diff --git a/config/plugins/webhooks/demo/tool_list/__init__.py b/config/plugins/webhooks/demo/tool_list/__init__.py
index 31db2b819c1..db8e58ceeca 100644
--- a/config/plugins/webhooks/demo/tool_list/__init__.py
+++ b/config/plugins/webhooks/demo/tool_list/__init__.py
@@ -3,7 +3,7 @@ import yaml
 
 def main(trans, webhook, params):
     data = {}
-    data['tools'] = []
+    data["tools"] = []
     unique_tools = []
 
     tools = trans.app.toolbox.tools()
@@ -16,24 +16,23 @@ def main(trans, webhook, params):
         except AttributeError:
             continue
 
-        if (ts_data['name'] + ts_data['installed_changeset_revision'] not in
-                unique_tools):
+        if ts_data["name"] + ts_data["installed_changeset_revision"] not in unique_tools:
 
-            unique_tools.append(
-                ts_data['name'] + ts_data['installed_changeset_revision']
+            unique_tools.append(ts_data["name"] + ts_data["installed_changeset_revision"])
+
+            data["tools"].append(
+                {
+                    "name": ts_data["name"],
+                    "owner": ts_data["owner"],
+                    "tool_panel_section_label": panel[1],
+                    "tool_shed_url": ts_data["tool_shed"],
+                    "install_tool_dependencies": True,
+                    "install_repository_dependencies": True,
+                    "install_resolver_dependencies": True,
+                    "revisions": [ts_data["installed_changeset_revision"]],
+                }
             )
-
-            data['tools'].append({
-                'name': ts_data['name'],
-                'owner': ts_data['owner'],
-                'tool_panel_section_label': panel[1],
-                'tool_shed_url': ts_data['tool_shed'],
-                'install_tool_dependencies': True,
-                'install_repository_dependencies': True,
-                'install_resolver_dependencies': True,
-                'revisions': [ts_data['installed_changeset_revision']]
-            })
             if panel[0]:
-                data['tools'][-1]['tool_panel_section_id'] = panel[0]
+                data["tools"][-1]["tool_panel_section_id"] = panel[0]
 
-    return {'yaml': yaml.safe_dump(data, default_flow_style=False)}
+    return {"yaml": yaml.safe_dump(data, default_flow_style=False)}
diff --git a/config/plugins/webhooks/demo/tour_generator/__init__.py b/config/plugins/webhooks/demo/tour_generator/__init__.py
index 8e4d77e5bfc..c132aff0501 100644
--- a/config/plugins/webhooks/demo/tour_generator/__init__.py
+++ b/config/plugins/webhooks/demo/tour_generator/__init__.py
@@ -28,13 +28,12 @@ class TourGenerator:
         section of the provided tool.
         """
         if not self._tool.tests:
-            raise ValueError('Tests are not defined.')
+            raise ValueError("Tests are not defined.")
 
         self._test = self._tool.tests[0]
 
         # All inputs with the type 'data'
-        self._data_inputs = {x.name: x for x in self._tool.input_params if
-                             x.type == 'data'}
+        self._data_inputs = {x.name: x for x in self._tool.input_params if x.type == "data"}
 
         # Datasets from the <test></test> section
         test_datasets = {
@@ -45,20 +44,17 @@ class TourGenerator:
 
         # Conditional datasets
         for name in self._test.inputs.keys():
-            if '|' in name:
-                input_name = name.split('|')[1]
+            if "|" in name:
+                input_name = name.split("|")[1]
                 if input_name in self._data_inputs.keys():
-                    test_datasets.update({
-                        input_name: self._test.inputs[name][0]
-                    })
+                    test_datasets.update({input_name: self._test.inputs[name][0]})
 
         if not test_datasets.keys():
             not_supported_input_types = [
-                k for k, v in self._tool.inputs.items() if
-                v.type == 'repeat' or v.type == 'data_collection'
+                k for k, v in self._tool.inputs.items() if v.type == "repeat" or v.type == "data_collection"
             ]
             if not_supported_input_types:
-                raise ValueError('Not supported input types.')
+                raise ValueError("Not supported input types.")
             else:
                 # Some tests don't have data inputs at all,
                 # so we can generate a tour without them
@@ -73,16 +69,15 @@ class TourGenerator:
                 if not input_path:
                     raise ValueError('Test dataset "%s" doesn\'t exist.' % input_name)
 
-                upload_tool = self._trans.app.toolbox.get_tool('upload1')
+                upload_tool = self._trans.app.toolbox.get_tool("upload1")
                 filename = os.path.basename(input_path)
 
-                with open(input_path, 'rb') as f:
+                with open(input_path, "rb") as f:
                     content = f.read()
                     headers = {
-                        'content-disposition':
-                            'form-data; name="{}"; filename="{}"'.format(
-                                'files_0|file_data', filename
-                            ),
+                        "content-disposition": 'form-data; name="{}"; filename="{}"'.format(
+                            "files_0|file_data", filename
+                        ),
                     }
 
                     input_file = cgi_FieldStorage(headers=headers)
@@ -90,76 +85,68 @@ class TourGenerator:
                     input_file.file.write(content)
 
                     inputs = {
-                        'dbkey': '?',  # is it always a question mark?
-                        'file_type': input.extensions[0],
-                        'files_0|type': 'upload_dataset',
-                        'files_0|space_to_tab': None,
-                        'files_0|to_posix_lines': 'Yes',
-                        'files_0|file_data': input_file,
+                        "dbkey": "?",  # is it always a question mark?
+                        "file_type": input.extensions[0],
+                        "files_0|type": "upload_dataset",
+                        "files_0|space_to_tab": None,
+                        "files_0|to_posix_lines": "Yes",
+                        "files_0|file_data": input_file,
                     }
 
                     params = Params(inputs, sanitize=False)
                     incoming = params.__dict__
-                    output = upload_tool.handle_input(self._trans, incoming,
-                                                      history=None)
+                    output = upload_tool.handle_input(self._trans, incoming, history=None)
 
-                    job_errors = output.get('job_errors', [])
+                    job_errors = output.get("job_errors", [])
                     if job_errors:
                         # self._errors.extend(job_errors)
-                        raise ValueError('Cannot upload a dataset.')
+                        raise ValueError("Cannot upload a dataset.")
                     else:
-                        self._hids.update({
-                            input_name: output['out_data'][0][1].hid
-                        })
+                        self._hids.update({input_name: output["out_data"][0][1].hid})
 
     def _generate_tour(self):
-        """ Generate a tour. """
-        tour_name = self._tool.name + ' Tour'
+        """Generate a tour."""
+        tour_name = self._tool.name + " Tour"
         test_inputs = self._test.inputs.keys()
 
-        steps = [{
-            'title': tour_name,
-            'content': 'This short tour will guide you through the <b>'
-                       + self._tool.name + '</b> tool.',
-            'orphan': True
-        }]
+        steps = [
+            {
+                "title": tour_name,
+                "content": "This short tour will guide you through the <b>" + self._tool.name + "</b> tool.",
+                "orphan": True,
+            }
+        ]
 
         for name, input in self._tool.inputs.items():
             cond_case_steps = []
 
-            if input.type == 'repeat':
+            if input.type == "repeat":
                 continue
 
-            step = {
-                'title': input.label,
-                'element': '[tour_id=%s]' % name,
-                'placement': 'right',
-                'content': ''
-            }
+            step = {"title": input.label, "element": "[tour_id=%s]" % name, "placement": "right", "content": ""}
 
-            if input.type == 'text':
+            if input.type == "text":
                 if name in test_inputs:
                     param = self._test.inputs[name]
-                    step['content'] = 'Enter value(s): <b>%s</b>' % param
+                    step["content"] = "Enter value(s): <b>%s</b>" % param
                 else:
-                    step['content'] = 'Enter a value'
+                    step["content"] = "Enter a value"
 
-            elif input.type == 'integer' or input.type == 'float':
+            elif input.type == "integer" or input.type == "float":
                 if name in test_inputs:
                     num_param = self._test.inputs[name][0]
-                    step['content'] = 'Enter number: <b>%s</b>' % num_param
+                    step["content"] = "Enter number: <b>%s</b>" % num_param
                 else:
-                    step['content'] = 'Enter a number'
+                    step["content"] = "Enter a number"
 
-            elif input.type == 'boolean':
+            elif input.type == "boolean":
                 if name in test_inputs:
-                    choice = 'Yes' if self._test.inputs[name][0] is True \
-                        else 'No'
-                    step['content'] = 'Choose <b>%s</b>' % choice
+                    choice = "Yes" if self._test.inputs[name][0] is True else "No"
+                    step["content"] = "Choose <b>%s</b>" % choice
                 else:
-                    step['content'] = 'Choose Yes/No'
+                    step["content"] = "Choose Yes/No"
 
-            elif input.type == 'select':
+            elif input.type == "select":
                 params = []
                 if name in test_inputs:
                     for option in input.static_options:
@@ -167,26 +154,23 @@ class TourGenerator:
                             if test_option == option[1]:
                                 params.append(option[0])
                 if params:
-                    select_param = ', '.join(params)
-                    step['content'] = 'Select parameter(s): <b>%s</b>' % \
-                                      select_param
+                    select_param = ", ".join(params)
+                    step["content"] = "Select parameter(s): <b>%s</b>" % select_param
                 else:
-                    step['content'] = 'Select a parameter'
+                    step["content"] = "Select a parameter"
 
-            elif input.type == 'data':
+            elif input.type == "data":
                 if name in test_inputs:
                     hid = self._hids[name]
                     dataset = self._test.inputs[name][0]
-                    step['content'] = 'Select dataset: <b>{}: {}</b>'.format(
-                        hid, dataset
-                    )
+                    step["content"] = "Select dataset: <b>{}: {}</b>".format(hid, dataset)
                 else:
-                    step['content'] = 'Select a dataset'
+                    step["content"] = "Select a dataset"
 
-            elif input.type == 'conditional':
-                param_id = f'{input.name}|{input.test_param.name}'
-                step['title'] = input.test_param.label
-                step['element'] = '[tour_id="%s"]' % param_id
+            elif input.type == "conditional":
+                param_id = f"{input.name}|{input.test_param.name}"
+                step["title"] = input.test_param.label
+                step["element"] = '[tour_id="%s"]' % param_id
                 params = []
 
                 if param_id in self._test.inputs.keys():
@@ -203,60 +187,60 @@ class TourGenerator:
                                 cases[key] = value.label
 
                     for case_id, case_title in cases.items():
-                        tour_id = f'{input.name}|{case_id}'
+                        tour_id = f"{input.name}|{case_id}"
                         if tour_id in self._test.inputs.keys():
                             if case_id in self._data_inputs.keys():
                                 hid = self._hids[case_id]
                                 dataset = self._test.inputs[tour_id][0]
-                                step_msg = 'Select dataset: <b>%s: %s</b>' % \
-                                           (hid, dataset)
+                                step_msg = "Select dataset: <b>%s: %s</b>" % (hid, dataset)
                             else:
-                                case_params = ', '.join(
-                                    self._test.inputs[tour_id])
-                                step_msg = 'Select parameter(s): ' + \
-                                           '<b>%s</b>' % case_params
-                            cond_case_steps.append({
-                                'title': case_title,
-                                'element': '[tour_id="%s"]' % tour_id,
-                                'placement': 'right',
-                                'content': step_msg
-                            })
+                                case_params = ", ".join(self._test.inputs[tour_id])
+                                step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params
+                            cond_case_steps.append(
+                                {
+                                    "title": case_title,
+                                    "element": '[tour_id="%s"]' % tour_id,
+                                    "placement": "right",
+                                    "content": step_msg,
+                                }
+                            )
 
                 if params:
-                    cond_param = ', '.join(params)
-                    step['content'] = 'Select parameter(s): <b>%s</b>' % \
-                                      cond_param
+                    cond_param = ", ".join(params)
+                    step["content"] = "Select parameter(s): <b>%s</b>" % cond_param
                 else:
-                    step['content'] = 'Select a parameter'
+                    step["content"] = "Select a parameter"
 
-            elif input.type == 'data_column':
+            elif input.type == "data_column":
                 if name in test_inputs:
                     column_param = self._test.inputs[name][0]
-                    step['content'] = 'Select <b>Column: %s</b>' % column_param
+                    step["content"] = "Select <b>Column: %s</b>" % column_param
                 else:
-                    step['content'] = 'Select a column'
+                    step["content"] = "Select a column"
 
             else:
-                step['content'] = 'Select a parameter'
+                step["content"] = "Select a parameter"
 
             steps.append(step)
             if cond_case_steps:
                 steps.extend(cond_case_steps)  # add conditional input steps
 
         # Add the last step
-        steps.append({
-            'title': 'Execute tool',
-            'content': 'Click <b>Execute</b> button to run the tool.',
-            'element': '#execute',
-            'placement': 'bottom',
-            # 'postclick': ['#execute']
-        })
+        steps.append(
+            {
+                "title": "Execute tool",
+                "content": "Click <b>Execute</b> button to run the tool.",
+                "element": "#execute",
+                "placement": "bottom",
+                # 'postclick': ['#execute']
+            }
+        )
 
         self._tour = {
-            'title_default': tour_name,
-            'name': tour_name,
-            'description': self._tool.name + ' ' + self._tool.description,
-            'steps': steps
+            "title_default": tour_name,
+            "name": tour_name,
+            "description": self._tool.name + " " + self._tool.description,
+            "steps": steps,
         }
 
     def get_data(self):
@@ -264,26 +248,22 @@ class TourGenerator:
         Return a dictionary with the uploaded datasets' history ids and
         the generated tour.
         """
-        return {
-            'useDatasets': self._use_datasets,
-            'hids': list(self._hids.values()),
-            'tour': self._tour
-        }
+        return {"useDatasets": self._use_datasets, "hids": list(self._hids.values()), "tour": self._tour}
 
 
 def main(trans, webhook, params):
-    error = ''
+    error = ""
     data = {}
 
     try:
-        if not params or 'tool_id' not in params.keys():
-            raise KeyError('Tool id is missing.')
+        if not params or "tool_id" not in params.keys():
+            raise KeyError("Tool id is missing.")
 
-        if not params or 'tool_version' not in params.keys():
-            raise KeyError('Tool version is missing.')
+        if not params or "tool_version" not in params.keys():
+            raise KeyError("Tool version is missing.")
 
-        tool_id = params['tool_id']
-        tool_version = params['tool_version']
+        tool_id = params["tool_id"]
+        tool_version = params["tool_version"]
         tour_generator = TourGenerator(trans, tool_id, tool_version)
         data = tour_generator.get_data()
 
@@ -291,4 +271,4 @@ def main(trans, webhook, params):
         error = str(e)
         log.exception(e)
 
-    return {'success': not error, 'error': error, 'data': data}
+    return {"success": not error, "error": error, "data": data}
diff --git a/contrib/galaxy_config_merger.py b/contrib/galaxy_config_merger.py
index 887e43434f4..f7d60f183aa 100644
--- a/contrib/galaxy_config_merger.py
+++ b/contrib/galaxy_config_merger.py
@@ -1,5 +1,5 @@
 #! /usr/bin/env python
-'''
+"""
 galaxy_config_merger.py
 
 Created by Anne Pajon on 31 Jan 2012
@@ -22,7 +22,7 @@ FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF
 THE ORIGINAL WORK IS WITH YOU.
 
 Script for merging specific local Galaxy config galaxy.ini.cri with default Galaxy galaxy.ini.sample
-'''
+"""
 
 import configparser
 import logging
@@ -32,16 +32,18 @@ import sys
 
 def main():
     # logging configuration
-    logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO)
+    logging.basicConfig(format="%(levelname)s: %(message)s", level=logging.INFO)
 
     # get the options
     parser = optparse.OptionParser()
     parser.add_option("-s", "--sample", dest="sample", action="store", help="path to Galaxy galaxy.ini.sample file")
     parser.add_option("-c", "--config", dest="config", action="store", help="path to your own galaxy.ini file")
-    parser.add_option("-o", "--output", dest="output", action="store", help="path to the new merged galaxy.ini.new file")
+    parser.add_option(
+        "-o", "--output", dest="output", action="store", help="path to the new merged galaxy.ini.new file"
+    )
     (options, args) = parser.parse_args()
 
-    for option in ['sample', 'config']:
+    for option in ["sample", "config"]:
         if getattr(options, option) is None:
             print("Please supply a --%s parameter.\n" % (option))
             parser.print_help()
@@ -63,18 +65,24 @@ def main():
             for (name, value) in config.items(section):
                 if not config_sample.has_option(section, name):
                     if not "#%s" % name in config_sample_content:
-                        logging.warning(f"-MISSING- section [{section}] option '{name}' not found in sample file. It will be ignored.")
+                        logging.warning(
+                            f"-MISSING- section [{section}] option '{name}' not found in sample file. It will be ignored."
+                        )
                     else:
-                        logging.info(f"-notset- section [{section}] option '{name}' not set in sample file. It will be added.")
+                        logging.info(
+                            f"-notset- section [{section}] option '{name}' not set in sample file. It will be added."
+                        )
                         config_sample.set(section, name, value)
                 else:
                     if not config_sample.get(section, name) == value:
-                        logging.info(f"- diff - section [{section}] option '{name}' has different value ('{config_sample.get(section, name)}':'{value}'). It will be modified.")
+                        logging.info(
+                            f"- diff - section [{section}] option '{name}' has different value ('{config_sample.get(section, name)}':'{value}'). It will be modified."
+                        )
                         config_sample.set(section, name, value)
     logging.info("---------- DIFFERENCE ANALYSIS END   ----------")
 
     if options.output:
-        outputfile = open(options.output, 'w')
+        outputfile = open(options.output, "w")
         config_sample.write(outputfile)
         outputfile.close()
     else:
@@ -83,5 +91,5 @@ def main():
     logging.info("read Galaxy galaxy.ini.sample for detailed information.")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/cron/add_manual_builds.py b/cron/add_manual_builds.py
index 8a4197eef5b..5138442e145 100644
--- a/cron/add_manual_builds.py
+++ b/cron/add_manual_builds.py
@@ -21,7 +21,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
             existing_builds.append(line.replace("\n", "").replace("\r", "").split("\t")[0])
         except Exception:
             continue
-    build_file_out = open(build_file, 'a')
+    build_file_out = open(build_file, "a")
     for line in open(input_file):
         try:
             fields = line.replace("\n", "").replace("\r", "").split("\t")
@@ -35,7 +35,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
                 chrs = []
             print(build + "\t" + name + " (" + build + ")", file=build_file_out)
             if chrs:  # create len file if provided chrom lens
-                chr_len_out = open(os.path.join(chr_dir, build + ".len"), 'w')
+                chr_len_out = open(os.path.join(chr_dir, build + ".len"), "w")
                 for chr in chrs:
                     print(chr.replace("=", "\t"), file=chr_len_out)
                 chr_len_out.close()
diff --git a/cron/build_chrom_db.py b/cron/build_chrom_db.py
index 7289dc72202..615e791e5c2 100644
--- a/cron/build_chrom_db.py
+++ b/cron/build_chrom_db.py
@@ -17,24 +17,26 @@ import os
 import sys
 from urllib.parse import urlencode
 
-import requests
-
 import parse_builds  # noqa: I100,I202
+import requests
 
 
 def getchrominfo(url, db):
     tableURL = "http://genome-test.gi.ucsc.edu/cgi-bin/hgTables?"
-    URL = tableURL + urlencode({
-        "clade": "",
-        "org": "",
-        "db": db,
-        "hgta_outputType": "primaryTable",
-        "hgta_group": "allTables",
-        "hgta_table": "chromInfo",
-        "hgta_track": db,
-        "hgta_regionType": "",
-        "position": "",
-        "hgta_doTopSubmit": "get info"})
+    URL = tableURL + urlencode(
+        {
+            "clade": "",
+            "org": "",
+            "db": db,
+            "hgta_outputType": "primaryTable",
+            "hgta_group": "allTables",
+            "hgta_table": "chromInfo",
+            "hgta_track": db,
+            "hgta_regionType": "",
+            "position": "",
+            "hgta_doTopSubmit": "get info",
+        }
+    )
     page = requests.get(URL).text
     for i, line in enumerate(page.splitlines()):
         line = line.rstrip("\r\n")
diff --git a/cron/cleanup_datasets.py b/cron/cleanup_datasets.py
index 184be129957..f20362d6b36 100644
--- a/cron/cleanup_datasets.py
+++ b/cron/cleanup_datasets.py
@@ -2,5 +2,7 @@
 
 import sys
 
-sys.exit("This script has been deprecated, replaced by the set of scripts in <galaxy_distribution>/scripts/cleanup_datsets/."
-         "See https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets for more information.")
+sys.exit(
+    "This script has been deprecated, replaced by the set of scripts in <galaxy_distribution>/scripts/cleanup_datsets/."
+    "See https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets for more information."
+)
diff --git a/cron/parse_builds.py b/cron/parse_builds.py
index 45361c3aeeb..dcd2005c537 100644
--- a/cron/parse_builds.py
+++ b/cron/parse_builds.py
@@ -29,7 +29,7 @@ def getbuilds(url):
     print("#Harvested from " + url)
     print("?\tunspecified (?)")
     for dsn in tree:
-        build = dsn.find("SOURCE").attrib['id']
+        build = dsn.find("SOURCE").attrib["id"]
         description = dsn.find("DESCRIPTION").text.replace(" - Genome at UCSC", "").replace(" Genome at UCSC", "")
 
         fields = description.split(" ")
diff --git a/cron/parse_builds_3_sites.py b/cron/parse_builds_3_sites.py
index c1eb4d0a147..52ad1bd6acd 100644
--- a/cron/parse_builds_3_sites.py
+++ b/cron/parse_builds_3_sites.py
@@ -7,10 +7,12 @@ import xml.etree.ElementTree as ElementTree
 
 import requests
 
-sites = ['http://genome.ucsc.edu/cgi-bin/',
-         'http://archaea.ucsc.edu/cgi-bin/',
-         'http://genome-test.gi.ucsc.edu/cgi-bin/']
-names = ['main', 'archaea', 'test']
+sites = [
+    "http://genome.ucsc.edu/cgi-bin/",
+    "http://archaea.ucsc.edu/cgi-bin/",
+    "http://genome-test.gi.ucsc.edu/cgi-bin/",
+]
+names = ["main", "archaea", "test"]
 
 
 def main():
@@ -32,7 +34,7 @@ def main():
         print("#Harvested from", site)
 
         for dsn in tree:
-            build = dsn.find("SOURCE").attrib['id']
+            build = dsn.find("SOURCE").attrib["id"]
             builds.append(build)
             build_dict = {}
         for build in builds:
diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py
index 382c7eee8ce..a74557fdf20 100644
--- a/doc/parse_gx_xsd.py
+++ b/doc/parse_gx_xsd.py
@@ -28,7 +28,7 @@ def main():
                 toc_list.append(tag.build_toc_entry())
                 content_list.append(tag.build_help())
             elif not found_tag:
-                print(line, end='')
+                print(line, end="")
             else:
                 raise Exception("No normal text allowed after the first $tag")
     print("## Contents\n")
@@ -36,11 +36,10 @@ def main():
         print(el)
     print("\n")
     for el in content_list:
-        print(el, end='')
+        print(el, end="")
 
 
 class Tag:
-
     def __init__(self, line):
         assert line.startswith("$tag:")
         line_parts = line.split(" ")
@@ -60,9 +59,9 @@ class Tag:
     @property
     def _anchor(self):
         anchor = self.title
-        for _ in ['|', '_']:
-            anchor = anchor.replace(_, '-')
-        return '#' + anchor
+        for _ in ["|", "_"]:
+            anchor = anchor.replace(_, "-")
+        return "#" + anchor
 
     @property
     def _pretty_title(self):
@@ -93,18 +92,24 @@ def _build_tag(tag, hide_attributes):
     text = _replace_attribute_list(tag, text, attributes)
     for line in text.splitlines():
         if line.startswith("$assertions"):
-            assertions_tag = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}complexType[@name='TestAssertions']")
+            assertions_tag = xmlschema_doc.find(
+                "//{http://www.w3.org/2001/XMLSchema}complexType[@name='TestAssertions']"
+            )
             assertions_buffer = StringIO()
             assertions_buffer.write(_doc_or_none(assertions_tag))
             assertions_buffer.write("\n\n")
 
-            assertion_groups = assertions_tag.xpath("xs:choice/xs:group", namespaces={'xs': 'http://www.w3.org/2001/XMLSchema'})
+            assertion_groups = assertions_tag.xpath(
+                "xs:choice/xs:group", namespaces={"xs": "http://www.w3.org/2001/XMLSchema"}
+            )
             for group in assertion_groups:
-                ref = group.attrib['ref']
+                ref = group.attrib["ref"]
                 assertion_tag = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}group[@name='" + ref + "']")
                 doc = _doc_or_none(assertion_tag)
                 assertions_buffer.write(f"### {doc}\n\n")
-                elements = assertion_tag.findall("{http://www.w3.org/2001/XMLSchema}choice/{http://www.w3.org/2001/XMLSchema}element")
+                elements = assertion_tag.findall(
+                    "{http://www.w3.org/2001/XMLSchema}choice/{http://www.w3.org/2001/XMLSchema}element"
+                )
                 for element in elements:
                     doc = _doc_or_none(element)
                     if doc is None:
@@ -121,9 +126,12 @@ def _build_tag(tag, hide_attributes):
     best_practices = _get_bp_link(annotation_el)
     if best_practices:
         tag_help.write("\n\n### Best Practices\n")
-        tag_help.write("""
+        tag_help.write(
+            """
 Find the Intergalactic Utilities Commision suggested best practices for this
-element [here](%s).""" % best_practices)
+element [here](%s)."""
+            % best_practices
+        )
     tag_help.write(_build_attributes_table(tag, attributes, hide_attributes))
 
     return tag_help.getvalue()
@@ -139,7 +147,9 @@ def _replace_attribute_list(tag, text, attributes):
         else:
             attribute_names = attributes_str.split(",")
         header_level = int(header_level)
-        text = text.replace(line, _build_attributes_table(tag, attributes, attribute_names=attribute_names, header_level=header_level))
+        text = text.replace(
+            line, _build_attributes_table(tag, attributes, attribute_names=attribute_names, header_level=header_level)
+        )
     return text
 
 
@@ -155,7 +165,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
     attribute_table = StringIO()
     attribute_table.write("\n\n")
     if attributes and not hide_attributes:
-        header_prefix = '#' * header_level
+        header_prefix = "#" * header_level
         attribute_table.write("\n%s Attributes\n\n" % header_prefix)
         attribute_table.write("Attribute | Details | Required\n")
         attribute_table.write("--- | --- | ---\n")
@@ -176,25 +186,42 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = details.replace("\n", " ").strip()
             best_practices = _get_bp_link(annotation_el)
             if best_practices:
-                details += """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s).""" % best_practices
+                details += (
+                    """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s)."""
+                    % best_practices
+                )
 
             attribute_table.write(f"``{name}`` | {details} | {use}\n")
     return attribute_table.getvalue()
 
 
 def _find_attributes(tag):
-    raw_attributes = tag.findall("{http://www.w3.org/2001/XMLSchema}attribute") or \
-        tag.findall("{http://www.w3.org/2001/XMLSchema}complexType/{http://www.w3.org/2001/XMLSchema}attribute") or \
-        tag.findall("{http://www.w3.org/2001/XMLSchema}complexContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attribute") or \
-        tag.findall("{http://www.w3.org/2001/XMLSchema}simpleContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attribute")
-    attribute_groups = tag.findall("{http://www.w3.org/2001/XMLSchema}attributeGroup") or \
-        tag.findall("{http://www.w3.org/2001/XMLSchema}complexType/{http://www.w3.org/2001/XMLSchema}attributeGroup") or \
-        tag.findall("{http://www.w3.org/2001/XMLSchema}complexContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attributeGroup") or \
-        tag.findall("{http://www.w3.org/2001/XMLSchema}simpleContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attributeGroup")
+    raw_attributes = (
+        tag.findall("{http://www.w3.org/2001/XMLSchema}attribute")
+        or tag.findall("{http://www.w3.org/2001/XMLSchema}complexType/{http://www.w3.org/2001/XMLSchema}attribute")
+        or tag.findall(
+            "{http://www.w3.org/2001/XMLSchema}complexContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attribute"
+        )
+        or tag.findall(
+            "{http://www.w3.org/2001/XMLSchema}simpleContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attribute"
+        )
+    )
+    attribute_groups = (
+        tag.findall("{http://www.w3.org/2001/XMLSchema}attributeGroup")
+        or tag.findall("{http://www.w3.org/2001/XMLSchema}complexType/{http://www.w3.org/2001/XMLSchema}attributeGroup")
+        or tag.findall(
+            "{http://www.w3.org/2001/XMLSchema}complexContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attributeGroup"
+        )
+        or tag.findall(
+            "{http://www.w3.org/2001/XMLSchema}simpleContent/{http://www.w3.org/2001/XMLSchema}extension/{http://www.w3.org/2001/XMLSchema}attributeGroup"
+        )
+    )
     attributes = list(raw_attributes)
     for attribute_group in attribute_groups:
         attribute_group_name = attribute_group.get("ref")
-        attribute_group_def = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}attributeGroup/[@name='%s']" % attribute_group_name)
+        attribute_group_def = xmlschema_doc.find(
+            "//{http://www.w3.org/2001/XMLSchema}attributeGroup/[@name='%s']" % attribute_group_name
+        )
         attributes.extend(_find_attributes(attribute_group_def))
     return attributes
 
@@ -222,5 +249,5 @@ def _doc_or_none(tag):
         return doc_el.text
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/doc/source/conf.py b/doc/source/conf.py
index c983beef6a1..8e364417cb7 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -15,6 +15,7 @@ import os
 import sys
 
 import sphinx_rtd_theme
+
 # Library to make .md to slideshow
 from recommonmark.transform import AutoStructify
 
@@ -30,35 +31,35 @@ SKIP_RELEASES = os.environ.get("GALAXY_DOCS_SKIP_RELEASES", False) == "1"
 
 # REQUIRED GALAXY INCLUDES
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['recommonmark', 'sphinx.ext.intersphinx', 'sphinx_markdown_tables']
+extensions = ["recommonmark", "sphinx.ext.intersphinx", "sphinx_markdown_tables"]
 if not SKIP_SOURCE:
     # TODO: Add https://pypi.org/project/sphinx-autodoc-typehints
-    extensions += ['sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.autodoc']
+    extensions += ["sphinx.ext.doctest", "sphinx.ext.todo", "sphinx.ext.coverage", "sphinx.ext.autodoc"]
     if not SKIP_VIEW_CODE:
-        extensions.append('sphinx.ext.viewcode')
+        extensions.append("sphinx.ext.viewcode")
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # Configure default autodoc's action
-autodoc_default_flags = ['members', 'undoc-members']
+autodoc_default_flags = ["members", "undoc-members"]
 
 # Prevent alphabetical reordering of module members.
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 
 
 def dont_skip_init(app, what, name, obj, skip, options):
@@ -70,26 +71,30 @@ def dont_skip_init(app, what, name, obj, skip, options):
 def setup(app):
     if not SKIP_SOURCE:
         app.connect("autodoc-skip-member", dont_skip_init)
-    app.add_config_value('recommonmark_config', {
-        'enable_auto_doc_ref': False,
-        'enable_auto_toc_tree': False,
-        'enable_inline_math': False,  # https://github.com/rtfd/recommonmark/pull/124
-    }, True)
+    app.add_config_value(
+        "recommonmark_config",
+        {
+            "enable_auto_doc_ref": False,
+            "enable_auto_toc_tree": False,
+            "enable_inline_math": False,  # https://github.com/rtfd/recommonmark/pull/124
+        },
+        True,
+    )
     app.add_transform(AutoStructify)
 
 
 # The suffix of source filenames.
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'Galaxy Project'
-copyright = str(datetime.datetime.now().year) + ', Galaxy Committers'
+project = "Galaxy Project"
+copyright = str(datetime.datetime.now().year) + ", Galaxy Committers"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -97,33 +102,34 @@ copyright = str(datetime.datetime.now().year) + ', Galaxy Committers'
 #
 # The short X.Y version.
 from galaxy.version import VERSION, VERSION_MAJOR
+
 version = VERSION_MAJOR
 # The full version, including alpha/beta/rc tags.
 release = VERSION
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['**/_*.rst']
+exclude_patterns = ["**/_*.rst"]
 if SKIP_SOURCE:
-    exclude_patterns.extend(['lib'])
+    exclude_patterns.extend(["lib"])
 if SKIP_RELEASES:
-    exclude_patterns.extend(['releases'])
+    exclude_patterns.extend(["releases"])
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
@@ -131,34 +137,34 @@ add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # Intersphinx mapping to Python documentation
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'requests': ("https://requests.readthedocs.io/en/master/", None),
+    "python": ("https://docs.python.org/3", None),
+    "requests": ("https://requests.readthedocs.io/en/master/", None),
 }
 
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    'collapse_navigation': False,
-    'display_version': True,
-    'navigation_depth': 2,
-    'canonical_url': 'https://docs.galaxyproject.org/en/master/',
+    "collapse_navigation": False,
+    "display_version": True,
+    "navigation_depth": 2,
+    "canonical_url": "https://docs.galaxyproject.org/en/master/",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -166,68 +172,68 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'Galaxydoc'
+htmlhelp_basename = "Galaxydoc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -235,10 +241,8 @@ htmlhelp_basename = 'Galaxydoc'
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #'preamble': '',
 }
@@ -246,42 +250,38 @@ latex_elements = {
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ('index', 'Galaxy.tex', 'Galaxy Code Documentation',
-     'Galaxy Team', 'manual'),
+    ("index", "Galaxy.tex", "Galaxy Code Documentation", "Galaxy Team", "manual"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output --------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'galaxy', 'Galaxy Documentation',
-     ['Galaxy Team'], 1)
-]
+man_pages = [("index", "galaxy", "Galaxy Documentation", ["Galaxy Team"], 1)]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ------------------------------------------------
@@ -290,19 +290,25 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'Galaxy', 'Galaxy Documentation',
-     'Galaxy Team', 'Galaxy', 'Data intensive biology for everyone.',
-     'Miscellaneous'),
+    (
+        "index",
+        "Galaxy",
+        "Galaxy Documentation",
+        "Galaxy Team",
+        "Galaxy",
+        "Data intensive biology for everyone.",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 
 # -- ReadTheDocs.org Settings ------------------------------------------------
@@ -315,8 +321,8 @@ class Mock:
 
     @classmethod
     def __getattr__(cls, name):
-        if name in ('__file__', '__path__'):
-            return '/dev/null'
+        if name in ("__file__", "__path__"):
+            return "/dev/null"
         elif name[0] == name[0].upper():
             mockType = type(name, (), {})
             mockType.__module__ = __name__
@@ -326,6 +332,6 @@ class Mock:
 
 
 # adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect.
-MOCK_MODULES = ['tables', 'decorator']
+MOCK_MODULES = ["tables", "decorator"]
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()
diff --git a/doc/source/conf.versioning.py b/doc/source/conf.versioning.py
index fb8c7eb94b1..3e45f6db296 100644
--- a/doc/source/conf.versioning.py
+++ b/doc/source/conf.versioning.py
@@ -7,7 +7,7 @@ from distutils.version import LooseVersion
 from subprocess import check_output
 
 # This is set in the Jenkins matrix config
-TARGET_GIT_BRANCH = os.environ.get('TARGET_BRANCH', 'dev')  # noqa: F821
+TARGET_GIT_BRANCH = os.environ.get("TARGET_BRANCH", "dev")  # noqa: F821
 
 # Version message templates
 OLD_BANNER = """This document is for an old release of Galaxy."""
@@ -17,58 +17,51 @@ BANNER_APPEND = """ You can alternatively <a href="%(stable_path)s">view this pa
 exists</a> or <a href="%(stable_root)s">view the top of the latest release's documentation</a>."""
 
 # Minimum version for linking to docs
-MIN_DOC_VERSION = LooseVersion('17.05')
+MIN_DOC_VERSION = LooseVersion("17.05")
 
 # Enable simpleversioning
-extensions += ['sphinxcontrib.simpleversioning']  # noqa: F821
+extensions += ["sphinxcontrib.simpleversioning"]  # noqa: F821
 
 # -- sphinxcontrib-simpleversioning Settings ---------------------------------
 
-simpleversioning_path_template = '/en/{version}/{pagename}'
-simpleversioning_stable_version = 'master'
+simpleversioning_path_template = "/en/{version}/{pagename}"
+simpleversioning_stable_version = "master"
 simpleversioning_current_version = TARGET_GIT_BRANCH
 simpleversioning_versions = [
-    {'id': 'latest', 'name': 'dev'},
-    {'id': 'master', 'name': 'stable'},
+    {"id": "latest", "name": "dev"},
+    {"id": "master", "name": "stable"},
     # Additional versions added below
 ]
 
 # Used for determining the latest stable release so the banner can be added to older releases.
 _stable = None
 # Use tags to determine versions - a stable version will have a branch before it's released, but not a tag.
-tags = check_output(('git', 'tag')).decode().splitlines()
+tags = check_output(("git", "tag")).decode().splitlines()
 for _tag in reversed(tags):
-    if _tag.startswith('v') and _tag.count('.') == 1:
+    if _tag.startswith("v") and _tag.count(".") == 1:
         # this version is released
         _ver = _tag[1:]
         if not _stable:
             _stable = _ver
         if LooseVersion(_ver) >= MIN_DOC_VERSION:
-            simpleversioning_versions.append(
-                {'id': 'release_%s' % _ver, 'name': _ver}
-            )
+            simpleversioning_versions.append({"id": "release_%s" % _ver, "name": _ver})
 
-if re.fullmatch(r'release_\d{2}\.\d{2}', TARGET_GIT_BRANCH):
+if re.fullmatch(r"release_\d{2}\.\d{2}", TARGET_GIT_BRANCH):
     if _stable:
         # The current stable release will go here but fail the next conditional, avoiding either banner.
-        if TARGET_GIT_BRANCH != 'release_%s' % _stable:
+        if TARGET_GIT_BRANCH != "release_%s" % _stable:
             simpleversioning_show_banner = True
-            _target_ver = TARGET_GIT_BRANCH[len('release_'):]
+            _target_ver = TARGET_GIT_BRANCH[len("release_") :]
             if LooseVersion(_target_ver) > LooseVersion(_stable):
                 # Pre-release
                 # Insert it between master and _stable
-                simpleversioning_versions.insert(
-                    2,
-                    {'id': TARGET_GIT_BRANCH, 'name': _target_ver}
-                )
+                simpleversioning_versions.insert(2, {"id": TARGET_GIT_BRANCH, "name": _target_ver})
                 simpleversioning_banner_message = PRE_BANNER + BANNER_APPEND
             else:
                 simpleversioning_banner_message = OLD_BANNER + BANNER_APPEND
-elif TARGET_GIT_BRANCH != 'master':
-    if TARGET_GIT_BRANCH != 'dev':
+elif TARGET_GIT_BRANCH != "master":
+    if TARGET_GIT_BRANCH != "dev":
         # Feature branch
-        simpleversioning_versions.append(
-            {'id': TARGET_GIT_BRANCH, 'name': TARGET_GIT_BRANCH}
-        )
+        simpleversioning_versions.append({"id": TARGET_GIT_BRANCH, "name": TARGET_GIT_BRANCH})
     simpleversioning_show_banner = True
     simpleversioning_banner_message = DEV_BANNER + BANNER_APPEND
diff --git a/lib/galaxy/__init__.py b/lib/galaxy/__init__.py
index 8c478621de6..70b3b112b71 100644
--- a/lib/galaxy/__init__.py
+++ b/lib/galaxy/__init__.py
@@ -3,4 +3,5 @@ Galaxy root package -- this is a namespace package.
 """
 
 from pkgutil import extend_path
+
 __path__ = extend_path(__path__, __name__)  # type: ignore[has-type]
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index 04be31f36ab..fdd365f0db2 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -22,19 +22,19 @@ from galaxy.tools.parameters import populate_state
 from galaxy.util.path import (
     safe_contains,
     safe_relpath,
-    unsafe_walk
+    unsafe_walk,
 )
 
 log = logging.getLogger(__name__)
 
 
 def validate_server_directory_upload(trans, server_dir):
-    if server_dir in [None, 'None', '']:
+    if server_dir in [None, "None", ""]:
         raise RequestParameterInvalidException("Invalid or unspecified server_dir parameter")
 
     if trans.user_is_admin:
         import_dir = trans.app.config.library_import_dir
-        import_dir_desc = 'library_import_dir'
+        import_dir_desc = "library_import_dir"
         if not import_dir:
             raise ConfigDoesNotAllowException('"library_import_dir" is not set in the Galaxy configuration')
     else:
@@ -43,17 +43,31 @@ def validate_server_directory_upload(trans, server_dir):
             raise ConfigDoesNotAllowException('"user_library_import_dir" is not set in the Galaxy configuration')
         if server_dir != trans.user.email:
             import_dir = os.path.join(import_dir, trans.user.email)
-        import_dir_desc = 'user_library_import_dir'
+        import_dir_desc = "user_library_import_dir"
 
     full_dir = os.path.join(import_dir, server_dir)
     unsafe = None
     if safe_relpath(server_dir):
         username = trans.user.username if trans.app.config.user_library_import_check_permissions else None
-        if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, allowlist=trans.app.config.user_library_import_symlink_allowlist):
-            for unsafe in unsafe_walk(full_dir, allowlist=[import_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username):
-                log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))
+        if import_dir_desc == "user_library_import_dir" and safe_contains(
+            import_dir, full_dir, allowlist=trans.app.config.user_library_import_symlink_allowlist
+        ):
+            for unsafe in unsafe_walk(
+                full_dir,
+                allowlist=[import_dir] + trans.app.config.user_library_import_symlink_allowlist,
+                username=username,
+            ):
+                log.error(
+                    "User attempted to import a path that resolves to a path outside of their import dir: %s -> %s",
+                    unsafe,
+                    os.path.realpath(unsafe),
+                )
     else:
-        log.error('User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s', server_dir, os.path.realpath(full_dir))
+        log.error(
+            "User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s",
+            server_dir,
+            os.path.realpath(full_dir),
+        )
         unsafe = True
     if unsafe:
         raise RequestParameterInvalidException("Invalid server_dir specified")
@@ -66,7 +80,7 @@ def validate_path_upload(trans):
         raise ConfigDoesNotAllowException('"allow_path_paste" is not set to True in the Galaxy configuration file')
 
     if not trans.user_is_admin:
-        raise AdminRequiredException('Uploading files via filesystem paths can only be performed by administrators')
+        raise AdminRequiredException("Uploading files via filesystem paths can only be performed by administrators")
 
 
 class LibraryActions:
@@ -76,10 +90,10 @@ class LibraryActions:
 
     def _upload_dataset(self, trans, folder_id: str, replace_dataset: Optional[LibraryDataset] = None, **kwd):
         # Set up the traditional tool state/params
-        cntrller = 'api'
-        tool_id = 'upload1'
+        cntrller = "api"
+        tool_id = "upload1"
         message = None
-        file_type = kwd.get('file_type')
+        file_type = kwd.get("file_type")
         try:
             upload_common.validate_datatype_extension(datatypes_registry=trans.app.datatypes_registry, ext=file_type)
         except RequestParameterInvalidException as e:
@@ -93,13 +107,13 @@ class LibraryActions:
             if input.type == "upload_dataset":
                 dataset_upload_inputs.append(input)
         # Library-specific params
-        server_dir = kwd.get('server_dir', '')
-        upload_option = kwd.get('upload_option', 'upload_file')
+        server_dir = kwd.get("server_dir", "")
+        upload_option = kwd.get("upload_option", "upload_file")
         response_code = 200
-        if upload_option == 'upload_directory':
+        if upload_option == "upload_directory":
             full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)
-            message = 'Select a directory'
-        elif upload_option == 'upload_paths':
+            message = "Select a directory"
+        elif upload_option == "upload_paths":
             # Library API already checked this - following check isn't actually needed.
             validate_path_upload(trans)
         # Some error handling should be added to this method.
@@ -112,28 +126,38 @@ class LibraryActions:
             message = "Unable to parse upload parameters, please report this error."
         # Proceed with (mostly) regular upload processing if we're still errorless
         if response_code == 200:
-            if upload_option == 'upload_file':
+            if upload_option == "upload_file":
                 tool_params = upload_common.persist_uploads(tool_params, trans)
-                uploaded_datasets = upload_common.get_uploaded_datasets(trans, cntrller, tool_params, dataset_upload_inputs, library_bunch=library_bunch)
-            elif upload_option == 'upload_directory':
-                uploaded_datasets, response_code, message = self._get_server_dir_uploaded_datasets(trans, kwd, full_dir, import_dir_desc, library_bunch, response_code, message)
-            elif upload_option == 'upload_paths':
-                uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(trans, kwd, library_bunch, response_code, message)
-            if upload_option == 'upload_file' and not uploaded_datasets:
+                uploaded_datasets = upload_common.get_uploaded_datasets(
+                    trans, cntrller, tool_params, dataset_upload_inputs, library_bunch=library_bunch
+                )
+            elif upload_option == "upload_directory":
+                uploaded_datasets, response_code, message = self._get_server_dir_uploaded_datasets(
+                    trans, kwd, full_dir, import_dir_desc, library_bunch, response_code, message
+                )
+            elif upload_option == "upload_paths":
+                uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(
+                    trans, kwd, library_bunch, response_code, message
+                )
+            if upload_option == "upload_file" and not uploaded_datasets:
                 response_code = 400
-                message = 'Select a file, enter a URL or enter text'
+                message = "Select a file, enter a URL or enter text"
         if response_code != 200:
             return (response_code, message)
         json_file_path = upload_common.create_paramfile(trans, uploaded_datasets)
         data_list = [ud.data for ud in uploaded_datasets]
         job_params = {}
-        job_params['link_data_only'] = json.dumps(kwd.get('link_data_only', 'copy_files'))
-        job_params['uuid'] = json.dumps(kwd.get('uuid', None))
-        job, output = upload_common.create_job(trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder, job_params=job_params)
+        job_params["link_data_only"] = json.dumps(kwd.get("link_data_only", "copy_files"))
+        job_params["uuid"] = json.dumps(kwd.get("uuid", None))
+        job, output = upload_common.create_job(
+            trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder, job_params=job_params
+        )
         trans.app.job_manager.enqueue(job, tool=tool)
         return output
 
-    def _get_server_dir_uploaded_datasets(self, trans, params, full_dir, import_dir_desc, library_bunch, response_code, message):
+    def _get_server_dir_uploaded_datasets(
+        self, trans, params, full_dir, import_dir_desc, library_bunch, response_code, message
+    ):
         dir_response = self._get_server_dir_files(params, full_dir, import_dir_desc)
         files = dir_response[0]
         if not files:
@@ -141,7 +165,9 @@ class LibraryActions:
         uploaded_datasets = []
         for file in files:
             name = os.path.basename(file)
-            uploaded_datasets.append(self._make_library_uploaded_dataset(trans, params, name, file, 'server_dir', library_bunch))
+            uploaded_datasets.append(
+                self._make_library_uploaded_dataset(trans, params, name, file, "server_dir", library_bunch)
+            )
         return uploaded_datasets, 200, None
 
     def _get_server_dir_files(self, params, full_dir, import_dir_desc):
@@ -150,8 +176,8 @@ class LibraryActions:
             for entry in os.listdir(full_dir):
                 # Only import regular files
                 path = os.path.join(full_dir, entry)
-                link_data_only = params.get('link_data_only', 'copy_files')
-                if os.path.islink(full_dir) and link_data_only == 'link_to_files':
+                link_data_only = params.get("link_data_only", "copy_files")
+                if os.path.islink(full_dir) and link_data_only == "link_to_files":
                     # If we're linking instead of copying and the
                     # sub-"directory" in the import dir is actually a symlink,
                     # dereference the symlink, but not any of its contents.
@@ -160,7 +186,7 @@ class LibraryActions:
                         path = os.path.join(link_path, entry)
                     else:
                         path = os.path.abspath(os.path.join(link_path, entry))
-                elif os.path.islink(path) and os.path.isfile(path) and link_data_only == 'link_to_files':
+                elif os.path.islink(path) and os.path.isfile(path) and link_data_only == "link_to_files":
                     # If we're linking instead of copying and the "file" in the
                     # sub-directory of the import dir is actually a symlink,
                     # dereference the symlink (one dereference only, Vasili).
@@ -182,13 +208,15 @@ class LibraryActions:
         return files, None, None
 
     def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, response_code, message):
-        preserve_dirs = util.string_as_bool(params.get('preserve_dirs', False))
+        preserve_dirs = util.string_as_bool(params.get("preserve_dirs", False))
         uploaded_datasets = []
         (files_and_folders, _response_code, _message) = self._get_path_files_and_folders(params, preserve_dirs)
         if _response_code:
             return (uploaded_datasets, _response_code, _message)
         for (path, name, folder) in files_and_folders:
-            uploaded_datasets.append(self._make_library_uploaded_dataset(trans, params, name, path, 'path_paste', library_bunch, folder))
+            uploaded_datasets.append(
+                self._make_library_uploaded_dataset(trans, params, name, path, "path_paste", library_bunch, folder)
+            )
         return uploaded_datasets, 200, None
 
     def _get_path_files_and_folders(self, params, preserve_dirs):
@@ -210,17 +238,21 @@ class LibraryActions:
             for file in files:
                 file_path = os.path.abspath(os.path.join(basedir, file))
                 if preserve_dirs:
-                    in_folder = os.path.dirname(file_path.replace(path, '', 1).lstrip('/'))
+                    in_folder = os.path.dirname(file_path.replace(path, "", 1).lstrip("/"))
                 else:
                     in_folder = None
                 files_and_folders.append((file_path, file, in_folder))
         return files_and_folders
 
     def _paths_list(self, params):
-        return [(line.strip(), os.path.abspath(line.strip())) for line in params.get('filesystem_paths', '').splitlines() if line.strip()]
+        return [
+            (line.strip(), os.path.abspath(line.strip()))
+            for line in params.get("filesystem_paths", "").splitlines()
+            if line.strip()
+        ]
 
     def _check_path_paste_params(self, params):
-        if params.get('filesystem_paths', '') == '':
+        if params.get("filesystem_paths", "") == "":
             message = "No paths entered in the upload form"
             response_code = 400
             return None, response_code, message
@@ -235,36 +267,36 @@ class LibraryActions:
         return None
 
     def _make_library_uploaded_dataset(self, trans, params, name, path, type, library_bunch, in_folder=None):
-        link_data_only = params.get('link_data_only', 'copy_files')
-        uuid_str = params.get('uuid', None)
-        file_type = params.get('file_type', None)
+        link_data_only = params.get("link_data_only", "copy_files")
+        uuid_str = params.get("uuid", None)
+        file_type = params.get("file_type", None)
         library_bunch.replace_dataset = None  # not valid for these types of upload
         uploaded_dataset = util.bunch.Bunch()
         new_name = name
         # Remove compressed file extensions, if any, but only if
         # we're copying files into Galaxy's file space.
-        if link_data_only == 'copy_files':
-            if new_name.endswith('.gz'):
-                new_name = new_name.rstrip('.gz')
-            elif new_name.endswith('.zip'):
-                new_name = new_name.rstrip('.zip')
+        if link_data_only == "copy_files":
+            if new_name.endswith(".gz"):
+                new_name = new_name.rstrip(".gz")
+            elif new_name.endswith(".zip"):
+                new_name = new_name.rstrip(".zip")
         uploaded_dataset.name = new_name
         uploaded_dataset.path = path
         uploaded_dataset.type = type
         uploaded_dataset.ext = None
         uploaded_dataset.file_type = file_type
-        uploaded_dataset.dbkey = params.get('dbkey', None)
-        uploaded_dataset.to_posix_lines = params.get('to_posix_lines', None)
-        uploaded_dataset.space_to_tab = params.get('space_to_tab', None)
-        uploaded_dataset.tag_using_filenames = params.get('tag_using_filenames', False)
-        uploaded_dataset.tags = params.get('tags', None)
-        uploaded_dataset.purge_source = getattr(trans.app.config, 'ftp_upload_purge', True)
+        uploaded_dataset.dbkey = params.get("dbkey", None)
+        uploaded_dataset.to_posix_lines = params.get("to_posix_lines", None)
+        uploaded_dataset.space_to_tab = params.get("space_to_tab", None)
+        uploaded_dataset.tag_using_filenames = params.get("tag_using_filenames", False)
+        uploaded_dataset.tags = params.get("tags", None)
+        uploaded_dataset.purge_source = getattr(trans.app.config, "ftp_upload_purge", True)
         if in_folder:
             uploaded_dataset.in_folder = in_folder
-        uploaded_dataset.data = upload_common.new_upload(trans, 'api', uploaded_dataset, library_bunch)
+        uploaded_dataset.data = upload_common.new_upload(trans, "api", uploaded_dataset, library_bunch)
         uploaded_dataset.link_data_only = link_data_only
         uploaded_dataset.uuid = uuid_str
-        if link_data_only == 'link_to_files':
+        if link_data_only == "link_to_files":
             uploaded_dataset.data.link_to(path)
             trans.sa_session.add_all((uploaded_dataset.data, uploaded_dataset.data.dataset))
             trans.sa_session.flush()
@@ -274,15 +306,16 @@ class LibraryActions:
         is_admin = trans.user_is_admin
         current_user_roles = trans.get_current_user_roles()
         try:
-            parent_folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(trans.security.decode_id(parent_id))
+            parent_folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(
+                trans.security.decode_id(parent_id)
+            )
         except Exception:
             parent_folder = None
         # Check the library which actually contains the user-supplied parent folder, not the user-supplied
         # library, which could be anything.
         self._check_access(trans, is_admin, parent_folder, current_user_roles)
         self._check_add(trans, is_admin, parent_folder, current_user_roles)
-        new_folder = trans.app.model.LibraryFolder(name=kwd.get('name', ''),
-                                                   description=kwd.get('description', ''))
+        new_folder = trans.app.model.LibraryFolder(name=kwd.get("name", ""), description=kwd.get("description", ""))
         # We are associating the last used genome build with folders, so we will always
         # initialize a new folder with the first dbkey in genome builds list which is currently
         # ?    unspecified (?)
@@ -300,7 +333,10 @@ class LibraryActions:
             if not item:
                 message = f"Invalid history dataset ({escape(str(item))}) specified."
                 raise ObjectNotFound(message)
-            elif not trans.app.security_agent.can_access_dataset(current_user_roles, item.dataset) and item.history.user == trans.user:
+            elif (
+                not trans.app.security_agent.can_access_dataset(current_user_roles, item.dataset)
+                and item.history.user == trans.user
+            ):
                 message = f"You do not have permission to access the history dataset with id ({str(item.id)})."
                 raise ItemAccessibilityException(message)
         else:
@@ -308,13 +344,15 @@ class LibraryActions:
             if not item:
                 message = f"Invalid library item ({escape(str(item))}) specified."
                 raise ObjectNotFound(message)
-            elif not (is_admin or trans.app.security_agent.can_access_library_item(current_user_roles, item, trans.user)):
+            elif not (
+                is_admin or trans.app.security_agent.can_access_library_item(current_user_roles, item, trans.user)
+            ):
                 if isinstance(item, trans.model.Library):
-                    item_type = 'data library'
+                    item_type = "data library"
                 elif isinstance(item, trans.model.LibraryFolder):
-                    item_type = 'folder'
+                    item_type = "folder"
                 else:
-                    item_type = '(unknown item type)'
+                    item_type = "(unknown item type)"
                 message = f"You do not have permission to access the {escape(item_type)} with id ({str(item.id)})."
                 raise ItemAccessibilityException(message)
 
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 0b131b4b3dc..f0647767282 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -2,13 +2,22 @@ import logging
 import signal
 import sys
 import time
-from typing import Any, Callable, List, Tuple
+from typing import (
+    Any,
+    Callable,
+    List,
+    Tuple,
+)
 
 import galaxy.model
 import galaxy.model.security
 import galaxy.queues
 import galaxy.security
-from galaxy import auth, config, jobs
+from galaxy import (
+    auth,
+    config,
+    jobs,
+)
 from galaxy.config_watchers import ConfigWatchers
 from galaxy.containers import build_container_interfaces
 from galaxy.datatypes.registry import Registry
@@ -43,11 +52,14 @@ from galaxy.queue_worker import (
     GalaxyQueueWorker,
     send_local_control_task,
 )
-from galaxy.quota import get_quota_agent, QuotaAgent
+from galaxy.quota import (
+    get_quota_agent,
+    QuotaAgent,
+)
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.security.vault import (
     Vault,
-    VaultFactory
+    VaultFactory,
 )
 from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from galaxy.tool_shed.galaxy_install.update_repository_manager import UpdateRepositoryManager
@@ -55,12 +67,15 @@ from galaxy.tool_util.deps.views import DependencyResolversView
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.tools.cache import (
     ToolCache,
-    ToolShedRepositoryCache
+    ToolShedRepositoryCache,
 )
 from galaxy.tools.data_manager.manager import DataManagers
 from galaxy.tools.error_reports import ErrorReports
 from galaxy.tools.special_tools import load_lib_tools
-from galaxy.tours import build_tours_registry, ToursRegistry
+from galaxy.tours import (
+    build_tours_registry,
+    ToursRegistry,
+)
 from galaxy.util import (
     ExecutionTimer,
     heartbeat,
@@ -72,11 +87,18 @@ from galaxy.visualization.genomes import Genomes
 from galaxy.visualization.plugins.registry import VisualizationsRegistry
 from galaxy.web import url_for
 from galaxy.web.proxy import ProxyManager
-from galaxy.web_stack import application_stack_instance, ApplicationStack
+from galaxy.web_stack import (
+    application_stack_instance,
+    ApplicationStack,
+)
 from galaxy.webhooks import WebhooksRegistry
 from galaxy.workflow.trs_proxy import TrsProxy
 from .di import Container
-from .structured_app import BasicSharedApp, MinimalManagerApp, StructuredApp
+from .structured_app import (
+    BasicSharedApp,
+    MinimalManagerApp,
+    StructuredApp,
+)
 
 log = logging.getLogger(__name__)
 app = None
@@ -106,7 +128,13 @@ class SentryClientMixin:
         self.sentry_client = None
         if self.config.sentry_dsn:
             event_level = self.config.sentry_event_level.upper()
-            assert event_level in ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'], f"Invalid sentry event level '{self.config.sentry.event_level}'"
+            assert event_level in [
+                "DEBUG",
+                "INFO",
+                "WARNING",
+                "ERROR",
+                "CRITICAL",
+            ], f"Invalid sentry event level '{self.config.sentry.event_level}'"
 
             def postfork_sentry_client():
                 import sentry_sdk
@@ -114,12 +142,12 @@ class SentryClientMixin:
 
                 sentry_logging = LoggingIntegration(
                     level=logging.INFO,  # Capture info and above as breadcrumbs
-                    event_level=getattr(logging, event_level)  # Send errors as events
+                    event_level=getattr(logging, event_level),  # Send errors as events
                 )
                 self.sentry_client = sentry_sdk.init(
                     self.config.sentry_dsn,
                     release=f"{self.config.version_major}.{self.config.version_minor}",
-                    integrations=[sentry_logging]
+                    integrations=[sentry_logging],
                 )
 
             self.application_stack.register_postfork_function(postfork_sentry_client)
@@ -141,7 +169,7 @@ class MinimalGalaxyApplication(BasicSharedApp, config.ConfiguresGalaxyMixin, Hal
             # an appropriately configured logger in configure_logging below.
             logging.basicConfig(level=logging.DEBUG)
         log.debug("python path is: %s", ", ".join(sys.path))
-        self.name = 'galaxy'
+        self.name = "galaxy"
         self.is_webapp = False
         self.new_installation = False
         # Read config file and check for errors
@@ -150,7 +178,7 @@ class MinimalGalaxyApplication(BasicSharedApp, config.ConfiguresGalaxyMixin, Hal
         if configure_logging:
             config.configure_logging(self.config)
         self._configure_object_store(fsmon=True)
-        config_file = kwargs.get('global_conf', {}).get('__file__', None)
+        config_file = kwargs.get("global_conf", {}).get("__file__", None)
         if config_file:
             log.debug('Using "galaxy.ini" config file: %s', config_file)
         self._configure_models(check_migrate_databases=self.config.check_migrate_databases, config_file=config_file)
@@ -165,7 +193,8 @@ class MinimalGalaxyApplication(BasicSharedApp, config.ConfiguresGalaxyMixin, Hal
     def configure_fluent_log(self):
         if self.config.fluent_log:
             from galaxy.util.custom_logging.fluent_log import FluentTraceLogger
-            self.trace_logger = FluentTraceLogger('galaxy', self.config.fluent_host, self.config.fluent_port)
+
+            self.trace_logger = FluentTraceLogger("galaxy", self.config.fluent_host, self.config.fluent_port)
         else:
             self.trace_logger = None
 
@@ -182,12 +211,16 @@ class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self._register_singleton(MinimalManagerApp, self)
-        self.execution_timer_factory = self._register_singleton(ExecutionTimerFactory, ExecutionTimerFactory(self.config))
+        self.execution_timer_factory = self._register_singleton(
+            ExecutionTimerFactory, ExecutionTimerFactory(self.config)
+        )
         self.configure_fluent_log()
         self.application_stack = self._register_singleton(ApplicationStack, application_stack_instance(app=self))
         # Initialize job metrics manager, needs to be in place before
         # config so per-destination modifications can be made.
-        self.job_metrics = self._register_singleton(JobMetrics, JobMetrics(self.config.job_metrics_config_file, app=self))
+        self.job_metrics = self._register_singleton(
+            JobMetrics, JobMetrics(self.config.job_metrics_config_file, app=self)
+        )
         # Initialize the job management configuration
         self.job_config = self._register_singleton(jobs.JobConfiguration)
 
@@ -206,17 +239,22 @@ class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication):
         self.library_datasets_manager = self._register_singleton(LibraryDatasetsManager)
         self.role_manager = self._register_singleton(RoleManager)
         from galaxy.jobs.manager import JobManager
+
         self.job_manager = self._register_singleton(JobManager)
 
         # ConfiguredFileSources
-        self.file_sources = self._register_singleton(ConfiguredFileSources, ConfiguredFileSources.from_app_config(self.config))
+        self.file_sources = self._register_singleton(
+            ConfiguredFileSources, ConfiguredFileSources.from_app_config(self.config)
+        )
 
         self.vault = self._register_singleton(Vault, VaultFactory.from_app(self))
 
         # We need the datatype registry for running certain tasks that modify HDAs, and to build the registry we need
         # to setup the installed repositories ... this is not ideal
         self._configure_tool_config_files()
-        self.installed_repository_manager = self._register_singleton(InstalledRepositoryManager, InstalledRepositoryManager(self))
+        self.installed_repository_manager = self._register_singleton(
+            InstalledRepositoryManager, InstalledRepositoryManager(self)
+        )
         self._configure_datatypes_registry(self.installed_repository_manager)
         self._register_singleton(Registry, self.datatypes_registry)
         galaxy.model.set_datatypes_registry(self.datatypes_registry)
@@ -244,7 +282,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         self._register_singleton(StructuredApp, self)
         # A lot of postfork initialization depends on the server name, ensure it is set immediately after forking before other postfork functions
         self.application_stack.register_postfork_function(self.application_stack.set_postfork_server_name, self)
-        self.config.reload_sanitize_allowlist(explicit='sanitize_allowlist_file' in kwargs)
+        self.config.reload_sanitize_allowlist(explicit="sanitize_allowlist_file" in kwargs)
         self.amqp_internal_connection_obj = galaxy.queues.connection_from_config(self.config)
         # queue_worker *can* be initialized with a queue, but here we don't
         # want to and we'll allow postfork to bind and start it.
@@ -252,8 +290,12 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
 
         self._configure_tool_shed_registry()
 
-        self.dependency_resolvers_view = self._register_singleton(DependencyResolversView, DependencyResolversView(self))
-        self.test_data_resolver = self._register_singleton(TestDataResolver, TestDataResolver(file_dirs=self.config.tool_test_data_directories))
+        self.dependency_resolvers_view = self._register_singleton(
+            DependencyResolversView, DependencyResolversView(self)
+        )
+        self.test_data_resolver = self._register_singleton(
+            TestDataResolver, TestDataResolver(file_dirs=self.config.tool_test_data_directories)
+        )
         self.dynamic_tool_manager = self._register_singleton(DynamicToolManager)
         self.api_keys_manager = self._register_singleton(ApiKeyManager)
 
@@ -268,7 +310,9 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         self.data_provider_registry = self._register_singleton(DataProviderRegistry)
 
         # Initialize error report plugins.
-        self.error_reports = self._register_singleton(ErrorReports, ErrorReports(self.config.error_report_file, app=self))
+        self.error_reports = self._register_singleton(
+            ErrorReports, ErrorReports(self.config.error_report_file, app=self)
+        )
 
         # Setup a Tool Cache
         self.tool_cache = self._register_singleton(ToolCache)
@@ -279,7 +323,9 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         # Load Data Manager
         self.data_managers = self._register_singleton(DataManagers)
         # Load the update repository manager.
-        self.update_repository_manager = self._register_singleton(UpdateRepositoryManager, UpdateRepositoryManager(self))
+        self.update_repository_manager = self._register_singleton(
+            UpdateRepositoryManager, UpdateRepositoryManager(self)
+        )
         # Load proprietary datatype converters and display applications.
         self.installed_repository_manager.load_proprietary_converters_and_display_applications()
         # Load datatype display applications defined in local datatypes_conf.xml
@@ -292,10 +338,14 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         load_lib_tools(self.toolbox)
         self.toolbox.persist_cache(register_postfork=True)
         # visualizations registry: associates resources with visualizations, controls how to render
-        self.visualizations_registry = self._register_singleton(VisualizationsRegistry, VisualizationsRegistry(
-            self,
-            directories_setting=self.config.visualization_plugins_directory,
-            template_cache_dir=self.config.template_cache_path))
+        self.visualizations_registry = self._register_singleton(
+            VisualizationsRegistry,
+            VisualizationsRegistry(
+                self,
+                directories_setting=self.config.visualization_plugins_directory,
+                template_cache_dir=self.config.template_cache_path,
+            ),
+        )
         # Tours registry
         tour_registry = build_tours_registry(self.config.tour_config_dir)
         self.tour_registry = tour_registry
@@ -305,8 +355,8 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         # Load security policy.
         self.security_agent = self.model.security_agent
         self.host_security_agent = galaxy.model.security.HostAgent(
-            model=self.security_agent.model,
-            permitted_actions=self.security_agent.permitted_actions)
+            model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions
+        )
         # Load quota management.
         self.quota_agent = self._register_singleton(QuotaAgent, get_quota_agent(self.config, self.model))
         # Heartbeat for thread profiling
@@ -317,9 +367,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         if self.config.use_heartbeat:
             if heartbeat.Heartbeat:
                 self.heartbeat = heartbeat.Heartbeat(
-                    self.config,
-                    period=self.config.heartbeat_interval,
-                    fname=self.config.heartbeat_log
+                    self.config, period=self.config.heartbeat_interval, fname=self.config.heartbeat_log
                 )
                 self.heartbeat.daemon = True
                 self.application_stack.register_postfork_function(self.heartbeat.start)
@@ -327,15 +375,15 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         self.authnz_manager = None
         if self.config.enable_oidc:
             from galaxy.authnz import managers
-            self.authnz_manager = managers.AuthnzManager(self,
-                                                         self.config.oidc_config_file,
-                                                         self.config.oidc_backends_config_file)
+
+            self.authnz_manager = managers.AuthnzManager(
+                self, self.config.oidc_config_file, self.config.oidc_backends_config_file
+            )
 
         self.containers = {}
         if self.config.enable_beta_containers_interface:
             self.containers = build_container_interfaces(
-                self.config.containers_config_file,
-                containers_conf=self.config.containers_conf
+                self.config.containers_config_file, containers_conf=self.config.containers_conf
             )
 
         if not self.config.enable_celery_tasks and self.config.history_audit_table_prune_interval > 0:
@@ -344,7 +392,8 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
                 name="HistoryAuditTablePruneTask",
                 interval=self.config.history_audit_table_prune_interval,
                 immediate_start=False,
-                time_execution=True)
+                time_execution=True,
+            )
             self.application_stack.register_postfork_function(self.prune_history_audit_task.start)
             self.haltables.append(("HistoryAuditTablePruneTask", self.prune_history_audit_task.shutdown))
         # Start the job manager
@@ -355,6 +404,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         self.proxy_manager = ProxyManager(self.config)
 
         from galaxy.workflow import scheduling_manager
+
         # Must be initialized after job_config.
         self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager(self)
 
@@ -372,9 +422,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
             handlers[signal.SIGUSR1] = self.heartbeat.dump_signal_handler
         self._configure_signal_handlers(handlers)
 
-        self.database_heartbeat = DatabaseHeartbeat(
-            application_stack=self.application_stack
-        )
+        self.database_heartbeat = DatabaseHeartbeat(application_stack=self.application_stack)
         self.database_heartbeat.add_change_callback(self.watchers.change_state)
         self.application_stack.register_postfork_function(self.database_heartbeat.start)
 
@@ -382,7 +430,9 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         self.application_stack.register_postfork_function(self.application_stack.start)
         self.application_stack.register_postfork_function(self.queue_worker.bind_and_start)
         # Delay toolbox index until after startup
-        self.application_stack.register_postfork_function(lambda: send_local_control_task(self, 'rebuild_toolbox_search_index'))
+        self.application_stack.register_postfork_function(
+            lambda: send_local_control_task(self, "rebuild_toolbox_search_index")
+        )
 
         # Inject url_for for components to more easily optionally depend
         # on url_for.
@@ -420,32 +470,33 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
 
     @property
     def is_job_handler(self) -> bool:
-        return (self.config.track_jobs_in_database and self.job_config.is_handler) or not self.config.track_jobs_in_database
+        return (
+            self.config.track_jobs_in_database and self.job_config.is_handler
+        ) or not self.config.track_jobs_in_database
 
 
 class StatsdStructuredExecutionTimer(StructuredExecutionTimer):
-
     def __init__(self, galaxy_statsd_client, *args, **kwds):
         self.galaxy_statsd_client = galaxy_statsd_client
         super().__init__(*args, **kwds)
 
     def to_str(self, **kwd):
-        self.galaxy_statsd_client.timing(self.timer_id, self.elapsed * 1000., kwd)
+        self.galaxy_statsd_client.timing(self.timer_id, self.elapsed * 1000.0, kwd)
         return super().to_str(**kwd)
 
 
 class ExecutionTimerFactory:
-
     def __init__(self, config):
         statsd_host = getattr(config, "statsd_host", None)
         if statsd_host:
             from galaxy.web.framework.middleware.statsd import GalaxyStatsdClient
+
             self.galaxy_statsd_client = GalaxyStatsdClient(
                 statsd_host,
-                getattr(config, 'statsd_port', 8125),
-                getattr(config, 'statsd_prefix', 'galaxy'),
-                getattr(config, 'statsd_influxdb', False),
-                getattr(config, 'statsd_mock_calls', False),
+                getattr(config, "statsd_port", 8125),
+                getattr(config, "statsd_prefix", "galaxy"),
+                getattr(config, "statsd_influxdb", False),
+                getattr(config, "statsd_mock_calls", False),
             )
         else:
             self.galaxy_statsd_client = None
diff --git a/lib/galaxy/app_unittest_utils/celery_helper.py b/lib/galaxy/app_unittest_utils/celery_helper.py
index fa4657ef065..d70e0eafb94 100644
--- a/lib/galaxy/app_unittest_utils/celery_helper.py
+++ b/lib/galaxy/app_unittest_utils/celery_helper.py
@@ -3,6 +3,7 @@ from functools import wraps
 
 def rebind_container_to_task(app):
     import galaxy.app
+
     galaxy.app.app = app
     from galaxy.celery import (
         CELERY_TASKS,
@@ -15,6 +16,6 @@ def rebind_container_to_task(app):
     for task in CELERY_TASKS:
         task_fn = getattr(tasks, task, None)
         if task_fn:
-            task_fn = getattr(task_fn, '__wrapped__', task_fn)
+            task_fn = getattr(task_fn, "__wrapped__", task_fn)
             container_bound_task = magic_bind_dynamic(task_fn)
             setattr(tasks, task, container_bound_task)
diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index 98e3574b028..53ece3ff6fa 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -18,9 +18,16 @@ from galaxy.model import tags
 from galaxy.model.base import SharedModelMapping
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.scoped_session import galaxy_scoped_session
-from galaxy.model.unittest_utils import GalaxyDataTestApp, GalaxyDataTestConfig
+from galaxy.model.unittest_utils import (
+    GalaxyDataTestApp,
+    GalaxyDataTestConfig,
+)
 from galaxy.security import idencoding
-from galaxy.structured_app import BasicSharedApp, MinimalManagerApp, StructuredApp
+from galaxy.structured_app import (
+    BasicSharedApp,
+    MinimalManagerApp,
+    StructuredApp,
+)
 from galaxy.tool_util.deps.containers import NullContainerFinder
 from galaxy.tools.data import ToolDataTableManager
 from galaxy.util import StructuredExecutionTimer
@@ -33,34 +40,34 @@ from .celery_helper import rebind_container_to_task
 # =============================================================================
 def buildMockEnviron(**kwargs):
     environ = {
-        'CONTENT_LENGTH': '0',
-        'CONTENT_TYPE': '',
-        'HTTP_ACCEPT': '*/*',
-        'HTTP_ACCEPT_ENCODING': 'gzip, deflate',
-        'HTTP_ACCEPT_LANGUAGE': 'en-US,en;q=0.8,zh;q=0.5,ja;q=0.3',
-        'HTTP_CACHE_CONTROL': 'no-cache',
-        'HTTP_CONNECTION': 'keep-alive',
-        'HTTP_DNT': '1',
-        'HTTP_HOST': 'localhost:8000',
-        'HTTP_ORIGIN': 'http://localhost:8000',
-        'HTTP_PRAGMA': 'no-cache',
-        'HTTP_REFERER': 'http://localhost:8000',
-        'HTTP_USER_AGENT': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:43.0) Gecko/20100101 Firefox/43.0',
-        'PATH_INFO': '/',
-        'QUERY_STRING': '',
-        'REMOTE_ADDR': '127.0.0.1',
-        'REQUEST_METHOD': 'GET',
-        'SCRIPT_NAME': '',
-        'SERVER_NAME': '127.0.0.1',
-        'SERVER_PORT': '8080',
-        'SERVER_PROTOCOL': 'HTTP/1.1'
+        "CONTENT_LENGTH": "0",
+        "CONTENT_TYPE": "",
+        "HTTP_ACCEPT": "*/*",
+        "HTTP_ACCEPT_ENCODING": "gzip, deflate",
+        "HTTP_ACCEPT_LANGUAGE": "en-US,en;q=0.8,zh;q=0.5,ja;q=0.3",
+        "HTTP_CACHE_CONTROL": "no-cache",
+        "HTTP_CONNECTION": "keep-alive",
+        "HTTP_DNT": "1",
+        "HTTP_HOST": "localhost:8000",
+        "HTTP_ORIGIN": "http://localhost:8000",
+        "HTTP_PRAGMA": "no-cache",
+        "HTTP_REFERER": "http://localhost:8000",
+        "HTTP_USER_AGENT": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:43.0) Gecko/20100101 Firefox/43.0",
+        "PATH_INFO": "/",
+        "QUERY_STRING": "",
+        "REMOTE_ADDR": "127.0.0.1",
+        "REQUEST_METHOD": "GET",
+        "SCRIPT_NAME": "",
+        "SERVER_NAME": "127.0.0.1",
+        "SERVER_PORT": "8080",
+        "SERVER_PROTOCOL": "HTTP/1.1",
     }
     environ.update(**kwargs)
     return environ
 
 
 class MockApp(di.Container, GalaxyDataTestApp):
-    config: 'MockAppConfig'
+    config: "MockAppConfig"
 
     def __init__(self, config=None, **kwargs):
         super().__init__()
@@ -70,7 +77,7 @@ class MockApp(di.Container, GalaxyDataTestApp):
         self[MinimalManagerApp] = self
         self[StructuredApp] = self
         self[idencoding.IdEncodingHelper] = self.security
-        self.name = kwargs.get('name', 'galaxy')
+        self.name = kwargs.get("name", "galaxy")
         self[SharedModelMapping] = self.model
         self[GalaxyModelMapping] = self.model
         self[galaxy_scoped_session] = self.model.context
@@ -79,10 +86,7 @@ class MockApp(di.Container, GalaxyDataTestApp):
         self[tags.GalaxyTagHandler] = self.tag_handler
         self.quota_agent = quota.DatabaseQuotaAgent(self.model)
         self.job_config = Bunch(
-            dynamic_params=None,
-            destinations={},
-            use_messaging=False,
-            assign_handler=lambda *args, **kwargs: None
+            dynamic_params=None, destinations={}, use_messaging=False, assign_handler=lambda *args, **kwargs: None
         )
         self.tool_data_tables = ToolDataTableManager(tool_data_path=self.config.tool_data_path)
         self.dataset_collections_service = None
@@ -103,6 +107,7 @@ class MockApp(di.Container, GalaxyDataTestApp):
 
         def url_for(*args, **kwds):
             return "/mock/url"
+
         self.url_for = url_for
 
     def wait_for_toolbox_reload(self, toolbox):
@@ -120,19 +125,18 @@ class MockLock:
 
 
 class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin):
-
     class MockSchema(Bunch):
         pass
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self.schema = self.MockSchema()
-        self.use_remote_user = kwargs.get('use_remote_user', False)
+        self.use_remote_user = kwargs.get("use_remote_user", False)
         self.enable_celery_tasks = False
-        self.tool_data_path = os.path.join(self.root, 'tool-data')
+        self.tool_data_path = os.path.join(self.root, "tool-data")
         self.galaxy_data_manager_data_path = self.tool_data_path
         self.tool_dependency_dir = None
-        self.metadata_strategy = 'directory'
+        self.metadata_strategy = "directory"
 
         self.user_activation_on = False
         self.new_user_dataset_access_role_default_private = False
@@ -152,8 +156,8 @@ class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin):
         self.redact_email_in_job_name = False
 
         # Follow two required by GenomeBuilds
-        self.len_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'chrom')
-        self.builds_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'builds.txt.sample')
+        self.len_file_path = os.path.join("tool-data", "shared", "ucsc", "chrom")
+        self.builds_file_path = os.path.join("tool-data", "shared", "ucsc", "builds.txt.sample")
 
         self.shed_tool_config_file = "config/shed_tool_conf.xml"
         self.shed_tool_config_file_set = False
@@ -165,7 +169,7 @@ class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin):
 
         # set by MockDir
         self.enable_tool_document_cache = False
-        self.tool_cache_data_dir = os.path.join(self.root, 'tool_cache')
+        self.tool_cache_data_dir = os.path.join(self.root, "tool_cache")
         self.delay_tool_initialization = True
         self.external_chown_script = None
         self.check_job_script_integrity = False
@@ -173,9 +177,9 @@ class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin):
         self.check_job_script_integrity_sleep = 0
 
         self.default_panel_view = "default"
-        self.panel_views_dir = ''
+        self.panel_views_dir = ""
         self.panel_views = {}
-        self.edam_panel_views = ''
+        self.edam_panel_views = ""
 
         self.config_file = None
 
@@ -189,7 +193,7 @@ class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin):
         self.enable_tool_shed_check = False
         self.monitor_thread_join_timeout = 1
         self.integrated_tool_panel_config = None
-        self.vault_config_file = kwargs.get('vault_config_file')
+        self.vault_config_file = kwargs.get("vault_config_file")
         self.max_discovered_files = 10000
 
     @property
@@ -198,23 +202,21 @@ class MockAppConfig(GalaxyDataTestConfig, CommonConfigurationMixin):
 
     def __getattr__(self, name):
         # Handle the automatic [option]_set options: for tests, assume none are set
-        if name == 'is_set':
+        if name == "is_set":
             return lambda x: False
         # Handle the automatic config file _set options
-        if name.endswith('_file_set'):
+        if name.endswith("_file_set"):
             return False
         raise AttributeError(name)
 
 
 class MockWebapp:
-
     def __init__(self, security: idencoding.IdEncodingHelper, **kwargs):
-        self.name = kwargs.get('name', 'galaxy')
+        self.name = kwargs.get("name", "galaxy")
         self.security = security
 
 
 class MockTrans:
-
     def __init__(self, app=None, user=None, history=None, **kwargs):
         self.app = app or MockApp(**kwargs)
         self.model = self.app.model
@@ -273,14 +275,13 @@ class MockTrans:
 
 
 class MockVisualizationsRegistry:
-    BUILT_IN_VISUALIZATIONS = ['trackster']
+    BUILT_IN_VISUALIZATIONS = ["trackster"]
 
     def get_visualizations(self, trans, target):
         return []
 
 
 class MockDir:
-
     def __init__(self, structure_dict, where=None):
         self.structure_dict = structure_dict
         self.create_root(structure_dict, where)
@@ -301,7 +302,7 @@ class MockDir:
                 self.create_structure(subdir_path, v)
 
     def create_file(self, path, contents):
-        with open(path, 'w') as newfile:
+        with open(path, "w") as newfile:
             newfile.write(contents)
 
     def remove(self):
diff --git a/lib/galaxy/app_unittest_utils/tools_support.py b/lib/galaxy/app_unittest_utils/tools_support.py
index 349bc291350..c36ac90911b 100644
--- a/lib/galaxy/app_unittest_utils/tools_support.py
+++ b/lib/galaxy/app_unittest_utils/tools_support.py
@@ -17,14 +17,12 @@ from galaxy.tool_util.parser import get_tool_source
 from galaxy.tools import create_tool_from_source
 from galaxy.util.bunch import Bunch
 
-
 datatypes_registry = galaxy.datatypes.registry.Registry()
 datatypes_registry.load_datatypes()
 galaxy.model.set_datatypes_registry(datatypes_registry)
 
 
 class UsesApp:
-
     def setup_app(self):
         self.test_directory = tempfile.mkdtemp()
         self.app = MockApp()
@@ -37,7 +35,7 @@ class UsesApp:
 
 
 # Simple tool with just one text parameter and output.
-SIMPLE_TOOL_CONTENTS = '''<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile">
+SIMPLE_TOOL_CONTENTS = """<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile">
     <command>echo "$param1" &lt; $out1</command>
     <inputs>
         <param type="text" name="param1" value="" />
@@ -46,11 +44,11 @@ SIMPLE_TOOL_CONTENTS = '''<tool id="${tool_id}" name="Test Tool" version="$versi
         <data name="out1" format="data" label="Output ($param1)" />
     </outputs>
 </tool>
-'''
+"""
 
 
 # A tool with data parameters (kind of like cat1) my favorite test tool :)
-SIMPLE_CAT_TOOL_CONTENTS = '''<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile">
+SIMPLE_CAT_TOOL_CONTENTS = """<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile">
     <command>cat "$param1" #for $r in $repeat# "$r.param2" #end for# &lt; $out1</command>
     <inputs>
         <param type="data" format="tabular" name="param1" value="" />
@@ -62,11 +60,10 @@ SIMPLE_CAT_TOOL_CONTENTS = '''<tool id="${tool_id}" name="Test Tool" version="$v
         <data name="out1" format="data" />
     </outputs>
 </tool>
-'''
+"""
 
 
 class MockActionI:
-
     def execute(self, tool, trans, **kwds):
         pass
 
@@ -122,7 +119,6 @@ class UsesTools(UsesApp):
 
 
 class MockContext:
-
     def __init__(self, model_objects=None):
         self.expunged_all = False
         self.flushed = False
@@ -144,7 +140,6 @@ class MockContext:
 
 
 class MockQuery:
-
     def __init__(self, class_objects):
         self.class_objects = class_objects
 
@@ -155,4 +150,4 @@ class MockQuery:
         return self.class_objects.get(id, None)
 
 
-__all__ = ('UsesApp', )
+__all__ = ("UsesApp",)
diff --git a/lib/galaxy/auth/__init__.py b/lib/galaxy/auth/__init__.py
index 064ae8af2af..1f4aa9986c6 100644
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -3,7 +3,10 @@ Contains implementations of the authentication logic.
 """
 import logging
 
-from galaxy.auth.util import get_authenticators, parse_auth_results
+from galaxy.auth.util import (
+    get_authenticators,
+    parse_auth_results,
+)
 from galaxy.exceptions import Conflict
 from galaxy.util import string_as_bool
 
@@ -11,30 +14,29 @@ log = logging.getLogger(__name__)
 
 
 class AuthManager:
-
     def __init__(self, config):
         self.redact_username_in_logs = config.redact_username_in_logs
-        self.authenticators = get_authenticators(config.auth_config_file, config.is_set('auth_config_file'))
+        self.authenticators = get_authenticators(config.auth_config_file, config.is_set("auth_config_file"))
 
     def check_registration_allowed(self, email, username, password):
         """Checks if the provided email/username is allowed to register."""
-        message = ''
-        status = 'done'
+        message = ""
+        status = "done"
         for provider, options in self.active_authenticators(email, username, password):
             allow_reg = _get_allow_register(options)
-            if allow_reg == 'challenge':
+            if allow_reg == "challenge":
                 auth_results = provider.authenticate(email, username, password, options)
                 if auth_results[0] is True:
                     break
                 if auth_results[0] is None:
-                    message = 'Invalid email address/username or password.'
-                    status = 'error'
+                    message = "Invalid email address/username or password."
+                    status = "error"
                     break
             elif allow_reg is True:
                 break
             elif allow_reg is False:
-                message = 'Account registration not required for your account.  Please simply login.'
-                status = 'error'
+                message = "Account registration not required for your account.  Please simply login."
+                status = "error"
                 break
         return message, status
 
@@ -43,22 +45,18 @@ class AuthManager:
         Checks the username/email & password using auth providers in order.
         If a match is found, returns the 'auto-register' option for that provider.
         """
-        if '@' in login:
+        if "@" in login:
             email = login
             username = None
         else:
             email = None
             username = login
-        auth_return = {
-            "auto_reg": False,
-            "email": "",
-            "username": ""
-        }
+        auth_return = {"auto_reg": False, "email": "", "username": ""}
         for provider, options in self.active_authenticators(email, username, password):
             if provider is None:
                 log.debug(f"Unable to find module: {options}")
             else:
-                options['no_password_check'] = no_password_check
+                options["no_password_check"] = no_password_check
                 auth_results = provider.authenticate(email, username, password, options)
                 if auth_results[0] is True:
                     try:
@@ -98,10 +96,10 @@ class AuthManager:
                     if string_as_bool(options.get("allow-password-change", False)):
                         return
                     else:
-                        return 'Password change not supported.'
+                        return "Password change not supported."
                 elif auth_result is None:
                     break  # end authentication (skip rest)
-        return 'Invalid current password.'
+        return "Invalid current password."
 
     def active_authenticators(self, email, username, password):
         """Yields AuthProvider instances for the provided configfile that match the
@@ -112,11 +110,11 @@ class AuthManager:
                 filter_template = authenticator.filter_template
                 if filter_template:
                     filter_str = filter_template.format(email=email, username=username, password=password)
-                    passed_filter = eval(filter_str, {"__builtins__": None}, {'str': str})
+                    passed_filter = eval(filter_str, {"__builtins__": None}, {"str": str})
                     if not passed_filter:
                         continue  # skip to next
                 options = authenticator.options
-                options['redact_username_in_logs'] = self.redact_username_in_logs
+                options["redact_username_in_logs"] = self.redact_username_in_logs
                 yield authenticator.plugin, options
         except Exception:
             log.exception("Active Authenticators Failure")
@@ -124,9 +122,9 @@ class AuthManager:
 
 
 def _get_allow_register(d):
-    s = d.get('allow-register', True)
+    s = d.get("allow-register", True)
     lower_s = str(s).lower()
-    if lower_s == 'challenge':
+    if lower_s == "challenge":
         return lower_s
     else:
         return string_as_bool(s)
diff --git a/lib/galaxy/auth/providers/__init__.py b/lib/galaxy/auth/providers/__init__.py
index 220fdf24898..f85051dabcb 100644
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -11,7 +11,7 @@ class AuthProvider(metaclass=abc.ABCMeta):
 
     @abc.abstractproperty
     def plugin_type(self):
-        """ Short string providing labelling this plugin """
+        """Short string providing labelling this plugin"""
 
     @abc.abstractmethod
     def authenticate(self, email, username, password, options):
diff --git a/lib/galaxy/auth/providers/alwaysreject.py b/lib/galaxy/auth/providers/alwaysreject.py
index e39990ae977..b4ffa043fbe 100644
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -14,13 +14,14 @@ class AlwaysReject(AuthProvider):
     """A simple authenticator that just accepts users (does not care about their
     password).
     """
-    plugin_type = 'alwaysreject'
+
+    plugin_type = "alwaysreject"
 
     def authenticate(self, email, username, password, options):
         """
         See abstract method documentation.
         """
-        return (None, '', '')
+        return (None, "", "")
 
     def authenticate_user(self, user, password, options):
         """
@@ -30,4 +31,4 @@ class AlwaysReject(AuthProvider):
         return None
 
 
-__all__ = ('AlwaysReject', )
+__all__ = ("AlwaysReject",)
diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index dac936f7386..fc7eef2af5b 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -43,11 +43,16 @@ def _parse_ldap_options(options_unparsed):
         try:
             key, value = opt.split("=")
         except ValueError:
-            log.warning("LDAP authenticate: Invalid syntax '%s' inside <ldap-options> element. Syntax should be option1=value1,option2=value2", opt)
+            log.warning(
+                "LDAP authenticate: Invalid syntax '%s' inside <ldap-options> element. Syntax should be option1=value1,option2=value2",
+                opt,
+            )
             continue
 
         if not key.startswith(prefix):
-            log.warning("LDAP authenticate: Invalid LDAP option '%s'. '%s' doesn't start with prefix '%s'", opt, key, prefix)
+            log.warning(
+                "LDAP authenticate: Invalid LDAP option '%s'. '%s' doesn't start with prefix '%s'", opt, key, prefix
+            )
             continue
         try:
             key = getattr(ldap, key)
@@ -58,7 +63,9 @@ def _parse_ldap_options(options_unparsed):
             try:
                 value = getattr(ldap, value)
             except AttributeError:
-                log.warning("LDAP authenticate: Invalid LDAP option '%s'. '%s' is not available in module ldap", opt, value)
+                log.warning(
+                    "LDAP authenticate: Invalid LDAP option '%s'. '%s' is not available in module ldap", opt, value
+                )
                 continue
         pair = (key, value)
         log.debug("LDAP authenticate: Valid LDAP option pair '%s' -> '%s=%s'", opt, *pair)
@@ -76,8 +83,9 @@ class LDAP(AuthProvider):
     those fields first.  After that it will bind to LDAP with the username
     (formatted as specified).
     """
-    plugin_type = 'ldap'
-    role_search_option = 'auto-register-roles'
+
+    plugin_type = "ldap"
+    role_search_option = "auto-register-roles"
 
     def __init__(self):
         super().__init__()
@@ -86,32 +94,36 @@ class LDAP(AuthProvider):
 
     def check_config(self, username, email, options):
         ok = True
-        if options.get('continue-on-failure', 'False') == 'False':
+        if options.get("continue-on-failure", "False") == "False":
             failure_mode = None  # reject and do not continue
         else:
             failure_mode = False  # reject but continue
 
-        if string_as_bool(options.get('login-use-username', False)):
+        if string_as_bool(options.get("login-use-username", False)):
             if not username:
-                log.debug('LDAP authenticate: username must be used to login, cannot be None')
+                log.debug("LDAP authenticate: username must be used to login, cannot be None")
                 return ok, failure_mode
         else:
             if not email:
-                log.debug('LDAP authenticate: email must be used to login, cannot be None')
+                log.debug("LDAP authenticate: email must be used to login, cannot be None")
                 return ok, failure_mode
 
-        auto_create_roles = string_as_bool(options.get('auto-create-roles', False))
-        auto_create_groups = string_as_bool(options.get('auto-create-groups', False))
+        auto_create_roles = string_as_bool(options.get("auto-create-roles", False))
+        auto_create_groups = string_as_bool(options.get("auto-create-groups", False))
         self.auto_create_roles_or_groups = auto_create_roles or auto_create_groups
-        auto_assign_roles_to_groups_only = string_as_bool(options.get('auto-assign-roles-to-groups-only', False))
+        auto_assign_roles_to_groups_only = string_as_bool(options.get("auto-assign-roles-to-groups-only", False))
         if auto_assign_roles_to_groups_only and not (auto_create_roles and auto_create_groups):
-            raise ConfigurationError("If 'auto-assign-roles-to-groups-only' is True, auto-create-roles and "
-                                     "auto-create-groups have to be True as well.")
+            raise ConfigurationError(
+                "If 'auto-assign-roles-to-groups-only' is True, auto-create-roles and "
+                "auto-create-groups have to be True as well."
+            )
 
         self.role_search_attribute = options.get(self.role_search_option)
         if self.auto_create_roles_or_groups and self.role_search_attribute is None:
-            raise ConfigurationError("If 'auto-create-roles' or 'auto-create-groups' is True, a '%s' attribute has to"
-                                     " be provided." % self.role_search_option)
+            raise ConfigurationError(
+                "If 'auto-create-roles' or 'auto-create-groups' is True, a '%s' attribute has to"
+                " be provided." % self.role_search_option
+            )
 
         return ok, failure_mode
 
@@ -123,10 +135,10 @@ class LDAP(AuthProvider):
         if not config_ok:
             return failure_mode, None
 
-        params = {'email': email, 'username': username}
+        params = {"email": email, "username": username}
 
         try:
-            ldap_options_raw = _get_subs(options, 'ldap-options', params)
+            ldap_options_raw = _get_subs(options, "ldap-options", params)
         except ConfigurationError:
             ldap_options = ()
         else:
@@ -139,34 +151,37 @@ class LDAP(AuthProvider):
             for opt in ldap_options:
                 ldap.set_option(*opt)
         except Exception:
-            log.exception('LDAP authenticate: set_option exception')
+            log.exception("LDAP authenticate: set_option exception")
             return (failure_mode, None)
 
-        if 'search-fields' in options:
+        if "search-fields" in options:
             try:
-                conn = ldap.initialize(_get_subs(options, 'server', params))
+                conn = ldap.initialize(_get_subs(options, "server", params))
                 conn.protocol_version = 3
 
-                if 'search-user' in options:
+                if "search-user" in options:
                     conn.simple_bind_s(
-                        _get_subs(options, 'search-user', params),
-                        _get_subs(options, 'search-password', params))
+                        _get_subs(options, "search-user", params), _get_subs(options, "search-password", params)
+                    )
                 else:
                     conn.simple_bind_s()
 
                 # setup search
-                attributes = {_.strip().format(**params) for _ in options['search-fields'].split(',')}
-                if 'search-memberof-filter' in options:
-                    attributes.add('memberOf')
+                attributes = {_.strip().format(**params) for _ in options["search-fields"].split(",")}
+                if "search-memberof-filter" in options:
+                    attributes.add("memberOf")
                 suser = conn.search_ext_s(
-                    _get_subs(options, 'search-base', params),
+                    _get_subs(options, "search-base", params),
                     ldap.SCOPE_SUBTREE,
-                    _get_subs(options, 'search-filter', params), attributes,
-                    timeout=60, sizelimit=1)
+                    _get_subs(options, "search-filter", params),
+                    attributes,
+                    timeout=60,
+                    sizelimit=1,
+                )
 
                 # parse results
                 if suser is None or len(suser) == 0:
-                    log.warning('LDAP authenticate: search returned no results')
+                    log.warning("LDAP authenticate: search returned no results")
                     return (failure_mode, None)
                 dn, attrs = suser[0]
                 log.debug("LDAP authenticate: dn is %s", dn)
@@ -175,7 +190,7 @@ class LDAP(AuthProvider):
                     if self.role_search_attribute and attr == self.role_search_attribute[1:-1]:  # strip curly brackets
                         # keep role names as list
                         params[self.role_search_option] = [unicodify(_) for _ in attrs[attr]]
-                    elif attr == 'memberOf':
+                    elif attr == "memberOf":
                         params[attr] = [unicodify(_) for _ in attrs[attr]]
                     elif attr in attrs:
                         params[attr] = unicodify(attrs[attr][0])
@@ -183,12 +198,13 @@ class LDAP(AuthProvider):
                         params[attr] = ""
 
                 if self.auto_create_roles_or_groups and self.role_search_option not in params:
-                    raise ConfigurationError("Missing or mismatching LDAP parameters for %s. Make sure the %s is "
-                                             "included in the 'search-fields'." %
-                                             (self.role_search_option, self.role_search_attribute))
-                params['dn'] = dn
+                    raise ConfigurationError(
+                        "Missing or mismatching LDAP parameters for %s. Make sure the %s is "
+                        "included in the 'search-fields'." % (self.role_search_option, self.role_search_attribute)
+                    )
+                params["dn"] = dn
             except Exception:
-                log.exception('LDAP authenticate: search exception')
+                log.exception("LDAP authenticate: search exception")
                 return (failure_mode, None)
 
         return failure_mode, params
@@ -197,7 +213,7 @@ class LDAP(AuthProvider):
         """
         See abstract method documentation.
         """
-        if not options['redact_username_in_logs']:
+        if not options["redact_username_in_logs"]:
             log.debug("LDAP authenticate: email is %s", email)
             log.debug("LDAP authenticate: username is %s", username)
 
@@ -205,39 +221,41 @@ class LDAP(AuthProvider):
 
         failure_mode, params = self.ldap_search(email, username, options)
         if not params:
-            return failure_mode, '', ''
+            return failure_mode, "", ""
 
         # allow to skip authentication to allow for pre-populating users
-        if not options.get('no_password_check', False):
-            params['password'] = password
+        if not options.get("no_password_check", False):
+            params["password"] = password
             if not self._authenticate(params, options):
-                return failure_mode, '', ''
+                return failure_mode, "", ""
 
         # check whether the user is a member of a specified group/domain/...
-        if 'search-memberof-filter' in options:
-            search_filter = _get_subs(options, 'search-memberof-filter', params)
-            if not any(search_filter in ad_node_name for ad_node_name in params['memberOf']):
-                return failure_mode, '', ''
+        if "search-memberof-filter" in options:
+            search_filter = _get_subs(options, "search-memberof-filter", params)
+            if not any(search_filter in ad_node_name for ad_node_name in params["memberOf"]):
+                return failure_mode, "", ""
 
         attributes = {}
         if self.auto_create_roles_or_groups:
-            attributes['roles'] = params[self.role_search_option]
-        return (True,
-                _get_subs(options, 'auto-register-email', params),
-                transform_publicname(_get_subs(options, 'auto-register-username', params)),
-                attributes)
+            attributes["roles"] = params[self.role_search_option]
+        return (
+            True,
+            _get_subs(options, "auto-register-email", params),
+            transform_publicname(_get_subs(options, "auto-register-username", params)),
+            attributes,
+        )
 
     def _authenticate(self, params, options):
         """
         Do the actual authentication by binding as the user to check their credentials
         """
         try:
-            conn = ldap.initialize(_get_subs(options, 'server', params))
+            conn = ldap.initialize(_get_subs(options, "server", params))
             conn.protocol_version = 3
-            bind_user = _get_subs(options, 'bind-user', params)
-            bind_password = _get_subs(options, 'bind-password', params)
+            bind_user = _get_subs(options, "bind-user", params)
+            bind_password = _get_subs(options, "bind-password", params)
         except Exception:
-            log.exception('LDAP authenticate: initialize exception')
+            log.exception("LDAP authenticate: initialize exception")
             return False
         try:
             conn.simple_bind_s(bind_user, bind_password)
@@ -248,13 +266,13 @@ class LDAP(AuthProvider):
                 pass
             else:
                 if whoami is None:
-                    raise RuntimeError('LDAP authenticate: anonymous bind')
-                if not options['redact_username_in_logs']:
+                    raise RuntimeError("LDAP authenticate: anonymous bind")
+                if not options["redact_username_in_logs"]:
                     log.debug("LDAP authenticate: whoami is %s", whoami)
         except Exception as e:
-            log.info('LDAP authenticate: bind exception: %s', unicodify(e))
+            log.info("LDAP authenticate: bind exception: %s", unicodify(e))
             return False
-        log.debug('LDAP authentication successful')
+        log.debug("LDAP authentication successful")
         return True
 
     def authenticate_user(self, user, password, options):
@@ -265,9 +283,10 @@ class LDAP(AuthProvider):
 
 
 class ActiveDirectory(LDAP):
-    """ Effectively just an alias for LDAP auth, but may contain active directory specific
-    logic in the future. """
-    plugin_type = 'activedirectory'
+    """Effectively just an alias for LDAP auth, but may contain active directory specific
+    logic in the future."""
+
+    plugin_type = "activedirectory"
 
 
-__all__ = ('LDAP', 'ActiveDirectory')
+__all__ = ("LDAP", "ActiveDirectory")
diff --git a/lib/galaxy/auth/providers/localdb.py b/lib/galaxy/auth/providers/localdb.py
index d17d865a7dc..168800a3e06 100644
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -12,13 +12,14 @@ log = logging.getLogger(__name__)
 
 class LocalDB(AuthProvider):
     """Authenticate users against the local Galaxy database (as per usual)."""
-    plugin_type = 'localdb'
+
+    plugin_type = "localdb"
 
     def authenticate(self, email, username, password, options):
         """
         See abstract method documentation.
         """
-        return (False, '', '')  # it can never auto-create based of localdb (chicken-egg)
+        return (False, "", "")  # it can never auto-create based of localdb (chicken-egg)
 
     def authenticate_user(self, user, password, options):
         """
@@ -29,4 +30,4 @@ class LocalDB(AuthProvider):
         return user_ok
 
 
-__all__ = ('LocalDB', )
+__all__ = ("LocalDB",)
diff --git a/lib/galaxy/auth/providers/pam_auth.py b/lib/galaxy/auth/providers/pam_auth.py
index 69a56186935..48794157bd2 100644
--- a/lib/galaxy/auth/providers/pam_auth.py
+++ b/lib/galaxy/auth/providers/pam_auth.py
@@ -8,7 +8,7 @@ import shlex
 
 from galaxy.util import (
     commands,
-    string_as_bool
+    string_as_bool,
 )
 from ..providers import AuthProvider
 
@@ -56,35 +56,37 @@ Configuration example (for internal authentication, use email for user details):
 
 class PAM(AuthProvider):
 
-    plugin_type = 'PAM'
+    plugin_type = "PAM"
 
     def authenticate(self, email, username, password, options):
         pam_username = None
         auto_register_username = None
         auto_register_email = None
         force_fail = False
-        if not options['redact_username_in_logs']:
-            log.debug(f"use username: {options.get('login-use-username')} use email {options.get('login-use-email', False)} email {email} username {username}")
+        if not options["redact_username_in_logs"]:
+            log.debug(
+                f"use username: {options.get('login-use-username')} use email {options.get('login-use-email', False)} email {email} username {username}"
+            )
         # check email based login first because if email exists in Galaxy DB
         # we will be given the "public name" as username
-        if string_as_bool(options.get('login-use-email', False)) and email is not None:
-            if '@' in email:
-                (email_user, email_domain) = email.split('@')
+        if string_as_bool(options.get("login-use-email", False)) and email is not None:
+            if "@" in email:
+                (email_user, email_domain) = email.split("@")
                 pam_username = email_user
-                if email_domain == options.get('maildomain', None):
+                if email_domain == options.get("maildomain", None):
                     auto_register_email = email
                     if username is not None:
                         auto_register_username = username
                     else:
                         auto_register_username = email_user
                 else:
-                    log.debug('PAM authenticate: warning: email does not match configured PAM maildomain')
+                    log.debug("PAM authenticate: warning: email does not match configured PAM maildomain")
                     # no need to fail: if auto-register is not enabled, this
                     # might still be a valid user
             else:
-                log.debug('PAM authenticate: email must be used to login, but no valid email found')
+                log.debug("PAM authenticate: email must be used to login, but no valid email found")
                 force_fail = True
-        elif string_as_bool(options.get('login-use-username', False)):
+        elif string_as_bool(options.get("login-use-username", False)):
             # if we get here via authenticate_user then
             # user will be "public name" and
             # email address will be as per registered user
@@ -92,42 +94,44 @@ class PAM(AuthProvider):
                 pam_username = username
                 if email is not None:
                     auto_register_email = email
-                elif options.get('maildomain', None) is not None:
+                elif options.get("maildomain", None) is not None:
                     # we can register a user with this username and mail domain
                     # if auto registration is enabled
                     auto_register_email = f"{username}@{options['maildomain']}"
                 auto_register_username = username
             else:
-                log.debug('PAM authenticate: username login selected but no username provided')
+                log.debug("PAM authenticate: username login selected but no username provided")
                 force_fail = True
         else:
-            log.debug('PAM authenticate: could not find username for PAM')
+            log.debug("PAM authenticate: could not find username for PAM")
             force_fail = True
 
         if force_fail:
-            return None, '', ''
+            return None, "", ""
 
-        pam_service = options.get('pam-service', 'galaxy')
-        use_helper = string_as_bool(options.get('use-external-helper', False))
+        pam_service = options.get("pam-service", "galaxy")
+        use_helper = string_as_bool(options.get("use-external-helper", False))
         log.debug(f"PAM auth: will use external helper: {use_helper}")
         authenticated = False
         if use_helper:
-            authentication_helper = options.get('authentication-helper-script', '/bin/false').strip()
+            authentication_helper = options.get("authentication-helper-script", "/bin/false").strip()
             log.debug(f"PAM auth: external helper script: {authentication_helper}")
-            if not authentication_helper.startswith('/'):
+            if not authentication_helper.startswith("/"):
                 # don't accept relative path
                 authenticated = False
             else:
-                auth_cmd = shlex.split(f'/usr/bin/sudo -n {authentication_helper}')
+                auth_cmd = shlex.split(f"/usr/bin/sudo -n {authentication_helper}")
                 log.debug(f"PAM auth: external helper cmd: {auth_cmd}")
-                message = f'{pam_service}\n{pam_username}\n{password}\n'
+                message = f"{pam_service}\n{pam_username}\n{password}\n"
                 try:
                     output = commands.execute(auth_cmd, input=message)
                 except commands.CommandLineException as e:
-                    if e.stderr != '':
-                        log.debug(f"PAM auth: external authentication script had errors: status {e.returncode} error {e.stderr}")
+                    if e.stderr != "":
+                        log.debug(
+                            f"PAM auth: external authentication script had errors: status {e.returncode} error {e.stderr}"
+                        )
                     output = e.stdout
-                if output.strip() == 'True':
+                if output.strip() == "True":
                     authenticated = True
                 else:
                     authenticated = False
@@ -135,21 +139,25 @@ class PAM(AuthProvider):
             try:
                 import pam
             except ImportError:
-                log.debug('PAM authenticate: could not load pam module, PAM authentication disabled')
-                return None, '', ''
+                log.debug("PAM authenticate: could not load pam module, PAM authentication disabled")
+                return None, "", ""
 
             p_auth = pam.pam()
             authenticated = p_auth.authenticate(pam_username, password, service=pam_service)
 
         if authenticated:
-            log.debug(f"PAM authentication successful for {'redacted' if options['redact_username_in_logs'] else pam_username}")
+            log.debug(
+                f"PAM authentication successful for {'redacted' if options['redact_username_in_logs'] else pam_username}"
+            )
             return True, auto_register_email, auto_register_username
         else:
-            log.debug(f"PAM authentication failed for {'redacted' if options['redact_username_in_logs'] else pam_username}")
-            return False, '', ''
+            log.debug(
+                f"PAM authentication failed for {'redacted' if options['redact_username_in_logs'] else pam_username}"
+            )
+            return False, "", ""
 
     def authenticate_user(self, user, password, options):
         return self.authenticate(user.email, user.username, password, options)[0]
 
 
-__all__ = ('PAM', )
+__all__ = ("PAM",)
diff --git a/lib/galaxy/auth/util.py b/lib/galaxy/auth/util.py
index 7f9f0f2dd1b..78168fda7de 100644
--- a/lib/galaxy/auth/util.py
+++ b/lib/galaxy/auth/util.py
@@ -12,7 +12,6 @@ from galaxy.util import (
     string_as_bool,
 )
 
-
 log = logging.getLogger(__name__)
 
 AUTH_CONF_XML = """<?xml version="1.0"?>
@@ -26,11 +25,11 @@ AUTH_CONF_XML = """<?xml version="1.0"?>
 </auth>
 """
 
-Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
+Authenticator = namedtuple("Authenticator", ["plugin", "filter_template", "options"])
 
 
 def get_authenticators(auth_config_file, auth_config_file_set):
-    __plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type')
+    __plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, "plugin_type")
     # parse XML
     try:
         ct = parse_xml(auth_config_file)
@@ -44,21 +43,23 @@ def get_authenticators(auth_config_file, auth_config_file_set):
     authenticators = []
     # process authenticators
     for auth_elem in conf_root:
-        type_elem_text = auth_elem.find('type').text
+        type_elem_text = auth_elem.find("type").text
         plugin_class = __plugins_dict.get(type_elem_text)
         if not plugin_class:
-            raise Exception(f"Authenticator type '{type_elem_text}' not recognized, should be one of {', '.join(__plugins_dict)}")
+            raise Exception(
+                f"Authenticator type '{type_elem_text}' not recognized, should be one of {', '.join(__plugins_dict)}"
+            )
         plugin = plugin_class()
 
         # check filterelem
-        filter_elem = auth_elem.find('filter')
+        filter_elem = auth_elem.find("filter")
         if filter_elem is not None:
             filter_template = str(filter_elem.text)
         else:
             filter_template = None
 
         # extract options
-        options_elem = auth_elem.find('options')
+        options_elem = auth_elem.find("options")
         options = {}
         if options_elem is not None:
             for opt in options_elem:
@@ -77,23 +78,24 @@ def parse_auth_results(trans, auth_results, options):
     auth_result, auto_email, auto_username = auth_results[:3]
     auto_username = str(auto_username).lower()
     # make username unique
-    if validate_publicname(trans, auto_username) != '':
+    if validate_publicname(trans, auto_username) != "":
         i = 1
         while i <= 10:  # stop after 10 tries
-            if validate_publicname(trans, "%s-%i" % (auto_username, i)) == '':
+            if validate_publicname(trans, "%s-%i" % (auto_username, i)) == "":
                 auto_username = "%s-%i" % (auto_username, i)
                 break
             i += 1
         else:
             raise Conflict("Cannot make unique username")
     log.debug(f"Email: {auto_email}, auto-register with username: {auto_username}")
-    auth_return["auto_reg"] = string_as_bool(options.get('auto-register', False))
+    auth_return["auto_reg"] = string_as_bool(options.get("auto-register", False))
     auth_return["email"] = auto_email
     auth_return["username"] = auto_username
-    auth_return["auto_create_roles"] = string_as_bool(options.get('auto-create-roles', False))
-    auth_return["auto_create_groups"] = string_as_bool(options.get('auto-create-groups', False))
+    auth_return["auto_create_roles"] = string_as_bool(options.get("auto-create-roles", False))
+    auth_return["auto_create_groups"] = string_as_bool(options.get("auto-create-groups", False))
     auth_return["auto_assign_roles_to_groups_only"] = string_as_bool(
-        options.get('auto-assign-roles-to-groups-only', False))
+        options.get("auto-assign-roles-to-groups-only", False)
+    )
 
     if len(auth_results) == 4:
         auth_return["attributes"] = auth_results[3]
diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index 579006246b2..f3aa897a7c1 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -3,7 +3,10 @@ import hashlib
 import json
 import logging
 import os
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from urllib.parse import quote
 
 import jwt
@@ -11,55 +14,61 @@ import requests
 from oauthlib.common import generate_nonce
 from requests_oauthlib import OAuth2Session
 
-from galaxy import exceptions
-from galaxy import util
-from galaxy.model import CustosAuthnzToken, User
+from galaxy import (
+    exceptions,
+    util,
+)
+from galaxy.model import (
+    CustosAuthnzToken,
+    User,
+)
 from ..authnz import IdentityProvider
 
 log = logging.getLogger(__name__)
-STATE_COOKIE_NAME = 'galaxy-oidc-state'
-NONCE_COOKIE_NAME = 'galaxy-oidc-nonce'
-KEYCLOAK_BACKENDS = {'custos', 'cilogon', 'keycloak'}
+STATE_COOKIE_NAME = "galaxy-oidc-state"
+NONCE_COOKIE_NAME = "galaxy-oidc-nonce"
+KEYCLOAK_BACKENDS = {"custos", "cilogon", "keycloak"}
 
 
 class CustosAuthnz(IdentityProvider):
     def __init__(self, provider, oidc_config, oidc_backend_config, idphint=None):
         provider = provider.lower()
-        self.config = {'provider': provider}
-        self.config['verify_ssl'] = oidc_config['VERIFY_SSL']
-        self.config['url'] = oidc_backend_config['url']
-        self.config['client_id'] = oidc_backend_config['client_id']
-        self.config['client_secret'] = oidc_backend_config['client_secret']
-        self.config['redirect_uri'] = oidc_backend_config['redirect_uri']
-        self.config['ca_bundle'] = oidc_backend_config.get('ca_bundle', None)
-        self.config['extra_params'] = {
-            'kc_idp_hint': oidc_backend_config.get('idphint', 'oidc' if self.config['provider'] in ['custos', 'keycloak'] else 'cilogon')
+        self.config = {"provider": provider}
+        self.config["verify_ssl"] = oidc_config["VERIFY_SSL"]
+        self.config["url"] = oidc_backend_config["url"]
+        self.config["client_id"] = oidc_backend_config["client_id"]
+        self.config["client_secret"] = oidc_backend_config["client_secret"]
+        self.config["redirect_uri"] = oidc_backend_config["redirect_uri"]
+        self.config["ca_bundle"] = oidc_backend_config.get("ca_bundle", None)
+        self.config["extra_params"] = {
+            "kc_idp_hint": oidc_backend_config.get(
+                "idphint", "oidc" if self.config["provider"] in ["custos", "keycloak"] else "cilogon"
+            )
         }
-        if provider == 'cilogon':
+        if provider == "cilogon":
             self._load_config_for_cilogon()
-        elif provider == 'custos':
+        elif provider == "custos":
             self._load_config_for_custos()
-        elif provider == 'keycloak':
+        elif provider == "keycloak":
             self._load_config_for_keycloak()
 
     def _decode_token_no_signature(self, token):
-        return jwt.decode(token, audience=self.config['client_id'], options={"verify_signature": False})
+        return jwt.decode(token, audience=self.config["client_id"], options={"verify_signature": False})
 
     def authenticate(self, trans, idphint=None):
-        base_authorize_url = self.config['authorization_endpoint']
-        scopes = ['openid', 'email', 'profile']
-        if self.config['provider'] in ['custos', 'cilogon']:
-            scopes.append('org.cilogon.userinfo')
+        base_authorize_url = self.config["authorization_endpoint"]
+        scopes = ["openid", "email", "profile"]
+        if self.config["provider"] in ["custos", "cilogon"]:
+            scopes.append("org.cilogon.userinfo")
         oauth2_session = self._create_oauth2_session(scope=scopes)
         nonce = generate_nonce()
         nonce_hash = self._hash_nonce(nonce)
         extra_params = {"nonce": nonce_hash}
         if idphint is not None:
-            extra_params['idphint'] = idphint
+            extra_params["idphint"] = idphint
         if "extra_params" in self.config:
-            extra_params.update(self.config['extra_params'])
-        authorization_url, state = oauth2_session.authorization_url(
-            base_authorize_url, **extra_params)
+            extra_params.update(self.config["extra_params"])
+        authorization_url, state = oauth2_session.authorization_url(base_authorize_url, **extra_params)
         trans.set_cookie(value=state, name=STATE_COOKIE_NAME)
         trans.set_cookie(value=nonce, name=NONCE_COOKIE_NAME)
         return authorization_url
@@ -71,29 +80,31 @@ class CustosAuthnz(IdentityProvider):
         state_cookie = trans.get_cookie(name=STATE_COOKIE_NAME)
         oauth2_session = self._create_oauth2_session(state=state_cookie)
         token = self._fetch_token(oauth2_session, trans)
-        access_token = token['access_token']
-        id_token = token['id_token']
-        refresh_token = token['refresh_token'] if 'refresh_token' in token else None
-        expiration_time = datetime.now() + timedelta(seconds=token.get('expires_in', 3600))
-        refresh_expiration_time = (datetime.now() + timedelta(seconds=token['refresh_expires_in'])) if 'refresh_expires_in' in token else None
+        access_token = token["access_token"]
+        id_token = token["id_token"]
+        refresh_token = token["refresh_token"] if "refresh_token" in token else None
+        expiration_time = datetime.now() + timedelta(seconds=token.get("expires_in", 3600))
+        refresh_expiration_time = (
+            (datetime.now() + timedelta(seconds=token["refresh_expires_in"])) if "refresh_expires_in" in token else None
+        )
 
         # Get nonce from token['id_token'] and validate. 'nonce' in the
         # id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME
         # cookie.
         id_token_decoded = self._decode_token_no_signature(id_token)
-        nonce_hash = id_token_decoded['nonce']
+        nonce_hash = id_token_decoded["nonce"]
         self._validate_nonce(trans, nonce_hash)
 
         # Get userinfo and lookup/create Galaxy user record
-        if id_token_decoded.get('email', None):
+        if id_token_decoded.get("email", None):
             userinfo = id_token_decoded
         else:
             userinfo = self._get_userinfo(oauth2_session)
-        email = userinfo['email']
-        user_id = userinfo['sub']
+        email = userinfo["email"]
+        user_id = userinfo["sub"]
 
         # Create or update custos_authnz_token record
-        custos_authnz_token = self._get_custos_authnz_token(trans.sa_session, user_id, self.config['provider'])
+        custos_authnz_token = self._get_custos_authnz_token(trans.sa_session, user_id, self.config["provider"])
         if custos_authnz_token is None:
             user = trans.user
             if not user:
@@ -105,15 +116,17 @@ class CustosAuthnz(IdentityProvider):
                     # TODO: Future work will expand on this and provide an
                     # interface for when there are multiple auth providers
                     # allowing explicit authenticated association.
-                    if (trans.app.config.enable_oidc
-                            and len(trans.app.config.oidc) == 1
-                            and len(trans.app.auth_manager.authenticators) == 0):
+                    if (
+                        trans.app.config.enable_oidc
+                        and len(trans.app.config.oidc) == 1
+                        and len(trans.app.auth_manager.authenticators) == 0
+                    ):
                         user = existing_user
                     else:
                         message = f"There already exists a user with email {email}.  To associate this external login, you must first be logged in as that existing account."
                         log.exception(message)
                         raise exceptions.AuthenticationFailed(message)
-                elif self.config['provider'] == 'custos':
+                elif self.config["provider"] == "custos":
                     login_redirect_url = f"{login_redirect_url}root/login?confirm=true&custos_token={json.dumps(token)}"
                     return login_redirect_url, None
                 else:
@@ -122,14 +135,16 @@ class CustosAuthnz(IdentityProvider):
                     if trans.app.config.user_activation_on:
                         trans.app.user_manager.send_activation_email(trans, email, username)
 
-            custos_authnz_token = CustosAuthnzToken(user=user,
-                                   external_user_id=user_id,
-                                   provider=self.config['provider'],
-                                   access_token=access_token,
-                                   id_token=id_token,
-                                   refresh_token=refresh_token,
-                                   expiration_time=expiration_time,
-                                   refresh_expiration_time=refresh_expiration_time)
+            custos_authnz_token = CustosAuthnzToken(
+                user=user,
+                external_user_id=user_id,
+                provider=self.config["provider"],
+                access_token=access_token,
+                id_token=id_token,
+                refresh_token=refresh_token,
+                expiration_time=expiration_time,
+                refresh_expiration_time=refresh_expiration_time,
+            )
         else:
             custos_authnz_token.access_token = access_token
             custos_authnz_token.id_token = id_token
@@ -143,11 +158,17 @@ class CustosAuthnz(IdentityProvider):
     def create_user(self, token, trans, login_redirect_url):
         token_dict = json.loads(token)
 
-        access_token = token_dict['access_token']
-        id_token = token_dict['id_token']
-        refresh_token = token_dict['refresh_token'] if 'refresh_token' in token_dict else None
-        expiration_time = datetime.now() + timedelta(seconds=token_dict.get('expires_in', 3600))  # might be a problem cause times no long valid
-        refresh_expiration_time = (datetime.now() + timedelta(seconds=token_dict['refresh_expires_in'])) if 'refresh_expires_in' in token_dict else None
+        access_token = token_dict["access_token"]
+        id_token = token_dict["id_token"]
+        refresh_token = token_dict["refresh_token"] if "refresh_token" in token_dict else None
+        expiration_time = datetime.now() + timedelta(
+            seconds=token_dict.get("expires_in", 3600)
+        )  # might be a problem cause times no long valid
+        refresh_expiration_time = (
+            (datetime.now() + timedelta(seconds=token_dict["refresh_expires_in"]))
+            if "refresh_expires_in" in token_dict
+            else None
+        )
 
         # Get nonce from token['id_token'] and validate. 'nonce' in the
         # id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME
@@ -155,23 +176,25 @@ class CustosAuthnz(IdentityProvider):
         userinfo = self._decode_token_no_signature(id_token)
 
         # Get userinfo and create Galaxy user record
-        email = userinfo['email']
+        email = userinfo["email"]
         # Check if username if already taken
         username = self._username_from_userinfo(trans, userinfo)
-        user_id = userinfo['sub']
+        user_id = userinfo["sub"]
 
         user = trans.app.user_manager.create(email=email, username=username)
         if trans.app.config.user_activation_on:
             trans.app.user_manager.send_activation_email(trans, email, username)
 
-        custos_authnz_token = CustosAuthnzToken(user=user,
-                               external_user_id=user_id,
-                               provider=self.config['provider'],
-                               access_token=access_token,
-                               id_token=id_token,
-                               refresh_token=refresh_token,
-                               expiration_time=expiration_time,
-                               refresh_expiration_time=refresh_expiration_time)
+        custos_authnz_token = CustosAuthnzToken(
+            user=user,
+            external_user_id=user_id,
+            provider=self.config["provider"],
+            access_token=access_token,
+            id_token=id_token,
+            refresh_token=refresh_token,
+            expiration_time=expiration_time,
+            refresh_expiration_time=refresh_expiration_time,
+        )
 
         trans.sa_session.add(user)
         trans.sa_session.add(custos_authnz_token)
@@ -189,7 +212,7 @@ class CustosAuthnz(IdentityProvider):
             if len(provider_tokens) > 1:
                 for idx, token in enumerate(provider_tokens):
                     id_token_decoded = self._decode_token_no_signature(token.id_token)
-                    if (id_token_decoded['email'] == email):
+                    if id_token_decoded["email"] == email:
                         index = idx
             trans.sa_session.delete(provider_tokens[index])
             trans.sa_session.flush()
@@ -199,7 +222,7 @@ class CustosAuthnz(IdentityProvider):
 
     def logout(self, trans, post_logout_redirect_url=None):
         try:
-            redirect_url = self.config['end_session_endpoint']
+            redirect_url = self.config["end_session_endpoint"]
             if post_logout_redirect_url is not None:
                 redirect_url += f"?redirect_uri={quote(post_logout_redirect_url)}"
             return redirect_url
@@ -208,43 +231,40 @@ class CustosAuthnz(IdentityProvider):
             return None
 
     def _create_oauth2_session(self, state=None, scope=None):
-        client_id = self.config['client_id']
-        redirect_uri = self.config['redirect_uri']
-        if (redirect_uri.startswith('http://localhost')
-                and os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None) != "1"):
+        client_id = self.config["client_id"]
+        redirect_uri = self.config["redirect_uri"]
+        if redirect_uri.startswith("http://localhost") and os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None) != "1":
             log.warning("Setting OAUTHLIB_INSECURE_TRANSPORT to '1' to allow plain HTTP (non-SSL) callback")
-            os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = "1"
-        session = OAuth2Session(client_id,
-                             scope=scope,
-                             redirect_uri=redirect_uri,
-                             state=state)
+            os.environ["OAUTHLIB_INSECURE_TRANSPORT"] = "1"
+        session = OAuth2Session(client_id, scope=scope, redirect_uri=redirect_uri, state=state)
         session.verify = self._get_verify_param()
         return session
 
     def _fetch_token(self, oauth2_session, trans):
 
-        if self.config.get('iam_client_secret'):
+        if self.config.get("iam_client_secret"):
             # Custos uses the Keycloak client secret to get the token
-            client_secret = self.config['iam_client_secret']
+            client_secret = self.config["iam_client_secret"]
         else:
-            client_secret = self.config['client_secret']
-        token_endpoint = self.config['token_endpoint']
+            client_secret = self.config["client_secret"]
+        token_endpoint = self.config["token_endpoint"]
         clientIdAndSec = f"{self.config['client_id']}:{self.config['client_secret']}"  # for custos
         return oauth2_session.fetch_token(
             token_endpoint,
             client_secret=client_secret,
             authorization_response=trans.request.url,
-            headers={"Authorization": f"Basic {util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}"},  # for custos
-            verify=self._get_verify_param())
+            headers={
+                "Authorization": f"Basic {util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}"
+            },  # for custos
+            verify=self._get_verify_param(),
+        )
 
     def _get_userinfo(self, oauth2_session):
-        userinfo_endpoint = self.config['userinfo_endpoint']
-        return oauth2_session.get(userinfo_endpoint,
-                                  verify=self._get_verify_param()).json()
+        userinfo_endpoint = self.config["userinfo_endpoint"]
+        return oauth2_session.get(userinfo_endpoint, verify=self._get_verify_param()).json()
 
     def _get_custos_authnz_token(self, sa_session, user_id, provider):
-        return sa_session.query(CustosAuthnzToken).filter_by(
-            external_user_id=user_id, provider=provider).one_or_none()
+        return sa_session.query(CustosAuthnzToken).filter_by(external_user_id=user_id, provider=provider).one_or_none()
 
     def _hash_nonce(self, nonce):
         return hashlib.sha256(util.smart_str(nonce)).hexdigest()
@@ -252,48 +272,53 @@ class CustosAuthnz(IdentityProvider):
     def _validate_nonce(self, trans, nonce_hash):
         nonce_cookie = trans.get_cookie(name=NONCE_COOKIE_NAME)
         # Delete the nonce cookie
-        trans.set_cookie('', name=NONCE_COOKIE_NAME, age=-1)
+        trans.set_cookie("", name=NONCE_COOKIE_NAME, age=-1)
         nonce_cookie_hash = self._hash_nonce(nonce_cookie)
         if nonce_hash != nonce_cookie_hash:
             raise Exception("Nonce mismatch!")
 
     def _load_config_for_cilogon(self):
         # Set cilogon endpoints
-        self.config['authorization_endpoint'] = "https://cilogon.org/authorize"
-        self.config['token_endpoint'] = "https://cilogon.org/oauth2/token"
-        self.config['userinfo_endpoint'] = "https://cilogon.org/oauth2/userinfo"
+        self.config["authorization_endpoint"] = "https://cilogon.org/authorize"
+        self.config["token_endpoint"] = "https://cilogon.org/oauth2/token"
+        self.config["userinfo_endpoint"] = "https://cilogon.org/oauth2/userinfo"
 
     def _load_config_for_custos(self):
-        self.config['well_known_oidc_config_uri'] = self._get_well_known_uri_from_url(self.config['provider'])
-        self.config['credential_url'] = f"{self.config['url'].rstrip('/')}/credentials"
+        self.config["well_known_oidc_config_uri"] = self._get_well_known_uri_from_url(self.config["provider"])
+        self.config["credential_url"] = f"{self.config['url'].rstrip('/')}/credentials"
         self._get_custos_credentials()
         # Set custos endpoints
         clientIdAndSec = f"{self.config['client_id']}:{self.config['client_secret']}"
-        eps = requests.get(self.config['well_known_oidc_config_uri'],
-                           headers={"Authorization": f"Basic {util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}"},
-                           verify=False,
-                           params={'client_id': self.config['client_id']},
-                           timeout=util.DEFAULT_SOCKET_TIMEOUT)
+        eps = requests.get(
+            self.config["well_known_oidc_config_uri"],
+            headers={"Authorization": f"Basic {util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}"},
+            verify=False,
+            params={"client_id": self.config["client_id"]},
+            timeout=util.DEFAULT_SOCKET_TIMEOUT,
+        )
         well_known_oidc_config = eps.json()
         self._load_well_known_oidc_config(well_known_oidc_config)
 
     def _load_config_for_keycloak(self):
-        self.config['well_known_oidc_config_uri'] = self._get_well_known_uri_from_url(self.config['provider'])
-        well_known_oidc_config = self._fetch_well_known_oidc_config(self.config['well_known_oidc_config_uri'])
+        self.config["well_known_oidc_config_uri"] = self._get_well_known_uri_from_url(self.config["provider"])
+        well_known_oidc_config = self._fetch_well_known_oidc_config(self.config["well_known_oidc_config_uri"])
         self._load_well_known_oidc_config(well_known_oidc_config)
 
     def _get_custos_credentials(self):
         clientIdAndSec = f"{self.config['client_id']}:{self.config['client_secret']}"
-        creds = requests.get(self.config['credential_url'],
-                            headers={"Authorization": f"Basic {util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}"},
-                            verify=False, params={'client_id': self.config['client_id']},
-                            timeout=util.DEFAULT_SOCKET_TIMEOUT)
+        creds = requests.get(
+            self.config["credential_url"],
+            headers={"Authorization": f"Basic {util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}"},
+            verify=False,
+            params={"client_id": self.config["client_id"]},
+            timeout=util.DEFAULT_SOCKET_TIMEOUT,
+        )
         credentials = creds.json()
-        self.config['iam_client_secret'] = credentials['iam_client_secret']
+        self.config["iam_client_secret"] = credentials["iam_client_secret"]
 
     def _get_well_known_uri_from_url(self, provider):
         # TODO: Look up this URL from a Python library
-        if provider in ['custos', 'keycloak']:
+        if provider in ["custos", "keycloak"]:
             base_url = self.config["url"]
             # Remove potential trailing slash to avoid "//realms"
             base_url = base_url if base_url[-1] != "/" else base_url[:-1]
@@ -303,35 +328,35 @@ class CustosAuthnz(IdentityProvider):
 
     def _fetch_well_known_oidc_config(self, well_known_uri):
         try:
-            return requests.get(well_known_uri,
-                                verify=self._get_verify_param(),
-                                timeout=util.DEFAULT_SOCKET_TIMEOUT).json()
+            return requests.get(
+                well_known_uri, verify=self._get_verify_param(), timeout=util.DEFAULT_SOCKET_TIMEOUT
+            ).json()
         except Exception:
             log.error(f"Failed to load well-known OIDC config URI: {well_known_uri}")
             raise
 
     def _load_well_known_oidc_config(self, well_known_oidc_config):
-        self.config['authorization_endpoint'] = well_known_oidc_config['authorization_endpoint']
-        self.config['token_endpoint'] = well_known_oidc_config['token_endpoint']
-        self.config['userinfo_endpoint'] = well_known_oidc_config['userinfo_endpoint']
-        self.config['end_session_endpoint'] = well_known_oidc_config.get('end_session_endpoint')
+        self.config["authorization_endpoint"] = well_known_oidc_config["authorization_endpoint"]
+        self.config["token_endpoint"] = well_known_oidc_config["token_endpoint"]
+        self.config["userinfo_endpoint"] = well_known_oidc_config["userinfo_endpoint"]
+        self.config["end_session_endpoint"] = well_known_oidc_config.get("end_session_endpoint")
 
     def _get_verify_param(self):
         """Return 'ca_bundle' if 'verify_ssl' is true and 'ca_bundle' is configured."""
         # in requests_oauthlib, the verify param can either be a boolean or a CA bundle path
-        if self.config['ca_bundle'] is not None and self.config['verify_ssl']:
-            return self.config['ca_bundle']
+        if self.config["ca_bundle"] is not None and self.config["verify_ssl"]:
+            return self.config["ca_bundle"]
         else:
-            return self.config['verify_ssl']
+            return self.config["verify_ssl"]
 
     def _username_from_userinfo(self, trans, userinfo):
-        username = userinfo.get('preferred_username', userinfo['email'])
+        username = userinfo.get("preferred_username", userinfo["email"])
         if "@" in username:
-            username = username.split('@')[0]  # username created from username portion of email
-        if (trans.sa_session.query(trans.app.model.User).filter_by(username=username).first()):
+            username = username.split("@")[0]  # username created from username portion of email
+        if trans.sa_session.query(trans.app.model.User).filter_by(username=username).first():
             # if username already exists in database, append integer and iterate until unique username found
             count = 0
-            while (trans.sa_session.query(trans.app.model.User).filter_by(username=(f"{username}{count}")).first()):
+            while trans.sa_session.query(trans.app.model.User).filter_by(username=(f"{username}{count}")).first():
                 count += 1
             return f"{username}{count}"
         else:
diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 479924f74fb..7049448c39f 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -8,12 +8,12 @@ import string
 
 import requests
 from cloudauthz import CloudAuthz
-from cloudauthz.exceptions import (
-    CloudAuthzBaseException
-)
+from cloudauthz.exceptions import CloudAuthzBaseException
 
-from galaxy import exceptions
-from galaxy import model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.util import (
     asbool,
     etree,
@@ -31,22 +31,20 @@ from .psa_authnz import (
     on_the_fly_config,
     PSAAuthnz,
     Storage,
-    Strategy
+    Strategy,
 )
 
-
 log = logging.getLogger(__name__)
 
 # Note: This if for backward compatibility. Icons can be specified in oidc_backends_config.xml.
 DEFAULT_OIDC_IDP_ICONS = {
-    'google': 'https://developers.google.com/identity/images/btn_google_signin_light_normal_web.png',
-    'elixir': 'https://elixir-europe.org/sites/default/files/images/login-button-orange.png',
-    'okta': 'https://www.okta.com/sites/all/themes/Okta/images/blog/Logos/Okta_Logo_BrightBlue_Medium.png'
+    "google": "https://developers.google.com/identity/images/btn_google_signin_light_normal_web.png",
+    "elixir": "https://elixir-europe.org/sites/default/files/images/login-button-orange.png",
+    "okta": "https://www.okta.com/sites/all/themes/Okta/images/blog/Logos/Okta_Logo_BrightBlue_Medium.png",
 }
 
 
 class AuthnzManager:
-
     def __init__(self, app, oidc_config_file, oidc_backends_config_file):
         """
         :type app: galaxy.app.UniverseApplication
@@ -66,35 +64,42 @@ class AuthnzManager:
         try:
             tree = parse_xml(config_file)
             root = tree.getroot()
-            if root.tag != 'OIDC':
-                raise etree.ParseError("The root element in OIDC_Config xml file is expected to be `OIDC`, "
-                                 "found `{}` instead -- unable to continue.".format(root.tag))
+            if root.tag != "OIDC":
+                raise etree.ParseError(
+                    "The root element in OIDC_Config xml file is expected to be `OIDC`, "
+                    "found `{}` instead -- unable to continue.".format(root.tag)
+                )
             for child in root:
-                if child.tag != 'Setter':
-                    log.error("Expect a node with `Setter` tag, found a node with `{}` tag instead; "
-                              "skipping this node.".format(child.tag))
+                if child.tag != "Setter":
+                    log.error(
+                        "Expect a node with `Setter` tag, found a node with `{}` tag instead; "
+                        "skipping this node.".format(child.tag)
+                    )
                     continue
-                if 'Property' not in child.attrib or 'Value' not in child.attrib or 'Type' not in child.attrib:
-                    log.error("Could not find the node attributes `Property` and/or `Value` and/or `Type`;"
-                              " found these attributes: `{}`; skipping this node.".format(child.attrib))
+                if "Property" not in child.attrib or "Value" not in child.attrib or "Type" not in child.attrib:
+                    log.error(
+                        "Could not find the node attributes `Property` and/or `Value` and/or `Type`;"
+                        " found these attributes: `{}`; skipping this node.".format(child.attrib)
+                    )
                     continue
                 try:
-                    if child.get('Type') == "bool":
+                    if child.get("Type") == "bool":
                         func = string_as_bool
                     else:
-                        func = getattr(builtins, child.get('Type'))
+                        func = getattr(builtins, child.get("Type"))
                 except AttributeError:
-                    log.error("The value of attribute `Type`, `{}`, is not a valid built-in type;"
-                              " skipping this node").format(child.get('Type'))
+                    log.error(
+                        "The value of attribute `Type`, `{}`, is not a valid built-in type;" " skipping this node"
+                    ).format(child.get("Type"))
                     continue
-                self.oidc_config[child.get('Property')] = func(child.get('Value'))
+                self.oidc_config[child.get("Property")] = func(child.get("Value"))
         except ImportError:
             raise
         except etree.ParseError as e:
             raise etree.ParseError(f"Invalid configuration at `{config_file}`: {e} -- unable to continue.")
 
     def _get_idp_icon(self, idp):
-        return self.oidc_backends_config[idp].get('icon') or DEFAULT_OIDC_IDP_ICONS.get(idp)
+        return self.oidc_backends_config[idp].get("icon") or DEFAULT_OIDC_IDP_ICONS.get(idp)
 
     def _parse_oidc_backends_config(self, config_file):
         self.oidc_backends_config = {}
@@ -102,26 +107,30 @@ class AuthnzManager:
         try:
             tree = parse_xml(config_file)
             root = tree.getroot()
-            if root.tag != 'OIDC':
-                raise etree.ParseError("The root element in OIDC config xml file is expected to be `OIDC`, "
-                                 "found `{}` instead -- unable to continue.".format(root.tag))
+            if root.tag != "OIDC":
+                raise etree.ParseError(
+                    "The root element in OIDC config xml file is expected to be `OIDC`, "
+                    "found `{}` instead -- unable to continue.".format(root.tag)
+                )
             for child in root:
-                if child.tag != 'provider':
-                    log.error("Expect a node with `provider` tag, found a node with `{}` tag instead; "
-                              "skipping the node.".format(child.tag))
+                if child.tag != "provider":
+                    log.error(
+                        "Expect a node with `provider` tag, found a node with `{}` tag instead; "
+                        "skipping the node.".format(child.tag)
+                    )
                     continue
-                if 'name' not in child.attrib:
+                if "name" not in child.attrib:
                     log.error(f"Could not find a node attribute 'name'; skipping the node '{child.tag}'.")
                     continue
-                idp = child.get('name').lower()
+                idp = child.get("name").lower()
                 if idp in BACKENDS_NAME:
                     self.oidc_backends_config[idp] = self._parse_idp_config(child)
-                    self.oidc_backends_implementation[idp] = 'psa'
-                    self.app.config.oidc[idp] = {'icon': self._get_idp_icon(idp)}
+                    self.oidc_backends_implementation[idp] = "psa"
+                    self.app.config.oidc[idp] = {"icon": self._get_idp_icon(idp)}
                 elif idp in KEYCLOAK_BACKENDS:
                     self.oidc_backends_config[idp] = self._parse_custos_config(child)
-                    self.oidc_backends_implementation[idp] = 'custos'
-                    self.app.config.oidc[idp] = {'icon': self._get_idp_icon(idp)}
+                    self.oidc_backends_implementation[idp] = "custos"
+                    self.app.config.oidc[idp] = {"icon": self._get_idp_icon(idp)}
                 else:
                     raise etree.ParseError("Unknown provider specified")
             if len(self.oidc_backends_config) == 0:
@@ -133,40 +142,42 @@ class AuthnzManager:
 
     def _parse_idp_config(self, config_xml):
         rtv = {
-            'client_id': config_xml.find('client_id').text,
-            'client_secret': config_xml.find('client_secret').text,
-            'redirect_uri': config_xml.find('redirect_uri').text,
-            'enable_idp_logout': asbool(config_xml.findtext('enable_idp_logout', 'false'))}
-        if config_xml.find('prompt') is not None:
-            rtv['prompt'] = config_xml.find('prompt').text
-        if config_xml.find('api_url') is not None:
-            rtv['api_url'] = config_xml.find('api_url').text
-        if config_xml.find('url') is not None:
-            rtv['url'] = config_xml.find('url').text
-        if config_xml.find('icon') is not None:
-            rtv['icon'] = config_xml.find('icon').text
-        if config_xml.find('extra_scopes') is not None:
-            rtv['extra_scopes'] = listify(config_xml.find('extra_scopes').text)
+            "client_id": config_xml.find("client_id").text,
+            "client_secret": config_xml.find("client_secret").text,
+            "redirect_uri": config_xml.find("redirect_uri").text,
+            "enable_idp_logout": asbool(config_xml.findtext("enable_idp_logout", "false")),
+        }
+        if config_xml.find("prompt") is not None:
+            rtv["prompt"] = config_xml.find("prompt").text
+        if config_xml.find("api_url") is not None:
+            rtv["api_url"] = config_xml.find("api_url").text
+        if config_xml.find("url") is not None:
+            rtv["url"] = config_xml.find("url").text
+        if config_xml.find("icon") is not None:
+            rtv["icon"] = config_xml.find("icon").text
+        if config_xml.find("extra_scopes") is not None:
+            rtv["extra_scopes"] = listify(config_xml.find("extra_scopes").text)
 
         return rtv
 
     def _parse_custos_config(self, config_xml):
         rtv = {
-            'url': config_xml.find('url').text,
-            'client_id': config_xml.find('client_id').text,
-            'client_secret': config_xml.find('client_secret').text,
-            'redirect_uri': config_xml.find('redirect_uri').text,
-            'enable_idp_logout': asbool(config_xml.findtext('enable_idp_logout', 'false'))}
-        if config_xml.find('credential_url') is not None:
-            rtv['credential_url'] = config_xml.find('credential_url').text
-        if config_xml.find('well_known_oidc_config_uri') is not None:
-            rtv['well_known_oidc_config_uri'] = config_xml.find('well_known_oidc_config_uri').text
-        if config_xml.findall('allowed_idp') is not None:
-            self.allowed_idps = list(map(lambda idp: idp.text, config_xml.findall('allowed_idp')))
-        if config_xml.find('ca_bundle') is not None:
-            rtv['ca_bundle'] = config_xml.find('ca_bundle').text
-        if config_xml.find('icon') is not None:
-            rtv['icon'] = config_xml.find('icon').text
+            "url": config_xml.find("url").text,
+            "client_id": config_xml.find("client_id").text,
+            "client_secret": config_xml.find("client_secret").text,
+            "redirect_uri": config_xml.find("redirect_uri").text,
+            "enable_idp_logout": asbool(config_xml.findtext("enable_idp_logout", "false")),
+        }
+        if config_xml.find("credential_url") is not None:
+            rtv["credential_url"] = config_xml.find("credential_url").text
+        if config_xml.find("well_known_oidc_config_uri") is not None:
+            rtv["well_known_oidc_config_uri"] = config_xml.find("well_known_oidc_config_uri").text
+        if config_xml.findall("allowed_idp") is not None:
+            self.allowed_idps = list(map(lambda idp: idp.text, config_xml.findall("allowed_idp")))
+        if config_xml.find("ca_bundle") is not None:
+            rtv["ca_bundle"] = config_xml.find("ca_bundle").text
+        if config_xml.find("icon") is not None:
+            rtv["icon"] = config_xml.find("icon").text
         return rtv
 
     def get_allowed_idps(self):
@@ -188,22 +199,37 @@ class AuthnzManager:
             identity_provider_class = self._get_identity_provider_class(self.oidc_backends_implementation[provider])
             try:
                 if provider in KEYCLOAK_BACKENDS:
-                    return True, "", identity_provider_class(unified_provider_name, self.oidc_config, self.oidc_backends_config[unified_provider_name], idphint=idphint)
+                    return (
+                        True,
+                        "",
+                        identity_provider_class(
+                            unified_provider_name,
+                            self.oidc_config,
+                            self.oidc_backends_config[unified_provider_name],
+                            idphint=idphint,
+                        ),
+                    )
                 else:
-                    return True, "", identity_provider_class(unified_provider_name, self.oidc_config, self.oidc_backends_config[unified_provider_name])
+                    return (
+                        True,
+                        "",
+                        identity_provider_class(
+                            unified_provider_name, self.oidc_config, self.oidc_backends_config[unified_provider_name]
+                        ),
+                    )
             except Exception as e:
-                log.exception(f'An error occurred when loading {identity_provider_class.__name__}')
+                log.exception(f"An error occurred when loading {identity_provider_class.__name__}")
                 return False, unicodify(e), None
         else:
-            msg = f'The requested identity provider, `{provider}`, is not a recognized/expected provider.'
+            msg = f"The requested identity provider, `{provider}`, is not a recognized/expected provider."
             log.debug(msg)
             return False, msg, None
 
     @staticmethod
     def _get_identity_provider_class(implementation):
-        if implementation == 'psa':
+        if implementation == "psa":
             return PSAAuthnz
-        elif implementation == 'custos':
+        elif implementation == "custos":
             return CustosAuthnz
         else:
             return None
@@ -215,17 +241,22 @@ class AuthnzManager:
             strategy = Strategy(request, None, Storage, backend.config)
             on_the_fly_config(sa_session)
             try:
-                config['id_token'] = cloudauthz.authn.get_id_token(strategy)
+                config["id_token"] = cloudauthz.authn.get_id_token(strategy)
             except requests.exceptions.HTTPError as e:
-                msg = "Sign-out from Galaxy and remove its access from `{}`, then log back in using `{}` " \
-                      "account.".format(self._unify_provider_name(cloudauthz.authn.provider), cloudauthz.authn.uid)
-                log.debug("Failed to get/refresh ID token for user with ID `{}` for assuming authz_id `{}`. "
-                          "User may not have a refresh token. If the problem persists, set the `prompt` key to "
-                          "`consent` in `oidc_backends_config.xml`, then restart Galaxy and ask user to: {}"
-                          "Error Message: `{}`".format(user_id, cloudauthz.id, msg, e.response.text))
+                msg = (
+                    "Sign-out from Galaxy and remove its access from `{}`, then log back in using `{}` "
+                    "account.".format(self._unify_provider_name(cloudauthz.authn.provider), cloudauthz.authn.uid)
+                )
+                log.debug(
+                    "Failed to get/refresh ID token for user with ID `{}` for assuming authz_id `{}`. "
+                    "User may not have a refresh token. If the problem persists, set the `prompt` key to "
+                    "`consent` in `oidc_backends_config.xml`, then restart Galaxy and ask user to: {}"
+                    "Error Message: `{}`".format(user_id, cloudauthz.id, msg, e.response.text)
+                )
                 raise exceptions.AuthenticationFailed(
                     err_msg="An error occurred getting your ID token. {}. If the problem persists, please "
-                            "contact Galaxy admin.".format(msg))
+                    "contact Galaxy admin.".format(msg)
+                )
         return config
 
     @staticmethod
@@ -233,12 +264,14 @@ class AuthnzManager:
         qres = trans.sa_session.query(model.UserAuthnzToken).get(authn_id)
         if qres is None:
             msg = "Authentication record with the given `authn_id` (`{}`) not found.".format(
-                trans.security.encode_id(authn_id))
+                trans.security.encode_id(authn_id)
+            )
             log.debug(msg)
             raise exceptions.ObjectNotFound(msg)
         if qres.user_id != trans.user.id:
-            msg = "The request authentication with ID `{}` is not accessible to user with ID " \
-                  "`{}`.".format(trans.security.encode_id(authn_id), trans.security.encode_id(trans.user.id))
+            msg = "The request authentication with ID `{}` is not accessible to user with ID " "`{}`.".format(
+                trans.security.encode_id(authn_id), trans.security.encode_id(trans.user.id)
+            )
             log.warning(msg)
             raise exceptions.ItemAccessibilityException(msg)
 
@@ -264,8 +297,10 @@ class AuthnzManager:
         if qres is None:
             raise exceptions.ObjectNotFound("An authorization configuration with given ID not found.")
         if user_id != qres.user_id:
-            msg = "The request authorization configuration (with ID:`{}`) is not accessible for user with " \
-                  "ID:`{}`.".format(qres.id, user_id)
+            msg = (
+                "The request authorization configuration (with ID:`{}`) is not accessible for user with "
+                "ID:`{}`.".format(qres.id, user_id)
+            )
             log.warning(msg)
             raise exceptions.ItemAccessibilityException(msg)
         return qres
@@ -284,14 +319,22 @@ class AuthnzManager:
             if success is False:
                 return False, message, None
             elif provider in KEYCLOAK_BACKENDS:
-                if (self.allowed_idps and (idphint not in self.allowed_idps)):
-                    msg = f'An error occurred when authenticating a user. Invalid EntityID: `{idphint}`'
+                if self.allowed_idps and (idphint not in self.allowed_idps):
+                    msg = f"An error occurred when authenticating a user. Invalid EntityID: `{idphint}`"
                     log.exception(msg)
                     return False, msg, None
-                return True, f"Redirecting to the `{provider}` identity provider for authentication", backend.authenticate(trans, idphint)
-            return True, f"Redirecting to the `{provider}` identity provider for authentication", backend.authenticate(trans)
+                return (
+                    True,
+                    f"Redirecting to the `{provider}` identity provider for authentication",
+                    backend.authenticate(trans, idphint),
+                )
+            return (
+                True,
+                f"Redirecting to the `{provider}` identity provider for authentication",
+                backend.authenticate(trans),
+            )
         except Exception:
-            msg = f'An error occurred when authenticating a user on `{provider}` identity provider'
+            msg = f"An error occurred when authenticating a user on `{provider}` identity provider"
             log.exception(msg)
             return False, msg, None
 
@@ -304,7 +347,7 @@ class AuthnzManager:
         except exceptions.AuthenticationFailed:
             raise
         except Exception:
-            msg = f'An error occurred when handling callback from `{provider}` identity provider.  Please contact an administrator for assistance.'
+            msg = f"An error occurred when handling callback from `{provider}` identity provider.  Please contact an administrator for assistance."
             log.exception(msg)
             return False, msg, (None, None)
 
@@ -318,7 +361,7 @@ class AuthnzManager:
             log.exception("Error creating user")
             raise
         except Exception:
-            msg = f'An error occurred when creating a user with `{provider}` identity provider.  Please contact an administrator for assistance.'
+            msg = f"An error occurred when creating a user with `{provider}` identity provider.  Please contact an administrator for assistance."
             log.exception(msg)
             return False, msg, (None, None)
 
@@ -338,7 +381,7 @@ class AuthnzManager:
         try:
             # check if logout is enabled for this idp and return false if not
             unified_provider_name = self._unify_provider_name(provider)
-            if self.oidc_backends_config[unified_provider_name]['enable_idp_logout'] is False:
+            if self.oidc_backends_config[unified_provider_name]["enable_idp_logout"] is False:
                 return False, f"IDP logout is not enabled for {provider}", None
 
             success, message, backend = self._get_authnz_backend(provider)
@@ -346,7 +389,7 @@ class AuthnzManager:
                 return False, message, None
             return True, message, backend.logout(trans, post_logout_redirect_url)
         except Exception:
-            msg = f'An error occurred when logging out from `{provider}` identity provider.  Please contact an administrator for assistance.'
+            msg = f"An error occurred when logging out from `{provider}` identity provider.  Please contact an administrator for assistance."
             log.exception(msg)
             return False, msg, None
 
@@ -359,8 +402,11 @@ class AuthnzManager:
                 return backend.disconnect(provider, trans, email, disconnect_redirect_url)
             return backend.disconnect(provider, trans, disconnect_redirect_url)
         except Exception:
-            msg = 'An error occurred when disconnecting authentication with `{}` identity provider for user `{}`' \
-                  .format(provider, trans.user.username)
+            msg = (
+                "An error occurred when disconnecting authentication with `{}` identity provider for user `{}`".format(
+                    provider, trans.user.username
+                )
+            )
             log.exception(msg)
             return False, msg, None
 
@@ -399,8 +445,11 @@ class AuthnzManager:
         config = self._extend_cloudauthz_config(cloudauthz, request, sa_session, user_id)
         try:
             ca = CloudAuthz()
-            log.info("Requesting credentials using CloudAuthz with config id `{}` on be half of user `{}`.".format(
-                cloudauthz.id, user_id))
+            log.info(
+                "Requesting credentials using CloudAuthz with config id `{}` on be half of user `{}`.".format(
+                    cloudauthz.id, user_id
+                )
+            )
             credentials = ca.authorize(cloudauthz.provider, config)
             return credentials
         except CloudAuthzBaseException as e:
@@ -439,12 +488,18 @@ class AuthnzManager:
         :rtype:                 str
         :return:                The filename to which credentials are written.
         """
-        filename = os.path.abspath(os.path.join(new_file_path,
-                                                "cd_" + ''.join(random.SystemRandom().choice(
-                                                    string.ascii_uppercase + string.digits) for _ in range(11))))
+        filename = os.path.abspath(
+            os.path.join(
+                new_file_path,
+                "cd_"
+                + "".join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(11)),
+            )
+        )
         credentials = self.get_cloud_access_credentials(cloudauthz, sa_session, user_id, request)
-        log.info("Writting credentials generated using CloudAuthz with config id `{}` to the following file: `{}`"
-                 "".format(cloudauthz.id, filename))
+        log.info(
+            "Writting credentials generated using CloudAuthz with config id `{}` to the following file: `{}`"
+            "".format(cloudauthz.id, filename)
+        )
         with open(filename, "w") as f:
             f.write(json.dumps(credentials))
         return filename
diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index 2139ab698a8..de6a6b4d576 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -1,39 +1,48 @@
 import json
 
 import requests
-from social_core.actions import do_auth, do_complete, do_disconnect
+from social_core.actions import (
+    do_auth,
+    do_complete,
+    do_disconnect,
+)
 from social_core.backends.utils import get_backend
 from social_core.strategy import BaseStrategy
-from social_core.utils import module_member, setting_name
+from social_core.utils import (
+    module_member,
+    setting_name,
+)
 from sqlalchemy.exc import IntegrityError
 
 from galaxy.exceptions import MalformedContents
 from galaxy.util import DEFAULT_SOCKET_TIMEOUT
 from ..authnz import IdentityProvider
-from ..model import PSAAssociation, PSACode, PSANonce, PSAPartial, UserAuthnzToken
-
+from ..model import (
+    PSAAssociation,
+    PSACode,
+    PSANonce,
+    PSAPartial,
+    UserAuthnzToken,
+)
 
 # key: a component name which PSA requests.
 # value: is the name of a class associated with that key.
-DEFAULTS = {
-    'STRATEGY': 'Strategy',
-    'STORAGE': 'Storage'
-}
+DEFAULTS = {"STRATEGY": "Strategy", "STORAGE": "Storage"}
 
 BACKENDS = {
-    'google': 'social_core.backends.google_openidconnect.GoogleOpenIdConnect',
-    'globus': 'social_core.backends.globus.GlobusOpenIdConnect',
-    'elixir': 'social_core.backends.elixir.ElixirOpenIdConnect',
-    'okta': 'social_core.backends.okta_openidconnect.OktaOpenIdConnect',
-    'azure': 'social_core.backends.azuread_tenant.AzureADTenantOAuth2'
+    "google": "social_core.backends.google_openidconnect.GoogleOpenIdConnect",
+    "globus": "social_core.backends.globus.GlobusOpenIdConnect",
+    "elixir": "social_core.backends.elixir.ElixirOpenIdConnect",
+    "okta": "social_core.backends.okta_openidconnect.OktaOpenIdConnect",
+    "azure": "social_core.backends.azuread_tenant.AzureADTenantOAuth2",
 }
 
 BACKENDS_NAME = {
-    'google': 'google-openidconnect',
-    'globus': 'globus',
-    'elixir': 'elixir',
-    'okta': 'okta-openidconnect',
-    'azure': 'azuread-tenant-oauth2'
+    "google": "google-openidconnect",
+    "globus": "globus",
+    "elixir": "elixir",
+    "okta": "okta-openidconnect",
+    "azure": "azuread-tenant-oauth2",
 }
 
 AUTH_PIPELINE = (
@@ -41,67 +50,52 @@ AUTH_PIPELINE = (
     # format to create the user instance later. On some cases the details are
     # already part of the auth response from the provider, but sometimes this
     # could hit a provider API.
-    'social_core.pipeline.social_auth.social_details',
-
+    "social_core.pipeline.social_auth.social_details",
     # Get the social uid from whichever service we're authing thru. The uid is
     # the unique identifier of the given user in the provider.
-    'social_core.pipeline.social_auth.social_uid',
-
+    "social_core.pipeline.social_auth.social_uid",
     # Verifies that the current auth process is valid within the current
     # project, this is where emails and domains allowlists are applied (if
     # defined).
-    'social_core.pipeline.social_auth.auth_allowed',
-
+    "social_core.pipeline.social_auth.auth_allowed",
     # Checks if the decoded response contains all the required fields such
     # as an ID token or a refresh token.
-    'galaxy.authnz.psa_authnz.contains_required_data',
-
-    'galaxy.authnz.psa_authnz.verify',
-
+    "galaxy.authnz.psa_authnz.contains_required_data",
+    "galaxy.authnz.psa_authnz.verify",
     # Checks if the current social-account is already associated in the site.
-    'social_core.pipeline.social_auth.social_user',
-
+    "social_core.pipeline.social_auth.social_user",
     # Make up a username for this person, appends a random string at the end if
     # there's any collision.
-    'social_core.pipeline.user.get_username',
-
+    "social_core.pipeline.user.get_username",
     # Send a validation email to the user to verify its email address.
     # 'social_core.pipeline.mail.mail_validation',
-
     # Associates the current social details with another user account with
     # a similar email address.
-    'social_core.pipeline.social_auth.associate_by_email',
-
+    "social_core.pipeline.social_auth.associate_by_email",
     # Create a user account if we haven't found one yet.
-    'social_core.pipeline.user.create_user',
-
+    "social_core.pipeline.user.create_user",
     # Create the record that associated the social account with this user.
-    'social_core.pipeline.social_auth.associate_user',
-
+    "social_core.pipeline.social_auth.associate_user",
     # Populate the extra_data field in the social record with the values
     # specified by settings (and the default ones like access_token, etc).
-    'social_core.pipeline.social_auth.load_extra_data',
-
+    "social_core.pipeline.social_auth.load_extra_data",
     # Update the user record with any changed info from the auth service.
-    'social_core.pipeline.user.user_details'
+    "social_core.pipeline.user.user_details",
 )
 
-DISCONNECT_PIPELINE = (
-    'galaxy.authnz.psa_authnz.allowed_to_disconnect',
-    'galaxy.authnz.psa_authnz.disconnect'
-)
+DISCONNECT_PIPELINE = ("galaxy.authnz.psa_authnz.allowed_to_disconnect", "galaxy.authnz.psa_authnz.disconnect")
 
 
 class PSAAuthnz(IdentityProvider):
     def __init__(self, provider, oidc_config, oidc_backend_config):
-        self.config = {'provider': provider.lower()}
+        self.config = {"provider": provider.lower()}
         for key, value in oidc_config.items():
             self.config[setting_name(key)] = value
 
-        self.config[setting_name('USER_MODEL')] = 'models.User'
-        self.config['SOCIAL_AUTH_PIPELINE'] = AUTH_PIPELINE
-        self.config['DISCONNECT_PIPELINE'] = DISCONNECT_PIPELINE
-        self.config[setting_name('AUTHENTICATION_BACKENDS')] = (BACKENDS[provider],)
+        self.config[setting_name("USER_MODEL")] = "models.User"
+        self.config["SOCIAL_AUTH_PIPELINE"] = AUTH_PIPELINE
+        self.config["DISCONNECT_PIPELINE"] = DISCONNECT_PIPELINE
+        self.config[setting_name("AUTHENTICATION_BACKENDS")] = (BACKENDS[provider],)
 
         self.config["VERIFY_SSL"] = oidc_config.get("VERIFY_SSL")
         self.config["REQUESTS_TIMEOUT"] = oidc_config.get("REQUESTS_TIMEOUT")
@@ -111,90 +105,95 @@ class PSAAuthnz(IdentityProvider):
         # logging in a user. If this setting is set to false, the `_login_user`
         # would not be called, and as a result Galaxy would not know who is
         # the just logged-in user.
-        self.config[setting_name('INACTIVE_USER_LOGIN')] = True
+        self.config[setting_name("INACTIVE_USER_LOGIN")] = True
 
         if provider in BACKENDS_NAME:
             self._setup_idp(oidc_backend_config)
 
         # Secondary AuthZ with Google identities is currently supported
         if provider != "google":
-            if 'SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER' in self.config:
+            if "SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER" in self.config:
                 del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
-            if 'SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT' in self.config:
+            if "SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT" in self.config:
                 del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
 
     def _setup_idp(self, oidc_backend_config):
-        self.config[setting_name('AUTH_EXTRA_ARGUMENTS')] = {'access_type': 'offline'}
-        self.config['KEY'] = oidc_backend_config.get('client_id')
-        self.config['SECRET'] = oidc_backend_config.get('client_secret')
-        self.config['redirect_uri'] = oidc_backend_config.get('redirect_uri')
-        self.config['EXTRA_SCOPES'] = oidc_backend_config.get('extra_scopes')
-        if oidc_backend_config.get('prompt') is not None:
-            self.config[setting_name('AUTH_EXTRA_ARGUMENTS')]['prompt'] = oidc_backend_config.get('prompt')
-        if oidc_backend_config.get('api_url') is not None:
-            self.config[setting_name('API_URL')] = oidc_backend_config.get('api_url')
-        if oidc_backend_config.get('url') is not None:
-            self.config[setting_name('URL')] = oidc_backend_config.get('url')
+        self.config[setting_name("AUTH_EXTRA_ARGUMENTS")] = {"access_type": "offline"}
+        self.config["KEY"] = oidc_backend_config.get("client_id")
+        self.config["SECRET"] = oidc_backend_config.get("client_secret")
+        self.config["redirect_uri"] = oidc_backend_config.get("redirect_uri")
+        self.config["EXTRA_SCOPES"] = oidc_backend_config.get("extra_scopes")
+        if oidc_backend_config.get("prompt") is not None:
+            self.config[setting_name("AUTH_EXTRA_ARGUMENTS")]["prompt"] = oidc_backend_config.get("prompt")
+        if oidc_backend_config.get("api_url") is not None:
+            self.config[setting_name("API_URL")] = oidc_backend_config.get("api_url")
+        if oidc_backend_config.get("url") is not None:
+            self.config[setting_name("URL")] = oidc_backend_config.get("url")
 
     def _get_helper(self, name, do_import=False):
         this_config = self.config.get(setting_name(name), DEFAULTS.get(name, None))
         return do_import and module_member(this_config) or this_config
 
     def _load_backend(self, strategy, redirect_uri):
-        backends = self._get_helper('AUTHENTICATION_BACKENDS')
-        backend = get_backend(backends, BACKENDS_NAME[self.config['provider']])
+        backends = self._get_helper("AUTHENTICATION_BACKENDS")
+        backend = get_backend(backends, BACKENDS_NAME[self.config["provider"]])
         return backend(strategy, redirect_uri)
 
     def _login_user(self, backend, user, social_user):
-        self.config['user'] = user
+        self.config["user"] = user
 
     def authenticate(self, trans):
         on_the_fly_config(trans.sa_session)
         strategy = Strategy(trans.request, trans.session, Storage, self.config)
-        backend = self._load_backend(strategy, self.config['redirect_uri'])
-        if backend.name is BACKENDS_NAME["google"] and \
-                "SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER" in self.config and \
-                "SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT" in self.config:
+        backend = self._load_backend(strategy, self.config["redirect_uri"])
+        if (
+            backend.name is BACKENDS_NAME["google"]
+            and "SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER" in self.config
+            and "SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT" in self.config
+        ):
             backend.DEFAULT_SCOPE.append("https://www.googleapis.com/auth/cloud-platform")
 
-        if self.config['EXTRA_SCOPES'] is not None:
-            backend.DEFAULT_SCOPE.extend(self.config['EXTRA_SCOPES'])
+        if self.config["EXTRA_SCOPES"] is not None:
+            backend.DEFAULT_SCOPE.extend(self.config["EXTRA_SCOPES"])
 
         return do_auth(backend)
 
     def callback(self, state_token, authz_code, trans, login_redirect_url):
         on_the_fly_config(trans.sa_session)
-        self.config[setting_name('LOGIN_REDIRECT_URL')] = login_redirect_url
+        self.config[setting_name("LOGIN_REDIRECT_URL")] = login_redirect_url
         strategy = Strategy(trans.request, trans.session, Storage, self.config)
         strategy.session_set(f"{BACKENDS_NAME[self.config['provider']]}_state", state_token)
-        backend = self._load_backend(strategy, self.config['redirect_uri'])
+        backend = self._load_backend(strategy, self.config["redirect_uri"])
         redirect_url = do_complete(
             backend,
             login=lambda backend, user, social_user: self._login_user(backend, user, social_user),
             user=trans.user,
-            state=state_token)
-        return redirect_url, self.config.get('user', None)
+            state=state_token,
+        )
+        return redirect_url, self.config.get("user", None)
 
     def disconnect(self, provider, trans, disconnect_redirect_url=None, association_id=None):
         on_the_fly_config(trans.sa_session)
-        self.config[setting_name('DISCONNECT_REDIRECT_URL')] =\
+        self.config[setting_name("DISCONNECT_REDIRECT_URL")] = (
             disconnect_redirect_url if disconnect_redirect_url is not None else ()
+        )
         strategy = Strategy(trans.request, trans.session, Storage, self.config)
-        backend = self._load_backend(strategy, self.config['redirect_uri'])
+        backend = self._load_backend(strategy, self.config["redirect_uri"])
         response = do_disconnect(backend, trans.user, association_id)
         if isinstance(response, str):
             return True, "", response
-        return response.get('success', False), response.get('message', ""), ""
+        return response.get("success", False), response.get("message", ""), ""
 
 
 class Strategy(BaseStrategy):
-
     def __init__(self, request, session, storage, config, tpl=None):
         self.request = request
         self.session = session if session else {}
         self.config = config
-        self.config['SOCIAL_AUTH_REDIRECT_IS_HTTPS'] = True if self.request and self.request.host.startswith('https:') else False
-        self.config['SOCIAL_AUTH_GOOGLE_OPENIDCONNECT_EXTRA_DATA'] = ['id_token']
+        self.config["SOCIAL_AUTH_REDIRECT_IS_HTTPS"] = (
+            True if self.request and self.request.host.startswith("https:") else False
+        )
+        self.config["SOCIAL_AUTH_GOOGLE_OPENIDCONNECT_EXTRA_DATA"] = ["id_token"]
         super().__init__(storage, tpl)
 
     def get_setting(self, name):
@@ -207,7 +206,7 @@ class Strategy(BaseStrategy):
         self.session[name] = value
 
     def session_pop(self, name):
-        raise NotImplementedError('Not implemented.')
+        raise NotImplementedError("Not implemented.")
 
     def request_data(self, merge=True):
         if not self.request:
@@ -215,7 +214,7 @@ class Strategy(BaseStrategy):
         if merge:
             data = self.request.GET.copy()
             data.update(self.request.POST)
-        elif self.request.method == 'POST':
+        elif self.request.method == "POST":
             data = self.request.POST
         else:
             data = self.request.GET
@@ -226,23 +225,25 @@ class Strategy(BaseStrategy):
             return self.request.host
 
     def build_absolute_uri(self, path=None):
-        path = path or ''
-        if path.startswith('http://') or path.startswith('https://'):
+        path = path or ""
+        if path.startswith("http://") or path.startswith("https://"):
             return path
         if self.request:
-            return \
-                self.request.host +\
-                '/authnz' + ('/' + self.config.get('provider')) if self.config.get('provider', None) is not None else ''
+            return (
+                self.request.host + "/authnz" + ("/" + self.config.get("provider"))
+                if self.config.get("provider", None) is not None
+                else ""
+            )
         return path
 
     def redirect(self, url):
         return url
 
     def html(self, content):
-        raise NotImplementedError('Not implemented.')
+        raise NotImplementedError("Not implemented.")
 
     def render_html(self, tpl=None, html=None, context=None):
-        raise NotImplementedError('Not implemented.')
+        raise NotImplementedError("Not implemented.")
 
     def start(self):
         self.clean_partial_pipeline()
@@ -316,11 +317,13 @@ def contains_required_data(response=None, is_new=False, **kwargs):
     :rtype:  void
     :return: Raises an exception if any of the required arguments is missing, and pass if all are given.
     """
-    hint_msg = "Visit the identity provider's permitted applications page " \
-               "(e.g., visit `https://myaccount.google.com/u/0/permissions` " \
-               "for Google), then revoke the access of this Galaxy instance, " \
-               "and then retry to login. If the problem persists, contact " \
-               "the Admin of this Galaxy instance."
+    hint_msg = (
+        "Visit the identity provider's permitted applications page "
+        "(e.g., visit `https://myaccount.google.com/u/0/permissions` "
+        "for Google), then revoke the access of this Galaxy instance, "
+        "and then retry to login. If the problem persists, contact "
+        "the Admin of this Galaxy instance."
+    )
     if response is None or not isinstance(response, dict):
         # This can happen only if PSA is not able to decode the `authnz code`
         # sent back from the identity provider. PSA internally handles such
@@ -356,10 +359,10 @@ def verify(strategy=None, response=None, details=None, **kwargs):
         result = requests.post(
             f"https://iam.googleapis.com/v1/projects/-/serviceAccounts/{endpoint}:getIamPolicy",
             headers={
-                'Authorization': f"Bearer {response.get('access_token')}",
-                'Accept': 'application/json',
+                "Authorization": f"Bearer {response.get('access_token')}",
+                "Accept": "application/json",
             },
-            timeout=DEFAULT_SOCKET_TIMEOUT
+            timeout=DEFAULT_SOCKET_TIMEOUT,
         )
         res = json.loads(result.content)
         if result.status_code == requests.codes.ok:
@@ -380,8 +383,9 @@ def verify(strategy=None, response=None, details=None, **kwargs):
         raise Exception(f"`{provider}` is an unsupported secondary authorization provider, contact admin.")
 
 
-def allowed_to_disconnect(name=None, user=None, user_storage=None, strategy=None,
-                          backend=None, request=None, details=None, **kwargs):
+def allowed_to_disconnect(
+    name=None, user=None, user_storage=None, strategy=None, backend=None, request=None, details=None, **kwargs
+):
     """
     Disconnect is the process of disassociating a Galaxy user and a third-party authnz.
     In other words, it is the process of removing any access and/or ID tokens of a user.
@@ -402,8 +406,9 @@ def allowed_to_disconnect(name=None, user=None, user_storage=None, strategy=None
     """
 
 
-def disconnect(name=None, user=None, user_storage=None, strategy=None,
-               backend=None, request=None, details=None, **kwargs):
+def disconnect(
+    name=None, user=None, user_storage=None, strategy=None, backend=None, request=None, details=None, **kwargs
+):
     """
     Disconnect is the process of disassociating a Galaxy user and a third-party authnz.
     In other words, it is the process of removing any access and/or ID tokens of a user.
@@ -422,10 +427,13 @@ def disconnect(name=None, user=None, user_storage=None, strategy=None,
     """
 
     sa_session = user_storage.sa_session
-    user_authnz = sa_session.query(user_storage).filter(user_storage.table.c.user_id == user.id,
-                                                        user_storage.table.c.provider == name).first()
+    user_authnz = (
+        sa_session.query(user_storage)
+        .filter(user_storage.table.c.user_id == user.id, user_storage.table.c.provider == name)
+        .first()
+    )
     if user_authnz is None:
-        return {'success': False, 'message': 'Not authenticated by any identity providers.'}
+        return {"success": False, "message": "Not authenticated by any identity providers."}
     # option A
     sa_session.delete(user_authnz)
     # option B
diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index 5bc16fb0d96..6aa5a4c8535 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -15,7 +15,10 @@ from galaxy.config import Configuration
 from galaxy.main_config import find_config
 from galaxy.util.custom_logging import get_logger
 from galaxy.util.properties import load_app_properties
-from ._serialization import schema_dumps, schema_loads
+from ._serialization import (
+    schema_dumps,
+    schema_loads,
+)
 
 log = get_logger(__name__)
 
@@ -23,11 +26,12 @@ log = get_logger(__name__)
 @lru_cache(maxsize=1)
 def get_galaxy_app():
     import galaxy.app
+
     if galaxy.app.app:
         return galaxy.app.app
     kwargs = get_app_properties()
     if kwargs:
-        kwargs['check_migrate_databases'] = False
+        kwargs["check_migrate_databases"] = False
         galaxy_app = galaxy.app.GalaxyManagerApplication(configure_logging=False, **kwargs)
         return galaxy_app
 
@@ -35,16 +39,16 @@ def get_galaxy_app():
 @lru_cache(maxsize=1)
 def get_app_properties():
     config_file = os.environ.get("GALAXY_CONFIG_FILE")
-    galaxy_root_dir = os.environ.get('GALAXY_ROOT_DIR')
+    galaxy_root_dir = os.environ.get("GALAXY_ROOT_DIR")
     if not config_file and galaxy_root_dir:
         config_file = find_config(config_file, galaxy_root_dir)
     if config_file:
         properties = load_app_properties(
             config_file=os.path.abspath(config_file),
-            config_section='galaxy',
+            config_section="galaxy",
         )
         if galaxy_root_dir:
-            properties['root_dir'] = galaxy_root_dir
+            properties["root_dir"] = galaxy_root_dir
         return properties
 
 
@@ -52,7 +56,7 @@ def get_app_properties():
 def get_config():
     kwargs = get_app_properties()
     if kwargs:
-        kwargs['override_tempdir'] = False
+        kwargs["override_tempdir"] = False
         return Configuration(**kwargs)
 
 
@@ -71,33 +75,30 @@ def get_history_audit_table_prune_interval():
 
 
 broker = get_broker()
-celery_app = Celery('galaxy', broker=broker, include=['galaxy.celery.tasks'])
+celery_app = Celery("galaxy", broker=broker, include=["galaxy.celery.tasks"])
 prune_interval = get_history_audit_table_prune_interval()
 if prune_interval > 0:
     celery_app.conf.beat_schedule = {
-        'prune-history-audit-table': {
-            'task': 'galaxy.celery.tasks.prune_history_audit_table',
-            'schedule': prune_interval,
+        "prune-history-audit-table": {
+            "task": "galaxy.celery.tasks.prune_history_audit_table",
+            "schedule": prune_interval,
         },
     }
-celery_app.conf.timezone = 'UTC'
+celery_app.conf.timezone = "UTC"
 
 
 CELERY_TASKS = []
-PYDANTIC_AWARE_SERIALIER_NAME = 'pydantic-aware-json'
+PYDANTIC_AWARE_SERIALIER_NAME = "pydantic-aware-json"
 
 
 serialization.register(
-    PYDANTIC_AWARE_SERIALIER_NAME,
-    encoder=schema_dumps,
-    decoder=schema_loads,
-    content_type='application/json'
+    PYDANTIC_AWARE_SERIALIER_NAME, encoder=schema_dumps, decoder=schema_loads, content_type="application/json"
 )
 
 
 def galaxy_task(*args, **celery_task_kwd):
-    if 'serializer' not in celery_task_kwd:
-        celery_task_kwd['serializer'] = PYDANTIC_AWARE_SERIALIER_NAME
+    if "serializer" not in celery_task_kwd:
+        celery_task_kwd["serializer"] = PYDANTIC_AWARE_SERIALIER_NAME
 
     def decorate(func):
         CELERY_TASKS.append(func.__name__)
@@ -117,5 +118,5 @@ def galaxy_task(*args, **celery_task_kwd):
         return decorate
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     celery_app.start()
diff --git a/lib/galaxy/celery/_serialization.py b/lib/galaxy/celery/_serialization.py
index a7a6b3a4670..8accdb632d3 100644
--- a/lib/galaxy/celery/_serialization.py
+++ b/lib/galaxy/celery/_serialization.py
@@ -10,32 +10,34 @@ SCHEMA_MODELS_PACKAGE_BASE = "galaxy.schema."
 def fullname(o):
     klass = o.__class__
     module = klass.__module__
-    if module == 'builtins':
+    if module == "builtins":
         return klass.__qualname__  # avoid outputs like 'builtins.str'
-    return module + '.' + klass.__qualname__
+    return module + "." + klass.__qualname__
 
 
 class SchemaEncoder(json.JSONEncoder):
     def default(self, obj):
         if isinstance(obj, BaseModel):
             return {
-                '__type__': '__pydantic_object__',
-                '__class__': fullname(obj),
-                '__object__': obj.dict(),
+                "__type__": "__pydantic_object__",
+                "__class__": fullname(obj),
+                "__object__": obj.dict(),
             }
         else:
             return json.JSONEncoder.default(self, obj)
 
 
 def schema_decoder(obj):
-    if '__type__' in obj:
-        if obj['__type__'] == '__pydantic_object__':
-            clazz_str = obj['__class__']
-            assert clazz_str.startswith(SCHEMA_MODELS_PACKAGE_BASE) and ".." not in clazz_str, f"Invalid class str {clazz_str}"
-            module_name, class_name = clazz_str.rsplit('.', 1)
+    if "__type__" in obj:
+        if obj["__type__"] == "__pydantic_object__":
+            clazz_str = obj["__class__"]
+            assert (
+                clazz_str.startswith(SCHEMA_MODELS_PACKAGE_BASE) and ".." not in clazz_str
+            ), f"Invalid class str {clazz_str}"
+            module_name, class_name = clazz_str.rsplit(".", 1)
             module = import_module(module_name)
             clazz = getattr(module, class_name, None)
-            obj = clazz(**obj['__object__'])
+            obj = clazz(**obj["__object__"])
             return obj
 
     return obj
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index 8b1d4a97faa..8914cfaf193 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -31,24 +31,27 @@ def purge_hda(hda_manager: HDAManager, hda_id):
 
 
 @galaxy_task
-def set_metadata(hda_manager: HDAManager, ldda_manager: LDDAManager, dataset_id, model_class='HistoryDatasetAssociation'):
-    if model_class == 'HistoryDatasetAssociation':
+def set_metadata(
+    hda_manager: HDAManager, ldda_manager: LDDAManager, dataset_id, model_class="HistoryDatasetAssociation"
+):
+    if model_class == "HistoryDatasetAssociation":
         dataset = hda_manager.by_id(dataset_id)
-    elif model_class == 'LibraryDatasetDatasetAssociation':
+    elif model_class == "LibraryDatasetDatasetAssociation":
         dataset = ldda_manager.by_id(dataset_id)
     dataset.datatype.set_meta(dataset)
 
 
 @galaxy_task(ignore_result=True)
 def export_history(
-        app: MinimalManagerApp,
-        sa_session: galaxy_scoped_session,
-        job_manager: JobManager,
-        store_directory: str,
-        history_id: int,
-        job_id: int,
-        include_hidden=False,
-        include_deleted=False):
+    app: MinimalManagerApp,
+    sa_session: galaxy_scoped_session,
+    job_manager: JobManager,
+    store_directory: str,
+    history_id: int,
+    job_id: int,
+    include_hidden=False,
+    include_deleted=False,
+):
     history = sa_session.query(model.History).get(history_id)
     with model.store.DirectoryModelExportStore(store_directory, app=app, export_files="symlink") as export_store:
         export_store.export_history(history, include_hidden=include_hidden, include_deleted=include_deleted)
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 0d76a4e39f6..15ac7dd8d16 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -61,7 +61,10 @@ from galaxy.util.properties import (
 )
 from galaxy.web.formatting import expand_pretty_datetime_format
 from galaxy.web_stack import get_stack_facts
-from ..version import VERSION_MAJOR, VERSION_MINOR
+from ..version import (
+    VERSION_MAJOR,
+    VERSION_MINOR,
+)
 
 try:
     from importlib.resources import files  # type: ignore[attr-defined]
@@ -78,60 +81,60 @@ if TYPE_CHECKING:
 
 log = logging.getLogger(__name__)
 
-GALAXY_APP_NAME = 'galaxy'
-GALAXY_SCHEMAS_PATH = files('galaxy.config') / 'schemas'
-GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / 'config_schema.yml'
-UWSGI_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / 'uwsgi_schema.yml'
+GALAXY_APP_NAME = "galaxy"
+GALAXY_SCHEMAS_PATH = files("galaxy.config") / "schemas"
+GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "config_schema.yml"
+UWSGI_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "uwsgi_schema.yml"
 LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
-    'disable_existing_loggers': False,
-    'version': 1,
-    'root': {
-        'handlers': ['console'],
-        'level': 'DEBUG',
+    "disable_existing_loggers": False,
+    "version": 1,
+    "root": {
+        "handlers": ["console"],
+        "level": "DEBUG",
     },
-    'loggers': {
-        'paste.httpserver.ThreadPool': {
-            'level': 'WARN',
-            'qualname': 'paste.httpserver.ThreadPool',
+    "loggers": {
+        "paste.httpserver.ThreadPool": {
+            "level": "WARN",
+            "qualname": "paste.httpserver.ThreadPool",
         },
-        'sqlalchemy_json.track': {
-            'level': 'WARN',
-            'qualname': 'sqlalchemy_json.track',
+        "sqlalchemy_json.track": {
+            "level": "WARN",
+            "qualname": "sqlalchemy_json.track",
         },
-        'urllib3.connectionpool': {
-            'level': 'WARN',
-            'qualname': 'urllib3.connectionpool',
+        "urllib3.connectionpool": {
+            "level": "WARN",
+            "qualname": "urllib3.connectionpool",
         },
-        'routes.middleware': {
-            'level': 'WARN',
-            'qualname': 'routes.middleware',
+        "routes.middleware": {
+            "level": "WARN",
+            "qualname": "routes.middleware",
         },
-        'amqp': {
-            'level': 'INFO',
-            'qualname': 'amqp',
+        "amqp": {
+            "level": "INFO",
+            "qualname": "amqp",
         },
-        'botocore': {
-            'level': 'INFO',
-            'qualname': 'botocore',
+        "botocore": {
+            "level": "INFO",
+            "qualname": "botocore",
         },
     },
-    'filters': {
-        'stack': {
-            '()': 'galaxy.web_stack.application_stack_log_filter',
+    "filters": {
+        "stack": {
+            "()": "galaxy.web_stack.application_stack_log_filter",
         },
     },
-    'handlers': {
-        'console': {
-            'class': 'logging.StreamHandler',
-            'formatter': 'stack',
-            'level': 'DEBUG',
-            'stream': 'ext://sys.stderr',
-            'filters': ['stack'],
+    "handlers": {
+        "console": {
+            "class": "logging.StreamHandler",
+            "formatter": "stack",
+            "level": "DEBUG",
+            "stream": "ext://sys.stderr",
+            "filters": ["stack"],
         },
     },
-    'formatters': {
-        'stack': {
-            '()': 'galaxy.web_stack.application_stack_log_formatter',
+    "formatters": {
+        "stack": {
+            "()": "galaxy.web_stack.application_stack_log_formatter",
         },
     },
 }
@@ -139,7 +142,7 @@ LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
 
 
 def find_root(kwargs):
-    return os.path.abspath(kwargs.get('root_dir', '.'))
+    return os.path.abspath(kwargs.get("root_dir", "."))
 
 
 OptStr = TypeVar("OptStr", None, str)
@@ -150,7 +153,9 @@ class BaseAppConfiguration(HasDynamicProperties):
     # If VALUE == first directory in a user-supplied path that resolves to KEY, it will be stripped from that path
     renamed_options: Optional[Dict[str, str]] = None
     deprecated_dirs: Dict[str, str] = {}
-    paths_to_check_against_root: Set[str] = set()  # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root
+    paths_to_check_against_root: Set[
+        str
+    ] = set()  # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root
     add_sample_file_to_defaults: Set[str] = set()  # for these options, add sample config files to their defaults
     listify_options: Set[str] = set()  # values for these options are processed as lists of values
     object_store_store_by: str
@@ -188,19 +193,21 @@ class BaseAppConfiguration(HasDynamicProperties):
         Fix deprecated database URLs (postgres... >> postgresql...)
         https://docs.sqlalchemy.org/en/14/changelog/changelog_14.html#change-3687655465c25a39b968b4f5f6e9170b
         """
-        old_dialect, new_dialect = 'postgres', 'postgresql'
-        old_prefixes = (f'{old_dialect}:', f'{old_dialect}+')  # check for postgres://foo and postgres+driver//foo
+        old_dialect, new_dialect = "postgres", "postgresql"
+        old_prefixes = (f"{old_dialect}:", f"{old_dialect}+")  # check for postgres://foo and postgres+driver//foo
         offset = len(old_dialect)
-        keys = ('database_connection', 'install_database_connection')
+        keys = ("database_connection", "install_database_connection")
         for key in keys:
             if key in kwargs:
                 value = kwargs[key]
                 for prefix in old_prefixes:
                     if value.startswith(prefix):
-                        value = f'{new_dialect}{value[offset:]}'
+                        value = f"{new_dialect}{value[offset:]}"
                         kwargs[key] = value
-                        log.warning('PostgreSQL database URLs of the form "postgres://" have been '
-                            'deprecated. Please use "postgresql://".')
+                        log.warning(
+                            'PostgreSQL database URLs of the form "postgres://" have been '
+                            'deprecated. Please use "postgresql://".'
+                        )
 
     def is_set(self, key):
         """Check if a configuration option has been explicitly set."""
@@ -215,13 +222,12 @@ class BaseAppConfiguration(HasDynamicProperties):
         return self._in_root_dir(path)
 
     def _set_config_base(self, config_kwargs):
-
         def _set_global_conf():
-            self.config_file = find_config_file('galaxy')
-            self.global_conf = config_kwargs.get('global_conf')
+            self.config_file = find_config_file("galaxy")
+            self.global_conf = config_kwargs.get("global_conf")
             self.global_conf_parser = configparser.ConfigParser()
             if not self.config_file and self.global_conf and "__file__" in self.global_conf:
-                self.config_file = os.path.join(self.root, self.global_conf['__file__'])
+                self.config_file = os.path.join(self.root, self.global_conf["__file__"])
 
             if self.config_file is None:
                 log.warning("No Galaxy config file found, running from current working directory: %s", os.getcwd())
@@ -236,40 +242,40 @@ class BaseAppConfiguration(HasDynamicProperties):
         def _set_config_directories():
             # Set config_dir to value from kwargs OR dirname of config_file OR None
             _config_dir = os.path.dirname(self.config_file) if self.config_file else None
-            self.config_dir = config_kwargs.get('config_dir', _config_dir)
+            self.config_dir = config_kwargs.get("config_dir", _config_dir)
             # Make path absolute before using it as base for other paths
             if self.config_dir:
                 self.config_dir = os.path.abspath(self.config_dir)
 
-            self.data_dir = config_kwargs.get('data_dir')
+            self.data_dir = config_kwargs.get("data_dir")
             if self.data_dir:
                 self.data_dir = os.path.abspath(self.data_dir)
 
-            self.sample_config_dir = os.path.join(os.path.dirname(__file__), 'sample')
+            self.sample_config_dir = os.path.join(os.path.dirname(__file__), "sample")
             if self.sample_config_dir:
                 self.sample_config_dir = os.path.abspath(self.sample_config_dir)
 
-            self.managed_config_dir = config_kwargs.get('managed_config_dir')
+            self.managed_config_dir = config_kwargs.get("managed_config_dir")
             if self.managed_config_dir:
                 self.managed_config_dir = os.path.abspath(self.managed_config_dir)
 
             if running_from_source:
                 if not self.config_dir:
-                    self.config_dir = os.path.join(self.root, 'config')
+                    self.config_dir = os.path.join(self.root, "config")
                 if not self.data_dir:
-                    self.data_dir = os.path.join(self.root, 'database')
+                    self.data_dir = os.path.join(self.root, "database")
                 if not self.managed_config_dir:
                     self.managed_config_dir = self.config_dir
             else:
                 if not self.config_dir:
                     self.config_dir = os.getcwd()
                 if not self.data_dir:
-                    self.data_dir = self._in_config_dir('data')
+                    self.data_dir = self._in_config_dir("data")
                 if not self.managed_config_dir:
-                    self.managed_config_dir = self._in_data_dir('config')
+                    self.managed_config_dir = self._in_data_dir("config")
 
             # TODO: do we still need to support ../shed_tools when running_from_source?
-            self.shed_tools_dir = self._in_data_dir('shed_tools')
+            self.shed_tools_dir = self._in_data_dir("shed_tools")
 
             log.debug("Configuration directory is %s", self.config_dir)
             log.debug("Data directory is %s", self.data_dir)
@@ -280,7 +286,7 @@ class BaseAppConfiguration(HasDynamicProperties):
 
     def _load_schema(self):
         # Override in subclasses
-        raise Exception('Not implemented')
+        raise Exception("Not implemented")
 
     def _preprocess_paths_to_resolve(self):
         # For these options, if option is not set, listify its defaults and add a sample config file.
@@ -288,17 +294,20 @@ class BaseAppConfiguration(HasDynamicProperties):
             for key in self.add_sample_file_to_defaults:
                 if not self.is_set(key):
                     defaults = listify(getattr(self, key), do_strip=True)
-                    sample = f'{defaults[-1]}.sample'  # if there are multiple defaults, use last as template
+                    sample = f"{defaults[-1]}.sample"  # if there are multiple defaults, use last as template
                     sample = self._in_sample_dir(sample)  # resolve w.r.t sample_dir
                     defaults.append(sample)
                     setattr(self, key, defaults)
 
     def _postprocess_paths_to_resolve(self):
-
         def select_one_path_from_list():
             # To consider: options with a sample file added to defaults except options that can have multiple values.
             # If value is not set, check each path in list; set to first path that exists; if none exist, set to last path in list.
-            keys = self.add_sample_file_to_defaults - self.listify_options if self.listify_options else self.add_sample_file_to_defaults
+            keys = (
+                self.add_sample_file_to_defaults - self.listify_options
+                if self.listify_options
+                else self.add_sample_file_to_defaults
+            )
             for key in keys:
                 if not self.is_set(key):
                     paths = getattr(self, key)
@@ -307,7 +316,9 @@ class BaseAppConfiguration(HasDynamicProperties):
                             setattr(self, key, path)
                             break
                     else:
-                        setattr(self, key, paths[-1])  # TODO: we assume it exists; but we've already checked in the loop! Raise error instead?
+                        setattr(
+                            self, key, paths[-1]
+                        )  # TODO: we assume it exists; but we've already checked in the loop! Raise error instead?
 
         def select_one_or_all_paths_from_list():
             # Values for these options are lists of paths. If value is not set, use defaults if all paths in list exist;
@@ -320,7 +331,9 @@ class BaseAppConfiguration(HasDynamicProperties):
                             setattr(self, key, [paths[-1]])  # value is a list
                             break
 
-        if self.add_sample_file_to_defaults:  # Currently, this is the ONLY case when we need to pick one file from a list
+        if (
+            self.add_sample_file_to_defaults
+        ):  # Currently, this is the ONLY case when we need to pick one file from a list
             select_one_path_from_list()
         if self.listify_options:
             select_one_or_all_paths_from_list()
@@ -346,7 +359,7 @@ class BaseAppConfiguration(HasDynamicProperties):
         }
 
         def convert_datatype(key, value):
-            datatype = self.schema.app_schema[key].get('type')
+            datatype = self.schema.app_schema[key].get("type")
             # check for `not None` explicitly (value can be falsy)
             if value is not None and datatype in type_converters:
                 # convert value or each item in value to type `datatype`
@@ -367,14 +380,18 @@ class BaseAppConfiguration(HasDynamicProperties):
                         ignore = first_dir + os.sep
                         log.warning(
                             "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
-                            "to suppress this warning: %s", key, resolves_to, ignore, path
+                            "to suppress this warning: %s",
+                            key,
+                            resolves_to,
+                            ignore,
+                            path,
                         )
-                        paths[i] = path[len(ignore):]
+                        paths[i] = path[len(ignore) :]
 
                 # return list or string, depending on type of `value`
                 if isinstance(value, list):
                     return paths
-                return ','.join(paths)
+                return ",".join(paths)
             return value
 
         for key, value in kwargs.items():
@@ -387,7 +404,7 @@ class BaseAppConfiguration(HasDynamicProperties):
     def _create_attributes_from_raw_config(self):
         # `base_configs` are a special case: these attributes have been created and will be ignored
         # by the code below. Trying to overwrite any other existing attributes will raise an error.
-        base_configs = {'config_dir', 'data_dir', 'managed_config_dir'}
+        base_configs = {"config_dir", "data_dir", "managed_config_dir"}
         for key, value in self._raw_config.items():
             if not hasattr(self, key):
                 setattr(self, key, value)
@@ -395,7 +412,6 @@ class BaseAppConfiguration(HasDynamicProperties):
                 raise ConfigurationError(f"Attempting to override existing attribute '{key}'")
 
     def _resolve_paths(self):
-
         def resolve(key):
             if key in _cache:  # resolve each path only once
                 return _cache[key]
@@ -420,7 +436,7 @@ class BaseAppConfiguration(HasDynamicProperties):
             # Check if value is a list or should be listified; if so, listify and resolve each item separately.
             if type(value) is list or (self.listify_options and key in self.listify_options):
                 saved_values = listify(getattr(self, key), do_strip=True)  # listify and save original value
-                setattr(self, key, '_')  # replace value with temporary placeholder
+                setattr(self, key, "_")  # replace value with temporary placeholder
                 resolve(key)  # resolve temporary value (`_` becomes `parent-path/_`)
                 resolved_base = getattr(self, key)[:-1]  # get rid of placeholder in resolved path
                 # apply resolved base to saved values
@@ -433,7 +449,6 @@ class BaseAppConfiguration(HasDynamicProperties):
                 self._check_against_root(key)
 
     def _check_against_root(self, key):
-
         def get_path(current_path, initial_path):
             # if path does not exist and was set as relative:
             if not self._path_exists(current_path) and not os.path.isabs(initial_path):
@@ -531,64 +546,71 @@ class CommonConfigurationMixin:
 
 
 class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
-    deprecated_options = ('database_file', 'track_jobs_in_database', 'blacklist_file', 'whitelist_file',
-                          'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist',
-                          'containers_resolvers_config_file')
+    deprecated_options = (
+        "database_file",
+        "track_jobs_in_database",
+        "blacklist_file",
+        "whitelist_file",
+        "sanitize_whitelist_file",
+        "user_library_import_symlink_whitelist",
+        "fetch_url_whitelist",
+        "containers_resolvers_config_file",
+    )
     renamed_options = {
-        'blacklist_file': 'email_domain_blocklist_file',
-        'whitelist_file': 'email_domain_allowlist_file',
-        'sanitize_whitelist_file': 'sanitize_allowlist_file',
-        'user_library_import_symlink_whitelist': 'user_library_import_symlink_allowlist',
-        'fetch_url_whitelist': 'fetch_url_allowlist',
-        'containers_resolvers_config_file': 'container_resolvers_config_file',
+        "blacklist_file": "email_domain_blocklist_file",
+        "whitelist_file": "email_domain_allowlist_file",
+        "sanitize_whitelist_file": "sanitize_allowlist_file",
+        "user_library_import_symlink_whitelist": "user_library_import_symlink_allowlist",
+        "fetch_url_whitelist": "fetch_url_allowlist",
+        "containers_resolvers_config_file": "container_resolvers_config_file",
     }
-    default_config_file_name = 'galaxy.yml'
-    deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
+    default_config_file_name = "galaxy.yml"
+    deprecated_dirs = {"config_dir": "config", "data_dir": "database"}
 
     paths_to_check_against_root = {
-        'auth_config_file',
-        'build_sites_config_file',
-        'containers_config_file',
-        'data_manager_config_file',
-        'datatypes_config_file',
-        'dependency_resolvers_config_file',
-        'error_report_file',
-        'job_config_file',
-        'job_metrics_config_file',
-        'job_resource_params_file',
-        'local_conda_mapping_file',
-        'migrated_tools_config',
-        'modules_mapping_files',
-        'object_store_config_file',
-        'oidc_backends_config_file',
-        'oidc_config_file',
-        'shed_data_manager_config_file',
-        'shed_tool_config_file',
-        'shed_tool_data_table_config',
-        'tool_destinations_config_file',
-        'tool_sheds_config_file',
-        'user_preferences_extra_conf_path',
-        'workflow_resource_params_file',
-        'workflow_schedulers_config_file',
-        'markdown_export_css',
-        'markdown_export_css_pages',
-        'markdown_export_css_invocation_reports',
-        'file_path',
-        'tool_data_table_config_path',
-        'tool_config_file',
+        "auth_config_file",
+        "build_sites_config_file",
+        "containers_config_file",
+        "data_manager_config_file",
+        "datatypes_config_file",
+        "dependency_resolvers_config_file",
+        "error_report_file",
+        "job_config_file",
+        "job_metrics_config_file",
+        "job_resource_params_file",
+        "local_conda_mapping_file",
+        "migrated_tools_config",
+        "modules_mapping_files",
+        "object_store_config_file",
+        "oidc_backends_config_file",
+        "oidc_config_file",
+        "shed_data_manager_config_file",
+        "shed_tool_config_file",
+        "shed_tool_data_table_config",
+        "tool_destinations_config_file",
+        "tool_sheds_config_file",
+        "user_preferences_extra_conf_path",
+        "workflow_resource_params_file",
+        "workflow_schedulers_config_file",
+        "markdown_export_css",
+        "markdown_export_css_pages",
+        "markdown_export_css_invocation_reports",
+        "file_path",
+        "tool_data_table_config_path",
+        "tool_config_file",
     }
 
     add_sample_file_to_defaults = {
-        'build_sites_config_file',
-        'datatypes_config_file',
-        'job_metrics_config_file',
-        'tool_data_table_config_path',
-        'tool_config_file',
+        "build_sites_config_file",
+        "datatypes_config_file",
+        "job_metrics_config_file",
+        "tool_data_table_config_path",
+        "tool_config_file",
     }
 
     listify_options = {
-        'tool_data_table_config_path',
-        'tool_config_file',
+        "tool_data_table_config_path",
+        "tool_config_file",
     }
     database_connection: str
     tool_path: str
@@ -637,17 +659,20 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         This method should be deleted after migration to SQLAlchemy 2.0 is complete.
         To enable warnings, set `GALAXY_CONFIG_SQLALCHEMY_WARN_20=1`,
         """
-        warn = string_as_bool(kwargs.get('sqlalchemy_warn_20', False))
+        warn = string_as_bool(kwargs.get("sqlalchemy_warn_20", False))
         if warn:
             import sqlalchemy
+
             sqlalchemy.util.deprecations.SQLALCHEMY_WARN_20 = True
             self._setup_sqlalchemy20_warnings_filters()
 
     def _setup_sqlalchemy20_warnings_filters(self):
         import warnings
+
         from sqlalchemy.exc import RemovedIn20Warning
+
         # Always display RemovedIn20Warning warnings.
-        warnings.filterwarnings('always', category=RemovedIn20Warning)
+        warnings.filterwarnings("always", category=RemovedIn20Warning)
         # Optionally, enable filters for specific warnings (raise error, or log, etc.)
         # messages = [
         #     r"replace with warning text to match",
@@ -693,13 +718,13 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.version_minor = VERSION_MINOR
 
         # Database related configuration
-        self.check_migrate_databases = kwargs.get('check_migrate_databases', True)
+        self.check_migrate_databases = kwargs.get("check_migrate_databases", True)
         if not self.database_connection:  # Provide default if not supplied by user
-            db_path = self._in_data_dir('universe.sqlite')
-            self.database_connection = f'sqlite:///{db_path}?isolation_level=IMMEDIATE'
+            db_path = self._in_data_dir("universe.sqlite")
+            self.database_connection = f"sqlite:///{db_path}?isolation_level=IMMEDIATE"
         self.database_engine_options = get_database_engine_options(kwargs)
-        self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
-        self.database_encoding = kwargs.get('database_encoding')  # Create new databases with this encoding
+        self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True"))
+        self.database_encoding = kwargs.get("database_encoding")  # Create new databases with this encoding
         self.thread_local_log = None
         if self.enable_per_request_sql_debugging:
             self.thread_local_log = threading.local()
@@ -710,12 +735,12 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.tool_path = self._in_root_dir(self.tool_path)
         self.tool_data_path = self._in_root_dir(self.tool_data_path)
         if not running_from_source and kwargs.get("tool_data_path") is None:
-            self.tool_data_path = self._in_data_dir(self.schema.defaults['tool_data_path'])
+            self.tool_data_path = self._in_data_dir(self.schema.defaults["tool_data_path"])
         self.builds_file_path = os.path.join(self.tool_data_path, self.builds_file_path)
         self.len_file_path = os.path.join(self.tool_data_path, self.len_file_path)
         self.oidc = {}
         self.integrated_tool_panel_config = self._in_managed_config_dir(self.integrated_tool_panel_config)
-        integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory')
+        integrated_tool_panel_tracking_directory = kwargs.get("integrated_tool_panel_tracking_directory")
         if integrated_tool_panel_tracking_directory:
             self.integrated_tool_panel_tracking_directory = self._in_root_dir(integrated_tool_panel_tracking_directory)
         else:
@@ -728,18 +753,18 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.user_tool_filters = listify(self.user_tool_filters, do_strip=True)
         self.user_tool_label_filters = listify(self.user_tool_label_filters, do_strip=True)
         self.user_tool_section_filters = listify(self.user_tool_section_filters, do_strip=True)
-        self.has_user_tool_filters = bool(self.user_tool_filters or self.user_tool_label_filters or self.user_tool_section_filters)
-
-        self.password_expiration_period = timedelta(
-            days=int(cast(SupportsInt, self.password_expiration_period))
+        self.has_user_tool_filters = bool(
+            self.user_tool_filters or self.user_tool_label_filters or self.user_tool_section_filters
         )
 
+        self.password_expiration_period = timedelta(days=int(cast(SupportsInt, self.password_expiration_period)))
+
         if self.shed_tool_data_path:
             self.shed_tool_data_path = self._in_root_dir(self.shed_tool_data_path)
         else:
             self.shed_tool_data_path = self.tool_data_path
 
-        self.running_functional_tests = string_as_bool(kwargs.get('running_functional_tests', False))
+        self.running_functional_tests = string_as_bool(kwargs.get("running_functional_tests", False))
         if isinstance(self.hours_between_check, str):
             self.hours_between_check = float(self.hours_between_check)
         try:
@@ -765,9 +790,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.use_remote_user = self.use_remote_user or self.single_user
         self.fetch_url_allowlist_ips = [
             ipaddress.ip_network(unicodify(ip.strip()))  # If it has a slash, assume 127.0.0.1/24 notation
-            if '/' in ip else
-            ipaddress.ip_address(unicodify(ip.strip()))  # Otherwise interpret it as an ip address.
-            for ip in kwargs.get("fetch_url_allowlist", "").split(',')
+            if "/" in ip
+            else ipaddress.ip_address(unicodify(ip.strip()))  # Otherwise interpret it as an ip address.
+            for ip in kwargs.get("fetch_url_allowlist", "").split(",")
             if len(ip.strip()) > 0
         ]
         self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
@@ -780,36 +805,47 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.preserve_python_environment = "legacy_only"
         self.nodejs_path = kwargs.get("nodejs_path")
         self.container_image_cache_path = self._in_data_dir(kwargs.get("container_image_cache_path", "container_cache"))
-        self.output_size_limit = int(kwargs.get('output_size_limit', 0))
+        self.output_size_limit = int(kwargs.get("output_size_limit", 0))
         # activation_email was used until release_15.03
-        activation_email = kwargs.get('activation_email')
+        activation_email = kwargs.get("activation_email")
         self.email_from = self.email_from or activation_email
 
-        self.email_domain_blocklist_content = self._load_list_from_file(self._in_config_dir(self.email_domain_blocklist_file)) if self.email_domain_blocklist_file else None
-        self.email_domain_allowlist_content = self._load_list_from_file(self._in_config_dir(self.email_domain_allowlist_file)) if self.email_domain_allowlist_file else None
+        self.email_domain_blocklist_content = (
+            self._load_list_from_file(self._in_config_dir(self.email_domain_blocklist_file))
+            if self.email_domain_blocklist_file
+            else None
+        )
+        self.email_domain_allowlist_content = (
+            self._load_list_from_file(self._in_config_dir(self.email_domain_allowlist_file))
+            if self.email_domain_allowlist_file
+            else None
+        )
 
         # These are not even beta - just experiments - don't use them unless
         # you want yours tools to be broken in the future.
-        self.enable_beta_tool_formats = string_as_bool(kwargs.get('enable_beta_tool_formats', 'False'))
+        self.enable_beta_tool_formats = string_as_bool(kwargs.get("enable_beta_tool_formats", "False"))
 
-        if self.workflow_resource_params_mapper and ':' not in self.workflow_resource_params_mapper:
+        if self.workflow_resource_params_mapper and ":" not in self.workflow_resource_params_mapper:
             # Assume it is not a Python function, so a file; else: a Python function
             self.workflow_resource_params_mapper = self._in_root_dir(self.workflow_resource_params_mapper)
 
-        self.pbs_application_server = kwargs.get('pbs_application_server', "")
-        self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "")
-        self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "")
-        self.pbs_stage_path = kwargs.get('pbs_stage_path', "")
+        self.pbs_application_server = kwargs.get("pbs_application_server", "")
+        self.pbs_dataset_server = kwargs.get("pbs_dataset_server", "")
+        self.pbs_dataset_path = kwargs.get("pbs_dataset_path", "")
+        self.pbs_stage_path = kwargs.get("pbs_stage_path", "")
 
         _sanitize_allowlist_path = self._in_managed_config_dir(self.sanitize_allowlist_file)
         if not os.path.isfile(_sanitize_allowlist_path):  # then check old default location
             for deprecated in (
-                    self._in_managed_config_dir('sanitize_whitelist.txt'),
-                    self._in_root_dir('config/sanitize_whitelist.txt')):
+                self._in_managed_config_dir("sanitize_whitelist.txt"),
+                self._in_root_dir("config/sanitize_whitelist.txt"),
+            ):
                 if os.path.isfile(deprecated):
-                    log.warning("The path '%s' for the 'sanitize_allowlist_file' config option is "
+                    log.warning(
+                        "The path '%s' for the 'sanitize_allowlist_file' config option is "
                         "deprecated and will be no longer checked in a future release. Please consult "
-                        "the latest version of the sample configuration file." % deprecated)
+                        "the latest version of the sample configuration file." % deprecated
+                    )
                     _sanitize_allowlist_path = deprecated
                     break
         self.sanitize_allowlist_file = _sanitize_allowlist_path
@@ -818,18 +854,24 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         if "trust_jupyter_notebook_conversion" not in kwargs:
             # if option not set, check IPython-named alternative, falling back to schema default if not set either
             _default = self.trust_jupyter_notebook_conversion
-            self.trust_jupyter_notebook_conversion = string_as_bool(kwargs.get('trust_ipython_notebook_conversion', _default))
+            self.trust_jupyter_notebook_conversion = string_as_bool(
+                kwargs.get("trust_ipython_notebook_conversion", _default)
+            )
         # Configuration for the message box directly below the masthead.
-        self.blog_url = kwargs.get('blog_url')
+        self.blog_url = kwargs.get("blog_url")
         self.user_library_import_symlink_allowlist = listify(self.user_library_import_symlink_allowlist, do_strip=True)
-        self.user_library_import_dir_auto_creation = self.user_library_import_dir_auto_creation if self.user_library_import_dir else False
+        self.user_library_import_dir_auto_creation = (
+            self.user_library_import_dir_auto_creation if self.user_library_import_dir else False
+        )
         # Searching data libraries
-        self.ftp_upload_dir_template = kwargs.get('ftp_upload_dir_template', '${ftp_upload_dir}%s${ftp_upload_dir_identifier}' % os.path.sep)
+        self.ftp_upload_dir_template = kwargs.get(
+            "ftp_upload_dir_template", "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep
+        )
         # Support older library-specific path paste option but just default to the new
         # allow_path_paste value.
-        self.allow_library_path_paste = string_as_bool(kwargs.get('allow_library_path_paste', self.allow_path_paste))
-        self.disable_library_comptypes = kwargs.get('disable_library_comptypes', '').lower().split(',')
-        self.check_upload_content = string_as_bool(kwargs.get('check_upload_content', True))
+        self.allow_library_path_paste = string_as_bool(kwargs.get("allow_library_path_paste", self.allow_path_paste))
+        self.disable_library_comptypes = kwargs.get("disable_library_comptypes", "").lower().split(",")
+        self.check_upload_content = string_as_bool(kwargs.get("check_upload_content", True))
         # On can mildly speed up Galaxy startup time by disabling index of help,
         # not needed on production systems but useful if running many functional tests.
         self.index_tool_help = string_as_bool(kwargs.get("index_tool_help", True))
@@ -839,7 +881,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         # Deployers may either specify a complete list of mapping files or get the default for free and just
         # specify a local mapping file to adapt and extend the default one.
         if "conda_mapping_files" not in kwargs:
-            _default_mapping = self._in_root_dir(os.path.join("lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"))
+            _default_mapping = self._in_root_dir(
+                os.path.join("lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml")
+            )
             # dependency resolution options are consumed via config_dict - so don't populate
             # self, populate config_dict
             self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping]
@@ -848,16 +892,16 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.container_resolvers_config_file = self._in_config_dir(self.container_resolvers_config_file)
 
         # tool_dependency_dir can be "none" (in old configs). If so, set it to None
-        if self.tool_dependency_dir and self.tool_dependency_dir.lower() == 'none':
+        if self.tool_dependency_dir and self.tool_dependency_dir.lower() == "none":
             self.tool_dependency_dir = None
         if self.involucro_path is None:
-            target_dir = self.tool_dependency_dir or self.schema.defaults['tool_dependency_dir']
+            target_dir = self.tool_dependency_dir or self.schema.defaults["tool_dependency_dir"]
             self.involucro_path = self._in_data_dir(os.path.join(target_dir, "involucro"))
         self.involucro_path = self._in_root_dir(self.involucro_path)
         if self.mulled_channels:
             self.mulled_channels = [c.strip() for c in self.mulled_channels.split(",")]  # type: ignore[attr-defined]
 
-        default_job_resubmission_condition = kwargs.get('default_job_resubmission_condition', '')
+        default_job_resubmission_condition = kwargs.get("default_job_resubmission_condition", "")
         if not default_job_resubmission_condition.strip():
             default_job_resubmission_condition = None
         self.default_job_resubmission_condition = default_job_resubmission_condition
@@ -866,92 +910,100 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         if self.nginx_upload_store:
             self.nginx_upload_store = os.path.abspath(self.nginx_upload_store)
 
-        self.object_store = kwargs.get('object_store', 'disk')
-        self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
-        self.object_store_cache_path = self._in_root_dir(kwargs.get("object_store_cache_path", self._in_data_dir("object_store_cache")))
+        self.object_store = kwargs.get("object_store", "disk")
+        self.object_store_check_old_style = string_as_bool(kwargs.get("object_store_check_old_style", False))
+        self.object_store_cache_path = self._in_root_dir(
+            kwargs.get("object_store_cache_path", self._in_data_dir("object_store_cache"))
+        )
         self._configure_dataset_storage()
 
         # Handle AWS-specific config options for backward compatibility
-        if kwargs.get('aws_access_key') is not None:
-            self.os_access_key = kwargs.get('aws_access_key')
-            self.os_secret_key = kwargs.get('aws_secret_key')
-            self.os_bucket_name = kwargs.get('s3_bucket')
-            self.os_use_reduced_redundancy = kwargs.get('use_reduced_redundancy', False)
+        if kwargs.get("aws_access_key") is not None:
+            self.os_access_key = kwargs.get("aws_access_key")
+            self.os_secret_key = kwargs.get("aws_secret_key")
+            self.os_bucket_name = kwargs.get("s3_bucket")
+            self.os_use_reduced_redundancy = kwargs.get("use_reduced_redundancy", False)
         else:
-            self.os_access_key = kwargs.get('os_access_key')
-            self.os_secret_key = kwargs.get('os_secret_key')
-            self.os_bucket_name = kwargs.get('os_bucket_name')
-            self.os_use_reduced_redundancy = kwargs.get('os_use_reduced_redundancy', False)
-        self.os_host = kwargs.get('os_host')
-        self.os_port = kwargs.get('os_port')
-        self.os_is_secure = string_as_bool(kwargs.get('os_is_secure', True))
-        self.os_conn_path = kwargs.get('os_conn_path', '/')
-        self.object_store_cache_size = float(kwargs.get('object_store_cache_size', -1))
-        self.distributed_object_store_config_file = kwargs.get('distributed_object_store_config_file')
+            self.os_access_key = kwargs.get("os_access_key")
+            self.os_secret_key = kwargs.get("os_secret_key")
+            self.os_bucket_name = kwargs.get("os_bucket_name")
+            self.os_use_reduced_redundancy = kwargs.get("os_use_reduced_redundancy", False)
+        self.os_host = kwargs.get("os_host")
+        self.os_port = kwargs.get("os_port")
+        self.os_is_secure = string_as_bool(kwargs.get("os_is_secure", True))
+        self.os_conn_path = kwargs.get("os_conn_path", "/")
+        self.object_store_cache_size = float(kwargs.get("object_store_cache_size", -1))
+        self.distributed_object_store_config_file = kwargs.get("distributed_object_store_config_file")
         if self.distributed_object_store_config_file is not None:
             self.distributed_object_store_config_file = self._in_root_dir(self.distributed_object_store_config_file)
-        self.irods_root_collection_path = kwargs.get('irods_root_collection_path')
-        self.irods_default_resource = kwargs.get('irods_default_resource')
+        self.irods_root_collection_path = kwargs.get("irods_root_collection_path")
+        self.irods_default_resource = kwargs.get("irods_default_resource")
         # Heartbeat log file name override
-        if self.global_conf is not None and 'heartbeat_log' in self.global_conf:
-            self.heartbeat_log = self.global_conf['heartbeat_log']
+        if self.global_conf is not None and "heartbeat_log" in self.global_conf:
+            self.heartbeat_log = self.global_conf["heartbeat_log"]
         # Determine which 'server:' this is
-        self.server_name = 'main'
+        self.server_name = "main"
         for arg in sys.argv:
             # Crummy, but PasteScript does not give you a way to determine this
-            if arg.lower().startswith('--server-name='):
-                self.server_name = arg.split('=', 1)[-1]
+            if arg.lower().startswith("--server-name="):
+                self.server_name = arg.split("=", 1)[-1]
         # Allow explicit override of server name in config params
         if "server_name" in kwargs:
             self.server_name = kwargs.get("server_name")
         # The application stack code may manipulate the server name. It also needs to be accessible via the get() method
         # for galaxy.util.facts()
-        self.config_dict['base_server_name'] = self.base_server_name = self.server_name
+        self.config_dict["base_server_name"] = self.base_server_name = self.server_name
         # Store all configured server names for the message queue routing
         self.server_names = []
         for section in self.global_conf_parser.sections():
-            if section.startswith('server:'):
-                self.server_names.append(section.replace('server:', '', 1))
+            if section.startswith("server:"):
+                self.server_names.append(section.replace("server:", "", 1))
 
         self._set_galaxy_infrastructure_url(kwargs)
 
         # Asynchronous execution process pools - limited functionality for now, attach_to_pools is designed to allow
         # webless Galaxy server processes to attach to arbitrary message queues (e.g. as job handlers) so they do not
         # have to be explicitly defined as such in the job configuration.
-        self.attach_to_pools = kwargs.get('attach_to_pools', []) or []
+        self.attach_to_pools = kwargs.get("attach_to_pools", []) or []
 
         # Store advanced job management config
-        self.job_handlers = [x.strip() for x in kwargs.get('job_handlers', self.server_name).split(',')]
-        self.default_job_handlers = [x.strip() for x in kwargs.get('default_job_handlers', ','.join(self.job_handlers)).split(',')]
+        self.job_handlers = [x.strip() for x in kwargs.get("job_handlers", self.server_name).split(",")]
+        self.default_job_handlers = [
+            x.strip() for x in kwargs.get("default_job_handlers", ",".join(self.job_handlers)).split(",")
+        ]
         # Galaxy internal control queue configuration.
         # If specified in universe, use it, otherwise we use whatever 'real'
         # database is specified.  Lastly, we create and use new sqlite database
         # (to minimize locking) as a final option.
-        if 'amqp_internal_connection' in kwargs:
-            self.amqp_internal_connection = kwargs.get('amqp_internal_connection')
+        if "amqp_internal_connection" in kwargs:
+            self.amqp_internal_connection = kwargs.get("amqp_internal_connection")
             # TODO Get extra amqp args as necessary for ssl
-        elif 'database_connection' in kwargs:
+        elif "database_connection" in kwargs:
             self.amqp_internal_connection = f"sqlalchemy+{self.database_connection}"
         else:
-            self.amqp_internal_connection = f"sqlalchemy+sqlite:///{self._in_data_dir('control.sqlite')}?isolation_level=IMMEDIATE"
+            self.amqp_internal_connection = (
+                f"sqlalchemy+sqlite:///{self._in_data_dir('control.sqlite')}?isolation_level=IMMEDIATE"
+            )
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         try:
             with open(self.user_preferences_extra_conf_path) as stream:
                 self.user_preferences_extra = yaml.safe_load(stream)
         except Exception:
-            if self.is_set('user_preferences_extra_conf_path'):
-                log.warning(f'Config file ({self.user_preferences_extra_conf_path}) could not be found or is malformed.')
-            self.user_preferences_extra = {'preferences': {}}
+            if self.is_set("user_preferences_extra_conf_path"):
+                log.warning(
+                    f"Config file ({self.user_preferences_extra_conf_path}) could not be found or is malformed."
+                )
+            self.user_preferences_extra = {"preferences": {}}
 
         # Experimental: This will not be enabled by default and will hide
         # nonproduction code.
         # The api_folders refers to whether the API exposes the /folders section.
-        self.api_folders = string_as_bool(kwargs.get('api_folders', False))
+        self.api_folders = string_as_bool(kwargs.get("api_folders", False))
         # This is for testing new library browsing capabilities.
-        self.new_lib_browse = string_as_bool(kwargs.get('new_lib_browse', False))
+        self.new_lib_browse = string_as_bool(kwargs.get("new_lib_browse", False))
         # Logging configuration with logging.config.configDict:
         # Statistics and profiling with statsd
-        self.statsd_host = kwargs.get('statsd_host', '')
+        self.statsd_host = kwargs.get("statsd_host", "")
 
         ie_dirs = self.interactive_environment_plugins_directory
         self.gie_dirs = [d.strip() for d in (ie_dirs.split(",") if ie_dirs else [])]
@@ -962,7 +1014,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.manage_dynamic_proxy = self.dynamic_proxy_manage  # Set to false if being launched externally
 
         # InteractiveTools propagator mapping file
-        self.interactivetools_map = self._in_root_dir(kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite")))
+        self.interactivetools_map = self._in_root_dir(
+            kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite"))
+        )
 
         self.containers_conf = parse_containers_config(self.containers_config_file)
 
@@ -989,58 +1043,56 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.redact_user_address_during_deletion = True
             self.allow_user_deletion = True
 
-            LOGGING_CONFIG_DEFAULT['formatters']['brief'] = {
-                'format': '%(asctime)s %(levelname)-8s %(name)-15s %(message)s'
+            LOGGING_CONFIG_DEFAULT["formatters"]["brief"] = {
+                "format": "%(asctime)s %(levelname)-8s %(name)-15s %(message)s"
             }
-            LOGGING_CONFIG_DEFAULT['handlers']['compliance_log'] = {
-                'class': 'logging.handlers.RotatingFileHandler',
-                'formatter': 'brief',
-                'filename': 'compliance.log',
-                'backupCount': 0,
+            LOGGING_CONFIG_DEFAULT["handlers"]["compliance_log"] = {
+                "class": "logging.handlers.RotatingFileHandler",
+                "formatter": "brief",
+                "filename": "compliance.log",
+                "backupCount": 0,
             }
-            LOGGING_CONFIG_DEFAULT['loggers']['COMPLIANCE'] = {
-                'handlers': ['compliance_log'],
-                'level': 'DEBUG',
-                'qualname': 'COMPLIANCE'
+            LOGGING_CONFIG_DEFAULT["loggers"]["COMPLIANCE"] = {
+                "handlers": ["compliance_log"],
+                "level": "DEBUG",
+                "qualname": "COMPLIANCE",
             }
 
         log_destination = kwargs.get("log_destination")
-        galaxy_daemon_log_destination = os.environ.get('GALAXY_DAEMON_LOG')
+        galaxy_daemon_log_destination = os.environ.get("GALAXY_DAEMON_LOG")
         if log_destination == "stdout":
-            LOGGING_CONFIG_DEFAULT['handlers']['console'] = {
-                'class': 'logging.StreamHandler',
-                'formatter': 'stack',
-                'level': 'DEBUG',
-                'stream': 'ext://sys.stdout',
-                'filters': ['stack']
+            LOGGING_CONFIG_DEFAULT["handlers"]["console"] = {
+                "class": "logging.StreamHandler",
+                "formatter": "stack",
+                "level": "DEBUG",
+                "stream": "ext://sys.stdout",
+                "filters": ["stack"],
             }
         elif log_destination:
-            LOGGING_CONFIG_DEFAULT['handlers']['console'] = {
-                'class': 'logging.FileHandler',
-                'formatter': 'stack',
-                'level': 'DEBUG',
-                'filename': log_destination,
-                'filters': ['stack']
+            LOGGING_CONFIG_DEFAULT["handlers"]["console"] = {
+                "class": "logging.FileHandler",
+                "formatter": "stack",
+                "level": "DEBUG",
+                "filename": log_destination,
+                "filters": ["stack"],
             }
         if galaxy_daemon_log_destination:
-            LOGGING_CONFIG_DEFAULT['handlers']['files'] = {
-                'class': 'logging.FileHandler',
-                'formatter': 'stack',
-                'level': 'DEBUG',
-                'filename': galaxy_daemon_log_destination,
-                'filters': ['stack']
+            LOGGING_CONFIG_DEFAULT["handlers"]["files"] = {
+                "class": "logging.FileHandler",
+                "formatter": "stack",
+                "level": "DEBUG",
+                "filename": galaxy_daemon_log_destination,
+                "filters": ["stack"],
             }
-            LOGGING_CONFIG_DEFAULT['root']['handlers'].append('files')
+            LOGGING_CONFIG_DEFAULT["root"]["handlers"].append("files")
 
     def _configure_dataset_storage(self):
         # The default for `file_path` has changed in 20.05; we may need to fall back to the old default
-        self._set_alt_paths('file_path', self._in_data_dir('files'))  # this is called BEFORE guessing id/uuid
-        ID, UUID = 'id', 'uuid'
-        if self.is_set('object_store_store_by'):
+        self._set_alt_paths("file_path", self._in_data_dir("files"))  # this is called BEFORE guessing id/uuid
+        ID, UUID = "id", "uuid"
+        if self.is_set("object_store_store_by"):
             if self.object_store_store_by not in [ID, UUID]:
-                raise Exception(
-                    f"Invalid value for object_store_store_by [{self.object_store_store_by}]"
-                )
+                raise Exception(f"Invalid value for object_store_store_by [{self.object_store_store_by}]")
         elif os.path.basename(self.file_path) == "objects":
             self.object_store_store_by = UUID
         else:
@@ -1053,35 +1105,41 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     def _set_galaxy_infrastructure_url(self, kwargs):
         # indicate if this was not set explicitly, so dependending on the context a better default
         # can be used (request url in a web thread, Docker parent in IE stuff, etc.)
-        self.galaxy_infrastructure_url_set = kwargs.get('galaxy_infrastructure_url') is not None
+        self.galaxy_infrastructure_url_set = kwargs.get("galaxy_infrastructure_url") is not None
         if "HOST_IP" in self.galaxy_infrastructure_url:
-            self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute({
-                'HOST_IP': socket.gethostbyname(socket.gethostname())
-            })
+            self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute(
+                {"HOST_IP": socket.gethostbyname(socket.gethostname())}
+            )
         if "GALAXY_WEB_PORT" in self.galaxy_infrastructure_url:
-            port = os.environ.get('GALAXY_WEB_PORT')
+            port = os.environ.get("GALAXY_WEB_PORT")
             if not port:
-                raise Exception('$GALAXY_WEB_PORT set in galaxy_infrastructure_url, but environment variable not set')
-            self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute({
-                'GALAXY_WEB_PORT': port
-            })
+                raise Exception("$GALAXY_WEB_PORT set in galaxy_infrastructure_url, but environment variable not set")
+            self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute(
+                {"GALAXY_WEB_PORT": port}
+            )
         if "UWSGI_PORT" in self.galaxy_infrastructure_url:
             import uwsgi
-            http = unicodify(uwsgi.opt['http'])
+
+            http = unicodify(uwsgi.opt["http"])
             host, port = http.split(":", 1)
             assert port, "galaxy_infrastructure_url depends on dynamic PORT determination but port unknown"
-            self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute({
-                'UWSGI_PORT': port
-            })
+            self.galaxy_infrastructure_url = string.Template(self.galaxy_infrastructure_url).safe_substitute(
+                {"UWSGI_PORT": port}
+            )
 
     def reload_sanitize_allowlist(self, explicit=True):
         self.sanitize_allowlist = []
         if not os.path.exists(self.sanitize_allowlist_file):
             if explicit:
-                log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools allowlisted.", self.sanitize_allowlist_file)
+                log.warning(
+                    "Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools allowlisted.",
+                    self.sanitize_allowlist_file,
+                )
         else:
             with open(self.sanitize_allowlist_file) as f:
-                self.sanitize_allowlist = sorted(line.strip() for line in f.readlines() if line.strip() and not line.startswith('#'))
+                self.sanitize_allowlist = sorted(
+                    line.strip() for line in f.readlines() if line.strip() and not line.startswith("#")
+                )
 
     def ensure_tempdir(self):
         self._ensure_directory(self.new_file_path)
@@ -1113,7 +1171,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         # Check for deprecated options.
         for key in self.config_dict.keys():
             if key in self.deprecated_options:
-                log.warning(f"Config option '{key}' is deprecated and will be removed in a future release.  Please consult the latest version of the sample configuration file.")
+                log.warning(
+                    f"Config option '{key}' is deprecated and will be removed in a future release.  Please consult the latest version of the sample configuration file."
+                )
 
     @staticmethod
     def _parse_allowed_origin_hostnames(allowed_origin_hostnames):
@@ -1127,7 +1187,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
         def parse(string):
             # a string enclosed in fwd slashes will be parsed as a regexp: e.g. /<some val>/
-            if string[0] == '/' and string[-1] == '/':
+            if string[0] == "/" and string[-1] == "/":
                 string = string[1:-1]
                 return re.compile(string, flags=(re.UNICODE))
             return string
@@ -1148,24 +1208,24 @@ def reload_config_options(current_config):
             if current_config._raw_config[option] != modified_config[option]:
                 current_config._raw_config[option] = modified_config[option]
                 setattr(current_config, option, modified_config[option])
-                log.info(f'Reloaded {option}')
+                log.info(f"Reloaded {option}")
 
 
-def get_database_engine_options(kwargs, model_prefix=''):
+def get_database_engine_options(kwargs, model_prefix=""):
     """
     Allow options for the SQLAlchemy database engine to be passed by using
     the prefix "database_engine_option".
     """
     conversions: Dict[str, Callable[[Any], Union[bool, int]]] = {
-        'convert_unicode': string_as_bool,
-        'pool_timeout': int,
-        'echo': string_as_bool,
-        'echo_pool': string_as_bool,
-        'pool_recycle': int,
-        'pool_size': int,
-        'max_overflow': int,
-        'pool_threadlocal': string_as_bool,
-        'server_side_cursors': string_as_bool
+        "convert_unicode": string_as_bool,
+        "pool_timeout": int,
+        "echo": string_as_bool,
+        "echo_pool": string_as_bool,
+        "pool_recycle": int,
+        "pool_size": int,
+        "max_overflow": int,
+        "pool_threadlocal": string_as_bool,
+        "server_side_cursors": string_as_bool,
     }
     prefix = f"{model_prefix}database_engine_option_"
     prefix_len = len(prefix)
@@ -1194,7 +1254,7 @@ def init_models_from_config(config, map_install_models=False, object_store=None,
         database_query_profiling_proxy=config.database_query_profiling_proxy,
         object_store=object_store,
         trace_logger=trace_logger,
-        use_pbkdf2=config.get_bool('use_pbkdf2', True),
+        use_pbkdf2=config.get_bool("use_pbkdf2", True),
         slow_query_log_threshold=config.slow_query_log_threshold,
         thread_local_log=config.thread_local_log,
         log_query_counts=config.database_log_query_counts,
@@ -1218,19 +1278,25 @@ def configure_logging(config):
         paste_configures_logging = config.global_conf_parser.has_section("loggers")
     else:
         paste_configures_logging = False
-    auto_configure_logging = not paste_configures_logging and string_as_bool(config.get("auto_configure_logging", "True"))
+    auto_configure_logging = not paste_configures_logging and string_as_bool(
+        config.get("auto_configure_logging", "True")
+    )
     if auto_configure_logging:
-        logging_conf = config.get('logging', None)
+        logging_conf = config.get("logging", None)
         if logging_conf is None:
             # if using the default logging config, honor the log_level setting
             logging_conf = LOGGING_CONFIG_DEFAULT
-            if config.get('log_level', 'DEBUG') != 'DEBUG':
-                logging_conf['handlers']['console']['level'] = config.get('log_level', 'DEBUG')
+            if config.get("log_level", "DEBUG") != "DEBUG":
+                logging_conf["handlers"]["console"]["level"] = config.get("log_level", "DEBUG")
         # configure logging with logging dict in config, template *FileHandler handler filenames with the `filename_template` option
-        for name, conf in logging_conf.get('handlers', {}).items():
-            if conf['class'].startswith('logging.') and conf['class'].endswith('FileHandler') and 'filename_template' in conf:
-                conf['filename'] = conf.pop('filename_template').format(**get_stack_facts(config=config))
-                logging_conf['handlers'][name] = conf
+        for name, conf in logging_conf.get("handlers", {}).items():
+            if (
+                conf["class"].startswith("logging.")
+                and conf["class"].endswith("FileHandler")
+                and "filename_template" in conf
+            ):
+                conf["filename"] = conf.pop("filename_template").format(**get_stack_facts(config=config))
+                logging_conf["handlers"][name] = conf
         logging.config.dictConfig(logging_conf)
 
 
@@ -1249,15 +1315,15 @@ class ConfiguresGalaxyMixin:
 
     def wait_for_toolbox_reload(self, old_toolbox):
         timer = ExecutionTimer()
-        log.debug('Waiting for toolbox reload')
+        log.debug("Waiting for toolbox reload")
         # Wait till toolbox reload has been triggered (or more than 60 seconds have passed)
         while timer.elapsed < 60:
             if self.toolbox.has_reloaded(old_toolbox):
-                log.debug('Finished waiting for toolbox reload %s', timer)
+                log.debug("Finished waiting for toolbox reload %s", timer)
                 break
             time.sleep(0.1)
         else:
-            log.warning('Waiting for toolbox reload timed out after 60 seconds')
+            log.warning("Waiting for toolbox reload timed out after 60 seconds")
 
     def _configure_tool_config_files(self):
         if self.config.shed_tool_config_file not in self.config.tool_configs:
@@ -1265,17 +1331,19 @@ class ConfiguresGalaxyMixin:
         # The value of migrated_tools_config is the file reserved for containing only those tools that have been
         # eliminated from the distribution and moved to the tool shed. If migration checking is disabled, only add it if
         # it exists (since this may be an existing deployment where migrations were previously run).
-        if (os.path.exists(self.config.migrated_tools_config)
-                and self.config.migrated_tools_config not in self.config.tool_configs):
+        if (
+            os.path.exists(self.config.migrated_tools_config)
+            and self.config.migrated_tools_config not in self.config.tool_configs
+        ):
             self.config.tool_configs.append(self.config.migrated_tools_config)
 
     def _configure_toolbox(self):
+        import galaxy.tools.search
         from galaxy import tools
-        from galaxy.tools.biotools import get_galaxy_biotools_metadata_source
         from galaxy.managers.citations import CitationsManager
         from galaxy.tool_util.deps import containers
         from galaxy.tool_util.deps.dependencies import AppInfo
-        import galaxy.tools.search
+        from galaxy.tools.biotools import get_galaxy_biotools_metadata_source
 
         if not isinstance(self, BasicSharedApp):
             raise Exception("Must inherit from BasicSharedApp")
@@ -1308,15 +1376,19 @@ class ConfiguresGalaxyMixin:
         mulled_resolution_cache = None
         if self.config.mulled_resolution_cache_type:
             cache_opts = {
-                'cache.type': self.config.mulled_resolution_cache_type,
-                'cache.data_dir': self.config.mulled_resolution_cache_data_dir,
-                'cache.lock_dir': self.config.mulled_resolution_cache_lock_dir,
+                "cache.type": self.config.mulled_resolution_cache_type,
+                "cache.data_dir": self.config.mulled_resolution_cache_data_dir,
+                "cache.lock_dir": self.config.mulled_resolution_cache_lock_dir,
             }
-            mulled_resolution_cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('mulled_resolution')
+            mulled_resolution_cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache(
+                "mulled_resolution"
+            )
         self.container_finder = containers.ContainerFinder(app_info, mulled_resolution_cache=mulled_resolution_cache)
         self._set_enabled_container_types()
         index_help = getattr(self.config, "index_tool_help", True)
-        self.toolbox_search = galaxy.tools.search.ToolBoxSearch(self.toolbox, index_dir=self.config.tool_search_index_dir, index_help=index_help)
+        self.toolbox_search = galaxy.tools.search.ToolBoxSearch(
+            self.toolbox, index_dir=self.config.tool_search_index_dir, index_help=index_help
+        )
 
     def reindex_tool_search(self):
         # Call this when tools are added or removed.
@@ -1330,28 +1402,37 @@ class ConfiguresGalaxyMixin:
                 for enabled_container_type in self.container_finder._enabled_container_types(destination.params):
                     container_types_to_destinations[enabled_container_type].append(destination)
         self.toolbox.dependency_manager.set_enabled_container_types(container_types_to_destinations)
-        self.toolbox.dependency_manager.resolver_classes.update(self.container_finder.default_container_registry.resolver_classes)
-        self.toolbox.dependency_manager.dependency_resolvers.extend(self.container_finder.default_container_registry.container_resolvers)
+        self.toolbox.dependency_manager.resolver_classes.update(
+            self.container_finder.default_container_registry.resolver_classes
+        )
+        self.toolbox.dependency_manager.dependency_resolvers.extend(
+            self.container_finder.default_container_registry.container_resolvers
+        )
 
     def _configure_tool_data_tables(self, from_shed_config):
         from galaxy.tools.data import ToolDataTableManager
 
         # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path.
-        self.tool_data_tables = ToolDataTableManager(tool_data_path=self.config.tool_data_path,
-                                                     config_filename=self.config.tool_data_table_config_path,
-                                                     other_config_dict=self.config)
+        self.tool_data_tables = ToolDataTableManager(
+            tool_data_path=self.config.tool_data_path,
+            config_filename=self.config.tool_data_table_config_path,
+            other_config_dict=self.config,
+        )
         # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables.
         try:
-            self.tool_data_tables.load_from_config_file(config_filename=self.config.shed_tool_data_table_config,
-                                                        tool_data_path=self.tool_data_tables.tool_data_path,
-                                                        from_shed_config=from_shed_config)
+            self.tool_data_tables.load_from_config_file(
+                config_filename=self.config.shed_tool_data_table_config,
+                tool_data_path=self.tool_data_tables.tool_data_path,
+                from_shed_config=from_shed_config,
+            )
         except OSError as exc:
             # Missing shed_tool_data_table_config is okay if it's the default
-            if exc.errno != errno.ENOENT or self.config.is_set('shed_tool_data_table_config'):
+            if exc.errno != errno.ENOENT or self.config.is_set("shed_tool_data_table_config"):
                 raise
 
     def _configure_datatypes_registry(self, installed_repository_manager=None):
         from galaxy.datatypes import registry
+
         # Create an empty datatypes registry.
         self.datatypes_registry = registry.Registry(self.config)
         if installed_repository_manager and self.config.load_tool_shed_datatypes:
@@ -1372,10 +1453,12 @@ class ConfiguresGalaxyMixin:
 
     def _configure_object_store(self, **kwds):
         from galaxy.objectstore import build_object_store_from_config
+
         self.object_store = build_object_store_from_config(self.config, **kwds)
 
     def _configure_security(self):
         from galaxy.security import idencoding
+
         self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
         BaseDatabaseIdField.security = self.security
 
@@ -1394,22 +1477,34 @@ class ConfiguresGalaxyMixin:
         install_db_url = self.config.install_database_connection
         # TODO: Consider more aggressive check here that this is not the same
         # database file under the hood.
-        combined_install_database = not(install_db_url and install_db_url != db_url)
+        combined_install_database = not (install_db_url and install_db_url != db_url)
         install_db_url = install_db_url or db_url
-        install_database_options = self.config.database_engine_options if combined_install_database else self.config.install_database_engine_options
+        install_database_options = (
+            self.config.database_engine_options
+            if combined_install_database
+            else self.config.install_database_engine_options
+        )
 
         if self.config.database_wait:
             self._wait_for_database(db_url)
 
         if getattr(self.config, "max_metadata_value_size", None):
             from galaxy.model import custom_types
+
             custom_types.MAX_METADATA_VALUE_SIZE = self.config.max_metadata_value_size
 
         if check_migrate_databases:
             # Initialize database / check for appropriate schema version.  # If this
             # is a new installation, we'll restrict the tool migration messaging.
             from galaxy.model.migrate.check import create_or_verify_database
-            create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self, map_install_models=combined_install_database)
+
+            create_or_verify_database(
+                db_url,
+                config_file,
+                self.config.database_engine_options,
+                app=self,
+                map_install_models=combined_install_database,
+            )
             if not combined_install_database:
                 tsi_create_or_verify_database(install_db_url, install_database_options, app=self)
 
@@ -1417,17 +1512,17 @@ class ConfiguresGalaxyMixin:
             self.config,
             map_install_models=combined_install_database,
             object_store=self.object_store,
-            trace_logger=getattr(self, "trace_logger", None)
+            trace_logger=getattr(self, "trace_logger", None),
         )
         if combined_install_database:
             log.info("Install database targetting Galaxy's database configuration.")
             self.install_model = self.model
         else:
             from galaxy.model.tool_shed_install import mapping as install_mapping
+
             install_db_url = self.config.install_database_connection
             log.info(f"Install database using its own connection {install_db_url}")
-            self.install_model = install_mapping.init(install_db_url,
-                                                      install_database_options)
+            self.install_model = install_mapping.init(install_db_url, install_database_options)
 
     def _configure_signal_handlers(self, handlers):
         for sig, handler in handlers.items():
diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index 26638a11ab4..8f508a1688d 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -7,7 +7,11 @@ import sys
 import tempfile
 from io import StringIO
 from textwrap import TextWrapper
-from typing import Any, List, NamedTuple
+from typing import (
+    Any,
+    List,
+    NamedTuple,
+)
 
 import requests
 import yaml
@@ -18,7 +22,7 @@ try:
 except ImportError:
     Core = None
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
 
 
@@ -38,7 +42,6 @@ from galaxy.util.yaml_util import (
     ordered_load,
 )
 
-
 DESCRIPTION = "Convert configuration files."
 
 APP_DESCRIPTION = """Application to target for operation (i.e. galaxy, tool_shed, or reports))"""
@@ -49,151 +52,224 @@ EXTRA_SERVER_MESSAGE = "Additional server section after [%s] encountered [%s], w
 MISSING_FILTER_TYPE_MESSAGE = "Missing filter type for section [%s], it will be ignored."
 UNHANDLED_FILTER_TYPE_MESSAGE = "Unhandled filter type encountered [%s] for section [%s]."
 NO_APP_MAIN_MESSAGE = "No app:main section found, using application defaults throughout."
-YAML_COMMENT_WRAPPER = TextWrapper(initial_indent="# ", subsequent_indent="# ", break_long_words=False, break_on_hyphens=False)
-RST_DESCRIPTION_WRAPPER = TextWrapper(initial_indent="    ", subsequent_indent="    ", break_long_words=False, break_on_hyphens=False)
+YAML_COMMENT_WRAPPER = TextWrapper(
+    initial_indent="# ", subsequent_indent="# ", break_long_words=False, break_on_hyphens=False
+)
+RST_DESCRIPTION_WRAPPER = TextWrapper(
+    initial_indent="    ", subsequent_indent="    ", break_long_words=False, break_on_hyphens=False
+)
 
-UWSGI_OPTIONS = dict([
-    ('http', {
-        'desc': """The address and port on which to listen.  By default, only listen to localhost ($app_name will not be accessible over the network).  Use ':$default_port' to listen on all available network interfaces.""",
-        'default': '127.0.0.1:$default_port',
-        'type': 'str',
-    }),
-    ('buffer-size', {
-        'desc': """By default uWSGI allocates a very small buffer (4096 bytes) for the headers of each request. If you start receiving "invalid request block size" in your logs, it could mean you need a bigger buffer. We recommend at least 16384.""",
-        'default': 16384,
-        'type': 'int',
-    }),
-    ('processes', {
-        'desc': """Number of web server (worker) processes to fork after the application has loaded. If this is set to greater than 1, thunder-lock likely should be enabled below.""",
-        'default': 1,
-        'type': 'int',
-    }),
-    ('threads', {
-        'desc': """Number of threads for each web server process.""",
-        'default': 4,
-        'type': 'int',
-    }),
-    ('offload-threads', {
-        'desc': """Number of threads for serving static content and handling internal routing requests.""",
-        'default': 2,
-        'type': 'int',
-    }),
-    ('static-map.1', {
-        'key': 'static-map',
-        'desc': """Mapping to serve static content.""",
-        'default': '/static=static',
-        'type': 'str',
-    }),
-    ('static-map.2', {
-        'key': 'static-map',
-        'desc': """Mapping to serve the favicon.""",
-        'default': '/favicon.ico=static/favicon.ico',
-        'type': 'str',
-    }),
-    ('static-safe', {
-        'key': 'static-safe',
-        'desc': """Allow serving certain assets out of `client`.  Most modern Galaxy interfaces bundle all of this, but some older pages still serve these via symlink, requiring this rule.""",
-        'default': 'client/src/assets',
-        'type': 'str',
-    }),
-    ('master', {
-        'desc': """Enable the master process manager. Disabled by default for maximum compatibility with CTRL+C, but should be enabled for use with --daemon and/or production deployments.""",
-        'default': False,
-        'type': 'bool',
-    }),
-    ('virtualenv', {
-        'desc': """Path to the application's Python virtual environment. If using Conda for Galaxy's framework dependencies (not tools!), do not set this.""",
-        'default': '.venv',
-        'type': 'str',
-    }),
-    ('pythonpath', {
-        'desc': """Path to the application's Python library.""",
-        'default': 'lib',
-        'type': 'str',
-    }),
-    ('module', {
-        'desc': """The entry point which returns the web application (e.g. Galaxy, Reports, etc.) that you are loading.""",
-        'default': '$uwsgi_module',
-        'type': 'str',
-    }),
-    ('#mount', {
-        'desc': """Mount the web application (e.g. Galaxy, Reports, etc.) at the given URL prefix. Cannot be used together with 'module:' above.""",
-        'default': '/galaxy=$uwsgi_module',
-        'type': 'str',
-    }),
-    ('manage-script-name', {
-        'desc': """Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-points. Set this to true if a URL prefix is used.""",
-        'default': False,
-        'type': 'bool',
-    }),
-    ('thunder-lock', {
-        'desc': """It is usually a good idea to set this to ``true`` if processes is greater than 1.""",
-        'default': False,
-        'type': 'bool',
-    }),
-    ('die-on-term', {
-        'desc': """Cause uWSGI to respect the traditional behavior of dying on SIGTERM (its default is to brutally reload workers)""",
-        'default': True,
-        'type': 'bool',
-    }),
-    ('hook-master-start.1', {
-        'key': 'hook-master-start',
-        'desc': """Cause uWSGI to gracefully reload workers and mules upon receipt of SIGINT (its default is to brutally kill workers)""",
-        'default': 'unix_signal:2 gracefully_kill_them_all',
-        'type': 'str',
-    }),
-    ('hook-master-start.2', {
-        'key': 'hook-master-start',
-        'desc': """Cause uWSGI to gracefully reload workers and mules upon receipt of SIGTERM (its default is to brutally kill workers)""",
-        'default': 'unix_signal:15 gracefully_kill_them_all',
-        'type': 'str',
-    }),
-    ('py-call-osafterfork', {
-        'desc': """Feature necessary for proper mule signal handling on Python versions below 3.7.2. The default is set to false to prevent a runtime error under Python 3.7.2 and newer (see https://github.com/unbit/uwsgi/issues/1978).""",
-        'default': False,
-        'type': 'bool',
-    }),
-    ('enable-threads', {
-        'desc': """Ensure application threads will run if `threads` is unset.""",
-        'default': True,
-        'type': 'bool',
-    }),
-    ('umask', {
-        'desc': """uWSGI default umask. On some systems uWSGI has a default umask of 000, for Galaxy a somewhat safer default is chosen. If Galaxy submits jobs as real user then all users needs to be able to read the files, i.e. the umask needs to be '022' or the Galaxy users need to be in the same group as the Galaxy system user""",
-        'default': '027',
-        'type': 'str',
-    }),
-    # ('route-uri', {
-    #     'default': '^/proxy/ goto:proxy'
-    # }),
-    # ('route', {
-    #     'default': '.* last:'
-    # }),
-    # ('route-label', {
-    #     'default': 'proxy'
-    # }),
-    # ('route-run', {
-    #     'default': 'rpcvar:TARGET_HOST galaxy_dynamic_proxy_mapper ${HTTP_HOST} ${cookie[galaxysession]}'
-    # }),
-    # ('route-run', {
-    #     'default': "['log:Proxy ${HTTP_HOST} to ${TARGET_HOST}', 'httpdumb:${TARGET_HOST}']",
-    # }),
-    # ('http-raw-body', {
-    #     'default': True
-    # }),
-])
+UWSGI_OPTIONS = dict(
+    [
+        (
+            "http",
+            {
+                "desc": """The address and port on which to listen.  By default, only listen to localhost ($app_name will not be accessible over the network).  Use ':$default_port' to listen on all available network interfaces.""",
+                "default": "127.0.0.1:$default_port",
+                "type": "str",
+            },
+        ),
+        (
+            "buffer-size",
+            {
+                "desc": """By default uWSGI allocates a very small buffer (4096 bytes) for the headers of each request. If you start receiving "invalid request block size" in your logs, it could mean you need a bigger buffer. We recommend at least 16384.""",
+                "default": 16384,
+                "type": "int",
+            },
+        ),
+        (
+            "processes",
+            {
+                "desc": """Number of web server (worker) processes to fork after the application has loaded. If this is set to greater than 1, thunder-lock likely should be enabled below.""",
+                "default": 1,
+                "type": "int",
+            },
+        ),
+        (
+            "threads",
+            {
+                "desc": """Number of threads for each web server process.""",
+                "default": 4,
+                "type": "int",
+            },
+        ),
+        (
+            "offload-threads",
+            {
+                "desc": """Number of threads for serving static content and handling internal routing requests.""",
+                "default": 2,
+                "type": "int",
+            },
+        ),
+        (
+            "static-map.1",
+            {
+                "key": "static-map",
+                "desc": """Mapping to serve static content.""",
+                "default": "/static=static",
+                "type": "str",
+            },
+        ),
+        (
+            "static-map.2",
+            {
+                "key": "static-map",
+                "desc": """Mapping to serve the favicon.""",
+                "default": "/favicon.ico=static/favicon.ico",
+                "type": "str",
+            },
+        ),
+        (
+            "static-safe",
+            {
+                "key": "static-safe",
+                "desc": """Allow serving certain assets out of `client`.  Most modern Galaxy interfaces bundle all of this, but some older pages still serve these via symlink, requiring this rule.""",
+                "default": "client/src/assets",
+                "type": "str",
+            },
+        ),
+        (
+            "master",
+            {
+                "desc": """Enable the master process manager. Disabled by default for maximum compatibility with CTRL+C, but should be enabled for use with --daemon and/or production deployments.""",
+                "default": False,
+                "type": "bool",
+            },
+        ),
+        (
+            "virtualenv",
+            {
+                "desc": """Path to the application's Python virtual environment. If using Conda for Galaxy's framework dependencies (not tools!), do not set this.""",
+                "default": ".venv",
+                "type": "str",
+            },
+        ),
+        (
+            "pythonpath",
+            {
+                "desc": """Path to the application's Python library.""",
+                "default": "lib",
+                "type": "str",
+            },
+        ),
+        (
+            "module",
+            {
+                "desc": """The entry point which returns the web application (e.g. Galaxy, Reports, etc.) that you are loading.""",
+                "default": "$uwsgi_module",
+                "type": "str",
+            },
+        ),
+        (
+            "#mount",
+            {
+                "desc": """Mount the web application (e.g. Galaxy, Reports, etc.) at the given URL prefix. Cannot be used together with 'module:' above.""",
+                "default": "/galaxy=$uwsgi_module",
+                "type": "str",
+            },
+        ),
+        (
+            "manage-script-name",
+            {
+                "desc": """Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-points. Set this to true if a URL prefix is used.""",
+                "default": False,
+                "type": "bool",
+            },
+        ),
+        (
+            "thunder-lock",
+            {
+                "desc": """It is usually a good idea to set this to ``true`` if processes is greater than 1.""",
+                "default": False,
+                "type": "bool",
+            },
+        ),
+        (
+            "die-on-term",
+            {
+                "desc": """Cause uWSGI to respect the traditional behavior of dying on SIGTERM (its default is to brutally reload workers)""",
+                "default": True,
+                "type": "bool",
+            },
+        ),
+        (
+            "hook-master-start.1",
+            {
+                "key": "hook-master-start",
+                "desc": """Cause uWSGI to gracefully reload workers and mules upon receipt of SIGINT (its default is to brutally kill workers)""",
+                "default": "unix_signal:2 gracefully_kill_them_all",
+                "type": "str",
+            },
+        ),
+        (
+            "hook-master-start.2",
+            {
+                "key": "hook-master-start",
+                "desc": """Cause uWSGI to gracefully reload workers and mules upon receipt of SIGTERM (its default is to brutally kill workers)""",
+                "default": "unix_signal:15 gracefully_kill_them_all",
+                "type": "str",
+            },
+        ),
+        (
+            "py-call-osafterfork",
+            {
+                "desc": """Feature necessary for proper mule signal handling on Python versions below 3.7.2. The default is set to false to prevent a runtime error under Python 3.7.2 and newer (see https://github.com/unbit/uwsgi/issues/1978).""",
+                "default": False,
+                "type": "bool",
+            },
+        ),
+        (
+            "enable-threads",
+            {
+                "desc": """Ensure application threads will run if `threads` is unset.""",
+                "default": True,
+                "type": "bool",
+            },
+        ),
+        (
+            "umask",
+            {
+                "desc": """uWSGI default umask. On some systems uWSGI has a default umask of 000, for Galaxy a somewhat safer default is chosen. If Galaxy submits jobs as real user then all users needs to be able to read the files, i.e. the umask needs to be '022' or the Galaxy users need to be in the same group as the Galaxy system user""",
+                "default": "027",
+                "type": "str",
+            },
+        ),
+        # ('route-uri', {
+        #     'default': '^/proxy/ goto:proxy'
+        # }),
+        # ('route', {
+        #     'default': '.* last:'
+        # }),
+        # ('route-label', {
+        #     'default': 'proxy'
+        # }),
+        # ('route-run', {
+        #     'default': 'rpcvar:TARGET_HOST galaxy_dynamic_proxy_mapper ${HTTP_HOST} ${cookie[galaxysession]}'
+        # }),
+        # ('route-run', {
+        #     'default': "['log:Proxy ${HTTP_HOST} to ${TARGET_HOST}', 'httpdumb:${TARGET_HOST}']",
+        # }),
+        # ('http-raw-body', {
+        #     'default': True
+        # }),
+    ]
+)
 
-SHED_ONLY_UWSGI_OPTIONS = [('cron', {
-    'desc': """Task for rebuilding Toolshed search indexes using the uWSGI cron-like interface.""",
-    'default': "0 -1 -1 -1 -1 python scripts/tool_shed/build_ts_whoosh_index.py -c config/tool_shed.yml --config-section tool_shed",
-    'type': 'str',
-})]
+SHED_ONLY_UWSGI_OPTIONS = [
+    (
+        "cron",
+        {
+            "desc": """Task for rebuilding Toolshed search indexes using the uWSGI cron-like interface.""",
+            "default": "0 -1 -1 -1 -1 python scripts/tool_shed/build_ts_whoosh_index.py -c config/tool_shed.yml --config-section tool_shed",
+            "type": "str",
+        },
+    )
+]
 
 DROP_OPTION_VALUE = object()
 
 
 class _OptionAction:
-
     def converted(self, args, app_desc, key, value):
         pass
 
@@ -202,13 +278,11 @@ class _OptionAction:
 
 
 class _DeprecatedAction(_OptionAction):
-
     def lint(self, args, app_desc, key, value):
         print(f"Option [{key}] has been deprecated, this will likely be dropped in future releases of Galaxy.")
 
 
 class _DeprecatedAndDroppedAction(_OptionAction):
-
     def converted(self, args, app_desc, key, value):
         print(f"Option [{key}] has been deprecated and dropped. It is not included in converted configuration.")
         return DROP_OPTION_VALUE
@@ -218,7 +292,6 @@ class _DeprecatedAndDroppedAction(_OptionAction):
 
 
 class _PasteAppFactoryAction(_OptionAction):
-
     def converted(self, args, app_desc, key, value):
         if value not in app_desc.expected_app_factories:
             raise Exception(f"Ending convert process - unknown paste factory encountered [{value}]")
@@ -230,7 +303,6 @@ class _PasteAppFactoryAction(_OptionAction):
 
 
 class _ProductionUnsafe(_OptionAction):
-
     def __init__(self, unsafe_value):
         self.unsafe_value = unsafe_value
 
@@ -242,7 +314,6 @@ class _ProductionUnsafe(_OptionAction):
 
 
 class _ProductionPerformance(_OptionAction):
-
     def lint(self, args, app_desc, key, value):
         template = "Problem - option [%s] should not be set to [%s] in production environments - it may cause performance issues or instability."
         message = template % (key, value)
@@ -250,14 +321,12 @@ class _ProductionPerformance(_OptionAction):
 
 
 class _HandleFilterWithAction(_OptionAction):
-
     def converted(self, args, app_desc, key, value):
         print("filter-with converted to prefixed module load of uwsgi module, dropping from converted configuration")
         return DROP_OPTION_VALUE
 
 
 class _RenameAction(_OptionAction):
-
     def __init__(self, new_name):
         self.new_name = new_name
 
@@ -271,50 +340,50 @@ class _RenameAction(_OptionAction):
 
 
 OPTION_ACTIONS = {
-    'use_beaker_session': _DeprecatedAndDroppedAction(),
-    'use_interactive': _DeprecatedAndDroppedAction(),
-    'session_type': _DeprecatedAndDroppedAction(),
-    'session_data_dir': _DeprecatedAndDroppedAction(),
-    'session_key': _DeprecatedAndDroppedAction(),
-    'session_secret': _DeprecatedAndDroppedAction(),
-    'paste.app_factory': _PasteAppFactoryAction(),
-    'filter-with': _HandleFilterWithAction(),
-    'debug': _ProductionUnsafe(True),
-    'serve_xss_vulnerable_mimetypes': _ProductionUnsafe(True),
-    'use_printdebug': _ProductionUnsafe(True),
-    'id_secret': _ProductionUnsafe('USING THE DEFAULT IS NOT SECURE!'),
-    'master_api_key': _ProductionUnsafe('changethis'),
-    'external_service_type_config_file': _DeprecatedAndDroppedAction(),
-    'external_service_type_path': _DeprecatedAndDroppedAction(),
-    'enable_sequencer_communication': _DeprecatedAndDroppedAction(),
-    'run_workflow_toolform_upgrade': _DeprecatedAndDroppedAction(),
+    "use_beaker_session": _DeprecatedAndDroppedAction(),
+    "use_interactive": _DeprecatedAndDroppedAction(),
+    "session_type": _DeprecatedAndDroppedAction(),
+    "session_data_dir": _DeprecatedAndDroppedAction(),
+    "session_key": _DeprecatedAndDroppedAction(),
+    "session_secret": _DeprecatedAndDroppedAction(),
+    "paste.app_factory": _PasteAppFactoryAction(),
+    "filter-with": _HandleFilterWithAction(),
+    "debug": _ProductionUnsafe(True),
+    "serve_xss_vulnerable_mimetypes": _ProductionUnsafe(True),
+    "use_printdebug": _ProductionUnsafe(True),
+    "id_secret": _ProductionUnsafe("USING THE DEFAULT IS NOT SECURE!"),
+    "master_api_key": _ProductionUnsafe("changethis"),
+    "external_service_type_config_file": _DeprecatedAndDroppedAction(),
+    "external_service_type_path": _DeprecatedAndDroppedAction(),
+    "enable_sequencer_communication": _DeprecatedAndDroppedAction(),
+    "run_workflow_toolform_upgrade": _DeprecatedAndDroppedAction(),
     # Next 4 were from library search which is no longer available.
-    'enable_lucene_library_search': _DeprecatedAndDroppedAction(),
-    'fulltext_max_size': _DeprecatedAndDroppedAction(),
-    'fulltext_noindex_filetypes': _DeprecatedAndDroppedAction(),
-    'fulltext_url': _DeprecatedAndDroppedAction(),
-    'enable_beta_job_managers': _DeprecatedAndDroppedAction(),
-    'enable_legacy_sample_tracking_api': _DeprecatedAction(),
-    'enable_new_user_preferences': _DeprecatedAndDroppedAction(),
-    'force_beta_workflow_scheduled_for_collections': _DeprecatedAndDroppedAction(),
-    'force_beta_workflow_scheduled_min_steps': _DeprecatedAndDroppedAction(),
-    'history_local_serial_workflow_scheduling': _ProductionPerformance(),
-    'allow_library_path_paste': _RenameAction("allow_path_paste"),
-    'trust_ipython_notebook_conversion': _RenameAction("trust_jupyter_notebook_conversion"),
-    'enable_beta_tool_command_isolation': _DeprecatedAndDroppedAction(),
-    'enable_beta_ts_api_install': _DeprecatedAndDroppedAction(),
-    'single_user': _ProductionUnsafe(True),
-    'tool_submission_burst_threads': _DeprecatedAndDroppedAction(),
-    'tool_submission_burst_at': _DeprecatedAndDroppedAction(),
-    'toolform_upgrade': _DeprecatedAndDroppedAction(),
-    'enable_beta_mulled_containers': _DeprecatedAndDroppedAction(),
-    'enable_communication_server': _DeprecatedAndDroppedAction(),
-    'communication_server_host': _DeprecatedAndDroppedAction(),
-    'communication_server_port': _DeprecatedAndDroppedAction(),
-    'persistent_communication_rooms': _DeprecatedAndDroppedAction(),
-    'legacy_eager_objectstore_initialization': _DeprecatedAndDroppedAction(),
-    'enable_openid': _DeprecatedAndDroppedAction(),
-    'openid_consumer_cache_path': _DeprecatedAndDroppedAction(),
+    "enable_lucene_library_search": _DeprecatedAndDroppedAction(),
+    "fulltext_max_size": _DeprecatedAndDroppedAction(),
+    "fulltext_noindex_filetypes": _DeprecatedAndDroppedAction(),
+    "fulltext_url": _DeprecatedAndDroppedAction(),
+    "enable_beta_job_managers": _DeprecatedAndDroppedAction(),
+    "enable_legacy_sample_tracking_api": _DeprecatedAction(),
+    "enable_new_user_preferences": _DeprecatedAndDroppedAction(),
+    "force_beta_workflow_scheduled_for_collections": _DeprecatedAndDroppedAction(),
+    "force_beta_workflow_scheduled_min_steps": _DeprecatedAndDroppedAction(),
+    "history_local_serial_workflow_scheduling": _ProductionPerformance(),
+    "allow_library_path_paste": _RenameAction("allow_path_paste"),
+    "trust_ipython_notebook_conversion": _RenameAction("trust_jupyter_notebook_conversion"),
+    "enable_beta_tool_command_isolation": _DeprecatedAndDroppedAction(),
+    "enable_beta_ts_api_install": _DeprecatedAndDroppedAction(),
+    "single_user": _ProductionUnsafe(True),
+    "tool_submission_burst_threads": _DeprecatedAndDroppedAction(),
+    "tool_submission_burst_at": _DeprecatedAndDroppedAction(),
+    "toolform_upgrade": _DeprecatedAndDroppedAction(),
+    "enable_beta_mulled_containers": _DeprecatedAndDroppedAction(),
+    "enable_communication_server": _DeprecatedAndDroppedAction(),
+    "communication_server_host": _DeprecatedAndDroppedAction(),
+    "communication_server_port": _DeprecatedAndDroppedAction(),
+    "persistent_communication_rooms": _DeprecatedAndDroppedAction(),
+    "legacy_eager_objectstore_initialization": _DeprecatedAndDroppedAction(),
+    "enable_openid": _DeprecatedAndDroppedAction(),
+    "openid_consumer_cache_path": _DeprecatedAndDroppedAction(),
 }
 
 
@@ -348,10 +417,12 @@ class OptionValue(NamedTuple):
 GALAXY_APP = App(
     ["universe_wsgi.ini", "config/galaxy.ini"],
     "8080",
-    ["galaxy.web.buildapp:app_factory"],  # TODO: Galaxy could call factory a few different things and they'd all be fine.
+    [
+        "galaxy.web.buildapp:app_factory"
+    ],  # TODO: Galaxy could call factory a few different things and they'd all be fine.
     "config/galaxy.yml",
     str(GALAXY_CONFIG_SCHEMA_PATH),
-    'galaxy.webapps.galaxy.buildapp:uwsgi_app()',
+    "galaxy.webapps.galaxy.buildapp:uwsgi_app()",
 )
 SHED_APP = App(
     ["tool_shed_wsgi.ini", "config/tool_shed.ini"],
@@ -359,7 +430,7 @@ SHED_APP = App(
     ["tool_shed.webapp.buildapp:app_factory"],
     "config/tool_shed.yml",
     "lib/tool_shed/webapp/config_schema.yml",
-    'tool_shed.webapp.buildapp:uwsgi_app()',
+    "tool_shed.webapp.buildapp:uwsgi_app()",
 )
 REPORTS_APP = App(
     ["reports_wsgi.ini", "config/reports.ini"],
@@ -367,7 +438,7 @@ REPORTS_APP = App(
     ["galaxy.webapps.reports.buildapp:app_factory"],
     "config/reports.yml",
     "lib/galaxy/webapps/reports/config_schema.yml",
-    'galaxy.webapps.reports.buildapp:uwsgi_app()',
+    "galaxy.webapps.reports.buildapp:uwsgi_app()",
 )
 APPS = {"galaxy": GALAXY_APP, "tool_shed": SHED_APP, "reports": REPORTS_APP}
 
@@ -386,15 +457,11 @@ def main(argv=None):
 
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
-    parser.add_argument('action', metavar='ACTION', type=str,
-                        choices=list(ACTIONS.keys()),
-                        help='action to perform')
-    parser.add_argument('app', metavar='APP', type=str, nargs="?",
-                        help=APP_DESCRIPTION)
-    parser.add_argument('--add-comments', default=False, action="store_true")
-    parser.add_argument('--dry-run', default=False, action="store_true",
-                        help=DRY_RUN_DESCRIPTION)
-    parser.add_argument('--galaxy_root', default=".", type=str)
+    parser.add_argument("action", metavar="ACTION", type=str, choices=list(ACTIONS.keys()), help="action to perform")
+    parser.add_argument("app", metavar="APP", type=str, nargs="?", help=APP_DESCRIPTION)
+    parser.add_argument("--add-comments", default=False, action="store_true")
+    parser.add_argument("--dry-run", default=False, action="store_true", help=DRY_RUN_DESCRIPTION)
+    parser.add_argument("--galaxy_root", default=".", type=str)
     return parser
 
 
@@ -438,7 +505,7 @@ def _write_option_rst(args, rst, key, heading_level, option_value):
 
 
 def _build_uwsgi_schema(args, app_desc):
-    req = requests.get('https://raw.githubusercontent.com/unbit/uwsgi-docs/master/Options.rst')
+    req = requests.get("https://raw.githubusercontent.com/unbit/uwsgi-docs/master/Options.rst")
     rst_options = req.text
     last_line = None
     current_opt = None
@@ -451,7 +518,7 @@ def _build_uwsgi_schema(args, app_desc):
         if line and (line == dots):
             current_opt = last_line
             option = {
-                'type': 'any',
+                "type": "any",
             }
             options[current_opt] = option
 
@@ -467,7 +534,7 @@ def _build_uwsgi_schema(args, app_desc):
     schema = {
         "type": "map",
         "desc": "uwsgi definition, see https://uwsgi-docs.readthedocs.io/en/latest/Options.html",
-        "mapping": options
+        "mapping": options,
     }
     contents = ordered_dump(schema)
     _write_to_file(args, contents, UWSGI_SCHEMA_PATH)
@@ -534,14 +601,14 @@ def _validate(args, app_desc):
     if raw_config.get(app_desc.app_name) is None:
         raw_config[app_desc.app_name] = {}
     # Rewrite the file any way to merge any duplicate keys
-    with tempfile.NamedTemporaryFile('w', delete=False, suffix=".yml") as config_p:
+    with tempfile.NamedTemporaryFile("w", delete=False, suffix=".yml") as config_p:
         ordered_dump(raw_config, config_p)
 
     def _clean(p, k, v):
-        return k not in ['reloadable', 'path_resolves_to', 'per_host']
+        return k not in ["reloadable", "path_resolves_to", "per_host"]
 
     clean_schema = remap(app_desc.schema.raw_schema, _clean)
-    with tempfile.NamedTemporaryFile('w', suffix=".yml") as fp:
+    with tempfile.NamedTemporaryFile("w", suffix=".yml") as fp:
         ordered_dump(clean_schema, fp)
         fp.flush()
         c = Core(
@@ -553,14 +620,12 @@ def _validate(args, app_desc):
 
 
 class PrefixFilter:
-
     def __init__(self, name, prefix):
         self.name = name
         self.prefix = prefix
 
 
 class GzipFilter:
-
     def __init__(self, name):
         self.name = name
 
@@ -585,7 +650,7 @@ def _run_conversion(args, app_desc):
                 server_section = section
 
         if section.startswith("filter:"):
-            filter_name = section[len("filter:"):]
+            filter_name = section[len("filter:") :]
             filter_type = p.get(section, "use")
             if filter_type is None:
                 MISSING_FILTER_TYPE_MESSAGE
@@ -681,18 +746,20 @@ def _build_sample_yaml(args, app_desc):
             if not isinstance(field_value, str):
                 continue
 
-            new_field_value = string.Template(field_value).safe_substitute(**{
-                'default_port': str(app_desc.default_port),
-                'app_name': app_desc.app_name,
-                'uwsgi_module': app_desc.uwsgi_module,
-            })
+            new_field_value = string.Template(field_value).safe_substitute(
+                **{
+                    "default_port": str(app_desc.default_port),
+                    "app_name": app_desc.app_name,
+                    "uwsgi_module": app_desc.uwsgi_module,
+                }
+            )
             value[field] = new_field_value
     description = getattr(schema, "description", None)
     if description:
         description = description.lstrip()
         as_comment = "\n".join(f"# {line}" for line in description.split("\n")) + "\n"
         f.write(as_comment)
-    _write_sample_section(args, f, 'uwsgi', Schema(UWSGI_OPTIONS), as_comment=False, uwsgi_hack=True)
+    _write_sample_section(args, f, "uwsgi", Schema(UWSGI_OPTIONS), as_comment=False, uwsgi_hack=True)
     _write_sample_section(args, f, app_desc.app_name, schema)
     destination = os.path.join(args.galaxy_root, app_desc.sample_destination)
     _write_to_file(args, f, destination)
@@ -729,7 +796,7 @@ def _write_sample_section(args, f, section_header, schema, as_comment=True, uwsg
         option = schema.get_app_option(key)
         option_value = OptionValue(key, default, option)
         # support uWSGI "dumb YAML parser" (unbit/uwsgi#863)
-        key = option.get('key', key)
+        key = option.get("key", key)
         _write_option(args, f, key, option_value, as_comment=as_comment, uwsgi_hack=uwsgi_hack)
 
 
@@ -835,5 +902,5 @@ ACTIONS = {
 }
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/config/schema.py b/lib/galaxy/config/schema.py
index ebd88e05c74..b8f87c7bc85 100644
--- a/lib/galaxy/config/schema.py
+++ b/lib/galaxy/config/schema.py
@@ -16,12 +16,11 @@ UNKNOWN_OPTION = {
     "type": "str",
     "required": False,
     "unknown_option": True,
-    "desc": "Unknown option, may want to remove or report to Galaxy team."
+    "desc": "Unknown option, may want to remove or report to Galaxy team.",
 }
 
 
 class Schema:
-
     def __init__(self, mapping):
         self.app_schema = mapping
 
@@ -36,11 +35,10 @@ class Schema:
 
 
 class AppSchema(Schema):
-
     def __init__(self, schema_path, app_name):
         self.raw_schema = self._read_schema(schema_path)
         self.description = self.raw_schema.get("desc", None)
-        app_schema = self.raw_schema['mapping'][app_name]['mapping']
+        app_schema = self.raw_schema["mapping"][app_name]["mapping"]
         self._preprocess(app_schema)
         super().__init__(app_schema)
 
@@ -55,13 +53,13 @@ class AppSchema(Schema):
         self._paths_to_resolve = {}  # {config option: referenced config option}
         self._per_host_options = set()  # config options that can be set using a per_host config parameter
         for key, data in app_schema.items():
-            self._defaults[key] = data.get('default')
-            if data.get('reloadable'):
+            self._defaults[key] = data.get("default")
+            if data.get("reloadable"):
                 self._reloadable_options.add(key)
-            if data.get('per_host'):
+            if data.get("per_host"):
                 self._per_host_options.add(key)
-            if data.get('path_resolves_to'):
-                self._paths_to_resolve[key] = data.get('path_resolves_to')
+            if data.get("path_resolves_to"):
+                self._paths_to_resolve[key] = data.get("path_resolves_to")
 
     @property
     def defaults(self):
@@ -81,16 +79,19 @@ class AppSchema(Schema):
 
     def validate_path_resolution_graph(self):
         """This method is for tests only: we SHOULD validate the schema's path resolution graph
-           as part of automated testing; but we should NOT validate it at runtime.
+        as part of automated testing; but we should NOT validate it at runtime.
         """
+
         def check_exists(option, key):
             if not option:
-                message = "Invalid schema: property '{}' listed as path resolution target " \
+                message = (
+                    "Invalid schema: property '{}' listed as path resolution target "
                     "for '{}' does not exist".format(resolves_to, key)
+                )
                 raise_error(message)
 
         def check_type_is_str_or_any(option, key):
-            if option.get('type') not in ('str', 'any'):
+            if option.get("type") not in ("str", "any"):
                 message = f"Invalid schema: property '{key}' should have type 'str'"
                 raise_error(message)
 
@@ -100,9 +101,9 @@ class AppSchema(Schema):
                 visited.clear()
                 while key:
                     visited.add(key)
-                    key = self.app_schema[key].get('path_resolves_to')
+                    key = self.app_schema[key].get("path_resolves_to")
                     if key and key in visited:
-                        raise_error('Invalid schema: cycle detected')
+                        raise_error("Invalid schema: cycle detected")
 
         def raise_error(message):
             log.error(message)
diff --git a/lib/galaxy/config/script.py b/lib/galaxy/config/script.py
index 82cdad9018a..b6f724fad91 100644
--- a/lib/galaxy/config/script.py
+++ b/lib/galaxy/config/script.py
@@ -17,26 +17,26 @@ DESCRIPTION = "Initialize a directory with a minimal Galaxy config."
 HELP_CONFIG_DIR = "Directory containing the configuration files for Galaxy."
 HELP_DATA_DIR = "Directory containing Galaxy-created data."
 HELP_FORCE = "Overwrite existing files if they already exist."
-HELP_WSGI_SERVER = ("Web server stack used to host Galaxy web application, and if uWSGI, which protocol to use.")
+HELP_WSGI_SERVER = "Web server stack used to host Galaxy web application, and if uWSGI, which protocol to use."
 HELP_LIBDRMAA = (
     "Configure Galaxy to submit jobs to a cluster via DRMAA by supplying the path to a libdrmaa.so file using this "
     "argument."
 )
-HELP_INSTALL = ("Install optional dependencies required by specified configuration (e.g. drmaa, etc...).")
+HELP_INSTALL = "Install optional dependencies required by specified configuration (e.g. drmaa, etc...)."
 HELP_HOST = (
     'Host to bind Galaxy to - defaults to localhost. Specify an IP address or "all" to listen on all interfaces.'
 )
-HELP_PORT = ("Port to bind Galaxy to.")
-HELP_DB_CONN = ("Galaxy database connection URI.")
+HELP_PORT = "Port to bind Galaxy to."
+HELP_DB_CONN = "Galaxy database connection URI."
 
 DEFAULT_HOST = "localhost"
 DEFAULT_YML = "galaxy.yml"
-DEFAULT_DB_CONN = 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
+DEFAULT_DB_CONN = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
 
-SAMPLES_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sample'))
-GALAXY_CONFIG_TEMPLATE_FILE = os.path.join(SAMPLES_PATH, 'galaxy.yml.sample')
-STATIC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'web', 'framework', 'static'))
-CLIENT_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'client'))
+SAMPLES_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), "sample"))
+GALAXY_CONFIG_TEMPLATE_FILE = os.path.join(SAMPLES_PATH, "galaxy.yml.sample")
+STATIC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "web", "framework", "static"))
+CLIENT_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "client"))
 
 MSG_CONFIG_SUMMARY = """
 For help on configuring Galaxy, consult the documentation at: \n {}
@@ -51,15 +51,15 @@ Start Galaxy by running the command from directory [{}]:
 # whole thing into galaxy.config for templating, so for now just substitute some lines. In the future we will build
 # configs differently.
 GALAXY_CONFIG_SUBSTITUTIONS = {
-    '  http: 127.0.0.1:8080': '  ${uwsgi_transport}: ${host}:${port}',
-    '  static-map: /static=static': '  static-map: /static=${static_path}',
-    '  static-map: /favicon.ico=static/favicon.ico': '  static-map: /static=${static_path}/favicon.ico',
-    '  static-safe: client/src/assets': '  ${client_path}/src/assets',
-    '  virtualenv: .venv': '  #venv: .venv   # not used when running installed',
-    '  pythonpath: lib': '  #pythonpath: lib  # not used  when running installed',
-    '  #config_dir: false': '  config_dir: ${config_dir}',
-    '  #data_dir: false': '  data_dir: ${data_dir}',
-    '  #database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE': '  database_connection: ${database_connection}',
+    "  http: 127.0.0.1:8080": "  ${uwsgi_transport}: ${host}:${port}",
+    "  static-map: /static=static": "  static-map: /static=${static_path}",
+    "  static-map: /favicon.ico=static/favicon.ico": "  static-map: /static=${static_path}/favicon.ico",
+    "  static-safe: client/src/assets": "  ${client_path}/src/assets",
+    "  virtualenv: .venv": "  #venv: .venv   # not used when running installed",
+    "  pythonpath: lib": "  #pythonpath: lib  # not used  when running installed",
+    "  #config_dir: false": "  config_dir: ${config_dir}",
+    "  #data_dir: false": "  data_dir: ${data_dir}",
+    "  #database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE": "  database_connection: ${database_connection}",
 }
 
 
@@ -68,8 +68,9 @@ def main(argv=None):
     arg_parser = ArgumentParser(description=DESCRIPTION)
     arg_parser.add_argument("--config-dir", default=".", help=HELP_CONFIG_DIR)
     arg_parser.add_argument("--data-dir", default="./data", help=HELP_DATA_DIR)
-    arg_parser.add_argument("--wsgi-server", choices=["uwsgi-http", "uwsgi-native"], default="uwsgi-http",
-                            help=HELP_WSGI_SERVER)
+    arg_parser.add_argument(
+        "--wsgi-server", choices=["uwsgi-http", "uwsgi-native"], default="uwsgi-http", help=HELP_WSGI_SERVER
+    )
     arg_parser.add_argument("--host", default=DEFAULT_HOST, help=HELP_HOST)
     arg_parser.add_argument("--port", default="8080", help=HELP_PORT)
     arg_parser.add_argument("--db-conn", default=DEFAULT_DB_CONN, help=HELP_DB_CONN)
@@ -129,7 +130,7 @@ def _determine_mode(args):
 
 
 def _determine_host(args):
-    return '0.0.0.0' if args.host == 'all' else args.host
+    return "0.0.0.0" if args.host == "all" else args.host
 
 
 def _determine_yml_file(config_dir):
@@ -140,7 +141,7 @@ def _handle_galaxy_yml(args, config_dir, data_dir):
     force = args.force
     yml_file = _determine_yml_file(config_dir)
     _check_file(yml_file, force)
-    uwsgi_transport = 'socket' if args.wsgi_server == 'uwsgi-native' else 'http'
+    uwsgi_transport = "socket" if args.wsgi_server == "uwsgi-native" else "http"
     config_dict = dict(
         port=args.port,
         host=_determine_host(args),
@@ -155,16 +156,14 @@ def _handle_galaxy_yml(args, config_dir, data_dir):
     galaxy_config_template = []
     with open(GALAXY_CONFIG_TEMPLATE_FILE) as fh:
         for line in fh:
-            line = line.rstrip('\n')
+            line = line.rstrip("\n")
             for k, v in GALAXY_CONFIG_SUBSTITUTIONS.items():
                 if line == k:
                     line = v
             galaxy_config_template.append(line)
-    galaxy_config_template = string.Template('\n'.join(galaxy_config_template))
+    galaxy_config_template = string.Template("\n".join(galaxy_config_template))
 
-    galaxy_config = galaxy_config_template.safe_substitute(
-        **config_dict
-    )
+    galaxy_config = galaxy_config_template.safe_substitute(**config_dict)
     open(yml_file, "w").write(galaxy_config)
 
 
@@ -182,5 +181,5 @@ def _check_file(path, force):
         sys.exit(1)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/config_watchers.py b/lib/galaxy/config_watchers.py
index 4601319deba..0482aa9ac40 100644
--- a/lib/galaxy/config_watchers.py
+++ b/lib/galaxy/config_watchers.py
@@ -31,42 +31,42 @@ class ConfigWatchers:
             try:
                 # Run and wait for toolbox reload on the process that watches the config files.
                 # The toolbox reload will update the integrated_tool_panel_file
-                self.app.queue_worker.send_local_control_task('reload_toolbox', get_response=True),
+                self.app.queue_worker.send_local_control_task("reload_toolbox", get_response=True),
             except Exception:
                 save_integrated_tool_panel = True
                 log.exception("Exception occured while reloading toolbox")
-            self.app.queue_worker.send_control_task('reload_toolbox', noop_self=True, kwargs={'save_integrated_tool_panel': save_integrated_tool_panel}),
+            self.app.queue_worker.send_control_task(
+                "reload_toolbox", noop_self=True, kwargs={"save_integrated_tool_panel": save_integrated_tool_panel}
+            ),
 
         self.tool_config_watcher = get_tool_conf_watcher(
             reload_callback=reload_toolbox,
             tool_cache=self.app.tool_cache,
         )
         self.data_manager_config_watcher = get_tool_conf_watcher(
-            reload_callback=lambda: self.app.queue_worker.send_control_task('reload_data_managers'),
+            reload_callback=lambda: self.app.queue_worker.send_control_task("reload_data_managers"),
         )
-        self.tool_data_watcher = get_watcher(self.app.config, 'watch_tool_data_dir', monitor_what_str='data tables')
+        self.tool_data_watcher = get_watcher(self.app.config, "watch_tool_data_dir", monitor_what_str="data tables")
         self.tool_watcher = get_tool_watcher(self, app.config)
-        if getattr(self.app, 'is_job_handler', False):
-            self.job_rule_watcher = get_watcher(app.config, 'watch_job_rules', monitor_what_str='job rules')
+        if getattr(self.app, "is_job_handler", False):
+            self.job_rule_watcher = get_watcher(app.config, "watch_job_rules", monitor_what_str="job rules")
         else:
-            self.job_rule_watcher = get_watcher(app.config, '__invalid__')
-        self.core_config_watcher = get_watcher(
-            app.config,
-            'watch_core_config',
-            monitor_what_str='core config file'
-        )
-        self.tour_watcher = get_watcher(app.config, 'watch_tours', monitor_what_str='tours')
+            self.job_rule_watcher = get_watcher(app.config, "__invalid__")
+        self.core_config_watcher = get_watcher(app.config, "watch_core_config", monitor_what_str="core config file")
+        self.tour_watcher = get_watcher(app.config, "watch_tours", monitor_what_str="tours")
 
     @property
     def watchers(self):
-        return (self.tool_watcher,
-                self.tool_config_watcher,
-                self.data_manager_config_watcher,
-                self.tool_data_watcher,
-                self.tool_watcher,
-                self.job_rule_watcher,
-                self.core_config_watcher,
-                self.tour_watcher)
+        return (
+            self.tool_watcher,
+            self.tool_config_watcher,
+            self.data_manager_config_watcher,
+            self.tool_data_watcher,
+            self.tool_watcher,
+            self.job_rule_watcher,
+            self.core_config_watcher,
+            self.tour_watcher,
+        )
 
     def change_state(self, active):
         if active:
@@ -82,24 +82,27 @@ class ConfigWatchers:
         for tool_data_path in self.tool_data_paths:
             self.tool_data_watcher.watch_directory(
                 tool_data_path,
-                callback=lambda path: self.app.queue_worker.send_control_task('reload_tool_data_tables', kwargs={'path': path}),
-                require_extensions=('.loc',),
+                callback=lambda path: self.app.queue_worker.send_control_task(
+                    "reload_tool_data_tables", kwargs={"path": path}
+                ),
+                require_extensions=(".loc",),
                 recursive=True,
             )
         for job_rules_directory in self.job_rules_paths:
             self.job_rule_watcher.watch_directory(
                 job_rules_directory,
-                callback=lambda: self.app.queue_worker.send_control_task('reload_job_rules'),
+                callback=lambda: self.app.queue_worker.send_control_task("reload_job_rules"),
                 recursive=True,
-                ignore_extensions=('.pyc', '.pyo', '.pyd'))
+                ignore_extensions=(".pyc", ".pyo", ".pyd"),
+            )
         if self.app.config.config_file:
             self.core_config_watcher.watch_file(
                 self.app.config.config_file,
-                callback=lambda path: self.app.queue_worker.send_control_task('reload_core_config')
+                callback=lambda path: self.app.queue_worker.send_control_task("reload_core_config"),
             )
             self.tour_watcher.watch_directory(
                 self.app.config.tour_config_dir,
-                callback=lambda path: self.app.queue_worker.send_control_task('reload_tour', kwargs={'path': path})
+                callback=lambda path: self.app.queue_worker.send_control_task("reload_tour", kwargs={"path": path}),
             )
         self.active = True
 
@@ -109,7 +112,7 @@ class ConfigWatchers:
         self.active = False
 
     def update_watch_data_table_paths(self):
-        if hasattr(self.tool_data_watcher, 'monitored_dirs'):
+        if hasattr(self.tool_data_watcher, "monitored_dirs"):
             for tool_data_table_path in self.tool_data_paths:
                 if tool_data_table_path not in self.tool_data_watcher.monitored_dirs:
                     self.tool_data_watcher.watch_directory(tool_data_table_path)
@@ -117,25 +120,25 @@ class ConfigWatchers:
     @property
     def data_manager_configs(self):
         data_manager_configs = []
-        if hasattr(self.app.config, 'data_manager_config_file'):
+        if hasattr(self.app.config, "data_manager_config_file"):
             data_manager_configs.append(self.app.config.data_manager_config_file)
-        if hasattr(self.app.config, 'shed_data_manager_config_file'):
+        if hasattr(self.app.config, "shed_data_manager_config_file"):
             data_manager_configs.append(self.app.config.shed_data_manager_config_file)
         return data_manager_configs
 
     @property
     def tool_data_paths(self):
         tool_data_paths = []
-        if hasattr(self.app.config, 'tool_data_path'):
+        if hasattr(self.app.config, "tool_data_path"):
             tool_data_paths.append(self.app.config.tool_data_path)
-        if hasattr(self.app.config, 'shed_tool_data_path'):
+        if hasattr(self.app.config, "shed_tool_data_path"):
             tool_data_paths.append(self.app.config.shed_tool_data_path)
         return tool_data_paths
 
     @property
     def tool_config_paths(self):
         tool_config_paths = []
-        if hasattr(self.app.config, 'tool_configs'):
+        if hasattr(self.app.config, "tool_configs"):
             tool_config_paths = self.app.config.tool_configs
         return tool_config_paths
 
diff --git a/lib/galaxy/containers/__init__.py b/lib/galaxy/containers/__init__.py
index ffb9c9e25c8..35d9cbf9012 100644
--- a/lib/galaxy/containers/__init__.py
+++ b/lib/galaxy/containers/__init__.py
@@ -12,24 +12,30 @@ import uuid
 from abc import (
     ABCMeta,
     abstractmethod,
-    abstractproperty
+    abstractproperty,
+)
+from typing import (
+    Any,
+    Dict,
+    NamedTuple,
+    Optional,
+    Type,
 )
-from typing import Any, Dict, NamedTuple, Optional, Type
 
 import yaml
 
 from galaxy.exceptions import ContainerCLIError
 from galaxy.util.submodules import import_submodules
 
-
-DEFAULT_CONTAINER_TYPE = 'docker'
-DEFAULT_CONF = {'_default_': {'type': DEFAULT_CONTAINER_TYPE}}
+DEFAULT_CONTAINER_TYPE = "docker"
+DEFAULT_CONF = {"_default_": {"type": DEFAULT_CONTAINER_TYPE}}
 
 log = logging.getLogger(__name__)
 
 
 class ContainerPort(NamedTuple):
     """Named tuple representing ports published by a container, with attributes"""
+
     port: int  # Port number (inside the container)
     protocol: str  # Port protocol, either ``tcp`` or ``udp``
     hostaddr: str  # Address or hostname where the published port can be accessed
@@ -57,13 +63,11 @@ class ContainerVolume(metaclass=ABCMeta):
 
     @abstractmethod
     def __str__(self):
-        """Return this container type's string representation of the volume.
-        """
+        """Return this container type's string representation of the volume."""
 
     @abstractmethod
     def to_native(self):
-        """Return this container type's native representation of the volume.
-        """
+        """Return this container type's native representation of the volume."""
 
     @property
     def mode_is_valid(self):
@@ -71,7 +75,6 @@ class ContainerVolume(metaclass=ABCMeta):
 
 
 class Container(metaclass=ABCMeta):
-
     def __init__(self, interface, id, name=None, **kwargs):
         """
 
@@ -149,9 +152,13 @@ class Container(metaclass=ABCMeta):
             if port == mapping.port:
                 return mapping
             if port is None:
-                log.warning("Container %s (%s): Don't know how to map ports to containers with multiple exposed ports "
-                            "when a specific port is not requested. Arbitrarily choosing first: %s",
-                            self.name, self.id, mapping)
+                log.warning(
+                    "Container %s (%s): Don't know how to map ports to containers with multiple exposed ports "
+                    "when a specific port is not requested. Arbitrarily choosing first: %s",
+                    self.name,
+                    self.id,
+                    mapping,
+                )
                 return mapping
         else:
             if port is None:
@@ -167,7 +174,7 @@ class ContainerInterface(metaclass=ABCMeta):
     container_class: Optional[Type[Container]] = None
     volume_class = Optional[Type[ContainerVolume]]
     conf_defaults: Dict[str, Optional[Any]] = {
-        'name_prefix': 'galaxy_',
+        "name_prefix": "galaxy_",
     }
     option_map: Dict[str, Dict] = {}
     publish_port_list_required = False
@@ -190,18 +197,18 @@ class ContainerInterface(metaclass=ABCMeta):
         return command
 
     def _guess_kwopt_type(self, val):
-        opttype = 'string'
+        opttype = "string"
         if isinstance(val, bool):
-            opttype = 'boolean'
+            opttype = "boolean"
         elif isinstance(val, list):
-            opttype = 'list'
+            opttype = "list"
             try:
                 if isinstance(val[0], tuple) and len(val[0]) == 3:
-                    opttype = 'list_of_kovtrips'
+                    opttype = "list_of_kovtrips"
             except IndexError:
                 pass
         elif isinstance(val, dict):
-            opttype = 'list_of_kvpairs'
+            opttype = "list_of_kvpairs"
         return opttype
 
     def _guess_kwopt_flag(self, opt):
@@ -214,34 +221,35 @@ class ContainerInterface(metaclass=ABCMeta):
                 optdef = self.option_map[opt]
             except KeyError:
                 optdef = {
-                    'flag': self._guess_kwopt_flag(opt),
-                    'type': self._guess_kwopt_type(val),
+                    "flag": self._guess_kwopt_flag(opt),
+                    "type": self._guess_kwopt_type(val),
                 }
-                log.warning("option '%s' not in %s.option_map, guessing flag '%s' type '%s'",
-                            opt, self.__class__.__name__, optdef['flag'], optdef['type'])
-            opts.append(getattr(self, f"_stringify_kwopt_{optdef['type']}")(optdef['flag'], val))
-        return ' '.join(opts)
+                log.warning(
+                    "option '%s' not in %s.option_map, guessing flag '%s' type '%s'",
+                    opt,
+                    self.__class__.__name__,
+                    optdef["flag"],
+                    optdef["type"],
+                )
+            opts.append(getattr(self, f"_stringify_kwopt_{optdef['type']}")(optdef["flag"], val))
+        return " ".join(opts)
 
     def _stringify_kwopt_boolean(self, flag, val):
-        """
-        """
-        return f'{flag}={str(val).lower()}'
+        """ """
+        return f"{flag}={str(val).lower()}"
 
     def _stringify_kwopt_string(self, flag, val):
-        """
-        """
-        return f'{flag} {shlex.quote(str(val))}'
+        """ """
+        return f"{flag} {shlex.quote(str(val))}"
 
     def _stringify_kwopt_list(self, flag, val):
-        """
-        """
+        """ """
         if isinstance(val, str):
             return self._stringify_kwopt_string(flag, val)
-        return ' '.join(f'{flag} {shlex.quote(str(v))}' for v in val)
+        return " ".join(f"{flag} {shlex.quote(str(v))}" for v in val)
 
     def _stringify_kwopt_list_of_kvpairs(self, flag, val):
-        """
-        """
+        """ """
         kwopt_list = []
         if isinstance(val, list):
             # ['foo=bar', 'baz=quux']
@@ -249,22 +257,21 @@ class ContainerInterface(metaclass=ABCMeta):
         else:
             # {'foo': 'bar', 'baz': 'quux'}
             for k, v in dict(val).items():
-                kwopt_list.append(f'{k}={v}')
+                kwopt_list.append(f"{k}={v}")
         return self._stringify_kwopt_list(flag, kwopt_list)
 
     def _stringify_kwopt_list_of_kovtrips(self, flag, val):
-        """
-        """
+        """ """
         if isinstance(val, str):
             return self._stringify_kwopt_string(flag, val)
         kwopt_list = []
         for k, o, v in val:
-            kwopt_list.append(f'{k}{o}{v}')
+            kwopt_list.append(f"{k}{o}{v}")
         return self._stringify_kwopt_list(flag, kwopt_list)
 
     def _run_command(self, command, verbose=False):
         if verbose:
-            log.debug('running command: [%s]', command)
+            log.debug("running command: [%s]", command)
         command_list = self._normalize_command(command)
         p = subprocess.Popen(command_list, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True)
         stdout, stderr = p.communicate()
@@ -279,7 +286,8 @@ class ContainerInterface(metaclass=ABCMeta):
                 stderr=stderr.strip(),
                 returncode=p.returncode,
                 command=command,
-                subprocess_command=command_list)
+                subprocess_command=command_list,
+            )
 
     @property
     def key(self):
@@ -294,25 +302,19 @@ class ContainerInterface(metaclass=ABCMeta):
 
     def set_kwopts_name(self, kwopts):
         if self._name_prefix is not None:
-            name = '{prefix}{name}'.format(
-                prefix=self._name_prefix,
-                name=kwopts.get('name', uuid.uuid4().hex)
-            )
-            kwopts['name'] = name
+            name = "{prefix}{name}".format(prefix=self._name_prefix, name=kwopts.get("name", uuid.uuid4().hex))
+            kwopts["name"] = name
 
     def validate_config(self):
-        """
-        """
+        """ """
         self._name_prefix = self._conf.name_prefix
 
     @abstractmethod
     def run_in_container(self, command, image=None, **kwopts):
-        """
-        """
+        """ """
 
 
 class ContainerInterfaceConfig(dict):
-
     def __setattr__(self, name, value):
         self[name] = value
 
@@ -345,7 +347,7 @@ def build_container_interfaces(containers_config_file, containers_conf=None):
     interface_classes = _get_interface_modules()
     interfaces = {}
     for k, conf in containers_conf.items():
-        container_type = conf.get('type', DEFAULT_CONTAINER_TYPE)
+        container_type = conf.get("type", DEFAULT_CONTAINER_TYPE)
         assert container_type in interface_classes, f"unknown container interface type: {container_type}"
         interfaces[k] = interface_classes[container_type](conf, k, containers_config_file)
     return interfaces
@@ -363,7 +365,7 @@ def parse_containers_config(containers_config_file):
     try:
         with open(containers_config_file) as fh:
             c = yaml.safe_load(fh)
-            conf.update(c.get('containers', {}))
+            conf.update(c.get("containers", {}))
     except OSError as exc:
         if exc.errno == errno.ENOENT:
             log.debug("config file '%s' does not exist, running with default config", containers_config_file)
@@ -377,7 +379,10 @@ def _get_interface_modules():
     modules = import_submodules(sys.modules[__name__])
     for module in modules:
         module_names = [getattr(module, _) for _ in dir(module)]
-        classes = [_ for _ in module_names if inspect.isclass(_)
-            and not _ == ContainerInterface and issubclass(_, ContainerInterface)]
+        classes = [
+            _
+            for _ in module_names
+            if inspect.isclass(_) and not _ == ContainerInterface and issubclass(_, ContainerInterface)
+        ]
         interfaces.extend(classes)
     return {x.container_type: x for x in interfaces}
diff --git a/lib/galaxy/containers/docker.py b/lib/galaxy/containers/docker.py
index 438483d70f7..3f08f84f053 100644
--- a/lib/galaxy/containers/docker.py
+++ b/lib/galaxy/containers/docker.py
@@ -6,9 +6,17 @@ import logging
 import os
 import shlex
 from functools import partial
-from itertools import cycle, repeat
+from itertools import (
+    cycle,
+    repeat,
+)
 from time import sleep
-from typing import Any, Dict, Optional, Type
+from typing import (
+    Any,
+    Dict,
+    Optional,
+    Type,
+)
 
 try:
     import docker
@@ -16,24 +24,30 @@ except ImportError:
     docker = None  # type: ignore[assignment]
 
 try:
-    from requests.exceptions import ConnectionError, ReadTimeout
+    from requests.exceptions import (
+        ConnectionError,
+        ReadTimeout,
+    )
 except ImportError:
     ConnectionError = None  # type: ignore[assignment,misc]
     ReadTimeout = None  # type: ignore[assignment,misc]
 
-from galaxy.containers import Container, ContainerInterface
+from galaxy.containers import (
+    Container,
+    ContainerInterface,
+)
 from galaxy.containers.docker_decorators import (
     docker_columns,
-    docker_json
+    docker_json,
 )
 from galaxy.containers.docker_model import (
     DockerContainer,
-    DockerVolume
+    DockerVolume,
 )
 from galaxy.exceptions import (
     ContainerCLIError,
     ContainerImageNotFound,
-    ContainerNotFound
+    ContainerNotFound,
 )
 from galaxy.util.json import safe_dumps_formatted
 
@@ -45,18 +59,18 @@ class DockerInterface(ContainerInterface):
     container_class: Type[Container] = DockerContainer
     volume_class = DockerVolume
     conf_defaults: Dict[str, Optional[Any]] = {
-        'host': None,
-        'tls': False,
-        'force_tlsverify': False,
-        'auto_remove': True,
-        'image': None,
-        'cpus': None,
-        'memory': None,
+        "host": None,
+        "tls": False,
+        "force_tlsverify": False,
+        "auto_remove": True,
+        "image": None,
+        "cpus": None,
+        "memory": None,
     }
     # These values are inserted into kwopts for run commands
     conf_run_kwopts = (
-        'cpus',
-        'memory',
+        "cpus",
+        "memory",
     )
 
     def validate_config(self):
@@ -92,7 +106,7 @@ class DockerInterface(ContainerInterface):
         """
         try:
             inspect = self.image_inspect(image)
-            return inspect['RepoDigests'][0]
+            return inspect["RepoDigests"][0]
         except ContainerImageNotFound:
             return image
 
@@ -107,45 +121,45 @@ class DockerInterface(ContainerInterface):
 
 class DockerCLIInterface(DockerInterface):
 
-    container_type = 'docker_cli'
+    container_type = "docker_cli"
     conf_defaults: Dict[str, Optional[Any]] = {
-        'command_template': '{executable} {global_kwopts} {subcommand} {args}',
-        'executable': 'docker',
+        "command_template": "{executable} {global_kwopts} {subcommand} {args}",
+        "executable": "docker",
     }
     option_map = {
         # `run` options
-        'environment': {'flag': '--env', 'type': 'list_of_kvpairs'},
-        'volumes': {'flag': '--volume', 'type': 'docker_volumes'},
-        'name': {'flag': '--name', 'type': 'string'},
-        'detach': {'flag': '--detach', 'type': 'boolean'},
-        'publish_all_ports': {'flag': '--publish-all', 'type': 'boolean'},
-        'publish_port_random': {'flag': '--publish', 'type': 'string'},
-        'auto_remove': {'flag': '--rm', 'type': 'boolean'},
-        'cpus': {'flag': '--cpus', 'type': 'string'},
-        'memory': {'flag': '--memory', 'type': 'string'},
+        "environment": {"flag": "--env", "type": "list_of_kvpairs"},
+        "volumes": {"flag": "--volume", "type": "docker_volumes"},
+        "name": {"flag": "--name", "type": "string"},
+        "detach": {"flag": "--detach", "type": "boolean"},
+        "publish_all_ports": {"flag": "--publish-all", "type": "boolean"},
+        "publish_port_random": {"flag": "--publish", "type": "string"},
+        "auto_remove": {"flag": "--rm", "type": "boolean"},
+        "cpus": {"flag": "--cpus", "type": "string"},
+        "memory": {"flag": "--memory", "type": "string"},
     }
 
     def validate_config(self):
-        log.warning('The `docker_cli` interface is deprecated and will be removed in Galaxy 18.09, please use `docker`')
+        log.warning("The `docker_cli` interface is deprecated and will be removed in Galaxy 18.09, please use `docker`")
         super().validate_config()
         global_kwopts = []
         if self._conf.host:
-            global_kwopts.append('--host')
+            global_kwopts.append("--host")
             global_kwopts.append(shlex.quote(self._conf.host))
         if self._conf.force_tlsverify:
-            global_kwopts.append('--tlsverify')
-        self._docker_command = self._conf['command_template'].format(
-            executable=self._conf['executable'],
-            global_kwopts=' '.join(global_kwopts),
-            subcommand='{subcommand}',
-            args='{args}'
+            global_kwopts.append("--tlsverify")
+        self._docker_command = self._conf["command_template"].format(
+            executable=self._conf["executable"],
+            global_kwopts=" ".join(global_kwopts),
+            subcommand="{subcommand}",
+            args="{args}",
         )
 
     def _filter_by_id_or_name(self, id, name):
         if id:
-            return f'--filter id={id}'
+            return f"--filter id={id}"
         elif name:
-            return f'--filter name={name}'
+            return f"--filter name={name}"
         return None
 
     def _stringify_kwopt_docker_volumes(self, flag, val):
@@ -160,20 +174,20 @@ class DockerCLIInterface(DockerInterface):
             for hostvol, guestopts in val.items():
                 if isinstance(guestopts, str):
                     # {'/host/vol': '/container/vol'}
-                    kwopt_list.append(f'{hostvol}:{guestopts}')
+                    kwopt_list.append(f"{hostvol}:{guestopts}")
                 else:
                     # {'/host/vol': {'bind': '/container/vol'}}
                     # {'/host/vol': {'bind': '/container/vol', 'mode': 'rw'}}
-                    mode = guestopts.get('mode', '')
-                    kwopt_list.append('{vol}:{bind}{mode}'.format(
-                        vol=hostvol,
-                        bind=guestopts['bind'],
-                        mode=f":{mode}" if mode else ''
-                    ))
+                    mode = guestopts.get("mode", "")
+                    kwopt_list.append(
+                        "{vol}:{bind}{mode}".format(
+                            vol=hostvol, bind=guestopts["bind"], mode=f":{mode}" if mode else ""
+                        )
+                    )
         return self._stringify_kwopt_list(flag, kwopt_list)
 
     def _run_docker(self, subcommand, args=None, verbose=False):
-        command = self._docker_command.format(subcommand=subcommand, args=args or '')
+        command = self._docker_command.format(subcommand=subcommand, args=args or "")
         return self._run_command(command, verbose=verbose)
 
     #
@@ -182,24 +196,24 @@ class DockerCLIInterface(DockerInterface):
 
     @docker_columns
     def ps(self, id=None, name=None):
-        return self._run_docker(subcommand='ps', args=self._filter_by_id_or_name(id, name))
+        return self._run_docker(subcommand="ps", args=self._filter_by_id_or_name(id, name))
 
     def run(self, command, image=None, **kwopts):
-        args = '{kwopts} {image} {command}'.format(
+        args = "{kwopts} {image} {command}".format(
             kwopts=self._stringify_kwopts(kwopts),
             image=image or self._default_image,
-            command=command if command else ''
+            command=command if command else "",
         ).strip()
-        container_id = self._run_docker(subcommand='run', args=args, verbose=True)
+        container_id = self._run_docker(subcommand="run", args=args, verbose=True)
         return DockerContainer.from_id(self, container_id)
 
     @docker_json
     def inspect(self, container_id):
         try:
-            return self._run_docker(subcommand='inspect', args=container_id)[0]
+            return self._run_docker(subcommand="inspect", args=container_id)[0]
         except (IndexError, ContainerCLIError) as exc:
             msg = f"Invalid container id: {container_id}"
-            if exc.stdout == '[]' and exc.stderr == f'Error: no such object: {container_id}':
+            if exc.stdout == "[]" and exc.stderr == f"Error: no such object: {container_id}":
                 log.warning(msg)
                 return []
             else:
@@ -208,10 +222,10 @@ class DockerCLIInterface(DockerInterface):
     @docker_json
     def image_inspect(self, image):
         try:
-            return self._run_docker(subcommand='image inspect', args=image)[0]
+            return self._run_docker(subcommand="image inspect", args=image)[0]
         except (IndexError, ContainerCLIError) as exc:
             msg = f"{image} not pulled, cannot get digest"
-            if exc.stdout == '[]' and exc.stderr == f'Error: no such image: {image}':
+            if exc.stdout == "[]" and exc.stderr == f"Error: no such image: {image}":
                 log.warning(msg, image)
                 return []
             else:
@@ -219,8 +233,7 @@ class DockerCLIInterface(DockerInterface):
 
 
 class DockerAPIClient:
-    """Wraps a ``docker.APIClient`` to catch exceptions.
-    """
+    """Wraps a ``docker.APIClient`` to catch exceptions."""
 
     _exception_retry_time = 5
     _default_max_tries = 10
@@ -234,7 +247,7 @@ class DockerAPIClient:
         if isinstance(f, partial):
             f = f.func
         try:
-            return getattr(f, '__qualname__', f"{f.im_class.__name__}.{f.__name__}")
+            return getattr(f, "__qualname__", f"{f.im_class.__name__}.{f.__name__}")
         except AttributeError:
             return f.__name__
 
@@ -253,15 +266,15 @@ class DockerAPIClient:
     @staticmethod
     def _init_client():
         kwargs = DockerAPIClient._client_kwargs.copy()
-        if DockerAPIClient._host_iter is not None and 'base_url' not in kwargs:
-            kwargs['base_url'] = next(DockerAPIClient._host_iter)
+        if DockerAPIClient._host_iter is not None and "base_url" not in kwargs:
+            kwargs["base_url"] = next(DockerAPIClient._host_iter)
         DockerAPIClient._client = docker.APIClient(*DockerAPIClient._client_args, **kwargs)
-        log.info('Initialized Docker API client for server: %s', kwargs.get('base_url', 'localhost'))
+        log.info("Initialized Docker API client for server: %s", kwargs.get("base_url", "localhost"))
 
     @staticmethod
     def _default_client_handler(fname, *args, **kwargs):
-        success_test = kwargs.pop('success_test', None)
-        max_tries = kwargs.pop('max_tries', DockerAPIClient._default_max_tries)
+        success_test = kwargs.pop("success_test", None)
+        max_tries = kwargs.pop("max_tries", DockerAPIClient._default_max_tries)
         for tries in range(1, max_tries + 1):
             retry_time = DockerAPIClient._exception_retry_time
             reinit = False
@@ -272,7 +285,7 @@ class DockerAPIClient:
             try:
                 r = f(*args, **kwargs)
                 if tries > 1:
-                    log.info('%s() succeeded on attempt %s', qualname, tries)
+                    log.info("%s() succeeded on attempt %s", qualname, tries)
                 return r
             except (ConnectionError, docker.errors.APIError, ReadTimeout) as exc:
                 if isinstance(exc, ConnectionError):
@@ -283,8 +296,9 @@ class DockerAPIClient:
                 else:  # ReadTimeout
                     reinit = True
                     retry_time = 0
-                log.warning("Caught exception on %s(): %s: %s",
-                            DockerAPIClient._qualname(f), exc.__class__.__name__, exc)
+                log.warning(
+                    "Caught exception on %s(): %s: %s", DockerAPIClient._qualname(f), exc.__class__.__name__, exc
+                )
                 if reinit:
                     log.warning("Reinitializing Docker API client due to connection-oriented failure")
                     DockerAPIClient._init_client()
@@ -299,7 +313,7 @@ class DockerAPIClient:
                     return r
                 elif tries >= max_tries:
                     log.error("Maximum number of attempts (%s) exceeded", max_tries)
-                    if 'response' in exc and DockerAPIClient._nonfatal_error(exc.response.status_code):
+                    if "response" in exc and DockerAPIClient._nonfatal_error(exc.response.status_code):
                         return None
                     else:
                         raise
@@ -309,15 +323,14 @@ class DockerAPIClient:
 
     def __init__(self, *args, **kwargs):
         # Only initialize the host iterator once
-        host_iter = kwargs.pop('host_iter', None)
+        host_iter = kwargs.pop("host_iter", None)
         DockerAPIClient._host_iter = DockerAPIClient._host_iter or host_iter
         DockerAPIClient._client_args = args
         DockerAPIClient._client_kwargs = kwargs
         DockerAPIClient._init_client()
 
     def __getattr__(self, attr):
-        """Allow the calling of methods on this class as if it were a docker.APIClient instance.
-        """
+        """Allow the calling of methods on this class as if it were a docker.APIClient instance."""
         cattr = DockerAPIClient._unwrapped_attr(attr)
         if callable(cattr):
             return partial(DockerAPIClient._default_client_handler, attr)
@@ -327,16 +340,16 @@ class DockerAPIClient:
 
 class DockerAPIInterface(DockerInterface):
 
-    container_type = 'docker'
+    container_type = "docker"
 
     # 'publish_port_random' and 'volumes' are special cases handled in _create_host_config()
     host_config_option_map = {
-        'auto_remove': {},
-        'publish_all_ports': {},
-        'cpus': {'param': 'nano_cpus', 'map': lambda x: int(x * 1000000000)},
-        'memory': {'param': 'mem_limit'},
-        'binds': {},
-        'port_bindings': {},
+        "auto_remove": {},
+        "publish_all_ports": {},
+        "cpus": {"param": "nano_cpus", "map": lambda x: int(x * 1000000000)},
+        "memory": {"param": "mem_limit"},
+        "binds": {},
+        "port_bindings": {},
     }
 
     def validate_config(self):
@@ -347,14 +360,13 @@ class DockerAPIInterface(DockerInterface):
     @property
     def _client(self):
         # TODO: add cert options to containers conf
-        cert_path = os.environ.get('DOCKER_CERT_PATH') or None
+        cert_path = os.environ.get("DOCKER_CERT_PATH") or None
         if not cert_path:
-            cert_path = os.path.join(os.path.expanduser('~'), '.docker')
+            cert_path = os.path.join(os.path.expanduser("~"), ".docker")
         if self._conf.force_tlsverify or self._conf.tls:
             tls_config = docker.tls.TLSConfig(
-                client_cert=(os.path.join(cert_path, 'cert.pem'),
-                             os.path.join(cert_path, 'key.pem')),
-                ca_cert=os.path.join(cert_path, 'ca.pem'),
+                client_cert=(os.path.join(cert_path, "cert.pem"), os.path.join(cert_path, "key.pem")),
+                ca_cert=os.path.join(cert_path, "ca.pem"),
                 verify=self._conf.force_tlsverify,
             )
         else:
@@ -376,9 +388,9 @@ class DockerAPIInterface(DockerInterface):
     @staticmethod
     def _filter_by_id_or_name(id, name):
         if id:
-            return {'id': id}
+            return {"id": id}
         elif name:
-            return {'name': name}
+            return {"name": name}
         return None
 
     @staticmethod
@@ -388,11 +400,11 @@ class DockerAPIInterface(DockerInterface):
         See :meth:`_create_docker_api_spec`.
         """
         params = []
-        if 'param' not in map_spec and 'params' not in map_spec:
+        if "param" not in map_spec and "params" not in map_spec:
             params.append(key)
-        elif 'param' in map_spec:
-            params.append(map_spec['param'])
-        params.extend(map_spec.get('params', ()))
+        elif "param" in map_spec:
+            params.append(map_spec["param"])
+        params.extend(map_spec.get("params", ()))
         return params
 
     @staticmethod
@@ -403,8 +415,8 @@ class DockerAPIInterface(DockerInterface):
         See :meth:`_create_docker_api_spec`.
         """
         params = {}
-        if 'map' in map_spec:
-            value = map_spec['map'](value)
+        if "map" in map_spec:
+            value = map_spec["map"](value)
         for param in DockerAPIInterface._kwopt_to_param_names(map_spec, key):
             params[param] = value
         return params
@@ -475,15 +487,17 @@ class DockerAPIInterface(DockerInterface):
         :returns:                   Instantiated ``spec_class`` object
         :rtype:                     ``type(spec_class)``
         """
+
         def _kwopt_to_arg(map_spec, key, value, param=None):
             # determines whether the given param is a positional or keyword argument in docker-py and adds it to the
             # list of arguments
-            if isinstance(map_spec.get('param'), int):
-                spec_opts.append((map_spec.get('param'), value))
+            if isinstance(map_spec.get("param"), int):
+                spec_opts.append((map_spec.get("param"), value))
             elif param is not None:
                 spec_kwopts[param] = value
             else:
                 spec_kwopts.update(DockerAPIInterface._kwopt_to_params(map_spec, key, value))
+
         # positional arguments
         spec_opts = []
         # keyword arguments
@@ -491,20 +505,20 @@ class DockerAPIInterface(DockerInterface):
         # retrieve the option map for the docker-py object we're creating
         option_map = getattr(self, f"{option_map_name}_option_map")
         # set defaults
-        for key in filter(lambda k: option_map[k].get('default'), option_map.keys()):
+        for key in filter(lambda k: option_map[k].get("default"), option_map.keys()):
             map_spec = option_map[key]
-            _kwopt_to_arg(map_spec, key, map_spec['default'])
+            _kwopt_to_arg(map_spec, key, map_spec["default"])
         # don't allow kwopts that start with _, those are reserved for "child" object params
-        for kwopt in filter(lambda k: not k.startswith('_') and k in option_map, list(kwopts.keys())):
+        for kwopt in filter(lambda k: not k.startswith("_") and k in option_map, list(kwopts.keys())):
             map_spec = option_map[kwopt]
             _v = kwopts.pop(kwopt)
             _kwopt_to_arg(map_spec, kwopt, _v)
         # find any child objects that need to be created and recurse to create them
-        for _sub_k in filter(lambda k: k.startswith('_') and 'spec_class' in option_map[k], option_map.keys()):
+        for _sub_k in filter(lambda k: k.startswith("_") and "spec_class" in option_map[k], option_map.keys()):
             map_spec = option_map[_sub_k]
-            param = _sub_k.lstrip('_')
-            _sub_v = self._create_docker_api_spec(param, map_spec['spec_class'], kwopts)
-            if _sub_v is not None or map_spec.get('required') or isinstance(map_spec.get('param'), int):
+            param = _sub_k.lstrip("_")
+            _sub_v = self._create_docker_api_spec(param, map_spec["spec_class"], kwopts)
+            if _sub_v is not None or map_spec.get("required") or isinstance(map_spec.get("param"), int):
                 _kwopt_to_arg(map_spec, None, _sub_v, param=param)
         # sort positional args and make into a flat tuple
         if spec_opts:
@@ -541,15 +555,15 @@ class DockerAPIInterface(DockerInterface):
         :returns:       The return value of `docker.APIClient.create_host_config()`
         :rtype:         dict
         """
-        if 'publish_port_random' in kwopts:
-            port = int(kwopts.pop('publish_port_random'))
-            kwopts['port_bindings'] = {port: None}
-            kwopts['ports'] = [port]
-        if 'volumes' in kwopts:
-            paths, binds = self._volumes_to_native(kwopts.pop('volumes'))
-            kwopts['binds'] = binds
-            kwopts['volumes'] = paths
-        return self._create_docker_api_spec('host_config', self._client.create_host_config, kwopts)
+        if "publish_port_random" in kwopts:
+            port = int(kwopts.pop("publish_port_random"))
+            kwopts["port_bindings"] = {port: None}
+            kwopts["ports"] = [port]
+        if "volumes" in kwopts:
+            paths, binds = self._volumes_to_native(kwopts.pop("volumes"))
+            kwopts["binds"] = binds
+            kwopts["volumes"] = paths
+        return self._create_docker_api_spec("host_config", self._client.create_host_config, kwopts)
 
     #
     # docker subcommands
@@ -565,7 +579,7 @@ class DockerAPIInterface(DockerInterface):
         host_config = self._create_host_config(kwopts)
         log.debug("Docker container host configuration:\n%s", safe_dumps_formatted(host_config))
         log.debug("Docker container creation parameters:\n%s", safe_dumps_formatted(kwopts))
-        success_test = partial(self._first, self.ps, name=kwopts['name'], running=False)
+        success_test = partial(self._first, self.ps, name=kwopts["name"], running=False)
         # this can raise exceptions, if necessary we could wrap them in a more generic "creation failed" exception class
         container = self._client.create_container(
             image,
@@ -573,10 +587,10 @@ class DockerAPIInterface(DockerInterface):
             host_config=host_config,
             success_test=success_test,
             max_tries=5,
-            **kwopts
+            **kwopts,
         )
-        container_id = container.get('Id')
-        log.debug("Starting container: %s (%s)", kwopts['name'], str(container_id))
+        container_id = container.get("Id")
+        log.debug("Starting container: %s (%s)", kwopts["name"], str(container_id))
         # start can safely be run more than once
         self._client.start(container=container_id)
         return DockerContainer.from_id(self, container_id)
diff --git a/lib/galaxy/containers/docker_decorators.py b/lib/galaxy/containers/docker_decorators.py
index ee5e9fa6fa2..a3e28de4860 100644
--- a/lib/galaxy/containers/docker_decorators.py
+++ b/lib/galaxy/containers/docker_decorators.py
@@ -28,22 +28,23 @@ def docker_columns(f):
         if not output:
             return parsed
         for i, c in enumerate(header):
-            if c != ' ' and spacect > 1:
+            if c != " " and spacect > 1:
                 colidx += 1
                 colstarts.append(i)
                 spacect = 0
-            elif c == ' ':
+            elif c == " ":
                 spacect += 1
         colstarts.append(None)
         colheadings = []
         for i in range(0, len(colstarts) - 1):
-            colheadings.append(header[colstarts[i]:colstarts[i + 1]].strip())
+            colheadings.append(header[colstarts[i] : colstarts[i + 1]].strip())
         for line in output[1:]:
             row = {}
             for i, key in enumerate(colheadings):
-                row[key] = line[colstarts[i]:colstarts[i + 1]].strip()
+                row[key] = line[colstarts[i] : colstarts[i + 1]].strip()
             parsed.append(row)
         return parsed
+
     return parse_docker_column_output
 
 
@@ -51,4 +52,5 @@ def docker_json(f):
     @wraps(f)
     def json_loads(*args, **kwargs):
         return json.loads(f(*args, **kwargs))
+
     return json_loads
diff --git a/lib/galaxy/containers/docker_model.py b/lib/galaxy/containers/docker_model.py
index 2d409e258db..a5f2656c46d 100644
--- a/lib/galaxy/containers/docker_model.py
+++ b/lib/galaxy/containers/docker_model.py
@@ -9,21 +9,21 @@ try:
     import docker
 except ImportError:
     from galaxy.util.bunch import Bunch
+
     docker = Bunch(errors=Bunch(NotFound=None))
 
 from galaxy.containers import (
     Container,
     ContainerPort,
-    ContainerVolume
+    ContainerVolume,
 )
 from galaxy.util import (
     pretty_print_time_interval,
     unicodify,
 )
 
-
-CPUS_LABEL = '_galaxy_cpus'
-IMAGE_LABEL = '_galaxy_image'
+CPUS_LABEL = "_galaxy_cpus"
+IMAGE_LABEL = "_galaxy_image"
 CPUS_CONSTRAINT = f"node.labels.{CPUS_LABEL}"
 IMAGE_CONSTRAINT = f"node.labels.{IMAGE_LABEL}"
 
@@ -31,7 +31,6 @@ log = logging.getLogger(__name__)
 
 
 class DockerAttributeContainer:
-
     def __init__(self, members=None):
         if members is None:
             members = set()
@@ -47,7 +46,7 @@ class DockerAttributeContainer:
         return hash(tuple(sorted(repr(x) for x in self._members)))
 
     def __str__(self):
-        return ', '.join(str(x) for x in self._members) or 'None'
+        return ", ".join(str(x) for x in self._members) or "None"
 
     def __iter__(self):
         return iter(self._members)
@@ -114,11 +113,10 @@ class DockerVolume(ContainerVolume):
 
     def to_native(self):
         host_path = self.host_path or self.path
-        return (self.path, {host_path: {'bind': self.path, 'mode': self.mode}})
+        return (self.path, {host_path: {"bind": self.path, "mode": self.mode}})
 
 
 class DockerContainer(Container):
-
     def __init__(self, interface, id, name=None, inspect=None):
         super().__init__(interface, id, name=name)
         self._inspect = inspect
@@ -126,7 +124,7 @@ class DockerContainer(Container):
     @classmethod
     def from_id(cls, interface, id):
         inspect = interface.inspect(id)
-        return cls(interface, id, name=inspect['Name'], inspect=inspect)
+        return cls(interface, id, name=inspect["Name"], inspect=inspect)
 
     @property
     def ports(self):
@@ -141,30 +139,36 @@ class DockerContainer(Container):
         #             ]
         rval = []
         try:
-            port_mappings = self.inspect['NetworkSettings']['Ports']
+            port_mappings = self.inspect["NetworkSettings"]["Ports"]
         except KeyError:
-            log.warning("Failed to get ports for container %s from `docker inspect` output at "
-                        "['NetworkSettings']['Ports']: %s: %s", self.id, exc_info=True)
+            log.warning(
+                "Failed to get ports for container %s from `docker inspect` output at "
+                "['NetworkSettings']['Ports']: %s: %s",
+                self.id,
+                exc_info=True,
+            )
             return None
         for port_name in port_mappings:
             for binding in port_mappings[port_name]:
-                rval.append(ContainerPort(
-                    int(port_name.split('/')[0]),
-                    port_name.split('/')[1],
-                    self.address,
-                    int(binding['HostPort']),
-                ))
+                rval.append(
+                    ContainerPort(
+                        int(port_name.split("/")[0]),
+                        port_name.split("/")[1],
+                        self.address,
+                        int(binding["HostPort"]),
+                    )
+                )
         return rval
 
     @property
     def address(self):
-        if self._interface.host and self._interface.host.startswith('tcp://'):
-            return self._interface.host.replace('tcp://', '').split(':', 1)[0]
+        if self._interface.host and self._interface.host.startswith("tcp://"):
+            return self._interface.host.replace("tcp://", "").split(":", 1)[0]
         else:
-            return 'localhost'
+            return "localhost"
 
     def is_ready(self):
-        return self.inspect['State']['Running']
+        return self.inspect["State"]["Running"]
 
     def __eq__(self, other):
         return self._id == other.id
@@ -183,7 +187,6 @@ class DockerContainer(Container):
 
 
 class DockerService(Container):
-
     def __init__(self, interface, id, name=None, image=None, inspect=None):
         super().__init__(interface, id, name=name)
         self._image = image
@@ -191,15 +194,15 @@ class DockerService(Container):
         self._env = {}
         self._tasks = []
         if inspect:
-            self._name = name or inspect['Spec']['Name']
-            self._image = image or inspect['Spec']['TaskTemplate']['ContainerSpec']['Image']
+            self._name = name or inspect["Spec"]["Name"]
+            self._image = image or inspect["Spec"]["TaskTemplate"]["ContainerSpec"]["Image"]
 
     @classmethod
     def from_cli(cls, interface, s, task_list):
-        service = cls(interface, s['ID'], name=s['NAME'], image=s['IMAGE'])
+        service = cls(interface, s["ID"], name=s["NAME"], image=s["IMAGE"])
         for task_dict in task_list:
-            if task_dict['NAME'].strip().startswith(r'\_'):
-                continue    # historical task
+            if task_dict["NAME"].strip().startswith(r"\_"):
+                continue  # historical task
             service.task_add(DockerTask.from_cli(interface, task_dict, service=service))
         return service
 
@@ -225,29 +228,35 @@ class DockerService(Container):
         #         ]
         rval = []
         try:
-            port_mappings = self.inspect['Endpoint']['Ports']
+            port_mappings = self.inspect["Endpoint"]["Ports"]
         except (IndexError, KeyError):
-            log.warning("Failed to get ports for container %s from `docker service inspect` output at "
-                        "['Endpoint']['Ports']: %s: %s", self.id, exc_info=True)
+            log.warning(
+                "Failed to get ports for container %s from `docker service inspect` output at "
+                "['Endpoint']['Ports']: %s: %s",
+                self.id,
+                exc_info=True,
+            )
             return None
         for binding in port_mappings:
-            rval.append(ContainerPort(
-                binding['TargetPort'],
-                binding['Protocol'],
-                self.address,               # use the routing mesh
-                binding['PublishedPort']
-            ))
+            rval.append(
+                ContainerPort(
+                    binding["TargetPort"],
+                    binding["Protocol"],
+                    self.address,  # use the routing mesh
+                    binding["PublishedPort"],
+                )
+            )
         return rval
 
     @property
     def address(self):
-        if self._interface.host and self._interface.host.startswith('tcp://'):
-            return self._interface.host.replace('tcp://', '').split(':', 1)[0]
+        if self._interface.host and self._interface.host.startswith("tcp://"):
+            return self._interface.host.replace("tcp://", "").split(":", 1)[0]
         else:
-            return 'localhost'
+            return "localhost"
 
     def is_ready(self):
-        return self.in_state('Running', 'Running')
+        return self.in_state("Running", "Running")
 
     def __eq__(self, other):
         return self._id == other.id
@@ -278,7 +287,7 @@ class DockerService(Container):
         state = None
         for task in self.tasks:
             state = task.state
-            if task.desired_state == 'running':
+            if task.desired_state == "running":
                 break
         return state
 
@@ -286,28 +295,26 @@ class DockerService(Container):
     def env(self):
         if not self._env:
             try:
-                for env_str in self.inspect['Spec']['TaskTemplate']['ContainerSpec']['Env']:
+                for env_str in self.inspect["Spec"]["TaskTemplate"]["ContainerSpec"]["Env"]:
                     try:
-                        self._env.update([env_str.split('=', 1)])
+                        self._env.update([env_str.split("=", 1)])
                     except ValueError:
                         self._env[env_str] = None
             except KeyError as exc:
-                log.debug('Cannot retrieve container environment: KeyError: %s', unicodify(exc))
+                log.debug("Cannot retrieve container environment: KeyError: %s", unicodify(exc))
         return self._env
 
     @property
     def terminal(self):
-        """Same caveats as :meth:`state`.
-        """
+        """Same caveats as :meth:`state`."""
         for task in self.tasks:
-            if task.desired_state == 'running':
+            if task.desired_state == "running":
                 return False
         return True
 
     @property
     def node(self):
-        """Same caveats as :meth:`state`.
-        """
+        """Same caveats as :meth:`state`."""
         for task in self.tasks:
             if task.node is not None:
                 return task.node
@@ -316,13 +323,13 @@ class DockerService(Container):
     @property
     def image(self):
         if self._image is None:
-            self._image = self.inspect['Spec']['TaskTemplate']['ContainerSpec']['Image']
+            self._image = self.inspect["Spec"]["TaskTemplate"]["ContainerSpec"]["Image"]
         return self._image
 
     @property
     def cpus(self):
         try:
-            cpus = self.inspect['Spec']['TaskTemplate']['Resources']['Limits']['NanoCPUs'] / 1000000000.0
+            cpus = self.inspect["Spec"]["TaskTemplate"]["Resources"]["Limits"]["NanoCPUs"] / 1000000000.0
             if cpus == int(cpus):
                 cpus = int(cpus)
             return cpus
@@ -331,13 +338,12 @@ class DockerService(Container):
 
     @property
     def constraints(self):
-        constraints = self.inspect['Spec']['TaskTemplate']['Placement'].get('Constraints', [])
+        constraints = self.inspect["Spec"]["TaskTemplate"]["Placement"].get("Constraints", [])
         return DockerServiceConstraints.from_constraint_string_list(constraints)
 
     @property
     def tasks(self):
-        """A list of *all* tasks, including terminal ones.
-        """
+        """A list of *all* tasks, including terminal ones."""
         if not self._tasks:
             self._tasks = []
             for task in self._interface.service_tasks(self):
@@ -346,45 +352,40 @@ class DockerService(Container):
 
     @property
     def task_count(self):
-        """A count of *all* tasks, including terminal ones.
-        """
+        """A count of *all* tasks, including terminal ones."""
         return len(self.tasks)
 
-    def in_state(self, desired, current, tasks='any'):
-        """Indicate if one of this service's tasks matches the desired state.
-        """
+    def in_state(self, desired, current, tasks="any"):
+        """Indicate if one of this service's tasks matches the desired state."""
         for task in self.tasks:
             if task.in_state(desired, current):
-                if tasks == 'any':
+                if tasks == "any":
                     # at least 1 task in desired state
                     return True
-            elif tasks == 'all':
+            elif tasks == "all":
                 # at least 1 task not in desired state
                 return False
         else:
-            return False if tasks == 'any' else True
+            return False if tasks == "any" else True
 
     def constraint_add(self, name, op, value):
         self._interface.service_constraint_add(self.id, name, op, value)
 
     def set_cpus(self):
-        self.constraint_add(CPUS_LABEL, '==', self.cpus)
+        self.constraint_add(CPUS_LABEL, "==", self.cpus)
 
     def set_image(self):
-        self.constraint_add(IMAGE_LABEL, '==', self.image)
+        self.constraint_add(IMAGE_LABEL, "==", self.image)
 
 
 class DockerServiceConstraint:
-
     def __init__(self, name=None, op=None, value=None):
         self._name = name
         self._op = op
         self._value = value
 
     def __eq__(self, other):
-        return self._name == other._name and \
-            self._op == other._op and \
-            self._value == other._value
+        return self._name == other._name and self._op == other._op and self._value == other._value
 
     def __ne__(self, other):
         return not self.__eq__(other)
@@ -393,20 +394,20 @@ class DockerServiceConstraint:
         return hash((self._name, self._op, self._value))
 
     def __repr__(self):
-        return f'{self.__class__.__name__}({self._name}{self._op}{self._value})'
+        return f"{self.__class__.__name__}({self._name}{self._op}{self._value})"
 
     def __str__(self):
-        return f'{self._name}{self._op}{self._value}'
+        return f"{self._name}{self._op}{self._value}"
 
     @staticmethod
     def split_constraint_string(constraint_str):
-        constraint = (constraint_str, '', '')
-        for op in '==', '!=':
+        constraint = (constraint_str, "", "")
+        for op in "==", "!=":
             t = constraint_str.partition(op)
             if len(t[0]) < len(constraint[0]):
                 constraint = t
         if constraint[0] == constraint_str:
-            raise Exception(f'Unable to parse constraint string: {constraint_str}')
+            raise Exception(f"Unable to parse constraint string: {constraint_str}")
         return [x.strip() for x in constraint]
 
     @classmethod
@@ -428,10 +429,7 @@ class DockerServiceConstraint:
 
     @property
     def label(self):
-        return DockerNodeLabel(
-            name=self.name.replace('node.labels.', ''),
-            value=self.value
-        )
+        return DockerNodeLabel(name=self.name.replace("node.labels.", ""), value=self.value)
 
 
 class DockerServiceConstraints(DockerAttributeContainer):
@@ -451,9 +449,7 @@ class DockerServiceConstraints(DockerAttributeContainer):
 
 
 class DockerNode:
-
-    def __init__(self, interface, id=None, name=None, status=None,
-                 availability=None, manager=False, inspect=None):
+    def __init__(self, interface, id=None, name=None, status=None, availability=None, manager=False, inspect=None):
         self._interface = interface
         self._id = id
         self._name = name
@@ -462,16 +458,22 @@ class DockerNode:
         self._manager = manager
         self._inspect = inspect
         if inspect:
-            self._name = name or inspect['Description']['Hostname']
-            self._status = status or inspect['Status']['State']
-            self._availability = inspect['Spec']['Availability']
-            self._manager = manager or inspect['Spec']['Role'] == 'manager'
+            self._name = name or inspect["Description"]["Hostname"]
+            self._status = status or inspect["Status"]["State"]
+            self._availability = inspect["Spec"]["Availability"]
+            self._manager = manager or inspect["Spec"]["Role"] == "manager"
         self._tasks = []
 
     @classmethod
     def from_cli(cls, interface, n, task_list):
-        node = cls(interface, id=n['ID'], name=n['HOSTNAME'], status=n['STATUS'],
-                   availability=n['AVAILABILITY'], manager=True if n['MANAGER STATUS'] else False)
+        node = cls(
+            interface,
+            id=n["ID"],
+            name=n["HOSTNAME"],
+            status=n["STATUS"],
+            availability=n["AVAILABILITY"],
+            manager=True if n["MANAGER STATUS"] else False,
+        )
         for task_dict in task_list:
             node.task_add(DockerTask.from_cli(interface, task_dict, node=node))
         return node
@@ -498,7 +500,7 @@ class DockerNode:
     @property
     def version(self):
         # this changes on update so don't cache
-        return self._interface.node_inspect(self._id or self._name)['Version']['Index']
+        return self._interface.node_inspect(self._id or self._name)["Version"]["Index"]
 
     @property
     def inspect(self):
@@ -508,15 +510,15 @@ class DockerNode:
 
     @property
     def state(self):
-        return (f'{self._status}-{self._availability}').lower()
+        return (f"{self._status}-{self._availability}").lower()
 
     @property
     def cpus(self):
-        return self.inspect['Description']['Resources']['NanoCPUs'] / 1000000000
+        return self.inspect["Description"]["Resources"]["NanoCPUs"] / 1000000000
 
     @property
     def labels(self):
-        labels = self.inspect['Spec'].get('Labels', {}) or {}
+        labels = self.inspect["Spec"].get("Labels", {}) or {}
         return DockerNodeLabels.from_label_dictionary(labels)
 
     def label_add(self, label, value):
@@ -534,14 +536,13 @@ class DockerNode:
                 self.label_add(label.name, label.value)
 
     def _constraints_to_label_args(self, constraints):
-        constraints = filter(lambda x: x.name.startswith('node.labels.') and x.op == '==', constraints)
-        labels = map(lambda x: DockerNodeLabel(name=x.name.replace('node.labels.', '', 1), value=x.value), constraints)
+        constraints = filter(lambda x: x.name.startswith("node.labels.") and x.op == "==", constraints)
+        labels = map(lambda x: DockerNodeLabel(name=x.name.replace("node.labels.", "", 1), value=x.value), constraints)
         return labels
 
     @property
     def tasks(self):
-        """A list of *all* tasks, including terminal ones.
-        """
+        """A list of *all* tasks, including terminal ones."""
         if not self._tasks:
             self._tasks = []
             for task in self._interface.node_tasks(self):
@@ -560,15 +561,14 @@ class DockerNode:
 
     @property
     def task_count(self):
-        """A count of *all* tasks, including terminal ones.
-        """
+        """A count of *all* tasks, including terminal ones."""
         return len(self.tasks)
 
     def in_state(self, status, availability):
         return self._status.lower() == status.lower() and self._availability.lower() == availability.lower()
 
     def is_ok(self):
-        return self.in_state('Ready', 'Active')
+        return self.in_state("Ready", "Active")
 
     def is_managed(self):
         return not self._manager
@@ -577,18 +577,16 @@ class DockerNode:
         return not self._manager and self.is_ok() and self.task_count == 0
 
     def drain(self):
-        self._interface.node_update(self.id, availability='drain')
+        self._interface.node_update(self.id, availability="drain")
 
 
 class DockerNodeLabel:
-
     def __init__(self, name=None, value=None):
         self._name = name
         self._value = value
 
     def __eq__(self, other):
-        return self._name == other._name and \
-            self._value == other._value
+        return self._name == other._name and self._value == other._value
 
     def __ne__(self, other):
         return not self.__eq__(other)
@@ -597,10 +595,10 @@ class DockerNodeLabel:
         return hash((self._name, self._value))
 
     def __repr__(self):
-        return f'{self.__class__.__name__}({self._name}: {self._value})'
+        return f"{self.__class__.__name__}({self._name}: {self._value})"
 
     def __str__(self):
-        return f'{self._name}: {self._value}'
+        return f"{self._name}: {self._value}"
 
     @property
     def name(self):
@@ -612,15 +610,11 @@ class DockerNodeLabel:
 
     @property
     def constraint_string(self):
-        return f'node.labels.{self.name}=={self.value}'
+        return f"node.labels.{self.name}=={self.value}"
 
     @property
     def constraint(self):
-        return DockerServiceConstraint(
-            name=f'node.labels.{self.name}',
-            op='==',
-            value=self.value
-        )
+        return DockerServiceConstraint(name=f"node.labels.{self.name}", op="==", value=self.value)
 
 
 class DockerNodeLabels(DockerAttributeContainer):
@@ -643,15 +637,26 @@ class DockerTask:
 
     # these are the possible *current* state terminal states
     terminal_states = (
-        'shutdown',  # this is normally only a desired state but I've seen a task with it as current as well
-        'complete',
-        'failed',
-        'rejected',
-        'orphaned',
+        "shutdown",  # this is normally only a desired state but I've seen a task with it as current as well
+        "complete",
+        "failed",
+        "rejected",
+        "orphaned",
     )
 
-    def __init__(self, interface, id=None, name=None, image=None, desired_state=None,
-                 state=None, error=None, ports=None, service=None, node=None):
+    def __init__(
+        self,
+        interface,
+        id=None,
+        name=None,
+        image=None,
+        desired_state=None,
+        state=None,
+        error=None,
+        ports=None,
+        service=None,
+        node=None,
+    ):
         self._interface = interface
         self._id = id
         self._name = name
@@ -666,23 +671,41 @@ class DockerTask:
 
     @classmethod
     def from_cli(cls, interface, t, service=None, node=None):
-        state = t['CURRENT STATE'].split()[0]
-        return cls(interface, id=t['ID'], name=t['NAME'], image=t['IMAGE'],
-                   desired_state=t['DESIRED STATE'], state=state, error=t['ERROR'],
-                   ports=t['PORTS'], service=service, node=node)
+        state = t["CURRENT STATE"].split()[0]
+        return cls(
+            interface,
+            id=t["ID"],
+            name=t["NAME"],
+            image=t["IMAGE"],
+            desired_state=t["DESIRED STATE"],
+            state=state,
+            error=t["ERROR"],
+            ports=t["PORTS"],
+            service=service,
+            node=node,
+        )
 
     @classmethod
     def from_api(cls, interface, t, service=None, node=None):
-        service = service or interface.service(id=t.get('ServiceID'))
-        node = node or interface.node(id=t.get('NodeID'))
+        service = service or interface.service(id=t.get("ServiceID"))
+        node = node or interface.node(id=t.get("NodeID"))
         if service:
             name = f"{service.name}.{str(t['Slot'])}"
         else:
-            name = t['ID']
-        image = t['Spec']['ContainerSpec']['Image'].split('@', 1)[0],  # remove pin
-        return cls(interface, id=t['ID'], name=name, image=image, desired_state=t['DesiredState'],
-                   state=t['Status']['State'], ports=t['Status']['PortStatus'], error=t['Status']['Message'],
-                   service=service, node=node)
+            name = t["ID"]
+        image = (t["Spec"]["ContainerSpec"]["Image"].split("@", 1)[0],)  # remove pin
+        return cls(
+            interface,
+            id=t["ID"],
+            name=name,
+            image=image,
+            desired_state=t["DesiredState"],
+            state=t["Status"]["State"],
+            ports=t["Status"]["PortStatus"],
+            error=t["Status"]["Message"],
+            service=service,
+            node=node,
+        )
 
     @property
     def id(self):
@@ -700,15 +723,16 @@ class DockerTask:
             except docker.errors.NotFound:
                 # This shouldn't be possible, appears to be some kind of Swarm bug (the node claims to have a task that
                 # does not actually exist anymore, nor does its service exist).
-                log.error('Task could not be inspected because Docker claims it does not exist: %s (%s)',
-                          self.name, self.id)
+                log.error(
+                    "Task could not be inspected because Docker claims it does not exist: %s (%s)", self.name, self.id
+                )
                 return None
         return self._inspect
 
     @property
     def slot(self):
         try:
-            return self.inspect['Slot']
+            return self.inspect["Slot"]
         except TypeError:
             return None
 
@@ -716,7 +740,7 @@ class DockerTask:
     def node(self):
         if not self._node:
             try:
-                self._node = self._interface.node(id=self.inspect['NodeID'])
+                self._node = self._interface.node(id=self.inspect["NodeID"])
             except TypeError:
                 return None
         return self._node
@@ -725,7 +749,7 @@ class DockerTask:
     def service(self):
         if not self._service:
             try:
-                self._service = self._interface.service(id=self.inspect['ServiceID'])
+                self._service = self._interface.service(id=self.inspect["ServiceID"])
             except TypeError:
                 return None
         return self._service
@@ -733,7 +757,7 @@ class DockerTask:
     @property
     def cpus(self):
         try:
-            cpus = self.inspect['Spec']['Resources']['Reservations']['NanoCPUs'] / 1000000000.0
+            cpus = self.inspect["Spec"]["Resources"]["Reservations"]["NanoCPUs"] / 1000000000.0
             if cpus == int(cpus):
                 cpus = int(cpus)
             return cpus
@@ -744,7 +768,7 @@ class DockerTask:
 
     @property
     def state(self):
-        return (f'{self._desired_state}-{self._state}').lower()
+        return (f"{self._desired_state}-{self._state}").lower()
 
     @property
     def current_state(self):
@@ -758,10 +782,10 @@ class DockerTask:
     def current_state_time(self):
         # Docker API returns a stamp w/ higher second precision than Python takes
         try:
-            stamp = self.inspect['Status']['Timestamp']
+            stamp = self.inspect["Status"]["Timestamp"]
         except TypeError:
             return None
-        return pretty_print_time_interval(time=stamp[:stamp.index('.') + 7], precise=True, utc=stamp[-1] == 'Z')
+        return pretty_print_time_interval(time=stamp[: stamp.index(".") + 7], precise=True, utc=stamp[-1] == "Z")
 
     @property
     def desired_state(self):
@@ -773,7 +797,7 @@ class DockerTask:
 
     @property
     def terminal(self):
-        return self.desired_state == 'shutdown' and self.current_state in self.terminal_states
+        return self.desired_state == "shutdown" and self.current_state in self.terminal_states
 
     def in_state(self, desired, current):
         return self.desired_state == desired.lower() and self.current_state == current.lower()
diff --git a/lib/galaxy/containers/docker_swarm.py b/lib/galaxy/containers/docker_swarm.py
index 6ac26c547df..840215950f9 100644
--- a/lib/galaxy/containers/docker_swarm.py
+++ b/lib/galaxy/containers/docker_swarm.py
@@ -6,31 +6,41 @@ import logging
 import os.path
 import subprocess
 from functools import partial
-from typing import Any, Dict, Optional
+from typing import (
+    Any,
+    Dict,
+    Optional,
+)
 
 try:
     import docker.types
 except ImportError:
     from galaxy.util.bunch import Bunch
-    docker = Bunch(types=Bunch(
-        ContainerSpec=None,
-        RestartPolicy=None,
-        Resources=None,
-        Placement=None,
-    ))
+
+    docker = Bunch(
+        types=Bunch(
+            ContainerSpec=None,
+            RestartPolicy=None,
+            Resources=None,
+            Placement=None,
+        )
+    )
 
 from galaxy.containers.docker import (
     DockerAPIInterface,
     DockerCLIInterface,
-    DockerInterface
+    DockerInterface,
+)
+from galaxy.containers.docker_decorators import (
+    docker_columns,
+    docker_json,
 )
-from galaxy.containers.docker_decorators import docker_columns, docker_json
 from galaxy.containers.docker_model import (
     CPUS_CONSTRAINT,
     DockerNode,
     DockerService,
     DockerTask,
-    IMAGE_CONSTRAINT
+    IMAGE_CONSTRAINT,
 )
 from galaxy.exceptions import ContainerRunError
 from galaxy.util import unicodify
@@ -40,25 +50,22 @@ log = logging.getLogger(__name__)
 
 SWARM_MANAGER_PATH = os.path.abspath(
     os.path.join(
-        os.path.dirname(__file__),
-        os.path.pardir,
-        os.path.pardir,
-        os.path.pardir,
-        'scripts',
-        'docker_swarm_manager.py'))
+        os.path.dirname(__file__), os.path.pardir, os.path.pardir, os.path.pardir, "scripts", "docker_swarm_manager.py"
+    )
+)
 
 
 class DockerSwarmInterface(DockerInterface):
 
     container_class = DockerService
     conf_defaults: Dict[str, Optional[Any]] = {
-        'ignore_volumes': False,
-        'node_prefix': None,
-        'service_create_image_constraint': False,
-        'service_create_cpus_constraint': False,
-        'resolve_image_digest': False,
-        'managed': True,
-        'manager_autostart': True,
+        "ignore_volumes": False,
+        "node_prefix": None,
+        "service_create_image_constraint": False,
+        "service_create_cpus_constraint": False,
+        "resolve_image_digest": False,
+        "managed": True,
+        "manager_autostart": True,
     }
     publish_port_list_required = True
     supports_volumes = False
@@ -68,48 +75,45 @@ class DockerSwarmInterface(DockerInterface):
         self._node_prefix = self._conf.node_prefix
 
     def run_in_container(self, command, image=None, **kwopts):
-        """Run a service like a detached container
-        """
-        kwopts['replicas'] = 1
-        kwopts['restart_condition'] = 'none'
-        if kwopts.get('publish_all_ports', False):
+        """Run a service like a detached container"""
+        kwopts["replicas"] = 1
+        kwopts["restart_condition"] = "none"
+        if kwopts.get("publish_all_ports", False):
             # not supported for services
             # TODO: inspect image (or query registry if possible) for port list
-            if kwopts.get('publish_port_random', False) or kwopts.get('ports', False):
+            if kwopts.get("publish_port_random", False) or kwopts.get("ports", False):
                 # assume this covers for publish_all_ports
-                del kwopts['publish_all_ports']
+                del kwopts["publish_all_ports"]
             else:
                 raise ContainerRunError(
                     "Publishing all ports is not supported in Docker swarm"
                     " mode, use `publish_port_random` or `ports`",
                     image=image,
-                    command=command
+                    command=command,
                 )
-        if not kwopts.get('detach', True):
+        if not kwopts.get("detach", True):
             raise ContainerRunError(
-                "Running attached containers is not supported in Docker swarm mode",
-                image=image,
-                command=command
+                "Running attached containers is not supported in Docker swarm mode", image=image, command=command
             )
-        elif kwopts.get('detach', None):
-            del kwopts['detach']
-        if kwopts.get('volumes', None):
+        elif kwopts.get("detach", None):
+            del kwopts["detach"]
+        if kwopts.get("volumes", None):
             if self._conf.ignore_volumes:
                 log.warning(
                     "'volumes' kwopt is set and not supported in Docker swarm "
                     "mode, volumes will not be passed (set 'ignore_volumes: "
-                    "False' in containers config to fail instead): %s" % kwopts['volumes']
+                    "False' in containers config to fail instead): %s" % kwopts["volumes"]
                 )
             else:
                 raise ContainerRunError(
                     "'volumes' kwopt is set and not supported in Docker swarm "
                     "mode (set 'ignore_volumes: True' in containers config to "
-                    "warn instead): %s" % kwopts['volumes'],
+                    "warn instead): %s" % kwopts["volumes"],
                     image=image,
-                    command=command
+                    command=command,
                 )
         # ensure the volumes key is removed from kwopts
-        kwopts.pop('volumes', None)
+        kwopts.pop("volumes", None)
         service = self.service_create(command, image=image, **kwopts)
         self._run_swarm_manager()
         return service
@@ -122,10 +126,18 @@ class DockerSwarmInterface(DockerInterface):
         if self._conf.managed and self._conf.manager_autostart:
             try:
                 # sys.exectuable would be preferable to using $PATH, but sys.executable is probably uwsgi
-                subprocess.check_call(['python', SWARM_MANAGER_PATH, '--containers-config-file',
-                                      self.containers_config_file, '--swarm', self.key])
+                subprocess.check_call(
+                    [
+                        "python",
+                        SWARM_MANAGER_PATH,
+                        "--containers-config-file",
+                        self.containers_config_file,
+                        "--swarm",
+                        self.key,
+                    ]
+                )
             except subprocess.CalledProcessError as exc:
-                log.error('Failed to launch swarm manager: %s', unicodify(exc))
+                log.error("Failed to launch swarm manager: %s", unicodify(exc))
 
     def _get_image(self, image):
         """Get the image string, either from the argument, or from the
@@ -143,7 +155,9 @@ class DockerSwarmInterface(DockerInterface):
         """
         if not image:
             image = self._conf.image
-        assert image is not None, "No image supplied as parameter and no image set as default in config, cannot create service"
+        assert (
+            image is not None
+        ), "No image supplied as parameter and no image set as default in config, cannot create service"
         if self._conf.resolve_image_digest:
             image = self.image_repodigest(image)
         return image
@@ -163,7 +177,7 @@ class DockerSwarmInterface(DockerInterface):
 
     def services(self, id=None, name=None):
         for service_dict in self.service_ls(id=id, name=name):
-            service_id = service_dict['ID']
+            service_id = service_dict["ID"]
             service = DockerService(self, service_id, inspect=service_dict)
             if service.name.startswith(self._name_prefix):
                 yield service
@@ -174,7 +188,7 @@ class DockerSwarmInterface(DockerInterface):
         except StopIteration:
             return None
 
-    def services_in_state(self, desired, current, tasks='any'):
+    def services_in_state(self, desired, current, tasks="any"):
         for service in self.services():
             if service.in_state(desired, current, tasks=tasks):
                 yield service
@@ -185,7 +199,7 @@ class DockerSwarmInterface(DockerInterface):
 
     def nodes(self, id=None, name=None):
         for node_dict in self.node_ls(id=id, name=name):
-            node_id = node_dict['ID']
+            node_id = node_dict["ID"]
             node = DockerNode(self, node_id, inspect=node_dict)
             if self._node_prefix and not node.name.startswith(self._node_prefix):
                 continue
@@ -211,22 +225,22 @@ class DockerSwarmInterface(DockerInterface):
     #
 
     def services_waiting(self):
-        return self.services_in_state('Running', 'Pending')
+        return self.services_in_state("Running", "Pending")
 
     def services_waiting_by_constraints(self):
-        return self._objects_by_attribute(self.services_waiting(), 'constraints')
+        return self._objects_by_attribute(self.services_waiting(), "constraints")
 
     def services_completed(self):
-        return self.services_in_state('Shutdown', 'Complete', tasks='all')
+        return self.services_in_state("Shutdown", "Complete", tasks="all")
 
     def services_terminal(self):
         return [s for s in self.services() if s.terminal]
 
     def nodes_active(self):
-        return self.nodes_in_state('Ready', 'Active')
+        return self.nodes_in_state("Ready", "Active")
 
     def nodes_active_by_constraints(self):
-        return self._objects_by_attribute(self.nodes_active(), 'labels_as_constraints')
+        return self._objects_by_attribute(self.nodes_active(), "labels_as_constraints")
 
     #
     # operations
@@ -239,7 +253,12 @@ class DockerSwarmInterface(DockerInterface):
             cleaned_service_ids.extend(self.service_rm([x.id for x in completed_services]))
         terminal_services = list(self.services_terminal())
         for service in terminal_services:
-            log.warning('cleaned service in abnormal terminal state: %s (%s). state: %s', service.name, service.id, service.state)
+            log.warning(
+                "cleaned service in abnormal terminal state: %s (%s). state: %s",
+                service.name,
+                service.id,
+                service.state,
+            )
         if terminal_services:
             cleaned_service_ids.extend(self.service_rm([x.id for x in terminal_services]))
         return filter(lambda x: x.id in cleaned_service_ids, completed_services + terminal_services)
@@ -247,23 +266,23 @@ class DockerSwarmInterface(DockerInterface):
 
 class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
 
-    container_type = 'docker_swarm_cli'
+    container_type = "docker_swarm_cli"
     option_map = {
         # `service create` options
-        'constraint': {'flag': '--constraint', 'type': 'list_of_kovtrips'},
-        'replicas': {'flag': '--replicas', 'type': 'string'},
-        'restart_condition': {'flag': '--restart-condition', 'type': 'string'},
-        'environment': {'flag': '--env', 'type': 'list_of_kvpairs'},
-        'name': {'flag': '--name', 'type': 'string'},
-        'publish_port_random': {'flag': '--publish', 'type': 'string'},
-        'cpu_limit': {'flag': '--limit-cpu', 'type': 'string'},
-        'mem_limit': {'flag': '--limit-memory', 'type': 'string'},
-        'cpu_reservation': {'flag': '--reserve-cpu', 'type': 'string'},
-        'mem_reservation': {'flag': '--reserve-memory', 'type': 'string'},
+        "constraint": {"flag": "--constraint", "type": "list_of_kovtrips"},
+        "replicas": {"flag": "--replicas", "type": "string"},
+        "restart_condition": {"flag": "--restart-condition", "type": "string"},
+        "environment": {"flag": "--env", "type": "list_of_kvpairs"},
+        "name": {"flag": "--name", "type": "string"},
+        "publish_port_random": {"flag": "--publish", "type": "string"},
+        "cpu_limit": {"flag": "--limit-cpu", "type": "string"},
+        "mem_limit": {"flag": "--limit-memory", "type": "string"},
+        "cpu_reservation": {"flag": "--reserve-cpu", "type": "string"},
+        "mem_reservation": {"flag": "--reserve-memory", "type": "string"},
         # `service update` options
-        'label_add': {'flag': '--label-add', 'type': 'list_of_kvpairs'},
-        'label_rm': {'flag': '--label-rm', 'type': 'list_of_kvpairs'},
-        'availability': {'flag': '--availability', 'type': 'string'},
+        "label_add": {"flag": "--label-add", "type": "list_of_kvpairs"},
+        "label_rm": {"flag": "--label-rm", "type": "list_of_kvpairs"},
+        "availability": {"flag": "--availability", "type": "string"},
     }
 
     #
@@ -272,8 +291,8 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
 
     def services(self, id=None, name=None):
         for service_dict in self.service_ls(id=id, name=name):
-            service_id = service_dict['ID']
-            service_name = service_dict['NAME']
+            service_id = service_dict["ID"]
+            service_name = service_dict["NAME"]
             if not service_name.startswith(self._name_prefix):
                 continue
             task_list = self.service_ps(service_id)
@@ -281,17 +300,17 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
 
     def service_tasks(self, service):
         for task_dict in self.service_ps(service.id):
-            if task_dict['NAME'].strip().startswith(r'\_'):
-                continue    # historical task
+            if task_dict["NAME"].strip().startswith(r"\_"):
+                continue  # historical task
             yield DockerTask.from_cli(self, task_dict, service=service)
 
     def nodes(self, id=None, name=None):
         for node_dict in self.node_ls(id=id, name=name):
-            node_id = node_dict['ID'].strip(' *')
-            node_name = node_dict['HOSTNAME']
+            node_id = node_dict["ID"].strip(" *")
+            node_name = node_dict["HOSTNAME"]
             if self._node_prefix and not node_name.startswith(self._node_prefix):
                 continue
-            task_list = filter(lambda x: x['NAME'].startswith(self._name_prefix), self.node_ps(node_id))
+            task_list = filter(lambda x: x["NAME"].startswith(self._name_prefix), self.node_ps(node_id))
             yield DockerNode.from_cli(self, node_dict, task_list)
 
     #
@@ -299,62 +318,64 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
     #
 
     def service_create(self, command, image=None, **kwopts):
-        if ('service_create_image_constraint' in self._conf or 'service_create_cpus_constraint' in self._conf) and 'constraint' not in kwopts:
-            kwopts['constraint'] = []
+        if (
+            "service_create_image_constraint" in self._conf or "service_create_cpus_constraint" in self._conf
+        ) and "constraint" not in kwopts:
+            kwopts["constraint"] = []
         image = self._get_image(image)
         if self._conf.service_create_image_constraint:
-            kwopts['constraint'].append((IMAGE_CONSTRAINT, '==', image))
+            kwopts["constraint"].append((IMAGE_CONSTRAINT, "==", image))
         if self._conf.service_create_cpus_constraint:
-            cpus = kwopts.get('reserve_cpus', kwopts.get('limit_cpus', '1'))
-            kwopts['constraint'].append((CPUS_CONSTRAINT, '==', cpus))
+            cpus = kwopts.get("reserve_cpus", kwopts.get("limit_cpus", "1"))
+            kwopts["constraint"].append((CPUS_CONSTRAINT, "==", cpus))
         if self._conf.cpus:
-            kwopts['cpu_limit'] = self._conf.cpus
-            kwopts['cpu_reservation'] = self._conf.cpus
+            kwopts["cpu_limit"] = self._conf.cpus
+            kwopts["cpu_reservation"] = self._conf.cpus
         if self._conf.memory:
-            kwopts['mem_limit'] = self._conf.memory
-            kwopts['mem_reservation'] = self._conf.memory
+            kwopts["mem_limit"] = self._conf.memory
+            kwopts["mem_reservation"] = self._conf.memory
         self.set_kwopts_name(kwopts)
-        args = '{kwopts} {image} {command}'.format(
+        args = "{kwopts} {image} {command}".format(
             kwopts=self._stringify_kwopts(kwopts),
-            image=image if image else '',
-            command=command if command else '',
+            image=image if image else "",
+            command=command if command else "",
         ).strip()
-        service_id = self._run_docker(subcommand='service create', args=args, verbose=True)
+        service_id = self._run_docker(subcommand="service create", args=args, verbose=True)
         return DockerService.from_id(self, service_id)
 
     @docker_json
     def service_inspect(self, service_id):
-        return self._run_docker(subcommand='service inspect', args=service_id)[0]
+        return self._run_docker(subcommand="service inspect", args=service_id)[0]
 
     @docker_columns
     def service_ls(self, id=None, name=None):
-        return self._run_docker(subcommand='service ls', args=self._filter_by_id_or_name(id, name))
+        return self._run_docker(subcommand="service ls", args=self._filter_by_id_or_name(id, name))
 
     @docker_columns
     def service_ps(self, service_id):
-        return self._run_docker(subcommand='service ps', args=f'--no-trunc {service_id}')
+        return self._run_docker(subcommand="service ps", args=f"--no-trunc {service_id}")
 
     def service_rm(self, service_ids):
-        service_ids = ' '.join(service_ids)
-        return self._run_docker(subcommand='service rm', args=service_ids).splitlines()
+        service_ids = " ".join(service_ids)
+        return self._run_docker(subcommand="service rm", args=service_ids).splitlines()
 
     @docker_json
     def node_inspect(self, node_id):
-        return self._run_docker(subcommand='node inspect', args=node_id)[0]
+        return self._run_docker(subcommand="node inspect", args=node_id)[0]
 
     @docker_columns
     def node_ls(self, id=None, name=None):
-        return self._run_docker(subcommand='node ls', args=self._filter_by_id_or_name(id, name))
+        return self._run_docker(subcommand="node ls", args=self._filter_by_id_or_name(id, name))
 
     @docker_columns
     def node_ps(self, node_id):
-        return self._run_docker(subcommand='node ps', args=f'--no-trunc {node_id}')
+        return self._run_docker(subcommand="node ps", args=f"--no-trunc {node_id}")
 
     def node_update(self, node_id, **kwopts):
-        return self._run_docker(subcommand='node update', args='{kwopts} {node_id}'.format(
-            kwopts=self._stringify_kwopts(kwopts),
-            node_id=node_id
-        ))
+        return self._run_docker(
+            subcommand="node update",
+            args="{kwopts} {node_id}".format(kwopts=self._stringify_kwopts(kwopts), node_id=node_id),
+        )
 
     @docker_json
     def task_inspect(self, task_id):
@@ -363,51 +384,51 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
 
 class DockerSwarmAPIInterface(DockerSwarmInterface, DockerAPIInterface):
 
-    container_type = 'docker_swarm'
+    container_type = "docker_swarm"
     placement_option_map = {
-        'constraint': {'param': 'constraints'},
+        "constraint": {"param": "constraints"},
     }
     service_mode_option_map = {
-        'service_mode': {'param': 0, 'default': 'replicated'},
-        'replicas': {'default': 1},
+        "service_mode": {"param": 0, "default": "replicated"},
+        "replicas": {"default": 1},
     }
     endpoint_spec_option_map: Dict[str, Dict] = {
-        'ports': {},
+        "ports": {},
     }
     resources_option_map = {
-        'cpus': {'params': ('cpu_limit', 'cpu_reservation'), 'map': lambda x: int(x * 1000000000)},
-        'memory': {'params': ('mem_limit', 'mem_reservation')},
+        "cpus": {"params": ("cpu_limit", "cpu_reservation"), "map": lambda x: int(x * 1000000000)},
+        "memory": {"params": ("mem_limit", "mem_reservation")},
     }
     container_spec_option_map = {
-        'image': {'param': 0},
-        'command': {},
-        'environment': {'param': 'env'},
-        'labels': {},
+        "image": {"param": 0},
+        "command": {},
+        "environment": {"param": "env"},
+        "labels": {},
     }
     restart_policy_option_map = {
-        'restart_condition': {'param': 'condition', 'default': 'none'},
-        'restart_delay': {'param': 'delay'},
-        'restart_max_attempts': {'param': 'max_attemps'},
+        "restart_condition": {"param": "condition", "default": "none"},
+        "restart_delay": {"param": "delay"},
+        "restart_max_attempts": {"param": "max_attemps"},
     }
     task_template_option_map = {
-        '_container_spec': {'spec_class': docker.types.ContainerSpec, 'required': True},
-        '_resources': {'spec_class': docker.types.Resources},
-        '_restart_policy': {'spec_class': docker.types.RestartPolicy},
-        '_placement': {'spec_class': docker.types.Placement},
+        "_container_spec": {"spec_class": docker.types.ContainerSpec, "required": True},
+        "_resources": {"spec_class": docker.types.Resources},
+        "_restart_policy": {"spec_class": docker.types.RestartPolicy},
+        "_placement": {"spec_class": docker.types.Placement},
     }
     node_spec_option_map = {
-        'availability': {'param': 'Availability'},
-        'name': {'param': 'Name'},
-        'role': {'param': 'Role'},
-        'labels': {'param': 'Labels'},
+        "availability": {"param": "Availability"},
+        "name": {"param": "Name"},
+        "role": {"param": "Role"},
+        "labels": {"param": "Labels"},
     }
 
     @staticmethod
     def create_random_port_spec(port):
         return {
-            'Protocol': 'tcp',
-            'PublishedPort': None,
-            'TargetPort': port,
+            "Protocol": "tcp",
+            "PublishedPort": None,
+            "TargetPort": port,
         }
 
     #
@@ -422,27 +443,27 @@ class DockerSwarmAPIInterface(DockerSwarmInterface, DockerAPIInterface):
             if self._conf[opt]:
                 kwopts[opt] = self._conf[opt]
         # image is part of the container spec
-        kwopts['image'] = self._get_image(image)
+        kwopts["image"] = self._get_image(image)
         # service constraints
-        kwopts['constraint'] = kwopts.get('constraint', [])
+        kwopts["constraint"] = kwopts.get("constraint", [])
         if self._conf.service_create_image_constraint:
-            kwopts['constraint'].append(f"{IMAGE_CONSTRAINT}=={image}")
+            kwopts["constraint"].append(f"{IMAGE_CONSTRAINT}=={image}")
         if self._conf.service_create_cpus_constraint:
-            cpus = kwopts.get('reserve_cpus', kwopts.get('limit_cpus', '1'))
-            kwopts['constraint'].append(f"{CPUS_CONSTRAINT}=={cpus}")
+            cpus = kwopts.get("reserve_cpus", kwopts.get("limit_cpus", "1"))
+            kwopts["constraint"].append(f"{CPUS_CONSTRAINT}=={cpus}")
         # ports
-        if 'publish_port_random' in kwopts:
-            kwopts['ports'] = [DockerSwarmAPIInterface.create_random_port_spec(kwopts.pop('publish_port_random'))]
+        if "publish_port_random" in kwopts:
+            kwopts["ports"] = [DockerSwarmAPIInterface.create_random_port_spec(kwopts.pop("publish_port_random"))]
         # create specs
-        service_mode = self._create_docker_api_spec('service_mode', docker.types.ServiceMode, kwopts)
-        endpoint_spec = self._create_docker_api_spec('endpoint_spec', docker.types.EndpointSpec, kwopts)
-        task_template = self._create_docker_api_spec('task_template', docker.types.TaskTemplate, kwopts)
+        service_mode = self._create_docker_api_spec("service_mode", docker.types.ServiceMode, kwopts)
+        endpoint_spec = self._create_docker_api_spec("endpoint_spec", docker.types.EndpointSpec, kwopts)
+        task_template = self._create_docker_api_spec("task_template", docker.types.TaskTemplate, kwopts)
         self.set_kwopts_name(kwopts)
         log.debug("Docker service task template:\n%s", safe_dumps_formatted(task_template))
         log.debug("Docker service endpoint specification:\n%s", safe_dumps_formatted(endpoint_spec))
         log.debug("Docker service mode:\n%s", safe_dumps_formatted(service_mode))
         log.debug("Docker service creation parameters:\n%s", safe_dumps_formatted(kwopts))
-        success_test = partial(self._first, self.service_ls, name=kwopts['name'])
+        success_test = partial(self._first, self.service_ls, name=kwopts["name"])
         # this can raise exceptions, if necessary we could wrap them in a more generic "creation failed" exception class
         service = self._client.create_service(
             task_template,
@@ -450,9 +471,10 @@ class DockerSwarmAPIInterface(DockerSwarmInterface, DockerAPIInterface):
             endpoint_spec=endpoint_spec,
             success_test=success_test,
             max_tries=5,
-            **kwopts)
-        service_id = service.get('ID')
-        log.debug('Created service: %s (%s)', kwopts['name'], service_id)
+            **kwopts,
+        )
+        service_id = service.get("ID")
+        log.debug("Created service: %s (%s)", kwopts["name"], service_id)
         return DockerService.from_id(self, service_id)
 
     def service_inspect(self, service_id):
@@ -463,7 +485,7 @@ class DockerSwarmAPIInterface(DockerSwarmInterface, DockerAPIInterface):
 
     # roughly `docker service ps`
     def service_ps(self, service_id):
-        return self.task_ls(filters={'service': service_id})
+        return self.task_ls(filters={"service": service_id})
 
     def service_rm(self, service_ids):
         r = []
@@ -480,15 +502,15 @@ class DockerSwarmAPIInterface(DockerSwarmInterface, DockerAPIInterface):
 
     # roughly `docker node ps`
     def node_ps(self, node_id):
-        return self.task_ls(filters={'node': node_id})
+        return self.task_ls(filters={"node": node_id})
 
     def node_update(self, node_id, **kwopts):
         node = DockerNode.from_id(self, node_id)
-        spec = node.inspect['Spec']
-        if 'label_add' in kwopts:
-            kwopts['labels'] = spec.get('Labels', {})
-            kwopts['labels'].update(kwopts.pop('label_add'))
-        spec.update(self._create_docker_api_spec('node_spec', dict, kwopts))
+        spec = node.inspect["Spec"]
+        if "label_add" in kwopts:
+            kwopts["labels"] = spec.get("Labels", {})
+            kwopts["labels"].update(kwopts.pop("label_add"))
+        spec.update(self._create_docker_api_spec("node_spec", dict, kwopts))
         return self._client.update_node(node.id, node.version, node_spec=spec)
 
     def task_inspect(self, task_id):
diff --git a/lib/galaxy/datatypes/_schema.py b/lib/galaxy/datatypes/_schema.py
index 6efb7cc4565..50c1774b614 100644
--- a/lib/galaxy/datatypes/_schema.py
+++ b/lib/galaxy/datatypes/_schema.py
@@ -7,44 +7,23 @@ from typing import (
 from pydantic import (
     BaseModel,
     Field,
-    HttpUrl
+    HttpUrl,
 )
 
 
 class CompositeFileInfo(BaseModel):
-    name: str = Field(
-        ...,  # Mark this field as required
-        title="Name",
-        description="The name of this composite file"
-    )
-    optional: bool = Field(
-        title="Optional",
-        description=""  # TODO add description
-    )
-    mimetype: Optional[str] = Field(
-        title="MIME type",
-        description="The MIME type of this file"
-    )
+    name: str = Field(..., title="Name", description="The name of this composite file")  # Mark this field as required
+    optional: bool = Field(title="Optional", description="")  # TODO add description
+    mimetype: Optional[str] = Field(title="MIME type", description="The MIME type of this file")
     description: Optional[str] = Field(
-        title="Description",
-        description="Summary description of the purpouse of this file"
+        title="Description", description="Summary description of the purpouse of this file"
     )
     substitute_name_with_metadata: Optional[str] = Field(
-        title="Substitute name with metadata",
-        description=""  # TODO add description
-    )
-    is_binary: bool = Field(
-        title="Is binary",
-        description="Whether this file is a binary file"
-    )
-    to_posix_lines: bool = Field(
-        title="To posix lines",
-        description=""  # TODO add description
-    )
-    space_to_tab: bool = Field(
-        title="Spaces to tabulation",
-        description=""  # TODO add description
+        title="Substitute name with metadata", description=""  # TODO add description
     )
+    is_binary: bool = Field(title="Is binary", description="Whether this file is a binary file")
+    to_posix_lines: bool = Field(title="To posix lines", description="")  # TODO add description
+    space_to_tab: bool = Field(title="Spaces to tabulation", description="")  # TODO add description
 
 
 class DatatypeDetails(BaseModel):
@@ -52,26 +31,21 @@ class DatatypeDetails(BaseModel):
         ...,  # Mark this field as required
         title="Extension",
         description="The data type’s Dataset file extension",
-        example="bed"
-    )
-    description: Optional[str] = Field(
-        title="Description",
-        description="A summary description for this data type"
+        example="bed",
     )
+    description: Optional[str] = Field(title="Description", description="A summary description for this data type")
     description_url: Optional[HttpUrl] = Field(
         title="Description URL",
         description="The URL to a detailed description for this datatype",
-        example="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"
+        example="https://wiki.galaxyproject.org/Learn/Datatypes#Bed",
     )
     display_in_upload: bool = Field(
         default=False,
         title="Display in upload",
-        description="If True, the associated file extension will be displayed in the `File Format` select list in the `Upload File from your computer` tool in the `Get Data` tool section of the tool panel"
+        description="If True, the associated file extension will be displayed in the `File Format` select list in the `Upload File from your computer` tool in the `Get Data` tool section of the tool panel",
     )
     composite_files: Optional[List[CompositeFileInfo]] = Field(
-        default=None,
-        title="Composite files",
-        description="A collection of files composing this data type"
+        default=None, title="Composite files", description="A collection of files composing this data type"
     )
 
 
@@ -123,7 +97,4 @@ class DatatypeConverter(BaseModel):
 
 
 class DatatypeConverterList(BaseModel):
-    __root__: List[DatatypeConverter] = Field(
-        title='List of data type converters',
-        default=[]
-    )
+    __root__: List[DatatypeConverter] = Field(title="List of data type converters", default=[])
diff --git a/lib/galaxy/datatypes/annotation.py b/lib/galaxy/datatypes/annotation.py
index 8d2e70d87b3..b8eb217bc66 100644
--- a/lib/galaxy/datatypes/annotation.py
+++ b/lib/galaxy/datatypes/annotation.py
@@ -2,7 +2,10 @@ import logging
 import tarfile
 
 from galaxy.datatypes.binary import CompressedArchive
-from galaxy.datatypes.data import get_file_peek, Text
+from galaxy.datatypes.data import (
+    get_file_peek,
+    Text,
+)
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
@@ -22,8 +25,8 @@ class SnapHmm(Text):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "SNAP HMM model"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def display_peek(self, dataset):
         try:
@@ -35,13 +38,14 @@ class SnapHmm(Text):
         """
         SNAP model files start with zoeHMM
         """
-        return file_prefix.startswith('zoeHMM')
+        return file_prefix.startswith("zoeHMM")
 
 
 class Augustus(CompressedArchive):
     """
-        Class describing an Augustus prediction model
+    Class describing an Augustus prediction model
     """
+
     file_ext = "augustus"
     edam_data = "data_0950"
     compressed = True
@@ -51,8 +55,8 @@ class Augustus(CompressedArchive):
             dataset.peek = "Augustus model"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -65,19 +69,21 @@ class Augustus(CompressedArchive):
         Augustus archives always contain the same files
         """
         if filename and tarfile.is_tarfile(filename):
-            with tarfile.open(filename, 'r') as temptar:
+            with tarfile.open(filename, "r") as temptar:
                 for f in temptar:
                     if not f.isfile():
                         continue
-                    if f.name.endswith('_exon_probs.pbl') \
-                            or f.name.endswith('_igenic_probs.pbl') \
-                            or f.name.endswith('_intron_probs.pbl') \
-                            or f.name.endswith('_metapars.cfg') \
-                            or f.name.endswith('_metapars.utr.cfg') \
-                            or f.name.endswith('_parameters.cfg') \
-                            or f.name.endswith('_parameters.cgp.cfg') \
-                            or f.name.endswith('_utr_probs.pbl') \
-                            or f.name.endswith('_weightmatrix.txt'):
+                    if (
+                        f.name.endswith("_exon_probs.pbl")
+                        or f.name.endswith("_igenic_probs.pbl")
+                        or f.name.endswith("_intron_probs.pbl")
+                        or f.name.endswith("_metapars.cfg")
+                        or f.name.endswith("_metapars.utr.cfg")
+                        or f.name.endswith("_parameters.cfg")
+                        or f.name.endswith("_parameters.cgp.cfg")
+                        or f.name.endswith("_utr_probs.pbl")
+                        or f.name.endswith("_weightmatrix.txt")
+                    ):
                         return True
                     else:
                         return False
diff --git a/lib/galaxy/datatypes/anvio.py b/lib/galaxy/datatypes/anvio.py
index 9e0d9828b57..51c8f9eecd7 100644
--- a/lib/galaxy/datatypes/anvio.py
+++ b/lib/galaxy/datatypes/anvio.py
@@ -19,8 +19,9 @@ class AnvioComposite(Html):
     Base class to use for Anvi'o composite datatypes.
     Generally consist of a sqlite database, plus optional additional files
     """
+
     file_ext = "anvio_composite"
-    composite_type = 'auto_primary_file'
+    composite_type = "auto_primary_file"
 
     def generate_primary_file(self, dataset=None):
         """
@@ -32,12 +33,12 @@ class AnvioComposite(Html):
         if defined_files:
             rval.append("<p/>This composite dataset is composed of the following defined files:<p/><ul>")
             for composite_name, composite_file in defined_files:
-                opt_text = ''
+                opt_text = ""
                 if composite_file.optional:
-                    opt_text = ' (optional)'
-                missing_text = ''
+                    opt_text = " (optional)"
+                missing_text = ""
                 if not os.path.exists(os.path.join(dataset.extra_files_path, composite_name)):
-                    missing_text = ' (missing)'
+                    missing_text = " (missing)"
                 rval.append(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}{missing_text}</li>')
             rval.append("</ul>")
         defined_files = map(lambda x: x[0], defined_files)
@@ -51,24 +52,24 @@ class AnvioComposite(Html):
             rval.append("<p/>This composite dataset contains these undefined files:<p/><ul>")
             for rel_path in extra_files:
                 rval.append(f'<li><a href="{rel_path}">{rel_path}</a></li>')
-            rval.append('</ul>')
+            rval.append("</ul>")
         if not (defined_files or extra_files):
             rval.append("<p/>This composite dataset does not contain any files!<p/><ul>")
-        rval.append('</html>')
+        rval.append("</html>")
         return "\n".join(rval)
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/html'
+        return "text/html"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
-            dataset.peek = 'Anvio database (multiple files)'
-            dataset.blurb = 'Anvio database (multiple files)'
+            dataset.peek = "Anvio database (multiple files)"
+            dataset.blurb = "Anvio database (multiple files)"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Create HTML content, used for displaying peek."""
@@ -80,9 +81,10 @@ class AnvioComposite(Html):
 
 class AnvioDB(AnvioComposite):
     """Class for AnvioDB database files."""
+
     _anvio_basename: Optional[str] = None
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_db'
+    file_ext = "anvio_db"
 
     def __init__(self, *args, **kwd):
         super().__init__(*args, **kwd)
@@ -94,7 +96,9 @@ class AnvioDB(AnvioComposite):
         Set the anvio_basename based upon actual extra_files_path contents.
         """
         super().set_meta(dataset, **kwd)
-        if dataset.metadata.anvio_basename is not None and os.path.exists(os.path.join(dataset.extra_files_path, dataset.metadata.anvio_basename)):
+        if dataset.metadata.anvio_basename is not None and os.path.exists(
+            os.path.join(dataset.extra_files_path, dataset.metadata.anvio_basename)
+        ):
             return
         found = False
         for basename in [dataset.metadata.anvio_basename, self._anvio_basename]:
@@ -109,57 +113,64 @@ class AnvioDB(AnvioComposite):
 
 class AnvioStructureDB(AnvioDB):
     """Class for Anvio Structure DB database files."""
-    _anvio_basename = 'STRUCTURE.db'
+
+    _anvio_basename = "STRUCTURE.db"
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_structure_db'
+    file_ext = "anvio_structure_db"
 
 
 class AnvioGenomesDB(AnvioDB):
     """Class for Anvio Genomes DB database files."""
-    _anvio_basename = '-GENOMES.db'
+
+    _anvio_basename = "-GENOMES.db"
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_genomes_db'
+    file_ext = "anvio_genomes_db"
 
 
 class AnvioContigsDB(AnvioDB):
     """Class for Anvio Contigs DB database files."""
-    _anvio_basename = 'CONTIGS.db'
+
+    _anvio_basename = "CONTIGS.db"
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_contigs_db'
+    file_ext = "anvio_contigs_db"
 
     def __init__(self, *args, **kwd):
         super().__init__(*args, **kwd)
-        self.add_composite_file('CONTIGS.h5', is_binary=True, optional=True)
+        self.add_composite_file("CONTIGS.h5", is_binary=True, optional=True)
 
 
 class AnvioProfileDB(AnvioDB):
     """Class for Anvio Profile DB database files."""
-    _anvio_basename = 'PROFILE.db'
+
+    _anvio_basename = "PROFILE.db"
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_profile_db'
+    file_ext = "anvio_profile_db"
 
     def __init__(self, *args, **kwd):
         super().__init__(*args, **kwd)
-        self.add_composite_file('RUNINFO.cp', is_binary=True, optional=True)
-        self.add_composite_file('RUNINFO.mcp', is_binary=True, optional=True)
-        self.add_composite_file('AUXILIARY_DATA.db', is_binary=True, optional=True)
-        self.add_composite_file('RUNLOG.txt', is_binary=False, optional=True)
+        self.add_composite_file("RUNINFO.cp", is_binary=True, optional=True)
+        self.add_composite_file("RUNINFO.mcp", is_binary=True, optional=True)
+        self.add_composite_file("AUXILIARY_DATA.db", is_binary=True, optional=True)
+        self.add_composite_file("RUNLOG.txt", is_binary=False, optional=True)
 
 
 class AnvioPanDB(AnvioDB):
     """Class for Anvio Pan DB database files."""
-    _anvio_basename = 'PAN.db'
+
+    _anvio_basename = "PAN.db"
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_pan_db'
+    file_ext = "anvio_pan_db"
 
 
 class AnvioSamplesDB(AnvioDB):
     """Class for Anvio Samples DB database files."""
-    _anvio_basename = 'SAMPLES.db'
+
+    _anvio_basename = "SAMPLES.db"
     MetadataElement(name="anvio_basename", default=_anvio_basename, desc="Basename", readonly=True)
-    file_ext = 'anvio_samples_db'
+    file_ext = "anvio_samples_db"
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/assembly.py b/lib/galaxy/datatypes/assembly.py
index 46b108942a2..c3855350ecf 100644
--- a/lib/galaxy/datatypes/assembly.py
+++ b/lib/galaxy/datatypes/assembly.py
@@ -9,8 +9,10 @@ import os
 import re
 import sys
 
-from galaxy.datatypes import data
-from galaxy.datatypes import sequence
+from galaxy.datatypes import (
+    data,
+    sequence,
+)
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
@@ -23,10 +25,11 @@ log = logging.getLogger(__name__)
 
 @build_sniff_from_prefix
 class Amos(data.Text):
-    """Class describing the AMOS assembly file """
+    """Class describing the AMOS assembly file"""
+
     edam_data = "data_0925"
     edam_format = "format_3582"
-    file_ext = 'afg'
+    file_ext = "afg"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -57,17 +60,18 @@ class Amos(data.Text):
                 break  # EOF
             line = line.strip()
             if line:  # first non-empty line
-                if line.startswith('{'):
-                    if re.match(r'{(RED|CTG|TLE)$', line):
+                if line.startswith("{"):
+                    if re.match(r"{(RED|CTG|TLE)$", line):
                         return True
         return False
 
 
 @build_sniff_from_prefix
 class Sequences(sequence.Fasta):
-    """Class describing the Sequences file generated by velveth """
+    """Class describing the Sequences file generated by velveth"""
+
     edam_data = "data_0925"
-    file_ext = 'sequences'
+    file_ext = "sequences"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -83,12 +87,12 @@ class Sequences(sequence.Fasta):
         for line in fh:
             line = line.strip()
             if line:  # first non-empty line
-                if line.startswith('>'):
-                    if not re.match(r'>[^\t]+\t\d+\t\d+$', line):
+                if line.startswith(">"):
+                    if not re.match(r">[^\t]+\t\d+\t\d+$", line):
                         return False
                     # The next line.strip() must not be '', nor startwith '>'
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         return False
                     return True
                 else:
@@ -98,9 +102,10 @@ class Sequences(sequence.Fasta):
 
 @build_sniff_from_prefix
 class Roadmaps(data.Text):
-    """Class describing the Sequences file generated by velveth """
+    """Class describing the Sequences file generated by velveth"""
+
     edam_format = "format_2561"
-    file_ext = 'roadmaps'
+    file_ext = "roadmaps"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -115,45 +120,72 @@ class Roadmaps(data.Text):
         for line in fh:
             line = line.strip()
             if line:  # first non-empty line
-                if not re.match(r'\d+\t\d+\t\d+$', line):
+                if not re.match(r"\d+\t\d+\t\d+$", line):
                     return False
                 # The next line.strip() should be 'ROADMAP 1'
                 line = fh.readline().strip()
-                return bool(re.match(r'ROADMAP \d+$', line))
+                return bool(re.match(r"ROADMAP \d+$", line))
             else:
                 return False  # we found a non-empty line, but it's not a fasta header
         return False
 
 
 class Velvet(Html):
-    MetadataElement(name="base_name", desc="base name for velveth dataset", default="velvet", readonly=True, set_in_upload=True)
-    MetadataElement(name="paired_end_reads", desc="has paired-end reads", default="False", readonly=False, set_in_upload=True)
+    MetadataElement(
+        name="base_name", desc="base name for velveth dataset", default="velvet", readonly=True, set_in_upload=True
+    )
+    MetadataElement(
+        name="paired_end_reads", desc="has paired-end reads", default="False", readonly=False, set_in_upload=True
+    )
     MetadataElement(name="long_reads", desc="has long reads", default="False", readonly=False, set_in_upload=True)
-    MetadataElement(name="short2_reads", desc="has 2nd short reads", default="False", readonly=False, set_in_upload=True)
-    composite_type = 'auto_primary_file'
-    file_ext = 'velvet'
+    MetadataElement(
+        name="short2_reads", desc="has 2nd short reads", default="False", readonly=False, set_in_upload=True
+    )
+    composite_type = "auto_primary_file"
+    file_ext = "velvet"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False)
-        self.add_composite_file('Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False)
-        self.add_composite_file('Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False)
+        self.add_composite_file(
+            "Sequences",
+            mimetype="text/html",
+            description="Sequences",
+            substitute_name_with_metadata=None,
+            is_binary=False,
+        )
+        self.add_composite_file(
+            "Roadmaps",
+            mimetype="text/html",
+            description="Roadmaps",
+            substitute_name_with_metadata=None,
+            is_binary=False,
+        )
+        self.add_composite_file(
+            "Log",
+            mimetype="text/html",
+            description="Log",
+            optional="True",
+            substitute_name_with_metadata=None,
+            is_binary=False,
+        )
 
     def generate_primary_file(self, dataset=None):
         log.debug(f"Velvet log info  JJ generate_primary_file {dataset}")
-        rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
             log.debug(f"Velvet log info  JJ generate_primary_file {fn} {composite_file}")
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                opt_text = " (optional)"
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
 
     def regenerate_primary_file(self, dataset):
@@ -161,21 +193,21 @@ class Velvet(Html):
         cannot do this until we are setting metadata
         """
         log.debug(f"Velvet log info  {'JJ regenerate_primary_file'}")
-        gen_msg = ''
+        gen_msg = ""
         try:
             efp = dataset.extra_files_path
-            log_path = os.path.join(efp, 'Log')
+            log_path = os.path.join(efp, "Log")
             with open(log_path) as f:
                 log_content = f.read(1000)
-            log_msg = re.sub(r'/\S*/', '', log_content)
+            log_msg = re.sub(r"/\S*/", "", log_content)
             log.debug(f"Velveth log info  {log_msg}")
-            paired_end_reads = re.search(r'-(short|long)Paired', log_msg) is not None
+            paired_end_reads = re.search(r"-(short|long)Paired", log_msg) is not None
             dataset.metadata.paired_end_reads = paired_end_reads
-            long_reads = re.search(r'-long', log_msg) is not None
+            long_reads = re.search(r"-long", log_msg) is not None
             dataset.metadata.long_reads = long_reads
-            short2_reads = re.search(r'-short(Paired)?2', log_msg) is not None
+            short2_reads = re.search(r"-short(Paired)?2", log_msg) is not None
             dataset.metadata.short2_reads = short2_reads
-            dataset.info = re.sub(r'.*velveth \S+', 'hash_length', re.sub(r'\n', ' ', log_msg))
+            dataset.info = re.sub(r".*velveth \S+", "hash_length", re.sub(r"\n", " ", log_msg))
             if paired_end_reads:
                 gen_msg = f"{gen_msg} Paired-End Reads"
             if long_reads:
@@ -185,31 +217,34 @@ class Velvet(Html):
         except Exception:
             log.debug(f"Velveth could not read Log file in {efp}")
         log.debug(f"Velveth log info  {gen_msg}")
-        rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
+        rval = ["<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>"]
         # rval.append('<div>Generated:<p/><code> %s </code></div>' %(re.sub('\n','<br>',log_msg)))
-        rval.append(f'<div>Generated:<p/> {gen_msg} </div>')
-        rval.append('<div>Velveth dataset:<p/><ul>')
+        rval.append(f"<div>Generated:<p/> {gen_msg} </div>")
+        rval.append("<div>Velveth dataset:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
             log.debug(f"Velvet log info  JJ regenerate_primary_file {fn} {composite_file}")
-            if re.search('Log', fn) is None:
-                opt_text = ''
+            if re.search("Log", fn) is None:
+                opt_text = ""
                 if composite_file.optional:
-                    opt_text = ' (optional)'
-                if composite_file.get('description'):
-                    rval.append(f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                    opt_text = " (optional)"
+                if composite_file.get("description"):
+                    rval.append(
+                        f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                    )
                 else:
                     rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
-        with open(dataset.file_name, 'w') as f:
+        rval.append("</ul></div></html>")
+        with open(dataset.file_name, "w") as f:
             f.write("\n".join(rval))
-            f.write('\n')
+            f.write("\n")
 
     def set_meta(self, dataset, **kwd):
         Html.set_meta(self, dataset, **kwd)
         self.regenerate_primary_file(dataset)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 908ad8999f6..0c7b410128a 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -20,7 +20,10 @@ import h5py
 import numpy as np
 import pysam
 import pysam.bcftools
-from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP
+from bx.seq.twobit import (
+    TWOBIT_MAGIC_NUMBER,
+    TWOBIT_MAGIC_NUMBER_SWAP,
+)
 
 from galaxy import util
 from galaxy.datatypes import metadata
@@ -36,11 +39,24 @@ from galaxy.datatypes.metadata import (
     MetadataElement,
     MetadataParameter,
 )
-from galaxy.datatypes.sniff import build_sniff_from_prefix, FilePrefix
+from galaxy.datatypes.sniff import (
+    build_sniff_from_prefix,
+    FilePrefix,
+)
 from galaxy.datatypes.text import Html
-from galaxy.util import compression_utils, nice_size, sqlite
-from galaxy.util.checkers import is_bz2, is_gzip
-from . import data, dataproviders
+from galaxy.util import (
+    compression_utils,
+    nice_size,
+    sqlite,
+)
+from galaxy.util.checkers import (
+    is_bz2,
+    is_gzip,
+)
+from . import (
+    data,
+    dataproviders,
+)
 
 log = logging.getLogger(__name__)
 # pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
@@ -52,6 +68,7 @@ pysam.set_verbosity(0)
 
 class Binary(data.Data):
     """Binary data"""
+
     edam_format = "format_2333"
     file_ext = "binary"
 
@@ -66,19 +83,20 @@ class Binary(data.Data):
     def set_peek(self, dataset, **kwd):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
-            dataset.peek = 'binary data'
+            dataset.peek = "binary data"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/octet-stream'
+        return "application/octet-stream"
 
 
 class Ab1(Binary):
     """Class describing an ab1 binary sequence file"""
+
     file_ext = "ab1"
     edam_format = "format_3000"
     edam_data = "data_0924"
@@ -88,8 +106,8 @@ class Ab1(Binary):
             dataset.peek = "Binary ab1 sequence file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -100,14 +118,15 @@ class Ab1(Binary):
 
 class Idat(Binary):
     """Binary data in idat format"""
+
     file_ext = "idat"
     edam_format = "format_2058"
     edam_data = "data_2603"
 
     def sniff(self, filename):
         try:
-            header = open(filename, 'rb').read(4)
-            if header == b'IDAT':
+            header = open(filename, "rb").read(4)
+            if header == b"IDAT":
                 return True
             return False
         except Exception:
@@ -115,15 +134,16 @@ class Idat(Binary):
 
 
 class Cel(Binary):
-    """ Cel File format described at:
-            http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html
+    """Cel File format described at:
+    http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html
     """
 
     file_ext = "cel"
     edam_format = "format_1638"
     edam_data = "data_3110"
-    MetadataElement(name="version", default="3", desc="Version", readonly=True, visible=True,
-                    optional=True, no_value="3")
+    MetadataElement(
+        name="version", default="3", desc="Version", readonly=True, visible=True, optional=True, no_value="3"
+    )
 
     def sniff(self, filename):
         """
@@ -142,7 +162,7 @@ class Cel(Binary):
         >>> Cel().sniff(fname)
         False
         """
-        with open(filename, 'rb') as handle:
+        with open(filename, "rb") as handle:
             header_bytes = handle.read(8)
         found_cel_4 = False
         found_cel_3 = False
@@ -151,7 +171,7 @@ class Cel(Binary):
             found_cel_4 = True
         elif struct.unpack(">bb", header_bytes[:2]) == (59, 1):
             found_cel_agcc = True
-        elif header_bytes.decode("utf8", errors="ignore").startswith('[CEL]'):
+        elif header_bytes.decode("utf8", errors="ignore").startswith("[CEL]"):
             found_cel_3 = True
         return found_cel_3 or found_cel_4 or found_cel_agcc
 
@@ -159,13 +179,13 @@ class Cel(Binary):
         """
         Set metadata for Cel file.
         """
-        with open(dataset.file_name, 'rb') as handle:
+        with open(dataset.file_name, "rb") as handle:
             header_bytes = handle.read(8)
         if struct.unpack("<ii", header_bytes[:9]) == (64, 4):
             dataset.metadata.version = "4"
         elif struct.unpack(">bb", header_bytes[:2]) == (59, 1):
             dataset.metadata.version = "agcc"
-        elif header_bytes.decode("utf8", errors="ignore").startswith('[CEL]'):
+        elif header_bytes.decode("utf8", errors="ignore").startswith("[CEL]"):
             dataset.metadata.version = "3"
 
     def set_peek(self, dataset):
@@ -173,27 +193,29 @@ class Cel(Binary):
             dataset.blurb = f"Cel version: {dataset.metadata.version}"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class MashSketch(Binary):
     """
-        Mash Sketch file.
-        Sketches are used by the MinHash algorithm to allow fast distance estimations
-        with low storage and memory requirements. To make a sketch, each k-mer in a sequence
-        is hashed, which creates a pseudo-random identifier. By sorting these identifiers (hashes),
-        a small subset from the top of the sorted list can represent the entire sequence (these are min-hashes).
-        The more similar another sequence is, the more min-hashes it is likely to share.
+    Mash Sketch file.
+    Sketches are used by the MinHash algorithm to allow fast distance estimations
+    with low storage and memory requirements. To make a sketch, each k-mer in a sequence
+    is hashed, which creates a pseudo-random identifier. By sorting these identifiers (hashes),
+    a small subset from the top of the sorted list can represent the entire sequence (these are min-hashes).
+    The more similar another sequence is, the more min-hashes it is likely to share.
     """
+
     file_ext = "msh"
 
 
 class CompressedArchive(Binary):
     """
-        Class describing an compressed binary file
-        This class can be sublass'ed to implement archive filetypes that will not be unpacked by upload.py.
+    Class describing an compressed binary file
+    This class can be sublass'ed to implement archive filetypes that will not be unpacked by upload.py.
     """
+
     file_ext = "compressed_archive"
     compressed = True
 
@@ -202,8 +224,8 @@ class CompressedArchive(Binary):
             dataset.peek = "Compressed binary file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -214,6 +236,7 @@ class CompressedArchive(Binary):
 
 class Meryldb(CompressedArchive):
     """MerylDB is a tar.gz archive, with 128 files. 64 data files and 64 index files."""
+
     file_ext = "meryldb"
 
     def sniff(self, filename):
@@ -229,14 +252,14 @@ class Meryldb(CompressedArchive):
         """
         try:
             if filename and tarfile.is_tarfile(filename):
-                with tarfile.open(filename, 'r') as temptar:
+                with tarfile.open(filename, "r") as temptar:
                     _tar_content = temptar.getnames()
                     # 64 data files ad 64 indices + 2 folders
                     if len(_tar_content) == 130:
-                        if len([_ for _ in _tar_content if _.endswith('.merylIndex')]) == 64:
+                        if len([_ for _ in _tar_content if _.endswith(".merylIndex")]) == 64:
                             return True
         except Exception as e:
-            log.warning('%s, sniff Exception: %s', self, e)
+            log.warning("%s, sniff Exception: %s", self, e)
         return False
 
 
@@ -257,8 +280,8 @@ class Bref3(Binary):
             dataset.peek = "Binary bref3 file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -273,13 +296,15 @@ class DynamicCompressedArchive(CompressedArchive):
     uncompressed_datatype_instance: Data
 
     def matches_any(self, target_datatypes) -> bool:
-        """Treat two aspects of compressed datatypes separately.
-        """
+        """Treat two aspects of compressed datatypes separately."""
         compressed_target_datatypes = []
         uncompressed_target_datatypes = []
 
         for target_datatype in target_datatypes:
-            if hasattr(target_datatype, "uncompressed_datatype_instance") and target_datatype.compressed_format == self.compressed_format:
+            if (
+                hasattr(target_datatype, "uncompressed_datatype_instance")
+                and target_datatype.compressed_format == self.compressed_format
+            ):
                 uncompressed_target_datatypes.append(target_datatype.uncompressed_datatype_instance)
             else:
                 compressed_target_datatypes.append(target_datatype)
@@ -304,9 +329,10 @@ class Bz2DynamicCompressedArchive(DynamicCompressedArchive):
 
 class CompressedZipArchive(CompressedArchive):
     """
-        Class describing an compressed binary file
-        This class can be sublass'ed to implement archive filetypes that will not be unpacked by upload.py.
+    Class describing an compressed binary file
+    This class can be sublass'ed to implement archive filetypes that will not be unpacked by upload.py.
     """
+
     file_ext = "zip"
 
     def set_peek(self, dataset):
@@ -314,8 +340,8 @@ class CompressedZipArchive(CompressedArchive):
             dataset.peek = "Compressed zip file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -328,7 +354,7 @@ class CompressedZipArchive(CompressedArchive):
             zf_files = zf.infolist()
             count = 0
             for f in zf_files:
-                if f.file_size > 0 and not f.filename.startswith('__MACOSX/') and not f.filename.endswith('.DS_Store'):
+                if f.file_size > 0 and not f.filename.startswith("__MACOSX/") and not f.filename.endswith(".DS_Store"):
                     count += 1
                 if count > 1:
                     return True
@@ -336,6 +362,7 @@ class CompressedZipArchive(CompressedArchive):
 
 class GenericAsn1Binary(Binary):
     """Class for generic ASN.1 binary format"""
+
     file_ext = "asn1-binary"
     edam_format = "format_1966"
     edam_data = "data_0849"
@@ -348,14 +375,16 @@ class _BamOrSam:
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         try:
-            bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb')
+            bam_file = pysam.AlignmentFile(dataset.file_name, mode="rb")
             # TODO: Reference names, lengths, read_groups and headers can become very large, truncate when necessary
             dataset.metadata.reference_names = list(bam_file.references)
             dataset.metadata.reference_lengths = list(bam_file.lengths)
             dataset.metadata.bam_header = dict(bam_file.header.items())
-            dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
-            dataset.metadata.sort_order = dataset.metadata.bam_header.get('HD', {}).get('SO', None)
-            dataset.metadata.bam_version = dataset.metadata.bam_header.get('HD', {}).get('VN', None)
+            dataset.metadata.read_groups = [
+                read_group["ID"] for read_group in dataset.metadata.bam_header.get("RG", []) if "ID" in read_group
+            ]
+            dataset.metadata.sort_order = dataset.metadata.bam_header.get("HD", {}).get("SO", None)
+            dataset.metadata.bam_version = dataset.metadata.bam_header.get("HD", {}).get("VN", None)
         except Exception:
             # Per Dan, don't log here because doing so will cause datasets that
             # fail metadata to end in the error state
@@ -364,21 +393,90 @@ class _BamOrSam:
 
 class BamNative(CompressedArchive, _BamOrSam):
     """Class describing a BAM binary file that is not necessarily sorted"""
+
     edam_format = "format_2572"
     edam_data = "data_0863"
     file_ext = "unsorted.bam"
     sort_flag: Optional[str] = None
 
     MetadataElement(name="columns", default=12, desc="Number of columns", readonly=True, visible=False, no_value=0)
-    MetadataElement(name="column_types", default=['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str'], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[])
-    MetadataElement(name="column_names", default=['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT'], desc="Column names", readonly=True, visible=False, optional=True, no_value=[])
+    MetadataElement(
+        name="column_types",
+        default=["str", "int", "str", "int", "int", "str", "str", "int", "int", "str", "str", "str"],
+        desc="Column types",
+        param=metadata.ColumnTypesParameter,
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
+    MetadataElement(
+        name="column_names",
+        default=["QNAME", "FLAG", "RNAME", "POS", "MAPQ", "CIGAR", "MRNM", "MPOS", "ISIZE", "SEQ", "QUAL", "OPT"],
+        desc="Column names",
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
 
-    MetadataElement(name="bam_version", default=None, desc="BAM Version", param=MetadataParameter, readonly=True, visible=False, optional=True)
-    MetadataElement(name="sort_order", default=None, desc="Sort Order", param=MetadataParameter, readonly=True, visible=False, optional=True)
-    MetadataElement(name="read_groups", default=[], desc="Read Groups", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="reference_names", default=[], desc="Chromosome Names", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="reference_lengths", default=[], desc="Chromosome Lengths", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="bam_header", default={}, desc="Dictionary of BAM Headers", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value={})
+    MetadataElement(
+        name="bam_version",
+        default=None,
+        desc="BAM Version",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
+    MetadataElement(
+        name="sort_order",
+        default=None,
+        desc="Sort Order",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
+    MetadataElement(
+        name="read_groups",
+        default=[],
+        desc="Read Groups",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="reference_names",
+        default=[],
+        desc="Chromosome Names",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="reference_lengths",
+        default=[],
+        desc="Chromosome Lengths",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="bam_header",
+        default={},
+        desc="Dictionary of BAM Headers",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value={},
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         _BamOrSam().set_meta(dataset)
@@ -391,7 +489,7 @@ class BamNative(CompressedArchive, _BamOrSam):
         :param split_files: List of bam file paths to merge
         :param output_file: Write merged bam file to this location
         """
-        pysam.merge('-O', 'BAM', output_file, *split_files)
+        pysam.merge("-O", "BAM", output_file, *split_files)
 
     def init_meta(self, dataset, copy_from=None):
         Binary.init_meta(self, dataset, copy_from=copy_from)
@@ -405,7 +503,7 @@ class BamNative(CompressedArchive, _BamOrSam):
         # The first 4 bytes of any bam file is 'BAM\1', and the file is binary.
         try:
             header = gzip.open(filename).read(4)
-            if header == b'BAM\1':
+            if header == b"BAM\1":
                 return True
             return False
         except Exception:
@@ -416,8 +514,8 @@ class BamNative(CompressedArchive, _BamOrSam):
             dataset.peek = "Binary bam alignments file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -447,13 +545,15 @@ class BamNative(CompressedArchive, _BamOrSam):
             # Don't re-sort if already sorted
             return
         tmp_dir = tempfile.mkdtemp()
-        tmp_sorted_dataset_file_name_prefix = os.path.join(tmp_dir, 'sorted')
+        tmp_sorted_dataset_file_name_prefix = os.path.join(tmp_dir, "sorted")
         sorted_file_name = f"{tmp_sorted_dataset_file_name_prefix}.bam"
-        slots = os.environ.get('GALAXY_SLOTS', 1)
+        slots = os.environ.get("GALAXY_SLOTS", 1)
         sort_args = []
         if self.sort_flag:
             sort_args = [self.sort_flag]
-        sort_args.extend([f"-@{slots}", file_name, '-T', tmp_sorted_dataset_file_name_prefix, '-O', 'BAM', '-o', sorted_file_name])
+        sort_args.extend(
+            [f"-@{slots}", file_name, "-T", tmp_sorted_dataset_file_name_prefix, "-O", "BAM", "-o", sorted_file_name]
+        )
         try:
             pysam.sort(*sort_args)
         except Exception:
@@ -472,8 +572,8 @@ class BamNative(CompressedArchive, _BamOrSam):
                     ck_data = ""
                     header_line_count = 0
                     if offset == 0:
-                        ck_data = bamfile.text.replace('\t', ' ')
-                        header_line_count = bamfile.text.count('\n')
+                        ck_data = bamfile.text.replace("\t", " ")
+                        header_line_count = bamfile.text.count("\n")
                     else:
                         bamfile.seek(offset)
                     for line_number, alignment in enumerate(bamfile):
@@ -486,7 +586,7 @@ class BamNative(CompressedArchive, _BamOrSam):
                             bamline = alignment.tostring(bamfile)
                             # Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
                             # Below code will remove spaces between each tag.
-                            bamline_modified = ('\t').join(bamline.split()[:11] + [(' ').join(bamline.split()[11:])])
+                            bamline_modified = ("\t").join(bamline.split()[:11] + [(" ").join(bamline.split()[11:])])
                             ck_data = f"{ck_data}\n{bamline_modified}"
                     else:
                         # Nothing to enumerate; we've either offset to the end
@@ -497,10 +597,9 @@ class BamNative(CompressedArchive, _BamOrSam):
                 offset = -1
                 ck_data = f"Could not display BAM file, error was:\n{e}"
         else:
-            ck_data = ''
+            ck_data = ""
             offset = -1
-        return dumps({'ck_data': util.unicodify(ck_data),
-                      'offset': offset})
+        return dumps({"ck_data": util.unicodify(ck_data), "offset": offset})
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
         headers = kwd.get("headers", {})
@@ -519,42 +618,66 @@ class BamNative(CompressedArchive, _BamOrSam):
             column_number = dataset.metadata.columns
             if column_number is None:
                 column_number = 1
-            return trans.fill_template("/dataset/tabular_chunked.mako",
-                                       dataset=dataset,
-                                       chunk=self.get_chunk(trans, dataset, 0),
-                                       column_number=column_number,
-                                       column_names=column_names,
-                                       column_types=column_types), headers
+            return (
+                trans.fill_template(
+                    "/dataset/tabular_chunked.mako",
+                    dataset=dataset,
+                    chunk=self.get_chunk(trans, dataset, 0),
+                    column_number=column_number,
+                    column_names=column_names,
+                    column_types=column_types,
+                ),
+                headers,
+            )
 
     def validate(self, dataset, **kwd):
         if not BamNative.is_bam(dataset.file_name):
             return DatatypeValidation.invalid("This dataset does not appear to a BAM file.")
         elif self.dataset_content_needs_grooming(dataset.file_name):
-            return DatatypeValidation.invalid("This BAM file does not appear to have the correct sorting for declared datatype.")
+            return DatatypeValidation.invalid(
+                "This BAM file does not appear to have the correct sorting for declared datatype."
+            )
         return DatatypeValidation.validated()
 
 
 @dataproviders.decorators.has_dataproviders
 class Bam(BamNative):
     """Class describing a BAM binary file"""
+
     edam_format = "format_2572"
     edam_data = "data_0863"
     file_ext = "bam"
     track_type = "ReadTrack"
     data_sources = {"data": "bai", "index": "bigwig"}
 
-    MetadataElement(name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, visible=False, optional=True)
-    MetadataElement(name="bam_csi_index", desc="BAM CSI Index File", param=metadata.FileParameter, file_ext="bam.csi", readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="bam_index",
+        desc="BAM Index File",
+        param=metadata.FileParameter,
+        file_ext="bai",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
+    MetadataElement(
+        name="bam_csi_index",
+        desc="BAM CSI Index File",
+        param=metadata.FileParameter,
+        file_ext="bam.csi",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def get_index_flag(self, file_name):
         """
         Return pysam flag for bai index (default) or csi index (contig size > (2**29 - 1) )
         """
-        index_flag = '-b'  # bai index
+        index_flag = "-b"  # bai index
         try:
             with pysam.AlignmentFile(file_name) as alignment_file:
-                if max(alignment_file.header.lengths) > (2 ** 29) - 1:
-                    index_flag = '-c'  # csi index
+                if max(alignment_file.header.lengths) > (2**29) - 1:
+                    index_flag = "-c"  # csi index
         except Exception:
             # File may not have a header, that's OK
             pass
@@ -572,12 +695,20 @@ class Bam(BamNative):
             # If pysam fails to index a file it will write to stderr,
             # and this causes the set_meta script to fail. So instead
             # we start another process and discard stderr.
-            if index_flag == '-b':
+            if index_flag == "-b":
                 # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
-                cmd = ['python', '-c', f"import pysam; pysam.set_verbosity(0); pysam.index('{file_name}', '{index_name}')"]
+                cmd = [
+                    "python",
+                    "-c",
+                    f"import pysam; pysam.set_verbosity(0); pysam.index('{file_name}', '{index_name}')",
+                ]
             else:
-                cmd = ['python', '-c', f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '{file_name}', '{index_name}')"]
-            with open(os.devnull, 'w') as devnull:
+                cmd = [
+                    "python",
+                    "-c",
+                    f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '{file_name}', '{index_name}')",
+                ]
+            with open(os.devnull, "w") as devnull:
                 subprocess.check_call(cmd, stderr=devnull, shell=False)
             needs_sorting = False
         except subprocess.CalledProcessError:
@@ -592,15 +723,15 @@ class Bam(BamNative):
         # These metadata values are not accessible by users, always overwrite
         super().set_meta(dataset=dataset, overwrite=overwrite, **kwd)
         index_flag = self.get_index_flag(dataset.file_name)
-        if index_flag == '-b':
-            spec_key = 'bam_index'
+        if index_flag == "-b":
+            spec_key = "bam_index"
             index_file = dataset.metadata.bam_index
         else:
-            spec_key = 'bam_csi_index'
+            spec_key = "bam_csi_index"
             index_file = dataset.metadata.bam_csi_index
         if not index_file:
             index_file = dataset.metadata.spec[spec_key].param.new_file(dataset=dataset)
-        if index_flag == '-b':
+        if index_flag == "-b":
             # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
             pysam.index(dataset.file_name, index_file.file_name)
         else:
@@ -616,28 +747,28 @@ class Bam(BamNative):
     # bam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers
     # TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char?
     # TODO: incorporate samtools options to control output: regions first, then flags, etc.
-    @dataproviders.decorators.dataprovider_factory('line', dataproviders.line.FilteredLineDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("line", dataproviders.line.FilteredLineDataProvider.settings)
     def line_dataprovider(self, dataset, **settings):
         samtools_source = dataproviders.dataset.SamtoolsDataProvider(dataset)
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return dataproviders.line.FilteredLineDataProvider(samtools_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('regex-line', dataproviders.line.RegexLineDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("regex-line", dataproviders.line.RegexLineDataProvider.settings)
     def regex_line_dataprovider(self, dataset, **settings):
         samtools_source = dataproviders.dataset.SamtoolsDataProvider(dataset)
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return dataproviders.line.RegexLineDataProvider(samtools_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('column', dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("column", dataproviders.column.ColumnarDataProvider.settings)
     def column_dataprovider(self, dataset, **settings):
         samtools_source = dataproviders.dataset.SamtoolsDataProvider(dataset)
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return dataproviders.column.ColumnarDataProvider(samtools_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dict', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dict", dataproviders.column.DictDataProvider.settings)
     def dict_dataprovider(self, dataset, **settings):
         samtools_source = dataproviders.dataset.SamtoolsDataProvider(dataset)
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return dataproviders.column.DictDataProvider(samtools_source, **settings)
 
     # these can't be used directly - may need BamColumn, BamDict (Bam metadata -> column/dict)
@@ -652,20 +783,20 @@ class Bam(BamNative):
     #    settings['comment_char'] = '@'
     #    return super().dataset_dict_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('header', dataproviders.line.RegexLineDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("header", dataproviders.line.RegexLineDataProvider.settings)
     def header_dataprovider(self, dataset, **settings):
         # in this case we can use an option of samtools view to provide just what we need (w/o regex)
-        samtools_source = dataproviders.dataset.SamtoolsDataProvider(dataset, '-H')
+        samtools_source = dataproviders.dataset.SamtoolsDataProvider(dataset, "-H")
         return dataproviders.line.RegexLineDataProvider(samtools_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('id-seq-qual', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("id-seq-qual", dataproviders.column.DictDataProvider.settings)
     def id_seq_qual_dataprovider(self, dataset, **settings):
-        settings['indeces'] = [0, 9, 10]
-        settings['column_types'] = ['str', 'str', 'str']
-        settings['column_names'] = ['id', 'seq', 'qual']
+        settings["indeces"] = [0, 9, 10]
+        settings["column_types"] = ["str", "str", "str"]
+        settings["column_names"] = ["id", "seq", "qual"]
         return self.dict_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region', dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("genomic-region", dataproviders.column.ColumnarDataProvider.settings)
     def genomic_region_dataprovider(self, dataset, **settings):
         # GenomicRegionDataProvider currently requires a dataset as source - may not be necc.
         # TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset),
@@ -675,18 +806,20 @@ class Bam(BamNative):
         #                                                        2, 3, 3, **settings)
 
         # instead, set manually and use in-class column gen
-        settings['indeces'] = [2, 3, 3]
-        settings['column_types'] = ['str', 'int', 'int']
+        settings["indeces"] = [2, 3, 3]
+        settings["column_types"] = ["str", "int", "int"]
         return self.column_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region-dict', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region-dict", dataproviders.column.DictDataProvider.settings
+    )
     def genomic_region_dict_dataprovider(self, dataset, **settings):
-        settings['indeces'] = [2, 3, 3]
-        settings['column_types'] = ['str', 'int', 'int']
-        settings['column_names'] = ['chrom', 'start', 'end']
+        settings["indeces"] = [2, 3, 3]
+        settings["column_types"] = ["str", "int", "int"]
+        settings["column_names"] = ["chrom", "start", "end"]
         return self.dict_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('samtools')
+    @dataproviders.decorators.dataprovider_factory("samtools")
     def samtools_dataprovider(self, dataset, **settings):
         """Generic samtools interface - all options available through settings."""
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
@@ -695,6 +828,7 @@ class Bam(BamNative):
 
 class ProBam(Bam):
     """Class describing a BAM binary file - extended for proteomics data"""
+
     edam_format = "format_3826"
     edam_data = "data_0863"
     file_ext = "probam"
@@ -707,8 +841,9 @@ class BamInputSorted(BamNative):
     or ordered by their queryname.
     This notaby keeps alignments produced by paired end sequencing adjacent.
     """
-    sort_flag = '-n'
-    file_ext = 'qname_input_sorted.bam'
+
+    sort_flag = "-n"
+    file_ext = "qname_input_sorted.bam"
 
     def sniff(self, file_name):
         # We never want to sniff to this datatype
@@ -722,13 +857,13 @@ class BamInputSorted(BamNative):
         # is to actually index them.
         with pysam.AlignmentFile(filename=file_name) as f:
             # The only sure thing we know here is that the sort order can't be coordinate
-            return f.header.get('HD', {}).get('SO') == 'coordinate'
+            return f.header.get("HD", {}).get("SO") == "coordinate"
 
 
 class BamQuerynameSorted(BamInputSorted):
     """A class for queryname sorted BAM files."""
 
-    sort_flag = '-n'
+    sort_flag = "-n"
     file_ext = "qname_sorted.bam"
 
     def sniff(self, file_name):
@@ -741,7 +876,7 @@ class BamQuerynameSorted(BamInputSorted):
         # The best way to ensure that BAM files are coordinate-sorted and indexable
         # is to actually index them.
         with pysam.AlignmentFile(filename=file_name) as f:
-            return f.header.get('HD', {}).get('SO') != 'queryname'
+            return f.header.get("HD", {}).get("SO") != "queryname"
 
 
 class CRAM(Binary):
@@ -749,8 +884,24 @@ class CRAM(Binary):
     edam_format = "format_3462"
     edam_data = "data_0863"
 
-    MetadataElement(name="cram_version", default=None, desc="CRAM Version", param=MetadataParameter, readonly=True, visible=False, optional=False)
-    MetadataElement(name="cram_index", desc="CRAM Index File", param=metadata.FileParameter, file_ext="crai", readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="cram_version",
+        default=None,
+        desc="CRAM Version",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=False,
+    )
+    MetadataElement(
+        name="cram_index",
+        desc="CRAM Index File",
+        param=metadata.FileParameter,
+        file_ext="crai",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         major_version, minor_version = self.get_cram_version(dataset.file_name)
@@ -758,7 +909,7 @@ class CRAM(Binary):
             dataset.metadata.cram_version = f"{str(major_version)}.{str(minor_version)}"
 
         if not dataset.metadata.cram_index:
-            index_file = dataset.metadata.spec['cram_index'].param.new_file(dataset=dataset)
+            index_file = dataset.metadata.spec["cram_index"].param.new_file(dataset=dataset)
             if self.set_index_file(dataset, index_file):
                 dataset.metadata.cram_index = index_file
 
@@ -768,7 +919,7 @@ class CRAM(Binary):
                 header = bytearray(fh.read(6))
             return header[4], header[5]
         except Exception as exc:
-            log.warning('%s, get_cram_version Exception: %s', self, exc)
+            log.warning("%s, get_cram_version Exception: %s", self, exc)
             return -1, -1
 
     def set_index_file(self, dataset, index_file):
@@ -776,20 +927,20 @@ class CRAM(Binary):
             pysam.index(dataset.file_name, index_file.file_name)
             return True
         except Exception as exc:
-            log.warning('%s, set_index_file Exception: %s', self, exc)
+            log.warning("%s, set_index_file Exception: %s", self, exc)
             return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = 'CRAM binary alignment file'
-            dataset.blurb = 'binary data'
+            dataset.peek = "CRAM binary alignment file"
+            dataset.blurb = "binary data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         try:
-            header = open(filename, 'rb').read(4)
+            header = open(filename, "rb").read(4)
             if header == b"CRAM":
                 return True
             return False
@@ -807,37 +958,48 @@ class Bcf(BaseBcf):
     Class describing a (BGZF-compressed) BCF file
 
     """
+
     file_ext = "bcf"
 
-    MetadataElement(name="bcf_index", desc="BCF Index File", param=metadata.FileParameter, file_ext="csi", readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="bcf_index",
+        desc="BCF Index File",
+        param=metadata.FileParameter,
+        file_ext="csi",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def sniff(self, filename):
         # BCF is compressed in the BGZF format, and must not be uncompressed in Galaxy.
         try:
             header = gzip.open(filename).read(3)
             # The first 3 bytes of any BCF file are 'BCF', and the file is binary.
-            if header == b'BCF':
+            if header == b"BCF":
                 return True
             return False
         except Exception:
             return False
 
     def set_meta(self, dataset, overwrite=True, **kwd):
-        """ Creates the index for the BCF file. """
+        """Creates the index for the BCF file."""
         # These metadata values are not accessible by users, always overwrite
         index_file = dataset.metadata.bcf_index
         if not index_file:
-            index_file = dataset.metadata.spec['bcf_index'].param.new_file(dataset=dataset)
+            index_file = dataset.metadata.spec["bcf_index"].param.new_file(dataset=dataset)
         # Create the bcf index
-        dataset_symlink = os.path.join(os.path.dirname(index_file.file_name),
-                                       '__dataset_%d_%s' % (dataset.id, os.path.basename(index_file.file_name)))
+        dataset_symlink = os.path.join(
+            os.path.dirname(index_file.file_name),
+            "__dataset_%d_%s" % (dataset.id, os.path.basename(index_file.file_name)),
+        )
         os.symlink(dataset.file_name, dataset_symlink)
         try:
-            cmd = ['python', '-c', f"import pysam.bcftools; pysam.bcftools.index('{dataset_symlink}')"]
+            cmd = ["python", "-c", f"import pysam.bcftools; pysam.bcftools.index('{dataset_symlink}')"]
             subprocess.check_call(cmd)
             shutil.move(f"{dataset_symlink}.csi", index_file.file_name)
         except Exception as e:
-            raise Exception(f'Error setting BCF metadata: {util.unicodify(e)}')
+            raise Exception(f"Error setting BCF metadata: {util.unicodify(e)}")
         finally:
             # Remove temp file and symlink
             os.remove(dataset_symlink)
@@ -856,13 +1018,14 @@ class BcfUncompressed(BaseBcf):
     >>> BcfUncompressed().sniff(fname)
     False
     """
+
     file_ext = "bcf_uncompressed"
 
     def sniff(self, filename):
         try:
-            header = open(filename, mode='rb').read(3)
+            header = open(filename, mode="rb").read(3)
             # The first 3 bytes of any BCF file are 'BCF', and the file is binary.
-            if header == b'BCF':
+            if header == b"BCF":
                 return True
             return False
         except Exception:
@@ -881,6 +1044,7 @@ class H5(Binary):
     >>> H5().sniff(fname)
     False
     """
+
     file_ext = "h5"
     edam_format = "format_3590"
 
@@ -891,7 +1055,7 @@ class H5(Binary):
     def sniff(self, filename):
         # The first 8 bytes of any hdf5 file are 0x894844460d0a1a0a
         try:
-            header = open(filename, 'rb').read(8)
+            header = open(filename, "rb").read(8)
             if header == self._magic:
                 return True
             return False
@@ -903,8 +1067,8 @@ class H5(Binary):
             dataset.peek = "Binary HDF5 file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -925,6 +1089,7 @@ class Loom(H5):
     >>> Loom().sniff(fname)
     False
     """
+
     file_ext = "loom"
     edam_format = "format_3590"
 
@@ -932,28 +1097,71 @@ class Loom(H5):
     MetadataElement(name="description", default="", desc="description", readonly=True, visible=True, no_value="")
     MetadataElement(name="url", default="", desc="url", readonly=True, visible=True, no_value="")
     MetadataElement(name="doi", default="", desc="doi", readonly=True, visible=True, no_value="")
-    MetadataElement(name="loom_spec_version", default="", desc="loom_spec_version", readonly=True, visible=True, no_value="")
+    MetadataElement(
+        name="loom_spec_version", default="", desc="loom_spec_version", readonly=True, visible=True, no_value=""
+    )
     MetadataElement(name="creation_date", default=None, desc="creation_date", readonly=True, visible=True)
-    MetadataElement(name="shape", default=(), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=())
+    MetadataElement(
+        name="shape", default=(), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=()
+    )
     MetadataElement(name="layers_count", default=0, desc="layers_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="layers_names", desc="layers_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="layers_names",
+        desc="layers_names",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
     MetadataElement(name="row_attrs_count", default=0, desc="row_attrs_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="row_attrs_names", desc="row_attrs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="row_attrs_names",
+        desc="row_attrs_names",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
     MetadataElement(name="col_attrs_count", default=0, desc="col_attrs_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="col_attrs_names", desc="col_attrs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
-    MetadataElement(name="col_graphs_count", default=0, desc="col_graphs_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="col_graphs_names", desc="col_graphs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
-    MetadataElement(name="row_graphs_count", default=0, desc="row_graphs_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="row_graphs_names", desc="row_graphs_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="col_attrs_names",
+        desc="col_attrs_names",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
+    MetadataElement(
+        name="col_graphs_count", default=0, desc="col_graphs_count", readonly=True, visible=True, no_value=0
+    )
+    MetadataElement(
+        name="col_graphs_names",
+        desc="col_graphs_names",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
+    MetadataElement(
+        name="row_graphs_count", default=0, desc="row_graphs_count", readonly=True, visible=True, no_value=0
+    )
+    MetadataElement(
+        name="row_graphs_names",
+        desc="row_graphs_names",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
 
     def sniff(self, filename):
         if super().sniff(filename):
-            with h5py.File(filename, 'r') as loom_file:
+            with h5py.File(filename, "r") as loom_file:
                 # Check the optional but distinctive LOOM_SPEC_VERSION attribute
-                if bool(loom_file.attrs.get('LOOM_SPEC_VERSION')):
+                if bool(loom_file.attrs.get("LOOM_SPEC_VERSION")):
                     return True
                 # Check some mandatory H5 datasets and groups
-                for el in ('matrix', 'row_attrs', 'col_attrs'):
+                for el in ("matrix", "row_attrs", "col_attrs"):
                     if loom_file.get(el) is None:
                         return False
                 else:
@@ -965,8 +1173,8 @@ class Loom(H5):
             dataset.peek = "Binary Loom file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -977,29 +1185,29 @@ class Loom(H5):
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
-            with h5py.File(dataset.file_name, 'r') as loom_file:
-                dataset.metadata.title = loom_file.attrs.get('title')
-                dataset.metadata.description = loom_file.attrs.get('description')
-                dataset.metadata.url = loom_file.attrs.get('url')
-                dataset.metadata.doi = loom_file.attrs.get('doi')
-                loom_spec_version = loom_file.attrs.get('LOOM_SPEC_VERSION')
+            with h5py.File(dataset.file_name, "r") as loom_file:
+                dataset.metadata.title = loom_file.attrs.get("title")
+                dataset.metadata.description = loom_file.attrs.get("description")
+                dataset.metadata.url = loom_file.attrs.get("url")
+                dataset.metadata.doi = loom_file.attrs.get("doi")
+                loom_spec_version = loom_file.attrs.get("LOOM_SPEC_VERSION")
                 if isinstance(loom_spec_version, np.ndarray):
                     loom_spec_version = loom_spec_version[0]
                     if isinstance(loom_spec_version, bytes):
                         loom_spec_version = loom_spec_version.decode()
                 dataset.metadata.loom_spec_version = loom_spec_version
-                dataset.creation_date = loom_file.attrs.get('creation_date')
-                dataset.metadata.shape = tuple(loom_file['matrix'].shape)
+                dataset.creation_date = loom_file.attrs.get("creation_date")
+                dataset.metadata.shape = tuple(loom_file["matrix"].shape)
 
-                tmp = list(loom_file.get('layers', {}).keys())
+                tmp = list(loom_file.get("layers", {}).keys())
                 dataset.metadata.layers_count = len(tmp)
                 dataset.metadata.layers_names = tmp
 
-                tmp = list(loom_file['row_attrs'].keys())
+                tmp = list(loom_file["row_attrs"].keys())
                 dataset.metadata.row_attrs_count = len(tmp)
                 dataset.metadata.row_attrs_names = tmp
 
-                tmp = list(loom_file['col_attrs'].keys())
+                tmp = list(loom_file["col_attrs"].keys())
                 dataset.metadata.col_attrs_count = len(tmp)
                 dataset.metadata.col_attrs_names = tmp
 
@@ -1007,15 +1215,15 @@ class Loom(H5):
                 # and row_graphs are mandatory groups, but files created by
                 # Bioconductor LoomExperiment do not always have them:
                 # https://github.com/Bioconductor/LoomExperiment/issues/7
-                tmp = list(loom_file.get('col_graphs', {}).keys())
+                tmp = list(loom_file.get("col_graphs", {}).keys())
                 dataset.metadata.col_graphs_count = len(tmp)
                 dataset.metadata.col_graphs_names = tmp
 
-                tmp = list(loom_file.get('row_graphs', {}).keys())
+                tmp = list(loom_file.get("row_graphs", {}).keys())
                 dataset.metadata.row_graphs_count = len(tmp)
                 dataset.metadata.row_graphs_names = tmp
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
 
 class Anndata(H5):
@@ -1041,57 +1249,92 @@ class Anndata(H5):
     >>> Anndata().sniff(get_test_fname('adata_unk.h5ad'))
     True
     """
-    file_ext = 'h5ad'
+
+    file_ext = "h5ad"
 
     MetadataElement(name="title", default="", desc="title", readonly=True, visible=True, no_value="")
     MetadataElement(name="description", default="", desc="description", readonly=True, visible=True, no_value="")
     MetadataElement(name="url", default="", desc="url", readonly=True, visible=True, no_value="")
     MetadataElement(name="doi", default="", desc="doi", readonly=True, visible=True, no_value="")
-    MetadataElement(name="anndata_spec_version", default="", desc="anndata_spec_version", readonly=True, visible=True, no_value="")
+    MetadataElement(
+        name="anndata_spec_version", default="", desc="anndata_spec_version", readonly=True, visible=True, no_value=""
+    )
     MetadataElement(name="creation_date", default=None, desc="creation_date", readonly=True, visible=True)
     MetadataElement(name="layers_count", default=0, desc="layers_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="layers_names", desc="layers_names", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="layers_names",
+        desc="layers_names",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
     MetadataElement(name="row_attrs_count", default=0, desc="row_attrs_count", readonly=True, visible=True, no_value=0)
     # obs_names: Cell1, Cell2, Cell3,...
     # obs_layers: louvain, leidein, isBcell
     # obs_count: number of obs_layers
     # obs_size: number of obs_names
     MetadataElement(name="obs_names", desc="obs_names", default=[], multiple=True, readonly=True)
-    MetadataElement(name="obs_layers", desc="obs_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="obs_layers", desc="obs_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
     MetadataElement(name="obs_count", default=0, desc="obs_count", readonly=True, visible=True, no_value=0)
     MetadataElement(name="obs_size", default=-1, desc="obs_size", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="obsm_layers", desc="obsm_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="obsm_layers", desc="obsm_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
     MetadataElement(name="obsm_count", default=0, desc="obsm_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="raw_var_layers", desc="raw_var_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="raw_var_layers",
+        desc="raw_var_layers",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+    )
     MetadataElement(name="raw_var_count", default=0, desc="raw_var_count", readonly=True, visible=True, no_value=0)
     MetadataElement(name="raw_var_size", default=0, desc="raw_var_size", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="var_layers", desc="var_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="var_layers", desc="var_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
     MetadataElement(name="var_count", default=0, desc="var_count", readonly=True, visible=True, no_value=0)
     MetadataElement(name="var_size", default=-1, desc="var_size", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="varm_layers", desc="varm_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="varm_layers", desc="varm_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
     MetadataElement(name="varm_count", default=0, desc="varm_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="uns_layers", desc="uns_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="uns_layers", desc="uns_layers", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
     MetadataElement(name="uns_count", default=0, desc="uns_count", readonly=True, visible=True, no_value=0)
-    MetadataElement(name="shape", default=(-1, -1), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=(0, 0))
+    MetadataElement(
+        name="shape",
+        default=(-1, -1),
+        desc="shape",
+        param=metadata.ListParameter,
+        readonly=True,
+        visible=True,
+        no_value=(0, 0),
+    )
 
     def sniff(self, filename):
         if super().sniff(filename):
             try:
-                with h5py.File(filename, 'r') as f:
-                    return all(attr in f for attr in ['X', 'obs', 'var'])
+                with h5py.File(filename, "r") as f:
+                    return all(attr in f for attr in ["X", "obs", "var"])
             except Exception:
                 return False
         return False
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
-        with h5py.File(dataset.file_name, 'r') as anndata_file:
-            dataset.metadata.title = anndata_file.attrs.get('title')
-            dataset.metadata.description = anndata_file.attrs.get('description')
-            dataset.metadata.url = anndata_file.attrs.get('url')
-            dataset.metadata.doi = anndata_file.attrs.get('doi')
-            dataset.creation_date = anndata_file.attrs.get('creation_date')
-            dataset.metadata.shape = anndata_file.attrs.get('shape', dataset.metadata.shape)
+        with h5py.File(dataset.file_name, "r") as anndata_file:
+            dataset.metadata.title = anndata_file.attrs.get("title")
+            dataset.metadata.description = anndata_file.attrs.get("description")
+            dataset.metadata.url = anndata_file.attrs.get("url")
+            dataset.metadata.doi = anndata_file.attrs.get("doi")
+            dataset.creation_date = anndata_file.attrs.get("creation_date")
+            dataset.metadata.shape = anndata_file.attrs.get("shape", dataset.metadata.shape)
             # none of the above appear to work in any dataset tested, but could be useful for
             # future AnnData datasets
             dataset.metadata.layers_count = len(anndata_file)
@@ -1099,7 +1342,7 @@ class Anndata(H5):
 
             def _layercountsize(tmp, lennames=0):
                 "From TMP and LENNAMES, return layers, their number, and the length of one of the layers (all equal)."
-                if hasattr(tmp, 'dtype'):
+                if hasattr(tmp, "dtype"):
                     layers = list(tmp.dtype.names)
                     count = len(tmp.dtype)
                     size = int(tmp.size)
@@ -1109,7 +1352,7 @@ class Anndata(H5):
                     size = lennames
                 return (layers, count, size)
 
-            if 'obs' in dataset.metadata.layers_names:
+            if "obs" in dataset.metadata.layers_names:
                 tmp = anndata_file["obs"]
                 obs_index = None
                 if "index" in tmp:
@@ -1119,7 +1362,7 @@ class Anndata(H5):
                 # Determine cell labels
                 if obs_index:
                     dataset.metadata.obs_names = list(tmp[obs_index])
-                elif hasattr(tmp, 'dtype'):
+                elif hasattr(tmp, "dtype"):
                     if "index" in tmp.dtype.names:
                         # Yes, we call tmp["index"], and not tmp.dtype["index"]
                         # here, despite the above tests.
@@ -1136,11 +1379,11 @@ class Anndata(H5):
                 dataset.metadata.obs_count = y
                 dataset.metadata.obs_size = z
 
-            if 'obsm' in dataset.metadata.layers_names:
+            if "obsm" in dataset.metadata.layers_names:
                 tmp = anndata_file["obsm"]
                 dataset.metadata.obsm_layers, dataset.metadata.obsm_count, _ = _layercountsize(tmp)
 
-            if 'raw.var' in dataset.metadata.layers_names:
+            if "raw.var" in dataset.metadata.layers_names:
                 tmp = anndata_file["raw.var"]
                 # full set of genes would never need to be previewed
                 # dataset.metadata.raw_var_names = tmp["index"]
@@ -1149,7 +1392,7 @@ class Anndata(H5):
                 dataset.metadata.raw_var_count = y
                 dataset.metadata.raw_var_size = z
 
-            if 'var' in dataset.metadata.layers_names:
+            if "var" in dataset.metadata.layers_names:
                 tmp = anndata_file["var"]
                 var_index = None
                 if "index" in tmp:
@@ -1169,22 +1412,22 @@ class Anndata(H5):
                 dataset.metadata.var_count = y
                 dataset.metadata.var_size = z
 
-            if 'varm' in dataset.metadata.layers_names:
+            if "varm" in dataset.metadata.layers_names:
                 tmp = anndata_file["varm"]
                 dataset.metadata.varm_layers, dataset.metadata.varm_count, _ = _layercountsize(tmp)
 
-            if 'uns' in dataset.metadata.layers_names:
+            if "uns" in dataset.metadata.layers_names:
                 tmp = anndata_file["uns"]
                 dataset.metadata.uns_layers, dataset.metadata.uns_count, _ = _layercountsize(tmp)
 
             # Resolving the problematic shape parameter
-            if 'X' in dataset.metadata.layers_names:
+            if "X" in dataset.metadata.layers_names:
                 # Shape we determine here due to the non-standard representation of 'X' dimensions
-                shape = anndata_file['X'].attrs.get("shape")
+                shape = anndata_file["X"].attrs.get("shape")
                 if shape is not None:
                     dataset.metadata.shape = tuple(shape)
-                elif hasattr(anndata_file['X'], 'shape'):
-                    dataset.metadata.shape = tuple(anndata_file['X'].shape)
+                elif hasattr(anndata_file["X"], "shape"):
+                    dataset.metadata.shape = tuple(anndata_file["X"].shape)
 
             if dataset.metadata.shape is None:
                 dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size))
@@ -1200,7 +1443,7 @@ class Anndata(H5):
                         layer,
                         count,
                         "layer" if count == 1 else "layers",
-                        ', '.join(sorted(names))
+                        ", ".join(sorted(names)),
                     )
                 return ""
 
@@ -1214,8 +1457,8 @@ class Anndata(H5):
             dataset.peek = peekstr
             dataset.blurb = f"Anndata file ({nice_size(dataset.get_size())})"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1237,14 +1480,17 @@ class Grib(Binary):
     >>> Grib().sniff_prefix(fname)
     False
     """
+
     file_ext = "grib"
     # GRIB not yet in EDAM (work in progress). For now, so set to binary
     edam_format = "format_2333"
-    MetadataElement(name="grib_edition", default=1, desc="GRIB edition", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="grib_edition", default=1, desc="GRIB edition", readonly=True, visible=True, optional=True, no_value=0
+    )
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self._magic = b'GRIB'
+        self._magic = b"GRIB"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         # The first 4 bytes of any GRIB file are GRIB
@@ -1264,8 +1510,8 @@ class Grib(Binary):
             dataset.peek = "Binary GRIB file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1282,7 +1528,7 @@ class Grib(Binary):
     def _get_grib_edition(self, filename):
         _uint8struct = struct.Struct(b">B")
         edition = 0
-        with open(filename, 'rb') as f:
+        with open(filename, "rb") as f:
             f.seek(4)
             tmp = f.read(4)
             edition = _uint8struct.unpack_from(tmp, 3)[0]
@@ -1300,15 +1546,15 @@ class GmxBinary(Binary):
 
     def sniff_prefix(self, sniff_prefix):
         # The first 4 bytes of any GROMACS binary file containing the magic number
-        return sniff_prefix.magic_header('>1i') == self.magic_number
+        return sniff_prefix.magic_header(">1i") == self.magic_number
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = f"Binary GROMACS {self.file_ext} file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1382,22 +1628,41 @@ class Edr(GmxBinary):
     """
 
     file_ext = "edr"
-    magic_number = -55555  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/enxio.cpp
+    magic_number = (
+        -55555
+    )  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/enxio.cpp
 
 
 class Biom2(H5):
     """
     Class describing a biom2 file (http://biom-format.org/documentation/biom_format.html)
     """
+
     MetadataElement(name="id", default=None, desc="table id", readonly=True, visible=True)
     MetadataElement(name="format_url", default=None, desc="format-url", readonly=True, visible=True)
-    MetadataElement(name="format_version", default=None, desc="format-version (equal to format)", readonly=True, visible=True)
+    MetadataElement(
+        name="format_version", default=None, desc="format-version (equal to format)", readonly=True, visible=True
+    )
     MetadataElement(name="format", default=None, desc="format (equal to format=version)", readonly=True, visible=True)
     MetadataElement(name="type", default=None, desc="table type", readonly=True, visible=True)
     MetadataElement(name="generated_by", default=None, desc="generated by", readonly=True, visible=True)
     MetadataElement(name="creation_date", default=None, desc="creation date", readonly=True, visible=True)
-    MetadataElement(name="nnz", default=-1, desc="nnz: The number of non-zero elements in the table", readonly=True, visible=True, no_value=-1)
-    MetadataElement(name="shape", default=(), desc="shape: The number of rows and columns in the dataset", readonly=True, visible=True, no_value=())
+    MetadataElement(
+        name="nnz",
+        default=-1,
+        desc="nnz: The number of non-zero elements in the table",
+        readonly=True,
+        visible=True,
+        no_value=-1,
+    )
+    MetadataElement(
+        name="shape",
+        default=(),
+        desc="shape: The number of rows and columns in the dataset",
+        readonly=True,
+        visible=True,
+        no_value=(),
+    )
 
     file_ext = "biom2"
     edam_format = "format_3746"
@@ -1416,47 +1681,47 @@ class Biom2(H5):
         False
         """
         if super().sniff(filename):
-            with h5py.File(filename, 'r') as f:
-                required_fields = {'id', 'format-url', 'type', 'generated-by', 'creation-date', 'nnz', 'shape'}
+            with h5py.File(filename, "r") as f:
+                required_fields = {"id", "format-url", "type", "generated-by", "creation-date", "nnz", "shape"}
                 return required_fields.issubset(f.attrs.keys())
         return False
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
-            with h5py.File(dataset.file_name, 'r') as f:
+            with h5py.File(dataset.file_name, "r") as f:
                 attributes = f.attrs
 
-                dataset.metadata.id = util.unicodify(attributes['id'])
-                dataset.metadata.format_url = util.unicodify(attributes['format-url'])
-                if 'format-version' in attributes:  # biom 2.1
-                    dataset.metadata.format_version = '.'.join(str(_) for _ in attributes['format-version'])
+                dataset.metadata.id = util.unicodify(attributes["id"])
+                dataset.metadata.format_url = util.unicodify(attributes["format-url"])
+                if "format-version" in attributes:  # biom 2.1
+                    dataset.metadata.format_version = ".".join(str(_) for _ in attributes["format-version"])
                     dataset.metadata.format = dataset.metadata.format_version
-                elif 'format' in attributes:  # biom 2.0
-                    dataset.metadata.format = util.unicodify(attributes['format'])
+                elif "format" in attributes:  # biom 2.0
+                    dataset.metadata.format = util.unicodify(attributes["format"])
                     dataset.metadata.format_version = dataset.metadata.format
-                dataset.metadata.type = util.unicodify(attributes['type'])
-                dataset.metadata.shape = tuple(int(_) for _ in attributes['shape'])
-                dataset.metadata.generated_by = util.unicodify(attributes['generated-by'])
-                dataset.metadata.creation_date = util.unicodify(attributes['creation-date'])
-                dataset.metadata.nnz = int(attributes['nnz'])
+                dataset.metadata.type = util.unicodify(attributes["type"])
+                dataset.metadata.shape = tuple(int(_) for _ in attributes["shape"])
+                dataset.metadata.generated_by = util.unicodify(attributes["generated-by"])
+                dataset.metadata.creation_date = util.unicodify(attributes["creation-date"])
+                dataset.metadata.nnz = int(attributes["nnz"])
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, util.unicodify(e))
+            log.warning("%s, set_meta Exception: %s", self, util.unicodify(e))
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            lines = ['Biom2 (HDF5) file']
+            lines = ["Biom2 (HDF5) file"]
             try:
                 with h5py.File(dataset.file_name) as f:
                     for k, v in f.attrs.items():
-                        lines.append(f'{k}:  {util.unicodify(v)}')
+                        lines.append(f"{k}:  {util.unicodify(v)}")
             except Exception as e:
-                log.warning('%s, set_peek Exception: %s', self, util.unicodify(e))
-            dataset.peek = '\n'.join(lines)
+                log.warning("%s, set_peek Exception: %s", self, util.unicodify(e))
+            dataset.peek = "\n".join(lines)
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1493,10 +1758,10 @@ class Cool(H5):
         URL = "https://github.com/mirnylab/cooler"
 
         if super().sniff(filename):
-            keys = ['chroms', 'bins', 'pixels', 'indexes']
-            with h5py.File(filename, 'r') as handle:
-                fmt = util.unicodify(handle.attrs.get('format'))
-                url = util.unicodify(handle.attrs.get('format-url'))
+            keys = ["chroms", "bins", "pixels", "indexes"]
+            with h5py.File(filename, "r") as handle:
+                fmt = util.unicodify(handle.attrs.get("format"))
+                url = util.unicodify(handle.attrs.get("format-url"))
                 if fmt == MAGIC or url == URL:
                     if not all(name in handle.keys() for name in keys):
                         return False
@@ -1508,8 +1773,8 @@ class Cool(H5):
             dataset.peek = "Cool (HDF5) file for storing genomic interaction data."
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1549,16 +1814,16 @@ class MCool(H5):
         URL = "https://github.com/mirnylab/cooler"
 
         if super().sniff(filename):
-            keys0 = ['resolutions']
-            with h5py.File(filename, 'r') as handle:
+            keys0 = ["resolutions"]
+            with h5py.File(filename, "r") as handle:
                 if not all(name in handle.keys() for name in keys0):
                     return False
-                res0 = next(iter(handle['resolutions'].keys()))
-                keys = ['chroms', 'bins', 'pixels', 'indexes']
-                fmt = util.unicodify(handle['resolutions'][res0].attrs.get('format'))
-                url = util.unicodify(handle['resolutions'][res0].attrs.get('format-url'))
+                res0 = next(iter(handle["resolutions"].keys()))
+                keys = ["chroms", "bins", "pixels", "indexes"]
+                fmt = util.unicodify(handle["resolutions"][res0].attrs.get("format"))
+                url = util.unicodify(handle["resolutions"][res0].attrs.get("format-url"))
                 if fmt == MAGIC or url == URL:
-                    if not all(name in handle['resolutions'][res0].keys() for name in keys):
+                    if not all(name in handle["resolutions"][res0].keys() for name in keys):
                         return False
                     return True
         return False
@@ -1568,8 +1833,8 @@ class MCool(H5):
             dataset.peek = "Multi-resolution Cool (HDF5) file for storing genomic interaction data."
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1582,13 +1847,22 @@ class H5MLM(H5):
     """
     Machine learning model generated by Galaxy-ML.
     """
+
     file_ext = "h5mlm"
     URL = "https://github.com/goeckslab/Galaxy-ML"
 
-    max_peek_size = 1000         # 1 KB
-    max_preview_size = 1000000   # 1 MB
+    max_peek_size = 1000  # 1 KB
+    max_preview_size = 1000000  # 1 MB
 
-    MetadataElement(name="hyper_params", desc="Hyperparameter File", param=FileParameter, file_ext="tabular", readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="hyper_params",
+        desc="Hyperparameter File",
+        param=FileParameter,
+        file_ext="tabular",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         try:
@@ -1605,7 +1879,7 @@ class H5MLM(H5):
                     f.write("\t".join(p) + "\n")
             dataset.metadata.hyper_params = params_file
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
@@ -1624,7 +1898,7 @@ class H5MLM(H5):
                 repr_ = util.unicodify(handle.attrs.get("-repr-"))
             return repr_
         except Exception as e:
-            log.warning('%s, get_repr Except: %s', self, e)
+            log.warning("%s, get_repr Except: %s", self, e)
             return ""
 
     def get_config_string(self, filename):
@@ -1633,17 +1907,17 @@ class H5MLM(H5):
                 config = util.unicodify(handle["-model_config-"][()])
             return config
         except Exception as e:
-            log.warning('%s, get model configuration Except: %s', self, e)
+            log.warning("%s, get model configuration Except: %s", self, e)
             return ""
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             repr_ = self.get_repr(dataset.file_name)
-            dataset.peek = repr_[:self.max_peek_size]
+            dataset.peek = repr_[: self.max_peek_size]
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1662,17 +1936,17 @@ class H5MLM(H5):
         rval = {}
         try:
             with h5py.File(dataset.file_name, "r") as handle:
-                rval['Attributes'] = {}
+                rval["Attributes"] = {}
                 attributes = handle.attrs
-                for k in (set(attributes.keys()) - {'-URL-', '-repr-'}):
-                    rval['Attributes'][k] = util.unicodify(attributes.get(k))
+                for k in set(attributes.keys()) - {"-URL-", "-repr-"}:
+                    rval["Attributes"][k] = util.unicodify(attributes.get(k))
         except Exception as e:
             log.warning(e)
 
         config = self.get_config_string(dataset.file_name)
-        rval['Config'] = json.loads(config) if config else ''
+        rval["Config"] = json.loads(config) if config else ""
         rval = json.dumps(rval, sort_keys=True, indent=2)
-        rval = rval[:self.max_preview_size]
+        rval = rval[: self.max_preview_size]
 
         repr_ = self.get_repr(dataset.file_name)
 
@@ -1683,26 +1957,29 @@ class LudwigModel(Html):
     """
     Composite datatype that encloses multiple files for a Ludwig trained model.
     """
-    composite_type = 'auto_primary_file'
+
+    composite_type = "auto_primary_file"
     file_ext = "ludwig_model"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
 
-        self.add_composite_file('model_hyperparameters.json', description='Model hyperparameters', is_binary=False)
-        self.add_composite_file('model_weights', description='Model weights', is_binary=True)
-        self.add_composite_file('training_set_metadata.json', description='Training set metadata', is_binary=False)
-        self.add_composite_file('training_progress.json', description='Training progress', is_binary=False, optional=True)
+        self.add_composite_file("model_hyperparameters.json", description="Model hyperparameters", is_binary=False)
+        self.add_composite_file("model_weights", description="Model weights", is_binary=True)
+        self.add_composite_file("training_set_metadata.json", description="Training set metadata", is_binary=False)
+        self.add_composite_file(
+            "training_progress.json", description="Training progress", is_binary=False, optional=True
+        )
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Ludwig Model Composite Dataset.</title></head><p/>']
-        rval.append('<div>This model dataset is composed of the following items:<p/><ul>')
+        rval = ["<html><head><title>Ludwig Model Composite Dataset.</title></head><p/>"]
+        rval.append("<div>This model dataset is composed of the following items:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
-            description = composite_file.get('description')
-            link_text = f'{composite_name} ({description})' if description else composite_name
-            opt_text = ' (optional)' if composite_file.optional else ''
+            description = composite_file.get("description")
+            link_text = f"{composite_name} ({description})" if description else composite_name
+            opt_text = " (optional)" if composite_file.optional else ""
             rval.append(f'<li><a href="{composite_name}" type="text/plain">{link_text}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
 
 
@@ -1718,17 +1995,36 @@ class HexrdMaterials(H5):
     >>> HexrdMaterials().sniff(fname)
     False
     """
+
     file_ext = "hexrd.materials.h5"
     edam_format = "format_3590"
 
-    MetadataElement(name="materials", desc="materials", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
-    MetadataElement(name="SpaceGroupNumber", default={}, param=DictParameter, desc="SpaceGroupNumber", readonly=True, visible=True, no_value={})
-    MetadataElement(name="LatticeParameters", default={}, param=DictParameter, desc="LatticeParameters", readonly=True, visible=True, no_value={})
+    MetadataElement(
+        name="materials", desc="materials", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
+    MetadataElement(
+        name="SpaceGroupNumber",
+        default={},
+        param=DictParameter,
+        desc="SpaceGroupNumber",
+        readonly=True,
+        visible=True,
+        no_value={},
+    )
+    MetadataElement(
+        name="LatticeParameters",
+        default={},
+        param=DictParameter,
+        desc="LatticeParameters",
+        readonly=True,
+        visible=True,
+        no_value={},
+    )
 
     def sniff(self, filename):
         if super().sniff(filename):
-            req = {'AtomData', 'Atomtypes', 'CrystalSystem', 'LatticeParameters'}
-            with h5py.File(filename, 'r') as mat_file:
+            req = {"AtomData", "Atomtypes", "CrystalSystem", "LatticeParameters"}
+            with h5py.File(filename, "r") as mat_file:
                 for k in mat_file.keys():
                     if isinstance(mat_file[k], h5py._hl.group.Group) and set(mat_file[k].keys()) >= req:
                         return True
@@ -1737,38 +2033,41 @@ class HexrdMaterials(H5):
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
-            with h5py.File(dataset.file_name, 'r') as mat_file:
+            with h5py.File(dataset.file_name, "r") as mat_file:
                 dataset.metadata.materials = list(mat_file.keys())
                 sgn = dict()
                 lp = dict()
                 for m in mat_file.keys():
-                    if 'SpaceGroupNumber' in mat_file[m] and len(mat_file[m]['SpaceGroupNumber']) > 0:
-                        sgn[m] = mat_file[m]['SpaceGroupNumber'][0].item()
-                    if 'LatticeParameters' in mat_file[m]:
-                        lp[m] = mat_file[m]['LatticeParameters'][0:].tolist()
+                    if "SpaceGroupNumber" in mat_file[m] and len(mat_file[m]["SpaceGroupNumber"]) > 0:
+                        sgn[m] = mat_file[m]["SpaceGroupNumber"][0].item()
+                    if "LatticeParameters" in mat_file[m]:
+                        lp[m] = mat_file[m]["LatticeParameters"][0:].tolist()
                 dataset.metadata.SpaceGroupNumber = sgn
                 dataset.metadata.LatticeParameters = lp
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            lines = ['Material SpaceGroup Lattice']
+            lines = ["Material SpaceGroup Lattice"]
             if dataset.metadata.materials:
                 for m in dataset.metadata.materials:
                     try:
-                        lines.append(f'{m} {dataset.metadata.SpaceGroupNumber[m]} {dataset.metadata.LatticeParameters[m]}')
+                        lines.append(
+                            f"{m} {dataset.metadata.SpaceGroupNumber[m]} {dataset.metadata.LatticeParameters[m]}"
+                        )
                     except Exception:
                         continue
-            dataset.peek = '\n'.join(lines)
+            dataset.peek = "\n".join(lines)
             dataset.blurb = f"Materials: {' '.join(dataset.metadata.materials)}"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class Scf(Binary):
     """Class describing an scf binary sequence file"""
+
     edam_format = "format_1632"
     edam_data = "data_0924"
     file_ext = "scf"
@@ -1778,8 +2077,8 @@ class Scf(Binary):
             dataset.peek = "Binary scf sequence file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1790,7 +2089,8 @@ class Scf(Binary):
 
 @build_sniff_from_prefix
 class Sff(Binary):
-    """ Standard Flowgram Format (SFF) """
+    """Standard Flowgram Format (SFF)"""
+
     edam_format = "format_3284"
     edam_data = "data_0924"
     file_ext = "sff"
@@ -1798,15 +2098,15 @@ class Sff(Binary):
     def sniff_prefix(self, sniff_prefix):
         # The first 4 bytes of any sff file is '.sff', and the file is binary. For details
         # about the format, see http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format
-        return sniff_prefix.startswith_bytes(b'.sff')
+        return sniff_prefix.startswith_bytes(b".sff")
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = "Binary sff file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1822,6 +2122,7 @@ class BigWig(Binary):
     The supplemental info in the paper has the binary details:
     http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351v1
     """
+
     edam_format = "format_3006"
     edam_data = "data_3002"
     file_ext = "bigwig"
@@ -1841,8 +2142,8 @@ class BigWig(Binary):
             dataset.peek = f"Binary UCSC {self._name} file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1853,6 +2154,7 @@ class BigWig(Binary):
 
 class BigBed(BigWig):
     """BigBed support from UCSC."""
+
     edam_format = "format_3004"
     edam_data = "data_3002"
     file_ext = "bigbed"
@@ -1867,6 +2169,7 @@ class BigBed(BigWig):
 @build_sniff_from_prefix
 class TwoBit(Binary):
     """Class describing a TwoBit format nucleotide file"""
+
     edam_format = "format_3009"
     edam_data = "data_0848"
     file_ext = "twobit"
@@ -1891,10 +2194,29 @@ class TwoBit(Binary):
 
 @dataproviders.decorators.has_dataproviders
 class SQlite(Binary):
-    """Class describing a Sqlite database """
-    MetadataElement(name="tables", default=[], param=ListParameter, desc="Database Tables", readonly=True, visible=True, no_value=[])
-    MetadataElement(name="table_columns", default={}, param=DictParameter, desc="Database Table Columns", readonly=True, visible=True, no_value={})
-    MetadataElement(name="table_row_count", default={}, param=DictParameter, desc="Database Table Row Count", readonly=True, visible=True, no_value={})
+    """Class describing a Sqlite database"""
+
+    MetadataElement(
+        name="tables", default=[], param=ListParameter, desc="Database Tables", readonly=True, visible=True, no_value=[]
+    )
+    MetadataElement(
+        name="table_columns",
+        default={},
+        param=DictParameter,
+        desc="Database Table Columns",
+        readonly=True,
+        visible=True,
+        no_value={},
+    )
+    MetadataElement(
+        name="table_row_count",
+        default={},
+        param=DictParameter,
+        desc="Database Table Row Count",
+        readonly=True,
+        visible=True,
+        no_value={},
+    )
     file_ext = "sqlite"
     edam_format = "format_3621"
 
@@ -1913,30 +2235,30 @@ class SQlite(Binary):
             for table, _ in rslt:
                 tables.append(table)
                 try:
-                    col_query = f'SELECT * FROM {table} LIMIT 0'
+                    col_query = f"SELECT * FROM {table} LIMIT 0"
                     cur = conn.cursor().execute(col_query)
                     cols = [col[0] for col in cur.description]
                     columns[table] = cols
                 except Exception as exc:
-                    log.warning('%s, set_meta Exception: %s', self, exc)
+                    log.warning("%s, set_meta Exception: %s", self, exc)
             for table in tables:
                 try:
                     row_query = f"SELECT count(*) FROM {table}"
                     rowcounts[table] = c.execute(row_query).fetchone()[0]
                 except Exception as exc:
-                    log.warning('%s, set_meta Exception: %s', self, exc)
+                    log.warning("%s, set_meta Exception: %s", self, exc)
             dataset.metadata.tables = tables
             dataset.metadata.table_columns = columns
             dataset.metadata.table_row_count = rowcounts
         except Exception as exc:
-            log.warning('%s, set_meta Exception: %s', self, exc)
+            log.warning("%s, set_meta Exception: %s", self, exc)
 
     def sniff(self, filename):
         # The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details
         # about the format, see http://www.sqlite.org/fileformat.html
         try:
-            header = open(filename, 'rb').read(16)
-            if header == b'SQLite format 3\0':
+            header = open(filename, "rb").read(16)
+            if header == b"SQLite format 3\0":
                 return True
             return False
         except Exception:
@@ -1955,24 +2277,24 @@ class SQlite(Binary):
                     return False
             return True
         except Exception as e:
-            log.warning('%s, sniff Exception: %s', self, e)
+            log.warning("%s, sniff Exception: %s", self, e)
         return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = "SQLite Database"
-            lines = ['SQLite Database']
+            lines = ["SQLite Database"]
             if dataset.metadata.tables:
                 for table in dataset.metadata.tables:
                     try:
-                        lines.append(f'{table} [{dataset.metadata.table_row_count[table]}]')
+                        lines.append(f"{table} [{dataset.metadata.table_row_count[table]}]")
                     except Exception:
                         continue
-            dataset.peek = '\n'.join(lines)
+            dataset.peek = "\n".join(lines)
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -1980,26 +2302,36 @@ class SQlite(Binary):
         except Exception:
             return f"SQLite Database ({nice_size(dataset.get_size())})"
 
-    @dataproviders.decorators.dataprovider_factory('sqlite', dataproviders.dataset.SQliteDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("sqlite", dataproviders.dataset.SQliteDataProvider.settings)
     def sqlite_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return dataproviders.dataset.SQliteDataProvider(dataset_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "sqlite-table", dataproviders.dataset.SQliteDataTableProvider.settings
+    )
     def sqlite_datatableprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return dataproviders.dataset.SQliteDataTableProvider(dataset_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("sqlite-dict", dataproviders.dataset.SQliteDataDictProvider.settings)
     def sqlite_datadictprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return dataproviders.dataset.SQliteDataDictProvider(dataset_source, **settings)
 
 
 class GeminiSQLite(SQlite):
-    """Class describing a Gemini Sqlite database """
-    MetadataElement(name="gemini_version", default='0.10.0', param=MetadataParameter, desc="Gemini Version",
-                    readonly=True, visible=True, no_value='0.10.0')
+    """Class describing a Gemini Sqlite database"""
+
+    MetadataElement(
+        name="gemini_version",
+        default="0.10.0",
+        param=MetadataParameter,
+        desc="Gemini Version",
+        readonly=True,
+        visible=True,
+        no_value="0.10.0",
+    )
     file_ext = "gemini.sqlite"
     edam_format = "format_3622"
     edam_data = "data_3498"
@@ -2011,36 +2343,46 @@ class GeminiSQLite(SQlite):
             c = conn.cursor()
             tables_query = "SELECT version FROM version"
             result = c.execute(tables_query).fetchall()
-            for version, in result:
+            for (version,) in result:
                 dataset.metadata.gemini_version = version
             # TODO: Can/should we detect even more attributes, such as use of PED file, what was input annotation type, etc.
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = ["gene_detailed", "gene_summary", "resources", "sample_genotype_counts",
-                           "sample_genotypes", "samples", "variant_impacts", "variants", "version"]
+            table_names = [
+                "gene_detailed",
+                "gene_summary",
+                "resources",
+                "sample_genotype_counts",
+                "sample_genotypes",
+                "samples",
+                "variant_impacts",
+                "variants",
+                "version",
+            ]
             return self.sniff_table_names(filename, table_names)
         return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or 'unknown')
+            dataset.peek = "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or "unknown")
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
             return dataset.peek
         except Exception:
-            return "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or 'unknown')
+            return "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or "unknown")
 
 
 class ChiraSQLite(SQlite):
-    """Class describing a ChiRAViz Sqlite database """
+    """Class describing a ChiRAViz Sqlite database"""
+
     file_ext = "chira.sqlite"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2048,18 +2390,28 @@ class ChiraSQLite(SQlite):
 
     def sniff(self, filename):
         if super().sniff(filename):
-            self.sniff_table_names(filename, ['Chimeras'])
+            self.sniff_table_names(filename, ["Chimeras"])
         return False
 
 
 class CuffDiffSQlite(SQlite):
-    """Class describing a CuffDiff SQLite database """
-    MetadataElement(name="cuffdiff_version", default='2.2.1', param=MetadataParameter, desc="CuffDiff Version",
-                    readonly=True, visible=True, no_value='2.2.1')
-    MetadataElement(name="genes", default=[], param=MetadataParameter, desc="Genes",
-                    readonly=True, visible=True, no_value=[])
-    MetadataElement(name="samples", default=[], param=MetadataParameter, desc="Samples",
-                    readonly=True, visible=True, no_value=[])
+    """Class describing a CuffDiff SQLite database"""
+
+    MetadataElement(
+        name="cuffdiff_version",
+        default="2.2.1",
+        param=MetadataParameter,
+        desc="CuffDiff Version",
+        readonly=True,
+        visible=True,
+        no_value="2.2.1",
+    )
+    MetadataElement(
+        name="genes", default=[], param=MetadataParameter, desc="Genes", readonly=True, visible=True, no_value=[]
+    )
+    MetadataElement(
+        name="samples", default=[], param=MetadataParameter, desc="Samples", readonly=True, visible=True, no_value=[]
+    )
     file_ext = "cuffdiff.sqlite"
     # TODO: Update this when/if there is a specific EDAM format for CuffDiff SQLite data.
     edam_format = "format_3621"
@@ -2073,50 +2425,51 @@ class CuffDiffSQlite(SQlite):
             c = conn.cursor()
             tables_query = "SELECT value FROM runInfo where param = 'version'"
             result = c.execute(tables_query).fetchall()
-            for version, in result:
+            for (version,) in result:
                 dataset.metadata.cuffdiff_version = version
-            genes_query = 'SELECT gene_id, gene_short_name FROM genes ORDER BY gene_short_name'
+            genes_query = "SELECT gene_id, gene_short_name FROM genes ORDER BY gene_short_name"
             result = c.execute(genes_query).fetchall()
             for gene_id, gene_name in result:
                 if gene_name is None:
                     continue
-                gene = f'{gene_id}: {gene_name}'
+                gene = f"{gene_id}: {gene_name}"
                 if gene not in genes:
                     genes.append(gene)
-            samples_query = 'SELECT DISTINCT(sample_name) as sample_name FROM samples ORDER BY sample_name'
+            samples_query = "SELECT DISTINCT(sample_name) as sample_name FROM samples ORDER BY sample_name"
             result = c.execute(samples_query).fetchall()
-            for sample_name, in result:
+            for (sample_name,) in result:
                 if sample_name not in samples:
                     samples.append(sample_name)
             dataset.metadata.genes = genes
             dataset.metadata.samples = samples
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
             # These tables should be in any CuffDiff SQLite output.
-            table_names = ['CDS', 'genes', 'isoforms', 'replicates', 'runInfo', 'samples', 'TSS']
+            table_names = ["CDS", "genes", "isoforms", "replicates", "runInfo", "samples", "TSS"]
             return self.sniff_table_names(filename, table_names)
         return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = "CuffDiff SQLite Database, version %s" % (dataset.metadata.cuffdiff_version or 'unknown')
+            dataset.peek = "CuffDiff SQLite Database, version %s" % (dataset.metadata.cuffdiff_version or "unknown")
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
             return dataset.peek
         except Exception:
-            return "CuffDiff SQLite Database, version %s" % (dataset.metadata.cuffdiff_version or 'unknown')
+            return "CuffDiff SQLite Database, version %s" % (dataset.metadata.cuffdiff_version or "unknown")
 
 
 class MzSQlite(SQlite):
-    """Class describing a Proteomics Sqlite database """
+    """Class describing a Proteomics Sqlite database"""
+
     file_ext = "mz.sqlite"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2124,8 +2477,19 @@ class MzSQlite(SQlite):
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = ["DBSequence", "Modification", "Peaks", "Peptide", "PeptideEvidence",
-                           "Score", "SearchDatabase", "Source", "SpectraData", "Spectrum", "SpectrumIdentification"]
+            table_names = [
+                "DBSequence",
+                "Modification",
+                "Peaks",
+                "Peptide",
+                "PeptideEvidence",
+                "Score",
+                "SearchDatabase",
+                "Source",
+                "SpectraData",
+                "Spectrum",
+                "SpectrumIdentification",
+            ]
             return self.sniff_table_names(filename, table_names)
         return False
 
@@ -2142,6 +2506,7 @@ class PQP(SQlite):
     >>> PQP().sniff(fname)
     False
     """
+
     file_ext = "pqp"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2155,10 +2520,19 @@ class PQP(SQlite):
         """
         if not super().sniff(filename):
             return False
-        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
-                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
-                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
-        osw_table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        table_names = [
+            "COMPOUND",
+            "PEPTIDE",
+            "PEPTIDE_PROTEIN_MAPPING",
+            "PRECURSOR",
+            "PRECURSOR_COMPOUND_MAPPING",
+            "PRECURSOR_PEPTIDE_MAPPING",
+            "PROTEIN",
+            "TRANSITION",
+            "TRANSITION_PEPTIDE_MAPPING",
+            "TRANSITION_PRECURSOR_MAPPING",
+        ]
+        osw_table_names = ["FEATURE", "FEATURE_MS1", "FEATURE_MS2", "FEATURE_TRANSITION", "RUN"]
         return self.sniff_table_names(filename, table_names) and not self.sniff_table_names(filename, osw_table_names)
 
 
@@ -2174,6 +2548,7 @@ class OSW(SQlite):
     >>> OSW().sniff(fname)
     False
     """
+
     file_ext = "osw"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2184,10 +2559,23 @@ class OSW(SQlite):
         # see also here https://github.com/OpenMS/OpenMS/issues/4365
         if not super().sniff(filename):
             return False
-        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
-                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
-                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING',
-                       'FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        table_names = [
+            "COMPOUND",
+            "PEPTIDE",
+            "PEPTIDE_PROTEIN_MAPPING",
+            "PRECURSOR",
+            "PRECURSOR_COMPOUND_MAPPING",
+            "PRECURSOR_PEPTIDE_MAPPING",
+            "PROTEIN",
+            "TRANSITION",
+            "TRANSITION_PEPTIDE_MAPPING",
+            "TRANSITION_PRECURSOR_MAPPING",
+            "FEATURE",
+            "FEATURE_MS1",
+            "FEATURE_MS2",
+            "FEATURE_TRANSITION",
+            "RUN",
+        ]
         return self.sniff_table_names(filename, table_names)
 
 
@@ -2203,6 +2591,7 @@ class SQmass(SQlite):
     >>> SQmass().sniff(fname)
     False
     """
+
     file_ext = "sqmass"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2216,9 +2605,17 @@ class SQmass(SQlite):
 
 
 class BlibSQlite(SQlite):
-    """Class describing a Proteomics Spectral Library Sqlite database """
-    MetadataElement(name="blib_version", default='1.8', param=MetadataParameter, desc="Blib Version",
-                    readonly=True, visible=True, no_value='1.8')
+    """Class describing a Proteomics Spectral Library Sqlite database"""
+
+    MetadataElement(
+        name="blib_version",
+        default="1.8",
+        param=MetadataParameter,
+        desc="Blib Version",
+        readonly=True,
+        visible=True,
+        no_value="1.8",
+    )
     file_ext = "blib"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2228,14 +2625,22 @@ class BlibSQlite(SQlite):
             c = conn.cursor()
             tables_query = "SELECT majorVersion,minorVersion FROM LibInfo"
             (majorVersion, minorVersion) = c.execute(tables_query).fetchall()[0]
-            dataset.metadata.blib_version = f'{majorVersion}.{minorVersion}'
+            dataset.metadata.blib_version = f"{majorVersion}.{minorVersion}"
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = ['IonMobilityTypes', 'LibInfo', 'Modifications', 'RefSpectra',
-                           'RefSpectraPeakAnnotations', 'RefSpectraPeaks', 'ScoreTypes', 'SpectrumSourceFiles']
+            table_names = [
+                "IonMobilityTypes",
+                "LibInfo",
+                "Modifications",
+                "RefSpectra",
+                "RefSpectraPeakAnnotations",
+                "RefSpectraPeaks",
+                "ScoreTypes",
+                "SpectrumSourceFiles",
+            ]
             return self.sniff_table_names(filename, table_names)
         return False
 
@@ -2254,8 +2659,16 @@ class DlibSQlite(SQlite):
     >>> DlibSQlite().sniff(fname)
     False
     """
-    MetadataElement(name="dlib_version", default='1.8', param=MetadataParameter, desc="Dlib Version",
-                    readonly=True, visible=True, no_value='1.8')
+
+    MetadataElement(
+        name="dlib_version",
+        default="1.8",
+        param=MetadataParameter,
+        desc="Dlib Version",
+        readonly=True,
+        visible=True,
+        no_value="1.8",
+    )
     file_ext = "dlib"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2265,13 +2678,13 @@ class DlibSQlite(SQlite):
             c = conn.cursor()
             tables_query = "SELECT Value FROM metadata WHERE Key = 'version'"
             version = c.execute(tables_query).fetchall()[0]
-            dataset.metadata.dlib_version = f'{version}'
+            dataset.metadata.dlib_version = f"{version}"
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = ['entries', 'metadata', 'peptidetoprotein']
+            table_names = ["entries", "metadata", "peptidetoprotein"]
             return self.sniff_table_names(filename, table_names)
         return False
 
@@ -2290,8 +2703,16 @@ class ElibSQlite(SQlite):
     >>> ElibSQlite().sniff(fname)
     False
     """
-    MetadataElement(name="version", default='0.1.14', param=MetadataParameter, desc="Elib Version",
-                    readonly=True, visible=True, no_value='0.1.14')
+
+    MetadataElement(
+        name="version",
+        default="0.1.14",
+        param=MetadataParameter,
+        desc="Elib Version",
+        readonly=True,
+        visible=True,
+        no_value="0.1.14",
+    )
     file_ext = "elib"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2301,14 +2722,23 @@ class ElibSQlite(SQlite):
             c = conn.cursor()
             tables_query = "SELECT Value FROM metadata WHERE Key = 'version'"
             version = c.execute(tables_query).fetchall()[0]
-            dataset.metadata.dlib_version = f'{version}'
+            dataset.metadata.dlib_version = f"{version}"
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = ['entries', 'fragmentquants', 'metadata', 'peptidelocalizations', 'peptidequants',
-                           'peptidescores', 'peptidetoprotein', 'proteinscores', 'retentiontimes']
+            table_names = [
+                "entries",
+                "fragmentquants",
+                "metadata",
+                "peptidelocalizations",
+                "peptidequants",
+                "peptidescores",
+                "peptidetoprotein",
+                "proteinscores",
+                "retentiontimes",
+            ]
             if self.sniff_table_names(filename, table_names):
                 try:
                     conn = sqlite.connect(filename)
@@ -2317,7 +2747,7 @@ class ElibSQlite(SQlite):
                     count = c.execute(row_query).fetchone()[0]
                     return int(count) > 0
                 except Exception as e:
-                    log.warning('%s, sniff Exception: %s', self, e)
+                    log.warning("%s, sniff Exception: %s", self, e)
         return False
 
 
@@ -2333,6 +2763,7 @@ class IdpDB(SQlite):
     >>> IdpDB().sniff(fname)
     False
     """
+
     file_ext = "idpdb"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2340,8 +2771,14 @@ class IdpDB(SQlite):
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = ["About", "Analysis", "AnalysisParameter", "PeptideSpectrumMatch",
-                           "Spectrum", "SpectrumSource"]
+            table_names = [
+                "About",
+                "Analysis",
+                "AnalysisParameter",
+                "PeptideSpectrumMatch",
+                "Spectrum",
+                "SpectrumSource",
+            ]
             return self.sniff_table_names(filename, table_names)
         return False
 
@@ -2350,8 +2787,8 @@ class IdpDB(SQlite):
             dataset.peek = "IDPickerDB SQLite file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -2362,62 +2799,85 @@ class IdpDB(SQlite):
 
 class GAFASQLite(SQlite):
     """Class describing a GAFA SQLite database"""
-    MetadataElement(name='gafa_schema_version', default='0.3.0', param=MetadataParameter, desc='GAFA schema version',
-                    readonly=True, visible=True, no_value='0.3.0')
-    file_ext = 'gafa.sqlite'
+
+    MetadataElement(
+        name="gafa_schema_version",
+        default="0.3.0",
+        param=MetadataParameter,
+        desc="GAFA schema version",
+        readonly=True,
+        visible=True,
+        no_value="0.3.0",
+    )
+    file_ext = "gafa.sqlite"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
             conn = sqlite.connect(dataset.file_name)
             c = conn.cursor()
-            version_query = 'SELECT version FROM meta'
+            version_query = "SELECT version FROM meta"
             results = c.execute(version_query).fetchall()
             if len(results) == 0:
-                raise Exception('version not found in meta table')
+                raise Exception("version not found in meta table")
             elif len(results) > 1:
-                raise Exception('Multiple versions found in meta table')
+                raise Exception("Multiple versions found in meta table")
             dataset.metadata.gafa_schema_version = results[0][0]
         except Exception as e:
             log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = frozenset({'gene', 'gene_family', 'gene_family_member', 'meta', 'transcript'})
+            table_names = frozenset({"gene", "gene_family", "gene_family_member", "meta", "transcript"})
             return self.sniff_table_names(filename, table_names)
         return False
 
 
 class NcbiTaxonomySQlite(SQlite):
     """Class describing the NCBI Taxonomy database stored in SQLite as done by rust-ncbitaxonomy"""
-    MetadataElement(name='ncbitaxonomy_schema_version', default='20200501095116', param=MetadataParameter, desc='ncbitaxonomy schema version',
-                    readonly=True, visible=True, no_value='20200501095116')
-    MetadataElement(name="taxon_count", default=[], param=MetadataParameter, desc="Count of taxa in the taxonomy",
-                    readonly=True, visible=True, no_value=[])
 
-    file_ext = 'ncbitaxonomy.sqlite'
+    MetadataElement(
+        name="ncbitaxonomy_schema_version",
+        default="20200501095116",
+        param=MetadataParameter,
+        desc="ncbitaxonomy schema version",
+        readonly=True,
+        visible=True,
+        no_value="20200501095116",
+    )
+    MetadataElement(
+        name="taxon_count",
+        default=[],
+        param=MetadataParameter,
+        desc="Count of taxa in the taxonomy",
+        readonly=True,
+        visible=True,
+        no_value=[],
+    )
+
+    file_ext = "ncbitaxonomy.sqlite"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
             conn = sqlite.connect(dataset.file_name)
             c = conn.cursor()
-            version_query = 'SELECT version FROM __diesel_schema_migrations ORDER BY run_on DESC LIMIT 1'
+            version_query = "SELECT version FROM __diesel_schema_migrations ORDER BY run_on DESC LIMIT 1"
             results = c.execute(version_query).fetchall()
             if len(results) == 0:
-                raise Exception('version not found in __diesel_schema_migrations table')
+                raise Exception("version not found in __diesel_schema_migrations table")
             dataset.metadata.ncbitaxonomy_schema_version = results[0][0]
-            taxons_query = 'SELECT count(name) FROM taxonomy'
+            taxons_query = "SELECT count(name) FROM taxonomy"
             results = c.execute(taxons_query).fetchall()
             if len(results) == 0:
-                raise Exception('could not count size of taxonomy table')
+                raise Exception("could not count size of taxonomy table")
             dataset.metadata.taxon_count = results[0][0]
         except Exception as e:
             log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super().sniff(filename):
-            table_names = frozenset({'__diesel_schema_migrations', 'taxonomy'})
+            table_names = frozenset({"__diesel_schema_migrations", "taxonomy"})
             return self.sniff_table_names(filename, table_names)
         return False
 
@@ -2425,12 +2885,12 @@ class NcbiTaxonomySQlite(SQlite):
         if not dataset.dataset.purged:
             dataset.peek = "NCBI Taxonomy SQLite Database, version {} ({} taxons)".format(
                 getattr(dataset.metadata, "ncbitaxonomy_schema_version", "unknown"),
-                getattr(dataset.metadata, "taxon_count", "unknown")
+                getattr(dataset.metadata, "taxon_count", "unknown"),
             )
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -2438,12 +2898,13 @@ class NcbiTaxonomySQlite(SQlite):
         except Exception:
             return "NCBI Taxonomy SQLite Database, version {} ({} taxons)".format(
                 getattr(dataset.metadata, "ncbitaxonomy_schema_version", "unknown"),
-                getattr(dataset.metadata, "taxon_count", "unknown")
+                getattr(dataset.metadata, "taxon_count", "unknown"),
             )
 
 
 class Xlsx(Binary):
     """Class for Excel 2007 (xlsx) files"""
+
     file_ext = "xlsx"
     compressed = True
 
@@ -2452,7 +2913,13 @@ class Xlsx(Binary):
         try:
             if zipfile.is_zipfile(filename):
                 tempzip = zipfile.ZipFile(filename)
-                if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1:
+                if (
+                    "[Content_Types].xml" in tempzip.namelist()
+                    and tempzip.read("[Content_Types].xml").find(
+                        b"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml"
+                    )
+                    != -1
+                ):
                     return True
             return False
         except Exception:
@@ -2461,24 +2928,25 @@ class Xlsx(Binary):
 
 class ExcelXls(Binary):
     """Class describing an Excel (xls) file"""
+
     file_ext = "excel.xls"
     edam_format = "format_3468"
 
     def sniff(self, filename):
-        mime_type = subprocess.check_output(['file', '--mime-type', filename])
+        mime_type = subprocess.check_output(["file", "--mime-type", filename])
         return b"application/vnd.ms-excel" in mime_type
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/vnd.ms-excel'
+        return "application/vnd.ms-excel"
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = "Microsoft Excel XLS file"
             dataset.blurb = data.nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -2489,28 +2957,29 @@ class ExcelXls(Binary):
 
 @build_sniff_from_prefix
 class Sra(Binary):
-    """ Sequence Read Archive (SRA) datatype originally from mdshw5/sra-tools-galaxy"""
-    file_ext = 'sra'
+    """Sequence Read Archive (SRA) datatype originally from mdshw5/sra-tools-galaxy"""
+
+    file_ext = "sra"
 
     def sniff_prefix(self, sniff_prefix):
-        """ The first 8 bytes of any NCBI sra file is 'NCBI.sra', and the file is binary.
+        """The first 8 bytes of any NCBI sra file is 'NCBI.sra', and the file is binary.
         For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
         """
-        return sniff_prefix.startswith_bytes(b'NCBI.sra')
+        return sniff_prefix.startswith_bytes(b"NCBI.sra")
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = 'Binary sra file'
+            dataset.peek = "Binary sra file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
             return dataset.peek
         except Exception:
-            return f'Binary sra file ({nice_size(dataset.get_size())})'
+            return f"Binary sra file ({nice_size(dataset.get_size())})"
 
 
 @build_sniff_from_prefix
@@ -2532,11 +3001,20 @@ class RData(CompressedArchive):
     >>> dataset.metadata.version
     '3'
     """
-    VERSION_2_PREFIX = b'RDX2\nX\n'
-    VERSION_3_PREFIX = b'RDX3\nX\n'
-    file_ext = 'rdata'
 
-    MetadataElement(name="version", default=None, desc="serialisation version", param=MetadataParameter, readonly=True, visible=False, optional=False)
+    VERSION_2_PREFIX = b"RDX2\nX\n"
+    VERSION_3_PREFIX = b"RDX3\nX\n"
+    file_ext = "rdata"
+
+    MetadataElement(
+        name="version",
+        default=None,
+        desc="serialisation version",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=False,
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
@@ -2590,17 +3068,47 @@ class RDS(CompressedArchive):
     >>> dataset.metadata.minrversion
     '3.5.0'
     """
-    file_ext = 'rds'
 
-    MetadataElement(name="version", default=None, desc="serialisation version", param=MetadataParameter, readonly=True, visible=False, optional=False)
-    MetadataElement(name="rversion", default=None, desc="R version", param=MetadataParameter, readonly=True, visible=False, optional=False)
-    MetadataElement(name="minrversion", default=None, desc="minimum R version", param=MetadataParameter, readonly=False, visible=True, optional=False)
+    file_ext = "rds"
+
+    MetadataElement(
+        name="version",
+        default=None,
+        desc="serialisation version",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=False,
+    )
+    MetadataElement(
+        name="rversion",
+        default=None,
+        desc="R version",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=False,
+    )
+    MetadataElement(
+        name="minrversion",
+        default=None,
+        desc="minimum R version",
+        param=MetadataParameter,
+        readonly=False,
+        visible=True,
+        optional=False,
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         _, fh = compression_utils.get_fileobj_raw(dataset.file_name, "rb")
         try:
-            _, dataset.metadata.version, dataset.metadata.rversion, dataset.metadata.minrversion = self._parse_rds_header(fh.read(14))
+            (
+                _,
+                dataset.metadata.version,
+                dataset.metadata.rversion,
+                dataset.metadata.minrversion,
+            ) = self._parse_rds_header(fh.read(14))
         except Exception:
             pass
         finally:
@@ -2623,9 +3131,9 @@ class RDS(CompressedArchive):
           - the minimum r version needed to read the file
         """
         header = header_bytes[:2]
-        if header == b'X\n':
+        if header == b"X\n":
             mode = "X"
-        elif header == b'A\n':
+        elif header == b"A\n":
             mode = "A"
         else:
             raise Exception()
@@ -2644,13 +3152,12 @@ class RDS(CompressedArchive):
 
 
 class OxliBinary(Binary):
-
     @staticmethod
     def _sniff(filename, oxlitype):
         try:
-            with open(filename, 'rb') as fileobj:
+            with open(filename, "rb") as fileobj:
                 header = fileobj.read(4)
-                if header == b'OXLI':
+                if header == b"OXLI":
                     fileobj.read(1)  # skip the version number
                     ftype = fileobj.read(1)
                     if binascii.hexlify(ftype) == oxlitype:
@@ -2679,7 +3186,8 @@ class OxliCountGraph(OxliBinary):
     >>> OxliCountGraph().sniff(fname)
     True
     """
-    file_ext = 'oxlicg'
+
+    file_ext = "oxlicg"
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"01")
@@ -2704,7 +3212,8 @@ class OxliNodeGraph(OxliBinary):
     >>> OxliNodeGraph().sniff(fname)
     True
     """
-    file_ext = 'oxling'
+
+    file_ext = "oxling"
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"02")
@@ -2730,7 +3239,8 @@ class OxliTagSet(OxliBinary):
     >>> OxliTagSet().sniff(fname)
     True
     """
-    file_ext = 'oxlits'
+
+    file_ext = "oxlits"
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"03")
@@ -2751,7 +3261,8 @@ class OxliStopTags(OxliBinary):
     >>> OxliStopTags().sniff(fname)
     True
     """
-    file_ext = 'oxlist'
+
+    file_ext = "oxlist"
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"04")
@@ -2777,7 +3288,8 @@ class OxliSubset(OxliBinary):
     >>> OxliSubset().sniff(fname)
     True
     """
-    file_ext = 'oxliss'
+
+    file_ext = "oxliss"
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"05")
@@ -2804,7 +3316,8 @@ class OxliGraphLabels(OxliBinary):
     >>> OxliGraphLabels().sniff(fname)
     True
     """
-    file_ext = 'oxligl'
+
+    file_ext = "oxligl"
 
     def sniff(self, filename):
         return OxliBinary._sniff(filename, b"06")
@@ -2822,33 +3335,40 @@ class PostgresqlArchive(CompressedArchive):
     >>> PostgresqlArchive().sniff(fname)
     False
     """
-    MetadataElement(name="version", default=None, param=MetadataParameter, desc="PostgreSQL database version",
-                    readonly=True, visible=True)
+
+    MetadataElement(
+        name="version",
+        default=None,
+        param=MetadataParameter,
+        desc="PostgreSQL database version",
+        readonly=True,
+        visible=True,
+    )
     file_ext = "postgresql"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
             if dataset and tarfile.is_tarfile(dataset.file_name):
-                with tarfile.open(dataset.file_name, 'r') as temptar:
-                    pg_version_file = temptar.extractfile('postgresql/db/PG_VERSION')
+                with tarfile.open(dataset.file_name, "r") as temptar:
+                    pg_version_file = temptar.extractfile("postgresql/db/PG_VERSION")
                     dataset.metadata.version = util.unicodify(pg_version_file.read()).strip()
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, util.unicodify(e))
+            log.warning("%s, set_meta Exception: %s", self, util.unicodify(e))
 
     def sniff(self, filename):
         if filename and tarfile.is_tarfile(filename):
-            with tarfile.open(filename, 'r') as temptar:
-                return 'postgresql/db/PG_VERSION' in temptar.getnames()
+            with tarfile.open(filename, "r") as temptar:
+                return "postgresql/db/PG_VERSION" in temptar.getnames()
         return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = f"PostgreSQL Archive ({nice_size(dataset.get_size())})"
-            dataset.blurb = "PostgreSQL version %s" % (dataset.metadata.version or 'unknown')
+            dataset.blurb = "PostgreSQL version %s" % (dataset.metadata.version or "unknown")
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -2866,43 +3386,43 @@ class Fast5Archive(CompressedArchive):
     >>> Fast5Archive().sniff(fname)
     True
     """
-    MetadataElement(name="fast5_count", default='0', param=MetadataParameter, desc="Read Count",
-                    readonly=True, visible=True)
+
+    MetadataElement(
+        name="fast5_count", default="0", param=MetadataParameter, desc="Read Count", readonly=True, visible=True
+    )
     file_ext = "fast5.tar"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
             if dataset and tarfile.is_tarfile(dataset.file_name):
-                with tarfile.open(dataset.file_name, 'r') as temptar:
-                    dataset.metadata.fast5_count = sum(
-                        1 for f in temptar if f.name.endswith('.fast5')
-                    )
+                with tarfile.open(dataset.file_name, "r") as temptar:
+                    dataset.metadata.fast5_count = sum(1 for f in temptar if f.name.endswith(".fast5"))
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         try:
             if filename and tarfile.is_tarfile(filename):
-                with tarfile.open(filename, 'r') as temptar:
+                with tarfile.open(filename, "r") as temptar:
                     for f in temptar:
                         if not f.isfile():
                             continue
-                        if f.name.endswith('.fast5'):
+                        if f.name.endswith(".fast5"):
                             return True
                         else:
                             return False
         except Exception as e:
-            log.warning('%s, sniff Exception: %s', self, e)
+            log.warning("%s, sniff Exception: %s", self, e)
         return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = f"FAST5 Archive ({nice_size(dataset.get_size())})"
-            dataset.blurb = "%s sequences" % (dataset.metadata.fast5_count or 'unknown')
+            dataset.blurb = "%s sequences" % (dataset.metadata.fast5_count or "unknown")
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -2926,6 +3446,7 @@ class Fast5ArchiveGz(Fast5Archive):
     >>> Fast5ArchiveGz().sniff(fname)
     False
     """
+
     file_ext = "fast5.tar.gz"
 
     def sniff(self, filename):
@@ -2949,6 +3470,7 @@ class Fast5ArchiveBz2(Fast5Archive):
     >>> Fast5ArchiveBz2().sniff(fname)
     False
     """
+
     file_ext = "fast5.tar.bz2"
 
     def sniff(self, filename):
@@ -2958,11 +3480,24 @@ class Fast5ArchiveBz2(Fast5Archive):
 
 
 class SearchGuiArchive(CompressedArchive):
-    """Class describing a SearchGUI archive """
-    MetadataElement(name="searchgui_version", default='1.28.0', param=MetadataParameter, desc="SearchGui Version",
-                    readonly=True, visible=True)
-    MetadataElement(name="searchgui_major_version", default='1', param=MetadataParameter, desc="SearchGui Major Version",
-                    readonly=True, visible=True)
+    """Class describing a SearchGUI archive"""
+
+    MetadataElement(
+        name="searchgui_version",
+        default="1.28.0",
+        param=MetadataParameter,
+        desc="SearchGui Version",
+        readonly=True,
+        visible=True,
+    )
+    MetadataElement(
+        name="searchgui_major_version",
+        default="1",
+        param=MetadataParameter,
+        desc="SearchGui Major Version",
+        readonly=True,
+        visible=True,
+    )
     file_ext = "searchgui_archive"
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -2970,44 +3505,45 @@ class SearchGuiArchive(CompressedArchive):
         try:
             if dataset and zipfile.is_zipfile(dataset.file_name):
                 with zipfile.ZipFile(dataset.file_name) as tempzip:
-                    if 'searchgui.properties' in tempzip.namelist():
-                        with tempzip.open('searchgui.properties') as fh:
+                    if "searchgui.properties" in tempzip.namelist():
+                        with tempzip.open("searchgui.properties") as fh:
                             for line in io.TextIOWrapper(fh):
-                                if line.startswith('searchgui.version'):
-                                    version = line.split('=')[1].strip()
+                                if line.startswith("searchgui.version"):
+                                    version = line.split("=")[1].strip()
                                     dataset.metadata.searchgui_version = version
-                                    dataset.metadata.searchgui_major_version = version.split('.')[0]
+                                    dataset.metadata.searchgui_major_version = version.split(".")[0]
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         try:
             if filename and zipfile.is_zipfile(filename):
-                with zipfile.ZipFile(filename, 'r') as tempzip:
-                    is_searchgui = 'searchgui.properties' in tempzip.namelist()
+                with zipfile.ZipFile(filename, "r") as tempzip:
+                    is_searchgui = "searchgui.properties" in tempzip.namelist()
                 return is_searchgui
         except Exception as e:
-            log.warning('%s, sniff Exception: %s', self, e)
+            log.warning("%s, sniff Exception: %s", self, e)
         return False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or 'unknown')
+            dataset.peek = "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or "unknown")
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
             return dataset.peek
         except Exception:
-            return "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or 'unknown')
+            return "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or "unknown")
 
 
 @build_sniff_from_prefix
 class NetCDF(Binary):
     """Binary data in netCDF format"""
+
     file_ext = "netcdf"
     edam_format = "format_3650"
     edam_data = "data_0943"
@@ -3017,8 +3553,8 @@ class NetCDF(Binary):
             dataset.peek = "Binary netCDF file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3027,7 +3563,7 @@ class NetCDF(Binary):
             return f"Binary netCDF file ({nice_size(dataset.get_size())})"
 
     def sniff_prefix(self, sniff_prefix):
-        return sniff_prefix.startswith_bytes(b'CDF')
+        return sniff_prefix.startswith_bytes(b"CDF")
 
 
 class Dcd(Binary):
@@ -3042,18 +3578,19 @@ class Dcd(Binary):
     >>> Dcd().sniff(fname)
     False
     """
+
     file_ext = "dcd"
     edam_data = "data_3842"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self._magic_number = b'CORD'
+        self._magic_number = b"CORD"
 
     def sniff(self, filename):
         # Match the keyword 'CORD' at position 4 or 8 - intsize dependent
         # Not checking for endianness
         try:
-            with open(filename, 'rb') as header:
+            with open(filename, "rb") as header:
                 intsize = 4
                 header.seek(intsize)
                 if header.read(intsize) == self._magic_number:
@@ -3072,8 +3609,8 @@ class Dcd(Binary):
             dataset.peek = "Binary CHARMM/NAMD dcd file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3094,17 +3631,18 @@ class Vel(Binary):
     >>> Vel().sniff(fname)
     False
     """
+
     file_ext = "vel"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self._magic_number = b'VELD'
+        self._magic_number = b"VELD"
 
     def sniff(self, filename):
         # Match the keyword 'VELD' at position 4 or 8 - intsize dependent
         # Not checking for endianness
         try:
-            with open(filename, 'rb') as header:
+            with open(filename, "rb") as header:
                 intsize = 4
                 header.seek(intsize)
                 if header.read(intsize) == self._magic_number:
@@ -3123,8 +3661,8 @@ class Vel(Binary):
             dataset.peek = "Binary CHARMM velocity file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3145,6 +3683,7 @@ class DAA(Binary):
     >>> DAA().sniff(fname)
     False
     """
+
     file_ext = "daa"
 
     def __init__(self, **kwd):
@@ -3168,6 +3707,7 @@ class RMA6(Binary):
     >>> RMA6().sniff(fname)
     False
     """
+
     file_ext = "rma6"
 
     def __init__(self, **kwd):
@@ -3190,6 +3730,7 @@ class DMND(Binary):
     >>> DMND().sniff(fname)
     False
     """
+
     file_ext = "dmnd"
 
     def __init__(self, **kwd):
@@ -3205,6 +3746,7 @@ class ICM(Binary):
     """
     Class describing an ICM (interpolated context model) file, used by Glimmer
     """
+
     file_ext = "icm"
     edam_data = "data_0950"
 
@@ -3213,12 +3755,18 @@ class ICM(Binary):
             dataset.peek = "Binary ICM (interpolated context model) file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, dataset):
         line = open(dataset).read(100)
-        if '>ver = ' in line and 'len = ' in line and 'depth = ' in line and 'periodicity =' in line and 'nodes = ' in line:
+        if (
+            ">ver = " in line
+            and "len = " in line
+            and "depth = " in line
+            and "periodicity =" in line
+            and "nodes = " in line
+        ):
             return True
 
         return False
@@ -3236,6 +3784,7 @@ class Parquet(Binary):
     >>> Parquet().sniff(fname)
     False
     """
+
     file_ext = "parquet"
 
     def __init__(self, **kwd):
@@ -3257,6 +3806,7 @@ class BafTar(CompressedArchive):
     >>> BafTar().sniff(fname)
     False
     """
+
     edam_data = "data_2536"  # mass spectrometry data
     edam_format = "format_3712"  # TODO: add more raw formats to EDAM?
     file_ext = "brukerbaf.d.tar"
@@ -3278,8 +3828,8 @@ class BafTar(CompressedArchive):
             dataset.peek = self.get_type()
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3289,7 +3839,8 @@ class BafTar(CompressedArchive):
 
 
 class YepTar(BafTar):
-    """ A tar'd up .d directory containing Agilent/Bruker YEP format data """
+    """A tar'd up .d directory containing Agilent/Bruker YEP format data"""
+
     file_ext = "agilentbrukeryep.d.tar"
 
     def get_signature_file(self):
@@ -3300,7 +3851,8 @@ class YepTar(BafTar):
 
 
 class TdfTar(BafTar):
-    """ A tar'd up .d directory containing Bruker TDF format data """
+    """A tar'd up .d directory containing Bruker TDF format data"""
+
     file_ext = "brukertdf.d.tar"
 
     def get_signature_file(self):
@@ -3311,7 +3863,8 @@ class TdfTar(BafTar):
 
 
 class MassHunterTar(BafTar):
-    """ A tar'd up .d directory containing Agilent MassHunter format data """
+    """A tar'd up .d directory containing Agilent MassHunter format data"""
+
     file_ext = "agilentmasshunter.d.tar"
 
     def get_signature_file(self):
@@ -3322,7 +3875,8 @@ class MassHunterTar(BafTar):
 
 
 class MassLynxTar(BafTar):
-    """ A tar'd up .d directory containing Waters MassLynx format data """
+    """A tar'd up .d directory containing Waters MassLynx format data"""
+
     file_ext = "watersmasslynx.raw.tar"
 
     def get_signature_file(self):
@@ -3346,6 +3900,7 @@ class WiffTar(BafTar):
     >>> WiffTar().sniff(fname)
     False
     """
+
     file_ext = "wiff.tar"
 
     def sniff(self, filename):
@@ -3368,20 +3923,21 @@ class Pretext(Binary):
     >>> Pretext().sniff(fname)
     True
     """
+
     file_ext = "pretext"
 
     def sniff_prefix(self, sniff_prefix):
         # The first 4 bytes of any pretext file is 'pstm', and the rest of the
         # file contains binary data.
-        return sniff_prefix.startswith_bytes(b'pstm')
+        return sniff_prefix.startswith_bytes(b"pstm")
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = "Binary pretext file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3401,6 +3957,7 @@ class JP2(Binary):
     >>> JP2().sniff(fname)
     False
     """
+
     file_ext = "jp2"
 
     def __init__(self, **kwd):
@@ -3410,7 +3967,7 @@ class JP2(Binary):
     def sniff(self, filename):
         # The first 12 bytes of any jp2 file are 0000000C6A5020200D0A870A
         try:
-            header = open(filename, 'rb').read(12)
+            header = open(filename, "rb").read(12)
             if header == self._magic:
                 return True
             return False
@@ -3422,8 +3979,8 @@ class JP2(Binary):
             dataset.peek = "Binary JPEG 2000 file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3444,6 +4001,7 @@ class Npz(CompressedArchive):
     >>> Npz().sniff(fname)
     False
     """
+
     file_ext = "npz"
     # edam_format = "format_4003"
 
@@ -3470,15 +4028,15 @@ class Npz(CompressedArchive):
                 dataset.metadata.nfiles = len(npz.files)
                 dataset.metadata.files = npz.files
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = f"Binary Numpy npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3499,10 +4057,22 @@ class HexrdImagesNpz(Npz):
     >>> HexrdImagesNpz().sniff(fname)
     False
     """
+
     file_ext = "hexrd.images.npz"
 
-    MetadataElement(name="panel_id", default='', desc="Detector Panel ID", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value='')
-    MetadataElement(name="shape", default=(), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=())
+    MetadataElement(
+        name="panel_id",
+        default="",
+        desc="Detector Panel ID",
+        param=MetadataParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="shape", default=(), desc="shape", param=metadata.ListParameter, readonly=True, visible=True, no_value=()
+    )
     MetadataElement(name="nframes", default=0, desc="nframes", readonly=True, visible=True, no_value=0)
     MetadataElement(name="omegas", desc="has omegas", default="False", visible=False)
 
@@ -3512,11 +4082,11 @@ class HexrdImagesNpz(Npz):
     def sniff(self, filename):
         if super().sniff(filename):
             try:
-                req_files = {'0_row', '0_col', '0_data', 'shape', 'nframes', 'dtype'}
+                req_files = {"0_row", "0_col", "0_data", "shape", "nframes", "dtype"}
                 with np.load(filename) as npz:
                     return set(npz.files) >= req_files
             except Exception as e:
-                log.warning('%s, sniff Exception: %s', self, e)
+                log.warning("%s, sniff Exception: %s", self, e)
                 return False
         return False
 
@@ -3524,24 +4094,26 @@ class HexrdImagesNpz(Npz):
         super().set_meta(dataset, **kwd)
         try:
             with np.load(dataset.file_name) as npz:
-                if 'panel_id' in npz.files:
-                    dataset.metadata.panel_id = str(npz['panel_id'])
-                if 'omega' in npz.files:
+                if "panel_id" in npz.files:
+                    dataset.metadata.panel_id = str(npz["panel_id"])
+                if "omega" in npz.files:
                     dataset.metadata.omegas = "True"
-                dataset.metadata.shape = npz['shape'].tolist()
-                dataset.metadata.nframes = npz['nframes'].tolist()
+                dataset.metadata.shape = npz["shape"].tolist()
+                dataset.metadata.nframes = npz["nframes"].tolist()
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            lines = [f"Binary Hexrd Image npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})",
-                     f"Panel: {dataset.metadata.panel_id} Frames: {dataset.metadata.nframes} Shape: {dataset.metadata.shape}"]
-            dataset.peek = '\n'.join(lines)
+            lines = [
+                f"Binary Hexrd Image npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})",
+                f"Panel: {dataset.metadata.panel_id} Frames: {dataset.metadata.nframes} Shape: {dataset.metadata.shape}",
+            ]
+            dataset.peek = "\n".join(lines)
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3562,9 +4134,12 @@ class HexrdEtaOmeNpz(Npz):
     >>> HexrdEtaOmeNpz().sniff(fname)
     False
     """
+
     file_ext = "hexrd.eta_ome.npz"
 
-    MetadataElement(name="HKLs", default=(), desc="HKLs", param=metadata.ListParameter, readonly=True, visible=True, no_value=())
+    MetadataElement(
+        name="HKLs", default=(), desc="HKLs", param=metadata.ListParameter, readonly=True, visible=True, no_value=()
+    )
     MetadataElement(name="nframes", default=0, desc="nframes", readonly=True, visible=True, no_value=0)
 
     def __init__(self, **kwd):
@@ -3573,11 +4148,11 @@ class HexrdEtaOmeNpz(Npz):
     def sniff(self, filename):
         if super().sniff(filename):
             try:
-                req_files = {'dataStore', 'etas', 'etaEdges', 'iHKLList', 'omegas', 'omeEdges', 'planeData_hkls'}
+                req_files = {"dataStore", "etas", "etaEdges", "iHKLList", "omegas", "omeEdges", "planeData_hkls"}
                 with np.load(filename) as npz:
                     return set(npz.files) >= req_files
             except Exception as e:
-                log.warning('%s, sniff Exception: %s', self, e)
+                log.warning("%s, sniff Exception: %s", self, e)
                 return False
         return False
 
@@ -3585,20 +4160,22 @@ class HexrdEtaOmeNpz(Npz):
         super().set_meta(dataset, **kwd)
         try:
             with np.load(dataset.file_name) as npz:
-                dataset.metadata.HKLs = npz['iHKLList'].tolist()
-                dataset.metadata.nframes = len(npz['omegas'])
+                dataset.metadata.HKLs = npz["iHKLList"].tolist()
+                dataset.metadata.nframes = len(npz["omegas"])
         except Exception as e:
-            log.warning('%s, set_meta Exception: %s', self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            lines = [f"Binary Hexrd Eta-Ome npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})",
-                     f"Eta-Ome HKLs: {dataset.metadata.HKLs} Frames: {dataset.metadata.nframes}"]
-            dataset.peek = '\n'.join(lines)
+            lines = [
+                f"Binary Hexrd Eta-Ome npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})",
+                f"Eta-Ome HKLs: {dataset.metadata.HKLs} Frames: {dataset.metadata.nframes}",
+            ]
+            dataset.peek = "\n".join(lines)
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -3607,6 +4184,7 @@ class HexrdEtaOmeNpz(Npz):
             return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/blast.py b/lib/galaxy/datatypes/blast.py
index 7d03e000532..31bfbd0b81b 100644
--- a/lib/galaxy/datatypes/blast.py
+++ b/lib/galaxy/datatypes/blast.py
@@ -42,7 +42,7 @@ from galaxy.util import smart_str
 from .data import (
     Data,
     get_file_peek,
-    Text
+    Text,
 )
 from .xml import GenericXml
 
@@ -52,6 +52,7 @@ log = logging.getLogger(__name__)
 @build_sniff_from_prefix
 class BlastXml(GenericXml):
     """NCBI Blast XML Output data"""
+
     file_ext = "blastxml"
     edam_format = "format_3331"
     edam_data = "data_0857"
@@ -60,10 +61,10 @@ class BlastXml(GenericXml):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name)
-            dataset.blurb = 'NCBI Blast XML data'
+            dataset.blurb = "NCBI Blast XML data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """Determines whether the file is blastxml
@@ -84,11 +85,13 @@ class BlastXml(GenericXml):
         if line.strip() != '<?xml version="1.0"?>':
             return False
         line = handle.readline()
-        if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
-                                '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
+        if line.strip() not in [
+            '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
+            '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">',
+        ]:
             return False
         line = handle.readline()
-        if line.strip() != '<BlastOutput>':
+        if line.strip() != "<BlastOutput>":
             return False
         return True
 
@@ -99,8 +102,7 @@ class BlastXml(GenericXml):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("Given no BLAST XML files, %r, to merge into %s"
-                             % (split_files, output_file))
+            raise ValueError("Given no BLAST XML files, %r, to merge into %s" % (split_files, output_file))
         with open(output_file, "w") as out:
             h = None
             old_header = None
@@ -129,8 +131,10 @@ class BlastXml(GenericXml):
                     raise ValueError(f"{f} is not an XML file!")
                 line = h.readline()
                 header += line
-                if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
-                                        '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
+                if line.strip() not in [
+                    '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
+                    '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">',
+                ]:
                     out.write(header)  # for diagnosis
                     h.close()
                     raise ValueError(f"{f} is not a BLAST XML file!")
@@ -158,8 +162,10 @@ class BlastXml(GenericXml):
                 elif old_header is not None and old_header[:300] != header[:300]:
                     # Enough to check <BlastOutput_program> and <BlastOutput_version> match
                     h.close()
-                    raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n"
-                                     % (split_files[0], f, old_header[:300], header[:300]))
+                    raise ValueError(
+                        "BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n"
+                        % (split_files[0], f, old_header[:300], header[:300])
+                    )
                 else:
                     out.write("    <Iteration>\n")
                 for line in h:
@@ -182,8 +188,8 @@ class _BlastDb(Data):
             dataset.peek = "BLAST database (multiple files)"
             dataset.blurb = "BLAST database (multiple files)"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Create HTML content, used for displaying peek."""
@@ -192,22 +198,16 @@ class _BlastDb(Data):
         except Exception:
             return "BLAST database (multiple files)"
 
-    def display_data(self, trans, data, preview=False, filename=None,
-                     to_ext=None, size=None, offset=None, **kwd):
+    def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
         """
         If preview is `True` allows us to format the data shown in the central pane via the "eye" icon.
         If preview is `False` triggers download.
         """
         headers = kwd.get("headers", {})
         if not preview:
-            return super().display_data(trans,
-                                        data=data,
-                                        preview=preview,
-                                        filename=filename,
-                                        to_ext=to_ext,
-                                        size=size,
-                                        offset=offset,
-                                        **kwd)
+            return super().display_data(
+                trans, data=data, preview=preview, filename=filename, to_ext=to_ext, size=size, offset=offset, **kwd
+            )
         if self.file_ext == "blastdbn":
             title = "This is a nucleotide BLAST database"
         elif self.file_ext == "blastdbp":
@@ -220,7 +220,7 @@ class _BlastDb(Data):
         msg = ""
         try:
             # Try to use any text recorded in the dummy index file:
-            with open(data.file_name, encoding='utf-8') as handle:
+            with open(data.file_name, encoding="utf-8") as handle:
                 msg = handle.read().strip()
         except Exception:
             pass
@@ -242,25 +242,46 @@ class _BlastDb(Data):
 
 class BlastNucDb(_BlastDb):
     """Class for nucleotide BLAST database files."""
-    file_ext = 'blastdbn'
-    composite_type = 'basic'
+
+    file_ext = "blastdbn"
+    composite_type = "basic"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('blastdb.nhr', is_binary=True)  # sequence headers
-        self.add_composite_file('blastdb.nin', is_binary=True)  # index file
-        self.add_composite_file('blastdb.nsq', is_binary=True)  # nucleotide sequences
-        self.add_composite_file('blastdb.nal', is_binary=False, optional=True)  # alias ( -gi_mask option of makeblastdb)
-        self.add_composite_file('blastdb.nhd', is_binary=True, optional=True)  # sorted sequence hash values ( -hash_index option of makeblastdb)
-        self.add_composite_file('blastdb.nhi', is_binary=True, optional=True)  # index of sequence hash values ( -hash_index option of makeblastdb)
-        self.add_composite_file('blastdb.nnd', is_binary=True, optional=True)  # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
-        self.add_composite_file('blastdb.nni', is_binary=True, optional=True)  # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
-        self.add_composite_file('blastdb.nog', is_binary=True, optional=True)  # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
-        self.add_composite_file('blastdb.nsd', is_binary=True, optional=True)  # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
-        self.add_composite_file('blastdb.nsi', is_binary=True, optional=True)  # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
-#        self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True)  # first volume of the MegaBLAST index generated by makembindex
-# The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
-        self.add_composite_file('blastdb.shd', is_binary=True, optional=True)  # MegaBLAST index superheader (-old_style_index false option of makembindex)
+        self.add_composite_file("blastdb.nhr", is_binary=True)  # sequence headers
+        self.add_composite_file("blastdb.nin", is_binary=True)  # index file
+        self.add_composite_file("blastdb.nsq", is_binary=True)  # nucleotide sequences
+        self.add_composite_file(
+            "blastdb.nal", is_binary=False, optional=True
+        )  # alias ( -gi_mask option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nhd", is_binary=True, optional=True
+        )  # sorted sequence hash values ( -hash_index option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nhi", is_binary=True, optional=True
+        )  # index of sequence hash values ( -hash_index option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nnd", is_binary=True, optional=True
+        )  # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
+        self.add_composite_file(
+            "blastdb.nni", is_binary=True, optional=True
+        )  # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
+        self.add_composite_file(
+            "blastdb.nog", is_binary=True, optional=True
+        )  # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nsd", is_binary=True, optional=True
+        )  # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nsi", is_binary=True, optional=True
+        )  # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
+        #        self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True)  # first volume of the MegaBLAST index generated by makembindex
+        # The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
+        self.add_composite_file(
+            "blastdb.shd", is_binary=True, optional=True
+        )  # MegaBLAST index superheader (-old_style_index false option of makembindex)
+
+
 #        self.add_composite_file('blastdb.naa', is_binary=True, optional=True)  # index of a WriteDB column for e.g. mask data
 #        self.add_composite_file('blastdb.nab', is_binary=True, optional=True)  # data of a WriteDB column
 #        self.add_composite_file('blastdb.nac', is_binary=True, optional=True)  # multiple byte order for a WriteDB column
@@ -269,22 +290,25 @@ class BlastNucDb(_BlastDb):
 
 class BlastProtDb(_BlastDb):
     """Class for protein BLAST database files."""
-    file_ext = 'blastdbp'
-    composite_type = 'basic'
+
+    file_ext = "blastdbp"
+    composite_type = "basic"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-# Component file comments are as in BlastNucDb except where noted
-        self.add_composite_file('blastdb.phr', is_binary=True)
-        self.add_composite_file('blastdb.pin', is_binary=True)
-        self.add_composite_file('blastdb.psq', is_binary=True)  # protein sequences
-        self.add_composite_file('blastdb.phd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.phi', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.pnd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.pni', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.pog', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
+        # Component file comments are as in BlastNucDb except where noted
+        self.add_composite_file("blastdb.phr", is_binary=True)
+        self.add_composite_file("blastdb.pin", is_binary=True)
+        self.add_composite_file("blastdb.psq", is_binary=True)  # protein sequences
+        self.add_composite_file("blastdb.phd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.phi", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.pnd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.pni", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.pog", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psi", is_binary=True, optional=True)
+
+
 #        self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
 #        self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
 #        self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
@@ -293,26 +317,28 @@ class BlastProtDb(_BlastDb):
 
 class BlastDomainDb(_BlastDb):
     """Class for domain BLAST database files."""
-    file_ext = 'blastdbd'
-    composite_type = 'basic'
+
+    file_ext = "blastdbd"
+    composite_type = "basic"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('blastdb.phr', is_binary=True)
-        self.add_composite_file('blastdb.pin', is_binary=True)
-        self.add_composite_file('blastdb.psq', is_binary=True)
-        self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.aux', is_binary=True, optional=True)
+        self.add_composite_file("blastdb.phr", is_binary=True)
+        self.add_composite_file("blastdb.pin", is_binary=True)
+        self.add_composite_file("blastdb.psq", is_binary=True)
+        self.add_composite_file("blastdb.freq", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.loo", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psi", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.rps", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.aux", is_binary=True, optional=True)
 
 
 class LastDb(Data):
     """Class for LAST database files."""
-    file_ext = 'lastdb'
-    composite_type = 'basic'
+
+    file_ext = "lastdb"
+    composite_type = "basic"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text."""
@@ -320,8 +346,8 @@ class LastDb(Data):
             dataset.peek = "LAST database (multiple files)"
             dataset.blurb = "LAST database (multiple files)"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Create HTML content, used for displaying peek."""
@@ -332,36 +358,57 @@ class LastDb(Data):
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('lastdb.bck', is_binary=True)
-        self.add_composite_file('lastdb.des', description="Description file", is_binary=False)
-        self.add_composite_file('lastdb.prj', description="Project resume file", is_binary=False)
-        self.add_composite_file('lastdb.sds', is_binary=True)
-        self.add_composite_file('lastdb.ssp', is_binary=True)
-        self.add_composite_file('lastdb.suf', is_binary=True)
-        self.add_composite_file('lastdb.tis', is_binary=True)
+        self.add_composite_file("lastdb.bck", is_binary=True)
+        self.add_composite_file("lastdb.des", description="Description file", is_binary=False)
+        self.add_composite_file("lastdb.prj", description="Project resume file", is_binary=False)
+        self.add_composite_file("lastdb.sds", is_binary=True)
+        self.add_composite_file("lastdb.ssp", is_binary=True)
+        self.add_composite_file("lastdb.suf", is_binary=True)
+        self.add_composite_file("lastdb.tis", is_binary=True)
 
 
 class BlastNucDb5(_BlastDb):
     """Class for nucleotide BLAST database files."""
-    file_ext = 'blastdbn5'
-    composite_type = 'basic'
+
+    file_ext = "blastdbn5"
+    composite_type = "basic"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('blastdb.nhr', is_binary=True)  # sequence headers
-        self.add_composite_file('blastdb.nin', is_binary=True)  # index file
-        self.add_composite_file('blastdb.nsq', is_binary=True)  # nucleotide sequences
-        self.add_composite_file('blastdb.nal', is_binary=False, optional=True)  # alias ( -gi_mask option of makeblastdb)
-        self.add_composite_file('blastdb.nhd', is_binary=True, optional=True)  # sorted sequence hash values ( -hash_index option of makeblastdb)
-        self.add_composite_file('blastdb.nhi', is_binary=True, optional=True)  # index of sequence hash values ( -hash_index option of makeblastdb)
-        self.add_composite_file('blastdb.nnd', is_binary=True, optional=True)  # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
-        self.add_composite_file('blastdb.nni', is_binary=True, optional=True)  # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
-        self.add_composite_file('blastdb.nog', is_binary=True, optional=True)  # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
-        self.add_composite_file('blastdb.nsd', is_binary=True, optional=True)  # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
-        self.add_composite_file('blastdb.nsi', is_binary=True, optional=True)  # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
-#        self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True)  # first volume of the MegaBLAST index generated by makembindex
-# The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
-        self.add_composite_file('blastdb.shd', is_binary=True, optional=True)  # MegaBLAST index superheader (-old_style_index false option of makembindex)
+        self.add_composite_file("blastdb.nhr", is_binary=True)  # sequence headers
+        self.add_composite_file("blastdb.nin", is_binary=True)  # index file
+        self.add_composite_file("blastdb.nsq", is_binary=True)  # nucleotide sequences
+        self.add_composite_file(
+            "blastdb.nal", is_binary=False, optional=True
+        )  # alias ( -gi_mask option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nhd", is_binary=True, optional=True
+        )  # sorted sequence hash values ( -hash_index option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nhi", is_binary=True, optional=True
+        )  # index of sequence hash values ( -hash_index option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nnd", is_binary=True, optional=True
+        )  # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
+        self.add_composite_file(
+            "blastdb.nni", is_binary=True, optional=True
+        )  # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
+        self.add_composite_file(
+            "blastdb.nog", is_binary=True, optional=True
+        )  # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nsd", is_binary=True, optional=True
+        )  # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
+        self.add_composite_file(
+            "blastdb.nsi", is_binary=True, optional=True
+        )  # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
+        #        self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True)  # first volume of the MegaBLAST index generated by makembindex
+        # The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
+        self.add_composite_file(
+            "blastdb.shd", is_binary=True, optional=True
+        )  # MegaBLAST index superheader (-old_style_index false option of makembindex)
+
+
 #        self.add_composite_file('blastdb.naa', is_binary=True, optional=True)  # index of a WriteDB column for e.g. mask data
 #        self.add_composite_file('blastdb.nab', is_binary=True, optional=True)  # data of a WriteDB column
 #        self.add_composite_file('blastdb.nac', is_binary=True, optional=True)  # multiple byte order for a WriteDB column
@@ -370,22 +417,25 @@ class BlastNucDb5(_BlastDb):
 
 class BlastProtDb5(_BlastDb):
     """Class for protein BLAST database files."""
-    file_ext = 'blastdbp5'
-    composite_type = 'basic'
+
+    file_ext = "blastdbp5"
+    composite_type = "basic"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-# Component file comments are as in BlastNucDb except where noted
-        self.add_composite_file('blastdb.phr', is_binary=True)
-        self.add_composite_file('blastdb.pin', is_binary=True)
-        self.add_composite_file('blastdb.psq', is_binary=True)  # protein sequences
-        self.add_composite_file('blastdb.phd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.phi', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.pnd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.pni', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.pog', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
+        # Component file comments are as in BlastNucDb except where noted
+        self.add_composite_file("blastdb.phr", is_binary=True)
+        self.add_composite_file("blastdb.pin", is_binary=True)
+        self.add_composite_file("blastdb.psq", is_binary=True)  # protein sequences
+        self.add_composite_file("blastdb.phd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.phi", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.pnd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.pni", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.pog", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psi", is_binary=True, optional=True)
+
+
 #        self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
 #        self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
 #        self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
@@ -394,17 +444,18 @@ class BlastProtDb5(_BlastDb):
 
 class BlastDomainDb5(_BlastDb):
     """Class for domain BLAST database files."""
-    file_ext = 'blastdbd5'
-    composite_type = 'basic'
+
+    file_ext = "blastdbd5"
+    composite_type = "basic"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('blastdb.phr', is_binary=True)
-        self.add_composite_file('blastdb.pin', is_binary=True)
-        self.add_composite_file('blastdb.psq', is_binary=True)
-        self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
-        self.add_composite_file('blastdb.aux', is_binary=True, optional=True)
+        self.add_composite_file("blastdb.phr", is_binary=True)
+        self.add_composite_file("blastdb.pin", is_binary=True)
+        self.add_composite_file("blastdb.psq", is_binary=True)
+        self.add_composite_file("blastdb.freq", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.loo", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psd", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.psi", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.rps", is_binary=True, optional=True)
+        self.add_composite_file("blastdb.aux", is_binary=True, optional=True)
diff --git a/lib/galaxy/datatypes/checkers.py b/lib/galaxy/datatypes/checkers.py
index ab2fce29024..600fecd8f18 100644
--- a/lib/galaxy/datatypes/checkers.py
+++ b/lib/galaxy/datatypes/checkers.py
@@ -14,12 +14,12 @@ from galaxy.util.checkers import (
 )
 
 __all__ = (
-    'check_binary',
-    'check_bz2',
-    'check_gzip',
-    'check_html',
-    'check_image',
-    'check_zip',
-    'is_gzip',
-    'is_bz2',
+    "check_binary",
+    "check_bz2",
+    "check_gzip",
+    "check_html",
+    "check_image",
+    "check_zip",
+    "is_gzip",
+    "is_bz2",
 )
diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py
index 3bee5711b3e..7c8f6686fc2 100644
--- a/lib/galaxy/datatypes/constructive_solid_geometry.py
+++ b/lib/galaxy/datatypes/constructive_solid_geometry.py
@@ -10,8 +10,10 @@ from typing import List
 from galaxy import util
 from galaxy.datatypes import data
 from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.data import get_file_peek
-from galaxy.datatypes.data import nice_size
+from galaxy.datatypes.data import (
+    get_file_peek,
+    nice_size,
+)
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
@@ -21,7 +23,7 @@ from galaxy.datatypes.tabular import Tabular
 
 MAX_HEADER_LINES = 500
 MAX_LINE_LEN = 2000
-COLOR_OPTS = ['COLOR_SCALARS', 'red', 'green', 'blue']
+COLOR_OPTS = ["COLOR_SCALARS", "red", "green", "blue"]
 
 
 @build_sniff_from_prefix
@@ -32,16 +34,21 @@ class Ply:
     normal direction that can be attached to these elements.  A PLY
     file contains the description of exactly one object.
     """
-    subtype = ''
+
+    subtype = ""
     # Add metadata elements.
-    MetadataElement(name="file_format", default=None, desc="File format",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="vertex", default=None, desc="Vertex",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="face", default=None, desc="Face",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="other_elements", default=[], desc="Other elements",
-                    readonly=True, optional=True, visible=True, no_value=[])
+    MetadataElement(name="file_format", default=None, desc="File format", readonly=True, optional=True, visible=True)
+    MetadataElement(name="vertex", default=None, desc="Vertex", readonly=True, optional=True, visible=True)
+    MetadataElement(name="face", default=None, desc="Face", readonly=True, optional=True, visible=True)
+    MetadataElement(
+        name="other_elements",
+        default=[],
+        desc="Other elements",
+        readonly=True,
+        optional=True,
+        visible=True,
+        no_value=[],
+    )
 
     @abc.abstractmethod
     def __init__(self, **kwd):
@@ -52,7 +59,7 @@ class Ply:
         The structure of a typical PLY file:
         Header, Vertex List, Face List, (lists of other elements)
         """
-        if not self._is_ply_header(file_prefix.text_io(errors='ignore'), self.subtype):
+        if not self._is_ply_header(file_prefix.text_io(errors="ignore"), self.subtype):
             return False
         return True
 
@@ -61,10 +68,10 @@ class Ply:
         The header is a series of carriage-return terminated lines of
         text that describe the remainder of the file.
         """
-        valid_header_items = ['comment', 'obj_info', 'element', 'property']
+        valid_header_items = ["comment", "obj_info", "element", "property"]
         # Line 1: ply
         line = get_next_line(fh)
-        if line != 'ply':
+        if line != "ply":
             return False
         # Line 2: format ascii 1.0
         line = get_next_line(fh)
@@ -74,7 +81,7 @@ class Ply:
         for line in util.iter_start_of_line(fh, MAX_LINE_LEN):
             line = line.strip()
             stop_index += 1
-            if line == 'end_header':
+            if line == "end_header":
                 return True
             items = line.split()
             if items[0] not in valid_header_items:
@@ -87,22 +94,22 @@ class Ply:
 
     def set_meta(self, dataset, **kwd):
         if dataset.has_data():
-            with open(dataset.file_name, errors='ignore') as fh:
+            with open(dataset.file_name, errors="ignore") as fh:
                 for line in fh:
                     line = line.strip()
                     if not line:
                         continue
-                    if line.startswith('format'):
+                    if line.startswith("format"):
                         items = line.split()
                         dataset.metadata.file_format = items[1]
-                    elif line == 'end_header':
+                    elif line == "end_header":
                         # Metadata is complete.
                         break
-                    elif line.startswith('element'):
+                    elif line.startswith("element"):
                         items = line.split()
-                        if items[1] == 'face':
+                        if items[1] == "face":
                             dataset.metadata.face = int(items[2])
-                        elif items[1] == 'vertex':
+                        elif items[1] == "vertex":
                             dataset.metadata.vertex = int(items[2])
                         else:
                             element_tuple = (items[1], int(items[2]))
@@ -113,8 +120,8 @@ class Ply:
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = f"Faces: {str(dataset.metadata.face)}, Vertices: {str(dataset.metadata.vertex)}"
         else:
-            dataset.peek = 'File does not exist'
-            dataset.blurb = 'File purged from disc'
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disc"
 
     def display_peek(self, dataset):
         try:
@@ -133,8 +140,9 @@ class PlyAscii(Ply, data.Text):  # type: ignore[misc]
     >>> PlyAscii().sniff(fname)
     False
     """
+
     file_ext = "plyascii"
-    subtype = 'ascii'
+    subtype = "ascii"
 
     def __init__(self, **kwd):
         data.Text.__init__(self, **kwd)
@@ -142,7 +150,7 @@ class PlyAscii(Ply, data.Text):  # type: ignore[misc]
 
 class PlyBinary(Ply, Binary):  # type: ignore[misc]
     file_ext = "plybinary"
-    subtype = 'binary'
+    subtype = "binary"
 
     def __init__(self, **kwd):
         Binary.__init__(self, **kwd)
@@ -173,46 +181,46 @@ class Vtk:
     TODO: only legacy formats are currently supported and support for XML formats
     should be added.
     """
-    subtype = ''
+    subtype = ""
     # Add metadata elements.
-    MetadataElement(name="vtk_version", default=None, desc="Vtk version",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="file_format", default=None, desc="File format",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="dataset_type", default=None, desc="Dataset type",
-                    readonly=True, optional=True, visible=True)
+    MetadataElement(name="vtk_version", default=None, desc="Vtk version", readonly=True, optional=True, visible=True)
+    MetadataElement(name="file_format", default=None, desc="File format", readonly=True, optional=True, visible=True)
+    MetadataElement(name="dataset_type", default=None, desc="Dataset type", readonly=True, optional=True, visible=True)
 
     # STRUCTURED_GRID data_type.
-    MetadataElement(name="dimensions", default=[], desc="Dimensions",
-                    readonly=True, optional=True, visible=True, no_value=[])
-    MetadataElement(name="origin", default=[], desc="Origin",
-                    readonly=True, optional=True, visible=True, no_value=[])
-    MetadataElement(name="spacing", default=[], desc="Spacing",
-                    readonly=True, optional=True, visible=True, no_value=[])
+    MetadataElement(
+        name="dimensions", default=[], desc="Dimensions", readonly=True, optional=True, visible=True, no_value=[]
+    )
+    MetadataElement(name="origin", default=[], desc="Origin", readonly=True, optional=True, visible=True, no_value=[])
+    MetadataElement(name="spacing", default=[], desc="Spacing", readonly=True, optional=True, visible=True, no_value=[])
 
     # POLYDATA data_type (Points element is also a component of UNSTRUCTURED_GRID..
-    MetadataElement(name="points", default=None, desc="Points",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="vertices", default=None, desc="Vertices",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="lines", default=None, desc="Lines",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="polygons", default=None, desc="Polygons",
-                    readonly=True, optional=True, visible=True)
-    MetadataElement(name="triangle_strips", default=None, desc="Triangle strips",
-                    readonly=True, optional=True, visible=True)
+    MetadataElement(name="points", default=None, desc="Points", readonly=True, optional=True, visible=True)
+    MetadataElement(name="vertices", default=None, desc="Vertices", readonly=True, optional=True, visible=True)
+    MetadataElement(name="lines", default=None, desc="Lines", readonly=True, optional=True, visible=True)
+    MetadataElement(name="polygons", default=None, desc="Polygons", readonly=True, optional=True, visible=True)
+    MetadataElement(
+        name="triangle_strips", default=None, desc="Triangle strips", readonly=True, optional=True, visible=True
+    )
 
     # UNSTRUCTURED_GRID data_type.
-    MetadataElement(name="cells", default=None, desc="Cells",
-                    readonly=True, optional=True, visible=True)
+    MetadataElement(name="cells", default=None, desc="Cells", readonly=True, optional=True, visible=True)
 
     # Additional elements not categorized by data_type.
-    MetadataElement(name="field_names", default=[], desc="Field names",
-                    readonly=True, optional=True, visible=True, no_value=[])
+    MetadataElement(
+        name="field_names", default=[], desc="Field names", readonly=True, optional=True, visible=True, no_value=[]
+    )
     # The keys in the field_components map to the list of field_names in the above element
     # which ensures order for select list options that are built from it.
-    MetadataElement(name="field_components", default={}, desc="Field names and components",
-                    readonly=True, optional=True, visible=True, no_value={})
+    MetadataElement(
+        name="field_components",
+        default={},
+        desc="Field names and components",
+        readonly=True,
+        optional=True,
+        visible=True,
+        no_value={},
+    )
 
     @abc.abstractmethod
     def __init__(self, **kwd):
@@ -224,7 +232,7 @@ class Vtk:
         styles of file formats: legacy or XML.  We'll assume if the
         file contains a valid VTK header, then it is a valid VTK file.
         """
-        if self._is_vtk_header(file_prefix.text_io(errors='ignore'), self.subtype):
+        if self._is_vtk_header(file_prefix.text_io(errors="ignore"), self.subtype):
             return True
         return False
 
@@ -236,7 +244,7 @@ class Vtk:
         data_kind) or the 4th line consists of the data_kind (in
         which case the 5th line is blank).
         """
-        data_kinds = ['STRUCTURED_GRID', 'POLYDATA', 'UNSTRUCTURED_GRID', 'STRUCTURED_POINTS', 'RECTILINEAR_GRID']
+        data_kinds = ["STRUCTURED_GRID", "POLYDATA", "UNSTRUCTURED_GRID", "STRUCTURED_POINTS", "RECTILINEAR_GRID"]
 
         def check_data_kind(line):
             for data_kind in data_kinds:
@@ -246,7 +254,7 @@ class Vtk:
 
         # Line 1: vtk DataFile Version 3.0
         line = get_next_line(fh)
-        if line.find('vtk') < 0:
+        if line.find("vtk") < 0:
             return False
         # Line 2: can be anything - skip it
         line = get_next_line(fh)
@@ -272,14 +280,14 @@ class Vtk:
             field_components = {}
             dataset_structure_complete = False
             processing_field_section = False
-            with open(dataset.file_name, errors='ignore') as fh:
+            with open(dataset.file_name, errors="ignore") as fh:
                 for i, line in enumerate(fh):
                     line = line.strip()
                     if not line:
                         continue
                     if i < 3:
                         dataset = self.set_initial_metadata(i, line, dataset)
-                    elif dataset.metadata.file_format == 'ASCII' or not util.is_binary(line):
+                    elif dataset.metadata.file_format == "ASCII" or not util.is_binary(line):
                         if dataset_structure_complete:
                             """
                             The final part of legacy VTK files describes the dataset attributes.
@@ -300,7 +308,7 @@ class Vtk:
                             reader, then the first data of that type is extracted from the file.
                             """
                             items = line.split()
-                            if items[0] == 'SCALARS':
+                            if items[0] == "SCALARS":
                                 # Example: SCALARS surface_field double 3
                                 # Scalar definition includes specification of a lookup table. The
                                 # definition of a lookup table is optional. If not specified, the
@@ -317,7 +325,7 @@ class Vtk:
                                     num_components = 1
                                 field_component_indexes = [str(i) for i in range(num_components)]
                                 field_components[field_name] = field_component_indexes
-                            elif items[0] == 'FIELD':
+                            elif items[0] == "FIELD":
                                 # The dataset consists of CELL_DATA.
                                 # FIELD FieldData 2
                                 processing_field_section = True
@@ -340,11 +348,11 @@ class Vtk:
                                         field_component_indexes = [str(i) for i in range(num_components)]
                                         field_components[field_name] = field_component_indexes
                                         fields_processed.append(field_name)
-                        elif line.startswith('CELL_DATA'):
+                        elif line.startswith("CELL_DATA"):
                             # CELL_DATA 3188
                             dataset_structure_complete = True
                             dataset.metadata.cells = int(line.split()[1])
-                        elif line.startswith('POINT_DATA'):
+                        elif line.startswith("POINT_DATA"):
                             # POINT_DATA 1876
                             dataset_structure_complete = True
                             dataset.metadata.points = int(line.split()[1])
@@ -358,7 +366,7 @@ class Vtk:
             # The first part of legacy VTK files is the file version and
             # identifier. This part contains the single line:
             # # vtk DataFile Version X.Y
-            dataset.metadata.vtk_version = line.lower().split('version')[1]
+            dataset.metadata.vtk_version = line.lower().split("version")[1]
             # The second part of legacy VTK files is the header. The header
             # consists of a character string terminated by end-of-line
             # character \n. The header is 256 characters maximum. The header
@@ -380,51 +388,51 @@ class Vtk:
         the type of dataset, other keyword/ data combinations define the
         actual data.
         """
-        if dataset_type is None and line.startswith('DATASET'):
+        if dataset_type is None and line.startswith("DATASET"):
             dataset_type = line.split()[1]
             dataset.metadata.dataset_type = dataset_type
-        if dataset_type == 'STRUCTURED_GRID':
+        if dataset_type == "STRUCTURED_GRID":
             # The STRUCTURED_GRID format supports 1D, 2D, and 3D structured
             # grid datasets.  The dimensions nx, ny, nz must be greater
             # than or equal to 1.  The point coordinates are defined by the
             # data in the POINTS section. This consists of x-y-z data values
             # for each point.
-            if line.startswith('DIMENSIONS'):
+            if line.startswith("DIMENSIONS"):
                 # DIMENSIONS 10 5 1
                 dataset.metadata.dimensions = [line.split()[1:]]
-            elif line.startswith('ORIGIN'):
+            elif line.startswith("ORIGIN"):
                 # ORIGIN 0 0 0
                 dataset.metadata.origin = [line.split()[1:]]
-            elif line.startswith('SPACING'):
+            elif line.startswith("SPACING"):
                 # SPACING 1 1 1
                 dataset.metadata.spacing = [line.split()[1:]]
-        elif dataset_type == 'POLYDATA':
+        elif dataset_type == "POLYDATA":
             # The polygonal dataset consists of arbitrary combinations
             # of surface graphics primitives vertices, lines, polygons
             # and triangle strips.  Polygonal data is defined by the POINTS,
             # VERTICES, LINES, POLYGONS, or TRIANGLE_STRIPS sections.
-            if line.startswith('POINTS'):
+            if line.startswith("POINTS"):
                 # POINTS 18 float
                 dataset.metadata.points = int(line.split()[1])
-            elif line.startswith('VERTICES'):
+            elif line.startswith("VERTICES"):
                 dataset.metadata.vertices = int(line.split()[1])
-            elif line.startswith('LINES'):
+            elif line.startswith("LINES"):
                 # LINES 5 17
                 dataset.metadata.lines = int(line.split()[1])
-            elif line.startswith('POLYGONS'):
+            elif line.startswith("POLYGONS"):
                 # POLYGONS 6 30
                 dataset.metadata.polygons = int(line.split()[1])
-            elif line.startswith('TRIANGLE_STRIPS'):
+            elif line.startswith("TRIANGLE_STRIPS"):
                 # TRIANGLE_STRIPS 2212 16158
                 dataset.metadata.triangle_strips = int(line.split()[1])
-        elif dataset_type == 'UNSTRUCTURED_GRID':
+        elif dataset_type == "UNSTRUCTURED_GRID":
             # The unstructured grid dataset consists of arbitrary combinations
             # of any possible cell type. Unstructured grids are defined by points,
             # cells, and cell types.
-            if line.startswith('POINTS'):
+            if line.startswith("POINTS"):
                 # POINTS 18 float
                 dataset.metadata.points = int(line.split()[1])
-            if line.startswith('CELLS'):
+            if line.startswith("CELLS"):
                 # CELLS 756 3024
                 dataset.metadata.cells = int(line.split()[1])
         return dataset, dataset_type
@@ -432,20 +440,20 @@ class Vtk:
     def get_blurb(self, dataset):
         blurb = ""
         if dataset.metadata.vtk_version is not None:
-            blurb += f'VTK Version {str(dataset.metadata.vtk_version)}'
+            blurb += f"VTK Version {str(dataset.metadata.vtk_version)}"
         if dataset.metadata.dataset_type is not None:
             if blurb:
-                blurb += ' '
+                blurb += " "
             blurb += str(dataset.metadata.dataset_type)
-        return blurb or 'VTK data'
+        return blurb or "VTK data"
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = self.get_blurb(dataset)
         else:
-            dataset.peek = 'File does not exist'
-            dataset.blurb = 'File purged from disc'
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disc"
 
     def display_peek(self, dataset):
         try:
@@ -464,14 +472,15 @@ class VtkAscii(Vtk, data.Text):  # type: ignore[misc]
     >>> VtkAscii().sniff(fname)
     False
     """
+
     file_ext = "vtkascii"
-    subtype = 'ASCII'
+    subtype = "ASCII"
 
     def __init__(self, **kwd):
         data.Text.__init__(self, **kwd)
 
 
-class VtkBinary(Vtk, Binary):   # type: ignore[misc]
+class VtkBinary(Vtk, Binary):  # type: ignore[misc]
     """
     >>> from galaxy.datatypes.sniff import get_test_fname
     >>> fname = get_test_fname('test.vtkbinary')
@@ -483,7 +492,7 @@ class VtkBinary(Vtk, Binary):   # type: ignore[misc]
     """
 
     file_ext = "vtkbinary"
-    subtype = 'BINARY'
+    subtype = "BINARY"
 
     def __init__(self, **kwd):
         Binary.__init__(self, **kwd)
@@ -505,6 +514,7 @@ class NeperTess(data.Text):
       **cell
         number_of_cells
     """
+
     file_ext = "neper.tess"
     MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True)
     MetadataElement(name="dimension", default=None, desc="dimension", readonly=True, visible=True)
@@ -524,16 +534,16 @@ class NeperTess(data.Text):
         >>> NeperTess().sniff(fname)
         False
         """
-        return file_prefix.text_io(errors='ignore').readline(10).startswith('***tess')
+        return file_prefix.text_io(errors="ignore").readline(10).startswith("***tess")
 
     def set_meta(self, dataset, **kwd):
         if dataset.has_data():
-            with open(dataset.file_name, errors='ignore') as fh:
+            with open(dataset.file_name, errors="ignore") as fh:
                 for i, line in enumerate(fh):
                     line = line.strip()
                     if not line or i > 6:
                         break
-                    if i == 0 and not line.startswith('***tess'):
+                    if i == 0 and not line.startswith("***tess"):
                         break
                     if i == 2:
                         dataset.metadata.format = line
@@ -545,10 +555,10 @@ class NeperTess(data.Text):
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name, LINE_COUNT=7)
-            dataset.blurb = f'format: {str(dataset.metadata.format)} dim: {str(dataset.metadata.dimension)} cells: {str(dataset.metadata.cells)}'
+            dataset.blurb = f"format: {str(dataset.metadata.format)} dim: {str(dataset.metadata.dimension)} cells: {str(dataset.metadata.cells)}"
         else:
-            dataset.peek = 'File does not exist'
-            dataset.blurb = 'File purged from disc'
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disc"
 
 
 @build_sniff_from_prefix
@@ -568,6 +578,7 @@ class NeperTesr(Binary):
       [**cell
         number_of_cells
     """
+
     file_ext = "neper.tesr"
     MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True)
     MetadataElement(name="dimension", default=None, desc="dimension", readonly=True, visible=True)
@@ -590,19 +601,19 @@ class NeperTesr(Binary):
         >>> NeperTesr().sniff(fname)
         False
         """
-        return file_prefix.text_io(errors='ignore').readline(10).startswith('***tesr')
+        return file_prefix.text_io(errors="ignore").readline(10).startswith("***tesr")
 
     def set_meta(self, dataset, **kwd):
         if dataset.has_data():
-            with open(dataset.file_name, errors='ignore') as fh:
-                field = ''
+            with open(dataset.file_name, errors="ignore") as fh:
+                field = ""
                 for i, line in enumerate(fh):
                     line = line.strip()
                     if not line or i > 12:
                         break
-                    if i == 0 and not line.startswith('***tesr'):
+                    if i == 0 and not line.startswith("***tesr"):
                         break
-                    if line.startswith('*'):
+                    if line.startswith("*"):
                         field = line
                         continue
                     if i == 2:
@@ -617,20 +628,20 @@ class NeperTesr(Binary):
                     if i == 6:
                         dataset.metadata.voxsize = line.split()
                         continue
-                    if field.startswith('*origin'):
+                    if field.startswith("*origin"):
                         dataset.metadata.origin = line.split()
                         continue
-                    if field.startswith('**cell'):
+                    if field.startswith("**cell"):
                         dataset.metadata.cells = int(line)
                         break
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name, LINE_COUNT=9)
-            dataset.blurb = f'format: {str(dataset.metadata.format)} dim: {str(dataset.metadata.dimension)} cells: {str(dataset.metadata.cells)}'
+            dataset.blurb = f"format: {str(dataset.metadata.format)} dim: {str(dataset.metadata.dimension)} cells: {str(dataset.metadata.cells)}"
         else:
-            dataset.peek = 'File does not exist'
-            dataset.blurb = 'File purged from disc'
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disc"
 
 
 class NeperPoints(data.Text):
@@ -638,6 +649,7 @@ class NeperPoints(data.Text):
     Neper Position File
     Neper position format has 1 - 3 floats per line separated by white space.
     """
+
     file_ext = "neper.points"
     MetadataElement(name="dimension", default=None, desc="dimension", readonly=True, visible=True)
 
@@ -647,7 +659,7 @@ class NeperPoints(data.Text):
     def set_meta(self, dataset, **kwd):
         data.Text.set_meta(self, dataset, **kwd)
         if dataset.has_data():
-            with open(dataset.file_name, errors='ignore') as fh:
+            with open(dataset.file_name, errors="ignore") as fh:
                 dataset.metadata.dimension = self._get_dimension(fh)
 
     def _get_dimension(self, fh, maxlines=100, sep=None):
@@ -672,7 +684,7 @@ class NeperPoints(data.Text):
     def set_peek(self, dataset):
         data.Text.set_peek(self, dataset)
         if not dataset.dataset.purged:
-            dataset.blurb += f' dim: {str(dataset.metadata.dimension)}'
+            dataset.blurb += f" dim: {str(dataset.metadata.dimension)}"
 
 
 class NeperPointsTabular(NeperPoints, Tabular):
@@ -680,6 +692,7 @@ class NeperPointsTabular(NeperPoints, Tabular):
     Neper Position File
     Neper position format has 1 - 3 floats per line separated by TABs.
     """
+
     file_ext = "neper.points.tsv"
 
     def __init__(self, **kwd):
@@ -688,25 +701,27 @@ class NeperPointsTabular(NeperPoints, Tabular):
     def set_meta(self, dataset, **kwd):
         Tabular.set_meta(self, dataset, **kwd)
         if dataset.has_data():
-            with open(dataset.file_name, errors='ignore') as fh:
+            with open(dataset.file_name, errors="ignore") as fh:
                 dataset.metadata.dimension = self._get_dimension(fh)
 
     def set_peek(self, dataset):
         Tabular.set_peek(self, dataset)
         if not dataset.dataset.purged:
-            dataset.blurb += f' dim: {str(dataset.metadata.dimension)}'
+            dataset.blurb += f" dim: {str(dataset.metadata.dimension)}"
 
 
 class NeperMultiScaleCell(data.Text):
     """
     Neper Multiscale Cell File
     """
+
     file_ext = "neper.mscell"
 
 
 @build_sniff_from_prefix
 class GmshMsh(Binary):
     """Gmsh Mesh File"""
+
     file_ext = "gmsh.msh"
     MetadataElement(name="version", default=None, desc="version", readonly=True, visible=True)
     MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True)
@@ -725,35 +740,36 @@ class GmshMsh(Binary):
         >>> GmshMsh().sniff(fname)
         False
         """
-        return file_prefix.text_io(errors='ignore').readline().startswith('$MeshFormat')
+        return file_prefix.text_io(errors="ignore").readline().startswith("$MeshFormat")
 
     def set_meta(self, dataset, **kwd):
         if dataset.has_data():
-            with open(dataset.file_name, errors='ignore') as fh:
+            with open(dataset.file_name, errors="ignore") as fh:
                 for i, line in enumerate(fh):
                     line = line.strip()
                     if not line or i > 1:
                         break
-                    if i == 0 and not line.startswith('$MeshFormat'):
+                    if i == 0 and not line.startswith("$MeshFormat"):
                         break
                     if i == 1:
                         fields = line.split()
                         if len(fields) > 0:
                             dataset.metadata.version = fields[0]
                         if len(fields) > 1:
-                            dataset.metadata.format = 'ASCII' if fields[1] == '0' else 'binary'
+                            dataset.metadata.format = "ASCII" if fields[1] == "0" else "binary"
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name, LINE_COUNT=3)
-            dataset.blurb = f'Gmsh verion: {str(dataset.metadata.version)} {str(dataset.metadata.format)}'
+            dataset.blurb = f"Gmsh verion: {str(dataset.metadata.version)} {str(dataset.metadata.format)}"
         else:
-            dataset.peek = 'File does not exist'
-            dataset.blurb = 'File purged from disc'
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disc"
 
 
 class GmshGeo(data.Text):
     """Gmsh geometry File"""
+
     file_ext = "gmsh.geo"
 
 
@@ -761,6 +777,7 @@ class ZsetGeof(data.Text):
     """
     Z-set geof File
     """
+
     file_ext = "zset.geof"
 
 
diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.py b/lib/galaxy/datatypes/converters/bed_to_gff_converter.py
index 8e72f45d9b8..eee7add9a8d 100644
--- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.py
+++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.py
@@ -12,15 +12,15 @@ def __main__():
     skipped_lines = 0
     first_skipped_line = 0
     i = 0
-    with open(input_name) as fh, open(output_name, 'w') as out:
+    with open(input_name) as fh, open(output_name, "w") as out:
         out.write("##gff-version 2\n")
         out.write("##bed_to_gff_converter.py\n\n")
         for i, line in enumerate(fh):
             complete_bed = False
-            line = line.rstrip('\r\n')
-            if line and not line.startswith('#') and not line.startswith('track') and not line.startswith('browser'):
+            line = line.rstrip("\r\n")
+            if line and not line.startswith("#") and not line.startswith("track") and not line.startswith("browser"):
                 try:
-                    elems = line.split('\t')
+                    elems = line.split("\t")
                     if len(elems) == 12:
                         complete_bed = True
                     chrom = elems[0]
@@ -30,34 +30,43 @@ def __main__():
                         try:
                             feature = elems[3]
                         except Exception:
-                            feature = 'feature%d' % (i + 1)
+                            feature = "feature%d" % (i + 1)
                     start = int(elems[1]) + 1
                     end = int(elems[2])
                     try:
                         score = elems[4]
                     except Exception:
-                        score = '0'
+                        score = "0"
                     try:
                         strand = elems[5]
                     except Exception:
-                        strand = '+'
+                        strand = "+"
                     try:
                         group = elems[3]
                     except Exception:
-                        group = 'group%d' % (i + 1)
+                        group = "group%d" % (i + 1)
                     if complete_bed:
-                        out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
+                        out.write(
+                            "%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n"
+                            % (chrom, feature, start, end, score, strand, feature, group)
+                        )
                     else:
-                        out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n' % (chrom, feature, start, end, score, strand, group))
+                        out.write(
+                            "%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n"
+                            % (chrom, feature, start, end, score, strand, group)
+                        )
                     if complete_bed:
                         # We have all the info necessary to annotate exons for genes and mRNAs
                         block_count = int(elems[9])
-                        block_sizes = elems[10].split(',')
-                        block_starts = elems[11].split(',')
+                        block_sizes = elems[10].split(",")
+                        block_starts = elems[11].split(",")
                         for j in range(block_count):
                             exon_start = int(start) + int(block_starts[j])
                             exon_end = exon_start + int(block_sizes[j]) - 1
-                            out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
+                            out.write(
+                                "%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n"
+                                % (chrom, exon_start, exon_end, score, strand, group)
+                            )
                 except Exception:
                     skipped_lines += 1
                     if not first_skipped_line:
@@ -68,7 +77,10 @@ def __main__():
                     first_skipped_line = i + 1
     info_msg = "%i lines converted to GFF version 2.  " % (i + 1 - skipped_lines)
     if skipped_lines > 0:
-        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)
+        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (
+            skipped_lines,
+            first_skipped_line,
+        )
     print(info_msg)
 
 
diff --git a/lib/galaxy/datatypes/converters/bgzip.py b/lib/galaxy/datatypes/converters/bgzip.py
index 4aa23ae2382..3e996c5442a 100644
--- a/lib/galaxy/datatypes/converters/bgzip.py
+++ b/lib/galaxy/datatypes/converters/bgzip.py
@@ -15,10 +15,10 @@ import pysam
 def main():
     # Read options, args.
     parser = optparse.OptionParser()
-    parser.add_option('-c', '--chr-col', type='int', dest='chrom_col')
-    parser.add_option('-s', '--start-col', type='int', dest='start_col')
-    parser.add_option('-e', '--end-col', type='int', dest='end_col')
-    parser.add_option('-P', '--preset', dest='preset')
+    parser.add_option("-c", "--chr-col", type="int", dest="chrom_col")
+    parser.add_option("-s", "--start-col", type="int", dest="start_col")
+    parser.add_option("-e", "--end-col", type="int", dest="end_col")
+    parser.add_option("-P", "--preset", dest="preset")
     (options, args) = parser.parse_args()
     input_fname, output_fname = args
 
@@ -29,8 +29,8 @@ def main():
         sort_params = [
             "sort",
             "-k{i},{i}".format(i=options.chrom_col),
-            "-k%(i)i,%(i)in" % {'i': options.start_col},
-            "-k%(i)i,%(i)in" % {'i': options.end_col}
+            "-k%(i)i,%(i)in" % {"i": options.start_col},
+            "-k%(i)i,%(i)in" % {"i": options.end_col},
         ]
     elif options.preset == "bed":
         sort_params = ["sort", "-k1,1", "-k2,2n", "-k3,3n"]
@@ -39,7 +39,9 @@ def main():
     elif options.preset == "gff":
         sort_params = ["sort", "-s", "-k1,1", "-k4,4n"]  # stable sort on start column
     # Skip any lines starting with "#" and "track"
-    grepped = subprocess.Popen(["grep", "-e", "^\"#\"", "-e", "^track", "-v", input_fname], stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+    grepped = subprocess.Popen(
+        ["grep", "-e", '^"#"', "-e", "^track", "-v", input_fname], stderr=subprocess.PIPE, stdout=subprocess.PIPE
+    )
     after_sort = subprocess.Popen(sort_params, stdin=grepped.stdout, stderr=subprocess.PIPE, stdout=tmpfile)
     grepped.stdout.close()
     output, err = after_sort.communicate()
diff --git a/lib/galaxy/datatypes/converters/cram_to_bam.py b/lib/galaxy/datatypes/converters/cram_to_bam.py
index f139442835f..673abff4f80 100644
--- a/lib/galaxy/datatypes/converters/cram_to_bam.py
+++ b/lib/galaxy/datatypes/converters/cram_to_bam.py
@@ -15,8 +15,8 @@ def main():
     parser = optparse.OptionParser()
     (options, args) = parser.parse_args()
     input_fname, output_fname = args
-    slots = os.getenv('GALAXY_SLOTS', 1)
-    pysam.sort(f"-@{slots}", '-o', output_fname, '-O', 'bam', '-T', '.', input_fname)
+    slots = os.getenv("GALAXY_SLOTS", 1)
+    pysam.sort(f"-@{slots}", "-o", output_fname, "-O", "bam", "-T", ".", input_fname)
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.py b/lib/galaxy/datatypes/converters/fasta_to_len.py
index 3447aba63c0..cec4bf35d68 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.py
@@ -14,7 +14,7 @@ def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=
     infile = fasta_file
     keep_first_char = int(keep_first_char)
 
-    fasta_title = ''
+    fasta_title = ""
     seq_len = 0
 
     # number of char to keep in the title
@@ -25,13 +25,13 @@ def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=
 
     first_entry = True
 
-    with open(out_file, 'w') as out:
+    with open(out_file, "w") as out:
         with open(infile) as fh:
             for line in fh:
                 line = line.strip()
-                if not line or line.startswith('#'):
+                if not line or line.startswith("#"):
                     continue
-                if line[0] == '>':
+                if line[0] == ">":
                     if first_entry is False:
                         if keep_first_word:
                             fasta_title = fasta_title.split()[0]
diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
index 18d5b18789f..45ba059dd35 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
@@ -23,26 +23,26 @@ def __main__():
         sys.exit(1)
 
     with open(infile) as inp:
-        with open(outfile, 'w') as out:
-            sequence = ''
+        with open(outfile, "w") as out:
+            sequence = ""
             for line in inp:
-                line = line.rstrip('\r\n')
-                if line.startswith('>'):
+                line = line.rstrip("\r\n")
+                if line.startswith(">"):
                     if sequence:
                         # Flush sequence from previous FASTA record,
                         # removing any white space
-                        out.write("".join(sequence.split()) + '\n')
-                        sequence = ''
+                        out.write("".join(sequence.split()) + "\n")
+                        sequence = ""
                     # Strip off the leading '>' and remove any pre-existing
                     # tabs which would trigger extra columns; write with
                     # tab to separate this from the sequence column:
-                    out.write(line[1:].replace('\t', ' ') + '\t')
+                    out.write(line[1:].replace("\t", " ") + "\t")
                 else:
                     # Continuing sequence,
                     sequence += line
             # End of FASTA file, flush last sequence
             if sequence:
-                out.write("".join(sequence.split()) + '\n')
+                out.write("".join(sequence.split()) + "\n")
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
index cb0fb34b0e9..1a15c47d65d 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
@@ -19,17 +19,17 @@ def main():
     """
     input_fname = sys.argv[1]
     if is_gzip(input_fname):
-        sys.exit('Conversion is only possible for uncompressed files')
+        sys.exit("Conversion is only possible for uncompressed files")
 
     current_line = 0
     sequences = 1000000
     lines_per_chunk = 4 * sequences
     chunk_begin = 0
 
-    with open(input_fname) as in_file, open(sys.argv[2], 'w') as out_file:
+    with open(input_fname) as in_file, open(sys.argv[2], "w") as out_file:
         out_file.write('{"sections" : [')
 
-        for _ in iter(in_file.readline, ''):
+        for _ in iter(in_file.readline, ""):
             current_line += 1
             if 0 == current_line % lines_per_chunk:
                 chunk_end = in_file.tell()
@@ -37,8 +37,10 @@ def main():
                 chunk_begin = chunk_end
 
         chunk_end = in_file.tell()
-        out_file.write(f'{{"start":"{chunk_begin}","end":"{chunk_end}","sequences":"{current_line % lines_per_chunk / 4}"}}')
-        out_file.write(']}\n')
+        out_file.write(
+            f'{{"start":"{chunk_begin}","end":"{chunk_end}","sequences":"{current_line % lines_per_chunk / 4}"}}'
+        )
+        out_file.write("]}\n")
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
index 18428f6c368..b7557de1481 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
@@ -25,12 +25,12 @@ def stop_err(msg):
 def __main__():
     infile_name = sys.argv[1]
     fastq_block_lines = 0
-    seq_title_startswith = ''
+    seq_title_startswith = ""
 
-    with open(infile_name) as fh, open(sys.argv[2], 'w') as outfile:
+    with open(infile_name) as fh, open(sys.argv[2], "w") as outfile:
         for i, line in enumerate(fh):
             line = line.rstrip()  # eliminate trailing space and new line characters
-            if not line or line.startswith('#'):
+            if not line or line.startswith("#"):
                 continue
             fastq_block_lines = (fastq_block_lines + 1) % 4
             line_startswith = line[0:1]
@@ -39,11 +39,11 @@ def __main__():
                 if not seq_title_startswith:
                     seq_title_startswith = line_startswith
                 if seq_title_startswith != line_startswith:
-                    stop_err('Invalid fastqsolexa format at line %d: %s.' % (i + 1, line))
-                outfile.write(f'>{line[1:]}\n')
+                    stop_err("Invalid fastqsolexa format at line %d: %s." % (i + 1, line))
+                outfile.write(f">{line[1:]}\n")
             elif fastq_block_lines == 2:
                 # line 2 is nucleotides
-                outfile.write(f'{line}\n')
+                outfile.write(f"{line}\n")
             else:
                 pass
 
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
index c48283ba535..c2f51cde20c 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
@@ -25,15 +25,15 @@ def stop_err(msg):
 def __main__():
     infile_name = sys.argv[1]
     # datatype = sys.argv[3]
-    qual_title_startswith = ''
-    seq_title_startswith = ''
+    qual_title_startswith = ""
+    seq_title_startswith = ""
     default_coding_value = 64
     fastq_block_lines = 0
 
-    with open(infile_name) as fh, open(sys.argv[2], 'w') as outfile_score:
+    with open(infile_name) as fh, open(sys.argv[2], "w") as outfile_score:
         for i, line in enumerate(fh):
             line = line.rstrip()
-            if not line or line.startswith('#'):
+            if not line or line.startswith("#"):
                 continue
             fastq_block_lines = (fastq_block_lines + 1) % 4
             line_startswith = line[0:1]
@@ -42,7 +42,7 @@ def __main__():
                 if not seq_title_startswith:
                     seq_title_startswith = line_startswith
                 if line_startswith != seq_title_startswith:
-                    stop_err('Invalid fastqsolexa format at line %d: %s.' % (i + 1, line))
+                    stop_err("Invalid fastqsolexa format at line %d: %s." % (i + 1, line))
                 read_title = line[1:]
             elif fastq_block_lines == 2:
                 # second line is nucleotides
@@ -52,17 +52,20 @@ def __main__():
                 if not qual_title_startswith:
                     qual_title_startswith = line_startswith
                 if line_startswith != qual_title_startswith:
-                    stop_err('Invalid fastqsolexa format at line %d: %s.' % (i + 1, line))
+                    stop_err("Invalid fastqsolexa format at line %d: %s." % (i + 1, line))
                 quality_title = line[1:]
                 if quality_title and read_title != quality_title:
-                    stop_err('Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % (i + 1, read_title, quality_title))
+                    stop_err(
+                        'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".'
+                        % (i + 1, read_title, quality_title)
+                    )
                 if not quality_title:
-                    outfile_score.write(f'>{read_title}\n')
+                    outfile_score.write(f">{read_title}\n")
                 else:
-                    outfile_score.write(f'>{line[1:]}\n')
+                    outfile_score.write(f">{line[1:]}\n")
             else:
                 # fourth line is quality scores
-                qual = ''
+                qual = ""
                 fastq_integer = True
                 # peek: ascii or digits?
                 val = line.split()[0]
@@ -84,11 +87,14 @@ def __main__():
                     elif quality_score_length == read_length:
                         quality_score_startswith = default_coding_value
                     else:
-                        stop_err('Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d ).' % (i + 1, quality_score_length, read_length))
+                        stop_err(
+                            "Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d )."
+                            % (i + 1, quality_score_length, read_length)
+                        )
                     for char in line:
-                        score = ord(char) - quality_score_startswith    # 64
+                        score = ord(char) - quality_score_startswith  # 64
                         qual = f"{qual}{str(score)} "
-                outfile_score.write(f'{qual}\n')
+                outfile_score.write(f"{qual}\n")
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/gff_to_bed_converter.py b/lib/galaxy/datatypes/converters/gff_to_bed_converter.py
index 1fe4ed4ef3b..379b3f3393c 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bed_converter.py
+++ b/lib/galaxy/datatypes/converters/gff_to_bed_converter.py
@@ -11,16 +11,16 @@ def __main__():
     skipped_lines = 0
     first_skipped_line = 0
     i = 0
-    with open(input_name) as fh, open(output_name, 'w') as out:
+    with open(input_name) as fh, open(output_name, "w") as out:
         for i, line in enumerate(fh):
-            line = line.rstrip('\r\n')
-            if line and not line.startswith('#'):
+            line = line.rstrip("\r\n")
+            if line and not line.startswith("#"):
                 try:
-                    elems = line.split('\t')
+                    elems = line.split("\t")
                     start = str(int(elems[3]) - 1)
                     strand = elems[6]
-                    if strand not in ['+', '-']:
-                        strand = '+'
+                    if strand not in ["+", "-"]:
+                        strand = "+"
                     # GFF format: chrom source, name, chromStart, chromEnd, score, strand
                     # Bed format: chrom, chromStart, chromEnd, name, score, strand
                     #
@@ -37,7 +37,10 @@ def __main__():
                     first_skipped_line = i + 1
     info_msg = "%i lines converted to BED.  " % (i + 1 - skipped_lines)
     if skipped_lines > 0:
-        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)
+        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (
+            skipped_lines,
+            first_skipped_line,
+        )
     print(info_msg)
 
 
diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
index 1f7d7670e2c..70ea0aa2f01 100644
--- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
@@ -12,7 +12,11 @@ import sys
 
 from bx.interval_index_file import Indexes
 
-from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GenomicInterval, GFFReaderWrapper
+from galaxy.datatypes.util.gff_util import (
+    convert_gff_coords_to_bed,
+    GenomicInterval,
+    GFFReaderWrapper,
+)
 
 
 def main():
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
index 4263962ebab..b5d5cddb423 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
@@ -18,15 +18,21 @@ def __main__():
     try:
         chromCol = int(sys.argv[3]) - 1
     except Exception:
-        stop_err(f"'{str(sys.argv[3])}' is an invalid chrom column, correct the column settings before attempting to convert the data format.")
+        stop_err(
+            f"'{str(sys.argv[3])}' is an invalid chrom column, correct the column settings before attempting to convert the data format."
+        )
     try:
         startCol = int(sys.argv[4]) - 1
     except Exception:
-        stop_err(f"'{str(sys.argv[4])}' is an invalid start column, correct the column settings before attempting to convert the data format.")
+        stop_err(
+            f"'{str(sys.argv[4])}' is an invalid start column, correct the column settings before attempting to convert the data format."
+        )
     try:
         endCol = int(sys.argv[5]) - 1
     except Exception:
-        stop_err(f"'{str(sys.argv[5])}' is an invalid end column, correct the column settings before attempting to convert the data format.")
+        stop_err(
+            f"'{str(sys.argv[5])}' is an invalid end column, correct the column settings before attempting to convert the data format."
+        )
     try:
         strandCol = int(sys.argv[6]) - 1
     except Exception:
@@ -38,8 +44,19 @@ def __main__():
     skipped_lines = 0
     first_skipped_line = 0
     count = 0
-    with open(input_name) as fh, open(output_name, 'w') as out:
-        for count, region in enumerate(bx.intervals.io.NiceReaderWrapper(fh, chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):
+    with open(input_name) as fh, open(output_name, "w") as out:
+        for count, region in enumerate(
+            bx.intervals.io.NiceReaderWrapper(
+                fh,
+                chrom_col=chromCol,
+                start_col=startCol,
+                end_col=endCol,
+                strand_col=strandCol,
+                fix_strand=True,
+                return_header=False,
+                return_comments=False,
+            )
+        ):
             try:
                 if nameCol >= 0:
                     name = region.fields[nameCol]
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
index 70f34cc7d82..ea2d1b01313 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
@@ -14,23 +14,23 @@ def stop_err(msg):
 
 def force_bed_field_count(fields, region_count, force_num_columns):
     if force_num_columns >= 4 and len(fields) < 4:
-        fields.append('region_%i' % (region_count))
+        fields.append("region_%i" % (region_count))
     if force_num_columns >= 5 and len(fields) < 5:
-        fields.append('0')
+        fields.append("0")
     if force_num_columns >= 6 and len(fields) < 6:
-        fields.append('+')
+        fields.append("+")
     if force_num_columns >= 7 and len(fields) < 7:
         fields.append(fields[1])
     if force_num_columns >= 8 and len(fields) < 8:
         fields.append(fields[2])
     if force_num_columns >= 9 and len(fields) < 9:
-        fields.append('0')
+        fields.append("0")
     if force_num_columns >= 10 and len(fields) < 10:
-        fields.append('0')
+        fields.append("0")
     if force_num_columns >= 11 and len(fields) < 11:
-        fields.append(',')
+        fields.append(",")
     if force_num_columns >= 12 and len(fields) < 12:
-        fields.append(',')
+        fields.append(",")
     return fields[:force_num_columns]
 
 
@@ -40,15 +40,21 @@ def __main__():
     try:
         chromCol = int(sys.argv[3]) - 1
     except Exception:
-        stop_err(f"'{str(sys.argv[3])}' is an invalid chrom column, correct the column settings before attempting to convert the data format.")
+        stop_err(
+            f"'{str(sys.argv[3])}' is an invalid chrom column, correct the column settings before attempting to convert the data format."
+        )
     try:
         startCol = int(sys.argv[4]) - 1
     except Exception:
-        stop_err(f"'{str(sys.argv[4])}' is an invalid start column, correct the column settings before attempting to convert the data format.")
+        stop_err(
+            f"'{str(sys.argv[4])}' is an invalid start column, correct the column settings before attempting to convert the data format."
+        )
     try:
         endCol = int(sys.argv[5]) - 1
     except Exception:
-        stop_err(f"'{str(sys.argv[5])}' is an invalid end column, correct the column settings before attempting to convert the data format.")
+        stop_err(
+            f"'{str(sys.argv[5])}' is an invalid end column, correct the column settings before attempting to convert the data format."
+        )
     try:
         strandCol = int(sys.argv[6]) - 1
     except Exception:
@@ -60,7 +66,7 @@ def __main__():
     try:
         extension = sys.argv[8]
     except IndexError:
-        extension = 'interval'  # default extension
+        extension = "interval"  # default extension
     try:
         force_num_columns = int(sys.argv[9])
     except Exception:
@@ -72,53 +78,77 @@ def __main__():
     # does file already conform to bed strict?
     # if so, we want to keep extended columns, otherwise we'll create a generic 6 column bed file
     strict_bed = True
-    if extension in ['bed', 'bedstrict', 'bed6', 'bed12'] and (chromCol, startCol, endCol) == (0, 1, 2) and (nameCol < 0 or nameCol == 3) and (strandCol < 0 or strandCol == 5):
-        with open(input_name) as fh, open(output_name, 'w') as out:
+    if (
+        extension in ["bed", "bedstrict", "bed6", "bed12"]
+        and (chromCol, startCol, endCol) == (0, 1, 2)
+        and (nameCol < 0 or nameCol == 3)
+        and (strandCol < 0 or strandCol == 5)
+    ):
+        with open(input_name) as fh, open(output_name, "w") as out:
             for count, line in enumerate(fh):
-                line = line.rstrip('\n\r')
+                line = line.rstrip("\n\r")
                 if line == "" or line.startswith("#"):
                     skipped_lines += 1
                     if first_skipped_line is None:
                         first_skipped_line = count + 1
                     continue
-                fields = line.split('\t')
+                fields = line.split("\t")
                 try:
-                    assert len(fields) >= 3, 'A BED file requires at least 3 columns'  # we can't fix this
+                    assert len(fields) >= 3, "A BED file requires at least 3 columns"  # we can't fix this
                     if len(fields) > 12:
                         strict_bed = False
                         break
                     # name (fields[3]) can be anything, no verification needed
                     if len(fields) > 4:
-                        float(fields[4])  # score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
+                        float(
+                            fields[4]
+                        )  # score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
                         if len(fields) > 5:
-                            assert fields[5] in ['+', '-'], 'Invalid strand'  # strand - Defines the strand - either '+' or '-'.
+                            assert fields[5] in [
+                                "+",
+                                "-",
+                            ], "Invalid strand"  # strand - Defines the strand - either '+' or '-'.
                             if len(fields) > 6:
-                                int(fields[6])  # thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
+                                int(
+                                    fields[6]
+                                )  # thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
                                 if len(fields) > 7:
-                                    int(fields[7])  # thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
+                                    int(
+                                        fields[7]
+                                    )  # thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
                                     if len(fields) > 8:
-                                        if fields[8] != '0':  # itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
-                                            fields2 = fields[8].split(',')
-                                            assert len(fields2) == 3, 'RGB value must be 0 or have length of 3'
+                                        if (
+                                            fields[8] != "0"
+                                        ):  # itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
+                                            fields2 = fields[8].split(",")
+                                            assert len(fields2) == 3, "RGB value must be 0 or have length of 3"
                                             for field in fields2:
                                                 int(field)  # rgb values are integers
                                         if len(fields) > 9:
                                             int(fields[9])  # blockCount - The number of blocks (exons) in the BED line.
                                             if len(fields) > 10:
-                                                if fields[10] != ',':  # blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
-                                                    fields2 = fields[10].rstrip(",").split(",")  # remove trailing comma and split on comma
+                                                if (
+                                                    fields[10] != ","
+                                                ):  # blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
+                                                    fields2 = (
+                                                        fields[10].rstrip(",").split(",")
+                                                    )  # remove trailing comma and split on comma
                                                     for field in fields2:
                                                         int(field)
                                                 if len(fields) > 11:
-                                                    if fields[11] != ',':  # blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
-                                                        fields2 = fields[11].rstrip(",").split(",")  # remove trailing comma and split on comma
+                                                    if (
+                                                        fields[11] != ","
+                                                    ):  # blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
+                                                        fields2 = (
+                                                            fields[11].rstrip(",").split(",")
+                                                        )  # remove trailing comma and split on comma
                                                         for field in fields2:
                                                             int(field)
                 except Exception:
                     strict_bed = False
                     break
                 if force_num_columns is not None and len(fields) != force_num_columns:
-                    line = '\t'.join(force_bed_field_count(fields, count, force_num_columns))
+                    line = "\t".join(force_bed_field_count(fields, count, force_num_columns))
                 out.write(f"{line}\n")
     else:
         strict_bed = False
@@ -127,8 +157,19 @@ def __main__():
         skipped_lines = 0
         first_skipped_line = None
         count = 0
-        with open(input_name) as fh, open(output_name, 'w') as out:
-            for count, region in enumerate(bx.intervals.io.NiceReaderWrapper(fh, chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):
+        with open(input_name) as fh, open(output_name, "w") as out:
+            for count, region in enumerate(
+                bx.intervals.io.NiceReaderWrapper(
+                    fh,
+                    chrom_col=chromCol,
+                    start_col=startCol,
+                    end_col=endCol,
+                    strand_col=strandCol,
+                    fix_strand=True,
+                    return_header=False,
+                    return_comments=False,
+                )
+            ):
                 try:
                     if nameCol >= 0:
                         name = region.fields[nameCol]
@@ -140,7 +181,7 @@ def __main__():
                     fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
                     if force_num_columns is not None and len(fields) != force_num_columns:
                         fields = force_bed_field_count(fields, count, force_num_columns)
-                    out.write("%s\n" % '\t'.join(fields))
+                    out.write("%s\n" % "\t".join(fields))
                 except Exception:
                     skipped_lines += 1
                     if first_skipped_line is None:
diff --git a/lib/galaxy/datatypes/converters/interval_to_fli.py b/lib/galaxy/datatypes/converters/interval_to_fli.py
index 16dcf4f88d3..fb2d1351460 100644
--- a/lib/galaxy/datatypes/converters/interval_to_fli.py
+++ b/lib/galaxy/datatypes/converters/interval_to_fli.py
@@ -1,4 +1,4 @@
-'''
+"""
 Creates a feature location index (FLI) for a given BED/GFF file.
 FLI index has the form::
 
@@ -12,29 +12,36 @@ where location is formatted as:
     contig:start-end
 
 and symbols are sorted in lexigraphical order.
-'''
+"""
 import optparse
 
-from bx.tabular.io import Comment, Header
+from bx.tabular.io import (
+    Comment,
+    Header,
+)
 
-from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf
+from galaxy.datatypes.util.gff_util import (
+    convert_gff_coords_to_bed,
+    GFFReaderWrapper,
+    read_unordered_gtf,
+)
 
 
 def main():
     # Process arguments.
     parser = optparse.OptionParser()
-    parser.add_option('-F', '--format', dest="input_format")
+    parser.add_option("-F", "--format", dest="input_format")
     (options, args) = parser.parse_args()
     in_fname, out_fname = args
     input_format = options.input_format.lower()
 
     # Create dict of name-location pairings.
     name_loc_dict = {}
-    if input_format in ['gff', 'gtf']:
+    if input_format in ["gff", "gtf"]:
         # GTF/GFF format
 
         # Create reader.
-        if input_format == 'gff':
+        if input_format == "gff":
             in_reader = GFFReaderWrapper(open(in_fname))
         else:  # input_format == 'gtf'
             in_reader = read_unordered_gtf(open(in_fname))
@@ -53,19 +60,15 @@ def main():
                     # Value is not a number, so it can be indexed.
                     if val not in name_loc_dict:
                         # Value is not in dictionary.
-                        name_loc_dict[val] = {
-                            'contig': feature.chrom,
-                            'start': feature.start,
-                            'end': feature.end
-                        }
+                        name_loc_dict[val] = {"contig": feature.chrom, "start": feature.start, "end": feature.end}
                     else:
                         # Value already in dictionary, so update dictionary.
                         loc = name_loc_dict[val]
-                        if feature.start < loc['start']:
-                            loc['start'] = feature.start
-                        if feature.end > loc['end']:
-                            loc['end'] = feature.end
-    elif input_format == 'bed':
+                        if feature.start < loc["start"]:
+                            loc["start"] = feature.start
+                        if feature.end > loc["end"]:
+                            loc["end"] = feature.end
+    elif input_format == "bed":
         # BED format.
         for line in open(in_fname):
             # Ignore track lines.
@@ -79,28 +82,24 @@ def main():
                 continue
 
             # Process line
-            name_loc_dict[fields[3]] = {
-                'contig': fields[0],
-                'start': int(fields[1]),
-                'end': int(fields[2])
-            }
+            name_loc_dict[fields[3]] = {"contig": fields[0], "start": int(fields[1]), "end": int(fields[2])}
 
     # Create sorted list of entries.
     max_len = 0
     entries = []
     for name in sorted(name_loc_dict.keys()):
         loc = name_loc_dict[name]
-        entry = '{}\t{}\t{}'.format(name.lower(), name, '%s:%i-%i' % (loc['contig'], loc['start'], loc['end']))
+        entry = "{}\t{}\t{}".format(name.lower(), name, "%s:%i-%i" % (loc["contig"], loc["start"], loc["end"]))
         if len(entry) > max_len:
             max_len = len(entry)
         entries.append(entry)
 
     # Write padded entries.
-    with open(out_fname, 'w') as out:
+    with open(out_fname, "w") as out:
         out.write(f"{str(max_len + 1).ljust(max_len)}\n")
         for entry in entries:
             out.write(f"{entry.ljust(max_len)}\n")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
index 68ff09f2bc1..60a9146fe20 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
@@ -18,9 +18,9 @@ def main():
 
     # Read options, args.
     parser = optparse.OptionParser()
-    parser.add_option('-c', '--chr-col', type='int', dest='chrom_col', default=1)
-    parser.add_option('-s', '--start-col', type='int', dest='start_col', default=2)
-    parser.add_option('-e', '--end-col', type='int', dest='end_col', default=3)
+    parser.add_option("-c", "--chr-col", type="int", dest="chrom_col", default=1)
+    parser.add_option("-s", "--start-col", type="int", dest="start_col", default=2)
+    parser.add_option("-e", "--end-col", type="int", dest="end_col", default=3)
     (options, args) = parser.parse_args()
     input_fname, output_fname = args
 
@@ -44,7 +44,7 @@ def main():
             index.add(chrom, chrom_start, chrom_end, offset)
             offset += len(line)
 
-    with open(output_fname, 'wb') as out:
+    with open(output_fname, "wb") as out:
         index.write(out)
 
 
diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
index a4fec2bef4d..29e66b518a0 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
@@ -16,31 +16,40 @@ import pysam
 def main():
     # Read options, args.
     parser = optparse.OptionParser()
-    parser.add_option('-c', '--chr-col', type='int', dest='chrom_col')
-    parser.add_option('-s', '--start-col', type='int', dest='start_col')
-    parser.add_option('-e', '--end-col', type='int', dest='end_col')
-    parser.add_option('-P', '--preset', dest='preset')
+    parser.add_option("-c", "--chr-col", type="int", dest="chrom_col")
+    parser.add_option("-s", "--start-col", type="int", dest="start_col")
+    parser.add_option("-e", "--end-col", type="int", dest="end_col")
+    parser.add_option("-P", "--preset", dest="preset")
     (options, args) = parser.parse_args()
     _, bgzip_fname, out_fname = args
-    to_tabix(bgzip_fname=bgzip_fname,
-             out_fname=out_fname,
-             preset=options.preset,
-             chrom_col=options.chrom_col,
-             start_col=options.start_col,
-             end_col=options.end_col)
+    to_tabix(
+        bgzip_fname=bgzip_fname,
+        out_fname=out_fname,
+        preset=options.preset,
+        chrom_col=options.chrom_col,
+        start_col=options.start_col,
+        end_col=options.end_col,
+    )
 
 
 def to_tabix(bgzip_fname, out_fname, preset=None, chrom_col=None, start_col=None, end_col=None):
     # Create index.
     if preset:
         # Preset type.
-        bgzip_fname = pysam.tabix_index(filename=bgzip_fname, preset=preset, keep_original=True,
-                                        index=out_fname, force=True)
+        bgzip_fname = pysam.tabix_index(
+            filename=bgzip_fname, preset=preset, keep_original=True, index=out_fname, force=True
+        )
     else:
         # For interval files; column indices are 0-based.
-        bgzip_fname = pysam.tabix_index(filename=bgzip_fname, seq_col=(chrom_col - 1),
-                                        start_col=(start_col - 1), end_col=(end_col - 1),
-                                        keep_original=True, index=out_fname, force=True)
+        bgzip_fname = pysam.tabix_index(
+            filename=bgzip_fname,
+            seq_col=(chrom_col - 1),
+            start_col=(start_col - 1),
+            end_col=(end_col - 1),
+            keep_original=True,
+            index=out_fname,
+            force=True,
+        )
     if os.path.getsize(out_fname) == 0:
         sys.exit("The converted tabix index file is empty, meaning the input data is invalid.")
     return bgzip_fname
diff --git a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
index 9ba6c738e1c..e1484529278 100644
--- a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
+++ b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
@@ -8,7 +8,7 @@ import sys
 import time
 
 prog = os.path.split(sys.argv[0])[-1]
-myversion = 'Oct 10 2009'
+myversion = "Oct 10 2009"
 
 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
@@ -25,36 +25,35 @@ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 
 
 def timenow():
-    """return current time as a string
-    """
-    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+    """return current time as a string"""
+    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
 
 
 def rgConv(inpedfilepath, outhtmlname, outfilepath):
     """convert linkage ped/map to fbat"""
-    recode = {'A': '1', 'C': '2', 'G': '3', 'T': '4', 'N': '0', '0': '0', '1': '1', '2': '2', '3': '3', '4': '4'}
+    recode = {"A": "1", "C": "2", "G": "3", "T": "4", "N": "0", "0": "0", "1": "1", "2": "2", "3": "3", "4": "4"}
     basename = os.path.split(inpedfilepath)[-1]  # get basename
-    inmap = f'{inpedfilepath}.map'
-    inped = f'{inpedfilepath}.ped'
-    outf = f'{basename}.ped'  # note the fbat exe insists that this is the extension for the ped data
+    inmap = f"{inpedfilepath}.map"
+    inped = f"{inpedfilepath}.ped"
+    outf = f"{basename}.ped"  # note the fbat exe insists that this is the extension for the ped data
     outfpath = os.path.join(outfilepath, outf)  # where to write the fbat format file to
     try:
         mf = open(inmap)
     except Exception:
-        sys.exit(f'{prog} cannot open inmap file {inmap} - do you have permission?\n')
+        sys.exit(f"{prog} cannot open inmap file {inmap} - do you have permission?\n")
     try:
         rsl = [x.split()[1] for x in mf]
     except Exception:
-        sys.exit(f'## cannot parse {inmap}')
+        sys.exit(f"## cannot parse {inmap}")
     try:
         os.makedirs(outfilepath)
     except Exception:
         pass  # already exists
-    head = ' '.join(rsl)  # list of rs numbers
+    head = " ".join(rsl)  # list of rs numbers
     # TODO add anno to rs but fbat will prolly barf?
-    with open(inped) as pedf, open(outfpath, 'w', 2 ** 20) as o:
+    with open(inped) as pedf, open(outfpath, "w", 2**20) as o:
         o.write(head)
-        o.write('\n')
+        o.write("\n")
         for i, row in enumerate(pedf):
             if i == 0:
                 lrow = row.split()
@@ -66,7 +65,7 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
                 lrow = row.strip().split()
                 p = lrow[:6]
                 g = lrow[6:]
-                gc = [recode.get(z, '0') for z in g]
+                gc = [recode.get(z, "0") for z in g]
                 lrow = p + gc
                 row = f"{' '.join(lrow)}\n"
             o.write(row)
@@ -82,7 +81,7 @@ def main():
     """
     nparm = 3
     if len(sys.argv) < nparm:
-        sys.exit('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
+        sys.exit("## %s called with %s - needs %d parameters \n" % (prog, sys.argv, nparm))
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
     outfilepath = sys.argv[3]
@@ -92,10 +91,10 @@ def main():
         pass
     rgConv(inpedfilepath, outhtmlname, outfilepath)
     flist = os.listdir(outfilepath)
-    with open(outhtmlname, 'w') as f:
+    with open(outhtmlname, "w") as f:
         f.write(galhtmlprefix % prog)
-        print(f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}')  # becomes info
-        f.write(f'<div>## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}\n<ol>')
+        print(f"## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}")  # becomes info
+        f.write(f"<div>## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}\n<ol>")
         for data in flist:
             f.write(f'<li><a href="{os.path.split(data)[-1]}">{os.path.split(data)[-1]}</a></li>\n')
         f.write("</div></body></html>")
diff --git a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
index 90bc0586926..c9258e22375 100644
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
@@ -11,7 +11,7 @@ import sys
 import time
 
 prog = os.path.split(sys.argv[0])[-1]
-myversion = 'Oct 10 2009'
+myversion = "Oct 10 2009"
 
 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
@@ -28,17 +28,16 @@ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 
 
 def timenow():
-    """return current time as a string
-    """
-    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+    """return current time as a string"""
+    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
 
 
-def getMissval(inped=''):
+def getMissval(inped=""):
     """
     read some lines...ugly hack - try to guess missing value
     should be N or 0 but might be . or -
     """
-    commonmissvals = {'N': 'N', '0': '0', 'n': 'n', '9': '9', '-': '-', '.': '.'}
+    commonmissvals = {"N": "N", "0": "0", "n": "n", "9": "9", "-": "-", ".": "."}
     try:
         f = open(inped)
     except Exception:
@@ -56,24 +55,24 @@ def getMissval(inped=''):
                 f.close()
                 return missval
     if not missval:
-        missval = 'N'  # punt
+        missval = "N"  # punt
     f.close()
     return missval
 
 
 def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
-    """
-    """
-    pedf = f'{inpedfilepath}.ped'
+    """ """
+    pedf = f"{inpedfilepath}.ped"
     basename = os.path.split(inpedfilepath)[-1]  # get basename
     outroot = os.path.join(outfilepath, basename)
     missval = getMissval(inped=pedf)
     if not missval:
-        print(f'### lped_to_pbed_converter.py cannot identify missing value in {pedf}')
-        missval = '0'
-    subprocess.check_call([plink, '--noweb', '--file', inpedfilepath,
-                           '--make-bed', '--out', outroot,
-                           '--missing-genotype', missval], cwd=outfilepath)
+        print(f"### lped_to_pbed_converter.py cannot identify missing value in {pedf}")
+        missval = "0"
+    subprocess.check_call(
+        [plink, "--noweb", "--file", inpedfilepath, "--make-bed", "--out", outroot, "--missing-genotype", missval],
+        cwd=outfilepath,
+    )
 
 
 def main():
@@ -86,7 +85,7 @@ def main():
     """
     nparm = 4
     if len(sys.argv) < nparm:
-        sys.exit('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
+        sys.exit("## %s called with %s - needs %d parameters \n" % (prog, sys.argv, nparm))
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
     outfilepath = sys.argv[3]
@@ -97,11 +96,11 @@ def main():
     plink = sys.argv[4]
     rgConv(inpedfilepath, outhtmlname, outfilepath, plink)
     flist = os.listdir(outfilepath)
-    with open(outhtmlname, 'w') as f:
+    with open(outhtmlname, "w") as f:
         f.write(galhtmlprefix % prog)
-        s = f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}'  # becomes info
+        s = f"## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}"  # becomes info
         print(s)
-        f.write(f'<div>{s}\n<ol>')
+        f.write(f"<div>{s}\n<ol>")
         for data in flist:
             f.write(f'<li><a href="{os.path.split(data)[-1]}">{os.path.split(data)[-1]}</a></li>\n')
         f.write("</ol></div></div></body></html>")
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
index 78906386ab4..0b968f3c753 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
@@ -14,7 +14,7 @@ def __main__():
     output_name = sys.argv.pop(1)
     input_name = sys.argv.pop(1)
     count = 0
-    with open(output_name, 'w') as out, open(input_name) as infile:
+    with open(output_name, "w") as out, open(input_name) as infile:
         for count, block in enumerate(bx.align.maf.Reader(infile)):
             spec_counts = {}
             for c in block.components:
@@ -23,7 +23,14 @@ def __main__():
                     spec_counts[spec] = 0
                 else:
                     spec_counts[spec] += 1
-                out.write("%s\n" % maf_utilities.get_fasta_header(c, {'block_index': count, 'species': spec, 'sequence_index': spec_counts[spec]}, suffix="%s_%i_%i" % (spec, count, spec_counts[spec])))
+                out.write(
+                    "%s\n"
+                    % maf_utilities.get_fasta_header(
+                        c,
+                        {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
+                        suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                    )
+                )
                 out.write(f"{c.text}\n")
             out.write("\n")
     print("%i MAF blocks converted to FASTA." % (count))
diff --git a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py
index 92bc7c2b4e8..05c9c4b1a73 100644
--- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py
@@ -15,7 +15,7 @@ def __main__():
     input_name = sys.argv.pop(1)
     species = sys.argv.pop(1)
     count = 0
-    with open(output_name, 'w') as out:
+    with open(output_name, "w") as out:
         # write interval header line
         out.write("#chrom\tstart\tend\tstrand\n")
         try:
@@ -23,7 +23,15 @@ def __main__():
                 for block in bx.align.maf.Reader(fh):
                     for c in maf_utilities.iter_components_by_src_start(block, species):
                         if c is not None:
-                            out.write("%s\t%i\t%i\t%s\n" % (maf_utilities.src_split(c.src)[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand))
+                            out.write(
+                                "%s\t%i\t%i\t%s\n"
+                                % (
+                                    maf_utilities.src_split(c.src)[-1],
+                                    c.get_forward_strand_start(),
+                                    c.get_forward_strand_end(),
+                                    c.strand,
+                                )
+                            )
                             count += 1
         except Exception as e:
             print(f"There was a problem processing your input: {e}", file=sys.stderr)
diff --git a/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py b/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py
index d4e6969d279..6646e7a9533 100644
--- a/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py
+++ b/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py
@@ -5,6 +5,7 @@ Output: csv
 """
 import os
 import sys
+
 try:
     import pyarrow.csv
     import pyarrow.parquet
diff --git a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
index 7835d7ad96a..cffebc2d8d6 100644
--- a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
@@ -22,46 +22,56 @@ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 <div class="document">
 """
 
-plinke = 'plink'
+plinke = "plink"
 
 
 def timenow():
-    """return current time as a string
-    """
-    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+    """return current time as a string"""
+    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
 
 
-def pruneLD(plinktasks=None, cd='./', vclbase=None):
-    """
-    """
+def pruneLD(plinktasks=None, cd="./", vclbase=None):
+    """ """
     plinktasks = plinktasks or []
     vclbase = vclbase or []
-    alog = ['## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n']
-    with tempfile.NamedTemporaryFile(mode='r+') as plog:
+    alog = ["## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n"]
+    with tempfile.NamedTemporaryFile(mode="r+") as plog:
         for task in plinktasks:  # each is a list
             vcl = vclbase + task
             subprocess.check_call(vcl, stdout=plog, stderr=plog, cwd=cd)
             try:
                 plog.seek(0)
-                lplog = [elem for elem in plog.readlines() if elem.find('Pruning SNP') == -1]
+                lplog = [elem for elem in plog.readlines() if elem.find("Pruning SNP") == -1]
                 alog += lplog
-                alog.append('\n')
+                alog.append("\n")
             except Exception:
-                alog.append(f"### {timenow()} Strange - no std out from plink when running command line\n{' '.join(vcl)}\n")
+                alog.append(
+                    f"### {timenow()} Strange - no std out from plink when running command line\n{' '.join(vcl)}\n"
+                )
     return alog
 
 
-def makeLDreduced(basename, infpath=None, outfpath=None, plinke='plink', forcerebuild=False, returnFname=False,
-                  winsize="60", winmove="40", r2thresh="0.1"):
-    """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
-    """
+def makeLDreduced(
+    basename,
+    infpath=None,
+    outfpath=None,
+    plinke="plink",
+    forcerebuild=False,
+    returnFname=False,
+    winsize="60",
+    winmove="40",
+    r2thresh="0.1",
+):
+    """not there so make and leave in output dir for post job hook to copy back into input extra files path for next time"""
     outbase = os.path.join(outfpath, basename)
     inbase = os.path.join(infpath)
     plinktasks = []
-    vclbase = [plinke, '--noweb']
-    plinktasks += [['--bfile', inbase, f'--indep-pairwise {winsize} {winmove} {r2thresh}', f'--out {outbase}'],
-                   ['--bfile', inbase, f'--extract {outbase}.prune.in --make-bed --out {outbase}']]
-    vclbase = [plinke, '--noweb']
+    vclbase = [plinke, "--noweb"]
+    plinktasks += [
+        ["--bfile", inbase, f"--indep-pairwise {winsize} {winmove} {r2thresh}", f"--out {outbase}"],
+        ["--bfile", inbase, f"--extract {outbase}.prune.in --make-bed --out {outbase}"],
+    ]
+    vclbase = [plinke, "--noweb"]
     pruneLD(plinktasks=plinktasks, cd=outfpath, vclbase=vclbase)
 
 
@@ -79,7 +89,7 @@ def main():
     """
     nparm = 7
     if len(sys.argv) < nparm:
-        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
+        sys.stderr.write("## %s called with %s - needs %d parameters \n" % (prog, sys.argv, nparm))
         sys.exit(1)
     inpedfilepath = sys.argv[1]
     base_name = os.path.split(inpedfilepath)[-1]
@@ -93,15 +103,24 @@ def main():
     except Exception:
         pass
     plink = sys.argv[7]
-    makeLDreduced(base_name, infpath=inpedfilepath, outfpath=outfilepath, plinke=plink, forcerebuild=False, returnFname=False,
-                  winsize=winsize, winmove=winmove, r2thresh=r2thresh)
+    makeLDreduced(
+        base_name,
+        infpath=inpedfilepath,
+        outfpath=outfilepath,
+        plinke=plink,
+        forcerebuild=False,
+        returnFname=False,
+        winsize=winsize,
+        winmove=winmove,
+        r2thresh=r2thresh,
+    )
     flist = os.listdir(outfilepath)
-    with open(outhtmlname, 'w') as f:
+    with open(outhtmlname, "w") as f:
         f.write(galhtmlprefix % prog)
-        s1 = f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}'  # becomes info
-        s2 = f'Input {base_name}, winsize={winsize}, winmove={winmove}, r2thresh={r2thresh}'
-        print(f'{s1} {s2}')
-        f.write(f'<div>{s1}\n{s2}\n<ol>')
+        s1 = f"## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}"  # becomes info
+        s2 = f"Input {base_name}, winsize={winsize}, winmove={winmove}, r2thresh={r2thresh}"
+        print(f"{s1} {s2}")
+        f.write(f"<div>{s1}\n{s2}\n<ol>")
         for data in flist:
             f.write(f'<li><a href="{os.path.split(data)[-1]}">{os.path.split(data)[-1]}</a></li>\n')
         f.write("</div></body></html>")
diff --git a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
index d967206bff5..eee21aa85da 100644
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
@@ -10,9 +10,8 @@ import subprocess
 import sys
 import time
 
-
 prog = os.path.split(sys.argv[0])[-1]
-myversion = 'Oct 10 2009'
+myversion = "Oct 10 2009"
 
 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
@@ -29,17 +28,15 @@ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
 
 
 def timenow():
-    """return current time as a string
-    """
-    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+    """return current time as a string"""
+    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
 
 
 def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
-    """
-    """
+    """ """
     basename = os.path.split(inpedfilepath)[-1]  # get basename
     outroot = os.path.join(outfilepath, basename)
-    subprocess.check_call([plink, '--noweb', '--bfile', inpedfilepath, '--recode', '--out', outroot], cwd=outfilepath)
+    subprocess.check_call([plink, "--noweb", "--bfile", inpedfilepath, "--recode", "--out", outroot], cwd=outfilepath)
 
 
 def main():
@@ -52,7 +49,7 @@ def main():
     """
     nparm = 4
     if len(sys.argv) < nparm:
-        sys.exit('PBED to LPED converter called with %s - needs %d parameters \n' % (sys.argv, nparm))
+        sys.exit("PBED to LPED converter called with %s - needs %d parameters \n" % (sys.argv, nparm))
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
     outfilepath = sys.argv[3]
@@ -63,11 +60,11 @@ def main():
     plink = sys.argv[4]
     rgConv(inpedfilepath, outhtmlname, outfilepath, plink)
     flist = os.listdir(outfilepath)
-    with open(outhtmlname, 'w') as f:
+    with open(outhtmlname, "w") as f:
         f.write(galhtmlprefix % prog)
-        s = f'## Rgenetics: http://bitbucket.org/rgalaxy Galaxy Tools {prog} {timenow()}'  # becomes info
+        s = f"## Rgenetics: http://bitbucket.org/rgalaxy Galaxy Tools {prog} {timenow()}"  # becomes info
         print(s)
-        f.write(f'<div>{s}\n<ol>')
+        f.write(f"<div>{s}\n<ol>")
         for data in flist:
             f.write(f'<li><a href="{os.path.split(data)[-1]}">{os.path.split(data)[-1]}</a></li>\n')
         f.write("</ol></div></div></body></html>")
diff --git a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
index 52a16deefff..dde54d6d6ad 100644
--- a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
+++ b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
@@ -4,7 +4,7 @@
 import sys
 
 assert sys.version_info[:2] >= (2, 6)
-HEADER_STARTS_WITH = ('@')
+HEADER_STARTS_WITH = "@"
 
 
 def __main__():
@@ -14,16 +14,16 @@ def __main__():
     first_skipped_line = 0
     header_lines = 0
     i = 0
-    with open(input_name) as fh, open(output_name, 'w') as out:
+    with open(input_name) as fh, open(output_name, "w") as out:
         for i, line in enumerate(fh):
-            line = line.rstrip('\r\n')
+            line = line.rstrip("\r\n")
             if line:
                 if line.startswith(HEADER_STARTS_WITH):
                     header_lines += 1
                 else:
                     try:
-                        elems = line.split('\t')
-                        out.write(f'{elems[0]}\t{int(elems[1]) - 1}\t{elems[2]}\t{elems[4]}\t0\t{elems[3]}\n')
+                        elems = line.split("\t")
+                        out.write(f"{elems[0]}\t{int(elems[1]) - 1}\t{elems[2]}\t{elems[4]}\t0\t{elems[3]}\n")
                     except Exception as e:
                         print(e)
                         skipped_lines += 1
@@ -35,7 +35,10 @@ def __main__():
                     first_skipped_line = i + 1
     info_msg = "%i lines converted to BED.  " % (i + 1 - skipped_lines)
     if skipped_lines > 0:
-        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)
+        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (
+            skipped_lines,
+            first_skipped_line,
+        )
     print(info_msg)
 
 
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
index 9847a909fa5..1366d5d15d2 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
@@ -29,7 +29,7 @@ def main():
             index.add(chrom, start, start + 1, offset)
             offset += len(line)
 
-    with open(output_fname, 'wb') as out:
+    with open(output_fname, "wb") as out:
         index.write(out)
 
 
diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
index c5c978a2da3..097459048de 100644
--- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
+++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
@@ -11,11 +11,11 @@ assert sys.version_info[:2] >= (2, 4)
 
 
 def __main__():
-    with open(sys.argv[1]) as infile, open(sys.argv[2], 'w') as outfile:
+    with open(sys.argv[1]) as infile, open(sys.argv[2], "w") as outfile:
         for line in infile:
             line = line.rstrip()
-            if line and not line.startswith('#'):
-                fields = line.split('\t')
+            if line and not line.startswith("#"):
+                fields = line.split("\t")
                 # make sure the 2nd field (taxonomy) ends with a ;
                 outfile.write(f"{fields[0]}\t{re.sub(';$', '', fields[1])};\n")
 
diff --git a/lib/galaxy/datatypes/converters/tabular_csv.py b/lib/galaxy/datatypes/converters/tabular_csv.py
index a323385037a..4170613b879 100644
--- a/lib/galaxy/datatypes/converters/tabular_csv.py
+++ b/lib/galaxy/datatypes/converters/tabular_csv.py
@@ -12,9 +12,9 @@ import csv
 def main():
     usage = "Usage: %prog [options]"
     parser = argparse.ArgumentParser(usage=usage)
-    parser.add_argument('-f', '--from-tabular', action='store_true', default=False, dest='fromtabular')
-    parser.add_argument('-i', '--input', type=str, dest='input')
-    parser.add_argument('-o', '--output', type=str, dest='output')
+    parser.add_argument("-f", "--from-tabular", action="store_true", default=False, dest="fromtabular")
+    parser.add_argument("-i", "--input", type=str, dest="input")
+    parser.add_argument("-o", "--output", type=str, dest="output")
     args = parser.parse_args()
     input_fname = args.input
     output_fname = args.output
@@ -25,17 +25,17 @@ def main():
 
 
 def convert_to_tsv(input_fname, output_fname):
-    with open(input_fname, newline="") as csvfile, open(output_fname, 'w') as ofh:
+    with open(input_fname, newline="") as csvfile, open(output_fname, "w") as ofh:
         reader = csv.reader(csvfile)
         for line in reader:
-            ofh.write('\t'.join(line) + '\n')
+            ofh.write("\t".join(line) + "\n")
 
 
 def convert_to_csv(input_fname, output_fname):
-    with open(input_fname) as tabfile, open(output_fname, 'w', newline='') as ofh:
-        writer = csv.writer(ofh, delimiter=',')
+    with open(input_fname) as tabfile, open(output_fname, "w", newline="") as ofh:
+        writer = csv.writer(ofh, delimiter=",")
         for line in tabfile.readlines():
-            writer.writerow(line.strip().split('\t'))
+            writer.writerow(line.strip().split("\t"))
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
index e6545b9d0de..a8c7c06ee5a 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
@@ -15,9 +15,9 @@ def main():
     # Read options, args.
     usage = "Usage: %prog [options] tabular_input_file bgzip_output_file"
     parser = optparse.OptionParser(usage=usage)
-    parser.add_option('-c', '--chr-col', type='int', default=0, dest='chrom_col')
-    parser.add_option('-s', '--start-col', type='int', default=1, dest='start_col')
-    parser.add_option('-e', '--end-col', type='int', default=1, dest='end_col')
+    parser.add_option("-c", "--chr-col", type="int", default=0, dest="chrom_col")
+    parser.add_option("-s", "--start-col", type="int", default=1, dest="start_col")
+    parser.add_option("-e", "--end-col", type="int", default=1, dest="end_col")
     (options, args) = parser.parse_args()
     if len(args) != 2:
         parser.print_usage()
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
index 30b6330b010..853d57e0172 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
@@ -12,7 +12,7 @@ import bx.wiggle
 
 from galaxy.util.ucsc import (
     UCSCLimitException,
-    UCSCOutWrapper
+    UCSCOutWrapper,
 )
 
 
@@ -23,7 +23,9 @@ def main():
                 out_file.write("%s\n" % "\t".join(map(str, fields)))
         except UCSCLimitException:
             # Wiggle data was truncated, at the very least need to warn the user.
-            sys.stderr.write('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
+            sys.stderr.write(
+                'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.'
+            )
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/coverage.py b/lib/galaxy/datatypes/coverage.py
index 50f7895bbcb..1d489c1fc48 100644
--- a/lib/galaxy/datatypes/coverage.py
+++ b/lib/galaxy/datatypes/coverage.py
@@ -18,8 +18,16 @@ class LastzCoverage(Tabular):
 
     MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter)
     MetadataElement(name="positionCol", default=2, desc="Position column", param=metadata.ColumnParameter)
-    MetadataElement(name="forwardCol", default=3, desc="Forward or aggregate read column", param=metadata.ColumnParameter)
-    MetadataElement(name="reverseCol", desc="Optional reverse read column", param=metadata.ColumnParameter, optional=True, no_value=0)
+    MetadataElement(
+        name="forwardCol", default=3, desc="Forward or aggregate read column", param=metadata.ColumnParameter
+    )
+    MetadataElement(
+        name="reverseCol",
+        desc="Optional reverse read column",
+        param=metadata.ColumnParameter,
+        optional=True,
+        no_value=0,
+    )
     MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
 
     def get_track_resolution(self, dataset, start, end):
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index bd42a995b94..98146ac554c 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -45,16 +45,16 @@ if TYPE_CHECKING:
     from galaxy.model import DatasetInstance
 
 XSS_VULNERABLE_MIME_TYPES = [
-    'image/svg+xml',  # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
-    'application/xml',  # Some browsers will evalute SVG embedded JS in such XML documents.
+    "image/svg+xml",  # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
+    "application/xml",  # Some browsers will evalute SVG embedded JS in such XML documents.
 ]
-DEFAULT_MIME_TYPE = 'text/plain'  # Vulnerable mime types will be replaced with this.
+DEFAULT_MIME_TYPE = "text/plain"  # Vulnerable mime types will be replaced with this.
 
 log = logging.getLogger(__name__)
 
 # Valid first column and strand column values vor bed, other formats
-col1_startswith = ['chr', 'chl', 'groupun', 'reftig_', 'scaffold', 'super_', 'vcho']
-valid_strand = ['+', '-', '.']
+col1_startswith = ["chr", "chl", "groupun", "reftig_", "scaffold", "super_", "vcho"]
+valid_strand = ["+", "-", "."]
 
 DOWNLOAD_FILENAME_PATTERN_DATASET = "Galaxy${hid}-[${name}].${ext}"
 DOWNLOAD_FILENAME_PATTERN_COLLECTION_ELEMENT = "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}"
@@ -68,7 +68,6 @@ class DatatypeConverterNotFoundException(Exception):
 
 
 class DatatypeValidation:
-
     def __init__(self, state, message):
         self.state = state
         self.message = message
@@ -101,17 +100,17 @@ def get_params_and_input_name(converter, deps, target_context=None):
     # Generate parameter dictionary
     params = {}
     # determine input parameter name and add to params
-    input_name = 'input1'
+    input_name = "input1"
     for key, value in converter.inputs.items():
         if deps and value.name in deps:
             params[value.name] = deps[value.name]
-        elif value.type == 'data':
+        elif value.type == "data":
             input_name = key
 
     # add potentially required/common internal tool parameters e.g. '__job_resource'
     if target_context:
         for key, value in target_context.items():
-            if key.startswith('__'):
+            if key.startswith("__"):
                 params[key] = value
     return params, input_name
 
@@ -120,6 +119,7 @@ class DataMeta(abc.ABCMeta):
     """
     Metaclass for Data class.  Sets up metadata spec.
     """
+
     def __init__(cls, name, bases, dict_):
         cls.metadata_spec = metadata.MetadataSpecCollection()
         for base in bases:  # loop through bases (class/types) of cls
@@ -144,9 +144,10 @@ class Data(metaclass=DataMeta):
     >>> type( DataTest.metadata_spec.test.param )
     <class 'galaxy.model.metadata.MetadataParameter'>
     """
+
     edam_data = "data_0006"
     edam_format = "format_1915"
-    file_ext = 'data'
+    file_ext = "data"
     # Data is not chunkable by default.
     CHUNKABLE = False
 
@@ -154,7 +155,15 @@ class Data(metaclass=DataMeta):
     metadata_spec: metadata.MetadataSpecCollection
 
     # Add metadata elements
-    MetadataElement(name="dbkey", desc="Database/Build", default="?", param=metadata.DBKeyParameter, multiple=False, optional=True, no_value="?")
+    MetadataElement(
+        name="dbkey",
+        desc="Database/Build",
+        default="?",
+        param=metadata.DBKeyParameter,
+        multiple=False,
+        optional=True,
+        no_value="?",
+    )
     # Stores the set of display applications, and viewing methods, supported by this datatype
     supported_display_apps: Dict[str, Any] = {}
     # If False, the peek is regenerated whenever a dataset of this type is copied
@@ -165,7 +174,7 @@ class Data(metaclass=DataMeta):
     # Composite datatypes
     composite_type: Optional[str] = None
     composite_files: Dict[str, Any] = {}
-    primary_file_name = 'index'
+    primary_file_name = "index"
     # Allow user to change between this datatype and others. If left to None,
     # datatype change is allowed if the datatype is not composite.
     allow_datatype_change: Optional[bool] = None
@@ -199,10 +208,10 @@ class Data(metaclass=DataMeta):
     def get_raw_data(self, dataset):
         """Returns the full data. To stream it open the file_name and read/write as needed"""
         try:
-            return open(dataset.file_name, 'rb').read(-1)
+            return open(dataset.file_name, "rb").read(-1)
         except OSError:
-            log.exception('%s reading a file that does not exist %s', self.__class__.__name__, dataset.file_name)
-            return ''
+            log.exception("%s reading a file that does not exist %s", self.__class__.__name__, dataset.file_name)
+            return ""
 
     def dataset_content_needs_grooming(self, file_name):
         """This function is called on an output dataset file after the content is initially generated."""
@@ -267,11 +276,11 @@ class Data(metaclass=DataMeta):
         Set the peek and blurb text
         """
         if not dataset.dataset.purged:
-            dataset.peek = ''
-            dataset.blurb = 'data'
+            dataset.peek = ""
+            dataset.blurb = "data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Create HTML table, used for displaying peek"""
@@ -286,7 +295,7 @@ class Data(metaclass=DataMeta):
                 if not line:
                     continue
                 out.append(f"<tr><td>{escape(unicodify(line, 'utf-8'))}</td></tr>")
-            out.append('</table>')
+            out.append("</table>")
             return "".join(out)
         except Exception as exc:
             return f"Can't create peek: {unicodify(exc)}"
@@ -301,7 +310,7 @@ class Data(metaclass=DataMeta):
         Returns a tuple of boolean, string, string: (error, msg, messagetype)
         """
         error, msg, messagetype = False, "", ""
-        archname = f'{display_name}.html'  # fake the real nature of the html file
+        archname = f"{display_name}.html"  # fake the real nature of the html file
         try:
             archive.write(data_filename, archname)
         except OSError:
@@ -311,17 +320,17 @@ class Data(metaclass=DataMeta):
             messagetype = "error"
         return error, msg, messagetype
 
-    def _archive_composite_dataset(self, trans, data, headers: Headers, do_action='zip'):
+    def _archive_composite_dataset(self, trans, data, headers: Headers, do_action="zip"):
         # save a composite object into a compressed archive for downloading
         outfname = data.name[0:150]
-        outfname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in outfname)
+        outfname = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in outfname)
         archive = ZipstreamWrapper(
             archive_name=outfname,
             upstream_mod_zip=trans.app.config.upstream_mod_zip,
-            upstream_gzip=trans.app.config.upstream_gzip
+            upstream_gzip=trans.app.config.upstream_gzip,
         )
         error = False
-        msg = ''
+        msg = ""
         ext = data.extension
         path = data.file_name
         efp = data.extra_files_path
@@ -329,7 +338,7 @@ class Data(metaclass=DataMeta):
 
         display_name = os.path.splitext(outfname)[0]
         if not display_name.endswith(ext):
-            display_name = f'{display_name}_{ext}'
+            display_name = f"{display_name}_{ext}"
 
         error, msg = self._archive_main_file(archive, display_name, path)[:2]
         if not error:
@@ -356,11 +365,19 @@ class Data(metaclass=DataMeta):
                 yield fpath, rpath
 
     def _serve_raw(self, dataset, to_ext, headers: Headers, **kwd):
-        headers['Content-Length'] = str(os.stat(dataset.file_name).st_size)
-        headers["content-type"] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
-        filename = self._download_filename(dataset, to_ext, hdca=kwd.get("hdca"), element_identifier=kwd.get("element_identifier"), filename_pattern=kwd.get("filename_pattern"))
+        headers["Content-Length"] = str(os.stat(dataset.file_name).st_size)
+        headers[
+            "content-type"
+        ] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+        filename = self._download_filename(
+            dataset,
+            to_ext,
+            hdca=kwd.get("hdca"),
+            element_identifier=kwd.get("element_identifier"),
+            filename_pattern=kwd.get("filename_pattern"),
+        )
         headers["Content-Disposition"] = f'attachment; filename="{filename}"'
-        return open(dataset.file_name, mode='rb'), headers
+        return open(dataset.file_name, mode="rb"), headers
 
     def to_archive(self, dataset, name=""):
         """
@@ -372,7 +389,7 @@ class Data(metaclass=DataMeta):
         """
         rel_paths = []
         file_paths = []
-        if dataset.datatype.composite_type or dataset.extension.endswith('html'):
+        if dataset.datatype.composite_type or dataset.extension.endswith("html"):
             main_file = f"{name}.html"
             rel_paths.append(main_file)
             file_paths.append(dataset.file_name)
@@ -397,10 +414,10 @@ class Data(metaclass=DataMeta):
         headers = kwd.get("headers", {})
         # Relocate all composite datatype display to a common location.
         composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
-        composite_extensions.append('html')  # for archiving composite datatypes
+        composite_extensions.append("html")  # for archiving composite datatypes
         # Prevent IE8 from sniffing content type since we're explicit about it.  This prevents intentionally text/plain
         # content from being rendered in the browser
-        headers['X-Content-Type-Options'] = 'nosniff'
+        headers["X-Content-Type-Options"] = "nosniff"
         if isinstance(data, str):
             return smart_str(data), headers
         if filename and filename != "index":
@@ -409,17 +426,22 @@ class Data(metaclass=DataMeta):
             file_path = trans.app.object_store.get_filename(data.dataset, extra_dir=extra_dir, alt_name=filename)
             if os.path.exists(file_path):
                 if os.path.isdir(file_path):
-                    with tempfile.NamedTemporaryFile(mode='w', delete=False, dir=trans.app.config.new_file_path, prefix='gx_html_autocreate_') as tmp_fh:
+                    with tempfile.NamedTemporaryFile(
+                        mode="w", delete=False, dir=trans.app.config.new_file_path, prefix="gx_html_autocreate_"
+                    ) as tmp_fh:
                         tmp_file_name = tmp_fh.name
                         dir_items = sorted(os.listdir(file_path))
                         base_path, item_name = os.path.split(file_path)
-                        tmp_fh.write('<html><head><h3>Directory %s contents: %d items</h3></head>\n' % (escape(item_name), len(dir_items)))
+                        tmp_fh.write(
+                            "<html><head><h3>Directory %s contents: %d items</h3></head>\n"
+                            % (escape(item_name), len(dir_items))
+                        )
                         tmp_fh.write('<body><p/><table cellpadding="2">\n')
                         for index, fname in enumerate(dir_items):
                             if index % 2 == 0:
-                                bgcolor = '#D8D8D8'
+                                bgcolor = "#D8D8D8"
                             else:
-                                bgcolor = '#FFFFFF'
+                                bgcolor = "#FFFFFF"
                             # Can't have an href link here because there is no route
                             # defined for files contained within multiple subdirectory
                             # levels of the primary dataset.  Something like this is
@@ -428,7 +450,7 @@ class Data(metaclass=DataMeta):
                             # dataset_id=trans.security.encode_id(data.dataset.id),
                             # preview=preview, filename=fname, to_ext=to_ext)
                             tmp_fh.write(f'<tr bgcolor="{bgcolor}"><td>{escape(fname)}</td></tr>\n')
-                        tmp_fh.write('</table></body></html>\n')
+                        tmp_fh.write("</table></body></html>\n")
                     return self._yield_user_file_content(trans, data, tmp_file_name, headers), headers
                 mime = mimetypes.guess_type(file_path)[0]
                 if not mime:
@@ -449,34 +471,39 @@ class Data(metaclass=DataMeta):
             text,
         )
 
-        if to_ext or isinstance(
-            data.datatype, binary.Binary
-        ):  # Saving the file, or binary file
+        if to_ext or isinstance(data.datatype, binary.Binary):  # Saving the file, or binary file
             if data.extension in composite_extensions:
-                return self._archive_composite_dataset(trans, data, headers, do_action=kwd.get('do_action', 'zip'))
+                return self._archive_composite_dataset(trans, data, headers, do_action=kwd.get("do_action", "zip"))
             else:
-                headers['Content-Length'] = str(os.stat(data.file_name).st_size)
-                filename = self._download_filename(data, to_ext, hdca=kwd.get("hdca"), element_identifier=kwd.get("element_identifier"), filename_pattern=kwd.get("filename_pattern"))
-                headers['content-type'] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+                headers["Content-Length"] = str(os.stat(data.file_name).st_size)
+                filename = self._download_filename(
+                    data,
+                    to_ext,
+                    hdca=kwd.get("hdca"),
+                    element_identifier=kwd.get("element_identifier"),
+                    filename_pattern=kwd.get("filename_pattern"),
+                )
+                headers[
+                    "content-type"
+                ] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
                 headers["Content-Disposition"] = f'attachment; filename="{filename}"'
-                return open(data.file_name, 'rb'), headers
+                return open(data.file_name, "rb"), headers
         if not os.path.exists(data.file_name):
             raise ObjectNotFound(f"File Not Found ({data.file_name}).")
         max_peek_size = DEFAULT_MAX_PEEK_SIZE  # 1 MB
         if isinstance(data.datatype, text.Html):
             max_peek_size = 10000000  # 10 MB for html
         preview = util.string_as_bool(preview)
-        if (
-            not preview
-            or isinstance(data.datatype, images.Image)
-            or os.stat(data.file_name).st_size < max_peek_size
-        ):
+        if not preview or isinstance(data.datatype, images.Image) or os.stat(data.file_name).st_size < max_peek_size:
             return self._yield_user_file_content(trans, data, data.file_name, headers), headers
         else:
             headers["content-type"] = "text/html"
-            return trans.fill_template_mako("/dataset/large_file.mako",
-                                            truncated_data=open(data.file_name, 'rb').read(max_peek_size),
-                                            data=data), headers
+            return (
+                trans.fill_template_mako(
+                    "/dataset/large_file.mako", truncated_data=open(data.file_name, "rb").read(max_peek_size), data=data
+                ),
+                headers,
+            )
 
     def display_as_markdown(self, dataset_instance, markdown_format_helpers):
         """Prepare for embedding dataset into a basic Markdown document.
@@ -494,7 +521,7 @@ class Data(metaclass=DataMeta):
         If the data cannot reasonably be displayed, just indicate this and do
         not throw an exception.
         """
-        if self.file_ext in {'png', 'jpg'}:
+        if self.file_ext in {"png", "jpg"}:
             return self.handle_dataset_as_image(dataset_instance)
         if self.is_binary:
             result = "*cannot display binary content*\n"
@@ -512,20 +539,22 @@ class Data(metaclass=DataMeta):
             # Sanitize anytime we respond with plain text/html content.
             # Check to see if this dataset's parent job is allowlisted
             # We cannot currently trust imported datasets for rendering.
-            if not from_dataset.creating_job.imported and from_dataset.creating_job.tool_id.startswith(tuple(trans.app.config.sanitize_allowlist)):
-                return open(filename, mode='rb')
+            if not from_dataset.creating_job.imported and from_dataset.creating_job.tool_id.startswith(
+                tuple(trans.app.config.sanitize_allowlist)
+            ):
+                return open(filename, mode="rb")
 
             # This is returning to the browser, it needs to be encoded.
             # TODO Ideally this happens a layer higher, but this is a bad
             # issue affecting many tools
             with open(filename) as f:
-                return sanitize_html(f.read()).encode('utf-8')
+                return sanitize_html(f.read()).encode("utf-8")
 
-        return open(filename, mode='rb')
+        return open(filename, mode="rb")
 
     def _download_filename(self, dataset, to_ext, hdca=None, element_identifier=None, filename_pattern=None):
         def escape(raw_identifier):
-            return ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in raw_identifier)[0:150]
+            return "".join(c in FILENAME_VALID_CHARS and c or "_" for c in raw_identifier)[0:150]
 
         if not to_ext or to_ext == "data":
             # If a client requests to_ext with the extension 'data', they are
@@ -555,7 +584,7 @@ class Data(metaclass=DataMeta):
     def display_name(self, dataset):
         """Returns formatted html of dataset name"""
         try:
-            return escape(unicodify(dataset.name, 'utf-8'))
+            return escape(unicodify(dataset.name, "utf-8"))
         except Exception:
             return "name unavailable"
 
@@ -564,14 +593,14 @@ class Data(metaclass=DataMeta):
         try:
             # Change new line chars to html
             info: str = escape(dataset.info)
-            if info.find('\r\n') >= 0:
-                info = info.replace('\r\n', '<br/>')
-            if info.find('\r') >= 0:
-                info = info.replace('\r', '<br/>')
-            if info.find('\n') >= 0:
-                info = info.replace('\n', '<br/>')
+            if info.find("\r\n") >= 0:
+                info = info.replace("\r\n", "<br/>")
+            if info.find("\r") >= 0:
+                info = info.replace("\r", "<br/>")
+            if info.find("\n") >= 0:
+                info = info.replace("\n", "<br/>")
 
-            info = unicodify(info, 'utf-8')
+            info = unicodify(info, "utf-8")
 
             return info
         except Exception:
@@ -583,7 +612,7 @@ class Data(metaclass=DataMeta):
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/octet-stream'
+        return "application/octet-stream"
 
     def add_display_app(self, app_id, label, file_function, links_function):
         """
@@ -594,7 +623,11 @@ class Data(metaclass=DataMeta):
         links_function is a string containing the name of the function that returns a list of (link_name,link)
         """
         self.supported_display_apps = self.supported_display_apps.copy()
-        self.supported_display_apps[app_id] = {'label': label, 'file_function': file_function, 'links_function': links_function}
+        self.supported_display_apps[app_id] = {
+            "label": label,
+            "file_function": file_function,
+            "links_function": links_function,
+        }
 
     def remove_display_app(self, app_id):
         """Removes a display app from the datatype"""
@@ -602,14 +635,18 @@ class Data(metaclass=DataMeta):
         try:
             del self.supported_display_apps[app_id]
         except Exception:
-            log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.', type, self.__class__.__name__)
+            log.exception(
+                "Tried to remove display app %s from datatype %s, but this display app is not declared.",
+                type,
+                self.__class__.__name__,
+            )
 
     def clear_display_apps(self):
         self.supported_display_apps = {}
 
     def add_display_application(self, display_application):
         """New style display applications"""
-        assert display_application.id not in self.display_applications, 'Attempted to add a display application twice'
+        assert display_application.id not in self.display_applications, "Attempted to add a display application twice"
         self.display_applications[display_application.id] = display_application
 
     def get_display_application(self, key, default=None):
@@ -630,20 +667,25 @@ class Data(metaclass=DataMeta):
     def get_display_label(self, type):
         """Returns primary label for display app"""
         try:
-            return self.supported_display_apps[type]['label']
+            return self.supported_display_apps[type]["label"]
         except Exception:
-            return 'unknown'
+            return "unknown"
 
     def as_display_type(self, dataset, type, **kwd):
-        """Returns modified file contents for a particular display type """
+        """Returns modified file contents for a particular display type"""
         try:
             if type in self.get_display_types():
-                return getattr(self, self.supported_display_apps[type]['file_function'])(dataset, **kwd)
+                return getattr(self, self.supported_display_apps[type]["file_function"])(dataset, **kwd)
         except Exception:
-            log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible', self.supported_display_apps[type]['file_function'], self.__class__.__name__, type)
+            log.exception(
+                "Function %s is referred to in datatype %s for displaying as type %s, but is not accessible",
+                self.supported_display_apps[type]["file_function"],
+                self.__class__.__name__,
+                type,
+            )
         return f"This display type ({type}) is not implemented for this datatype ({dataset.ext})."
 
-    def get_display_links(self, dataset, type, app, base_url, target_frame='_blank', **kwd):
+    def get_display_links(self, dataset, type, app, base_url, target_frame="_blank", **kwd):
         """
         Returns a list of tuples of (name, link) for a particular display type.  No check on
         'access' permissions is done here - if you can view the dataset, you can also save it
@@ -652,10 +694,16 @@ class Data(metaclass=DataMeta):
         """
         try:
             if app.config.enable_old_display_applications and type in self.get_display_types():
-                return target_frame, getattr(self, self.supported_display_apps[type]['links_function'])(dataset, type, app, base_url, **kwd)
+                return target_frame, getattr(self, self.supported_display_apps[type]["links_function"])(
+                    dataset, type, app, base_url, **kwd
+                )
         except Exception:
-            log.exception('Function %s is referred to in datatype %s for generating links for type %s, but is not accessible',
-                          self.supported_display_apps[type]['links_function'], self.__class__.__name__, type)
+            log.exception(
+                "Function %s is referred to in datatype %s for generating links for type %s, but is not accessible",
+                self.supported_display_apps[type]["links_function"],
+                self.__class__.__name__,
+                type,
+            )
         return target_frame, []
 
     def get_converter_types(self, original_dataset, datatypes_registry):
@@ -666,20 +714,34 @@ class Data(metaclass=DataMeta):
         self, dataset, accepted_formats: List[str], datatypes_registry, **kwd
     ) -> Tuple[bool, Optional[str], Optional["DatasetInstance"]]:
         """Returns ( direct_match, converted_ext, existing converted dataset )"""
-        return datatypes_registry.find_conversion_destination_for_dataset_by_extensions(dataset, accepted_formats, **kwd)
+        return datatypes_registry.find_conversion_destination_for_dataset_by_extensions(
+            dataset, accepted_formats, **kwd
+        )
 
-    def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None, history=None):
+    def convert_dataset(
+        self,
+        trans,
+        original_dataset,
+        target_type,
+        return_output=False,
+        visible=True,
+        deps=None,
+        target_context=None,
+        history=None,
+    ):
         """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure."""
         converter = trans.app.datatypes_registry.get_converter_by_target_type(original_dataset.ext, target_type)
 
         if converter is None:
-            raise DatatypeConverterNotFoundException(f"A converter does not exist for {original_dataset.ext} to {target_type}.")
+            raise DatatypeConverterNotFoundException(
+                f"A converter does not exist for {original_dataset.ext} to {target_type}."
+            )
 
         params, input_name = get_params_and_input_name(converter, deps, target_context)
 
         params[input_name] = original_dataset
         # Make the target datatype available to the converter
-        params['__target_datatype__'] = target_type
+        params["__target_datatype__"] = target_type
         # Run converter, job is dispatched through Queue
         job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
         trans.app.job_manager.enqueue(job, tool=converter)
@@ -703,15 +765,26 @@ class Data(metaclass=DataMeta):
         """This function is called on the dataset before metadata is set."""
         dataset.clear_associated_files(metadata_safe=True)
 
-    def __new_composite_file(self, name, optional=False, mimetype=None, description=None, substitute_name_with_metadata=None, is_binary=False, to_posix_lines=True, space_to_tab=False, **kwds):
-        kwds['name'] = name
-        kwds['optional'] = optional
-        kwds['mimetype'] = mimetype
-        kwds['description'] = description
-        kwds['substitute_name_with_metadata'] = substitute_name_with_metadata
-        kwds['is_binary'] = is_binary
-        kwds['to_posix_lines'] = to_posix_lines
-        kwds['space_to_tab'] = space_to_tab
+    def __new_composite_file(
+        self,
+        name,
+        optional=False,
+        mimetype=None,
+        description=None,
+        substitute_name_with_metadata=None,
+        is_binary=False,
+        to_posix_lines=True,
+        space_to_tab=False,
+        **kwds,
+    ):
+        kwds["name"] = name
+        kwds["optional"] = optional
+        kwds["mimetype"] = mimetype
+        kwds["description"] = description
+        kwds["substitute_name_with_metadata"] = substitute_name_with_metadata
+        kwds["is_binary"] = is_binary
+        kwds["to_posix_lines"] = to_posix_lines
+        kwds["space_to_tab"] = space_to_tab
         return Bunch(**kwds)
 
     def add_composite_file(self, name, **kwds):
@@ -730,7 +803,7 @@ class Data(metaclass=DataMeta):
     @property
     def writable_files(self):
         files = {}
-        if self.composite_type != 'auto_primary_file':
+        if self.composite_type != "auto_primary_file":
             files[self.primary_file_name] = self.__new_composite_file(self.primary_file_name)
         for key, value in self.get_composite_files().items():
             files[key] = value
@@ -745,6 +818,7 @@ class Data(metaclass=DataMeta):
                     meta_value = self.metadata_spec[composite_file.substitute_name_with_metadata].default
                 return key % meta_value
             return key
+
         files = {}
         for key, value in self.composite_files.items():
             files[substitute_composite_key(key, value)] = value
@@ -768,17 +842,17 @@ class Data(metaclass=DataMeta):
     @staticmethod
     def merge(split_files, output_file):
         """
-            Merge files with copy.copyfileobj() will not hit the
-            max argument limitation of cat. gz and bz2 files are also working.
+        Merge files with copy.copyfileobj() will not hit the
+        max argument limitation of cat. gz and bz2 files are also working.
         """
         if not split_files:
-            raise ValueError(f'Asked to merge zero files as {output_file}')
+            raise ValueError(f"Asked to merge zero files as {output_file}")
         elif len(split_files) == 1:
-            shutil.copyfileobj(open(split_files[0], 'rb'), open(output_file, 'wb'))
+            shutil.copyfileobj(open(split_files[0], "rb"), open(output_file, "wb"))
         else:
-            with open(output_file, 'wb') as fdst:
+            with open(output_file, "wb") as fdst:
                 for fsrc in split_files:
-                    shutil.copyfileobj(open(fsrc, 'rb'), fdst)
+                    shutil.copyfileobj(open(fsrc, "rb"), fdst)
 
     def get_visualizations(self, dataset):
         """
@@ -786,7 +860,7 @@ class Data(metaclass=DataMeta):
         """
 
         if self.track_type:
-            return ['trackster', 'circster']
+            return ["trackster", "circster"]
         return []
 
     # ------------- Dataproviders
@@ -813,16 +887,12 @@ class Data(metaclass=DataMeta):
         dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
         return p_dataproviders.base.DataProvider(dataset_source, **settings)
 
-    @p_dataproviders.decorators.dataprovider_factory(
-        "chunk", p_dataproviders.chunk.ChunkDataProvider.settings
-    )
+    @p_dataproviders.decorators.dataprovider_factory("chunk", p_dataproviders.chunk.ChunkDataProvider.settings)
     def chunk_dataprovider(self, dataset, **settings):
         dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
         return p_dataproviders.chunk.ChunkDataProvider(dataset_source, **settings)
 
-    @p_dataproviders.decorators.dataprovider_factory(
-        "chunk64", p_dataproviders.chunk.Base64ChunkDataProvider.settings
-    )
+    @p_dataproviders.decorators.dataprovider_factory("chunk64", p_dataproviders.chunk.Base64ChunkDataProvider.settings)
     def chunk64_dataprovider(self, dataset, **settings):
         dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
         return p_dataproviders.chunk.Base64ChunkDataProvider(dataset_source, **settings)
@@ -840,17 +910,25 @@ class Data(metaclass=DataMeta):
 @p_dataproviders.decorators.has_dataproviders
 class Text(Data):
     edam_format = "format_2330"
-    file_ext = 'txt'
-    line_class = 'line'
+    file_ext = "txt"
+    line_class = "line"
 
     is_binary = False
 
     # Add metadata elements
-    MetadataElement(name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0)
+    MetadataElement(
+        name="data_lines",
+        default=0,
+        desc="Number of data lines",
+        readonly=True,
+        optional=True,
+        visible=False,
+        no_value=0,
+    )
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/plain'
+        return "text/plain"
 
     def set_meta(self, dataset, **kwd):
         """
@@ -866,10 +944,10 @@ class Text(Data):
         try:
             with compression_utils.get_fileobj(dataset.file_name) as dataset_fh:
                 dataset_read = dataset_fh.read(sample_size)
-            sample_lines = dataset_read.count('\n')
+            sample_lines = dataset_read.count("\n")
             return int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
         except UnicodeDecodeError:
-            log.error(f'Unable to estimate lines in file {dataset.file_name}')
+            log.error(f"Unable to estimate lines in file {dataset.file_name}")
             return None
 
     def count_data_lines(self, dataset):
@@ -877,7 +955,7 @@ class Text(Data):
         Count the number of lines of data in dataset,
         skipping all blank lines and comments.
         """
-        CHUNK_SIZE = 2 ** 15  # 32Kb
+        CHUNK_SIZE = 2**15  # 32Kb
         data_lines = 0
         with compression_utils.get_fileobj(dataset.file_name) as in_file:
             # FIXME: Potential encoding issue can prevent the ability to iterate over lines
@@ -886,10 +964,10 @@ class Text(Data):
             try:
                 for line in iter_start_of_line(in_file, CHUNK_SIZE):
                     line = line.strip()
-                    if line and not line.startswith('#'):
+                    if line and not line.startswith("#"):
                         data_lines += 1
             except UnicodeDecodeError:
-                log.error(f'Unable to count lines in file {dataset.file_name}')
+                log.error(f"Unable to count lines in file {dataset.file_name}")
                 return None
         return data_lines
 
@@ -925,8 +1003,8 @@ class Text(Data):
             else:
                 dataset.blurb = f"{util.commaify(str(line_count))} {inflector.cond_plural(line_count, self.line_class)}"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     @classmethod
     def split(cls, input_datasets, subdir_generator_function, split_params):
@@ -942,15 +1020,16 @@ class Text(Data):
 
         lines_per_file = None
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
+        if split_params["split_mode"] == "number_of_parts":
             lines_per_file = []
 
             # Computing the length is expensive!
             def _file_len(fname):
                 with open(fname) as f:
                     return sum(1 for _ in f)
+
             length = _file_len(input_files[0])
-            parts = int(split_params['split_size'])
+            parts = int(split_params["split_size"])
             if length < parts:
                 parts = length
             len_each, remainder = divmod(length, parts)
@@ -961,8 +1040,8 @@ class Text(Data):
                 lines_per_file.append(chunk)
                 remainder -= 1
                 length -= chunk
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
             raise Exception(f"Unsupported split mode {split_params['split_mode']}")
 
@@ -981,17 +1060,17 @@ class Text(Data):
                 part_file = None
                 while lines_remaining > 0:
                     a_line = f.readline()
-                    if a_line == '':
+                    if a_line == "":
                         file_done = True
                         break
                     if part_file is None:
                         part_dir = subdir_generator_function()
                         part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
-                        part_file = open(part_path, 'w')
+                        part_file = open(part_path, "w")
                     part_file.write(a_line)
                     lines_remaining -= 1
         except Exception as e:
-            log.error('Unable to split files: %s', unicodify(e))
+            log.error("Unable to split files: %s", unicodify(e))
             raise
         finally:
             f.close()
@@ -999,9 +1078,7 @@ class Text(Data):
                 part_file.close()
 
     # ------------- Dataproviders
-    @p_dataproviders.decorators.dataprovider_factory(
-        "line", p_dataproviders.line.FilteredLineDataProvider.settings
-    )
+    @p_dataproviders.decorators.dataprovider_factory("line", p_dataproviders.line.FilteredLineDataProvider.settings)
     def line_dataprovider(self, dataset, **settings):
         """
         Returns an iterator over the dataset's lines (that have been stripped)
@@ -1010,9 +1087,7 @@ class Text(Data):
         dataset_source = p_dataproviders.dataset.DatasetDataProvider(dataset)
         return p_dataproviders.line.FilteredLineDataProvider(dataset_source, **settings)
 
-    @p_dataproviders.decorators.dataprovider_factory(
-        "regex-line", p_dataproviders.line.RegexLineDataProvider.settings
-    )
+    @p_dataproviders.decorators.dataprovider_factory("regex-line", p_dataproviders.line.RegexLineDataProvider.settings)
     def regex_line_dataprovider(self, dataset, **settings):
         """
         Returns an iterator over the dataset's lines
@@ -1028,9 +1103,10 @@ class Directory(Data):
 
 class GenericAsn1(Text):
     """Class for generic ASN.1 text format"""
+
     edam_data = "data_0849"
     edam_format = "format_1966"
-    file_ext = 'asn1'
+    file_ext = "asn1"
 
 
 class LineCount(Text):
@@ -1042,24 +1118,26 @@ class LineCount(Text):
 
 class Newick(Text):
     """New Hampshire/Newick Format"""
+
     edam_data = "data_0872"
     edam_format = "format_1910"
     file_ext = "newick"
 
     def sniff(self, filename):
-        """ Returning false as the newick format is too general and cannot be sniffed."""
+        """Returning false as the newick format is too general and cannot be sniffed."""
         return False
 
     def get_visualizations(self, dataset):
         """
         Returns a list of visualizations for datatype.
         """
-        return ['phyloviz']
+        return ["phyloviz"]
 
 
 @build_sniff_from_prefix
 class Nexus(Text):
     """Nexus format as used By Paup, Mr Bayes, etc"""
+
     edam_data = "data_0872"
     edam_format = "format_1912"
     file_ext = "nex"
@@ -1072,7 +1150,7 @@ class Nexus(Text):
         """
         Returns a list of visualizations for datatype.
         """
-        return ['phyloviz']
+        return ["phyloviz"]
 
 
 # ------------- Utility methods --------------
@@ -1086,7 +1164,7 @@ nice_size = util.nice_size
 def get_test_fname(fname):
     """Returns test data filename"""
     path = os.path.dirname(__file__)
-    full_path = os.path.join(path, 'test', fname)
+    full_path = os.path.join(path, "test", fname)
     return full_path
 
 
@@ -1106,7 +1184,7 @@ def get_file_peek(file_name, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=
     # Set size for file.readline() to a negative number to force it to
     # read until either a newline or EOF.  Needed for datasets with very
     # long lines.
-    if WIDTH == 'unlimited':
+    if WIDTH == "unlimited":
         WIDTH = -1
     if skipchars is None:
         skipchars = []
@@ -1123,14 +1201,14 @@ def get_file_peek(file_name, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=
             if line == "":
                 break
             last_line_break = False
-            if line.endswith('\n'):
+            if line.endswith("\n"):
                 line = line[:-1]
                 last_line_break = True
             elif not line_wrap:
                 for i in file_reader(temp, 1):
-                    if i == '\n':
+                    if i == "\n":
                         last_line_break = True
-                    if not i or i == '\n':
+                    if not i or i == "\n":
                         break
             skip_line = False
             for skipchar in skipchars:
@@ -1140,4 +1218,4 @@ def get_file_peek(file_name, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=
             if not skip_line:
                 lines.append(line)
                 count += 1
-    return '\n'.join(lines) + ('\n' if last_line_break else '')
+    return "\n".join(lines) + ("\n" if last_line_break else "")
diff --git a/lib/galaxy/datatypes/dataproviders/__init__.py b/lib/galaxy/datatypes/dataproviders/__init__.py
index ee258fd5713..b18734eda2c 100644
--- a/lib/galaxy/datatypes/dataproviders/__init__.py
+++ b/lib/galaxy/datatypes/dataproviders/__init__.py
@@ -24,7 +24,7 @@ from . import (
     exceptions,
     external,
     hierarchy,
-    line
+    line,
 )
 
-__all__ = ('decorators', 'exceptions', 'base', 'chunk', 'line', 'hierarchy', 'column', 'external', 'dataset')
+__all__ = ("decorators", "exceptions", "base", "chunk", "line", "hierarchy", "column", "external", "dataset")
diff --git a/lib/galaxy/datatypes/dataproviders/base.py b/lib/galaxy/datatypes/dataproviders/base.py
index 3d0a536b8e0..22dbb6abcb1 100644
--- a/lib/galaxy/datatypes/dataproviders/base.py
+++ b/lib/galaxy/datatypes/dataproviders/base.py
@@ -46,19 +46,20 @@ class HasSettings(type):
     Useful for allowing class level access to expected variable types
     passed to class `__init__` functions so they can be parsed from a query string.
     """
+
     # yeah - this is all too acrobatic
     def __new__(cls, name, base_classes, attributes):
         settings = {}
         # get settings defined in base classes
         for base_class in base_classes:
-            base_settings = getattr(base_class, 'settings', None)
+            base_settings = getattr(base_class, "settings", None)
             if base_settings:
                 settings.update(base_settings)
         # get settings defined in this class
-        new_settings = attributes.pop('settings', None)
+        new_settings = attributes.pop("settings", None)
         if new_settings:
             settings.update(new_settings)
-        attributes['settings'] = settings
+        attributes["settings"] = settings
         return type.__new__(cls, name, base_classes, attributes)
 
 
@@ -72,6 +73,7 @@ class DataProvider(metaclass=HasSettings):
     - do not allow write methods (but otherwise implement the other file object interface methods)
 
     """
+
     # a definition of expected types for keyword arguments sent to __init__
     #   useful for controlling how query string dictionaries can be parsed into correct types for __init__
     #   empty in this base class
@@ -95,7 +97,7 @@ class DataProvider(metaclass=HasSettings):
 
         Meant to be overridden in subclasses.
         """
-        if not source or not hasattr(source, '__iter__'):
+        if not source or not hasattr(source, "__iter__"):
             # that's by no means a thorough check
             raise exceptions.InvalidDataProviderSource(source)
         return source
@@ -103,7 +105,7 @@ class DataProvider(metaclass=HasSettings):
     # TODO: (this might cause problems later...)
     # TODO: some providers (such as chunk's seek and read) rely on this... remove
     def __getattr__(self, name):
-        if name == 'source':
+        if name == "source":
             # if we're inside this fn, source hasn't been set - provide some safety just for this attr
             return None
         # otherwise, try to get the attr from the source - allows us to get things like provider.encoding, etc.
@@ -114,13 +116,13 @@ class DataProvider(metaclass=HasSettings):
 
     # write methods should not be allowed
     def truncate(self, size):
-        raise NotImplementedError('Write methods are purposely disabled')
+        raise NotImplementedError("Write methods are purposely disabled")
 
     def write(self, string):
-        raise NotImplementedError('Write methods are purposely disabled')
+        raise NotImplementedError("Write methods are purposely disabled")
 
     def writelines(self, sequence):
-        raise NotImplementedError('Write methods are purposely disabled')
+        raise NotImplementedError("Write methods are purposely disabled")
 
     # TODO: route read methods through next?
     # def readline( self ):
@@ -140,16 +142,16 @@ class DataProvider(metaclass=HasSettings):
     # context manager interface
     def __enter__(self):
         # make the source's context manager interface optional
-        if hasattr(self.source, '__enter__'):
+        if hasattr(self.source, "__enter__"):
             self.source.__enter__()
         return self
 
     def __exit__(self, *args):
         # make the source's context manager interface optional, call on source if there
-        if hasattr(self.source, '__exit__'):
+        if hasattr(self.source, "__exit__"):
             self.source.__exit__(*args)
         # alternately, call close()
-        elif hasattr(self.source, 'close'):
+        elif hasattr(self.source, "close"):
             self.source.close()
 
     def __str__(self):
@@ -159,8 +161,8 @@ class DataProvider(metaclass=HasSettings):
         Will call `__str__` on its source so this will display piped dataproviders.
         """
         # we need to protect against recursion (in __getattr__) if self.source hasn't been set
-        source_str = str(self.source) if hasattr(self, 'source') else ''
-        return f'{self.__class__.__name__}({str(source_str)})'
+        source_str = str(self.source) if hasattr(self, "source") else ""
+        return f"{self.__class__.__name__}({str(source_str)})"
 
 
 class FilteredDataProvider(DataProvider):
@@ -173,6 +175,7 @@ class FilteredDataProvider(DataProvider):
         - `num_valid_data_read`: how many data have been returned from `filter`.
         - `num_data_returned`: how many data has this provider yielded.
     """
+
     # not useful here - we don't want functions over the query string
     # settings.update({ 'filter_fn': 'function' })
 
@@ -225,11 +228,9 @@ class LimitedOffsetDataProvider(FilteredDataProvider):
 
     Useful for grabbing sections from a source (e.g. pagination).
     """
+
     # define the expected types of these __init__ arguments so they can be parsed out from query strings
-    settings = {
-        'limit': 'int',
-        'offset': 'int'
-    }
+    settings = {"limit": "int", "offset": "int"}
 
     # TODO: may want to squash this into DataProvider
     def __init__(self, source, offset=0, limit=None, **kwargs):
diff --git a/lib/galaxy/datatypes/dataproviders/chunk.py b/lib/galaxy/datatypes/dataproviders/chunk.py
index 16aa2016182..66cd3540ac0 100644
--- a/lib/galaxy/datatypes/dataproviders/chunk.py
+++ b/lib/galaxy/datatypes/dataproviders/chunk.py
@@ -10,7 +10,7 @@ import os
 
 from . import (
     base,
-    exceptions
+    exceptions,
 )
 
 log = logging.getLogger(__name__)
@@ -22,12 +22,10 @@ class ChunkDataProvider(base.DataProvider):
 
     Note: this version does not account for lines and works with Binary datatypes.
     """
-    MAX_CHUNK_SIZE = 2 ** 16
+
+    MAX_CHUNK_SIZE = 2**16
     DEFAULT_CHUNK_SIZE = MAX_CHUNK_SIZE
-    settings = {
-        'chunk_index': 'int',
-        'chunk_size': 'int'
-    }
+    settings = {"chunk_index": "int", "chunk_size": "int"}
 
     # TODO: subclass from LimitedOffsetDataProvider?
     # see web/framework/base.iterate_file, util/__init__.file_reader, and datatypes.tabular
@@ -49,7 +47,7 @@ class ChunkDataProvider(base.DataProvider):
         :raises InvalidDataProviderSource: if not.
         """
         source = super().validate_source(source)
-        if((not hasattr(source, 'seek')) or (not hasattr(source, 'read'))):
+        if (not hasattr(source, "seek")) or (not hasattr(source, "read")):
             raise exceptions.InvalidDataProviderSource(source)
         return source
 
diff --git a/lib/galaxy/datatypes/dataproviders/column.py b/lib/galaxy/datatypes/dataproviders/column.py
index 6a94597bcf4..34cee4b8d76 100644
--- a/lib/galaxy/datatypes/dataproviders/column.py
+++ b/lib/galaxy/datatypes/dataproviders/column.py
@@ -31,18 +31,28 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
     the same number of columns as the number of indeces asked for (even if they
     are filled with None).
     """
+
     settings = {
-        'indeces': 'list:int',
-        'column_count': 'int',
-        'column_types': 'list:str',
-        'parse_columns': 'bool',
-        'deliminator': 'str',
-        'filters': 'list:str'
+        "indeces": "list:int",
+        "column_count": "int",
+        "column_types": "list:str",
+        "parse_columns": "bool",
+        "deliminator": "str",
+        "filters": "list:str",
     }
 
-    def __init__(self, source, indeces=None,
-                 column_count=None, column_types=None, parsers=None, parse_columns=True,
-                 deliminator='\t', filters=None, **kwargs):
+    def __init__(
+        self,
+        source,
+        indeces=None,
+        column_count=None,
+        column_types=None,
+        parsers=None,
+        parse_columns=True,
+        deliminator="\t",
+        filters=None,
+        **kwargs,
+    ):
         """
 
         :param indeces: a list of indeces of columns to gather from each row
@@ -114,7 +124,7 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
                 self.column_filters.append(parsed)
 
     def parse_filter(self, filter_param_str):
-        split = filter_param_str.split('-', 2)
+        split = filter_param_str.split("-", 2)
         if not len(split) >= 3:
             return None
         column, op, val = split
@@ -123,11 +133,11 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
         column = int(column)
         if column > len(self.column_types):
             return None
-        if self.column_types[column] in ('float', 'int'):
+        if self.column_types[column] in ("float", "int"):
             return self.create_numeric_filter(column, op, val)
-        if self.column_types[column] in ('str'):
+        if self.column_types[column] in ("str"):
             return self.create_string_filter(column, op, val)
-        if self.column_types[column] in ('list'):
+        if self.column_types[column] in ("list"):
             return self.create_list_filter(column, op, val)
         return None
 
@@ -153,17 +163,17 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
             val = float(val)
         except ValueError:
             return None
-        if 'lt' == op:
+        if "lt" == op:
             return lambda d: d[column] < val
-        elif 'le' == op:
+        elif "le" == op:
             return lambda d: d[column] <= val
-        elif 'eq' == op:
+        elif "eq" == op:
             return lambda d: d[column] == val
-        elif 'ne' == op:
+        elif "ne" == op:
             return lambda d: d[column] != val
-        elif 'ge' == op:
+        elif "ge" == op:
             return lambda d: d[column] >= val
-        elif 'gt' == op:
+        elif "gt" == op:
             return lambda d: d[column] > val
         return None
 
@@ -180,11 +190,11 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
         - has: the column contains the substring `val`
         - re: the column matches the regular expression in `val`
         """
-        if 'eq' == op:
+        if "eq" == op:
             return lambda d: d[column] == val
-        elif 'has' == op:
+        elif "has" == op:
             return lambda d: val in d[column]
-        elif 're' == op:
+        elif "re" == op:
             val = unquote_plus(val)
             val = re.compile(val)
             return lambda d: val.match(d[column]) is not None
@@ -202,10 +212,10 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
         - eq: the list `val` exactly matches the list in the column
         - has: the list in the column contains the sublist `val`
         """
-        if 'eq' == op:
-            val = self.parse_value(val, 'list')
+        if "eq" == op:
+            val = self.parse_value(val, "list")
             return lambda d: d[column] == val
-        elif 'has' == op:
+        elif "has" == op:
             return lambda d: val in d[column]
         return None
 
@@ -223,10 +233,9 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
         # TODO: move to module level (or datatypes, util)
         return {
             # str is default and not needed here
-            'int': int,
-            'float': float,
-            'bool': bool,
-
+            "int": int,
+            "float": float,
+            "bool": bool,
             # unfortunately, 'list' is used in dataset metadata both for
             #   query style maps (9th col gff) AND comma-sep strings.
             #   (disabled for now)
@@ -235,12 +244,9 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
             # i don't like how urlparses does sub-lists...
             # 'querystr' : lambda v: dict([ ( p.split( '=', 1 ) if '=' in p else ( p, True ) )
             #                              for p in v.split( ';', 1 ) ])
-
             # 'scifloat': #floating point which may be in scientific notation
-
             # always with the 1 base, biologists?
             # 'int1'  : ( lambda i: int( i ) - 1 ),
-
             # 'gffval': string or '.' for None
             # 'gffint': # int or '.' for None
             # 'gffphase': # 0, 1, 2, or '.' for None
@@ -290,7 +296,7 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
             or `value` if no `type` found in `parsers`
             or `None` if there was a parser error (ValueError)
         """
-        if type == 'str' or type is None:
+        if type == "str" or type is None:
             return val
         try:
             return self.parsers[type](val)
@@ -332,8 +338,9 @@ class DictDataProvider(ColumnarDataProvider):
     .. note:: The subclass constructors are passed kwargs - so their
         params (limit, offset, etc.) are also applicable here.
     """
+
     settings = {
-        'column_names': 'list:str',
+        "column_names": "list:str",
     }
 
     def __init__(self, source, column_names=None, **kwargs):
diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py
index 7d856ad847a..b7d68021696 100644
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -8,17 +8,15 @@ Dataproviders that use either:
 import logging
 import sys
 
-from bx import (
-    seq as bx_seq,
-    wiggle as bx_wig
-)
+from bx import seq as bx_seq
+from bx import wiggle as bx_wig
 
 from galaxy.util import sqlite
 from . import (
     base,
     column,
     external,
-    line
+    line,
 )
 
 _TODO = """
@@ -52,7 +50,7 @@ class DatasetDataProvider(base.DataProvider):
         self.dataset = dataset
         # this dataset file is obviously the source
         # TODO: this might be a good place to interface with the object_store...
-        mode = 'rb' if dataset.datatype.is_binary else 'r'
+        mode = "rb" if dataset.datatype.is_binary else "r"
         super().__init__(open(dataset.file_name, mode))
 
     # TODO: this is a bit of a mess
@@ -66,9 +64,9 @@ class DatasetDataProvider(base.DataProvider):
         """
         # re-map keys to fit ColumnarProvider.__init__ kwargs
         params = {}
-        params['column_count'] = dataset.metadata.columns
-        params['column_types'] = dataset.metadata.column_types
-        params['column_names'] = dataset.metadata.column_names or getattr(dataset.datatype, 'column_names', None)
+        params["column_count"] = dataset.metadata.columns
+        params["column_types"] = dataset.metadata.column_types
+        params["column_names"] = dataset.metadata.column_names or getattr(dataset.datatype, "column_names", None)
         return params
 
     def get_metadata_column_types(self, indeces=None):
@@ -79,8 +77,9 @@ class DatasetDataProvider(base.DataProvider):
             Optional: defaults to None (return all types)
         :type indeces: list of ints
         """
-        metadata_column_types = (self.dataset.metadata.column_types
-                                 or getattr(self.dataset.datatype, 'column_types', None) or None)
+        metadata_column_types = (
+            self.dataset.metadata.column_types or getattr(self.dataset.datatype, "column_types", None) or None
+        )
         if not metadata_column_types:
             return metadata_column_types
         if indeces:
@@ -99,8 +98,9 @@ class DatasetDataProvider(base.DataProvider):
             Optional: defaults to None (return all names)
         :type indeces: list of ints
         """
-        metadata_column_names = (self.dataset.metadata.column_names
-                                 or getattr(self.dataset.datatype, 'column_names', None) or None)
+        metadata_column_names = (
+            self.dataset.metadata.column_names or getattr(self.dataset.datatype, "column_names", None) or None
+        )
         if not metadata_column_names:
             return metadata_column_names
         if indeces:
@@ -122,11 +122,13 @@ class DatasetDataProvider(base.DataProvider):
         :raises KeyError: if column_names are not found
         :raises ValueError: if an entry in list_of_column_names is not in column_names
         """
-        metadata_column_names = (self.dataset.metadata.column_names
-                                 or getattr(self.dataset.datatype, 'column_names', None) or None)
+        metadata_column_names = (
+            self.dataset.metadata.column_names or getattr(self.dataset.datatype, "column_names", None) or None
+        )
         if not metadata_column_names:
-            raise KeyError('No column_names found for '
-                           + f'datatype: {str(self.dataset.datatype)}, dataset: {str(self.dataset)}')
+            raise KeyError(
+                "No column_names found for " + f"datatype: {str(self.dataset.datatype)}, dataset: {str(self.dataset)}"
+            )
         indeces = []  # if indeces and column_names:
         # pull using indeces and re-name with given names - no need to alter (does as super would)
         #    pass
@@ -152,7 +154,7 @@ class DatasetDataProvider(base.DataProvider):
         :raises ValueError: if check is `True` and one or more indeces were not found.
         :returns: list of column indeces for the named columns.
         """
-        region_column_names = ('chromCol', 'startCol', 'endCol')
+        region_column_names = ("chromCol", "startCol", "endCol")
         region_indices = [self.get_metadata_column_index_by_name(name) for name in region_column_names]
         if check and not all(_ is not None for _ in region_indices):
             raise ValueError(f"Could not determine proper column indices for chrom, start, end: {str(region_indices)}")
@@ -166,7 +168,7 @@ class ConvertedDatasetDataProvider(DatasetDataProvider):
     """
 
     def __init__(self, dataset, **kwargs):
-        raise NotImplementedError('Abstract class')
+        raise NotImplementedError("Abstract class")
         # self.original_dataset = dataset
         # self.converted_dataset = self.convert_dataset(dataset, **kwargs)
         # super(ConvertedDatasetDataProvider, self).__init__(self.converted_dataset, **kwargs)
@@ -198,9 +200,9 @@ class DatasetColumnarDataProvider(column.ColumnarDataProvider):
         any metadata available.
         """
         dataset_source = DatasetDataProvider(dataset)
-        if not kwargs.get('column_types', None):
-            indeces = kwargs.get('indeces', None)
-            kwargs['column_types'] = dataset_source.get_metadata_column_types(indeces=indeces)
+        if not kwargs.get("column_types", None):
+            indeces = kwargs.get("indeces", None)
+            kwargs["column_types"] = dataset_source.get_metadata_column_types(indeces=indeces)
         super().__init__(dataset_source, **kwargs)
 
 
@@ -234,24 +236,24 @@ class DatasetDictDataProvider(column.DictDataProvider):
 
         # TODO: getting too complicated - simplify at some lvl, somehow
         # if no column_types given, get column_types from indeces (or all if indeces == None)
-        indeces = kwargs.get('indeces', None)
-        column_names = kwargs.get('column_names', None)
+        indeces = kwargs.get("indeces", None)
+        column_names = kwargs.get("column_names", None)
 
         if not indeces and column_names:
             # pull columns by name
-            indeces = kwargs['indeces'] = dataset_source.get_indeces_by_column_names(column_names)
+            indeces = kwargs["indeces"] = dataset_source.get_indeces_by_column_names(column_names)
 
         elif indeces and not column_names:
             # pull using indeces, name with meta
-            column_names = kwargs['column_names'] = dataset_source.get_metadata_column_names(indeces=indeces)
+            column_names = kwargs["column_names"] = dataset_source.get_metadata_column_names(indeces=indeces)
 
         elif not indeces and not column_names:
             # pull all indeces and name using metadata
-            column_names = kwargs['column_names'] = dataset_source.get_metadata_column_names(indeces=indeces)
+            column_names = kwargs["column_names"] = dataset_source.get_metadata_column_names(indeces=indeces)
 
         # if no column_types given, use metadata column_types
-        if not kwargs.get('column_types', None):
-            kwargs['column_types'] = dataset_source.get_metadata_column_types(indeces=indeces)
+        if not kwargs.get("column_types", None):
+            kwargs["column_types"] = dataset_source.get_metadata_column_types(indeces=indeces)
 
         super().__init__(dataset_source, **kwargs)
 
@@ -267,13 +269,14 @@ class GenomicRegionDataProvider(column.ColumnarDataProvider):
     If `named_columns` is true, will return dictionaries with the keys
     'chrom', 'start', 'end'.
     """
+
     # dictionary keys when named_columns=True
-    COLUMN_NAMES = ['chrom', 'start', 'end']
+    COLUMN_NAMES = ["chrom", "start", "end"]
     settings = {
-        'chrom_column': 'int',
-        'start_column': 'int',
-        'end_column': 'int',
-        'named_columns': 'bool',
+        "chrom_column": "int",
+        "start_column": "int",
+        "end_column": "int",
+        "named_columns": "bool",
     }
 
     def __init__(self, dataset, chrom_column=None, start_column=None, end_column=None, named_columns=False, **kwargs):
@@ -297,19 +300,18 @@ class GenomicRegionDataProvider(column.ColumnarDataProvider):
         dataset_source = DatasetDataProvider(dataset)
 
         if chrom_column is None:
-            chrom_column = dataset_source.get_metadata_column_index_by_name('chromCol')
+            chrom_column = dataset_source.get_metadata_column_index_by_name("chromCol")
         if start_column is None:
-            start_column = dataset_source.get_metadata_column_index_by_name('startCol')
+            start_column = dataset_source.get_metadata_column_index_by_name("startCol")
         if end_column is None:
-            end_column = dataset_source.get_metadata_column_index_by_name('endCol')
+            end_column = dataset_source.get_metadata_column_index_by_name("endCol")
         indeces = [chrom_column, start_column, end_column]
         if not all(_ is not None for _ in indeces):
-            raise ValueError("Could not determine proper column indeces for"
-                             + f" chrom, start, end: {str(indeces)}")
-        kwargs.update({'indeces': indeces})
+            raise ValueError("Could not determine proper column indeces for" + f" chrom, start, end: {str(indeces)}")
+        kwargs.update({"indeces": indeces})
 
-        if not kwargs.get('column_types', None):
-            kwargs.update({'column_types': dataset_source.get_metadata_column_types(indeces=indeces)})
+        if not kwargs.get("column_types", None):
+            kwargs.update({"column_types": dataset_source.get_metadata_column_types(indeces=indeces)})
 
         self.named_columns = named_columns
         if self.named_columns:
@@ -336,18 +338,28 @@ class IntervalDataProvider(column.ColumnarDataProvider):
     If `named_columns` is true, will return dictionaries with the keys
     'chrom', 'start', 'end' (and 'strand' and 'name' if available).
     """
-    COLUMN_NAMES = ['chrom', 'start', 'end', 'strand', 'name']
+
+    COLUMN_NAMES = ["chrom", "start", "end", "strand", "name"]
     settings = {
-        'chrom_column': 'int',
-        'start_column': 'int',
-        'end_column': 'int',
-        'strand_column': 'int',
-        'name_column': 'int',
-        'named_columns': 'bool',
+        "chrom_column": "int",
+        "start_column": "int",
+        "end_column": "int",
+        "strand_column": "int",
+        "name_column": "int",
+        "named_columns": "bool",
     }
 
-    def __init__(self, dataset, chrom_column=None, start_column=None, end_column=None,
-                 strand_column=None, name_column=None, named_columns=False, **kwargs):
+    def __init__(
+        self,
+        dataset,
+        chrom_column=None,
+        start_column=None,
+        end_column=None,
+        strand_column=None,
+        name_column=None,
+        named_columns=False,
+        **kwargs,
+    ):
         """
         :param dataset: the Galaxy dataset whose file will be the source
         :type dataset: model.DatasetInstance
@@ -365,34 +377,34 @@ class IntervalDataProvider(column.ColumnarDataProvider):
         indeces = []
         # TODO: this is sort of involved and oogly
         if chrom_column is None:
-            chrom_column = dataset_source.get_metadata_column_index_by_name('chromCol')
+            chrom_column = dataset_source.get_metadata_column_index_by_name("chromCol")
             if chrom_column is not None:
-                self.column_names.append('chrom')
+                self.column_names.append("chrom")
                 indeces.append(chrom_column)
         if start_column is None:
-            start_column = dataset_source.get_metadata_column_index_by_name('startCol')
+            start_column = dataset_source.get_metadata_column_index_by_name("startCol")
             if start_column is not None:
-                self.column_names.append('start')
+                self.column_names.append("start")
                 indeces.append(start_column)
         if end_column is None:
-            end_column = dataset_source.get_metadata_column_index_by_name('endCol')
+            end_column = dataset_source.get_metadata_column_index_by_name("endCol")
             if end_column is not None:
-                self.column_names.append('end')
+                self.column_names.append("end")
                 indeces.append(end_column)
         if strand_column is None:
-            strand_column = dataset_source.get_metadata_column_index_by_name('strandCol')
+            strand_column = dataset_source.get_metadata_column_index_by_name("strandCol")
             if strand_column is not None:
-                self.column_names.append('strand')
+                self.column_names.append("strand")
                 indeces.append(strand_column)
         if name_column is None:
-            name_column = dataset_source.get_metadata_column_index_by_name('nameCol')
+            name_column = dataset_source.get_metadata_column_index_by_name("nameCol")
             if name_column is not None:
-                self.column_names.append('name')
+                self.column_names.append("name")
                 indeces.append(name_column)
 
-        kwargs.update({'indeces': indeces})
-        if not kwargs.get('column_types', None):
-            kwargs.update({'column_types': dataset_source.get_metadata_column_types(indeces=indeces)})
+        kwargs.update({"indeces": indeces})
+        if not kwargs.get("column_types", None):
+            kwargs.update({"column_types": dataset_source.get_metadata_column_types(indeces=indeces)})
 
         self.named_columns = named_columns
 
@@ -418,8 +430,9 @@ class FastaDataProvider(base.FilteredDataProvider):
             sequence: <joined lines of nucleotide/amino data>
         }
     """
+
     settings = {
-        'ids': 'list:str',
+        "ids": "list:str",
     }
 
     def __init__(self, source, ids=None, **kwargs):
@@ -437,10 +450,7 @@ class FastaDataProvider(base.FilteredDataProvider):
     def __iter__(self):
         parent_gen = super().__iter__()
         for fasta_record in parent_gen:
-            yield {
-                'id': fasta_record.name,
-                'seq': fasta_record.text
-            }
+            yield {"id": fasta_record.name, "seq": fasta_record.text}
 
 
 class TwoBitFastaDataProvider(DatasetDataProvider):
@@ -452,8 +462,9 @@ class TwoBitFastaDataProvider(DatasetDataProvider):
             sequence: <joined lines of nucleotide/amino data>
         }
     """
+
     settings = {
-        'ids': 'list:str',
+        "ids": "list:str",
     }
 
     def __init__(self, source, ids=None, **kwargs):
@@ -470,10 +481,7 @@ class TwoBitFastaDataProvider(DatasetDataProvider):
 
     def __iter__(self):
         for id_ in self.ids:
-            yield {
-                'id': id_,
-                'seq': self.source[id_]
-            }
+            yield {"id": id_, "seq": self.source[id_]}
 
 
 # TODO:
@@ -481,10 +489,11 @@ class WiggleDataProvider(base.LimitedOffsetDataProvider):
     """
     Class that returns chrom, pos, data from a wiggle source.
     """
-    COLUMN_NAMES = ['chrom', 'pos', 'value']
+
+    COLUMN_NAMES = ["chrom", "pos", "value"]
     settings = {
-        'named_columns': 'bool',
-        'column_names': 'list:str',
+        "named_columns": "bool",
+        "column_names": "list:str",
     }
 
     def __init__(self, source, named_columns=False, column_names=None, **kwargs):
@@ -523,10 +532,11 @@ class BigWigDataProvider(base.LimitedOffsetDataProvider):
     """
     Class that returns chrom, pos, data from a wiggle source.
     """
-    COLUMN_NAMES = ['chrom', 'pos', 'value']
+
+    COLUMN_NAMES = ["chrom", "pos", "value"]
     settings = {
-        'named_columns': 'bool',
-        'column_names': 'list:str',
+        "named_columns": "bool",
+        "column_names": "list:str",
     }
 
     def __init__(self, source, chrom, start, end, named_columns=False, column_names=None, **kwargs):
@@ -551,7 +561,7 @@ class BigWigDataProvider(base.LimitedOffsetDataProvider):
         :type column_names:
 
         """
-        raise NotImplementedError('Work in progress')
+        raise NotImplementedError("Work in progress")
         # TODO: validate is a wig
         # still good to maintain a ref to the raw source bc Reader won't
         # self.raw_source = source
@@ -579,6 +589,7 @@ class DatasetSubprocessDataProvider(external.SubprocessDataProvider):
     Uses a subprocess as its source and has a dataset (gen. as an input file
     for the process).
     """
+
     # TODO: below should be a subclass of this and not RegexSubprocess
 
     def __init__(self, dataset, *args, **kwargs):
@@ -586,7 +597,7 @@ class DatasetSubprocessDataProvider(external.SubprocessDataProvider):
         :param args: the list of strings used to build commands.
         :type args: variadic function args
         """
-        raise NotImplementedError('Abstract class')
+        raise NotImplementedError("Abstract class")
         # super(DatasetSubprocessDataProvider, self).__init__(*args, **kwargs)
         # self.dataset = dataset
 
@@ -599,11 +610,12 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
 
     .. note:: that only the samtools 'view' command is currently implemented.
     """
-    FLAGS_WO_ARGS = 'bhHSu1xXcB'
-    FLAGS_W_ARGS = 'fFqlrs'
+
+    FLAGS_WO_ARGS = "bhHSu1xXcB"
+    FLAGS_W_ARGS = "fFqlrs"
     VALID_FLAGS = FLAGS_WO_ARGS + FLAGS_W_ARGS
 
-    def __init__(self, dataset, options_string='', options_dict=None, regions=None, **kwargs):
+    def __init__(self, dataset, options_string="", options_dict=None, regions=None, **kwargs):
         """
         :param options_string: samtools options in string form (flags separated
             by spaces)
@@ -627,10 +639,10 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
 
         # TODO: view only for now
         # TODO: not properly using overriding super's validate_opts, command here
-        subcommand = 'view'
+        subcommand = "view"
         # TODO:?? do we need a path to samtools?
         subproc_args = self.build_command_list(subcommand, options_string, options_dict, regions)
-# TODO: the composition/inheritance here doesn't make a lot sense
+        # TODO: the composition/inheritance here doesn't make a lot sense
         subproc_provider = external.SubprocessDataProvider(*subproc_args)
         super().__init__(subproc_provider, **kwargs)
 
@@ -638,7 +650,7 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
         """
         Convert all init args to list form.
         """
-        command = ['samtools', subcommand]
+        command = ["samtools", subcommand]
         # add options and switches, input file, regions list (if any)
         command.extend(self.to_options_list(options_string, options_dict))
         command.append(self.dataset.file_name)
@@ -654,14 +666,13 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
 
         # strip out any user supplied bash switch formating -> string of option chars
         #   then compress to single option string of unique, VALID flags with prefixed bash switch char '-'
-        options_string = options_string.strip('- ')
+        options_string = options_string.strip("- ")
         validated_flag_list = {flag for flag in options_string if flag in self.FLAGS_WO_ARGS}
 
         # if sam add -S
         # TODO: not the best test in the world...
-        if((self.dataset.ext == 'sam')
-                and ('S' not in validated_flag_list)):
-            validated_flag_list.append('S')
+        if (self.dataset.ext == "sam") and ("S" not in validated_flag_list):
+            validated_flag_list.append("S")
 
         if validated_flag_list:
             opt_list.append(f"-{''.join(validated_flag_list)}")
@@ -696,9 +707,8 @@ class SQliteDataProvider(base.DataProvider):
 
     Allows any query to be run and returns the resulting rows as sqlite3 row objects
     """
-    settings = {
-        'query': 'str'
-    }
+
+    settings = {"query": "str"}
 
     def __init__(self, source, query=None, **kwargs):
         self.query = query
@@ -717,11 +727,8 @@ class SQliteDataTableProvider(base.DataProvider):
     Data provider that uses a sqlite database file as its source.
     Allows any query to be run and returns the resulting rows as arrays of arrays
     """
-    settings = {
-        'query': 'str',
-        'headers': 'bool',
-        'limit': 'int'
-    }
+
+    settings = {"query": "str", "headers": "bool", "limit": "int"}
 
     def __init__(self, source, query=None, headers=False, limit=sys.maxsize, **kwargs):
         self.query = query
@@ -749,9 +756,8 @@ class SQliteDataDictProvider(base.DataProvider):
     Data provider that uses a sqlite database file as its source.
     Allows any query to be run and returns the resulting rows as arrays of dicts
     """
-    settings = {
-        'query': 'str'
-    }
+
+    settings = {"query": "str"}
 
     def __init__(self, source, query=None, **kwargs):
         self.query = query
diff --git a/lib/galaxy/datatypes/dataproviders/decorators.py b/lib/galaxy/datatypes/dataproviders/decorators.py
index 6a2579260b3..a20c2bb5146 100644
--- a/lib/galaxy/datatypes/dataproviders/decorators.py
+++ b/lib/galaxy/datatypes/dataproviders/decorators.py
@@ -21,8 +21,8 @@ from urllib.parse import unquote
 
 log = logging.getLogger(__name__)
 
-_DATAPROVIDER_CLASS_MAP_KEY = 'dataproviders'
-_DATAPROVIDER_METHOD_NAME_KEY = '_dataprovider_name'
+_DATAPROVIDER_CLASS_MAP_KEY = "dataproviders"
+_DATAPROVIDER_METHOD_NAME_KEY = "_dataprovider_name"
 
 
 def has_dataproviders(cls):
@@ -67,9 +67,11 @@ def has_dataproviders(cls):
     #       where it's possible to override a super's provider with a sub's
     for attr_key, attr_value in cls.__dict__.items():
         # can't use isinstance( attr_value, MethodType ) bc of wrapping
-        if((callable(attr_value))
-                and (not attr_key.startswith("__"))
-                and (getattr(attr_value, _DATAPROVIDER_METHOD_NAME_KEY, None))):
+        if (
+            (callable(attr_value))
+            and (not attr_key.startswith("__"))
+            and (getattr(attr_value, _DATAPROVIDER_METHOD_NAME_KEY, None))
+        ):
             name = getattr(attr_value, _DATAPROVIDER_METHOD_NAME_KEY)
             dataproviders[name] = attr_value
     return cls
@@ -110,7 +112,9 @@ def dataprovider_factory(name, settings=None):
         @wraps(func)
         def wrapped_dataprovider_factory(self, *args, **kwargs):
             return func(self, *args, **kwargs)
+
         return wrapped_dataprovider_factory
+
     return named_dataprovider_factory
 
 
@@ -122,15 +126,15 @@ def _parse_query_string_settings(query_kwargs, settings=None):
     # TODO: this was a relatively late addition: review and re-think
     def list_from_query_string(s):
         # assume csv
-        return s.split(',')
+        return s.split(",")
 
     parsers = {
-        'int': int,
-        'float': float,
-        'bool': bool,
-        'list:str': lambda s: list_from_query_string(s),
-        'list:escaped': lambda s: [unquote(e) for e in list_from_query_string(s)],
-        'list:int': lambda s: [int(i) for i in list_from_query_string(s)],
+        "int": int,
+        "float": float,
+        "bool": bool,
+        "list:str": lambda s: list_from_query_string(s),
+        "list:escaped": lambda s: [unquote(e) for e in list_from_query_string(s)],
+        "list:int": lambda s: [int(i) for i in list_from_query_string(s)],
     }
     settings = settings or {}
     # yay! yet another set of query string parsers! <-- sarcasm
@@ -142,7 +146,7 @@ def _parse_query_string_settings(query_kwargs, settings=None):
             # TODO: this would be the place to sanitize any strings
             query_value = query_kwargs[key]
             needed_type = settings[key]
-            if needed_type != 'str':
+            if needed_type != "str":
                 try:
                     query_kwargs[key] = parsers[needed_type](query_value)
                 except (KeyError, ValueError):
diff --git a/lib/galaxy/datatypes/dataproviders/exceptions.py b/lib/galaxy/datatypes/dataproviders/exceptions.py
index a3d9fbd2dd4..b40e001ccd0 100644
--- a/lib/galaxy/datatypes/dataproviders/exceptions.py
+++ b/lib/galaxy/datatypes/dataproviders/exceptions.py
@@ -8,8 +8,8 @@ class InvalidDataProviderSource(TypeError):
     Raised when a unusable source is passed to a provider.
     """
 
-    def __init__(self, source=None, msg=''):
-        msg = msg or f'Invalid source for provider: {source}'
+    def __init__(self, source=None, msg=""):
+        msg = msg or f"Invalid source for provider: {source}"
         super().__init__(msg)
 
 
@@ -27,7 +27,7 @@ class NoProviderAvailable(TypeError):
     Meant to be used within a class that builds dataproviders (e.g. a Datatype)
     """
 
-    def __init__(self, factory_source, format_requested=None, msg=''):
+    def __init__(self, factory_source, format_requested=None, msg=""):
         self.factory_source = factory_source
         self.format_requested = format_requested
         msg = msg or f'No provider available in factory_source "{str(factory_source)}" for format requested'
diff --git a/lib/galaxy/datatypes/dataproviders/external.py b/lib/galaxy/datatypes/dataproviders/external.py
index a0e2c00b0a2..fea7a8b665d 100644
--- a/lib/galaxy/datatypes/dataproviders/external.py
+++ b/lib/galaxy/datatypes/dataproviders/external.py
@@ -15,7 +15,7 @@ from urllib.request import urlopen
 from galaxy.util import DEFAULT_SOCKET_TIMEOUT
 from . import (
     base,
-    line
+    line,
 )
 
 _TODO = """
@@ -33,6 +33,7 @@ class SubprocessDataProvider(base.DataProvider):
     Data provider that uses the output from an intermediate program and
     subprocess as its data source.
     """
+
     # TODO: need better ways of checking returncode, stderr for errors and raising
 
     def __init__(self, *args, **kwargs):
@@ -57,32 +58,33 @@ class SubprocessDataProvider(base.DataProvider):
         try:
             # how expensive is this?
             popen = subprocess.Popen(command_list, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
-            log.info(f'opened subrocess ({str(command_list)}), PID: {str(popen.pid)}')
+            log.info(f"opened subrocess ({str(command_list)}), PID: {str(popen.pid)}")
 
         except OSError as os_err:
-            command_str = ' '.join(self.command)
-            raise OSError(' '.join((str(os_err), ':', command_str)))
+            command_str = " ".join(self.command)
+            raise OSError(" ".join((str(os_err), ":", command_str)))
 
         return popen
 
     def __exit__(self, *args):
         # poll the subrocess for an exit code
         self.exit_code = self.popen.poll()
-        log.info(f'{str(self)}.__exit__, exit_code: {str(self.exit_code)}')
+        log.info(f"{str(self)}.__exit__, exit_code: {str(self.exit_code)}")
         return super().__exit__(*args)
 
     def __str__(self):
         # provide the pid and current return code
-        source_str = ''
-        if hasattr(self, 'popen'):
-            source_str = f'{str(self.popen.pid)}:{str(self.popen.poll())}'
-        return f'{self.__class__.__name__}({str(source_str)})'
+        source_str = ""
+        if hasattr(self, "popen"):
+            source_str = f"{str(self.popen.pid)}:{str(self.popen.poll())}"
+        return f"{self.__class__.__name__}({str(source_str)})"
 
 
 class RegexSubprocessDataProvider(line.RegexLineDataProvider):
     """
     RegexLineDataProvider that uses a SubprocessDataProvider as its data source.
     """
+
     # this is a conv. class and not really all that necc...
 
     def __init__(self, *args, **kwargs):
@@ -98,9 +100,10 @@ class URLDataProvider(base.DataProvider):
 
     This can be piped through other providers (column, map, genome region, etc.).
     """
-    VALID_METHODS = ('GET', 'POST')
 
-    def __init__(self, url, method='GET', data=None, **kwargs):
+    VALID_METHODS = ("GET", "POST")
+
+    def __init__(self, url, method="GET", data=None, **kwargs):
         """
         :param url: the base URL to open.
         :param method: the HTTP method to use.
@@ -116,15 +119,15 @@ class URLDataProvider(base.DataProvider):
         encoded_data = urlencode(self.data)
 
         scheme = urlparse(url).scheme
-        assert scheme in ('http', 'https', 'ftp'), f'Invalid URL scheme: {scheme}'
+        assert scheme in ("http", "https", "ftp"), f"Invalid URL scheme: {scheme}"
 
-        if method == 'GET':
-            self.url += f'?{encoded_data}'
+        if method == "GET":
+            self.url += f"?{encoded_data}"
             opened = urlopen(url, timeout=DEFAULT_SOCKET_TIMEOUT)
-        elif method == 'POST':
+        elif method == "POST":
             opened = urlopen(url, encoded_data, timeout=DEFAULT_SOCKET_TIMEOUT)
         else:
-            raise ValueError(f'Not a valid method: {method}')
+            raise ValueError(f"Not a valid method: {method}")
 
         super().__init__(opened, **kwargs)
         # NOTE: the request object is now accessible as self.source
@@ -145,7 +148,7 @@ class GzipDataProvider(base.DataProvider):
     """
 
     def __init__(self, source, **kwargs):
-        unzipped = gzip.GzipFile(source, 'rb')
+        unzipped = gzip.GzipFile(source, "rb")
         super().__init__(unzipped, **kwargs)
         # NOTE: the GzipFile is now accessible in self.source
 
@@ -171,6 +174,6 @@ class TempfileDataProvider(base.DataProvider):
 
     def write_to_file(self):
         parent_gen = super().__iter__()
-        with open(self.tmp_file, 'w') as open_file:
+        with open(self.tmp_file, "w") as open_file:
             for datum in parent_gen:
                 open_file.write(f"{datum}\n")
diff --git a/lib/galaxy/datatypes/dataproviders/hierarchy.py b/lib/galaxy/datatypes/dataproviders/hierarchy.py
index 7a52dd76b29..e0773975548 100644
--- a/lib/galaxy/datatypes/dataproviders/hierarchy.py
+++ b/lib/galaxy/datatypes/dataproviders/hierarchy.py
@@ -31,13 +31,14 @@ class XMLDataProvider(HierarchalDataProvider):
     """
     Data provider that converts selected XML elements to dictionaries.
     """
+
     # using lxml.etree's iterparse method to keep mem down
     # TODO:   this, however (AFAIK), prevents the use of xpath
     settings = {
-        'selector': 'str',  # urlencoded
-        'max_depth': 'int',
+        "selector": "str",  # urlencoded
+        "max_depth": "int",
     }
-    ITERPARSE_ALL_EVENTS = ('start', 'end', 'start-ns', 'end-ns')
+    ITERPARSE_ALL_EVENTS = ("start", "end", "start-ns", "end-ns")
     # TODO: move appropo into super
 
     def __init__(self, source, selector=None, max_depth=None, **kwargs):
@@ -64,9 +65,8 @@ class XMLDataProvider(HierarchalDataProvider):
         # TODO: add more flexibility here w/o re-implementing xpath
         # TODO: fails with '#' - browser thinks it's an anchor - use urlencode
         # TODO: need removal/replacement of etree namespacing here - then move to string match
-        Element = getattr(etree, '_Element', etree.Element)
-        return bool((selector is None)
-                    or (isinstance(element, Element) and selector in element.tag))
+        Element = getattr(etree, "_Element", etree.Element)
+        return bool((selector is None) or (isinstance(element, Element) and selector in element.tag))
 
     def element_as_dict(self, element):
         """
@@ -76,10 +76,10 @@ class XMLDataProvider(HierarchalDataProvider):
         """
         # TODO: Key collision is unlikely here, but still should be better handled
         return {
-            'tag': element.tag,
-            'text': element.text.strip() if element.text else None,
+            "tag": element.tag,
+            "text": element.text.strip() if element.text else None,
             # needs shallow copy to protect v. element.clear()
-            'attrib': dict(element.attrib)
+            "attrib": dict(element.attrib),
         }
 
     def get_children(self, element, max_depth=None):
@@ -96,7 +96,7 @@ class XMLDataProvider(HierarchalDataProvider):
                 next_depth = max_depth - 1 if isinstance(max_depth, int) else None
                 grand_children = list(self.get_children(child, next_depth))
                 if grand_children:
-                    child_data['children'] = grand_children
+                    child_data["children"] = grand_children
 
                 yield child_data
 
@@ -106,18 +106,17 @@ class XMLDataProvider(HierarchalDataProvider):
 
         selected_element = None
         for event, element in context:
-            if event == 'start-ns':
+            if event == "start-ns":
                 ns, uri = element
                 self.namespaces[ns] = uri
 
-            elif event == 'start':
-                if((selected_element is None)
-                        and (self.matches_selector(element, self.selector))):
+            elif event == "start":
+                if (selected_element is None) and (self.matches_selector(element, self.selector)):
                     # start tag of selected element - wait for 'end' to emit/yield
                     selected_element = element
 
-            elif event == 'end':
-                if((selected_element is not None) and (element == selected_element)):
+            elif event == "end":
+                if (selected_element is not None) and (element == selected_element):
                     self.num_valid_data_read += 1
 
                     # offset
@@ -126,7 +125,7 @@ class XMLDataProvider(HierarchalDataProvider):
                         selected_element_dict = self.element_as_dict(selected_element)
                         children = list(self.get_children(selected_element, self.max_depth))
                         if children:
-                            selected_element_dict['children'] = children
+                            selected_element_dict["children"] = children
                         yield selected_element_dict
 
                         # limit
diff --git a/lib/galaxy/datatypes/dataproviders/line.py b/lib/galaxy/datatypes/dataproviders/line.py
index 3a95521e992..dcbdfc44012 100644
--- a/lib/galaxy/datatypes/dataproviders/line.py
+++ b/lib/galaxy/datatypes/dataproviders/line.py
@@ -23,16 +23,24 @@ class FilteredLineDataProvider(base.LimitedOffsetDataProvider):
     optional control over which line to start on and how many lines
     to return.
     """
-    DEFAULT_COMMENT_CHAR = '#'
+
+    DEFAULT_COMMENT_CHAR = "#"
     settings = {
-        'strip_lines': 'bool',
-        'strip_newlines': 'bool',
-        'provide_blank': 'bool',
-        'comment_char': 'str',
+        "strip_lines": "bool",
+        "strip_newlines": "bool",
+        "provide_blank": "bool",
+        "comment_char": "str",
     }
 
-    def __init__(self, source, strip_lines=True, strip_newlines=False, provide_blank=False,
-                 comment_char=DEFAULT_COMMENT_CHAR, **kwargs):
+    def __init__(
+        self,
+        source,
+        strip_lines=True,
+        strip_newlines=False,
+        provide_blank=False,
+        comment_char=DEFAULT_COMMENT_CHAR,
+        **kwargs,
+    ):
         """
         :param strip_lines: remove whitespace from the beginning an ending
             of each line (or not).
@@ -72,8 +80,8 @@ class FilteredLineDataProvider(base.LimitedOffsetDataProvider):
             if self.strip_lines:
                 line = line.strip()
             elif self.strip_newlines:
-                line = line.strip('\n')
-            if not self.provide_blank and line == '':
+                line = line.strip("\n")
+            if not self.provide_blank and line == "":
                 return None
             elif self.comment_char and line.startswith(self.comment_char):
                 return None
@@ -90,9 +98,10 @@ class RegexLineDataProvider(FilteredLineDataProvider):
     .. note:: the regex matches are effectively OR'd (if **any** regex matches
         the line it is considered valid and will be provided).
     """
+
     settings = {
-        'regex_list': 'list:escaped',
-        'invert': 'bool',
+        "regex_list": "list:escaped",
+        "invert": "bool",
     }
 
     def __init__(self, source, regex_list=None, invert=False, **kwargs):
@@ -153,8 +162,7 @@ class BlockDataProvider(base.LimitedOffsetDataProvider):
         """
         # composition - not inheritance
         # TODO: not a fan of this:
-        (filter_fn, limit, offset) = (kwargs.pop('filter_fn', None),
-                                      kwargs.pop('limit', None), kwargs.pop('offset', 0))
+        (filter_fn, limit, offset) = (kwargs.pop("filter_fn", None), kwargs.pop("limit", None), kwargs.pop("offset", 0))
         line_provider = FilteredLineDataProvider(source, **kwargs)
         super().__init__(line_provider, filter_fn=filter_fn, limit=limit, offset=offset)
 
diff --git a/lib/galaxy/datatypes/display_applications/application.py b/lib/galaxy/datatypes/display_applications/application.py
index f9519752040..a978e9c61d7 100644
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -5,13 +5,13 @@ from urllib.parse import quote_plus
 
 from galaxy.util import (
     parse_xml,
-    string_as_bool
+    string_as_bool,
 )
 from galaxy.util.template import fill_template
 from .parameters import (
     DEFAULT_DATASET_NAME,
     DisplayApplicationDataParameter,
-    DisplayApplicationParameter
+    DisplayApplicationParameter,
 )
 from .util import encode_dataset_user
 
@@ -29,16 +29,16 @@ class DisplayApplicationLink:
     @classmethod
     def from_elem(cls, elem, display_application, other_values=None):
         rval = DisplayApplicationLink(display_application)
-        rval.id = elem.get('id', None)
-        assert rval.id, 'Link elements require a id.'
-        rval.name = elem.get('name', rval.id)
-        rval.url = elem.find('url')
-        assert rval.url is not None, 'A url element must be provided for link elements.'
+        rval.id = elem.get("id", None)
+        assert rval.id, "Link elements require a id."
+        rval.name = elem.get("name", rval.id)
+        rval.url = elem.find("url")
+        assert rval.url is not None, "A url element must be provided for link elements."
         rval.other_values = other_values
-        rval.filters = elem.findall('filter')
-        for param_elem in elem.findall('param'):
+        rval.filters = elem.findall("filter")
+        for param_elem in elem.findall("param"):
             param = DisplayApplicationParameter.from_elem(param_elem, rval)
-            assert param, f'Unable to load parameter from element: {param_elem}'
+            assert param, f"Unable to load parameter from element: {param_elem}"
             rval.parameters[param.name] = param
             rval.url_param_name_map[param.url] = param.name
         return rval
@@ -53,21 +53,25 @@ class DisplayApplicationLink:
 
     def get_display_url(self, data, trans):
         dataset_hash, user_hash = encode_dataset_user(trans, data, None)
-        return trans.app.url_for(controller='dataset',
-                                 action="display_application",
-                                 dataset_id=dataset_hash,
-                                 user_id=user_hash,
-                                 app_name=quote_plus(self.display_application.id),
-                                 link_name=quote_plus(self.id),
-                                 app_action=None)
+        return trans.app.url_for(
+            controller="dataset",
+            action="display_application",
+            dataset_id=dataset_hash,
+            user_id=user_hash,
+            app_name=quote_plus(self.display_application.id),
+            link_name=quote_plus(self.id),
+            app_action=None,
+        )
 
     def get_inital_values(self, data, trans):
         if self.other_values:
             rval = dict(self.other_values)
         else:
             rval = {}
-        rval.update({'BASE_URL': trans.request.base, 'APP': trans.app})  # trans automatically appears as a response, need to add properties of trans that we want here
-        BASE_PARAMS = {'qp': quote_plus_string, 'url_for': trans.app.url_for}
+        rval.update(
+            {"BASE_URL": trans.request.base, "APP": trans.app}
+        )  # trans automatically appears as a response, need to add properties of trans that we want here
+        BASE_PARAMS = {"qp": quote_plus_string, "url_for": trans.app.url_for}
         for key, value in BASE_PARAMS.items():  # add helper functions/variables
             rval[key] = value
         rval[DEFAULT_DATASET_NAME] = data  # always have the display dataset name available
@@ -75,8 +79,8 @@ class DisplayApplicationLink:
 
     def build_parameter_dict(self, data, dataset_hash, user_hash, trans, app_kwds):
         other_values = self.get_inital_values(data, trans)
-        other_values['DATASET_HASH'] = dataset_hash
-        other_values['USER_HASH'] = user_hash
+        other_values["DATASET_HASH"] = dataset_hash
+        other_values["USER_HASH"] = user_hash
         ready = True
         for name, param in self.parameters.items():
             assert name not in other_values, f"The display parameter '{name}' has been defined more than once."
@@ -84,10 +88,14 @@ class DisplayApplicationLink:
                 if name in app_kwds and param.allow_override:
                     other_values[name] = app_kwds[name]
                 else:
-                    other_values[name] = param.get_value(other_values, dataset_hash, user_hash, trans)  # subsequent params can rely on this value
+                    other_values[name] = param.get_value(
+                        other_values, dataset_hash, user_hash, trans
+                    )  # subsequent params can rely on this value
             else:
                 ready = False
-                other_values[name] = param.get_value(other_values, dataset_hash, user_hash, trans)  # subsequent params can rely on this value
+                other_values[name] = param.get_value(
+                    other_values, dataset_hash, user_hash, trans
+                )  # subsequent params can rely on this value
                 if other_values[name] is None:
                     # Need to stop here, next params may need this value to determine its own value
                     return False, other_values
@@ -96,51 +104,50 @@ class DisplayApplicationLink:
     def filter_by_dataset(self, data, trans):
         context = self.get_inital_values(data, trans)
         for filter_elem in self.filters:
-            if fill_template(filter_elem.text, context=context) != filter_elem.get('value', 'True'):
+            if fill_template(filter_elem.text, context=context) != filter_elem.get("value", "True"):
                 return False
         return True
 
 
 class DynamicDisplayApplicationBuilder:
-
     def __init__(self, elem, display_application, build_sites):
         filename = None
         data_table = None
-        if elem.get('site_type', None) is not None:
-            filename = build_sites.get(elem.get('site_type'))
+        if elem.get("site_type", None) is not None:
+            filename = build_sites.get(elem.get("site_type"))
         else:
-            filename = elem.get('from_file', None)
+            filename = elem.get("from_file", None)
         if filename is None:
-            data_table_name = elem.get('from_data_table', None)
+            data_table_name = elem.get("from_data_table", None)
             if data_table_name:
                 data_table = display_application.app.tool_data_tables.get(data_table_name, None)
                 assert data_table is not None, f'Unable to find data table named "{data_table_name}".'
 
-        assert filename is not None or data_table is not None, 'Filename or data Table is required for dynamic_links.'
-        skip_startswith = elem.get('skip_startswith', None)
-        separator = elem.get('separator', '\t')
-        id_col = elem.get('id', None)
+        assert filename is not None or data_table is not None, "Filename or data Table is required for dynamic_links."
+        skip_startswith = elem.get("skip_startswith", None)
+        separator = elem.get("separator", "\t")
+        id_col = elem.get("id", None)
         try:
             id_col = int(id_col)
         except (TypeError, ValueError):
             if data_table:
                 if id_col is None:
-                    id_col = data_table.columns.get('id', None)
+                    id_col = data_table.columns.get("id", None)
                 if id_col is None:
-                    id_col = data_table.columns.get('value', None)
+                    id_col = data_table.columns.get("value", None)
                 try:
                     id_col = int(id_col)
                 except (TypeError, ValueError):
                     # id is set to a string or None, use column by that name if available
                     id_col = data_table.columns.get(id_col, None)
                     id_col = int(id_col)
-        name_col = elem.get('name', None)
+        name_col = elem.get("name", None)
         try:
             name_col = int(name_col)
         except (TypeError, ValueError):
             if data_table:
                 if name_col is None:
-                    name_col = data_table.columns.get('name', None)
+                    name_col = data_table.columns.get("name", None)
                 else:
                     name_col = data_table.columns.get(name_col, None)
             else:
@@ -152,14 +159,14 @@ class DynamicDisplayApplicationBuilder:
         if data_table is not None:
             max_col = max([max_col] + list(data_table.columns.values()))
             for key, value in data_table.columns.items():
-                dynamic_params[key] = {'column': value, 'split': False, 'separator': ','}
-        for dynamic_param in elem.findall('dynamic_param'):
-            name = dynamic_param.get('name')
-            value = int(dynamic_param.get('value'))
-            split = string_as_bool(dynamic_param.get('split', False))
-            param_separator = dynamic_param.get('separator', ',')
+                dynamic_params[key] = {"column": value, "split": False, "separator": ","}
+        for dynamic_param in elem.findall("dynamic_param"):
+            name = dynamic_param.get("name")
+            value = int(dynamic_param.get("value"))
+            split = string_as_bool(dynamic_param.get("split", False))
+            param_separator = dynamic_param.get("separator", ",")
             max_col = max(max_col, value)
-            dynamic_params[name] = {'column': value, 'split': split, 'separator': param_separator}
+            dynamic_params[name] = {"column": value, "split": split, "separator": param_separator}
         if filename:
             data_iter = open(filename)
         elif data_table:
@@ -169,7 +176,7 @@ class DynamicDisplayApplicationBuilder:
         for line in data_iter:
             if isinstance(line, str):
                 if not skip_startswith or not line.startswith(skip_startswith):
-                    line = line.rstrip('\n\r')
+                    line = line.rstrip("\n\r")
                     if not line:
                         continue
                     fields = line.split(separator)
@@ -179,16 +186,18 @@ class DynamicDisplayApplicationBuilder:
                 fields = line
             if len(fields) > max_col:
                 new_elem = deepcopy(elem)
-                new_elem.set('id', fields[id_col])
-                new_elem.set('name', fields[name_col])
+                new_elem.set("id", fields[id_col])
+                new_elem.set("name", fields[name_col])
                 dynamic_values = {}
                 for key, attributes in dynamic_params.items():
-                    value = fields[attributes['column']]
-                    if attributes['split']:
-                        value = value.split(attributes['separator'])
+                    value = fields[attributes["column"]]
+                    if attributes["split"]:
+                        value = value.split(attributes["separator"])
                     dynamic_values[key] = value
                 # now populate
-                links.append(DisplayApplicationLink.from_elem(new_elem, display_application, other_values=dynamic_values))
+                links.append(
+                    DisplayApplicationLink.from_elem(new_elem, display_application, other_values=dynamic_values)
+                )
             else:
                 log.warning(f'Invalid dynamic display application link specified in {filename}: "{line}"')
         self.links = links
@@ -204,7 +213,9 @@ class PopulatedDisplayApplicationLink:
         self.dataset_hash = dataset_hash
         self.user_hash = user_hash
         self.trans = trans
-        self.ready, self.parameters = self.link.build_parameter_dict(self.data, self.dataset_hash, self.user_hash, trans, app_kwds)
+        self.ready, self.parameters = self.link.build_parameter_dict(
+            self.data, self.dataset_hash, self.user_hash, trans, app_kwds
+        )
 
     def display_ready(self):
         return self.ready
@@ -213,7 +224,7 @@ class PopulatedDisplayApplicationLink:
         value = None
         if self.ready:
             value = self.parameters.get(name, None)
-            assert value, 'Unknown parameter requested'
+            assert value, "Unknown parameter requested"
         return value
 
     def preparing_display(self):
@@ -230,7 +241,7 @@ class PopulatedDisplayApplicationLink:
                 if found_last or list(other_values.keys())[-1] == name:  # found last parameter to be populated
                     found_last = True
                     value = param.prepare(other_values, self.dataset_hash, self.user_hash, self.trans)
-                    rval.append({'name': name, 'value': value, 'param': param})
+                    rval.append({"name": name, "value": value, "param": param})
                     other_values[name] = value
                     if value is None:
                         # We can go no further until we have a value for this parameter
@@ -243,11 +254,11 @@ class PopulatedDisplayApplicationLink:
             if datasets_only and not isinstance(param, DisplayApplicationDataParameter):
                 continue
             value = self.parameters.get(name, None)
-            rval.append({'name': name, 'value': value, 'param': param, 'ready': param.ready(self.parameters)})
+            rval.append({"name": name, "value": value, "param": param, "ready": param.ready(self.parameters)})
         return rval
 
     def display_url(self):
-        assert self.display_ready(), 'Display is not yet ready, cannot generate display link'
+        assert self.display_ready(), "Display is not yet ready, cannot generate display link"
         return fill_template(self.link.url.text, context=self.parameters)
 
     def get_param_name_by_url(self, url):
@@ -269,16 +280,18 @@ class DisplayApplication:
     @classmethod
     def from_elem(cls, elem, app, filename=None):
         att_dict = cls._get_attributes_from_elem(elem)
-        rval = DisplayApplication(att_dict['id'], att_dict['name'], app, att_dict['version'], filename=filename, elem=elem)
+        rval = DisplayApplication(
+            att_dict["id"], att_dict["name"], app, att_dict["version"], filename=filename, elem=elem
+        )
         rval._load_links_from_elem(elem)
         return rval
 
     @classmethod
     def _get_attributes_from_elem(cls, elem):
-        display_id = elem.get('id', None)
+        display_id = elem.get("id", None)
         assert display_id, "ID tag is required for a Display Application"
-        name = elem.get('name', display_id)
-        version = elem.get('version', None)
+        name = elem.get("name", display_id)
+        version = elem.get("version", None)
         return dict(id=display_id, name=name, version=version)
 
     def __init__(self, display_id, name, app, version=None, filename=None, elem=None):
@@ -294,13 +307,15 @@ class DisplayApplication:
         self._data_table_versions = {}
 
     def _load_links_from_elem(self, elem):
-        for link_elem in elem.findall('link'):
+        for link_elem in elem.findall("link"):
             link = DisplayApplicationLink.from_elem(link_elem, self)
             if link:
                 self.links[link.id] = link
         try:
-            for dynamic_links in elem.findall('dynamic_links'):
-                for link in DynamicDisplayApplicationBuilder(dynamic_links, self, self.app.datatypes_registry.build_sites):
+            for dynamic_links in elem.findall("dynamic_links"):
+                for link in DynamicDisplayApplicationBuilder(
+                    dynamic_links, self, self.app.datatypes_registry.build_sites
+                ):
                     self.links[link.id] = link
         except Exception as e:
             log.error("Error loading a set of Dynamic Display Application links: %s", e)
@@ -328,7 +343,9 @@ class DisplayApplication:
         # All toolshed-specific attributes added by e.g the registry will remain
         attr_dict = self._get_attributes_from_elem(elem)
         # We will not allow changing the id at this time (we'll need to fix several mappings upstream to handle this case)
-        assert attr_dict.get('id') == self.id, ValueError("You cannot reload a Display application where the ID has changed. You will need to restart the server instead.")
+        assert attr_dict.get("id") == self.id, ValueError(
+            "You cannot reload a Display application where the ID has changed. You will need to restart the server instead."
+        )
         # clear old links
         self.links = {}
         # clear data table versions:
diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py
index f5e6c3659bf..c1a28fc8147 100644
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -7,35 +7,41 @@ from galaxy.util import string_as_bool
 from galaxy.util.bunch import Bunch
 from galaxy.util.template import fill_template
 
-DEFAULT_DATASET_NAME = 'dataset'
+DEFAULT_DATASET_NAME = "dataset"
 
 
 class DisplayApplicationParameter:
-    """ Abstract Class for Display Application Parameters """
+    """Abstract Class for Display Application Parameters"""
 
     type: Optional[str] = None
 
     @classmethod
     def from_elem(cls, elem, link):
-        param_type = elem.get('type', None)
-        assert param_type, 'DisplayApplicationParameter requires a type'
+        param_type = elem.get("type", None)
+        assert param_type, "DisplayApplicationParameter requires a type"
         return parameter_type_to_class[param_type](elem, link)
 
     def __init__(self, elem, link):
-        self.name = elem.get('name', None)
-        assert self.name, 'DisplayApplicationParameter requires a name'
+        self.name = elem.get("name", None)
+        assert self.name, "DisplayApplicationParameter requires a name"
         self.link = link
-        self.url = elem.get('url', self.name)  # name used in url for display purposes defaults to name; e.g. want the form of file.ext, where a '.' is not allowed as python variable name/keyword
-        self.mime_type = elem.get('mimetype', None)
-        self.guess_mime_type = string_as_bool(elem.get('guess_mimetype', 'False'))
-        self.viewable = string_as_bool(elem.get('viewable', 'False'))  # only allow these to be viewed via direct url when explicitly set to viewable
-        self.strip = string_as_bool(elem.get('strip', 'False'))
-        self.strip_https = string_as_bool(elem.get('strip_https', 'False'))
-        self.allow_override = string_as_bool(elem.get('allow_override', 'False'))  # Passing query param app_<name>=<value> to dataset controller allows override if this is true.
-        self.allow_cors = string_as_bool(elem.get('allow_cors', 'False'))
+        self.url = elem.get(
+            "url", self.name
+        )  # name used in url for display purposes defaults to name; e.g. want the form of file.ext, where a '.' is not allowed as python variable name/keyword
+        self.mime_type = elem.get("mimetype", None)
+        self.guess_mime_type = string_as_bool(elem.get("guess_mimetype", "False"))
+        self.viewable = string_as_bool(
+            elem.get("viewable", "False")
+        )  # only allow these to be viewed via direct url when explicitly set to viewable
+        self.strip = string_as_bool(elem.get("strip", "False"))
+        self.strip_https = string_as_bool(elem.get("strip_https", "False"))
+        self.allow_override = string_as_bool(
+            elem.get("allow_override", "False")
+        )  # Passing query param app_<name>=<value> to dataset controller allows override if this is true.
+        self.allow_cors = string_as_bool(elem.get("allow_cors", "False"))
 
     def get_value(self, other_values, dataset_hash, user_hash, trans):
-        raise Exception('get_value() is unimplemented for DisplayApplicationDataParameter')
+        raise Exception("get_value() is unimplemented for DisplayApplicationDataParameter")
 
     def prepare(self, other_values, dataset_hash, user_hash, trans):
         return self.get_value(other_values, dataset_hash, user_hash, trans)
@@ -51,40 +57,53 @@ class DisplayApplicationParameter:
 
 
 class DisplayApplicationDataParameter(DisplayApplicationParameter):
-    """ Parameter that returns a file_name containing the requested content """
+    """Parameter that returns a file_name containing the requested content"""
 
-    type = 'data'
+    type = "data"
 
     def __init__(self, elem, link):
         DisplayApplicationParameter.__init__(self, elem, link)
-        self.extensions = elem.get('format', None)
+        self.extensions = elem.get("format", None)
         if self.extensions:
             self.extensions = self.extensions.split(",")
-        self.metadata = elem.get('metadata', None)
-        self.allow_extra_files_access = string_as_bool(elem.get('allow_extra_files_access', 'False'))
-        self.dataset = elem.get('dataset', DEFAULT_DATASET_NAME)  # 'dataset' is default name assigned to dataset to be displayed
-        assert not (self.extensions and self.metadata), 'A format or a metadata can be defined for a DisplayApplicationParameter, but not both.'
-        assert not (self.allow_extra_files_access and self.metadata), 'allow_extra_files_access or metadata can be defined for a DisplayApplicationParameter, but not both.'
-        self.viewable = string_as_bool(elem.get('viewable', 'True'))  # data params should be viewable
-        self.force_url_param = string_as_bool(elem.get('force_url_param', 'False'))
-        self.force_conversion = string_as_bool(elem.get('force_conversion', 'False'))
+        self.metadata = elem.get("metadata", None)
+        self.allow_extra_files_access = string_as_bool(elem.get("allow_extra_files_access", "False"))
+        self.dataset = elem.get(
+            "dataset", DEFAULT_DATASET_NAME
+        )  # 'dataset' is default name assigned to dataset to be displayed
+        assert not (
+            self.extensions and self.metadata
+        ), "A format or a metadata can be defined for a DisplayApplicationParameter, but not both."
+        assert not (
+            self.allow_extra_files_access and self.metadata
+        ), "allow_extra_files_access or metadata can be defined for a DisplayApplicationParameter, but not both."
+        self.viewable = string_as_bool(elem.get("viewable", "True"))  # data params should be viewable
+        self.force_url_param = string_as_bool(elem.get("force_url_param", "False"))
+        self.force_conversion = string_as_bool(elem.get("force_conversion", "False"))
 
     @property
     def formats(self):
         if self.extensions:
-            return tuple(map(type, map(self.link.display_application.app.datatypes_registry.get_datatype_by_extension, self.extensions)))
+            return tuple(
+                map(
+                    type,
+                    map(
+                        self.link.display_application.app.datatypes_registry.get_datatype_by_extension, self.extensions
+                    ),
+                )
+            )
         return None
 
     def _get_dataset_like_object(self, other_values):
         # this returned object has file_name, state, and states attributes equivalent to a DatasetAssociation
         data = other_values.get(self.dataset, None)
-        assert data, 'Base dataset could not be found in values provided to DisplayApplicationDataParameter'
+        assert data, "Base dataset could not be found in values provided to DisplayApplicationDataParameter"
         if isinstance(data, DisplayDataValueWrapper):
             data = data.value
         if self.metadata:
             rval = getattr(data.metadata, self.metadata, None)
             assert rval, f'Unknown metadata name "{self.metadata}" provided for dataset type "{data.ext}".'
-            return Bunch(file_name=rval.file_name, state=data.state, states=data.states, extension='data')
+            return Bunch(file_name=rval.file_name, state=data.state, states=data.states, extension="data")
         elif self.extensions and (self.force_conversion or not isinstance(data.datatype, self.formats)):
             for ext in self.extensions:
                 rval = data.get_converted_files_by_type(ext)
@@ -110,16 +129,26 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
             # start conversion
             # FIXME: Much of this is copied (more than once...); should be some abstract method elsewhere called from here
             # find target ext
-            direct_match, target_ext, converted_dataset = data.find_conversion_destination(self.formats, converter_safe=True)
+            direct_match, target_ext, converted_dataset = data.find_conversion_destination(
+                self.formats, converter_safe=True
+            )
             if not direct_match:
                 if target_ext and not converted_dataset:
                     if isinstance(data, DisplayDataValueWrapper):
                         data = data.value
-                    new_data = next(iter(data.datatype.convert_dataset(trans, data, target_ext, return_output=True, visible=False).values()))
+                    new_data = next(
+                        iter(
+                            data.datatype.convert_dataset(
+                                trans, data, target_ext, return_output=True, visible=False
+                            ).values()
+                        )
+                    )
                     new_data.hid = data.hid
                     new_data.name = data.name
                     trans.sa_session.add(new_data)
-                    assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False)
+                    assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
+                        parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False
+                    )
                     trans.sa_session.add(assoc)
                     trans.sa_session.flush()
                 elif converted_dataset and converted_dataset.state == converted_dataset.states.ERROR:
@@ -138,18 +167,18 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
             if value.state == value.states.OK:
                 return True
             elif value.state == value.states.ERROR:
-                raise Exception(f'A data display parameter is in the error state: {self.name}')
+                raise Exception(f"A data display parameter is in the error state: {self.name}")
         return False
 
 
 class DisplayApplicationTemplateParameter(DisplayApplicationParameter):
-    """ Parameter that returns a string containing the requested content """
+    """Parameter that returns a string containing the requested content"""
 
-    type = 'template'
+    type = "template"
 
     def __init__(self, elem, link):
         DisplayApplicationParameter.__init__(self, elem, link)
-        self.text = elem.text or ''
+        self.text = elem.text or ""
 
     def get_value(self, other_values, dataset_hash, user_hash, trans):
         value = fill_template(self.text, context=other_values)
@@ -158,12 +187,14 @@ class DisplayApplicationTemplateParameter(DisplayApplicationParameter):
         return DisplayParameterValueWrapper(value, self, other_values, dataset_hash, user_hash, trans)
 
 
-parameter_type_to_class = {DisplayApplicationDataParameter.type: DisplayApplicationDataParameter,
-                           DisplayApplicationTemplateParameter.type: DisplayApplicationTemplateParameter}
+parameter_type_to_class = {
+    DisplayApplicationDataParameter.type: DisplayApplicationDataParameter,
+    DisplayApplicationTemplateParameter.type: DisplayApplicationTemplateParameter,
+}
 
 
 class DisplayParameterValueWrapper:
-    ACTION_NAME = 'param'
+    ACTION_NAME = "param"
 
     def __init__(self, value, parameter, other_values, dataset_hash, user_hash, trans):
         self.value = value
@@ -186,22 +217,26 @@ class DisplayParameterValueWrapper:
                 mime = self.trans.app.datatypes_registry.get_mimetype_by_extension(".".split(self._url)[-1], None)
             if mime:
                 return mime
-        return 'text/plain'
+        return "text/plain"
 
     @property
     def url(self):
         base_url = self.trans.request.base
-        if self.parameter.strip_https and base_url[: 5].lower() == 'https':
+        if self.parameter.strip_https and base_url[:5].lower() == "https":
             base_url = f"http{base_url[5:]}"
-        return "{}{}".format(base_url,
-                             self.trans.app.url_for(controller='dataset',
-                                                    action="display_application",
-                                                    dataset_id=self._dataset_hash,
-                                                    user_id=self._user_hash,
-                                                    app_name=quote_plus(self.parameter.link.display_application.id),
-                                                    link_name=quote_plus(self.parameter.link.id),
-                                                    app_action=self.action_name,
-                                                    action_param=self._url))
+        return "{}{}".format(
+            base_url,
+            self.trans.app.url_for(
+                controller="dataset",
+                action="display_application",
+                dataset_id=self._dataset_hash,
+                user_id=self._user_hash,
+                app_name=quote_plus(self.parameter.link.display_application.id),
+                link_name=quote_plus(self.parameter.link.id),
+                app_action=self.action_name,
+                action_param=self._url,
+            ),
+        )
 
     @property
     def action_name(self):
@@ -210,14 +245,14 @@ class DisplayParameterValueWrapper:
     @property
     def qp(self):
         # returns quoted str contents
-        return self.other_values['qp'](str(self))
+        return self.other_values["qp"](str(self))
 
     def __getattr__(self, key):
         return getattr(self.value, key)
 
 
 class DisplayDataValueWrapper(DisplayParameterValueWrapper):
-    ACTION_NAME = 'data'
+    ACTION_NAME = "data"
 
     def __str__(self):
         # string of data param is filename
@@ -233,12 +268,14 @@ class DisplayDataValueWrapper(DisplayParameterValueWrapper):
                 mime, encoding = mimetypes.guess_type(self._url)
             if not mime:
                 if action_param_extra:
-                    mime = self.trans.app.datatypes_registry.get_mimetype_by_extension(".".split(action_param_extra)[-1], None)
+                    mime = self.trans.app.datatypes_registry.get_mimetype_by_extension(
+                        ".".split(action_param_extra)[-1], None
+                    )
                 if not mime:
                     mime = self.trans.app.datatypes_registry.get_mimetype_by_extension(".".split(self._url)[-1], None)
             if mime:
                 return mime
-        if hasattr(self.value, 'get_mime'):
+        if hasattr(self.value, "get_mime"):
             return self.value.get_mime()
         return self.other_values[DEFAULT_DATASET_NAME].get_mime()
 
@@ -251,4 +288,4 @@ class DisplayDataValueWrapper(DisplayParameterValueWrapper):
     @property
     def qp(self):
         # returns quoted url contents
-        return self.other_values['qp'](self.url)
+        return self.other_values["qp"](self.url)
diff --git a/lib/galaxy/datatypes/display_applications/util.py b/lib/galaxy/datatypes/display_applications/util.py
index 6af23bf5b94..aefc65d9ff1 100644
--- a/lib/galaxy/datatypes/display_applications/util.py
+++ b/lib/galaxy/datatypes/display_applications/util.py
@@ -6,7 +6,7 @@ def encode_dataset_user(trans, dataset, user):
     # encode user id using the dataset create time as the key
     dataset_hash = trans.security.encode_id(dataset.id)
     if user is None:
-        user_hash = 'None'
+        user_hash = "None"
     else:
         security = IdEncodingHelper(id_secret=dataset.create_time)
         user_hash = security.encode_id(user.id)
@@ -19,7 +19,7 @@ def decode_dataset_user(trans, dataset_hash, user_hash):
     dataset_id = trans.security.decode_id(dataset_hash)
     dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dataset_id)
     assert dataset, "Bad Dataset id provided to decode_dataset_user"
-    if user_hash in [None, 'None']:
+    if user_hash in [None, "None"]:
         user = None
     else:
         security = IdEncodingHelper(id_secret=dataset.create_time)
diff --git a/lib/galaxy/datatypes/flow.py b/lib/galaxy/datatypes/flow.py
index 48a7a4a2495..34f6de4c90b 100644
--- a/lib/galaxy/datatypes/flow.py
+++ b/lib/galaxy/datatypes/flow.py
@@ -17,6 +17,7 @@ log = logging.getLogger(__name__)
 @build_sniff_from_prefix
 class FCS(Binary):
     """Class describing an FCS binary file"""
+
     file_ext = "fcs"
 
     def set_peek(self, dataset):
@@ -24,8 +25,8 @@ class FCS(Binary):
             dataset.peek = "Binary FCS file"
             dataset.blurb = data.nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -45,8 +46,8 @@ class FCS(Binary):
         version = content[:6]
         if version not in ["FCS2.0", "FCS3.0", "FCS3.1"]:
             return False
-        if content[6:10] != '    ':
+        if content[6:10] != "    ":
             return False
         # we only need to check ioffs 2 to 5
-        int(content[10:42].replace(' ', ''))
+        int(content[10:42].replace(" ", ""))
         return True
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 6b32f006ebe..1c10d06ab77 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -40,8 +40,8 @@ gal_Log = logging.getLogger(__name__)
 verbose = False
 
 # https://genome.ucsc.edu/goldenpath/help/hgGenomeHelp.html
-VALID_GENOME_GRAPH_MARKERS = re.compile(r'^(chr.*|RH.*|rs.*|SNP_.*|CN.*|A_.*)')
-VALID_GENOTYPES_LINE = re.compile(r'^([a-zA-Z0-9]+)(\s([0-9]{2}|[A-Z]{2}|NC|\?\?))+\s*$')
+VALID_GENOME_GRAPH_MARKERS = re.compile(r"^(chr.*|RH.*|rs.*|SNP_.*|CN.*|A_.*)")
+VALID_GENOTYPES_LINE = re.compile(r"^([a-zA-Z0-9]+)(\s([0-9]{2}|[A-Z]{2}|NC|\?\?))+\s*$")
 
 
 @build_sniff_from_prefix
@@ -53,22 +53,22 @@ class GenomeGraphs(Tabular):
     MetadataElement(name="markerCol", default=1, desc="Marker ID column", param=metadata.ColumnParameter)
     MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True)
     MetadataElement(name="column_types", default=[], desc="Column types", readonly=True, visible=False)
-    file_ext = 'gg'
+    file_ext = "gg"
 
     def __init__(self, **kwd):
         """
         Initialize gg datatype, by adding UCSC display apps
         """
         super().__init__(**kwd)
-        self.add_display_app('ucsc', 'Genome Graph', 'as_ucsc_display_file', 'ucsc_links')
+        self.add_display_app("ucsc", "Genome Graph", "as_ucsc_display_file", "ucsc_links")
 
     def set_meta(self, dataset, **kwd):
         super().set_meta(dataset, **kwd)
         dataset.metadata.markerCol = 1
-        header = open(dataset.file_name).readlines()[0].strip().split('\t')
+        header = open(dataset.file_name).readlines()[0].strip().split("\t")
         dataset.metadata.columns = len(header)
-        t = ['numeric' for x in header]
-        t[0] = 'string'
+        t = ["numeric" for x in header]
+        t[0] = "string"
         dataset.metadata.column_types = t
         return True
 
@@ -76,7 +76,7 @@ class GenomeGraphs(Tabular):
         """
         Returns file
         """
-        return open(dataset.file_name, 'rb')
+        return open(dataset.file_name, "rb")
 
     def ucsc_links(self, dataset, type, app, base_url):
         """
@@ -97,30 +97,36 @@ class GenomeGraphs(Tabular):
         """
         ret_val = []
         if not dataset.dbkey:
-            dataset.dbkey = 'hg18'  # punt!
+            dataset.dbkey = "hg18"  # punt!
         if dataset.has_data():
-            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
-                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
-                    site_url = site_url.replace('/hgTracks?', '/hgGenome?')  # for genome graphs
-                    internal_url = "%s" % app.url_for(controller='dataset',
-                                                      dataset_id=dataset.id,
-                                                      action='display_at',
-                                                      filename=f"ucsc_{site_name}")
-                    display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, app.url_for(controller='root'), dataset.id, type)
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites("ucsc"):
+                    site_url = site_url.replace("/hgTracks?", "/hgGenome?")  # for genome graphs
+                    internal_url = "%s" % app.url_for(
+                        controller="dataset", dataset_id=dataset.id, action="display_at", filename=f"ucsc_{site_name}"
+                    )
+                    display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (
+                        base_url,
+                        app.url_for(controller="root"),
+                        dataset.id,
+                        type,
+                    )
                     display_url = quote_plus(display_url)
                     # was display_url = quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
                     # redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
-                    sl = [f"{site_url}db={dataset.dbkey}", ]
+                    sl = [
+                        f"{site_url}db={dataset.dbkey}",
+                    ]
                     # sl.append("&hgt.customText=%s")
                     sl.append(f"&hgGenome_dataSetName={dataset.name}&hgGenome_dataSetDescription=GalaxyGG_data")
                     sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
                     sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=")
                     sl.append("&hgGenome_doSubmitUpload=submit")
                     sl.append(f"&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile={display_url}")
-                    s = ''.join(sl)
+                    s = "".join(sl)
                     s = quote_plus(s)
                     redirect_url = s
-                    link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
+                    link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -137,21 +143,21 @@ class GenomeGraphs(Tabular):
                 return out
             hasheader = 0
             try:
-                [f'{x:f}' for x in d[0][1:]]  # first is name - see if starts all numerics
+                [f"{x:f}" for x in d[0][1:]]  # first is name - see if starts all numerics
             except Exception:
                 hasheader = 1
             # Generate column header
-            out.append('<tr>')
+            out.append("<tr>")
             if hasheader:
                 for i, name in enumerate(d[0].split()):
-                    out.append(f'<th>{i + 1}.{name}</th>')
+                    out.append(f"<th>{i + 1}.{name}</th>")
                 d.pop(0)
-                out.append('</tr>')
+                out.append("</tr>")
             for row in d:
-                out.append('<tr>')
-                out.append(''.join(f'<td>{x}</td>' for x in row.split()))
-                out.append('</tr>')
-            out.append('</table>')
+                out.append("<tr>")
+                out.append("".join(f"<td>{x}</td>" for x in row.split()))
+                out.append("</tr>")
+            out.append("</table>")
             out = "".join(out)
         except Exception as exc:
             out = f"Can't create peek {exc}"
@@ -164,7 +170,7 @@ class GenomeGraphs(Tabular):
         with open(dataset.file_name) as infile:
             next(infile)  # header
             for row in infile:
-                ll = row.strip().split('\t')[1:]  # first is alpha feature identifier
+                ll = row.strip().split("\t")[1:]  # first is alpha feature identifier
                 for x in ll:
                     x = float(x)
         return DatatypeValidation.validated()
@@ -203,7 +209,7 @@ class GenomeGraphs(Tabular):
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/vnd.ms-excel'
+        return "application/vnd.ms-excel"
 
 
 class rgTabList(Tabular):
@@ -211,6 +217,7 @@ class rgTabList(Tabular):
     for sampleid and for featureid lists of exclusions or inclusions in the clean tool
     featureid subsets on statistical criteria -> specialized display such as gg
     """
+
     file_ext = "rgTList"
 
     def __init__(self, **kwd):
@@ -226,7 +233,7 @@ class rgTabList(Tabular):
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/html'
+        return "text/html"
 
 
 class rgSampleList(rgTabList):
@@ -237,6 +244,7 @@ class rgSampleList(rgTabList):
     but they are persistent at least
     same infrastructure for expression?
     """
+
     file_ext = "rgSList"
 
     def __init__(self, **kwd):
@@ -244,8 +252,8 @@ class rgSampleList(rgTabList):
         Initialize samplelist datatype
         """
         super().__init__(**kwd)
-        self.column_names[0] = 'FID'
-        self.column_names[1] = 'IID'
+        self.column_names[0] = "FID"
+        self.column_names[1] = "IID"
         # this is what Plink wants as at 2009
 
 
@@ -256,12 +264,13 @@ class rgFeatureList(rgTabList):
     featureid subsets on statistical criteria -> specialized display such as gg
     same infrastructure for expression?
     """
+
     file_ext = "rgFList"
 
     def __init__(self, **kwd):
         """Initialize featurelist datatype"""
         super().__init__(**kwd)
-        for i, s in enumerate(['#FeatureId', 'Chr', 'Genpos', 'Mappos']):
+        for i, s in enumerate(["#FeatureId", "Chr", "Genpos", "Mappos"]):
             self.column_names[i] = s
 
 
@@ -272,25 +281,32 @@ class Rgenetics(Html):
     stored in extra files path
     """
 
-    MetadataElement(name="base_name", desc="base name for all transformed versions of this genetic dataset", default='RgeneticsData',
-                    readonly=True, set_in_upload=True)
+    MetadataElement(
+        name="base_name",
+        desc="base name for all transformed versions of this genetic dataset",
+        default="RgeneticsData",
+        readonly=True,
+        set_in_upload=True,
+    )
 
-    composite_type = 'auto_primary_file'
-    file_ext = 'rgenetics'
+    composite_type = "auto_primary_file"
+    file_ext = "rgenetics"
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"application/binary\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                opt_text = " (optional)"
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"application/binary\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
 
     def regenerate_primary_file(self, dataset):
@@ -299,19 +315,21 @@ class Rgenetics(Html):
         """
         efp = dataset.extra_files_path
         flist = os.listdir(efp)
-        rval = [f'<html><head><title>Files for Composite Dataset {dataset.name}</title></head><body><p/>Composite {dataset.name} contains:<p/><ul>']
+        rval = [
+            f"<html><head><title>Files for Composite Dataset {dataset.name}</title></head><body><p/>Composite {dataset.name} contains:<p/><ul>"
+        ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
             f, e = os.path.splitext(fname)
             rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
-        rval.append('</ul></body></html>')
-        with open(dataset.file_name, 'w') as f:
+        rval.append("</ul></body></html>")
+        with open(dataset.file_name, "w") as f:
             f.write("\n".join(rval))
-            f.write('\n')
+            f.write("\n")
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/html'
+        return "text/html"
 
     def set_meta(self, dataset, **kwd):
         """
@@ -319,31 +337,31 @@ class Rgenetics(Html):
 
         """
         super().set_meta(dataset, **kwd)
-        if not kwd.get('overwrite'):
+        if not kwd.get("overwrite"):
             if verbose:
-                gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
+                gal_Log.debug("@@@ rgenetics set_meta called with overwrite = False")
             return True
         try:
             efp = dataset.extra_files_path
         except Exception:
             if verbose:
-                gal_Log.debug(f'@@@rgenetics set_meta failed {sys.exc_info()[0]} - dataset {dataset.name} has no efp ?')
+                gal_Log.debug(f"@@@rgenetics set_meta failed {sys.exc_info()[0]} - dataset {dataset.name} has no efp ?")
             return False
         try:
             flist = os.listdir(efp)
         except Exception:
             if verbose:
-                gal_Log.debug(f'@@@rgenetics set_meta failed {sys.exc_info()[0]} - dataset {dataset.name} has no efp ?')
+                gal_Log.debug(f"@@@rgenetics set_meta failed {sys.exc_info()[0]} - dataset {dataset.name} has no efp ?")
             return False
         if len(flist) == 0:
             if verbose:
-                gal_Log.debug(f'@@@rgenetics set_meta failed - {dataset.name} efp {efp} is empty?')
+                gal_Log.debug(f"@@@rgenetics set_meta failed - {dataset.name} efp {efp} is empty?")
             return False
         self.regenerate_primary_file(dataset)
         if not dataset.info:
-            dataset.info = 'Galaxy genotype datatype object'
+            dataset.info = "Galaxy genotype datatype object"
         if not dataset.blurb:
-            dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
+            dataset.blurb = "Composite file - Rgenetics Galaxy toolkit"
         return True
 
 
@@ -351,6 +369,7 @@ class SNPMatrix(Rgenetics):
     """
     BioC SNPMatrix Rgenetics data collections
     """
+
     file_ext = "snpmatrix"
 
     def set_peek(self, dataset, **kwd):
@@ -358,16 +377,15 @@ class SNPMatrix(Rgenetics):
             dataset.peek = "Binary RGenetics file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
-        """ need to check the file header hex code
-        """
+        """need to check the file header hex code"""
         with open(filename, "b") as infile:
             head = infile.read(16)
         head = [hex(x) for x in head]
-        if head != '':
+        if head != "":
             return False
         else:
             return True
@@ -377,32 +395,31 @@ class Lped(Rgenetics):
     """
     linkage pedigree (ped,map) Rgenetics data collections
     """
+
     file_ext = "lped"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.ped',
-                                description='Pedigree File',
-                                substitute_name_with_metadata='base_name',
-                                is_binary=False)
-        self.add_composite_file('%s.map',
-                                description='Map File',
-                                substitute_name_with_metadata='base_name',
-                                is_binary=False)
+        self.add_composite_file(
+            "%s.ped", description="Pedigree File", substitute_name_with_metadata="base_name", is_binary=False
+        )
+        self.add_composite_file(
+            "%s.map", description="Map File", substitute_name_with_metadata="base_name", is_binary=False
+        )
 
 
 class Pphe(Rgenetics):
     """
     Plink phenotype file - header must have FID\tIID... Rgenetics data collections
     """
+
     file_ext = "pphe"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.pphe',
-                                description='Plink Phenotype File',
-                                substitute_name_with_metadata='base_name',
-                                is_binary=False)
+        self.add_composite_file(
+            "%s.pphe", description="Plink Phenotype File", substitute_name_with_metadata="base_name", is_binary=False
+        )
 
 
 class Fphe(Rgenetics):
@@ -410,27 +427,26 @@ class Fphe(Rgenetics):
     fbat pedigree file - mad format with ! as first char on header row
     Rgenetics data collections
     """
+
     file_ext = "fphe"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.fphe',
-                                description='FBAT Phenotype File',
-                                substitute_name_with_metadata='base_name')
+        self.add_composite_file("%s.fphe", description="FBAT Phenotype File", substitute_name_with_metadata="base_name")
 
 
 class Phe(Rgenetics):
     """
     Phenotype file
     """
+
     file_ext = "phe"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.phe',
-                                description='Phenotype File',
-                                substitute_name_with_metadata='base_name',
-                                is_binary=False)
+        self.add_composite_file(
+            "%s.phe", description="Phenotype File", substitute_name_with_metadata="base_name", is_binary=False
+        )
 
 
 class Fped(Rgenetics):
@@ -438,26 +454,28 @@ class Fped(Rgenetics):
     FBAT pedigree format - single file, map is header row of rs numbers. Strange.
     Rgenetics data collections
     """
+
     file_ext = "fped"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.fped', description='FBAT format pedfile',
-                                substitute_name_with_metadata='base_name',
-                                is_binary=False)
+        self.add_composite_file(
+            "%s.fped", description="FBAT format pedfile", substitute_name_with_metadata="base_name", is_binary=False
+        )
 
 
 class Pbed(Rgenetics):
     """
     Plink Binary compressed 2bit/geno Rgenetics data collections
     """
+
     file_ext = "pbed"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.bim', substitute_name_with_metadata='base_name', is_binary=False)
-        self.add_composite_file('%s.bed', substitute_name_with_metadata='base_name', is_binary=True)
-        self.add_composite_file('%s.fam', substitute_name_with_metadata='base_name', is_binary=False)
+        self.add_composite_file("%s.bim", substitute_name_with_metadata="base_name", is_binary=False)
+        self.add_composite_file("%s.bed", substitute_name_with_metadata="base_name", is_binary=True)
+        self.add_composite_file("%s.fam", substitute_name_with_metadata="base_name", is_binary=False)
 
 
 class ldIndep(Rgenetics):
@@ -466,13 +484,14 @@ class ldIndep(Rgenetics):
     This is really a plink binary, but some tools work better with less redundancy so are constrained to
     these files
     """
+
     file_ext = "ldreduced"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.bim', substitute_name_with_metadata='base_name', is_binary=False)
-        self.add_composite_file('%s.bed', substitute_name_with_metadata='base_name', is_binary=True)
-        self.add_composite_file('%s.fam', substitute_name_with_metadata='base_name', is_binary=False)
+        self.add_composite_file("%s.bim", substitute_name_with_metadata="base_name", is_binary=False)
+        self.add_composite_file("%s.bed", substitute_name_with_metadata="base_name", is_binary=True)
+        self.add_composite_file("%s.fam", substitute_name_with_metadata="base_name", is_binary=False)
 
 
 class Eigenstratgeno(Rgenetics):
@@ -481,13 +500,14 @@ class Eigenstratgeno(Rgenetics):
     if we move to shellfish
     Rgenetics data collections
     """
+
     file_ext = "eigenstratgeno"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.eigenstratgeno', substitute_name_with_metadata='base_name', is_binary=False)
-        self.add_composite_file('%s.ind', substitute_name_with_metadata='base_name', is_binary=False)
-        self.add_composite_file('%s.map', substitute_name_with_metadata='base_name', is_binary=False)
+        self.add_composite_file("%s.eigenstratgeno", substitute_name_with_metadata="base_name", is_binary=False)
+        self.add_composite_file("%s.ind", substitute_name_with_metadata="base_name", is_binary=False)
+        self.add_composite_file("%s.map", substitute_name_with_metadata="base_name", is_binary=False)
 
 
 class Eigenstratpca(Rgenetics):
@@ -495,18 +515,21 @@ class Eigenstratpca(Rgenetics):
     Eigenstrat PCA file for case control adjustment
     Rgenetics data collections
     """
+
     file_ext = "eigenstratpca"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.eigenstratpca',
-                                description='Eigenstrat PCA file', substitute_name_with_metadata='base_name')
+        self.add_composite_file(
+            "%s.eigenstratpca", description="Eigenstrat PCA file", substitute_name_with_metadata="base_name"
+        )
 
 
 class Snptest(Rgenetics):
     """
     BioC snptest Rgenetics data collections
     """
+
     file_ext = "snptest"
 
 
@@ -523,21 +546,27 @@ class IdeasPre(Html):
     - compressed archived tmp directory containing a number of compressed bed files.
     """
 
-    MetadataElement(name="base_name", desc="Base name for this dataset", default='IDEASData', readonly=True, set_in_upload=True)
+    MetadataElement(
+        name="base_name", desc="Base name for this dataset", default="IDEASData", readonly=True, set_in_upload=True
+    )
     MetadataElement(name="chrom_bed", desc="Bed file specifying window positions", default=None, readonly=True)
     MetadataElement(name="chrom_windows", desc="Chromosome window positions", default=None, readonly=True)
     MetadataElement(name="input_config", desc="IDEAS input config", default=None, readonly=True)
     MetadataElement(name="tmp_archive", desc="Compressed archive of compressed bed files", default=None, readonly=True)
 
-    composite_type = 'auto_primary_file'
-    file_ext = 'ideaspre'
+    composite_type = "auto_primary_file"
+    file_ext = "ideaspre"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('chromosome_windows.txt', description='Chromosome window positions', is_binary=False, optional=True)
-        self.add_composite_file('chromosomes.bed', description='Bed file specifying window positions', is_binary=False, optional=True)
-        self.add_composite_file('IDEAS_input_config.txt', description='IDEAS input config', is_binary=False)
-        self.add_composite_file('tmp.tar.gz', description='Compressed archive of compressed bed files', is_binary=True)
+        self.add_composite_file(
+            "chromosome_windows.txt", description="Chromosome window positions", is_binary=False, optional=True
+        )
+        self.add_composite_file(
+            "chromosomes.bed", description="Bed file specifying window positions", is_binary=False, optional=True
+        )
+        self.add_composite_file("IDEAS_input_config.txt", description="IDEAS input config", is_binary=False)
+        self.add_composite_file("tmp.tar.gz", description="Compressed archive of compressed bed files", is_binary=True)
 
     def set_meta(self, dataset, **kwd):
         super().set_meta(dataset, **kwd)
@@ -553,34 +582,35 @@ class IdeasPre(Html):
         self.regenerate_primary_file(dataset)
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head></head><body>']
-        rval.append('<h3>Files prepared for IDEAS</h3>')
-        rval.append('<ul>')
+        rval = ["<html><head></head><body>"]
+        rval.append("<h3>Files prepared for IDEAS</h3>")
+        rval.append("<ul>")
         for composite_name in self.get_composite_files(dataset=dataset).keys():
             fn = composite_name
             rval.append(f'<li><a href="{fn}>{fn}</a></li>')
-        rval.append('</ul></body></html>\n')
+        rval.append("</ul></body></html>\n")
         return "\n".join(rval)
 
     def regenerate_primary_file(self, dataset):
         # Cannot do this until we are setting metadata.
-        rval = ['<html><head></head><body>']
-        rval.append('<h3>Files prepared for IDEAS</h3>')
-        rval.append('<ul>')
+        rval = ["<html><head></head><body>"]
+        rval.append("<h3>Files prepared for IDEAS</h3>")
+        rval.append("<ul>")
         for fname in os.listdir(dataset.extra_files_path):
             fn = os.path.split(fname)[-1]
             rval.append(f'<li><a href="{fn}">{fn}</a></li>')
-        rval.append('</ul></body></html>')
-        with open(dataset.file_name, 'w') as f:
+        rval.append("</ul></body></html>")
+        with open(dataset.file_name, "w") as f:
             f.write("\n".join(rval))
-            f.write('\n')
+            f.write("\n")
 
 
 class Pheno(Tabular):
     """
     base class for pheno files
     """
-    file_ext = 'pheno'
+
+    file_ext = "pheno"
 
 
 class RexpBase(Html):
@@ -589,31 +619,42 @@ class RexpBase(Html):
     must be constructed with the pheno data in place since that
     goes into the metadata for each instance
     """
+
     MetadataElement(name="columns", default=0, desc="Number of columns", visible=True)
     MetadataElement(name="column_names", default=[], desc="Column names", visible=True)
     MetadataElement(name="pheCols", default=[], desc="Select list for potentially interesting variables", visible=True)
-    MetadataElement(name="base_name",
-                    desc="base name for all transformed versions of this expression dataset", default='rexpression', set_in_upload=True)
-    MetadataElement(name="pheno_path", desc="Path to phenotype data for this experiment", default="rexpression.pheno", visible=True)
-    file_ext = 'rexpbase'
+    MetadataElement(
+        name="base_name",
+        desc="base name for all transformed versions of this expression dataset",
+        default="rexpression",
+        set_in_upload=True,
+    )
+    MetadataElement(
+        name="pheno_path", desc="Path to phenotype data for this experiment", default="rexpression.pheno", visible=True
+    )
+    file_ext = "rexpbase"
     html_table = None
-    composite_type = 'auto_primary_file'
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.pheno', description='Phenodata tab text file',
-                                substitute_name_with_metadata='base_name', is_binary=False)
+        self.add_composite_file(
+            "%s.pheno",
+            description="Phenodata tab text file",
+            substitute_name_with_metadata="base_name",
+            is_binary=False,
+        )
 
     def generate_primary_file(self, dataset=None):
         """
         This is called only at upload to write the html file
         cannot rename the datasets here - they come with the default unfortunately
         """
-        return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
+        return "<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>"
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/html'
+        return "text/html"
 
     def get_phecols(self, phenolist, maxConc=20):
         """
@@ -632,7 +673,7 @@ class RexpBase(Html):
         for nrows, row in enumerate(phenolist):  # construct concordance
             if len(row.strip()) == 0:
                 break
-            row = row.strip().split('\t')
+            row = row.strip().split("\t")
             if nrows == 0:  # set up from header
                 head = row
                 totcols = len(row)
@@ -640,7 +681,10 @@ class RexpBase(Html):
             else:
                 for col, code in enumerate(row):  # keep column order correct
                     if col >= totcols:
-                        gal_Log.warning('### get_phecols error in pheno file - row %d col %d (%s) longer than header %s' % (nrows, col, row, head))
+                        gal_Log.warning(
+                            "### get_phecols error in pheno file - row %d col %d (%s) longer than header %s"
+                            % (nrows, col, row, head)
+                        )
                     else:
                         concordance[col].setdefault(code, 0)  # first one is zero
                         concordance[col][code] += 1
@@ -656,15 +700,15 @@ class RexpBase(Html):
         # now to check for pairs of concordant columns - drop one of these.
         delme = []
         p = phenolist[1:]  # drop header
-        plist = [x.strip().split('\t') for x in p]  # list of lists
+        plist = [x.strip().split("\t") for x in p]  # list of lists
         phe = [[x[i] for i in useCols] for x in plist if len(x) >= totcols]  # strip unused data
         for i in range(0, (nuse - 1)):  # for each interesting column
             for j in range(i + 1, nuse):
                 kdict = {}
                 for row in phe:  # row is a list of lists
-                    k = f'{row[i]}{row[j]}'  # composite key
+                    k = f"{row[i]}{row[j]}"  # composite key
                     kdict[k] = k
-                if (len(kdict.keys()) == len(concordance[useCols[j]])):  # i and j are always matched
+                if len(kdict.keys()) == len(concordance[useCols[j]]):  # i and j are always matched
                     delme.append(j)
         delme = list(set(delme))  # remove dupes
         listCol = []
@@ -682,7 +726,14 @@ class RexpBase(Html):
             res = listCol
             # metadata.pheCols becomes [('bar;22,zot;113','foo'), ...]
         else:
-            res = [('no usable phenotype columns found', [('?', 0), ]), ]
+            res = [
+                (
+                    "no usable phenotype columns found",
+                    [
+                        ("?", 0),
+                    ],
+                ),
+            ]
         return res
 
     def get_pheno(self, dataset):
@@ -695,14 +746,14 @@ class RexpBase(Html):
         """
         p = open(dataset.metadata.pheno_path).readlines()
         if len(p) > 0:  # should only need to fix an R pheno file once
-            head = p[0].strip().split('\t')
-            line1 = p[1].strip().split('\t')
+            head = p[0].strip().split("\t")
+            line1 = p[1].strip().split("\t")
             if len(head) < len(line1):
-                head.insert(0, 'ChipFileName')  # fix R write.table b0rken-ness
-                p[0] = '\t'.join(head)
+                head.insert(0, "ChipFileName")  # fix R write.table b0rken-ness
+                p[0] = "\t".join(head)
         else:
             p = []
-        return '\n'.join(p)
+        return "\n".join(p)
 
     def set_peek(self, dataset, **kwd):
         """
@@ -710,41 +761,43 @@ class RexpBase(Html):
         note that R is weird and does not include the row.name in
         the header. why?"""
         if not dataset.dataset.purged:
-            pp = os.path.join(dataset.extra_files_path, f'{dataset.metadata.base_name}.pheno')
+            pp = os.path.join(dataset.extra_files_path, f"{dataset.metadata.base_name}.pheno")
             try:
                 with open(pp) as f:
                     p = f.readlines()
             except Exception:
-                p = [f'##failed to find {pp}', ]
-            dataset.peek = ''.join(p[:5])
-            dataset.blurb = 'Galaxy Rexpression composite file'
+                p = [
+                    f"##failed to find {pp}",
+                ]
+            dataset.peek = "".join(p[:5])
+            dataset.blurb = "Galaxy Rexpression composite file"
         else:
-            dataset.peek = 'file does not exist\n'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist\n"
+            dataset.blurb = "file purged from disk"
 
     def get_peek(self, dataset):
         """
         expects a .pheno file in the extra_files_dir - ugh
         """
-        pp = os.path.join(dataset.extra_files_path, f'{dataset.metadata.base_name}.pheno')
+        pp = os.path.join(dataset.extra_files_path, f"{dataset.metadata.base_name}.pheno")
         try:
             with open(pp) as f:
                 p = f.readlines()
         except Exception:
-            p = [f'##failed to find {pp}']
-        return ''.join(p[:5])
+            p = [f"##failed to find {pp}"]
+        return "".join(p[:5])
 
     def get_file_peek(self, filename):
         """
         can't really peek at a filename - need the extra_files_path and such?
         """
-        h = '## rexpression get_file_peek: no file found'
+        h = "## rexpression get_file_peek: no file found"
         try:
             with open(filename) as f:
                 h = f.readlines()
         except Exception:
             pass
-        return ''.join(h[:5])
+        return "".join(h[:5])
 
     def regenerate_primary_file(self, dataset):
         """
@@ -752,14 +805,16 @@ class RexpBase(Html):
         """
         bn = dataset.metadata.base_name
         flist = os.listdir(dataset.extra_files_path)
-        rval = [f'<html><head><title>Files for Composite Dataset {bn}</title></head><p/>Comprises the following files:<p/><ul>']
+        rval = [
+            f"<html><head><title>Files for Composite Dataset {bn}</title></head><p/>Comprises the following files:<p/><ul>"
+        ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
             rval.append(f'<li><a href="{sfname}">{sfname}</a>')
-        rval.append('</ul></html>')
-        with open(dataset.file_name, 'w') as f:
+        rval.append("</ul></html>")
+        with open(dataset.file_name, "w") as f:
             f.write("\n".join(rval))
-            f.write('\n')
+            f.write("\n")
 
     def init_meta(self, dataset, copy_from=None):
         if copy_from:
@@ -776,7 +831,7 @@ class RexpBase(Html):
             flist = os.listdir(dataset.extra_files_path)
         except Exception:
             if verbose:
-                gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
+                gal_Log.debug("@@@rexpression set_meta failed - no dataset?")
             return False
         bn = dataset.metadata.base_name
         if not bn:
@@ -785,9 +840,9 @@ class RexpBase(Html):
                 bn = n
                 dataset.metadata.base_name = bn
         if not bn:
-            bn = '?'
+            bn = "?"
             dataset.metadata.base_name = bn
-        pn = f'{bn}.pheno'
+        pn = f"{bn}.pheno"
         pp = os.path.join(dataset.extra_files_path, pn)
         dataset.metadata.pheno_path = pp
         try:
@@ -797,45 +852,49 @@ class RexpBase(Html):
             pf = None
         if pf:
             h = pf[0].strip()
-            h = h.split('\t')  # hope is header
+            h = h.split("\t")  # hope is header
             h = [escape(x) for x in h]
             dataset.metadata.column_names = h
             dataset.metadata.columns = len(h)
-            dataset.peek = ''.join(pf[:5])
+            dataset.peek = "".join(pf[:5])
         else:
             dataset.metadata.column_names = []
             dataset.metadata.columns = 0
-            dataset.peek = 'No pheno file found'
+            dataset.peek = "No pheno file found"
         if pf and len(pf) > 1:
             dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
         else:
-            dataset.metadata.pheCols = [('', 'No useable phenotypes found', False), ]
+            dataset.metadata.pheCols = [
+                ("", "No useable phenotypes found", False),
+            ]
         if not dataset.info:
-            dataset.info = 'Galaxy Expression datatype object'
+            dataset.info = "Galaxy Expression datatype object"
         if not dataset.blurb:
-            dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
+            dataset.blurb = "R loadable BioC expression object for the Rexpression Galaxy toolkit"
         return True
 
-    def make_html_table(self, pp='nothing supplied from peek\n'):
+    def make_html_table(self, pp="nothing supplied from peek\n"):
         """
         Create HTML table, used for displaying peek
         """
-        out = ['<table cellspacing="0" cellpadding="3">', ]
+        out = [
+            '<table cellspacing="0" cellpadding="3">',
+        ]
         try:
             # Generate column header
-            p = pp.split('\n')
+            p = pp.split("\n")
             for i, row in enumerate(p):
-                lrow = row.strip().split('\t')
+                lrow = row.strip().split("\t")
                 if i == 0:
-                    orow = [f'<th>{escape(x)}</th>' for x in lrow]
-                    orow.insert(0, '<tr>')
-                    orow.append('</tr>')
+                    orow = [f"<th>{escape(x)}</th>" for x in lrow]
+                    orow.insert(0, "<tr>")
+                    orow.append("</tr>")
                 else:
-                    orow = [f'<td>{escape(x)}</td>' for x in lrow]
-                    orow.insert(0, '<tr>')
-                    orow.append('</tr>')
-                out.append(''.join(orow))
-            out.append('</table>')
+                    orow = [f"<td>{escape(x)}</td>" for x in lrow]
+                    orow.insert(0, "<tr>")
+                    orow.append("</tr>")
+                out.append("".join(orow))
+            out.append("</table>")
             out = "\n".join(out)
         except Exception as exc:
             out = f"Can't create html table {unicodify(exc)}"
@@ -858,44 +917,58 @@ class Affybatch(RexpBase):
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.affybatch',
-                                description='AffyBatch R object saved to file',
-                                substitute_name_with_metadata='base_name', is_binary=True)
+        self.add_composite_file(
+            "%s.affybatch",
+            description="AffyBatch R object saved to file",
+            substitute_name_with_metadata="base_name",
+            is_binary=True,
+        )
 
 
 class Eset(RexpBase):
     """
     derived class for BioC data structures in Galaxy
     """
+
     file_ext = "eset"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.eset',
-                                description='ESet R object saved to file',
-                                substitute_name_with_metadata='base_name', is_binary=True)
+        self.add_composite_file(
+            "%s.eset",
+            description="ESet R object saved to file",
+            substitute_name_with_metadata="base_name",
+            is_binary=True,
+        )
 
 
 class MAlist(RexpBase):
     """
     derived class for BioC data structures in Galaxy
     """
+
     file_ext = "malist"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.malist',
-                                description='MAlist R object saved to file',
-                                substitute_name_with_metadata='base_name', is_binary=True)
+        self.add_composite_file(
+            "%s.malist",
+            description="MAlist R object saved to file",
+            substitute_name_with_metadata="base_name",
+            is_binary=True,
+        )
 
 
 class LinkageStudies(Text):
     """
     superclass for classical linkage analysis suites
     """
+
     test_files = [
-        'linkstudies.allegro_fparam', 'linkstudies.alohomora_gts',
-        'linkstudies.linkage_datain', 'linkstudies.linkage_map'
+        "linkstudies.allegro_fparam",
+        "linkstudies.alohomora_gts",
+        "linkstudies.linkage_datain",
+        "linkstudies.linkage_map",
     ]
 
     def __init__(self, **kwd):
@@ -909,13 +982,14 @@ class GenotypeMatrix(LinkageStudies):
     Sample matrix of genotypes
     - GTs as columns
     """
+
     file_ext = "alohomora_gts"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
 
     def header_check(self, fio):
-        header_elems = fio.readline().split('\t')
+        header_elems = fio.readline().split("\t")
 
         if header_elems[0] != "Name":
             return False
@@ -957,7 +1031,7 @@ class GenotypeMatrix(LinkageStudies):
             if lcount > self.max_lines:
                 return True
 
-            tokens = line.split('\t')
+            tokens = line.split("\t")
 
             if num_cols == -1:
                 num_cols = len(tokens)
@@ -977,6 +1051,7 @@ class MarkerMap(LinkageStudies):
 
     chrom, genetic pos, markername, physical pos, Nr
     """
+
     file_ext = "linkage_map"
 
     def header_check(self, fio):
@@ -1023,7 +1098,7 @@ class MarkerMap(LinkageStudies):
                 try:
                     int(chrm)
                 except ValueError:
-                    if not chrm.lower()[0] in ('x', 'y', 'm'):
+                    if not chrm.lower()[0] in ("x", "y", "m"):
                         return False
 
             except ValueError:
@@ -1038,6 +1113,7 @@ class DataIn(LinkageStudies):
     Common linkage input file for intermarker distances
     and recombination rates
     """
+
     file_ext = "linkage_datain"
 
     def __init__(self, **kwd):
@@ -1108,13 +1184,12 @@ class AllegroLOD(LinkageStudies):
     """
     Allegro output format for LOD scores
     """
+
     file_ext = "allegro_fparam"
 
     def header_check(self, fio):
         header = fio.readline().splitlines()[0].split()
-        if len(header) == 4 and header == [
-                "family", "location", "LOD", "marker"
-        ]:
+        if len(header) == 4 and header == ["family", "location", "LOD", "marker"]:
             return True
 
         return False
@@ -1163,6 +1238,7 @@ class AllegroLOD(LinkageStudies):
         return True
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/gis.py b/lib/galaxy/datatypes/gis.py
index 02a5f8931dc..040db4495ed 100644
--- a/lib/galaxy/datatypes/gis.py
+++ b/lib/galaxy/datatypes/gis.py
@@ -6,44 +6,76 @@ from galaxy.datatypes.binary import Binary
 
 
 class Shapefile(Binary):
-    """ The Shapefile data format:
-            For more information please see http://en.wikipedia.org/wiki/Shapefile
+    """The Shapefile data format:
+    For more information please see http://en.wikipedia.org/wiki/Shapefile
     """
 
-    composite_type = 'auto_primary_file'
+    composite_type = "auto_primary_file"
     file_ext = "shp"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('shapefile.shp', description='Geometry File (shp)', is_binary=True, optional=False)
-        self.add_composite_file('shapefile.shx', description='Geometry index File (shx)', is_binary=True, optional=False)
-        self.add_composite_file('shapefile.dbf', description='Columnar attributes for each shape (dbf)', is_binary=True, optional=False)
+        self.add_composite_file("shapefile.shp", description="Geometry File (shp)", is_binary=True, optional=False)
+        self.add_composite_file(
+            "shapefile.shx", description="Geometry index File (shx)", is_binary=True, optional=False
+        )
+        self.add_composite_file(
+            "shapefile.dbf", description="Columnar attributes for each shape (dbf)", is_binary=True, optional=False
+        )
         # optional
-        self.add_composite_file('shapefile.prj', description='Projection description (prj)', is_binary=False, optional=True)
-        self.add_composite_file('shapefile.sbn', description='Spatial index of the features (sbn)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.sbx', description='Spatial index of the features (sbx)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.fbn', description='Read only spatial index of the features (fbn)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.fbx', description='Read only spatial index of the features (fbx)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.ain', description='Attribute index of the active fields in a table (ain)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.aih', description='Attribute index of the active fields in a table (aih)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.atx', description='Attribute index for the dbf file (atx)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.ixs', description='Geocoding index (ixs)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.mxs', description='Geocoding index in ODB format (mxs)', is_binary=True, optional=True)
-        self.add_composite_file('shapefile.shp.xml', description='Geospatial metadata in XML format (xml)', is_binary=False, optional=True)
+        self.add_composite_file(
+            "shapefile.prj", description="Projection description (prj)", is_binary=False, optional=True
+        )
+        self.add_composite_file(
+            "shapefile.sbn", description="Spatial index of the features (sbn)", is_binary=True, optional=True
+        )
+        self.add_composite_file(
+            "shapefile.sbx", description="Spatial index of the features (sbx)", is_binary=True, optional=True
+        )
+        self.add_composite_file(
+            "shapefile.fbn", description="Read only spatial index of the features (fbn)", is_binary=True, optional=True
+        )
+        self.add_composite_file(
+            "shapefile.fbx", description="Read only spatial index of the features (fbx)", is_binary=True, optional=True
+        )
+        self.add_composite_file(
+            "shapefile.ain",
+            description="Attribute index of the active fields in a table (ain)",
+            is_binary=True,
+            optional=True,
+        )
+        self.add_composite_file(
+            "shapefile.aih",
+            description="Attribute index of the active fields in a table (aih)",
+            is_binary=True,
+            optional=True,
+        )
+        self.add_composite_file(
+            "shapefile.atx", description="Attribute index for the dbf file (atx)", is_binary=True, optional=True
+        )
+        self.add_composite_file("shapefile.ixs", description="Geocoding index (ixs)", is_binary=True, optional=True)
+        self.add_composite_file(
+            "shapefile.mxs", description="Geocoding index in ODB format (mxs)", is_binary=True, optional=True
+        )
+        self.add_composite_file(
+            "shapefile.shp.xml", description="Geospatial metadata in XML format (xml)", is_binary=False, optional=True
+        )
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"application/binary\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                opt_text = " (optional)"
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"application/binary\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>\n')
+        rval.append("</ul></div></html>\n")
         return "\n".join(rval)
 
     def set_peek(self, dataset):
diff --git a/lib/galaxy/datatypes/goldenpath.py b/lib/galaxy/datatypes/goldenpath.py
index 6f200a57fb4..49dd46cecb0 100755
--- a/lib/galaxy/datatypes/goldenpath.py
+++ b/lib/galaxy/datatypes/goldenpath.py
@@ -16,8 +16,9 @@ from .tabular import Tabular
 @build_sniff_from_prefix
 class GoldenPath(Tabular):
     """Class describing NCBI's Golden Path assembly format"""
-    edam_format = 'format_3693'
-    file_ext = 'agp'
+
+    edam_format = "format_3693"
+    file_ext = "agp"
 
     def set_meta(self, dataset, **kwd):
         # AGPFile reads and validates entire file.
@@ -44,21 +45,40 @@ class GoldenPath(Tabular):
         """
         found_non_comment_lines = False
         try:
-            for line in iter_headers(file_prefix, '\t', comment_designator='#'):
+            for line in iter_headers(file_prefix, "\t", comment_designator="#"):
                 if line:
                     if len(line) != 9:
                         return False
-                    assert line[4] in ['A', 'D', 'F', 'G', 'O', 'P', 'W', 'N', 'U']
+                    assert line[4] in ["A", "D", "F", "G", "O", "P", "W", "N", "U"]
                     ostensible_numbers = line[1:3]
-                    if line[4] in ['U', 'N']:
+                    if line[4] in ["U", "N"]:
                         ostensible_numbers.append(line[5])
-                        assert line[6] in ['scaffold', 'contig', 'centromere', 'short_arm', 'heterochromatin', 'telomere', 'repeat']
-                        assert line[7] in ['yes', 'no']
-                        assert line[8] in ['na', 'paired-ends', 'align_genus', 'align_xgenus', 'align_trnscript', 'within_clone', 'clone_contig', 'map', 'strobe', 'unspecified']
+                        assert line[6] in [
+                            "scaffold",
+                            "contig",
+                            "centromere",
+                            "short_arm",
+                            "heterochromatin",
+                            "telomere",
+                            "repeat",
+                        ]
+                        assert line[7] in ["yes", "no"]
+                        assert line[8] in [
+                            "na",
+                            "paired-ends",
+                            "align_genus",
+                            "align_xgenus",
+                            "align_trnscript",
+                            "within_clone",
+                            "clone_contig",
+                            "map",
+                            "strobe",
+                            "unspecified",
+                        ]
                     else:
                         ostensible_numbers.extend([line[6], line[7]])
-                        assert line[8] in ['+', '-', '?', '0', 'na']
-                    if line[4] == 'U':
+                        assert line[8] in ["+", "-", "?", "0", "na"]
+                    if line[4] == "U":
                         assert int(line[5]) == 100
                     assert all(map(lambda x: str(x).isnumeric() and int(x) > 0, ostensible_numbers))
                     found_non_comment_lines = True
@@ -192,16 +212,16 @@ class AGPFile:
 
     @property
     def num_lines(self):
-        """ Calculate the number of lines in the current state of the AGP file. """
+        """Calculate the number of lines in the current state of the AGP file."""
         return len(self._comment_lines) + sum(obj.num_lines for obj in self._objects)
 
     def iterate_objs(self):
-        """ Iterate over the objects of the AGP file. """
+        """Iterate over the objects of the AGP file."""
         for obj in self._objects:
             yield obj
 
     def iterate_lines(self):
-        """ Iterate over the non-comment lines of AGP file. """
+        """Iterate over the non-comment lines of AGP file."""
         for obj in self.iterate_objs():
             for j in obj.iterate_lines():
                 yield j
@@ -271,7 +291,11 @@ class AGPObject:
         # Check that the object intervals are sequential
         if self.obj_intervals:
             if self.obj_intervals[-1][1] != agp_line.obj_beg - 1:
-                raise AGPError(self.fname, agp_line.line_number, f"some positions in {agp_line.obj} are not accounted for or overlapping")
+                raise AGPError(
+                    self.fname,
+                    agp_line.line_number,
+                    f"some positions in {agp_line.obj} are not accounted for or overlapping",
+                )
 
         self.previous_pid = agp_line.pid
         self.obj_intervals.append((agp_line.obj_beg - 1, agp_line.obj_end))
@@ -312,27 +336,29 @@ class AGPLine(object, metaclass=abc.ABCMeta):
 
     @abc.abstractmethod
     def __str__(self):
-        """ Return the tab delimited AGP line"""
+        """Return the tab delimited AGP line"""
         pass
 
     @abc.abstractmethod
     def __iter__(self):
-        """ Return the AGP line's iterator"""
+        """Return the AGP line's iterator"""
         pass
 
     @abc.abstractmethod
     def _validate_numerics(self):
-        """ Ensure all numeric fields and positive integers. """
+        """Ensure all numeric fields and positive integers."""
         pass
 
     @abc.abstractmethod
     def _validate_strings(self):
-        """ Ensure all text fields are strings. """
+        """Ensure all text fields are strings."""
         pass
 
     def _validate_obj_coords(self):
         if self.obj_beg > self.obj_end:
-            raise AGPError(self.fname, self.line_number, f"object_beg ({self.obj_beg}) must be <= object_end ({self.obj_end})")
+            raise AGPError(
+                self.fname, self.line_number, f"object_beg ({self.obj_beg}) must be <= object_end ({self.obj_end})"
+            )
 
     def _validate_component_type(self):
         if self.comp_type not in self.allowed_comp_types:
@@ -340,7 +366,7 @@ class AGPLine(object, metaclass=abc.ABCMeta):
 
     @abc.abstractmethod
     def _validate_line(self):
-        """ Final remaining validations specific to the gap or sequence AGP lines. """
+        """Final remaining validations specific to the gap or sequence AGP lines."""
         pass
 
 
@@ -353,7 +379,9 @@ class AGPSeqLine(AGPLine):
     allowed_comp_types = {"A", "D", "F", "G", "O", "P", "W"}
     allowed_orientations = {"+", "-", "?", "0", "na"}
 
-    def __init__(self, fname, line_number, obj, obj_beg, obj_end, pid, comp_type, comp, comp_beg, comp_end, orientation):
+    def __init__(
+        self, fname, line_number, obj, obj_beg, obj_end, pid, comp_type, comp, comp_beg, comp_end, orientation
+    ):
         self.comp = comp
         self.comp_beg = comp_beg
         self.comp_end = comp_end
@@ -363,28 +391,32 @@ class AGPSeqLine(AGPLine):
         super(AGPSeqLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
 
         self.is_gap = False
-        self.seqdict = dict(obj=str(self.obj),
-                            obj_beg=int(self.obj_beg),
-                            obj_end=int(self.obj_end),
-                            pid=int(self.pid),
-                            comp_type=str(self.comp_type),
-                            comp=str(self.comp),
-                            comp_beg=int(self.comp_beg),
-                            comp_end=int(self.comp_end),
-                            orientation=str(self.orientation))
+        self.seqdict = dict(
+            obj=str(self.obj),
+            obj_beg=int(self.obj_beg),
+            obj_end=int(self.obj_end),
+            pid=int(self.pid),
+            comp_type=str(self.comp_type),
+            comp=str(self.comp),
+            comp_beg=int(self.comp_beg),
+            comp_end=int(self.comp_end),
+            orientation=str(self.orientation),
+        )
 
     def __str__(self):
-        return "\t".join([
-            self.obj,
-            str(self.obj_beg),
-            str(self.obj_end),
-            str(self.pid),
-            self.comp_type,
-            self.comp,
-            str(self.comp_beg),
-            str(self.comp_end),
-            self.orientation
-        ])
+        return "\t".join(
+            [
+                self.obj,
+                str(self.obj_beg),
+                str(self.obj_end),
+                str(self.pid),
+                self.comp_type,
+                self.comp,
+                str(self.comp_beg),
+                str(self.comp_end),
+                self.orientation,
+            ]
+        )
 
     def __iter__(self):
         for key in self.seqdict:
@@ -403,21 +435,23 @@ class AGPSeqLine(AGPLine):
             raise AGPError(self.fname, self.line_number, "encountered an invalid non-integer numeric AGP field")
 
         # Ensure that all numeric values are positive
-        if not all([
-            self.obj_beg > 0,
-            self.obj_end > 0,
-            self.pid > 0,
-            self.comp_beg > 0,
-            self.comp_end > 0
-        ]):
+        if not all([self.obj_beg > 0, self.obj_end > 0, self.pid > 0, self.comp_beg > 0, self.comp_end > 0]):
             raise AGPError(self.fname, self.line_number, "encountered an invalid zero or negative numeric AGP field.")
 
         # Check the coordinates
         if self.comp_beg > self.comp_end:
-            raise AGPError(self.fname, self.line_number, f"component_beg ({self.comp_beg}) must be <= component_end ({self.comp_end})")
+            raise AGPError(
+                self.fname,
+                self.line_number,
+                f"component_beg ({self.comp_beg}) must be <= component_end ({self.comp_end})",
+            )
 
         if self.obj_end - (self.obj_beg - 1) != self.comp_end - (self.comp_beg - 1):
-            raise AGPError(self.fname, self.line_number, f"object coordinates ({self.obj_beg}, {self.obj_end}) and component coordinates ({self.comp_beg}, {self.comp_end}) do not have the same length")
+            raise AGPError(
+                self.fname,
+                self.line_number,
+                f"object coordinates ({self.obj_beg}, {self.obj_end}) and component coordinates ({self.comp_beg}, {self.comp_end}) do not have the same length",
+            )
 
     def _validate_strings(self):
         try:
@@ -442,15 +476,33 @@ class AGPGapLine(AGPLine):
     allowed_comp_types = {"N", "U"}
     allowed_linkage_types = {"yes", "no"}
     allowed_gap_types = {
-        "scaffold", "contig", "centromere", "short_arm", "heterochromatin", "telomere", "repeat", "contamination"
+        "scaffold",
+        "contig",
+        "centromere",
+        "short_arm",
+        "heterochromatin",
+        "telomere",
+        "repeat",
+        "contamination",
     }
     allowed_evidence_types = {
-        "na", "paired-ends", "align_genus", "align_xgenus",
-        "align_trnscpt", "within_clone", "clone_contig", "map",
-        "pcr", "proximity_ligation", "strobe", "unspecified"
+        "na",
+        "paired-ends",
+        "align_genus",
+        "align_xgenus",
+        "align_trnscpt",
+        "within_clone",
+        "clone_contig",
+        "map",
+        "pcr",
+        "proximity_ligation",
+        "strobe",
+        "unspecified",
     }
 
-    def __init__(self, fname, line_number, obj, obj_beg, obj_end, pid, comp_type, gap_len, gap_type, linkage, linkage_evidence):
+    def __init__(
+        self, fname, line_number, obj, obj_beg, obj_end, pid, comp_type, gap_len, gap_type, linkage, linkage_evidence
+    ):
         self.gap_len = gap_len
         self.gap_type = gap_type
         self.linkage = linkage
@@ -460,28 +512,32 @@ class AGPGapLine(AGPLine):
         super(AGPGapLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
 
         self.is_gap = True
-        self.gapdict = dict(obj=str(self.obj),
-                            obj_beg=int(self.obj_beg),
-                            obj_end=int(self.obj_end),
-                            pid=int(self.pid),
-                            comp_type=str(self.comp_type),
-                            gap_len=int(self.gap_len),
-                            gap_type=str(self.gap_type),
-                            linkage=str(self.linkage),
-                            linkage_evidence=str(self.linkage_evidence))
+        self.gapdict = dict(
+            obj=str(self.obj),
+            obj_beg=int(self.obj_beg),
+            obj_end=int(self.obj_end),
+            pid=int(self.pid),
+            comp_type=str(self.comp_type),
+            gap_len=int(self.gap_len),
+            gap_type=str(self.gap_type),
+            linkage=str(self.linkage),
+            linkage_evidence=str(self.linkage_evidence),
+        )
 
     def __str__(self):
-        return "\t".join([
-            self.obj,
-            str(self.obj_beg),
-            str(self.obj_end),
-            str(self.pid),
-            self.comp_type,
-            str(self.gap_len),
-            self.gap_type,
-            self.linkage,
-            self.linkage_evidence
-        ])
+        return "\t".join(
+            [
+                self.obj,
+                str(self.obj_beg),
+                str(self.obj_end),
+                str(self.pid),
+                self.comp_type,
+                str(self.gap_len),
+                self.gap_type,
+                self.linkage,
+                self.linkage_evidence,
+            ]
+        )
 
     def __iter__(self):
         for key in self.gapdict:
@@ -499,17 +555,16 @@ class AGPGapLine(AGPLine):
             raise AGPError(self.fname, self.line_number, "encountered an invalid non-integer numeric AGP field")
 
         # Ensure that all numeric values are positive
-        if not all([
-            self.obj_beg > 0,
-            self.obj_end > 0,
-            self.pid > 0,
-            self.gap_len > 0
-        ]):
+        if not all([self.obj_beg > 0, self.obj_end > 0, self.pid > 0, self.gap_len > 0]):
             raise AGPError(self.fname, self.line_number, "encountered an invalid negative numeric AGP field")
 
         # Make sure the coordinates match
         if self.obj_end - (self.obj_beg - 1) != self.gap_len:
-            raise AGPError(self.fname, self.line_number, f"object coordinates ({self.obj_beg}, {self.obj_end}) and gap length ({self.gap_len}) are not the same length")
+            raise AGPError(
+                self.fname,
+                self.line_number,
+                f"object coordinates ({self.obj_beg}, {self.obj_end}) and gap length ({self.gap_len}) are not the same length",
+            )
 
     def _validate_strings(self):
         try:
@@ -522,9 +577,13 @@ class AGPGapLine(AGPLine):
             raise AGPError(self.fname, self.line_number, "encountered an invalid type for an AGP text field")
 
     def _validate_line(self):
-        """ Validation specific to AGP gap lines. """
+        """Validation specific to AGP gap lines."""
         if self.comp_type == "U" and self.gap_len != 100:
-            raise AGPError(self.fname, self.line_number, f"invalid gap length for component type 'U': {self.gap_len} (should be 100)")
+            raise AGPError(
+                self.fname,
+                self.line_number,
+                f"invalid gap length for component type 'U': {self.gap_len} (should be 100)",
+            )
 
         if self.gap_type not in AGPGapLine.allowed_gap_types:
             raise AGPError(self.fname, self.line_number, f"invalid gap type: {self.gap_type}")
@@ -542,7 +601,11 @@ class AGPGapLine(AGPLine):
                 raise AGPError(self.fname, self.line_number, "invalid 'scaffold' gap without linkage evidence")
 
             if self.linkage_evidence != "na":
-                raise AGPError(self.fname, self.line_number, f"linkage evidence must be 'na' when not asserting linkage. Got {self.linkage_evidence}")
+                raise AGPError(
+                    self.fname,
+                    self.line_number,
+                    f"linkage evidence must be 'na' when not asserting linkage. Got {self.linkage_evidence}",
+                )
         else:
             if "na" in all_evidence:
                 raise AGPError(self.fname, self.line_number, "'na' is invalid linkage evidence when asserting linkage")
diff --git a/lib/galaxy/datatypes/graph.py b/lib/galaxy/datatypes/graph.py
index 94f0156b1f4..7b3f5c97cfb 100644
--- a/lib/galaxy/datatypes/graph.py
+++ b/lib/galaxy/datatypes/graph.py
@@ -8,7 +8,7 @@ from . import (
     data,
     dataproviders,
     tabular,
-    xml
+    xml,
 )
 
 log = logging.getLogger(__name__)
@@ -20,6 +20,7 @@ class Xgmml(xml.GenericXml):
     XGMML graph format
     (http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats).
     """
+
     file_ext = "xgmml"
 
     def set_peek(self, dataset):
@@ -28,10 +29,10 @@ class Xgmml(xml.GenericXml):
         """
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'XGMML data'
+            dataset.blurb = "XGMML data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         """
@@ -45,12 +46,13 @@ class Xgmml(xml.GenericXml):
         Merging multiple XML files is non-trivial and must be done in subclasses.
         """
         if len(split_files) > 1:
-            raise NotImplementedError("Merging multiple XML files is non-trivial "
-                                      + "and must be implemented for each XML type")
+            raise NotImplementedError(
+                "Merging multiple XML files is non-trivial " + "and must be implemented for each XML type"
+            )
         # For one file only, use base class method (move/copy)
         data.Text.merge(split_files, output_file)
 
-    @dataproviders.decorators.dataprovider_factory('node-edge', dataproviders.hierarchy.XMLDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("node-edge", dataproviders.hierarchy.XMLDataProvider.settings)
     def node_edge_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return XGMMLGraphDataProvider(dataset_source, **settings)
@@ -66,6 +68,7 @@ class Sif(tabular.Tabular):
     Second column: relationship type
     Third to Nth column: target ids for link
     """
+
     file_ext = "sif"
 
     def set_peek(self, dataset):
@@ -74,10 +77,10 @@ class Sif(tabular.Tabular):
         """
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'SIF data'
+            dataset.blurb = "SIF data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         """
@@ -89,7 +92,7 @@ class Sif(tabular.Tabular):
     def merge(split_files, output_file):
         data.Text.merge(split_files, output_file)
 
-    @dataproviders.decorators.dataprovider_factory('node-edge', dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("node-edge", dataproviders.column.ColumnarDataProvider.settings)
     def node_edge_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return SIFGraphDataProvider(dataset_source, **settings)
@@ -113,18 +116,18 @@ class XGMMLGraphDataProvider(dataproviders.hierarchy.XMLDataProvider):
 
         parent_gen = super().__iter__()
         for graph_elem in parent_gen:
-            if 'children' not in graph_elem:
+            if "children" not in graph_elem:
                 continue
-            for elem in graph_elem['children']:
+            for elem in graph_elem["children"]:
                 # use endswith to work around Elementtree namespaces
-                if elem['tag'].endswith('node'):
-                    node_id = elem['attrib']['id']
+                if elem["tag"].endswith("node"):
+                    node_id = elem["attrib"]["id"]
                     # pass the entire, parsed xml element as the data
                     graph.add_node(node_id, **elem)
 
-                elif elem['tag'].endswith('edge'):
-                    source_id = elem['attrib']['source']
-                    target_id = elem['attrib']['target']
+                elif elem["tag"].endswith("edge"):
+                    source_id = elem["attrib"]["source"]
+                    target_id = elem["attrib"]["target"]
                     graph.add_edge(source_id, target_id, **elem)
 
         yield graph.as_dict()
diff --git a/lib/galaxy/datatypes/hdf5.py b/lib/galaxy/datatypes/hdf5.py
index 388998bf11e..13a9e57126d 100644
--- a/lib/galaxy/datatypes/hdf5.py
+++ b/lib/galaxy/datatypes/hdf5.py
@@ -28,20 +28,20 @@ class HDF5SummarizedExperiment(Data):
         set_in_upload=True,
     )
 
-    file_ext = 'rdata.se'
-    composite_type = 'auto_primary_file'
+    file_ext = "rdata.se"
+    composite_type = "auto_primary_file"
     allow_datatype_change = False
 
     def __init__(self, **kwd):
         """Construct object from input files."""
         Data.__init__(self, **kwd)
         self.add_composite_file(
-            'se.rds',
+            "se.rds",
             is_binary=True,
             description="Summarized experiment RDS object",
         )
         self.add_composite_file(
-            'assays.h5',
+            "assays.h5",
             is_binary=True,
             description="Summarized experiment data array",
         )
@@ -52,8 +52,7 @@ class HDF5SummarizedExperiment(Data):
 
     def generate_primary_file(self, dataset=None):
         """Generate primary file to represent dataset."""
-        return (
-            f'''
+        return f"""
               <html>
                 <head>
                   <title> Files for Composite Dataset ({self.file_ext})</title>
@@ -66,8 +65,7 @@ class HDF5SummarizedExperiment(Data):
                   <li><a href="array.h5">array.h5</a>
                 </ul>
               </html>
-              '''
-        )
+              """
 
     def sniff(self, filename):
         """Not sure whether this is necessary (or possible) with binaries."""
@@ -75,4 +73,4 @@ class HDF5SummarizedExperiment(Data):
 
     def get_mime(self):
         """Return the mime type of the datatype."""
-        return 'text/html'
+        return "text/html"
diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py
index faaefbc7d39..3ef57bb3620 100644
--- a/lib/galaxy/datatypes/images.py
+++ b/lib/galaxy/datatypes/images.py
@@ -42,9 +42,10 @@ log = logging.getLogger(__name__)
 
 class Image(data.Data):
     """Class describing an image"""
-    edam_data = 'data_2968'
+
+    edam_data = "data_2968"
     edam_format = "format_3547"
-    file_ext = ''
+    file_ext = ""
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -52,11 +53,11 @@ class Image(data.Data):
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = f'Image in {dataset.extension} format'
+            dataset.peek = f"Image in {dataset.extension} format"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         """Determine if the file is in this format"""
@@ -64,7 +65,7 @@ class Image(data.Data):
 
     def handle_dataset_as_image(self, hda):
         dataset = hda.dataset
-        name = hda.name or ''
+        name = hda.name or ""
         with open(dataset.file_name, "rb") as f:
             base64_image_data = base64.b64encode(f.read()).decode("utf-8")
         return f"![{name}](data:image/{self.file_ext};base64,{base64_image_data})"
@@ -76,7 +77,7 @@ class Jpg(Image):
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.image_formats = ['JPEG']
+        self.image_formats = ["JPEG"]
 
 
 class Png(Image):
@@ -91,16 +92,24 @@ class Tiff(Image):
 
 class OMETiff(Tiff):
     file_ext = "ome.tiff"
-    MetadataElement(name="offsets", desc="Offsets File", param=FileParameter, file_ext="json", readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="offsets",
+        desc="Offsets File",
+        param=FileParameter,
+        file_ext="json",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
-        spec_key = 'offsets'
+        spec_key = "offsets"
         offsets_file = dataset.metadata.offsets
         if not offsets_file:
             offsets_file = dataset.metadata.spec[spec_key].param.new_file(dataset=dataset)
         with tifffile.TiffFile(dataset.file_name) as tif:
             offsets = [page.offset for page in tif.pages]
-        with open(offsets_file.file_name, 'w') as f:
+        with open(offsets_file.file_name, "w") as f:
             json.dump(offsets, f)
         dataset.metadata.offsets = offsets_file
 
@@ -203,7 +212,7 @@ class Pdf(Image):
 
     def sniff(self, filename):
         """Determine if the file is in pdf format."""
-        with open(filename, 'rb') as fh:
+        with open(filename, "rb") as fh:
             return fh.read(4) == b"%PDF"
 
 
@@ -242,11 +251,17 @@ class Tck(Binary):
     >>> Tck().sniff( fname )
     False
     """
-    file_ext = 'tck'
+
+    file_ext = "tck"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        format_def = [[b'mrtrix tracks'], [b'datatype: Float32LE', b'datatype: Float32BE', b'datatype: Float64BE', b'datatype: Float64LE'],
-                      [b'count: '], [b'file: .'], [b'END']]
+        format_def = [
+            [b"mrtrix tracks"],
+            [b"datatype: Float32LE", b"datatype: Float32BE", b"datatype: Float64BE", b"datatype: Float64LE"],
+            [b"count: "],
+            [b"file: ."],
+            [b"END"],
+        ]
         matches = 0
 
         for elem in format_def:
@@ -272,40 +287,41 @@ class Trk(Binary):
     >>> Trk().sniff( fname )
     False
     """
-    file_ext = 'trk'
+
+    file_ext = "trk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         # quick check
         header_raw = None
         header_raw = file_prefix.contents_header_bytes[:1000]
 
-        if header_raw[:5] != b'TRACK':
+        if header_raw[:5] != b"TRACK":
             return False
         # detailed check
         header_def = [
-            ('magic', 'S6'),
-            ('dim', 'h', 3),
-            ('voxel_size', 'f4', 3),
-            ('origin', 'f4', 3),
-            ('n_scalars', 'h'),
-            ('scalar_name', 'S20', 10),
-            ('n_properties', 'h'),
-            ('property_name', 'S20', 10),
-            ('vox_to_ras', 'f4', (4, 4)),
-            ('reserved', 'S444'),
-            ('voxel_order', 'S4'),
-            ('pad2', 'S4'),
-            ('image_orientation_patient', 'f4', 6),
-            ('pad1', 'S2'),
-            ('invert_x', 'S1'),
-            ('invert_y', 'S1'),
-            ('invert_z', 'S1'),
-            ('swap_xy', 'S1'),
-            ('swap_yz', 'S1'),
-            ('swap_zx', 'S1'),
-            ('n_count', 'i4'),
-            ('version', 'i4'),
-            ('header_size', 'i4'),
+            ("magic", "S6"),
+            ("dim", "h", 3),
+            ("voxel_size", "f4", 3),
+            ("origin", "f4", 3),
+            ("n_scalars", "h"),
+            ("scalar_name", "S20", 10),
+            ("n_properties", "h"),
+            ("property_name", "S20", 10),
+            ("vox_to_ras", "f4", (4, 4)),
+            ("reserved", "S444"),
+            ("voxel_order", "S4"),
+            ("pad2", "S4"),
+            ("image_orientation_patient", "f4", 6),
+            ("pad1", "S2"),
+            ("invert_x", "S1"),
+            ("invert_y", "S1"),
+            ("invert_z", "S1"),
+            ("swap_xy", "S1"),
+            ("swap_yz", "S1"),
+            ("swap_zx", "S1"),
+            ("n_count", "i4"),
+            ("version", "i4"),
+            ("header_size", "i4"),
         ]
         np_dtype = np.dtype(header_def)
         header: np.ndarray = np.ndarray(shape=(), dtype=np_dtype, buffer=header_raw)
@@ -332,7 +348,8 @@ class Mrc2014(Binary):
     >>> Mrc2014().sniff(fname)
     False
     """
-    file_ext = 'mrc'
+
+    file_ext = "mrc"
 
     def sniff(self, filename):
         # Handle the wierdness of mrcfile:
@@ -350,31 +367,43 @@ class Mrc2014(Binary):
 
 class Gmaj(data.Data):
     """Class describing a GMAJ Applet"""
+
     edam_format = "format_3547"
     file_ext = "gmaj.zip"
     copy_safe_peek = False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            if hasattr(dataset, 'history_id'):
+            if hasattr(dataset, "history_id"):
                 params = {
                     "bundle": f"display?id={dataset.id}&tofile=yes&toext=.zip",
                     "buttonlabel": "Launch GMAJ",
                     "nobutton": "false",
                     "urlpause": "100",
                     "debug": "false",
-                    "posturl": "history_add_to?%s" % "&".join(f"{x[0]}={quote_plus(str(x[1]))}" for x in [('copy_access_from', dataset.id), ('history_id', dataset.history_id), ('ext', 'maf'), ('name', f'GMAJ Output on data {dataset.hid}'), ('info', 'Added by GMAJ'), ('dbkey', dataset.dbkey)])
+                    "posturl": "history_add_to?%s"
+                    % "&".join(
+                        f"{x[0]}={quote_plus(str(x[1]))}"
+                        for x in [
+                            ("copy_access_from", dataset.id),
+                            ("history_id", dataset.history_id),
+                            ("ext", "maf"),
+                            ("name", f"GMAJ Output on data {dataset.hid}"),
+                            ("info", "Added by GMAJ"),
+                            ("dbkey", dataset.dbkey),
+                        ]
+                    ),
                 }
                 class_name = "edu.psu.bx.gmaj.MajApplet.class"
                 archive = "/static/gmaj/gmaj.jar"
                 dataset.peek = create_applet_tag_peek(class_name, archive, params)
-                dataset.blurb = 'GMAJ Multiple Alignment Viewer'
+                dataset.blurb = "GMAJ Multiple Alignment Viewer"
             else:
                 dataset.peek = "After you add this item to your history, you will be able to launch the GMAJ applet."
-                dataset.blurb = 'GMAJ Multiple Alignment Viewer'
+                dataset.blurb = "GMAJ Multiple Alignment Viewer"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -384,7 +413,7 @@ class Gmaj(data.Data):
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/zip'
+        return "application/zip"
 
     def sniff(self, filename):
         """
@@ -397,7 +426,7 @@ class Gmaj(data.Data):
         contains_gmaj_file = False
         with zipfile.ZipFile(filename, "r") as zip_file:
             for name in zip_file.namelist():
-                if name.split(".")[1].strip().lower() == 'gmaj':
+                if name.split(".")[1].strip().lower() == "gmaj":
                     contains_gmaj_file = True
                     break
         if not contains_gmaj_file:
@@ -407,48 +436,41 @@ class Gmaj(data.Data):
 
 class Analyze75(Binary):
     """
-        Mayo Analyze 7.5 files
-        http://www.imzml.org
+    Mayo Analyze 7.5 files
+    http://www.imzml.org
     """
-    file_ext = 'analyze75'
-    composite_type = 'auto_primary_file'
+
+    file_ext = "analyze75"
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
 
         # The header file provides information about dimensions, identification,
         # and processing history.
-        self.add_composite_file(
-            'hdr',
-            description='The Analyze75 header file.',
-            is_binary=True)
+        self.add_composite_file("hdr", description="The Analyze75 header file.", is_binary=True)
 
         # The image file contains the actual data, whose data type and ordering
         # are described by the header file.
-        self.add_composite_file(
-            'img',
-            description='The Analyze75 image file.',
-            is_binary=True)
+        self.add_composite_file("img", description="The Analyze75 image file.", is_binary=True)
 
-        self.add_composite_file(
-            't2m',
-            description='The Analyze75 t2m file.',
-            optional=True,
-            is_binary=True)
+        self.add_composite_file("t2m", description="The Analyze75 t2m file.", optional=True, is_binary=True)
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Analyze75 Composite Dataset.</title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>Analyze75 Composite Dataset.</title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                opt_text = " (optional)"
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
 
 
@@ -466,11 +488,12 @@ class Nifti1(Binary):
     >>> Nifti1().sniff( fname )
     False
     """
-    file_ext = 'nii1'
+
+    file_ext = "nii1"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         magic = file_prefix.contents_header_bytes[344:348]
-        if magic == b'n+1\0':
+        if magic == b"n+1\0":
             return True
         return False
 
@@ -489,11 +512,12 @@ class Nifti2(Binary):
     >>> Nifti2().sniff( fname )
     False
     """
-    file_ext = 'nii2'
+
+    file_ext = "nii2"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         magic = file_prefix.contents_header_bytes[4:8]
-        if magic in [b'n+2\0', b'ni2\0']:
+        if magic in [b"n+2\0", b"ni2\0"]:
             return True
         return False
 
@@ -501,6 +525,7 @@ class Nifti2(Binary):
 @build_sniff_from_prefix
 class Gifti(GenericXml):
     """Class describing a Gifti format"""
+
     file_ext = "gii"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -528,7 +553,7 @@ class Gifti(GenericXml):
         if line.strip() == '<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/1594/gifti.dtd">':
             return True
         line = handle.readline()
-        if line.strip().startswith('<GIFTI'):
+        if line.strip().startswith("<GIFTI"):
             return True
         return False
 
@@ -538,16 +563,17 @@ class Star(data.Text):
     """Base format class for Relion STAR (Self-defining
     Text Archiving and Retrieval) image files.
     https://relion.readthedocs.io/en/latest/Reference/Conventions.html"""
+
     file_ext = "star"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'Relion STAR data'
+            dataset.blurb = "Relion STAR data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """Each file must have one or more data blocks.
@@ -593,28 +619,31 @@ class Html(HtmlFromText):
 
 class Laj(data.Text):
     """Class describing a LAJ Applet"""
+
     file_ext = "laj"
     copy_safe_peek = False
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            if hasattr(dataset, 'history_id'):
+            if hasattr(dataset, "history_id"):
                 params = {
                     "alignfile1": f"display?id={dataset.id}",
                     "buttonlabel": "Launch LAJ",
                     "title": "LAJ in Galaxy",
-                    "posturl": quote_plus(f"history_add_to?{'&'.join(f'{key}={value}' for key, value in {'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id}.items())}"),
-                    "noseq": "true"
+                    "posturl": quote_plus(
+                        f"history_add_to?{'&'.join(f'{key}={value}' for key, value in {'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id}.items())}"
+                    ),
+                    "noseq": "true",
                 }
                 class_name = "edu.psu.cse.bio.laj.LajApplet.class"
                 archive = "/static/laj/laj.jar"
                 dataset.peek = create_applet_tag_peek(class_name, archive, params)
             else:
                 dataset.peek = "After you add this item to your history, you will be able to launch the LAJ applet."
-                dataset.blurb = 'LAJ Multiple Alignment Viewer'
+                dataset.blurb = "LAJ Multiple Alignment Viewer"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 330e9c473ae..32fa628e87e 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -7,7 +7,10 @@ import sys
 import tempfile
 from urllib.parse import quote_plus
 
-from bx.intervals.io import GenomicIntervalReader, ParseError
+from bx.intervals.io import (
+    GenomicIntervalReader,
+    ParseError,
+)
 
 from galaxy import util
 from galaxy.datatypes import metadata
@@ -17,14 +20,17 @@ from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
     get_headers,
-    iter_headers
+    iter_headers,
 )
 from galaxy.datatypes.tabular import Tabular
-from galaxy.datatypes.util.gff_util import parse_gff3_attributes, parse_gff_attributes
+from galaxy.datatypes.util.gff_util import (
+    parse_gff3_attributes,
+    parse_gff_attributes,
+)
 from galaxy.util import compression_utils
 from . import (
     data,
-    dataproviders
+    dataproviders,
 )
 
 log = logging.getLogger(__name__)
@@ -32,11 +38,21 @@ log = logging.getLogger(__name__)
 # Contains the meta columns and the words that map to it; list aliases on the
 # right side of the : in decreasing order of priority
 alias_spec = {
-    'chromCol': ['chrom', 'CHROMOSOME', 'CHROM', 'Chromosome Name'],
-    'startCol': ['start', 'START', 'chromStart', 'txStart', 'Start Position (bp)'],
-    'endCol': ['end', 'END', 'STOP', 'chromEnd', 'txEnd', 'End Position (bp)'],
-    'strandCol': ['strand', 'STRAND', 'Strand'],
-    'nameCol': ['name', 'NAME', 'Name', 'name2', 'NAME2', 'Name2', 'Ensembl Gene ID', 'Ensembl Transcript ID', 'Ensembl Peptide ID']
+    "chromCol": ["chrom", "CHROMOSOME", "CHROM", "Chromosome Name"],
+    "startCol": ["start", "START", "chromStart", "txStart", "Start Position (bp)"],
+    "endCol": ["end", "END", "STOP", "chromEnd", "txEnd", "End Position (bp)"],
+    "strandCol": ["strand", "STRAND", "Strand"],
+    "nameCol": [
+        "name",
+        "NAME",
+        "Name",
+        "name2",
+        "NAME2",
+        "Name2",
+        "Ensembl Gene ID",
+        "Ensembl Transcript ID",
+        "Ensembl Peptide ID",
+    ],
 }
 
 # a little faster lookup
@@ -56,6 +72,7 @@ VIEWPORT_MAX_READS_PER_LINE = 10
 @build_sniff_from_prefix
 class Interval(Tabular):
     """Tab delimited data containing interval information"""
+
     edam_data = "data_3002"
     edam_format = "format_3475"
     file_ext = "interval"
@@ -66,14 +83,26 @@ class Interval(Tabular):
     MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter)
     MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter)
     MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)
-    MetadataElement(name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0)
-    MetadataElement(name="nameCol", desc="Name/Identifier column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0)
+    MetadataElement(
+        name="strandCol",
+        desc="Strand column (click box & select)",
+        param=metadata.ColumnParameter,
+        optional=True,
+        no_value=0,
+    )
+    MetadataElement(
+        name="nameCol",
+        desc="Name/Identifier column (click box & select)",
+        param=metadata.ColumnParameter,
+        optional=True,
+        no_value=0,
+    )
     MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
 
     def __init__(self, **kwd):
         """Initialize interval datatype, by adding UCSC display apps"""
         Tabular.__init__(self, **kwd)
-        self.add_display_app('ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links')
+        self.add_display_app("ucsc", "display at UCSC", "as_ucsc_display_file", "ucsc_links")
 
     def init_meta(self, dataset, copy_from=None):
         Tabular.init_meta(self, dataset, copy_from=copy_from)
@@ -86,12 +115,12 @@ class Interval(Tabular):
             num_check_lines = 100  # only check up to this many non empty lines
             with compression_utils.get_fileobj(dataset.file_name) as in_fh:
                 for i, line in enumerate(in_fh):
-                    line = line.rstrip('\r\n')
+                    line = line.rstrip("\r\n")
                     if line:
-                        if (first_line_is_header or line[0] == '#'):
+                        if first_line_is_header or line[0] == "#":
                             self.init_meta(dataset)
-                            line = line.strip('#')
-                            elems = line.split('\t')
+                            line = line.strip("#")
+                            elems = line.split("\t")
                             for meta_name, header_list in alias_spec.items():
                                 for header_val in header_list:
                                     if header_val in elems:
@@ -102,19 +131,19 @@ class Interval(Tabular):
                         else:
                             # Header lines in Interval files are optional. For example, BED is Interval but has no header.
                             # We'll make a best guess at the location of the metadata columns.
-                            elems = line.split('\t')
+                            elems = line.split("\t")
                             if len(elems) > 2:
-                                if overwrite or not dataset.metadata.element_is_set('chromCol'):
+                                if overwrite or not dataset.metadata.element_is_set("chromCol"):
                                     dataset.metadata.chromCol = 1
                                 try:
                                     int(elems[1])
-                                    if overwrite or not dataset.metadata.element_is_set('startCol'):
+                                    if overwrite or not dataset.metadata.element_is_set("startCol"):
                                         dataset.metadata.startCol = 2
                                 except Exception:
                                     pass  # Metadata default will be used
                                 try:
                                     int(elems[2])
-                                    if overwrite or not dataset.metadata.element_is_set('endCol'):
+                                    if overwrite or not dataset.metadata.element_is_set("endCol"):
                                         dataset.metadata.endCol = 3
                                 except Exception:
                                     pass  # Metadata default will be used
@@ -127,10 +156,10 @@ class Interval(Tabular):
                                 #        if overwrite or not dataset.metadata.element_is_set( 'nameCol' ):
                                 #            dataset.metadata.nameCol = 4
                                 if len(elems) < 6 or elems[5] not in data.valid_strand:
-                                    if overwrite or not dataset.metadata.element_is_set('strandCol'):
+                                    if overwrite or not dataset.metadata.element_is_set("strandCol"):
                                         dataset.metadata.strandCol = 0
                                 else:
-                                    if overwrite or not dataset.metadata.element_is_set('strandCol'):
+                                    if overwrite or not dataset.metadata.element_is_set("strandCol"):
                                         dataset.metadata.strandCol = 6
                                 break
                             if (i - empty_line_count) > num_check_lines:
@@ -140,13 +169,15 @@ class Interval(Tabular):
 
     def displayable(self, dataset):
         try:
-            return dataset.has_data() \
-                and dataset.state == dataset.states.OK \
-                and dataset.metadata.columns > 0 \
-                and dataset.metadata.data_lines != 0 \
-                and dataset.metadata.chromCol \
-                and dataset.metadata.startCol \
+            return (
+                dataset.has_data()
+                and dataset.state == dataset.states.OK
+                and dataset.metadata.columns > 0
+                and dataset.metadata.data_lines != 0
+                and dataset.metadata.chromCol
+                and dataset.metadata.startCol
                 and dataset.metadata.endCol
+            )
         except Exception:
             return False
 
@@ -172,9 +203,9 @@ class Interval(Tabular):
             with compression_utils.get_fileobj(dataset.file_name) as fh:
                 for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
                     # Skip comment lines
-                    if not line.startswith('#'):
+                    if not line.startswith("#"):
                         try:
-                            fields = line.rstrip().split('\t')
+                            fields = line.rstrip().split("\t")
                             if len(fields) > max_col:
                                 if chrom is None or chrom == fields[chrom_col]:
                                     start = min(start, int(fields[start_col]))
@@ -189,8 +220,10 @@ class Interval(Tabular):
                             pass
                     # Make sure we are at the next new line
                     readline_count = VIEWPORT_MAX_READS_PER_LINE
-                    while line.rstrip('\n\r') == line:
-                        assert readline_count > 0, Exception(f'Viewport readline count exceeded for dataset {dataset.id}.')
+                    while line.rstrip("\n\r") == line:
+                        assert readline_count > 0, Exception(
+                            f"Viewport readline count exceeded for dataset {dataset.id}."
+                        )
                         line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
                         if not line:
                             break  # EOF
@@ -208,8 +241,14 @@ class Interval(Tabular):
 
     def as_ucsc_display_file(self, dataset, **kwd):
         """Returns file contents with only the bed data"""
-        with tempfile.NamedTemporaryFile(delete=False, mode='w') as fh:
-            c, s, e, t, n = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol, dataset.metadata.strandCol or 0, dataset.metadata.nameCol or 0
+        with tempfile.NamedTemporaryFile(delete=False, mode="w") as fh:
+            c, s, e, t, n = (
+                dataset.metadata.chromCol,
+                dataset.metadata.startCol,
+                dataset.metadata.endCol,
+                dataset.metadata.strandCol or 0,
+                dataset.metadata.nameCol or 0,
+            )
             c, s, e, t, n = int(c) - 1, int(s) - 1, int(e) - 1, int(t) - 1, int(n) - 1
             if t >= 0:  # strand column (should) exists
                 for i, elems in enumerate(compression_utils.file_iter(dataset.file_name)):
@@ -219,24 +258,33 @@ class Interval(Tabular):
                         name = elems[n]
                     if t < len(elems):
                         strand = elems[t]
-                    tmp = [elems[c], elems[s], elems[e], name, '0', strand]
-                    fh.write('%s\n' % '\t'.join(tmp))
+                    tmp = [elems[c], elems[s], elems[e], name, "0", strand]
+                    fh.write("%s\n" % "\t".join(tmp))
             elif n >= 0:  # name column (should) exists
                 for i, elems in enumerate(compression_utils.file_iter(dataset.file_name)):
                     name = "region_%i" % i
                     if n >= 0 and n < len(elems):
                         name = elems[n]
                     tmp = [elems[c], elems[s], elems[e], name]
-                    fh.write('%s\n' % '\t'.join(tmp))
+                    fh.write("%s\n" % "\t".join(tmp))
             else:
                 for elems in compression_utils.file_iter(dataset.file_name):
                     tmp = [elems[c], elems[s], elems[e]]
-                    fh.write('%s\n' % '\t'.join(tmp))
-            return compression_utils.get_fileobj(fh.name, mode='rb')
+                    fh.write("%s\n" % "\t".join(tmp))
+            return compression_utils.get_fileobj(fh.name, mode="rb")
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
-        return self.make_html_table(dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'endCol': 'End', 'strandCol': 'Strand', 'nameCol': 'Name'})
+        return self.make_html_table(
+            dataset,
+            column_parameter_alias={
+                "chromCol": "Chrom",
+                "startCol": "Start",
+                "endCol": "End",
+                "strandCol": "Strand",
+                "nameCol": "Name",
+            },
+        )
 
     def ucsc_links(self, dataset, type, app, base_url):
         """
@@ -245,9 +293,11 @@ class Interval(Tabular):
         """
         # Filter UCSC sites to only those that are supported by this build and
         # enabled.
-        valid_sites = [(name, url)
-                       for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey)
-                       if name in app.datatypes_registry.get_display_sites('ucsc')]
+        valid_sites = [
+            (name, url)
+            for name, url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey)
+            if name in app.datatypes_registry.get_display_sites("ucsc")
+        ]
         if not valid_sites:
             return []
         # If there are any valid sites, we need to generate the estimated
@@ -258,27 +308,31 @@ class Interval(Tabular):
         # Accumulate links for valid sites
         ret_val = []
         for site_name, site_url in valid_sites:
-            internal_url = app.url_for(controller='dataset', dataset_id=dataset.id,
-                                       action='display_at', filename='ucsc_' + site_name)
-            display_url = quote_plus("%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
-                                     (base_url, app.url_for(controller='root'), dataset.id, type))
-            redirect_url = quote_plus("%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
-                                      (site_url, dataset.dbkey, chrom, start, stop))
-            link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
+            internal_url = app.url_for(
+                controller="dataset", dataset_id=dataset.id, action="display_at", filename="ucsc_" + site_name
+            )
+            display_url = quote_plus(
+                "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
+                % (base_url, app.url_for(controller="root"), dataset.id, type)
+            )
+            redirect_url = quote_plus(
+                "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop)
+            )
+            link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
             ret_val.append((site_name, link))
         return ret_val
 
     def validate(self, dataset, **kwd):
         """Validate an interval file using the bx GenomicIntervalReader"""
-        c, s, e, t = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol, dataset.metadata.strandCol
+        c, s, e, t = (
+            dataset.metadata.chromCol,
+            dataset.metadata.startCol,
+            dataset.metadata.endCol,
+            dataset.metadata.strandCol,
+        )
         c, s, e, t = int(c) - 1, int(s) - 1, int(e) - 1, int(t) - 1
         with compression_utils.get_fileobj(dataset.file_name, "r") as infile:
-            reader = GenomicIntervalReader(
-                infile,
-                chrom_col=c,
-                start_col=s,
-                end_col=e,
-                strand_col=t)
+            reader = GenomicIntervalReader(infile, chrom_col=c, start_col=s, end_col=e, strand_col=t)
 
             while True:
                 try:
@@ -309,7 +363,7 @@ class Interval(Tabular):
         """
         found_valid_lines = False
         try:
-            headers = iter_headers(file_prefix, '\t', comment_designator='#')
+            headers = iter_headers(file_prefix, "\t", comment_designator="#")
             # If we got here, we already know the file is_column_based and is not bed,
             # so we'll just look for some valid data.
             for hdr in headers:
@@ -329,31 +383,32 @@ class Interval(Tabular):
         return None
 
     # ------------- Dataproviders
-    @dataproviders.decorators.dataprovider_factory('genomic-region',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dataprovider(self, dataset, **settings):
         return dataproviders.dataset.GenomicRegionDataProvider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region-dict',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region-dict", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dict_dataprovider(self, dataset, **settings):
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return self.genomic_region_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('interval',
-                                                   dataproviders.dataset.IntervalDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("interval", dataproviders.dataset.IntervalDataProvider.settings)
     def interval_dataprovider(self, dataset, **settings):
         return dataproviders.dataset.IntervalDataProvider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('interval-dict',
-                                                   dataproviders.dataset.IntervalDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("interval-dict", dataproviders.dataset.IntervalDataProvider.settings)
     def interval_dict_dataprovider(self, dataset, **settings):
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return self.interval_dataprovider(dataset, **settings)
 
 
 class BedGraph(Interval):
     """Tab delimited chrom/start/end/datavalue dataset"""
+
     edam_format = "format_3583"
     file_ext = "bedgraph"
     track_type = "LineTrack"
@@ -361,33 +416,62 @@ class BedGraph(Interval):
 
     def as_ucsc_display_file(self, dataset, **kwd):
         """
-            Returns file contents as is with no modifications.
-            TODO: this is a functional stub and will need to be enhanced moving forward to provide additional support for bedgraph.
+        Returns file contents as is with no modifications.
+        TODO: this is a functional stub and will need to be enhanced moving forward to provide additional support for bedgraph.
         """
-        return open(dataset.file_name, 'rb')
+        return open(dataset.file_name, "rb")
 
     def get_estimated_display_viewport(self, dataset, chrom_col=0, start_col=1, end_col=2):
         """
-            Set viewport based on dataset's first 100 lines.
+        Set viewport based on dataset's first 100 lines.
         """
-        return Interval.get_estimated_display_viewport(self, dataset, chrom_col=chrom_col, start_col=start_col, end_col=end_col)
+        return Interval.get_estimated_display_viewport(
+            self, dataset, chrom_col=chrom_col, start_col=start_col, end_col=end_col
+        )
 
 
 class Bed(Interval):
     """Tab delimited data in BED format"""
+
     edam_format = "format_3003"
     file_ext = "bed"
     data_sources = {"data": "tabix", "index": "bigwig", "feature_search": "fli"}
     track_type = Interval.track_type
 
-    column_names = ['Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'ThickStart', 'ThickEnd', 'ItemRGB', 'BlockCount', 'BlockSizes', 'BlockStarts']
+    column_names = [
+        "Chrom",
+        "Start",
+        "End",
+        "Name",
+        "Score",
+        "Strand",
+        "ThickStart",
+        "ThickEnd",
+        "ItemRGB",
+        "BlockCount",
+        "BlockSizes",
+        "BlockStarts",
+    ]
 
     MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter)
     MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter)
     MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)
-    MetadataElement(name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0)
+    MetadataElement(
+        name="strandCol",
+        desc="Strand column (click box & select)",
+        param=metadata.ColumnParameter,
+        optional=True,
+        no_value=0,
+    )
     MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="viz_filter_cols", desc="Score column for visualization", default=[4], param=metadata.ColumnParameter, optional=True, multiple=True)
+    MetadataElement(
+        name="viz_filter_cols",
+        desc="Score column for visualization",
+        default=[4],
+        param=metadata.ColumnParameter,
+        optional=True,
+        multiple=True,
+    )
     # do we need to repeat these? they are the same as should be inherited from interval type
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -395,18 +479,18 @@ class Bed(Interval):
         if dataset.has_data():
             i = 0
             for i, line in enumerate(open(dataset.file_name)):  # noqa: B007
-                line = line.rstrip('\r\n')
-                if line and not line.startswith('#'):
-                    elems = line.split('\t')
+                line = line.rstrip("\r\n")
+                if line and not line.startswith("#"):
+                    elems = line.split("\t")
                     if len(elems) > 2:
                         if len(elems) > 3:
-                            if overwrite or not dataset.metadata.element_is_set('nameCol'):
+                            if overwrite or not dataset.metadata.element_is_set("nameCol"):
                                 dataset.metadata.nameCol = 4
                         if len(elems) < 6:
-                            if overwrite or not dataset.metadata.element_is_set('strandCol'):
+                            if overwrite or not dataset.metadata.element_is_set("strandCol"):
                                 dataset.metadata.strandCol = 0
                         else:
-                            if overwrite or not dataset.metadata.element_is_set('strandCol'):
+                            if overwrite or not dataset.metadata.element_is_set("strandCol"):
                                 dataset.metadata.strandCol = 6
                         break
             Tabular.set_meta(self, dataset, overwrite=overwrite, skip=i)
@@ -417,7 +501,7 @@ class Bed(Interval):
             line = line.strip()
             if line == "" or line.startswith("#"):
                 continue
-            fields = line.split('\t')
+            fields = line.split("\t")
             """check to see if this file doesn't conform to strict genome browser accepted bed"""
             try:
                 if len(fields) > 12:
@@ -432,11 +516,15 @@ class Bed(Interval):
                             if len(fields) > 9:
                                 int(fields[9])
                                 if len(fields) > 10:
-                                    fields2 = fields[10].rstrip(",").split(",")  # remove trailing comma and split on comma
+                                    fields2 = (
+                                        fields[10].rstrip(",").split(",")
+                                    )  # remove trailing comma and split on comma
                                     for field in fields2:
                                         int(field)
                                     if len(fields) > 11:
-                                        fields2 = fields[11].rstrip(",").split(",")  # remove trailing comma and split on comma
+                                        fields2 = (
+                                            fields[11].rstrip(",").split(",")
+                                        )  # remove trailing comma and split on comma
                                         for field in fields2:
                                             int(field)
             except Exception:
@@ -445,7 +533,7 @@ class Bed(Interval):
             break
 
         try:
-            return open(dataset.file_name, 'rb')
+            return open(dataset.file_name, "rb")
         except Exception:
             return "This item contains no content"
 
@@ -473,12 +561,12 @@ class Bed(Interval):
         >>> Bed().sniff( fname )
         True
         """
-        if not get_headers(file_prefix, '\t', comment_designator='#', count=1):
+        if not get_headers(file_prefix, "\t", comment_designator="#", count=1):
             return False
         try:
             found_valid_lines = False
-            for hdr in iter_headers(file_prefix, '\t', comment_designator='#'):
-                if not hdr or hdr == ['']:
+            for hdr in iter_headers(file_prefix, "\t", comment_designator="#"):
+                if not hdr or hdr == [""]:
                     continue
                 if len(hdr) < 3 or len(hdr) > 12:
                     return False
@@ -517,7 +605,7 @@ class Bed(Interval):
                         int(hdr[8])
                     except Exception:
                         try:
-                            hdr[8].split(',')
+                            hdr[8].split(",")
                         except Exception:
                             return False
                 if len(hdr) > 9:
@@ -530,13 +618,13 @@ class Bed(Interval):
                     # hdr[10] is blockSizes - A comma-separated list of the block sizes.
                     # Sometimes the blosck_sizes and block_starts lists end in extra commas
                     try:
-                        block_sizes = hdr[10].rstrip(',').split(',')
+                        block_sizes = hdr[10].rstrip(",").split(",")
                     except Exception:
                         return False
                 if len(hdr) > 11:
                     # hdr[11] is blockStarts - A comma-separated list of block starts.
                     try:
-                        block_starts = hdr[11].rstrip(',').split(',')
+                        block_starts = hdr[11].rstrip(",").split(",")
                     except Exception:
                         return False
                     if len(block_sizes) != block_count or len(block_starts) != block_count:
@@ -549,13 +637,41 @@ class Bed(Interval):
 
 class ProBed(Bed):
     """Tab delimited data in proBED format - adaptation of BED for proteomics data."""
+
     edam_format = "format_3827"
     file_ext = "probed"
-    column_names = ['Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'ThickStart', 'ThickEnd', 'ItemRGB', 'BlockCount', 'BlockSizes', 'BlockStarts', 'ProteinAccession', 'PeptideSequence', 'Uniqueness', 'GenomeReferenceVersion', 'PsmScore', 'Fdr', 'Modifications', 'Charge', 'ExpMassToCharge', 'CalcMassToCharge', 'PsmRank', 'DatasetID', 'Uri']
+    column_names = [
+        "Chrom",
+        "Start",
+        "End",
+        "Name",
+        "Score",
+        "Strand",
+        "ThickStart",
+        "ThickEnd",
+        "ItemRGB",
+        "BlockCount",
+        "BlockSizes",
+        "BlockStarts",
+        "ProteinAccession",
+        "PeptideSequence",
+        "Uniqueness",
+        "GenomeReferenceVersion",
+        "PsmScore",
+        "Fdr",
+        "Modifications",
+        "Charge",
+        "ExpMassToCharge",
+        "CalcMassToCharge",
+        "PsmRank",
+        "DatasetID",
+        "Uri",
+    ]
 
 
 class BedStrict(Bed):
     """Tab delimited data in strict BED format - no non-standard columns allowed"""
+
     edam_format = "format_3584"
     file_ext = "bedstrict"
 
@@ -564,10 +680,26 @@ class BedStrict(Bed):
 
     # Read only metadata elements
     MetadataElement(name="chromCol", default=1, desc="Chrom column", readonly=True, param=metadata.MetadataParameter)
-    MetadataElement(name="startCol", default=2, desc="Start column", readonly=True, param=metadata.MetadataParameter)  # TODO: start and end should be able to be set to these or the proper thick[start/end]?
+    MetadataElement(
+        name="startCol", default=2, desc="Start column", readonly=True, param=metadata.MetadataParameter
+    )  # TODO: start and end should be able to be set to these or the proper thick[start/end]?
     MetadataElement(name="endCol", default=3, desc="End column", readonly=True, param=metadata.MetadataParameter)
-    MetadataElement(name="strandCol", desc="Strand column (click box & select)", readonly=True, param=metadata.MetadataParameter, no_value=0, optional=True)
-    MetadataElement(name="nameCol", desc="Name/Identifier column (click box & select)", readonly=True, param=metadata.MetadataParameter, no_value=0, optional=True)
+    MetadataElement(
+        name="strandCol",
+        desc="Strand column (click box & select)",
+        readonly=True,
+        param=metadata.MetadataParameter,
+        no_value=0,
+        optional=True,
+    )
+    MetadataElement(
+        name="nameCol",
+        desc="Name/Identifier column (click box & select)",
+        readonly=True,
+        param=metadata.MetadataParameter,
+        no_value=0,
+        optional=True,
+    )
     MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
 
     def __init__(self, **kwd):
@@ -587,12 +719,14 @@ class BedStrict(Bed):
 
 class Bed6(BedStrict):
     """Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6"""
+
     edam_format = "format_3585"
     file_ext = "bed6"
 
 
 class Bed12(BedStrict):
     """Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12"""
+
     edam_format = "format_3586"
     file_ext = "bed12"
 
@@ -606,9 +740,11 @@ class _RemoteCallMixin:
         """
         internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
         base_url = app.config.get("display_at_callback", base_url)
-        display_url = quote_plus("%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
-                                 (base_url, app.url_for(controller='root'), dataset.id, type))
-        link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
+        display_url = quote_plus(
+            "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
+            % (base_url, app.url_for(controller="root"), dataset.id, type)
+        )
+        link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
         return link
 
 
@@ -616,26 +752,41 @@ class _RemoteCallMixin:
 @build_sniff_from_prefix
 class Gff(Tabular, _RemoteCallMixin):
     """Tab delimited data in Gff format"""
+
     edam_data = "data_1255"
     edam_format = "format_2305"
     file_ext = "gff"
-    valid_gff_frame = ['.', '0', '1', '2']
-    column_names = ['Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group']
+    valid_gff_frame = [".", "0", "1", "2"]
+    column_names = ["Seqname", "Source", "Feature", "Start", "End", "Score", "Strand", "Frame", "Group"]
     data_sources = {"data": "interval_index", "index": "bigwig", "feature_search": "fli"}
     track_type = Interval.track_type
 
     MetadataElement(name="columns", default=9, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=['str', 'str', 'str', 'int', 'int', 'int', 'str', 'str', 'str'],
-                    param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
+    MetadataElement(
+        name="column_types",
+        default=["str", "str", "str", "int", "int", "int", "str", "str", "str"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+    )
 
     MetadataElement(name="attributes", default=0, desc="Number of attributes", readonly=True, visible=False, no_value=0)
-    MetadataElement(name="attribute_types", default={}, desc="Attribute types", param=metadata.DictParameter, readonly=True, visible=False, no_value=[])
+    MetadataElement(
+        name="attribute_types",
+        default={},
+        desc="Attribute types",
+        param=metadata.DictParameter,
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
 
     def __init__(self, **kwd):
         """Initialize datatype, by adding GBrowse display app"""
         Tabular.__init__(self, **kwd)
-        self.add_display_app('ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links')
-        self.add_display_app('gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links')
+        self.add_display_app("ucsc", "display at UCSC", "as_ucsc_display_file", "ucsc_links")
+        self.add_display_app("gbrowse", "display in Gbrowse", "as_gbrowse_display_file", "gbrowse_links")
 
     def set_attribute_metadata(self, dataset):
         """
@@ -648,8 +799,8 @@ class Gff(Tabular, _RemoteCallMixin):
         attribute_types = {}
         with compression_utils.get_fileobj(dataset.file_name) as in_fh:
             for i, line in enumerate(in_fh):
-                if line and not line.startswith('#'):
-                    elems = line.split('\t')
+                if line and not line.startswith("#"):
+                    elems = line.split("\t")
                     if len(elems) == 9:
                         try:
                             # Loop through attributes to set types.
@@ -683,9 +834,9 @@ class Gff(Tabular, _RemoteCallMixin):
         i = 0
         with compression_utils.get_fileobj(dataset.file_name) as in_fh:
             for i, line in enumerate(in_fh):  # noqa: B007
-                line = line.rstrip('\r\n')
-                if line and not line.startswith('#'):
-                    elems = line.split('\t')
+                line = line.rstrip("\r\n")
+                if line and not line.startswith("#"):
+                    elems = line.split("\t")
                     if len(elems) == 9:
                         try:
                             int(elems[3])
@@ -714,8 +865,8 @@ class Gff(Tabular, _RemoteCallMixin):
                 with compression_utils.get_fileobj(dataset.file_name) as fh:
                     for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
                         try:
-                            if line.startswith('##sequence-region'):  # ##sequence-region IV 6000000 6030000
-                                elems = line.rstrip('\n\r').split()
+                            if line.startswith("##sequence-region"):  # ##sequence-region IV 6000000 6030000
+                                elems = line.rstrip("\n\r").split()
                                 if len(elems) > 3:
                                     # line looks like:
                                     # sequence-region   ctg123 1 1497228
@@ -723,13 +874,13 @@ class Gff(Tabular, _RemoteCallMixin):
                                     start = int(elems[2])  # 6000000
                                     stop = int(elems[3])  # 6030000
                                     break  # use location declared in file
-                                elif len(elems) == 2 and elems[1].find('..') > 0:
+                                elif len(elems) == 2 and elems[1].find("..") > 0:
                                     # line looks like this:
                                     # sequence-region X:120000..140000
-                                    elems = elems[1].split(':')
+                                    elems = elems[1].split(":")
                                     seqid = elems[0]
-                                    start = int(elems[1].split('..')[0])
-                                    stop = int(elems[1].split('..')[1])
+                                    start = int(elems[1].split("..")[0])
+                                    stop = int(elems[1].split("..")[1])
                                     break  # use location declared in file
                                 else:
                                     log.debug(f"line ({str(line)}) uses an unsupported ##sequence-region definition.")
@@ -740,9 +891,9 @@ class Gff(Tabular, _RemoteCallMixin):
                                 seqid, startend = pos_info.split(":")
                                 start, stop = map(int, startend.split("-"))
                                 break  # use location declared in file
-                            elif not line.startswith(('#', 'track', 'browser')):
+                            elif not line.startswith(("#", "track", "browser")):
                                 viewport_feature_count -= 1
-                                elems = line.rstrip('\n\r').split('\t')
+                                elems = line.rstrip("\n\r").split("\t")
                                 if len(elems) > 3:
                                     if not seqid:
                                         # We can only set the viewport for a single chromosome
@@ -756,8 +907,10 @@ class Gff(Tabular, _RemoteCallMixin):
                             pass
                         # make sure we are at the next new line
                         readline_count = VIEWPORT_MAX_READS_PER_LINE
-                        while line.rstrip('\n\r') == line:
-                            assert readline_count > 0, Exception(f'Viewport readline count exceeded for dataset {dataset.id}.')
+                        while line.rstrip("\n\r") == line:
+                            assert readline_count > 0, Exception(
+                                f"Viewport readline count exceeded for dataset {dataset.id}."
+                            )
                             line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
                             if not line:
                                 break  # EOF
@@ -769,18 +922,18 @@ class Gff(Tabular, _RemoteCallMixin):
                     if seqid is not None:
                         return (seqid, str(start), str(stop))  # Necessary to return strings?
             except Exception:
-                log.exception('Unexpected error')
+                log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
     def ucsc_links(self, dataset, type, app, base_url):
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
-            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
-                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     redirect_url = quote_plus(
-                        "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
-                        (site_url, dataset.dbkey, seqid, start, stop))
+                        "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, seqid, start, stop)
+                    )
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
@@ -789,9 +942,9 @@ class Gff(Tabular, _RemoteCallMixin):
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
-            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey):
-                if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
-                    if seqid.startswith('chr') and len(seqid) > 3:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("gbrowse", dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites("gbrowse"):
+                    if seqid.startswith("chr") and len(seqid) > 3:
                         seqid = seqid[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={seqid}:{start}..{stop}&eurl=%s")
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
@@ -814,18 +967,18 @@ class Gff(Tabular, _RemoteCallMixin):
         >>> Gff().sniff( fname )
         True
         """
-        if len(get_headers(file_prefix, '\t', count=2)) < 2:
+        if len(get_headers(file_prefix, "\t", count=2)) < 2:
             return False
         try:
             found_valid_lines = False
-            for hdr in iter_headers(file_prefix, '\t'):
-                if not hdr or hdr == ['']:
+            for hdr in iter_headers(file_prefix, "\t"):
+                if not hdr or hdr == [""]:
                     continue
                 hdr0_parts = hdr[0].split()
-                if hdr0_parts[0] == '##gff-version':
-                    return hdr0_parts[1].startswith('2')
+                if hdr0_parts[0] == "##gff-version":
+                    return hdr0_parts[1].startswith("2")
                 # The gff-version header comment may have been stripped, so inspect the data
-                if hdr[0].startswith('#'):
+                if hdr[0].startswith("#"):
                     continue
                 if len(hdr) != 9:
                     return False
@@ -834,7 +987,7 @@ class Gff(Tabular, _RemoteCallMixin):
                     int(hdr[4])
                 except Exception:
                     return False
-                if hdr[5] != '.':
+                if hdr[5] != ".":
                     try:
                         float(hdr[5])
                     except Exception:
@@ -850,40 +1003,47 @@ class Gff(Tabular, _RemoteCallMixin):
 
     # ------------- Dataproviders
     # redefine bc super is Tabular
-    @dataproviders.decorators.dataprovider_factory('genomic-region',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dataprovider(self, dataset, **settings):
         return dataproviders.dataset.GenomicRegionDataProvider(dataset, 0, 3, 4, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region-dict',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region-dict", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dict_dataprovider(self, dataset, **settings):
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return self.genomic_region_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('interval',
-                                                   dataproviders.dataset.IntervalDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("interval", dataproviders.dataset.IntervalDataProvider.settings)
     def interval_dataprovider(self, dataset, **settings):
         return dataproviders.dataset.IntervalDataProvider(dataset, 0, 3, 4, 6, 2, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('interval-dict',
-                                                   dataproviders.dataset.IntervalDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("interval-dict", dataproviders.dataset.IntervalDataProvider.settings)
     def interval_dict_dataprovider(self, dataset, **settings):
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return self.interval_dataprovider(dataset, **settings)
 
 
 class Gff3(Gff):
     """Tab delimited data in Gff3 format"""
+
     edam_format = "format_1975"
     file_ext = "gff3"
-    valid_gff3_strand = ['+', '-', '.', '?']
+    valid_gff3_strand = ["+", "-", ".", "?"]
     valid_gff3_phase = Gff.valid_gff_frame
-    column_names = ['Seqid', 'Source', 'Type', 'Start', 'End', 'Score', 'Strand', 'Phase', 'Attributes']
+    column_names = ["Seqid", "Source", "Type", "Start", "End", "Score", "Strand", "Phase", "Attributes"]
     track_type = Interval.track_type
 
-    MetadataElement(name="column_types", default=['str', 'str', 'str', 'int', 'int', 'float', 'str', 'int', 'list'],
-                    param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
+    MetadataElement(
+        name="column_types",
+        default=["str", "str", "str", "int", "int", "float", "str", "int", "list"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+    )
 
     def __init__(self, **kwd):
         """Initialize datatype, by adding GBrowse display app"""
@@ -894,9 +1054,9 @@ class Gff3(Gff):
         i = 0
         with compression_utils.get_fileobj(dataset.file_name) as in_fh:
             for i, line in enumerate(in_fh):  # noqa: B007
-                line = line.rstrip('\r\n')
-                if line and not line.startswith('#'):
-                    elems = line.split('\t')
+                line = line.rstrip("\r\n")
+                if line and not line.startswith("#"):
+                    elems = line.split("\t")
                     valid_start = False
                     valid_end = False
                     if len(elems) == 9:
@@ -904,17 +1064,23 @@ class Gff3(Gff):
                             start = int(elems[3])
                             valid_start = True
                         except Exception:
-                            if elems[3] == '.':
+                            if elems[3] == ".":
                                 valid_start = True
                         try:
                             end = int(elems[4])
                             valid_end = True
                         except Exception:
-                            if elems[4] == '.':
+                            if elems[4] == ".":
                                 valid_end = True
                         strand = elems[6]
                         phase = elems[7]
-                        if valid_start and valid_end and start < end and strand in self.valid_gff3_strand and phase in self.valid_gff3_phase:
+                        if (
+                            valid_start
+                            and valid_end
+                            and start < end
+                            and strand in self.valid_gff3_strand
+                            and phase in self.valid_gff3_phase
+                        ):
                             break
         Tabular.set_meta(self, dataset, overwrite=overwrite, skip=i)
 
@@ -954,32 +1120,32 @@ class Gff3(Gff):
         >>> Gff3().sniff( fname )
         False
         """
-        if len(get_headers(file_prefix, '\t', count=2)) < 2:
+        if len(get_headers(file_prefix, "\t", count=2)) < 2:
             return False
         try:
             found_valid_lines = False
-            for hdr in iter_headers(file_prefix, '\t'):
-                if not hdr or hdr == ['']:
+            for hdr in iter_headers(file_prefix, "\t"):
+                if not hdr or hdr == [""]:
                     continue
                 hdr0_parts = hdr[0].split()
-                if hdr0_parts[0] == '##gff-version':
-                    return hdr0_parts[1].startswith('3')
+                if hdr0_parts[0] == "##gff-version":
+                    return hdr0_parts[1].startswith("3")
                 # The gff-version header comment may have been stripped, so inspect the data
-                if hdr[0].startswith('#'):
+                if hdr[0].startswith("#"):
                     continue
                 if len(hdr) != 9:
                     return False
                 try:
                     int(hdr[3])
                 except Exception:
-                    if hdr[3] != '.':
+                    if hdr[3] != ".":
                         return False
                 try:
                     int(hdr[4])
                 except Exception:
-                    if hdr[4] != '.':
+                    if hdr[4] != ".":
                         return False
-                if hdr[5] != '.':
+                if hdr[5] != ".":
                     try:
                         float(hdr[5])
                     except Exception:
@@ -997,14 +1163,21 @@ class Gff3(Gff):
 
 class Gtf(Gff):
     """Tab delimited data in Gtf format"""
+
     edam_format = "format_2306"
     file_ext = "gtf"
-    column_names = ['Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Attributes']
+    column_names = ["Seqname", "Source", "Feature", "Start", "End", "Score", "Strand", "Frame", "Attributes"]
     track_type = Interval.track_type
 
     MetadataElement(name="columns", default=9, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=['str', 'str', 'str', 'int', 'int', 'float', 'str', 'int', 'list'],
-                    param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
+    MetadataElement(
+        name="column_types",
+        default=["str", "str", "str", "int", "int", "float", "str", "int", "list"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+    )
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -1034,18 +1207,18 @@ class Gtf(Gff):
         >>> Gtf().sniff( fname )
         True
         """
-        if len(get_headers(file_prefix, '\t', count=2)) < 2:
+        if len(get_headers(file_prefix, "\t", count=2)) < 2:
             return False
         try:
             found_valid_lines = False
-            for hdr in iter_headers(file_prefix, '\t'):
-                if not hdr or hdr == ['']:
+            for hdr in iter_headers(file_prefix, "\t"):
+                if not hdr or hdr == [""]:
                     continue
                 hdr0_parts = hdr[0].split()
-                if hdr0_parts[0] == '##gff-version' and not hdr0_parts[1].startswith('2'):
+                if hdr0_parts[0] == "##gff-version" and not hdr0_parts[1].startswith("2"):
                     return False
                 # The gff-version header comment may have been stripped, so inspect the data
-                if hdr[0].startswith('#'):
+                if hdr[0].startswith("#"):
                     continue
                 if len(hdr) != 9:
                     return False
@@ -1054,7 +1227,7 @@ class Gtf(Gff):
                     int(hdr[4])
                 except Exception:
                     return False
-                if hdr[5] != '.':
+                if hdr[5] != ".":
                     try:
                         float(hdr[5])
                     except Exception:
@@ -1066,7 +1239,7 @@ class Gtf(Gff):
                 # Check attributes for gene_id (transcript_id is also mandatory
                 # but not for genes)
                 attributes = parse_gff_attributes(hdr[8])
-                if 'gene_id' not in attributes:
+                if "gene_id" not in attributes:
                     return False
                 found_valid_lines = True
             return found_valid_lines
@@ -1078,6 +1251,7 @@ class Gtf(Gff):
 @build_sniff_from_prefix
 class Wiggle(Tabular, _RemoteCallMixin):
     """Tab delimited data in wiggle format"""
+
     edam_format = "format_3005"
     file_ext = "wig"
     track_type = "LineTrack"
@@ -1087,8 +1261,8 @@ class Wiggle(Tabular, _RemoteCallMixin):
 
     def __init__(self, **kwd):
         Tabular.__init__(self, **kwd)
-        self.add_display_app('ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links')
-        self.add_display_app('gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links')
+        self.add_display_app("ucsc", "display at UCSC", "as_ucsc_display_file", "ucsc_links")
+        self.add_display_app("gbrowse", "display in Gbrowse", "as_gbrowse_display_file", "gbrowse_links")
 
     def get_estimated_display_viewport(self, dataset):
         """Return a chrom, start, stop tuple for viewing a file."""
@@ -1105,22 +1279,24 @@ class Wiggle(Tabular, _RemoteCallMixin):
                     for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
                         try:
                             if line.startswith("browser"):
-                                chr_info = line.rstrip('\n\r').split()[-1]
+                                chr_info = line.rstrip("\n\r").split()[-1]
                                 chrom, coords = chr_info.split(":")
                                 start, end = map(int, coords.split("-"))
                                 break  # use the browser line
                             # variableStep chrom=chr20
-                            if line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
+                            if line and (
+                                line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")
+                            ):
                                 if chrom is not None:
                                     break  # different chrom or different section of the chrom
-                                chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
-                                if 'span=' in line:
-                                    span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
-                                if 'step=' in line:
-                                    step = int(line.rstrip('\n\r').split("step=")[1].split()[0])
-                                    start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
+                                chrom = line.rstrip("\n\r").split("chrom=")[1].split()[0]
+                                if "span=" in line:
+                                    span = int(line.rstrip("\n\r").split("span=")[1].split()[0])
+                                if "step=" in line:
+                                    step = int(line.rstrip("\n\r").split("step=")[1].split()[0])
+                                    start = int(line.rstrip("\n\r").split("start=")[1].split()[0])
                             else:
-                                fields = line.rstrip('\n\r').split()
+                                fields = line.rstrip("\n\r").split()
                                 if fields:
                                     if step is not None:
                                         if not end:
@@ -1135,8 +1311,10 @@ class Wiggle(Tabular, _RemoteCallMixin):
                             pass
                         # make sure we are at the next new line
                         readline_count = VIEWPORT_MAX_READS_PER_LINE
-                        while line.rstrip('\n\r') == line:
-                            assert readline_count > 0, Exception(f'Viewport readline count exceeded for dataset {dataset.id}.')
+                        while line.rstrip("\n\r") == line:
+                            assert readline_count > 0, Exception(
+                                f"Viewport readline count exceeded for dataset {dataset.id}."
+                            )
                             line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
                             if not line:
                                 break  # EOF
@@ -1148,16 +1326,16 @@ class Wiggle(Tabular, _RemoteCallMixin):
                 if chrom is not None:
                     return (chrom, str(start), str(end))  # Necessary to return strings?
             except Exception:
-                log.exception('Unexpected error')
+                log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
     def gbrowse_links(self, dataset, type, app, base_url):
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
-            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey):
-                if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
-                    if chrom.startswith('chr') and len(chrom) > 3:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("gbrowse", dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites("gbrowse"):
+                    if chrom.startswith("chr") and len(chrom) > 3:
                         chrom = chrom[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={chrom}:{start}..{stop}&eurl=%s")
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
@@ -1168,24 +1346,26 @@ class Wiggle(Tabular, _RemoteCallMixin):
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
-            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
-                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
-                    redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites("ucsc"):
+                    redirect_url = quote_plus(
+                        f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
+                    )
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
-        return self.make_html_table(dataset, skipchars=['track', '#'])
+        return self.make_html_table(dataset, skipchars=["track", "#"])
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         max_data_lines = None
         i = 0
         for i, line in enumerate(open(dataset.file_name)):  # noqa: B007
-            line = line.rstrip('\r\n')
-            if line and not line.startswith('#'):
-                elems = line.split('\t')
+            line = line.rstrip("\r\n")
+            if line and not line.startswith("#"):
+                elems = line.split("\t")
                 try:
                     # variableStep format is nucleotide position\tvalue\n,
                     # fixedStep is value\n
@@ -1229,7 +1409,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
         try:
             headers = iter_headers(file_prefix, None)
             for hdr in headers:
-                if len(hdr) > 1 and hdr[0] == 'track' and hdr[1].startswith('type=wiggle'):
+                if len(hdr) > 1 and hdr[0] == "track" and hdr[1].startswith("type=wiggle"):
                     return True
             return False
         except Exception:
@@ -1245,35 +1425,36 @@ class Wiggle(Tabular, _RemoteCallMixin):
         return resolution
 
     # ------------- Dataproviders
-    @dataproviders.decorators.dataprovider_factory('wiggle', dataproviders.dataset.WiggleDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("wiggle", dataproviders.dataset.WiggleDataProvider.settings)
     def wiggle_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return dataproviders.dataset.WiggleDataProvider(dataset_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('wiggle-dict', dataproviders.dataset.WiggleDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("wiggle-dict", dataproviders.dataset.WiggleDataProvider.settings)
     def wiggle_dict_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return dataproviders.dataset.WiggleDataProvider(dataset_source, **settings)
 
 
 @build_sniff_from_prefix
 class CustomTrack(Tabular):
     """UCSC CustomTrack"""
+
     edam_format = "format_3588"
     file_ext = "customtrack"
 
     def __init__(self, **kwd):
         """Initialize interval datatype, by adding UCSC display app"""
         Tabular.__init__(self, **kwd)
-        self.add_display_app('ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links')
+        self.add_display_app("ucsc", "display at UCSC", "as_ucsc_display_file", "ucsc_links")
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         Tabular.set_meta(self, dataset, overwrite=overwrite, skip=1)
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
-        return self.make_html_table(dataset, skipchars=['track', '#'])
+        return self.make_html_table(dataset, skipchars=["track", "#"])
 
     def get_estimated_display_viewport(self, dataset, chrom_col=None, start_col=None, end_col=None):
         """Return a chrom, start, stop tuple for viewing a file."""
@@ -1287,24 +1468,26 @@ class CustomTrack(Tabular):
             try:
                 with open(dataset.file_name) as fh:
                     for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
-                        if not line.startswith('#'):
+                        if not line.startswith("#"):
                             try:
                                 if variable_step_wig:
                                     fields = line.rstrip().split()
                                     if len(fields) == 2:
                                         start = int(fields[0])
                                         return (chrom, str(start), str(start + span))
-                                elif line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
-                                    chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
-                                    if 'span=' in line:
-                                        span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
-                                    if 'start=' in line:
-                                        start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
+                                elif line and (
+                                    line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")
+                                ):
+                                    chrom = line.rstrip("\n\r").split("chrom=")[1].split()[0]
+                                    if "span=" in line:
+                                        span = int(line.rstrip("\n\r").split("span=")[1].split()[0])
+                                    if "start=" in line:
+                                        start = int(line.rstrip("\n\r").split("start=")[1].split()[0])
                                         return (chrom, str(start), str(start + span))
                                     else:
                                         variable_step_wig = True
                                 else:
-                                    fields = line.rstrip().split('\t')
+                                    fields = line.rstrip().split("\t")
                                     if len(fields) >= 3:
                                         chrom = fields[0]
                                         start = int(fields[1])
@@ -1315,8 +1498,10 @@ class CustomTrack(Tabular):
                                 continue
                         # make sure we are at the next new line
                         readline_count = VIEWPORT_MAX_READS_PER_LINE
-                        while line.rstrip('\n\r') == line:
-                            assert readline_count > 0, Exception(f'Viewport readline count exceeded for dataset {dataset.id}.')
+                        while line.rstrip("\n\r") == line:
+                            assert readline_count > 0, Exception(
+                                f"Viewport readline count exceeded for dataset {dataset.id}."
+                            )
                             line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
                             if not line:
                                 break  # EOF
@@ -1326,19 +1511,24 @@ class CustomTrack(Tabular):
                             # exceeded viewport or total line count to check
                             break
             except Exception:
-                log.exception('Unexpected error')
+                log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
     def ucsc_links(self, dataset, type, app, base_url):
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
-            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
-                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
-                    display_url = quote_plus("%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, app.url_for(controller='root'), dataset.id, type))
-                    redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
-                    link = f'{internal_url}?redirect_url={redirect_url}&display_url={display_url}'
+                    display_url = quote_plus(
+                        "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
+                        % (base_url, app.url_for(controller="root"), dataset.id, type)
+                    )
+                    redirect_url = quote_plus(
+                        f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
+                    )
+                    link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1366,13 +1556,13 @@ class CustomTrack(Tabular):
             if first_line:
                 first_line = False
                 try:
-                    if hdr[0].startswith('track'):
+                    if hdr[0].startswith("track"):
                         color_found = False
                         visibility_found = False
                         for elem in hdr[1:]:
-                            if elem.startswith('color'):
+                            if elem.startswith("color"):
                                 color_found = True
-                            if elem.startswith('visibility'):
+                            if elem.startswith("visibility"):
                                 visibility_found = True
                             if color_found and visibility_found:
                                 break
@@ -1384,7 +1574,7 @@ class CustomTrack(Tabular):
                     return False
             else:
                 try:
-                    if hdr[0] and not hdr[0].startswith('#'):
+                    if hdr[0] and not hdr[0].startswith("#"):
                         if len(hdr) < 3:
                             return False
                         try:
@@ -1399,7 +1589,7 @@ class CustomTrack(Tabular):
 
 
 class ENCODEPeak(Interval):
-    '''
+    """
     Human ENCODE peak format. There are both broad and narrow peak formats.
     Formats are very similar; narrow peak has an additional column, though.
 
@@ -1410,16 +1600,23 @@ class ENCODEPeak(Interval):
     Narrow peak http://genome.ucsc.edu/FAQ/FAQformat#format12 and :
     This format is used to provide called peaks of signal enrichment based on
     pooled, normalized (interpreted) data. It is a BED6+4 format.
-    '''
+    """
+
     edam_format = "format_3612"
     file_ext = "encodepeak"
-    column_names = ['Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak']
+    column_names = ["Chrom", "Start", "End", "Name", "Score", "Strand", "SignalValue", "pValue", "qValue", "Peak"]
     data_sources = {"data": "tabix", "index": "bigwig"}
 
     MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter)
     MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter)
     MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)
-    MetadataElement(name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0)
+    MetadataElement(
+        name="strandCol",
+        desc="Strand column (click box & select)",
+        param=metadata.ColumnParameter,
+        optional=True,
+        no_value=0,
+    )
     MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
 
     def sniff(self, filename):
@@ -1427,13 +1624,14 @@ class ENCODEPeak(Interval):
 
 
 class ChromatinInteractions(Interval):
-    '''
+    """
     Chromatin interactions obtained from 3C/5C/Hi-C experiments.
-    '''
+    """
+
     file_ext = "chrint"
     track_type = "DiagonalHeatmapTrack"
     data_sources = {"data": "tabix", "index": "bigwig"}
-    column_names = ['Chrom1', 'Start1', 'End1', 'Chrom2', 'Start2', 'End2', 'Value']
+    column_names = ["Chrom1", "Start1", "End1", "Chrom2", "Start2", "End2", "Value"]
 
     MetadataElement(name="chrom1Col", default=1, desc="Chrom1 column", param=metadata.ColumnParameter)
     MetadataElement(name="start1Col", default=2, desc="Start1 column", param=metadata.ColumnParameter)
@@ -1471,10 +1669,19 @@ class ScIdx(Tabular):
     >>> ScIdx().sniff(fname)
     False
     """
+
     file_ext = "scidx"
 
     MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=[], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[])
+    MetadataElement(
+        name="column_types",
+        default=[],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
 
     def __init__(self, **kwd):
         """
@@ -1483,18 +1690,18 @@ class ScIdx(Tabular):
         Tabular.__init__(self, **kwd)
         # Don't set column names since the first
         # line of the dataset displays them.
-        self.column_names = ['chrom', 'index', 'forward', 'reverse', 'value']
+        self.column_names = ["chrom", "index", "forward", "reverse", "value"]
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
         Checks for 'scidx-ness.'
         """
         count = 0
-        for count, line in enumerate(iter_headers(file_prefix, '\t')):
+        for count, line in enumerate(iter_headers(file_prefix, "\t")):
             # The first line is always a comment like this:
             # 2015-11-23 20:18:56.51;input.bam;READ1
             if count == 0:
-                if not line[0].startswith('#'):
+                if not line[0].startswith("#"):
                     return False
             # The 2nd line is always a specific header
             elif count == 1:
@@ -1517,6 +1724,7 @@ class ScIdx(Tabular):
         return False
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/isa.py b/lib/galaxy/datatypes/isa.py
index 66a3338e892..f991e6e6a65 100644
--- a/lib/galaxy/datatypes/isa.py
+++ b/lib/galaxy/datatypes/isa.py
@@ -16,7 +16,7 @@ import tempfile
 logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
 from isatools import (
     isajson,
-    isatab_meta
+    isatab_meta,
 )
 from markupsafe import escape
 
@@ -50,9 +50,11 @@ logger = logging.getLogger(__name__)
 # ISA class {{{1
 ################################################################
 
+
 class _Isa(data.Data):
-    """ Base class for implementing ISA datatypes """
-    composite_type = 'auto_primary_file'
+    """Base class for implementing ISA datatypes"""
+
+    composite_type = "auto_primary_file"
     is_binary = True
     _main_file_regex = None
 
@@ -78,7 +80,7 @@ class _Isa(data.Data):
     def _get_isa_folder_path(self, dataset):
         isa_folder = dataset.extra_files_path
         if not isa_folder:
-            raise Exception('Unvalid dataset object, or no extra files path found for this dataset.')
+            raise Exception("Unvalid dataset object, or no extra files path found for this dataset.")
         return isa_folder
 
     # Get main file {{{2
@@ -99,7 +101,7 @@ class _Isa(data.Data):
             main_file = self._find_main_file_in_archive(isa_files)
 
             if main_file is None:
-                raise Exception('Invalid ISA archive. No main file found.')
+                raise Exception("Invalid ISA archive. No main file found.")
 
             # Make full path
             main_file = os.path.join(isa_folder, main_file)
@@ -111,7 +113,7 @@ class _Isa(data.Data):
 
     def _get_investigation(self, dataset):
         """Create a contained instance specific to the exact ISA type (Tab or Json).
-           We will use it to parse and access information from the archive."""
+        We will use it to parse and access information from the archive."""
 
         investigation = None
         main_file = self._get_main_file(dataset)
@@ -134,7 +136,11 @@ class _Isa(data.Data):
                 if found_file is None:
                     found_file = match.group()
                 else:
-                    raise Exception('More than one file match the pattern "', str(self._main_file_regex), '" to identify the investigation file')
+                    raise Exception(
+                        'More than one file match the pattern "',
+                        str(self._main_file_regex),
+                        '" to identify the investigation file',
+                    )
 
         return found_file
 
@@ -150,7 +156,7 @@ class _Isa(data.Data):
             raise RuntimeError("Unable to find the main file within the 'files_path' folder")
 
         # Read first lines of main file
-        with open(main_file, encoding='utf-8') as f:
+        with open(main_file, encoding="utf-8") as f:
             data = []
             for line in f:
                 if len(data) < _MAX_LINES_HISTORY_PEEK:
@@ -159,10 +165,10 @@ class _Isa(data.Data):
                     break
             if not dataset.dataset.purged and data:
                 dataset.peek = json.dumps({"data": data})
-                dataset.blurb = 'data'
+                dataset.blurb = "data"
             else:
-                dataset.peek = 'file does not exist'
-                dataset.blurb = 'file purged from disk'
+                dataset.peek = "file does not exist"
+                dataset.blurb = "file purged from disk"
 
     # Display peek {{{2
     ################################################################
@@ -180,7 +186,7 @@ class _Isa(data.Data):
                 if not line:
                     continue
                 out.append(f"<tr><td>{escape(util.unicodify(line, 'utf-8'))}</td></tr>")
-            out.append('</table>')
+            out.append("</table>")
             out = "".join(out)
         except Exception as exc:
             out = f"Can't create peek: {util.unicodify(exc)}"
@@ -191,17 +197,17 @@ class _Isa(data.Data):
 
     def generate_primary_file(self, dataset=None):
         """Generate the primary file. It is an HTML file containing description of the composite dataset
-           as well as a list of the composite files that it contains."""
+        as well as a list of the composite files that it contains."""
 
         if dataset:
-            rval = ['<html><head><title>ISA Dataset </title></head><p/>']
+            rval = ["<html><head><title>ISA Dataset </title></head><p/>"]
             if hasattr(dataset, "extra_files_path"):
-                rval.append('<div>ISA Dataset composed of the following files:<p/><ul>')
+                rval.append("<div>ISA Dataset composed of the following files:<p/><ul>")
                 for cmp_file in os.listdir(dataset.extra_files_path):
                     rval.append(f'<li><a href="{cmp_file}" type="text/plain">{escape(cmp_file)}</a></li>')
-                rval.append('</ul></div></html>')
+                rval.append("</ul></div></html>")
             else:
-                rval.append('<div>ISA Dataset is empty!<p/><ul>')
+                rval.append("<div>ISA Dataset is empty!<p/><ul>")
             return "\n".join(rval)
         return "<div>No dataset available</div>"
 
@@ -232,7 +238,7 @@ class _Isa(data.Data):
             CompressedFile(file_name).extract(temp_folder)
             shutil.rmtree(output_path)
             extracted_files = os.listdir(temp_folder)
-            logger.debug(' '.join(extracted_files))
+            logger.debug(" ".join(extracted_files))
             if len(extracted_files) == 0:
                 os.makedirs(output_path)
                 shutil.rmtree(temp_folder)
@@ -247,8 +253,8 @@ class _Isa(data.Data):
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
         """Downloads the ISA dataset if `preview` is `False`;
-           if `preview` is `True`, it returns a preview of the ISA dataset as a HTML page.
-           The preview is triggered when user clicks on the eye icon of the composite dataset."""
+        if `preview` is `True`, it returns a preview of the ISA dataset as a HTML page.
+        The preview is triggered when user clicks on the eye icon of the composite dataset."""
 
         headers = kwd.get("headers", {})
         # if it is not required a preview use the default behaviour of `display_data`
@@ -265,45 +271,46 @@ class _Isa(data.Data):
                         <p>You may also try to look into your zip file in order to find out if this is a proper ISA archive. If you see a file i_Investigation.txt inside, then it is an ISA-Tab archive. If you see a file with extension .json inside, then it is an ISA-JSON archive. If you see nothing like that, then either your ISA archive is corrupted, or it is not an ISA archive.</p>
                    </body></html>"""
         else:
-            html = '<html><body>'
-            html += f'<h1>{investigation.title} {investigation.identifier}</h1>'
+            html = "<html><body>"
+            html += f"<h1>{investigation.title} {investigation.identifier}</h1>"
 
             # Loop on all studies
             for study in investigation.studies:
-                html += f'<h2>Study {study.identifier}</h2>'
-                html += f'<h3>{study.title}</h3>'
-                html += f'<p>{study.description}</p>'
-                html += f'<p>Submitted the {study.submission_date}</p>'
-                html += f'<p>Released on {study.public_release_date}</p>'
+                html += f"<h2>Study {study.identifier}</h2>"
+                html += f"<h3>{study.title}</h3>"
+                html += f"<p>{study.description}</p>"
+                html += f"<p>Submitted the {study.submission_date}</p>"
+                html += f"<p>Released on {study.public_release_date}</p>"
 
                 html += f"<p>Experimental factors used: {', '.join(x.name for x in study.factors)}</p>"
 
                 # Loop on all assays of this study
                 for assay in study.assays:
-                    html += f'<h3>Assay {assay.filename}</h3>'
-                    html += f'<p>Measurement type: {assay.measurement_type.term}</p>'  # OntologyAnnotation
-                    html += f'<p>Technology type: {assay.technology_type.term}</p>'    # OntologyAnnotation
-                    html += f'<p>Technology platform: {assay.technology_platform}</p>'
+                    html += f"<h3>Assay {assay.filename}</h3>"
+                    html += f"<p>Measurement type: {assay.measurement_type.term}</p>"  # OntologyAnnotation
+                    html += f"<p>Technology type: {assay.technology_type.term}</p>"  # OntologyAnnotation
+                    html += f"<p>Technology platform: {assay.technology_platform}</p>"
                     if assay.data_files is not None:
-                        html += '<p>Data files:</p>'
-                        html += '<ul>'
+                        html += "<p>Data files:</p>"
+                        html += "<ul>"
                         for data_file in assay.data_files:
-                            if data_file.filename != '':
+                            if data_file.filename != "":
                                 html += f"<li>{escape(util.unicodify(str(data_file.filename), 'utf-8'))} - {escape(util.unicodify(str(data_file.label), 'utf-8'))}</li>"
-                        html += '</ul>'
+                        html += "</ul>"
 
-            html += '</body></html>'
+            html += "</body></html>"
 
         # Set mime type
-        mime = 'text/html'
+        mime = "text/html"
         self._clean_and_set_mime_type(trans, mime, headers)
 
-        return sanitize_html(html).encode('utf-8'), headers
+        return sanitize_html(html).encode("utf-8"), headers
 
 
 # ISA-Tab class {{{1
 ################################################################
 
+
 class IsaTab(_Isa):
     file_ext = "isa-tab"
 
@@ -321,7 +328,7 @@ class IsaTab(_Isa):
         # Parse ISA-Tab investigation file
         parser = isatab_meta.InvestigationParser()
         isa_dir = os.path.dirname(filename)
-        with open(filename, newline='', encoding='utf8') as fp:
+        with open(filename, newline="", encoding="utf8") as fp:
             parser.parse(fp)
         for study in parser.isa.studies:
             s_parser = isatab_meta.LazyStudySampleTableParser(parser.isa)
@@ -337,6 +344,7 @@ class IsaTab(_Isa):
 # ISA-JSON class {{{1
 ################################################################
 
+
 class IsaJson(_Isa):
     file_ext = "isa-json"
 
@@ -352,7 +360,7 @@ class IsaJson(_Isa):
     def _make_investigation_instance(self, filename):
 
         # Parse JSON file
-        with open(filename, newline='', encoding='utf8') as fp:
+        with open(filename, newline="", encoding="utf8") as fp:
             isa = isajson.load(fp)
 
         return isa
diff --git a/lib/galaxy/datatypes/media.py b/lib/galaxy/datatypes/media.py
index 9b3e9ab9ddc..4c7b54418eb 100644
--- a/lib/galaxy/datatypes/media.py
+++ b/lib/galaxy/datatypes/media.py
@@ -4,75 +4,176 @@ import subprocess
 import wave
 
 from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.metadata import ListParameter, MetadataElement
+from galaxy.datatypes.metadata import (
+    ListParameter,
+    MetadataElement,
+)
 from galaxy.util import which
 
 
 def ffprobe(path):
-    data = json.loads(subprocess.check_output(['ffprobe', '-loglevel', 'quiet', '-show_format', '-show_streams', '-of', 'json', path]).decode("utf-8"))
-    return data['format'], data['streams']
+    data = json.loads(
+        subprocess.check_output(
+            ["ffprobe", "-loglevel", "quiet", "-show_format", "-show_streams", "-of", "json", path]
+        ).decode("utf-8")
+    )
+    return data["format"], data["streams"]
 
 
 class Audio(Binary):
 
-    MetadataElement(name="duration", default=0, desc="Length of audio sample", readonly=True, visible=True, optional=True, no_value=0)
-    MetadataElement(name="audio_codecs", default=[], desc="Audio codec(s)", param=ListParameter, readonly=True, visible=True, optional=True, no_value=[])
-    MetadataElement(name="sample_rates", default=[], desc="Sampling Rate(s)", param=ListParameter, readonly=True, visible=True, optional=True, no_value=[])
-    MetadataElement(name="audio_streams", default=0, desc="Number of audio streams", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="duration",
+        default=0,
+        desc="Length of audio sample",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
+    MetadataElement(
+        name="audio_codecs",
+        default=[],
+        desc="Audio codec(s)",
+        param=ListParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="sample_rates",
+        default=[],
+        desc="Sampling Rate(s)",
+        param=ListParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="audio_streams",
+        default=0,
+        desc="Number of audio streams",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_meta(self, dataset, **kwd):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(dataset.file_name)
 
-            dataset.metadata.duration = metadata['duration']
-            dataset.metadata.audio_codecs = [stream['codec_name'] for stream in streams if stream['codec_type'] == 'audio']
-            dataset.metadata.sample_rates = [stream['sample_rate'] for stream in streams if stream['codec_type'] == 'audio']
-            dataset.metadata.audio_streams = len([stream for stream in streams if stream['codec_type'] == 'audio'])
+            dataset.metadata.duration = metadata["duration"]
+            dataset.metadata.audio_codecs = [
+                stream["codec_name"] for stream in streams if stream["codec_type"] == "audio"
+            ]
+            dataset.metadata.sample_rates = [
+                stream["sample_rate"] for stream in streams if stream["codec_type"] == "audio"
+            ]
+            dataset.metadata.audio_streams = len([stream for stream in streams if stream["codec_type"] == "audio"])
 
 
 class Video(Binary):
 
-    MetadataElement(name="resolution_w", default=0, desc="Width of video stream", readonly=True, visible=True, optional=True, no_value=0)
-    MetadataElement(name="resolution_h", default=0, desc="Height of video stream", readonly=True, visible=True, optional=True, no_value=0)
-    MetadataElement(name="fps", default=0, desc="FPS of video stream", readonly=True, visible=True, optional=True, no_value=0)
-    MetadataElement(name="video_codecs", default=[], desc="Video codec(s)", param=ListParameter, readonly=True, visible=True, optional=True, no_value=[])
-    MetadataElement(name="audio_codecs", default=[], desc="Audio codec(s)", param=ListParameter, readonly=True, visible=True, optional=True, no_value=[])
-    MetadataElement(name="video_streams", default=0, desc="Number of video streams", readonly=True, visible=True, optional=True, no_value=0)
-    MetadataElement(name="audio_streams", default=0, desc="Number of audio streams", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="resolution_w",
+        default=0,
+        desc="Width of video stream",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
+    MetadataElement(
+        name="resolution_h",
+        default=0,
+        desc="Height of video stream",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
+    MetadataElement(
+        name="fps", default=0, desc="FPS of video stream", readonly=True, visible=True, optional=True, no_value=0
+    )
+    MetadataElement(
+        name="video_codecs",
+        default=[],
+        desc="Video codec(s)",
+        param=ListParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="audio_codecs",
+        default=[],
+        desc="Audio codec(s)",
+        param=ListParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="video_streams",
+        default=0,
+        desc="Number of video streams",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
+    MetadataElement(
+        name="audio_streams",
+        default=0,
+        desc="Number of audio streams",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def _get_resolution(self, streams):
         for stream in streams:
-            if stream['codec_type'] == 'video':
-                w = stream['width']
-                h = stream['height']
-                dividend, divisor = stream['avg_frame_rate'].split('/')
+            if stream["codec_type"] == "video":
+                w = stream["width"]
+                h = stream["height"]
+                dividend, divisor = stream["avg_frame_rate"].split("/")
                 fps = float(dividend) / float(divisor)
         else:
             w = h = fps = 0
         return w, h, fps
 
     def set_meta(self, dataset, **kwd):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(dataset.file_name)
             (w, h, fps) = self._get_resolution(streams)
             dataset.metadata.resolution_w = w
             dataset.metadata.resolution_h = h
             dataset.metadata.fps = fps
 
-            dataset.metadata.audio_codecs = [stream['codec_name'] for stream in streams if stream['codec_type'] == 'audio']
-            dataset.metadata.video_codecs = [stream['codec_name'] for stream in streams if stream['codec_type'] == 'video']
+            dataset.metadata.audio_codecs = [
+                stream["codec_name"] for stream in streams if stream["codec_type"] == "audio"
+            ]
+            dataset.metadata.video_codecs = [
+                stream["codec_name"] for stream in streams if stream["codec_type"] == "video"
+            ]
 
-            dataset.metadata.audio_streams = len([stream for stream in streams if stream['codec_type'] == 'audio'])
-            dataset.metadata.video_streams = len([stream for stream in streams if stream['codec_type'] == 'video'])
+            dataset.metadata.audio_streams = len([stream for stream in streams if stream["codec_type"] == "audio"])
+            dataset.metadata.video_streams = len([stream for stream in streams if stream["codec_type"] == "video"])
 
 
 class Mkv(Video):
     file_ext = "mkv"
 
     def sniff(self, filename):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(filename)
-            return 'matroska' in metadata['format_name'].split(',')
+            return "matroska" in metadata["format_name"].split(",")
 
 
 class Mp4(Video):
@@ -88,27 +189,27 @@ class Mp4(Video):
     file_ext = "mp4"
 
     def sniff(self, filename):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(filename)
-            return 'mp4' in metadata['format_name'].split(',')
+            return "mp4" in metadata["format_name"].split(",")
 
 
 class Flv(Video):
     file_ext = "flv"
 
     def sniff(self, filename):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(filename)
-            return 'flv' in metadata['format_name'].split(',')
+            return "flv" in metadata["format_name"].split(",")
 
 
 class Mpg(Video):
     file_ext = "mpg"
 
     def sniff(self, filename):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(filename)
-            return 'mpegvideo' in metadata['format_name'].split(',')
+            return "mpegvideo" in metadata["format_name"].split(",")
 
 
 class Mp3(Audio):
@@ -120,12 +221,13 @@ class Mp3(Audio):
     >>> sniff_with_cls(Mp3, 'audio_1.wav')
     False
     """
+
     file_ext = "mp3"
 
     def sniff(self, filename):
-        if which('ffprobe'):
+        if which("ffprobe"):
             metadata, streams = ffprobe(filename)
-            return 'mp3' in metadata['format_name'].split(',')
+            return "mp3" in metadata["format_name"].split(",")
 
 
 class Wav(Audio):
@@ -138,27 +240,34 @@ class Wav(Audio):
     >>> sniff_with_cls(Wav, 'drugbank_drugs.cml')
     False
     """
+
     file_ext = "wav"
     blurb = "RIFF WAV Audio file"
     is_binary = True
 
     MetadataElement(name="rate", desc="Sample Rate", default=0, no_value=0, readonly=True, visible=True, optional=True)
-    MetadataElement(name="nframes", desc="Number of Samples", default=0, no_value=0, readonly=True, visible=True, optional=True)
-    MetadataElement(name="nchannels", desc="Number of Channels", default=0, no_value=0, readonly=True, visible=True, optional=True)
-    MetadataElement(name="sampwidth", desc="Sample Width", default=0, no_value=0, readonly=True, visible=True, optional=True)
+    MetadataElement(
+        name="nframes", desc="Number of Samples", default=0, no_value=0, readonly=True, visible=True, optional=True
+    )
+    MetadataElement(
+        name="nchannels", desc="Number of Channels", default=0, no_value=0, readonly=True, visible=True, optional=True
+    )
+    MetadataElement(
+        name="sampwidth", desc="Sample Width", default=0, no_value=0, readonly=True, visible=True, optional=True
+    )
 
     def get_mime(self):
         """Returns the mime type of the datatype."""
-        return 'audio/wav'
+        return "audio/wav"
 
     def sniff(self, filename):
-        with wave.open(filename, 'rb'):
+        with wave.open(filename, "rb"):
             return True
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         """Set the metadata for this dataset from the file contents."""
         try:
-            with wave.open(dataset.dataset.file_name, 'rb') as fd:
+            with wave.open(dataset.dataset.file_name, "rb") as fd:
                 dataset.metadata.rate = fd.getframerate()
                 dataset.metadata.nframes = fd.getnframes()
                 dataset.metadata.sampwidth = fd.getsampwidth()
diff --git a/lib/galaxy/datatypes/metacyto.py b/lib/galaxy/datatypes/metacyto.py
index d18759fcb34..33e05752fb9 100644
--- a/lib/galaxy/datatypes/metacyto.py
+++ b/lib/galaxy/datatypes/metacyto.py
@@ -12,13 +12,14 @@ log = logging.getLogger(__name__)
 
 class mStats(Tabular):
     """Class describing the table of cluster statistics output from MetaCyto"""
+
     file_ext = "metacyto_stats.txt"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """Quick test on file headings"""
         if file_prefix.startswith("fcs_files\tcluster_id\tlabel\tfcs_names"):
             header_line = file_prefix.string_io().readline()
-            if header_line.strip().split("\t")[-1] == 'fraction':
+            if header_line.strip().split("\t")[-1] == "fraction":
                 return True
             elif file_prefix.truncated and file_prefix.string_io().read() == header_line:
                 return True
@@ -27,7 +28,8 @@ class mStats(Tabular):
 
 class mSummary(Tabular):
     """Class describing the summary table output by MetaCyto after FCS preprocessing"""
+
     file_ext = "metacyto_summary.txt"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        return file_prefix.startswith('study_id\tantibodies\tfilenames')
+        return file_prefix.startswith("study_id\tantibodies\tfilenames")
diff --git a/lib/galaxy/datatypes/microarrays.py b/lib/galaxy/datatypes/microarrays.py
index fc83c051f2e..56ab225198c 100644
--- a/lib/galaxy/datatypes/microarrays.py
+++ b/lib/galaxy/datatypes/microarrays.py
@@ -7,7 +7,7 @@ from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
-    get_headers
+    get_headers,
 )
 
 log = logging.getLogger(__name__)
@@ -17,24 +17,64 @@ class GenericMicroarrayFile(data.Text):
     """
     Abstract class for most of the microarray files.
     """
-    MetadataElement(name="version_number", default="1.0", desc="Version number", readonly=True, visible=True,
-                    optional=True, no_value="1.0")
-    MetadataElement(name="file_format", default="ATF", desc="File format", readonly=True, visible=True,
-                    optional=True, no_value="ATF")
-    MetadataElement(name="number_of_optional_header_records", default=1, desc="Number of optional header records",
-                    readonly=True, visible=True, optional=True, no_value=1)
-    MetadataElement(name="number_of_data_columns", default=1, desc="Number of data columns",
-                    readonly=True, visible=True,
-                    optional=True, no_value=1)
-    MetadataElement(name="file_type", default="GenePix", desc="File type",
-                    readonly=True, visible=True,
-                    optional=True, no_value="GenePix")
-    MetadataElement(name="block_count", default=1, desc="Number of blocks described in the file",
-                    readonly=True, visible=True,
-                    optional=True, no_value=1)
-    MetadataElement(name="block_type", default=0, desc="Type of block",
-                    readonly=True, visible=True,
-                    optional=True, no_value=0)
+
+    MetadataElement(
+        name="version_number",
+        default="1.0",
+        desc="Version number",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="1.0",
+    )
+    MetadataElement(
+        name="file_format",
+        default="ATF",
+        desc="File format",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="ATF",
+    )
+    MetadataElement(
+        name="number_of_optional_header_records",
+        default=1,
+        desc="Number of optional header records",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=1,
+    )
+    MetadataElement(
+        name="number_of_data_columns",
+        default=1,
+        desc="Number of data columns",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=1,
+    )
+    MetadataElement(
+        name="file_type",
+        default="GenePix",
+        desc="File type",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="GenePix",
+    )
+    MetadataElement(
+        name="block_count",
+        default=1,
+        desc="Number of blocks described in the file",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=1,
+    )
+    MetadataElement(
+        name="block_type", default=0, desc="Type of block", readonly=True, visible=True, optional=True, no_value=0
+    )
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
@@ -44,17 +84,17 @@ class GenericMicroarrayFile(data.Text):
                 dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, {dataset.metadata.block_count} blocks, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def get_mime(self):
-        return 'text/plain'
+        return "text/plain"
 
 
 @build_sniff_from_prefix
 class Gal(GenericMicroarrayFile):
-    """ Gal File format described at:
-            http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gal
+    """Gal File format described at:
+    http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gal
     """
 
     edam_format = "format_3829"
@@ -94,8 +134,8 @@ class Gal(GenericMicroarrayFile):
 
 @build_sniff_from_prefix
 class Gpr(GenericMicroarrayFile):
-    """ Gpr File format described at:
-            http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gpr
+    """Gpr File format described at:
+    http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gpr
     """
 
     edam_format = "format_3829"
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index 5c95158a9e2..852b6f2206e 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -13,14 +13,14 @@ from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
     get_headers,
-    iter_headers
+    iter_headers,
 )
 from galaxy.datatypes.tabular import Tabular
 from galaxy.datatypes.util.generic_util import count_special_lines
 from galaxy.datatypes.xml import GenericXml
 from galaxy.util import (
     commands,
-    unicodify
+    unicodify,
 )
 
 log = logging.getLogger(__name__)
@@ -31,9 +31,9 @@ def count_lines(filename, non_empty=False):
     counting the number of lines from the 'filename' file
     """
     if non_empty:
-        cmd = ['grep', '-cve', r'^\s*$', filename]
+        cmd = ["grep", "-cve", r"^\s*$", filename]
     else:
-        cmd = ['wc', '-l', filename]
+        cmd = ["wc", "-l", filename]
     try:
         out = commands.execute(cmd)
     except commands.CommandLineException as e:
@@ -46,21 +46,30 @@ class GenericMolFile(Text):
     """
     Abstract class for most of the molecule files.
     """
-    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+
+    MetadataElement(
+        name="number_of_molecules",
+        default=0,
+        desc="Number of molecules",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            if (dataset.metadata.number_of_molecules == 1):
+            if dataset.metadata.number_of_molecules == 1:
                 dataset.blurb = "1 molecule"
             else:
                 dataset.blurb = f"{dataset.metadata.number_of_molecules} molecules"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def get_mime(self):
-        return 'text/plain'
+        return "text/plain"
 
 
 class MOL(GenericMolFile):
@@ -104,17 +113,16 @@ class SDF(GenericMolFile):
         idx = 0
         for line in file_prefix.line_iterator():
             idx += 1
-            line = line.rstrip('\n\r')
+            line = line.rstrip("\n\r")
             if idx < 4:
                 continue
             elif idx == 4:
-                if len(line) != 39 or not(line.endswith(' V2000')
-                        or line.endswith(' V3000')):
+                if len(line) != 39 or not (line.endswith(" V2000") or line.endswith(" V3000")):
                     return False
             elif not m_end_found:
-                if line == 'M  END':
+                if line == "M  END":
                     m_end_found = True
-            elif line == '$$$$':
+            elif line == "$$$$":
                 return True
             if idx == limit:
                 break
@@ -139,10 +147,10 @@ class SDF(GenericMolFile):
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
+        if split_params["split_mode"] == "number_of_parts":
             raise Exception(f"Split mode \"{split_params['split_mode']}\" is currently not implemented for SD-files.")
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
             raise Exception(f"Unsupported split mode {split_params['split_mode']}")
 
@@ -158,7 +166,7 @@ class SDF(GenericMolFile):
         def _write_part_sdf_file(accumulated_lines):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
-            with open(part_path, 'w') as part_file:
+            with open(part_path, "w") as part_file:
                 part_file.writelines(accumulated_lines)
 
         try:
@@ -172,7 +180,7 @@ class SDF(GenericMolFile):
             if sdf_lines_accumulated:
                 _write_part_sdf_file(sdf_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s', unicodify(e))
+            log.error("Unable to split files: %s", unicodify(e))
             raise
 
 
@@ -195,8 +203,8 @@ class MOL2(GenericMolFile):
         limit = 60
         idx = 0
         for line in file_prefix.line_iterator():
-            line = line.rstrip('\n\r')
-            if line == '@<TRIPOS>MOLECULE':
+            line = line.rstrip("\n\r")
+            if line == "@<TRIPOS>MOLECULE":
                 return True
             idx += 1
             if idx == limit:
@@ -222,10 +230,10 @@ class MOL2(GenericMolFile):
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
+        if split_params["split_mode"] == "number_of_parts":
             raise Exception(f"Split mode \"{split_params['split_mode']}\" is currently not implemented for MOL2-files.")
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
             raise Exception(f"Unsupported split mode {split_params['split_mode']}")
 
@@ -245,7 +253,7 @@ class MOL2(GenericMolFile):
         def _write_part_mol2_file(accumulated_lines):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
-            with open(part_path, 'w') as part_file:
+            with open(part_path, "w") as part_file:
                 part_file.writelines(accumulated_lines)
 
         try:
@@ -259,7 +267,7 @@ class MOL2(GenericMolFile):
             if mol2_lines_accumulated:
                 _write_part_mol2_file(mol2_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s', unicodify(e))
+            log.error("Unable to split files: %s", unicodify(e))
             raise
 
 
@@ -268,6 +276,7 @@ class FPS(GenericMolFile):
     """
     chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS
     """
+
     file_ext = "fps"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -282,8 +291,8 @@ class FPS(GenericMolFile):
         >>> FPS().sniff(fname)
         False
         """
-        header = get_headers(file_prefix, sep='\t', count=1)
-        if header[0][0].strip() == '#FPS1':
+        header = get_headers(file_prefix, sep="\t", count=1)
+        if header[0][0].strip() == "#FPS1":
             return True
         else:
             return False
@@ -292,7 +301,7 @@ class FPS(GenericMolFile):
         """
         Set the number of lines of data in dataset.
         """
-        dataset.metadata.number_of_molecules = count_special_lines('^#', dataset.file_name, invert=True)
+        dataset.metadata.number_of_molecules = count_special_lines("^#", dataset.file_name, invert=True)
 
     @classmethod
     def split(cls, input_datasets, subdir_generator_function, split_params):
@@ -307,17 +316,17 @@ class FPS(GenericMolFile):
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
+        if split_params["split_mode"] == "number_of_parts":
             raise Exception(f"Split mode \"{split_params['split_mode']}\" is currently not implemented for MOL2-files.")
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
             raise Exception(f"Unsupported split mode {split_params['split_mode']}")
 
         def _write_part_fingerprint_file(accumulated_lines):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
-            with open(part_path, 'w') as part_file:
+            with open(part_path, "w") as part_file:
                 part_file.writelines(accumulated_lines)
 
         try:
@@ -327,7 +336,7 @@ class FPS(GenericMolFile):
             for line in open(input_files[0]):
                 if not line.strip():
                     continue
-                if line.startswith('#'):
+                if line.startswith("#"):
                     header_lines.append(line)
                 else:
                     fingerprint_counter += 1
@@ -338,7 +347,7 @@ class FPS(GenericMolFile):
             if lines_accumulated:
                 _write_part_fingerprint_file(header_lines + lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s', unicodify(e))
+            log.error("Unable to split files: %s", unicodify(e))
             raise
 
     @staticmethod
@@ -351,14 +360,13 @@ class FPS(GenericMolFile):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("No fps files given, %r, to merge into %s"
-                             % (split_files, output_file))
+            raise ValueError("No fps files given, %r, to merge into %s" % (split_files, output_file))
         with open(output_file, "w") as out:
             first = True
             for filename in split_files:
                 with open(filename) as handle:
                     for line in handle:
-                        if line.startswith('#'):
+                        if line.startswith("#"):
                             if first:
                                 out.write(line)
                         else:
@@ -369,30 +377,30 @@ class FPS(GenericMolFile):
 
 class OBFS(Binary):
     """OpenBabel Fastsearch format (fs)."""
-    file_ext = 'obfs'
-    composite_type = 'basic'
 
-    MetadataElement(name="base_name", default='OpenBabel Fastsearch Index',
-                    readonly=True, visible=True, optional=True,)
+    file_ext = "obfs"
+    composite_type = "basic"
+
+    MetadataElement(
+        name="base_name",
+        default="OpenBabel Fastsearch Index",
+        readonly=True,
+        visible=True,
+        optional=True,
+    )
 
     def __init__(self, **kwd):
         """
-            A Fastsearch Index consists of a binary file with the fingerprints
-            and a pointer the actual molecule file.
+        A Fastsearch Index consists of a binary file with the fingerprints
+        and a pointer the actual molecule file.
         """
         super().__init__(**kwd)
-        self.add_composite_file('molecule.fs', is_binary=True,
-                                description='OpenBabel Fastsearch Index')
-        self.add_composite_file('molecule.sdf', optional=True,
-                                is_binary=False, description='Molecule File')
-        self.add_composite_file('molecule.smi', optional=True,
-                                is_binary=False, description='Molecule File')
-        self.add_composite_file('molecule.inchi', optional=True,
-                                is_binary=False, description='Molecule File')
-        self.add_composite_file('molecule.mol2', optional=True,
-                                is_binary=False, description='Molecule File')
-        self.add_composite_file('molecule.cml', optional=True,
-                                is_binary=False, description='Molecule File')
+        self.add_composite_file("molecule.fs", is_binary=True, description="OpenBabel Fastsearch Index")
+        self.add_composite_file("molecule.sdf", optional=True, is_binary=False, description="Molecule File")
+        self.add_composite_file("molecule.smi", optional=True, is_binary=False, description="Molecule File")
+        self.add_composite_file("molecule.inchi", optional=True, is_binary=False, description="Molecule File")
+        self.add_composite_file("molecule.mol2", optional=True, is_binary=False, description="Molecule File")
+        self.add_composite_file("molecule.cml", optional=True, is_binary=False, description="Molecule File")
 
     def set_peek(self, dataset):
         """Set the peek and blurb text."""
@@ -412,7 +420,7 @@ class OBFS(Binary):
 
     def get_mime(self):
         """Returns the mime type of the datatype (pretend it is text for peek)"""
-        return 'text/plain'
+        return "text/plain"
 
     def merge(split_files, output_file, extra_merge_args):
         """Merging Fastsearch indices is not supported."""
@@ -432,13 +440,14 @@ class DRF(GenericMolFile):
         """
         Set the number of lines of data in dataset.
         """
-        dataset.metadata.number_of_molecules = count_special_lines('\"ligand id\"', dataset.file_name, invert=True)
+        dataset.metadata.number_of_molecules = count_special_lines('"ligand id"', dataset.file_name, invert=True)
 
 
 class PHAR(GenericMolFile):
     """
     Pharmacophore database format from silicos-it.
     """
+
     file_ext = "phar"
 
     def set_peek(self, dataset):
@@ -446,8 +455,8 @@ class PHAR(GenericMolFile):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "pharmacophore"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -456,6 +465,7 @@ class PDB(GenericMolFile):
     Protein Databank format.
     http://www.wwpdb.org/documentation/format33/v3.3.html
     """
+
     file_ext = "pdb"
     MetadataElement(name="chain_ids", default=[], desc="Chain IDs", readonly=False, visible=True)
 
@@ -471,21 +481,21 @@ class PDB(GenericMolFile):
         >>> PDB().sniff(fname)
         False
         """
-        headers = iter_headers(file_prefix, sep=' ', count=300)
+        headers = iter_headers(file_prefix, sep=" ", count=300)
         h = t = c = s = k = e = False
         for line in headers:
             section_name = line[0].strip()
-            if section_name == 'HEADER':
+            if section_name == "HEADER":
                 h = True
-            elif section_name == 'TITLE':
+            elif section_name == "TITLE":
                 t = True
-            elif section_name == 'COMPND':
+            elif section_name == "COMPND":
                 c = True
-            elif section_name == 'SOURCE':
+            elif section_name == "SOURCE":
                 s = True
-            elif section_name == 'KEYWDS':
+            elif section_name == "KEYWDS":
                 k = True
-            elif section_name == 'EXPDTA':
+            elif section_name == "EXPDTA":
                 e = True
 
         if h * t * c * s * k * e:
@@ -501,24 +511,24 @@ class PDB(GenericMolFile):
             chain_ids = set()
             with open(dataset.file_name) as fh:
                 for line in fh:
-                    if line.startswith('ATOM  ') or line.startswith('HETATM'):
-                        if line[21] != ' ':
+                    if line.startswith("ATOM  ") or line.startswith("HETATM"):
+                        if line[21] != " ":
                             chain_ids.add(line[21])
             dataset.metadata.chain_ids = list(chain_ids)
         except Exception as e:
-            log.error('Error finding chain_ids: %s', unicodify(e))
+            log.error("Error finding chain_ids: %s", unicodify(e))
             raise
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             atom_numbers = count_special_lines("^ATOM", dataset.file_name)
             hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
-            chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
+            chain_ids = ",".join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else "None"
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = f"{atom_numbers} atoms and {hetatm_numbers} HET-atoms\nchain_ids: {chain_ids}"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -527,6 +537,7 @@ class PDBQT(GenericMolFile):
     PDBQT Autodock and Autodock Vina format
     http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
     """
+
     file_ext = "pdbqt"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -541,19 +552,19 @@ class PDBQT(GenericMolFile):
         >>> PDBQT().sniff(fname)
         False
         """
-        headers = iter_headers(file_prefix, sep=' ', count=300)
+        headers = iter_headers(file_prefix, sep=" ", count=300)
         h = t = c = s = k = False
         for line in headers:
             section_name = line[0].strip()
-            if section_name == 'REMARK':
+            if section_name == "REMARK":
                 h = True
-            elif section_name == 'ROOT':
+            elif section_name == "ROOT":
                 t = True
-            elif section_name == 'ENDROOT':
+            elif section_name == "ENDROOT":
                 c = True
-            elif section_name == 'BRANCH':
+            elif section_name == "BRANCH":
                 s = True
-            elif section_name == 'TORSDOF':
+            elif section_name == "TORSDOF":
                 k = True
 
         if h * t * c * s * k:
@@ -568,8 +579,8 @@ class PDBQT(GenericMolFile):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = f"{root_numbers} roots and {branch_numbers} branches"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -578,6 +589,7 @@ class PQR(GenericMolFile):
     Protein Databank format.
     https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
     """
+
     file_ext = "pqr"
     MetadataElement(name="chain_ids", default=[], desc="Chain IDs", readonly=False, visible=True)
 
@@ -604,16 +616,18 @@ class PQR(GenericMolFile):
           11: Radius
               A float which provides the atomic radius (in angstroms).
         """
-        pat = r'(ATOM|HETATM)\s+' +\
-              r'(\d+)\s+' +\
-              r'([A-Z0-9]+)\s+' +\
-              r'([A-Z0-9]+)\s+' +\
-              r'(([A-Z]?)\s+)?' +\
-              r'([-+]?\d*\.\d+|\d+)\s+' +\
-              r'([-+]?\d*\.\d+|\d+)\s+' +\
-              r'([-+]?\d*\.\d+|\d+)\s+' +\
-              r'([-+]?\d*\.\d+|\d+)\s+' +\
-              r'([-+]?\d*\.\d+|\d+)\s+'
+        pat = (
+            r"(ATOM|HETATM)\s+"
+            + r"(\d+)\s+"
+            + r"([A-Z0-9]+)\s+"
+            + r"([A-Z0-9]+)\s+"
+            + r"(([A-Z]?)\s+)?"
+            + r"([-+]?\d*\.\d+|\d+)\s+"
+            + r"([-+]?\d*\.\d+|\d+)\s+"
+            + r"([-+]?\d*\.\d+|\d+)\s+"
+            + r"([-+]?\d*\.\d+|\d+)\s+"
+            + r"([-+]?\d*\.\d+|\d+)\s+"
+        )
         return re.compile(pat)
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -628,14 +642,14 @@ class PQR(GenericMolFile):
         False
         """
         prog = self.get_matcher()
-        headers = iter_headers(file_prefix, sep=None, comment_designator='REMARK   5', count=3000)
+        headers = iter_headers(file_prefix, sep=None, comment_designator="REMARK   5", count=3000)
         h = a = False
         for line in headers:
             section_name = line[0].strip()
-            if section_name == 'REMARK':
+            if section_name == "REMARK":
                 h = True
-            elif section_name == 'ATOM' or section_name == 'HETATM':
-                if prog.match(' '.join(line)):
+            elif section_name == "ATOM" or section_name == "HETATM":
+                if prog.match(" ".join(line)):
                     a = True
                     break
         if h * a:
@@ -652,26 +666,26 @@ class PQR(GenericMolFile):
             chain_ids = set()
             with open(dataset.file_name) as fh:
                 for line in fh:
-                    if line.startswith('REMARK'):
+                    if line.startswith("REMARK"):
                         continue
                     match = prog.match(line.rstrip())
                     if match and match.groups()[5]:
                         chain_ids.add(match.groups()[5])
             dataset.metadata.chain_ids = list(chain_ids)
         except Exception as e:
-            log.error('Error finding chain_ids: %s', unicodify(e))
+            log.error("Error finding chain_ids: %s", unicodify(e))
             raise
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             atom_numbers = count_special_lines("^ATOM", dataset.file_name)
             hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
-            chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
+            chain_ids = ",".join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else "None"
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = f"{atom_numbers} atoms and {hetatm_numbers} HET-atoms\nchain_ids: {str(chain_ids)}"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class grd(Text):
@@ -682,8 +696,8 @@ class grd(Text):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "grids for docking"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class grdtgz(Binary):
@@ -691,70 +705,35 @@ class grdtgz(Binary):
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = 'binary data'
+            dataset.peek = "binary data"
             dataset.blurb = "compressed grids for docking"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
 class InChI(Tabular):
     file_ext = "inchi"
-    column_names = ['InChI']
+    column_names = ["InChI"]
     MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=['str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
-    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
-
-    def set_meta(self, dataset, **kwd):
-        """
-        Set the number of lines of data in dataset.
-        """
-        dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
-
-    def set_peek(self, dataset):
-        if not dataset.dataset.purged:
-            if (dataset.metadata.number_of_molecules == 1):
-                dataset.blurb = "1 molecule"
-            else:
-                dataset.blurb = f"{dataset.metadata.number_of_molecules} molecules"
-            dataset.peek = get_file_peek(dataset.file_name)
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-
-    def sniff_prefix(self, file_prefix: FilePrefix):
-        """
-        Try to guess if the file is a InChI file.
-
-        >>> from galaxy.datatypes.sniff import get_test_fname
-        >>> fname = get_test_fname('drugbank_drugs.inchi')
-        >>> InChI().sniff(fname)
-        True
-        >>> fname = get_test_fname('drugbank_drugs.cml')
-        >>> InChI().sniff(fname)
-        False
-        """
-        inchi_lines = iter_headers(file_prefix, sep=' ', count=10)
-        found_lines = False
-        for inchi in inchi_lines:
-            if not inchi[0].startswith('InChI='):
-                return False
-            found_lines = True
-        return found_lines
-
-
-class SMILES(Tabular):
-    # It is hard or impossible to sniff a SMILES File. We can try to import the
-    # first SMILES and check if it is a molecule, but currently it is not
-    # possible to use external libraries in datatype definition files.
-    # Moreover it seems impossible to include OpenBabel as Python library
-    # because OpenBabel is GPL licensed.
-    file_ext = "smi"
-    column_names = ['SMILES', 'TITLE']
-    MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
-    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="column_types",
+        default=["str"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+    )
+    MetadataElement(
+        name="number_of_molecules",
+        default=0,
+        desc="Number of molecules",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_meta(self, dataset, **kwd):
         """
@@ -770,8 +749,73 @@ class SMILES(Tabular):
                 dataset.blurb = f"{dataset.metadata.number_of_molecules} molecules"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def sniff_prefix(self, file_prefix: FilePrefix):
+        """
+        Try to guess if the file is a InChI file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('drugbank_drugs.inchi')
+        >>> InChI().sniff(fname)
+        True
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> InChI().sniff(fname)
+        False
+        """
+        inchi_lines = iter_headers(file_prefix, sep=" ", count=10)
+        found_lines = False
+        for inchi in inchi_lines:
+            if not inchi[0].startswith("InChI="):
+                return False
+            found_lines = True
+        return found_lines
+
+
+class SMILES(Tabular):
+    # It is hard or impossible to sniff a SMILES File. We can try to import the
+    # first SMILES and check if it is a molecule, but currently it is not
+    # possible to use external libraries in datatype definition files.
+    # Moreover it seems impossible to include OpenBabel as Python library
+    # because OpenBabel is GPL licensed.
+    file_ext = "smi"
+    column_names = ["SMILES", "TITLE"]
+    MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
+    MetadataElement(
+        name="column_types",
+        default=["str", "str"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+    )
+    MetadataElement(
+        name="number_of_molecules",
+        default=0,
+        desc="Number of molecules",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
+
+    def set_peek(self, dataset):
+        if not dataset.dataset.purged:
+            if dataset.metadata.number_of_molecules == 1:
+                dataset.blurb = "1 molecule"
+            else:
+                dataset.blurb = f"{dataset.metadata.number_of_molecules} molecules"
+            dataset.peek = get_file_peek(dataset.file_name)
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -780,25 +824,34 @@ class CML(GenericXml):
     Chemical Markup Language
     http://cml.sourceforge.net/
     """
+
     file_ext = "cml"
-    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="number_of_molecules",
+        default=0,
+        desc="Number of molecules",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_meta(self, dataset, **kwd):
         """
         Set the number of lines of data in dataset.
         """
-        dataset.metadata.number_of_molecules = count_special_lines(r'^\s*<molecule', dataset.file_name)
+        dataset.metadata.number_of_molecules = count_special_lines(r"^\s*<molecule", dataset.file_name)
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            if (dataset.metadata.number_of_molecules == 1):
+            if dataset.metadata.number_of_molecules == 1:
                 dataset.blurb = "1 molecule"
             else:
                 dataset.blurb = f"{dataset.metadata.number_of_molecules} molecules"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -812,7 +865,7 @@ class CML(GenericXml):
         >>> CML().sniff(fname)
         True
         """
-        for expected_string in ['<?xml version="1.0"?>', 'http://www.xml-cml.org/schema']:
+        for expected_string in ['<?xml version="1.0"?>', "http://www.xml-cml.org/schema"]:
             if expected_string not in file_prefix.contents_header:
                 return False
 
@@ -831,10 +884,10 @@ class CML(GenericXml):
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
+        if split_params["split_mode"] == "number_of_parts":
             raise Exception(f"Split mode \"{split_params['split_mode']}\" is currently not implemented for CML-files.")
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
             raise Exception(f"Unsupported split mode {split_params['split_mode']}")
 
@@ -842,22 +895,24 @@ class CML(GenericXml):
             lines = []
             with open(filename) as handle:
                 for line in handle:
-                    if line.lstrip().startswith('<?xml version="1.0"?>') or \
-                       line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema') or \
-                       line.lstrip().startswith('</cml>'):
+                    if (
+                        line.lstrip().startswith('<?xml version="1.0"?>')
+                        or line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema')
+                        or line.lstrip().startswith("</cml>")
+                    ):
                         continue
                     lines.append(line)
-                    if line.lstrip().startswith('</molecule>'):
+                    if line.lstrip().startswith("</molecule>"):
                         yield lines
                         lines = []
 
         header_lines = ['<?xml version="1.0"?>\n', '<cml xmlns="http://www.xml-cml.org/schema">\n']
-        footer_line = ['</cml>\n']
+        footer_line = ["</cml>\n"]
 
         def _write_part_cml_file(accumulated_lines):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
-            with open(part_path, 'w') as part_file:
+            with open(part_path, "w") as part_file:
                 part_file.writelines(header_lines)
                 part_file.writelines(accumulated_lines)
                 part_file.writelines(footer_line)
@@ -873,7 +928,7 @@ class CML(GenericXml):
             if cml_lines_accumulated:
                 _write_part_cml_file(cml_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s', unicodify(e))
+            log.error("Unable to split files: %s", unicodify(e))
             raise
 
     @staticmethod
@@ -885,8 +940,7 @@ class CML(GenericXml):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("Given no CML files, %r, to merge into %s"
-                             % (split_files, output_file))
+            raise ValueError("Given no CML files, %r, to merge into %s" % (split_files, output_file))
         with open(output_file, "w") as out:
             for filename in split_files:
                 with open(filename) as handle:
@@ -904,9 +958,9 @@ class CML(GenericXml):
                     molecule_found = False
                     for line in handle.readlines():
                         # We found two required header lines, the next line should start with <molecule >
-                        if line.lstrip().startswith('</cml>'):
+                        if line.lstrip().startswith("</cml>"):
                             continue
-                        if line.lstrip().startswith('<molecule'):
+                        if line.lstrip().startswith("<molecule"):
                             molecule_found = True
                         if molecule_found:
                             out.write(line)
@@ -918,6 +972,7 @@ class GRO(GenericMolFile):
     GROMACS structure format.
     https://manual.gromacs.org/current/reference-manual/file-formats.html#gro
     """
+
     file_ext = "gro"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -932,21 +987,24 @@ class GRO(GenericMolFile):
         >>> GRO().sniff_prefix(fname)
         False
         """
-        headers = get_headers(file_prefix, sep='\n', count=300)
+        headers = get_headers(file_prefix, sep="\n", count=300)
         try:
             int(headers[1][0])  # the second line should just be the number of atoms
         except ValueError:
             return False
         for line in headers[2:-1]:  # skip the first, second and last lines
-            if not re.search(r'^[0-9 ]{5}[a-zA-Z0-9 ]{10}[0-9 ]{5}[0-9 -]{4}\.[0-9]{3}[0-9 -]{4}\.[0-9]{3}[0-9 -]{4}\.[0-9]{3}', line[0]):
+            if not re.search(
+                r"^[0-9 ]{5}[a-zA-Z0-9 ]{10}[0-9 ]{5}[0-9 -]{4}\.[0-9]{3}[0-9 -]{4}\.[0-9]{3}[0-9 -]{4}\.[0-9]{3}",
+                line[0],
+            ):
                 return False
         return True
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name)
-            atom_number = int(dataset.peek.split('\n')[1])
+            atom_number = int(dataset.peek.split("\n")[1])
             dataset.blurb = f"{atom_number} atoms"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index 2c7cd917b31..f1ac6c353e6 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -11,7 +11,7 @@ from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
     get_headers,
-    iter_headers
+    iter_headers,
 )
 from galaxy.datatypes.tabular import Tabular
 from galaxy.util import unicodify
@@ -21,7 +21,7 @@ log = logging.getLogger(__name__)
 
 @build_sniff_from_prefix
 class Otu(Text):
-    file_ext = 'mothur.otu'
+    file_ext = "mothur.otu"
     MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0)
     MetadataElement(name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[])
     MetadataElement(name="otulabels", default=[], desc="OTU Names", readonly=True, visible=True, no_value=[])
@@ -57,8 +57,8 @@ class Otu(Text):
             data_lines = 0
             comment_lines = 0
 
-            headers = iter_headers(dataset.file_name, sep='\t', count=-1)
-            first_line = get_headers(dataset.file_name, sep='\t', count=1)
+            headers = iter_headers(dataset.file_name, sep="\t", count=-1)
+            first_line = get_headers(dataset.file_name, sep="\t", count=1)
             if first_line:
                 first_line = first_line[0]
             # set otulabels
@@ -66,7 +66,7 @@ class Otu(Text):
                 otulabel_names = first_line[2:]
             # set label names and number of lines
             for line in headers:
-                if len(line) >= 2 and not line[0].startswith('@'):
+                if len(line) >= 2 and not line[0].startswith("@"):
                     data_lines += 1
                     ncols = max(ncols, len(line))
                     label_names.add(line[0])
@@ -90,10 +90,10 @@ class Otu(Text):
         >>> Otu().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 if len(line) < 2:
                     return False
                 if count >= 1:
@@ -111,7 +111,7 @@ class Otu(Text):
 
 
 class Sabund(Otu):
-    file_ext = 'mothur.sabund'
+    file_ext = "mothur.sabund"
 
     def __init__(self, **kwd):
         """
@@ -135,10 +135,10 @@ class Sabund(Otu):
         >>> Sabund().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 if len(line) < 2:
                     return False
                 try:
@@ -157,7 +157,7 @@ class Sabund(Otu):
 
 
 class GroupAbund(Otu):
-    file_ext = 'mothur.shared'
+    file_ext = "mothur.shared"
     MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[])
 
     def __init__(self, **kwd):
@@ -177,9 +177,9 @@ class GroupAbund(Otu):
             comment_lines = 0
             ncols = 0
 
-            headers = iter_headers(dataset.file_name, sep='\t', count=-1)
+            headers = iter_headers(dataset.file_name, sep="\t", count=-1)
             for line in headers:
-                if line[0] == 'label' and line[1] == 'Group':
+                if line[0] == "label" and line[1] == "Group":
                     skip = 1
                     comment_lines += 1
                 else:
@@ -211,13 +211,13 @@ class GroupAbund(Otu):
         >>> GroupAbund().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 if len(line) < 3:
                     return False
-                if count > 0 or line[0] != 'label':
+                if count > 0 or line[0] != "label":
                     try:
                         check = int(line[2])
                         if check + 3 != len(line):
@@ -237,12 +237,12 @@ class GroupAbund(Otu):
 
 @build_sniff_from_prefix
 class SecondaryStructureMap(Tabular):
-    file_ext = 'mothur.map'
+    file_ext = "mothur.map"
 
     def __init__(self, **kwd):
         """Initialize secondary structure map datatype"""
         super().__init__(**kwd)
-        self.column_names = ['Map']
+        self.column_names = ["Map"]
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -259,7 +259,7 @@ class SecondaryStructureMap(Tabular):
         >>> SecondaryStructureMap().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         line_num = 0
         rowidxmap = {}
         for line in headers:
@@ -281,13 +281,13 @@ class SecondaryStructureMap(Tabular):
 
 
 class AlignCheck(Tabular):
-    file_ext = 'mothur.align.check'
+    file_ext = "mothur.align.check"
 
     def __init__(self, **kwd):
         """Initialize AlignCheck datatype"""
         super().__init__(**kwd)
-        self.column_names = ['name', 'pound', 'dash', 'plus', 'equal', 'loop', 'tilde', 'total']
-        self.column_types = ['str', 'int', 'int', 'int', 'int', 'int', 'int', 'int']
+        self.column_names = ["name", "pound", "dash", "plus", "equal", "loop", "tilde", "total"]
+        self.column_types = ["str", "int", "int", "int", "int", "int", "int", "int"]
         self.comment_lines = 1
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -305,21 +305,44 @@ class AlignReport(Tabular):
     QueryName	QueryLength	TemplateName	TemplateLength	SearchMethod	SearchScore	AlignmentMethod	QueryStart	QueryEnd	TemplateStart	TemplateEnd	PairwiseAlignmentLength	GapsInQuery	GapsInTemplate	LongestInsert	SimBtwnQuery&Template
     AY457915	501		82283		1525		kmer		89.07		needleman	5		501		1		499		499			2		0		0		97.6
     """
-    file_ext = 'mothur.align.report'
+
+    file_ext = "mothur.align.report"
 
     def __init__(self, **kwd):
         """Initialize AlignCheck datatype"""
         super().__init__(**kwd)
-        self.column_names = ['QueryName', 'QueryLength', 'TemplateName', 'TemplateLength', 'SearchMethod', 'SearchScore',
-                             'AlignmentMethod', 'QueryStart', 'QueryEnd', 'TemplateStart', 'TemplateEnd',
-                             'PairwiseAlignmentLength', 'GapsInQuery', 'GapsInTemplate', 'LongestInsert', 'SimBtwnQuery&Template'
-                             ]
+        self.column_names = [
+            "QueryName",
+            "QueryLength",
+            "TemplateName",
+            "TemplateLength",
+            "SearchMethod",
+            "SearchScore",
+            "AlignmentMethod",
+            "QueryStart",
+            "QueryEnd",
+            "TemplateStart",
+            "TemplateEnd",
+            "PairwiseAlignmentLength",
+            "GapsInQuery",
+            "GapsInTemplate",
+            "LongestInsert",
+            "SimBtwnQuery&Template",
+        ]
 
 
 class DistanceMatrix(Text):
-    file_ext = 'mothur.dist'
+    file_ext = "mothur.dist"
 
-    MetadataElement(name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?')
+    MetadataElement(
+        name="sequence_count",
+        default=0,
+        desc="Number of sequences",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="?",
+    )
 
     def init_meta(self, dataset, copy_from=None):
         super().init_meta(dataset, copy_from=copy_from)
@@ -327,11 +350,11 @@ class DistanceMatrix(Text):
     def set_meta(self, dataset, overwrite=True, skip=0, **kwd):
         super().set_meta(dataset, overwrite=overwrite, skip=skip, **kwd)
 
-        headers = iter_headers(dataset.file_name, sep='\t')
+        headers = iter_headers(dataset.file_name, sep="\t")
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 try:
-                    dataset.metadata.sequence_count = int(''.join(line))  # seq count sometimes preceded by tab
+                    dataset.metadata.sequence_count = int("".join(line))  # seq count sometimes preceded by tab
                     break
                 except Exception as e:
                     if not isinstance(self, PairwiseDistanceMatrix):
@@ -340,7 +363,7 @@ class DistanceMatrix(Text):
 
 @build_sniff_from_prefix
 class LowerTriangleDistanceMatrix(DistanceMatrix):
-    file_ext = 'mothur.lower.dist'
+    file_ext = "mothur.lower.dist"
 
     def __init__(self, **kwd):
         """Initialize secondary structure map datatype"""
@@ -371,17 +394,17 @@ class LowerTriangleDistanceMatrix(DistanceMatrix):
         False
         """
         numlines = 300
-        headers = iter_headers(file_prefix, sep='\t', count=numlines)
+        headers = iter_headers(file_prefix, sep="\t", count=numlines)
         line_num = 0
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 # first line should contain the number of sequences in the file
                 if line_num == 0:
                     if len(line) > 2:
                         return False
                     else:
                         try:
-                            sequence_count = int(''.join(line))
+                            sequence_count = int("".join(line))
                             assert sequence_count > 0
                         except ValueError:
                             return False
@@ -406,7 +429,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix):
 
 @build_sniff_from_prefix
 class SquareDistanceMatrix(DistanceMatrix):
-    file_ext = 'mothur.square.dist'
+    file_ext = "mothur.square.dist"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -435,16 +458,16 @@ class SquareDistanceMatrix(DistanceMatrix):
         False
         """
         numlines = 300
-        headers = iter_headers(file_prefix, sep='\t', count=numlines)
+        headers = iter_headers(file_prefix, sep="\t", count=numlines)
         line_num = 0
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 if line_num == 0:
                     if len(line) > 2:
                         return False
                     else:
                         try:
-                            sequence_count = int(''.join(line))
+                            sequence_count = int("".join(line))
                             assert sequence_count > 0
                         except ValueError:
                             return False
@@ -469,13 +492,13 @@ class SquareDistanceMatrix(DistanceMatrix):
 
 @build_sniff_from_prefix
 class PairwiseDistanceMatrix(DistanceMatrix, Tabular):
-    file_ext = 'mothur.pair.dist'
+    file_ext = "mothur.pair.dist"
 
     def __init__(self, **kwd):
         """Initialize secondary structure map datatype"""
         super().__init__(**kwd)
-        self.column_names = ['Sequence', 'Sequence', 'Distance']
-        self.column_types = ['str', 'str', 'float']
+        self.column_names = ["Sequence", "Sequence", "Distance"]
+        self.column_types = ["str", "str", "float"]
 
     def set_meta(self, dataset, overwrite=True, skip=None, **kwd):
         super().set_meta(dataset, overwrite=overwrite, skip=skip, **kwd)
@@ -493,11 +516,11 @@ class PairwiseDistanceMatrix(DistanceMatrix, Tabular):
         >>> PairwiseDistanceMatrix().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         names = [False, False]
         for line in headers:
-            if line[0].startswith('@'):
+            if line[0].startswith("@"):
                 continue
             if len(line) != 3:
                 return False
@@ -530,7 +553,7 @@ class PairwiseDistanceMatrix(DistanceMatrix, Tabular):
 
 
 class Names(Tabular):
-    file_ext = 'mothur.names'
+    file_ext = "mothur.names"
 
     def __init__(self, **kwd):
         """
@@ -538,22 +561,22 @@ class Names(Tabular):
         Name file shows the relationship between a representative sequence(col 1)  and the sequences(comma-separated) it represents(col 2)
         """
         super().__init__(**kwd)
-        self.column_names = ['name', 'representatives']
+        self.column_names = ["name", "representatives"]
         self.columns = 2
 
 
 class Summary(Tabular):
-    file_ext = 'mothur.summary'
+    file_ext = "mothur.summary"
 
     def __init__(self, **kwd):
         """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file"""
         super().__init__(**kwd)
-        self.column_names = ['seqname', 'start', 'end', 'nbases', 'ambigs', 'polymer']
+        self.column_names = ["seqname", "start", "end", "nbases", "ambigs", "polymer"]
         self.columns = 6
 
 
 class Group(Tabular):
-    file_ext = 'mothur.groups'
+    file_ext = "mothur.groups"
     MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[])
 
     def __init__(self, **kwd):
@@ -562,14 +585,14 @@ class Group(Tabular):
         Group file assigns sequence (col 1)  to a group (col 2)
         """
         super().__init__(**kwd)
-        self.column_names = ['name', 'group']
+        self.column_names = ["name", "group"]
         self.columns = 2
 
     def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=None, **kwd):
         super().set_meta(dataset, overwrite, skip, max_data_lines)
 
         group_names = set()
-        headers = iter_headers(dataset.file_name, sep='\t', count=-1)
+        headers = iter_headers(dataset.file_name, sep="\t", count=-1)
         for line in headers:
             if len(line) > 1:
                 group_names.add(line[1])
@@ -577,18 +600,18 @@ class Group(Tabular):
 
 
 class AccNos(Tabular):
-    file_ext = 'mothur.accnos'
+    file_ext = "mothur.accnos"
 
     def __init__(self, **kwd):
         """A list of names"""
         super().__init__(**kwd)
-        self.column_names = ['name']
+        self.column_names = ["name"]
         self.columns = 1
 
 
 @build_sniff_from_prefix
 class Oligos(Text):
-    file_ext = 'mothur.oligos'
+    file_ext = "mothur.oligos"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -603,14 +626,14 @@ class Oligos(Text):
         >>> Oligos().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         for line in headers:
-            if not line[0].startswith('@') and not line[0].startswith('#'):
-                if len(line) == 2 and line[0] in ['forward', 'reverse']:
+            if not line[0].startswith("@") and not line[0].startswith("#"):
+                if len(line) == 2 and line[0] in ["forward", "reverse"]:
                     count += 1
                     continue
-                elif len(line) == 3 and line[0] == 'barcode':
+                elif len(line) == 3 and line[0] == "barcode":
                     count += 1
                     continue
                 else:
@@ -623,13 +646,13 @@ class Oligos(Text):
 
 @build_sniff_from_prefix
 class Frequency(Tabular):
-    file_ext = 'mothur.freq'
+    file_ext = "mothur.freq"
 
     def __init__(self, **kwd):
         """A list of names"""
         super().__init__(**kwd)
-        self.column_names = ['position', 'frequency']
-        self.column_types = ['int', 'float']
+        self.column_names = ["position", "frequency"]
+        self.column_types = ["int", "float"]
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -655,13 +678,13 @@ class Frequency(Tabular):
         >>> Frequency().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         for line in headers:
-            if not line[0].startswith('@'):
+            if not line[0].startswith("@"):
                 # first line should be #<version string>
                 if count == 0:
-                    if not line[0].startswith('#') or len(line) != 1:
+                    if not line[0].startswith("#") or len(line) != 1:
                         return False
 
                 else:
@@ -672,7 +695,7 @@ class Frequency(Tabular):
                         int(line[0])
                         float(line[1])
 
-                        if line[1].find('.') == -1:
+                        if line[1].find(".") == -1:
                             return False
                     except Exception:
                         return False
@@ -686,15 +709,29 @@ class Frequency(Tabular):
 
 @build_sniff_from_prefix
 class Quantile(Tabular):
-    file_ext = 'mothur.quan'
-    MetadataElement(name="filtered", default=False, no_value=False, optional=True, desc="Quantiles calculated using a mask", readonly=True)
-    MetadataElement(name="masked", default=False, no_value=False, optional=True, desc="Quantiles calculated using a frequency filter", readonly=True)
+    file_ext = "mothur.quan"
+    MetadataElement(
+        name="filtered",
+        default=False,
+        no_value=False,
+        optional=True,
+        desc="Quantiles calculated using a mask",
+        readonly=True,
+    )
+    MetadataElement(
+        name="masked",
+        default=False,
+        no_value=False,
+        optional=True,
+        desc="Quantiles calculated using a frequency filter",
+        readonly=True,
+    )
 
     def __init__(self, **kwd):
         """Quantiles for chimera analysis"""
         super().__init__(**kwd)
-        self.column_names = ['num', 'ten', 'twentyfive', 'fifty', 'seventyfive', 'ninetyfive', 'ninetynine']
-        self.column_types = ['int', 'float', 'float', 'float', 'float', 'float', 'float']
+        self.column_names = ["num", "ten", "twentyfive", "fifty", "seventyfive", "ninetyfive", "ninetynine"]
+        self.column_types = ["int", "float", "float", "float", "float", "float", "float"]
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -715,10 +752,10 @@ class Quantile(Tabular):
         >>> Quantile().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         for line in headers:
-            if not line[0].startswith('@') and not line[0].startswith('#'):
+            if not line[0].startswith("@") and not line[0].startswith("#"):
                 if len(line) != 7:
                     return False
                 try:
@@ -740,7 +777,7 @@ class Quantile(Tabular):
 
 @build_sniff_from_prefix
 class LaneMask(Text):
-    file_ext = 'mothur.filter'
+    file_ext = "mothur.filter"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -754,7 +791,7 @@ class LaneMask(Text):
         >>> LaneMask().sniff( fname )
         False
         """
-        headers = get_headers(file_prefix, sep='\t', count=2)
+        headers = get_headers(file_prefix, sep="\t", count=2)
         if len(headers) != 1 or len(headers[0]) != 1:
             return False
 
@@ -762,7 +799,7 @@ class LaneMask(Text):
             # these filter files should be relatively big
             return False
 
-        if not re.match('^[01]+$', headers[0][0]):
+        if not re.match("^[01]+$", headers[0][0]):
             return False
 
         return True
@@ -770,7 +807,7 @@ class LaneMask(Text):
 
 class CountTable(Tabular):
     MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[])
-    file_ext = 'mothur.count_table'
+    file_ext = "mothur.count_table"
 
     def __init__(self, **kwd):
         """
@@ -790,14 +827,14 @@ class CountTable(Tabular):
         U68647  1       0       1
         """
         super().__init__(**kwd)
-        self.column_names = ['name', 'total']
+        self.column_names = ["name", "total"]
 
     def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd):
         super().set_meta(dataset, overwrite=overwrite, **kwd)
 
-        headers = get_headers(dataset.file_name, sep='\t', count=1)
+        headers = get_headers(dataset.file_name, sep="\t", count=1)
         colnames = headers[0]
-        dataset.metadata.column_types = ['str'] + (['int'] * (len(headers[0]) - 1))
+        dataset.metadata.column_types = ["str"] + (["int"] * (len(headers[0]) - 1))
         if len(colnames) > 1:
             dataset.metadata.columns = len(colnames)
         if len(colnames) > 2:
@@ -810,11 +847,11 @@ class CountTable(Tabular):
 
 @build_sniff_from_prefix
 class RefTaxonomy(Tabular):
-    file_ext = 'mothur.ref.taxonomy'
+    file_ext = "mothur.ref.taxonomy"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.column_names = ['name', 'taxonomy']
+        self.column_names = ["name", "taxonomy"]
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -851,17 +888,17 @@ class RefTaxonomy(Tabular):
         >>> RefTaxonomy().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t', count=300)
+        headers = iter_headers(file_prefix, sep="\t", count=300)
         count = 0
-        pat_prog = re.compile('^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$')
+        pat_prog = re.compile("^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$")
         found_semicolons = False
         for line in headers:
-            if not line[0].startswith('@') and not line[0].startswith('#'):
+            if not line[0].startswith("@") and not line[0].startswith("#"):
                 if not (2 <= len(line) <= 3):
                     return False
                 if not pat_prog.match(line[1]):
                     return False
-                if not found_semicolons and line[1].find(';') > -1:
+                if not found_semicolons and line[1].find(";") > -1:
                     found_semicolons = True
                 if len(line) == 3:
                     try:
@@ -878,26 +915,26 @@ class RefTaxonomy(Tabular):
 
 
 class ConsensusTaxonomy(Tabular):
-    file_ext = 'mothur.cons.taxonomy'
+    file_ext = "mothur.cons.taxonomy"
 
     def __init__(self, **kwd):
         """A list of names"""
         super().__init__(**kwd)
-        self.column_names = ['OTU', 'count', 'taxonomy']
+        self.column_names = ["OTU", "count", "taxonomy"]
 
 
 class TaxonomySummary(Tabular):
-    file_ext = 'mothur.tax.summary'
+    file_ext = "mothur.tax.summary"
 
     def __init__(self, **kwd):
         """A Summary of taxon classification"""
         super().__init__(**kwd)
-        self.column_names = ['taxlevel', 'rankID', 'taxon', 'daughterlevels', 'total']
+        self.column_names = ["taxlevel", "rankID", "taxon", "daughterlevels", "total"]
 
 
 @build_sniff_from_prefix
 class Axes(Tabular):
-    file_ext = 'mothur.axes'
+    file_ext = "mothur.axes"
 
     def __init__(self, **kwd):
         """Initialize axes datatype"""
@@ -930,7 +967,7 @@ class Axes(Tabular):
         >>> Axes().sniff( fname )
         False
         """
-        headers = iter_headers(file_prefix, sep='\t')
+        headers = iter_headers(file_prefix, sep="\t")
         count = 0
         col_cnt = None
         all_integers = True
@@ -984,10 +1021,15 @@ class SffFlow(Tabular):
         GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ...
 
     """
-    file_ext = 'mothur.sff.flow'
 
-    MetadataElement(name="flow_values", default="", no_value="", optional=True, desc="Total number of flow values", readonly=True)
-    MetadataElement(name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False)
+    file_ext = "mothur.sff.flow"
+
+    MetadataElement(
+        name="flow_values", default="", no_value="", optional=True, desc="Total number of flow values", readonly=True
+    )
+    MetadataElement(
+        name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False
+    )
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -995,7 +1037,7 @@ class SffFlow(Tabular):
     def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd):
         super().set_meta(dataset, overwrite, 1, max_data_lines)
 
-        headers = get_headers(dataset.file_name, sep='\t', count=1)
+        headers = get_headers(dataset.file_name, sep="\t", count=1)
         try:
             flow_values = int(headers[0][0])
             dataset.metadata.flow_values = flow_values
@@ -1010,20 +1052,21 @@ class SffFlow(Tabular):
             out = '<table cellspacing="0" cellpadding="3">'
 
             # Generate column header
-            out += '<tr>'
-            out += '<th>1. Name</th>'
-            out += '<th>2. Flows</th>'
+            out += "<tr>"
+            out += "<th>1. Name</th>"
+            out += "<th>2. Flows</th>"
             for i in range(3, dataset.metadata.columns + 1):
                 base = dataset.metadata.flow_order[(i + 1) % 4]
-                out += '<th>%d. %s</th>' % (i - 2, base)
-            out += '</tr>'
+                out += "<th>%d. %s</th>" % (i - 2, base)
+            out += "</tr>"
             out += self.make_html_peek_rows(dataset, skipchars=skipchars)
-            out += '</table>'
+            out += "</table>"
         except Exception as exc:
             out = f"Can't create peek: {unicodify(exc)}"
         return out
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/msa.py b/lib/galaxy/datatypes/msa.py
index e187d663f31..c5c8feab069 100644
--- a/lib/galaxy/datatypes/msa.py
+++ b/lib/galaxy/datatypes/msa.py
@@ -4,7 +4,10 @@ import os
 import re
 
 from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.data import get_file_peek, Text
+from galaxy.datatypes.data import (
+    get_file_peek,
+    Text,
+)
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
@@ -18,18 +21,32 @@ from galaxy.util import (
 
 log = logging.getLogger(__name__)
 
-STOCKHOLM_SEARCH_PATTERN = re.compile(r'#\s+STOCKHOLM\s+1\.0')
+STOCKHOLM_SEARCH_PATTERN = re.compile(r"#\s+STOCKHOLM\s+1\.0")
 
 
 @build_sniff_from_prefix
 class InfernalCM(Text):
     file_ext = "cm"
 
-    MetadataElement(name="number_of_models", default=0, desc="Number of covariance models",
-                    readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="number_of_models",
+        default=0,
+        desc="Number of covariance models",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
-    MetadataElement(name="cm_version", default="1/a", desc="Infernal Covariance Model version",
-                    readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="cm_version",
+        default="1/a",
+        desc="Infernal Covariance Model version",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
@@ -40,8 +57,8 @@ class InfernalCM(Text):
                 dataset.blurb = f"{dataset.metadata.number_of_models} models"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -59,11 +76,11 @@ class InfernalCM(Text):
         """
         Set the number of models and the version of CM file in dataset.
         """
-        dataset.metadata.number_of_models = generic_util.count_special_lines('^INFERNAL', dataset.file_name)
+        dataset.metadata.number_of_models = generic_util.count_special_lines("^INFERNAL", dataset.file_name)
         with open(dataset.file_name) as f:
             first_line = f.readline()
             if first_line.startswith("INFERNAL"):
-                dataset.metadata.cm_version = (first_line.split()[0]).replace('INFERNAL', '')
+                dataset.metadata.cm_version = (first_line.split()[0]).replace("INFERNAL", "")
 
 
 @build_sniff_from_prefix
@@ -76,8 +93,8 @@ class Hmmer(Text):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "HMMER Database"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def display_peek(self, dataset):
         try:
@@ -95,9 +112,8 @@ class Hmmer2(Hmmer):
     file_ext = "hmm2"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """HMMER2 files start with HMMER2.0
-        """
-        return file_prefix.startswith('HMMER2.0')
+        """HMMER2 files start with HMMER2.0"""
+        return file_prefix.startswith("HMMER2.0")
 
 
 class Hmmer3(Hmmer):
@@ -105,15 +121,15 @@ class Hmmer3(Hmmer):
     file_ext = "hmm3"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """HMMER3 files start with HMMER3/f
-        """
-        return file_prefix.startswith('HMMER3/f')
+        """HMMER3 files start with HMMER3/f"""
+        return file_prefix.startswith("HMMER3/f")
 
 
 class HmmerPress(Binary):
     """Class for hmmpress database files."""
-    file_ext = 'hmmpress'
-    composite_type = 'basic'
+
+    file_ext = "hmmpress"
+    composite_type = "basic"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text."""
@@ -121,8 +137,8 @@ class HmmerPress(Binary):
             dataset.peek = "HMMER Binary database"
             dataset.blurb = "HMMER Binary database"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Create HTML content, used for displaying peek."""
@@ -134,13 +150,13 @@ class HmmerPress(Binary):
     def __init__(self, **kwd):
         super().__init__(**kwd)
         # Binary model
-        self.add_composite_file('model.hmm.h3m', is_binary=True)
+        self.add_composite_file("model.hmm.h3m", is_binary=True)
         # SSI index for binary model
-        self.add_composite_file('model.hmm.h3i', is_binary=True)
+        self.add_composite_file("model.hmm.h3i", is_binary=True)
         # Profiles (MSV part)
-        self.add_composite_file('model.hmm.h3f', is_binary=True)
+        self.add_composite_file("model.hmm.h3f", is_binary=True)
         # Profiles (remained)
-        self.add_composite_file('model.hmm.h3p', is_binary=True)
+        self.add_composite_file("model.hmm.h3p", is_binary=True)
 
 
 @build_sniff_from_prefix
@@ -149,18 +165,26 @@ class Stockholm_1_0(Text):
     edam_format = "format_1961"
     file_ext = "stockholm"
 
-    MetadataElement(name="number_of_models", default=0, desc="Number of multiple alignments", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="number_of_models",
+        default=0,
+        desc="Number of multiple alignments",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            if (dataset.metadata.number_of_models == 1):
+            if dataset.metadata.number_of_models == 1:
                 dataset.blurb = "1 alignment"
             else:
                 dataset.blurb = f"{dataset.metadata.number_of_models} alignments"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         return file_prefix.search(STOCKHOLM_SEARCH_PATTERN)
@@ -170,7 +194,9 @@ class Stockholm_1_0(Text):
 
         Set the number of models in dataset.
         """
-        dataset.metadata.number_of_models = generic_util.count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
+        dataset.metadata.number_of_models = generic_util.count_special_lines(
+            "^#[[:space:]+]STOCKHOLM[[:space:]+]1.0", dataset.file_name
+        )
 
     @classmethod
     def split(cls, input_datasets, subdir_generator_function, split_params):
@@ -186,10 +212,12 @@ class Stockholm_1_0(Text):
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
-            raise Exception(f"Split mode \"{split_params['split_mode']}\" is currently not implemented for STOCKHOLM-files.")
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        if split_params["split_mode"] == "number_of_parts":
+            raise Exception(
+                f"Split mode \"{split_params['split_mode']}\" is currently not implemented for STOCKHOLM-files."
+            )
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
             raise Exception(f"Unsupported split mode {split_params['split_mode']}")
 
@@ -198,14 +226,14 @@ class Stockholm_1_0(Text):
             with open(filename) as handle:
                 for line in handle:
                     lines.append(line)
-                    if line.strip() == '//':
+                    if line.strip() == "//":
                         yield lines
                         lines = []
 
         def _write_part_stockholm_file(accumulated_lines):
             part_dir = subdir_generator_function()
             part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
-            with open(part_path, 'w') as part_file:
+            with open(part_path, "w") as part_file:
                 part_file.writelines(accumulated_lines)
 
         try:
@@ -220,7 +248,7 @@ class Stockholm_1_0(Text):
             if stockholm_lines_accumulated:
                 _write_part_stockholm_file(stockholm_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s', unicodify(e))
+            log.error("Unable to split files: %s", unicodify(e))
             raise
 
 
@@ -228,24 +256,34 @@ class Stockholm_1_0(Text):
 class MauveXmfa(Text):
     file_ext = "xmfa"
 
-    MetadataElement(name="number_of_models", default=0, desc="Number of alignmened sequences", readonly=True, visible=True, optional=True, no_value=0)
+    MetadataElement(
+        name="number_of_models",
+        default=0,
+        desc="Number of alignmened sequences",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            if (dataset.metadata.number_of_models == 1):
+            if dataset.metadata.number_of_models == 1:
                 dataset.blurb = "1 alignment"
             else:
                 dataset.blurb = f"{dataset.metadata.number_of_models} alignments"
             dataset.peek = get_file_peek(dataset.file_name)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        return file_prefix.startswith('#FormatVersion Mauve1')
+        return file_prefix.startswith("#FormatVersion Mauve1")
 
     def set_meta(self, dataset, **kwd):
-        dataset.metadata.number_of_models = generic_util.count_special_lines('^#Sequence([[:digit:]]+)Entry', dataset.file_name)
+        dataset.metadata.number_of_models = generic_util.count_special_lines(
+            "^#Sequence([[:digit:]]+)Entry", dataset.file_name
+        )
 
 
 class Msf(Text):
@@ -253,6 +291,7 @@ class Msf(Text):
     Multiple sequence alignment format produced by the Accelrys GCG suite and
     other programs.
     """
+
     edam_data = "data_0863"
     edam_format = "format_1947"
-    file_ext = 'msf'
+    file_ext = "msf"
diff --git a/lib/galaxy/datatypes/neo4j.py b/lib/galaxy/datatypes/neo4j.py
index c4191706aec..c2706a8917a 100644
--- a/lib/galaxy/datatypes/neo4j.py
+++ b/lib/galaxy/datatypes/neo4j.py
@@ -26,30 +26,30 @@ class Neo4j(Html):
         """
         # self.regenerate_primary_file(dataset)
         rval = [
-            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
-            This composite dataset is composed of the following files:<p/><ul>' % (
-                self.file_ext)]
+            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>"
+            % (self.file_ext)
+        ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            rval.append('<li><a href="%s">%s</a>%s' %
-                        (composite_name, composite_name, opt_text))
-        rval.append('</ul></html>')
+                opt_text = " (optional)"
+            rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
+        rval.append("</ul></html>")
         return "\n".join(rval)
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/html'
+        return "text/html"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
-            dataset.peek = 'Neo4j database (multiple files)'
-            dataset.blurb = 'Neo4j database (multiple files)'
+            dataset.peek = "Neo4j database (multiple files)"
+            dataset.blurb = "Neo4j database (multiple files)"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Create HTML content, used for displaying peek."""
@@ -61,80 +61,80 @@ class Neo4j(Html):
 
 class Neo4jDB(Neo4j, Data):
     """Class for neo4jDB database files."""
-    file_ext = 'neostore'
-    composite_type = 'auto_primary_file'
+
+    file_ext = "neostore"
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         Data.__init__(self, **kwd)
-        self.add_composite_file('neostore', is_binary=True)
-        self.add_composite_file('neostore.id', is_binary=True)
-        self.add_composite_file('neostore.counts.db.a', optional=True, is_binary=True)
-        self.add_composite_file('neostore.counts.db.b', optional=True, is_binary=True)
-        self.add_composite_file('neostore.labeltokenstore.db', is_binary=True)
-        self.add_composite_file(
-            'neostore.labeltokenstore.db.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.labeltokenstore.db.names', is_binary=True)
-        self.add_composite_file(
-            'neostore.labeltokenstore.db.names.id', is_binary=True)
-        self.add_composite_file('neostore.nodestore.db', is_binary=True)
-        self.add_composite_file('neostore.nodestore.db.id', is_binary=True)
-        self.add_composite_file('neostore.nodestore.db.labels', is_binary=True)
-        self.add_composite_file(
-            'neostore.nodestore.db.labels.id', is_binary=True)
+        self.add_composite_file("neostore", is_binary=True)
+        self.add_composite_file("neostore.id", is_binary=True)
+        self.add_composite_file("neostore.counts.db.a", optional=True, is_binary=True)
+        self.add_composite_file("neostore.counts.db.b", optional=True, is_binary=True)
+        self.add_composite_file("neostore.labeltokenstore.db", is_binary=True)
+        self.add_composite_file("neostore.labeltokenstore.db.id", is_binary=True)
+        self.add_composite_file("neostore.labeltokenstore.db.names", is_binary=True)
+        self.add_composite_file("neostore.labeltokenstore.db.names.id", is_binary=True)
+        self.add_composite_file("neostore.nodestore.db", is_binary=True)
+        self.add_composite_file("neostore.nodestore.db.id", is_binary=True)
+        self.add_composite_file("neostore.nodestore.db.labels", is_binary=True)
+        self.add_composite_file("neostore.nodestore.db.labels.id", is_binary=True)
 
-        self.add_composite_file('neostore.propertystore.db', is_binary=True)
-        self.add_composite_file('neostore.propertystore.db.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.arrays', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.arrays.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.index', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.index.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.index.keys', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.index.keys.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.strings', is_binary=True)
-        self.add_composite_file(
-            'neostore.propertystore.db.strings.id', is_binary=True)
+        self.add_composite_file("neostore.propertystore.db", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.id", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.arrays", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.arrays.id", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.index", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.index.id", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.index.keys", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.index.keys.id", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.strings", is_binary=True)
+        self.add_composite_file("neostore.propertystore.db.strings.id", is_binary=True)
 
-        self.add_composite_file(
-            'neostore.relationshipgroupstore.db', is_binary=True)
-        self.add_composite_file(
-            'neostore.relationshipgroupstore.db.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.relationshipstore.db', is_binary=True)
-        self.add_composite_file(
-            'neostore.relationshipstore.db.id', is_binary=True)
-        self.add_composite_file(
-            'neostore.relationshiptypestore.db.names', is_binary=True)
-        self.add_composite_file(
-            'neostore.relationshiptypestore.db.names.id', is_binary=True)
-        self.add_composite_file('neostore.schemastore.db', is_binary=True)
-        self.add_composite_file('neostore.schemastore.db.id', is_binary=True)
-        self.add_composite_file('neostore.transaction.db.0', is_binary=True)
+        self.add_composite_file("neostore.relationshipgroupstore.db", is_binary=True)
+        self.add_composite_file("neostore.relationshipgroupstore.db.id", is_binary=True)
+        self.add_composite_file("neostore.relationshipstore.db", is_binary=True)
+        self.add_composite_file("neostore.relationshipstore.db.id", is_binary=True)
+        self.add_composite_file("neostore.relationshiptypestore.db.names", is_binary=True)
+        self.add_composite_file("neostore.relationshiptypestore.db.names.id", is_binary=True)
+        self.add_composite_file("neostore.schemastore.db", is_binary=True)
+        self.add_composite_file("neostore.schemastore.db.id", is_binary=True)
+        self.add_composite_file("neostore.transaction.db.0", is_binary=True)
 
 
 class Neo4jDBzip(Neo4j, Data):
     """Class for neo4jDB database files."""
-    MetadataElement(name='reference_name', default='neostore_file', desc='Reference Name',
-                    readonly=True, visible=True, set_in_upload=True, no_value='neostore')
-    MetadataElement(name="neostore_zip", default=None, desc="Neostore zip",
-                    readonly=True, visible=True, set_in_upload=True, optional=True)
+
+    MetadataElement(
+        name="reference_name",
+        default="neostore_file",
+        desc="Reference Name",
+        readonly=True,
+        visible=True,
+        set_in_upload=True,
+        no_value="neostore",
+    )
+    MetadataElement(
+        name="neostore_zip",
+        default=None,
+        desc="Neostore zip",
+        readonly=True,
+        visible=True,
+        set_in_upload=True,
+        optional=True,
+    )
 
     file_ext = "neostore.zip"
-    composite_type = 'auto_primary_file'
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         Data.__init__(self, **kwd)
-        self.add_composite_file('%s.zip', description='neostore zip', substitute_name_with_metadata='reference_name',
-                                is_binary=True)
+        self.add_composite_file(
+            "%s.zip", description="neostore zip", substitute_name_with_metadata="reference_name", is_binary=True
+        )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/ngsindex.py b/lib/galaxy/datatypes/ngsindex.py
index e734db4df65..d065005ce29 100644
--- a/lib/galaxy/datatypes/ngsindex.py
+++ b/lib/galaxy/datatypes/ngsindex.py
@@ -15,17 +15,30 @@ class BowtieIndex(Html):
     base class for BowtieIndex
     is subclassed by BowtieColorIndex and BowtieBaseIndex
     """
-    MetadataElement(name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True)
-    MetadataElement(name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True)
 
-    composite_type = 'auto_primary_file'
+    MetadataElement(
+        name="base_name",
+        desc="base name for this index set",
+        default="galaxy_generated_bowtie_index",
+        set_in_upload=True,
+        readonly=True,
+    )
+    MetadataElement(
+        name="sequence_space",
+        desc="sequence_space for this index set",
+        default="unknown",
+        set_in_upload=True,
+        readonly=True,
+    )
+
+    composite_type = "auto_primary_file"
 
     def generate_primary_file(self, dataset=None):
         """
         This is called only at upload to write the html file
         cannot rename the datasets here - they come with the default unfortunately
         """
-        return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
+        return "<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>"
 
     def regenerate_primary_file(self, dataset):
         """
@@ -33,22 +46,24 @@ class BowtieIndex(Html):
         """
         bn = dataset.metadata.base_name
         flist = os.listdir(dataset.extra_files_path)
-        rval = [f'<html><head><title>Files for Composite Dataset {bn}</title></head><p/>Comprises the following files:<p/><ul>']
+        rval = [
+            f"<html><head><title>Files for Composite Dataset {bn}</title></head><p/>Comprises the following files:<p/><ul>"
+        ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
             rval.append(f'<li><a href="{sfname}">{sfname}</a>')
-        rval.append('</ul></html>')
-        with open(dataset.file_name, 'w') as f:
+        rval.append("</ul></html>")
+        with open(dataset.file_name, "w") as f:
             f.write("\n".join(rval))
-            f.write('\n')
+            f.write("\n")
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = f"Bowtie index file ({dataset.metadata.sequence_space})"
             dataset.blurb = f"{dataset.metadata.sequence_space} space"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -61,15 +76,29 @@ class BowtieColorIndex(BowtieIndex):
     """
     Bowtie color space index
     """
-    MetadataElement(name="sequence_space", desc="sequence_space for this index set", default='color', set_in_upload=True, readonly=True)
 
-    file_ext = 'bowtie_color_index'
+    MetadataElement(
+        name="sequence_space",
+        desc="sequence_space for this index set",
+        default="color",
+        set_in_upload=True,
+        readonly=True,
+    )
+
+    file_ext = "bowtie_color_index"
 
 
 class BowtieBaseIndex(BowtieIndex):
     """
     Bowtie base space index
     """
-    MetadataElement(name="sequence_space", desc="sequence_space for this index set", default='base', set_in_upload=True, readonly=True)
 
-    file_ext = 'bowtie_base_index'
+    MetadataElement(
+        name="sequence_space",
+        desc="sequence_space for this index set",
+        default="base",
+        set_in_upload=True,
+        readonly=True,
+    )
+
+    file_ext = "bowtie_base_index"
diff --git a/lib/galaxy/datatypes/phylip.py b/lib/galaxy/datatypes/phylip.py
index 305d74f0f87..dd0f2798289 100644
--- a/lib/galaxy/datatypes/phylip.py
+++ b/lib/galaxy/datatypes/phylip.py
@@ -8,7 +8,10 @@ Created on January. 05, 2018
 Phylip datatype sniffer
 """
 from galaxy import util
-from galaxy.datatypes.data import get_file_peek, Text
+from galaxy.datatypes.data import (
+    get_file_peek,
+    Text,
+)
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
@@ -20,12 +23,14 @@ from .metadata import MetadataElement
 @build_sniff_from_prefix
 class Phylip(Text):
     """Phylip format stores a multiple sequence alignment"""
+
     edam_data = "data_0863"
     edam_format = "format_1997"
     file_ext = "phylip"
 
-    MetadataElement(name="sequences", default=0, desc="Number of sequences", readonly=True,
-                    visible=False, optional=True, no_value=0)
+    MetadataElement(
+        name="sequences", default=0, desc="Number of sequences", readonly=True, visible=False, optional=True, no_value=0
+    )
 
     def set_meta(self, dataset, **kwd):
         """
@@ -45,8 +50,8 @@ class Phylip(Text):
             else:
                 dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_strict_interleaved(self, nb_seq, seq_length, alignment_prefix):
         found_seq_length = None
@@ -70,7 +75,7 @@ class Phylip(Text):
                 # All sequence parts should have the same length
                 return False
             # Fail if sequence is not ascii
-            seq.encode('ascii')
+            seq.encode("ascii")
             if any(str.isdigit(c) for c in seq):
                 # Could tighten up further by requiring IUPAC strings chars
                 return False
@@ -100,7 +105,7 @@ class Phylip(Text):
                 # All sequence parts should have the same length
                 return False
             # Fail if sequence is not ascii
-            seq.encode('ascii')
+            seq.encode("ascii")
             if any(str.isdigit(c) for c in seq):
                 # Could tighten up further by requiring IUPAC strings chars
                 return False
diff --git a/lib/galaxy/datatypes/plant_tribes.py b/lib/galaxy/datatypes/plant_tribes.py
index 2d1cda45641..12c37747eee 100644
--- a/lib/galaxy/datatypes/plant_tribes.py
+++ b/lib/galaxy/datatypes/plant_tribes.py
@@ -1,7 +1,10 @@
 import logging
 import re
 
-from galaxy.datatypes.data import get_file_peek, Text
+from galaxy.datatypes.data import (
+    get_file_peek,
+    Text,
+)
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
@@ -29,8 +32,8 @@ class Smat(Text):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "ESTScan scores matrices"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -61,11 +64,11 @@ class Smat(Text):
             line_no += 1
             if line_no > 10000:
                 return True
-            if line_no == 1 and not line.startswith('FORMAT'):
+            if line_no == 1 and not line.startswith("FORMAT"):
                 # The first line is always the start of a format section.
                 return False
-            if not line.startswith('FORMAT'):
-                if line.find('\t') >= 0:
+            if not line.startswith("FORMAT"):
+                if line.find("\t") >= 0:
                     # Smat files are not tabular.
                     return False
                 items = line.split()
@@ -101,7 +104,14 @@ class Smat(Text):
 
 class PlantTribesKsComponents(Tabular):
     file_ext = "ptkscmp"
-    MetadataElement(name="number_comp", default=0, desc="Number of significant components in the Ks distribution", readonly=True, visible=True, no_value=0)
+    MetadataElement(
+        name="number_comp",
+        default=0,
+        desc="Number of significant components in the Ks distribution",
+        readonly=True,
+        visible=True,
+        no_value=0,
+    )
 
     def display_peek(self, dataset):
         try:
@@ -134,13 +144,13 @@ class PlantTribesKsComponents(Tabular):
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.file_name)
-            if (dataset.metadata.number_comp == 1):
+            if dataset.metadata.number_comp == 1:
                 dataset.blurb = "1 significant component"
             else:
                 dataset.blurb = f"{dataset.metadata.number_comp} significant components"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         """
@@ -153,11 +163,12 @@ class PlantTribesKsComponents(Tabular):
         True
         """
         try:
-            line_item_str = get_headers(filename, '\\t', 1)[0][0]
-            return line_item_str == 'species\tn\tnumber_comp\tlnL\tAIC\tBIC\tmean\tvariance\tporportion'
+            line_item_str = get_headers(filename, "\\t", 1)[0][0]
+            return line_item_str == "species\tn\tnumber_comp\tlnL\tAIC\tBIC\tmean\tvariance\tporportion"
         except Exception:
             return False
 
+
 # class PlantTribesOrtho(PlantTribes):
 #    """
 #    PlantTribes sequences classified into precomputed, orthologous gene family
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 93a1dfa2f02..a9878667abd 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -12,47 +12,55 @@ from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
 )
-from galaxy.datatypes.tabular import Tabular, TabularData
+from galaxy.datatypes.tabular import (
+    Tabular,
+    TabularData,
+)
 from galaxy.datatypes.xml import GenericXml
 from galaxy.util import nice_size
 
-
 log = logging.getLogger(__name__)
 
 
 class Wiff(Binary):
     """Class for wiff files."""
+
     edam_data = "data_2536"
     edam_format = "format_3710"
-    file_ext = 'wiff'
-    composite_type = 'auto_primary_file'
+    file_ext = "wiff"
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
 
         self.add_composite_file(
-            'wiff',
-            description='AB SCIEX files in .wiff format. This can contain all needed information or only metadata.',
-            is_binary=True)
+            "wiff",
+            description="AB SCIEX files in .wiff format. This can contain all needed information or only metadata.",
+            is_binary=True,
+        )
 
         self.add_composite_file(
-            'wiff_scan',
-            description='AB SCIEX spectra file (wiff.scan), if the corresponding .wiff file only contains metadata.',
-            optional='True', is_binary=True)
+            "wiff_scan",
+            description="AB SCIEX spectra file (wiff.scan), if the corresponding .wiff file only contains metadata.",
+            optional="True",
+            is_binary=True,
+        )
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Wiff Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>Wiff Composite Dataset </title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                opt_text = " (optional)"
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
 
 
@@ -69,15 +77,18 @@ class MzTab(Text):
     >>> MzTab().sniff(fname)
     False
     """
+
     edam_data = "data_3681"
     file_ext = "mztab"
     # section names (except MTD)
     _sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
     # mandatory metadata fields and list of allowed entries (in lower case)
     # (or None if everything is allowed)
-    _man_mtd = {"mzTab-mode": ["complete", "summary"],
-                "mzTab-type": ['quantification', 'identification'],
-                "description": None}
+    _man_mtd = {
+        "mzTab-mode": ["complete", "summary"],
+        "mzTab-type": ["quantification", "identification"],
+        "description": None,
+    }
     _version_re = r"(1)(\.[0-9])?(\.[0-9])?"
 
     def __init__(self, **kwd):
@@ -87,13 +98,13 @@ class MzTab(Text):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'mzTab Format'
+            dataset.blurb = "mzTab Format"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """ Determines whether the file is the correct type. """
+        """Determines whether the file is the correct type."""
         has_version = False
         found_man_mtd = set()
         contents = file_prefix.string_io()
@@ -125,6 +136,7 @@ class MzTab2(MzTab):
     >>> MzTab2().sniff(fname)
     False
     """
+
     file_ext = "mztab2"
     _sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
     _version_re = r"(2)(\.[0-9])?(\.[0-9])?-M$"
@@ -137,10 +149,10 @@ class MzTab2(MzTab):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'mzTab2 Format'
+            dataset.blurb = "mzTab2 Format"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -156,11 +168,27 @@ class Kroenik(Tabular):
     >>> Kroenik().sniff(fname)
     False
     """
+
     file_ext = "kroenik"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.column_names = ["File", "First Scan", "Last Scan", "Num of Scans", "Charge", "Monoisotopic Mass", "Base Isotope Peak", "Best Intensity", "Summed Intensity", "First RTime", "Last RTime", "Best RTime", "Best Correlation", "Modifications"]
+        self.column_names = [
+            "File",
+            "First Scan",
+            "Last Scan",
+            "Num of Scans",
+            "Charge",
+            "Monoisotopic Mass",
+            "Base Isotope Peak",
+            "Best Intensity",
+            "Summed Intensity",
+            "First RTime",
+            "Last RTime",
+            "Best RTime",
+            "Best Correlation",
+            "Modifications",
+        ]
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
@@ -194,6 +222,7 @@ class PepList(Tabular):
     >>> PepList().sniff(fname)
     False
     """
+
     file_ext = "peplist"
 
     def __init__(self, **kwd):
@@ -230,6 +259,7 @@ class PSMS(Tabular):
     >>> PSMS().sniff(fname)
     False
     """
+
     file_ext = "psms"
 
     def __init__(self, **kwd):
@@ -254,6 +284,7 @@ class PEFF(Sequence):
     PSI Extended FASTA Format
     https://github.com/HUPO-PSI/PEFF
     """
+
     file_ext = "peff"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -275,12 +306,25 @@ class PEFF(Sequence):
 
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
+
     edam_data = "data_2536"
     file_ext = "pepxml.tsv"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probability']
+        self.column_names = [
+            "Protein",
+            "Peptide",
+            "Assumed Charge",
+            "Neutral Pep Mass (calculated)",
+            "Neutral Mass",
+            "Retention Time",
+            "Start Scan",
+            "End Scan",
+            "Search Engine",
+            "PeptideProphet Probability",
+            "Interprophet Probability",
+        ]
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
@@ -289,6 +333,7 @@ class PepXmlReport(Tabular):
 
 class ProtXmlReport(Tabular):
     """protxml converted to tabular report"""
+
     edam_data = "data_2536"
     file_ext = "protxml.tsv"
     comment_lines = 1
@@ -296,16 +341,31 @@ class ProtXmlReport(Tabular):
     def __init__(self, **kwd):
         super().__init__(**kwd)
         self.column_names = [
-            "Entry Number", "Group Probability",
-            "Protein", "Protein Link", "Protein Probability",
-            "Percent Coverage", "Number of Unique Peptides",
-            "Total Independent Spectra", "Percent Share of Spectrum ID's",
-            "Description", "Protein Molecular Weight", "Protein Length",
-            "Is Nondegenerate Evidence", "Weight", "Precursor Ion Charge",
-            "Peptide sequence", "Peptide Link", "NSP Adjusted Probability",
-            "Initial Probability", "Number of Total Termini",
-            "Number of Sibling Peptides Bin", "Number of Instances",
-            "Peptide Group Designator", "Is Evidence?"]
+            "Entry Number",
+            "Group Probability",
+            "Protein",
+            "Protein Link",
+            "Protein Probability",
+            "Percent Coverage",
+            "Number of Unique Peptides",
+            "Total Independent Spectra",
+            "Percent Share of Spectrum ID's",
+            "Description",
+            "Protein Molecular Weight",
+            "Protein Length",
+            "Is Nondegenerate Evidence",
+            "Weight",
+            "Precursor Ion Charge",
+            "Peptide sequence",
+            "Peptide Link",
+            "NSP Adjusted Probability",
+            "Initial Probability",
+            "Number of Total Termini",
+            "Number of Sibling Peptides Bin",
+            "Number of Instances",
+            "Peptide Group Designator",
+            "Is Evidence?",
+        ]
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
@@ -318,6 +378,7 @@ class Dta(TabularData):
     peptide charge state separated by a space. Subsequent lines contain space
     separated pairs of fragment ion m/z and intensity values.
     """
+
     file_ext = "dta"
     comment_lines = 0
 
@@ -337,9 +398,9 @@ class Dta(TabularData):
         # Set metadata
         dataset.metadata.data_lines = data_lines
         dataset.metadata.comment_lines = 0
-        dataset.metadata.column_types = ['float', 'float']
+        dataset.metadata.column_types = ["float", "float"]
         dataset.metadata.columns = 2
-        dataset.metadata.column_names = ['m/z', 'intensity']
+        dataset.metadata.column_names = ["m/z", "intensity"]
         dataset.metadata.delimiter = " "
 
 
@@ -365,6 +426,7 @@ class Dta2d(TabularData):
     >>> Dta2d().sniff(fname)
     False
     """
+
     file_ext = "dta2d"
     comment_lines = 0
 
@@ -373,7 +435,7 @@ class Dta2d(TabularData):
             return None
         line[0] = line[0].lstrip("#")
         line = [_.strip() for _ in line]
-        if 'MZ' not in line or 'INT' not in line or ('MIN' not in line and 'SEC' not in line):
+        if "MZ" not in line or "INT" not in line or ("MIN" not in line and "SEC" not in line):
             return None
         return line
 
@@ -410,12 +472,12 @@ class Dta2d(TabularData):
 
         dataset.metadata.data_lines = data_lines
         dataset.metadata.comment_lines = 0
-        dataset.metadata.column_types = ['float', 'float', 'float']
+        dataset.metadata.column_types = ["float", "float", "float"]
         dataset.metadata.columns = 3
         if dataset.metadata.column_names is None or dataset.metadata.column_names == []:
             dataset.metadata.comment_lines += 1
             dataset.metadata.data_lines -= 1
-            dataset.metadata.column_names = ['SEC', 'MZ', 'INT']
+            dataset.metadata.column_names = ["SEC", "MZ", "INT"]
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         sep = None
@@ -466,6 +528,7 @@ class Edta(TabularData):
     >>> Edta().sniff(fname)
     False
     """
+
     file_ext = "edta"
     comment_lines = 0
 
@@ -585,20 +648,21 @@ class Edta(TabularData):
 
 
 class ProteomicsXml(GenericXml):
-    """ An enhanced XML datatype used to reuse code across several
-    proteomic/mass-spec datatypes. """
+    """An enhanced XML datatype used to reuse code across several
+    proteomic/mass-spec datatypes."""
+
     edam_data = "data_2536"
     edam_format = "format_2032"
     root: str
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """ Determines whether the file is the correct XML type. """
+        """Determines whether the file is the correct XML type."""
         for line in file_prefix.line_iterator():
             line = line.strip()
-            if not line.startswith('<?'):
+            if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r'<(\w*:)?%s' % self.root
+        pattern = r"<(\w*:)?%s" % self.root
         return re.search(pattern, line) is not None
 
     def set_peek(self, dataset):
@@ -607,12 +671,13 @@ class ProteomicsXml(GenericXml):
             dataset.peek = data.get_file_peek(dataset.file_name)
             dataset.blurb = self.blurb
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class ParamXml(ProteomicsXml):
     """store Parameters in XML formal"""
+
     file_ext = "paramxml"
     blurb = "parameters in xmls"
     root = "parameters|PARAMETERS"
@@ -620,14 +685,16 @@ class ParamXml(ProteomicsXml):
 
 class PepXml(ProteomicsXml):
     """pepXML data"""
+
     edam_format = "format_3655"
     file_ext = "pepxml"
-    blurb = 'pepXML data'
+    blurb = "pepXML data"
     root = "msms_pipeline_analysis"
 
 
 class MascotXML(ProteomicsXml):
     """mzXML data"""
+
     file_ext = "mascotxml"
     blurb = "mascot Mass Spectrometry data"
     root = "mascot_search_results"
@@ -635,29 +702,33 @@ class MascotXML(ProteomicsXml):
 
 class MzML(ProteomicsXml):
     """mzML data"""
+
     edam_format = "format_3244"
     file_ext = "mzml"
-    blurb = 'mzML Mass Spectrometry data'
+    blurb = "mzML Mass Spectrometry data"
     root = "(mzML|indexedmzML)"
 
 
 class NmrML(ProteomicsXml):
     """nmrML data"""
+
     # No edam format number yet.
     file_ext = "nmrml"
-    blurb = 'nmrML NMR data'
+    blurb = "nmrML NMR data"
     root = "nmrML"
 
 
 class ProtXML(ProteomicsXml):
     """protXML data"""
+
     file_ext = "protxml"
-    blurb = 'prot XML Search Results'
+    blurb = "prot XML Search Results"
     root = "protein_summary"
 
 
 class MzXML(ProteomicsXml):
     """mzXML data"""
+
     edam_format = "format_3654"
     file_ext = "mzxml"
     blurb = "mzXML Mass Spectrometry data"
@@ -666,6 +737,7 @@ class MzXML(ProteomicsXml):
 
 class MzData(ProteomicsXml):
     """mzData data"""
+
     edam_format = "format_3245"
     file_ext = "mzdata"
     blurb = "mzData Mass Spectrometry data"
@@ -738,8 +810,9 @@ class XquestXML(ProteomicsXml):
 
 class XquestSpecXML(ProteomicsXml):
     """spec.xml"""
+
     file_ext = "spec.xml"
-    blurb = 'xquest_spectra'
+    blurb = "xquest_spectra"
     root = "xquest_spectra"
 
 
@@ -748,13 +821,15 @@ class QCML(ProteomicsXml):
     https://github.com/OpenMS/OpenMS/blob/113c49d01677f7f03343ce7cd542d83c99b351ee/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
     https://github.com/OpenMS/OpenMS/blob/3cfc57ad1788e7ab2bd6dd9862818b2855234c3f/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
     """
+
     file_ext = "qcml"
-    blurb = 'QualityAssessments to runs'
+    blurb = "QualityAssessments to runs"
     root = "qcML|MzQualityML)"
 
 
 class Mgf(Text):
     """Mascot Generic Format data"""
+
     edam_data = "data_2536"
     edam_format = "format_3651"
     file_ext = "mgf"
@@ -763,10 +838,10 @@ class Mgf(Text):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'mgf Mascot Generic Format'
+            dataset.blurb = "mgf Mascot Generic Format"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         mgf_begin_ions = "BEGIN IONS"
@@ -782,7 +857,8 @@ class Mgf(Text):
 
 
 class MascotDat(Text):
-    """Mascot search results """
+    """Mascot search results"""
+
     edam_data = "data_2536"
     edam_format = "format_3713"
     file_ext = "mascotdat"
@@ -791,10 +867,10 @@ class MascotDat(Text):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'mascotdat Mascot Search Results'
+            dataset.blurb = "mascotdat Mascot Search Results"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         mime_version = "MIME-Version: 1.0 (Generated by Mascot version 1.0)"
@@ -811,6 +887,7 @@ class MascotDat(Text):
 
 class ThermoRAW(Binary):
     """Class describing a Thermo Finnigan binary RAW file"""
+
     edam_data = "data_2536"
     edam_format = "format_3712"
     file_ext = "thermo.raw"
@@ -821,8 +898,8 @@ class ThermoRAW(Binary):
         # This combination represents 17 bytes, but to play safe we read 20 bytes from
         # the start of the file.
         try:
-            header = open(filename, 'rb').read(20)
-            finnigan = b'F\0i\0n\0n\0i\0g\0a\0n'
+            header = open(filename, "rb").read(20)
+            finnigan = b"F\0i\0n\0n\0i\0g\0a\0n"
             if header.find(finnigan) != -1:
                 return True
             return False
@@ -834,8 +911,8 @@ class ThermoRAW(Binary):
             dataset.peek = "Thermo Finnigan RAW file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
@@ -846,7 +923,8 @@ class ThermoRAW(Binary):
 
 @build_sniff_from_prefix
 class Msp(Text):
-    """ Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf """
+    """Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf"""
+
     file_ext = "msp"
 
     @staticmethod
@@ -855,7 +933,7 @@ class Msp(Text):
         return next_line is not None and next_line.startswith(prefix)
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """ Determines whether the file is a NIST MSP output file."""
+        """Determines whether the file is a NIST MSP output file."""
         begin_contents = file_prefix.contents_header
         if "\n" not in begin_contents:
             return False
@@ -866,62 +944,63 @@ class Msp(Text):
 
 
 class SPLibNoIndex(Text):
-    """SPlib without index file """
+    """SPlib without index file"""
+
     file_ext = "splib_noindex"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'Spectral Library without index files'
+            dataset.blurb = "Spectral Library without index files"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
 class SPLib(Msp):
     """SpectraST Spectral Library. Closely related to msp format"""
+
     file_ext = "splib"
-    composite_type = 'auto_primary_file'
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('library.splib',
-                                description='Spectral Library. Contains actual library spectra',
-                                is_binary=False)
-        self.add_composite_file('library.spidx',
-                                description='Spectrum index', is_binary=False)
-        self.add_composite_file('library.pepidx',
-                                description='Peptide index', is_binary=False)
+        self.add_composite_file(
+            "library.splib", description="Spectral Library. Contains actual library spectra", is_binary=False
+        )
+        self.add_composite_file("library.spidx", description="Spectrum index", is_binary=False)
+        self.add_composite_file("library.pepidx", description="Peptide index", is_binary=False)
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Spectral Library Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>Spectral Library Composite Dataset </title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+                opt_text = " (optional)"
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'splib Spectral Library Format'
+            dataset.blurb = "splib Spectral Library Format"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """ Determines whether the file is a SpectraST generated file.
-        """
+        """Determines whether the file is a SpectraST generated file."""
         contents = file_prefix.string_io()
         return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "LibID:")
 
@@ -931,20 +1010,20 @@ class Ms2(Text):
     file_ext = "ms2"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """ Determines whether the file is a valid ms2 file."""
+        """Determines whether the file is a valid ms2 file."""
         header_lines = []
         for line in file_prefix.line_iterator():
             if line.strip() == "":
                 continue
-            elif line.startswith('H\t'):
+            elif line.startswith("H\t"):
                 header_lines.append(line)
             else:
                 break
 
-        for header_field in ['CreationDate', 'Extractor', 'ExtractorVersion', 'ExtractorOptions']:
+        for header_field in ["CreationDate", "Extractor", "ExtractorVersion", "ExtractorOptions"]:
             found_header = False
             for header_line in header_lines:
-                if header_line.startswith(f'H\t{header_field}'):
+                if header_line.startswith(f"H\t{header_field}"):
                     found_header = True
                     break
             if not found_header:
@@ -955,46 +1034,45 @@ class Ms2(Text):
 
 # unsniffable binary format, should do something about this
 class XHunterAslFormat(Binary):
-    """ Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html """
+    """Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html"""
+
     file_ext = "hlf"
 
 
 class Sf3(Binary):
     """Class describing a Scaffold SF3 files"""
+
     file_ext = "sf3"
 
 
 class ImzML(Binary):
     """
-        Class for imzML files.
-        http://www.imzml.org
+    Class for imzML files.
+    http://www.imzml.org
     """
+
     edam_format = "format_3682"
-    file_ext = 'imzml'
-    composite_type = 'auto_primary_file'
+    file_ext = "imzml"
+    composite_type = "auto_primary_file"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
 
-        self.add_composite_file(
-            'imzml',
-            description='The imzML metadata component.',
-            is_binary=False)
+        self.add_composite_file("imzml", description="The imzML metadata component.", is_binary=False)
 
-        self.add_composite_file(
-            'ibd',
-            description='The mass spectral data component.',
-            is_binary=True)
+        self.add_composite_file("ibd", description="The mass spectral data component.", is_binary=True)
 
     def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>imzML Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        rval = ["<html><head><title>imzML Composite Dataset </title></head><p/>"]
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
-            opt_text = ''
-            if composite_file.get('description'):
-                rval.append(f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>")
+            opt_text = ""
+            if composite_file.get("description"):
+                rval.append(
+                    f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
+                )
             else:
                 rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
-        rval.append('</ul></div></html>')
+        rval.append("</ul></div></html>")
         return "\n".join(rval)
diff --git a/lib/galaxy/datatypes/qualityscore.py b/lib/galaxy/datatypes/qualityscore.py
index 1e987be499d..1ce98a17600 100644
--- a/lib/galaxy/datatypes/qualityscore.py
+++ b/lib/galaxy/datatypes/qualityscore.py
@@ -7,9 +7,7 @@ from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
 )
-from . import (
-    data,
-)
+from . import data
 
 log = logging.getLogger(__name__)
 
@@ -18,6 +16,7 @@ class QualityScore(data.Text):
     """
     until we know more about quality score formats
     """
+
     edam_data = "data_2048"
     edam_format = "format_3606"
     file_ext = "qual"
@@ -28,6 +27,7 @@ class QualityScoreSOLiD(QualityScore):
     """
     until we know more about quality score formats
     """
+
     edam_format = "format_3610"
     file_ext = "qualsolid"
 
@@ -46,10 +46,10 @@ class QualityScoreSOLiD(QualityScore):
         goodblock = 0
         for line in fh:
             line = line.strip()
-            if not line.startswith('#'):  # first non-empty non-comment line
-                if line.startswith('>'):
+            if not line.startswith("#"):  # first non-empty non-comment line
+                if line.startswith(">"):
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         return False
                     try:
                         [int(x) for x in line.split()]
@@ -77,6 +77,7 @@ class QualityScore454(QualityScore):
     """
     until we know more about quality score formats
     """
+
     edam_format = "format_3611"
     file_ext = "qual454"
 
@@ -93,10 +94,10 @@ class QualityScore454(QualityScore):
         fh = file_prefix.string_io()
         for line in fh:
             line = line.strip()
-            if line and not line.startswith('#'):  # first non-empty non-comment line
-                if line.startswith('>'):
+            if line and not line.startswith("#"):  # first non-empty non-comment line
+                if line.startswith(">"):
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         break
                     try:
                         [int(x) for x in line.split()]
@@ -112,6 +113,7 @@ class QualityScoreSolexa(QualityScore):
     """
     until we know more about quality score formats
     """
+
     edam_format = "format_3608"
     file_ext = "qualsolexa"
 
@@ -120,5 +122,6 @@ class QualityScoreIllumina(QualityScore):
     """
     until we know more about quality score formats
     """
+
     edam_format = "format_3609"
     file_ext = "qualillumina"
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index bb0c508bd19..3cc5f1d4e68 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -6,7 +6,13 @@ import imp
 import logging
 import os
 from string import Template
-from typing import Dict, List, Optional, Tuple, TYPE_CHECKING
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    TYPE_CHECKING,
+)
 
 import yaml
 
@@ -24,7 +30,7 @@ from . import (
     tabular,
     text,
     tracks,
-    xml
+    xml,
 )
 from .display_applications.application import DisplayApplication
 
@@ -37,7 +43,6 @@ class ConfigurationError(Exception):
 
 
 class Registry:
-
     def __init__(self, config=None):
         self.log = logging.getLogger(__name__)
         self.log.addHandler(logging.NullHandler())
@@ -85,7 +90,16 @@ class Registry:
         self.display_sites = {}
         self.legacy_build_sites = {}
 
-    def load_datatypes(self, root_dir=None, config=None, deactivate=False, override=True, use_converters=True, use_display_applications=True, use_build_sites=True):
+    def load_datatypes(
+        self,
+        root_dir=None,
+        config=None,
+        deactivate=False,
+        override=True,
+        use_converters=True,
+        use_display_applications=True,
+        use_build_sites=True,
+    ):
         """
         Parse a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within
         an installed Tool Shed repository.  If deactivate is True, an installed Tool Shed repository that includes custom datatypes
@@ -115,63 +129,71 @@ class Registry:
                 root = tree.getroot()
                 # Load datatypes and converters from config
                 if deactivate:
-                    self.log.debug(f'Deactivating datatypes from {config}')
+                    self.log.debug(f"Deactivating datatypes from {config}")
                 else:
-                    self.log.debug(f'Loading datatypes from {config}')
+                    self.log.debug(f"Loading datatypes from {config}")
             else:
                 root = config
-            registration = root.find('registration')
+            registration = root.find("registration")
             # Set default paths defined in local datatypes_conf.xml.
             if use_converters:
                 if not self.converters_path:
-                    self.converters_path_attr = registration.get('converters_path', 'lib/galaxy/datatypes/converters')
+                    self.converters_path_attr = registration.get("converters_path", "lib/galaxy/datatypes/converters")
                     self.converters_path = os.path.join(root_dir, self.converters_path_attr)
-                    if self.converters_path_attr == 'lib/galaxy/datatypes/converters' \
-                            and not os.path.isdir(self.converters_path):
+                    if self.converters_path_attr == "lib/galaxy/datatypes/converters" and not os.path.isdir(
+                        self.converters_path
+                    ):
                         # Deal with the old default of this path being set in
                         # datatypes_conf.xml.sample (this path is not useful in an
                         # "installed Galaxy" world)
-                        self.converters_path_attr = os.path.abspath(os.path.join(os.path.dirname(__file__), 'converters'))
+                        self.converters_path_attr = os.path.abspath(
+                            os.path.join(os.path.dirname(__file__), "converters")
+                        )
                         self.converters_path = self.converters_path_attr
                     if not os.path.isdir(self.converters_path):
                         raise ConfigurationError(f"Directory does not exist: {self.converters_path}")
             if use_display_applications:
                 if not self.display_applications_path:
-                    self.display_path_attr = registration.get('display_path', 'display_applications')
+                    self.display_path_attr = registration.get("display_path", "display_applications")
                     self.display_applications_path = os.path.join(root_dir, self.display_path_attr)
-                    if self.display_path_attr == 'display_applications' \
-                            and not os.path.isdir('display_applications'):
+                    if self.display_path_attr == "display_applications" and not os.path.isdir("display_applications"):
                         # Ditto as with converters_path
-                        self.display_path_attr = os.path.abspath(os.path.join(os.path.dirname(__file__), 'display_applications', 'configs'))
+                        self.display_path_attr = os.path.abspath(
+                            os.path.join(os.path.dirname(__file__), "display_applications", "configs")
+                        )
                         self.display_applications_path = self.display_path_attr
             # Proprietary datatype's <registration> tag may have special attributes, proprietary_converter_path and proprietary_display_path.
-            proprietary_converter_path = registration.get('proprietary_converter_path', None)
-            proprietary_display_path = registration.get('proprietary_display_path', None)
-            if proprietary_converter_path is not None or proprietary_display_path is not None and not handling_proprietary_datatypes:
+            proprietary_converter_path = registration.get("proprietary_converter_path", None)
+            proprietary_display_path = registration.get("proprietary_display_path", None)
+            if (
+                proprietary_converter_path is not None
+                or proprietary_display_path is not None
+                and not handling_proprietary_datatypes
+            ):
                 handling_proprietary_datatypes = True
-            for elem in registration.findall('datatype'):
+            for elem in registration.findall("datatype"):
                 # Keep a status of the process steps to enable stopping the process of handling the datatype if necessary.
                 ok = True
                 extension = self.get_extension(elem)
-                dtype = elem.get('type', None)
-                type_extension = elem.get('type_extension', None)
-                auto_compressed_types = galaxy.util.listify(elem.get('auto_compressed_types', ''))
+                dtype = elem.get("type", None)
+                type_extension = elem.get("type_extension", None)
+                auto_compressed_types = galaxy.util.listify(elem.get("auto_compressed_types", ""))
                 sniff_compressed_types = galaxy.util.string_as_bool_or_none(elem.get("sniff_compressed_types", "None"))
                 if sniff_compressed_types is None:
                     sniff_compressed_types = getattr(self.config, "sniff_compressed_dynamic_datatypes_default", True)
                     # Make sure this is set in the elems we write out so the config option is passed to the upload
                     # tool which does not have a config object.
                     elem.set("sniff_compressed_types", str(sniff_compressed_types))
-                mimetype = elem.get('mimetype', None)
-                display_in_upload = galaxy.util.string_as_bool(elem.get('display_in_upload', False))
+                mimetype = elem.get("mimetype", None)
+                display_in_upload = galaxy.util.string_as_bool(elem.get("display_in_upload", False))
                 # If make_subclass is True, it does not necessarily imply that we are subclassing a datatype that is contained
                 # in the distribution.
-                make_subclass = galaxy.util.string_as_bool(elem.get('subclass', False))
-                edam_format = elem.get('edam_format', None)
+                make_subclass = galaxy.util.string_as_bool(elem.get("subclass", False))
+                edam_format = elem.get("edam_format", None)
                 if edam_format and not make_subclass:
                     self.log.warning("Cannot specify edam_format without setting subclass to True, skipping datatype.")
                     continue
-                edam_data = elem.get('edam_data', None)
+                edam_data = elem.get("edam_data", None)
                 if edam_data and not make_subclass:
                     self.log.warning("Cannot specify edam_data without setting subclass to True, skipping datatype.")
                     continue
@@ -179,26 +201,34 @@ class Registry:
                 # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes.
                 # The value of proprietary_path is the path to the cloned location of the tool shed repository's contained
                 # datatypes_conf.xml file.
-                proprietary_path = elem.get('proprietary_path', None)
-                proprietary_datatype_module = elem.get('proprietary_datatype_module', None)
-                if proprietary_path is not None or proprietary_datatype_module is not None and not handling_proprietary_datatypes:
+                proprietary_path = elem.get("proprietary_path", None)
+                proprietary_datatype_module = elem.get("proprietary_datatype_module", None)
+                if (
+                    proprietary_path is not None
+                    or proprietary_datatype_module is not None
+                    and not handling_proprietary_datatypes
+                ):
                     handling_proprietary_datatypes = True
                 if deactivate:
                     # We are deactivating or uninstalling an installed tool shed repository, so eliminate the datatype
                     # elem from the in-memory list of datatype elems.
                     for in_memory_elem in self.datatype_elems:
-                        in_memory_extension = in_memory_elem.get('extension', None)
+                        in_memory_extension = in_memory_elem.get("extension", None)
                         if in_memory_extension == extension:
-                            in_memory_dtype = elem.get('type', None)
-                            in_memory_type_extension = elem.get('type_extension', None)
-                            in_memory_mimetype = elem.get('mimetype', None)
-                            in_memory_display_in_upload = galaxy.util.string_as_bool(elem.get('display_in_upload', False))
-                            in_memory_make_subclass = galaxy.util.string_as_bool(elem.get('subclass', False))
-                            if in_memory_dtype == dtype and \
-                                    in_memory_type_extension == type_extension and \
-                                    in_memory_mimetype == mimetype and \
-                                    in_memory_display_in_upload == display_in_upload and \
-                                    in_memory_make_subclass == make_subclass:
+                            in_memory_dtype = elem.get("type", None)
+                            in_memory_type_extension = elem.get("type_extension", None)
+                            in_memory_mimetype = elem.get("mimetype", None)
+                            in_memory_display_in_upload = galaxy.util.string_as_bool(
+                                elem.get("display_in_upload", False)
+                            )
+                            in_memory_make_subclass = galaxy.util.string_as_bool(elem.get("subclass", False))
+                            if (
+                                in_memory_dtype == dtype
+                                and in_memory_type_extension == type_extension
+                                and in_memory_mimetype == mimetype
+                                and in_memory_display_in_upload == display_in_upload
+                                and in_memory_make_subclass == make_subclass
+                            ):
                                 self.datatype_elems.remove(in_memory_elem)
                     if extension is not None and extension in self.datatypes_by_extension:
                         # We are deactivating or uninstalling an installed tool shed repository, so eliminate the datatype
@@ -218,11 +248,11 @@ class Registry:
                     if can_process_datatype:
                         if dtype is not None:
                             try:
-                                fields = dtype.split(':')
+                                fields = dtype.split(":")
                                 datatype_module = fields[0]
                                 datatype_class_name = fields[1]
                             except Exception:
-                                self.log.exception('Error parsing datatype definition for dtype %s', str(dtype))
+                                self.log.exception("Error parsing datatype definition for dtype %s", str(dtype))
                                 ok = False
                             if ok:
                                 datatype_class = None
@@ -230,36 +260,46 @@ class Registry:
                                     # TODO: previously comments suggested this needs to be locked because it modifies
                                     # the sys.path, probably true but the previous lock wasn't doing that.
                                     try:
-                                        imported_module = __import_module(proprietary_path,
-                                                                          proprietary_datatype_module,
-                                                                          datatype_class_name)
+                                        imported_module = __import_module(
+                                            proprietary_path, proprietary_datatype_module, datatype_class_name
+                                        )
                                         if imported_module not in self.imported_modules:
                                             self.imported_modules.append(imported_module)
                                         if hasattr(imported_module, datatype_class_name):
                                             datatype_class = getattr(imported_module, datatype_class_name)
                                     except Exception as e:
                                         full_path = os.path.join(proprietary_path, proprietary_datatype_module)
-                                        self.log.debug("Exception importing proprietary code file %s: %s", full_path, galaxy.util.unicodify(e))
+                                        self.log.debug(
+                                            "Exception importing proprietary code file %s: %s",
+                                            full_path,
+                                            galaxy.util.unicodify(e),
+                                        )
                                 # Either the above exception was thrown because the proprietary_datatype_module is not derived from a class
                                 # in the repository, or we are loading Galaxy's datatypes. In either case we'll look in the registry.
                                 if datatype_class is None:
                                     try:
                                         # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution.
-                                        fields = datatype_module.split('.')[1:]
+                                        fields = datatype_module.split(".")[1:]
                                         module = __import__(datatype_module)
                                         for mod in fields:
                                             module = getattr(module, mod)
                                         datatype_class = getattr(module, datatype_class_name)
-                                        self.log.debug(f'Retrieved datatype module {str(datatype_module)}:{datatype_class_name} from the datatype registry for extension {extension}.')
+                                        self.log.debug(
+                                            f"Retrieved datatype module {str(datatype_module)}:{datatype_class_name} from the datatype registry for extension {extension}."
+                                        )
                                     except Exception:
-                                        self.log.exception('Error importing datatype module %s', str(datatype_module))
+                                        self.log.exception("Error importing datatype module %s", str(datatype_module))
                                         ok = False
                         elif type_extension is not None:
                             try:
                                 datatype_class = self.datatypes_by_extension[type_extension].__class__
-                                self.log.debug(f'Retrieved datatype module {str(datatype_class.__name__)} from type_extension {type_extension} for extension {extension}.')
+                                self.log.debug(
+                                    f"Retrieved datatype module {str(datatype_class.__name__)} from type_extension {type_extension} for extension {extension}."
+                                )
                             except Exception:
-                                self.log.exception('Error determining datatype_class for type_extension %s', str(type_extension))
+                                self.log.exception(
+                                    "Error determining datatype_class for type_extension %s", str(type_extension)
+                                )
                                 ok = False
                         if ok:
                             if not deactivate:
@@ -269,10 +309,12 @@ class Registry:
                                 if extension in self.datatypes_by_extension:
                                     # Because of the way that the value of can_process_datatype was set above, we know that the value of
                                     # override is True.
-                                    self.log.debug("Overriding conflicting datatype with extension '%s', using datatype from %s." %
-                                                   (str(extension), str(config)))
+                                    self.log.debug(
+                                        "Overriding conflicting datatype with extension '%s', using datatype from %s."
+                                        % (str(extension), str(config))
+                                    )
                                 if make_subclass:
-                                    datatype_class = type(datatype_class_name, (datatype_class, ), {})
+                                    datatype_class = type(datatype_class_name, (datatype_class,), {})
                                     if edam_format:
                                         datatype_class.edam_format = edam_format
                                     if edam_data:
@@ -291,30 +333,38 @@ class Registry:
                                 if display_in_upload and extension not in self.upload_file_formats:
                                     self.upload_file_formats.append(extension)
                                 # Max file size cut off for setting optional metadata.
-                                self.datatypes_by_extension[extension].max_optional_metadata_filesize = elem.get('max_optional_metadata_filesize', None)
-                                for converter in elem.findall('converter'):
+                                self.datatypes_by_extension[extension].max_optional_metadata_filesize = elem.get(
+                                    "max_optional_metadata_filesize", None
+                                )
+                                for converter in elem.findall("converter"):
                                     # Build the list of datatype converters which will later be loaded into the calling app's toolbox.
-                                    converter_config = converter.get('file', None)
-                                    target_datatype = converter.get('target_datatype', None)
-                                    depends_on = converter.get('depends_on', None)
+                                    converter_config = converter.get("file", None)
+                                    target_datatype = converter.get("target_datatype", None)
+                                    depends_on = converter.get("depends_on", None)
                                     if depends_on is not None and target_datatype is not None:
                                         if extension not in self.converter_deps:
                                             self.converter_deps[extension] = {}
-                                        self.converter_deps[extension][target_datatype] = depends_on.split(',')
+                                        self.converter_deps[extension][target_datatype] = depends_on.split(",")
                                     if converter_config and target_datatype:
                                         if proprietary_converter_path:
-                                            self.proprietary_converters.append((converter_config, extension, target_datatype))
+                                            self.proprietary_converters.append(
+                                                (converter_config, extension, target_datatype)
+                                            )
                                         else:
                                             self.converters.append((converter_config, extension, target_datatype))
                                 # Add composite files.
-                                for composite_file in elem.findall('composite_file'):
-                                    name = composite_file.get('name', None)
+                                for composite_file in elem.findall("composite_file"):
+                                    name = composite_file.get("name", None)
                                     if name is None:
-                                        self.log.warning(f"You must provide a name for your composite_file ({composite_file}).")
-                                    optional = composite_file.get('optional', False)
-                                    mimetype = composite_file.get('mimetype', None)
-                                    self.datatypes_by_extension[extension].add_composite_file(name, optional=optional, mimetype=mimetype)
-                                for _display_app in elem.findall('display'):
+                                        self.log.warning(
+                                            f"You must provide a name for your composite_file ({composite_file})."
+                                        )
+                                    optional = composite_file.get("optional", False)
+                                    mimetype = composite_file.get("mimetype", None)
+                                    self.datatypes_by_extension[extension].add_composite_file(
+                                        name, optional=optional, mimetype=mimetype
+                                    )
+                                for _display_app in elem.findall("display"):
                                     if proprietary_display_path:
                                         if elem not in self.proprietary_display_app_containers:
                                             self.proprietary_display_app_containers.append(elem)
@@ -329,7 +379,7 @@ class Registry:
                                 }
                                 composite_files = datatype_instance.composite_files
                                 if composite_files:
-                                    datatype_info_dict['composite_files'] = [_.dict() for _ in composite_files.values()]
+                                    datatype_info_dict["composite_files"] = [_.dict() for _ in composite_files.values()]
                                 self.datatype_info_dicts.append(datatype_info_dict)
 
                                 for auto_compressed_type in auto_compressed_types:
@@ -345,7 +395,14 @@ class Registry:
                                         raise Exception(f"Unknown auto compression type [{auto_compressed_type}]")
                                     attributes["file_ext"] = compressed_extension
                                     attributes["uncompressed_datatype_instance"] = datatype_instance
-                                    compressed_datatype_class = type(auto_compressed_type_name, (datatype_class, dynamic_parent, ), attributes)
+                                    compressed_datatype_class = type(
+                                        auto_compressed_type_name,
+                                        (
+                                            datatype_class,
+                                            dynamic_parent,
+                                        ),
+                                        attributes,
+                                    )
                                     if edam_format:
                                         compressed_datatype_class.edam_format = edam_format
                                     if edam_data:
@@ -354,15 +411,25 @@ class Registry:
                                     self.datatypes_by_extension[compressed_extension] = compressed_datatype_instance
                                     if display_in_upload and compressed_extension not in self.upload_file_formats:
                                         self.upload_file_formats.append(compressed_extension)
-                                    self.datatype_info_dicts.append({
-                                        "display_in_upload": display_in_upload,
-                                        "extension": compressed_extension,
-                                        "description": description,
-                                        "description_url": description_url,
-                                    })
-                                    if auto_compressed_type == 'gz':
-                                        self.converters.append((f"uncompressed_to_{auto_compressed_type}.xml", extension, compressed_extension))
-                                    self.converters.append((f"{auto_compressed_type}_to_uncompressed.xml", compressed_extension, extension))
+                                    self.datatype_info_dicts.append(
+                                        {
+                                            "display_in_upload": display_in_upload,
+                                            "extension": compressed_extension,
+                                            "description": description,
+                                            "description_url": description_url,
+                                        }
+                                    )
+                                    if auto_compressed_type == "gz":
+                                        self.converters.append(
+                                            (
+                                                f"uncompressed_to_{auto_compressed_type}.xml",
+                                                extension,
+                                                compressed_extension,
+                                            )
+                                        )
+                                    self.converters.append(
+                                        (f"{auto_compressed_type}_to_uncompressed.xml", compressed_extension, extension)
+                                    )
                                     if datatype_class not in compressed_sniffers:
                                         compressed_sniffers[datatype_class] = []
                                     if sniff_compressed_types:
@@ -377,14 +444,18 @@ class Registry:
                                     if not override:
                                         # Do not load the datatype since it conflicts with an existing datatype which we are not supposed
                                         # to override.
-                                        self.log.debug(f"Ignoring conflicting datatype with extension '{extension}' from {config}.")
+                                        self.log.debug(
+                                            f"Ignoring conflicting datatype with extension '{extension}' from {config}."
+                                        )
             # Load datatype sniffers from the config - we'll do this even if one or more datatypes were not properly processed in the config
             # since sniffers are not tightly coupled with datatypes.
-            self.load_datatype_sniffers(root,
-                                        deactivate=deactivate,
-                                        handling_proprietary_datatypes=handling_proprietary_datatypes,
-                                        override=override,
-                                        compressed_sniffers=compressed_sniffers)
+            self.load_datatype_sniffers(
+                root,
+                deactivate=deactivate,
+                handling_proprietary_datatypes=handling_proprietary_datatypes,
+                override=override,
+                compressed_sniffers=compressed_sniffers,
+            )
             self.upload_file_formats.sort()
             # Load build sites
             if use_build_sites:
@@ -398,23 +469,25 @@ class Registry:
                 # has a sniff() method and was not defined with subclass="true".
                 # Do not add dynamic compressed types - these were carefully added or not
                 # to the sniff order in the proper position above.
-                if type(datatype) not in sniff_order_classes and \
-                        hasattr(datatype, 'sniff') and not datatype.is_subclass and \
-                        not hasattr(datatype, "uncompressed_datatype_instance"):
+                if (
+                    type(datatype) not in sniff_order_classes
+                    and hasattr(datatype, "sniff")
+                    and not datatype.is_subclass
+                    and not hasattr(datatype, "uncompressed_datatype_instance")
+                ):
                     self.sniff_order.append(datatype)
 
         append_to_sniff_order()
 
     def _load_build_sites(self, root):
-
         def load_build_site(build_site_config):
             # Take in either an XML element or simple dictionary from YAML and add build site for this.
-            if not (build_site_config.get('type') and build_site_config.get('file')):
+            if not (build_site_config.get("type") and build_site_config.get("file")):
                 self.log.exception("Site is missing required 'type' and 'file' attributes")
                 return
 
-            site_type = build_site_config.get('type')
-            path = build_site_config.get('file')
+            site_type = build_site_config.get("type")
+            path = build_site_config.get("file")
             if not os.path.exists(path):
                 sample_path = f"{path}.sample"
                 if os.path.exists(sample_path):
@@ -422,19 +495,19 @@ class Registry:
                     path = sample_path
 
             self.build_sites[site_type] = path
-            if site_type in ('ucsc', 'gbrowse'):
+            if site_type in ("ucsc", "gbrowse"):
                 self.legacy_build_sites[site_type] = galaxy.util.read_build_sites(path)
-            if build_site_config.get('display', None):
-                display = build_site_config.get('display')
+            if build_site_config.get("display", None):
+                display = build_site_config.get("display")
                 if not isinstance(display, list):
-                    display = [x.strip() for x in display.lower().split(',')]
+                    display = [x.strip() for x in display.lower().split(",")]
                 self.display_sites[site_type] = display
                 self.log.debug("Loaded build site '%s': %s with display sites: %s", site_type, path, display)
             else:
                 self.log.debug("Loaded build site '%s': %s", site_type, path)
 
-        if root.find('build_sites') is not None:
-            for elem in root.find('build_sites').findall('site'):
+        if root.find("build_sites") is not None:
+            for elem in root.find("build_sites").findall("site"):
                 load_build_site(elem)
         else:
             build_sites_config_file = getattr(self.config, "build_sites_config_file", None)
@@ -453,14 +526,16 @@ class Registry:
     def get_legacy_sites_by_build(self, site_type, build):
         sites = []
         for site in self.legacy_build_sites.get(site_type, []):
-            if build in site['builds']:
-                sites.append((site['name'], site['url']))
+            if build in site["builds"]:
+                sites.append((site["name"], site["url"]))
         return sites
 
     def get_display_sites(self, site_type):
         return self.display_sites.get(site_type, [])
 
-    def load_datatype_sniffers(self, root, deactivate=False, handling_proprietary_datatypes=False, override=False, compressed_sniffers=None):
+    def load_datatype_sniffers(
+        self, root, deactivate=False, handling_proprietary_datatypes=False, override=False, compressed_sniffers=None
+    ):
         """
         Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy
         distributed config) or contained within an installed Tool Shed repository.  If deactivate is True, an installed Tool
@@ -469,13 +544,13 @@ class Registry:
         Since installation is occurring after the datatypes registry has been initialized at server startup, its contents
         cannot be overridden by newly introduced conflicting sniffers.
         """
-        sniffer_elem_classes = [e.attrib['type'] for e in self.sniffer_elems]
-        sniffers = root.find('sniffers')
+        sniffer_elem_classes = [e.attrib["type"] for e in self.sniffer_elems]
+        sniffers = root.find("sniffers")
         if sniffers is not None:
-            for elem in sniffers.findall('sniffer'):
+            for elem in sniffers.findall("sniffer"):
                 # Keep a status of the process steps to enable stopping the process of handling the sniffer if necessary.
                 ok = True
-                dtype = elem.get('type', None)
+                dtype = elem.get("type", None)
                 if dtype is not None:
                     try:
                         fields = dtype.split(":")
@@ -483,7 +558,7 @@ class Registry:
                         datatype_class_name = fields[1]
                         module = None
                     except Exception:
-                        self.log.exception('Error determining datatype class or module for dtype %s', str(dtype))
+                        self.log.exception("Error determining datatype class or module for dtype %s", str(dtype))
                         ok = False
                     if ok:
                         if handling_proprietary_datatypes:
@@ -496,7 +571,7 @@ class Registry:
                             try:
                                 # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution.
                                 module = __import__(datatype_module)
-                                for comp in datatype_module.split('.')[1:]:
+                                for comp in datatype_module.split(".")[1:]:
                                     module = getattr(module, comp)
                             except Exception:
                                 self.log.exception("Error importing datatype class for '%s'", str(dtype))
@@ -505,23 +580,29 @@ class Registry:
                             try:
                                 aclass = getattr(module, datatype_class_name)()
                             except Exception:
-                                self.log.exception('Error calling method %s from class %s', str(datatype_class_name), str(module))
+                                self.log.exception(
+                                    "Error calling method %s from class %s", str(datatype_class_name), str(module)
+                                )
                                 ok = False
                             if ok:
                                 if deactivate:
                                     # We are deactivating or uninstalling an installed Tool Shed repository, so eliminate the appropriate sniffers.
-                                    sniffer_class = elem.get('type', None)
+                                    sniffer_class = elem.get("type", None)
                                     if sniffer_class is not None:
                                         for index, s_e_c in enumerate(sniffer_elem_classes):
                                             if sniffer_class == s_e_c:
                                                 del self.sniffer_elems[index]
-                                                sniffer_elem_classes = [elem.attrib['type'] for elem in self.sniffer_elems]
+                                                sniffer_elem_classes = [
+                                                    elem.attrib["type"] for elem in self.sniffer_elems
+                                                ]
                                                 self.log.debug(f"Removed sniffer element for datatype '{str(dtype)}'")
                                                 break
                                         for sniffer_class in self.sniff_order:
                                             if sniffer_class.__class__ == aclass.__class__:
                                                 self.sniff_order.remove(sniffer_class)
-                                                self.log.debug(f"Removed sniffer class for datatype '{str(dtype)}' from sniff order")
+                                                self.log.debug(
+                                                    f"Removed sniffer class for datatype '{str(dtype)}' from sniff order"
+                                                )
                                                 break
                                 else:
                                     # We are loading new sniffer, so see if we have a conflicting sniffer already loaded.
@@ -541,14 +622,14 @@ class Registry:
                                         self.sniff_order.append(aclass)
                                         self.log.debug(f"Loaded sniffer for datatype '{dtype}'")
                                     # Processing the new sniffer elem is now complete, so make sure the element defining it is loaded if necessary.
-                                    sniffer_class = elem.get('type', None)
+                                    sniffer_class = elem.get("type", None)
                                     if sniffer_class is not None:
                                         if sniffer_class not in sniffer_elem_classes:
                                             self.sniffer_elems.append(elem)
 
     def is_extension_unsniffable_binary(self, ext):
         datatype = self.get_datatype_by_extension(ext)
-        return datatype is not None and isinstance(datatype, binary.Binary) and not hasattr(datatype, 'sniff')
+        return datatype is not None and isinstance(datatype, binary.Binary) and not hasattr(datatype, "sniff")
 
     def get_datatype_class_by_name(self, name):
         """
@@ -557,7 +638,7 @@ class Registry:
         """
         # TODO: obviously not ideal but some of these base classes that are useful for testing datatypes
         # aren't loaded into the datatypes registry, so we'd need to test for them here
-        if name == 'images.Image':
+        if name == "images.Image":
             return images.Image
 
         # TODO: too inefficient - would be better to generate this once as a map and store in this object
@@ -571,14 +652,14 @@ class Registry:
     def get_available_tracks(self):
         return self.available_tracks
 
-    def get_mimetype_by_extension(self, ext, default='application/octet-stream'):
+    def get_mimetype_by_extension(self, ext, default="application/octet-stream"):
         """Returns a mimetype based on an extension"""
         try:
             mimetype = self.mimetypes_by_extension[ext]
         except KeyError:
             # datatype was never declared
             mimetype = default
-            self.log.warning(f'unknown mimetype in data factory {str(ext)}')
+            self.log.warning(f"unknown mimetype in data factory {str(ext)}")
         return mimetype
 
     def get_datatype_by_extension(self, ext):
@@ -612,7 +693,7 @@ class Registry:
             source_datatype = elem[1]
             target_datatype = elem[2]
             if installed_repository_dict:
-                converter_path = installed_repository_dict['converter_path']
+                converter_path = installed_repository_dict["converter_path"]
             else:
                 converter_path = self.converters_path
             try:
@@ -622,17 +703,17 @@ class Registry:
                 if installed_repository_dict:
                     # If the converter is included in an installed tool shed repository, set the tool
                     # shed related tool attributes.
-                    converter.tool_shed = installed_repository_dict['tool_shed']
-                    converter.repository_name = installed_repository_dict['repository_name']
-                    converter.repository_owner = installed_repository_dict['repository_owner']
-                    converter.installed_changeset_revision = installed_repository_dict['installed_changeset_revision']
+                    converter.tool_shed = installed_repository_dict["tool_shed"]
+                    converter.repository_name = installed_repository_dict["repository_name"]
+                    converter.repository_owner = installed_repository_dict["repository_owner"]
+                    converter.installed_changeset_revision = installed_repository_dict["installed_changeset_revision"]
                     converter.old_id = converter.id
                     # The converter should be included in the list of tools defined in tool_dicts.
-                    tool_dicts = installed_repository_dict['tool_dicts']
+                    tool_dicts = installed_repository_dict["tool_dicts"]
                     for tool_dict in tool_dicts:
-                        if tool_dict['id'] == converter.id:
-                            converter.guid = tool_dict['guid']
-                            converter.id = tool_dict['guid']
+                        if tool_dict["id"] == converter.id:
+                            converter.guid = tool_dict["guid"]
+                            converter.id = tool_dict["guid"]
                             break
                 if deactivate:
                     toolbox.remove_tool_by_id(converter.id, remove_from_panel=False)
@@ -645,7 +726,7 @@ class Registry:
                     if source_datatype not in self.datatype_converters:
                         self.datatype_converters[source_datatype] = {}
                     self.datatype_converters[source_datatype][target_datatype] = converter
-                    if not hasattr(toolbox.app, 'tool_cache') or converter.id in toolbox.app.tool_cache._new_tool_ids:
+                    if not hasattr(toolbox.app, "tool_cache") or converter.id in toolbox.app.tool_cache._new_tool_ids:
                         self.log.debug("Loaded converter: %s", converter.id)
             except Exception:
                 if deactivate:
@@ -667,16 +748,16 @@ class Registry:
             datatype_elems = self.display_app_containers
         for elem in datatype_elems:
             extension = self.get_extension(elem)
-            for display_app in elem.findall('display'):
-                display_file = display_app.get('file', None)
+            for display_app in elem.findall("display"):
+                display_file = display_app.get("file", None)
                 if installed_repository_dict:
-                    display_path = installed_repository_dict['display_path']
+                    display_path = installed_repository_dict["display_path"]
                     display_file_head, display_file_tail = os.path.split(display_file)
                     config_path = os.path.join(display_path, display_file_tail)
                 else:
                     config_path = os.path.join(self.display_applications_path, display_file)
                 try:
-                    inherit = galaxy.util.string_as_bool(display_app.get('inherit', 'False'))
+                    inherit = galaxy.util.string_as_bool(display_app.get("inherit", "False"))
                     display_app = DisplayApplication.from_file(config_path, app)
                     if display_app:
                         if display_app.id in self.display_applications:
@@ -688,17 +769,19 @@ class Registry:
                         elif installed_repository_dict:
                             # If the display application is included in an installed tool shed repository,
                             # set the tool shed related tool attributes.
-                            display_app.tool_shed = installed_repository_dict['tool_shed']
-                            display_app.repository_name = installed_repository_dict['repository_name']
-                            display_app.repository_owner = installed_repository_dict['repository_owner']
-                            display_app.installed_changeset_revision = installed_repository_dict['installed_changeset_revision']
+                            display_app.tool_shed = installed_repository_dict["tool_shed"]
+                            display_app.repository_name = installed_repository_dict["repository_name"]
+                            display_app.repository_owner = installed_repository_dict["repository_owner"]
+                            display_app.installed_changeset_revision = installed_repository_dict[
+                                "installed_changeset_revision"
+                            ]
                             display_app.old_id = display_app.id
                             # The display application should be included in the list of tools defined in tool_dicts.
-                            tool_dicts = installed_repository_dict['tool_dicts']
+                            tool_dicts = installed_repository_dict["tool_dicts"]
                             for tool_dict in tool_dicts:
-                                if tool_dict['id'] == display_app.id:
-                                    display_app.guid = tool_dict['guid']
-                                    display_app.id = tool_dict['guid']
+                                if tool_dict["id"] == display_app.id:
+                                    display_app.guid = tool_dict["guid"]
+                                    display_app.id = tool_dict["guid"]
                                     break
                         if deactivate:
                             if display_app.id in self.display_applications:
@@ -706,15 +789,31 @@ class Registry:
                             if extension in self.datatypes_by_extension:
                                 if display_app.id in self.datatypes_by_extension[extension].display_applications:
                                     del self.datatypes_by_extension[extension].display_applications[display_app.id]
-                            if inherit and (self.datatypes_by_extension[extension], display_app) in self.inherit_display_application_by_class:
-                                self.inherit_display_application_by_class.remove((self.datatypes_by_extension[extension], display_app))
-                            self.log.debug(f"Deactivated display application '{display_app.id}' for datatype '{extension}'.")
+                            if (
+                                inherit
+                                and (self.datatypes_by_extension[extension], display_app)
+                                in self.inherit_display_application_by_class
+                            ):
+                                self.inherit_display_application_by_class.remove(
+                                    (self.datatypes_by_extension[extension], display_app)
+                                )
+                            self.log.debug(
+                                f"Deactivated display application '{display_app.id}' for datatype '{extension}'."
+                            )
                         else:
                             self.display_applications[display_app.id] = display_app
                             self.datatypes_by_extension[extension].add_display_application(display_app)
-                            if inherit and (self.datatypes_by_extension[extension], display_app) not in self.inherit_display_application_by_class:
-                                self.inherit_display_application_by_class.append((self.datatypes_by_extension[extension], display_app))
-                            self.log.debug(f"Loaded display application '{display_app.id}' for datatype '{extension}', inherit={inherit}.")
+                            if (
+                                inherit
+                                and (self.datatypes_by_extension[extension], display_app)
+                                not in self.inherit_display_application_by_class
+                            ):
+                                self.inherit_display_application_by_class.append(
+                                    (self.datatypes_by_extension[extension], display_app)
+                                )
+                            self.log.debug(
+                                f"Loaded display application '{display_app.id}' for datatype '{extension}', inherit={inherit}."
+                            )
                 except Exception:
                     if deactivate:
                         self.log.exception(f"Error deactivating display application ({config_path})")
@@ -744,7 +843,9 @@ class Registry:
                 self.display_applications[display_application_id].reload()
                 reloaded.append(display_application_id)
             except Exception as e:
-                self.log.debug('Requested to reload display application "%s", but failed: %s.', display_application_id, e)
+                self.log.debug(
+                    'Requested to reload display application "%s", but failed: %s.', display_application_id, e
+                )
                 failed.append(display_application_id)
         return (reloaded, failed)
 
@@ -753,7 +854,9 @@ class Registry:
         # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated
         # tool.  We'll load a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective
         # Properly building a tool without relying on parsing an XML file is near difficult...so we bundle with Galaxy.
-        set_meta_tool = toolbox.load_hidden_lib_tool(os.path.abspath(os.path.join(os.path.dirname(__file__), "set_metadata_tool.xml")))
+        set_meta_tool = toolbox.load_hidden_lib_tool(
+            os.path.abspath(os.path.join(os.path.dirname(__file__), "set_metadata_tool.xml"))
+        )
         self.set_external_metadata_tool = set_meta_tool
         self.log.debug("Loaded external metadata tool: %s", self.set_external_metadata_tool.id)
 
@@ -761,80 +864,80 @@ class Registry:
         # Default values.
         if not self.datatypes_by_extension:
             self.datatypes_by_extension = {
-                'ab1': binary.Ab1(),
-                'axt': sequence.Axt(),
-                'bam': binary.Bam(),
-                'jp2': binary.JP2(),
-                'bed': interval.Bed(),
-                'coverage': coverage.LastzCoverage(),
-                'customtrack': interval.CustomTrack(),
-                'csfasta': sequence.csFasta(),
-                'fasta': sequence.Fasta(),
-                'eland': tabular.Eland(),
-                'fastq': sequence.Fastq(),
-                'fastqsanger': sequence.FastqSanger(),
-                'gtf': interval.Gtf(),
-                'gff': interval.Gff(),
-                'gff3': interval.Gff3(),
-                'genetrack': tracks.GeneTrack(),
-                'h5': binary.H5(),
-                'interval': interval.Interval(),
-                'laj': images.Laj(),
-                'lav': sequence.Lav(),
-                'maf': sequence.Maf(),
-                'pileup': tabular.Pileup(),
-                'qualsolid': qualityscore.QualityScoreSOLiD(),
-                'qualsolexa': qualityscore.QualityScoreSolexa(),
-                'qual454': qualityscore.QualityScore454(),
-                'sam': tabular.Sam(),
-                'scf': binary.Scf(),
-                'sff': binary.Sff(),
-                'tabular': tabular.Tabular(),
-                'csv': tabular.CSV(),
-                'taxonomy': tabular.Taxonomy(),
-                'txt': data.Text(),
-                'wig': interval.Wiggle(),
-                'xml': xml.GenericXml(),
+                "ab1": binary.Ab1(),
+                "axt": sequence.Axt(),
+                "bam": binary.Bam(),
+                "jp2": binary.JP2(),
+                "bed": interval.Bed(),
+                "coverage": coverage.LastzCoverage(),
+                "customtrack": interval.CustomTrack(),
+                "csfasta": sequence.csFasta(),
+                "fasta": sequence.Fasta(),
+                "eland": tabular.Eland(),
+                "fastq": sequence.Fastq(),
+                "fastqsanger": sequence.FastqSanger(),
+                "gtf": interval.Gtf(),
+                "gff": interval.Gff(),
+                "gff3": interval.Gff3(),
+                "genetrack": tracks.GeneTrack(),
+                "h5": binary.H5(),
+                "interval": interval.Interval(),
+                "laj": images.Laj(),
+                "lav": sequence.Lav(),
+                "maf": sequence.Maf(),
+                "pileup": tabular.Pileup(),
+                "qualsolid": qualityscore.QualityScoreSOLiD(),
+                "qualsolexa": qualityscore.QualityScoreSolexa(),
+                "qual454": qualityscore.QualityScore454(),
+                "sam": tabular.Sam(),
+                "scf": binary.Scf(),
+                "sff": binary.Sff(),
+                "tabular": tabular.Tabular(),
+                "csv": tabular.CSV(),
+                "taxonomy": tabular.Taxonomy(),
+                "txt": data.Text(),
+                "wig": interval.Wiggle(),
+                "xml": xml.GenericXml(),
             }
             self.mimetypes_by_extension = {
-                'ab1': 'application/octet-stream',
-                'axt': 'text/plain',
-                'bam': 'application/octet-stream',
-                'jp2': 'application/octet-stream',
-                'bed': 'text/plain',
-                'customtrack': 'text/plain',
-                'csfasta': 'text/plain',
-                'eland': 'application/octet-stream',
-                'fasta': 'text/plain',
-                'fastq': 'text/plain',
-                'fastqsanger': 'text/plain',
-                'gtf': 'text/plain',
-                'gff': 'text/plain',
-                'gff3': 'text/plain',
-                'h5': 'application/octet-stream',
-                'interval': 'text/plain',
-                'laj': 'text/plain',
-                'lav': 'text/plain',
-                'maf': 'text/plain',
-                'memexml': 'application/xml',
-                'pileup': 'text/plain',
-                'qualsolid': 'text/plain',
-                'qualsolexa': 'text/plain',
-                'qual454': 'text/plain',
-                'sam': 'text/plain',
-                'scf': 'application/octet-stream',
-                'sff': 'application/octet-stream',
-                'tabular': 'text/plain',
-                'csv': 'text/plain',
-                'taxonomy': 'text/plain',
-                'txt': 'text/plain',
-                'wig': 'text/plain',
-                'xml': 'application/xml',
+                "ab1": "application/octet-stream",
+                "axt": "text/plain",
+                "bam": "application/octet-stream",
+                "jp2": "application/octet-stream",
+                "bed": "text/plain",
+                "customtrack": "text/plain",
+                "csfasta": "text/plain",
+                "eland": "application/octet-stream",
+                "fasta": "text/plain",
+                "fastq": "text/plain",
+                "fastqsanger": "text/plain",
+                "gtf": "text/plain",
+                "gff": "text/plain",
+                "gff3": "text/plain",
+                "h5": "application/octet-stream",
+                "interval": "text/plain",
+                "laj": "text/plain",
+                "lav": "text/plain",
+                "maf": "text/plain",
+                "memexml": "application/xml",
+                "pileup": "text/plain",
+                "qualsolid": "text/plain",
+                "qualsolexa": "text/plain",
+                "qual454": "text/plain",
+                "sam": "text/plain",
+                "scf": "application/octet-stream",
+                "sff": "application/octet-stream",
+                "tabular": "text/plain",
+                "csv": "text/plain",
+                "taxonomy": "text/plain",
+                "txt": "text/plain",
+                "wig": "text/plain",
+                "xml": "application/xml",
             }
         # super supertype fix for input steps in workflows.
-        if 'data' not in self.datatypes_by_extension:
-            self.datatypes_by_extension['data'] = data.Data()
-            self.mimetypes_by_extension['data'] = 'application/octet-stream'
+        if "data" not in self.datatypes_by_extension:
+            self.datatypes_by_extension["data"] = data.Data()
+            self.mimetypes_by_extension["data"] = "application/octet-stream"
         # Default values - the order in which we attempt to determine data types is critical
         # because some formats are much more flexibly defined than others.
         if len(self.sniff_order) < 1:
@@ -865,7 +968,7 @@ class Registry:
                 interval.Interval(),
                 tabular.Sam(),
                 tabular.Eland(),
-                tabular.CSV()
+                tabular.CSV(),
             ]
 
     def get_converters_by_datatype(self, ext):
@@ -905,13 +1008,17 @@ class Registry:
             ext = dataset_or_ext
             dataset = None
 
-        if self.get_datatype_by_extension(ext) is not None and self.get_datatype_by_extension(ext).matches_any(accepted_formats):
+        if self.get_datatype_by_extension(ext) is not None and self.get_datatype_by_extension(ext).matches_any(
+            accepted_formats
+        ):
             return True, None, None
 
         for convert_ext in self.get_converters_by_datatype(ext):
             convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
             if convert_ext_datatype is None:
-                self.log.warning(f"Datatype class not found for extension '{convert_ext}', which is used as target for conversion from datatype '{dataset.ext}'")
+                self.log.warning(
+                    f"Datatype class not found for extension '{convert_ext}', which is used as target for conversion from datatype '{dataset.ext}'"
+                )
             elif convert_ext_datatype.matches_any(accepted_formats):
                 converted_dataset = dataset and dataset.get_converted_files_by_type(convert_ext)
                 if converted_dataset:
@@ -936,31 +1043,32 @@ class Registry:
                     help_txt = meta_spec.desc
                     if not help_txt or help_txt == meta_name:
                         help_txt = ""
-                    inputs.append(f'<param type="text" name="{meta_name}" label="Set metadata value for &quot;{meta_name}&quot;" value="{meta_spec.default}" help="{help_txt}"/>')
+                    inputs.append(
+                        f'<param type="text" name="{meta_name}" label="Set metadata value for &quot;{meta_name}&quot;" value="{meta_spec.default}" help="{help_txt}"/>'
+                    )
             rval[ext] = "\n".join(inputs)
-        if 'auto' not in rval and 'txt' in rval:  # need to manually add 'auto' datatype
-            rval['auto'] = rval['txt']
+        if "auto" not in rval and "txt" in rval:  # need to manually add 'auto' datatype
+            rval["auto"] = rval["txt"]
         return rval
 
     @property
     def edam_formats(self):
-        """
-        """
+        """ """
         if not self._edam_formats_mapping:
             self._edam_formats_mapping = {k: v.edam_format for k, v in self.datatypes_by_extension.items()}
         return self._edam_formats_mapping
 
     @property
     def edam_data(self):
-        """
-        """
+        """ """
         if not self._edam_data_mapping:
             self._edam_data_mapping = {k: v.edam_data for k, v in self.datatypes_by_extension.items()}
         return self._edam_data_mapping
 
     def to_xml_file(self, path):
         if not self._registry_xml_string:
-            registry_string_template = Template("""<?xml version="1.0"?>
+            registry_string_template = Template(
+                """<?xml version="1.0"?>
             <datatypes>
               <registration converters_path="$converters_path" display_path="$display_path">
                 $datatype_elems
@@ -969,16 +1077,19 @@ class Registry:
                 $sniffer_elems
               </sniffers>
             </datatypes>
-            """)
-            converters_path = self.converters_path_attr or ''
-            display_path = self.display_path_attr or ''
+            """
+            )
+            converters_path = self.converters_path_attr or ""
+            display_path = self.display_path_attr or ""
             datatype_elems = "".join(galaxy.util.xml_to_string(elem) for elem in self.datatype_elems)
             sniffer_elems = "".join(galaxy.util.xml_to_string(elem) for elem in self.sniffer_elems)
-            self._registry_xml_string = registry_string_template.substitute(converters_path=converters_path,
-                                                                            display_path=display_path,
-                                                                            datatype_elems=datatype_elems,
-                                                                            sniffer_elems=sniffer_elems)
-        with open(os.path.abspath(path), 'w') as registry_xml:
+            self._registry_xml_string = registry_string_template.substitute(
+                converters_path=converters_path,
+                display_path=display_path,
+                datatype_elems=datatype_elems,
+                sniffer_elems=sniffer_elems,
+            )
+        with open(os.path.abspath(path), "w") as registry_xml:
             os.chmod(path, RW_R__R__)
             registry_xml.write(self._registry_xml_string)
 
@@ -988,11 +1099,14 @@ class Registry:
         :param elem:
         :return extension:
         """
-        extension = elem.get('extension', None)
+        extension = elem.get("extension", None)
         # If extension is not None and is uppercase or mixed case, we need to lowercase it
         if extension is not None and not extension.islower():
-            self.log.debug("%s is not lower case, that could cause troubles in the future. \
-            Please change it to lower case" % extension)
+            self.log.debug(
+                "%s is not lower case, that could cause troubles in the future. \
+            Please change it to lower case"
+                % extension
+            )
             extension = extension.lower()
         return extension
 
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 4e5e6028e2d..ad02b1239fd 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -16,11 +16,12 @@ from markupsafe import escape
 
 from galaxy import util
 from galaxy.datatypes import metadata
-from galaxy.datatypes.binary import (
-    Binary
-)
+from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.data import DatatypeValidation
-from galaxy.datatypes.metadata import DictParameter, MetadataElement
+from galaxy.datatypes.metadata import (
+    DictParameter,
+    MetadataElement,
+)
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
@@ -29,11 +30,9 @@ from galaxy.datatypes.sniff import (
 )
 from galaxy.util import (
     compression_utils,
-    nice_size
-)
-from galaxy.util.checkers import (
-    is_gzip
+    nice_size,
 )
+from galaxy.util.checkers import is_gzip
 from galaxy.util.image_util import check_image_type
 from . import data
 
@@ -54,6 +53,7 @@ class SequenceSplitLocations(data.Text):
       ]}
 
     """
+
     file_ext = "fqtoc"
 
     def set_peek(self, dataset):
@@ -62,21 +62,21 @@ class SequenceSplitLocations(data.Text):
                 parsed_data = json.load(open(dataset.file_name))
                 # dataset.peek = json.dumps(data, sort_keys=True, indent=4)
                 dataset.peek = data.get_file_peek(dataset.file_name)
-                dataset.blurb = '%d sections' % len(parsed_data['sections'])
+                dataset.blurb = "%d sections" % len(parsed_data["sections"])
             except Exception:
-                dataset.peek = 'Not FQTOC file'
-                dataset.blurb = 'Not FQTOC file'
+                dataset.peek = "Not FQTOC file"
+                dataset.blurb = "Not FQTOC file"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         if file_prefix.file_size < 50000 and not file_prefix.truncated:
             try:
                 data = json.loads(file_prefix.contents_header)
-                sections = data['sections']
+                sections = data["sections"]
                 for section in sections:
-                    if 'start' not in section or 'end' not in section or 'sequences' not in section:
+                    if "start" not in section or "end" not in section or "sequences" not in section:
                         return False
                 return True
             except Exception:
@@ -86,9 +86,12 @@ class SequenceSplitLocations(data.Text):
 
 class Sequence(data.Text):
     """Class describing a sequence"""
+
     edam_data = "data_2044"
 
-    MetadataElement(name="sequences", default=0, desc="Number of sequences", readonly=True, visible=False, optional=True, no_value=0)
+    MetadataElement(
+        name="sequences", default=0, desc="Number of sequences", readonly=True, visible=False, optional=True, no_value=0
+    )
 
     def set_meta(self, dataset, **kwd):
         """
@@ -99,10 +102,10 @@ class Sequence(data.Text):
         with compression_utils.get_fileobj(dataset.file_name) as fh:
             for line in fh:
                 line = line.strip()
-                if line and line.startswith('#'):
+                if line and line.startswith("#"):
                     # We don't count comment lines for sequence data types
                     continue
-                if line and line.startswith('>'):
+                if line and line.startswith(">"):
                     sequences += 1
                     data_lines += 1
                 else:
@@ -118,20 +121,20 @@ class Sequence(data.Text):
             else:
                 dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     @staticmethod
     def get_sequences_per_file(total_sequences, split_params):
-        if split_params['split_mode'] == 'number_of_parts':
+        if split_params["split_mode"] == "number_of_parts":
             # legacy basic mode - split into a specified number of parts
-            parts = int(split_params['split_size'])
+            parts = int(split_params["split_size"])
             sequences_per_file = [total_sequences / parts for i in range(parts)]
             for i in range(total_sequences % parts):
                 sequences_per_file[i] += 1
-        elif split_params['split_mode'] == 'to_size':
+        elif split_params["split_mode"] == "to_size":
             # loop through the sections and calculate the number of sequences
-            chunk_size = int(split_params['split_size'])
+            chunk_size = int(split_params["split_size"])
             rem = total_sequences % chunk_size
             sequences_per_file = [chunk_size for i in range(total_sequences / chunk_size)]
             # TODO: Should we invest the time in a better way to handle small remainders?
@@ -158,10 +161,10 @@ class Sequence(data.Text):
     @classmethod
     def do_fast_split(cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
         data = json.load(open(toc_file_datasets[0].file_name))
-        sections = data['sections']
+        sections = data["sections"]
         total_sequences = int(0)
         for section in sections:
-            total_sequences += int(section['sequences'])
+            total_sequences += int(section["sequences"])
         sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
         return cls.write_split_files(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file)
 
@@ -186,14 +189,16 @@ class Sequence(data.Text):
                 ds = input_datasets[ds_no]
                 base_name = os.path.basename(ds.file_name)
                 part_path = os.path.join(dir, base_name)
-                split_data = dict(class_name=f'{cls.__module__}.{cls.__name__}',
-                                  output_name=part_path,
-                                  input_name=ds.file_name,
-                                  args=dict(start_sequence=start_sequence, num_sequences=sequences_per_file[part_no]))
+                split_data = dict(
+                    class_name=f"{cls.__module__}.{cls.__name__}",
+                    output_name=part_path,
+                    input_name=ds.file_name,
+                    args=dict(start_sequence=start_sequence, num_sequences=sequences_per_file[part_no]),
+                )
                 if toc_file_datasets is not None:
                     toc = toc_file_datasets[ds_no]
-                    split_data['args']['toc_file'] = toc.file_name
-                with open(os.path.join(dir, f'split_info_{base_name}.json'), 'w') as f:
+                    split_data["args"]["toc_file"] = toc.file_name
+                with open(os.path.join(dir, f"split_info_{base_name}.json"), "w") as f:
                     json.dump(split_data, f)
             start_sequence += sequences_per_file[part_no]
         return directories
@@ -223,40 +228,49 @@ class Sequence(data.Text):
         >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=20)
         ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', 'dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz', '(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz']
         """
-        sections = toc_file['sections']
+        sections = toc_file["sections"]
         result = []
 
         current_sequence = int(0)
         i = 0
         # skip to the section that contains my starting sequence
-        while i < len(sections) and start_sequence >= current_sequence + int(sections[i]['sequences']):
-            current_sequence += int(sections[i]['sequences'])
+        while i < len(sections) and start_sequence >= current_sequence + int(sections[i]["sequences"]):
+            current_sequence += int(sections[i]["sequences"])
             i += 1
         if i == len(sections):  # bad input data!
-            raise Exception(f'No FQTOC section contains starting sequence {start_sequence}')
+            raise Exception(f"No FQTOC section contains starting sequence {start_sequence}")
 
         # These two variables act as an accumulator for consecutive entire blocks that
         # can be copied verbatim (without decompressing)
         start_chunk = int(-1)
         end_chunk = int(-1)
-        copy_chunk_cmd = 'dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s'
+        copy_chunk_cmd = "dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s"
 
         while sequence_count > 0 and i < len(sections):
             # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need
             # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the
             # right number of lines
-            sequences = int(sections[i]['sequences'])
+            sequences = int(sections[i]["sequences"])
             skip_sequences = start_sequence - current_sequence
             sequences_to_extract = min(sequence_count, sequences - skip_sequences)
-            start_copy = int(sections[i]['start'])
-            end_copy = int(sections[i]['end'])
+            start_copy = int(sections[i]["start"])
+            end_copy = int(sections[i]["end"])
             if sequences_to_extract < sequences:
                 if start_chunk > -1:
                     result.append(copy_chunk_cmd % (start_chunk, end_chunk - start_chunk, input_name, output_name))
                     start_chunk = -1
                 # extract, unzip, trim, recompress
-                result.append('(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s' %
-                              (start_copy, end_copy - start_copy, input_name, skip_sequences * 4 + 1, sequences_to_extract * 4, output_name))
+                result.append(
+                    "(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s"
+                    % (
+                        start_copy,
+                        end_copy - start_copy,
+                        input_name,
+                        skip_sequences * 4 + 1,
+                        sequences_to_extract * 4,
+                        output_name,
+                    )
+                )
             else:  # whole section - add it to the start_chunk/end_chunk accumulator
                 if start_chunk == -1:
                     start_chunk = start_copy
@@ -269,7 +283,7 @@ class Sequence(data.Text):
             result.append(copy_chunk_cmd % (start_chunk, end_chunk - start_chunk, input_name, output_name))
 
         if sequence_count > 0:
-            raise Exception(f'{sequence_count} sequences not found in file')
+            raise Exception(f"{sequence_count} sequences not found in file")
 
         return result
 
@@ -296,9 +310,12 @@ class Sequence(data.Text):
 
 class Alignment(data.Text):
     """Class describing an alignment"""
+
     edam_data = "data_0863"
 
-    MetadataElement(name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True)
+    MetadataElement(
+        name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True
+    )
 
     def split(cls, input_datasets, subdir_generator_function, split_params):
         """Split a generic alignment file (not sensible or possible, see subclasses)."""
@@ -310,6 +327,7 @@ class Alignment(data.Text):
 @build_sniff_from_prefix
 class Fasta(Sequence):
     """Class representing a FASTA sequence"""
+
     edam_format = "format_1929"
     file_ext = "fasta"
 
@@ -351,17 +369,17 @@ class Fasta(Sequence):
         for line in fh:
             line = line.strip()
             if line:  # first non-empty line
-                if line.startswith('>'):
+                if line.startswith(">"):
                     # The next line.strip() must not be '', nor startwith '>'
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         return False
 
                     # If there is a third line, and it isn't a header line, it may not contain chars like '()[].' otherwise it's most likely a DotBracket file
                     line = fh.readline()
                     if not line:
                         return True
-                    if not line.startswith('>') and re.search(r"[\(\)\[\]\.]", line):
+                    if not line.startswith(">") and re.search(r"[\(\)\[\]\.]", line):
                         return False
                     return True
                 else:
@@ -385,10 +403,10 @@ class Fasta(Sequence):
         input_file = input_datasets[0].file_name
 
         # Counting chunk size as number of sequences.
-        if 'split_mode' not in split_params:
-            raise Exception('Tool does not define a split mode')
-        elif split_params['split_mode'] == 'number_of_parts':
-            split_size = int(split_params['split_size'])
+        if "split_mode" not in split_params:
+            raise Exception("Tool does not define a split mode")
+        elif split_params["split_mode"] == "number_of_parts":
+            split_size = int(split_params["split_size"])
             log.debug("Split %s into %i parts..." % (input_file, split_size))
             # if split_mode = number_of_parts, and split_size = 10, and
             # we know the number of sequences (say 1234), then divide by
@@ -404,10 +422,10 @@ class Fasta(Sequence):
                 # the file size.
                 chunk_size = os.path.getsize(input_file) // split_size
                 cls._size_split(input_file, chunk_size, subdir_generator_function)
-        elif split_params['split_mode'] == 'to_size':
+        elif split_params["split_mode"] == "to_size":
             # Split the input file into as many sub-files as required,
             # each containing to_size many sequences
-            batch_size = int(split_params['split_size'])
+            batch_size = int(split_params["split_size"])
             log.debug("Split %s into batches of %i records..." % (input_file, batch_size))
             cls._count_split(input_file, batch_size, subdir_generator_function)
         else:
@@ -428,10 +446,10 @@ class Fasta(Sequence):
                 # produce just one sub-file which will be a copy of it.
                 part_dir = subdir_generator_function()
                 part_path = os.path.join(part_dir, os.path.basename(input_file))
-                part_file = open(part_path, 'w')
+                part_file = open(part_path, "w")
                 log.debug(f"Writing {input_file} part to {part_path}")
                 start_offset = 0
-                for line in iter(f.readline, ''):
+                for line in iter(f.readline, ""):
                     offset = f.tell()
                     if not line:
                         break
@@ -440,12 +458,12 @@ class Fasta(Sequence):
                         part_file.close()
                         part_dir = subdir_generator_function()
                         part_path = os.path.join(part_dir, os.path.basename(input_file))
-                        part_file = open(part_path, 'w')
+                        part_file = open(part_path, "w")
                         log.debug(f"Writing {input_file} part to {part_path}")
                         start_offset = f.tell()
                     part_file.write(line)
             except Exception as e:
-                log.error('Unable to size split FASTA file: %s', util.unicodify(e))
+                log.error("Unable to size split FASTA file: %s", util.unicodify(e))
                 raise
             finally:
                 if part_file:
@@ -462,7 +480,7 @@ class Fasta(Sequence):
                 # produce just one sub-file which will be a copy of it.
                 part_dir = subdir_generator_function()
                 part_path = os.path.join(part_dir, os.path.basename(input_file))
-                part_file = open(part_path, 'w')
+                part_file = open(part_path, "w")
                 log.debug(f"Writing {input_file} part to {part_path}")
                 rec_count = 0
                 for line in f:
@@ -475,12 +493,12 @@ class Fasta(Sequence):
                             part_file.close()
                             part_dir = subdir_generator_function()
                             part_path = os.path.join(part_dir, os.path.basename(input_file))
-                            part_file = open(part_path, 'w')
+                            part_file = open(part_path, "w")
                             log.debug(f"Writing {input_file} part to {part_path}")
                             rec_count = 1
                     part_file.write(line)
             except Exception as e:
-                log.error('Unable to count split FASTA file: %s', util.unicodify(e))
+                log.error("Unable to count split FASTA file: %s", util.unicodify(e))
                 raise
             finally:
                 if part_file:
@@ -489,7 +507,8 @@ class Fasta(Sequence):
 
 @build_sniff_from_prefix
 class csFasta(Sequence):
-    """ Class representing the SOLID Color-Space sequence ( csfasta ) """
+    """Class representing the SOLID Color-Space sequence ( csfasta )"""
+
     edam_format = "format_3589"
     file_ext = "csfasta"
 
@@ -510,14 +529,14 @@ class csFasta(Sequence):
         fh = file_prefix.string_io()
         for line in fh:
             line = line.strip()
-            if line and not line.startswith('#'):  # first non-empty non-comment line
-                if line.startswith('>'):
+            if line and not line.startswith("#"):  # first non-empty non-comment line
+                if line.startswith(">"):
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         break
                     elif line[0] not in string.ascii_uppercase:
                         return False
-                    elif len(line) > 1 and not re.search(r'^[\d.]+$', line[1:]):
+                    elif len(line) > 1 and not re.search(r"^[\d.]+$", line[1:]):
                         return False
                     return True
                 else:
@@ -534,13 +553,24 @@ class csFasta(Sequence):
 
 @build_sniff_from_prefix
 class Fastg(Sequence):
-    """ Class representing a FASTG sequence
-    http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf """
+    """Class representing a FASTG sequence
+    http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"""
+
     edam_format = "format_3823"
     file_ext = "fastg"
 
-    MetadataElement(name="version", default='1.0', desc="FASTG format version", readonly=True, visible=True, no_value='1.0')
-    MetadataElement(name="properties", default={}, param=DictParameter, desc="FASTG properites", readonly=True, visible=True, no_value={})
+    MetadataElement(
+        name="version", default="1.0", desc="FASTG format version", readonly=True, visible=True, no_value="1.0"
+    )
+    MetadataElement(
+        name="properties",
+        default={},
+        param=DictParameter,
+        desc="FASTG properites",
+        readonly=True,
+        visible=True,
+        no_value={},
+    )
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """FASTG must begin with lines:
@@ -577,13 +607,13 @@ class Fastg(Sequence):
                 break  # EOF
             line = line.strip()
             if i == 0:
-                if not line.startswith('#FASTG:begin'):
+                if not line.startswith("#FASTG:begin"):
                     break
-            elif line and not line.startswith('#'):  # first non-empty non-comment line
-                if line.startswith('>'):
+            elif line and not line.startswith("#"):  # first non-empty non-comment line
+                if line.startswith(">"):
                     # The next line.strip() must not be '', nor startwith '>'
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         break
                     return True
                 else:
@@ -597,14 +627,17 @@ class Fastg(Sequence):
                     break  # EOF
                 line = line.strip()
                 if i == 0:
-                    if not line.startswith('#FASTG:begin'):
+                    if not line.startswith("#FASTG:begin"):
                         break
-                if line.startswith('#FASTG'):
-                    props = {x.split('=')[0][1:]: x.split('=')[1] for x in re.findall(':[a-zA-Z0-9_]+=[a-zA-Z0-9_().,\" ]+', line)}
+                if line.startswith("#FASTG"):
+                    props = {
+                        x.split("=")[0][1:]: x.split("=")[1]
+                        for x in re.findall(':[a-zA-Z0-9_]+=[a-zA-Z0-9_().," ]+', line)
+                    }
                     dataset.metadata.properties.update(props)
-                    if 'version' in props:
-                        dataset.metadata.version = props['version']
-                if line and line.startswith('>'):
+                    if "version" in props:
+                        dataset.metadata.version = props["version"]
+                if line and line.startswith(">"):
                     break
         if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
             dataset.metadata.data_lines = None
@@ -619,18 +652,19 @@ class Fastg(Sequence):
                 dataset.blurb = f"{util.commaify(str(dataset.metadata.sequences))} sequences"
             else:
                 dataset.blurb = nice_size(dataset.get_size())
-            dataset.blurb += f'\nversion={dataset.metadata.version}'
+            dataset.blurb += f"\nversion={dataset.metadata.version}"
             for k, v in dataset.metadata.properties.items():
-                if k != 'version':
-                    dataset.blurb += f'\n{k}={v}'
+                if k != "version":
+                    dataset.blurb += f"\n{k}={v}"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
 class BaseFastq(Sequence):
     """Base class for FastQ sequences"""
+
     edam_format = "format_1930"
     file_ext = "fastq"
     bases_regexp = re.compile(r"^[NGTAC 0123\.]*$", re.IGNORECASE)
@@ -647,16 +681,16 @@ class BaseFastq(Sequence):
             return
         data_lines = 0
         sequences = 0
-        seq_counter = 0     # blocks should be 4 lines long
+        seq_counter = 0  # blocks should be 4 lines long
         with compression_utils.get_fileobj(dataset.file_name) as in_file:
             for line in in_file:
                 line = line.strip()
-                if line and line.startswith('#') and not data_lines:
+                if line and line.startswith("#") and not data_lines:
                     # We don't count comment lines for sequence data types
                     continue
                 seq_counter += 1
                 data_lines += 1
-                if line and line.startswith('@'):
+                if line and line.startswith("@"):
                     if seq_counter >= 4:
                         # count previous block
                         # blocks should be 4 lines long
@@ -707,7 +741,7 @@ class BaseFastq(Sequence):
         compressed = file_prefix.compressed_format is not None
         if compressed and not isinstance(self, Binary):
             return False
-        headers = iter_headers(file_prefix, sep='\n', count=1000)
+        headers = iter_headers(file_prefix, sep="\n", count=1000)
         # check to see if the base qualities match
         if not self.quality_check(headers):
             return False
@@ -722,9 +756,12 @@ class BaseFastq(Sequence):
                     mime = "text/plain"
                     self._clean_and_set_mime_type(trans, mime, headers)
                     return fh.read(), headers
-                return trans.fill_template_mako("/dataset/large_file.mako",
-                                                truncated_data=fh.read(max_peek_size),
-                                                data=dataset), headers
+                return (
+                    trans.fill_template_mako(
+                        "/dataset/large_file.mako", truncated_data=fh.read(max_peek_size), data=dataset
+                    ),
+                    headers,
+                )
         else:
             return Sequence.display_data(self, trans, dataset, preview, filename, to_ext, **kwd)
 
@@ -743,7 +780,7 @@ class BaseFastq(Sequence):
             tmp_ds = ds
             fqtoc_file = None
             while fqtoc_file is None and tmp_ds is not None:
-                fqtoc_file = tmp_ds.get_converted_files_by_type('fqtoc')
+                fqtoc_file = tmp_ds.get_converted_files_by_type("fqtoc")
                 tmp_ds = tmp_ds.copied_from_library_dataset_dataset_association
 
             if fqtoc_file is not None:
@@ -760,18 +797,22 @@ class BaseFastq(Sequence):
         to create the input files for the Task. The parameters:
         data - a dict containing the contents of the split file
         """
-        args = data['args']
-        input_name = data['input_name']
-        output_name = data['output_name']
-        start_sequence = int(args['start_sequence'])
-        sequence_count = int(args['num_sequences'])
+        args = data["args"]
+        input_name = data["input_name"]
+        output_name = data["output_name"]
+        start_sequence = int(args["start_sequence"])
+        sequence_count = int(args["num_sequences"])
 
-        if 'toc_file' in args:
-            with open(args['toc_file']) as f:
+        if "toc_file" in args:
+            with open(args["toc_file"]) as f:
                 toc_file = json.load(f)
-            commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count)
+            commands = Sequence.get_split_commands_with_toc(
+                input_name, output_name, toc_file, start_sequence, sequence_count
+            )
         else:
-            commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count)
+            commands = Sequence.get_split_commands_sequential(
+                is_gzip(input_name), input_name, output_name, start_sequence, sequence_count
+            )
         for cmd in commands:
             subprocess.check_call(cmd, shell=True)
         return True
@@ -783,12 +824,19 @@ class BaseFastq(Sequence):
     @classmethod
     def check_first_block(cls, file_prefix: FilePrefix):
         # check that first block looks like a fastq block
-        block = get_headers(file_prefix, sep='\n', count=4)
+        block = get_headers(file_prefix, sep="\n", count=4)
         return cls.check_block(block)
 
     @classmethod
     def check_block(cls, block):
-        if len(block) == 4 and block[0][0] and block[0][0][0] == "@" and block[2][0] and block[2][0][0] == "+" and block[1][0]:
+        if (
+            len(block) == 4
+            and block[0][0]
+            and block[0][0][0] == "@"
+            and block[2][0]
+            and block[2][0][0] == "+"
+            and block[1][0]
+        ):
             # Check the sequence line, make sure it contains only G/C/A/T/N
             match = cls.bases_regexp.match(block[1][0])
             if match:
@@ -798,12 +846,12 @@ class BaseFastq(Sequence):
         return False
 
     def validate(self, dataset, **kwd):
-        headers = iter_headers(dataset.file_name, sep='\n', count=-1)
+        headers = iter_headers(dataset.file_name, sep="\n", count=-1)
         # check to see if the base qualities match
         if not self.quality_check(headers):
             return DatatypeValidation.invalid("Invalid quality score(s) found for this fastq datatype.")
 
-        headers = iter_headers(dataset.file_name, sep='\n', count=-1)
+        headers = iter_headers(dataset.file_name, sep="\n", count=-1)
         while True:
             block = list(islice(headers, 4))
             if len(block) == 0:
@@ -816,6 +864,7 @@ class BaseFastq(Sequence):
 
 class Fastq(BaseFastq):
     """Class representing a generic FASTQ sequence"""
+
     edam_format = "format_1930"
     file_ext = "fastq"
 
@@ -825,6 +874,7 @@ class FastqSanger(Fastq):
 
     phred scored quality values 0:50 represented by ASCII 33:83
     """
+
     edam_format = "format_1932"
     file_ext = "fastqsanger"
     bases_regexp = re.compile("^[NGTAC]*$", re.IGNORECASE)
@@ -836,7 +886,7 @@ class FastqSanger(Fastq):
         return True if the qualities are compatible with sanger encoding
         """
         for line in islice(lines, 3, None, 4):
-            if not all(q >= '!' and q <= 'S' for q in line[0]):
+            if not all(q >= "!" and q <= "S" for q in line[0]):
                 return False
         return True
 
@@ -846,6 +896,7 @@ class FastqSolexa(Fastq):
 
     solexa scored quality values -5:40 represented by ASCII 59:104
     """
+
     edam_format = "format_1933"
     file_ext = "fastqsolexa"
 
@@ -856,7 +907,7 @@ class FastqSolexa(Fastq):
         return True if the qualities are compatible with sanger encoding
         """
         for line in islice(lines, 3, None, 4):
-            if not all(q >= ';' and q <= 'h' for q in line[0]):
+            if not all(q >= ";" and q <= "h" for q in line[0]):
                 return False
         return True
 
@@ -871,6 +922,7 @@ class FastqIllumina(Fastq):
 
     phred scored quality values 0:40 represented by ASCII 64:104
     """
+
     edam_format = "format_1931"
     file_ext = "fastqillumina"
 
@@ -881,7 +933,7 @@ class FastqIllumina(Fastq):
         return True if the qualities are compatible with sanger encoding
         """
         for line in islice(lines, 3, None, 4):
-            if not all(q >= '@' and q <= 'h' for q in line[0]):
+            if not all(q >= "@" and q <= "h" for q in line[0]):
                 return False
         return True
 
@@ -897,6 +949,7 @@ class FastqCSSanger(Fastq):
     sequence in in color space
     phred scored quality values 0:93 represented by ASCII 33:126
     """
+
     file_ext = "fastqcssanger"
     bases_regexp = re.compile(r"^[NGTAC][0123\.]*$", re.IGNORECASE)
 
@@ -904,13 +957,30 @@ class FastqCSSanger(Fastq):
 @build_sniff_from_prefix
 class Maf(Alignment):
     """Class describing a Maf alignment"""
+
     edam_format = "format_3008"
     file_ext = "maf"
 
     # Readonly and optional, users can't unset it, but if it is not set, we are generally ok; if required use a metadata validator in the tool definition
-    MetadataElement(name="blocks", default=0, desc="Number of blocks", readonly=True, optional=True, visible=False, no_value=0)
-    MetadataElement(name="species_chromosomes", desc="Species Chromosomes", param=metadata.FileParameter, readonly=True, visible=False, optional=True)
-    MetadataElement(name="maf_index", desc="MAF Index File", param=metadata.FileParameter, readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="blocks", default=0, desc="Number of blocks", readonly=True, optional=True, visible=False, no_value=0
+    )
+    MetadataElement(
+        name="species_chromosomes",
+        desc="Species Chromosomes",
+        param=metadata.FileParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
+    MetadataElement(
+        name="maf_index",
+        desc="MAF Index File",
+        param=metadata.FileParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def init_meta(self, dataset, copy_from=None):
         Alignment.init_meta(self, dataset, copy_from=copy_from)
@@ -922,6 +992,7 @@ class Maf(Alignment):
         # these metadata values are not accessable by users, always overwrite
         # Imported here to avoid circular dependency
         from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes
+
         indexes, species, species_chromosomes, blocks = build_maf_index_species_chromosomes(dataset.file_name)
         if indexes is None:
             return  # this is not a MAF file
@@ -931,16 +1002,16 @@ class Maf(Alignment):
         # write species chromosomes to a file
         chrom_file = dataset.metadata.species_chromosomes
         if not chrom_file:
-            chrom_file = dataset.metadata.spec['species_chromosomes'].param.new_file(dataset=dataset)
-        with open(chrom_file.file_name, 'w') as chrom_out:
+            chrom_file = dataset.metadata.spec["species_chromosomes"].param.new_file(dataset=dataset)
+        with open(chrom_file.file_name, "w") as chrom_out:
             for spec, chroms in species_chromosomes.items():
                 chrom_out.write("{}\t{}\n".format(spec, "\t".join(chroms)))
         dataset.metadata.species_chromosomes = chrom_file
 
         index_file = dataset.metadata.maf_index
         if not index_file:
-            index_file = dataset.metadata.spec['maf_index'].param.new_file(dataset=dataset)
-        indexes.write(open(index_file.file_name, 'wb'))
+            index_file = dataset.metadata.spec["maf_index"].param.new_file(dataset=dataset)
+        indexes.write(open(index_file.file_name, "wb"))
         dataset.metadata.maf_index = index_file
 
     def set_peek(self, dataset):
@@ -954,8 +1025,8 @@ class Maf(Alignment):
                 # needed to set metadata
                 dataset.blurb = "? blocks"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
@@ -966,10 +1037,10 @@ class Maf(Alignment):
         skipchars = skipchars or []
         out = ['<table cellspacing="0" cellpadding="3">']
         try:
-            out.append('<tr><th>Species:&nbsp;')
+            out.append("<tr><th>Species:&nbsp;")
             for species in dataset.metadata.species:
-                out.append(f'{species}&nbsp;')
-            out.append('</th></tr>')
+                out.append(f"{species}&nbsp;")
+            out.append("</th></tr>")
             if not dataset.peek:
                 dataset.set_peek()
             data = dataset.peek
@@ -978,8 +1049,8 @@ class Maf(Alignment):
                 line = line.strip()
                 if not line:
                     continue
-                out.append(f'<tr><td>{escape(line)}</td></tr>')
-            out.append('</table>')
+                out.append(f"<tr><td>{escape(line)}</td></tr>")
+            out.append("</table>")
             out = "".join(out)
         except Exception as exc:
             out = f"Can't create peek {exc}"
@@ -1021,9 +1092,21 @@ class Maf(Alignment):
 class MafCustomTrack(data.Text):
     file_ext = "mafcustomtrack"
 
-    MetadataElement(name="vp_chromosome", default='chr1', desc="Viewport Chromosome", readonly=True, optional=True, visible=False, no_value='')
-    MetadataElement(name="vp_start", default='1', desc="Viewport Start", readonly=True, optional=True, visible=False, no_value='')
-    MetadataElement(name="vp_end", default='100', desc="Viewport End", readonly=True, optional=True, visible=False, no_value='')
+    MetadataElement(
+        name="vp_chromosome",
+        default="chr1",
+        desc="Viewport Chromosome",
+        readonly=True,
+        optional=True,
+        visible=False,
+        no_value="",
+    )
+    MetadataElement(
+        name="vp_start", default="1", desc="Viewport Start", readonly=True, optional=True, visible=False, no_value=""
+    )
+    MetadataElement(
+        name="vp_end", default="100", desc="Viewport End", readonly=True, optional=True, visible=False, no_value=""
+    )
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         """
@@ -1059,6 +1142,7 @@ class MafCustomTrack(data.Text):
 @build_sniff_from_prefix
 class Axt(data.Text):
     """Class describing an axt alignment"""
+
     # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is
     # here simply for backward compatibility ( although it is still in the datatypes registry ).  Subclassing
     # from data.Text eliminates managing metadata elements inherited from the Alignemnt class.
@@ -1116,6 +1200,7 @@ class Axt(data.Text):
 @build_sniff_from_prefix
 class Lav(data.Text):
     """Class describing a LAV alignment"""
+
     # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is
     # here simply for backward compatibility ( although it is still in the datatypes registry ).  Subclassing
     # from data.Text eliminates managing metadata elements inherited from the Alignment class.
@@ -1143,7 +1228,7 @@ class Lav(data.Text):
         """
         headers = get_headers(file_prefix, None)
         try:
-            if len(headers) > 1 and headers[0][0] and headers[0][0].startswith('#:lav'):
+            if len(headers) > 1 and headers[0][0] and headers[0][0].startswith("#:lav"):
                 return True
             else:
                 return False
@@ -1157,15 +1242,15 @@ class RNADotPlotMatrix(data.Data):
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
-            dataset.peek = 'RNA Dot Plot format (Postscript derivative)'
+            dataset.peek = "RNA Dot Plot format (Postscript derivative)"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff(self, filename):
         """Determine if the file is in RNA dot plot format."""
-        if check_image_type(filename, ['EPS']):
+        if check_image_type(filename, ["EPS"]):
             seq = False
             coor = False
             pairs = False
@@ -1173,11 +1258,11 @@ class RNADotPlotMatrix(data.Data):
                 for line in handle:
                     line = line.strip()
                     if line:
-                        if line.startswith('/sequence'):
+                        if line.startswith("/sequence"):
                             seq = True
-                        elif line.startswith('/coor'):
+                        elif line.startswith("/coor"):
                             coor = True
-                        elif line.startswith('/pairs'):
+                        elif line.startswith("/pairs"):
                             pairs = True
                     if seq and coor and pairs:
                         return True
@@ -1211,7 +1296,7 @@ class DotBracket(Sequence):
             line = line.strip()
             data_lines += 1
 
-            if line and line.startswith('>'):
+            if line and line.startswith(">"):
                 sequences += 1
 
         dataset.metadata.data_lines = data_lines
@@ -1245,7 +1330,7 @@ class DotBracket(Sequence):
             * Sniffing is only applied on the first entry.
 
         * Empty lines are allowed.
-         """
+        """
 
         state = 0
 
@@ -1255,7 +1340,7 @@ class DotBracket(Sequence):
             if line:
                 # header line
                 if state == 0:
-                    if(line[0] != '>'):
+                    if line[0] != ">":
                         return False
                     else:
                         state = 1
@@ -1270,10 +1355,13 @@ class DotBracket(Sequence):
 
                 # dot-bracket structure line
                 elif state == 2:
-                    if sequence_size != len(line) or not self.structure_regexp.match(line) or \
-                            line.count('(') != line.count(')') or \
-                            line.count('[') != line.count(']') or \
-                            line.count('{') != line.count('}'):
+                    if (
+                        sequence_size != len(line)
+                        or not self.structure_regexp.match(line)
+                        or line.count("(") != line.count(")")
+                        or line.count("[") != line.count("]")
+                        or line.count("{") != line.count("}")
+                    ):
                         return False
                     else:
                         return True
@@ -1285,6 +1373,7 @@ class DotBracket(Sequence):
 @build_sniff_from_prefix
 class Genbank(data.Text):
     """Class representing a Genbank sequence"""
+
     edam_format = "format_1936"
     edam_data = "data_0849"
     file_ext = "genbank"
@@ -1302,12 +1391,13 @@ class Genbank(data.Text):
         compressed = file_prefix.compressed_format
         if compressed and not isinstance(self, Binary):
             return False
-        return 'LOCUS ' == file_prefix.contents_header[0:6]
+        return "LOCUS " == file_prefix.contents_header[0:6]
 
 
 @build_sniff_from_prefix
 class MemePsp(Sequence):
     """Class representing MEME Position Specific Priors"""
+
     file_ext = "memepsp"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -1327,6 +1417,7 @@ class MemePsp(Sequence):
         >>> MemePsp().sniff(fname)
         False
         """
+
         def floats_verified(line):
             for item in line.split():
                 try:
@@ -1338,6 +1429,7 @@ class MemePsp(Sequence):
                 except ValueError:
                     return True
             return False
+
         num_lines = 0
         fh = file_prefix.string_io()
         got_header = False
@@ -1350,11 +1442,11 @@ class MemePsp(Sequence):
             num_lines += 1
             line = line.strip()
             if line:
-                if line.startswith('>'):
+                if line.startswith(">"):
                     got_header = True
                     # The line must not be blank, nor start with '>'
                     line = fh.readline().strip()
-                    if line == '' or line.startswith('>'):
+                    if line == "" or line.startswith(">"):
                         return False
                     # All items within the line must be floats.
                     if not floats_verified(line):
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 40341e0bc6b..840b499dd60 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -29,7 +29,7 @@ from galaxy.files import ConfiguredFileSources
 from galaxy.util import (
     compression_utils,
     file_reader,
-    stream_to_open_named_file
+    stream_to_open_named_file,
 )
 from galaxy.util.checkers import (
     check_binary,
@@ -40,13 +40,13 @@ from galaxy.util.checkers import (
 
 log = logging.getLogger(__name__)
 
-SNIFF_PREFIX_BYTES = int(os.environ.get("GALAXY_SNIFF_PREFIX_BYTES", None) or 2 ** 20)
+SNIFF_PREFIX_BYTES = int(os.environ.get("GALAXY_SNIFF_PREFIX_BYTES", None) or 2**20)
 
 
 def get_test_fname(fname):
     """Returns test data filename"""
     path, name = os.path.split(__file__)
-    full_path = os.path.join(path, 'test', fname)
+    full_path = os.path.join(path, "test", fname)
     return full_path
 
 
@@ -67,12 +67,16 @@ def stream_url_to_file(path: str, file_sources: Optional[ConfiguredFileSources]
         file_source_path.file_source.realize_to(file_source_path.path, temp_name)
         return temp_name
     else:
-        page = urllib.request.urlopen(path, timeout=util.DEFAULT_SOCKET_TIMEOUT)  # page will be .close()ed in stream_to_file
-        temp_name = stream_to_file(page, prefix=prefix, source_encoding=util.get_charset_from_http_headers(page.headers))
+        page = urllib.request.urlopen(
+            path, timeout=util.DEFAULT_SOCKET_TIMEOUT
+        )  # page will be .close()ed in stream_to_file
+        temp_name = stream_to_file(
+            page, prefix=prefix, source_encoding=util.get_charset_from_http_headers(page.headers)
+        )
         return temp_name
 
 
-def stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd):
+def stream_to_file(stream, suffix="", prefix="", dir=None, text=False, **kwd):
     """Writes a stream to a temporary file, returns the temporary file's name"""
     fd, temp_name = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir, text=text)
     return stream_to_open_named_file(stream, fd, temp_name, **kwd)
@@ -80,7 +84,7 @@ def stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd):
 
 def handle_composite_file(datatype, src_path, extra_files, name, is_binary, tmp_dir, tmp_prefix, upload_opts):
     if not is_binary:
-        if upload_opts.get('space_to_tab'):
+        if upload_opts.get("space_to_tab"):
             convert_newlines_sep2tabs(src_path, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix)
         else:
             convert_newlines(src_path, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix)
@@ -101,12 +105,20 @@ class ConvertResult(NamedTuple):
 
 
 class ConvertFunction(Protocol):
-
-    def __call__(self, fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload") -> ConvertResult:
+    def __call__(
+        self, fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload"
+    ) -> ConvertResult:
         ...
 
 
-def convert_newlines(fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload", block_size: int = 128 * 1024, regexp=None) -> ConvertResult:
+def convert_newlines(
+    fname: str,
+    in_place: bool = True,
+    tmp_dir: Optional[str] = None,
+    tmp_prefix: Optional[str] = "gxupload",
+    block_size: int = 128 * 1024,
+    regexp=None,
+) -> ConvertResult:
     """
     Converts in place a file from universal line endings
     to Posix line endings.
@@ -116,7 +128,9 @@ def convert_newlines(fname: str, in_place: bool = True, tmp_dir: Optional[str] =
     converted_regex = False
     NEWLINE_BYTE = 10
     CR_BYTE = 13
-    with tempfile.NamedTemporaryFile(mode='wb', prefix=tmp_prefix, dir=tmp_dir, delete=False) as fp, open(fname, mode='rb') as fi:
+    with tempfile.NamedTemporaryFile(mode="wb", prefix=tmp_prefix, dir=tmp_dir, delete=False) as fp, open(
+        fname, mode="rb"
+    ) as fi:
         last_char = None
         block = fi.read(block_size)
         last_block = b""
@@ -151,16 +165,24 @@ def convert_newlines(fname: str, in_place: bool = True, tmp_dir: Optional[str] =
         return ConvertResult(i, fp.name, converted_newlines, converted_regex)
 
 
-def convert_sep2tabs(fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload", block_size: int = 128 * 1024):
+def convert_sep2tabs(
+    fname: str,
+    in_place: bool = True,
+    tmp_dir: Optional[str] = None,
+    tmp_prefix: Optional[str] = "gxupload",
+    block_size: int = 128 * 1024,
+):
     """
     Transforms in place a 'sep' separated file to a tab separated one
     """
-    patt: bytes = br"[^\S\r\n]+"
+    patt: bytes = rb"[^\S\r\n]+"
     regexp = re.compile(patt)
     i = 0
     converted_newlines = False
     converted_regex = False
-    with tempfile.NamedTemporaryFile(mode='wb', prefix=tmp_prefix, dir=tmp_dir, delete=False) as fp, open(fname, mode='rb') as fi:
+    with tempfile.NamedTemporaryFile(mode="wb", prefix=tmp_prefix, dir=tmp_dir, delete=False) as fp, open(
+        fname, mode="rb"
+    ) as fi:
         block = fi.read(block_size)
         while block:
             if block:
@@ -179,11 +201,13 @@ def convert_sep2tabs(fname: str, in_place: bool = True, tmp_dir: Optional[str] =
         return ConvertResult(i, fp.name, converted_newlines, converted_regex)
 
 
-def convert_newlines_sep2tabs(fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload") -> ConvertResult:
+def convert_newlines_sep2tabs(
+    fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload"
+) -> ConvertResult:
     """
     Converts newlines in a file to posix newlines and replaces spaces with tabs.
     """
-    patt: bytes = br"[^\S\n]+"
+    patt: bytes = rb"[^\S\n]+"
     regexp = re.compile(patt)
     return convert_newlines(fname, in_place, tmp_dir, tmp_prefix, regexp=regexp)
 
@@ -195,8 +219,8 @@ def iter_headers(fname_or_file_prefix, sep, count=60, comment_designator=None):
     else:
         file_iterator = compression_utils.get_fileobj(fname_or_file_prefix)
     for line in file_iterator:
-        line = line.rstrip('\n\r')
-        if comment_designator is not None and comment_designator != '' and line.startswith(comment_designator):
+        line = line.rstrip("\n\r")
+        if comment_designator is not None and comment_designator != "" and line.startswith(comment_designator):
             continue
         yield line.split(sep)
         idx += 1
@@ -221,10 +245,14 @@ def get_headers(fname_or_file_prefix, sep, count=60, comment_designator=None):
     >>> get_headers(fname, '\\t', count=5, comment_designator='#') == [[''], ['chr7', 'bed2gff', 'AR', '26731313', '26731437', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731491', '26731536', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731541', '26731649', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731659', '26731841', '.', '+', '.', 'score']]
     True
     """
-    return list(iter_headers(fname_or_file_prefix=fname_or_file_prefix, sep=sep, count=count, comment_designator=comment_designator))
+    return list(
+        iter_headers(
+            fname_or_file_prefix=fname_or_file_prefix, sep=sep, count=count, comment_designator=comment_designator
+        )
+    )
 
 
-def is_column_based(fname_or_file_prefix, sep='\t', skip=0):
+def is_column_based(fname_or_file_prefix, sep="\t", skip=0):
     """
     Checks whether the file is column based with respect to a separator
     (defaults to tab separator).
@@ -256,14 +284,14 @@ def is_column_based(fname_or_file_prefix, sep='\t', skip=0):
         return False
 
     try:
-        headers = get_headers(fname_or_file_prefix, sep, comment_designator='#')[skip:]
+        headers = get_headers(fname_or_file_prefix, sep, comment_designator="#")[skip:]
     except UnicodeDecodeError:
         return False
     count = 0
     if not headers:
         return False
     for hdr in headers:
-        if hdr and hdr != ['']:
+        if hdr and hdr != [""]:
             if count:
                 if len(hdr) != count:
                     return False
@@ -492,26 +520,25 @@ def guess_ext(fname, sniff_order, is_binary=False):
     # Ugly hack for tsv vs tabular sniffing, we want to prefer tabular
     # to tsv but it doesn't have a sniffer - is TSV was sniffed just check
     # if it is an okay tabular and use that instead.
-    if file_ext == 'tsv':
-        if is_column_based(file_prefix, '\t', 1):
-            file_ext = 'tabular'
+    if file_ext == "tsv":
+        if is_column_based(file_prefix, "\t", 1):
+            file_ext = "tabular"
     if file_ext is not None:
         return file_ext
 
     # skip header check if data is already known to be binary
     if is_binary:
-        return file_ext or 'binary'
+        return file_ext or "binary"
     try:
         get_headers(file_prefix, None)
     except UnicodeDecodeError:
-        return 'data'  # default data type file extension
-    if is_column_based(file_prefix, '\t', 1):
-        return 'tabular'  # default tabular data type file extension
-    return 'txt'  # default text data type file extension
+        return "data"  # default data type file extension
+    if is_column_based(file_prefix, "\t", 1):
+        return "tabular"  # default tabular data type file extension
+    return "txt"  # default text data type file extension
 
 
 class FilePrefix:
-
     def __init__(self, filename):
         non_utf8_error = None
         compressed_format = None
@@ -564,7 +591,7 @@ class FilePrefix:
     def line_iterator(self):
         s = self.string_io()
         s_len = len(s.getvalue())
-        for line in iter(s.readline, ''):
+        for line in iter(s.readline, ""):
             if line.endswith("\n") or line.endswith("\r"):
                 yield line
             elif s.tell() == s_len and not self.truncated:
@@ -600,8 +627,7 @@ def _get_file_prefix(filename_or_file_prefix: Union[str, FilePrefix]) -> FilePre
 
 
 def run_sniffers_raw(filename_or_file_prefix: Union[str, FilePrefix], sniff_order, is_binary=False):
-    """Run through sniffers specified by sniff_order, return None of None match.
-    """
+    """Run through sniffers specified by sniff_order, return None of None match."""
     file_prefix = _get_file_prefix(filename_or_file_prefix)
     fname = file_prefix.filename
     file_ext = None
@@ -643,7 +669,7 @@ def run_sniffers_raw(filename_or_file_prefix: Union[str, FilePrefix], sniff_orde
 def zip_single_fileobj(path):
     z = zipfile.ZipFile(path)
     for name in z.namelist():
-        if not name.endswith('/'):
+        if not name.endswith("/"):
             return z.open(name)
 
 
@@ -684,14 +710,14 @@ class HandleCompressedFileResponse(NamedTuple):
 
 
 def handle_compressed_file(
-        filename: str,
-        datatypes_registry,
-        ext: str = 'auto',
-        tmp_prefix: Optional[str] = 'sniff_uncompress_',
-        tmp_dir: Optional[str] = None,
-        in_place: bool = False,
-        check_content: bool = True,
-        auto_decompress: bool = True,
+    filename: str,
+    datatypes_registry,
+    ext: str = "auto",
+    tmp_prefix: Optional[str] = "sniff_uncompress_",
+    tmp_dir: Optional[str] = None,
+    in_place: bool = False,
+    check_content: bool = True,
+    auto_decompress: bool = True,
 ) -> HandleCompressedFileResponse:
     """
     Check uploaded files for compression, check compressed file contents, and uncompress if necessary.
@@ -708,7 +734,7 @@ def handle_compressed_file(
     in the case of a zip file), this is so lengthy decompression can be bypassed if there is invalid content in the
     first 32KB. Otherwise the caller should be checking content.
     """
-    CHUNK_SIZE = 2 ** 20  # 1Mb
+    CHUNK_SIZE = 2**20  # 1Mb
     is_compressed = False
     compressed_type = None
     keep_compressed = False
@@ -723,14 +749,14 @@ def handle_compressed_file(
     if is_compressed and is_valid:
         if ext in AUTO_DETECT_EXTENSIONS:
             # attempt to sniff for a keep-compressed datatype (observing the sniff order)
-            sniff_datatypes = filter(lambda d: getattr(d, 'compressed', False), datatypes_registry.sniff_order)
+            sniff_datatypes = filter(lambda d: getattr(d, "compressed", False), datatypes_registry.sniff_order)
             sniffed_ext = run_sniffers_raw(filename, sniff_datatypes)
             if sniffed_ext:
                 ext = sniffed_ext
                 keep_compressed = True
         else:
             datatype = datatypes_registry.get_datatype_by_extension(ext)
-            keep_compressed = getattr(datatype, 'compressed', False)
+            keep_compressed = getattr(datatype, "compressed", False)
     # don't waste time decompressing if we sniff invalid contents
     if is_compressed and is_valid and auto_decompress and not keep_compressed:
         assert compressed_type  # Tell type checker is_compressed will only be true if compressed_type is also set.
@@ -744,7 +770,11 @@ def handle_compressed_file(
                         uncompressed.write(chunk)
                 except OSError as e:
                     os.remove(uncompressed.name)
-                    raise OSError('Problem uncompressing {} data, please try retrieving the data uncompressed: {}'.format(compressed_type, util.unicodify(e)))
+                    raise OSError(
+                        "Problem uncompressing {} data, please try retrieving the data uncompressed: {}".format(
+                            compressed_type, util.unicodify(e)
+                        )
+                    )
         uncompressed_path = uncompressed.name
         if in_place:
             # Replace the compressed file with the uncompressed file
@@ -780,18 +810,18 @@ def convert_function(convert_to_posix_lines, convert_spaces_to_tabs) -> ConvertF
 
 
 def handle_uploaded_dataset_file_internal(
-        filename: str,
-        datatypes_registry,
-        ext: str = 'auto',
-        tmp_prefix: Optional[str] = 'sniff_upload_',
-        tmp_dir: Optional[str] = None,
-        in_place: bool = False,
-        check_content: bool = True,
-        is_binary: Optional[bool] = None,
-        auto_decompress: bool = True,
-        uploaded_file_ext: Optional[str] = None,
-        convert_to_posix_lines: Optional[bool] = None,
-        convert_spaces_to_tabs: Optional[bool] = None,
+    filename: str,
+    datatypes_registry,
+    ext: str = "auto",
+    tmp_prefix: Optional[str] = "sniff_upload_",
+    tmp_dir: Optional[str] = None,
+    in_place: bool = False,
+    check_content: bool = True,
+    is_binary: Optional[bool] = None,
+    auto_decompress: bool = True,
+    uploaded_file_ext: Optional[str] = None,
+    convert_to_posix_lines: Optional[bool] = None,
+    convert_spaces_to_tabs: Optional[bool] = None,
 ) -> HandleUploadedDatasetFileInternalResponse:
     is_valid, ext, converted_path, compressed_type = handle_compressed_file(
         filename,
@@ -808,8 +838,8 @@ def handle_uploaded_dataset_file_internal(
     try:
         if not is_valid:
             if is_tar(converted_path):
-                raise InappropriateDatasetContentError('TAR file uploads are not supported')
-            raise InappropriateDatasetContentError('The uploaded compressed file contains invalid content')
+                raise InappropriateDatasetContentError("TAR file uploads are not supported")
+            raise InappropriateDatasetContentError("The uploaded compressed file contains invalid content")
 
         # This needs to be checked again after decompression
         is_binary = check_binary(converted_path)
@@ -825,7 +855,9 @@ def handle_uploaded_dataset_file_internal(
         if not is_binary and (convert_to_posix_lines or convert_spaces_to_tabs):
             # Convert universal line endings to Posix line endings, spaces to tabs (if desired)
             convert_fxn = convert_function(convert_to_posix_lines, convert_spaces_to_tabs)
-            line_count, _converted_path, converted_newlines, converted_spaces = convert_fxn(converted_path, in_place=in_place, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix)
+            line_count, _converted_path, converted_newlines, converted_spaces = convert_fxn(
+                converted_path, in_place=in_place, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix
+            )
             if not in_place:
                 if converted_path and filename != converted_path:
                     os.unlink(converted_path)
@@ -837,19 +869,20 @@ def handle_uploaded_dataset_file_internal(
             ext = guessed_ext
 
         if not is_binary and check_content and check_html(converted_path):
-            raise InappropriateDatasetContentError('The uploaded file contains invalid HTML content')
+            raise InappropriateDatasetContentError("The uploaded file contains invalid HTML content")
     except Exception:
         if filename != converted_path:
             os.unlink(converted_path)
         raise
-    return HandleUploadedDatasetFileInternalResponse(ext, converted_path, compressed_type, converted_newlines, converted_spaces)
+    return HandleUploadedDatasetFileInternalResponse(
+        ext, converted_path, compressed_type, converted_newlines, converted_spaces
+    )
 
 
-AUTO_DETECT_EXTENSIONS = ['auto']  # should 'data' also cause auto detect?
+AUTO_DETECT_EXTENSIONS = ["auto"]  # should 'data' also cause auto detect?
 
 
 class Decompress(Protocol):
-
     def __call__(self, path: str) -> IO[bytes]:
         ...
 
@@ -861,6 +894,7 @@ class InappropriateDatasetContentError(Exception):
     pass
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__])
diff --git a/lib/galaxy/datatypes/spaln.py b/lib/galaxy/datatypes/spaln.py
index 19ad30c083d..528def8473b 100644
--- a/lib/galaxy/datatypes/spaln.py
+++ b/lib/galaxy/datatypes/spaln.py
@@ -54,12 +54,8 @@ class _SpalnDb(Data):
 
     def generate_primary_file(self, dataset=None):
         rval = ["<html><head><title>Spaln Database</title></head><p/>"]
-        rval.append(
-            "<div>This composite dataset is composed of the following files:<p/><ul>"
-        )
-        for composite_name, composite_file in self.get_composite_files(
-            dataset=dataset
-        ).items():
+        rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
+        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
             opt_text = ""
             if composite_file.get("description"):
@@ -68,10 +64,7 @@ class _SpalnDb(Data):
                     % (fn, fn, composite_file.get("description"), opt_text)
                 )
             else:
-                rval.append(
-                    '<li><a href="%s" type="application/binary">%s</a>%s</li>'
-                    % (fn, fn, opt_text)
-                )
+                rval.append('<li><a href="%s" type="application/binary">%s</a>%s</li>' % (fn, fn, opt_text))
         rval.append("</ul></div></html>")
         return "\n".join(rval)
 
@@ -110,17 +103,7 @@ class _SpalnDb(Data):
         except Exception:
             return "spaln database (multiple files)"
 
-    def display_data(
-        self,
-        trans,
-        data,
-        preview=False,
-        filename=None,
-        to_ext=None,
-        size=None,
-        offset=None,
-        **kwd
-    ):
+    def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):
         """
         If preview is `True` allows us to format the data shown in the central pane via the "eye" icon.
         If preview is `False` triggers download.
@@ -136,7 +119,7 @@ class _SpalnDb(Data):
                 size=size,
                 offset=offset,
                 headers=headers,
-                **kwd
+                **kwd,
             )
         if self.file_ext == "spalndbn":
             title = "This is a nucleotide-query spaln database"
@@ -157,10 +140,10 @@ class _SpalnDb(Data):
         if not msg:
             msg = title
         # Galaxy assumes HTML for the display of composite datatypes,
-        return smart_str(
-            "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>"
-            % (title, msg)
-        ), headers
+        return (
+            smart_str("<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)),
+            headers,
+        )
 
     def merge(split_files, output_file):
         """Merge spaln databases (not implemented)."""
diff --git a/lib/galaxy/datatypes/speech.py b/lib/galaxy/datatypes/speech.py
index b45eee0336f..6be6a96fc94 100644
--- a/lib/galaxy/datatypes/speech.py
+++ b/lib/galaxy/datatypes/speech.py
@@ -1,4 +1,7 @@
-from galaxy.datatypes.metadata import ListParameter, MetadataElement
+from galaxy.datatypes.metadata import (
+    ListParameter,
+    MetadataElement,
+)
 from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.text import Text
 
@@ -21,7 +24,16 @@ class TextGrid(Text):
 
     blurb = "Praat TextGrid file"
 
-    MetadataElement(name="annotations", default=[], desc="Annotation types", param=ListParameter, readonly=True, visible=True, optional=True, no_value=[])
+    MetadataElement(
+        name="annotations",
+        default=[],
+        desc="Annotation types",
+        param=ListParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
 
     def sniff(self, filename):
 
@@ -49,9 +61,41 @@ class BPF(Text):
 
     file_ext = "par"
 
-    MetadataElement(name="annotations", default=[], desc="Annotation types", param=ListParameter, readonly=True, visible=True, optional=True, no_value=[])
-    mandatory_headers = ['LHD', 'REP', 'SNB', 'SAM', 'SBF', 'SSB', 'NCH', 'SPN', 'LBD']
-    optional_headers = ['FIL', 'TYP', 'DBN', 'VOL', 'DIR', 'SRC', 'BEG', 'END', 'RED', 'RET', 'RCC', 'CMT', 'SPI', 'PCF', 'PCN', 'EXP', 'SYS', 'DAT', 'SPA', 'MAO', 'GPO', 'SAO']
+    MetadataElement(
+        name="annotations",
+        default=[],
+        desc="Annotation types",
+        param=ListParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    mandatory_headers = ["LHD", "REP", "SNB", "SAM", "SBF", "SSB", "NCH", "SPN", "LBD"]
+    optional_headers = [
+        "FIL",
+        "TYP",
+        "DBN",
+        "VOL",
+        "DIR",
+        "SRC",
+        "BEG",
+        "END",
+        "RED",
+        "RET",
+        "RCC",
+        "CMT",
+        "SPI",
+        "PCF",
+        "PCN",
+        "EXP",
+        "SYS",
+        "DAT",
+        "SPA",
+        "MAO",
+        "GPO",
+        "SAO",
+    ]
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         """Set the metadata for this dataset from the file contents"""
@@ -59,7 +103,7 @@ class BPF(Text):
         with open(dataset.dataset.file_name) as fd:
             for line in fd:
                 # Split the line on a colon rather than regexing it
-                parts = line.split(':')
+                parts = line.split(":")
 
                 # And if the first part is a 3 character string, then it's
                 # interesting.
@@ -74,12 +118,12 @@ class BPF(Text):
         # We loop over 30 as there are 9 mandatory headers (the last should be
         # `LBD:`), while there are 21 optional headers that can be
         # interspersed.
-        seen_headers = [line[0] for line in get_headers(filename, sep=':', count=40)]
+        seen_headers = [line[0] for line in get_headers(filename, sep=":", count=40)]
 
         # We cut everything after LBD, where the headers end and contents
         # start. We choose not to validate contents.
-        if 'LBD' in seen_headers:
-            seen_headers = seen_headers[0:seen_headers.index('LBD') + 1]
+        if "LBD" in seen_headers:
+            seen_headers = seen_headers[0 : seen_headers.index("LBD") + 1]
 
         # Check that every mandatory header is present in the seen headers
         for header in self.mandatory_headers:
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 2bf9a7a6de0..4fbb2100493 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -17,7 +17,11 @@ import pysam
 from markupsafe import escape
 
 from galaxy import util
-from galaxy.datatypes import binary, data, metadata
+from galaxy.datatypes import (
+    binary,
+    data,
+    metadata,
+)
 from galaxy.datatypes.binary import _BamOrSam
 from galaxy.datatypes.metadata import (
     MetadataElement,
@@ -41,18 +45,41 @@ MAX_DATA_LINES = 100000
 @dataproviders.decorators.has_dataproviders
 class TabularData(data.Text):
     """Generic tabular data"""
+
     edam_format = "format_3475"
     # All tabular data is chunkable.
     CHUNKABLE = True
     data_line_offset = 0
     max_peek_columns = 50
 
-    MetadataElement(name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0)
-    MetadataElement(name="data_lines", default=0, desc="Number of data lines", readonly=True, visible=False, optional=True, no_value=0)
+    MetadataElement(
+        name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0
+    )
+    MetadataElement(
+        name="data_lines",
+        default=0,
+        desc="Number of data lines",
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=0,
+    )
     MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0)
-    MetadataElement(name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[])
-    MetadataElement(name="column_names", default=[], desc="Column names", readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="delimiter", default='\t', desc="Data delimiter", readonly=True, visible=False, optional=True, no_value=[])
+    MetadataElement(
+        name="column_types",
+        default=[],
+        desc="Column types",
+        param=metadata.ColumnTypesParameter,
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
+    MetadataElement(
+        name="column_names", default=[], desc="Column names", readonly=True, visible=False, optional=True, no_value=[]
+    )
+    MetadataElement(
+        name="delimiter", default="\t", desc="Data delimiter", readonly=True, visible=False, optional=True, no_value=[]
+    )
 
     @abc.abstractmethod
     def set_meta(self, dataset, **kwd):
@@ -65,10 +92,12 @@ class TabularData(data.Text):
 
     def displayable(self, dataset):
         try:
-            return dataset.has_data() \
-                and dataset.state == dataset.states.OK \
-                and dataset.metadata.columns > 0 \
+            return (
+                dataset.has_data()
+                and dataset.state == dataset.states.OK
+                and dataset.metadata.columns > 0
                 and dataset.metadata.data_lines != 0
+            )
         except Exception:
             return False
 
@@ -76,16 +105,19 @@ class TabularData(data.Text):
         with compression_utils.get_fileobj(dataset.file_name) as f:
             f.seek(offset)
             ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
-            if ck_data and ck_data[-1] != '\n':
+            if ck_data and ck_data[-1] != "\n":
                 cursor = f.read(1)
-                while cursor and cursor != '\n':
+                while cursor and cursor != "\n":
                     ck_data += cursor
                     cursor = f.read(1)
             last_read = f.tell()
-        return dumps({'ck_data': util.unicodify(ck_data),
-                      'offset': last_read,
-                      'data_line_offset': self.data_line_offset,
-                      })
+        return dumps(
+            {
+                "ck_data": util.unicodify(ck_data),
+                "offset": last_read,
+                "data_line_offset": self.data_line_offset,
+            }
+        )
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
         headers = kwd.get("headers", {})
@@ -102,30 +134,40 @@ class TabularData(data.Text):
             max_peek_size = 1000000  # 1 MB
             if os.stat(dataset.file_name).st_size < max_peek_size:
                 self._clean_and_set_mime_type(trans, dataset.get_mime(), headers)
-                return open(dataset.file_name, mode='rb'), headers
+                return open(dataset.file_name, mode="rb"), headers
             else:
                 headers["content-type"] = "text/html"
-                return trans.fill_template_mako("/dataset/large_file.mako",
-                                                truncated_data=open(dataset.file_name).read(max_peek_size),
-                                                data=dataset), headers
+                return (
+                    trans.fill_template_mako(
+                        "/dataset/large_file.mako",
+                        truncated_data=open(dataset.file_name).read(max_peek_size),
+                        data=dataset,
+                    ),
+                    headers,
+                )
         else:
-            column_names = 'null'
+            column_names = "null"
             if dataset.metadata.column_names:
                 column_names = dataset.metadata.column_names
-            elif hasattr(dataset.datatype, 'column_names'):
+            elif hasattr(dataset.datatype, "column_names"):
                 column_names = dataset.datatype.column_names
             column_types = dataset.metadata.column_types
             if not column_types:
                 column_types = []
             column_number = dataset.metadata.columns
             if column_number is None:
-                column_number = 'null'
-            return trans.fill_template("/dataset/tabular_chunked.mako",
-                                       dataset=dataset,
-                                       chunk=self.get_chunk(trans, dataset, 0),
-                                       column_number=column_number,
-                                       column_names=column_names,
-                                       column_types=column_types), headers
+                column_number = "null"
+            return (
+                trans.fill_template(
+                    "/dataset/tabular_chunked.mako",
+                    dataset=dataset,
+                    chunk=self.get_chunk(trans, dataset, 0),
+                    column_number=column_number,
+                    column_names=column_names,
+                    column_types=column_types,
+                ),
+                headers,
+            )
 
     def display_as_markdown(self, dataset_instance, markdown_format_helpers):
         with open(dataset_instance.file_name) as f:
@@ -141,13 +183,21 @@ class TabularData(data.Text):
         try:
             out.append(self.make_html_peek_header(dataset, **kwargs))
             out.append(self.make_html_peek_rows(dataset, **kwargs))
-            out.append('</table>')
+            out.append("</table>")
             out = "".join(out)
         except Exception as exc:
             out = f"Can't create peek: {util.unicodify(exc)}"
         return out
 
-    def make_html_peek_header(self, dataset, skipchars=None, column_names=None, column_number_format='%s', column_parameter_alias=None, **kwargs):
+    def make_html_peek_header(
+        self,
+        dataset,
+        skipchars=None,
+        column_names=None,
+        column_number_format="%s",
+        column_parameter_alias=None,
+        **kwargs,
+    ):
         if skipchars is None:
             skipchars = []
         if column_names is None:
@@ -180,17 +230,17 @@ class TabularData(data.Text):
                     if 0 <= i < columns and column_headers[i] is None:
                         column_headers[i] = column_parameter_alias.get(name, name)
 
-            out.append('<tr>')
+            out.append("<tr>")
             for i, header in enumerate(column_headers):
-                out.append('<th>')
+                out.append("<th>")
                 if header is None:
                     out.append(column_number_format % str(i + 1))
                 else:
-                    out.append(f'{str(i + 1)}.{escape(header)}')
-                out.append('</th>')
-            out.append('</tr>')
+                    out.append(f"{str(i + 1)}.{escape(header)}")
+                out.append("</th>")
+            out.append("</tr>")
         except Exception as exc:
-            log.exception('make_html_peek_header failed on HDA %s', dataset.id)
+            log.exception("make_html_peek_header failed on HDA %s", dataset.id)
             raise Exception(f"Can't create peek header: {util.unicodify(exc)}")
         return "".join(out)
 
@@ -214,20 +264,20 @@ class TabularData(data.Text):
                         out.append(f'<tr><td colspan="100%">{escape(line)}</td></tr>')
                     elif line:
                         elems = line.split(dataset.metadata.delimiter)
-                        elems = elems[:min(len(elems), self.max_peek_columns)]
+                        elems = elems[: min(len(elems), self.max_peek_columns)]
                         # pad shortened elems, since lines could have been truncated by width
                         if len(elems) < columns:
-                            elems.extend([''] * (columns - len(elems)))
+                            elems.extend([""] * (columns - len(elems)))
                         # we may have an invalid comment line or invalid data
                         if len(elems) != columns:
                             out.append(f'<tr><td colspan="100%">{escape(line)}</td></tr>')
                         else:
-                            out.append('<tr>')
+                            out.append("<tr>")
                             for elem in elems:
-                                out.append(f'<td>{escape(elem)}</td>')
-                            out.append('</tr>')
+                                out.append(f"<td>{escape(elem)}</td>")
+                            out.append("</tr>")
         except Exception as exc:
-            log.exception('make_html_peek_rows failed on HDA %s', dataset.id)
+            log.exception("make_html_peek_rows failed on HDA %s", dataset.id)
             raise Exception(f"Can't create peek rows: {util.unicodify(exc)}")
         return "".join(out)
 
@@ -236,28 +286,27 @@ class TabularData(data.Text):
         return self.make_html_table(dataset)
 
     # ------------- Dataproviders
-    @dataproviders.decorators.dataprovider_factory('column', dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("column", dataproviders.column.ColumnarDataProvider.settings)
     def column_dataprovider(self, dataset, **settings):
         """Uses column settings that are passed in"""
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         delimiter = dataset.metadata.delimiter
         return dataproviders.column.ColumnarDataProvider(dataset_source, deliminator=delimiter, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dataset-column',
-                                                   dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dataset-column", dataproviders.column.ColumnarDataProvider.settings)
     def dataset_column_dataprovider(self, dataset, **settings):
         """Attempts to get column settings from dataset.metadata"""
         delimiter = dataset.metadata.delimiter
         return dataproviders.dataset.DatasetColumnarDataProvider(dataset, deliminator=delimiter, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dict', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dict", dataproviders.column.DictDataProvider.settings)
     def dict_dataprovider(self, dataset, **settings):
         """Uses column settings that are passed in"""
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         delimiter = dataset.metadata.delimiter
         return dataproviders.column.DictDataProvider(dataset_source, deliminator=delimiter, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dataset-dict', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dataset-dict", dataproviders.column.DictDataProvider.settings)
     def dataset_dict_dataprovider(self, dataset, **settings):
         """Attempts to get column settings from dataset.metadata"""
         delimiter = dataset.metadata.delimiter
@@ -267,12 +316,15 @@ class TabularData(data.Text):
 @dataproviders.decorators.has_dataproviders
 class Tabular(TabularData):
     """Tab delimited data"""
+
     file_ext = "tabular"
 
     def get_column_names(self, first_line=None):
         return None
 
-    def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=MAX_DATA_LINES, max_guess_type_data_lines=None, **kwd):
+    def set_meta(
+        self, dataset, overwrite=True, skip=None, max_data_lines=MAX_DATA_LINES, max_guess_type_data_lines=None, **kwd
+    ):
         """
         Tries to determine the number of columns as well as those columns that
         contain numerical values in the dataset.  A skip parameter is used
@@ -301,7 +353,7 @@ class Tabular(TabularData):
         requested_skip = skip
         if skip is None:
             skip = 0
-        column_type_set_order = ['int', 'float', 'list', 'str']  # Order to set column types in
+        column_type_set_order = ["int", "float", "list", "str"]  # Order to set column types in
         default_column_type = column_type_set_order[-1]  # Default column type is lowest in list
         column_type_compare_order = list(column_type_set_order)  # Order to compare column types
         column_type_compare_order.reverse()
@@ -321,7 +373,7 @@ class Tabular(TabularData):
 
         def is_int(column_text):
             # Don't allow underscores in numeric literals (PEP 515)
-            if '_' in column_text:
+            if "_" in column_text:
                 return False
             try:
                 int(column_text)
@@ -331,13 +383,13 @@ class Tabular(TabularData):
 
         def is_float(column_text):
             # Don't allow underscores in numeric literals (PEP 515)
-            if '_' in column_text:
+            if "_" in column_text:
                 return False
             try:
                 float(column_text)
                 return True
             except ValueError:
-                if column_text.strip().lower() == 'na':
+                if column_text.strip().lower() == "na":
                     return True  # na is special cased to be a float
                 return False
 
@@ -369,19 +421,21 @@ class Tabular(TabularData):
             # NOTE: if skip > num_check_lines, we won't detect any metadata, and will use default
             with compression_utils.get_fileobj(dataset.file_name) as dataset_fh:
                 i = 0
-                for line in iter(dataset_fh.readline, ''):
-                    line = line.rstrip('\r\n')
+                for line in iter(dataset_fh.readline, ""):
+                    line = line.rstrip("\r\n")
                     if i == 0:
                         column_names = self.get_column_names(first_line=line)
-                    if i < skip or not line or line.startswith('#'):
+                    if i < skip or not line or line.startswith("#"):
                         # We'll call blank lines comments
                         comment_lines += 1
                     else:
                         data_lines += 1
                         if max_guess_type_data_lines is None or data_lines <= max_guess_type_data_lines:
-                            fields = line.split('\t')
+                            fields = line.split("\t")
                             for field_count, field in enumerate(fields):
-                                if field_count >= len(column_types):  # found a previously unknown column, we append None
+                                if field_count >= len(
+                                    column_types
+                                ):  # found a previously unknown column, we append None
                                     column_types.append(None)
                                 column_type = guess_column_type(field)
                                 if type_overrules_type(column_type, column_types[field_count]):
@@ -412,7 +466,7 @@ class Tabular(TabularData):
         # we error on the larger number of columns
         # first we pad our column_types by using data from first line
         if len(first_line_column_types) > len(column_types):
-            for column_type in first_line_column_types[len(column_types):]:
+            for column_type in first_line_column_types[len(column_types) :]:
                 column_types.append(column_type)
         # Now we fill any unknown (None) column_types with data from first line
         for i in range(len(column_types)):
@@ -426,20 +480,21 @@ class Tabular(TabularData):
         dataset.metadata.comment_lines = comment_lines
         dataset.metadata.column_types = column_types
         dataset.metadata.columns = len(column_types)
-        dataset.metadata.delimiter = '\t'
+        dataset.metadata.delimiter = "\t"
         if column_names is not None:
             dataset.metadata.column_names = column_names
 
     def as_gbrowse_display_file(self, dataset, **kwd):
-        return open(dataset.file_name, 'rb')
+        return open(dataset.file_name, "rb")
 
     def as_ucsc_display_file(self, dataset, **kwd):
-        return open(dataset.file_name, 'rb')
+        return open(dataset.file_name, "rb")
 
 
 class SraManifest(Tabular):
     """A manifest received from the sra_source tool."""
-    file_ext = 'sra_manifest.tabular'
+
+    file_ext = "sra_manifest.tabular"
     data_line_offset = 1
 
     def set_meta(self, dataset, **kwds):
@@ -447,7 +502,7 @@ class SraManifest(Tabular):
         dataset.metadata.comment_lines = 1
 
     def get_column_names(self, first_line):
-        return first_line.strip().split('\t')
+        return first_line.strip().split("\t")
 
 
 class Taxonomy(Tabular):
@@ -456,11 +511,32 @@ class Taxonomy(Tabular):
     def __init__(self, **kwd):
         """Initialize taxonomy datatype"""
         super().__init__(**kwd)
-        self.column_names = ['Name', 'TaxId', 'Root', 'Superkingdom', 'Kingdom', 'Subkingdom',
-                             'Superphylum', 'Phylum', 'Subphylum', 'Superclass', 'Class', 'Subclass',
-                             'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily',
-                             'Tribe', 'Subtribe', 'Genus', 'Subgenus', 'Species', 'Subspecies'
-                             ]
+        self.column_names = [
+            "Name",
+            "TaxId",
+            "Root",
+            "Superkingdom",
+            "Kingdom",
+            "Subkingdom",
+            "Superphylum",
+            "Phylum",
+            "Subphylum",
+            "Superclass",
+            "Class",
+            "Subclass",
+            "Superorder",
+            "Order",
+            "Suborder",
+            "Superfamily",
+            "Family",
+            "Subfamily",
+            "Tribe",
+            "Subtribe",
+            "Genus",
+            "Subgenus",
+            "Species",
+            "Subspecies",
+        ]
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
@@ -472,23 +548,86 @@ class Taxonomy(Tabular):
 class Sam(Tabular, _BamOrSam):
     edam_format = "format_2573"
     edam_data = "data_0863"
-    file_ext = 'sam'
+    file_ext = "sam"
     track_type = "ReadTrack"
     data_sources = {"data": "bam", "index": "bigwig"}
 
-    MetadataElement(name="bam_version", default=None, desc="BAM Version", param=MetadataParameter, readonly=True, visible=False, optional=True)
-    MetadataElement(name="sort_order", default=None, desc="Sort Order", param=MetadataParameter, readonly=True, visible=False, optional=True)
-    MetadataElement(name="read_groups", default=[], desc="Read Groups", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="reference_names", default=[], desc="Chromosome Names", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="reference_lengths", default=[], desc="Chromosome Lengths", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="bam_header", default={}, desc="Dictionary of BAM Headers", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value={})
+    MetadataElement(
+        name="bam_version",
+        default=None,
+        desc="BAM Version",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
+    MetadataElement(
+        name="sort_order",
+        default=None,
+        desc="Sort Order",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
+    MetadataElement(
+        name="read_groups",
+        default=[],
+        desc="Read Groups",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="reference_names",
+        default=[],
+        desc="Chromosome Names",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="reference_lengths",
+        default=[],
+        desc="Chromosome Lengths",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="bam_header",
+        default={},
+        desc="Dictionary of BAM Headers",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value={},
+    )
 
     def __init__(self, **kwd):
         """Initialize sam datatype"""
         super().__init__(**kwd)
-        self.column_names = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR',
-                             'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT'
-                             ]
+        self.column_names = [
+            "QNAME",
+            "FLAG",
+            "RNAME",
+            "POS",
+            "MAPQ",
+            "CIGAR",
+            "MRNM",
+            "MPOS",
+            "ISIZE",
+            "SEQ",
+            "QUAL",
+            "OPT",
+        ]
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
@@ -527,8 +666,8 @@ class Sam(Tabular, _BamOrSam):
         for line in file_prefix.line_iterator():
             line = line.strip()
             if line:
-                if line[0] != '@':
-                    line_pieces = line.split('\t')
+                if line[0] != "@":
+                    line_pieces = line.split("\t")
                     if len(line_pieces) < 11:
                         return False
                     try:
@@ -570,10 +709,13 @@ class Sam(Tabular, _BamOrSam):
         if dataset.has_data():
             with open(dataset.file_name) as dataset_fh:
                 comment_lines = 0
-                if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
+                if (
+                    self.max_optional_metadata_filesize >= 0
+                    and dataset.get_size() > self.max_optional_metadata_filesize
+                ):
                     # If the dataset is larger than optional_metadata, just count comment lines.
                     for line in dataset_fh:
-                        if line.startswith('@'):
+                        if line.startswith("@"):
                             comment_lines += 1
                         else:
                             # No more comments, and the file is too big to look at the whole thing. Give up.
@@ -582,12 +724,25 @@ class Sam(Tabular, _BamOrSam):
                 else:
                     # Otherwise, read the whole thing and set num data lines.
                     for i, l in enumerate(dataset_fh):  # noqa: B007
-                        if l.startswith('@'):
+                        if l.startswith("@"):
                             comment_lines += 1
                     dataset.metadata.data_lines = i + 1 - comment_lines
             dataset.metadata.comment_lines = comment_lines
             dataset.metadata.columns = 12
-            dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
+            dataset.metadata.column_types = [
+                "str",
+                "int",
+                "str",
+                "int",
+                "int",
+                "str",
+                "str",
+                "int",
+                "int",
+                "str",
+                "str",
+                "str",
+            ]
 
             _BamOrSam().set_meta(dataset)
 
@@ -600,66 +755,67 @@ class Sam(Tabular, _BamOrSam):
         shutil.move(split_files[0], output_file)
 
         if len(split_files) > 1:
-            cmd = ['egrep', '-v', '-h', '^@'] + split_files[1:] + ['>>', output_file]
+            cmd = ["egrep", "-v", "-h", "^@"] + split_files[1:] + [">>", output_file]
             subprocess.check_call(cmd, shell=True)
 
     # Dataproviders
     # sam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers
     # TODO:?? seems like there should be an easier way to do this - metadata.comment_char?
-    @dataproviders.decorators.dataprovider_factory('line', dataproviders.line.FilteredLineDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("line", dataproviders.line.FilteredLineDataProvider.settings)
     def line_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return super().line_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('regex-line', dataproviders.line.RegexLineDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("regex-line", dataproviders.line.RegexLineDataProvider.settings)
     def regex_line_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return super().regex_line_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('column', dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("column", dataproviders.column.ColumnarDataProvider.settings)
     def column_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return super().column_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dataset-column',
-                                                   dataproviders.column.ColumnarDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dataset-column", dataproviders.column.ColumnarDataProvider.settings)
     def dataset_column_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return super().dataset_column_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dict', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dict", dataproviders.column.DictDataProvider.settings)
     def dict_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return super().dict_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('dataset-dict', dataproviders.column.DictDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("dataset-dict", dataproviders.column.DictDataProvider.settings)
     def dataset_dict_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return super().dataset_dict_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('header', dataproviders.line.RegexLineDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("header", dataproviders.line.RegexLineDataProvider.settings)
     def header_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
-        headers_source = dataproviders.line.RegexLineDataProvider(dataset_source, regex_list=['^@'])
+        headers_source = dataproviders.line.RegexLineDataProvider(dataset_source, regex_list=["^@"])
         return dataproviders.line.RegexLineDataProvider(headers_source, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('id-seq-qual', dict_dataprovider.settings)
+    @dataproviders.decorators.dataprovider_factory("id-seq-qual", dict_dataprovider.settings)
     def id_seq_qual_dataprovider(self, dataset, **settings):
         # provided as an example of a specified column dict (w/o metadata)
-        settings['indeces'] = [0, 9, 10]
-        settings['column_names'] = ['id', 'seq', 'qual']
+        settings["indeces"] = [0, 9, 10]
+        settings["column_names"] = ["id", "seq", "qual"]
         return self.dict_dataprovider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return dataproviders.dataset.GenomicRegionDataProvider(dataset, 2, 3, 3, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region-dict',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region-dict", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dict_dataprovider(self, dataset, **settings):
-        settings['comment_char'] = '@'
+        settings["comment_char"] = "@"
         return dataproviders.dataset.GenomicRegionDataProvider(dataset, 2, 3, 3, True, **settings)
 
     # @dataproviders.decorators.dataprovider_factory( 'samtools' )
@@ -672,6 +828,7 @@ class Sam(Tabular, _BamOrSam):
 @build_sniff_from_prefix
 class Pileup(Tabular):
     """Tab delimited data in pileup (6- or 10-column) format"""
+
     edam_format = "format_3015"
     file_ext = "pileup"
     line_class = "genomic coordinate"
@@ -687,7 +844,9 @@ class Pileup(Tabular):
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
-        return self.make_html_table(dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'})
+        return self.make_html_table(
+            dataset, column_parameter_alias={"chromCol": "Chrom", "startCol": "Start", "baseCol": "Base"}
+        )
 
     def repair_methods(self, dataset):
         """Return options for removing errors along with a description"""
@@ -723,54 +882,74 @@ class Pileup(Tabular):
         """
         found_non_comment_lines = False
         try:
-            headers = iter_headers(file_prefix, '\t')
+            headers = iter_headers(file_prefix, "\t")
             for hdr in headers:
-                if hdr and not hdr[0].startswith('#'):
+                if hdr and not hdr[0].startswith("#"):
                     if len(hdr) < 5:
                         return False
                     # chrom start in column 1 (with 0-based columns)
                     # and reference base is in column 2
                     chrom = int(hdr[1])
                     assert chrom >= 0
-                    assert hdr[2] in ['A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n']
+                    assert hdr[2] in ["A", "C", "G", "T", "N", "a", "c", "g", "t", "n"]
                     found_non_comment_lines = True
         except Exception:
             return False
         return found_non_comment_lines
 
     # Dataproviders
-    @dataproviders.decorators.dataprovider_factory('genomic-region',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dataprovider(self, dataset, **settings):
         return dataproviders.dataset.GenomicRegionDataProvider(dataset, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region-dict',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region-dict", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dict_dataprovider(self, dataset, **settings):
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return self.genomic_region_dataprovider(dataset, **settings)
 
 
 @dataproviders.decorators.has_dataproviders
 @build_sniff_from_prefix
 class BaseVcf(Tabular):
-    """ Variant Call Format for describing SNPs and other simple genome variations. """
+    """Variant Call Format for describing SNPs and other simple genome variations."""
+
     edam_format = "format_3016"
     track_type = "VariantTrack"
     data_sources = {"data": "tabix", "index": "bigwig"}
 
-    column_names = ['Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data']
+    column_names = ["Chrom", "Pos", "ID", "Ref", "Alt", "Qual", "Filter", "Info", "Format", "data"]
 
     MetadataElement(name="columns", default=10, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=['str', 'int', 'str', 'str', 'str', 'int', 'str', 'list', 'str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
-    MetadataElement(name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, optional=True, multiple=True, visible=False)
-    MetadataElement(name="sample_names", default=[], desc="Sample names", readonly=True, visible=False, optional=True, no_value=[])
+    MetadataElement(
+        name="column_types",
+        default=["str", "int", "str", "str", "str", "int", "str", "list", "str", "str"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+    )
+    MetadataElement(
+        name="viz_filter_cols",
+        desc="Score column for visualization",
+        default=[5],
+        param=metadata.ColumnParameter,
+        optional=True,
+        multiple=True,
+        visible=False,
+    )
+    MetadataElement(
+        name="sample_names", default=[], desc="Sample names", readonly=True, visible=False, optional=True, no_value=[]
+    )
 
     def _sniff(self, fname_or_file_prefix):
         # Because this sniffer is run on compressed files that might be BGZF (due to the VcfGz subclass), we should
         # handle unicode decode errors. This should ultimately be done in get_headers(), but guess_ext() currently
         # relies on get_headers() raising this exception.
-        headers = get_headers(fname_or_file_prefix, '\n', count=1)
+        headers = get_headers(fname_or_file_prefix, "\n", count=1)
         return headers[0][0].startswith("##fileformat=VCF")
 
     def display_peek(self, dataset):
@@ -783,10 +962,10 @@ class BaseVcf(Tabular):
         with compression_utils.get_fileobj(dataset.file_name) as fh:
             # Skip comments.
             for line in fh:
-                if not line.startswith('##'):
+                if not line.startswith("##"):
                     break
 
-        if line and line.startswith('#'):
+        if line and line.startswith("#"):
             # Found header line, get sample names.
             dataset.metadata.sample_names = line.split()[9:]
 
@@ -796,7 +975,7 @@ class BaseVcf(Tabular):
         stderr_name = stderr_f.name
         command = ["bcftools", "concat"] + split_files + ["-o", output_file]
         log.info(f"Merging vcf files with command [{' '.join(command)}]")
-        exit_code = subprocess.call(args=command, stderr=open(stderr_name, 'wb'))
+        exit_code = subprocess.call(args=command, stderr=open(stderr_name, "wb"))
         with open(stderr_name, "rb") as f:
             stderr = f.read().strip()
         # Did merge succeed?
@@ -807,24 +986,27 @@ class BaseVcf(Tabular):
         def validate_row(row):
             if len(row) < 8:
                 raise Exception("Not enough columns in row %s" % row.join("\t"))
-        validate_tabular(dataset.file_name, sep='\t', validate_row=validate_row, comment_designator="#")
+
+        validate_tabular(dataset.file_name, sep="\t", validate_row=validate_row, comment_designator="#")
         return data.DatatypeValidation.validated()
 
     # Dataproviders
-    @dataproviders.decorators.dataprovider_factory('genomic-region',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dataprovider(self, dataset, **settings):
         return dataproviders.dataset.GenomicRegionDataProvider(dataset, 0, 1, 1, **settings)
 
-    @dataproviders.decorators.dataprovider_factory('genomic-region-dict',
-                                                   dataproviders.dataset.GenomicRegionDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory(
+        "genomic-region-dict", dataproviders.dataset.GenomicRegionDataProvider.settings
+    )
     def genomic_region_dict_dataprovider(self, dataset, **settings):
-        settings['named_columns'] = True
+        settings["named_columns"] = True
         return self.genomic_region_dataprovider(dataset, **settings)
 
 
 class Vcf(BaseVcf):
-    file_ext = 'vcf'
+    file_ext = "vcf"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         return self._sniff(file_prefix)
@@ -832,12 +1014,20 @@ class Vcf(BaseVcf):
 
 class VcfGz(BaseVcf, binary.Binary):
     # This class name is a misnomer, should be VcfBgzip
-    file_ext = 'vcf_bgzip'
-    file_ext_export_alias = 'vcf.gz'
+    file_ext = "vcf_bgzip"
+    file_ext_export_alias = "vcf.gz"
     compressed = True
     compressed_format = "gzip"
 
-    MetadataElement(name="tabix_index", desc="Vcf Index File", param=metadata.FileParameter, file_ext="tbi", readonly=True, visible=False, optional=True)
+    MetadataElement(
+        name="tabix_index",
+        desc="Vcf Index File",
+        param=metadata.FileParameter,
+        file_ext="tbi",
+        readonly=True,
+        visible=False,
+        optional=True,
+    )
 
     def sniff(self, filename):
         if not self._sniff(filename):
@@ -845,10 +1035,10 @@ class VcfGz(BaseVcf, binary.Binary):
         # Check that the file is compressed with bgzip (not gzip), i.e. the
         # compressed format is BGZF, as explained in
         # http://samtools.github.io/hts-specs/SAMv1.pdf
-        with open(filename, 'rb') as fh:
+        with open(filename, "rb") as fh:
             fh.seek(-28, 2)
             last28 = fh.read()
-            return binascii.hexlify(last28) == b'1f8b08040000000000ff0600424302001b0003000000000000000000'
+            return binascii.hexlify(last28) == b"1f8b08040000000000ff0600424302001b0003000000000000000000"
 
     def set_meta(self, dataset, **kwd):
         super().set_meta(dataset, **kwd)
@@ -856,37 +1046,98 @@ class VcfGz(BaseVcf, binary.Binary):
         # These metadata values are not accessible by users, always overwrite
         index_file = dataset.metadata.tabix_index
         if not index_file:
-            index_file = dataset.metadata.spec['tabix_index'].param.new_file(dataset=dataset)
+            index_file = dataset.metadata.spec["tabix_index"].param.new_file(dataset=dataset)
 
         try:
-            pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', keep_original=True, force=True)
+            pysam.tabix_index(
+                dataset.file_name, index=index_file.file_name, preset="vcf", keep_original=True, force=True
+            )
         except Exception as e:
-            raise Exception(f'Error setting VCF.gz metadata: {util.unicodify(e)}')
+            raise Exception(f"Error setting VCF.gz metadata: {util.unicodify(e)}")
         dataset.metadata.tabix_index = index_file
 
 
 @build_sniff_from_prefix
 class Eland(Tabular):
     """Support for the export.txt.gz file used by Illumina's ELANDv2e aligner"""
+
     compressed = True
     compressed_format = "gzip"
-    file_ext = '_export.txt.gz'
+    file_ext = "_export.txt.gz"
     MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=[], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[])
+    MetadataElement(
+        name="column_types",
+        default=[],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
     MetadataElement(name="comment_lines", default=0, desc="Number of comments", readonly=True, visible=False)
-    MetadataElement(name="tiles", default=[], param=metadata.ListParameter, desc="Set of tiles", readonly=True, visible=False, no_value=[])
-    MetadataElement(name="reads", default=[], param=metadata.ListParameter, desc="Set of reads", readonly=True, visible=False, no_value=[])
-    MetadataElement(name="lanes", default=[], param=metadata.ListParameter, desc="Set of lanes", readonly=True, visible=False, no_value=[])
-    MetadataElement(name="barcodes", default=[], param=metadata.ListParameter, desc="Set of barcodes", readonly=True, visible=False, no_value=[])
+    MetadataElement(
+        name="tiles",
+        default=[],
+        param=metadata.ListParameter,
+        desc="Set of tiles",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
+    MetadataElement(
+        name="reads",
+        default=[],
+        param=metadata.ListParameter,
+        desc="Set of reads",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
+    MetadataElement(
+        name="lanes",
+        default=[],
+        param=metadata.ListParameter,
+        desc="Set of lanes",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
+    MetadataElement(
+        name="barcodes",
+        default=[],
+        param=metadata.ListParameter,
+        desc="Set of barcodes",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
 
     def __init__(self, **kwd):
         """Initialize eland datatype"""
         super().__init__(**kwd)
-        self.column_names = ['MACHINE', 'RUN_NO', 'LANE', 'TILE', 'X', 'Y',
-                             'INDEX', 'READ_NO', 'SEQ', 'QUAL', 'CHROM', 'CONTIG',
-                             'POSITION', 'STRAND', 'DESC', 'SRAS', 'PRAS', 'PART_CHROM'
-                             'PART_CONTIG', 'PART_OFFSET', 'PART_STRAND', 'FILT'
-                             ]
+        self.column_names = [
+            "MACHINE",
+            "RUN_NO",
+            "LANE",
+            "TILE",
+            "X",
+            "Y",
+            "INDEX",
+            "READ_NO",
+            "SEQ",
+            "QUAL",
+            "CHROM",
+            "CONTIG",
+            "POSITION",
+            "STRAND",
+            "DESC",
+            "SRAS",
+            "PRAS",
+            "PART_CHROM" "PART_CONTIG",
+            "PART_OFFSET",
+            "PART_STRAND",
+            "FILT",
+        ]
 
     def make_html_table(self, dataset, skipchars=None, peek=None):
         """Create HTML table, used for displaying peek"""
@@ -895,16 +1146,16 @@ class Eland(Tabular):
         out = ['<table cellspacing="0" cellpadding="3">']
         try:
             # Generate column header
-            out.append('<tr>')
+            out.append("<tr>")
             for i, name in enumerate(self.column_names):
-                out.append(f'<th>{str(i + 1)}.{name}</th>')
+                out.append(f"<th>{str(i + 1)}.{name}</th>")
             # This data type requires at least 11 columns in the data
             if dataset.metadata.columns - len(self.column_names) > 0:
                 for i in range(len(self.column_names), max(dataset.metadata.columns, self.max_peek_columns)):
-                    out.append(f'<th>{str(i + 1)}</th>')
-                out.append('</tr>')
+                    out.append(f"<th>{str(i + 1)}</th>")
+                out.append("</tr>")
             out.append(self.make_html_peek_rows(dataset, skipchars=skipchars, peek=peek))
-            out.append('</table>')
+            out.append("</table>")
             out = "".join(out)
         except Exception as exc:
             out = f"Can't create peek {exc}"
@@ -929,15 +1180,15 @@ class Eland(Tabular):
             if not line:
                 break  # Had a EOF comment previously, but this does not indicate EOF. I assume empty lines are not valid and this was intentional.
             if line:
-                line_pieces = line.split('\t')
+                line_pieces = line.split("\t")
                 if len(line_pieces) != 22:
                     return False
                 if int(line_pieces[1]) < 0:
-                    raise Exception('Out of range')
+                    raise Exception("Out of range")
                 if int(line_pieces[2]) < 0:
-                    raise Exception('Out of range')
+                    raise Exception("Out of range")
                 if int(line_pieces[3]) < 0:
-                    raise Exception('Out of range')
+                    raise Exception("Out of range")
                 int(line_pieces[4])
                 int(line_pieces[5])
                 # can get a lot more specific
@@ -949,7 +1200,7 @@ class Eland(Tabular):
 
     def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=5, **kwd):
         if dataset.has_data():
-            with compression_utils.get_fileobj(dataset.file_name, compressed_formats=['gzip']) as dataset_fh:
+            with compression_utils.get_fileobj(dataset.file_name, compressed_formats=["gzip"]) as dataset_fh:
                 lanes = {}
                 tiles = {}
                 barcodes = {}
@@ -962,9 +1213,9 @@ class Eland(Tabular):
                 # Otherwise, read the whole thing and set num data lines.
                 for i, line in enumerate(dataset_fh):
                     if line:
-                        line_pieces = line.split('\t')
+                        line_pieces = line.split("\t")
                         if len(line_pieces) != 22:
-                            raise Exception('%s:%d:Corrupt line!' % (dataset.file_name, i))
+                            raise Exception("%s:%d:Corrupt line!" % (dataset.file_name, i))
                         lanes[line_pieces[2]] = 1
                         tiles[line_pieces[3]] = 1
                         barcodes[line_pieces[6]] = 1
@@ -972,16 +1223,40 @@ class Eland(Tabular):
                 dataset.metadata.data_lines = i + 1
             dataset.metadata.comment_lines = 0
             dataset.metadata.columns = 21
-            dataset.metadata.column_types = ['str', 'int', 'int', 'int', 'int', 'int', 'str', 'int', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str']
+            dataset.metadata.column_types = [
+                "str",
+                "int",
+                "int",
+                "int",
+                "int",
+                "int",
+                "str",
+                "int",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+                "str",
+            ]
             dataset.metadata.lanes = list(lanes.keys())
             dataset.metadata.tiles = ["%04d" % int(t) for t in tiles.keys()]
-            dataset.metadata.barcodes = [_ for _ in barcodes.keys() if _ != '0'] + ['NoIndex' for _ in barcodes.keys() if _ == '0']
+            dataset.metadata.barcodes = [_ for _ in barcodes.keys() if _ != "0"] + [
+                "NoIndex" for _ in barcodes.keys() if _ == "0"
+            ]
             dataset.metadata.reads = list(reads.keys())
 
 
 @build_sniff_from_prefix
 class ElandMulti(Tabular):
-    file_ext = 'elandmulti'
+    file_ext = "elandmulti"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         return False
@@ -991,9 +1266,18 @@ class FeatureLocationIndex(Tabular):
     """
     An index that stores feature locations in tabular format.
     """
-    file_ext = 'fli'
+
+    file_ext = "fli"
     MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
-    MetadataElement(name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[])
+    MetadataElement(
+        name="column_types",
+        default=["str", "str"],
+        param=metadata.ColumnTypesParameter,
+        desc="Column types",
+        readonly=True,
+        visible=False,
+        no_value=[],
+    )
 
 
 @dataproviders.decorators.has_dataproviders
@@ -1005,13 +1289,14 @@ class BaseCSV(TabularData):
     Must be extended to define the dialect to use, strict_width and file_ext.
     See the Python module csv for documentation of dialect settings
     """
-    delimiter = ','
+
+    delimiter = ","
     peek_size = 1024  # File chunk used for sniffing CSV dialect
     big_peek_size = 10240  # Large File chunk used for sniffing CSV dialect
 
     def is_int(self, column_text):
         # Don't allow underscores in numeric literals (PEP 515)
-        if '_' in column_text:
+        if "_" in column_text:
             return False
         try:
             int(column_text)
@@ -1021,28 +1306,28 @@ class BaseCSV(TabularData):
 
     def is_float(self, column_text):
         # Don't allow underscores in numeric literals (PEP 515)
-        if '_' in column_text:
+        if "_" in column_text:
             return False
         try:
             float(column_text)
             return True
         except ValueError:
-            if column_text.strip().lower() == 'na':
+            if column_text.strip().lower() == "na":
                 return True  # na is special cased to be a float
             return False
 
     def guess_type(self, text):
         if self.is_int(text):
-            return 'int'
+            return "int"
         if self.is_float(text):
-            return 'float'
+            return "float"
         else:
-            return 'str'
+            return "str"
 
     def sniff(self, filename):
-        """ Return True if if recognizes dialect and header. """
+        """Return True if if recognizes dialect and header."""
         # check the dialect works
-        with open(filename, newline='') as f:
+        with open(filename, newline="") as f:
             reader = csv.reader(f, self.dialect)
             # Check we can read header and get columns
             header_row = next(reader)
@@ -1075,9 +1360,9 @@ class BaseCSV(TabularData):
         with open(filename) as f:
             big_peek = f.read(self.big_peek_size)
         auto_dialect = csv.Sniffer().sniff(big_peek)
-        if (auto_dialect.delimiter != self.dialect.delimiter):
+        if auto_dialect.delimiter != self.dialect.delimiter:
             return False
-        if (auto_dialect.quotechar != self.dialect.quotechar):
+        if auto_dialect.quotechar != self.dialect.quotechar:
             return False
         # Not checking for other dialect options
         # They may be mis detected from just the sample.
@@ -1097,7 +1382,7 @@ class BaseCSV(TabularData):
         data_row = []
         data_lines = 0
         if dataset.has_data():
-            with open(dataset.file_name, newline='') as csvfile:
+            with open(dataset.file_name, newline="") as csvfile:
                 # Parse file with the correct dialect
                 reader = csv.reader(csvfile, self.dialect)
                 try:
@@ -1108,7 +1393,7 @@ class BaseCSV(TabularData):
                 except StopIteration:
                     pass
                 except csv.Error as e:
-                    raise Exception('CSV reader error - line %d: %s' % (reader.line_num, e))
+                    raise Exception("CSV reader error - line %d: %s" % (reader.line_num, e))
                 else:
                     data_lines = reader.line_num - 1
 
@@ -1131,7 +1416,8 @@ class CSV(BaseCSV):
     Comma-separated table data.
     Only sniffs comma-separated files with at least 2 rows and 2 columns.
     """
-    file_ext = 'csv'
+
+    file_ext = "csv"
     dialect = csv.excel  # This is the default
     strict_width = False  # Previous csv type did not check column width
 
@@ -1150,7 +1436,8 @@ class TSV(BaseCSV):
     column less to indicate first column is row names. This kind of file is
     handled fine by the tabular datatype.
     """
-    file_ext = 'tsv'
+
+    file_ext = "tsv"
     dialect = csv.excel_tab
     strict_width = True  # Leave files with different width to tabular
 
@@ -1161,13 +1448,15 @@ class ConnectivityTable(Tabular):
     file_ext = "ct"
 
     header_regexp = re.compile("^[0-9]+(?:	|[ ]+).*?(?:ENERGY|energy|dG)[ 	].*?=")
-    structure_regexp = re.compile("^[0-9]+(?:	|[ ]+)[ACGTURYKMSWBDHVN]+(?:	|[ ]+)[^	]+(?:	|[ ]+)[^	]+(?:	|[ ]+)[^	]+(?:	|[ ]+)[^	]+")
+    structure_regexp = re.compile(
+        "^[0-9]+(?:	|[ ]+)[ACGTURYKMSWBDHVN]+(?:	|[ ]+)[^	]+(?:	|[ ]+)[^	]+(?:	|[ ]+)[^	]+(?:	|[ ]+)[^	]+"
+    )
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
         self.columns = 6
-        self.column_names = ['base_index', 'base', 'neighbor_left', 'neighbor_right', 'partner', 'natural_numbering']
-        self.column_types = ['int', 'str', 'int', 'int', 'int', 'int']
+        self.column_names = ["base_index", "base", "neighbor_left", "neighbor_right", "partner", "natural_numbering"]
+        self.column_types = ["int", "str", "int", "int", "int", "int"]
 
     def set_meta(self, dataset, **kwd):
         data_lines = 0
@@ -1222,12 +1511,12 @@ class ConnectivityTable(Tabular):
                     if not self.header_regexp.match(line):
                         return False
                     else:
-                        length = int(re.split(r'\W+', line, 1)[0])
+                        length = int(re.split(r"\W+", line, 1)[0])
                 else:
                     if not self.structure_regexp.match(line.upper()):
                         return False
                     else:
-                        if j != int(re.split(r'\W+', line, 1)[0]):
+                        if j != int(re.split(r"\W+", line, 1)[0]):
                             return False
                         elif j == length:  # Last line of first sequence has been reached
                             return True
@@ -1243,22 +1532,22 @@ class ConnectivityTable(Tabular):
         # If we aren't at the start of the file, seek to next newline.  Do this better eventually.
         if f.tell() != 0:
             cursor = f.read(1)
-            while cursor and cursor != '\n':
+            while cursor and cursor != "\n":
                 cursor = f.read(1)
         ck_data = f.read(trans.app.config.display_chunk_size)
         cursor = f.read(1)
-        while cursor and ck_data[-1] != '\n':
+        while cursor and ck_data[-1] != "\n":
             ck_data += cursor
             cursor = f.read(1)
 
         # The ConnectivityTable format has several derivatives of which one is delimited by (multiple) spaces.
         # By converting these spaces back to tabs, chucks can still be interpreted by tab delimited file parsers
-        ck_data_header, ck_data_body = ck_data.split('\n', 1)
-        ck_data_header = re.sub('^([0-9]+)[ ]+', r'\1\t', ck_data_header)
-        ck_data_body = re.sub('\n[ \t]+', '\n', ck_data_body)
-        ck_data_body = re.sub('[ ]+', '\t', ck_data_body)
+        ck_data_header, ck_data_body = ck_data.split("\n", 1)
+        ck_data_header = re.sub("^([0-9]+)[ ]+", r"\1\t", ck_data_header)
+        ck_data_body = re.sub("\n[ \t]+", "\n", ck_data_body)
+        ck_data_body = re.sub("[ ]+", "\t", ck_data_body)
 
-        return dumps({'ck_data': util.unicodify(f"{ck_data_header}\n{ck_data_body}"), 'ck_index': ck_index + 1})
+        return dumps({"ck_data": util.unicodify(f"{ck_data_header}\n{ck_data_body}"), "ck_index": ck_index + 1})
 
 
 @build_sniff_from_prefix
@@ -1296,39 +1585,43 @@ class MatrixMarket(TabularData):
     >>> MatrixMarket().sniff( get_test_fname( '3.mtx' ) )
     True
     """
+
     file_ext = "mtx"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        return file_prefix.startswith('%%MatrixMarket matrix coordinate')
+        return file_prefix.startswith("%%MatrixMarket matrix coordinate")
 
     def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=5, **kwd):
         if dataset.has_data():
             # If the dataset is larger than optional_metadata, just count comment lines.
             with open(dataset.file_name) as dataset_fh:
-                line = ''
+                line = ""
                 data_lines = 0
                 comment_lines = 0
                 # If the dataset is larger than optional_metadata, just count comment lines.
-                count_comments_only = self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize
+                count_comments_only = (
+                    self.max_optional_metadata_filesize >= 0
+                    and dataset.get_size() > self.max_optional_metadata_filesize
+                )
                 for line in dataset_fh:
-                    if line.startswith('%'):
+                    if line.startswith("%"):
                         comment_lines += 1
                     elif count_comments_only:
                         data_lines = None
                         break
                     else:
                         data_lines += 1
-                if ' ' in line:
-                    dataset.metadata.delimiter = ' '
+                if " " in line:
+                    dataset.metadata.delimiter = " "
                 else:
-                    dataset.metadata.delimiter = '\t'
+                    dataset.metadata.delimiter = "\t"
             dataset.metadata.comment_lines = comment_lines
             dataset.metadata.data_lines = data_lines
             dataset.metadata.columns = 3
-            dataset.metadata.column_types = ['int', 'int', 'float']
+            dataset.metadata.column_types = ["int", "int", "float"]
 
 
 @build_sniff_from_prefix
@@ -1346,22 +1639,79 @@ class CMAP(TabularData):
     182 58474736.7  10235   1   1   58820.9 35.4    13.5    13.5    -1.00   -1.00   -1.00   3.63    0.00    0.00    -1.00   0
     182 58474736.7  10235   1   1   58820.9 35.4    13.5    13.5    -1.00   -1.00   -1.00   3.63    0.00    0.00    -1.00   0
     """
+
     file_ext = "cmap"
 
-    MetadataElement(name="cmap_version", default='0.2', desc="version of cmap", readonly=True, visible=True, optional=False, no_value='0.2')
-    MetadataElement(name="label_channels", default=1, desc="the number of label channels", readonly=True, visible=True, optional=False, no_value=1)
-    MetadataElement(name="nickase_recognition_site_1", default=[], desc="comma separated list of label motif recognition sequences for channel 1", readonly=True, visible=True, optional=False, no_value=[])
-    MetadataElement(name="number_of_consensus_nanomaps", default=0, desc="the total number of consensus genome maps in the CMAP file", readonly=True, visible=True, optional=False, no_value=0)
-    MetadataElement(name="nickase_recognition_site_2", default=[], desc="comma separated list of label motif recognition sequences for channel 2", readonly=True, visible=True, optional=True, no_value=[])
-    MetadataElement(name="channel_1_color", default=[], desc="channel 1 color", readonly=True, visible=True, optional=True, no_value=[])
-    MetadataElement(name="channel_2_color", default=[], desc="channel 2 color", readonly=True, visible=True, optional=True, no_value=[])
+    MetadataElement(
+        name="cmap_version",
+        default="0.2",
+        desc="version of cmap",
+        readonly=True,
+        visible=True,
+        optional=False,
+        no_value="0.2",
+    )
+    MetadataElement(
+        name="label_channels",
+        default=1,
+        desc="the number of label channels",
+        readonly=True,
+        visible=True,
+        optional=False,
+        no_value=1,
+    )
+    MetadataElement(
+        name="nickase_recognition_site_1",
+        default=[],
+        desc="comma separated list of label motif recognition sequences for channel 1",
+        readonly=True,
+        visible=True,
+        optional=False,
+        no_value=[],
+    )
+    MetadataElement(
+        name="number_of_consensus_nanomaps",
+        default=0,
+        desc="the total number of consensus genome maps in the CMAP file",
+        readonly=True,
+        visible=True,
+        optional=False,
+        no_value=0,
+    )
+    MetadataElement(
+        name="nickase_recognition_site_2",
+        default=[],
+        desc="comma separated list of label motif recognition sequences for channel 2",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="channel_1_color",
+        default=[],
+        desc="channel 1 color",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="channel_2_color",
+        default=[],
+        desc="channel 2 color",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         handle = file_prefix.string_io()
         for line in handle:
-            if not line.startswith('#'):
+            if not line.startswith("#"):
                 return False
-            if line.startswith('# CMAP File Version:'):
+            if line.startswith("# CMAP File Version:"):
                 return True
         return False
 
@@ -1373,49 +1723,55 @@ class CMAP(TabularData):
                 cleaned_column_types = None
                 number_of_columns = 0
                 for i, line in enumerate(dataset_fh):
-                    line = line.strip('\n')
-                    if line.startswith('#'):
+                    line = line.strip("\n")
+                    if line.startswith("#"):
 
-                        if line.startswith('#h'):
+                        if line.startswith("#h"):
 
                             column_headers = line.split("\t")[1:]
-                        elif line.startswith('#f'):
+                        elif line.startswith("#f"):
                             cleaned_column_types = []
-                            for column_type in line.split('\t')[1:]:
-                                if column_type == 'Hex':
-                                    cleaned_column_types.append('str')
+                            for column_type in line.split("\t")[1:]:
+                                if column_type == "Hex":
+                                    cleaned_column_types.append("str")
                                 else:
                                     cleaned_column_types.append(column_type)
                         comment_lines += 1
-                        fields = line.split('\t')
+                        fields = line.split("\t")
                         if len(fields) == 2:
-                            if fields[0] == '# CMAP File Version:':
+                            if fields[0] == "# CMAP File Version:":
                                 dataset.metadata.cmap_version = fields[1]
-                            elif fields[0] == '# Label Channels:':
+                            elif fields[0] == "# Label Channels:":
                                 dataset.metadata.label_channels = int(fields[1])
-                            elif fields[0] == '# Nickase Recognition Site 1:':
-                                fields2 = fields[1].split(';')
+                            elif fields[0] == "# Nickase Recognition Site 1:":
+                                fields2 = fields[1].split(";")
                                 if len(fields2) == 2:
                                     dataset.metadata.channel_1_color = fields2[1]
-                                dataset.metadata.nickase_recognition_site_1 = fields2[0].split(',')
-                            elif fields[0] == '# Number of Consensus Maps:':
+                                dataset.metadata.nickase_recognition_site_1 = fields2[0].split(",")
+                            elif fields[0] == "# Number of Consensus Maps:":
                                 dataset.metadata.number_of_consensus_nanomaps = int(fields[1])
-                            elif fields[0] == '# Nickase Recognition Site 2:':
-                                fields2 = fields[1].split(';')
+                            elif fields[0] == "# Nickase Recognition Site 2:":
+                                fields2 = fields[1].split(";")
                                 if len(fields2) == 2:
                                     dataset.metadata.channel_2_color = fields2[1]
-                                dataset.metadata.nickase_recognition_site_2 = fields2[0].split(',')
-                    elif self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
+                                dataset.metadata.nickase_recognition_site_2 = fields2[0].split(",")
+                    elif (
+                        self.max_optional_metadata_filesize >= 0
+                        and dataset.get_size() > self.max_optional_metadata_filesize
+                    ):
                         # If the dataset is larger than optional_metadata, just count comment lines.
                         # No more comments, and the file is too big to look at the whole thing. Give up.
                         dataset.metadata.data_lines = None
                         break
                     elif i == comment_lines + 1:
-                        number_of_columns = len(line.split('\t'))
-                if not (self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize):
+                        number_of_columns = len(line.split("\t"))
+                if not (
+                    self.max_optional_metadata_filesize >= 0
+                    and dataset.get_size() > self.max_optional_metadata_filesize
+                ):
                     dataset.metadata.data_lines = i + 1 - comment_lines
             dataset.metadata.comment_lines = comment_lines
             dataset.metadata.column_names = column_headers
             dataset.metadata.column_types = cleaned_column_types
             dataset.metadata.columns = number_of_columns
-            dataset.metadata.delimiter = '\t'
+            dataset.metadata.delimiter = "\t"
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index a5bdb09dcb4..c4f84555202 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -12,8 +12,15 @@ import tempfile
 
 import yaml
 
-from galaxy.datatypes.data import get_file_peek, Headers, Text
-from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
+from galaxy.datatypes.data import (
+    get_file_peek,
+    Headers,
+    Text,
+)
+from galaxy.datatypes.metadata import (
+    MetadataElement,
+    MetadataParameter,
+)
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
@@ -31,6 +38,7 @@ log = logging.getLogger(__name__)
 @build_sniff_from_prefix
 class Html(Text):
     """Class describing an html file"""
+
     edam_format = "format_2331"
     file_ext = "html"
 
@@ -39,12 +47,12 @@ class Html(Text):
             dataset.peek = "HTML file"
             dataset.blurb = nice_size(dataset.get_size())
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'text/html'
+        return "text/html"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -60,7 +68,7 @@ class Html(Text):
         """
         headers = iter_headers(file_prefix, None)
         for hdr in headers:
-            if hdr and hdr[0].lower().find('<html>') >= 0:
+            if hdr and hdr[0].lower().find("<html>") >= 0:
                 return True
         return False
 
@@ -75,16 +83,16 @@ class Json(Text):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "JavaScript Object Notation (JSON)"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/json'
+        return "application/json"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Try to load the string with the json module. If successful it's a json file.
+        Try to load the string with the json module. If successful it's a json file.
         """
         return self._looks_like_json(file_prefix)
 
@@ -115,14 +123,15 @@ class Json(Text):
 
 
 class ExpressionJson(Json):
-    """ Represents the non-data input or output to a tool or workflow.
-    """
+    """Represents the non-data input or output to a tool or workflow."""
+
     file_ext = "json"
-    MetadataElement(name="json_type", default=None, desc="JavaScript or JSON type of expression", readonly=True, visible=True)
+    MetadataElement(
+        name="json_type", default=None, desc="JavaScript or JSON type of expression", readonly=True, visible=True
+    )
 
     def set_meta(self, dataset, **kwd):
-        """
-        """
+        """ """
         if dataset.has_data():
             json_type = "null"
             file_path = dataset.file_name
@@ -153,18 +162,18 @@ class Ipynb(Json):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "Jupyter Notebook"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Try to load the string with the json module. If successful it's a json file.
+        Try to load the string with the json module. If successful it's a json file.
         """
         if self._looks_like_json(file_prefix):
             try:
                 with open(file_prefix.filename) as f:
                     ipynb = json.load(f)
-                if ipynb.get('nbformat', False) is not False and ipynb.get('metadata', False):
+                if ipynb.get("nbformat", False) is not False and ipynb.get("metadata", False):
                     return True
                 else:
                     return False
@@ -174,11 +183,15 @@ class Ipynb(Json):
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
         headers = kwd.get("headers", {})
         config = trans.app.config
-        trust = getattr(config, 'trust_jupyter_notebook_conversion', False)
+        trust = getattr(config, "trust_jupyter_notebook_conversion", False)
         if trust:
-            return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, headers=headers, **kwd)
+            return self._display_data_trusted(
+                trans, dataset, preview=preview, filename=filename, to_ext=to_ext, headers=headers, **kwd
+            )
         else:
-            return super().display_data(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, headers=headers, **kwd)
+            return super().display_data(
+                trans, dataset, preview=preview, filename=filename, to_ext=to_ext, headers=headers, **kwd
+            )
 
     def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
         headers = kwd.get("headers", {})
@@ -189,13 +202,26 @@ class Ipynb(Json):
             with tempfile.NamedTemporaryFile(delete=False) as ofile_handle:
                 ofilename = ofile_handle.name
             try:
-                cmd = ['jupyter', 'nbconvert', '--to', 'html', '--template', 'full', dataset.file_name, '--output', ofilename]
+                cmd = [
+                    "jupyter",
+                    "nbconvert",
+                    "--to",
+                    "html",
+                    "--template",
+                    "full",
+                    dataset.file_name,
+                    "--output",
+                    ofilename,
+                ]
                 subprocess.check_call(cmd)
-                ofilename = f'{ofilename}.html'
+                ofilename = f"{ofilename}.html"
             except subprocess.CalledProcessError:
                 ofilename = dataset.file_name
-                log.exception('Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', ' '.join(map(shlex.quote, cmd)))
-            return open(ofilename, mode='rb'), headers
+                log.exception(
+                    'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.',
+                    " ".join(map(shlex.quote, cmd)),
+                )
+            return open(ofilename, mode="rb"), headers
 
     def set_meta(self, dataset, **kwd):
         """
@@ -206,24 +232,132 @@ class Ipynb(Json):
 @build_sniff_from_prefix
 class Biom1(Json):
     """
-        BIOM version 1.0 file format description
-        http://biom-format.org/documentation/format_versions/biom-1.0.html
+    BIOM version 1.0 file format description
+    http://biom-format.org/documentation/format_versions/biom-1.0.html
     """
+
     file_ext = "biom1"
     edam_format = "format_3746"
 
-    MetadataElement(name="table_rows", default=[], desc="table_rows", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="table_matrix_element_type", default="", desc="table_matrix_element_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
-    MetadataElement(name="table_format", default="", desc="table_format", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
-    MetadataElement(name="table_generated_by", default="", desc="table_generated_by", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="")
-    MetadataElement(name="table_matrix_type", default="", desc="table_matrix_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
-    MetadataElement(name="table_shape", default=[], desc="table_shape", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="table_format_url", default="", desc="table_format_url", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
-    MetadataElement(name="table_date", default="", desc="table_date", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="")
-    MetadataElement(name="table_type", default="", desc="table_type", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="")
-    MetadataElement(name="table_id", default=None, desc="table_id", param=MetadataParameter, readonly=True, visible=True, optional=True)
-    MetadataElement(name="table_columns", default=[], desc="table_columns", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
-    MetadataElement(name="table_column_metadata_headers", default=[], desc="table_column_metadata_headers", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value=[])
+    MetadataElement(
+        name="table_rows",
+        default=[],
+        desc="table_rows",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="table_matrix_element_type",
+        default="",
+        desc="table_matrix_element_type",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_format",
+        default="",
+        desc="table_format",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_generated_by",
+        default="",
+        desc="table_generated_by",
+        param=MetadataParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_matrix_type",
+        default="",
+        desc="table_matrix_type",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_shape",
+        default=[],
+        desc="table_shape",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="table_format_url",
+        default="",
+        desc="table_format_url",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_date",
+        default="",
+        desc="table_date",
+        param=MetadataParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_type",
+        default="",
+        desc="table_type",
+        param=MetadataParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value="",
+    )
+    MetadataElement(
+        name="table_id",
+        default=None,
+        desc="table_id",
+        param=MetadataParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+    )
+    MetadataElement(
+        name="table_columns",
+        default=[],
+        desc="table_columns",
+        param=MetadataParameter,
+        readonly=True,
+        visible=False,
+        optional=True,
+        no_value=[],
+    )
+    MetadataElement(
+        name="table_column_metadata_headers",
+        default=[],
+        desc="table_column_metadata_headers",
+        param=MetadataParameter,
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=[],
+    )
 
     def set_peek(self, dataset):
         super().set_peek(dataset)
@@ -248,11 +382,11 @@ class Biom1(Json):
             with open(file_prefix.filename) as fh:
                 prev_str = ""
                 segment_str = fh.read(segment_size)
-                if segment_str.strip().startswith('{'):
+                if segment_str.strip().startswith("{"):
                     while segment_str:
                         current_str = prev_str + segment_str
                         if '"format"' in current_str:
-                            current_str = re.sub(r'\s', '', current_str)
+                            current_str = re.sub(r"\s", "", current_str)
                             if '"format":"BiologicalObservationMatrix' in current_str:
                                 is_biom = True
                                 break
@@ -264,7 +398,7 @@ class Biom1(Json):
 
     def set_meta(self, dataset, **kwd):
         """
-            Store metadata information from the BIOM file.
+        Store metadata information from the BIOM file.
         """
         if dataset.has_data():
             with open(dataset.file_name) as fh:
@@ -275,28 +409,30 @@ class Biom1(Json):
 
                 def _transform_dict_list_ids(dict_list):
                     if dict_list:
-                        return [x.get('id', None) for x in dict_list]
+                        return [x.get("id", None) for x in dict_list]
                     return []
 
-                b_transform = {'rows': _transform_dict_list_ids, 'columns': _transform_dict_list_ids}
-                for (m_name, b_name) in [('table_rows', 'rows'),
-                                         ('table_matrix_element_type', 'matrix_element_type'),
-                                         ('table_format', 'format'),
-                                         ('table_generated_by', 'generated_by'),
-                                         ('table_matrix_type', 'matrix_type'),
-                                         ('table_shape', 'shape'),
-                                         ('table_format_url', 'format_url'),
-                                         ('table_date', 'date'),
-                                         ('table_type', 'type'),
-                                         ('table_id', 'id'),
-                                         ('table_columns', 'columns')]:
+                b_transform = {"rows": _transform_dict_list_ids, "columns": _transform_dict_list_ids}
+                for (m_name, b_name) in [
+                    ("table_rows", "rows"),
+                    ("table_matrix_element_type", "matrix_element_type"),
+                    ("table_format", "format"),
+                    ("table_generated_by", "generated_by"),
+                    ("table_matrix_type", "matrix_type"),
+                    ("table_shape", "shape"),
+                    ("table_format_url", "format_url"),
+                    ("table_date", "date"),
+                    ("table_type", "type"),
+                    ("table_id", "id"),
+                    ("table_columns", "columns"),
+                ]:
                     try:
                         metadata_value = json_dict.get(b_name, None)
                         if b_name == "columns" and metadata_value:
                             keep_columns = set()
                             for column in metadata_value:
-                                if column['metadata'] is not None:
-                                    for k, v in column['metadata'].items():
+                                if column["metadata"] is not None:
+                                    for k, v in column["metadata"].items():
                                         if v is not None:
                                             keep_columns.add(k)
                             final_list = sorted(list(keep_columns))
@@ -317,6 +453,7 @@ class ImgtJson(Json):
     "IMGT®, the international ImMunoGeneTics information system®
     http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."
     """
+
     file_ext = "imgt.json"
 
     MetadataElement(name="taxon_names", default=[], desc="taxonID: names", readonly=True, visible=True, no_value=[])
@@ -353,7 +490,7 @@ class ImgtJson(Json):
         try:
             with open(file_prefix.filename) as fh:
                 segment_str = fh.read(load_size)
-                if segment_str.strip().startswith('['):
+                if segment_str.strip().startswith("["):
                     if '"taxonId"' in segment_str and '"anchorPoints"' in segment_str:
                         is_imgt = True
         except Exception:
@@ -362,7 +499,7 @@ class ImgtJson(Json):
 
     def set_meta(self, dataset, **kwd):
         """
-            Store metadata information from the imgt file.
+        Store metadata information from the imgt file.
         """
         if dataset.has_data():
             with open(dataset.file_name) as fh:
@@ -370,8 +507,8 @@ class ImgtJson(Json):
                     json_dict = json.load(fh)
                     tax_names = []
                     for entry in json_dict:
-                        if 'taxonId' in entry:
-                            names = "%d: %s" % (entry['taxonId'], ','.join(entry['speciesNames']))
+                        if "taxonId" in entry:
+                            names = "%d: %s" % (entry["taxonId"], ",".join(entry["speciesNames"]))
                             tax_names.append(names)
                     dataset.metadata.taxon_names = tax_names
                 except Exception:
@@ -381,9 +518,10 @@ class ImgtJson(Json):
 @build_sniff_from_prefix
 class GeoJson(Json):
     """
-        GeoJSON is a geospatial data interchange format based on JavaScript Object Notation (JSON).
-        https://tools.ietf.org/html/rfc7946
+    GeoJSON is a geospatial data interchange format based on JavaScript Object Notation (JSON).
+    https://tools.ietf.org/html/rfc7946
     """
+
     file_ext = "geojson"
 
     def set_peek(self, dataset):
@@ -417,7 +555,18 @@ class GeoJson(Json):
         try:
             with open(file_prefix.filename) as fh:
                 segment_str = fh.read(load_size)
-                if any(x in segment_str for x in ["Point", "MultiPoint", "LineString", "MultiLineString", "Polygon", "MultiPolygon", "GeometryCollection"]):
+                if any(
+                    x in segment_str
+                    for x in [
+                        "Point",
+                        "MultiPoint",
+                        "LineString",
+                        "MultiLineString",
+                        "Polygon",
+                        "MultiPolygon",
+                        "GeometryCollection",
+                    ]
+                ):
                     if all(x in segment_str for x in ["type", "geometry", "coordinates"]):
                         return True
         except Exception:
@@ -428,9 +577,10 @@ class GeoJson(Json):
 @build_sniff_from_prefix
 class Obo(Text):
     """
-        OBO file format description
-        https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html
+    OBO file format description
+    https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html
     """
+
     edam_data = "data_0582"
     edam_format = "format_2549"
     file_ext = "obo"
@@ -440,24 +590,24 @@ class Obo(Text):
             dataset.peek = get_file_peek(dataset.file_name)
             dataset.blurb = "Open Biomedical Ontology (OBO)"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Try to guess the Obo filetype.
-            It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
+        Try to guess the Obo filetype.
+        It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
         """
-        stanza = re.compile(r'^\[.*\]$')
+        stanza = re.compile(r"^\[.*\]$")
         handle = file_prefix.string_io()
         first_line = handle.readline()
-        if not first_line.startswith('format-version:'):
+        if not first_line.startswith("format-version:"):
             return False
 
         for line in handle:
             if stanza.match(line.strip()):
                 # a stanza needs to begin with an ID tag
-                if next(handle).startswith('id:'):
+                if next(handle).startswith("id:"):
                     return True
         return False
 
@@ -468,10 +618,13 @@ class Arff(Text):
     An ARFF (Attribute-Relation File Format) file is an ASCII text file that describes a list of instances sharing a set of attributes.
     http://weka.wikispaces.com/ARFF
     """
+
     edam_format = "format_3581"
     file_ext = "arff"
 
-    MetadataElement(name="comment_lines", default=0, desc="Number of comment lines", readonly=True, optional=True, no_value=0)
+    MetadataElement(
+        name="comment_lines", default=0, desc="Number of comment lines", readonly=True, optional=True, no_value=0
+    )
     MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0)
 
     def set_peek(self, dataset):
@@ -480,13 +633,13 @@ class Arff(Text):
             dataset.blurb = "Attribute-Relation File Format (ARFF)"
             dataset.blurb += f", {dataset.metadata.comment_lines} comments, {dataset.metadata.columns} attributes"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Try to guess the Arff filetype.
-            It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
+        Try to guess the Arff filetype.
+        It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
         """
         handle = file_prefix.string_io()
         relation_found = False
@@ -512,11 +665,11 @@ class Arff(Text):
 
     def set_meta(self, dataset, **kwd):
         """
-            Trying to count the comment lines and the number of columns included.
-            A typical ARFF data block looks like this:
-            @DATA
-            5.1,3.5,1.4,0.2,Iris-setosa
-            4.9,3.0,1.4,0.2,Iris-setosa
+        Trying to count the comment lines and the number of columns included.
+        A typical ARFF data block looks like this:
+        @DATA
+        5.1,3.5,1.4,0.2,Iris-setosa
+        4.9,3.0,1.4,0.2,Iris-setosa
         """
         comment_lines = column_count = 0
         if dataset.has_data():
@@ -527,12 +680,12 @@ class Arff(Text):
                     line = line.strip()
                     if not line:
                         continue
-                    if line.startswith('%') and not first_real_line:
+                    if line.startswith("%") and not first_real_line:
                         comment_lines += 1
                     else:
                         first_real_line = True
                     if data_block:
-                        if line.startswith('{'):
+                        if line.startswith("{"):
                             # Sparse representation
                             """
                                 @data
@@ -541,18 +694,18 @@ class Arff(Text):
                                 @data
                                 {1 X, 3 Y, 4 "class A"}, {5}
                             """
-                            token = line.split('}', 1)
+                            token = line.split("}", 1)
                             first_part = token[0]
-                            last_column = first_part.split(',')[-1].strip()
+                            last_column = first_part.split(",")[-1].strip()
                             numeric_value = last_column.split()[0]
                             column_count = int(numeric_value)
                             if len(token) > 1:
                                 # we have an additional weight
                                 column_count -= 1
                         else:
-                            columns = line.strip().split(',')
+                            columns = line.strip().split(",")
                             column_count = len(columns)
-                            if columns[-1].strip().startswith('{'):
+                            if columns[-1].strip().startswith("{"):
                                 # we have an additional weight at the end
                                 column_count -= 1
 
@@ -566,12 +719,17 @@ class Arff(Text):
 
 class SnpEffDb(Text):
     """Class describing a SnpEff genome build"""
+
     edam_format = "format_3624"
     file_ext = "snpeffdb"
     MetadataElement(name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True)
     MetadataElement(name="snpeff_version", default="SnpEff4.0", desc="SnpEff Version", readonly=True, visible=True)
-    MetadataElement(name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[], optional=True)
-    MetadataElement(name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True)
+    MetadataElement(
+        name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[], optional=True
+    )
+    MetadataElement(
+        name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True
+    )
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -580,10 +738,10 @@ class SnpEffDb(Text):
     def getSnpeffVersionFromFile(self, path):
         snpeff_version = None
         try:
-            with gzip.open(path, 'rt') as fh:
+            with gzip.open(path, "rt") as fh:
                 buf = fh.read(100)
                 lines = buf.splitlines()
-                m = re.match(r'^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
+                m = re.match(r"^(SnpEff)\s+(\d+\.\d+).*$", lines[0].strip())
                 if m:
                     snpeff_version = m.groups()[0] + m.groups()[1]
         except Exception:
@@ -594,9 +752,9 @@ class SnpEffDb(Text):
         super().set_meta(dataset, **kwd)
         data_dir = dataset.extra_files_path
         # search data_dir/genome_version for files
-        regulation_pattern = 'regulation_(.+).bin'
+        regulation_pattern = "regulation_(.+).bin"
         #  annotation files that are included in snpEff by a flag
-        annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
+        annotations_dict = {"nextProt.bin": "-nextprot", "motif.bin": "-motif", "interactions.bin": "-interaction"}
         regulations = []
         annotations = []
         genome_version = None
@@ -604,7 +762,7 @@ class SnpEffDb(Text):
         if data_dir and os.path.isdir(data_dir):
             for root, _, files in os.walk(data_dir):
                 for fname in files:
-                    if fname.startswith('snpEffectPredictor'):
+                    if fname.startswith("snpEffectPredictor"):
                         # if snpEffectPredictor.bin download succeeded
                         genome_version = os.path.basename(root)
                         dataset.metadata.genome_version = genome_version
@@ -619,14 +777,14 @@ class SnpEffDb(Text):
                             regulations.append(name)
                         elif fname in annotations_dict:
                             value = annotations_dict[fname]
-                            name = value.lstrip('-')
+                            name = value.lstrip("-")
                             annotations.append(name)
             dataset.metadata.regulation = regulations
             dataset.metadata.annotation = annotations
             try:
-                with open(dataset.file_name, 'w') as fh:
-                    fh.write(f"{genome_version}\n" if genome_version else 'Genome unknown')
-                    fh.write(f"{snpeff_version}\n" if snpeff_version else 'SnpEff version unknown')
+                with open(dataset.file_name, "w") as fh:
+                    fh.write(f"{genome_version}\n" if genome_version else "Genome unknown")
+                    fh.write(f"{snpeff_version}\n" if snpeff_version else "SnpEff version unknown")
                     if annotations:
                         fh.write(f"annotations: {','.join(annotations)}\n")
                     if regulations:
@@ -650,36 +808,49 @@ class SnpSiftDbNSFP(Text):
     - Create tabix index
     $ tabix -s 1 -b 2 -e 2 dbNSFP2.3.txt.gz
     """
-    file_ext = "snpsiftdbnsfp"
-    composite_type = 'auto_primary_file'
 
-    MetadataElement(name='reference_name', default='dbSNFP', desc='Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='dbSNFP')
+    file_ext = "snpsiftdbnsfp"
+    composite_type = "auto_primary_file"
+
+    MetadataElement(
+        name="reference_name",
+        default="dbSNFP",
+        desc="Reference Name",
+        readonly=True,
+        visible=True,
+        set_in_upload=True,
+        no_value="dbSNFP",
+    )
     MetadataElement(name="bgzip", default=None, desc="dbNSFP bgzip", readonly=True, visible=True)
     MetadataElement(name="index", default=None, desc="Tabix Index File", readonly=True, visible=True)
     MetadataElement(name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[])
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
-        self.add_composite_file('%s.gz', description='dbNSFP bgzip', substitute_name_with_metadata='reference_name', is_binary=True)
-        self.add_composite_file('%s.gz.tbi', description='Tabix Index File', substitute_name_with_metadata='reference_name', is_binary=True)
+        self.add_composite_file(
+            "%s.gz", description="dbNSFP bgzip", substitute_name_with_metadata="reference_name", is_binary=True
+        )
+        self.add_composite_file(
+            "%s.gz.tbi", description="Tabix Index File", substitute_name_with_metadata="reference_name", is_binary=True
+        )
 
     def generate_primary_file(self, dataset=None):
         """
         This is called only at upload to write the html file
         cannot rename the datasets here - they come with the default unfortunately
         """
-        return '<html><head><title>SnpSiftDbNSFP Composite Dataset</title></head></html>'
+        return "<html><head><title>SnpSiftDbNSFP Composite Dataset</title></head></html>"
 
     def regenerate_primary_file(self, dataset):
         """
         cannot do this until we are setting metadata
         """
         annotations = f"dbNSFP Annotations: {','.join(dataset.metadata.annotation)}\n"
-        with open(dataset.file_name, 'a') as f:
+        with open(dataset.file_name, "a") as f:
             if dataset.metadata.bgzip:
                 bn = dataset.metadata.bgzip
                 f.write(bn)
-                f.write('\n')
+                f.write("\n")
             f.write(annotations)
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -688,35 +859,40 @@ class SnpSiftDbNSFP(Text):
             if os.path.exists(efp):
                 flist = os.listdir(efp)
                 for fname in flist:
-                    if fname.endswith('.gz'):
+                    if fname.endswith(".gz"):
                         dataset.metadata.bgzip = fname
                         try:
-                            with gzip.open(os.path.join(efp, fname), 'rt') as fh:
+                            with gzip.open(os.path.join(efp, fname), "rt") as fh:
                                 buf = fh.read(5000)
                                 lines = buf.splitlines()
-                                headers = lines[0].split('\t')
+                                headers = lines[0].split("\t")
                                 dataset.metadata.annotation = headers[4:]
                         except Exception as e:
                             log.warning("set_meta fname: %s  %s", fname, unicodify(e))
-                    if fname.endswith('.tbi'):
+                    if fname.endswith(".tbi"):
                         dataset.metadata.index = fname
             self.regenerate_primary_file(dataset)
         except Exception as e:
-            log.warning("set_meta fname: %s  %s", dataset.file_name if dataset and dataset.file_name else 'Unkwown', unicodify(e))
+            log.warning(
+                "set_meta fname: %s  %s",
+                dataset.file_name if dataset and dataset.file_name else "Unkwown",
+                unicodify(e),
+            )
 
         def set_peek(self, dataset):
             if not dataset.dataset.purged:
                 dataset.peek = f"{dataset.metadata.reference_name} :  {','.join(dataset.metadata.annotation)}"
-                dataset.blurb = f'{dataset.metadata.reference_name}'
+                dataset.blurb = f"{dataset.metadata.reference_name}"
             else:
-                dataset.peek = 'file does not exist'
-                dataset.blurb = 'file purged from disc'
+                dataset.peek = "file does not exist"
+                dataset.blurb = "file purged from disc"
 
 
 @build_sniff_from_prefix
 class IQTree(Text):
     """IQ-TREE format"""
-    file_ext = 'iqtree'
+
+    file_ext = "iqtree"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -748,6 +924,7 @@ class Paf(Text):
 
     https://github.com/lh3/miniasm/blob/master/PAF.md
     """
+
     file_ext = "paf"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -763,13 +940,13 @@ class Paf(Text):
                 return False
             for i in (1, 2, 3, 6, 7, 8, 9, 10, 11):
                 int(line[i])
-            if line[4] not in ('+', '-'):
+            if line[4] not in ("+", "-"):
                 return False
             if not (0 <= int(line[11]) <= 255):
                 return False
             # Check that the optional columns after the 12th contain SAM-like typed key-value pairs
             for i in range(12, len(line)):
-                if len(line[i].split(':')) != 3:
+                if len(line[i].split(":")) != 3:
                     return False
             found_valid_lines = True
         return found_valid_lines
@@ -782,6 +959,7 @@ class Gfa1(Text):
 
     http://gfa-spec.github.io/GFA-spec/GFA1.html
     """
+
     file_ext = "gfa1"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -795,27 +973,27 @@ class Gfa1(Text):
         """
         found_valid_lines = False
         for line in iter_headers(file_prefix, "\t"):
-            if line[0].startswith('#'):
+            if line[0].startswith("#"):
                 continue
-            if line[0] == 'H':
-                return len(line) == 2 and line[1] == 'VN:Z:1.0'
-            elif line[0] == 'S':
+            if line[0] == "H":
+                return len(line) == 2 and line[1] == "VN:Z:1.0"
+            elif line[0] == "S":
                 if len(line) < 3:
                     return False
-            elif line[0] == 'L':
+            elif line[0] == "L":
                 if len(line) < 6:
                     return False
                 for i in (2, 4):
-                    if line[i] not in ('+', '-'):
+                    if line[i] not in ("+", "-"):
                         return False
-            elif line[0] == 'C':
+            elif line[0] == "C":
                 if len(line) < 7:
                     return False
                 for i in (2, 4):
-                    if line[i] not in ('+', '-'):
+                    if line[i] not in ("+", "-"):
                         return False
                 int(line[5])
-            elif line[0] == 'P':
+            elif line[0] == "P":
                 if len(line) < 4:
                     return False
             else:
@@ -831,6 +1009,7 @@ class Gfa2(Text):
 
     https://github.com/GFA-spec/GFA-spec/blob/master/GFA2.md
     """
+
     file_ext = "gfa2"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -844,23 +1023,23 @@ class Gfa2(Text):
         """
         found_valid_lines = False
         for line in iter_headers(file_prefix, "\t"):
-            if line[0].startswith('#'):
+            if line[0].startswith("#"):
                 continue
-            if line[0] == 'H':
-                return len(line) >= 2 and line[1] == 'VN:Z:2.0'
-            elif line[0] == 'S':
+            if line[0] == "H":
+                return len(line) >= 2 and line[1] == "VN:Z:2.0"
+            elif line[0] == "S":
                 if len(line) < 3:
                     return False
-            elif line[0] == 'F':
+            elif line[0] == "F":
                 if len(line) < 8:
                     return False
-            elif line[0] == 'E':
+            elif line[0] == "E":
                 if len(line) < 9:
                     return False
-            elif line[0] == 'G':
+            elif line[0] == "G":
                 if len(line) < 6:
                     return False
-            elif line[0] == 'O' or line[0] == 'U':
+            elif line[0] == "O" or line[0] == "U":
                 if len(line) < 3:
                     return False
             else:
@@ -872,23 +1051,24 @@ class Gfa2(Text):
 @build_sniff_from_prefix
 class Yaml(Text):
     """Yaml files"""
+
     file_ext = "yaml"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Try to load the string with the yaml module. If successful it's a yaml file.
+        Try to load the string with the yaml module. If successful it's a yaml file.
         """
         return self._looks_like_yaml(file_prefix)
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
-        return 'application/yaml'
+        return "application/yaml"
 
     def _yield_user_file_content(self, trans, from_dataset, filename, headers: Headers):
         # Override non-standard application/yaml mediatype with
         # non-standard text/x-yaml, so preview is shown in preview iframe,
         # instead of downloading the file.
-        headers['content-type'] = 'text/x-yaml'
+        headers["content-type"] = "text/x-yaml"
         return super()._yield_user_file_content(trans, from_dataset, filename, headers)
 
     def _looks_like_yaml(self, file_prefix: FilePrefix):
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index 6d28363c8da..02fd0f50882 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -22,8 +22,8 @@ class UCSCTrackHub(Html):
     Datatype for UCSC TrackHub
     """
 
-    file_ext = 'trackhub'
-    composite_type = 'auto_primary_file'
+    file_ext = "trackhub"
+    composite_type = "auto_primary_file"
 
     def generate_primary_file(self, dataset=None):
         """
@@ -31,23 +31,24 @@ class UCSCTrackHub(Html):
         cannot rename the datasets here - they come with the default unfortunately
         """
         rval = [
-            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
-            This composite dataset is composed of the following files:<p/><ul>' % (
-                self.file_ext)]
+            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>"
+            % (self.file_ext)
+        ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
-            opt_text = ''
+            opt_text = ""
             if composite_file.optional:
-                opt_text = ' (optional)'
+                opt_text = " (optional)"
             rval.append(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}')
-        rval.append('</ul></html>')
+        rval.append("</ul></html>")
         return "\n".join(rval)
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def display_peek(self, dataset):
         try:
diff --git a/lib/galaxy/datatypes/triples.py b/lib/galaxy/datatypes/triples.py
index 29e9611761c..711c71d92a3 100644
--- a/lib/galaxy/datatypes/triples.py
+++ b/lib/galaxy/datatypes/triples.py
@@ -12,19 +12,20 @@ from . import (
     binary,
     data,
     text,
-    xml
+    xml,
 )
 
 log = logging.getLogger(__name__)
 
-TURTLE_PREFIX_PATTERN = re.compile(r'@prefix\s+[^:]*:\s+<[^>]*>\s\.')
-TURTLE_BASE_PATTERN = re.compile(r'@base\s+<[^>]*>\s\.')
+TURTLE_PREFIX_PATTERN = re.compile(r"@prefix\s+[^:]*:\s+<[^>]*>\s\.")
+TURTLE_BASE_PATTERN = re.compile(r"@base\s+<[^>]*>\s\.")
 
 
 class Triples(data.Data):
     """
     The abstract base class for the file format that can contain triples
     """
+
     edam_data = "data_0582"
     edam_format = "format_2376"
     file_ext = "triples"
@@ -39,10 +40,10 @@ class Triples(data.Data):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'Triple data'
+            dataset.blurb = "Triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -50,12 +51,13 @@ class NTriples(data.Text, Triples):
     """
     The N-Triples triple data format
     """
+
     edam_format = "format_3256"
     file_ext = "nt"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         # <http://example.org/dir/relfile> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://example.org/type> .
-        if re.compile(r'<[^>]*>\s<[^>]*>\s<[^>]*>\s\.').search(file_prefix.contents_header):
+        if re.compile(r"<[^>]*>\s<[^>]*>\s<[^>]*>\s\.").search(file_prefix.contents_header):
             return True
         return False
 
@@ -63,16 +65,17 @@ class NTriples(data.Text, Triples):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'N-Triples triple data'
+            dataset.blurb = "N-Triples triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class N3(data.Text, Triples):
     """
     The N3 triple data format
     """
+
     edam_format = "format_3257"
     file_ext = "n3"
 
@@ -86,10 +89,10 @@ class N3(data.Text, Triples):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'Notation-3 Triple data'
+            dataset.blurb = "Notation-3 Triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -97,6 +100,7 @@ class Turtle(data.Text, Triples):
     """
     The Turtle triple data format
     """
+
     edam_format = "format_3255"
     file_ext = "ttl"
 
@@ -113,10 +117,10 @@ class Turtle(data.Text, Triples):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'Turtle triple data'
+            dataset.blurb = "Turtle triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 # TODO: we might want to look at rdflib or a similar, larger lib/egg
@@ -125,12 +129,15 @@ class Rdf(xml.GenericXml, Triples):
     """
     Resource Description Framework format (http://www.w3.org/RDF/).
     """
+
     edam_format = "format_3261"
     file_ext = "rdf"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         # <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" ...
-        match = re.compile(r'xmlns:([^=]*)="http://www.w3.org/1999/02/22-rdf-syntax-ns#"').search(file_prefix.contents_header)
+        match = re.compile(r'xmlns:([^=]*)="http://www.w3.org/1999/02/22-rdf-syntax-ns#"').search(
+            file_prefix.contents_header
+        )
         if match and (f"{match.group(1)}:RDF") in file_prefix.contents_header:
             return True
         return False
@@ -139,10 +146,10 @@ class Rdf(xml.GenericXml, Triples):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'RDF/XML triple data'
+            dataset.blurb = "RDF/XML triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @build_sniff_from_prefix
@@ -150,13 +157,14 @@ class Jsonld(text.Json, Triples):
     """
     The JSON-LD data format
     """
+
     # format not defined in edam so we use the json format number
     edam_format = "format_3464"
     file_ext = "jsonld"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         if self._looks_like_json(file_prefix):
-            if "\"@id\"" in file_prefix.contents_header or "\"@context\"" in file_prefix.contents_header:
+            if '"@id"' in file_prefix.contents_header or '"@context"' in file_prefix.contents_header:
                 return True
         return False
 
@@ -164,16 +172,17 @@ class Jsonld(text.Json, Triples):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'JSON-LD triple data'
+            dataset.blurb = "JSON-LD triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class HDT(binary.Binary, Triples):
     """
     The HDT triple data format
     """
+
     edam_format = "format_2376"
     file_ext = "hdt"
 
@@ -186,7 +195,7 @@ class HDT(binary.Binary, Triples):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'HDT triple data'
+            dataset.blurb = "HDT triple data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
diff --git a/lib/galaxy/datatypes/upload_util.py b/lib/galaxy/datatypes/upload_util.py
index c4772c35332..98d3f97a971 100644
--- a/lib/galaxy/datatypes/upload_util.py
+++ b/lib/galaxy/datatypes/upload_util.py
@@ -1,7 +1,13 @@
 import os
-from typing import NamedTuple, Optional
+from typing import (
+    NamedTuple,
+    Optional,
+)
 
-from galaxy.datatypes import data, sniff
+from galaxy.datatypes import (
+    data,
+    sniff,
+)
 from galaxy.util.checkers import (
     check_binary,
     is_single_file_zip,
@@ -52,7 +58,13 @@ def handle_upload(
         if auto_decompress and is_zip(path) and not is_single_file_zip(path):
             multi_file_zip = True
         try:
-            ext, converted_path, compression_type, converted_newlines, converted_spaces = sniff.handle_uploaded_dataset_file_internal(
+            (
+                ext,
+                converted_path,
+                compression_type,
+                converted_newlines,
+                converted_spaces,
+            ) = sniff.handle_uploaded_dataset_file_internal(
                 path,
                 registry,
                 ext=requested_ext,
@@ -62,13 +74,13 @@ def handle_upload(
                 check_content=check_content,
                 is_binary=is_binary,
                 auto_decompress=auto_decompress,
-                uploaded_file_ext=os.path.splitext(name)[1].lower().lstrip('.'),
+                uploaded_file_ext=os.path.splitext(name)[1].lower().lstrip("."),
                 convert_to_posix_lines=convert_to_posix_lines,
                 convert_spaces_to_tabs=convert_spaces_to_tabs,
             )
         except sniff.InappropriateDatasetContentError as exc:
             raise UploadProblemException(exc)
-    elif requested_ext == 'auto':
+    elif requested_ext == "auto":
         ext = sniff.guess_ext(path, registry.sniff_order, is_binary=is_binary)
     else:
         ext = requested_ext
@@ -77,10 +89,10 @@ def handle_upload(
     converted_path = None if converted_path == path else converted_path
 
     # Validate datasets where the filetype was explicitly set using the filetype's sniffer (if any)
-    if requested_ext != 'auto':
+    if requested_ext != "auto":
         datatype = registry.get_datatype_by_extension(requested_ext)
         # Enable sniffer "validate mode" (prevents certain sniffers from disabling themselves)
-        if check_content and hasattr(datatype, 'sniff'):
+        if check_content and hasattr(datatype, "sniff"):
             try:
                 is_of_datatype = datatype.sniff(path)
             except Exception:
@@ -89,19 +101,23 @@ def handle_upload(
                 stdout = f"Warning: The file 'Type' was set to '{requested_ext}' but the file does not appear to be of that type"
 
     # Handle unsniffable binaries
-    if is_binary and ext == 'binary':
-        upload_ext = os.path.splitext(name)[1].lower().lstrip('.')
+    if is_binary and ext == "binary":
+        upload_ext = os.path.splitext(name)[1].lower().lstrip(".")
         if registry.is_extension_unsniffable_binary(upload_ext):
-            stdout = ("Warning: The file's datatype cannot be determined from its contents and was guessed based on"
-                     " its extension, to avoid this warning, manually set the file 'Type' to '{ext}' when uploading"
-                     " this type of file".format(ext=upload_ext))
+            stdout = (
+                "Warning: The file's datatype cannot be determined from its contents and was guessed based on"
+                " its extension, to avoid this warning, manually set the file 'Type' to '{ext}' when uploading"
+                " this type of file".format(ext=upload_ext)
+            )
             ext = upload_ext
         else:
-            stdout = ("The uploaded binary file format cannot be determined automatically, please set the file 'Type'"
-                      " manually")
+            stdout = (
+                "The uploaded binary file format cannot be determined automatically, please set the file 'Type'"
+                " manually"
+            )
 
     datatype = registry.get_datatype_by_extension(ext)
-    if multi_file_zip and not getattr(datatype, 'compressed', False):
-        stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.'
+    if multi_file_zip and not getattr(datatype, "compressed", False):
+        stdout = "ZIP file contained more than one file, only the first file was added to Galaxy."
 
     return HandleUploadResponse(stdout, ext, datatype, is_binary, converted_path, converted_newlines, converted_spaces)
diff --git a/lib/galaxy/datatypes/util/generic_util.py b/lib/galaxy/datatypes/util/generic_util.py
index 574f09586c0..105f1a4792c 100644
--- a/lib/galaxy/datatypes/util/generic_util.py
+++ b/lib/galaxy/datatypes/util/generic_util.py
@@ -9,7 +9,7 @@ def count_special_lines(word, filename, invert=False):
     """
     cmd = ["grep", "-c", "-E"]
     if invert:
-        cmd.append('-v')
+        cmd.append("-v")
     cmd.extend([word, filename])
     try:
         out = commands.execute(cmd)
diff --git a/lib/galaxy/datatypes/util/gff_util.py b/lib/galaxy/datatypes/util/gff_util.py
index 31ac20de25a..d0ec30b91ca 100644
--- a/lib/galaxy/datatypes/util/gff_util.py
+++ b/lib/galaxy/datatypes/util/gff_util.py
@@ -3,12 +3,21 @@ Provides utilities for working with GFF files.
 """
 import copy
 
-from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError
-from bx.tabular.io import Comment, Header
+from bx.intervals.io import (
+    GenomicInterval,
+    GenomicIntervalReader,
+    MissingFieldError,
+    NiceReaderWrapper,
+    ParseError,
+)
+from bx.tabular.io import (
+    Comment,
+    Header,
+)
 
 from galaxy.util import unicodify
 
-FASTA_DIRECTIVE = '##FASTA'
+FASTA_DIRECTIVE = "##FASTA"
 
 
 class GFFInterval(GenomicInterval):
@@ -17,19 +26,31 @@ class GFFInterval(GenomicInterval):
     only attribute is 'group.'
     """
 
-    def __init__(self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4,
-                 strand_col=6, score_col=5, default_strand='.', fix_strand=False):
+    def __init__(
+        self,
+        reader,
+        fields,
+        chrom_col=0,
+        feature_col=2,
+        start_col=3,
+        end_col=4,
+        strand_col=6,
+        score_col=5,
+        default_strand=".",
+        fix_strand=False,
+    ):
         # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this,
         # temporarily set strand and then unset after initing GenomicInterval.
         unknown_strand = False
-        if not fix_strand and fields[strand_col] == '.':
+        if not fix_strand and fields[strand_col] == ".":
             unknown_strand = True
-            fields[strand_col] = '+'
-        GenomicInterval.__init__(self, reader, fields, chrom_col, start_col, end_col, strand_col,
-                                 default_strand, fix_strand=fix_strand)
+            fields[strand_col] = "+"
+        GenomicInterval.__init__(
+            self, reader, fields, chrom_col, start_col, end_col, strand_col, default_strand, fix_strand=fix_strand
+        )
         if unknown_strand:
-            self.strand = '.'
-            self.fields[strand_col] = '.'
+            self.strand = "."
+            self.fields[strand_col] = "."
 
         # Handle feature, score column.
         self.feature_col = feature_col
@@ -47,8 +68,17 @@ class GFFInterval(GenomicInterval):
         self.attributes = parse_gff_attributes(fields[8])
 
     def copy(self):
-        return GFFInterval(self.reader, list(self.fields), self.chrom_col, self.feature_col, self.start_col,
-                           self.end_col, self.strand_col, self.score_col, self.strand)
+        return GFFInterval(
+            self.reader,
+            list(self.fields),
+            self.chrom_col,
+            self.feature_col,
+            self.start_col,
+            self.end_col,
+            self.strand_col,
+            self.score_col,
+            self.strand,
+        )
 
 
 class GFFFeature(GFFInterval):
@@ -56,22 +86,42 @@ class GFFFeature(GFFInterval):
     A GFF feature, which can include multiple intervals.
     """
 
-    def __init__(self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4,
-                 strand_col=6, score_col=5, default_strand='.', fix_strand=False, intervals=None,
-                 raw_size=0):
+    def __init__(
+        self,
+        reader,
+        chrom_col=0,
+        feature_col=2,
+        start_col=3,
+        end_col=4,
+        strand_col=6,
+        score_col=5,
+        default_strand=".",
+        fix_strand=False,
+        intervals=None,
+        raw_size=0,
+    ):
         # Use copy so that first interval and feature do not share fields.
         intervals = intervals or []
-        GFFInterval.__init__(self, reader, copy.deepcopy(intervals[0].fields), chrom_col, feature_col,
-                             start_col, end_col, strand_col, score_col, default_strand,
-                             fix_strand=fix_strand)
+        GFFInterval.__init__(
+            self,
+            reader,
+            copy.deepcopy(intervals[0].fields),
+            chrom_col,
+            feature_col,
+            start_col,
+            end_col,
+            strand_col,
+            score_col,
+            default_strand,
+            fix_strand=fix_strand,
+        )
         self.intervals = intervals
         self.raw_size = raw_size
         # Use intervals to set feature attributes.
         for interval in self.intervals:
             # Error checking. NOTE: intervals need not share the same strand.
             if interval.chrom != self.chrom:
-                raise ValueError("interval chrom does not match self chrom: %s != %s" %
-                                 (interval.chrom, self.chrom))
+                raise ValueError("interval chrom does not match self chrom: %s != %s" % (interval.chrom, self.chrom))
             # Set start, end of interval.
             if interval.start < self.start:
                 self.start = interval.start
@@ -79,16 +129,19 @@ class GFFFeature(GFFInterval):
                 self.end = interval.end
 
     def name(self):
-        """ Returns feature's name. """
+        """Returns feature's name."""
         name = None
         # Preference for name: GTF, GFF3, GFF.
         for attr_name in [
-                # GTF:
-                'gene_id', 'transcript_id',
-                # GFF3:
-                'ID', 'id',
-                # GFF (TODO):
-                'group']:
+            # GTF:
+            "gene_id",
+            "transcript_id",
+            # GFF3:
+            "ID",
+            "id",
+            # GFF (TODO):
+            "group",
+        ]:
             name = self.attributes.get(attr_name, None)
             if name is not None:
                 break
@@ -98,13 +151,22 @@ class GFFFeature(GFFInterval):
         intervals_copy = []
         for interval in self.intervals:
             intervals_copy.append(interval.copy())
-        return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col, self.strand_col,
-                          self.score_col, self.strand, intervals=intervals_copy)
+        return GFFFeature(
+            self.reader,
+            self.chrom_col,
+            self.feature_col,
+            self.start_col,
+            self.end_col,
+            self.strand_col,
+            self.score_col,
+            self.strand,
+            intervals=intervals_copy,
+        )
 
     def lines(self):
         lines = []
         for interval in self.intervals:
-            lines.append('\t'.join(interval.fields))
+            lines.append("\t".join(interval.fields))
         return lines
 
 
@@ -117,9 +179,16 @@ class GFFIntervalToBEDReaderWrapper(NiceReaderWrapper):
     def parse_row(self, line):
         # HACK: this should return a GFF interval, but bx-python operations
         # require GenomicInterval objects and subclasses will not work.
-        interval = GenomicInterval(self, line.split("\t"), self.chrom_col, self.start_col,
-                                   self.end_col, self.strand_col, self.default_strand,
-                                   fix_strand=self.fix_strand)
+        interval = GenomicInterval(
+            self,
+            line.split("\t"),
+            self.chrom_col,
+            self.start_col,
+            self.end_col,
+            self.strand_col,
+            self.default_strand,
+            fix_strand=self.fix_strand,
+        )
         interval = convert_gff_coords_to_bed(interval)
         return interval
 
@@ -138,10 +207,29 @@ class GFFReaderWrapper(NiceReaderWrapper):
        expect traditional interval format.
     """
 
-    def __init__(self, reader, chrom_col=0, feature_col=2, start_col=3,
-                 end_col=4, strand_col=6, score_col=5, fix_strand=False, convert_to_bed_coord=False, **kwargs):
-        NiceReaderWrapper.__init__(self, reader, chrom_col=chrom_col, start_col=start_col, end_col=end_col,
-                                   strand_col=strand_col, fix_strand=fix_strand, **kwargs)
+    def __init__(
+        self,
+        reader,
+        chrom_col=0,
+        feature_col=2,
+        start_col=3,
+        end_col=4,
+        strand_col=6,
+        score_col=5,
+        fix_strand=False,
+        convert_to_bed_coord=False,
+        **kwargs,
+    ):
+        NiceReaderWrapper.__init__(
+            self,
+            reader,
+            chrom_col=chrom_col,
+            start_col=start_col,
+            end_col=end_col,
+            strand_col=strand_col,
+            fix_strand=fix_strand,
+            **kwargs,
+        )
         self.feature_col = feature_col
         self.score_col = score_col
         self.convert_to_bed_coord = convert_to_bed_coord
@@ -152,20 +240,29 @@ class GFFReaderWrapper(NiceReaderWrapper):
         self.__end_of_intervals = False
 
     def parse_row(self, line):
-        interval = GFFInterval(self, line.split("\t"), self.chrom_col, self.feature_col,
-                               self.start_col, self.end_col, self.strand_col, self.score_col,
-                               self.default_strand, fix_strand=self.fix_strand)
+        interval = GFFInterval(
+            self,
+            line.split("\t"),
+            self.chrom_col,
+            self.feature_col,
+            self.start_col,
+            self.end_col,
+            self.strand_col,
+            self.score_col,
+            self.default_strand,
+            fix_strand=self.fix_strand,
+        )
         return interval
 
     def __next__(self):
-        """ Returns next GFFFeature. """
+        """Returns next GFFFeature."""
 
         #
         # Helper function.
         #
 
         def handle_parse_error(e):
-            """ Actions to take when ParseError found. """
+            """Actions to take when ParseError found."""
             if self.outstream:
                 if self.print_delegate and callable(self.print_delegate):
                     self.print_delegate(self.outstream, e, self)
@@ -207,11 +304,11 @@ class GFFReaderWrapper(NiceReaderWrapper):
             return return_val
 
         # Initialize feature identifier from seed.
-        feature_group = self.seed_interval.attributes.get('group', None)  # For GFF
+        feature_group = self.seed_interval.attributes.get("group", None)  # For GFF
         # For GFF3
-        feature_id = self.seed_interval.attributes.get('ID', None)
+        feature_id = self.seed_interval.attributes.get("ID", None)
         # For GTF.
-        feature_transcript_id = self.seed_interval.attributes.get('transcript_id', None)
+        feature_transcript_id = self.seed_interval.attributes.get("transcript_id", None)
 
         # Read all intervals associated with seed.
         feature_intervals = []
@@ -239,17 +336,17 @@ class GFFReaderWrapper(NiceReaderWrapper):
 
             # Determine if interval is part of feature.
             part_of = False
-            group = interval.attributes.get('group', None)
+            group = interval.attributes.get("group", None)
             # GFF test:
             if group and feature_group == group:
                 part_of = True
             # GFF3 test:
-            parent_id = interval.attributes.get('Parent', None)
-            cur_id = interval.attributes.get('ID', None)
+            parent_id = interval.attributes.get("Parent", None)
+            cur_id = interval.attributes.get("ID", None)
             if (cur_id and cur_id == feature_id) or (parent_id and parent_id == feature_id):
                 part_of = True
             # GTF test:
-            transcript_id = interval.attributes.get('transcript_id', None)
+            transcript_id = interval.attributes.get("transcript_id", None)
             if transcript_id and transcript_id == feature_transcript_id:
                 part_of = True
 
@@ -267,10 +364,19 @@ class GFFReaderWrapper(NiceReaderWrapper):
         self.seed_interval_line_len = len(self.current_line)
 
         # Return feature.
-        feature = GFFFeature(self, self.chrom_col, self.feature_col, self.start_col,
-                             self.end_col, self.strand_col, self.score_col,
-                             self.default_strand, fix_strand=self.fix_strand,
-                             intervals=feature_intervals, raw_size=raw_size)
+        feature = GFFFeature(
+            self,
+            self.chrom_col,
+            self.feature_col,
+            self.start_col,
+            self.end_col,
+            self.strand_col,
+            self.score_col,
+            self.default_strand,
+            fix_strand=self.fix_strand,
+            intervals=feature_intervals,
+            raw_size=raw_size,
+        )
 
         # Convert to BED coords?
         if self.convert_to_bed_coord:
@@ -335,23 +441,23 @@ def parse_gff_attributes(attr_str):
         # attribute; next, try double quotes for GTF.
         pair = name_value_pair.strip().split("=")
         if len(pair) == 1:
-            pair = name_value_pair.strip().split("\"")
+            pair = name_value_pair.strip().split('"')
         if len(pair) == 1:
             # Could not split for some reason -- raise exception?
             continue
-        if pair == '':
+        if pair == "":
             continue
         name = pair[0].strip()
-        if name == '':
+        if name == "":
             continue
         # Need to strip double quote from values
-        value = pair[1].strip(" \"")
+        value = pair[1].strip(' "')
         attributes[name] = value
 
     if len(attributes) == 0:
         # Could not split attributes string, so entire string must be
         # 'group' attribute. This is the case for strictly GFF files.
-        attributes['group'] = attr_str
+        attributes["group"] = attr_str
     return attributes
 
 
@@ -366,15 +472,15 @@ def parse_gff3_attributes(attr_str):
     attributes = {}
     for tag_value_pair in attributes_list:
         tag_value_pair = tag_value_pair.strip()
-        if tag_value_pair == '':
+        if tag_value_pair == "":
             continue
         pair = tag_value_pair.split("=")
         if len(pair) == 1:
             raise Exception(f"Attribute '{tag_value_pair}' does not contain a '='")
-        if pair == '':
+        if pair == "":
             continue
         tag = pair[0].strip()
-        if tag == '':
+        if tag == "":
             raise Exception(f"Empty tag in attribute '{tag_value_pair}'")
         value = pair[1].strip()
         attributes[tag] = value
@@ -385,20 +491,20 @@ def gff_attributes_to_str(attrs, gff_format):
     """
     Convert GFF attributes to string. Supported formats are GFF3, GTF.
     """
-    if gff_format == 'GTF':
+    if gff_format == "GTF":
         format_string = '%s "%s"'
         # Convert group (GFF) and ID, parent (GFF3) attributes to transcript_id, gene_id
         id_attr = None
-        if 'group' in attrs:
-            id_attr = 'group'
-        elif 'ID' in attrs:
-            id_attr = 'ID'
-        elif 'Parent' in attrs:
-            id_attr = 'Parent'
+        if "group" in attrs:
+            id_attr = "group"
+        elif "ID" in attrs:
+            id_attr = "ID"
+        elif "Parent" in attrs:
+            id_attr = "Parent"
         if id_attr:
-            attrs['transcript_id'] = attrs['gene_id'] = attrs[id_attr]
-    elif gff_format == 'GFF3':
-        format_string = '%s=%s'
+            attrs["transcript_id"] = attrs["gene_id"] = attrs[id_attr]
+    elif gff_format == "GFF3":
+        format_string = "%s=%s"
     attrs_strs = []
     for name, value in attrs.items():
         attrs_strs.append(format_string % (name, value))
@@ -414,7 +520,8 @@ def read_unordered_gtf(iterator, strict=False):
 
     # -- Get function that generates line/feature key. --
     def get_transcript_id(fields):
-        return parse_gff_attributes(fields[8])['transcript_id']
+        return parse_gff_attributes(fields[8])["transcript_id"]
+
     if strict:
         # Strict GTF parsing uses transcript_id only to group lines into feature.
         key_fn = get_transcript_id
@@ -429,17 +536,17 @@ def read_unordered_gtf(iterator, strict=False):
     feature_intervals = {}
     comments = []
     for line in iterator:
-        if line.startswith('#'):
+        if line.startswith("#"):
             comments.append(Comment(line))
             continue
 
-        line_key = key_fn(line.split('\t'))
+        line_key = key_fn(line.split("\t"))
         if line_key in feature_intervals:
             feature = feature_intervals[line_key]
         else:
             feature = []
             feature_intervals[line_key] = feature
-        feature.append(GFFInterval(None, line.split('\t')))
+        feature.append(GFFInterval(None, line.split("\t")))
 
     # Create features.
     chroms_features = {}
diff --git a/lib/galaxy/datatypes/util/maf_utilities.py b/lib/galaxy/datatypes/util/maf_utilities.py
index 28fda0fd885..8d8c9efecd4 100644
--- a/lib/galaxy/datatypes/util/maf_utilities.py
+++ b/lib/galaxy/datatypes/util/maf_utilities.py
@@ -21,8 +21,8 @@ maketrans = str.maketrans
 
 log = logging.getLogger(__name__)
 
-GAP_CHARS = ['-']
-SRC_SPLIT_CHAR = '.'
+GAP_CHARS = ["-"]
+SRC_SPLIT_CHAR = "."
 
 
 def src_split(src):
@@ -55,10 +55,10 @@ def tool_fail(msg="Unknown Error"):
 
 
 class TempFileHandler:
-    '''
+    """
     Handles creating, opening, closing, and deleting of Temp files, with a
     maximum number of files open at one time.
-    '''
+    """
 
     DEFAULT_MAX_OPEN_FILES = max(resource.getrlimit(resource.RLIMIT_NOFILE)[0] / 2, 1)
 
@@ -80,7 +80,7 @@ class TempFileHandler:
             if index is None:
                 index = len(self.files)
                 temp_kwds = dict(self.kwds)
-                temp_kwds['delete'] = False
+                temp_kwds["delete"] = False
                 temp_kwds.update(kwds)
                 # Being able to use delete=True here, would simplify a bit,
                 # but we support python2.4 in these tools
@@ -96,11 +96,11 @@ class TempFileHandler:
                         else:
                             raise e
                 tmp_file.close()
-                self.files.append(open(filename, 'r+'))
+                self.files.append(open(filename, "r+"))
             else:
                 while True:
                     try:
-                        self.files[index] = open(self.files[index].name, 'r+')
+                        self.files[index] = open(self.files[index].name, "r+")
                         break
                     except OSError as e:
                         if self.open_file_indexes and e.errno == EMFILE:
@@ -139,7 +139,12 @@ class RegionAlignment:
     MAX_SEQUENCE_SIZE = sys.maxsize  # Maximum length of sequence allowed
 
     def __init__(self, size, species=None, temp_file_handler=None):
-        assert size <= self.MAX_SEQUENCE_SIZE, "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % (size, self.MAX_SEQUENCE_SIZE)
+        assert (
+            size <= self.MAX_SEQUENCE_SIZE
+        ), "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % (
+            size,
+            self.MAX_SEQUENCE_SIZE,
+        )
         species = species or []
         self.size = size
         if not temp_file_handler:
@@ -188,6 +193,7 @@ class RegionAlignment:
         if len(base) != 1:
             raise Exception("A genomic position can only have a length of 1.")
         return self.set_range(index, species, base)
+
     # sets a range for a species
 
     def set_range(self, index, species, bases):
@@ -212,7 +218,6 @@ class RegionAlignment:
 
 
 class GenomicRegionAlignment(RegionAlignment):
-
     def __init__(self, start, end, species=None, temp_file_handler=None):
         species = species or []
         RegionAlignment.__init__(self, end - start, species, temp_file_handler=temp_file_handler)
@@ -236,7 +241,9 @@ class SplicedAlignment:
             temp_file_handler = TempFileHandler()
         self.temp_file_handler = temp_file_handler
         for i in range(len(exon_starts)):
-            self.exons.append(GenomicRegionAlignment(exon_starts[i], exon_ends[i], species, temp_file_handler=temp_file_handler))
+            self.exons.append(
+                GenomicRegionAlignment(exon_starts[i], exon_ends[i], species, temp_file_handler=temp_file_handler)
+            )
 
     # returns the names for species found in alignment, skipping names as requested
     def get_species_names(self, skip=None):
@@ -290,13 +297,13 @@ def maf_index_by_uid(maf_uid, index_location_file):
             # read each line, if not enough fields, go to next line
             if line[0:1] == "#":
                 continue
-            fields = line.split('\t')
+            fields = line.split("\t")
             if maf_uid == fields[1]:
                 try:
                     maf_files = fields[4].replace("\n", "").replace("\r", "").split(",")
                     return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False)
                 except Exception as e:
-                    raise Exception(f'MAF UID ({maf_uid}) found, but configuration appears to be malformed: {e}')
+                    raise Exception(f"MAF UID ({maf_uid}) found, but configuration appears to be malformed: {e}")
         except Exception:
             pass
     return None
@@ -348,7 +355,7 @@ def build_maf_index_species_chromosomes(filename, index_species=None):
                         indexes.add(c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size)
     except Exception as e:
         # most likely a bad MAF
-        log.debug(f'Building MAF index on {filename} failed: {e}')
+        log.debug(f"Building MAF index on {filename} failed: {e}")
         return (None, [], {}, 0)
     return (indexes, species, species_chromosomes, blocks)
 
@@ -357,9 +364,12 @@ def build_maf_index_species_chromosomes(filename, index_species=None):
 def build_maf_index(maf_file, species=None):
     indexes, *_ = build_maf_index_species_chromosomes(maf_file, species)
     if indexes is not None:
-        with tempfile.NamedTemporaryFile(mode='w', delete=False) as index:
+        with tempfile.NamedTemporaryFile(mode="w", delete=False) as index:
             indexes.write(index)
-        return (bx.align.maf.Indexed(maf_file, index_filename=index.name, keep_open=True, parse_e_rows=False), index.name)
+        return (
+            bx.align.maf.Indexed(maf_file, index_filename=index.name, keep_open=True, parse_e_rows=False),
+            index.name,
+        )
     return (None, None)
 
 
@@ -420,17 +430,25 @@ def orient_block_by_region(block, src, region, force_strand=None):
     # if force_strand / region.strand not in strand cache, reverse complement
     # we could have 2 sequences with same src, overlapping region, on different strands, this would cause no reverse_complementing
     strands = [c.strand for c in iter_components_by_src(block, src) if component_overlaps_region(c, region)]
-    if strands and (force_strand is None and region.strand not in strands) or (force_strand is not None and force_strand not in strands):
+    if (
+        strands
+        and (force_strand is None and region.strand not in strands)
+        or (force_strand is not None and force_strand not in strands)
+    ):
         block = block.reverse_complement()
     return block
 
 
 def get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None):
-    for block, _, _ in get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols, force_strand):
+    for block, _, _ in get_oriented_chopped_blocks_with_index_offset_for_region(
+        index, src, region, species, mincols, force_strand
+    ):
         yield block
 
 
-def get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0, force_strand=None):
+def get_oriented_chopped_blocks_with_index_offset_for_region(
+    index, src, region, species=None, mincols=0, force_strand=None
+):
     for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols):
         yield orient_block_by_region(block, src, region, force_strand), idx, offset
 
@@ -442,7 +460,9 @@ def iter_blocks_split_by_src(block, src):
         new_block.text_size = block.text_size
         for c in block.components:
             if c == src_c or c.src != src:
-                new_block.add_component(deepcopy(c))  # components have reference to alignment, don't want to lose reference to original alignment block in original components
+                new_block.add_component(
+                    deepcopy(c)
+                )  # components have reference to alignment, don't want to lose reference to original alignment block in original components
         yield new_block
 
 
@@ -477,7 +497,9 @@ def iter_blocks_split_by_species(block, species=None):
             for c in iter_components_by_src_start(block, spec):
                 spec_dict[spec].append(c)
 
-    empty_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes))  # should we copy attributes?
+    empty_block = bx.align.Alignment(
+        score=block.score, attributes=deepcopy(block.attributes)
+    )  # should we copy attributes?
     empty_block.text_size = block.text_size
     # call recursive function to split into each combo of spec/blocks
     for value in __split_components_by_species(list(spec_dict.values()), empty_block):
@@ -499,12 +521,25 @@ def get_chopped_blocks_with_index_offset_for_region(index, src, region, species=
 
 
 # returns a filled region alignment for specified regions
-def get_region_alignment(index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None):
+def get_region_alignment(
+    index,
+    primary_species,
+    chrom,
+    start,
+    end,
+    strand="+",
+    species=None,
+    mincols=0,
+    overwrite_with_gaps=True,
+    temp_file_handler=None,
+):
     if species is not None:
         alignment = RegionAlignment(end - start, species, temp_file_handler=temp_file_handler)
     else:
         alignment = RegionAlignment(end - start, primary_species, temp_file_handler=temp_file_handler)
-    return fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps)
+    return fill_region_alignment(
+        alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps
+    )
 
 
 # reduces a block to only positions exisiting in the src provided
@@ -516,19 +551,21 @@ def reduce_block_by_primary_genome(block, species, chromosome, region_start):
     start_offset = ref.start - region_start
     species_texts = {}
     for c in block.components:
-        species_texts[c.src.split('.')[0]] = list(c.text)
+        species_texts[c.src.split(".")[0]] = list(c.text)
     # remove locations which are gaps in the primary species, starting from the downstream end
     for i in range(len(species_texts[species]) - 1, -1, -1):
-        if species_texts[species][i] == '-':
+        if species_texts[species][i] == "-":
             for text in species_texts.values():
                 text.pop(i)
     for spec, text in species_texts.items():
-        species_texts[spec] = ''.join(text)
+        species_texts[spec] = "".join(text)
     return (start_offset, species_texts)
 
 
 # fills a region alignment
-def fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True):
+def fill_region_alignment(
+    alignment, index, primary_species, chrom, start, end, strand="+", species=None, mincols=0, overwrite_with_gaps=True
+):
     region = bx.intervals.Interval(start, end)
     region.chrom = chrom
     region.strand = strand
@@ -546,10 +583,12 @@ def fill_region_alignment(alignment, index, primary_species, chrom, start, end,
             blocks.append((score, idx, offset))
 
     # gap_chars_tuple = tuple( GAP_CHARS )
-    gap_chars_str = ''.join(GAP_CHARS)
+    gap_chars_str = "".join(GAP_CHARS)
     # Loop through ordered blocks and layer by increasing score
     for block_dict in blocks:
-        for block in iter_blocks_split_by_species(block_dict[1].get_at_offset(block_dict[2])):  # need to handle each occurance of sequence in block seperately
+        for block in iter_blocks_split_by_species(
+            block_dict[1].get_at_offset(block_dict[2])
+        ):  # need to handle each occurance of sequence in block seperately
             if component_overlaps_region(block.get_component_by_src(primary_src), region):
                 block = chop_block_by_region(block, primary_src, region, species, mincols)  # chop block
                 block = orient_block_by_region(block, primary_src, region)  # orient block
@@ -559,7 +598,9 @@ def fill_region_alignment(alignment, index, primary_species, chrom, start, end,
                     text = text.rstrip(gap_chars_str)
                     gap_offset = 0
                     # while text.startswith( gap_chars_tuple ):
-                    while True in [text.startswith(gap_char) for gap_char in GAP_CHARS]:  # python2.4 doesn't accept a tuple for .startswith()
+                    while True in [
+                        text.startswith(gap_char) for gap_char in GAP_CHARS
+                    ]:  # python2.4 doesn't accept a tuple for .startswith()
                         gap_offset += 1
                         text = text[1:]
                         if not text:
@@ -575,19 +616,32 @@ def fill_region_alignment(alignment, index, primary_species, chrom, start, end,
 
 
 # returns a filled spliced region alignment for specified region with start and end lists
-def get_spliced_region_alignment(index, primary_species, chrom, starts, ends, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None):
+def get_spliced_region_alignment(
+    index,
+    primary_species,
+    chrom,
+    starts,
+    ends,
+    strand="+",
+    species=None,
+    mincols=0,
+    overwrite_with_gaps=True,
+    temp_file_handler=None,
+):
     # create spliced alignment object
     if species is not None:
         alignment = SplicedAlignment(starts, ends, species, temp_file_handler=temp_file_handler)
     else:
         alignment = SplicedAlignment(starts, ends, [primary_species], temp_file_handler=temp_file_handler)
     for exon in alignment.exons:
-        fill_region_alignment(exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps)
+        fill_region_alignment(
+            exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps
+        )
     return alignment
 
 
 # loop through string array, only return non-commented lines
-def line_enumerator(lines, comment_start='#'):
+def line_enumerator(lines, comment_start="#"):
     i = 0
     for line in lines:
         if not line.startswith(comment_start):
@@ -607,16 +661,16 @@ def get_starts_ends_fields_from_gene_bed(line):
         raise Exception(f"Not a proper 12 column BED line ({line}).")
     tx_start = int(fields[1])
     strand = fields[5]
-    if strand != '-':
-        strand = '+'  # Default strand is +
+    if strand != "-":
+        strand = "+"  # Default strand is +
     cds_start = int(fields[6])
     cds_end = int(fields[7])
 
     # Calculate and store starts and ends of coding exons
     region_start, region_end = cds_start, cds_end
-    exon_starts = list(map(int, fields[11].rstrip(',\n').split(',')))
+    exon_starts = list(map(int, fields[11].rstrip(",\n").split(",")))
     exon_starts = [x + tx_start for x in exon_starts]
-    exon_ends = list(map(int, fields[10].rstrip(',').split(',')))
+    exon_ends = list(map(int, fields[10].rstrip(",").split(",")))
     exon_ends = [x + y for x, y in zip(exon_starts, exon_ends)]
     for start, end in zip(exon_starts, exon_ends):
         start = max(start, region_start)
@@ -651,7 +705,9 @@ def sort_block_components_by_block(block1, block2):
     # orders the components in block1 by the index of the component in block2
     # block1 must be a subset of block2
     # occurs in-place
-    return block1.components.sort(key=functools.cmp_to_key(lambda x, y: block2.components.index(x) - block2.components.index(y)))
+    return block1.components.sort(
+        key=functools.cmp_to_key(lambda x, y: block2.components.index(x) - block2.components.index(y))
+    )
 
 
 def get_species_in_maf(maf_filename):
@@ -665,8 +721,8 @@ def get_species_in_maf(maf_filename):
 
 def parse_species_option(species):
     if species:
-        species = species.split(',')
-        if 'None' not in species:
+        species = species.split(",")
+        if "None" not in species:
             return species
     return None  # provided species was '', None, or had 'None' in it
 
@@ -677,12 +733,18 @@ def remove_temp_index_file(index_filename):
     except Exception:
         pass
 
+
 # Below are methods to deal with FASTA files
 
 
 def get_fasta_header(component, attributes=None, suffix=None):
     attributes = attributes or {}
-    header = ">%s(%s):%i-%i|" % (component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end())
+    header = ">%s(%s):%i-%i|" % (
+        component.src,
+        component.strand,
+        component.get_forward_strand_start(),
+        component.get_forward_strand_end(),
+    )
     for key, value in attributes.items():
         header = f"{header}{key}={value}|"
     if suffix:
@@ -696,33 +758,33 @@ def get_attributes_from_fasta_header(header):
     if not header:
         return {}
     attributes = {}
-    header = header.lstrip('>')
+    header = header.lstrip(">")
     header = header.strip()
-    fields = header.split('|')
+    fields = header.split("|")
     try:
         region = fields[0]
-        region = region.split('(', 1)
-        temp = region[0].split('.', 1)
-        attributes['species'] = temp[0]
+        region = region.split("(", 1)
+        temp = region[0].split(".", 1)
+        attributes["species"] = temp[0]
         if len(temp) == 2:
-            attributes['chrom'] = temp[1]
+            attributes["chrom"] = temp[1]
         else:
-            attributes['chrom'] = temp[0]
-        region = region[1].split(')', 1)
-        attributes['strand'] = region[0]
-        region = region[1].lstrip(':').split('-')
-        attributes['start'] = int(region[0])
-        attributes['end'] = int(region[1])
+            attributes["chrom"] = temp[0]
+        region = region[1].split(")", 1)
+        attributes["strand"] = region[0]
+        region = region[1].lstrip(":").split("-")
+        attributes["start"] = int(region[0])
+        attributes["end"] = int(region[1])
     except Exception:
         # fields 0 is not a region coordinate
         pass
     if len(fields) > 2:
         for i in range(1, len(fields) - 1):
-            prop = fields[i].split('=', 1)
+            prop = fields[i].split("=", 1)
             if len(prop) == 2:
                 attributes[prop[0]] = prop[1]
     if len(fields) > 1:
-        attributes['__suffix__'] = fields[-1]
+        attributes["__suffix__"] = fields[-1]
     return attributes
 
 
@@ -733,9 +795,10 @@ def iter_fasta_alignment(filename):
             self.text = text
 
         def extend(self, text):
-            self.text = self.text + text.replace('\n', '').replace('\r', '').strip()
+            self.text = self.text + text.replace("\n", "").replace("\r", "").strip()
+
     # yields a list of fastaComponents for a FASTA file
-    f = open(filename, 'rb')
+    f = open(filename, "rb")
     components = []
     # cur_component = None
     while True:
@@ -749,8 +812,8 @@ def iter_fasta_alignment(filename):
             if components:
                 yield components
             components = []
-        elif line.startswith('>'):
+        elif line.startswith(">"):
             attributes = get_attributes_from_fasta_header(line)
-            components.append(fastaComponent(attributes['species']))
+            components.append(fastaComponent(attributes["species"]))
         elif components:
             components[-1].extend(line)
diff --git a/lib/galaxy/datatypes/xml.py b/lib/galaxy/datatypes/xml.py
index e3a1dfd5e15..a975d8ba761 100644
--- a/lib/galaxy/datatypes/xml.py
+++ b/lib/galaxy/datatypes/xml.py
@@ -18,14 +18,15 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-OWL_MARKER = re.compile(r'\<owl:')
-SBML_MARKER = re.compile(r'\<sbml')
+OWL_MARKER = re.compile(r"\<owl:")
+SBML_MARKER = re.compile(r"\<sbml")
 
 
 @dataproviders.decorators.has_dataproviders
 @build_sniff_from_prefix
 class GenericXml(data.Text):
     """Base format class for any XML file."""
+
     edam_format = "format_2332"
     file_ext = "xml"
 
@@ -33,17 +34,17 @@ class GenericXml(data.Text):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'XML data'
+            dataset.blurb = "XML data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def _has_root_element_in_prefix(self, file_prefix: FilePrefix, root):
         for line in file_prefix.line_iterator():
-            if not line.startswith('<?'):
+            if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r'^<(\w*:)?%s' % root
+        pattern = r"^<(\w*:)?%s" % root
         return re.match(pattern, line) is not None
 
     def sniff_prefix(self, file_prefix: FilePrefix):
@@ -58,17 +59,19 @@ class GenericXml(data.Text):
         >>> GenericXml().sniff( fname )
         False
         """
-        return file_prefix.startswith('<?xml ')
+        return file_prefix.startswith("<?xml ")
 
     @staticmethod
     def merge(split_files, output_file):
         """Merging multiple XML files is non-trivial and must be done in subclasses."""
         if len(split_files) > 1:
-            raise NotImplementedError("Merging multiple XML files is non-trivial and must be implemented for each XML type")
+            raise NotImplementedError(
+                "Merging multiple XML files is non-trivial and must be implemented for each XML type"
+            )
         # For one file only, use base class method (move/copy)
         data.Text.merge(split_files, output_file)
 
-    @dataproviders.decorators.dataprovider_factory('xml', dataproviders.hierarchy.XMLDataProvider.settings)
+    @dataproviders.decorators.dataprovider_factory("xml", dataproviders.hierarchy.XMLDataProvider.settings)
     def xml_dataprovider(self, dataset, **settings):
         dataset_source = dataproviders.dataset.DatasetDataProvider(dataset)
         return dataproviders.hierarchy.XMLDataProvider(dataset_source, **settings)
@@ -77,31 +80,33 @@ class GenericXml(data.Text):
 @disable_parent_class_sniffing
 class MEMEXml(GenericXml):
     """MEME XML Output data"""
+
     file_ext = "memexml"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'MEME XML data'
+            dataset.blurb = "MEME XML data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 @disable_parent_class_sniffing
 class CisML(GenericXml):
     """CisML XML data"""  # see: http://www.ncbi.nlm.nih.gov/pubmed/15001475
+
     file_ext = "cisml"
 
     def set_peek(self, dataset):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'CisML data'
+            dataset.blurb = "CisML data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
 
 class Dzi(GenericXml):
@@ -111,18 +116,29 @@ class Dzi(GenericXml):
     """
 
     # General elements.
-    MetadataElement(name="base_name", desc="Base name for this dataset", default='DeepZoomImage', readonly=True, set_in_upload=True)
+    MetadataElement(
+        name="base_name", desc="Base name for this dataset", default="DeepZoomImage", readonly=True, set_in_upload=True
+    )
     MetadataElement(name="format", desc="File format of the tiles", default=None, readonly=True, visible=True)
     MetadataElement(name="tile_size", desc="Size of tiles", default=None, readonly=True, visible=True)
     # Collection elements.
-    MetadataElement(name="max_level", desc="Max pyramid level", default=None, readonly=True, optional=True, visible=True)
+    MetadataElement(
+        name="max_level", desc="Max pyramid level", default=None, readonly=True, optional=True, visible=True
+    )
     MetadataElement(name="quality", desc="Quality", default=None, readonly=True, optional=True, visible=True)
     # Image elements.
     MetadataElement(name="height", desc="Size height", default=None, readonly=True, optional=True, visible=True)
-    MetadataElement(name="overlap", desc="Overlap of all four sides of tiles", default=None, readonly=True, optional=True, visible=True)
+    MetadataElement(
+        name="overlap",
+        desc="Overlap of all four sides of tiles",
+        default=None,
+        readonly=True,
+        optional=True,
+        visible=True,
+    )
     MetadataElement(name="width", desc="Size width", default=None, readonly=True, optional=True, visible=True)
 
-    file_ext = 'dzi'
+    file_ext = "dzi"
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -130,31 +146,31 @@ class Dzi(GenericXml):
     def set_meta(self, dataset, **kwd):
         tree = util.parse_xml(dataset.file_name)
         root = tree.getroot()
-        dataset.metadata.format = root.get('Format')
-        dataset.metadata.tile_size = root.get('TileSize')
+        dataset.metadata.format = root.get("Format")
+        dataset.metadata.tile_size = root.get("TileSize")
         # DeepZoom image files can include
         # xml namespace attributes.
-        if root.tag.find('Collection') >= 0:
-            dataset.metadata.max_level = root.get('MaxLevel')
-            dataset.metadata.quality = root.get('Quality')
-        elif root.tag.find('Image') >= 0:
-            dataset.metadata.overlap = root.get('Overlap')
+        if root.tag.find("Collection") >= 0:
+            dataset.metadata.max_level = root.get("MaxLevel")
+            dataset.metadata.quality = root.get("Quality")
+        elif root.tag.find("Image") >= 0:
+            dataset.metadata.overlap = root.get("Overlap")
         for elem in root:
-            if elem.tag.find('Size') >= 0:
-                dataset.metadata.width = elem.get('Width')
-                dataset.metadata.height = elem.get('Height')
+            if elem.tag.find("Size") >= 0:
+                dataset.metadata.width = elem.get("Width")
+                dataset.metadata.height = elem.get("Height")
 
     def get_visualizations(self, dataset):
-        """ Returns a list of visualizations for datatype"""
-        return ['openseadragon']
+        """Returns a list of visualizations for datatype"""
+        return ["openseadragon"]
 
     def set_peek(self, dataset):
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
             dataset.blurb = "Deep Zoom Image"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
@@ -169,13 +185,14 @@ class Dzi(GenericXml):
         """
         for line in file_prefix.line_iterator():
             line = line.lower()
-            if line.find('<collection') >= 0 or line.find('<image') >= 0:
+            if line.find("<collection") >= 0 or line.find("<image") >= 0:
                 return True
         return False
 
 
 class Phyloxml(GenericXml):
     """Format for defining phyloxml data http://www.phyloxml.org/"""
+
     edam_data = "data_0872"
     edam_format = "format_3159"
     file_ext = "phyloxml"
@@ -184,13 +201,13 @@ class Phyloxml(GenericXml):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = data.get_file_peek(dataset.file_name)
-            dataset.blurb = 'Phyloxml data'
+            dataset.blurb = "Phyloxml data"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
-        """"Checking for keyword - 'phyloxml' always in lowercase in the first few lines.
+        """ "Checking for keyword - 'phyloxml' always in lowercase in the first few lines.
 
         >>> from galaxy.datatypes.sniff import get_test_fname
         >>> fname = get_test_fname( '1.phyloxml' )
@@ -210,14 +227,15 @@ class Phyloxml(GenericXml):
         Returns a list of visualizations for datatype.
         """
 
-        return ['phyloviz']
+        return ["phyloviz"]
 
 
 class Owl(GenericXml):
     """
-        Web Ontology Language OWL format description
-        http://www.w3.org/TR/owl-ref/
+    Web Ontology Language OWL format description
+    http://www.w3.org/TR/owl-ref/
     """
+
     edam_format = "format_3262"
     file_ext = "owl"
 
@@ -226,21 +244,22 @@ class Owl(GenericXml):
             dataset.peek = data.get_file_peek(dataset.file_name)
             dataset.blurb = "Web Ontology Language OWL"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Checking for keyword - '<owl' in the first 200 lines.
+        Checking for keyword - '<owl' in the first 200 lines.
         """
         return file_prefix.search(OWL_MARKER)
 
 
 class Sbml(GenericXml):
     """
-        System Biology Markup Language
-        http://sbml.org
+    System Biology Markup Language
+    http://sbml.org
     """
+
     file_ext = "sbml"
     edam_data = "data_2024"
     edam_format = "format_2585"
@@ -250,11 +269,11 @@ class Sbml(GenericXml):
             dataset.peek = data.get_file_peek(dataset.file_name)
             dataset.blurb = "System Biology Markup Language SBML"
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
-            Checking for keyword - '<sbml' in the first 200 lines.
+        Checking for keyword - '<sbml' in the first 200 lines.
         """
         return file_prefix.search(SBML_MARKER)
diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 8f98f0075a6..26d4eaa2faf 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -4,7 +4,11 @@ Determine what optional dependencies are needed.
 
 import os
 import sys
-from os.path import dirname, exists, join
+from os.path import (
+    dirname,
+    exists,
+    join,
+)
 
 import pkg_resources
 import yaml
@@ -18,7 +22,7 @@ from galaxy.util import (
 )
 from galaxy.util.properties import (
     find_config_file,
-    load_app_properties
+    load_app_properties,
 )
 
 
@@ -42,7 +46,6 @@ class ConditionalDependencies:
         self.get_conditional_requirements()
 
     def parse_configs(self):
-
         def load_job_config_dict(job_conf_dict):
             runners = job_conf_dict.get("runners", {})
             for runner in runners.values():
@@ -54,15 +57,13 @@ class ConditionalDependencies:
         if "job_config" in self.config:
             load_job_config_dict(self.config.get("job_config"))
         else:
-            job_conf_path = self.config.get(
-                "job_config_file",
-                join(dirname(self.config_file), 'job_conf.xml'))
-            if '.xml' in job_conf_path:
+            job_conf_path = self.config.get("job_config_file", join(dirname(self.config_file), "job_conf.xml"))
+            if ".xml" in job_conf_path:
                 try:
                     try:
-                        for plugin in parse_xml(job_conf_path).find('plugins').findall('plugin'):
-                            if 'load' in plugin.attrib:
-                                self.job_runners.append(plugin.attrib['load'])
+                        for plugin in parse_xml(job_conf_path).find("plugins").findall("plugin"):
+                            if "load" in plugin.attrib:
+                                self.job_runners.append(plugin.attrib["load"])
                     except OSError:
                         pass
                     try:
@@ -81,13 +82,13 @@ class ConditionalDependencies:
                     pass
 
         object_store_conf_path = self.config.get(
-            "object_store_config_file",
-            join(dirname(self.config_file), 'object_store_conf.xml'))
+            "object_store_config_file", join(dirname(self.config_file), "object_store_conf.xml")
+        )
         try:
-            if '.xml' in object_store_conf_path:
-                for store in parse_xml(object_store_conf_path).iter('object_store'):
-                    if 'type' in store.attrib:
-                        self.object_stores.append(store.attrib['type'])
+            if ".xml" in object_store_conf_path:
+                for store in parse_xml(object_store_conf_path).iter("object_store"):
+                    if "type" in store.attrib:
+                        self.object_stores.append(store.attrib["type"])
             else:
                 with open(object_store_conf_path) as f:
                     job_conf_dict = yaml.safe_load(f)
@@ -96,8 +97,8 @@ class ConditionalDependencies:
                     if not isinstance(from_dict, dict):
                         return
 
-                    if 'type' in from_dict:
-                        self.object_stores.append(from_dict['type'])
+                    if "type" in from_dict:
+                        self.object_stores.append(from_dict["type"])
 
                     for value in from_dict.values():
                         if isinstance(value, list):
@@ -112,12 +113,10 @@ class ConditionalDependencies:
             pass
 
         # Parse auth conf
-        auth_conf_xml = self.config.get(
-            "auth_config_file",
-            join(dirname(self.config_file), 'auth_conf.xml'))
+        auth_conf_xml = self.config.get("auth_config_file", join(dirname(self.config_file), "auth_conf.xml"))
         try:
-            for auth in parse_xml(auth_conf_xml).findall('authenticator'):
-                auth_type = auth.find('type')
+            for auth in parse_xml(auth_conf_xml).findall("authenticator"):
+                auth_type = auth.find("type")
                 if auth_type is not None:
                     self.authenticators.append(auth_type.text)
         except OSError:
@@ -125,52 +124,48 @@ class ConditionalDependencies:
 
         # Parse containers config
         containers_conf_yml = self.config.get(
-            "containers_config_file",
-            join(dirname(self.config_file), 'containers_conf.yml'))
+            "containers_config_file", join(dirname(self.config_file), "containers_conf.yml")
+        )
         containers_conf = parse_containers_config(containers_conf_yml)
-        self.container_interface_types = [c.get('type', None) for c in containers_conf.values()]
+        self.container_interface_types = [c.get("type", None) for c in containers_conf.values()]
 
         # Parse error report config
-        error_report_yml = self.config.get(
-            "error_report_file",
-            join(dirname(self.config_file), 'error_report.yml'))
+        error_report_yml = self.config.get("error_report_file", join(dirname(self.config_file), "error_report.yml"))
         try:
             with open(error_report_yml) as f:
                 error_reporters = yaml.safe_load(f)
-                self.error_report_modules = [er.get('type', None) for er in error_reporters]
+                self.error_report_modules = [er.get("type", None) for er in error_reporters]
         except OSError:
             pass
 
         # Parse file sources config
         file_sources_conf_yml = self.config.get(
-            "file_sources_config_file",
-            join(dirname(self.config_file), 'file_sources_conf.yml'))
+            "file_sources_config_file", join(dirname(self.config_file), "file_sources_conf.yml")
+        )
         if exists(file_sources_conf_yml):
             with open(file_sources_conf_yml) as f:
                 file_sources_conf = yaml.safe_load(f)
         else:
             file_sources_conf = []
-        self.file_sources = [c.get('type', None) for c in file_sources_conf]
+        self.file_sources = [c.get("type", None) for c in file_sources_conf]
 
         # Parse vault config
-        vault_conf_yml = self.config.get(
-            "vault_config_file",
-            join(dirname(self.config_file), 'vault_conf.yml'))
+        vault_conf_yml = self.config.get("vault_config_file", join(dirname(self.config_file), "vault_conf.yml"))
         if exists(vault_conf_yml):
             with open(vault_conf_yml) as f:
                 vault_conf = yaml.safe_load(f)
         else:
             vault_conf = {}
-        self.vault_type = vault_conf.get('type', '').lower()
+        self.vault_type = vault_conf.get("type", "").lower()
 
     def get_conditional_requirements(self):
-        crfile = join(dirname(__file__), 'conditional-requirements.txt')
+        crfile = join(dirname(__file__), "conditional-requirements.txt")
         for req in pkg_resources.parse_requirements(open(crfile).readlines()):
             self.conditional_reqs.append(req)
 
     def check(self, name):
         try:
-            name = name.replace('-', '_').replace('.', '_')
+            name = name.replace("-", "_").replace(".", "_")
             return getattr(self, f"check_{name}")()
         except Exception:
             return False
@@ -182,18 +177,20 @@ class ConditionalDependencies:
         return self.config["database_connection"].startswith("mysql")
 
     def check_drmaa(self):
-        return ("galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners
-                or "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners
-                or "galaxy.jobs.runners.univa:UnivaJobRunner" in self.job_runners)
+        return (
+            "galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners
+            or "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners
+            or "galaxy.jobs.runners.univa:UnivaJobRunner" in self.job_runners
+        )
 
     def check_galaxycloudrunner(self):
-        return ("galaxycloudrunner.rules" in self.job_rule_modules)
+        return "galaxycloudrunner.rules" in self.job_rule_modules
 
     def check_pbs_python(self):
         return "galaxy.jobs.runners.pbs:PBSJobRunner" in self.job_runners
 
     def check_pykube(self):
-        return "galaxy.jobs.runners.kubernetes:KubernetesJobRunner" in self.job_runners or which('kubectl')
+        return "galaxy.jobs.runners.kubernetes:KubernetesJobRunner" in self.job_runners or which("kubectl")
 
     def check_chronos_python(self):
         return "galaxy.jobs.runners.chronos:ChronosJobRunner" in self.job_runners
@@ -208,72 +205,70 @@ class ConditionalDependencies:
         return self.config.get("statsd_host", None) is not None
 
     def check_python_ldap(self):
-        return ('ldap' in self.authenticators
-                or 'activedirectory' in self.authenticators)
+        return "ldap" in self.authenticators or "activedirectory" in self.authenticators
 
     def check_python_pam(self):
-        return 'PAM' in self.authenticators
+        return "PAM" in self.authenticators
 
     def check_azure_storage(self):
-        return 'azure_blob' in self.object_stores
+        return "azure_blob" in self.object_stores
 
     def check_kamaki(self):
-        return 'pithos' in self.object_stores
+        return "pithos" in self.object_stores
 
     def check_python_irodsclient(self):
-        return 'irods' in self.object_stores
+        return "irods" in self.object_stores
 
     def check_fs_dropboxfs(self):
-        return 'dropbox' in self.file_sources
+        return "dropbox" in self.file_sources
 
     def check_fs_webdavfs(self):
-        return 'webdav' in self.file_sources
+        return "webdav" in self.file_sources
 
     def check_fs_s3fs(self):
         # pyfilesystem plugin access to s3
-        return 's3' in self.file_sources
+        return "s3" in self.file_sources
 
     def check_fs_anvilfs(self):
         # pyfilesystem plugin access to terra on anvil
-        return 'anvil' in self.file_sources
+        return "anvil" in self.file_sources
 
     def check_fs_sshfs(self):
-        return 'ssh' in self.file_sources
+        return "ssh" in self.file_sources
 
     def check_s3fs(self):
         # use s3fs directly (skipping pyfilesystem) for direct access to more options
-        return 's3fs' in self.file_sources
+        return "s3fs" in self.file_sources
 
     def check_fs_googledrivefs(self):
-        return 'googledrive' in self.file_sources
+        return "googledrive" in self.file_sources
 
     def check_fs_gcsfs(self):
-        return 'googlecloudstorage' in self.file_sources
+        return "googlecloudstorage" in self.file_sources
 
     def check_fs_onedatafs(self):
-        return 'onedata' in self.file_sources
+        return "onedata" in self.file_sources
 
     def check_fs_basespace(self):
-        return 'basespace' in self.file_sources
+        return "basespace" in self.file_sources
 
     def check_watchdog(self):
-        install_set = {'auto', 'True', 'true', 'polling', True}
-        return (self.config['watch_tools'] in install_set
-                or self.config['watch_tool_data_dir'] in install_set)
+        install_set = {"auto", "True", "true", "polling", True}
+        return self.config["watch_tools"] in install_set or self.config["watch_tool_data_dir"] in install_set
 
     def check_docker(self):
-        return (self.config.get("enable_beta_containers_interface", False)
-                and ('docker' in self.container_interface_types
-                     or 'docker_swarm' in self.container_interface_types))
+        return self.config.get("enable_beta_containers_interface", False) and (
+            "docker" in self.container_interface_types or "docker_swarm" in self.container_interface_types
+        )
 
     def check_python_gitlab(self):
-        return 'gitlab' in self.error_report_modules
+        return "gitlab" in self.error_report_modules
 
     def check_pygithub(self):
-        return 'github' in self.error_report_modules
+        return "github" in self.error_report_modules
 
     def check_influxdb(self):
-        return 'influxdb' in self.error_report_modules
+        return "influxdb" in self.error_report_modules
 
     def check_keras(self):
         return asbool(self.config["enable_tool_recommendations"])
@@ -286,15 +281,15 @@ class ConditionalDependencies:
         return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"
 
     def check_custos_sdk(self):
-        return 'custos' == self.vault_type
+        return "custos" == self.vault_type
 
     def check_hvac(self):
-        return 'hashicorp' == self.vault_type
+        return "hashicorp" == self.vault_type
 
 
 def optional(config_file=None):
     if not config_file:
-        config_file = find_config_file(['galaxy', 'universe_wsgi'], include_samples=True)
+        config_file = find_config_file(["galaxy", "universe_wsgi"], include_samples=True)
     if not config_file:
         print("galaxy.dependencies.optional: no config file found", file=sys.stderr)
         return []
diff --git a/lib/galaxy/di.py b/lib/galaxy/di.py
index 8736140b996..e1f31bd57cd 100644
--- a/lib/galaxy/di.py
+++ b/lib/galaxy/di.py
@@ -1,5 +1,9 @@
 """Dependency injection framework for Galaxy-type apps."""
-from typing import Optional, Type, TypeVar
+from typing import (
+    Optional,
+    Type,
+    TypeVar,
+)
 
 from lagom import Container as LagomContainer
 from lagom.exceptions import UnresolvableType
diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index f1240ef95c6..f0742fbee54 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -24,10 +24,11 @@ from ..exceptions.error_codes import (
 
 class MessageException(Exception):
     """Most generic Galaxy exception - indicates merely that some exceptional condition happened."""
+
     # status code to be set when used with API.
     status_code: int = 400
     # Error code information embedded into API json responses.
-    err_code: ErrorCode = error_codes_by_name['UNKNOWN']
+    err_code: ErrorCode = error_codes_by_name["UNKNOWN"]
 
     def __init__(self, err_msg=None, type="info", **extra_error_info):
         self.err_msg = err_msg or self.err_code.default_error_message
@@ -52,14 +53,15 @@ class ItemDeletionException(MessageException):
 
 
 class ObjectInvalid(Exception):
-    """ Accessed object store ID is invalid """
+    """Accessed object store ID is invalid"""
+
 
 # Please keep the exceptions ordered by status code
 
 
 class ActionInputError(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_REQUEST_INVALID_PARAMETER']
+    err_code = error_codes_by_name["USER_REQUEST_INVALID_PARAMETER"]
 
     def __init__(self, err_msg, type="error"):
         super().__init__(err_msg, type)
@@ -67,57 +69,57 @@ class ActionInputError(MessageException):
 
 class DuplicatedSlugException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_SLUG_DUPLICATE']
+    err_code = error_codes_by_name["USER_SLUG_DUPLICATE"]
 
 
 class DuplicatedIdentifierException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_IDENTIFIER_DUPLICATE']
+    err_code = error_codes_by_name["USER_IDENTIFIER_DUPLICATE"]
 
 
 class ObjectAttributeInvalidException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_OBJECT_ATTRIBUTE_INVALID']
+    err_code = error_codes_by_name["USER_OBJECT_ATTRIBUTE_INVALID"]
 
 
 class ObjectAttributeMissingException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_OBJECT_ATTRIBUTE_MISSING']
+    err_code = error_codes_by_name["USER_OBJECT_ATTRIBUTE_MISSING"]
 
 
 class MalformedId(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['MALFORMED_ID']
+    err_code = error_codes_by_name["MALFORMED_ID"]
 
 
 class UserInvalidRunAsException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_INVALID_RUN_AS']
+    err_code = error_codes_by_name["USER_INVALID_RUN_AS"]
 
 
 class MalformedContents(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['MALFORMED_CONTENTS']
+    err_code = error_codes_by_name["MALFORMED_CONTENTS"]
 
 
 class UnknownContentsType(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['UNKNOWN_CONTENTS_TYPE']
+    err_code = error_codes_by_name["UNKNOWN_CONTENTS_TYPE"]
 
 
 class RequestParameterMissingException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_REQUEST_MISSING_PARAMETER']
+    err_code = error_codes_by_name["USER_REQUEST_MISSING_PARAMETER"]
 
 
 class ToolMetaParameterException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_TOOL_META_PARAMETER_PROBLEM']
+    err_code = error_codes_by_name["USER_TOOL_META_PARAMETER_PROBLEM"]
 
 
 class ToolMissingException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_TOOL_MISSING_PROBLEM']
+    err_code = error_codes_by_name["USER_TOOL_MISSING_PROBLEM"]
 
     def __init__(self, err_msg=None, type="info", tool_id=None, **extra_error_info):
         super().__init__(err_msg, type, **extra_error_info)
@@ -126,103 +128,105 @@ class ToolMissingException(MessageException):
 
 class RequestParameterInvalidException(MessageException):
     status_code = 400
-    err_code = error_codes_by_name['USER_REQUEST_INVALID_PARAMETER']
+    err_code = error_codes_by_name["USER_REQUEST_INVALID_PARAMETER"]
 
 
 class ToolInputsNotReadyException(MessageException):
     status_code = 400
-    error_code = error_codes_by_name['TOOL_INPUTS_NOT_READY']
+    error_code = error_codes_by_name["TOOL_INPUTS_NOT_READY"]
 
 
 class RealUserRequiredException(MessageException):
     status_code = 400
-    error_code = error_codes_by_name['REAL_USER_REQUIRED']
+    error_code = error_codes_by_name["REAL_USER_REQUIRED"]
 
 
 class AuthenticationFailed(MessageException):
     status_code = 401
-    err_code = error_codes_by_name['USER_AUTHENTICATION_FAILED']
+    err_code = error_codes_by_name["USER_AUTHENTICATION_FAILED"]
 
 
 class AuthenticationRequired(MessageException):
     status_code = 403
     # TODO: as 401 and send WWW-Authenticate: ???
-    err_code = error_codes_by_name['USER_NO_API_KEY']
+    err_code = error_codes_by_name["USER_NO_API_KEY"]
 
 
 class ItemAccessibilityException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['USER_CANNOT_ACCESS_ITEM']
+    err_code = error_codes_by_name["USER_CANNOT_ACCESS_ITEM"]
 
 
 class ItemOwnershipException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['USER_DOES_NOT_OWN_ITEM']
+    err_code = error_codes_by_name["USER_DOES_NOT_OWN_ITEM"]
 
 
 class ConfigDoesNotAllowException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['CONFIG_DOES_NOT_ALLOW']
+    err_code = error_codes_by_name["CONFIG_DOES_NOT_ALLOW"]
 
 
 class InsufficientPermissionsException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['INSUFFICIENT_PERMISSIONS']
+    err_code = error_codes_by_name["INSUFFICIENT_PERMISSIONS"]
 
 
 class UserCannotRunAsException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['USER_CANNOT_RUN_AS']
+    err_code = error_codes_by_name["USER_CANNOT_RUN_AS"]
 
 
 class AdminRequiredException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['ADMIN_REQUIRED']
+    err_code = error_codes_by_name["ADMIN_REQUIRED"]
 
 
 class UserActivationRequiredException(MessageException):
     status_code = 403
-    err_code = error_codes_by_name['USER_ACTIVATION_REQUIRED']
+    err_code = error_codes_by_name["USER_ACTIVATION_REQUIRED"]
 
 
 class ObjectNotFound(MessageException):
-    """ Accessed object was not found """
+    """Accessed object was not found"""
+
     status_code = 404
-    err_code = error_codes_by_name['USER_OBJECT_NOT_FOUND']
+    err_code = error_codes_by_name["USER_OBJECT_NOT_FOUND"]
 
 
 class DeprecatedMethod(MessageException):
     """
     Method (or a particular form/arg signature) has been removed and won't be available later
     """
+
     status_code = 404
     # TODO:?? 410 Gone?
-    err_code = error_codes_by_name['DEPRECATED_API_CALL']
+    err_code = error_codes_by_name["DEPRECATED_API_CALL"]
 
 
 class Conflict(MessageException):
     status_code = 409
-    err_code = error_codes_by_name['CONFLICT']
+    err_code = error_codes_by_name["CONFLICT"]
 
 
 class ConfigurationError(Exception):
     status_code = 500
-    err_code = error_codes_by_name['CONFIG_ERROR']
+    err_code = error_codes_by_name["CONFIG_ERROR"]
 
 
 class InconsistentDatabase(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['INCONSISTENT_DATABASE']
+    err_code = error_codes_by_name["INCONSISTENT_DATABASE"]
 
 
 class InternalServerError(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['INTERNAL_SERVER_ERROR']
+    err_code = error_codes_by_name["INTERNAL_SERVER_ERROR"]
 
 
 class ToolExecutionError(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['TOOL_EXECUTION_ERROR']
+    err_code = error_codes_by_name["TOOL_EXECUTION_ERROR"]
 
     def __init__(self, err_msg, type="error", job=None):
         super().__init__(err_msg, type)
@@ -231,31 +235,33 @@ class ToolExecutionError(MessageException):
 
 class NotImplemented(MessageException):
     status_code = 501
-    err_code = error_codes_by_name['NOT_IMPLEMENTED']
+    err_code = error_codes_by_name["NOT_IMPLEMENTED"]
 
 
 class InvalidFileFormatError(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['INVALID_FILE_FORMAT']
+    err_code = error_codes_by_name["INVALID_FILE_FORMAT"]
 
 
 class ReferenceDataError(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['REFERENCE_DATA_ERROR']
+    err_code = error_codes_by_name["REFERENCE_DATA_ERROR"]
 
 
 class ServerNotConfiguredForRequest(MessageException):
     # A bit like ConfigDoesNotAllowException but it has nothing to do with the user of the
     # request being "forbidden". It just isn't configured.
     status_code = 501
-    err_code = error_codes_by_name['SERVER_NOT_CONFIGURED_FOR_REQUEST']
+    err_code = error_codes_by_name["SERVER_NOT_CONFIGURED_FOR_REQUEST"]
 
 
 # non-web exceptions
 
+
 class ContainerCLIError(Exception):
-    def __init__(self, msg=None, stdout=None, stderr=None, returncode=None,
-                 command=None, subprocess_command=None, **kwargs):
+    def __init__(
+        self, msg=None, stdout=None, stderr=None, returncode=None, command=None, subprocess_command=None, **kwargs
+    ):
         super().__init__(msg)
         self.stdout = stdout
         self.stderr = stderr
diff --git a/lib/galaxy/exceptions/error_codes.py b/lib/galaxy/exceptions/error_codes.py
index f4415686411..420acad1bb9 100644
--- a/lib/galaxy/exceptions/error_codes.py
+++ b/lib/galaxy/exceptions/error_codes.py
@@ -9,7 +9,6 @@ from pkg_resources import resource_string
 
 from galaxy.util import unicodify
 
-
 # Error codes are provided as a convience to Galaxy API clients, but at this
 # time they do represent part of the more stable interface. They can change
 # without warning between releases.
@@ -45,7 +44,7 @@ def _from_dict(entry):
     return (name, ErrorCode(code, message))
 
 
-error_codes_json = unicodify(resource_string(__name__, 'error_codes.json'))
+error_codes_json = unicodify(resource_string(__name__, "error_codes.json"))
 error_codes_by_name: Dict[str, ErrorCode] = {}
 
 for entry in loads(error_codes_json):
diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py
index ebcac4c9942..f2178ce6257 100644
--- a/lib/galaxy/files/__init__.py
+++ b/lib/galaxy/files/__init__.py
@@ -7,20 +7,24 @@ from collections import (
 from typing import Set
 
 from galaxy import exceptions
-from galaxy.util import (
-    plugin_config
-)
+from galaxy.util import plugin_config
 from galaxy.util.dictifiable import Dictifiable
 
 log = logging.getLogger(__name__)
 
-FileSourcePath = namedtuple('FileSourcePath', ['file_source', 'path'])
+FileSourcePath = namedtuple("FileSourcePath", ["file_source", "path"])
 
 
 class ConfiguredFileSources:
     """Load plugins and resolve Galaxy URIs to FileSource objects."""
 
-    def __init__(self, file_sources_config: 'ConfiguredFileSourcesConfig', conf_file=None, conf_dict=None, load_stock_plugins=False):
+    def __init__(
+        self,
+        file_sources_config: "ConfiguredFileSourcesConfig",
+        conf_file=None,
+        conf_dict=None,
+        load_stock_plugins=False,
+    ):
         self._file_sources_config = file_sources_config
         self._plugin_classes = self._file_source_plugins_dict()
         file_sources = []
@@ -39,14 +43,14 @@ class ConfiguredFileSources:
                 for file_source in file_sources:
                     if file_source.plugin_type == plugin_type:
                         return
-                stock_file_source_conf_dict.append({'type': plugin_type})
+                stock_file_source_conf_dict.append({"type": plugin_type})
 
             if file_sources_config.ftp_upload_dir is not None:
-                _ensure_loaded('gxftp')
+                _ensure_loaded("gxftp")
             if file_sources_config.library_import_dir is not None:
-                _ensure_loaded('gximport')
+                _ensure_loaded("gximport")
             if file_sources_config.user_library_import_dir is not None:
-                _ensure_loaded('gxuserimport')
+                _ensure_loaded("gxuserimport")
             if stock_file_source_conf_dict:
                 stock_plugin_source = plugin_config.plugin_source_from_dict(stock_file_source_conf_dict)
                 # insert at begining instead of append so FTP and library import appear
@@ -63,11 +67,12 @@ class ConfiguredFileSources:
 
     def _file_source_plugins_dict(self):
         import galaxy.files.sources
-        return plugin_config.plugins_dict(galaxy.files.sources, 'plugin_type')
+
+        return plugin_config.plugins_dict(galaxy.files.sources, "plugin_type")
 
     def _parse_plugin_source(self, plugin_source):
         extra_kwds = {
-            'file_sources_config': self._file_sources_config,
+            "file_sources_config": self._file_sources_config,
         }
         return plugin_config.load_plugins(
             self._plugin_classes,
@@ -104,21 +109,29 @@ class ConfiguredFileSources:
             user_login = user_context.email
             user_base_dir = self._file_sources_config.user_library_import_dir
             if user_base_dir is None:
-                raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow upload from user directories.')
+                raise exceptions.ConfigDoesNotAllowException(
+                    "The configuration of this Galaxy instance does not allow upload from user directories."
+                )
             full_import_dir = os.path.join(user_base_dir, user_login)
             if not os.path.exists(full_import_dir):
-                raise exceptions.ObjectNotFound('Your user import directory does not exist.')
+                raise exceptions.ObjectNotFound("Your user import directory does not exist.")
         elif uri.startswith("gximport://"):
             base_dir = self._file_sources_config.library_import_dir
             if base_dir is None:
-                raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow usage of import directory.')
+                raise exceptions.ConfigDoesNotAllowException(
+                    "The configuration of this Galaxy instance does not allow usage of import directory."
+                )
         elif uri.startswith("gxftp://"):
             user_ftp_base_dir = self._file_sources_config.ftp_upload_dir
             if user_ftp_base_dir is None:
-                raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow upload from FTP directories.')
+                raise exceptions.ConfigDoesNotAllowException(
+                    "The configuration of this Galaxy instance does not allow upload from FTP directories."
+                )
             user_ftp_dir = user_context.ftp_dir
             if not user_ftp_dir or not os.path.exists(user_ftp_dir):
-                raise exceptions.ObjectNotFound('Your FTP directory does not exist, attempting to upload files to it may cause it to be created.')
+                raise exceptions.ObjectNotFound(
+                    "Your FTP directory does not exist, attempting to upload files to it may cause it to be created."
+                )
 
     def get_file_source(self, id_prefix, scheme):
         for file_source in self._file_sources:
@@ -156,8 +169,8 @@ class ConfiguredFileSources:
 
     def to_dict(self, for_serialization=False, user_context=None):
         return {
-            'file_sources': self.plugins_to_dict(for_serialization=for_serialization, user_context=user_context),
-            'config': self._file_sources_config.to_dict()
+            "file_sources": self.plugins_to_dict(for_serialization=for_serialization, user_context=user_context),
+            "config": self._file_sources_config.to_dict(),
         }
 
     @staticmethod
@@ -181,8 +194,14 @@ class ConfiguredFileSources:
 
 
 class ConfiguredFileSourcesConfig:
-
-    def __init__(self, symlink_allowlist=None, library_import_dir=None, user_library_import_dir=None, ftp_upload_dir=None, ftp_upload_purge=True):
+    def __init__(
+        self,
+        symlink_allowlist=None,
+        library_import_dir=None,
+        user_library_import_dir=None,
+        ftp_upload_dir=None,
+        ftp_upload_purge=True,
+    ):
         symlink_allowlist = symlink_allowlist or []
         self.symlink_allowlist = symlink_allowlist
         self.library_import_dir = library_import_dir
@@ -204,31 +223,31 @@ class ConfiguredFileSourcesConfig:
 
     def to_dict(self):
         return {
-            'symlink_allowlist': self.symlink_allowlist,
-            'library_import_dir': self.library_import_dir,
-            'user_library_import_dir': self.user_library_import_dir,
-            'ftp_upload_dir': self.ftp_upload_dir,
-            'ftp_upload_purge': self.ftp_upload_purge,
+            "symlink_allowlist": self.symlink_allowlist,
+            "library_import_dir": self.library_import_dir,
+            "user_library_import_dir": self.user_library_import_dir,
+            "ftp_upload_dir": self.ftp_upload_dir,
+            "ftp_upload_purge": self.ftp_upload_purge,
         }
 
     @staticmethod
     def from_dict(as_dict):
         return ConfiguredFileSourcesConfig(
-            symlink_allowlist=as_dict['symlink_allowlist'],
-            library_import_dir=as_dict['library_import_dir'],
-            user_library_import_dir=as_dict['user_library_import_dir'],
-            ftp_upload_dir=as_dict['ftp_upload_dir'],
-            ftp_upload_purge=as_dict['ftp_upload_purge'],
+            symlink_allowlist=as_dict["symlink_allowlist"],
+            library_import_dir=as_dict["library_import_dir"],
+            user_library_import_dir=as_dict["user_library_import_dir"],
+            ftp_upload_dir=as_dict["ftp_upload_dir"],
+            ftp_upload_purge=as_dict["ftp_upload_purge"],
         )
 
 
 class FileSourceDictifiable(Dictifiable):
-    dict_collection_visible_keys = ('email', 'username', 'ftp_dir', 'preferences', 'is_admin')
+    dict_collection_visible_keys = ("email", "username", "ftp_dir", "preferences", "is_admin")
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        rval['role_names'] = list(self.role_names)
-        rval['group_names'] = list(self.group_names)
+        rval["role_names"] = list(self.role_names)
+        rval["group_names"] = list(self.group_names)
         return rval
 
     @property
@@ -296,7 +315,6 @@ class ProvidesUserFileSourcesUserContext(FileSourceDictifiable):
 
 
 class DictFileSourcesUserContext(FileSourceDictifiable):
-
     def __init__(self, **kwd):
         self._kwd = kwd
 
diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 2b97d955fb0..20f8eb2ad16 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -20,8 +20,7 @@ DEFAULT_WRITABLE = False
 
 
 class FilesSource(metaclass=abc.ABCMeta):
-    """
-    """
+    """ """
 
     @abc.abstractmethod
     def get_uri_root(self) -> str:
@@ -49,8 +48,7 @@ class FilesSource(metaclass=abc.ABCMeta):
         """Realize source path (relative to uri root) to local file system path."""
 
     def write_from(self, target_path, native_path, user_context=None):
-        """Write file at native path to target_path (relative to uri root).
-        """
+        """Write file at native path to target_path (relative to uri root)."""
 
     @abc.abstractmethod
     def to_dict(self, for_serialization=False, user_context=None):
@@ -79,10 +77,7 @@ class BaseFilesSource(FilesSource):
         return (
             user_context is None
             or user_context.is_admin
-            or (
-                self._user_has_required_roles(user_context)
-                and self._user_has_required_groups(user_context)
-            )
+            or (self._user_has_required_roles(user_context) and self._user_has_required_groups(user_context))
         )
 
     @property
diff --git a/lib/galaxy/files/sources/_pyfilesystem2.py b/lib/galaxy/files/sources/_pyfilesystem2.py
index 8dba207caf4..13e0f9d2102 100644
--- a/lib/galaxy/files/sources/_pyfilesystem2.py
+++ b/lib/galaxy/files/sources/_pyfilesystem2.py
@@ -2,7 +2,13 @@ import abc
 import functools
 import logging
 import os
-from typing import Any, Dict, List, Optional, Type
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Type,
+)
 
 import fs
 from fs.base import FS
@@ -41,16 +47,16 @@ class PyFilesystem2FilesSource(BaseFilesSource):
                     res.extend(map(to_dict, files))
                 return res
             else:
-                res = h.scandir(path, namespaces=['details'])
+                res = h.scandir(path, namespaces=["details"])
                 to_dict = functools.partial(self._resource_info_to_dict, path)
                 return list(map(to_dict, res))
 
     def _realize_to(self, source_path, native_path, user_context=None):
-        with open(native_path, 'wb') as write_file:
+        with open(native_path, "wb") as write_file:
             self._open_fs(user_context=user_context).download(source_path, write_file)
 
     def _write_from(self, target_path, native_path, user_context=None):
-        with open(native_path, 'rb') as read_file:
+        with open(native_path, "rb") as read_file:
             openfs = self._open_fs(user_context=user_context)
             dirname = fs.path.dirname(target_path)
             if not openfs.isdir(dirname):
diff --git a/lib/galaxy/files/sources/anvil.py b/lib/galaxy/files/sources/anvil.py
index 5ed894aed2b..aaaf31f134b 100644
--- a/lib/galaxy/files/sources/anvil.py
+++ b/lib/galaxy/files/sources/anvil.py
@@ -6,7 +6,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class AnVILFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'anvil'
+    plugin_type = "anvil"
     required_module = AnVILFS
     required_package = "fs.anvilfs"
 
@@ -16,4 +16,4 @@ class AnVILFilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('AnVILFilesSource', )
+__all__ = ("AnVILFilesSource",)
diff --git a/lib/galaxy/files/sources/basespace.py b/lib/galaxy/files/sources/basespace.py
index 95c09b250b7..3ed27bdb227 100644
--- a/lib/galaxy/files/sources/basespace.py
+++ b/lib/galaxy/files/sources/basespace.py
@@ -7,7 +7,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class BaseSpaceFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'basespace'
+    plugin_type = "basespace"
     required_module = BASESPACEFS
     required_package = "fs-basespace"
 
@@ -17,4 +17,4 @@ class BaseSpaceFilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('BaseSpaceFilesSource',)
+__all__ = ("BaseSpaceFilesSource",)
diff --git a/lib/galaxy/files/sources/dropbox.py b/lib/galaxy/files/sources/dropbox.py
index 49a9b2f958d..6fa2a3b9d3c 100644
--- a/lib/galaxy/files/sources/dropbox.py
+++ b/lib/galaxy/files/sources/dropbox.py
@@ -7,7 +7,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class DropboxFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'dropbox'
+    plugin_type = "dropbox"
     required_module = DropboxFS
     required_package = "fs.dropboxfs"
 
@@ -17,4 +17,4 @@ class DropboxFilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('DropboxFilesSource',)
+__all__ = ("DropboxFilesSource",)
diff --git a/lib/galaxy/files/sources/galaxy.py b/lib/galaxy/files/sources/galaxy.py
index 2ce2e8a4ef2..0f344906156 100644
--- a/lib/galaxy/files/sources/galaxy.py
+++ b/lib/galaxy/files/sources/galaxy.py
@@ -4,7 +4,7 @@ from .posix import PosixFilesSource
 
 
 class UserFtpFilesSource(PosixFilesSource):
-    plugin_type = 'gxftp'
+    plugin_type = "gxftp"
 
     def __init__(self, label="FTP Directory", doc="Galaxy User's FTP Directory", root="${user.ftp_dir}", **kwd):
         posix_kwds = dict(
@@ -28,9 +28,15 @@ class UserFtpFilesSource(PosixFilesSource):
 
 
 class LibraryImportFilesSource(PosixFilesSource):
-    plugin_type = 'gximport'
+    plugin_type = "gximport"
 
-    def __init__(self, label="Library Import Directory", doc="Galaxy's library import directory", root="${config.library_import_dir}", **kwd):
+    def __init__(
+        self,
+        label="Library Import Directory",
+        doc="Galaxy's library import directory",
+        root="${config.library_import_dir}",
+        **kwd,
+    ):
         posix_kwds = dict(
             id="_import",
             root=root,
@@ -48,9 +54,15 @@ class LibraryImportFilesSource(PosixFilesSource):
 
 
 class UserLibraryImportFilesSource(PosixFilesSource):
-    plugin_type = 'gxuserimport'
+    plugin_type = "gxuserimport"
 
-    def __init__(self, label="Library User Import Directory", doc="Galaxy's user library import directory", root="${config.user_library_import_dir}/${user.email}", **kwd):
+    def __init__(
+        self,
+        label="Library User Import Directory",
+        doc="Galaxy's user library import directory",
+        root="${config.user_library_import_dir}/${user.email}",
+        **kwd,
+    ):
         posix_kwds = dict(
             id="_userimport",
             root=root,
@@ -67,4 +79,4 @@ class UserLibraryImportFilesSource(PosixFilesSource):
         return "gxuserimport"
 
 
-__all__ = ('UserFtpFilesSource', 'LibraryImportFilesSource', 'UserLibraryImportFilesSource')
+__all__ = ("UserFtpFilesSource", "LibraryImportFilesSource", "UserLibraryImportFilesSource")
diff --git a/lib/galaxy/files/sources/googlecloudstorage.py b/lib/galaxy/files/sources/googlecloudstorage.py
index e2d7ad08a87..bbe64e6a983 100644
--- a/lib/galaxy/files/sources/googlecloudstorage.py
+++ b/lib/galaxy/files/sources/googlecloudstorage.py
@@ -9,22 +9,22 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class GoogleCloudStorageFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'googlecloudstorage'
+    plugin_type = "googlecloudstorage"
     required_module = GCSFS
     required_package = "fs-gcsfs"
 
     def _open_fs(self, user_context):
         props = self._serialization_props(user_context)
-        bucket_name = props.pop('bucket_name', None)
-        root_path = props.pop('root_path', None)
-        project = props.pop('project', None)
+        bucket_name = props.pop("bucket_name", None)
+        root_path = props.pop("root_path", None)
+        project = props.pop("project", None)
         args = {}
-        if props.get('anonymous'):
-            args['client'] = Client.create_anonymous_client()
-        elif props.get('token'):
-            args['client'] = Client(project=project, credentials=Credentials(**props))
+        if props.get("anonymous"):
+            args["client"] = Client.create_anonymous_client()
+        elif props.get("token"):
+            args["client"] = Client(project=project, credentials=Credentials(**props))
         handle = GCSFS(bucket_name, root_path=root_path, retry=0, **args)
         return handle
 
 
-__all__ = ('GoogleCloudStorageFilesSource',)
+__all__ = ("GoogleCloudStorageFilesSource",)
diff --git a/lib/galaxy/files/sources/googledrive.py b/lib/galaxy/files/sources/googledrive.py
index 1c8da18849c..f0a4bb7249a 100644
--- a/lib/galaxy/files/sources/googledrive.py
+++ b/lib/galaxy/files/sources/googledrive.py
@@ -8,7 +8,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class GoogleDriveFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'googledrive'
+    plugin_type = "googledrive"
     required_module = GoogleDriveFS
     required_package = "fs.googledrivefs"
 
@@ -19,4 +19,4 @@ class GoogleDriveFilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('GoogleDriveFilesSource',)
+__all__ = ("GoogleDriveFilesSource",)
diff --git a/lib/galaxy/files/sources/onedata.py b/lib/galaxy/files/sources/onedata.py
index d9e29d33c9b..59b98765f3d 100644
--- a/lib/galaxy/files/sources/onedata.py
+++ b/lib/galaxy/files/sources/onedata.py
@@ -7,7 +7,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class OneDataFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'onedata'
+    plugin_type = "onedata"
     required_module = OnedataFS
     required_package = "fs-onedatafs"
 
@@ -17,4 +17,4 @@ class OneDataFilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('OneDataFilesSource',)
+__all__ = ("OneDataFilesSource",)
diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index 11aaa7378e8..937c6be397a 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -1,7 +1,11 @@
 import functools
 import os
 import shutil
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 
 from galaxy import exceptions
 from galaxy.util.path import (
@@ -17,7 +21,7 @@ DEFAULT_ALLOW_SUBDIR_CREATION = True
 
 
 class PosixFilesSource(BaseFilesSource):
-    plugin_type = 'posix'
+    plugin_type = "posix"
 
     # If this were a PyFilesystem2FilesSource all that would be needed would be,
     # but we couldn't enforce security our way I suspect.
@@ -36,7 +40,7 @@ class PosixFilesSource(BaseFilesSource):
     def _list(self, path="/", recursive=True, user_context=None):
         dir_path = self._to_native_path(path, user_context=user_context)
         if not self._safe_directory(dir_path):
-            raise exceptions.ObjectNotFound(f'The specified directory does not exist [{dir_path}].')
+            raise exceptions.ObjectNotFound(f"The specified directory does not exist [{dir_path}].")
         if recursive:
             res: List[Dict[str, Any]] = []
             effective_root = self._effective_root(user_context)
@@ -114,7 +118,9 @@ class PosixFilesSource(BaseFilesSource):
     def _safe_directory(self, directory):
         if self.enforce_symlink_security:
             if not safe_path(directory, allowlist=self._allowlist):
-                raise exceptions.ConfigDoesNotAllowException(f'directory ({directory}) is a symlink to a location not on the allowlist')
+                raise exceptions.ConfigDoesNotAllowException(
+                    f"directory ({directory}) is a symlink to a location not on the allowlist"
+                )
 
         if not os.path.exists(directory):
             return False
@@ -135,4 +141,4 @@ class PosixFilesSource(BaseFilesSource):
         return self._file_sources_config.symlink_allowlist
 
 
-__all__ = ('PosixFilesSource',)
+__all__ = ("PosixFilesSource",)
diff --git a/lib/galaxy/files/sources/s3.py b/lib/galaxy/files/sources/s3.py
index 6ef398d7402..4e5652f0712 100644
--- a/lib/galaxy/files/sources/s3.py
+++ b/lib/galaxy/files/sources/s3.py
@@ -7,7 +7,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class S3FilesSource(PyFilesystem2FilesSource):
-    plugin_type = 's3'
+    plugin_type = "s3"
     required_module = S3FS
     required_package = "fs-s3fs"
 
@@ -17,4 +17,4 @@ class S3FilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('S3FilesSource',)
+__all__ = ("S3FilesSource",)
diff --git a/lib/galaxy/files/sources/s3fs.py b/lib/galaxy/files/sources/s3fs.py
index ffa6b15d7da..2c85609dd33 100644
--- a/lib/galaxy/files/sources/s3fs.py
+++ b/lib/galaxy/files/sources/s3fs.py
@@ -1,7 +1,11 @@
 import functools
 import logging
 import os
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 
 try:
     import s3fs
@@ -17,14 +21,14 @@ log = logging.getLogger(__name__)
 
 
 class S3FsFilesSource(BaseFilesSource):
-    plugin_type = 's3fs'
+    plugin_type = "s3fs"
 
     def __init__(self, **kwd):
         if s3fs is None:
             raise Exception("Package s3fs unavailable but required for this file source plugin.")
         props = self._parse_common_config_opts(kwd)
-        self._bucket = props.pop("bucket", '')
-        self._endpoint_url = props.pop('endpoint_url', None)
+        self._bucket = props.pop("bucket", "")
+        self._endpoint_url = props.pop("endpoint_url", None)
         assert self._endpoint_url or self._bucket
         self._props = props
 
@@ -58,7 +62,7 @@ class S3FsFilesSource(BaseFilesSource):
 
     def _open_fs(self, user_context=None):
         if self._endpoint_url:
-            self._props.update({'client_kwargs': {'endpoint_url': self._endpoint_url}})
+            self._props.update({"client_kwargs": {"endpoint_url": self._endpoint_url}})
         fs = s3fs.S3FileSystem(**self._props)
         return fs
 
@@ -87,4 +91,4 @@ class S3FsFilesSource(BaseFilesSource):
         return effective_props
 
 
-__all__ = ('S3FsFilesSource',)
+__all__ = ("S3FsFilesSource",)
diff --git a/lib/galaxy/files/sources/ssh.py b/lib/galaxy/files/sources/ssh.py
index ed2ec98f30c..15114ce687f 100644
--- a/lib/galaxy/files/sources/ssh.py
+++ b/lib/galaxy/files/sources/ssh.py
@@ -13,7 +13,7 @@ class SshFilesSource(PyFilesystem2FilesSource):
 
     def _open_fs(self, user_context):
         props = self._serialization_props(user_context)
-        path = props.pop('path')
+        path = props.pop("path")
         handle = SSHFS(**props)
         if path:
             handle = handle.opendir(path)
diff --git a/lib/galaxy/files/sources/webdav.py b/lib/galaxy/files/sources/webdav.py
index ba43e106b2d..4a9a3f0e7ce 100644
--- a/lib/galaxy/files/sources/webdav.py
+++ b/lib/galaxy/files/sources/webdav.py
@@ -7,7 +7,7 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
 class WebDavFilesSource(PyFilesystem2FilesSource):
-    plugin_type = 'webdav'
+    plugin_type = "webdav"
     required_module = WebDAVFS
     required_package = "fs.webdavfs"
 
@@ -17,4 +17,4 @@ class WebDavFilesSource(PyFilesystem2FilesSource):
         return handle
 
 
-__all__ = ('WebDavFilesSource',)
+__all__ = ("WebDavFilesSource",)
diff --git a/lib/galaxy/files/unittest_utils/__init__.py b/lib/galaxy/files/unittest_utils/__init__.py
index d500de23e4f..b823894a5ad 100644
--- a/lib/galaxy/files/unittest_utils/__init__.py
+++ b/lib/galaxy/files/unittest_utils/__init__.py
@@ -2,11 +2,13 @@ import os
 import tempfile
 from typing import Tuple
 
-from galaxy.files import ConfiguredFileSources, ConfiguredFileSourcesConfig
+from galaxy.files import (
+    ConfiguredFileSources,
+    ConfiguredFileSourcesConfig,
+)
 
 
 class TestConfiguredFileSources(ConfiguredFileSources):
-
     def __init__(self, file_sources_config: ConfiguredFileSourcesConfig, conf_dict: dict, test_root: str):
         super().__init__(file_sources_config, conf_dict=conf_dict)
         self.test_root = test_root
diff --git a/lib/galaxy/forms/forms.py b/lib/galaxy/forms/forms.py
index a2a8effc116..80e6c9067f1 100644
--- a/lib/galaxy/forms/forms.py
+++ b/lib/galaxy/forms/forms.py
@@ -5,7 +5,7 @@ FormDefinition and field factories
 # Can this functionality be further abstracted and merged with form_builder?
 from galaxy.model import (
     FormDefinition,
-    FormDefinitionCurrent
+    FormDefinitionCurrent,
 )
 from galaxy.util import string_as_bool
 
@@ -21,10 +21,12 @@ class FormDefinitionFactory:
         """
         Return new FormDefinition.
         """
-        assert form_type in self.form_types, f'Invalid FormDefinition type ( {form_type} not in {self.form_types.keys()} )'
-        assert name, 'FormDefinition requires a name'
+        assert (
+            form_type in self.form_types
+        ), f"Invalid FormDefinition type ( {form_type} not in {self.form_types.keys()} )"
+        assert name, "FormDefinition requires a name"
         if description is None:
-            description = ''
+            description = ""
         if layout is None:
             layout = []
         if fields is None:
@@ -32,12 +34,14 @@ class FormDefinitionFactory:
         # Create new FormDefinitionCurrent
         if form_definition_current is None:
             form_definition_current = FormDefinitionCurrent()
-        rval = FormDefinition(name=name,
-                              desc=description,
-                              form_type=self.form_types[form_type],
-                              form_definition_current=form_definition_current,
-                              layout=layout,
-                              fields=fields)
+        rval = FormDefinition(
+            name=name,
+            desc=description,
+            form_type=self.form_types[form_type],
+            form_definition_current=form_definition_current,
+            layout=layout,
+            fields=fields,
+        )
         form_definition_current.latest_form = rval
         return rval
 
@@ -45,97 +49,121 @@ class FormDefinitionFactory:
         """
         Return FormDefinition created from an xml element.
         """
-        name = elem.get('name', None)
-        description = elem.get('description', None)
-        form_type = elem.get('type', None)
+        name = elem.get("name", None)
+        description = elem.get("description", None)
+        form_type = elem.get("type", None)
         # load layout
         layout = []
-        layouts_elem = elem.find('layout')
+        layouts_elem = elem.find("layout")
         if layouts_elem:
-            for layout_elem in layouts_elem.findall('grid'):
-                layout_name = layout_elem.get('name', None)
-                assert layout_name and layout_name not in layout, 'Layout grid element requires a unique name.'
+            for layout_elem in layouts_elem.findall("grid"):
+                layout_name = layout_elem.get("name", None)
+                assert layout_name and layout_name not in layout, "Layout grid element requires a unique name."
                 layout.append(layout_name)
         # load fields
         fields = []
-        fields_elem = elem.find('fields')
+        fields_elem = elem.find("fields")
         if fields_elem is not None:
-            for field_elem in fields_elem.findall('field'):
-                field_type = field_elem.get('type')
-                assert field_type in self.field_type_factories, f'Invalid form field type ( {field_type} ).'
+            for field_elem in fields_elem.findall("field"):
+                field_type = field_elem.get("type")
+                assert field_type in self.field_type_factories, f"Invalid form field type ( {field_type} )."
                 fields.append(self.field_type_factories[field_type].from_elem(field_elem, layout))
         # create and return new form
-        return self.new(form_type, name, description=description, fields=fields, layout=layout, form_definition_current=form_definition_current)
+        return self.new(
+            form_type,
+            name,
+            description=description,
+            fields=fields,
+            layout=layout,
+            form_definition_current=form_definition_current,
+        )
 
 
 class FormDefinitionFieldFactory:
     type: str
 
     def __get_stored_field_type(self, **kwds):
-        raise Exception('not implemented')
+        raise Exception("not implemented")
 
     def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None):
         """
         Return new FormDefinition field.
         """
         rval = {}
-        assert name, 'Must provide a name'
-        rval['name'] = name
+        assert name, "Must provide a name"
+        rval["name"] = name
         if not label:
-            rval['label'] = name
+            rval["label"] = name
         else:
-            rval['label'] = label
+            rval["label"] = label
         if required:
-            rval['required'] = 'required'
+            rval["required"] = "required"
         else:
-            rval['required'] = 'optional'
+            rval["required"] = "optional"
         if helptext is None:
-            helptext = ''
-        rval['helptext'] = helptext
+            helptext = ""
+        rval["helptext"] = helptext
         if default is None:
-            default = ''
-        rval['default'] = default
-        rval['visible'] = visible
+            default = ""
+        rval["default"] = default
+        rval["visible"] = visible
         # if layout is None: #is this needed?
         #    layout = ''
-        rval['layout'] = layout
+        rval["layout"] = layout
         return rval
 
     def from_elem(self, elem, layout=None):
         """
         Return FormDefinition created from an xml element.
         """
-        name = elem.get('name')
-        label = elem.get('label')
-        required = string_as_bool(elem.get('required', 'false'))
-        default = elem.get('value')
-        helptext = elem.get('helptext')
-        visible = string_as_bool(elem.get('visible', 'true'))
-        field_layout = elem.get('layout', None)
+        name = elem.get("name")
+        label = elem.get("label")
+        required = string_as_bool(elem.get("required", "false"))
+        default = elem.get("value")
+        helptext = elem.get("helptext")
+        visible = string_as_bool(elem.get("visible", "true"))
+        field_layout = elem.get("layout", None)
         if field_layout:
-            assert layout and field_layout in layout, f'Invalid layout specified: {field_layout} not in {layout}'
-            field_layout = str(layout.index(field_layout))  # existing behavior: integer indexes are stored as strings. why?
-        return self.new(name=name, label=label, required=required, helptext=helptext, default=default, visible=visible, layout=field_layout)
+            assert layout and field_layout in layout, f"Invalid layout specified: {field_layout} not in {layout}"
+            field_layout = str(
+                layout.index(field_layout)
+            )  # existing behavior: integer indexes are stored as strings. why?
+        return self.new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=field_layout,
+        )
 
 
 class FormDefinitionTextFieldFactory(FormDefinitionFieldFactory):
-    type = 'text'
+    type = "text"
 
     def __get_stored_field_type(self, area):
         if area:
-            return 'TextArea'
+            return "TextArea"
         else:
-            return 'TextField'
+            return "TextField"
 
-    def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None, area=False):
+    def new(
+        self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None, area=False
+    ):
         """
         Return new FormDefinition field.
         """
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type(area)
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type(area)
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -143,25 +171,32 @@ class FormDefinitionTextFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type(string_as_bool(elem.get('area', 'false')))
+        rval["type"] = self.__get_stored_field_type(string_as_bool(elem.get("area", "false")))
         return rval
 
 
 class FormDefinitionPasswordFieldFactory(FormDefinitionFieldFactory):
-    type = 'password'
+    type = "password"
 
     def __get_stored_field_type(self):
-        return 'PasswordField'
+        return "PasswordField"
 
-    def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None, area=False):
+    def new(
+        self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None, area=False
+    ):
         """
         Return new FormDefinition field.
         """
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -169,25 +204,30 @@ class FormDefinitionPasswordFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
 
 class FormDefinitionAddressFieldFactory(FormDefinitionFieldFactory):
-    type = 'address'
+    type = "address"
 
     def __get_stored_field_type(self):
-        return 'AddressField'
+        return "AddressField"
 
     def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None):
         """
         Return new FormDefinition field.
         """
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -195,25 +235,30 @@ class FormDefinitionAddressFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
 
 class FormDefinitionWorkflowFieldFactory(FormDefinitionFieldFactory):
-    type = 'workflow'
+    type = "workflow"
 
     def __get_stored_field_type(self):
-        return 'WorkflowField'
+        return "WorkflowField"
 
     def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None):
         """
         Return new FormDefinition field.
         """
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -221,25 +266,30 @@ class FormDefinitionWorkflowFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
 
 class FormDefinitionWorkflowMappingFieldFactory(FormDefinitionFieldFactory):
-    type = 'workflowmapping'
+    type = "workflowmapping"
 
     def __get_stored_field_type(self):
-        return 'WorkflowMappingField'
+        return "WorkflowMappingField"
 
     def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None):
         """
         Return new FormDefinition field.
         """
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -247,25 +297,30 @@ class FormDefinitionWorkflowMappingFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
 
 class FormDefinitionHistoryFieldFactory(FormDefinitionFieldFactory):
-    type = 'history'
+    type = "history"
 
     def __get_stored_field_type(self):
-        return 'HistoryField'
+        return "HistoryField"
 
     def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None):
         """
         Return new FormDefinition field.
         """
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -273,32 +328,48 @@ class FormDefinitionHistoryFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type()
+        rval["type"] = self.__get_stored_field_type()
         return rval
 
 
 class FormDefinitionSelectFieldFactory(FormDefinitionFieldFactory):
-    type = 'select'
+    type = "select"
 
     def __get_stored_field_type(self, checkboxes):
         if checkboxes:
-            return 'CheckboxField'
+            return "CheckboxField"
         else:
-            return 'SelectField'
+            return "SelectField"
 
-    def new(self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None, options=None, checkboxes=False):
+    def new(
+        self,
+        name=None,
+        label=None,
+        required=False,
+        helptext=None,
+        default=None,
+        visible=True,
+        layout=None,
+        options=None,
+        checkboxes=False,
+    ):
         """
         Return new FormDefinition field.
         """
         options = options or []
-        rval = super().new(name=name, label=label,
-                           required=required, helptext=helptext,
-                           default=default, visible=visible,
-                           layout=layout)
-        rval['type'] = self.__get_stored_field_type(checkboxes)
+        rval = super().new(
+            name=name,
+            label=label,
+            required=required,
+            helptext=helptext,
+            default=default,
+            visible=visible,
+            layout=layout,
+        )
+        rval["type"] = self.__get_stored_field_type(checkboxes)
         if options is None:
             options = []
-        rval['selectlist'] = options
+        rval["selectlist"] = options
         return rval
 
     def from_elem(self, elem, layout=None):
@@ -306,22 +377,27 @@ class FormDefinitionSelectFieldFactory(FormDefinitionFieldFactory):
         Return FormDefinition field created from an xml element.
         """
         rval = super().from_elem(elem, layout=layout)
-        rval['type'] = self.__get_stored_field_type(string_as_bool(elem.get('checkboxes', 'false')))
+        rval["type"] = self.__get_stored_field_type(string_as_bool(elem.get("checkboxes", "false")))
         # load select options
-        rval['selectlist'] = []
-        for select_option in elem.findall('option'):
-            value = select_option.get('value', None)
+        rval["selectlist"] = []
+        for select_option in elem.findall("option"):
+            value = select_option.get("value", None)
             assert value is not None, 'Must provide a "value" for a select option'
-            rval['selectlist'].append(value)
+            rval["selectlist"].append(value)
         return rval
 
 
-field_type_factories = {field.type: field() for field in (FormDefinitionTextFieldFactory,
-                                                          FormDefinitionPasswordFieldFactory,
-                                                          FormDefinitionAddressFieldFactory,
-                                                          FormDefinitionSelectFieldFactory,
-                                                          FormDefinitionWorkflowFieldFactory,
-                                                          FormDefinitionWorkflowMappingFieldFactory,
-                                                          FormDefinitionHistoryFieldFactory)}
+field_type_factories = {
+    field.type: field()
+    for field in (
+        FormDefinitionTextFieldFactory,
+        FormDefinitionPasswordFieldFactory,
+        FormDefinitionAddressFieldFactory,
+        FormDefinitionSelectFieldFactory,
+        FormDefinitionWorkflowFieldFactory,
+        FormDefinitionWorkflowMappingFieldFactory,
+        FormDefinitionHistoryFieldFactory,
+    )
+}
 
 form_factory = FormDefinitionFactory(FORM_TYPES, field_type_factories)
diff --git a/lib/galaxy/job_execution/actions/post.py b/lib/galaxy/job_execution/actions/post.py
index ede02a4a0ca..21e0215a9cf 100644
--- a/lib/galaxy/job_execution/actions/post.py
+++ b/lib/galaxy/job_execution/actions/post.py
@@ -20,6 +20,7 @@ class DefaultJobAction:
     """
     Base job action.
     """
+
     name = "DefaultJobAction"
     verbose_name = "Default Job"
 
@@ -28,7 +29,9 @@ class DefaultJobAction:
         pass
 
     @classmethod
-    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None):
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
         pass
 
     @classmethod
@@ -43,6 +46,7 @@ class EmailAction(DefaultJobAction):
     """
     This action sends an email to the galaxy user responsible for a job.
     """
+
     name = "EmailAction"
     verbose_name = "Email Notification"
 
@@ -53,14 +57,14 @@ class EmailAction(DefaultJobAction):
             history_id_encoded = app.security.encode_id(job.history_id)
             link = f"{app.config.galaxy_infrastructure_url}/histories/view?id={history_id_encoded}"
             if frm is None:
-                if action.action_arguments and 'host' in action.action_arguments:
-                    host = action.action_arguments['host']
+                if action.action_arguments and "host" in action.action_arguments:
+                    host = action.action_arguments["host"]
                 else:
                     host = socket.getfqdn()
-                frm = f'galaxy-no-reply@{host}'
+                frm = f"galaxy-no-reply@{host}"
             to = job.get_user_email()
             subject = f"Galaxy job completion notification from history '{job.history.name}'"
-            outdata = ',\n'.join(ds.dataset.display_name() for ds in job.output_datasets)
+            outdata = ",\n".join(ds.dataset.display_name() for ds in job.output_datasets)
             body = f"Your Galaxy job generating dataset(s):\n\n{outdata}\n\nis complete as of {datetime.datetime.now().strftime('%I:%M')}. Click the link below to access your data: \n{link}"
             send_mail(frm, to, subject, body, app.config)
         except Exception as e:
@@ -68,8 +72,10 @@ class EmailAction(DefaultJobAction):
 
     @classmethod
     def get_short_str(cls, pja):
-        if pja.action_arguments and 'host' in pja.action_arguments:
-            return f"Email the current user from server {escape(pja.action_arguments['host'])} when this job is complete."
+        if pja.action_arguments and "host" in pja.action_arguments:
+            return (
+                f"Email the current user from server {escape(pja.action_arguments['host'])} when this job is complete."
+            )
         else:
             return "Email the current user when this job is complete."
 
@@ -78,6 +84,7 @@ class ValidateOutputsAction(DefaultJobAction):
     """
     This action validates the produced outputs against the expected datatype.
     """
+
     name = "ValidateOutputsAction"
     verbose_name = "Validate Tool Outputs"
 
@@ -98,18 +105,19 @@ class ChangeDatatypeAction(DefaultJobAction):
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         for dataset_assoc in job.output_datasets:
-            if action.output_name == '' or dataset_assoc.name == action.output_name:
-                app.datatypes_registry.change_datatype(dataset_assoc.dataset, action.action_arguments['newtype'])
+            if action.output_name == "" or dataset_assoc.name == action.output_name:
+                app.datatypes_registry.change_datatype(dataset_assoc.dataset, action.action_arguments["newtype"])
         for dataset_collection_assoc in job.output_dataset_collection_instances:
-            if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
+            if action.output_name == "" or dataset_collection_assoc.name == action.output_name:
                 for dataset_instance in dataset_collection_assoc.dataset_collection_instance.dataset_instances:
                     if dataset_instance:
-                        app.datatypes_registry.change_datatype(dataset_instance, action.action_arguments['newtype'])
+                        app.datatypes_registry.change_datatype(dataset_instance, action.action_arguments["newtype"])
 
     @classmethod
     def get_short_str(cls, pja):
-        return "Set the datatype of output '{}' to '{}'".format(escape(pja.output_name),
-                                                            escape(pja.action_arguments['newtype']))
+        return "Set the datatype of output '{}' to '{}'".format(
+            escape(pja.output_name), escape(pja.action_arguments["newtype"])
+        )
 
 
 class RenameDatasetAction(DefaultJobAction):
@@ -117,7 +125,9 @@ class RenameDatasetAction(DefaultJobAction):
     verbose_name = "Rename Dataset"
 
     @classmethod
-    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None):
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
         # Prevent renaming a dataset to the empty string.
         input_names = {}
         #  Lookp through inputs find one with "to_be_replaced" input
@@ -129,15 +139,15 @@ class RenameDatasetAction(DefaultJobAction):
         new_name = cls._gen_new_name(action, input_names, replacement_dict)
         if new_name:
             for name, step_output in step_outputs.items():
-                if action.output_name == '' or name == action.output_name:
+                if action.output_name == "" or name == action.output_name:
                     step_output.name = new_name
 
     @classmethod
     def _gen_new_name(self, action, input_names, replacement_dict):
         new_name = None
 
-        if action.action_arguments and action.action_arguments.get('newname', ''):
-            new_name = action.action_arguments['newname']
+        if action.action_arguments and action.action_arguments.get("newname", ""):
+            new_name = action.action_arguments["newname"]
             #  TODO: Unify and simplify replacement options.
             #      Add interface through workflow editor UI
 
@@ -183,7 +193,7 @@ class RenameDatasetAction(DefaultJobAction):
                 replacement = input_names.get(input_file_var, "")
 
                 # In case name was None.
-                replacement = replacement or ''
+                replacement = replacement or ""
                 #  Do operations on replacement
                 #  Any control that is not defined will be ignored.
                 #  This should be moved out to a class or module function
@@ -229,19 +239,20 @@ class RenameDatasetAction(DefaultJobAction):
         new_name = cls._gen_new_name(action, input_names, replacement_dict)
         if new_name:
             for dataset_assoc in job.output_datasets:
-                if action.output_name == '' or dataset_assoc.name == action.output_name:
+                if action.output_name == "" or dataset_assoc.name == action.output_name:
                     dataset_assoc.dataset.name = new_name
 
             for dataset_collection_assoc in job.output_dataset_collection_instances:
-                if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
+                if action.output_name == "" or dataset_collection_assoc.name == action.output_name:
                     dataset_collection_assoc.dataset_collection_instance.name = new_name
 
     @classmethod
     def get_short_str(cls, pja):
         # Prevent renaming a dataset to the empty string.
-        if pja.action_arguments and pja.action_arguments.get('newname', ''):
-            return "Rename output '{}' to '{}'.".format(escape(pja.output_name),
-                                                    escape(pja.action_arguments['newname']))
+        if pja.action_arguments and pja.action_arguments.get("newname", ""):
+            return "Rename output '{}' to '{}'.".format(
+                escape(pja.output_name), escape(pja.action_arguments["newname"])
+            )
         else:
             return "Rename action used without a new name specified.  Output name will be unchanged."
 
@@ -254,13 +265,15 @@ class HideDatasetAction(DefaultJobAction):
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         if final_job_state != job.states.ERROR:
             for output_association in job.output_datasets + job.output_dataset_collection_instances:
-                if action.output_name == '' or output_association.name == action.output_name:
+                if action.output_name == "" or output_association.name == action.output_name:
                     output_association.item.visible = False
 
     @classmethod
-    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None):
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
         for name, step_output in step_outputs.items():
-            if action.output_name == '' or name == action.output_name:
+            if action.output_name == "" or name == action.output_name:
                 step_output.visible = False
 
     @classmethod
@@ -276,13 +289,15 @@ class DeleteDatasetAction(DefaultJobAction):
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         for output_association in job.output_datasets + job.output_dataset_collection_instances:
-            if action.output_name == '' or output_association.name == action.output_name:
+            if action.output_name == "" or output_association.name == action.output_name:
                 output_association.item.deleted = True
 
     @classmethod
-    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None):
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
         for name, step_output in step_outputs.items():
-            if action.output_name == '' or name == action.output_name:
+            if action.output_name == "" or name == action.output_name:
                 step_output.deleted = True
 
     @classmethod
@@ -297,12 +312,12 @@ class ColumnSetAction(DefaultJobAction):
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         for dataset_assoc in job.output_datasets:
-            if action.output_name == '' or dataset_assoc.name == action.output_name:
+            if action.output_name == "" or dataset_assoc.name == action.output_name:
                 for k, v in action.action_arguments.items():
                     if v:
                         # Try to use both pure integer and 'cX' format.
                         if not isinstance(v, int):
-                            if v[0] == 'c':
+                            if v[0] == "c":
                                 v = v[1:]
                             v = int(v)
                         if v != 0:
@@ -320,7 +335,7 @@ class SetMetadataAction(DefaultJobAction):
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         for data in job.output_datasets:
-            data.set_metadata(action.action_arguments['newtype'])
+            data.set_metadata(action.action_arguments["newtype"])
 
 
 class DeleteIntermediatesAction(DefaultJobAction):
@@ -353,7 +368,11 @@ class DeleteIntermediatesAction(DefaultJobAction):
             return
         outputs_defined = wfi.workflow.has_outputs_defined()
         if outputs_defined:
-            wfi_steps = [wfistep for wfistep in wfi.steps if not wfistep.workflow_step.workflow_outputs and wfistep.workflow_step.type == "tool"]
+            wfi_steps = [
+                wfistep
+                for wfistep in wfi.steps
+                if not wfistep.workflow_step.workflow_outputs and wfistep.workflow_step.type == "tool"
+            ]
             jobs_to_check = []
             for wfi_step in wfi_steps:
                 sa_session.refresh(wfi_step)
@@ -366,21 +385,32 @@ class DeleteIntermediatesAction(DefaultJobAction):
                 creating_jobs = []
                 for input_dataset in j2c.input_datasets:
                     if not input_dataset.dataset:
-                        log.debug(f"PJA Async Issue: No dataset attached to input_dataset {input_dataset.id} during handling of workflow invocation {wfi}")
+                        log.debug(
+                            f"PJA Async Issue: No dataset attached to input_dataset {input_dataset.id} during handling of workflow invocation {wfi}"
+                        )
                     elif not input_dataset.dataset.creating_job:
-                        log.debug(f"PJA Async Issue: No creating job attached to dataset {input_dataset.dataset.id} during handling of workflow invocation {wfi}")
+                        log.debug(
+                            f"PJA Async Issue: No creating job attached to dataset {input_dataset.dataset.id} during handling of workflow invocation {wfi}"
+                        )
                     else:
                         creating_jobs.append((input_dataset, input_dataset.dataset.creating_job))
                 for (input_dataset, creating_job) in creating_jobs:
                     sa_session.refresh(creating_job)
                     sa_session.refresh(input_dataset)
-                for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step and creating_job.workflow_invocation_step.workflow_invocation == wfi]:
+                for input_dataset in [
+                    x.dataset
+                    for (x, creating_job) in creating_jobs
+                    if creating_job.workflow_invocation_step
+                    and creating_job.workflow_invocation_step.workflow_invocation == wfi
+                ]:
                     # note that the above input_dataset is a reference to a
                     # job.input_dataset.dataset at this point
                     safe_to_delete = True
                     for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]:
                         if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]:
-                            log.trace(f"Workflow Intermediates cleanup attempted, but non-terminal state '{job_to_check.state}' detected for job {job_to_check.id}")
+                            log.trace(
+                                f"Workflow Intermediates cleanup attempted, but non-terminal state '{job_to_check.state}' detected for job {job_to_check.id}"
+                            )
                             safe_to_delete = False
                     if safe_to_delete:
                         # Support purging here too.
@@ -402,27 +432,35 @@ class TagDatasetAction(DefaultJobAction):
     direction = "to"
 
     @classmethod
-    def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None):
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
         tag_handler = trans.app.tag_handler.create_tag_handler_session()
         if action.action_arguments:
-            tags = [t.replace('#', 'name:') if t.startswith('#') else t for t in [t.strip() for t in action.action_arguments.get('tags', '').split(',') if t.strip()]]
+            tags = [
+                t.replace("#", "name:") if t.startswith("#") else t
+                for t in [t.strip() for t in action.action_arguments.get("tags", "").split(",") if t.strip()]
+            ]
             if tags:
                 for name, step_output in step_outputs.items():
-                    if action.output_name == '' or name == action.output_name:
+                    if action.output_name == "" or name == action.output_name:
                         cls._execute(tag_handler, trans.user, step_output, tags)
 
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         if action.action_arguments:
             tag_handler = app.tag_handler.create_tag_handler_session()
-            tags = [t.replace('#', 'name:') if t.startswith('#') else t for t in [t.strip() for t in action.action_arguments.get('tags', '').split(',') if t.strip()]]
+            tags = [
+                t.replace("#", "name:") if t.startswith("#") else t
+                for t in [t.strip() for t in action.action_arguments.get("tags", "").split(",") if t.strip()]
+            ]
             if tags:
                 for dataset_assoc in job.output_datasets:
-                    if action.output_name == '' or dataset_assoc.name == action.output_name:
+                    if action.output_name == "" or dataset_assoc.name == action.output_name:
                         cls._execute(tag_handler, job.user, dataset_assoc.dataset, tags)
 
                 for dataset_collection_assoc in job.output_dataset_collection_instances:
-                    if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
+                    if action.output_name == "" or dataset_collection_assoc.name == action.output_name:
                         cls._execute(tag_handler, job.user, dataset_collection_assoc.dataset_collection_instance, tags)
 
     @classmethod
@@ -431,11 +469,10 @@ class TagDatasetAction(DefaultJobAction):
 
     @classmethod
     def get_short_str(cls, pja):
-        if pja.action_arguments and pja.action_arguments.get('tags', ''):
-            return "{} tag(s) '{}' {} '{}'.".format(cls.action,
-                                                escape(pja.action_arguments['tags']),
-                                                cls.direction,
-                                                escape(pja.output_name))
+        if pja.action_arguments and pja.action_arguments.get("tags", ""):
+            return "{} tag(s) '{}' {} '{}'.".format(
+                cls.action, escape(pja.action_arguments["tags"]), cls.direction, escape(pja.output_name)
+            )
         else:
             return f"{cls.action} Tag action used without a tag specified.  No tag will be added."
 
@@ -453,26 +490,36 @@ class RemoveTagDatasetAction(TagDatasetAction):
 
 class ActionBox:
 
-    actions = {"RenameDatasetAction": RenameDatasetAction,
-               "HideDatasetAction": HideDatasetAction,
-               "ChangeDatatypeAction": ChangeDatatypeAction,
-               "ColumnSetAction": ColumnSetAction,
-               "EmailAction": EmailAction,
-               "DeleteIntermediatesAction": DeleteIntermediatesAction,
-               "TagDatasetAction": TagDatasetAction,
-               "RemoveTagDatasetAction": RemoveTagDatasetAction}
-    public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction',
-                      'ColumnSetAction', 'EmailAction',
-                      'DeleteIntermediatesAction', 'TagDatasetAction',
-                      'RemoveTagDatasetAction']
+    actions = {
+        "RenameDatasetAction": RenameDatasetAction,
+        "HideDatasetAction": HideDatasetAction,
+        "ChangeDatatypeAction": ChangeDatatypeAction,
+        "ColumnSetAction": ColumnSetAction,
+        "EmailAction": EmailAction,
+        "DeleteIntermediatesAction": DeleteIntermediatesAction,
+        "TagDatasetAction": TagDatasetAction,
+        "RemoveTagDatasetAction": RemoveTagDatasetAction,
+    }
+    public_actions = [
+        "RenameDatasetAction",
+        "ChangeDatatypeAction",
+        "ColumnSetAction",
+        "EmailAction",
+        "DeleteIntermediatesAction",
+        "TagDatasetAction",
+        "RemoveTagDatasetAction",
+    ]
     # Actions that can be applied ahead of the job execution while workflow is still
     # being scheduled and jobs created.
-    immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction',
-                         'TagDatasetAction', 'RemoveTagDatasetAction']
+    immediate_actions = ["ChangeDatatypeAction", "RenameDatasetAction", "TagDatasetAction", "RemoveTagDatasetAction"]
     # Actions that will be applied to implicit mapped over collection outputs and not
     # just individual outputs when steps include mapped over tools and implicit collection outputs.
-    mapped_over_output_actions = ['RenameDatasetAction', 'HideDatasetAction',
-                                  'TagDatasetAction', 'RemoveTagDatasetAction']
+    mapped_over_output_actions = [
+        "RenameDatasetAction",
+        "HideDatasetAction",
+        "TagDatasetAction",
+        "RemoveTagDatasetAction",
+    ]
 
     @classmethod
     def get_short_str(cls, action):
@@ -485,30 +532,34 @@ class ActionBox:
     def handle_incoming(cls, incoming):
         npd = {}
         for key, val in incoming.items():
-            if key.startswith('pja'):
-                sp = key.split('__')
+            if key.startswith("pja"):
+                sp = key.split("__")
                 ao_key = sp[2] + sp[1]
                 # flag / output_name / pjatype / desc
                 if ao_key not in npd:
-                    npd[ao_key] = {'action_type': sp[2],
-                                   'output_name': sp[1],
-                                   'action_arguments': {}}
+                    npd[ao_key] = {"action_type": sp[2], "output_name": sp[1], "action_arguments": {}}
                 if len(sp) > 3:
-                    if sp[3] == 'output_name':
-                        npd[ao_key]['output_name'] = val
+                    if sp[3] == "output_name":
+                        npd[ao_key]["output_name"] = val
                     else:
-                        npd[ao_key]['action_arguments'][sp[3]] = val
+                        npd[ao_key]["action_arguments"][sp[3]] = val
             else:
                 # Not pja stuff.
                 pass
         return npd
 
     @classmethod
-    def execute_on_mapped_over(cls, trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None, final_job_state=None):
+    def execute_on_mapped_over(
+        cls, trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None, final_job_state=None
+    ):
         if pja.action_type in ActionBox.actions:
-            ActionBox.actions[pja.action_type].execute_on_mapped_over(trans, sa_session, pja, step_inputs, step_outputs, replacement_dict, final_job_state=final_job_state)
+            ActionBox.actions[pja.action_type].execute_on_mapped_over(
+                trans, sa_session, pja, step_inputs, step_outputs, replacement_dict, final_job_state=final_job_state
+            )
 
     @classmethod
     def execute(cls, app, sa_session, pja, job, replacement_dict=None, final_job_state=None):
         if pja.action_type in ActionBox.actions:
-            ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict, final_job_state=final_job_state)
+            ActionBox.actions[pja.action_type].execute(
+                app, sa_session, pja, job, replacement_dict, final_job_state=final_job_state
+            )
diff --git a/lib/galaxy/job_execution/compute_environment.py b/lib/galaxy/job_execution/compute_environment.py
index 3de4e16aeee..66966e06797 100644
--- a/lib/galaxy/job_execution/compute_environment.py
+++ b/lib/galaxy/job_execution/compute_environment.py
@@ -9,13 +9,13 @@ from galaxy.model import Job
 
 
 class ComputeEnvironment(metaclass=ABCMeta):
-    """ Definition of the job as it will be run on the (potentially) remote
+    """Definition of the job as it will be run on the (potentially) remote
     compute server.
     """
 
     @abstractmethod
     def output_names(self):
-        """ Output unqualified filenames defined by job. """
+        """Output unqualified filenames defined by job."""
 
     @abstractmethod
     def input_path_rewrite(self, dataset):
@@ -43,11 +43,11 @@ class ComputeEnvironment(metaclass=ABCMeta):
 
     @abstractmethod
     def working_directory(self):
-        """ Job working directory (potentially remote) """
+        """Job working directory (potentially remote)"""
 
     @abstractmethod
     def config_directory(self):
-        """ Directory containing config files (potentially remote) """
+        """Directory containing config files (potentially remote)"""
 
     @abstractmethod
     def env_config_directory(self):
@@ -55,20 +55,19 @@ class ComputeEnvironment(metaclass=ABCMeta):
 
     @abstractmethod
     def sep(self):
-        """ os.path.sep for the platform this job will execute in.
-        """
+        """os.path.sep for the platform this job will execute in."""
 
     @abstractmethod
     def new_file_path(self):
-        """ Absolute path to dump new files for this job on compute server. """
+        """Absolute path to dump new files for this job on compute server."""
 
     @abstractmethod
     def tool_directory(self):
-        """ Absolute path to tool files for this job on compute server. """
+        """Absolute path to tool files for this job on compute server."""
 
     @abstractmethod
     def version_path(self):
-        """ Location of the version file for the underlying tool. """
+        """Location of the version file for the underlying tool."""
 
     @abstractmethod
     def home_directory(self):
@@ -88,7 +87,6 @@ class ComputeEnvironment(metaclass=ABCMeta):
 
 
 class SimpleComputeEnvironment:
-
     def config_directory(self):
         return os.path.join(self.working_directory(), "configs")  # type: ignore[attr-defined]
 
@@ -97,7 +95,7 @@ class SimpleComputeEnvironment:
 
 
 class SharedComputeEnvironment(SimpleComputeEnvironment, ComputeEnvironment):
-    """ Default ComputeEnvironment for job and task wrapper to pass
+    """Default ComputeEnvironment for job and task wrapper to pass
     to ToolEvaluator - valid when Galaxy and compute share all the relevant
     file systems.
     """
diff --git a/lib/galaxy/job_execution/datasets.py b/lib/galaxy/job_execution/datasets.py
index 9a872b59eba..d06e68fee71 100644
--- a/lib/galaxy/job_execution/datasets.py
+++ b/lib/galaxy/job_execution/datasets.py
@@ -4,7 +4,7 @@ Utility classes allowing Job interface to reason about datasets.
 import os.path
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
 
@@ -14,7 +14,6 @@ def dataset_path_rewrites(dataset_paths):
 
 
 class DatasetPath:
-
     def __init__(
         self,
         dataset_id,
@@ -59,7 +58,7 @@ class DatasetPath:
 
 
 class DatasetPathRewriter(metaclass=ABCMeta):
-    """ Used by runner to rewrite paths. """
+    """Used by runner to rewrite paths."""
 
     @abstractmethod
     def rewrite_dataset_path(self, dataset, dataset_type):
@@ -70,17 +69,15 @@ class DatasetPathRewriter(metaclass=ABCMeta):
 
 
 class NullDatasetPathRewriter:
-    """ Used by default for jobwrapper, do not rewrite anything.
-    """
+    """Used by default for jobwrapper, do not rewrite anything."""
 
     def rewrite_dataset_path(self, dataset, dataset_type):
-        """ Keep path the same.
-        """
+        """Keep path the same."""
         return None
 
 
 class OutputsToWorkingDirectoryPathRewriter:
-    """ Rewrites all paths to place them in the specified working
+    """Rewrites all paths to place them in the specified working
     directory for normal jobs when Galaxy is configured with
     app.config.outputs_to_working_directory. Job runner base class
     is responsible for copying these out after job is complete.
@@ -91,9 +88,8 @@ class OutputsToWorkingDirectoryPathRewriter:
         self.outputs_directory_name = outputs_directory_name
 
     def rewrite_dataset_path(self, dataset, dataset_type):
-        """ Keep path the same.
-        """
-        if dataset_type == 'output':
+        """Keep path the same."""
+        if dataset_type == "output":
             base_output_directory = os.path.abspath(self.working_directory)
             if self.outputs_directory_name is not None:
                 base_output_directory = os.path.join(base_output_directory, self.outputs_directory_name)
@@ -105,7 +101,7 @@ class OutputsToWorkingDirectoryPathRewriter:
 
 
 class TaskPathRewriter:
-    """ Rewrites all paths to place them in the specified working
+    """Rewrites all paths to place them in the specified working
     directory for TaskWrapper. TaskWrapper is responsible for putting
     them there and pulling them out.
     """
@@ -115,15 +111,18 @@ class TaskPathRewriter:
         self.job_dataset_path_rewriter = job_dataset_path_rewriter
 
     def rewrite_dataset_path(self, dataset, dataset_type):
-        """
-        """
+        """ """
         dataset_file_name = dataset.file_name
         job_file_name = self.job_dataset_path_rewriter.rewrite_dataset_path(dataset, dataset_type) or dataset_file_name
         return os.path.join(self.working_directory, os.path.basename(job_file_name))
 
 
 def get_path_rewriter(outputs_to_working_directory, working_directory, outputs_directory, is_task):
-    job_dataset_path_rewriter = OutputsToWorkingDirectoryPathRewriter(working_directory, outputs_directory) if outputs_to_working_directory else NullDatasetPathRewriter()
+    job_dataset_path_rewriter = (
+        OutputsToWorkingDirectoryPathRewriter(working_directory, outputs_directory)
+        if outputs_to_working_directory
+        else NullDatasetPathRewriter()
+    )
     if is_task:
         return TaskPathRewriter(working_directory, job_dataset_path_rewriter=job_dataset_path_rewriter)
     return job_dataset_path_rewriter
diff --git a/lib/galaxy/job_execution/output_collect.py b/lib/galaxy/job_execution/output_collect.py
index 05dbc41b29a..d5fe7ac089a 100644
--- a/lib/galaxy/job_execution/output_collect.py
+++ b/lib/galaxy/job_execution/output_collect.py
@@ -5,7 +5,13 @@ import operator
 import os
 import re
 from tempfile import NamedTemporaryFile
-from typing import Callable, Dict, List, Optional, Union
+from typing import (
+    Callable,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
 
 from sqlalchemy.orm.scoping import ScopedSession
 
@@ -23,9 +29,11 @@ from galaxy.model.store.discover import (
     discover_target_directory,
     DiscoveredFile,
     JsonCollectedDatasetMatch,
-    MetadataSourceProvider as AbstractMetadataSourceProvider,
-    ModelPersistenceContext,
-    PermissionProvider as AbstractPermissionProvider,
+)
+from galaxy.model.store.discover import MetadataSourceProvider as AbstractMetadataSourceProvider
+from galaxy.model.store.discover import ModelPersistenceContext
+from galaxy.model.store.discover import PermissionProvider as AbstractPermissionProvider
+from galaxy.model.store.discover import (
     persist_elements_to_folder,
     persist_elements_to_hdca,
     persist_hdas,
@@ -56,7 +64,6 @@ log = logging.getLogger(__name__)
 # PermissionProvider and MetadataSourceProvider are abstractions over input data used to
 # collect and produce dynamic outputs.
 class PermissionProvider(AbstractPermissionProvider):
-
     def __init__(self, inp_data, security_agent, job):
         self._job = job
         self._security_agent = security_agent
@@ -88,7 +95,6 @@ class PermissionProvider(AbstractPermissionProvider):
 
 
 class MetadataSourceProvider(AbstractMetadataSourceProvider):
-
     def __init__(self, inp_data):
         self._inp_data = inp_data
 
@@ -162,7 +168,9 @@ def collect_dynamic_outputs(
 
         try:
             collection_builder = builder.BoundCollectionBuilder(collection)
-            dataset_collectors = [dataset_collector(description) for description in output_collection_def.dataset_collector_descriptions]
+            dataset_collectors = [
+                dataset_collector(description) for description in output_collection_def.dataset_collector_descriptions
+            ]
             output_name = output_collection_def.name
             filenames = job_context.find_files(output_name, collection, dataset_collectors)
             job_context.populate_collection_elements(
@@ -190,7 +198,9 @@ class BaseJobContext:
 
     def find_files(self, output_name, collection, dataset_collectors):
         filenames = {}
-        for discovered_file in discover_files(output_name, self.tool_provided_metadata, dataset_collectors, self.job_working_directory, collection):
+        for discovered_file in discover_files(
+            output_name, self.tool_provided_metadata, dataset_collectors, self.job_working_directory, collection
+        ):
             self.increment_discovered_file_count()
             filenames[discovered_file.path] = discovered_file
         return filenames
@@ -200,20 +210,19 @@ class BaseJobContext:
 
 
 class JobContext(ModelPersistenceContext, BaseJobContext):
-
     def __init__(
-            self,
-            tool,
-            tool_provided_metadata,
-            job,
-            job_working_directory,
-            permission_provider,
-            metadata_source_provider,
-            input_dbkey,
-            object_store,
-            final_job_state,
-            max_discovered_files: Optional[int],
-            flush_per_n_datasets=None,
+        self,
+        tool,
+        tool_provided_metadata,
+        job,
+        job_working_directory,
+        permission_provider,
+        metadata_source_provider,
+        input_dbkey,
+        object_store,
+        final_job_state,
+        max_discovered_files: Optional[int],
+        flush_per_n_datasets=None,
     ):
         self.tool = tool
         self._metadata_source_provider = metadata_source_provider
@@ -227,7 +236,7 @@ class JobContext(ModelPersistenceContext, BaseJobContext):
         self._object_store = object_store
         self.final_job_state = final_job_state
         self._flush_per_n_datasets = flush_per_n_datasets
-        self.max_discovered_files = float('inf') if max_discovered_files is None else max_discovered_files
+        self.max_discovered_files = float("inf") if max_discovered_files is None else max_discovered_files
         self.discovered_file_count = 0
         self._tag_handler = None
 
@@ -240,6 +249,7 @@ class JobContext(ModelPersistenceContext, BaseJobContext):
     @property
     def work_context(self):
         from galaxy.work.context import WorkRequestContext
+
         return WorkRequestContext(self.app, user=self.user)
 
     @property
@@ -287,7 +297,9 @@ class JobContext(ModelPersistenceContext, BaseJobContext):
     def get_library_folder(self, destination):
         app = self.app
         library_folder_manager = app.library_folder_manager
-        library_folder = library_folder_manager.get(self.work_context, app.security.decode_id(destination.get("library_folder_id")))
+        library_folder = library_folder_manager.get(
+            self.work_context, app.security.decode_id(destination.get("library_folder_id"))
+        )
         return library_folder
 
     def get_hdca(self, object_id):
@@ -304,9 +316,7 @@ class JobContext(ModelPersistenceContext, BaseJobContext):
         history = self.job.history
         trans = self.work_context
         collection_manager = self.app.dataset_collection_manager
-        hdca = collection_manager.precreate_dataset_collection_instance(
-            trans, history, name, structure=structure
-        )
+        hdca = collection_manager.precreate_dataset_collection_instance(trans, history, name, structure=structure)
         return hdca
 
     def add_output_dataset_association(self, name, dataset):
@@ -327,7 +337,9 @@ class JobContext(ModelPersistenceContext, BaseJobContext):
         # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
         trans.app.security_agent.copy_library_permissions(trans, ld, ldda)
         # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset
-        trans.app.security_agent.set_all_dataset_permissions(ldda.dataset, trans.app.security_agent.user_get_default_permissions(trans.user))
+        trans.app.security_agent.set_all_dataset_permissions(
+            ldda.dataset, trans.app.security_agent.user_get_default_permissions(trans.user)
+        )
         library_folder.add_library_dataset(ld, genome_build=ldda.dbkey)
         trans.sa_session.add(library_folder)
         trans.sa_session.flush()
@@ -378,15 +390,24 @@ class JobContext(ModelPersistenceContext, BaseJobContext):
 
 
 class SessionlessJobContext(SessionlessModelPersistenceContext, BaseJobContext):
-
-    def __init__(self, metadata_params, tool_provided_metadata, object_store, export_store, import_store, working_directory, final_job_state, max_discovered_files: Optional[int]):
+    def __init__(
+        self,
+        metadata_params,
+        tool_provided_metadata,
+        object_store,
+        export_store,
+        import_store,
+        working_directory,
+        final_job_state,
+        max_discovered_files: Optional[int],
+    ):
         # TODO: use a metadata source provider... (pop from inputs and add parameter)
         super().__init__(object_store, export_store, working_directory)
         self.metadata_params = metadata_params
         self.tool_provided_metadata = tool_provided_metadata
         self.import_store = import_store
         self.final_job_state = final_job_state
-        self.max_discovered_files = float('inf') if max_discovered_files is None else max_discovered_files
+        self.max_discovered_files = float("inf") if max_discovered_files is None else max_discovered_files
         self.discovered_file_count = 0
 
     def output_collection_def(self, name):
@@ -453,9 +474,13 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
         dataset_collectors = [DEFAULT_DATASET_COLLECTOR]
         output_def = job_context.output_def(name)
         if output_def is not None:
-            dataset_collectors = [dataset_collector(description) for description in output_def.dataset_collector_descriptions]
+            dataset_collectors = [
+                dataset_collector(description) for description in output_def.dataset_collector_descriptions
+            ]
         filenames = {}
-        for discovered_file in discover_files(name, job_context.tool_provided_metadata, dataset_collectors, job_working_directory, outdata):
+        for discovered_file in discover_files(
+            name, job_context.tool_provided_metadata, dataset_collectors, job_working_directory, outdata
+        ):
             job_context.increment_discovered_file_count()
             filenames[discovered_file.path] = discovered_file
         for filename_index, (filename, discovered_file) in enumerate(filenames.items()):
@@ -490,10 +515,12 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
 
             # TODO: should be able to disambiguate files in different directories...
             new_primary_filename = os.path.split(filename)[-1]
-            new_primary_datasets_attributes = job_context.tool_provided_metadata.get_new_dataset_meta_by_basename(name, new_primary_filename)
+            new_primary_datasets_attributes = job_context.tool_provided_metadata.get_new_dataset_meta_by_basename(
+                name, new_primary_filename
+            )
             extra_files = None
             if new_primary_datasets_attributes:
-                extra_files_path = new_primary_datasets_attributes.get('extra_files', None)
+                extra_files_path = new_primary_datasets_attributes.get("extra_files", None)
                 if extra_files_path:
                     extra_files = os.path.join(job_working_directory, extra_files_path)
             primary_data = job_context.create_dataset(
@@ -508,10 +535,10 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
                 init_from=outdata,
                 dataset_attributes=new_primary_datasets_attributes,
                 creating_job_id=job_context.get_job_id() if job_context else None,
-                storage_callbacks=storage_callbacks
+                storage_callbacks=storage_callbacks,
             )
             # Associate new dataset with job
-            job_context.add_output_dataset_association(f'__new_primary_file_{name}|{designation}__', primary_data)
+            job_context.add_output_dataset_association(f"__new_primary_file_{name}|{designation}__", primary_data)
             job_context.add_datasets_to_history([primary_data], for_output_dataset=outdata)
             # Add dataset to return dict
             primary_datasets[name][designation] = primary_data
@@ -540,7 +567,11 @@ def discover_files(output_name, tool_provided_metadata, extra_file_collectors, j
         for dataset in tool_provided_metadata.get_new_datasets(output_name):
             filename = dataset["filename"]
             path = os.path.join(target_directory, filename)
-            yield DiscoveredFile(path, extra_file_collector, JsonCollectedDatasetMatch(dataset, extra_file_collector, filename, path=path))
+            yield DiscoveredFile(
+                path,
+                extra_file_collector,
+                JsonCollectedDatasetMatch(dataset, extra_file_collector, filename, path=path),
+            )
     else:
         for (match, collector) in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable):
             yield DiscoveredFile(match.path, collector, match)
@@ -549,7 +580,9 @@ def discover_files(output_name, tool_provided_metadata, extra_file_collectors, j
 def walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable):
     for extra_file_collector in extra_file_collectors:
         assert extra_file_collector.discover_via == "pattern"
-        for match in walk_over_extra_files(extra_file_collector.directory, extra_file_collector, job_working_directory, matchable):
+        for match in walk_over_extra_files(
+            extra_file_collector.directory, extra_file_collector, job_working_directory, matchable
+        ):
             yield match, extra_file_collector
 
 
@@ -570,7 +603,9 @@ def walk_over_extra_files(target_dir, extra_file_collector, job_working_director
                     new_parent_paths = parent_paths[:]
                     new_parent_paths.append(filename)
                     # The current directory is already validated, so use that as the next job_working_directory when recursing
-                    for match in walk_over_extra_files(filename, extra_file_collector, directory, matchable, parent_paths=new_parent_paths):
+                    for match in walk_over_extra_files(
+                        filename, extra_file_collector, directory, matchable, parent_paths=new_parent_paths
+                    ):
                         yield match
             else:
                 match = extra_file_collector.match(matchable, filename, path=path, parent_paths=parent_paths)
@@ -594,7 +629,6 @@ def dataset_collector(dataset_collection_description):
 
 
 class ToolMetadataDatasetCollector:
-
     def __init__(self, dataset_collection_description):
         self.discover_via = dataset_collection_description.discover_via
         self.default_dbkey = dataset_collection_description.default_dbkey
@@ -605,7 +639,6 @@ class ToolMetadataDatasetCollector:
 
 
 class DatasetCollector:
-
     def __init__(self, dataset_collection_description):
         self.discover_via = dataset_collection_description.discover_via
         # dataset_collection_description is an abstract description
@@ -623,7 +656,7 @@ class DatasetCollector:
         self.match_relative_path = dataset_collection_description.match_relative_path
 
     def _pattern_for_dataset(self, dataset_instance=None):
-        token_replacement = r'\d+'
+        token_replacement = r"\d+"
         if dataset_instance:
             token_replacement = str(dataset_instance.id)
         return self.pattern.replace(DATASET_ID_TOKEN, token_replacement)
@@ -680,7 +713,7 @@ def read_exit_code_from(exit_code_file, id_tag):
 
 
 def default_exit_code_file(files_dir, id_tag):
-    return os.path.join(files_dir, f'galaxy_{id_tag}.ec')
+    return os.path.join(files_dir, f"galaxy_{id_tag}.ec")
 
 
 def collect_extra_files(object_store, dataset, job_working_directory):
@@ -693,7 +726,7 @@ def collect_extra_files(object_store, dataset, job_working_directory):
         # not be created in the object store at all, which might be a
         # problem.
         for root, _dirs, files in os.walk(temp_file_path):
-            extra_dir = root.replace(os.path.join(job_working_directory, "working"), '', 1).lstrip(os.path.sep)
+            extra_dir = root.replace(os.path.join(job_working_directory, "working"), "", 1).lstrip(os.path.sep)
             for f in files:
                 object_store.update_from_file(
                     dataset.dataset,
@@ -701,26 +734,28 @@ def collect_extra_files(object_store, dataset, job_working_directory):
                     alt_name=f,
                     file_name=os.path.join(root, f),
                     create=True,
-                    preserve_symlinks=True
+                    preserve_symlinks=True,
                 )
     except Exception as e:
         log.debug("Error in collect_associated_files: %s", unicodify(e))
 
     # Handle composite datatypes of auto_primary_file type
-    if dataset.datatype.composite_type == 'auto_primary_file' and not dataset.has_data():
+    if dataset.datatype.composite_type == "auto_primary_file" and not dataset.has_data():
         try:
-            with NamedTemporaryFile(mode='w') as temp_fh:
+            with NamedTemporaryFile(mode="w") as temp_fh:
                 temp_fh.write(dataset.datatype.generate_primary_file(dataset))
                 temp_fh.flush()
                 object_store.update_from_file(dataset.dataset, file_name=temp_fh.name, create=True)
                 dataset.set_size()
         except Exception as e:
-            log.warning('Unable to generate primary composite file automatically for %s: %s', dataset.dataset.id, unicodify(e))
+            log.warning(
+                "Unable to generate primary composite file automatically for %s: %s", dataset.dataset.id, unicodify(e)
+            )
 
 
 def collect_shrinked_content_from_path(path):
     try:
-        with open(path, 'rb') as fh:
+        with open(path, "rb") as fh:
             return shrink_and_unicodify(fh.read().strip())
     except FileNotFoundError:
         return None
diff --git a/lib/galaxy/job_execution/ports/__init__.py b/lib/galaxy/job_execution/ports/__init__.py
index a8838df5aa0..db717ad245e 100644
--- a/lib/galaxy/job_execution/ports/__init__.py
+++ b/lib/galaxy/job_execution/ports/__init__.py
@@ -1,3 +1,3 @@
 from .view import JobPortsView
 
-__all__ = ('JobPortsView', )
+__all__ = ("JobPortsView",)
diff --git a/lib/galaxy/job_execution/ports/view.py b/lib/galaxy/job_execution/ports/view.py
index 0b4c94c5c7e..807c2d5d4b7 100644
--- a/lib/galaxy/job_execution/ports/view.py
+++ b/lib/galaxy/job_execution/ports/view.py
@@ -2,15 +2,17 @@ import logging
 
 from galaxy import (
     model,
-    util
+    util,
+)
+from galaxy.exceptions import (
+    ItemAccessibilityException,
+    ObjectAttributeMissingException,
 )
-from galaxy.exceptions import ItemAccessibilityException, ObjectAttributeMissingException
 
 log = logging.getLogger(__name__)
 
 
 class JobPortsView:
-
     def __init__(self, app):
         self._app = app
 
diff --git a/lib/galaxy/job_execution/setup.py b/lib/galaxy/job_execution/setup.py
index e4f827bbc43..709580bc578 100644
--- a/lib/galaxy/job_execution/setup.py
+++ b/lib/galaxy/job_execution/setup.py
@@ -1,7 +1,15 @@
 """Utilities to help job and tool code setup jobs."""
 import json
 import os
-from typing import Any, cast, Dict, List, Optional, Tuple, Union
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
 
 from galaxy.files import (
     ConfiguredFileSources,
@@ -21,8 +29,8 @@ from galaxy.model import (
 from galaxy.util import safe_makedirs
 from galaxy.util.dictifiable import Dictifiable
 
-TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json'
-TOOL_PROVIDED_JOB_METADATA_KEYS = ['name', 'info', 'dbkey', 'created_from_basename']
+TOOL_PROVIDED_JOB_METADATA_FILE = "galaxy.json"
+TOOL_PROVIDED_JOB_METADATA_KEYS = ["name", "info", "dbkey", "created_from_basename"]
 
 
 OutputHdasAndType = Dict[str, Tuple[DatasetInstance, DatasetPath]]
@@ -31,56 +39,57 @@ OutputPaths = List[DatasetPath]
 
 class JobIO(Dictifiable):
     dict_collection_visible_keys = (
-        'job_id',
-        'working_directory',
-        'outputs_directory',
-        'outputs_to_working_directory',
-        'galaxy_url',
-        'version_path',
-        'tool_directory',
-        'home_directory',
-        'tmp_directory',
-        'tool_data_path',
-        'galaxy_data_manager_data_path',
-        'new_file_path',
-        'len_file_path',
-        'builds_file_path',
-        'file_sources_dict',
-        'check_job_script_integrity',
-        'check_job_script_integrity_count',
-        'check_job_script_integrity_sleep',
-        'tool_source',
-        'tool_source_class',
-        'tool_dir',
-        'is_task',
+        "job_id",
+        "working_directory",
+        "outputs_directory",
+        "outputs_to_working_directory",
+        "galaxy_url",
+        "version_path",
+        "tool_directory",
+        "home_directory",
+        "tmp_directory",
+        "tool_data_path",
+        "galaxy_data_manager_data_path",
+        "new_file_path",
+        "len_file_path",
+        "builds_file_path",
+        "file_sources_dict",
+        "check_job_script_integrity",
+        "check_job_script_integrity_count",
+        "check_job_script_integrity_sleep",
+        "tool_source",
+        "tool_source_class",
+        "tool_dir",
+        "is_task",
     )
 
     def __init__(
-            self,
-            sa_session,
-            job: Job,
-            working_directory: str,
-            outputs_directory: str,
-            outputs_to_working_directory: bool,
-            galaxy_url: str,
-            version_path: str,
-            tool_directory: str,
-            home_directory: str,
-            tmp_directory: str,
-            tool_data_path: str,
-            galaxy_data_manager_data_path: str,
-            new_file_path: str,
-            len_file_path: str,
-            builds_file_path: str,
-            check_job_script_integrity: bool,
-            check_job_script_integrity_count: int,
-            check_job_script_integrity_sleep: float,
-            file_sources_dict: Dict[str, Any],
-            user_context: Union[ProvidesUserFileSourcesUserContext, Dict['str', Any]],
-            tool_source: Optional[str] = None,
-            tool_source_class: Optional['str'] = 'XmlToolSource',
-            tool_dir: Optional[str] = None,
-            is_task: bool = False):
+        self,
+        sa_session,
+        job: Job,
+        working_directory: str,
+        outputs_directory: str,
+        outputs_to_working_directory: bool,
+        galaxy_url: str,
+        version_path: str,
+        tool_directory: str,
+        home_directory: str,
+        tmp_directory: str,
+        tool_data_path: str,
+        galaxy_data_manager_data_path: str,
+        new_file_path: str,
+        len_file_path: str,
+        builds_file_path: str,
+        check_job_script_integrity: bool,
+        check_job_script_integrity_count: int,
+        check_job_script_integrity_sleep: float,
+        file_sources_dict: Dict[str, Any],
+        user_context: Union[ProvidesUserFileSourcesUserContext, Dict["str", Any]],
+        tool_source: Optional[str] = None,
+        tool_source_class: Optional["str"] = "XmlToolSource",
+        tool_dir: Optional[str] = None,
+        is_task: bool = False,
+    ):
         user_context_instance: Union[ProvidesUserFileSourcesUserContext, DictFileSourcesUserContext]
         if isinstance(user_context, dict):
             user_context_instance = DictFileSourcesUserContext(**user_context)
@@ -123,18 +132,18 @@ class JobIO(Dictifiable):
 
     @classmethod
     def from_dict(cls, io_dict, sa_session):
-        io_dict.pop('model_class')
-        job_id = io_dict.pop('job_id')
+        io_dict.pop("model_class")
+        job_id = io_dict.pop("job_id")
         job = sa_session.query(Job).get(job_id)
         return cls(sa_session=sa_session, job=job, **io_dict)
 
     def to_dict(self):
         io_dict = super().to_dict()
-        io_dict['user_context'] = self.user_context.to_dict()
+        io_dict["user_context"] = self.user_context.to_dict()
         return io_dict
 
     def to_json(self, path):
-        with open(path, 'w') as out:
+        with open(path, "w") as out:
             out.write(json.dumps(self.to_dict()))
 
     @property
@@ -191,7 +200,7 @@ class JobIO(Dictifiable):
 
     def get_input_path(self, dataset: DatasetInstance):
         real_path = dataset.file_name
-        false_path = self.dataset_path_rewriter.rewrite_dataset_path(dataset, 'input')
+        false_path = self.dataset_path_rewriter.rewrite_dataset_path(dataset, "input")
         return DatasetPath(
             dataset.dataset.id,
             real_path=real_path,
@@ -232,15 +241,17 @@ class JobIO(Dictifiable):
 
         results = []
         for da in job.output_datasets + job.output_library_datasets:
-            da_false_path = dataset_path_rewriter.rewrite_dataset_path(da.dataset, 'output')
+            da_false_path = dataset_path_rewriter.rewrite_dataset_path(da.dataset, "output")
             mutable = da.dataset.dataset.external_filename is None
-            dataset_path = DatasetPath(da.dataset.dataset.id, da.dataset.file_name, false_path=da_false_path, mutable=mutable)
+            dataset_path = DatasetPath(
+                da.dataset.dataset.id, da.dataset.file_name, false_path=da_false_path, mutable=mutable
+            )
             results.append((da.name, da.dataset, dataset_path))
 
         self._output_paths = [t[2] for t in results]
         self._output_hdas_and_paths = {t[0]: t[1:] for t in results}
         if special:
-            false_path = dataset_path_rewriter.rewrite_dataset_path(special, 'output')
+            false_path = dataset_path_rewriter.rewrite_dataset_path(special, "output")
             dsp = DatasetPath(special.dataset.id, special.dataset.file_name, false_path)
             self._output_paths.append(dsp)
             self._output_hdas_and_paths["output_file"] = (special.fda, dsp)
@@ -262,8 +273,6 @@ def ensure_configs_directory(work_dir):
 
 
 def create_working_directory_for_job(object_store, job):
-    object_store.create(
-        job, base_dir='job_work', dir_only=True, obj_dir=True)
-    working_directory = object_store.get_filename(
-        job, base_dir='job_work', dir_only=True, obj_dir=True)
+    object_store.create(job, base_dir="job_work", dir_only=True, obj_dir=True)
+    working_directory = object_store.get_filename(job, base_dir="job_work", dir_only=True, obj_dir=True)
     return working_directory
diff --git a/lib/galaxy/job_metrics/__init__.py b/lib/galaxy/job_metrics/__init__.py
index bbc79ac4840..50a79af9745 100644
--- a/lib/galaxy/job_metrics/__init__.py
+++ b/lib/galaxy/job_metrics/__init__.py
@@ -47,12 +47,12 @@ class JobMetrics:
         self.set_destination_instrumenter(destination_id, instrumenter)
 
     def set_destination_conf_element(self, destination_id, element):
-        plugin_source = plugin_config.PluginConfigSource('xml', element)
+        plugin_source = plugin_config.PluginConfigSource("xml", element)
         instrumenter = JobInstrumenter(self.plugin_classes, plugin_source)
         self.set_destination_instrumenter(destination_id, instrumenter)
 
     def set_destination_conf_dicts(self, destination_id, conf_dicts):
-        plugin_source = plugin_config.PluginConfigSource('dict', conf_dicts)
+        plugin_source = plugin_config.PluginConfigSource("dict", conf_dicts)
         instrumenter = JobInstrumenter(self.plugin_classes, plugin_source)
         self.set_destination_instrumenter(destination_id, instrumenter)
 
@@ -66,11 +66,11 @@ class JobMetrics:
 
     def __plugins_dict(self):
         import galaxy.job_metrics.instrumenters
-        return plugin_config.plugins_dict(galaxy.job_metrics.instrumenters, 'plugin_type')
+
+        return plugin_config.plugins_dict(galaxy.job_metrics.instrumenters, "plugin_type")
 
 
 class NullJobInstrumenter:
-
     def pre_execute_commands(self, job_directory):
         return None
 
@@ -85,7 +85,6 @@ NULL_JOB_INSTRUMENTER = NullJobInstrumenter()
 
 
 class JobInstrumenter:
-
     def __init__(self, plugin_classes, plugins_source, **kwargs):
         self.extra_kwargs = kwargs
         self.plugin_classes = plugin_classes
diff --git a/lib/galaxy/job_metrics/collectl/cli.py b/lib/galaxy/job_metrics/collectl/cli.py
index bea4e4a7ba6..1c370fe1858 100644
--- a/lib/galaxy/job_metrics/collectl/cli.py
+++ b/lib/galaxy/job_metrics/collectl/cli.py
@@ -138,4 +138,4 @@ class CollectlCli:
             raise Exception("Problem running collectl command.")
 
 
-__all__ = ('CollectlCli', )
+__all__ = ("CollectlCli",)
diff --git a/lib/galaxy/job_metrics/collectl/processes.py b/lib/galaxy/job_metrics/collectl/processes.py
index c06037c0368..a665e76b82a 100644
--- a/lib/galaxy/job_metrics/collectl/processes.py
+++ b/lib/galaxy/job_metrics/collectl/processes.py
@@ -84,7 +84,7 @@ DEFAULT_STATISTICS = [
 
 
 def parse_process_statistics(statistics):
-    """ Turn string or list of strings into list of tuples in format ( stat,
+    """Turn string or list of strings into list of tuples in format ( stat,
     resource ) where stat is a value from STATISTIC_TYPES and resource is a
     value from PROCESS_COLUMNS.
     """
@@ -103,8 +103,7 @@ def parse_process_statistics(statistics):
 
 
 def generate_process_statistics(collectl_playback_cli, pid, statistics=DEFAULT_STATISTICS):
-    """ Playback collectl file and generate summary statistics.
-    """
+    """Playback collectl file and generate summary statistics."""
     with tempfile.NamedTemporaryFile() as tmp_tsv:
         collectl_playback_cli.run(stdout=tmp_tsv)
         with open(tmp_tsv.name) as tsv_file:
@@ -139,7 +138,6 @@ def _read_process_statistics(tsv_file, pid, statistics):
 
 
 class CollectlProcessSummarizer:
-
     def __init__(self, pid, statistics):
         self.pid = pid
         self.statistics = statistics
@@ -223,7 +221,7 @@ class CollectlProcessSummarizer:
 
 
 class CollectlProcessInterval:
-    """ Represent all rows in collectl playback file for given time slice with
+    """Represent all rows in collectl playback file for given time slice with
     ability to filter out just rows corresponding to the process tree
     corresponding to a given pid.
     """
@@ -248,4 +246,4 @@ def _tuplize_statistic(statistic):
     return statistic
 
 
-__all__ = ('generate_process_statistics', )
+__all__ = ("generate_process_statistics",)
diff --git a/lib/galaxy/job_metrics/collectl/stats.py b/lib/galaxy/job_metrics/collectl/stats.py
index ff974bacc76..a5685dd4288 100644
--- a/lib/galaxy/job_metrics/collectl/stats.py
+++ b/lib/galaxy/job_metrics/collectl/stats.py
@@ -4,7 +4,6 @@ memory.
 
 
 class StatisticsTracker:
-
     def __init__(self):
         self.min = None
         self.max = None
diff --git a/lib/galaxy/job_metrics/collectl/subsystems.py b/lib/galaxy/job_metrics/collectl/subsystems.py
index bac7e50eb19..d4816593c20 100644
--- a/lib/galaxy/job_metrics/collectl/subsystems.py
+++ b/lib/galaxy/job_metrics/collectl/subsystems.py
@@ -4,25 +4,22 @@ Subsystems are essentially monitoring plugins available within collectl.
 """
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
 
 class CollectlSubsystem(metaclass=ABCMeta):
-    """ Class providing an abstraction of collectl subsytems.
-    """
+    """Class providing an abstraction of collectl subsytems."""
 
     @property
     @abstractmethod
     def command_line_arg(self):
-        """ Return single letter command-line argument used by collectl CLI.
-        """
+        """Return single letter command-line argument used by collectl CLI."""
 
     @property
     @abstractmethod
     def name(self):
-        """ High-level name for subsystem as consumed by this module.
-        """
+        """High-level name for subsystem as consumed by this module."""
 
 
 class ProcessesSubsystem(CollectlSubsystem):
@@ -75,4 +72,4 @@ def get_subsystem(name):
     return SUBSYSTEM_DICT[name]
 
 
-__all__ = ('get_subsystem', )
+__all__ = ("get_subsystem",)
diff --git a/lib/galaxy/job_metrics/instrumenters/__init__.py b/lib/galaxy/job_metrics/instrumenters/__init__.py
index 27a21a7114c..cc15408da54 100644
--- a/lib/galaxy/job_metrics/instrumenters/__init__.py
+++ b/lib/galaxy/job_metrics/instrumenters/__init__.py
@@ -5,10 +5,9 @@ These are responsible for collecting and formatting a coherent set of metrics.
 import os.path
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
-
 from .. import formatting
 
 INSTRUMENT_FILE_PREFIX = "__instrument"
@@ -16,22 +15,23 @@ INSTRUMENT_FILE_PREFIX = "__instrument"
 
 class InstrumentPlugin(metaclass=ABCMeta):
     """Describes how to instrument job scripts and retrieve collected metrics."""
+
     formatter = formatting.JobMetricFormatter()
 
     @property
     @abstractmethod
     def plugin_type(self):
-        """ Short string providing labelling this plugin """
+        """Short string providing labelling this plugin"""
 
     def pre_execute_instrument(self, job_directory):
-        """ Optionally return one or more commands to instrument job. These
+        """Optionally return one or more commands to instrument job. These
         commands will be executed on the compute server prior to the job
         running.
         """
         return None
 
     def post_execute_instrument(self, job_directory):
-        """ Optionally return one or more commands to instrument job. These
+        """Optionally return one or more commands to instrument job. These
         commands will be executed on the compute server after the tool defined
         command is ran.
         """
@@ -39,14 +39,14 @@ class InstrumentPlugin(metaclass=ABCMeta):
 
     @abstractmethod
     def job_properties(self, job_id, job_directory):
-        """ Collect properties for this plugin from specified job directory.
+        """Collect properties for this plugin from specified job directory.
         This method will run on the Galaxy server and can assume files created
         in job_directory with pre_execute_instrument and
         post_execute_instrument are available.
         """
 
     def _instrument_file_name(self, name):
-        """ Provide a common pattern for naming files used by instrumentation
+        """Provide a common pattern for naming files used by instrumentation
         plugins - to ease their staging out of remote job directories.
         """
         return f"{INSTRUMENT_FILE_PREFIX}_{self.plugin_type}_{name}"
diff --git a/lib/galaxy/job_metrics/instrumenters/cgroup.py b/lib/galaxy/job_metrics/instrumenters/cgroup.py
index 5273465999e..48f07c1499a 100644
--- a/lib/galaxy/job_metrics/instrumenters/cgroup.py
+++ b/lib/galaxy/job_metrics/instrumenters/cgroup.py
@@ -3,7 +3,10 @@ import logging
 import numbers
 from collections import namedtuple
 
-from galaxy.util import asbool, nice_size
+from galaxy.util import (
+    asbool,
+    nice_size,
+)
 from . import InstrumentPlugin
 from .. import formatting
 
@@ -18,12 +21,12 @@ TITLES = {
     "memory.failcnt": "Failed to allocate memory count",
     "memory.oom_control.oom_kill_disable": "OOM Control enabled",
     "memory.oom_control.under_oom": "Was OOM Killer active?",
-    "cpuacct.usage": "CPU Time"
+    "cpuacct.usage": "CPU Time",
 }
 CONVERSION = {
     "memory.oom_control.oom_kill_disable": lambda x: "No" if x == 1 else "Yes",
     "memory.oom_control.under_oom": lambda x: "Yes" if x == 1 else "No",
-    "cpuacct.usage": lambda x: formatting.seconds_to_str(x / 10**9)  # convert nanoseconds
+    "cpuacct.usage": lambda x: formatting.seconds_to_str(x / 10**9),  # convert nanoseconds
 }
 CPU_USAGE_TEMPLATE = r"""
 if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" ]; then
@@ -37,7 +40,9 @@ if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" ]; then
         fi;
     done;
 fi
-""".replace("\n", " ").strip()
+""".replace(
+    "\n", " "
+).strip()
 MEMORY_USAGE_TEMPLATE = """
 if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" ]; then
     cgroup_path=$(cat "/proc/$$/cgroup" | awk -F':' '$2=="memory"{{print $3}}');
@@ -48,14 +53,15 @@ if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" ]; then
         echo "__$(basename $f)__" >> {metrics}; cat "$f" >> {metrics} 2>/dev/null;
     done;
 fi
-""".replace("\n", " ").strip()
+""".replace(
+    "\n", " "
+).strip()
 
 
 Metric = namedtuple("Metric", ("key", "subkey", "value"))
 
 
 class CgroupPluginFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         title = TITLES.get(key, key)
         if key in CONVERSION:
@@ -71,8 +77,8 @@ class CgroupPluginFormatter(formatting.JobMetricFormatter):
 
 
 class CgroupPlugin(InstrumentPlugin):
-    """ Plugin that collects memory and cpu utilization from within a cgroup.
-    """
+    """Plugin that collects memory and cpu utilization from within a cgroup."""
+
     plugin_type = "cgroup"
     formatter = CgroupPluginFormatter()
 
@@ -98,10 +104,14 @@ class CgroupPlugin(InstrumentPlugin):
 
     def __record_cgroup_cpu_usage(self, job_directory):
         # comounted cgroups (which cpu and cpuacct are on the supported Linux distros) can appear in any order (cpu,cpuacct or cpuacct,cpu)
-        return CPU_USAGE_TEMPLATE.format(metrics=self.__cgroup_metrics_file(job_directory), cgroup_mount=self.cgroup_mount)
+        return CPU_USAGE_TEMPLATE.format(
+            metrics=self.__cgroup_metrics_file(job_directory), cgroup_mount=self.cgroup_mount
+        )
 
     def __record_cgroup_memory_usage(self, job_directory):
-        return MEMORY_USAGE_TEMPLATE.format(metrics=self.__cgroup_metrics_file(job_directory), cgroup_mount=self.cgroup_mount)
+        return MEMORY_USAGE_TEMPLATE.format(
+            metrics=self.__cgroup_metrics_file(job_directory), cgroup_mount=self.cgroup_mount
+        )
 
     def __cgroup_metrics_file(self, job_directory):
         return self._instrument_file_path(job_directory, "_metrics")
@@ -126,7 +136,7 @@ class CgroupPlugin(InstrumentPlugin):
             metrics[metric.subkey] = metric.value
 
     def __read_key_value(self, line, key):
-        if line.startswith('__') and line.endswith('__'):
+        if line.startswith("__") and line.endswith("__"):
             # line is the beginning of a new param
             key = line[2:][:-2]
             return (None, key)
@@ -151,4 +161,4 @@ class CgroupPlugin(InstrumentPlugin):
             return value
 
 
-__all__ = ('CgroupPlugin', )
+__all__ = ("CgroupPlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/collectl.py b/lib/galaxy/job_metrics/instrumenters/collectl.py
index 3b696f0d89d..ee740c274d9 100644
--- a/lib/galaxy/job_metrics/instrumenters/collectl.py
+++ b/lib/galaxy/job_metrics/instrumenters/collectl.py
@@ -9,7 +9,7 @@ from .. import formatting
 from ..collectl import (
     cli,
     processes,
-    subsystems
+    subsystems,
 )
 
 log = logging.getLogger(__name__)
@@ -27,11 +27,12 @@ FORMATTED_RESOURCE_TITLES = {
     "WSYS": "Disk Writes",
 }
 
-EMPTY_COLLECTL_FILE_MESSAGE = "Skipping process summary due to empty file... job probably did not run long enough for collectl to gather data."
+EMPTY_COLLECTL_FILE_MESSAGE = (
+    "Skipping process summary due to empty file... job probably did not run long enough for collectl to gather data."
+)
 
 
 class CollectlFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         if key == "pid":
             return ("Process ID", int(value))
@@ -52,9 +53,10 @@ class CollectlFormatter(formatting.JobMetricFormatter):
 
 
 class CollectlPlugin(InstrumentPlugin):
-    """ Run collectl along with job to capture system and/or process data
+    """Run collectl along with job to capture system and/or process data
     according to specified collectl subsystems.
     """
+
     plugin_type = "collectl"
     formatter = CollectlFormatter()
 
@@ -71,7 +73,9 @@ class CollectlPlugin(InstrumentPlugin):
         self.log_collectl_program_output = util.asbool(kwargs.get("log_collectl_program_output", False))
         if self.summarize_process_data:
             if subsystems.get_subsystem("process") not in self.subsystems:
-                raise Exception("Collectl plugin misconfigured - cannot summarize_process_data without process subsystem being enabled.")
+                raise Exception(
+                    "Collectl plugin misconfigured - cannot summarize_process_data without process subsystem being enabled."
+                )
 
             process_statistics = kwargs.get("process_statistics", None)
             # None will let processes module use default set of statistics
@@ -82,7 +86,7 @@ class CollectlPlugin(InstrumentPlugin):
         commands = []
         # Capture PID of process so we can walk its ancestors when building
         # statistics for the whole job.
-        commands.append(f'''echo "$$" > '{self.__pid_file(job_directory)}' ''')
+        commands.append(f"""echo "$$" > '{self.__pid_file(job_directory)}' """)
         # Run collectl in record mode to capture process and system level
         # statistics according to supplied subsystems.
         commands.append(self.__collectl_record_command(job_directory))
@@ -167,11 +171,7 @@ class CollectlPlugin(InstrumentPlugin):
         self.collectl_recorder_args = collectl_recorder_args
 
     def __summarize_process_data(self, pid, collectl_log_path):
-        playback_cli_args = dict(
-            collectl_path=self.local_collectl_path,
-            playback_path=collectl_log_path,
-            sep="9"
-        )
+        playback_cli_args = dict(collectl_path=self.local_collectl_path, playback_path=collectl_log_path, sep="9")
         if not os.stat(collectl_log_path).st_size:
             log.debug(EMPTY_COLLECTL_FILE_MESSAGE)
             return []
@@ -212,4 +212,4 @@ def procfilt_argument(procfilt_on):
         return ""
 
 
-__all__ = ('CollectlPlugin', )
+__all__ = ("CollectlPlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/core.py b/lib/galaxy/job_metrics/instrumenters/core.py
index 9118d4b36ba..756524979cc 100644
--- a/lib/galaxy/job_metrics/instrumenters/core.py
+++ b/lib/galaxy/job_metrics/instrumenters/core.py
@@ -15,7 +15,6 @@ RUNTIME_SECONDS_KEY = "runtime_seconds"
 
 
 class CorePluginFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         value = int(value)
         if key == GALAXY_SLOTS_KEY:
@@ -27,13 +26,14 @@ class CorePluginFormatter(formatting.JobMetricFormatter):
         else:
             # TODO: Use localized version of this from galaxy.ini
             title = "Job Start Time" if key == START_EPOCH_KEY else "Job End Time"
-            return (title, time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(value)))
+            return (title, time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(value)))
 
 
 class CorePlugin(InstrumentPlugin):
-    """ Simple plugin that collects data without external dependencies. In
+    """Simple plugin that collects data without external dependencies. In
     particular it currently collects value set for Galaxy slots.
     """
+
     plugin_type = "core"
     formatter = CorePluginFormatter()
 
@@ -69,15 +69,15 @@ class CorePlugin(InstrumentPlugin):
 
     def __record_galaxy_slots_command(self, job_directory):
         galaxy_slots_file = self.__galaxy_slots_file(job_directory)
-        return f'''echo "$GALAXY_SLOTS" > '{galaxy_slots_file}' '''
+        return f"""echo "$GALAXY_SLOTS" > '{galaxy_slots_file}' """
 
     def __record_galaxy_memory_mb_command(self, job_directory):
         galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
-        return f'''echo "$GALAXY_MEMORY_MB" > '{galaxy_memory_mb_file}' '''
+        return f"""echo "$GALAXY_MEMORY_MB" > '{galaxy_memory_mb_file}' """
 
     def __record_seconds_since_epoch_to_file(self, job_directory, name):
         path = self._instrument_file_path(job_directory, f"epoch_{name}")
-        return f"date +\"%s\" > {path}"
+        return f'date +"%s" > {path}'
 
     def __read_seconds_since_epoch(self, job_directory, name):
         path = self._instrument_file_path(job_directory, f"epoch_{name}")
@@ -98,4 +98,4 @@ class CorePlugin(InstrumentPlugin):
         return value
 
 
-__all__ = ('CorePlugin', )
+__all__ = ("CorePlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/cpuinfo.py b/lib/galaxy/job_metrics/instrumenters/cpuinfo.py
index 9d6ed45e176..4c1672d3fbf 100644
--- a/lib/galaxy/job_metrics/instrumenters/cpuinfo.py
+++ b/lib/galaxy/job_metrics/instrumenters/cpuinfo.py
@@ -12,7 +12,6 @@ PROCESSOR_LINE = re.compile(r"processor\s*\:\s*(\d+)")
 
 
 class CpuInfoFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         if key == "processor_count":
             return "Processor Count", f"{int(value)}"
@@ -21,9 +20,10 @@ class CpuInfoFormatter(formatting.JobMetricFormatter):
 
 
 class CpuInfoPlugin(InstrumentPlugin):
-    """ Gather information about processor configuration from /proc/cpuinfo.
+    """Gather information about processor configuration from /proc/cpuinfo.
     Linux only.
     """
+
     plugin_type = "cpuinfo"
     formatter = CpuInfoFormatter()
 
@@ -60,4 +60,4 @@ class CpuInfoPlugin(InstrumentPlugin):
         return self._instrument_file_path(job_directory, "cpuinfo")
 
 
-__all__ = ('CpuInfoPlugin', )
+__all__ = ("CpuInfoPlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/env.py b/lib/galaxy/job_metrics/instrumenters/env.py
index 8e21dcd5709..b46d4a68796 100644
--- a/lib/galaxy/job_metrics/instrumenters/env.py
+++ b/lib/galaxy/job_metrics/instrumenters/env.py
@@ -13,9 +13,10 @@ class EnvFormatter(formatting.JobMetricFormatter):
 
 
 class EnvPlugin(InstrumentPlugin):
-    """ Instrumentation plugin capable of recording all or specific environment
+    """Instrumentation plugin capable of recording all or specific environment
     variables for a job at runtime.
     """
+
     plugin_type = "env"
     formatter = EnvFormatter()
 
@@ -28,29 +29,28 @@ class EnvPlugin(InstrumentPlugin):
         self.variables = variables
 
     def pre_execute_instrument(self, job_directory):
-        """ Use env to dump all environment variables to a file.
-        """
+        """Use env to dump all environment variables to a file."""
         return f"env > '{self.__env_file(job_directory)}'"
 
     def post_execute_instrument(self, job_directory):
         return None
 
     def job_properties(self, job_id, job_directory):
-        """ Recover environment variables dumped out on compute server and filter
+        """Recover environment variables dumped out on compute server and filter
         out specific variables if needed.
         """
         variables = self.variables
 
         properties = {}
-        env_string = ''.join(open(self.__env_file(job_directory)).readlines())
+        env_string = "".join(open(self.__env_file(job_directory)).readlines())
         while env_string:
             # Check if the next lines contain a shell function.
             # We use '\n\}\n' as regex termination because shell
             # functions can be nested.
             # We use the non-greedy '.+?' because of re.DOTALL .
-            m = re.match(r'([^=]+)=(\(\) \{.+?\n\})\n', env_string, re.DOTALL)
+            m = re.match(r"([^=]+)=(\(\) \{.+?\n\})\n", env_string, re.DOTALL)
             if m is None:
-                m = re.match('([^=]+)=(.*)\n', env_string)
+                m = re.match("([^=]+)=(.*)\n", env_string)
             if m is None:
                 # Some problem recording or reading back env output.
                 message_template = "Problem parsing env metric output for job %s - properties will be incomplete"
@@ -60,7 +60,7 @@ class EnvPlugin(InstrumentPlugin):
             (var, value) = m.groups()
             if not variables or var in variables:
                 properties[var] = value
-            env_string = env_string[m.end():]
+            env_string = env_string[m.end() :]
 
         return properties
 
@@ -68,4 +68,4 @@ class EnvPlugin(InstrumentPlugin):
         return self._instrument_file_path(job_directory, "vars")
 
 
-__all__ = ('EnvPlugin', )
+__all__ = ("EnvPlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/hostname.py b/lib/galaxy/job_metrics/instrumenters/hostname.py
index f8cbe26b8d3..813c44297ac 100644
--- a/lib/galaxy/job_metrics/instrumenters/hostname.py
+++ b/lib/galaxy/job_metrics/instrumenters/hostname.py
@@ -8,14 +8,13 @@ log = logging.getLogger(__name__)
 
 
 class HostnameFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         return key, value
 
 
 class HostnamePlugin(InstrumentPlugin):
-    """ Gather hostname
-    """
+    """Gather hostname"""
+
     plugin_type = "hostname"
     formatter = HostnameFormatter()
 
@@ -27,10 +26,10 @@ class HostnamePlugin(InstrumentPlugin):
 
     def job_properties(self, job_id, job_directory):
         with open(self.__instrument_hostname_path(job_directory)) as f:
-            return {'hostname': f.read().strip()}
+            return {"hostname": f.read().strip()}
 
     def __instrument_hostname_path(self, job_directory):
         return self._instrument_file_path(job_directory, "hostname")
 
 
-__all__ = ('HostnamePlugin', )
+__all__ = ("HostnamePlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/meminfo.py b/lib/galaxy/job_metrics/instrumenters/meminfo.py
index 7cdb212cc34..9c10a381f02 100644
--- a/lib/galaxy/job_metrics/instrumenters/meminfo.py
+++ b/lib/galaxy/job_metrics/instrumenters/meminfo.py
@@ -5,27 +5,23 @@ from galaxy import util
 from . import InstrumentPlugin
 from .. import formatting
 
-
 MEMINFO_LINE = re.compile(r"(\w+)\s*\:\s*(\d+) kB")
 
 # Important (non-verbose) meminfo property titles.
-MEMINFO_TITLES = {
-    "memtotal": "Total System Memory",
-    "swaptotal": "Total System Swap"
-}
+MEMINFO_TITLES = {"memtotal": "Total System Memory", "swaptotal": "Total System Swap"}
 
 
 class MemInfoFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         title = MEMINFO_TITLES.get(key, key)
         return title, util.nice_size(value * 1000)  # kB = *1000, KB = *1024 - wikipedia
 
 
 class MemInfoPlugin(InstrumentPlugin):
-    """ Gather information about processor configuration from /proc/cpuinfo.
+    """Gather information about processor configuration from /proc/cpuinfo.
     Linux only.
     """
+
     plugin_type = "meminfo"
     formatter = MemInfoFormatter()
 
@@ -58,4 +54,4 @@ class MemInfoPlugin(InstrumentPlugin):
         return self._instrument_file_path(job_directory, "meminfo")
 
 
-__all__ = ('MemInfoPlugin', )
+__all__ = ("MemInfoPlugin",)
diff --git a/lib/galaxy/job_metrics/instrumenters/uname.py b/lib/galaxy/job_metrics/instrumenters/uname.py
index 288ba2f5c42..b4f96434d6e 100644
--- a/lib/galaxy/job_metrics/instrumenters/uname.py
+++ b/lib/galaxy/job_metrics/instrumenters/uname.py
@@ -4,15 +4,15 @@ from .. import formatting
 
 
 class UnameFormatter(formatting.JobMetricFormatter):
-
     def format(self, key, value):
         return "Operating System", value
 
 
 class UnamePlugin(InstrumentPlugin):
-    """ Use uname to gather operating system information about remote system
+    """Use uname to gather operating system information about remote system
     job is running on. Linux only.
     """
+
     plugin_type = "uname"
     formatter = UnameFormatter()
 
@@ -32,4 +32,4 @@ class UnamePlugin(InstrumentPlugin):
         return self._instrument_file_path(job_directory, "uname")
 
 
-__all__ = ('UnamePlugin', )
+__all__ = ("UnamePlugin",)
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 7524e216adb..499210b86cd 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -13,7 +13,12 @@ import sys
 import time
 import traceback
 from json import loads
-from typing import Any, Dict, List, TYPE_CHECKING
+from typing import (
+    Any,
+    Dict,
+    List,
+    TYPE_CHECKING,
+)
 
 import packaging.version
 import yaml
@@ -36,11 +41,10 @@ from galaxy.job_execution.output_collect import (
     collect_extra_files,
     collect_shrinked_content_from_path,
 )
-from galaxy.job_execution.setup import (  # noqa: F401
+from galaxy.job_execution.setup import (  # noqa: F401; This is read by certain misbehaving tool wrappers that import Galaxy internals
     create_working_directory_for_job,
     ensure_configs_directory,
     JobIO,
-    # This is read by certain misbehaving tool wrappers that import Galaxy internals
     TOOL_PROVIDED_JOB_METADATA_FILE,
     TOOL_PROVIDED_JOB_METADATA_KEYS,
 )
@@ -48,7 +52,10 @@ from galaxy.jobs.mapper import (
     JobMappingException,
     JobRunnerMapper,
 )
-from galaxy.jobs.runners import BaseJobRunner, JobState
+from galaxy.jobs.runners import (
+    BaseJobRunner,
+    JobState,
+)
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.model import store
 from galaxy.model.store.discover import MaxDiscoveredFilesExceededError
@@ -67,7 +74,7 @@ from galaxy.util import (
     parse_xml_string,
     RWXRWXRWX,
     safe_makedirs,
-    unicodify
+    unicodify,
 )
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
@@ -82,7 +89,7 @@ if TYPE_CHECKING:
 log = logging.getLogger(__name__)
 
 # Override with config.default_job_shell.
-DEFAULT_JOB_SHELL = '/bin/bash'
+DEFAULT_JOB_SHELL = "/bin/bash"
 DEFAULT_LOCAL_WORKERS = 4
 
 DEFAULT_CLEANUP_JOB = "always"
@@ -95,22 +102,22 @@ class JobDestination(Bunch):
     """
 
     def __init__(self, **kwds):
-        self['id'] = None
-        self['url'] = None
-        self['tags'] = None
-        self['runner'] = None
-        self['legacy'] = False
-        self['converted'] = False
-        self['shell'] = None
-        self['env'] = []
-        self['resubmit'] = []
+        self["id"] = None
+        self["url"] = None
+        self["tags"] = None
+        self["runner"] = None
+        self["legacy"] = False
+        self["converted"] = False
+        self["shell"] = None
+        self["env"] = []
+        self["resubmit"] = []
         # dict is appropriate (rather than a bunch) since keys may not be valid as attributes
-        self['params'] = dict()
+        self["params"] = dict()
 
         # Use the values persisted in an existing job
-        if 'from_job' in kwds and kwds['from_job'].destination_id is not None:
-            self['id'] = kwds['from_job'].destination_id
-            self['params'] = kwds['from_job'].destination_params
+        if "from_job" in kwds and kwds["from_job"].destination_id is not None:
+            self["id"] = kwds["from_job"].destination_id
+            self["params"] = kwds["from_job"].destination_params
 
         super().__init__(**kwds)
 
@@ -124,9 +131,9 @@ class JobToolConfiguration(Bunch):
     """
 
     def __init__(self, **kwds):
-        self['handler'] = None
-        self['destination'] = None
-        self['params'] = dict()
+        self["handler"] = None
+        self["destination"] = None
+        self["params"] = dict()
         super().__init__(**kwds)
 
     def get_resource_group(self):
@@ -135,8 +142,8 @@ class JobToolConfiguration(Bunch):
 
 def config_exception(e, file):
     abs_path = os.path.abspath(file)
-    message = f'Problem parsing the XML in file {abs_path}, '
-    message += 'please correct the indicated portion of the file and restart Galaxy. '
+    message = f"Problem parsing the XML in file {abs_path}, "
+    message += "please correct the indicated portion of the file and restart Galaxy. "
     message += unicodify(e)
     log.exception(message)
     return Exception(message)
@@ -149,23 +156,20 @@ def job_config_xml_to_dict(config, root):
     config_dict["runners"] = runners
 
     # Parser plugins section populate 'runners' and 'dynamic' in config_dict.
-    plugins = root.find('plugins')
+    plugins = root.find("plugins")
     if plugins is not None:
-        for plugin in ConfiguresHandlers._findall_with_required(plugins, 'plugin', ('id', 'type', 'load')):
-            if plugin.get('type') == 'runner':
-                workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS))
+        for plugin in ConfiguresHandlers._findall_with_required(plugins, "plugin", ("id", "type", "load")):
+            if plugin.get("type") == "runner":
+                workers = plugin.get("workers", plugins.get("workers", JobConfiguration.DEFAULT_NWORKERS))
                 runner_kwds = JobConfiguration.get_params(config, plugin)
-                plugin_id = plugin.get('id')
-                runner_info = dict(id=plugin_id,
-                                   load=plugin.get('load'),
-                                   workers=int(workers),
-                                   kwds=runner_kwds)
+                plugin_id = plugin.get("id")
+                runner_info = dict(id=plugin_id, load=plugin.get("load"), workers=int(workers), kwds=runner_kwds)
                 runners[plugin_id] = runner_info
             else:
                 log.error(f"Unknown plugin type: {plugin.get('type')}")
 
-        for plugin in ConfiguresHandlers._findall_with_required(plugins, 'plugin', ('id', 'type')):
-            if plugin.get('id') == 'dynamic' and plugin.get('type') == 'runner':
+        for plugin in ConfiguresHandlers._findall_with_required(plugins, "plugin", ("id", "type")):
+            if plugin.get("id") == "dynamic" and plugin.get("type") == "runner":
                 config_dict["dynamic"] = JobConfiguration.get_params(config, plugin)
 
     handling_config_dict = ConfiguresHandlers.xml_to_dict(config, root.find("handlers"))
@@ -174,9 +178,9 @@ def job_config_xml_to_dict(config, root):
     # Parse destinations
     environments = []
 
-    destinations = root.find('destinations')
-    for destination in ConfiguresHandlers._findall_with_required(destinations, 'destination', ('id', 'runner')):
-        destination_id = destination.get('id')
+    destinations = root.find("destinations")
+    for destination in ConfiguresHandlers._findall_with_required(destinations, "destination", ("id", "runner")):
+        destination_id = destination.get("id")
         destination_metrics = destination.get("metrics", None)
 
         environment = {"id": destination_id}
@@ -188,9 +192,9 @@ def job_config_xml_to_dict(config, root):
             else:
                 metrics_to_dict = {"src": "path", "path": destination_metrics}
         else:
-            metrics_elements = ConfiguresHandlers._findall_with_required(destination, 'job_metrics', ())
+            metrics_elements = ConfiguresHandlers._findall_with_required(destination, "job_metrics", ())
             if metrics_elements:
-                metrics_to_dict = {"src": "xml_element", 'xml_element': metrics_elements[0]}
+                metrics_to_dict = {"src": "xml_element", "xml_element": metrics_elements[0]}
 
         environment["metrics"] = metrics_to_dict
 
@@ -200,45 +204,45 @@ def job_config_xml_to_dict(config, root):
             params["docker_sudo"] = "true"
 
         # TODO: handle enabled/disabled in configure_from
-        environment['params'] = params
-        environment['env'] = JobConfiguration.get_envs(destination)
+        environment["params"] = params
+        environment["env"] = JobConfiguration.get_envs(destination)
         destination_resubmits = JobConfiguration.get_resubmits(destination)
         if destination_resubmits:
-            environment['resubmit'] = destination_resubmits
+            environment["resubmit"] = destination_resubmits
         # TODO: handle empty resubmits defaults in configure_from
 
-        runner = destination.get('runner')
+        runner = destination.get("runner")
         if runner:
-            environment['runner'] = runner
+            environment["runner"] = runner
 
-        tags = destination.get('tags')
+        tags = destination.get("tags")
         # Store tags as a list
         if tags is not None:
-            tags = [x.strip() for x in tags.split(',')]
-            environment['tags'] = tags
+            tags = [x.strip() for x in tags.split(",")]
+            environment["tags"] = tags
 
         environments.append(environment)
 
-    config_dict['execution'] = {
-        'environments': environments,
+    config_dict["execution"] = {
+        "environments": environments,
     }
     default_destination = ConfiguresHandlers.get_xml_default(config, destinations)
     if default_destination:
-        config_dict['execution']['default'] = default_destination
+        config_dict["execution"]["default"] = default_destination
 
     resources_config_dict = {}
     resource_groups = {}
 
     # Parse resources...
-    resources = root.find('resources')
+    resources = root.find("resources")
     if resources is not None:
         default_resource_group = resources.get("default", None)
         if default_resource_group:
             resources_config_dict["default"] = default_resource_group
 
-        for group in ConfiguresHandlers._findall_with_required(resources, 'group'):
-            group_id = group.get('id')
-            fields_str = group.get('fields', None) or group.text or ''
+        for group in ConfiguresHandlers._findall_with_required(resources, "group"):
+            group_id = group.get("id")
+            fields_str = group.get("fields", None) or group.text or ""
             fields = [f for f in fields_str.split(",") if f]
             resource_groups[group_id] = fields
 
@@ -246,36 +250,36 @@ def job_config_xml_to_dict(config, root):
     config_dict["resources"] = resources_config_dict
 
     # Parse tool mappings
-    tools = root.find('tools')
-    config_dict['tools'] = []
+    tools = root.find("tools")
+    config_dict["tools"] = []
     if tools is not None:
-        for tool in tools.findall('tool'):
+        for tool in tools.findall("tool"):
             # There can be multiple definitions with identical ids, but different params
             tool_mapping_conf = {}
-            for key in ['handler', 'destination', 'id', 'resources', 'class']:
+            for key in ["handler", "destination", "id", "resources", "class"]:
                 value = tool.get(key)
                 if value:
                     if key == "destination":
                         key = "environment"
                     tool_mapping_conf[key] = value
             tool_mapping_conf["params"] = JobConfiguration.get_params(config, tool)
-            config_dict['tools'].append(tool_mapping_conf)
+            config_dict["tools"].append(tool_mapping_conf)
 
     limits_config = []
-    limits = root.find('limits')
+    limits = root.find("limits")
     if limits is not None:
-        for limit in JobConfiguration._findall_with_required(limits, 'limit', ('type',)):
+        for limit in JobConfiguration._findall_with_required(limits, "limit", ("type",)):
             limit_dict = {}
-            for key in ['type', 'tag', 'id', 'window']:
-                if key == 'type' and key.startswith('destination_'):
+            for key in ["type", "tag", "id", "window"]:
+                if key == "type" and key.startswith("destination_"):
                     key = f"environment_{key[len('destination_'):]}"
                 value = limit.get(key)
                 if value:
                     limit_dict[key] = value
-                limit_dict['value'] = limit.text
+                limit_dict["value"] = limit.text
             limits_config.append(limit_dict)
 
-    config_dict['limits'] = limits_config
+    config_dict["limits"] = limits_config
     return config_dict
 
 
@@ -284,6 +288,7 @@ class JobConfiguration(ConfiguresHandlers):
 
     These features are configured in the job configuration, by default, ``job_conf.xml``
     """
+
     runner_plugins: List[dict]
     handlers: dict
     handler_runner_plugins: Dict[str, str]
@@ -292,7 +297,7 @@ class JobConfiguration(ConfiguresHandlers):
     resource_groups: Dict[str, list]
     destinations: Dict[str, tuple]
     resource_parameters: Dict[str, Any]
-    DEFAULT_BASE_HANDLER_POOLS = ('job-handlers',)
+    DEFAULT_BASE_HANDLER_POOLS = ("job-handlers",)
 
     DEFAULT_NWORKERS = 4
 
@@ -308,8 +313,7 @@ class JobConfiguration(ConfiguresHandlers):
     </conditional>"""
 
     def __init__(self, app: MinimalManagerApp):
-        """Parse the job configuration XML.
-        """
+        """Parse the job configuration XML."""
         self.app = app
         self.runner_plugins = []
         self.dynamic_params = None
@@ -327,34 +331,38 @@ class JobConfiguration(ConfiguresHandlers):
         self.resource_groups = {}
         self.default_resource_group = None
         self.resource_parameters = {}
-        self.limits = Bunch(registered_user_concurrent_jobs=None,
-                            anonymous_user_concurrent_jobs=None,
-                            walltime=None,
-                            walltime_delta=None,
-                            total_walltime={},
-                            output_size=None,
-                            destination_user_concurrent_jobs={},
-                            destination_total_concurrent_jobs={})
+        self.limits = Bunch(
+            registered_user_concurrent_jobs=None,
+            anonymous_user_concurrent_jobs=None,
+            walltime=None,
+            walltime_delta=None,
+            total_walltime={},
+            output_size=None,
+            destination_user_concurrent_jobs={},
+            destination_total_concurrent_jobs={},
+        )
 
         default_resubmits = []
         default_resubmit_condition = self.app.config.default_job_resubmission_condition
         if default_resubmit_condition:
-            default_resubmits.append(dict(
-                environment=None,
-                condition=default_resubmit_condition,
-                handler=None,
-                delay=None,
-            ))
+            default_resubmits.append(
+                dict(
+                    environment=None,
+                    condition=default_resubmit_condition,
+                    handler=None,
+                    delay=None,
+                )
+            )
         self.default_resubmits = default_resubmits
 
         self.__parse_resource_parameters()
         # Initialize the config
         try:
-            if 'job_config' in self.app.config.config_dict:
+            if "job_config" in self.app.config.config_dict:
                 job_config_dict = self.app.config.config_dict["job_config"]
             else:
                 job_config_file = self.app.config.job_config_file
-                if '.xml' in job_config_file:
+                if ".xml" in job_config_file:
                     tree = load(job_config_file)
                     job_config_dict = self.__parse_job_conf_xml(tree)
                 else:
@@ -363,15 +371,19 @@ class JobConfiguration(ConfiguresHandlers):
 
             # Load tasks if configured
             if self.app.config.use_tasked_jobs:
-                job_config_dict["runners"]["tasks"] = dict(id='tasks', load='tasks', workers=self.app.config.local_task_queue_workers, kwds={})
+                job_config_dict["runners"]["tasks"] = dict(
+                    id="tasks", load="tasks", workers=self.app.config.local_task_queue_workers, kwds={}
+                )
 
             self._configure_from_dict(job_config_dict)
 
-            log.debug('Done loading job configuration')
+            log.debug("Done loading job configuration")
 
         except OSError:
-            log.warning('Job configuration "%s" does not exist, using default job configuration',
-                        self.app.config.job_config_file)
+            log.warning(
+                'Job configuration "%s" does not exist, using default job configuration',
+                self.app.config.job_config_file,
+            )
             self.__set_default_job_conf()
         except Exception as e:
             raise config_exception(e, job_config_file)
@@ -383,7 +395,7 @@ class JobConfiguration(ConfiguresHandlers):
                 # with a flat dictionary.
                 kwds = {}
                 for key, value in runner_info.items():
-                    if key in ['id', 'load', 'workers']:
+                    if key in ["id", "load", "workers"]:
                         continue
                     kwds[key] = value
                 runner_info["kwds"] = kwds
@@ -392,7 +404,7 @@ class JobConfiguration(ConfiguresHandlers):
                 continue
             runner_info["id"] = runner_id
             if runner_id == "dynamic":
-                log.warning('Deprecated treatment of dynamic running configuration as an actual job runner.')
+                log.warning("Deprecated treatment of dynamic running configuration as an actual job runner.")
                 self.dynamic_params = runner_info["kwds"]
                 continue
             self.runner_plugins.append(runner_info)
@@ -407,17 +419,20 @@ class JobConfiguration(ConfiguresHandlers):
             self._set_default_handler_assignment_methods()
         else:
             self.app.application_stack.init_job_handling(self)
-        log.info("Job handler assignment methods set to: %s", ', '.join(self.handler_assignment_methods))
+        log.info("Job handler assignment methods set to: %s", ", ".join(self.handler_assignment_methods))
         for tag, handlers in [(t, h) for t, h in self.handlers.items() if isinstance(h, list)]:
-            log.info("Tag [%s] handlers: %s", tag, ', '.join(handlers))
-        self.handler_ready_window_size = int(handling_config_dict.get(
-            'ready_window_size', JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE))
+            log.info("Tag [%s] handlers: %s", tag, ", ".join(handlers))
+        self.handler_ready_window_size = int(
+            handling_config_dict.get("ready_window_size", JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE)
+        )
 
         # Parse environments
         job_metrics = self.app.job_metrics
-        execution_dict = job_config_dict.get('execution', {})
+        execution_dict = job_config_dict.get("execution", {})
         environments = execution_dict.get("environments", [])
-        enviroment_iter = map(lambda e: (e["id"], e), environments) if isinstance(environments, list) else environments.items()
+        enviroment_iter = (
+            map(lambda e: (e["id"], e), environments) if isinstance(environments, list) else environments.items()
+        )
         for environment_id, environment_dict in enviroment_iter:
             metrics = environment_dict.get("metrics")
             if metrics is None:
@@ -445,12 +460,12 @@ class JobConfiguration(ConfiguresHandlers):
                 # allowing a flat configuration of these things.
                 params = {}
                 for key, value in environment_dict.items():
-                    if key in ['id', 'tags', 'runner', 'shell', 'env', 'resubmit']:
+                    if key in ["id", "tags", "runner", "shell", "env", "resubmit"]:
                         continue
                     params[key] = value
                 environment_dict["params"] = params
 
-            for key in ['tags', 'runner', 'shell', 'env', 'resubmit', 'params']:
+            for key in ["tags", "runner", "shell", "env", "resubmit", "params"]:
                 if key in environment_dict:
                     destination_kwds[key] = environment_dict[key]
             destination_kwds["id"] = environment_id
@@ -470,7 +485,9 @@ class JobConfiguration(ConfiguresHandlers):
                     self.destinations[tag].append(job_destination)
 
         # Determine the default destination
-        self.default_destination_id = self._ensure_default_set(execution_dict.get("default"), list(self.destinations.keys()), auto=True)
+        self.default_destination_id = self._ensure_default_set(
+            execution_dict.get("default"), list(self.destinations.keys()), auto=True
+        )
 
         # Read in resources
         resources = job_config_dict.get("resources", {})
@@ -478,13 +495,13 @@ class JobConfiguration(ConfiguresHandlers):
         for group_id, fields in resources.get("groups", {}).items():
             self.resource_groups[group_id] = fields
 
-        tools = job_config_dict.get('tools', [])
+        tools = job_config_dict.get("tools", [])
         for tool in tools:
-            raw_tool_id = tool.get('id')
-            tool_class = tool.get('class')
+            raw_tool_id = tool.get("id")
+            tool_class = tool.get("class")
             if raw_tool_id is not None:
                 assert tool_class is None
-                tool_id = raw_tool_id.lower().rstrip('/')
+                tool_id = raw_tool_id.lower().rstrip("/")
                 if tool_id not in self.tools:
                     self.tools[tool_id] = list()
             else:
@@ -509,46 +526,45 @@ class JobConfiguration(ConfiguresHandlers):
             else:
                 self.tool_classes[tool_class].append(jtc)
 
-        types = dict(registered_user_concurrent_jobs=int,
-                     anonymous_user_concurrent_jobs=int,
-                     walltime=str,
-                     total_walltime=str,
-                     output_size=util.size_to_bytes)
+        types = dict(
+            registered_user_concurrent_jobs=int,
+            anonymous_user_concurrent_jobs=int,
+            walltime=str,
+            total_walltime=str,
+            output_size=util.size_to_bytes,
+        )
 
         # Parse job limits
         for limit_dict in job_config_dict.get("limits", []):
-            limit_type = limit_dict.get('type')
+            limit_type = limit_dict.get("type")
             if limit_type.startswith("environment_"):
                 limit_type = f"destination_{limit_type[len('environment_'):]}"
 
             limit_value = limit_dict.get("value")
             # concurrent_jobs renamed to destination_user_concurrent_jobs in job_conf.xml
-            if limit_type in ('destination_user_concurrent_jobs', 'concurrent_jobs', 'destination_total_concurrent_jobs'):
-                id = limit_dict.get('tag', None) or limit_dict.get('id')
-                if limit_type == 'destination_total_concurrent_jobs':
+            if limit_type in (
+                "destination_user_concurrent_jobs",
+                "concurrent_jobs",
+                "destination_total_concurrent_jobs",
+            ):
+                id = limit_dict.get("tag", None) or limit_dict.get("id")
+                if limit_type == "destination_total_concurrent_jobs":
                     self.limits.destination_total_concurrent_jobs[id] = int(limit_value)
                 else:
                     self.limits.destination_user_concurrent_jobs[id] = int(limit_value)
-            elif limit_type == 'total_walltime':
-                self.limits.total_walltime["window"] = (
-                    int(limit_dict.get('window')) or 30
-                )
-                self.limits.total_walltime["raw"] = (
-                    types.get(limit_type, str)(limit_value)
-                )
+            elif limit_type == "total_walltime":
+                self.limits.total_walltime["window"] = int(limit_dict.get("window")) or 30
+                self.limits.total_walltime["raw"] = types.get(limit_type, str)(limit_value)
             elif limit_value:
                 self.limits.__dict__[limit_type] = types.get(limit_type, str)(limit_value)
 
         if self.limits.walltime is not None:
-            h, m, s = (int(v) for v in self.limits.walltime.split(':'))
+            h, m, s = (int(v) for v in self.limits.walltime.split(":"))
             self.limits.walltime_delta = datetime.timedelta(0, s, 0, 0, m, h)
 
         if "raw" in self.limits.total_walltime:
-            h, m, s = (int(v) for v in
-                       self.limits.total_walltime["raw"].split(':'))
-            self.limits.total_walltime["delta"] = datetime.timedelta(
-                0, s, 0, 0, m, h
-            )
+            h, m, s = (int(v) for v in self.limits.total_walltime["raw"].split(":"))
+            self.limits.total_walltime["delta"] = datetime.timedelta(0, s, 0, 0, m, h)
 
     def __parse_job_conf_xml(self, tree):
         """Loads the new-style job configuration from options in the job config file (by default, job_conf.xml).
@@ -557,7 +573,7 @@ class JobConfiguration(ConfiguresHandlers):
         :type tree: ``lxml.etree._Element``
         """
         root = tree.getroot()
-        log.debug(f'Loading job configuration from {self.app.config.job_config_file}')
+        log.debug(f"Loading job configuration from {self.app.config.job_config_file}")
 
         job_config_dict = job_config_xml_to_dict(self.app.config, root)
         return job_config_dict
@@ -570,10 +586,10 @@ class JobConfiguration(ConfiguresHandlers):
 
     def __set_default_job_conf(self):
         # Run jobs locally
-        self.runner_plugins = [dict(id='local', load='local', workers=DEFAULT_LOCAL_WORKERS)]
+        self.runner_plugins = [dict(id="local", load="local", workers=DEFAULT_LOCAL_WORKERS)]
         # Load tasks if configured
         if self.app.config.use_tasked_jobs:
-            self.runner_plugins.append(dict(id='tasks', load='tasks', workers=DEFAULT_LOCAL_WORKERS))
+            self.runner_plugins.append(dict(id="tasks", load="tasks", workers=DEFAULT_LOCAL_WORKERS))
         # Set the handlers
         self._init_handler_assignment_methods()
         if not self.handler_assignment_methods_configured:
@@ -582,12 +598,12 @@ class JobConfiguration(ConfiguresHandlers):
             self.app.application_stack.init_job_handling(self)
         self.handler_ready_window_size = JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE
         # Set the destination
-        self.default_destination_id = 'local'
-        self.destinations['local'] = [JobDestination(id='local', runner='local')]
-        log.debug('Done loading job configuration')
+        self.default_destination_id = "local"
+        self.destinations["local"] = [JobDestination(id="local", runner="local")]
+        log.debug("Done loading job configuration")
 
     def get_tool_resource_xml(self, tool_id, tool_type):
-        """ Given a tool id, return XML elements describing parameters to
+        """Given a tool id, return XML elements describing parameters to
         insert into job resources.
 
         :tool id: A tool ID (a string)
@@ -595,7 +611,7 @@ class JobConfiguration(ConfiguresHandlers):
 
         :returns: List of parameter elements.
         """
-        if tool_id and tool_type in ('default', 'manage_data'):
+        if tool_id and tool_type in ("default", "manage_data"):
             # TODO: Only works with exact matches, should handle different kinds of ids
             # the way destination lookup does.
             resource_group = None
@@ -615,7 +631,7 @@ class JobConfiguration(ConfiguresHandlers):
 
                 if fields:
                     conditional_element = parse_xml_string(self.JOB_RESOURCE_CONDITIONAL_XML)
-                    when_yes_elem = conditional_element.findall('when')[1]
+                    when_yes_elem = conditional_element.findall("when")[1]
                     for parameter in fields:
                         when_yes_elem.append(parameter)
                     return conditional_element
@@ -626,19 +642,19 @@ class JobConfiguration(ConfiguresHandlers):
     @staticmethod
     def get_params(config, parent):
         rval = {}
-        for param in parent.findall('param'):
-            key = param.get('id')
+        for param in parent.findall("param"):
+            key = param.get("id")
             if key in ["container", "container_override"]:
-                containers = map(requirements.container_from_element, param.findall('container'))
+                containers = map(requirements.container_from_element, param.findall("container"))
                 param_value = list(map(lambda c: c.to_dict(), containers))
             else:
                 param_value = param.text
 
-            if 'from_environ' in param.attrib:
-                environ_var = param.attrib['from_environ']
+            if "from_environ" in param.attrib:
+                environ_var = param.attrib["from_environ"]
                 param_value = os.environ.get(environ_var, param_value)
-            elif 'from_config' in param.attrib:
-                config_val = param.attrib['from_config']
+            elif "from_config" in param.attrib:
+                config_val = param.attrib["from_config"]
                 param_value = config.config_dict.get(config_val, param_value)
 
             rval[key] = param_value
@@ -664,14 +680,16 @@ class JobConfiguration(ConfiguresHandlers):
         :returns: dict
         """
         rval = []
-        for param in parent.findall('env'):
-            rval.append(dict(
-                name=param.get('id'),
-                file=param.get('file'),
-                execute=param.get('exec'),
-                value=param.text,
-                raw=util.asbool(param.get('raw', 'false'))
-            ))
+        for param in parent.findall("env"):
+            rval.append(
+                dict(
+                    name=param.get("id"),
+                    file=param.get("file"),
+                    execute=param.get("exec"),
+                    value=param.text,
+                    raw=util.asbool(param.get("raw", "false")),
+                )
+            )
         return rval
 
     @staticmethod
@@ -684,13 +702,15 @@ class JobConfiguration(ConfiguresHandlers):
         :returns: dict
         """
         rval = []
-        for resubmit in parent.findall('resubmit'):
-            rval.append(dict(
-                condition=resubmit.get('condition'),
-                environment=resubmit.get('destination'),
-                handler=resubmit.get('handler'),
-                delay=resubmit.get('delay'),
-            ))
+        for resubmit in parent.findall("resubmit"):
+            rval.append(
+                dict(
+                    condition=resubmit.get("condition"),
+                    environment=resubmit.get("destination"),
+                    handler=resubmit.get("handler"),
+                    delay=resubmit.get("delay"),
+                )
+            )
         return rval
 
     def __is_enabled(self, params):
@@ -711,7 +731,9 @@ class JobConfiguration(ConfiguresHandlers):
 
         :returns: JobToolConfiguration -- a representation of a <tool> element that uses the default handler and destination
         """
-        return JobToolConfiguration(id='_default_', handler=self.default_handler_id, destination=self.default_destination_id)
+        return JobToolConfiguration(
+            id="_default_", handler=self.default_handler_id, destination=self.default_destination_id
+        )
 
     # Called upon instantiation of a Tool object
     def get_job_tool_configurations(self, ids, tool_classes):
@@ -793,24 +815,28 @@ class JobConfiguration(ConfiguresHandlers):
         """
         rval = {}
         if handler_id in self.handler_runner_plugins:
-            plugins_to_load = [rp for rp in self.runner_plugins if rp['id'] in self.handler_runner_plugins[handler_id]]
-            log.info("Handler '%s' will load specified runner plugins: %s", handler_id, ', '.join(rp['id'] for rp in plugins_to_load))
+            plugins_to_load = [rp for rp in self.runner_plugins if rp["id"] in self.handler_runner_plugins[handler_id]]
+            log.info(
+                "Handler '%s' will load specified runner plugins: %s",
+                handler_id,
+                ", ".join(rp["id"] for rp in plugins_to_load),
+            )
         else:
             plugins_to_load = self.runner_plugins
             log.info("Handler '%s' will load all configured runner plugins", handler_id)
         for runner in plugins_to_load:
             class_names = []
             module = None
-            id = runner['id']
-            load = runner['load']
-            if ':' in load:
+            id = runner["id"]
+            load = runner["load"]
+            if ":" in load:
                 # Name to load was specified as '<module>:<class>'
-                module_name, class_name = load.rsplit(':', 1)
+                module_name, class_name = load.rsplit(":", 1)
                 class_names = [class_name]
                 module = __import__(module_name)
             else:
                 # Name to load was specified as '<module>'
-                if '.' not in load:
+                if "." not in load:
                     # For legacy reasons, try from galaxy.jobs.runners first if there's no '.' in the name
                     module_name = f"galaxy.jobs.runners.{load}"
                     try:
@@ -844,13 +870,20 @@ class JobConfiguration(ConfiguresHandlers):
                     log.warning(f"A non-class name was found in __all__, ignoring: {id}")
                     continue
                 except AssertionError:
-                    log.warning(f"Job runner classes must be subclassed from BaseJobRunner, {id} has bases: {runner_class.__bases__}")
+                    log.warning(
+                        f"Job runner classes must be subclassed from BaseJobRunner, {id} has bases: {runner_class.__bases__}"
+                    )
                     continue
                 try:
-                    rval[id] = runner_class(self.app, runner.get('workers', JobConfiguration.DEFAULT_NWORKERS), **runner.get('kwds', {}))
+                    rval[id] = runner_class(
+                        self.app, runner.get("workers", JobConfiguration.DEFAULT_NWORKERS), **runner.get("kwds", {})
+                    )
                 except TypeError:
-                    log.exception("Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load",
-                                  module_name, class_name)
+                    log.exception(
+                        "Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load",
+                        module_name,
+                        class_name,
+                    )
                     rval[id] = runner_class(self.app)
                 log.debug(f"Loaded job runner '{module_name}:{class_name}' as '{id}'")
         return rval
@@ -881,7 +914,9 @@ class JobConfiguration(ConfiguresHandlers):
         :param job_runners: All loaded job runner plugins.
         :type job_runners: list of job runner plugins
         """
-        for id, destination in [(id, destinations[0]) for id, destinations in self.destinations.items() if self.is_id(destinations)]:
+        for id, destination in [
+            (id, destinations[0]) for id, destinations in self.destinations.items() if self.is_id(destinations)
+        ]:
             # Only need to deal with real destinations, not members of tags
             if destination.legacy and not destination.converted:
                 if destination.runner in job_runners:
@@ -894,11 +929,12 @@ class JobConfiguration(ConfiguresHandlers):
                     else:
                         log.debug(f"Legacy destination with id '{id}', url '{destination.url}' converted, got params:")
                 else:
-                    log.warning(f"Legacy destination with id '{id}' could not be converted: Unknown runner plugin: {destination.runner}")
+                    log.warning(
+                        f"Legacy destination with id '{id}' could not be converted: Unknown runner plugin: {destination.runner}"
+                    )
 
 
 class HasResourceParameters:
-
     def get_resource_parameters(self, job=None):
         # Find the dymically inserted resource parameters and give them
         # to rule.
@@ -925,9 +961,10 @@ class JobWrapper(HasResourceParameters):
     Wraps a 'model.Job' with convenience methods for running processes and
     state management.
     """
+
     is_task = False
 
-    def __init__(self, job, queue: 'JobHandlerQueue', use_persisted_destination=False):
+    def __init__(self, job, queue: "JobHandlerQueue", use_persisted_destination=False):
         self.job_id = job.id
         self.session_id = job.session_id
         self.user_id = job.user_id
@@ -971,19 +1008,28 @@ class JobWrapper(HasResourceParameters):
     def external_output_metadata(self):
         if self.__external_output_metadata is None:
             try:
-                metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
+                metadata_strategy_override = self.get_destination_configuration("metadata_strategy", None)
             except JobMappingException:
                 metadata_strategy_override = None
             if self.__has_tasks:
                 metadata_strategy_override = "directory"
-            self.__external_output_metadata = get_metadata_compute_strategy(self.app.config, self.job_id, metadata_strategy_override=metadata_strategy_override, tool_id=self.tool.id)
+            self.__external_output_metadata = get_metadata_compute_strategy(
+                self.app.config,
+                self.job_id,
+                metadata_strategy_override=metadata_strategy_override,
+                tool_id=self.tool.id,
+            )
         return self.__external_output_metadata
 
     @property
     def remote_command_line(self):
-        use_remote = self.get_destination_configuration('tool_evaluation_strategy') == 'remote'
+        use_remote = self.get_destination_configuration("tool_evaluation_strategy") == "remote"
         # It wouldn't be hard to support history export, but we want to do this in task queue workers anyway ...
-        return use_remote and self.external_output_metadata.extended and not self.sa_session.query(model.JobExportHistoryArchive).filter_by(job=self.get_job()).first()
+        return (
+            use_remote
+            and self.external_output_metadata.extended
+            and not self.sa_session.query(model.JobExportHistoryArchive).filter_by(job=self.get_job()).first()
+        )
 
     def tool_directory(self):
         tool_dir = self.tool.tool_dir
@@ -1027,8 +1073,7 @@ class JobWrapper(HasResourceParameters):
 
     @property
     def outputs_directory(self):
-        """Default location of ``outputs_to_working_directory``.
-        """
+        """Default location of ``outputs_to_working_directory``."""
         return None if self.created_with_galaxy_version < packaging.version.parse("20.01") else "outputs"
 
     @property
@@ -1051,8 +1096,7 @@ class JobWrapper(HasResourceParameters):
 
     @property
     def cleanup_job(self):
-        """ Remove the job after it is complete, should return "always", "onsuccess", or "never".
-        """
+        """Remove the job after it is complete, should return "always", "onsuccess", or "never"."""
         return self.get_destination_configuration("cleanup_job", DEFAULT_CLEANUP_JOB)
 
     @property
@@ -1061,14 +1105,14 @@ class JobWrapper(HasResourceParameters):
 
     @property
     def use_metadata_binary(self):
-        return util.asbool(self.get_destination_configuration('use_metadata_binary', "False"))
+        return util.asbool(self.get_destination_configuration("use_metadata_binary", "False"))
 
     def can_split(self):
         # Should the job handler split this job up?
         return self.app.config.use_tasked_jobs and self.tool.parallelism
 
     def get_job_runner_url(self):
-        log.warning(f'({self.job_id}) Job runner URLs are deprecated, use destinations instead.')
+        log.warning(f"({self.job_id}) Job runner URLs are deprecated, use destinations instead.")
         return self.job_destination.url
 
     def get_parallelism(self):
@@ -1076,7 +1120,7 @@ class JobWrapper(HasResourceParameters):
 
     @property
     def shell(self):
-        return self.job_destination.shell or getattr(self.app.config, 'default_job_shell', DEFAULT_JOB_SHELL)
+        return self.job_destination.shell or getattr(self.app.config, "default_job_shell", DEFAULT_JOB_SHELL)
 
     def disable_commands_in_new_shell(self):
         """Provide an extension point to disable this isolation,
@@ -1100,7 +1144,7 @@ class JobWrapper(HasResourceParameters):
 
     @property
     def galaxy_virtual_env(self):
-        return os.environ.get('VIRTUAL_ENV', None)
+        return os.environ.get("VIRTUAL_ENV", None)
 
     # legacy naming
     get_job_runner = get_job_runner_url
@@ -1156,10 +1200,9 @@ class JobWrapper(HasResourceParameters):
         return os.path.abspath(os.path.join(self.working_directory, COMMAND_VERSION_FILENAME))
 
     def __prepare_upload_paramfile(self, job):
-        """Special case paramfile handling for the upload tool. Copies the paramfile to the working directory
-        """
-        new = os.path.join(self.working_directory, 'upload_params.json')
-        param_file_path = json.loads(next(iter(param.value for param in job.parameters if param.name == 'paramfile')))
+        """Special case paramfile handling for the upload tool. Copies the paramfile to the working directory"""
+        new = os.path.join(self.working_directory, "upload_params.json")
+        param_file_path = json.loads(next(iter(param.value for param in job.parameters if param.name == "paramfile")))
         try:
             shutil.copy2(param_file_path, new)
         except OSError as exc:
@@ -1186,7 +1229,7 @@ class JobWrapper(HasResourceParameters):
             return self.sa_session.query(model.GenomeIndexToolData).filter_by(job=job).first()
 
         # TODO: The upload tool actions that create the paramfile can probably be turned in to a configfile to remove this special casing
-        if job.tool_id == 'upload1':
+        if job.tool_id == "upload1":
             self.__prepare_upload_paramfile(job)
 
         tool_evaluator = self._get_tool_evaluator(job)
@@ -1201,11 +1244,13 @@ class JobWrapper(HasResourceParameters):
         self.galaxy_lib_dir
         if self.tool.requires_galaxy_python_environment or self.remote_command_line:
             # These tools (upload, metadata, data_source) may need access to the datatypes registry.
-            self.app.datatypes_registry.to_xml_file(os.path.join(self.working_directory, 'registry.xml'))
+            self.app.datatypes_registry.to_xml_file(os.path.join(self.working_directory, "registry.xml"))
         if self.remote_command_line:
-            os.makedirs(os.path.join(self.working_directory, 'metadata', 'outputs_new'), exist_ok=True)
-            self.job_io.to_json(path=os.path.join(self.working_directory, 'metadata', 'outputs_new', 'job_io.json'))
-            self.app.tool_data_tables.to_json(path=os.path.join(self.working_directory, 'metadata', 'outputs_new', 'tool_data_tables.json'))
+            os.makedirs(os.path.join(self.working_directory, "metadata", "outputs_new"), exist_ok=True)
+            self.job_io.to_json(path=os.path.join(self.working_directory, "metadata", "outputs_new", "job_io.json"))
+            self.app.tool_data_tables.to_json(
+                path=os.path.join(self.working_directory, "metadata", "outputs_new", "tool_data_tables.json")
+            )
         job.dependencies = self.tool.dependencies
         self.sa_session.add(job)
         self.sa_session.flush()
@@ -1220,18 +1265,16 @@ class JobWrapper(HasResourceParameters):
             # The tool execution is given a working directory beneath the
             # "job" working directory.
             safe_makedirs(self.tool_working_directory)
-            safe_makedirs(os.path.join(working_directory, 'outputs'))
-            log.debug('(%s) Working directory for job is: %s',
-                      self.job_id, self.working_directory)
+            safe_makedirs(os.path.join(working_directory, "outputs"))
+            log.debug("(%s) Working directory for job is: %s", self.job_id, self.working_directory)
         except ObjectInvalid:
-            raise Exception('(%s) Unable to create job working directory',
-                            job.id)
+            raise Exception("(%s) Unable to create job working directory", job.id)
 
     @property
     def guest_ports(self):
         if hasattr(self, "interactivetools"):
             # This works when the job is being prepared
-            guest_ports = [ep.get('port') for ep in self.interactivetools]
+            guest_ports = [ep.get("port") for ep in self.interactivetools]
             return guest_ports
         else:
             # This works when handling a running job
@@ -1251,12 +1294,13 @@ class JobWrapper(HasResourceParameters):
                 self._set_object_store_ids(job)
 
             self.__working_directory = self.app.object_store.get_filename(
-                job, base_dir='job_work', dir_only=True, obj_dir=True)
+                job, base_dir="job_work", dir_only=True, obj_dir=True
+            )
         return self.__working_directory
 
     def working_directory_exists(self):
         job = self.get_job()
-        return self.app.object_store.exists(job, base_dir='job_work', dir_only=True, obj_dir=True)
+        return self.app.object_store.exists(job, base_dir="job_work", dir_only=True, obj_dir=True)
 
     @property
     def tool_working_directory(self):
@@ -1268,24 +1312,22 @@ class JobWrapper(HasResourceParameters):
     def clear_working_directory(self):
         job = self.get_job()
         if not os.path.exists(self.working_directory):
-            log.warning('(%s): Working directory clear requested but %s does '
-                        'not exist',
-                        self.job_id,
-                        self.working_directory)
+            log.warning(
+                "(%s): Working directory clear requested but %s does " "not exist", self.job_id, self.working_directory
+            )
             return
 
         self.object_store.create(
-            job, base_dir='job_work', dir_only=True, obj_dir=True,
-            extra_dir='_cleared_contents', extra_dir_at_root=True)
+            job, base_dir="job_work", dir_only=True, obj_dir=True, extra_dir="_cleared_contents", extra_dir_at_root=True
+        )
         base = self.object_store.get_filename(
-            job, base_dir='job_work', dir_only=True, obj_dir=True,
-            extra_dir='_cleared_contents', extra_dir_at_root=True)
-        date_str = datetime.datetime.now().strftime('%Y%m%d-%H%M%S')
+            job, base_dir="job_work", dir_only=True, obj_dir=True, extra_dir="_cleared_contents", extra_dir_at_root=True
+        )
+        date_str = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
         arc_dir = os.path.join(base, date_str)
         shutil.move(self.working_directory, arc_dir)
         self._setup_working_directory(job=job)
-        log.debug('(%s) Previous working directory moved to %s',
-                  self.job_id, arc_dir)
+        log.debug("(%s) Previous working directory moved to %s", self.job_id, arc_dir)
 
     def default_compute_environment(self, job=None):
         if not job:
@@ -1297,7 +1339,7 @@ class JobWrapper(HasResourceParameters):
         # Restore parameters from the database
         job = self.get_job()
         if job.user is None and job.galaxy_session is None:
-            raise Exception(f'Job {job.id} has no user and no session.')
+            raise Exception(f"Job {job.id} has no user and no session.")
         return job
 
     def _get_tool_evaluator(self, job):
@@ -1315,7 +1357,9 @@ class JobWrapper(HasResourceParameters):
             if os.path.exists(path):
                 util.umask_fix_perms(path, self.app.config.umask, 0o666, self.app.config.gid)
 
-    def fail(self, message, exception=False, tool_stdout="", tool_stderr="", exit_code=None, job_stdout=None, job_stderr=None):
+    def fail(
+        self, message, exception=False, tool_stdout="", tool_stderr="", exit_code=None, job_stdout=None, job_stderr=None
+    ):
         """
         Indicate job failure by setting state and message on all output
         datasets.
@@ -1329,9 +1373,13 @@ class JobWrapper(HasResourceParameters):
         try:
             self.job_destination
         except JobMappingException as exc:
-            log.debug("(%s) fail(): Job destination raised JobMappingException('%s'), caching fake '__fail__' "
-                      "destination for completion of fail method", self.get_id_tag(), unicodify(exc.failure_message))
-            self.job_runner_mapper.cached_job_destination = JobDestination(id='__fail__')
+            log.debug(
+                "(%s) fail(): Job destination raised JobMappingException('%s'), caching fake '__fail__' "
+                "destination for completion of fail method",
+                self.get_id_tag(),
+                unicodify(exc.failure_message),
+            )
+            self.job_runner_mapper.cached_job_destination = JobDestination(id="__fail__")
 
         # Might be AssertionError or other exception
         message = str(message)
@@ -1359,30 +1407,38 @@ class JobWrapper(HasResourceParameters):
                 dataset = dataset_assoc.dataset
                 self.sa_session.refresh(dataset)
                 dataset.state = dataset.states.ERROR
-                dataset.blurb = 'tool error'
+                dataset.blurb = "tool error"
                 dataset.info = message
                 dataset.set_size()
                 dataset.dataset.set_total_size()
                 dataset.mark_unhidden()
-                if dataset.ext == 'auto':
-                    dataset.extension = 'data'
+                if dataset.ext == "auto":
+                    dataset.extension = "data"
                 try:
                     self.__update_output(job, dataset)
                 except Exception:
                     # Failure to update the output of a failed job should not prevent completion of the failure method
-                    log.exception("(%s) fail(): Failed to update job output dataset with id: %s", self.get_id_tag(),
-                                  dataset.dataset.id)
+                    log.exception(
+                        "(%s) fail(): Failed to update job output dataset with id: %s",
+                        self.get_id_tag(),
+                        dataset.dataset.id,
+                    )
                 # Pause any dependent jobs (and those jobs' outputs)
                 for dep_job_assoc in dataset.dependent_jobs:
-                    self.pause(dep_job_assoc.job, "Execution of this dataset's job is paused because its input datasets are in an error state.")
-            job.set_final_state(job.states.ERROR, supports_skip_locked=self.app.application_stack.supports_skip_locked())
+                    self.pause(
+                        dep_job_assoc.job,
+                        "Execution of this dataset's job is paused because its input datasets are in an error state.",
+                    )
+            job.set_final_state(
+                job.states.ERROR, supports_skip_locked=self.app.application_stack.supports_skip_locked()
+            )
             job.command_line = self.command_line
             job.info = message
             # TODO: Put setting the stdout, stderr, and exit code in one place
             # (not duplicated with the finish method).
             job.set_streams(tool_stdout, tool_stderr, job_stdout=job_stdout, job_stderr=job_stderr)
             # Let the exit code be Null if one is not provided:
-            if (exit_code is not None):
+            if exit_code is not None:
                 job.exit_code = exit_code
 
             self.sa_session.add(job)
@@ -1398,7 +1454,9 @@ class JobWrapper(HasResourceParameters):
             self._fix_output_permissions()
         self._report_error()
         # Perform email action even on failure.
-        for pja in [pjaa.post_job_action for pjaa in job.post_job_actions if pjaa.post_job_action.action_type == "EmailAction"]:
+        for pja in [
+            pjaa.post_job_action for pjaa in job.post_job_actions if pjaa.post_job_action.action_type == "EmailAction"
+        ]:
             ActionBox.execute(self.app, self.sa_session, pja, job)
         # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
         if self.tool:
@@ -1407,7 +1465,7 @@ class JobWrapper(HasResourceParameters):
             except Exception:
                 log.exception(f"Error occured while calling tool specific fail actions for job {job.id}")
         cleanup_job = self.cleanup_job
-        delete_files = cleanup_job == 'always' or (cleanup_job == 'onsuccess' and job.state == job.states.DELETED)
+        delete_files = cleanup_job == "always" or (cleanup_job == "onsuccess" and job.state == job.states.DELETED)
         self.cleanup(delete_files=delete_files)
 
     def pause(self, job=None, message=None):
@@ -1455,8 +1513,12 @@ class JobWrapper(HasResourceParameters):
         # thread and no other threads are working on the job yet - so don't refresh.
 
         if job.state in model.Job.terminal_states:
-            log.warning("(%s) Ignoring state change from '%s' to '%s' for job "
-                        "that is already terminal", job.id, job.state, state)
+            log.warning(
+                "(%s) Ignoring state change from '%s' to '%s' for job " "that is already terminal",
+                job.id,
+                job.state,
+                state,
+            )
             return
         if info:
             job.info = info
@@ -1472,7 +1534,7 @@ class JobWrapper(HasResourceParameters):
         return job.state
 
     def set_runner(self, runner_url, external_id):
-        log.warning('set_runner() is deprecated, use set_job_destination()')
+        log.warning("set_runner() is deprecated, use set_job_destination()")
         self.set_job_destination(self.job_destination, external_id)
 
     def set_job_destination(self, job_destination, external_id=None, flush=True, job=None):
@@ -1484,7 +1546,7 @@ class JobWrapper(HasResourceParameters):
         """
         if job is None:
             job = self.get_job()
-        log.debug(f'({job.id}) Persisting job destination (destination id: {job_destination.id})')
+        log.debug(f"({job.id}) Persisting job destination (destination id: {job_destination.id})")
         job.destination_id = job_destination.id
         job.destination_params = job_destination.params
         job.job_runner_name = job_destination.runner
@@ -1511,13 +1573,11 @@ class JobWrapper(HasResourceParameters):
         return self.tool.tmp_target
 
     def get_destination_configuration(self, key, default=None):
-        """ Get a destination parameter that can be defaulted back
+        """Get a destination parameter that can be defaulted back
         in app.config if it needs to be applied globally.
         """
         dest_params = self.job_destination.params
-        return self.get_job().get_destination_configuration(
-            dest_params, self.app.config, key, default
-        )
+        return self.get_job().get_destination_configuration(dest_params, self.app.config, key, default)
 
     def enqueue(self):
         job = self.get_job()
@@ -1566,23 +1626,23 @@ class JobWrapper(HasResourceParameters):
                     trynum = self.app.config.retry_job_output_collection
                 except (OSError, ObjectNotFound) as e:
                     trynum += 1
-                    log.warning('Error accessing dataset with ID %i, will retry: %s', dataset.dataset.id, unicodify(e))
+                    log.warning("Error accessing dataset with ID %i, will retry: %s", dataset.dataset.id, unicodify(e))
                     time.sleep(2)
         if getattr(dataset, "hidden_beneath_collection_instance", None):
             dataset.visible = False
-        dataset.blurb = 'done'
-        dataset.peek = 'no peek'
-        dataset.info = (dataset.info or '')
-        if context['stdout'].strip():
+        dataset.blurb = "done"
+        dataset.peek = "no peek"
+        dataset.info = dataset.info or ""
+        if context["stdout"].strip():
             # Ensure white space between entries
             dataset.info = f"{dataset.info.rstrip()}\n{context['stdout'].strip()}"
-        if context['stderr'].strip():
+        if context["stderr"].strip():
             # Ensure white space between entries
             dataset.info = f"{dataset.info.rstrip()}\n{context['stderr'].strip()}"
         dataset.tool_version = self.version_string
         dataset.set_size()
-        if 'uuid' in context:
-            dataset.dataset.uuid = context['uuid']
+        if "uuid" in context:
+            dataset.dataset.uuid = context["uuid"]
         self.__update_output(job, dataset)
         if not purged:
             collect_extra_files(self.object_store, dataset, self.working_directory)
@@ -1593,30 +1653,42 @@ class JobWrapper(HasResourceParameters):
                 dataset.mark_unhidden()
         elif not purged:
             # If the tool was expected to set the extension, attempt to retrieve it
-            if dataset.ext == 'auto':
-                dataset.extension = context.get('ext', 'data')
+            if dataset.ext == "auto":
+                dataset.extension = context.get("ext", "data")
                 dataset.init_meta(copy_from=dataset)
             # if a dataset was copied, it won't appear in our dictionary:
             # either use the metadata from originating output dataset, or call set_meta on the copies
             # it would be quicker to just copy the metadata from the originating output dataset,
             # but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
             retry_internally = util.asbool(self.get_destination_configuration("retry_metadata_internally", True))
-            if not retry_internally and self.tool.tool_type == 'interactive':
-                retry_internally = util.asbool(self.get_destination_configuration("retry_interactivetool_metadata_internally", retry_internally))
-            metadata_set_successfully = self.external_output_metadata.external_metadata_set_successfully(dataset, output_name, self.sa_session, working_directory=self.working_directory)
+            if not retry_internally and self.tool.tool_type == "interactive":
+                retry_internally = util.asbool(
+                    self.get_destination_configuration("retry_interactivetool_metadata_internally", retry_internally)
+                )
+            metadata_set_successfully = self.external_output_metadata.external_metadata_set_successfully(
+                dataset, output_name, self.sa_session, working_directory=self.working_directory
+            )
             if retry_internally and not metadata_set_successfully:
                 # If Galaxy was expected to sniff type and didn't - do so.
                 if dataset.ext == "_sniff_":
-                    extension = sniff.handle_uploaded_dataset_file(dataset.dataset.file_name, self.app.datatypes_registry)
+                    extension = sniff.handle_uploaded_dataset_file(
+                        dataset.dataset.file_name, self.app.datatypes_registry
+                    )
                     dataset.extension = extension
 
                 # call datatype.set_meta directly for the initial set_meta call during dataset creation
                 dataset.datatype.set_meta(dataset, overwrite=False)
-            elif (job.states.ERROR != final_job_state and not metadata_set_successfully):
+            elif job.states.ERROR != final_job_state and not metadata_set_successfully:
                 dataset._state = model.Dataset.states.FAILED_METADATA
             else:
-                self.external_output_metadata.load_metadata(dataset, output_name, self.sa_session, working_directory=self.working_directory, remote_metadata_directory=remote_metadata_directory)
-            line_count = context.get('line_count', None)
+                self.external_output_metadata.load_metadata(
+                    dataset,
+                    output_name,
+                    self.sa_session,
+                    working_directory=self.working_directory,
+                    remote_metadata_directory=remote_metadata_directory,
+                )
+            line_count = context.get("line_count", None)
             try:
                 # Certain datatype's set_peek methods contain a line_count argument
                 dataset.set_peek(line_count=line_count)
@@ -1626,8 +1698,8 @@ class JobWrapper(HasResourceParameters):
         else:
             # Handle purged datasets.
             dataset.blurb = "empty"
-            if dataset.ext == 'auto':
-                dataset.extension = context.get('ext', 'txt')
+            if dataset.ext == "auto":
+                dataset.extension = context.get("ext", "txt")
 
         for context_key in TOOL_PROVIDED_JOB_METADATA_KEYS:
             if context_key in context:
@@ -1653,8 +1725,7 @@ class JobWrapper(HasResourceParameters):
         the contents of the output files.
         """
         finish_timer = self.app.execution_timer_factory.get_timer(
-            'internals.galaxy.jobs.job_wrapper_finish',
-            'job_wrapper.finish for job ${job_id} executed'
+            "internals.galaxy.jobs.job_wrapper_finish", "job_wrapper.finish for job ${job_id} executed"
         )
 
         # default post job setup
@@ -1665,13 +1736,21 @@ class JobWrapper(HasResourceParameters):
             if not isinstance(exception, (AssertionError, MessageException)):
                 # Only attach MessageException and AssertionErrors to job.traceback
                 exception = None
-            return self.fail(message, tool_stdout=tool_stdout, tool_stderr=tool_stderr, exit_code=tool_exit_code, job_stdout=job_stdout, job_stderr=job_stderr, exception=exception)
+            return self.fail(
+                message,
+                tool_stdout=tool_stdout,
+                tool_stderr=tool_stderr,
+                exit_code=tool_exit_code,
+                job_stdout=job_stdout,
+                job_stderr=job_stderr,
+                exception=exception,
+            )
 
         # TODO: After failing here, consider returning from the function.
         try:
             self.reclaim_ownership()
         except Exception:
-            log.exception(f'({job.id}) Failed to change ownership of {self.working_directory}, failing')
+            log.exception(f"({job.id}) Failed to change ownership of {self.working_directory}, failing")
             return fail()
 
         # if the job was deleted, don't finish it
@@ -1683,7 +1762,7 @@ class JobWrapper(HasResourceParameters):
             # the tasks failed. So include the stderr, stdout, and exit code:
             return fail()
 
-        extended_metadata = self.external_output_metadata.extended and not self.tool.tool_type == 'interactive'
+        extended_metadata = self.external_output_metadata.extended and not self.tool.tool_type == "interactive"
 
         # We collect the stderr from tools that write their stderr to galaxy.json
         tool_provided_metadata = self.get_tool_provided_job_metadata()
@@ -1695,7 +1774,14 @@ class JobWrapper(HasResourceParameters):
         # We set final_job_state to use for dataset management, but *don't* set
         # job.state until after dataset discovery to prevent history issues
         if check_output_detected_state is None:
-            check_output_detected_state = self.check_tool_output(tool_stdout, tool_stderr, tool_exit_code=tool_exit_code, job=job, job_stdout=job_stdout, job_stderr=job_stderr)
+            check_output_detected_state = self.check_tool_output(
+                tool_stdout,
+                tool_stderr,
+                tool_exit_code=tool_exit_code,
+                job=job,
+                job_stdout=job_stdout,
+                job_stderr=job_stderr,
+            )
 
         if check_output_detected_state == DETECTED_JOB_STATE.OK and not tool_provided_metadata.has_failed_outputs():
             final_job_state = job.states.OK
@@ -1713,8 +1799,10 @@ class JobWrapper(HasResourceParameters):
                     # finish method - the false_path file has already moved,
                     # and when the job is recovered, it won't be found.
                     if os.path.exists(dataset_path.real_path) and os.stat(dataset_path.real_path).st_size > 0:
-                        log.warning("finish(): %s not found, but %s is not empty, so it will be used instead"
-                                    % (dataset_path.false_path, dataset_path.real_path))
+                        log.warning(
+                            "finish(): %s not found, but %s is not empty, so it will be used instead"
+                            % (dataset_path.false_path, dataset_path.real_path)
+                        )
                     else:
                         # Prior to fail we need to set job.state
                         job.set_state(final_job_state)
@@ -1725,7 +1813,7 @@ class JobWrapper(HasResourceParameters):
             try:
                 import_options = store.ImportOptions(allow_dataset_object_edit=True, allow_edit=True)
                 import_model_store = store.get_import_model_store_for_directory(
-                    os.path.join(self.working_directory, 'metadata', 'outputs_populated'),
+                    os.path.join(self.working_directory, "metadata", "outputs_populated"),
                     app=self.app,
                     import_options=import_options,
                     user=job.user,
@@ -1756,13 +1844,14 @@ class JobWrapper(HasResourceParameters):
                 # should this also be checking library associations? - can a library item be added from a history before the job has ended? -
                 # lets not allow this to occur
                 # need to update all associated output hdas, i.e. history was shared with job running
-                for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
+                for dataset in (
+                    dataset_assoc.dataset.dataset.history_associations
+                    + dataset_assoc.dataset.dataset.library_associations
+                ):
                     output_name = dataset_assoc.name
 
                     # Handles retry internally on error for instance...
-                    self._finish_dataset(
-                        output_name, dataset, job, context, final_job_state, remote_metadata_directory
-                    )
+                    self._finish_dataset(output_name, dataset, job, context, final_job_state, remote_metadata_directory)
                 if not final_job_state == job.states.ERROR:
                     dataset_assoc.dataset.dataset.state = model.Dataset.states.OK
             try:
@@ -1778,7 +1867,10 @@ class JobWrapper(HasResourceParameters):
                 dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
                 # Pause any dependent jobs (and those jobs' outputs)
                 for dep_job_assoc in dataset_assoc.dataset.dependent_jobs:
-                    self.pause(dep_job_assoc.job, "Execution of this dataset's job is paused because its input datasets are in an error state.")
+                    self.pause(
+                        dep_job_assoc.job,
+                        "Execution of this dataset's job is paused because its input datasets are in an error state.",
+                    )
 
         for pja in job.post_job_actions:
             ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job, final_job_state=final_job_state)
@@ -1803,15 +1895,24 @@ class JobWrapper(HasResourceParameters):
         # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ).
         param_dict = self.get_param_dict(job)
         try:
-            self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
+            self.tool.exec_after_process(
+                self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state
+            )
         except Exception as e:
             log.exception(f"exec_after_process hook failed for job {self.job_id}")
             return fail("exec_after_process hook failed", exception=e)
 
         # Call 'exec_after_process' hook
-        self.tool.call_hook('exec_after_process', self.app, inp_data=inp_data,
-                            out_data=out_data, param_dict=param_dict,
-                            tool=self.tool, stdout=job.stdout, stderr=job.stderr)
+        self.tool.call_hook(
+            "exec_after_process",
+            self.app,
+            inp_data=inp_data,
+            out_data=out_data,
+            param_dict=param_dict,
+            tool=self.tool,
+            stdout=job.stdout,
+            stderr=job.stderr,
+        )
 
         self._fix_output_permissions()
 
@@ -1835,7 +1936,7 @@ class JobWrapper(HasResourceParameters):
         if job.state == job.states.ERROR:
             self._report_error()
         cleanup_job = self.cleanup_job
-        delete_files = cleanup_job == 'always' or (job.state == job.states.OK and cleanup_job == 'onsuccess')
+        delete_files = cleanup_job == "always" or (job.state == job.states.OK and cleanup_job == "onsuccess")
         self.cleanup(delete_files=delete_files)
         log.debug(finish_timer.to_str(job_id=self.job_id, tool_id=job.tool_id))
 
@@ -1851,14 +1952,14 @@ class JobWrapper(HasResourceParameters):
             input_dbkey = loads(input_dbkey)
         else:
             # Legacy jobs without __input_ext.
-            input_ext = 'data'
-            input_dbkey = '?'
+            input_ext = "data"
+            input_dbkey = "?"
             for _, data in inp_data.items():
                 # For loop odd, but sort simulating behavior in galaxy.tools.actions
                 if not data:
                     continue
                 input_ext = data.ext
-                input_dbkey = data.dbkey or '?'
+                input_dbkey = data.dbkey or "?"
 
         # Create generated output children and primary datasets.
         tool_working_directory = self.tool_working_directory
@@ -1880,11 +1981,15 @@ class JobWrapper(HasResourceParameters):
         if job is not None:
             job_id_tag = job.get_id_tag()
 
-        state, tool_stdout, tool_stderr, job_messages = check_output(self.tool.stdio_regexes, self.tool.stdio_exit_codes, tool_stdout, tool_stderr, tool_exit_code, job_id_tag)
+        state, tool_stdout, tool_stderr, job_messages = check_output(
+            self.tool.stdio_regexes, self.tool.stdio_exit_codes, tool_stdout, tool_stderr, tool_exit_code, job_id_tag
+        )
 
         # Store the modified stdout and stderr in the job:
         if job is not None:
-            job.set_streams(tool_stdout, tool_stderr, job_messages=job_messages, job_stdout=job_stdout, job_stderr=job_stderr)
+            job.set_streams(
+                tool_stdout, tool_stderr, job_messages=job_messages, job_stdout=job_stdout, job_stderr=job_stderr
+            )
 
         return state
 
@@ -1902,16 +2007,22 @@ class JobWrapper(HasResourceParameters):
                             raise
                 self.external_output_metadata.cleanup_external_metadata(self.sa_session)
             if delete_files:
-                self.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, obj_dir=True)
+                self.object_store.delete(
+                    self.get_job(), base_dir="job_work", entire_dir=True, dir_only=True, obj_dir=True
+                )
         except Exception:
             log.exception("Unable to cleanup job %d", self.job_id)
 
     def _collect_metrics(self, has_metrics, job_metrics_directory=None):
         job = has_metrics.get_job()
         job_metrics_directory = job_metrics_directory or self.working_directory
-        per_plugin_properties = self.app.job_metrics.collect_properties(job.destination_id, self.job_id, job_metrics_directory)
+        per_plugin_properties = self.app.job_metrics.collect_properties(
+            job.destination_id, self.job_id, job_metrics_directory
+        )
         if per_plugin_properties:
-            log.info(f"Collecting metrics for {type(has_metrics).__name__} {getattr(has_metrics, 'id', None)} in {job_metrics_directory}")
+            log.info(
+                f"Collecting metrics for {type(has_metrics).__name__} {getattr(has_metrics, 'id', None)} in {job_metrics_directory}"
+            )
         for plugin, properties in per_plugin_properties.items():
             for metric_name, metric_value in properties.items():
                 if metric_value is not None:
@@ -1931,16 +2042,28 @@ class JobWrapper(HasResourceParameters):
         if self.app.job_config.limits.output_size and self.app.job_config.limits.output_size > 0:
             for outfile, size in self.get_output_sizes():
                 if size > self.app.job_config.limits.output_size:
-                    log.warning('(%s) Job output size %s has exceeded the global output size limit', self.get_id_tag(), os.path.basename(outfile))
-                    return (JobState.runner_states.OUTPUT_SIZE_LIMIT,
-                            'Job output file grew too large (greater than %s), please try different inputs or parameters'
-                            % util.nice_size(self.app.job_config.limits.output_size))
+                    log.warning(
+                        "(%s) Job output size %s has exceeded the global output size limit",
+                        self.get_id_tag(),
+                        os.path.basename(outfile),
+                    )
+                    return (
+                        JobState.runner_states.OUTPUT_SIZE_LIMIT,
+                        "Job output file grew too large (greater than %s), please try different inputs or parameters"
+                        % util.nice_size(self.app.job_config.limits.output_size),
+                    )
         if self.app.job_config.limits.walltime_delta is not None and runtime is not None:
             if runtime > self.app.job_config.limits.walltime_delta:
-                log.warning('(%s) Job runtime %s has exceeded the global walltime, it will be terminated', self.get_id_tag(), runtime)
-                return (JobState.runner_states.GLOBAL_WALLTIME_REACHED,
-                        'Job ran longer than the maximum allowed execution time (runtime: %s, limit: %s), please try different inputs or parameters'
-                        % (str(runtime).split('.')[0], self.app.job_config.limits.walltime))
+                log.warning(
+                    "(%s) Job runtime %s has exceeded the global walltime, it will be terminated",
+                    self.get_id_tag(),
+                    runtime,
+                )
+                return (
+                    JobState.runner_states.GLOBAL_WALLTIME_REACHED,
+                    "Job ran longer than the maximum allowed execution time (runtime: %s, limit: %s), please try different inputs or parameters"
+                    % (str(runtime).split(".")[0], self.app.job_config.limits.walltime),
+                )
         return None
 
     def has_limits(self):
@@ -1956,7 +2079,7 @@ class JobWrapper(HasResourceParameters):
 
     def get_env_setup_clause(self):
         if self.app.config.environment_setup_file is None:
-            return ''
+            return ""
         return f'[ -f "{self.app.config.environment_setup_file}" ] && . {self.app.config.environment_setup_file}'
 
     @property
@@ -1969,7 +2092,9 @@ class JobWrapper(HasResourceParameters):
         try:
             if not tmp_dir or util.asbool(tmp_dir):
                 working_directory = self.working_directory
-                return '''$([ ! -e '{0}/tmp' ] || mv '{0}/tmp' '{0}'/tmp.$(date +%Y%m%d-%H%M%S) ; mkdir '{0}/tmp'; echo '{0}/tmp')'''.format(working_directory)
+                return """$([ ! -e '{0}/tmp' ] || mv '{0}/tmp' '{0}'/tmp.$(date +%Y%m%d-%H%M%S) ; mkdir '{0}/tmp'; echo '{0}/tmp')""".format(
+                    working_directory
+                )
             else:
                 return tmp_dir
         except ValueError:
@@ -2018,23 +2143,33 @@ class JobWrapper(HasResourceParameters):
 
     def invalidate_external_metadata(self):
         job = self.get_job()
-        self.external_output_metadata.invalidate_external_metadata([output_dataset_assoc.dataset for
-                                                                    output_dataset_assoc in
-                                                                    job.output_datasets + job.output_library_datasets],
-                                                                   self.sa_session)
+        self.external_output_metadata.invalidate_external_metadata(
+            [
+                output_dataset_assoc.dataset
+                for output_dataset_assoc in job.output_datasets + job.output_library_datasets
+            ],
+            self.sa_session,
+        )
 
-    def setup_external_metadata(self, exec_dir=None, tmp_dir=None,
-                                dataset_files_path=None, config_root=None,
-                                config_file=None, datatypes_config=None,
-                                resolve_metadata_dependencies=False,
-                                set_extension=True, **kwds):
+    def setup_external_metadata(
+        self,
+        exec_dir=None,
+        tmp_dir=None,
+        dataset_files_path=None,
+        config_root=None,
+        config_file=None,
+        datatypes_config=None,
+        resolve_metadata_dependencies=False,
+        set_extension=True,
+        **kwds,
+    ):
         # extension could still be 'auto' if this is the upload tool.
         job = self.get_job()
         if set_extension:
             for output_dataset_assoc in job.output_datasets:
-                if output_dataset_assoc.dataset.ext == 'auto':
+                if output_dataset_assoc.dataset.ext == "auto":
                     context = self.get_dataset_finish_context(dict(), output_dataset_assoc)
-                    output_dataset_assoc.dataset.extension = context.get('ext', 'data')
+                    output_dataset_assoc.dataset.extension = context.get("ext", "data")
             self.sa_session.flush()
         if tmp_dir is None:
             # this dir should should relative to the exec_dir
@@ -2046,38 +2181,42 @@ class JobWrapper(HasResourceParameters):
         if config_file is None:
             config_file = self.app.config.config_file
         if datatypes_config is None:
-            datatypes_config = os.path.join(self.working_directory, 'metadata', 'registry.xml')
-            safe_makedirs(os.path.join(self.working_directory, 'metadata'))
+            datatypes_config = os.path.join(self.working_directory, "metadata", "registry.xml")
+            safe_makedirs(os.path.join(self.working_directory, "metadata"))
             self.app.datatypes_registry.to_xml_file(path=datatypes_config)
 
         inp_data, out_data, out_collections = job.io_dicts(exclude_implicit_outputs=True)
         job_metadata = os.path.join(self.tool_working_directory, self.tool.provided_metadata_file)
         object_store_conf = self.object_store.to_dict()
-        command = self.external_output_metadata.setup_external_metadata(out_data,
-                                                                        out_collections,
-                                                                        self.sa_session,
-                                                                        exec_dir=exec_dir,
-                                                                        tmp_dir=tmp_dir,
-                                                                        dataset_files_path=dataset_files_path,
-                                                                        config_root=config_root,
-                                                                        config_file=config_file,
-                                                                        datatypes_config=datatypes_config,
-                                                                        job_metadata=job_metadata,
-                                                                        provided_metadata_style=self.tool.provided_metadata_style,
-                                                                        object_store_conf=object_store_conf,
-                                                                        tool=self.tool,
-                                                                        job=job,
-                                                                        max_metadata_value_size=self.app.config.max_metadata_value_size,
-                                                                        max_discovered_files=self.app.config.max_discovered_files,
-                                                                        validate_outputs=self.validate_outputs,
-                                                                        link_data_only=self.__link_file_check(),
-                                                                        **kwds)
+        command = self.external_output_metadata.setup_external_metadata(
+            out_data,
+            out_collections,
+            self.sa_session,
+            exec_dir=exec_dir,
+            tmp_dir=tmp_dir,
+            dataset_files_path=dataset_files_path,
+            config_root=config_root,
+            config_file=config_file,
+            datatypes_config=datatypes_config,
+            job_metadata=job_metadata,
+            provided_metadata_style=self.tool.provided_metadata_style,
+            object_store_conf=object_store_conf,
+            tool=self.tool,
+            job=job,
+            max_metadata_value_size=self.app.config.max_metadata_value_size,
+            max_discovered_files=self.app.config.max_discovered_files,
+            validate_outputs=self.validate_outputs,
+            link_data_only=self.__link_file_check(),
+            **kwds,
+        )
         if resolve_metadata_dependencies:
             metadata_tool = self.app.toolbox.get_tool("__SET_METADATA__")
             if metadata_tool is not None:
                 # Due to tool shed hacks for migrate and installed tool tests...
                 # see (``setup_shed_tools_for_test`` in test/base/driver_util.py).
-                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory, metadata=True)
+                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(
+                    job_directory=self.working_directory, metadata=True
+                )
                 if dependency_shell_commands:
                     dependency_shell_commands = "; ".join(dependency_shell_commands)
                     command = f"{dependency_shell_commands}; {command}"
@@ -2114,10 +2253,14 @@ class JobWrapper(HasResourceParameters):
             return True
 
     def container_monitor_command(self, container, **kwds):
-        if not container or not self.tool.produces_entry_points or not self.get_destination_configuration("container_monitor", True):
+        if (
+            not container
+            or not self.tool.produces_entry_points
+            or not self.get_destination_configuration("container_monitor", True)
+        ):
             return None
 
-        exec_dir = kwds.get('exec_dir', os.path.abspath(os.getcwd()))
+        exec_dir = kwds.get("exec_dir", os.path.abspath(os.getcwd()))
         work_dir = self.working_directory
         configs_dir = ensure_configs_directory(work_dir)
         container_config = os.path.join(configs_dir, "container_config.json")
@@ -2136,11 +2279,7 @@ class JobWrapper(HasResourceParameters):
             encoded_job_id = self.app.security.encode_id(job_id)
             job_key = self.app.security.encode_id(job_id, kind="jobs_files")
             endpoint_base = "%s/api/jobs/%s/ports?job_key=%s"
-            callback_url = endpoint_base % (
-                galaxy_url,
-                encoded_job_id,
-                job_key
-            )
+            callback_url = endpoint_base % (galaxy_url, encoded_job_id, job_key)
             container_config_dict["callback_url"] = callback_url
 
         with open(container_config, "w") as f:
@@ -2157,7 +2296,7 @@ class JobWrapper(HasResourceParameters):
         elif job.galaxy_session is not None:
             return f"anonymous@{job.galaxy_session.remote_addr.split()[-1]}"
         else:
-            return 'anonymous@unknown'
+            return "anonymous@unknown"
 
     def __update_output(self, job, hda, clean_only=False):
         """Handle writing outputs to the object store.
@@ -2182,7 +2321,7 @@ class JobWrapper(HasResourceParameters):
                     pass
 
     def __link_file_check(self):
-        """ outputs_to_working_directory breaks library uploads where data is
+        """outputs_to_working_directory breaks library uploads where data is
         linked.  This method is a hack that solves that problem, but is
         specific to the upload tool and relies on an injected job param.  This
         method should be removed ASAP and replaced with some properly generic
@@ -2191,7 +2330,7 @@ class JobWrapper(HasResourceParameters):
         if self.tool:
             job = self.get_job()
             param_dict = job.get_param_values(self.app)
-            return self.tool.id == 'upload1' and param_dict.get('link_data_only', None) == 'link_to_files'
+            return self.tool.id == "upload1" and param_dict.get("link_data_only", None) == "link_to_files"
         else:
             # The tool is unavailable, we try to move the outputs.
             return False
@@ -2200,8 +2339,9 @@ class JobWrapper(HasResourceParameters):
         job = self.get_job()
         external_chown_script = self.get_destination_configuration("external_chown_script", None)
         if job.user is not None and external_chown_script:
-            ret = external_chown(self.working_directory, self.user_system_pwent,
-                           external_chown_script, description="working directory")
+            ret = external_chown(
+                self.working_directory, self.user_system_pwent, external_chown_script, description="working directory"
+            )
             if not ret:
                 os.chmod(self.working_directory, RWXRWXRWX)
 
@@ -2209,8 +2349,9 @@ class JobWrapper(HasResourceParameters):
         job = self.get_job()
         external_chown_script = self.get_destination_configuration("external_chown_script", None)
         if job.user is not None and external_chown_script:
-            external_chown(self.working_directory, self.galaxy_system_pwent,
-                           external_chown_script, description="working directory")
+            external_chown(
+                self.working_directory, self.galaxy_system_pwent, external_chown_script, description="working directory"
+            )
 
     @property
     def user_system_pwent(self):
@@ -2246,7 +2387,12 @@ class JobWrapper(HasResourceParameters):
 
     def set_container(self, container):
         if container:
-            cont = model.JobContainerAssociation(job=self.get_job(), container_type=container.container_type, container_name=container.container_name, container_info=container.container_info)
+            cont = model.JobContainerAssociation(
+                job=self.get_job(),
+                container_type=container.container_type,
+                container_name=container.container_name,
+                container_info=container.container_info,
+            )
             self.sa_session.add(cont)
             self.sa_session.flush()
 
@@ -2256,6 +2402,7 @@ class TaskWrapper(JobWrapper):
     Extension of JobWrapper intended for running tasks.
     Should be refactored into a generalized executable unit wrapper parent, then jobs and tasks.
     """
+
     # Abstract this to be more useful for running tasks that *don't* necessarily compose a job.
 
     is_task = True
@@ -2317,12 +2464,12 @@ class TaskWrapper(JobWrapper):
         self.sa_session.add(task)
         self.sa_session.flush()
 
-        self.status = 'prepared'
+        self.status = "prepared"
         return self.extra_filenames
 
     def fail(self, message, exception=False):
         log.error(f"TaskWrapper Failure {message}")
-        self.status = 'error'
+        self.status = "error"
         # How do we want to handle task failure?  Fail the job and let it clean up?
 
     def change_state(self, state, info=False, flush=True, job=None):
@@ -2363,16 +2510,17 @@ class TaskWrapper(JobWrapper):
         """
 
         # This may have ended too soon
-        log.debug('task %s for job %d ended; exit code: %d'
-                  % (self.task_id, self.job_id,
-                      tool_exit_code if tool_exit_code is not None else -256))
+        log.debug(
+            "task %s for job %d ended; exit code: %d"
+            % (self.task_id, self.job_id, tool_exit_code if tool_exit_code is not None else -256)
+        )
         # default post job setup_external_metadata
         self.sa_session.expunge_all()
         task = self.get_task()
         # if the job was deleted, don't finish it
         if task.state == task.states.DELETED:
             # Job was deleted by an administrator
-            delete_files = self.cleanup_job in ('always', 'onsuccess')
+            delete_files = self.cleanup_job in ("always", "onsuccess")
             self.cleanup(delete_files=delete_files)
             return
         elif task.state == task.states.ERROR:
@@ -2416,9 +2564,17 @@ class TaskWrapper(JobWrapper):
         # Handled at the parent job level.  Do nothing here.
         pass
 
-    def setup_external_metadata(self, exec_dir=None, tmp_dir=None, dataset_files_path=None,
-                                config_root=None, config_file=None, datatypes_config=None,
-                                set_extension=True, **kwds):
+    def setup_external_metadata(
+        self,
+        exec_dir=None,
+        tmp_dir=None,
+        dataset_files_path=None,
+        config_root=None,
+        config_file=None,
+        datatypes_config=None,
+        set_extension=True,
+        **kwds,
+    ):
         # There is no metadata setting for tasks.  This is handled after the merge, at the job level.
         return ""
 
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index eb76d84c39f..5b8a90dd5bb 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -2,7 +2,7 @@ from logging import getLogger
 from os import getcwd
 from os.path import (
     abspath,
-    join
+    join,
 )
 
 from galaxy import util
@@ -77,7 +77,9 @@ def build_command(
             external_command_shell = container.shell
         else:
             external_command_shell = shell
-        externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params, container=container)
+        externalized_commands = __externalize_commands(
+            job_wrapper, external_command_shell, commands_builder, remote_command_params, container=container
+        )
         if container and modify_command_for_container:
             # Stop now and build command before handling metadata and copying
             # working directory files back. These should always happen outside
@@ -85,9 +87,7 @@ def build_command(
             # metadata and means no need for Galaxy to be available to container
             # and not copying workdir outputs back means on can be more restrictive
             # of where container can write to in some circumstances.
-            run_in_container_command = container.containerize_command(
-                externalized_commands
-            )
+            run_in_container_command = container.containerize_command(externalized_commands)
             commands_builder = CommandsBuilder(run_in_container_command)
         else:
             commands_builder = CommandsBuilder(externalized_commands)
@@ -102,7 +102,7 @@ def build_command(
         # xref https://github.com/galaxyproject/galaxy/issues/3289
         commands_builder.prepend_command(PREPARE_DIRS)
 
-    for_pulsar = 'script_directory' in remote_command_params
+    for_pulsar = "script_directory" in remote_command_params
     __handle_remote_command_line_building(commands_builder, job_wrapper, for_pulsar=for_pulsar)
 
     container_monitor_command = job_wrapper.container_monitor_command(container)
@@ -124,14 +124,16 @@ def build_command(
     return commands_builder.build()
 
 
-def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh", container=None):
+def __externalize_commands(
+    job_wrapper, shell, commands_builder, remote_command_params, script_name="tool_script.sh", container=None
+):
     local_container_script = join(job_wrapper.working_directory, script_name)
     tool_commands = commands_builder.build()
     integrity_injection = ""
     # Setting shell to none in job_conf.xml disables creating a tool command script,
     # set -e doesn't work for composite commands but this is necessary for Windows jobs
     # for instance.
-    if shell and shell.lower() == 'none':
+    if shell and shell.lower() == "none":
         return tool_commands
     if job_wrapper.job_io.check_job_script_integrity:
         integrity_injection = INTEGRITY_INJECTION
@@ -162,7 +164,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
     #   doesn't need to mount the job directory (rw) and then eliminate this hack
     #   (or restrict to older Pulsar versions).
     #   https://github.com/galaxyproject/galaxy/pull/8449
-    for_pulsar = 'script_directory' in remote_command_params
+    for_pulsar = "script_directory" in remote_command_params
     if for_pulsar:
         commands = f"{shell} {join(remote_command_params['script_directory'], script_name)}"
     else:
@@ -172,7 +174,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
 
 
 def __handle_remote_command_line_building(commands_builder, job_wrapper, for_pulsar=False):
-    if getattr(job_wrapper, 'remote_command_line', False):
+    if getattr(job_wrapper, "remote_command_line", False):
         sep = "" if for_pulsar else "&&"
         command = 'PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" python "$GALAXY_LIB"/galaxy/tools/remote_tool_eval.py'
         if for_pulsar:
@@ -184,7 +186,7 @@ def __handle_remote_command_line_building(commands_builder, job_wrapper, for_pul
 
 def __handle_task_splitting(commands_builder, job_wrapper):
     # prepend getting input files (if defined)
-    if getattr(job_wrapper, 'prepare_input_files_cmds', None):
+    if getattr(job_wrapper, "prepare_input_files_cmds", None):
         commands_builder.prepend_commands(job_wrapper.prepare_input_files_cmds)
 
 
@@ -198,8 +200,8 @@ def __handle_dependency_resolution(commands_builder, job_wrapper, remote_command
 def __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params):
     # Append commands to copy job outputs based on from_work_dir attribute.
     work_dir_outputs_kwds = {}
-    if 'working_directory' in remote_command_params:
-        work_dir_outputs_kwds['job_working_directory'] = remote_command_params['working_directory']
+    if "working_directory" in remote_command_params:
+        work_dir_outputs_kwds["job_working_directory"] = remote_command_params["working_directory"]
     work_dir_outputs = runner.get_work_dir_outputs(job_wrapper, **work_dir_outputs_kwds)
     if work_dir_outputs:
         commands_builder.capture_return_code()
@@ -210,30 +212,33 @@ def __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_comm
 def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_params):
     # Append metadata setting commands, we don't want to overwrite metadata
     # that was copied over in init_meta(), as per established behavior
-    metadata_kwds = remote_command_params.get('metadata_kwds', {})
-    exec_dir = metadata_kwds.get('exec_dir', abspath(getcwd()))
-    tmp_dir = metadata_kwds.get('tmp_dir', job_wrapper.working_directory)
-    dataset_files_path = metadata_kwds.get('dataset_files_path', runner.app.model.Dataset.file_path)
-    output_fnames = metadata_kwds.get('output_fnames', job_wrapper.job_io.get_output_fnames())
-    config_root = metadata_kwds.get('config_root', None)
-    config_file = metadata_kwds.get('config_file', None)
-    datatypes_config = metadata_kwds.get('datatypes_config', None)
-    compute_tmp_dir = metadata_kwds.get('compute_tmp_dir', None)
+    metadata_kwds = remote_command_params.get("metadata_kwds", {})
+    exec_dir = metadata_kwds.get("exec_dir", abspath(getcwd()))
+    tmp_dir = metadata_kwds.get("tmp_dir", job_wrapper.working_directory)
+    dataset_files_path = metadata_kwds.get("dataset_files_path", runner.app.model.Dataset.file_path)
+    output_fnames = metadata_kwds.get("output_fnames", job_wrapper.job_io.get_output_fnames())
+    config_root = metadata_kwds.get("config_root", None)
+    config_file = metadata_kwds.get("config_file", None)
+    datatypes_config = metadata_kwds.get("datatypes_config", None)
+    compute_tmp_dir = metadata_kwds.get("compute_tmp_dir", None)
     resolve_metadata_dependencies = job_wrapper.commands_in_new_shell
-    metadata_command = job_wrapper.setup_external_metadata(
-        exec_dir=exec_dir,
-        tmp_dir=tmp_dir,
-        dataset_files_path=dataset_files_path,
-        output_fnames=output_fnames,
-        set_extension=False,
-        config_root=config_root,
-        config_file=config_file,
-        datatypes_config=datatypes_config,
-        compute_tmp_dir=compute_tmp_dir,
-        resolve_metadata_dependencies=resolve_metadata_dependencies,
-        use_bin=job_wrapper.use_metadata_binary,
-        kwds={'overwrite': False}
-    ) or ''
+    metadata_command = (
+        job_wrapper.setup_external_metadata(
+            exec_dir=exec_dir,
+            tmp_dir=tmp_dir,
+            dataset_files_path=dataset_files_path,
+            output_fnames=output_fnames,
+            set_extension=False,
+            config_root=config_root,
+            config_file=config_file,
+            datatypes_config=datatypes_config,
+            compute_tmp_dir=compute_tmp_dir,
+            resolve_metadata_dependencies=resolve_metadata_dependencies,
+            use_bin=job_wrapper.use_metadata_binary,
+            kwds={"overwrite": False},
+        )
+        or ""
+    )
     metadata_command = metadata_command.strip()
     if metadata_command:
         # Place Galaxy and its dependencies in environment for metadata regardless of tool.
@@ -244,18 +249,17 @@ def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_para
 
 def __copy_if_exists_command(work_dir_output):
     source_file, destination = work_dir_output
-    if '?' in source_file or '*' in source_file:
-        source_file = source_file.replace('*', '"*"').replace('?', '"?"')
+    if "?" in source_file or "*" in source_file:
+        source_file = source_file.replace("*", '"*"').replace("?", '"?"')
     return f'\nif [ -f "{source_file}" ] ; then cp "{source_file}" "{destination}" ; fi'
 
 
 class CommandsBuilder:
-
-    def __init__(self, initial_command=''):
+    def __init__(self, initial_command=""):
         # Remove trailing semi-colon so we can start hacking up this command.
         # TODO: Refactor to compose a list and join with ';', would be more clean.
         self.raw_command = initial_command
-        initial_command = util.unicodify(initial_command or '')
+        initial_command = util.unicodify(initial_command or "")
         commands = initial_command.rstrip("; ")
         self.commands = commands
 
@@ -272,7 +276,7 @@ class CommandsBuilder:
     def prepend_commands(self, commands):
         return self.prepend_command("; ".join(c for c in commands if c))
 
-    def append_command(self, command, sep=';'):
+    def append_command(self, command, sep=";"):
         if command:
             self.commands = f"{self.commands}{sep} {command}"
         return self
@@ -281,14 +285,15 @@ class CommandsBuilder:
         self.append_command("; ".join(c for c in commands if c))
 
     def capture_stdout_stderr(self, stdout_file, stderr_file):
-        self.prepend_command("""out="${TMPDIR:-/tmp}/out.$$" err="${TMPDIR:-/tmp}/err.$$"
+        self.prepend_command(
+            """out="${TMPDIR:-/tmp}/out.$$" err="${TMPDIR:-/tmp}/err.$$"
 mkfifo "$out" "$err"
 trap 'rm "$out" "$err"' EXIT
 tee -a stdout.log < "$out" &
 tee -a stderr.log < "$err" >&2 &""",
-                             sep="")
-        self.append_command(f"> '{stdout_file}' 2> '{stderr_file}'",
-                            sep="")
+            sep="",
+        )
+        self.append_command(f"> '{stdout_file}' 2> '{stderr_file}'", sep="")
 
     def capture_return_code(self):
         if not self.return_code_captured:
@@ -301,4 +306,4 @@ tee -a stderr.log < "$err" >&2 &""",
         return self.commands
 
 
-__all__ = ("build_command", )
+__all__ = ("build_command",)
diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py
index 3ab28227a22..e327c5eee39 100755
--- a/lib/galaxy/jobs/dynamic_tool_destination.py
+++ b/lib/galaxy/jobs/dynamic_tool_destination.py
@@ -15,7 +15,7 @@ import yaml
 
 from galaxy.util import parse_xml
 
-__version__ = '1.1.0'
+__version__ = "1.1.0"
 
 # log to galaxy's logger
 log = logging.getLogger(__name__)
@@ -46,13 +46,16 @@ max_edit_dist = 2
 """
 List of valid categories that can be expected in the configuration.
 """
-valid_categories = ['verbose', 'tools', 'default_destination',
-                    'users', 'default_priority']
+valid_categories = ["verbose", "tools", "default_destination", "users", "default_priority"]
 
 # --- destination validation error messages --- #
 dest_err_default_dest = "Default destination '%s' does not appear in the job configuration."  # destination
-dest_err_tool_default_dest = "Default destination for '%s': '%s' does not appear in the job configuration."  # tool, destination
-dest_err_tool_rule_dest = "Destination for '%s', rule %s: '%s' does not exist in job configuration."  # tool, counter, destination
+dest_err_tool_default_dest = (
+    "Default destination for '%s': '%s' does not appear in the job configuration."  # tool, destination
+)
+dest_err_tool_rule_dest = (
+    "Destination for '%s', rule %s: '%s' does not exist in job configuration."  # tool, counter, destination
+)
 
 
 class MalformedYMLException(Exception):
@@ -96,21 +99,20 @@ class RuleValidator:
         :returns: validated rule or result of validation (depending on
                   return_bool)
         """
-        if rule_type == 'file_size':
+        if rule_type == "file_size":
             return cls.__validate_file_size_rule(app, return_bool, *args, **kwargs)
 
-        elif rule_type == 'num_input_datasets':
+        elif rule_type == "num_input_datasets":
             return cls.__validate_num_input_datasets_rule(app, return_bool, *args, **kwargs)
 
-        elif rule_type == 'records':
+        elif rule_type == "records":
             return cls.__validate_records_rule(app, return_bool, *args, **kwargs)
 
-        elif rule_type == 'arguments':
+        elif rule_type == "arguments":
             return cls.__validate_arguments_rule(app, return_bool, *args, **kwargs)
 
     @classmethod
-    def __validate_file_size_rule(
-            cls, app, return_bool, original_rule, counter, tool):
+    def __validate_file_size_rule(cls, app, return_bool, original_rule, counter, tool):
         """
         This function is responsible for validating 'file_size' rules.
 
@@ -138,23 +140,19 @@ class RuleValidator:
 
         # Users Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_users(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_users(valid_rule, return_bool, rule, tool, counter)
 
         # Nice_value Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_nice_value(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_nice_value(valid_rule, return_bool, rule, tool, counter)
 
         # Destination Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_destination(
-                valid_rule, app, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_destination(valid_rule, app, return_bool, rule, tool, counter)
 
         # Bounds Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_bounds(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_bounds(valid_rule, return_bool, rule, tool, counter)
 
         if return_bool:
             return valid_rule
@@ -163,8 +161,7 @@ class RuleValidator:
             return rule
 
     @classmethod
-    def __validate_num_input_datasets_rule(
-            cls, app, return_bool, original_rule, counter, tool):
+    def __validate_num_input_datasets_rule(cls, app, return_bool, original_rule, counter, tool):
         """
         This function is responsible for validating 'num_input_datasets' rules.
 
@@ -192,23 +189,19 @@ class RuleValidator:
 
         # Users Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_users(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_users(valid_rule, return_bool, rule, tool, counter)
 
         # Nice_value Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_nice_value(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_nice_value(valid_rule, return_bool, rule, tool, counter)
 
         # Destination Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_destination(
-                valid_rule, app, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_destination(valid_rule, app, return_bool, rule, tool, counter)
 
         # Bounds Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_bounds(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_bounds(valid_rule, return_bool, rule, tool, counter)
 
         if return_bool:
             return valid_rule
@@ -245,23 +238,19 @@ class RuleValidator:
 
         # Users Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_users(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_users(valid_rule, return_bool, rule, tool, counter)
 
         # Nice_value Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_nice_value(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_nice_value(valid_rule, return_bool, rule, tool, counter)
 
         # Destination Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_destination(
-                valid_rule, app, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_destination(valid_rule, app, return_bool, rule, tool, counter)
 
         # Bounds Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_bounds(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_bounds(valid_rule, return_bool, rule, tool, counter)
 
         if return_bool:
             return valid_rule
@@ -270,8 +259,7 @@ class RuleValidator:
             return rule
 
     @classmethod
-    def __validate_arguments_rule(
-            cls, app, return_bool, original_rule, counter, tool):
+    def __validate_arguments_rule(cls, app, return_bool, original_rule, counter, tool):
         """
         This is responsible for validating 'arguments' rules.
 
@@ -299,24 +287,20 @@ class RuleValidator:
 
         # Users Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_users(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_users(valid_rule, return_bool, rule, tool, counter)
 
         # Nice_value Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_nice_value(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_nice_value(valid_rule, return_bool, rule, tool, counter)
 
         # Destination Verification #
         if rule is not None:
-            valid_rule, rule = cls.__validate_destination(
-                valid_rule, app, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_destination(valid_rule, app, return_bool, rule, tool, counter)
 
         # Arguments Verification (for rule_type arguments; read comment block at top
         # of function for clarification.
         if rule is not None:
-            valid_rule, rule = cls.__validate_arguments(
-                valid_rule, return_bool, rule, tool, counter)
+            valid_rule, rule = cls.__validate_arguments(valid_rule, return_bool, rule, tool, counter)
 
         if return_bool:
             return valid_rule
@@ -394,7 +378,7 @@ class RuleValidator:
         """
 
         if "fail_message" in rule:
-            if "destination" not in rule or rule['destination'] != "fail":
+            if "destination" not in rule or rule["destination"] != "fail":
                 error = f"Found a fail_message for rule {str(counter)}"
                 error += f" in '{str(tool)}', but destination is not 'fail'!"
                 if not return_bool:
@@ -421,22 +405,24 @@ class RuleValidator:
                         log.debug(error)
                     valid_rule = False
                 else:
-                    is_valid = validate_destination(app, rule["destination"],
-                               dest_err_tool_rule_dest, (tool, counter, rule["destination"]),
-                               return_bool)
+                    is_valid = validate_destination(
+                        app,
+                        rule["destination"],
+                        dest_err_tool_rule_dest,
+                        (tool, counter, rule["destination"]),
+                        return_bool,
+                    )
                     if not is_valid:
                         valid_rule = False
             elif isinstance(rule["destination"], dict):
-                if ("priority" in rule["destination"]
-                        and isinstance(rule["destination"]["priority"], dict)):
+                if "priority" in rule["destination"] and isinstance(rule["destination"]["priority"], dict):
 
                     for priority in rule["destination"]["priority"]:
                         if priority not in priority_list:
                             error = "Invalid priority '"
                             error += f"{str(priority)}' for rule "
                             error += f"{str(counter)} in '{str(tool)}'."
-                            suggestion = get_typo_correction(priority,
-                                         priority_list, max_edit_dist)
+                            suggestion = get_typo_correction(priority, priority_list, max_edit_dist)
                             if suggestion:
                                 error += f" Did you mean '{str(suggestion)}'?"
                             if not return_bool:
@@ -456,11 +442,13 @@ class RuleValidator:
                                 log.debug(error)
                             valid_rule = False
                         else:
-                            is_valid = validate_destination(app,
+                            is_valid = validate_destination(
+                                app,
                                 rule["destination"]["priority"][priority],
                                 dest_err_tool_rule_dest,
                                 (tool, counter, rule["destination"]["priority"][priority]),
-                                return_bool)
+                                return_bool,
+                            )
                             if not is_valid:
                                 valid_rule = False
                 else:
@@ -685,9 +673,13 @@ class RuleValidator:
         return valid_rule, rule
 
 
-def parse_yaml(path: str = "/config/tool_destinations.yml",
-               job_conf_path: str = "/config/job_conf.xml", app=None, test: bool = False,
-               return_bool: bool = False):
+def parse_yaml(
+    path: str = "/config/tool_destinations.yml",
+    job_conf_path: str = "/config/job_conf.xml",
+    app=None,
+    test: bool = False,
+    return_bool: bool = False,
+):
     """
     Get a yaml file from path and send it to validate_config for validation.
 
@@ -715,8 +707,8 @@ def parse_yaml(path: str = "/config/tool_destinations.yml",
                 # os.path.realpath gets the path of DynamicToolDestination.py
                 # and then os.path.join is used to go back four directories
                 config_directory = os.path.join(
-                    os.path.dirname(os.path.realpath(__file__)), os.pardir,
-                    os.pardir, os.pardir, os.pardir)
+                    os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, os.pardir
+                )
 
                 opt_file = config_directory + path
 
@@ -748,8 +740,7 @@ def parse_yaml(path: str = "/config/tool_destinations.yml",
         return config
 
 
-def validate_destination(app, destination: str, err_message: str, err_message_contents,
-                         return_bool: bool = True):
+def validate_destination(app, destination: str, err_message: str, err_message_contents, return_bool: bool = True):
     """
     Validate received destination id.
 
@@ -773,14 +764,15 @@ def validate_destination(app, destination: str, err_message: str, err_message_co
     valid_destination = False
     suggestion = None
 
-    if destination == 'fail' and err_message is dest_err_tool_rule_dest:  # It's a tool rule that is set to fail. It's valid
+    if (
+        destination == "fail" and err_message is dest_err_tool_rule_dest
+    ):  # It's a tool rule that is set to fail. It's valid
         valid_destination = True
     elif app is None:
         if destination in destination_list:
             valid_destination = True
         else:
-            suggestion = get_typo_correction(destination,
-                                             destination_list, max_edit_dist)
+            suggestion = get_typo_correction(destination, destination_list, max_edit_dist)
     elif app.job_config.get_destination(destination):
         valid_destination = True
 
@@ -824,8 +816,8 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
 
     if return_bool:
         verbose = True
-    elif obj is not None and 'verbose' in obj and isinstance(obj['verbose'], bool):
-        verbose = obj['verbose']
+    elif obj is not None and "verbose" in obj and isinstance(obj["verbose"], bool):
+        verbose = obj["verbose"]
     else:
         valid_config = False
         if obj:
@@ -840,57 +832,64 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
         log.debug("Missing mandatory field 'verbose' in config!")
 
     # a list with the available rule_types. Can be expanded on easily in the future
-    available_rule_types = ['file_size', 'num_input_datasets', 'records', 'arguments']
+    available_rule_types = ["file_size", "num_input_datasets", "records", "arguments"]
 
     if obj is not None:
         # in obj, there should always be only 5 categories: tools, default_destination,
         # default_priority, users, and verbose
 
-        if 'default_destination' in obj:
+        if "default_destination" in obj:
             suggestion = None
-            if isinstance(obj['default_destination'], str):
-                is_valid = validate_destination(app, obj['default_destination'],
-                                                dest_err_default_dest,
-                                                (obj['default_destination']))
+            if isinstance(obj["default_destination"], str):
+                is_valid = validate_destination(
+                    app, obj["default_destination"], dest_err_default_dest, (obj["default_destination"])
+                )
                 if is_valid:
-                    new_config["default_destination"] = obj['default_destination']
+                    new_config["default_destination"] = obj["default_destination"]
                 else:
                     valid_config = False
 
-            elif isinstance(obj['default_destination'], dict):
+            elif isinstance(obj["default_destination"], dict):
 
-                if ('priority' in obj['default_destination']
-                        and isinstance(obj['default_destination']['priority'], dict)):
+                if "priority" in obj["default_destination"] and isinstance(
+                    obj["default_destination"]["priority"], dict
+                ):
 
-                    for priority in obj['default_destination']['priority']:
-                        if isinstance(obj['default_destination']['priority'][priority],
-                                      str):
+                    for priority in obj["default_destination"]["priority"]:
+                        if isinstance(obj["default_destination"]["priority"][priority], str):
                             priority_list.add(priority)
                             is_valid = validate_destination(
-                                app, obj['default_destination']['priority'][priority],
+                                app,
+                                obj["default_destination"]["priority"][priority],
                                 dest_err_default_dest,
-                                (obj['default_destination']['priority'][priority]))
+                                (obj["default_destination"]["priority"][priority]),
+                            )
 
                             if is_valid:
-                                new_config["default_destination"]['priority'][priority] = (
-                                    obj['default_destination']['priority'][priority])
+                                new_config["default_destination"]["priority"][priority] = obj["default_destination"][
+                                    "priority"
+                                ][priority]
                             else:
                                 valid_config = False
                     if len(priority_list) < 1:
-                        error = ("No valid priorities found!")
+                        error = "No valid priorities found!"
                         if verbose:
                             log.debug(error)
                         valid_config = False
                     else:
-                        if 'default_priority' in obj:
-                            if isinstance(obj['default_priority'], str):
-                                if obj['default_priority'] in priority_list:
-                                    new_config['default_priority'] = obj['default_priority']
+                        if "default_priority" in obj:
+                            if isinstance(obj["default_priority"], str):
+                                if obj["default_priority"] in priority_list:
+                                    new_config["default_priority"] = obj["default_priority"]
                                 else:
-                                    error = ("Default priority '" + str(obj['default_priority'])
-                                          + "' is not a valid priority.")
-                                    suggestion = get_typo_correction(obj['default_priority'],
-                                                 priority_list, max_edit_dist)
+                                    error = (
+                                        "Default priority '"
+                                        + str(obj["default_priority"])
+                                        + "' is not a valid priority."
+                                    )
+                                    suggestion = get_typo_correction(
+                                        obj["default_priority"], priority_list, max_edit_dist
+                                    )
                                     if suggestion:
                                         error += f" Did you mean '{str(suggestion)}'?"
                                     if verbose:
@@ -902,11 +901,11 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                                 valid_config = False
                         else:
                             error = "No default_priority section found in config."
-                            if 'med' in priority_list:
+                            if "med" in priority_list:
                                 # set 'med' as fallback default priority, so
                                 # old tool_destination.yml configs still work
                                 error += " Setting 'med' as default priority."
-                                new_config['default_priority'] = 'med'
+                                new_config["default_priority"] = "med"
                             else:
                                 error += " Things may not run as expected!"
                                 valid_config = False
@@ -930,22 +929,26 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                 log.debug(error)
             valid_config = False
 
-        if 'users' in obj:
-            if isinstance(obj['users'], dict):
-                for user in obj['users']:
-                    curr = obj['users'][user]
+        if "users" in obj:
+            if isinstance(obj["users"], dict):
+                for user in obj["users"]:
+                    curr = obj["users"][user]
 
                     if isinstance(curr, dict):
-                        if 'priority' in curr and isinstance(curr['priority'], str):
+                        if "priority" in curr and isinstance(curr["priority"], str):
 
-                            if curr['priority'] in priority_list:
-                                new_config['users'][user]['priority'] = curr['priority']
+                            if curr["priority"] in priority_list:
+                                new_config["users"][user]["priority"] = curr["priority"]
                             else:
-                                error = ("User '" + user + "', priority '"
-                                      + str(curr['priority']) + "' is not defined "
-                                      + "in the global default_destination section")
-                                suggestion = get_typo_correction(curr['priority'],
-                                             priority_list, max_edit_dist)
+                                error = (
+                                    "User '"
+                                    + user
+                                    + "', priority '"
+                                    + str(curr["priority"])
+                                    + "' is not defined "
+                                    + "in the global default_destination section"
+                                )
+                                suggestion = get_typo_correction(curr["priority"], priority_list, max_edit_dist)
                                 if suggestion:
                                     error += f" Did you mean '{str(suggestion)}'?"
                                 if verbose:
@@ -967,9 +970,9 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                     log.debug(error)
                 valid_config = False
 
-        if 'tools' in obj:
-            for tool in obj['tools']:
-                curr = obj['tools'][tool]
+        if "tools" in obj:
+            for tool in obj["tools"]:
+                curr = obj["tools"][tool]
 
                 # This check is to make sure we have a tool name, and not just
                 # rules right way.
@@ -982,51 +985,64 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                         # default_destination (not mandatory) and rules (mandatory)
                         if "default_destination" in curr:
                             suggestion = None
-                            if isinstance(curr['default_destination'], str):
-                                is_valid = validate_destination(app,
-                                    curr['default_destination'],
+                            if isinstance(curr["default_destination"], str):
+                                is_valid = validate_destination(
+                                    app,
+                                    curr["default_destination"],
                                     dest_err_tool_default_dest,
-                                    (tool, curr['default_destination']))
+                                    (tool, curr["default_destination"]),
+                                )
                                 if is_valid:
-                                    new_config['tools'][tool]['default_destination'] = (
-                                        curr['default_destination'])
+                                    new_config["tools"][tool]["default_destination"] = curr["default_destination"]
                                     tool_has_default = True
                                 else:
                                     valid_config = False
-                            elif isinstance(curr['default_destination'], dict):
+                            elif isinstance(curr["default_destination"], dict):
 
-                                if ('priority' in curr['default_destination']
-                                        and isinstance(curr['default_destination']['priority'], dict)):
+                                if "priority" in curr["default_destination"] and isinstance(
+                                    curr["default_destination"]["priority"], dict
+                                ):
 
-                                    for priority in curr['default_destination']['priority']:
-                                        destination = curr['default_destination']['priority'][priority]
+                                    for priority in curr["default_destination"]["priority"]:
+                                        destination = curr["default_destination"]["priority"][priority]
                                         if priority in priority_list:
                                             if isinstance(destination, str):
 
                                                 is_valid = validate_destination(
-                                                    app, destination,
+                                                    app,
+                                                    destination,
                                                     dest_err_tool_default_dest,
-                                                    (tool, curr['default_destination']['priority'][priority]))
+                                                    (tool, curr["default_destination"]["priority"][priority]),
+                                                )
                                                 if is_valid:
-                                                    new_config['tools'][tool]['default_destination']['priority'][priority] = destination
+                                                    new_config["tools"][tool]["default_destination"]["priority"][
+                                                        priority
+                                                    ] = destination
                                                     tool_has_default = True
                                                 else:
                                                     valid_config = False
 
                                             else:
-                                                error = ("No default '" + str(priority)
-                                                         + "' priority destination  for tool "
-                                                         + str(tool) + " in config!")
+                                                error = (
+                                                    "No default '"
+                                                    + str(priority)
+                                                    + "' priority destination  for tool "
+                                                    + str(tool)
+                                                    + " in config!"
+                                                )
                                                 if verbose:
                                                     log.debug(error)
                                                 valid_config = False
 
                                         else:
-                                            error = ("Invalid default destination priority '"
-                                                     + str(priority) + "' for '" + str(tool)
-                                                     + "'.")
-                                            suggestion = get_typo_correction(priority,
-                                                         priority_list, max_edit_dist)
+                                            error = (
+                                                "Invalid default destination priority '"
+                                                + str(priority)
+                                                + "' for '"
+                                                + str(tool)
+                                                + "'."
+                                            )
+                                            suggestion = get_typo_correction(priority, priority_list, max_edit_dist)
                                             if suggestion:
                                                 error += f" Did you mean '{str(suggestion)}'?"
                                             if verbose:
@@ -1039,14 +1055,14 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                                         log.debug(error)
                                     valid_config = False
 
-                        if "rules" in curr and isinstance(curr['rules'], list):
+                        if "rules" in curr and isinstance(curr["rules"], list):
                             # under rules, there should only be a list of rules
                             curr_tool = curr
                             counter = 0
 
-                            for rule in curr_tool['rules']:
+                            for rule in curr_tool["rules"]:
                                 if "rule_type" in rule:
-                                    if rule['rule_type'] in available_rule_types:
+                                    if rule["rule_type"] in available_rule_types:
                                         validated_rule = None
                                         counter += 1
 
@@ -1055,16 +1071,14 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                                         # result
                                         if return_bool:
                                             valid_rule = RuleValidator.validate_rule(
-                                                rule['rule_type'], app, return_bool,
-                                                rule, counter, tool)
+                                                rule["rule_type"], app, return_bool, rule, counter, tool
+                                            )
 
                                         # otherwise, retrieve the processed rule
                                         else:
-                                            validated_rule = (
-                                                RuleValidator.validate_rule(
-                                                    rule['rule_type'],
-                                                    app, return_bool,
-                                                    rule, counter, tool))
+                                            validated_rule = RuleValidator.validate_rule(
+                                                rule["rule_type"], app, return_bool, rule, counter, tool
+                                            )
 
                                         # if the result we get is False, then
                                         # indicate that the whole config is invalid
@@ -1074,10 +1088,8 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                                         # if we got a rule back that seems to be
                                         # valid (or was fixable) then append it to
                                         # list of ready-to-use tools
-                                        if (not return_bool
-                                                and validated_rule is not None):
-                                            curr_tool_rules.append(
-                                                copy.deepcopy(validated_rule))
+                                        if not return_bool and validated_rule is not None:
+                                            curr_tool_rules.append(copy.deepcopy(validated_rule))
 
                                     # if rule['rule_type'] in available_rule_types
                                     else:
@@ -1116,7 +1128,7 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
                             log.debug(error)
 
                     if curr_tool_rules:
-                        new_config['tools'][str(tool)]['rules'] = curr_tool_rules
+                        new_config["tools"][str(tool)]["rules"] = curr_tool_rules
 
                 # if not isinstance(curr, list)
                 else:
@@ -1153,7 +1165,7 @@ def validate_config(obj: dict, app=None, return_bool: bool = False):
 
 
 def bytes_to_str(size, unit="YB"):
-    '''
+    """
     Uses the bi convention: 1024 B = 1 KB since this method primarily
     has inputs of bytes for RAM
 
@@ -1162,7 +1174,7 @@ def bytes_to_str(size, unit="YB"):
 
     @rtype: str
     @return return_str: the resulting string
-    '''
+    """
     # converts size in bytes to most readable unit
     units = ["B", "KB", "MB", "GB", "TB", "PB", "EB", "ZB", "YB"]
     i = 0
@@ -1196,7 +1208,7 @@ def bytes_to_str(size, unit="YB"):
 
 
 def str_to_bytes(size):
-    '''
+    """
     Uses the bi convention: 1024 B = 1 KB since this method primarily
     has inputs of bytes for RAM
 
@@ -1205,7 +1217,7 @@ def str_to_bytes(size):
 
     @rtype: int
     @return curr_size: the resulting size converted from str
-    '''
+    """
     units = ["", "b", "kb", "mb", "gb", "tb", "pb", "eb", "zb", "yb"]
     curr_size = size
 
@@ -1258,19 +1270,20 @@ def importer(test):
     global JobDestination
     global JobMappingException
     if test:
+
         class JobDestination:
             def __init__(self, *kwd):
-                self.id = kwd.get('id')
-                self.nativeSpec = kwd.get('params')['nativeSpecification']
-                self.runner = kwd.get('runner')
+                self.id = kwd.get("id")
+                self.nativeSpec = kwd.get("params")["nativeSpecification"]
+                self.runner = kwd.get("runner")
+
         from galaxy.jobs.mapper import JobMappingException
     else:
         from galaxy.jobs import JobDestination
         from galaxy.jobs.mapper import JobMappingException
 
 
-def map_tool_to_destination(
-        job, app, tool, user_email, test=False, path=None, job_conf_path=None):
+def map_tool_to_destination(job, app, tool, user_email, test=False, path=None, job_conf_path=None):
     """
     Dynamically allocate resources
 
@@ -1312,9 +1325,9 @@ def map_tool_to_destination(
     inp_data = {da.name: da.dataset for da in job.input_datasets}
     inp_data.update([(da.name, da.dataset) for da in job.input_library_datasets])
 
-    if config is not None and str(tool.old_id) in config['tools']:
-        if 'rules' in config['tools'][str(tool.old_id)]:
-            for rule in config['tools'][str(tool.old_id)]['rules']:
+    if config is not None and str(tool.old_id) in config["tools"]:
+        if "rules" in config["tools"][str(tool.old_id)]:
+            for rule in config["tools"][str(tool.old_id)]["rules"]:
                 if rule["rule_type"] == "file_size":
                     filesize_rule_present = True
 
@@ -1392,18 +1405,21 @@ def map_tool_to_destination(
         # Get the default priority from the config if necessary.
         # If there isn't one, choose an arbitrary one as a fallback
         if "default_destination" in config:
-            if isinstance(config['default_destination'], dict):
-                if 'default_priority' in config:
-                    default_priority = config['default_priority']
+            if isinstance(config["default_destination"], dict):
+                if "default_priority" in config:
+                    default_priority = config["default_priority"]
                     priority = default_priority
 
                 else:
                     if len(priority_list) > 0:
                         default_priority = next(iter(priority_list))
                         priority = default_priority
-                        error = ("No default priority found, arbitrarily setting '"
-                                 + default_priority + "' as the default priority."
-                                 + " Things may not work as expected!")
+                        error = (
+                            "No default priority found, arbitrarily setting '"
+                            + default_priority
+                            + "' as the default priority."
+                            + " Things may not work as expected!"
+                        )
                         if verbose:
                             log.debug(error)
 
@@ -1421,17 +1437,17 @@ def map_tool_to_destination(
         # Priority coming from workflow invocation takes precedence over job specific priorities
         if workflow_params is not None:
             resource_params = json.loads(workflow_params)
-            if 'priority' in resource_params:
+            if "priority" in resource_params:
                 # For by_group mapping, this priority has already been validated when the
                 # request was created.
-                if resource_params['priority'] is not None:
-                    priority = resource_params['priority']
+                if resource_params["priority"] is not None:
+                    priority = resource_params["priority"]
 
         elif job_params is not None:
             resource_params = json.loads(job_params)
-            if 'priority' in resource_params:
-                if resource_params['priority'] is not None:
-                    priority = resource_params['priority']
+            if "priority" in resource_params:
+                if resource_params["priority"] is not None:
+                    priority = resource_params["priority"]
 
         # get the user's priority
         if "users" in config:
@@ -1439,21 +1455,21 @@ def map_tool_to_destination(
                 priority = config["users"][user_email]["priority"]
 
         if "default_destination" in config:
-            if isinstance(config['default_destination'], str):
-                destination = config['default_destination']
+            if isinstance(config["default_destination"], str):
+                destination = config["default_destination"]
             else:
-                if priority in config['default_destination']['priority']:
-                    destination = config['default_destination']['priority'][priority]
-                elif default_priority in config['default_destination']['priority']:
-                    destination = (config['default_destination']['priority'][default_priority])
-            config = config['tools']
+                if priority in config["default_destination"]["priority"]:
+                    destination = config["default_destination"]["priority"][priority]
+                elif default_priority in config["default_destination"]["priority"]:
+                    destination = config["default_destination"]["priority"][default_priority]
+            config = config["tools"]
             if str(tool.old_id) in config:
-                if 'rules' in config[str(tool.old_id)]:
-                    for rule in config[str(tool.old_id)]['rules']:
+                if "rules" in config[str(tool.old_id)]:
+                    for rule in config[str(tool.old_id)]["rules"]:
                         rule_counter += 1
                         user_authorized = False
-                        if 'users' in rule and isinstance(rule['users'], list):
-                            if user_email in rule['users']:
+                        if "users" in rule and isinstance(rule["users"], list):
+                            if user_email in rule["users"]:
                                 user_authorized = True
                         else:
                             user_authorized = True
@@ -1471,7 +1487,7 @@ def map_tool_to_destination(
                                         matched = True
 
                                 else:
-                                    if (lower_bound <= file_size and file_size < upper_bound):
+                                    if lower_bound <= file_size and file_size < upper_bound:
                                         matched = True
 
                             elif rule["rule_type"] == "num_input_datasets":
@@ -1484,7 +1500,7 @@ def map_tool_to_destination(
                                     if lower_bound <= num_input_datasets:
                                         matched = True
                                 else:
-                                    if (lower_bound <= num_input_datasets and num_input_datasets < upper_bound):
+                                    if lower_bound <= num_input_datasets and num_input_datasets < upper_bound:
                                         matched = True
 
                             elif rule["rule_type"] == "records":
@@ -1512,7 +1528,7 @@ def map_tool_to_destination(
                                     try:
                                         options_value = reduce(dict.__getitem__, arg_keys_list, options)
                                         arg_value = reduce(dict.__getitem__, arg_keys_list, arg_dict)
-                                        if (arg_value != options_value):
+                                        if arg_value != options_value:
                                             matched = False
                                     except KeyError:
                                         matched = False
@@ -1523,8 +1539,7 @@ def map_tool_to_destination(
 
                             # if we matched a rule
                             if matched:
-                                if (matched_rule is None or rule["nice_value"]
-                                        < matched_rule["nice_value"]):
+                                if matched_rule is None or rule["nice_value"] < matched_rule["nice_value"]:
                                     matched_rule = rule
                         # if user_authorized
                         else:
@@ -1544,14 +1559,14 @@ def map_tool_to_destination(
 
             if matched_rule is None:
                 if "default_destination" in config[str(tool.old_id)]:
-                    default_tool_destination = (config[str(tool.old_id)]['default_destination'])
+                    default_tool_destination = config[str(tool.old_id)]["default_destination"]
                     if isinstance(default_tool_destination, str):
                         destination = default_tool_destination
                     else:
-                        if priority in default_tool_destination['priority']:
-                            destination = default_tool_destination['priority'][priority]
-                        elif default_priority in default_tool_destination['priority']:
-                            destination = (default_tool_destination['priority'][default_priority])
+                        if priority in default_tool_destination["priority"]:
+                            destination = default_tool_destination["priority"][priority]
+                        elif default_priority in default_tool_destination["priority"]:
+                            destination = default_tool_destination["priority"][default_priority]
                         # else global default destination is used
             else:
                 if isinstance(matched_rule["destination"], str):
@@ -1560,7 +1575,7 @@ def map_tool_to_destination(
                     if priority in matched_rule["destination"]["priority"]:
                         destination = matched_rule["destination"]["priority"][priority]
                     elif default_priority in matched_rule["destination"]["priority"]:
-                        destination = (matched_rule["destination"]["priority"][default_priority])
+                        destination = matched_rule["destination"]["priority"][default_priority]
                     # else global default destination is used
 
         # if "default_destination" in config
@@ -1615,11 +1630,10 @@ def get_destination_list_from_job_config(job_config_location) -> set:
     # os.path.realpath gets the path of DynamicToolDestination.py
     # and then os.path.join is used to go back four directories
 
-    config_location = os.path.join(
-        os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir)
+    config_location = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir)
 
     if job_config_location:
-        local_path = re.compile('^/config/.+$')
+        local_path = re.compile("^/config/.+$")
         if local_path.match(job_config_location):
             job_config_location = os.path.join(config_location, job_config_location)
     else:  # Pick one of the default ones
@@ -1636,8 +1650,7 @@ def get_destination_list_from_job_config(job_config_location) -> set:
                 message += f"using '{f}'. *"
                 break
         else:
-            message += ("and no default job configs in 'config/'. "
-                    + "Expect lots of failures. *")
+            message += "and no default job configs in 'config/'. " + "Expect lots of failures. *"
 
         if verbose:
             log.debug(message)
@@ -1698,14 +1711,10 @@ def get_edit_distance(source, target):
         # Substitution or matching:
         # Target and source items are aligned, and either
         # are different (cost of 1), or are the same (cost of 0).
-        current_row[1:] = np.minimum(
-            current_row[1:],
-            np.add(previous_row[:-1], target != s))
+        current_row[1:] = np.minimum(current_row[1:], np.add(previous_row[:-1], target != s))
 
         # Deletion (target grows shorter than source):
-        current_row[1:] = np.minimum(
-            current_row[1:],
-            current_row[0:-1] + 1)
+        current_row[1:] = np.minimum(current_row[1:], current_row[0:-1] + 1)
 
         previous_row = current_row
 
@@ -1757,7 +1766,7 @@ def get_typo_correction(typo_str, word_set, max_dist):
     return suggestion
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     """
     This function is responsible for running the app if directly run through
     the commandline. It offers the ability to specify a config through the
@@ -1773,18 +1782,20 @@ if __name__ == '__main__':
     logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
 
     parser.add_argument(
-        '-c', '--check-config', dest='check_config', nargs='?',
-        help='Use this option to validate tool_destinations.yml.'
-             + ' Optionally, provide the path to the tool_destinations.yml'
-             + ' that you would like to check, and/or the path to the related'
-             + ' job_conf.xml. Default: galaxy/config/tool_destinations.yml'
-             + 'and galaxy/config/job_conf.xml')
+        "-c",
+        "--check-config",
+        dest="check_config",
+        nargs="?",
+        help="Use this option to validate tool_destinations.yml."
+        + " Optionally, provide the path to the tool_destinations.yml"
+        + " that you would like to check, and/or the path to the related"
+        + " job_conf.xml. Default: galaxy/config/tool_destinations.yml"
+        + "and galaxy/config/job_conf.xml",
+    )
 
-    parser.add_argument(
-        '-j', '--job-config', dest='job_config')
+    parser.add_argument("-j", "--job-config", dest="job_config")
 
-    parser.add_argument(
-        '-V', '--version', action='version', version=f"%(prog)s {__version__}")
+    parser.add_argument("-V", "--version", action="version", version=f"%(prog)s {__version__}")
 
     args = parser.parse_args()
 
@@ -1796,13 +1807,11 @@ if __name__ == '__main__':
     job_config_location = args.job_config
 
     if args.check_config:
-        valid_config = parse_yaml(path=args.check_config,
-                                  job_conf_path=job_config_location,
-                                  return_bool=True)
+        valid_config = parse_yaml(path=args.check_config, job_conf_path=job_config_location, return_bool=True)
     else:
-        valid_config = parse_yaml(path="/config/tool_destinations.yml",
-                                  job_conf_path=job_config_location,
-                                  return_bool=True)
+        valid_config = parse_yaml(
+            path="/config/tool_destinations.yml", job_conf_path=job_config_location, return_bool=True
+        )
 
     if valid_config:
         print("Configuration is valid!")
diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 0085a74cfa5..58aaecd5ea2 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -9,7 +9,11 @@ from queue import (
     Empty,
     Queue,
 )
-from typing import Dict, List, Tuple
+from typing import (
+    Dict,
+    List,
+    Tuple,
+)
 
 from sqlalchemy.exc import OperationalError
 from sqlalchemy.sql.expression import (
@@ -18,7 +22,7 @@ from sqlalchemy.sql.expression import (
     null,
     or_,
     select,
-    true
+    true,
 )
 
 from galaxy import model
@@ -26,7 +30,7 @@ from galaxy.exceptions import ObjectNotFound
 from galaxy.jobs import (
     JobDestination,
     JobWrapper,
-    TaskWrapper
+    TaskWrapper,
 )
 from galaxy.jobs.mapper import JobNotReadyException
 from galaxy.structured_app import MinimalManagerApp
@@ -39,12 +43,31 @@ from galaxy.web_stack.message import JobHandlerMessage
 log = get_logger(__name__)
 
 # States for running a job. These are NOT the same as data states
-JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_READY, JOB_DELETED, JOB_ADMIN_DELETED, JOB_USER_OVER_QUOTA, JOB_USER_OVER_TOTAL_WALLTIME = 'wait', 'error', 'input_error', 'input_deleted', 'ready', 'deleted', 'admin_deleted', 'user_over_quota', 'user_over_total_walltime'
-DEFAULT_JOB_PUT_FAILURE_MESSAGE = 'Unable to run job due to a misconfiguration of the Galaxy job running system.  Please contact a site administrator.'
+(
+    JOB_WAIT,
+    JOB_ERROR,
+    JOB_INPUT_ERROR,
+    JOB_INPUT_DELETED,
+    JOB_READY,
+    JOB_DELETED,
+    JOB_ADMIN_DELETED,
+    JOB_USER_OVER_QUOTA,
+    JOB_USER_OVER_TOTAL_WALLTIME,
+) = (
+    "wait",
+    "error",
+    "input_error",
+    "input_deleted",
+    "ready",
+    "deleted",
+    "admin_deleted",
+    "user_over_quota",
+    "user_over_total_walltime",
+)
+DEFAULT_JOB_PUT_FAILURE_MESSAGE = "Unable to run job due to a misconfiguration of the Galaxy job running system.  Please contact a site administrator."
 
 
 class JobHandlerI:
-
     def start(self):
         pass
 
@@ -76,8 +99,15 @@ class JobHandler(JobHandlerI):
 
 
 class ItemGrabber:
-
-    def __init__(self, app, grab_type='Job', handler_assignment_method=None, max_grab=None, self_handler_tags=None, handler_tags=None):
+    def __init__(
+        self,
+        app,
+        grab_type="Job",
+        handler_assignment_method=None,
+        max_grab=None,
+        self_handler_tags=None,
+        handler_tags=None,
+    ):
         self.app = app
         self.sa_session = app.model.context
         self.grab_this = getattr(model, grab_type)
@@ -86,30 +116,39 @@ class ItemGrabber:
         self.self_handler_tags = self_handler_tags
         self.max_grab = max_grab
         self.handler_tags = handler_tags
-        self._grab_conn_opts = {'autocommit': False}
+        self._grab_conn_opts = {"autocommit": False}
         self._grab_query = None
         self._supports_returning = self.app.application_stack.supports_returning()
 
     def setup_query(self):
-        subq = select([self.grab_this.id]) \
-            .where(and_(
-                self.grab_this.table.c.handler.in_(self.self_handler_tags),
-                self.grab_this.table.c.state == self.grab_this.states.NEW)) \
+        subq = (
+            select([self.grab_this.id])
+            .where(
+                and_(
+                    self.grab_this.table.c.handler.in_(self.self_handler_tags),
+                    self.grab_this.table.c.state == self.grab_this.states.NEW,
+                )
+            )
             .order_by(self.grab_this.table.c.id)
+        )
         if self.max_grab:
             subq = subq.limit(self.max_grab)
         if self.handler_assignment_method == HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED:
             subq = subq.with_for_update(skip_locked=True)
-        self._grab_query = self.grab_this.table.update() \
-            .where(self.grab_this.table.c.id.in_(subq)) \
+        self._grab_query = (
+            self.grab_this.table.update()
+            .where(self.grab_this.table.c.id.in_(subq))
             .values(handler=self.app.config.server_name)
+        )
         if self._supports_returning:
             self._grab_query = self._grab_query.returning(self.grab_this.table.c.id)
         if self.handler_assignment_method == HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION:
-            self._grab_conn_opts['isolation_level'] = 'SERIALIZABLE'
+            self._grab_conn_opts["isolation_level"] = "SERIALIZABLE"
         log.info(
-            "Handler job grabber initialized with '%s' assignment method for handler '%s', tag(s): %s", self.handler_assignment_method,
-            self.app.config.server_name, ', '.join(str(x) for x in self.handler_tags)
+            "Handler job grabber initialized with '%s' assignment method for handler '%s', tag(s): %s",
+            self.handler_assignment_method,
+            self.app.config.server_name,
+            ", ".join(str(x) for x in self.handler_tags),
         )
 
     @staticmethod
@@ -151,8 +190,8 @@ class ItemGrabber:
             except OperationalError as e:
                 # If this is a serialization failure on PostgreSQL, then e.orig is a psycopg2 TransactionRollbackError
                 # and should have attribute `code`. Other engines should just report the message and move on.
-                if int(getattr(e.orig, 'pgcode', -1)) != 40001:
-                    log.debug('Grabbing %s failed (serialization failures are ok): %s', self.grab_type, unicodify(e))
+                if int(getattr(e.orig, "pgcode", -1)) != 40001:
+                    log.debug("Grabbing %s failed (serialization failures are ok): %s", self.grab_type, unicodify(e))
                 trans.rollback()
 
 
@@ -161,6 +200,7 @@ class JobHandlerQueue(Monitors):
     Job Handler's Internal Queue, this is what actually implements waiting for
     jobs to be runnable and dispatching to a JobRunner.
     """
+
     STOP_SIGNAL = object()
 
     def __init__(self, app: MinimalManagerApp, dispatcher):
@@ -186,11 +226,13 @@ class JobHandlerQueue(Monitors):
         name = "JobHandlerQueue.monitor_thread"
         self._init_monitor_thread(name, target=self.__monitor, config=app.config)
         self.job_grabber = None
-        handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.app.job_config.handler_assignment_methods)
+        handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(
+            self.app.job_config.handler_assignment_methods
+        )
         if handler_assignment_method:
             self.job_grabber = ItemGrabber(
                 app=app,
-                grab_type='Job',
+                grab_type="Job",
                 handler_assignment_method=handler_assignment_method,
                 max_grab=self.app.job_config.handler_max_grab,
                 self_handler_tags=self.app.job_config.self_handler_tags,
@@ -201,13 +243,13 @@ class JobHandlerQueue(Monitors):
         """
         Starts the JobHandler's thread after checking for any unhandled jobs.
         """
-        log.debug('Handler queue starting for jobs assigned to handler: %s', self.app.config.server_name)
+        log.debug("Handler queue starting for jobs assigned to handler: %s", self.app.config.server_name)
         # Recover jobs at startup
         self.__check_jobs_at_startup()
         # Start the queue
         self.monitor_thread.start()
         # The stack code is initialized in the application
-        JobHandlerMessage().bind_default_handler(self, '_handle_message')
+        JobHandlerMessage().bind_default_handler(self, "_handle_message")
         self.app.application_stack.register_message_handler(self._handle_message, name=JobHandlerMessage.target)
         log.info("job handler queue started")
 
@@ -227,48 +269,63 @@ class JobHandlerQueue(Monitors):
         """
         jobs_at_startup = []
         if self.track_jobs_in_database:
-            in_list = (model.Job.states.QUEUED,
-                       model.Job.states.RUNNING,
-                       model.Job.states.STOPPED)
+            in_list = (model.Job.states.QUEUED, model.Job.states.RUNNING, model.Job.states.STOPPED)
         else:
-            in_list = (model.Job.states.NEW,
-                       model.Job.states.QUEUED,
-                       model.Job.states.RUNNING)
+            in_list = (model.Job.states.NEW, model.Job.states.QUEUED, model.Job.states.RUNNING)
         if self.app.config.user_activation_on:
-            jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                .outerjoin(model.User) \
-                .filter(model.Job.state.in_(in_list)
-                        & (model.Job.handler == self.app.config.server_name)
-                        & or_((model.Job.user_id == null()), (model.User.active == true()))).yield_per(model.YIELD_PER_ROWS)
+            jobs_at_startup = (
+                self.sa_session.query(model.Job)
+                .enable_eagerloads(False)
+                .outerjoin(model.User)
+                .filter(
+                    model.Job.state.in_(in_list)
+                    & (model.Job.handler == self.app.config.server_name)
+                    & or_((model.Job.user_id == null()), (model.User.active == true()))
+                )
+                .yield_per(model.YIELD_PER_ROWS)
+            )
         else:
-            jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                .filter(model.Job.state.in_(in_list)
-                        & (model.Job.handler == self.app.config.server_name)).yield_per(model.YIELD_PER_ROWS)
+            jobs_at_startup = (
+                self.sa_session.query(model.Job)
+                .enable_eagerloads(False)
+                .filter(model.Job.state.in_(in_list) & (model.Job.handler == self.app.config.server_name))
+                .yield_per(model.YIELD_PER_ROWS)
+            )
 
         for job in jobs_at_startup:
             if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
                 log.warning(f"({job.id}) Tool '{job.tool_id}' removed from tool config, unable to recover job")
-                self.job_wrapper(job).fail('This tool was disabled before the job completed.  Please contact your Galaxy administrator.')
+                self.job_wrapper(job).fail(
+                    "This tool was disabled before the job completed.  Please contact your Galaxy administrator."
+                )
             elif job.job_runner_name is not None and job.job_runner_external_id is None:
                 # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
-                log.debug(f"({job.id}) Job runner assigned but no external ID recorded, adding to the job handler queue")
+                log.debug(
+                    f"({job.id}) Job runner assigned but no external ID recorded, adding to the job handler queue"
+                )
                 job.job_runner_name = None
                 if self.track_jobs_in_database:
                     job.set_state(model.Job.states.NEW)
                 else:
                     self.queue.put((job.id, job.tool_id))
-            elif job.job_runner_name is not None and job.job_runner_external_id is not None and job.destination_id is None:
+            elif (
+                job.job_runner_name is not None
+                and job.job_runner_external_id is not None
+                and job.destination_id is None
+            ):
                 # This is the first start after upgrading from URLs to destinations, convert the URL to a destination and persist
                 job_wrapper = self.job_wrapper(job)
                 job_destination = self.dispatcher.url_to_destination(job.job_runner_name)
                 if job_destination.id is None:
-                    job_destination.id = 'legacy_url'
+                    job_destination.id = "legacy_url"
                 job_wrapper.set_job_destination(job_destination, job.job_runner_external_id)
                 self.dispatcher.recover(job, job_wrapper)
-                log.info(f'({job.id}) Converted job from a URL to a destination and recovered')
+                log.info(f"({job.id}) Converted job from a URL to a destination and recovered")
             elif job.job_runner_name is None:
                 # Never (fully) dispatched
-                log.debug(f"({job.id}) No job runner assigned and job still in '{job.state}' state, adding to the job handler queue")
+                log.debug(
+                    f"({job.id}) No job runner assigned and job still in '{job.state}' state, adding to the job handler queue"
+                )
                 if self.track_jobs_in_database:
                     job.set_state(model.Job.states.NEW)
                 else:
@@ -285,14 +342,20 @@ class JobHandlerQueue(Monitors):
         job_wrapper = self.job_wrapper(job)
         # Use the persisted destination as its params may differ from
         # what's in the job_conf xml
-        job_destination = JobDestination(id=job.destination_id, runner=job.job_runner_name, params=job.destination_params)
+        job_destination = JobDestination(
+            id=job.destination_id, runner=job.job_runner_name, params=job.destination_params
+        )
         # resubmits are not persisted (it's a good thing) so they
         # should be added back to the in-memory destination on startup
         try:
             config_job_destination = self.app.job_config.get_destination(job.destination_id)
             job_destination.resubmit = config_job_destination.resubmit
         except KeyError:
-            log.debug('(%s) Recovered destination id (%s) does not exist in job config (but this may be normal in the case of a dynamically generated destination)', job.id, job.destination_id)
+            log.debug(
+                "(%s) Recovered destination id (%s) does not exist in job config (but this may be normal in the case of a dynamically generated destination)",
+                job.id,
+                job.destination_id,
+            )
         job_wrapper.job_runner_mapper.cached_job_destination = job_destination
         return job_wrapper
 
@@ -319,8 +382,7 @@ class JobHandlerQueue(Monitors):
         Called repeatedly by `monitor` to process waiting jobs.
         """
         monitor_step_timer = self.app.execution_timer_factory.get_timer(
-            'internal.galaxy.jobs.handlers.monitor_step',
-            'Job handler monitor step complete.'
+            "internal.galaxy.jobs.handlers.monitor_step", "Job handler monitor step complete."
         )
         if self.job_grabber is not None:
             self.job_grabber.grab_unhandled_items()
@@ -341,50 +403,79 @@ class JobHandlerQueue(Monitors):
             # Clear the session so we get fresh states for job and all datasets
             self.sa_session.expunge_all()
             # Fetch all new jobs
-            hda_not_ready = self.sa_session.query(model.Job.id).enable_eagerloads(False) \
-                .join(model.JobToInputDatasetAssociation) \
-                .join(model.HistoryDatasetAssociation) \
-                .join(model.Dataset) \
-                .filter(and_(model.Job.state == model.Job.states.NEW,
-                             model.Dataset.state.in_(model.Dataset.non_ready_states))).subquery()
-            ldda_not_ready = self.sa_session.query(model.Job.id).enable_eagerloads(False) \
-                .join(model.JobToInputLibraryDatasetAssociation) \
-                .join(model.LibraryDatasetDatasetAssociation) \
-                .join(model.Dataset) \
-                .filter(and_(model.Job.state == model.Job.states.NEW,
-                             model.Dataset.state.in_(model.Dataset.non_ready_states))).subquery()
-            rank = func.rank().over(partition_by=model.Job.table.c.user_id,
-                                    order_by=model.Job.table.c.id).label('rank')
+            hda_not_ready = (
+                self.sa_session.query(model.Job.id)
+                .enable_eagerloads(False)
+                .join(model.JobToInputDatasetAssociation)
+                .join(model.HistoryDatasetAssociation)
+                .join(model.Dataset)
+                .filter(
+                    and_(
+                        model.Job.state == model.Job.states.NEW, model.Dataset.state.in_(model.Dataset.non_ready_states)
+                    )
+                )
+                .subquery()
+            )
+            ldda_not_ready = (
+                self.sa_session.query(model.Job.id)
+                .enable_eagerloads(False)
+                .join(model.JobToInputLibraryDatasetAssociation)
+                .join(model.LibraryDatasetDatasetAssociation)
+                .join(model.Dataset)
+                .filter(
+                    and_(
+                        model.Job.state == model.Job.states.NEW, model.Dataset.state.in_(model.Dataset.non_ready_states)
+                    )
+                )
+                .subquery()
+            )
+            rank = func.rank().over(partition_by=model.Job.table.c.user_id, order_by=model.Job.table.c.id).label("rank")
             job_filter_conditions = (
                 (model.Job.state == model.Job.states.NEW),
                 (model.Job.handler == self.app.config.server_name),
                 ~model.Job.table.c.id.in_(select(hda_not_ready)),
-                ~model.Job.table.c.id.in_(select(ldda_not_ready)))
+                ~model.Job.table.c.id.in_(select(ldda_not_ready)),
+            )
             if self.app.config.user_activation_on:
                 job_filter_conditions = job_filter_conditions + (
-                    or_((model.Job.user_id == null()), (model.User.active == true())),)
-            if self.sa_session.bind.name == 'sqlite':
+                    or_((model.Job.user_id == null()), (model.User.active == true())),
+                )
+            if self.sa_session.bind.name == "sqlite":
                 query_objects = (model.Job,)
             else:
                 query_objects = (model.Job, rank)
-            ready_query = self.sa_session.query(*query_objects).enable_eagerloads(False) \
-                .outerjoin(model.User) \
-                .filter(and_(*job_filter_conditions)) \
+            ready_query = (
+                self.sa_session.query(*query_objects)
+                .enable_eagerloads(False)
+                .outerjoin(model.User)
+                .filter(and_(*job_filter_conditions))
                 .order_by(model.Job.id)
-            if self.sa_session.bind.name == 'sqlite':
+            )
+            if self.sa_session.bind.name == "sqlite":
                 jobs_to_check = ready_query.all()
             else:
                 ranked = ready_query.subquery()
-                jobs_to_check = self.sa_session.query(model.Job) \
-                    .join(ranked, model.Job.id == ranked.c.id) \
-                    .filter(ranked.c.rank <= self.app.job_config.handler_ready_window_size).all()
+                jobs_to_check = (
+                    self.sa_session.query(model.Job)
+                    .join(ranked, model.Job.id == ranked.c.id)
+                    .filter(ranked.c.rank <= self.app.job_config.handler_ready_window_size)
+                    .all()
+                )
             # Filter jobs with invalid input states
             jobs_to_check = self.__filter_jobs_with_invalid_input_states(jobs_to_check)
             # Fetch all "resubmit" jobs
-            resubmit_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                .filter(and_((model.Job.state == model.Job.states.RESUBMITTED),
-                             (model.Job.handler == self.app.config.server_name))) \
-                .order_by(model.Job.id).all()
+            resubmit_jobs = (
+                self.sa_session.query(model.Job)
+                .enable_eagerloads(False)
+                .filter(
+                    and_(
+                        (model.Job.state == model.Job.states.RESUBMITTED),
+                        (model.Job.handler == self.app.config.server_name),
+                    )
+                )
+                .order_by(model.Job.id)
+                .all()
+            )
         else:
             # Get job objects and append to watch queue for any which were
             # previously waiting
@@ -405,7 +496,7 @@ class JobHandlerQueue(Monitors):
         self.__clear_job_count()
         # Check resubmit jobs first so that limits of new jobs will still be enforced
         for job in resubmit_jobs:
-            log.debug('(%s) Job was resubmitted and is being dispatched immediately', job.id)
+            log.debug("(%s) Job was resubmitted and is being dispatched immediately", job.id)
             # Reassemble resubmit job destination from persisted value
             jw = self.__recover_job_wrapper(job)
             if jw.is_ready_for_resubmission(job):
@@ -449,8 +540,7 @@ class JobHandlerQueue(Monitors):
                     log.info("(%d) Job deleted by user while still queued" % job.id)
                 elif job_state == JOB_ADMIN_DELETED:
                     log.info("(%d) Job deleted by admin while still queued" % job.id)
-                elif job_state in (JOB_USER_OVER_QUOTA,
-                                   JOB_USER_OVER_TOTAL_WALLTIME):
+                elif job_state in (JOB_USER_OVER_QUOTA, JOB_USER_OVER_TOTAL_WALLTIME):
                     if job_state == JOB_USER_OVER_QUOTA:
                         log.info("(%d) User (%s) is over quota: job paused" % (job.id, job.user_id))
                         what = "your disk quota"
@@ -489,25 +579,34 @@ class JobHandlerQueue(Monitors):
         """
         job_ids_to_check = [j.id for j in jobs]
         queries = []
-        for job_to_input, input_association in [(model.JobToInputDatasetAssociation, model.HistoryDatasetAssociation),
-                                                (model.JobToInputLibraryDatasetAssociation, model.LibraryDatasetDatasetAssociation)]:
-            q = self.sa_session.query(
-                model.Job.id,
-                input_association.deleted,
-                input_association._state,
-                input_association.name,
-                model.Dataset.deleted,
-                model.Dataset.purged,
-                model.Dataset.state,
-            ).join(job_to_input.job) \
-                .join(input_association) \
-                .join(model.Dataset) \
-                .filter(model.Job.id.in_(job_ids_to_check)) \
-                .filter(or_(model.Dataset.deleted == true(),
-                            model.Dataset.state != model.Dataset.states.OK,
-                            input_association.deleted == true(),
-                            input_association._state == input_association.states.FAILED_METADATA
-                            )).all()
+        for job_to_input, input_association in [
+            (model.JobToInputDatasetAssociation, model.HistoryDatasetAssociation),
+            (model.JobToInputLibraryDatasetAssociation, model.LibraryDatasetDatasetAssociation),
+        ]:
+            q = (
+                self.sa_session.query(
+                    model.Job.id,
+                    input_association.deleted,
+                    input_association._state,
+                    input_association.name,
+                    model.Dataset.deleted,
+                    model.Dataset.purged,
+                    model.Dataset.state,
+                )
+                .join(job_to_input.job)
+                .join(input_association)
+                .join(model.Dataset)
+                .filter(model.Job.id.in_(job_ids_to_check))
+                .filter(
+                    or_(
+                        model.Dataset.deleted == true(),
+                        model.Dataset.state != model.Dataset.states.OK,
+                        input_association.deleted == true(),
+                        input_association._state == input_association.states.FAILED_METADATA,
+                    )
+                )
+                .all()
+            )
             queries.extend(q)
         jobs_to_pause = defaultdict(list)
         jobs_to_fail = defaultdict(list)
@@ -586,14 +685,16 @@ class JobHandlerQueue(Monitors):
         return state
 
     def __verify_job_ready(self, job, job_wrapper):
-        """ Compute job destination and verify job is ready at that
+        """Compute job destination and verify job is ready at that
         destination by checking job limits and quota. If this method
         return a job state of JOB_READY - it MUST also return a job
         destination.
         """
         job_destination = None
         try:
-            assert job_wrapper.tool is not None, 'This tool was disabled before the job completed.  Please contact your Galaxy administrator.'
+            assert (
+                job_wrapper.tool is not None
+            ), "This tool was disabled before the job completed.  Please contact your Galaxy administrator."
             # Cause the job_destination to be set and cached by the mapper
             job_destination = job_wrapper.job_destination
         except AssertionError as e:
@@ -604,9 +705,9 @@ class JobHandlerQueue(Monitors):
             job_state = e.job_state or JOB_WAIT
             return job_state, None
         except Exception as e:
-            failure_message = getattr(e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE)
+            failure_message = getattr(e, "failure_message", DEFAULT_JOB_PUT_FAILURE_MESSAGE)
             if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE:
-                log.exception('Failed to generate job destination')
+                log.exception("Failed to generate job destination")
             else:
                 log.debug(f"Intentionally failing job with message ({failure_message})")
             job_wrapper.fail(failure_message)
@@ -620,10 +721,11 @@ class JobHandlerQueue(Monitors):
         if state == JOB_READY and self.app.quota_agent.is_over_quota(self.app, job, job_destination):
             return JOB_USER_OVER_QUOTA, job_destination
         # Check total walltime limits
-        if (state == JOB_READY and "delta" in self.app.job_config.limits.total_walltime):
+        if state == JOB_READY and "delta" in self.app.job_config.limits.total_walltime:
             jobs_to_check = self.sa_session.query(model.Job).filter(
-                model.Job.update_time >= datetime.datetime.now() - datetime.timedelta(self.app.job_config.limits.total_walltime["window"]),
-                model.Job.state == 'ok'
+                model.Job.update_time
+                >= datetime.datetime.now() - datetime.timedelta(self.app.job_config.limits.total_walltime["window"]),
+                model.Job.state == "ok",
             )
             if job.user_id:
                 jobs_to_check = jobs_to_check.filter(model.Job.user_id == job.user_id)
@@ -634,9 +736,7 @@ class JobHandlerQueue(Monitors):
                 # History is job.state_history
                 started = None
                 finished = None
-                for history in sorted(
-                        job.state_history,
-                        key=lambda history: history.update_time):
+                for history in sorted(job.state_history, key=lambda history: history.update_time):
                     if history.state == "running":
                         started = history.create_time
                     elif history.state == "ok":
@@ -645,8 +745,12 @@ class JobHandlerQueue(Monitors):
                 if started is not None and finished is not None:
                     time_spent += finished - started
                 else:
-                    log.warning("Unable to calculate time spent for job %s; started: %s, finished: %s",
-                                job.id, started, finished)
+                    log.warning(
+                        "Unable to calculate time spent for job %s; started: %s, finished: %s",
+                        job.id,
+                        started,
+                        finished,
+                    )
 
             if time_spent > self.app.job_config.limits.total_walltime["delta"]:
                 return JOB_USER_OVER_TOTAL_WALLTIME, job_destination
@@ -654,7 +758,7 @@ class JobHandlerQueue(Monitors):
         return state, job_destination
 
     def __verify_in_memory_job_inputs(self, job):
-        """ Perform the same checks that happen via SQL for in-memory managed
+        """Perform the same checks that happen via SQL for in-memory managed
         jobs.
         """
         if job.state == model.Job.states.DELETED:
@@ -667,16 +771,24 @@ class JobHandlerQueue(Monitors):
                 continue
             # don't run jobs for which the input dataset was deleted
             if idata.deleted:
-                self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail(f"input data {idata.hid} (file: {idata.file_name}) was deleted before the job started")
+                self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail(
+                    f"input data {idata.hid} (file: {idata.file_name}) was deleted before the job started"
+                )
                 return JOB_INPUT_DELETED
             # an error in the input data causes us to bail immediately
             elif idata.state == idata.states.ERROR:
                 self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail(f"input data {idata.hid} is in error state")
                 return JOB_INPUT_ERROR
             elif idata.state == idata.states.FAILED_METADATA:
-                self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail(f"input data {idata.hid} failed to properly set metadata")
+                self.job_wrappers.pop(job.id, self.job_wrapper(job)).fail(
+                    f"input data {idata.hid} failed to properly set metadata"
+                )
                 return JOB_INPUT_ERROR
-            elif idata.state != idata.states.OK and not (idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id):
+            elif idata.state != idata.states.OK and not (
+                idata.state == idata.states.SETTING_METADATA
+                and job.tool_id is not None
+                and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id
+            ):
                 # need to requeue
                 return JOB_WAIT
 
@@ -693,11 +805,16 @@ class JobHandlerQueue(Monitors):
         # This could have been incremented by a previous job dispatched on this iteration, even if we're not caching
         rval = self.user_job_count.get(user_id, 0)
         if not self.app.config.cache_user_job_count:
-            result = self.sa_session.execute(select([func.count(model.Job.table.c.id)])
-                                             .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED,
-                                                         model.Job.states.RUNNING,
-                                                         model.Job.states.RESUBMITTED)),
-                                                         (model.Job.table.c.user_id == user_id))))
+            result = self.sa_session.execute(
+                select([func.count(model.Job.table.c.id)]).where(
+                    and_(
+                        model.Job.table.c.state.in_(
+                            (model.Job.states.QUEUED, model.Job.states.RUNNING, model.Job.states.RESUBMITTED)
+                        ),
+                        (model.Job.table.c.user_id == user_id),
+                    )
+                )
+            )
             for row in result:
                 # there should only be one row
                 rval += row[0]
@@ -707,12 +824,18 @@ class JobHandlerQueue(Monitors):
         # Cache the job count if necessary
         if self.user_job_count is None and self.app.config.cache_user_job_count:
             self.user_job_count = {}
-            query = self.sa_session.execute(select([model.Job.table.c.user_id, func.count(model.Job.table.c.user_id)])
-                                            .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED,
-                                                                                     model.Job.states.RUNNING,
-                                                                                     model.Job.states.RESUBMITTED)),
-                                                        (model.Job.table.c.user_id != null())))
-                                            .group_by(model.Job.table.c.user_id))
+            query = self.sa_session.execute(
+                select([model.Job.table.c.user_id, func.count(model.Job.table.c.user_id)])
+                .where(
+                    and_(
+                        model.Job.table.c.state.in_(
+                            (model.Job.states.QUEUED, model.Job.states.RUNNING, model.Job.states.RESUBMITTED)
+                        ),
+                        (model.Job.table.c.user_id != null()),
+                    )
+                )
+                .group_by(model.Job.table.c.user_id)
+            )
             for row in query:
                 self.user_job_count[row[0]] = row[1]
         elif self.user_job_count is None:
@@ -730,32 +853,51 @@ class JobHandlerQueue(Monitors):
             # queue.
             rval = {}
             rval.update(cached)
-            result = self.sa_session.execute(select([model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label('job_count')])
-                                             .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING)), (model.Job.table.c.user_id == user_id)))
-                                             .group_by(model.Job.table.c.destination_id))
+            result = self.sa_session.execute(
+                select(
+                    [model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label("job_count")]
+                )
+                .where(
+                    and_(
+                        model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING)),
+                        (model.Job.table.c.user_id == user_id),
+                    )
+                )
+                .group_by(model.Job.table.c.destination_id)
+            )
             for row in result:
                 # Add the count from the database to the cached count
-                rval[row['destination_id']] = rval.get(row['destination_id'], 0) + row['job_count']
+                rval[row["destination_id"]] = rval.get(row["destination_id"], 0) + row["job_count"]
         return rval
 
     def __cache_user_job_count_per_destination(self):
         # Cache the job count if necessary
         if self.user_job_count_per_destination is None and self.app.config.cache_user_job_count:
             self.user_job_count_per_destination = {}
-            result = self.sa_session.execute(select([model.Job.table.c.user_id, model.Job.table.c.destination_id, func.count(model.Job.table.c.user_id).label('job_count')])
-                                             .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING))))
-                                             .group_by(model.Job.table.c.user_id, model.Job.table.c.destination_id))
+            result = self.sa_session.execute(
+                select(
+                    [
+                        model.Job.table.c.user_id,
+                        model.Job.table.c.destination_id,
+                        func.count(model.Job.table.c.user_id).label("job_count"),
+                    ]
+                )
+                .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING))))
+                .group_by(model.Job.table.c.user_id, model.Job.table.c.destination_id)
+            )
             for row in result:
-                if row['user_id'] not in self.user_job_count_per_destination:
-                    self.user_job_count_per_destination[row['user_id']] = {}
-                self.user_job_count_per_destination[row['user_id']][row['destination_id']] = row['job_count']
+                if row["user_id"] not in self.user_job_count_per_destination:
+                    self.user_job_count_per_destination[row["user_id"]] = {}
+                self.user_job_count_per_destination[row["user_id"]][row["destination_id"]] = row["job_count"]
         elif self.user_job_count_per_destination is None:
             self.user_job_count_per_destination = {}
 
     def increase_running_job_count(self, user_id, destination_id):
-        if self.app.job_config.limits.registered_user_concurrent_jobs or \
-           self.app.job_config.limits.anonymous_user_concurrent_jobs or \
-           self.app.job_config.limits.destination_user_concurrent_jobs:
+        if (
+            self.app.job_config.limits.registered_user_concurrent_jobs
+            or self.app.job_config.limits.anonymous_user_concurrent_jobs
+            or self.app.job_config.limits.destination_user_concurrent_jobs
+        ):
             if self.user_job_count is None:
                 self.user_job_count = {}
             if self.user_job_count_per_destination is None:
@@ -763,11 +905,15 @@ class JobHandlerQueue(Monitors):
             self.user_job_count[user_id] = self.user_job_count.get(user_id, 0) + 1
             if user_id not in self.user_job_count_per_destination:
                 self.user_job_count_per_destination[user_id] = {}
-            self.user_job_count_per_destination[user_id][destination_id] = self.user_job_count_per_destination[user_id].get(destination_id, 0) + 1
+            self.user_job_count_per_destination[user_id][destination_id] = (
+                self.user_job_count_per_destination[user_id].get(destination_id, 0) + 1
+            )
         if self.app.job_config.limits.destination_total_concurrent_jobs:
             if self.total_job_count_per_destination is None:
                 self.total_job_count_per_destination = {}
-            self.total_job_count_per_destination[destination_id] = self.total_job_count_per_destination.get(destination_id, 0) + 1
+            self.total_job_count_per_destination[destination_id] = (
+                self.total_job_count_per_destination.get(destination_id, 0) + 1
+            )
 
     def __check_user_jobs(self, job, job_wrapper):
         # TODO: Update output datasets' _state = LIMITED or some such new
@@ -803,25 +949,40 @@ class JobHandlerQueue(Monitors):
         elif job.galaxy_session:
             # Anonymous users only get the hard limit
             if self.app.job_config.limits.anonymous_user_concurrent_jobs:
-                count = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                            .filter(and_(model.Job.session_id == job.galaxy_session.id,
-                                         or_(model.Job.state == model.Job.states.RUNNING,
-                                             model.Job.state == model.Job.states.QUEUED))).count()
+                count = (
+                    self.sa_session.query(model.Job)
+                    .enable_eagerloads(False)
+                    .filter(
+                        and_(
+                            model.Job.session_id == job.galaxy_session.id,
+                            or_(
+                                model.Job.state == model.Job.states.RUNNING, model.Job.state == model.Job.states.QUEUED
+                            ),
+                        )
+                    )
+                    .count()
+                )
                 if count >= self.app.job_config.limits.anonymous_user_concurrent_jobs:
                     return JOB_WAIT
         else:
-            log.warning(f'Job {job.id} is not associated with a user or session so job concurrency limit cannot be checked.')
+            log.warning(
+                f"Job {job.id} is not associated with a user or session so job concurrency limit cannot be checked."
+            )
         return JOB_READY
 
     def __cache_total_job_count_per_destination(self):
         # Cache the job count if necessary
         if self.total_job_count_per_destination is None:
             self.total_job_count_per_destination = {}
-            result = self.sa_session.execute(select([model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label('job_count')])
-                                             .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING))))
-                                             .group_by(model.Job.table.c.destination_id))
+            result = self.sa_session.execute(
+                select(
+                    [model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label("job_count")]
+                )
+                .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING))))
+                .group_by(model.Job.table.c.destination_id)
+            )
             for row in result:
-                self.total_job_count_per_destination[row['destination_id']] = row['job_count']
+                self.total_job_count_per_destination[row["destination_id"]] = row["job_count"]
 
     def get_total_job_count_per_destination(self):
         self.__cache_total_job_count_per_destination()
@@ -862,7 +1023,12 @@ class JobHandlerQueue(Monitors):
             # If not tracking jobs in the database
             self.put(job.id, job.tool_id)
         else:
-            log.warning("(%s) Handler '%s' received setup message but handler '%s' is already assigned, ignoring", job.id, self.app.config.server_name, job.handler)
+            log.warning(
+                "(%s) Handler '%s' received setup message but handler '%s' is already assigned, ignoring",
+                job.id,
+                self.app.config.server_name,
+                job.handler,
+            )
 
     def put(self, job_id, tool_id):
         """Add a job to the queue (by job identifier)"""
@@ -892,6 +1058,7 @@ class JobHandlerStopQueue(Monitors):
     """
     A queue for jobs which need to be terminated prematurely.
     """
+
     STOP_SIGNAL = object()
 
     def __init__(self, app: MinimalManagerApp, dispatcher):
@@ -957,11 +1124,19 @@ class JobHandlerStopQueue(Monitors):
             # Clear the session so we get fresh states for job and all datasets
             self.sa_session.expunge_all()
             # Fetch all new jobs
-            newly_deleted_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                                     .filter((model.Job.state.in_((model.Job.states.DELETED_NEW,
-                                                                   model.Job.states.DELETING,
-                                                                   model.Job.states.STOPPING)))
-                                             & (model.Job.handler == self.app.config.server_name)).all()
+            newly_deleted_jobs = (
+                self.sa_session.query(model.Job)
+                .enable_eagerloads(False)
+                .filter(
+                    (
+                        model.Job.state.in_(
+                            (model.Job.states.DELETED_NEW, model.Job.states.DELETING, model.Job.states.STOPPING)
+                        )
+                    )
+                    & (model.Job.handler == self.app.config.server_name)
+                )
+                .all()
+            )
             for job in newly_deleted_jobs:
                 # job.stderr is always a string (job.job_stderr + job.tool_stderr, possibly `''`),
                 # while any `not None` message returned in self.queue.get_nowait() is interpreted
@@ -980,15 +1155,19 @@ class JobHandlerStopQueue(Monitors):
         except Empty:
             pass
         for job, error_msg in jobs_to_check:
-            if (job.state not in
-                    (job.states.DELETED_NEW,
-                     job.states.DELETING,
-                     job.states.DELETED,
-                     job.states.STOPPING,
-                     job.states.STOPPED)
-                    and job.finished):
+            if (
+                job.state
+                not in (
+                    job.states.DELETED_NEW,
+                    job.states.DELETING,
+                    job.states.DELETED,
+                    job.states.STOPPING,
+                    job.states.STOPPED,
+                )
+                and job.finished
+            ):
                 # terminated before it got here
-                log.debug('Job %s already finished, not deleting or stopping', job.id)
+                log.debug("Job %s already finished, not deleting or stopping", job.id)
                 continue
             if job.state in (job.states.DELETED_NEW, job.states.DELETING):
                 self.__delete(job, error_msg)
@@ -1018,7 +1197,6 @@ class JobHandlerStopQueue(Monitors):
 
 
 class DefaultJobDispatcher:
-
     def __init__(self, app):
         self.app = app
         self.job_runners = self.app.job_config.get_job_runner_plugins(self.app.config.server_name)
@@ -1045,11 +1223,15 @@ class DefaultJobDispatcher:
 
         New-style runner plugin IDs must match the URL's scheme for this to work.
         """
-        runner_name = url.split(':', 1)[0]
+        runner_name = url.split(":", 1)[0]
         try:
             return self.job_runners[runner_name].url_to_destination(url)
         except Exception:
-            log.exception("Unable to convert legacy job runner URL '%s' to job destination, destination will be the '%s' runner with no params", url, runner_name)
+            log.exception(
+                "Unable to convert legacy job runner URL '%s' to job destination, destination will be the '%s' runner with no params",
+                url,
+                runner_name,
+            )
             return JobDestination(runner=runner_name)
 
     def put(self, job_wrapper):
@@ -1062,7 +1244,7 @@ class DefaultJobDispatcher:
                 log.debug(f"({job_wrapper.job_id}) Dispatching to {runner_name} runner")
             self.job_runners[runner_name].put(job_wrapper)
         except KeyError:
-            log.error(f'put(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}')
+            log.error(f"put(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}")
             job_wrapper.fail(DEFAULT_JOB_PUT_FAILURE_MESSAGE)
 
     def stop(self, job, job_wrapper):
@@ -1084,7 +1266,7 @@ class DefaultJobDispatcher:
             try:
                 self.job_runners[runner_name].stop_job(job_wrapper)
             except KeyError:
-                log.error(f'stop(): ({job_wrapper.get_id_tag()}) Invalid job runner: {runner_name}')
+                log.error(f"stop(): ({job_wrapper.get_id_tag()}) Invalid job runner: {runner_name}")
                 # Job and output dataset states have already been updated, so nothing is done here.
 
     def recover(self, job, job_wrapper):
@@ -1093,7 +1275,7 @@ class DefaultJobDispatcher:
         try:
             self.job_runners[runner_name].recover(job, job_wrapper)
         except KeyError:
-            log.error(f'recover(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}')
+            log.error(f"recover(): ({job_wrapper.job_id}) Invalid job runner: {runner_name}")
             job_wrapper.fail(DEFAULT_JOB_PUT_FAILURE_MESSAGE)
         except ObjectNotFound:
             msg = "Could not recover job working directory after Galaxy restart"
diff --git a/lib/galaxy/jobs/manager.py b/lib/galaxy/jobs/manager.py
index 7184e6a4771..4d58a001f35 100644
--- a/lib/galaxy/jobs/manager.py
+++ b/lib/galaxy/jobs/manager.py
@@ -6,8 +6,14 @@ from functools import partial
 
 from sqlalchemy.sql.expression import null
 
-from galaxy.exceptions import HandlerAssignmentError, ToolExecutionError
-from galaxy.jobs import handler, NoopQueue
+from galaxy.exceptions import (
+    HandlerAssignmentError,
+    ToolExecutionError,
+)
+from galaxy.jobs import (
+    handler,
+    NoopQueue,
+)
 from galaxy.model import Job
 from galaxy.structured_app import MinimalManagerApp
 from galaxy.web_stack.message import JobHandlerMessage
@@ -19,6 +25,7 @@ class JobManager:
     """
     Highest level interface to job management.
     """
+
     job_handler: handler.JobHandlerI
 
     def __init__(self, app: MinimalManagerApp):
@@ -32,12 +39,17 @@ class JobManager:
 
     def __check_jobs_at_startup(self):
         if self.app.job_config.use_messaging:
-            jobs_at_startup = self.app.model.context.query(Job).enable_eagerloads(False) \
-                .filter((Job.state == Job.states.NEW) & (Job.handler == null())).all()
+            jobs_at_startup = (
+                self.app.model.context.query(Job)
+                .enable_eagerloads(False)
+                .filter((Job.state == Job.states.NEW) & (Job.handler == null()))
+                .all()
+            )
             if jobs_at_startup:
                 log.info(
-                    'No handler assigned at startup for the following jobs, will dispatch via message: %s',
-                    ', '.join(str(j.id) for j in jobs_at_startup))
+                    "No handler assigned at startup for the following jobs, will dispatch via message: %s",
+                    ", ".join(str(j.id) for j in jobs_at_startup),
+                )
             for job in jobs_at_startup:
                 tool = self.app.toolbox.get_tool(job.tool_id, job.tool_version, exact=True)
                 self.enqueue(job, tool)
@@ -52,7 +64,7 @@ class JobManager:
         self.job_handler.job_queue.put(job.id, tool_id)
 
     def _message_callback(self, job):
-        return JobHandlerMessage(task='setup', job_id=job.id)
+        return JobHandlerMessage(task="setup", job_id=job.id)
 
     def enqueue(self, job, tool=None, flush=True):
         """Queue a job for execution.
@@ -76,12 +88,19 @@ class JobManager:
             configured_handler = tool.get_configured_job_handler(job.params)
             if configured_handler is not None:
                 p = f" (with job params: {str(job.params)})" if job.params else ""
-                log.debug("(%s) Configured job handler for tool '%s'%s is: %s", job.log_str(), tool_id, p, configured_handler)
+                log.debug(
+                    "(%s) Configured job handler for tool '%s'%s is: %s", job.log_str(), tool_id, p, configured_handler
+                )
         queue_callback = partial(self._queue_callback, job, tool_id)
         message_callback = partial(self._message_callback, job)
         try:
             return self.app.job_config.assign_handler(
-                job, configured=configured_handler, queue_callback=queue_callback, message_callback=message_callback, flush=flush)
+                job,
+                configured=configured_handler,
+                queue_callback=queue_callback,
+                message_callback=message_callback,
+                flush=flush,
+            )
         except HandlerAssignmentError as exc:
             raise ToolExecutionError(exc.args[0], job=exc.obj)
 
@@ -105,6 +124,7 @@ class NoopManager:
     """
     Implements the JobManager interface but does nothing
     """
+
     def __init__(self, *args, **kwargs):
         self.job_handler = NoopHandler()
 
@@ -119,6 +139,7 @@ class NoopHandler(handler.JobHandlerI):
     """
     Implements the JobHandler interface but does nothing
     """
+
     def __init__(self, *args, **kwargs):
         self.job_queue = NoopQueue()
         self.job_stop_queue = NoopQueue()
diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index cf762ed9b45..93222311836 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -15,7 +15,9 @@ DYNAMIC_RUNNER_NAME = "dynamic"
 DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url"
 
 ERROR_MESSAGE_NO_RULE_FUNCTION = "Galaxy misconfigured - cannot find dynamic rule function name for destination %s."
-ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND = "Galaxy misconfigured - no rule function named %s found in dynamic rule modules."
+ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND = (
+    "Galaxy misconfigured - no rule function named %s found in dynamic rule modules."
+)
 ERROR_MESSAGE_RULE_EXCEPTION = "Encountered an unhandled exception while caching job destination dynamic rule."
 
 
@@ -24,13 +26,11 @@ class JobMappingConfigurationException(Exception):
 
 
 class JobMappingException(Exception):
-
     def __init__(self, failure_message):
         self.failure_message = failure_message
 
 
 class JobNotReadyException(Exception):
-
     def __init__(self, job_state=None, message=None):
         self.job_state = job_state
         self.message = message
@@ -49,6 +49,7 @@ class JobRunnerMapper:
     This class is responsible to managing the mapping of jobs
     (in the form of job_wrappers) to job runner url strings.
     """
+
     rules_module: ModuleType
 
     def __init__(self, job_wrapper, url_to_destination, job_config):
@@ -59,7 +60,7 @@ class JobRunnerMapper:
         self.rules_module = galaxy.jobs.rules
 
         if job_config.dynamic_params is not None:
-            module_name = job_config.dynamic_params['rules_module']
+            module_name = job_config.dynamic_params["rules_module"]
             self.rules_module = importlib.import_module(module_name)
 
     def __invoke_expand_function(self, expand_function, destination):
@@ -72,7 +73,7 @@ class JobRunnerMapper:
             "job_wrapper": self.job_wrapper,
             "rule_helper": RuleHelper(app),
             "app": app,
-            "referrer": destination
+            "referrer": destination,
         }
 
         actual_args = {}
@@ -138,7 +139,7 @@ class JobRunnerMapper:
         calls the url_to_destination method for the appropriate runner.
         """
         dest = self.url_to_destination(url)
-        dest['id'] = DYNAMIC_DESTINATION_ID
+        dest["id"] = DYNAMIC_DESTINATION_ID
         return dest
 
     def __find_function_by_tool_id(self, rule_modules):
@@ -155,13 +156,12 @@ class JobRunnerMapper:
         is specified, search within that rules_module, or default to the plugin's
         top level rules_module.
         """
-        rules_module_name = destination.params.get('rules_module')
+        rules_module_name = destination.params.get("rules_module")
         rule_modules = self.__get_rule_modules_or_defaults(rules_module_name)
         expand_function = None
-        expand_function_name = destination.params.get('function')
+        expand_function_name = destination.params.get("function")
         if expand_function_name:
-            expand_function = self.__last_matching_function_in_modules(
-                rule_modules, expand_function_name)
+            expand_function = self.__last_matching_function_in_modules(rule_modules, expand_function_name)
             if not expand_function:
                 message = ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND % expand_function_name
                 raise JobMappingConfigurationException(message)
@@ -192,7 +192,7 @@ class JobRunnerMapper:
         return None
 
     def __handle_dynamic_job_destination(self, destination):
-        expand_type = destination.params.get('type', "python")
+        expand_type = destination.params.get("type", "python")
         expand_function = None
         if expand_type == "python":
             expand_function = self.__get_expand_function(destination)
@@ -207,7 +207,7 @@ class JobRunnerMapper:
         job_destination = self.__invoke_expand_function(rule_function, destination)
         if not isinstance(job_destination, galaxy.jobs.JobDestination):
             job_destination_rep = str(job_destination)  # Should be either id or url
-            if '://' in job_destination_rep:
+            if "://" in job_destination_rep:
                 job_destination = self.__convert_url_to_destination(job_destination_rep)
             else:
                 job_destination = self.job_config.get_destination(job_destination_rep)
@@ -233,7 +233,9 @@ class JobRunnerMapper:
 
     def __cache_job_destination(self, params, raw_job_destination=None):
         try:
-            self.cached_job_destination = self.__determine_job_destination(params, raw_job_destination=raw_job_destination)
+            self.cached_job_destination = self.__determine_job_destination(
+                params, raw_job_destination=raw_job_destination
+            )
         except (JobMappingConfigurationException, JobMappingException, JobNotReadyException):
             raise
         except Exception:
@@ -249,7 +251,7 @@ class JobRunnerMapper:
         externally set to short-circuit the mapper, such as during resubmits.
         get_job_destination will respect that and not run the mapper if so.
         """
-        if not hasattr(self, 'cached_job_destination'):
+        if not hasattr(self, "cached_job_destination"):
             return self.__cache_job_destination(params)
         return self.cached_job_destination
 
@@ -258,5 +260,4 @@ class JobRunnerMapper:
         Force update of cached_job_destination to mapper determined job
         destination, overwriting any externally set cached_job_destination
         """
-        return self.__cache_job_destination(
-            None, raw_job_destination=raw_job_destination)
+        return self.__cache_job_destination(None, raw_job_destination=raw_job_destination)
diff --git a/lib/galaxy/jobs/rule_helper.py b/lib/galaxy/jobs/rule_helper.py
index b70b183ddad..677eba7077a 100644
--- a/lib/galaxy/jobs/rule_helper.py
+++ b/lib/galaxy/jobs/rule_helper.py
@@ -7,7 +7,7 @@ from sqlalchemy import func
 
 from galaxy import (
     model,
-    util
+    util,
 )
 from galaxy.tool_util.deps.dependencies import ToolInfo
 
@@ -17,7 +17,7 @@ VALID_JOB_HASH_STRATEGIES = ["job", "user", "history", "workflow_invocation"]
 
 
 class RuleHelper:
-    """ Utility to allow job rules to interface cleanly with the rest of
+    """Utility to allow job rules to interface cleanly with the rest of
     Galaxy and shield them from low-level details of models, metrics, etc....
 
     Currently focus is on figuring out job statistics for a given user, but
@@ -40,16 +40,17 @@ class RuleHelper:
         # developers from the details and they shouldn't have to know how to
         # interrogate tool or job to figure out if it can be run in a
         # container.
-        if hasattr(job_or_tool, 'containers'):
+        if hasattr(job_or_tool, "containers"):
             tool = job_or_tool
-        elif hasattr(job_or_tool, 'tool'):
+        elif hasattr(job_or_tool, "tool"):
             # Have a JobWrapper-like
             tool = job_or_tool.tool
         else:
             # Have a Job object.
             tool = self.app.toolbox.get_tool(job_or_tool.tool_id, tool_version=job_or_tool.tool_version)
-        tool_info = ToolInfo(tool.containers, tool.requirements, tool.requires_galaxy_python_environment,
-                             tool.docker_env_pass_through)
+        tool_info = ToolInfo(
+            tool.containers, tool.requirements, tool.requires_galaxy_python_environment, tool.docker_env_pass_through
+        )
         container_description = self.app.container_finder.find_best_container_description([container_type], tool_info)
         return container_description is not None
 
@@ -71,17 +72,11 @@ class RuleHelper:
         """
         return self.supports_container(job_or_tool, container_type="singularity")
 
-    def job_count(
-        self,
-        **kwds
-    ):
+    def job_count(self, **kwds):
         query = self.query(model.Job)
         return self._filter_job_query(query, **kwds).count()
 
-    def sum_job_runtime(
-        self,
-        **kwds
-    ):
+    def sum_job_runtime(self, **kwds):
         # TODO: Consider sum_core_hours or something that scales runtime by
         # by calculated cores per job.
         query = self.metric_query(
@@ -147,7 +142,7 @@ class RuleHelper:
         return query
 
     def should_burst(self, destination_ids, num_jobs, job_states=None):
-        """ Check if the specified destinations ``destination_ids`` have at
+        """Check if the specified destinations ``destination_ids`` have at
         least ``num_jobs`` assigned to it - send in ``job_state`` as ``queued``
         to limit this check to number of jobs queued.
 
@@ -159,8 +154,7 @@ class RuleHelper:
         if job_states is None:
             job_states = "queued,running"
         from_destination_job_count = self.job_count(
-            for_destinations=destination_ids,
-            for_job_states=util.listify(job_states)
+            for_destinations=destination_ids, for_job_states=util.listify(job_states)
         )
         # Would this job push us over maximum job count before requiring
         # bursting (roughly... very roughly given many handler threads may be
@@ -168,7 +162,7 @@ class RuleHelper:
         return (from_destination_job_count + 1) > int(num_jobs)
 
     def choose_one(self, lst, hash_value=None):
-        """ Choose a random value from supplied list. If hash_value is passed
+        """Choose a random value from supplied list. If hash_value is passed
         in then every request with that same hash_value would produce the same
         choice from the supplied list.
         """
@@ -184,7 +178,7 @@ class RuleHelper:
         return lst[random_index]
 
     def job_hash(self, job, hash_by=None):
-        """ Produce a reproducible hash for the given job on various
+        """Produce a reproducible hash for the given job on various
         criteria - for instance if hash_by is "workflow_invocation,history" -
         all jobs within the same workflow invocation will receive the same
         hash - for jobs outside of workflows all jobs within the same history
@@ -206,7 +200,7 @@ class RuleHelper:
         return self._try_hash_for_job(job, "job")
 
     def _try_hash_for_job(self, job, hash_by):
-        """ May return False or None if hash type is invalid for that job -
+        """May return False or None if hash type is invalid for that job -
         e.g. attempting to hash by user for anonymous job or by workflow
         invocation for jobs outside of workflows.
         """
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 2d9dbbf2273..61859b77741 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -16,17 +16,20 @@ from queue import (
 
 import galaxy.jobs
 from galaxy import model
-from galaxy.job_execution.output_collect import default_exit_code_file, read_exit_code_from
+from galaxy.job_execution.output_collect import (
+    default_exit_code_file,
+    read_exit_code_from,
+)
 from galaxy.jobs.command_factory import build_command
 from galaxy.jobs.runners.util import runner_states
 from galaxy.jobs.runners.util.env import env_to_statement
 from galaxy.jobs.runners.util.job_script import (
     job_script,
-    write_script
+    write_script,
 )
 from galaxy.tool_util.deps.dependencies import (
     JobInfo,
-    ToolInfo
+    ToolInfo,
 )
 from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
 from galaxy.util import (
@@ -47,7 +50,9 @@ STOP_SIGNAL = object()
 
 
 JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE = "Invalid job runner parameter for this plugin: %s"
-JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE = "Job runner parameter '%s' value '%s' could not be converted to the correct type"
+JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE = (
+    "Job runner parameter '%s' value '%s' could not be converted to the correct type"
+)
 JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE = "Job runner parameter %s failed validation"
 
 GALAXY_LIB_ADJUST_TEMPLATE = """GALAXY_LIB="%s"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi;"""
@@ -55,7 +60,6 @@ GALAXY_VENV_TEMPLATE = """GALAXY_VIRTUAL_ENV="%s"; if [ "$GALAXY_VIRTUAL_ENV" !=
 
 
 class RunnerParams(ParamsWithSpecs):
-
     def _param_unknown_error(self, name):
         raise Exception(JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE % name)
 
@@ -68,21 +72,20 @@ class RunnerParams(ParamsWithSpecs):
 
 class BaseJobRunner:
 
-    start_methods = ['_init_monitor_thread', '_init_worker_threads']
+    start_methods = ["_init_monitor_thread", "_init_worker_threads"]
     DEFAULT_SPECS = dict(recheck_missing_job_retries=dict(map=int, valid=lambda x: int(x) >= 0, default=0))
 
     def __init__(self, app, nworkers, **kwargs):
-        """Start the job runner
-        """
+        """Start the job runner"""
         self.app = app
         self.redact_email_in_job_name = self.app.config.redact_email_in_job_name
         self.sa_session = app.model.context
         self.nworkers = nworkers
         runner_param_specs = self.DEFAULT_SPECS.copy()
-        if 'runner_param_specs' in kwargs:
-            runner_param_specs.update(kwargs.pop('runner_param_specs'))
+        if "runner_param_specs" in kwargs:
+            runner_param_specs.update(kwargs.pop("runner_param_specs"))
         if kwargs:
-            log.debug('Loading %s with params: %s', self.runner_name, kwargs)
+            log.debug("Loading %s with params: %s", self.runner_name, kwargs)
         self.runner_params = RunnerParams(specs=runner_param_specs, params=kwargs)
         self.runner_state_handlers = build_state_handlers()
         self._should_stop = False
@@ -92,11 +95,10 @@ class BaseJobRunner:
             getattr(self, start_method, lambda: None)()
 
     def _init_worker_threads(self):
-        """Start ``nworkers`` worker threads.
-        """
+        """Start ``nworkers`` worker threads."""
         self.work_queue = Queue()
         self.work_threads = []
-        log.debug(f'Starting {self.nworkers} {self.runner_name} workers')
+        log.debug(f"Starting {self.nworkers} {self.runner_name} workers")
         for i in range(self.nworkers):
             worker = threading.Thread(name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next)
             worker.daemon = True
@@ -115,8 +117,7 @@ class BaseJobRunner:
                     yield thread
 
     def run_next(self):
-        """Run the next item in the work queue (a job waiting to run)
-        """
+        """Run the next item in the work queue (a job waiting to run)"""
         while self._should_stop is False:
             try:
                 (method, arg) = self.work_queue.get(timeout=1)
@@ -132,16 +133,15 @@ class BaseJobRunner:
                     # arg should be a JobWrapper/TaskWrapper
                     job_id = arg.get_id_tag()
             except Exception:
-                job_id = 'unknown'
+                job_id = "unknown"
             try:
                 name = method.__name__
             except Exception:
-                name = 'unknown'
+                name = "unknown"
             try:
-                action_str = f'galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}'
+                action_str = f"galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}"
                 action_timer = self.app.execution_timer_factory.get_timer(
-                    f'internals.{action_str}',
-                    'job runner action %s for job ${job_id} executed' % (action_str)
+                    f"internals.{action_str}", "job runner action %s for job ${job_id} executed" % (action_str)
                 )
                 method(arg)
                 log.trace(action_timer.to_str(job_id=job_id))
@@ -157,8 +157,7 @@ class BaseJobRunner:
 
     # Causes a runner's `queue_job` method to be called from a worker thread
     def put(self, job_wrapper):
-        """Add a job to the queue (by job identifier), indicate that the job is ready to run.
-        """
+        """Add a job to the queue (by job identifier), indicate that the job is ready to run."""
         put_timer = ExecutionTimer()
         job_wrapper.enqueue()
         self.mark_as_queued(job_wrapper)
@@ -168,8 +167,7 @@ class BaseJobRunner:
         self.work_queue.put((self.queue_job, job_wrapper))
 
     def shutdown(self):
-        """Attempts to gracefully shut down the worker threads
-        """
+        """Attempts to gracefully shut down the worker threads"""
         log.info("%s: Sending stop signal to %s job worker threads", self.runner_name, len(self.work_threads))
         self._should_stop = True
         for _ in range(len(self.work_threads)):
@@ -199,8 +197,12 @@ class BaseJobRunner:
                 except KeyError:
                     # thread is now stopped
                     continue
-                log.warning("Timed out waiting for job worker thread %s to terminate, shutdown will be unclean! Thread "
-                            "stack is:\n%s", thread.name, ''.join(traceback.format_stack(frame)))
+                log.warning(
+                    "Timed out waiting for job worker thread %s to terminate, shutdown will be unclean! Thread "
+                    "stack is:\n%s",
+                    thread.name,
+                    "".join(traceback.format_stack(frame)),
+                )
 
     # Most runners should override the legacy URL handler methods and destination param method
     def url_to_destination(self, url):
@@ -211,22 +213,22 @@ class BaseJobRunner:
         This base class method converts from a URL to a very basic
         JobDestination without destination params.
         """
-        return galaxy.jobs.JobDestination(runner=url.split(':')[0])
+        return galaxy.jobs.JobDestination(runner=url.split(":")[0])
 
     def parse_destination_params(self, params):
-        """Parse the JobDestination ``params`` dict and return the runner's native representation of those params.
-        """
+        """Parse the JobDestination ``params`` dict and return the runner's native representation of those params."""
         raise NotImplementedError()
 
-    def prepare_job(self,
-                    job_wrapper,
-                    include_metadata=False,
-                    include_work_dir_outputs=True,
-                    modify_command_for_container=True,
-                    stdout_file=None,
-                    stderr_file=None):
-        """Some sanity checks that all runners' queue_job() methods are likely to want to do
-        """
+    def prepare_job(
+        self,
+        job_wrapper,
+        include_metadata=False,
+        include_work_dir_outputs=True,
+        modify_command_for_container=True,
+        stdout_file=None,
+        stderr_file=None,
+    ):
+        """Some sanity checks that all runners' queue_job() methods are likely to want to do"""
         job_id = job_wrapper.get_id_tag()
         job_state = job_wrapper.get_state()
         job_wrapper.is_ready = False
@@ -260,7 +262,7 @@ class BaseJobRunner:
             return False
 
         if not job_wrapper.runner_command_line:
-            job_wrapper.finish('', '')
+            job_wrapper.finish("", "")
             return False
 
         return True
@@ -275,13 +277,15 @@ class BaseJobRunner:
     def recover(self, job, job_wrapper):
         raise NotImplementedError()
 
-    def build_command_line(self,
-                           job_wrapper,
-                           include_metadata=False,
-                           include_work_dir_outputs=True,
-                           modify_command_for_container=True,
-                           stdout_file=None,
-                           stderr_file=None):
+    def build_command_line(
+        self,
+        job_wrapper,
+        include_metadata=False,
+        include_work_dir_outputs=True,
+        modify_command_for_container=True,
+        stdout_file=None,
+        stderr_file=None,
+    ):
         container = self._find_container(job_wrapper)
         if not container and job_wrapper.requires_containerization:
             raise Exception("Failed to find a container when required, contact Galaxy admin.")
@@ -302,7 +306,9 @@ class BaseJobRunner:
         to work_dir output file and ultimate destination.
         """
         if tool_working_directory is not None and job_working_directory is not None:
-            raise Exception("get_work_dir_outputs called with both a job and tool working directory, only one may be specified")
+            raise Exception(
+                "get_work_dir_outputs called with both a job and tool working directory, only one may be specified"
+            )
 
         if tool_working_directory is None:
             if not job_working_directory:
@@ -334,14 +340,24 @@ class BaseJobRunner:
                         output_pairs.append((source_file, destination))
                     else:
                         # Security violation.
-                        log.exception("from_work_dir specified a location not in the working directory: %s, %s", source_file, job_wrapper.working_directory)
+                        log.exception(
+                            "from_work_dir specified a location not in the working directory: %s, %s",
+                            source_file,
+                            job_wrapper.working_directory,
+                        )
         return output_pairs
 
     def _walk_dataset_outputs(self, job):
         for dataset_assoc in job.output_datasets + job.output_library_datasets:
-            for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
+            for dataset in (
+                dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations
+            ):
                 if isinstance(dataset, self.app.model.HistoryDatasetAssociation):
-                    joda = self.sa_session.query(self.app.model.JobToOutputDatasetAssociation).filter_by(job=job, dataset=dataset).first()
+                    joda = (
+                        self.sa_session.query(self.app.model.JobToOutputDatasetAssociation)
+                        .filter_by(job=job, dataset=dataset)
+                        .first()
+                    )
                     yield (joda, dataset)
         # TODO: why is this not just something easy like:
         # for dataset_assoc in job.output_datasets + job.output_library_datasets:
@@ -356,37 +372,52 @@ class BaseJobRunner:
         # run the metadata setting script here
         # this is terminate-able when output dataset/job is deleted
         # so that long running set_meta()s can be canceled without having to reboot the server
-        if job_wrapper.get_state() not in [model.Job.states.ERROR, model.Job.states.DELETED] and job_wrapper.job_io.output_paths:
+        if (
+            job_wrapper.get_state() not in [model.Job.states.ERROR, model.Job.states.DELETED]
+            and job_wrapper.job_io.output_paths
+        ):
             lib_adjust = GALAXY_LIB_ADJUST_TEMPLATE % job_wrapper.galaxy_lib_dir
             venv = GALAXY_VENV_TEMPLATE % job_wrapper.galaxy_virtual_env
-            external_metadata_script = job_wrapper.setup_external_metadata(output_fnames=job_wrapper.job_io.get_output_fnames(),
-                                                                           set_extension=True,
-                                                                           tmp_dir=job_wrapper.working_directory,
-                                                                           # We don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
-                                                                           kwds={'overwrite': False})
+            external_metadata_script = job_wrapper.setup_external_metadata(
+                output_fnames=job_wrapper.job_io.get_output_fnames(),
+                set_extension=True,
+                tmp_dir=job_wrapper.working_directory,
+                # We don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
+                kwds={"overwrite": False},
+            )
             external_metadata_script = f"{lib_adjust} {venv} {external_metadata_script}"
             if resolve_requirements:
-                dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands(job_directory=job_wrapper.working_directory)
+                dependency_shell_commands = (
+                    self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands(
+                        job_directory=job_wrapper.working_directory
+                    )
+                )
                 if dependency_shell_commands:
                     if isinstance(dependency_shell_commands, list):
                         dependency_shell_commands = "&&".join(dependency_shell_commands)
                     external_metadata_script = f"{dependency_shell_commands}&&{external_metadata_script}"
-            log.debug('executing external set_meta script for job %d: %s' % (job_wrapper.job_id, external_metadata_script))
-            external_metadata_proc = subprocess.Popen(args=external_metadata_script,
-                                                      shell=True,
-                                                      cwd=job_wrapper.working_directory,
-                                                      env=os.environ,
-                                                      preexec_fn=os.setpgrp)
-            job_wrapper.external_output_metadata.set_job_runner_external_pid(external_metadata_proc.pid, self.sa_session)
+            log.debug(
+                "executing external set_meta script for job %d: %s" % (job_wrapper.job_id, external_metadata_script)
+            )
+            external_metadata_proc = subprocess.Popen(
+                args=external_metadata_script,
+                shell=True,
+                cwd=job_wrapper.working_directory,
+                env=os.environ,
+                preexec_fn=os.setpgrp,
+            )
+            job_wrapper.external_output_metadata.set_job_runner_external_pid(
+                external_metadata_proc.pid, self.sa_session
+            )
             external_metadata_proc.wait()
-            log.debug('execution of external set_meta for job %d finished' % job_wrapper.job_id)
+            log.debug("execution of external set_meta for job %d finished" % job_wrapper.job_id)
 
     def get_job_file(self, job_wrapper, **kwds):
         job_metrics = job_wrapper.app.job_metrics
         job_instrumenter = job_metrics.job_instrumenters[job_wrapper.job_destination.id]
 
-        env_setup_commands = kwds.get('env_setup_commands', [])
-        env_setup_commands.append(job_wrapper.get_env_setup_clause() or '')
+        env_setup_commands = kwds.get("env_setup_commands", [])
+        env_setup_commands.append(job_wrapper.get_env_setup_clause() or "")
         destination = job_wrapper.job_destination or {}
         envs = destination.get("env", [])
         envs.extend(job_wrapper.environment_variables)
@@ -408,7 +439,7 @@ class BaseJobRunner:
         # Additional logging to enable if debugging from_work_dir handling, metadata
         # commands, etc... (or just peak in the job script.)
         job_id = job_wrapper.job_id
-        log.debug(f'({job_id}) command is: {command_line}')
+        log.debug(f"({job_id}) command is: {command_line}")
         options.update(**kwds)
         return job_script(**options)
 
@@ -458,11 +489,7 @@ class BaseJobRunner:
         )
 
         destination_info = job_wrapper.job_destination.params
-        container = self.app.container_finder.find_container(
-            tool_info,
-            destination_info,
-            job_info
-        )
+        container = self.app.container_finder.find_container(tool_info, destination_info, job_info)
         if container:
             job_wrapper.set_container(container)
         return container
@@ -474,17 +501,17 @@ class BaseJobRunner:
                 if job_state.runner_state_handled:
                     break
         except Exception:
-            log.exception('Caught exception in runner state handler')
+            log.exception("Caught exception in runner state handler")
 
     def fail_job(self, job_state, exception=False):
-        if getattr(job_state, 'stop_job', True):
+        if getattr(job_state, "stop_job", True):
             self.stop_job(job_state.job_wrapper)
         job_state.job_wrapper.reclaim_ownership()
-        self._handle_runner_state('failure', job_state)
+        self._handle_runner_state("failure", job_state)
         # Not convinced this is the best way to indicate this state, but
         # something necessary
         if not job_state.runner_state_handled:
-            job_state.job_wrapper.fail(getattr(job_state, 'fail_message', 'Job failed'), exception=exception)
+            job_state.job_wrapper.fail(getattr(job_state, "fail_message", "Job failed"), exception=exception)
             if job_state.job_wrapper.cleanup_job == "always":
                 job_state.cleanup()
 
@@ -495,7 +522,9 @@ class BaseJobRunner:
             self.app.job_manager.job_handler.dispatcher.put(job_state.job_wrapper)
 
     def _job_io_for_db(self, stream):
-        return shrink_stream_by_size(stream, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
+        return shrink_stream_by_size(
+            stream, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True
+        )
 
     def _finish_or_resubmit_job(self, job_state, job_stdout, job_stderr, job_id=None, external_job_id=None):
         job_wrapper = job_state.job_wrapper
@@ -527,7 +556,14 @@ class BaseJobRunner:
                 tool_stderr = job_stderr
                 job_stderr = None
 
-            check_output_detected_state = job_wrapper.check_tool_output(tool_stdout, tool_stderr, tool_exit_code=exit_code, job=job, job_stdout=job_stdout, job_stderr=job_stderr)
+            check_output_detected_state = job_wrapper.check_tool_output(
+                tool_stdout,
+                tool_stderr,
+                tool_exit_code=exit_code,
+                job=job,
+                job_stdout=job_stdout,
+                job_stderr=job_stderr,
+            )
             job_ok = check_output_detected_state == DETECTED_JOB_STATE.OK
 
             # clean up the job files
@@ -544,12 +580,19 @@ class BaseJobRunner:
                 if check_output_detected_state == DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR:
                     job_runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
                 job_state.runner_state = job_runner_state
-                self._handle_runner_state('failure', job_state)
+                self._handle_runner_state("failure", job_state)
                 # Was resubmitted or something - I think we are done with it.
                 if job_state.runner_state_handled:
                     return
 
-            job_wrapper.finish(tool_stdout, tool_stderr, exit_code, check_output_detected_state=check_output_detected_state, job_stdout=job_stdout, job_stderr=job_stderr)
+            job_wrapper.finish(
+                tool_stdout,
+                tool_stderr,
+                exit_code,
+                check_output_detected_state=check_output_detected_state,
+                job_stdout=job_stdout,
+                job_stderr=job_stderr,
+            )
         except Exception:
             log.exception(f"({job_id or ''}/{external_job_id or ''}) Job wrapper finish method failed")
             job_wrapper.fail("Unable to finish job", exception=True)
@@ -559,6 +602,7 @@ class JobState:
     """
     Encapsulate state of jobs.
     """
+
     runner_states = runner_states
 
     def __init__(self, job_wrapper, job_destination):
@@ -570,26 +614,26 @@ class JobState:
         if self.job_wrapper:
             self.redact_email_in_job_name = self.job_wrapper.app.config.redact_email_in_job_name
 
-        self.cleanup_file_attributes = ['job_file', 'output_file', 'error_file', 'exit_code_file']
+        self.cleanup_file_attributes = ["job_file", "output_file", "error_file", "exit_code_file"]
 
     def set_defaults(self, files_dir):
         if self.job_wrapper is not None:
             id_tag = self.job_wrapper.get_id_tag()
             if files_dir is not None:
                 self.job_file = JobState.default_job_file(files_dir, id_tag)
-                self.output_file = os.path.join(files_dir, f'galaxy_{id_tag}.o')
-                self.error_file = os.path.join(files_dir, f'galaxy_{id_tag}.e')
+                self.output_file = os.path.join(files_dir, f"galaxy_{id_tag}.o")
+                self.error_file = os.path.join(files_dir, f"galaxy_{id_tag}.e")
                 self.exit_code_file = default_exit_code_file(files_dir, id_tag)
-            job_name = f'g{id_tag}'
+            job_name = f"g{id_tag}"
             if self.job_wrapper.tool.old_id:
-                job_name += f'_{self.job_wrapper.tool.old_id}'
+                job_name += f"_{self.job_wrapper.tool.old_id}"
             if not self.redact_email_in_job_name and self.job_wrapper.user:
-                job_name += f'_{self.job_wrapper.user}'
-            self.job_name = ''.join(x if x in (f"{string.ascii_letters + string.digits}_") else '_' for x in job_name)
+                job_name += f"_{self.job_wrapper.user}"
+            self.job_name = "".join(x if x in (f"{string.ascii_letters + string.digits}_") else "_" for x in job_name)
 
     @staticmethod
     def default_job_file(files_dir, id_tag):
-        return os.path.join(files_dir, f'galaxy_{id_tag}.sh')
+        return os.path.join(files_dir, f"galaxy_{id_tag}.sh")
 
     def read_exit_code(self):
         return read_exit_code_from(self.exit_code_file, self.job_wrapper.get_id_tag())
@@ -615,7 +659,18 @@ class AsynchronousJobState(JobState):
     to communicate with distributed resource manager.
     """
 
-    def __init__(self, files_dir=None, job_wrapper=None, job_id=None, job_file=None, output_file=None, error_file=None, exit_code_file=None, job_name=None, job_destination=None):
+    def __init__(
+        self,
+        files_dir=None,
+        job_wrapper=None,
+        job_id=None,
+        job_file=None,
+        output_file=None,
+        error_file=None,
+        exit_code_file=None,
+        job_name=None,
+        job_destination=None,
+    ):
         super().__init__(job_wrapper, job_destination)
         self.old_state = None
         self._running = False
@@ -711,7 +766,7 @@ class AsynchronousJobRunner(BaseJobRunner, Monitors):
             try:
                 self.check_watched_items()
             except Exception:
-                log.exception('Unhandled exception checking active jobs')
+                log.exception("Unhandled exception checking active jobs")
             # Sleep a bit before the next state check
             time.sleep(self.app.config.job_runner_monitor_sleep)
 
@@ -761,15 +816,15 @@ class AsynchronousJobRunner(BaseJobRunner, Monitors):
         collect_output_success = True
         while which_try < self.app.config.retry_job_output_collection + 1:
             try:
-                with open(job_state.output_file, "rb") as stdout_file, open(job_state.error_file, 'rb') as stderr_file:
+                with open(job_state.output_file, "rb") as stdout_file, open(job_state.error_file, "rb") as stderr_file:
                     stdout = self._job_io_for_db(stdout_file)
                     stderr = self._job_io_for_db(stderr_file)
                 break
             except Exception as e:
                 if which_try == self.app.config.retry_job_output_collection:
-                    stdout = ''
+                    stdout = ""
                     stderr = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
-                    log.error('(%s/%s) %s: %s', galaxy_id_tag, external_job_id, stderr, unicodify(e))
+                    log.error("(%s/%s) %s: %s", galaxy_id_tag, external_job_id, stderr, unicodify(e))
                     collect_output_success = False
                 else:
                     time.sleep(1)
diff --git a/lib/galaxy/jobs/runners/chronos.py b/lib/galaxy/jobs/runners/chronos.py
index ae161b4b772..297726fb1da 100644
--- a/lib/galaxy/jobs/runners/chronos.py
+++ b/lib/galaxy/jobs/runners/chronos.py
@@ -3,15 +3,21 @@ import logging
 import os
 
 from galaxy import model
-from galaxy.jobs.runners import AsynchronousJobRunner, AsynchronousJobState
+from galaxy.jobs.runners import (
+    AsynchronousJobRunner,
+    AsynchronousJobState,
+)
 from galaxy.util import unicodify
 
-CHRONOS_IMPORT_MSG = ('The Python \'chronos\' package is required to use '
-                      'this feature, please install it or correct the '
-                      'following error:\nImportError {msg!s}')
+CHRONOS_IMPORT_MSG = (
+    "The Python 'chronos' package is required to use "
+    "this feature, please install it or correct the "
+    "following error:\nImportError {msg!s}"
+)
 
 try:
     import chronos
+
     chronos_exceptions = (
         chronos.ChronosAPIError,
         chronos.UnauthorizedError,
@@ -23,7 +29,7 @@ except ImportError as e:
     CHRONOS_IMPORT_MSG.format(msg=unicodify(e))
 
 
-__all__ = ('ChronosJobRunner',)
+__all__ = ("ChronosJobRunner",)
 LOGGER = logging.getLogger(__name__)
 
 
@@ -52,19 +58,19 @@ def to_dict(segments, v):
 
 
 def _write_logfile(logfile, msg):
-    with open(logfile, 'w') as fil:
+    with open(logfile, "w") as fil:
         fil.write(msg)
 
 
 def _parse_job_volumes_list(li):
     # Convert comma separated string to list
-    volume_list = list(li.split(','))
+    volume_list = list(li.split(","))
     # Create the list with right mountpoint and permissions
     mountpoint_list = []
     # Convert each element to right format
     for i in volume_list:
-        hpath, cpath, mode = i.split(':')
-        mountpoint_list.append({'hostPath': hpath, 'containerPath': cpath, 'mode': mode})
+        hpath, cpath, mode = i.split(":")
+        mountpoint_list.append({"hostPath": hpath, "containerPath": cpath, "mode": mode})
     return mountpoint_list
 
 
@@ -72,60 +78,56 @@ def _add_galaxy_environment_variables(cpus, memory):
     # Set:
     # GALAXY_SLOTS: to docker_cpu
     # GALAXY_MEMORY_MB to docker_memory
-    return [{'name': 'GALAXY_SLOTS', 'value': cpus}, {'name': 'GALAXY_MEMORY_MB', 'value': memory}]
+    return [{"name": "GALAXY_SLOTS", "value": cpus}, {"name": "GALAXY_MEMORY_MB", "value": memory}]
 
 
 class ChronosJobRunner(AsynchronousJobRunner):
-    runner_name = 'ChronosRunner'
-    RUNNER_PARAM_SPEC_KEY = 'runner_param_specs'
-    JOB_NAME_PREFIX = 'galaxy-chronos-'
+    runner_name = "ChronosRunner"
+    RUNNER_PARAM_SPEC_KEY = "runner_param_specs"
+    JOB_NAME_PREFIX = "galaxy-chronos-"
 
     RUNNER_PARAM_SPEC = {
-        'chronos': {
-            'map': str,
+        "chronos": {
+            "map": str,
         },
-        'insecure': {
-            'map': lambda x: x in ['true', 'True', 'TRUE'],
-            'default': True,
+        "insecure": {
+            "map": lambda x: x in ["true", "True", "TRUE"],
+            "default": True,
         },
-        'username': {
-            'map': str,
+        "username": {
+            "map": str,
         },
-        'password': {
-            'map': str,
-        },
-        'owner': {
-            'map': str
+        "password": {
+            "map": str,
         },
+        "owner": {"map": str},
     }
 
     DESTINATION_PARAMS_SPEC = {
-        'docker_cpu': {
-            'default': 0.1,
-            'map_name': 'cpus',
-            'map': float,
+        "docker_cpu": {
+            "default": 0.1,
+            "map_name": "cpus",
+            "map": float,
         },
-        'docker_memory': {
-            'default': 128,
-            'map_name': 'mem',
-            'map': int,
+        "docker_memory": {
+            "default": 128,
+            "map_name": "mem",
+            "map": int,
         },
-        'docker_disk': {
-            'default': 256,
-            'map_name': 'disk',
-            'map': int,
+        "docker_disk": {
+            "default": 256,
+            "map_name": "disk",
+            "map": int,
         },
-        'volumes': {
-            'default': None,
-            'map_name': 'container/volumes',
-            'map': (
-                lambda x: _parse_job_volumes_list(x)
-                if x is not None else [])
+        "volumes": {
+            "default": None,
+            "map_name": "container/volumes",
+            "map": (lambda x: _parse_job_volumes_list(x) if x is not None else []),
         },
-        'max_retries': {
-            'default': 2,
-            'map_name': 'retries',
-            'map': int,
+        "max_retries": {
+            "default": 2,
+            "map_name": "retries",
+            "map": int,
         },
     }
 
@@ -136,28 +138,30 @@ class ChronosJobRunner(AsynchronousJobRunner):
             kwargs[self.RUNNER_PARAM_SPEC_KEY] = {}
         kwargs[self.RUNNER_PARAM_SPEC_KEY].update(self.RUNNER_PARAM_SPEC)
         super().__init__(app, nworkers, **kwargs)
-        protocol = 'http' if self.runner_params.get('insecure', True) else 'https'
+        protocol = "http" if self.runner_params.get("insecure", True) else "https"
         self._chronos_client = chronos.connect(
-            self.runner_params['chronos'],
-            username=self.runner_params.get('username'),
-            password=self.runner_params.get('password'),
-            proto=protocol)
+            self.runner_params["chronos"],
+            username=self.runner_params.get("username"),
+            password=self.runner_params.get("password"),
+            proto=protocol,
+        )
 
     @handle_exception_call
     def queue_job(self, job_wrapper):
         LOGGER.debug(f"Starting queue_job for job {job_wrapper.get_id_tag()}")
-        if not self.prepare_job(job_wrapper, include_metadata=False,
-                                modify_command_for_container=False):
+        if not self.prepare_job(job_wrapper, include_metadata=False, modify_command_for_container=False):
             LOGGER.debug(f"Not ready {job_wrapper.get_id_tag()}")
             return
         job_destination = job_wrapper.job_destination
         chronos_job_spec = self._get_job_spec(job_wrapper)
-        job_name = chronos_job_spec['name']
+        job_name = chronos_job_spec["name"]
         self._chronos_client.add(chronos_job_spec)
-        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
-                                   job_wrapper=job_wrapper,
-                                   job_id=job_name,
-                                   job_destination=job_destination)
+        ajs = AsynchronousJobState(
+            files_dir=job_wrapper.working_directory,
+            job_wrapper=job_wrapper,
+            job_id=job_name,
+            job_destination=job_destination,
+        )
         self.monitor_queue.put(ajs)
 
     @handle_exception_call
@@ -166,46 +170,40 @@ class ChronosJobRunner(AsynchronousJobRunner):
         job_name = self.JOB_NAME_PREFIX + job_id
         job = self._retrieve_job(job_name)
         if job:
-            msg = 'Job {name!r} is terminated'
+            msg = "Job {name!r} is terminated"
             self._chronos_client.delete(job_name)
             LOGGER.debug(msg.format(name=job_name))
         else:
-            msg = 'Job {name!r} not found. It cannot be terminated.'
+            msg = "Job {name!r} not found. It cannot be terminated."
             LOGGER.error(msg.format(name=job_name))
 
     def recover(self, job, job_wrapper):
-        msg = ('(name!r/runner!r) is still in {state!s} state, adding to'
-               ' the runner monitor queue')
+        msg = "(name!r/runner!r) is still in {state!s} state, adding to" " the runner monitor queue"
         job_id = job.get_job_runner_external_id()
-        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
-                                   job_wrapper=job_wrapper)
+        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
         ajs.job_id = self.JOB_NAME_PREFIX + str(job_id)
         ajs.command_line = job.command_line
         ajs.job_wrapper = job_wrapper
         ajs.job_destination = job_wrapper.job_destination
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            LOGGER.debug(msg.format(
-                name=job.id, runner=job.job_runner_external_id,
-                state=job.state))
+            LOGGER.debug(msg.format(name=job.id, runner=job.job_runner_external_id, state=job.state))
             ajs.old_state = model.Job.states.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
         elif job.state == model.Job.states.QUEUED:
-            LOGGER.debug(msg.format(
-                name=job.id, runner=job.job_runner_external_id,
-                state='queued'))
+            LOGGER.debug(msg.format(name=job.id, runner=job.job_runner_external_id, state="queued"))
             ajs.old_state = model.Job.states.QUEUED
             ajs.running = False
             self.monitor_queue.put(ajs)
 
     def fail_job(self, job_state, exception=False):
-        if getattr(job_state, 'stop_job', True):
+        if getattr(job_state, "stop_job", True):
             self.stop_job(job_state.job_wrapper)
         job_state.job_wrapper.reclaim_ownership()
-        self._handle_runner_state('failure', job_state)
+        self._handle_runner_state("failure", job_state)
         if not job_state.runner_state_handled:
-            job_state.job_wrapper.fail(getattr(job_state, 'fail_message', 'Job failed'), exception=exception)
-            self._finish_or_resubmit_job(job_state, '', job_state.fail_message, job_id=job_state.job_id)
+            job_state.job_wrapper.fail(getattr(job_state, "fail_message", "Job failed"), exception=exception)
+            self._finish_or_resubmit_job(job_state, "", job_state.fail_message, job_id=job_state.job_id)
             if job_state.job_wrapper.cleanup_job == "always":
                 job_state.cleanup()
 
@@ -215,28 +213,27 @@ class ChronosJobRunner(AsynchronousJobRunner):
         job = self._retrieve_job(job_name)
         # TODO: how can stopped GxIT jobs be handled here?
         if job:
-            succeeded = job['successCount']
-            errors = job['errorCount']
+            succeeded = job["successCount"]
+            errors = job["errorCount"]
             if succeeded > 0:
                 return self._mark_as_successful(job_state)
             elif not succeeded and not errors:
                 return self._mark_as_active(job_state)
             elif errors:
-                max_retries = job['retries']
+                max_retries = job["retries"]
                 if max_retries == 0:
-                    msg = 'Job {name!r} failed. No retries performed.'
+                    msg = "Job {name!r} failed. No retries performed."
                 else:
-                    msg = 'Job {name!r} failed more than {retries!s} times.'
+                    msg = "Job {name!r} failed more than {retries!s} times."
                 reason = msg.format(name=job_name, retries=str(max_retries))
                 return self._mark_as_failed(job_state, reason)
-        reason = f'Job {job_name!r} not found'
+        reason = f"Job {job_name!r} not found"
         return self._mark_as_failed(job_state, reason)
 
     def _mark_as_successful(self, job_state):
-        msg = 'Job {name!r} finished successfully'
-        _write_logfile(job_state.output_file,
-                       msg.format(name=job_state.job_id))
-        _write_logfile(job_state.error_file, '')
+        msg = "Job {name!r} finished successfully"
+        _write_logfile(job_state.output_file, msg.format(name=job_state.job_id))
+        _write_logfile(job_state.error_file, "")
         job_state.running = False
         job_state.job_wrapper.change_state(model.Job.states.OK)
         self.mark_as_finished(job_state)
@@ -264,10 +261,10 @@ class ChronosJobRunner(AsynchronousJobRunner):
     def parse_destination_params(self, params):
         parsed_params = {}
         for k, spec in self.DESTINATION_PARAMS_SPEC.items():
-            value = params.get(k, spec.get('default'))
-            map_to = spec.get('map_name')
-            mapper = spec.get('map')
-            segments = map_to.split('/')
+            value = params.get(k, spec.get("default"))
+            map_to = spec.get("map_name")
+            mapper = spec.get("map")
+            segments = map_to.split("/")
             parsed_params.update(to_dict(segments, mapper(value)))
         return parsed_params
 
@@ -280,8 +277,8 @@ class ChronosJobRunner(AsynchronousJobRunner):
         path = f"{job_wrapper.working_directory}/chronos_{job_wrapper.get_id_tag()}.sh"
         mode = 0o755
 
-        with open(path, 'w', encoding='utf-8') as f:
-            f.write('#!/bin/bash\n')
+        with open(path, "w", encoding="utf-8") as f:
+            f.write("#!/bin/bash\n")
             f.write(job_wrapper.runner_command_line)
         os.chmod(path, mode)
         return path
@@ -291,34 +288,33 @@ class ChronosJobRunner(AsynchronousJobRunner):
         job_destination = job_wrapper.job_destination
         command_script_path = self.write_command(job_wrapper)
         template = {
-            'async': False,
+            "async": False,
             # 'command': job_wrapper.runner_command_line,
-            'command': f"$SHELL {command_script_path}",
-            'owner': self.runner_params['owner'],
-            'disabled': False,
-            'schedule': 'R1//PT1S',
-            'name': job_name,
+            "command": f"$SHELL {command_script_path}",
+            "owner": self.runner_params["owner"],
+            "disabled": False,
+            "schedule": "R1//PT1S",
+            "name": job_name,
             # Add Galaxy environemnt variables to json
-            'environmentVariables': _add_galaxy_environment_variables(job_destination.params.get('docker_cpu'), job_destination.params.get('docker_memory')),
+            "environmentVariables": _add_galaxy_environment_variables(
+                job_destination.params.get("docker_cpu"), job_destination.params.get("docker_memory")
+            ),
         }
-        if not job_destination.params.get('docker_enabled'):
-            raise ChronosRunnerException(
-                'ChronosJobRunner needs \'docker_enabled\' to be set as True')
-        destination_params = self.parse_destination_params(
-            job_destination.params)
+        if not job_destination.params.get("docker_enabled"):
+            raise ChronosRunnerException("ChronosJobRunner needs 'docker_enabled' to be set as True")
+        destination_params = self.parse_destination_params(job_destination.params)
         template.update(destination_params)
-        template['container']['type'] = 'DOCKER'
-        template['container']['image'] = self._find_container(
-            job_wrapper).container_id
+        template["container"]["type"] = "DOCKER"
+        template["container"]["image"] = self._find_container(job_wrapper).container_id
         # Fix the working directory inside the container
-        template['container']['parameters'] = [{"key": "workdir", "value": job_wrapper.working_directory}]
+        template["container"]["parameters"] = [{"key": "workdir", "value": job_wrapper.working_directory}]
         return template
 
     def _retrieve_job(self, job_id):
         jobs = self._chronos_client.list()
-        job = [x for x in jobs if x['name'] == job_id]
+        job = [x for x in jobs if x["name"] == job_id]
         if len(job) > 1:
-            msg = f'Multiple jobs found with name {job_id!r}'
+            msg = f"Multiple jobs found with name {job_id!r}"
             LOGGER.error(msg)
             raise ChronosRunnerException(msg)
         return job[0] if job else None
diff --git a/lib/galaxy/jobs/runners/cli.py b/lib/galaxy/jobs/runners/cli.py
index 0f064e2304b..14605ce7d8c 100644
--- a/lib/galaxy/jobs/runners/cli.py
+++ b/lib/galaxy/jobs/runners/cli.py
@@ -10,13 +10,17 @@ from galaxy.jobs import JobDestination
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
     AsynchronousJobState,
-    JobState)
+    JobState,
+)
 from galaxy.util import asbool
-from .util.cli import CliInterface, split_params
+from .util.cli import (
+    CliInterface,
+    split_params,
+)
 
 log = logging.getLogger(__name__)
 
-__all__ = ('ShellJobRunner', )
+__all__ = ("ShellJobRunner",)
 
 DEFAULT_EMBED_METADATA_IN_JOB = True
 MAX_SUBMIT_RETRY = 3
@@ -26,10 +30,11 @@ class ShellJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "ShellRunner"
 
     def __init__(self, app, nworkers):
-        """Start the job runner """
+        """Start the job runner"""
         super().__init__(app, nworkers)
 
         self.cli_interface = CliInterface()
@@ -39,15 +44,15 @@ class ShellJobRunner(AsynchronousJobRunner):
 
     def url_to_destination(self, url):
         params = {}
-        shell_params, job_params = url.split('/')[2:4]
+        shell_params, job_params = url.split("/")[2:4]
         # split 'foo=bar&baz=quux' into { 'foo' : 'bar', 'baz' : 'quux' }
-        shell_params = {f"shell_{k}": v for k, v in [kv.split('=', 1) for kv in shell_params.split('&')]}
-        job_params = {f"job_{k}": v for k, v in [kv.split('=', 1) for kv in job_params.split('&')]}
+        shell_params = {f"shell_{k}": v for k, v in [kv.split("=", 1) for kv in shell_params.split("&")]}
+        job_params = {f"job_{k}": v for k, v in [kv.split("=", 1) for kv in job_params.split("&")]}
         params.update(shell_params)
         params.update(job_params)
         log.debug(f"Converted URL '{url}' to destination runner=cli, params={params}")
         # Create a dynamic JobDestination
-        return JobDestination(runner='cli', params=params)
+        return JobDestination(runner="cli", params=params)
 
     def parse_destination_params(self, params):
         return split_params(params)
@@ -55,7 +60,9 @@ class ShellJobRunner(AsynchronousJobRunner):
     def queue_job(self, job_wrapper):
         """Create job script and submit it to the DRM"""
         # prepare the job
-        include_metadata = asbool(job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
+        include_metadata = asbool(
+            job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB)
+        )
         if not self.prepare_job(job_wrapper, include_metadata=include_metadata):
             return
 
@@ -72,10 +79,7 @@ class ShellJobRunner(AsynchronousJobRunner):
 
         job_file_kwargs = job_interface.job_script_kwargs(ajs.output_file, ajs.error_file, ajs.job_name)
         script = self.get_job_file(
-            job_wrapper,
-            exit_code_path=ajs.exit_code_file,
-            shell=job_wrapper.shell,
-            **job_file_kwargs
+            job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell, **job_file_kwargs
         )
 
         try:
@@ -102,7 +106,7 @@ class ShellJobRunner(AsynchronousJobRunner):
         # Strip and split to get job ID.
         external_job_id = stdout.strip().split()[-1]
         if not external_job_id:
-            log.error(f'({galaxy_id_tag}) submission did not return a job identifier, failing job')
+            log.error(f"({galaxy_id_tag}) submission did not return a job identifier, failing job")
             job_wrapper.fail("failure submitting job")
             return
 
@@ -113,7 +117,7 @@ class ShellJobRunner(AsynchronousJobRunner):
 
         # Store state information for job
         ajs.job_id = external_job_id
-        ajs.old_state = 'new'
+        ajs.old_state = "new"
         ajs.job_destination = job_destination
 
         # Add to our 'queue' of jobs to monitor
@@ -129,8 +133,8 @@ class ShellJobRunner(AsynchronousJobRunner):
         cmd_out = shell.execute(job_interface.submit(job_file))
         if cmd_out.returncode == 0:
             return cmd_out.returncode, cmd_out.stdout
-        stdout = f'({galaxy_id_tag}) submission failed (stdout): {cmd_out.stdout}'
-        stderr = f'({galaxy_id_tag}) submission failed (stderr): {cmd_out.stderr}'
+        stdout = f"({galaxy_id_tag}) submission failed (stdout): {cmd_out.stdout}"
+        stderr = f"({galaxy_id_tag}) submission failed (stderr): {cmd_out.stderr}"
         if retry > 0:
             log.debug("%s, retrying in %s seconds", stdout, timeout)
             log.debug("%s, retrying in %s seconds", stderr, timeout)
@@ -165,7 +169,9 @@ class ShellJobRunner(AsynchronousJobRunner):
                 cmd_out = shell.execute(job_interface.get_single_status(external_job_id))
                 state = job_interface.parse_single_status(cmd_out.stdout, external_job_id)
                 if not state == model.Job.states.OK:
-                    log.warning(f'({id_tag}/{external_job_id}) job not found in batch state check, but found in individual state check')
+                    log.warning(
+                        f"({id_tag}/{external_job_id}) job not found in batch state check, but found in individual state check"
+                    )
             job_state = ajs.job_wrapper.get_state()
             if state != old_state:
                 log.debug(f"({id_tag}/{external_job_id}) state change: from {old_state} to {state}")
@@ -183,10 +189,12 @@ class ShellJobRunner(AsynchronousJobRunner):
                 ajs.running = True
             ajs.old_state = state
             if state == model.Job.states.OK or job_state == model.Job.states.STOPPED:
-                external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
+                external_metadata = not asbool(
+                    ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB)
+                )
                 if external_metadata:
                     self.work_queue.put((self.handle_metadata_externally, ajs))
-                log.debug(f'({id_tag}/{external_job_id}) job execution finished, running job wrapper finish method')
+                log.debug(f"({id_tag}/{external_job_id}) job execution finished, running job wrapper finish method")
                 self.work_queue.put((self.finish_job, ajs))
             else:
                 new_watched.append(ajs)
@@ -201,8 +209,10 @@ class ShellJobRunner(AsynchronousJobRunner):
         shell, job_interface = self.get_cli_plugins(shell_params, job_params)
         cmd_out = shell.execute(job_interface.get_failure_reason(external_job_id))
         if cmd_out is not None:
-            if job_interface.parse_failure_reason(cmd_out.stdout, external_job_id) \
-                    == JobState.runner_states.MEMORY_LIMIT_REACHED:
+            if (
+                job_interface.parse_failure_reason(cmd_out.stdout, external_job_id)
+                == JobState.runner_states.MEMORY_LIMIT_REACHED
+            ):
                 ajs.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
                 ajs.fail_message = "Tool failed due to insufficient memory. Try with more memory."
 
@@ -212,13 +222,15 @@ class ShellJobRunner(AsynchronousJobRunner):
         # unique the list of destinations
         for ajs in self.watched:
             if ajs.job_destination.id not in job_destinations:
-                job_destinations[ajs.job_destination.id] = dict(job_destination=ajs.job_destination, job_ids=[ajs.job_id])
+                job_destinations[ajs.job_destination.id] = dict(
+                    job_destination=ajs.job_destination, job_ids=[ajs.job_id]
+                )
             else:
-                job_destinations[ajs.job_destination.id]['job_ids'].append(ajs.job_id)
+                job_destinations[ajs.job_destination.id]["job_ids"].append(ajs.job_id)
         # check each destination for the listed job ids
         for v in job_destinations.values():
-            job_destination = v['job_destination']
-            job_ids = v['job_ids']
+            job_destination = v["job_destination"]
+            job_ids = v["job_ids"]
             shell_params, job_params = self.parse_destination_params(job_destination.params)
             shell, job_interface = self.get_cli_plugins(shell_params, job_params)
             cmd_out = shell.execute(job_interface.get_status(job_ids))
@@ -236,7 +248,9 @@ class ShellJobRunner(AsynchronousJobRunner):
             assert cmd_out.returncode == 0, cmd_out.stderr
             log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")
         except Exception as e:
-            log.debug(f"({job.id}/{job.job_runner_external_id}) User killed running job, but error encountered during termination: {e}")
+            log.debug(
+                f"({job.id}/{job.job_runner_external_id}) User killed running job, but error encountered during termination: {e}"
+            )
 
     def recover(self, job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
@@ -250,12 +264,16 @@ class ShellJobRunner(AsynchronousJobRunner):
         ajs.job_wrapper = job_wrapper
         ajs.job_destination = job_wrapper.job_destination
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            log.debug(f"({job.id}/{job.job_runner_external_id}) is still in {job.state} state, adding to the runner monitor queue")
+            log.debug(
+                f"({job.id}/{job.job_runner_external_id}) is still in {job.state} state, adding to the runner monitor queue"
+            )
             ajs.old_state = model.Job.states.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
         elif job.state == model.Job.states.QUEUED:
-            log.debug(f"({job.id}/{job.job_runner_external_id}) is still in queued state, adding to the runner monitor queue")
+            log.debug(
+                f"({job.id}/{job.job_runner_external_id}) is still in queued state, adding to the runner monitor queue"
+            )
             ajs.old_state = model.Job.states.QUEUED
             ajs.running = False
             self.monitor_queue.put(ajs)
diff --git a/lib/galaxy/jobs/runners/condor.py b/lib/galaxy/jobs/runners/condor.py
index 41dcab79a53..da7b5556959 100644
--- a/lib/galaxy/jobs/runners/condor.py
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -17,20 +17,20 @@ import subprocess
 from galaxy import model
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
-    AsynchronousJobState
+    AsynchronousJobState,
 )
 from galaxy.jobs.runners.util.condor import (
     build_submit_description,
     condor_stop,
     condor_submit,
     submission_params,
-    summarize_condor_log
+    summarize_condor_log,
 )
 from galaxy.util import asbool
 
 log = logging.getLogger(__name__)
 
-__all__ = ('CondorJobRunner', )
+__all__ = ("CondorJobRunner",)
 
 
 class CondorJobState(AsynchronousJobState):
@@ -49,6 +49,7 @@ class CondorJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "CondorRunner"
 
     def queue_job(self, job_wrapper):
@@ -68,28 +69,25 @@ class CondorJobRunner(AsynchronousJobRunner):
         # get destination params
         query_params = submission_params(prefix="", **job_destination.params)
         container = None
-        universe = query_params.get('universe', None)
-        if universe and universe.strip().lower() == 'docker':
+        universe = query_params.get("universe", None)
+        if universe and universe.strip().lower() == "docker":
             container = self._find_container(job_wrapper)
             if container:
                 # HTCondor needs the image as 'docker_image'
-                query_params.update({'docker_image': container.container_id})
+                query_params.update({"docker_image": container.container_id})
 
-        galaxy_slots = query_params.get('request_cpus', None)
+        galaxy_slots = query_params.get("request_cpus", None)
         if galaxy_slots:
             galaxy_slots_statement = f'GALAXY_SLOTS="{galaxy_slots}"; export GALAXY_SLOTS; GALAXY_SLOTS_CONFIGURED="1"; export GALAXY_SLOTS_CONFIGURED;'
         else:
             galaxy_slots_statement = 'GALAXY_SLOTS="1"; export GALAXY_SLOTS;'
 
         # define job attributes
-        cjs = CondorJobState(
-            files_dir=job_wrapper.working_directory,
-            job_wrapper=job_wrapper
-        )
+        cjs = CondorJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
 
-        cjs.user_log = os.path.join(job_wrapper.working_directory, f'galaxy_{galaxy_id_tag}.condor.log')
-        cjs.register_cleanup_file_attribute('user_log')
-        submit_file = os.path.join(job_wrapper.working_directory, f'galaxy_{galaxy_id_tag}.condor.desc')
+        cjs.user_log = os.path.join(job_wrapper.working_directory, f"galaxy_{galaxy_id_tag}.condor.log")
+        cjs.register_cleanup_file_attribute("user_log")
+        submit_file = os.path.join(job_wrapper.working_directory, f"galaxy_{galaxy_id_tag}.condor.desc")
         executable = cjs.job_file
 
         build_submit_params = dict(
@@ -169,7 +167,10 @@ class CondorJobRunner(AsynchronousJobRunner):
             job_id = cjs.job_id
             galaxy_id_tag = cjs.job_wrapper.get_id_tag()
             try:
-                if cjs.job_wrapper.tool.tool_type != 'interactive' and os.stat(cjs.user_log).st_size == cjs.user_log_size:
+                if (
+                    cjs.job_wrapper.tool.tool_type != "interactive"
+                    and os.stat(cjs.user_log).st_size == cjs.user_log_size
+                ):
                     new_watched.append(cjs)
                     continue
                 s1, s4, s7, s5, s9, log_size = summarize_condor_log(cjs.user_log, job_id)
@@ -199,7 +200,9 @@ class CondorJobRunner(AsynchronousJobRunner):
             job_state = cjs.job_wrapper.get_state()
             if job_complete or job_state == model.Job.states.STOPPED:
                 if job_state != model.Job.states.DELETED:
-                    external_metadata = not asbool(cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True))
+                    external_metadata = not asbool(
+                        cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True)
+                    )
                     if external_metadata:
                         self._handle_metadata_externally(cjs.job_wrapper, resolve_requirements=True)
                     log.debug(f"({galaxy_id_tag}/{job_id}) job has completed")
@@ -236,7 +239,9 @@ class CondorJobRunner(AsynchronousJobRunner):
                 self._stop_container(job_wrapper)
                 # self.watched.append(cjs)
                 if cjs.job_wrapper.get_state() != model.Job.states.DELETED:
-                    external_metadata = not asbool(cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True))
+                    external_metadata = not asbool(
+                        cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True)
+                    )
                     if external_metadata:
                         self._handle_metadata_externally(cjs.job_wrapper, resolve_requirements=True)
                     log.debug(f"({galaxy_id_tag}/{external_id}) job has completed")
@@ -268,10 +273,12 @@ class CondorJobRunner(AsynchronousJobRunner):
         cjs.command_line = job.get_command_line()
         cjs.job_wrapper = job_wrapper
         cjs.job_destination = job_wrapper.job_destination
-        cjs.user_log = os.path.join(job_wrapper.working_directory, f'galaxy_{galaxy_id_tag}.condor.log')
-        cjs.register_cleanup_file_attribute('user_log')
+        cjs.user_log = os.path.join(job_wrapper.working_directory, f"galaxy_{galaxy_id_tag}.condor.log")
+        cjs.register_cleanup_file_attribute("user_log")
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the DRM queue")
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the DRM queue"
+            )
             cjs.running = True
             self.monitor_queue.put(cjs)
         elif job.state == model.Job.states.QUEUED:
@@ -280,10 +287,10 @@ class CondorJobRunner(AsynchronousJobRunner):
             self.monitor_queue.put(cjs)
 
     def _stop_container(self, job_wrapper):
-        return self._run_container_command(job_wrapper, 'stop')
+        return self._run_container_command(job_wrapper, "stop")
 
     def _kill_container(self, job_wrapper):
-        return self._run_container_command(job_wrapper, 'kill')
+        return self._run_container_command(job_wrapper, "kill")
 
     def _run_container_command(self, job_wrapper, command):
         job = job_wrapper.get_job()
@@ -291,13 +298,15 @@ class CondorJobRunner(AsynchronousJobRunner):
         if job:
             cont = job.container
             if cont:
-                if cont.container_type == 'docker':
-                    return self._run_command(cont.container_info['commands'][command], external_id)[0]
+                if cont.container_type == "docker":
+                    return self._run_command(cont.container_info["commands"][command], external_id)[0]
 
     def _run_command(self, command, external_job_id):
-        command = f'condor_ssh_to_job {external_job_id} {command}'
+        command = f"condor_ssh_to_job {external_job_id} {command}"
 
-        p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, close_fds=True, preexec_fn=os.setpgrp)
+        p = subprocess.Popen(
+            command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, close_fds=True, preexec_fn=os.setpgrp
+        )
         stdout, stderr = p.communicate()
         exit_code = p.returncode
         ret = None
@@ -308,5 +317,5 @@ class CondorJobRunner(AsynchronousJobRunner):
         # exit_code = subprocess.call(command,
         #                            shell=True,
         #                            preexec_fn=os.setpgrp)
-        log.debug('_run_command(%s) exit code (%s) and failure: %s', command, exit_code, stderr)
+        log.debug("_run_command(%s) exit code (%s) and failure: %s", command, exit_code, stderr)
         return (exit_code, ret)
diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index 081a22fd9fc..903a5688489 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -14,27 +14,28 @@ from galaxy.jobs import JobDestination
 from galaxy.jobs.handler import DEFAULT_JOB_PUT_FAILURE_MESSAGE
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
-    AsynchronousJobState
+    AsynchronousJobState,
 )
 from galaxy.util import (
     asbool,
     commands,
-    unicodify
+    unicodify,
 )
 
 drmaa = None
 
 log = logging.getLogger(__name__)
 
-__all__ = ('DRMAAJobRunner',)
+__all__ = ("DRMAAJobRunner",)
 
-RETRY_EXCEPTIONS_LOWER = frozenset({'invalidjobexception', 'internalexception'})
+RETRY_EXCEPTIONS_LOWER = frozenset({"invalidjobexception", "internalexception"})
 
 
 class DRMAAJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "DRMAARunner"
     restrict_job_name_length = 15
 
@@ -42,32 +43,37 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         """Start the job runner"""
         global drmaa
 
-        runner_param_specs = {
-            'drmaa_library_path': dict(map=str, default=os.environ.get('DRMAA_LIBRARY_PATH', None))}
+        runner_param_specs = {"drmaa_library_path": dict(map=str, default=os.environ.get("DRMAA_LIBRARY_PATH", None))}
         for retry_exception in RETRY_EXCEPTIONS_LOWER:
-            runner_param_specs[f"{retry_exception}_state"] = dict(map=str, valid=lambda x: x in (model.Job.states.OK, model.Job.states.ERROR), default=model.Job.states.OK)
+            runner_param_specs[f"{retry_exception}_state"] = dict(
+                map=str, valid=lambda x: x in (model.Job.states.OK, model.Job.states.ERROR), default=model.Job.states.OK
+            )
             runner_param_specs[f"{retry_exception}_retries"] = dict(map=int, valid=lambda x: int(x) >= 0, default=0)
 
-        if 'runner_param_specs' not in kwargs:
-            kwargs['runner_param_specs'] = dict()
-        kwargs['runner_param_specs'].update(runner_param_specs)
+        if "runner_param_specs" not in kwargs:
+            kwargs["runner_param_specs"] = dict()
+        kwargs["runner_param_specs"].update(runner_param_specs)
 
         super().__init__(app, nworkers, **kwargs)
 
         # This allows multiple drmaa runners (although only one per handler) in the same job config file
-        if 'drmaa_library_path' in kwargs:
-            log.info('Overriding DRMAA_LIBRARY_PATH due to runner plugin parameter: %s', self.runner_params.drmaa_library_path)
-            os.environ['DRMAA_LIBRARY_PATH'] = self.runner_params.drmaa_library_path
+        if "drmaa_library_path" in kwargs:
+            log.info(
+                "Overriding DRMAA_LIBRARY_PATH due to runner plugin parameter: %s",
+                self.runner_params.drmaa_library_path,
+            )
+            os.environ["DRMAA_LIBRARY_PATH"] = self.runner_params.drmaa_library_path
 
         # Import is delayed until runner initialization to allow for the
         # drmaa_library_path plugin param to override $DRMAA_LIBRARY_PATH
         try:
             drmaa = __import__("drmaa")
         except (ImportError, RuntimeError) as exc:
-            raise exc.__class__('The Python drmaa package is required to use this '
-                                'feature, please install it or correct the '
-                                'following error:\n%s: %s' %
-                                (exc.__class__.__name__, str(exc)))
+            raise exc.__class__(
+                "The Python drmaa package is required to use this "
+                "feature, please install it or correct the "
+                "following error:\n%s: %s" % (exc.__class__.__name__, str(exc))
+            )
         from pulsar.managers.util.drmaa import DrmaaSessionFactory
 
         # make the drmaa library also available to subclasses
@@ -78,16 +84,16 @@ class DRMAAJobRunner(AsynchronousJobRunner):
 
         # Descriptive state strings pulled from the drmaa lib itself
         self.drmaa_job_state_strings = {
-            drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
-            drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
-            drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
-            drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
-            drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
-            drmaa.JobState.RUNNING: 'job is running',
-            drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
-            drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
-            drmaa.JobState.DONE: 'job finished normally',
-            drmaa.JobState.FAILED: 'job finished, but failed',
+            drmaa.JobState.UNDETERMINED: "process status cannot be determined",
+            drmaa.JobState.QUEUED_ACTIVE: "job is queued and active",
+            drmaa.JobState.SYSTEM_ON_HOLD: "job is queued and in system hold",
+            drmaa.JobState.USER_ON_HOLD: "job is queued and in user hold",
+            drmaa.JobState.USER_SYSTEM_ON_HOLD: "job is queued and in user and system hold",
+            drmaa.JobState.RUNNING: "job is running",
+            drmaa.JobState.SYSTEM_SUSPENDED: "job is system suspended",
+            drmaa.JobState.USER_SUSPENDED: "job is user suspended",
+            drmaa.JobState.DONE: "job finished normally",
+            drmaa.JobState.FAILED: "job finished, but failed",
         }
 
         # Ensure a DRMAA session exists and is initialized
@@ -101,19 +107,19 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         """Convert a legacy URL to a job destination"""
         if not url:
             return
-        native_spec = url.split('/')[2]
+        native_spec = url.split("/")[2]
         if native_spec:
             params = dict(nativeSpecification=native_spec)
             log.debug(f"Converted URL '{url}' to destination runner=drmaa, params={params}")
-            return JobDestination(runner='drmaa', params=params)
+            return JobDestination(runner="drmaa", params=params)
         else:
             log.debug(f"Converted URL '{url}' to destination runner=drmaa")
-            return JobDestination(runner='drmaa')
+            return JobDestination(runner="drmaa")
 
     def get_native_spec(self, url):
         """Get any native DRM arguments specified by the site configuration"""
         try:
-            return url.split('/')[2] or None
+            return url.split("/")[2] or None
         except Exception:
             return None
 
@@ -143,15 +149,15 @@ class DRMAAJobRunner(AsynchronousJobRunner):
             jobName=ajs.job_name,
             workingDirectory=job_wrapper.working_directory,
             outputPath=f":{ajs.output_file}",
-            errorPath=f":{ajs.error_file}"
+            errorPath=f":{ajs.error_file}",
         )
 
         # Avoid a jt.exitCodePath for now - it's only used when finishing.
-        native_spec = job_destination.params.get('nativeSpecification', None)
+        native_spec = job_destination.params.get("nativeSpecification", None)
         if native_spec is None:
-            native_spec = job_destination.params.get('native_specification', None)
+            native_spec = job_destination.params.get("native_specification", None)
         if native_spec is not None:
-            jt['nativeSpecification'] = native_spec
+            jt["nativeSpecification"] = native_spec
 
         # fill in the DRM's job run template
         script = self.get_job_file(job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell)
@@ -186,11 +192,11 @@ class DRMAAJobRunner(AsynchronousJobRunner):
                     break
                 except (drmaa.InternalException, drmaa.DeniedByDrmException) as e:
                     trynum += 1
-                    log.warning('(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e)
+                    log.warning("(%s) drmaa.Session.runJob() failed, will retry: %s", galaxy_id_tag, e)
                     fail_msg = "Unable to run this job due to a cluster error, please retry it later"
                     time.sleep(5)
                 except Exception:
-                    log.exception('(%s) drmaa.Session.runJob() failed unconditionally', galaxy_id_tag)
+                    log.exception("(%s) drmaa.Session.runJob() failed unconditionally", galaxy_id_tag)
                     trynum = 5
             else:
                 log.error(f"({galaxy_id_tag}) All attempts to submit job failed")
@@ -205,11 +211,13 @@ class DRMAAJobRunner(AsynchronousJobRunner):
             pwent = job_wrapper.user_system_pwent
             if pwent is None:
                 if not allow_guests:
-                    fail_msg = f"User {job_wrapper.user} is not mapped to any real user, and not permitted to start jobs."
+                    fail_msg = (
+                        f"User {job_wrapper.user} is not mapped to any real user, and not permitted to start jobs."
+                    )
                     job_wrapper.fail(fail_msg)
                     return
                 pwent = job_wrapper.galaxy_system_pwent
-            log.debug(f'({galaxy_id_tag}) submitting with credentials: {pwent[0]} [uid: {pwent[2]}]')
+            log.debug(f"({galaxy_id_tag}) submitting with credentials: {pwent[0]} [uid: {pwent[2]}]")
             filename = self.store_jobtemplate(job_wrapper, jt)
             self.userid = pwent[2]
             external_job_id = self.external_runjob(external_runjob_script, filename, pwent[2])
@@ -223,7 +231,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
 
         # Store DRM related state information for job
         ajs.job_id = external_job_id
-        ajs.old_state = 'new'
+        ajs.old_state = "new"
         ajs.job_destination = job_destination
 
         # Add to our 'queue' of jobs to monitor
@@ -277,7 +285,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         galaxy_id_tag = ajs.job_wrapper.get_id_tag()
         state = None
         try:
-            assert external_job_id not in (None, 'None'), f'({galaxy_id_tag}/{external_job_id}) Invalid job id'
+            assert external_job_id not in (None, "None"), f"({galaxy_id_tag}/{external_job_id}) Invalid job id"
             state = self.ds.job_status(external_job_id)
             # Reset exception retries
             for retry_exception in RETRY_EXCEPTIONS_LOWER:
@@ -287,7 +295,14 @@ class DRMAAJobRunner(AsynchronousJobRunner):
             retry_param = f"{ecn.lower()}_retries"
             state_param = f"{ecn.lower()}_state"
             retries = getattr(ajs, retry_param, 0)
-            log.warning("(%s/%s) unable to check job status because of %s exception for %d consecutive tries: %s", galaxy_id_tag, external_job_id, ecn, retries + 1, e)
+            log.warning(
+                "(%s/%s) unable to check job status because of %s exception for %d consecutive tries: %s",
+                galaxy_id_tag,
+                external_job_id,
+                ecn,
+                retries + 1,
+                e,
+            )
             if self.runner_params[retry_param] > 0:
                 if retries < self.runner_params[retry_param]:
                     # will retry check on next iteration
@@ -301,7 +316,11 @@ class DRMAAJobRunner(AsynchronousJobRunner):
                 log.warning("(%s/%s) job will now be errored", galaxy_id_tag, external_job_id)
                 self.work_queue.put((self.fail_job, ajs))
             else:
-                raise Exception("%s is set to an invalid value (%s), this should not be possible. See galaxy.jobs.drmaa.__init__()", state_param, self.runner_params[state_param])
+                raise Exception(
+                    "%s is set to an invalid value (%s), this should not be possible. See galaxy.jobs.drmaa.__init__()",
+                    state_param,
+                    self.runner_params[state_param],
+                )
             return None
         except drmaa.DrmCommunicationException as e:
             log.warning("(%s/%s) unable to communicate with DRM: %s", galaxy_id_tag, external_job_id, e)
@@ -356,7 +375,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         job = job_wrapper.get_job()
         try:
             ext_id = job.get_job_runner_external_id()
-            assert ext_id not in (None, 'None'), 'External job id is None'
+            assert ext_id not in (None, "None"), "External job id is None"
             kill_script = job_wrapper.get_destination_configuration("drmaa_external_killjob_script")
             if kill_script is None:
                 self.ds.kill(ext_id)
@@ -384,28 +403,32 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         ajs.job_wrapper = job_wrapper
         ajs.job_destination = job_wrapper.job_destination
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the DRM queue")
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the DRM queue"
+            )
             ajs.old_state = drmaa.JobState.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
         elif job.get_state() == model.Job.states.QUEUED:
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in DRM queued state, adding to the DRM queue")
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in DRM queued state, adding to the DRM queue"
+            )
             ajs.old_state = drmaa.JobState.QUEUED_ACTIVE
             ajs.running = False
             self.monitor_queue.put(ajs)
 
     def store_jobtemplate(self, job_wrapper, jt):
-        """ Stores the content of a DRMAA JobTemplate object in a file as a JSON string.
+        """Stores the content of a DRMAA JobTemplate object in a file as a JSON string.
         Path is hard-coded, but it's no worse than other path in this module.
         Uses Galaxy's JobID, so file is expected to be unique."""
         filename = f"{self.app.config.cluster_files_directory}/{job_wrapper.get_id_tag()}.jt_json"
-        with open(filename, 'w+') as fp:
+        with open(filename, "w+") as fp:
             json.dump(jt, fp)
-        log.debug(f'({job_wrapper.job_id}) Job script for external submission is: {filename}')
+        log.debug(f"({job_wrapper.job_id}) Job script for external submission is: {filename}")
         return filename
 
     def external_runjob(self, external_runjob_script, jobtemplate_filename, username):
-        """ runs an external script that will QSUB a new job.
+        """runs an external script that will QSUB a new job.
         The external script needs to be run with sudo, and will setuid() to the specified user.
         Effectively, will QSUB as a different user (than the one used by Galaxy).
         """
@@ -429,12 +452,12 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         galaxy_id_tag = job_wrapper.get_id_tag()
 
         # define job attributes
-        job_name = f'g{galaxy_id_tag}'
+        job_name = f"g{galaxy_id_tag}"
         if job_wrapper.tool.old_id:
-            job_name += f'_{job_wrapper.tool.old_id}'
+            job_name += f"_{job_wrapper.tool.old_id}"
         if not self.redact_email_in_job_name and external_runjob_script is None:
-            job_name += f'_{job_wrapper.user}'
-        job_name = ''.join(x if x in (f"{string.ascii_letters + string.digits}_") else '_' for x in job_name)
+            job_name += f"_{job_wrapper.user}"
+        job_name = "".join(x if x in (f"{string.ascii_letters + string.digits}_") else "_" for x in job_name)
         if self.restrict_job_name_length:
-            job_name = job_name[:self.restrict_job_name_length]
+            job_name = job_name[: self.restrict_job_name_length]
         return job_name
diff --git a/lib/galaxy/jobs/runners/godocker.py b/lib/galaxy/jobs/runners/godocker.py
index db499c9da30..69ef5ec61bc 100644
--- a/lib/galaxy/jobs/runners/godocker.py
+++ b/lib/galaxy/jobs/runners/godocker.py
@@ -8,17 +8,16 @@ import requests
 from galaxy import model
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
-    AsynchronousJobState
+    AsynchronousJobState,
 )
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     unicodify,
 )
 
-
 log = logging.getLogger(__name__)
 
-__all__ = ('GodockerJobRunner', )
+__all__ = ("GodockerJobRunner",)
 
 
 class Godocker:
@@ -37,7 +36,7 @@ class Godocker:
         self.token = token
 
     def http_post_request(self, query, data, header):
-        """ post request with query """
+        """post request with query"""
 
         verify_ssl = not self.noCert
         try:
@@ -45,13 +44,13 @@ class Godocker:
             res = requests.post(url, data, headers=header, verify=verify_ssl, timeout=DEFAULT_SOCKET_TIMEOUT)
 
         except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
-            log.error('A transport error occurred in the GoDocker job runner:', e)
+            log.error("A transport error occurred in the GoDocker job runner:", e)
             return False
 
         return self.test_status_code(res)
 
     def http_get_request(self, query, header):
-        """ get request with query, server and header required """
+        """get request with query, server and header required"""
 
         # remove warnings if using --no-certificate
         requests.packages.urllib3.disable_warnings()
@@ -61,13 +60,13 @@ class Godocker:
             res = requests.get(url, headers=header, verify=verify_ssl, timeout=DEFAULT_SOCKET_TIMEOUT)
 
         except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
-            log.error('A communication error occurred in the GoDocker job runner:', e)
+            log.error("A communication error occurred in the GoDocker job runner:", e)
             return False
 
         return self.test_status_code(res)
 
     def http_delete_request(self, query, header):
-        """ delete request with query, server and header required """
+        """delete request with query, server and header required"""
 
         # remove warnings if using --no-certificate
         requests.packages.urllib3.disable_warnings()
@@ -77,13 +76,13 @@ class Godocker:
             res = requests.delete(url, headers=header, verify=verify_ssl, timeout=DEFAULT_SOCKET_TIMEOUT)
 
         except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
-            log.error('A communication error occurred in the GoDocker job runner:', e)
+            log.error("A communication error occurred in the GoDocker job runner:", e)
             return False
 
         return self.test_status_code(res)
 
     def http_put_request(self, query, data, header):
-        """ put request with query """
+        """put request with query"""
 
         # remove warnings if using --no-certificate
         requests.packages.urllib3.disable_warnings()
@@ -93,21 +92,23 @@ class Godocker:
             res = requests.put(url, data, headers=header, verify=verify_ssl, timeout=DEFAULT_SOCKET_TIMEOUT)
 
         except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
-            log.error('A communication error occurred in the GoDocker job runner:', e)
+            log.error("A communication error occurred in the GoDocker job runner:", e)
             return False
 
         return self.test_status_code(res)
 
     def test_status_code(self, httpresult):
-        """ exit if status code is 401 or 403 or 404 or 200"""
+        """exit if status code is 401 or 403 or 404 or 200"""
         if httpresult.status_code == 401:
-            log.debug('Unauthorized : this server could not verify that you are authorized to access the document you requested.')
+            log.debug(
+                "Unauthorized : this server could not verify that you are authorized to access the document you requested."
+            )
 
         elif httpresult.status_code == 403:
-            log.debug('Forbidden : Access was denied to this resource. Not authorized to access this resource.')
+            log.debug("Forbidden : Access was denied to this resource. Not authorized to access this resource.")
 
         elif httpresult.status_code == 404:
-            log.debug('Not Found : The resource could not be found.')
+            log.debug("Not Found : The resource could not be found.")
 
         elif httpresult.status_code == 200:
             return httpresult
@@ -119,28 +120,35 @@ class GodockerJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "GodockerJobRunner"
 
     def __init__(self, app, nworkers, **kwargs):
-        """ 1: Get runner_param_specs from job_conf.xml
-            2: Initialise job runner parent object
-            3: Login to godocker and store the token
-            4: Start the worker and monitor threads
+        """1: Get runner_param_specs from job_conf.xml
+        2: Initialise job runner parent object
+        3: Login to godocker and store the token
+        4: Start the worker and monitor threads
         """
-        runner_param_specs = dict(godocker_master=dict(map=str), user=dict(map=str), key=dict(map=str), godocker_project=dict(map=str))
-        if 'runner_param_specs' not in kwargs:
-            kwargs['runner_param_specs'] = dict()
-        kwargs['runner_param_specs'].update(runner_param_specs)
+        runner_param_specs = dict(
+            godocker_master=dict(map=str), user=dict(map=str), key=dict(map=str), godocker_project=dict(map=str)
+        )
+        if "runner_param_specs" not in kwargs:
+            kwargs["runner_param_specs"] = dict()
+        kwargs["runner_param_specs"].update(runner_param_specs)
 
         # Start the job runner parent object
         super().__init__(app, nworkers, **kwargs)
 
         # godocker API login call
-        self.auth = self.login(self.runner_params["key"], self.runner_params["user"], self.runner_params["godocker_master"])
+        self.auth = self.login(
+            self.runner_params["key"], self.runner_params["user"], self.runner_params["godocker_master"]
+        )
 
     def queue_job(self, job_wrapper):
-        """ Create job script and submit it to godocker """
-        if not self.prepare_job(job_wrapper, include_metadata=False, include_work_dir_outputs=True, modify_command_for_container=False):
+        """Create job script and submit it to godocker"""
+        if not self.prepare_job(
+            job_wrapper, include_metadata=False, include_work_dir_outputs=True, modify_command_for_container=False
+        ):
             return
 
         job_destination = job_wrapper.job_destination
@@ -152,18 +160,23 @@ class GodockerJobRunner(AsynchronousJobRunner):
         else:
             log.debug(f"Starting queue_job for job {job_id}")
             # Create an object of AsynchronousJobState and add it to the monitor queue.
-            ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_id=job_id, job_destination=job_destination)
+            ajs = AsynchronousJobState(
+                files_dir=job_wrapper.working_directory,
+                job_wrapper=job_wrapper,
+                job_id=job_id,
+                job_destination=job_destination,
+            )
             self.monitor_queue.put(ajs)
 
     def check_watched_item(self, job_state):
-        """ Get the job current status from GoDocker
-                    using job_id and update the status in galaxy.
-            If the job execution is successful, call
-                    mark_as_finished() and return 'None' to galaxy.
-            else if the job failed, call mark_as_failed()
-                    and return 'None' to galaxy.
-            else if the job is running or in pending state, simply
-                    return the 'AsynchronousJobState object' (job_state).
+        """Get the job current status from GoDocker
+                using job_id and update the status in galaxy.
+        If the job execution is successful, call
+                mark_as_finished() and return 'None' to galaxy.
+        else if the job failed, call mark_as_failed()
+                and return 'None' to galaxy.
+        else if the job is running or in pending state, simply
+                return the 'AsynchronousJobState object' (job_state).
         """
         # This function is called by check_watched_items() where param job_state
         # is an object of AsynchronousJobState.
@@ -175,14 +188,14 @@ class GodockerJobRunner(AsynchronousJobRunner):
         job_status_god = self.get_task(job_state.job_id)
         log.debug(f"Job ID: {str(job_state.job_id)} Job Status: {str(job_status_god['status']['primary'])}")
 
-        if job_status_god['status']['primary'] == "over" or job_persisted_state == model.Job.states.STOPPED:
+        if job_status_god["status"]["primary"] == "over" or job_persisted_state == model.Job.states.STOPPED:
             job_state.running = False
             job_state.job_wrapper.change_state(model.Job.states.OK)
             if self.create_log_file(job_state, job_status_god):
                 self.mark_as_finished(job_state)
             else:
                 self.mark_as_failed(job_state)
-            '''The function mark_as_finished() executes:
+            """The function mark_as_finished() executes:
                         self.work_queue.put((self.finish_job, job_state))
            *self.finish_job ->
             job_state.job_wrapper.finish( stdout, stderr, exit_code )
@@ -196,18 +209,18 @@ class GodockerJobRunner(AsynchronousJobRunner):
             job_state.job_wrapper.finish( stdout, stderr, exit_code )
             job_state.job_wrapper.fail( "Unable to finish job", exception=True)
            *Similar workflow is done for mark_as_failed() method.
-            '''
+            """
             return None
 
-        elif job_status_god['status']['primary'] == "running":
+        elif job_status_god["status"]["primary"] == "running":
             job_state.running = True
             job_state.job_wrapper.change_state(model.Job.states.RUNNING)
             return job_state
 
-        elif job_status_god['status']['primary'] == "pending":
+        elif job_status_god["status"]["primary"] == "pending":
             return job_state
 
-        elif job_status_god['status']['exitcode'] not in [None, 0] and job_persisted_state != model.Job.states.STOPPED:
+        elif job_status_god["status"]["exitcode"] not in [None, 0] and job_persisted_state != model.Job.states.STOPPED:
             job_state.running = False
             job_state.job_wrapper.change_state(model.Job.states.ERROR)
             self.create_log_file(job_state, job_status_god)
@@ -221,7 +234,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
             return None
 
     def stop_job(self, job_wrapper):
-        """ Attempts to delete a dispatched executing Job in GoDocker """
+        """Attempts to delete a dispatched executing Job in GoDocker"""
         # This function is called by fail_job() where
         # param job = self.sa_session.query(self.app.model.Job).get(job_state.job_wrapper.job_id)
         # No Return data expected
@@ -229,13 +242,13 @@ class GodockerJobRunner(AsynchronousJobRunner):
         log.debug(f"STOP JOB EXECUTION OF JOB ID: {str(job_id)}")
         # Get task status from GoDocker.
         job_status_god = self.get_task_status(job_id)
-        if job_status_god['status']['primary'] != "over":
+        if job_status_god["status"]["primary"] != "over":
             # Initiate a delete call,if the job is running in GoDocker.
             self.delete_task(job_id)
         return None
 
     def recover(self, job, job_wrapper):
-        """ Recovers jobs stuck in the queued/running state when Galaxy started """
+        """Recovers jobs stuck in the queued/running state when Galaxy started"""
         # This method is called by Galaxy at startup time.
         # Jobs in Running & Queued state in galaxy are put in the monitor_queue
         # by creating an AsynchronousJobState object
@@ -246,27 +259,31 @@ class GodockerJobRunner(AsynchronousJobRunner):
         job_wrapper.command_line = job.command_line
         ajs.job_wrapper = job_wrapper
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the god queue")
-            ajs.old_state = 'R'
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the god queue"
+            )
+            ajs.old_state = "R"
             ajs.running = True
             self.monitor_queue.put(ajs)
 
         elif job.state == model.Job.states.QUEUED:
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in god queued state, adding to the god queue")
-            ajs.old_state = 'Q'
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in god queued state, adding to the god queue"
+            )
+            ajs.old_state = "Q"
             ajs.running = False
             self.monitor_queue.put(ajs)
 
     # Helper functions
 
     def create_log_file(self, job_state, job_status_god):
-        """ Create log files in galaxy, namely error_file, output_file, exit_code_file
-            Return true, if all the file creations are successful
+        """Create log files in galaxy, namely error_file, output_file, exit_code_file
+        Return true, if all the file creations are successful
         """
         path = None
-        for vol in job_status_god['container']['volumes']:
-            if vol['name'] == "go-docker":
-                path = str(vol['path'])
+        for vol in job_status_god["container"]["volumes"]:
+            if vol["name"] == "go-docker":
+                path = str(vol["path"])
         if path:
             god_output_file = f"{path}/god.log"
             god_error_file = f"{path}/god.err"
@@ -286,7 +303,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
                 log_file.close()
                 f.close()
                 # Read from GoDocker exit_code and write it into galaxy exit_code_file.
-                out_log = str(job_status_god['status']['exitcode'])
+                out_log = str(job_status_god["status"]["exitcode"])
                 log_file = open(job_state.exit_code_file, "w")
                 log_file.write(out_log)
                 log_file.close()
@@ -295,7 +312,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
                 log.debug(f"CREATE ERROR FILE: {job_state.error_file}")
                 log.debug(f"CREATE EXIT CODE FILE: {job_state.exit_code_file}")
             except OSError as e:
-                log.error('Could not access task log file: %s', unicodify(e))
+                log.error("Could not access task log file: %s", unicodify(e))
                 log.debug("IO Error occurred when accessing the files.")
                 return False
         return True
@@ -303,27 +320,29 @@ class GodockerJobRunner(AsynchronousJobRunner):
     # GoDocker API helper functions
 
     def login(self, apikey, login, server, noCert=False):
-        """ Login to GoDocker and return the token
-            Create Login model schema of GoDocker and call the http_post_request method.
+        """Login to GoDocker and return the token
+        Create Login model schema of GoDocker and call the http_post_request method.
         """
         log.debug("LOGIN TASK TO BE EXECUTED \n")
         log.debug(f"GODOCKER LOGIN: {str(login)}")
-        data = json.dumps({'user': login, 'apikey': apikey})
+        data = json.dumps({"user": login, "apikey": apikey})
         # Create object of Godocker class
         g_auth = Godocker(server, login, apikey, noCert)
-        auth = g_auth.http_post_request("/api/1.0/authenticate", data, {'Content-type': 'application/json', 'Accept': 'application/json'})
+        auth = g_auth.http_post_request(
+            "/api/1.0/authenticate", data, {"Content-type": "application/json", "Accept": "application/json"}
+        )
         if not auth:
             raise Exception("Authentication failure, GoDocker runner cannot be started")
         else:
             log.debug("GoDocker authentication successful.")
-            token = auth.json()['token']
+            token = auth.json()["token"]
             g_auth.setToken(token)
         # Return the object of Godocker class
         return g_auth
 
     def post_task(self, job_wrapper):
-        """ Sumbit job to GoDocker and return jobid
-            Create Job model schema of GoDocker and call the http_post_request method.
+        """Sumbit job to GoDocker and return jobid
+        Create Job model schema of GoDocker and call the http_post_request method.
         """
         # Get the params from <destination> tag in job_conf by using job_destination.params[param]
         if self.auth.token:
@@ -345,7 +364,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
 
             volumes = []
             labels = []
-            tags_tab = ['galaxy', job_wrapper.tool.id]
+            tags_tab = ["galaxy", job_wrapper.tool.id]
             tasks_depends = []
             name = job_wrapper.tool.name
             description = "galaxy job"
@@ -367,10 +386,12 @@ class GodockerJobRunner(AsynchronousJobRunner):
             dt = datetime.now()
             # Enable galaxy venv in the docker containers
             try:
-                if(job_destination.params["virtualenv"] == "true"):
+                if job_destination.params["virtualenv"] == "true":
                     GALAXY_VENV_TEMPLATE = """GALAXY_VIRTUAL_ENV="%s"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi;"""
                     venv = GALAXY_VENV_TEMPLATE % job_wrapper.galaxy_virtual_env
-                    command = f"#!/bin/bash\ncd {job_wrapper.working_directory}\n{venv}\n{job_wrapper.runner_command_line}"
+                    command = (
+                        f"#!/bin/bash\ncd {job_wrapper.working_directory}\n{venv}\n{job_wrapper.runner_command_line}"
+                    )
                 else:
                     command = f"#!/bin/bash\ncd {job_wrapper.working_directory}\n{job_wrapper.runner_command_line}"
             except Exception:
@@ -378,89 +399,95 @@ class GodockerJobRunner(AsynchronousJobRunner):
 
             # GoDocker Job model schema
             job = {
-                'date': time.mktime(dt.timetuple()),
-                'meta': {
-                    'name': name,
-                    'description': description,
-                    'tags': tags_tab
+                "date": time.mktime(dt.timetuple()),
+                "meta": {"name": name, "description": description, "tags": tags_tab},
+                "requirements": {
+                    "cpu": docker_cpu,
+                    "ram": docker_ram,
+                    "array": {"values": array},
+                    "label": labels,
+                    "tasks": tasks_depends,
+                    "tmpstorage": None,
                 },
-                'requirements': {
-                    'cpu': docker_cpu,
-                    'ram': docker_ram,
-                    'array': {'values': array},
-                    'label': labels,
-                    'tasks': tasks_depends,
-                    'tmpstorage': None
+                "container": {
+                    "image": str(docker_image),
+                    "volumes": volumes,
+                    "network": True,
+                    "id": None,
+                    "meta": None,
+                    "stats": None,
+                    "ports": [],
+                    "root": False,
                 },
-                'container': {
-                    'image': str(docker_image),
-                    'volumes': volumes,
-                    'network': True,
-                    'id': None,
-                    'meta': None,
-                    'stats': None,
-                    'ports': [],
-                    'root': False
+                "command": {
+                    "interactive": False,
+                    "cmd": command,
                 },
-                'command': {
-                    'interactive': False,
-                    'cmd': command,
-                },
-                'status': {
-                    'primary': None,
-                    'secondary': None
-                }
+                "status": {"primary": None, "secondary": None},
             }
             if project is not None:
-                job['user'] = {"project": project}
+                job["user"] = {"project": project}
 
             result = self.auth.http_post_request(
-                "/api/1.0/task", json.dumps(job),
-                {'Authorization': f"Bearer {self.auth.token}", 'Content-type': 'application/json', 'Accept': 'application/json'}
+                "/api/1.0/task",
+                json.dumps(job),
+                {
+                    "Authorization": f"Bearer {self.auth.token}",
+                    "Content-type": "application/json",
+                    "Accept": "application/json",
+                },
             )
             # Return job_id
-            return str(result.json()['id'])
+            return str(result.json()["id"])
 
     def get_task(self, job_id):
-        """ Get job details from GoDocker and return the job.
-            Pass job_id to the http_get_request method.
+        """Get job details from GoDocker and return the job.
+        Pass job_id to the http_get_request method.
         """
         job = False
         if self.auth.token:
-            result = self.auth.http_get_request(f"/api/1.0/task/{str(job_id)}", {'Authorization': f"Bearer {self.auth.token}"})
+            result = self.auth.http_get_request(
+                f"/api/1.0/task/{str(job_id)}", {"Authorization": f"Bearer {self.auth.token}"}
+            )
             job = result.json()
         # Return the job
         return job
 
     def task_suspend(self, job_id):
-        """ Suspend actively running job in galaxy.
-            Pass job_id to the http_get_request method.
+        """Suspend actively running job in galaxy.
+        Pass job_id to the http_get_request method.
         """
         job = False
         if self.auth.token:
-            result = self.auth.http_get_request(f"/api/1.0/task/{str(job_id)}/suspend", {'Authorization': f"Bearer {self.auth.token}"})
+            result = self.auth.http_get_request(
+                f"/api/1.0/task/{str(job_id)}/suspend", {"Authorization": f"Bearer {self.auth.token}"}
+            )
             job = result.json()
         # Return the job
         return job
 
     def get_task_status(self, job_id):
-        """ Get job status from GoDocker and return the status of job.
-            Pass job_id to http_get_request method.
+        """Get job status from GoDocker and return the status of job.
+        Pass job_id to http_get_request method.
         """
         job = False
         if self.auth.token:
-            result = self.auth.http_get_request(f"/api/1.0/task/{str(job_id)}/status", {'Authorization': f"Bearer {self.auth.token}"})
+            result = self.auth.http_get_request(
+                f"/api/1.0/task/{str(job_id)}/status", {"Authorization": f"Bearer {self.auth.token}"}
+            )
             job = result.json()
         # Return task status
         return job
 
     def delete_task(self, job_id):
-        """ Delete a suspended task in GoDocker.
-            Pass job_id to http_delete_request method.
+        """Delete a suspended task in GoDocker.
+        Pass job_id to http_delete_request method.
         """
         job = False
         if self.auth.token:
-            result = self.auth.http_delete_request(f"/api/1.0/task/{str(job_id)}", {'Authorization': f"Bearer {self.auth.token}"})
+            result = self.auth.http_delete_request(
+                f"/api/1.0/task/{str(job_id)}", {"Authorization": f"Bearer {self.auth.token}"}
+            )
             job = result.json()
         # Return the job
         return job
diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 505e1e0b7bd..5c8886a3e63 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -14,7 +14,7 @@ from galaxy import model
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
     AsynchronousJobState,
-    JobState
+    JobState,
 )
 from galaxy.jobs.runners.util.pykube_util import (
     deduplicate_entries,
@@ -41,19 +41,20 @@ from galaxy.jobs.runners.util.pykube_util import (
     pull_policy,
     pykube_client_from_dict,
     Service,
-    service_object_dict
+    service_object_dict,
 )
 from galaxy.util.bytesize import ByteSize
 
 log = logging.getLogger(__name__)
 
-__all__ = ('KubernetesJobRunner', )
+__all__ = ("KubernetesJobRunner",)
 
 
 class KubernetesJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "KubernetesRunner"
 
     LABEL_START = re.compile("^[A-Za-z0-9]")
@@ -80,21 +81,30 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             k8s_job_api_version=dict(map=str, default=DEFAULT_JOB_API_VERSION),
             k8s_job_ttl_secs_after_finished=dict(map=int, valid=lambda x: x is None or int(x) >= 0, default=None),
             k8s_job_metadata=dict(map=str, default=None),
-            k8s_supplemental_group_id=dict(map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or s.isdigit(), default=None),
+            k8s_supplemental_group_id=dict(
+                map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or s.isdigit(), default=None
+            ),
             k8s_pull_policy=dict(map=str, default="Default"),
-            k8s_run_as_user_id=dict(map=str, valid=lambda s: s == "$uid" or isinstance(s, int) or not s or s.isdigit(), default=None),
-            k8s_run_as_group_id=dict(map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or s.isdigit(), default=None),
-            k8s_fs_group_id=dict(map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or s.isdigit(), default=None),
+            k8s_run_as_user_id=dict(
+                map=str, valid=lambda s: s == "$uid" or isinstance(s, int) or not s or s.isdigit(), default=None
+            ),
+            k8s_run_as_group_id=dict(
+                map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or s.isdigit(), default=None
+            ),
+            k8s_fs_group_id=dict(
+                map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or s.isdigit(), default=None
+            ),
             k8s_cleanup_job=dict(map=str, valid=lambda s: s in {"onsuccess", "always", "never"}, default="always"),
             k8s_pod_retries=dict(map=int, valid=lambda x: int(x) >= 0, default=3),
             k8s_walltime_limit=dict(map=int, valid=lambda x: int(x) >= 0, default=172800),
             k8s_unschedulable_walltime_limit=dict(map=int, valid=lambda x: not x or int(x) >= 0, default=None),
             k8s_interactivetools_use_ssl=dict(map=bool, default=False),
-            k8s_interactivetools_ingress_annotations=dict(map=str),)
+            k8s_interactivetools_ingress_annotations=dict(map=str),
+        )
 
-        if 'runner_param_specs' not in kwargs:
-            kwargs['runner_param_specs'] = dict()
-        kwargs['runner_param_specs'].update(runner_param_specs)
+        if "runner_param_specs" not in kwargs:
+            kwargs["runner_param_specs"] = dict()
+        kwargs["runner_param_specs"].update(runner_param_specs)
 
         # Start the job runner parent object
         super().__init__(app, nworkers, **kwargs)
@@ -111,23 +121,23 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         self.setup_base_volumes()
 
     def setup_base_volumes(self):
-
         def generate_volumes(pvc_list):
-            return [{'name': pvc["name"], 'persistentVolumeClaim': {'claimName': pvc["name"]}} for pvc in pvc_list]
+            return [{"name": pvc["name"], "persistentVolumeClaim": {"claimName": pvc["name"]}} for pvc in pvc_list]
 
         def get_volume_mounts_for(claim):
             if self.runner_params.get(claim):
-                volume_mounts = [parse_pvc_param_line(pvc) for pvc in self.runner_params[claim].split(',')]
+                volume_mounts = [parse_pvc_param_line(pvc) for pvc in self.runner_params[claim].split(",")]
                 # generate default list of volumes for all jobs
                 volumes = generate_volumes(volume_mounts)
                 return volumes, volume_mounts
             return [], []
 
-        self.runner_params['k8s_volumes'], self.runner_params['k8s_volume_mounts'] = \
-            get_volume_mounts_for('k8s_persistent_volume_claims')
+        self.runner_params["k8s_volumes"], self.runner_params["k8s_volume_mounts"] = get_volume_mounts_for(
+            "k8s_persistent_volume_claims"
+        )
         # ignore volume mounts for the following two, as they are generated per job
-        self.runner_params['k8s_volumes'].extend(get_volume_mounts_for('k8s_data_volume_claim')[0])
-        self.runner_params['k8s_volumes'].extend(get_volume_mounts_for('k8s_working_volume_claim')[0])
+        self.runner_params["k8s_volumes"].extend(get_volume_mounts_for("k8s_data_volume_claim")[0])
+        self.runner_params["k8s_volumes"].extend(get_volume_mounts_for("k8s_working_volume_claim")[0])
 
     def queue_job(self, job_wrapper):
         """Create job script and submit it to Kubernetes cluster"""
@@ -136,18 +146,24 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         # where galaxy will expect results.
         log.debug(f"Starting queue_job for job {job_wrapper.get_id_tag()}")
 
-        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
-                                   job_wrapper=job_wrapper,
-                                   job_destination=job_wrapper.job_destination)
+        ajs = AsynchronousJobState(
+            files_dir=job_wrapper.working_directory,
+            job_wrapper=job_wrapper,
+            job_destination=job_wrapper.job_destination,
+        )
 
-        if not self.prepare_job(job_wrapper,
-                                include_metadata=False,
-                                modify_command_for_container=False,
-                                stdout_file=ajs.output_file,
-                                stderr_file=ajs.error_file):
+        if not self.prepare_job(
+            job_wrapper,
+            include_metadata=False,
+            modify_command_for_container=False,
+            stdout_file=ajs.output_file,
+            stderr_file=ajs.error_file,
+        ):
             return
 
-        script = self.get_job_file(job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell, galaxy_virtual_env=None)
+        script = self.get_job_file(
+            job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell, galaxy_virtual_env=None
+        )
         try:
             self.write_executable_script(ajs.job_file, script, job_io=job_wrapper.job_io)
         except Exception:
@@ -167,11 +183,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 return
 
         k8s_job_prefix = self.__produce_k8s_job_prefix()
-        k8s_job_obj = job_object_dict(
-            self.runner_params,
-            k8s_job_prefix,
-            self.__get_k8s_job_spec(ajs)
-        )
+        k8s_job_obj = job_object_dict(self.runner_params, k8s_job_prefix, self.__get_k8s_job_spec(ajs))
 
         job = Job(self._pykube_api, k8s_job_obj)
         try:
@@ -204,24 +216,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         guest_ports = ajs.job_wrapper.guest_ports
         ports_dict = {}
         for guest_port in guest_ports:
-            ports_dict[str(guest_port)] = dict(host='manual', port=guest_port, protocol="https")
+            ports_dict[str(guest_port)] = dict(host="manual", port=guest_port, protocol="https")
         self.app.interactivetool_manager.configure_entry_points(ajs.job_wrapper.get_job(), ports_dict)
 
         # Configure additional k8s service and ingress for tools with guest ports
         k8s_job_prefix = self.__produce_k8s_job_prefix()
         k8s_job_name = self.__get_k8s_job_name(k8s_job_prefix, ajs.job_wrapper)
-        log.debug(f'Configuring entry points and deploying service/ingress for job with ID {ajs.job_id}')
-        k8s_service_obj = service_object_dict(
-            self.runner_params,
-            k8s_job_name,
-            self.__get_k8s_service_spec(ajs)
-        )
+        log.debug(f"Configuring entry points and deploying service/ingress for job with ID {ajs.job_id}")
+        k8s_service_obj = service_object_dict(self.runner_params, k8s_job_name, self.__get_k8s_service_spec(ajs))
 
-        k8s_ingress_obj = ingress_object_dict(
-            self.runner_params,
-            k8s_job_name,
-            self.__get_k8s_ingress_spec(ajs)
-        )
+        k8s_ingress_obj = ingress_object_dict(self.runner_params, k8s_job_name, self.__get_k8s_ingress_spec(ajs))
         service = Service(self._pykube_api, k8s_service_obj)
         service.create()
         ingress = Ingress(self._pykube_api, k8s_ingress_obj)
@@ -243,8 +247,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 try:
                     return int(self.runner_params["k8s_run_as_user_id"])
                 except Exception:
-                    log.warning("User ID passed for Kubernetes runner needs to be an integer or \"$uid\", value "
-                             + self.runner_params["k8s_run_as_user_id"] + " passed is invalid")
+                    log.warning(
+                        'User ID passed for Kubernetes runner needs to be an integer or "$uid", value '
+                        + self.runner_params["k8s_run_as_user_id"]
+                        + " passed is invalid"
+                    )
                     return None
         return None
 
@@ -257,17 +264,26 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 try:
                     return int(self.runner_params["k8s_run_as_group_id"])
                 except Exception:
-                    log.warning("Group ID passed for Kubernetes runner needs to be an integer or \"$gid\", value "
-                             + self.runner_params["k8s_run_as_group_id"] + " passed is invalid")
+                    log.warning(
+                        'Group ID passed for Kubernetes runner needs to be an integer or "$gid", value '
+                        + self.runner_params["k8s_run_as_group_id"]
+                        + " passed is invalid"
+                    )
         return None
 
     def __get_supplemental_group(self):
-        if self.runner_params.get("k8s_supplemental_group_id") or self.runner_params.get("k8s_supplemental_group_id") == 0:
+        if (
+            self.runner_params.get("k8s_supplemental_group_id")
+            or self.runner_params.get("k8s_supplemental_group_id") == 0
+        ):
             try:
                 return int(self.runner_params["k8s_supplemental_group_id"])
             except Exception:
-                log.warning("Supplemental group passed for Kubernetes runner needs to be an integer or \"$gid\", value "
-                         + self.runner_params["k8s_supplemental_group_id"] + " passed is invalid")
+                log.warning(
+                    'Supplemental group passed for Kubernetes runner needs to be an integer or "$gid", value '
+                    + self.runner_params["k8s_supplemental_group_id"]
+                    + " passed is invalid"
+                )
                 return None
         return None
 
@@ -276,8 +292,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             try:
                 return int(self.runner_params["k8s_fs_group_id"])
             except Exception:
-                log.warning("FS group passed for Kubernetes runner needs to be an integer or \"$gid\", value "
-                         + self.runner_params["k8s_fs_group_id"] + " passed is invalid")
+                log.warning(
+                    'FS group passed for Kubernetes runner needs to be an integer or "$gid", value '
+                    + self.runner_params["k8s_fs_group_id"]
+                    + " passed is invalid"
+                )
                 return None
         return None
 
@@ -286,14 +305,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         return galaxy_instance_id(self.runner_params)
 
     def __produce_k8s_job_prefix(self):
-        instance_id = self._galaxy_instance_id or ''
-        return produce_k8s_job_prefix(app_prefix='gxy', instance_id=instance_id)
+        instance_id = self._galaxy_instance_id or ""
+        return produce_k8s_job_prefix(app_prefix="gxy", instance_id=instance_id)
 
     def __get_k8s_job_spec(self, ajs):
         """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template.
         If the job hangs around unlimited it will be ended after k8s wall time limit, which sets activeDeadlineSeconds"""
-        k8s_job_spec = {"template": self.__get_k8s_job_spec_template(ajs),
-                        "activeDeadlineSeconds": int(self.runner_params['k8s_walltime_limit'])}
+        k8s_job_spec = {
+            "template": self.__get_k8s_job_spec_template(ajs),
+            "activeDeadlineSeconds": int(self.runner_params["k8s_walltime_limit"]),
+        }
         job_ttl = self.runner_params["k8s_job_ttl_secs_after_finished"]
         if self.runner_params["k8s_cleanup_job"] != "never" and job_ttl is not None:
             k8s_job_spec["ttlSecondsAfterFinished"] = job_ttl
@@ -310,7 +331,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         if not self.LABEL_START.search(label_val):
             label_val = f"x{label_val}"
         if not self.LABEL_END.search(label_val):
-            label_val += 'x'
+            label_val += "x"
         return label_val
 
     def __get_k8s_job_spec_template(self, ajs):
@@ -329,32 +350,31 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                     "app.galaxyproject.org/job_id": self.__force_label_conformity(ajs.job_wrapper.get_id_tag()),
                     "app.galaxyproject.org/handler": self.__force_label_conformity(self.app.config.server_name),
                     "app.galaxyproject.org/destination": self.__force_label_conformity(
-                        str(ajs.job_wrapper.job_destination.id))
+                        str(ajs.job_wrapper.job_destination.id)
+                    ),
                 },
-                "annotations": {
-                    "app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id
-                }
+                "annotations": {"app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id},
             },
             "spec": {
-                "volumes": deduplicate_entries(self.runner_params['k8s_volumes']),
+                "volumes": deduplicate_entries(self.runner_params["k8s_volumes"]),
                 "restartPolicy": self.__get_k8s_restart_policy(ajs.job_wrapper),
                 "containers": self.__get_k8s_containers(ajs),
-                "priorityClassName": self.runner_params['k8s_pod_priority_class'],
-                "tolerations": yaml.safe_load(self.runner_params['k8s_tolerations'] or "[]"),
-                "affinity": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper,
-                                                                         'k8s_affinity') or "{}"),
-                "nodeSelector": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper,
-                                                                             'k8s_node_selector') or "{}")
-            }
+                "priorityClassName": self.runner_params["k8s_pod_priority_class"],
+                "tolerations": yaml.safe_load(self.runner_params["k8s_tolerations"] or "[]"),
+                "affinity": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper, "k8s_affinity") or "{}"),
+                "nodeSelector": yaml.safe_load(
+                    self.__get_overridable_params(ajs.job_wrapper, "k8s_node_selector") or "{}"
+                ),
+            },
         }
         # TODO include other relevant elements that people might want to use from
         # TODO http://kubernetes.io/docs/api-reference/v1/definitions/#_v1_podspec
         k8s_spec_template["spec"]["securityContext"] = self.__get_k8s_security_context()
-        extra_metadata = self.runner_params['k8s_job_metadata'] or '{}'
+        extra_metadata = self.runner_params["k8s_job_metadata"] or "{}"
         if isinstance(extra_metadata, str):
             extra_metadata = yaml.safe_load(extra_metadata)
-        k8s_spec_template["metadata"]["labels"].update(extra_metadata.get('labels', {}))
-        k8s_spec_template["metadata"]["annotations"].update(extra_metadata.get('annotations', {}))
+        k8s_spec_template["metadata"]["labels"].update(extra_metadata.get("labels", {}))
+        k8s_spec_template["metadata"]["annotations"].update(extra_metadata.get("annotations", {}))
         return k8s_spec_template
 
     def __get_k8s_service_spec(self, ajs):
@@ -366,24 +386,28 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 "labels": {
                     "app.galaxyproject.org/handler": self.__force_label_conformity(self.app.config.server_name),
                     "app.galaxyproject.org/destination": self.__force_label_conformity(
-                        str(ajs.job_wrapper.job_destination.id))
+                        str(ajs.job_wrapper.job_destination.id)
+                    ),
                 },
-                "annotations": {
-                    "app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id
-                }
+                "annotations": {"app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id},
             },
             "spec": {
-                "ports": [{"name": f"job-{self.__force_label_conformity(ajs.job_wrapper.get_id_tag())}-{p}",
-                           "port": int(p),
-                           "protocol": "TCP",
-                           "targetPort": int(p)} for p in guest_ports],
+                "ports": [
+                    {
+                        "name": f"job-{self.__force_label_conformity(ajs.job_wrapper.get_id_tag())}-{p}",
+                        "port": int(p),
+                        "protocol": "TCP",
+                        "targetPort": int(p),
+                    }
+                    for p in guest_ports
+                ],
                 "selector": {
                     "app.kubernetes.io/name": self.__force_label_conformity(ajs.job_wrapper.tool.old_id),
                     "app.kubernetes.io/component": "tool",
-                    "app.galaxyproject.org/job_id": self.__force_label_conformity(ajs.job_wrapper.get_id_tag())
+                    "app.galaxyproject.org/job_id": self.__force_label_conformity(ajs.job_wrapper.get_id_tag()),
                 },
-                "type": "ClusterIP"
-            }
+                "type": "ClusterIP",
+            },
         }
         return k8s_spec_template
 
@@ -397,45 +421,61 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             for entry_point in configured_eps:
                 # sending in self.app as `trans` since it's only used for `.security` so seems to work
                 entry_point_path = self.app.interactivetool_manager.get_entry_point_path(self.app, entry_point)
-                if '?' in entry_point_path:
+                if "?" in entry_point_path:
                     # Removing all the parameters from the ingress path, but they will still be in the database
                     # so the link that the user clicks on will still have them
-                    log.warning("IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S")
-                    entry_point_path = entry_point_path.split('?')[0]
-                entry_point_domain = f'{self.app.config.interactivetools_proxy_host}'
+                    log.warning(
+                        "IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S"
+                    )
+                    entry_point_path = entry_point_path.split("?")[0]
+                entry_point_domain = f"{self.app.config.interactivetools_proxy_host}"
                 if entry_point.requires_domain:
-                    entry_point_subdomain = self.app.interactivetool_manager.get_entry_point_subdomain(self.app, entry_point)
-                    entry_point_domain = f'{entry_point_subdomain}.{entry_point_domain}'
-                    entry_point_path = '/'
-                entry_points.append({"tool_port": entry_point.tool_port, "domain": entry_point_domain, "entry_path": entry_point_path})
+                    entry_point_subdomain = self.app.interactivetool_manager.get_entry_point_subdomain(
+                        self.app, entry_point
+                    )
+                    entry_point_domain = f"{entry_point_subdomain}.{entry_point_domain}"
+                    entry_point_path = "/"
+                entry_points.append(
+                    {"tool_port": entry_point.tool_port, "domain": entry_point_domain, "entry_path": entry_point_path}
+                )
         k8s_spec_template = {
             "metadata": {
                 "labels": {
                     "app.galaxyproject.org/handler": self.__force_label_conformity(self.app.config.server_name),
                     "app.galaxyproject.org/destination": self.__force_label_conformity(
-                        str(ajs.job_wrapper.job_destination.id))
+                        str(ajs.job_wrapper.job_destination.id)
+                    ),
                 },
-                "annotations": {
-                    "app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id
-                }
+                "annotations": {"app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id},
             },
             "spec": {
-                "rules": [{"host": ep["domain"],
-                           "http": {
-                               "paths": [{
-                                   "backend": {
-                                       "serviceName": self.__get_k8s_job_name(self.__produce_k8s_job_prefix(), ajs.job_wrapper),
-                                       "servicePort": int(ep["tool_port"])
-                                   },
-                                   "path": ep.get("entry_path", '/'),
-                                   "pathType": "Prefix"
-                               }]}} for ep in entry_points]
-            }
+                "rules": [
+                    {
+                        "host": ep["domain"],
+                        "http": {
+                            "paths": [
+                                {
+                                    "backend": {
+                                        "serviceName": self.__get_k8s_job_name(
+                                            self.__produce_k8s_job_prefix(), ajs.job_wrapper
+                                        ),
+                                        "servicePort": int(ep["tool_port"]),
+                                    },
+                                    "path": ep.get("entry_path", "/"),
+                                    "pathType": "Prefix",
+                                }
+                            ]
+                        },
+                    }
+                    for ep in entry_points
+                ]
+            },
         }
         if self.runner_params.get("k8s_interactivetools_use_ssl"):
             domains = list({e["domain"] for e in entry_points})
-            k8s_spec_template["spec"]["tls"] = [{"hosts": [domain],
-                                                 "secretName": re.sub("[^a-z0-9-]", "-", domain)} for domain in domains]
+            k8s_spec_template["spec"]["tls"] = [
+                {"hosts": [domain], "secretName": re.sub("[^a-z0-9-]", "-", domain)} for domain in domains
+            ]
         if self.runner_params.get("k8s_interactivetools_ingress_annotations"):
             new_ann = yaml.safe_load(self.runner_params.get("k8s_interactivetools_ingress_annotations"))
             k8s_spec_template["metadata"]["annotations"].update(new_ann)
@@ -459,16 +499,20 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def __get_k8s_containers(self, ajs):
         """Fills in all required for setting up the docker containers to be used, including setting a pull policy if
-           this has been set.
-           $GALAXY_VIRTUAL_ENV is set to None to avoid the galaxy virtualenv inside the tool container.
-           $GALAXY_LIB is set to None to avoid changing the python path inside the container.
-           Setting these variables changes the described behaviour in the job file shell script
-           used to execute the tool inside the container.
+        this has been set.
+        $GALAXY_VIRTUAL_ENV is set to None to avoid the galaxy virtualenv inside the tool container.
+        $GALAXY_LIB is set to None to avoid changing the python path inside the container.
+        Setting these variables changes the described behaviour in the job file shell script
+        used to execute the tool inside the container.
         """
         container = self._find_container(ajs.job_wrapper)
 
-        mounts = get_volume_mounts_for_job(ajs.job_wrapper, self.runner_params.get('k8s_data_volume_claim'), self.runner_params.get('k8s_working_volume_claim'))
-        mounts.extend(self.runner_params['k8s_volume_mounts'])
+        mounts = get_volume_mounts_for_job(
+            ajs.job_wrapper,
+            self.runner_params.get("k8s_data_volume_claim"),
+            self.runner_params.get("k8s_working_volume_claim"),
+        )
+        mounts.extend(self.runner_params["k8s_volume_mounts"])
 
         k8s_container = {
             "name": self.__get_k8s_container_name(ajs.job_wrapper),
@@ -479,56 +523,60 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             "command": [ajs.job_wrapper.shell],
             "args": ["-c", ajs.job_file],
             "workingDir": ajs.job_wrapper.working_directory,
-            "volumeMounts": deduplicate_entries(mounts)
+            "volumeMounts": deduplicate_entries(mounts),
         }
 
         resources = self.__get_resources(ajs.job_wrapper)
         if resources:
             envs = []
             cpu_val = None
-            if 'requests' in resources:
-                requests = resources['requests']
-                if 'cpu' in requests:
-                    cpu_val = int(math.ceil(float(requests['cpu'])))
-                    envs.append({'name': 'GALAXY_SLOTS', 'value': str(cpu_val)})
-                if 'memory' in requests:
-                    mem_val = ByteSize(requests['memory']).to_unit('M', as_string=False)
-                    envs.append({'name': 'GALAXY_MEMORY_MB', 'value': str(mem_val)})
+            if "requests" in resources:
+                requests = resources["requests"]
+                if "cpu" in requests:
+                    cpu_val = int(math.ceil(float(requests["cpu"])))
+                    envs.append({"name": "GALAXY_SLOTS", "value": str(cpu_val)})
+                if "memory" in requests:
+                    mem_val = ByteSize(requests["memory"]).to_unit("M", as_string=False)
+                    envs.append({"name": "GALAXY_MEMORY_MB", "value": str(mem_val)})
                     if cpu_val:
-                        envs.append({'name': 'GALAXY_MEMORY_MB_PER_SLOT', 'value': str(math.floor(mem_val / cpu_val))})
-            elif 'limits' in resources:
-                limits = resources['limits']
-                if 'cpu' in limits:
-                    cpu_val = int(math.floor(float(limits['cpu'])))
+                        envs.append({"name": "GALAXY_MEMORY_MB_PER_SLOT", "value": str(math.floor(mem_val / cpu_val))})
+            elif "limits" in resources:
+                limits = resources["limits"]
+                if "cpu" in limits:
+                    cpu_val = int(math.floor(float(limits["cpu"])))
                     cpu_val = cpu_val or 1
-                    envs.append({'name': 'GALAXY_SLOTS', 'value': str(cpu_val)})
-                if 'memory' in limits:
-                    mem_val = ByteSize(limits['memory']).to_unit('M', as_string=False)
-                    envs.append({'name': 'GALAXY_MEMORY_MB', 'value': str(mem_val)})
+                    envs.append({"name": "GALAXY_SLOTS", "value": str(cpu_val)})
+                if "memory" in limits:
+                    mem_val = ByteSize(limits["memory"]).to_unit("M", as_string=False)
+                    envs.append({"name": "GALAXY_MEMORY_MB", "value": str(mem_val)})
                     if cpu_val:
-                        envs.append({'name': 'GALAXY_MEMORY_MB_PER_SLOT', 'value': str(math.floor(mem_val / cpu_val))})
-            extra_envs = yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper, 'k8s_extra_job_envs') or "{}")
+                        envs.append({"name": "GALAXY_MEMORY_MB_PER_SLOT", "value": str(math.floor(mem_val / cpu_val))})
+            extra_envs = yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper, "k8s_extra_job_envs") or "{}")
             for key in extra_envs:
-                envs.append({'name': key, 'value': extra_envs[key]})
+                envs.append({"name": key, "value": extra_envs[key]})
             if self.__has_guest_ports(ajs.job_wrapper):
                 configured_eps = [ep for ep in ajs.job_wrapper.get_job().interactivetool_entry_points if ep.configured]
                 for entry_point in configured_eps:
                     # sending in self.app as `trans` since it's only used for `.security` so seems to work
                     entry_point_path = self.app.interactivetool_manager.get_entry_point_path(self.app, entry_point)
-                    if '?' in entry_point_path:
+                    if "?" in entry_point_path:
                         # Removing all the parameters from the ingress path, but they will still be in the database
                         # so the link that the user clicks on will still have them
-                        log.warning("IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S")
-                        entry_point_path = entry_point_path.split('?')[0]
-                    entry_point_domain = f'{self.app.config.interactivetools_proxy_host}'
+                        log.warning(
+                            "IT urls including parameters (eg: /myit?mykey=myvalue) are only experimentally supported on K8S"
+                        )
+                        entry_point_path = entry_point_path.split("?")[0]
+                    entry_point_domain = f"{self.app.config.interactivetools_proxy_host}"
                     if entry_point.requires_domain:
-                        entry_point_subdomain = self.app.interactivetool_manager.get_entry_point_subdomain(self.app, entry_point)
-                        entry_point_domain = f'{entry_point_subdomain}.{entry_point_domain}'
-                    envs.append({'name': 'INTERACTIVETOOL_PORT', 'value': str(entry_point.tool_port)})
-                    envs.append({'name': 'INTERACTIVETOOL_DOMAIN', 'value': str(entry_point_domain)})
-                    envs.append({'name': 'INTERACTIVETOOL_PATH', 'value': str(entry_point_path)})
-            k8s_container['resources'] = resources
-            k8s_container['env'] = envs
+                        entry_point_subdomain = self.app.interactivetool_manager.get_entry_point_subdomain(
+                            self.app, entry_point
+                        )
+                        entry_point_domain = f"{entry_point_subdomain}.{entry_point_domain}"
+                    envs.append({"name": "INTERACTIVETOOL_PORT", "value": str(entry_point.tool_port)})
+                    envs.append({"name": "INTERACTIVETOOL_DOMAIN", "value": str(entry_point_domain)})
+                    envs.append({"name": "INTERACTIVETOOL_PATH", "value": str(entry_point_path)})
+            k8s_container["resources"] = resources
+            k8s_container["env"] = envs
 
         if self._default_pull_policy:
             k8s_container["imagePullPolicy"] = self._default_pull_policy
@@ -546,20 +594,20 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         limits = {}
 
         if mem_request:
-            requests['memory'] = mem_request
+            requests["memory"] = mem_request
         if cpu_request:
-            requests['cpu'] = cpu_request
+            requests["cpu"] = cpu_request
 
         if mem_limit:
-            limits['memory'] = mem_limit
+            limits["memory"] = mem_limit
         if cpu_limit:
-            limits['cpu'] = cpu_limit
+            limits["cpu"] = cpu_limit
 
         resources = {}
         if requests:
-            resources['requests'] = requests
+            resources["requests"] = requests
         if limits:
-            resources['limits'] = limits
+            resources["limits"] = limits
 
         return resources
 
@@ -567,32 +615,32 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         """Obtains memory requests for job, checking if available on the destination, otherwise using the default"""
         job_destination = job_wrapper.job_destination
 
-        if 'requests_memory' in job_destination.params:
-            return self.__transform_memory_value(job_destination.params['requests_memory'])
+        if "requests_memory" in job_destination.params:
+            return self.__transform_memory_value(job_destination.params["requests_memory"])
         return None
 
     def __get_memory_limit(self, job_wrapper):
         """Obtains memory limits for job, checking if available on the destination, otherwise using the default"""
         job_destination = job_wrapper.job_destination
 
-        if 'limits_memory' in job_destination.params:
-            return self.__transform_memory_value(job_destination.params['limits_memory'])
+        if "limits_memory" in job_destination.params:
+            return self.__transform_memory_value(job_destination.params["limits_memory"])
         return None
 
     def __get_cpu_request(self, job_wrapper):
         """Obtains cpu requests for job, checking if available on the destination, otherwise using the default"""
         job_destination = job_wrapper.job_destination
 
-        if 'requests_cpu' in job_destination.params:
-            return job_destination.params['requests_cpu']
+        if "requests_cpu" in job_destination.params:
+            return job_destination.params["requests_cpu"]
         return None
 
     def __get_cpu_limit(self, job_wrapper):
         """Obtains cpu requests for job, checking if available on the destination, otherwise using the default"""
         job_destination = job_wrapper.job_destination
 
-        if 'limits_cpu' in job_destination.params:
-            return job_destination.params['limits_cpu']
+        if "limits_cpu" in job_destination.params:
+            return job_destination.params["limits_cpu"]
         return None
 
     def __transform_memory_value(self, mem_value):
@@ -609,14 +657,14 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         # definition
         repo = ""
         owner = ""
-        if 'repo' in job_destination.params:
+        if "repo" in job_destination.params:
             repo = f"{job_destination.params['repo']}/"
-        if 'owner' in job_destination.params:
+        if "owner" in job_destination.params:
             owner = f"{job_destination.params['owner']}/"
 
-        k8s_cont_image = repo + owner + job_destination.params['image']
+        k8s_cont_image = repo + owner + job_destination.params["image"]
 
-        if 'tag' in job_destination.params:
+        if "tag" in job_destination.params:
             k8s_cont_image += f":{job_destination.params['tag']}"
 
         return k8s_cont_image
@@ -646,19 +694,19 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def check_watched_item(self, job_state):
         """Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState"""
-        jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
+        jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
 
-        if len(jobs.response['items']) == 1:
-            job = Job(self._pykube_api, jobs.response['items'][0])
+        if len(jobs.response["items"]) == 1:
+            job = Job(self._pykube_api, jobs.response["items"][0])
             job_destination = job_state.job_wrapper.job_destination
             succeeded = 0
             active = 0
             failed = 0
 
-            if 'max_pod_retries' in job_destination.params:
-                max_pod_retries = int(job_destination.params['max_pod_retries'])
-            elif 'k8s_pod_retries' in self.runner_params:
-                max_pod_retries = int(self.runner_params['k8s_pod_retries'])
+            if "max_pod_retries" in job_destination.params:
+                max_pod_retries = int(job_destination.params["max_pod_retries"])
+            elif "k8s_pod_retries" in self.runner_params:
+                max_pod_retries = int(self.runner_params["k8s_pod_retries"])
             else:
                 max_pod_retries = 1
 
@@ -667,14 +715,14 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             # as probably this means that the k8s API server hasn't
             # had time to fill in the object status since the
             # job was created only too recently.
-            if len(job.obj['status']) == 0:
+            if len(job.obj["status"]) == 0:
                 return job_state
-            if 'succeeded' in job.obj['status']:
-                succeeded = job.obj['status']['succeeded']
-            if 'active' in job.obj['status']:
-                active = job.obj['status']['active']
-            if 'failed' in job.obj['status']:
-                failed = job.obj['status']['failed']
+            if "succeeded" in job.obj["status"]:
+                succeeded = job.obj["status"]["succeeded"]
+            if "active" in job.obj["status"]:
+                active = job.obj["status"]["active"]
+            if "failed" in job.obj["status"]:
+                failed = job.obj["status"]["failed"]
 
             job_persisted_state = job_state.job_wrapper.get_state()
 
@@ -686,11 +734,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             elif active > 0 and failed <= max_pod_retries:
                 if not job_state.running:
                     if self.__job_pending_due_to_unschedulable_pod(job_state):
-                        if self.runner_params.get('k8s_unschedulable_walltime_limit'):
-                            creation_time_str = job.obj['metadata'].get('creationTimestamp')
-                            creation_time = datetime.strptime(creation_time_str, '%Y-%m-%dT%H:%M:%SZ')
+                        if self.runner_params.get("k8s_unschedulable_walltime_limit"):
+                            creation_time_str = job.obj["metadata"].get("creationTimestamp")
+                            creation_time = datetime.strptime(creation_time_str, "%Y-%m-%dT%H:%M:%SZ")
                             elapsed_seconds = (datetime.utcnow() - creation_time).total_seconds()
-                            if elapsed_seconds > self.runner_params['k8s_unschedulable_walltime_limit']:
+                            if elapsed_seconds > self.runner_params["k8s_unschedulable_walltime_limit"]:
                                 return self._handle_unschedulable_job(job, job_state)
                             else:
                                 pass
@@ -709,7 +757,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             else:
                 return self._handle_job_failure(job, job_state)
 
-        elif len(jobs.response['items']) == 0:
+        elif len(jobs.response["items"]) == 0:
             if job_state.job_wrapper.get_job().state == model.Job.states.DELETED:
                 # Job has been deleted via stop_job and job has been deleted,
                 # cleanup and remove from watched_jobs by returning `None`
@@ -744,7 +792,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def _handle_job_failure(self, job, job_state):
         # Figure out why job has failed
-        with open(job_state.error_file, 'a') as error_file:
+        with open(job_state.error_file, "a") as error_file:
             if self.__job_failed_due_to_low_memory(job_state):
                 error_file.write("Job killed after running out of memory. Try with more memory.\n")
                 job_state.fail_message = "Tool failed due to insufficient memory. Try with more memory."
@@ -767,28 +815,29 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         return None
 
     def __cleanup_k8s_job(self, job):
-        k8s_cleanup_job = self.runner_params['k8s_cleanup_job']
+        k8s_cleanup_job = self.runner_params["k8s_cleanup_job"]
         delete_job(job, k8s_cleanup_job)
 
     def __cleanup_k8s_ingress(self, ingress, job_failed):
-        k8s_cleanup_job = self.runner_params['k8s_cleanup_job']
+        k8s_cleanup_job = self.runner_params["k8s_cleanup_job"]
         delete_ingress(ingress, k8s_cleanup_job, job_failed)
 
     def __cleanup_k8s_service(self, service, job_failed):
-        k8s_cleanup_job = self.runner_params['k8s_cleanup_job']
+        k8s_cleanup_job = self.runner_params["k8s_cleanup_job"]
         delete_service(service, k8s_cleanup_job, job_failed)
 
     def __job_failed_due_to_walltime_limit(self, job):
-        conditions = job.obj['status'].get('conditions') or []
-        return any(True for c in conditions if c['type'] == 'Failed' and c['reason'] == 'DeadlineExceeded')
+        conditions = job.obj["status"].get("conditions") or []
+        return any(True for c in conditions if c["type"] == "Failed" and c["reason"] == "DeadlineExceeded")
 
     def _get_pod_for_job(self, job_state):
-        pods = Pod.objects(self._pykube_api).filter(selector=f"app={job_state.job_id}",
-                                                    namespace=self.runner_params['k8s_namespace'])
-        if not pods.response['items']:
+        pods = Pod.objects(self._pykube_api).filter(
+            selector=f"app={job_state.job_id}", namespace=self.runner_params["k8s_namespace"]
+        )
+        if not pods.response["items"]:
             return None
 
-        pod = Pod(self._pykube_api, pods.response['items'][0])
+        pod = Pod(self._pykube_api, pods.response["items"][0])
         return pod
 
     def __job_failed_due_to_low_memory(self, job_state):
@@ -797,13 +846,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         for being out of memory (pod status OOMKilled). If that is the case
         marks the job for resubmission (resubmit logic is part of destinations).
         """
-        pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
-        if not pods.response['items']:
+        pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
+        if not pods.response["items"]:
             return False
 
         pod = self._get_pod_for_job(job_state)
-        if pod and pod.obj['status']['phase'] == "Failed" and \
-                pod.obj['status']['containerStatuses'][0]['state']['terminated']['reason'] == "OOMKilled":
+        if (
+            pod
+            and pod.obj["status"]["phase"] == "Failed"
+            and pod.obj["status"]["containerStatuses"][0]["state"]["terminated"]["reason"] == "OOMKilled"
+        ):
             return True
 
         return False
@@ -812,35 +864,40 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         """
         checks the state of the pod to see if it is unschedulable.
         """
-        pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
-        if not pods.response['items']:
+        pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
+        if not pods.response["items"]:
             return False
 
-        pod = Pod(self._pykube_api, pods.response['items'][0])
-        return is_pod_unschedulable(self._pykube_api, pod, self.runner_params['k8s_namespace'])
+        pod = Pod(self._pykube_api, pods.response["items"][0])
+        return is_pod_unschedulable(self._pykube_api, pod, self.runner_params["k8s_namespace"])
 
     def __cleanup_k8s_guest_ports(self, job_wrapper, k8s_job):
         k8s_job_prefix = self.__produce_k8s_job_prefix()
         k8s_job_name = f"{k8s_job_prefix}-{self.__force_label_conformity(job_wrapper.get_id_tag())}"
-        log.debug(f'Deleting service/ingress for job with ID {job_wrapper.get_id_tag()}')
-        job_failed = (k8s_job.obj['status']['failed'] > 0
-                      if 'failed' in k8s_job.obj['status'] else False)
-        ingress_to_delete = find_ingress_object_by_name(self._pykube_api, k8s_job_name, self.runner_params['k8s_namespace'])
-        if ingress_to_delete and len(ingress_to_delete.response['items']) > 0:
-            k8s_ingress = Ingress(self._pykube_api, ingress_to_delete.response['items'][0])
+        log.debug(f"Deleting service/ingress for job with ID {job_wrapper.get_id_tag()}")
+        job_failed = k8s_job.obj["status"]["failed"] > 0 if "failed" in k8s_job.obj["status"] else False
+        ingress_to_delete = find_ingress_object_by_name(
+            self._pykube_api, k8s_job_name, self.runner_params["k8s_namespace"]
+        )
+        if ingress_to_delete and len(ingress_to_delete.response["items"]) > 0:
+            k8s_ingress = Ingress(self._pykube_api, ingress_to_delete.response["items"][0])
             self.__cleanup_k8s_ingress(k8s_ingress, job_failed)
-        service_to_delete = find_service_object_by_name(self._pykube_api, k8s_job_name, self.runner_params['k8s_namespace'])
-        if service_to_delete and len(service_to_delete.response['items']) > 0:
-            k8s_service = Service(self._pykube_api, service_to_delete.response['items'][0])
+        service_to_delete = find_service_object_by_name(
+            self._pykube_api, k8s_job_name, self.runner_params["k8s_namespace"]
+        )
+        if service_to_delete and len(service_to_delete.response["items"]) > 0:
+            k8s_service = Service(self._pykube_api, service_to_delete.response["items"][0])
             self.__cleanup_k8s_service(k8s_service, job_failed)
 
     def stop_job(self, job_wrapper):
         """Attempts to delete a dispatched job to the k8s cluster"""
         job = job_wrapper.get_job()
         try:
-            job_to_delete = find_job_object_by_name(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace'])
-            if job_to_delete and len(job_to_delete.response['items']) > 0:
-                k8s_job = Job(self._pykube_api, job_to_delete.response['items'][0])
+            job_to_delete = find_job_object_by_name(
+                self._pykube_api, job.get_job_runner_external_id(), self.runner_params["k8s_namespace"]
+            )
+            if job_to_delete and len(job_to_delete.response["items"]) > 0:
+                k8s_job = Job(self._pykube_api, job_to_delete.response["items"][0])
                 if self.__has_guest_ports(job_wrapper):
                     self.__cleanup_k8s_guest_ports(job_wrapper, k8s_job)
                 self.__cleanup_k8s_job(k8s_job)
@@ -849,8 +906,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")
 
         except Exception as e:
-            log.exception("({}/{}) User killed running job, but error encountered during termination: {}".format(
-                job.id, job.get_job_runner_external_id(), e))
+            log.exception(
+                "({}/{}) User killed running job, but error encountered during termination: {}".format(
+                    job.id, job.get_job_runner_external_id(), e
+                )
+            )
 
     def recover(self, job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
@@ -865,14 +925,20 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         ajs.job_wrapper = job_wrapper
         ajs.job_destination = job_wrapper.job_destination
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            log.debug("({}/{}) is still in {} state, adding to the runner monitor queue".format(
-                job.id, job.job_runner_external_id, job.state))
+            log.debug(
+                "({}/{}) is still in {} state, adding to the runner monitor queue".format(
+                    job.id, job.job_runner_external_id, job.state
+                )
+            )
             ajs.old_state = model.Job.states.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
         elif job.state == model.Job.states.QUEUED:
-            log.debug("({}/{}) is still in queued state, adding to the runner monitor queue".format(
-                job.id, job.job_runner_external_id))
+            log.debug(
+                "({}/{}) is still in queued state, adding to the runner monitor queue".format(
+                    job.id, job.job_runner_external_id
+                )
+            )
             ajs.old_state = model.Job.states.QUEUED
             ajs.running = False
             self.monitor_queue.put(ajs)
@@ -880,14 +946,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
     def finish_job(self, job_state):
         self._handle_metadata_externally(job_state.job_wrapper, resolve_requirements=True)
         super().finish_job(job_state)
-        jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
-        if len(jobs.response['items']) > 1:
-            log.warning("More than one job matches selector: %s. Possible configuration error"
-                        " in job id '%s'" % (jobs.response['items'], job_state.job_id))
-        elif len(jobs.response['items']) == 0:
+        jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
+        if len(jobs.response["items"]) > 1:
+            log.warning(
+                "More than one job matches selector: %s. Possible configuration error"
+                " in job id '%s'" % (jobs.response["items"], job_state.job_id)
+            )
+        elif len(jobs.response["items"]) == 0:
             log.warning("No k8s job found which matches job id '%s'. Ignoring...", job_state.job_id)
         else:
-            job = Job(self._pykube_api, jobs.response['items'][0])
+            job = Job(self._pykube_api, jobs.response["items"][0])
             if self.__has_guest_ports(job_state.job_wrapper):
                 self.__cleanup_k8s_guest_ports(job_state.job_wrapper, job)
             self.__cleanup_k8s_job(job)
diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py
index 395ab3ceeef..c0e9cb4fdca 100644
--- a/lib/galaxy/jobs/runners/local.py
+++ b/lib/galaxy/jobs/runners/local.py
@@ -11,22 +11,20 @@ from time import sleep
 
 from galaxy import model
 from galaxy.job_execution.output_collect import default_exit_code_file
-from galaxy.util import (
-    asbool,
-)
+from galaxy.util import asbool
 from galaxy.util.commands import new_clean_env
 from . import (
     BaseJobRunner,
-    JobState
+    JobState,
 )
 from .util.process_groups import (
     check_pg,
-    kill_pg
+    kill_pg,
 )
 
 log = logging.getLogger(__name__)
 
-__all__ = ('LocalJobRunner', )
+__all__ = ("LocalJobRunner",)
 
 DEFAULT_POOL_SLEEP_TIME = 1
 # TODO: Set to false and just get rid of this option. It would simplify this
@@ -38,10 +36,11 @@ class LocalJobRunner(BaseJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "LocalRunner"
 
     def __init__(self, app, nworkers):
-        """Start the job runner """
+        """Start the job runner"""
 
         self._proc_lock = threading.Lock()
         self._procs = []
@@ -51,8 +50,7 @@ class LocalJobRunner(BaseJobRunner):
         super().__init__(app, nworkers)
 
     def __command_line(self, job_wrapper):
-        """
-        """
+        """ """
         command_line = job_wrapper.runner_command_line
 
         # slots would be cleaner name, but don't want deployers to see examples and think it
@@ -67,11 +65,11 @@ class LocalJobRunner(BaseJobRunner):
         job_file = JobState.default_job_file(job_wrapper.working_directory, job_id)
         exit_code_path = default_exit_code_file(job_wrapper.working_directory, job_id)
         job_script_props = {
-            'slots_statement': slots_statement,
-            'command': command_line,
-            'exit_code_path': exit_code_path,
-            'working_directory': job_wrapper.working_directory,
-            'shell': job_wrapper.shell,
+            "slots_statement": slots_statement,
+            "command": command_line,
+            "exit_code_path": exit_code_path,
+            "working_directory": job_wrapper.working_directory,
+            "shell": job_wrapper.shell,
         }
         job_file_contents = self.get_job_file(job_wrapper, **job_script_props)
         self.write_executable_script(job_file, job_file_contents, job_io=job_wrapper.job_io)
@@ -81,26 +79,28 @@ class LocalJobRunner(BaseJobRunner):
         if not self._prepare_job_local(job_wrapper):
             return
 
-        stderr = stdout = ''
+        stderr = stdout = ""
 
         # command line has been added to the wrapper by prepare_job()
         job_file, exit_code_path = self.__command_line(job_wrapper)
         job_id = job_wrapper.get_id_tag()
 
         try:
-            stdout_file = tempfile.NamedTemporaryFile(mode='wb+', suffix='_stdout', dir=job_wrapper.working_directory)
-            stderr_file = tempfile.NamedTemporaryFile(mode='wb+', suffix='_stderr', dir=job_wrapper.working_directory)
-            log.debug(f'({job_id}) executing job script: {job_file}')
+            stdout_file = tempfile.NamedTemporaryFile(mode="wb+", suffix="_stdout", dir=job_wrapper.working_directory)
+            stderr_file = tempfile.NamedTemporaryFile(mode="wb+", suffix="_stderr", dir=job_wrapper.working_directory)
+            log.debug(f"({job_id}) executing job script: {job_file}")
             # The preexec_fn argument of Popen() is used to call os.setpgrp() in
             # the child process just before the child is executed. This will set
             # the PGID of the child process to its PID (i.e. ensures that it is
             # the root of its own process group instead of Galaxy's one).
-            proc = subprocess.Popen(args=[job_file],
-                                    cwd=job_wrapper.working_directory,
-                                    stdout=stdout_file,
-                                    stderr=stderr_file,
-                                    env=self._environ,
-                                    preexec_fn=os.setpgrp)
+            proc = subprocess.Popen(
+                args=[job_file],
+                cwd=job_wrapper.working_directory,
+                stdout=stdout_file,
+                stderr=stderr_file,
+                env=self._environ,
+                preexec_fn=os.setpgrp,
+            )
 
             proc.terminated_by_shutdown = False
             with self._proc_lock:
@@ -133,7 +133,7 @@ class LocalJobRunner(BaseJobRunner):
             stderr = self._job_io_for_db(stderr_file)
             stdout_file.close()
             stderr_file.close()
-            log.debug(f'execution finished: {job_file}')
+            log.debug(f"execution finished: {job_file}")
         except Exception:
             log.exception("failure running job %d", job_wrapper.job_id)
             self._fail_job_local(job_wrapper, "failure running job")
@@ -152,24 +152,28 @@ class LocalJobRunner(BaseJobRunner):
         job = job_wrapper.get_job()
         job_ext_output_metadata = job.get_external_output_metadata()
         try:
-            pid = job_ext_output_metadata[0].job_runner_external_pid  # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
-            assert pid not in [None, '']
+            pid = job_ext_output_metadata[
+                0
+            ].job_runner_external_pid  # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
+            assert pid not in [None, ""]
         except Exception:
             # metadata internal or job not complete yet
             pid = job.get_job_runner_external_id()
-        if pid in [None, '']:
+        if pid in [None, ""]:
             log.warning(f"stop_job(): {job.id}: no PID in database for job, unable to stop")
             return
         pid = int(pid)
         if not check_pg(pid):
             log.warning("stop_job(): %s: Process group %d was already dead or can't be signaled" % (job.id, pid))
             return
-        log.debug('stop_job(): %s: Terminating process group %d', job.id, pid)
+        log.debug("stop_job(): %s: Terminating process group %d", job.id, pid)
         kill_pg(pid)
 
     def recover(self, job, job_wrapper):
         # local jobs can't be recovered
-        job_wrapper.change_state(model.Job.states.ERROR, info="This job was killed when Galaxy was restarted.  Please retry the job.")
+        job_wrapper.change_state(
+            model.Job.states.ERROR, info="This job was killed when Galaxy was restarted.  Please retry the job."
+        )
 
     def shutdown(self):
         super().shutdown()
@@ -223,7 +227,7 @@ class LocalJobRunner(BaseJobRunner):
                 limit_state = job_wrapper.check_limits(runtime=datetime.datetime.now() - job_start)
                 if limit_state is not None:
                     job_wrapper.fail(limit_state[1])
-                    log.debug('(%s) Terminating process group %d', job_id, pgid)
+                    log.debug("(%s) Terminating process group %d", job_id, pgid)
                     kill_pg(pgid)
                     return True
             else:
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 5cf1871bda8..72e0876d39e 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -6,27 +6,30 @@ from datetime import timedelta
 
 try:
     import pbs
+
     PBS_IMPORT_MESSAGE = None
 except ImportError as exc:
     pbs = None
-    PBS_IMPORT_MESSAGE = ('The Python pbs-python package is required to use '
-                          'this feature, please install it or correct the '
-                          'following error:\nImportError %s' % str(exc))
+    PBS_IMPORT_MESSAGE = (
+        "The Python pbs-python package is required to use "
+        "this feature, please install it or correct the "
+        "following error:\nImportError %s" % str(exc)
+    )
 
 from galaxy import (
     model,
-    util
+    util,
 )
 from galaxy.jobs import JobDestination
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
-    AsynchronousJobState
+    AsynchronousJobState,
 )
 from galaxy.util.bunch import Bunch
 
 log = logging.getLogger(__name__)
 
-__all__ = ('PBSJobRunner', )
+__all__ = ("PBSJobRunner",)
 
 CLUSTER_ERROR_MESSAGE = "Job cannot be completed due to a cluster error, please retry it later: %s"
 
@@ -43,26 +46,26 @@ mkdir -p %s
 """
 
 PBS_ARGMAP = {
-    'destination': '-q',
-    'Execution_Time': '-a',
-    'Account_Name': '-A',
-    'Checkpoint': '-c',
-    'Error_Path': '-e',
-    'Group_List': '-g',
-    'Hold_Types': '-h',
-    'Join_Paths': '-j',
-    'Keep_Files': '-k',
-    'Resource_List': '-l',
-    'Mail_Points': '-m',
-    'Mail_Users': '-M',
-    'Job_Name': '-N',
-    'Output_Path': '-o',
-    'Priority': '-p',
-    'Rerunable': '-r',
-    'Shell_Path_List': '-S',
-    'job_array_request': '-t',
-    'User_List': '-u',
-    'Variable_List': '-v',
+    "destination": "-q",
+    "Execution_Time": "-a",
+    "Account_Name": "-A",
+    "Checkpoint": "-c",
+    "Error_Path": "-e",
+    "Group_List": "-g",
+    "Hold_Types": "-h",
+    "Join_Paths": "-j",
+    "Keep_Files": "-k",
+    "Resource_List": "-l",
+    "Mail_Points": "-m",
+    "Mail_Users": "-M",
+    "Job_Name": "-N",
+    "Output_Path": "-o",
+    "Priority": "-p",
+    "Rerunable": "-r",
+    "Shell_Path_List": "-S",
+    "job_array_request": "-t",
+    "User_List": "-u",
+    "Variable_List": "-v",
 }
 
 # From pbs' pbs_job.h
@@ -87,18 +90,21 @@ class PBSJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "PBSRunner"
 
     def __init__(self, app, nworkers):
-        """Start the job runner """
+        """Start the job runner"""
         # Check if PBS was importable, fail if not
         assert pbs is not None, PBS_IMPORT_MESSAGE
         if app.config.pbs_application_server and app.config.outputs_to_working_directory:
-            raise Exception("pbs_application_server (file staging) and outputs_to_working_directory options are mutually exclusive")
+            raise Exception(
+                "pbs_application_server (file staging) and outputs_to_working_directory options are mutually exclusive"
+            )
 
         # Set the default server during startup
         self.__default_pbs_server = None
-        self.default_pbs_server     # this is a method with a property decorator, so this causes the default server to be set
+        self.default_pbs_server  # this is a method with a property decorator, so this causes the default server to be set
 
         # Proceed with general initialization
         super().__init__(app, nworkers)
@@ -119,23 +125,23 @@ class PBSJobRunner(AsynchronousJobRunner):
         # Determine the the PBS server
         url_split = url.split("/")
         server = url_split[2]
-        if server == '':
+        if server == "":
             server = self.default_pbs_server
         if server is None:
             raise Exception("Could not find TORQUE server")
 
         # Determine the queue, set the PBS destination (not the same thing as a Galaxy job destination)
-        pbs_destination = f'@{server}'
+        pbs_destination = f"@{server}"
         pbs_queue = url_split[3] or None
         if pbs_queue is not None:
-            pbs_destination = f'{pbs_queue}{pbs_destination}'
+            pbs_destination = f"{pbs_queue}{pbs_destination}"
 
         params = dict(destination=pbs_destination)
 
         # Determine the args (long-format args were never supported in URLs so they are not supported here)
         try:
-            opts = url.split('/')[4].strip().lstrip('-').split(' -')
-            assert opts != ['']
+            opts = url.split("/")[4].strip().lstrip("-").split(" -")
+            assert opts != [""]
             # stripping the - comes later (in parse_destination_params)
             for i, opt in enumerate(opts):
                 opts[i] = f"-{opt}"
@@ -148,7 +154,7 @@ class PBSJobRunner(AsynchronousJobRunner):
         log.debug(f"Converted URL '{url}' to destination runner=pbs, params={params}")
 
         # Create a dynamic JobDestination
-        return JobDestination(runner='pbs', params=params)
+        return JobDestination(runner="pbs", params=params)
 
     def parse_destination_params(self, params):
         """A wrapper method around __args_to_attrs() that allow administrators to define PBS
@@ -160,12 +166,12 @@ class PBSJobRunner(AsynchronousJobRunner):
         args = {}
         for arg, value in params.items():
             try:
-                if not arg.startswith('-'):
+                if not arg.startswith("-"):
                     arg = PBS_ARGMAP[arg]
-                arg = arg.lstrip('-')
+                arg = arg.lstrip("-")
                 args[arg] = value
             except Exception:
-                log.warning(f'Unrecognized long argument in destination params: {arg}')
+                log.warning(f"Unrecognized long argument in destination params: {arg}")
         return self.__args_to_attrs(args)
 
     # Internal stuff
@@ -176,9 +182,9 @@ class PBSJobRunner(AsynchronousJobRunner):
         """
         rval = []
         for arg, value in args.items():
-            if arg == 'l':
-                resource_attrs = value.split(',')
-                for res, val in [a.split('=', 1) for a in resource_attrs]:
+            if arg == "l":
+                resource_attrs = value.split(",")
+                for res, val in [a.split("=", 1) for a in resource_attrs]:
                     rval.append(dict(name=pbs.ATTR_l, value=val, resource=res))
             else:
                 try:
@@ -190,12 +196,12 @@ class PBSJobRunner(AsynchronousJobRunner):
     def __get_pbs_server(self, job_destination_params):
         if job_destination_params is None:
             return None
-        return job_destination_params['destination'].split('@')[-1]
+        return job_destination_params["destination"].split("@")[-1]
 
     def queue_job(self, job_wrapper):
         """Create PBS script for a job and submit it to the PBS queue"""
         # prepare the job
-        if not self.prepare_job(job_wrapper, include_metadata=not(self.app.config.pbs_stage_path)):
+        if not self.prepare_job(job_wrapper, include_metadata=not (self.app.config.pbs_stage_path)):
             return
 
         job_destination = job_wrapper.job_destination
@@ -204,25 +210,25 @@ class PBSJobRunner(AsynchronousJobRunner):
         pbs_queue_name = None
         pbs_server_name = self.default_pbs_server
         pbs_options = []
-        if '-q' in job_destination.params and 'destination' not in job_destination.params:
-            job_destination.params['destination'] = job_destination.params.pop('-q')
-        if 'destination' in job_destination.params:
-            if '@' in job_destination.params['destination']:
+        if "-q" in job_destination.params and "destination" not in job_destination.params:
+            job_destination.params["destination"] = job_destination.params.pop("-q")
+        if "destination" in job_destination.params:
+            if "@" in job_destination.params["destination"]:
                 # Destination includes a server
-                pbs_queue_name, pbs_server_name = job_destination.params['destination'].split('@')
-                if pbs_queue_name == '':
+                pbs_queue_name, pbs_server_name = job_destination.params["destination"].split("@")
+                if pbs_queue_name == "":
                     # e.g. `qsub -q @server`
                     pbs_queue_name = None
             else:
                 # Destination is just a queue
-                pbs_queue_name = job_destination.params['destination']
-            job_destination.params.pop('destination')
+                pbs_queue_name = job_destination.params["destination"]
+            job_destination.params.pop("destination")
 
         # Parse PBS params
         pbs_options = self.parse_destination_params(job_destination.params)
 
         # Explicitly set the determined PBS destination in the persisted job destination for recovery
-        job_destination.params['destination'] = f"{pbs_queue_name or ''}@{pbs_server_name}"
+        job_destination.params["destination"] = f"{pbs_queue_name or ''}@{pbs_server_name}"
 
         c = pbs.pbs_connect(util.smart_str(pbs_server_name))
         if c <= 0:
@@ -263,16 +269,16 @@ class PBSJobRunner(AsynchronousJobRunner):
         attrs.append(dict(name=pbs.ATTR_N, value=str(f"{job_wrapper.job_id}_{job_wrapper.tool.id}_{job_wrapper.user}")))
         job_attrs = pbs.new_attropl(len(attrs) + len(pbs_options))
         for i, attr in enumerate(attrs + pbs_options):
-            job_attrs[i].name = attr['name']
-            job_attrs[i].value = attr['value']
-            if 'resource' in attr:
-                job_attrs[i].resource = attr['resource']
+            job_attrs[i].name = attr["name"]
+            job_attrs[i].value = attr["value"]
+            if "resource" in attr:
+                job_attrs[i].resource = attr["resource"]
         exec_dir = os.path.abspath(job_wrapper.working_directory)
 
         # write the job script
-        if self.app.config.pbs_stage_path != '':
+        if self.app.config.pbs_stage_path != "":
             # touch the ecfile so that it gets staged
-            with open(ecfile, 'a'):
+            with open(ecfile, "a"):
                 os.utime(ecfile, None)
 
             stage_commands = pbs_symlink_template % (
@@ -281,10 +287,12 @@ class PBSJobRunner(AsynchronousJobRunner):
                 exec_dir,
             )
         else:
-            stage_commands = ''
+            stage_commands = ""
 
         env_setup_commands = [stage_commands]
-        script = self.get_job_file(job_wrapper, exit_code_path=ecfile, env_setup_commands=env_setup_commands, shell=job_wrapper.shell)
+        script = self.get_job_file(
+            job_wrapper, exit_code_path=ecfile, env_setup_commands=env_setup_commands, shell=job_wrapper.shell
+        )
         job_file = f"{self.app.config.cluster_files_directory}/{job_wrapper.job_id}.sh"
         self.write_executable_script(job_file, script, job_io=job_wrapper.job_io)
         # job was deleted while we were preparing it
@@ -333,7 +341,7 @@ class PBSJobRunner(AsynchronousJobRunner):
         job_state.output_file = ofile
         job_state.error_file = efile
         job_state.exit_code_file = ecfile
-        job_state.old_state = 'N'
+        job_state.old_state = "N"
         job_state.running = False
         job_state.job_destination = job_destination
 
@@ -365,7 +373,9 @@ class PBSJobRunner(AsynchronousJobRunner):
                 try:
                     # Recheck to make sure it wasn't a communication problem
                     self.check_single_job(pbs_server_name, job_id)
-                    log.warning(f"({galaxy_job_id}/{job_id}) PBS job was not in state check list, but was found with individual state check")
+                    log.warning(
+                        f"({galaxy_job_id}/{job_id}) PBS job was not in state check list, but was found with individual state check"
+                    )
                     new_watched.append(pbs_job_state)
                 except Exception:
                     errno, text = pbs.error()
@@ -375,7 +385,9 @@ class PBSJobRunner(AsynchronousJobRunner):
                         self.work_queue.put((self.finish_job, pbs_job_state))
                     else:
                         # Unhandled error, continue to monitor
-                        log.info("(%s/%s) PBS state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text))
+                        log.info(
+                            "(%s/%s) PBS state check resulted in error (%d): %s" % (galaxy_job_id, job_id, errno, text)
+                        )
                         new_watched.append(pbs_job_state)
                 continue
             if status.job_state != old_state:
@@ -383,9 +395,9 @@ class PBSJobRunner(AsynchronousJobRunner):
             if status.job_state == "R" and not pbs_job_state.running:
                 pbs_job_state.running = True
                 pbs_job_state.job_wrapper.change_state(model.Job.states.RUNNING)
-            if status.job_state == "R" and status.get('resources_used', False):
+            if status.job_state == "R" and status.get("resources_used", False):
                 # resources_used may not be in the status for new jobs
-                h, m, s = (int(i) for i in status.resources_used.walltime.split(':'))
+                h, m, s = (int(i) for i in status.resources_used.walltime.split(":"))
                 runtime = timedelta(0, s, 0, 0, m, h)
                 if pbs_job_state.check_limits(runtime=runtime):
                     self.work_queue.put((self.fail_job, pbs_job_state))
@@ -393,13 +405,16 @@ class PBSJobRunner(AsynchronousJobRunner):
             elif status.job_state == "C":
                 # "keep_completed" is enabled in PBS, so try to check exit status
                 try:
-                    assert int(status.exit_status) == 0 or pbs_job_state.job_wrapper.get_state() == model.Job.states.STOPPED
+                    assert (
+                        int(status.exit_status) == 0
+                        or pbs_job_state.job_wrapper.get_state() == model.Job.states.STOPPED
+                    )
                     log.debug(f"({galaxy_job_id}/{job_id}) PBS job has completed successfully")
                 except AssertionError:
                     exit_status = int(status.exit_status)
-                    error_message = JOB_EXIT_STATUS.get(exit_status, f'Unknown error: {status.exit_status}')
+                    error_message = JOB_EXIT_STATUS.get(exit_status, f"Unknown error: {status.exit_status}")
                     pbs_job_state.fail_message = CLUSTER_ERROR_MESSAGE % error_message
-                    log.error(f'({galaxy_job_id}/{job_id}) PBS job failed: {error_message}')
+                    log.error(f"({galaxy_job_id}/{job_id}) PBS job failed: {error_message}")
                     pbs_job_state.stop_job = False
                     self.work_queue.put((self.fail_job, pbs_job_state))
                     continue
@@ -440,7 +455,7 @@ class PBSJobRunner(AsynchronousJobRunner):
             jobs = pbs.pbs_statjob(c, None, stat_attrl, None)
             pbs.pbs_disconnect(c)
             statuses.update(self.convert_statjob_to_bunches(jobs))
-        return((failures, statuses))
+        return (failures, statuses)
 
     def convert_statjob_to_bunches(self, statjob_out):
         statuses = {}
@@ -481,15 +496,22 @@ class PBSJobRunner(AsynchronousJobRunner):
             self.stop_job(pbs_job_state.job_wrapper)
         pbs_job_state.job_wrapper.fail(pbs_job_state.fail_message)
         if pbs_job_state.job_wrapper.cleanup_job == "always":
-            self.cleanup((pbs_job_state.output_file, pbs_job_state.error_file, pbs_job_state.exit_code_file, pbs_job_state.job_file))
+            self.cleanup(
+                (
+                    pbs_job_state.output_file,
+                    pbs_job_state.error_file,
+                    pbs_job_state.exit_code_file,
+                    pbs_job_state.job_file,
+                )
+            )
 
     def get_stage_in_out(self, fnames, symlink=False):
         """Convenience function to create a stagein/stageout list"""
-        stage = ''
+        stage = ""
         for fname in fnames:
             if os.access(fname, os.R_OK):
                 if stage:
-                    stage += ','
+                    stage += ","
                 # pathnames are now absolute
                 if symlink and self.app.config.pbs_stage_path:
                     stage_name = os.path.join(self.app.config.pbs_stage_path, os.path.split(fname)[1])
@@ -501,7 +523,7 @@ class PBSJobRunner(AsynchronousJobRunner):
     def stop_job(self, job_wrapper):
         """Attempts to delete a job from the PBS queue"""
         job = job_wrapper.get_job()
-        job_id = job.get_job_runner_external_id().encode('utf-8')
+        job_id = job.get_job_runner_external_id().encode("utf-8")
         job_tag = f"({job.get_id_tag()}/{job_id})"
         log.debug(f"{job_tag} Stopping PBS job")
 
@@ -511,21 +533,20 @@ class PBSJobRunner(AsynchronousJobRunner):
         try:
             pbs_server_name = self.__get_pbs_server(job.destination_params)
             if pbs_server_name is None:
-                log.debug("(%s) Job queued but no destination stored in job params, cannot delete"
-                          % job_tag)
+                log.debug("(%s) Job queued but no destination stored in job params, cannot delete" % job_tag)
                 return
             c = pbs.pbs_connect(util.smart_str(pbs_server_name))
             if c <= 0:
                 log.debug(f"({job_tag}) Connection to PBS server for job delete failed")
                 return
-            pbs.pbs_deljob(c, job_id, '')
+            pbs.pbs_deljob(c, job_id, "")
             log.debug(f"{job_tag} Removed from PBS queue before job completion")
         except Exception:
             e = traceback.format_exc()
             log.debug(f"{job_tag} Unable to stop job: {e}")
         finally:
             # Cleanup: disconnect from the server.
-            if (None is not c):
+            if None is not c:
                 pbs.pbs_disconnect(c)
 
     def recover(self, job, job_wrapper):
@@ -542,12 +563,16 @@ class PBSJobRunner(AsynchronousJobRunner):
         job_wrapper.command_line = job.command_line
         pbs_job_state.job_wrapper = job_wrapper
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the PBS queue")
-            pbs_job_state.old_state = 'R'
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the PBS queue"
+            )
+            pbs_job_state.old_state = "R"
             pbs_job_state.running = True
             self.monitor_queue.put(pbs_job_state)
         elif job.state == model.Job.states.QUEUED:
-            log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in PBS queued state, adding to the PBS queue")
-            pbs_job_state.old_state = 'Q'
+            log.debug(
+                f"({job.id}/{job.get_job_runner_external_id()}) is still in PBS queued state, adding to the PBS queue"
+            )
+            pbs_job_state.old_state = "Q"
             pbs_job_state.running = False
             self.monitor_queue.put(pbs_job_state)
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 9132ef9ea12..22b72282110 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -21,13 +21,16 @@ from pulsar.client import (
     ClientJobDescription,
     ClientOutputs,
     EXTENDED_METADATA_DYNAMIC_COLLECTION_PATTERN,
-    finish_job as pulsar_finish_job,
+)
+from pulsar.client import finish_job as pulsar_finish_job
+from pulsar.client import (
     PathMapper,
     PulsarClientTransportError,
     PulsarOutputs,
-    submit_job as pulsar_submit_job,
-    url_to_destination_params
 )
+from pulsar.client import submit_job as pulsar_submit_job
+from pulsar.client import url_to_destination_params
+
 # TODO: Perform pulsar release with this included in the client package
 from pulsar.client.staging import DEFAULT_DYNAMIC_COLLECTION_PATTERN
 
@@ -37,30 +40,30 @@ from galaxy.jobs import JobDestination
 from galaxy.jobs.command_factory import build_command
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
-    AsynchronousJobState
+    AsynchronousJobState,
 )
 from galaxy.tool_util.deps import dependencies
 from galaxy.util import (
     galaxy_directory,
     specs,
-    string_as_bool_or_none
+    string_as_bool_or_none,
 )
 from galaxy.util.bunch import Bunch
 
 log = logging.getLogger(__name__)
 
 __all__ = (
-    'PulsarLegacyJobRunner',
-    'PulsarRESTJobRunner',
-    'PulsarMQJobRunner',
-    'PulsarEmbeddedJobRunner',
-    'PulsarEmbeddedMQJobRunner',
+    "PulsarLegacyJobRunner",
+    "PulsarRESTJobRunner",
+    "PulsarMQJobRunner",
+    "PulsarEmbeddedJobRunner",
+    "PulsarEmbeddedMQJobRunner",
 )
 
 MINIMUM_PULSAR_VERSIONS = {
-    '_default_': packaging.version.parse("0.7.0.dev3"),
-    'remote_metadata': packaging.version.parse("0.8.0"),
-    'remote_container_handling': packaging.version.parse("0.9.1.dev0")  # probably 0.10 ultimately?
+    "_default_": packaging.version.parse("0.7.0.dev3"),
+    "remote_metadata": packaging.version.parse("0.8.0"),
+    "remote_container_handling": packaging.version.parse("0.9.1.dev0"),  # probably 0.10 ultimately?
 }
 
 NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory."
@@ -76,11 +79,7 @@ UPGRADE_PULSAR_ERROR = "Galaxy is misconfigured, please contact administrator. T
 DEFAULT_GALAXY_URL = "http://localhost:8080"
 
 PULSAR_PARAM_SPECS = dict(
-    transport=dict(
-        map=specs.to_str_or_none,
-        valid=specs.is_in("urllib", "curl", None),
-        default=None
-    ),
+    transport=dict(map=specs.to_str_or_none, valid=specs.is_in("urllib", "curl", None), default=None),
     transport_timeout=dict(
         map=lambda val: None if val == "None" else int(val),
         default=None,
@@ -116,10 +115,7 @@ PULSAR_PARAM_SPECS = dict(
         map=specs.to_str_or_none,
         default=None,
     ),
-    amqp_acknowledge=dict(
-        map=specs.to_bool_or_none,
-        default=None
-    ),
+    amqp_acknowledge=dict(map=specs.to_bool_or_none, default=None),
     amqp_ack_republish_time=dict(
         map=lambda val: None if val == "None" else int(val),
         default=None,
@@ -186,7 +182,7 @@ PARAMETER_SPECIFICATION_IGNORED = object()
 class PulsarJobRunner(AsynchronousJobRunner):
     """Base class for pulsar job runners."""
 
-    start_methods = ['_init_worker_threads', '_init_client_manager', '_monitor']
+    start_methods = ["_init_worker_threads", "_init_client_manager", "_monitor"]
     runner_name = "PulsarJobRunner"
     default_build_pulsar_app = False
     use_mq = False
@@ -215,14 +211,14 @@ class PulsarJobRunner(AsynchronousJobRunner):
             self._init_noop_monitor()
 
     def _init_client_manager(self):
-        pulsar_conf = self.runner_params.get('pulsar_app_config', None)
+        pulsar_conf = self.runner_params.get("pulsar_app_config", None)
         pulsar_conf_file = None
         if pulsar_conf is None:
-            pulsar_conf_file = self.runner_params.get('pulsar_config', None)
+            pulsar_conf_file = self.runner_params.get("pulsar_config", None)
         self.__init_pulsar_app(pulsar_conf, pulsar_conf_file)
 
         client_manager_kwargs = {}
-        for kwd in 'manager', 'cache', 'transport', 'persistence_directory':
+        for kwd in "manager", "cache", "transport", "persistence_directory":
             client_manager_kwargs[kwd] = self.runner_params[kwd]
         if self.pulsar_app is not None:
             client_manager_kwargs["pulsar_app"] = self.pulsar_app
@@ -231,7 +227,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             client_manager_kwargs["file_cache"] = None
 
         for kwd in self.runner_params.keys():
-            if kwd.startswith('amqp_') or kwd.startswith('transport_'):
+            if kwd.startswith("amqp_") or kwd.startswith("transport_"):
                 client_manager_kwargs[kwd] = self.runner_params[kwd]
         self.client_manager = build_client_manager(**client_manager_kwargs)
 
@@ -269,7 +265,11 @@ class PulsarJobRunner(AsynchronousJobRunner):
             if len(guest_ports) > 0:
                 persisted_state = job_wrapper.get_state()
                 if persisted_state in model.Job.terminal_states + [model.Job.states.DELETED_NEW]:
-                    log.debug("(%s) Watched job in terminal state, will stop monitoring: %s", job_state.job_id, persisted_state)
+                    log.debug(
+                        "(%s) Watched job in terminal state, will stop monitoring: %s",
+                        job_state.job_id,
+                        persisted_state,
+                    )
                     job_state = None
                 elif persisted_state == model.Job.states.RUNNING:
                     client = self.get_client_from_state(job_state)
@@ -304,7 +304,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
         return job_state
 
     def _update_job_state_for_status(self, job_state, pulsar_status, full_status=None):
-        log.debug('(%s) Received status update: %s %s', job_state.job_id, type(pulsar_status), pulsar_status)
+        log.debug("(%s) Received status update: %s %s", job_state.job_id, type(pulsar_status), pulsar_status)
         if pulsar_status in ["complete", "cancelled"] or job_state.job_wrapper.get_state() == model.Job.states.STOPPED:
             self.mark_as_finished(job_state)
             return None
@@ -325,7 +325,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
         job_destination = job_wrapper.job_destination
         self._populate_parameter_defaults(job_destination)
 
-        command_line, client, remote_job_config, compute_environment, remote_container = self.__prepare_job(job_wrapper, job_destination)
+        command_line, client, remote_job_config, compute_environment, remote_container = self.__prepare_job(
+            job_wrapper, job_destination
+        )
 
         if not command_line:
             return
@@ -348,15 +350,21 @@ class PulsarJobRunner(AsynchronousJobRunner):
                         "dataset_uuid": str(input_dataset_wrapper.dataset_uuid),
                         "object_store_id": input_dataset_wrapper.object_store_id,
                     }
-                    client_inputs_list.append(ClientInput(path, CLIENT_INPUT_PATH_TYPES.INPUT_PATH, object_store_ref=object_store_ref))
+                    client_inputs_list.append(
+                        ClientInput(path, CLIENT_INPUT_PATH_TYPES.INPUT_PATH, object_store_ref=object_store_ref)
+                    )
 
                 for input_extra_path in compute_environment.path_rewrites_input_extra.keys():
                     # TODO: track dataset for object_Store_ref...
-                    client_inputs_list.append(ClientInput(input_extra_path, CLIENT_INPUT_PATH_TYPES.INPUT_EXTRA_FILES_PATH))
+                    client_inputs_list.append(
+                        ClientInput(input_extra_path, CLIENT_INPUT_PATH_TYPES.INPUT_EXTRA_FILES_PATH)
+                    )
 
                 for input_metadata_path in compute_environment.path_rewrites_input_metadata.keys():
                     # TODO: track dataset for object_Store_ref...
-                    client_inputs_list.append(ClientInput(input_metadata_path, CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH))
+                    client_inputs_list.append(
+                        ClientInput(input_metadata_path, CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH)
+                    )
 
                 input_files = None
                 client_inputs = ClientInputs(client_inputs_list)
@@ -436,8 +444,8 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     def __needed_features(self, client):
         return {
-            'remote_metadata': PulsarJobRunner.__remote_metadata(client),
-            'remote_container_handling': PulsarJobRunner.__remote_container_handling(client),
+            "remote_metadata": PulsarJobRunner.__remote_metadata(client),
+            "remote_container_handling": PulsarJobRunner.__remote_container_handling(client),
         }
 
     def __prepare_job(self, job_wrapper, job_destination):
@@ -466,17 +474,17 @@ class PulsarJobRunner(AsynchronousJobRunner):
             prepare_kwds = {}
             if rewrite_parameters:
                 compute_environment = PulsarComputeEnvironment(client, job_wrapper, remote_job_config)
-                prepare_kwds['compute_environment'] = compute_environment
+                prepare_kwds["compute_environment"] = compute_environment
             job_wrapper.prepare(**prepare_kwds)
             self.__prepare_input_files_locally(job_wrapper)
             remote_metadata = PulsarJobRunner.__remote_metadata(client)
             dependency_resolution = PulsarJobRunner.__dependency_resolution(client)
             metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config)
-            remote_working_directory = remote_job_config['working_directory']
+            remote_working_directory = remote_job_config["working_directory"]
             remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir))
             remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files"))
             remote_command_params = dict(
-                working_directory=remote_job_config['metadata_directory'],
+                working_directory=remote_job_config["metadata_directory"],
                 script_directory=remote_job_directory,
                 metadata_kwds=metadata_kwds,
                 dependency_resolution=dependency_resolution,
@@ -525,7 +533,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     def __prepare_input_files_locally(self, job_wrapper):
         """Run task splitting commands locally."""
-        prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None)
+        prepare_input_files_cmds = getattr(job_wrapper, "prepare_input_files_cmds", None)
         if prepare_input_files_cmds is not None:
             for cmd in prepare_input_files_cmds:  # run the commands to stage the input files
                 subprocess.check_call(cmd, shell=True)
@@ -558,7 +566,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     def get_output_files(self, job_wrapper):
         output_paths = job_wrapper.job_io.get_output_fnames()
-        return [str(o) for o in output_paths]   # Force job_path from DatasetPath objects.
+        return [str(o) for o in output_paths]  # Force job_path from DatasetPath objects.
 
     def get_input_files(self, job_wrapper):
         input_paths = job_wrapper.job_io.get_input_paths()
@@ -566,7 +574,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     def get_client_from_wrapper(self, job_wrapper):
         job_id = job_wrapper.job_id
-        if hasattr(job_wrapper, 'task_id'):
+        if hasattr(job_wrapper, "task_id"):
             job_id = f"{job_id}_{job_wrapper.task_id}"
         params = job_wrapper.job_destination.params.copy()
         user = job_wrapper.get_job().user
@@ -592,33 +600,23 @@ class PulsarJobRunner(AsynchronousJobRunner):
         job_key = self.app.security.encode_id(job_id, kind="jobs_files")
         endpoint_base = "%s/api/jobs/%s/files?job_key=%s"
         if self.app.config.nginx_upload_job_files_path:
-            endpoint_base = "%s" + \
-                            self.app.config.nginx_upload_job_files_path + \
-                            "?job_id=%s&job_key=%s"
-        files_endpoint = endpoint_base % (
-            self.galaxy_url,
-            encoded_job_id,
-            job_key
-        )
-        get_client_kwds = dict(
-            job_id=str(job_id),
-            files_endpoint=files_endpoint,
-            env=env
-        )
+            endpoint_base = "%s" + self.app.config.nginx_upload_job_files_path + "?job_id=%s&job_key=%s"
+        files_endpoint = endpoint_base % (self.galaxy_url, encoded_job_id, job_key)
+        get_client_kwds = dict(job_id=str(job_id), files_endpoint=files_endpoint, env=env)
         # Turn MutableDict into standard dict for pulsar consumption
         job_destination_params = dict(job_destination_params.items())
         return self.client_manager.get_client(job_destination_params, **get_client_kwds)
 
     def finish_job(self, job_state):
-        stderr = stdout = ''
+        stderr = stdout = ""
         job_wrapper = job_state.job_wrapper
         try:
             client = self.get_client_from_state(job_state)
             run_results = client.full_status()
             remote_metadata_directory = run_results.get("metadata_directory", None)
-            stdout = run_results.get('stdout', '')
-            stderr = run_results.get('stderr', '')
-            exit_code = run_results.get('returncode', None)
+            stdout = run_results.get("stdout", "")
+            stderr = run_results.get("stderr", "")
+            exit_code = run_results.get("returncode", None)
             pulsar_outputs = PulsarOutputs.from_status_response(run_results)
             job_state = job_wrapper.get_state()
             # Use Pulsar client code to transfer/copy files back
@@ -630,14 +628,18 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 exit_code = 0
             cleanup_job = job_wrapper.cleanup_job
             client_outputs = self.__client_outputs(client, job_wrapper)
-            finish_args = dict(client=client,
-                               job_completed_normally=completed_normally,
-                               cleanup_job=cleanup_job,
-                               client_outputs=client_outputs,
-                               pulsar_outputs=pulsar_outputs)
+            finish_args = dict(
+                client=client,
+                job_completed_normally=completed_normally,
+                cleanup_job=cleanup_job,
+                client_outputs=client_outputs,
+                pulsar_outputs=pulsar_outputs,
+            )
             failed = pulsar_finish_job(**finish_args)
             if failed:
-                job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True)
+                job_wrapper.fail(
+                    "Failed to find or download one or more job outputs from remote server.", exception=True
+                )
         except Exception:
             self.fail_job(job_state, message=GENERIC_REMOTE_ERROR, exception=True)
             log.exception("failure finishing job %d", job_wrapper.job_id)
@@ -650,7 +652,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
             # Following check is a hack for jobs started during 19.01 or earlier release
             # and finishing with a 19.05 code base. Eliminate the hack in 19.09 or later
             # along with hacks for legacy metadata compute strategy.
-            if not os.path.exists(job_metrics_directory) or not any("__instrument" in f for f in os.listdir(job_metrics_directory)):
+            if not os.path.exists(job_metrics_directory) or not any(
+                "__instrument" in f for f in os.listdir(job_metrics_directory)
+            ):
                 job_metrics_directory = job_wrapper.working_directory
             job_wrapper.finish(
                 stdout,
@@ -671,10 +675,11 @@ class PulsarJobRunner(AsynchronousJobRunner):
         if full_status:
             stdout = full_status.get("stdout", "")
             stderr = full_status.get("stderr", "")
-        self._handle_runner_state('failure', job_state)
+        self._handle_runner_state("failure", job_state)
         if not job_state.runner_state_handled:
-            job_state.job_wrapper.fail(getattr(job_state, "fail_message", message),
-                                       tool_stdout=stdout, tool_stderr=stderr, exception=exception)
+            job_state.job_wrapper.fail(
+                getattr(job_state, "fail_message", message), tool_stdout=stdout, tool_stderr=stderr, exception=exception
+            )
 
     def check_pid(self, pid):
         try:
@@ -684,7 +689,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
             if e.errno == errno.ESRCH:
                 log.debug("check_pid(): PID %d is dead" % pid)
             else:
-                log.warning("check_pid(): Got errno %s when attempting to check PID %d: %s" % (errno.errorcode[e.errno], pid, e.strerror))
+                log.warning(
+                    "check_pid(): Got errno %s when attempting to check PID %d: %s"
+                    % (errno.errorcode[e.errno], pid, e.strerror)
+                )
             return False
 
     def stop_job(self, job_wrapper):
@@ -695,8 +703,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
         client = self.get_client(job.destination_params, job.job_runner_external_id)
         job_ext_output_metadata = job.get_external_output_metadata()
         if not PulsarJobRunner.__remote_metadata(client) and job_ext_output_metadata:
-            pid = job_ext_output_metadata[0].job_runner_external_pid  # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
-            if pid in [None, '']:
+            pid = job_ext_output_metadata[
+                0
+            ].job_runner_external_pid  # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
+            if pid in [None, ""]:
                 log.warning(f"stop_job(): {job.id}: no PID in database for job, unable to stop")
                 return
             pid = int(pid)
@@ -707,7 +717,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 try:
                     os.killpg(pid, sig)
                 except OSError as e:
-                    log.warning("stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % (job.id, errno.errorcode[e.errno], sig, pid, e.strerror))
+                    log.warning(
+                        "stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s"
+                        % (job.id, errno.errorcode[e.errno], sig, pid, e.strerror)
+                    )
                     return  # give up
                 sleep(2)
                 if not self.check_pid(pid):
@@ -753,7 +766,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     def __client_outputs(self, client, job_wrapper):
         metadata_directory = os.path.join(job_wrapper.working_directory, "metadata")
-        metadata_strategy = job_wrapper.get_destination_configuration('metadata_strategy', None)
+        metadata_strategy = job_wrapper.get_destination_configuration("metadata_strategy", None)
         tool = job_wrapper.tool
         tool_provided_metadata_file_path = tool.provided_metadata_file
         tool_provided_metadata_style = tool.provided_metadata_style
@@ -775,7 +788,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
             output_files = self.get_output_files(job_wrapper)
             work_dir_outputs = self.get_work_dir_outputs(job_wrapper)
         dynamic_file_sources = [
-            {"path": tool_provided_metadata_file_path, "type": "galaxy" if tool_provided_metadata_style == "default" else "legacy_galaxy"}
+            {
+                "path": tool_provided_metadata_file_path,
+                "type": "galaxy" if tool_provided_metadata_style == "default" else "legacy_galaxy",
+            }
         ]
         client_outputs = ClientOutputs(
             working_directory=job_wrapper.tool_working_directory,
@@ -792,10 +808,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
     def check_job_config(remote_job_config, check_features=None):
         check_features = check_features or {}
         # 0.6.0 was newest Pulsar version that did not report it's version.
-        pulsar_version = packaging.version.parse(remote_job_config.get('pulsar_version', "0.6.0"))
+        pulsar_version = packaging.version.parse(remote_job_config.get("pulsar_version", "0.6.0"))
         needed_version = packaging.version.parse("0.0.0")
         log.info(f"pulsar_version is {pulsar_version}")
-        for feature, needed in list(check_features.items()) + [('_default_', True)]:
+        for feature, needed in list(check_features.items()) + [("_default_", True)]:
             if not needed:
                 continue
             if pulsar_version < MINIMUM_PULSAR_VERSIONS[feature]:
@@ -830,7 +846,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     @staticmethod
     def __remote_container_handling(pulsar_client):
-        remote_container_handling = string_as_bool_or_none(pulsar_client.destination_params.get("remote_container_handling", False))
+        remote_container_handling = string_as_bool_or_none(
+            pulsar_client.destination_params.get("remote_container_handling", False)
+        )
         return remote_container_handling
 
     @staticmethod
@@ -848,7 +866,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
         there is no guarentee that it will contain all the datatypes available
         to this Galaxy.
         """
-        use_remote_datatypes = string_as_bool_or_none(pulsar_client.destination_params.get("use_remote_datatypes", False))
+        use_remote_datatypes = string_as_bool_or_none(
+            pulsar_client.destination_params.get("use_remote_datatypes", False)
+        )
         return use_remote_datatypes
 
     @staticmethod
@@ -862,10 +882,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
             remote_galaxy_home = remote_system_properties.get("galaxy_home", None)
             if not remote_galaxy_home:
                 raise Exception(NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE)
-            metadata_kwds['exec_dir'] = remote_galaxy_home
-            outputs_directory = remote_job_config['outputs_directory']
-            working_directory = remote_job_config['working_directory']
-            metadata_directory = remote_job_config['metadata_directory']
+            metadata_kwds["exec_dir"] = remote_galaxy_home
+            outputs_directory = remote_job_config["outputs_directory"]
+            working_directory = remote_job_config["working_directory"]
+            metadata_directory = remote_job_config["metadata_directory"]
             # For metadata calculation, we need to build a list of of output
             # file objects with real path indicating location on Galaxy server
             # and false path indicating location on compute server. Since the
@@ -876,29 +896,32 @@ class PulsarJobRunner(AsynchronousJobRunner):
             # server relative to the remote working directory as the
             # false_path to send the metadata command generation module.
             work_dir_outputs = self.get_work_dir_outputs(job_wrapper, tool_working_directory=working_directory)
-            outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)]
+            outputs = [
+                Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path)
+                for path in self.get_output_files(job_wrapper)
+            ]
             for output in outputs:
                 for pulsar_workdir_path, real_path in work_dir_outputs:
                     if real_path == output.real_path:
                         output.false_path = pulsar_workdir_path
-            metadata_kwds['output_fnames'] = outputs
-            metadata_kwds['compute_tmp_dir'] = metadata_directory
-            metadata_kwds['config_root'] = remote_galaxy_home
-            default_config_file = os.path.join(remote_galaxy_home, 'config/galaxy.ini')
-            metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file)
-            metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None)
+            metadata_kwds["output_fnames"] = outputs
+            metadata_kwds["compute_tmp_dir"] = metadata_directory
+            metadata_kwds["config_root"] = remote_galaxy_home
+            default_config_file = os.path.join(remote_galaxy_home, "config/galaxy.ini")
+            metadata_kwds["config_file"] = remote_system_properties.get("galaxy_config_file", default_config_file)
+            metadata_kwds["dataset_files_path"] = remote_system_properties.get("galaxy_dataset_files_path", None)
             if PulsarJobRunner.__use_remote_datatypes_conf(client):
-                remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None)
+                remote_datatypes_config = remote_system_properties.get("galaxy_datatypes_config_file", None)
                 if not remote_datatypes_config:
                     log.warning(NO_REMOTE_DATATYPES_CONFIG)
-                    remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml')
-                metadata_kwds['datatypes_config'] = remote_datatypes_config
+                    remote_datatypes_config = os.path.join(remote_galaxy_home, "datatypes_conf.xml")
+                metadata_kwds["datatypes_config"] = remote_datatypes_config
             else:
-                datatypes_config = os.path.join(job_wrapper.working_directory, 'registry.xml')
+                datatypes_config = os.path.join(job_wrapper.working_directory, "registry.xml")
                 self.app.datatypes_registry.to_xml_file(path=datatypes_config)
                 # Ensure this file gets pushed out to the remote config dir.
                 job_wrapper.extra_filenames.append(datatypes_config)
-                metadata_kwds['datatypes_config'] = datatypes_config
+                metadata_kwds["datatypes_config"] = datatypes_config
         return metadata_kwds
 
     def __async_update(self, full_status):
@@ -908,7 +931,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
             if len(remote_job_id) == 32:
                 # It is a UUID - assign_ids = uuid in destination params...
                 sa_session = self.app.model.session
-                galaxy_job_id = sa_session.query(model.Job).filter(model.Job.job_runner_external_id == remote_job_id).one().id
+                galaxy_job_id = (
+                    sa_session.query(model.Job).filter(model.Job.job_runner_external_id == remote_job_id).one().id
+                )
             else:
                 galaxy_job_id = remote_job_id
             job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(galaxy_job_id)
@@ -931,6 +956,7 @@ class PulsarLegacyJobRunner(PulsarJobRunner):
 
 class PulsarMQJobRunner(PulsarJobRunner):
     """Flavor of Pulsar job runner with sensible defaults for message queue communication."""
+
     use_mq = True
     poll = False
 
@@ -940,7 +966,7 @@ class PulsarMQJobRunner(PulsarJobRunner):
         dependency_resolution="remote",
         jobs_directory=PARAMETER_SPECIFICATION_REQUIRED,
         url=PARAMETER_SPECIFICATION_IGNORED,
-        private_token=PARAMETER_SPECIFICATION_IGNORED
+        private_token=PARAMETER_SPECIFICATION_IGNORED,
     )
 
 
@@ -1003,7 +1029,6 @@ class PulsarEmbeddedMQJobRunner(PulsarMQJobRunner):
 
 
 class PulsarComputeEnvironment(ComputeEnvironment):
-
     def __init__(self, pulsar_client, job_wrapper, remote_job_config):
         self.pulsar_client = pulsar_client
         self.job_wrapper = job_wrapper
@@ -1020,8 +1045,8 @@ class PulsarComputeEnvironment(ComputeEnvironment):
         self._working_directory = remote_job_config["working_directory"]
         self._sep = remote_job_config["system_properties"]["separator"]
         self._tool_dir = remote_job_config["tools_directory"]
-        self._tmp_dir = remote_job_config.get('tmp_dir')
-        self._shared_home_dir = remote_job_config.get('shared_home_dir')
+        self._tmp_dir = remote_job_config.get("tmp_dir")
+        self._shared_home_dir = remote_job_config.get("shared_home_dir")
         version_path = self.local_path_config.version_path()
         new_version_path = self.path_mapper.remote_version_path_rewrite(version_path)
         if new_version_path:
@@ -1052,21 +1077,23 @@ class PulsarComputeEnvironment(ComputeEnvironment):
 
     def input_extra_files_rewrite(self, dataset):
         input_path_rewrite = self.input_path_rewrite(dataset)
-        base_input_path = input_path_rewrite[0:-len(".dat")]
+        base_input_path = input_path_rewrite[0 : -len(".dat")]
         remote_extra_files_path_rewrite = f"{base_input_path}_files"
         self.path_rewrites_input_extra[dataset.extra_files_path] = remote_extra_files_path_rewrite
         return remote_extra_files_path_rewrite
 
     def output_extra_files_rewrite(self, dataset):
         output_path_rewrite = self.output_path_rewrite(dataset)
-        base_output_path = output_path_rewrite[0:-len(".dat")]
+        base_output_path = output_path_rewrite[0 : -len(".dat")]
         remote_extra_files_path_rewrite = f"{base_output_path}_files"
         return remote_extra_files_path_rewrite
 
     def input_metadata_rewrite(self, dataset, metadata_val):
         # May technically be incorrect to not pass through local_path_config.input_metadata_rewrite
         # first but that adds untested logic that wouln't ever be used.
-        remote_input_path = self.path_mapper.remote_input_path_rewrite(metadata_val, client_input_path_type=CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH)
+        remote_input_path = self.path_mapper.remote_input_path_rewrite(
+            metadata_val, client_input_path_type=CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH
+        )
         if remote_input_path:
             log.info(f"input_metadata_rewrite is {remote_input_path} from {metadata_val}")
             self.path_rewrites_input_metadata[metadata_val] = remote_input_path
@@ -1137,6 +1164,5 @@ class PulsarComputeEnvironment(ComputeEnvironment):
 
 
 class UnsupportedPulsarException(Exception):
-
     def __init__(self, needed):
         super().__init__(UPGRADE_PULSAR_ERROR % needed)
diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
index 794d9bde7ae..92573c8e679 100644
--- a/lib/galaxy/jobs/runners/slurm.py
+++ b/lib/galaxy/jobs/runners/slurm.py
@@ -11,23 +11,25 @@ from galaxy.util.custom_logging import get_logger
 
 log = get_logger(__name__)
 
-__all__ = ('SlurmJobRunner', )
+__all__ = ("SlurmJobRunner",)
 
 # Error message printed to job stderr when SLURM itself kills a job.
 # See src/common/slurm_jobacct_gather.c and src/slurmd/slurmd/req.c in
 # https://github.com/SchedMD/slurm/
-SLURM_MEMORY_LIMIT_EXCEEDED_MSG = 'slurmstepd: error: Exceeded job memory limit'
+SLURM_MEMORY_LIMIT_EXCEEDED_MSG = "slurmstepd: error: Exceeded job memory limit"
 # Warning messages which may be printed to job stderr by SLURM after termination
 # of a job step when using the cgroup task plugin. The exceeded memory is not
 # always the cause of the step termination, which can be successful.
 # See src/plugins/task/cgroup/task_cgroup_memory.c in
 # https://github.com/SchedMD/slurm/
-SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS = [': Exceeded job memory limit at some point.',
-                                                ': Exceeded step memory limit at some point.']
+SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS = [
+    ": Exceeded job memory limit at some point.",
+    ": Exceeded step memory limit at some point.",
+]
 
 # These messages are returned to the user
-OUT_OF_MEMORY_MSG = 'This job was terminated because it used more memory than it was allocated.'
-PROBABLY_OUT_OF_MEMORY_MSG = 'This job was cancelled probably because it used more memory than it was allocated.'
+OUT_OF_MEMORY_MSG = "This job was terminated because it used more memory than it was allocated."
+PROBABLY_OUT_OF_MEMORY_MSG = "This job was cancelled probably because it used more memory than it was allocated."
 
 
 class SlurmJobRunner(DRMAAJobRunner):
@@ -36,15 +38,15 @@ class SlurmJobRunner(DRMAAJobRunner):
 
     def _complete_terminal_job(self, ajs, drmaa_state, **kwargs):
         def _get_slurm_state_with_sacct(job_id, cluster):
-            cmd = ['sacct', '-n', '-o', 'state%-32']
+            cmd = ["sacct", "-n", "-o", "state%-32"]
             if cluster:
-                cmd.extend(['-M', cluster])
-            cmd.extend(['-j', job_id])
+                cmd.extend(["-M", cluster])
+            cmd.extend(["-j", job_id])
             try:
                 stdout = commands.execute(cmd)
             except commands.CommandLineException as e:
-                if e.stderr.strip() == 'SLURM accounting storage is disabled':
-                    log.warning('SLURM accounting storage is not properly configured, unable to run sacct')
+                if e.stderr.strip() == "SLURM accounting storage is disabled":
+                    log.warning("SLURM accounting storage is not properly configured, unable to run sacct")
                     return
                 raise e
             # First line is for 'job_id'
@@ -52,27 +54,27 @@ class SlurmJobRunner(DRMAAJobRunner):
             # Following lines are for the steps 'job_id.0', 'job_id.1', ... (but Galaxy does not use steps)
             first_line = stdout.splitlines()[0]
             # Strip whitespaces and the final '+' (if present), only return the first word
-            return first_line.strip().rstrip('+').split()[0]
+            return first_line.strip().rstrip("+").split()[0]
 
         def _get_slurm_state():
-            cmd = ['scontrol', '-o']
-            if '.' in ajs.job_id:
+            cmd = ["scontrol", "-o"]
+            if "." in ajs.job_id:
                 # custom slurm-drmaa-with-cluster-support job id syntax
-                job_id, cluster = ajs.job_id.split('.', 1)
-                cmd.extend(['-M', cluster])
+                job_id, cluster = ajs.job_id.split(".", 1)
+                cmd.extend(["-M", cluster])
             else:
                 job_id = ajs.job_id
                 cluster = None
-            cmd.extend(['show', 'job', job_id])
+            cmd.extend(["show", "job", job_id])
             try:
                 stdout = commands.execute(cmd).strip()
             except commands.CommandLineException as e:
-                if e.stderr == 'slurm_load_jobs error: Invalid job id specified\n':
+                if e.stderr == "slurm_load_jobs error: Invalid job id specified\n":
                     # The job may be old, try to get its state with sacct
                     job_state = _get_slurm_state_with_sacct(job_id, cluster)
                     if job_state:
                         return job_state
-                    return 'NOT_FOUND'
+                    return "NOT_FOUND"
                 raise e
             # stdout is a single line in format "key1=value1 key2=value2 ..."
             job_info_keys = []
@@ -80,72 +82,122 @@ class SlurmJobRunner(DRMAAJobRunner):
             for job_info in stdout.split():
                 try:
                     # Some value may contain `=` (e.g. `StdIn=StdIn=/dev/null`)
-                    k, v = job_info.split('=', 1)
+                    k, v = job_info.split("=", 1)
                     job_info_keys.append(k)
                     job_info_values.append(v)
                 except ValueError:
                     # Some value may contain spaces (e.g. `Comment=** time_limit (60m) min_nodes (1) **`)
                     job_info_values[-1] += f" {job_info}"
             job_info_dict = dict(zip(job_info_keys, job_info_values))
-            return job_info_dict['JobState']
+            return job_info_dict["JobState"]
 
         try:
             if drmaa_state == self.drmaa_job_states.FAILED:
                 slurm_state = _get_slurm_state()
                 sleep = 1
-                while slurm_state == 'COMPLETING':
-                    log.debug('(%s/%s) Waiting %s seconds for failed job to exit COMPLETING state for post-mortem', ajs.job_wrapper.get_id_tag(), ajs.job_id, sleep)
+                while slurm_state == "COMPLETING":
+                    log.debug(
+                        "(%s/%s) Waiting %s seconds for failed job to exit COMPLETING state for post-mortem",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                        sleep,
+                    )
                     time.sleep(sleep)
                     sleep *= 2
                     if sleep > 64:
                         ajs.fail_message = "This job failed and the system timed out while trying to determine the cause of the failure."
                         break
                     slurm_state = _get_slurm_state()
-                if slurm_state == 'NOT_FOUND':
-                    log.warning('(%s/%s) Job not found, assuming job check exceeded MinJobAge and completing as successful', ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                if slurm_state == "NOT_FOUND":
+                    log.warning(
+                        "(%s/%s) Job not found, assuming job check exceeded MinJobAge and completing as successful",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                    )
                     drmaa_state = self.drmaa_job_states.DONE
-                elif slurm_state == 'COMPLETED':
-                    log.debug("(%s/%s) SLURM reported job success, assuming job check exceeded MinJobAge and completing as successful", ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                elif slurm_state == "COMPLETED":
+                    log.debug(
+                        "(%s/%s) SLURM reported job success, assuming job check exceeded MinJobAge and completing as successful",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                    )
                     drmaa_state = self.drmaa_job_states.DONE
-                elif slurm_state == 'TIMEOUT':
-                    log.info('(%s/%s) Job hit walltime', ajs.job_wrapper.get_id_tag(), ajs.job_id)
-                    ajs.fail_message = "This job was terminated because it ran longer than the maximum allowed job run time."
+                elif slurm_state == "TIMEOUT":
+                    log.info("(%s/%s) Job hit walltime", ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                    ajs.fail_message = (
+                        "This job was terminated because it ran longer than the maximum allowed job run time."
+                    )
                     ajs.runner_state = ajs.runner_states.WALLTIME_REACHED
-                elif slurm_state == 'NODE_FAIL':
-                    log.warning('(%s/%s) Job failed due to node failure, attempting resubmission', ajs.job_wrapper.get_id_tag(), ajs.job_id)
-                    ajs.job_wrapper.change_state(model.Job.states.QUEUED, info='Job was resubmitted due to node failure')
+                elif slurm_state == "NODE_FAIL":
+                    log.warning(
+                        "(%s/%s) Job failed due to node failure, attempting resubmission",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                    )
+                    ajs.job_wrapper.change_state(
+                        model.Job.states.QUEUED, info="Job was resubmitted due to node failure"
+                    )
                     try:
                         self.queue_job(ajs.job_wrapper)
                         return
                     except Exception:
-                        ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed."
-                elif slurm_state == 'OUT_OF_MEMORY':
-                    log.info('(%s/%s) Job hit memory limit (SLURM state: OUT_OF_MEMORY)', ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                        ajs.fail_message = (
+                            "This job failed due to a cluster node failure, and an attempt to resubmit the job failed."
+                        )
+                elif slurm_state == "OUT_OF_MEMORY":
+                    log.info(
+                        "(%s/%s) Job hit memory limit (SLURM state: OUT_OF_MEMORY)",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                    )
                     ajs.fail_message = OUT_OF_MEMORY_MSG
                     ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED
-                elif slurm_state == 'CANCELLED':
+                elif slurm_state == "CANCELLED":
                     # Check to see if the job was killed for exceeding memory consumption
                     check_memory_limit_msg = self.__check_memory_limit(ajs.error_file)
                     if check_memory_limit_msg:
-                        log.info('(%s/%s) Job hit memory limit (SLURM state: CANCELLED)', ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                        log.info(
+                            "(%s/%s) Job hit memory limit (SLURM state: CANCELLED)",
+                            ajs.job_wrapper.get_id_tag(),
+                            ajs.job_id,
+                        )
                         ajs.fail_message = check_memory_limit_msg
                         ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED
                     else:
-                        log.info('(%s/%s) Job was cancelled via SLURM (e.g. with scancel(1))', ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                        log.info(
+                            "(%s/%s) Job was cancelled via SLURM (e.g. with scancel(1))",
+                            ajs.job_wrapper.get_id_tag(),
+                            ajs.job_id,
+                        )
                         ajs.fail_message = "This job failed because it was cancelled by an administrator."
-                elif slurm_state in ('PENDING', 'RUNNING'):
-                    log.warning('(%s/%s) Job was reported by drmaa as terminal but job state in SLURM is: %s, returning to monitor queue', ajs.job_wrapper.get_id_tag(), ajs.job_id, slurm_state)
+                elif slurm_state in ("PENDING", "RUNNING"):
+                    log.warning(
+                        "(%s/%s) Job was reported by drmaa as terminal but job state in SLURM is: %s, returning to monitor queue",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                        slurm_state,
+                    )
                     return True
                 else:
-                    log.warning('(%s/%s) Job failed due to unknown reasons, job state in SLURM was: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, slurm_state)
+                    log.warning(
+                        "(%s/%s) Job failed due to unknown reasons, job state in SLURM was: %s",
+                        ajs.job_wrapper.get_id_tag(),
+                        ajs.job_id,
+                        slurm_state,
+                    )
                     ajs.fail_message = "This job failed for reasons that could not be determined."
                 if drmaa_state == self.drmaa_job_states.FAILED:
-                    ajs.fail_message += '\nPlease click the bug icon to report this problem if you need help.'
+                    ajs.fail_message += "\nPlease click the bug icon to report this problem if you need help."
                     ajs.stop_job = False
                     self.work_queue.put((self.fail_job, ajs))
                     return
         except Exception:
-            log.exception('(%s/%s) Failure in SLURM _complete_terminal_job(), job final state will be: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, drmaa_state)
+            log.exception(
+                "(%s/%s) Failure in SLURM _complete_terminal_job(), job final state will be: %s",
+                ajs.job_wrapper.get_id_tag(),
+                ajs.job_id,
+                drmaa_state,
+            )
         # by default, finish the job with the state from drmaa
         return super()._complete_terminal_job(ajs, drmaa_state=drmaa_state)
 
@@ -155,7 +207,7 @@ class SlurmJobRunner(DRMAAJobRunner):
         since we are only searching the last 2K
         """
         try:
-            log.debug('Checking %s for exceeded memory message from SLURM', efile_path)
+            log.debug("Checking %s for exceeded memory message from SLURM", efile_path)
             with open(efile_path) as f:
                 if os.path.getsize(efile_path) > 2048:
                     f.seek(-2048, os.SEEK_END)
@@ -167,6 +219,6 @@ class SlurmJobRunner(DRMAAJobRunner):
                     elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):
                         return PROBABLY_OUT_OF_MEMORY_MSG
         except Exception:
-            log.exception('Error reading end of %s:', efile_path)
+            log.exception("Error reading end of %s:", efile_path)
 
         return False
diff --git a/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py b/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
index e900071cde9..6c04fede96f 100644
--- a/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
+++ b/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
@@ -5,17 +5,54 @@ from ast import (
 )
 
 AST_NODE_TYPE_ALLOWLIST = [
-    'Expr', 'Load', 'Str', 'Num', 'BoolOp', 'Compare', 'And', 'Eq', 'NotEq',
-    'Or', 'GtE', 'LtE', 'Lt', 'Gt', 'BinOp', 'Add', 'Div', 'Sub', 'Mult', 'Mod',
-    'Pow', 'LShift', 'GShift', 'BitAnd', 'BitOr', 'BitXor', 'UnaryOp', 'Invert',
-    'Not', 'NotIn', 'In', 'Is', 'IsNot', 'List', 'Index', 'Subscript', 'Constant',
+    "Expr",
+    "Load",
+    "Str",
+    "Num",
+    "BoolOp",
+    "Compare",
+    "And",
+    "Eq",
+    "NotEq",
+    "Or",
+    "GtE",
+    "LtE",
+    "Lt",
+    "Gt",
+    "BinOp",
+    "Add",
+    "Div",
+    "Sub",
+    "Mult",
+    "Mod",
+    "Pow",
+    "LShift",
+    "GShift",
+    "BitAnd",
+    "BitOr",
+    "BitXor",
+    "UnaryOp",
+    "Invert",
+    "Not",
+    "NotIn",
+    "In",
+    "Is",
+    "IsNot",
+    "List",
+    "Index",
+    "Subscript",
+    "Constant",
     # Further checks
-    'Name', 'Call', 'Attribute',
+    "Name",
+    "Call",
+    "Attribute",
 ]
 
 
-BUILTIN_AND_MATH_FUNCTIONS = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor'.split('|')
-STRING_AND_LIST_METHODS = [name for name in dir('') + dir([]) if not name.startswith('_')]
+BUILTIN_AND_MATH_FUNCTIONS = "abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor".split(
+    "|"
+)
+STRING_AND_LIST_METHODS = [name for name in dir("") + dir([]) if not name.startswith("_")]
 VALID_FUNCTIONS = BUILTIN_AND_MATH_FUNCTIONS + STRING_AND_LIST_METHODS
 
 
@@ -38,10 +75,10 @@ def _check_call(ast_node):
     # string or list function.
     ast_func = ast_node.func
     ast_func_class = ast_func.__class__.__name__
-    if ast_func_class == 'Name':
+    if ast_func_class == "Name":
         if ast_func.id not in BUILTIN_AND_MATH_FUNCTIONS:
             return False
-    elif ast_func_class == 'Attribute':
+    elif ast_func_class == "Attribute":
         if not _check_attribute(ast_func):
             return False
     else:
@@ -96,7 +133,7 @@ def _check_expression(text, allowed_variables=None):
     if not len(statements) == 1:
         return False
     expression = statements[0]
-    if expression.__class__.__name__ != 'Expr':
+    if expression.__class__.__name__ != "Expr":
         return False
 
     for ast_node in walk(expression):
@@ -108,17 +145,17 @@ def _check_expression(text, allowed_variables=None):
             return False
 
         # White-list more potentially dangerous types AST elements.
-        if ast_node_class == 'Name':
+        if ast_node_class == "Name":
             # In order to prevent loading 'exec', 'eval', etc...
             # put string restriction on names allowed.
             if not _check_name(ast_node, allowed_variables):
                 return False
         # Check only valid, white-listed functions are called.
-        elif ast_node_class == 'Call':
+        elif ast_node_class == "Call":
             if not _check_call(ast_node):
                 return False
         # Check only valid, white-listed attributes are accessed
-        elif ast_node_class == 'Attribute':
+        elif ast_node_class == "Attribute":
             if not _check_attribute(ast_node):
                 return False
 
diff --git a/lib/galaxy/jobs/runners/state_handlers/resubmit.py b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
index 2c09923a2e5..3ad5530aa38 100644
--- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py
+++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
@@ -5,20 +5,20 @@ from galaxy import model
 from galaxy.jobs.runners import JobState
 from ._safe_eval import safe_eval
 
-__all__ = ('failure', )
+__all__ = ("failure",)
 
 log = logging.getLogger(__name__)
 
 MESSAGES = dict(
-    walltime_reached='it reached the walltime',
-    memory_limit_reached='it exceeded the amount of allocated memory',
-    unknown_error='it encountered an unknown error',
-    tool_detected='it encountered a tool detected error condition',
+    walltime_reached="it reached the walltime",
+    memory_limit_reached="it exceeded the amount of allocated memory",
+    unknown_error="it encountered an unknown error",
+    tool_detected="it encountered a tool detected error condition",
 )
 
 
 def eval_condition(condition, job_state):
-    runner_state = getattr(job_state, 'runner_state', None) or JobState.runner_states.UNKNOWN_ERROR
+    runner_state = getattr(job_state, "runner_state", None) or JobState.runner_states.UNKNOWN_ERROR
 
     attempt = 1
     now = datetime.utcnow()
@@ -60,16 +60,18 @@ def eval_condition(condition, job_state):
 
 def failure(app, job_runner, job_state):
     # Leave handler quickly if no resubmit conditions specified or if the runner state doesn't allow resubmission.
-    resubmit_definitions = job_state.job_destination.get('resubmit')
+    resubmit_definitions = job_state.job_destination.get("resubmit")
     if not resubmit_definitions:
         return
 
-    runner_state = getattr(job_state, 'runner_state', None) or JobState.runner_states.UNKNOWN_ERROR
-    if (runner_state not in (JobState.runner_states.WALLTIME_REACHED,
-                             JobState.runner_states.MEMORY_LIMIT_REACHED,
-                             JobState.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER,
-                             JobState.runner_states.TOOL_DETECT_ERROR,
-                             JobState.runner_states.UNKNOWN_ERROR)):
+    runner_state = getattr(job_state, "runner_state", None) or JobState.runner_states.UNKNOWN_ERROR
+    if runner_state not in (
+        JobState.runner_states.WALLTIME_REACHED,
+        JobState.runner_states.MEMORY_LIMIT_REACHED,
+        JobState.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER,
+        JobState.runner_states.TOOL_DETECT_ERROR,
+        JobState.runner_states.UNKNOWN_ERROR,
+    ):
         # not set or not a handleable runner state
         return
 
@@ -77,7 +79,7 @@ def failure(app, job_runner, job_state):
 
 
 def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_state):
-    runner_state = getattr(job_state, 'runner_state', None) or JobState.runner_states.UNKNOWN_ERROR
+    runner_state = getattr(job_state, "runner_state", None) or JobState.runner_states.UNKNOWN_ERROR
 
     # Setup environment for evaluating resubmission conditions and related expression.
     expression_context = _ExpressionContext(job_state)
@@ -85,7 +87,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
     # Intercept jobs that hit the walltime and have a walltime or
     # nonspecific resubmit destination configured
     for resubmit in resubmit_definitions:
-        condition = resubmit.get('condition', None)
+        condition = resubmit.get("condition", None)
         if condition and not expression_context.safe_eval(condition):
             # There is a resubmit defined for the destination but
             # its condition is not for the encountered state
@@ -98,13 +100,14 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
             job_log_prefix = f"({job_state.job_wrapper.job_id})"
 
         # Is destination needed here, might these be serialized to the database?
-        destination = resubmit.get('environment') or resubmit.get('destination')
-        log.info("%s Job will be resubmitted to '%s' because %s at "
-                 "the '%s' destination",
-                 job_log_prefix,
-                 destination,
-                 MESSAGES[runner_state],
-                 job_state.job_wrapper.job_destination.id)
+        destination = resubmit.get("environment") or resubmit.get("destination")
+        log.info(
+            "%s Job will be resubmitted to '%s' because %s at " "the '%s' destination",
+            job_log_prefix,
+            destination,
+            MESSAGES[runner_state],
+            job_state.job_wrapper.job_destination.id,
+        )
         # fetch JobDestination for the id or tag
         if destination:
             new_destination = app.job_config.get_destination(destination)
@@ -112,32 +115,28 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
             new_destination = job_state.job_destination
 
         # Resolve dynamic if necessary
-        new_destination = (job_state.job_wrapper.job_runner_mapper
-                           .cache_job_destination(new_destination))
+        new_destination = job_state.job_wrapper.job_runner_mapper.cache_job_destination(new_destination)
         # Reset job state
         job_state.job_wrapper.clear_working_directory()
         job_state.job_wrapper.invalidate_external_metadata()
         job = job_state.job_wrapper.get_job()
-        if resubmit.get('handler', None):
-            log.debug('%s Job reassigned to handler %s',
-                      job_log_prefix,
-                      resubmit['handler'])
-            job.set_handler(resubmit['handler'])
+        if resubmit.get("handler", None):
+            log.debug("%s Job reassigned to handler %s", job_log_prefix, resubmit["handler"])
+            job.set_handler(resubmit["handler"])
             job_runner.sa_session.add(job)
             # Is this safe to do here?
             job_runner.sa_session.flush()
         # Cache the destination to prevent rerunning dynamic after
         # resubmit
-        job_state.job_wrapper.job_runner_mapper \
-            .cached_job_destination = new_destination
+        job_state.job_wrapper.job_runner_mapper.cached_job_destination = new_destination
         # Handle delaying before resubmission if needed.
-        raw_delay = resubmit.get('delay')
+        raw_delay = resubmit.get("delay")
         if raw_delay:
             delay = str(expression_context.safe_eval(str(raw_delay)))
             try:
                 # ensure result acts like a number when persisted.
                 float(delay)
-                new_destination.params['__resubmit_delay_seconds'] = str(delay)
+                new_destination.params["__resubmit_delay_seconds"] = str(delay)
             except ValueError:
                 log.warning(f"Cannot delay job with delay [{delay}], does not appear to be a number.")
         job_state.job_wrapper.set_job_destination(new_destination)
@@ -147,14 +146,12 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         if job.params is None:
             job.params = {}
         job_state.runner_state_handled = True
-        info = "This job was resubmitted to the queue because %s on its " \
-               "compute resource." % MESSAGES[runner_state]
+        info = "This job was resubmitted to the queue because %s on its " "compute resource." % MESSAGES[runner_state]
         job_runner.mark_as_resubmitted(job_state, info=info)
         return
 
 
 class _ExpressionContext:
-
     def __init__(self, job_state):
         self._job_state = job_state
         self._lazy_context = None
@@ -164,7 +161,7 @@ class _ExpressionContext:
             return int(condition)
 
         if self._lazy_context is None:
-            runner_state = getattr(self._job_state, 'runner_state', None) or JobState.runner_states.UNKNOWN_ERROR
+            runner_state = getattr(self._job_state, "runner_state", None) or JobState.runner_states.UNKNOWN_ERROR
             attempt = 1
             now = datetime.utcnow()
             last_running_state = None
diff --git a/lib/galaxy/jobs/runners/tasks.py b/lib/galaxy/jobs/runners/tasks.py
index d9af589a4b9..72249681d97 100644
--- a/lib/galaxy/jobs/runners/tasks.py
+++ b/lib/galaxy/jobs/runners/tasks.py
@@ -9,13 +9,14 @@ from galaxy.jobs.runners import BaseJobRunner
 
 log = logging.getLogger(__name__)
 
-__all__ = ('TaskedJobRunner', )
+__all__ = ("TaskedJobRunner",)
 
 
 class TaskedJobRunner(BaseJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
     """
+
     runner_name = "TaskRunner"
 
     def __init__(self, app, nworkers):
@@ -31,7 +32,7 @@ class TaskedJobRunner(BaseJobRunner):
         # command line has been added to the wrapper by prepare_job()
         command_line = job_wrapper.runner_command_line
 
-        stderr = stdout = ''
+        stderr = stdout = ""
 
         # Persist the destination
         job_wrapper.set_job_destination(job_wrapper.job_destination)
@@ -51,7 +52,9 @@ class TaskedJobRunner(BaseJobRunner):
             # Split with the defined method.
             parallelism = job_wrapper.get_parallelism()
             try:
-                splitter = getattr(__import__('galaxy.jobs.splitters', globals(), locals(), [parallelism.method]), parallelism.method)
+                splitter = getattr(
+                    __import__("galaxy.jobs.splitters", globals(), locals(), [parallelism.method]), parallelism.method
+                )
             except Exception:
                 job_wrapper.change_state(model.Job.states.ERROR)
                 job_wrapper.fail(f"Job Splitting Failed, no match for '{parallelism}'")
@@ -75,9 +78,7 @@ class TaskedJobRunner(BaseJobRunner):
             sleep_time = 1
             # sleep/loop until no more progress can be made. That is when
             # all tasks are one of { OK, ERROR, DELETED }. If a task
-            completed_states = [model.Task.states.OK,
-                                model.Task.states.ERROR,
-                                model.Task.states.DELETED]
+            completed_states = [model.Task.states.OK, model.Task.states.ERROR, model.Task.states.DELETED]
 
             # TODO: Should we report an error (and not merge outputs) if
             # one of the subtasks errored out?  Should we prevent any that
@@ -94,10 +95,9 @@ class TaskedJobRunner(BaseJobRunner):
                 tasks_complete = True
                 for tw in task_wrappers:
                     task_state = tw.get_state()
-                    if (model.Task.states.ERROR == task_state):
+                    if model.Task.states.ERROR == task_state:
                         job_exit_code = tw.get_exit_code()
-                        log.debug("Canceling job %d: Task %s returned an error"
-                                  % (tw.job_id, tw.task_id))
+                        log.debug("Canceling job %d: Task %s returned an error" % (tw.job_id, tw.task_id))
                         self._cancel_job(job_wrapper, task_wrappers)
                         tasks_complete = True
                         break
@@ -110,8 +110,8 @@ class TaskedJobRunner(BaseJobRunner):
                     sleep(sleep_time)
                     if sleep_time < 8:
                         sleep_time *= 2
-            job_wrapper.reclaim_ownership()      # if running as the actual user, change ownership before merging.
-            log.debug(f'execution finished - beginning merge: {command_line}')
+            job_wrapper.reclaim_ownership()  # if running as the actual user, change ownership before merging.
+            log.debug(f"execution finished - beginning merge: {command_line}")
             stdout, stderr = splitter.do_merge(job_wrapper, task_wrappers)
         except Exception:
             job_wrapper.fail("failure running job", exception=True)
@@ -136,7 +136,7 @@ class TaskedJobRunner(BaseJobRunner):
         # to retrieve a job's list of tasks.
         job = job_wrapper.get_job()
         tasks = job.get_tasks()
-        if (len(tasks) > 0):
+        if len(tasks) > 0:
             for task in tasks:
                 log.debug(f"Killing task's job {task.id}")
                 self.app.job_manager.job_handler.dispatcher.stop(task)
@@ -148,17 +148,21 @@ class TaskedJobRunner(BaseJobRunner):
             # if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished
             job_ext_output_metadata = job.get_external_output_metadata()
             if job_ext_output_metadata:
-                pid = job_ext_output_metadata[0].job_runner_external_pid  # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
+                pid = job_ext_output_metadata[
+                    0
+                ].job_runner_external_pid  # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
             else:
                 pid = job.job_runner_external_id
-            if pid in [None, '']:
+            if pid in [None, ""]:
                 log.warning(f"stop_job(): {job.id}: no PID in database for job, unable to stop")
                 return
             self._stop_pid(pid, job.id)
 
     def recover(self, job, job_wrapper):
         # DBTODO Task Recovery, this should be possible.
-        job_wrapper.change_state(model.Job.states.ERROR, info="This job was killed when Galaxy was restarted.  Please retry the job.")
+        job_wrapper.change_state(
+            model.Job.states.ERROR, info="This job was killed when Galaxy was restarted.  Please retry the job."
+        )
 
     def _cancel_job(self, job_wrapper, task_wrappers):
         """
@@ -188,9 +192,10 @@ class TaskedJobRunner(BaseJobRunner):
         for task_wrapper in task_wrappers:
             task = task_wrapper.get_task()
             task_state = task.get_state()
-            if (model.Task.states.QUEUED == task_state):
-                log.debug("_cancel_job for job %d: Task %d is not running; setting state to DELETED"
-                          % (job.id, task.id))
+            if model.Task.states.QUEUED == task_state:
+                log.debug(
+                    "_cancel_job for job %d: Task %d is not running; setting state to DELETED" % (job.id, task.id)
+                )
                 task_wrapper.change_state(task.states.DELETED)
         # If a task failed, then the caller will have waited a few seconds
         # before recognizing the failure. In that time, a queued task could
@@ -199,10 +204,9 @@ class TaskedJobRunner(BaseJobRunner):
         # are running.
         sleep(5)
         for task_wrapper in task_wrappers:
-            if (model.Task.states.RUNNING == task_wrapper.get_state()):
+            if model.Task.states.RUNNING == task_wrapper.get_state():
                 task = task_wrapper.get_task()
-                log.debug("_cancel_job for job %d: Stopping running task %d"
-                          % (job.id, task.id))
+                log.debug("_cancel_job for job %d: Stopping running task %d" % (job.id, task.id))
                 job_wrapper.app.job_manager.job_handler.dispatcher.stop(task)
 
     def _check_pid(self, pid):
@@ -227,7 +231,10 @@ class TaskedJobRunner(BaseJobRunner):
             except OSError as e:
                 # This warning could be bogus; many tasks are stopped with
                 # SIGTERM (signal 15), but ymmv depending on the platform.
-                log.warning("_stop_pid(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % (job_id, errno.errorcode[e.errno], sig, pid, e.strerror))
+                log.warning(
+                    "_stop_pid(): %s: Got errno %s when attempting to signal %d to PID %d: %s"
+                    % (job_id, errno.errorcode[e.errno], sig, pid, e.strerror)
+                )
                 return
             # TODO: If we're stopping lots of tasks, then we will want to put this
             # avoid a two-second overhead using some other asynchronous method.
diff --git a/lib/galaxy/jobs/runners/univa.py b/lib/galaxy/jobs/runners/univa.py
index 2fe1a5c76ca..018e99caebb 100644
--- a/lib/galaxy/jobs/runners/univa.py
+++ b/lib/galaxy/jobs/runners/univa.py
@@ -37,12 +37,12 @@ from galaxy.jobs.runners.drmaa import DRMAAJobRunner
 from galaxy.util import (
     commands,
     size_to_bytes,
-    unicodify
+    unicodify,
 )
 
 log = logging.getLogger(__name__)
 
-__all__ = ('UnivaJobRunner',)
+__all__ = ("UnivaJobRunner",)
 
 MEMORY_LIMIT_SCAN_SIZE = 1024 * 1024  # 1MB
 
@@ -80,7 +80,7 @@ class UnivaJobRunner(DRMAAJobRunner):
         if state in [self.drmaa.JobState.DONE, self.drmaa.JobState.FAILED]:
             # get configured job destination
             job_destination = ajs.job_wrapper.job_destination
-            native_spec = job_destination.params.get('nativeSpecification', None)
+            native_spec = job_destination.params.get("nativeSpecification", None)
             # determine time and memory that was granted for the job
             time_granted, mem_granted = _parse_native_specs(ajs.job_id, native_spec)
             time_wasted = extinfo["time_wasted"]
@@ -91,26 +91,40 @@ class UnivaJobRunner(DRMAAJobRunner):
 
             # check job for run time or memory violation
             if "deleted" in extinfo and extinfo["deleted"]:
-                log.info('(%s/%s) Job was cancelled (e.g. with qdel)', ajs.job_wrapper.get_id_tag(), ajs.job_id)
+                log.info("(%s/%s) Job was cancelled (e.g. with qdel)", ajs.job_wrapper.get_id_tag(), ajs.job_id)
                 ajs.fail_message = "This job failed because it was cancelled."
                 drmaa_state = self.drmaa.JobState.FAILED
             elif ("signal" in extinfo and extinfo["signal"] == "SIGKILL") and time_wasted > time_granted:
-                log.error(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job hit walltime')
-                ajs.fail_message = "This job was terminated because it ran longer than the maximum allowed job run time."
+                log.error(f"({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job hit walltime")
+                ajs.fail_message = (
+                    "This job was terminated because it ran longer than the maximum allowed job run time."
+                )
                 ajs.runner_state = ajs.runner_states.WALLTIME_REACHED
                 drmaa_state = self.drmaa.JobState.FAILED
             # test wasted>granted memory only if failed != 0 and exit_status != 0, ie if marked as failed
             elif state == self.drmaa.JobState.FAILED and mem_wasted > mem_granted * slots:
-                log.error(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job hit memory limit ({mem_wasted}>{mem_granted})')
+                log.error(
+                    f"({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job hit memory limit ({mem_wasted}>{mem_granted})"
+                )
                 ajs.fail_message = "This job was terminated because it used more than the maximum allowed memory."
                 ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED
                 drmaa_state = self.drmaa_job_states.FAILED
-        elif state in [self.drmaa.JobState.QUEUED_ACTIVE, self.drmaa.JobState.SYSTEM_ON_HOLD, self.drmaa.JobState.USER_ON_HOLD, self.drmaa.JobState.USER_SYSTEM_ON_HOLD, self.drmaa.JobState.RUNNING, self.drmaa.JobState.SYSTEM_SUSPENDED, self.drmaa.JobState.USER_SUSPENDED]:
-            log.warning(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job is {self.drmaa_job_state_strings[state]}, returning to monitor queue')
+        elif state in [
+            self.drmaa.JobState.QUEUED_ACTIVE,
+            self.drmaa.JobState.SYSTEM_ON_HOLD,
+            self.drmaa.JobState.USER_ON_HOLD,
+            self.drmaa.JobState.USER_SYSTEM_ON_HOLD,
+            self.drmaa.JobState.RUNNING,
+            self.drmaa.JobState.SYSTEM_SUSPENDED,
+            self.drmaa.JobState.USER_SUSPENDED,
+        ]:
+            log.warning(
+                f"({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job is {self.drmaa_job_state_strings[state]}, returning to monitor queue"
+            )
             # TODO return True?
             return True  # job was not actually terminal
         elif state == self.drmaa.JobState.UNDETERMINED:
-            log.warning(f'({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job state could not be determined')
+            log.warning(f"({ajs.job_wrapper.get_id_tag()}/{ajs.job_id}) Job state could not be determined")
             drmaa_state = self.drmaa_job_states.FAILED
         else:
             log.error(f"DRMAAUniva: job {ajs.job_id} determined unknown state {state}")
@@ -160,14 +174,14 @@ class UnivaJobRunner(DRMAAJobRunner):
         # exit code in case of error as well as if the jobid is not found (if job is finished).
         # even if this could be disambiguated by the stderr message the `qstat -u "*"`
         # way seems more generic
-        cmd = ['qstat', '-u', '"*"']
+        cmd = ["qstat", "-u", '"*"']
         try:
             stdout = commands.execute(cmd).strip()
         except commands.CommandLineException as e:
             log.error(unicodify(e))
             raise self.drmaa.InternalException()
         state = self.drmaa.JobState.UNDETERMINED
-        for line in stdout.split('\n'):
+        for line in stdout.split("\n"):
             line = line.split()
             if len(line) >= 5 and line[0] == str(job_id):
                 state = self._map_qstat_drmaa_states(job_id, line[5], extinfo)
@@ -176,7 +190,7 @@ class UnivaJobRunner(DRMAAJobRunner):
         return state
 
     def _get_drmaa_state_qacct(self, job_id, extinfo):
-        '''
+        """
         get the job (drmaa) state with qacct.
 
         extinfo: dict where signal, exit_status, deleted = True, time_wasted, and memory_wasted can be stored:
@@ -194,11 +208,14 @@ class UnivaJobRunner(DRMAAJobRunner):
         - FAILED if exit state != 0
         - RUNNING if failed in 24,25
         - FAILED if failed not in [0,24,25,100]
-        '''
+        """
         # log.debug("UnivaJobRunner._get_drmaa_state_qacct ({jobid})".format(jobid=job_id))
-        signals = {k: v for v, k in reversed(sorted(signal.__dict__.items()))
-           if v.startswith('SIG') and not v.startswith('SIG_')}
-        cmd = ['qacct', '-j', job_id]
+        signals = {
+            k: v
+            for v, k in reversed(sorted(signal.__dict__.items()))
+            if v.startswith("SIG") and not v.startswith("SIG_")
+        }
+        cmd = ["qacct", "-j", job_id]
         slp = 1
         # run qacct -j JOBID (since the accounting data for the job might not be
         # available immediately a simple retry mechanism is implemented ..
@@ -277,7 +294,7 @@ class UnivaJobRunner(DRMAAJobRunner):
                 state = self.drmaa.JobState.DONE
             elif 0 < qacct["exit_status"] < 129:
                 log.error(f"DRMAAUniva: job {job_id} has exit status {qacct['exit_status']}")
-                extinfo['exit_status'] = qacct["exit_status"]
+                extinfo["exit_status"] = qacct["exit_status"]
                 state = self.drmaa.JobState.FAILED
             else:
                 log.error(f"DRMAAUniva: job {job_id} was killed by signal {qacct['exit_status'] - 128}")
@@ -306,7 +323,7 @@ class UnivaJobRunner(DRMAAJobRunner):
         return state
 
     def _get_drmaa_state_wait(self, job_id, ds, extinfo):
-        '''
+        """
         get the (drmaa) job state with the python-drmaa wait function
         this function will not work if the job was started as real user
         since the external runner uses a different drmaa session.
@@ -315,7 +332,7 @@ class UnivaJobRunner(DRMAAJobRunner):
         jobid: the jobid
         ds: drmaa session
         extinfo dict where signal, exit_status, deleted = True, time_wasted, and memory_wasted can be stored
-        '''
+        """
         # log.debug("UnivaJobRunner._get_drmaa_state_wait ({jobid})".format(jobid=job_id))
 
         # experiments
@@ -395,10 +412,10 @@ class UnivaJobRunner(DRMAAJobRunner):
         # check if job was aborted
 
         # get the used time and memory
-        extinfo["time_wasted"] = float(rv.resourceUsage['wallclock'])
-        extinfo["memory_wasted"] = float(rv.resourceUsage['maxvmem'])
+        extinfo["time_wasted"] = float(rv.resourceUsage["wallclock"])
+        extinfo["memory_wasted"] = float(rv.resourceUsage["maxvmem"])
         # TODO unsure if the resourceUsage key is really slots -> test in submit as galaxy user setting
-        extinfo["slots"] = float(rv.resourceUsage['slots'])
+        extinfo["slots"] = float(rv.resourceUsage["slots"])
         # log.debug("wait -> \texitStatus {0}\thasCoreDump {1}\thasExited {2}\thasSignal {3}\tjobId {4}\t\tterminatedSignal {5}\twasAborted {6}\tresourceUsage {7}".format(rv.exitStatus, rv.hasCoreDump, rv.hasExited, rv.hasSignal, rv.jobId, rv.terminatedSignal, rv.wasAborted, rv.resourceUsage))
         if rv.wasAborted:
             log.error(f"DRMAAUniva: job {job_id} was aborted according to wait()")
@@ -448,7 +465,11 @@ class UnivaJobRunner(DRMAAJobRunner):
         # if the job is finished (in whatever state) get (additional) infos
         # drmaa.wait or qacct (oposed to job_status/qstat these methods work
         # only for finished jobs)
-        if waitqacct and state in [self.drmaa.JobState.UNDETERMINED, self.drmaa.JobState.DONE, self.drmaa.JobState.FAILED]:
+        if waitqacct and state in [
+            self.drmaa.JobState.UNDETERMINED,
+            self.drmaa.JobState.DONE,
+            self.drmaa.JobState.FAILED,
+        ]:
             try:
                 # log.debug("UnivaJobRunner trying wait ({jobid})".format(jobid=job_id))
                 wstate = self._get_drmaa_state_wait(job_id, ds, extinfo)
@@ -530,7 +551,7 @@ class UnivaJobRunner(DRMAAJobRunner):
             return self.drmaa.JobState.FAILED
         elif "s" in state:
             return self.drmaa.JobState.USER_SUSPENDED
-        elif "S" in state or "T" in state or 'N' in state or 'P' in state:
+        elif "S" in state or "T" in state or "N" in state or "P" in state:
             return self.drmaa.JobState.SYSTEM_SUSPENDED
         elif "h" in state:
             return self.drmaa.JobState.USER_SYSTEM_ON_HOLD
@@ -547,7 +568,7 @@ def _parse_time(tstring):
     tme = None
     m = re.search("([0-9:.]+)", tstring)
     if m is not None:
-        timespl = m.group(1).split(':')
+        timespl = m.group(1).split(":")
         tme = float(timespl[-1])  # sec
         if len(timespl) > 1:  # min
             tme += float(timespl[-2]) * 60
diff --git a/lib/galaxy/jobs/runners/util/__init__.py b/lib/galaxy/jobs/runners/util/__init__.py
index 73bac582bbb..4aa4cce543e 100644
--- a/lib/galaxy/jobs/runners/util/__init__.py
+++ b/lib/galaxy/jobs/runners/util/__init__.py
@@ -6,19 +6,18 @@ functionality shared between Galaxy and the Pulsar.
 from galaxy.util.bunch import Bunch
 from .kill import kill_pid
 
-
 runner_states = Bunch(
-    WALLTIME_REACHED='walltime_reached',
-    MEMORY_LIMIT_REACHED='memory_limit_reached',
-    JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER='Job output not returned from cluster',
-    UNKNOWN_ERROR='unknown_error',
-    GLOBAL_WALLTIME_REACHED='global_walltime_reached',
-    OUTPUT_SIZE_LIMIT='output_size_limit',
-    TOOL_DETECT_ERROR='tool_detected',  # job runner interaction worked fine but the tool indicated error
+    WALLTIME_REACHED="walltime_reached",
+    MEMORY_LIMIT_REACHED="memory_limit_reached",
+    JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER="Job output not returned from cluster",
+    UNKNOWN_ERROR="unknown_error",
+    GLOBAL_WALLTIME_REACHED="global_walltime_reached",
+    OUTPUT_SIZE_LIMIT="output_size_limit",
+    TOOL_DETECT_ERROR="tool_detected",  # job runner interaction worked fine but the tool indicated error
 )
 
 
 __all__ = (
-    'kill_pid',
-    'runner_states',
+    "kill_pid",
+    "runner_states",
 )
diff --git a/lib/galaxy/jobs/runners/util/cli/__init__.py b/lib/galaxy/jobs/runners/util/cli/__init__.py
index 5e199fe787b..9b677bea0a8 100644
--- a/lib/galaxy/jobs/runners/util/cli/__init__.py
+++ b/lib/galaxy/jobs/runners/util/cli/__init__.py
@@ -4,7 +4,7 @@ import json
 
 from galaxy.util.plugin_config import plugins_dict
 
-DEFAULT_SHELL_PLUGIN = 'LocalShell'
+DEFAULT_SHELL_PLUGIN = "LocalShell"
 
 ERROR_MESSAGE_NO_JOB_PLUGIN = "No job plugin parameter found, cannot create CLI job interface"
 ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN = "Failed to find job_plugin of type %s, available types include %s"
@@ -17,8 +17,7 @@ class CliInterface:
     """
 
     def __init__(self):
-        """
-        """
+        """ """
         module_prefix = self.__module__
         self.cli_shells = plugins_dict(f"{module_prefix}.shell", "__name__")
         self.cli_job_interfaces = plugins_dict(f"{module_prefix}.job", "__name__")
@@ -34,17 +33,19 @@ class CliInterface:
         return shell, job_interface
 
     def get_shell_plugin(self, shell_params):
-        shell_plugin = shell_params.get('plugin', DEFAULT_SHELL_PLUGIN)
+        shell_plugin = shell_params.get("plugin", DEFAULT_SHELL_PLUGIN)
         requested_shell_settings = json.dumps(shell_params, sort_keys=True)
         if requested_shell_settings not in self.active_cli_shells:
             shell_plugin_class = self.cli_shells.get(shell_plugin)
             if not shell_plugin_class:
-                raise ValueError(f"Unknown shell_plugin [{shell_plugin}], available plugins are {list(self.cli_shells.keys())}")
+                raise ValueError(
+                    f"Unknown shell_plugin [{shell_plugin}], available plugins are {list(self.cli_shells.keys())}"
+                )
             self.active_cli_shells[requested_shell_settings] = shell_plugin_class(**shell_params)
         return self.active_cli_shells[requested_shell_settings]
 
     def get_job_interface(self, job_params):
-        job_plugin = job_params.get('plugin')
+        job_plugin = job_params.get("plugin")
         if not job_plugin:
             raise ValueError(ERROR_MESSAGE_NO_JOB_PLUGIN)
         job_plugin_class = self.cli_job_interfaces.get(job_plugin)
@@ -54,6 +55,6 @@ class CliInterface:
 
 
 def split_params(params):
-    shell_params = {k.replace('shell_', '', 1): v for k, v in params.items() if k.startswith('shell_')}
-    job_params = {k.replace('job_', '', 1): v for k, v in params.items() if k.startswith('job_')}
+    shell_params = {k.replace("shell_", "", 1): v for k, v in params.items() if k.startswith("shell_")}
+    job_params = {k.replace("job_", "", 1): v for k, v in params.items() if k.startswith("job_")}
     return shell_params, job_params
diff --git a/lib/galaxy/jobs/runners/util/cli/factory.py b/lib/galaxy/jobs/runners/util/cli/factory.py
index 64f8cb944f9..e7fe72b3c37 100644
--- a/lib/galaxy/jobs/runners/util/cli/factory.py
+++ b/lib/galaxy/jobs/runners/util/cli/factory.py
@@ -1,12 +1,12 @@
 try:
     from galaxy.jobs.runners.util.cli import (
         CliInterface,
-        split_params
+        split_params,
     )
 except ImportError:
     from pulsar.managers.util.cli import (  # type: ignore[no-redef]
         CliInterface,
-        split_params
+        split_params,
     )
 
 
diff --git a/lib/galaxy/jobs/runners/util/cli/job/__init__.py b/lib/galaxy/jobs/runners/util/cli/job/__init__.py
index 73d3f0b53e3..829724143ed 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/__init__.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/__init__.py
@@ -3,25 +3,25 @@ Abstract base class for cli job plugins.
 """
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 from enum import Enum
 
 try:
     from galaxy.model import Job
+
     job_states = Job.states
 except ImportError:
 
     # Not in Galaxy, map Galaxy job states to Pulsar ones.
     class job_states(str, Enum):  # type: ignore[no-redef]
-        RUNNING = 'running'
-        OK = 'complete'
-        QUEUED = 'queued'
+        RUNNING = "running"
+        OK = "complete"
+        QUEUED = "queued"
         ERROR = "failed"
 
 
 class BaseJobExec(metaclass=ABCMeta):
-
     def __init__(self, **params):
         """
         Constructor for CLI job executor.
@@ -29,7 +29,7 @@ class BaseJobExec(metaclass=ABCMeta):
         self.params = params.copy()
 
     def job_script_kwargs(self, ofile, efile, job_name):
-        """ Return extra keyword argument for consumption by job script
+        """Return extra keyword argument for consumption by job script
         module.
         """
         return {}
@@ -86,6 +86,6 @@ class BaseJobExec(metaclass=ABCMeta):
 
 
 __all__ = (
-    'BaseJobExec',
-    'job_states',
+    "BaseJobExec",
+    "job_states",
 )
diff --git a/lib/galaxy/jobs/runners/util/cli/job/lsf.py b/lib/galaxy/jobs/runners/util/cli/job/lsf.py
index a1e871b732d..68c96345096 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/lsf.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/lsf.py
@@ -3,48 +3,48 @@
 from logging import getLogger
 from os import path
 
-from ..job import BaseJobExec, job_states
+from ..job import (
+    BaseJobExec,
+    job_states,
+)
 from ... import runner_states
 
 log = getLogger(__name__)
 
 argmap = {
-    'memory': '-M',  # There is code in job_script_kwargs relying on this name's setting
-    'cores': '-n',
-    'queue': '-q',
-    'working_dir': '-cwd',
-    'project': '-P'
+    "memory": "-M",  # There is code in job_script_kwargs relying on this name's setting
+    "cores": "-n",
+    "queue": "-q",
+    "working_dir": "-cwd",
+    "project": "-P",
 }
 
 
 class LSF(BaseJobExec):
-
     def job_script_kwargs(self, ofile, efile, job_name):
-        scriptargs = {'-o': ofile,
-                      '-e': efile,
-                      '-J': job_name}
+        scriptargs = {"-o": ofile, "-e": efile, "-J": job_name}
 
         # Map arguments using argmap.
         for k, v in self.params.items():
-            if k == 'plugin' or k == 'excluded_hosts':
+            if k == "plugin" or k == "excluded_hosts":
                 continue
             try:
-                if k == 'memory':
+                if k == "memory":
                     # Memory requires both -m and -R rusage[mem=v] request
-                    scriptargs['-R'] = f"\"rusage[mem={v}]\""
-                if not k.startswith('-'):
+                    scriptargs["-R"] = f'"rusage[mem={v}]"'
+                if not k.startswith("-"):
                     k = argmap[k]
                 scriptargs[k] = v
             except Exception:
-                log.warning(f'Unrecognized long argument passed to LSF CLI plugin: {k}')
+                log.warning(f"Unrecognized long argument passed to LSF CLI plugin: {k}")
 
         # Generated template.
-        template_scriptargs = ''
+        template_scriptargs = ""
         for k, v in scriptargs.items():
-            template_scriptargs += f'#BSUB {k} {v}\n'
+            template_scriptargs += f"#BSUB {k} {v}\n"
         # Excluded hosts use the same -R option already in use for mem, so easier adding here.
         for host in self._get_excluded_hosts():
-            template_scriptargs += f'#BSUB -R \"select[hname!=\'{host}\']\"\n'
+            template_scriptargs += f"#BSUB -R \"select[hname!='{host}']\"\n"
         return dict(headers=template_scriptargs)
 
     def submit(self, script_file):
@@ -55,10 +55,10 @@ class LSF(BaseJobExec):
         return "bsub <%s | awk '{ print $2}' | sed 's/[<>]//g'" % script_file
 
     def delete(self, job_id):
-        return f'bkill {job_id}'
+        return f"bkill {job_id}"
 
     def get_status(self, job_ids=None):
-        return "bjobs -a -o \"id stat\" -noheader"  # check this
+        return 'bjobs -a -o "id stat" -noheader'  # check this
 
     def get_single_status(self, job_id):
         return f"bjobs -o stat -noheader {job_id}"
@@ -103,16 +103,16 @@ class LSF(BaseJobExec):
         # https://www.ibm.com/support/knowledgecenter/en/SSETD4_9.1.2/lsf_command_ref/bjobs.1.html
         try:
             return {
-                'EXIT': job_states.ERROR,
-                'RUN': job_states.RUNNING,
-                'PEND': job_states.QUEUED,
-                'DONE': job_states.OK,
-                'PSUSP': job_states.ERROR,
-                'USUSP': job_states.ERROR,
-                'SSUSP': job_states.ERROR,
-                'UNKWN': job_states.ERROR,
-                'WAIT': job_states.QUEUED,
-                'ZOMBI': job_states.ERROR
+                "EXIT": job_states.ERROR,
+                "RUN": job_states.RUNNING,
+                "PEND": job_states.QUEUED,
+                "DONE": job_states.OK,
+                "PSUSP": job_states.ERROR,
+                "USUSP": job_states.ERROR,
+                "SSUSP": job_states.ERROR,
+                "UNKWN": job_states.ERROR,
+                "WAIT": job_states.QUEUED,
+                "ZOMBI": job_states.ERROR,
             }.get(state)
         except KeyError:
             raise KeyError(f"Failed to map LSF status code [{state}] to job state.")
@@ -143,4 +143,4 @@ class LSF(BaseJobExec):
         return []
 
 
-__all__ = ('LSF',)
+__all__ = ("LSF",)
diff --git a/lib/galaxy/jobs/runners/util/cli/job/pbs.py b/lib/galaxy/jobs/runners/util/cli/job/pbs.py
index 19746660ae3..b885a2de118 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/pbs.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/pbs.py
@@ -8,25 +8,25 @@ log = getLogger(__name__)
 
 class OpenPBS(Torque):
 
-    ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to OpenPBS CLI plugin: %s'
+    ERROR_MESSAGE_UNRECOGNIZED_ARG = "Unrecognized long argument passed to OpenPBS CLI plugin: %s"
 
     def get_status(self, job_ids=None):
-        return 'qstat -f -F json'
+        return "qstat -f -F json"
 
     def get_single_status(self, job_id):
-        return f'qstat -f {job_id}'
+        return f"qstat -f {job_id}"
 
     def parse_status(self, status, job_ids):
         try:
             data = json.loads(status)
         except Exception:
-            log.warning(f'No valid qstat JSON return from `qstat -f -F json`, got the following: {status}')
+            log.warning(f"No valid qstat JSON return from `qstat -f -F json`, got the following: {status}")
         rval = {}
-        for job_id, job in data.get('Jobs', {}).items():
+        for job_id, job in data.get("Jobs", {}).items():
             if job_id in job_ids:
                 # map PBS job states to Galaxy job states.
-                rval[id] = self._get_job_state(job['job_state'])
+                rval[id] = self._get_job_state(job["job_state"])
         return rval
 
 
-__all__ = ('OpenPBS',)
+__all__ = ("OpenPBS",)
diff --git a/lib/galaxy/jobs/runners/util/cli/job/slurm.py b/lib/galaxy/jobs/runners/util/cli/job/slurm.py
index 9ae10295ace..5b694b13253 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py
@@ -2,46 +2,42 @@
 # non-submit host and using a Slurm cluster.
 from logging import getLogger
 
-from ..job import BaseJobExec, job_states
+from ..job import (
+    BaseJobExec,
+    job_states,
+)
 
 log = getLogger(__name__)
 
-argmap = {
-    'time': '-t',
-    'ncpus': '-c',
-    'partition': '-p'
-}
+argmap = {"time": "-t", "ncpus": "-c", "partition": "-p"}
 
 
 class Slurm(BaseJobExec):
-
     def job_script_kwargs(self, ofile, efile, job_name):
-        scriptargs = {'-o': ofile,
-                      '-e': efile,
-                      '-J': job_name}
+        scriptargs = {"-o": ofile, "-e": efile, "-J": job_name}
 
         # Map arguments using argmap.
         for k, v in self.params.items():
-            if k == 'plugin':
+            if k == "plugin":
                 continue
             try:
-                if not k.startswith('-'):
+                if not k.startswith("-"):
                     k = argmap[k]
                 scriptargs[k] = v
             except Exception:
-                log.warning(f'Unrecognized long argument passed to Slurm CLI plugin: {k}')
+                log.warning(f"Unrecognized long argument passed to Slurm CLI plugin: {k}")
 
         # Generated template.
-        template_scriptargs = ''
+        template_scriptargs = ""
         for k, v in scriptargs.items():
-            template_scriptargs += f'#SBATCH {k} {v}\n'
+            template_scriptargs += f"#SBATCH {k} {v}\n"
         return dict(headers=template_scriptargs)
 
     def submit(self, script_file):
-        return f'sbatch {script_file}'
+        return f"sbatch {script_file}"
 
     def delete(self, job_id):
-        return f'scancel {job_id}'
+        return f"scancel {job_id}"
 
     def get_status(self, job_ids=None):
         return "squeue -a -o '%A %t'"
@@ -71,14 +67,14 @@ class Slurm(BaseJobExec):
     def _get_job_state(self, state):
         try:
             return {
-                'F': job_states.ERROR,
-                'R': job_states.RUNNING,
-                'CG': job_states.RUNNING,
-                'PD': job_states.QUEUED,
-                'CD': job_states.OK
+                "F": job_states.ERROR,
+                "R": job_states.RUNNING,
+                "CG": job_states.RUNNING,
+                "PD": job_states.QUEUED,
+                "CD": job_states.OK,
             }.get(state)
         except KeyError:
             raise KeyError(f"Failed to map slurm status code [{state}] to job state.")
 
 
-__all__ = ('Slurm',)
+__all__ = ("Slurm",)
diff --git a/lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py b/lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
index 78f2576ca38..1cc09708767 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
@@ -2,17 +2,17 @@ import re
 
 from .torque import Torque
 
-__all__ = ('SlurmTorque',)
+__all__ = ("SlurmTorque",)
 
 
 class SlurmTorque(Torque):
-    """ A CLI job executor for Slurm's Torque compatibility mode. This differs
+    """A CLI job executor for Slurm's Torque compatibility mode. This differs
     from real torque CLI in that -x command line is not available so job status
     needs to be parsed from qstat table instead of XML.
     """
 
     def get_status(self, job_ids=None):
-        return 'qstat'
+        return "qstat"
 
     def parse_status(self, status, job_ids):
         rval = {}
diff --git a/lib/galaxy/jobs/runners/util/cli/job/torque.py b/lib/galaxy/jobs/runners/util/cli/job/torque.py
index a1a988d8cf3..cb801ed1c0a 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/torque.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py
@@ -1,66 +1,69 @@
 from logging import getLogger
 
 from galaxy.util import parse_xml_string
-from ..job import BaseJobExec, job_states
+from ..job import (
+    BaseJobExec,
+    job_states,
+)
 
 log = getLogger(__name__)
 
 
-argmap = {'destination': '-q',
-          'Execution_Time': '-a',
-          'Account_Name': '-A',
-          'Checkpoint': '-c',
-          'Error_Path': '-e',
-          'Group_List': '-g',
-          'Hold_Types': '-h',
-          'Join_Paths': '-j',
-          'Keep_Files': '-k',
-          'Resource_List': '-l',
-          'Mail_Points': '-m',
-          'Mail_Users': '-M',
-          'Job_Name': '-N',
-          'Output_Path': '-o',
-          'Priority': '-p',
-          'Rerunable': '-r',
-          'Shell_Path_List': '-S',
-          'job_array_request': '-t',
-          'User_List': '-u',
-          'Variable_List': '-v'}
+argmap = {
+    "destination": "-q",
+    "Execution_Time": "-a",
+    "Account_Name": "-A",
+    "Checkpoint": "-c",
+    "Error_Path": "-e",
+    "Group_List": "-g",
+    "Hold_Types": "-h",
+    "Join_Paths": "-j",
+    "Keep_Files": "-k",
+    "Resource_List": "-l",
+    "Mail_Points": "-m",
+    "Mail_Users": "-M",
+    "Job_Name": "-N",
+    "Output_Path": "-o",
+    "Priority": "-p",
+    "Rerunable": "-r",
+    "Shell_Path_List": "-S",
+    "job_array_request": "-t",
+    "User_List": "-u",
+    "Variable_List": "-v",
+}
 
 
 class Torque(BaseJobExec):
 
-    ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s'
+    ERROR_MESSAGE_UNRECOGNIZED_ARG = "Unrecognized long argument passed to Torque CLI plugin: %s"
 
     def job_script_kwargs(self, ofile, efile, job_name):
-        pbsargs = {'-o': ofile,
-                   '-e': efile,
-                   '-N': job_name}
+        pbsargs = {"-o": ofile, "-e": efile, "-N": job_name}
         for k, v in self.params.items():
-            if k == 'plugin':
+            if k == "plugin":
                 continue
             try:
-                if not k.startswith('-'):
+                if not k.startswith("-"):
                     k = argmap[k]
                 pbsargs[k] = v
             except KeyError:
                 log.warning(self.ERROR_MESSAGE_UNRECOGNIZED_ARG, k)
-        template_pbsargs = ''
+        template_pbsargs = ""
         for k, v in pbsargs.items():
-            template_pbsargs += f'#PBS {k} {v}\n'
+            template_pbsargs += f"#PBS {k} {v}\n"
         return dict(headers=template_pbsargs)
 
     def submit(self, script_file):
-        return f'qsub {script_file}'
+        return f"qsub {script_file}"
 
     def delete(self, job_id):
-        return f'qdel {job_id}'
+        return f"qdel {job_id}"
 
     def get_status(self, job_ids=None):
-        return 'qstat -x'
+        return "qstat -x"
 
     def get_single_status(self, job_id):
-        return f'qstat -f {job_id}'
+        return f"qstat -f {job_id}"
 
     def parse_status(self, status, job_ids):
         # in case there's noise in the output, find the big blob 'o xml
@@ -69,40 +72,37 @@ class Torque(BaseJobExec):
         for line in status.strip().splitlines():
             try:
                 tree = parse_xml_string(line.strip())
-                assert tree.tag == 'Data'
+                assert tree.tag == "Data"
                 break
             except Exception:
                 tree = None
         if tree is None:
-            log.warning(f'No valid qstat XML return from `qstat -x`, got the following: {status}')
+            log.warning(f"No valid qstat XML return from `qstat -x`, got the following: {status}")
             return None
         else:
-            for job in tree.findall('Job'):
-                id = job.find('Job_Id').text
+            for job in tree.findall("Job"):
+                id = job.find("Job_Id").text
                 if id in job_ids:
-                    state = job.find('job_state').text
+                    state = job.find("job_state").text
                     # map PBS job states to Galaxy job states.
                     rval[id] = self._get_job_state(state)
         return rval
 
     def parse_single_status(self, status, job_id):
         for line in status.splitlines():
-            line = line.split(' = ')
-            if line[0].strip() == 'job_state':
+            line = line.split(" = ")
+            if line[0].strip() == "job_state":
                 return self._get_job_state(line[1].strip())
         # no state found, job has exited
         return job_states.OK
 
     def _get_job_state(self, state):
         try:
-            return {
-                'E': job_states.RUNNING,
-                'R': job_states.RUNNING,
-                'Q': job_states.QUEUED,
-                'C': job_states.OK
-            }.get(state)
+            return {"E": job_states.RUNNING, "R": job_states.RUNNING, "Q": job_states.QUEUED, "C": job_states.OK}.get(
+                state
+            )
         except KeyError:
             raise KeyError(f"Failed to map torque status code [{state}] to job state.")
 
 
-__all__ = ('Torque',)
+__all__ = ("Torque",)
diff --git a/lib/galaxy/jobs/runners/util/cli/shell/__init__.py b/lib/galaxy/jobs/runners/util/cli/shell/__init__.py
index 54e77e22bd1..5e650fc2835 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/__init__.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/__init__.py
@@ -3,12 +3,11 @@ Abstract base class for runners which execute commands via a shell.
 """
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
 
 class BaseShellExec(metaclass=ABCMeta):
-
     @abstractmethod
     def __init__(self, *args, **kwargs):
         """
diff --git a/lib/galaxy/jobs/runners/util/cli/shell/local.py b/lib/galaxy/jobs/runners/util/cli/shell/local.py
index 440eccda437..933ba622f69 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/local.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/local.py
@@ -2,22 +2,21 @@ import os
 from logging import getLogger
 from subprocess import (
     PIPE,
-    Popen
+    Popen,
 )
 from tempfile import TemporaryFile
 from time import sleep
 
-
 from galaxy.util.bunch import Bunch
 from . import BaseShellExec
 from ....util.process_groups import (
     check_pg,
-    kill_pg
+    kill_pg,
 )
 
 log = getLogger(__name__)
 
-TIMEOUT_ERROR_MESSAGE = 'Execution timed out'
+TIMEOUT_ERROR_MESSAGE = "Execution timed out"
 TIMEOUT_RETURN_CODE = -1
 DEFAULT_TIMEOUT = 60
 DEFAULT_TIMEOUT_CHECK_INTERVAL = 3
@@ -49,7 +48,9 @@ class LocalShell(BaseShellExec):
     def __init__(self, **kwds):
         pass
 
-    def execute(self, cmd, persist=False, timeout=DEFAULT_TIMEOUT, timeout_check_interval=DEFAULT_TIMEOUT_CHECK_INTERVAL, **kwds):
+    def execute(
+        self, cmd, persist=False, timeout=DEFAULT_TIMEOUT, timeout_check_interval=DEFAULT_TIMEOUT_CHECK_INTERVAL, **kwds
+    ):
         is_cmd_string = isinstance(cmd, str)
         outf = TemporaryFile()
         p = Popen(cmd, stdin=None, stdout=outf, stderr=PIPE, shell=is_cmd_string, preexec_fn=os.setpgrp)
@@ -62,7 +63,7 @@ class LocalShell(BaseShellExec):
             sleep(timeout_check_interval)
         else:
             kill_pg(p.pid)
-            return Bunch(stdout='', stderr=TIMEOUT_ERROR_MESSAGE, returncode=TIMEOUT_RETURN_CODE)
+            return Bunch(stdout="", stderr=TIMEOUT_ERROR_MESSAGE, returncode=TIMEOUT_RETURN_CODE)
         outf.seek(0)
         # Need to poll once to establish return code
         p.poll()
@@ -71,7 +72,7 @@ class LocalShell(BaseShellExec):
 
 def _read_str(stream):
     contents = stream.read()
-    return contents.decode('UTF-8') if isinstance(contents, bytes) else contents
+    return contents.decode("UTF-8") if isinstance(contents, bytes) else contents
 
 
-__all__ = ('LocalShell',)
+__all__ = ("LocalShell",)
diff --git a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
index 18c128bde68..9302a3fdc41 100644
--- a/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
+++ b/lib/galaxy/jobs/runners/util/cli/shell/rsh.py
@@ -15,12 +15,11 @@ from .local import LocalShell
 log = logging.getLogger(__name__)
 logging.getLogger("paramiko").setLevel(logging.WARNING)  # paramiko logging is very verbose
 
-__all__ = ('RemoteShell', 'SecureShell', 'GlobusSecureShell', 'ParamikoShell')
+__all__ = ("RemoteShell", "SecureShell", "GlobusSecureShell", "ParamikoShell")
 
 
 class RemoteShell(LocalShell):
-
-    def __init__(self, rsh='rsh', rcp='rcp', hostname='localhost', username=None, options=None, **kwargs):
+    def __init__(self, rsh="rsh", rcp="rcp", hostname="localhost", username=None, options=None, **kwargs):
         super().__init__(**kwargs)
         self.rsh = rsh
         self.rcp = rcp
@@ -41,22 +40,30 @@ class RemoteShell(LocalShell):
 
 
 class SecureShell(RemoteShell):
-
-    def __init__(self, rsh='ssh', rcp='scp', private_key=None, port=None, strict_host_key_checking=True, **kwargs):
+    def __init__(self, rsh="ssh", rcp="scp", private_key=None, port=None, strict_host_key_checking=True, **kwargs):
         options = []
         if not string_as_bool(strict_host_key_checking):
             options.extend(["-o", "StrictHostKeyChecking=no", "-o", "UserKnownHostsFile=/dev/null"])
         options.extend(["-o", "ConnectTimeout=60"])
         if private_key:
-            options.extend(['-i', private_key])
+            options.extend(["-i", private_key])
         if port:
-            options.extend(['-p', str(port)])
+            options.extend(["-p", str(port)])
         super().__init__(rsh=rsh, rcp=rcp, options=options, **kwargs)
 
 
 class ParamikoShell:
-
-    def __init__(self, username, hostname, password=None, private_key=None, port=22, timeout=60, strict_host_key_checking=True, **kwargs):
+    def __init__(
+        self,
+        username,
+        hostname,
+        password=None,
+        private_key=None,
+        port=22,
+        timeout=60,
+        strict_host_key_checking=True,
+        **kwargs,
+    ):
         self.username = username
         self.hostname = hostname
         self.password = password
@@ -71,17 +78,20 @@ class ParamikoShell:
     def connect(self):
         log.info("Attempting establishment of new paramiko SSH channel")
         self.ssh = paramiko.SSHClient()
-        self.ssh.set_missing_host_key_policy(paramiko.RejectPolicy() if self.strict_host_key_checking else paramiko.WarningPolicy())
+        self.ssh.set_missing_host_key_policy(
+            paramiko.RejectPolicy() if self.strict_host_key_checking else paramiko.WarningPolicy()
+        )
         self.ssh.load_system_host_keys()
-        self.ssh.connect(hostname=self.hostname,
-                         port=self.port,
-                         username=self.username,
-                         password=self.password,
-                         key_filename=self.private_key,
-                         timeout=self.timeout)
+        self.ssh.connect(
+            hostname=self.hostname,
+            port=self.port,
+            username=self.username,
+            password=self.password,
+            key_filename=self.private_key,
+            timeout=self.timeout,
+        )
 
     def execute(self, cmd, timeout=60):
-
         def retry():
             try:
                 _, stdout, stderr = self._execute(cmd, timeout)
@@ -101,6 +111,5 @@ class ParamikoShell:
 
 
 class GlobusSecureShell(SecureShell):
-
-    def __init__(self, rsh='gsissh', rcp='gsiscp', **kwargs):
+    def __init__(self, rsh="gsissh", rcp="gsiscp", **kwargs):
         super().__init__(rsh=rsh, rcp=rcp, **kwargs)
diff --git a/lib/galaxy/jobs/runners/util/condor/__init__.py b/lib/galaxy/jobs/runners/util/condor/__init__.py
index 93b2c5cdf5b..c608d13e9ca 100644
--- a/lib/galaxy/jobs/runners/util/condor/__init__.py
+++ b/lib/galaxy/jobs/runners/util/condor/__init__.py
@@ -3,23 +3,22 @@ Condor helper utilities.
 """
 from subprocess import (
     CalledProcessError,
-    check_call
+    check_call,
 )
 
 from galaxy.util import (
     commands,
-    unicodify
+    unicodify,
 )
 from ..external import parse_external_id
 
 DEFAULT_QUERY_CLASSAD = dict(
-    universe='vanilla',
-    getenv='true',
-    notification='NEVER',
+    universe="vanilla",
+    getenv="true",
+    notification="NEVER",
 )
 
-PROBLEM_PARSING_EXTERNAL_ID = \
-    "Failed to find job id from condor_submit"
+PROBLEM_PARSING_EXTERNAL_ID = "Failed to find job id from condor_submit"
 
 SUBMIT_PARAM_PREFIX = "submit_"
 
@@ -59,13 +58,13 @@ def build_submit_description(executable, output, error, user_log, query_params):
 
     submit_description = []
     for key, value in all_query_params.items():
-        submit_description.append(f'{key} = {value}')
+        submit_description.append(f"{key} = {value}")
     submit_description.append(f"executable = {executable}")
     submit_description.append(f"output = {output}")
     submit_description.append(f"error = {error}")
     submit_description.append(f"log = {user_log}")
-    submit_description.append('queue')
-    return '\n'.join(submit_description)
+    submit_description.append("queue")
+    return "\n".join(submit_description)
 
 
 def condor_submit(submit_file):
@@ -76,12 +75,12 @@ def condor_submit(submit_file):
     external_id = None
     failure_message = None
     try:
-        condor_message = commands.execute(('condor_submit', submit_file))
+        condor_message = commands.execute(("condor_submit", submit_file))
     except commands.CommandLineException as e:
         failure_message = unicodify(e)
     else:
         try:
-            external_id = parse_external_id(condor_message, type='condor')
+            external_id = parse_external_id(condor_message, type="condor")
         except Exception:
             failure_message = f"{PROBLEM_PARSING_EXTERNAL_ID}: {condor_message}"
     return external_id, failure_message
@@ -94,7 +93,7 @@ def condor_stop(external_id):
     """
     failure_message = None
     try:
-        check_call(('condor_rm', external_id))
+        check_call(("condor_rm", external_id))
     except CalledProcessError:
         failure_message = "condor_rm failed"
     except Exception as e:
@@ -103,8 +102,7 @@ def condor_stop(external_id):
 
 
 def summarize_condor_log(log_file, external_id):
-    """
-    """
+    """ """
     log_job_id = external_id.zfill(3)
     s1 = s4 = s7 = s5 = s9 = False
     with open(log_file) as log_handle:
diff --git a/lib/galaxy/jobs/runners/util/env.py b/lib/galaxy/jobs/runners/util/env.py
index 3de52700078..b7a30d89505 100644
--- a/lib/galaxy/jobs/runners/util/env.py
+++ b/lib/galaxy/jobs/runners/util/env.py
@@ -2,7 +2,7 @@ RAW_VALUE_BY_DEFAULT = False
 
 
 def env_to_statement(env):
-    ''' Return the abstraction description of an environment variable definition
+    """Return the abstraction description of an environment variable definition
     into a statement for shell script.
 
     >>> env_to_statement(dict(name='X', value='Y'))
@@ -20,20 +20,20 @@ def env_to_statement(env):
     '. "S"'
     >>> env_to_statement(dict(execute="module load java/1.5.1"))
     'module load java/1.5.1'
-    '''
-    source_file = env.get('file', None)
+    """
+    source_file = env.get("file", None)
     if source_file:
-        return f'. {__escape(source_file, env)}'
-    execute = env.get('execute', None)
+        return f". {__escape(source_file, env)}"
+    execute = env.get("execute", None)
     if execute:
         return execute
-    name = env['name']
-    value = __escape(env['value'], env)
-    return f'{name}={value}; export {name}'
+    name = env["name"]
+    value = __escape(env["value"], env)
+    return f"{name}={value}; export {name}"
 
 
 def __escape(value, env):
-    raw = env.get('raw', RAW_VALUE_BY_DEFAULT)
+    raw = env.get("raw", RAW_VALUE_BY_DEFAULT)
     if not raw:
         value = '"' + value.replace('"', '\\"') + '"'
     return value
diff --git a/lib/galaxy/jobs/runners/util/external.py b/lib/galaxy/jobs/runners/util/external.py
index a02b448fec0..863ee002933 100644
--- a/lib/galaxy/jobs/runners/util/external.py
+++ b/lib/galaxy/jobs/runners/util/external.py
@@ -3,9 +3,9 @@ from re import search
 EXTERNAL_ID_TYPE_ANY = None
 
 EXTERNAL_ID_PATTERNS = [
-    ('condor', r'submitted to cluster (\d+)\.'),
-    ('slurm', r'Submitted batch job (\w+)'),
-    ('torque', r'(.+)'),  # Default 'pattern' assumed by Galaxy code circa August 2013.
+    ("condor", r"submitted to cluster (\d+)\."),
+    ("slurm", r"Submitted batch job (\w+)"),
+    ("torque", r"(.+)"),  # Default 'pattern' assumed by Galaxy code circa August 2013.
 ]
 
 
diff --git a/lib/galaxy/jobs/runners/util/job_script/__init__.py b/lib/galaxy/jobs/runners/util/job_script/__init__.py
index 61f13eb7b49..f48b2e41063 100644
--- a/lib/galaxy/jobs/runners/util/job_script/__init__.py
+++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py
@@ -3,7 +3,10 @@ import os
 import subprocess
 import time
 from string import Template
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 from pkg_resources import resource_string
 
@@ -14,17 +17,13 @@ from galaxy.util import (
 )
 
 log = logging.getLogger(__name__)
-DEFAULT_SHELL = '/bin/bash'
+DEFAULT_SHELL = "/bin/bash"
 
-DEFAULT_JOB_FILE_TEMPLATE = Template(
-    unicodify(resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh'))
-)
+DEFAULT_JOB_FILE_TEMPLATE = Template(unicodify(resource_string(__name__, "DEFAULT_JOB_FILE_TEMPLATE.sh")))
 
-SLOTS_STATEMENT_CLUSTER_DEFAULT = \
-    unicodify(resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh'))
+SLOTS_STATEMENT_CLUSTER_DEFAULT = unicodify(resource_string(__name__, "CLUSTER_SLOTS_STATEMENT.sh"))
 
-MEMORY_STATEMENT_DEFAULT = \
-    unicodify(resource_string(__name__, 'MEMORY_STATEMENT.sh'))
+MEMORY_STATEMENT_DEFAULT = unicodify(resource_string(__name__, "MEMORY_STATEMENT.sh"))
 
 SLOTS_STATEMENT_SINGLE = """
 GALAXY_SLOTS="1"
@@ -42,21 +41,21 @@ fi
 INTEGRITY_SYNC_COMMAND = "/bin/sync"
 DEFAULT_INTEGRITY_CHECK = True
 DEFAULT_INTEGRITY_COUNT = 35
-DEFAULT_INTEGRITY_SLEEP = .25
-REQUIRED_TEMPLATE_PARAMS = ['working_directory', 'command', 'exit_code_path']
+DEFAULT_INTEGRITY_SLEEP = 0.25
+REQUIRED_TEMPLATE_PARAMS = ["working_directory", "command", "exit_code_path"]
 OPTIONAL_TEMPLATE_PARAMS: Dict[str, Any] = {
-    'galaxy_lib': None,
-    'galaxy_virtual_env': None,
-    'headers': '',
-    'env_setup_commands': [],
-    'slots_statement': SLOTS_STATEMENT_CLUSTER_DEFAULT,
-    'memory_statement': MEMORY_STATEMENT_DEFAULT,
-    'instrument_pre_commands': '',
-    'instrument_post_commands': '',
-    'integrity_injection': INTEGRITY_INJECTION,
-    'shell': DEFAULT_SHELL,
-    'preserve_python_environment': True,
-    'tmp_dir_creation_statement': '""',
+    "galaxy_lib": None,
+    "galaxy_virtual_env": None,
+    "headers": "",
+    "env_setup_commands": [],
+    "slots_statement": SLOTS_STATEMENT_CLUSTER_DEFAULT,
+    "memory_statement": MEMORY_STATEMENT_DEFAULT,
+    "instrument_pre_commands": "",
+    "instrument_post_commands": "",
+    "integrity_injection": INTEGRITY_INJECTION,
+    "shell": DEFAULT_SHELL,
+    "preserve_python_environment": True,
+    "tmp_dir_creation_statement": '""',
 }
 
 
@@ -93,8 +92,8 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     if job_instrumenter:
         del kwds["job_instrumenter"]
         working_directory = kwds.get("metadata_directory", kwds["working_directory"])
-        kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(working_directory) or ''
-        kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(working_directory) or ''
+        kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(working_directory) or ""
+        kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(working_directory) or ""
 
     template_params = OPTIONAL_TEMPLATE_PARAMS.copy()
     template_params.update(**kwds)
@@ -107,16 +106,12 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     return template.safe_substitute(template_params)
 
 
-def write_script(
-        path,
-        contents,
-        job_io: JobIO,
-        mode=RWXR_XR_X):
+def write_script(path, contents, job_io: JobIO, mode=RWXR_XR_X):
     dir = os.path.dirname(path)
     if not os.path.exists(dir):
         os.makedirs(dir)
 
-    with open(path, 'w', encoding='utf-8') as f:
+    with open(path, "w", encoding="utf-8") as f:
         f.write(unicodify(contents))
     os.chmod(path, mode)
     if job_io.check_job_script_integrity:
@@ -155,7 +150,7 @@ def _handle_script_integrity(path, check_job_script_integrity_count, check_job_s
 
 
 __all__ = (
-    'job_script',
-    'write_script',
-    'INTEGRITY_INJECTION',
+    "job_script",
+    "write_script",
+    "INTEGRITY_INJECTION",
 )
diff --git a/lib/galaxy/jobs/runners/util/kill.py b/lib/galaxy/jobs/runners/util/kill.py
index 6b4e3f8854d..f0abd62fede 100644
--- a/lib/galaxy/jobs/runners/util/kill.py
+++ b/lib/galaxy/jobs/runners/util/kill.py
@@ -5,9 +5,12 @@ from platform import system
 from time import sleep
 
 try:
-    from psutil import NoSuchProcess, Process
+    from psutil import (
+        NoSuchProcess,
+        Process,
+    )
 except ImportError:
-    """ Don't make psutil a strict requirement, but use if available. """
+    """Don't make psutil a strict requirement, but use if available."""
     Process = None
 
 
@@ -32,7 +35,7 @@ def _psutil_kill_pid(pid):
 
 
 def _stock_kill_pid(pid):
-    is_windows = system() == 'Windows'
+    is_windows = system() == "Windows"
 
     if is_windows:
         __kill_windows(pid)
@@ -42,7 +45,7 @@ def _stock_kill_pid(pid):
 
 def __kill_windows(pid):
     try:
-        subprocess.check_call(['taskkill', '/F', '/T', '/PID', pid])
+        subprocess.check_call(["taskkill", "/F", "/T", "/PID", pid])
     except subprocess.CalledProcessError:
         pass
 
diff --git a/lib/galaxy/jobs/runners/util/process_groups.py b/lib/galaxy/jobs/runners/util/process_groups.py
index c35d5397f9a..c56042b31c3 100644
--- a/lib/galaxy/jobs/runners/util/process_groups.py
+++ b/lib/galaxy/jobs/runners/util/process_groups.py
@@ -15,7 +15,12 @@ def check_pg(pgid):
         if e.errno == errno.ECHILD:
             log.debug("check_pg(): No process found in process group %d", pgid)
         else:
-            log.warning("check_pg(): Got errno %s when checking process group %d: %s", errno.errorcode[e.errno], pgid, e.strerror)
+            log.warning(
+                "check_pg(): Got errno %s when checking process group %d: %s",
+                errno.errorcode[e.errno],
+                pgid,
+                e.strerror,
+            )
         return False
     # Since we are passing os.WNOHANG to os.waitpid(), pid is 0 if no process
     # status is available immediately.
@@ -30,7 +35,13 @@ def kill_pg(pgid):
         except OSError as e:
             if e.errno == errno.ESRCH:
                 return
-            log.warning("Got errno %s when sending signal %d to process group %d: %s", errno.errorcode[e.errno], sig, pgid, e.strerror)
+            log.warning(
+                "Got errno %s when sending signal %d to process group %d: %s",
+                errno.errorcode[e.errno],
+                sig,
+                pgid,
+                e.strerror,
+            )
         sleep(1)
         if not check_pg(pgid):
             log.debug("Processes in process group %d successfully killed with signal %d", pgid, sig)
diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py
index 7c500646cf2..a77733c54a5 100644
--- a/lib/galaxy/jobs/runners/util/pykube_util.py
+++ b/lib/galaxy/jobs/runners/util/pykube_util.py
@@ -6,14 +6,14 @@ from pathlib import PurePath
 
 try:
     from pykube.config import KubeConfig
+    from pykube.exceptions import HTTPError
     from pykube.http import HTTPClient
     from pykube.objects import (
+        Ingress,
         Job,
         Pod,
         Service,
-        Ingress,
     )
-    from pykube.exceptions import HTTPError
 except ImportError as exc:
     KubeConfig = None
     Ingress = None
@@ -21,9 +21,11 @@ except ImportError as exc:
     Pod = None
     Service = None
     HTTPError = None
-    K8S_IMPORT_MESSAGE = ('The Python pykube package is required to use '
-                          'this feature, please install it or correct the '
-                          'following error:\nImportError %s' % str(exc))
+    K8S_IMPORT_MESSAGE = (
+        "The Python pykube package is required to use "
+        "this feature, please install it or correct the "
+        "following error:\nImportError %s" % str(exc)
+    )
 
 log = logging.getLogger(__name__)
 
@@ -31,9 +33,11 @@ DEFAULT_JOB_API_VERSION = "batch/v1"
 DEFAULT_SERVICE_API_VERSION = "v1"
 DEFAULT_INGRESS_API_VERSION = "extensions/v1beta1"
 DEFAULT_NAMESPACE = "default"
-INSTANCE_ID_INVALID_MESSAGE = ("Galaxy instance [%s] is either too long "
-                               "(>20 characters) or it includes non DNS "
-                               "acceptable characters, ignoring it.")
+INSTANCE_ID_INVALID_MESSAGE = (
+    "Galaxy instance [%s] is either too long "
+    "(>20 characters) or it includes non DNS "
+    "acceptable characters, ignoring it."
+)
 
 
 def ensure_pykube():
@@ -47,23 +51,23 @@ def pykube_client_from_dict(params):
     else:
         config_path = params.get("k8s_config_path")
         if config_path is None:
-            config_path = os.environ.get('KUBECONFIG', None)
+            config_path = os.environ.get("KUBECONFIG", None)
         if config_path is None:
-            config_path = '~/.kube/config'
+            config_path = "~/.kube/config"
         pykube_client = HTTPClient(KubeConfig.from_file(config_path))
     return pykube_client
 
 
 def produce_k8s_job_prefix(app_prefix=None, instance_id=None):
     job_name_elems = [app_prefix or "", instance_id or ""]
-    return '-'.join(elem for elem in job_name_elems if elem)
+    return "-".join(elem for elem in job_name_elems if elem)
 
 
 def pull_policy(params):
     # If this doesn't validate it returns None, that seems odd?
     if "k8s_pull_policy" in params:
-        if params['k8s_pull_policy'] in ["Always", "IfNotPresent", "Never"]:
-            return params['k8s_pull_policy']
+        if params["k8s_pull_policy"] in ["Always", "IfNotPresent", "Never"]:
+            return params["k8s_pull_policy"]
     return None
 
 
@@ -90,27 +94,22 @@ def find_pod_object_by_name(pykube_api, job_name, namespace=None):
 
 
 def is_pod_unschedulable(pykube_api, pod, namespace=None):
-    is_unschedulable = any(c.get("reason") == "Unschedulable" for c in pod.obj['status'].get('conditions', []))
-    if pod.obj['status'].get('phase') == "Pending" and is_unschedulable:
+    is_unschedulable = any(c.get("reason") == "Unschedulable" for c in pod.obj["status"].get("conditions", []))
+    if pod.obj["status"].get("phase") == "Pending" and is_unschedulable:
         return True
 
     return False
 
 
 def delete_job(job, cleanup="always"):
-    job_failed = (job.obj['status']['failed'] > 0
-                  if 'failed' in job.obj['status'] else False)
+    job_failed = job.obj["status"]["failed"] > 0 if "failed" in job.obj["status"] else False
     # Scale down the job just in case even if cleanup is never
     job.scale(replicas=0)
     api_delete = cleanup == "always"
     if not api_delete and cleanup == "onsuccess" and not job_failed:
         api_delete = True
     if api_delete:
-        delete_options = {
-            "apiVersion": "v1",
-            "kind": "DeleteOptions",
-            "propagationPolicy": "Background"
-        }
+        delete_options = {"apiVersion": "v1", "kind": "DeleteOptions", "propagationPolicy": "Background"}
         r = job.api.delete(json=delete_options, **job.api_kwargs())
         job.api.raise_for_status(r)
 
@@ -120,11 +119,7 @@ def delete_ingress(ingress, cleanup="always", job_failed=False):
     if not api_delete and cleanup == "onsuccess" and not job_failed:
         api_delete = True
     if api_delete:
-        delete_options = {
-            "apiVersion": "v1",
-            "kind": "DeleteOptions",
-            "propagationPolicy": "Background"
-        }
+        delete_options = {"apiVersion": "v1", "kind": "DeleteOptions", "propagationPolicy": "Background"}
         r = ingress.api.delete(json=delete_options, **ingress.api_kwargs())
         ingress.api.raise_for_status(r)
 
@@ -134,22 +129,18 @@ def delete_service(service, cleanup="always", job_failed=False):
     if not api_delete and cleanup == "onsuccess" and not job_failed:
         api_delete = True
     if api_delete:
-        delete_options = {
-            "apiVersion": "v1",
-            "kind": "DeleteOptions",
-            "propagationPolicy": "Background"
-        }
+        delete_options = {"apiVersion": "v1", "kind": "DeleteOptions", "propagationPolicy": "Background"}
         r = service.api.delete(json=delete_options, **service.api_kwargs())
         service.api.raise_for_status(r)
 
 
 def job_object_dict(params, job_prefix, spec):
     k8s_job_obj = {
-        "apiVersion": params.get('k8s_job_api_version', DEFAULT_JOB_API_VERSION),
+        "apiVersion": params.get("k8s_job_api_version", DEFAULT_JOB_API_VERSION),
         "kind": "Job",
         "metadata": {
-                "generateName": f"{job_prefix}-",
-                "namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE),
+            "generateName": f"{job_prefix}-",
+            "namespace": params.get("k8s_namespace", DEFAULT_NAMESPACE),
         },
         "spec": spec,
     }
@@ -158,11 +149,11 @@ def job_object_dict(params, job_prefix, spec):
 
 def service_object_dict(params, service_name, spec):
     k8s_service_obj = {
-        "apiVersion": params.get('k8s_service_api_version', DEFAULT_SERVICE_API_VERSION),
+        "apiVersion": params.get("k8s_service_api_version", DEFAULT_SERVICE_API_VERSION),
         "kind": "Service",
         "metadata": {
-                "name": service_name,
-                "namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE),
+            "name": service_name,
+            "namespace": params.get("k8s_namespace", DEFAULT_NAMESPACE),
         },
     }
     k8s_service_obj["metadata"].update(spec.pop("metadata", {}))
@@ -172,11 +163,11 @@ def service_object_dict(params, service_name, spec):
 
 def ingress_object_dict(params, ingress_name, spec):
     k8s_ingress_obj = {
-        "apiVersion": params.get('k8s_ingress_api_version', DEFAULT_INGRESS_API_VERSION),
+        "apiVersion": params.get("k8s_ingress_api_version", DEFAULT_INGRESS_API_VERSION),
         "kind": "Ingress",
         "metadata": {
-                "name": ingress_name,
-                "namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE),
+            "name": ingress_name,
+            "namespace": params.get("k8s_namespace", DEFAULT_NAMESPACE),
             # TODO: Add default annotations
         },
     }
@@ -201,10 +192,10 @@ def parse_pvc_param_line(pvc_param):
     read_only = mode == "r"
     claim_name, _, subpath = claim.partition("/")
     return {
-        'name': claim_name.strip(),
-        'subPath': subpath.strip(),
-        'mountPath': mount_path.strip(),
-        'readOnly': read_only
+        "name": claim_name.strip(),
+        "subPath": subpath.strip(),
+        "mountPath": mount_path.strip(),
+        "readOnly": read_only,
     }
 
 
@@ -244,8 +235,8 @@ def generate_relative_mounts(pvc_param, files):
     if not pvc_param:
         return
     param_claim = parse_pvc_param_line(pvc_param)
-    claim_name = param_claim['name']
-    base_subpath = PurePath(param_claim.get('subPath', ""))
+    claim_name = param_claim["name"]
+    base_subpath = PurePath(param_claim.get("subPath", ""))
     base_mount = PurePath(param_claim["mountPath"])
     read_only = param_claim["readOnly"]
     volume_mounts = []
@@ -257,14 +248,15 @@ def generate_relative_mounts(pvc_param, files):
         relpath = file_path.relative_to(base_mount)
         subpath = base_subpath.joinpath(relpath)
         volume_mounts.append(
-            {'name': claim_name, 'mountPath': str(file_path), 'subPath': str(subpath), 'readOnly': read_only})
+            {"name": claim_name, "mountPath": str(file_path), "subPath": str(subpath), "readOnly": read_only}
+        )
     return volume_mounts
 
 
 def deduplicate_entries(obj_list):
     # remove duplicate entries in a list of dictionaries
     # based on: https://stackoverflow.com/a/9428041
-    return [i for n, i in enumerate(obj_list) if i not in obj_list[n + 1:]]
+    return [i for n, i in enumerate(obj_list) if i not in obj_list[n + 1 :]]
 
 
 def get_volume_mounts_for_job(job_wrapper, data_claim=None, working_claim=None):
@@ -273,7 +265,8 @@ def get_volume_mounts_for_job(job_wrapper, data_claim=None, working_claim=None):
         volume_mounts.extend(generate_relative_mounts(data_claim, job_wrapper.job_io.get_input_fnames()))
         # for individual output files, mount the parent folder of each output as there could be wildcard outputs
         output_folders = deduplicate_entries(
-            [str(PurePath(str(f)).parent) for f in job_wrapper.job_io.get_output_fnames()])
+            [str(PurePath(str(f)).parent) for f in job_wrapper.job_io.get_output_fnames()]
+        )
         volume_mounts.extend(generate_relative_mounts(data_claim, output_folders))
 
     if working_claim:
@@ -295,7 +288,7 @@ def galaxy_instance_id(params):
     setup of a Job that is being recovered or restarted after a downtime/reboot.
     """
     if "k8s_galaxy_instance_id" in params:
-        raw_value = params['k8s_galaxy_instance_id']
+        raw_value = params["k8s_galaxy_instance_id"]
         if re.match(r"(?!-)[a-z\d-]{1,20}(?<!-)$", raw_value):
             return raw_value
         else:
@@ -329,5 +322,5 @@ __all__ = (
     "delete_service",
     "delete_ingress",
     "get_volume_mounts_for_job",
-    "parse_pvc_param_line"
+    "parse_pvc_param_line",
 )
diff --git a/lib/galaxy/jobs/runners/util/sudo.py b/lib/galaxy/jobs/runners/util/sudo.py
index 72fc3f06ee2..fdc8d74feda 100644
--- a/lib/galaxy/jobs/runners/util/sudo.py
+++ b/lib/galaxy/jobs/runners/util/sudo.py
@@ -1,12 +1,12 @@
 import logging
 from subprocess import (
     PIPE,
-    Popen
+    Popen,
 )
 
-SUDO_PATH = '/usr/bin/sudo'
-SUDO_PRESERVE_ENVIRONMENT_ARG = '-E'
-SUDO_USER_ARG = '-u'
+SUDO_PATH = "/usr/bin/sudo"
+SUDO_PRESERVE_ENVIRONMENT_ARG = "-E"
+SUDO_USER_ARG = "-u"
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/jobs/splitters/basic.py b/lib/galaxy/jobs/splitters/basic.py
index 01b557c9bca..f19f0bd8163 100644
--- a/lib/galaxy/jobs/splitters/basic.py
+++ b/lib/galaxy/jobs/splitters/basic.py
@@ -8,8 +8,8 @@ log = logging.getLogger(__name__)
 def set_basic_defaults(job_wrapper):
     parent_job = job_wrapper.get_job()
     parallelism = job_wrapper.get_parallelism()
-    parallelism.attributes['split_inputs'] = parent_job.input_datasets[0].name
-    parallelism.attributes['merge_outputs'] = next(iter(job_wrapper.job_io.get_output_hdas_and_fnames()))
+    parallelism.attributes["split_inputs"] = parent_job.input_datasets[0].name
+    parallelism.attributes["merge_outputs"] = next(iter(job_wrapper.job_io.get_output_hdas_and_fnames()))
 
 
 def do_split(job_wrapper):
diff --git a/lib/galaxy/jobs/splitters/multi.py b/lib/galaxy/jobs/splitters/multi.py
index 13ef12dc8d5..5e6b2dd8f40 100644
--- a/lib/galaxy/jobs/splitters/multi.py
+++ b/lib/galaxy/jobs/splitters/multi.py
@@ -3,8 +3,10 @@ import os
 import shutil
 from inspect import getfullargspec
 
-from galaxy import model, util
-
+from galaxy import (
+    model,
+    util,
+)
 
 log = logging.getLogger(__name__)
 
@@ -37,7 +39,7 @@ def do_split(job_wrapper):
     task_dirs = []
 
     def get_new_working_directory_name():
-        dir = os.path.join(working_directory, 'task_%d' % subdir_index[0])
+        dir = os.path.join(working_directory, "task_%d" % subdir_index[0])
         subdir_index[0] = subdir_index[0] + 1
         if not os.path.exists(dir):
             os.makedirs(dir)
@@ -92,7 +94,7 @@ def do_split(job_wrapper):
         log_error = f"The type '{str(input_type)}' does not define a method for splitting files"
         log.error(log_error)
         raise
-    log.debug('do_split created %d parts' % len(task_dirs))
+    log.debug("do_split created %d parts" % len(task_dirs))
     # next, after we know how many divisions there are, add the shared inputs via soft links
     for input in parent_job.input_datasets:
         if input and input.name in shared_inputs:
@@ -125,21 +127,21 @@ def do_merge(job_wrapper, task_wrappers):
 
     illegal_outputs = [x for x in merge_outputs if x in pickone_outputs]
     if len(illegal_outputs) > 0:
-        return ('Tool file error', f'Outputs have conflicting parallelism attributes: {str(illegal_outputs)}')
+        return ("Tool file error", f"Outputs have conflicting parallelism attributes: {str(illegal_outputs)}")
 
-    stdout = ''
-    stderr = ''
+    stdout = ""
+    stderr = ""
 
     try:
         working_directory = job_wrapper.working_directory
-        task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
+        task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith("task_")]
         assert task_dirs, "Should be at least one sub-task!"
         # TODO: Output datasets can be very complex. This doesn't handle metadata files
         outputs = job_wrapper.job_io.get_output_hdas_and_fnames()
         output_paths = job_wrapper.job_io.get_output_fnames()
         pickone_done = []
-        task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
-        task_dirs.sort(key=lambda x: int(x.split('task_')[-1]))
+        task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith("task_")]
+        task_dirs.sort(key=lambda x: int(x.split("task_")[-1]))
         for index, output in enumerate(outputs):
             output_file_name = str(output_paths[index])  # Use false_path if set, else real path.
             base_output_name = os.path.basename(output_file_name)
@@ -151,10 +153,12 @@ def do_merge(job_wrapper, task_wrappers):
                 # file f exists; some files may not exist if a task fails.
                 output_files = [f for f in output_files if os.path.exists(f)]
                 if output_files:
-                    log.debug(f'files {output_files} ')
+                    log.debug(f"files {output_files} ")
                     if len(output_files) < len(task_dirs):
-                        log.debug('merging only %i out of expected %i files for %s'
-                                  % (len(output_files), len(task_dirs), output_file_name))
+                        log.debug(
+                            "merging only %i out of expected %i files for %s"
+                            % (len(output_files), len(task_dirs), output_file_name)
+                        )
                     # First two args to merge always output_files and path of dataset. More
                     # complicated merge methods may require more parameters. Set those up here.
                     extra_merge_arg_names = getfullargspec(output_type.merge).args[2:]
@@ -162,10 +166,9 @@ def do_merge(job_wrapper, task_wrappers):
                     if "output_dataset" in extra_merge_arg_names:
                         extra_merge_args["output_dataset"] = output_dataset
                     output_type.merge(output_files, output_file_name, **extra_merge_args)
-                    log.debug(f'merge finished: {output_file_name}')
+                    log.debug(f"merge finished: {output_file_name}")
                 else:
-                    msg = 'nothing to merge for %s (expected %i files)' \
-                          % (output_file_name, len(task_dirs))
+                    msg = "nothing to merge for %s (expected %i files)" % (output_file_name, len(task_dirs))
                     log.debug(msg)
                     stderr += f"{msg}\n"
             elif output in pickone_outputs:
@@ -179,7 +182,7 @@ def do_merge(job_wrapper, task_wrappers):
                 log.exception(log_error)
                 raise Exception(log_error)
     except Exception as e:
-        stdout = 'Error merging files'
+        stdout = "Error merging files"
         log.exception(stdout)
         stderr = util.unicodify(e)
 
diff --git a/lib/galaxy/main_config.py b/lib/galaxy/main_config.py
index 6c433cfe460..a3f9b8a126d 100644
--- a/lib/galaxy/main_config.py
+++ b/lib/galaxy/main_config.py
@@ -12,7 +12,6 @@ from typing import (
 from galaxy.util.properties import find_config_file
 from galaxy.web_stack import get_app_kwds
 
-
 DEFAULT_INI_APP = "main"
 DEFAULT_CONFIG_SECTION = "galaxy"
 
@@ -28,7 +27,7 @@ def absolute_config_path(path, galaxy_root):
 
 
 def config_is_ini(config_file):
-    return config_file and (config_file.endswith('.ini') or config_file.endswith('.ini.sample'))
+    return config_file and (config_file.endswith(".ini") or config_file.endswith(".ini.sample"))
 
 
 def find_config(supplied_config, galaxy_root, app_name="galaxy"):
@@ -36,7 +35,7 @@ def find_config(supplied_config, galaxy_root, app_name="galaxy"):
         return supplied_config
 
     if galaxy_root is None:
-        return os.path.abspath(f'{app_name}.yml')
+        return os.path.abspath(f"{app_name}.yml")
 
     # If not explicitly supplied an config, check galaxy.ini and then
     # just resort to sample if that has not been configured.
@@ -52,6 +51,7 @@ def find_config(supplied_config, galaxy_root, app_name="galaxy"):
 class WebappSetupProps(NamedTuple):
     """Basic properties to provide information about the App and the environment variables
     used to resolve the App configuration."""
+
     app_name: str
     default_section_name: str
     env_config_file: str
@@ -61,13 +61,13 @@ class WebappSetupProps(NamedTuple):
 
 class WebappConfig(NamedTuple):
     """The resolved configuration values for a Webapp."""
+
     global_conf: dict
     load_app_kwds: dict
     wsgi_preflight: bool = False
 
 
 class WebappConfigResolver:
-
     def __init__(self, props: WebappSetupProps) -> None:
         self.props = props
         self.app_kwds = get_app_kwds(props.default_section_name, props.app_name)
diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index abf3ca9ac06..00f60a78294 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -74,7 +74,7 @@ class AnnotatableSerializerMixin:
     serializers: Dict[str, Serializer]
 
     def add_serializers(self):
-        self.serializers['annotation'] = self.serialize_annotation
+        self.serializers["annotation"] = self.serialize_annotation
 
     def serialize_annotation(self, item, key, user=None, **context):
         """
@@ -88,7 +88,7 @@ class AnnotatableDeserializerMixin:
     deserializers: Dict[str, Deserializer]
 
     def add_deserializers(self):
-        self.deserializers['annotation'] = self.deserialize_annotation
+        self.deserializers["annotation"] = self.deserialize_annotation
 
     def deserialize_annotation(self, item, key, val, user=None, **context):
         """
@@ -121,10 +121,10 @@ class AnnotatableFilterMixin:
     def _add_parsers(self):
         self.fn_filter_parsers.update(
             {
-                'annotation': {
-                    'op': {
-                        'has': self.filter_annotation_contains,
-                        'contains': self.filter_annotation_contains,
+                "annotation": {
+                    "op": {
+                        "has": self.filter_annotation_contains,
+                        "contains": self.filter_annotation_contains,
                     },
                 },
             }
diff --git a/lib/galaxy/managers/api_keys.py b/lib/galaxy/managers/api_keys.py
index 4c7e7659ea6..1adbede04ec 100644
--- a/lib/galaxy/managers/api_keys.py
+++ b/lib/galaxy/managers/api_keys.py
@@ -2,7 +2,6 @@ from galaxy.structured_app import BasicSharedApp
 
 
 class ApiKeyManager:
-
     def __init__(self, app: BasicSharedApp):
         self.app = app
 
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 298ebc0b2b3..46c30ba1296 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -48,12 +48,17 @@ from sqlalchemy.orm import Query
 from sqlalchemy.orm.scoping import scoped_session
 from typing_extensions import Protocol
 
-from galaxy import exceptions
-from galaxy import model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.model import tool_shed_install
 from galaxy.schema import FilterQueryParams
 from galaxy.security.idencoding import IdEncodingHelper
-from galaxy.structured_app import BasicSharedApp, MinimalManagerApp
+from galaxy.structured_app import (
+    BasicSharedApp,
+    MinimalManagerApp,
+)
 from galaxy.web import url_for as gx_url_for
 
 log = logging.getLogger(__name__)
@@ -88,20 +93,34 @@ def security_check(trans, item, check_ownership=False, check_accessible=False):
     # Verify ownership: there is a current user and that user is the same as the item's
     if check_ownership:
         if not trans.user:
-            raise exceptions.ItemOwnershipException("Must be logged in to manage Galaxy items", type='error')
+            raise exceptions.ItemOwnershipException("Must be logged in to manage Galaxy items", type="error")
         if item.user != trans.user:
-            raise exceptions.ItemOwnershipException(f"{item.__class__.__name__} is not owned by the current user", type='error')
+            raise exceptions.ItemOwnershipException(
+                f"{item.__class__.__name__} is not owned by the current user", type="error"
+            )
 
     # Verify accessible:
     #   if it's part of a lib - can they access via security
     #   if it's something else (sharable) have they been added to the item's users_shared_with_dot_users
     if check_accessible:
-        if type(item) in (trans.app.model.LibraryFolder, trans.app.model.LibraryDatasetDatasetAssociation, trans.app.model.LibraryDataset):
+        if type(item) in (
+            trans.app.model.LibraryFolder,
+            trans.app.model.LibraryDatasetDatasetAssociation,
+            trans.app.model.LibraryDataset,
+        ):
             if not trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), item, trans.user):
-                raise exceptions.ItemAccessibilityException(f"{item.__class__.__name__} is not accessible to the current user", type='error')
+                raise exceptions.ItemAccessibilityException(
+                    f"{item.__class__.__name__} is not accessible to the current user", type="error"
+                )
         else:
-            if (item.user != trans.user) and (not item.importable) and (trans.user not in item.users_shared_with_dot_users):
-                raise exceptions.ItemAccessibilityException(f"{item.__class__.__name__} is not accessible to the current user", type='error')
+            if (
+                (item.user != trans.user)
+                and (not item.importable)
+                and (trans.user not in item.users_shared_with_dot_users)
+            ):
+                raise exceptions.ItemAccessibilityException(
+                    f"{item.__class__.__name__} is not accessible to the current user", type="error"
+                )
     return item
 
 
@@ -110,7 +129,7 @@ def get_class(class_name):
     Returns the class object that a string denotes. Without this method, we'd have
     to do eval(<class_name>).
     """
-    if class_name == 'ToolShedRepository':
+    if class_name == "ToolShedRepository":
         item_class = tool_shed_install.ToolShedRepository
     else:
         if not hasattr(model, class_name):
@@ -153,11 +172,13 @@ def get_object(trans, id, class_name, check_ownership=False, check_accessible=Fa
     if check_ownership or check_accessible:
         security_check(trans, item, check_ownership, check_accessible)
     if deleted is True and not item.deleted:
-        raise exceptions.ItemDeletionException('%s "%s" is not deleted'
-                                               % (class_name, getattr(item, 'name', id)), type="warning")
+        raise exceptions.ItemDeletionException(
+            '%s "%s" is not deleted' % (class_name, getattr(item, "name", id)), type="warning"
+        )
     elif deleted is False and item.deleted:
-        raise exceptions.ItemDeletionException('%s "%s" is deleted'
-                                               % (class_name, getattr(item, 'name', id)), type="warning")
+        raise exceptions.ItemDeletionException(
+            '%s "%s" is deleted' % (class_name, getattr(item, "name", id)), type="warning"
+        )
     return item
 
 
@@ -188,6 +209,7 @@ class ModelManager:
     Provides common queries and CRUD operations as a (hopefully) light layer
     over the ORM.
     """
+
     model_class: Type[model._HasTable]
     foreign_key_name: str
     app: BasicSharedApp
@@ -207,7 +229,14 @@ class ModelManager:
         return item
 
     # .... query foundation wrapper
-    def query(self, eagerloads: bool = True, filters=None, order_by=None, limit: Optional[int] = None, offset: Optional[int] = None) -> Query:
+    def query(
+        self,
+        eagerloads: bool = True,
+        filters=None,
+        order_by=None,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
+    ) -> Query:
         """
         Return a basic query from model_class, filters, order_by, and limit and offset.
 
@@ -219,7 +248,9 @@ class ModelManager:
             query = query.enable_eagerloads(False)
         return self._filter_and_order_query(query, filters=filters, order_by=order_by, limit=limit, offset=offset)
 
-    def _filter_and_order_query(self, query: Query, filters=None, order_by=None, limit: Optional[int] = None, offset: Optional[int] = None) -> Query:
+    def _filter_and_order_query(
+        self, query: Query, filters=None, order_by=None, limit: Optional[int] = None, offset: Optional[int] = None
+    ) -> Query:
         # TODO: not a lot of functional cohesion here
         query = self._apply_orm_filters(query, filters)
         query = self._apply_order_by(query, order_by)
@@ -267,7 +298,7 @@ class ModelManager:
         """
         Returns a tuple of columns for the default order when getting multiple models.
         """
-        return (self.model_class.table.c.create_time, )
+        return (self.model_class.table.c.create_time,)
 
     def _apply_orm_limit_offset(self, query: Query, limit: Optional[int], offset: Optional[int]) -> Query:
         """
@@ -333,8 +364,7 @@ class ModelManager:
         orm_filters, fn_filters = self._split_filters(filters)
         if not fn_filters:
             # if no fn_filtering required, we can use the 'all orm' version with limit offset
-            return self._orm_list(filters=orm_filters, order_by=order_by,
-                limit=limit, offset=offset, **kwargs)
+            return self._orm_list(filters=orm_filters, order_by=order_by, limit=limit, offset=offset, **kwargs)
 
         # fn filters will change the number of items returnable by limit/offset - remove them here from the orm query
         query = self.query(filters=orm_filters, order_by=order_by, limit=None, offset=None, **kwargs)
@@ -357,11 +387,11 @@ class ModelManager:
         if not isinstance(filters, list):
             filters = [filters]
         for filter_ in filters:
-            if not hasattr(filter_, 'filter_type'):
+            if not hasattr(filter_, "filter_type"):
                 orm_filters.append(filter_)
-            elif filter_.filter_type == 'function':
+            elif filter_.filter_type == "function":
                 fn_filters.append(filter_.filter)
-            elif filter_.filter_type == 'orm_function':
+            elif filter_.filter_type == "orm_function":
                 orm_filters.append(filter_.filter(self.model_class))
             else:
                 orm_filters.append(filter_.filter)
@@ -430,7 +460,7 @@ class ModelManager:
         If an id in ids is not found or if an item in items doesn't have a given
         id, they will not be in the returned list.
         """
-        ID_ATTR_NAME = 'id'
+        ID_ATTR_NAME = "id"
         # TODO:?? aside from sqlalx.get mentioned above, I haven't seen an in-SQL way
         #   to make this happen. This may not be the most efficient way either.
         # NOTE: that this isn't sorting by id - this is matching the order in items to the order in ids
@@ -462,7 +492,7 @@ class ModelManager:
         """
         Clone or copy an item.
         """
-        raise exceptions.NotImplemented('Abstract method')
+        raise exceptions.NotImplemented("Abstract method")
 
     def update(self, item, new_values, flush=True, **kwargs):
         """
@@ -502,7 +532,7 @@ class ModelManager:
     #    return item
 
 
-T = TypeVar('T')
+T = TypeVar("T")
 
 
 # ---- code for classes that use one *main* model manager
@@ -515,7 +545,9 @@ class HasAModelManager(Generic[T]):
     """
 
     #: the class used to create this serializer's generically accessible model_manager
-    model_manager_class: Type[T]  # ideally this would be Type[ModelManager] but HistoryContentsManager cannot be a ModelManager
+    model_manager_class: Type[
+        T
+    ]  # ideally this would be Type[ModelManager] but HistoryContentsManager cannot be a ModelManager
     # examples where this doesn't really work are ConfigurationSerializer (no manager)
     # and contents (2 managers)
     app: MinimalManagerApp
@@ -554,7 +586,6 @@ class SkipAttribute(Exception):
 
 
 class Serializer(Protocol):
-
     def __call__(self, item: Any, key: str, **context) -> Any:
         ...
 
@@ -576,6 +607,7 @@ class ModelSerializer(HasAModelManager[T]):
         keys_to_serialize = [ 'id', 'name', 'attr1', 'attr2', ... ]
         item_dict = MySerializer.serialize( my_item, keys_to_serialize )
     """
+
     #: 'service' to use for getting urls - use class var to allow overriding when testing
     url_for = staticmethod(gx_url_for)
     default_view: Optional[str]
@@ -609,11 +641,13 @@ class ModelSerializer(HasAModelManager[T]):
         Register a map of attribute keys -> serializing functions that will serialize
         the attribute.
         """
-        self.serializers.update({
-            'id': self.serialize_id,
-            'create_time': self.serialize_date,
-            'update_time': self.serialize_date,
-        })
+        self.serializers.update(
+            {
+                "id": self.serialize_id,
+                "create_time": self.serialize_date,
+                "update_time": self.serialize_date,
+            }
+        )
 
     def add_view(self, view_name, key_list, include_keys_from=None):
         """
@@ -651,7 +685,7 @@ class ModelSerializer(HasAModelManager[T]):
             # ignore bad/unreg keys
         return returned
 
-    def skip(self, msg='skipped'):
+    def skip(self, msg="skipped"):
         """
         To be called from inside a serializer to skip it.
 
@@ -693,7 +727,7 @@ class ModelSerializer(HasAModelManager[T]):
         """
         Serialize an type-id for `item`.
         """
-        TYPE_ID_SEP = '-'
+        TYPE_ID_SEP = "-"
         type_id = getattr(item, key)
         if type_id is None:
             return None
@@ -740,7 +774,7 @@ class ModelSerializer(HasAModelManager[T]):
         if view is None:
             view = self.default_view
         if view not in self.views:
-            raise ModelSerializingError('unknown view', view=view, available_views=self.views)
+            raise ModelSerializingError("unknown view", view=view, available_views=self.views)
         return self.views[view][:]
 
 
@@ -759,7 +793,7 @@ class ModelValidator:
         :raises exceptions.RequestParameterInvalidException: if not an instance.
         """
         if not isinstance(val, types):
-            msg = f'must be a type: {str(types)}'
+            msg = f"must be a type: {str(types)}"
             raise exceptions.RequestParameterInvalidException(msg, key=key, val=val)
         return val
 
@@ -812,7 +846,7 @@ class ModelValidator:
         """
         # TODO: is this correct?
         if val is None:
-            return '?'
+            return "?"
         # currently, data source sites like UCSC are able to set the genome build to non-local build names
         # afterwards, attempting to validate the whole model will choke here
         # for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ):
@@ -828,7 +862,6 @@ class ModelValidator:
 
 
 class Deserializer(Protocol):
-
     def __call__(self, item: Any, key: Any, val: Any, **kwargs) -> Any:
         ...
 
@@ -838,6 +871,7 @@ class ModelDeserializer(HasAModelManager[T]):
     An object that converts an incoming serialized dict into values that can be
     directly assigned to an item's attributes and assigns them.
     """
+
     validate = ModelValidator()
     app: MinimalManagerApp
 
@@ -894,7 +928,7 @@ class ModelDeserializer(HasAModelManager[T]):
         return val
 
     def deserialize_basestring(self, item, key, val, convert_none_to_empty=False, **context):
-        val = '' if (convert_none_to_empty and val is None) else self.validate.basestring(key, val)
+        val = "" if (convert_none_to_empty and val is None) else self.validate.basestring(key, val)
         return self.default_deserializer(item, key, val, **context)
 
     def deserialize_bool(self, item, key, val, **context):
@@ -939,6 +973,7 @@ class ModelFilterParser(HasAModelManager):
     These might be safely be replaced in the future by creating SQLAlchemy
     hybrid properties or more thoroughly mapping derived values.
     """
+
     # ??: this class kindof 'lives' in both the world of the controllers/param-parsing and to models/orm
     # (as the model informs how the filter params are parsed)
     # I have no great idea where this 'belongs', so it's here for now
@@ -955,7 +990,9 @@ class ModelFilterParser(HasAModelManager):
         super().__init__(app, **kwargs)
 
         #: regex for testing/dicing iso8601 date strings, with optional time and ms, but allowing only UTC timezone
-        self.date_string_re = re.compile(r'^(\d{4}\-\d{2}\-\d{2})[T| ]{0,1}(\d{2}:\d{2}:\d{2}(?:\.\d{1,6}){0,1}){0,1}Z{0,1}$')
+        self.date_string_re = re.compile(
+            r"^(\d{4}\-\d{2}\-\d{2})[T| ]{0,1}(\d{2}:\d{2}:\d{2}(?:\.\d{1,6}){0,1}){0,1}Z{0,1}$"
+        )
 
         # dictionary containing parsing data for ORM/SQLAlchemy-based filters
         # ..note: although kind of a pain in the ass and verbose, opt-in/allowlisting allows more control
@@ -973,27 +1010,29 @@ class ModelFilterParser(HasAModelManager):
         Set up, extend, or alter `orm_filter_parsers` and `fn_filter_parsers`.
         """
         # note: these are the default filters for all models
-        self.orm_filter_parsers.update({
-            # (prob.) applicable to all models
-            'id': {'op': ('in')},
-            'encoded_id': {'column': 'id', 'op': ('in'), 'val': self.parse_id_list},
-            # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
-            'extension': {'op': ('eq', 'like', 'in')},
-            'create_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
-            'update_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
-        })
+        self.orm_filter_parsers.update(
+            {
+                # (prob.) applicable to all models
+                "id": {"op": ("in")},
+                "encoded_id": {"column": "id", "op": ("in"), "val": self.parse_id_list},
+                # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
+                "extension": {"op": ("eq", "like", "in")},
+                "create_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
+                "update_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
+            }
+        )
 
     def build_filter_params(
         self,
         query_params: FilterQueryParams,
-        filter_attr_key: str = 'q',
-        filter_value_key: str = 'qv',
-        attr_op_split_char: str = '-',
+        filter_attr_key: str = "q",
+        filter_value_key: str = "qv",
+        attr_op_split_char: str = "-",
     ) -> List[Tuple[str, str, str]]:
         """
         Builds a list of tuples containing filtering information in the form of (attribute, operator, value).
         """
-        DEFAULT_OP = 'eq'
+        DEFAULT_OP = "eq"
         qdict = query_params.dict(exclude_defaults=True)
         if filter_attr_key not in qdict:
             return []
@@ -1059,12 +1098,13 @@ class ModelFilterParser(HasAModelManager):
 
         # by convention, assume most val parsers raise ValueError
         except ValueError as val_err:
-            raise exceptions.RequestParameterInvalidException('unparsable value for filter',
-                column=attr, operation=op, value=val, ValueError=str(val_err))
+            raise exceptions.RequestParameterInvalidException(
+                "unparsable value for filter", column=attr, operation=op, value=val, ValueError=str(val_err)
+            )
 
         # if neither of the above work, raise an error with how-to info
         # TODO: send back all valid filter keys in exception for added user help
-        raise exceptions.RequestParameterInvalidException('bad filter', column=attr, operation=op)
+        raise exceptions.RequestParameterInvalidException("bad filter", column=attr, operation=op)
 
     # ---- fn filters
     def _parse_fn_filter(self, attr, op, val):
@@ -1077,13 +1117,13 @@ class ModelFilterParser(HasAModelManager):
         attr_map = self.fn_filter_parsers.get(attr, None)
         if not attr_map:
             return None
-        allowed_ops = attr_map['op']
+        allowed_ops = attr_map["op"]
         # allowed ops is a map here, op => fn
         filter_fn = allowed_ops.get(op, None)
         if not filter_fn:
             return None
         # parse the val from string using the 'val' parser if present (otherwise, leave as string)
-        val_parser = attr_map.get('val', None)
+        val_parser = attr_map.get("val", None)
         if val_parser:
             val = val_parser(val)
 
@@ -1106,8 +1146,8 @@ class ModelFilterParser(HasAModelManager):
             return self.parsed_filter(filter_type="orm_function", filter=column_map(attr, op, val))
         # attr must be an allowlisted column by attr name or by key passed in column_map
         # note: column_map[ 'column' ] takes precedence
-        if 'column' in column_map:
-            attr = column_map['column']
+        if "column" in column_map:
+            attr = column_map["column"]
         column = self.model_class.table.columns.get(attr)
         if column is None:
             # could be a property (hybrid_property, etc.) - assume we can make a filter from it
@@ -1117,7 +1157,7 @@ class ModelFilterParser(HasAModelManager):
             return None
 
         # op must be allowlisted: contained in the list orm_filter_list[ attr ][ 'op' ]
-        allowed_ops = column_map['op']
+        allowed_ops = column_map["op"]
         if op not in allowed_ops:
             return None
         op = self._convert_op_string_to_fn(column, op)
@@ -1125,7 +1165,7 @@ class ModelFilterParser(HasAModelManager):
             return None
 
         # parse the val from string using the 'val' parser if present (otherwise, leave as string)
-        val_parser = column_map.get('val', None)
+        val_parser = column_map.get("val", None)
         if val_parser:
             val = val_parser(val)
 
@@ -1133,7 +1173,7 @@ class ModelFilterParser(HasAModelManager):
         return self.parsed_filter(filter_type="orm", filter=orm_filter)
 
     #: these are the easier/shorter string equivalents to the python operator fn names that need '__' around them
-    UNDERSCORED_OPS = ('lt', 'le', 'eq', 'ne', 'ge', 'gt')
+    UNDERSCORED_OPS = ("lt", "le", "eq", "ne", "ge", "gt")
 
     def _convert_op_string_to_fn(self, column, op_string):
         """
@@ -1144,8 +1184,8 @@ class ModelFilterParser(HasAModelManager):
         fn_name = op_string
         if op_string in self.UNDERSCORED_OPS:
             fn_name = f"__{op_string}__"
-        elif op_string == 'in':
-            fn_name = 'in_'
+        elif op_string == "in":
+            fn_name = "in_"
 
         # get the column fn using the op_string and error if not a callable attr
         # TODO: special case 'not in' - or disallow?
@@ -1157,15 +1197,15 @@ class ModelFilterParser(HasAModelManager):
     # ---- preset fn_filters: dictionaries of standard filter ops for standard datatypes
     def string_standard_ops(self, key):
         return {
-            'op': {
-                'eq': lambda i, v: v == getattr(i, key),
-                'contains': lambda i, v: v in getattr(i, key),
+            "op": {
+                "eq": lambda i, v: v == getattr(i, key),
+                "contains": lambda i, v: v in getattr(i, key),
             }
         }
 
     # --- more parsers! yay!
     # TODO: These should go somewhere central - we've got ~6 parser modules/sections now
-    def parse_id_list(self, id_list_string, sep=','):
+    def parse_id_list(self, id_list_string, sep=","):
         """
         Split `id_list_string` at `sep`.
         """
@@ -1173,7 +1213,7 @@ class ModelFilterParser(HasAModelManager):
         id_list = [self.app.security.decode_id(id_) for id_ in id_list_string.split(sep)]
         return id_list
 
-    def parse_int_list(self, int_list_string, sep=','):
+    def parse_int_list(self, int_list_string, sep=","):
         """
         Split `int_list_string` at `sep` and parse as ints.
         """
@@ -1192,15 +1232,15 @@ class ModelFilterParser(HasAModelManager):
         try:
             epoch = float(date_string)
             datetime_obj = datetime.datetime.fromtimestamp(epoch)
-            return datetime_obj.isoformat(sep=' ')
+            return datetime_obj.isoformat(sep=" ")
         except ValueError:
             pass
 
         match = self.date_string_re.match(date_string)
         if match:
-            date_string = ' '.join(group for group in match.groups() if group)
+            date_string = " ".join(group for group in match.groups() if group)
             return date_string
-        raise ValueError('datetime strings must be in the ISO 8601 format and in the UTC')
+        raise ValueError("datetime strings must be in the ISO 8601 format and in the UTC")
 
 
 def parse_bool(bool_string: Union[str, bool]) -> bool:
@@ -1208,9 +1248,9 @@ def parse_bool(bool_string: Union[str, bool]) -> bool:
     Parse a boolean from a string.
     """
     # Be strict here to remove complexity of options (but allow already parsed).
-    if bool_string in ('True', True):
+    if bool_string in ("True", True):
         return True
-    if bool_string in ('False', False):
+    if bool_string in ("False", False):
         return False
     raise ValueError(f"invalid boolean: {str(bool_string)}")
 
diff --git a/lib/galaxy/managers/citations.py b/lib/galaxy/managers/citations.py
index 3e97901e192..84e9ab17bea 100644
--- a/lib/galaxy/managers/citations.py
+++ b/lib/galaxy/managers/citations.py
@@ -12,7 +12,6 @@ log = logging.getLogger(__name__)
 
 
 class CitationsManager:
-
     def __init__(self, app: BasicSharedApp) -> None:
         self.app = app
         self.doi_cache = DoiCache(app.config)
@@ -37,18 +36,17 @@ class CitationsManager:
 
 
 class DoiCache:
-
     def __init__(self, config):
         cache_opts = {
-            'cache.type': getattr(config, 'citation_cache_type', 'file'),
-            'cache.data_dir': getattr(config, 'citation_cache_data_dir', None),
-            'cache.lock_dir': getattr(config, 'citation_cache_lock_dir', None),
+            "cache.type": getattr(config, "citation_cache_type", "file"),
+            "cache.data_dir": getattr(config, "citation_cache_data_dir", None),
+            "cache.lock_dir": getattr(config, "citation_cache_lock_dir", None),
         }
-        self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('doi')
+        self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache("doi")
 
     def _raw_get_bibtex(self, doi):
         doi_url = f"https://doi.org/{doi}"
-        headers = {'Accept': 'application/x-bibtex'}
+        headers = {"Accept": "application/x-bibtex"}
         req = requests.get(doi_url, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
         req.encoding = req.apparent_encoding
         return req.text
@@ -62,7 +60,7 @@ def parse_citation(elem, citation_manager):
     """
     Parse an abstract citation entry from the specified XML element.
     """
-    citation_type = elem.attrib.get('type', None)
+    citation_type = elem.attrib.get("type", None)
     citation_class = CITATION_CLASSES.get(citation_type, None)
     if not citation_class:
         log.warning(f"Unknown or unspecified citation type: {citation_type}")
@@ -75,7 +73,6 @@ def parse_citation(elem, citation_manager):
 
 
 class CitationCollection:
-
     def __init__(self):
         self.citations = []
 
@@ -97,7 +94,6 @@ class CitationCollection:
 
 
 class BaseCitation:
-
     def to_dict(self, citation_format):
         if citation_format == "bibtex":
             return dict(
@@ -119,7 +115,6 @@ class BaseCitation:
 
 
 class BibtexCitation(BaseCitation):
-
     def __init__(self, elem, citation_manager):
         self.raw_bibtex = elem.text.strip()
 
@@ -152,7 +147,9 @@ class DoiCitation(BaseCitation):
             return """@MISC{{{doi},
                 DOI = {{{doi}}},
                 note = {{Failed to fetch BibTeX for DOI.}}
-            }}""".format(doi=self.__doi)
+            }}""".format(
+                doi=self.__doi
+            )
         else:
             return self.raw_bibtex
 
diff --git a/lib/galaxy/managers/cloud.py b/lib/galaxy/managers/cloud.py
index 66af9720068..1d04ea4f2e4 100644
--- a/lib/galaxy/managers/cloud.py
+++ b/lib/galaxy/managers/cloud.py
@@ -5,20 +5,25 @@ Manager and serializer for cloud-based storages.
 import json
 import logging
 
-from galaxy import model
-from galaxy import util
+from galaxy import (
+    model,
+    util,
+)
 from galaxy.exceptions import (
     ItemAccessibilityException,
     MessageException,
     ObjectNotFound,
     RequestParameterInvalidException,
-    RequestParameterMissingException
+    RequestParameterMissingException,
 )
 from galaxy.managers import sharable
 from galaxy.util import Params
 
 try:
-    from cloudbridge.factory import CloudProviderFactory, ProviderList
+    from cloudbridge.factory import (
+        CloudProviderFactory,
+        ProviderList,
+    )
 except ImportError:
     CloudProviderFactory = None
     ProviderList = None
@@ -68,46 +73,50 @@ class CloudManager(sharable.SharableModelManager):
         :return: a cloudbridge connection to the specified provider.
         """
         missing_credentials = []
-        if provider == 'aws':
-            access = credentials.get('access_key', None)
+        if provider == "aws":
+            access = credentials.get("access_key", None)
             if access is None:
                 access = credentials.get("AccessKeyId", None)
                 if access is None:
-                    missing_credentials.append('access_key')
-            secret = credentials.get('secret_key', None)
+                    missing_credentials.append("access_key")
+            secret = credentials.get("secret_key", None)
             if secret is None:
                 secret = credentials.get("SecretAccessKey", None)
                 if secret is None:
-                    missing_credentials.append('secret_key')
+                    missing_credentials.append("secret_key")
             if len(missing_credentials) > 0:
-                raise RequestParameterMissingException("The following required key(s) are missing from the provided "
-                                                       "credentials object: {}".format(missing_credentials))
+                raise RequestParameterMissingException(
+                    "The following required key(s) are missing from the provided "
+                    "credentials object: {}".format(missing_credentials)
+                )
             session_token = credentials.get("SessionToken")
-            config = {'aws_access_key': access,
-                      'aws_secret_key': secret,
-                      "aws_session_token": session_token}
+            config = {"aws_access_key": access, "aws_secret_key": secret, "aws_session_token": session_token}
             connection = CloudProviderFactory().create_provider(ProviderList.AWS, config)
         elif provider == "azure":
-            subscription = credentials.get('subscription_id', None)
+            subscription = credentials.get("subscription_id", None)
             if subscription is None:
-                missing_credentials.append('subscription_id')
-            client = credentials.get('client_id', None)
+                missing_credentials.append("subscription_id")
+            client = credentials.get("client_id", None)
             if client is None:
-                missing_credentials.append('client_id')
-            secret = credentials.get('secret', None)
+                missing_credentials.append("client_id")
+            secret = credentials.get("secret", None)
             if secret is None:
-                missing_credentials.append('secret')
-            tenant = credentials.get('tenant', None)
+                missing_credentials.append("secret")
+            tenant = credentials.get("tenant", None)
             if tenant is None:
-                missing_credentials.append('tenant')
+                missing_credentials.append("tenant")
             if len(missing_credentials) > 0:
-                raise RequestParameterMissingException("The following required key(s) are missing from the provided "
-                                                       "credentials object: {}".format(missing_credentials))
+                raise RequestParameterMissingException(
+                    "The following required key(s) are missing from the provided "
+                    "credentials object: {}".format(missing_credentials)
+                )
 
-            config = {'azure_subscription_id': subscription,
-                      'azure_client_id': client,
-                      'azure_secret': secret,
-                      'azure_tenant': tenant}
+            config = {
+                "azure_subscription_id": subscription,
+                "azure_client_id": client,
+                "azure_secret": secret,
+                "azure_tenant": tenant,
+            }
             storage_account = credentials.get("storage_account")
             if storage_account:
                 config["azure_storage_account"] = storage_account
@@ -116,40 +125,46 @@ class CloudManager(sharable.SharableModelManager):
                 config["azure_resource_group"] = resource_group
             connection = CloudProviderFactory().create_provider(ProviderList.AZURE, config)
         elif provider == "openstack":
-            username = credentials.get('username', None)
+            username = credentials.get("username", None)
             if username is None:
-                missing_credentials.append('username')
-            password = credentials.get('password', None)
+                missing_credentials.append("username")
+            password = credentials.get("password", None)
             if password is None:
-                missing_credentials.append('password')
-            auth_url = credentials.get('auth_url', None)
+                missing_credentials.append("password")
+            auth_url = credentials.get("auth_url", None)
             if auth_url is None:
-                missing_credentials.append('auth_url')
-            prj_name = credentials.get('project_name', None)
+                missing_credentials.append("auth_url")
+            prj_name = credentials.get("project_name", None)
             if prj_name is None:
-                missing_credentials.append('project_name')
-            prj_domain_name = credentials.get('project_domain_name', None)
+                missing_credentials.append("project_name")
+            prj_domain_name = credentials.get("project_domain_name", None)
             if prj_domain_name is None:
-                missing_credentials.append('project_domain_name')
-            user_domain_name = credentials.get('user_domain_name', None)
+                missing_credentials.append("project_domain_name")
+            user_domain_name = credentials.get("user_domain_name", None)
             if user_domain_name is None:
-                missing_credentials.append('user_domain_name')
+                missing_credentials.append("user_domain_name")
             if len(missing_credentials) > 0:
-                raise RequestParameterMissingException("The following required key(s) are missing from the provided "
-                                                       "credentials object: {}".format(missing_credentials))
-            config = {'os_username': username,
-                      'os_password': password,
-                      'os_auth_url': auth_url,
-                      'os_project_name': prj_name,
-                      'os_project_domain_name': prj_domain_name,
-                      'os_user_domain_name': user_domain_name}
+                raise RequestParameterMissingException(
+                    "The following required key(s) are missing from the provided "
+                    "credentials object: {}".format(missing_credentials)
+                )
+            config = {
+                "os_username": username,
+                "os_password": password,
+                "os_auth_url": auth_url,
+                "os_project_name": prj_name,
+                "os_project_domain_name": prj_domain_name,
+                "os_user_domain_name": user_domain_name,
+            }
             connection = CloudProviderFactory().create_provider(ProviderList.OPENSTACK, config)
         elif provider == "gcp":
             config = {"gcp_service_creds_dict": credentials}
             connection = CloudProviderFactory().create_provider(ProviderList.GCP, config)
         else:
-            raise RequestParameterInvalidException("Unrecognized provider '{}'; the following are the supported "
-                                                   "providers: {}.".format(provider, SUPPORTED_PROVIDERS.keys()))
+            raise RequestParameterInvalidException(
+                "Unrecognized provider '{}'; the following are the supported "
+                "providers: {}.".format(provider, SUPPORTED_PROVIDERS.keys())
+            )
 
         # The authorization-assertion mechanism of Cloudbridge assumes a user has an elevated privileges,
         # such as Admin-level access to all resources (see https://github.com/CloudVE/cloudbridge/issues/135).
@@ -169,29 +184,33 @@ class CloudManager(sharable.SharableModelManager):
     @staticmethod
     def _get_inputs(obj, key, input_args):
         space_to_tab = None
-        if input_args.get('space_to_tab', "").lower() == "true":
+        if input_args.get("space_to_tab", "").lower() == "true":
             space_to_tab = "Yes"
-        elif input_args.get('space_to_tab', "").lower() not in ["false", ""]:
+        elif input_args.get("space_to_tab", "").lower() not in ["false", ""]:
             raise RequestParameterInvalidException(
                 "The valid values for `space_to_tab` argument are `true` and `false`; received {}".format(
-                    input_args.get('space_to_tab')))
+                    input_args.get("space_to_tab")
+                )
+            )
 
         to_posix_lines = None
-        if input_args.get('to_posix_lines', "").lower() == "true":
+        if input_args.get("to_posix_lines", "").lower() == "true":
             to_posix_lines = "Yes"
-        elif input_args.get('to_posix_lines', "").lower() not in ["false", ""]:
+        elif input_args.get("to_posix_lines", "").lower() not in ["false", ""]:
             raise RequestParameterInvalidException(
                 "The valid values for `to_posix_lines` argument are `true` and `false`; received {}".format(
-                    input_args.get('to_posix_lines')))
+                    input_args.get("to_posix_lines")
+                )
+            )
 
         return {
-            'dbkey': input_args.get("dbkey", "?"),
-            'file_type': input_args.get("file_type", "auto"),
-            'files_0|type': 'upload_dataset',
-            'files_0|space_to_tab': space_to_tab,
-            'files_0|to_posix_lines': to_posix_lines,
-            'files_0|NAME': obj,
-            'files_0|url_paste': key.generate_url(expires_in=SINGED_URL_TTL),
+            "dbkey": input_args.get("dbkey", "?"),
+            "file_type": input_args.get("file_type", "auto"),
+            "files_0|type": "upload_dataset",
+            "files_0|space_to_tab": space_to_tab,
+            "files_0|to_posix_lines": to_posix_lines,
+            "files_0|NAME": obj,
+            "files_0|url_paste": key.generate_url(expires_in=SINGED_URL_TTL),
         }
 
     def get(self, trans, history_id, bucket_name, objects, authz_id, input_args=None):
@@ -233,14 +252,18 @@ class CloudManager(sharable.SharableModelManager):
         if input_args is None:
             input_args = {}
 
-        if not hasattr(trans.app, 'authnz_manager'):
-            err_msg = "The OpenID Connect protocol, a required feature for getting data from cloud, " \
-                      "is not enabled on this Galaxy instance."
+        if not hasattr(trans.app, "authnz_manager"):
+            err_msg = (
+                "The OpenID Connect protocol, a required feature for getting data from cloud, "
+                "is not enabled on this Galaxy instance."
+            )
             log.debug(err_msg)
             raise MessageException(err_msg)
 
         cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
-        credentials = trans.app.authnz_manager.get_cloud_access_credentials(cloudauthz, trans.sa_session, trans.user.id, trans.request)
+        credentials = trans.app.authnz_manager.get_cloud_access_credentials(
+            cloudauthz, trans.sa_session, trans.user.id, trans.request
+        )
         connection = self.configure_provider(cloudauthz.provider, credentials)
         try:
             bucket = connection.storage.buckets.get(bucket_name)
@@ -254,28 +277,35 @@ class CloudManager(sharable.SharableModelManager):
             try:
                 key = bucket.objects.get(obj)
             except Exception as e:
-                raise MessageException(f"The following error occurred while getting the object {obj}: {util.unicodify(e)}")
+                raise MessageException(
+                    f"The following error occurred while getting the object {obj}: {util.unicodify(e)}"
+                )
             if key is None:
                 log.exception(
                     "Could not get object `{}` for user `{}`. Object may not exist, or the provided credentials are "
-                    "invalid or not authorized to read the bucket/object.".format(obj, trans.user.id))
+                    "invalid or not authorized to read the bucket/object.".format(obj, trans.user.id)
+                )
                 raise ObjectNotFound(
                     "Could not get the object `{}`. Please check if the object exists, and credentials are valid and "
-                    "authorized to read the bucket and object. ".format(obj))
+                    "authorized to read the bucket and object. ".format(obj)
+                )
 
             params = Params(self._get_inputs(obj, key, input_args), sanitize=False)
             incoming = params.__dict__
             history = trans.sa_session.query(trans.app.model.History).get(history_id)
             if not history:
                 raise ObjectNotFound(f"History with ID `{trans.app.security.encode_id(history_id)}` not found.")
-            output = trans.app.toolbox.get_tool('upload1').handle_input(trans, incoming, history=history)
+            output = trans.app.toolbox.get_tool("upload1").handle_input(trans, incoming, history=history)
 
-            job_errors = output.get('job_errors', [])
+            job_errors = output.get("job_errors", [])
             if job_errors:
-                raise ValueError('Following error occurred while getting the given object(s) from {}: {}'.format(
-                    cloudauthz.provider, job_errors))
+                raise ValueError(
+                    "Following error occurred while getting the given object(s) from {}: {}".format(
+                        cloudauthz.provider, job_errors
+                    )
+                )
             else:
-                for d in output['out_data']:
+                for d in output["out_data"]:
                     datasets.append(d[1].dataset)
 
         return datasets
@@ -319,9 +349,11 @@ class CloudManager(sharable.SharableModelManager):
         if CloudProviderFactory is None:
             raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
 
-        if not hasattr(trans.app, 'authnz_manager'):
-            err_msg = "The OpenID Connect protocol, a required feature for sending data to cloud, " \
-                      "is not enabled on this Galaxy instance."
+        if not hasattr(trans.app, "authnz_manager"):
+            err_msg = (
+                "The OpenID Connect protocol, a required feature for sending data to cloud, "
+                "is not enabled on this Galaxy instance."
+            )
             log.debug(err_msg)
             raise MessageException(err_msg)
 
@@ -346,32 +378,23 @@ class CloudManager(sharable.SharableModelManager):
                         "bucket": bucket_name,
                         "object_label": object_label,
                         "filename": hda,
-                        "overwrite_existing": overwrite_existing
+                        "overwrite_existing": overwrite_existing,
                     }
                     incoming = (util.Params(args, sanitize=False)).__dict__
                     d2c = trans.app.toolbox.get_tool(SEND_TOOL, SEND_TOOL_VERSION)
                     if not d2c:
                         log.debug(f"Failed to get the `send` tool per user `{trans.user.id}` request.")
-                        failed.append(json.dumps(
-                            {
-                                "object": object_label,
-                                "error": "Unable to get the `send` tool."
-                            }))
+                        failed.append(json.dumps({"object": object_label, "error": "Unable to get the `send` tool."}))
                         continue
                     res = d2c.execute(trans, incoming, history=history)
                     job = res[0]
-                    sent.append(json.dumps(
-                        {
-                            "object": object_label,
-                            "job_id": trans.app.security.encode_id(job.id)
-                        }))
+                    sent.append(json.dumps({"object": object_label, "job_id": trans.app.security.encode_id(job.id)}))
                 except Exception as e:
                     err_msg = f"maybe invalid or unauthorized credentials. {util.unicodify(e)}"
-                    log.debug("Failed to send the dataset `{}` per user `{}` request to cloud, {}".format(
-                        object_label, trans.user.id, err_msg))
-                    failed.append(json.dumps(
-                        {
-                            "object": object_label,
-                            "error": err_msg
-                        }))
+                    log.debug(
+                        "Failed to send the dataset `{}` per user `{}` request to cloud, {}".format(
+                            object_label, trans.user.id, err_msg
+                        )
+                    )
+                    failed.append(json.dumps({"object": object_label, "error": err_msg}))
         return sent, failed
diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py
index 005fbe780eb..392bc0147d8 100644
--- a/lib/galaxy/managers/cloudauthzs.py
+++ b/lib/galaxy/managers/cloudauthzs.py
@@ -6,11 +6,11 @@ import logging
 from typing import Dict
 
 from galaxy import model
-from galaxy.exceptions import (
-    InternalServerError,
+from galaxy.exceptions import InternalServerError
+from galaxy.managers import (
+    base,
+    sharable,
 )
-from galaxy.managers import base
-from galaxy.managers import sharable
 
 log = logging.getLogger(__name__)
 
@@ -18,32 +18,36 @@ log = logging.getLogger(__name__)
 class CloudAuthzManager(sharable.SharableModelManager):
 
     model_class = model.CloudAuthz
-    foreign_key_name = 'cloudauthz'
+    foreign_key_name = "cloudauthz"
 
 
 class CloudAuthzsSerializer(base.ModelSerializer):
     """
     Interface/service object for serializing cloud authorizations (cloudauthzs) into dictionaries.
     """
+
     model_manager_class = CloudAuthzManager
 
     def __init__(self, app, **kwargs):
         super().__init__(app, **kwargs)
         self.cloudauthzs_manager = self.manager
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'model_class',
-            'user_id',
-            'provider',
-            'config',
-            'authn_id',
-            'last_update',
-            'last_activity',
-            'create_time',
-            'description'
-        ])
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "model_class",
+                "user_id",
+                "provider",
+                "config",
+                "authn_id",
+                "last_update",
+                "last_activity",
+                "create_time",
+                "description",
+            ],
+        )
 
     def add_serializers(self):
         super().add_serializers()
@@ -53,16 +57,18 @@ class CloudAuthzsSerializer(base.ModelSerializer):
         # k  : serialized dictionary key (e.g., 'model_class', 'provider').
         # **c: a dictionary containing 'trans' and 'user' objects.
         serializers: Dict[str, base.Serializer] = {
-            'id': lambda item, key, **context: self.app.security.encode_id(item.id),
-            'model_class': lambda item, key, **context: 'CloudAuthz',
-            'user_id': lambda item, key, **context: self.app.security.encode_id(item.user_id),
-            'provider': lambda item, key, **context: str(item.provider),
-            'config': lambda item, key, **context: item.config,
-            'authn_id': lambda item, key, **context: self.app.security.encode_id(item.authn_id) if item.authn_id else None,
-            'last_update': lambda item, key, **context: str(item.last_update),
-            'last_activity': lambda item, key, **context: str(item.last_activity),
-            'create_time': lambda item, key, **context: str(item.create_time),
-            'description': lambda item, key, **context: str(item.description)
+            "id": lambda item, key, **context: self.app.security.encode_id(item.id),
+            "model_class": lambda item, key, **context: "CloudAuthz",
+            "user_id": lambda item, key, **context: self.app.security.encode_id(item.user_id),
+            "provider": lambda item, key, **context: str(item.provider),
+            "config": lambda item, key, **context: item.config,
+            "authn_id": lambda item, key, **context: self.app.security.encode_id(item.authn_id)
+            if item.authn_id
+            else None,
+            "last_update": lambda item, key, **context: str(item.last_update),
+            "last_activity": lambda item, key, **context: str(item.last_activity),
+            "create_time": lambda item, key, **context: str(item.create_time),
+            "description": lambda item, key, **context: str(item.description),
         }
         self.serializers.update(serializers)
 
@@ -72,16 +78,19 @@ class CloudAuthzsDeserializer(base.ModelDeserializer):
     Service object for validating and deserializing dictionaries that
     update/alter cloudauthz configurations.
     """
+
     model_manager_class = CloudAuthzManager
 
     def add_deserializers(self):
         super().add_deserializers()
-        self.deserializers.update({
-            'authn_id': self.deserialize_and_validate_authn_id,
-            'provider': self.default_deserializer,
-            'config': self.default_deserializer,
-            'description': self.default_deserializer
-        })
+        self.deserializers.update(
+            {
+                "authn_id": self.deserialize_and_validate_authn_id,
+                "provider": self.default_deserializer,
+                "config": self.default_deserializer,
+                "description": self.default_deserializer,
+            }
+        )
 
     def deserialize_and_validate_authn_id(self, item, key, val, **context):
         """
@@ -104,7 +113,7 @@ class CloudAuthzsDeserializer(base.ModelDeserializer):
         :return:        decoded authentication ID.
         """
 
-        decoded_authn_id = self.app.security.decode_id(val, object_name='authz')
+        decoded_authn_id = self.app.security.decode_id(val, object_name="authz")
 
         trans = context.get("trans")
         if trans is None:
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 3318d3f0aa9..0ed7c6e9778 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -1,14 +1,22 @@
 import logging
-from typing import Any, Dict, List, Union
+from typing import (
+    Any,
+    Dict,
+    List,
+    Union,
+)
 
-from sqlalchemy.orm import joinedload, Query
+from sqlalchemy.orm import (
+    joinedload,
+    Query,
+)
 
 from galaxy import model
 from galaxy.datatypes.registry import Registry
 from galaxy.exceptions import (
     ItemAccessibilityException,
     MessageException,
-    RequestParameterInvalidException
+    RequestParameterInvalidException,
 )
 from galaxy.managers.collections_util import validate_input_element_identifiers
 from galaxy.model.dataset_collections import builder
@@ -18,9 +26,7 @@ from galaxy.model.dataset_collections.type_description import COLLECTION_TYPE_DE
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.tags import GalaxyTagHandler
 from galaxy.security.idencoding import IdEncodingHelper
-from galaxy.util import (
-    validation
-)
+from galaxy.util import validation
 from .hdas import (
     HDAManager,
     HistoryDatasetAssociationNoHistoryException,
@@ -28,7 +34,6 @@ from .hdas import (
 from .histories import HistoryManager
 from .lddas import LDDAManager
 
-
 log = logging.getLogger(__name__)
 
 ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers."
@@ -40,6 +45,7 @@ class DatasetCollectionManager:
     Abstraction for interfacing with dataset collections instance - ideally abstracts
     out model and plugin details.
     """
+
     ELEMENTS_UNINITIALIZED = object()
 
     def __init__(
@@ -61,15 +67,39 @@ class DatasetCollectionManager:
         self.tag_handler = tag_handler.create_tag_handler_session()
         self.ldda_manager = ldda_manager
 
-    def precreate_dataset_collection_instance(self, trans, parent, name, structure, implicit_inputs=None, implicit_output_name=None, tags=None, completed_collection=None):
+    def precreate_dataset_collection_instance(
+        self,
+        trans,
+        parent,
+        name,
+        structure,
+        implicit_inputs=None,
+        implicit_output_name=None,
+        tags=None,
+        completed_collection=None,
+    ):
         # TODO: prebuild all required HIDs and send them in so no need to flush in between.
-        dataset_collection = self.precreate_dataset_collection(structure, allow_unitialized_element=implicit_output_name is not None, completed_collection=completed_collection, implicit_output_name=implicit_output_name)
+        dataset_collection = self.precreate_dataset_collection(
+            structure,
+            allow_unitialized_element=implicit_output_name is not None,
+            completed_collection=completed_collection,
+            implicit_output_name=implicit_output_name,
+        )
         instance = self._create_instance_for_collection(
-            trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, flush=False, tags=tags
+            trans,
+            parent,
+            name,
+            dataset_collection,
+            implicit_inputs=implicit_inputs,
+            implicit_output_name=implicit_output_name,
+            flush=False,
+            tags=tags,
         )
         return instance
 
-    def precreate_dataset_collection(self, structure, allow_unitialized_element=True, completed_collection=None, implicit_output_name=None):
+    def precreate_dataset_collection(
+        self, structure, allow_unitialized_element=True, completed_collection=None, implicit_output_name=None
+    ):
         has_structure = not structure.is_leaf and structure.children_known
         if not has_structure and allow_unitialized_element:
             dataset_collection = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
@@ -88,13 +118,19 @@ class DatasetCollectionManager:
                 if completed_collection and implicit_output_name:
                     job = completed_collection[index]
                     if job:
-                        it = (jtiodca.dataset_collection for jtiodca in job.output_dataset_collections if jtiodca.name == implicit_output_name)
+                        it = (
+                            jtiodca.dataset_collection
+                            for jtiodca in job.output_dataset_collections
+                            if jtiodca.name == implicit_output_name
+                        )
                         element = next(it, None)
                 if element is None:
                     if substructure.is_leaf:
                         element = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
                     else:
-                        element = self.precreate_dataset_collection(substructure, allow_unitialized_element=allow_unitialized_element)
+                        element = self.precreate_dataset_collection(
+                            substructure, allow_unitialized_element=allow_unitialized_element
+                        )
 
                 element = model.DatasetCollectionElement(
                     collection=dataset_collection,
@@ -107,10 +143,25 @@ class DatasetCollectionManager:
 
         return dataset_collection
 
-    def create(self, trans, parent, name, collection_type, element_identifiers=None,
-               elements=None, implicit_collection_info=None, trusted_identifiers=None,
-               hide_source_items=False, tags=None, copy_elements=False, history=None,
-               set_hid=True, flush=True, completed_job=None, output_name=None):
+    def create(
+        self,
+        trans,
+        parent,
+        name,
+        collection_type,
+        element_identifiers=None,
+        elements=None,
+        implicit_collection_info=None,
+        trusted_identifiers=None,
+        hide_source_items=False,
+        tags=None,
+        copy_elements=False,
+        history=None,
+        set_hid=True,
+        flush=True,
+        completed_job=None,
+        output_name=None,
+    ):
         """
         PRECONDITION: security checks on ability to add to parent
         occurred during load.
@@ -138,17 +189,36 @@ class DatasetCollectionManager:
 
         implicit_inputs = []
         if implicit_collection_info:
-            implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
+            implicit_inputs = implicit_collection_info.get("implicit_inputs", [])
 
         implicit_output_name = None
         if implicit_collection_info:
             implicit_output_name = implicit_collection_info["implicit_output_name"]
 
         return self._create_instance_for_collection(
-            trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, tags=tags, set_hid=set_hid, flush=flush,
+            trans,
+            parent,
+            name,
+            dataset_collection,
+            implicit_inputs=implicit_inputs,
+            implicit_output_name=implicit_output_name,
+            tags=tags,
+            set_hid=set_hid,
+            flush=flush,
         )
 
-    def _create_instance_for_collection(self, trans, parent, name, dataset_collection, implicit_output_name=None, implicit_inputs=None, tags=None, set_hid=True, flush=True):
+    def _create_instance_for_collection(
+        self,
+        trans,
+        parent,
+        name,
+        dataset_collection,
+        implicit_output_name=None,
+        implicit_inputs=None,
+        tags=None,
+        set_hid=True,
+        flush=True,
+    ):
         if isinstance(parent, model.History):
             dataset_collection_instance: Union[
                 model.HistoryDatasetCollectionAssociation,
@@ -157,9 +227,7 @@ class DatasetCollectionManager:
                 collection=dataset_collection,
                 name=name,
             )
-            assert isinstance(
-                dataset_collection_instance, model.HistoryDatasetCollectionAssociation
-            )
+            assert isinstance(dataset_collection_instance, model.HistoryDatasetCollectionAssociation)
             if implicit_inputs:
                 for input_name, input_collection in implicit_inputs:
                     dataset_collection_instance.add_implicit_input_collection(input_name, input_collection)
@@ -194,8 +262,16 @@ class DatasetCollectionManager:
             tags = self._append_tags(dataset_collection_instance, implicit_inputs, tags)
         return self.__persist(dataset_collection_instance, flush=flush)
 
-    def create_dataset_collection(self, trans, collection_type, element_identifiers=None, elements=None,
-                                  hide_source_items=None, copy_elements=False, history=None):
+    def create_dataset_collection(
+        self,
+        trans,
+        collection_type,
+        element_identifiers=None,
+        elements=None,
+        hide_source_items=None,
+        copy_elements=False,
+        history=None,
+    ):
         # Make sure at least one of these is None.
         assert element_identifiers is None or elements is None
 
@@ -209,18 +285,22 @@ class DatasetCollectionManager:
         # If we have elements, this is an internal request, don't need to load
         # objects from identifiers.
         if elements is None:
-            elements = self._element_identifiers_to_elements(trans,
-                                                             collection_type_description=collection_type_description,
-                                                             element_identifiers=element_identifiers,
-                                                             hide_source_items=hide_source_items,
-                                                             copy_elements=copy_elements,
-                                                             history=history)
+            elements = self._element_identifiers_to_elements(
+                trans,
+                collection_type_description=collection_type_description,
+                element_identifiers=element_identifiers,
+                hide_source_items=hide_source_items,
+                copy_elements=copy_elements,
+                history=history,
+            )
             if history:
                 history.add_pending_items()
         else:
             if has_subcollections:
                 # Nested collection - recursively create collections as needed.
-                self.__recursively_create_collections_for_elements(trans, elements, hide_source_items, copy_elements=copy_elements, history=history)
+                self.__recursively_create_collections_for_elements(
+                    trans, elements, hide_source_items, copy_elements=copy_elements, history=history
+                )
         # else if elements is set, it better be an ordered dict!
 
         if elements is not self.ELEMENTS_UNINITIALIZED:
@@ -233,10 +313,7 @@ class DatasetCollectionManager:
 
     def get_converters_for_collection(self, trans, id, datatypes_registry: Registry, instance_type="history"):
         dataset_collection_instance = self.get_dataset_collection_instance(
-            trans,
-            id=id,
-            instance_type=instance_type,
-            check_ownership=True
+            trans, id=id, instance_type=instance_type, check_ownership=True
         )
         dbkeys_and_extensions = dataset_collection_instance.dataset_dbkeys_and_extensions_summary
         suitable_converters = set()
@@ -249,7 +326,7 @@ class DatasetCollectionManager:
             for tgt_type, tgt_val in new_converters.items():
                 converter = (tgt_type, tgt_val)
                 set_of_new_converters.add(converter)
-            if (first_extension is True):
+            if first_extension is True:
                 suitable_converters = set_of_new_converters
                 most_recent_datatype = datatype
                 first_extension = False
@@ -259,35 +336,48 @@ class DatasetCollectionManager:
                     most_recent_datatype = datatype
         suitable_tool_ids = list()
         for tool in suitable_converters:
-            tool_info = {"tool_id": tool[1].id, "name": tool[1].name, "target_type": tool[0], "original_type": most_recent_datatype}
+            tool_info = {
+                "tool_id": tool[1].id,
+                "name": tool[1].name,
+                "target_type": tool[0],
+                "original_type": most_recent_datatype,
+            }
             suitable_tool_ids.append(tool_info)
         return suitable_tool_ids
 
-    def _element_identifiers_to_elements(self,
-                                         trans,
-                                         collection_type_description,
-                                         element_identifiers,
-                                         hide_source_items=False,
-                                         copy_elements=False,
-                                         history=None):
+    def _element_identifiers_to_elements(
+        self,
+        trans,
+        collection_type_description,
+        element_identifiers,
+        hide_source_items=False,
+        copy_elements=False,
+        history=None,
+    ):
         if collection_type_description.has_subcollections():
             # Nested collection - recursively create collections and update identifiers.
-            self.__recursively_create_collections_for_identifiers(trans, element_identifiers, hide_source_items, copy_elements, history=history)
+            self.__recursively_create_collections_for_identifiers(
+                trans, element_identifiers, hide_source_items, copy_elements, history=history
+            )
         new_collection = False
         for element_identifier in element_identifiers:
-            if element_identifier.get("src") == "new_collection" and element_identifier.get('collection_type') == '':
+            if element_identifier.get("src") == "new_collection" and element_identifier.get("collection_type") == "":
                 new_collection = True
-                elements = self.__load_elements(trans=trans,
-                                                element_identifiers=element_identifier['element_identifiers'],
-                                                hide_source_items=hide_source_items,
-                                                copy_elements=copy_elements,
-                                                history=history)
+                elements = self.__load_elements(
+                    trans=trans,
+                    element_identifiers=element_identifier["element_identifiers"],
+                    hide_source_items=hide_source_items,
+                    copy_elements=copy_elements,
+                    history=history,
+                )
         if not new_collection:
-            elements = self.__load_elements(trans=trans,
-                                            element_identifiers=element_identifiers,
-                                            hide_source_items=hide_source_items,
-                                            copy_elements=copy_elements,
-                                            history=history)
+            elements = self.__load_elements(
+                trans=trans,
+                element_identifiers=element_identifiers,
+                hide_source_items=hide_source_items,
+                copy_elements=copy_elements,
+                history=history,
+            )
         return elements
 
     def _append_tags(self, dataset_collection_instance, implicit_inputs=None, tags=None):
@@ -303,7 +393,9 @@ class DatasetCollectionManager:
         return builder.BoundCollectionBuilder(dataset_collection)
 
     def delete(self, trans, instance_type, id, recursive=False, purge=False):
-        dataset_collection_instance = self.get_dataset_collection_instance(trans, instance_type, id, check_ownership=True)
+        dataset_collection_instance = self.get_dataset_collection_instance(
+            trans, instance_type, id, check_ownership=True
+        )
         dataset_collection_instance.deleted = True
         trans.sa_session.add(dataset_collection_instance)
 
@@ -312,7 +404,9 @@ class DatasetCollectionManager:
                 try:
                     self.hda_manager.error_unless_owner(dataset, user=trans.get_user(), current_history=trans.history)
                 except HistoryDatasetAssociationNoHistoryException:
-                    log.info(f"Cannot delete HistoryDatasetAssociation {dataset.id}, HistoryDatasetAssociation has no associated History, cannot verify owner")
+                    log.info(
+                        f"Cannot delete HistoryDatasetAssociation {dataset.id}, HistoryDatasetAssociation has no associated History, cannot verify owner"
+                    )
                     continue
                 if not dataset.deleted:
                     dataset.deleted = True
@@ -323,13 +417,15 @@ class DatasetCollectionManager:
         trans.sa_session.flush()
 
     def update(self, trans, instance_type, id, payload):
-        dataset_collection_instance = self.get_dataset_collection_instance(trans, instance_type, id, check_ownership=True)
+        dataset_collection_instance = self.get_dataset_collection_instance(
+            trans, instance_type, id, check_ownership=True
+        )
         if trans.user is None:
             anon_allowed_payload = {}
-            if 'deleted' in payload:
-                anon_allowed_payload['deleted'] = payload['deleted']
-            if 'visible' in payload:
-                anon_allowed_payload['visible'] = payload['visible']
+            if "deleted" in payload:
+                anon_allowed_payload["deleted"] = payload["deleted"]
+            if "visible" in payload:
+                anon_allowed_payload["visible"] = payload["visible"]
             payload = self._validate_and_parse_update_payload(anon_allowed_payload)
         else:
             payload = self._validate_and_parse_update_payload(payload)
@@ -360,23 +456,27 @@ class DatasetCollectionManager:
         changed = dataset_collection_instance.set_from_dict(new_data)
 
         # the rest (often involving the trans) - do here
-        if 'annotation' in new_data.keys() and trans.get_user():
-            dataset_collection_instance.add_item_annotation(trans.sa_session, trans.get_user(), dataset_collection_instance, new_data['annotation'])
-            changed['annotation'] = new_data['annotation']
+        if "annotation" in new_data.keys() and trans.get_user():
+            dataset_collection_instance.add_item_annotation(
+                trans.sa_session, trans.get_user(), dataset_collection_instance, new_data["annotation"]
+            )
+            changed["annotation"] = new_data["annotation"]
 
         # the api promises a list of changed fields, but tags are not marked as changed to avoid the
         # flush, so we must handle changed tag responses manually
         new_tags = None
-        if 'tags' in new_data.keys() and trans.get_user():
+        if "tags" in new_data.keys() and trans.get_user():
             # set_tags_from_list will flush on its own, no need to add to 'changed' here and incur a second flush.
-            new_tags = self.tag_handler.set_tags_from_list(trans.get_user(), dataset_collection_instance, new_data['tags'])
+            new_tags = self.tag_handler.set_tags_from_list(
+                trans.get_user(), dataset_collection_instance, new_data["tags"]
+            )
 
         if changed.keys():
             trans.sa_session.flush()
 
         # set client tag field response after the flush
         if new_tags is not None:
-            changed['tags'] = dataset_collection_instance.make_tag_string_list()
+            changed["tags"] = dataset_collection_instance.make_tag_string_list()
 
         return changed
 
@@ -385,12 +485,12 @@ class DatasetCollectionManager:
         for key, val in payload.items():
             if val is None:
                 continue
-            if key in ('name'):
+            if key in ("name"):
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
-            if key in ('deleted', 'visible'):
+            if key in ("deleted", "visible"):
                 validated_payload[key] = validation.validate_boolean(key, val)
-            elif key == 'tags':
+            elif key == "tags":
                 validated_payload[key] = validation.validate_and_sanitize_basestring_list(key, val)
         return validated_payload
 
@@ -406,7 +506,9 @@ class DatasetCollectionManager:
             context.flush()
         return dataset_collection_instance
 
-    def __recursively_create_collections_for_identifiers(self, trans, element_identifiers, hide_source_items, copy_elements, history=None):
+    def __recursively_create_collections_for_identifiers(
+        self, trans, element_identifiers, hide_source_items, copy_elements, history=None
+    ):
         for element_identifier in element_identifiers:
             try:
                 if element_identifier.get("src") != "new_collection":
@@ -430,7 +532,9 @@ class DatasetCollectionManager:
 
         return element_identifiers
 
-    def __recursively_create_collections_for_elements(self, trans, elements, hide_source_items, copy_elements, history=None):
+    def __recursively_create_collections_for_elements(
+        self, trans, elements, hide_source_items, copy_elements, history=None
+    ):
         if elements is self.ELEMENTS_UNINITIALIZED:
             return
 
@@ -460,11 +564,13 @@ class DatasetCollectionManager:
     def __load_elements(self, trans, element_identifiers, hide_source_items=False, copy_elements=False, history=None):
         elements = {}
         for element_identifier in element_identifiers:
-            elements[element_identifier["name"]] = self.__load_element(trans,
-                                                                       element_identifier=element_identifier,
-                                                                       hide_source_items=hide_source_items,
-                                                                       copy_elements=copy_elements,
-                                                                       history=history)
+            elements[element_identifier["name"]] = self.__load_element(
+                trans,
+                element_identifier=element_identifier,
+                hide_source_items=hide_source_items,
+                copy_elements=copy_elements,
+                history=history,
+            )
         return elements
 
     def __load_element(self, trans, element_identifier, hide_source_items, copy_elements, history=None):
@@ -485,34 +591,38 @@ class DatasetCollectionManager:
 
         # dataset_identifier is dict {src=hda|ldda|hdca|new_collection, id=<encoded_id>}
         try:
-            src_type = element_identifier.get('src', 'hda')
+            src_type = element_identifier.get("src", "hda")
         except AttributeError:
             raise MessageException(f"Dataset collection element definition ({element_identifier}) not dictionary-like.")
-        encoded_id = element_identifier.get('id')
+        encoded_id = element_identifier.get("id")
         if not src_type or not encoded_id:
             message_template = "Problem decoding element identifier %s - must contain a 'src' and a 'id'."
             message = message_template % element_identifier
             raise RequestParameterInvalidException(message)
 
-        tags = element_identifier.pop('tags', None)
-        tag_str = ''
+        tags = element_identifier.pop("tags", None)
+        tag_str = ""
         if tags:
             tag_str = ",".join(str(_) for _ in tags)
-        if src_type == 'hda':
+        if src_type == "hda":
             decoded_id = int(trans.app.security.decode_id(encoded_id))
             hda = self.hda_manager.get_accessible(decoded_id, trans.user)
             if copy_elements:
                 element = self.hda_manager.copy(hda, history=history or trans.history, hide_copy=True, flush=False)
             else:
                 element = hda
-            if hide_source_items and self.hda_manager.get_owned(hda.id, user=trans.user, current_history=history or trans.history):
+            if hide_source_items and self.hda_manager.get_owned(
+                hda.id, user=trans.user, current_history=history or trans.history
+            ):
                 hda.visible = False
             self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str, flush=False)
-        elif src_type == 'ldda':
+        elif src_type == "ldda":
             element = self.ldda_manager.get(trans, encoded_id, check_accessible=True)
-            element = element.to_history_dataset_association(history or trans.history, add_to_history=True, visible=not hide_source_items)
+            element = element.to_history_dataset_association(
+                history or trans.history, add_to_history=True, visible=not hide_source_items
+            )
             self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str, flush=False)
-        elif src_type == 'hdca':
+        elif src_type == "hdca":
             # TODO: Option to copy? Force copy? Copy or allow if not owned?
             element = self.__get_history_collection_instance(trans, encoded_id).collection
         # TODO: ldca.
@@ -528,8 +638,7 @@ class DatasetCollectionManager:
         return MatchingCollections.for_collections(collections_to_match, self.collection_type_descriptions)
 
     def get_dataset_collection_instance(self, trans, instance_type, id, **kwds):
-        """
-        """
+        """ """
         if instance_type == "history":
             return self.__get_history_collection_instance(trans, id, **kwds)
         elif instance_type == "library":
@@ -550,7 +659,9 @@ class DatasetCollectionManager:
 
         collection_type = rule_set.collection_type
         collection_type_description = self.collection_type_descriptions.for_collection_type(collection_type)
-        elements = self._build_elements_from_rule_data(collection_type_description, rule_set, data, sources, handle_dataset)
+        elements = self._build_elements_from_rule_data(
+            collection_type_description, rule_set, data, sources, handle_dataset
+        )
         return elements
 
     def _build_elements_from_rule_data(self, collection_type_description, rule_set, data, sources, handle_dataset):
@@ -573,7 +684,9 @@ class DatasetCollectionManager:
                         elif identifier.lower() in ["r", "2", "r2", "reverse"]:
                             identifier = "reverse"
                         else:
-                            raise Exception("Unknown indicator of paired status encountered - only values of F, R, 1, 2, R1, R2, forward, or reverse are allowed.")
+                            raise Exception(
+                                "Unknown indicator of paired status encountered - only values of F, R, 1, 2, R1, R2, forward, or reverse are allowed."
+                            )
 
                     tags = []
                     if "group_tags" in mapping_as_dict:
@@ -620,7 +733,11 @@ class DatasetCollectionManager:
             identifiers = parent_identifiers + [element.element_identifier]
             if not element.is_collection:
                 data.append([])
-                source = {"identifiers": identifiers, "dataset": element_object, "tags": element_object.make_tag_string_list()}
+                source = {
+                    "identifiers": identifiers,
+                    "dataset": element_object,
+                    "tags": element_object.make_tag_string_list(),
+                }
                 sources.append(source)
             else:
                 child_collection_type_description = collection_type_description.child_collection_type_description()
@@ -634,26 +751,38 @@ class DatasetCollectionManager:
 
     def __get_history_collection_instance(self, trans, id, check_ownership=False, check_accessible=True):
         instance_id = int(trans.app.security.decode_id(id))
-        collection_instance = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(instance_id)
+        collection_instance = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(
+            instance_id
+        )
         if not collection_instance:
             raise RequestParameterInvalidException(f"History dataset collection association {id} not found")
-        history = getattr(trans, 'history', collection_instance.history)
+        history = getattr(trans, "history", collection_instance.history)
         if check_ownership:
             self.history_manager.error_unless_owner(collection_instance.history, trans.user, current_history=history)
         if check_accessible:
-            self.history_manager.error_unless_accessible(collection_instance.history, trans.user, current_history=history)
+            self.history_manager.error_unless_accessible(
+                collection_instance.history, trans.user, current_history=history
+            )
         return collection_instance
 
     def __get_library_collection_instance(self, trans, id, check_ownership=False, check_accessible=True):
         if check_ownership:
-            raise NotImplementedError("Functionality (getting library dataset collection with ownership check) unimplemented.")
+            raise NotImplementedError(
+                "Functionality (getting library dataset collection with ownership check) unimplemented."
+            )
         instance_id = int(trans.security.decode_id(id))
-        collection_instance = trans.sa_session.query(trans.app.model.LibraryDatasetCollectionAssociation).get(instance_id)
+        collection_instance = trans.sa_session.query(trans.app.model.LibraryDatasetCollectionAssociation).get(
+            instance_id
+        )
         if not collection_instance:
             raise RequestParameterInvalidException(f"Library dataset collection association {id} not found")
         if check_accessible:
-            if not trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), collection_instance, trans.user):
-                raise ItemAccessibilityException("LibraryDatasetCollectionAssociation is not accessible to the current user", type='error')
+            if not trans.app.security_agent.can_access_library_item(
+                trans.get_current_user_roles(), collection_instance, trans.user
+            ):
+                raise ItemAccessibilityException(
+                    "LibraryDatasetCollectionAssociation is not accessible to the current user", type="error"
+                )
         return collection_instance
 
     def get_collection_contents(self, trans, parent_id, limit=None, offset=None):
@@ -667,7 +796,7 @@ class DatasetCollectionManager:
         DCE = model.DatasetCollectionElement
         qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)
         qry = qry.order_by(DCE.element_index)
-        qry = qry.options(joinedload('child_collection'), joinedload('hda'))
+        qry = qry.options(joinedload("child_collection"), joinedload("hda"))
         if limit is not None:
             qry = qry.limit(int(limit))
         if offset is not None:
diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py
index 12b04706343..dcf5c68c4f9 100644
--- a/lib/galaxy/managers/collections_util.py
+++ b/lib/galaxy/managers/collections_util.py
@@ -1,13 +1,18 @@
 import logging
 import math
 
-from galaxy import exceptions, model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.util import string_as_bool
 
 log = logging.getLogger(__name__)
 
 ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s."
-ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection."
+ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = (
+    "Dataset source new_collection requires nested element_identifiers for new collection."
+)
 ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s"
 ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s."
 ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s."
@@ -29,13 +34,13 @@ def api_payload_to_create_params(payload):
         element_identifiers=payload.get("element_identifiers"),
         name=payload.get("name", None),
         hide_source_items=string_as_bool(payload.get("hide_source_items", False)),
-        copy_elements=string_as_bool(payload.get("copy_elements", False))
+        copy_elements=string_as_bool(payload.get("copy_elements", False)),
     )
     return params
 
 
 def validate_input_element_identifiers(element_identifiers):
-    """ Scan through the list of element identifiers supplied by the API consumer
+    """Scan through the list of element identifiers supplied by the API consumer
     and verify the structure is valid.
     """
     log.debug("Validating %d element identifiers for collection creation." % len(element_identifiers))
@@ -78,7 +83,9 @@ def get_collection(collection, name=""):
     hdas = []
     if collection.has_subcollections:
         for element in collection.elements:
-            subnames, subhdas = get_collection_elements(element.child_collection, name=f"{name}/{element.element_identifier}")
+            subnames, subhdas = get_collection_elements(
+                element.child_collection, name=f"{name}/{element.element_identifier}"
+            )
             names.extend(subnames)
             hdas.extend(subhdas)
     else:
@@ -103,34 +110,40 @@ def get_collection_elements(collection, name=""):
     return names, hdas
 
 
-def dictify_dataset_collection_instance(dataset_collection_instance, parent, security, url_builder, view="element", fuzzy_count=None):
+def dictify_dataset_collection_instance(
+    dataset_collection_instance, parent, security, url_builder, view="element", fuzzy_count=None
+):
     hdca_view = "element" if view in ["element", "element-reference"] else "collection"
     dict_value = dataset_collection_instance.to_dict(view=hdca_view)
     encoded_id = security.encode_id(dataset_collection_instance.id)
     if isinstance(parent, model.History):
         encoded_history_id = security.encode_id(parent.id)
-        dict_value['url'] = url_builder('history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection")
+        dict_value["url"] = url_builder(
+            "history_content_typed", history_id=encoded_history_id, id=encoded_id, type="dataset_collection"
+        )
     elif isinstance(parent, model.LibraryFolder):
         encoded_library_id = security.encode_id(parent.library_root.id)
         encoded_folder_id = security.encode_id(parent.id)
         # TODO: Work in progress - this end-point is not right yet...
-        dict_value['url'] = url_builder('library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id)
+        dict_value["url"] = url_builder(
+            "library_content", library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id
+        )
 
-    dict_value['contents_url'] = url_builder(
-        'contents_dataset_collection',
+    dict_value["contents_url"] = url_builder(
+        "contents_dataset_collection",
         hdca_id=encoded_id,
-        parent_id=security.encode_id(dataset_collection_instance.collection_id)
+        parent_id=security.encode_id(dataset_collection_instance.collection_id),
     )
     if view in ["element", "element-reference"]:
         collection = dataset_collection_instance.collection
         rank_fuzzy_counts = gen_rank_fuzzy_counts(collection.collection_type, fuzzy_count)
         elements, rest_fuzzy_counts = get_fuzzy_count_elements(collection, rank_fuzzy_counts)
         if view == "element":
-            dict_value['populated'] = collection.populated
+            dict_value["populated"] = collection.populated
             element_func = dictify_element
         else:
             element_func = dictify_element_reference
-        dict_value['elements'] = [element_func(_, rank_fuzzy_counts=rest_fuzzy_counts) for _ in elements]
+        dict_value["elements"] = [element_func(_, rank_fuzzy_counts=rest_fuzzy_counts) for _ in elements]
 
     security.encode_all_ids(dict_value, recursive=True)  # TODO: Use Kyle's recursive formulation of this.
     return dict_value
@@ -156,11 +169,14 @@ def dictify_element_reference(element, rank_fuzzy_counts=None, recursive=True, s
             if recursive:
                 child_collection = element.child_collection
                 elements, rest_fuzzy_counts = get_fuzzy_count_elements(child_collection, rank_fuzzy_counts)
-                object_details["elements"] = [dictify_element_reference(_, rank_fuzzy_counts=rest_fuzzy_counts, recursive=recursive) for _ in elements]
+                object_details["elements"] = [
+                    dictify_element_reference(_, rank_fuzzy_counts=rest_fuzzy_counts, recursive=recursive)
+                    for _ in elements
+                ]
                 object_details["element_count"] = child_collection.element_count
         else:
             object_details["state"] = element_object.state
-            object_details["hda_ldda"] = 'hda'
+            object_details["hda_ldda"] = "hda"
             object_details["history_id"] = element_object.history_id
 
         dictified["object"] = object_details
@@ -265,15 +281,19 @@ def gen_rank_fuzzy_counts(collection_type, fuzzy_count=None):
         list_count = len(rank_collection_types) - paired_count
         paired_fuzzy_count_mult = 1 if paired_count == 0 else 2 << (paired_count - 1)
         list_fuzzy_count_mult = math.floor((fuzzy_count * 1.0) / paired_fuzzy_count_mult)
-        list_rank_fuzzy_count = int(math.floor(math.pow(list_fuzzy_count_mult, 1.0 / list_count)) + 1) if list_count > 0 else 1.0
+        list_rank_fuzzy_count = (
+            int(math.floor(math.pow(list_fuzzy_count_mult, 1.0 / list_count)) + 1) if list_count > 0 else 1.0
+        )
         pair_rank_fuzzy_count = 2
         if list_rank_fuzzy_count > fuzzy_count:
             list_rank_fuzzy_count = fuzzy_count
         if pair_rank_fuzzy_count > fuzzy_count:
             pair_rank_fuzzy_count = fuzzy_count
-        rank_fuzzy_counts = [pair_rank_fuzzy_count if rt == "paired" else list_rank_fuzzy_count for rt in rank_collection_types]
+        rank_fuzzy_counts = [
+            pair_rank_fuzzy_count if rt == "paired" else list_rank_fuzzy_count for rt in rank_collection_types
+        ]
 
         return rank_fuzzy_counts
 
 
-__all__ = ('api_payload_to_create_params', 'dictify_dataset_collection_instance')
+__all__ = ("api_payload_to_create_params", "dictify_dataset_collection_instance")
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 2201abe6e1f..55b5c2115f1 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -22,9 +22,10 @@ from galaxy.managers.markdown_util import weasyprint_available
 from galaxy.schema import SerializationParams
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.web.framework.base import server_starttime
+
 log = logging.getLogger(__name__)
 
-VERSION_JSON_FILE = 'version.json'
+VERSION_JSON_FILE = "version.json"
 
 
 class ConfigurationManager:
@@ -34,9 +35,7 @@ class ConfigurationManager:
         self._app = app
 
     def get_configuration(
-        self,
-        trans: ProvidesUserContext,
-        serialization_params: SerializationParams
+        self, trans: ProvidesUserContext, serialization_params: SerializationParams
     ) -> Dict[str, Any]:
         is_admin = trans.user_is_admin
         host = getattr(trans, "host", None)
@@ -56,9 +55,9 @@ class ConfigurationManager:
             with open(json_file) as f:
                 extra_info = json.load(f)
         except OSError:
-            log.info('Galaxy extra version JSON file %s not loaded.', json_file)
+            log.info("Galaxy extra version JSON file %s not loaded.", json_file)
         else:
-            version_info['extra'] = extra_info
+            version_info["extra"] = extra_info
         return version_info
 
     def decode_id(
@@ -66,7 +65,7 @@ class ConfigurationManager:
         encoded_id: EncodedDatabaseIdField,
     ) -> Dict[str, int]:
         # Handle the special case for library folders
-        if ((len(encoded_id) % 16 == 1) and encoded_id.startswith('F')):
+        if (len(encoded_id) % 16 == 1) and encoded_id.startswith("F"):
             encoded_id = cast(EncodedDatabaseIdField, encoded_id[1:])
         decoded_id = self._app.security.decode_id(encoded_id)
         return {"decoded_id": decoded_id}
@@ -79,7 +78,7 @@ class ConfigurationManager:
             except AttributeError:
                 pass
             else:
-                entry = {'id': id, 'lineage': lineage_dict}
+                entry = {"id": id, "lineage": lineage_dict}
                 rval.append(entry)
         return rval
 
@@ -89,14 +88,15 @@ class ConfigurationManager:
         # server. A dedicated endpoint should probably be added to do that instead.
         def tool_conf_to_dict(conf):
             return dict(
-                config_filename=conf['config_filename'],
-                tool_path=conf['tool_path'],
+                config_filename=conf["config_filename"],
+                tool_path=conf["tool_path"],
             )
+
         confs = self._app.toolbox.dynamic_confs(include_migrated_tool_conf=True)
         return list(map(tool_conf_to_dict, confs))
 
     def reload_toolbox(self):
-        self._app.queue_worker.send_control_task('reload_toolbox')
+        self._app.queue_worker.send_control_task("reload_toolbox")
 
 
 # TODO: this is a bit of an odd duck. It uses the serializer structure from managers
@@ -108,14 +108,13 @@ class ConfigSerializer(base.ModelSerializer):
     def __init__(self, app):
         super().__init__(app)
 
-        self.default_view = 'all'
-        self.add_view('all', list(self.serializers.keys()))
+        self.default_view = "all"
+        self.add_view("all", list(self.serializers.keys()))
 
     def default_serializer(self, config, key):
         return getattr(config, key, None)
 
     def add_serializers(self):
-
         def _defaults_to(default) -> base.Serializer:
             return lambda item, key, **context: getattr(item, key, default)
 
@@ -129,87 +128,87 @@ class ConfigSerializer(base.ModelSerializer):
 
         self.serializers: Dict[str, base.Serializer] = {
             # TODO: this is available from user data, remove
-            'is_admin_user': lambda *a, **c: False,
-            'brand': _use_config,
-            'display_galaxy_brand': _use_config,
-            'logo_url': _use_config,
-            'logo_src': _use_config,
-            'logo_src_secondary': _use_config,
-            'terms_url': _use_config,
-            'myexperiment_target_url': _use_config,
-            'wiki_url': _use_config,
-            'search_url': _use_config,
-            'mailing_lists': _defaults_to(self.app.config.mailing_lists_url),
-            'screencasts_url': _use_config,
-            'citation_url': _use_config,
-            'support_url': _use_config,
-            'quota_url': _use_config,
-            'helpsite_url': _use_config,
-            'lims_doc_url': _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"),
-            'default_locale': _use_config,
-            'enable_tool_recommendations': _use_config,
-            'enable_account_interface': _use_config,
-            'tool_recommendation_model_path': _use_config,
-            'admin_tool_recommendations_path': _use_config,
-            'overwrite_model_recommendations': _use_config,
-            'topk_recommendations': _use_config,
-            'allow_user_impersonation': _use_config,
-            'allow_user_creation': _defaults_to(False),  # schema default is True
-            'use_remote_user': _defaults_to(None),  # schema default is False; or config.single_user
-            'single_user': _config_is_truthy,
-            'enable_oidc': _use_config,
-            'oidc': _use_config,
-            'enable_quotas': _use_config,
-            'remote_user_logout_href': _use_config,
-            'datatypes_disable_auto': _use_config,
-            'allow_user_dataset_purge': _defaults_to(False),  # schema default is True
-            'ga_code': _use_config,
-            'plausible_server': _use_config,
-            'plausible_domain': _use_config,
-            'markdown_to_pdf_available': lambda item, key, **context: weasyprint_available(),
-            'matomo_server': _use_config,
-            'matomo_site_id': _use_config,
-            'enable_unique_workflow_defaults': _use_config,
-            'enable_beta_markdown_export': _use_config,
-            'simplified_workflow_run_ui': _use_config,
-            'simplified_workflow_run_ui_target_history': _use_config,
-            'simplified_workflow_run_ui_job_cache': _use_config,
-            'simplified_workflow_run_ui': _use_config,
-            'has_user_tool_filters': _defaults_to(False),
+            "is_admin_user": lambda *a, **c: False,
+            "brand": _use_config,
+            "display_galaxy_brand": _use_config,
+            "logo_url": _use_config,
+            "logo_src": _use_config,
+            "logo_src_secondary": _use_config,
+            "terms_url": _use_config,
+            "myexperiment_target_url": _use_config,
+            "wiki_url": _use_config,
+            "search_url": _use_config,
+            "mailing_lists": _defaults_to(self.app.config.mailing_lists_url),
+            "screencasts_url": _use_config,
+            "citation_url": _use_config,
+            "support_url": _use_config,
+            "quota_url": _use_config,
+            "helpsite_url": _use_config,
+            "lims_doc_url": _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"),
+            "default_locale": _use_config,
+            "enable_tool_recommendations": _use_config,
+            "enable_account_interface": _use_config,
+            "tool_recommendation_model_path": _use_config,
+            "admin_tool_recommendations_path": _use_config,
+            "overwrite_model_recommendations": _use_config,
+            "topk_recommendations": _use_config,
+            "allow_user_impersonation": _use_config,
+            "allow_user_creation": _defaults_to(False),  # schema default is True
+            "use_remote_user": _defaults_to(None),  # schema default is False; or config.single_user
+            "single_user": _config_is_truthy,
+            "enable_oidc": _use_config,
+            "oidc": _use_config,
+            "enable_quotas": _use_config,
+            "remote_user_logout_href": _use_config,
+            "datatypes_disable_auto": _use_config,
+            "allow_user_dataset_purge": _defaults_to(False),  # schema default is True
+            "ga_code": _use_config,
+            "plausible_server": _use_config,
+            "plausible_domain": _use_config,
+            "markdown_to_pdf_available": lambda item, key, **context: weasyprint_available(),
+            "matomo_server": _use_config,
+            "matomo_site_id": _use_config,
+            "enable_unique_workflow_defaults": _use_config,
+            "enable_beta_markdown_export": _use_config,
+            "simplified_workflow_run_ui": _use_config,
+            "simplified_workflow_run_ui_target_history": _use_config,
+            "simplified_workflow_run_ui_job_cache": _use_config,
+            "simplified_workflow_run_ui": _use_config,
+            "has_user_tool_filters": _defaults_to(False),
             # TODO: is there no 'correct' way to get an api url? controller='api', action='tools' is a hack
             # at any rate: the following works with path_prefix but is still brittle
             # TODO: change this to (more generic) upload_path and incorporate config.nginx_upload_path into building it
-            'nginx_upload_path': lambda item, key, **context: getattr(item, key, False),
-            'chunk_upload_size': _use_config,
-            'ftp_upload_site': _use_config,
-            'version_major': _defaults_to(None),
-            'version_minor': _defaults_to(None),
-            'require_login': _use_config,
-            'inactivity_box_content': _use_config,
-            'visualizations_visible': _use_config,
-            'interactivetools_enable': _use_config,
-            'aws_estimate': _use_config,
-            'message_box_content': _use_config,
-            'message_box_visible': _use_config,
-            'message_box_class': _use_config,
-            'server_startttime': lambda item, key, **context: server_starttime,
-            'mailing_join_addr': _defaults_to('galaxy-announce-join@bx.psu.edu'),  # should this be the schema default?
-            'server_mail_configured': lambda item, key, **context: bool(item.smtp_server),
-            'registration_warning_message': _use_config,
-            'welcome_url': _use_config,
-            'show_welcome_with_login': _defaults_to(True),  # schema default is False
-            'cookie_domain': _use_config,
-            'python': _defaults_to((sys.version_info.major, sys.version_info.minor)),
-            'select_type_workflow_threshold': _use_config,
-            'file_sources_configured': lambda item, key, **context: self.app.file_sources.custom_sources_configured,
-            'panel_views': lambda item, key, **context: self.app.toolbox.panel_view_dicts(),
-            'default_panel_view': _use_config,
-            'upload_from_form_button': _use_config,
-            'release_doc_base_url': _use_config,
-            'expose_user_email': _use_config,
-            'enable_tool_source_display': _use_config,
-            'user_library_import_dir_available': lambda item, key, **context: bool(item.get('user_library_import_dir')),
-            'welcome_directory': _use_config,
+            "nginx_upload_path": lambda item, key, **context: getattr(item, key, False),
+            "chunk_upload_size": _use_config,
+            "ftp_upload_site": _use_config,
+            "version_major": _defaults_to(None),
+            "version_minor": _defaults_to(None),
+            "require_login": _use_config,
+            "inactivity_box_content": _use_config,
+            "visualizations_visible": _use_config,
+            "interactivetools_enable": _use_config,
+            "aws_estimate": _use_config,
+            "message_box_content": _use_config,
+            "message_box_visible": _use_config,
+            "message_box_class": _use_config,
+            "server_startttime": lambda item, key, **context: server_starttime,
+            "mailing_join_addr": _defaults_to("galaxy-announce-join@bx.psu.edu"),  # should this be the schema default?
+            "server_mail_configured": lambda item, key, **context: bool(item.smtp_server),
+            "registration_warning_message": _use_config,
+            "welcome_url": _use_config,
+            "show_welcome_with_login": _defaults_to(True),  # schema default is False
+            "cookie_domain": _use_config,
+            "python": _defaults_to((sys.version_info.major, sys.version_info.minor)),
+            "select_type_workflow_threshold": _use_config,
+            "file_sources_configured": lambda item, key, **context: self.app.file_sources.custom_sources_configured,
+            "panel_views": lambda item, key, **context: self.app.toolbox.panel_view_dicts(),
+            "default_panel_view": _use_config,
+            "upload_from_form_button": _use_config,
+            "release_doc_base_url": _use_config,
+            "expose_user_email": _use_config,
+            "enable_tool_source_display": _use_config,
+            "user_library_import_dir_available": lambda item, key, **context: bool(item.get("user_library_import_dir")),
+            "welcome_directory": _use_config,
         }
 
 
@@ -222,12 +221,13 @@ class AdminConfigSerializer(ConfigSerializer):
         def _defaults_to(default):
             return lambda config, key, **context: getattr(config, key, default)
 
-        self.serializers.update({
-            # TODO: this is available from user serialization: remove
-            'is_admin_user': lambda *a, **context: True,
-
-            'library_import_dir': _defaults_to(None),
-            'user_library_import_dir': _defaults_to(None),
-            'allow_library_path_paste': _defaults_to(False),
-            'allow_user_deletion': _defaults_to(False),
-        })
+        self.serializers.update(
+            {
+                # TODO: this is available from user serialization: remove
+                "is_admin_user": lambda *a, **context: True,
+                "library_import_dir": _defaults_to(None),
+                "user_library_import_dir": _defaults_to(None),
+                "allow_library_path_paste": _defaults_to(False),
+                "allow_user_deletion": _defaults_to(False),
+            }
+        )
diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py
index d4c850e70c8..aee813e7ceb 100644
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -37,7 +37,11 @@ A method that requires a user but not a history should declare its
 import abc
 import string
 from json import dumps
-from typing import Callable, List, Optional
+from typing import (
+    Callable,
+    List,
+    Optional,
+)
 
 from galaxy.exceptions import UserActivationRequiredException
 from galaxy.model import (
@@ -55,7 +59,7 @@ from galaxy.util import bunch
 
 
 class ProvidesAppContext:
-    """ For transaction-like objects to provide Galaxy convenience layer for
+    """For transaction-like objects to provide Galaxy convenience layer for
     database and event handling.
 
     Mixed in class must provide `app` property.
@@ -63,8 +67,7 @@ class ProvidesAppContext:
 
     @abc.abstractproperty
     def app(self) -> MinimalManagerApp:
-        """Provide access to the Galaxy ``app`` object.
-        """
+        """Provide access to the Galaxy ``app`` object."""
 
     @abc.abstractproperty
     def url_builder(self) -> Optional[Callable[..., str]]:
@@ -149,7 +152,7 @@ class ProvidesAppContext:
         context = app.model.context
         context.expunge_all()
         # This is a bit hacky, should refctor this. Maybe refactor to app -> expunge_all()
-        if hasattr(app, 'install_model'):
+        if hasattr(app, "install_model"):
             install_model = app.install_model
             if install_model != app.model:
                 install_model.context.expunge_all()
@@ -187,7 +190,7 @@ class ProvidesAppContext:
 
 
 class ProvidesUserContext(ProvidesAppContext):
-    """ For transaction-like objects to provide Galaxy convenience layer for
+    """For transaction-like objects to provide Galaxy convenience layer for
     reasoning about users.
 
     Mixed in class must provide `user` and `app`
@@ -247,15 +250,17 @@ class ProvidesUserContext(ProvidesAppContext):
             identifier_attr = self.app.config.ftp_upload_dir_identifier
             identifier_value = getattr(self.user, identifier_attr)
             template = self.app.config.ftp_upload_dir_template
-            path = string.Template(template).safe_substitute(dict(
-                ftp_upload_dir=base_dir,
-                ftp_upload_dir_identifier=identifier_value,
-            ))
+            path = string.Template(template).safe_substitute(
+                dict(
+                    ftp_upload_dir=base_dir,
+                    ftp_upload_dir_identifier=identifier_value,
+                )
+            )
             return path
 
 
 class ProvidesHistoryContext(ProvidesUserContext):
-    """ For transaction-like objects to provide Galaxy convenience layer for
+    """For transaction-like objects to provide Galaxy convenience layer for
     reasoning about histories.
 
     Mixed in class must provide `user`, `history`, and `app`
@@ -270,8 +275,7 @@ class ProvidesHistoryContext(ProvidesUserContext):
         """
 
     def db_dataset_for(self, dbkey) -> Optional[HistoryDatasetAssociation]:
-        """Optionally return the db_file dataset associated/needed by `dataset`.
-        """
+        """Optionally return the db_file dataset associated/needed by `dataset`."""
         # If no history, return None.
         if self.history is None:
             return None
@@ -282,14 +286,12 @@ class ProvidesHistoryContext(ProvidesUserContext):
             return None
         non_ready_or_ok = set(Dataset.non_ready_states)
         non_ready_or_ok.add(HistoryDatasetAssociation.states.OK)
-        datasets = self.sa_session.query(
-            HistoryDatasetAssociation
-        ).filter_by(
-            deleted=False,
-            history_id=self.history.id,
-            extension="len"
-        ).filter(
-            HistoryDatasetAssociation.table.c._state.in_(non_ready_or_ok),
+        datasets = (
+            self.sa_session.query(HistoryDatasetAssociation)
+            .filter_by(deleted=False, history_id=self.history.id, extension="len")
+            .filter(
+                HistoryDatasetAssociation.table.c._state.in_(non_ready_or_ok),
+            )
         )
         valid_ds = None
         for ds in datasets:
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index cf3bd0128bf..67ff9afa6ff 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -4,11 +4,16 @@ Manager and Serializer for Datasets.
 import glob
 import logging
 import os
-from typing import Dict, List, Type, TypeVar
+from typing import (
+    Dict,
+    List,
+    Type,
+    TypeVar,
+)
 
 from galaxy import (
     exceptions,
-    model
+    model,
 )
 from galaxy.datatypes import sniff
 from galaxy.managers import (
@@ -16,22 +21,23 @@ from galaxy.managers import (
     deletable,
     rbac_secured,
     secured,
-    users
+    users,
 )
 from galaxy.structured_app import MinimalManagerApp
 from galaxy.util.checkers import check_binary
 
 log = logging.getLogger(__name__)
 
-T = TypeVar('T')
+T = TypeVar("T")
 
 
 class DatasetManager(base.ModelManager, secured.AccessibleManagerMixin, deletable.PurgableManagerMixin):
     """
     Manipulate datasets: the components contained in DatasetAssociations/DatasetInstances/HDAs/LDDAs
     """
+
     model_class = model.Dataset
-    foreign_key_name = 'dataset'
+    foreign_key_name = "dataset"
     app: MinimalManagerApp
 
     # TODO:?? get + error_if_uploading is common pattern, should upload check be worked into access/owed?
@@ -47,7 +53,7 @@ class DatasetManager(base.ModelManager, secured.AccessibleManagerMixin, deletabl
         Create and return a new Dataset object.
         """
         # default to NEW state on new datasets
-        kwargs.update(dict(state=(kwargs.get('state', model.Dataset.states.NEW))))
+        kwargs.update(dict(state=(kwargs.get("state", model.Dataset.states.NEW))))
         dataset = model.Dataset(**kwargs)
         self.session().add(dataset)
 
@@ -58,7 +64,7 @@ class DatasetManager(base.ModelManager, secured.AccessibleManagerMixin, deletabl
         return dataset
 
     def copy(self, dataset, **kwargs):
-        raise exceptions.NotImplemented('Datasets cannot be copied')
+        raise exceptions.NotImplemented("Datasets cannot be copied")
 
     def purge(self, dataset, flush=True):
         """
@@ -80,7 +86,7 @@ class DatasetManager(base.ModelManager, secured.AccessibleManagerMixin, deletabl
     # TODO: how to allow admin bypass?
     def error_unless_dataset_purge_allowed(self, msg=None):
         if not self.app.config.allow_user_dataset_purge:
-            msg = msg or 'This instance does not allow user dataset purging'
+            msg = msg or "This instance does not allow user dataset purging"
             raise exceptions.ConfigDoesNotAllowException(msg)
 
     # .... accessibility
@@ -110,15 +116,15 @@ class DatasetManager(base.ModelManager, secured.AccessibleManagerMixin, deletabl
 
 # TODO: SecurityAgentDatasetRBACPermissions( object ):
 
-class DatasetRBACPermissions:
 
+class DatasetRBACPermissions:
     def __init__(self, app):
         self.app = app
         self.access = rbac_secured.AccessDatasetRBACPermission(app)
         self.manage = rbac_secured.ManageDatasetRBACPermission(app)
 
     # TODO: temporary facade over security_agent
-    def available_roles(self, trans, dataset, controller='root'):
+    def available_roles(self, trans, dataset, controller="root"):
         return self.app.security_agent.get_legitimate_roles(trans, dataset, controller)
 
     def get(self, dataset, flush=True):
@@ -152,38 +158,39 @@ class DatasetSerializer(base.ModelSerializer[DatasetManager], deletable.Purgable
         # needed for admin test
         self.user_manager = user_manager
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'create_time',
-            'update_time',
-            'state',
-            'deleted',
-            'purged',
-            'purgable',
-            # 'object_store_id',
-            # 'external_filename',
-            # 'extra_files_path',
-            'file_size',
-            'total_size',
-            'uuid',
-        ])
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "create_time",
+                "update_time",
+                "state",
+                "deleted",
+                "purged",
+                "purgable",
+                # 'object_store_id',
+                # 'external_filename',
+                # 'extra_files_path',
+                "file_size",
+                "total_size",
+                "uuid",
+            ],
+        )
         # could do visualizations and/or display_apps
 
     def add_serializers(self):
         super().add_serializers()
         deletable.PurgableSerializerMixin.add_serializers(self)
         serializers: Dict[str, base.Serializer] = {
-            'create_time': self.serialize_date,
-            'update_time': self.serialize_date,
-
-            'uuid': lambda item, key, **context: str(item.uuid) if item.uuid else None,
-            'file_name': self.serialize_file_name,
-            'extra_files_path': self.serialize_extra_files_path,
-            'permissions': self.serialize_permissions,
-
-            'total_size': lambda item, key, **context: int(item.get_total_size()),
-            'file_size': lambda item, key, **context: int(item.get_size())
+            "create_time": self.serialize_date,
+            "update_time": self.serialize_date,
+            "uuid": lambda item, key, **context: str(item.uuid) if item.uuid else None,
+            "file_name": self.serialize_file_name,
+            "extra_files_path": self.serialize_extra_files_path,
+            "permissions": self.serialize_permissions,
+            "total_size": lambda item, key, **context: int(item.get_total_size()),
+            "file_size": lambda item, key, **context: int(item.get_size()),
         }
         self.serializers.update(serializers)
 
@@ -213,8 +220,7 @@ class DatasetSerializer(base.ModelSerializer[DatasetManager], deletable.Purgable
         self.skip()
 
     def serialize_permissions(self, item, key, user=None, **context):
-        """
-        """
+        """ """
         dataset = item
         trans = context.get("trans")
         if not self.dataset_manager.permissions.manage.is_permitted(dataset, user, trans=trans):
@@ -223,21 +229,20 @@ class DatasetSerializer(base.ModelSerializer[DatasetManager], deletable.Purgable
         management_permissions = self.dataset_manager.permissions.manage.by_dataset(dataset)
         access_permissions = self.dataset_manager.permissions.access.by_dataset(dataset)
         permissions = {
-            'manage': [self.app.security.encode_id(perm.role.id) for perm in management_permissions],
-            'access': [self.app.security.encode_id(perm.role.id) for perm in access_permissions],
+            "manage": [self.app.security.encode_id(perm.role.id) for perm in management_permissions],
+            "access": [self.app.security.encode_id(perm.role.id) for perm in access_permissions],
         }
         return permissions
 
 
 # ============================================================================= AKA DatasetInstanceManager
-class DatasetAssociationManager(base.ModelManager,
-                                secured.AccessibleManagerMixin,
-                                deletable.PurgableManagerMixin):
+class DatasetAssociationManager(base.ModelManager, secured.AccessibleManagerMixin, deletable.PurgableManagerMixin):
     """
     DatasetAssociation/DatasetInstances are intended to be working
     proxies to a Dataset, associated with either a library or a
     user/history (HistoryDatasetAssociation).
     """
+
     # DA's were meant to be proxies - but were never fully implemented as them
     # Instead, a dataset association HAS a dataset but contains metadata specific to a library (lda) or user (hda)
     model_class: Type[model.DatasetInstance]
@@ -278,7 +283,7 @@ class DatasetAssociationManager(base.ModelManager,
         return dataset_assoc
 
     def by_user(self, user):
-        raise exceptions.NotImplemented('Abstract Method')
+        raise exceptions.NotImplemented("Abstract Method")
 
     # .... associated job
     def creating_job(self, dataset_assoc):
@@ -328,7 +333,7 @@ class DatasetAssociationManager(base.ModelManager,
         """Return a list of file paths for composite files, an empty list otherwise."""
         if not self.is_composite(dataset_assoc):
             return []
-        return glob.glob(os.path.join(dataset_assoc.dataset.extra_files_path, '*'))
+        return glob.glob(os.path.join(dataset_assoc.dataset.extra_files_path, "*"))
 
     def serialize_dataset_association_roles(self, trans, dataset_assoc):
         if hasattr(dataset_assoc, "library_dataset_dataset_association"):
@@ -343,12 +348,22 @@ class DatasetAssociationManager(base.ModelManager,
         access_roles = set(dataset.get_access_roles(security_agent))
         manage_roles = set(dataset.get_manage_permissions_roles(security_agent))
 
-        access_dataset_role_list = [(access_role.name, trans.security.encode_id(access_role.id)) for access_role in access_roles]
-        manage_dataset_role_list = [(manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles]
+        access_dataset_role_list = [
+            (access_role.name, trans.security.encode_id(access_role.id)) for access_role in access_roles
+        ]
+        manage_dataset_role_list = [
+            (manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles
+        ]
         rval = dict(access_dataset_roles=access_dataset_role_list, manage_dataset_roles=manage_dataset_role_list)
         if library_dataset is not None:
-            modify_roles = set(security_agent.get_roles_for_action(library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY))
-            modify_item_role_list = [(modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles]
+            modify_roles = set(
+                security_agent.get_roles_for_action(
+                    library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY
+                )
+            )
+            modify_item_role_list = [
+                (modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles
+            ]
             rval["modify_item_roles"] = modify_item_role_list
         return rval
 
@@ -357,7 +372,9 @@ class DatasetAssociationManager(base.ModelManager,
         data = trans.sa_session.query(self.model_class).get(dataset_assoc.id)
         if data.datatype.is_datatype_change_allowed():
             if not data.ok_to_edit_metadata():
-                raise exceptions.ItemAccessibilityException('This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them.')
+                raise exceptions.ItemAccessibilityException(
+                    "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them."
+                )
             else:
                 path = data.dataset.file_name
                 is_binary = check_binary(path)
@@ -372,25 +389,32 @@ class DatasetAssociationManager(base.ModelManager,
         """Trigger a job that detects and sets metadata on a given dataset association (ldda or hda)"""
         data = trans.sa_session.query(self.model_class).get(dataset_assoc.id)
         if not data.ok_to_edit_metadata():
-            raise exceptions.ItemAccessibilityException('This dataset is currently being used as input or output. You cannot edit metadata until the jobs have completed or you have canceled them.')
+            raise exceptions.ItemAccessibilityException(
+                "This dataset is currently being used as input or output. You cannot edit metadata until the jobs have completed or you have canceled them."
+            )
         else:
             if overwrite:
                 for name, spec in data.metadata.spec.items():
                     # We need to be careful about the attributes we are resetting
-                    if name not in ['name', 'info', 'dbkey', 'base_name']:
-                        if spec.get('default'):
-                            setattr(data.metadata, name, spec.unwrap(spec.get('default')))
+                    if name not in ["name", "info", "dbkey", "base_name"]:
+                        if spec.get("default"):
+                            setattr(data.metadata, name, spec.unwrap(spec.get("default")))
 
             job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
-                self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': data, 'validate': validate},
-                overwrite=overwrite)
+                self.app.datatypes_registry.set_external_metadata_tool,
+                trans,
+                incoming={"input1": data, "validate": validate},
+                overwrite=overwrite,
+            )
             self.app.job_manager.enqueue(job, tool=self.app.datatypes_registry.set_external_metadata_tool)
 
     def update_permissions(self, trans, dataset_assoc, **kwd):
-        action = kwd.get('action', 'set_permissions')
-        if action not in ['remove_restrictions', 'make_private', 'set_permissions']:
-            raise exceptions.RequestParameterInvalidException('The mandatory parameter "action" has an invalid value. '
-                                                              'Allowed values are: "remove_restrictions", "make_private", "set_permissions"')
+        action = kwd.get("action", "set_permissions")
+        if action not in ["remove_restrictions", "make_private", "set_permissions"]:
+            raise exceptions.RequestParameterInvalidException(
+                'The mandatory parameter "action" has an invalid value. '
+                'Allowed values are: "remove_restrictions", "make_private", "set_permissions"'
+            )
         if hasattr(dataset_assoc, "library_dataset_dataset_association"):
             library_dataset = dataset_assoc
             dataset = library_dataset.library_dataset_dataset_association.dataset
@@ -401,22 +425,26 @@ class DatasetAssociationManager(base.ModelManager,
         current_user_roles = trans.get_current_user_roles()
         can_manage = trans.app.security_agent.can_manage_dataset(current_user_roles, dataset) or trans.user_is_admin
         if not can_manage:
-            raise exceptions.InsufficientPermissionsException('You do not have proper permissions to manage permissions on this dataset.')
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permissions to manage permissions on this dataset."
+            )
 
-        if action == 'remove_restrictions':
+        if action == "remove_restrictions":
             trans.app.security_agent.make_dataset_public(dataset)
             if not trans.app.security_agent.dataset_is_public(dataset):
-                raise exceptions.InternalServerError('An error occurred while making dataset public.')
-        elif action == 'make_private':
+                raise exceptions.InternalServerError("An error occurred while making dataset public.")
+        elif action == "make_private":
             if not trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
                 private_role = trans.app.security_agent.get_private_user_role(trans.user)
-                dp = trans.app.model.DatasetPermissions(trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role)
+                dp = trans.app.model.DatasetPermissions(
+                    trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role
+                )
                 trans.sa_session.add(dp)
                 trans.sa_session.flush()
             if not trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
                 # Check again and inform the user if dataset is not private.
-                raise exceptions.InternalServerError('An error occurred and the dataset is NOT private.')
-        elif action == 'set_permissions':
+                raise exceptions.InternalServerError("An error occurred and the dataset is NOT private.")
+        elif action == "set_permissions":
 
             def to_role_id(encoded_role_id):
                 role_id = base.decode_id(self.app, encoded_role_id)
@@ -429,12 +457,12 @@ class DatasetAssociationManager(base.ModelManager,
                 else:
                     return None
 
-            access_roles = parameters_roles_or_none('access')
-            manage_roles = parameters_roles_or_none('manage')
-            modify_roles = parameters_roles_or_none('modify')
+            access_roles = parameters_roles_or_none("access")
+            manage_roles = parameters_roles_or_none("manage")
+            modify_roles = parameters_roles_or_none("modify")
             role_ids_dict = {
-                'DATASET_MANAGE_PERMISSIONS': manage_roles,
-                'DATASET_ACCESS': access_roles,
+                "DATASET_MANAGE_PERMISSIONS": manage_roles,
+                "DATASET_ACCESS": access_roles,
             }
             if library_dataset is not None:
                 role_ids_dict["LIBRARY_MODIFY"] = modify_roles
@@ -445,9 +473,7 @@ class DatasetAssociationManager(base.ModelManager,
         raise exceptions.NotImplemented()
 
 
-class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
-                                                       deletable.PurgableSerializerMixin):
-
+class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T], deletable.PurgableSerializerMixin):
     def __init__(self, app):
         self.dataset_serializer = app[DatasetSerializer]
         super().__init__(app)
@@ -457,55 +483,48 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         serializers: Dict[str, base.Serializer] = {
-            'create_time': self.serialize_date,
-            'update_time': self.serialize_date,
-
+            "create_time": self.serialize_date,
+            "update_time": self.serialize_date,
             # underlying dataset
-            'dataset': lambda item, key, **context: self.dataset_serializer.serialize_to_view(item.dataset, view='summary', **context),
-            'dataset_id': self._proxy_to_dataset(proxy_key='id'),
+            "dataset": lambda item, key, **context: self.dataset_serializer.serialize_to_view(
+                item.dataset, view="summary", **context
+            ),
+            "dataset_id": self._proxy_to_dataset(proxy_key="id"),
             # TODO: why is this named uuid!? The da doesn't have a uuid - it's the underlying dataset's uuid!
-            'uuid': self._proxy_to_dataset(proxy_key='uuid'),
+            "uuid": self._proxy_to_dataset(proxy_key="uuid"),
             # 'dataset_uuid': self._proxy_to_dataset( key='uuid' ),
-            'file_name': self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_file_name),
-            'extra_files_path': self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_extra_files_path),
-            'permissions': self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_permissions),
+            "file_name": self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_file_name),
+            "extra_files_path": self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_extra_files_path),
+            "permissions": self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_permissions),
             # TODO: do the sizes proxy accurately/in the same way?
-            'size': lambda item, key, **context: int(item.get_size()),
-            'file_size': lambda item, key, **context: self.serializers['size'](item, key, **context),
-            'nice_size': lambda item, key, **context: item.get_size(nice_size=True),
-
+            "size": lambda item, key, **context: int(item.get_size()),
+            "file_size": lambda item, key, **context: self.serializers["size"](item, key, **context),
+            "nice_size": lambda item, key, **context: item.get_size(nice_size=True),
             # common to lddas and hdas - from mapping.py
-            'copied_from_history_dataset_association_id': self.serialize_id,
-            'copied_from_library_dataset_dataset_association_id': self.serialize_id,
-            'info': lambda item, key, **context: item.info.strip() if isinstance(item.info, str) else item.info,
-            'blurb': lambda item, key, **context: item.blurb,
-            'peek': lambda item, key, **context: item.display_peek() if item.peek and item.peek != 'no peek' else None,
-
-            'meta_files': self.serialize_meta_files,
-            'metadata': self.serialize_metadata,
-
-            'creating_job': self.serialize_creating_job,
-            'rerunnable': self.serialize_rerunnable,
-
-            'parent_id': self.serialize_id,
-            'designation': lambda item, key, **context: item.designation,
-
+            "copied_from_history_dataset_association_id": self.serialize_id,
+            "copied_from_library_dataset_dataset_association_id": self.serialize_id,
+            "info": lambda item, key, **context: item.info.strip() if isinstance(item.info, str) else item.info,
+            "blurb": lambda item, key, **context: item.blurb,
+            "peek": lambda item, key, **context: item.display_peek() if item.peek and item.peek != "no peek" else None,
+            "meta_files": self.serialize_meta_files,
+            "metadata": self.serialize_metadata,
+            "creating_job": self.serialize_creating_job,
+            "rerunnable": self.serialize_rerunnable,
+            "parent_id": self.serialize_id,
+            "designation": lambda item, key, **context: item.designation,
             # 'extended_metadata': self.serialize_extended_metadata,
             # 'extended_metadata_id': self.serialize_id,
-
             # remapped
-            'genome_build': lambda item, key, **context: item.dbkey,
-
+            "genome_build": lambda item, key, **context: item.dbkey,
             # derived (not mapped) attributes
-            'data_type': lambda item, key, **context: f"{item.datatype.__class__.__module__}.{item.datatype.__class__.__name__}",
-
-            'converted': self.serialize_converted_datasets,
+            "data_type": lambda item, key, **context: f"{item.datatype.__class__.__module__}.{item.datatype.__class__.__name__}",
+            "converted": self.serialize_converted_datasets,
             # TODO: metadata/extra files
         }
         self.serializers.update(serializers)
         # this an abstract superclass, so no views created
         # because of that: we need to add a few keys that will use the default serializer
-        self.serializable_keyset.update(['name', 'state', 'tool_version', 'extension', 'visible', 'dbkey'])
+        self.serializable_keyset.update(["name", "state", "tool_version", "extension", "visible", "dbkey"])
 
     def _proxy_to_dataset(self, serializer: base.Serializer = None, proxy_key=None):
         # dataset associations are (rough) proxies to datasets - access their serializer using this remapping fn
@@ -515,7 +534,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
             serializer = self.dataset_serializer.serializers.get(proxy_key)
         if serializer:
             return lambda item, key, **context: serializer(item.dataset, proxy_key or key, **context)
-        raise TypeError('kwarg serializer or key needed')
+        raise TypeError("kwarg serializer or key needed")
 
     def serialize_meta_files(self, item, key, **context):
         """
@@ -526,11 +545,16 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
         for meta_type in dataset_assoc.metadata_file_types:
             if getattr(dataset_assoc.metadata, meta_type, None):
                 meta_files.append(
-                    dict(file_type=meta_type,
-                         download_url=self.url_for('history_contents_metadata_file',
-                                                   history_id=self.app.security.encode_id(dataset_assoc.history_id),
-                                                   history_content_id=self.app.security.encode_id(dataset_assoc.id),
-                                                   metadata_file=meta_type)))
+                    dict(
+                        file_type=meta_type,
+                        download_url=self.url_for(
+                            "history_contents_metadata_file",
+                            history_id=self.app.security.encode_id(dataset_assoc.history_id),
+                            history_content_id=self.app.security.encode_id(dataset_assoc.id),
+                            metadata_file=meta_type,
+                        ),
+                    )
+                )
         return meta_files
 
     def serialize_metadata(self, item, key, excluded=None, **context):
@@ -570,7 +594,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
         """
         dataset = item
         if dataset.creating_job:
-            return self.serialize_id(dataset.creating_job, 'id')
+            return self.serialize_id(dataset.creating_job, "id")
         else:
             return None
 
@@ -597,7 +621,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
         id_map = {}
         for converted in dataset_assoc.implicitly_converted_datasets:
             if not converted.deleted and converted.dataset:
-                id_map[converted.type] = self.serialize_id(converted.dataset, 'id')
+                id_map[converted.type] = self.serialize_id(converted.dataset, "id")
         return id_map
 
 
@@ -607,7 +631,7 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
     def add_serializers(self):
         super().add_serializers()
         # remove the single nesting key here
-        del self.serializers['metadata']
+        del self.serializers["metadata"]
 
     def serialize(self, dataset_assoc, keys, **context):
         """
@@ -615,12 +639,12 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
         """
         # if 'metadata' isn't removed from keys here serialize will retrieve the un-serializable MetadataCollection
         # TODO: remove these when metadata is sub-object
-        KEYS_HANDLED_SEPARATELY = ('metadata', )
+        KEYS_HANDLED_SEPARATELY = ("metadata",)
         left_to_handle = self._pluck_from_list(keys, KEYS_HANDLED_SEPARATELY)
         serialized = super().serialize(dataset_assoc, keys, **context)
 
         # add metadata directly to the dict instead of as a sub-object
-        if 'metadata' in left_to_handle:
+        if "metadata" in left_to_handle:
             metadata = self._prefixed_metadata(dataset_assoc)
             serialized.update(metadata)
         return serialized
@@ -645,7 +669,7 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
         prefixing each key with 'metadata_'.
         """
         # build the original, nested dictionary
-        metadata = self.serialize_metadata(dataset_assoc, 'metadata')
+        metadata = self.serialize_metadata(dataset_assoc, "metadata")
 
         # prefix each key within and return
         prefixed = {}
@@ -656,22 +680,22 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
 
 
 class DatasetAssociationDeserializer(base.ModelDeserializer, deletable.PurgableDeserializerMixin):
-
     def add_deserializers(self):
         super().add_deserializers()
         deletable.PurgableDeserializerMixin.add_deserializers(self)
 
-        self.deserializers.update({
-            'name': self.deserialize_basestring,
-            'info': self.deserialize_basestring,
-            'datatype': self.deserialize_datatype,
-        })
+        self.deserializers.update(
+            {
+                "name": self.deserialize_basestring,
+                "info": self.deserialize_basestring,
+                "datatype": self.deserialize_datatype,
+            }
+        )
         self.deserializable_keyset.update(self.deserializers.keys())
 
-# TODO: untested
+    # TODO: untested
     def deserialize_metadata(self, dataset_assoc, metadata_key, metadata_dict, **context):
-        """
-        """
+        """ """
         self.validate.matches_type(metadata_key, metadata_dict, dict)
         returned = {}
         for key, val in metadata_dict.items():
@@ -679,12 +703,11 @@ class DatasetAssociationDeserializer(base.ModelDeserializer, deletable.PurgableD
         return returned
 
     def deserialize_metadatum(self, dataset_assoc, key, val, **context):
-        """
-        """
+        """ """
         if key not in dataset_assoc.datatype.metadata_spec:
             return
         metadata_specification = dataset_assoc.datatype.metadata_spec[key]
-        if metadata_specification.get('readonly'):
+        if metadata_specification.get("readonly"):
             return
         unwrapped_val = metadata_specification.unwrap(val)
         setattr(dataset_assoc.metadata, key, unwrapped_val)
@@ -700,37 +723,41 @@ class DatasetAssociationDeserializer(base.ModelDeserializer, deletable.PurgableD
         if not target_datatype.is_datatype_change_allowed():
             raise exceptions.RequestParameterInvalidException("The target datatype does not allow datatype changes.")
         if not item.ok_to_edit_metadata():
-            raise exceptions.RequestParameterInvalidException("Dataset metadata could not be updated because it is used as input or output of a running job.")
+            raise exceptions.RequestParameterInvalidException(
+                "Dataset metadata could not be updated because it is used as input or output of a running job."
+            )
         item.change_datatype(val)
         sa_session = self.app.model.context
         sa_session.flush()
         trans = context.get("trans")
-        assert trans, "Logic error in Galaxy, deserialize_datatype not send a transation object"  # TODO: restructure this for stronger typing
-        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': item}, overwrite=False)  # overwrite is False as per existing behavior
+        assert (
+            trans
+        ), "Logic error in Galaxy, deserialize_datatype not send a transation object"  # TODO: restructure this for stronger typing
+        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
+            self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={"input1": item}, overwrite=False
+        )  # overwrite is False as per existing behavior
         trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)
         return item.datatype
 
 
 class DatasetAssociationFilterParser(base.ModelFilterParser, deletable.PurgableFiltersMixin):
-
     def _add_parsers(self):
         super()._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers(self)
 
-        self.orm_filter_parsers.update({
-            'name': {'op': ('eq', 'contains', 'like')},
-            'state': {'column': '_state', 'op': ('eq', 'in')},
-            'visible': {'op': ('eq'), 'val': base.parse_bool},
-        })
-        self.fn_filter_parsers.update({
-            'genome_build': self.string_standard_ops('dbkey'),
-            'data_type': {
-                'op': {
-                    'eq': self.eq_datatype,
-                    'isinstance': self.isinstance_datatype
-                }
+        self.orm_filter_parsers.update(
+            {
+                "name": {"op": ("eq", "contains", "like")},
+                "state": {"column": "_state", "op": ("eq", "in")},
+                "visible": {"op": ("eq"), "val": base.parse_bool},
             }
-        })
+        )
+        self.fn_filter_parsers.update(
+            {
+                "genome_build": self.string_standard_ops("dbkey"),
+                "data_type": {"op": {"eq": self.eq_datatype, "isinstance": self.isinstance_datatype}},
+            }
+        )
 
     def eq_datatype(self, dataset_assoc, class_str):
         """
@@ -746,7 +773,7 @@ class DatasetAssociationFilterParser(base.ModelFilterParser, deletable.PurgableF
         """
         parse_datatype_fn = self.app.datatypes_registry.get_datatype_class_by_name
         comparison_classes: List[Type] = []
-        for class_str in class_strs.split(','):
+        for class_str in class_strs.split(","):
             datatype_class = parse_datatype_fn(class_str)
             if datatype_class:
                 comparison_classes.append(datatype_class)
diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
index 6913bc32104..37f4df8c953 100644
--- a/lib/galaxy/managers/datatypes.py
+++ b/lib/galaxy/managers/datatypes.py
@@ -18,9 +18,7 @@ from galaxy.datatypes.registry import Registry
 
 
 def view_index(
-    datatypes_registry: Registry,
-    extension_only: Optional[bool] = True,
-    upload_only: Optional[bool] = True
+    datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
 ) -> Union[List[DatatypeDetails], List[str]]:
     if extension_only:
         if upload_only:
@@ -30,7 +28,7 @@ def view_index(
     else:
         rval = []
         for datatype_info_dict in datatypes_registry.datatype_info_dicts:
-            if upload_only and not datatype_info_dict.get('display_in_upload'):
+            if upload_only and not datatype_info_dict.get("display_in_upload"):
                 continue
             rval.append(datatype_info_dict)
         return rval
@@ -60,20 +58,18 @@ def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
 
 
 def view_types_and_mapping(
-    datatypes_registry: Registry,
-    extension_only: Optional[bool] = True,
-    upload_only: Optional[bool] = True
+    datatypes_registry: Registry, extension_only: Optional[bool] = True, upload_only: Optional[bool] = True
 ) -> DatatypesCombinedMap:
     return DatatypesCombinedMap(
         datatypes=view_index(datatypes_registry, extension_only, upload_only),
-        datatypes_mapping=view_mapping(datatypes_registry)
+        datatypes_mapping=view_mapping(datatypes_registry),
     )
 
 
 def view_sniffers(datatypes_registry: Registry) -> List[str]:
     rval: List[str] = []
     for sniffer_elem in datatypes_registry.sniffer_elems:
-        datatype = sniffer_elem.get('type')
+        datatype = sniffer_elem.get("type")
         if datatype is not None:
             rval.append(datatype)
     return rval
@@ -83,11 +79,13 @@ def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
     converters = []
     for (source_type, targets) in datatypes_registry.datatype_converters.items():
         for target_type in targets:
-            converters.append({
-                'source': source_type,
-                'target': target_type,
-                'tool_id': targets[target_type].id,
-            })
+            converters.append(
+                {
+                    "source": source_type,
+                    "target": target_type,
+                    "tool_id": targets[target_type].id,
+                }
+            )
     return parse_obj_as(DatatypeConverterList, converters)
 
 
diff --git a/lib/galaxy/managers/deletable.py b/lib/galaxy/managers/deletable.py
index a9c8ce6d6a8..b3aaf3802f9 100644
--- a/lib/galaxy/managers/deletable.py
+++ b/lib/galaxy/managers/deletable.py
@@ -8,7 +8,11 @@ models have some backing/supporting resources that can be removed as well
 the supporting resources as well. These models also have the boolean
 attribute 'purged'.
 """
-from typing import Any, Dict, Set
+from typing import (
+    Any,
+    Dict,
+    Set,
+)
 
 from galaxy.model import _HasTable
 from .base import (
@@ -35,20 +39,20 @@ class DeletableManagerMixin:
         """
         Mark as deleted and return.
         """
-        return self._session_setattr(item, 'deleted', True, flush=flush)
+        return self._session_setattr(item, "deleted", True, flush=flush)
 
     def undelete(self, item, flush=True, **kwargs):
         """
         Mark as not deleted and return.
         """
-        return self._session_setattr(item, 'deleted', False, flush=flush)
+        return self._session_setattr(item, "deleted", False, flush=flush)
 
 
 class DeletableSerializerMixin:
     serializable_keyset: Set[str]
 
     def add_serializers(self):
-        self.serializable_keyset.add('deleted')
+        self.serializable_keyset.add("deleted")
 
 
 # TODO: these are of questionable value if we don't want to enable users to delete/purge via update
@@ -56,7 +60,7 @@ class DeletableDeserializerMixin:
     deserializers: Dict[str, Deserializer]
 
     def add_deserializers(self):
-        self.deserializers['deleted'] = self.deserialize_deleted
+        self.deserializers["deleted"] = self.deserialize_deleted
 
     def deserialize_deleted(self, item, key, val, **context):
         """
@@ -77,9 +81,7 @@ class DeletableFiltersMixin:
     orm_filter_parsers: OrmFilterParsersType
 
     def _add_parsers(self):
-        self.orm_filter_parsers.update({
-            'deleted': {'op': ('eq'), 'val': parse_bool}
-        })
+        self.orm_filter_parsers.update({"deleted": {"op": ("eq"), "val": parse_bool}})
 
 
 class PurgableManagerMixin(DeletableManagerMixin):
@@ -99,7 +101,7 @@ class PurgableManagerMixin(DeletableManagerMixin):
         Override this in subclasses to do the additional resource removal.
         """
         self.delete(item, flush=False)
-        return self._session_setattr(item, 'purged', True, flush=flush)
+        return self._session_setattr(item, "purged", True, flush=flush)
 
 
 class PurgableSerializerMixin(DeletableSerializerMixin):
@@ -107,7 +109,7 @@ class PurgableSerializerMixin(DeletableSerializerMixin):
 
     def add_serializers(self):
         DeletableSerializerMixin.add_serializers(self)
-        self.serializable_keyset.add('purged')
+        self.serializable_keyset.add("purged")
 
 
 class PurgableDeserializerMixin(DeletableDeserializerMixin):
@@ -115,7 +117,7 @@ class PurgableDeserializerMixin(DeletableDeserializerMixin):
 
     def add_deserializers(self):
         DeletableDeserializerMixin.add_deserializers(self)
-        self.deserializers['purged'] = self.deserialize_purged
+        self.deserializers["purged"] = self.deserialize_purged
 
     def deserialize_purged(self, item, key, val, **context):
         """
@@ -131,9 +133,6 @@ class PurgableDeserializerMixin(DeletableDeserializerMixin):
 
 
 class PurgableFiltersMixin(DeletableFiltersMixin):
-
     def _add_parsers(self):
         DeletableFiltersMixin._add_parsers(self)
-        self.orm_filter_parsers.update({
-            'purged': {'op': ('eq'), 'val': parse_bool}
-        })
+        self.orm_filter_parsers.update({"purged": {"op": ("eq"), "val": parse_bool}})
diff --git a/lib/galaxy/managers/display_applications.py b/lib/galaxy/managers/display_applications.py
index de88e8b9a9d..ec8572e8238 100644
--- a/lib/galaxy/managers/display_applications.py
+++ b/lib/galaxy/managers/display_applications.py
@@ -1,6 +1,7 @@
 import logging
 from typing import (
-    Any, Dict,
+    Any,
+    Dict,
     List,
 )
 
@@ -29,13 +30,15 @@ class DisplayApplicationsManager:
         """
         rval = []
         for display_app in self.datatypes_registry.display_applications.values():
-            rval.append({
-                'id': display_app.id,
-                'name': display_app.name,
-                'version': display_app.version,
-                'filename_': display_app._filename,
-                'links': [{'name': link.name} for link in display_app.links.values()]
-            })
+            rval.append(
+                {
+                    "id": display_app.id,
+                    "name": display_app.name,
+                    "version": display_app.version,
+                    "filename_": display_app._filename,
+                    "links": [{"name": link.name} for link in display_app.links.values()],
+                }
+            )
         return rval
 
     def reload(self, ids: List[str]) -> Dict[str, Any]:
@@ -46,17 +49,21 @@ class DisplayApplicationsManager:
         :type   ids:  list
         """
         self._app.queue_worker.send_control_task(
-            'reload_display_application',
-            noop_self=True,
-            kwargs={'display_application_ids': ids}
+            "reload_display_application", noop_self=True, kwargs={"display_application_ids": ids}
         )
         reloaded, failed = self.datatypes_registry.reload_display_applications(ids)
         if not reloaded and failed:
-            message = 'Unable to reload any of the %i requested display applications ("%s").' % (len(failed), '", "'.join(failed))
+            message = 'Unable to reload any of the %i requested display applications ("%s").' % (
+                len(failed),
+                '", "'.join(failed),
+            )
         elif failed:
-            message = 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").' % (len(reloaded), '", "'.join(reloaded), len(failed), '", "'.join(failed))
+            message = (
+                'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").'
+                % (len(reloaded), '", "'.join(reloaded), len(failed), '", "'.join(failed))
+            )
         elif not reloaded:
-            message = 'You need to request at least one display application to reload.'
+            message = "You need to request at least one display application to reload."
         else:
             message = 'Reloaded %i requested display applications ("%s").' % (len(reloaded), '", "'.join(reloaded))
-        return {'message': message, 'reloaded': reloaded, 'failed': failed}
+        return {"message": message, "reloaded": reloaded, "failed": failed}
diff --git a/lib/galaxy/managers/executables.py b/lib/galaxy/managers/executables.py
index 776f7299367..8fb95eacdaf 100644
--- a/lib/galaxy/managers/executables.py
+++ b/lib/galaxy/managers/executables.py
@@ -34,6 +34,4 @@ def artifact_class(trans, as_dict):
     return artifact_class, as_dict, object_id
 
 
-__all__ = (
-    'artifact_class',
-)
+__all__ = ("artifact_class",)
diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py
index 3dda0f85bca..4fe5daea419 100644
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -5,7 +5,7 @@ import logging
 
 from sqlalchemy.orm.exc import (
     MultipleResultsFound,
-    NoResultFound
+    NoResultFound,
 )
 
 from galaxy import util
@@ -45,11 +45,15 @@ class FolderManager:
         :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
         """
         try:
-            folder = trans.sa_session.query(trans.app.model.LibraryFolder).filter(trans.app.model.LibraryFolder.table.c.id == decoded_folder_id).one()
+            folder = (
+                trans.sa_session.query(trans.app.model.LibraryFolder)
+                .filter(trans.app.model.LibraryFolder.table.c.id == decoded_folder_id)
+                .one()
+            )
         except MultipleResultsFound:
-            raise InconsistentDatabase('Multiple folders found with the same id.')
+            raise InconsistentDatabase("Multiple folders found with the same id.")
         except NoResultFound:
-            raise RequestParameterInvalidException('No folder found with the id provided.')
+            raise RequestParameterInvalidException("No folder found with the id provided.")
         except Exception as e:
             raise InternalServerError(f"Error loading from the database.{util.unicodify(e)}")
         folder = self.secure(trans, folder, check_manageable, check_accessible)
@@ -88,10 +92,10 @@ class FolderManager:
         :raises: AuthenticationRequired, InsufficientPermissionsException
         """
         if not trans.user:
-            raise AuthenticationRequired("Must be logged in to manage Galaxy items.", type='error')
+            raise AuthenticationRequired("Must be logged in to manage Galaxy items.", type="error")
         current_user_roles = trans.get_current_user_roles()
         if not trans.app.security_agent.can_modify_library_item(current_user_roles, folder):
-            raise InsufficientPermissionsException("You don't have permissions to modify this folder.", type='error')
+            raise InsufficientPermissionsException("You don't have permissions to modify this folder.", type="error")
         else:
             return folder
 
@@ -105,10 +109,10 @@ class FolderManager:
         :raises: AuthenticationRequired, InsufficientPermissionsException
         """
         if not trans.user:
-            raise AuthenticationRequired("Must be logged in to manage Galaxy items.", type='error')
+            raise AuthenticationRequired("Must be logged in to manage Galaxy items.", type="error")
         current_user_roles = trans.get_current_user_roles()
         if not trans.app.security_agent.can_manage_library_item(current_user_roles, folder):
-            raise InsufficientPermissionsException("You don't have permissions to manage this folder.", type='error')
+            raise InsufficientPermissionsException("You don't have permissions to manage this folder.", type="error")
         else:
             return folder
 
@@ -130,15 +134,15 @@ class FolderManager:
         :rtype:     dictionary
 
         """
-        folder_dict = folder.to_dict(view='element')
+        folder_dict = folder.to_dict(view="element")
         folder_dict = trans.security.encode_all_ids(folder_dict, True)
-        folder_dict['id'] = f"F{folder_dict['id']}"
-        if folder_dict['parent_id'] is not None:
-            folder_dict['parent_id'] = f"F{folder_dict['parent_id']}"
-        folder_dict['update_time'] = folder.update_time
+        folder_dict["id"] = f"F{folder_dict['id']}"
+        if folder_dict["parent_id"] is not None:
+            folder_dict["parent_id"] = f"F{folder_dict['parent_id']}"
+        folder_dict["update_time"] = folder.update_time
         return folder_dict
 
-    def create(self, trans, parent_folder_id, new_folder_name, new_folder_description=''):
+    def create(self, trans, parent_folder_id, new_folder_name, new_folder_description=""):
         """
         Create a new folder under the given folder.
 
@@ -156,8 +160,12 @@ class FolderManager:
         """
         parent_folder = self.get(trans, parent_folder_id)
         current_user_roles = trans.get_current_user_roles()
-        if not (trans.user_is_admin or trans.app.security_agent.can_add_library_item(current_user_roles, parent_folder)):
-            raise InsufficientPermissionsException('You do not have proper permission to create folders under given folder.')
+        if not (
+            trans.user_is_admin or trans.app.security_agent.can_add_library_item(current_user_roles, parent_folder)
+        ):
+            raise InsufficientPermissionsException(
+                "You do not have proper permission to create folders under given folder."
+            )
         new_folder = trans.app.model.LibraryFolder(name=new_folder_name, description=new_folder_description)
         # We are associating the last used genome build with folders, so we will always
         # initialize a new folder with the first dbkey in genome builds list which is currently
@@ -238,16 +246,34 @@ class FolderManager:
         :rtype:     dictionary
         """
         # Omit duplicated roles by converting to set
-        modify_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY))
-        manage_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE))
-        add_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD))
+        modify_roles = set(
+            trans.app.security_agent.get_roles_for_action(
+                folder, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY
+            )
+        )
+        manage_roles = set(
+            trans.app.security_agent.get_roles_for_action(
+                folder, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE
+            )
+        )
+        add_roles = set(
+            trans.app.security_agent.get_roles_for_action(
+                folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD
+            )
+        )
 
-        modify_folder_role_list = [(modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles]
-        manage_folder_role_list = [(manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles]
+        modify_folder_role_list = [
+            (modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles
+        ]
+        manage_folder_role_list = [
+            (manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles
+        ]
         add_library_item_role_list = [(add_role.name, trans.security.encode_id(add_role.id)) for add_role in add_roles]
-        return dict(modify_folder_role_list=modify_folder_role_list,
-                    manage_folder_role_list=manage_folder_role_list,
-                    add_library_item_role_list=add_library_item_role_list)
+        return dict(
+            modify_folder_role_list=modify_folder_role_list,
+            manage_folder_role_list=manage_folder_role_list,
+            add_library_item_role_list=add_library_item_role_list,
+        )
 
     def can_add_item(self, trans, folder):
         """
@@ -256,7 +282,11 @@ class FolderManager:
         if trans.user_is_admin:
             return True
         current_user_roles = trans.get_current_user_roles()
-        add_roles = set(trans.app.security_agent.get_roles_for_action(folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD))
+        add_roles = set(
+            trans.app.security_agent.get_roles_for_action(
+                folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD
+            )
+        )
         for role in current_user_roles:
             if role in add_roles:
                 return True
@@ -274,10 +304,10 @@ class FolderManager:
 
         :raises: MalformedId
         """
-        if ((len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith('F')):
+        if (len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith("F"):
             cut_id = encoded_folder_id[1:]
         else:
-            raise MalformedId(f'Malformed folder id ( {str(encoded_folder_id)} ) specified, unable to decode.')
+            raise MalformedId(f"Malformed folder id ( {str(encoded_folder_id)} ) specified, unable to decode.")
         return cut_id
 
     def decode_folder_id(self, trans, encoded_folder_id):
diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
index 9ea0f3a565e..47cde121746 100644
--- a/lib/galaxy/managers/genomes.py
+++ b/lib/galaxy/managers/genomes.py
@@ -13,7 +13,6 @@ from galaxy.structured_app import StructuredApp
 
 
 class GenomesManager:
-
     def __init__(self, app: StructuredApp):
         self._app = app
         self.genomes = app.genomes
@@ -22,36 +21,22 @@ class GenomesManager:
         return self.genomes.get_dbkeys(user, chrom_info)
 
     def get_genome(
-        self,
-        trans: ProvidesUserContext,
-        id: str,
-        num: int,
-        chrom: str,
-        low: int,
-        high: int,
-        reference: bool
+        self, trans: ProvidesUserContext, id: str, num: int, chrom: str, low: int, high: int, reference: bool
     ) -> Any:
         if reference:
             region = self.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
-            return {'dataset_type': 'refseq', 'data': region.sequence}
+            return {"dataset_type": "refseq", "data": region.sequence}
         else:
             return self.genomes.chroms(trans, dbkey=id, num=num, chrom=chrom, low=low)
 
-    def get_sequence(
-        self,
-        trans: ProvidesUserContext,
-        id: str,
-        chrom: str,
-        low: int,
-        high: int
-    ) -> Any:
+    def get_sequence(self, trans: ProvidesUserContext, id: str, chrom: str, low: int, high: int) -> Any:
         region = self.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
         return region.sequence
 
     def get_indexes(self, id: str, index_type: str) -> Any:
-        index_extensions = {'fasta_indexes': '.fai'}
+        index_extensions = {"fasta_indexes": ".fai"}
         if index_type not in index_extensions:
-            raise RequestParameterInvalidException(f'Invalid index type: {index_type}')
+            raise RequestParameterInvalidException(f"Invalid index type: {index_type}")
 
         tbl_entries = self._app.tool_data_tables.data_tables[index_type].data
         ext = index_extensions[index_type]
@@ -60,15 +45,15 @@ class GenomesManager:
             with open(index_filename) as f:
                 return f.read()
         except OSError:
-            raise ReferenceDataError(f'Failed to load index file for {id}')
+            raise ReferenceDataError(f"Failed to load index file for {id}")
 
     def _get_index_filename(self, id, tbl_entries, ext, index_type):
         try:
             paths = [x[-1] for x in tbl_entries if id in x]
             file_name = paths.pop()
         except TypeError:
-            raise ReferenceDataError(f'Data tables not found for {index_type}')
+            raise ReferenceDataError(f"Data tables not found for {index_type}")
         except IndexError:
-            raise ReferenceDataError(f'Data tables not found for {index_type} for {id}')
+            raise ReferenceDataError(f"Data tables not found for {index_type} for {id}")
         else:
             return f"{file_name}{ext}"
diff --git a/lib/galaxy/managers/group_roles.py b/lib/galaxy/managers/group_roles.py
index 2a149dd7df9..728c2bdc0d9 100644
--- a/lib/galaxy/managers/group_roles.py
+++ b/lib/galaxy/managers/group_roles.py
@@ -6,9 +6,7 @@ from typing import (
 
 from galaxy import model
 from galaxy.app import MinimalManagerApp
-from galaxy.exceptions import (
-    ObjectNotFound,
-)
+from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.base import decode_id
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.schema.fields import EncodedDatabaseIdField
@@ -80,11 +78,14 @@ class GroupRolesManager:
             raise ObjectNotFound(f"Role with id {encoded_role_id} was not found.")
         return role
 
-    def _get_group_role(self, trans: ProvidesAppContext, group: model.Group, role: model.Role) -> Optional[model.GroupRoleAssociation]:
-        return trans.sa_session.query(model.GroupRoleAssociation).filter(
-            model.GroupRoleAssociation.group == group,
-            model.GroupRoleAssociation.role == role
-        ).one_or_none()
+    def _get_group_role(
+        self, trans: ProvidesAppContext, group: model.Group, role: model.Role
+    ) -> Optional[model.GroupRoleAssociation]:
+        return (
+            trans.sa_session.query(model.GroupRoleAssociation)
+            .filter(model.GroupRoleAssociation.group == group, model.GroupRoleAssociation.role == role)
+            .one_or_none()
+        )
 
     def _add_role_to_group(self, trans: ProvidesAppContext, group: model.Group, role: model.Role):
         gra = model.GroupRoleAssociation(group, role)
diff --git a/lib/galaxy/managers/group_users.py b/lib/galaxy/managers/group_users.py
index 1bbef7ec4a2..5cc6438f08d 100644
--- a/lib/galaxy/managers/group_users.py
+++ b/lib/galaxy/managers/group_users.py
@@ -8,9 +8,7 @@ from typing import (
 
 from galaxy import model
 from galaxy.app import MinimalManagerApp
-from galaxy.exceptions import (
-    ObjectNotFound,
-)
+from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.base import decode_id
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.schema.fields import EncodedDatabaseIdField
@@ -36,7 +34,9 @@ class GroupUsersManager:
             rval.append(group_user)
         return rval
 
-    def show(self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField) -> Dict[str, Any]:
+    def show(
+        self, trans: ProvidesAppContext, id: EncodedDatabaseIdField, group_id: EncodedDatabaseIdField
+    ) -> Dict[str, Any]:
         """
         Returns information about a group user.
         """
@@ -89,11 +89,14 @@ class GroupUsersManager:
             raise ObjectNotFound(f"User with id {encoded_user_id} was not found.")
         return user
 
-    def _get_group_user(self, trans: ProvidesAppContext, group: model.Group, user: model.User) -> Optional[model.UserGroupAssociation]:
-        return trans.sa_session.query(model.UserGroupAssociation).filter(
-            model.UserGroupAssociation.user == user,
-            model.UserGroupAssociation.group == group
-        ).one_or_none()
+    def _get_group_user(
+        self, trans: ProvidesAppContext, group: model.Group, user: model.User
+    ) -> Optional[model.UserGroupAssociation]:
+        return (
+            trans.sa_session.query(model.UserGroupAssociation)
+            .filter(model.UserGroupAssociation.user == user, model.UserGroupAssociation.group == group)
+            .one_or_none()
+        )
 
     def _add_user_to_group(self, trans: ProvidesAppContext, group: model.Group, user: model.User):
         gra = model.UserGroupAssociation(user, group)
@@ -109,5 +112,5 @@ class GroupUsersManager:
         return {
             "id": encoded_user_id,
             "email": user.email,
-            "url": url_for('group_user', group_id=encoded_group_id, id=encoded_user_id)
+            "url": url_for("group_user", group_id=encoded_group_id, id=encoded_user_id),
         }
diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index d1d47468251..b401158ffde 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -31,9 +31,9 @@ class GroupsManager:
         """
         rval = []
         for group in trans.sa_session.query(model.Group).filter(model.Group.deleted == false()):
-            item = group.to_dict(value_mapper={'id': trans.security.encode_id})
+            item = group.to_dict(value_mapper={"id": trans.security.encode_id})
             encoded_id = trans.security.encode_id(group.id)
-            item['url'] = url_for('group', id=encoded_id)
+            item["url"] = url_for("group", id=encoded_id)
             rval.append(item)
         return rval
 
@@ -41,23 +41,23 @@ class GroupsManager:
         """
         Creates a new group.
         """
-        name = payload.get('name', None)
+        name = payload.get("name", None)
         if name is None:
             raise ObjectAttributeMissingException("Missing required name")
         self._check_duplicated_group_name(trans, name)
 
         group = model.Group(name=name)
         trans.sa_session.add(group)
-        encoded_user_ids = payload.get('user_ids', [])
+        encoded_user_ids = payload.get("user_ids", [])
         users = self._get_users_by_encoded_ids(trans, encoded_user_ids)
-        encoded_role_ids = payload.get('role_ids', [])
+        encoded_role_ids = payload.get("role_ids", [])
         roles = self._get_roles_by_encoded_ids(trans, encoded_role_ids)
         trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
         trans.sa_session.flush()
 
         encoded_id = trans.security.encode_id(group.id)
-        item = group.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
-        item['url'] = url_for('group', id=encoded_id)
+        item = group.to_dict(view="element", value_mapper={"id": trans.security.encode_id})
+        item["url"] = url_for("group", id=encoded_id)
         return [item]
 
     def show(self, trans: ProvidesAppContext, encoded_id: EncodedDatabaseIdField):
@@ -65,10 +65,10 @@ class GroupsManager:
         Displays information about a group.
         """
         group = self._get_group(trans, encoded_id)
-        item = group.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
-        item['url'] = url_for('group', id=encoded_id)
-        item['users_url'] = url_for('group_users', group_id=encoded_id)
-        item['roles_url'] = url_for('group_roles', group_id=encoded_id)
+        item = group.to_dict(view="element", value_mapper={"id": trans.security.encode_id})
+        item["url"] = url_for("group", id=encoded_id)
+        item["users_url"] = url_for("group_users", group_id=encoded_id)
+        item["roles_url"] = url_for("group_roles", group_id=encoded_id)
         return item
 
     def update(self, trans: ProvidesAppContext, encoded_id: EncodedDatabaseIdField, payload: Dict[str, Any]):
@@ -76,16 +76,18 @@ class GroupsManager:
         Modifies a group.
         """
         group = self._get_group(trans, encoded_id)
-        name = payload.get('name', None)
+        name = payload.get("name", None)
         if name:
             self._check_duplicated_group_name(trans, name)
             group.name = name
             trans.sa_session.add(group)
-        encoded_user_ids = payload.get('user_ids', [])
+        encoded_user_ids = payload.get("user_ids", [])
         users = self._get_users_by_encoded_ids(trans, encoded_user_ids)
-        encoded_role_ids = payload.get('role_ids', [])
+        encoded_role_ids = payload.get("role_ids", [])
         roles = self._get_roles_by_encoded_ids(trans, encoded_role_ids)
-        trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users, delete_existing_assocs=False)
+        trans.app.security_agent.set_entity_group_associations(
+            groups=[group], roles=roles, users=users, delete_existing_assocs=False
+        )
         trans.sa_session.flush()
 
     def _decode_id(self, encoded_id: EncodedDatabaseIdField) -> int:
@@ -105,12 +107,16 @@ class GroupsManager:
             raise ObjectNotFound(f"Group with id {encoded_id} was not found.")
         return group
 
-    def _get_users_by_encoded_ids(self, trans: ProvidesAppContext, encoded_user_ids: List[EncodedDatabaseIdField]) -> List[model.User]:
+    def _get_users_by_encoded_ids(
+        self, trans: ProvidesAppContext, encoded_user_ids: List[EncodedDatabaseIdField]
+    ) -> List[model.User]:
         decoded_user_ids = self._decode_ids(encoded_user_ids)
         users = trans.sa_session.query(model.User).filter(model.User.table.c.id.in_(decoded_user_ids)).all()
         return users
 
-    def _get_roles_by_encoded_ids(self, trans: ProvidesAppContext, encoded_role_ids: List[EncodedDatabaseIdField]) -> List[model.Role]:
+    def _get_roles_by_encoded_ids(
+        self, trans: ProvidesAppContext, encoded_role_ids: List[EncodedDatabaseIdField]
+    ) -> List[model.Role]:
         decoded_role_ids = self._decode_ids(encoded_role_ids)
         roles = trans.sa_session.query(model.Role).filter(model.Role.id.in_(decoded_role_ids)).all()
         return roles
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index fd59c1585a9..50f6ac76582 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -7,14 +7,18 @@ history.
 import gettext
 import logging
 import os
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 
 from sqlalchemy.orm.session import object_session
 
 from galaxy import (
     datatypes,
     exceptions,
-    model
+    model,
 )
 from galaxy.managers import (
     annotatable,
@@ -25,7 +29,10 @@ from galaxy.managers import (
     users,
 )
 from galaxy.model.tags import GalaxyTagHandler
-from galaxy.structured_app import MinimalManagerApp, StructuredApp
+from galaxy.structured_app import (
+    MinimalManagerApp,
+    StructuredApp,
+)
 
 log = logging.getLogger(__name__)
 
@@ -34,15 +41,18 @@ class HistoryDatasetAssociationNoHistoryException(Exception):
     pass
 
 
-class HDAManager(datasets.DatasetAssociationManager,
-                 secured.OwnableManagerMixin,
-                 taggable.TaggableManagerMixin,
-                 annotatable.AnnotatableManagerMixin):
+class HDAManager(
+    datasets.DatasetAssociationManager,
+    secured.OwnableManagerMixin,
+    taggable.TaggableManagerMixin,
+    annotatable.AnnotatableManagerMixin,
+):
     """
     Interface/service object for interacting with HDAs.
     """
+
     model_class = model.HistoryDatasetAssociation
-    foreign_key_name = 'history_dataset_association'
+    foreign_key_name = "history_dataset_association"
 
     tag_assoc = model.HistoryDatasetAssociationTagAssociation
     annotation_assoc = model.HistoryDatasetAssociationAnnotationAssociation
@@ -60,8 +70,7 @@ class HDAManager(datasets.DatasetAssociationManager,
         self.tag_handler = tag_handler
 
     def get_owned_ids(self, object_ids, history=None):
-        """Get owned IDs.
-        """
+        """Get owned IDs."""
         filters = [self.model_class.table.c.id.in_(object_ids), self.model_class.table.c.history_id == history.id]
         return self.list(filters=filters)
 
@@ -104,12 +113,13 @@ class HDAManager(datasets.DatasetAssociationManager,
         it will be automatically set.
         """
         if not dataset:
-            kwargs['create_dataset'] = True
-        hda = model.HistoryDatasetAssociation(history=history, dataset=dataset,
-                                              sa_session=self.app.model.context, **kwargs)
+            kwargs["create_dataset"] = True
+        hda = model.HistoryDatasetAssociation(
+            history=history, dataset=dataset, sa_session=self.app.model.context, **kwargs
+        )
 
         if history:
-            history.add_dataset(hda, set_hid=('hid' not in kwargs))
+            history.add_dataset(hda, set_hid=("hid" not in kwargs))
         # TODO:?? some internal sanity check here (or maybe in add_dataset) to make sure hids are not duped?
 
         self.session().add(hda)
@@ -121,7 +131,7 @@ class HDAManager(datasets.DatasetAssociationManager,
         """
         Copy hda, including annotation and tags, add to history and return the given HDA.
         """
-        copy = hda.copy(parent_id=kwargs.get('parent_id'), copy_hid=False, copy_tags=hda.tags, flush=flush)
+        copy = hda.copy(parent_id=kwargs.get("parent_id"), copy_hid=False, copy_tags=hda.tags, flush=flush)
         if hide_copy:
             copy.visible = False
         if history:
@@ -148,6 +158,7 @@ class HDAManager(datasets.DatasetAssociationManager,
     def purge(self, hda, flush=True):
         if self.app.config.enable_celery_tasks:
             from galaxy.celery.tasks import purge_hda
+
             purge_hda.delay(hda_id=hda.id)
         else:
             self._purge(hda, flush=flush)
@@ -180,8 +191,7 @@ class HDAManager(datasets.DatasetAssociationManager,
         Return True if the hda's job was resubmitted at any point.
         """
         job_states = model.Job.states
-        query = (self._job_state_history_query(hda)
-                 .filter(model.JobStateHistory.state == job_states.RESUBMITTED))
+        query = self._job_state_history_query(hda).filter(model.JobStateHistory.state == job_states.RESUBMITTED)
         return self.app.model.context.query(query.exists()).scalar()
 
     def _job_state_history_query(self, hda):
@@ -195,10 +205,12 @@ class HDAManager(datasets.DatasetAssociationManager,
         # TODO: this does not play well with copied hdas
         # NOTE: don't eagerload (JODA will load the hda were using!)
         hda_id = hda.id
-        query = (session.query(JobToOutputDatasetAssociation, JobStateHistory)
-                 .filter(JobToOutputDatasetAssociation.dataset_id == hda_id)
-                 .filter(JobStateHistory.job_id == JobToOutputDatasetAssociation.job_id)
-                 .enable_eagerloads(False))
+        query = (
+            session.query(JobToOutputDatasetAssociation, JobStateHistory)
+            .filter(JobToOutputDatasetAssociation.dataset_id == hda_id)
+            .filter(JobStateHistory.job_id == JobToOutputDatasetAssociation.job_id)
+            .enable_eagerloads(False)
+        )
         return query
 
     def data_conversion_status(self, hda):
@@ -244,8 +256,9 @@ class HDAManager(datasets.DatasetAssociationManager,
         # The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles.  We
         # need to ensure that they did not associate roles that would cause accessibility problems.
         security_agent = trans.app.security_agent
-        permissions, in_roles, error, message = \
-            security_agent.derive_roles_from_access(trans, hda.dataset.id, 'root', **role_ids_dict)
+        permissions, in_roles, error, message = security_agent.derive_roles_from_access(
+            trans, hda.dataset.id, "root", **role_ids_dict
+        )
         if error:
             # Keep the original role associations for the DATASET_ACCESS permission on the dataset.
             access_action = security_agent.get_action(security_agent.permitted_actions.DATASET_ACCESS.action)
@@ -260,9 +273,10 @@ class HDAManager(datasets.DatasetAssociationManager,
 
 
 class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerializer,
-        datasets.DatasetAssociationSerializer[HDAManager],
-        taggable.TaggableSerializerMixin,
-        annotatable.AnnotatableSerializerMixin):
+    datasets.DatasetAssociationSerializer[HDAManager],
+    taggable.TaggableSerializerMixin,
+    annotatable.AnnotatableSerializerMixin,
+):
     model_manager_class = HDAManager
     app: StructuredApp
 
@@ -270,125 +284,139 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         super().__init__(app)
         self.hda_manager = self.manager
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'type_id',
-            'name',
-            'history_id',
-            'hid',
-            'history_content_type',
-            'dataset_id',
-            'state',
-            'extension',
-            'deleted', 'purged', 'visible',
-            'tags',
-            'type',
-            'url',
-            'create_time',
-            'update_time',
-        ])
-        self.add_view('detailed', [
-            'model_class',
-            'history_id', 'hid',
-            # why include if model_class is there?
-            'hda_ldda',
-            'copied_from_ldda_id',
-            # TODO: accessible needs to go away
-            'accessible',
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "type_id",
+                "name",
+                "history_id",
+                "hid",
+                "history_content_type",
+                "dataset_id",
+                "state",
+                "extension",
+                "deleted",
+                "purged",
+                "visible",
+                "tags",
+                "type",
+                "url",
+                "create_time",
+                "update_time",
+            ],
+        )
+        self.add_view(
+            "detailed",
+            [
+                "model_class",
+                "history_id",
+                "hid",
+                # why include if model_class is there?
+                "hda_ldda",
+                "copied_from_ldda_id",
+                # TODO: accessible needs to go away
+                "accessible",
+                # remapped
+                "genome_build",
+                "misc_info",
+                "misc_blurb",
+                "file_ext",
+                "file_size",
+                "resubmitted",
+                "metadata",
+                "meta_files",
+                "data_type",
+                "peek",
+                "creating_job",
+                "rerunnable",
+                "uuid",
+                "permissions",
+                "file_name",
+                "display_apps",
+                "display_types",
+                "visualizations",
+                "validated_state",
+                "validated_state_message",
+                # 'url',
+                "download_url",
+                "annotation",
+                "api_type",
+                "created_from_basename",
+                "hashes",
+                "sources",
+            ],
+            include_keys_from="summary",
+        )
 
-            # remapped
-            'genome_build', 'misc_info', 'misc_blurb',
-            'file_ext', 'file_size',
-
-            'resubmitted',
-            'metadata', 'meta_files', 'data_type',
-            'peek',
-
-            'creating_job',
-            'rerunnable',
-
-            'uuid',
-            'permissions',
-            'file_name',
-
-            'display_apps',
-            'display_types',
-            'visualizations',
-
-            'validated_state',
-            'validated_state_message',
-
-            # 'url',
-            'download_url',
-
-            'annotation',
-
-            'api_type',
-            'created_from_basename',
-            'hashes',
-            'sources',
-        ], include_keys_from='summary')
-
-        self.add_view('extended', [
-            'tool_version', 'parent_id', 'designation',
-        ], include_keys_from='detailed')
+        self.add_view(
+            "extended",
+            [
+                "tool_version",
+                "parent_id",
+                "designation",
+            ],
+            include_keys_from="detailed",
+        )
 
         # keyset returned to create show a dataset where the owner has no access
-        self.add_view('inaccessible', [
-            'accessible',
-            'id', 'name', 'history_id', 'hid', 'history_content_type',
-            'state', 'deleted', 'visible'
-        ])
+        self.add_view(
+            "inaccessible",
+            ["accessible", "id", "name", "history_id", "hid", "history_content_type", "state", "deleted", "visible"],
+        )
 
         # fields for new beta web client, there is no summary/detailed split any more
-        self.add_view('betawebclient', [
-            # common to hdca
-            'create_time',
-            'deleted',
-            'hid',
-            'history_content_type',
-            'history_id',
-            'id',
-            'name',
-            'tags',
-            'type',
-            'type_id',
-            'update_time',
-            'url',
-            'visible',
-            # dataset only
-            'accessible',
-            'api_type',
-            'annotation',
-            'created_from_basename',
-            'creating_job',
-            'dataset_id',
-            'data_type',
-            'display_apps',
-            'display_types',
-            'download_url',
-            'extension',
-            'file_ext',
-            'file_name',
-            'file_size',
-            'genome_build',
-            'hda_ldda',
-            'meta_files',
-            'misc_blurb',
-            'misc_info',
-            'model_class',
-            'peek',
-            'purged',
-            'rerunnable',
-            'resubmitted',
-            'state',
-            'uuid',
-            'validated_state',
-            'validated_state_message',
-            'hashes',
-            'sources',
-        ])
+        self.add_view(
+            "betawebclient",
+            [
+                # common to hdca
+                "create_time",
+                "deleted",
+                "hid",
+                "history_content_type",
+                "history_id",
+                "id",
+                "name",
+                "tags",
+                "type",
+                "type_id",
+                "update_time",
+                "url",
+                "visible",
+                # dataset only
+                "accessible",
+                "api_type",
+                "annotation",
+                "created_from_basename",
+                "creating_job",
+                "dataset_id",
+                "data_type",
+                "display_apps",
+                "display_types",
+                "download_url",
+                "extension",
+                "file_ext",
+                "file_name",
+                "file_size",
+                "genome_build",
+                "hda_ldda",
+                "meta_files",
+                "misc_blurb",
+                "misc_info",
+                "model_class",
+                "peek",
+                "purged",
+                "rerunnable",
+                "resubmitted",
+                "state",
+                "uuid",
+                "validated_state",
+                "validated_state_message",
+                "hashes",
+                "sources",
+            ],
+        )
 
     def serialize_copied_from_ldda_id(self, item, key, **context):
         """
@@ -404,44 +432,45 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
 
         serializers: Dict[str, base.Serializer] = {
-            'model_class': lambda item, key, **context: 'HistoryDatasetAssociation',
-            'history_content_type': lambda item, key, **context: 'dataset',
-            'hda_ldda': lambda item, key, **context: 'hda',
-            'type_id': self.serialize_type_id,
-            'copied_from_ldda_id': self.serialize_copied_from_ldda_id,
-            'history_id': self.serialize_id,
-
+            "model_class": lambda item, key, **context: "HistoryDatasetAssociation",
+            "history_content_type": lambda item, key, **context: "dataset",
+            "hda_ldda": lambda item, key, **context: "hda",
+            "type_id": self.serialize_type_id,
+            "copied_from_ldda_id": self.serialize_copied_from_ldda_id,
+            "history_id": self.serialize_id,
             # remapped
-            'misc_info': self._remap_from('info'),
-            'misc_blurb': self._remap_from('blurb'),
-            'file_ext': self._remap_from('extension'),
-            'file_path': self._remap_from('file_name'),
-            'resubmitted': lambda item, key, **context: self.hda_manager.has_been_resubmitted(item),
-            'display_apps': self.serialize_display_apps,
-            'display_types': self.serialize_old_display_applications,
-            'visualizations': self.serialize_visualization_links,
-
+            "misc_info": self._remap_from("info"),
+            "misc_blurb": self._remap_from("blurb"),
+            "file_ext": self._remap_from("extension"),
+            "file_path": self._remap_from("file_name"),
+            "resubmitted": lambda item, key, **context: self.hda_manager.has_been_resubmitted(item),
+            "display_apps": self.serialize_display_apps,
+            "display_types": self.serialize_old_display_applications,
+            "visualizations": self.serialize_visualization_links,
             # 'url'   : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ),
             # TODO: this intermittently causes a routes.GenerationException - temp use the legacy route to prevent this
             #   see also: https://trello.com/c/5d6j4X5y
             #   see also: https://sentry.galaxyproject.org/galaxy/galaxy-main/group/20769/events/9352883/
-            'url': lambda item, key, **context: self.url_for('history_content',
-                                                             history_id=self.app.security.encode_id(item.history_id),
-                                                             id=self.app.security.encode_id(item.id)),
-            'urls': self.serialize_urls,
-
+            "url": lambda item, key, **context: self.url_for(
+                "history_content",
+                history_id=self.app.security.encode_id(item.history_id),
+                id=self.app.security.encode_id(item.id),
+            ),
+            "urls": self.serialize_urls,
             # TODO: backwards compat: need to go away
-            'download_url': lambda item, key, **context: self.url_for('history_contents_display',
-                                                                      history_id=self.app.security.encode_id(item.history.id),
-                                                                      history_content_id=self.app.security.encode_id(item.id)),
-            'parent_id': self.serialize_id,
+            "download_url": lambda item, key, **context: self.url_for(
+                "history_contents_display",
+                history_id=self.app.security.encode_id(item.history.id),
+                history_content_id=self.app.security.encode_id(item.id),
+            ),
+            "parent_id": self.serialize_id,
             # TODO: to DatasetAssociationSerializer
-            'accessible': lambda item, key, user=None, **c: self.manager.is_accessible(item, user, **c),
-            'api_type': lambda item, key, **context: 'file',
-            'type': lambda item, key, **context: 'file',
-            'created_from_basename': lambda item, key, **context: item.created_from_basename,
-            'hashes': lambda item, key, **context: [h.to_dict() for h in item.hashes],
-            'sources': lambda item, key, **context: [s.to_dict() for s in item.sources],
+            "accessible": lambda item, key, user=None, **c: self.manager.is_accessible(item, user, **c),
+            "api_type": lambda item, key, **context: "file",
+            "type": lambda item, key, **context: "file",
+            "created_from_basename": lambda item, key, **context: item.created_from_basename,
+            "hashes": lambda item, key, **context: [h.to_dict() for h in item.hashes],
+            "sources": lambda item, key, **context: [s.to_dict() for s in item.sources],
         }
         self.serializers.update(serializers)
 
@@ -451,7 +480,7 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         """
         # TODO: to DatasetAssociationSerializer
         if not self.manager.is_accessible(hda, user, **context):
-            keys = self._view_to_keys('inaccessible')
+            keys = self._view_to_keys("inaccessible")
         return super().serialize(hda, keys, user=user, **context)
 
     def serialize_display_apps(self, item, key, trans=None, **context):
@@ -464,11 +493,13 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
 
             app_links = []
             for link_app in display_app.links.values():
-                app_links.append({
-                    'target': link_app.url.get('target_frame', '_blank'),
-                    'href': link_app.get_display_url(hda, trans),
-                    'text': gettext.gettext(link_app.name)
-                })
+                app_links.append(
+                    {
+                        "target": link_app.url.get("target_frame", "_blank"),
+                        "href": link_app.get_display_url(hda, trans),
+                        "text": gettext.gettext(link_app.name),
+                    }
+                )
             if app_links:
                 display_apps.append(dict(label=display_app.name, links=app_links))
 
@@ -492,11 +523,9 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
 
                 app_links = []
                 for display_name, display_link in display_links:
-                    app_links.append({
-                        'target': target_frame,
-                        'href': display_link,
-                        'text': gettext.gettext(display_name)
-                    })
+                    app_links.append(
+                        {"target": target_frame, "href": display_link, "text": gettext.gettext(display_name)}
+                    )
                 if app_links:
                     display_apps.append(dict(label=display_label, links=app_links))
 
@@ -521,28 +550,32 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         url_for = self.url_for
         encoded_id = self.app.security.encode_id(hda.id)
         urls = {
-            'purge': url_for(controller='dataset', action='purge_async', dataset_id=encoded_id),
-            'display': url_for(controller='dataset', action='display', dataset_id=encoded_id, preview=True),
-            'edit': url_for(controller='dataset', action='edit', dataset_id=encoded_id),
-            'download': url_for(controller='dataset', action='display',
-                                dataset_id=encoded_id, to_ext=hda.extension),
-            'report_error': url_for(controller='dataset', action='errors', id=encoded_id),
-            'rerun': url_for(controller='tool_runner', action='rerun', id=encoded_id),
-            'show_params': url_for(controller='dataset', action='details', dataset_id=encoded_id),
-            'visualization': url_for(controller='visualization', action='index',
-                                     id=encoded_id, model='HistoryDatasetAssociation'),
-            'meta_download': url_for(controller='dataset', action='get_metadata_file',
-                                     hda_id=encoded_id, metadata_name=''),
+            "purge": url_for(controller="dataset", action="purge_async", dataset_id=encoded_id),
+            "display": url_for(controller="dataset", action="display", dataset_id=encoded_id, preview=True),
+            "edit": url_for(controller="dataset", action="edit", dataset_id=encoded_id),
+            "download": url_for(controller="dataset", action="display", dataset_id=encoded_id, to_ext=hda.extension),
+            "report_error": url_for(controller="dataset", action="errors", id=encoded_id),
+            "rerun": url_for(controller="tool_runner", action="rerun", id=encoded_id),
+            "show_params": url_for(controller="dataset", action="details", dataset_id=encoded_id),
+            "visualization": url_for(
+                controller="visualization", action="index", id=encoded_id, model="HistoryDatasetAssociation"
+            ),
+            "meta_download": url_for(
+                controller="dataset", action="get_metadata_file", hda_id=encoded_id, metadata_name=""
+            ),
         }
         return urls
 
 
-class HDADeserializer(datasets.DatasetAssociationDeserializer,
-                      taggable.TaggableDeserializerMixin,
-                      annotatable.AnnotatableDeserializerMixin):
+class HDADeserializer(
+    datasets.DatasetAssociationDeserializer,
+    taggable.TaggableDeserializerMixin,
+    annotatable.AnnotatableDeserializerMixin,
+):
     """
     Interface/service object for validating and deserializing dictionaries into histories.
     """
+
     model_manager_class = HDAManager
 
     def __init__(self, app: MinimalManagerApp):
@@ -555,19 +588,22 @@ class HDADeserializer(datasets.DatasetAssociationDeserializer,
         taggable.TaggableDeserializerMixin.add_deserializers(self)
         annotatable.AnnotatableDeserializerMixin.add_deserializers(self)
 
-        self.deserializers.update({
-            'visible': self.deserialize_bool,
-            # remapped
-            'genome_build': lambda item, key, val, **c: self.deserialize_genome_build(item, 'dbkey', val),
-            'misc_info': lambda item, key, val, **c: self.deserialize_basestring(item, 'info', val,
-                                                                                 convert_none_to_empty=True),
-        })
+        self.deserializers.update(
+            {
+                "visible": self.deserialize_bool,
+                # remapped
+                "genome_build": lambda item, key, val, **c: self.deserialize_genome_build(item, "dbkey", val),
+                "misc_info": lambda item, key, val, **c: self.deserialize_basestring(
+                    item, "info", val, convert_none_to_empty=True
+                ),
+            }
+        )
         self.deserializable_keyset.update(self.deserializers.keys())
 
 
-class HDAFilterParser(datasets.DatasetAssociationFilterParser,
-                      taggable.TaggableFilterMixin,
-                      annotatable.AnnotatableFilterMixin):
+class HDAFilterParser(
+    datasets.DatasetAssociationFilterParser, taggable.TaggableFilterMixin, annotatable.AnnotatableFilterMixin
+):
     model_manager_class = HDAManager
     model_class = model.HistoryDatasetAssociation
 
diff --git a/lib/galaxy/managers/hdcas.py b/lib/galaxy/managers/hdcas.py
index 9f6b4fe9b92..ec9b23d1649 100644
--- a/lib/galaxy/managers/hdcas.py
+++ b/lib/galaxy/managers/hdcas.py
@@ -14,14 +14,16 @@ from galaxy.managers import (
     deletable,
     hdas,
     secured,
-    taggable
+    taggable,
 )
 from galaxy.managers.collections_util import get_hda_and_element_identifiers
 from galaxy.model.tags import GalaxyTagHandler
-from galaxy.structured_app import MinimalManagerApp, StructuredApp
+from galaxy.structured_app import (
+    MinimalManagerApp,
+    StructuredApp,
+)
 from galaxy.util.zipstream import ZipstreamWrapper
 
-
 log = logging.getLogger(__name__)
 
 
@@ -48,17 +50,19 @@ def set_collection_attributes(dataset_element, *payload):
 
 # TODO: to DatasetCollectionInstanceManager
 class HDCAManager(
-        base.ModelManager,
-        secured.AccessibleManagerMixin,
-        secured.OwnableManagerMixin,
-        deletable.PurgableManagerMixin,
-        taggable.TaggableManagerMixin,
-        annotatable.AnnotatableManagerMixin):
+    base.ModelManager,
+    secured.AccessibleManagerMixin,
+    secured.OwnableManagerMixin,
+    deletable.PurgableManagerMixin,
+    taggable.TaggableManagerMixin,
+    annotatable.AnnotatableManagerMixin,
+):
     """
     Interface/service object for interacting with HDCAs.
     """
+
     model_class = model.HistoryDatasetCollectionAssociation
-    foreign_key_name = 'history_dataset_collection_association'
+    foreign_key_name = "history_dataset_collection_association"
 
     tag_assoc = model.HistoryDatasetCollectionTagAssociation
     annotation_assoc = model.HistoryDatasetCollectionAssociationAnnotationAssociation
@@ -79,10 +83,10 @@ class HDCAManager(
         """
         returned = []
         # lots of nesting going on within the nesting
-        collection = content.collection if hasattr(content, 'collection') else content
-        this_parents = (content, ) + parents
+        collection = content.collection if hasattr(content, "collection") else content
+        this_parents = (content,) + parents
         for element in collection.elements:
-            next_parents = (element, ) + this_parents
+            next_parents = (element,) + this_parents
             if element.is_collection:
                 processed_list = self.map_datasets(element.child_collection, fn, *next_parents)
                 returned.extend(processed_list)
@@ -108,28 +112,21 @@ class DCESerializer(base.ModelSerializer):
         self.hda_serializer = hdas.HDASerializer(app)
         self.dc_serializer = DCSerializer(app, dce_serializer=self)
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id', 'model_class',
-            'element_index',
-            'element_identifier',
-            'element_type',
-            'object'
-        ])
+        self.default_view = "summary"
+        self.add_view("summary", ["id", "model_class", "element_index", "element_identifier", "element_type", "object"])
 
     def add_serializers(self):
         super().add_serializers()
-        self.serializers.update({
-            'model_class': lambda *a, **c: 'DatasetCollectionElement',
-            'object': self.serialize_object
-        })
+        self.serializers.update(
+            {"model_class": lambda *a, **c: "DatasetCollectionElement", "object": self.serialize_object}
+        )
 
     def serialize_object(self, item, key, **context):
         if item.hda:
-            return self.hda_serializer.serialize_to_view(item.hda, view='summary', **context)
+            return self.hda_serializer.serialize_to_view(item.hda, view="summary", **context)
         if item.child_collection:
-            return self.dc_serializer.serialize_to_view(item.child_collection, view='detailed', **context)
-        return 'object'
+            return self.dc_serializer.serialize_to_view(item.child_collection, view="detailed", **context)
+        return "object"
 
 
 class DCSerializer(base.ModelSerializer):
@@ -141,32 +138,41 @@ class DCSerializer(base.ModelSerializer):
         super().__init__(app)
         self.dce_serializer = dce_serializer or DCESerializer(app)
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'create_time',
-            'update_time',
-            'collection_type',
-            'populated_state',
-            'populated_state_message',
-            'element_count',
-        ])
-        self.add_view('detailed', [
-            'populated',
-            'elements',
-        ], include_keys_from='summary')
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "create_time",
+                "update_time",
+                "collection_type",
+                "populated_state",
+                "populated_state_message",
+                "element_count",
+            ],
+        )
+        self.add_view(
+            "detailed",
+            [
+                "populated",
+                "elements",
+            ],
+            include_keys_from="summary",
+        )
 
     def add_serializers(self):
         super().add_serializers()
-        self.serializers.update({
-            'model_class': lambda *a, **c: 'DatasetCollection',
-            'elements': self.serialize_elements,
-        })
+        self.serializers.update(
+            {
+                "model_class": lambda *a, **c: "DatasetCollection",
+                "elements": self.serialize_elements,
+            }
+        )
 
     def serialize_elements(self, item, key, **context):
         returned = []
         for element in item.elements:
-            serialized = self.dce_serializer.serialize_to_view(element, view='summary', **context)
+            serialized = self.dce_serializer.serialize_to_view(element, view="summary", **context)
             returned.append(serialized)
         return returned
 
@@ -175,25 +181,34 @@ class DCASerializer(base.ModelSerializer):
     """
     Base (abstract) Serializer class for HDCAs and LDCAs.
     """
+
     app: StructuredApp
 
     def __init__(self, app: StructuredApp, dce_serializer=None):
         super().__init__(app)
         self.dce_serializer = dce_serializer or DCESerializer(app)
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'create_time', 'update_time',
-            'collection_type',
-            'populated_state',
-            'populated_state_message',
-            'element_count',
-        ])
-        self.add_view('detailed', [
-            'populated',
-            'elements',
-        ], include_keys_from='summary')
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "create_time",
+                "update_time",
+                "collection_type",
+                "populated_state",
+                "populated_state_message",
+                "element_count",
+            ],
+        )
+        self.add_view(
+            "detailed",
+            [
+                "populated",
+                "elements",
+            ],
+            include_keys_from="summary",
+        )
 
     def add_serializers(self):
         super().add_serializers()
@@ -201,14 +216,14 @@ class DCASerializer(base.ModelSerializer):
         self.dc_serializer = DCSerializer(self.app)
         # then set the serializers to point to it for those attrs
         collection_keys = [
-            'create_time',
-            'update_time',
-            'collection_type',
-            'populated',
-            'populated_state',
-            'populated_state_message',
-            'elements',
-            'element_count',
+            "create_time",
+            "update_time",
+            "collection_type",
+            "populated",
+            "populated_state",
+            "populated_state_message",
+            "elements",
+            "element_count",
         ]
         for key in collection_keys:
             self.serializers[key] = self._proxy_to_dataset_collection(key=key)
@@ -221,13 +236,10 @@ class DCASerializer(base.ModelSerializer):
             return lambda i, k, **c: self.dc_serializer.serialize(i.collection, [k], **c)[k]
         if serializer:
             return lambda i, k, **c: serializer(i.collection, key or k, **c)
-        raise TypeError('kwarg serializer or key needed')
+        raise TypeError("kwarg serializer or key needed")
 
 
-class HDCASerializer(
-        DCASerializer,
-        taggable.TaggableSerializerMixin,
-        annotatable.AnnotatableSerializerMixin):
+class HDCASerializer(DCASerializer, taggable.TaggableSerializerMixin, annotatable.AnnotatableSerializerMixin):
     """
     Serializer for HistoryDatasetCollectionAssociations.
     """
@@ -236,87 +248,92 @@ class HDCASerializer(
         super().__init__(app)
         self.hdca_manager = HDCAManager(app)
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'type_id',
-            'name',
-            'history_id', 'hid',
-            'history_content_type',
-
-            'collection_type',
-            'populated_state',
-            'populated_state_message',
-            'element_count',
-
-            'job_source_id',
-            'job_source_type',
-
-            'name',
-            'type_id',
-            'deleted',
-            # 'purged',
-            'visible',
-            'type', 'url',
-            'create_time', 'update_time',
-            'tags',  # TODO: detail view only (maybe),
-            'contents_url'
-        ])
-        self.add_view('detailed', [
-            'populated',
-            'elements'
-        ], include_keys_from='summary')
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "type_id",
+                "name",
+                "history_id",
+                "hid",
+                "history_content_type",
+                "collection_type",
+                "populated_state",
+                "populated_state_message",
+                "element_count",
+                "job_source_id",
+                "job_source_type",
+                "name",
+                "type_id",
+                "deleted",
+                # 'purged',
+                "visible",
+                "type",
+                "url",
+                "create_time",
+                "update_time",
+                "tags",  # TODO: detail view only (maybe),
+                "contents_url",
+            ],
+        )
+        self.add_view("detailed", ["populated", "elements"], include_keys_from="summary")
 
         # fields for new beta web client, there is no summary/detailed split any more
-        self.add_view('betawebclient', [
-            # common to hda
-            'create_time',
-            'deleted',
-            'hid',
-            'history_content_type',
-            'history_id',
-            'id',
-            'name',
-            'tags',
-            'type',
-            'type_id',
-            'update_time',
-            'url',
-            'visible',
-            # hdca only
-            'collection_id',
-            'collection_type',
-            'contents_url',
-            'element_count',
-            'job_source_id',
-            'job_source_type',
-            'job_state_summary',
-            'populated',
-            'populated_state',
-            'populated_state_message',
-            'elements_datatypes',
-        ])
+        self.add_view(
+            "betawebclient",
+            [
+                # common to hda
+                "create_time",
+                "deleted",
+                "hid",
+                "history_content_type",
+                "history_id",
+                "id",
+                "name",
+                "tags",
+                "type",
+                "type_id",
+                "update_time",
+                "url",
+                "visible",
+                # hdca only
+                "collection_id",
+                "collection_type",
+                "contents_url",
+                "element_count",
+                "job_source_id",
+                "job_source_type",
+                "job_state_summary",
+                "populated",
+                "populated_state",
+                "populated_state_message",
+                "elements_datatypes",
+            ],
+        )
 
     def add_serializers(self):
         super().add_serializers()
         taggable.TaggableSerializerMixin.add_serializers(self)
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
         serializers: Dict[str, base.Serializer] = {
-            'model_class': lambda item, key, **context: self.hdca_manager.model_class.__class__.__name__,
+            "model_class": lambda item, key, **context: self.hdca_manager.model_class.__class__.__name__,
             # TODO: remove
-            'type': lambda item, key, **context: 'collection',
+            "type": lambda item, key, **context: "collection",
             # part of a history and container
-            'history_id': self.serialize_id,
-            'history_content_type': lambda item, key, **context: self.hdca_manager.model_class.content_type,
-            'type_id': self.serialize_type_id,
-            'job_source_id': self.serialize_id,
-            'url': lambda item, key, **context: self.url_for('history_content_typed',
-                                                             history_id=self.app.security.encode_id(item.history_id),
-                                                             id=self.app.security.encode_id(item.id),
-                                                             type=self.hdca_manager.model_class.content_type),
-            'contents_url': self.generate_contents_url,
-            'job_state_summary': self.serialize_job_state_summary,
-            'elements_datatypes': self.serialize_elements_datatypes,
+            "history_id": self.serialize_id,
+            "history_content_type": lambda item, key, **context: self.hdca_manager.model_class.content_type,
+            "type_id": self.serialize_type_id,
+            "job_source_id": self.serialize_id,
+            "url": lambda item, key, **context: self.url_for(
+                "history_content_typed",
+                history_id=self.app.security.encode_id(item.history_id),
+                id=self.app.security.encode_id(item.id),
+                type=self.hdca_manager.model_class.content_type,
+            ),
+            "contents_url": self.generate_contents_url,
+            "job_state_summary": self.serialize_job_state_summary,
+            "elements_datatypes": self.serialize_elements_datatypes,
         }
         self.serializers.update(serializers)
 
@@ -324,15 +341,15 @@ class HDCASerializer(
         encode_id = self.app.security.encode_id
         trans = context.get("trans")
         url_for = trans.url_builder if trans and trans.url_builder else self.url_for
-        contents_url = url_for('contents_dataset_collection',
-            hdca_id=encode_id(item.id),
-            parent_id=encode_id(item.collection_id))
+        contents_url = url_for(
+            "contents_dataset_collection", hdca_id=encode_id(item.id), parent_id=encode_id(item.collection_id)
+        )
         return contents_url
 
     def serialize_job_state_summary(self, item, key, **context):
         states = item.job_state_summary.__dict__.copy()
-        del states['_sa_instance_state']
-        del states['hdca_id']
+        del states["_sa_instance_state"]
+        del states["hdca_id"]
         return states
 
     def serialize_elements_datatypes(self, item, key, **context):
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index 098a91a044f..59ce2a84bc8 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -19,15 +19,13 @@ from sqlalchemy import (
     desc,
 )
 
-from galaxy import (
-    exceptions as glx_exceptions,
-    model
-)
+from galaxy import exceptions as glx_exceptions
+from galaxy import model
 from galaxy.managers import (
     deletable,
     hdas,
     history_contents,
-    sharable
+    sharable,
 )
 from galaxy.managers.base import (
     Serializer,
@@ -45,7 +43,7 @@ log = logging.getLogger(__name__)
 class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMixin, SortableManager):
 
     model_class = model.History
-    foreign_key_name = 'history'
+    foreign_key_name = "history"
     user_share_model = model.HistoryUserShareAssociation
 
     tag_assoc = model.HistoryTagAssociation
@@ -54,7 +52,13 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
 
     # TODO: incorporate imp/exp (or alias to)
 
-    def __init__(self, app: MinimalManagerApp, hda_manager: hdas.HDAManager, contents_manager: history_contents.HistoryContentsManager, contents_filters: history_contents.HistoryContentsFilters):
+    def __init__(
+        self,
+        app: MinimalManagerApp,
+        hda_manager: hdas.HDAManager,
+        contents_manager: history_contents.HistoryContentsManager,
+        contents_filters: history_contents.HistoryContentsFilters,
+    ):
         super().__init__(app)
         self.hda_manager = hda_manager
         self.contents_manager = contents_manager
@@ -149,28 +153,29 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
         """Return an ORM compatible order_by using the given string"""
         # TODO: generalize into class
         # TODO: general (enough) columns
-        if order_by_string in ('create_time', 'create_time-dsc'):
+        if order_by_string in ("create_time", "create_time-dsc"):
             return desc(self.model_class.create_time)
-        if order_by_string == 'create_time-asc':
+        if order_by_string == "create_time-asc":
             return asc(self.model_class.create_time)
-        if order_by_string in ('update_time', 'update_time-dsc'):
+        if order_by_string in ("update_time", "update_time-dsc"):
             return desc(self.model_class.update_time)
-        if order_by_string == 'update_time-asc':
+        if order_by_string == "update_time-asc":
             return asc(self.model_class.update_time)
-        if order_by_string in ('name', 'name-asc'):
+        if order_by_string in ("name", "name-asc"):
             return asc(self.model_class.name)
-        if order_by_string == 'name-dsc':
+        if order_by_string == "name-dsc":
             return desc(self.model_class.name)
         # TODO: history columns
-        if order_by_string in ('size', 'size-dsc'):
+        if order_by_string in ("size", "size-dsc"):
             return desc(self.model_class.disk_size)
-        if order_by_string == 'size-asc':
+        if order_by_string == "size-asc":
             return asc(self.model_class.disk_size)
         # TODO: add functional/non-orm orders (such as rating)
         if default:
             return self.parse_order_by(default)
-        raise glx_exceptions.RequestParameterInvalidException('Unkown order_by', order_by=order_by_string,
-            available=['create_time', 'update_time', 'name', 'size'])
+        raise glx_exceptions.RequestParameterInvalidException(
+            "Unkown order_by", order_by=order_by_string, available=["create_time", "update_time", "name", "size"]
+        )
 
     def non_ready_jobs(self, history):
         """Return the currently running job objects associated with this history.
@@ -180,15 +185,18 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
         """
         # TODO: defer to jobModelManager (if there was one)
         # TODO: genericize the params to allow other filters
-        jobs = (self.session().query(model.Job)
+        jobs = (
+            self.session()
+            .query(model.Job)
             .filter(model.Job.history == history)
-            .filter(model.Job.state.in_(model.Job.non_ready_states)))
+            .filter(model.Job.state.in_(model.Job.non_ready_states))
+        )
         return jobs
 
     def queue_history_import(self, trans, archive_type, archive_source):
         # Run job to do import.
-        history_imp_tool = trans.app.toolbox.get_tool('__IMPORT_HISTORY__')
-        incoming = {'__ARCHIVE_SOURCE__': archive_source, '__ARCHIVE_TYPE__': archive_type}
+        history_imp_tool = trans.app.toolbox.get_tool("__IMPORT_HISTORY__")
+        incoming = {"__ARCHIVE_SOURCE__": archive_source, "__ARCHIVE_TYPE__": archive_type}
         job, *_ = history_imp_tool.execute(trans, incoming=incoming)
         trans.app.job_manager.enqueue(job, tool=history_imp_tool)
         return job
@@ -197,13 +205,13 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
     def legacy_serve_ready_history_export(self, trans, jeha):
         assert jeha.ready
         if jeha.compressed:
-            trans.response.set_content_type('application/x-gzip')
+            trans.response.set_content_type("application/x-gzip")
         else:
-            trans.response.set_content_type('application/x-tar')
+            trans.response.set_content_type("application/x-tar")
         disposition = f'attachment; filename="{jeha.export_name}"'
         trans.response.headers["Content-Disposition"] = disposition
         archive = trans.app.object_store.get_filename(jeha.dataset)
-        return open(archive, mode='rb')
+        return open(archive, mode="rb")
 
     def get_ready_history_export_file_path(self, trans, jeha) -> str:
         """
@@ -213,28 +221,30 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
         assert jeha.ready
         return trans.app.object_store.get_filename(jeha.dataset)
 
-    def queue_history_export(self, trans, history, gzip=True, include_hidden=False, include_deleted=False, directory_uri=None, file_name=None):
+    def queue_history_export(
+        self, trans, history, gzip=True, include_hidden=False, include_deleted=False, directory_uri=None, file_name=None
+    ):
         # Convert options to booleans.
         if isinstance(gzip, str):
-            gzip = (gzip in ['True', 'true', 'T', 't'])
+            gzip = gzip in ["True", "true", "T", "t"]
         if isinstance(include_hidden, str):
-            include_hidden = (include_hidden in ['True', 'true', 'T', 't'])
+            include_hidden = include_hidden in ["True", "true", "T", "t"]
         if isinstance(include_deleted, str):
-            include_deleted = (include_deleted in ['True', 'true', 'T', 't'])
+            include_deleted = include_deleted in ["True", "true", "T", "t"]
 
         params = {
-            'history_to_export': history,
-            'compress': gzip,
-            'include_hidden': include_hidden,
-            'include_deleted': include_deleted
+            "history_to_export": history,
+            "compress": gzip,
+            "include_hidden": include_hidden,
+            "include_deleted": include_deleted,
         }
 
         if directory_uri is None:
-            export_tool_id = '__EXPORT_HISTORY__'
+            export_tool_id = "__EXPORT_HISTORY__"
         else:
-            params['directory_uri'] = directory_uri
-            params['file_name'] = file_name or None
-            export_tool_id = '__EXPORT_HISTORY_TO_URI__'
+            params["directory_uri"] = directory_uri
+            params["file_name"] = file_name or None
+            export_tool_id = "__EXPORT_HISTORY_TO_URI__"
 
         # Run job to do export.
         history_exp_tool = trans.app.toolbox.get_tool(export_tool_id)
@@ -291,21 +301,28 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
         extra.cannot_change = list(cannot_change_dict.values())
         extra.accessible_count = total_dataset_count - len(extra.can_change) - len(extra.cannot_change)
         if not extra.accessible_count and not extra.can_change and not share_anyway:
-            errors.add("The history you are sharing do not contain any datasets that can be accessed by the users with which you are sharing.")
+            errors.add(
+                "The history you are sharing do not contain any datasets that can be accessed by the users with which you are sharing."
+            )
 
         extra.can_share = not errors and (extra.accessible_count == total_dataset_count or option is not None)
         return extra
 
     def is_history_shared_with(self, history, user) -> bool:
-        return bool(self.session().query(self.user_share_model).filter(
-            and_(
-                self.user_share_model.table.c.user_id == user.id,
-                self.user_share_model.table.c.history_id == history.id,
+        return bool(
+            self.session()
+            .query(self.user_share_model)
+            .filter(
+                and_(
+                    self.user_share_model.table.c.user_id == user.id,
+                    self.user_share_model.table.c.history_id == history.id,
+                )
             )
-        ).first())
+            .first()
+        )
 
     def make_members_public(self, trans, item):
-        """ Make the non-purged datasets in history public.
+        """Make the non-purged datasets in history public.
         Performs permissions check.
         """
         for hda in item.activatable_datasets:
@@ -321,7 +338,6 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
 
 
 class HistoryExportView:
-
     def __init__(self, app: MinimalManagerApp):
         self.app = app
 
@@ -335,7 +351,9 @@ class HistoryExportView:
         encoded_jeha_id = trans.security.encode_id(jeha.id)
         api_url = trans.url_builder("history_archive_download", id=history_id, jeha_id=encoded_jeha_id)
         external_url = trans.url_builder("history_archive_download", id=history_id, jeha_id="latest", qualified=True)
-        external_permanent_url = trans.url_builder("history_archive_download", id=history_id, jeha_id=encoded_jeha_id, qualified=True)
+        external_permanent_url = trans.url_builder(
+            "history_archive_download", id=history_id, jeha_id=encoded_jeha_id, qualified=True
+        )
         rval["download_url"] = api_url
         rval["external_download_latest_url"] = external_url
         rval["external_download_permanent_url"] = external_permanent_url
@@ -359,7 +377,9 @@ class HistoryExportView:
 
     def _history(self, trans, history_id):
         if history_id is not None:
-            history = self.app.history_manager.get_accessible(trans.security.decode_id(history_id), trans.user, current_history=trans.history)
+            history = self.app.history_manager.get_accessible(
+                trans.security.decode_id(history_id), trans.user, current_history=trans.history
+            )
         else:
             history = trans.history
         return history
@@ -369,10 +389,17 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
     """
     Interface/service object for serializing histories into dictionaries.
     """
-    model_manager_class = HistoryManager
-    SINGLE_CHAR_ABBR = 'h'
 
-    def __init__(self, app: MinimalManagerApp, hda_manager: hdas.HDAManager, hda_serializer: hdas.HDASerializer, history_contents_serializer: history_contents.HistoryContentsSerializer):
+    model_manager_class = HistoryManager
+    SINGLE_CHAR_ABBR = "h"
+
+    def __init__(
+        self,
+        app: MinimalManagerApp,
+        hda_manager: hdas.HDAManager,
+        hda_serializer: hdas.HDASerializer,
+        history_contents_serializer: history_contents.HistoryContentsSerializer,
+    ):
         super().__init__(app)
 
         self.history_manager = self.manager
@@ -380,83 +407,97 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
         self.hda_serializer = hda_serializer
         self.history_contents_serializer = history_contents_serializer
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id',
-            'model_class',
-            'name',
-            'deleted',
-            'purged',
-            # 'count'
-            'url',
-            # TODO: why these?
-            'published',
-            'annotation',
-            'tags',
-            'update_time',
-        ])
-        self.add_view('detailed', [
-            'contents_url',
-            'empty',
-            'size',
-            'user_id',
-            'create_time',
-            'update_time',
-            'importable',
-            'slug',
-            'username_and_slug',
-            'genome_build',
-            # TODO: remove the next three - instead getting the same info from the 'hdas' list
-            'state',
-            'state_details',
-            'state_ids',
-            # 'community_rating',
-            # 'user_rating',
-        ], include_keys_from='summary')
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "model_class",
+                "name",
+                "deleted",
+                "purged",
+                # 'count'
+                "url",
+                # TODO: why these?
+                "published",
+                "annotation",
+                "tags",
+                "update_time",
+            ],
+        )
+        self.add_view(
+            "detailed",
+            [
+                "contents_url",
+                "empty",
+                "size",
+                "user_id",
+                "create_time",
+                "update_time",
+                "importable",
+                "slug",
+                "username_and_slug",
+                "genome_build",
+                # TODO: remove the next three - instead getting the same info from the 'hdas' list
+                "state",
+                "state_details",
+                "state_ids",
+                # 'community_rating',
+                # 'user_rating',
+            ],
+            include_keys_from="summary",
+        )
         # in the Historys' case, each of these views includes the keys from the previous
 
         #: ..note: this is a custom view for newer (2016/3) UI and should be considered volatile
-        self.add_view('dev-detailed', [
-            'contents_url',
-            'size',
-            'user_id',
-            'create_time',
-            'update_time',
-            'importable',
-            'slug',
-            'username_and_slug',
-            'genome_build',
-            # 'contents_states',
-            'contents_active',
-            'hid_counter',
-        ], include_keys_from='summary')
+        self.add_view(
+            "dev-detailed",
+            [
+                "contents_url",
+                "size",
+                "user_id",
+                "create_time",
+                "update_time",
+                "importable",
+                "slug",
+                "username_and_slug",
+                "genome_build",
+                # 'contents_states',
+                "contents_active",
+                "hid_counter",
+            ],
+            include_keys_from="summary",
+        )
 
         # beta web client fields, no summary/detailed/dev-detailed blah
-        self.add_view('betawebclient', [
-            'annotation',
-            'contents_active',
-            'contents_url',
-            'create_time',
-            'deleted',
-            'empty',
-            'genome_build',
-            'hid_counter',
-            'id',
-            'importable',
-            'name',
-            'nice_size',
-            'published',
-            'purged',
-            # 'shared',
-            'size',
-            'slug',
-            'state',
-            'tags',
-            'update_time',
-            'url',
-            'username_and_slug',
-            'user_id',
-        ])
+        self.add_view(
+            "betawebclient",
+            [
+                "annotation",
+                "contents_active",
+                "contents_url",
+                "create_time",
+                "deleted",
+                "empty",
+                "genome_build",
+                "hid_counter",
+                "id",
+                "importable",
+                "name",
+                "nice_size",
+                "published",
+                "purged",
+                # 'shared',
+                "size",
+                "slug",
+                "state",
+                "tags",
+                "update_time",
+                "url",
+                "username_and_slug",
+                "user_id",
+            ],
+        )
 
     # assumes: outgoing to json.dumps and sanitized
     def add_serializers(self):
@@ -464,29 +505,30 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         serializers: Dict[str, Serializer] = {
-            'model_class': lambda item, key, **context: 'History',
-            'size': lambda item, key, **context: int(item.disk_size),
-            'nice_size': lambda item, key, **context: item.disk_nice_size,
-            'state': self.serialize_history_state,
-
-            'url': lambda item, key, **context: self.url_for('history', id=self.app.security.encode_id(item.id)),
-            'contents_url': lambda item, key, **context: self.url_for('history_contents',
-                                                           history_id=self.app.security.encode_id(item.id)),
-
-            'empty': lambda item, key, **context: (len(item.datasets) + len(item.dataset_collections)) <= 0,
-            'count': lambda item, key, **context: len(item.datasets),
-            'hdas': lambda item, key, **context: [self.app.security.encode_id(hda.id) for hda in item.datasets],
-            'state_details': self.serialize_state_counts,
-            'state_ids': self.serialize_state_ids,
-            'contents': self.serialize_contents,
-            'non_ready_jobs': lambda item, key, **context: [self.app.security.encode_id(job.id) for job
-                                                 in self.manager.non_ready_jobs(item)],
-
-            'contents_states': self.serialize_contents_states,
-            'contents_active': self.serialize_contents_active,
+            "model_class": lambda item, key, **context: "History",
+            "size": lambda item, key, **context: int(item.disk_size),
+            "nice_size": lambda item, key, **context: item.disk_nice_size,
+            "state": self.serialize_history_state,
+            "url": lambda item, key, **context: self.url_for("history", id=self.app.security.encode_id(item.id)),
+            "contents_url": lambda item, key, **context: self.url_for(
+                "history_contents", history_id=self.app.security.encode_id(item.id)
+            ),
+            "empty": lambda item, key, **context: (len(item.datasets) + len(item.dataset_collections)) <= 0,
+            "count": lambda item, key, **context: len(item.datasets),
+            "hdas": lambda item, key, **context: [self.app.security.encode_id(hda.id) for hda in item.datasets],
+            "state_details": self.serialize_state_counts,
+            "state_ids": self.serialize_state_ids,
+            "contents": self.serialize_contents,
+            "non_ready_jobs": lambda item, key, **context: [
+                self.app.security.encode_id(job.id) for job in self.manager.non_ready_jobs(item)
+            ],
+            "contents_states": self.serialize_contents_states,
+            "contents_active": self.serialize_contents_active,
             #  TODO: Use base manager's serialize_id for user_id (and others)
             #  after refactoring hierarchy here?
-            'user_id': lambda item, key, **context: self.app.security.encode_id(item.user_id) if item.user_id is not None else None
+            "user_id": lambda item, key, **context: self.app.security.encode_id(item.user_id)
+            if item.user_id is not None
+            else None,
         }
         self.serializers.update(serializers)
 
@@ -540,21 +582,21 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
         state = states.ERROR
         # TODO: history_state and state_counts are classically calc'd at the same time
         #   so this is rel. ineff. - if we keep this...
-        hda_state_counts = self.serialize_state_counts(history, 'counts', exclude_deleted=True, **context)
+        hda_state_counts = self.serialize_state_counts(history, "counts", exclude_deleted=True, **context)
         if history.empty:
             state = states.NEW
         else:
             num_hdas = sum(hda_state_counts.values())
-            if (hda_state_counts[states.RUNNING] > 0
-                    or hda_state_counts[states.SETTING_METADATA] > 0
-                    or hda_state_counts[states.UPLOAD] > 0):
+            if (
+                hda_state_counts[states.RUNNING] > 0
+                or hda_state_counts[states.SETTING_METADATA] > 0
+                or hda_state_counts[states.UPLOAD] > 0
+            ):
                 state = states.RUNNING
             # TODO: this method may be more useful if we *also* polled the histories jobs here too
-            elif (hda_state_counts[states.QUEUED] > 0
-                    or hda_state_counts[states.NEW] > 0):
+            elif hda_state_counts[states.QUEUED] > 0 or hda_state_counts[states.NEW] > 0:
                 state = states.QUEUED
-            elif (hda_state_counts[states.ERROR] > 0
-                    or hda_state_counts[states.FAILED_METADATA] > 0):
+            elif hda_state_counts[states.ERROR] > 0 or hda_state_counts[states.FAILED_METADATA] > 0:
                 state = states.ERROR
             elif hda_state_counts[states.OK] == num_hdas:
                 state = states.OK
@@ -565,8 +607,9 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
         history = item
         returned = []
         for content in self.manager.contents_manager._union_of_contents_query(history).all():
-            serialized = self.history_contents_serializer.serialize_to_view(content,
-                view='summary', trans=trans, user=user)
+            serialized = self.history_contents_serializer.serialize_to_view(
+                content, view="summary", trans=trans, user=user
+            )
             returned.append(serialized)
         return returned
 
@@ -596,6 +639,7 @@ class HistoryDeserializer(sharable.SharableModelDeserializer, deletable.Purgable
     """
     Interface/service object for validating and deserializing dictionaries into histories.
     """
+
     model_manager_class = HistoryManager
 
     def __init__(self, app: MinimalManagerApp):
@@ -606,10 +650,12 @@ class HistoryDeserializer(sharable.SharableModelDeserializer, deletable.Purgable
         super().add_deserializers()
         deletable.PurgableDeserializerMixin.add_deserializers(self)
 
-        self.deserializers.update({
-            'name': self.deserialize_basestring,
-            'genome_build': self.deserialize_genome_build,
-        })
+        self.deserializers.update(
+            {
+                "name": self.deserialize_basestring,
+                "genome_build": self.deserialize_genome_build,
+            }
+        )
 
 
 class HistoryFilters(sharable.SharableModelFilters, deletable.PurgableFiltersMixin):
@@ -619,10 +665,12 @@ class HistoryFilters(sharable.SharableModelFilters, deletable.PurgableFiltersMix
     def _add_parsers(self):
         super()._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers(self)
-        self.orm_filter_parsers.update({
-            # history specific
-            'name': {'op': ('eq', 'contains', 'like')},
-            'genome_build': {'op': ('eq', 'contains', 'like')},
-            'create_time': {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
-            'update_time': {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
-        })
+        self.orm_filter_parsers.update(
+            {
+                # history specific
+                "name": {"op": ("eq", "contains", "like")},
+                "genome_build": {"op": ("eq", "contains", "like")},
+                "create_time": {"op": ("le", "ge", "gt", "lt"), "val": self.parse_date},
+                "update_time": {"op": ("le", "ge", "gt", "lt"), "val": self.parse_date},
+            }
+        )
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 5c6e6b8160d..63ff7ae385c 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -3,7 +3,11 @@ Heterogenous lists/contents are difficult to query properly since unions are
 not easily made.
 """
 import logging
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 
 from sqlalchemy import (
     asc,
@@ -12,17 +16,15 @@ from sqlalchemy import (
     func,
     literal,
     sql,
-    true
+    true,
 )
 from sqlalchemy.orm import (
     eagerload,
-    undefer
+    undefer,
 )
 
-from galaxy import (
-    exceptions as glx_exceptions,
-    model
-)
+from galaxy import exceptions as glx_exceptions
+from galaxy import model
 from galaxy.managers import (
     annotatable,
     base,
@@ -30,7 +32,7 @@ from galaxy.managers import (
     hdas,
     hdcas,
     taggable,
-    tools
+    tools,
 )
 from galaxy.structured_app import MinimalManagerApp
 from .base import (
@@ -50,11 +52,11 @@ class HistoryContentsManager(base.SortableManager):
 
     contained_class = model.HistoryDatasetAssociation
     contained_class_manager_class = hdas.HDAManager
-    contained_class_type_name = 'dataset'
+    contained_class_type_name = "dataset"
 
     subcontainer_class = model.HistoryDatasetCollectionAssociation
     subcontainer_class_manager_class = hdcas.HDCAManager
-    subcontainer_class_type_name = 'dataset_collection'
+    subcontainer_class_type_name = "dataset_collection"
 
     #: the columns which are common to both subcontainers and non-subcontainers.
     #  (Also the attributes that may be filtered or orderered_by)
@@ -76,7 +78,7 @@ class HistoryContentsManager(base.SortableManager):
         "create_time",
         "update_time",
     )
-    default_order_by = 'hid'
+    default_order_by = "hid"
 
     def __init__(self, app: MinimalManagerApp):
         self.app = app
@@ -108,38 +110,42 @@ class HistoryContentsManager(base.SortableManager):
         """
         # TODO?: we could branch here based on 'if limit is None and offset is None' - to a simpler (non-union) query
         # for now, I'm just using this (even for non-limited/offset queries) to reduce code paths
-        return self._union_of_contents(container,
-            filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs)
+        return self._union_of_contents(
+            container, filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs
+        )
 
     def contents_count(self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs):
         """
         Returns a count of both/all types of contents, based on the given filters.
         """
-        return self.contents_query(container,
-            filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs).count()
+        return self.contents_query(
+            container, filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs
+        ).count()
 
     def contents_query(self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs):
         """
         Returns the contents union query for subqueries, etc.
         """
-        return self._union_of_contents_query(container,
-            filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs)
+        return self._union_of_contents_query(
+            container, filters=filters, limit=limit, offset=offset, order_by=order_by, **kwargs
+        )
 
     # order_by parsing - similar to FilterParser but not enough yet to warrant a class?
     def parse_order_by(self, order_by_string, default=None):
         """Return an ORM compatible order_by using the given string"""
-        available = ['create_time', 'extension', 'hid', 'history_id', 'name', 'update_time']
+        available = ["create_time", "extension", "hid", "history_id", "name", "update_time"]
         for attribute in available:
-            attribute_dsc = f'{attribute}-dsc'
-            attribute_asc = f'{attribute}-asc'
+            attribute_dsc = f"{attribute}-dsc"
+            attribute_asc = f"{attribute}-asc"
             if order_by_string in (attribute, attribute_dsc):
                 return desc(attribute)
             if order_by_string == attribute_asc:
                 return asc(attribute)
         if default:
             return self.parse_order_by(default)
-        raise glx_exceptions.RequestParameterInvalidException('Unknown order_by', order_by=order_by_string,
-            available=available)
+        raise glx_exceptions.RequestParameterInvalidException(
+            "Unknown order_by", order_by=order_by_string, available=available
+        )
 
     # history specific methods
     def state_counts(self, history):
@@ -150,13 +156,15 @@ class HistoryContentsManager(base.SortableManager):
         Note: does not include deleted/hidden contents.
         """
         filters = [
-            base.ModelFilterParser.parsed_filter("orm", sql.column('deleted') == false()),
-            base.ModelFilterParser.parsed_filter("orm", sql.column('visible') == true())
+            base.ModelFilterParser.parsed_filter("orm", sql.column("deleted") == false()),
+            base.ModelFilterParser.parsed_filter("orm", sql.column("visible") == true()),
         ]
         contents_subquery = self._union_of_contents_query(history, filters=filters).subquery()
-        statement = (sql.select([sql.column('state'), func.count('*')])
+        statement = (
+            sql.select([sql.column("state"), func.count("*")])
             .select_from(contents_subquery)
-            .group_by(sql.column('state')))
+            .group_by(sql.column("state"))
+        )
         counts = self.app.model.context.execute(statement).fetchall()
         return dict(counts)
 
@@ -170,22 +178,18 @@ class HistoryContentsManager(base.SortableManager):
         """
         returned = dict(deleted=0, hidden=0, active=0)
         contents_subquery = self._union_of_contents_query(history).subquery()
-        columns = [
-            sql.column('deleted'),
-            sql.column('visible'),
-            func.count('*')
-        ]
-        statement = (sql.select(columns)
-            .select_from(contents_subquery)
-            .group_by(sql.column('deleted'), sql.column('visible')))
+        columns = [sql.column("deleted"), sql.column("visible"), func.count("*")]
+        statement = (
+            sql.select(columns).select_from(contents_subquery).group_by(sql.column("deleted"), sql.column("visible"))
+        )
         groups = self.app.model.context.execute(statement).fetchall()
         for deleted, visible, count in groups:
             if deleted:
-                returned['deleted'] += count
+                returned["deleted"] += count
             if not visible:
-                returned['hidden'] += count
+                returned["hidden"] += count
             if not deleted and visible:
-                returned['active'] += count
+                returned["active"] += count
         return returned
 
     def map_datasets(self, history, fn, **kwargs):
@@ -229,25 +233,29 @@ class HistoryContentsManager(base.SortableManager):
             return contents_results
 
         # partition ids into a map of { component_class names -> list of ids } from the above union query
-        id_map: Dict[str, List[int]] = dict([(self.contained_class_type_name, []), (self.subcontainer_class_type_name, [])])
+        id_map: Dict[str, List[int]] = dict(
+            [(self.contained_class_type_name, []), (self.subcontainer_class_type_name, [])]
+        )
         for result in contents_results:
             result_type = self._get_union_type(result)
             contents_id = self._get_union_id(result)
             if result_type in id_map:
                 id_map[result_type].append(contents_id)
             else:
-                raise TypeError('Unknown contents type:', result_type)
+                raise TypeError("Unknown contents type:", result_type)
 
         # query 2 & 3: use the ids to query each component_class, returning an id->full component model map
         contained_ids = id_map[self.contained_class_type_name]
         id_map[self.contained_class_type_name] = self._contained_id_map(contained_ids)
         subcontainer_ids = id_map[self.subcontainer_class_type_name]
-        serialization_params = kwargs.get('serialization_params', None)
-        id_map[self.subcontainer_class_type_name] = self._subcontainer_id_map(subcontainer_ids, serialization_params=serialization_params)
+        serialization_params = kwargs.get("serialization_params", None)
+        id_map[self.subcontainer_class_type_name] = self._subcontainer_id_map(
+            subcontainer_ids, serialization_params=serialization_params
+        )
 
         # cycle back over the union query to create an ordered list of the objects returned in queries 2 & 3 above
         contents = []
-        filters = kwargs.get('filters') or []
+        filters = kwargs.get("filters") or []
         # TODO: or as generator?
         for result in contents_results:
             result_type = self._get_union_type(result)
@@ -260,25 +268,20 @@ class HistoryContentsManager(base.SortableManager):
     @staticmethod
     def passes_filters(content, filters):
         for filter_fn in filters:
-            if filter_fn.filter_type == 'function':
+            if filter_fn.filter_type == "function":
                 if not filter_fn.filter(content):
                     return False
         return True
 
-    def _union_of_contents_query(self,
-                                 container,
-                                 filters=None,
-                                 limit=None,
-                                 offset=None,
-                                 order_by=None,
-                                 user_id=None,
-                                 **kwargs):
+    def _union_of_contents_query(
+        self, container, filters=None, limit=None, offset=None, order_by=None, user_id=None, **kwargs
+    ):
         """
         Returns a query for a limited and offset list of both types of contents,
         filtered and in some order.
         """
         order_by = order_by if order_by is not None else self.default_order_by
-        order_by = order_by if isinstance(order_by, (tuple, list)) else (order_by, )
+        order_by = order_by if isinstance(order_by, (tuple, list)) else (order_by,)
 
         # TODO: 3 queries and 3 iterations over results - this is undoubtedly better solved in the actual SQL layer
         # via one common table for contents, Some Yonder Resplendent and Fanciful Join, or ORM functionality
@@ -290,10 +293,12 @@ class HistoryContentsManager(base.SortableManager):
         # note: I'm trying to keep these private functions as generic as possible in order to move them toward base later
 
         # query 1: create a union of common columns for which the component_classes can be filtered/limited
-        contained_query = self._contents_common_query_for_contained(history_id=container.id if container else None,
-                                                                    user_id=user_id)
-        subcontainer_query = self._contents_common_query_for_subcontainer(history_id=container.id if container else None,
-                                                                          user_id=user_id)
+        contained_query = self._contents_common_query_for_contained(
+            history_id=container.id if container else None, user_id=user_id
+        )
+        subcontainer_query = self._contents_common_query_for_subcontainer(
+            history_id=container.id if container else None, user_id=user_id
+        )
 
         filters = filters or []
         # Apply filters that are specific to a model
@@ -316,8 +321,8 @@ class HistoryContentsManager(base.SortableManager):
 
     def _apply_orm_filter(self, qry, orm_filter):
         if isinstance(orm_filter, sql.elements.BinaryExpression):
-            for match in filter(lambda col: col['name'] == orm_filter.left.name, qry.column_descriptions):
-                column = match['expr']
+            for match in filter(lambda col: col["name"] == orm_filter.left.name, qry.column_descriptions):
+                column = match["expr"]
                 new_filter = orm_filter._clone()
                 new_filter.left = column
                 qry = qry.filter(new_filter)
@@ -340,11 +345,12 @@ class HistoryContentsManager(base.SortableManager):
     def _contents_common_query_for_contained(self, history_id, user_id):
         component_class = self.contained_class
         # TODO: and now a join with Dataset - this is getting sad
-        columns = self._contents_common_columns(component_class,
-            history_content_type=literal('dataset'),
+        columns = self._contents_common_columns(
+            component_class,
+            history_content_type=literal("dataset"),
             state=model.Dataset.state,
             # do not have inner collections
-            collection_id=literal(None)
+            collection_id=literal(None),
         )
         subquery = self._session().query(*columns)
         # for the HDA's we need to join the Dataset since it has an actual state column
@@ -355,14 +361,16 @@ class HistoryContentsManager(base.SortableManager):
             # Make sure we only return items that are user-accessible by checking that they are in a history
             # owned by the current user.
             # TODO: move into filter mixin, and implement accessible logic as SQL query
-            subquery = subquery.filter(component_class.table.c.history_id == model.History.table.c.id,
-                                       model.History.table.c.user_id == user_id)
+            subquery = subquery.filter(
+                component_class.table.c.history_id == model.History.table.c.id, model.History.table.c.user_id == user_id
+            )
         return subquery
 
     def _contents_common_query_for_subcontainer(self, history_id, user_id):
         component_class = self.subcontainer_class
-        columns = self._contents_common_columns(component_class,
-            history_content_type=literal('dataset_collection'),
+        columns = self._contents_common_columns(
+            component_class,
+            history_content_type=literal("dataset_collection"),
             # do not have datasets
             dataset_id=literal(None),
             state=model.DatasetCollection.populated_state,
@@ -372,13 +380,13 @@ class HistoryContentsManager(base.SortableManager):
         )
         subquery = self._session().query(*columns)
         # for the HDCA's we need to join the DatasetCollection since it has the populated_state
-        subquery = subquery.join(model.DatasetCollection,
-            model.DatasetCollection.id == component_class.collection_id)
+        subquery = subquery.join(model.DatasetCollection, model.DatasetCollection.id == component_class.collection_id)
         if history_id:
             subquery = subquery.filter(component_class.history_id == history_id)
         else:
-            subquery = subquery.filter(component_class.history_id == model.History.table.c.id,
-                                       model.History.table.c.user_id == user_id)
+            subquery = subquery.filter(
+                component_class.history_id == model.History.table.c.id, model.History.table.c.user_id == user_id
+            )
         return subquery
 
     def _get_union_type(self, union):
@@ -394,12 +402,15 @@ class HistoryContentsManager(base.SortableManager):
         if not id_list:
             return []
         component_class = self.contained_class
-        query = (self._session().query(component_class)
+        query = (
+            self._session()
+            .query(component_class)
             .filter(component_class.id.in_(id_list))
-            .options(undefer('_metadata'))
-            .options(eagerload('dataset.actions'))
-            .options(eagerload('tags'))
-            .options(eagerload('annotations')))
+            .options(undefer("_metadata"))
+            .options(eagerload("dataset.actions"))
+            .options(eagerload("tags"))
+            .options(eagerload("annotations"))
+        )
         return {row.id: row for row in query.all()}
 
     def _subcontainer_id_map(self, id_list, serialization_params=None):
@@ -407,18 +418,21 @@ class HistoryContentsManager(base.SortableManager):
         if not id_list:
             return []
         component_class = self.subcontainer_class
-        query = (self._session().query(component_class)
+        query = (
+            self._session()
+            .query(component_class)
             .filter(component_class.id.in_(id_list))
-            .options(eagerload('collection'))
-            .options(eagerload('tags'))
-            .options(eagerload('annotations')))
+            .options(eagerload("collection"))
+            .options(eagerload("tags"))
+            .options(eagerload("annotations"))
+        )
 
         # This will conditionally join a potentially costly job_state summary
         # All the paranoia if-checking makes me wonder if serialization_params
         # should really be a property of the manager class instance
         if serialization_params and serialization_params.keys:
-            if 'job_state_summary' in serialization_params.keys:
-                query = query.options(eagerload('job_state_summary'))
+            if "job_state_summary" in serialization_params.keys:
+                query = query.options(eagerload("job_state_summary"))
 
         return {row.id: row for row in query.all()}
 
@@ -427,53 +441,59 @@ class HistoryContentsSerializer(base.ModelSerializer, deletable.PurgableSerializ
     """
     Interface/service object for serializing histories into dictionaries.
     """
+
     model_manager_class = HistoryContentsManager
 
     def __init__(self, app: MinimalManagerApp, **kwargs):
         super().__init__(app, **kwargs)
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            "id",
-            "type_id",
-            "history_id",
-            "hid",
-            "history_content_type",
-            "visible",
-            "dataset_id",
-            "collection_id",
-            "name",
-            "state",
-            "deleted",
-            "purged",
-            "create_time",
-            "update_time",
-        ])
+        self.default_view = "summary"
+        self.add_view(
+            "summary",
+            [
+                "id",
+                "type_id",
+                "history_id",
+                "hid",
+                "history_content_type",
+                "visible",
+                "dataset_id",
+                "collection_id",
+                "name",
+                "state",
+                "deleted",
+                "purged",
+                "create_time",
+                "update_time",
+            ],
+        )
 
     # assumes: outgoing to json.dumps and sanitized
     def add_serializers(self):
         super().add_serializers()
         deletable.PurgableSerializerMixin.add_serializers(self)
         serializers: Dict[str, Serializer] = {
-            'type_id': self.serialize_type_id,
-            'history_id': self.serialize_id,
-            'dataset_id': self.serialize_id_or_skip,
-            'collection_id': self.serialize_id_or_skip,
+            "type_id": self.serialize_type_id,
+            "history_id": self.serialize_id,
+            "dataset_id": self.serialize_id_or_skip,
+            "collection_id": self.serialize_id_or_skip,
         }
         self.serializers.update(serializers)
 
     def serialize_id_or_skip(self, item: Any, key: str, **context):
         """Serialize id or skip if attribute with `key` is not present."""
         if not hasattr(item, key):
-            raise base.SkipAttribute('no such attribute')
+            raise base.SkipAttribute("no such attribute")
         return self.serialize_id(item, key, **context)
 
 
-class HistoryContentsFilters(base.ModelFilterParser,
-                             annotatable.AnnotatableFilterMixin,
-                             deletable.PurgableFiltersMixin,
-                             taggable.TaggableFilterMixin,
-                             tools.ToolFilterMixin):
+class HistoryContentsFilters(
+    base.ModelFilterParser,
+    annotatable.AnnotatableFilterMixin,
+    deletable.PurgableFiltersMixin,
+    taggable.TaggableFilterMixin,
+    tools.ToolFilterMixin,
+):
     # surprisingly (but ominously), this works for both content classes in the union that's filtered
     model_class = model.HistoryDatasetAssociation
 
@@ -485,54 +505,54 @@ class HistoryContentsFilters(base.ModelFilterParser,
         # TODO: genericize these - can probably extract a _get_column( attr, ... ) or something
         # special cases...special cases everywhere
         def get_filter(attr, op, val):
-            if attr == 'history_content_type' and op == 'eq':
-                if val in ('dataset', 'dataset_collection'):
-                    return sql.column('history_content_type') == val
-                raise_filter_err(attr, op, val, 'bad op in filter')
+            if attr == "history_content_type" and op == "eq":
+                if val in ("dataset", "dataset_collection"):
+                    return sql.column("history_content_type") == val
+                raise_filter_err(attr, op, val, "bad op in filter")
 
-            if attr == 'type_id':
-                if op == 'eq':
-                    return sql.column('type_id') == val
-                if op == 'in':
-                    return sql.column('type_id').in_(self.parse_type_id_list(val))
-                raise_filter_err(attr, op, val, 'bad op in filter')
+            if attr == "type_id":
+                if op == "eq":
+                    return sql.column("type_id") == val
+                if op == "in":
+                    return sql.column("type_id").in_(self.parse_type_id_list(val))
+                raise_filter_err(attr, op, val, "bad op in filter")
 
-            if attr in ('update_time', 'create_time'):
-                if op == 'ge':
+            if attr in ("update_time", "create_time"):
+                if op == "ge":
                     return sql.column(attr) >= self.parse_date(val)
-                if op == 'le':
+                if op == "le":
                     return sql.column(attr) <= self.parse_date(val)
-                if op == 'gt':
+                if op == "gt":
                     return sql.column(attr) > self.parse_date(val)
-                if op == 'lt':
+                if op == "lt":
                     return sql.column(attr) < self.parse_date(val)
-                raise_filter_err(attr, op, val, 'bad op in filter')
+                raise_filter_err(attr, op, val, "bad op in filter")
 
-            if attr == 'state':
+            if attr == "state":
                 valid_states = model.Dataset.states.values()
-                if op == 'eq':
+                if op == "eq":
                     if val not in valid_states:
-                        raise_filter_err(attr, op, val, 'invalid state in filter')
-                    return sql.column('state') == val
-                if op == 'in':
-                    states = [s for s in val.split(',') if s]
+                        raise_filter_err(attr, op, val, "invalid state in filter")
+                    return sql.column("state") == val
+                if op == "in":
+                    states = [s for s in val.split(",") if s]
                     for state in states:
                         if state not in valid_states:
-                            raise_filter_err(attr, op, state, 'invalid state in filter')
-                    return sql.column('state').in_(states)
-                raise_filter_err(attr, op, val, 'bad op in filter')
+                            raise_filter_err(attr, op, state, "invalid state in filter")
+                    return sql.column("state").in_(states)
+                raise_filter_err(attr, op, val, "bad op in filter")
 
         column_filter = get_filter(attr, op, val)
         if column_filter is not None:
-            return self.parsed_filter(filter_type='orm', filter=column_filter)
+            return self.parsed_filter(filter_type="orm", filter=column_filter)
         return super()._parse_orm_filter(attr, op, val)
 
     def decode_type_id(self, type_id):
-        TYPE_ID_SEP = '-'
+        TYPE_ID_SEP = "-"
         split = type_id.split(TYPE_ID_SEP, 1)
         return TYPE_ID_SEP.join((split[0], str(self.app.security.decode_id(split[1]))))
 
-    def parse_type_id_list(self, type_id_list_string, sep=','):
+    def parse_type_id_list(self, type_id_list_string, sep=","):
         """
         Split `type_id_list_string` at `sep`.
         """
@@ -544,15 +564,17 @@ class HistoryContentsFilters(base.ModelFilterParser,
         deletable.PurgableFiltersMixin._add_parsers(self)
         taggable.TaggableFilterMixin._add_parsers(self)
         tools.ToolFilterMixin._add_parsers(self)
-        self.orm_filter_parsers.update({
-            'history_content_type': {'op': ('eq')},
-            'type_id': {'op': ('eq', 'in'), 'val': self.parse_type_id_list},
-            'hid': {'op': ('eq', 'ge', 'le', 'gt', 'lt'), 'val': int},
-            # TODO: needs a different val parser - but no way to add to the above
-            # 'hid-in'        : { 'op': ( 'in' ), 'val': self.parse_int_list },
-            'name': {'op': ('eq', 'contains', 'like')},
-            'state': {'op': ('eq', 'in')},
-            'visible': {'op': ('eq'), 'val': parse_bool},
-            'create_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
-            'update_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
-        })
+        self.orm_filter_parsers.update(
+            {
+                "history_content_type": {"op": ("eq")},
+                "type_id": {"op": ("eq", "in"), "val": self.parse_type_id_list},
+                "hid": {"op": ("eq", "ge", "le", "gt", "lt"), "val": int},
+                # TODO: needs a different val parser - but no way to add to the above
+                # 'hid-in'        : { 'op': ( 'in' ), 'val': self.parse_int_list },
+                "name": {"op": ("eq", "contains", "like")},
+                "state": {"op": ("eq", "in")},
+                "visible": {"op": ("eq"), "val": parse_bool},
+                "create_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
+                "update_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
+            }
+        )
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index df3b83ab97c..35c1b51c451 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -3,21 +3,18 @@ import sqlite3
 
 from sqlalchemy import or_
 
-
 from galaxy import (
     exceptions,
-    model
+    model,
 )
 from galaxy.util.filelock import FileLock
 
-
 log = logging.getLogger(__name__)
 
-DATABASE_TABLE_NAME = 'gxitproxy'
+DATABASE_TABLE_NAME = "gxitproxy"
 
 
 class InteractiveToolSqlite:
-
     def __init__(self, sqlite_filename, encode_id):
         self.sqlite_filename = sqlite_filename
         self.encode_id = encode_id
@@ -27,22 +24,22 @@ class InteractiveToolSqlite:
             conn = sqlite3.connect(self.sqlite_filename)
             try:
                 c = conn.cursor()
-                select = f'''SELECT token, host, port, info
+                select = f"""SELECT token, host, port, info
                             FROM {DATABASE_TABLE_NAME}
-                            WHERE key=? and key_type=?'''
-                c.execute(select, (key, key_type,))
+                            WHERE key=? and key_type=?"""
+                c.execute(
+                    select,
+                    (
+                        key,
+                        key_type,
+                    ),
+                )
                 try:
                     token, host, port, info = c.fetchone()
                 except TypeError:
-                    log.warning('get(): invalid key: %s key_type %s', key, key_type)
+                    log.warning("get(): invalid key: %s key_type %s", key, key_type)
                     return None
-                return dict(
-                    key=key,
-                    key_type=key_type,
-                    token=token,
-                    host=host,
-                    port=port,
-                    info=info)
+                return dict(key=key, key_type=key_type, token=token, host=host, port=port, info=info)
             finally:
                 conn.close()
 
@@ -60,7 +57,8 @@ class InteractiveToolSqlite:
                 c = conn.cursor()
                 try:
                     # Create table
-                    c.execute('''CREATE TABLE %s
+                    c.execute(
+                        """CREATE TABLE %s
                                  (key text,
                                   key_type text,
                                   token text,
@@ -68,22 +66,35 @@ class InteractiveToolSqlite:
                                   port integer,
                                   info text,
                                   PRIMARY KEY (key, key_type)
-                                  )''' % (DATABASE_TABLE_NAME))
+                                  )"""
+                        % (DATABASE_TABLE_NAME)
+                    )
                 except Exception:
                     pass
-                delete = f'''DELETE FROM {DATABASE_TABLE_NAME} WHERE key=? and key_type=?'''
-                c.execute(delete, (key, key_type,))
-                insert = '''INSERT INTO %s
+                delete = f"""DELETE FROM {DATABASE_TABLE_NAME} WHERE key=? and key_type=?"""
+                c.execute(
+                    delete,
+                    (
+                        key,
+                        key_type,
+                    ),
+                )
+                insert = """INSERT INTO %s
                             (key, key_type, token, host, port, info)
-                            VALUES (?, ?, ?, ?, ?, ?)''' % (DATABASE_TABLE_NAME)
-                c.execute(insert,
-                          (key,
-                           key_type,
-                           token,
-                           host,
-                           port,
-                           info,
-                           ))
+                            VALUES (?, ?, ?, ?, ?, ?)""" % (
+                    DATABASE_TABLE_NAME
+                )
+                c.execute(
+                    insert,
+                    (
+                        key,
+                        key_type,
+                        token,
+                        host,
+                        port,
+                        info,
+                    ),
+                )
                 conn.commit()
             finally:
                 conn.close()
@@ -94,12 +105,12 @@ class InteractiveToolSqlite:
         with external resources. Remove entries that match all provided key=values
         """
         assert kwd, ValueError("You must provide some values to key upon")
-        delete = f'DELETE FROM {DATABASE_TABLE_NAME} WHERE'
+        delete = f"DELETE FROM {DATABASE_TABLE_NAME} WHERE"
         value_list = []
         for i, (key, value) in enumerate(kwd.items()):
             if i != 0:
-                delete += ' and'
-            delete += f' {key}=?'
+                delete += " and"
+            delete += f" {key}=?"
             value_list.append(value)
         with FileLock(self.sqlite_filename):
             conn = sqlite3.connect(self.sqlite_filename)
@@ -110,19 +121,24 @@ class InteractiveToolSqlite:
                     # NB: This does not invalidate in-memory caches used by uwsgi (if any)
                     c.execute(delete, tuple(value_list))
                 except Exception as e:
-                    log.debug('Error removing entry (%s): %s', delete, e)
+                    log.debug("Error removing entry (%s): %s", delete, e)
                 conn.commit()
             finally:
                 conn.close()
 
     def save_entry_point(self, entry_point):
-        """Convenience method to easily save an entry_point.
-        """
-        return self.save(self.encode_id(entry_point.id), entry_point.__class__.__name__.lower(), entry_point.token, entry_point.host, entry_point.port, None)
+        """Convenience method to easily save an entry_point."""
+        return self.save(
+            self.encode_id(entry_point.id),
+            entry_point.__class__.__name__.lower(),
+            entry_point.token,
+            entry_point.host,
+            entry_point.port,
+            None,
+        )
 
     def remove_entry_point(self, entry_point):
-        """Convenience method to easily remove an entry_point.
-        """
+        """Convenience method to easily remove an entry_point."""
         return self.remove(key=self.encode_id(entry_point.id), key_type=entry_point.__class__.__name__.lower())
 
 
@@ -142,13 +158,21 @@ class InteractiveToolManager:
     def create_entry_points(self, job, tool, entry_points=None, flush=True):
         entry_points = entry_points or tool.ports
         for entry in entry_points:
-            ep = self.model.InteractiveToolEntryPoint(job=job, tool_port=entry['port'], entry_url=entry['url'], name=entry['name'], requires_domain=entry['requires_domain'])
+            ep = self.model.InteractiveToolEntryPoint(
+                job=job,
+                tool_port=entry["port"],
+                entry_url=entry["url"],
+                name=entry["name"],
+                requires_domain=entry["requires_domain"],
+            )
             self.sa_session.add(ep)
         if flush:
             self.sa_session.flush()
 
     def configure_entry_point(self, job, tool_port=None, host=None, port=None, protocol=None):
-        return self.configure_entry_points(job, {tool_port: dict(tool_port=tool_port, host=host, port=port, protocol=protocol)})
+        return self.configure_entry_points(
+            job, {tool_port: dict(tool_port=tool_port, host=host, port=port, protocol=protocol)}
+        )
 
     def configure_entry_points(self, job, ports_dict):
         # There can be multiple entry points that reference the same tool port (could have different entry URLs)
@@ -160,9 +184,9 @@ class InteractiveToolManager:
                 log.error("Did not find port to assign to InteractiveToolEntryPoint by tool port: %s.", ep.tool_port)
                 not_configured.append(ep)
             else:
-                ep.host = port_dict['host']
-                ep.port = port_dict['port']
-                ep.protocol = port_dict['protocol']
+                ep.host = port_dict["host"]
+                ep.port = port_dict["port"]
+                ep.protocol = port_dict["protocol"]
                 ep.configured = True
                 self.sa_session.add(ep)
                 self.save_entry_point(ep)
@@ -182,13 +206,17 @@ class InteractiveToolManager:
         if job and tool:
             self.create_entry_points(job, tool, entry_points)
         else:
-            log.warning('Called InteractiveToolManager.create_interactivetool, but job (%s) or tool (%s) is None', job, tool)
+            log.warning(
+                "Called InteractiveToolManager.create_interactivetool, but job (%s) or tool (%s) is None", job, tool
+            )
 
     def get_nonterminal_for_user_by_trans(self, trans):
         if trans.user:
             jobs = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.user == trans.user)
         else:
-            jobs = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.session_id == trans.get_galaxy_session().id)
+            jobs = trans.sa_session.query(trans.app.model.Job).filter(
+                trans.app.model.Job.session_id == trans.get_galaxy_session().id
+            )
 
         def build_and_apply_filters(query, objects, filter_func):
             if objects is not None:
@@ -200,8 +228,13 @@ class InteractiveToolManager:
                         t.append(filter_func(obj))
                     query = query.filter(or_(*t))
             return query
-        jobs = build_and_apply_filters(jobs, trans.app.model.Job.non_ready_states, lambda s: trans.app.model.Job.state == s)
-        return trans.sa_session.query(trans.app.model.InteractiveToolEntryPoint).filter(trans.app.model.InteractiveToolEntryPoint.job_id.in_([job.id for job in jobs]))
+
+        jobs = build_and_apply_filters(
+            jobs, trans.app.model.Job.non_ready_states, lambda s: trans.app.model.Job.state == s
+        )
+        return trans.sa_session.query(trans.app.model.InteractiveToolEntryPoint).filter(
+            trans.app.model.InteractiveToolEntryPoint.job_id.in_([job.id for job in jobs])
+        )
 
     def can_access_job(self, trans, job):
         if job:
@@ -230,7 +263,7 @@ class InteractiveToolManager:
         self.remove_entry_point(entry_point)
         job = entry_point.job
         if not job.finished:
-            log.debug('Stopping Job: %s for InteractiveToolEntryPoint: %s', job, entry_point)
+            log.debug("Stopping Job: %s for InteractiveToolEntryPoint: %s", job, entry_point)
             job.mark_stopped(trans.app.config.track_jobs_in_database)
             # This self.job_manager.stop(job) does nothing without changing job.state, manually or e.g. with .mark_deleted()
             self.job_manager.stop(job)
@@ -253,11 +286,11 @@ class InteractiveToolManager:
     def target_if_active(self, trans, entry_point):
         if entry_point.active and not entry_point.deleted:
             request_host = trans.request.host
-            protocol = trans.request.host_url.split('//', 1)[0]
+            protocol = trans.request.host_url.split("//", 1)[0]
             if entry_point.requires_domain:
-                rval = f'{protocol}//{self.get_entry_point_subdomain(trans, entry_point)}.{request_host}/'
+                rval = f"{protocol}//{self.get_entry_point_subdomain(trans, entry_point)}.{request_host}/"
                 if entry_point.entry_url:
-                    rval = '{}/{}'.format(rval.rstrip('/'), entry_point.entry_url.lstrip('/'))
+                    rval = "{}/{}".format(rval.rstrip("/"), entry_point.entry_url.lstrip("/"))
             else:
                 rval = self.get_entry_point_path(trans, entry_point)
 
@@ -269,8 +302,8 @@ class InteractiveToolManager:
         entry_point_prefix = self.app.config.interactivetools_prefix
         entry_point_token = entry_point.token
         if self.app.config.interactivetools_shorten_url:
-            return f'{entry_point_encoded_id}-{entry_point_token[:10]}.{entry_point_prefix}'
-        return f'{entry_point_encoded_id}-{entry_point_token}.{entry_point_class}.{entry_point_prefix}'
+            return f"{entry_point_encoded_id}-{entry_point_token[:10]}.{entry_point_prefix}"
+        return f"{entry_point_encoded_id}-{entry_point_token}.{entry_point_class}.{entry_point_prefix}"
 
     def get_entry_point_path(self, trans, entry_point):
         entry_point_encoded_id = trans.security.encode_id(entry_point.id)
@@ -280,13 +313,13 @@ class InteractiveToolManager:
         if not entry_point.requires_domain:
             rval = str(self.app.config.interactivetools_base_path).rstrip("/").lstrip("/")
             if self.app.config.interactivetools_shorten_url:
-                rval = f'/{rval}/{entry_point_prefix}/{entry_point_encoded_id}/{entry_point.token[:10]}/'
+                rval = f"/{rval}/{entry_point_prefix}/{entry_point_encoded_id}/{entry_point.token[:10]}/"
             else:
-                rval = f'/{rval}/{entry_point_prefix}/access/{entry_point_class}/{entry_point_encoded_id}/{entry_point.token}/'
+                rval = f"/{rval}/{entry_point_prefix}/access/{entry_point_class}/{entry_point_encoded_id}/{entry_point.token}/"
         if entry_point.entry_url:
             rval = f"{rval.rstrip('/')}/{entry_point.entry_url.lstrip('/')}"
         if rval[0] != "/":
-            rval = f'/{rval}'
+            rval = f"/{rval}"
         return rval
 
     def access_entry_point_target(self, trans, entry_point_id):
@@ -295,7 +328,9 @@ class InteractiveToolManager:
             if entry_point.active:
                 return self.target_if_active(trans, entry_point)
             elif entry_point.deleted:
-                raise exceptions.MessageException('InteractiveTool has ended. You will have to start a new one.')
+                raise exceptions.MessageException("InteractiveTool has ended. You will have to start a new one.")
             else:
-                raise exceptions.MessageException('InteractiveTool is not active. If you recently launched this tool it may not be ready yet, please wait a moment and refresh this page.')
+                raise exceptions.MessageException(
+                    "InteractiveTool is not active. If you recently launched this tool it may not be ready yet, please wait a moment and refresh this page."
+                )
         raise exceptions.ItemAccessibilityException("You do not have access to this InteractiveTool entry point.")
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 37cd15debbb..4c7cca0ed4c 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -7,7 +7,12 @@ from pydantic import (
     BaseModel,
     Field,
 )
-from sqlalchemy import and_, false, func, or_
+from sqlalchemy import (
+    and_,
+    false,
+    func,
+    or_,
+)
 from sqlalchemy.orm import aliased
 from sqlalchemy.sql import select
 
@@ -42,10 +47,10 @@ def get_path_key(path_tuple):
     tuple_elements = len(path_tuple)
     for i, p in enumerate(path_tuple):
         if isinstance(p, int):
-            sep = '_'
+            sep = "_"
         else:
-            sep = '|'
-        if i == (tuple_elements - 2) and p == 'values':
+            sep = "|"
+        if i == (tuple_elements - 2) and p == "values":
             # dataset inputs are always wrapped in lists. To avoid 'rep_factorName_0|rep_factorLevel_2|countsFile|values_0',
             # we remove the last 2 items of the path tuple (values and list index)
             return path_key
@@ -57,7 +62,6 @@ def get_path_key(path_tuple):
 
 
 class JobManager:
-
     def __init__(self, app: StructuredApp):
         self.app = app
         self.dataset_manager = DatasetManager(app)
@@ -66,14 +70,20 @@ class JobManager:
         return JobLock(active=self.app.job_manager.job_lock)
 
     def update_job_lock(self, job_lock: JobLock):
-        self.app.queue_worker.send_control_task('admin_job_lock', kwargs={'job_lock': job_lock.active}, get_response=True)
+        self.app.queue_worker.send_control_task(
+            "admin_job_lock", kwargs={"job_lock": job_lock.active}, get_response=True
+        )
         return self.job_lock()
 
     def get_accessible_job(self, trans, decoded_job_id):
         job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
         if job is None:
             raise ObjectNotFound()
-        belongs_to_user = (job.user_id == trans.user.id) if job.user_id and trans.user else (job.session_id == trans.get_galaxy_session().id)
+        belongs_to_user = (
+            (job.user_id == trans.user.id)
+            if job.user_id and trans.user
+            else (job.session_id == trans.get_galaxy_session().id)
+        )
         if not trans.user_is_admin and not belongs_to_user:
             # Check access granted via output datasets.
             if not job.output_datasets:
@@ -96,6 +106,7 @@ class JobManager:
 
 class JobSearch:
     """Search for jobs using tool inputs or other jobs"""
+
     def __init__(
         self,
         sa_session: galaxy_scoped_session,
@@ -110,72 +121,85 @@ class JobSearch:
         self.ldda_manager = ldda_manager
         self.decode_id = id_encoding_helper.decode_id
 
-    def by_tool_input(self, trans, tool_id, tool_version, param=None, param_dump=None, job_state='ok'):
+    def by_tool_input(self, trans, tool_id, tool_version, param=None, param_dump=None, job_state="ok"):
         """Search for jobs producing same results using the 'inputs' part of a tool POST."""
         user = trans.user
         input_data = defaultdict(list)
 
         def populate_input_data_input_id(path, key, value):
             """Traverses expanded incoming using remap and collects input_ids and input_data."""
-            if key == 'id':
+            if key == "id":
                 path_key = get_path_key(path[:-2])
                 current_case = param_dump
                 for p in path:
                     current_case = current_case[p]
-                src = current_case['src']
+                src = current_case["src"]
                 current_case = param
                 for i, p in enumerate(path):
-                    if p == 'values' and i == len(path) - 2:
+                    if p == "values" and i == len(path) - 2:
                         continue
                     if isinstance(current_case, (list, dict)):
                         current_case = current_case[p]
                 identifier = getattr(current_case, "element_identifier", None)
-                input_data[path_key].append({'src': src,
-                                             'id': value,
-                                             'identifier': identifier,
-                                             })
+                input_data[path_key].append(
+                    {
+                        "src": src,
+                        "id": value,
+                        "identifier": identifier,
+                    }
+                )
                 return key, "__id_wildcard__"
             return key, value
 
         wildcard_param_dump = remap(param_dump, visit=populate_input_data_input_id)
-        return self.__search(tool_id=tool_id,
-                             tool_version=tool_version,
-                             user=user,
-                             input_data=input_data,
-                             job_state=job_state,
-                             param_dump=param_dump,
-                             wildcard_param_dump=wildcard_param_dump)
+        return self.__search(
+            tool_id=tool_id,
+            tool_version=tool_version,
+            user=user,
+            input_data=input_data,
+            job_state=job_state,
+            param_dump=param_dump,
+            wildcard_param_dump=wildcard_param_dump,
+        )
 
-    def __search(self, tool_id, tool_version, user, input_data, job_state=None, param_dump=None, wildcard_param_dump=None):
+    def __search(
+        self, tool_id, tool_version, user, input_data, job_state=None, param_dump=None, wildcard_param_dump=None
+    ):
         search_timer = ExecutionTimer()
 
         def replace_dataset_ids(path, key, value):
             """Exchanges dataset_ids (HDA, LDA, HDCA, not Dataset) in param_dump with dataset ids used in job."""
-            if key == 'id':
+            if key == "id":
                 current_case = param_dump
                 for p in path:
                     current_case = current_case[p]
-                src = current_case['src']
+                src = current_case["src"]
                 value = job_input_ids[src][value]
                 return key, value
             return key, value
 
-        job_conditions = [and_(
-            model.Job.tool_id == tool_id,
-            model.Job.user == user,
-            model.Job.copied_from_job_id.is_(None)  # Always pick original job
-        )]
+        job_conditions = [
+            and_(
+                model.Job.tool_id == tool_id,
+                model.Job.user == user,
+                model.Job.copied_from_job_id.is_(None),  # Always pick original job
+            )
+        ]
 
         if tool_version:
             job_conditions.append(model.Job.tool_version == str(tool_version))
 
         if job_state is None:
             job_conditions.append(
-                model.Job.state.in_([model.Job.states.NEW,
-                                     model.Job.states.QUEUED,
-                                     model.Job.states.WAITING,
-                                     model.Job.states.RUNNING,
-                                     model.Job.states.OK])
+                model.Job.state.in_(
+                    [
+                        model.Job.states.NEW,
+                        model.Job.states.QUEUED,
+                        model.Job.states.WAITING,
+                        model.Job.states.RUNNING,
+                        model.Job.states.OK,
+                    ]
+                )
             )
         else:
             if isinstance(job_state, str):
@@ -184,19 +208,17 @@ class JobSearch:
                 o = []
                 for s in job_state:
                     o.append(model.Job.state == s)
-                job_conditions.append(
-                    or_(*o)
-                )
+                job_conditions.append(or_(*o))
 
         for k, v in wildcard_param_dump.items():
             wildcard_value = None
-            if v == {'__class__': 'RuntimeValue'}:
+            if v == {"__class__": "RuntimeValue"}:
                 # TODO: verify this is always None. e.g. run with runtime input input
                 v = None
-            elif k.endswith('|__identifier__'):
+            elif k.endswith("|__identifier__"):
                 # We've taken care of this while constructing the conditions based on ``input_data`` above
                 continue
-            elif k == 'chromInfo' and '?.len' in v:
+            elif k == "chromInfo" and "?.len" in v:
                 continue
                 wildcard_value = '"%?.len"'
             if not wildcard_value:
@@ -204,22 +226,22 @@ class JobSearch:
                 wildcard_value = value_dump.replace('"id": "__id_wildcard__"', '"id": %')
             a = aliased(model.JobParameter)
             if value_dump == wildcard_value:
-                job_conditions.append(and_(
-                    model.Job.id == a.job_id,
-                    a.name == k,
-                    a.value == value_dump,
-                ))
+                job_conditions.append(
+                    and_(
+                        model.Job.id == a.job_id,
+                        a.name == k,
+                        a.value == value_dump,
+                    )
+                )
             else:
-                job_conditions.append(and_(
-                    model.Job.id == a.job_id,
-                    a.name == k,
-                    a.value.like(wildcard_value)
-                ))
+                job_conditions.append(and_(model.Job.id == a.job_id, a.name == k, a.value.like(wildcard_value)))
 
-        job_conditions.append(and_(
-            model.Job.any_output_dataset_collection_instances_deleted == false(),
-            model.Job.any_output_dataset_deleted == false()
-        ))
+        job_conditions.append(
+            and_(
+                model.Job.any_output_dataset_collection_instances_deleted == false(),
+                model.Job.any_output_dataset_deleted == false(),
+            )
+        )
 
         subq = self.sa_session.query(model.Job.id).filter(*job_conditions).subquery()
         data_conditions = []
@@ -234,14 +256,14 @@ class JobSearch:
         for k, input_list in input_data.items():
             # k will be matched against the JobParameter.name column. This can be prefixed depending on whethter
             # the input is in a repeat, or not (section and conditional)
-            k = {k, k.split('|')[-1]}
+            k = {k, k.split("|")[-1]}
             for type_values in input_list:
-                t = type_values['src']
-                v = type_values['id']
+                t = type_values["src"]
+                v = type_values["id"]
                 requested_ids.append(v)
                 data_types.append(t)
-                identifier = type_values['identifier']
-                if t == 'hda':
+                identifier = type_values["identifier"]
+                if t == "hda":
                     a = aliased(model.JobToInputDatasetAssociation)
                     b = aliased(model.HistoryDatasetAssociation)
                     c = aliased(model.HistoryDatasetAssociation)
@@ -252,86 +274,105 @@ class JobSearch:
                     )
                     name_condition = []
                     if identifier:
-                        data_conditions.append(and_(model.Job.id == d.job_id,
-                                             d.name.in_({f"{_}|__identifier__" for _ in k}),
-                                             d.value == json.dumps(identifier)))
+                        data_conditions.append(
+                            and_(
+                                model.Job.id == d.job_id,
+                                d.name.in_({f"{_}|__identifier__" for _ in k}),
+                                d.value == json.dumps(identifier),
+                            )
+                        )
                     else:
                         stmt = stmt.where(e.name == c.name)
                         name_condition.append(b.name == c.name)
-                    stmt = stmt.where(
-                        e.extension == c.extension,
-                    ).where(
-                        a.dataset_version == e.version,
-                    ).where(
-                        e._metadata == c._metadata,
+                    stmt = (
+                        stmt.where(
+                            e.extension == c.extension,
+                        )
+                        .where(
+                            a.dataset_version == e.version,
+                        )
+                        .where(
+                            e._metadata == c._metadata,
+                        )
+                    )
+                    data_conditions.append(
+                        and_(
+                            a.name.in_(k),
+                            a.dataset_id == b.id,  # b is the HDA used for the job
+                            c.dataset_id == b.dataset_id,
+                            c.id == v,  # c is the requested job input HDA
+                            # We need to make sure that the job we are looking for has been run with identical inputs.
+                            # Here we deal with 3 requirements:
+                            #  - the jobs' input dataset (=b) version is 0, meaning the job's input dataset is not yet ready
+                            #  - b's update_time is older than the job create time, meaning no changes occurred
+                            #  - the job has a dataset_version recorded, and that versions' metadata matches c's metadata.
+                            or_(
+                                and_(
+                                    or_(a.dataset_version.in_([0, b.version]), b.update_time < model.Job.create_time),
+                                    b.extension == c.extension,
+                                    b.metadata == c.metadata,
+                                    *name_condition,
+                                ),
+                                b.id.in_(stmt),
+                            ),
+                            or_(b.deleted == false(), c.deleted == false()),
+                        )
                     )
-                    data_conditions.append(and_(
-                        a.name.in_(k),
-                        a.dataset_id == b.id,  # b is the HDA used for the job
-                        c.dataset_id == b.dataset_id,
-                        c.id == v,  # c is the requested job input HDA
-                        # We need to make sure that the job we are looking for has been run with identical inputs.
-                        # Here we deal with 3 requirements:
-                        #  - the jobs' input dataset (=b) version is 0, meaning the job's input dataset is not yet ready
-                        #  - b's update_time is older than the job create time, meaning no changes occurred
-                        #  - the job has a dataset_version recorded, and that versions' metadata matches c's metadata.
-                        or_(
-                            and_(or_(a.dataset_version.in_([0, b.version]),
-                                     b.update_time < model.Job.create_time),
-                                 b.extension == c.extension,
-                                 b.metadata == c.metadata,
-                                 *name_condition,
-                                 ),
-                            b.id.in_(stmt)
-                        ),
-                        or_(b.deleted == false(), c.deleted == false())
-
-                    ))
 
                     used_ids.append(a.dataset_id)
-                elif t == 'ldda':
+                elif t == "ldda":
                     a = aliased(model.JobToInputLibraryDatasetAssociation)
-                    data_conditions.append(and_(
-                        model.Job.id == a.job_id,
-                        a.name.in_(k),
-                        a.ldda_id == v
-                    ))
+                    data_conditions.append(and_(model.Job.id == a.job_id, a.name.in_(k), a.ldda_id == v))
                     used_ids.append(a.ldda_id)
-                elif t == 'hdca':
+                elif t == "hdca":
                     a = aliased(model.JobToInputDatasetCollectionAssociation)
                     b = aliased(model.HistoryDatasetCollectionAssociation)
                     c = aliased(model.HistoryDatasetCollectionAssociation)
-                    data_conditions.append(and_(
-                        model.Job.id == a.job_id,
-                        a.name.in_(k),
-                        b.id == a.dataset_collection_id,
-                        c.id == v,
-                        b.name == c.name,
-                        or_(and_(b.deleted == false(), b.id == v),
-                            and_(or_(c.copied_from_history_dataset_collection_association_id == b.id,
-                                     b.copied_from_history_dataset_collection_association_id == c.id),
-                                 c.deleted == false(),
-                                 )
-                            )
-                    ))
+                    data_conditions.append(
+                        and_(
+                            model.Job.id == a.job_id,
+                            a.name.in_(k),
+                            b.id == a.dataset_collection_id,
+                            c.id == v,
+                            b.name == c.name,
+                            or_(
+                                and_(b.deleted == false(), b.id == v),
+                                and_(
+                                    or_(
+                                        c.copied_from_history_dataset_collection_association_id == b.id,
+                                        b.copied_from_history_dataset_collection_association_id == c.id,
+                                    ),
+                                    c.deleted == false(),
+                                ),
+                            ),
+                        )
+                    )
                     used_ids.append(a.dataset_collection_id)
-                elif t == 'dce':
+                elif t == "dce":
                     a = aliased(model.JobToInputDatasetCollectionElementAssociation)
                     b = aliased(model.DatasetCollectionElement)
                     c = aliased(model.DatasetCollectionElement)
-                    data_conditions.append(and_(
-                        model.Job.id == a.job_id,
-                        a.name.in_(k),
-                        a.dataset_collection_element_id == b.id,
-                        b.element_identifier == c.element_identifier,
-                        c.child_collection_id == b.child_collection_id,
-                        c.id == v,
-                    ))
+                    data_conditions.append(
+                        and_(
+                            model.Job.id == a.job_id,
+                            a.name.in_(k),
+                            a.dataset_collection_element_id == b.id,
+                            b.element_identifier == c.element_identifier,
+                            c.child_collection_id == b.child_collection_id,
+                            c.id == v,
+                        )
+                    )
                     used_ids.append(a.dataset_collection_element_id)
                 else:
                     return []
 
-        query = self.sa_session.query(model.Job.id, *used_ids).join(subq, model.Job.id == subq.c.id).filter(*data_conditions).group_by(model.Job.id, *used_ids).order_by(model.Job.id.desc())
+        query = (
+            self.sa_session.query(model.Job.id, *used_ids)
+            .join(subq, model.Job.id == subq.c.id)
+            .filter(*data_conditions)
+            .group_by(model.Job.id, *used_ids)
+            .order_by(model.Job.id.desc())
+        )
         for job in query:
             # We found a job that is equal in terms of tool_id, user, state and input datasets,
             # but to be able to verify that the parameters match we need to modify all instances of
@@ -351,23 +392,21 @@ class JobSearch:
                 # new_param_dump has its dataset ids remapped to those used by the job.
                 # We now ask if the remapped job parameters match the current job.
                 for k, v in new_param_dump.items():
-                    if v == {'__class__': 'RuntimeValue'}:
+                    if v == {"__class__": "RuntimeValue"}:
                         # TODO: verify this is always None. e.g. run with runtime input input
                         v = None
-                    elif k.endswith('|__identifier__'):
+                    elif k.endswith("|__identifier__"):
                         # We've taken care of this while constructing the conditions based on ``input_data`` above
                         continue
-                    elif k == 'chromInfo' and '?.len' in v:
+                    elif k == "chromInfo" and "?.len" in v:
                         continue
                         wildcard_value = '"%?.len"'
                     if not wildcard_value:
                         wildcard_value = json.dumps(v, sort_keys=True).replace('"id": "__id_wildcard__"', '"id": %')
                     a = aliased(model.JobParameter)
-                    job_parameter_conditions.append(and_(
-                        model.Job.id == a.job_id,
-                        a.name == k,
-                        a.value == json.dumps(v, sort_keys=True)
-                    ))
+                    job_parameter_conditions.append(
+                        and_(model.Job.id == a.job_id, a.name == k, a.value == json.dumps(v, sort_keys=True))
+                    )
             else:
                 job_parameter_conditions = [model.Job.id == job]
             query = self.sa_session.query(model.Job).filter(*job_parameter_conditions)
@@ -382,10 +421,14 @@ class JobSearch:
             for parameter in job.parameters:
                 if parameter.name.startswith("__"):
                     continue
-                if parameter.name in {'chromInfo', 'dbkey'} or parameter.name.endswith('|__identifier__'):
+                if parameter.name in {"chromInfo", "dbkey"} or parameter.name.endswith("|__identifier__"):
                     continue
                 n_parameters += 1
-            if not n_parameters == sum(1 for k in param_dump if not k.startswith('__') and not k.endswith('|__identifier__') and k not in {'chromInfo', 'dbkey'}):
+            if not n_parameters == sum(
+                1
+                for k in param_dump
+                if not k.startswith("__") and not k.endswith("|__identifier__") and k not in {"chromInfo", "dbkey"}
+            ):
                 continue
             log.info("Found equivalent job %s", search_timer)
             return job
@@ -395,44 +438,48 @@ class JobSearch:
 
 def view_show_job(trans, job, full: bool) -> typing.Dict:
     is_admin = trans.user_is_admin
-    job_dict = trans.app.security.encode_all_ids(job.to_dict('element', system_details=is_admin), True)
-    if trans.app.config.expose_dataset_path and 'command_line' not in job_dict:
-        job_dict['command_line'] = job.command_line
+    job_dict = trans.app.security.encode_all_ids(job.to_dict("element", system_details=is_admin), True)
+    if trans.app.config.expose_dataset_path and "command_line" not in job_dict:
+        job_dict["command_line"] = job.command_line
     if full:
-        job_dict.update(dict(
-            tool_stdout=job.tool_stdout,
-            tool_stderr=job.tool_stderr,
-            job_stdout=job.job_stdout,
-            job_stderr=job.job_stderr,
-            stderr=job.stderr,
-            stdout=job.stdout,
-            job_messages=job.job_messages,
-            dependencies=job.dependencies
-        ))
+        job_dict.update(
+            dict(
+                tool_stdout=job.tool_stdout,
+                tool_stderr=job.tool_stderr,
+                job_stdout=job.job_stdout,
+                job_stderr=job.job_stderr,
+                stderr=job.stderr,
+                stdout=job.stdout,
+                job_messages=job.job_messages,
+                dependencies=job.dependencies,
+            )
+        )
 
         if is_admin:
-            job_dict['user_email'] = job.get_user_email()
-            job_dict['job_metrics'] = summarize_job_metrics(trans, job)
+            job_dict["user_email"] = job.get_user_email()
+            job_dict["job_metrics"] = summarize_job_metrics(trans, job)
     return job_dict
 
 
 def invocation_job_source_iter(sa_session, invocation_id):
     # TODO: Handle subworkflows.
-    join = model.WorkflowInvocationStep.table.join(
-        model.WorkflowInvocation
-    )
-    statement = select(
-        [model.WorkflowInvocationStep.job_id, model.WorkflowInvocationStep.implicit_collection_jobs_id, model.WorkflowInvocationStep.state]
-    ).select_from(
-        join
-    ).where(
-        model.WorkflowInvocation.id == invocation_id
+    join = model.WorkflowInvocationStep.table.join(model.WorkflowInvocation)
+    statement = (
+        select(
+            [
+                model.WorkflowInvocationStep.job_id,
+                model.WorkflowInvocationStep.implicit_collection_jobs_id,
+                model.WorkflowInvocationStep.state,
+            ]
+        )
+        .select_from(join)
+        .where(model.WorkflowInvocation.id == invocation_id)
     )
     for row in sa_session.execute(statement):
         if row[0]:
-            yield ('Job', row[0], row[2])
+            yield ("Job", row[0], row[2])
         if row[1]:
-            yield ('ImplicitCollectionJobs', row[1], row[2])
+            yield ("ImplicitCollectionJobs", row[1], row[2])
 
 
 def fetch_job_states(sa_session, job_source_ids, job_source_types):
@@ -440,7 +487,9 @@ def fetch_job_states(sa_session, job_source_ids, job_source_types):
     job_ids = set()
     implicit_collection_job_ids = set()
     workflow_invocations_job_sources = {}
-    workflow_invocation_states = {}  # should be set before we walk step states to be conservative on whether things are done expanding yet
+    workflow_invocation_states = (
+        {}
+    )  # should be set before we walk step states to be conservative on whether things are done expanding yet
 
     for job_source_id, job_source_type in zip(job_source_ids, job_source_types):
         if job_source_type == "Job":
@@ -451,8 +500,14 @@ def fetch_job_states(sa_session, job_source_ids, job_source_types):
             invocation_state = sa_session.query(model.WorkflowInvocation).get(job_source_id).state
             workflow_invocation_states[job_source_id] = invocation_state
             workflow_invocation_job_sources = []
-            for (invocation_step_source_type, invocation_step_source_id, invocation_step_state) in invocation_job_source_iter(sa_session, job_source_id):
-                workflow_invocation_job_sources.append((invocation_step_source_type, invocation_step_source_id, invocation_step_state))
+            for (
+                invocation_step_source_type,
+                invocation_step_source_id,
+                invocation_step_state,
+            ) in invocation_job_source_iter(sa_session, job_source_id):
+                workflow_invocation_job_sources.append(
+                    (invocation_step_source_type, invocation_step_source_id, invocation_step_state)
+                )
                 if invocation_step_source_type == "Job":
                     job_ids.add(invocation_step_source_id)
                 elif invocation_step_source_type == "ImplicitCollectionJobs":
@@ -467,7 +522,9 @@ def fetch_job_states(sa_session, job_source_ids, job_source_types):
     for job_id in job_ids:
         job_summaries[job_id] = summarize_jobs_to_dict(sa_session, sa_session.query(model.Job).get(job_id))
     for implicit_collection_jobs_id in implicit_collection_job_ids:
-        implicit_collection_jobs_summaries[implicit_collection_jobs_id] = summarize_jobs_to_dict(sa_session, sa_session.query(model.ImplicitCollectionJobs).get(implicit_collection_jobs_id))
+        implicit_collection_jobs_summaries[implicit_collection_jobs_id] = summarize_jobs_to_dict(
+            sa_session, sa_session.query(model.ImplicitCollectionJobs).get(implicit_collection_jobs_id)
+        )
 
     rval = []
     for job_source_id, job_source_type in zip(job_source_ids, job_source_types):
@@ -480,18 +537,34 @@ def fetch_job_states(sa_session, job_source_ids, job_source_types):
             invocation_job_summaries = []
             invocation_implicit_collection_job_summaries = []
             invocation_step_states = []
-            for (invocation_step_source_type, invocation_step_source_id, invocation_step_state) in workflow_invocations_job_sources[job_source_id]:
+            for (
+                invocation_step_source_type,
+                invocation_step_source_id,
+                invocation_step_state,
+            ) in workflow_invocations_job_sources[job_source_id]:
                 invocation_step_states.append(invocation_step_state)
                 if invocation_step_source_type == "Job":
                     invocation_job_summaries.append(job_summaries[invocation_step_source_id])
                 else:
-                    invocation_implicit_collection_job_summaries.append(implicit_collection_jobs_summaries[invocation_step_source_id])
-            rval.append(summarize_invocation_jobs(job_source_id, invocation_job_summaries, invocation_implicit_collection_job_summaries, invocation_state, invocation_step_states))
+                    invocation_implicit_collection_job_summaries.append(
+                        implicit_collection_jobs_summaries[invocation_step_source_id]
+                    )
+            rval.append(
+                summarize_invocation_jobs(
+                    job_source_id,
+                    invocation_job_summaries,
+                    invocation_implicit_collection_job_summaries,
+                    invocation_state,
+                    invocation_step_states,
+                )
+            )
 
     return rval
 
 
-def summarize_invocation_jobs(invocation_id, job_summaries, implicit_collection_job_summaries, invocation_state, invocation_step_states):
+def summarize_invocation_jobs(
+    invocation_id, job_summaries, implicit_collection_job_summaries, invocation_state, invocation_step_states
+):
     states = {}
     if invocation_state == "scheduled":
         all_scheduled = True
@@ -567,14 +640,11 @@ def summarize_jobs_to_dict(sa_session, jobs_source):
             join = model.ImplicitCollectionJobs.table.join(
                 model.ImplicitCollectionJobsJobAssociation.table.join(model.Job)
             )
-            statement = select(
-                [model.Job.state, func.count("*")]
-            ).select_from(
-                join
-            ).where(
-                model.ImplicitCollectionJobs.id == jobs_source.id
-            ).group_by(
-                model.Job.state
+            statement = (
+                select([model.Job.state, func.count("*")])
+                .select_from(join)
+                .where(model.ImplicitCollectionJobs.id == jobs_source.id)
+                .group_by(model.Job.state)
             )
             for row in sa_session.execute(statement):
                 states[row[0]] = row[1]
@@ -604,7 +674,7 @@ def summarize_job_metrics(trans, job):
             raw_value=str(metric_value),
         )
 
-    metrics = [m for m in job.metrics if m.plugin != 'env' or trans.user_is_admin]
+    metrics = [m for m in job.metrics if m.plugin != "env" or trans.user_is_admin]
     return list(map(metric_to_dict, metrics))
 
 
@@ -615,9 +685,11 @@ def summarize_destination_params(trans, job):
     represented by the trans parameter.
     """
 
-    destination_params = {'Runner': job.job_runner_name,
-                          'Runner Job ID': job.job_runner_external_id,
-                          'Handler': job.handler}
+    destination_params = {
+        "Runner": job.job_runner_name,
+        "Runner Job ID": job.job_runner_external_id,
+        "Handler": job.handler,
+    }
     job_destination_params = job.destination_params
     if job_destination_params:
         destination_params.update(job_destination_params)
@@ -630,6 +702,7 @@ def summarize_job_parameters(trans, job):
     Precondition: the caller has verified the job is accessible to the user
     represented by the trans parameter.
     """
+
     def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None):
         if upgrade_messages is None:
             upgrade_messages = {}
@@ -644,21 +717,50 @@ def summarize_job_parameters(trans, job):
                 elif input.type == "section":
                     # Get the value of the current Section parameter
                     rval.append(dict(text=input.name, depth=depth))
-                    rval.extend(inputs_recursive(input.inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name)))
+                    rval.extend(
+                        inputs_recursive(
+                            input.inputs,
+                            param_values[input.name],
+                            depth=depth + 1,
+                            upgrade_messages=upgrade_messages.get(input.name),
+                        )
+                    )
                 elif input.type == "conditional":
                     try:
-                        current_case = param_values[input.name]['__current_case__']
+                        current_case = param_values[input.name]["__current_case__"]
                         is_valid = True
                     except Exception:
                         current_case = None
                         is_valid = False
                     if is_valid:
-                        rval.append(dict(text=input.test_param.label, depth=depth, value=input.cases[current_case].value))
-                        rval.extend(inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name)))
+                        rval.append(
+                            dict(text=input.test_param.label, depth=depth, value=input.cases[current_case].value)
+                        )
+                        rval.extend(
+                            inputs_recursive(
+                                input.cases[current_case].inputs,
+                                param_values[input.name],
+                                depth=depth + 1,
+                                upgrade_messages=upgrade_messages.get(input.name),
+                            )
+                        )
                     else:
-                        rval.append(dict(text=input.name, depth=depth, notes="The previously used value is no longer valid.", error=True))
+                        rval.append(
+                            dict(
+                                text=input.name,
+                                depth=depth,
+                                notes="The previously used value is no longer valid.",
+                                error=True,
+                            )
+                        )
                 elif input.type == "upload_dataset":
-                    rval.append(dict(text=input.group_title(param_values), depth=depth, value=f"{len(param_values[input.name])} uploaded datasets"))
+                    rval.append(
+                        dict(
+                            text=input.group_title(param_values),
+                            depth=depth,
+                            value=f"{len(param_values[input.name])} uploaded datasets",
+                        )
+                    )
                 elif input.type == "data":
                     value = []
                     for element in listify(param_values[input.name]):
@@ -667,11 +769,13 @@ def summarize_job_parameters(trans, job):
                             hda = element
                             value.append({"src": "hda", "id": encoded_id, "hid": hda.hid, "name": hda.name})
                         elif isinstance(element, model.DatasetCollectionElement):
-                            value.append({'src': "dce", "id": encoded_id, "name": element.element_identifier})
+                            value.append({"src": "dce", "id": encoded_id, "name": element.element_identifier})
                         elif isinstance(element, model.HistoryDatasetCollectionAssociation):
                             value.append({"src": "hdca", "id": encoded_id, "hid": element.hid, "name": element.name})
                         else:
-                            raise Exception(f"Unhandled data input parameter type encountered {element.__class__.__name__}")
+                            raise Exception(
+                                f"Unhandled data input parameter type encountered {element.__class__.__name__}"
+                            )
                     rval.append(dict(text=input.label, depth=depth, value=value))
                 elif input.visible:
                     if hasattr(input, "label") and input.label:
@@ -679,7 +783,14 @@ def summarize_job_parameters(trans, job):
                     else:
                         # value for label not required, fallback to input name (same as tool panel)
                         label = input.name
-                    rval.append(dict(text=label, depth=depth, value=input.value_to_display_text(param_values[input.name]), notes=upgrade_messages.get(input.name, '')))
+                    rval.append(
+                        dict(
+                            text=label,
+                            depth=depth,
+                            value=input.value_to_display_text(param_values[input.name]),
+                            notes=upgrade_messages.get(input.name, ""),
+                        )
+                    )
             else:
                 # Parameter does not have a stored value.
                 # Get parameter label.
@@ -689,7 +800,9 @@ def summarize_job_parameters(trans, job):
                     label = input.label()
                 else:
                     label = input.label or input.name
-                rval.append(dict(text=label, depth=depth, notes="not used (parameter was added after this job was run)"))
+                rval.append(
+                    dict(text=label, depth=depth, notes="not used (parameter was added after this job was run)")
+                )
 
         return rval
 
@@ -710,15 +823,19 @@ def summarize_job_parameters(trans, job):
         except Exception:
             params_objects = job.get_param_values(app, ignore_errors=True)
             # use different param_objects in the following line, since we want to display original values as much as possible
-            upgrade_messages = tool.check_and_update_param_values(job.get_param_values(app, ignore_errors=True),
-                                                                  trans,
-                                                                  update_values=False)
+            upgrade_messages = tool.check_and_update_param_values(
+                job.get_param_values(app, ignore_errors=True), trans, update_values=False
+            )
             has_parameter_errors = True
         parameters = inputs_recursive(tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages)
     else:
         has_parameter_errors = True
 
-    return {"parameters": parameters, "has_parameter_errors": has_parameter_errors, 'outputs': summarize_job_outputs(job=job, tool=tool, params=params_objects, security=trans.security)}
+    return {
+        "parameters": parameters,
+        "has_parameter_errors": has_parameter_errors,
+        "outputs": summarize_job_outputs(job=job, tool=tool, params=params_objects, security=trans.security),
+    }
 
 
 def get_output_name(tool, output, params):
@@ -736,16 +853,23 @@ def summarize_job_outputs(job: model.Job, tool, params, security):
     outputs = defaultdict(list)
     output_labels = {}
     possible_outputs = (
-        ('hda', 'dataset_id', job.output_datasets),
-        ('ldda', 'ldda_id', job.output_library_datasets),
-        ('hdca', 'dataset_collection_id', job.output_dataset_collection_instances),
+        ("hda", "dataset_id", job.output_datasets),
+        ("ldda", "ldda_id", job.output_library_datasets),
+        ("hdca", "dataset_collection_id", job.output_dataset_collection_instances),
     )
     for src, attribute, output_associations in possible_outputs:
         for output_association in output_associations:
             output_name = output_association.name
             if output_name not in output_labels and tool:
-                tool_output = tool.output_collections if src == 'hdca' else tool.outputs
-                output_labels[output_name] = get_output_name(tool=tool, output=tool_output.get(output_name), params=params)
+                tool_output = tool.output_collections if src == "hdca" else tool.outputs
+                output_labels[output_name] = get_output_name(
+                    tool=tool, output=tool_output.get(output_name), params=params
+                )
             label = output_labels.get(output_name)
-            outputs[output_name].append({'label': label, 'value': {'src': src, 'id': security.encode_id(getattr(output_association, attribute))}})
+            outputs[output_name].append(
+                {
+                    "label": label,
+                    "value": {"src": src, "id": security.encode_id(getattr(output_association, attribute))},
+                }
+            )
     return outputs
diff --git a/lib/galaxy/managers/lddas.py b/lib/galaxy/managers/lddas.py
index 7de07fd38a3..8d08e67c87d 100644
--- a/lib/galaxy/managers/lddas.py
+++ b/lib/galaxy/managers/lddas.py
@@ -12,6 +12,7 @@ class LDDAManager(DatasetAssociationManager):
     """
     A fairly sparse manager for LDDAs.
     """
+
     model_class = model.LibraryDatasetDatasetAssociation
 
     def __init__(self, app: MinimalManagerApp):
@@ -21,10 +22,9 @@ class LDDAManager(DatasetAssociationManager):
         super().__init__(app)
 
     def get(self, trans, id, check_accessible=True):
-        return manager_base.get_object(trans, id,
-                                       'LibraryDatasetDatasetAssociation',
-                                       check_ownership=False,
-                                       check_accessible=check_accessible)
+        return manager_base.get_object(
+            trans, id, "LibraryDatasetDatasetAssociation", check_ownership=False, check_accessible=check_accessible
+        )
 
     def _set_permissions(self, trans, library_dataset, role_ids_dict):
         # Check Git history for an older broken implementation, but it was broken
diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py
index 1aedd9e0fb5..71eba2d361c 100644
--- a/lib/galaxy/managers/libraries.py
+++ b/lib/galaxy/managers/libraries.py
@@ -2,17 +2,21 @@
 Manager and Serializer for libraries.
 """
 import logging
-from typing import (
-    Optional,
+from typing import Optional
+
+from sqlalchemy import (
+    and_,
+    false,
+    not_,
+    or_,
+    true,
+)
+from sqlalchemy.orm.exc import (
+    MultipleResultsFound,
+    NoResultFound,
 )
 
-from sqlalchemy import and_, false, not_, or_, true
-from sqlalchemy.orm.exc import MultipleResultsFound
-from sqlalchemy.orm.exc import NoResultFound
-
-from galaxy import (
-    exceptions,
-)
+from galaxy import exceptions
 from galaxy.managers.folders import FolderManager
 from galaxy.util import (
     pretty_print_time_interval,
@@ -41,25 +45,29 @@ class LibraryManager:
         :rtype:     galaxy.model.Library
         """
         try:
-            library = trans.sa_session.query(trans.app.model.Library).filter(trans.app.model.Library.table.c.id == decoded_library_id).one()
+            library = (
+                trans.sa_session.query(trans.app.model.Library)
+                .filter(trans.app.model.Library.table.c.id == decoded_library_id)
+                .one()
+            )
         except MultipleResultsFound:
-            raise exceptions.InconsistentDatabase('Multiple libraries found with the same id.')
+            raise exceptions.InconsistentDatabase("Multiple libraries found with the same id.")
         except NoResultFound:
-            raise exceptions.RequestParameterInvalidException('No library found with the id provided.')
+            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
         except Exception as e:
             raise exceptions.InternalServerError(f"Error loading from the database.{unicodify(e)}")
         library = self.secure(trans, library, check_accessible)
         return library
 
-    def create(self, trans, name, description='', synopsis=''):
+    def create(self, trans, name, description="", synopsis=""):
         """
         Create a new library.
         """
         if not trans.user_is_admin:
-            raise exceptions.ItemAccessibilityException('Only administrators can create libraries.')
+            raise exceptions.ItemAccessibilityException("Only administrators can create libraries.")
         else:
             library = trans.app.model.Library(name=name, description=description, synopsis=synopsis)
-            root_folder = trans.app.model.LibraryFolder(name=name, description='')
+            root_folder = trans.app.model.LibraryFolder(name=name, description="")
             library.root_folder = root_folder
             trans.sa_session.add_all((library, root_folder))
             trans.sa_session.flush()
@@ -77,7 +85,7 @@ class LibraryManager:
             if not user_can_modify:
                 raise exceptions.ItemAccessibilityException("You don't have permission update libraries.")
         if library.deleted:
-            raise exceptions.RequestParameterInvalidException('You cannot modify a deleted library. Undelete it first.')
+            raise exceptions.RequestParameterInvalidException("You cannot modify a deleted library. Undelete it first.")
         if name is not None:
             library.name = name
             changed = True
@@ -100,7 +108,7 @@ class LibraryManager:
         Mark given library deleted/undeleted based on the flag.
         """
         if not trans.user_is_admin:
-            raise exceptions.ItemAccessibilityException('Only administrators can delete and undelete libraries.')
+            raise exceptions.ItemAccessibilityException("Only administrators can delete and undelete libraries.")
         if undelete:
             library.deleted = False
         else:
@@ -127,11 +135,15 @@ class LibraryManager:
         is_admin = trans.user_is_admin
         query = trans.sa_session.query(trans.app.model.Library)
         library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action
-        restricted_library_ids = {lp.library_id for lp in (
-            trans.sa_session.query(trans.model.LibraryPermissions).filter(
-                trans.model.LibraryPermissions.table.c.action == library_access_action
-            ).distinct())}
-        prefetched_ids = {'restricted_library_ids': restricted_library_ids}
+        restricted_library_ids = {
+            lp.library_id
+            for lp in (
+                trans.sa_session.query(trans.model.LibraryPermissions)
+                .filter(trans.model.LibraryPermissions.table.c.action == library_access_action)
+                .distinct()
+            )
+        }
+        prefetched_ids = {"restricted_library_ids": restricted_library_ids}
         if is_admin:
             if deleted is None:
                 #  Flag is not specified, do not filter on it.
@@ -147,7 +159,9 @@ class LibraryManager:
             else:
                 query = query.filter(trans.app.model.Library.table.c.deleted == false())
                 current_user_role_ids = [role.id for role in trans.get_current_user_roles()]
-                all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids))
+                all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(
+                    trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids)
+                )
                 library_add_action = trans.app.security_agent.permitted_actions.LIBRARY_ADD.action
                 library_modify_action = trans.app.security_agent.permitted_actions.LIBRARY_MODIFY.action
                 library_manage_action = trans.app.security_agent.permitted_actions.LIBRARY_MANAGE.action
@@ -164,13 +178,15 @@ class LibraryManager:
                         allowed_library_modify_ids.add(action.library_id)
                     if action.action == library_manage_action:
                         allowed_library_manage_ids.add(action.library_id)
-                query = query.filter(or_(
-                    not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
-                    trans.model.Library.table.c.id.in_(accessible_restricted_library_ids)
-                ))
-                prefetched_ids['allowed_library_add_ids'] = allowed_library_add_ids
-                prefetched_ids['allowed_library_modify_ids'] = allowed_library_modify_ids
-                prefetched_ids['allowed_library_manage_ids'] = allowed_library_manage_ids
+                query = query.filter(
+                    or_(
+                        not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
+                        trans.model.Library.table.c.id.in_(accessible_restricted_library_ids),
+                    )
+                )
+                prefetched_ids["allowed_library_add_ids"] = allowed_library_add_ids
+                prefetched_ids["allowed_library_modify_ids"] = allowed_library_modify_ids
+                prefetched_ids["allowed_library_manage_ids"] = allowed_library_manage_ids
         return query, prefetched_ids
 
     def secure(self, trans, library, check_accessible=True):
@@ -197,9 +213,9 @@ class LibraryManager:
         Check whether the library is accessible to current user.
         """
         if not trans.app.security_agent.can_access_library(trans.get_current_user_roles(), library):
-            raise exceptions.ObjectNotFound('Library with the id provided was not found.')
+            raise exceptions.ObjectNotFound("Library with the id provided was not found.")
         elif library.deleted:
-            raise exceptions.ObjectNotFound('Library with the id provided is deleted.')
+            raise exceptions.ObjectNotFound("Library with the id provided is deleted.")
         else:
             return library
 
@@ -218,27 +234,41 @@ class LibraryManager:
         :returns:   dict with data about the library
         :rtype:     dictionary
         """
-        restricted_library_ids = prefetched_ids.get('restricted_library_ids', None) if prefetched_ids else None
-        allowed_library_add_ids = prefetched_ids.get('allowed_library_add_ids', None) if prefetched_ids else None
-        allowed_library_modify_ids = prefetched_ids.get('allowed_library_modify_ids', None) if prefetched_ids else None
-        allowed_library_manage_ids = prefetched_ids.get('allowed_library_manage_ids', None) if prefetched_ids else None
-        library_dict = library.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id})
-        library_dict['public'] = False if (restricted_library_ids and library.id in restricted_library_ids) else True
-        library_dict['create_time_pretty'] = pretty_print_time_interval(library.create_time, precise=True)
+        restricted_library_ids = prefetched_ids.get("restricted_library_ids", None) if prefetched_ids else None
+        allowed_library_add_ids = prefetched_ids.get("allowed_library_add_ids", None) if prefetched_ids else None
+        allowed_library_modify_ids = prefetched_ids.get("allowed_library_modify_ids", None) if prefetched_ids else None
+        allowed_library_manage_ids = prefetched_ids.get("allowed_library_manage_ids", None) if prefetched_ids else None
+        library_dict = library.to_dict(
+            view="element", value_mapper={"id": trans.security.encode_id, "root_folder_id": trans.security.encode_id}
+        )
+        library_dict["public"] = False if (restricted_library_ids and library.id in restricted_library_ids) else True
+        library_dict["create_time_pretty"] = pretty_print_time_interval(library.create_time, precise=True)
         if not trans.user_is_admin:
             if prefetched_ids:
-                library_dict['can_user_add'] = True if (allowed_library_add_ids and library.id in allowed_library_add_ids) else False
-                library_dict['can_user_modify'] = True if (allowed_library_modify_ids and library.id in allowed_library_modify_ids) else False
-                library_dict['can_user_manage'] = True if (allowed_library_manage_ids and library.id in allowed_library_manage_ids) else False
+                library_dict["can_user_add"] = (
+                    True if (allowed_library_add_ids and library.id in allowed_library_add_ids) else False
+                )
+                library_dict["can_user_modify"] = (
+                    True if (allowed_library_modify_ids and library.id in allowed_library_modify_ids) else False
+                )
+                library_dict["can_user_manage"] = (
+                    True if (allowed_library_manage_ids and library.id in allowed_library_manage_ids) else False
+                )
             else:
                 current_user_roles = trans.get_current_user_roles()
-                library_dict['can_user_add'] = trans.app.security_agent.can_add_library_item(current_user_roles, library)
-                library_dict['can_user_modify'] = trans.app.security_agent.can_modify_library_item(current_user_roles, library)
-                library_dict['can_user_manage'] = trans.app.security_agent.can_manage_library_item(current_user_roles, library)
+                library_dict["can_user_add"] = trans.app.security_agent.can_add_library_item(
+                    current_user_roles, library
+                )
+                library_dict["can_user_modify"] = trans.app.security_agent.can_modify_library_item(
+                    current_user_roles, library
+                )
+                library_dict["can_user_manage"] = trans.app.security_agent.can_manage_library_item(
+                    current_user_roles, library
+                )
         else:
-            library_dict['can_user_add'] = True
-            library_dict['can_user_modify'] = True
-            library_dict['can_user_manage'] = True
+            library_dict["can_user_add"] = True
+            library_dict["can_user_modify"] = True
+            library_dict["can_user_manage"] = True
         return library_dict
 
     def get_current_roles(self, trans, library):
@@ -251,14 +281,27 @@ class LibraryManager:
         :rtype:     dictionary
         :returns:   dict of current roles for all available permission types
         """
-        access_library_role_list = [(access_role.name, trans.security.encode_id(access_role.id)) for access_role in self.get_access_roles(trans, library)]
-        modify_library_role_list = [(modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in self.get_modify_roles(trans, library)]
-        manage_library_role_list = [(manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in self.get_manage_roles(trans, library)]
-        add_library_item_role_list = [(add_role.name, trans.security.encode_id(add_role.id)) for add_role in self.get_add_roles(trans, library)]
-        return dict(access_library_role_list=access_library_role_list,
-                    modify_library_role_list=modify_library_role_list,
-                    manage_library_role_list=manage_library_role_list,
-                    add_library_item_role_list=add_library_item_role_list)
+        access_library_role_list = [
+            (access_role.name, trans.security.encode_id(access_role.id))
+            for access_role in self.get_access_roles(trans, library)
+        ]
+        modify_library_role_list = [
+            (modify_role.name, trans.security.encode_id(modify_role.id))
+            for modify_role in self.get_modify_roles(trans, library)
+        ]
+        manage_library_role_list = [
+            (manage_role.name, trans.security.encode_id(manage_role.id))
+            for manage_role in self.get_manage_roles(trans, library)
+        ]
+        add_library_item_role_list = [
+            (add_role.name, trans.security.encode_id(add_role.id)) for add_role in self.get_add_roles(trans, library)
+        ]
+        return dict(
+            access_library_role_list=access_library_role_list,
+            modify_library_role_list=modify_library_role_list,
+            manage_library_role_list=manage_library_role_list,
+            add_library_item_role_list=add_library_item_role_list,
+        )
 
     def get_access_roles(self, trans, library):
         """
@@ -270,19 +313,31 @@ class LibraryManager:
         """
         Load modify roles for all library permissions
         """
-        return set(trans.app.security_agent.get_roles_for_action(library, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY))
+        return set(
+            trans.app.security_agent.get_roles_for_action(
+                library, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY
+            )
+        )
 
     def get_manage_roles(self, trans, library):
         """
         Load manage roles for all library permissions
         """
-        return set(trans.app.security_agent.get_roles_for_action(library, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE))
+        return set(
+            trans.app.security_agent.get_roles_for_action(
+                library, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE
+            )
+        )
 
     def get_add_roles(self, trans, library):
         """
         Load add roles for all library permissions
         """
-        return set(trans.app.security_agent.get_roles_for_action(library, trans.app.security_agent.permitted_actions.LIBRARY_ADD))
+        return set(
+            trans.app.security_agent.get_roles_for_action(
+                library, trans.app.security_agent.permitted_actions.LIBRARY_ADD
+            )
+        )
 
     def set_permission_roles(self, trans, library, access_roles, modify_roles, manage_roles, add_roles):
         """
@@ -310,8 +365,8 @@ def get_containing_library_from_library_dataset(trans, library_dataset):
         folder = folder.parent
     # We have folder set to the library's root folder, which has the same name as the library
     for library in trans.sa_session.query(trans.model.Library).filter(
-        and_(trans.model.Library.table.c.deleted == false(),
-            trans.model.Library.table.c.name == folder.name)):
+        and_(trans.model.Library.table.c.deleted == false(), trans.model.Library.table.c.name == folder.name)
+    ):
         # Just to double-check
         if library.root_folder == folder:
             return library
diff --git a/lib/galaxy/managers/library_datasets.py b/lib/galaxy/managers/library_datasets.py
index b26314c0d7e..f2a2eab8973 100644
--- a/lib/galaxy/managers/library_datasets.py
+++ b/lib/galaxy/managers/library_datasets.py
@@ -3,17 +3,15 @@ import logging
 
 from galaxy import (
     model,
-    util
+    util,
 )
 from galaxy.exceptions import (
     InsufficientPermissionsException,
     InternalServerError,
     ObjectNotFound,
-    RequestParameterInvalidException
-)
-from galaxy.managers import (
-    datasets,
+    RequestParameterInvalidException,
 )
+from galaxy.managers import datasets
 from galaxy.model import tags
 from galaxy.structured_app import MinimalManagerApp
 from galaxy.util import validation
@@ -23,6 +21,7 @@ log = logging.getLogger(__name__)
 
 class LibraryDatasetsManager(datasets.DatasetAssociationManager):
     """Interface/service object for interacting with library datasets."""
+
     model_class = model.LibraryDatasetDatasetAssociation
 
     def __init__(self, app: MinimalManagerApp):
@@ -42,7 +41,11 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         :rtype:     galaxy.model.LibraryDataset
         """
         try:
-            ld = trans.sa_session.query(trans.app.model.LibraryDataset).filter(trans.app.model.LibraryDataset.table.c.id == decoded_library_dataset_id).one()
+            ld = (
+                trans.sa_session.query(trans.app.model.LibraryDataset)
+                .filter(trans.app.model.LibraryDataset.table.c.id == decoded_library_dataset_id)
+                .one()
+            )
         except Exception as e:
             raise InternalServerError(f"Error loading from the database.{util.unicodify(e)}")
         ld = self.secure(trans, ld, check_accessible)
@@ -80,30 +83,30 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
 
     def _set_from_dict(self, trans, ldda, new_data):
         changed = False
-        new_name = new_data.get('name', None)
+        new_name = new_data.get("name", None)
         if new_name is not None and new_name != ldda.name:
             ldda.name = new_name
             changed = True
-        new_misc_info = new_data.get('misc_info', None)
+        new_misc_info = new_data.get("misc_info", None)
         if new_misc_info is not None and new_misc_info != ldda.info:
             ldda.info = new_misc_info
             changed = True
-        new_message = new_data.get('message', None)
+        new_message = new_data.get("message", None)
         if new_message is not None and new_message != ldda.message:
             ldda.message = new_message
             changed = True
-        new_file_ext = new_data.get('file_ext', None)
-        if new_file_ext == 'auto':
+        new_file_ext = new_data.get("file_ext", None)
+        if new_file_ext == "auto":
             self.detect_datatype(trans, ldda)
         elif new_file_ext is not None and new_file_ext != ldda.extension:
             ldda.extension = new_file_ext
             self.set_metadata(trans, ldda)
             changed = True
-        new_genome_build = new_data.get('genome_build', None)
+        new_genome_build = new_data.get("genome_build", None)
         if new_genome_build is not None and new_genome_build != ldda.dbkey:
             ldda.dbkey = new_genome_build
             changed = True
-        new_tags = new_data.get('tags', None)
+        new_tags = new_data.get("tags", None)
         if new_tags is not None and new_tags != ldda.tags:
             self.tag_handler.delete_item_tags(item=ldda, user=trans.user)
             tag_list = self.tag_handler.parse_tags_list(new_tags)
@@ -122,25 +125,29 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         for key, val in payload.items():
             if val is None:
                 continue
-            if key in ('name'):
+            if key in ("name"):
                 if len(val) < MINIMUM_STRING_LENGTH:
-                    raise RequestParameterInvalidException(f'{key} must have at least length of {MINIMUM_STRING_LENGTH}')
+                    raise RequestParameterInvalidException(
+                        f"{key} must have at least length of {MINIMUM_STRING_LENGTH}"
+                    )
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
-            if key in ('misc_info', 'message'):
+            if key in ("misc_info", "message"):
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
-            if key in ('file_ext'):
+            if key in ("file_ext"):
                 datatype = self.app.datatypes_registry.get_datatype_by_extension(val)
                 if datatype is None and val not in ("auto",):
-                    raise RequestParameterInvalidException(f'This Galaxy does not recognize the datatype of: {val}')
+                    raise RequestParameterInvalidException(f"This Galaxy does not recognize the datatype of: {val}")
                 validated_payload[key] = val
-            if key in ('genome_build'):
+            if key in ("genome_build"):
                 if len(val) < MINIMUM_STRING_LENGTH:
-                    raise RequestParameterInvalidException(f'{key} must have at least length of {MINIMUM_STRING_LENGTH}')
+                    raise RequestParameterInvalidException(
+                        f"{key} must have at least length of {MINIMUM_STRING_LENGTH}"
+                    )
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
-            if key in ('tags'):
+            if key in ("tags"):
                 val = validation.validate_and_sanitize_basestring_list(key, util.listify(val))
                 validated_payload[key] = val
         return validated_payload
@@ -177,9 +184,9 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         :raises:    ObjectNotFound
         """
         if not trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), ld, trans.user):
-            raise ObjectNotFound('Library dataset with the id provided was not found.')
+            raise ObjectNotFound("Library dataset with the id provided was not found.")
         elif ld.deleted:
-            raise ObjectNotFound('Library dataset with the id provided is deleted.')
+            raise ObjectNotFound("Library dataset with the id provided is deleted.")
         else:
             return ld
 
@@ -196,11 +203,11 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         :raises:    ObjectNotFound
         """
         if ld.deleted:
-            raise ObjectNotFound('Library dataset with the id provided is deleted.')
+            raise ObjectNotFound("Library dataset with the id provided is deleted.")
         elif trans.user_is_admin:
             return ld
         if not trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), ld):
-            raise InsufficientPermissionsException('You do not have proper permission to modify this library dataset.')
+            raise InsufficientPermissionsException("You do not have proper permission to modify this library dataset.")
         else:
             return ld
 
@@ -221,29 +228,33 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
 
         rval = trans.security.encode_all_ids(ld.to_dict())
         if len(expired_ldda_versions) > 0:
-            rval['has_versions'] = True
-            rval['expired_versions'] = expired_ldda_versions
+            rval["has_versions"] = True
+            rval["expired_versions"] = expired_ldda_versions
 
         ldda = ld.library_dataset_dataset_association
         if ldda.creating_job_associations:
             if ldda.creating_job_associations[0].job.stdout:
-                rval['job_stdout'] = ldda.creating_job_associations[0].job.stdout.strip()
+                rval["job_stdout"] = ldda.creating_job_associations[0].job.stdout.strip()
             if ldda.creating_job_associations[0].job.stderr:
-                rval['job_stderr'] = ldda.creating_job_associations[0].job.stderr.strip()
+                rval["job_stderr"] = ldda.creating_job_associations[0].job.stderr.strip()
         if ldda.dataset.uuid:
-            rval['uuid'] = str(ldda.dataset.uuid)
-        rval['deleted'] = ld.deleted
-        rval['folder_id'] = f"F{rval['folder_id']}"
-        rval['full_path'] = full_path
-        rval['file_size'] = util.nice_size(int(ldda.get_size()))
-        rval['date_uploaded'] = ldda.create_time.strftime("%Y-%m-%d %I:%M %p")
-        rval['update_time'] = ldda.update_time.strftime("%Y-%m-%d %I:%M %p")
-        rval['can_user_modify'] = trans.user_is_admin or trans.app.security_agent.can_modify_library_item(current_user_roles, ld)
-        rval['is_unrestricted'] = trans.app.security_agent.dataset_is_public(ldda.dataset)
-        rval['tags'] = self.tag_handler.get_tags_str(ldda.tags)
+            rval["uuid"] = str(ldda.dataset.uuid)
+        rval["deleted"] = ld.deleted
+        rval["folder_id"] = f"F{rval['folder_id']}"
+        rval["full_path"] = full_path
+        rval["file_size"] = util.nice_size(int(ldda.get_size()))
+        rval["date_uploaded"] = ldda.create_time.strftime("%Y-%m-%d %I:%M %p")
+        rval["update_time"] = ldda.update_time.strftime("%Y-%m-%d %I:%M %p")
+        rval["can_user_modify"] = trans.user_is_admin or trans.app.security_agent.can_modify_library_item(
+            current_user_roles, ld
+        )
+        rval["is_unrestricted"] = trans.app.security_agent.dataset_is_public(ldda.dataset)
+        rval["tags"] = self.tag_handler.get_tags_str(ldda.tags)
 
         #  Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency
-        rval['can_user_manage'] = trans.user_is_admin or trans.app.security_agent.can_manage_dataset(current_user_roles, ldda.dataset)
+        rval["can_user_manage"] = trans.user_is_admin or trans.app.security_agent.can_manage_dataset(
+            current_user_roles, ldda.dataset
+        )
         return rval
 
     def _build_path(self, trans, folder):
diff --git a/lib/galaxy/managers/licenses.py b/lib/galaxy/managers/licenses.py
index 8af0d02e39d..dae5c996287 100644
--- a/lib/galaxy/managers/licenses.py
+++ b/lib/galaxy/managers/licenses.py
@@ -6,7 +6,7 @@ from pkg_resources import resource_string
 from pydantic import (
     BaseModel,
     Field,
-    HttpUrl
+    HttpUrl,
 )
 
 from galaxy import exceptions
@@ -16,57 +16,33 @@ log = logging.getLogger(__name__)
 
 # https://github.com/spdx/license-list-data/blob/master/accessingLicenses.md#license-list-table-of-contents
 class LicenseMetadataModel(BaseModel):
-    licenseId: str = Field(
-        title="Identifier",
-        description="SPDX Identifier",
-        example="Apache-2.0"
-    )
-    name: str = Field(
-        title="Name",
-        description="Full name of the license",
-        example="Apache License 2.0"
-    )
+    licenseId: str = Field(title="Identifier", description="SPDX Identifier", example="Apache-2.0")
+    name: str = Field(title="Name", description="Full name of the license", example="Apache License 2.0")
     reference: str = Field(
-        title="Reference",
-        description="Reference to the HTML format for the license file",
-        example="./Apache-2.0.html"
+        title="Reference", description="Reference to the HTML format for the license file", example="./Apache-2.0.html"
     )
     referenceNumber: int = Field(
-        title="Reference number",
-        description="*Deprecated* - this field is generated and is no longer in use"
+        title="Reference number", description="*Deprecated* - this field is generated and is no longer in use"
     )
     isDeprecatedLicenseId: bool = Field(
-        title="Deprecated License",
-        description="True if the entire license is deprecated",
-        example=False
+        title="Deprecated License", description="True if the entire license is deprecated", example=False
     )
     isOsiApproved: bool = Field(
         title="OSI approved",
         description="Indicates if the [OSI](https://opensource.org/) has approved the license",
-        example=True
+        example=True,
     )
     seeAlso: List[HttpUrl] = Field(
-        title="Reference URLs",
-        description="Cross reference URL pointing to additional copies of the license"
+        title="Reference URLs", description="Cross reference URL pointing to additional copies of the license"
     )
     detailsUrl: HttpUrl = Field(
         title="Details URL",
         description="URL to the SPDX json details for this license",
-        example="http://spdx.org/licenses/Apache-2.0.json"
-    )
-    recommended: bool = Field(
-        title="Recommended",
-        description="True if this license is recommended to be used"
-    )
-    url: HttpUrl = Field(
-        title="URL",
-        description="License URL",
-        example="http://www.apache.org/licenses/LICENSE-2.0"
-    )
-    spdxUrl: HttpUrl = Field(
-        title="SPDX URL",
-        example="https://spdx.org/licenses/Apache-2.0.html"
+        example="http://spdx.org/licenses/Apache-2.0.json",
     )
+    recommended: bool = Field(title="Recommended", description="True if this license is recommended to be used")
+    url: HttpUrl = Field(title="URL", description="License URL", example="http://www.apache.org/licenses/LICENSE-2.0")
+    spdxUrl: HttpUrl = Field(title="SPDX URL", example="https://spdx.org/licenses/Apache-2.0.html")
 
 
 # https://docs.google.com/document/d/16vnRtDjrx5eHSl4jXs2vMaDTI6luyyLzU6xMvRHsnbI/edit#heading=h.1pihjj16olz2
@@ -85,7 +61,7 @@ RECOMMENDED_LICENSES = [
     "MPL-2.0",
     "PDDL-1.0",
 ]
-SPDX_LICENSES_STRING = resource_string(__name__, 'licenses.json').decode("UTF-8")
+SPDX_LICENSES_STRING = resource_string(__name__, "licenses.json").decode("UTF-8")
 SPDX_LICENSES = json.loads(SPDX_LICENSES_STRING)
 for license in SPDX_LICENSES["licenses"]:
     license["recommended"] = license["licenseId"] in RECOMMENDED_LICENSES
@@ -99,7 +75,6 @@ for license in SPDX_LICENSES["licenses"]:
 
 
 class LicensesManager:
-
     def __init__(self):
         by_index = {}
         for spdx_license in self.index():
@@ -118,9 +93,7 @@ class LicensesManager:
             return self._by_index[uri]
         else:
             log.warning(f"Unknown license URI encountered [{uri}]")
-        return {
-            "url": uri
-        }
+        return {"url": uri}
 
     def get_licenses(self) -> List[LicenseMetadataModel]:
         return SPDX_LICENSES["licenses"]
diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py
index 1408dd50954..e5ee92258e5 100644
--- a/lib/galaxy/managers/markdown_parse.py
+++ b/lib/galaxy/managers/markdown_parse.py
@@ -6,14 +6,16 @@ Galaxy Markdown. Keeping things isolated to allow re-use of these utilities in o
 projects (e.g. gxformat2).
 """
 import re
-from typing import cast, Dict, List, Union
-
-
-BLOCK_FENCE_START = re.compile(r'```.*')
-BLOCK_FENCE_END = re.compile(r'```[\s]*')
-GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
-    r"```\s*galaxy\s*"
+from typing import (
+    cast,
+    Dict,
+    List,
+    Union,
 )
+
+BLOCK_FENCE_START = re.compile(r"```.*")
+BLOCK_FENCE_END = re.compile(r"```[\s]*")
+GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(r"```\s*galaxy\s*")
 VALID_CONTAINER_END_PATTERN = re.compile(r"^```\s*$")
 
 
@@ -48,12 +50,12 @@ VALID_ARGUMENTS: Dict[str, Union[List[str], DynamicArguments]] = {
     "invocation_inputs": [],
 }
 GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
-GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r'(?P<container>%s)' % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
+GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>%s)" % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
 
-ARG_VAL_REGEX = r'''[\w_\-]+|\"[^\"]+\"|\'[^\']+\''''
-FUNCTION_ARG = r'\s*[\w\|]+\s*=\s*(?:%s)\s*' % ARG_VAL_REGEX
+ARG_VAL_REGEX = r"""[\w_\-]+|\"[^\"]+\"|\'[^\']+\'"""
+FUNCTION_ARG = r"\s*[\w\|]+\s*=\s*(?:%s)\s*" % ARG_VAL_REGEX
 # embed commas between arguments
-FUNCTION_MULTIPLE_ARGS = fr'(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)'
+FUNCTION_MULTIPLE_ARGS = rf"(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)"
 FUNCTION_MULTIPLE_ARGS_PATTERN = re.compile(FUNCTION_MULTIPLE_ARGS)
 FUNCTION_CALL_LINE_TEMPLATE = f"\\s*%s\\s*\\((?:{FUNCTION_MULTIPLE_ARGS})?\\)\\s*"
 GALAXY_MARKDOWN_FUNCTION_CALL_LINE = re.compile(FUNCTION_CALL_LINE_TEMPLATE % GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX)
@@ -75,7 +77,11 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
 
         expecting_container_close = expecting_container_close_for is not None
         if not fenced and expecting_container_close:
-            invalid_line("[{line}] is not expected close line for [{expected_for}]", line=line, expected_for=expecting_container_close_for)
+            invalid_line(
+                "[{line}] is not expected close line for [{expected_for}]",
+                line=line,
+                expected_for=expecting_container_close_for,
+            )
             continue
         elif not fenced:
             continue
@@ -86,7 +92,11 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
         elif open_fence and GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
             if expecting_container_close:
                 if not VALID_CONTAINER_END_PATTERN.match(line):
-                    invalid_line("Invalid command close line [{line}] for [{expected_for}]", line=line, expected_for=expecting_container_close_for)
+                    invalid_line(
+                        "Invalid command close line [{line}] for [{expected_for}]",
+                        line=line,
+                        expected_for=expecting_container_close_for,
+                    )
                 # else closing container and we're done
                 expecting_container_close_for = None
                 function_calls = 0
@@ -159,6 +169,6 @@ def _split_markdown_lines(markdown):
 
 
 __all__ = (
-    'validate_galaxy_markdown',
-    'GALAXY_MARKDOWN_FUNCTION_CALL_LINE',
+    "validate_galaxy_markdown",
+    "GALAXY_MARKDOWN_FUNCTION_CALL_LINE",
 )
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index 26787fc452d..4e816663c26 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -28,6 +28,7 @@ from typing import (
 
 import markdown
 import pkg_resources
+
 try:
     import weasyprint
 except Exception:
@@ -48,22 +49,27 @@ from galaxy.model.item_attrs import get_item_annotation_str
 from galaxy.model.orm.now import now
 from galaxy.schema import PdfDocumentType
 from galaxy.util.sanitize_html import sanitize_html
-from .markdown_parse import GALAXY_MARKDOWN_FUNCTION_CALL_LINE, validate_galaxy_markdown
+from .markdown_parse import (
+    GALAXY_MARKDOWN_FUNCTION_CALL_LINE,
+    validate_galaxy_markdown,
+)
 
 log = logging.getLogger(__name__)
 
-ARG_VAL_CAPTURED_REGEX = r'''(?:([\w_\-\|]+)|\"([^\"]+)\"|\'([^\']+)\')'''
-OUTPUT_LABEL_PATTERN = re.compile(r'output=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
-INPUT_LABEL_PATTERN = re.compile(r'input=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
-STEP_LABEL_PATTERN = re.compile(r'step=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
-PATH_LABEL_PATTERN = re.compile(r'path=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
+ARG_VAL_CAPTURED_REGEX = r"""(?:([\w_\-\|]+)|\"([^\"]+)\"|\'([^\']+)\')"""
+OUTPUT_LABEL_PATTERN = re.compile(r"output=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
+INPUT_LABEL_PATTERN = re.compile(r"input=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
+STEP_LABEL_PATTERN = re.compile(r"step=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
+PATH_LABEL_PATTERN = re.compile(r"path=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
 # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)')
-UNENCODED_ID_PATTERN = re.compile(r'(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([\d]+)')
-ENCODED_ID_PATTERN = re.compile(r'(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([a-z0-9]+)')
-INVOCATION_SECTION_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
-    r"```\s*galaxy\s*"
+UNENCODED_ID_PATTERN = re.compile(
+    r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([\d]+)"
 )
-GALAXY_FENCED_BLOCK = re.compile(r'^```\s*galaxy\s*(.*?)^```', re.MULTILINE ^ re.DOTALL)
+ENCODED_ID_PATTERN = re.compile(
+    r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([a-z0-9]+)"
+)
+INVOCATION_SECTION_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(r"```\s*galaxy\s*")
+GALAXY_FENCED_BLOCK = re.compile(r"^```\s*galaxy\s*(.*?)^```", re.MULTILINE ^ re.DOTALL)
 VALID_CONTAINER_START_PATTERN = re.compile(r"^```\s+[\w]+.*$")
 
 
@@ -86,7 +92,6 @@ def ready_galaxy_markdown_for_import(trans, external_galaxy_markdown):
 
 
 class GalaxyInternalMarkdownDirectiveHandler(metaclass=abc.ABCMeta):
-
     def walk(self, trans, internal_galaxy_markdown):
         hda_manager = trans.app.hda_manager
         history_manager = trans.app.history_manager
@@ -264,7 +269,6 @@ class GalaxyInternalMarkdownDirectiveHandler(metaclass=abc.ABCMeta):
 
 
 class ReadyForExportMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHandler):
-
     def __init__(self, trans, extra_rendering_data=None):
         extra_rendering_data = extra_rendering_data or {}
         self.trans = trans
@@ -300,9 +304,7 @@ class ReadyForExportMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHand
 
     def handle_dataset_collection_display(self, line, hdca):
         hdca_serializer = HDCASerializer(self.trans.app)
-        hdca_view = hdca_serializer.serialize_to_view(
-            hdca, user=self.trans.user, trans=self.trans, view="summary"
-        )
+        hdca_view = hdca_serializer.serialize_to_view(hdca, user=self.trans.user, trans=self.trans, view="summary")
         self.ensure_rendering_data_for("history_dataset_collections", hdca).update(hdca_view)
 
     def handle_tool_stdout(self, line, job):
@@ -345,11 +347,13 @@ class ReadyForExportMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHand
     def handle_error(self, container, line, error):
         if "errors" not in self.extra_rendering_data:
             self.extra_rendering_data["errors"] = []
-        self.extra_rendering_data["errors"].append({
-            "error": error,
-            "line": line,
-            "container": container,
-        })
+        self.extra_rendering_data["errors"].append(
+            {
+                "error": error,
+                "line": line,
+                "container": container,
+            }
+        )
         return (line, False)
 
 
@@ -373,17 +377,16 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
 
 
 class ToBasicMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHandler):
-
     def __init__(self, trans, markdown_formatting_helpers):
         self.trans = trans
         self.markdown_formatting_helpers = markdown_formatting_helpers
 
     def handle_dataset_display(self, line, hda):
         name = hda.name or ""
-        markdown = '---\n'
+        markdown = "---\n"
         markdown += f"**Dataset:** {name}\n\n"
         markdown += self._display_dataset_content(hda)
-        markdown += '\n---\n'
+        markdown += "\n---\n"
         return (markdown, True)
 
     def handle_dataset_embedded(self, line, hda):
@@ -408,7 +411,7 @@ class ToBasicMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHandler):
 
     def handle_dataset_as_image(self, line, hda):
         dataset = hda.dataset
-        name = hda.name or ''
+        name = hda.name or ""
         path_match = re.search(PATH_LABEL_PATTERN, line)
 
         if path_match:
@@ -445,7 +448,7 @@ class ToBasicMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHandler):
 
     def handle_workflow_display(self, line, stored_workflow):
         # workflows/display.mako as markdown... meh...
-        markdown = '---\n'
+        markdown = "---\n"
         markdown += f"**Workflow:** {stored_workflow.name}\n\n"
         markdown += "**Steps:**\n\n"
         markdown += "|Step|Annotation|\n"
@@ -453,7 +456,7 @@ class ToBasicMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHandler):
         # Pass two should add tool information, labels, etc.. but
         # it requires module_injector and such.
         for order_index, step in enumerate(stored_workflow.latest_workflow.steps):
-            annotation = get_item_annotation_str(self.trans.sa_session, self.trans.user, step) or ''
+            annotation = get_item_annotation_str(self.trans.sa_session, self.trans.user, step) or ""
             markdown += "|{}|{}|\n".format(step.label or "Step %d" % (order_index + 1), annotation)
         markdown += "\n---\n"
         return (markdown, True)
@@ -471,8 +474,9 @@ class ToBasicMarkdownDirectiveHandler(GalaxyInternalMarkdownDirectiveHandler):
                 for element in collection.elements:
                     markdown_wrapper[0] += f"**Element:** {element_prefix}{element.element_identifier}\n\n"
                     markdown_wrapper[0] += self._display_dataset_content(element.hda, header="Element Contents")
+
         walk_elements(hdca.collection)
-        markdown = f'---\n{markdown_wrapper[0]}\n---\n'
+        markdown = f"---\n{markdown_wrapper[0]}\n---\n"
         return (markdown, True)
 
     def handle_tool_stdout(self, line, job):
@@ -571,8 +575,7 @@ class MarkdownFormatHelpers:
 
 
 def to_basic_markdown(trans, internal_galaxy_markdown: str) -> str:
-    """Replace Galaxy Markdown extensions with plain Markdown for PDF/HTML export.
-    """
+    """Replace Galaxy Markdown extensions with plain Markdown for PDF/HTML export."""
     markdown_formatting_helpers = MarkdownFormatHelpers()
     directive_handler = ToBasicMarkdownDirectiveHandler(trans, markdown_formatting_helpers)
     plain_markdown = directive_handler.walk(trans, internal_galaxy_markdown)
@@ -589,14 +592,14 @@ def to_pdf_raw(basic_markdown: str, css_paths: Optional[List[str]] = None) -> by
     """Convert RAW markdown with specified CSS paths into bytes of a PDF."""
     css_paths = css_paths or []
     as_html = to_html(basic_markdown)
-    directory = tempfile.mkdtemp('gxmarkdown')
+    directory = tempfile.mkdtemp("gxmarkdown")
     index = os.path.join(directory, "index.html")
     try:
         output_file = codecs.open(index, "w", encoding="utf-8", errors="xmlcharrefreplace")
         output_file.write(as_html)
         output_file.close()
         html = weasyprint.HTML(filename=index)
-        stylesheets = [weasyprint.CSS(string=pkg_resources.resource_string(__name__, 'markdown_export_base.css'))]
+        stylesheets = [weasyprint.CSS(string=pkg_resources.resource_string(__name__, "markdown_export_base.css"))]
         for css_path in css_paths:
             with open(css_path) as f:
                 css_content = f.read()
@@ -625,10 +628,10 @@ def internal_galaxy_markdown_to_pdf(trans, internal_galaxy_markdown: str, docume
 
 
 def to_branded_pdf(basic_markdown: str, document_type: PdfDocumentType, config: GalaxyAppConfiguration) -> bytes:
-    document_type_prologue = getattr(config, f"markdown_export_prologue_{document_type}s", '') or ''
-    document_type_epilogue = getattr(config, f"markdown_export_epilogue_{document_type}s", '') or ''
-    general_prologue = config.markdown_export_prologue or ''
-    general_epilogue = config.markdown_export_epilogue or ''
+    document_type_prologue = getattr(config, f"markdown_export_prologue_{document_type}s", "") or ""
+    document_type_epilogue = getattr(config, f"markdown_export_epilogue_{document_type}s", "") or ""
+    general_prologue = config.markdown_export_prologue or ""
+    general_epilogue = config.markdown_export_epilogue or ""
     effective_prologue = document_type_prologue or general_prologue
     effective_epilogue = document_type_epilogue or general_epilogue
     branded_markdown = effective_prologue + basic_markdown + effective_epilogue
@@ -671,13 +674,17 @@ def resolve_invocation_markdown(trans, invocation, workflow_markdown):
 ```galaxy
 history_dataset_display(output="{}")
 ```
-""".format(output_assoc.workflow_output.label, output_assoc.workflow_output.label)
+""".format(
+                        output_assoc.workflow_output.label, output_assoc.workflow_output.label
+                    )
                 else:
                     section_markdown += """#### Output Dataset Collection: {}
 ```galaxy
 history_dataset_collection_display(output="{}")
 ```
-""".format(output_assoc.workflow_output.label, output_assoc.workflow_output.label)
+""".format(
+                        output_assoc.workflow_output.label, output_assoc.workflow_output.label
+                    )
         elif container == "invocation_inputs":
             for input_assoc in invocation.input_associations:
                 if not input_assoc.workflow_step.label:
@@ -688,13 +695,17 @@ history_dataset_collection_display(output="{}")
 ```galaxy
 history_dataset_display(input="{}")
 ```
-""".format(input_assoc.workflow_step.label, input_assoc.workflow_step.label)
+""".format(
+                        input_assoc.workflow_step.label, input_assoc.workflow_step.label
+                    )
                 else:
                     section_markdown += """#### Input Dataset Collection: {}
 ```galaxy
 history_dataset_collection_display(input={})
 ```
-""".format(input_assoc.workflow_step.label, input_assoc.workflow_step.label)
+""".format(
+                        input_assoc.workflow_step.label, input_assoc.workflow_step.label
+                    )
         else:
             return line, False
         return section_markdown, True
@@ -781,7 +792,6 @@ def _remap_galaxy_markdown_containers(func, markdown):
 
 
 def _remap_galaxy_markdown_calls(func, markdown):
-
     def _remap_container(container):
         matching_line = None
         for line in container.splitlines():
@@ -808,8 +818,8 @@ def _validate(*args, **kwds):
 
 
 __all__ = (
-    'internal_galaxy_markdown_to_pdf',
-    'ready_galaxy_markdown_for_export',
-    'ready_galaxy_markdown_for_import',
-    'resolve_invocation_markdown',
+    "internal_galaxy_markdown_to_pdf",
+    "ready_galaxy_markdown_for_export",
+    "ready_galaxy_markdown_for_import",
+    "resolve_invocation_markdown",
 )
diff --git a/lib/galaxy/managers/metrics.py b/lib/galaxy/managers/metrics.py
index 6ff09336451..5e49dfd241b 100644
--- a/lib/galaxy/managers/metrics.py
+++ b/lib/galaxy/managers/metrics.py
@@ -36,7 +36,7 @@ class Metric(BaseModel):
         ...,  # Required
         title="Timestamp",
         description="The timestamp in ISO format.",
-        example=datetime_to_iso8601(datetime.utcnow())
+        example=datetime_to_iso8601(datetime.utcnow()),
     )
     level: int = Field(
         ...,  # Required
@@ -53,15 +53,12 @@ class Metric(BaseModel):
 class CreateMetricsPayload(BaseModel):
     metrics: List[Metric] = Field(
         default=[],
-        title='List of metrics to be recorded.',
+        title="List of metrics to be recorded.",
         example=[
             Metric(
-                namespace="test-source",
-                time=datetime_to_iso8601(datetime.utcnow()),
-                level=0,
-                args='{"test":"value"}'
+                namespace="test-source", time=datetime_to_iso8601(datetime.utcnow()), level=0, args='{"test":"value"}'
             )
-        ]
+        ],
     )
 
 
@@ -103,10 +100,7 @@ class MetricsManager:
         return response
 
     def _parse_metrics(
-        self,
-        metrics: Optional[List[Metric]] = None,
-        user_id=None,
-        session_id=None
+        self, metrics: Optional[List[Metric]] = None, user_id=None, session_id=None
     ) -> TimeSeriesTupleGenerator:
         """
         Return a generator yielding the each given metric as a tuple:
@@ -122,12 +116,7 @@ class MetricsManager:
         for metric in metrics:
             label = metric.namespace
             time = self._deserialize_isoformat_date(metric.time)
-            kwargs = {
-                'level': metric.level,
-                'args': metric.args,
-                'user': user_id,
-                'session': session_id
-            }
+            kwargs = {"level": metric.level, "args": metric.args, "user": user_id, "session": session_id}
             yield (label, time, kwargs)
 
     def _send_metrics(self, trans, metrics: TimeSeriesTupleGenerator) -> None:
@@ -142,7 +131,7 @@ class MetricsManager:
                 trans.app.trace_logger.log(label, event_time=int(time.timestamp()), **kwargs)
         elif self.debugging:
             for label, time, kwargs in metrics:
-                log.debug(f'{label} {time} {kwargs}')
+                log.debug(f"{label} {time} {kwargs}")
 
     def _get_server_pong(self, trans) -> Any:
         """
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index 0d599be6782..57a575771d2 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -9,12 +9,16 @@ import logging
 import re
 from html.entities import name2codepoint
 from html.parser import HTMLParser
-from typing import (
-    Callable,
-)
+from typing import Callable
 
-from galaxy import exceptions, model
-from galaxy.managers import base, sharable
+from galaxy import (
+    exceptions,
+    model,
+)
+from galaxy.managers import (
+    base,
+    sharable,
+)
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.managers.markdown_util import (
     ready_galaxy_markdown_for_export,
@@ -30,33 +34,33 @@ log = logging.getLogger(__name__)
 
 # Copied from https://github.com/kurtmckee/feedparser
 _cp1252 = {
-    128: '\u20ac',  # euro sign
-    130: '\u201a',  # single low-9 quotation mark
-    131: '\u0192',  # latin small letter f with hook
-    132: '\u201e',  # double low-9 quotation mark
-    133: '\u2026',  # horizontal ellipsis
-    134: '\u2020',  # dagger
-    135: '\u2021',  # double dagger
-    136: '\u02c6',  # modifier letter circumflex accent
-    137: '\u2030',  # per mille sign
-    138: '\u0160',  # latin capital letter s with caron
-    139: '\u2039',  # single left-pointing angle quotation mark
-    140: '\u0152',  # latin capital ligature oe
-    142: '\u017d',  # latin capital letter z with caron
-    145: '\u2018',  # left single quotation mark
-    146: '\u2019',  # right single quotation mark
-    147: '\u201c',  # left double quotation mark
-    148: '\u201d',  # right double quotation mark
-    149: '\u2022',  # bullet
-    150: '\u2013',  # en dash
-    151: '\u2014',  # em dash
-    152: '\u02dc',  # small tilde
-    153: '\u2122',  # trade mark sign
-    154: '\u0161',  # latin small letter s with caron
-    155: '\u203a',  # single right-pointing angle quotation mark
-    156: '\u0153',  # latin small ligature oe
-    158: '\u017e',  # latin small letter z with caron
-    159: '\u0178',  # latin capital letter y with diaeresis
+    128: "\u20ac",  # euro sign
+    130: "\u201a",  # single low-9 quotation mark
+    131: "\u0192",  # latin small letter f with hook
+    132: "\u201e",  # double low-9 quotation mark
+    133: "\u2026",  # horizontal ellipsis
+    134: "\u2020",  # dagger
+    135: "\u2021",  # double dagger
+    136: "\u02c6",  # modifier letter circumflex accent
+    137: "\u2030",  # per mille sign
+    138: "\u0160",  # latin capital letter s with caron
+    139: "\u2039",  # single left-pointing angle quotation mark
+    140: "\u0152",  # latin capital ligature oe
+    142: "\u017d",  # latin capital letter z with caron
+    145: "\u2018",  # left single quotation mark
+    146: "\u2019",  # right single quotation mark
+    147: "\u201c",  # left double quotation mark
+    148: "\u201d",  # right double quotation mark
+    149: "\u2022",  # bullet
+    150: "\u2013",  # en dash
+    151: "\u2014",  # em dash
+    152: "\u02dc",  # small tilde
+    153: "\u2122",  # trade mark sign
+    154: "\u0161",  # latin small letter s with caron
+    155: "\u203a",  # single right-pointing angle quotation mark
+    156: "\u0153",  # latin small ligature oe
+    158: "\u017e",  # latin small letter z with caron
+    159: "\u0178",  # latin capital letter y with diaeresis
 }
 
 
@@ -64,7 +68,7 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
     """Provides operations for managing a Page."""
 
     model_class = model.Page
-    foreign_key_name = 'page'
+    foreign_key_name = "page"
     user_share_model = model.PageUserShareAssociation
 
     tag_assoc = model.PageTagAssociation
@@ -72,8 +76,7 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
     rating_assoc = model.PageRatingAssociation
 
     def __init__(self, app: MinimalManagerApp):
-        """
-        """
+        """ """
         super().__init__(app)
         self.workflow_manager = app.workflow_manager
 
@@ -85,8 +88,14 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
         elif not payload.get("slug"):
             raise exceptions.ObjectAttributeMissingException("Page id is required")
         elif not base.is_valid_slug(payload["slug"]):
-            raise exceptions.ObjectAttributeInvalidException("Page identifier must consist of only lowercase letters, numbers, and the '-' character")
-        elif trans.sa_session.query(trans.app.model.Page).filter_by(user=user, slug=payload["slug"], deleted=False).first():
+            raise exceptions.ObjectAttributeInvalidException(
+                "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
+            )
+        elif (
+            trans.sa_session.query(trans.app.model.Page)
+            .filter_by(user=user, slug=payload["slug"], deleted=False)
+            .first()
+        ):
             raise exceptions.DuplicatedSlugException("Page identifier must be unique")
 
         if payload.get("invocation_id"):
@@ -101,8 +110,8 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
 
         # Create the new stored page
         page = trans.app.model.Page()
-        page.title = payload['title']
-        page.slug = payload['slug']
+        page.title = payload["title"]
+        page.slug = payload["slug"]
         page_annotation = payload.get("annotation", None)
         if page_annotation is not None:
             page_annotation = sanitize_html(page_annotation)
@@ -111,7 +120,7 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
         page.user = user
         # And the first (empty) page revision
         page_revision = trans.app.model.PageRevision()
-        page_revision.title = payload['title']
+        page_revision.title = payload["title"]
         page_revision.page = page
         page.latest_revision = page_revision
         page_revision.content = content
@@ -129,10 +138,12 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
         if not content:
             raise exceptions.ObjectAttributeMissingException("content undefined or empty")
         if content_format not in [None, PageContentFormat.html.value, PageContentFormat.markdown.value]:
-            raise exceptions.RequestParameterInvalidException(f"content_format [{content_format}], if specified, must be either html or markdown")
+            raise exceptions.RequestParameterInvalidException(
+                f"content_format [{content_format}], if specified, must be either html or markdown"
+            )
 
-        if 'title' in payload:
-            title = payload['title']
+        if "title" in payload:
+            title = payload["title"]
         else:
             title = page.title
 
@@ -159,7 +170,7 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
                 processor = PageContentProcessor(trans, placeholderRenderForSave)
                 processor.feed(content)
                 # Output is string, so convert to unicode for saving.
-                content = unicodify(processor.output(), 'utf-8')
+                content = unicodify(processor.output(), "utf-8")
             except exceptions.MessageException:
                 raise
             except Exception:
@@ -167,7 +178,9 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
         elif content_format == PageContentFormat.markdown.value:
             content = ready_galaxy_markdown_for_import(trans, content)
         else:
-            raise exceptions.RequestParameterInvalidException(f"content_format [{content_format}] must be either html or markdown")
+            raise exceptions.RequestParameterInvalidException(
+                f"content_format [{content_format}] must be either html or markdown"
+            )
         return content
 
     def rewrite_content_for_export(self, trans, as_dict):
@@ -176,14 +189,16 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
         if content_format == PageContentFormat.html.value:
             processor = PageContentProcessor(trans, placeholderRenderForEdit)
             processor.feed(content)
-            content = unicodify(processor.output(), 'utf-8')
+            content = unicodify(processor.output(), "utf-8")
             as_dict["content"] = content
         elif content_format == PageContentFormat.markdown.value:
             content, extra_attributes = ready_galaxy_markdown_for_export(trans, content)
             as_dict["content"] = content
             as_dict.update(extra_attributes)
         else:
-            raise exceptions.RequestParameterInvalidException(f"content_format [{content_format}] must be either html or markdown")
+            raise exceptions.RequestParameterInvalidException(
+                f"content_format [{content_format}] must be either html or markdown"
+            )
         return as_dict
 
 
@@ -191,21 +206,21 @@ class PageSerializer(sharable.SharableModelSerializer):
     """
     Interface/service object for serializing pages into dictionaries.
     """
+
     model_manager_class = PageManager
-    SINGLE_CHAR_ABBR = 'p'
+    SINGLE_CHAR_ABBR = "p"
 
     def __init__(self, app: MinimalManagerApp):
         super().__init__(app)
         self.page_manager = PageManager(app)
 
-        self.default_view = 'summary'
-        self.add_view('summary', [])
-        self.add_view('detailed', [])
+        self.default_view = "summary"
+        self.add_view("summary", [])
+        self.add_view("detailed", [])
 
     def add_serializers(self):
         super().add_serializers()
-        self.serializers.update({
-        })
+        self.serializers.update({})
 
 
 class PageDeserializer(sharable.SharableModelDeserializer):
@@ -213,6 +228,7 @@ class PageDeserializer(sharable.SharableModelDeserializer):
     Interface/service object for validating and deserializing dictionaries
     into pages.
     """
+
     model_manager_class = PageManager
 
     def __init__(self, app: MinimalManagerApp):
@@ -221,8 +237,7 @@ class PageDeserializer(sharable.SharableModelDeserializer):
 
     def add_deserializers(self):
         super().add_deserializers()
-        self.deserializers.update({
-        })
+        self.deserializers.update({})
         self.deserializable_keyset.update(self.deserializers.keys())
 
 
@@ -231,11 +246,28 @@ class PageContentProcessor(HTMLParser):
     Processes page content to produce HTML that is suitable for display.
     For now, processor renders embedded objects.
     """
+
     bare_ampersand = re.compile(r"&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)")
     elements_no_end_tag = {
-        'area', 'base', 'basefont', 'br', 'col', 'command', 'embed', 'frame',
-        'hr', 'img', 'input', 'isindex', 'keygen', 'link', 'meta', 'param',
-        'source', 'track', 'wbr'
+        "area",
+        "base",
+        "basefont",
+        "br",
+        "col",
+        "command",
+        "embed",
+        "frame",
+        "hr",
+        "img",
+        "input",
+        "isindex",
+        "keygen",
+        "link",
+        "meta",
+        "param",
+        "source",
+        "track",
+        "wbr",
     }
 
     def __init__(self, trans, render_embed_html_fn: Callable):
@@ -257,10 +289,10 @@ class PageContentProcessor(HTMLParser):
             return f"<{tag}></{tag}>"
 
     def feed(self, data):
-        data = re.compile(r'<!((?!DOCTYPE|--|\[))', re.IGNORECASE).sub(r'&lt;!\1', data)
-        data = re.sub(r'<([^<>\s]+?)\s*/>', self._shorttag_replace, data)
-        data = data.replace('&#39;', "'")
-        data = data.replace('&#34;', '"')
+        data = re.compile(r"<!((?!DOCTYPE|--|\[))", re.IGNORECASE).sub(r"&lt;!\1", data)
+        data = re.sub(r"<([^<>\s]+?)\s*/>", self._shorttag_replace, data)
+        data = data.replace("&#39;", "'")
+        data = data.replace("&#34;", '"')
         HTMLParser.feed(self, data)
         HTMLParser.close(self)
 
@@ -301,17 +333,17 @@ class PageContentProcessor(HTMLParser):
 
         # Default behavior: not ignoring and no embedded content.
         uattrs = []
-        strattrs = ''
+        strattrs = ""
         if attrs:
             for key, value in attrs:
-                value = value.replace('>', '&gt;').replace('<', '&lt;').replace('"', '&quot;')
+                value = value.replace(">", "&gt;").replace("<", "&lt;").replace('"', "&quot;")
                 value = self.bare_ampersand.sub("&amp;", value)
                 uattrs.append((key, value))
-            strattrs = ''.join(f' {k}="{v}"' for k, v in uattrs)
+            strattrs = "".join(f' {k}="{v}"' for k, v in uattrs)
         if tag in self.elements_no_end_tag:
-            self.pieces.append(f'<{tag}{strattrs} />')
+            self.pieces.append(f"<{tag}{strattrs} />")
         else:
-            self.pieces.append(f'<{tag}{strattrs}>')
+            self.pieces.append(f"<{tag}{strattrs}>")
 
     def handle_endtag(self, tag):
         """
@@ -335,23 +367,23 @@ class PageContentProcessor(HTMLParser):
         # called for each character reference, e.g. for '&#160;', ref will be '160'
         # Reconstruct the original character reference.
         ref = ref.lower()
-        if ref.startswith('x'):
+        if ref.startswith("x"):
             value = int(ref[1:], 16)
         else:
             value = int(ref)
 
         if value in _cp1252:
-            self.pieces.append(f'&#{hex(ord(_cp1252[value]))[1:]};')
+            self.pieces.append(f"&#{hex(ord(_cp1252[value]))[1:]};")
         else:
-            self.pieces.append(f'&#{ref};')
+            self.pieces.append(f"&#{ref};")
 
     def handle_entityref(self, ref):
         # called for each entity reference, e.g. for '&copy;', ref will be 'copy'
         # Reconstruct the original entity reference.
-        if ref in name2codepoint or ref == 'apos':
-            self.pieces.append(f'&{ref};')
+        if ref in name2codepoint or ref == "apos":
+            self.pieces.append(f"&{ref};")
         else:
-            self.pieces.append(f'&amp;{ref}')
+            self.pieces.append(f"&amp;{ref}")
 
     def handle_data(self, text):
         """
@@ -367,23 +399,23 @@ class PageContentProcessor(HTMLParser):
     def handle_comment(self, text):
         # called for each HTML comment, e.g. <!-- insert Javascript code here -->
         # Reconstruct the original comment.
-        self.pieces.append(f'<!--{text}-->')
+        self.pieces.append(f"<!--{text}-->")
 
     def handle_decl(self, text):
         # called for the DOCTYPE, if present, e.g.
         # <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
         #     "http://www.w3.org/TR/html4/loose.dtd">
         # Reconstruct original DOCTYPE
-        self.pieces.append(f'<!{text}>')
+        self.pieces.append(f"<!{text}>")
 
     def handle_pi(self, text):
         # called for each processing instruction, e.g. <?instruction>
         # Reconstruct original processing instruction.
-        self.pieces.append(f'<?{text}>')
+        self.pieces.append(f"<?{text}>")
 
     def output(self):
-        '''Return processed HTML as a single string'''
-        return ''.join(self.pieces)
+        """Return processed HTML as a single string"""
+        return "".join(self.pieces)
 
 
 PAGE_MAXRAW = 10**15
@@ -404,14 +436,14 @@ def get_page_identifiers(item_id, app):
 
 
 # Utilities for encoding/decoding HTML content.
-PLACEHOLDER_TEMPLATE = '''<div class="embedded-item {class_shorthand_lower} placeholder" id="{item_class}-{item_id}"><p class="title">Embedded Galaxy {class_shorthand} - '{item_name}'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]</p></div>'''
+PLACEHOLDER_TEMPLATE = """<div class="embedded-item {class_shorthand_lower} placeholder" id="{item_class}-{item_id}"><p class="title">Embedded Galaxy {class_shorthand} - '{item_name}'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]</p></div>"""
 
 # This is a mapping of the id portion of page contents to the cssclass/shortname.
 PAGE_CLASS_MAPPING = {
-    'History': 'History',
-    'HistoryDatasetAssociation': 'Dataset',
-    'StoredWorkflow': 'Workflow',
-    'Visualization': 'Visualization'
+    "History": "History",
+    "HistoryDatasetAssociation": "Dataset",
+    "StoredWorkflow": "Workflow",
+    "Visualization": "Visualization",
 }
 
 
@@ -421,21 +453,21 @@ def placeholderRenderForEdit(trans: ProvidesHistoryContext, item_class, item_id)
 
 def placeholderRenderForSave(trans: ProvidesHistoryContext, item_class, item_id, encode=False):
     encoded_item_id, decoded_item_id = get_page_identifiers(item_id, trans.app)
-    item_name = ''
-    if item_class == 'History':
+    item_name = ""
+    if item_class == "History":
         history = trans.sa_session.query(model.History).get(decoded_item_id)
         history = base.security_check(trans, history, False, True)
         item_name = history.name
-    elif item_class == 'HistoryDatasetAssociation':
+    elif item_class == "HistoryDatasetAssociation":
         hda = trans.sa_session.query(model.HistoryDatasetAssociation).get(decoded_item_id)
         hda_manager = trans.app.hda_manager
         hda = hda_manager.get_accessible(decoded_item_id, trans.user)
         item_name = hda.name
-    elif item_class == 'StoredWorkflow':
+    elif item_class == "StoredWorkflow":
         wf = trans.sa_session.query(model.StoredWorkflow).get(decoded_item_id)
         wf = base.security_check(trans, wf, False, True)
         item_name = wf.name
-    elif item_class == 'Visualization':
+    elif item_class == "Visualization":
         visualization = trans.sa_session.query(model.Visualization).get(decoded_item_id)
         visualization = base.security_check(trans, visualization, False, True)
         item_name = visualization.title
@@ -449,5 +481,5 @@ def placeholderRenderForSave(trans: ProvidesHistoryContext, item_class, item_id,
         class_shorthand=class_shorthand,
         class_shorthand_lower=class_shorthand.lower(),
         item_id=item_id,
-        item_name=item_name
+        item_name=item_name,
     )
diff --git a/lib/galaxy/managers/quotas.py b/lib/galaxy/managers/quotas.py
index 90194d862a8..e0a71eb5c5c 100644
--- a/lib/galaxy/managers/quotas.py
+++ b/lib/galaxy/managers/quotas.py
@@ -11,7 +11,10 @@ from typing import (
     Union,
 )
 
-from galaxy import model, util
+from galaxy import (
+    model,
+    util,
+)
 from galaxy.app import StructuredApp
 from galaxy.exceptions import ActionInputError
 from galaxy.managers import base
@@ -44,7 +47,9 @@ class QuotaManager:
         params = CreateQuotaParams.parse_obj(payload)
         create_amount = self._parse_amount(params.amount)
         if self.sa_session.query(model.Quota).filter(model.Quota.name == params.name).first():
-            raise ActionInputError("Quota names must be unique and a quota with that name already exists, please choose another name.")
+            raise ActionInputError(
+                "Quota names must be unique and a quota with that name already exists, please choose another name."
+            )
         elif create_amount is False:
             raise ActionInputError("Unable to parse the provided amount.")
         elif params.operation not in model.Quota.valid_operations:
@@ -54,7 +59,9 @@ class QuotaManager:
         elif create_amount is None and params.operation != QuotaOperation.EXACT:
             raise ActionInputError("Operation for an unlimited quota must be '='.")
         # Create the quota
-        quota = model.Quota(name=params.name, description=params.description, amount=create_amount, operation=params.operation)
+        quota = model.Quota(
+            name=params.name, description=params.description, amount=create_amount, operation=params.operation
+        )
         self.sa_session.add(quota)
         # If this is a default quota, create the DefaultQuotaAssociation
         if params.default != DefaultQuotaValues.NO:
@@ -62,8 +69,14 @@ class QuotaManager:
             message = f"Default quota '{quota.name}' has been created."
         else:
             # Create the UserQuotaAssociations
-            in_users = [self.sa_session.query(model.User).get(decode_id(x) if decode_id else x) for x in util.listify(params.in_users)]
-            in_groups = [self.sa_session.query(model.Group).get(decode_id(x) if decode_id else x) for x in util.listify(params.in_groups)]
+            in_users = [
+                self.sa_session.query(model.User).get(decode_id(x) if decode_id else x)
+                for x in util.listify(params.in_users)
+            ]
+            in_groups = [
+                self.sa_session.query(model.Group).get(decode_id(x) if decode_id else x)
+                for x in util.listify(params.in_groups)
+            ]
             if None in in_users:
                 raise ActionInputError("One or more invalid user id has been provided.")
             for user in in_users:
@@ -80,7 +93,7 @@ class QuotaManager:
         return quota, message
 
     def _parse_amount(self, amount: str) -> Optional[Union[int, bool]]:
-        if amount.lower() in ('unlimited', 'none', 'no limit'):
+        if amount.lower() in ("unlimited", "none", "no limit"):
             return None
         try:
             return util.size_to_bytes(amount)
@@ -89,9 +102,12 @@ class QuotaManager:
 
     def rename_quota(self, quota, params) -> str:
         if not params.name:
-            raise ActionInputError('Enter a valid name.')
-        elif params.name != quota.name and self.sa_session.query(model.Quota).filter(model.Quota.name == params.name).first():
-            raise ActionInputError('A quota with that name already exists.')
+            raise ActionInputError("Enter a valid name.")
+        elif (
+            params.name != quota.name
+            and self.sa_session.query(model.Quota).filter(model.Quota.name == params.name).first()
+        ):
+            raise ActionInputError("A quota with that name already exists.")
         else:
             old_name = quota.name
             quota.name = params.name
@@ -104,12 +120,18 @@ class QuotaManager:
 
     def manage_users_and_groups_for_quota(self, quota, params, decode_id=None) -> str:
         if quota.default:
-            raise ActionInputError('Default quotas cannot be associated with specific users and groups.')
+            raise ActionInputError("Default quotas cannot be associated with specific users and groups.")
         else:
-            in_users = [self.sa_session.query(model.User).get(decode_id(x) if decode_id else x) for x in util.listify(params.in_users)]
+            in_users = [
+                self.sa_session.query(model.User).get(decode_id(x) if decode_id else x)
+                for x in util.listify(params.in_users)
+            ]
             if None in in_users:
                 raise ActionInputError("One or more invalid user id has been provided.")
-            in_groups = [self.sa_session.query(model.Group).get(decode_id(x) if decode_id else x) for x in util.listify(params.in_groups)]
+            in_groups = [
+                self.sa_session.query(model.Group).get(decode_id(x) if decode_id else x)
+                for x in util.listify(params.in_groups)
+            ]
             if None in in_groups:
                 raise ActionInputError("One or more invalid group id has been provided.")
             self.quota_agent.set_entity_quota_associations(quotas=[quota], users=in_users, groups=in_groups)
@@ -118,7 +140,7 @@ class QuotaManager:
             return message
 
     def edit_quota(self, quota, params) -> str:
-        if params.amount.lower() in ('unlimited', 'none', 'no limit'):
+        if params.amount.lower() in ("unlimited", "none", "no limit"):
             new_amount = None
         else:
             try:
@@ -126,11 +148,11 @@ class QuotaManager:
             except (AssertionError, ValueError):
                 new_amount = False
         if not params.amount:
-            raise ActionInputError('Enter a valid amount.')
+            raise ActionInputError("Enter a valid amount.")
         elif new_amount is False:
-            raise ActionInputError('Unable to parse the provided amount.')
+            raise ActionInputError("Unable to parse the provided amount.")
         elif params.operation not in model.Quota.valid_operations:
-            raise ActionInputError('Enter a valid operation.')
+            raise ActionInputError("Enter a valid operation.")
         else:
             quota.amount = new_amount
             quota.operation = params.operation
@@ -140,10 +162,10 @@ class QuotaManager:
             return message
 
     def set_quota_default(self, quota, params) -> str:
-        if params.default != 'no' and params.default not in model.DefaultQuotaAssociation.types.__members__.values():
-            raise ActionInputError('Enter a valid default type.')
+        if params.default != "no" and params.default not in model.DefaultQuotaAssociation.types.__members__.values():
+            raise ActionInputError("Enter a valid default type.")
         else:
-            if params.default != 'no':
+            if params.default != "no":
                 self.quota_agent.set_default_quota(params.default, quota)
                 message = f"Quota '{quota.name}' is now the default for {params.default} users."
             else:
@@ -175,14 +197,16 @@ class QuotaManager:
         if len(names) == 1:
             raise ActionInputError(f"Quota '{names[0]}' is a default, please unset it as a default before deleting it.")
         elif len(names) > 1:
-            raise ActionInputError(f"Quotas are defaults, please unset them as defaults before deleting them: {', '.join(names)}")
+            raise ActionInputError(
+                f"Quotas are defaults, please unset them as defaults before deleting them: {', '.join(names)}"
+            )
         message = f"Deleted {len(quotas)} quotas: "
         for q in quotas:
             q.deleted = True
             self.sa_session.add(q)
             names.append(q.name)
         self.sa_session.flush()
-        message += ', '.join(names)
+        message += ", ".join(names)
         return message
 
     def undelete_quota(self, quota, params=None) -> str:
@@ -201,7 +225,7 @@ class QuotaManager:
             self.sa_session.add(q)
             names.append(q.name)
         self.sa_session.flush()
-        message += ', '.join(names)
+        message += ", ".join(names)
         return message
 
     def purge_quota(self, quota, params=None):
@@ -230,8 +254,8 @@ class QuotaManager:
                 self.sa_session.delete(gqa)
             names.append(q.name)
         self.sa_session.flush()
-        message += ', '.join(names)
+        message += ", ".join(names)
         return message
 
     def get_quota(self, trans, id: EncodedDatabaseIdField, deleted: Optional[bool] = None) -> model.Quota:
-        return base.get_object(trans, id, 'Quota', check_ownership=False, check_accessible=False, deleted=deleted)
+        return base.get_object(trans, id, "Quota", check_ownership=False, check_accessible=False, deleted=deleted)
diff --git a/lib/galaxy/managers/ratable.py b/lib/galaxy/managers/ratable.py
index b86c5505e3d..e2bb1f08fea 100644
--- a/lib/galaxy/managers/ratable.py
+++ b/lib/galaxy/managers/ratable.py
@@ -62,16 +62,16 @@ class RatableManagerMixin:
 
 
 class RatableSerializerMixin:
-
     def add_serializers(self):
-        self.serializers['user_rating'] = self.serialize_user_rating
-        self.serializers['community_rating'] = self.serialize_community_rating
+        self.serializers["user_rating"] = self.serialize_user_rating
+        self.serializers["community_rating"] = self.serialize_community_rating
 
     def serialize_user_rating(self, item, key, user=None, **context):
         """Returns the integer rating given to this item by the user."""
         if not user:
-            raise base.ModelSerializingError('user_rating requires a user',
-                model_class=self.manager.model_class, id=self.serialize_id(item, 'id'))
+            raise base.ModelSerializingError(
+                "user_rating requires a user", model_class=self.manager.model_class, id=self.serialize_id(item, "id")
+            )
         return self.manager.rating(item, user)
 
     def serialize_community_rating(self, item, key, **context):
@@ -84,26 +84,25 @@ class RatableSerializerMixin:
         # than getting the rows and calc'ing both here with one query
         manager = self.manager
         return {
-            'average': manager.ratings_avg(item),
-            'count': manager.ratings_count(item),
+            "average": manager.ratings_avg(item),
+            "count": manager.ratings_count(item),
         }
 
 
 class RatableDeserializerMixin:
-
     def add_deserializers(self):
-        self.deserializers['user_rating'] = self.deserialize_rating
+        self.deserializers["user_rating"] = self.deserialize_rating
 
     def deserialize_rating(self, item, key, val, user=None, **context):
         if not user:
-            raise base.ModelDeserializingError('user_rating requires a user',
-                model_class=self.manager.model_class, id=self.serialize_id(item, 'id'))
+            raise base.ModelDeserializingError(
+                "user_rating requires a user", model_class=self.manager.model_class, id=self.serialize_id(item, "id")
+            )
         val = self.validate.int_range(key, val, 0, 5)
         return self.manager.rate(item, user, val, flush=False)
 
 
 class RatableFilterMixin:
-
     def _ratings_avg_accessor(self, item):
         return self.manager.ratings_avg(item)
 
@@ -112,14 +111,16 @@ class RatableFilterMixin:
         Adds the following filters:
             `community_rating`: filter
         """
-        self.fn_filter_parsers.update({
-            'community_rating': {
-                'op': {
-                    'eq': lambda i, v: self._ratings_avg_accessor(i) == v,
-                    # TODO: default to greater than (currently 'eq' due to base/controller.py)
-                    'ge': lambda i, v: self._ratings_avg_accessor(i) >= v,
-                    'le': lambda i, v: self._ratings_avg_accessor(i) <= v,
-                },
-                'val': float
+        self.fn_filter_parsers.update(
+            {
+                "community_rating": {
+                    "op": {
+                        "eq": lambda i, v: self._ratings_avg_accessor(i) == v,
+                        # TODO: default to greater than (currently 'eq' due to base/controller.py)
+                        "ge": lambda i, v: self._ratings_avg_accessor(i) >= v,
+                        "le": lambda i, v: self._ratings_avg_accessor(i) <= v,
+                    },
+                    "val": float,
+                }
             }
-        })
+        )
diff --git a/lib/galaxy/managers/rbac_secured.py b/lib/galaxy/managers/rbac_secured.py
index 3587089b6b4..ccbc81d0264 100644
--- a/lib/galaxy/managers/rbac_secured.py
+++ b/lib/galaxy/managers/rbac_secured.py
@@ -3,7 +3,7 @@ import logging
 import galaxy.exceptions
 from galaxy import (
     model,
-    security
+    security,
 )
 from galaxy.managers import users
 
@@ -38,7 +38,7 @@ class RBACPermission:
 
     def error_unless_permitted(self, item, user, trans=None):
         if not self.is_permitted(item, user, trans=trans):
-            error_info = dict(model_class=item.__class__, id=getattr(item, 'id', None))
+            error_info = dict(model_class=item.__class__, id=getattr(item, "id", None))
             raise self.permission_failed_error_class(**error_info)
 
     def grant(self, item, user, flush=True):
@@ -52,7 +52,7 @@ class RBACPermission:
 
     def _error_unless_role_permitted(self, item, role):
         if not self._role_is_permitted(item, role):
-            error_info = dict(model_class=item.__class__, id=getattr(item, 'id', None))
+            error_info = dict(model_class=item.__class__, id=getattr(item, "id", None))
             raise self.permission_failed_error_class(**error_info)
 
     def _grant_role(self, item, role, flush=True):
@@ -75,6 +75,7 @@ class DatasetRBACPermission(RBACPermission):
     - manage permissions : can a role manage the permissions on a dataset
     - access : can a role read/look at/copy a dataset
     """
+
     permissions_class = model.DatasetPermissions
     action_name = None
 
@@ -167,8 +168,9 @@ class ManageDatasetRBACPermission(DatasetRBACPermission):
     When checking permissions for a user, if any of the user's roles
     have permission on the dataset
     """
+
     # TODO: We may also be able to infer/record the dataset 'owner' as well.
-    action_name = security.RBACAgent.permitted_actions.get('DATASET_MANAGE_PERMISSIONS').action
+    action_name = security.RBACAgent.permitted_actions.get("DATASET_MANAGE_PERMISSIONS").action
     permission_failed_error_class = DatasetManagePermissionFailedException
 
     # ---- interface
@@ -227,7 +229,8 @@ class AccessDatasetRBACPermission(DatasetRBACPermission):
     An user must have all the Roles of all the access permissions associated
     with a dataset in order to access it.
     """
-    action_name = security.RBACAgent.permitted_actions.get('DATASET_ACCESS').action
+
+    action_name = security.RBACAgent.permitted_actions.get("DATASET_ACCESS").action
     permission_failed_error_class = DatasetAccessPermissionFailedException
 
     # ---- interface
@@ -238,9 +241,11 @@ class AccessDatasetRBACPermission(DatasetRBACPermission):
         current_roles = self._roles(dataset)
         # NOTE: that because of short circuiting this allows
         #   anonymous access to public datasets
-        return (self._is_public_based_on_roles(current_roles)
-                or self.user_manager.is_admin(user)  # admin is always permitted
-                or self._user_has_all_roles(user, current_roles))
+        return (
+            self._is_public_based_on_roles(current_roles)
+            or self.user_manager.is_admin(user)  # admin is always permitted
+            or self._user_has_all_roles(user, current_roles)
+        )
 
     def grant(self, item, user):
         pass
@@ -273,6 +278,8 @@ class AccessDatasetRBACPermission(DatasetRBACPermission):
 
     def _role_is_permitted(self, dataset, role):
         current_roles = self._roles(dataset)
-        return (self._is_public_based_on_roles(current_roles)
-                # if there's only one role and this is it, let em in
-                or ((len(current_roles) == 1) and (role == current_roles[0])))
+        return (
+            self._is_public_based_on_roles(current_roles)
+            # if there's only one role and this is it, let em in
+            or ((len(current_roles) == 1) and (role == current_roles[0]))
+        )
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index 2e9bfbd96db..6fb6830e966 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -58,11 +58,11 @@ class RemoteFilesManager:
             default_format = RemoteFilesFormat.flat
             default_recursive = True
         elif target == RemoteFilesTarget.importdir:
-            uri = 'gximport://'
+            uri = "gximport://"
             default_format = RemoteFilesFormat.flat
             default_recursive = True
-        elif target in [RemoteFilesTarget.ftpdir, 'ftp']:  # legacy, allow both
-            uri = 'gxftp://'
+        elif target in [RemoteFilesTarget.ftpdir, "ftp"]:  # legacy, allow both
+            uri = "gxftp://"
             default_format = RemoteFilesFormat.flat
             default_recursive = True
         else:
@@ -100,13 +100,19 @@ class RemoteFilesManager:
                 path = ent["path"]
                 path_hash = hashlib.sha1(smart_str(path)).hexdigest()
                 if ent["class"] == "Directory":
-                    path_type = 'folder'
+                    path_type = "folder"
                     disabled = True if disable == RemoteFilesDisableMode.folders else False
                 else:
-                    path_type = 'file'
+                    path_type = "file"
                     disabled = True if disable == RemoteFilesDisableMode.files else False
 
-                jstree_paths.append(jstree.Path(path, path_hash, {'type': path_type, 'state': {'disabled': disabled}, 'li_attr': {'full_path': path}}))
+                jstree_paths.append(
+                    jstree.Path(
+                        path,
+                        path_hash,
+                        {"type": path_type, "state": {"disabled": disabled}, "li_attr": {"full_path": path}},
+                    )
+                )
             userdir_jstree = jstree.JSTree(jstree_paths)
             index = userdir_jstree.jsonData()
 
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index 9eec5893248..42a3b491679 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -21,8 +21,9 @@ class RoleManager(base.ModelManager):
     """
     Business logic for roles.
     """
+
     model_class = model.Role
-    foreign_key_name = 'role'
+    foreign_key_name = "role"
 
     user_assoc = model.UserRoleAssociation
     group_assoc = model.GroupRoleAssociation
@@ -40,17 +41,16 @@ class RoleManager(base.ModelManager):
         :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
         """
         try:
-            role = (self.session().query(self.model_class)
-                    .filter(self.model_class.id == decoded_role_id).one())
+            role = self.session().query(self.model_class).filter(self.model_class.id == decoded_role_id).one()
         except sqlalchemy_exceptions.MultipleResultsFound:
-            raise galaxy.exceptions.InconsistentDatabase('Multiple roles found with the same id.')
+            raise galaxy.exceptions.InconsistentDatabase("Multiple roles found with the same id.")
         except sqlalchemy_exceptions.NoResultFound:
-            raise galaxy.exceptions.RequestParameterInvalidException('No accessible role found with the id provided.')
+            raise galaxy.exceptions.RequestParameterInvalidException("No accessible role found with the id provided.")
         except Exception as e:
             raise galaxy.exceptions.InternalServerError(f"Error loading from the database.{unicodify(e)}")
 
         if not (trans.user_is_admin or trans.app.security_agent.ok_to_display(trans.user, role)):
-            raise galaxy.exceptions.RequestParameterInvalidException('No accessible role found with the id provided.')
+            raise galaxy.exceptions.RequestParameterInvalidException("No accessible role found with the id provided.")
 
         return role
 
diff --git a/lib/galaxy/managers/secured.py b/lib/galaxy/managers/secured.py
index 70f37c6f22b..7103c435a18 100644
--- a/lib/galaxy/managers/secured.py
+++ b/lib/galaxy/managers/secured.py
@@ -5,7 +5,10 @@ Owned models can be modified and deleted.
 """
 from typing import Type
 
-from galaxy import exceptions, model
+from galaxy import (
+    exceptions,
+    model,
+)
 
 
 class AccessibleManagerMixin:
@@ -81,6 +84,7 @@ class OwnableManagerMixin:
 
     This can also be thought of as write/edit privileges.
     """
+
     # declare what we are using from base ModelManager
     model_class: Type[model._HasTable]
 
diff --git a/lib/galaxy/managers/session.py b/lib/galaxy/managers/session.py
index 8ec49cd23ad..5d9fc238af8 100644
--- a/lib/galaxy/managers/session.py
+++ b/lib/galaxy/managers/session.py
@@ -4,9 +4,7 @@ from sqlalchemy import (
     and_,
     true,
 )
-from sqlalchemy.orm import (
-    joinedload,
-)
+from sqlalchemy.orm import joinedload
 
 from galaxy.model.base import SharedModelMapping
 
@@ -24,9 +22,15 @@ class GalaxySessionManager:
         """Returns GalaxySession if session_key is valid."""
         # going through self.model since this can be used by Galaxy or Toolshed despite
         # type annotations
-        galaxy_session = self.sa_session.query(self.model.GalaxySession).filter(
-            and_(
-                self.model.GalaxySession.table.c.session_key == session_key,
-                self.model.GalaxySession.table.c.is_valid == true())
-        ).options(joinedload("user")).first()
+        galaxy_session = (
+            self.sa_session.query(self.model.GalaxySession)
+            .filter(
+                and_(
+                    self.model.GalaxySession.table.c.session_key == session_key,
+                    self.model.GalaxySession.table.c.is_valid == true(),
+                )
+            )
+            .options(joinedload("user"))
+            .first()
+        )
         return galaxy_session
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index cf1ddcf2bb3..f013f182be5 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -29,7 +29,7 @@ from galaxy.managers import (
     ratable,
     secured,
     taggable,
-    users
+    users,
 )
 from galaxy.model import (
     User,
@@ -46,8 +46,14 @@ from galaxy.util import ready_name_for_url
 log = logging.getLogger(__name__)
 
 
-class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secured.AccessibleManagerMixin,
-        taggable.TaggableManagerMixin, annotatable.AnnotatableManagerMixin, ratable.RatableManagerMixin):
+class SharableModelManager(
+    base.ModelManager,
+    secured.OwnableManagerMixin,
+    secured.AccessibleManagerMixin,
+    taggable.TaggableManagerMixin,
+    annotatable.AnnotatableManagerMixin,
+    ratable.RatableManagerMixin,
+):
     # e.g. histories, pages, stored workflows, visualizations
     # base.DeleteableModelMixin? (all four are deletable)
 
@@ -107,7 +113,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         importable, and slug attributes.
         """
         self.create_unique_slug(item, flush=False)
-        return self._session_setattr(item, 'importable', True, flush=flush)
+        return self._session_setattr(item, "importable", True, flush=flush)
 
     def make_non_importable(self, item, flush=True):
         """
@@ -118,7 +124,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         # item must be unpublished if non-importable
         if item.published:
             self.unpublish(item, flush=False)
-        return self._session_setattr(item, 'importable', False, flush=flush)
+        return self._session_setattr(item, "importable", False, flush=flush)
 
     # .... published
     def publish(self, item, flush=True):
@@ -128,13 +134,13 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         # item must be importable to be published
         if not item.importable:
             self.make_importable(item, flush=False)
-        return self._session_setattr(item, 'published', True, flush=flush)
+        return self._session_setattr(item, "published", True, flush=flush)
 
     def unpublish(self, item, flush=True):
         """
         Set the published flag on `item` to False.
         """
-        return self._session_setattr(item, 'published', False, flush=flush)
+        return self._session_setattr(item, "published", False, flush=flush)
 
     def _query_published(self, filters=None, **kwargs):
         """
@@ -209,7 +215,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         Return a query for this model already filtered to models shared
         with a particular user.
         """
-        query = self.session().query(self.model_class).join('users_shared_with')
+        query = self.session().query(self.model_class).join("users_shared_with")
         if eagerloads is False:
             query = query.enable_eagerloads(False)
         # TODO: as filter in FilterParser also
@@ -224,13 +230,13 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         orm_filters, fn_filters = self._split_filters(filters)
         if not fn_filters:
             # if no fn_filtering required, we can use the 'all orm' version with limit offset
-            query = self._query_shared_with(user, filters=orm_filters,
-                order_by=order_by, limit=limit, offset=offset, **kwargs)
+            query = self._query_shared_with(
+                user, filters=orm_filters, order_by=order_by, limit=limit, offset=offset, **kwargs
+            )
             return self._orm_list(query=query, **kwargs)
 
         # fn filters will change the number of items returnable by limit/offset - remove them here from the orm query
-        query = self._query_shared_with(user, filters=orm_filters,
-            order_by=order_by, limit=None, offset=None, **kwargs)
+        query = self._query_shared_with(user, filters=orm_filters, order_by=order_by, limit=None, offset=None, **kwargs)
         # apply limit and offset afterwards
         items = self._apply_fn_filters_gen(query.all(), fn_filters)
         return list(self._apply_fn_limit_offset_gen(items, limit, offset))
@@ -245,7 +251,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         return None
 
     def make_members_public(self, trans, item):
-        """ Make potential elements of this item public.
+        """Make potential elements of this item public.
 
         This method must be overridden in managers that need to change permissions of internal elements
         contained associated with the given item.
@@ -301,9 +307,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         return VALID_SLUG_RE.match(slug)
 
     def _slug_exists(self, user, slug):
-        query = (self.session().query(self.model_class)
-                 .filter_by(user_id=user.id, slug=slug)
-                 .with_entities(func.count()))
+        query = self.session().query(self.model_class).filter_by(user_id=user.id, slug=slug).with_entities(func.count())
         return query.scalar() != 0
 
     def _slugify(self, start_with):
@@ -312,13 +316,13 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         # Remove all non-alphanumeric characters.
         slug_base = re.sub(r"[^a-zA-Z0-9\-]", "", slug_base)
         # Remove trailing '-'.
-        if slug_base.endswith('-'):
+        if slug_base.endswith("-"):
             slug_base = slug_base[:-1]
         return slug_base
 
     def _default_slug_base(self, item):
         # override in subclasses
-        if hasattr(item, 'title'):
+        if hasattr(item, "title"):
             return item.title.lower()
         return item.name.lower()
 
@@ -339,12 +343,12 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
         # add integer to end.
         new_slug = slug_base
         count = 1
-        while (self.session().query(item.__class__)
-               .filter_by(user=item.user, slug=new_slug, importable=True)
-               .count() != 0):
+        while (
+            self.session().query(item.__class__).filter_by(user=item.user, slug=new_slug, importable=True).count() != 0
+        ):
             # Slug taken; choose a new slug based on count. This approach can
             # handle numerous items with the same name gracefully.
-            new_slug = '%s-%i' % (slug_base, count)
+            new_slug = "%s-%i" % (slug_base, count)
             count += 1
 
         return new_slug
@@ -362,37 +366,34 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
     # TODO: def by_slug( self, user, **kwargs ):
 
 
-class SharableModelSerializer(base.ModelSerializer,
-       taggable.TaggableSerializerMixin, annotatable.AnnotatableSerializerMixin, ratable.RatableSerializerMixin):
+class SharableModelSerializer(
+    base.ModelSerializer,
+    taggable.TaggableSerializerMixin,
+    annotatable.AnnotatableSerializerMixin,
+    ratable.RatableSerializerMixin,
+):
     # TODO: stub
     SINGLE_CHAR_ABBR: Optional[str] = None
 
     def __init__(self, app, **kwargs):
         super().__init__(app, **kwargs)
-        self.add_view('sharing', [
-            'id',
-            'title',
-            'importable',
-            'published',
-            'username_and_slug',
-            'users_shared_with'
-        ])
+        self.add_view("sharing", ["id", "title", "importable", "published", "username_and_slug", "users_shared_with"])
 
     def add_serializers(self):
         super().add_serializers()
         taggable.TaggableSerializerMixin.add_serializers(self)
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
         ratable.RatableSerializerMixin.add_serializers(self)
-        self.serializers.update({
-            'id': self.serialize_id,
-            'title': self.serialize_title,
-            'username_and_slug': self.serialize_username_and_slug,
-            'users_shared_with': self.serialize_users_shared_with
-        })
+        self.serializers.update(
+            {
+                "id": self.serialize_id,
+                "title": self.serialize_title,
+                "username_and_slug": self.serialize_username_and_slug,
+                "users_shared_with": self.serialize_users_shared_with,
+            }
+        )
         # these use the default serializer but must still be white-listed
-        self.serializable_keyset.update([
-            'importable', 'published', 'slug'
-        ])
+        self.serializable_keyset.update(["importable", "published", "slug"])
 
     def serialize_title(self, item, key, **context):
         if hasattr(item, "title"):
@@ -403,7 +404,7 @@ class SharableModelSerializer(base.ModelSerializer,
     def serialize_username_and_slug(self, item, key, **context):
         if not (item.user and item.user.username and item.slug and self.SINGLE_CHAR_ABBR):
             return None
-        return ('/').join(('u', item.user.username, self.SINGLE_CHAR_ABBR, item.slug))
+        return ("/").join(("u", item.user.username, self.SINGLE_CHAR_ABBR, item.slug))
 
     # the only ones that needs any fns:
     #   user/user_id
@@ -421,12 +422,15 @@ class SharableModelSerializer(base.ModelSerializer,
             self.skip()
 
         share_assocs = self.manager.get_share_assocs(item)
-        return [self.serialize_id(share, 'user_id') for share in share_assocs]
+        return [self.serialize_id(share, "user_id") for share in share_assocs]
 
 
-class SharableModelDeserializer(base.ModelDeserializer,
-        taggable.TaggableDeserializerMixin, annotatable.AnnotatableDeserializerMixin, ratable.RatableDeserializerMixin):
-
+class SharableModelDeserializer(
+    base.ModelDeserializer,
+    taggable.TaggableDeserializerMixin,
+    annotatable.AnnotatableDeserializerMixin,
+    ratable.RatableDeserializerMixin,
+):
     def __init__(self, app: MinimalManagerApp, **kwargs):
         super().__init__(app, **kwargs)
         self.tag_handler = app.tag_handler
@@ -437,15 +441,16 @@ class SharableModelDeserializer(base.ModelDeserializer,
         annotatable.AnnotatableDeserializerMixin.add_deserializers(self)
         ratable.RatableDeserializerMixin.add_deserializers(self)
 
-        self.deserializers.update({
-            'published': self.deserialize_published,
-            'importable': self.deserialize_importable,
-            'users_shared_with': self.deserialize_users_shared_with,
-        })
+        self.deserializers.update(
+            {
+                "published": self.deserialize_published,
+                "importable": self.deserialize_importable,
+                "users_shared_with": self.deserialize_users_shared_with,
+            }
+        )
 
     def deserialize_published(self, item, key, val, **context):
-        """
-        """
+        """ """
         val = self.validate.bool(key, val)
         if item.published == val:
             return val
@@ -457,8 +462,7 @@ class SharableModelDeserializer(base.ModelDeserializer,
         return item.published
 
     def deserialize_importable(self, item, key, val, **context):
-        """
-        """
+        """ """
         val = self.validate.bool(key, val)
         if item.importable == val:
             return val
@@ -484,22 +488,24 @@ class SharableModelDeserializer(base.ModelDeserializer,
         return current_shares
 
 
-class SharableModelFilters(base.ModelFilterParser,
-        taggable.TaggableFilterMixin, annotatable.AnnotatableFilterMixin, ratable.RatableFilterMixin):
-
+class SharableModelFilters(
+    base.ModelFilterParser, taggable.TaggableFilterMixin, annotatable.AnnotatableFilterMixin, ratable.RatableFilterMixin
+):
     def _add_parsers(self):
         super()._add_parsers()
         taggable.TaggableFilterMixin._add_parsers(self)
         annotatable.AnnotatableFilterMixin._add_parsers(self)
         ratable.RatableFilterMixin._add_parsers(self)
 
-        self.orm_filter_parsers.update({
-            'importable': {'op': ('eq'), 'val': base.parse_bool},
-            'published': {'op': ('eq'), 'val': base.parse_bool},
-            'slug': {'op': ('eq', 'contains', 'like')},
-            # chose by user should prob. only be available for admin? (most often we'll only need trans.user)
-            # 'user'          : { 'op': ( 'eq' ), 'val': self.parse_id_list },
-        })
+        self.orm_filter_parsers.update(
+            {
+                "importable": {"op": ("eq"), "val": base.parse_bool},
+                "published": {"op": ("eq"), "val": base.parse_bool},
+                "slug": {"op": ("eq", "contains", "like")},
+                # chose by user should prob. only be available for admin? (most often we'll only need trans.user)
+                # 'user'          : { 'op': ( 'eq' ), 'val': self.parse_id_list },
+            }
+        )
 
 
 class SlugBuilder:
@@ -519,12 +525,12 @@ class SlugBuilder:
         cur_slug = item.slug
 
         # Setup slug base.
-        if cur_slug is None or cur_slug == '':
+        if cur_slug is None or cur_slug == "":
             # Item can have either a name or a title.
-            item_name = ''
-            if hasattr(item, 'name'):
+            item_name = ""
+            if hasattr(item, "name"):
                 item_name = item.name
-            elif hasattr(item, 'title'):
+            elif hasattr(item, "title"):
                 item_name = item.title
             slug_base = ready_name_for_url(item_name.lower())
         else:
@@ -536,10 +542,15 @@ class SlugBuilder:
         count = 1
         # Ensure unique across model class and user and don't include this item
         # in the check in case it has previously been assigned a valid slug.
-        while sa_session.query(item.__class__).filter(item.__class__.user == item.user, item.__class__.slug == new_slug, item.__class__.id != item.id).count() != 0:
+        while (
+            sa_session.query(item.__class__)
+            .filter(item.__class__.user == item.user, item.__class__.slug == new_slug, item.__class__.id != item.id)
+            .count()
+            != 0
+        ):
             # Slug taken; choose a new slug based on count. This approach can
             # handle numerous items with the same name gracefully.
-            new_slug = f'{slug_base}-{count}'
+            new_slug = f"{slug_base}-{count}"
             count += 1
 
         # Set slug and return.
diff --git a/lib/galaxy/managers/taggable.py b/lib/galaxy/managers/taggable.py
index 233fc417c9d..9a6377ecf2b 100644
--- a/lib/galaxy/managers/taggable.py
+++ b/lib/galaxy/managers/taggable.py
@@ -12,7 +12,10 @@ from sqlalchemy import sql
 from galaxy import model
 from galaxy.model.tags import GalaxyTagHandler
 from galaxy.util import unicodify
-from .base import ModelValidator, raise_filter_err
+from .base import (
+    ModelValidator,
+    raise_filter_err,
+)
 
 log = logging.getLogger(__name__)
 
@@ -28,7 +31,7 @@ def _tag_str_gen(item):
 
 
 def _tags_to_strings(item):
-    if not hasattr(item, 'tags'):
+    if not hasattr(item, "tags"):
         return None
     return sorted(list(_tag_str_gen(item)))
 
@@ -42,8 +45,8 @@ def _tags_from_strings(item, tag_handler, new_tags_list, user=None):
         return
     # TODO: duped from tags manager - de-dupe when moved to taggable mixin
     tag_handler.delete_item_tags(user, item)
-    new_tags_str = ','.join(new_tags_list)
-    tag_handler.apply_item_tags(user, item, unicodify(new_tags_str, 'utf-8'))
+    new_tags_str = ",".join(new_tags_list)
+    tag_handler.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"))
     # TODO:!! does the creation of new_tags_list mean there are now more and more unused tag rows in the db?
 
 
@@ -70,9 +73,8 @@ class TaggableManagerMixin:
 
 
 class TaggableSerializerMixin:
-
     def add_serializers(self):
-        self.serializers['tags'] = self.serialize_tags
+        self.serializers["tags"] = self.serialize_tags
 
     def serialize_tags(self, item, key, **context):
         """
@@ -86,7 +88,7 @@ class TaggableDeserializerMixin:
     validate: ModelValidator
 
     def add_deserializers(self):
-        self.deserializers['tags'] = self.deserialize_tags
+        self.deserializers["tags"] = self.deserialize_tags
 
     def deserialize_tags(self, item, key, val, user=None, **context):
         """
@@ -101,24 +103,23 @@ class TaggableDeserializerMixin:
 
 class TaggableFilterMixin:
 
-    valid_ops = ('eq', 'contains', 'has')
+    valid_ops = ("eq", "contains", "has")
 
     def create_tag_filter(self, attr, op, val):
-
         def _create_tag_filter(model_class=None):
             if op not in TaggableFilterMixin.valid_ops:
-                raise_filter_err(attr, op, val, 'bad op in filter')
+                raise_filter_err(attr, op, val, "bad op in filter")
             if model_class is None:
                 return True
             class_name = model_class.__name__
-            if class_name == 'HistoryDatasetCollectionAssociation':
+            if class_name == "HistoryDatasetCollectionAssociation":
                 # Unfortunately we were a little inconsistent with our naming scheme
-                class_name = 'HistoryDatasetCollection'
+                class_name = "HistoryDatasetCollection"
             target_model = getattr(model, f"{class_name}TagAssociation")
             id_column = f"{target_model.table.name.rsplit('_tag_association')[0]}_id"
             column = target_model.table.c.user_tname + ":" + target_model.table.c.user_value
-            if op == 'eq':
-                if ':' not in val:
+            if op == "eq":
+                if ":" not in val:
                     # We require an exact match and the tag to look for has no user_value,
                     # so we can't just concatenate user_tname, ':' and user_vale
                     cond = target_model.table.c.user_tname == val
@@ -126,13 +127,9 @@ class TaggableFilterMixin:
                     cond = column == val
             else:
                 cond = column.contains(val, autoescape=True)
-            return sql.expression.and_(
-                model_class.table.c.id == getattr(target_model.table.c, id_column),
-                cond
-            )
+            return sql.expression.and_(model_class.table.c.id == getattr(target_model.table.c, id_column), cond)
+
         return _create_tag_filter
 
     def _add_parsers(self):
-        self.orm_filter_parsers.update({
-            'tag': self.create_tag_filter
-        })
+        self.orm_filter_parsers.update({"tag": self.create_tag_filter})
diff --git a/lib/galaxy/managers/tags.py b/lib/galaxy/managers/tags.py
index 3afbe9862e0..9fe308f163e 100644
--- a/lib/galaxy/managers/tags.py
+++ b/lib/galaxy/managers/tags.py
@@ -1,7 +1,5 @@
 from enum import Enum
-from typing import (
-    Optional,
-)
+from typing import Optional
 
 from pydantic import (
     BaseModel,
@@ -17,7 +15,7 @@ from galaxy.schema.schema import TagCollection
 taggable_item_names = {item: item for item in ItemTagAssociation.associated_item_names}
 # This Enum is generated dynamically and mypy can not statically infer it's real type
 # so it should be ignored. See: https://github.com/python/mypy/issues/4865#issuecomment-592560696
-TaggableItemClass = Enum('TaggableItemClass', taggable_item_names)  # type: ignore[misc]
+TaggableItemClass = Enum("TaggableItemClass", taggable_item_names)  # type: ignore[misc]
 
 
 class ItemTagsPayload(BaseModel):
diff --git a/lib/galaxy/managers/tool_data.py b/lib/galaxy/managers/tool_data.py
index c03d3bdc39f..d4f50f7eed4 100644
--- a/lib/galaxy/managers/tool_data.py
+++ b/lib/galaxy/managers/tool_data.py
@@ -37,7 +37,7 @@ class ToolDataManager:
     def show(self, table_name: str) -> ToolDataDetails:
         """Get details of a given data table"""
         data_table = self._data_table(table_name)
-        element_view = data_table.to_dict(view='element')
+        element_view = data_table.to_dict(view="element")
         return ToolDataDetails.parse_obj(element_view)
 
     def show_field(self, table_name: str, field_name: str) -> ToolDataField:
@@ -69,7 +69,9 @@ class ToolDataManager:
         split_values = values.split("\t")
 
         if len(split_values) != len(data_table.get_column_name_list()):
-            raise exceptions.RequestParameterInvalidException(f"Invalid data table item ( {values} ) specified. Wrong number of columns ({len(split_values)} given, {len(data_table.get_column_name_list())} required).")
+            raise exceptions.RequestParameterInvalidException(
+                f"Invalid data table item ( {values} ) specified. Wrong number of columns ({len(split_values)} given, {len(data_table.get_column_name_list())} required)."
+            )
 
         data_table.remove_entry(split_values)
         return self._reload_data_table(table_name)
@@ -87,9 +89,5 @@ class ToolDataManager:
         return out
 
     def _reload_data_table(self, name: str) -> ToolDataDetails:
-        self._app.queue_worker.send_control_task(
-            'reload_tool_data_tables',
-            noop_self=True,
-            kwargs={'table_name': name}
-        )
+        self._app.queue_worker.send_control_task("reload_tool_data_tables", noop_self=True, kwargs={"table_name": name})
         return self.show(name)
diff --git a/lib/galaxy/managers/tools.py b/lib/galaxy/managers/tools.py
index a9f4d6222ab..1b05ff43b46 100644
--- a/lib/galaxy/managers/tools.py
+++ b/lib/galaxy/managers/tools.py
@@ -1,14 +1,23 @@
 import logging
-from typing import Optional, TYPE_CHECKING, Union
+from typing import (
+    Optional,
+    TYPE_CHECKING,
+    Union,
+)
 from uuid import UUID
 
 from sqlalchemy import sql
 
-from galaxy import exceptions
-from galaxy import model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.exceptions import DuplicatedIdentifierException
 from galaxy.tool_util.cwl import tool_proxy
-from .base import ModelManager, raise_filter_err
+from .base import (
+    ModelManager,
+    raise_filter_err,
+)
 from .executables import artifact_class
 
 log = logging.getLogger(__name__)
@@ -18,31 +27,27 @@ if TYPE_CHECKING:
 
 
 class DynamicToolManager(ModelManager):
-    """ Manages dynamic tools stored in Galaxy's database.
-    """
+    """Manages dynamic tools stored in Galaxy's database."""
+
     model_class = model.DynamicTool
 
     def get_tool_by_uuid(self, uuid: Optional[Union[UUID, str]]):
-        dynamic_tool = self._one_or_none(
-            self.query().filter(self.model_class.uuid == uuid)
-        )
+        dynamic_tool = self._one_or_none(self.query().filter(self.model_class.uuid == uuid))
         return dynamic_tool
 
     def get_tool_by_tool_id(self, tool_id):
-        dynamic_tool = self._one_or_none(
-            self.query().filter(self.model_class.tool_id == tool_id)
-        )
+        dynamic_tool = self._one_or_none(self.query().filter(self.model_class.tool_id == tool_id))
         return dynamic_tool
 
     def get_tool_by_id(self, object_id):
-        dynamic_tool = self._one_or_none(
-            self.query().filter(self.model_class.id == object_id)
-        )
+        dynamic_tool = self._one_or_none(self.query().filter(self.model_class.id == object_id))
         return dynamic_tool
 
     def create_tool(self, trans, tool_payload, allow_load=True):
         if not getattr(self.app.config, "enable_beta_tool_formats", False):
-            raise exceptions.ConfigDoesNotAllowException("Set 'enable_beta_tool_formats' in Galaxy config to create dynamic tools.")
+            raise exceptions.ConfigDoesNotAllowException(
+                "Set 'enable_beta_tool_formats' in Galaxy config to create dynamic tools."
+            )
 
         dynamic_tool = None
         uuid_str = tool_payload.get("uuid")
@@ -66,15 +71,11 @@ class DynamicToolManager(ModelManager):
                 assert src == "representation"
                 representation = tool_payload.get("representation")
                 if not representation:
-                    raise exceptions.ObjectAttributeMissingException(
-                        "A tool 'representation' is required."
-                    )
+                    raise exceptions.ObjectAttributeMissingException("A tool 'representation' is required.")
 
                 tool_format = representation.get("class")
                 if not tool_format:
-                    raise exceptions.ObjectAttributeMissingException(
-                        "Current tool representations require 'class'."
-                    )
+                    raise exceptions.ObjectAttributeMissingException("Current tool representations require 'class'.")
 
             tool_path = tool_payload.get("path")
             tool_directory = tool_payload.get("tool_directory")
@@ -122,32 +123,36 @@ class ToolFilterMixin:
     orm_filter_parsers: "OrmFilterParsersType"
 
     def create_tool_filter(self, attr, op, val):
-
         def _create_tool_filter(model_class=None):
-            if op == 'eq':
+            if op == "eq":
                 cond = model.Job.table.c.tool_id == val
-            elif op == 'contains':
+            elif op == "contains":
                 cond = model.Job.table.c.tool_id.contains(val, autoescape=True)
             else:
-                raise_filter_err(attr, op, val, 'bad op in filter')
+                raise_filter_err(attr, op, val, "bad op in filter")
             if model_class is model.HistoryDatasetAssociation:
                 return sql.expression.and_(
                     model.Job.table.c.id == model.JobToOutputDatasetAssociation.table.c.job_id,
-                    model.HistoryDatasetAssociation.table.c.id == model.JobToOutputDatasetAssociation.table.c.dataset_id,
-                    cond
+                    model.HistoryDatasetAssociation.table.c.id
+                    == model.JobToOutputDatasetAssociation.table.c.dataset_id,
+                    cond,
                 )
             elif model_class is model.HistoryDatasetCollectionAssociation:
                 return sql.expression.and_(
                     model.Job.id == model.JobToOutputDatasetAssociation.job_id,
                     model.JobToOutputDatasetAssociation.dataset_id == model.DatasetCollectionElement.hda_id,
-                    model.DatasetCollectionElement.dataset_collection_id == model.HistoryDatasetCollectionAssociation.collection_id,
+                    model.DatasetCollectionElement.dataset_collection_id
+                    == model.HistoryDatasetCollectionAssociation.collection_id,
                     cond,
                 )
             else:
                 return True
+
         return _create_tool_filter
 
     def _add_parsers(self):
-        self.orm_filter_parsers.update({
-            'tool_id': self.create_tool_filter,
-        })
+        self.orm_filter_parsers.update(
+            {
+                "tool_id": self.create_tool_filter,
+            }
+        )
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 05d7b2bc4ea..09bf8eeb49e 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -9,7 +9,13 @@ import time
 from datetime import datetime
 
 from markupsafe import escape
-from sqlalchemy import and_, desc, exc, func, true
+from sqlalchemy import (
+    and_,
+    desc,
+    exc,
+    func,
+    true,
+)
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import (
@@ -21,15 +27,18 @@ from galaxy import (
 from galaxy.managers import (
     api_keys,
     base,
-    deletable
+    deletable,
 )
 from galaxy.security.validate_user_input import (
     VALID_EMAIL_RE,
     validate_email,
     validate_password,
-    validate_publicname
+    validate_publicname,
+)
+from galaxy.structured_app import (
+    BasicSharedApp,
+    MinimalManagerApp,
 )
-from galaxy.structured_app import BasicSharedApp, MinimalManagerApp
 from galaxy.util.hash_util import new_secure_hash
 from galaxy.web import url_for
 
@@ -50,7 +59,7 @@ can also copy and paste it into your browser.
 
 
 class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
-    foreign_key_name = 'user'
+    foreign_key_name = "user"
 
     # TODO: there is quite a bit of functionality around the user (authentication, permissions, quotas, groups/roles)
     #   most of which it may be unneccessary to have here
@@ -73,9 +82,13 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             return None, message
         if not email or not username or not password or not confirm:
             return None, "Please provide email, username and password."
-        message = "\n".join((validate_email(trans, email),
-                             validate_password(trans, password, confirm),
-                             validate_publicname(trans, username))).rstrip()
+        message = "\n".join(
+            (
+                validate_email(trans, email),
+                validate_password(trans, password, confirm),
+                validate_publicname(trans, username),
+            )
+        ).rstrip()
         if message:
             return None, message
         email = util.restore_text(email)
@@ -120,23 +133,29 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
     def delete(self, user, flush=True):
         """Mark the given user deleted."""
         if not self.app.config.allow_user_deletion:
-            raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow admins to delete users.')
+            raise exceptions.ConfigDoesNotAllowException(
+                "The configuration of this Galaxy instance does not allow admins to delete users."
+            )
         super().delete(user, flush=flush)
 
     def undelete(self, user, flush=True):
         """Remove the deleted flag for the given user."""
         if not self.app.config.allow_user_deletion:
-            raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow admins to undelete users.')
+            raise exceptions.ConfigDoesNotAllowException(
+                "The configuration of this Galaxy instance does not allow admins to undelete users."
+            )
         if user.purged:
-            raise exceptions.ItemDeletionException('Purged user cannot be undeleted.')
+            raise exceptions.ItemDeletionException("Purged user cannot be undeleted.")
         super().undelete(user, flush=flush)
 
     def purge(self, user, flush=True):
         """Purge the given user. They must have the deleted flag already."""
         if not self.app.config.allow_user_deletion:
-            raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow admins to delete or purge users.')
+            raise exceptions.ConfigDoesNotAllowException(
+                "The configuration of this Galaxy instance does not allow admins to delete or purge users."
+            )
         if not user.deleted:
-            raise exceptions.MessageException('User \'%s\' has not been deleted, so they cannot be purged.' % user.email)
+            raise exceptions.MessageException("User '%s' has not been deleted, so they cannot be purged." % user.email)
         private_role = self.app.security_agent.get_private_user_role(user)
         # Delete History
         for active_history in user.active_histories:
@@ -157,8 +176,8 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         # Delete UserAddresses
         for address in user.addresses:
             self.session().delete(address)
-        compliance_log = logging.getLogger('COMPLIANCE')
-        compliance_log.info(f'delete-user-event: {user.username}')
+        compliance_log = logging.getLogger("COMPLIANCE")
+        compliance_log.info(f"delete-user-event: {user.username}")
         # Maybe there is some case in the future where an admin needs
         # to prove that a user was using a server for some reason (e.g.
         # a court case.) So we make this painfully hard to recover (and
@@ -188,8 +207,12 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             user.username = uname_hash
         # Redact user addresses as well
         if self.app.config.redact_user_address_during_deletion:
-            user_addresses = self.session().query(self.app.model.UserAddress) \
-                .filter(self.app.model.UserAddress.user_id == user.id).all()
+            user_addresses = (
+                self.session()
+                .query(self.app.model.UserAddress)
+                .filter(self.app.model.UserAddress.user_id == user.id)
+                .all()
+            )
             for addr in user_addresses:
                 addr.desc = new_secure_hash(addr.desc + pseudorandom_value)
                 addr.name = new_secure_hash(addr.name + pseudorandom_value)
@@ -212,7 +235,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         """
         # TODO: remove this check when unique=True is added to the email column
         if self.by_email(email) is not None:
-            raise exceptions.Conflict('Email must be unique', email=email)
+            raise exceptions.Conflict("Email must be unique", email=email)
 
     def by_id(self, user_id):
         return self.app.model.session.query(self.model_class).get(user_id)
@@ -239,17 +262,17 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         try:
             provided_key = sa_session.query(self.app.model.APIKeys).filter(self.app.model.APIKeys.key == api_key).one()
         except NoResultFound:
-            raise exceptions.AuthenticationFailed('Provided API key is not valid.')
+            raise exceptions.AuthenticationFailed("Provided API key is not valid.")
         if provided_key.user.deleted:
-            raise exceptions.AuthenticationFailed('User account is deactivated, please contact an administrator.')
+            raise exceptions.AuthenticationFailed("User account is deactivated, please contact an administrator.")
         sa_session.refresh(provided_key.user)
         newest_key = provided_key.user.api_keys[0]
         if newest_key.key != provided_key.key:
-            raise exceptions.AuthenticationFailed('Provided API key has expired.')
+            raise exceptions.AuthenticationFailed("Provided API key has expired.")
         return provided_key.user
 
     def check_master_api_key(self, api_key):
-        master_api_key = getattr(self.app.config, 'master_api_key', None)
+        master_api_key = getattr(self.app.config, "master_api_key", None)
         if not master_api_key:
             return False
         # Hash keys to make them the same size, so we can do safe comparison.
@@ -311,15 +334,17 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         user = None
         if VALID_EMAIL_RE.match(identity):
             # VALID_PUBLICNAME and VALID_EMAIL do not overlap, so 'identity' here is an email address
-            user = self.session().query(self.model_class).filter(
-                self.model_class.table.c.email == identity).first()
+            user = self.session().query(self.model_class).filter(self.model_class.table.c.email == identity).first()
             if not user:
                 # Try a case-insensitive match on the email
-                user = self.session().query(self.model_class).filter(
-                    func.lower(self.model_class.table.c.email) == identity.lower()).first()
+                user = (
+                    self.session()
+                    .query(self.model_class)
+                    .filter(func.lower(self.model_class.table.c.email) == identity.lower())
+                    .first()
+                )
         else:
-            user = self.session().query(self.model_class).filter(
-                self.model_class.table.c.username == identity).first()
+            user = self.session().query(self.model_class).filter(self.model_class.table.c.username == identity).first()
         return user
 
     # ---- current
@@ -351,9 +376,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         """
         Return this most recent APIKey for this user or None if none have been created.
         """
-        query = (self.session().query(model.APIKeys)
-                 .filter_by(user=user)
-                 .order_by(desc(model.APIKeys.create_time)))
+        query = self.session().query(model.APIKeys).filter_by(user=user).order_by(desc(model.APIKeys.create_time))
         all = query.all()
         if len(all):
             return all[0]
@@ -404,8 +427,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         # create a union of subqueries for each for this user - getting only the tname and user_value
         all_tags_query = None
         for tag_model in tag_models:
-            subq = (self.session().query(tag_model.user_tname, tag_model.user_value)
-                    .filter(tag_model.user == user))
+            subq = self.session().query(tag_model.user_tname, tag_model.user_value).filter(tag_model.user == user)
             all_tags_query = subq if all_tags_query is None else all_tags_query.union(subq)
 
         # if nothing init'd the query, bail
@@ -460,10 +482,13 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
                 user.set_password_cleartext(password)
                 # Invalidate all other sessions
                 if trans.galaxy_session:
-                    for other_galaxy_session in trans.sa_session.query(self.app.model.GalaxySession) \
-                                                     .filter(and_(self.app.model.GalaxySession.table.c.user_id == user.id,
-                                                                  self.app.model.GalaxySession.table.c.is_valid == true(),
-                                                                  self.app.model.GalaxySession.table.c.id != trans.galaxy_session.id)):
+                    for other_galaxy_session in trans.sa_session.query(self.app.model.GalaxySession).filter(
+                        and_(
+                            self.app.model.GalaxySession.table.c.user_id == user.id,
+                            self.app.model.GalaxySession.table.c.is_valid == true(),
+                            self.app.model.GalaxySession.table.c.id != trans.galaxy_session.id,
+                        )
+                    ):
                         other_galaxy_session.is_valid = False
                         trans.sa_session.add(other_galaxy_session)
                 trans.sa_session.add(user)
@@ -477,43 +502,50 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         Send the verification email containing the activation link to the user's email.
         """
         activation_token = self.__get_activation_token(trans, email)
-        activation_link = url_for(controller='user', action='activate', activation_token=activation_token, email=escape(email), qualified=True)
+        activation_link = url_for(
+            controller="user", action="activate", activation_token=activation_token, email=escape(email), qualified=True
+        )
         host = self.__get_host(trans)
-        custom_message = ''
+        custom_message = ""
         if self.app.config.custom_activation_email_message:
             custom_message = f"{self.app.config.custom_activation_email_message}\n\n"
-        body = ("Hello %s,\n\n"
-                "In order to complete the activation process for %s begun on %s at %s, please click "
-                "on the following link to verify your account:\n\n" "%s \n\n"
-                "By clicking on the above link and opening a Galaxy account you are also confirming "
-                "that you have read and agreed to Galaxy's Terms and Conditions for use of this "
-                "service (%s). This includes a quota limit of one account per user. Attempts to "
-                "subvert this limit by creating multiple accounts or through any other method may "
-                "result in termination of all associated accounts and data.\n\n"
-                "Please contact us if you need help with your account at: %s. You can also browse "
-                "resources available" " at: %s. \n\n"
-                "More about the Galaxy Project can be found at galaxyproject.org\n\n"
-                "%s"
-                "Your Galaxy Team" % (
-                    escape(username),
-                    escape(email),
-                    datetime.utcnow().strftime("%D"),
-                    trans.request.host,
-                    activation_link,
-                    self.app.config.terms_url,
-                    self.app.config.error_email_to,
-                    self.app.config.instance_resource_url,
-                    custom_message)
-                )
+        body = (
+            "Hello %s,\n\n"
+            "In order to complete the activation process for %s begun on %s at %s, please click "
+            "on the following link to verify your account:\n\n"
+            "%s \n\n"
+            "By clicking on the above link and opening a Galaxy account you are also confirming "
+            "that you have read and agreed to Galaxy's Terms and Conditions for use of this "
+            "service (%s). This includes a quota limit of one account per user. Attempts to "
+            "subvert this limit by creating multiple accounts or through any other method may "
+            "result in termination of all associated accounts and data.\n\n"
+            "Please contact us if you need help with your account at: %s. You can also browse "
+            "resources available"
+            " at: %s. \n\n"
+            "More about the Galaxy Project can be found at galaxyproject.org\n\n"
+            "%s"
+            "Your Galaxy Team"
+            % (
+                escape(username),
+                escape(email),
+                datetime.utcnow().strftime("%D"),
+                trans.request.host,
+                activation_link,
+                self.app.config.terms_url,
+                self.app.config.error_email_to,
+                self.app.config.instance_resource_url,
+                custom_message,
+            )
+        )
         to = email
         frm = self.app.config.email_from or f"galaxy-no-reply@{host}"
-        subject = 'Galaxy Account Activation'
+        subject = "Galaxy Account Activation"
         try:
             util.send_mail(frm, to, subject, body, self.app.config)
             return True
         except Exception:
             log.debug(body)
-            log.exception('Unable to send the activation email.')
+            log.exception("Unable to send the activation email.")
             return False
 
     def __get_activation_token(self, trans, email):
@@ -543,16 +575,20 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             reset_user, prt = self.get_reset_token(trans, email)
             if prt:
                 host = self.__get_host(trans)
-                reset_url = url_for(controller='root', action='login', token=prt.token)
-                body = PASSWORD_RESET_TEMPLATE % (host, prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
-                                                  trans.request.host, reset_url)
+                reset_url = url_for(controller="root", action="login", token=prt.token)
+                body = PASSWORD_RESET_TEMPLATE % (
+                    host,
+                    prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
+                    trans.request.host,
+                    reset_url,
+                )
                 frm = trans.app.config.email_from or f"galaxy-no-reply@{host}"
-                subject = 'Galaxy Password Reset'
+                subject = "Galaxy Password Reset"
                 try:
                     util.send_mail(frm, email, subject, body, self.app.config)
                     trans.sa_session.add(reset_user)
                     trans.sa_session.flush()
-                    trans.log_event(f'User reset password: {email}')
+                    trans.log_event(f"User reset password: {email}")
                 except Exception as e:
                     log.debug(body)
                     return f"Failed to submit email. Please contact the administrator: {util.unicodify(e)}"
@@ -560,9 +596,15 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
                 return "Failed to produce password reset token. User not found."
 
     def get_reset_token(self, trans, email):
-        reset_user = trans.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == email).first()
+        reset_user = (
+            trans.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == email).first()
+        )
         if not reset_user and email != email.lower():
-            reset_user = trans.sa_session.query(self.app.model.User).filter(func.lower(self.app.model.User.table.c.email) == email.lower()).first()
+            reset_user = (
+                trans.sa_session.query(self.app.model.User)
+                .filter(func.lower(self.app.model.User.table.c.email) == email.lower())
+                .first()
+            )
         if reset_user:
             prt = self.app.model.PasswordResetToken(reset_user)
             trans.sa_session.add(prt)
@@ -571,8 +613,8 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         return None, None
 
     def __get_host(self, trans):
-        host = trans.request.host.split(':')[0]
-        if host in ['localhost', '127.0.0.1', '0.0.0.0']:
+        host = trans.request.host.split(":")[0]
+        if host in ["localhost", "127.0.0.1", "0.0.0.0"]:
             host = socket.getfqdn()
         return host
 
@@ -580,14 +622,14 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         if self.app.config.smtp_server is None:
             return "Subscribing to the mailing list has failed because mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator."
         else:
-            body = (self.app.config.mailing_join_body or '') + '\n'
+            body = (self.app.config.mailing_join_body or "") + "\n"
             to = self.app.config.mailing_join_addr
             frm = email
-            subject = self.app.config.mailing_join_subject or ''
+            subject = self.app.config.mailing_join_subject or ""
             try:
                 util.send_mail(frm, to, subject, body, self.app.config)
             except Exception:
-                log.exception('Subscribing to the mailing list has failed.')
+                log.exception("Subscribing to the mailing list has failed.")
                 return "Subscribing to the mailing list has failed."
 
     def activate(self, user):
@@ -606,47 +648,47 @@ class UserSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin):
         super().__init__(app)
         self.user_manager = self.manager
 
-        self.default_view = 'summary'
-        self.add_view('summary', [
-            'id', 'email', 'username'
-        ])
-        self.add_view('detailed', [
-            # 'update_time',
-            # 'create_time',
-            'is_admin',
-            'total_disk_usage',
-            'nice_total_disk_usage',
-            'quota_percent',
-            'quota',
-            'deleted',
-            'purged',
-            # 'active',
-
-            'preferences',
-            #  all tags
-            'tags_used',
-            # all annotations
-            # 'annotations'
-        ], include_keys_from='summary')
+        self.default_view = "summary"
+        self.add_view("summary", ["id", "email", "username"])
+        self.add_view(
+            "detailed",
+            [
+                # 'update_time',
+                # 'create_time',
+                "is_admin",
+                "total_disk_usage",
+                "nice_total_disk_usage",
+                "quota_percent",
+                "quota",
+                "deleted",
+                "purged",
+                # 'active',
+                "preferences",
+                #  all tags
+                "tags_used",
+                # all annotations
+                # 'annotations'
+            ],
+            include_keys_from="summary",
+        )
 
     def add_serializers(self):
         super().add_serializers()
         deletable.PurgableSerializerMixin.add_serializers(self)
 
-        self.serializers.update({
-            'id': self.serialize_id,
-            'create_time': self.serialize_date,
-            'update_time': self.serialize_date,
-            'is_admin': lambda i, k, **c: self.user_manager.is_admin(i),
-
-            'preferences': lambda i, k, **c: self.user_manager.preferences(i),
-
-            'total_disk_usage': lambda i, k, **c: float(i.total_disk_usage),
-            'quota_percent': lambda i, k, **c: self.user_manager.quota(i),
-            'quota': lambda i, k, **c: self.user_manager.quota(i, total=True),
-
-            'tags_used': lambda i, k, **c: self.user_manager.tags_used(i),
-        })
+        self.serializers.update(
+            {
+                "id": self.serialize_id,
+                "create_time": self.serialize_date,
+                "update_time": self.serialize_date,
+                "is_admin": lambda i, k, **c: self.user_manager.is_admin(i),
+                "preferences": lambda i, k, **c: self.user_manager.preferences(i),
+                "total_disk_usage": lambda i, k, **c: float(i.total_disk_usage),
+                "quota_percent": lambda i, k, **c: self.user_manager.quota(i),
+                "quota": lambda i, k, **c: self.user_manager.quota(i, total=True),
+                "tags_used": lambda i, k, **c: self.user_manager.tags_used(i),
+            }
+        )
 
 
 class UserDeserializer(base.ModelDeserializer):
@@ -654,13 +696,16 @@ class UserDeserializer(base.ModelDeserializer):
     Service object for validating and deserializing dictionaries that
     update/alter users.
     """
+
     model_manager_class = UserManager
 
     def add_deserializers(self):
         super().add_deserializers()
-        self.deserializers.update({
-            'username': self.deserialize_username,
-        })
+        self.deserializers.update(
+            {
+                "username": self.deserialize_username,
+            }
+        )
 
     def deserialize_username(self, item, key, username, trans=None, **context):
         # TODO: validate_publicname requires trans and should(?) raise exceptions
@@ -678,7 +723,7 @@ class CurrentUserSerializer(UserSerializer):
         """
         Override to return at least some usage info if user is anonymous.
         """
-        kwargs['current_user'] = user
+        kwargs["current_user"] = user
         if self.user_manager.is_anonymous(user):
             return self.serialize_current_anonymous_user(user, keys, **kwargs)
         return super(UserSerializer, self).serialize(user, keys, **kwargs)
@@ -696,10 +741,10 @@ class CurrentUserSerializer(UserSerializer):
 
         # a very small subset of keys available
         values = {
-            'id': None,
-            'total_disk_usage': float(usage),
-            'nice_total_disk_usage': util.nice_size(usage),
-            'quota_percent': percent,
+            "id": None,
+            "total_disk_usage": float(usage),
+            "nice_total_disk_usage": util.nice_size(usage),
+            "quota_percent": percent,
         }
         serialized = {}
         for key in keys:
@@ -717,11 +762,13 @@ class AdminUserFilterParser(base.ModelFilterParser, deletable.PurgableFiltersMix
         deletable.PurgableFiltersMixin._add_parsers(self)
 
         # PRECONDITION: user making the query has been verified as an admin
-        self.orm_filter_parsers.update({
-            'email': {'op': ('eq', 'contains', 'like')},
-            'username': {'op': ('eq', 'contains', 'like')},
-            'active': {'op': ('eq')},
-            'disk_usage': {'op': ('le', 'ge')}
-        })
+        self.orm_filter_parsers.update(
+            {
+                "email": {"op": ("eq", "contains", "like")},
+                "username": {"op": ("eq", "contains", "like")},
+                "active": {"op": ("eq")},
+                "disk_usage": {"op": ("le", "ge")},
+            }
+        )
 
         self.fn_filter_parsers.update({})
diff --git a/lib/galaxy/managers/visualizations.py b/lib/galaxy/managers/visualizations.py
index 9f89c476f32..59657a90285 100644
--- a/lib/galaxy/managers/visualizations.py
+++ b/lib/galaxy/managers/visualizations.py
@@ -21,7 +21,7 @@ class VisualizationManager(sharable.SharableModelManager):
     # TODO: revisions
 
     model_class = model.Visualization
-    foreign_key_name = 'visualization'
+    foreign_key_name = "visualization"
     user_share_model = model.VisualizationUserShareAssociation
 
     tag_assoc = model.VisualizationTagAssociation
@@ -38,21 +38,21 @@ class VisualizationSerializer(sharable.SharableModelSerializer):
     """
     Interface/service object for serializing visualizations into dictionaries.
     """
+
     model_manager_class = VisualizationManager
-    SINGLE_CHAR_ABBR = 'v'
+    SINGLE_CHAR_ABBR = "v"
 
     def __init__(self, app: MinimalManagerApp):
         super().__init__(app)
         self.visualization_manager = self.manager
 
-        self.default_view = 'summary'
-        self.add_view('summary', [])
-        self.add_view('detailed', [])
+        self.default_view = "summary"
+        self.add_view("summary", [])
+        self.add_view("detailed", [])
 
     def add_serializers(self):
         super().add_serializers()
-        self.serializers.update({
-        })
+        self.serializers.update({})
 
 
 class VisualizationDeserializer(sharable.SharableModelDeserializer):
@@ -60,6 +60,7 @@ class VisualizationDeserializer(sharable.SharableModelDeserializer):
     Interface/service object for validating and deserializing
     dictionaries into visualizations.
     """
+
     model_manager_class = VisualizationManager
 
     def __init__(self, app):
@@ -68,6 +69,5 @@ class VisualizationDeserializer(sharable.SharableModelDeserializer):
 
     def add_deserializers(self):
         super().add_deserializers()
-        self.deserializers.update({
-        })
+        self.deserializers.update({})
         self.deserializable_keyset.update(self.deserializers.keys())
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 1d5769e86bb..19fb78ce4bf 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -19,25 +19,28 @@ from gxformat2 import (
 )
 from pydantic import BaseModel
 from sqlalchemy import and_
-from sqlalchemy.orm import joinedload, subqueryload
+from sqlalchemy.orm import (
+    joinedload,
+    subqueryload,
+)
 
 from galaxy import (
     exceptions,
     model,
-    util
+    util,
 )
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.structured_app import MinimalManagerApp
 from galaxy.tools.parameters import (
     params_to_incoming,
-    visit_input_values
+    visit_input_values,
 )
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     DataToolParameter,
     RuntimeValue,
-    workflow_building_modes
+    workflow_building_modes,
 )
 from galaxy.util.json import (
     safe_dumps,
@@ -49,7 +52,7 @@ from galaxy.workflow.modules import (
     is_tool_module_type,
     module_factory,
     ToolModule,
-    WorkflowModuleInjector
+    WorkflowModuleInjector,
 )
 from galaxy.workflow.refactor.execute import WorkflowRefactorExecutor
 from galaxy.workflow.refactor.schema import (
@@ -66,7 +69,7 @@ log = logging.getLogger(__name__)
 
 
 class WorkflowsManager:
-    """ Handle CRUD type operations related to workflows. More interesting
+    """Handle CRUD type operations related to workflows. More interesting
     stuff regarding workflow execution, step sorting, etc... can be found in
     the galaxy.workflow module.
     """
@@ -75,29 +78,36 @@ class WorkflowsManager:
         self.app = app
 
     def get_stored_workflow(self, trans, workflow_id, by_stored_id=True):
-        """ Use a supplied ID (UUID or encoded stored workflow ID) to find
+        """Use a supplied ID (UUID or encoded stored workflow ID) to find
         a workflow.
         """
         if util.is_uuid(workflow_id):
             # see if they have passed in the UUID for a workflow that is attached to a stored workflow
             workflow_uuid = uuid.UUID(workflow_id)
-            workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(and_(
-                trans.app.model.StoredWorkflow.id == trans.app.model.Workflow.stored_workflow_id,
-                trans.app.model.Workflow.uuid == workflow_uuid
-            ))
+            workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(
+                and_(
+                    trans.app.model.StoredWorkflow.id == trans.app.model.Workflow.stored_workflow_id,
+                    trans.app.model.Workflow.uuid == workflow_uuid,
+                )
+            )
         elif by_stored_id:
             workflow_id = decode_id(self.app, workflow_id)
-            workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).\
-                filter(trans.app.model.StoredWorkflow.id == workflow_id)
+            workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(
+                trans.app.model.StoredWorkflow.id == workflow_id
+            )
         else:
             workflow_id = decode_id(self.app, workflow_id)
-            workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(and_(
-                trans.app.model.StoredWorkflow.id == trans.app.model.Workflow.stored_workflow_id,
-                trans.app.model.Workflow.id == workflow_id
-            ))
-        stored_workflow = workflow_query.options(joinedload('annotations'),
-                                                 joinedload('tags'),
-                                                 subqueryload('latest_workflow').joinedload('steps').joinedload('*')).first()
+            workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(
+                and_(
+                    trans.app.model.StoredWorkflow.id == trans.app.model.Workflow.stored_workflow_id,
+                    trans.app.model.Workflow.id == workflow_id,
+                )
+            )
+        stored_workflow = workflow_query.options(
+            joinedload("annotations"),
+            joinedload("tags"),
+            subqueryload("latest_workflow").joinedload("steps").joinedload("*"),
+        ).first()
         if stored_workflow is None:
             if not by_stored_id:
                 # May have a subworkflow without attached StoredWorkflow object, this was the default prior to 20.09 release.
@@ -109,14 +119,19 @@ class WorkflowsManager:
         return stored_workflow
 
     def get_stored_accessible_workflow(self, trans, workflow_id, by_stored_id=True):
-        """ Get a stored workflow from a encoded stored workflow id and
+        """Get a stored workflow from a encoded stored workflow id and
         make sure it accessible to the user.
         """
         stored_workflow = self.get_stored_workflow(trans, workflow_id, by_stored_id=by_stored_id)
 
         # check to see if user has permissions to selected workflow
         if stored_workflow.user != trans.user and not trans.user_is_admin and not stored_workflow.published:
-            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
+            if (
+                trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation)
+                .filter_by(user=trans.user, stored_workflow=stored_workflow)
+                .count()
+                == 0
+            ):
                 message = "Workflow is not owned by or shared with current user"
                 raise exceptions.ItemAccessibilityException(message)
 
@@ -128,13 +143,15 @@ class WorkflowsManager:
         # To properly serialize them we do need a StoredWorkflow, so we create and attach one here.
         # We hide the new StoredWorkflow to avoid cluttering the default workflow view.
         if workflow and workflow.stored_workflow is None and self.check_security(trans, has_workflow=workflow):
-            stored_workflow = trans.app.model.StoredWorkflow(user=trans.user, name=workflow.name, workflow=workflow, hidden=True)
+            stored_workflow = trans.app.model.StoredWorkflow(
+                user=trans.user, name=workflow.name, workflow=workflow, hidden=True
+            )
             trans.sa_session.add(stored_workflow)
             trans.sa_session.flush()
             return stored_workflow
 
     def get_owned_workflow(self, trans, encoded_workflow_id):
-        """ Get a workflow (non-stored) from a encoded workflow id and
+        """Get a workflow (non-stored) from a encoded workflow id and
         make sure it accessible to the user.
         """
         workflow_id = decode_id(self.app, encoded_workflow_id)
@@ -143,7 +160,7 @@ class WorkflowsManager:
         return workflow
 
     def check_security(self, trans, has_workflow, check_ownership=True, check_accessible=True):
-        """ check accessibility or ownership of workflows, storedworkflows, and
+        """check accessibility or ownership of workflows, storedworkflows, and
         workflowinvocations. Throw an exception or returns True if user has
         needed level of access.
         """
@@ -170,21 +187,25 @@ class WorkflowsManager:
             if check_ownership:
                 raise exceptions.ItemOwnershipException()
             # else check_accessible...
-            if trans.sa_session.query(model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
+            if (
+                trans.sa_session.query(model.StoredWorkflowUserShareAssociation)
+                .filter_by(user=trans.user, stored_workflow=stored_workflow)
+                .count()
+                == 0
+            ):
                 raise exceptions.ItemAccessibilityException()
 
         return True
 
     def get_invocation(self, trans, decoded_invocation_id, eager=False):
-        q = trans.sa_session.query(
-            self.app.model.WorkflowInvocation
-        )
+        q = trans.sa_session.query(self.app.model.WorkflowInvocation)
         if eager:
-            q = q.options(subqueryload(self.app.model.WorkflowInvocation.steps).joinedload(
-                'implicit_collection_jobs').joinedload(
-                    'jobs').joinedload(
-                        'job').joinedload(
-                            'input_datasets')
+            q = q.options(
+                subqueryload(self.app.model.WorkflowInvocation.steps)
+                .joinedload("implicit_collection_jobs")
+                .joinedload("jobs")
+                .joinedload("job")
+                .joinedload("input_datasets")
             )
         workflow_invocation = q.get(decoded_invocation_id)
         if not workflow_invocation:
@@ -204,7 +225,8 @@ class WorkflowsManager:
         if invocation_markdown:
             runtime_report_config_json = {"markdown": invocation_markdown}
         return generate_report(
-            trans, workflow_invocation,
+            trans,
+            workflow_invocation,
             runtime_report_config_json=runtime_report_config_json,
             plugin_type=generator_plugin_type,
             target_format=target_format,
@@ -225,22 +247,28 @@ class WorkflowsManager:
 
     def get_invocation_step(self, trans, decoded_workflow_invocation_step_id):
         try:
-            workflow_invocation_step = trans.sa_session.query(
-                model.WorkflowInvocationStep
-            ).get(decoded_workflow_invocation_step_id)
+            workflow_invocation_step = trans.sa_session.query(model.WorkflowInvocationStep).get(
+                decoded_workflow_invocation_step_id
+            )
         except Exception:
             raise exceptions.ObjectNotFound()
-        self.check_security(trans, workflow_invocation_step.workflow_invocation, check_ownership=True, check_accessible=False)
+        self.check_security(
+            trans, workflow_invocation_step.workflow_invocation, check_ownership=True, check_accessible=False
+        )
         return workflow_invocation_step
 
     def update_invocation_step(self, trans, decoded_workflow_invocation_step_id, action):
         if action is None:
-            raise exceptions.RequestParameterMissingException("Updating workflow invocation step requires an action parameter. ")
+            raise exceptions.RequestParameterMissingException(
+                "Updating workflow invocation step requires an action parameter. "
+            )
 
         workflow_invocation_step = self.get_invocation_step(trans, decoded_workflow_invocation_step_id)
         workflow_invocation = workflow_invocation_step.workflow_invocation
         if not workflow_invocation.active:
-            raise exceptions.RequestParameterInvalidException("Attempting to modify the state of a completed workflow invocation.")
+            raise exceptions.RequestParameterInvalidException(
+                "Attempting to modify the state of a completed workflow invocation."
+            )
 
         step = workflow_invocation_step.workflow_step
         module = module_factory.from_workflow_step(trans, step)
@@ -250,8 +278,19 @@ class WorkflowsManager:
         trans.sa_session.flush()
         return workflow_invocation_step
 
-    def build_invocations_query(self, trans, stored_workflow_id=None, history_id=None, job_id=None, user_id=None,
-                                include_terminal=True, limit=None, offset=None, sort_by=None, sort_desc=None):
+    def build_invocations_query(
+        self,
+        trans,
+        stored_workflow_id=None,
+        history_id=None,
+        job_id=None,
+        user_id=None,
+        include_terminal=True,
+        limit=None,
+        offset=None,
+        sort_by=None,
+        sort_desc=None,
+    ):
         """Get invocations owned by the current user."""
         sa_session = trans.sa_session
         invocations_query = sa_session.query(model.WorkflowInvocation)
@@ -259,25 +298,17 @@ class WorkflowsManager:
             stored_workflow = sa_session.query(model.StoredWorkflow).get(stored_workflow_id)
             if not stored_workflow:
                 raise exceptions.ObjectNotFound()
-            invocations_query = invocations_query.join(
-                model.Workflow
-            ).filter(
+            invocations_query = invocations_query.join(model.Workflow).filter(
                 model.Workflow.table.c.stored_workflow_id == stored_workflow_id
             )
         if user_id is not None:
-            invocations_query = invocations_query.join(
-                model.History
-            ).filter(
-                model.History.table.c.user_id == user_id
-            )
+            invocations_query = invocations_query.join(model.History).filter(model.History.table.c.user_id == user_id)
         if history_id is not None:
-            invocations_query = invocations_query.filter(
-                model.WorkflowInvocation.table.c.history_id == history_id
-            )
+            invocations_query = invocations_query.filter(model.WorkflowInvocation.table.c.history_id == history_id)
         if job_id is not None:
-            invocations_query = invocations_query.join(
-                model.WorkflowInvocationStep
-            ).filter(model.WorkflowInvocationStep.table.c.job_id == job_id)
+            invocations_query = invocations_query.join(model.WorkflowInvocationStep).filter(
+                model.WorkflowInvocationStep.table.c.job_id == job_id
+            )
         if not include_terminal:
             invocations_query = invocations_query.filter(
                 model.WorkflowInvocation.table.c.state.in_(model.WorkflowInvocation.non_terminal_states)
@@ -294,17 +325,18 @@ class WorkflowsManager:
             invocations_query = invocations_query.limit(limit)
         if offset is not None:
             invocations_query = invocations_query.offset(offset)
-        invocations = [inv for inv in invocations_query if self.check_security(trans,
-                                                                        inv,
-                                                                        check_ownership=True,
-                                                                        check_accessible=False)]
+        invocations = [
+            inv
+            for inv in invocations_query
+            if self.check_security(trans, inv, check_ownership=True, check_accessible=False)
+        ]
         return invocations, total_matches
 
     def serialize_workflow_invocation(self, invocation, **kwd):
         app = self.app
         view = kwd.get("view", "element")
-        step_details = util.string_as_bool(kwd.get('step_details', False))
-        legacy_job_state = util.string_as_bool(kwd.get('legacy_job_state', False))
+        step_details = util.string_as_bool(kwd.get("step_details", False))
+        legacy_job_state = util.string_as_bool(kwd.get("legacy_job_state", False))
         as_dict = invocation.to_dict(view, step_details=step_details, legacy_job_state=legacy_job_state)
         return app.security.encode_all_ids(as_dict, recursive=True)
 
@@ -318,7 +350,6 @@ CreatedWorkflow = namedtuple("CreatedWorkflow", ["stored_workflow", "workflow",
 
 
 class WorkflowContentsManager(UsesAnnotations):
-
     def __init__(self, app: MinimalManagerApp):
         self.app = app
         self._resource_mapper_function = get_resource_mapper_function(app)
@@ -353,7 +384,9 @@ class WorkflowContentsManager(UsesAnnotations):
             galaxy_interface = Format2ConverterGalaxyInterface()
             import_options = ImportOptions()
             import_options.deduplicate_subworkflows = True
-            as_dict = python_to_workflow(as_dict, galaxy_interface, workflow_directory=workflow_directory, import_options=import_options)
+            as_dict = python_to_workflow(
+                as_dict, galaxy_interface, workflow_directory=workflow_directory, import_options=import_options
+            )
 
         return RawWorkflowDescription(as_dict, workflow_path)
 
@@ -370,10 +403,10 @@ class WorkflowContentsManager(UsesAnnotations):
         # Put parameters in workflow mode
         trans.workflow_building_mode = workflow_building_modes.ENABLED
         # If there's a source, put it in the workflow name.
-        if 'name' not in data:
+        if "name" not in data:
             raise exceptions.RequestParameterInvalidException(f"Invalid workflow format detected [{data}]")
 
-        workflow_input_name = data['name']
+        workflow_input_name = data["name"]
         imported_sufix = f"(imported from {source})"
         if source and imported_sufix not in workflow_input_name:
             name = f"{workflow_input_name} {imported_sufix}"
@@ -385,8 +418,8 @@ class WorkflowContentsManager(UsesAnnotations):
             workflow_create_options,
             name=name,
         )
-        if 'uuid' in data:
-            workflow.uuid = data['uuid']
+        if "uuid" in data:
+            workflow.uuid = data["uuid"]
 
         # Connect up
         stored = model.StoredWorkflow()
@@ -397,10 +430,10 @@ class WorkflowContentsManager(UsesAnnotations):
         stored.user = trans.user
         stored.published = workflow_create_options.publish
         stored.hidden = hidden
-        if data['annotation']:
-            annotation = sanitize_html(data['annotation'])
+        if data["annotation"]:
+            annotation = sanitize_html(data["annotation"])
             self.add_item_annotation(trans.sa_session, stored.user, stored, annotation)
-        workflow_tags = data.get('tags', [])
+        workflow_tags = data.get("tags", [])
         trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored, new_tags_list=workflow_tags)
 
         # Persist
@@ -415,13 +448,11 @@ class WorkflowContentsManager(UsesAnnotations):
 
         trans.sa_session.flush()
 
-        return CreatedWorkflow(
-            stored_workflow=stored,
-            workflow=workflow,
-            missing_tools=missing_tool_tups
-        )
+        return CreatedWorkflow(stored_workflow=stored, workflow=workflow, missing_tools=missing_tool_tups)
 
-    def update_workflow_from_raw_description(self, trans, stored_workflow, raw_workflow_description, workflow_update_options):
+    def update_workflow_from_raw_description(
+        self, trans, stored_workflow, raw_workflow_description, workflow_update_options
+    ):
         raw_workflow_description = self.ensure_raw_description(raw_workflow_description)
 
         # Put parameters in workflow mode
@@ -452,12 +483,12 @@ class WorkflowContentsManager(UsesAnnotations):
 
         if workflow_update_options.update_stored_workflow_attributes:
             update_dict = raw_workflow_description.as_dict
-            if 'name' in update_dict:
-                sanitized_name = sanitize_html(update_dict['name'])
+            if "name" in update_dict:
+                sanitized_name = sanitize_html(update_dict["name"])
                 workflow.name = sanitized_name
                 stored_workflow.name = sanitized_name
-            if 'annotation' in update_dict:
-                newAnnotation = sanitize_html(update_dict['annotation'])
+            if "annotation" in update_dict:
+                newAnnotation = sanitize_html(update_dict["annotation"])
                 sa_session = None if dry_run else trans.sa_session
                 self.add_item_annotation(sa_session, stored_workflow.user, stored_workflow, newAnnotation)
 
@@ -474,7 +505,9 @@ class WorkflowContentsManager(UsesAnnotations):
             errors.append("This workflow contains cycles")
         return workflow, errors
 
-    def _workflow_from_raw_description(self, trans, raw_workflow_description, workflow_state_resolution_options, name, **kwds):
+    def _workflow_from_raw_description(
+        self, trans, raw_workflow_description, workflow_state_resolution_options, name, **kwds
+    ):
         # don't commit the workflow or attach its part to the sa session - just build a
         # a transient model to operate on or render.
         dry_run = kwds.pop("dry_run", False)
@@ -487,16 +520,16 @@ class WorkflowContentsManager(UsesAnnotations):
         workflow = model.Workflow()
         workflow.name = name
 
-        if 'report' in data:
-            workflow.reports_config = data['report']
-        workflow.license = data.get('license')
-        workflow.creator_metadata = data.get('creator')
+        if "report" in data:
+            workflow.reports_config = data["report"]
+        workflow.license = data.get("license")
+        workflow.creator_metadata = data.get("creator")
 
-        if 'license' in data:
-            workflow.license = data['license']
+        if "license" in data:
+            workflow.license = data["license"]
 
-        if 'creator' in data:
-            workflow.creator_metadata = data['creator']
+        if "creator" in data:
+            workflow.creator_metadata = data["creator"]
 
         # Assume no errors until we find a step that has some
         workflow.has_errors = False
@@ -512,7 +545,9 @@ class WorkflowContentsManager(UsesAnnotations):
         if subworkflows:
             subworkflow_id_map = {}
             for key, subworkflow_dict in subworkflows.items():
-                subworkflow = self.__build_embedded_subworkflow(trans, subworkflow_dict, workflow_state_resolution_options)
+                subworkflow = self.__build_embedded_subworkflow(
+                    trans, subworkflow_dict, workflow_state_resolution_options
+                )
                 subworkflow_id_map[key] = subworkflow
 
         # Keep track of tools required by the workflow that are not available in
@@ -521,7 +556,9 @@ class WorkflowContentsManager(UsesAnnotations):
         missing_tool_tups = []
         for step_dict in self.__walk_step_dicts(data):
             if not dry_run:
-                self.__load_subworkflows(trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=dry_run)
+                self.__load_subworkflows(
+                    trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=dry_run
+                )
 
         module_kwds = workflow_state_resolution_options.dict()
         module_kwds.update(kwds)  # TODO: maybe drop this?
@@ -529,7 +566,7 @@ class WorkflowContentsManager(UsesAnnotations):
             module, step = self.__module_from_dict(trans, steps, steps_by_external_id, step_dict, **module_kwds)
             is_tool = is_tool_module_type(module.type)
             if is_tool and module.tool is None:
-                missing_tool_tup = (module.tool_id, module.get_name(), module.tool_version, step_dict['id'])
+                missing_tool_tup = (module.tool_id, module.get_name(), module.tool_version, step_dict["id"])
                 if missing_tool_tup not in missing_tool_tups:
                     missing_tool_tups.append(missing_tool_tup)
             if module.get_errors():
@@ -544,7 +581,7 @@ class WorkflowContentsManager(UsesAnnotations):
         return workflow, missing_tool_tups
 
     def workflow_to_dict(self, trans, stored, style="export", version=None, history=None):
-        """ Export the workflow contents to a dictionary ready for JSON-ification and to be
+        """Export the workflow contents to a dictionary ready for JSON-ification and to be
         sent out via API for instance. There are three styles of export allowed 'export', 'instance', and
         'editor'. The Galaxy team will do its best to preserve the backward compatibility of the
         'export' style - this is the export method meant to be portable across Galaxy instances and over
@@ -552,10 +589,11 @@ class WorkflowContentsManager(UsesAnnotations):
         option describes the workflow in a context more tied to the current Galaxy instance and includes
         fields like 'url' and 'url' and actual unencoded step ids instead of 'order_index'.
         """
+
         def to_format_2(wf_dict, **kwds):
             return from_galaxy_native(wf_dict, None, **kwds)
 
-        if version == '':
+        if version == "":
             version = None
         if version is not None:
             version = int(version)
@@ -581,11 +619,11 @@ class WorkflowContentsManager(UsesAnnotations):
         elif style == "ga":
             wf_dict = self._workflow_to_dict_export(trans, stored, workflow=workflow)
         else:
-            raise exceptions.RequestParameterInvalidException(f'Unknown workflow style {style}')
+            raise exceptions.RequestParameterInvalidException(f"Unknown workflow style {style}")
         if version is not None:
-            wf_dict['version'] = version
+            wf_dict["version"] = version
         else:
-            wf_dict['version'] = len(stored.workflows) - 1
+            wf_dict["version"] = len(stored.workflows) - 1
         return wf_dict
 
     def _sync_stored_workflow(self, trans, stored_workflow):
@@ -605,9 +643,9 @@ class WorkflowContentsManager(UsesAnnotations):
         Builds workflow dictionary used by run workflow form
         """
         if len(workflow.steps) == 0:
-            raise exceptions.MessageException('Workflow cannot be run because it does not have any steps.')
+            raise exceptions.MessageException("Workflow cannot be run because it does not have any steps.")
         if attach_ordered_steps(workflow, workflow.steps):
-            raise exceptions.MessageException('Workflow cannot be run because it contains cycles.')
+            raise exceptions.MessageException("Workflow cannot be run because it contains cycles.")
         trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
         module_injector = WorkflowModuleInjector(trans)
         has_upgrade_messages = False
@@ -624,7 +662,7 @@ class WorkflowContentsManager(UsesAnnotations):
                 continue
             if step.upgrade_messages:
                 has_upgrade_messages = True
-            if step.type in ('tool', 'subworkflow', None):
+            if step.type in ("tool", "subworkflow", None):
                 if step.module.version_changes:
                     step_version_changes.extend(step.module.version_changes)
                 step_errors = step.module.get_errors()
@@ -640,47 +678,55 @@ class WorkflowContentsManager(UsesAnnotations):
         step_models = []
         for step in workflow.steps:
             step_model = None
-            if step.type == 'tool':
+            if step.type == "tool":
                 incoming: Dict[str, Any] = {}
-                tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version, tool_uuid=step.tool_uuid)
+                tool = trans.app.toolbox.get_tool(
+                    step.tool_id, tool_version=step.tool_version, tool_uuid=step.tool_uuid
+                )
                 params_to_incoming(incoming, tool.inputs, step.state.inputs, trans.app)
-                step_model = tool.to_json(trans, incoming, workflow_building_mode=workflow_building_modes.USE_HISTORY, history=history)
-                step_model['post_job_actions'] = [{
-                    'short_str': ActionBox.get_short_str(pja),
-                    'action_type': pja.action_type,
-                    'output_name': pja.output_name,
-                    'action_arguments': pja.action_arguments
-                } for pja in step.post_job_actions]
+                step_model = tool.to_json(
+                    trans, incoming, workflow_building_mode=workflow_building_modes.USE_HISTORY, history=history
+                )
+                step_model["post_job_actions"] = [
+                    {
+                        "short_str": ActionBox.get_short_str(pja),
+                        "action_type": pja.action_type,
+                        "output_name": pja.output_name,
+                        "action_arguments": pja.action_arguments,
+                    }
+                    for pja in step.post_job_actions
+                ]
             else:
                 inputs = step.module.get_runtime_inputs(connections=step.output_connections)
-                step_model = {
-                    'inputs': [input.to_dict(trans) for input in inputs.values()]
+                step_model = {"inputs": [input.to_dict(trans) for input in inputs.values()]}
+            step_model["replacement_parameters"] = step.module.get_replacement_parameters(step)
+            step_model["step_type"] = step.type
+            step_model["step_label"] = step.label
+            step_model["step_name"] = step.module.get_name()
+            step_model["step_version"] = step.module.get_version()
+            step_model["step_index"] = step.order_index
+            step_model["output_connections"] = [
+                {
+                    "input_step_index": step_order_indices.get(oc.input_step_id),
+                    "output_step_index": step_order_indices.get(oc.output_step_id),
+                    "input_name": oc.input_name,
+                    "output_name": oc.output_name,
                 }
-            step_model['replacement_parameters'] = step.module.get_replacement_parameters(step)
-            step_model['step_type'] = step.type
-            step_model['step_label'] = step.label
-            step_model['step_name'] = step.module.get_name()
-            step_model['step_version'] = step.module.get_version()
-            step_model['step_index'] = step.order_index
-            step_model['output_connections'] = [{
-                'input_step_index': step_order_indices.get(oc.input_step_id),
-                'output_step_index': step_order_indices.get(oc.output_step_id),
-                'input_name': oc.input_name,
-                'output_name': oc.output_name
-            } for oc in step.output_connections]
+                for oc in step.output_connections
+            ]
             if step.annotations:
-                step_model['annotation'] = step.annotations[0].annotation
+                step_model["annotation"] = step.annotations[0].annotation
             if step.upgrade_messages:
-                step_model['messages'] = step.upgrade_messages
+                step_model["messages"] = step.upgrade_messages
             step_models.append(step_model)
         return {
-            'id': trans.app.security.encode_id(stored.id),
-            'history_id': trans.app.security.encode_id(history.id) if history else None,
-            'name': stored.name,
-            'steps': step_models,
-            'step_version_changes': step_version_changes,
-            'has_upgrade_messages': has_upgrade_messages,
-            'workflow_resource_parameters': self._workflow_resource_parameters(trans, stored, workflow),
+            "id": trans.app.security.encode_id(stored.id),
+            "history_id": trans.app.security.encode_id(history.id) if history else None,
+            "name": stored.name,
+            "steps": step_models,
+            "step_version_changes": step_version_changes,
+            "has_upgrade_messages": has_upgrade_messages,
+            "workflow_resource_parameters": self._workflow_resource_parameters(trans, stored, workflow),
         }
 
     def _workflow_to_dict_preview(self, trans, workflow):
@@ -689,9 +735,9 @@ class WorkflowContentsManager(UsesAnnotations):
         Used to create embedded workflow previews.
         """
         if len(workflow.steps) == 0:
-            raise exceptions.MessageException('Workflow cannot be run because it does not have any steps.')
+            raise exceptions.MessageException("Workflow cannot be run because it does not have any steps.")
         if attach_ordered_steps(workflow, workflow.steps):
-            raise exceptions.MessageException('Workflow cannot be run because it contains cycles.')
+            raise exceptions.MessageException("Workflow cannot be run because it contains cycles.")
 
         # Ensure that the user has a history
         trans.get_history(most_recent=True, create=True)
@@ -704,14 +750,17 @@ class WorkflowContentsManager(UsesAnnotations):
                     conns = step.input_connections_by_name[prefix + param.name]
                     if not isinstance(conns, list):
                         conns = [conns]
-                    value_list = ["Output '%s' from Step %d." % (conn.output_name, int(conn.output_step.order_index) + 1) for conn in conns]
+                    value_list = [
+                        "Output '%s' from Step %d." % (conn.output_name, int(conn.output_step.order_index) + 1)
+                        for conn in conns
+                    ]
                     value = ",".join(value_list)
                 else:
                     value = "Select at Runtime."
             else:
-                value = param.value_to_display_text(raw_value) or 'Unavailable.'
+                value = param.value_to_display_text(raw_value) or "Unavailable."
             input_dict["value"] = value
-            if hasattr(step, 'upgrade_messages') and step.upgrade_messages and param.name in step.upgrade_messages:
+            if hasattr(step, "upgrade_messages") and step.upgrade_messages and param.name in step.upgrade_messages:
                 input_dict["upgrade_messages"] = step.upgrade_messages[param.name]
 
         def do_inputs(inputs, values, prefix, step, other_values=None):
@@ -726,17 +775,27 @@ class WorkflowContentsManager(UsesAnnotations):
                         nested_input_dicts = []
                         for i in range(len(repeat_values)):
                             nested_input_dict = {}
-                            index = repeat_values[i]['__index__']
+                            index = repeat_values[i]["__index__"]
                             nested_input_dict["title"] = "%i. %s" % (i + 1, input.title)
-                            nested_input_dict["inputs"] = do_inputs(input.inputs, repeat_values[i], f"{prefix + input.name}_{str(index)}|", step, other_values)
+                            nested_input_dict["inputs"] = do_inputs(
+                                input.inputs,
+                                repeat_values[i],
+                                f"{prefix + input.name}_{str(index)}|",
+                                step,
+                                other_values,
+                            )
                             nested_input_dicts.append(nested_input_dict)
                         input_dict["inputs"] = nested_input_dicts
                 elif input.type == "conditional":
                     group_values = values[input.name]
-                    current_case = group_values['__current_case__']
+                    current_case = group_values["__current_case__"]
                     new_prefix = f"{prefix + input.name}|"
-                    row_for_param(input_dict, input.test_param, group_values[input.test_param.name], other_values, prefix, step)
-                    input_dict["inputs"] = do_inputs(input.cases[current_case].inputs, group_values, new_prefix, step, other_values)
+                    row_for_param(
+                        input_dict, input.test_param, group_values[input.test_param.name], other_values, prefix, step
+                    )
+                    input_dict["inputs"] = do_inputs(
+                        input.cases[current_case].inputs, group_values, new_prefix, step, other_values
+                    )
                 elif input.type == "section":
                     new_prefix = f"{prefix + input.name}|"
                     group_values = values[input.name]
@@ -760,14 +819,14 @@ class WorkflowContentsManager(UsesAnnotations):
                 step_dict["label"] = f"Unknown Tool with id '{e.tool_id}'"
                 step_dicts.append(step_dict)
                 continue
-            if step.type == 'tool' or step.type is None:
+            if step.type == "tool" or step.type is None:
                 tool = trans.app.toolbox.get_tool(step.tool_id)
                 if tool:
                     step_dict["label"] = step.label or tool.name
                 else:
                     step_dict["label"] = f"Unknown Tool with id '{step.tool_id}'"
                 step_dict["inputs"] = do_inputs(tool.inputs, step.state.inputs, "", step)
-            elif step.type == 'subworkflow':
+            elif step.type == "subworkflow":
                 step_dict["label"] = step.label or (step.subworkflow.name if step.subworkflow else "Missing workflow.")
                 errors = step.module.get_errors()
                 if errors:
@@ -784,20 +843,19 @@ class WorkflowContentsManager(UsesAnnotations):
         }
 
     def _workflow_resource_parameters(self, trans, stored, workflow):
-        """Get workflow scheduling resource parameters for this user and workflow or None if not configured.
-        """
+        """Get workflow scheduling resource parameters for this user and workflow or None if not configured."""
         return self._resource_mapper_function(trans=trans, stored_workflow=stored, workflow=workflow)
 
     def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_subworkflow=False):
         # Pack workflow data into a dictionary and return
         data = {}
-        data['name'] = workflow.name
-        data['steps'] = {}
-        data['upgrade_messages'] = {}
-        data['report'] = workflow.reports_config or {}
-        data['license'] = workflow.license
-        data['creator'] = workflow.creator_metadata
-        data['annotation'] = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ''
+        data["name"] = workflow.name
+        data["steps"] = {}
+        data["upgrade_messages"] = {}
+        data["report"] = workflow.reports_config or {}
+        data["license"] = workflow.license
+        data["creator"] = workflow.creator_metadata
+        data["annotation"] = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ""
 
         output_label_index = set()
         input_step_types = set(workflow.input_step_types)
@@ -806,7 +864,7 @@ class WorkflowContentsManager(UsesAnnotations):
             # Load from database representation
             module = module_factory.from_workflow_step(trans, step, exact_tools=False)
             if not module:
-                raise exceptions.MessageException(f'Unrecognized step type: {step.type}')
+                raise exceptions.MessageException(f"Unrecognized step type: {step.type}")
             # Load label from state of data input modules, necessary for backward compatibility
             self.__set_default_label(step, module, step.tool_inputs)
             # Fix any missing parameters
@@ -815,31 +873,31 @@ class WorkflowContentsManager(UsesAnnotations):
                 upgrade_message_dict[module.get_name()] = "\n".join(module.version_changes)
             # Get user annotation.
             config_form = module.get_config_form(step=step)
-            annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
+            annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ""
             # Pack attributes into plain dictionary
             step_dict = {
-                'id': step.order_index,
-                'type': module.type,
-                'label': module.label,
-                'content_id': module.get_content_id(),
-                'name': module.get_name(),
-                'tool_state': module.get_tool_state(),
-                'errors': module.get_errors(),
-                'inputs': module.get_all_inputs(connectable_only=True),
-                'outputs': module.get_all_outputs(),
-                'config_form': config_form,
-                'annotation': annotation_str,
-                'post_job_actions': {},
-                'uuid': str(step.uuid) if step.uuid else None,
-                'workflow_outputs': []
+                "id": step.order_index,
+                "type": module.type,
+                "label": module.label,
+                "content_id": module.get_content_id(),
+                "name": module.get_name(),
+                "tool_state": module.get_tool_state(),
+                "errors": module.get_errors(),
+                "inputs": module.get_all_inputs(connectable_only=True),
+                "outputs": module.get_all_outputs(),
+                "config_form": config_form,
+                "annotation": annotation_str,
+                "post_job_actions": {},
+                "uuid": str(step.uuid) if step.uuid else None,
+                "workflow_outputs": [],
             }
             if tooltip:
-                step_dict['tooltip'] = module.get_tooltip(static_path=url_for('/static'))
+                step_dict["tooltip"] = module.get_tooltip(static_path=url_for("/static"))
             # Connections
             input_connections = step.input_connections
             input_connections_type = {}
             multiple_input = {}  # Boolean value indicating if this can be multiple
-            if (step.type is None or step.type == 'tool') and module.tool:
+            if (step.type is None or step.type == "tool") and module.tool:
                 # Determine full (prefixed) names of valid input datasets
                 data_input_names = {}
 
@@ -851,16 +909,15 @@ class WorkflowContentsManager(UsesAnnotations):
                             input_connections_type[input.name] = "dataset"
                         if isinstance(input, DataCollectionToolParameter):
                             input_connections_type[input.name] = "dataset_collection"
+
                 visit_input_values(module.tool.inputs, module.state.inputs, callback)
                 # post_job_actions
                 pja_dict = {}
                 for pja in step.post_job_actions:
                     pja_dict[pja.action_type + pja.output_name] = dict(
-                        action_type=pja.action_type,
-                        output_name=pja.output_name,
-                        action_arguments=pja.action_arguments
+                        action_type=pja.action_type, output_name=pja.output_name, action_arguments=pja.action_arguments
                     )
-                step_dict['post_job_actions'] = pja_dict
+                step_dict["post_job_actions"] = pja_dict
 
             # workflow outputs
             outputs = []
@@ -870,21 +927,21 @@ class WorkflowContentsManager(UsesAnnotations):
                     output_label = output.label
                     output_name = output.output_name
                     output_uuid = str(output.uuid) if output.uuid else None
-                    outputs.append({"output_name": output_name,
-                                    "uuid": output_uuid,
-                                    "label": output_label})
+                    outputs.append({"output_name": output_name, "uuid": output_uuid, "label": output_label})
                     if output_label is not None:
                         if output_label in output_label_index:
                             if output_label not in output_label_duplicate:
                                 output_label_duplicate.add(output_label)
                         else:
                             output_label_index.add(output_label)
-            step_dict['workflow_outputs'] = outputs
+            step_dict["workflow_outputs"] = outputs
             if len(output_label_duplicate) > 0:
                 output_label_duplicate_string = ", ".join(output_label_duplicate)
-                upgrade_message_dict['output_label_duplicate'] = f"Ignoring duplicate labels: {output_label_duplicate_string}."
+                upgrade_message_dict[
+                    "output_label_duplicate"
+                ] = f"Ignoring duplicate labels: {output_label_duplicate_string}."
             if upgrade_message_dict:
-                data['upgrade_messages'][step.order_index] = upgrade_message_dict
+                data["upgrade_messages"][step.order_index] = upgrade_message_dict
 
             # Encode input connections as dictionary
             input_conn_dict: model.InputConnDictType = {}
@@ -900,14 +957,14 @@ class WorkflowContentsManager(UsesAnnotations):
                         input_conn_dict[conn.input_name] = [conn_dict]
                 else:
                     input_conn_dict[conn.input_name] = conn_dict
-            step_dict['input_connections'] = input_conn_dict
+            step_dict["input_connections"] = input_conn_dict
 
             # Position
-            step_dict['position'] = step.position
+            step_dict["position"] = step.position
             # Add to return value
-            data['steps'][step.order_index] = step_dict
+            data["steps"][step.order_index] = step_dict
         if is_subworkflow:
-            data['steps'] = self._resolve_collection_type(data['steps'])
+            data["steps"] = self._resolve_collection_type(data["steps"])
         return data
 
     @staticmethod
@@ -916,40 +973,40 @@ class WorkflowContentsManager(UsesAnnotations):
         Given a tool step and its input steps guess that maximum level of mapping over.
         All data outputs of a step need to be mapped over to this level.
         """
-        max_map_over = ''
-        for input_name, input_connections in current_step['input_connections'].items():
+        max_map_over = ""
+        for input_name, input_connections in current_step["input_connections"].items():
             if isinstance(input_connections, dict):
                 # if input does not accept multiple inputs
                 input_connections = [input_connections]
             for input_value in input_connections:
                 current_data_input = None
-                for current_input in current_step['inputs']:
-                    if current_input['name'] == input_name:
+                for current_input in current_step["inputs"]:
+                    if current_input["name"] == input_name:
                         current_data_input = current_input
                         # we've got one of the tools' input data definitions
                         break
                 if current_data_input is None:
                     log.info(f"failed to find input {input_name} for get_step_map_over")
                     continue
-                input_step = steps[input_value['id']]
-                for input_step_data_output in input_step['outputs']:
-                    if input_step_data_output['name'] == input_value['output_name']:
-                        collection_type = input_step_data_output.get('collection_type')
+                input_step = steps[input_value["id"]]
+                for input_step_data_output in input_step["outputs"]:
+                    if input_step_data_output["name"] == input_value["output_name"]:
+                        collection_type = input_step_data_output.get("collection_type")
                         # This is the defined incoming collection type, in reality there may be additional
                         # mapping over of the workflows' data input, but this should be taken care of by the workflow editor /
                         # outer workflow.
                         if collection_type:
-                            if current_data_input.get('input_type') == 'dataset' and current_data_input.get('multiple'):
+                            if current_data_input.get("input_type") == "dataset" and current_data_input.get("multiple"):
                                 # We reduce the innermost collection
-                                if ':' in collection_type:
+                                if ":" in collection_type:
                                     # more than one layer of nesting and multiple="true" input,
                                     # we consume the innermost collection
-                                    collection_type = ":".join(collection_type.rsplit(':')[:-1])
+                                    collection_type = ":".join(collection_type.rsplit(":")[:-1])
                                 else:
                                     # We've reduced a list or a pair
                                     collection_type = None
-                            elif current_data_input.get('input_type') == 'dataset_collection':
-                                current_collection_types = current_data_input['collection_types']
+                            elif current_data_input.get("input_type") == "dataset_collection":
+                                current_collection_types = current_data_input["collection_types"]
                                 if not current_collection_types:
                                     # Accepts any input dataset collection, no mapping
                                     collection_type = None
@@ -958,19 +1015,19 @@ class WorkflowContentsManager(UsesAnnotations):
                                     collection_type = None
                                 else:
                                     outer_map_over = collection_type
-                                    for accepted_collection_type in current_data_input['collection_types']:
+                                    for accepted_collection_type in current_data_input["collection_types"]:
                                         # need to find the lowest level of mapping over,
                                         # for collection_type = 'list:list:list' and accepted_collection_type = ['list:list', 'list']
                                         # it'd be outer_map_over == 'list'
                                         if collection_type.endswith(accepted_collection_type):
-                                            _outer_map_over = collection_type[:-(len(accepted_collection_type) + 1)]
-                                            if len(_outer_map_over.split(':')) < len(outer_map_over.split(':')):
+                                            _outer_map_over = collection_type[: -(len(accepted_collection_type) + 1)]
+                                            if len(_outer_map_over.split(":")) < len(outer_map_over.split(":")):
                                                 outer_map_over = _outer_map_over
                                     collection_type = outer_map_over
                             # If there is mapping over, we're going to assume it is linked, everything else is (probably)
                             # too hard to display in the workflow editor. With this assumption we should be able to
                             # set the maximum mapping over level to the most deeply nested map_over
-                            if collection_type and len(collection_type.split(':')) >= len(max_map_over.split(':')):
+                            if collection_type and len(collection_type.split(":")) >= len(max_map_over.split(":")):
                                 max_map_over = collection_type
         if max_map_over:
             return max_map_over
@@ -985,26 +1042,26 @@ class WorkflowContentsManager(UsesAnnotations):
         """
         for order_index in sorted(steps):
             step = steps[order_index]
-            if step['type'] == 'tool' and not step.get('errors'):
+            if step["type"] == "tool" and not step.get("errors"):
                 map_over = self.get_step_map_over(step, steps)
-                for step_data_output in step['outputs']:
-                    if step_data_output.get('collection_type_source') and step_data_output['collection_type'] is None:
-                        collection_type_source = step_data_output['collection_type_source']
-                        for input_connection in step['input_connections'].get(collection_type_source, []):
-                            input_step = steps[input_connection['id']]
-                            for input_step_data_output in input_step['outputs']:
-                                if input_step_data_output['name'] == input_connection['output_name']:
-                                    step_data_output['collection_type'] = input_step_data_output.get('collection_type')
+                for step_data_output in step["outputs"]:
+                    if step_data_output.get("collection_type_source") and step_data_output["collection_type"] is None:
+                        collection_type_source = step_data_output["collection_type_source"]
+                        for input_connection in step["input_connections"].get(collection_type_source, []):
+                            input_step = steps[input_connection["id"]]
+                            for input_step_data_output in input_step["outputs"]:
+                                if input_step_data_output["name"] == input_connection["output_name"]:
+                                    step_data_output["collection_type"] = input_step_data_output.get("collection_type")
                     if map_over:
                         collection_type = map_over
-                        step_data_output['collection'] = True
-                        if step_data_output.get('collection_type'):
+                        step_data_output["collection"] = True
+                        if step_data_output.get("collection_type"):
                             collection_type = f"{map_over}:{step_data_output['collection_type']}"
-                        step_data_output['collection_type'] = collection_type
+                        step_data_output["collection_type"] = collection_type
         return steps
 
     def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=False):
-        """ Export the workflow contents to a dictionary ready for JSON-ification and export.
+        """Export the workflow contents to a dictionary ready for JSON-ification and export.
 
         If internal, use content_ids instead subworkflow definitions.
         """
@@ -1012,7 +1069,7 @@ class WorkflowContentsManager(UsesAnnotations):
         tag_str = ""
         if stored is not None:
             if stored.id:
-                annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ''
+                annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ""
                 tag_str = stored.make_tag_string_list()
             else:
                 # dry run with flushed workflow objects, just use the annotation
@@ -1022,91 +1079,86 @@ class WorkflowContentsManager(UsesAnnotations):
 
         # Pack workflow data into a dictionary and return
         data: Dict[str, Any] = {}
-        data['a_galaxy_workflow'] = 'true'  # Placeholder for identifying galaxy workflow
-        data['format-version'] = "0.1"
-        data['name'] = workflow.name
-        data['annotation'] = annotation_str
-        data['tags'] = tag_str
+        data["a_galaxy_workflow"] = "true"  # Placeholder for identifying galaxy workflow
+        data["format-version"] = "0.1"
+        data["name"] = workflow.name
+        data["annotation"] = annotation_str
+        data["tags"] = tag_str
         if workflow.uuid is not None:
-            data['uuid'] = str(workflow.uuid)
+            data["uuid"] = str(workflow.uuid)
         steps: Dict[int, Dict[str, Any]] = {}
-        data['steps'] = steps
+        data["steps"] = steps
         if workflow.reports_config:
-            data['report'] = workflow.reports_config
+            data["report"] = workflow.reports_config
         if workflow.creator_metadata:
-            data['creator'] = workflow.creator_metadata
+            data["creator"] = workflow.creator_metadata
         if workflow.license:
-            data['license'] = workflow.license
+            data["license"] = workflow.license
         # For each step, rebuild the form and encode the state
         for step in workflow.steps:
             # Load from database representation
             module = module_factory.from_workflow_step(trans, step)
             if not module:
-                raise exceptions.MessageException(f'Unrecognized step type: {step.type}')
+                raise exceptions.MessageException(f"Unrecognized step type: {step.type}")
             # Get user annotation.
-            annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
+            annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ""
             content_id = module.get_content_id()
             # Export differences for backward compatibility
             tool_state = module.get_export_state()
             # Step info
             step_dict = {
-                'id': step.order_index,
-                'type': module.type,
-                'content_id': content_id,
-                'tool_id': content_id,  # For workflows exported to older Galaxies,
-                                        # eliminate after a few years...
-                'tool_version': step.tool_version,
-                'name': module.get_name(),
-                'tool_state': json.dumps(tool_state),
-                'errors': module.get_errors(),
-                'uuid': str(step.uuid),
-                'label': step.label or None,
-                'annotation': annotation_str
+                "id": step.order_index,
+                "type": module.type,
+                "content_id": content_id,
+                "tool_id": content_id,  # For workflows exported to older Galaxies,
+                # eliminate after a few years...
+                "tool_version": step.tool_version,
+                "name": module.get_name(),
+                "tool_state": json.dumps(tool_state),
+                "errors": module.get_errors(),
+                "uuid": str(step.uuid),
+                "label": step.label or None,
+                "annotation": annotation_str,
             }
             # Add tool shed repository information and post-job actions to step dict.
-            if module.type == 'tool':
+            if module.type == "tool":
                 if module.tool and module.tool.tool_shed:
                     step_dict["tool_shed_repository"] = {
-                        'name': module.tool.repository_name,
-                        'owner': module.tool.repository_owner,
-                        'changeset_revision': module.tool.changeset_revision,
-                        'tool_shed': module.tool.tool_shed
+                        "name": module.tool.repository_name,
+                        "owner": module.tool.repository_owner,
+                        "changeset_revision": module.tool.changeset_revision,
+                        "tool_shed": module.tool.tool_shed,
                     }
 
                 tool_representation = None
                 dynamic_tool = step.dynamic_tool
                 if dynamic_tool:
                     tool_representation = dynamic_tool.value
-                    step_dict['tool_representation'] = tool_representation
-                    if util.is_uuid(step_dict['content_id']):
-                        step_dict['content_id'] = None
-                        step_dict['tool_id'] = None
+                    step_dict["tool_representation"] = tool_representation
+                    if util.is_uuid(step_dict["content_id"]):
+                        step_dict["content_id"] = None
+                        step_dict["tool_id"] = None
 
                 pja_dict = {}
                 for pja in step.post_job_actions:
                     pja_dict[pja.action_type + pja.output_name] = dict(
-                        action_type=pja.action_type,
-                        output_name=pja.output_name,
-                        action_arguments=pja.action_arguments)
-                step_dict['post_job_actions'] = pja_dict
+                        action_type=pja.action_type, output_name=pja.output_name, action_arguments=pja.action_arguments
+                    )
+                step_dict["post_job_actions"] = pja_dict
 
-            if module.type == 'subworkflow' and not internal:
-                del step_dict['content_id']
-                del step_dict['errors']
-                del step_dict['tool_version']
-                del step_dict['tool_state']
+            if module.type == "subworkflow" and not internal:
+                del step_dict["content_id"]
+                del step_dict["errors"]
+                del step_dict["tool_version"]
+                del step_dict["tool_state"]
                 subworkflow = step.subworkflow
-                subworkflow_as_dict = self._workflow_to_dict_export(
-                    trans,
-                    stored=None,
-                    workflow=subworkflow
-                )
-                step_dict['subworkflow'] = subworkflow_as_dict
+                subworkflow_as_dict = self._workflow_to_dict_export(trans, stored=None, workflow=subworkflow)
+                step_dict["subworkflow"] = subworkflow_as_dict
 
             # Data inputs, legacy section not used anywhere within core
             input_dicts = []
             step_state = module.state.inputs or {}
-            if module.type != 'tool':
+            if module.type != "tool":
                 name = step_state.get("name") or module.label
                 if name:
                     input_dicts.append({"name": name, "description": annotation_str})
@@ -1118,8 +1170,10 @@ class WorkflowContentsManager(UsesAnnotations):
                     # Input type is described by a dict, e.g. indexed parameters.
                     for partval in val.values():
                         if type(partval) == RuntimeValue:
-                            input_dicts.append({"name": name, "description": f"runtime parameter for tool {module.get_name()}"})
-            step_dict['inputs'] = input_dicts
+                            input_dicts.append(
+                                {"name": name, "description": f"runtime parameter for tool {module.get_name()}"}
+                            )
+            step_dict["inputs"] = input_dicts
 
             # User outputs
             workflow_outputs_dicts = []
@@ -1130,13 +1184,13 @@ class WorkflowContentsManager(UsesAnnotations):
                     uuid=str(workflow_output.uuid) if workflow_output.uuid is not None else None,
                 )
                 workflow_outputs_dicts.append(workflow_output_dict)
-            step_dict['workflow_outputs'] = workflow_outputs_dicts
+            step_dict["workflow_outputs"] = workflow_outputs_dicts
 
             # All step outputs
-            step_dict['outputs'] = []
+            step_dict["outputs"] = []
             if type(module) is ToolModule:
                 for output in module.get_data_outputs():
-                    step_dict['outputs'].append({'name': output['name'], 'type': output['extensions'][0]})
+                    step_dict["outputs"].append({"name": output["name"], "type": output["extensions"][0]})
 
             step_in = {}
             for step_input in step.inputs:
@@ -1148,13 +1202,14 @@ class WorkflowContentsManager(UsesAnnotations):
 
             # Connections
             input_connections = step.input_connections
-            if step.type is None or step.type == 'tool':
+            if step.type is None or step.type == "tool":
                 # Determine full (prefixed) names of valid input datasets
                 data_input_names = {}
 
                 def callback(input, prefixed_name, **kwargs):
                     if isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter):
                         data_input_names[prefixed_name] = True
+
                 # FIXME: this updates modules silently right now; messages from updates should be provided.
                 module.check_and_update_state()
                 if module.tool:
@@ -1170,10 +1225,7 @@ class WorkflowContentsManager(UsesAnnotations):
                 for conn in input_connections:
                     if conn.input_name != input_name:
                         continue
-                    input_conn = dict(
-                        id=conn.output_step.order_index,
-                        output_name=conn.output_name
-                    )
+                    input_conn = dict(id=conn.output_step.order_index, output_name=conn.output_name)
                     if conn.input_subworkflow_step is not None:
                         subworkflow_step_id = conn.input_subworkflow_step.order_index
                         input_conn["input_subworkflow_step_id"] = subworkflow_step_id
@@ -1196,9 +1248,9 @@ class WorkflowContentsManager(UsesAnnotations):
                     back_compat_input_conn_dict[input_name] = input_conn_list[0]
                 else:
                     back_compat_input_conn_dict[input_name] = input_conn_list
-            step_dict['input_connections'] = back_compat_input_conn_dict
+            step_dict["input_connections"] = back_compat_input_conn_dict
             # Position
-            step_dict['position'] = step.position
+            step_dict["position"] = step.position
             # Add to return value
             steps[step.order_index] = step_dict
         return data
@@ -1206,21 +1258,21 @@ class WorkflowContentsManager(UsesAnnotations):
     def _workflow_to_dict_instance(self, stored, workflow, legacy=True):
         encode = self.app.security.encode_id
         sa_session = self.app.model.context
-        item = stored.to_dict(view='element', value_mapper={'id': encode})
-        item['name'] = workflow.name
-        item['url'] = url_for('workflow', id=item['id'])
-        item['owner'] = stored.user.username
+        item = stored.to_dict(view="element", value_mapper={"id": encode})
+        item["name"] = workflow.name
+        item["url"] = url_for("workflow", id=item["id"])
+        item["owner"] = stored.user.username
         inputs = {}
         for step in workflow.input_steps:
             step_type = step.type
-            step_label = step.label or step.tool_inputs.get('name')
+            step_label = step.label or step.tool_inputs.get("name")
             if step_label:
                 label = step_label
             elif step_type == "data_input":
                 label = "Input Dataset"
             elif step_type == "data_collection_input":
                 label = "Input Dataset Collection"
-            elif step_type == 'parameter_input':
+            elif step_type == "parameter_input":
                 label = "Input Parameter"
             else:
                 raise ValueError(f"Invalid step_type {step_type}")
@@ -1229,11 +1281,11 @@ class WorkflowContentsManager(UsesAnnotations):
             else:
                 index = step.order_index
             step_uuid = str(step.uuid) if step.uuid else None
-            inputs[index] = {'label': label, 'value': '', 'uuid': step_uuid}
-        item['inputs'] = inputs
-        item['annotation'] = self.get_item_annotation_str(sa_session, stored.user, stored)
-        item['license'] = workflow.license
-        item['creator'] = workflow.creator_metadata
+            inputs[index] = {"label": label, "value": "", "uuid": step_uuid}
+        item["inputs"] = inputs
+        item["annotation"] = self.get_item_annotation_str(sa_session, stored.user, stored)
+        item["license"] = workflow.license
+        item["creator"] = workflow.creator_metadata
         steps = {}
         steps_to_order_index = {}
         for step in workflow.steps:
@@ -1241,37 +1293,41 @@ class WorkflowContentsManager(UsesAnnotations):
         for step in workflow.steps:
             step_id = step.id if legacy else step.order_index
             step_type = step.type
-            step_dict = {'id': step_id,
-                         'type': step_type,
-                         'tool_id': step.tool_id,
-                         'tool_version': step.tool_version,
-                         'annotation': self.get_item_annotation_str(sa_session, stored.user, step),
-                         'tool_inputs': step.tool_inputs,
-                         'input_steps': {}}
+            step_dict = {
+                "id": step_id,
+                "type": step_type,
+                "tool_id": step.tool_id,
+                "tool_version": step.tool_version,
+                "annotation": self.get_item_annotation_str(sa_session, stored.user, step),
+                "tool_inputs": step.tool_inputs,
+                "input_steps": {},
+            }
 
-            if step_type == 'subworkflow':
-                del step_dict['tool_id']
-                del step_dict['tool_version']
-                del step_dict['tool_inputs']
-                step_dict['workflow_id'] = encode(step.subworkflow.id)
+            if step_type == "subworkflow":
+                del step_dict["tool_id"]
+                del step_dict["tool_version"]
+                del step_dict["tool_inputs"]
+                step_dict["workflow_id"] = encode(step.subworkflow.id)
 
             for conn in step.input_connections:
                 step_id = step.id if legacy else step.order_index
                 source_id = conn.output_step_id
                 source_step = source_id if legacy else steps_to_order_index[source_id]
-                step_dict['input_steps'][conn.input_name] = {'source_step': source_step,
-                                                             'step_output': conn.output_name}
+                step_dict["input_steps"][conn.input_name] = {
+                    "source_step": source_step,
+                    "step_output": conn.output_name,
+                }
 
             steps[step_id] = step_dict
 
-        item['steps'] = steps
+        item["steps"] = steps
         return item
 
     def __walk_step_dicts(self, data):
-        """ Walk over the supplied step dictionaries and return them in a way
+        """Walk over the supplied step dictionaries and return them in a way
         designed to preserve step order when possible.
         """
-        supplied_steps = data['steps']
+        supplied_steps = data["steps"]
         # Try to iterate through imported workflow in such a way as to
         # preserve step order.
         step_indices = list(supplied_steps.keys())
@@ -1301,8 +1357,8 @@ class WorkflowContentsManager(UsesAnnotations):
                     raise exceptions.DuplicatedIdentifierException(f"Duplicated step label '{label}' in request.")
                 discovered_labels.add(label)
 
-            if 'workflow_outputs' in step_dict:
-                outputs = step_dict['workflow_outputs']
+            if "workflow_outputs" in step_dict:
+                outputs = step_dict["workflow_outputs"]
                 # outputs may be list of name (deprecated legacy behavior)
                 # or dictionary of names to {uuid: <uuid>, label: <label>}
                 if isinstance(outputs, dict):
@@ -1311,18 +1367,24 @@ class WorkflowContentsManager(UsesAnnotations):
                         output_label = output_dict.get("label", None)
                         if output_label:
                             if label in discovered_output_labels:
-                                raise exceptions.DuplicatedIdentifierException(f"Duplicated workflow output label '{label}' in request.")
+                                raise exceptions.DuplicatedIdentifierException(
+                                    f"Duplicated workflow output label '{label}' in request."
+                                )
                             discovered_output_labels.add(label)
 
                         output_uuid = step_dict.get("output_uuid", None)
                         if output_uuid:
                             if output_uuid in discovered_output_uuids:
-                                raise exceptions.DuplicatedIdentifierException(f"Duplicate workflow output UUID '{output_uuid}' in request.")
+                                raise exceptions.DuplicatedIdentifierException(
+                                    f"Duplicate workflow output UUID '{output_uuid}' in request."
+                                )
                             discovered_output_uuids.add(uuid)
 
             yield step_dict
 
-    def __load_subworkflows(self, trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=False):
+    def __load_subworkflows(
+        self, trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=False
+    ):
         step_type = step_dict.get("type", None)
         if step_type == "subworkflow":
             subworkflow = self.__load_subworkflow_from_step_dict(
@@ -1330,37 +1392,44 @@ class WorkflowContentsManager(UsesAnnotations):
             )
             step_dict["subworkflow"] = subworkflow
 
-    def __module_from_dict(self, trans, steps: List[model.WorkflowStep], steps_by_external_id: Dict[str, model.WorkflowStep], step_dict, **kwds):
-        """ Create a WorkflowStep model object and corresponding module
+    def __module_from_dict(
+        self,
+        trans,
+        steps: List[model.WorkflowStep],
+        steps_by_external_id: Dict[str, model.WorkflowStep],
+        step_dict,
+        **kwds,
+    ):
+        """Create a WorkflowStep model object and corresponding module
         representing type-specific functionality from the incoming dictionary.
         """
         dry_run = kwds.get("dry_run", False)
         step = model.WorkflowStep()
-        step.position = step_dict.get('position', model.WorkflowStep.DEFAULT_POSITION)
-        if step_dict.get("uuid", None) and step_dict['uuid'] != "None":
+        step.position = step_dict.get("position", model.WorkflowStep.DEFAULT_POSITION)
+        if step_dict.get("uuid", None) and step_dict["uuid"] != "None":
             step.uuid = step_dict["uuid"]
         if "label" in step_dict:
             step.label = step_dict["label"]
 
         module = module_factory.from_dict(trans, step_dict, detached=dry_run, **kwds)
-        self.__set_default_label(step, module, step_dict.get('tool_state'))
+        self.__set_default_label(step, module, step_dict.get("tool_state"))
         module.save_to_step(step, detached=dry_run)
 
-        annotation = step_dict.get('annotation')
+        annotation = step_dict.get("annotation")
         if annotation:
             annotation = sanitize_html(annotation)
             sa_session = None if dry_run else trans.sa_session
             self.add_item_annotation(sa_session, trans.get_user(), step, annotation)
 
         # Stick this in the step temporarily
-        step.temp_input_connections = step_dict.get('input_connections', {})
+        step.temp_input_connections = step_dict.get("input_connections", {})
 
         # Create the model class for the step
         steps.append(step)
         external_id = step_dict["id"]
         steps_by_external_id[external_id] = step
-        if 'workflow_outputs' in step_dict:
-            workflow_outputs = step_dict['workflow_outputs']
+        if "workflow_outputs" in step_dict:
+            workflow_outputs = step_dict["workflow_outputs"]
             found_output_names = set()
             for workflow_output in workflow_outputs:
                 # Allow workflow outputs as list of output_names for backward compatibility.
@@ -1368,7 +1437,9 @@ class WorkflowContentsManager(UsesAnnotations):
                     workflow_output = {"output_name": workflow_output}
                 output_name = workflow_output["output_name"]
                 if output_name in found_output_names:
-                    raise exceptions.ObjectAttributeInvalidException(f"Duplicate workflow outputs with name [{output_name}] found.")
+                    raise exceptions.ObjectAttributeInvalidException(
+                        f"Duplicate workflow outputs with name [{output_name}] found."
+                    )
                 if not output_name:
                     raise exceptions.ObjectAttributeInvalidException("Workflow output with empty name encountered.")
                 found_output_names.add(output_name)
@@ -1395,7 +1466,9 @@ class WorkflowContentsManager(UsesAnnotations):
             trans.sa_session.expunge(step)
         return module, step
 
-    def __load_subworkflow_from_step_dict(self, trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=False):
+    def __load_subworkflow_from_step_dict(
+        self, trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=False
+    ):
         embedded_subworkflow = step_dict.get("subworkflow", None)
         subworkflow_id = step_dict.get("content_id", None)
         if embedded_subworkflow and subworkflow_id:
@@ -1406,15 +1479,15 @@ class WorkflowContentsManager(UsesAnnotations):
 
         if embedded_subworkflow:
             assert not dry_run
-            subworkflow = self.__build_embedded_subworkflow(trans, embedded_subworkflow, workflow_state_resolution_options)
+            subworkflow = self.__build_embedded_subworkflow(
+                trans, embedded_subworkflow, workflow_state_resolution_options
+            )
         elif subworkflow_id_map is not None:
             assert not dry_run
             # Interpret content_id as a workflow local thing.
             subworkflow = subworkflow_id_map[subworkflow_id[1:]]
         else:
-            subworkflow = self.app.workflow_manager.get_owned_workflow(
-                trans, subworkflow_id
-            )
+            subworkflow = self.app.workflow_manager.get_owned_workflow(trans, subworkflow_id)
 
         return subworkflow
 
@@ -1426,7 +1499,7 @@ class WorkflowContentsManager(UsesAnnotations):
         return subworkflow
 
     def __connect_workflow_steps(self, steps: List[model.WorkflowStep], steps_by_external_id, dry_run: bool) -> None:
-        """ Second pass to deal with connections between steps.
+        """Second pass to deal with connections between steps.
 
         Create workflow connection objects using externally specified ids
         using during creation or update.
@@ -1441,17 +1514,17 @@ class WorkflowContentsManager(UsesAnnotations):
                         conn_list = [conn_list]
 
                     for conn_dict in conn_list:
-                        if 'output_name' not in conn_dict or 'id' not in conn_dict:
+                        if "output_name" not in conn_dict or "id" not in conn_dict:
                             template = "Invalid connection [%s] - must be dict with output_name and id fields."
                             message = template % conn_dict
                             raise exceptions.MessageException(message)
-                        external_id = conn_dict['id']
+                        external_id = conn_dict["id"]
                         if external_id not in steps_by_external_id:
                             raise KeyError(f"Failed to find external id {external_id} in {steps_by_external_id.keys()}")
                         output_step = steps_by_external_id[external_id]
 
                         output_name = conn_dict["output_name"]
-                        input_subworkflow_step_index = conn_dict.get('input_subworkflow_step_id', None)
+                        input_subworkflow_step_index = conn_dict.get("input_subworkflow_step_id", None)
 
                         if dry_run:
                             input_subworkflow_step_index = None
@@ -1460,18 +1533,20 @@ class WorkflowContentsManager(UsesAnnotations):
             step.temp_input_connections = None
 
     def __set_default_label(self, step, module, state):
-        """ Previously data input modules had a `name` attribute to rename individual steps. Here, this value is transferred
+        """Previously data input modules had a `name` attribute to rename individual steps. Here, this value is transferred
         to the actual `label` attribute which is available for all module types, unique, and mapped to its own database column.
         """
-        if not module.label and module.type in ['data_input', 'data_collection_input']:
+        if not module.label and module.type in ["data_input", "data_collection_input"]:
             new_state = safe_loads(state)
-            default_label = new_state.get('name')
-            if default_label and util.unicodify(default_label).lower() not in ['input dataset', 'input dataset collection']:
+            default_label = new_state.get("name")
+            if default_label and util.unicodify(default_label).lower() not in [
+                "input dataset",
+                "input dataset collection",
+            ]:
                 step.label = module.label = default_label
 
     def do_refactor(self, trans, stored_workflow, refactor_request):
-        """Apply supplied actions to stored_workflow.latest_workflow to build a new version.
-        """
+        """Apply supplied actions to stored_workflow.latest_workflow to build a new version."""
         workflow = stored_workflow.latest_workflow
         as_dict = self._workflow_to_dict_export(trans, stored_workflow, workflow=workflow, internal=True)
         raw_workflow_description = self.normalize_workflow_format(trans, as_dict)
@@ -1509,10 +1584,10 @@ class WorkflowContentsManager(UsesAnnotations):
     def get_all_tool_ids(self, workflow):
         tool_ids = set()
         for step in workflow.steps:
-            if step.type == 'tool':
+            if step.type == "tool":
                 if step.tool_id:
                     tool_ids.add(step.tool_id)
-            elif step.type == 'subworkflow':
+            elif step.type == "subworkflow":
                 tool_ids.update(self.get_all_tool_ids(step.subworkflow))
         return tool_ids
 
@@ -1563,8 +1638,8 @@ class WorkflowCreateOptions(WorkflowStateResolutionOptions):
     install_repository_dependencies: bool = False
     install_resolver_dependencies: bool = False
     install_tool_dependencies: bool = False
-    new_tool_panel_section_label: str = ''
-    tool_panel_section_id: str = ''
+    new_tool_panel_section_label: str = ""
+    tool_panel_section_id: str = ""
     tool_panel_section_mapping: Dict = {}
     shed_tool_conf: Optional[str] = None
 
@@ -1579,31 +1654,30 @@ class WorkflowCreateOptions(WorkflowStateResolutionOptions):
     @property
     def install_options(self):
         return {
-            'install_repository_dependencies': self.install_repository_dependencies,
-            'install_resolver_dependencies': self.install_resolver_dependencies,
-            'install_tool_dependencies': self.install_tool_dependencies,
-            'new_tool_panel_section_label': self.new_tool_panel_section_label,
-            'tool_panel_section_id': self.tool_panel_section_id,
-            'tool_panel_section_mapping': self.tool_panel_section_mapping,
-            'shed_tool_conf': self.shed_tool_conf
+            "install_repository_dependencies": self.install_repository_dependencies,
+            "install_resolver_dependencies": self.install_resolver_dependencies,
+            "install_tool_dependencies": self.install_tool_dependencies,
+            "new_tool_panel_section_label": self.new_tool_panel_section_label,
+            "tool_panel_section_id": self.tool_panel_section_id,
+            "tool_panel_section_mapping": self.tool_panel_section_mapping,
+            "shed_tool_conf": self.shed_tool_conf,
         }
 
 
 class MissingToolsException(exceptions.MessageException):
-
     def __init__(self, workflow, errors):
         self.workflow = workflow
         self.errors = errors
 
 
 class RawWorkflowDescription:
-
     def __init__(self, as_dict, workflow_path=None):
         self.as_dict = as_dict
         self.workflow_path = workflow_path
 
 
 class Format2ConverterGalaxyInterface(ImporterGalaxyInterface):
-
     def import_workflow(self, workflow, **kwds):
-        raise NotImplementedError("Direct format 2 import of nested workflows is not yet implemented, use bioblend client.")
+        raise NotImplementedError(
+            "Direct format 2 import of nested workflows is not yet implemented, use bioblend client."
+        )
diff --git a/lib/galaxy/metadata/__init__.py b/lib/galaxy/metadata/__init__.py
index 89d3185d9ed..b79f14dee2e 100644
--- a/lib/galaxy/metadata/__init__.py
+++ b/lib/galaxy/metadata/__init__.py
@@ -8,19 +8,22 @@ from logging import getLogger
 
 import galaxy.model
 from galaxy.model import store
-from galaxy.model.metadata import FileParameter, MetadataTempFile
+from galaxy.model.metadata import (
+    FileParameter,
+    MetadataTempFile,
+)
 from galaxy.model.store import DirectoryModelExportStore
 from galaxy.util import safe_makedirs
 
 log = getLogger(__name__)
 
-SET_METADATA_SCRIPT = 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()'
+SET_METADATA_SCRIPT = "from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()"
 
 
 def get_metadata_compute_strategy(config, job_id, metadata_strategy_override=None, tool_id=None):
     metadata_strategy = metadata_strategy_override or config.metadata_strategy
     if metadata_strategy == "legacy":
-        raise Exception('legacy metadata_strategy has been removed')
+        raise Exception("legacy metadata_strategy has been removed")
     elif metadata_strategy == "extended" and tool_id != "__SET_METADATA__":
         return ExtendedDirectoryMetadataGenerator(job_id)
     else:
@@ -28,8 +31,8 @@ def get_metadata_compute_strategy(config, job_id, metadata_strategy_override=Non
 
 
 class MetadataCollectionStrategy(metaclass=abc.ABCMeta):
-    """Interface describing the abstract process of writing out and collecting output metadata.
-    """
+    """Interface describing the abstract process of writing out and collecting output metadata."""
+
     extended = False
 
     def invalidate_external_metadata(self, datasets, sa_session):
@@ -42,14 +45,30 @@ class MetadataCollectionStrategy(metaclass=abc.ABCMeta):
         pass
 
     @abc.abstractmethod
-    def setup_external_metadata(self, datasets_dict, out_collections, sa_session, exec_dir=None,
-                                tmp_dir=None, dataset_files_path=None,
-                                output_fnames=None, config_root=None, use_bin=False,
-                                config_file=None, datatypes_config=None,
-                                job_metadata=None, provided_metadata_style=None, compute_tmp_dir=None,
-                                include_command=True, max_metadata_value_size=0, max_discovered_files=None,
-                                object_store_conf=None, tool=None, job=None,
-                                kwds=None):
+    def setup_external_metadata(
+        self,
+        datasets_dict,
+        out_collections,
+        sa_session,
+        exec_dir=None,
+        tmp_dir=None,
+        dataset_files_path=None,
+        output_fnames=None,
+        config_root=None,
+        use_bin=False,
+        config_file=None,
+        datatypes_config=None,
+        job_metadata=None,
+        provided_metadata_style=None,
+        compute_tmp_dir=None,
+        include_command=True,
+        max_metadata_value_size=0,
+        max_discovered_files=None,
+        object_store_conf=None,
+        tool=None,
+        job=None,
+        kwds=None,
+    ):
         """Setup files needed for external metadata collection.
 
         If include_command is True, return full Python command to externally compute metadata
@@ -65,11 +84,12 @@ class MetadataCollectionStrategy(metaclass=abc.ABCMeta):
         """Load metadata calculated externally into specified dataset."""
 
     def _load_metadata_from_path(self, dataset, metadata_output_path, working_directory, remote_metadata_directory):
-
         def path_rewriter(path):
             if not path:
                 return path
-            normalized_remote_metadata_directory = remote_metadata_directory and os.path.normpath(remote_metadata_directory)
+            normalized_remote_metadata_directory = remote_metadata_directory and os.path.normpath(
+                remote_metadata_directory
+            )
             normalized_path = os.path.normpath(path)
             if remote_metadata_directory and normalized_path.startswith(normalized_remote_metadata_directory):
                 if self.portable:
@@ -90,7 +110,7 @@ class MetadataCollectionStrategy(metaclass=abc.ABCMeta):
             rstring = f"Metadata results could not be read from '{filename_results_code}'"
 
         if not rval:
-            log.debug(f'setting metadata externally failed for {dataset.__class__.__name__} {dataset.id}: {rstring}')
+            log.debug(f"setting metadata externally failed for {dataset.__class__.__name__} {dataset.id}: {rstring}")
         return rval
 
 
@@ -101,15 +121,32 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
     def __init__(self, job_id):
         self.job_id = job_id
 
-    def setup_external_metadata(self, datasets_dict, out_collections, sa_session, exec_dir=None,
-                                tmp_dir=None, dataset_files_path=None,
-                                output_fnames=None, config_root=None, use_bin=False,
-                                config_file=None, datatypes_config=None,
-                                job_metadata=None, provided_metadata_style=None, compute_tmp_dir=None,
-                                include_command=True, max_metadata_value_size=0, max_discovered_files=None,
-                                validate_outputs=False,
-                                object_store_conf=None, tool=None, job=None, link_data_only=False,
-                                kwds=None):
+    def setup_external_metadata(
+        self,
+        datasets_dict,
+        out_collections,
+        sa_session,
+        exec_dir=None,
+        tmp_dir=None,
+        dataset_files_path=None,
+        output_fnames=None,
+        config_root=None,
+        use_bin=False,
+        config_file=None,
+        datatypes_config=None,
+        job_metadata=None,
+        provided_metadata_style=None,
+        compute_tmp_dir=None,
+        include_command=True,
+        max_metadata_value_size=0,
+        max_discovered_files=None,
+        validate_outputs=False,
+        object_store_conf=None,
+        tool=None,
+        job=None,
+        link_data_only=False,
+        kwds=None,
+    ):
         assert job_metadata, "setup_external_metadata must be supplied with job_metadata path"
         kwds = kwds or {}
         if not job:
@@ -135,14 +172,18 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
             def _metadata_path(what):
                 return os.path.join(metadata_dir, f"metadata_{what}_{key}")
 
-            _initialize_metadata_inputs(dataset, _metadata_path, tmp_dir, kwds, real_metadata_object=self.write_object_store_conf)
+            _initialize_metadata_inputs(
+                dataset, _metadata_path, tmp_dir, kwds, real_metadata_object=self.write_object_store_conf
+            )
 
             outputs[name] = {
                 "filename_override": _get_filename_override(output_fnames, dataset.file_name),
                 "validate": validate_outputs,
                 "object_store_store_by": dataset.dataset.store_by,
-                'id': dataset.id,
-                'model_class': 'LibraryDatasetDatasetAssociation' if isinstance(dataset, galaxy.model.LibraryDatasetDatasetAssociation) else 'HistoryDatasetAssociation'
+                "id": dataset.id,
+                "model_class": "LibraryDatasetDatasetAssociation"
+                if isinstance(dataset, galaxy.model.LibraryDatasetDatasetAssociation)
+                else "HistoryDatasetAssociation",
             }
 
         metadata_params_path = os.path.join(metadata_dir, "params.json")
@@ -158,7 +199,13 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
 
         # export model objects and object store configuration for extended metadata also.
         export_directory = os.path.join(metadata_dir, "outputs_new")
-        with DirectoryModelExportStore(export_directory, for_edit=True, strip_metadata_files=False, serialize_dataset_objects=True, serialize_jobs=False) as export_store:
+        with DirectoryModelExportStore(
+            export_directory,
+            for_edit=True,
+            strip_metadata_files=False,
+            serialize_dataset_objects=True,
+            serialize_jobs=False,
+        ) as export_store:
             export_store.export_job(job, tool=tool)
             for dataset in datasets_dict.values():
                 export_store.add_dataset(dataset)
@@ -166,8 +213,8 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
             for name, dataset_collection in out_collections.items():
                 export_store.export_collection(dataset_collection)
                 output_collections[name] = {
-                    'id': dataset_collection.id,
-                    'model_class': dataset_collection.__class__.__name__
+                    "id": dataset_collection.id,
+                    "model_class": dataset_collection.__class__.__name__,
                 }
 
         if self.write_object_store_conf:
@@ -179,14 +226,18 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
             tool_as_dict["stdio_exit_codes"] = [e.to_dict() for e in tool.stdio_exit_codes]
             tool_as_dict["stdio_regexes"] = [r.to_dict() for r in tool.stdio_regexes]
             tool_as_dict["outputs"] = {name: output.to_dict() for name, output in tool.outputs.items()}
-            tool_as_dict["output_collections"] = {name: output.to_dict() for name, output in tool.output_collections.items()}
+            tool_as_dict["output_collections"] = {
+                name: output.to_dict() for name, output in tool.output_collections.items()
+            }
 
             # setup the rest
             metadata_params["tool"] = tool_as_dict
             metadata_params["link_data_only"] = link_data_only
             metadata_params["tool_path"] = tool.config_file
             metadata_params["job_id_tag"] = job.get_id_tag()
-            metadata_params["implicit_collection_jobs_association_id"] = job.implicit_collection_jobs_association and job.implicit_collection_jobs_association.id
+            metadata_params["implicit_collection_jobs_association_id"] = (
+                job.implicit_collection_jobs_association and job.implicit_collection_jobs_association.id
+            )
             metadata_params["job_params"] = job.raw_param_dict()
             metadata_params["output_collections"] = output_collections
 
@@ -204,7 +255,7 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
                 return 'python "metadata/set.py"'
         else:
             # return args to galaxy_ext.metadata.set_metadata required to build
-            return ''
+            return ""
 
     def load_metadata(self, dataset, name, sa_session, working_directory, remote_metadata_directory=None):
         metadata_output_path = os.path.join(working_directory, "metadata", f"metadata_out_{name}")
@@ -236,7 +287,9 @@ class ExtendedDirectoryMetadataGenerator(PortableDirectoryMetadataGenerator):
         # the target model store within the context of a session to bring in all the changed objects.
         # However, this method is part of the metadata interface and is used by unit tests,
         # so we allow a sessionless import and loading of individual dataset as below.
-        import_model_store = store.imported_store_for_metadata(os.path.join(working_directory, 'metadata', 'outputs_populated'))
+        import_model_store = store.imported_store_for_metadata(
+            os.path.join(working_directory, "metadata", "outputs_populated")
+        )
         imported_dataset = import_model_store.sa_session.query(galaxy.model.HistoryDatasetAssociation).find(dataset.id)
         dataset.metadata = imported_dataset.metadata
         return dataset
@@ -248,10 +301,10 @@ def _initialize_metadata_inputs(dataset, path_for_part, tmp_dir, kwds, real_meta
     filename_kwds = path_for_part("kwds")
     filename_override_metadata = path_for_part("override")
 
-    open(filename_out, 'wt+')  # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
+    open(filename_out, "wt+")  # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
     # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
-    json.dump((False, 'External set_meta() not called'), open(filename_results_code, 'wt+'))
-    json.dump(kwds, open(filename_kwds, 'wt+'), ensure_ascii=True)
+    json.dump((False, "External set_meta() not called"), open(filename_results_code, "wt+"))
+    json.dump(kwds, open(filename_kwds, "wt+"), ensure_ascii=True)
 
     override_metadata = []
     for meta_key, spec_value in dataset.metadata.spec.items():
@@ -262,7 +315,7 @@ def _initialize_metadata_inputs(dataset, path_for_part, tmp_dir, kwds, real_meta
                 shutil.copy(dataset.metadata.get(meta_key, None).file_name, metadata_temp.file_name)
                 override_metadata.append((meta_key, metadata_temp.to_JSON()))
 
-    json.dump(override_metadata, open(filename_override_metadata, 'wt+'))
+    json.dump(override_metadata, open(filename_override_metadata, "wt+"))
 
     return filename_out, filename_results_code, filename_kwds, filename_override_metadata
 
diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index 90755ce774c..1f381d91f09 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -22,7 +22,7 @@ try:
     from pulsar.client.staging import COMMAND_VERSION_FILENAME
 except ImportError:
     # Package unit tests
-    COMMAND_VERSION_FILENAME = 'COMMAND_VERSION'
+    COMMAND_VERSION_FILENAME = "COMMAND_VERSION"
 
 import galaxy.datatypes.registry
 import galaxy.model.mapping
@@ -67,7 +67,7 @@ logging.basicConfig()
 log = logging.getLogger(__name__)
 
 
-MAX_STDIO_READ_BYTES = 100 * 10 ** 6  # 100 MB
+MAX_STDIO_READ_BYTES = 100 * 10**6  # 100 MB
 
 
 def set_validated_state(dataset_instance):
@@ -81,7 +81,9 @@ def set_validated_state(dataset_instance):
     dataset_instance.metadata.__validated_state_message__ = datatype_validation.message
 
 
-def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size):
+def set_meta_with_tool_provided(
+    dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size
+):
     # This method is somewhat odd, in that we set the metadata attributes from tool,
     # then call set_meta, then set metadata attributes from tool again.
     # This is intentional due to interplay of overwrite kwd, the fact that some metadata
@@ -90,7 +92,9 @@ def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, data
     extension = dataset_instance.extension
     if extension == "_sniff_":
         try:
-            extension = sniff.handle_uploaded_dataset_file(dataset_instance.dataset.external_filename, datatypes_registry)
+            extension = sniff.handle_uploaded_dataset_file(
+                dataset_instance.dataset.external_filename, datatypes_registry
+            )
             # We need to both set the extension so it is available to set_meta
             # and record it in the metadata so it can be reloaded on the server
             # side and the model updated (see MetadataCollection.{from,to}_JSON_dict)
@@ -100,10 +104,10 @@ def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, data
         except Exception:
             log.exception("Problem sniffing datatype.")
 
-    for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
+    for metadata_name, metadata_value in file_dict.get("metadata", {}).items():
         setattr(dataset_instance.metadata, metadata_name, metadata_value)
     dataset_instance.datatype.set_meta(dataset_instance, **set_meta_kwds)
-    for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
+    for metadata_name, metadata_value in file_dict.get("metadata", {}).items():
         setattr(dataset_instance.metadata, metadata_name, metadata_value)
 
     if max_metadata_value_size:
@@ -153,7 +157,9 @@ def set_metadata_portable():
     tool_provided_metadata = load_job_metadata(job_metadata, provided_metadata_style)
 
     def set_meta(new_dataset_instance, file_dict):
-        set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
+        set_meta_with_tool_provided(
+            new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size
+        )
 
     try:
         object_store = get_object_store(tool_job_working_directory=tool_job_working_directory)
@@ -178,29 +184,29 @@ def set_metadata_portable():
 
         # TODO: constants...
         locations = [
-            (outputs_directory, 'tool_'),
-            (tool_job_working_directory, ''),
-            (outputs_directory, ''),  # # Pulsar style output directory? Was this ever used - did this ever work?
+            (outputs_directory, "tool_"),
+            (tool_job_working_directory, ""),
+            (outputs_directory, ""),  # # Pulsar style output directory? Was this ever used - did this ever work?
         ]
         for directory, prefix in locations:
             if os.path.exists(os.path.join(directory, f"{prefix}stdout")):
-                with open(os.path.join(directory, f"{prefix}stdout"), 'rb') as f:
+                with open(os.path.join(directory, f"{prefix}stdout"), "rb") as f:
                     tool_stdout = f.read(MAX_STDIO_READ_BYTES)
-                with open(os.path.join(directory, f"{prefix}stderr"), 'rb') as f:
+                with open(os.path.join(directory, f"{prefix}stderr"), "rb") as f:
                     tool_stderr = f.read(MAX_STDIO_READ_BYTES)
                 break
         else:
-            if os.path.exists(os.path.join(tool_job_working_directory, 'task_0')):
+            if os.path.exists(os.path.join(tool_job_working_directory, "task_0")):
                 # We have a task splitting job
-                tool_stdout = b''
-                tool_stderr = b''
-                paths = Path(tool_job_working_directory).glob('task_*')
+                tool_stdout = b""
+                tool_stderr = b""
+                paths = Path(tool_job_working_directory).glob("task_*")
                 for path in paths:
-                    with open(path / 'outputs' / 'tool_stdout', 'rb') as f:
+                    with open(path / "outputs" / "tool_stdout", "rb") as f:
                         task_stdout = f.read(MAX_STDIO_READ_BYTES)
                         if task_stdout:
                             tool_stdout = b"%s[%s stdout]\n%s\n" % (tool_stdout, path.name.encode(), task_stdout)
-                    with open(path / 'outputs' / 'tool_stderr', 'rb') as f:
+                    with open(path / "outputs" / "tool_stderr", "rb") as f:
                         task_stderr = f.read(MAX_STDIO_READ_BYTES)
                         if task_stderr:
                             tool_stderr = b"%s[%s stdout]\n%s\n" % (tool_stderr, path.name.encode(), task_stderr)
@@ -217,26 +223,34 @@ def set_metadata_portable():
         exit_code_file = default_exit_code_file(".", job_id_tag)
         tool_exit_code = read_exit_code_from(exit_code_file, job_id_tag)
 
-        check_output_detected_state, tool_stdout, tool_stderr, job_messages = check_output(stdio_regexes, stdio_exit_codes, tool_stdout, tool_stderr, tool_exit_code, job_id_tag)
+        check_output_detected_state, tool_stdout, tool_stderr, job_messages = check_output(
+            stdio_regexes, stdio_exit_codes, tool_stdout, tool_stderr, tool_exit_code, job_id_tag
+        )
         if check_output_detected_state == DETECTED_JOB_STATE.OK and not tool_provided_metadata.has_failed_outputs():
             final_job_state = Job.states.OK
         else:
             final_job_state = Job.states.ERROR
 
-        version_string_path = os.path.join('outputs', COMMAND_VERSION_FILENAME)
+        version_string_path = os.path.join("outputs", COMMAND_VERSION_FILENAME)
         version_string = collect_shrinked_content_from_path(version_string_path)
 
         expression_context = ExpressionContext(dict(stdout=tool_stdout[:255], stderr=tool_stderr[:255]))
 
         # Load outputs.
-        export_store = store.DirectoryModelExportStore('metadata/outputs_populated', serialize_dataset_objects=True, for_edit=True, strip_metadata_files=False, serialize_jobs=True)
+        export_store = store.DirectoryModelExportStore(
+            "metadata/outputs_populated",
+            serialize_dataset_objects=True,
+            for_edit=True,
+            strip_metadata_files=False,
+            serialize_jobs=True,
+        )
     try:
-        import_model_store = store.imported_store_for_metadata('metadata/outputs_new', object_store=object_store)
+        import_model_store = store.imported_store_for_metadata("metadata/outputs_new", object_store=object_store)
     except AssertionError:
         # Remove in 21.09, this should only happen for jobs that started on <= 20.09 and finish now
         import_model_store = None
 
-    tool_script_file = os.path.join(tool_job_working_directory, 'tool_script.sh')
+    tool_script_file = os.path.join(tool_job_working_directory, "tool_script.sh")
     job = None
     if import_model_store and export_store:
         job = next(iter(import_model_store.sa_session.objects[Job].values()))
@@ -257,12 +271,14 @@ def set_metadata_portable():
         output_collections = {}
         for name, output_collection in metadata_params["output_collections"].items():
             # TODO: remove HistoryDatasetCollectionAssociation fallback on 22.01, model_class used to not be serialized prior to 21.09
-            model_class = output_collection.get('model_class', 'HistoryDatasetCollectionAssociation')
-            collection = import_model_store.sa_session.query(getattr(galaxy.model, model_class)).find(output_collection["id"])
+            model_class = output_collection.get("model_class", "HistoryDatasetCollectionAssociation")
+            collection = import_model_store.sa_session.query(getattr(galaxy.model, model_class)).find(
+                output_collection["id"]
+            )
             output_collections[name] = collection
         output_instances = {}
         for name, output in metadata_params["outputs"].items():
-            klass = getattr(galaxy.model, output.get('model_class', 'HistoryDatasetAssociation'))
+            klass = getattr(galaxy.model, output.get("model_class", "HistoryDatasetAssociation"))
             output_instances[name] = import_model_store.sa_session.query(klass).find(output["id"])
 
         input_ext = json.loads(metadata_params["job_params"].get("__input_ext") or '"data"')
@@ -289,16 +305,16 @@ def set_metadata_portable():
         destination = unnamed_output_dict["destination"]
         elements = unnamed_output_dict["elements"]
         destination_type = destination["type"]
-        if destination_type == 'hdas':
+        if destination_type == "hdas":
             for element in elements:
-                filename = element.get('filename')
-                object_id = element.get('object_id')
+                filename = element.get("filename")
+                object_id = element.get("object_id")
                 if filename and object_id:
                     unnamed_id_to_path[object_id] = os.path.join(job_context.job_working_directory, filename)
 
     for output_name, output_dict in outputs.items():
         dataset_instance_id = output_dict["id"]
-        klass = getattr(galaxy.model, output_dict.get('model_class', 'HistoryDatasetAssociation'))
+        klass = getattr(galaxy.model, output_dict.get("model_class", "HistoryDatasetAssociation"))
         dataset = None
         if import_model_store:
             dataset = import_model_store.sa_session.query(klass).find(dataset_instance_id)
@@ -306,7 +322,8 @@ def set_metadata_portable():
             # legacy check for jobs that started before 21.01, remove on 21.05
             filename_in = os.path.join(f"metadata/metadata_in_{output_name}")
             import pickle
-            dataset = pickle.load(open(filename_in, 'rb'))  # load DatasetInstance
+
+            dataset = pickle.load(open(filename_in, "rb"))  # load DatasetInstance
         assert dataset is not None
 
         filename_kwds = os.path.join(f"metadata/metadata_kwds_{output_name}")
@@ -318,15 +335,21 @@ def set_metadata_portable():
         legacy_object_store_store_by = metadata_params.get("object_store_store_by", "id")
 
         # Same block as below...
-        set_meta_kwds = stringify_dictionary_keys(json.load(open(filename_kwds)))  # load kwds; need to ensure our keywords are not unicode
+        set_meta_kwds = stringify_dictionary_keys(
+            json.load(open(filename_kwds))
+        )  # load kwds; need to ensure our keywords are not unicode
         try:
             external_filename = unnamed_id_to_path.get(dataset_instance_id, dataset_filename_override)
             if not os.path.exists(external_filename):
                 matches = glob.glob(external_filename)
                 assert len(matches) == 1, f"More than one file matched by output glob '{external_filename}'"
                 external_filename = matches[0]
-                assert safe_contains(tool_job_working_directory, external_filename), f"Cannot collect output '{external_filename}' from outside of working directory"
-                created_from_basename = os.path.relpath(external_filename, os.path.join(tool_job_working_directory, 'working'))
+                assert safe_contains(
+                    tool_job_working_directory, external_filename
+                ), f"Cannot collect output '{external_filename}' from outside of working directory"
+                created_from_basename = os.path.relpath(
+                    external_filename, os.path.join(tool_job_working_directory, "working")
+                )
                 dataset.dataset.created_from_basename = created_from_basename
             # override filename if we're dealing with outputs to working directory and dataset is not linked to
             link_data_only = metadata_params.get("link_data_only")
@@ -339,8 +362,8 @@ def set_metadata_portable():
                 files_path = os.path.abspath(os.path.join(tool_job_working_directory, "working", extra_files_dir_name))
                 dataset.dataset.external_extra_files_path = files_path
             file_dict = tool_provided_metadata.get_dataset_meta(output_name, dataset.dataset.id, dataset.dataset.uuid)
-            if 'ext' in file_dict:
-                dataset.extension = file_dict['ext']
+            if "ext" in file_dict:
+                dataset.extension = file_dict["ext"]
             # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
             override_metadata = json.load(open(override_metadata))
             for metadata_name, metadata_file_override in override_metadata:
@@ -368,20 +391,20 @@ def set_metadata_portable():
                     context = ExpressionContext(meta, expression_context)
                 else:
                     context = expression_context
-                dataset.blurb = 'done'
-                dataset.peek = 'no peek'
-                dataset.info = (dataset.info or '')
-                if context['stdout'].strip():
+                dataset.blurb = "done"
+                dataset.peek = "no peek"
+                dataset.info = dataset.info or ""
+                if context["stdout"].strip():
                     # Ensure white space between entries
                     dataset.info = f"{dataset.info.rstrip()}\n{context['stdout'].strip()}"
-                if context['stderr'].strip():
+                if context["stderr"].strip():
                     # Ensure white space between entries
                     dataset.info = f"{dataset.info.rstrip()}\n{context['stderr'].strip()}"
                 dataset.tool_version = version_string
-                if 'uuid' in context:
-                    dataset.dataset.uuid = context['uuid']
+                if "uuid" in context:
+                    dataset.dataset.uuid = context["uuid"]
                 if not final_job_state == Job.states.ERROR:
-                    line_count = context.get('line_count', None)
+                    line_count = context.get("line_count", None)
                     try:
                         # Certain datatype's set_peek methods contain a line_count argument
                         dataset.set_peek(line_count=line_count)
@@ -400,9 +423,13 @@ def set_metadata_portable():
             else:
                 dataset.metadata.to_JSON_dict(filename_out)  # write out results of set_meta
 
-            json.dump((True, 'Metadata has been set successfully'), open(filename_results_code, 'wt+'))  # setting metadata has succeeded
+            json.dump(
+                (True, "Metadata has been set successfully"), open(filename_results_code, "wt+")
+            )  # setting metadata has succeeded
         except Exception:
-            json.dump((False, traceback.format_exc()), open(filename_results_code, 'wt+'))  # setting metadata has failed somehow
+            json.dump(
+                (False, traceback.format_exc()), open(filename_results_code, "wt+")
+            )  # setting metadata has failed somehow
 
     if export_store:
         export_store._finalize()
@@ -417,10 +444,18 @@ def validate_and_load_datatypes_config(datatypes_config):
         datatypes_config = "configs/registry.xml"
 
     if not os.path.exists(datatypes_config):
-        print(f"Metadata setting failed because registry.xml [{datatypes_config}] could not be found. You may retry setting metadata.")
+        print(
+            f"Metadata setting failed because registry.xml [{datatypes_config}] could not be found. You may retry setting metadata."
+        )
         sys.exit(1)
     datatypes_registry = galaxy.datatypes.registry.Registry()
-    datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config, use_build_sites=False, use_converters=False, use_display_applications=False)
+    datatypes_registry.load_datatypes(
+        root_dir=galaxy_root,
+        config=datatypes_config,
+        use_build_sites=False,
+        use_converters=False,
+        use_display_applications=False,
+    )
     galaxy.model.set_datatypes_registry(datatypes_registry)
     return datatypes_registry
 
@@ -434,12 +469,16 @@ def write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_
         filename = file_dict["filename"]
         new_dataset_filename = os.path.join(tool_job_working_directory, "working", filename)
         new_dataset = Dataset(id=-i, external_filename=new_dataset_filename)
-        extra_files = file_dict.get('extra_files', None)
+        extra_files = file_dict.get("extra_files", None)
         if extra_files is not None:
             new_dataset._extra_files_path = os.path.join(tool_job_working_directory, "working", extra_files)
         new_dataset.state = new_dataset.states.OK
-        new_dataset_instance = HistoryDatasetAssociation(id=-i, dataset=new_dataset, extension=file_dict.get('ext', 'data'))
+        new_dataset_instance = HistoryDatasetAssociation(
+            id=-i, dataset=new_dataset, extension=file_dict.get("ext", "data")
+        )
         set_meta(new_dataset_instance, file_dict)
-        file_dict['metadata'] = json.loads(new_dataset_instance.metadata.to_JSON_dict())  # storing metadata in external form, need to turn back into dict, then later jsonify
+        file_dict["metadata"] = json.loads(
+            new_dataset_instance.metadata.to_JSON_dict()
+        )  # storing metadata in external form, need to turn back into dict, then later jsonify
 
     tool_provided_metadata.rewrite()
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 6e7b6ff84bb..318d0e16ef0 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -17,7 +17,10 @@ import random
 import string
 from collections import defaultdict
 from collections.abc import Callable
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from enum import Enum
 from string import Template
 from typing import (
@@ -32,11 +35,20 @@ from typing import (
     TYPE_CHECKING,
     Union,
 )
-from uuid import UUID, uuid4
+from uuid import (
+    UUID,
+    uuid4,
+)
 
 import sqlalchemy
 from boltons.iterutils import remap
-from social_core.storage import AssociationMixin, CodeMixin, NonceMixin, PartialMixin, UserMixin
+from social_core.storage import (
+    AssociationMixin,
+    CodeMixin,
+    NonceMixin,
+    PartialMixin,
+    UserMixin,
+)
 from sqlalchemy import (
     alias,
     and_,
@@ -102,7 +114,10 @@ from galaxy.model.custom_types import (
     TrimmedString,
     UUIDType,
 )
-from galaxy.model.item_attrs import get_item_annotation_str, UsesAnnotations
+from galaxy.model.item_attrs import (
+    get_item_annotation_str,
+    UsesAnnotations,
+)
 from galaxy.model.orm.now import now
 from galaxy.model.view import HistoryDatasetCollectionJobStateSummary
 from galaxy.security import get_permitted_actions
@@ -115,10 +130,21 @@ from galaxy.util import (
     unicodify,
     unique_id,
 )
-from galaxy.util.dictifiable import dict_for, Dictifiable
-from galaxy.util.form_builder import (AddressField, CheckboxField, HistoryField,
-                                      PasswordField, SelectField, TextArea, TextField, WorkflowField,
-                                      WorkflowMappingField)
+from galaxy.util.dictifiable import (
+    dict_for,
+    Dictifiable,
+)
+from galaxy.util.form_builder import (
+    AddressField,
+    CheckboxField,
+    HistoryField,
+    PasswordField,
+    SelectField,
+    TextArea,
+    TextField,
+    WorkflowField,
+    WorkflowMappingField,
+)
 from galaxy.util.hash_util import new_secure_hash
 from galaxy.util.json import safe_loads
 from galaxy.util.sanitize_html import sanitize_html
@@ -151,6 +177,7 @@ if TYPE_CHECKING:
     class _HasTable:
         table: Table
         __table__: Table
+
 else:
     _HasTable = object
 
@@ -179,7 +206,7 @@ class RepresentById(_HasTable):
 
     def __repr__(self):
         try:
-            r = f'<galaxy.model.{self.__class__.__name__}({cached_id(self)}) at {hex(id(self))}>'
+            r = f"<galaxy.model.{self.__class__.__name__}({cached_id(self)}) at {hex(id(self))}>"
         except Exception:
             r = object.__repr__(self)
             log.exception("Caught exception attempting to generate repr for: %s", r)
@@ -204,7 +231,9 @@ class ConverterDependencyException(Exception):
 
 def _get_datatypes_registry():
     if _datatypes_registry is None:
-        raise Exception("galaxy.model.set_datatypes_registry must be called before performing certain DatasetInstance operations.")
+        raise Exception(
+            "galaxy.model.set_datatypes_registry must be called before performing certain DatasetInstance operations."
+        )
     return _datatypes_registry
 
 
@@ -223,7 +252,7 @@ class HasTags:
 
     def to_dict(self, *args, **kwargs):
         rval = super().to_dict(*args, **kwargs)
-        rval['tags'] = self.make_tag_string_list()
+        rval["tags"] = self.make_tag_string_list()
         return rval
 
     def make_tag_string_list(self):
@@ -248,8 +277,9 @@ class HasTags:
 
 
 class SerializationOptions:
-
-    def __init__(self, for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None):
+    def __init__(
+        self, for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None
+    ):
         self.for_edit = for_edit
         if serialize_dataset_objects is None:
             serialize_dataset_objects = for_edit
@@ -265,7 +295,7 @@ class SerializationOptions:
         if self.for_edit and obj.id:
             ret_val["id"] = obj.id
         elif obj.id:
-            ret_val["encoded_id"] = id_encoder.encode_id(obj.id, kind='model_export')
+            ret_val["encoded_id"] = id_encoder.encode_id(obj.id, kind="model_export")
         else:
             if not hasattr(obj, "temp_id"):
                 obj.temp_id = uuid4().hex
@@ -275,7 +305,7 @@ class SerializationOptions:
         if self.for_edit and obj.id:
             return obj.id
         elif obj.id:
-            return id_encoder.encode_id(obj.id, kind='model_export')
+            return id_encoder.encode_id(obj.id, kind="model_export")
         else:
             if not hasattr(obj, "temp_id"):
                 obj.temp_id = uuid4().hex
@@ -285,7 +315,7 @@ class SerializationOptions:
         if self.for_edit and obj_id:
             return obj_id
         elif obj_id:
-            return id_encoder.encode_id(obj_id, kind='model_export')
+            return id_encoder.encode_id(obj_id, kind="model_export")
         else:
             raise NotImplementedError()
 
@@ -295,13 +325,12 @@ class SerializationOptions:
 
 
 class Serializable(RepresentById):
-
-    def serialize(self, id_encoder: IdEncodingHelper, serialization_options: SerializationOptions, for_link: bool = False) -> Dict[str, Any]:
+    def serialize(
+        self, id_encoder: IdEncodingHelper, serialization_options: SerializationOptions, for_link: bool = False
+    ) -> Dict[str, Any]:
         """Serialize model for a re-population in (potentially) another Galaxy instance."""
         if for_link:
-            rval = dict_for(
-                self
-            )
+            rval = dict_for(self)
             serialization_options.attach_identifier(id_encoder, self, rval)
             return rval
         return self._serialize(id_encoder, serialization_options)
@@ -312,14 +341,13 @@ class Serializable(RepresentById):
 
 
 class HasName:
-
     def get_display_name(self):
         """
         These objects have a name attribute can be either a string or a unicode
         object. If string, convert to unicode object assuming 'utf-8' format.
         """
         name = self.name
-        name = unicodify(name, 'utf-8')
+        name = unicodify(name, "utf-8")
         return name
 
 
@@ -342,10 +370,8 @@ class UsesCreateAndUpdateTime:
 
 
 class WorkerProcess(Base, UsesCreateAndUpdateTime, _HasTable):
-    __tablename__ = 'worker_process'
-    __table_args__ = (
-        UniqueConstraint('server_name', 'hostname'),
-    )
+    __tablename__ = "worker_process"
+    __table_args__ = (UniqueConstraint("server_name", "hostname"),)
 
     id = Column(Integer, primary_key=True)
     server_name = Column(String(255), index=True)
@@ -381,28 +407,32 @@ def cached_id(galaxy_model_object):
 
 
 class JobLike:
-    MAX_NUMERIC = 10**(JOB_METRIC_PRECISION - JOB_METRIC_SCALE) - 1
+    MAX_NUMERIC = 10 ** (JOB_METRIC_PRECISION - JOB_METRIC_SCALE) - 1
 
     def _init_metrics(self):
         self.text_metrics = []
         self.numeric_metrics = []
 
     def add_metric(self, plugin, metric_name, metric_value):
-        plugin = unicodify(plugin, 'utf-8')
-        metric_name = unicodify(metric_name, 'utf-8')
+        plugin = unicodify(plugin, "utf-8")
+        metric_name = unicodify(metric_name, "utf-8")
         number = isinstance(metric_value, numbers.Number)
         if number and int(metric_value) <= JobLike.MAX_NUMERIC:
             metric = self._numeric_metric(plugin, metric_name, metric_value)
             self.numeric_metrics.append(metric)
         elif number:
-            log.warning("Cannot store metric due to database column overflow (max: %s): %s: %s",
-                        JobLike.MAX_NUMERIC, metric_name, metric_value)
+            log.warning(
+                "Cannot store metric due to database column overflow (max: %s): %s: %s",
+                JobLike.MAX_NUMERIC,
+                metric_name,
+                metric_value,
+            )
         else:
-            metric_value = unicodify(metric_value, 'utf-8')
+            metric_value = unicodify(metric_value, "utf-8")
             if len(metric_value) > (JOB_METRIC_MAX_LENGTH - 1):
                 # Truncate these values - not needed with sqlite
                 # but other backends must need it.
-                metric_value = metric_value[:(JOB_METRIC_MAX_LENGTH - 1)]
+                metric_value = metric_value[: (JOB_METRIC_MAX_LENGTH - 1)]
             metric = self._text_metric(plugin, metric_name, metric_value)
             self.text_metrics.append(metric)
 
@@ -414,22 +444,24 @@ class JobLike:
     def set_streams(self, tool_stdout, tool_stderr, job_stdout=None, job_stderr=None, job_messages=None):
         def shrink_and_unicodify(what, stream):
             if len(stream) > galaxy.util.DATABASE_MAX_STRING_SIZE:
-                log.info("%s for %s %d is greater than %s, only a portion will be logged to database",
-                         what,
-                         type(self),
-                         self.id,
-                         galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY)
+                log.info(
+                    "%s for %s %d is greater than %s, only a portion will be logged to database",
+                    what,
+                    type(self),
+                    self.id,
+                    galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY,
+                )
             return galaxy.util.shrink_and_unicodify(stream)
 
-        self.tool_stdout = shrink_and_unicodify('tool_stdout', tool_stdout)
-        self.tool_stderr = shrink_and_unicodify('tool_stderr', tool_stderr)
+        self.tool_stdout = shrink_and_unicodify("tool_stdout", tool_stdout)
+        self.tool_stderr = shrink_and_unicodify("tool_stderr", tool_stderr)
         if job_stdout is not None:
-            self.job_stdout = shrink_and_unicodify('job_stdout', job_stdout)
+            self.job_stdout = shrink_and_unicodify("job_stdout", job_stdout)
         else:
             self.job_stdout = None
 
         if job_stderr is not None:
-            self.job_stderr = shrink_and_unicodify('job_stderr', job_stderr)
+            self.job_stderr = shrink_and_unicodify("job_stderr", job_stderr)
         else:
             self.job_stderr = None
 
@@ -448,7 +480,7 @@ class JobLike:
 
     @property
     def stdout(self):
-        stdout = self.tool_stdout or ''
+        stdout = self.tool_stdout or ""
         if self.job_stdout:
             stdout += f"\n{self.job_stdout}"
         return stdout
@@ -459,7 +491,7 @@ class JobLike:
 
     @property
     def stderr(self):
-        stderr = self.tool_stderr or ''
+        stderr = self.tool_stderr or ""
         if self.job_stderr:
             stderr += f"\n{self.job_stderr}"
         return stderr
@@ -474,11 +506,12 @@ class User(Base, Dictifiable, RepresentById):
     Data for a Galaxy user or admin and relations to their
     histories, credentials, and roles.
     """
+
     use_pbkdf2 = True
     bootstrap_admin_user = False
     # api_keys: 'List[APIKeys]'  already declared as relationship()
 
-    __tablename__ = 'galaxy_user'
+    __tablename__ = "galaxy_user"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -488,7 +521,7 @@ class User(Base, Dictifiable, RepresentById):
     password = Column(TrimmedString(255), nullable=False)
     last_password_change = Column(DateTime, default=now)
     external = Column(Boolean, default=False)
-    form_values_id = Column(Integer, ForeignKey('form_values.id'), index=True)
+    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
     deleted = Column(Boolean, index=True, default=False)
     purged = Column(Boolean, index=True, default=False)
     disk_usage = Column(Numeric(15, 0), index=True)
@@ -496,60 +529,74 @@ class User(Base, Dictifiable, RepresentById):
     active = Column(Boolean, index=True, default=True, nullable=False)
     activation_token = Column(TrimmedString(64), nullable=True, index=True)
 
-    addresses = relationship('UserAddress',
-        back_populates='user',
-        order_by=lambda: desc(UserAddress.update_time))
-    cloudauthz = relationship('CloudAuthz', back_populates='user')
-    custos_auth = relationship('CustosAuthnzToken', back_populates='user')
-    default_permissions = relationship('DefaultUserPermissions', back_populates='user')
-    groups = relationship('UserGroupAssociation', back_populates='user')
-    histories = relationship('History',
-        back_populates='user',
-        order_by=lambda: desc(History.update_time))  # type: ignore[has-type]
-    active_histories = relationship('History',
+    addresses = relationship("UserAddress", back_populates="user", order_by=lambda: desc(UserAddress.update_time))
+    cloudauthz = relationship("CloudAuthz", back_populates="user")
+    custos_auth = relationship("CustosAuthnzToken", back_populates="user")
+    default_permissions = relationship("DefaultUserPermissions", back_populates="user")
+    groups = relationship("UserGroupAssociation", back_populates="user")
+    histories = relationship(
+        "History", back_populates="user", order_by=lambda: desc(History.update_time)
+    )  # type: ignore[has-type]
+    active_histories = relationship(
+        "History",
         primaryjoin=(lambda: (History.user_id == User.id) & (not_(History.deleted))),  # type: ignore[has-type]
         viewonly=True,
-        order_by=lambda: desc(History.update_time))  # type: ignore[has-type]
-    galaxy_sessions = relationship('GalaxySession',
-        back_populates='user',
-        order_by=lambda: desc(GalaxySession.update_time))  # type: ignore[has-type]
-    quotas = relationship('UserQuotaAssociation', back_populates='user')
-    social_auth = relationship('UserAuthnzToken', back_populates='user')
-    stored_workflow_menu_entries = relationship('StoredWorkflowMenuEntry',
-        primaryjoin=(lambda:
-            (StoredWorkflowMenuEntry.user_id == User.id)
+        order_by=lambda: desc(History.update_time),
+    )  # type: ignore[has-type]
+    galaxy_sessions = relationship(
+        "GalaxySession", back_populates="user", order_by=lambda: desc(GalaxySession.update_time)
+    )  # type: ignore[has-type]
+    quotas = relationship("UserQuotaAssociation", back_populates="user")
+    social_auth = relationship("UserAuthnzToken", back_populates="user")
+    stored_workflow_menu_entries = relationship(
+        "StoredWorkflowMenuEntry",
+        primaryjoin=(
+            lambda: (StoredWorkflowMenuEntry.user_id == User.id)
             & (StoredWorkflowMenuEntry.stored_workflow_id == StoredWorkflow.id)  # type: ignore[has-type]
             & not_(StoredWorkflow.deleted)  # type: ignore[has-type]
         ),
-        back_populates='user',
-        cascade='all, delete-orphan',
-        collection_class=ordering_list('order_index'))
-    _preferences = relationship('UserPreference', collection_class=attribute_mapped_collection('name'))
-    values = relationship('FormValues',
-        primaryjoin=(lambda: User.form_values_id == FormValues.id))  # type: ignore[has-type]
+        back_populates="user",
+        cascade="all, delete-orphan",
+        collection_class=ordering_list("order_index"),
+    )
+    _preferences = relationship("UserPreference", collection_class=attribute_mapped_collection("name"))
+    values = relationship(
+        "FormValues", primaryjoin=(lambda: User.form_values_id == FormValues.id)
+    )  # type: ignore[has-type]
     # Add type hint (will this work w/SA?)
-    api_keys: 'List[APIKeys]' = relationship('APIKeys',
-        back_populates='user',
-        order_by=lambda: desc(APIKeys.create_time))
-    data_manager_histories = relationship('DataManagerHistoryAssociation', back_populates='user')
-    roles = relationship('UserRoleAssociation', back_populates='user')
-    stored_workflows = relationship('StoredWorkflow', back_populates='user',
-        primaryjoin=(lambda: User.id == StoredWorkflow.user_id))  # type: ignore[has-type]
+    api_keys: "List[APIKeys]" = relationship(
+        "APIKeys", back_populates="user", order_by=lambda: desc(APIKeys.create_time)
+    )
+    data_manager_histories = relationship("DataManagerHistoryAssociation", back_populates="user")
+    roles = relationship("UserRoleAssociation", back_populates="user")
+    stored_workflows = relationship(
+        "StoredWorkflow", back_populates="user", primaryjoin=(lambda: User.id == StoredWorkflow.user_id)
+    )  # type: ignore[has-type]
     non_private_roles = relationship(
-        'UserRoleAssociation',
+        "UserRoleAssociation",
         viewonly=True,
-        primaryjoin=(lambda:
-            (User.id == UserRoleAssociation.user_id)  # type: ignore[has-type]
+        primaryjoin=(
+            lambda: (User.id == UserRoleAssociation.user_id)  # type: ignore[has-type]
             & (UserRoleAssociation.role_id == Role.id)  # type: ignore[has-type]
-            & not_(Role.name == User.email))  # type: ignore[has-type]
+            & not_(Role.name == User.email)
+        ),  # type: ignore[has-type]
     )
 
     preferences: association_proxy  # defined at the end of this module
 
     # attributes that will be accessed and returned when calling to_dict( view='collection' )
-    dict_collection_visible_keys = ['id', 'email', 'username', 'deleted', 'active', 'last_password_change']
+    dict_collection_visible_keys = ["id", "email", "username", "deleted", "active", "last_password_change"]
     # attributes that will be accessed and returned when calling to_dict( view='element' )
-    dict_element_visible_keys = ['id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change']
+    dict_element_visible_keys = [
+        "id",
+        "email",
+        "username",
+        "total_disk_usage",
+        "nice_total_disk_usage",
+        "deleted",
+        "active",
+        "last_password_change",
+    ]
 
     def __init__(self, email=None, password=None, username=None):
         self.email = email
@@ -563,7 +610,7 @@ class User(Base, Dictifiable, RepresentById):
     @property
     def extra_preferences(self):
         data = defaultdict(lambda: None)
-        extra_user_preferences = self.preferences.get('extra_user_preferences')
+        extra_user_preferences = self.preferences.get("extra_user_preferences")
         if extra_user_preferences:
             try:
                 data.update(json.loads(extra_user_preferences))
@@ -590,7 +637,8 @@ class User(Base, Dictifiable, RepresentById):
         :return: void
         """
         self.set_password_cleartext(
-            ''.join(random.SystemRandom().choice(string.ascii_letters + string.digits) for _ in range(length)))
+            "".join(random.SystemRandom().choice(string.ascii_letters + string.digits) for _ in range(length))
+        )
 
     def check_password(self, cleartext):
         """
@@ -603,9 +651,9 @@ class User(Base, Dictifiable, RepresentById):
         Gives the system user pwent entry based on e-mail or username depending
         on the value in real_system_username
         """
-        if real_system_username == 'user_email':
-            username = self.email.split('@')[0]
-        elif real_system_username == 'username':
+        if real_system_username == "user_email":
+            username = self.email.split("@")[0]
+        elif real_system_username == "username":
             username = self.username
         else:
             username = real_system_username
@@ -621,18 +669,19 @@ class User(Base, Dictifiable, RepresentById):
         """
         try:
             db_session = object_session(self)
-            user = db_session.query(
-                User
-            ).filter_by(  # don't use get, it will use session variant.
-                id=self.id
-            ).options(
-                joinedload("roles"),
-                joinedload("roles.role"),
-                joinedload("groups"),
-                joinedload("groups.group"),
-                joinedload("groups.group.roles"),
-                joinedload("groups.group.roles.role")
-            ).one()
+            user = (
+                db_session.query(User)
+                .filter_by(id=self.id)  # don't use get, it will use session variant.
+                .options(
+                    joinedload("roles"),
+                    joinedload("roles.role"),
+                    joinedload("groups"),
+                    joinedload("groups.group"),
+                    joinedload("groups.group.roles"),
+                    joinedload("groups.group.roles.role"),
+                )
+                .one()
+            )
         except Exception:
             # If not persistent user, just use models normaly and
             # skip optimizations...
@@ -646,8 +695,7 @@ class User(Base, Dictifiable, RepresentById):
         return roles
 
     def all_roles_exploiting_cache(self):
-        """
-        """
+        """ """
         roles = [ura.role for ura in self.roles]
         for group in [uga.group for uga in self.groups]:
             for role in [gra.role for gra in group.roles]:
@@ -726,7 +774,7 @@ class User(Base, Dictifiable, RepresentById):
                 AND library_dataset_dataset_association.id IS NULL
         """
         sa_session = object_session(self)
-        usage = sa_session.scalar(sql_calc, {'id': self.id})
+        usage = sa_session.scalar(sql_calc, {"id": self.id})
         if not dryrun:
             self.set_disk_usage(usage)
             sa_session.flush()
@@ -751,25 +799,24 @@ class User(Base, Dictifiable, RepresentById):
         'foo2'
         """
         if user:
-            user_id = '%d' % user.id
+            user_id = "%d" % user.id
             user_email = str(user.email)
             user_name = str(user.username)
         else:
             user = None
-            user_id = 'Anonymous'
-            user_email = 'Anonymous'
-            user_name = 'Anonymous'
+            user_id = "Anonymous"
+            user_email = "Anonymous"
+            user_name = "Anonymous"
         environment = {}
-        environment['__user__'] = user
-        environment['__user_id__'] = environment['userId'] = user_id
-        environment['__user_email__'] = environment['userEmail'] = user_email
-        environment['__user_name__'] = user_name
+        environment["__user__"] = user
+        environment["__user_id__"] = environment["userId"] = user_id
+        environment["__user_email__"] = environment["userEmail"] = user_email
+        environment["__user_name__"] = user_name
         return environment
 
     @staticmethod
     def expand_user_properties(user, in_string):
-        """
-        """
+        """ """
         environment = User.user_template_environment(user)
         return Template(in_string).safe_substitute(environment)
 
@@ -788,7 +835,7 @@ class User(Base, Dictifiable, RepresentById):
     def attempt_create_private_role(self):
         session = object_session(self)
         role_name = self.email
-        role_desc = f'Private Role for {self.email}'
+        role_desc = f"Private Role for {self.email}"
         role_type = Role.types.PRIVATE
         role = Role(name=role_name, description=role_desc, type=role_type)
         assoc = UserRoleAssociation(self, role)
@@ -797,12 +844,12 @@ class User(Base, Dictifiable, RepresentById):
 
 
 class PasswordResetToken(Base, _HasTable):
-    __tablename__ = 'password_reset_token'
+    __tablename__ = "password_reset_token"
 
     token = Column(String(32), primary_key=True, unique=True, index=True)
     expiration_time = Column(DateTime)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    user = relationship('User')
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user = relationship("User")
 
     def __init__(self, user, token=None):
         if token:
@@ -814,7 +861,7 @@ class PasswordResetToken(Base, _HasTable):
 
 
 class DynamicTool(Base, Dictifiable, RepresentById):
-    __tablename__ = 'dynamic_tool'
+    __tablename__ = "dynamic_tool"
 
     id = Column(Integer, primary_key=True)
     uuid = Column(UUIDType())
@@ -829,14 +876,14 @@ class DynamicTool(Base, Dictifiable, RepresentById):
     active = Column(Boolean, default=True)
     value = Column(MutableJSONType)
 
-    dict_collection_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
-    dict_element_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
+    dict_collection_visible_keys = ("id", "tool_id", "tool_format", "tool_version", "uuid", "active", "hidden")
+    dict_element_visible_keys = ("id", "tool_id", "tool_format", "tool_version", "uuid", "active", "hidden")
 
     def __init__(self, active=True, hidden=True, **kwd):
         super().__init__(**kwd)
         self.active = active
         self.hidden = hidden
-        _uuid = kwd.get('uuid')
+        _uuid = kwd.get("uuid")
         self.uuid = get_uuid(_uuid)
 
 
@@ -851,40 +898,40 @@ class BaseJobMetric(Base):
 
 
 class JobMetricText(BaseJobMetric, RepresentById):
-    __tablename__ = 'job_metric_text'
+    __tablename__ = "job_metric_text"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
     plugin = Column(Unicode(255))
     metric_name = Column(Unicode(255))
     metric_value = Column(Unicode(JOB_METRIC_MAX_LENGTH))
 
 
 class JobMetricNumeric(BaseJobMetric, RepresentById):
-    __tablename__ = 'job_metric_numeric'
+    __tablename__ = "job_metric_numeric"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
     plugin = Column(Unicode(255))
     metric_name = Column(Unicode(255))
     metric_value = Column(Numeric(JOB_METRIC_PRECISION, JOB_METRIC_SCALE))
 
 
 class TaskMetricText(BaseJobMetric, RepresentById):
-    __tablename__ = 'task_metric_text'
+    __tablename__ = "task_metric_text"
 
     id = Column(Integer, primary_key=True)
-    task_id = Column(Integer, ForeignKey('task.id'), index=True)
+    task_id = Column(Integer, ForeignKey("task.id"), index=True)
     plugin = Column(Unicode(255))
     metric_name = Column(Unicode(255))
     metric_value = Column(Unicode(JOB_METRIC_MAX_LENGTH))
 
 
 class TaskMetricNumeric(BaseJobMetric, RepresentById):
-    __tablename__ = 'task_metric_numeric'
+    __tablename__ = "task_metric_numeric"
 
     id = Column(Integer, primary_key=True)
-    task_id = Column(Integer, ForeignKey('task.id'), index=True)
+    task_id = Column(Integer, ForeignKey("task.id"), index=True)
     plugin = Column(Unicode(255))
     metric_name = Column(Unicode(255))
     metric_value = Column(Numeric(JOB_METRIC_PRECISION, JOB_METRIC_SCALE))
@@ -895,17 +942,18 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     A job represents a request to run a tool given input datasets, tool
     parameters, and output datasets.
     """
-    __tablename__ = 'job'
+
+    __tablename__ = "job"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now, index=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    library_folder_id = Column(Integer, ForeignKey('library_folder.id'), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
     tool_id = Column(String(255))
-    tool_version = Column(TEXT, default='1.0.0')
+    tool_version = Column(TEXT, default="1.0.0")
     galaxy_version = Column(String(64), default=None)
-    dynamic_tool_id = Column(Integer, ForeignKey('dynamic_tool.id'), index=True, nullable=True)
+    dynamic_tool_id = Column(Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True)
     state = Column(String(64), index=True)
     info = Column(TrimmedString(255))
     copied_from_job_id = Column(Integer, nullable=True)
@@ -920,8 +968,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     tool_stderr = Column(TEXT)
     exit_code = Column(Integer, nullable=True)
     traceback = Column(TEXT)
-    session_id = Column(Integer, ForeignKey('galaxy_session.id'), index=True, nullable=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True, nullable=True)
+    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
     job_runner_name = Column(String(255))
     job_runner_external_id = Column(String(255), index=True)
     destination_id = Column(String(255), nullable=True)
@@ -931,72 +979,71 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     params = Column(TrimmedString(255), index=True)
     handler = Column(TrimmedString(255), index=True)
 
-    user = relationship('User')
-    galaxy_session = relationship('GalaxySession')
-    history = relationship('History', back_populates='jobs')
-    library_folder = relationship('LibraryFolder')
-    parameters = relationship('JobParameter')
-    input_datasets = relationship('JobToInputDatasetAssociation', back_populates='job')
-    input_dataset_collections = relationship('JobToInputDatasetCollectionAssociation',
-        back_populates='job')
-    input_dataset_collection_elements = relationship('JobToInputDatasetCollectionElementAssociation',
-        back_populates='job')
-    output_dataset_collection_instances = relationship('JobToOutputDatasetCollectionAssociation',
-        back_populates='job')
-    output_dataset_collections = relationship('JobToImplicitOutputDatasetCollectionAssociation',
-        back_populates='job')
-    post_job_actions = relationship('PostJobActionAssociation', back_populates='job')
-    input_library_datasets = relationship('JobToInputLibraryDatasetAssociation',
-        back_populates='job')
-    output_library_datasets = relationship('JobToOutputLibraryDatasetAssociation',
-        back_populates='job')
-    external_output_metadata = relationship('JobExternalOutputMetadata', back_populates='job')
-    tasks = relationship('Task', back_populates='job')
-    output_datasets = relationship('JobToOutputDatasetAssociation', back_populates='job')
-    state_history = relationship('JobStateHistory')
-    text_metrics = relationship('JobMetricText')
-    numeric_metrics = relationship('JobMetricNumeric')
-    interactivetool_entry_points = relationship('InteractiveToolEntryPoint',
-        back_populates='job', uselist=True)
-    implicit_collection_jobs_association = relationship('ImplicitCollectionJobsJobAssociation',
-        back_populates='job', uselist=False)
-    container = relationship('JobContainerAssociation', back_populates='job', uselist=False)
-    data_manager_association = relationship('DataManagerJobAssociation',
-        back_populates='job', uselist=False)
-    history_dataset_collection_associations = relationship('HistoryDatasetCollectionAssociation',
-        back_populates='job')
-    workflow_invocation_step = relationship('WorkflowInvocationStep',
-        back_populates='job', uselist=False)
+    user = relationship("User")
+    galaxy_session = relationship("GalaxySession")
+    history = relationship("History", back_populates="jobs")
+    library_folder = relationship("LibraryFolder")
+    parameters = relationship("JobParameter")
+    input_datasets = relationship("JobToInputDatasetAssociation", back_populates="job")
+    input_dataset_collections = relationship("JobToInputDatasetCollectionAssociation", back_populates="job")
+    input_dataset_collection_elements = relationship(
+        "JobToInputDatasetCollectionElementAssociation", back_populates="job"
+    )
+    output_dataset_collection_instances = relationship("JobToOutputDatasetCollectionAssociation", back_populates="job")
+    output_dataset_collections = relationship("JobToImplicitOutputDatasetCollectionAssociation", back_populates="job")
+    post_job_actions = relationship("PostJobActionAssociation", back_populates="job")
+    input_library_datasets = relationship("JobToInputLibraryDatasetAssociation", back_populates="job")
+    output_library_datasets = relationship("JobToOutputLibraryDatasetAssociation", back_populates="job")
+    external_output_metadata = relationship("JobExternalOutputMetadata", back_populates="job")
+    tasks = relationship("Task", back_populates="job")
+    output_datasets = relationship("JobToOutputDatasetAssociation", back_populates="job")
+    state_history = relationship("JobStateHistory")
+    text_metrics = relationship("JobMetricText")
+    numeric_metrics = relationship("JobMetricNumeric")
+    interactivetool_entry_points = relationship("InteractiveToolEntryPoint", back_populates="job", uselist=True)
+    implicit_collection_jobs_association = relationship(
+        "ImplicitCollectionJobsJobAssociation", back_populates="job", uselist=False
+    )
+    container = relationship("JobContainerAssociation", back_populates="job", uselist=False)
+    data_manager_association = relationship("DataManagerJobAssociation", back_populates="job", uselist=False)
+    history_dataset_collection_associations = relationship("HistoryDatasetCollectionAssociation", back_populates="job")
+    workflow_invocation_step = relationship("WorkflowInvocationStep", back_populates="job", uselist=False)
 
     any_output_dataset_collection_instances_deleted: column_property  # defined at the end of this module
     any_output_dataset_deleted: column_property  # defined at the end of this module
 
-    dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version']
-    dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version', 'command_version']
+    dict_collection_visible_keys = ["id", "state", "exit_code", "update_time", "create_time", "galaxy_version"]
+    dict_element_visible_keys = [
+        "id",
+        "state",
+        "exit_code",
+        "update_time",
+        "create_time",
+        "galaxy_version",
+        "command_version",
+    ]
 
     _numeric_metric = JobMetricNumeric
     _text_metric = JobMetricText
 
     class states(str, Enum):
-        NEW = 'new'
-        RESUBMITTED = 'resubmitted'
-        UPLOAD = 'upload'
-        WAITING = 'waiting'
-        QUEUED = 'queued'
-        RUNNING = 'running'
-        OK = 'ok'
-        ERROR = 'error'
-        FAILED = 'failed'
-        PAUSED = 'paused'
-        DELETING = 'deleting'
-        DELETED = 'deleted'
-        DELETED_NEW = 'deleted_new'  # now DELETING, remove after 21.0
-        STOPPING = 'stop'
-        STOPPED = 'stopped'
+        NEW = "new"
+        RESUBMITTED = "resubmitted"
+        UPLOAD = "upload"
+        WAITING = "waiting"
+        QUEUED = "queued"
+        RUNNING = "running"
+        OK = "ok"
+        ERROR = "error"
+        FAILED = "failed"
+        PAUSED = "paused"
+        DELETING = "deleting"
+        DELETED = "deleted"
+        DELETED_NEW = "deleted_new"  # now DELETING, remove after 21.0
+        STOPPING = "stop"
+        STOPPED = "stopped"
 
-    terminal_states = [states.OK,
-                       states.ERROR,
-                       states.DELETED]
+    terminal_states = [states.OK, states.ERROR, states.DELETED]
     #: job states where the job hasn't finished and the model may still change
     non_ready_states = [
         states.NEW,
@@ -1037,7 +1084,9 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         out_data.update([(da.name, da.dataset) for da in self.output_library_datasets])
 
         if not exclude_implicit_outputs:
-            out_collections = {obj.name: obj.dataset_collection_instance for obj in self.output_dataset_collection_instances}
+            out_collections = {
+                obj.name: obj.dataset_collection_instance for obj in self.output_dataset_collection_instances
+            }
         else:
             out_collections = {}
             for obj in self.output_dataset_collection_instances:
@@ -1228,13 +1277,19 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         self.input_dataset_collections.append(JobToInputDatasetCollectionAssociation(name, dataset_collection))
 
     def add_input_dataset_collection_element(self, name, dataset_collection_element):
-        self.input_dataset_collection_elements.append(JobToInputDatasetCollectionElementAssociation(name, dataset_collection_element))
+        self.input_dataset_collection_elements.append(
+            JobToInputDatasetCollectionElementAssociation(name, dataset_collection_element)
+        )
 
     def add_output_dataset_collection(self, name, dataset_collection_instance):
-        self.output_dataset_collection_instances.append(JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance))
+        self.output_dataset_collection_instances.append(
+            JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)
+        )
 
     def add_implicit_output_dataset_collection(self, name, dataset_collection):
-        self.output_dataset_collections.append(JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection))
+        self.output_dataset_collections.append(
+            JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection)
+        )
 
     def add_input_library_dataset(self, name, dataset):
         self.input_library_datasets.append(JobToInputLibraryDatasetAssociation(name, dataset))
@@ -1318,9 +1373,9 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
             for dataset in dataset.dataset.history_associations:
                 # propagate info across shared datasets
                 dataset.deleted = True
-                dataset.blurb = 'deleted'
-                dataset.peek = 'Job deleted'
-                dataset.info = 'Job output deleted by user before job completed'
+                dataset.blurb = "deleted"
+                dataset.peek = "Job deleted"
+                dataset.info = "Job output deleted by user before job completed"
 
     def mark_failed(self, info="Job execution failed", blurb=None, peek=None):
         """
@@ -1353,21 +1408,21 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     def _serialize(self, id_encoder, serialization_options):
         job_attrs = dict_for(self)
         serialization_options.attach_identifier(id_encoder, self, job_attrs)
-        job_attrs['tool_id'] = self.tool_id
-        job_attrs['tool_version'] = self.tool_version
-        job_attrs['galaxy_version'] = self.galaxy_version
-        job_attrs['state'] = self.state
-        job_attrs['info'] = self.info
-        job_attrs['traceback'] = self.traceback
-        job_attrs['command_line'] = self.command_line
-        job_attrs['tool_stderr'] = self.tool_stderr
-        job_attrs['job_stderr'] = self.job_stderr
-        job_attrs['tool_stdout'] = self.tool_stdout
-        job_attrs['job_stdout'] = self.job_stdout
-        job_attrs['exit_code'] = self.exit_code
-        job_attrs['create_time'] = self.create_time.isoformat()
-        job_attrs['update_time'] = self.update_time.isoformat()
-        job_attrs['job_messages'] = self.job_messages
+        job_attrs["tool_id"] = self.tool_id
+        job_attrs["tool_version"] = self.tool_version
+        job_attrs["galaxy_version"] = self.galaxy_version
+        job_attrs["state"] = self.state
+        job_attrs["info"] = self.info
+        job_attrs["traceback"] = self.traceback
+        job_attrs["command_line"] = self.command_line
+        job_attrs["tool_stderr"] = self.tool_stderr
+        job_attrs["job_stderr"] = self.job_stderr
+        job_attrs["tool_stdout"] = self.tool_stdout
+        job_attrs["job_stdout"] = self.job_stdout
+        job_attrs["exit_code"] = self.exit_code
+        job_attrs["create_time"] = self.create_time.isoformat()
+        job_attrs["update_time"] = self.update_time.isoformat()
+        job_attrs["job_messages"] = self.job_messages
 
         # Get the job's parameters
         param_dict = self.raw_param_dict()
@@ -1388,87 +1443,100 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         params_dict = {}
         for name, value in params_objects.items():
             params_dict[name] = value
-        job_attrs['params'] = params_dict
+        job_attrs["params"] = params_dict
         return job_attrs
 
-    def to_dict(self, view='collection', system_details=False):
-        if view == 'admin_job_list':
-            rval = super().to_dict(view='collection')
+    def to_dict(self, view="collection", system_details=False):
+        if view == "admin_job_list":
+            rval = super().to_dict(view="collection")
         else:
             rval = super().to_dict(view=view)
-        rval['tool_id'] = self.tool_id
-        rval['history_id'] = self.history_id
-        if system_details or view == 'admin_job_list':
+        rval["tool_id"] = self.tool_id
+        rval["history_id"] = self.history_id
+        if system_details or view == "admin_job_list":
             # System level details that only admins should have.
-            rval['external_id'] = self.job_runner_external_id
-            rval['command_line'] = self.command_line
-            rval['traceback'] = self.traceback
-        if view == 'admin_job_list':
-            rval['user_email'] = self.user.email if self.user else None
-            rval['handler'] = self.handler
-            rval['job_runner_name'] = self.job_runner_name
-            rval['info'] = self.info
-            rval['session_id'] = self.session_id
+            rval["external_id"] = self.job_runner_external_id
+            rval["command_line"] = self.command_line
+            rval["traceback"] = self.traceback
+        if view == "admin_job_list":
+            rval["user_email"] = self.user.email if self.user else None
+            rval["handler"] = self.handler
+            rval["job_runner_name"] = self.job_runner_name
+            rval["info"] = self.info
+            rval["session_id"] = self.session_id
             if self.galaxy_session and self.galaxy_session.remote_host:
-                rval['remote_host'] = self.galaxy_session.remote_host
-        if view == 'element':
+                rval["remote_host"] = self.galaxy_session.remote_host
+        if view == "element":
             param_dict = {p.name: p.value for p in self.parameters}
-            rval['params'] = param_dict
+            rval["params"] = param_dict
 
             input_dict = {}
             for i in self.input_datasets:
                 if i.dataset is not None:
                     input_dict[i.name] = {
-                        "id": i.dataset.id, "src": "hda",
-                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id,
+                        "src": "hda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None,
                     }
             for i in self.input_library_datasets:
                 if i.dataset is not None:
                     input_dict[i.name] = {
-                        "id": i.dataset.id, "src": "ldda",
-                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id,
+                        "src": "ldda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None,
                     }
             for k in input_dict:
                 if k in param_dict:
                     del param_dict[k]
-            rval['inputs'] = input_dict
+            rval["inputs"] = input_dict
 
             output_dict = {}
             for i in self.output_datasets:
                 if i.dataset is not None:
                     output_dict[i.name] = {
-                        "id": i.dataset.id, "src": "hda",
-                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id,
+                        "src": "hda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None,
                     }
             for i in self.output_library_datasets:
                 if i.dataset is not None:
                     output_dict[i.name] = {
-                        "id": i.dataset.id, "src": "ldda",
-                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id,
+                        "src": "ldda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None,
                     }
-            rval['outputs'] = output_dict
-            rval['output_collections'] = {jtodca.name: {'id': jtodca.dataset_collection_instance.id, 'src': 'hdca'} for jtodca in self.output_dataset_collection_instances}
+            rval["outputs"] = output_dict
+            rval["output_collections"] = {
+                jtodca.name: {"id": jtodca.dataset_collection_instance.id, "src": "hdca"}
+                for jtodca in self.output_dataset_collection_instances
+            }
 
         return rval
 
     def update_hdca_update_time_for_job(self, update_time, sa_session, supports_skip_locked):
-        subq = sa_session.query(HistoryDatasetCollectionAssociation.id) \
-            .join(ImplicitCollectionJobs) \
-            .join(ImplicitCollectionJobsJobAssociation) \
+        subq = (
+            sa_session.query(HistoryDatasetCollectionAssociation.id)
+            .join(ImplicitCollectionJobs)
+            .join(ImplicitCollectionJobsJobAssociation)
             .filter(ImplicitCollectionJobsJobAssociation.job_id == self.id)
+        )
         if supports_skip_locked:
             subq = subq.with_for_update(skip_locked=True).subquery()
-        implicit_statement = HistoryDatasetCollectionAssociation.table.update() \
-            .where(HistoryDatasetCollectionAssociation.table.c.id.in_(select(subq))) \
+        implicit_statement = (
+            HistoryDatasetCollectionAssociation.table.update()
+            .where(HistoryDatasetCollectionAssociation.table.c.id.in_(select(subq)))
             .values(update_time=update_time)
-        explicit_statement = HistoryDatasetCollectionAssociation.table.update() \
-            .where(HistoryDatasetCollectionAssociation.table.c.job_id == self.id) \
+        )
+        explicit_statement = (
+            HistoryDatasetCollectionAssociation.table.update()
+            .where(HistoryDatasetCollectionAssociation.table.c.job_id == self.id)
             .values(update_time=update_time)
+        )
         sa_session.execute(explicit_statement)
         if supports_skip_locked:
             sa_session.execute(implicit_statement)
         else:
-            conn = sa_session.connection(execution_options={'isolation_level': 'SERIALIZABLE'})
+            conn = sa_session.connection(execution_options={"isolation_level": "SERIALIZABLE"})
             with conn.begin() as trans:
                 try:
                     conn.execute(implicit_statement)
@@ -1476,29 +1544,30 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                 except OperationalError as e:
                     # If this is a serialization failure on PostgreSQL, then e.orig is a psycopg2 TransactionRollbackError
                     # and should have attribute `code`. Other engines should just report the message and move on.
-                    if int(getattr(e.orig, 'pgcode', -1)) != 40001:
-                        log.debug(f"Updating implicit collection uptime_time for job {self.id} failed (this is expected for large collections and not a problem): {unicodify(e)}")
+                    if int(getattr(e.orig, "pgcode", -1)) != 40001:
+                        log.debug(
+                            f"Updating implicit collection uptime_time for job {self.id} failed (this is expected for large collections and not a problem): {unicodify(e)}"
+                        )
                     trans.rollback()
 
     def set_final_state(self, final_state, supports_skip_locked):
         self.set_state(final_state)
         # TODO: migrate to where-in subqueries?
-        statement = '''
+        statement = """
             UPDATE workflow_invocation_step
             SET update_time = :update_time
             WHERE job_id = :job_id;
-        '''
+        """
         sa_session = object_session(self)
         update_time = now()
-        self.update_hdca_update_time_for_job(update_time=update_time, sa_session=sa_session, supports_skip_locked=supports_skip_locked)
-        params = {
-            'job_id': self.id,
-            'update_time': update_time
-        }
+        self.update_hdca_update_time_for_job(
+            update_time=update_time, sa_session=sa_session, supports_skip_locked=supports_skip_locked
+        )
+        params = {"job_id": self.id, "update_time": update_time}
         sa_session.execute(statement, params)
 
     def get_destination_configuration(self, dest_params, config, key, default=None):
-        """ Get a destination parameter that can be defaulted back
+        """Get a destination parameter that can be defaulted back
         in specified config if it needs to be applied globally.
         """
         param_unspecified = object()
@@ -1519,7 +1588,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
 
     def update_output_states(self, supports_skip_locked):
         # TODO: migrate to where-in subqueries?
-        statements = ['''
+        statements = [
+            """
             UPDATE dataset
             SET
                 state = :state,
@@ -1529,7 +1599,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                 INNER JOIN job_to_output_dataset jtod
                 ON jtod.dataset_id = hda.id AND jtod.job_id = :job_id
             );
-        ''', '''
+        """,
+            """
             UPDATE dataset
             SET
                 state = :state,
@@ -1539,7 +1610,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                 INNER JOIN job_to_output_library_dataset jtold
                 ON jtold.ldda_id = ldda.id AND jtold.job_id = :job_id
             );
-        ''', '''
+        """,
+            """
             UPDATE history_dataset_association
             SET
                 info = :info,
@@ -1549,7 +1621,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                 FROM job_to_output_dataset jtod
                 WHERE jtod.job_id = :job_id
             );
-        ''', '''
+        """,
+            """
             UPDATE library_dataset_dataset_association
             SET
                 info = :info,
@@ -1559,16 +1632,14 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                 FROM job_to_output_library_dataset jtold
                 WHERE jtold.job_id = :job_id
             );
-        ''']
+        """,
+        ]
         sa_session = object_session(self)
         update_time = now()
-        self.update_hdca_update_time_for_job(update_time=update_time, sa_session=sa_session, supports_skip_locked=supports_skip_locked)
-        params = {
-            'job_id': self.id,
-            'state': self.state,
-            'info': self.info,
-            'update_time': update_time
-        }
+        self.update_hdca_update_time_for_job(
+            update_time=update_time, sa_session=sa_session, supports_skip_locked=supports_skip_locked
+        )
+        params = {"job_id": self.id, "state": self.state, "info": self.info, "update_time": update_time}
         for statement in statements:
             sa_session.execute(statement, params)
 
@@ -1583,7 +1654,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                         return True
                 if self.output_dataset_collection_instances:
                     # We'll want to replace this item
-                    return 'job_produced_collection_elements'
+                    return "job_produced_collection_elements"
             except Exception:
                 log.exception(f"Error trying to determine if job {self.id} is remappable")
         return False
@@ -1599,7 +1670,8 @@ class Task(Base, JobLike, RepresentById):
     """
     A task represents a single component of a job.
     """
-    __tablename__ = 'task'
+
+    __tablename__ = "task"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -1617,26 +1689,26 @@ class Task(Base, JobLike, RepresentById):
     job_messages = Column(MutableJSONType, nullable=True)
     info = Column(TrimmedString(255))
     traceback = Column(TEXT)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True, nullable=False)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=False)
     working_directory = Column(String(1024))
     task_runner_name = Column(String(255))
     task_runner_external_id = Column(String(255))
     prepare_input_files_cmd = Column(TEXT)
-    job = relationship('Job', back_populates='tasks')
-    text_metrics = relationship('TaskMetricText')
-    numeric_metrics = relationship('TaskMetricNumeric')
+    job = relationship("Job", back_populates="tasks")
+    text_metrics = relationship("TaskMetricText")
+    numeric_metrics = relationship("TaskMetricNumeric")
 
     _numeric_metric = TaskMetricNumeric
     _text_metric = TaskMetricText
 
     class states(str, Enum):
-        NEW = 'new'
-        WAITING = 'waiting'
-        QUEUED = 'queued'
-        RUNNING = 'running'
-        OK = 'ok'
-        ERROR = 'error'
-        DELETED = 'deleted'
+        NEW = "new"
+        WAITING = "waiting"
+        QUEUED = "queued"
+        RUNNING = "running"
+        OK = "ok"
+        ERROR = "error"
+        DELETED = "deleted"
 
     # Please include an accessor (get/set pair) for any new columns/members.
     def __init__(self, job, working_directory, prepare_files_cmd):
@@ -1754,8 +1826,7 @@ class Task(Base, JobLike, RepresentById):
         # This method is available for runners that do not want/need to
         # differentiate between the kinds of Runnable things (Jobs and Tasks)
         # that they're using.
-        log.debug("Task %d: Set external id to %s"
-                  % (self.id, task_runner_external_id))
+        log.debug("Task %d: Set external id to %s" % (self.id, task_runner_external_id))
         self.task_runner_external_id = task_runner_external_id
 
     def set_task_runner_external_id(self, task_runner_external_id):
@@ -1769,10 +1840,10 @@ class Task(Base, JobLike, RepresentById):
 
 
 class JobParameter(Base, RepresentById):
-    __tablename__ = 'job_parameter'
+    __tablename__ = "job_parameter"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
     name = Column(String(255))
     value = Column(TEXT)
 
@@ -1785,16 +1856,15 @@ class JobParameter(Base, RepresentById):
 
 
 class JobToInputDatasetAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_input_dataset'
+    __tablename__ = "job_to_input_dataset"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    dataset_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
     dataset_version = Column(Integer)
     name = Column(String(255))
-    dataset = relationship('HistoryDatasetAssociation', lazy="joined", back_populates='dependent_jobs')
-    job = relationship('Job', back_populates='input_datasets')
+    dataset = relationship("HistoryDatasetAssociation", lazy="joined", back_populates="dependent_jobs")
+    job = relationship("Job", back_populates="input_datasets")
 
     def __init__(self, name, dataset):
         self.name = name
@@ -1803,15 +1873,14 @@ class JobToInputDatasetAssociation(Base, RepresentById):
 
 
 class JobToOutputDatasetAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_output_dataset'
+    __tablename__ = "job_to_output_dataset"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    dataset_id = Column(Integer, ForeignKey('history_dataset_association.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
     name = Column(String(255))
-    dataset = relationship('HistoryDatasetAssociation',
-        lazy="joined", back_populates='creating_job_associations')
-    job = relationship('Job', back_populates='output_datasets')
+    dataset = relationship("HistoryDatasetAssociation", lazy="joined", back_populates="creating_job_associations")
+    job = relationship("Job", back_populates="output_datasets")
 
     def __init__(self, name, dataset):
         self.name = name
@@ -1823,15 +1892,14 @@ class JobToOutputDatasetAssociation(Base, RepresentById):
 
 
 class JobToInputDatasetCollectionAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_input_dataset_collection'
+    __tablename__ = "job_to_input_dataset_collection"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    dataset_collection_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
     name = Column(String(255))
-    dataset_collection = relationship('HistoryDatasetCollectionAssociation', lazy="joined")
-    job = relationship('Job', back_populates='input_dataset_collections')
+    dataset_collection = relationship("HistoryDatasetCollectionAssociation", lazy="joined")
+    job = relationship("Job", back_populates="input_dataset_collections")
 
     def __init__(self, name, dataset_collection):
         self.name = name
@@ -1839,15 +1907,14 @@ class JobToInputDatasetCollectionAssociation(Base, RepresentById):
 
 
 class JobToInputDatasetCollectionElementAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_input_dataset_collection_element'
+    __tablename__ = "job_to_input_dataset_collection_element"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    dataset_collection_element_id = Column(Integer,
-        ForeignKey('dataset_collection_element.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_element_id = Column(Integer, ForeignKey("dataset_collection_element.id"), index=True)
     name = Column(Unicode(255))
-    dataset_collection_element = relationship('DatasetCollectionElement', lazy="joined")
-    job = relationship('Job', back_populates='input_dataset_collection_elements')
+    dataset_collection_element = relationship("DatasetCollectionElement", lazy="joined")
+    job = relationship("Job", back_populates="input_dataset_collection_elements")
 
     def __init__(self, name, dataset_collection_element):
         self.name = name
@@ -1857,15 +1924,14 @@ class JobToInputDatasetCollectionElementAssociation(Base, RepresentById):
 # Many jobs may map to one HistoryDatasetCollection using these for a given
 # tool output (if mapping over an input collection).
 class JobToOutputDatasetCollectionAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_output_dataset_collection'
+    __tablename__ = "job_to_output_dataset_collection"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    dataset_collection_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
     name = Column(Unicode(255))
-    dataset_collection_instance = relationship('HistoryDatasetCollectionAssociation', lazy="joined")
-    job = relationship('Job', back_populates='output_dataset_collection_instances')
+    dataset_collection_instance = relationship("HistoryDatasetCollectionAssociation", lazy="joined")
+    job = relationship("Job", back_populates="output_dataset_collection_instances")
 
     def __init__(self, name, dataset_collection_instance):
         self.name = name
@@ -1880,14 +1946,14 @@ class JobToOutputDatasetCollectionAssociation(Base, RepresentById):
 # using these. (You can think of many of these models as going into the
 # creation of a JobToOutputDatasetCollectionAssociation.)
 class JobToImplicitOutputDatasetCollectionAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_implicit_output_dataset_collection'
+    __tablename__ = "job_to_implicit_output_dataset_collection"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    dataset_collection_id = Column(Integer, ForeignKey('dataset_collection.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    dataset_collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True)
     name = Column(Unicode(255))
-    dataset_collection = relationship('DatasetCollection')
-    job = relationship('Job', back_populates='output_dataset_collections')
+    dataset_collection = relationship("DatasetCollection")
+    job = relationship("Job", back_populates="output_dataset_collections")
 
     def __init__(self, name, dataset_collection):
         self.name = name
@@ -1895,15 +1961,14 @@ class JobToImplicitOutputDatasetCollectionAssociation(Base, RepresentById):
 
 
 class JobToInputLibraryDatasetAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_input_library_dataset'
+    __tablename__ = "job_to_input_library_dataset"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    ldda_id = Column(Integer, ForeignKey('library_dataset_dataset_association.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
     name = Column(Unicode(255))
-    job = relationship('Job', back_populates='input_library_datasets')
-    dataset = relationship(
-        'LibraryDatasetDatasetAssociation', lazy="joined", back_populates='dependent_jobs')
+    job = relationship("Job", back_populates="input_library_datasets")
+    dataset = relationship("LibraryDatasetDatasetAssociation", lazy="joined", back_populates="dependent_jobs")
 
     def __init__(self, name, dataset):
         self.name = name
@@ -1911,15 +1976,16 @@ class JobToInputLibraryDatasetAssociation(Base, RepresentById):
 
 
 class JobToOutputLibraryDatasetAssociation(Base, RepresentById):
-    __tablename__ = 'job_to_output_library_dataset'
+    __tablename__ = "job_to_output_library_dataset"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    ldda_id = Column(Integer, ForeignKey('library_dataset_dataset_association.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
     name = Column(Unicode(255))
-    job = relationship('Job', back_populates='output_library_datasets')
+    job = relationship("Job", back_populates="output_library_datasets")
     dataset = relationship(
-        'LibraryDatasetDatasetAssociation', lazy="joined", back_populates='creating_job_associations')
+        "LibraryDatasetDatasetAssociation", lazy="joined", back_populates="creating_job_associations"
+    )
 
     def __init__(self, name, dataset):
         self.name = name
@@ -1927,12 +1993,12 @@ class JobToOutputLibraryDatasetAssociation(Base, RepresentById):
 
 
 class JobStateHistory(Base, RepresentById):
-    __tablename__ = 'job_state_history'
+    __tablename__ = "job_state_history"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
     state = Column(String(64), index=True)
     info = Column(TrimmedString(255))
 
@@ -1943,18 +2009,19 @@ class JobStateHistory(Base, RepresentById):
 
 
 class ImplicitlyCreatedDatasetCollectionInput(Base, RepresentById):
-    __tablename__ = 'implicitly_created_dataset_collection_inputs'
+    __tablename__ = "implicitly_created_dataset_collection_inputs"
 
     id = Column(Integer, primary_key=True)
-    dataset_collection_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id'), index=True)
-    input_dataset_collection_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id'), index=True)
+    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
+    input_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
     name = Column(Unicode(255))
 
-    input_dataset_collection = relationship('HistoryDatasetCollectionAssociation',
-        primaryjoin=(lambda: HistoryDatasetCollectionAssociation.id  # type: ignore[has-type]
-            == ImplicitlyCreatedDatasetCollectionInput.input_dataset_collection_id)  # type: ignore[has-type]
+    input_dataset_collection = relationship(
+        "HistoryDatasetCollectionAssociation",
+        primaryjoin=(
+            lambda: HistoryDatasetCollectionAssociation.id  # type: ignore[has-type]
+            == ImplicitlyCreatedDatasetCollectionInput.input_dataset_collection_id
+        ),  # type: ignore[has-type]
     )
 
     def __init__(self, name, input_dataset_collection):
@@ -1963,17 +2030,16 @@ class ImplicitlyCreatedDatasetCollectionInput(Base, RepresentById):
 
 
 class ImplicitCollectionJobs(Base, Serializable):
-    __tablename__ = 'implicit_collection_jobs'
+    __tablename__ = "implicit_collection_jobs"
 
     id = Column(Integer, primary_key=True)
-    populated_state = Column(TrimmedString(64), default='new', nullable=False)
-    jobs = relationship('ImplicitCollectionJobsJobAssociation',
-        back_populates='implicit_collection_jobs')
+    populated_state = Column(TrimmedString(64), default="new", nullable=False)
+    jobs = relationship("ImplicitCollectionJobsJobAssociation", back_populates="implicit_collection_jobs")
 
     class populated_states(str, Enum):
-        NEW = 'new'  # New implicit jobs object, unpopulated job associations
-        OK = 'ok'  # Job associations are set and fixed.
-        FAILED = 'failed'  # There were issues populating job associations, object is in error.
+        NEW = "new"  # New implicit jobs object, unpopulated job associations
+        OK = "ok"  # Job associations are set and fixed.
+        FAILED = "failed"  # There were issues populating job associations, object is in error.
 
     def __init__(self, populated_state=None):
         self.populated_state = populated_state or ImplicitCollectionJobs.populated_states.NEW
@@ -1986,34 +2052,35 @@ class ImplicitCollectionJobs(Base, Serializable):
         rval = dict_for(
             self,
             populated_state=self.populated_state,
-            jobs=[serialization_options.get_identifier(id_encoder, j_a.job) for j_a in self.jobs]
+            jobs=[serialization_options.get_identifier(id_encoder, j_a.job) for j_a in self.jobs],
         )
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 
 
 class ImplicitCollectionJobsJobAssociation(Base, RepresentById):
-    __tablename__ = 'implicit_collection_jobs_job_association'
+    __tablename__ = "implicit_collection_jobs_job_association"
 
     id = Column(Integer, primary_key=True)
-    implicit_collection_jobs_id = Column(Integer, ForeignKey('implicit_collection_jobs.id'), index=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)  # Consider making this nullable...
+    implicit_collection_jobs_id = Column(Integer, ForeignKey("implicit_collection_jobs.id"), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)  # Consider making this nullable...
     order_index = Column(Integer, nullable=False)
-    implicit_collection_jobs = relationship('ImplicitCollectionJobs', back_populates='jobs')
-    job = relationship('Job', back_populates='implicit_collection_jobs_association')
+    implicit_collection_jobs = relationship("ImplicitCollectionJobs", back_populates="jobs")
+    job = relationship("Job", back_populates="implicit_collection_jobs_association")
 
 
 class PostJobAction(Base, RepresentById):
-    __tablename__ = 'post_job_action'
+    __tablename__ = "post_job_action"
 
     id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True, nullable=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=True)
     action_type = Column(String(255), nullable=False)
     output_name = Column(String(255), nullable=True)
     action_arguments = Column(MutableJSONType, nullable=True)
-    workflow_step = relationship('WorkflowStep',
-        back_populates='post_job_actions',
-        primaryjoin=(lambda: WorkflowStep.id == PostJobAction.workflow_step_id)  # type: ignore[has-type]
+    workflow_step = relationship(
+        "WorkflowStep",
+        back_populates="post_job_actions",
+        primaryjoin=(lambda: WorkflowStep.id == PostJobAction.workflow_step_id),  # type: ignore[has-type]
     )
 
     def __init__(self, action_type, workflow_step=None, output_name=None, action_arguments=None):
@@ -2024,13 +2091,13 @@ class PostJobAction(Base, RepresentById):
 
 
 class PostJobActionAssociation(Base, RepresentById):
-    __tablename__ = 'post_job_action_association'
+    __tablename__ = "post_job_action_association"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True, nullable=False)
-    post_job_action_id = Column(Integer, ForeignKey('post_job_action.id'), index=True, nullable=False)
-    post_job_action = relationship('PostJobAction')
-    job = relationship('Job', back_populates='post_job_actions')
+    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=False)
+    post_job_action_id = Column(Integer, ForeignKey("post_job_action.id"), index=True, nullable=False)
+    post_job_action = relationship("PostJobAction")
+    job = relationship("Job", back_populates="post_job_actions")
 
     def __init__(self, pja, job=None, job_id=None):
         if job is not None:
@@ -2043,14 +2110,16 @@ class PostJobActionAssociation(Base, RepresentById):
 
 
 class JobExternalOutputMetadata(Base, RepresentById):
-    __tablename__ = 'job_external_output_metadata'
+    __tablename__ = "job_external_output_metadata"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True, nullable=True)
-    library_dataset_dataset_association_id = Column(Integer,
-        ForeignKey('library_dataset_dataset_association.id'), index=True, nullable=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    history_dataset_association_id = Column(
+        Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True
+    )
+    library_dataset_dataset_association_id = Column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True
+    )
     is_valid = Column(Boolean, default=True)
     filename_in = Column(String(255))
     filename_out = Column(String(255))
@@ -2058,9 +2127,9 @@ class JobExternalOutputMetadata(Base, RepresentById):
     filename_kwds = Column(String(255))
     filename_override_metadata = Column(String(255))
     job_runner_external_pid = Column(String(255))
-    history_dataset_association = relationship('HistoryDatasetAssociation', lazy="joined")
-    library_dataset_dataset_association = relationship('LibraryDatasetDatasetAssociation', lazy="joined")
-    job = relationship('Job', back_populates='external_output_metadata')
+    history_dataset_association = relationship("HistoryDatasetAssociation", lazy="joined")
+    library_dataset_dataset_association = relationship("LibraryDatasetDatasetAssociation", lazy="joined")
+    job = relationship("Job", back_populates="external_output_metadata")
 
     def __init__(self, job=None, dataset=None):
         self.job = job
@@ -2095,19 +2164,19 @@ class FakeDatasetAssociation:
 
 
 class JobExportHistoryArchive(Base, RepresentById):
-    __tablename__ = 'job_export_history_archive'
+    __tablename__ = "job_export_history_archive"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    dataset_id = Column(Integer, ForeignKey('dataset.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
     compressed = Column(Boolean, index=True, default=False)
     history_attrs_filename = Column(TEXT)
-    job = relationship('Job')
-    dataset = relationship('Dataset')
-    history = relationship('History', back_populates='exports')
+    job = relationship("Job")
+    dataset = relationship("Dataset")
+    history = relationship("History", back_populates="exports")
 
-    ATTRS_FILENAME_HISTORY = 'history_attrs.txt'
+    ATTRS_FILENAME_HISTORY = "history_attrs.txt"
 
     def __init__(self, compressed=False, **kwd):
         super().__init__(**kwd)
@@ -2123,12 +2192,11 @@ class JobExportHistoryArchive(Base, RepresentById):
 
     @property
     def up_to_date(self):
-        """ Return False, if a new export should be generated for corresponding
+        """Return False, if a new export should be generated for corresponding
         history.
         """
         job = self.job
-        return job.state not in [Job.states.ERROR, Job.states.DELETED] \
-            and job.update_time > self.history.update_time
+        return job.state not in [Job.states.ERROR, Job.states.DELETED] and job.update_time > self.history.update_time
 
     @property
     def ready(self):
@@ -2155,11 +2223,7 @@ class JobExportHistoryArchive(Base, RepresentById):
         sa_session.flush()  # ensure job.id and archive_dataset.id are available
         object_store.create(archive_dataset)  # set the object store id, create dataset (if applicable)
         # Add association for keeping track of job, history, archive relationship.
-        jeha = JobExportHistoryArchive(
-            job=job, history=history,
-            dataset=archive_dataset,
-            compressed=compressed
-        )
+        jeha = JobExportHistoryArchive(job=job, history=history, dataset=archive_dataset, compressed=compressed)
         sa_session.add(jeha)
 
         #
@@ -2174,36 +2238,36 @@ class JobExportHistoryArchive(Base, RepresentById):
 
     def to_dict(self):
         return {
-            'id': self.id,
-            'job_id': self.job.id,
-            'ready': self.ready,
-            'preparing': self.preparing,
-            'up_to_date': self.up_to_date,
+            "id": self.id,
+            "job_id": self.job.id,
+            "ready": self.ready,
+            "preparing": self.preparing,
+            "up_to_date": self.up_to_date,
         }
 
 
 class JobImportHistoryArchive(Base, RepresentById):
-    __tablename__ = 'job_import_history_archive'
+    __tablename__ = "job_import_history_archive"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
     archive_dir = Column(TEXT)
-    job = relationship('Job')
-    history = relationship('History')
+    job = relationship("Job")
+    history = relationship("History")
 
 
 class JobContainerAssociation(Base, RepresentById):
-    __tablename__ = 'job_container_association'
+    __tablename__ = "job_container_association"
 
     id = Column(Integer, primary_key=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True)
     container_type = Column(TEXT)
     container_name = Column(TEXT)
     container_info = Column(MutableJSONType, nullable=True)
     created_time = Column(DateTime, default=now)
     modified_time = Column(DateTime, default=now, onupdate=now)
-    job = relationship('Job', back_populates='container')
+    job = relationship("Job", back_populates="container")
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -2211,7 +2275,7 @@ class JobContainerAssociation(Base, RepresentById):
 
 
 class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
-    __tablename__ = 'interactivetool_entry_point'
+    __tablename__ = "interactivetool_entry_point"
 
     id = Column(Integer, primary_key=True)
     job_id = Column(Integer, ForeignKey("job.id"), index=True)
@@ -2228,10 +2292,10 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
     deleted = Column(Boolean, default=False)
     created_time = Column(DateTime, default=now)
     modified_time = Column(DateTime, default=now, onupdate=now)
-    job = relationship('Job', back_populates='interactivetool_entry_points', uselist=False)
+    job = relationship("Job", back_populates="interactivetool_entry_points", uselist=False)
 
-    dict_collection_visible_keys = ['id', 'name', 'active', 'created_time', 'modified_time']
-    dict_element_visible_keys = ['id', 'name', 'active', 'created_time', 'modified_time']
+    dict_collection_visible_keys = ["id", "name", "active", "created_time", "modified_time"]
+    dict_element_visible_keys = ["id", "name", "active", "created_time", "modified_time"]
 
     def __init__(self, requires_domain=True, configured=False, deleted=False, **kwd):
         super().__init__(**kwd)
@@ -2250,35 +2314,35 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
 
 
 class GenomeIndexToolData(Base, RepresentById):  # TODO: params arg is lost
-    __tablename__ = 'genome_index_tool_data'
+    __tablename__ = "genome_index_tool_data"
 
     id = Column(Integer, primary_key=True)
     job_id = Column(Integer, ForeignKey("job.id"), index=True)
-    dataset_id = Column(Integer, ForeignKey('dataset.id'), index=True)
+    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
     fasta_path = Column(String(255))
     created_time = Column(DateTime, default=now)
     modified_time = Column(DateTime, default=now, onupdate=now)
     indexer = Column(String(64))
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    job = relationship('Job')
-    dataset = relationship('Dataset')
-    user = relationship('User')
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    job = relationship("Job")
+    dataset = relationship("Dataset")
+    user = relationship("User")
 
 
 class Group(Base, Dictifiable, RepresentById):
-    __tablename__ = 'galaxy_group'
+    __tablename__ = "galaxy_group"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     name = Column(String(255), index=True, unique=True)
     deleted = Column(Boolean, index=True, default=False)
-    quotas = relationship('GroupQuotaAssociation', back_populates='group')
-    roles = relationship('GroupRoleAssociation', back_populates='group')
-    users = relationship('UserGroupAssociation', back_populates='group')
+    quotas = relationship("GroupQuotaAssociation", back_populates="group")
+    roles = relationship("GroupRoleAssociation", back_populates="group")
+    users = relationship("UserGroupAssociation", back_populates="group")
 
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'name']
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = ["id", "name"]
 
     def __init__(self, name=None):
         self.name = name
@@ -2286,15 +2350,15 @@ class Group(Base, Dictifiable, RepresentById):
 
 
 class UserGroupAssociation(Base, RepresentById):
-    __tablename__ = 'user_group_association'
+    __tablename__ = "user_group_association"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    group_id = Column(Integer, ForeignKey('galaxy_group.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    group_id = Column(Integer, ForeignKey("galaxy_group.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user = relationship('User', back_populates='groups')
-    group = relationship('Group', back_populates='users')
+    user = relationship("User", back_populates="groups")
+    group = relationship("Group", back_populates="users")
 
     def __init__(self, user, group):
         self.user = user
@@ -2306,12 +2370,10 @@ def is_hda(d):
 
 
 class HistoryAudit(Base, RepresentById):
-    __tablename__ = 'history_audit'
-    __table_args__ = (
-        PrimaryKeyConstraint(sqlite_on_conflict='IGNORE'),
-    )
+    __tablename__ = "history_audit"
+    __table_args__ = (PrimaryKeyConstraint(sqlite_on_conflict="IGNORE"),)
 
-    history_id = Column(Integer, ForeignKey('history.id'), primary_key=True, nullable=False)
+    history_id = Column(Integer, ForeignKey("history.id"), primary_key=True, nullable=False)
     update_time = Column(DateTime, default=now, primary_key=True, nullable=False)
 
     # This class should never be instantiated.
@@ -2320,29 +2382,35 @@ class HistoryAudit(Base, RepresentById):
 
     @classmethod
     def prune(cls, sa_session):
-        latest_subq = sa_session.query(
-            cls.history_id,
-            func.max(cls.update_time).label('max_update_time')).group_by(cls.history_id).subquery()
-        not_latest_query = sa_session.query(
-            cls.history_id, cls.update_time
-        ).select_from(latest_subq).join(
-            cls, and_(
-                cls.update_time < latest_subq.columns.max_update_time,
-                cls.history_id == latest_subq.columns.history_id)).subquery()
+        latest_subq = (
+            sa_session.query(cls.history_id, func.max(cls.update_time).label("max_update_time"))
+            .group_by(cls.history_id)
+            .subquery()
+        )
+        not_latest_query = (
+            sa_session.query(cls.history_id, cls.update_time)
+            .select_from(latest_subq)
+            .join(
+                cls,
+                and_(
+                    cls.update_time < latest_subq.columns.max_update_time,
+                    cls.history_id == latest_subq.columns.history_id,
+                ),
+            )
+            .subquery()
+        )
         q = cls.__table__.delete().where(tuple_(cls.history_id, cls.update_time).in_(select(not_latest_query)))
         sa_session.execute(q)
 
 
 class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable):
-    __tablename__ = 'history'
-    __table_args__ = (
-        Index('ix_history_slug', 'slug', mysql_length=200),
-    )
+    __tablename__ = "history"
+    __table_args__ = (Index("ix_history_slug", "slug", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    _update_time = Column('update_time', DateTime, index=True, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    _update_time = Column("update_time", DateTime, index=True, default=now, onupdate=now)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     name = Column(TrimmedString(255))
     hid_counter = Column(Integer, default=1)
     deleted = Column(Boolean, index=True, default=False)
@@ -2353,59 +2421,79 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     slug = Column(TEXT)
     published = Column(Boolean, index=True, default=False)
 
-    datasets = relationship('HistoryDatasetAssociation',
-        back_populates='history',
-        order_by=lambda: asc(HistoryDatasetAssociation.hid))  # type: ignore[has-type]
-    exports = relationship('JobExportHistoryArchive',
-        back_populates='history',
+    datasets = relationship(
+        "HistoryDatasetAssociation", back_populates="history", order_by=lambda: asc(HistoryDatasetAssociation.hid)
+    )  # type: ignore[has-type]
+    exports = relationship(
+        "JobExportHistoryArchive",
+        back_populates="history",
         primaryjoin=lambda: JobExportHistoryArchive.history_id == History.id,
-        order_by=lambda: desc(JobExportHistoryArchive.id))
-    active_datasets = relationship('HistoryDatasetAssociation',
+        order_by=lambda: desc(JobExportHistoryArchive.id),
+    )
+    active_datasets = relationship(
+        "HistoryDatasetAssociation",
         primaryjoin=(
-            lambda: and_(HistoryDatasetAssociation.history_id  # type: ignore[attr-defined]
-                == History.id, not_(HistoryDatasetAssociation.deleted))  # type: ignore[has-type]
+            lambda: and_(
+                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[attr-defined]
+                not_(HistoryDatasetAssociation.deleted),
+            )  # type: ignore[has-type]
         ),
         order_by=lambda: asc(HistoryDatasetAssociation.hid),  # type: ignore[has-type]
-        viewonly=True)
-    dataset_collections = relationship('HistoryDatasetCollectionAssociation', back_populates='history')
-    active_dataset_collections = relationship('HistoryDatasetCollectionAssociation',
+        viewonly=True,
+    )
+    dataset_collections = relationship("HistoryDatasetCollectionAssociation", back_populates="history")
+    active_dataset_collections = relationship(
+        "HistoryDatasetCollectionAssociation",
         primaryjoin=(
-            lambda: (and_(HistoryDatasetCollectionAssociation.history_id == History.id,  # type: ignore[has-type]
-             not_(HistoryDatasetCollectionAssociation.deleted)))  # type: ignore[has-type]
+            lambda: (
+                and_(
+                    HistoryDatasetCollectionAssociation.history_id == History.id,  # type: ignore[has-type]
+                    not_(HistoryDatasetCollectionAssociation.deleted),
+                )
+            )  # type: ignore[has-type]
         ),
         order_by=lambda: asc(HistoryDatasetCollectionAssociation.hid),  # type: ignore[has-type]
-        viewonly=True)
-    visible_datasets = relationship('HistoryDatasetAssociation',
+        viewonly=True,
+    )
+    visible_datasets = relationship(
+        "HistoryDatasetAssociation",
         primaryjoin=(
-            lambda: and_(HistoryDatasetAssociation.history_id == History.id,  # type: ignore[attr-defined]
-             not_(HistoryDatasetAssociation.deleted), HistoryDatasetAssociation.visible)  # type: ignore[has-type]
+            lambda: and_(
+                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[attr-defined]
+                not_(HistoryDatasetAssociation.deleted),
+                HistoryDatasetAssociation.visible,
+            )  # type: ignore[has-type]
         ),
         order_by=lambda: asc(HistoryDatasetAssociation.hid),  # type: ignore[has-type]
-        viewonly=True)
-    visible_dataset_collections = relationship('HistoryDatasetCollectionAssociation',
+        viewonly=True,
+    )
+    visible_dataset_collections = relationship(
+        "HistoryDatasetCollectionAssociation",
         primaryjoin=(
             lambda: and_(
                 HistoryDatasetCollectionAssociation.history_id == History.id,  # type: ignore[has-type]
                 not_(HistoryDatasetCollectionAssociation.deleted),  # type: ignore[has-type]
-                HistoryDatasetCollectionAssociation.visible)  # type: ignore[has-type]
+                HistoryDatasetCollectionAssociation.visible,
+            )  # type: ignore[has-type]
         ),
         order_by=lambda: asc(HistoryDatasetCollectionAssociation.hid),  # type: ignore[has-type]
-        viewonly=True)
-    tags = relationship('HistoryTagAssociation',
-        order_by=lambda: HistoryTagAssociation.id,
-        back_populates='history')
-    annotations = relationship('HistoryAnnotationAssociation',
-        order_by=lambda: HistoryAnnotationAssociation.id,
-        back_populates='history')
-    ratings = relationship('HistoryRatingAssociation',
+        viewonly=True,
+    )
+    tags = relationship("HistoryTagAssociation", order_by=lambda: HistoryTagAssociation.id, back_populates="history")
+    annotations = relationship(
+        "HistoryAnnotationAssociation", order_by=lambda: HistoryAnnotationAssociation.id, back_populates="history"
+    )
+    ratings = relationship(
+        "HistoryRatingAssociation",
         order_by=lambda: HistoryRatingAssociation.id,  # type: ignore[has-type]
-        back_populates='history')
-    default_permissions = relationship('DefaultHistoryPermissions', back_populates='history')
-    users_shared_with = relationship('HistoryUserShareAssociation', back_populates='history')
-    galaxy_sessions = relationship('GalaxySessionToHistoryAssociation', back_populates='history')
-    workflow_invocations = relationship('WorkflowInvocation', back_populates='history')
-    user = relationship('User', back_populates='histories')
-    jobs = relationship('Job', back_populates='history')
+        back_populates="history",
+    )
+    default_permissions = relationship("DefaultHistoryPermissions", back_populates="history")
+    users_shared_with = relationship("HistoryUserShareAssociation", back_populates="history")
+    galaxy_sessions = relationship("GalaxySessionToHistoryAssociation", back_populates="history")
+    workflow_invocations = relationship("WorkflowInvocation", back_populates="history")
+    user = relationship("User", back_populates="histories")
+    jobs = relationship("Job", back_populates="history")
 
     update_time = column_property(
         select(func.max(HistoryAudit.update_time)).where(HistoryAudit.history_id == id).scalar_subquery(),
@@ -2416,12 +2504,22 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     # Set up proxy so that
     #   History.users_shared_with
     # returns a list of users that history is shared with.
-    users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+    users_shared_with_dot_users = association_proxy("users_shared_with", "user")
 
-    dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']
-    dict_element_visible_keys = ['id', 'name', 'genome_build', 'deleted', 'purged', 'update_time',
-                                 'published', 'importable', 'slug', 'empty']
-    default_name = 'Unnamed history'
+    dict_collection_visible_keys = ["id", "name", "published", "deleted"]
+    dict_element_visible_keys = [
+        "id",
+        "name",
+        "genome_build",
+        "deleted",
+        "purged",
+        "update_time",
+        "published",
+        "importable",
+        "slug",
+        "empty",
+    ]
+    default_name = "Unnamed history"
 
     def __init__(self, id=None, name=None, user=None):
         self.id = id
@@ -2455,7 +2553,9 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     def add_pending_items(self, set_output_hid=True):
         # These are assumed to be either copies of existing datasets or new, empty datasets,
         # so we don't need to set the quota.
-        self.add_datasets(object_session(self), self._pending_additions, set_hid=set_output_hid, quota=False, flush=False)
+        self.add_datasets(
+            object_session(self), self._pending_additions, set_hid=set_output_hid, quota=False, flush=False
+        )
         self._pending_additions = []
 
     def _next_hid(self, n=1):
@@ -2475,7 +2575,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         update_stmt = update(table).where(table.c.id == history_id).values(hid_counter=table.c.hid_counter + n)
 
         with engine.begin() as conn:
-            if engine.name in ['postgres', 'postgresql']:
+            if engine.name in ["postgres", "postgresql"]:
                 stmt = update_stmt.returning(table.c.hid_counter)
                 updated_hid = conn.execute(stmt).scalar()
                 hid = updated_hid - n
@@ -2484,7 +2584,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
                 hid = conn.execute(select_stmt).scalar()
                 conn.execute(update_stmt)
 
-        session.expire(self, ['hid_counter'])
+        session.expire(self, ["hid_counter"])
         return hid
 
     def add_galaxy_session(self, galaxy_session, association=None):
@@ -2499,8 +2599,10 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
             object_session(self).add(dataset)
             object_session(self).flush()
         elif not isinstance(dataset, (HistoryDatasetAssociation, HistoryDatasetCollectionAssociation)):
-            raise TypeError("You can only add Dataset and HistoryDatasetAssociation instances to a history"
-                            + f" ( you tried to add {str(dataset)} ).")
+            raise TypeError(
+                "You can only add Dataset and HistoryDatasetAssociation instances to a history"
+                + f" ( you tried to add {str(dataset)} )."
+            )
         is_dataset = is_hda(dataset)
         if parent_id:
             for data in self.datasets:
@@ -2516,13 +2618,15 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         if quota and is_dataset and self.user:
             self.user.adjust_total_disk_usage(dataset.quota_amount(self.user))
         dataset.history = self
-        if is_dataset and genome_build not in [None, '?']:
+        if is_dataset and genome_build not in [None, "?"]:
             self.genome_build = genome_build
         dataset.history_id = self.id
         return dataset
 
-    def add_datasets(self, sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False):
-        """ Optimized version of add_dataset above that minimizes database
+    def add_datasets(
+        self, sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False
+    ):
+        """Optimized version of add_dataset above that minimizes database
         interactions when adding many datasets and collections to history at once.
         """
         optimize = len(datasets) > 1 and parent_id is None and set_hid
@@ -2542,14 +2646,14 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
                     sa_session.flush()
 
     def __add_datasets_optimized(self, datasets, genome_build=None):
-        """ Optimized version of add_dataset above that minimizes database
+        """Optimized version of add_dataset above that minimizes database
         interactions when adding many datasets to history at once under
         certain circumstances.
         """
         n = len(datasets)
 
         base_hid = self._next_hid(n=n)
-        set_genome = genome_build not in [None, '?']
+        set_genome = genome_build not in [None, "?"]
         for i, dataset in enumerate(datasets):
             dataset.hid = base_hid + i
             dataset.history = self
@@ -2650,13 +2754,13 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         serialization_options.attach_identifier(id_encoder, self, history_attrs)
         return history_attrs
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
 
         # Get basic value.
         rval = super().to_dict(view=view, value_mapper=value_mapper)
 
-        if view == 'element':
-            rval['size'] = int(self.disk_size)
+        if view == "element":
+            rval["size"] = int(self.disk_size)
 
         return rval
 
@@ -2680,8 +2784,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     @property
     def paused_jobs(self):
         db_session = object_session(self)
-        return db_session.query(Job).filter(Job.history_id == self.id,
-                                            Job.state == Job.states.PAUSED).all()
+        return db_session.query(Job).filter(Job.history_id == self.id, Job.state == Job.states.PAUSED).all()
 
     @hybrid.hybrid_property
     def disk_size(self):
@@ -2692,12 +2795,18 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         # non-.expression part of hybrid.hybrid_property: called when an instance is the namespace (not the class)
         db_session = object_session(self)
         rval = db_session.query(
-            func.sum(db_session.query(HistoryDatasetAssociation.dataset_id, Dataset.total_size).join(Dataset)
-                    .filter(HistoryDatasetAssociation.table.c.history_id == self.id)
-                    .filter(HistoryDatasetAssociation.purged != true())
-                    .filter(Dataset.purged != true())
-                    # unique datasets only
-                    .distinct().subquery().c.total_size)).first()[0]
+            func.sum(
+                db_session.query(HistoryDatasetAssociation.dataset_id, Dataset.total_size)
+                .join(Dataset)
+                .filter(HistoryDatasetAssociation.table.c.history_id == self.id)
+                .filter(HistoryDatasetAssociation.purged != true())
+                .filter(Dataset.purged != true())
+                # unique datasets only
+                .distinct()
+                .subquery()
+                .c.total_size
+            )
+        ).first()[0]
         if rval is None:
             rval = 0
         return rval
@@ -2710,15 +2819,18 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         """
         # .expression acts as a column_property and should return a scalar
         # first, get the distinct datasets within a history that are not purged
-        hda_to_dataset_join = join(HistoryDatasetAssociation, Dataset,
-            HistoryDatasetAssociation.table.c.dataset_id == Dataset.table.c.id)
+        hda_to_dataset_join = join(
+            HistoryDatasetAssociation, Dataset, HistoryDatasetAssociation.table.c.dataset_id == Dataset.table.c.id
+        )
         distinct_datasets = (
-            select([
-                # use labels here to better access from the query above
-                HistoryDatasetAssociation.table.c.history_id.label('history_id'),
-                Dataset.total_size.label('dataset_size'),
-                Dataset.id.label('dataset_id')
-            ])
+            select(
+                [
+                    # use labels here to better access from the query above
+                    HistoryDatasetAssociation.table.c.history_id.label("history_id"),
+                    Dataset.total_size.label("dataset_size"),
+                    Dataset.id.label("dataset_id"),
+                ]
+            )
             .where(HistoryDatasetAssociation.table.c.purged != true())
             .where(Dataset.table.c.purged != true())
             .select_from(hda_to_dataset_join)
@@ -2729,14 +2841,12 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         distinct_datasets_alias = aliased(distinct_datasets, name="datasets")
         # then, bind as property of history using the cls.id
         size_query = (
-            select([
-                func.coalesce(func.sum(distinct_datasets_alias.c.dataset_size), 0)
-            ])
+            select([func.coalesce(func.sum(distinct_datasets_alias.c.dataset_size), 0)])
             .select_from(distinct_datasets_alias)
             .where(distinct_datasets_alias.c.history_id == cls.id)
         )
         # label creates a scalar
-        return size_query.label('disk_size')
+        return size_query.label("disk_size")
 
     @property
     def disk_nice_size(self):
@@ -2746,45 +2856,51 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     @property
     def active_dataset_and_roles_query(self):
         db_session = object_session(self)
-        return (db_session.query(HistoryDatasetAssociation)
+        return (
+            db_session.query(HistoryDatasetAssociation)
             .filter(HistoryDatasetAssociation.table.c.history_id == self.id)
             .filter(not_(HistoryDatasetAssociation.deleted))
             .order_by(HistoryDatasetAssociation.table.c.hid.asc())
-            .options(joinedload("dataset"),
-                     joinedload("dataset.actions"),
-                     joinedload("dataset.actions.role"),
-                     joinedload("tags")))
+            .options(
+                joinedload("dataset"),
+                joinedload("dataset.actions"),
+                joinedload("dataset.actions.role"),
+                joinedload("tags"),
+            )
+        )
 
     @property
     def active_datasets_and_roles(self):
-        if not hasattr(self, '_active_datasets_and_roles'):
+        if not hasattr(self, "_active_datasets_and_roles"):
             self._active_datasets_and_roles = self.active_dataset_and_roles_query.all()
         return self._active_datasets_and_roles
 
     @property
     def active_visible_datasets_and_roles(self):
-        if not hasattr(self, '_active_visible_datasets_and_roles'):
-            self._active_visible_datasets_and_roles = self.active_dataset_and_roles_query.filter(HistoryDatasetAssociation.visible).all()
+        if not hasattr(self, "_active_visible_datasets_and_roles"):
+            self._active_visible_datasets_and_roles = self.active_dataset_and_roles_query.filter(
+                HistoryDatasetAssociation.visible
+            ).all()
         return self._active_visible_datasets_and_roles
 
     @property
     def active_visible_dataset_collections(self):
-        if not hasattr(self, '_active_visible_dataset_collections'):
+        if not hasattr(self, "_active_visible_dataset_collections"):
             db_session = object_session(self)
-            query = (db_session.query(HistoryDatasetCollectionAssociation)
+            query = (
+                db_session.query(HistoryDatasetCollectionAssociation)
                 .filter(HistoryDatasetCollectionAssociation.table.c.history_id == self.id)
                 .filter(not_(HistoryDatasetCollectionAssociation.deleted))
                 .filter(HistoryDatasetCollectionAssociation.visible)
                 .order_by(HistoryDatasetCollectionAssociation.table.c.hid.asc())
-                .options(joinedload("collection"),
-                         joinedload("tags")))
+                .options(joinedload("collection"), joinedload("tags"))
+            )
             self._active_visible_dataset_collections = query.all()
         return self._active_visible_dataset_collections
 
     @property
     def active_contents(self):
-        """ Return all active contents ordered by hid.
-        """
+        """Return all active contents ordered by hid."""
         return self.contents_iter(types=["dataset", "dataset_collection"], deleted=False, visible=True)
 
     def contents_iter(self, **kwds):
@@ -2792,13 +2908,13 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         Fetch filtered list of contents of history.
         """
         default_contents_types = [
-            'dataset',
+            "dataset",
         ]
-        types = kwds.get('types', default_contents_types)
+        types = kwds.get("types", default_contents_types)
         iters = []
-        if 'dataset' in types:
+        if "dataset" in types:
             iters.append(self.__dataset_contents_iter(**kwds))
-        if 'dataset_collection' in types:
+        if "dataset_collection" in types:
             iters.append(self.__collection_contents_iter(**kwds))
         return galaxy.util.merge_sorted_iterables(operator.attrgetter("hid"), *iters)
 
@@ -2810,15 +2926,15 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         assert db_session is not None
         query = db_session.query(content_class).filter(content_class.table.c.history_id == self.id)
         query = query.order_by(content_class.table.c.hid.asc())
-        deleted = galaxy.util.string_as_bool_or_none(kwds.get('deleted', None))
+        deleted = galaxy.util.string_as_bool_or_none(kwds.get("deleted", None))
         if deleted is not None:
             query = query.filter(content_class.deleted == deleted)
-        visible = galaxy.util.string_as_bool_or_none(kwds.get('visible', None))
+        visible = galaxy.util.string_as_bool_or_none(kwds.get("visible", None))
         if visible is not None:
             query = query.filter(content_class.visible == visible)
-        if 'ids' in kwds:
-            ids = kwds['ids']
-            max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH)
+        if "ids" in kwds:
+            ids = kwds["ids"]
+            max_in_filter_length = kwds.get("max_in_filter_length", MAX_IN_FILTER_LENGTH)
             if len(ids) < max_in_filter_length:
                 query = query.filter(content_class.id.in_(ids))
             else:
@@ -2834,26 +2950,26 @@ class UserShareAssociation(RepresentById):
 
 
 class HistoryUserShareAssociation(Base, UserShareAssociation):
-    __tablename__ = 'history_user_share_association'
+    __tablename__ = "history_user_share_association"
 
     id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    user = relationship('User')
-    history = relationship('History', back_populates='users_shared_with')
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user = relationship("User")
+    history = relationship("History", back_populates="users_shared_with")
 
 
 class UserRoleAssociation(Base, RepresentById):
-    __tablename__ = 'user_role_association'
+    __tablename__ = "user_role_association"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
 
-    user = relationship('User', back_populates="roles")
-    role = relationship('Role', back_populates="users")
+    user = relationship("User", back_populates="roles")
+    role = relationship("Role", back_populates="users")
 
     def __init__(self, user, role):
         self.user = user
@@ -2861,15 +2977,15 @@ class UserRoleAssociation(Base, RepresentById):
 
 
 class GroupRoleAssociation(Base, RepresentById):
-    __tablename__ = 'group_role_association'
+    __tablename__ = "group_role_association"
 
     id = Column(Integer, primary_key=True)
-    group_id = Column(Integer, ForeignKey('galaxy_group.id'), index=True)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
+    group_id = Column(Integer, ForeignKey("galaxy_group.id"), index=True)
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    group = relationship('Group', back_populates='roles')
-    role = relationship('Role', back_populates='groups')
+    group = relationship("Group", back_populates="roles")
+    role = relationship("Role", back_populates="groups")
 
     def __init__(self, group, role):
         self.group = group
@@ -2877,7 +2993,7 @@ class GroupRoleAssociation(Base, RepresentById):
 
 
 class Role(Base, Dictifiable, RepresentById):
-    __tablename__ = 'role'
+    __tablename__ = "role"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -2886,20 +3002,20 @@ class Role(Base, Dictifiable, RepresentById):
     description = Column(TEXT)
     type = Column(String(40), index=True)
     deleted = Column(Boolean, index=True, default=False)
-    dataset_actions = relationship('DatasetPermissions', back_populates='role')
-    groups = relationship('GroupRoleAssociation', back_populates='role')
-    users = relationship('UserRoleAssociation', back_populates='role')
+    dataset_actions = relationship("DatasetPermissions", back_populates="role")
+    groups = relationship("GroupRoleAssociation", back_populates="role")
+    users = relationship("UserRoleAssociation", back_populates="role")
 
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'name', 'description', 'type']
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = ["id", "name", "description", "type"]
     private_id = None
 
     class types(str, Enum):
-        PRIVATE = 'private'
-        SYSTEM = 'system'
-        USER = 'user'
-        ADMIN = 'admin'
-        SHARING = 'sharing'
+        PRIVATE = "private"
+        SYSTEM = "system"
+        USER = "user"
+        ADMIN = "admin"
+        SHARING = "sharing"
 
     def __init__(self, name=None, description=None, type=types.SYSTEM, deleted=False):
         self.name = name
@@ -2909,17 +3025,17 @@ class Role(Base, Dictifiable, RepresentById):
 
 
 class UserQuotaAssociation(Base, Dictifiable, RepresentById):
-    __tablename__ = 'user_quota_association'
+    __tablename__ = "user_quota_association"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    quota_id = Column(Integer, ForeignKey('quota.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    quota_id = Column(Integer, ForeignKey("quota.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user = relationship('User', back_populates='quotas')
-    quota = relationship('Quota', back_populates='users')
+    user = relationship("User", back_populates="quotas")
+    quota = relationship("Quota", back_populates="users")
 
-    dict_element_visible_keys = ['user']
+    dict_element_visible_keys = ["user"]
 
     def __init__(self, user, quota):
         self.user = user
@@ -2927,17 +3043,17 @@ class UserQuotaAssociation(Base, Dictifiable, RepresentById):
 
 
 class GroupQuotaAssociation(Base, Dictifiable, RepresentById):
-    __tablename__ = 'group_quota_association'
+    __tablename__ = "group_quota_association"
 
     id = Column(Integer, primary_key=True)
     group_id = Column(Integer, ForeignKey("galaxy_group.id"), index=True)
-    quota_id = Column(Integer, ForeignKey('quota.id'), index=True)
+    quota_id = Column(Integer, ForeignKey("quota.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    group = relationship('Group', back_populates='quotas')
-    quota = relationship('Quota', back_populates='groups')
+    group = relationship("Group", back_populates="quotas")
+    quota = relationship("Quota", back_populates="groups")
 
-    dict_element_visible_keys = ['group']
+    dict_element_visible_keys = ["group"]
 
     def __init__(self, group, quota):
         self.group = group
@@ -2945,7 +3061,7 @@ class GroupQuotaAssociation(Base, Dictifiable, RepresentById):
 
 
 class Quota(Base, Dictifiable, RepresentById):
-    __tablename__ = 'quota'
+    __tablename__ = "quota"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -2955,15 +3071,25 @@ class Quota(Base, Dictifiable, RepresentById):
     bytes = Column(BigInteger)
     operation = Column(String(8))
     deleted = Column(Boolean, index=True, default=False)
-    default = relationship('DefaultQuotaAssociation', back_populates='quota')
-    groups = relationship('GroupQuotaAssociation', back_populates='quota')
-    users = relationship('UserQuotaAssociation', back_populates='quota')
+    default = relationship("DefaultQuotaAssociation", back_populates="quota")
+    groups = relationship("GroupQuotaAssociation", back_populates="quota")
+    users = relationship("UserQuotaAssociation", back_populates="quota")
 
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups']
-    valid_operations = ('+', '-', '=')
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = [
+        "id",
+        "name",
+        "description",
+        "bytes",
+        "operation",
+        "display_amount",
+        "default",
+        "users",
+        "groups",
+    ]
+    valid_operations = ("+", "-", "=")
 
-    def __init__(self, name=None, description=None, amount=0, operation='='):
+    def __init__(self, name=None, description=None, amount=0, operation="="):
         self.name = name
         self.description = description
         if amount is None:
@@ -2982,6 +3108,7 @@ class Quota(Base, Dictifiable, RepresentById):
             self.bytes = -1
         else:
             self.bytes = amount
+
     amount = property(get_amount, set_amount)
 
     @property
@@ -2993,38 +3120,38 @@ class Quota(Base, Dictifiable, RepresentById):
 
 
 class DefaultQuotaAssociation(Base, Dictifiable, RepresentById):
-    __tablename__ = 'default_quota_association'
+    __tablename__ = "default_quota_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     type = Column(String(32), index=True, unique=True)
-    quota_id = Column(Integer, ForeignKey('quota.id'), index=True)
-    quota = relationship('Quota', back_populates='default')
+    quota_id = Column(Integer, ForeignKey("quota.id"), index=True)
+    quota = relationship("Quota", back_populates="default")
 
-    dict_element_visible_keys = ['type']
+    dict_element_visible_keys = ["type"]
 
     class types(str, Enum):
-        UNREGISTERED = 'unregistered'
-        REGISTERED = 'registered'
+        UNREGISTERED = "unregistered"
+        REGISTERED = "registered"
 
     def __init__(self, type, quota):
-        assert type in self.types.__members__.values(), 'Invalid type'
+        assert type in self.types.__members__.values(), "Invalid type"
         self.type = type
         self.quota = quota
 
 
 class DatasetPermissions(Base, RepresentById):
-    __tablename__ = 'dataset_permissions'
+    __tablename__ = "dataset_permissions"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     action = Column(TEXT)
-    dataset_id = Column(Integer, ForeignKey('dataset.id'), index=True)
+    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
     role_id = Column(Integer, ForeignKey("role.id"), index=True)
-    dataset = relationship('Dataset', back_populates='actions')
-    role = relationship('Role', back_populates='dataset_actions')
+    dataset = relationship("Dataset", back_populates="actions")
+    role = relationship("Role", back_populates="dataset_actions")
 
     def __init__(self, action, dataset, role=None, role_id=None):
         self.action = action
@@ -3036,16 +3163,16 @@ class DatasetPermissions(Base, RepresentById):
 
 
 class LibraryPermissions(Base, RepresentById):
-    __tablename__ = 'library_permissions'
+    __tablename__ = "library_permissions"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     action = Column(TEXT)
-    library_id = Column(Integer, ForeignKey('library.id'), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
-    library = relationship('Library', back_populates='actions')
-    role = relationship('Role')
+    library_id = Column(Integer, ForeignKey("library.id"), nullable=True, index=True)
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    library = relationship("Library", back_populates="actions")
+    role = relationship("Role")
 
     def __init__(self, action, library_item, role):
         self.action = action
@@ -3057,16 +3184,16 @@ class LibraryPermissions(Base, RepresentById):
 
 
 class LibraryFolderPermissions(Base, RepresentById):
-    __tablename__ = 'library_folder_permissions'
+    __tablename__ = "library_folder_permissions"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     action = Column(TEXT)
-    library_folder_id = Column(Integer, ForeignKey('library_folder.id'), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
-    folder = relationship('LibraryFolder', back_populates='actions')
-    role = relationship('Role')
+    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), nullable=True, index=True)
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    folder = relationship("LibraryFolder", back_populates="actions")
+    role = relationship("Role")
 
     def __init__(self, action, library_item, role):
         self.action = action
@@ -3078,16 +3205,16 @@ class LibraryFolderPermissions(Base, RepresentById):
 
 
 class LibraryDatasetPermissions(Base, RepresentById):
-    __tablename__ = 'library_dataset_permissions'
+    __tablename__ = "library_dataset_permissions"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     action = Column(TEXT)
-    library_dataset_id = Column(Integer, ForeignKey('library_dataset.id'), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
-    library_dataset = relationship('LibraryDataset', back_populates='actions')
-    role = relationship('Role')
+    library_dataset_id = Column(Integer, ForeignKey("library_dataset.id"), nullable=True, index=True)
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    library_dataset = relationship("LibraryDataset", back_populates="actions")
+    role = relationship("Role")
 
     def __init__(self, action, library_item, role):
         self.action = action
@@ -3099,18 +3226,18 @@ class LibraryDatasetPermissions(Base, RepresentById):
 
 
 class LibraryDatasetDatasetAssociationPermissions(Base, RepresentById):
-    __tablename__ = 'library_dataset_dataset_association_permissions'
+    __tablename__ = "library_dataset_dataset_association_permissions"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     action = Column(TEXT)
     library_dataset_dataset_association_id = Column(
-        Integer, ForeignKey('library_dataset_dataset_association.id'), nullable=True, index=True)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
-    library_dataset_dataset_association = relationship('LibraryDatasetDatasetAssociation',
-        back_populates='actions')
-    role = relationship('Role')
+        Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True, index=True
+    )
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    library_dataset_dataset_association = relationship("LibraryDatasetDatasetAssociation", back_populates="actions")
+    role = relationship("Role")
 
     def __init__(self, action, library_item, role):
         self.action = action
@@ -3122,14 +3249,14 @@ class LibraryDatasetDatasetAssociationPermissions(Base, RepresentById):
 
 
 class DefaultUserPermissions(Base, RepresentById):
-    __tablename__ = 'default_user_permissions'
+    __tablename__ = "default_user_permissions"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     action = Column(TEXT)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
-    user = relationship('User', back_populates='default_permissions')
-    role = relationship('Role')
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    user = relationship("User", back_populates="default_permissions")
+    role = relationship("Role")
 
     def __init__(self, user, action, role):
         self.user = user
@@ -3138,14 +3265,14 @@ class DefaultUserPermissions(Base, RepresentById):
 
 
 class DefaultHistoryPermissions(Base, RepresentById):
-    __tablename__ = 'default_history_permissions'
+    __tablename__ = "default_history_permissions"
 
     id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
     action = Column(TEXT)
-    role_id = Column(Integer, ForeignKey('role.id'), index=True)
-    history = relationship('History', back_populates='default_permissions')
-    role = relationship('Role')
+    role_id = Column(Integer, ForeignKey("role.id"), index=True)
+    history = relationship("History", back_populates="default_permissions")
+    role = relationship("Role")
 
     def __init__(self, history, action, role):
         self.history = history
@@ -3154,7 +3281,6 @@ class DefaultHistoryPermissions(Base, RepresentById):
 
 
 class StorableObject:
-
     def flush(self):
         sa_session = object_session(self)
         if sa_session:
@@ -3162,36 +3288,28 @@ class StorableObject:
 
 
 class Dataset(StorableObject, Serializable, _HasTable):
-
     class states(str, Enum):
-        NEW = 'new'
-        UPLOAD = 'upload'
-        QUEUED = 'queued'
-        RUNNING = 'running'
-        OK = 'ok'
-        EMPTY = 'empty'
-        ERROR = 'error'
-        DISCARDED = 'discarded'
-        PAUSED = 'paused'
-        SETTING_METADATA = 'setting_metadata'
-        FAILED_METADATA = 'failed_metadata'
+        NEW = "new"
+        UPLOAD = "upload"
+        QUEUED = "queued"
+        RUNNING = "running"
+        OK = "ok"
+        EMPTY = "empty"
+        ERROR = "error"
+        DISCARDED = "discarded"
+        PAUSED = "paused"
+        SETTING_METADATA = "setting_metadata"
+        FAILED_METADATA = "failed_metadata"
 
         @classmethod
         def values(self):
             return self.__members__.values()
+
     # failed_metadata is only valid as DatasetInstance state currently
 
-    non_ready_states = (
-        states.NEW,
-        states.UPLOAD,
-        states.QUEUED,
-        states.RUNNING,
-        states.SETTING_METADATA
-    )
+    non_ready_states = (states.NEW, states.UPLOAD, states.QUEUED, states.RUNNING, states.SETTING_METADATA)
     ready_states = tuple(set(states.__members__.values()) - set(non_ready_states))
-    valid_input_states = tuple(
-        set(states.__members__.values()) - {states.ERROR, states.DISCARDED}
-    )
+    valid_input_states = tuple(set(states.__members__.values()) - {states.ERROR, states.DISCARDED})
     terminal_states = (
         states.OK,
         states.EMPTY,
@@ -3210,12 +3328,21 @@ class Dataset(StorableObject, Serializable, _HasTable):
         ERROR = "error"
         OK = "ok"
 
-    permitted_actions = get_permitted_actions(filter='DATASET')
+    permitted_actions = get_permitted_actions(filter="DATASET")
     file_path = "/tmp/"
     object_store = None  # This get initialized in mapping.py (method init) by app.py
     engine = None
 
-    def __init__(self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None):
+    def __init__(
+        self,
+        id=None,
+        state=None,
+        external_filename=None,
+        extra_files_path=None,
+        file_size=None,
+        purgable=True,
+        uuid=None,
+    ):
         self.id = id
         self.uuid = get_uuid(uuid)
         self.state = state
@@ -3242,7 +3369,7 @@ class Dataset(StorableObject, Serializable, _HasTable):
             if self.object_store.exists(self):
                 return self.object_store.get_filename(self)
             else:
-                return ''
+                return ""
         else:
             filename = self.external_filename
         # Make filename absolute
@@ -3253,6 +3380,7 @@ class Dataset(StorableObject, Serializable, _HasTable):
             self.external_filename = None
         else:
             self.external_filename = filename
+
     file_name = property(get_file_name, set_file_name)
 
     def get_extra_files_path(self):
@@ -3262,7 +3390,7 @@ class Dataset(StorableObject, Serializable, _HasTable):
         if not getattr(self, "external_extra_files_path", None):
             if self.object_store.exists(self, dir_only=True, extra_dir=self._extra_files_rel_path):
                 return self.object_store.get_filename(self, dir_only=True, extra_dir=self._extra_files_rel_path)
-            return ''
+            return ""
         else:
             return os.path.abspath(self.external_extra_files_path)
 
@@ -3275,6 +3403,7 @@ class Dataset(StorableObject, Serializable, _HasTable):
             self.external_extra_files_path = None
         else:
             self.external_extra_files_path = extra_files_path
+
     extra_files_path = property(get_extra_files_path, set_extra_files_path)
 
     def extra_files_path_exists(self):
@@ -3351,7 +3480,11 @@ class Dataset(StorableObject, Serializable, _HasTable):
         if rel_path is not None:
             if self.object_store.exists(self, extra_dir=rel_path, dir_only=True):
                 for root, _, files in os.walk(self.extra_files_path):
-                    self.total_size += sum(os.path.getsize(os.path.join(root, file)) for file in files if os.path.exists(os.path.join(root, file)))
+                    self.total_size += sum(
+                        os.path.getsize(os.path.join(root, file))
+                        for file in files
+                        if os.path.exists(os.path.join(root, file))
+                    )
         return self.total_size
 
     def has_data(self):
@@ -3368,9 +3501,11 @@ class Dataset(StorableObject, Serializable, _HasTable):
 
     @property
     def user_can_purge(self):
-        return self.purged is False \
-            and not bool(self.library_associations) \
+        return (
+            self.purged is False
+            and not bool(self.library_associations)
             and len(self.history_associations) == len(self.purged_history_associations)
+        )
 
     def full_delete(self):
         """Remove the file and extra files, marks deleted and purged"""
@@ -3425,7 +3560,7 @@ class Dataset(StorableObject, Serializable, _HasTable):
             object_store_id=self.object_store_id,
             total_size=to_int(self.total_size),
             created_from_basename=self.created_from_basename,
-            uuid=str(self.uuid or '') or None,
+            uuid=str(self.uuid or "") or None,
             hashes=list(map(lambda h: h.serialize(id_encoder, serialization_options), self.hashes)),
             sources=list(map(lambda s: s.serialize(id_encoder, serialization_options), self.sources)),
         )
@@ -3434,17 +3569,22 @@ class Dataset(StorableObject, Serializable, _HasTable):
 
 
 class DatasetSource(Base, Dictifiable, Serializable):
-    __tablename__ = 'dataset_source'
+    __tablename__ = "dataset_source"
 
     id = Column(Integer, primary_key=True)
-    dataset_id = Column(Integer, ForeignKey('dataset.id'), index=True)
+    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
     source_uri = Column(TEXT)
     extra_files_path = Column(TEXT)
     transform = Column(MutableJSONType)
-    dataset = relationship('Dataset', back_populates='sources')
-    hashes = relationship('DatasetSourceHash', back_populates='source')
-    dict_collection_visible_keys = ['id', 'source_uri', 'extra_files_path', "transform"]
-    dict_element_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']  # TODO: implement to_dict and add hashes...
+    dataset = relationship("Dataset", back_populates="sources")
+    hashes = relationship("DatasetSourceHash", back_populates="source")
+    dict_collection_visible_keys = ["id", "source_uri", "extra_files_path", "transform"]
+    dict_element_visible_keys = [
+        "id",
+        "source_uri",
+        "extra_files_path",
+        "transform",
+    ]  # TODO: implement to_dict and add hashes...
 
     def _serialize(self, id_encoder, serialization_options):
         rval = dict_for(
@@ -3459,13 +3599,13 @@ class DatasetSource(Base, Dictifiable, Serializable):
 
 
 class DatasetSourceHash(Base, Serializable):
-    __tablename__ = 'dataset_source_hash'
+    __tablename__ = "dataset_source_hash"
 
     id = Column(Integer, primary_key=True)
-    dataset_source_id = Column(Integer, ForeignKey('dataset_source.id'), index=True)
+    dataset_source_id = Column(Integer, ForeignKey("dataset_source.id"), index=True)
     hash_function = Column(TEXT)
     hash_value = Column(TEXT)
-    source = relationship('DatasetSource', back_populates='hashes')
+    source = relationship("DatasetSource", back_populates="hashes")
 
     def _serialize(self, id_encoder, serialization_options):
         rval = dict_for(
@@ -3478,16 +3618,16 @@ class DatasetSourceHash(Base, Serializable):
 
 
 class DatasetHash(Base, Dictifiable, Serializable):
-    __tablename__ = 'dataset_hash'
+    __tablename__ = "dataset_hash"
 
     id = Column(Integer, primary_key=True)
-    dataset_id = Column(Integer, ForeignKey('dataset.id'), index=True)
+    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
     hash_function = Column(TEXT)
     hash_value = Column(TEXT)
     extra_files_path = Column(TEXT)
-    dataset = relationship('Dataset', back_populates='hashes')
-    dict_collection_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']
-    dict_element_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']
+    dataset = relationship("Dataset", back_populates="hashes")
+    dict_collection_visible_keys = ["id", "hash_function", "hash_value", "extra_files_path"]
+    dict_element_visible_keys = ["id", "hash_function", "hash_value", "extra_files_path"]
 
     def _serialize(self, id_encoder, serialization_options):
         rval = dict_for(
@@ -3505,31 +3645,53 @@ def datatype_for_extension(extension, datatypes_registry=None) -> "Data":
         extension = extension.lower()
     if datatypes_registry is None:
         datatypes_registry = _get_datatypes_registry()
-    if not extension or extension == 'auto' or extension == '_sniff_':
-        extension = 'data'
+    if not extension or extension == "auto" or extension == "_sniff_":
+        extension = "data"
     ret = datatypes_registry.get_datatype_by_extension(extension)
     if ret is None:
         log.warning(f"Datatype class not found for extension '{extension}'")
-        return datatypes_registry.get_datatype_by_extension('data')
+        return datatypes_registry.get_datatype_by_extension("data")
     return ret
 
 
 class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
     """A base class for all 'dataset instances', HDAs, LDAs, etc"""
+
     states = Dataset.states
     conversion_messages = Dataset.conversion_messages
     permitted_actions = Dataset.permitted_actions
 
     class validated_states(str, Enum):
-        UNKNOWN = 'unknown'
-        INVALID = 'invalid'
-        OK = 'ok'
+        UNKNOWN = "unknown"
+        INVALID = "invalid"
+        OK = "ok"
 
-    def __init__(self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None,
-                 extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False,
-                 designation=None, parent_id=None, validated_state='unknown', validated_state_message=None,
-                 visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True,
-                 creating_job_id=None):
+    def __init__(
+        self,
+        id=None,
+        hid=None,
+        name=None,
+        info=None,
+        blurb=None,
+        peek=None,
+        tool_version=None,
+        extension=None,
+        dbkey=None,
+        metadata=None,
+        history=None,
+        dataset=None,
+        deleted=False,
+        designation=None,
+        parent_id=None,
+        validated_state="unknown",
+        validated_state_message=None,
+        visible=True,
+        create_dataset=False,
+        sa_session=None,
+        extended_metadata=None,
+        flush=True,
+        creating_job_id=None,
+    ):
         self.name = name or "Unnamed dataset"
         self.id = id
         self.info = info
@@ -3542,8 +3704,10 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
         self._metadata = None
         self.metadata = metadata or dict()
         self.extended_metadata = extended_metadata
-        if dbkey:  # dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata'
-            self._metadata['dbkey'] = dbkey
+        if (
+            dbkey
+        ):  # dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata'
+            self._metadata["dbkey"] = dbkey
         self.deleted = deleted
         self.visible = visible
         self.validated_state = validated_state
@@ -3591,6 +3755,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
             if sa_session:
                 object_session(self).add(self.dataset)
                 object_session(self).flush()  # flush here, because hda.flush() won't flush the Dataset object
+
     state = property(get_dataset_state, set_dataset_state)
 
     def get_file_name(self) -> str:
@@ -3600,6 +3765,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
 
     def set_file_name(self, filename: str):
         return self.dataset.set_file_name(filename)
+
     file_name = property(get_file_name, set_file_name)
 
     def link_to(self, path):
@@ -3622,7 +3788,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
     def get_metadata(self):
         # using weakref to store parent (to prevent circ ref),
         #   does a Session.clear() cause parent to be invalidated, while still copying over this non-database attribute?
-        if not hasattr(self, '_metadata_collection') or self._metadata_collection.parent != self:
+        if not hasattr(self, "_metadata_collection") or self._metadata_collection.parent != self:
             self._metadata_collection = galaxy.model.metadata.MetadataCollection(self)
         return self._metadata_collection
 
@@ -3633,6 +3799,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
     def set_metadata(self, bunch):
         # Needs to accept a MetadataCollection, a bunch, or a dict
         self._metadata = self.metadata.make_dict_copy(bunch)
+
     metadata = property(get_metadata, set_metadata)
 
     @property
@@ -3673,15 +3840,17 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
         if "dbkey" in self.datatype.metadata_spec:
             if not isinstance(value, list):
                 self.metadata.dbkey = [value]
+
     dbkey = property(get_dbkey, set_dbkey)
 
     def ok_to_edit_metadata(self):
         # prevent modifying metadata when dataset is queued or running as input/output
         # This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now
         sa_session = object_session(self)
-        for job_to_dataset_association in sa_session.query(
-                JobToInputDatasetAssociation).filter_by(dataset_id=self.id).all() \
-                + sa_session.query(JobToOutputDatasetAssociation).filter_by(dataset_id=self.id).all():
+        for job_to_dataset_association in (
+            sa_session.query(JobToInputDatasetAssociation).filter_by(dataset_id=self.id).all()
+            + sa_session.query(JobToOutputDatasetAssociation).filter_by(dataset_id=self.id).all()
+        ):
             if job_to_dataset_association.job.state not in Job.terminal_states:
                 return False
         return True
@@ -3738,7 +3907,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
             return _get_datatypes_registry().get_mimetype_by_extension(self.extension.lower())
         except AttributeError:
             # extension is None
-            return 'data'
+            return "data"
 
     def set_peek(self, **kwd):
         return self.datatype.set_peek(self, **kwd)
@@ -3823,10 +3992,25 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
             raise NoConverterException(f"A dependency ({dependency}) is missing a converter.")
         except KeyError:
             pass  # No deps
-        new_dataset = next(iter(self.datatype.convert_dataset(trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context, history=history).values()))
+        new_dataset = next(
+            iter(
+                self.datatype.convert_dataset(
+                    trans,
+                    self,
+                    target_ext,
+                    return_output=True,
+                    visible=False,
+                    deps=deps,
+                    target_context=target_context,
+                    history=history,
+                ).values()
+            )
+        )
         new_dataset.name = self.name
         self.copy_attributes(new_dataset)
-        assoc = ImplicitlyConvertedDatasetAssociation(parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False)
+        assoc = ImplicitlyConvertedDatasetAssociation(
+            parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False
+        )
         session = trans.sa_session
         session.add(new_dataset)
         session.add(assoc)
@@ -3846,7 +4030,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
         for name, value in self.metadata.items():
             # HACK: MetadataFile objects do not have a type/ext, so need to use metadata name
             # to determine type.
-            if dataset_ext == 'bai' and name == 'bam_index' and isinstance(value, MetadataFile):
+            if dataset_ext == "bai" and name == "bam_index" and isinstance(value, MetadataFile):
                 # HACK: MetadataFile objects cannot be used by tools, so return
                 # a fake HDA that points to metadata file.
                 fake_dataset = Dataset(state=Dataset.states.OK, external_filename=value.file_name)
@@ -3897,9 +4081,13 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
         """
         Return true if the dataset is neither ready nor in error
         """
-        return self.state in (self.states.NEW, self.states.UPLOAD,
-                              self.states.QUEUED, self.states.RUNNING,
-                              self.states.SETTING_METADATA)
+        return self.state in (
+            self.states.NEW,
+            self.states.UPLOAD,
+            self.states.QUEUED,
+            self.states.RUNNING,
+            self.states.SETTING_METADATA,
+        )
 
     @property
     def source_library_dataset(self):
@@ -3916,6 +4104,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
                 if source:
                     return source
             return (None, None)
+
         return get_source(self)
 
     @property
@@ -3936,6 +4125,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
             except Exception as e:
                 log.warning(e)
             return lst
+
         return _source_dataset_chain(self, [])
 
     @property
@@ -4005,15 +4195,19 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
         except NoConverterException:
             return self.conversion_messages.NO_CONVERTER
         except ConverterDependencyException as dep_error:
-            return {'kind': self.conversion_messages.ERROR, 'message': dep_error.value}
+            return {"kind": self.conversion_messages.ERROR, "message": dep_error.value}
 
         # Check dataset state and return any messages.
         msg = None
         if converted_dataset and converted_dataset.state == Dataset.states.ERROR:
-            job_id = trans.sa_session.query(JobToOutputDatasetAssociation) \
-                .filter_by(dataset_id=converted_dataset.id).first().job_id
+            job_id = (
+                trans.sa_session.query(JobToOutputDatasetAssociation)
+                .filter_by(dataset_id=converted_dataset.id)
+                .first()
+                .job_id
+            )
             job = trans.sa_session.query(Job).get(job_id)
-            msg = {'kind': self.conversion_messages.ERROR, 'message': job.stderr}
+            msg = {"kind": self.conversion_messages.ERROR, "message": job.stderr}
         elif not converted_dataset or converted_dataset.state != Dataset.states.OK:
             msg = self.conversion_messages.PENDING
 
@@ -4061,19 +4255,20 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
             rval["file_metadata"] = file_metadata
 
 
-class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnotations,
-                                HasName, Serializable):
+class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable):
     """
     Resource class that creates a relation between a dataset and a user history.
     """
 
-    def __init__(self,
-                 hid=None,
-                 history=None,
-                 copied_from_history_dataset_association=None,
-                 copied_from_library_dataset_dataset_association=None,
-                 sa_session=None,
-                 **kwd):
+    def __init__(
+        self,
+        hid=None,
+        history=None,
+        copied_from_history_dataset_association=None,
+        copied_from_library_dataset_dataset_association=None,
+        sa_session=None,
+        **kwd,
+    ):
         """
         Create a a new HDA and associate it with the given history.
         """
@@ -4102,18 +4297,17 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         if self.update_time and self.state == self.states.OK:
             # We only record changes to HDAs that exist in the database and have a update_time
             new_values = {}
-            new_values['name'] = changes.get('name', self.name)
-            new_values['dbkey'] = changes.get('dbkey', self.dbkey)
-            new_values['extension'] = changes.get('extension', self.extension)
-            new_values['extended_metadata_id'] = changes.get('extended_metadata_id', self.extended_metadata_id)
+            new_values["name"] = changes.get("name", self.name)
+            new_values["dbkey"] = changes.get("dbkey", self.dbkey)
+            new_values["extension"] = changes.get("extension", self.extension)
+            new_values["extended_metadata_id"] = changes.get("extended_metadata_id", self.extended_metadata_id)
             for k, v in new_values.items():
                 if isinstance(v, list):
                     new_values[k] = v[0]
-            new_values['update_time'] = self.update_time
-            new_values['version'] = self.version or 1
-            new_values['metadata'] = self._metadata
-            past_hda = HistoryDatasetAssociationHistory(history_dataset_association_id=self.id,
-                                                        **new_values)
+            new_values["update_time"] = self.update_time
+            new_values["version"] = self.version or 1
+            new_values["metadata"] = self._metadata
+            past_hda = HistoryDatasetAssociationHistory(history_dataset_association_id=self.id, **new_values)
             self.version = self.version + 1 if self.version else 1
             session.add(past_hda)
 
@@ -4143,20 +4337,22 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         hid = None
         if copy_hid:
             hid = self.hid
-        hda = HistoryDatasetAssociation(hid=hid,
-                                        name=new_name or self.name,
-                                        info=self.info,
-                                        blurb=self.blurb,
-                                        peek=self.peek,
-                                        tool_version=self.tool_version,
-                                        extension=self.extension,
-                                        dbkey=self.dbkey,
-                                        dataset=self.dataset,
-                                        visible=self.visible,
-                                        deleted=self.deleted,
-                                        parent_id=parent_id,
-                                        copied_from_history_dataset_association=self,
-                                        flush=False)
+        hda = HistoryDatasetAssociation(
+            hid=hid,
+            name=new_name or self.name,
+            info=self.info,
+            blurb=self.blurb,
+            peek=self.peek,
+            tool_version=self.tool_version,
+            extension=self.extension,
+            dbkey=self.dbkey,
+            dataset=self.dataset,
+            visible=self.visible,
+            deleted=self.deleted,
+            parent_id=parent_id,
+            copied_from_history_dataset_association=self,
+            flush=False,
+        )
         # update init non-keywords as well
         hda.purged = self.purged
 
@@ -4182,8 +4378,16 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
     def copy_attributes(self, new_dataset):
         new_dataset.hid = self.hid
 
-    def to_library_dataset_dataset_association(self, trans, target_folder, replace_dataset=None,
-                                               parent_id=None, roles=None, ldda_message='', element_identifier=None):
+    def to_library_dataset_dataset_association(
+        self,
+        trans,
+        target_folder,
+        replace_dataset=None,
+        parent_id=None,
+        roles=None,
+        ldda_message="",
+        element_identifier=None,
+    ):
         """
         Copy this HDA to a library optionally replacing an existing LDDA.
         """
@@ -4197,27 +4401,30 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             #   to the associated Dataset.
             library_dataset = LibraryDataset(folder=target_folder, name=self.name, info=self.info)
         user = trans.user or self.history.user
-        ldda = LibraryDatasetDatasetAssociation(name=element_identifier or self.name,
-                                                info=self.info,
-                                                blurb=self.blurb,
-                                                peek=self.peek,
-                                                tool_version=self.tool_version,
-                                                extension=self.extension,
-                                                dbkey=self.dbkey,
-                                                dataset=self.dataset,
-                                                library_dataset=library_dataset,
-                                                visible=self.visible,
-                                                deleted=self.deleted,
-                                                parent_id=parent_id,
-                                                copied_from_history_dataset_association=self,
-                                                user=user)
+        ldda = LibraryDatasetDatasetAssociation(
+            name=element_identifier or self.name,
+            info=self.info,
+            blurb=self.blurb,
+            peek=self.peek,
+            tool_version=self.tool_version,
+            extension=self.extension,
+            dbkey=self.dbkey,
+            dataset=self.dataset,
+            library_dataset=library_dataset,
+            visible=self.visible,
+            deleted=self.deleted,
+            parent_id=parent_id,
+            copied_from_history_dataset_association=self,
+            user=user,
+        )
         library_dataset.library_dataset_dataset_association = ldda
         object_session(self).add(library_dataset)
         # If roles were selected on the upload form, restrict access to the Dataset to those roles
         roles = roles or []
         for role in roles:
-            dp = trans.model.DatasetPermissions(trans.app.security_agent.permitted_actions.DATASET_ACCESS.action,
-                                                ldda.dataset, role)
+            dp = trans.model.DatasetPermissions(
+                trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, ldda.dataset, role
+            )
             trans.sa_session.add(dp)
         # Must set metadata after ldda flushed, as MetadataFiles require ldda.id
         flushed = False
@@ -4241,8 +4448,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         return ldda
 
     def clear_associated_files(self, metadata_safe=False, purge=False):
-        """
-        """
+        """ """
         # metadata_safe = True means to only clear when assoc.metadata_safe == False
         for assoc in self.implicitly_converted_datasets:
             if not assoc.deleted and (not metadata_safe or not assoc.metadata_safe):
@@ -4257,8 +4463,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         return self.dataset.get_access_roles(security_agent)
 
     def purge_usage_from_quota(self, user):
-        """Remove this HDA's quota_amount from user's quota.
-        """
+        """Remove this HDA's quota_amount from user's quota."""
         if user:
             user.adjust_total_disk_usage(-self.quota_amount(user))
 
@@ -4287,11 +4492,11 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
 
     def _serialize(self, id_encoder, serialization_options):
         rval = super()._serialize(id_encoder, serialization_options)
-        rval['state'] = self.state
+        rval["state"] = self.state
         rval["hid"] = self.hid
-        rval["annotation"] = unicodify(getattr(self, 'annotation', ''))
+        rval["annotation"] = unicodify(getattr(self, "annotation", ""))
         rval["tags"] = self.make_tag_string_list()
-        rval['tool_version'] = self.tool_version
+        rval["tool_version"] = self.tool_version
         if self.history:
             rval["history_encoded_id"] = serialization_options.get_identifier(id_encoder, self.history)
 
@@ -4300,12 +4505,14 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         src_hda = self
         while src_hda.copied_from_history_dataset_association:
             src_hda = src_hda.copied_from_history_dataset_association
-            copied_from_history_dataset_association_chain.append(serialization_options.get_identifier(id_encoder, src_hda))
+            copied_from_history_dataset_association_chain.append(
+                serialization_options.get_identifier(id_encoder, src_hda)
+            )
         rval["copied_from_history_dataset_association_id_chain"] = copied_from_history_dataset_association_chain
         self._handle_serialize_files(id_encoder, serialization_options, rval)
         return rval
 
-    def to_dict(self, view='collection', expose_dataset_path=False):
+    def to_dict(self, view="collection", expose_dataset_path=False):
         """
         Return attributes of this HDA that are exposed using the API.
         """
@@ -4314,39 +4521,41 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         # other model classes.
         original_rval = super().to_dict(view=view)
         hda = self
-        rval = dict(id=hda.id,
-                    hda_ldda='hda',
-                    uuid=(lambda uuid: str(uuid) if uuid else None)(hda.dataset.uuid),
-                    hid=hda.hid,
-                    file_ext=hda.ext,
-                    peek=unicodify(hda.display_peek()) if hda.peek and hda.peek != 'no peek' else None,
-                    model_class=self.__class__.__name__,
-                    name=hda.name,
-                    deleted=hda.deleted,
-                    purged=hda.purged,
-                    visible=hda.visible,
-                    state=hda.state,
-                    history_content_type=hda.history_content_type,
-                    file_size=int(hda.get_size()),
-                    create_time=hda.create_time.isoformat(),
-                    update_time=hda.update_time.isoformat(),
-                    data_type=f"{hda.datatype.__class__.__module__}.{hda.datatype.__class__.__name__}",
-                    genome_build=hda.dbkey,
-                    validated_state=hda.validated_state,
-                    validated_state_message=hda.validated_state_message,
-                    misc_info=hda.info.strip() if isinstance(hda.info, str) else hda.info,
-                    misc_blurb=hda.blurb)
+        rval = dict(
+            id=hda.id,
+            hda_ldda="hda",
+            uuid=(lambda uuid: str(uuid) if uuid else None)(hda.dataset.uuid),
+            hid=hda.hid,
+            file_ext=hda.ext,
+            peek=unicodify(hda.display_peek()) if hda.peek and hda.peek != "no peek" else None,
+            model_class=self.__class__.__name__,
+            name=hda.name,
+            deleted=hda.deleted,
+            purged=hda.purged,
+            visible=hda.visible,
+            state=hda.state,
+            history_content_type=hda.history_content_type,
+            file_size=int(hda.get_size()),
+            create_time=hda.create_time.isoformat(),
+            update_time=hda.update_time.isoformat(),
+            data_type=f"{hda.datatype.__class__.__module__}.{hda.datatype.__class__.__name__}",
+            genome_build=hda.dbkey,
+            validated_state=hda.validated_state,
+            validated_state_message=hda.validated_state_message,
+            misc_info=hda.info.strip() if isinstance(hda.info, str) else hda.info,
+            misc_blurb=hda.blurb,
+        )
 
         rval.update(original_rval)
 
         if hda.copied_from_library_dataset_dataset_association is not None:
-            rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id
+            rval["copied_from_ldda_id"] = hda.copied_from_library_dataset_dataset_association.id
 
         if hda.history is not None:
-            rval['history_id'] = hda.history.id
+            rval["history_id"] = hda.history.id
 
         if hda.extended_metadata is not None:
-            rval['extended_metadata'] = hda.extended_metadata.data
+            rval["extended_metadata"] = hda.extended_metadata.data
 
         for name in hda.metadata.spec.keys():
             val = hda.metadata.get(name)
@@ -4370,9 +4579,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             if jtida.job not in jobs_to_unpause:
                 jobs_to_unpause.add(jtida.job)
                 for jtoda in jtida.job.output_datasets:
-                    jobs_to_unpause.update(
-                        jtoda.dataset.unpause_dependent_jobs(jobs=jobs_to_unpause)
-                    )
+                    jobs_to_unpause.update(jtoda.dataset.unpause_dependent_jobs(jobs=jobs_to_unpause))
         return jobs_to_unpause
 
     @property
@@ -4380,41 +4587,40 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         return "dataset"
 
     # TODO: down into DatasetInstance
-    content_type = 'dataset'
+    content_type = "dataset"
 
     @hybrid.hybrid_property
     def type_id(self):
-        return '-'.join((self.content_type, str(self.id)))
+        return "-".join((self.content_type, str(self.id)))
 
     @type_id.expression  # type: ignore[no-redef]
     def type_id(cls):
-        return ((type_coerce(cls.content_type, Unicode) + '-'
-                 + type_coerce(cls.id, Unicode)).label('type_id'))
+        return (type_coerce(cls.content_type, Unicode) + "-" + type_coerce(cls.id, Unicode)).label("type_id")
 
 
 class HistoryDatasetAssociationHistory(Base, Serializable):
-    __tablename__ = 'history_dataset_association_history'
+    __tablename__ = "history_dataset_association_history"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey("history_dataset_association.id"), index=True)
+    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
     update_time = Column(DateTime, default=now)
     version = Column(Integer)
     name = Column(TrimmedString(255))
     extension = Column(TrimmedString(64))
-    _metadata = Column('metadata', JSONType)
+    _metadata = Column("metadata", JSONType)
     extended_metadata_id = Column(Integer, ForeignKey("extended_metadata.id"), index=True)
 
-    def __init__(self,
-                 history_dataset_association_id,
-                 name,
-                 dbkey,
-                 update_time,
-                 version,
-                 extension,
-                 extended_metadata_id,
-                 metadata,
-                 ):
+    def __init__(
+        self,
+        history_dataset_association_id,
+        name,
+        dbkey,
+        update_time,
+        version,
+        extension,
+        extended_metadata_id,
+        metadata,
+    ):
         self.history_dataset_association_id = history_dataset_association_id
         self.name = name
         self.dbkey = dbkey
@@ -4427,17 +4633,16 @@ class HistoryDatasetAssociationHistory(Base, Serializable):
 
 # hda read access permission given by a user to a specific site (gen. for external display applications)
 class HistoryDatasetAssociationDisplayAtAuthorization(Base, RepresentById):
-    __tablename__ = 'history_dataset_association_display_at_authorization'
+    __tablename__ = "history_dataset_association_display_at_authorization"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     site = Column(TrimmedString(255))
-    history_dataset_association = relationship('HistoryDatasetAssociation')
-    user = relationship('User')
+    history_dataset_association = relationship("HistoryDatasetAssociation")
+    user = relationship("User")
 
     def __init__(self, hda=None, user=None, site=None):
         self.history_dataset_association = hda
@@ -4446,21 +4651,26 @@ class HistoryDatasetAssociationDisplayAtAuthorization(Base, RepresentById):
 
 
 class HistoryDatasetAssociationSubset(Base, RepresentById):
-    __tablename__ = 'history_dataset_association_subset'
+    __tablename__ = "history_dataset_association_subset"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
-    history_dataset_association_subset_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
+    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    history_dataset_association_subset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
     location = Column(Unicode(255), index=True)
 
-    hda = relationship('HistoryDatasetAssociation',
-        primaryjoin=(lambda: HistoryDatasetAssociationSubset.history_dataset_association_id
-            == HistoryDatasetAssociation.id))
-    subset = relationship('HistoryDatasetAssociation',
-        primaryjoin=(lambda: HistoryDatasetAssociationSubset.history_dataset_association_subset_id
-            == HistoryDatasetAssociation.id))
+    hda = relationship(
+        "HistoryDatasetAssociation",
+        primaryjoin=(
+            lambda: HistoryDatasetAssociationSubset.history_dataset_association_id == HistoryDatasetAssociation.id
+        ),
+    )
+    subset = relationship(
+        "HistoryDatasetAssociation",
+        primaryjoin=(
+            lambda: HistoryDatasetAssociationSubset.history_dataset_association_subset_id
+            == HistoryDatasetAssociation.id
+        ),
+    )
 
     def __init__(self, hda, subset, location):
         self.hda = hda
@@ -4469,7 +4679,7 @@ class HistoryDatasetAssociationSubset(Base, RepresentById):
 
 
 class Library(Base, Dictifiable, HasName, Serializable):
-    __tablename__ = 'library'
+    __tablename__ = "library"
 
     id = Column(Integer, primary_key=True)
     root_folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
@@ -4480,12 +4690,12 @@ class Library(Base, Dictifiable, HasName, Serializable):
     purged = Column(Boolean, index=True, default=False)
     description = Column(TEXT)
     synopsis = Column(TEXT)
-    root_folder = relationship('LibraryFolder', back_populates='library_root')
-    actions = relationship('LibraryPermissions', back_populates='library')
+    root_folder = relationship("LibraryFolder", back_populates="library_root")
+    actions = relationship("LibraryPermissions", back_populates="library")
 
-    permitted_actions = get_permitted_actions(filter='LIBRARY')
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time']
+    permitted_actions = get_permitted_actions(filter="LIBRARY")
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = ["id", "deleted", "name", "description", "synopsis", "root_folder_id", "create_time"]
 
     def __init__(self, name=None, description=None, synopsis=None, root_folder=None):
         self.name = name or "Unnamed library"
@@ -4506,13 +4716,13 @@ class Library(Base, Dictifiable, HasName, Serializable):
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         """
         We prepend an F to folders.
         """
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        if 'root_folder_id' in rval:
-            rval['root_folder_id'] = f"F{str(rval['root_folder_id'])}"
+        if "root_folder_id" in rval:
+            rval["root_folder_id"] = f"F{str(rval['root_folder_id'])}"
         return rval
 
     def get_active_folders(self, folder, folders=None):
@@ -4532,11 +4742,12 @@ class Library(Base, Dictifiable, HasName, Serializable):
             intermed = [(getattr(v, attr), i, v) for i, v in enumerate(seq)]
             intermed.sort()
             return [_[-1] for _ in intermed]
+
         if folders is None:
             active_folders = [folder]
         for active_folder in folder.active_folders:
             active_folders.extend(self.get_active_folders(active_folder, folders))
-        return sort_by_attr(active_folders, 'id')
+        return sort_by_attr(active_folders, "id")
 
     def get_access_roles(self, security_agent):
         roles = []
@@ -4547,13 +4758,11 @@ class Library(Base, Dictifiable, HasName, Serializable):
 
 
 class LibraryFolder(Base, Dictifiable, HasName, Serializable):
-    __tablename__ = 'library_folder'
-    __table_args__ = (
-        Index('ix_library_folder_name', 'name', mysql_length=200),
-    )
+    __tablename__ = "library_folder"
+    __table_args__ = (Index("ix_library_folder_name", "name", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    parent_id = Column(Integer, ForeignKey('library_folder.id'), nullable=True, index=True)
+    parent_id = Column(Integer, ForeignKey("library_folder.id"), nullable=True, index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     name = Column(TEXT)
@@ -4564,37 +4773,57 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
     purged = Column(Boolean, index=True, default=False)
     genome_build = Column(TrimmedString(40))
 
-    folders = relationship('LibraryFolder',
+    folders = relationship(
+        "LibraryFolder",
         primaryjoin=(lambda: LibraryFolder.id == LibraryFolder.parent_id),
         order_by=asc(name),
-        back_populates='parent')
-    parent = relationship('LibraryFolder', back_populates='folders', remote_side=[id])
+        back_populates="parent",
+    )
+    parent = relationship("LibraryFolder", back_populates="folders", remote_side=[id])
 
-    active_folders = relationship('LibraryFolder',
-        primaryjoin=(
-            'and_(LibraryFolder.parent_id == LibraryFolder.id, not_(LibraryFolder.deleted))'),
+    active_folders = relationship(
+        "LibraryFolder",
+        primaryjoin=("and_(LibraryFolder.parent_id == LibraryFolder.id, not_(LibraryFolder.deleted))"),
         order_by=asc(name),
         # """sqlalchemy.exc.ArgumentError: Error creating eager relationship 'active_folders'
         # on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>':
         # Cant use eager loading on a self referential relationship."""
         # TODO: This is no longer the case. Fix this: https://docs.sqlalchemy.org/en/14/orm/self_referential.html#configuring-self-referential-eager-loading
-        viewonly=True)
+        viewonly=True,
+    )
 
-    datasets = relationship('LibraryDataset',
-        primaryjoin=(lambda: LibraryDataset.folder_id == LibraryFolder.id and LibraryDataset.library_dataset_dataset_association_id.isnot(None)),
-        order_by=(lambda: asc(LibraryDataset._name)),
-        viewonly=True)
-
-    active_datasets = relationship('LibraryDataset',
+    datasets = relationship(
+        "LibraryDataset",
         primaryjoin=(
-            'and_(LibraryDataset.folder_id == LibraryFolder.id, not_(LibraryDataset.deleted), LibraryDataset.library_dataset_dataset_association_id.isnot(None))'),
+            lambda: LibraryDataset.folder_id == LibraryFolder.id
+            and LibraryDataset.library_dataset_dataset_association_id.isnot(None)
+        ),
         order_by=(lambda: asc(LibraryDataset._name)),
-        viewonly=True)
+        viewonly=True,
+    )
 
-    library_root = relationship('Library', back_populates='root_folder')
-    actions = relationship('LibraryFolderPermissions', back_populates='folder')
+    active_datasets = relationship(
+        "LibraryDataset",
+        primaryjoin=(
+            "and_(LibraryDataset.folder_id == LibraryFolder.id, not_(LibraryDataset.deleted), LibraryDataset.library_dataset_dataset_association_id.isnot(None))"
+        ),
+        order_by=(lambda: asc(LibraryDataset._name)),
+        viewonly=True,
+    )
 
-    dict_element_visible_keys = ['id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted']
+    library_root = relationship("Library", back_populates="root_folder")
+    actions = relationship("LibraryFolderPermissions", back_populates="folder")
+
+    dict_element_visible_keys = [
+        "id",
+        "parent_id",
+        "name",
+        "description",
+        "item_count",
+        "genome_build",
+        "update_time",
+        "deleted",
+    ]
 
     def __init__(self, name=None, description=None, item_count=0, order_id=None, genome_build=None):
         self.name = name or "Unnamed folder"
@@ -4607,7 +4836,7 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
         library_dataset.folder_id = self.id
         library_dataset.order_id = self.item_count
         self.item_count += 1
-        if genome_build not in [None, '?']:
+        if genome_build not in [None, "?"]:
             self.genome_build = genome_build
 
     def add_folder(self, folder):
@@ -4618,7 +4847,11 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
     @property
     def activatable_library_datasets(self):
         # This needs to be a list
-        return [ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted]
+        return [
+            ld
+            for ld in self.datasets
+            if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted
+        ]
 
     def _serialize(self, id_encoder, serialization_options):
         rval = dict_for(
@@ -4639,14 +4872,14 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
         datasets = []
         for dataset in self.datasets:
             datasets.append(dataset.serialize(id_encoder, serialization_options))
-        rval['datasets'] = datasets
+        rval["datasets"] = datasets
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        rval['library_path'] = self.library_path
-        rval['parent_library_id'] = self.parent_library.id
+        rval["library_path"] = self.library_path
+        rval["parent_library_id"] = self.parent_library.id
         return rval
 
     @property
@@ -4667,44 +4900,52 @@ class LibraryFolder(Base, Dictifiable, HasName, Serializable):
 
 
 class LibraryDataset(Base, Serializable):
-    __tablename__ = 'library_dataset'
+    __tablename__ = "library_dataset"
 
     id = Column(Integer, primary_key=True)
     # current version of dataset, if null, there is not a current version selected
-    library_dataset_dataset_association_id = Column(Integer,
-        ForeignKey('library_dataset_dataset_association.id',
-            use_alter=True, name='library_dataset_dataset_association_id_fk'),
-        nullable=True, index=True)
-    folder_id = Column(Integer, ForeignKey('library_folder.id'), index=True)
+    library_dataset_dataset_association_id = Column(
+        Integer,
+        ForeignKey(
+            "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk"
+        ),
+        nullable=True,
+        index=True,
+    )
+    folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
     # not currently being used, but for possible future use
     order_id = Column(Integer)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     # when not None/null this will supercede display in library (but not when imported into user's history?)
-    _name = Column('name', TrimmedString(255), index=True)
+    _name = Column("name", TrimmedString(255), index=True)
     # when not None/null this will supercede display in library (but not when imported into user's history?)
-    _info = Column('info', TrimmedString(255))
+    _info = Column("info", TrimmedString(255))
     deleted = Column(Boolean, index=True, default=False)
     purged = Column(Boolean, index=True, default=False)
-    folder = relationship('LibraryFolder')
-    library_dataset_dataset_association = relationship('LibraryDatasetDatasetAssociation',
-            foreign_keys=library_dataset_dataset_association_id,
-            post_update=True)
-    expired_datasets = relationship('LibraryDatasetDatasetAssociation',
+    folder = relationship("LibraryFolder")
+    library_dataset_dataset_association = relationship(
+        "LibraryDatasetDatasetAssociation", foreign_keys=library_dataset_dataset_association_id, post_update=True
+    )
+    expired_datasets = relationship(
+        "LibraryDatasetDatasetAssociation",
         foreign_keys=[id, library_dataset_dataset_association_id],
         primaryjoin=(
-            'and_(LibraryDataset.id == LibraryDatasetDatasetAssociation.library_dataset_id, \
-             not_(LibraryDataset.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.id))'
+            "and_(LibraryDataset.id == LibraryDatasetDatasetAssociation.library_dataset_id, \
+             not_(LibraryDataset.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.id))"
         ),
         viewonly=True,
-        uselist=True)
-    actions = relationship('LibraryDatasetPermissions', back_populates='library_dataset')
+        uselist=True,
+    )
+    actions = relationship("LibraryDatasetPermissions", back_populates="library_dataset")
 
     # This class acts as a proxy to the currently selected LDDA
-    upload_options = [('upload_file', 'Upload files'),
-                      ('upload_directory', 'Upload directory of files'),
-                      ('upload_paths', 'Upload files from filesystem paths'),
-                      ('import_from_history', 'Import datasets from your current history')]
+    upload_options = [
+        ("upload_file", "Upload files"),
+        ("upload_directory", "Upload directory of files"),
+        ("upload_paths", "Upload files from filesystem paths"),
+        ("import_from_history", "Import datasets from your current history"),
+    ]
 
     def get_info(self):
         if self.library_dataset_dataset_association:
@@ -4712,10 +4953,11 @@ class LibraryDataset(Base, Serializable):
         elif self._info:
             return self._info
         else:
-            return 'no info'
+            return "no info"
 
     def set_info(self, info):
         self._info = info
+
     info = property(get_info, set_info)
 
     def get_name(self):
@@ -4724,10 +4966,11 @@ class LibraryDataset(Base, Serializable):
         elif self._name:
             return self._name
         else:
-            return 'Unnamed dataset'
+            return "Unnamed dataset"
 
     def set_name(self, name):
         self._name = name
+
     name = property(get_name, set_name)
 
     def display_name(self):
@@ -4744,54 +4987,57 @@ class LibraryDataset(Base, Serializable):
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 
-    def to_dict(self, view='collection'):
+    def to_dict(self, view="collection"):
         # Since this class is a proxy to rather complex attributes we want to
         # display in other objects, we can't use the simpler method used by
         # other model classes.
         ldda = self.library_dataset_dataset_association
-        rval = dict(id=self.id,
-                    ldda_id=ldda.id,
-                    parent_library_id=self.folder.parent_library.id,
-                    folder_id=self.folder_id,
-                    model_class=self.__class__.__name__,
-                    state=ldda.state,
-                    name=ldda.name,
-                    file_name=ldda.file_name,
-                    created_from_basename=ldda.created_from_basename,
-                    uploaded_by=ldda.user and ldda.user.email,
-                    message=ldda.message,
-                    date_uploaded=ldda.create_time.isoformat(),
-                    update_time=ldda.update_time.isoformat(),
-                    file_size=int(ldda.get_size()),
-                    file_ext=ldda.ext,
-                    data_type=f"{ldda.datatype.__class__.__module__}.{ldda.datatype.__class__.__name__}",
-                    genome_build=ldda.dbkey,
-                    misc_info=ldda.info,
-                    misc_blurb=ldda.blurb,
-                    peek=(lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None)(ldda))
+        rval = dict(
+            id=self.id,
+            ldda_id=ldda.id,
+            parent_library_id=self.folder.parent_library.id,
+            folder_id=self.folder_id,
+            model_class=self.__class__.__name__,
+            state=ldda.state,
+            name=ldda.name,
+            file_name=ldda.file_name,
+            created_from_basename=ldda.created_from_basename,
+            uploaded_by=ldda.user and ldda.user.email,
+            message=ldda.message,
+            date_uploaded=ldda.create_time.isoformat(),
+            update_time=ldda.update_time.isoformat(),
+            file_size=int(ldda.get_size()),
+            file_ext=ldda.ext,
+            data_type=f"{ldda.datatype.__class__.__module__}.{ldda.datatype.__class__.__name__}",
+            genome_build=ldda.dbkey,
+            misc_info=ldda.info,
+            misc_blurb=ldda.blurb,
+            peek=(lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != "no peek" else None)(ldda),
+        )
         if ldda.dataset.uuid is None:
-            rval['uuid'] = None
+            rval["uuid"] = None
         else:
-            rval['uuid'] = str(ldda.dataset.uuid)
+            rval["uuid"] = str(ldda.dataset.uuid)
         for name in ldda.metadata.spec.keys():
             val = ldda.metadata.get(name)
             if isinstance(val, MetadataFile):
                 val = val.file_name
             elif isinstance(val, list):
-                val = ', '.join(str(v) for v in val)
+                val = ", ".join(str(v) for v in val)
             rval[f"metadata_{name}"] = val
         return rval
 
 
 class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
-
-    def __init__(self,
-                 copied_from_history_dataset_association=None,
-                 copied_from_library_dataset_dataset_association=None,
-                 library_dataset=None,
-                 user=None,
-                 sa_session=None,
-                 **kwd):
+    def __init__(
+        self,
+        copied_from_history_dataset_association=None,
+        copied_from_library_dataset_dataset_association=None,
+        library_dataset=None,
+        user=None,
+        sa_session=None,
+        **kwd,
+    ):
         # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
         # parameter in kwd is True so that the new object can be flushed.  Is there a better way?
         DatasetInstance.__init__(self, sa_session=sa_session, **kwd)
@@ -4804,19 +5050,21 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
 
     def to_history_dataset_association(self, target_history, parent_id=None, add_to_history=False, visible=None):
         sa_session = object_session(self)
-        hda = HistoryDatasetAssociation(name=self.name,
-                                        info=self.info,
-                                        blurb=self.blurb,
-                                        peek=self.peek,
-                                        tool_version=self.tool_version,
-                                        extension=self.extension,
-                                        dbkey=self.dbkey,
-                                        dataset=self.dataset,
-                                        visible=visible if visible is not None else self.visible,
-                                        deleted=self.deleted,
-                                        parent_id=parent_id,
-                                        copied_from_library_dataset_dataset_association=self,
-                                        history=target_history)
+        hda = HistoryDatasetAssociation(
+            name=self.name,
+            info=self.info,
+            blurb=self.blurb,
+            peek=self.peek,
+            tool_version=self.tool_version,
+            extension=self.extension,
+            dbkey=self.dbkey,
+            dataset=self.dataset,
+            visible=visible if visible is not None else self.visible,
+            deleted=self.deleted,
+            parent_id=parent_id,
+            copied_from_library_dataset_dataset_association=self,
+            history=target_history,
+        )
 
         tag_manager = galaxy.model.tags.GalaxyTagHandler(sa_session)
         src_ldda_tags = tag_manager.get_tags_str(self.tags)
@@ -4834,19 +5082,21 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
 
     def copy(self, parent_id=None, target_folder=None):
         sa_session = object_session(self)
-        ldda = LibraryDatasetDatasetAssociation(name=self.name,
-                                                info=self.info,
-                                                blurb=self.blurb,
-                                                peek=self.peek,
-                                                tool_version=self.tool_version,
-                                                extension=self.extension,
-                                                dbkey=self.dbkey,
-                                                dataset=self.dataset,
-                                                visible=self.visible,
-                                                deleted=self.deleted,
-                                                parent_id=parent_id,
-                                                copied_from_library_dataset_dataset_association=self,
-                                                folder=target_folder)
+        ldda = LibraryDatasetDatasetAssociation(
+            name=self.name,
+            info=self.info,
+            blurb=self.blurb,
+            peek=self.peek,
+            tool_version=self.tool_version,
+            extension=self.extension,
+            dbkey=self.dbkey,
+            dataset=self.dataset,
+            visible=self.visible,
+            deleted=self.deleted,
+            parent_id=parent_id,
+            copied_from_library_dataset_dataset_association=self,
+            folder=target_folder,
+        )
 
         tag_manager = galaxy.model.tags.GalaxyTagHandler(sa_session)
         src_ldda_tags = tag_manager.get_tags_str(self.tags)
@@ -4879,7 +5129,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
         self._handle_serialize_files(id_encoder, serialization_options, rval)
         return rval
 
-    def to_dict(self, view='collection'):
+    def to_dict(self, view="collection"):
         # Since this class is a proxy to rather complex attributes we want to
         # display in other objects, we can't use the simpler method used by
         # other model classes.
@@ -4890,30 +5140,32 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
             file_size = 0
 
         # TODO: render tags here
-        rval = dict(id=ldda.id,
-                    hda_ldda='ldda',
-                    model_class=self.__class__.__name__,
-                    name=ldda.name,
-                    deleted=ldda.deleted,
-                    visible=ldda.visible,
-                    state=ldda.state,
-                    library_dataset_id=ldda.library_dataset_id,
-                    file_size=file_size,
-                    file_name=ldda.file_name,
-                    update_time=ldda.update_time.isoformat(),
-                    file_ext=ldda.ext,
-                    data_type=f"{ldda.datatype.__class__.__module__}.{ldda.datatype.__class__.__name__}",
-                    genome_build=ldda.dbkey,
-                    misc_info=ldda.info,
-                    misc_blurb=ldda.blurb,
-                    created_from_basename=ldda.created_from_basename)
+        rval = dict(
+            id=ldda.id,
+            hda_ldda="ldda",
+            model_class=self.__class__.__name__,
+            name=ldda.name,
+            deleted=ldda.deleted,
+            visible=ldda.visible,
+            state=ldda.state,
+            library_dataset_id=ldda.library_dataset_id,
+            file_size=file_size,
+            file_name=ldda.file_name,
+            update_time=ldda.update_time.isoformat(),
+            file_ext=ldda.ext,
+            data_type=f"{ldda.datatype.__class__.__module__}.{ldda.datatype.__class__.__name__}",
+            genome_build=ldda.dbkey,
+            misc_info=ldda.info,
+            misc_blurb=ldda.blurb,
+            created_from_basename=ldda.created_from_basename,
+        )
         if ldda.dataset.uuid is None:
-            rval['uuid'] = None
+            rval["uuid"] = None
         else:
-            rval['uuid'] = str(ldda.dataset.uuid)
-        rval['parent_library_id'] = ldda.library_dataset.folder.parent_library.id
+            rval["uuid"] = str(ldda.dataset.uuid)
+        rval["parent_library_id"] = ldda.library_dataset.folder.parent_library.id
         if ldda.extended_metadata is not None:
-            rval['extended_metadata'] = ldda.extended_metadata.data
+            rval["extended_metadata"] = ldda.extended_metadata.data
         for name in ldda.metadata.spec.keys():
             val = ldda.metadata.get(name)
             if isinstance(val, MetadataFile):
@@ -4929,7 +5181,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
         ldda = self
 
         sql = text(
-            '''
+            """
                 WITH RECURSIVE parent_folders_of(folder_id) AS
                     (SELECT folder_id
                     FROM library_dataset
@@ -4945,32 +5197,34 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
                     WHERE id = :ldda_id)
                 WHERE exists (SELECT 1 FROM parent_folders_of
                     WHERE library_folder.id = parent_folders_of.folder_id)
-            ''').execution_options(autocommit=True)
-        ret = object_session(self).execute(sql, {'library_dataset_id': ldda.library_dataset_id, 'ldda_id': ldda.id})
+            """
+        ).execution_options(autocommit=True)
+        ret = object_session(self).execute(sql, {"library_dataset_id": ldda.library_dataset_id, "ldda_id": ldda.id})
         if ret.rowcount < 1:
-            log.warning(f'Attempt to updated parent folder times failed: {ret.rowcount} records updated.')
+            log.warning(f"Attempt to updated parent folder times failed: {ret.rowcount} records updated.")
 
 
 class ExtendedMetadata(Base, RepresentById):
-    __tablename__ = 'extended_metadata'
+    __tablename__ = "extended_metadata"
 
     id = Column(Integer, primary_key=True)
     data = Column(MutableJSONType)
-    children = relationship('ExtendedMetadataIndex', back_populates='extended_metadata')
+    children = relationship("ExtendedMetadataIndex", back_populates="extended_metadata")
 
     def __init__(self, data):
         self.data = data
 
 
 class ExtendedMetadataIndex(Base, RepresentById):
-    __tablename__ = 'extended_metadata_index'
+    __tablename__ = "extended_metadata_index"
 
     id = Column(Integer, primary_key=True)
-    extended_metadata_id = Column(Integer,
-        ForeignKey('extended_metadata.id', onupdate='CASCADE', ondelete='CASCADE'), index=True)
+    extended_metadata_id = Column(
+        Integer, ForeignKey("extended_metadata.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
+    )
     path = Column(String(255))
     value = Column(TEXT)
-    extended_metadata = relationship('ExtendedMetadata', back_populates='children')
+    extended_metadata = relationship("ExtendedMetadata", back_populates="children")
 
     def __init__(self, extended_metadata, path, value):
         self.extended_metadata = extended_metadata
@@ -4979,25 +5233,27 @@ class ExtendedMetadataIndex(Base, RepresentById):
 
 
 class LibraryInfoAssociation(Base, RepresentById):
-    __tablename__ = 'library_info_association'
+    __tablename__ = "library_info_association"
 
     id = Column(Integer, primary_key=True)
-    library_id = Column(Integer, ForeignKey('library.id'), index=True)
-    form_definition_id = Column(Integer, ForeignKey('form_definition.id'), index=True)
-    form_values_id = Column(Integer, ForeignKey('form_values.id'), index=True)
+    library_id = Column(Integer, ForeignKey("library.id"), index=True)
+    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
+    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
     inheritable = Column(Boolean, index=True, default=False)
     deleted = Column(Boolean, index=True, default=False)
 
-    library = relationship('Library',
+    library = relationship(
+        "Library",
         primaryjoin=(
-            lambda: and_(
-                LibraryInfoAssociation.library_id == Library.id,
-                not_(LibraryInfoAssociation.deleted))
-        ))
-    template = relationship('FormDefinition',
-        primaryjoin=lambda: LibraryInfoAssociation.form_definition_id == FormDefinition.id)
-    info = relationship('FormValues',
-        primaryjoin=lambda: LibraryInfoAssociation.form_values_id == FormValues.id)  # type: ignore[has-type]
+            lambda: and_(LibraryInfoAssociation.library_id == Library.id, not_(LibraryInfoAssociation.deleted))
+        ),
+    )
+    template = relationship(
+        "FormDefinition", primaryjoin=lambda: LibraryInfoAssociation.form_definition_id == FormDefinition.id
+    )
+    info = relationship(
+        "FormValues", primaryjoin=lambda: LibraryInfoAssociation.form_values_id == FormValues.id
+    )  # type: ignore[has-type]
 
     def __init__(self, library, form_definition, info, inheritable=False):
         self.library = library
@@ -5007,23 +5263,28 @@ class LibraryInfoAssociation(Base, RepresentById):
 
 
 class LibraryFolderInfoAssociation(Base, RepresentById):
-    __tablename__ = 'library_folder_info_association'
+    __tablename__ = "library_folder_info_association"
 
     id = Column(Integer, primary_key=True)
-    library_folder_id = Column(Integer, ForeignKey('library_folder.id'), nullable=True, index=True)
-    form_definition_id = Column(Integer, ForeignKey('form_definition.id'), index=True)
-    form_values_id = Column(Integer, ForeignKey('form_values.id'), index=True)
+    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), nullable=True, index=True)
+    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
+    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
     inheritable = Column(Boolean, index=True, default=False)
     deleted = Column(Boolean, index=True, default=False)
 
-    folder = relationship('LibraryFolder',
-        primaryjoin=(lambda:
-            (LibraryFolderInfoAssociation.library_folder_id == LibraryFolder.id)
-            & (not_(LibraryFolderInfoAssociation.deleted))))
-    template = relationship('FormDefinition',
-        primaryjoin=(lambda: LibraryFolderInfoAssociation.form_definition_id == FormDefinition.id))
-    info = relationship('FormValues',
-        primaryjoin=(lambda: LibraryFolderInfoAssociation.form_values_id == FormValues.id))  # type: ignore[has-type]
+    folder = relationship(
+        "LibraryFolder",
+        primaryjoin=(
+            lambda: (LibraryFolderInfoAssociation.library_folder_id == LibraryFolder.id)
+            & (not_(LibraryFolderInfoAssociation.deleted))
+        ),
+    )
+    template = relationship(
+        "FormDefinition", primaryjoin=(lambda: LibraryFolderInfoAssociation.form_definition_id == FormDefinition.id)
+    )
+    info = relationship(
+        "FormValues", primaryjoin=(lambda: LibraryFolderInfoAssociation.form_values_id == FormValues.id)
+    )  # type: ignore[has-type]
 
     def __init__(self, folder, form_definition, info, inheritable=False):
         self.folder = folder
@@ -5033,27 +5294,33 @@ class LibraryFolderInfoAssociation(Base, RepresentById):
 
 
 class LibraryDatasetDatasetInfoAssociation(Base, RepresentById):
-    __tablename__ = 'library_dataset_dataset_info_association'
+    __tablename__ = "library_dataset_dataset_info_association"
 
     id = Column(Integer, primary_key=True)
-    library_dataset_dataset_association_id = Column(Integer,
-        ForeignKey('library_dataset_dataset_association.id'), nullable=True, index=True)
-    form_definition_id = Column(Integer, ForeignKey('form_definition.id'), index=True)
-    form_values_id = Column(Integer, ForeignKey('form_values.id'), index=True)
+    library_dataset_dataset_association_id = Column(
+        Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True, index=True
+    )
+    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
+    form_values_id = Column(Integer, ForeignKey("form_values.id"), index=True)
     deleted = Column(Boolean, index=True, default=False)
 
-    library_dataset_dataset_association = relationship('LibraryDatasetDatasetAssociation',
-        primaryjoin=(lambda:
-            (LibraryDatasetDatasetInfoAssociation.library_dataset_dataset_association_id
-             == LibraryDatasetDatasetAssociation.id)
+    library_dataset_dataset_association = relationship(
+        "LibraryDatasetDatasetAssociation",
+        primaryjoin=(
+            lambda: (
+                LibraryDatasetDatasetInfoAssociation.library_dataset_dataset_association_id
+                == LibraryDatasetDatasetAssociation.id
+            )
             & (not_(LibraryDatasetDatasetInfoAssociation.deleted))
-        ))
-    template = relationship('FormDefinition',
-        primaryjoin=(lambda:
-            LibraryDatasetDatasetInfoAssociation.form_definition_id == FormDefinition.id))
-    info = relationship('FormValues',
-        primaryjoin=(lambda:
-            LibraryDatasetDatasetInfoAssociation.form_values_id == FormValues.id))  # type: ignore[has-type]
+        ),
+    )
+    template = relationship(
+        "FormDefinition",
+        primaryjoin=(lambda: LibraryDatasetDatasetInfoAssociation.form_definition_id == FormDefinition.id),
+    )
+    info = relationship(
+        "FormValues", primaryjoin=(lambda: LibraryDatasetDatasetInfoAssociation.form_values_id == FormValues.id)
+    )  # type: ignore[has-type]
 
     def __init__(self, library_dataset_dataset_association, form_definition, info):
         # TODO: need to figure out if this should be inheritable to the associated LibraryDataset
@@ -5067,51 +5334,58 @@ class LibraryDatasetDatasetInfoAssociation(Base, RepresentById):
 
 
 class ImplicitlyConvertedDatasetAssociation(Base, RepresentById):
-    __tablename__ = 'implicitly_converted_dataset_association'
+    __tablename__ = "implicitly_converted_dataset_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    hda_id = Column(Integer, ForeignKey('history_dataset_association.id'), index=True, nullable=True)
-    ldda_id = Column(Integer,
-        ForeignKey('library_dataset_dataset_association.id'), index=True, nullable=True)
-    hda_parent_id = Column(Integer, ForeignKey('history_dataset_association.id'), index=True)
-    ldda_parent_id = Column(Integer, ForeignKey('library_dataset_dataset_association.id'), index=True)
+    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True)
+    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
+    hda_parent_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    ldda_parent_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
     deleted = Column(Boolean, index=True, default=False)
     metadata_safe = Column(Boolean, index=True, default=True)
     type = Column(TrimmedString(255))
 
-    parent_hda = relationship('HistoryDatasetAssociation',
-        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_parent_id
-            == HistoryDatasetAssociation.id),
-        back_populates='implicitly_converted_datasets')
-    dataset_ldda = relationship('LibraryDatasetDatasetAssociation',
-        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.ldda_id
-            == LibraryDatasetDatasetAssociation.id),
-        back_populates='implicitly_converted_parent_datasets')
-    dataset = relationship('HistoryDatasetAssociation',
-        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_id
-            == HistoryDatasetAssociation.id),
-        back_populates='implicitly_converted_parent_datasets')
-    parent_ldda = relationship('LibraryDatasetDatasetAssociation',
-        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.ldda_parent_id
-            == LibraryDatasetDatasetAssociation.table.c.id),
-        back_populates='implicitly_converted_datasets')
+    parent_hda = relationship(
+        "HistoryDatasetAssociation",
+        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_parent_id == HistoryDatasetAssociation.id),
+        back_populates="implicitly_converted_datasets",
+    )
+    dataset_ldda = relationship(
+        "LibraryDatasetDatasetAssociation",
+        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.ldda_id == LibraryDatasetDatasetAssociation.id),
+        back_populates="implicitly_converted_parent_datasets",
+    )
+    dataset = relationship(
+        "HistoryDatasetAssociation",
+        primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_id == HistoryDatasetAssociation.id),
+        back_populates="implicitly_converted_parent_datasets",
+    )
+    parent_ldda = relationship(
+        "LibraryDatasetDatasetAssociation",
+        primaryjoin=(
+            lambda: ImplicitlyConvertedDatasetAssociation.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id
+        ),
+        back_populates="implicitly_converted_datasets",
+    )
 
-    def __init__(self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True):
+    def __init__(
+        self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True
+    ):
         self.id = id
         if isinstance(dataset, HistoryDatasetAssociation):
             self.dataset = dataset
         elif isinstance(dataset, LibraryDatasetDatasetAssociation):
             self.dataset_ldda = dataset
         else:
-            raise AttributeError(f'Unknown dataset type provided for dataset: {type(dataset)}')
+            raise AttributeError(f"Unknown dataset type provided for dataset: {type(dataset)}")
         if isinstance(parent, HistoryDatasetAssociation):
             self.parent_hda = parent
         elif isinstance(parent, LibraryDatasetDatasetAssociation):
             self.parent_ldda = parent
         else:
-            raise AttributeError(f'Unknown dataset type provided for parent: {type(parent)}')
+            raise AttributeError(f"Unknown dataset type provided for parent: {type(parent)}")
         self.type = file_type
         self.deleted = deleted
         self.purged = purged
@@ -5145,36 +5419,32 @@ class InnerCollectionFilter(NamedTuple):
 
 
 class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
-    __tablename__ = 'dataset_collection'
+    __tablename__ = "dataset_collection"
 
     id = Column(Integer, primary_key=True)
     collection_type = Column(Unicode(255), nullable=False)
-    populated_state = Column(TrimmedString(64), default='ok', nullable=False)
+    populated_state = Column(TrimmedString(64), default="ok", nullable=False)
     populated_state_message = Column(TEXT)
     element_count = Column(Integer, nullable=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
 
-    elements = relationship('DatasetCollectionElement',
+    elements = relationship(
+        "DatasetCollectionElement",
         primaryjoin=(lambda: DatasetCollection.id == DatasetCollectionElement.dataset_collection_id),  # type: ignore[has-type]
-        back_populates='collection',
-        order_by=lambda: DatasetCollectionElement.element_index)  # type: ignore[has-type]
+        back_populates="collection",
+        order_by=lambda: DatasetCollectionElement.element_index,
+    )  # type: ignore[has-type]
 
-    dict_collection_visible_keys = ['id', 'collection_type']
-    dict_element_visible_keys = ['id', 'collection_type']
+    dict_collection_visible_keys = ["id", "collection_type"]
+    dict_element_visible_keys = ["id", "collection_type"]
 
     class populated_states(str, Enum):
-        NEW = 'new'  # New dataset collection, unpopulated elements
-        OK = 'ok'  # Collection elements populated (HDAs may or may not have errors)
-        FAILED = 'failed'  # some problem populating state, won't be populated
+        NEW = "new"  # New dataset collection, unpopulated elements
+        OK = "ok"  # Collection elements populated (HDAs may or may not have errors)
+        FAILED = "failed"  # some problem populating state, won't be populated
 
-    def __init__(
-        self,
-        id=None,
-        collection_type=None,
-        populated=True,
-        element_count=None
-    ):
+    def __init__(self, id=None, collection_type=None, populated=True, element_count=None):
         self.id = id
         self.collection_type = collection_type
         if not populated:
@@ -5188,8 +5458,18 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         hda_attributes: Optional[Iterable[str]] = None,
         dataset_attributes: Optional[Iterable[str]] = None,
         dataset_permission_attributes: Optional[Iterable[str]] = None,
-        return_entities: Optional[Iterable[Union[Type[HistoryDatasetAssociation], Type[Dataset], Type[DatasetPermissions], Type['DatasetCollection'], Type['DatasetCollectionElement']]]] = None,
-        inner_filter: Optional[InnerCollectionFilter] = None
+        return_entities: Optional[
+            Iterable[
+                Union[
+                    Type[HistoryDatasetAssociation],
+                    Type[Dataset],
+                    Type[DatasetPermissions],
+                    Type["DatasetCollection"],
+                    Type["DatasetCollectionElement"],
+                ]
+            ]
+        ] = None,
+        inner_filter: Optional[InnerCollectionFilter] = None,
     ):
         collection_attributes = collection_attributes or ()
         element_attributes = element_attributes or ()
@@ -5210,22 +5490,21 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
             label_fragment = f"_{nesting_level}" if nesting_level is not None else ""
             return [getattr(column_collection, a).label(f"{a}{label_fragment}") for a in attributes]
 
-        q = db_session.query(
-            *attribute_columns(dce.c, element_attributes, nesting_level),
-            *attribute_columns(dc.c, collection_attributes, nesting_level),
-        ).select_from(
-            dce, dc
-        ).join(
-            dce, dce.c.dataset_collection_id == dc.c.id
-        ).filter(dc.c.id == dataset_collection.id)
-        while ':' in depth_collection_type:
+        q = (
+            db_session.query(
+                *attribute_columns(dce.c, element_attributes, nesting_level),
+                *attribute_columns(dc.c, collection_attributes, nesting_level),
+            )
+            .select_from(dce, dc)
+            .join(dce, dce.c.dataset_collection_id == dc.c.id)
+            .filter(dc.c.id == dataset_collection.id)
+        )
+        while ":" in depth_collection_type:
             nesting_level += 1
             inner_dc = alias(DatasetCollection)
             inner_dce = alias(DatasetCollectionElement)
             order_by_columns.append(inner_dce.c.element_index)
-            q = q.join(
-                inner_dc, inner_dc.c.id == dce.c.child_collection_id
-            ).outerjoin(
+            q = q.join(inner_dc, inner_dc.c.id == dce.c.child_collection_id).outerjoin(
                 inner_dce, inner_dce.c.dataset_collection_id == inner_dc.c.id
             )
             q = q.add_columns(
@@ -5238,16 +5517,20 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         if inner_filter:
             q = q.filter(inner_filter.produce_filter(dc.c))
 
-        if hda_attributes or dataset_attributes or dataset_permission_attributes or return_entities and not return_entities == (DatasetCollectionElement,):
+        if (
+            hda_attributes
+            or dataset_attributes
+            or dataset_permission_attributes
+            or return_entities
+            and not return_entities == (DatasetCollectionElement,)
+        ):
             q = q.join(HistoryDatasetAssociation).join(Dataset)
         if dataset_permission_attributes:
             q = q.join(DatasetPermissions)
-        q = q.add_columns(
-            *attribute_columns(HistoryDatasetAssociation, hda_attributes)
-        ).add_columns(
-            *attribute_columns(Dataset, dataset_attributes)
-        ).add_columns(
-            *attribute_columns(DatasetPermissions, dataset_permission_attributes)
+        q = (
+            q.add_columns(*attribute_columns(HistoryDatasetAssociation, hda_attributes))
+            .add_columns(*attribute_columns(Dataset, dataset_attributes))
+            .add_columns(*attribute_columns(DatasetPermissions, dataset_permission_attributes))
         )
         for entity in return_entities:
             q = q.add_entity(entity)
@@ -5257,11 +5540,8 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
 
     @property
     def dataset_states_and_extensions_summary(self):
-        if not hasattr(self, '_dataset_states_and_extensions_summary'):
-            q = self._get_nested_collection_attributes(
-                hda_attributes=('extension',),
-                dataset_attributes=('state',)
-            )
+        if not hasattr(self, "_dataset_states_and_extensions_summary"):
+            q = self._get_nested_collection_attributes(hda_attributes=("extension",), dataset_attributes=("state",))
             extensions = set()
             states = set()
             for extension, state in q:
@@ -5274,14 +5554,16 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
 
     @property
     def populated_optimized(self):
-        if not hasattr(self, '_populated_optimized'):
+        if not hasattr(self, "_populated_optimized"):
             _populated_optimized = True
             if ":" not in self.collection_type:
                 _populated_optimized = self.populated_state == DatasetCollection.populated_states.OK
             else:
                 q = self._get_nested_collection_attributes(
-                    collection_attributes=('populated_state',),
-                    inner_filter=InnerCollectionFilter('populated_state', operator.__ne__, DatasetCollection.populated_states.OK)
+                    collection_attributes=("populated_state",),
+                    inner_filter=InnerCollectionFilter(
+                        "populated_state", operator.__ne__, DatasetCollection.populated_states.OK
+                    ),
                 )
                 _populated_optimized = q.session.query(~exists(q.subquery())).scalar()
 
@@ -5298,10 +5580,8 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
 
     @property
     def dataset_action_tuples(self):
-        if not hasattr(self, '_dataset_action_tuples'):
-            q = self._get_nested_collection_attributes(
-                dataset_permission_attributes=('action', 'role_id')
-            )
+        if not hasattr(self, "_dataset_action_tuples"):
+            q = self._get_nested_collection_attributes(dataset_permission_attributes=("action", "role_id"))
             _dataset_action_tuples = []
             for _dataset_action_tuple in q:
                 if _dataset_action_tuple[0] is None:
@@ -5315,9 +5595,7 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
     @property
     def element_identifiers_extensions_and_paths(self):
         q = self._get_nested_collection_attributes(
-            element_attributes=('element_identifier',),
-            hda_attributes=('extension',),
-            return_entities=(Dataset,)
+            element_attributes=("element_identifier",), hda_attributes=("extension",), return_entities=(Dataset,)
         )
         return [(row[:-2], row.extension, row.Dataset.file_name) for row in q]
 
@@ -5328,9 +5606,9 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         results = []
         if object_session(self):
             q = self._get_nested_collection_attributes(
-                element_attributes=('element_identifier',),
-                hda_attributes=('extension',),
-                return_entities=(HistoryDatasetAssociation, Dataset)
+                element_attributes=("element_identifier",),
+                hda_attributes=("extension",),
+                return_entities=(HistoryDatasetAssociation, Dataset),
             )
             # element_identifiers, extension, path
             for row in q:
@@ -5342,7 +5620,14 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
             # This will be in a remote tool evaluation context, so can't query database
             for dataset_element in self.dataset_elements_and_identifiers():
                 # Let's pretend name is element identifier
-                results.append([dataset_element._identifiers, dataset_element.hda.extension, dataset_element.hda.file_name, dataset_element.hda.get_metadata_file_paths_and_extensions()])
+                results.append(
+                    [
+                        dataset_element._identifiers,
+                        dataset_element.hda.extension,
+                        dataset_element.hda.file_name,
+                        dataset_element.hda.get_metadata_file_paths_and_extensions(),
+                    ]
+                )
         return results
 
     @property
@@ -5425,7 +5710,7 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
     @property
     def state(self):
         # TODO: DatasetCollection state handling...
-        return 'ok'
+        return "ok"
 
     def validate(self):
         if self.collection_type is None:
@@ -5446,11 +5731,15 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         error_message = f"Dataset collection has no {get_by_attribute} with key {key}."
         raise KeyError(error_message)
 
-    def copy(self, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False):
-        new_collection = DatasetCollection(
-            collection_type=self.collection_type,
-            element_count=self.element_count
-        )
+    def copy(
+        self,
+        destination=None,
+        element_destination=None,
+        dataset_instance_attributes=None,
+        flush=True,
+        minimize_copies=False,
+    ):
+        new_collection = DatasetCollection(collection_type=self.collection_type, element_count=self.element_count)
         for element in self.elements:
             element.copy_to_collection(
                 new_collection,
@@ -5466,7 +5755,9 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         return new_collection
 
     def replace_failed_elements(self, replacements):
-        hda_id_to_element = dict(self._get_nested_collection_attributes(return_entities=[DatasetCollectionElement], hda_attributes=['id']))
+        hda_id_to_element = dict(
+            self._get_nested_collection_attributes(return_entities=[DatasetCollectionElement], hda_attributes=["id"])
+        )
         for failed, replacement in replacements.items():
             element = hda_id_to_element.get(failed.id)
             if element:
@@ -5486,14 +5777,13 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
             type=self.collection_type,
             populated_state=self.populated_state,
             populated_state_message=self.populated_state_message,
-            elements=list(map(lambda e: e.serialize(id_encoder, serialization_options), self.elements))
+            elements=list(map(lambda e: e.serialize(id_encoder, serialization_options), self.elements)),
         )
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 
 
 class DatasetCollectionInstance(HasName, UsesCreateAndUpdateTime):
-
     @property
     def state(self):
         return self.collection.state
@@ -5552,74 +5842,81 @@ class HistoryDatasetCollectionAssociation(
     UsesAnnotations,
     Serializable,
 ):
-    """ Associates a DatasetCollection with a History. """
-    __tablename__ = 'history_dataset_collection_association'
+    """Associates a DatasetCollection with a History."""
+
+    __tablename__ = "history_dataset_collection_association"
 
     id = Column(Integer, primary_key=True)
-    collection_id = Column(Integer, ForeignKey('dataset_collection.id'), index=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
+    collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
     name = Column(TrimmedString(255))
     hid = Column(Integer)
     visible = Column(Boolean)
     deleted = Column(Boolean, default=False)
-    copied_from_history_dataset_collection_association_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id'), nullable=True)
+    copied_from_history_dataset_collection_association_id = Column(
+        Integer, ForeignKey("history_dataset_collection_association.id"), nullable=True
+    )
     implicit_output_name = Column(Unicode(255), nullable=True)
-    job_id = Column(ForeignKey('job.id'), index=True, nullable=True)
-    implicit_collection_jobs_id = Column(
-        ForeignKey('implicit_collection_jobs.id'), index=True, nullable=True)
+    job_id = Column(ForeignKey("job.id"), index=True, nullable=True)
+    implicit_collection_jobs_id = Column(ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now, index=True)
 
-    collection = relationship('DatasetCollection')
-    history = relationship('History', back_populates='dataset_collections')
+    collection = relationship("DatasetCollection")
+    history = relationship("History", back_populates="dataset_collections")
 
     copied_from_history_dataset_collection_association = relationship(
-        'HistoryDatasetCollectionAssociation',
+        "HistoryDatasetCollectionAssociation",
         primaryjoin=copied_from_history_dataset_collection_association_id == id,
         remote_side=[id],
         uselist=False,
-        back_populates='copied_to_history_dataset_collection_association',
+        back_populates="copied_to_history_dataset_collection_association",
     )
     copied_to_history_dataset_collection_association = relationship(
-        'HistoryDatasetCollectionAssociation',
-        back_populates='copied_from_history_dataset_collection_association',
+        "HistoryDatasetCollectionAssociation",
+        back_populates="copied_from_history_dataset_collection_association",
     )
-    implicit_input_collections = relationship('ImplicitlyCreatedDatasetCollectionInput',
-        primaryjoin=(lambda: HistoryDatasetCollectionAssociation.id
-                == ImplicitlyCreatedDatasetCollectionInput.dataset_collection_id)
+    implicit_input_collections = relationship(
+        "ImplicitlyCreatedDatasetCollectionInput",
+        primaryjoin=(
+            lambda: HistoryDatasetCollectionAssociation.id
+            == ImplicitlyCreatedDatasetCollectionInput.dataset_collection_id
+        ),
     )
-    implicit_collection_jobs = relationship('ImplicitCollectionJobs', uselist=False)
+    implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False)
     job = relationship(
-        'Job',
-        back_populates='history_dataset_collection_associations',
+        "Job",
+        back_populates="history_dataset_collection_associations",
         uselist=False,
     )
-    job_state_summary = relationship(HistoryDatasetCollectionJobStateSummary,
-        primaryjoin=(lambda: HistoryDatasetCollectionAssociation.id
-            == HistoryDatasetCollectionJobStateSummary.__table__.c.hdca_id),
+    job_state_summary = relationship(
+        HistoryDatasetCollectionJobStateSummary,
+        primaryjoin=(
+            lambda: HistoryDatasetCollectionAssociation.id
+            == HistoryDatasetCollectionJobStateSummary.__table__.c.hdca_id
+        ),
         foreign_keys=HistoryDatasetCollectionJobStateSummary.__table__.c.hdca_id,
         uselist=False,
     )
     tags = relationship(
-        'HistoryDatasetCollectionTagAssociation',
+        "HistoryDatasetCollectionTagAssociation",
         order_by=lambda: HistoryDatasetCollectionTagAssociation.id,
-        back_populates='dataset_collection',
+        back_populates="dataset_collection",
     )
     annotations = relationship(
-        'HistoryDatasetCollectionAssociationAnnotationAssociation',
+        "HistoryDatasetCollectionAssociationAnnotationAssociation",
         order_by=lambda: HistoryDatasetCollectionAssociationAnnotationAssociation.id,
-        back_populates='history_dataset_collection',
+        back_populates="history_dataset_collection",
     )
     ratings = relationship(
-        'HistoryDatasetCollectionRatingAssociation',
+        "HistoryDatasetCollectionRatingAssociation",
         order_by=lambda: HistoryDatasetCollectionRatingAssociation.id,  # type: ignore[has-type]
-        back_populates='dataset_collection',
+        back_populates="dataset_collection",
     )
-    creating_job_associations = relationship('JobToOutputDatasetCollectionAssociation', viewonly=True)
+    creating_job_associations = relationship("JobToOutputDatasetCollectionAssociation", viewonly=True)
 
-    dict_dbkeysandextensions_visible_keys = ['dbkeys', 'extensions']
-    editable_keys = ('name', 'deleted', 'visible')
+    dict_dbkeysandextensions_visible_keys = ["dbkeys", "extensions"]
+    editable_keys = ("name", "deleted", "visible")
 
     def __init__(self, deleted=False, visible=True, **kwd):
         super().__init__(**kwd)
@@ -5635,16 +5932,15 @@ class HistoryDatasetCollectionAssociation(
         return "dataset_collection"
 
     # TODO: down into DatasetCollectionInstance
-    content_type = 'dataset_collection'
+    content_type = "dataset_collection"
 
     @hybrid.hybrid_property
     def type_id(self):
-        return '-'.join((self.content_type, str(self.id)))
+        return "-".join((self.content_type, str(self.id)))
 
     @type_id.expression  # type: ignore[no-redef]
     def type_id(cls):
-        return ((type_coerce(cls.content_type, Unicode) + '-'
-                 + type_coerce(cls.id, Unicode)).label('type_id'))
+        return (type_coerce(cls.content_type, Unicode) + "-" + type_coerce(cls.id, Unicode)).label("type_id")
 
     @property
     def job_source_type(self):
@@ -5657,13 +5953,13 @@ class HistoryDatasetCollectionAssociation(
 
     @property
     def dataset_dbkeys_and_extensions_summary(self):
-        if not hasattr(self, '_dataset_dbkeys_and_extensions_summary'):
-            rows = self.collection._get_nested_collection_attributes(hda_attributes=('_metadata', 'extension'))
+        if not hasattr(self, "_dataset_dbkeys_and_extensions_summary"):
+            rows = self.collection._get_nested_collection_attributes(hda_attributes=("_metadata", "extension"))
             extensions = set()
             dbkeys = set()
             for row in rows:
                 if row is not None:
-                    dbkey_field = row._metadata.get('dbkey')
+                    dbkey_field = row._metadata.get("dbkey")
                     if isinstance(dbkey_field, list):
                         for dbkey in dbkey_field:
                             dbkeys.add(dbkey)
@@ -5701,10 +5997,12 @@ class HistoryDatasetCollectionAssociation(
         implicit_input_collections = []
         for implicit_input_collection in self.implicit_input_collections:
             input_hdca = implicit_input_collection.input_dataset_collection
-            implicit_input_collections.append({
-                "name": implicit_input_collection.name,
-                "input_dataset_collection": serialization_options.get_identifier(id_encoder, input_hdca)
-            })
+            implicit_input_collections.append(
+                {
+                    "name": implicit_input_collection.name,
+                    "input_dataset_collection": serialization_options.get_identifier(id_encoder, input_hdca),
+                }
+            )
         if implicit_input_collections:
             rval["implicit_input_collections"] = implicit_input_collections
 
@@ -5713,18 +6011,22 @@ class HistoryDatasetCollectionAssociation(
         src_hdca = self
         while src_hdca.copied_from_history_dataset_collection_association:
             src_hdca = src_hdca.copied_from_history_dataset_collection_association
-            copied_from_history_dataset_collection_association_chain.append(serialization_options.get_identifier(id_encoder, src_hdca))
-        rval["copied_from_history_dataset_collection_association_id_chain"] = copied_from_history_dataset_collection_association_chain
+            copied_from_history_dataset_collection_association_chain.append(
+                serialization_options.get_identifier(id_encoder, src_hdca)
+            )
+        rval[
+            "copied_from_history_dataset_collection_association_id_chain"
+        ] = copied_from_history_dataset_collection_association_chain
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 
-    def to_dict(self, view='collection'):
+    def to_dict(self, view="collection"):
         original_dict_value = super().to_dict(view=view)
-        if (view == 'dbkeysandextensions'):
+        if view == "dbkeysandextensions":
             (dbkeys, extensions) = self.dataset_dbkeys_and_extensions_summary
             dict_value = dict(
                 dbkey=dbkeys.pop() if len(dbkeys) == 1 else "?",
-                extension=extensions.pop() if len(extensions) == 1 else "auto"
+                extension=extensions.pop() if len(extensions) == 1 else "auto",
             )
         else:
             dict_value = dict(
@@ -5737,7 +6039,7 @@ class HistoryDatasetCollectionAssociation(
                 job_source_type=self.job_source_type,
                 create_time=self.create_time.isoformat(),
                 update_time=self.update_time.isoformat(),
-                **self._base_to_dict(view=view)
+                **self._base_to_dict(view=view),
             )
 
         dict_value.update(original_dict_value)
@@ -5745,7 +6047,9 @@ class HistoryDatasetCollectionAssociation(
         return dict_value
 
     def add_implicit_input_collection(self, name, history_dataset_collection):
-        self.implicit_input_collections.append(ImplicitlyCreatedDatasetCollectionInput(name, history_dataset_collection))
+        self.implicit_input_collections.append(
+            ImplicitlyCreatedDatasetCollectionInput(name, history_dataset_collection)
+        )
 
     def find_implicit_input_collection(self, name):
         matching_collection = None
@@ -5755,7 +6059,14 @@ class HistoryDatasetCollectionAssociation(
                 break
         return matching_collection
 
-    def copy(self, element_destination=None, dataset_instance_attributes=None, flush=True, set_hid=True, minimize_copies=False):
+    def copy(
+        self,
+        element_destination=None,
+        dataset_instance_attributes=None,
+        flush=True,
+        set_hid=True,
+        minimize_copies=False,
+    ):
         """
         Create a copy of this history dataset collection association. Copy
         underlying collection.
@@ -5808,15 +6119,18 @@ class HistoryDatasetCollectionAssociation(
         HDCA = HistoryDatasetCollectionAssociation
 
         # non-recursive part of the cte (starting point)
-        parents_cte = Query(DCE.dataset_collection_id) \
-            .filter(or_(DCE.child_collection_id == collection_id, DCE.dataset_collection_id == collection_id)) \
+        parents_cte = (
+            Query(DCE.dataset_collection_id)
+            .filter(or_(DCE.child_collection_id == collection_id, DCE.dataset_collection_id == collection_id))
             .cte(name="element_parents", recursive="True")
+        )
         ep = aliased(parents_cte, name="ep")
 
         # add the recursive part of the cte expression
         dce = aliased(DCE, name="dce")
-        rec = Query(dce.dataset_collection_id.label('dataset_collection_id')) \
-            .filter(dce.child_collection_id == ep.c.dataset_collection_id)
+        rec = Query(dce.dataset_collection_id.label("dataset_collection_id")).filter(
+            dce.child_collection_id == ep.c.dataset_collection_id
+        )
         parents_cte = parents_cte.union(rec)
 
         # join parents to hdca, look for matching hdca_id
@@ -5829,29 +6143,36 @@ class HistoryDatasetCollectionAssociation(
 
 
 class LibraryDatasetCollectionAssociation(Base, DatasetCollectionInstance, RepresentById):
-    """ Associates a DatasetCollection with a library folder. """
-    __tablename__ = 'library_dataset_collection_association'
+    """Associates a DatasetCollection with a library folder."""
+
+    __tablename__ = "library_dataset_collection_association"
 
     id = Column(Integer, primary_key=True)
-    collection_id = Column(Integer, ForeignKey('dataset_collection.id'), index=True)
-    folder_id = Column(Integer, ForeignKey('library_folder.id'), index=True)
+    collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True)
+    folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
     name = Column(TrimmedString(255))
     deleted = Column(Boolean, default=False)
 
-    collection = relationship('DatasetCollection')
-    folder = relationship('LibraryFolder')
+    collection = relationship("DatasetCollection")
+    folder = relationship("LibraryFolder")
 
-    tags = relationship('LibraryDatasetCollectionTagAssociation',
+    tags = relationship(
+        "LibraryDatasetCollectionTagAssociation",
         order_by=lambda: LibraryDatasetCollectionTagAssociation.id,
-        back_populates='dataset_collection')
-    annotations = relationship('LibraryDatasetCollectionAnnotationAssociation',
+        back_populates="dataset_collection",
+    )
+    annotations = relationship(
+        "LibraryDatasetCollectionAnnotationAssociation",
         order_by=lambda: LibraryDatasetCollectionAnnotationAssociation.id,
-        back_populates="dataset_collection")
-    ratings = relationship('LibraryDatasetCollectionRatingAssociation',
+        back_populates="dataset_collection",
+    )
+    ratings = relationship(
+        "LibraryDatasetCollectionRatingAssociation",
         order_by=lambda: LibraryDatasetCollectionRatingAssociation.id,  # type: ignore[has-type]
-        back_populates="dataset_collection")
+        back_populates="dataset_collection",
+    )
 
-    editable_keys = ('name', 'deleted')
+    editable_keys = ("name", "deleted")
 
     def __init__(self, deleted=False, **kwd):
         super().__init__(**kwd)
@@ -5860,47 +6181,47 @@ class LibraryDatasetCollectionAssociation(Base, DatasetCollectionInstance, Repre
         # it is on instance instead of collection.
         self.deleted = deleted
 
-    def to_dict(self, view='collection'):
-        dict_value = dict(
-            folder_id=self.folder.id,
-            **self._base_to_dict(view=view)
-        )
+    def to_dict(self, view="collection"):
+        dict_value = dict(folder_id=self.folder.id, **self._base_to_dict(view=view))
         return dict_value
 
 
 class DatasetCollectionElement(Base, Dictifiable, Serializable):
-    """ Associates a DatasetInstance (hda or ldda) with a DatasetCollection. """
-    __tablename__ = 'dataset_collection_element'
+    """Associates a DatasetInstance (hda or ldda) with a DatasetCollection."""
+
+    __tablename__ = "dataset_collection_element"
 
     id = Column(Integer, primary_key=True)
     # Parent collection id describing what collection this element belongs to.
-    dataset_collection_id = Column(Integer,
-        ForeignKey('dataset_collection.id'), index=True, nullable=False)
+    dataset_collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True, nullable=False)
     # Child defined by this association - HDA, LDDA, or another dataset association...
-    hda_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True, nullable=True)
-    ldda_id = Column(Integer,
-        ForeignKey('library_dataset_dataset_association.id'), index=True, nullable=True)
-    child_collection_id = Column(Integer,
-        ForeignKey('dataset_collection.id'), index=True, nullable=True)
+    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True)
+    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
+    child_collection_id = Column(Integer, ForeignKey("dataset_collection.id"), index=True, nullable=True)
     # Element index and identifier to define this parent-child relationship.
     element_index = Column(Integer)
     element_identifier = Column(Unicode(255))
 
-    hda = relationship('HistoryDatasetAssociation',
-        primaryjoin=(lambda: DatasetCollectionElement.hda_id == HistoryDatasetAssociation.id))
-    ldda = relationship('LibraryDatasetDatasetAssociation',
-        primaryjoin=(lambda: DatasetCollectionElement.ldda_id == LibraryDatasetDatasetAssociation.id))
-    child_collection = relationship('DatasetCollection',
-        primaryjoin=(lambda: DatasetCollectionElement.child_collection_id == DatasetCollection.id))
-    collection = relationship('DatasetCollection',
+    hda = relationship(
+        "HistoryDatasetAssociation",
+        primaryjoin=(lambda: DatasetCollectionElement.hda_id == HistoryDatasetAssociation.id),
+    )
+    ldda = relationship(
+        "LibraryDatasetDatasetAssociation",
+        primaryjoin=(lambda: DatasetCollectionElement.ldda_id == LibraryDatasetDatasetAssociation.id),
+    )
+    child_collection = relationship(
+        "DatasetCollection", primaryjoin=(lambda: DatasetCollectionElement.child_collection_id == DatasetCollection.id)
+    )
+    collection = relationship(
+        "DatasetCollection",
         primaryjoin=(lambda: DatasetCollection.id == DatasetCollectionElement.dataset_collection_id),
-        back_populates='elements',
+        back_populates="elements",
     )
 
     # actionable dataset id needs to be available via API...
-    dict_collection_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
-    dict_element_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
+    dict_collection_visible_keys = ["id", "element_type", "element_index", "element_identifier"]
+    dict_element_visible_keys = ["id", "element_type", "element_index", "element_identifier"]
 
     UNINITIALIZED_ELEMENT = object()
 
@@ -5919,7 +6240,7 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):
         elif isinstance(element, DatasetCollection):
             self.child_collection = element
         elif element != self.UNINITIALIZED_ELEMENT:
-            raise AttributeError(f'Unknown element type provided: {type(element)}')
+            raise AttributeError(f"Unknown element type provided: {type(element)}")
 
         self.id = id
         self.collection = collection
@@ -5979,7 +6300,15 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):
         else:
             return [element_object]
 
-    def copy_to_collection(self, collection, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False):
+    def copy_to_collection(
+        self,
+        collection,
+        destination=None,
+        element_destination=None,
+        dataset_instance_attributes=None,
+        flush=True,
+        minimize_copies=False,
+    ):
         dataset_instance_attributes = dataset_instance_attributes or {}
         element_object = self.element_object
         if element_destination:
@@ -5995,7 +6324,11 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):
                 new_element_object = None
                 if minimize_copies:
                     new_element_object = element_destination.get_dataset_by_hid(element_object.hid)
-                if new_element_object and new_element_object.dataset and new_element_object.dataset.id == element_object.dataset_id:
+                if (
+                    new_element_object
+                    and new_element_object.dataset
+                    and new_element_object.dataset.id == element_object.dataset_id
+                ):
                     element_object = new_element_object
                 else:
                     new_element_object = element_object.copy(flush=flush, copy_tags=element_object.tags)
@@ -6024,7 +6357,7 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):
             self,
             element_type=self.element_type,
             element_index=self.element_index,
-            element_identifier=self.element_identifier
+            element_identifier=self.element_identifier,
         )
         serialization_options.attach_identifier(id_encoder, self, rval)
         element_obj = self.element_object
@@ -6036,33 +6369,33 @@ class DatasetCollectionElement(Base, Dictifiable, Serializable):
 
 
 class Event(Base, RepresentById):
-    __tablename__ = 'event'
+    __tablename__ = "event"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True, nullable=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True, nullable=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True, nullable=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
     message = Column(TrimmedString(1024))
-    session_id = Column(Integer, ForeignKey('galaxy_session.id'), index=True, nullable=True)
+    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True)
     tool_id = Column(String(255))
 
-    history = relationship('History')
-    user = relationship('User')
-    galaxy_session = relationship('GalaxySession')
+    history = relationship("History")
+    user = relationship("User")
+    galaxy_session = relationship("GalaxySession")
 
 
 class GalaxySession(Base, RepresentById):
-    __tablename__ = 'galaxy_session'
+    __tablename__ = "galaxy_session"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True, nullable=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
     remote_host = Column(String(255))
     remote_addr = Column(String(255))
     referer = Column(TEXT)
-    current_history_id = Column(Integer, ForeignKey('history.id'), nullable=True)
+    current_history_id = Column(Integer, ForeignKey("history.id"), nullable=True)
     # unique 128 bit random number coerced to a string
     session_key = Column(TrimmedString(255), index=True, unique=True)
     is_valid = Column(Boolean, default=False)
@@ -6070,9 +6403,9 @@ class GalaxySession(Base, RepresentById):
     prev_session_id = Column(Integer)
     disk_usage = Column(Numeric(15, 0), index=True)
     last_action = Column(DateTime)
-    current_history = relationship('History')
-    histories = relationship('GalaxySessionToHistoryAssociation', back_populates='galaxy_session')
-    user = relationship('User', back_populates='galaxy_sessions')
+    current_history = relationship("History")
+    histories = relationship("GalaxySessionToHistoryAssociation", back_populates="galaxy_session")
+    user = relationship("User", back_populates="galaxy_sessions")
 
     def __init__(self, is_valid=False, **kwd):
         super().__init__(**kwd)
@@ -6092,18 +6425,19 @@ class GalaxySession(Base, RepresentById):
 
     def set_disk_usage(self, bytes):
         self.disk_usage = bytes
+
     total_disk_usage = property(get_disk_usage, set_disk_usage)
 
 
 class GalaxySessionToHistoryAssociation(Base, RepresentById):
-    __tablename__ = 'galaxy_session_to_history'
+    __tablename__ = "galaxy_session_to_history"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    session_id = Column(Integer, ForeignKey('galaxy_session.id'), index=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    galaxy_session = relationship('GalaxySession', back_populates='histories')
-    history = relationship('History', back_populates='galaxy_sessions')
+    session_id = Column(Integer, ForeignKey("galaxy_session.id"), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    galaxy_session = relationship("GalaxySession", back_populates="histories")
+    history = relationship("History", back_populates="galaxy_sessions")
 
     def __init__(self, galaxy_session, history):
         self.galaxy_session = galaxy_session
@@ -6124,18 +6458,17 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
     Each time a workflow is modified a revision is created, represented by a new :class:`galaxy.model.Workflow` instance.
     See :class:`galaxy.model.Workflow` for more information
     """
-    __tablename__ = 'stored_workflow'
-    __table_args__ = (
-        Index('ix_stored_workflow_slug', 'slug', mysql_length=200),
-    )
+
+    __tablename__ = "stored_workflow"
+    __table_args__ = (Index("ix_stored_workflow_slug", "slug", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now, index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True, nullable=False)
-    latest_workflow_id = Column(Integer,
-        ForeignKey('workflow.id', use_alter=True, name='stored_workflow_latest_workflow_id_fk'),
-        index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    latest_workflow_id = Column(
+        Integer, ForeignKey("workflow.id", use_alter=True, name="stored_workflow_latest_workflow_id_fk"), index=True
+    )
     name = Column(TEXT)
     deleted = Column(Boolean, default=False)
     hidden = Column(Boolean, default=False)
@@ -6144,48 +6477,72 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
     from_path = Column(TEXT)
     published = Column(Boolean, index=True, default=False)
 
-    user = relationship('User',
-        primaryjoin=(lambda: User.id == StoredWorkflow.user_id),
-        back_populates='stored_workflows')
-    workflows = relationship('Workflow',
-        back_populates='stored_workflow',
+    user = relationship(
+        "User", primaryjoin=(lambda: User.id == StoredWorkflow.user_id), back_populates="stored_workflows"
+    )
+    workflows = relationship(
+        "Workflow",
+        back_populates="stored_workflow",
         cascade="all, delete-orphan",
         primaryjoin=(lambda: StoredWorkflow.id == Workflow.stored_workflow_id),  # type: ignore[has-type]
-        order_by=lambda: -Workflow.id)  # type: ignore[has-type]
-    latest_workflow = relationship('Workflow',
+        order_by=lambda: -Workflow.id,
+    )  # type: ignore[has-type]
+    latest_workflow = relationship(
+        "Workflow",
         post_update=True,
         primaryjoin=(lambda: StoredWorkflow.latest_workflow_id == Workflow.id),  # type: ignore[has-type]
-        lazy=False)
-    tags = relationship('StoredWorkflowTagAssociation',
+        lazy=False,
+    )
+    tags = relationship(
+        "StoredWorkflowTagAssociation",
         order_by=lambda: StoredWorkflowTagAssociation.id,
-        back_populates="stored_workflow")
-    owner_tags = relationship('StoredWorkflowTagAssociation',
-        primaryjoin=(lambda:
-            and_(StoredWorkflow.id == StoredWorkflowTagAssociation.stored_workflow_id,
-                StoredWorkflow.user_id == StoredWorkflowTagAssociation.user_id)
+        back_populates="stored_workflow",
+    )
+    owner_tags = relationship(
+        "StoredWorkflowTagAssociation",
+        primaryjoin=(
+            lambda: and_(
+                StoredWorkflow.id == StoredWorkflowTagAssociation.stored_workflow_id,
+                StoredWorkflow.user_id == StoredWorkflowTagAssociation.user_id,
+            )
         ),
         viewonly=True,
-        order_by=lambda: StoredWorkflowTagAssociation.id)
-    annotations = relationship('StoredWorkflowAnnotationAssociation',
+        order_by=lambda: StoredWorkflowTagAssociation.id,
+    )
+    annotations = relationship(
+        "StoredWorkflowAnnotationAssociation",
         order_by=lambda: StoredWorkflowAnnotationAssociation.id,
-        back_populates="stored_workflow")
-    ratings = relationship('StoredWorkflowRatingAssociation',
+        back_populates="stored_workflow",
+    )
+    ratings = relationship(
+        "StoredWorkflowRatingAssociation",
         order_by=lambda: StoredWorkflowRatingAssociation.id,  # type: ignore[has-type]
-        back_populates="stored_workflow")
-    users_shared_with = relationship('StoredWorkflowUserShareAssociation',
-        back_populates='stored_workflow')
+        back_populates="stored_workflow",
+    )
+    users_shared_with = relationship("StoredWorkflowUserShareAssociation", back_populates="stored_workflow")
 
     average_rating: column_property
 
     # Set up proxy so that
     #   StoredWorkflow.users_shared_with
     # returns a list of users that workflow is shared with.
-    users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+    users_shared_with_dot_users = association_proxy("users_shared_with", "user")
 
-    dict_collection_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', 'deleted', 'hidden']
-    dict_element_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', 'deleted', 'hidden']
+    dict_collection_visible_keys = ["id", "name", "create_time", "update_time", "published", "deleted", "hidden"]
+    dict_element_visible_keys = ["id", "name", "create_time", "update_time", "published", "deleted", "hidden"]
 
-    def __init__(self, user=None, name=None, slug=None, create_time=None, update_time=None, published=False, latest_workflow_id=None, workflow=None, hidden=False):
+    def __init__(
+        self,
+        user=None,
+        name=None,
+        slug=None,
+        create_time=None,
+        update_time=None,
+        published=False,
+        latest_workflow_id=None,
+        workflow=None,
+        hidden=False,
+    ):
         self.user = user
         self.name = name
         self.slug = slug
@@ -6205,10 +6562,14 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
 
     def show_in_tool_panel(self, user_id):
         sa_session = object_session(self)
-        return bool(sa_session.query(StoredWorkflowMenuEntry).filter(
-            StoredWorkflowMenuEntry.stored_workflow_id == self.id,
-            StoredWorkflowMenuEntry.user_id == user_id,
-        ).count())
+        return bool(
+            sa_session.query(StoredWorkflowMenuEntry)
+            .filter(
+                StoredWorkflowMenuEntry.stored_workflow_id == self.id,
+                StoredWorkflowMenuEntry.user_id == user_id,
+            )
+            .count()
+        )
 
     def copy_tags_from(self, target_user, source_workflow):
         # Override to only copy owner tags.
@@ -6217,9 +6578,11 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById):
             new_swta.user = target_user
             self.tags.append(new_swta)
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        rval['latest_workflow_uuid'] = (lambda uuid: str(uuid) if self.latest_workflow.uuid else None)(self.latest_workflow.uuid)
+        rval["latest_workflow_uuid"] = (lambda uuid: str(uuid) if self.latest_workflow.uuid else None)(
+            self.latest_workflow.uuid
+        )
         return rval
 
 
@@ -6230,14 +6593,15 @@ class Workflow(Base, Dictifiable, RepresentById):
 
     See :class:`galaxy.model.WorkflowStep` for more information
     """
-    __tablename__ = 'workflow'
+
+    __tablename__ = "workflow"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     # workflows will belong to either a stored workflow or a parent/nesting workflow.
-    stored_workflow_id = Column(Integer, ForeignKey('stored_workflow.id'), index=True, nullable=True)
-    parent_workflow_id = Column(Integer, ForeignKey('workflow.id'), index=True, nullable=True)
+    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True, nullable=True)
+    parent_workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=True)
     name = Column(TEXT)
     has_cycles = Column(Boolean)
     has_errors = Column(Boolean)
@@ -6246,25 +6610,30 @@ class Workflow(Base, Dictifiable, RepresentById):
     license = Column(TEXT)
     uuid = Column(UUIDType, nullable=True)
 
-    steps = relationship('WorkflowStep',
-        back_populates='workflow',
+    steps = relationship(
+        "WorkflowStep",
+        back_populates="workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),  # type: ignore[has-type]
         order_by=lambda: asc(WorkflowStep.order_index),  # type: ignore[has-type]
         cascade="all, delete-orphan",
-        lazy=False)
+        lazy=False,
+    )
     parent_workflow_steps = relationship(
-        'WorkflowStep',
+        "WorkflowStep",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.subworkflow_id),  # type: ignore[has-type]
-        back_populates='subworkflow')
-    stored_workflow = relationship('StoredWorkflow',
+        back_populates="subworkflow",
+    )
+    stored_workflow = relationship(
+        "StoredWorkflow",
         primaryjoin=(lambda: StoredWorkflow.id == Workflow.stored_workflow_id),
-        back_populates='workflows')
+        back_populates="workflows",
+    )
 
     step_count: column_property
 
-    dict_collection_visible_keys = ['name', 'has_cycles', 'has_errors']
-    dict_element_visible_keys = ['name', 'has_cycles', 'has_errors']
-    input_step_types = ['data_input', 'data_collection_input', 'parameter_input']
+    dict_collection_visible_keys = ["name", "has_cycles", "has_errors"]
+    dict_element_visible_keys = ["name", "has_cycles", "has_errors"]
+    input_step_types = ["data_input", "data_collection_input", "parameter_input"]
 
     def __init__(self, uuid=None):
         self.user = None
@@ -6279,9 +6648,9 @@ class Workflow(Base, Dictifiable, RepresentById):
                 return True
         return False
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        rval['uuid'] = (lambda uuid: str(uuid) if uuid else None)(self.uuid)
+        rval["uuid"] = (lambda uuid: str(uuid) if uuid else None)(self.uuid)
         return rval
 
     @property
@@ -6332,7 +6701,7 @@ class Workflow(Base, Dictifiable, RepresentById):
 
     @property
     def top_level_workflow(self):
-        """ If this workflow is not attached to stored workflow directly,
+        """If this workflow is not attached to stored workflow directly,
         recursively grab its parents until it is the top level workflow
         which must have a stored workflow associated with it.
         """
@@ -6345,7 +6714,7 @@ class Workflow(Base, Dictifiable, RepresentById):
 
     @property
     def top_level_stored_workflow(self):
-        """ If this workflow is not attached to stored workflow directly,
+        """If this workflow is not attached to stored workflow directly,
         recursively grab its parents until it is the top level workflow
         which must have a stored workflow associated with it and then
         grab that stored workflow.
@@ -6353,7 +6722,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         return self.top_level_workflow.stored_workflow
 
     def copy(self, user=None):
-        """ Copy a workflow for a new StoredWorkflow object.
+        """Copy a workflow for a new StoredWorkflow object.
 
         Pass user if user-specific information needed.
         """
@@ -6394,14 +6763,15 @@ class WorkflowStep(Base, RepresentById):
 
     See :class:`galaxy.model.WorkflowStepInput` and :class:`galaxy.model.WorkflowStepConnection` for more information.
     """
-    __tablename__ = 'workflow_step'
+
+    __tablename__ = "workflow_step"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    workflow_id = Column(Integer, ForeignKey('workflow.id'), index=True, nullable=False)
-    subworkflow_id = Column(Integer, ForeignKey('workflow.id'), index=True, nullable=True)
-    dynamic_tool_id = Column(Integer, ForeignKey('dynamic_tool.id'), index=True, nullable=True)
+    workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
+    subworkflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=True)
+    dynamic_tool_id = Column(Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True)
     type = Column(String(64))
     tool_id = Column(TEXT)
     tool_version = Column(TEXT)
@@ -6414,26 +6784,28 @@ class WorkflowStep(Base, RepresentById):
     label = Column(Unicode(255))
     temp_input_connections: Optional[InputConnDictType]
 
-    subworkflow = relationship('Workflow',
+    subworkflow = relationship(
+        "Workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.subworkflow_id),
-        back_populates='parent_workflow_steps')
-    dynamic_tool = relationship('DynamicTool',
-        primaryjoin=(lambda: DynamicTool.id == WorkflowStep.dynamic_tool_id))
-    tags = relationship('WorkflowStepTagAssociation',
-        order_by=lambda: WorkflowStepTagAssociation.id,
-        back_populates='workflow_step')
-    annotations = relationship('WorkflowStepAnnotationAssociation',
-        order_by=lambda: WorkflowStepAnnotationAssociation.id,
-        back_populates="workflow_step")
-    post_job_actions = relationship('PostJobAction', back_populates='workflow_step')
-    inputs = relationship('WorkflowStepInput', back_populates='workflow_step')
-    workflow_outputs = relationship('WorkflowOutput', back_populates='workflow_step')
-    output_connections = relationship('WorkflowStepConnection',
-        primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
+        back_populates="parent_workflow_steps",
     )
-    workflow = relationship('Workflow',
-        primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),
-        back_populates='steps'
+    dynamic_tool = relationship("DynamicTool", primaryjoin=(lambda: DynamicTool.id == WorkflowStep.dynamic_tool_id))
+    tags = relationship(
+        "WorkflowStepTagAssociation", order_by=lambda: WorkflowStepTagAssociation.id, back_populates="workflow_step"
+    )
+    annotations = relationship(
+        "WorkflowStepAnnotationAssociation",
+        order_by=lambda: WorkflowStepAnnotationAssociation.id,
+        back_populates="workflow_step",
+    )
+    post_job_actions = relationship("PostJobAction", back_populates="workflow_step")
+    inputs = relationship("WorkflowStepInput", back_populates="workflow_step")
+    workflow_outputs = relationship("WorkflowOutput", back_populates="workflow_step")
+    output_connections = relationship(
+        "WorkflowStepConnection", primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
+    )
+    workflow = relationship(
+        "Workflow", primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id), back_populates="steps"
     )
 
     STEP_TYPE_TO_INPUT_TYPE = {
@@ -6453,7 +6825,9 @@ class WorkflowStep(Base, RepresentById):
 
     @property
     def input_type(self):
-        assert self.type and self.type in self.STEP_TYPE_TO_INPUT_TYPE, "step.input_type can only be called on input step types"
+        assert (
+            self.type and self.type in self.STEP_TYPE_TO_INPUT_TYPE
+        ), "step.input_type can only be called on input step types"
         return self.STEP_TYPE_TO_INPUT_TYPE[self.type]
 
     @property
@@ -6597,10 +6971,12 @@ class WorkflowStep(Base, RepresentById):
             if old_conn.input_subworkflow_step_id:
                 new_conn.input_subworkflow_step = subworkflow_step_mapping[old_conn.input_subworkflow_step_id]
         for orig_pja in self.post_job_actions:
-            PostJobAction(orig_pja.action_type,
-                          copied_step,
-                          output_name=orig_pja.output_name,
-                          action_arguments=orig_pja.action_arguments)
+            PostJobAction(
+                orig_pja.action_type,
+                copied_step,
+                output_name=orig_pja.output_name,
+                action_arguments=orig_pja.action_arguments,
+            )
         copied_step.workflow_outputs = copy_list(self.workflow_outputs, copied_step)
 
     def log_str(self):
@@ -6617,14 +6993,19 @@ class WorkflowStep(Base, RepresentById):
 
 
 class WorkflowStepInput(Base, RepresentById):
-    __tablename__ = 'workflow_step_input'
+    __tablename__ = "workflow_step_input"
     __table_args__ = (
-        Index('ix_workflow_step_input_workflow_step_id_name_unique',
-            'workflow_step_id', 'name', unique=True, mysql_length={'name': 200}),
+        Index(
+            "ix_workflow_step_input_workflow_step_id_name_unique",
+            "workflow_step_id",
+            "name",
+            unique=True,
+            mysql_length={"name": 200},
+        ),
     )
 
     id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
     name = Column(TEXT)
     merge_type = Column(TEXT)
     scatter_type = Column(TEXT)
@@ -6634,14 +7015,17 @@ class WorkflowStepInput(Base, RepresentById):
     default_value_set = Column(Boolean, default=False)
     runtime_value = Column(Boolean, default=False)
 
-    workflow_step = relationship('WorkflowStep',
-        back_populates='inputs',
-        cascade='all',
-        primaryjoin=(lambda: WorkflowStepInput.workflow_step_id == WorkflowStep.id))
+    workflow_step = relationship(
+        "WorkflowStep",
+        back_populates="inputs",
+        cascade="all",
+        primaryjoin=(lambda: WorkflowStepInput.workflow_step_id == WorkflowStep.id),
+    )
     connections = relationship(
-        'WorkflowStepConnection',
-        back_populates='input_step_input',
-        primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id))
+        "WorkflowStepConnection",
+        back_populates="input_step_input",
+        primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),
+    )
 
     def __init__(self, workflow_step):
         self.workflow_step = workflow_step
@@ -6660,24 +7044,29 @@ class WorkflowStepInput(Base, RepresentById):
 
 
 class WorkflowStepConnection(Base, RepresentById):
-    __tablename__ = 'workflow_step_connection'
+    __tablename__ = "workflow_step_connection"
 
     id = Column(Integer, primary_key=True)
-    output_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True)
-    input_step_input_id = Column(Integer, ForeignKey('workflow_step_input.id'), index=True)
+    output_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
+    input_step_input_id = Column(Integer, ForeignKey("workflow_step_input.id"), index=True)
     output_name = Column(TEXT)
-    input_subworkflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True)
+    input_subworkflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
 
-    input_step_input = relationship('WorkflowStepInput',
-        back_populates='connections',
-        cascade='all',
-        primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id))
-    input_subworkflow_step = relationship('WorkflowStep',
-        primaryjoin=(lambda: WorkflowStepConnection.input_subworkflow_step_id == WorkflowStep.id))
-    output_step = relationship('WorkflowStep',
-        back_populates='output_connections',
-        cascade='all',
-        primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id))
+    input_step_input = relationship(
+        "WorkflowStepInput",
+        back_populates="connections",
+        cascade="all",
+        primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),
+    )
+    input_subworkflow_step = relationship(
+        "WorkflowStep", primaryjoin=(lambda: WorkflowStepConnection.input_subworkflow_step_id == WorkflowStep.id)
+    )
+    output_step = relationship(
+        "WorkflowStep",
+        back_populates="output_connections",
+        cascade="all",
+        primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id),
+    )
 
     # Constant used in lieu of output_name and input_name to indicate an
     # implicit connection between two steps that is not dependent on a dataset
@@ -6688,7 +7077,7 @@ class WorkflowStepConnection(Base, RepresentById):
 
     @property
     def non_data_connection(self):
-        return (self.output_name == self.input_name == WorkflowStepConnection.NON_DATA_CONNECTION)
+        return self.output_name == self.input_name == WorkflowStepConnection.NON_DATA_CONNECTION
 
     @property
     def input_name(self):
@@ -6711,16 +7100,18 @@ class WorkflowStepConnection(Base, RepresentById):
 
 
 class WorkflowOutput(Base, RepresentById):
-    __tablename__ = 'workflow_output'
+    __tablename__ = "workflow_output"
 
     id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True, nullable=False)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=False)
     output_name = Column(String(255), nullable=True)
     label = Column(Unicode(255))
     uuid = Column(UUIDType)
-    workflow_step = relationship('WorkflowStep',
-        back_populates='workflow_outputs',
-        primaryjoin=(lambda: WorkflowStep.id == WorkflowOutput.workflow_step_id))
+    workflow_step = relationship(
+        "WorkflowStep",
+        back_populates="workflow_outputs",
+        primaryjoin=(lambda: WorkflowStep.id == WorkflowOutput.workflow_step_id),
+    )
 
     def __init__(self, workflow_step, output_name=None, label=None, uuid=None):
         self.workflow_step = workflow_step
@@ -6736,79 +7127,81 @@ class WorkflowOutput(Base, RepresentById):
 
 
 class StoredWorkflowUserShareAssociation(Base, UserShareAssociation):
-    __tablename__ = 'stored_workflow_user_share_connection'
+    __tablename__ = "stored_workflow_user_share_connection"
 
     id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey('stored_workflow.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    user = relationship('User')
-    stored_workflow = relationship('StoredWorkflow', back_populates='users_shared_with')
+    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user = relationship("User")
+    stored_workflow = relationship("StoredWorkflow", back_populates="users_shared_with")
 
 
 class StoredWorkflowMenuEntry(Base, RepresentById):
-    __tablename__ = 'stored_workflow_menu_entry'
+    __tablename__ = "stored_workflow_menu_entry"
 
     id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey('stored_workflow.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     order_index = Column(Integer)
 
-    stored_workflow = relationship('StoredWorkflow')
-    user = relationship('User', back_populates='stored_workflow_menu_entries',
-        primaryjoin=(lambda:
-            (StoredWorkflowMenuEntry.user_id == User.id)
+    stored_workflow = relationship("StoredWorkflow")
+    user = relationship(
+        "User",
+        back_populates="stored_workflow_menu_entries",
+        primaryjoin=(
+            lambda: (StoredWorkflowMenuEntry.user_id == User.id)
             & (StoredWorkflowMenuEntry.stored_workflow_id == StoredWorkflow.id)
-            & not_(StoredWorkflow.deleted))
+            & not_(StoredWorkflow.deleted)
+        ),
     )
 
 
 class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
-    __tablename__ = 'workflow_invocation'
+    __tablename__ = "workflow_invocation"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now, index=True)
-    workflow_id = Column(Integer, ForeignKey('workflow.id'), index=True, nullable=False)
+    workflow_id = Column(Integer, ForeignKey("workflow.id"), index=True, nullable=False)
     state = Column(TrimmedString(64), index=True)
     scheduler = Column(TrimmedString(255), index=True)
     handler = Column(TrimmedString(255), index=True)
     uuid = Column(UUIDType())
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
 
-    history = relationship('History', back_populates='workflow_invocations')
-    input_parameters = relationship('WorkflowRequestInputParameter',
-        back_populates='workflow_invocation')
-    step_states = relationship('WorkflowRequestStepState', back_populates='workflow_invocation')
-    input_step_parameters = relationship('WorkflowRequestInputStepParameter',
-        back_populates='workflow_invocation')
-    input_datasets = relationship('WorkflowRequestToInputDatasetAssociation',
-        back_populates='workflow_invocation')
-    input_dataset_collections = relationship('WorkflowRequestToInputDatasetCollectionAssociation',
-        back_populates='workflow_invocation')
-    subworkflow_invocations = relationship('WorkflowInvocationToSubworkflowInvocationAssociation',
-        primaryjoin=(lambda:
-            WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id
-                == WorkflowInvocation.id),
-        back_populates='parent_workflow_invocation',
+    history = relationship("History", back_populates="workflow_invocations")
+    input_parameters = relationship("WorkflowRequestInputParameter", back_populates="workflow_invocation")
+    step_states = relationship("WorkflowRequestStepState", back_populates="workflow_invocation")
+    input_step_parameters = relationship("WorkflowRequestInputStepParameter", back_populates="workflow_invocation")
+    input_datasets = relationship("WorkflowRequestToInputDatasetAssociation", back_populates="workflow_invocation")
+    input_dataset_collections = relationship(
+        "WorkflowRequestToInputDatasetCollectionAssociation", back_populates="workflow_invocation"
+    )
+    subworkflow_invocations = relationship(
+        "WorkflowInvocationToSubworkflowInvocationAssociation",
+        primaryjoin=(
+            lambda: WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id == WorkflowInvocation.id
+        ),
+        back_populates="parent_workflow_invocation",
         uselist=True,
     )
-    steps = relationship('WorkflowInvocationStep', back_populates='workflow_invocation')
-    workflow = relationship('Workflow')
-    output_dataset_collections = relationship('WorkflowInvocationOutputDatasetCollectionAssociation',
-        back_populates='workflow_invocation')
-    output_datasets = relationship('WorkflowInvocationOutputDatasetAssociation',
-        back_populates='workflow_invocation')
-    output_values = relationship('WorkflowInvocationOutputValue', back_populates='workflow_invocation')
+    steps = relationship("WorkflowInvocationStep", back_populates="workflow_invocation")
+    workflow = relationship("Workflow")
+    output_dataset_collections = relationship(
+        "WorkflowInvocationOutputDatasetCollectionAssociation", back_populates="workflow_invocation"
+    )
+    output_datasets = relationship("WorkflowInvocationOutputDatasetAssociation", back_populates="workflow_invocation")
+    output_values = relationship("WorkflowInvocationOutputValue", back_populates="workflow_invocation")
 
-    dict_collection_visible_keys = ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']
-    dict_element_visible_keys = ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']
+    dict_collection_visible_keys = ["id", "update_time", "create_time", "workflow_id", "history_id", "uuid", "state"]
+    dict_element_visible_keys = ["id", "update_time", "create_time", "workflow_id", "history_id", "uuid", "state"]
 
     class states(str, Enum):
-        NEW = 'new'  # Brand new workflow invocation... maybe this should be same as READY
-        READY = 'ready'  # Workflow ready for another iteration of scheduling.
-        SCHEDULED = 'scheduled'  # Workflow has been scheduled.
-        CANCELLED = 'cancelled'
-        FAILED = 'failed'
+        NEW = "new"  # Brand new workflow invocation... maybe this should be same as READY
+        READY = "ready"  # Workflow ready for another iteration of scheduling.
+        SCHEDULED = "scheduled"  # Workflow has been scheduled.
+        CANCELLED = "cancelled"
+        FAILED = "failed"
 
     non_terminal_states = [states.NEW, states.READY]
 
@@ -6844,7 +7237,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
 
     @property
     def active(self):
-        """ Indicates the workflow invocation is somehow active - and in
+        """Indicates the workflow invocation is somehow active - and in
         particular valid actions may be performed on its
         WorkflowInvocationSteps.
         """
@@ -6894,23 +7287,21 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
     def poll_unhandled_workflow_ids(sa_session):
         and_conditions = [
             WorkflowInvocation.state == WorkflowInvocation.states.NEW,
-            WorkflowInvocation.handler.is_(None)
+            WorkflowInvocation.handler.is_(None),
         ]
-        query = sa_session.query(
-            WorkflowInvocation.id
-        ).filter(and_(*and_conditions)).order_by(WorkflowInvocation.table.c.id.asc())
+        query = (
+            sa_session.query(WorkflowInvocation.id)
+            .filter(and_(*and_conditions))
+            .order_by(WorkflowInvocation.table.c.id.asc())
+        )
         return [wid for wid in query.all()]
 
     @staticmethod
-    def poll_active_workflow_ids(
-        sa_session,
-        scheduler=None,
-        handler=None
-    ):
+    def poll_active_workflow_ids(sa_session, scheduler=None, handler=None):
         and_conditions = [
             or_(
                 WorkflowInvocation.state == WorkflowInvocation.states.NEW,
-                WorkflowInvocation.state == WorkflowInvocation.states.READY
+                WorkflowInvocation.state == WorkflowInvocation.states.READY,
             ),
         ]
         if scheduler is not None:
@@ -6918,9 +7309,11 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
         if handler is not None:
             and_conditions.append(WorkflowInvocation.handler == handler)
 
-        query = sa_session.query(
-            WorkflowInvocation.id
-        ).filter(and_(*and_conditions)).order_by(WorkflowInvocation.table.c.id.asc())
+        query = (
+            sa_session.query(WorkflowInvocation.id)
+            .filter(and_(*and_conditions))
+            .order_by(WorkflowInvocation.table.c.id.asc())
+        )
         # Immediately just load all ids into memory so time slicing logic
         # is relatively intutitive.
         return [wid for wid in query.all()]
@@ -6963,9 +7356,13 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
         # That probably isn't good.
         workflow_output = self.workflow.workflow_output_for(label)
         if workflow_output:
-            raise Exception(f"Failed to find workflow output named [{label}], one was defined but none registered during execution.")
+            raise Exception(
+                f"Failed to find workflow output named [{label}], one was defined but none registered during execution."
+            )
         else:
-            raise Exception(f"Failed to find workflow output named [{label}], workflow doesn't define output by that name - valid names are {self.workflow.workflow_output_labels}.")
+            raise Exception(
+                f"Failed to find workflow output named [{label}], workflow doesn't define output by that name - valid names are {self.workflow.workflow_output_labels}."
+            )
 
     def get_input_object(self, label):
         for input_dataset_assoc in self.input_datasets:
@@ -6994,15 +7391,15 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
             inputs.append(input_dataset_collection_assoc)
         return inputs
 
-    def to_dict(self, view='collection', value_mapper=None, step_details=False, legacy_job_state=False):
+    def to_dict(self, view="collection", value_mapper=None, step_details=False, legacy_job_state=False):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        if view == 'element':
+        if view == "element":
             steps = []
             for step in self.steps:
                 if step_details:
-                    v = step.to_dict(view='element')
+                    v = step.to_dict(view="element")
                 else:
-                    v = step.to_dict(view='collection')
+                    v = step.to_dict(view="collection")
                 if legacy_job_state:
                     step_jobs = step.jobs
                     if step_jobs:
@@ -7016,28 +7413,28 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
                         steps.append(v)
                 else:
                     steps.append(v)
-            rval['steps'] = steps
+            rval["steps"] = steps
 
             inputs = {}
             for input_item_association in self.input_datasets + self.input_dataset_collections:
-                if input_item_association.history_content_type == 'dataset':
-                    src = 'hda'
+                if input_item_association.history_content_type == "dataset":
+                    src = "hda"
                     item = input_item_association.dataset
-                elif input_item_association.history_content_type == 'dataset_collection':
-                    src = 'hdca'
+                elif input_item_association.history_content_type == "dataset_collection":
+                    src = "hdca"
                     item = input_item_association.dataset_collection
                 else:
                     # TODO: LDDAs are not implemented in workflow_request_to_input_dataset table
                     raise Exception(f"Unknown history content type '{input_item_association.history_content_type}'")
                 # Should this maybe also be by label ? Would break backwards compatibility though
                 inputs[str(input_item_association.workflow_step.order_index)] = {
-                    'id': item.id,
-                    'src': src,
-                    'label': input_item_association.workflow_step.label,
-                    'workflow_step_id': input_item_association.workflow_step_id,
+                    "id": item.id,
+                    "src": src,
+                    "label": input_item_association.workflow_step.label,
+                    "workflow_step_id": input_item_association.workflow_step_id,
                 }
 
-            rval['inputs'] = inputs
+            rval["inputs"] = inputs
 
             input_parameters = {}
             for input_step_parameter in self.input_step_parameters:
@@ -7045,11 +7442,11 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
                 if not label:
                     continue
                 input_parameters[label] = {
-                    'parameter_value': input_step_parameter.parameter_value,
-                    'label': label,
-                    'workflow_step_id': input_step_parameter.workflow_step_id,
+                    "parameter_value": input_step_parameter.parameter_value,
+                    "label": label,
+                    "workflow_step_id": input_step_parameter.workflow_step_id,
                 }
-            rval['input_step_parameters'] = input_parameters
+            rval["input_step_parameters"] = input_parameters
 
             outputs = {}
             for output_assoc in self.output_datasets:
@@ -7059,9 +7456,9 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
                     continue
 
                 outputs[label] = {
-                    'src': 'hda',
-                    'id': output_assoc.dataset_id,
-                    'workflow_step_id': output_assoc.workflow_step_id,
+                    "src": "hda",
+                    "id": output_assoc.dataset_id,
+                    "workflow_step_id": output_assoc.workflow_step_id,
                 }
 
             output_collections = {}
@@ -7071,13 +7468,13 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
                     continue
 
                 output_collections[label] = {
-                    'src': 'hdca',
-                    'id': output_assoc.dataset_collection_id,
-                    'workflow_step_id': output_assoc.workflow_step_id,
+                    "src": "hdca",
+                    "id": output_assoc.dataset_collection_id,
+                    "workflow_step_id": output_assoc.workflow_step_id,
                 }
 
-            rval['outputs'] = outputs
-            rval['output_collections'] = output_collections
+            rval["outputs"] = outputs
+            rval["output_collections"] = output_collections
 
             output_values = {}
             for output_param in self.output_values:
@@ -7085,7 +7482,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
                 if not label:
                     continue
                 output_values[label] = output_param.value
-            rval['output_values'] = output_values
+            rval["output_values"] = output_values
 
         return rval
 
@@ -7148,78 +7545,95 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, RepresentBy
 
 
 class WorkflowInvocationToSubworkflowInvocationAssociation(Base, Dictifiable, RepresentById):
-    __tablename__ = 'workflow_invocation_to_subworkflow_invocation_association'
+    __tablename__ = "workflow_invocation_to_subworkflow_invocation_association"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer,
-        ForeignKey('workflow_invocation.id', name='fk_wfi_swi_wfi'), index=True)
-    subworkflow_invocation_id = Column(Integer,
-        ForeignKey('workflow_invocation.id', name='fk_wfi_swi_swi'), index=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id', name='fk_wfi_swi_ws'))
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id", name="fk_wfi_swi_wfi"), index=True)
+    subworkflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id", name="fk_wfi_swi_swi"), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id", name="fk_wfi_swi_ws"))
 
-    subworkflow_invocation = relationship('WorkflowInvocation',
-        primaryjoin=(lambda:
-            WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id
-                == WorkflowInvocation.id),
+    subworkflow_invocation = relationship(
+        "WorkflowInvocation",
+        primaryjoin=(
+            lambda: WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id
+            == WorkflowInvocation.id
+        ),
         uselist=False,
     )
-    workflow_step = relationship('WorkflowStep')
-    parent_workflow_invocation = relationship('WorkflowInvocation',
-        primaryjoin=(lambda:
-            WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id
-                == WorkflowInvocation.id),
-        back_populates='subworkflow_invocations',
+    workflow_step = relationship("WorkflowStep")
+    parent_workflow_invocation = relationship(
+        "WorkflowInvocation",
+        primaryjoin=(
+            lambda: WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id == WorkflowInvocation.id
+        ),
+        back_populates="subworkflow_invocations",
         uselist=False,
     )
-    dict_collection_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']
-    dict_element_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']
+    dict_collection_visible_keys = ["id", "workflow_step_id", "workflow_invocation_id", "subworkflow_invocation_id"]
+    dict_element_visible_keys = ["id", "workflow_step_id", "workflow_invocation_id", "subworkflow_invocation_id"]
 
 
 class WorkflowInvocationStep(Base, Dictifiable, RepresentById):
-    __tablename__ = 'workflow_invocation_step'
+    __tablename__ = "workflow_invocation_step"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    workflow_invocation_id = Column(Integer,
-        ForeignKey('workflow_invocation.id'), index=True, nullable=False)
-    workflow_step_id = Column(Integer,
-        ForeignKey('workflow_step.id'), index=True, nullable=False)
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True, nullable=False)
     state = Column(TrimmedString(64), index=True)
-    job_id = Column(Integer, ForeignKey('job.id'), index=True, nullable=True)
-    implicit_collection_jobs_id = Column(Integer,
-        ForeignKey('implicit_collection_jobs.id'), index=True, nullable=True)
+    job_id = Column(Integer, ForeignKey("job.id"), index=True, nullable=True)
+    implicit_collection_jobs_id = Column(Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True)
     action = Column(MutableJSONType, nullable=True)
 
-    workflow_step = relationship('WorkflowStep')
-    job = relationship('Job', back_populates='workflow_invocation_step', uselist=False)
-    implicit_collection_jobs = relationship('ImplicitCollectionJobs', uselist=False)
+    workflow_step = relationship("WorkflowStep")
+    job = relationship("Job", back_populates="workflow_invocation_step", uselist=False)
+    implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False)
     output_dataset_collections = relationship(
-        'WorkflowInvocationStepOutputDatasetCollectionAssociation',
-        back_populates='workflow_invocation_step')
-    output_datasets = relationship('WorkflowInvocationStepOutputDatasetAssociation',
-        back_populates='workflow_invocation_step')
-    workflow_invocation = relationship('WorkflowInvocation', back_populates='steps')
-    output_value = relationship('WorkflowInvocationOutputValue',
-        foreign_keys='[WorkflowInvocationStep.workflow_invocation_id, WorkflowInvocationStep.workflow_step_id]',
-        primaryjoin=(lambda: and_(
-            WorkflowInvocationStep.workflow_invocation_id
-            == WorkflowInvocationOutputValue.workflow_invocation_id,
-            WorkflowInvocationStep.workflow_step_id == WorkflowInvocationOutputValue.workflow_step_id,
-        )),
-        back_populates='workflow_invocation_step',
-        viewonly=True
+        "WorkflowInvocationStepOutputDatasetCollectionAssociation", back_populates="workflow_invocation_step"
+    )
+    output_datasets = relationship(
+        "WorkflowInvocationStepOutputDatasetAssociation", back_populates="workflow_invocation_step"
+    )
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="steps")
+    output_value = relationship(
+        "WorkflowInvocationOutputValue",
+        foreign_keys="[WorkflowInvocationStep.workflow_invocation_id, WorkflowInvocationStep.workflow_step_id]",
+        primaryjoin=(
+            lambda: and_(
+                WorkflowInvocationStep.workflow_invocation_id == WorkflowInvocationOutputValue.workflow_invocation_id,
+                WorkflowInvocationStep.workflow_step_id == WorkflowInvocationOutputValue.workflow_step_id,
+            )
+        ),
+        back_populates="workflow_invocation_step",
+        viewonly=True,
     )
 
     subworkflow_invocation_id: column_property
 
-    dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'subworkflow_invocation_id', 'state', 'action']
-    dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'subworkflow_invocation_id', 'state', 'action']
+    dict_collection_visible_keys = [
+        "id",
+        "update_time",
+        "job_id",
+        "workflow_step_id",
+        "subworkflow_invocation_id",
+        "state",
+        "action",
+    ]
+    dict_element_visible_keys = [
+        "id",
+        "update_time",
+        "job_id",
+        "workflow_step_id",
+        "subworkflow_invocation_id",
+        "state",
+        "action",
+    ]
 
     class states(str, Enum):
-        NEW = 'new'  # Brand new workflow invocation step
-        READY = 'ready'  # Workflow invocation step ready for another iteration of scheduling.
-        SCHEDULED = 'scheduled'  # Workflow invocation step has been scheduled.
+        NEW = "new"  # Brand new workflow invocation step
+        READY = "ready"  # Workflow invocation step ready for another iteration of scheduling.
+        SCHEDULED = "scheduled"  # Workflow invocation step has been scheduled.
         # CANCELLED = 'cancelled',  TODO: implement and expose
         # FAILED = 'failed',  TODO: implement and expose
 
@@ -7252,14 +7666,14 @@ class WorkflowInvocationStep(Base, Dictifiable, RepresentById):
         else:
             return []
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        rval['order_index'] = self.workflow_step.order_index
-        rval['workflow_step_label'] = self.workflow_step.label
-        rval['workflow_step_uuid'] = str(self.workflow_step.uuid)
+        rval["order_index"] = self.workflow_step.order_index
+        rval["workflow_step_label"] = self.workflow_step.label
+        rval["workflow_step_uuid"] = str(self.workflow_step.uuid)
         # Following no longer makes sense...
         # rval['state'] = self.job.state if self.job is not None else None
-        if view == 'element':
+        if view == "element":
             jobs = []
             for job in self.jobs:
                 jobs.append(job.to_dict())
@@ -7268,67 +7682,71 @@ class WorkflowInvocationStep(Base, Dictifiable, RepresentById):
             for output_assoc in self.output_datasets:
                 name = output_assoc.output_name
                 outputs[name] = {
-                    'src': 'hda',
-                    'id': output_assoc.dataset.id,
-                    'uuid': str(output_assoc.dataset.dataset.uuid) if output_assoc.dataset.dataset.uuid is not None else None
+                    "src": "hda",
+                    "id": output_assoc.dataset.id,
+                    "uuid": str(output_assoc.dataset.dataset.uuid)
+                    if output_assoc.dataset.dataset.uuid is not None
+                    else None,
                 }
 
             output_collections = {}
             for output_assoc in self.output_dataset_collections:
                 name = output_assoc.output_name
                 output_collections[name] = {
-                    'src': 'hdca',
-                    'id': output_assoc.dataset_collection.id,
+                    "src": "hdca",
+                    "id": output_assoc.dataset_collection.id,
                 }
 
-            rval['outputs'] = outputs
-            rval['output_collections'] = output_collections
-            rval['jobs'] = jobs
+            rval["outputs"] = outputs
+            rval["output_collections"] = output_collections
+            rval["jobs"] = jobs
         return rval
 
 
 class WorkflowRequestInputParameter(Base, Dictifiable, RepresentById):
-    """ Workflow-related parameters not tied to steps or inputs.
-    """
-    __tablename__ = 'workflow_request_input_parameters'
+    """Workflow-related parameters not tied to steps or inputs."""
+
+    __tablename__ = "workflow_request_input_parameters"
 
     id = Column(Integer, primary_key=True)
     workflow_invocation_id = Column(
-        Integer, ForeignKey('workflow_invocation.id', onupdate='CASCADE', ondelete='CASCADE'))
+        Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")
+    )
     name = Column(Unicode(255))
     value = Column(TEXT)
     type = Column(Unicode(255))
-    workflow_invocation = relationship('WorkflowInvocation', back_populates='input_parameters')
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="input_parameters")
 
-    dict_collection_visible_keys = ['id', 'name', 'value', 'type']
+    dict_collection_visible_keys = ["id", "name", "value", "type"]
 
     class types(str, Enum):
-        REPLACEMENT_PARAMETERS = 'replacements'
-        STEP_PARAMETERS = 'step'
-        META_PARAMETERS = 'meta'
-        RESOURCE_PARAMETERS = 'resource'
+        REPLACEMENT_PARAMETERS = "replacements"
+        STEP_PARAMETERS = "step"
+        META_PARAMETERS = "meta"
+        RESOURCE_PARAMETERS = "resource"
 
 
 class WorkflowRequestStepState(Base, Dictifiable, RepresentById):
-    """ Workflow step value parameters.
-    """
-    __tablename__ = 'workflow_request_step_states'
+    """Workflow step value parameters."""
+
+    __tablename__ = "workflow_request_step_states"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer,
-        ForeignKey('workflow_invocation.id', onupdate='CASCADE', ondelete='CASCADE'))
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'))
+    workflow_invocation_id = Column(
+        Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")
+    )
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
     value = Column(MutableJSONType)
-    workflow_step = relationship('WorkflowStep')
-    workflow_invocation = relationship('WorkflowInvocation', back_populates='step_states')
+    workflow_step = relationship("WorkflowStep")
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="step_states")
 
-    dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']
+    dict_collection_visible_keys = ["id", "name", "value", "workflow_step_id"]
 
 
 class WorkflowRequestToInputDatasetAssociation(Base, Dictifiable, RepresentById):
-    """ Workflow step input dataset parameters.
-    """
-    __tablename__ = 'workflow_request_to_input_dataset'
+    """Workflow step input dataset parameters."""
+
+    __tablename__ = "workflow_request_to_input_dataset"
 
     id = Column(Integer, primary_key=True)
     name = Column(String(255))
@@ -7336,167 +7754,165 @@ class WorkflowRequestToInputDatasetAssociation(Base, Dictifiable, RepresentById)
     workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
     dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
 
-    workflow_step = relationship('WorkflowStep')
-    dataset = relationship('HistoryDatasetAssociation')
-    workflow_invocation = relationship('WorkflowInvocation', back_populates='input_datasets')
+    workflow_step = relationship("WorkflowStep")
+    dataset = relationship("HistoryDatasetAssociation")
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="input_datasets")
 
     history_content_type = "dataset"
-    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
+    dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_id", "name"]
 
 
 class WorkflowRequestToInputDatasetCollectionAssociation(Base, Dictifiable, RepresentById):
-    """ Workflow step input dataset collection parameters.
-    """
-    __tablename__ = 'workflow_request_to_input_collection_dataset'
+    """Workflow step input dataset collection parameters."""
+
+    __tablename__ = "workflow_request_to_input_collection_dataset"
 
     id = Column(Integer, primary_key=True)
     name = Column(String(255))
-    workflow_invocation_id = Column(Integer, ForeignKey('workflow_invocation.id'), index=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'))
-    dataset_collection_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id'), index=True)
-    workflow_step = relationship('WorkflowStep')
-    dataset_collection = relationship('HistoryDatasetCollectionAssociation')
-    workflow_invocation = relationship('WorkflowInvocation',
-        back_populates='input_dataset_collections')
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
+    dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
+    workflow_step = relationship("WorkflowStep")
+    dataset_collection = relationship("HistoryDatasetCollectionAssociation")
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="input_dataset_collections")
 
     history_content_type = "dataset_collection"
-    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
+    dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_collection_id", "name"]
 
 
 class WorkflowRequestInputStepParameter(Base, Dictifiable, RepresentById):
-    """ Workflow step parameter inputs.
-    """
-    __tablename__ = 'workflow_request_input_step_parameter'
+    """Workflow step parameter inputs."""
+
+    __tablename__ = "workflow_request_input_step_parameter"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey('workflow_invocation.id'), index=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'))
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
     parameter_value = Column(MutableJSONType)
 
-    workflow_step = relationship('WorkflowStep')
-    workflow_invocation = relationship('WorkflowInvocation', back_populates='input_step_parameters')
+    workflow_step = relationship("WorkflowStep")
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="input_step_parameters")
 
-    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']
+    dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "parameter_value"]
 
 
 class WorkflowInvocationOutputDatasetAssociation(Base, Dictifiable, RepresentById):
     """Represents links to output datasets for the workflow."""
-    __tablename__ = 'workflow_invocation_output_dataset_association'
+
+    __tablename__ = "workflow_invocation_output_dataset_association"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey('workflow_invocation.id'), index=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True)
-    dataset_id = Column(Integer, ForeignKey('history_dataset_association.id'), index=True)
-    workflow_output_id = Column(Integer, ForeignKey('workflow_output.id'), index=True)
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
+    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    workflow_output_id = Column(Integer, ForeignKey("workflow_output.id"), index=True)
 
-    workflow_invocation = relationship('WorkflowInvocation', back_populates='output_datasets')
-    workflow_step = relationship('WorkflowStep')
-    dataset = relationship('HistoryDatasetAssociation')
-    workflow_output = relationship('WorkflowOutput')
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="output_datasets")
+    workflow_step = relationship("WorkflowStep")
+    dataset = relationship("HistoryDatasetAssociation")
+    workflow_output = relationship("WorkflowOutput")
 
     history_content_type = "dataset"
-    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
+    dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_id", "name"]
 
 
 class WorkflowInvocationOutputDatasetCollectionAssociation(Base, Dictifiable, RepresentById):
     """Represents links to output dataset collections for the workflow."""
-    __tablename__ = 'workflow_invocation_output_dataset_collection_association'
+
+    __tablename__ = "workflow_invocation_output_dataset_collection_association"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer,
-        ForeignKey('workflow_invocation.id', name='fk_wiodca_wii'), index=True)
-    workflow_step_id = Column(Integer,
-        ForeignKey('workflow_step.id', name='fk_wiodca_wsi'), index=True)
-    dataset_collection_id = Column(Integer,
-        ForeignKey('history_dataset_collection_association.id', name='fk_wiodca_dci'), index=True)
-    workflow_output_id = Column(Integer,
-        ForeignKey('workflow_output.id', name='fk_wiodca_woi'), index=True)
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id", name="fk_wiodca_wii"), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id", name="fk_wiodca_wsi"), index=True)
+    dataset_collection_id = Column(
+        Integer, ForeignKey("history_dataset_collection_association.id", name="fk_wiodca_dci"), index=True
+    )
+    workflow_output_id = Column(Integer, ForeignKey("workflow_output.id", name="fk_wiodca_woi"), index=True)
 
-    workflow_invocation = relationship('WorkflowInvocation',
-        back_populates='output_dataset_collections')
-    workflow_step = relationship('WorkflowStep')
-    dataset_collection = relationship('HistoryDatasetCollectionAssociation')
-    workflow_output = relationship('WorkflowOutput')
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="output_dataset_collections")
+    workflow_step = relationship("WorkflowStep")
+    dataset_collection = relationship("HistoryDatasetCollectionAssociation")
+    workflow_output = relationship("WorkflowOutput")
 
     history_content_type = "dataset_collection"
-    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
+    dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_collection_id", "name"]
 
 
 class WorkflowInvocationOutputValue(Base, Dictifiable, RepresentById):
     """Represents a link to a specified or computed workflow parameter."""
-    __tablename__ = 'workflow_invocation_output_value'
+
+    __tablename__ = "workflow_invocation_output_value"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_id = Column(Integer, ForeignKey('workflow_invocation.id'), index=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'))
-    workflow_output_id = Column(Integer, ForeignKey('workflow_output.id'), index=True)
+    workflow_invocation_id = Column(Integer, ForeignKey("workflow_invocation.id"), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"))
+    workflow_output_id = Column(Integer, ForeignKey("workflow_output.id"), index=True)
     value = Column(MutableJSONType)
 
-    workflow_invocation = relationship('WorkflowInvocation', back_populates="output_values")
+    workflow_invocation = relationship("WorkflowInvocation", back_populates="output_values")
 
-    workflow_invocation_step = relationship('WorkflowInvocationStep',
-        foreign_keys='[WorkflowInvocationStep.workflow_invocation_id, WorkflowInvocationStep.workflow_step_id]',
-        primaryjoin=(lambda: and_(
-            WorkflowInvocationStep.workflow_invocation_id == WorkflowInvocationOutputValue.workflow_invocation_id,
-            WorkflowInvocationStep.workflow_step_id == WorkflowInvocationOutputValue.workflow_step_id,
-        )),
-        back_populates='output_value',
-        viewonly=True
+    workflow_invocation_step = relationship(
+        "WorkflowInvocationStep",
+        foreign_keys="[WorkflowInvocationStep.workflow_invocation_id, WorkflowInvocationStep.workflow_step_id]",
+        primaryjoin=(
+            lambda: and_(
+                WorkflowInvocationStep.workflow_invocation_id == WorkflowInvocationOutputValue.workflow_invocation_id,
+                WorkflowInvocationStep.workflow_step_id == WorkflowInvocationOutputValue.workflow_step_id,
+            )
+        ),
+        back_populates="output_value",
+        viewonly=True,
     )
 
-    workflow_step = relationship('WorkflowStep')
-    workflow_output = relationship('WorkflowOutput')
+    workflow_step = relationship("WorkflowStep")
+    workflow_output = relationship("WorkflowOutput")
 
-    dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'value']
+    dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "value"]
 
 
 class WorkflowInvocationStepOutputDatasetAssociation(Base, Dictifiable, RepresentById):
     """Represents links to output datasets for the workflow."""
-    __tablename__ = 'workflow_invocation_step_output_dataset_association'
+
+    __tablename__ = "workflow_invocation_step_output_dataset_association"
 
     id = Column(Integer, primary_key=True)
-    workflow_invocation_step_id = Column(Integer,
-        ForeignKey('workflow_invocation_step.id'), index=True)
-    dataset_id = Column(Integer, ForeignKey('history_dataset_association.id'), index=True)
+    workflow_invocation_step_id = Column(Integer, ForeignKey("workflow_invocation_step.id"), index=True)
+    dataset_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
     output_name = Column(String(255), nullable=True)
-    workflow_invocation_step = relationship('WorkflowInvocationStep',
-        back_populates='output_datasets')
-    dataset = relationship('HistoryDatasetAssociation')
+    workflow_invocation_step = relationship("WorkflowInvocationStep", back_populates="output_datasets")
+    dataset = relationship("HistoryDatasetAssociation")
 
-    dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']
+    dict_collection_visible_keys = ["id", "workflow_invocation_step_id", "dataset_id", "output_name"]
 
 
 class WorkflowInvocationStepOutputDatasetCollectionAssociation(Base, Dictifiable, RepresentById):
     """Represents links to output dataset collections for the workflow."""
-    __tablename__ = 'workflow_invocation_step_output_dataset_collection_association'
+
+    __tablename__ = "workflow_invocation_step_output_dataset_collection_association"
 
     id = Column(Integer, primary_key=True)
     workflow_invocation_step_id = Column(
-        Integer, ForeignKey('workflow_invocation_step.id', name='fk_wisodca_wisi'), index=True)
-    workflow_step_id = Column(
-        Integer, ForeignKey('workflow_step.id', name='fk_wisodca_wsi'), index=True)
+        Integer, ForeignKey("workflow_invocation_step.id", name="fk_wisodca_wisi"), index=True
+    )
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id", name="fk_wisodca_wsi"), index=True)
     dataset_collection_id = Column(
-        Integer,
-        ForeignKey('history_dataset_collection_association.id', name='fk_wisodca_dci'), index=True)
+        Integer, ForeignKey("history_dataset_collection_association.id", name="fk_wisodca_dci"), index=True
+    )
     output_name = Column(String(255), nullable=True)
 
-    workflow_invocation_step = relationship('WorkflowInvocationStep',
-        back_populates='output_dataset_collections')
-    dataset_collection = relationship('HistoryDatasetCollectionAssociation')
+    workflow_invocation_step = relationship("WorkflowInvocationStep", back_populates="output_dataset_collections")
+    dataset_collection = relationship("HistoryDatasetCollectionAssociation")
 
-    dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']
+    dict_collection_visible_keys = ["id", "workflow_invocation_step_id", "dataset_collection_id", "output_name"]
 
 
 class MetadataFile(Base, StorableObject, Serializable):
-    __tablename__ = 'metadata_file'
+    __tablename__ = "metadata_file"
 
     id = Column(Integer, primary_key=True)
     name = Column(TEXT)
-    hda_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True, nullable=True)
-    lda_id = Column(Integer,
-        ForeignKey('library_dataset_dataset_association.id'), index=True, nullable=True)
+    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True)
+    lda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, index=True, default=now, onupdate=now)
     object_store_id = Column(TrimmedString(255), index=True)
@@ -7504,8 +7920,8 @@ class MetadataFile(Base, StorableObject, Serializable):
     deleted = Column(Boolean, index=True, default=False)
     purged = Column(Boolean, index=True, default=False)
 
-    history_dataset = relationship('HistoryDatasetAssociation')
-    library_dataset = relationship('LibraryDatasetDatasetAssociation')
+    history_dataset = relationship("HistoryDatasetAssociation")
+    library_dataset = relationship("LibraryDatasetDatasetAssociation")
 
     def __init__(self, dataset=None, name=None, uuid=None):
         self.uuid = get_uuid(uuid)
@@ -7524,18 +7940,22 @@ class MetadataFile(Base, StorableObject, Serializable):
                 self.object_store_id = da.dataset.object_store_id
             object_store = da.dataset.object_store
             store_by = object_store.get_store_by(da.dataset)
-            if store_by == 'id' and self.id is None:
+            if store_by == "id" and self.id is None:
                 self.flush()
             identifier = getattr(self, store_by)
             alt_name = f"metadata_{identifier}.dat"
-            if not object_store.exists(self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=alt_name):
-                object_store.create(self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=alt_name)
-            path = object_store.get_filename(self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=alt_name)
+            if not object_store.exists(self, extra_dir="_metadata_files", extra_dir_at_root=True, alt_name=alt_name):
+                object_store.create(self, extra_dir="_metadata_files", extra_dir_at_root=True, alt_name=alt_name)
+            path = object_store.get_filename(
+                self, extra_dir="_metadata_files", extra_dir_at_root=True, alt_name=alt_name
+            )
             return path
         except AttributeError:
-            assert self.id is not None, "ID must be set before MetadataFile used without an HDA/LDDA (commit the object)"
+            assert (
+                self.id is not None
+            ), "ID must be set before MetadataFile used without an HDA/LDDA (commit the object)"
             # In case we're not working with the history_dataset
-            path = os.path.join(Dataset.file_path, '_metadata_files', *directory_hash_id(self.id))
+            path = os.path.join(Dataset.file_path, "_metadata_files", *directory_hash_id(self.id))
             # Create directory if it does not exist
             try:
                 os.makedirs(path)
@@ -7549,50 +7969,70 @@ class MetadataFile(Base, StorableObject, Serializable):
     def _serialize(self, id_encoder, serialization_options):
         as_dict = dict_for(self)
         serialization_options.attach_identifier(id_encoder, self, as_dict)
-        as_dict["uuid"] = str(self.uuid or '') or None
+        as_dict["uuid"] = str(self.uuid or "") or None
         return as_dict
 
 
 class FormDefinition(Base, Dictifiable, RepresentById):
-    __tablename__ = 'form_definition'
+    __tablename__ = "form_definition"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     name = Column(TrimmedString(255), nullable=False)
     desc = Column(TEXT)
-    form_definition_current_id = Column(Integer,
-        ForeignKey('form_definition_current.id', use_alter=True), index=True, nullable=False)
+    form_definition_current_id = Column(
+        Integer, ForeignKey("form_definition_current.id", use_alter=True), index=True, nullable=False
+    )
     fields = Column(MutableJSONType)
     type = Column(TrimmedString(255), index=True)
     layout = Column(MutableJSONType)
     form_definition_current = relationship(
-        'FormDefinitionCurrent',
-        back_populates='forms',
-        primaryjoin=(lambda: FormDefinitionCurrent.id == FormDefinition.form_definition_current_id))  # type: ignore[has-type]
+        "FormDefinitionCurrent",
+        back_populates="forms",
+        primaryjoin=(lambda: FormDefinitionCurrent.id == FormDefinition.form_definition_current_id),
+    )  # type: ignore[has-type]
 
     # The following form_builder classes are supported by the FormDefinition class.
-    supported_field_types = [AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField]
+    supported_field_types = [
+        AddressField,
+        CheckboxField,
+        PasswordField,
+        SelectField,
+        TextArea,
+        TextField,
+        WorkflowField,
+        WorkflowMappingField,
+        HistoryField,
+    ]
 
     class types(str, Enum):
-        USER_INFO = 'User Information'
+        USER_INFO = "User Information"
 
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout']
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = ["id", "name", "desc", "form_definition_current_id", "fields", "layout"]
 
     def to_dict(self, user=None, values=None, security=None):
         values = values or {}
-        form_def = {'id': security.encode_id(self.id) if security else self.id, 'name': self.name, 'inputs': []}
+        form_def = {"id": security.encode_id(self.id) if security else self.id, "name": self.name, "inputs": []}
         for field in self.fields:
-            FieldClass = ({'AddressField': AddressField,
-                           'CheckboxField': CheckboxField,
-                           'HistoryField': HistoryField,
-                           'PasswordField': PasswordField,
-                           'SelectField': SelectField,
-                           'TextArea': TextArea,
-                           'TextField': TextField,
-                           'WorkflowField': WorkflowField}).get(field['type'], TextField)
-            form_def['inputs'].append(FieldClass(user=user, value=values.get(field['name'], field['default']), security=security, **field).to_dict())
+            FieldClass = (
+                {
+                    "AddressField": AddressField,
+                    "CheckboxField": CheckboxField,
+                    "HistoryField": HistoryField,
+                    "PasswordField": PasswordField,
+                    "SelectField": SelectField,
+                    "TextArea": TextArea,
+                    "TextField": TextField,
+                    "WorkflowField": WorkflowField,
+                }
+            ).get(field["type"], TextField)
+            form_def["inputs"].append(
+                FieldClass(
+                    user=user, value=values.get(field["name"], field["default"]), security=security, **field
+                ).to_dict()
+            )
         return form_def
 
     def grid_fields(self, grid_index):
@@ -7600,44 +8040,46 @@ class FormDefinition(Base, Dictifiable, RepresentById):
         # on the grid and whose values are the field.
         gridfields = {}
         for i, f in enumerate(self.fields):
-            if str(f['layout']) == str(grid_index):
+            if str(f["layout"]) == str(grid_index):
                 gridfields[i] = f
         return gridfields
 
 
 class FormDefinitionCurrent(Base, RepresentById):
-    __tablename__ = 'form_definition_current'
+    __tablename__ = "form_definition_current"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    latest_form_id = Column(Integer, ForeignKey('form_definition.id'), index=True)
+    latest_form_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
     deleted = Column(Boolean, index=True, default=False)
     forms = relationship(
-        'FormDefinition',
-        back_populates='form_definition_current',
-        cascade='all, delete-orphan',
-        primaryjoin=(lambda: FormDefinitionCurrent.id == FormDefinition.form_definition_current_id))
+        "FormDefinition",
+        back_populates="form_definition_current",
+        cascade="all, delete-orphan",
+        primaryjoin=(lambda: FormDefinitionCurrent.id == FormDefinition.form_definition_current_id),
+    )
     latest_form = relationship(
-        'FormDefinition',
+        "FormDefinition",
         post_update=True,
-        primaryjoin=(lambda: FormDefinitionCurrent.latest_form_id == FormDefinition.id))
+        primaryjoin=(lambda: FormDefinitionCurrent.latest_form_id == FormDefinition.id),
+    )
 
     def __init__(self, form_definition=None):
         self.latest_form = form_definition
 
 
 class FormValues(Base, RepresentById):
-    __tablename__ = 'form_values'
+    __tablename__ = "form_values"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    form_definition_id = Column(Integer, ForeignKey('form_definition.id'), index=True)
+    form_definition_id = Column(Integer, ForeignKey("form_definition.id"), index=True)
     content = Column(MutableJSONType)
     form_definition = relationship(
-        'FormDefinition',
-        primaryjoin=(lambda: FormValues.form_definition_id == FormDefinition.id))
+        "FormDefinition", primaryjoin=(lambda: FormValues.form_definition_id == FormDefinition.id)
+    )
 
     def __init__(self, form_def=None, content=None):
         self.form_definition = form_def
@@ -7645,12 +8087,12 @@ class FormValues(Base, RepresentById):
 
 
 class UserAddress(Base, RepresentById):
-    __tablename__ = 'user_address'
+    __tablename__ = "user_address"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     desc = Column(TrimmedString(255))
     name = Column(TrimmedString(255), nullable=False)
     institution = Column(TrimmedString(255))
@@ -7664,23 +8106,25 @@ class UserAddress(Base, RepresentById):
     purged = Column(Boolean, index=True, default=False)
     # `desc` needs to be fully qualified because it is shadowed by `desc` Column defined above
     # TODO: db migration to rename column, then use `desc`
-    user = relationship('User', back_populates='addresses', order_by=sqlalchemy.desc('update_time'))
+    user = relationship("User", back_populates="addresses", order_by=sqlalchemy.desc("update_time"))
 
     def to_dict(self, trans):
-        return {'id': trans.security.encode_id(self.id),
-                'name': sanitize_html(self.name),
-                'desc': sanitize_html(self.desc),
-                'institution': sanitize_html(self.institution),
-                'address': sanitize_html(self.address),
-                'city': sanitize_html(self.city),
-                'state': sanitize_html(self.state),
-                'postal_code': sanitize_html(self.postal_code),
-                'country': sanitize_html(self.country),
-                'phone': sanitize_html(self.phone)}
+        return {
+            "id": trans.security.encode_id(self.id),
+            "name": sanitize_html(self.name),
+            "desc": sanitize_html(self.desc),
+            "institution": sanitize_html(self.institution),
+            "address": sanitize_html(self.address),
+            "city": sanitize_html(self.city),
+            "state": sanitize_html(self.state),
+            "postal_code": sanitize_html(self.postal_code),
+            "country": sanitize_html(self.country),
+            "phone": sanitize_html(self.phone),
+        }
 
 
 class PSAAssociation(Base, AssociationMixin, RepresentById):
-    __tablename__ = 'psa_association'
+    __tablename__ = "psa_association"
 
     id = Column(Integer, primary_key=True)
     server_url = Column(VARCHAR(255))
@@ -7716,14 +8160,12 @@ class PSAAssociation(Base, AssociationMixin, RepresentById):
 
     @classmethod
     def remove(cls, ids_to_delete):
-        cls.sa_session.query(cls).filter(cls.id.in_(ids_to_delete)).delete(synchronize_session='fetch')
+        cls.sa_session.query(cls).filter(cls.id.in_(ids_to_delete)).delete(synchronize_session="fetch")
 
 
 class PSACode(Base, CodeMixin, RepresentById):
-    __tablename__ = 'psa_code'
-    __table_args__ = (
-        UniqueConstraint('code', 'email'),
-    )
+    __tablename__ = "psa_code"
+    __table_args__ = (UniqueConstraint("code", "email"),)
 
     id = Column(Integer, primary_key=True)
     email = Column(VARCHAR(200))
@@ -7746,7 +8188,7 @@ class PSACode(Base, CodeMixin, RepresentById):
 
 
 class PSANonce(Base, NonceMixin, RepresentById):
-    __tablename__ = 'psa_nonce'
+    __tablename__ = "psa_nonce"
 
     id = Column(Integer, primary_key=True)
     server_url = Column(VARCHAR(255))
@@ -7777,7 +8219,7 @@ class PSANonce(Base, NonceMixin, RepresentById):
 
 
 class PSAPartial(Base, PartialMixin, RepresentById):
-    __tablename__ = 'psa_partial'
+    __tablename__ = "psa_partial"
 
     id = Column(Integer, primary_key=True)
     token = Column(VARCHAR(32))
@@ -7810,8 +8252,8 @@ class PSAPartial(Base, PartialMixin, RepresentById):
 
 
 class UserAuthnzToken(Base, UserMixin, RepresentById):
-    __tablename__ = 'oidc_user_authnz_tokens'
-    __table_args__ = (UniqueConstraint('provider', 'uid'),)
+    __tablename__ = "oidc_user_authnz_tokens"
+    __table_args__ = (UniqueConstraint("provider", "uid"),)
 
     id = Column(Integer, primary_key=True)
     user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
@@ -7820,7 +8262,7 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
     extra_data = Column(MutableJSONType, nullable=True)
     lifetime = Column(Integer)
     assoc_type = Column(VARCHAR(64))
-    user = relationship('User', back_populates='social_auth')
+    user = relationship("User", back_populates="social_auth")
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -7838,7 +8280,7 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
             # Access and ID tokens have same expiration time;
             # hence, if one is expired, the other is expired too.
             self.refresh_token(strategy)
-        return self.extra_data.get('id_token', None) if self.extra_data is not None else None
+        return self.extra_data.get("id_token", None) if self.extra_data is not None else None
 
     def set_extra_data(self, extra_data=None):
         if super().set_extra_data(extra_data):
@@ -7874,7 +8316,7 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
 
     @classmethod
     def get_username(cls, user):
-        return getattr(user, 'username', None)
+        return getattr(user, "username", None)
 
     @classmethod
     def create_user(cls, *args, **kwargs):
@@ -7926,14 +8368,14 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
 
 
 class CustosAuthnzToken(Base, RepresentById):
-    __tablename__ = 'custos_authnz_token'
+    __tablename__ = "custos_authnz_token"
     __table_args__ = (
-        UniqueConstraint('user_id', 'external_user_id', 'provider'),
-        UniqueConstraint('external_user_id', 'provider'),
+        UniqueConstraint("user_id", "external_user_id", "provider"),
+        UniqueConstraint("external_user_id", "provider"),
     )
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'))
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"))
     external_user_id = Column(String(64))
     provider = Column(String(255))
     access_token = Column(Text)
@@ -7941,24 +8383,24 @@ class CustosAuthnzToken(Base, RepresentById):
     refresh_token = Column(Text)
     expiration_time = Column(DateTime)
     refresh_expiration_time = Column(DateTime)
-    user = relationship('User', back_populates='custos_auth')
+    user = relationship("User", back_populates="custos_auth")
 
 
 class CloudAuthz(Base, _HasTable):
-    __tablename__ = 'cloudauthz'
+    __tablename__ = "cloudauthz"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     provider = Column(String(255))
     config = Column(MutableJSONType)
-    authn_id = Column(Integer, ForeignKey('oidc_user_authnz_tokens.id'), index=True)
+    authn_id = Column(Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True)
     tokens = Column(MutableJSONType)
     last_update = Column(DateTime)
     last_activity = Column(DateTime)
     description = Column(TEXT)
     create_time = Column(DateTime, default=now)
-    user = relationship('User', back_populates='cloudauthz')
-    authn = relationship('UserAuthnzToken')
+    user = relationship("User", back_populates="cloudauthz")
+    authn = relationship("UserAuthnzToken")
 
     def __init__(self, user_id, provider, config, authn_id, description=None):
         self.user_id = user_id
@@ -7970,73 +8412,80 @@ class CloudAuthz(Base, _HasTable):
         self.description = description
 
     def equals(self, user_id, provider, authn_id, config):
-        return (self.user_id == user_id
-                and self.provider == provider
-                and self.authn_id
-                and self.authn_id == authn_id
-                and len({k: self.config[k] for k in self.config if k in config
-                         and self.config[k] == config[k]}) == len(self.config))
+        return (
+            self.user_id == user_id
+            and self.provider == provider
+            and self.authn_id
+            and self.authn_id == authn_id
+            and len({k: self.config[k] for k in self.config if k in config and self.config[k] == config[k]})
+            == len(self.config)
+        )
 
 
 class Page(Base, Dictifiable, RepresentById):
-    __tablename__ = 'page'
-    __table_args__ = (
-        Index('ix_page_slug', 'slug', mysql_length=200),
-    )
+    __tablename__ = "page"
+    __table_args__ = (Index("ix_page_slug", "slug", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True, nullable=False)
-    latest_revision_id = Column(Integer,
-        ForeignKey('page_revision.id', use_alter=True, name='page_latest_revision_id_fk'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    latest_revision_id = Column(
+        Integer, ForeignKey("page_revision.id", use_alter=True, name="page_latest_revision_id_fk"), index=True
+    )
     title = Column(TEXT)
     deleted = Column(Boolean, index=True, default=False)
     importable = Column(Boolean, index=True, default=False)
     slug = Column(TEXT)
     published = Column(Boolean, index=True, default=False)
-    user = relationship('User')
+    user = relationship("User")
     revisions = relationship(
-        'PageRevision',
+        "PageRevision",
         cascade="all, delete-orphan",
         primaryjoin=(lambda: Page.id == PageRevision.page_id),  # type: ignore[has-type]
-        back_populates='page')
+        back_populates="page",
+    )
     latest_revision = relationship(
-        'PageRevision',
+        "PageRevision",
         post_update=True,
         primaryjoin=(lambda: Page.latest_revision_id == PageRevision.id),  # type: ignore[has-type]
-        lazy=False)
-    tags = relationship(
-        'PageTagAssociation',
-        order_by=lambda: PageTagAssociation.id,
-        back_populates='page')
+        lazy=False,
+    )
+    tags = relationship("PageTagAssociation", order_by=lambda: PageTagAssociation.id, back_populates="page")
     annotations = relationship(
-        'PageAnnotationAssociation',
-        order_by=lambda: PageAnnotationAssociation.id,
-        back_populates='page')
+        "PageAnnotationAssociation", order_by=lambda: PageAnnotationAssociation.id, back_populates="page"
+    )
     ratings = relationship(
-        'PageRatingAssociation',
+        "PageRatingAssociation",
         order_by=lambda: PageRatingAssociation.id,  # type: ignore[has-type]
-        back_populates='page')
-    users_shared_with = relationship(
-        'PageUserShareAssociation',
-        back_populates='page')
+        back_populates="page",
+    )
+    users_shared_with = relationship("PageUserShareAssociation", back_populates="page")
 
     average_rating: column_property  # defined at the end of this module
 
     # Set up proxy so that
     #   Page.users_shared_with
     # returns a list of users that page is shared with.
-    users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+    users_shared_with_dot_users = association_proxy("users_shared_with", "user")
 
-    dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted', 'username']
+    dict_element_visible_keys = [
+        "id",
+        "title",
+        "latest_revision_id",
+        "slug",
+        "published",
+        "importable",
+        "deleted",
+        "username",
+    ]
 
-    def to_dict(self, view='element'):
+    def to_dict(self, view="element"):
         rval = super().to_dict(view=view)
         rev = []
         for a in self.revisions:
             rev.append(a.id)
-        rval['revision_ids'] = rev
+        rval["revision_ids"] = rev
         return rval
 
     # username needed for slug generation
@@ -8046,54 +8495,55 @@ class Page(Base, Dictifiable, RepresentById):
 
 
 class PageRevision(Base, Dictifiable, RepresentById):
-    __tablename__ = 'page_revision'
+    __tablename__ = "page_revision"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    page_id = Column(Integer, ForeignKey('page.id'), index=True, nullable=False)
+    page_id = Column(Integer, ForeignKey("page.id"), index=True, nullable=False)
     title = Column(TEXT)
     content = Column(TEXT)
     content_format = Column(TrimmedString(32))
-    page = relationship('Page',
-        primaryjoin=(lambda: Page.id == PageRevision.page_id))
-    DEFAULT_CONTENT_FORMAT = 'html'
-    dict_element_visible_keys = ['id', 'page_id', 'title', 'content', 'content_format']
+    page = relationship("Page", primaryjoin=(lambda: Page.id == PageRevision.page_id))
+    DEFAULT_CONTENT_FORMAT = "html"
+    dict_element_visible_keys = ["id", "page_id", "title", "content", "content_format"]
 
     def __init__(self):
         self.content_format = PageRevision.DEFAULT_CONTENT_FORMAT
 
-    def to_dict(self, view='element'):
+    def to_dict(self, view="element"):
         rval = super().to_dict(view=view)
-        rval['create_time'] = str(self.create_time)
-        rval['update_time'] = str(self.update_time)
+        rval["create_time"] = str(self.create_time)
+        rval["update_time"] = str(self.update_time)
         return rval
 
 
 class PageUserShareAssociation(Base, UserShareAssociation):
-    __tablename__ = 'page_user_share_association'
+    __tablename__ = "page_user_share_association"
 
     id = Column(Integer, primary_key=True)
     page_id = Column(Integer, ForeignKey("page.id"), index=True)
     user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
-    user = relationship('User')
-    page = relationship('Page', back_populates='users_shared_with')
+    user = relationship("User")
+    page = relationship("Page", back_populates="users_shared_with")
 
 
 class Visualization(Base, RepresentById):
-    __tablename__ = 'visualization'
+    __tablename__ = "visualization"
     __table_args__ = (
-        Index('ix_visualization_dbkey', 'dbkey', mysql_length=200),
-        Index('ix_visualization_slug', 'slug', mysql_length=200),
+        Index("ix_visualization_dbkey", "dbkey", mysql_length=200),
+        Index("ix_visualization_slug", "slug", mysql_length=200),
     )
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True, nullable=False)
-    latest_revision_id = Column(Integer,
-        ForeignKey('visualization_revision.id', use_alter=True, name='visualization_latest_revision_id_fk'),
-        index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    latest_revision_id = Column(
+        Integer,
+        ForeignKey("visualization_revision.id", use_alter=True, name="visualization_latest_revision_id_fk"),
+        index=True,
+    )
     title = Column(TEXT)
     type = Column(TEXT)
     dbkey = Column(TEXT)
@@ -8102,32 +8552,40 @@ class Visualization(Base, RepresentById):
     slug = Column(TEXT)
     published = Column(Boolean, default=False, index=True)
 
-    user = relationship('User')
-    revisions = relationship('VisualizationRevision',
-        back_populates='visualization',
+    user = relationship("User")
+    revisions = relationship(
+        "VisualizationRevision",
+        back_populates="visualization",
         cascade="all, delete-orphan",
-        primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id))
-    latest_revision = relationship('VisualizationRevision',
+        primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id),
+    )
+    latest_revision = relationship(
+        "VisualizationRevision",
         post_update=True,
         primaryjoin=(lambda: Visualization.latest_revision_id == VisualizationRevision.id),
-        lazy=False)
-    tags = relationship('VisualizationTagAssociation',
-        order_by=lambda: VisualizationTagAssociation.id,
-        back_populates="visualization")
-    annotations = relationship('VisualizationAnnotationAssociation',
+        lazy=False,
+    )
+    tags = relationship(
+        "VisualizationTagAssociation", order_by=lambda: VisualizationTagAssociation.id, back_populates="visualization"
+    )
+    annotations = relationship(
+        "VisualizationAnnotationAssociation",
         order_by=lambda: VisualizationAnnotationAssociation.id,
-        back_populates="visualization")
-    ratings = relationship('VisualizationRatingAssociation',
+        back_populates="visualization",
+    )
+    ratings = relationship(
+        "VisualizationRatingAssociation",
         order_by=lambda: VisualizationRatingAssociation.id,  # type: ignore[has-type]
-        back_populates="visualization")
-    users_shared_with = relationship('VisualizationUserShareAssociation', back_populates='visualization')
+        back_populates="visualization",
+    )
+    users_shared_with = relationship("VisualizationUserShareAssociation", back_populates="visualization")
 
     average_rating: column_property  # defined at the end of this module
 
     # Set up proxy so that
     #   Visualization.users_shared_with
     # returns a list of users that visualization is shared with.
-    users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+    users_shared_with_dot_users = association_proxy("users_shared_with", "user")
 
     def __init__(self, **kwd):
         super().__init__(**kwd)
@@ -8157,21 +8615,21 @@ class Visualization(Base, RepresentById):
 
 
 class VisualizationRevision(Base, RepresentById):
-    __tablename__ = 'visualization_revision'
-    __table_args__ = (
-        Index('ix_visualization_revision_dbkey', 'dbkey', mysql_length=200),
-    )
+    __tablename__ = "visualization_revision"
+    __table_args__ = (Index("ix_visualization_revision_dbkey", "dbkey", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    visualization_id = Column(Integer, ForeignKey('visualization.id'), index=True, nullable=False)
+    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True, nullable=False)
     title = Column(TEXT)
     dbkey = Column(TEXT)
     config = Column(MutableJSONType)
-    visualization = relationship('Visualization',
-        back_populates='revisions',
-        primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id))
+    visualization = relationship(
+        "Visualization",
+        back_populates="revisions",
+        primaryjoin=(lambda: Visualization.id == VisualizationRevision.visualization_id),
+    )
 
     def copy(self, visualization=None):
         """
@@ -8181,42 +8639,37 @@ class VisualizationRevision(Base, RepresentById):
             visualization = self.visualization
 
         return VisualizationRevision(
-            visualization=visualization,
-            title=self.title,
-            dbkey=self.dbkey,
-            config=self.config
+            visualization=visualization, title=self.title, dbkey=self.dbkey, config=self.config
         )
 
 
 class VisualizationUserShareAssociation(Base, UserShareAssociation):
-    __tablename__ = 'visualization_user_share_association'
+    __tablename__ = "visualization_user_share_association"
 
     id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey('visualization.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    user = relationship('User')
-    visualization = relationship('Visualization', back_populates='users_shared_with')
+    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    user = relationship("User")
+    visualization = relationship("Visualization", back_populates="users_shared_with")
 
 
 class Tag(Base, RepresentById):
-    __tablename__ = 'tag'
-    __table_args__ = (
-        UniqueConstraint('name'),
-    )
+    __tablename__ = "tag"
+    __table_args__ = (UniqueConstraint("name"),)
 
     id = Column(Integer, primary_key=True)
     type = Column(Integer)
-    parent_id = Column(Integer, ForeignKey('tag.id'))
+    parent_id = Column(Integer, ForeignKey("tag.id"))
     name = Column(TrimmedString(255))
-    children = relationship('Tag', back_populates='parent')
-    parent = relationship('Tag', back_populates='children', remote_side=[id])
+    children = relationship("Tag", back_populates="parent")
+    parent = relationship("Tag", back_populates="children", remote_side=[id])
 
     def __str__(self):
         return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % (self.id, self.type or -1, self.parent_id, self.name)
 
 
 class ItemTagAssociation(Dictifiable):
-    dict_collection_visible_keys = ['id', 'user_tname', 'user_value']
+    dict_collection_visible_keys = ["id", "user_tname", "user_value"]
     dict_element_visible_keys = dict_collection_visible_keys
     associated_item_names: List[str] = []
     user_tname: Column
@@ -8239,268 +8692,248 @@ class ItemTagAssociation(Dictifiable):
 
 
 class HistoryTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'history_tag_association'
+    __tablename__ = "history_tag_association"
 
     id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    history = relationship('History', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    history = relationship("History", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class HistoryDatasetAssociationTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'history_dataset_association_tag_association'
+    __tablename__ = "history_dataset_association_tag_association"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    history_dataset_association = relationship('HistoryDatasetAssociation', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    history_dataset_association = relationship("HistoryDatasetAssociation", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class LibraryDatasetDatasetAssociationTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'library_dataset_dataset_association_tag_association'
+    __tablename__ = "library_dataset_dataset_association_tag_association"
 
     id = Column(Integer, primary_key=True)
     library_dataset_dataset_association_id = Column(
-        Integer, ForeignKey('library_dataset_dataset_association.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+        Integer, ForeignKey("library_dataset_dataset_association.id"), index=True
+    )
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    library_dataset_dataset_association = relationship(
-        'LibraryDatasetDatasetAssociation', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    library_dataset_dataset_association = relationship("LibraryDatasetDatasetAssociation", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class PageTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'page_tag_association'
+    __tablename__ = "page_tag_association"
 
     id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey('page.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    page_id = Column(Integer, ForeignKey("page.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    page = relationship('Page', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    page = relationship("Page", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class WorkflowStepTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'workflow_step_tag_association'
+    __tablename__ = "workflow_step_tag_association"
 
     id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    workflow_step = relationship('WorkflowStep', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    workflow_step = relationship("WorkflowStep", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class StoredWorkflowTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'stored_workflow_tag_association'
+    __tablename__ = "stored_workflow_tag_association"
 
     id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey('stored_workflow.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    stored_workflow = relationship('StoredWorkflow', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    stored_workflow = relationship("StoredWorkflow", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class VisualizationTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'visualization_tag_association'
+    __tablename__ = "visualization_tag_association"
 
     id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey('visualization.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    visualization = relationship('Visualization', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    visualization = relationship("Visualization", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class HistoryDatasetCollectionTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'history_dataset_collection_tag_association'
+    __tablename__ = "history_dataset_collection_tag_association"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_collection_id = Column(
-        Integer, ForeignKey('history_dataset_collection_association.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    dataset_collection = relationship('HistoryDatasetCollectionAssociation', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    dataset_collection = relationship("HistoryDatasetCollectionAssociation", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class LibraryDatasetCollectionTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'library_dataset_collection_tag_association'
+    __tablename__ = "library_dataset_collection_tag_association"
 
     id = Column(Integer, primary_key=True)
-    library_dataset_collection_id = Column(
-        Integer, ForeignKey('library_dataset_collection_association.id'), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    library_dataset_collection_id = Column(Integer, ForeignKey("library_dataset_collection_association.id"), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    dataset_collection = relationship('LibraryDatasetCollectionAssociation', back_populates='tags')
-    tag = relationship('Tag')
-    user = relationship('User')
+    dataset_collection = relationship("LibraryDatasetCollectionAssociation", back_populates="tags")
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 class ToolTagAssociation(Base, ItemTagAssociation, RepresentById):
-    __tablename__ = 'tool_tag_association'
+    __tablename__ = "tool_tag_association"
 
     id = Column(Integer, primary_key=True)
     tool_id = Column(TrimmedString(255), index=True)
-    tag_id = Column(Integer, ForeignKey('tag.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    tag_id = Column(Integer, ForeignKey("tag.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    tag = relationship('Tag')
-    user = relationship('User')
+    tag = relationship("Tag")
+    user = relationship("User")
 
 
 # Item annotation classes.
 class HistoryAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'history_annotation_association'
-    __table_args__ = (
-        Index('ix_history_anno_assoc_annotation', 'annotation', mysql_length=200),
-    )
+    __tablename__ = "history_annotation_association"
+    __table_args__ = (Index("ix_history_anno_assoc_annotation", "annotation", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    history = relationship('History', back_populates='annotations')
-    user = relationship('User')
+    history = relationship("History", back_populates="annotations")
+    user = relationship("User")
 
 
 class HistoryDatasetAssociationAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'history_dataset_association_annotation_association'
-    __table_args__ = (
-        Index('ix_history_dataset_anno_assoc_annotation', 'annotation', mysql_length=200),
-    )
+    __tablename__ = "history_dataset_association_annotation_association"
+    __table_args__ = (Index("ix_history_dataset_anno_assoc_annotation", "annotation", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    hda = relationship('HistoryDatasetAssociation', back_populates='annotations')
-    user = relationship('User')
+    hda = relationship("HistoryDatasetAssociation", back_populates="annotations")
+    user = relationship("User")
 
 
 class StoredWorkflowAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'stored_workflow_annotation_association'
-    __table_args__ = (
-        Index('ix_stored_workflow_ann_assoc_annotation', 'annotation', mysql_length=200),
-    )
+    __tablename__ = "stored_workflow_annotation_association"
+    __table_args__ = (Index("ix_stored_workflow_ann_assoc_annotation", "annotation", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey('stored_workflow.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    stored_workflow = relationship('StoredWorkflow', back_populates='annotations')
-    user = relationship('User')
+    stored_workflow = relationship("StoredWorkflow", back_populates="annotations")
+    user = relationship("User")
 
 
 class WorkflowStepAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'workflow_step_annotation_association'
-    __table_args__ = (
-        Index('ix_workflow_step_ann_assoc_annotation', 'annotation', mysql_length=200),
-    )
+    __tablename__ = "workflow_step_annotation_association"
+    __table_args__ = (Index("ix_workflow_step_ann_assoc_annotation", "annotation", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    workflow_step_id = Column(Integer, ForeignKey('workflow_step.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    workflow_step_id = Column(Integer, ForeignKey("workflow_step.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    workflow_step = relationship('WorkflowStep', back_populates='annotations')
-    user = relationship('User')
+    workflow_step = relationship("WorkflowStep", back_populates="annotations")
+    user = relationship("User")
 
 
 class PageAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'page_annotation_association'
-    __table_args__ = (
-        Index('ix_page_annotation_association_annotation', 'annotation', mysql_length=200),
-    )
+    __tablename__ = "page_annotation_association"
+    __table_args__ = (Index("ix_page_annotation_association_annotation", "annotation", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey('page.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    page_id = Column(Integer, ForeignKey("page.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    page = relationship('Page', back_populates='annotations')
-    user = relationship('User')
+    page = relationship("Page", back_populates="annotations")
+    user = relationship("User")
 
 
 class VisualizationAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'visualization_annotation_association'
-    __table_args__ = (
-        Index('ix_visualization_annotation_association_annotation', 'annotation', mysql_length=200),
-    )
+    __tablename__ = "visualization_annotation_association"
+    __table_args__ = (Index("ix_visualization_annotation_association_annotation", "annotation", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey('visualization.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    visualization = relationship('Visualization', back_populates='annotations')
-    user = relationship('User')
+    visualization = relationship("Visualization", back_populates="annotations")
+    user = relationship("User")
 
 
 class HistoryDatasetCollectionAssociationAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'history_dataset_collection_annotation_association'
+    __tablename__ = "history_dataset_collection_annotation_association"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_collection_id = Column(
-        Integer, ForeignKey('history_dataset_collection_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    history_dataset_collection = relationship('HistoryDatasetCollectionAssociation',
-        back_populates='annotations')
-    user = relationship('User')
+    history_dataset_collection = relationship("HistoryDatasetCollectionAssociation", back_populates="annotations")
+    user = relationship("User")
 
 
 class LibraryDatasetCollectionAnnotationAssociation(Base, RepresentById):
-    __tablename__ = 'library_dataset_collection_annotation_association'
+    __tablename__ = "library_dataset_collection_annotation_association"
 
     id = Column(Integer, primary_key=True)
-    library_dataset_collection_id = Column(
-        Integer, ForeignKey('library_dataset_collection_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    library_dataset_collection_id = Column(Integer, ForeignKey("library_dataset_collection_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     annotation = Column(TEXT)
-    dataset_collection = relationship('LibraryDatasetCollectionAssociation',
-        back_populates='annotations')
-    user = relationship('User')
+    dataset_collection = relationship("LibraryDatasetCollectionAssociation", back_populates="annotations")
+    user = relationship("User")
 
 
 class Vault(Base):
-    __tablename__ = 'vault'
+    __tablename__ = "vault"
 
     key = Column(Text, primary_key=True)
     parent_key = Column(Text, ForeignKey(key), index=True, nullable=True)
-    children = relationship('Vault', back_populates='parent')
-    parent = relationship('Vault', back_populates='children', remote_side=[key])
+    children = relationship("Vault", back_populates="parent")
+    parent = relationship("Vault", back_populates="children", remote_side=[key])
     value = Column(Text, nullable=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
@@ -8516,106 +8949,103 @@ class ItemRatingAssociation(Base):
         self._set_item(item)
 
     def _set_item(self, item):
-        """ Set association's item. """
+        """Set association's item."""
         raise NotImplementedError()
 
 
 class HistoryRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'history_rating_association'
+    __tablename__ = "history_rating_association"
 
     id = Column(Integer, primary_key=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    history = relationship('History', back_populates='ratings')
-    user = relationship('User')
+    history = relationship("History", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, history):
         self.history = history
 
 
 class HistoryDatasetAssociationRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'history_dataset_association_rating_association'
+    __tablename__ = "history_dataset_association_rating_association"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_association_id = Column(Integer,
-        ForeignKey('history_dataset_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_association_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    history_dataset_association = relationship('HistoryDatasetAssociation', back_populates='ratings')
-    user = relationship('User')
+    history_dataset_association = relationship("HistoryDatasetAssociation", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, history_dataset_association):
         self.history_dataset_association = history_dataset_association
 
 
 class StoredWorkflowRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'stored_workflow_rating_association'
+    __tablename__ = "stored_workflow_rating_association"
 
     id = Column(Integer, primary_key=True)
-    stored_workflow_id = Column(Integer, ForeignKey('stored_workflow.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    stored_workflow_id = Column(Integer, ForeignKey("stored_workflow.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    stored_workflow = relationship('StoredWorkflow', back_populates='ratings')
-    user = relationship('User')
+    stored_workflow = relationship("StoredWorkflow", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, stored_workflow):
         self.stored_workflow = stored_workflow
 
 
 class PageRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'page_rating_association'
+    __tablename__ = "page_rating_association"
 
     id = Column(Integer, primary_key=True)
-    page_id = Column(Integer, ForeignKey('page.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    page_id = Column(Integer, ForeignKey("page.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    page = relationship('Page', back_populates='ratings')
-    user = relationship('User')
+    page = relationship("Page", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, page):
         self.page = page
 
 
 class VisualizationRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'visualization_rating_association'
+    __tablename__ = "visualization_rating_association"
 
     id = Column(Integer, primary_key=True)
-    visualization_id = Column(Integer, ForeignKey('visualization.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    visualization_id = Column(Integer, ForeignKey("visualization.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    visualization = relationship('Visualization', back_populates='ratings')
-    user = relationship('User')
+    visualization = relationship("Visualization", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, visualization):
         self.visualization = visualization
 
 
 class HistoryDatasetCollectionRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'history_dataset_collection_rating_association'
+    __tablename__ = "history_dataset_collection_rating_association"
 
     id = Column(Integer, primary_key=True)
-    history_dataset_collection_id = Column(
-        Integer, ForeignKey('history_dataset_collection_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    history_dataset_collection_id = Column(Integer, ForeignKey("history_dataset_collection_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    dataset_collection = relationship('HistoryDatasetCollectionAssociation', back_populates='ratings')
-    user = relationship('User')
+    dataset_collection = relationship("HistoryDatasetCollectionAssociation", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, dataset_collection):
         self.dataset_collection = dataset_collection
 
 
 class LibraryDatasetCollectionRatingAssociation(ItemRatingAssociation, RepresentById):
-    __tablename__ = 'library_dataset_collection_rating_association'
+    __tablename__ = "library_dataset_collection_rating_association"
 
     id = Column(Integer, primary_key=True)
-    library_dataset_collection_id = Column(
-        Integer, ForeignKey('library_dataset_collection_association.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    library_dataset_collection_id = Column(Integer, ForeignKey("library_dataset_collection_association.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
-    dataset_collection = relationship('LibraryDatasetCollectionAssociation', back_populates='ratings')
-    user = relationship('User')
+    dataset_collection = relationship("LibraryDatasetCollectionAssociation", back_populates="ratings")
+    user = relationship("User")
 
     def _set_item(self, dataset_collection):
         self.dataset_collection = dataset_collection
@@ -8623,36 +9053,34 @@ class LibraryDatasetCollectionRatingAssociation(ItemRatingAssociation, Represent
 
 # Data manager classes.
 class DataManagerHistoryAssociation(Base, RepresentById):
-    __tablename__ = 'data_manager_history_association'
+    __tablename__ = "data_manager_history_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, index=True, default=now, onupdate=now)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
-    history = relationship('History')
-    user = relationship('User', back_populates='data_manager_histories')
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
+    history = relationship("History")
+    user = relationship("User", back_populates="data_manager_histories")
 
 
 class DataManagerJobAssociation(Base, RepresentById):
-    __tablename__ = 'data_manager_job_association'
-    __table_args__ = (
-        Index('ix_data_manager_job_association_data_manager_id', 'data_manager_id', mysql_length=200),
-    )
+    __tablename__ = "data_manager_job_association"
+    __table_args__ = (Index("ix_data_manager_job_association_data_manager_id", "data_manager_id", mysql_length=200),)
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, index=True, default=now, onupdate=now)
     job_id = Column(Integer, ForeignKey("job.id"), index=True)
     data_manager_id = Column(TEXT)
-    job = relationship('Job', back_populates='data_manager_association', uselist=False)
+    job = relationship("Job", back_populates="data_manager_association", uselist=False)
 
 
 class UserPreference(Base, RepresentById):
-    __tablename__ = 'user_preference'
+    __tablename__ = "user_preference"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     name = Column(Unicode(255), index=True)
     value = Column(Text)
 
@@ -8664,7 +9092,7 @@ class UserPreference(Base, RepresentById):
 
 
 class UserAction(Base, RepresentById):
-    __tablename__ = 'user_action'
+    __tablename__ = "user_action"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -8673,17 +9101,17 @@ class UserAction(Base, RepresentById):
     action = Column(Unicode(255))
     context = Column(Unicode(512))
     params = Column(Unicode(1024))
-    user = relationship('User')
+    user = relationship("User")
 
 
 class APIKeys(Base, RepresentById):
-    __tablename__ = 'api_keys'
+    __tablename__ = "api_keys"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
+    user_id = Column(Integer, ForeignKey("galaxy_user.id"), index=True)
     key = Column(TrimmedString(32), index=True, unique=True)
-    user = relationship('User', back_populates='api_keys')
+    user = relationship("User", back_populates="api_keys")
 
 
 def copy_list(lst, *args, **kwds):
@@ -8694,7 +9122,7 @@ def copy_list(lst, *args, **kwds):
 
 
 def _prepare_metadata_for_serialization(id_encoder, serialization_options, metadata):
-    """ Prepare metatdata for exporting. """
+    """Prepare metatdata for exporting."""
     processed_metadata = {}
     for name, value in metadata.items():
         # Metadata files are not needed for export because they can be
@@ -8712,8 +9140,9 @@ def _prepare_metadata_for_serialization(id_encoder, serialization_options, metad
 # The following CleanupEvent* models could be defined as tables only;
 # however making them models keeps things simple and consistent.
 
+
 class CleanupEvent(Base):
-    __tablename__ = 'cleanup_event'
+    __tablename__ = "cleanup_event"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -8721,84 +9150,84 @@ class CleanupEvent(Base):
 
 
 class CleanupEventDatasetAssociation(Base):
-    __tablename__ = 'cleanup_event_dataset_association'
+    __tablename__ = "cleanup_event_dataset_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    dataset_id = Column(Integer, ForeignKey('dataset.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    dataset_id = Column(Integer, ForeignKey("dataset.id"), index=True)
 
 
 class CleanupEventMetadataFileAssociation(Base):
-    __tablename__ = 'cleanup_event_metadata_file_association'
+    __tablename__ = "cleanup_event_metadata_file_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    metadata_file_id = Column(Integer, ForeignKey('metadata_file.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    metadata_file_id = Column(Integer, ForeignKey("metadata_file.id"), index=True)
 
 
 class CleanupEventHistoryAssociation(Base):
-    __tablename__ = 'cleanup_event_history_association'
+    __tablename__ = "cleanup_event_history_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    history_id = Column(Integer, ForeignKey('history.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    history_id = Column(Integer, ForeignKey("history.id"), index=True)
 
 
 class CleanupEventHistoryDatasetAssociationAssociation(Base):
-    __tablename__ = 'cleanup_event_hda_association'
+    __tablename__ = "cleanup_event_hda_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    hda_id = Column(Integer, ForeignKey('history_dataset_association.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    hda_id = Column(Integer, ForeignKey("history_dataset_association.id"), index=True)
 
 
 class CleanupEventLibraryAssociation(Base):
-    __tablename__ = 'cleanup_event_library_association'
+    __tablename__ = "cleanup_event_library_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    library_id = Column(Integer, ForeignKey('library.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    library_id = Column(Integer, ForeignKey("library.id"), index=True)
 
 
 class CleanupEventLibraryFolderAssociation(Base):
-    __tablename__ = 'cleanup_event_library_folder_association'
+    __tablename__ = "cleanup_event_library_folder_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    library_folder_id = Column(Integer, ForeignKey('library_folder.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    library_folder_id = Column(Integer, ForeignKey("library_folder.id"), index=True)
 
 
 class CleanupEventLibraryDatasetAssociation(Base):
-    __tablename__ = 'cleanup_event_library_dataset_association'
+    __tablename__ = "cleanup_event_library_dataset_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    library_dataset_id = Column(Integer, ForeignKey('library_dataset.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    library_dataset_id = Column(Integer, ForeignKey("library_dataset.id"), index=True)
 
 
 class CleanupEventLibraryDatasetDatasetAssociationAssociation(Base):
-    __tablename__ = 'cleanup_event_ldda_association'
+    __tablename__ = "cleanup_event_ldda_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    ldda_id = Column(Integer, ForeignKey('library_dataset_dataset_association.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    ldda_id = Column(Integer, ForeignKey("library_dataset_dataset_association.id"), index=True)
 
 
 class CleanupEventImplicitlyConvertedDatasetAssociationAssociation(Base):
-    __tablename__ = 'cleanup_event_icda_association'
+    __tablename__ = "cleanup_event_icda_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    cleanup_event_id = Column(Integer, ForeignKey('cleanup_event.id'), index=True, nullable=True)
-    icda_id = Column(Integer, ForeignKey('implicitly_converted_dataset_association.id'), index=True)
+    cleanup_event_id = Column(Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True)
+    icda_id = Column(Integer, ForeignKey("implicitly_converted_dataset_association.id"), index=True)
 
 
 # The following models (Dataset, HDA, LDDA) are mapped imperatively (for details see discussion in PR #12064)
@@ -8808,294 +9237,391 @@ class CleanupEventImplicitlyConvertedDatasetAssociationAssociation(Base):
 # mapping into the test; however, having all models mapped in the same module is cleaner.
 
 Dataset.table = Table(
-    'dataset', mapper_registry.metadata,
-    Column('id', Integer, primary_key=True),
-    Column('job_id', Integer, ForeignKey('job.id'), index=True, nullable=True),
-    Column('create_time', DateTime, default=now),
-    Column('update_time', DateTime, index=True, default=now, onupdate=now),
-    Column('state', TrimmedString(64), index=True),
-    Column('deleted', Boolean, index=True, default=False),
-    Column('purged', Boolean, index=True, default=False),
-    Column('purgable', Boolean, default=True),
-    Column('object_store_id', TrimmedString(255), index=True),
-    Column('external_filename', TEXT),
-    Column('_extra_files_path', TEXT),
-    Column('created_from_basename', TEXT),
-    Column('file_size', Numeric(15, 0)),
-    Column('total_size', Numeric(15, 0)),
-    Column('uuid', UUIDType()))
+    "dataset",
+    mapper_registry.metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, index=True, default=now, onupdate=now),
+    Column("state", TrimmedString(64), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+    Column("purged", Boolean, index=True, default=False),
+    Column("purgable", Boolean, default=True),
+    Column("object_store_id", TrimmedString(255), index=True),
+    Column("external_filename", TEXT),
+    Column("_extra_files_path", TEXT),
+    Column("created_from_basename", TEXT),
+    Column("file_size", Numeric(15, 0)),
+    Column("total_size", Numeric(15, 0)),
+    Column("uuid", UUIDType()),
+)
 
 HistoryDatasetAssociation.table = Table(
-    'history_dataset_association', mapper_registry.metadata,
-    Column('id', Integer, primary_key=True),
-    Column('history_id', Integer, ForeignKey('history.id'), index=True),
-    Column('dataset_id', Integer, ForeignKey('dataset.id'), index=True),
-    Column('create_time', DateTime, default=now),
-    Column('update_time', DateTime, default=now, onupdate=now, index=True),
-    Column('state', TrimmedString(64), index=True, key='_state'),
-    Column('copied_from_history_dataset_association_id', Integer,
-           ForeignKey('history_dataset_association.id'), nullable=True),
-    Column('copied_from_library_dataset_dataset_association_id', Integer,
-           ForeignKey('library_dataset_dataset_association.id'), nullable=True),
-    Column('name', TrimmedString(255)),
-    Column('info', TrimmedString(255)),
-    Column('blurb', TrimmedString(255)),
-    Column('peek', TEXT, key='_peek'),
-    Column('tool_version', TEXT),
-    Column('extension', TrimmedString(64)),
-    Column('metadata', JSONType, key='_metadata'),
-    Column('parent_id', Integer, ForeignKey('history_dataset_association.id'), nullable=True),
-    Column('designation', TrimmedString(255)),
-    Column('deleted', Boolean, index=True, default=False),
-    Column('visible', Boolean),
-    Column('extended_metadata_id', Integer, ForeignKey('extended_metadata.id'), index=True),
-    Column('version', Integer, default=1, nullable=True, index=True),
-    Column('hid', Integer),
-    Column('purged', Boolean, index=True, default=False),
-    Column('validated_state', TrimmedString(64), default='unvalidated', nullable=False),
-    Column('validated_state_message', TEXT),
-    Column('hidden_beneath_collection_instance_id',
-           ForeignKey('history_dataset_collection_association.id'), nullable=True))
+    "history_dataset_association",
+    mapper_registry.metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now, index=True),
+    Column("state", TrimmedString(64), index=True, key="_state"),
+    Column(
+        "copied_from_history_dataset_association_id",
+        Integer,
+        ForeignKey("history_dataset_association.id"),
+        nullable=True,
+    ),
+    Column(
+        "copied_from_library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        nullable=True,
+    ),
+    Column("name", TrimmedString(255)),
+    Column("info", TrimmedString(255)),
+    Column("blurb", TrimmedString(255)),
+    Column("peek", TEXT, key="_peek"),
+    Column("tool_version", TEXT),
+    Column("extension", TrimmedString(64)),
+    Column("metadata", JSONType, key="_metadata"),
+    Column("parent_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
+    Column("designation", TrimmedString(255)),
+    Column("deleted", Boolean, index=True, default=False),
+    Column("visible", Boolean),
+    Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
+    Column("version", Integer, default=1, nullable=True, index=True),
+    Column("hid", Integer),
+    Column("purged", Boolean, index=True, default=False),
+    Column("validated_state", TrimmedString(64), default="unvalidated", nullable=False),
+    Column("validated_state_message", TEXT),
+    Column(
+        "hidden_beneath_collection_instance_id", ForeignKey("history_dataset_collection_association.id"), nullable=True
+    ),
+)
 
 LibraryDatasetDatasetAssociation.table = Table(
-    'library_dataset_dataset_association', mapper_registry.metadata,
-    Column('id', Integer, primary_key=True),
-    Column('library_dataset_id', Integer, ForeignKey('library_dataset.id'), index=True),
-    Column('dataset_id', Integer, ForeignKey('dataset.id'), index=True),
-    Column('create_time', DateTime, default=now),
-    Column('update_time', DateTime, default=now, onupdate=now, index=True),
-    Column('state', TrimmedString(64), index=True, key='_state'),
-    Column('copied_from_history_dataset_association_id', Integer,
-        ForeignKey('history_dataset_association.id',
-            use_alter=True, name='history_dataset_association_dataset_id_fkey'),
-        nullable=True),
-    Column('copied_from_library_dataset_dataset_association_id', Integer,
-        ForeignKey('library_dataset_dataset_association.id',
-            use_alter=True, name='library_dataset_dataset_association_id_fkey'),
-        nullable=True),
-    Column('name', TrimmedString(255), index=True),
-    Column('info', TrimmedString(255)),
-    Column('blurb', TrimmedString(255)),
-    Column('peek', TEXT, key='_peek'),
-    Column('tool_version', TEXT),
-    Column('extension', TrimmedString(64)),
-    Column('metadata', JSONType, key='_metadata'),
-    Column('parent_id', Integer, ForeignKey('library_dataset_dataset_association.id'), nullable=True),
-    Column('designation', TrimmedString(255)),
-    Column('deleted', Boolean, index=True, default=False),
-    Column('validated_state', TrimmedString(64), default='unvalidated', nullable=False),
-    Column('validated_state_message', TEXT),
-    Column('visible', Boolean),
-    Column('extended_metadata_id', Integer, ForeignKey('extended_metadata.id'), index=True),
-    Column('user_id', Integer, ForeignKey('galaxy_user.id'), index=True),
-    Column('message', TrimmedString(255)))
+    "library_dataset_dataset_association",
+    mapper_registry.metadata,
+    Column("id", Integer, primary_key=True),
+    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now, index=True),
+    Column("state", TrimmedString(64), index=True, key="_state"),
+    Column(
+        "copied_from_history_dataset_association_id",
+        Integer,
+        ForeignKey(
+            "history_dataset_association.id", use_alter=True, name="history_dataset_association_dataset_id_fkey"
+        ),
+        nullable=True,
+    ),
+    Column(
+        "copied_from_library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey(
+            "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fkey"
+        ),
+        nullable=True,
+    ),
+    Column("name", TrimmedString(255), index=True),
+    Column("info", TrimmedString(255)),
+    Column("blurb", TrimmedString(255)),
+    Column("peek", TEXT, key="_peek"),
+    Column("tool_version", TEXT),
+    Column("extension", TrimmedString(64)),
+    Column("metadata", JSONType, key="_metadata"),
+    Column("parent_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
+    Column("designation", TrimmedString(255)),
+    Column("deleted", Boolean, index=True, default=False),
+    Column("validated_state", TrimmedString(64), default="unvalidated", nullable=False),
+    Column("validated_state_message", TEXT),
+    Column("visible", Boolean),
+    Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("message", TrimmedString(255)),
+)
 
 mapper_registry.map_imperatively(
     Dataset,
     Dataset.table,
     properties=dict(
-        actions=relationship(DatasetPermissions, back_populates='dataset'),
+        actions=relationship(DatasetPermissions, back_populates="dataset"),
         job=relationship(Job, primaryjoin=(Dataset.table.c.job_id == Job.id)),
-        active_history_associations=relationship(HistoryDatasetAssociation,
+        active_history_associations=relationship(
+            HistoryDatasetAssociation,
             primaryjoin=(
                 (Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id)
                 & (HistoryDatasetAssociation.table.c.deleted == false())
-                & (HistoryDatasetAssociation.table.c.purged == false())),
-            viewonly=True),
-        purged_history_associations=relationship(HistoryDatasetAssociation,
+                & (HistoryDatasetAssociation.table.c.purged == false())
+            ),
+            viewonly=True,
+        ),
+        purged_history_associations=relationship(
+            HistoryDatasetAssociation,
             primaryjoin=(
                 (Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id)
-                & (HistoryDatasetAssociation.table.c.purged == true())),
-            viewonly=True),
-        active_library_associations=relationship(LibraryDatasetDatasetAssociation,
+                & (HistoryDatasetAssociation.table.c.purged == true())
+            ),
+            viewonly=True,
+        ),
+        active_library_associations=relationship(
+            LibraryDatasetDatasetAssociation,
             primaryjoin=(
                 (Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id)
-                & (LibraryDatasetDatasetAssociation.table.c.deleted == false())),
-            viewonly=True),
-        hashes=relationship(DatasetHash, back_populates='dataset'),
-        sources=relationship(DatasetSource, back_populates='dataset'),
-        history_associations=relationship(HistoryDatasetAssociation, back_populates='dataset'),
-        library_associations=relationship(LibraryDatasetDatasetAssociation,
+                & (LibraryDatasetDatasetAssociation.table.c.deleted == false())
+            ),
+            viewonly=True,
+        ),
+        hashes=relationship(DatasetHash, back_populates="dataset"),
+        sources=relationship(DatasetSource, back_populates="dataset"),
+        history_associations=relationship(HistoryDatasetAssociation, back_populates="dataset"),
+        library_associations=relationship(
+            LibraryDatasetDatasetAssociation,
             primaryjoin=(LibraryDatasetDatasetAssociation.table.c.dataset_id == Dataset.table.c.id),
-            back_populates='dataset'),
-    )
+            back_populates="dataset",
+        ),
+    ),
 )
 
 mapper_registry.map_imperatively(
     HistoryDatasetAssociation,
     HistoryDatasetAssociation.table,
     properties=dict(
-        dataset=relationship(Dataset,
+        dataset=relationship(
+            Dataset,
             primaryjoin=(Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id),
             lazy="joined",
-            back_populates='history_associations'),
-        copied_from_history_dataset_association=relationship(HistoryDatasetAssociation,
-            primaryjoin=(HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
-                == HistoryDatasetAssociation.table.c.id),
+            back_populates="history_associations",
+        ),
+        copied_from_history_dataset_association=relationship(
+            HistoryDatasetAssociation,
+            primaryjoin=(
+                HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
+                == HistoryDatasetAssociation.table.c.id
+            ),
             remote_side=[HistoryDatasetAssociation.table.c.id],
             uselist=False,
-            back_populates='copied_to_history_dataset_associations'),
-        copied_from_library_dataset_dataset_association=relationship(LibraryDatasetDatasetAssociation,
-            primaryjoin=(LibraryDatasetDatasetAssociation.table.c.id
-                == HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id),
-            back_populates='copied_to_history_dataset_associations'),
-        copied_to_history_dataset_associations=relationship(HistoryDatasetAssociation,
-            primaryjoin=(HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
-                == HistoryDatasetAssociation.table.c.id),
-            back_populates='copied_from_history_dataset_association'),
-        copied_to_library_dataset_dataset_associations=relationship(LibraryDatasetDatasetAssociation,
-            primaryjoin=(HistoryDatasetAssociation.table.c.id
-                == LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id),
-            back_populates='copied_from_history_dataset_association'),
-        tags=relationship(HistoryDatasetAssociationTagAssociation,
+            back_populates="copied_to_history_dataset_associations",
+        ),
+        copied_from_library_dataset_dataset_association=relationship(
+            LibraryDatasetDatasetAssociation,
+            primaryjoin=(
+                LibraryDatasetDatasetAssociation.table.c.id
+                == HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+            ),
+            back_populates="copied_to_history_dataset_associations",
+        ),
+        copied_to_history_dataset_associations=relationship(
+            HistoryDatasetAssociation,
+            primaryjoin=(
+                HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
+                == HistoryDatasetAssociation.table.c.id
+            ),
+            back_populates="copied_from_history_dataset_association",
+        ),
+        copied_to_library_dataset_dataset_associations=relationship(
+            LibraryDatasetDatasetAssociation,
+            primaryjoin=(
+                HistoryDatasetAssociation.table.c.id
+                == LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id
+            ),
+            back_populates="copied_from_history_dataset_association",
+        ),
+        tags=relationship(
+            HistoryDatasetAssociationTagAssociation,
             order_by=HistoryDatasetAssociationTagAssociation.id,
-            back_populates='history_dataset_association'),
-        annotations=relationship(HistoryDatasetAssociationAnnotationAssociation,
+            back_populates="history_dataset_association",
+        ),
+        annotations=relationship(
+            HistoryDatasetAssociationAnnotationAssociation,
             order_by=HistoryDatasetAssociationAnnotationAssociation.id,
-            back_populates="hda"),
-        ratings=relationship(HistoryDatasetAssociationRatingAssociation,
+            back_populates="hda",
+        ),
+        ratings=relationship(
+            HistoryDatasetAssociationRatingAssociation,
             order_by=HistoryDatasetAssociationRatingAssociation.id,
-            back_populates="history_dataset_association"),
-        extended_metadata=relationship(ExtendedMetadata,
-            primaryjoin=(HistoryDatasetAssociation.table.c.extended_metadata_id
-                == ExtendedMetadata.id)),
-        hidden_beneath_collection_instance=relationship(HistoryDatasetCollectionAssociation,
-            primaryjoin=(HistoryDatasetAssociation.table.c.hidden_beneath_collection_instance_id
-                == HistoryDatasetCollectionAssociation.id),
-            uselist=False),
+            back_populates="history_dataset_association",
+        ),
+        extended_metadata=relationship(
+            ExtendedMetadata,
+            primaryjoin=(HistoryDatasetAssociation.table.c.extended_metadata_id == ExtendedMetadata.id),
+        ),
+        hidden_beneath_collection_instance=relationship(
+            HistoryDatasetCollectionAssociation,
+            primaryjoin=(
+                HistoryDatasetAssociation.table.c.hidden_beneath_collection_instance_id
+                == HistoryDatasetCollectionAssociation.id
+            ),
+            uselist=False,
+        ),
         _metadata=deferred(HistoryDatasetAssociation.table.c._metadata),
-        dependent_jobs=relationship(JobToInputDatasetAssociation, back_populates='dataset'),
-        creating_job_associations=relationship(
-            JobToOutputDatasetAssociation, back_populates='dataset'),
-        history=relationship(History, back_populates='datasets'),
-        implicitly_converted_datasets=relationship(ImplicitlyConvertedDatasetAssociation,
-            primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_parent_id
-                == HistoryDatasetAssociation.id),
-            back_populates='parent_hda'),
-        implicitly_converted_parent_datasets=relationship(ImplicitlyConvertedDatasetAssociation,
-            primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_id
-                == HistoryDatasetAssociation.id),
-            back_populates='dataset')
-    )
+        dependent_jobs=relationship(JobToInputDatasetAssociation, back_populates="dataset"),
+        creating_job_associations=relationship(JobToOutputDatasetAssociation, back_populates="dataset"),
+        history=relationship(History, back_populates="datasets"),
+        implicitly_converted_datasets=relationship(
+            ImplicitlyConvertedDatasetAssociation,
+            primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_parent_id == HistoryDatasetAssociation.id),
+            back_populates="parent_hda",
+        ),
+        implicitly_converted_parent_datasets=relationship(
+            ImplicitlyConvertedDatasetAssociation,
+            primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.hda_id == HistoryDatasetAssociation.id),
+            back_populates="dataset",
+        ),
+    ),
 )
 
 mapper_registry.map_imperatively(
     LibraryDatasetDatasetAssociation,
     LibraryDatasetDatasetAssociation.table,
     properties=dict(
-        dataset=relationship(Dataset,
+        dataset=relationship(
+            Dataset,
             primaryjoin=(LibraryDatasetDatasetAssociation.table.c.dataset_id == Dataset.table.c.id),
-            back_populates='library_associations'),
-        library_dataset=relationship(LibraryDataset,
-            foreign_keys=LibraryDatasetDatasetAssociation.table.c.library_dataset_id),
+            back_populates="library_associations",
+        ),
+        library_dataset=relationship(
+            LibraryDataset, foreign_keys=LibraryDatasetDatasetAssociation.table.c.library_dataset_id
+        ),
         user=relationship(User),
-        copied_from_library_dataset_dataset_association=relationship(LibraryDatasetDatasetAssociation,
+        copied_from_library_dataset_dataset_association=relationship(
+            LibraryDatasetDatasetAssociation,
             primaryjoin=(
                 LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
-                == LibraryDatasetDatasetAssociation.table.c.id),
+                == LibraryDatasetDatasetAssociation.table.c.id
+            ),
             remote_side=[LibraryDatasetDatasetAssociation.table.c.id],
             uselist=False,
-            back_populates='copied_to_library_dataset_dataset_associations'),
-        copied_to_library_dataset_dataset_associations=relationship(LibraryDatasetDatasetAssociation,
+            back_populates="copied_to_library_dataset_dataset_associations",
+        ),
+        copied_to_library_dataset_dataset_associations=relationship(
+            LibraryDatasetDatasetAssociation,
             primaryjoin=(
                 LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
-                == LibraryDatasetDatasetAssociation.table.c.id),
-            back_populates='copied_from_library_dataset_dataset_association'),
-        copied_to_history_dataset_associations=relationship(HistoryDatasetAssociation,
-            primaryjoin=(LibraryDatasetDatasetAssociation.table.c.id
-                == HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id),
-            back_populates='copied_from_library_dataset_dataset_association'),
-        implicitly_converted_datasets=relationship(ImplicitlyConvertedDatasetAssociation,
-            primaryjoin=(ImplicitlyConvertedDatasetAssociation.ldda_parent_id
-                         == LibraryDatasetDatasetAssociation.table.c.id),
-            back_populates='parent_ldda'),
-        tags=relationship(LibraryDatasetDatasetAssociationTagAssociation,
-                      order_by=LibraryDatasetDatasetAssociationTagAssociation.id,
-                      back_populates='library_dataset_dataset_association'),
-        extended_metadata=relationship(ExtendedMetadata,
-            primaryjoin=(LibraryDatasetDatasetAssociation.table.c.extended_metadata_id
-                == ExtendedMetadata.id)
+                == LibraryDatasetDatasetAssociation.table.c.id
+            ),
+            back_populates="copied_from_library_dataset_dataset_association",
+        ),
+        copied_to_history_dataset_associations=relationship(
+            HistoryDatasetAssociation,
+            primaryjoin=(
+                LibraryDatasetDatasetAssociation.table.c.id
+                == HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+            ),
+            back_populates="copied_from_library_dataset_dataset_association",
+        ),
+        implicitly_converted_datasets=relationship(
+            ImplicitlyConvertedDatasetAssociation,
+            primaryjoin=(
+                ImplicitlyConvertedDatasetAssociation.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id
+            ),
+            back_populates="parent_ldda",
+        ),
+        tags=relationship(
+            LibraryDatasetDatasetAssociationTagAssociation,
+            order_by=LibraryDatasetDatasetAssociationTagAssociation.id,
+            back_populates="library_dataset_dataset_association",
+        ),
+        extended_metadata=relationship(
+            ExtendedMetadata,
+            primaryjoin=(LibraryDatasetDatasetAssociation.table.c.extended_metadata_id == ExtendedMetadata.id),
         ),
         _metadata=deferred(LibraryDatasetDatasetAssociation.table.c._metadata),
         actions=relationship(
-            LibraryDatasetDatasetAssociationPermissions,
-            back_populates='library_dataset_dataset_association'),
-        dependent_jobs=relationship(
-            JobToInputLibraryDatasetAssociation, back_populates='dataset'),
-        creating_job_associations=relationship(
-            JobToOutputLibraryDatasetAssociation, back_populates='dataset'),
-        implicitly_converted_parent_datasets=relationship(ImplicitlyConvertedDatasetAssociation,
-            primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.ldda_id
-                == LibraryDatasetDatasetAssociation.id),
-            back_populates='dataset_ldda'),
-        copied_from_history_dataset_association=relationship(HistoryDatasetAssociation,
-            primaryjoin=(HistoryDatasetAssociation.table.c.id
-                == LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id),
-            back_populates='copied_to_library_dataset_dataset_associations'),
-    )
+            LibraryDatasetDatasetAssociationPermissions, back_populates="library_dataset_dataset_association"
+        ),
+        dependent_jobs=relationship(JobToInputLibraryDatasetAssociation, back_populates="dataset"),
+        creating_job_associations=relationship(JobToOutputLibraryDatasetAssociation, back_populates="dataset"),
+        implicitly_converted_parent_datasets=relationship(
+            ImplicitlyConvertedDatasetAssociation,
+            primaryjoin=(lambda: ImplicitlyConvertedDatasetAssociation.ldda_id == LibraryDatasetDatasetAssociation.id),
+            back_populates="dataset_ldda",
+        ),
+        copied_from_history_dataset_association=relationship(
+            HistoryDatasetAssociation,
+            primaryjoin=(
+                HistoryDatasetAssociation.table.c.id
+                == LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id
+            ),
+            back_populates="copied_to_library_dataset_dataset_associations",
+        ),
+    ),
 )
 
 # ----------------------------------------------------------------------------------------
 # The following statements must not precede the mapped models defined above.
 
 Job.any_output_dataset_collection_instances_deleted = column_property(
-    exists(HistoryDatasetCollectionAssociation.id).where(and_(
-        Job.id == JobToOutputDatasetCollectionAssociation.job_id,
-        HistoryDatasetCollectionAssociation.id == JobToOutputDatasetCollectionAssociation.dataset_collection_id,
-        HistoryDatasetCollectionAssociation.deleted == true())
+    exists(HistoryDatasetCollectionAssociation.id).where(
+        and_(
+            Job.id == JobToOutputDatasetCollectionAssociation.job_id,
+            HistoryDatasetCollectionAssociation.id == JobToOutputDatasetCollectionAssociation.dataset_collection_id,
+            HistoryDatasetCollectionAssociation.deleted == true(),
+        )
     )
 )
 
 Job.any_output_dataset_deleted = column_property(
-    exists(HistoryDatasetAssociation).where(and_(
-        Job.id == JobToOutputDatasetAssociation.job_id,
-        HistoryDatasetAssociation.table.c.id == JobToOutputDatasetAssociation.dataset_id,
-        HistoryDatasetAssociation.table.c.deleted == true())
+    exists(HistoryDatasetAssociation).where(
+        and_(
+            Job.id == JobToOutputDatasetAssociation.job_id,
+            HistoryDatasetAssociation.table.c.id == JobToOutputDatasetAssociation.dataset_id,
+            HistoryDatasetAssociation.table.c.deleted == true(),
+        )
     )
 )
 
 History.average_rating = column_property(
-    select(func.avg(HistoryRatingAssociation.rating)).where(
-        HistoryRatingAssociation.history_id == History.id).scalar_subquery(),
-    deferred=True
+    select(func.avg(HistoryRatingAssociation.rating))
+    .where(HistoryRatingAssociation.history_id == History.id)
+    .scalar_subquery(),
+    deferred=True,
 )
 
 History.users_shared_with_count = column_property(
-    select(func.count(HistoryUserShareAssociation.id)).where(
-        History.id == HistoryUserShareAssociation.history_id).scalar_subquery(),
-    deferred=True
+    select(func.count(HistoryUserShareAssociation.id))
+    .where(History.id == HistoryUserShareAssociation.history_id)
+    .scalar_subquery(),
+    deferred=True,
 )
 
 Page.average_rating = column_property(
-    select(func.avg(PageRatingAssociation.rating)).where(
-        PageRatingAssociation.page_id == Page.id).scalar_subquery(),
-    deferred=True
+    select(func.avg(PageRatingAssociation.rating)).where(PageRatingAssociation.page_id == Page.id).scalar_subquery(),
+    deferred=True,
 )
 
 StoredWorkflow.average_rating = column_property(
-    select(func.avg(StoredWorkflowRatingAssociation.rating)).where(
-        StoredWorkflowRatingAssociation.stored_workflow_id == StoredWorkflow.id).scalar_subquery(),
-    deferred=True
+    select(func.avg(StoredWorkflowRatingAssociation.rating))
+    .where(StoredWorkflowRatingAssociation.stored_workflow_id == StoredWorkflow.id)
+    .scalar_subquery(),
+    deferred=True,
 )
 
 Visualization.average_rating = column_property(
-    select(func.avg(VisualizationRatingAssociation.rating)).where(
-        VisualizationRatingAssociation.visualization_id == Visualization.id).scalar_subquery(),
-    deferred=True
+    select(func.avg(VisualizationRatingAssociation.rating))
+    .where(VisualizationRatingAssociation.visualization_id == Visualization.id)
+    .scalar_subquery(),
+    deferred=True,
 )
 
 Workflow.step_count = column_property(
-    select(func.count(WorkflowStep.id)).where(Workflow.id == WorkflowStep.workflow_id).scalar_subquery(),
-    deferred=True
+    select(func.count(WorkflowStep.id)).where(Workflow.id == WorkflowStep.workflow_id).scalar_subquery(), deferred=True
 )
 
 WorkflowInvocationStep.subworkflow_invocation_id = column_property(
-    select(WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id).where(and_(
-        WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id == WorkflowInvocationStep.workflow_invocation_id,
-        WorkflowInvocationToSubworkflowInvocationAssociation.workflow_step_id == WorkflowInvocationStep.workflow_step_id,
-    )).scalar_subquery(),
+    select(WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id)
+    .where(
+        and_(
+            WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id
+            == WorkflowInvocationStep.workflow_invocation_id,
+            WorkflowInvocationToSubworkflowInvocationAssociation.workflow_step_id
+            == WorkflowInvocationStep.workflow_step_id,
+        )
+    )
+    .scalar_subquery(),
 )
 
 # Set up proxy so that this syntax is possible:
 # <user_obj>.preferences[pref_name] = pref_value
-User.preferences = association_proxy('_preferences', 'value', creator=UserPreference)
+User.preferences = association_proxy("_preferences", "value", creator=UserPreference)
diff --git a/lib/galaxy/model/base.py b/lib/galaxy/model/base.py
index 05bee1fd279..8c7a2efa06c 100644
--- a/lib/galaxy/model/base.py
+++ b/lib/galaxy/model/base.py
@@ -7,30 +7,31 @@ import threading
 from contextvars import ContextVar
 from inspect import (
     getmembers,
-    isclass
+    isclass,
+)
+from typing import (
+    Dict,
+    Type,
 )
-from typing import Dict, Type
 
 from sqlalchemy import event
 from sqlalchemy.orm import (
     scoped_session,
-    sessionmaker
+    sessionmaker,
 )
 
 from galaxy.util.bunch import Bunch
 
-
 # Create a ContextVar with mutable state, this allows sync tasks in the context
 # of a request (which run within a threadpool) to see changes to the ContextVar
 # state. See https://github.com/tiangolo/fastapi/issues/953#issuecomment-586006249
 # for details
 _request_state: Dict[str, str] = {}
-REQUEST_ID = ContextVar('request_id', default=_request_state.copy())
+REQUEST_ID = ContextVar("request_id", default=_request_state.copy())
 
 
 # TODO: Refactor this to be a proper class, not a bunch.
 class ModelMapping(Bunch):
-
     def __init__(self, model_modules, engine):
         self.engine = engine
         SessionLocal = sessionmaker(autoflush=False, autocommit=True)
@@ -60,14 +61,14 @@ class ModelMapping(Bunch):
         This ensures that threads or request contexts will receive a single identical session
         from the ScopedRegistry.
         """
-        return REQUEST_ID.get().get('request') or threading.get_ident()
+        return REQUEST_ID.get().get("request") or threading.get_ident()
 
     @staticmethod
     def set_request_id(request_id):
         # Set REQUEST_ID to a new dict.
         # This new ContextVar value will only be seen by the current asyncio context
         # and descendant threadpools, but not other threads or asyncio contexts.
-        return REQUEST_ID.set({'request': request_id})
+        return REQUEST_ID.set({"request": request_id})
 
     def unset_request_id(self, request_id):
         # Unconditionally calling self.gx_app.model.session.remove()
@@ -96,6 +97,7 @@ class SharedModelMapping(ModelMapping):
     Generally things can be more strongly typed when importing models directly, but we need
     a way to do app.model.<CLASS> for common code shared by the tool shed and Galaxy.
     """
+
     User: Type
     GalaxySession: Type
     APIKeys: Type
@@ -104,21 +106,21 @@ class SharedModelMapping(ModelMapping):
 
 def versioned_objects(iter):
     for obj in iter:
-        if hasattr(obj, '__create_version__'):
+        if hasattr(obj, "__create_version__"):
             yield obj
 
 
 def versioned_objects_strict(iter):
     for obj in iter:
-        if hasattr(obj, '__create_version__'):
+        if hasattr(obj, "__create_version__"):
             if obj.extension != "len":
                 # TODO: Custom builds (with .len extension) do not get a history or a HID.
                 # These should get some other type of permanent storage, perhaps UserDatasetAssociation ?
                 # Everything else needs to have a hid and a history
                 if not obj.history and not obj.history_id:
-                    raise Exception(f'HistoryDatsetAssociation {obj} without history detected, this is not valid')
+                    raise Exception(f"HistoryDatsetAssociation {obj} without history detected, this is not valid")
                 elif not obj.hid:
-                    raise Exception(f'HistoryDatsetAssociation {obj} without has no hid, this is not valid')
+                    raise Exception(f"HistoryDatsetAssociation {obj} without has no hid, this is not valid")
             yield obj
 
 
@@ -127,7 +129,7 @@ if os.environ.get("GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA"):
 
 
 def versioned_session(session):
-    @event.listens_for(session, 'before_flush')
+    @event.listens_for(session, "before_flush")
     def before_flush(session, flush_context, instances):
         for obj in versioned_objects(session.dirty):
             obj.__create_version__(session)
diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index 1c1896ea8ac..b212e6b9695 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -15,12 +15,12 @@ from sqlalchemy.types import (
     CHAR,
     LargeBinary,
     String,
-    TypeDecorator
+    TypeDecorator,
 )
 
 from galaxy.util import (
     smart_str,
-    unicodify
+    unicodify,
 )
 from galaxy.util.aliaspickler import AliasPickleModule
 
@@ -51,9 +51,9 @@ def _sniffnfix_pg9_hex(value):
     Sniff for and fix postgres 9 hex decoding issue
     """
     try:
-        if value[0] == 'x':
+        if value[0] == "x":
             return binascii.unhexlify(value[1:])
-        elif smart_str(value).startswith(b'\\x'):
+        elif smart_str(value).startswith(b"\\x"):
             return binascii.unhexlify(value[2:])
         else:
             return value
@@ -71,10 +71,11 @@ class GalaxyLargeBinary(LargeBinary):
         def process(value):
             if value is not None:
                 if isinstance(value, str):
-                    value = bytes(value, encoding='utf-8')
+                    value = bytes(value, encoding="utf-8")
                 else:
                     value = bytes(value)
             return value
+
         return process
 
 
@@ -112,7 +113,7 @@ class JSONType(TypeDecorator):
         return copy.deepcopy(value)
 
     def compare_values(self, x, y):
-        return (x == y)
+        return x == y
 
 
 class MutableJSONType(JSONType):
@@ -172,20 +173,20 @@ class MutationObj(Mutable):
         def pickle(state, state_dict):
             val = state.dict.get(key, None)
             if isinstance(val, cls):
-                if 'ext.mutable.values' not in state_dict:
-                    state_dict['ext.mutable.values'] = []
-                state_dict['ext.mutable.values'].append(val)
+                if "ext.mutable.values" not in state_dict:
+                    state_dict["ext.mutable.values"] = []
+                state_dict["ext.mutable.values"].append(val)
 
         def unpickle(state, state_dict):
-            if 'ext.mutable.values' in state_dict:
-                for val in state_dict['ext.mutable.values']:
+            if "ext.mutable.values" in state_dict:
+                for val in state_dict["ext.mutable.values"]:
                     val._parents[state] = key
 
-        sqlalchemy.event.listen(parent_cls, 'load', load, raw=True, propagate=True)
-        sqlalchemy.event.listen(parent_cls, 'refresh', load, raw=True, propagate=True)
-        sqlalchemy.event.listen(attribute, 'set', set, raw=True, retval=True, propagate=True)
-        sqlalchemy.event.listen(parent_cls, 'pickle', pickle, raw=True, propagate=True)
-        sqlalchemy.event.listen(parent_cls, 'unpickle', unpickle, raw=True, propagate=True)
+        sqlalchemy.event.listen(parent_cls, "load", load, raw=True, propagate=True)
+        sqlalchemy.event.listen(parent_cls, "refresh", load, raw=True, propagate=True)
+        sqlalchemy.event.listen(attribute, "set", set, raw=True, retval=True, propagate=True)
+        sqlalchemy.event.listen(parent_cls, "pickle", pickle, raw=True, propagate=True)
+        sqlalchemy.event.listen(parent_cls, "unpickle", unpickle, raw=True, propagate=True)
 
 
 class MutationDict(MutationObj, dict):
@@ -278,13 +279,11 @@ class MutationList(MutationObj, list):
 MutationObj.associate_with(MutableJSONType)
 
 
-metadata_pickler = AliasPickleModule({
-    ("cookbook.patterns", "Bunch"): ("galaxy.util.bunch", "Bunch")
-})
+metadata_pickler = AliasPickleModule({("cookbook.patterns", "Bunch"): ("galaxy.util.bunch", "Bunch")})
 
 
 def total_size(o, handlers=None, verbose=False):
-    """ Returns the approximate memory footprint an object and all of its contents.
+    """Returns the approximate memory footprint an object and all of its contents.
 
     Automatically finds the contents of the following builtin containers and
     their subclasses:  tuple, list, deque, dict, set and frozenset.
@@ -300,18 +299,13 @@ def total_size(o, handlers=None, verbose=False):
     def dict_handler(d):
         return chain.from_iterable(d.items())
 
-    all_handlers = {tuple: iter,
-                    list: iter,
-                    deque: iter,
-                    dict: dict_handler,
-                    set: iter,
-                    frozenset: iter}
-    all_handlers.update(handlers)     # user handlers take precedence
-    seen = set()                      # track which object id's have already been seen
-    default_size = getsizeof(0)       # estimate sizeof object without __sizeof__
+    all_handlers = {tuple: iter, list: iter, deque: iter, dict: dict_handler, set: iter, frozenset: iter}
+    all_handlers.update(handlers)  # user handlers take precedence
+    seen = set()  # track which object id's have already been seen
+    default_size = getsizeof(0)  # estimate sizeof object without __sizeof__
 
     def sizeof(o):
-        if id(o) in seen:       # do not double count the same object
+        if id(o) in seen:  # do not double count the same object
             return 0
         seen.add(id(o))
         s = getsizeof(o, default_size)
@@ -338,7 +332,7 @@ class MetadataType(JSONType):
                     sz = total_size(v)
                     if sz > MAX_METADATA_VALUE_SIZE:
                         del value[k]
-                        log.warning(f'Refusing to bind metadata key {k} due to size ({sz})')
+                        log.warning(f"Refusing to bind metadata key {k} due to size ({sz})")
             value = json_encoder.encode(value).encode()
         return value
 
@@ -367,6 +361,7 @@ class UUIDType(TypeDecorator):
 
     CHAR(32), storing as stringified hex values.
     """
+
     impl = CHAR
     cache_ok = True
 
@@ -395,5 +390,5 @@ class TrimmedString(TypeDecorator):
     def process_bind_param(self, value, dialect):
         """Automatically truncate string values"""
         if self.impl.length and value is not None:
-            value = unicodify(value)[0:self.impl.length]
+            value = unicodify(value)[0 : self.impl.length]
         return value
diff --git a/lib/galaxy/model/database_heartbeat.py b/lib/galaxy/model/database_heartbeat.py
index 8a4e19e1b27..7321015f0b8 100644
--- a/lib/galaxy/model/database_heartbeat.py
+++ b/lib/galaxy/model/database_heartbeat.py
@@ -11,7 +11,6 @@ log = logging.getLogger(__name__)
 
 
 class DatabaseHeartbeat:
-
     def __init__(self, application_stack, heartbeat_interval=60):
         self.application_stack = application_stack
         self.heartbeat_interval = heartbeat_interval
@@ -34,7 +33,9 @@ class DatabaseHeartbeat:
 
     def start(self):
         if not self.active:
-            self.thread = threading.Thread(target=self.send_database_heartbeat, name=f"database_heartbeart_{self.server_name}.thread")
+            self.thread = threading.Thread(
+                target=self.send_database_heartbeat, name=f"database_heartbeart_{self.server_name}.thread"
+            )
             self.thread.daemon = True
             self.active = True
             self.thread.start()
@@ -49,7 +50,7 @@ class DatabaseHeartbeat:
         if worker_process:
             self.sa_session.delete(worker_process)
             self.sa_session.flush()
-            self.application_stack.app.queue_worker.send_control_task('reconfigure_watcher', noop_self=True)
+            self.application_stack.app.queue_worker.send_control_task("reconfigure_watcher", noop_self=True)
 
     def get_active_processes(self, last_seen_seconds=None):
         """Return all processes seen in ``last_seen_seconds`` seconds."""
@@ -68,16 +69,21 @@ class DatabaseHeartbeat:
     @is_config_watcher.setter
     def is_config_watcher(self, value):
         self._is_config_watcher = value
-        log.debug('%s %s config watcher', self.server_name, 'is' if self.is_config_watcher else 'is not')
+        log.debug("%s %s config watcher", self.server_name, "is" if self.is_config_watcher else "is not")
         for callback in self._observers:
             callback(self._is_config_watcher)
 
     @property
     def worker_process(self):
-        return self.sa_session.query(WorkerProcess).with_for_update(of=WorkerProcess).filter_by(
-            server_name=self.server_name,
-            hostname=self.hostname,
-        ).first()
+        return (
+            self.sa_session.query(WorkerProcess)
+            .with_for_update(of=WorkerProcess)
+            .filter_by(
+                server_name=self.server_name,
+                hostname=self.hostname,
+            )
+            .first()
+        )
 
     def update_watcher_designation(self):
         worker_process = self.worker_process
@@ -90,7 +96,8 @@ class DatabaseHeartbeat:
         # We only want a single process watching the various config files on the file system.
         # We just pick the max server name for simplicity
         is_config_watcher = self.server_name == max(
-            p.server_name for p in self.get_active_processes(self.heartbeat_interval + 1))
+            p.server_name for p in self.get_active_processes(self.heartbeat_interval + 1)
+        )
         if is_config_watcher != self.is_config_watcher:
             self.is_config_watcher = is_config_watcher
 
diff --git a/lib/galaxy/model/database_utils.py b/lib/galaxy/model/database_utils.py
index 4baf6d6da4a..ec0312bce65 100644
--- a/lib/galaxy/model/database_utils.py
+++ b/lib/galaxy/model/database_utils.py
@@ -18,7 +18,7 @@ def database_exists(db_url, database=None):
     return dbm.exists()
 
 
-def create_database(db_url, database=None, encoding='utf8', template=None):
+def create_database(db_url, database=None, encoding="utf8", template=None):
     """Create database; connect with db_url.
 
     If database is None, use the database name from db_url.
@@ -37,17 +37,16 @@ def sqlalchemy_engine(url):
 
 
 class DatabaseManager:
-
     @staticmethod
     def make_manager(db_url, database):
-        if db_url.startswith('postgres'):
+        if db_url.startswith("postgres"):
             return PosgresDatabaseManager(db_url, database)
-        elif db_url.startswith('sqlite'):
+        elif db_url.startswith("sqlite"):
             return SqliteDatabaseManager(db_url, database)
-        elif db_url.startswith('mysql'):
+        elif db_url.startswith("mysql"):
             return MySQLDatabaseManager(db_url, database)
         else:
-            raise ConfigurationError(f'Invalid database URL: {db_url}')
+            raise ConfigurationError(f"Invalid database URL: {db_url}")
 
     def __init__(self, db_url, database):
         self.url = make_url(db_url)
@@ -57,14 +56,13 @@ class DatabaseManager:
 
 
 class PosgresDatabaseManager(DatabaseManager):
-
     def _handle_no_database(self):
         self.database = self.url.database  # use database from db_url
-        self.url = self.url.set(database='postgres')
+        self.url = self.url.set(database="postgres")
 
     def exists(self):
         with sqlalchemy_engine(self.url) as engine:
-            stmt = text('SELECT 1 FROM pg_database WHERE datname=:database')
+            stmt = text("SELECT 1 FROM pg_database WHERE datname=:database")
             stmt = stmt.bindparams(database=self.database)
             with engine.connect() as conn:
                 return bool(conn.scalar(stmt))
@@ -72,23 +70,21 @@ class PosgresDatabaseManager(DatabaseManager):
     def create(self, encoding, template):
         with sqlalchemy_engine(self.url) as engine:
             preparer = IdentifierPreparer(engine.dialect)
-            template = template or 'template1'
+            template = template or "template1"
             database, template = preparer.quote(self.database), preparer.quote(template)
             stmt = f"CREATE DATABASE {database} ENCODING '{encoding}' TEMPLATE {template}"
-            with engine.connect().execution_options(isolation_level='AUTOCOMMIT') as conn:
+            with engine.connect().execution_options(isolation_level="AUTOCOMMIT") as conn:
                 conn.execute(stmt)
 
 
 class SqliteDatabaseManager(DatabaseManager):
-
     def _handle_no_database(self):
         self.database = self.url.database  # use database from db_url
 
     def exists(self):
-
         def can_connect_to_dbfile():
             try:
-                sqlite3.connect(f'file:{db}?mode=ro', uri=True)
+                sqlite3.connect(f"file:{db}?mode=ro", uri=True)
             except sqlite3.OperationalError:
                 return False
             else:
@@ -96,15 +92,14 @@ class SqliteDatabaseManager(DatabaseManager):
 
         db = self.url.database
         # No database or ':memory:' creates an in-memory database
-        return not db or db == ':memory:' or can_connect_to_dbfile()
+        return not db or db == ":memory:" or can_connect_to_dbfile()
 
     def create(self, *args):
         # Ignore any args (encoding, template)
-        sqlite3.connect(f'file:{self.url.database}', uri=True)
+        sqlite3.connect(f"file:{self.url.database}", uri=True)
 
 
 class MySQLDatabaseManager(DatabaseManager):
-
     def _handle_no_database(self):
         self.database = self.url.database  # use database from db_url
 
@@ -121,5 +116,5 @@ class MySQLDatabaseManager(DatabaseManager):
             preparer = IdentifierPreparer(engine.dialect)
             database = preparer.quote(self.database)
             stmt = f"CREATE DATABASE {database} CHARACTER SET = '{encoding}'"
-            with engine.connect().execution_options(isolation_level='AUTOCOMMIT') as conn:
+            with engine.connect().execution_options(isolation_level="AUTOCOMMIT") as conn:
                 conn.execute(stmt)
diff --git a/lib/galaxy/model/dataset_collections/builder.py b/lib/galaxy/model/dataset_collections/builder.py
index e32d5b9f932..601a0a57d1d 100644
--- a/lib/galaxy/model/dataset_collections/builder.py
+++ b/lib/galaxy/model/dataset_collections/builder.py
@@ -34,7 +34,7 @@ def set_collection_elements(dataset_collection, type, dataset_instances, associa
 
 
 class CollectionBuilder:
-    """ Purely functional builder pattern for building a dataset collection. """
+    """Purely functional builder pattern for building a dataset collection."""
 
     def __init__(self, collection_type_description):
         self._collection_type_description = collection_type_description
@@ -57,12 +57,13 @@ class CollectionBuilder:
                     collection_type_description=self._collection_type_description.child_collection_type_description()
                 )
                 collection_builder.replace_elements_in_collection(
-                    template_collection=element.child_collection,
-                    replacement_dict=replacement_dict
+                    template_collection=element.child_collection, replacement_dict=replacement_dict
                 )
                 elements[element.element_identifier] = collection_builder
             else:
-                elements[element.element_identifier] = replacement_dict.get(element.element_object, element.element_object)
+                elements[element.element_identifier] = replacement_dict.get(
+                    element.element_object, element.element_object
+                )
         return elements
 
     def get_level(self, identifier):
@@ -71,9 +72,7 @@ class CollectionBuilder:
             message = message_template % (self._collection_type_description)
             raise AssertionError(message)
         if identifier not in self._current_elements:
-            subcollection_builder = CollectionBuilder(
-                self._subcollection_type_description
-            )
+            subcollection_builder = CollectionBuilder(self._subcollection_type_description)
             self._current_elements[identifier] = subcollection_builder
 
         return self._current_elements[identifier]
@@ -94,7 +93,9 @@ class CollectionBuilder:
 
     def build(self):
         type_plugin = self._collection_type_description.rank_type_plugin()
-        self.collection = build_collection(type_plugin, self.build_elements(), self.collection, self.associated_identifiers)
+        self.collection = build_collection(
+            type_plugin, self.build_elements(), self.collection, self.associated_identifiers
+        )
         self.collection.collection_type = self._collection_type_description.collection_type
         return self.collection
 
@@ -108,7 +109,7 @@ class CollectionBuilder:
 
 
 class BoundCollectionBuilder(CollectionBuilder):
-    """ More stateful builder that is bound to a particular model object. """
+    """More stateful builder that is bound to a particular model object."""
 
     def __init__(self, dataset_collection):
         self.dataset_collection = dataset_collection
diff --git a/lib/galaxy/model/dataset_collections/matching.py b/lib/galaxy/model/dataset_collections/matching.py
index 43bc8cd703a..5679893bd9a 100644
--- a/lib/galaxy/model/dataset_collections/matching.py
+++ b/lib/galaxy/model/dataset_collections/matching.py
@@ -2,14 +2,14 @@ from galaxy import exceptions
 from galaxy.util import bunch
 from .structure import (
     get_structure,
-    leaf
+    leaf,
 )
 
 CANNOT_MATCH_ERROR_MESSAGE = "Cannot match collection types."
 
 
 class CollectionsToMatch:
-    """ Structure representing a set of collections that need to be matched up
+    """Structure representing a set of collections that need to be matched up
     when running tools (possibly workflows in the future as well).
     """
 
@@ -31,7 +31,7 @@ class CollectionsToMatch:
 
 
 class MatchingCollections:
-    """ Structure holding the result of matching a list of collections
+    """Structure holding the result of matching a list of collections
     together. This class being different than the class above and being
     created in the DatasetCollectionManager layer may seem like
     overkill but I suspect in the future plugins will be subtypable for
@@ -94,11 +94,15 @@ class MatchingCollections:
         matching_collections = MatchingCollections()
         for input_key, to_match in sorted(collections_to_match.items()):
             hdca = to_match.hdca
-            collection_type_description = collection_type_descriptions.for_collection_type(hdca.collection.collection_type)
+            collection_type_description = collection_type_descriptions.for_collection_type(
+                hdca.collection.collection_type
+            )
             subcollection_type = to_match.subcollection_type
 
             if to_match.linked:
-                matching_collections.__attempt_add_to_linked_match(input_key, hdca, collection_type_description, subcollection_type)
+                matching_collections.__attempt_add_to_linked_match(
+                    input_key, hdca, collection_type_description, subcollection_type
+                )
             else:
                 structure = get_structure(hdca, collection_type_description, leaf_subcollection_type=subcollection_type)
                 matching_collections.unlinked_structures.append(structure)
diff --git a/lib/galaxy/model/dataset_collections/registry.py b/lib/galaxy/model/dataset_collections/registry.py
index dd3b83d5a10..9c849dfdad6 100644
--- a/lib/galaxy/model/dataset_collections/registry.py
+++ b/lib/galaxy/model/dataset_collections/registry.py
@@ -1,14 +1,13 @@
 from galaxy import model
 from .types import (
     list,
-    paired
+    paired,
 )
 
 PLUGIN_CLASSES = [list.ListDatasetCollectionType, paired.PairedDatasetCollectionType]
 
 
 class DatasetCollectionTypesRegistry:
-
     def __init__(self):
         self.__plugins = {p.collection_type: p() for p in PLUGIN_CLASSES}
 
@@ -17,7 +16,7 @@ class DatasetCollectionTypesRegistry:
 
     def prototype(self, plugin_type):
         plugin_type_object = self.get(plugin_type)
-        if not hasattr(plugin_type_object, 'prototype_elements'):
+        if not hasattr(plugin_type_object, "prototype_elements"):
             raise Exception(f"Cannot pre-determine structure for collection of type {plugin_type}")
 
         dataset_collection = model.DatasetCollection()
diff --git a/lib/galaxy/model/dataset_collections/structure.py b/lib/galaxy/model/dataset_collections/structure.py
index 9814a3580c2..b8b73daa9f4 100644
--- a/lib/galaxy/model/dataset_collections/structure.py
+++ b/lib/galaxy/model/dataset_collections/structure.py
@@ -2,7 +2,6 @@
 """
 import logging
 
-
 log = logging.getLogger(__name__)
 
 
@@ -33,7 +32,6 @@ leaf = Leaf()
 
 
 class BaseTree:
-
     def __init__(self, collection_type_description):
         self.collection_type_description = collection_type_description
 
@@ -75,8 +73,12 @@ class Tree(BaseTree):
         for element in dataset_collection.elements:
             if collection_type_description.has_subcollections():
                 child_collection = element.child_collection
-                subcollection_type_description = collection_type_description.subcollection_type_description()  # Type description of children
-                tree = Tree.for_dataset_collection(child_collection, collection_type_description=subcollection_type_description)
+                subcollection_type_description = (
+                    collection_type_description.subcollection_type_description()
+                )  # Type description of children
+                tree = Tree.for_dataset_collection(
+                    child_collection, collection_type_description=subcollection_type_description
+                )
                 children.append((element.element_identifier, tree))
             else:
                 children.append((element.element_identifier, leaf))
@@ -87,6 +89,7 @@ class Tree(BaseTree):
 
     def _walk_collections(self, collection_dict):
         for index, (_identifier, substructure) in enumerate(self.children):
+
             def element(collection):
                 return collection[index]
 
@@ -158,7 +161,9 @@ def tool_output_to_structure(get_sliced_input_collection_structure, tool_output,
         else:
             # Can't pre-compute the structure in this case, see if we can find a collection type.
             if collection_type is None and tool_output.structure.collection_type_source:
-                collection_type = get_sliced_input_collection_structure(tool_output.structure.collection_type_source).collection_type_description.collection_type
+                collection_type = get_sliced_input_collection_structure(
+                    tool_output.structure.collection_type_source
+                ).collection_type_description.collection_type
 
             if not collection_type:
                 raise Exception(f"Failed to determine collection type for mapping over output {tool_output.name}")
@@ -178,9 +183,15 @@ def dict_map(func, input_dict):
 
 def get_structure(dataset_collection_instance, collection_type_description, leaf_subcollection_type=None):
     if leaf_subcollection_type:
-        collection_type_description = collection_type_description.effective_collection_type_description(leaf_subcollection_type)
-        if hasattr(dataset_collection_instance, 'child_collection'):
-            collection_type_description = collection_type_description.collection_type_description_factory.for_collection_type(leaf_subcollection_type)
+        collection_type_description = collection_type_description.effective_collection_type_description(
+            leaf_subcollection_type
+        )
+        if hasattr(dataset_collection_instance, "child_collection"):
+            collection_type_description = (
+                collection_type_description.collection_type_description_factory.for_collection_type(
+                    leaf_subcollection_type
+                )
+            )
             return UninitializedTree(collection_type_description)
 
     collection = dataset_collection_instance.collection
diff --git a/lib/galaxy/model/dataset_collections/subcollections.py b/lib/galaxy/model/dataset_collections/subcollections.py
index 99bd289e28b..af6c2a39732 100644
--- a/lib/galaxy/model/dataset_collections/subcollections.py
+++ b/lib/galaxy/model/dataset_collections/subcollections.py
@@ -2,8 +2,7 @@ from galaxy import exceptions
 
 
 def split_dataset_collection_instance(dataset_collection_instance, collection_type):
-    """ Split up collection into collection.
-    """
+    """Split up collection into collection."""
     return _split_dataset_collection(dataset_collection_instance.collection, collection_type)
 
 
diff --git a/lib/galaxy/model/dataset_collections/type_description.py b/lib/galaxy/model/dataset_collections/type_description.py
index 1297d294db5..7cb905e3b0f 100644
--- a/lib/galaxy/model/dataset_collections/type_description.py
+++ b/lib/galaxy/model/dataset_collections/type_description.py
@@ -2,7 +2,6 @@ from .registry import DATASET_COLLECTION_TYPES_REGISTRY
 
 
 class CollectionTypeDescriptionFactory:
-
     def __init__(self, type_registry=DATASET_COLLECTION_TYPES_REGISTRY):
         # taking in type_registry though not using it, because we will someday
         # I think.
@@ -14,7 +13,7 @@ class CollectionTypeDescriptionFactory:
 
 
 class CollectionTypeDescription:
-    """ Abstraction over dataset collection type that ties together string
+    """Abstraction over dataset collection type that ties together string
     reprentation in database/model with type registry.
 
     >>> factory = CollectionTypeDescriptionFactory(None)
@@ -51,7 +50,7 @@ class CollectionTypeDescription:
 
     def child_collection_type(self):
         rank_collection_type = self.rank_collection_type()
-        return self.collection_type[len(rank_collection_type) + 1:]
+        return self.collection_type[len(rank_collection_type) + 1 :]
 
     def child_collection_type_description(self):
         child_collection_type = self.child_collection_type()
@@ -62,16 +61,16 @@ class CollectionTypeDescription:
         return self.collection_type_description_factory.for_collection_type(effective_collection_type)
 
     def effective_collection_type(self, subcollection_type):
-        if hasattr(subcollection_type, 'collection_type'):
+        if hasattr(subcollection_type, "collection_type"):
             subcollection_type = subcollection_type.collection_type
 
         if not self.has_subcollections_of_type(subcollection_type):
             raise ValueError(f"Cannot compute effective subcollection type of {subcollection_type} over {self}")
 
-        return self.collection_type[:-(len(subcollection_type) + 1)]
+        return self.collection_type[: -(len(subcollection_type) + 1)]
 
     def has_subcollections_of_type(self, other_collection_type):
-        """ Take in another type (either flat string or another
+        """Take in another type (either flat string or another
         CollectionTypeDescription) and determine if this collection contains
         subcollections matching that type.
 
@@ -79,18 +78,18 @@ class CollectionTypeDescription:
         for this to return True if these subtypes are proper (i.e. a type
         is not considered to have subcollections of its own type).
         """
-        if hasattr(other_collection_type, 'collection_type'):
+        if hasattr(other_collection_type, "collection_type"):
             other_collection_type = other_collection_type.collection_type
         collection_type = self.collection_type
         return collection_type.endswith(other_collection_type) and collection_type != other_collection_type
 
     def is_subcollection_of_type(self, other_collection_type):
-        if not hasattr(other_collection_type, 'collection_type'):
+        if not hasattr(other_collection_type, "collection_type"):
             other_collection_type = self.collection_type_description_factory.for_collection_type(other_collection_type)
         return other_collection_type.has_subcollections_of_type(self)
 
     def can_match_type(self, other_collection_type):
-        if hasattr(other_collection_type, 'collection_type'):
+        if hasattr(other_collection_type, "collection_type"):
             other_collection_type = other_collection_type.collection_type
         collection_type = self.collection_type
         return other_collection_type == collection_type
@@ -105,7 +104,7 @@ class CollectionTypeDescription:
         return self.__has_subcollections
 
     def rank_collection_type(self):
-        """ Return the top-level collection type corresponding to this
+        """Return the top-level collection type corresponding to this
         collection type. For instance the "rank" type of a list of paired
         data ("list:paired") is "list".
         """
@@ -127,13 +126,13 @@ class CollectionTypeDescription:
 
 
 def map_over_collection_type(mapped_over_collection_type, target_collection_type):
-    if hasattr(mapped_over_collection_type, 'collection_type'):
+    if hasattr(mapped_over_collection_type, "collection_type"):
         mapped_over_collection_type = mapped_over_collection_type.collection_type
 
     if not target_collection_type:
         return mapped_over_collection_type
     else:
-        if hasattr(target_collection_type, 'collection_type'):
+        if hasattr(target_collection_type, "collection_type"):
             target_collection_type = target_collection_type.collection_type
 
         return f"{mapped_over_collection_type}:{target_collection_type}"
diff --git a/lib/galaxy/model/dataset_collections/types/__init__.py b/lib/galaxy/model/dataset_collections/types/__init__.py
index 6558ec5bb7c..bfcf7bae79a 100644
--- a/lib/galaxy/model/dataset_collections/types/__init__.py
+++ b/lib/galaxy/model/dataset_collections/types/__init__.py
@@ -1,26 +1,23 @@
 import logging
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
-
 from galaxy import exceptions
 
 log = logging.getLogger(__name__)
 
 
 class DatasetCollectionType(metaclass=ABCMeta):
-
     @abstractmethod
     def generate_elements(self, dataset_instances):
-        """ Generate DatasetCollectionElements with corresponding
+        """Generate DatasetCollectionElements with corresponding
         to the supplied dataset instances or throw exception if
         this is not a valid collection of the specified type.
         """
 
 
 class BaseDatasetCollectionType(DatasetCollectionType):
-
     def _validation_failed(self, message):
         raise exceptions.ObjectAttributeInvalidException(message)
diff --git a/lib/galaxy/model/dataset_collections/types/list.py b/lib/galaxy/model/dataset_collections/types/list.py
index 7297f051469..74a274138c7 100644
--- a/lib/galaxy/model/dataset_collections/types/list.py
+++ b/lib/galaxy/model/dataset_collections/types/list.py
@@ -3,8 +3,8 @@ from ..types import BaseDatasetCollectionType
 
 
 class ListDatasetCollectionType(BaseDatasetCollectionType):
-    """ A flat list of named elements.
-    """
+    """A flat list of named elements."""
+
     collection_type = "list"
 
     def __init__(self):
diff --git a/lib/galaxy/model/dataset_collections/types/paired.py b/lib/galaxy/model/dataset_collections/types/paired.py
index 335dcb15779..71e24f471c8 100644
--- a/lib/galaxy/model/dataset_collections/types/paired.py
+++ b/lib/galaxy/model/dataset_collections/types/paired.py
@@ -1,4 +1,7 @@
-from galaxy.model import DatasetCollectionElement, HistoryDatasetAssociation
+from galaxy.model import (
+    DatasetCollectionElement,
+    HistoryDatasetAssociation,
+)
 from ..types import BaseDatasetCollectionType
 
 FORWARD_IDENTIFIER = "forward"
@@ -9,6 +12,7 @@ class PairedDatasetCollectionType(BaseDatasetCollectionType):
     """
     Paired (left/right) datasets.
     """
+
     collection_type = "paired"
 
     def __init__(self):
diff --git a/lib/galaxy/model/item_attrs.py b/lib/galaxy/model/item_attrs.py
index fde16e71515..ad01926a274 100644
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -10,16 +10,16 @@ log = logging.getLogger(__name__)
 
 class UsesItemRatings:
     """
-        Mixin for getting and setting item ratings.
+    Mixin for getting and setting item ratings.
 
-        Class makes two assumptions:
-        (1) item-rating association table is named <item_class>RatingAssocation
-        (2) item-rating association table has a column with a foreign key referencing
-        item table that contains the item's id.
+    Class makes two assumptions:
+    (1) item-rating association table is named <item_class>RatingAssocation
+    (2) item-rating association table has a column with a foreign key referencing
+    item table that contains the item's id.
     """
 
     def get_ave_item_rating_data(self, db_session, item, webapp_model=None):
-        """ Returns the average rating for an item."""
+        """Returns the average rating for an item."""
         if webapp_model is None:
             webapp_model = galaxy.model
         item_rating_assoc_class = self._get_item_rating_assoc_class(item, webapp_model=webapp_model)
@@ -36,7 +36,7 @@ class UsesItemRatings:
         return (ave_rating, num_ratings)
 
     def rate_item(self, db_session, user, item, rating, webapp_model=None):
-        """ Rate an item. Return type is <item_class>RatingAssociation. """
+        """Rate an item. Return type is <item_class>RatingAssociation."""
         if webapp_model is None:
             webapp_model = galaxy.model
         item_rating = self.get_user_item_rating(db_session, user, item, webapp_model=webapp_model)
@@ -53,7 +53,7 @@ class UsesItemRatings:
         return item_rating
 
     def get_user_item_rating(self, db_session, user, item, webapp_model=None):
-        """ Returns user's rating for an item. Return type is <item_class>RatingAssociation. """
+        """Returns user's rating for an item. Return type is <item_class>RatingAssociation."""
         if webapp_model is None:
             webapp_model = galaxy.model
         item_rating_assoc_class = self._get_item_rating_assoc_class(item, webapp_model=webapp_model)
@@ -65,10 +65,10 @@ class UsesItemRatings:
         return db_session.query(item_rating_assoc_class).filter_by(user=user).filter(item_id_filter).first()
 
     def _get_item_rating_assoc_class(self, item, webapp_model=None):
-        """ Returns an item's item-rating association class. """
+        """Returns an item's item-rating association class."""
         if webapp_model is None:
             webapp_model = galaxy.model
-        item_rating_assoc_class = f'{item.__class__.__name__}RatingAssociation'
+        item_rating_assoc_class = f"{item.__class__.__name__}RatingAssociation"
         return getattr(webapp_model, item_rating_assoc_class, None)
 
     def _get_item_id_filter_str(self, item, item_rating_assoc_class):
@@ -78,7 +78,7 @@ class UsesItemRatings:
 
 
 class UsesAnnotations:
-    """ Mixin for getting and setting item annotations. """
+    """Mixin for getting and setting item annotations."""
 
     def get_item_annotation_str(self, db_session, user, item):
         return get_item_annotation_str(db_session, user, item)
@@ -96,7 +96,7 @@ class UsesAnnotations:
             db_session.flush()
 
     def copy_item_annotation(self, db_session, source_user, source_item, target_user, target_item):
-        """ Copy an annotation from a user/item source to a user/item target. """
+        """Copy an annotation from a user/item source to a user/item target."""
         if source_user and target_user:
             annotation_str = self.get_item_annotation_str(db_session, source_user, source_item)
             if annotation_str:
@@ -134,8 +134,8 @@ def get_item_annotation_obj(db_session, user, item):
 
 
 def get_item_annotation_str(db_session, user, item):
-    """ Returns a user's annotation string for an item. """
-    if hasattr(item, 'annotations'):
+    """Returns a user's annotation string for an item."""
+    if hasattr(item, "annotations"):
         # If we already have an annotations object we use it.
         annotation_obj = None
         for annotation in item.annotations:
@@ -150,7 +150,7 @@ def get_item_annotation_str(db_session, user, item):
 
 
 def add_item_annotation(db_session, user, item, annotation):
-    """ Add or update an item's annotation; a user can only have a single annotation for an item. """
+    """Add or update an item's annotation; a user can only have a single annotation for an item."""
     # Get/create annotation association object.
     annotation_assoc = get_item_annotation_obj(db_session, user, item)
     if not annotation_assoc:
@@ -166,13 +166,13 @@ def add_item_annotation(db_session, user, item, annotation):
 
 
 def _get_annotation_assoc_class(item):
-    """ Returns an item's item-annotation association class. """
-    class_name = f'{item.__class__.__name__}AnnotationAssociation'
+    """Returns an item's item-annotation association class."""
+    class_name = f"{item.__class__.__name__}AnnotationAssociation"
     return getattr(galaxy.model, class_name, None)
 
 
 def get_foreign_key(source_class, target_class):
-    """ Returns foreign key in source class that references target class. """
+    """Returns foreign key in source class that references target class."""
     target_fk = None
     for fk in source_class.table.foreign_keys:
         if fk.references(target_class.table):
@@ -184,7 +184,7 @@ def get_foreign_key(source_class, target_class):
 
 
 __all__ = (
-    'get_foreign_key',
-    'UsesAnnotations',
-    'UsesItemRatings',
+    "get_foreign_key",
+    "UsesAnnotations",
+    "UsesItemRatings",
 )
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index c41e6f6efdd..edbd2210e4f 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -6,7 +6,10 @@ The module will be revised during migration from SQLAlchemy Migrate to Alembic.
 
 import logging
 from threading import local
-from typing import Optional, Type
+from typing import (
+    Optional,
+    Type,
+)
 
 from galaxy import model
 from galaxy.model import mapper_registry
@@ -29,9 +32,20 @@ class GalaxyModelMapping(SharedModelMapping):
     GalaxySession: Type
 
 
-def init(file_path, url, engine_options=None, create_tables=False, map_install_models=False,
-        database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True,
-        slow_query_log_threshold=0, thread_local_log: Optional[local] = None, log_query_counts=False) -> GalaxyModelMapping:
+def init(
+    file_path,
+    url,
+    engine_options=None,
+    create_tables=False,
+    map_install_models=False,
+    database_query_profiling_proxy=False,
+    object_store=None,
+    trace_logger=None,
+    use_pbkdf2=True,
+    slow_query_log_threshold=0,
+    thread_local_log: Optional[local] = None,
+    log_query_counts=False,
+) -> GalaxyModelMapping:
     """Connect mappings to the database"""
     if engine_options is None:
         engine_options = {}
@@ -42,12 +56,21 @@ def init(file_path, url, engine_options=None, create_tables=False, map_install_m
     # Use PBKDF2 password hashing?
     model.User.use_pbkdf2 = use_pbkdf2
     # Load the appropriate db module
-    engine = build_engine(url, engine_options, database_query_profiling_proxy, trace_logger, slow_query_log_threshold, thread_local_log=thread_local_log, log_query_counts=log_query_counts)
+    engine = build_engine(
+        url,
+        engine_options,
+        database_query_profiling_proxy,
+        trace_logger,
+        slow_query_log_threshold,
+        thread_local_log=thread_local_log,
+        log_query_counts=log_query_counts,
+    )
 
     model_modules = [model]
     if map_install_models:
         import galaxy.model.tool_shed_install.mapping  # noqa: F401
         from galaxy.model import tool_shed_install
+
         galaxy.model.tool_shed_install.mapping.init(url=url, engine_options=engine_options, create_tables=create_tables)
         model_modules.append(tool_shed_install)
 
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
index 1a3e429dfde..a42f6cedab3 100644
--- a/lib/galaxy/model/metadata.py
+++ b/lib/galaxy/model/metadata.py
@@ -13,7 +13,13 @@ import weakref
 from collections import OrderedDict
 from collections.abc import Mapping
 from os.path import abspath
-from typing import Any, Iterator, Optional, TYPE_CHECKING, Union
+from typing import (
+    Any,
+    Iterator,
+    Optional,
+    TYPE_CHECKING,
+    Union,
+)
 
 from sqlalchemy.orm import object_session
 from sqlalchemy.orm.attributes import flag_modified
@@ -62,7 +68,9 @@ class Statement:
     @classmethod
     def process(cls, element):
         for statement, args, kwargs in getattr(element, STATEMENTS, []):
-            statement.target(element, *args, **kwargs)  # statement.target is MetadataElementSpec, element is a Datatype class
+            statement.target(
+                element, *args, **kwargs
+            )  # statement.target is MetadataElementSpec, element is a Datatype class
 
 
 class MetadataCollection(Mapping):
@@ -73,7 +81,11 @@ class MetadataCollection(Mapping):
     retrieved, returning default values in cases when metadata is not set.
     """
 
-    def __init__(self, parent: Union["DatasetInstance", "NoneDataset"], session: Optional[Union[galaxy_scoped_session, 'SessionlessContext']] = None) -> None:
+    def __init__(
+        self,
+        parent: Union["DatasetInstance", "NoneDataset"],
+        session: Optional[Union[galaxy_scoped_session, "SessionlessContext"]] = None,
+    ) -> None:
         self.parent = parent
         self._session = session
         # initialize dict if needed
@@ -90,6 +102,7 @@ class MetadataCollection(Mapping):
         # collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be
         # hashable, so cannot use proxy.
         self.__dict__["_parent"] = weakref.ref(parent)
+
     parent = property(get_parent, set_parent)
 
     @property
@@ -125,6 +138,7 @@ class MetadataCollection(Mapping):
 
     def __bool__(self):
         return bool(self.parent._metadata)
+
     __nonzero__ = __bool__
 
     def __getattr__(self, name):
@@ -140,14 +154,14 @@ class MetadataCollection(Mapping):
     def __setattr__(self, name, value):
         if name == "parent":
             return self.set_parent(value)
-        elif name == '_session':
+        elif name == "_session":
             super().__setattr__(name, value)
         else:
             if name in self.spec:
                 self.parent._metadata[name] = self.spec[name].unwrap(value)
             else:
                 self.parent._metadata[name] = value
-            flag_modified(self.parent, '_metadata')
+            flag_modified(self.parent, "_metadata")
 
     def remove_key(self, name):
         if name in self.parent._metadata:
@@ -200,11 +214,11 @@ class MetadataCollection(Mapping):
     def from_JSON_dict(self, filename=None, path_rewriter=None, json_dict=None):
         dataset = self.parent
         if filename is not None:
-            log.debug(f'loading metadata from file for: {dataset.__class__.__name__} {dataset.id}')
+            log.debug(f"loading metadata from file for: {dataset.__class__.__name__} {dataset.id}")
             with open(filename) as fh:
                 JSONified_dict = json.load(fh)
         elif json_dict is not None:
-            log.debug(f'loading metadata from dict for: {dataset.__class__.__name__} {dataset.id}')
+            log.debug(f"loading metadata from dict for: {dataset.__class__.__name__} {dataset.id}")
             if isinstance(json_dict, str):
                 JSONified_dict = json.loads(json_dict)
             elif isinstance(json_dict, dict):
@@ -226,7 +240,7 @@ class MetadataCollection(Mapping):
                 external_value = JSONified_dict[name]
                 param = spec.param
                 if isinstance(param, FileParameter):
-                    from_ext_kwds['path_rewriter'] = path_rewriter
+                    from_ext_kwds["path_rewriter"] = path_rewriter
                 value = param.from_external_value(external_value, dataset, **from_ext_kwds)
                 metadata_name_value[name] = value
             elif name in dataset._metadata:
@@ -235,13 +249,13 @@ class MetadataCollection(Mapping):
                 del dataset._metadata[name]
         for name, value in metadata_name_value.items():
             dataset._metadata[name] = value
-        if '__extension__' in JSONified_dict:
-            dataset.extension = JSONified_dict['__extension__']
-        if '__validated_state__' in JSONified_dict:
-            dataset.validated_state = JSONified_dict['__validated_state__']
-        if '__validated_state_message__' in JSONified_dict:
-            dataset.validated_state_message = JSONified_dict['__validated_state_message__']
-        flag_modified(dataset, '_metadata')
+        if "__extension__" in JSONified_dict:
+            dataset.extension = JSONified_dict["__extension__"]
+        if "__validated_state__" in JSONified_dict:
+            dataset.validated_state = JSONified_dict["__validated_state__"]
+        if "__validated_state_message__" in JSONified_dict:
+            dataset.validated_state_message = JSONified_dict["__validated_state_message__"]
+        flag_modified(dataset, "_metadata")
 
     def to_JSON_dict(self, filename=None):
         meta_dict = {}
@@ -249,19 +263,19 @@ class MetadataCollection(Mapping):
         for name, spec in self.spec.items():
             if name in dataset_meta_dict:
                 meta_dict[name] = spec.param.to_external_value(dataset_meta_dict[name])
-        if '__extension__' in dataset_meta_dict:
-            meta_dict['__extension__'] = dataset_meta_dict['__extension__']
-        if '__validated_state__' in dataset_meta_dict:
-            meta_dict['__validated_state__'] = dataset_meta_dict['__validated_state__']
-        if '__validated_state_message__' in dataset_meta_dict:
-            meta_dict['__validated_state_message__'] = dataset_meta_dict['__validated_state_message__']
+        if "__extension__" in dataset_meta_dict:
+            meta_dict["__extension__"] = dataset_meta_dict["__extension__"]
+        if "__validated_state__" in dataset_meta_dict:
+            meta_dict["__validated_state__"] = dataset_meta_dict["__validated_state__"]
+        if "__validated_state_message__" in dataset_meta_dict:
+            meta_dict["__validated_state_message__"] = dataset_meta_dict["__validated_state_message__"]
         try:
             encoded_meta_dict = galaxy.model.custom_types.json_encoder.encode(meta_dict)
         except Exception as e:
             raise Exception(f"Failed encoding metadata dictionary: {meta_dict}") from e
         if filename is None:
             return encoded_meta_dict
-        with open(filename, 'wt+') as fh:
+        with open(filename, "wt+") as fh:
             fh.write(encoded_meta_dict)
 
     def __getstate__(self):
@@ -291,7 +305,7 @@ class MetadataSpecCollection(OrderedDict):
 
     def __repr__(self):
         # force elements to draw with __str__ for sphinx-apidoc
-        return ', '.join(item.__str__() for item in self.values())
+        return ", ".join(item.__str__() for item in self.values())
 
 
 class MetadataParameter:
@@ -358,9 +372,18 @@ class MetadataElementSpec:
     is a MetadataSpecCollection) of datatype.
     """
 
-    def __init__(self, datatype, name=None, desc=None,
-                 param=MetadataParameter, default=None, no_value=None,
-                 visible=True, set_in_upload=False, **kwargs):
+    def __init__(
+        self,
+        datatype,
+        name=None,
+        desc=None,
+        param=MetadataParameter,
+        default=None,
+        no_value=None,
+        visible=True,
+        set_in_upload=False,
+        **kwargs,
+    ):
         self.name = name
         self.desc = desc or name
         self.default = default
@@ -393,7 +416,7 @@ class MetadataElementSpec:
         # TODO??: assuming param is the class of this MetadataElementSpec - add the plain class name for that
         spec_dict = dict(param_class=self.param.__class__.__name__)
         spec_dict.update(self.__dict__)
-        return ("{name} ({param_class}): {desc}, defaults to '{default}'".format(**spec_dict))
+        return "{name} ({param_class}): {desc}, defaults to '{default}'".format(**spec_dict)
 
 
 # create a statement class that, when called,
@@ -465,19 +488,17 @@ class SelectParameter(MetadataParameter):
 
 
 class DBKeyParameter(SelectParameter):
-
     def get_field(self, value=None, context=None, other_values=None, values=None, **kwd):
         context = context or {}
         other_values = other_values or {}
         try:
-            values = kwd['trans'].app.genome_builds.get_genome_build_names(kwd['trans'])
+            values = kwd["trans"].app.genome_builds.get_genome_build_names(kwd["trans"])
         except KeyError:
             pass
         return super().get_field(value, context, other_values, values, **kwd)
 
 
 class RangeParameter(SelectParameter):
-
     def __init__(self, spec):
         SelectParameter.__init__(self, spec)
         # The spec must be set with min and max values
@@ -491,7 +512,9 @@ class RangeParameter(SelectParameter):
 
         if values is None:
             values = list(zip(range(self.min, self.max, self.step), range(self.min, self.max, self.step)))
-        return SelectParameter.get_field(self, value=value, context=context, other_values=other_values, values=values, **kwd)
+        return SelectParameter.get_field(
+            self, value=value, context=context, other_values=other_values, values=values, **kwd
+        )
 
     @classmethod
     def marshal(cls, value):
@@ -501,7 +524,6 @@ class RangeParameter(SelectParameter):
 
 
 class ColumnParameter(RangeParameter):
-
     def get_field(self, value=None, context=None, other_values=None, values=None, **kwd):
         context = context or {}
         other_values = other_values or {}
@@ -509,23 +531,22 @@ class ColumnParameter(RangeParameter):
         if values is None and context:
             column_range = range(1, (context.columns or 0) + 1, 1)
             values = list(zip(column_range, column_range))
-        return RangeParameter.get_field(self, value=value, context=context, other_values=other_values, values=values, **kwd)
+        return RangeParameter.get_field(
+            self, value=value, context=context, other_values=other_values, values=values, **kwd
+        )
 
 
 class ColumnTypesParameter(MetadataParameter):
-
     def to_string(self, value):
         return ",".join(map(str, value))
 
 
 class ListParameter(MetadataParameter):
-
     def to_string(self, value):
         return ",".join(str(x) for x in value)
 
 
 class DictParameter(MetadataParameter):
-
     def to_string(self, value):
         return json.dumps(value)
 
@@ -535,7 +556,6 @@ class DictParameter(MetadataParameter):
 
 
 class PythonObjectParameter(MetadataParameter):
-
     def to_string(self, value):
         if not value:
             return self.spec._to_string(self.spec.no_value)
@@ -552,7 +572,6 @@ class PythonObjectParameter(MetadataParameter):
 
 
 class FileParameter(MetadataParameter):
-
     def to_string(self, value):
         if not value:
             return str(self.spec.no_value)
@@ -622,11 +641,13 @@ class FileParameter(MetadataParameter):
                 # Job may have run with a different (non-local) tmp/working
                 # directory. Correct.
                 file_name = path_rewriter(file_name)
-            parent.dataset.object_store.update_from_file(mf,
-                                                         file_name=file_name,
-                                                         extra_dir='_metadata_files',
-                                                         extra_dir_at_root=True,
-                                                         alt_name=os.path.basename(mf.file_name))
+            parent.dataset.object_store.update_from_file(
+                mf,
+                file_name=file_name,
+                extra_dir="_metadata_files",
+                extra_dir_at_root=True,
+                alt_name=os.path.basename(mf.file_name),
+            )
             os.unlink(file_name)
             value = mf.id
         return value
@@ -661,7 +682,7 @@ class FileParameter(MetadataParameter):
 
 # This class is used when a database file connection is not available
 class MetadataTempFile:
-    tmp_dir = 'database/tmp'  # this should be overwritten as necessary in calling scripts
+    tmp_dir = "database/tmp"  # this should be overwritten as necessary in calling scripts
 
     def __init__(self, **kwds):
         self.kwds = kwds
@@ -672,24 +693,22 @@ class MetadataTempFile:
         if self._filename is None:
             # we need to create a tmp file, accessable across all nodes/heads, save the name, and return it
             self._filename = abspath(tempfile.NamedTemporaryFile(dir=self.tmp_dir, prefix="metadata_temp_file_").name)
-            open(self._filename, 'wb+')  # create an empty file, so it can't be reused using tempfile
+            open(self._filename, "wb+")  # create an empty file, so it can't be reused using tempfile
         return self._filename
 
     def to_JSON(self):
-        return {'__class__': self.__class__.__name__,
-                'filename': self.file_name,
-                'kwds': self.kwds}
+        return {"__class__": self.__class__.__name__, "filename": self.file_name, "kwds": self.kwds}
 
     @classmethod
     def from_JSON(cls, json_dict):
         # need to ensure our keywords are not unicode
-        rval = cls(**stringify_dictionary_keys(json_dict['kwds']))
-        rval._filename = json_dict['filename']
+        rval = cls(**stringify_dictionary_keys(json_dict["kwds"]))
+        rval._filename = json_dict["filename"]
         return rval
 
     @classmethod
     def is_JSONified_value(cls, value):
-        return (isinstance(value, dict) and value.get('__class__', None) == cls.__name__)
+        return isinstance(value, dict) and value.get("__class__", None) == cls.__name__
 
     @classmethod
     def cleanup_from_JSON_dict_filename(cls, filename):
@@ -699,10 +718,10 @@ class MetadataTempFile:
                     if cls.is_JSONified_value(value):
                         value = cls.from_JSON(value)
                     if isinstance(value, cls) and os.path.exists(value.file_name):
-                        log.debug('Cleaning up abandoned MetadataTempFile file: %s', value.file_name)
+                        log.debug("Cleaning up abandoned MetadataTempFile file: %s", value.file_name)
                         os.unlink(value.file_name)
         except Exception as e:
-            log.debug('Failed to cleanup MetadataTempFile temp files from %s: %s', filename, unicodify(e))
+            log.debug("Failed to cleanup MetadataTempFile temp files from %s: %s", filename, unicodify(e))
 
 
 __all__ = (
diff --git a/lib/galaxy/model/migrate/check.py b/lib/galaxy/model/migrate/check.py
index 2659afeb564..bbdabad360c 100644
--- a/lib/galaxy/model/migrate/check.py
+++ b/lib/galaxy/model/migrate/check.py
@@ -2,21 +2,27 @@ import logging
 import os.path
 import sys
 
-from migrate.versioning import repository, schema
+from migrate.versioning import (
+    repository,
+    schema,
+)
 from sqlalchemy import (
     create_engine,
     MetaData,
-    Table
+    Table,
 )
 from sqlalchemy.exc import NoSuchTableError
 
 from galaxy.model import mapping
-from galaxy.model.database_utils import create_database, database_exists
+from galaxy.model.database_utils import (
+    create_database,
+    database_exists,
+)
 
 log = logging.getLogger(__name__)
 
 # path relative to galaxy
-migrate_repository_directory = os.path.abspath(os.path.dirname(__file__)).replace(os.getcwd() + os.path.sep, '', 1)
+migrate_repository_directory = os.path.abspath(os.path.dirname(__file__)).replace(os.getcwd() + os.path.sep, "", 1)
 migrate_repository = repository.Repository(migrate_repository_directory)
 
 
@@ -66,7 +72,7 @@ def create_or_verify_database(url, galaxy_config_file, engine_options=None, app=
         if not os.environ.get("GALAXY_TEST_FORCE_DATABASE_MIGRATION"):
             log.info("Creating new database from scratch, skipping migrations")
             current_version = migrate_repository.version().version
-            mapping.init(file_path='/tmp', url=url, map_install_models=map_install_models, create_tables=True)
+            mapping.init(file_path="/tmp", url=url, map_install_models=map_install_models, create_tables=True)
             schema.ControlledSchema.create(engine, migrate_repository, version=current_version)
             db_schema = schema.ControlledSchema(engine, migrate_repository)
             assert db_schema.version == current_version
@@ -79,7 +85,7 @@ def create_or_verify_database(url, galaxy_config_file, engine_options=None, app=
     if new_database:
         migrate_from_scratch()
         return
-    elif app and getattr(app.config, 'database_auto_migrate', False):
+    elif app and getattr(app.config, "database_auto_migrate", False):
         migrate()
         return
 
@@ -94,17 +100,21 @@ def create_or_verify_database(url, galaxy_config_file, engine_options=None, app=
     try:
         hda_table = Table("history_dataset_association", meta, autoload=True)
     except NoSuchTableError:
-        raise Exception("Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually")
+        raise Exception(
+            "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually"
+        )
     # There is a 'history_dataset_association' table, so we (hopefully) have
     # version 1 of the database, but without the migrate_version table. This
     # happens if the user has a build from right before migration was added.
     # Verify that this is true, if it is any older they'll have to update
     # manually
-    if 'copied_from_history_dataset_association_id' not in hda_table.c:
+    if "copied_from_history_dataset_association_id" not in hda_table.c:
         # The 'copied_from_history_dataset_association_id' column was added in
         # rev 1464:c7acaa1bb88f.  This is the oldest revision we currently do
         # automated versioning for, so stop here
-        raise Exception("Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually")
+        raise Exception(
+            "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually"
+        )
     # At revision 1464:c7acaa1bb88f or greater (database version 1), make sure
     # that the db has version information. This is the trickiest case -- we
     # have a database but no version control, and are assuming it is a certain
@@ -123,10 +133,16 @@ def create_or_verify_database(url, galaxy_config_file, engine_options=None, app=
     # Verify that the code and the DB are in sync
     db_schema = schema.ControlledSchema(engine, migrate_repository)
     if migrate_repository.versions.latest != db_schema.version:
-        config_arg = ''
-        if galaxy_config_file and os.path.abspath(os.path.join(os.getcwd(), 'config', 'galaxy.ini')) != galaxy_config_file:
+        config_arg = ""
+        if (
+            galaxy_config_file
+            and os.path.abspath(os.path.join(os.getcwd(), "config", "galaxy.ini")) != galaxy_config_file
+        ):
             config_arg = f" -c {galaxy_config_file.replace(os.path.abspath(os.getcwd()), '.')}"
-        expect_msg = "Your database has version '%d' but this code expects version '%d'" % (db_schema.version, migrate_repository.versions.latest)
+        expect_msg = "Your database has version '%d' but this code expects version '%d'" % (
+            db_schema.version,
+            migrate_repository.versions.latest,
+        )
         instructions = ""
         if db_schema.version > migrate_repository.versions.latest:
             instructions = "To downgrade the database schema you have to checkout the Galaxy version that you were running previously. "
@@ -136,7 +152,9 @@ def create_or_verify_database(url, galaxy_config_file, engine_options=None, app=
         backup_msg = f"Please backup your database and then migrate the database schema by running '{cmd_msg}'."
         allow_future_database = os.environ.get("GALAXY_ALLOW_FUTURE_DATABASE", False)
         if db_schema.version > migrate_repository.versions.latest and allow_future_database:
-            log.warning("WARNING: Database is from the future, but GALAXY_ALLOW_FUTURE_DATABASE is set, so Galaxy will continue to start.")
+            log.warning(
+                "WARNING: Database is from the future, but GALAXY_ALLOW_FUTURE_DATABASE is set, so Galaxy will continue to start."
+            )
         else:
             raise Exception(f"{expect_msg}. {instructions}{backup_msg}")
     else:
@@ -152,7 +170,7 @@ def migrate_to_current_version(engine, schema):
         raise e
     for ver, change in changeset:
         nextver = ver + changeset.step
-        log.info(f'Migrating {ver} -> {nextver}... ')
+        log.info(f"Migrating {ver} -> {nextver}... ")
         old_stdout = sys.stdout
 
         class FakeStdout:
@@ -164,6 +182,7 @@ def migrate_to_current_version(engine, schema):
 
             def flush(self):
                 pass
+
         sys.stdout = FakeStdout()
         try:
             schema.runchange(ver, change, changeset.step)
diff --git a/lib/galaxy/model/migrate/triggers/history_update_time_field.py b/lib/galaxy/model/migrate/triggers/history_update_time_field.py
index 3cbfa83eb9f..f25208eeae1 100644
--- a/lib/galaxy/model/migrate/triggers/history_update_time_field.py
+++ b/lib/galaxy/model/migrate/triggers/history_update_time_field.py
@@ -28,38 +28,34 @@ def get_timestamp_install_sql(variant):
 
     sql = get_timestamp_drop_sql(variant)
 
-    if 'postgres' in variant:
+    if "postgres" in variant:
         # PostgreSQL has a separate function definition and a trigger
         # assignment. The first two statements the functions, and
         # the later assign those functions to triggers on tables
 
-        fn_name = 'update_history_update_time'
-        sql.append(build_pg_timestamp_fn(fn_name, 'history', source_key='history_id'))
-        sql.append(build_pg_trigger('history_dataset_association', fn_name))
-        sql.append(build_pg_trigger('history_dataset_collection_association', fn_name))
+        fn_name = "update_history_update_time"
+        sql.append(build_pg_timestamp_fn(fn_name, "history", source_key="history_id"))
+        sql.append(build_pg_trigger("history_dataset_association", fn_name))
+        sql.append(build_pg_trigger("history_dataset_collection_association", fn_name))
 
     else:
         # Other database variants are more granular. Requiring separate
         # statements for INSERT/UPDATE/DELETE, and the body of the trigger
         # is not necessarily reusable with a function
 
-        for operation in ['INSERT', 'UPDATE', 'DELETE']:
+        for operation in ["INSERT", "UPDATE", "DELETE"]:
 
             # change hda -> update history
-            sql.append(build_timestamp_trigger(
-                operation,
-                'history_dataset_association',
-                'history',
-                source_key='history_id'
-            ))
+            sql.append(
+                build_timestamp_trigger(operation, "history_dataset_association", "history", source_key="history_id")
+            )
 
             # change hdca -> update history
-            sql.append(build_timestamp_trigger(
-                operation,
-                'history_dataset_collection_association',
-                'history',
-                source_key='history_id'
-            ))
+            sql.append(
+                build_timestamp_trigger(
+                    operation, "history_dataset_collection_association", "history", source_key="history_id"
+                )
+            )
 
     return sql
 
@@ -71,18 +67,18 @@ def get_timestamp_drop_sql(variant):
 
     sql = []
 
-    if 'postgres' in variant:
+    if "postgres" in variant:
         sql.append("DROP FUNCTION IF EXISTS update_history_update_time() CASCADE;")
     else:
-        for operation in ['INSERT', 'UPDATE', 'DELETE']:
-            for when in ['BEFORE', 'AFTER']:
-                sql.append(build_drop_trigger(operation, 'history_dataset_association', when))
-                sql.append(build_drop_trigger(operation, 'history_dataset_collection_association', when))
+        for operation in ["INSERT", "UPDATE", "DELETE"]:
+            for when in ["BEFORE", "AFTER"]:
+                sql.append(build_drop_trigger(operation, "history_dataset_association", when))
+                sql.append(build_drop_trigger(operation, "history_dataset_collection_association", when))
 
     return sql
 
 
-def build_pg_timestamp_fn(fn_name, target_table, source_key, target_key='id'):
+def build_pg_timestamp_fn(fn_name, target_table, source_key, target_key="id"):
     """Generates a PostgreSQL history update timestamp function"""
 
     return f"""
@@ -112,7 +108,7 @@ def build_pg_timestamp_fn(fn_name, target_table, source_key, target_key='id'):
     """
 
 
-def build_pg_trigger(source_table, fn_name, when='AFTER'):
+def build_pg_trigger(source_table, fn_name, when="AFTER"):
     """Assigns a PostgreSQL trigger to indicated table, calling user-defined function"""
     when_initial = when.lower()[0]
     trigger_name = f"trigger_{source_table}_{when_initial}iudr"
@@ -125,7 +121,7 @@ def build_pg_trigger(source_table, fn_name, when='AFTER'):
     """
 
 
-def build_timestamp_trigger(operation, source_table, target_table, source_key, target_key='id', when='AFTER'):
+def build_timestamp_trigger(operation, source_table, target_table, source_key, target_key="id", when="AFTER"):
     """Creates a non-PostgreSQL update_time trigger"""
 
     trigger_name = get_trigger_name(operation, source_table, when)
@@ -152,7 +148,7 @@ def build_timestamp_trigger(operation, source_table, target_table, source_key, t
     """
 
 
-def build_drop_trigger(operation, source_table, when='AFTER'):
+def build_drop_trigger(operation, source_table, when="AFTER"):
     """Drops a non-PostgreSQL trigger by name"""
     trigger_name = get_trigger_name(operation, source_table, when)
     return f"DROP TRIGGER IF EXISTS {trigger_name}"
diff --git a/lib/galaxy/model/migrate/triggers/update_audit_table.py b/lib/galaxy/model/migrate/triggers/update_audit_table.py
index 7966875566d..59f69f6f5ac 100644
--- a/lib/galaxy/model/migrate/triggers/update_audit_table.py
+++ b/lib/galaxy/model/migrate/triggers/update_audit_table.py
@@ -1,26 +1,25 @@
 from galaxy.model.migrate.versions.util import execute_statements
 
-
 # function name prefix
 fn_prefix = "fn_audit_history_by"
 
 # map between source table and associated incoming id field
 trigger_config = {
-    'history_dataset_association': "history_id",
-    'history_dataset_collection_association': "history_id",
-    'history': "id",
+    "history_dataset_association": "history_id",
+    "history_dataset_collection_association": "history_id",
+    "history": "id",
 }
 
 
 def install(engine):
     """Install history audit table triggers"""
-    sql = _postgres_install(engine) if 'postgres' in engine.name else _sqlite_install()
+    sql = _postgres_install(engine) if "postgres" in engine.name else _sqlite_install()
     execute_statements(engine, sql)
 
 
 def remove(engine):
     """Uninstall history audit table triggers"""
-    sql = _postgres_remove() if 'postgres' in engine.name else _sqlite_remove()
+    sql = _postgres_remove() if "postgres" in engine.name else _sqlite_remove()
     execute_statements(engine, sql)
 
 
diff --git a/lib/galaxy/model/migrate/versions/0001_initial_tables.py b/lib/galaxy/model/migrate/versions/0001_initial_tables.py
index 6248b2ca0bb..f9f4fcf116d 100644
--- a/lib/galaxy/model/migrate/versions/0001_initial_tables.py
+++ b/lib/galaxy/model/migrate/versions/0001_initial_tables.py
@@ -11,14 +11,14 @@ from sqlalchemy import (
     Numeric,
     String,
     Table,
-    TEXT
+    TEXT,
 )
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import (
     JSONType,
     MetadataType,
-    TrimmedString
+    TrimmedString,
 )
 
 log = logging.getLogger(__name__)
@@ -26,15 +26,20 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 # Tables as of changeset 1464:c7acaa1bb88f
-User_table = Table("galaxy_user", metadata,
+User_table = Table(
+    "galaxy_user",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("email", TrimmedString(255), nullable=False),
     Column("password", TrimmedString(40), nullable=False),
-    Column("external", Boolean, default=False))
+    Column("external", Boolean, default=False),
+)
 
-History_table = Table("history", metadata,
+History_table = Table(
+    "history",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, index=True, default=now, onupdate=now),
@@ -43,15 +48,23 @@ History_table = Table("history", metadata,
     Column("hid_counter", Integer, default=1),
     Column("deleted", Boolean, index=True, default=False),
     Column("purged", Boolean, index=True, default=False),
-    Column("genome_build", TrimmedString(40)))
+    Column("genome_build", TrimmedString(40)),
+)
 
-HistoryDatasetAssociation_table = Table("history_dataset_association", metadata,
+HistoryDatasetAssociation_table = Table(
+    "history_dataset_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("history_id", Integer, ForeignKey("history.id"), index=True),
     Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
-    Column("copied_from_history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
+    Column(
+        "copied_from_history_dataset_association_id",
+        Integer,
+        ForeignKey("history_dataset_association.id"),
+        nullable=True,
+    ),
     Column("hid", Integer),
     Column("name", TrimmedString(255)),
     Column("info", TrimmedString(255)),
@@ -62,9 +75,12 @@ HistoryDatasetAssociation_table = Table("history_dataset_association", metadata,
     Column("parent_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
     Column("designation", TrimmedString(255)),
     Column("deleted", Boolean, index=True, default=False),
-    Column("visible", Boolean))
+    Column("visible", Boolean),
+)
 
-Dataset_table = Table("dataset", metadata,
+Dataset_table = Table(
+    "dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, index=True, default=now, onupdate=now),
@@ -74,9 +90,12 @@ Dataset_table = Table("dataset", metadata,
     Column("purgable", Boolean, default=True),
     Column("external_filename", TEXT),
     Column("_extra_files_path", TEXT),
-    Column('file_size', Numeric(15, 0)))
+    Column("file_size", Numeric(15, 0)),
+)
 
-ImplicitlyConvertedDatasetAssociation_table = Table("implicitly_converted_dataset_association", metadata,
+ImplicitlyConvertedDatasetAssociation_table = Table(
+    "implicitly_converted_dataset_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -84,16 +103,22 @@ ImplicitlyConvertedDatasetAssociation_table = Table("implicitly_converted_datase
     Column("hda_parent_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
     Column("deleted", Boolean, index=True, default=False),
     Column("metadata_safe", Boolean, index=True, default=True),
-    Column("type", TrimmedString(255)))
+    Column("type", TrimmedString(255)),
+)
 
-ValidationError_table = Table("validation_error", metadata,
+ValidationError_table = Table(
+    "validation_error",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
     Column("message", TrimmedString(255)),
     Column("err_type", TrimmedString(64)),
-    Column("attributes", TEXT))
+    Column("attributes", TEXT),
+)
 
-Job_table = Table("job", metadata,
+Job_table = Table(
+    "job",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -110,27 +135,39 @@ Job_table = Table("job", metadata,
     Column("traceback", TEXT),
     Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True),
     Column("job_runner_name", String(255)),
-    Column("job_runner_external_id", String(255)))
+    Column("job_runner_external_id", String(255)),
+)
 
-JobParameter_table = Table("job_parameter", metadata,
+JobParameter_table = Table(
+    "job_parameter",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("name", String(255)),
-    Column("value", TEXT))
+    Column("value", TEXT),
+)
 
-JobToInputDatasetAssociation_table = Table("job_to_input_dataset", metadata,
+JobToInputDatasetAssociation_table = Table(
+    "job_to_input_dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-    Column("name", String(255)))
+    Column("name", String(255)),
+)
 
-JobToOutputDatasetAssociation_table = Table("job_to_output_dataset", metadata,
+JobToOutputDatasetAssociation_table = Table(
+    "job_to_output_dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-    Column("name", String(255)))
+    Column("name", String(255)),
+)
 
-Event_table = Table("event", metadata,
+Event_table = Table(
+    "event",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -138,9 +175,12 @@ Event_table = Table("event", metadata,
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True),
     Column("message", TrimmedString(1024)),
     Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True),
-    Column("tool_id", String(255)))
+    Column("tool_id", String(255)),
+)
 
-GalaxySession_table = Table("galaxy_session", metadata,
+GalaxySession_table = Table(
+    "galaxy_session",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -151,34 +191,50 @@ GalaxySession_table = Table("galaxy_session", metadata,
     Column("current_history_id", Integer, ForeignKey("history.id"), nullable=True),
     Column("session_key", TrimmedString(255), index=True, unique=True),
     Column("is_valid", Boolean, default=False),
-    Column("prev_session_id", Integer))
+    Column("prev_session_id", Integer),
+)
 
-GalaxySessionToHistoryAssociation_table = Table("galaxy_session_to_history", metadata,
+GalaxySessionToHistoryAssociation_table = Table(
+    "galaxy_session_to_history",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
-    Column("history_id", Integer, ForeignKey("history.id"), index=True))
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+)
 
-StoredWorkflow_table = Table("stored_workflow", metadata,
+StoredWorkflow_table = Table(
+    "stored_workflow",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-    Column("latest_workflow_id", Integer,
-           ForeignKey("workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk'), index=True),
+    Column(
+        "latest_workflow_id",
+        Integer,
+        ForeignKey("workflow.id", use_alter=True, name="stored_workflow_latest_workflow_id_fk"),
+        index=True,
+    ),
     Column("name", TEXT),
-    Column("deleted", Boolean, default=False))
+    Column("deleted", Boolean, default=False),
+)
 
-Workflow_table = Table("workflow", metadata,
+Workflow_table = Table(
+    "workflow",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True, nullable=False),
     Column("name", TEXT),
     Column("has_cycles", Boolean),
-    Column("has_errors", Boolean))
+    Column("has_errors", Boolean),
+)
 
-WorkflowStep_table = Table("workflow_step", metadata,
+WorkflowStep_table = Table(
+    "workflow_step",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -190,25 +246,35 @@ WorkflowStep_table = Table("workflow_step", metadata,
     Column("tool_errors", JSONType),
     Column("position", JSONType),
     Column("config", JSONType),
-    Column("order_index", Integer))
+    Column("order_index", Integer),
+)
 
-WorkflowStepConnection_table = Table("workflow_step_connection", metadata,
+WorkflowStepConnection_table = Table(
+    "workflow_step_connection",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
     Column("input_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
     Column("output_name", TEXT),
-    Column("input_name", TEXT))
+    Column("input_name", TEXT),
+)
 
-StoredWorkflowUserShareAssociation_table = Table("stored_workflow_user_share_connection", metadata,
-    Column("id", Integer, primary_key=True),
-    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
-
-StoredWorkflowMenuEntry_table = Table("stored_workflow_menu_entry", metadata,
+StoredWorkflowUserShareAssociation_table = Table(
+    "stored_workflow_user_share_connection",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-    Column("order_index", Integer))
+)
+
+StoredWorkflowMenuEntry_table = Table(
+    "stored_workflow_menu_entry",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("order_index", Integer),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0002_metadata_file_table.py b/lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
index 056f9d219b9..b61fe4bf580 100644
--- a/lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
+++ b/lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
@@ -12,12 +12,12 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -25,14 +25,17 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 # New table in changeset 1568:0b022adfdc34
-MetadataFile_table = Table("metadata_file", metadata,
+MetadataFile_table = Table(
+    "metadata_file",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("name", TEXT),
     Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, index=True, default=now, onupdate=now),
     Column("deleted", Boolean, index=True, default=False),
-    Column("purged", Boolean, index=True, default=False))
+    Column("purged", Boolean, index=True, default=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
index c79d72e94a8..27b09337bca 100644
--- a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
+++ b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
@@ -15,13 +15,13 @@ from sqlalchemy import (
     MetaData,
     String,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import (
     JSONType,
     MetadataType,
-    TrimmedString
+    TrimmedString,
 )
 from galaxy.model.migrate.versions.util import (
     add_column,
@@ -31,7 +31,7 @@ from galaxy.model.migrate.versions.util import (
     drop_table,
     engine_false,
     localtimestamp,
-    nextval
+    nextval,
 )
 
 log = logging.getLogger(__name__)
@@ -39,132 +39,215 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 # New tables as of changeset 2341:5498ac35eedd
-Group_table = Table("galaxy_group", metadata,
+Group_table = Table(
+    "galaxy_group",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("name", String(255), index=True, unique=True),
-    Column("deleted", Boolean, index=True, default=False))
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-UserGroupAssociation_table = Table("user_group_association", metadata,
+UserGroupAssociation_table = Table(
+    "user_group_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
     Column("create_time", DateTime, default=now),
-    Column("update_time", DateTime, default=now, onupdate=now))
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-UserRoleAssociation_table = Table("user_role_association", metadata,
+UserRoleAssociation_table = Table(
+    "user_role_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("role_id", Integer, ForeignKey("role.id"), index=True),
     Column("create_time", DateTime, default=now),
-    Column("update_time", DateTime, default=now, onupdate=now))
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-GroupRoleAssociation_table = Table("group_role_association", metadata,
+GroupRoleAssociation_table = Table(
+    "group_role_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
     Column("role_id", Integer, ForeignKey("role.id"), index=True),
     Column("create_time", DateTime, default=now),
-    Column("update_time", DateTime, default=now, onupdate=now))
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-Role_table = Table("role", metadata,
+Role_table = Table(
+    "role",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("name", String(255), index=True, unique=True),
     Column("description", TEXT),
     Column("type", String(40), index=True),
-    Column("deleted", Boolean, index=True, default=False))
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-DatasetPermissions_table = Table("dataset_permissions", metadata,
+DatasetPermissions_table = Table(
+    "dataset_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
     Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-LibraryPermissions_table = Table("library_permissions", metadata,
+LibraryPermissions_table = Table(
+    "library_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
     Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-LibraryFolderPermissions_table = Table("library_folder_permissions", metadata,
+LibraryFolderPermissions_table = Table(
+    "library_folder_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
     Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-LibraryDatasetPermissions_table = Table("library_dataset_permissions", metadata,
+LibraryDatasetPermissions_table = Table(
+    "library_dataset_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
     Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-LibraryDatasetDatasetAssociationPermissions_table = Table("library_dataset_dataset_association_permissions", metadata,
+LibraryDatasetDatasetAssociationPermissions_table = Table(
+    "library_dataset_dataset_association_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
-    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
-Index("ix_lddap_library_dataset_dataset_association_id", LibraryDatasetDatasetAssociationPermissions_table.c.library_dataset_dataset_association_id)
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        nullable=True,
+    ),
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
+Index(
+    "ix_lddap_library_dataset_dataset_association_id",
+    LibraryDatasetDatasetAssociationPermissions_table.c.library_dataset_dataset_association_id,
+)
 
-LibraryItemInfoPermissions_table = Table("library_item_info_permissions", metadata,
+LibraryItemInfoPermissions_table = Table(
+    "library_item_info_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
     Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), nullable=True, index=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-LibraryItemInfoTemplatePermissions_table = Table("library_item_info_template_permissions", metadata,
+LibraryItemInfoTemplatePermissions_table = Table(
+    "library_item_info_template_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("action", TEXT),
     Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id"), nullable=True),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
-Index("ix_liitp_library_item_info_template_id", LibraryItemInfoTemplatePermissions_table.c.library_item_info_template_id)
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
+Index(
+    "ix_liitp_library_item_info_template_id", LibraryItemInfoTemplatePermissions_table.c.library_item_info_template_id
+)
 
-DefaultUserPermissions_table = Table("default_user_permissions", metadata,
+DefaultUserPermissions_table = Table(
+    "default_user_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("action", TEXT),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-DefaultHistoryPermissions_table = Table("default_history_permissions", metadata,
+DefaultHistoryPermissions_table = Table(
+    "default_history_permissions",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("history_id", Integer, ForeignKey("history.id"), index=True),
     Column("action", TEXT),
-    Column("role_id", Integer, ForeignKey("role.id"), index=True))
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
-LibraryDataset_table = Table("library_dataset", metadata,
+LibraryDataset_table = Table(
+    "library_dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk"), nullable=True, index=True),  # current version of dataset, if null, there is not a current version selected
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey(
+            "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk"
+        ),
+        nullable=True,
+        index=True,
+    ),  # current version of dataset, if null, there is not a current version selected
     Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True),
     Column("order_id", Integer),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
-    Column("name", TrimmedString(255), key="_name"),  # when not None/null this will supercede display in library (but not when imported into user's history?)
-    Column("info", TrimmedString(255), key="_info"),  # when not None/null this will supercede display in library (but not when imported into user's history?)
-    Column("deleted", Boolean, index=True, default=False))
+    Column(
+        "name", TrimmedString(255), key="_name"
+    ),  # when not None/null this will supercede display in library (but not when imported into user's history?)
+    Column(
+        "info", TrimmedString(255), key="_info"
+    ),  # when not None/null this will supercede display in library (but not when imported into user's history?)
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata,
+LibraryDatasetDatasetAssociation_table = Table(
+    "library_dataset_dataset_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), index=True),
     Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
-    Column("copied_from_history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey'), nullable=True),
-    Column("copied_from_library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey'), nullable=True),
+    Column(
+        "copied_from_history_dataset_association_id",
+        Integer,
+        ForeignKey(
+            "history_dataset_association.id", use_alter=True, name="history_dataset_association_dataset_id_fkey"
+        ),
+        nullable=True,
+    ),
+    Column(
+        "copied_from_library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey(
+            "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fkey"
+        ),
+        nullable=True,
+    ),
     Column("name", TrimmedString(255)),
     Column("info", TrimmedString(255)),
     Column("blurb", TrimmedString(255)),
@@ -176,9 +259,12 @@ LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_associat
     Column("deleted", Boolean, index=True, default=False),
     Column("visible", Boolean),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-    Column("message", TrimmedString(255)))
+    Column("message", TrimmedString(255)),
+)
 
-Library_table = Table("library", metadata,
+Library_table = Table(
+    "library",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("root_folder_id", Integer, ForeignKey("library_folder.id"), index=True),
     Column("create_time", DateTime, default=now),
@@ -186,9 +272,12 @@ Library_table = Table("library", metadata,
     Column("name", String(255), index=True),
     Column("deleted", Boolean, index=True, default=False),
     Column("purged", Boolean, index=True, default=False),
-    Column("description", TEXT))
+    Column("description", TEXT),
+)
 
-LibraryFolder_table = Table("library_folder", metadata,
+LibraryFolder_table = Table(
+    "library_folder",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("parent_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
     Column("create_time", DateTime, default=now),
@@ -199,9 +288,12 @@ LibraryFolder_table = Table("library_folder", metadata,
     Column("item_count", Integer),
     Column("deleted", Boolean, index=True, default=False),
     Column("purged", Boolean, index=True, default=False),
-    Column("genome_build", TrimmedString(40)))
+    Column("genome_build", TrimmedString(40)),
+)
 
-LibraryItemInfoTemplateElement_table = Table("library_item_info_template_element", metadata,
+LibraryItemInfoTemplateElement_table = Table(
+    "library_item_info_template_element",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -209,13 +301,16 @@ LibraryItemInfoTemplateElement_table = Table("library_item_info_template_element
     Column("deleted", Boolean, index=True, default=False),
     Column("name", TEXT),
     Column("description", TEXT),
-    Column("type", TEXT, default='string'),
+    Column("type", TEXT, default="string"),
     Column("order_id", Integer),
     Column("options", JSONType),
-    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
+    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")),
+)
 Index("ix_liite_library_item_info_template_id", LibraryItemInfoTemplateElement_table.c.library_item_info_template_id)
 
-LibraryItemInfoTemplate_table = Table("library_item_info_template", metadata,
+LibraryItemInfoTemplate_table = Table(
+    "library_item_info_template",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -223,103 +318,180 @@ LibraryItemInfoTemplate_table = Table("library_item_info_template", metadata,
     Column("deleted", Boolean, index=True, default=False),
     Column("name", TEXT),
     Column("description", TEXT),
-    Column("item_count", Integer, default=0))
+    Column("item_count", Integer, default=0),
+)
 
-LibraryInfoTemplateAssociation_table = Table("library_info_template_association", metadata,
+LibraryInfoTemplateAssociation_table = Table(
+    "library_info_template_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
-    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
+    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")),
+)
 Index("ix_lita_library_item_info_template_id", LibraryInfoTemplateAssociation_table.c.library_item_info_template_id)
 
-LibraryFolderInfoTemplateAssociation_table = Table("library_folder_info_template_association", metadata,
+LibraryFolderInfoTemplateAssociation_table = Table(
+    "library_folder_info_template_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
-    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
-Index("ix_lfita_library_item_info_template_id", LibraryFolderInfoTemplateAssociation_table.c.library_item_info_template_id)
+    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")),
+)
+Index(
+    "ix_lfita_library_item_info_template_id", LibraryFolderInfoTemplateAssociation_table.c.library_item_info_template_id
+)
 
-LibraryDatasetInfoTemplateAssociation_table = Table("library_dataset_info_template_association", metadata,
+LibraryDatasetInfoTemplateAssociation_table = Table(
+    "library_dataset_info_template_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
-    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
-Index("ix_ldita_library_item_info_template_id", LibraryDatasetInfoTemplateAssociation_table.c.library_item_info_template_id)
+    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")),
+)
+Index(
+    "ix_ldita_library_item_info_template_id",
+    LibraryDatasetInfoTemplateAssociation_table.c.library_item_info_template_id,
+)
 
-LibraryDatasetDatasetInfoTemplateAssociation_table = Table("library_dataset_dataset_info_template_association", metadata,
+LibraryDatasetDatasetInfoTemplateAssociation_table = Table(
+    "library_dataset_dataset_info_template_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
-    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
-    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
-Index("ix_lddita_library_dataset_dataset_association_id", LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_dataset_dataset_association_id)
-Index("ix_lddita_library_item_info_template_id", LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_item_info_template_id)
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        nullable=True,
+    ),
+    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")),
+)
+Index(
+    "ix_lddita_library_dataset_dataset_association_id",
+    LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_dataset_dataset_association_id,
+)
+Index(
+    "ix_lddita_library_item_info_template_id",
+    LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_item_info_template_id,
+)
 
-LibraryItemInfoElement_table = Table("library_item_info_element", metadata,
+LibraryItemInfoElement_table = Table(
+    "library_item_info_element",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("contents", JSONType),
     Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
-    Column("library_item_info_template_element_id", Integer, ForeignKey("library_item_info_template_element.id")))
-Index("ix_liie_library_item_info_template_element_id", LibraryItemInfoElement_table.c.library_item_info_template_element_id)
+    Column("library_item_info_template_element_id", Integer, ForeignKey("library_item_info_template_element.id")),
+)
+Index(
+    "ix_liie_library_item_info_template_element_id",
+    LibraryItemInfoElement_table.c.library_item_info_template_element_id,
+)
 
-LibraryItemInfo_table = Table("library_item_info", metadata,
+LibraryItemInfo_table = Table(
+    "library_item_info",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("deleted", Boolean, index=True, default=False),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True),
-    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id"), nullable=True, index=True))
+    Column(
+        "library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id"), nullable=True, index=True
+    ),
+)
 
-LibraryInfoAssociation_table = Table("library_info_association", metadata,
+LibraryInfoAssociation_table = Table(
+    "library_info_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
     Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True),
+)
 
-LibraryFolderInfoAssociation_table = Table("library_folder_info_association", metadata,
+LibraryFolderInfoAssociation_table = Table(
+    "library_folder_info_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
     Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True),
+)
 
-LibraryDatasetInfoAssociation_table = Table("library_dataset_info_association", metadata,
+LibraryDatasetInfoAssociation_table = Table(
+    "library_dataset_info_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
     Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True),
+)
 
-LibraryDatasetDatasetInfoAssociation_table = Table("library_dataset_dataset_info_association", metadata,
+LibraryDatasetDatasetInfoAssociation_table = Table(
+    "library_dataset_dataset_info_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
-    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        nullable=True,
+    ),
     Column("library_item_info_id", Integer, ForeignKey("library_item_info.id")),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))
-Index("ix_lddia_library_dataset_dataset_association_id", LibraryDatasetDatasetInfoAssociation_table.c.library_dataset_dataset_association_id)
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True),
+)
+Index(
+    "ix_lddia_library_dataset_dataset_association_id",
+    LibraryDatasetDatasetInfoAssociation_table.c.library_dataset_dataset_association_id,
+)
 Index("ix_lddia_library_item_info_id", LibraryDatasetDatasetInfoAssociation_table.c.library_item_info_id)
 
-JobExternalOutputMetadata_table = Table("job_external_output_metadata", metadata,
+JobExternalOutputMetadata_table = Table(
+    "job_external_output_metadata",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
-    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True),
-    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
+    Column(
+        "history_dataset_association_id",
+        Integer,
+        ForeignKey("history_dataset_association.id"),
+        index=True,
+        nullable=True,
+    ),
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        nullable=True,
+    ),
     Column("filename_in", String(255)),
     Column("filename_out", String(255)),
     Column("filename_results_code", String(255)),
     Column("filename_kwds", String(255)),
-    Column("job_runner_external_pid", String(255)))
-Index("ix_jeom_library_dataset_dataset_association_id", JobExternalOutputMetadata_table.c.library_dataset_dataset_association_id)
+    Column("job_runner_external_pid", String(255)),
+)
+Index(
+    "ix_jeom_library_dataset_dataset_association_id",
+    JobExternalOutputMetadata_table.c.library_dataset_dataset_association_id,
+)
 
 
 def upgrade(migrate_engine):
@@ -329,47 +501,61 @@ def upgrade(migrate_engine):
 
     # Add 2 new columns to the galaxy_user table
     User_table = Table("galaxy_user", metadata, autoload=True)
-    col = Column('deleted', Boolean, index=True, default=False)
-    add_column(col, User_table, metadata, index_name='ix_galaxy_user_deleted')
-    col = Column('purged', Boolean, index=True, default=False)
-    add_column(col, User_table, metadata, index_name='ix_galaxy_user_purged')
+    col = Column("deleted", Boolean, index=True, default=False)
+    add_column(col, User_table, metadata, index_name="ix_galaxy_user_deleted")
+    col = Column("purged", Boolean, index=True, default=False)
+    add_column(col, User_table, metadata, index_name="ix_galaxy_user_purged")
     # Add 1 new column to the history_dataset_association table
     HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True)
-    col = Column('copied_from_library_dataset_dataset_association_id', Integer, nullable=True)
+    col = Column("copied_from_library_dataset_dataset_association_id", Integer, nullable=True)
     add_column(col, HistoryDatasetAssociation_table, metadata)
     # Add 1 new column to the metadata_file table
     MetadataFile_table = Table("metadata_file", metadata, autoload=True)
-    col = Column('lda_id', Integer, index=True, nullable=True)
-    add_column(col, MetadataFile_table, metadata, index_name='ix_metadata_file_lda_id')
+    col = Column("lda_id", Integer, index=True, nullable=True)
+    add_column(col, MetadataFile_table, metadata, index_name="ix_metadata_file_lda_id")
     # Add 1 new column to the stored_workflow table - changeset 2328
-    StoredWorkflow_table = Table("stored_workflow", metadata,
-        Column("latest_workflow_id", Integer,
-            ForeignKey("workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk'), index=True),
-        autoload=True, extend_existing=True)
-    col = Column('importable', Boolean, default=False)
+    StoredWorkflow_table = Table(
+        "stored_workflow",
+        metadata,
+        Column(
+            "latest_workflow_id",
+            Integer,
+            ForeignKey("workflow.id", use_alter=True, name="stored_workflow_latest_workflow_id_fk"),
+            index=True,
+        ),
+        autoload=True,
+        extend_existing=True,
+    )
+    col = Column("importable", Boolean, default=False)
     add_column(col, StoredWorkflow_table, metadata)
     # Create an index on the Job.state column - changeset 2192
-    add_index('ix_job_state', 'job', 'state', metadata)
+    add_index("ix_job_state", "job", "state", metadata)
     # Add all of the new tables above
     metadata.create_all()
     # Add 1 foreign key constraint to the history_dataset_association table
     LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True)
     try:
-        cons = ForeignKeyConstraint([HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id],
-                                    [LibraryDatasetDatasetAssociation_table.c.id],
-                                    name='history_dataset_association_copied_from_library_dataset_da_fkey')
+        cons = ForeignKeyConstraint(
+            [HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id],
+            [LibraryDatasetDatasetAssociation_table.c.id],
+            name="history_dataset_association_copied_from_library_dataset_da_fkey",
+        )
         # Create the constraint
         cons.create()
     except Exception:
-        log.exception("Adding foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' to table 'history_dataset_association' failed.")
+        log.exception(
+            "Adding foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' to table 'history_dataset_association' failed."
+        )
     # Add 1 foreign key constraint to the metadata_file table
     LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True)
-    if migrate_engine.name != 'sqlite':
+    if migrate_engine.name != "sqlite":
         # Sqlite can't alter table add foreign key.
         try:
-            cons = ForeignKeyConstraint([MetadataFile_table.c.lda_id],
-                                        [LibraryDatasetDatasetAssociation_table.c.id],
-                                        name='metadata_file_lda_id_fkey')
+            cons = ForeignKeyConstraint(
+                [MetadataFile_table.c.lda_id],
+                [LibraryDatasetDatasetAssociation_table.c.id],
+                name="metadata_file_lda_id_fkey",
+            )
             # Create the constraint
             cons.create()
         except Exception:
@@ -382,78 +568,97 @@ def upgrade(migrate_engine):
         roles = migrate_engine.execute(cmd).fetchall()
         if not roles:
             # Create private roles for each user - pass 1
-            cmd = \
-                "INSERT INTO role " + \
-                "SELECT %s AS id," + \
-                "%s AS create_time," + \
-                "%s AS update_time," + \
-                "email AS name," + \
-                "email AS description," + \
-                "'private' As type," + \
-                "%s AS deleted " + \
-                "FROM galaxy_user " + \
-                "ORDER BY id;"
-            cmd = cmd % (nextval(migrate_engine, 'role'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), engine_false(migrate_engine))
+            cmd = (
+                "INSERT INTO role "
+                + "SELECT %s AS id,"
+                + "%s AS create_time,"
+                + "%s AS update_time,"
+                + "email AS name,"
+                + "email AS description,"
+                + "'private' As type,"
+                + "%s AS deleted "
+                + "FROM galaxy_user "
+                + "ORDER BY id;"
+            )
+            cmd = cmd % (
+                nextval(migrate_engine, "role"),
+                localtimestamp(migrate_engine),
+                localtimestamp(migrate_engine),
+                engine_false(migrate_engine),
+            )
             migrate_engine.execute(cmd)
             # Create private roles for each user - pass 2
-            if migrate_engine.name in ['postgres', 'postgresql', 'sqlite']:
+            if migrate_engine.name in ["postgres", "postgresql", "sqlite"]:
                 cmd = "UPDATE role SET description = 'Private role for ' || description;"
-            elif migrate_engine.name == 'mysql':
+            elif migrate_engine.name == "mysql":
                 cmd = "UPDATE role SET description = CONCAT( 'Private role for ', description );"
             migrate_engine.execute(cmd)
             # Create private roles for each user - pass 3
-            cmd = \
-                "INSERT INTO user_role_association " + \
-                "SELECT %s AS id," + \
-                "galaxy_user.id AS user_id," + \
-                "role.id AS role_id," + \
-                "%s AS create_time," + \
-                "%s AS update_time " + \
-                "FROM galaxy_user, role " + \
-                "WHERE galaxy_user.email = role.name " + \
-                "ORDER BY galaxy_user.id;"
-            cmd = cmd % (nextval(migrate_engine, 'user_role_association'), localtimestamp(migrate_engine), localtimestamp(migrate_engine))
+            cmd = (
+                "INSERT INTO user_role_association "
+                + "SELECT %s AS id,"
+                + "galaxy_user.id AS user_id,"
+                + "role.id AS role_id,"
+                + "%s AS create_time,"
+                + "%s AS update_time "
+                + "FROM galaxy_user, role "
+                + "WHERE galaxy_user.email = role.name "
+                + "ORDER BY galaxy_user.id;"
+            )
+            cmd = cmd % (
+                nextval(migrate_engine, "user_role_association"),
+                localtimestamp(migrate_engine),
+                localtimestamp(migrate_engine),
+            )
             migrate_engine.execute(cmd)
             # Create default permissions for each user
-            cmd = \
-                "INSERT INTO default_user_permissions " + \
-                "SELECT %s AS id," + \
-                "galaxy_user.id AS user_id," + \
-                "'manage permissions' AS action," + \
-                "user_role_association.role_id AS role_id " + \
-                "FROM galaxy_user " + \
-                "JOIN user_role_association ON user_role_association.user_id = galaxy_user.id " + \
-                "ORDER BY galaxy_user.id;"
-            cmd = cmd % nextval(migrate_engine, 'default_user_permissions')
+            cmd = (
+                "INSERT INTO default_user_permissions "
+                + "SELECT %s AS id,"
+                + "galaxy_user.id AS user_id,"
+                + "'manage permissions' AS action,"
+                + "user_role_association.role_id AS role_id "
+                + "FROM galaxy_user "
+                + "JOIN user_role_association ON user_role_association.user_id = galaxy_user.id "
+                + "ORDER BY galaxy_user.id;"
+            )
+            cmd = cmd % nextval(migrate_engine, "default_user_permissions")
             migrate_engine.execute(cmd)
             # Create default history permissions for each active history associated with a user
 
-            cmd = \
-                "INSERT INTO default_history_permissions " + \
-                "SELECT %s AS id," + \
-                "history.id AS history_id," + \
-                "'manage permissions' AS action," + \
-                "user_role_association.role_id AS role_id " + \
-                "FROM history " + \
-                "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \
-                "WHERE history.purged = %s AND history.user_id IS NOT NULL;"
-            cmd = cmd % (nextval(migrate_engine, 'default_history_permissions'), engine_false(migrate_engine))
+            cmd = (
+                "INSERT INTO default_history_permissions "
+                + "SELECT %s AS id,"
+                + "history.id AS history_id,"
+                + "'manage permissions' AS action,"
+                + "user_role_association.role_id AS role_id "
+                + "FROM history "
+                + "JOIN user_role_association ON user_role_association.user_id = history.user_id "
+                + "WHERE history.purged = %s AND history.user_id IS NOT NULL;"
+            )
+            cmd = cmd % (nextval(migrate_engine, "default_history_permissions"), engine_false(migrate_engine))
             migrate_engine.execute(cmd)
             # Create "manage permissions" dataset_permissions for all activate-able datasets
-            cmd = \
-                "INSERT INTO dataset_permissions " + \
-                "SELECT %s AS id," + \
-                "%s AS create_time," + \
-                "%s AS update_time," + \
-                "'manage permissions' AS action," + \
-                "history_dataset_association.dataset_id AS dataset_id," + \
-                "user_role_association.role_id AS role_id " + \
-                "FROM history " + \
-                "JOIN history_dataset_association ON history_dataset_association.history_id = history.id " + \
-                "JOIN dataset ON history_dataset_association.dataset_id = dataset.id " + \
-                "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \
-                "WHERE dataset.purged = %s AND history.user_id IS NOT NULL;"
-            cmd = cmd % (nextval(migrate_engine, 'dataset_permissions'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), engine_false(migrate_engine))
+            cmd = (
+                "INSERT INTO dataset_permissions "
+                + "SELECT %s AS id,"
+                + "%s AS create_time,"
+                + "%s AS update_time,"
+                + "'manage permissions' AS action,"
+                + "history_dataset_association.dataset_id AS dataset_id,"
+                + "user_role_association.role_id AS role_id "
+                + "FROM history "
+                + "JOIN history_dataset_association ON history_dataset_association.history_id = history.id "
+                + "JOIN dataset ON history_dataset_association.dataset_id = dataset.id "
+                + "JOIN user_role_association ON user_role_association.user_id = history.user_id "
+                + "WHERE dataset.purged = %s AND history.user_id IS NOT NULL;"
+            )
+            cmd = cmd % (
+                nextval(migrate_engine, "dataset_permissions"),
+                localtimestamp(migrate_engine),
+                localtimestamp(migrate_engine),
+                engine_false(migrate_engine),
+            )
             migrate_engine.execute(cmd)
 
 
@@ -466,9 +671,11 @@ def downgrade(migrate_engine):
     MetadataFile_table = Table("metadata_file", metadata, autoload=True)
     LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True)
     try:
-        cons = ForeignKeyConstraint([MetadataFile_table.c.lda_id],
-                                    [LibraryDatasetDatasetAssociation_table.c.id],
-                                    name='metadata_file_lda_id_fkey')
+        cons = ForeignKeyConstraint(
+            [MetadataFile_table.c.lda_id],
+            [LibraryDatasetDatasetAssociation_table.c.id],
+            name="metadata_file_lda_id_fkey",
+        )
         # Drop the constraint
         cons.drop()
     except Exception:
@@ -477,13 +684,17 @@ def downgrade(migrate_engine):
     HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True)
     LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True)
     try:
-        cons = ForeignKeyConstraint([HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id],
-                                    [LibraryDatasetDatasetAssociation_table.c.id],
-                                    name='history_dataset_association_copied_from_library_dataset_da_fkey')
+        cons = ForeignKeyConstraint(
+            [HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id],
+            [LibraryDatasetDatasetAssociation_table.c.id],
+            name="history_dataset_association_copied_from_library_dataset_da_fkey",
+        )
         # Drop the constraint
         cons.drop()
     except Exception:
-        log.exception("Dropping foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' from table 'history_dataset_association' failed.")
+        log.exception(
+            "Dropping foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' from table 'history_dataset_association' failed."
+        )
     # Drop all of the new tables above
     TABLES = [
         UserGroupAssociation_table,
@@ -521,14 +732,14 @@ def downgrade(migrate_engine):
     for table in TABLES:
         drop_table(table)
     # Drop the index on the Job.state column - changeset 2192
-    drop_index('ix_job_state', 'job', 'state', metadata)
+    drop_index("ix_job_state", "job", "state", metadata)
     # Drop 1 column from the stored_workflow table - changeset 2328
-    drop_column('importable', 'stored_workflow', metadata)
+    drop_column("importable", "stored_workflow", metadata)
     # Drop 1 column from the metadata_file table
-    drop_column('lda_id', 'metadata_file', metadata)
+    drop_column("lda_id", "metadata_file", metadata)
     # Drop 1 column from the history_dataset_association table
-    drop_column('copied_from_library_dataset_dataset_association_id', HistoryDatasetAssociation_table)
+    drop_column("copied_from_library_dataset_dataset_association_id", HistoryDatasetAssociation_table)
     # Drop 2 columns from the galaxy_user table
     User_table = Table("galaxy_user", metadata, autoload=True)
-    drop_column('deleted', User_table)
-    drop_column('purged', User_table)
+    drop_column("deleted", User_table)
+    drop_column("purged", User_table)
diff --git a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
index e050e1384d7..a3c3d72e17b 100644
--- a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
+++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
@@ -5,12 +5,12 @@ import logging
 
 from sqlalchemy import (
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    engine_false
+    engine_false,
 )
 
 log = logging.getLogger(__name__)
@@ -25,8 +25,8 @@ def upgrade(migrate_engine):
     User_table = Table("galaxy_user", metadata, autoload=True)
     # The next add_index() calls are not needed any more after commit
     # 7ee93c0995123b0f357abd649326295dfa06766c , but harmless
-    add_index('ix_galaxy_user_deleted', User_table, 'deleted')
-    add_index('ix_galaxy_user_purged', User_table, 'purged')
+    add_index("ix_galaxy_user_deleted", User_table, "deleted")
+    add_index("ix_galaxy_user_purged", User_table, "purged")
     # Set the default data in the galaxy_user table, but only for null values
     cmd = f"UPDATE galaxy_user SET deleted = {engine_false(migrate_engine)} WHERE deleted is null"
     try:
@@ -38,9 +38,12 @@ def upgrade(migrate_engine):
         migrate_engine.execute(cmd)
     except Exception:
         log.exception("Setting default data for galaxy_user.purged column failed.")
-    add_index('ix_hda_copied_from_library_dataset_dataset_association_id',
-        'history_dataset_association',
-        'copied_from_library_dataset_dataset_association_id', metadata)
+    add_index(
+        "ix_hda_copied_from_library_dataset_dataset_association_id",
+        "history_dataset_association",
+        "copied_from_library_dataset_dataset_association_id",
+        metadata,
+    )
 
 
 def downgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
index 805e6faf07e..d73bb40c1d2 100644
--- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
+++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
@@ -17,12 +17,12 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     # Set the default data in the galaxy_user table, but only for null values
-    cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like \'>%%\'"
+    cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like '>%%'"
     try:
         migrate_engine.execute(cmd)
     except Exception:
         log.exception("Resetting extension qual to qual454 in history_dataset_association failed.")
-    cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like \'>%%\'"
+    cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like '>%%'"
     try:
         migrate_engine.execute(cmd)
     except Exception:
diff --git a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py
index a8e75b961b0..fdfd555a57c 100644
--- a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py
+++ b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py
@@ -12,23 +12,26 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-HistoryUserShareAssociation_table = Table("history_user_share_association", metadata,
-                                          Column("id", Integer, primary_key=True),
-                                          Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                          Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+HistoryUserShareAssociation_table = Table(
+    "history_user_share_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
@@ -37,13 +40,13 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     create_table(HistoryUserShareAssociation_table)
-    col = Column('importable', Boolean, index=True, default=False)
-    add_column(col, 'history', metadata, index_name='ix_history_importable')
+    col = Column("importable", Boolean, index=True, default=False)
+    add_column(col, "history", metadata, index_name="ix_history_importable")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('importable', 'history', metadata)
+    drop_column("importable", "history", metadata)
     drop_table(HistoryUserShareAssociation_table)
diff --git a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
index 8cd1b5d40d1..f7b3fb91487 100644
--- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
+++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
@@ -21,91 +21,121 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import (
     JSONType,
-    TrimmedString
+    TrimmedString,
 )
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-FormDefinition_table = Table('form_definition', metadata,
-                             Column("id", Integer, primary_key=True),
-                             Column("create_time", DateTime, default=now),
-                             Column("update_time", DateTime, default=now, onupdate=now),
-                             Column("name", TrimmedString(255), nullable=False),
-                             Column("desc", TEXT),
-                             Column("form_definition_current_id", Integer, ForeignKey("form_definition_current.id", use_alter=True), index=True, nullable=False),
-                             Column("fields", JSONType))
+FormDefinition_table = Table(
+    "form_definition",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("desc", TEXT),
+    Column(
+        "form_definition_current_id",
+        Integer,
+        ForeignKey("form_definition_current.id", use_alter=True),
+        index=True,
+        nullable=False,
+    ),
+    Column("fields", JSONType),
+)
 
-FormDefinitionCurrent_table = Table('form_definition_current', metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("create_time", DateTime, default=now),
-                                    Column("update_time", DateTime, default=now, onupdate=now),
-                                    Column("latest_form_id", Integer, ForeignKey("form_definition.id"), index=True),
-                                    Column("deleted", Boolean, index=True, default=False))
+FormDefinitionCurrent_table = Table(
+    "form_definition_current",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("latest_form_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-FormValues_table = Table('form_values', metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, default=now, onupdate=now),
-                         Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
-                         Column("content", JSONType))
+FormValues_table = Table(
+    "form_values",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("content", JSONType),
+)
 
-RequestType_table = Table('request_type', metadata,
-                          Column("id", Integer, primary_key=True),
-                          Column("create_time", DateTime, default=now),
-                          Column("update_time", DateTime, default=now, onupdate=now),
-                          Column("name", TrimmedString(255), nullable=False),
-                          Column("desc", TEXT),
-                          Column("request_form_id", Integer, ForeignKey("form_definition.id"), index=True),
-                          Column("sample_form_id", Integer, ForeignKey("form_definition.id"), index=True))
+RequestType_table = Table(
+    "request_type",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("desc", TEXT),
+    Column("request_form_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("sample_form_id", Integer, ForeignKey("form_definition.id"), index=True),
+)
 
-Request_table = Table('request', metadata,
-                      Column("id", Integer, primary_key=True),
-                      Column("create_time", DateTime, default=now),
-                      Column("update_time", DateTime, default=now, onupdate=now),
-                      Column("name", TrimmedString(255), nullable=False),
-                      Column("desc", TEXT),
-                      Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
-                      Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
-                      Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                      Column("library_id", Integer, ForeignKey("library.id"), index=True),
-                      Column("deleted", Boolean, index=True, default=False))
+Request_table = Table(
+    "request",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("desc", TEXT),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+    Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("library_id", Integer, ForeignKey("library.id"), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-Sample_table = Table('sample', metadata,
-                     Column("id", Integer, primary_key=True),
-                     Column("create_time", DateTime, default=now),
-                     Column("update_time", DateTime, default=now, onupdate=now),
-                     Column("name", TrimmedString(255), nullable=False),
-                     Column("desc", TEXT),
-                     Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
-                     Column("request_id", Integer, ForeignKey("request.id"), index=True),
-                     Column("deleted", Boolean, index=True, default=False))
+Sample_table = Table(
+    "sample",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("desc", TEXT),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+    Column("request_id", Integer, ForeignKey("request.id"), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-SampleState_table = Table('sample_state', metadata,
-                          Column("id", Integer, primary_key=True),
-                          Column("create_time", DateTime, default=now),
-                          Column("update_time", DateTime, default=now, onupdate=now),
-                          Column("name", TrimmedString(255), nullable=False),
-                          Column("desc", TEXT),
-                          Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True))
+SampleState_table = Table(
+    "sample_state",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("desc", TEXT),
+    Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
+)
 
-SampleEvent_table = Table('sample_event', metadata,
-                          Column("id", Integer, primary_key=True),
-                          Column("create_time", DateTime, default=now),
-                          Column("update_time", DateTime, default=now, onupdate=now),
-                          Column("sample_id", Integer, ForeignKey("sample.id"), index=True),
-                          Column("sample_state_id", Integer, ForeignKey("sample_state.id"), index=True),
-                          Column("comment", TEXT))
+SampleEvent_table = Table(
+    "sample_event",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("sample_id", Integer, ForeignKey("sample.id"), index=True),
+    Column("sample_state_id", Integer, ForeignKey("sample_state.id"), index=True),
+    Column("comment", TEXT),
+)
 
 TABLES = [
     FormDefinition_table,
@@ -115,7 +145,7 @@ TABLES = [
     Request_table,
     Sample_table,
     SampleState_table,
-    SampleEvent_table
+    SampleEvent_table,
 ]
 
 
diff --git a/lib/galaxy/model/migrate/versions/0009_request_table.py b/lib/galaxy/model/migrate/versions/0009_request_table.py
index 08887102b37..2c26a82b27a 100644
--- a/lib/galaxy/model/migrate/versions/0009_request_table.py
+++ b/lib/galaxy/model/migrate/versions/0009_request_table.py
@@ -9,13 +9,13 @@ import logging
 from sqlalchemy import (
     Boolean,
     Column,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -27,18 +27,18 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    col = Column('submitted', Boolean, default=False)
-    add_column(col, 'request', metadata)
+    col = Column("submitted", Boolean, default=False)
+    add_column(col, "request", metadata)
 
     col = Column("bar_code", TrimmedString(255), index=True)
-    add_column(col, 'sample', metadata, index_name='ix_sample_bar_code')
+    add_column(col, "sample", metadata, index_name="ix_sample_bar_code")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('bar_code', 'sample', metadata)
+    drop_column("bar_code", "sample", metadata)
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('submitted', 'request', metadata)
+    if migrate_engine.name != "sqlite":
+        drop_column("submitted", "request", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
index 61956c9e8d4..8f3675a2e10 100644
--- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
+++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
@@ -18,7 +18,7 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -27,13 +27,16 @@ log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-HistoryDatasetAssociationDisplayAtAuthorization_table = Table("history_dataset_association_display_at_authorization", metadata,
-                                                              Column("id", Integer, primary_key=True),
-                                                              Column("create_time", DateTime, default=now),
-                                                              Column("update_time", DateTime, index=True, default=now, onupdate=now),
-                                                              Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-                                                              Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                              Column("site", TrimmedString(255)))
+HistoryDatasetAssociationDisplayAtAuthorization_table = Table(
+    "history_dataset_association_display_at_authorization",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, index=True, default=now, onupdate=now),
+    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("site", TrimmedString(255)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
index 56e5ecd2221..397c878a35f 100644
--- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
+++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
@@ -25,13 +25,23 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    if migrate_engine.name == 'mysql':
-        add_index('ix_hdadaa_history_dataset_association_id', 'history_dataset_association_display_at_authorization', 'history_dataset_association_id', metadata)
+    if migrate_engine.name == "mysql":
+        add_index(
+            "ix_hdadaa_history_dataset_association_id",
+            "history_dataset_association_display_at_authorization",
+            "history_dataset_association_id",
+            metadata,
+        )
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    if migrate_engine.name == 'mysql':
-        drop_index('ix_hdadaa_history_dataset_association_id', 'history_dataset_association_display_at_authorization', 'history_dataset_association_id', metadata)
+    if migrate_engine.name == "mysql":
+        drop_index(
+            "ix_hdadaa_history_dataset_association_id",
+            "history_dataset_association_display_at_authorization",
+            "history_dataset_association_id",
+            metadata,
+        )
diff --git a/lib/galaxy/model/migrate/versions/0012_user_address.py b/lib/galaxy/model/migrate/versions/0012_user_address.py
index 4f7e82cb3df..06bda287d47 100644
--- a/lib/galaxy/model/migrate/versions/0012_user_address.py
+++ b/lib/galaxy/model/migrate/versions/0012_user_address.py
@@ -16,36 +16,39 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-UserAddress_table = Table("user_address", metadata,
-                          Column("id", Integer, primary_key=True),
-                          Column("create_time", DateTime, default=now),
-                          Column("update_time", DateTime, default=now, onupdate=now),
-                          Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                          Column("desc", TEXT),
-                          Column("name", TrimmedString(255), nullable=False),
-                          Column("institution", TrimmedString(255)),
-                          Column("address", TrimmedString(255), nullable=False),
-                          Column("city", TrimmedString(255), nullable=False),
-                          Column("state", TrimmedString(255), nullable=False),
-                          Column("postal_code", TrimmedString(255), nullable=False),
-                          Column("country", TrimmedString(255), nullable=False),
-                          Column("phone", TrimmedString(255)),
-                          Column("deleted", Boolean, index=True, default=False),
-                          Column("purged", Boolean, index=True, default=False))
+UserAddress_table = Table(
+    "user_address",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("desc", TEXT),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("institution", TrimmedString(255)),
+    Column("address", TrimmedString(255), nullable=False),
+    Column("city", TrimmedString(255), nullable=False),
+    Column("state", TrimmedString(255), nullable=False),
+    Column("postal_code", TrimmedString(255), nullable=False),
+    Column("country", TrimmedString(255), nullable=False),
+    Column("phone", TrimmedString(255)),
+    Column("deleted", Boolean, index=True, default=False),
+    Column("purged", Boolean, index=True, default=False),
+)
 
 
 def upgrade(migrate_engine):
@@ -57,16 +60,16 @@ def upgrade(migrate_engine):
     create_table(UserAddress_table)
     # Add 1 column to the request_type table
     col = Column("deleted", Boolean, index=True, default=False)
-    add_column(col, 'request_type', metadata, index_name='ix_request_type_deleted')
+    add_column(col, "request_type", metadata, index_name="ix_request_type_deleted")
 
     # Delete the submitted column
     # This fails for sqlite, so skip the drop -- no conflicts in the future
     Request_table = Table("request", metadata, autoload=True)
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('submitted', Request_table)
+    if migrate_engine.name != "sqlite":
+        drop_column("submitted", Request_table)
     col = Column("state", TrimmedString(255), index=True)
-    add_column(col, Request_table, metadata, index_name='ix_request_state')
+    add_column(col, Request_table, metadata, index_name="ix_request_state")
 
 
 def downgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
index bbd6b273220..57b6440e573 100644
--- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
+++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
@@ -19,56 +19,71 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 OLD_TABLE_NAMES = [
-    'library_item_info_permissions',
-    'library_item_info_template_permissions',
-    'library_item_info_element',
-    'library_item_info_template_element',
-    'library_info_template_association',
-    'library_folder_info_template_association',
-    'library_dataset_info_template_association',
-    'library_dataset_dataset_info_template_association',
-    'library_info_association',
-    'library_folder_info_association',
-    'library_dataset_info_association',
-    'library_dataset_dataset_info_association',
-    'library_item_info',
-    'library_item_info_template',
+    "library_item_info_permissions",
+    "library_item_info_template_permissions",
+    "library_item_info_element",
+    "library_item_info_template_element",
+    "library_info_template_association",
+    "library_folder_info_template_association",
+    "library_dataset_info_template_association",
+    "library_dataset_dataset_info_template_association",
+    "library_info_association",
+    "library_folder_info_association",
+    "library_dataset_info_association",
+    "library_dataset_dataset_info_association",
+    "library_item_info",
+    "library_item_info_template",
 ]
 
-LibraryInfoAssociation_table = Table('library_info_association', metadata,
-                                     Column("id", Integer, primary_key=True),
-                                     Column("library_id", Integer, ForeignKey("library.id"), index=True),
-                                     Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
-                                     Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True))
+LibraryInfoAssociation_table = Table(
+    "library_info_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("library_id", Integer, ForeignKey("library.id"), index=True),
+    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+)
 
-LibraryFolderInfoAssociation_table = Table('library_folder_info_association', metadata,
-                                           Column("id", Integer, primary_key=True),
-                                           Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
-                                           Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
-                                           Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True))
+LibraryFolderInfoAssociation_table = Table(
+    "library_folder_info_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
+    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+)
 
-LibraryDatasetDatasetInfoAssociation_table = Table('library_dataset_dataset_info_association', metadata,
-                                                   Column("id", Integer, primary_key=True),
-                                                   Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True, index=True),
-                                                   Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
-                                                   Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True))
+LibraryDatasetDatasetInfoAssociation_table = Table(
+    "library_dataset_dataset_info_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        nullable=True,
+        index=True,
+    ),
+    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+)
 
 NEW_TABLES = [
     LibraryInfoAssociation_table,
     LibraryFolderInfoAssociation_table,
-    LibraryDatasetDatasetInfoAssociation_table
+    LibraryDatasetDatasetInfoAssociation_table,
 ]
 
 
diff --git a/lib/galaxy/model/migrate/versions/0014_pages.py b/lib/galaxy/model/migrate/versions/0014_pages.py
index a17c6a59f57..dd454ae228b 100644
--- a/lib/galaxy/model/migrate/versions/0014_pages.py
+++ b/lib/galaxy/model/migrate/versions/0014_pages.py
@@ -7,13 +7,23 @@ Migration script to add support for "Pages".
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Index, Integer, MetaData, String, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Index,
+    Integer,
+    MetaData,
+    String,
+    Table,
+    TEXT,
+)
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 now = datetime.datetime.utcnow
@@ -21,25 +31,33 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 Page_table = Table(
-    "page", metadata,
+    "page",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-    Column("latest_revision_id", Integer,
-        ForeignKey("page_revision.id", use_alter=True, name='page_latest_revision_id_fk'), index=True),
+    Column(
+        "latest_revision_id",
+        Integer,
+        ForeignKey("page_revision.id", use_alter=True, name="page_latest_revision_id_fk"),
+        index=True,
+    ),
     Column("title", TEXT),
     Column("slug", TEXT),
-    Index('ix_page_slug', 'slug', unique=True, mysql_length=200),
+    Index("ix_page_slug", "slug", unique=True, mysql_length=200),
 )
 
-PageRevision_table = Table("page_revision", metadata,
-                           Column("id", Integer, primary_key=True),
-                           Column("create_time", DateTime, default=now),
-                           Column("update_time", DateTime, default=now, onupdate=now),
-                           Column("page_id", Integer, ForeignKey("page.id"), index=True, nullable=False),
-                           Column("title", TEXT),
-                           Column("content", TEXT))
+PageRevision_table = Table(
+    "page_revision",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("page_id", Integer, ForeignKey("page.id"), index=True, nullable=False),
+    Column("title", TEXT),
+    Column("content", TEXT),
+)
 
 
 def upgrade(migrate_engine):
@@ -50,14 +68,14 @@ def upgrade(migrate_engine):
     create_table(Page_table)
     create_table(PageRevision_table)
 
-    col = Column('username', String(255), index=True, unique=True, default=False)
-    add_column(col, 'galaxy_user', metadata, index_name='ix_galaxy_user_username', unique_name='username')
+    col = Column("username", String(255), index=True, unique=True, default=False)
+    add_column(col, "galaxy_user", metadata, index_name="ix_galaxy_user_username", unique_name="username")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('username', 'galaxy_user', metadata)
+    drop_column("username", "galaxy_user", metadata)
     drop_table(PageRevision_table)
     drop_table(Page_table)
diff --git a/lib/galaxy/model/migrate/versions/0015_tagging.py b/lib/galaxy/model/migrate/versions/0015_tagging.py
index ae53a72ac26..835635bea03 100644
--- a/lib/galaxy/model/migrate/versions/0015_tagging.py
+++ b/lib/galaxy/model/migrate/versions/0015_tagging.py
@@ -6,42 +6,63 @@ datasets, and history-dataset associations (user views of datasets).
 import logging
 
 from migrate import UniqueConstraint
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # New tables to support tagging of histories, datasets, and history-dataset associations.
-Tag_table = Table("tag", metadata,
-                  Column("id", Integer, primary_key=True),
-                  Column("type", Integer),
-                  Column("parent_id", Integer, ForeignKey("tag.id")),
-                  Column("name", TrimmedString(255)),
-                  UniqueConstraint("name"))
+Tag_table = Table(
+    "tag",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("type", Integer),
+    Column("parent_id", Integer, ForeignKey("tag.id")),
+    Column("name", TrimmedString(255)),
+    UniqueConstraint("name"),
+)
 
-HistoryTagAssociation_table = Table("history_tag_association", metadata,
-                                    Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                    Column("user_tname", TrimmedString(255), index=True),
-                                    Column("value", TrimmedString(255), index=True),
-                                    Column("user_value", TrimmedString(255), index=True))
+HistoryTagAssociation_table = Table(
+    "history_tag_association",
+    metadata,
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
-DatasetTagAssociation_table = Table("dataset_tag_association", metadata,
-                                    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-                                    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                    Column("user_tname", TrimmedString(255), index=True),
-                                    Column("value", TrimmedString(255), index=True),
-                                    Column("user_value", TrimmedString(255), index=True))
+DatasetTagAssociation_table = Table(
+    "dataset_tag_association",
+    metadata,
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
-HistoryDatasetAssociationTagAssociation_table = Table("history_dataset_association_tag_association", metadata,
-                                                      Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-                                                      Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                                      Column("user_tname", TrimmedString(255), index=True),
-                                                      Column("value", TrimmedString(255), index=True),
-                                                      Column("user_value", TrimmedString(255), index=True))
+HistoryDatasetAssociationTagAssociation_table = Table(
+    "history_dataset_association_tag_association",
+    metadata,
+    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py b/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
index 929b290269f..ff5b0cfc9b8 100644
--- a/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
+++ b/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
@@ -10,12 +10,12 @@ import logging
 
 from sqlalchemy import (
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
@@ -27,13 +27,27 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    HistoryDatasetAssociationTagAssociation_table = Table('history_dataset_association_tag_association', metadata, autoload=True)
-    if not any([_.name for _ in index.columns] == ['history_dataset_association_id'] for index in HistoryDatasetAssociationTagAssociation_table.indexes):
-        add_index('ix_hda_ta_history_dataset_association_id', HistoryDatasetAssociationTagAssociation_table, 'history_dataset_association_id')
+    HistoryDatasetAssociationTagAssociation_table = Table(
+        "history_dataset_association_tag_association", metadata, autoload=True
+    )
+    if not any(
+        [_.name for _ in index.columns] == ["history_dataset_association_id"]
+        for index in HistoryDatasetAssociationTagAssociation_table.indexes
+    ):
+        add_index(
+            "ix_hda_ta_history_dataset_association_id",
+            HistoryDatasetAssociationTagAssociation_table,
+            "history_dataset_association_id",
+        )
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_index('ix_hda_ta_history_dataset_association_id', 'history_dataset_association_tag_association', 'history_dataset_association_id', metadata)
+    drop_index(
+        "ix_hda_ta_history_dataset_association_id",
+        "history_dataset_association_tag_association",
+        "history_dataset_association_id",
+        metadata,
+    )
diff --git a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
index d6bf805d351..7a29439fd97 100644
--- a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
+++ b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
@@ -9,7 +9,7 @@ from sqlalchemy import MetaData
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
@@ -21,15 +21,15 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    add_index('ix_library_folder_name', 'library_folder', 'name', metadata)
-    add_index('ix_library_dataset_dataset_association_name', 'library_dataset_dataset_association', 'name', metadata)
-    add_index('ix_library_dataset_name', 'library_dataset', 'name', metadata)
+    add_index("ix_library_folder_name", "library_folder", "name", metadata)
+    add_index("ix_library_dataset_dataset_association_name", "library_dataset_dataset_association", "name", metadata)
+    add_index("ix_library_dataset_name", "library_dataset", "name", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_index('ix_library_dataset_name', 'library_dataset', 'name', metadata)
-    drop_index('ix_library_dataset_dataset_association_name', 'library_dataset_dataset_association', 'name', metadata)
-    drop_index('ix_library_folder_name', 'library_folder', 'name', metadata)
+    drop_index("ix_library_dataset_name", "library_dataset", "name", metadata)
+    drop_index("ix_library_dataset_dataset_association_name", "library_dataset_dataset_association", "name", metadata)
+    drop_index("ix_library_folder_name", "library_folder", "name", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
index 2b5b8faa3b6..f64c84ff1b0 100644
--- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
+++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
@@ -5,7 +5,14 @@ This migration script provides support for (a) ordering tags by recency and
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Index, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Index,
+    Integer,
+    MetaData,
+    Table,
+)
 from sqlalchemy.exc import OperationalError
 
 # Need our custom types, but don't import anything else from model
@@ -14,37 +21,49 @@ from galaxy.model.custom_types import TrimmedString
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-HistoryTagAssociation_table = Table("history_tag_association", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                    Column("user_tname", TrimmedString(255), index=True),
-                                    Column("value", TrimmedString(255), index=True),
-                                    Column("user_value", TrimmedString(255), index=True))
+HistoryTagAssociation_table = Table(
+    "history_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
-DatasetTagAssociation_table = Table("dataset_tag_association", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-                                    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                    Column("user_tname", TrimmedString(255), index=True),
-                                    Column("value", TrimmedString(255), index=True),
-                                    Column("user_value", TrimmedString(255), index=True))
+DatasetTagAssociation_table = Table(
+    "dataset_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
-HistoryDatasetAssociationTagAssociation_table = Table("history_dataset_association_tag_association", metadata,
-                                                      Column("id", Integer, primary_key=True),
-                                                      Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-                                                      Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                                      Column("user_tname", TrimmedString(255), index=True),
-                                                      Column("value", TrimmedString(255), index=True),
-                                                      Column("user_value", TrimmedString(255), index=True))
+HistoryDatasetAssociationTagAssociation_table = Table(
+    "history_dataset_association_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
-PageTagAssociation_table = Table("page_tag_association", metadata,
-                                 Column("id", Integer, primary_key=True),
-                                 Column("page_id", Integer, ForeignKey("page.id"), index=True),
-                                 Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                 Column("user_tname", TrimmedString(255), index=True),
-                                 Column("value", TrimmedString(255), index=True),
-                                 Column("user_value", TrimmedString(255), index=True))
+PageTagAssociation_table = Table(
+    "page_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("page_id", Integer, ForeignKey("page.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
 
 def upgrade(migrate_engine):
@@ -75,11 +94,16 @@ def upgrade(migrate_engine):
         # in MySQL.
         if str(e).find("CREATE INDEX") != -1:
             # Manually create index.
-            i = Index("ix_hda_ta_history_dataset_association_id", HistoryDatasetAssociationTagAssociation_table.c.history_dataset_association_id)
+            i = Index(
+                "ix_hda_ta_history_dataset_association_id",
+                HistoryDatasetAssociationTagAssociation_table.c.history_dataset_association_id,
+            )
             try:
                 i.create()
             except Exception:
-                log.exception("Adding index 'ix_hda_ta_history_dataset_association_id' to table 'history_dataset_association_tag_association' table failed.")
+                log.exception(
+                    "Adding index 'ix_hda_ta_history_dataset_association_id' to table 'history_dataset_association_tag_association' table failed."
+                )
     except Exception:
         log.exception("Recreating history_dataset_association_tag_association table failed.")
 
diff --git a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py
index 17cfff7b1b1..98937561d62 100644
--- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py
+++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py
@@ -11,16 +11,14 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import (
     JSONType,
-    TrimmedString
-)
-from galaxy.model.migrate.versions.util import (
-    add_column,
+    TrimmedString,
 )
+from galaxy.model.migrate.versions.util import add_column
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -32,12 +30,12 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     # Create the folder_id column
-    col = Column("folder_id", Integer, ForeignKey('library_folder.id'), index=True)
-    add_column(col, 'request', metadata, index_name='ix_request_folder_id')
+    col = Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True)
+    add_column(col, "request", metadata, index_name="ix_request_folder_id")
     # Create the type column in form_definition
     FormDefinition_table = Table("form_definition", metadata, autoload=True)
     col = Column("type", TrimmedString(255), index=True)
-    add_column(col, FormDefinition_table, metadata, index_name='ix_form_definition_type')
+    add_column(col, FormDefinition_table, metadata, index_name="ix_form_definition_type")
     col = Column("layout", JSONType)
     add_column(col, FormDefinition_table, metadata)
 
diff --git a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py
index 53a4f6e8c7a..340c3f60245 100644
--- a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py
+++ b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py
@@ -14,7 +14,7 @@ from sqlalchemy import (
     Integer,
     MetaData,
     String,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
@@ -23,17 +23,20 @@ from galaxy.model.migrate.versions.util import (
     create_table,
     drop_column,
     drop_index,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-JobToOutputLibraryDataset_table = Table("job_to_output_library_dataset", metadata,
+JobToOutputLibraryDataset_table = Table(
+    "job_to_output_library_dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True),
-    Column("name", String(255)))
+    Column("name", String(255)),
+)
 
 
 def upgrade(migrate_engine):
@@ -45,11 +48,13 @@ def upgrade(migrate_engine):
     create_table(JobToOutputLibraryDataset_table)
 
     # Create the library_folder_id column
-    col = Column("library_folder_id", Integer, ForeignKey('library_folder.id', name='job_library_folder_id_fk'), index=True)
-    add_column(col, 'job', metadata, index_name='ix_job_library_folder_id')
+    col = Column(
+        "library_folder_id", Integer, ForeignKey("library_folder.id", name="job_library_folder_id_fk"), index=True
+    )
+    add_column(col, "job", metadata, index_name="ix_job_library_folder_id")
 
     # Create the ix_dataset_state index
-    add_index('ix_dataset_state', 'dataset', 'state', metadata)
+    add_index("ix_dataset_state", "dataset", "state", metadata)
 
 
 def downgrade(migrate_engine):
@@ -57,10 +62,10 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     # Drop the ix_dataset_state index
-    drop_index('ix_dataset_state', 'dataset', 'state', metadata)
+    drop_index("ix_dataset_state", "dataset", "state", metadata)
 
     # Drop the library_folder_id column
-    drop_column('library_folder_id', 'job', metadata)
+    drop_column("library_folder_id", "job", metadata)
 
     # Drop the job_to_output_library_dataset table
     drop_table(JobToOutputLibraryDataset_table)
diff --git a/lib/galaxy/model/migrate/versions/0021_user_prefs.py b/lib/galaxy/model/migrate/versions/0021_user_prefs.py
index 4c7879bd0c2..02b52b2d53f 100644
--- a/lib/galaxy/model/migrate/versions/0021_user_prefs.py
+++ b/lib/galaxy/model/migrate/versions/0021_user_prefs.py
@@ -4,19 +4,32 @@ This migration script adds a user preferences table to Galaxy.
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table, Unicode
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    Unicode,
+)
 
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # New table to support user preferences.
-UserPreference_table = Table("user_preference", metadata,
-                             Column("id", Integer, primary_key=True),
-                             Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                             Column("name", Unicode(255), index=True),
-                             Column("value", Unicode(1024)))
+UserPreference_table = Table(
+    "user_preference",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("name", Unicode(255), index=True),
+    Column("value", Unicode(1024)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0022_visualization_tables.py b/lib/galaxy/model/migrate/versions/0022_visualization_tables.py
index 65c38e351df..03b06635e6c 100644
--- a/lib/galaxy/model/migrate/versions/0022_visualization_tables.py
+++ b/lib/galaxy/model/migrate/versions/0022_visualization_tables.py
@@ -6,29 +6,47 @@ Migration script to add support for storing visualizations.
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-Visualization_table = Table("visualization", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("latest_revision_id", Integer,
-                                   ForeignKey("visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk'), index=True),
-                            Column("title", TEXT),
-                            Column("type", TEXT))
+Visualization_table = Table(
+    "visualization",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column(
+        "latest_revision_id",
+        Integer,
+        ForeignKey("visualization_revision.id", use_alter=True, name="visualization_latest_revision_id_fk"),
+        index=True,
+    ),
+    Column("title", TEXT),
+    Column("type", TEXT),
+)
 
-VisualizationRevision_table = Table("visualization_revision", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("create_time", DateTime, default=now),
-                                    Column("update_time", DateTime, default=now, onupdate=now),
-                                    Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True, nullable=False),
-                                    Column("title", TEXT),
-                                    Column("config", TEXT))
+VisualizationRevision_table = Table(
+    "visualization_revision",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True, nullable=False),
+    Column("title", TEXT),
+    Column("config", TEXT),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py b/lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
index 7c03ba926eb..c2c09605e2d 100644
--- a/lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
+++ b/lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
@@ -5,7 +5,12 @@ publicly accessible.
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -20,11 +25,11 @@ def upgrade(migrate_engine):
     Page_table = Table("page", metadata, autoload=True)
 
     c = Column("published", Boolean, index=True, default=False)
-    c.create(Page_table, index_name='ix_page_published')
+    c.create(Page_table, index_name="ix_page_published")
     assert c is Page_table.c.published
 
     c = Column("deleted", Boolean, index=True, default=False)
-    c.create(Page_table, index_name='ix_page_deleted')
+    c.create(Page_table, index_name="ix_page_deleted")
     assert c is Page_table.c.deleted
 
 
diff --git a/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py b/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
index 50df7b5e889..c69d563444e 100644
--- a/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
+++ b/lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
@@ -7,12 +7,12 @@ import logging
 
 from sqlalchemy import (
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
@@ -27,9 +27,9 @@ def upgrade(migrate_engine):
     Page_table = Table("page", metadata, autoload=True)
     try:
         # Sqlite doesn't support .alter, so we need to drop an recreate
-        drop_index("ix_page_slug", Page_table, 'slug')
+        drop_index("ix_page_slug", Page_table, "slug")
 
-        add_index("ix_page_slug", Page_table, 'slug', unique=False)
+        add_index("ix_page_slug", Page_table, "slug", unique=False)
     except Exception:
         # Mysql doesn't have a named index, but alter should work
         Page_table.c.slug.alter(unique=False)
diff --git a/lib/galaxy/model/migrate/versions/0025_user_info.py b/lib/galaxy/model/migrate/versions/0025_user_info.py
index e5b4a1fa777..72c537cc9cd 100644
--- a/lib/galaxy/model/migrate/versions/0025_user_info.py
+++ b/lib/galaxy/model/migrate/versions/0025_user_info.py
@@ -8,12 +8,12 @@ from sqlalchemy import (
     Column,
     ForeignKey,
     Integer,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -25,12 +25,12 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    col = Column("form_values_id", Integer, ForeignKey('form_values.id', name='user_form_values_id_fk'), index=True)
-    add_column(col, 'galaxy_user', metadata, index_name='ix_galaxy_user_form_values_id')
+    col = Column("form_values_id", Integer, ForeignKey("form_values.id", name="user_form_values_id_fk"), index=True)
+    add_column(col, "galaxy_user", metadata, index_name="ix_galaxy_user_form_values_id")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('form_values_id', 'galaxy_user', metadata)
+    drop_column("form_values_id", "galaxy_user", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py
index 615c3cbb901..ee9440bf887 100644
--- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py
+++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py
@@ -5,122 +5,155 @@ This script adds tables needed for Galaxy cloud functionality.
 import datetime
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-CloudImage_table = Table("cloud_image", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, default=now, onupdate=now),
-                         Column("provider_type", TEXT),
-                         Column("image_id", TEXT, nullable=False),
-                         Column("manifest", TEXT),
-                         Column("state", TEXT),
-                         Column("architecture", TEXT),
-                         Column("deleted", Boolean, default=False))
+CloudImage_table = Table(
+    "cloud_image",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("provider_type", TEXT),
+    Column("image_id", TEXT, nullable=False),
+    Column("manifest", TEXT),
+    Column("state", TEXT),
+    Column("architecture", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
 """ UserConfiguredInstance (UCI) table """
-UCI_table = Table("cloud_uci", metadata,
-                  Column("id", Integer, primary_key=True),
-                  Column("create_time", DateTime, default=now),
-                  Column("update_time", DateTime, default=now, onupdate=now),
-                  Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                  Column("credentials_id", Integer, ForeignKey("cloud_user_credentials.id"), index=True),
-                  Column("key_pair_name", TEXT),
-                  Column("key_pair_material", TEXT),
-                  Column("name", TEXT),
-                  Column("state", TEXT),
-                  Column("error", TEXT),
-                  Column("total_size", Integer),
-                  Column("launch_time", DateTime),
-                  Column("deleted", Boolean, default=False))
+UCI_table = Table(
+    "cloud_uci",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("credentials_id", Integer, ForeignKey("cloud_user_credentials.id"), index=True),
+    Column("key_pair_name", TEXT),
+    Column("key_pair_material", TEXT),
+    Column("name", TEXT),
+    Column("state", TEXT),
+    Column("error", TEXT),
+    Column("total_size", Integer),
+    Column("launch_time", DateTime),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudInstance_table = Table("cloud_instance", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("launch_time", DateTime),
-                            Column("stop_time", DateTime),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
-                            Column("type", TEXT),
-                            Column("reservation_id", TEXT),
-                            Column("instance_id", TEXT),
-                            Column("mi_id", Integer, ForeignKey("cloud_image.id"), index=True),
-                            Column("state", TEXT),
-                            Column("error", TEXT),
-                            Column("public_dns", TEXT),
-                            Column("private_dns", TEXT),
-                            Column("security_group", TEXT),
-                            Column("availability_zone", TEXT))
+CloudInstance_table = Table(
+    "cloud_instance",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("launch_time", DateTime),
+    Column("stop_time", DateTime),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
+    Column("type", TEXT),
+    Column("reservation_id", TEXT),
+    Column("instance_id", TEXT),
+    Column("mi_id", Integer, ForeignKey("cloud_image.id"), index=True),
+    Column("state", TEXT),
+    Column("error", TEXT),
+    Column("public_dns", TEXT),
+    Column("private_dns", TEXT),
+    Column("security_group", TEXT),
+    Column("availability_zone", TEXT),
+)
 
-CloudStore_table = Table("cloud_store", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, default=now, onupdate=now),
-                         Column("attach_time", DateTime),
-                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                         Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True, nullable=False),
-                         Column("volume_id", TEXT),
-                         Column("size", Integer, nullable=False),
-                         Column("availability_zone", TEXT),
-                         Column("inst_id", Integer, ForeignKey("cloud_instance.id")),
-                         Column("status", TEXT),
-                         Column("device", TEXT),
-                         Column("space_consumed", Integer),
-                         Column("error", TEXT),
-                         Column("deleted", Boolean, default=False))
+CloudStore_table = Table(
+    "cloud_store",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("attach_time", DateTime),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True, nullable=False),
+    Column("volume_id", TEXT),
+    Column("size", Integer, nullable=False),
+    Column("availability_zone", TEXT),
+    Column("inst_id", Integer, ForeignKey("cloud_instance.id")),
+    Column("status", TEXT),
+    Column("device", TEXT),
+    Column("space_consumed", Integer),
+    Column("error", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudSnapshot_table = Table("cloud_snapshot", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
-                            Column("store_id", Integer, ForeignKey("cloud_store.id"), index=True, nullable=False),
-                            Column("snapshot_id", TEXT),
-                            Column("status", TEXT),
-                            Column("description", TEXT),
-                            Column("error", TEXT),
-                            Column("deleted", Boolean, default=False))
+CloudSnapshot_table = Table(
+    "cloud_snapshot",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
+    Column("store_id", Integer, ForeignKey("cloud_store.id"), index=True, nullable=False),
+    Column("snapshot_id", TEXT),
+    Column("status", TEXT),
+    Column("description", TEXT),
+    Column("error", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudUserCredentials_table = Table("cloud_user_credentials", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("create_time", DateTime, default=now),
-                                   Column("update_time", DateTime, default=now, onupdate=now),
-                                   Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                                   Column("provider_id", Integer, ForeignKey("cloud_provider.id"), index=True, nullable=False),
-                                   Column("name", TEXT),
-                                   Column("access_key", TEXT),
-                                   Column("secret_key", TEXT),
-                                   Column("deleted", Boolean, default=False))
+CloudUserCredentials_table = Table(
+    "cloud_user_credentials",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("provider_id", Integer, ForeignKey("cloud_provider.id"), index=True, nullable=False),
+    Column("name", TEXT),
+    Column("access_key", TEXT),
+    Column("secret_key", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudProvider_table = Table("cloud_provider", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("type", TEXT, nullable=False),
-                            Column("name", TEXT),
-                            Column("region_connection", TEXT),
-                            Column("region_name", TEXT),
-                            Column("region_endpoint", TEXT),
-                            Column("is_secure", Boolean),
-                            Column("host", TEXT),
-                            Column("port", Integer),
-                            Column("proxy", TEXT),
-                            Column("proxy_port", TEXT),
-                            Column("proxy_user", TEXT),
-                            Column("proxy_pass", TEXT),
-                            Column("debug", Integer),
-                            Column("https_connection_factory", TEXT),
-                            Column("path", TEXT),
-                            Column("deleted", Boolean, default=False))
+CloudProvider_table = Table(
+    "cloud_provider",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("type", TEXT, nullable=False),
+    Column("name", TEXT),
+    Column("region_connection", TEXT),
+    Column("region_name", TEXT),
+    Column("region_endpoint", TEXT),
+    Column("is_secure", Boolean),
+    Column("host", TEXT),
+    Column("port", Integer),
+    Column("proxy", TEXT),
+    Column("proxy_port", TEXT),
+    Column("proxy_user", TEXT),
+    Column("proxy_pass", TEXT),
+    Column("debug", Integer),
+    Column("https_connection_factory", TEXT),
+    Column("path", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0027_request_events.py b/lib/galaxy/model/migrate/versions/0027_request_events.py
index 538bdc2bb81..4cb033b64e5 100644
--- a/lib/galaxy/model/migrate/versions/0027_request_events.py
+++ b/lib/galaxy/model/migrate/versions/0027_request_events.py
@@ -13,7 +13,7 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -21,20 +21,23 @@ from galaxy.model.migrate.versions.util import (
     create_table,
     drop_column,
     localtimestamp,
-    nextval
+    nextval,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-RequestEvent_table = Table('request_event', metadata,
+RequestEvent_table = Table(
+    "request_event",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("request_id", Integer, ForeignKey("request.id"), index=True),
     Column("state", TrimmedString(255), index=True),
-    Column("comment", TEXT))
+    Column("comment", TEXT),
+)
 
 
 def upgrade(migrate_engine):
@@ -44,19 +47,25 @@ def upgrade(migrate_engine):
 
     create_table(RequestEvent_table)
     # move the current state of all existing requests to the request_event table
-    cmd = \
-        "INSERT INTO request_event " + \
-        "SELECT %s AS id," + \
-        "%s AS create_time," + \
-        "%s AS update_time," + \
-        "request.id AS request_id," + \
-        "request.state AS state," + \
-        "'%s' AS comment " + \
-        "FROM request;"
-    cmd = cmd % (nextval(migrate_engine, 'request_event'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), 'Imported from request table')
+    cmd = (
+        "INSERT INTO request_event "
+        + "SELECT %s AS id,"
+        + "%s AS create_time,"
+        + "%s AS update_time,"
+        + "request.id AS request_id,"
+        + "request.state AS state,"
+        + "'%s' AS comment "
+        + "FROM request;"
+    )
+    cmd = cmd % (
+        nextval(migrate_engine, "request_event"),
+        localtimestamp(migrate_engine),
+        localtimestamp(migrate_engine),
+        "Imported from request table",
+    )
     migrate_engine.execute(cmd)
 
-    drop_column('state', 'request', metadata)
+    drop_column("state", "request", metadata)
 
 
 def downgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py b/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
index 23c2c5295ad..db6fcd0c702 100644
--- a/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
+++ b/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
@@ -14,7 +14,7 @@ from sqlalchemy import (
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -27,11 +27,11 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     col = Column("filename_override_metadata", String(255))
-    add_column(col, 'job_external_output_metadata', metadata)
+    add_column(col, "job_external_output_metadata", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('filename_override_metadata', 'job_external_output_metadata', metadata)
+    drop_column("filename_override_metadata", "job_external_output_metadata", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0029_user_actions.py b/lib/galaxy/model/migrate/versions/0029_user_actions.py
index e0701b936a8..4848fbd41a6 100644
--- a/lib/galaxy/model/migrate/versions/0029_user_actions.py
+++ b/lib/galaxy/model/migrate/versions/0029_user_actions.py
@@ -5,21 +5,32 @@ This migration script adds a user actions table to Galaxy.
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, Unicode
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    Unicode,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # New table to store user actions.
-UserAction_table = Table("user_action", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                         Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
-                         Column("action", Unicode(255)),
-                         Column("context", Unicode(512)),
-                         Column("params", Unicode(1024)))
+UserAction_table = Table(
+    "user_action",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
+    Column("action", Unicode(255)),
+    Column("context", Unicode(512)),
+    Column("params", Unicode(1024)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0030_history_slug_column.py b/lib/galaxy/model/migrate/versions/0030_history_slug_column.py
index 06b454f8dd8..09df4baeef9 100644
--- a/lib/galaxy/model/migrate/versions/0030_history_slug_column.py
+++ b/lib/galaxy/model/migrate/versions/0030_history_slug_column.py
@@ -8,13 +8,13 @@ from sqlalchemy import (
     Column,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     add_index,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -31,11 +31,11 @@ def upgrade(migrate_engine):
     add_column(c, History_table, metadata)
     # Index needs to be added separately because MySQL cannot index a TEXT/BLOB
     # column without specifying mysql_length
-    add_index('ix_history_slug', History_table, 'slug')
+    add_index("ix_history_slug", History_table, "slug")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('slug', 'history', metadata)
+    drop_column("slug", "history", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py b/lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
index 0ed87155282..03ed15d4348 100644
--- a/lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
+++ b/lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
@@ -11,36 +11,42 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-StoredWorkflowTagAssociation_table = Table("stored_workflow_tag_association", metadata,
-                                           Column("id", Integer, primary_key=True),
-                                           Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
-                                           Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                           Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                           Column("user_tname", Unicode(255), index=True),
-                                           Column("value", Unicode(255), index=True),
-                                           Column("user_value", Unicode(255), index=True))
+StoredWorkflowTagAssociation_table = Table(
+    "stored_workflow_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", Unicode(255), index=True),
+    Column("value", Unicode(255), index=True),
+    Column("user_value", Unicode(255), index=True),
+)
 
-WorkflowTagAssociation_table = Table("workflow_tag_association", metadata,
-                                     Column("id", Integer, primary_key=True),
-                                     Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True),
-                                     Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                     Column("user_tname", Unicode(255), index=True),
-                                     Column("value", Unicode(255), index=True),
-                                     Column("user_value", Unicode(255), index=True))
+WorkflowTagAssociation_table = Table(
+    "workflow_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", Unicode(255), index=True),
+    Column("value", Unicode(255), index=True),
+    Column("user_value", Unicode(255), index=True),
+)
 
 
 def upgrade(migrate_engine):
@@ -50,27 +56,35 @@ def upgrade(migrate_engine):
 
     # Create user_id column in history_tag_association table.
     c = Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True)
-    add_column(c, 'history_tag_association', metadata, index_name='ix_history_tag_association_user_id')
+    add_column(c, "history_tag_association", metadata, index_name="ix_history_tag_association_user_id")
 
     # Populate column so that user_id is the id of the user who owns the history (and, up to now, was the only person able to tag the history).
     migrate_engine.execute(
-        "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )")
+        "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )"
+    )
 
     # Create user_id column in history_dataset_association_tag_association table.
     c = Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True)
-    add_column(c, 'history_dataset_association_tag_association', metadata, index_name='ix_history_dataset_association_tag_association_user_id')
+    add_column(
+        c,
+        "history_dataset_association_tag_association",
+        metadata,
+        index_name="ix_history_dataset_association_tag_association_user_id",
+    )
 
     # Populate column so that user_id is the id of the user who owns the history_dataset_association (and, up to now, was the only person able to tag the page).
     migrate_engine.execute(
-        "UPDATE history_dataset_association_tag_association SET user_id=( SELECT history.user_id FROM history, history_dataset_association WHERE history_dataset_association.history_id = history.id AND history_dataset_association.id = history_dataset_association_tag_association.history_dataset_association_id)")
+        "UPDATE history_dataset_association_tag_association SET user_id=( SELECT history.user_id FROM history, history_dataset_association WHERE history_dataset_association.history_id = history.id AND history_dataset_association.id = history_dataset_association_tag_association.history_dataset_association_id)"
+    )
 
     # Create user_id column in page_tag_association table.
     c = Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True)
-    add_column(c, 'page_tag_association', metadata, index_name='ix_page_tag_association_user_id')
+    add_column(c, "page_tag_association", metadata, index_name="ix_page_tag_association_user_id")
 
     # Populate column so that user_id is the id of the user who owns the page (and, up to now, was the only person able to tag the page).
     migrate_engine.execute(
-        "UPDATE page_tag_association SET user_id=( SELECT user_id FROM page WHERE page_tag_association.page_id = page.id )")
+        "UPDATE page_tag_association SET user_id=( SELECT user_id FROM page WHERE page_tag_association.page_id = page.id )"
+    )
 
     # Create stored_workflow_tag_association table.
     create_table(StoredWorkflowTagAssociation_table)
@@ -90,10 +104,10 @@ def downgrade(migrate_engine):
     drop_table(StoredWorkflowTagAssociation_table)
 
     # Drop user_id column from page_tag_association table.
-    drop_column('user_id', 'page_tag_association', metadata)
+    drop_column("user_id", "page_tag_association", metadata)
 
     # Drop user_id column from history_dataset_association_tag_association table.
-    drop_column('user_id', 'history_dataset_association_tag_association', metadata)
+    drop_column("user_id", "history_dataset_association_tag_association", metadata)
 
     # Drop user_id column from history_tag_association table.
-    drop_column('user_id', 'history_tag_association', metadata)
+    drop_column("user_id", "history_tag_association", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py b/lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
index eed3b2a9f11..579bd9bbf48 100644
--- a/lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
+++ b/lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
@@ -8,13 +8,13 @@ from sqlalchemy import (
     Column,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     add_index,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -31,11 +31,11 @@ def upgrade(migrate_engine):
     add_column(c, StoredWorkflow_table, metadata)
     # Index needs to be added separately because MySQL cannot index a TEXT/BLOB
     # column without specifying mysql_length
-    add_index('ix_stored_workflow_slug', StoredWorkflow_table, 'slug')
+    add_index("ix_stored_workflow_slug", StoredWorkflow_table, "slug")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('slug', 'stored_workflow', metadata)
+    drop_column("slug", "stored_workflow", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py b/lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
index a1bfc60a430..3e965229466 100644
--- a/lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
+++ b/lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
@@ -5,9 +5,18 @@ workflows, and pages. Script adds published column to histories and workflows an
 
 import logging
 
-from sqlalchemy import Boolean, Column, Index, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    Index,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -21,8 +30,8 @@ def upgrade(migrate_engine):
     # Create published column in history table.
     History_table = Table("history", metadata, autoload=True)
     c = Column("published", Boolean, index=True)
-    add_column(c, History_table, metadata, index_name='ix_history_published')
-    if migrate_engine.name != 'sqlite':
+    add_column(c, History_table, metadata, index_name="ix_history_published")
+    if migrate_engine.name != "sqlite":
         # Create index for published column in history table.
         try:
             i = Index("ix_history_published", History_table.c.published)
@@ -34,8 +43,8 @@ def upgrade(migrate_engine):
     # Create published column in stored workflows table.
     StoredWorkflow_table = Table("stored_workflow", metadata, autoload=True)
     c = Column("published", Boolean, index=True)
-    add_column(c, StoredWorkflow_table, metadata, index_name='ix_stored_workflow_published')
-    if migrate_engine.name != 'sqlite':
+    add_column(c, StoredWorkflow_table, metadata, index_name="ix_stored_workflow_published")
+    if migrate_engine.name != "sqlite":
         # Create index for published column in stored workflows table.
         try:
             i = Index("ix_stored_workflow_published", StoredWorkflow_table.c.published)
@@ -47,8 +56,8 @@ def upgrade(migrate_engine):
     # Create importable column in page table.
     Page_table = Table("page", metadata, autoload=True)
     c = Column("importable", Boolean, index=True)
-    add_column(c, Page_table, metadata, index_name='ix_page_importable')
-    if migrate_engine.name != 'sqlite':
+    add_column(c, Page_table, metadata, index_name="ix_page_importable")
+    if migrate_engine.name != "sqlite":
         # Create index for importable column in page table.
         try:
             i = Index("ix_page_importable", Page_table.c.importable)
@@ -62,6 +71,6 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('published', 'history', metadata)
-    drop_column('published', 'stored_workflow', metadata)
-    drop_column('importable', 'page', metadata)
+    drop_column("published", "history", metadata)
+    drop_column("published", "stored_workflow", metadata)
+    drop_column("importable", "page", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0034_page_user_share_association.py b/lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
index 75f7988fa72..fa8b3fb3c07 100644
--- a/lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
+++ b/lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
@@ -4,15 +4,24 @@ Migration script to create a table for page-user share association.
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-PageUserShareAssociation_table = Table("page_user_share_association", metadata,
-                                       Column("id", Integer, primary_key=True),
-                                       Column("page_id", Integer, ForeignKey("page.id"), index=True),
-                                       Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+PageUserShareAssociation_table = Table(
+    "page_user_share_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("page_id", Integer, ForeignKey("page.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py b/lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
index c60a19749a2..35b6fe37214 100644
--- a/lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
+++ b/lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
@@ -12,12 +12,12 @@ from sqlalchemy import (
     MetaData,
     Table,
     TEXT,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -26,59 +26,65 @@ metadata = MetaData()
 # Annotation tables.
 
 HistoryAnnotationAssociation_table = Table(
-    "history_annotation_association", metadata,
+    "history_annotation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("history_id", Integer, ForeignKey("history.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("annotation", TEXT),
-    Index("ix_history_anno_assoc_annotation", 'annotation', mysql_length=200),
+    Index("ix_history_anno_assoc_annotation", "annotation", mysql_length=200),
 )
 
 HistoryDatasetAssociationAnnotationAssociation_table = Table(
-    "history_dataset_association_annotation_association", metadata,
+    "history_dataset_association_annotation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("history_dataset_association_id", Integer,
-        ForeignKey("history_dataset_association.id"), index=True),
+    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("annotation", TEXT),
-    Index("ix_history_dataset_anno_assoc_annotation", 'annotation', mysql_length=200),
+    Index("ix_history_dataset_anno_assoc_annotation", "annotation", mysql_length=200),
 )
 
 StoredWorkflowAnnotationAssociation_table = Table(
-    "stored_workflow_annotation_association", metadata,
+    "stored_workflow_annotation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("annotation", TEXT),
-    Index("ix_stored_workflow_ann_assoc_annotation", 'annotation', mysql_length=200),
+    Index("ix_stored_workflow_ann_assoc_annotation", "annotation", mysql_length=200),
 )
 
 WorkflowStepAnnotationAssociation_table = Table(
-    "workflow_step_annotation_association", metadata,
+    "workflow_step_annotation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("annotation", TEXT),
-    Index("ix_workflow_step_ann_assoc_annotation", 'annotation', mysql_length=200),
+    Index("ix_workflow_step_ann_assoc_annotation", "annotation", mysql_length=200),
 )
 
 # Tagging tables.
 
-WorkflowStepTagAssociation_table = Table("workflow_step_tag_association", metadata,
-                                         Column("id", Integer, primary_key=True),
-                                         Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
-                                         Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                         Column("user_tname", Unicode(255), index=True),
-                                         Column("value", Unicode(255), index=True),
-                                         Column("user_value", Unicode(255), index=True))
+WorkflowStepTagAssociation_table = Table(
+    "workflow_step_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", Unicode(255), index=True),
+    Column("value", Unicode(255), index=True),
+    Column("user_value", Unicode(255), index=True),
+)
 
 TABLES = [
     HistoryAnnotationAssociation_table,
     HistoryDatasetAssociationAnnotationAssociation_table,
     StoredWorkflowAnnotationAssociation_table,
     WorkflowStepAnnotationAssociation_table,
-    WorkflowStepTagAssociation_table
+    WorkflowStepTagAssociation_table,
 ]
 
 
diff --git a/lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py b/lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
index 9d7d9359c59..7fc398a4ea2 100644
--- a/lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
+++ b/lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
@@ -5,7 +5,12 @@ library_info_association, library_folder_info_association, library_dataset_datas
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.migrate.versions.util import engine_false
 
@@ -21,7 +26,7 @@ def upgrade(migrate_engine):
     try:
         LibraryInfoAssociation_table = Table("library_info_association", metadata, autoload=True)
         c = Column("deleted", Boolean, index=True, default=False)
-        c.create(LibraryInfoAssociation_table, index_name='ix_library_info_association_deleted')
+        c.create(LibraryInfoAssociation_table, index_name="ix_library_info_association_deleted")
         assert c is LibraryInfoAssociation_table.c.deleted
     except Exception:
         log.exception("Adding column 'deleted' to 'library_info_association' table failed.")
@@ -33,7 +38,7 @@ def upgrade(migrate_engine):
     try:
         LibraryFolderInfoAssociation_table = Table("library_folder_info_association", metadata, autoload=True)
         c = Column("deleted", Boolean, index=True, default=False)
-        c.create(LibraryFolderInfoAssociation_table, index_name='ix_library_folder_info_association_deleted')
+        c.create(LibraryFolderInfoAssociation_table, index_name="ix_library_folder_info_association_deleted")
         assert c is LibraryFolderInfoAssociation_table.c.deleted
     except Exception:
         log.exception("Adding column 'deleted' to 'library_folder_info_association' table failed.")
@@ -43,9 +48,13 @@ def upgrade(migrate_engine):
     except Exception:
         log.exception("deleted to false in library_folder_info_association failed.")
     try:
-        LibraryDatasetDatasetInfoAssociation_table = Table("library_dataset_dataset_info_association", metadata, autoload=True)
+        LibraryDatasetDatasetInfoAssociation_table = Table(
+            "library_dataset_dataset_info_association", metadata, autoload=True
+        )
         c = Column("deleted", Boolean, index=True, default=False)
-        c.create(LibraryDatasetDatasetInfoAssociation_table, index_name='ix_library_dataset_dataset_info_association_deleted')
+        c.create(
+            LibraryDatasetDatasetInfoAssociation_table, index_name="ix_library_dataset_dataset_info_association_deleted"
+        )
         assert c is LibraryDatasetDatasetInfoAssociation_table.c.deleted
     except Exception:
         log.exception("Adding column 'deleted' to 'library_dataset_dataset_info_association' table failed.")
diff --git a/lib/galaxy/model/migrate/versions/0037_samples_library.py b/lib/galaxy/model/migrate/versions/0037_samples_library.py
index 154ec7c3839..ec536e88e2f 100644
--- a/lib/galaxy/model/migrate/versions/0037_samples_library.py
+++ b/lib/galaxy/model/migrate/versions/0037_samples_library.py
@@ -16,12 +16,10 @@ from sqlalchemy import (
     Table,
 )
 
-from galaxy.model.custom_types import (
-    JSONType,
-)
+from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -36,16 +34,16 @@ def upgrade(migrate_engine):
 
     # Add the datatx_info column in 'request_type' table
     col = Column("datatx_info", JSONType)
-    add_column(col, 'request_type', metadata)
+    add_column(col, "request_type", metadata)
 
     # Delete the library_id column in 'request' table
     Request_table = Table("request", metadata, autoload=True)
     # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first.
-    drop_column('library_id', Request_table)
+    drop_column("library_id", Request_table)
 
     # Delete the folder_id column in 'request' table
     # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first.
-    drop_column('folder_id', Request_table)
+    drop_column("folder_id", Request_table)
 
     # Add the dataset_files column in 'sample' table
     Sample_table = Table("sample", metadata, autoload=True)
@@ -54,11 +52,11 @@ def upgrade(migrate_engine):
 
     # Add the library_id column in 'sample' table
     col = Column("library_id", Integer, ForeignKey("library.id"), index=True)
-    add_column(col, Sample_table, metadata, index_name='ix_sample_library_id')
+    add_column(col, Sample_table, metadata, index_name="ix_sample_library_id")
 
     # Add the library_id column in 'sample' table
     col = Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True)
-    add_column(col, Sample_table, metadata, index_name='ix_sample_library_folder_id')
+    add_column(col, Sample_table, metadata, index_name="ix_sample_library_folder_id")
 
 
 def downgrade(migrate_engine):
@@ -66,15 +64,15 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     Sample_table = Table("sample", metadata, autoload=True)
-    drop_column('folder_id', Sample_table)
-    drop_column('library_id', Sample_table)
-    drop_column('dataset_files', Sample_table)
+    drop_column("folder_id", Sample_table)
+    drop_column("library_id", Sample_table)
+    drop_column("dataset_files", Sample_table)
 
     Request_table = Table("request", metadata, autoload=True)
-    col = Column('folder_id', Integer, ForeignKey('library_folder.id'), index=True)
-    add_column(col, Request_table, metadata, index_name='ix_request_folder_id')
+    col = Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True)
+    add_column(col, Request_table, metadata, index_name="ix_request_folder_id")
 
-    col = Column('library_id', Integer, ForeignKey("library.id"), index=True)
-    add_column(col, Request_table, metadata, index_name='ix_request_library_id')
+    col = Column("library_id", Integer, ForeignKey("library.id"), index=True)
+    add_column(col, Request_table, metadata, index_name="ix_request_library_id")
 
-    drop_column('datatx_info', 'request_type', metadata)
+    drop_column("datatx_info", "request_type", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py b/lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
index 9a607346d2c..1e0d4ada2b5 100644
--- a/lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
+++ b/lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
@@ -8,7 +8,16 @@ request table and if so, restore the table.
 import datetime
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import engine_false
@@ -24,21 +33,24 @@ def upgrade(migrate_engine):
 
     # In case of sqlite, check if the previous migration script deleted the
     # request table and if so, restore the table.
-    if migrate_engine.name == 'sqlite':
-        if not migrate_engine.has_table('request'):
+    if migrate_engine.name == "sqlite":
+        if not migrate_engine.has_table("request"):
             # load the tables referenced in foreign keys
-            metadata.reflect(only=['form_values', 'request_type', 'galaxy_user'])
+            metadata.reflect(only=["form_values", "request_type", "galaxy_user"])
             # create a temporary table
-            Request_table = Table('request', metadata,
-                                  Column("id", Integer, primary_key=True),
-                                  Column("create_time", DateTime, default=now),
-                                  Column("update_time", DateTime, default=now, onupdate=now),
-                                  Column("name", TrimmedString(255), nullable=False),
-                                  Column("desc", TEXT),
-                                  Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
-                                  Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
-                                  Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                  Column("deleted", Boolean, index=True, default=False))
+            Request_table = Table(
+                "request",
+                metadata,
+                Column("id", Integer, primary_key=True),
+                Column("create_time", DateTime, default=now),
+                Column("update_time", DateTime, default=now, onupdate=now),
+                Column("name", TrimmedString(255), nullable=False),
+                Column("desc", TEXT),
+                Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+                Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
+                Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+                Column("deleted", Boolean, index=True, default=False),
+            )
             try:
                 Request_table.create()
             except Exception:
@@ -48,7 +60,7 @@ def upgrade(migrate_engine):
     try:
         LibraryInfoAssociation_table = Table("library_info_association", metadata, autoload=True)
         c = Column("inheritable", Boolean, index=True, default=False)
-        c.create(LibraryInfoAssociation_table, index_name='ix_library_info_association_inheritable')
+        c.create(LibraryInfoAssociation_table, index_name="ix_library_info_association_inheritable")
         assert c is LibraryInfoAssociation_table.c.inheritable
     except Exception:
         log.exception("Adding column 'inheritable' to 'library_info_association' table failed.")
@@ -60,7 +72,7 @@ def upgrade(migrate_engine):
     try:
         LibraryFolderInfoAssociation_table = Table("library_folder_info_association", metadata, autoload=True)
         c = Column("inheritable", Boolean, index=True, default=False)
-        c.create(LibraryFolderInfoAssociation_table, index_name='ix_library_folder_info_association_inheritable')
+        c.create(LibraryFolderInfoAssociation_table, index_name="ix_library_folder_info_association_inheritable")
         assert c is LibraryFolderInfoAssociation_table.c.inheritable
     except Exception:
         log.exception("Adding column 'inheritable' to 'library_folder_info_association' table failed.")
diff --git a/lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py b/lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
index 4e61d488885..469987c29db 100644
--- a/lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
+++ b/lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
@@ -8,7 +8,7 @@ from sqlalchemy import (
     Column,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/model/migrate/versions/0040_page_annotations.py b/lib/galaxy/model/migrate/versions/0040_page_annotations.py
index 7f89c1fc1fc..35b12b27a3c 100644
--- a/lib/galaxy/model/migrate/versions/0040_page_annotations.py
+++ b/lib/galaxy/model/migrate/versions/0040_page_annotations.py
@@ -11,24 +11,25 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 PageAnnotationAssociation_table = Table(
-    "page_annotation_association", metadata,
+    "page_annotation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("page_id", Integer, ForeignKey("page.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("annotation", TEXT),
-    Index('ix_page_annotation_association_annotation', 'annotation', mysql_length=200),
+    Index("ix_page_annotation_association_annotation", "annotation", mysql_length=200),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0041_workflow_invocation.py b/lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
index 9b4ed386cd5..a30d56d5375 100644
--- a/lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
+++ b/lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
@@ -11,31 +11,37 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-WorkflowInvocation_table = Table("workflow_invocation", metadata,
-                                 Column("id", Integer, primary_key=True),
-                                 Column("create_time", DateTime, default=now),
-                                 Column("update_time", DateTime, default=now, onupdate=now),
-                                 Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=False))
+WorkflowInvocation_table = Table(
+    "workflow_invocation",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=False),
+)
 
-WorkflowInvocationStep_table = Table("workflow_invocation_step", metadata,
-                                     Column("id", Integer, primary_key=True),
-                                     Column("create_time", DateTime, default=now),
-                                     Column("update_time", DateTime, default=now, onupdate=now),
-                                     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
-                                     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-                                     Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False))
+WorkflowInvocationStep_table = Table(
+    "workflow_invocation_step",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
+)
 
 tables = [WorkflowInvocation_table, WorkflowInvocationStep_table]
 
diff --git a/lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py b/lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
index 63a451d0141..0164a00746c 100644
--- a/lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
+++ b/lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
@@ -11,12 +11,12 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -36,19 +36,25 @@ def upgrade(migrate_engine):
         metadata.remove(t)
 
     # 2) Re-add
-    WorkflowInvocation_table = Table("workflow_invocation", metadata,
-                                     Column("id", Integer, primary_key=True),
-                                     Column("create_time", DateTime, default=now),
-                                     Column("update_time", DateTime, default=now, onupdate=now),
-                                     Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=False))
+    WorkflowInvocation_table = Table(
+        "workflow_invocation",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=False),
+    )
 
-    WorkflowInvocationStep_table = Table("workflow_invocation_step", metadata,
-                                         Column("id", Integer, primary_key=True),
-                                         Column("create_time", DateTime, default=now),
-                                         Column("update_time", DateTime, default=now, onupdate=now),
-                                         Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
-                                         Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-                                         Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True))
+    WorkflowInvocationStep_table = Table(
+        "workflow_invocation_step",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True, nullable=False),
+        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
+        Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True),
+    )
 
     for table in [WorkflowInvocation_table, WorkflowInvocationStep_table]:
         create_table(table)
diff --git a/lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py b/lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
index d0230b9a3d6..833371fb269 100644
--- a/lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
+++ b/lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
@@ -13,7 +13,7 @@ from sqlalchemy import (
     MetaData,
     Table,
     TEXT,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.migrate.versions.util import (
@@ -22,7 +22,7 @@ from galaxy.model.migrate.versions.util import (
     create_table,
     drop_column,
     drop_table,
-    engine_false
+    engine_false,
 )
 
 log = logging.getLogger(__name__)
@@ -30,37 +30,44 @@ metadata = MetaData()
 
 # Sharing visualizations.
 
-VisualizationUserShareAssociation_table = Table("visualization_user_share_association", metadata,
-                                                Column("id", Integer, primary_key=True),
-                                                Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
-                                                Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+VisualizationUserShareAssociation_table = Table(
+    "visualization_user_share_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 # Tagging visualizations.
 
-VisualizationTagAssociation_table = Table("visualization_tag_association", metadata,
-                                          Column("id", Integer, primary_key=True),
-                                          Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
-                                          Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                          Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                          Column("user_tname", Unicode(255), index=True),
-                                          Column("value", Unicode(255), index=True),
-                                          Column("user_value", Unicode(255), index=True))
+VisualizationTagAssociation_table = Table(
+    "visualization_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", Unicode(255), index=True),
+    Column("value", Unicode(255), index=True),
+    Column("user_value", Unicode(255), index=True),
+)
 
 # Annotating visualizations.
 
 VisualizationAnnotationAssociation_table = Table(
-    "visualization_annotation_association", metadata,
+    "visualization_annotation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
     Column("annotation", TEXT),
-    Index('ix_visualization_annotation_association_annotation', 'annotation', mysql_length=200),
+    Index("ix_visualization_annotation_association_annotation", "annotation", mysql_length=200),
 )
 
 TABLES = [
     VisualizationUserShareAssociation_table,
     VisualizationTagAssociation_table,
-    VisualizationAnnotationAssociation_table
+    VisualizationAnnotationAssociation_table,
 ]
 
 
@@ -84,7 +91,7 @@ def upgrade(migrate_engine):
         log.exception("Updating column 'deleted' of table 'visualization' failed.")
 
     importable_column = Column("importable", Boolean, default=False, index=True)
-    add_column(importable_column, Visualization_table, metadata, index_name='ix_visualization_importable')
+    add_column(importable_column, Visualization_table, metadata, index_name="ix_visualization_importable")
     try:
         # Fill column with default value.
         cmd = f"UPDATE visualization SET importable = {engine_false(migrate_engine)}"
@@ -96,10 +103,10 @@ def upgrade(migrate_engine):
     add_column(slug_column, Visualization_table, metadata)
     # Index needs to be added separately because MySQL cannot index a TEXT/BLOB
     # column without specifying mysql_length
-    add_index('ix_visualization_slug', Visualization_table, 'slug')
+    add_index("ix_visualization_slug", Visualization_table, "slug")
 
     published_column = Column("published", Boolean, index=True)
-    add_column(published_column, Visualization_table, metadata, index_name='ix_visualization_published')
+    add_column(published_column, Visualization_table, metadata, index_name="ix_visualization_published")
     try:
         # Fill column with default value.
         cmd = f"UPDATE visualization SET published = {engine_false(migrate_engine)}"
@@ -113,10 +120,10 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     Visualization_table = Table("visualization", metadata, autoload=True)
-    drop_column('deleted', Visualization_table)
-    drop_column('importable', Visualization_table)
-    drop_column('slug', Visualization_table)
-    drop_column('published', Visualization_table)
+    drop_column("deleted", Visualization_table)
+    drop_column("importable", Visualization_table)
+    drop_column("slug", Visualization_table)
+    drop_column("published", Visualization_table)
 
     for table in TABLES:
         drop_table(table)
diff --git a/lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py b/lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
index 9b85b84d9c7..f9257ec9e8f 100644
--- a/lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
+++ b/lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
@@ -7,7 +7,7 @@ import logging
 from sqlalchemy import (
     Boolean,
     Column,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.migrate.versions.util import (
@@ -25,11 +25,11 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     c = Column("notify", Boolean, default=False)
-    add_column(c, 'request', metadata)
+    add_column(c, "request", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('notify', 'request', metadata)
+    drop_column("notify", "request", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py b/lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
index 18accef4afb..e32db165e51 100644
--- a/lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
+++ b/lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
@@ -5,19 +5,30 @@ Migration script to add the request_type_permissions table.
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-RequestTypePermissions_table = Table("request_type_permissions", metadata,
-                                     Column("id", Integer, primary_key=True),
-                                     Column("create_time", DateTime, default=now),
-                                     Column("update_time", DateTime, default=now, onupdate=now),
-                                     Column("action", TEXT),
-                                     Column("request_type_id", Integer, ForeignKey("request_type.id"), nullable=True, index=True),
-                                     Column("role_id", Integer, ForeignKey("role.id"), index=True))
+RequestTypePermissions_table = Table(
+    "request_type_permissions",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("action", TEXT),
+    Column("request_type_id", Integer, ForeignKey("request_type.id"), nullable=True, index=True),
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0046_post_job_actions.py b/lib/galaxy/model/migrate/versions/0046_post_job_actions.py
index f5cca656a29..c2dc6fa0b4e 100644
--- a/lib/galaxy/model/migrate/versions/0046_post_job_actions.py
+++ b/lib/galaxy/model/migrate/versions/0046_post_job_actions.py
@@ -10,24 +10,27 @@ from sqlalchemy import (
     Integer,
     MetaData,
     String,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-PostJobAction_table = Table("post_job_action", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-                            Column("action_type", String(255), nullable=False),
-                            Column("output_name", String(255), nullable=True),
-                            Column("action_arguments", JSONType, nullable=True))
+PostJobAction_table = Table(
+    "post_job_action",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
+    Column("action_type", String(255), nullable=False),
+    Column("output_name", String(255), nullable=True),
+    Column("action_arguments", JSONType, nullable=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py b/lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
index a46cf1f789f..b24b89dbc60 100644
--- a/lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
+++ b/lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
@@ -9,12 +9,12 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -28,12 +28,14 @@ def upgrade(migrate_engine):
 
     Job_table = Table("job", metadata, autoload=True)
     col = Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    add_column(col, Job_table, metadata, index_name='ix_job_user_id')
+    add_column(col, Job_table, metadata, index_name="ix_job_user_id")
     try:
-        cmd = "SELECT job.id AS galaxy_job_id, " \
-            + "galaxy_session.user_id AS galaxy_user_id " \
-            + "FROM job " \
+        cmd = (
+            "SELECT job.id AS galaxy_job_id, "
+            + "galaxy_session.user_id AS galaxy_user_id "
+            + "FROM job "
             + "JOIN galaxy_session ON job.session_id = galaxy_session.id;"
+        )
         job_users = migrate_engine.execute(cmd).fetchall()
         print("Updating user_id column in job table for ", len(job_users), " rows...")
         print("")
@@ -44,7 +46,9 @@ def upgrade(migrate_engine):
                 update_count += 1
             migrate_engine.execute(cmd)
         print("Updated column 'user_id' for ", update_count, " rows of table 'job'.")
-        print(len(job_users) - update_count, " rows have no user_id since the value was NULL in the galaxy_session table.")
+        print(
+            len(job_users) - update_count, " rows have no user_id since the value was NULL in the galaxy_session table."
+        )
         print("")
     except Exception:
         log.exception("Updating column 'user_id' of table 'job' failed.")
@@ -54,4 +58,4 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('user_id', 'job', metadata)
+    drop_column("user_id", "job", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py b/lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
index a68b0fd7942..5187ce14bc4 100644
--- a/lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
+++ b/lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
@@ -12,13 +12,13 @@ from sqlalchemy import (
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-DATASET_INSTANCE_TABLE_NAMES = ['history_dataset_association', 'library_dataset_dataset_association']
+DATASET_INSTANCE_TABLE_NAMES = ["history_dataset_association", "library_dataset_dataset_association"]
 
 
 def upgrade(migrate_engine):
@@ -37,4 +37,4 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     for table_name in DATASET_INSTANCE_TABLE_NAMES:
-        drop_column('state', table_name, metadata)
+        drop_column("state", table_name, metadata)
diff --git a/lib/galaxy/model/migrate/versions/0049_api_keys_table.py b/lib/galaxy/model/migrate/versions/0049_api_keys_table.py
index dd75ab7e68d..5bde68d9201 100644
--- a/lib/galaxy/model/migrate/versions/0049_api_keys_table.py
+++ b/lib/galaxy/model/migrate/versions/0049_api_keys_table.py
@@ -5,7 +5,14 @@ Migration script to add the api_keys table.
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
@@ -13,11 +20,14 @@ now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-APIKeys_table = Table("api_keys", metadata,
-                      Column("id", Integer, primary_key=True),
-                      Column("create_time", DateTime, default=now),
-                      Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                      Column("key", TrimmedString(32), index=True, unique=True))
+APIKeys_table = Table(
+    "api_keys",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("key", TrimmedString(32), index=True, unique=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py b/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
index 3eabd23174b..3b7abf2ebfd 100644
--- a/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
+++ b/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
@@ -5,122 +5,155 @@ This script drops tables that were associated with the old Galaxy Cloud function
 import datetime
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-CloudImage_table = Table("cloud_image", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, default=now, onupdate=now),
-                         Column("provider_type", TEXT),
-                         Column("image_id", TEXT, nullable=False),
-                         Column("manifest", TEXT),
-                         Column("state", TEXT),
-                         Column("architecture", TEXT),
-                         Column("deleted", Boolean, default=False))
+CloudImage_table = Table(
+    "cloud_image",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("provider_type", TEXT),
+    Column("image_id", TEXT, nullable=False),
+    Column("manifest", TEXT),
+    Column("state", TEXT),
+    Column("architecture", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
 """ UserConfiguredInstance (UCI) table """
-UCI_table = Table("cloud_uci", metadata,
-                  Column("id", Integer, primary_key=True),
-                  Column("create_time", DateTime, default=now),
-                  Column("update_time", DateTime, default=now, onupdate=now),
-                  Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                  Column("credentials_id", Integer, ForeignKey("cloud_user_credentials.id"), index=True),
-                  Column("key_pair_name", TEXT),
-                  Column("key_pair_material", TEXT),
-                  Column("name", TEXT),
-                  Column("state", TEXT),
-                  Column("error", TEXT),
-                  Column("total_size", Integer),
-                  Column("launch_time", DateTime),
-                  Column("deleted", Boolean, default=False))
+UCI_table = Table(
+    "cloud_uci",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("credentials_id", Integer, ForeignKey("cloud_user_credentials.id"), index=True),
+    Column("key_pair_name", TEXT),
+    Column("key_pair_material", TEXT),
+    Column("name", TEXT),
+    Column("state", TEXT),
+    Column("error", TEXT),
+    Column("total_size", Integer),
+    Column("launch_time", DateTime),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudInstance_table = Table("cloud_instance", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("launch_time", DateTime),
-                            Column("stop_time", DateTime),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
-                            Column("type", TEXT),
-                            Column("reservation_id", TEXT),
-                            Column("instance_id", TEXT),
-                            Column("mi_id", Integer, ForeignKey("cloud_image.id"), index=True),
-                            Column("state", TEXT),
-                            Column("error", TEXT),
-                            Column("public_dns", TEXT),
-                            Column("private_dns", TEXT),
-                            Column("security_group", TEXT),
-                            Column("availability_zone", TEXT))
+CloudInstance_table = Table(
+    "cloud_instance",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("launch_time", DateTime),
+    Column("stop_time", DateTime),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
+    Column("type", TEXT),
+    Column("reservation_id", TEXT),
+    Column("instance_id", TEXT),
+    Column("mi_id", Integer, ForeignKey("cloud_image.id"), index=True),
+    Column("state", TEXT),
+    Column("error", TEXT),
+    Column("public_dns", TEXT),
+    Column("private_dns", TEXT),
+    Column("security_group", TEXT),
+    Column("availability_zone", TEXT),
+)
 
-CloudStore_table = Table("cloud_store", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, default=now, onupdate=now),
-                         Column("attach_time", DateTime),
-                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                         Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True, nullable=False),
-                         Column("volume_id", TEXT),
-                         Column("size", Integer, nullable=False),
-                         Column("availability_zone", TEXT),
-                         Column("inst_id", Integer, ForeignKey("cloud_instance.id")),
-                         Column("status", TEXT),
-                         Column("device", TEXT),
-                         Column("space_consumed", Integer),
-                         Column("error", TEXT),
-                         Column("deleted", Boolean, default=False))
+CloudStore_table = Table(
+    "cloud_store",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("attach_time", DateTime),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True, nullable=False),
+    Column("volume_id", TEXT),
+    Column("size", Integer, nullable=False),
+    Column("availability_zone", TEXT),
+    Column("inst_id", Integer, ForeignKey("cloud_instance.id")),
+    Column("status", TEXT),
+    Column("device", TEXT),
+    Column("space_consumed", Integer),
+    Column("error", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudSnapshot_table = Table("cloud_snapshot", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
-                            Column("store_id", Integer, ForeignKey("cloud_store.id"), index=True, nullable=False),
-                            Column("snapshot_id", TEXT),
-                            Column("status", TEXT),
-                            Column("description", TEXT),
-                            Column("error", TEXT),
-                            Column("deleted", Boolean, default=False))
+CloudSnapshot_table = Table(
+    "cloud_snapshot",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("uci_id", Integer, ForeignKey("cloud_uci.id"), index=True),
+    Column("store_id", Integer, ForeignKey("cloud_store.id"), index=True, nullable=False),
+    Column("snapshot_id", TEXT),
+    Column("status", TEXT),
+    Column("description", TEXT),
+    Column("error", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudUserCredentials_table = Table("cloud_user_credentials", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("create_time", DateTime, default=now),
-                                   Column("update_time", DateTime, default=now, onupdate=now),
-                                   Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                                   Column("provider_id", Integer, ForeignKey("cloud_provider.id"), index=True, nullable=False),
-                                   Column("name", TEXT),
-                                   Column("access_key", TEXT),
-                                   Column("secret_key", TEXT),
-                                   Column("deleted", Boolean, default=False))
+CloudUserCredentials_table = Table(
+    "cloud_user_credentials",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("provider_id", Integer, ForeignKey("cloud_provider.id"), index=True, nullable=False),
+    Column("name", TEXT),
+    Column("access_key", TEXT),
+    Column("secret_key", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
-CloudProvider_table = Table("cloud_provider", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                            Column("type", TEXT, nullable=False),
-                            Column("name", TEXT),
-                            Column("region_connection", TEXT),
-                            Column("region_name", TEXT),
-                            Column("region_endpoint", TEXT),
-                            Column("is_secure", Boolean),
-                            Column("host", TEXT),
-                            Column("port", Integer),
-                            Column("proxy", TEXT),
-                            Column("proxy_port", TEXT),
-                            Column("proxy_user", TEXT),
-                            Column("proxy_pass", TEXT),
-                            Column("debug", Integer),
-                            Column("https_connection_factory", TEXT),
-                            Column("path", TEXT),
-                            Column("deleted", Boolean, default=False))
+CloudProvider_table = Table(
+    "cloud_provider",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("type", TEXT, nullable=False),
+    Column("name", TEXT),
+    Column("region_connection", TEXT),
+    Column("region_name", TEXT),
+    Column("region_endpoint", TEXT),
+    Column("is_secure", Boolean),
+    Column("host", TEXT),
+    Column("port", Integer),
+    Column("proxy", TEXT),
+    Column("proxy_port", TEXT),
+    Column("proxy_user", TEXT),
+    Column("proxy_pass", TEXT),
+    Column("debug", Integer),
+    Column("https_connection_factory", TEXT),
+    Column("path", TEXT),
+    Column("deleted", Boolean, default=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py b/lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
index fb547d3b30e..410e78d2dca 100644
--- a/lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
+++ b/lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
@@ -4,9 +4,18 @@ Migration script to add imported column for jobs table.
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column, engine_false
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+    engine_false,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -31,4 +40,4 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('imported', 'job', metadata)
+    drop_column("imported", "job", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
index 792d2c43a72..c597856ad91 100644
--- a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
+++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
@@ -7,27 +7,41 @@ import datetime
 import logging
 from json import loads
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 from sqlalchemy.exc import NoSuchTableError
 
 from galaxy.model.custom_types import TrimmedString
-from galaxy.model.migrate.versions.util import localtimestamp, nextval
+from galaxy.model.migrate.versions.util import (
+    localtimestamp,
+    nextval,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 
-SampleDataset_table = Table('sample_dataset', metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("sample_id", Integer, ForeignKey("sample.id"), index=True),
-                            Column("name", TrimmedString(255), nullable=False),
-                            Column("file_path", TrimmedString(255), nullable=False),
-                            Column("status", TrimmedString(255), nullable=False),
-                            Column("error_msg", TEXT),
-                            Column("size", TrimmedString(255)))
+SampleDataset_table = Table(
+    "sample_dataset",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("sample_id", Integer, ForeignKey("sample.id"), index=True),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("file_path", TrimmedString(255), nullable=False),
+    Column("status", TrimmedString(255), nullable=False),
+    Column("error_msg", TEXT),
+    Column("size", TrimmedString(255)),
+)
 
 
 def upgrade(migrate_engine):
@@ -49,15 +63,21 @@ def upgrade(migrate_engine):
             for df in dataset_files:
                 if isinstance(df, dict):
                     cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')"
-                    cmd = cmd % (nextval(migrate_engine, 'sample_dataset'),
-                                 localtimestamp(migrate_engine),
-                                 localtimestamp(migrate_engine),
-                                 str(sample_id),
-                                 df.get('name', ''),
-                                 df.get('filepath', ''),
-                                 df.get('status', '').replace('"', '').replace("'", ""),
-                                 "",
-                                 df.get('size', '').replace('"', '').replace("'", "").replace(df.get('filepath', ''), '').strip())
+                    cmd = cmd % (
+                        nextval(migrate_engine, "sample_dataset"),
+                        localtimestamp(migrate_engine),
+                        localtimestamp(migrate_engine),
+                        str(sample_id),
+                        df.get("name", ""),
+                        df.get("filepath", ""),
+                        df.get("status", "").replace('"', "").replace("'", ""),
+                        "",
+                        df.get("size", "")
+                        .replace('"', "")
+                        .replace("'", "")
+                        .replace(df.get("filepath", ""), "")
+                        .strip(),
+                    )
                 migrate_engine.execute(cmd)
 
     # Delete the dataset_files column in the Sample table
diff --git a/lib/galaxy/model/migrate/versions/0053_item_ratings.py b/lib/galaxy/model/migrate/versions/0053_item_ratings.py
index 5aea118a571..c3fa9b91b6a 100644
--- a/lib/galaxy/model/migrate/versions/0053_item_ratings.py
+++ b/lib/galaxy/model/migrate/versions/0053_item_ratings.py
@@ -9,48 +9,63 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_index,
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # Rating tables.
-HistoryRatingAssociation_table = Table("history_rating_association", metadata,
-                                       Column("id", Integer, primary_key=True),
-                                       Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                       Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                       Column("rating", Integer, index=True))
+HistoryRatingAssociation_table = Table(
+    "history_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
-HistoryDatasetAssociationRatingAssociation_table = Table("history_dataset_association_rating_association", metadata,
-                                                         Column("id", Integer, primary_key=True),
-                                                         Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-                                                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                         Column("rating", Integer, index=True))
+HistoryDatasetAssociationRatingAssociation_table = Table(
+    "history_dataset_association_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
-StoredWorkflowRatingAssociation_table = Table("stored_workflow_rating_association", metadata,
-                                              Column("id", Integer, primary_key=True),
-                                              Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
-                                              Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                              Column("rating", Integer, index=True))
+StoredWorkflowRatingAssociation_table = Table(
+    "stored_workflow_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
-PageRatingAssociation_table = Table("page_rating_association", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("page_id", Integer, ForeignKey("page.id"), index=True),
-                                    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                    Column("rating", Integer, index=True))
+PageRatingAssociation_table = Table(
+    "page_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("page_id", Integer, ForeignKey("page.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
-VisualizationRatingAssociation_table = Table("visualization_rating_association", metadata,
-                                             Column("id", Integer, primary_key=True),
-                                             Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
-                                             Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                             Column("rating", Integer, index=True))
+VisualizationRatingAssociation_table = Table(
+    "visualization_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
 
 def upgrade(migrate_engine):
@@ -65,9 +80,14 @@ def upgrade(migrate_engine):
         HistoryDatasetAssociationRatingAssociation_table.create()
     except Exception as e:
         # MySQL cannot handle long index names; when we see this error, create the index name manually.
-        if migrate_engine.name == 'mysql' and \
-                str(e).lower().find("identifier name 'ix_history_dataset_association_rating_association_history_dataset_association_id' is too long"):
-            add_index('ix_hda_rating_association_hda_id', HistoryDatasetAssociationRatingAssociation_table, 'history_dataset_association_id')
+        if migrate_engine.name == "mysql" and str(e).lower().find(
+            "identifier name 'ix_history_dataset_association_rating_association_history_dataset_association_id' is too long"
+        ):
+            add_index(
+                "ix_hda_rating_association_hda_id",
+                HistoryDatasetAssociationRatingAssociation_table,
+                "history_dataset_association_id",
+            )
         else:
             log.exception("Creating history_dataset_association_rating_association table failed.")
 
diff --git a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
index 7500028c29a..a5c42e4e8df 100644
--- a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
+++ b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
@@ -9,13 +9,13 @@ from sqlalchemy import (
     Column,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     add_index,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -37,16 +37,18 @@ def upgrade(migrate_engine):
     add_column(y, Visualization_revision_table, metadata)
     # Indexes need to be added separately because MySQL cannot index a TEXT/BLOB
     # column without specifying mysql_length
-    add_index("ix_visualization_dbkey", Visualization_table, 'dbkey')
-    add_index("ix_visualization_revision_dbkey", Visualization_revision_table, 'dbkey')
+    add_index("ix_visualization_dbkey", Visualization_table, "dbkey")
+    add_index("ix_visualization_revision_dbkey", Visualization_revision_table, "dbkey")
 
-    all_viz = migrate_engine.execute("SELECT visualization.id as viz_id, visualization_revision.id as viz_rev_id, visualization_revision.config FROM visualization_revision \
-                    LEFT JOIN visualization ON visualization.id=visualization_revision.visualization_id")
+    all_viz = migrate_engine.execute(
+        "SELECT visualization.id as viz_id, visualization_revision.id as viz_rev_id, visualization_revision.config FROM visualization_revision \
+                    LEFT JOIN visualization ON visualization.id=visualization_revision.visualization_id"
+    )
     for viz in all_viz:
-        viz_id = viz['viz_id']
-        viz_rev_id = viz['viz_rev_id']
+        viz_id = viz["viz_id"]
+        viz_rev_id = viz["viz_rev_id"]
         if viz[Visualization_revision_table.c.config]:
-            dbkey = loads(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'")
+            dbkey = loads(viz[Visualization_revision_table.c.config]).get("dbkey", "").replace("'", "\\'")
             migrate_engine.execute(f"UPDATE visualization_revision SET dbkey='{dbkey}' WHERE id={viz_rev_id}")
             migrate_engine.execute(f"UPDATE visualization SET dbkey='{dbkey}' WHERE id={viz_id}")
 
@@ -55,5 +57,5 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('dbkey', 'visualization', metadata)
-    drop_column('dbkey', 'visualization_revision', metadata)
+    drop_column("dbkey", "visualization", metadata)
+    drop_column("dbkey", "visualization_revision", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py b/lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
index 072ea174d83..ae05437922d 100644
--- a/lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
+++ b/lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
@@ -4,17 +4,29 @@ Migration script to add the post_job_action_association table.
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-PostJobActionAssociation_table = Table("post_job_action_association", metadata,
-                                       Column("id", Integer, primary_key=True),
-                                       Column("post_job_action_id", Integer, ForeignKey("post_job_action.id"), index=True, nullable=False),
-                                       Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False))
+PostJobActionAssociation_table = Table(
+    "post_job_action_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("post_job_action_id", Integer, ForeignKey("post_job_action.id"), index=True, nullable=False),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0056_workflow_outputs.py b/lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
index 234b9919bdb..08de99ff700 100644
--- a/lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
+++ b/lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
@@ -10,21 +10,24 @@ from sqlalchemy import (
     Integer,
     MetaData,
     String,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-WorkflowOutput_table = Table("workflow_output", metadata,
-                             Column("id", Integer, primary_key=True),
-                             Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
-                             Column("output_name", String(255), nullable=True))
+WorkflowOutput_table = Table(
+    "workflow_output",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
+    Column("output_name", String(255), nullable=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0057_request_notify.py b/lib/galaxy/model/migrate/versions/0057_request_notify.py
index f28c6562132..3a134efc7fd 100644
--- a/lib/galaxy/model/migrate/versions/0057_request_notify.py
+++ b/lib/galaxy/model/migrate/versions/0057_request_notify.py
@@ -10,7 +10,7 @@ from sqlalchemy import (
     Boolean,
     Column,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import JSONType
@@ -38,13 +38,13 @@ def upgrade(migrate_engine):
     result = migrate_engine.execute(cmd)
     for r in result:
         id = int(r[0])
-        notify_new = dict(email=[], sample_states=[], body='', subject='')
+        notify_new = dict(email=[], sample_states=[], body="", subject="")
         cmd = "UPDATE request SET notification='%s' WHERE id=%i" % (dumps(notify_new), id)
         migrate_engine.execute(cmd)
 
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('notify', Request_table)
+    if migrate_engine.name != "sqlite":
+        drop_column("notify", Request_table)
 
 
 def downgrade(migrate_engine):
@@ -52,8 +52,8 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     Request_table = Table("request", metadata, autoload=True)
-    if migrate_engine.name != 'sqlite':
+    if migrate_engine.name != "sqlite":
         c = Column("notify", Boolean, default=False)
         add_column(c, Request_table, metadata)
 
-    drop_column('notification', Request_table)
+    drop_column("notification", Request_table)
diff --git a/lib/galaxy/model/migrate/versions/0058_history_import_export.py b/lib/galaxy/model/migrate/versions/0058_history_import_export.py
index 509b4f9f7cf..669111d2589 100644
--- a/lib/galaxy/model/migrate/versions/0058_history_import_export.py
+++ b/lib/galaxy/model/migrate/versions/0058_history_import_export.py
@@ -4,22 +4,33 @@ Migration script to create table for exporting histories to archives.
 
 import logging
 
-from sqlalchemy import Boolean, Column, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # Table to add.
 
-JobExportHistoryArchive_table = Table("job_export_history_archive", metadata,
-                                      Column("id", Integer, primary_key=True),
-                                      Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                                      Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                      Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-                                      Column("compressed", Boolean, index=True, default=False),
-                                      Column("history_attrs_filename", TEXT),
-                                      Column("datasets_attrs_filename", TEXT),
-                                      Column("jobs_attrs_filename", TEXT))
+JobExportHistoryArchive_table = Table(
+    "job_export_history_archive",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+    Column("compressed", Boolean, index=True, default=False),
+    Column("history_attrs_filename", TEXT),
+    Column("datasets_attrs_filename", TEXT),
+    Column("jobs_attrs_filename", TEXT),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
index 164746248ea..f112668990d 100644
--- a/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
+++ b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
@@ -5,7 +5,12 @@ to 'TEXT' so that it can support large file paths exceeding 255 characters
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+    TEXT,
+)
 from sqlalchemy.exc import NoSuchTableError
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/model/migrate/versions/0060_history_archive_import.py b/lib/galaxy/model/migrate/versions/0060_history_archive_import.py
index cc42c710608..11bb16030e8 100644
--- a/lib/galaxy/model/migrate/versions/0060_history_archive_import.py
+++ b/lib/galaxy/model/migrate/versions/0060_history_archive_import.py
@@ -5,7 +5,15 @@ file archives.
 
 import logging
 
-from sqlalchemy import Boolean, Column, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 from galaxy.model.migrate.versions.util import engine_false
 
@@ -19,11 +27,14 @@ ldda_parent_col = Column("ldda_parent_id", Integer, ForeignKey("library_dataset_
 
 # Table to add.
 
-JobImportHistoryArchive_table = Table("job_import_history_archive", metadata,
-                                      Column("id", Integer, primary_key=True),
-                                      Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                                      Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                      Column("archive_dir", TEXT))
+JobImportHistoryArchive_table = Table(
+    "job_import_history_archive",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("archive_dir", TEXT),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0061_tasks.py b/lib/galaxy/model/migrate/versions/0061_tasks.py
index 3df41c06f74..c4523f223fe 100644
--- a/lib/galaxy/model/migrate/versions/0061_tasks.py
+++ b/lib/galaxy/model/migrate/versions/0061_tasks.py
@@ -13,34 +13,37 @@ from sqlalchemy import (
     MetaData,
     String,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-Task_table = Table("task", metadata,
-                   Column("id", Integer, primary_key=True),
-                   Column("create_time", DateTime, default=now),
-                   Column("execution_time", DateTime),
-                   Column("update_time", DateTime, default=now, onupdate=now),
-                   Column("state", String(64), index=True),
-                   Column("command_line", TEXT),
-                   Column("param_filename", String(1024)),
-                   Column("runner_name", String(255)),
-                   Column("stdout", TEXT),
-                   Column("stderr", TEXT),
-                   Column("traceback", TEXT),
-                   Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
-                   Column("part_file", String(1024)),
-                   Column("task_runner_name", String(255)),
-                   Column("task_runner_external_id", String(255)))
+Task_table = Table(
+    "task",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("execution_time", DateTime),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("state", String(64), index=True),
+    Column("command_line", TEXT),
+    Column("param_filename", String(1024)),
+    Column("runner_name", String(255)),
+    Column("stdout", TEXT),
+    Column("stderr", TEXT),
+    Column("traceback", TEXT),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
+    Column("part_file", String(1024)),
+    Column("task_runner_name", String(255)),
+    Column("task_runner_external_id", String(255)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0062_user_openid_table.py b/lib/galaxy/model/migrate/versions/0062_user_openid_table.py
index 1cd72e82724..130ffd57661 100644
--- a/lib/galaxy/model/migrate/versions/0062_user_openid_table.py
+++ b/lib/galaxy/model/migrate/versions/0062_user_openid_table.py
@@ -6,7 +6,16 @@ OpenIDs.
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Index, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Index,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -14,13 +23,16 @@ metadata = MetaData()
 
 # Table to add
 
-UserOpenID_table = Table("galaxy_user_openid", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, index=True, default=now, onupdate=now),
-                         Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
-                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                         Column("openid", TEXT))
+UserOpenID_table = Table(
+    "galaxy_user_openid",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, index=True, default=now, onupdate=now),
+    Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("openid", TEXT),
+)
 
 
 def upgrade(migrate_engine):
@@ -34,8 +46,8 @@ def upgrade(migrate_engine):
     except Exception:
         log.exception("Creating galaxy_user_openid table failed.")
 
-    ix_name = 'ix_galaxy_user_openid_openid'
-    if migrate_engine.name == 'mysql':
+    ix_name = "ix_galaxy_user_openid_openid"
+    if migrate_engine.name == "mysql":
         i = "ALTER TABLE galaxy_user_openid ADD UNIQUE INDEX ( openid( 255 ) )"
         migrate_engine.execute(i)
     else:
diff --git a/lib/galaxy/model/migrate/versions/0063_sequencer_table.py b/lib/galaxy/model/migrate/versions/0063_sequencer_table.py
index d19d53dcb5a..0cc2489a2e2 100644
--- a/lib/galaxy/model/migrate/versions/0063_sequencer_table.py
+++ b/lib/galaxy/model/migrate/versions/0063_sequencer_table.py
@@ -5,7 +5,16 @@ Migration script to create a new 'sequencer' table
 import datetime
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
@@ -14,17 +23,20 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # Table to add
-Sequencer_table = Table('sequencer', metadata,
-                        Column("id", Integer, primary_key=True),
-                        Column("create_time", DateTime, default=now),
-                        Column("update_time", DateTime, default=now, onupdate=now),
-                        Column("name", TrimmedString(255), nullable=False),
-                        Column("description", TEXT),
-                        Column("sequencer_type_id", TrimmedString(255), nullable=False),
-                        Column("version", TrimmedString(255)),
-                        Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
-                        Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
-                        Column("deleted", Boolean, index=True, default=False))
+Sequencer_table = Table(
+    "sequencer",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), nullable=False),
+    Column("description", TEXT),
+    Column("sequencer_type_id", TrimmedString(255), nullable=False),
+    Column("version", TrimmedString(255)),
+    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py b/lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
index 3b5aed500a2..e94c790ef64 100644
--- a/lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
+++ b/lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
@@ -5,31 +5,51 @@ Migration script to add the run and sample_run_association tables.
 import datetime
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-Run_table = Table("run", metadata,
-                  Column("id", Integer, primary_key=True),
-                  Column("create_time", DateTime, default=now),
-                  Column("update_time", DateTime, default=now, onupdate=now),
-                  Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
-                  Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
-                  Column("deleted", Boolean, index=True, default=False))
+Run_table = Table(
+    "run",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
+    Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-RequestTypeRunAssociation_table = Table("request_type_run_association", metadata,
-                                        Column("id", Integer, primary_key=True),
-                                        Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True, nullable=False),
-                                        Column("run_id", Integer, ForeignKey("run.id"), index=True, nullable=False))
+RequestTypeRunAssociation_table = Table(
+    "request_type_run_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True, nullable=False),
+    Column("run_id", Integer, ForeignKey("run.id"), index=True, nullable=False),
+)
 
-SampleRunAssociation_table = Table("sample_run_association", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("sample_id", Integer, ForeignKey("sample.id"), index=True, nullable=False),
-                                   Column("run_id", Integer, ForeignKey("run.id"), index=True, nullable=False))
+SampleRunAssociation_table = Table(
+    "sample_run_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("sample_id", Integer, ForeignKey("sample.id"), index=True, nullable=False),
+    Column("run_id", Integer, ForeignKey("run.id"), index=True, nullable=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py b/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
index a019a4a50a6..7ff1d99aacc 100644
--- a/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
+++ b/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
@@ -7,12 +7,12 @@ table, the 'content' column is now a JSON dict instead of a list.
 import logging
 from json import (
     dumps,
-    loads
+    loads,
 )
 
 from sqlalchemy import (
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import _sniffnfix_pg9_hex
@@ -33,7 +33,7 @@ def upgrade(migrate_engine):
         try:
             return str(lst[index]).replace("'", "''")
         except IndexError:
-            return ''
+            return ""
 
     # Go through the entire table and add a 'name' attribute for each field
     # in the list of fields for each form definition
@@ -47,26 +47,28 @@ def upgrade(migrate_engine):
         fields_list = loads(_sniffnfix_pg9_hex(fields))
         if len(fields_list):
             for index, field in enumerate(fields_list):
-                field['name'] = 'field_%i' % index
-                field['helptext'] = field['helptext'].replace("'", "''").replace('"', "")
-                field['label'] = field['label'].replace("'", "''")
+                field["name"] = "field_%i" % index
+                field["helptext"] = field["helptext"].replace("'", "''").replace('"', "")
+                field["label"] = field["label"].replace("'", "''")
             fields_json = dumps(fields_list)
-            if migrate_engine.name == 'mysql':
+            if migrate_engine.name == "mysql":
                 cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" % (fields_json, form_definition_id)
             else:
                 cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" % (fields_json, form_definition_id)
             migrate_engine.execute(cmd)
     # replace the values list in the content field of the form_values table with a name:value dict
-    cmd = "SELECT form_values.id, form_values.content, form_definition.fields" \
-          " FROM form_values, form_definition" \
-          " WHERE form_values.form_definition_id=form_definition.id" \
-          " ORDER BY form_values.id ASC"
+    cmd = (
+        "SELECT form_values.id, form_values.content, form_definition.fields"
+        " FROM form_values, form_definition"
+        " WHERE form_values.form_definition_id=form_definition.id"
+        " ORDER BY form_values.id ASC"
+    )
     result = migrate_engine.execute(cmd)
     for row in result:
         form_values_id = int(row[0])
         if not str(row[1]).strip():
             continue
-        row1 = str(row[1]).replace('\n', '').replace('\r', '')
+        row1 = str(row[1]).replace("\n", "").replace("\r", "")
         values_list = loads(str(row1).strip())
         if not str(row[2]).strip():
             continue
@@ -74,7 +76,7 @@ def upgrade(migrate_engine):
         if fields_list and isinstance(values_list, list):
             values_dict = {}
             for field_index, field in enumerate(fields_list):
-                field_name = field['name']
+                field_name = field["name"]
                 values_dict[field_name] = get_value(values_list, field_index)
             cmd = "UPDATE form_values SET content='%s' WHERE id=%i" % (dumps(values_dict), form_values_id)
             migrate_engine.execute(cmd)
@@ -88,10 +90,12 @@ def downgrade(migrate_engine):
     Table("form_values", metadata, autoload=True)
     # remove the name attribute in the content column JSON dict in the form_values table
     # and restore it to a list of values
-    cmd = "SELECT form_values.id, form_values.content, form_definition.fields" \
-          " FROM form_values, form_definition" \
-          " WHERE form_values.form_definition_id=form_definition.id" \
-          " ORDER BY form_values.id ASC"
+    cmd = (
+        "SELECT form_values.id, form_values.content, form_definition.fields"
+        " FROM form_values, form_definition"
+        " WHERE form_values.form_definition_id=form_definition.id"
+        " ORDER BY form_values.id ASC"
+    )
     result = migrate_engine.execute(cmd)
     for row in result:
         form_values_id = int(row[0])
@@ -104,7 +108,7 @@ def downgrade(migrate_engine):
         if fields_list:
             values_list = []
             for field in fields_list:
-                field_name = field['name']
+                field_name = field["name"]
                 field_value = values_dict[field_name]
                 values_list.append(field_value)
             cmd = "UPDATE form_values SET content='%s' WHERE id=%i" % (dumps(values_list), form_values_id)
@@ -120,10 +124,13 @@ def downgrade(migrate_engine):
         fields_list = loads(_sniffnfix_pg9_hex(fields))
         if len(fields_list):
             for field in fields_list:
-                if 'name' in field:
-                    del field['name']
-            if migrate_engine.name == 'mysql':
-                cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" % (dumps(fields_list), form_definition_id)
+                if "name" in field:
+                    del field["name"]
+            if migrate_engine.name == "mysql":
+                cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" % (
+                    dumps(fields_list),
+                    form_definition_id,
+                )
             else:
                 cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" % (dumps(fields_list), form_definition_id)
         migrate_engine.execute(cmd)
diff --git a/lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py b/lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
index 9f21c92fd3d..4e1ec88f454 100644
--- a/lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
+++ b/lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
@@ -6,7 +6,14 @@ information.
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, Integer, MetaData, String, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    Integer,
+    MetaData,
+    String,
+    Table,
+)
 
 from galaxy.model.custom_types import JSONType
 
@@ -16,21 +23,27 @@ metadata = MetaData()
 
 # Table to add
 
-DeferredJob_table = Table("deferred_job", metadata,
-                          Column("id", Integer, primary_key=True),
-                          Column("create_time", DateTime, default=now),
-                          Column("update_time", DateTime, default=now, onupdate=now),
-                          Column("state", String(64), index=True),
-                          Column("plugin", String(128), index=True),
-                          Column("params", JSONType))
+DeferredJob_table = Table(
+    "deferred_job",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("state", String(64), index=True),
+    Column("plugin", String(128), index=True),
+    Column("params", JSONType),
+)
 
-TransferJob_table = Table("transfer_job", metadata,
-                          Column("id", Integer, primary_key=True),
-                          Column("create_time", DateTime, default=now),
-                          Column("update_time", DateTime, default=now, onupdate=now),
-                          Column("state", String(64), index=True),
-                          Column("path", String(1024)),
-                          Column("params", JSONType))
+TransferJob_table = Table(
+    "transfer_job",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("state", String(64), index=True),
+    Column("path", String(1024)),
+    Column("params", JSONType),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py b/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
index b23a3907299..4ed8cfa7c30 100644
--- a/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
+++ b/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
@@ -6,14 +6,17 @@ actual contents of the datatx_info column are stored as form_values.
 """
 
 import logging
-from json import dumps, loads
+from json import (
+    dumps,
+    loads,
+)
 
 from sqlalchemy import (
     Column,
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import JSONType
@@ -22,7 +25,7 @@ from galaxy.model.migrate.versions.util import (
     drop_column,
     engine_false,
     localtimestamp,
-    nextval
+    nextval,
 )
 
 log = logging.getLogger(__name__)
@@ -35,78 +38,96 @@ def get_latest_id(migrate_engine, table):
     if row:
         return row[0]
     else:
-        raise Exception(f'Unable to get the latest id in the {table} table.')
+        raise Exception(f"Unable to get the latest id in the {table} table.")
 
 
 def create_sequencer_form_definition(migrate_engine):
-    '''
+    """
     Create a new form_definition containing 5 fields (host, username, password,
     data_dir & rename_datasets) which described the existing datatx_info json
     dict in the request_type table
-    '''
+    """
     # create new form_definition_current in the db
     cmd = "INSERT INTO form_definition_current VALUES ( {}, {}, {}, {}, {} )".format(
-        nextval(migrate_engine, 'form_definition_current'),
+        nextval(migrate_engine, "form_definition_current"),
         localtimestamp(migrate_engine),
         localtimestamp(migrate_engine),
-        'NULL',
-        engine_false(migrate_engine))
+        "NULL",
+        engine_false(migrate_engine),
+    )
     migrate_engine.execute(cmd)
     # get this form_definition_current id
-    form_definition_current_id = get_latest_id(migrate_engine, 'form_definition_current')
+    form_definition_current_id = get_latest_id(migrate_engine, "form_definition_current")
     # create new form_definition in the db
-    form_definition_name = 'Generic sequencer form'
-    form_definition_desc = ''
+    form_definition_name = "Generic sequencer form"
+    form_definition_desc = ""
     form_definition_fields = []
-    fields = [('Host', 'TextField'),
-              ('User name', 'TextField'),
-              ('Password', 'PasswordField'),
-              ('Data directory', 'TextField')]
+    fields = [
+        ("Host", "TextField"),
+        ("User name", "TextField"),
+        ("Password", "PasswordField"),
+        ("Data directory", "TextField"),
+    ]
     for index, (label, field_type) in enumerate(fields):
-        form_definition_fields.append({'name': 'field_%i' % index,
-                                       'label': label,
-                                       'helptext': '',
-                                       'visible': True,
-                                       'required': False,
-                                       'type': field_type,
-                                       'selectlist': [],
-                                       'layout': 'none',
-                                       'default': ''})
-    form_definition_fields.append({'name': 'field_%i' % len(fields),
-                                   'label': 'Prepend the experiment name and sample name to the dataset name?',
-                                   'helptext': 'Galaxy datasets are renamed by prepending the experiment name and sample name to the dataset name, ensuring dataset names remain unique in Galaxy even when multiple datasets have the same name on the sequencer.',
-                                   'visible': True,
-                                   'required': False,
-                                   'type': 'SelectField',
-                                   'selectlist': ['Do not rename',
-                                                  'Preprend sample name',
-                                                  'Prepend experiment name',
-                                                  'Prepend experiment and sample name'],
-                                   'layout': 'none',
-                                   'default': ''})
-    form_definition_type = 'Sequencer Information Form'
-    form_definition_layout = dumps('[]')
+        form_definition_fields.append(
+            {
+                "name": "field_%i" % index,
+                "label": label,
+                "helptext": "",
+                "visible": True,
+                "required": False,
+                "type": field_type,
+                "selectlist": [],
+                "layout": "none",
+                "default": "",
+            }
+        )
+    form_definition_fields.append(
+        {
+            "name": "field_%i" % len(fields),
+            "label": "Prepend the experiment name and sample name to the dataset name?",
+            "helptext": "Galaxy datasets are renamed by prepending the experiment name and sample name to the dataset name, ensuring dataset names remain unique in Galaxy even when multiple datasets have the same name on the sequencer.",
+            "visible": True,
+            "required": False,
+            "type": "SelectField",
+            "selectlist": [
+                "Do not rename",
+                "Preprend sample name",
+                "Prepend experiment name",
+                "Prepend experiment and sample name",
+            ],
+            "layout": "none",
+            "default": "",
+        }
+    )
+    form_definition_type = "Sequencer Information Form"
+    form_definition_layout = dumps("[]")
     cmd = "INSERT INTO form_definition VALUES ( %s, %s, %s, '%s', '%s', %s, '%s', '%s', '%s' )"
-    cmd = cmd % (nextval(migrate_engine, 'form_definition'),
-                 localtimestamp(migrate_engine),
-                 localtimestamp(migrate_engine),
-                 form_definition_name,
-                 form_definition_desc,
-                 form_definition_current_id,
-                 dumps(form_definition_fields),
-                 form_definition_type,
-                 form_definition_layout)
+    cmd = cmd % (
+        nextval(migrate_engine, "form_definition"),
+        localtimestamp(migrate_engine),
+        localtimestamp(migrate_engine),
+        form_definition_name,
+        form_definition_desc,
+        form_definition_current_id,
+        dumps(form_definition_fields),
+        form_definition_type,
+        form_definition_layout,
+    )
     migrate_engine.execute(cmd)
     # get this form_definition id
-    form_definition_id = get_latest_id(migrate_engine, 'form_definition')
+    form_definition_id = get_latest_id(migrate_engine, "form_definition")
     # update the form_definition_id column in form_definition_current
-    cmd = "UPDATE form_definition_current SET latest_form_id=%i WHERE id=%i" % (form_definition_id, form_definition_current_id)
+    cmd = "UPDATE form_definition_current SET latest_form_id=%i WHERE id=%i" % (
+        form_definition_id,
+        form_definition_current_id,
+    )
     migrate_engine.execute(cmd)
     return form_definition_id
 
 
 def get_sequencer_id(migrate_engine, sequencer_info):
-    '''Get the sequencer id corresponding to the sequencer information'''
+    """Get the sequencer id corresponding to the sequencer information"""
     # Check if there is any existing sequencer which have the same sequencer
     # information fields & values
     cmd = "SELECT sequencer.id, form_values.content FROM sequencer, form_values WHERE sequencer.form_values_id=form_values.id"
@@ -119,37 +140,45 @@ def get_sequencer_id(migrate_engine, sequencer_info):
         values = loads(values)
         # proceed only if sequencer_info is a valid list
         if values and isinstance(values, dict):
-            if sequencer_info.get('host', '') == values.get('field_0', '') \
-               and sequencer_info.get('username', '') == values.get('field_1', '') \
-               and sequencer_info.get('password', '') == values.get('field_2', '') \
-               and sequencer_info.get('data_dir', '') == values.get('field_3', '') \
-               and sequencer_info.get('rename_dataset', '') == values.get('field_4', ''):
+            if (
+                sequencer_info.get("host", "") == values.get("field_0", "")
+                and sequencer_info.get("username", "") == values.get("field_1", "")
+                and sequencer_info.get("password", "") == values.get("field_2", "")
+                and sequencer_info.get("data_dir", "") == values.get("field_3", "")
+                and sequencer_info.get("rename_dataset", "") == values.get("field_4", "")
+            ):
                 return sequencer_id
     return None
 
 
 def add_sequencer(migrate_engine, sequencer_index, sequencer_form_definition_id, sequencer_info):
-    '''Adds a new sequencer to the sequencer table along with its form values.'''
+    """Adds a new sequencer to the sequencer table along with its form values."""
     # Create a new form values record with the supplied sequencer information
-    values = dumps({'field_0': sequencer_info.get('host', ''),
-                    'field_1': sequencer_info.get('username', ''),
-                    'field_2': sequencer_info.get('password', ''),
-                    'field_3': sequencer_info.get('data_dir', ''),
-                    'field_4': sequencer_info.get('rename_dataset', '')})
-    cmd = "INSERT INTO form_values VALUES ( {}, {}, {}, {}, '{}' )".format(nextval(migrate_engine, 'form_values'),
-                                                                       localtimestamp(migrate_engine),
-                                                                       localtimestamp(migrate_engine),
-                                                                       sequencer_form_definition_id,
-                                                                       values)
+    values = dumps(
+        {
+            "field_0": sequencer_info.get("host", ""),
+            "field_1": sequencer_info.get("username", ""),
+            "field_2": sequencer_info.get("password", ""),
+            "field_3": sequencer_info.get("data_dir", ""),
+            "field_4": sequencer_info.get("rename_dataset", ""),
+        }
+    )
+    cmd = "INSERT INTO form_values VALUES ( {}, {}, {}, {}, '{}' )".format(
+        nextval(migrate_engine, "form_values"),
+        localtimestamp(migrate_engine),
+        localtimestamp(migrate_engine),
+        sequencer_form_definition_id,
+        values,
+    )
     migrate_engine.execute(cmd)
-    sequencer_form_values_id = get_latest_id(migrate_engine, 'form_values')
+    sequencer_form_values_id = get_latest_id(migrate_engine, "form_values")
     # Create a new sequencer record with reference to the form value created above.
-    name = 'Sequencer_%i' % sequencer_index
-    desc = ''
-    version = ''
-    sequencer_type_id = 'simple_unknown_sequencer'
+    name = "Sequencer_%i" % sequencer_index
+    desc = ""
+    version = ""
+    sequencer_type_id = "simple_unknown_sequencer"
     cmd = "INSERT INTO sequencer VALUES ( {}, {}, {}, '{}', '{}', '{}', '{}', {}, {}, {} )".format(
-        nextval(migrate_engine, 'sequencer'),
+        nextval(migrate_engine, "sequencer"),
         localtimestamp(migrate_engine),
         localtimestamp(migrate_engine),
         name,
@@ -158,13 +187,14 @@ def add_sequencer(migrate_engine, sequencer_index, sequencer_form_definition_id,
         version,
         sequencer_form_definition_id,
         sequencer_form_values_id,
-        engine_false(migrate_engine))
+        engine_false(migrate_engine),
+    )
     migrate_engine.execute(cmd)
-    return get_latest_id(migrate_engine, 'sequencer')
+    return get_latest_id(migrate_engine, "sequencer")
 
 
 def update_sequencer_id_in_request_type(migrate_engine, request_type_id, sequencer_id):
-    '''Update the foreign key to the sequencer table in the request_type table'''
+    """Update the foreign key to the sequencer table in the request_type table"""
     cmd = "UPDATE request_type SET sequencer_id=%i WHERE id=%i" % (sequencer_id, request_type_id)
     migrate_engine.execute(cmd)
 
@@ -197,7 +227,7 @@ def upgrade(migrate_engine):
             request_type_id = row[0]
             sequencer_info = str(row[2])  # datatx_info column
             # skip if sequencer_info is empty
-            if not sequencer_info.strip() or sequencer_info in ['None', 'null']:
+            if not sequencer_info.strip() or sequencer_info in ["None", "null"]:
                 continue
             sequencer_info = loads(sequencer_info.strip())
             # proceed only if sequencer_info is a valid dict
@@ -206,13 +236,15 @@ def upgrade(migrate_engine):
                 sequencer_id = get_sequencer_id(migrate_engine, sequencer_info)
                 if not sequencer_id:
                     # add to the sequencer table
-                    sequencer_id = add_sequencer(migrate_engine, sequencer_index, sequencer_form_definition_id, sequencer_info)
+                    sequencer_id = add_sequencer(
+                        migrate_engine, sequencer_index, sequencer_form_definition_id, sequencer_info
+                    )
                 # now update the sequencer_id column in request_type table
                 update_sequencer_id_in_request_type(migrate_engine, request_type_id, sequencer_id)
                 sequencer_index = sequencer_index + 1
 
     # Finally delete the 'datatx_info' column from the request_type table
-    drop_column('datatx_info', RequestType_table)
+    drop_column("datatx_info", RequestType_table)
 
 
 def downgrade(migrate_engine):
@@ -225,22 +257,28 @@ def downgrade(migrate_engine):
     add_column(col, RequestType_table, metadata)
     # restore the datatx_info column data in the request_type table with data from
     # the sequencer and the form_values table
-    cmd = "SELECT request_type.id, form_values.content "\
-          + " FROM request_type, sequencer, form_values "\
-          + " WHERE request_type.sequencer_id=sequencer.id AND sequencer.form_values_id=form_values.id "\
-          + " ORDER  BY request_type.id ASC"
+    cmd = (
+        "SELECT request_type.id, form_values.content "
+        + " FROM request_type, sequencer, form_values "
+        + " WHERE request_type.sequencer_id=sequencer.id AND sequencer.form_values_id=form_values.id "
+        + " ORDER  BY request_type.id ASC"
+    )
     result = migrate_engine.execute(cmd)
     for row in result:
         request_type_id = row[0]
         seq_values = loads(str(row[1]))
         # create the datatx_info json dict
-        datatx_info = dumps(dict(host=seq_values.get('field_0', ''),
-                                 username=seq_values.get('field_1', ''),
-                                 password=seq_values.get('field_2', ''),
-                                 data_dir=seq_values.get('field_3', ''),
-                                 rename_dataset=seq_values.get('field_4', '')))
+        datatx_info = dumps(
+            dict(
+                host=seq_values.get("field_0", ""),
+                username=seq_values.get("field_1", ""),
+                password=seq_values.get("field_2", ""),
+                data_dir=seq_values.get("field_3", ""),
+                rename_dataset=seq_values.get("field_4", ""),
+            )
+        )
         # update the column
         cmd = "UPDATE request_type SET datatx_info='%s' WHERE id=%i" % (datatx_info, request_type_id)
         migrate_engine.execute(cmd)
     # delete foreign key field to the sequencer table in the request_type table
-    drop_column('sequencer_id', RequestType_table)
+    drop_column("sequencer_id", RequestType_table)
diff --git a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
index c9dcb3904da..cef6baa7ca3 100644
--- a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
+++ b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
@@ -15,7 +15,7 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -24,7 +24,7 @@ from galaxy.model.migrate.versions.util import (
     create_table,
     drop_column,
     drop_table,
-    nextval
+    nextval,
 )
 
 now = datetime.datetime.utcnow
@@ -39,23 +39,30 @@ def upgrade(migrate_engine):
 
     # rename 'sequencer' table to 'external_service'
     Sequencer_table = Table("sequencer", metadata, autoload=True)
-    Sequencer_table.rename('external_service')
+    Sequencer_table.rename("external_service")
 
     # if running PostgreSQL, rename the primary key sequence too
-    if migrate_engine.name in ['postgres', 'postgresql']:
+    if migrate_engine.name in ["postgres", "postgresql"]:
         cmd = "ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_id_seq"
         migrate_engine.execute(cmd)
 
     # Add 'external_services_id' column to 'sample_dataset' table
     SampleDataset_table = Table("sample_dataset", metadata, autoload=True)
-    col = Column("external_service_id", Integer, ForeignKey("external_service.id", name='sample_dataset_external_services_id_fk'), index=True)
+    col = Column(
+        "external_service_id",
+        Integer,
+        ForeignKey("external_service.id", name="sample_dataset_external_services_id_fk"),
+        index=True,
+    )
     add_column(col, SampleDataset_table, metadata, index_name="ix_sample_dataset_external_service_id")
 
     # populate the column
-    cmd = "SELECT sample_dataset.id, request_type.sequencer_id " \
-          + " FROM sample_dataset, sample, request, request_type " \
-          + " WHERE sample.id=sample_dataset.sample_id and request.id=sample.request_id and request.request_type_id=request_type.id " \
-          + " ORDER BY sample_dataset.id"
+    cmd = (
+        "SELECT sample_dataset.id, request_type.sequencer_id "
+        + " FROM sample_dataset, sample, request, request_type "
+        + " WHERE sample.id=sample_dataset.sample_id and request.id=sample.request_id and request.request_type_id=request_type.id "
+        + " ORDER BY sample_dataset.id"
+    )
     try:
         result = migrate_engine.execute(cmd)
         for r in result:
@@ -77,13 +84,16 @@ def upgrade(migrate_engine):
     migrate_engine.execute(cmd)
 
     # remove the 'sequencer_type_id' column
-    drop_column('sequencer_type_id', ExternalServices_table)
+    drop_column("sequencer_type_id", ExternalServices_table)
 
     # create 'request_type_external_service_association' table
-    RequestTypeExternalServiceAssociation_table = Table("request_type_external_service_association", metadata,
-                                                        Column("id", Integer, primary_key=True),
-                                                        Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
-                                                        Column("external_service_id", Integer, ForeignKey("external_service.id"), index=True))
+    RequestTypeExternalServiceAssociation_table = Table(
+        "request_type_external_service_association",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True),
+        Column("external_service_id", Integer, ForeignKey("external_service.id"), index=True),
+    )
     create_table(RequestTypeExternalServiceAssociation_table)
 
     # populate 'request_type_external_service_association' table
@@ -95,15 +105,14 @@ def upgrade(migrate_engine):
         request_type_id = row[0]
         sequencer_id = row[1]
         if not sequencer_id:
-            sequencer_id = 'null'
+            sequencer_id = "null"
         cmd = "INSERT INTO request_type_external_service_association VALUES ( {}, {}, {} )".format(
-            nextval(migrate_engine, 'request_type_external_service_association'),
-            request_type_id,
-            sequencer_id)
+            nextval(migrate_engine, "request_type_external_service_association"), request_type_id, sequencer_id
+        )
         migrate_engine.execute(cmd)
 
     # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first.
-    drop_column('sequencer_id', 'request_type', metadata)
+    drop_column("sequencer_id", "request_type", metadata)
 
 
 def downgrade(migrate_engine):
@@ -114,16 +123,16 @@ def downgrade(migrate_engine):
     # table is renamed, so we start with the table rename.
     # rename the 'external_service' table to 'sequencer'
     ExternalServices_table = Table("external_service", metadata, autoload=True)
-    ExternalServices_table.rename('sequencer')
+    ExternalServices_table.rename("sequencer")
 
     # if running PostgreSQL, rename the primary key sequence too
-    if migrate_engine.name in ['postgres', 'postgresql']:
+    if migrate_engine.name in ["postgres", "postgresql"]:
         cmd = "ALTER SEQUENCE external_service_id_seq RENAME TO sequencer_id_seq"
         migrate_engine.execute(cmd)
 
     # create the 'sequencer_id' column in the 'request_type' table
     col = Column("sequencer_id", Integer, ForeignKey("sequencer.id"), nullable=True)
-    add_column(col, 'request_type', metadata)
+    add_column(col, "request_type", metadata)
 
     # populate 'sequencer_id' column in the 'request_type' table from the
     # 'request_type_external_service_association' table
@@ -137,7 +146,9 @@ def downgrade(migrate_engine):
         migrate_engine.execute(cmd)
 
     # remove the 'request_type_external_service_association' table
-    RequestTypeExternalServiceAssociation_table = Table("request_type_external_service_association", metadata, autoload=True)
+    RequestTypeExternalServiceAssociation_table = Table(
+        "request_type_external_service_association", metadata, autoload=True
+    )
     drop_table(RequestTypeExternalServiceAssociation_table)
 
     # rename 'external_service_type_id' column to 'sequencer_type_id' in the table 'sequencer'
@@ -151,7 +162,7 @@ def downgrade(migrate_engine):
     migrate_engine.execute(cmd)
 
     # remove the 'external_service_type_id' column
-    drop_column('external_service_type_id', Sequencer_table)
+    drop_column("external_service_type_id", Sequencer_table)
 
     # drop the 'external_service_id' column in the 'sample_dataset' table
-    drop_column('external_service_id', 'sample_dataset', metadata)
+    drop_column("external_service_id", "sample_dataset", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py b/lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
index 51175dd1441..a005987cabc 100644
--- a/lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
+++ b/lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
@@ -14,7 +14,7 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     print(__doc__)
     metadata.reflect()
-    current_form_type = 'Sequencer Information Form'
+    current_form_type = "Sequencer Information Form"
     new_form_type = "External Service Information Form"
     cmd = f"update form_definition set type='{new_form_type}' where type='{current_form_type}'"
     migrate_engine.execute(cmd)
@@ -23,7 +23,7 @@ def upgrade(migrate_engine):
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
-    new_form_type = 'Sequencer Information Form'
+    new_form_type = "Sequencer Information Form"
     current_form_type = "External Service Information Form"
     cmd = f"update form_definition set type='{new_form_type}' where type='{current_form_type}'"
     migrate_engine.execute(cmd)
diff --git a/lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py b/lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
index 6153a5b1878..64826809bb5 100644
--- a/lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
+++ b/lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
@@ -4,7 +4,12 @@ Migration script to add 'info' column to the transfer_job table.
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py b/lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
index 110c2911c41..97b11977d80 100644
--- a/lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
+++ b/lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
@@ -4,10 +4,19 @@ Migration script to add 'workflow' and 'history' columns for a sample.
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import JSONType
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -31,5 +40,5 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     Sample_table = Table("sample", metadata, autoload=True)
-    drop_column('workflow', Sample_table)
-    drop_column('history_id', Sample_table)
+    drop_column("workflow", Sample_table)
+    drop_column("history_id", Sample_table)
diff --git a/lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py b/lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
index 8dd4ddee3e4..d7b5c7904f9 100644
--- a/lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
+++ b/lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
@@ -4,7 +4,12 @@ Migration script to add 'pid' and 'socket' columns to the transfer_job table.
 
 import logging
 
-from sqlalchemy import Column, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py b/lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
index b1f8b3c15dd..ebc8f3f50c5 100644
--- a/lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
+++ b/lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
@@ -8,12 +8,12 @@ from sqlalchemy import (
     Column,
     ForeignKey,
     Integer,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -25,12 +25,19 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    c = Column("ldda_parent_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
-    add_column(c, 'implicitly_converted_dataset_association', metadata, index_name='ix_implicitly_converted_dataset_assoc_ldda_parent_id')
+    c = Column(
+        "ldda_parent_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True
+    )
+    add_column(
+        c,
+        "implicitly_converted_dataset_association",
+        metadata,
+        index_name="ix_implicitly_converted_dataset_assoc_ldda_parent_id",
+    )
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('ldda_parent_id', 'implicitly_converted_dataset_association', metadata)
+    drop_column("ldda_parent_id", "implicitly_converted_dataset_association", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py b/lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
index 71c465bfc08..9284f3a179f 100644
--- a/lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
+++ b/lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
@@ -4,9 +4,18 @@ Migration script to add 'purged' column to the library_dataset table.
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column, engine_false, engine_true
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+    engine_false,
+    engine_true,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -17,8 +26,8 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    c = Column('purged', Boolean, index=True, default=False)
-    add_column(c, 'library_dataset', metadata, index_name='ix_library_dataset_purged')
+    c = Column("purged", Boolean, index=True, default=False)
+    add_column(c, "library_dataset", metadata, index_name="ix_library_dataset_purged")
     # Update the purged flag to the default False
     cmd = f"UPDATE library_dataset SET purged = {engine_false(migrate_engine)};"
     try:
@@ -31,7 +40,10 @@ def upgrade(migrate_engine):
     cmd = f"SELECT * FROM library_dataset WHERE deleted = {engine_true(migrate_engine)};"
     deleted_lds = migrate_engine.execute(cmd).fetchall()
     for row in deleted_lds:
-        cmd = "SELECT * FROM library_dataset_dataset_association WHERE library_dataset_id = %d AND library_dataset_dataset_association.deleted = %s;" % (int(row.id), engine_false(migrate_engine))
+        cmd = (
+            "SELECT * FROM library_dataset_dataset_association WHERE library_dataset_id = %d AND library_dataset_dataset_association.deleted = %s;"
+            % (int(row.id), engine_false(migrate_engine))
+        )
         active_lddas = migrate_engine.execute(cmd).fetchall()
         if not active_lddas:
             print("Updating purged column to True for LibraryDataset id : ", int(row.id))
@@ -44,5 +56,5 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('purged', 'library_dataset', metadata)
+    if migrate_engine.name != "sqlite":
+        drop_column("purged", "library_dataset", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py b/lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
index 26f87361106..536682a913d 100644
--- a/lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
+++ b/lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
@@ -4,7 +4,11 @@ Migration script to add a 'subindex' column to the run table.
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
diff --git a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
index fad58b7507e..f0d43923041 100644
--- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
+++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
@@ -1,10 +1,13 @@
-'''
+"""
 This migration script fixes the data corruption caused in the form_values
 table (content json field) by migrate script 65.
-'''
+"""
 
 import logging
-from json import dumps, loads
+from json import (
+    dumps,
+    loads,
+)
 
 from sqlalchemy import MetaData
 
@@ -18,22 +21,24 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     print(__doc__)
     metadata.reflect()
-    cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fdfields " \
-          + " FROM form_definition, form_values " \
-          + " WHERE form_values.form_definition_id=form_definition.id " \
-          + " ORDER BY form_values.id"
+    cmd = (
+        "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fdfields "
+        + " FROM form_definition, form_values "
+        + " WHERE form_values.form_definition_id=form_definition.id "
+        + " ORDER BY form_values.id"
+    )
     result = migrate_engine.execute(cmd)
     corrupted_rows = 0
     for row in result:
         # first check if loading the dict from the json succeeds
         # if that fails, it means that the content field is corrupted.
         try:
-            field_values_dict = loads(_sniffnfix_pg9_hex(str(row['field_values'])))
+            field_values_dict = loads(_sniffnfix_pg9_hex(str(row["field_values"])))
         except Exception:
             corrupted_rows = corrupted_rows + 1
             # content field is corrupted
-            fields_list = loads(_sniffnfix_pg9_hex(str(row['fdfields'])))
-            field_values_str = _sniffnfix_pg9_hex(str(row['field_values']))
+            fields_list = loads(_sniffnfix_pg9_hex(str(row["fdfields"])))
+            field_values_str = _sniffnfix_pg9_hex(str(row["field_values"]))
             try:
                 # Encoding errors?  Just to be safe.
                 print(f"Attempting to fix row {row['id']}")
@@ -49,39 +54,44 @@ def upgrade(migrate_engine):
                 if field_index == -1:
                     # if the field name is not present the field values dict then
                     # inform the admin that this form values cannot be fixed
-                    print("The 'content' field of row 'id' %i does not have the field '%s' in the 'form_values' table and could not be fixed by this migration script." % (int(field['id']), field['name']))
+                    print(
+                        "The 'content' field of row 'id' %i does not have the field '%s' in the 'form_values' table and could not be fixed by this migration script."
+                        % (int(field["id"]), field["name"])
+                    )
                 else:
                     # check if this is the last field
                     if index == len(fields_list) - 1:
                         # since this is the last field, the value string lies between the
                         # field name and the '"}' string at the end, hence len(field_values_str) - 2
-                        value = field_values_str[field_index + len(field_name_key):len(field_values_str) - 2]
+                        value = field_values_str[field_index + len(field_name_key) : len(field_values_str) - 2]
                     else:
                         # if this is not the last field then the value string lies between
                         # this field name and the next field name
                         next_field = fields_list[index + 1]
                         next_field_index = field_values_str.find(f"\", \"{next_field['name']}\": \"")
-                        value = field_values_str[field_index + len(field_name_key):next_field_index]
+                        value = field_values_str[field_index + len(field_name_key) : next_field_index]
                     # clean up the value string, escape the required quoutes and newline characters
-                    value = value.replace("'", "\''")\
-                                 .replace('"', '\\\\"')\
-                                 .replace('\r', "\\\\r")\
-                                 .replace('\n', "\\\\n")\
-                                 .replace('\t', "\\\\t")
+                    value = (
+                        value.replace("'", "''")
+                        .replace('"', '\\\\"')
+                        .replace("\r", "\\\\r")
+                        .replace("\n", "\\\\n")
+                        .replace("\t", "\\\\t")
+                    )
                     # add to the new values dict
-                    field_values_dict[field['name']] = value
+                    field_values_dict[field["name"]] = value
             # update the db
             json_values = dumps(field_values_dict)
-            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" % (json_values, int(row['id']))
+            cmd = "UPDATE form_values SET content='%s' WHERE id=%i" % (json_values, int(row["id"]))
             migrate_engine.execute(cmd)
             try:
                 print(f"Post replacement: {json_values}")
             except Exception:
                 pass
     if corrupted_rows:
-        print('Fixed %i corrupted rows.' % corrupted_rows)
+        print("Fixed %i corrupted rows." % corrupted_rows)
     else:
-        print('No corrupted rows found.')
+        print("No corrupted rows found.")
 
 
 def downgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py b/lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
index e61e108b13d..58763437c8c 100644
--- a/lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
+++ b/lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
@@ -4,7 +4,13 @@ Migration script to create table for storing tool tag associations.
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
@@ -13,14 +19,17 @@ metadata = MetaData()
 
 # Table to add
 
-ToolTagAssociation_table = Table("tool_tag_association", metadata,
-                                 Column("id", Integer, primary_key=True),
-                                 Column("tool_id", TrimmedString(255), index=True),
-                                 Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                 Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                 Column("user_tname", TrimmedString(255), index=True),
-                                 Column("value", TrimmedString(255), index=True),
-                                 Column("user_value", TrimmedString(255), index=True))
+ToolTagAssociation_table = Table(
+    "tool_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("tool_id", TrimmedString(255), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py b/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
index 87400587533..cab4ea2bf6f 100644
--- a/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
+++ b/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
@@ -6,9 +6,18 @@ tables.
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData, Numeric, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Numeric,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -19,8 +28,8 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    c = Column('total_size', Numeric(15, 0))
-    add_column(c, 'dataset', metadata)
+    c = Column("total_size", Numeric(15, 0))
+    add_column(c, "dataset", metadata)
 
     HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True)
     c = Column("purged", Boolean, index=True, default=False)
@@ -30,22 +39,22 @@ def upgrade(migrate_engine):
     except Exception:
         log.exception("Updating column 'purged' of table 'history_dataset_association' failed.")
 
-    c = Column('disk_usage', Numeric(15, 0), index=True)
-    add_column(c, 'galaxy_user', metadata, index_name="ix_galaxy_user_disk_usage")
+    c = Column("disk_usage", Numeric(15, 0), index=True)
+    add_column(c, "galaxy_user", metadata, index_name="ix_galaxy_user_disk_usage")
 
-    c = Column('disk_usage', Numeric(15, 0), index=True)
-    add_column(c, 'galaxy_session', metadata, index_name="ix_galaxy_session_disk_usage")
+    c = Column("disk_usage", Numeric(15, 0), index=True)
+    add_column(c, "galaxy_session", metadata, index_name="ix_galaxy_session_disk_usage")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('disk_usage', 'galaxy_session', metadata)
-    drop_column('disk_usage', 'galaxy_user', metadata)
+    drop_column("disk_usage", "galaxy_session", metadata)
+    drop_column("disk_usage", "galaxy_user", metadata)
 
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('purged', 'history_dataset_association', metadata)
+    if migrate_engine.name != "sqlite":
+        drop_column("purged", "history_dataset_association", metadata)
 
-    drop_column('total_size', 'dataset', metadata)
+    drop_column("total_size", "dataset", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py b/lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
index 6dd1e4f05d8..5ddfb97d613 100644
--- a/lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
+++ b/lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
@@ -4,17 +4,27 @@ Migration script to add the job_to_input_library_dataset table.
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, String, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 
 metadata = MetaData()
 
-JobToInputLibraryDatasetAssociation_table = Table("job_to_input_library_dataset", metadata,
-                                                  Column("id", Integer, primary_key=True),
-                                                  Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                                                  Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True),
-                                                  Column("name", String(255)))
+JobToInputLibraryDatasetAssociation_table = Table(
+    "job_to_input_library_dataset",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True),
+    Column("name", String(255)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0080_quota_tables.py b/lib/galaxy/model/migrate/versions/0080_quota_tables.py
index a4d356da6d5..0973ea2ea0c 100644
--- a/lib/galaxy/model/migrate/versions/0080_quota_tables.py
+++ b/lib/galaxy/model/migrate/versions/0080_quota_tables.py
@@ -5,7 +5,18 @@ Migration script to create tables for disk quotas.
 import datetime
 import logging
 
-from sqlalchemy import BigInteger, Boolean, Column, DateTime, ForeignKey, Integer, MetaData, String, Table, TEXT
+from sqlalchemy import (
+    BigInteger,
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+    TEXT,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -13,36 +24,48 @@ metadata = MetaData()
 
 # Tables to add
 
-Quota_table = Table("quota", metadata,
-                    Column("id", Integer, primary_key=True),
-                    Column("create_time", DateTime, default=now),
-                    Column("update_time", DateTime, default=now, onupdate=now),
-                    Column("name", String(255), index=True, unique=True),
-                    Column("description", TEXT),
-                    Column("bytes", BigInteger),
-                    Column("operation", String(8)),
-                    Column("deleted", Boolean, index=True, default=False))
+Quota_table = Table(
+    "quota",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", String(255), index=True, unique=True),
+    Column("description", TEXT),
+    Column("bytes", BigInteger),
+    Column("operation", String(8)),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-UserQuotaAssociation_table = Table("user_quota_association", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                   Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
-                                   Column("create_time", DateTime, default=now),
-                                   Column("update_time", DateTime, default=now, onupdate=now))
+UserQuotaAssociation_table = Table(
+    "user_quota_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-GroupQuotaAssociation_table = Table("group_quota_association", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
-                                    Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
-                                    Column("create_time", DateTime, default=now),
-                                    Column("update_time", DateTime, default=now, onupdate=now))
+GroupQuotaAssociation_table = Table(
+    "group_quota_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
+    Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-DefaultQuotaAssociation_table = Table("default_quota_association", metadata,
-                                      Column("id", Integer, primary_key=True),
-                                      Column("create_time", DateTime, default=now),
-                                      Column("update_time", DateTime, default=now, onupdate=now),
-                                      Column("type", String(32), index=True, unique=True),
-                                      Column("quota_id", Integer, ForeignKey("quota.id"), index=True))
+DefaultQuotaAssociation_table = Table(
+    "default_quota_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("type", String(32), index=True, unique=True),
+    Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py b/lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
index 2367be206d4..040f7e62967 100644
--- a/lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
+++ b/lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
@@ -4,7 +4,12 @@ Migration script to add a 'tool_version' column to the hda/ldda tables.
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py b/lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
index 3d5749ea825..52acd68fd13 100644
--- a/lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
+++ b/lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
@@ -12,13 +12,13 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -26,16 +26,19 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 # New table to store information about cloned tool shed repositories.
-ToolShedRepository_table = Table("tool_shed_repository", metadata,
-                                 Column("id", Integer, primary_key=True),
-                                 Column("create_time", DateTime, default=now),
-                                 Column("update_time", DateTime, default=now, onupdate=now),
-                                 Column("tool_shed", TrimmedString(255), index=True),
-                                 Column("name", TrimmedString(255), index=True),
-                                 Column("description", TEXT),
-                                 Column("owner", TrimmedString(255), index=True),
-                                 Column("changeset_revision", TrimmedString(255), index=True),
-                                 Column("deleted", Boolean, index=True, default=False))
+ToolShedRepository_table = Table(
+    "tool_shed_repository",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("tool_shed", TrimmedString(255), index=True),
+    Column("name", TrimmedString(255), index=True),
+    Column("description", TEXT),
+    Column("owner", TrimmedString(255), index=True),
+    Column("changeset_revision", TrimmedString(255), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py b/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
index bf45eb2667b..d37b17c6829 100644
--- a/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
+++ b/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
@@ -4,9 +4,18 @@ Migration script to add 'prepare_input_files_cmd' column to the task table and t
 
 import logging
 
-from sqlalchemy import Column, MetaData, String, Table, TEXT
+from sqlalchemy import (
+    Column,
+    MetaData,
+    String,
+    Table,
+    TEXT,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -25,7 +34,7 @@ def upgrade(migrate_engine):
     add_column(c, task_table, metadata)
 
     # remove the 'part_file' column - nobody used tasks before this, so no data needs to be migrated
-    drop_column('part_file', task_table)
+    drop_column("part_file", task_table)
 
 
 def downgrade(migrate_engine):
@@ -36,5 +45,5 @@ def downgrade(migrate_engine):
     c = Column("part_file", String(1024), nullable=True)
     add_column(c, task_table, metadata)
 
-    drop_column('working_directory', task_table)
-    drop_column('prepare_input_files_cmd', task_table)
+    drop_column("working_directory", task_table)
+    drop_column("prepare_input_files_cmd", task_table)
diff --git a/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py b/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
index bcc882ff7ba..770e715c7bb 100644
--- a/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
+++ b/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
@@ -8,12 +8,12 @@ from sqlalchemy import (
     Column,
     ForeignKey,
     Integer,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -26,11 +26,13 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     c = Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True)
-    add_column(c, 'implicitly_converted_dataset_association', metadata, index_name='ix_implicitly_converted_ds_assoc_ldda_id')
+    add_column(
+        c, "implicitly_converted_dataset_association", metadata, index_name="ix_implicitly_converted_ds_assoc_ldda_id"
+    )
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('ldda_id', 'implicitly_converted_dataset_association', metadata)
+    drop_column("ldda_id", "implicitly_converted_dataset_association", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0085_add_task_info.py b/lib/galaxy/model/migrate/versions/0085_add_task_info.py
index e45bf1f869b..289188cb6e4 100644
--- a/lib/galaxy/model/migrate/versions/0085_add_task_info.py
+++ b/lib/galaxy/model/migrate/versions/0085_add_task_info.py
@@ -4,7 +4,11 @@ Migration script to add 'info' column to the task table.
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
diff --git a/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py b/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
index d916fac0476..168e21d9d42 100644
--- a/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
+++ b/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
@@ -8,14 +8,14 @@ from sqlalchemy import (
     Boolean,
     Column,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     add_column,
     drop_column,
-    engine_false
+    engine_false,
 )
 
 log = logging.getLogger(__name__)
@@ -49,8 +49,8 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     ToolShedRepository_table = Table("tool_shed_repository", metadata, autoload=True)
-    drop_column('metadata', ToolShedRepository_table)
+    drop_column("metadata", ToolShedRepository_table)
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('includes_datatypes', ToolShedRepository_table)
-        drop_column('update_available', ToolShedRepository_table)
+    if migrate_engine.name != "sqlite":
+        drop_column("includes_datatypes", ToolShedRepository_table)
+        drop_column("update_available", ToolShedRepository_table)
diff --git a/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py b/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
index 386ecb22501..056faf991f4 100644
--- a/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
+++ b/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
@@ -13,13 +13,13 @@ from sqlalchemy import (
     MetaData,
     String,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -27,7 +27,8 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 ToolIdGuidMap_table = Table(
-    "tool_id_guid_map", metadata,
+    "tool_id_guid_map",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
@@ -37,7 +38,7 @@ ToolIdGuidMap_table = Table(
     Column("repository_owner", TrimmedString(255)),
     Column("repository_name", TrimmedString(255)),
     Column("guid", TEXT),
-    Index('ix_tool_id_guid_map_guid', 'guid', unique=True, mysql_length=200),
+    Index("ix_tool_id_guid_map_guid", "guid", unique=True, mysql_length=200),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py b/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
index b4f806577b4..499e08d1ab0 100644
--- a/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
+++ b/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
@@ -6,13 +6,13 @@ import logging
 
 from sqlalchemy import (
     Column,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -25,29 +25,35 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     col = Column("installed_changeset_revision", TrimmedString(255))
-    add_column(col, 'tool_shed_repository', metadata)
+    add_column(col, "tool_shed_repository", metadata)
     # Update each row by setting the value of installed_changeset_revison to be the value of changeset_revision.
     # This will be problematic if the value of changeset_revision was updated to something other than the value
     # that it was when the repository was installed (because the install path determined in real time will attempt to
     # find the repository using the updated changeset_revison instead of the required installed_changeset_revision),
     # but at the time this script was written, this scenario is extremely unlikely.
-    cmd = "SELECT id AS id, " \
-        + "installed_changeset_revision AS installed_changeset_revision, " \
-        + "changeset_revision AS changeset_revision " \
+    cmd = (
+        "SELECT id AS id, "
+        + "installed_changeset_revision AS installed_changeset_revision, "
+        + "changeset_revision AS changeset_revision "
         + "FROM tool_shed_repository;"
+    )
     tool_shed_repositories = migrate_engine.execute(cmd).fetchall()
     update_count = 0
     for row in tool_shed_repositories:
-        cmd = "UPDATE tool_shed_repository " \
-            + f"SET installed_changeset_revision = '{row.changeset_revision}' " \
+        cmd = (
+            "UPDATE tool_shed_repository "
+            + f"SET installed_changeset_revision = '{row.changeset_revision}' "
             + f"WHERE changeset_revision = '{row.changeset_revision}';"
+        )
         migrate_engine.execute(cmd)
         update_count += 1
-    print("Updated the installed_changeset_revision column for ", update_count, " rows in the tool_shed_repository table.")
+    print(
+        "Updated the installed_changeset_revision column for ", update_count, " rows in the tool_shed_repository table."
+    )
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('installed_changeset_revision', 'tool_shed_repository', metadata)
+    drop_column("installed_changeset_revision", "tool_shed_repository", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py b/lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
index 660dbda7731..4b276f2215b 100644
--- a/lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
+++ b/lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
@@ -4,7 +4,11 @@ Migration script to add 'object_store_id' column to various tables
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
@@ -17,7 +21,7 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    for t_name in ('dataset', 'job', 'metadata_file'):
+    for t_name in ("dataset", "job", "metadata_file"):
         t = Table(t_name, metadata, autoload=True)
         c = Column("object_store_id", TrimmedString(255), index=True)
         try:
@@ -31,7 +35,7 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    for t_name in ('dataset', 'job', 'metadata_file'):
+    for t_name in ("dataset", "job", "metadata_file"):
         t = Table(t_name, metadata, autoload=True)
         try:
             t.c.object_store_id.drop()
diff --git a/lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py b/lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
index e5ee9f78347..b50fcd2fa56 100644
--- a/lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
+++ b/lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
@@ -8,13 +8,13 @@ from sqlalchemy import (
     Boolean,
     Column,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
     drop_column,
-    engine_false
+    engine_false,
 )
 
 log = logging.getLogger(__name__)
@@ -47,6 +47,6 @@ def downgrade(migrate_engine):
 
     ToolShedRepository_table = Table("tool_shed_repository", metadata, autoload=True)
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('uninstalled', ToolShedRepository_table)
-        drop_column('dist_to_shed', ToolShedRepository_table)
+    if migrate_engine.name != "sqlite":
+        drop_column("uninstalled", ToolShedRepository_table)
+        drop_column("dist_to_shed", ToolShedRepository_table)
diff --git a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
index 31988a401d8..b0c2626dbc2 100644
--- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
+++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
@@ -15,16 +15,16 @@ from sqlalchemy import (
     MetaData,
     String,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import (
     _sniffnfix_pg9_hex,
-    TrimmedString
+    TrimmedString,
 )
 from galaxy.model.migrate.versions.util import (
     localtimestamp,
-    nextval
+    nextval,
 )
 
 log = logging.getLogger(__name__)
@@ -32,17 +32,23 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 
-ToolVersion_table = Table("tool_version", metadata,
+ToolVersion_table = Table(
+    "tool_version",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, default=now, onupdate=now),
     Column("tool_id", String(255)),
-    Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=True))
+    Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=True),
+)
 
-ToolVersionAssociation_table = Table("tool_version_association", metadata,
+ToolVersionAssociation_table = Table(
+    "tool_version_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("tool_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False),
-    Column("parent_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False))
+    Column("parent_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False),
+)
 
 
 def upgrade(migrate_engine):
@@ -69,10 +75,15 @@ def upgrade(migrate_engine):
             repository_metadata = loads(_sniffnfix_pg9_hex(str(row[1])))
             # Create a new row in the tool table for each tool included in repository.  We will NOT
             # handle tool_version_associaions because we do not have the information we need to do so.
-            tools = repository_metadata.get('tools', [])
+            tools = repository_metadata.get("tools", [])
             for tool_dict in tools:
-                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % \
-                    (nextval(migrate_engine, 'tool_version'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), tool_dict['guid'], tool_shed_repository_id)
+                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % (
+                    nextval(migrate_engine, "tool_version"),
+                    localtimestamp(migrate_engine),
+                    localtimestamp(migrate_engine),
+                    tool_dict["guid"],
+                    tool_shed_repository_id,
+                )
                 migrate_engine.execute(cmd)
                 count += 1
     print("Added %d rows to the new tool_version table." % count)
@@ -88,7 +99,8 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
 
     ToolIdGuidMap_table = Table(
-        "tool_id_guid_map", metadata,
+        "tool_id_guid_map",
+        metadata,
         Column("id", Integer, primary_key=True),
         Column("create_time", DateTime, default=now),
         Column("update_time", DateTime, default=now, onupdate=now),
@@ -98,7 +110,7 @@ def downgrade(migrate_engine):
         Column("repository_owner", TrimmedString(255)),
         Column("repository_name", TrimmedString(255)),
         Column("guid", TEXT),
-        Index('ix_tool_id_guid_map_guid', 'guid', unique=True, mysql_length=200),
+        Index("ix_tool_id_guid_map_guid", "guid", unique=True, mysql_length=200),
     )
 
     metadata.reflect()
diff --git a/lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py b/lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
index e995834f0ff..9fdb919349a 100644
--- a/lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
+++ b/lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
@@ -9,22 +9,25 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-MigrateTools_table = Table("migrate_tools", metadata,
-                           Column("repository_id", TrimmedString(255)),
-                           Column("repository_path", TEXT),
-                           Column("version", Integer))
+MigrateTools_table = Table(
+    "migrate_tools",
+    metadata,
+    Column("repository_id", TrimmedString(255)),
+    Column("repository_path", TEXT),
+    Column("version", Integer),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0093_add_job_params_col.py b/lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
index ecbe6a299c3..ffd2936845d 100644
--- a/lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
+++ b/lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
@@ -4,7 +4,11 @@ Migration script to add a 'params' column to the 'job' table.
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
diff --git a/lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py b/lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
index 0fea793c82b..1654d678901 100644
--- a/lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
+++ b/lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
@@ -4,10 +4,16 @@ Migration script to add a 'handler' column to the 'job' table.
 
 import logging
 
-from sqlalchemy import Column, MetaData
+from sqlalchemy import (
+    Column,
+    MetaData,
+)
 
 from galaxy.model.custom_types import TrimmedString
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -21,11 +27,11 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    add_column(handler_col, 'job', metadata, index_name="ix_job_handler")
+    add_column(handler_col, "job", metadata, index_name="ix_job_handler")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('handler', 'job', metadata)
+    drop_column("handler", "job", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0095_hda_subsets.py b/lib/galaxy/model/migrate/versions/0095_hda_subsets.py
index 8deebf77e19..f6a4c6a4395 100644
--- a/lib/galaxy/model/migrate/versions/0095_hda_subsets.py
+++ b/lib/galaxy/model/migrate/versions/0095_hda_subsets.py
@@ -4,18 +4,29 @@ Migration script to create table for tracking history_dataset_association subset
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Index, Integer, MetaData, Table, Unicode
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Index,
+    Integer,
+    MetaData,
+    Table,
+    Unicode,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 # Table to add.
 
-HistoryDatasetAssociationSubset_table = Table("history_dataset_association_subset", metadata,
-                                              Column("id", Integer, primary_key=True),
-                                              Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id")),
-                                              Column("history_dataset_association_subset_id", Integer, ForeignKey("history_dataset_association.id")),
-                                              Column("location", Unicode(255), index=True))
+HistoryDatasetAssociationSubset_table = Table(
+    "history_dataset_association_subset",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id")),
+    Column("history_dataset_association_subset_id", Integer, ForeignKey("history_dataset_association.id")),
+    Column("location", Unicode(255), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0096_openid_provider.py b/lib/galaxy/model/migrate/versions/0096_openid_provider.py
index 752991ff9c7..2a19e269073 100644
--- a/lib/galaxy/model/migrate/versions/0096_openid_provider.py
+++ b/lib/galaxy/model/migrate/versions/0096_openid_provider.py
@@ -5,12 +5,16 @@ Remove any OpenID entries with nonunique GenomeSpace Identifier
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
 log = logging.getLogger(__name__)
-BAD_IDENTIFIER = 'https://identity.genomespace.org/identityServer/xrd.jsp'
+BAD_IDENTIFIER = "https://identity.genomespace.org/identityServer/xrd.jsp"
 metadata = MetaData()
 
 
diff --git a/lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py b/lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
index 368cfda2b2e..81ff20f8f5b 100644
--- a/lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
+++ b/lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
@@ -6,13 +6,13 @@ import logging
 
 from sqlalchemy import (
     Column,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -25,11 +25,11 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     col = Column("ctx_rev", TrimmedString(10))
-    add_column(col, 'tool_shed_repository', metadata)
+    add_column(col, "tool_shed_repository", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('ctx_rev', 'tool_shed_repository', metadata)
+    drop_column("ctx_rev", "tool_shed_repository", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py b/lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
index 1c56cb28658..5bae2518624 100644
--- a/lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
+++ b/lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
@@ -12,29 +12,32 @@ from sqlalchemy import (
     Integer,
     MetaData,
     String,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-GenomeIndexToolData_table = Table("genome_index_tool_data", metadata,
-                                  Column("id", Integer, primary_key=True),
-                                  Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                                  Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-                                  Column("deferred_job_id", Integer, ForeignKey("deferred_job.id"), index=True),
-                                  Column("transfer_job_id", Integer, ForeignKey("transfer_job.id"), index=True),
-                                  Column("fasta_path", String(255)),
-                                  Column("created_time", DateTime, default=now),
-                                  Column("modified_time", DateTime, default=now, onupdate=now),
-                                  Column("indexer", String(64)),
-                                  Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+GenomeIndexToolData_table = Table(
+    "genome_index_tool_data",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+    Column("deferred_job_id", Integer, ForeignKey("deferred_job.id"), index=True),
+    Column("transfer_job_id", Integer, ForeignKey("transfer_job.id"), index=True),
+    Column("fasta_path", String(255)),
+    Column("created_time", DateTime, default=now),
+    Column("modified_time", DateTime, default=now, onupdate=now),
+    Column("indexer", String(64)),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py b/lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
index 830c257d7eb..b8b6ef35c61 100644
--- a/lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
+++ b/lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
@@ -12,13 +12,13 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -26,16 +26,19 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 # New table to store information about cloned tool shed repositories.
-ToolDependency_table = Table("tool_dependency", metadata,
-                             Column("id", Integer, primary_key=True),
-                             Column("create_time", DateTime, default=now),
-                             Column("update_time", DateTime, default=now, onupdate=now),
-                             Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False),
-                             Column("installed_changeset_revision", TrimmedString(255)),
-                             Column("name", TrimmedString(255)),
-                             Column("version", TrimmedString(40)),
-                             Column("type", TrimmedString(40)),
-                             Column("uninstalled", Boolean, default=False))
+ToolDependency_table = Table(
+    "tool_dependency",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False),
+    Column("installed_changeset_revision", TrimmedString(255)),
+    Column("name", TrimmedString(255)),
+    Column("version", TrimmedString(40)),
+    Column("type", TrimmedString(40)),
+    Column("uninstalled", Boolean, default=False),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py b/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
index ce3bda016d1..ea0a274b430 100644
--- a/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
+++ b/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
@@ -6,7 +6,7 @@ import logging
 
 from sqlalchemy import (
     MetaData,
-    Table
+    Table,
 )
 
 log = logging.getLogger(__name__)
@@ -20,9 +20,9 @@ def upgrade(migrate_engine):
 
     Table("tool_dependency", metadata, autoload=True)
     # Change the tool_dependency table's version column from TrimmedString to Text.
-    if migrate_engine.name in ['postgres', 'postgresql']:
+    if migrate_engine.name in ["postgres", "postgresql"]:
         cmd = "ALTER TABLE tool_dependency ALTER COLUMN version TYPE Text;"
-    elif migrate_engine.name == 'mysql':
+    elif migrate_engine.name == "mysql":
         cmd = "ALTER TABLE tool_dependency MODIFY COLUMN version Text;"
     else:
         # We don't have to do anything for sqlite tables.  From the sqlite documentation at http://sqlite.org/datatype3.html:
diff --git a/lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py b/lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
index 171be2ea563..353ae12bb59 100644
--- a/lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
+++ b/lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
@@ -6,13 +6,13 @@ import logging
 
 from sqlalchemy import (
     Column,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -24,7 +24,7 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('installed_changeset_revision', 'tool_dependency', metadata)
+    drop_column("installed_changeset_revision", "tool_dependency", metadata)
 
 
 def downgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py b/lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
index 2e7e83219c2..3dd65fd7a8c 100644
--- a/lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
+++ b/lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
@@ -9,13 +9,13 @@ from sqlalchemy import (
     Column,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import TrimmedString
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -28,7 +28,7 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     ToolDependency_table = Table("tool_dependency", metadata, autoload=True)
-    if migrate_engine.name == 'sqlite':
+    if migrate_engine.name == "sqlite":
         col = Column("status", TrimmedString(255))
     else:
         col = Column("status", TrimmedString(255), nullable=False)
@@ -39,8 +39,8 @@ def upgrade(migrate_engine):
 
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
     # TODO move to alembic.
-    if migrate_engine.name != 'sqlite':
-        drop_column('uninstalled', ToolDependency_table)
+    if migrate_engine.name != "sqlite":
+        drop_column("uninstalled", ToolDependency_table)
 
 
 def downgrade(migrate_engine):
@@ -48,9 +48,9 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     ToolDependency_table = Table("tool_dependency", metadata, autoload=True)
-    if migrate_engine.name != 'sqlite':
+    if migrate_engine.name != "sqlite":
         col = Column("uninstalled", Boolean, default=False)
         add_column(col, ToolDependency_table, metadata)
 
-    drop_column('error_message', ToolDependency_table)
-    drop_column('status', ToolDependency_table)
+    drop_column("error_message", ToolDependency_table)
+    drop_column("status", ToolDependency_table)
diff --git a/lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py b/lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
index 523648adac7..e98c41bc9c7 100644
--- a/lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
+++ b/lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
@@ -2,7 +2,12 @@
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
diff --git a/lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py b/lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
index 5b65879302d..578969f5dd3 100644
--- a/lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
+++ b/lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
@@ -11,7 +11,7 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -21,64 +21,94 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 # New table to log cleanup events
-CleanupEvent_table = Table("cleanup_event", metadata,
-                           Column("id", Integer, primary_key=True),
-                           Column("create_time", DateTime, default=now),
-                           Column("message", TrimmedString(1024)))
+CleanupEvent_table = Table(
+    "cleanup_event",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("message", TrimmedString(1024)),
+)
 
-CleanupEventDatasetAssociation_table = Table("cleanup_event_dataset_association", metadata,
-                                             Column("id", Integer, primary_key=True),
-                                             Column("create_time", DateTime, default=now),
-                                             Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                             Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True))
+CleanupEventDatasetAssociation_table = Table(
+    "cleanup_event_dataset_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
+)
 
-CleanupEventMetadataFileAssociation_table = Table("cleanup_event_metadata_file_association", metadata,
-                                                  Column("id", Integer, primary_key=True),
-                                                  Column("create_time", DateTime, default=now),
-                                                  Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                                  Column("metadata_file_id", Integer, ForeignKey("metadata_file.id"), index=True))
+CleanupEventMetadataFileAssociation_table = Table(
+    "cleanup_event_metadata_file_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("metadata_file_id", Integer, ForeignKey("metadata_file.id"), index=True),
+)
 
-CleanupEventHistoryAssociation_table = Table("cleanup_event_history_association", metadata,
-                                             Column("id", Integer, primary_key=True),
-                                             Column("create_time", DateTime, default=now),
-                                             Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                             Column("history_id", Integer, ForeignKey("history.id"), index=True))
+CleanupEventHistoryAssociation_table = Table(
+    "cleanup_event_history_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+)
 
-CleanupEventHistoryDatasetAssociationAssociation_table = Table("cleanup_event_hda_association", metadata,
-                                                               Column("id", Integer, primary_key=True),
-                                                               Column("create_time", DateTime, default=now),
-                                                               Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                                               Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True))
+CleanupEventHistoryDatasetAssociationAssociation_table = Table(
+    "cleanup_event_hda_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
+)
 
-CleanupEventLibraryAssociation_table = Table("cleanup_event_library_association", metadata,
-                                             Column("id", Integer, primary_key=True),
-                                             Column("create_time", DateTime, default=now),
-                                             Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                             Column("library_id", Integer, ForeignKey("library.id"), index=True))
+CleanupEventLibraryAssociation_table = Table(
+    "cleanup_event_library_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("library_id", Integer, ForeignKey("library.id"), index=True),
+)
 
-CleanupEventLibraryFolderAssociation_table = Table("cleanup_event_library_folder_association", metadata,
-                                                   Column("id", Integer, primary_key=True),
-                                                   Column("create_time", DateTime, default=now),
-                                                   Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                                   Column("library_folder_id", Integer, ForeignKey("library_folder.id"), index=True))
+CleanupEventLibraryFolderAssociation_table = Table(
+    "cleanup_event_library_folder_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("library_folder_id", Integer, ForeignKey("library_folder.id"), index=True),
+)
 
-CleanupEventLibraryDatasetAssociation_table = Table("cleanup_event_library_dataset_association", metadata,
-                                                    Column("id", Integer, primary_key=True),
-                                                    Column("create_time", DateTime, default=now),
-                                                    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                                    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), index=True))
+CleanupEventLibraryDatasetAssociation_table = Table(
+    "cleanup_event_library_dataset_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), index=True),
+)
 
-CleanupEventLibraryDatasetDatasetAssociationAssociation_table = Table("cleanup_event_ldda_association", metadata,
-                                                                      Column("id", Integer, primary_key=True),
-                                                                      Column("create_time", DateTime, default=now),
-                                                                      Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                                                      Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True))
+CleanupEventLibraryDatasetDatasetAssociationAssociation_table = Table(
+    "cleanup_event_ldda_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True),
+)
 
-CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table = Table("cleanup_event_icda_association", metadata,
-                                                                           Column("id", Integer, primary_key=True),
-                                                                           Column("create_time", DateTime, default=now),
-                                                                           Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-                                                                           Column("icda_id", Integer, ForeignKey("implicitly_converted_dataset_association.id"), index=True))
+CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table = Table(
+    "cleanup_event_icda_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
+    Column("icda_id", Integer, ForeignKey("implicitly_converted_dataset_association.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py b/lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
index bb22ff5fd72..817b44d531f 100644
--- a/lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
+++ b/lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
@@ -8,47 +8,47 @@ from sqlalchemy import MetaData
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 indexes = (
-    ("ix_metadata_file_lda_id", 'metadata_file', 'lda_id'),                                   # 0003
-    ("ix_history_importable", 'history', 'importable'),                                       # 0007
-    ("ix_sample_bar_code", 'sample', 'bar_code'),                                             # 0009
-    ("ix_request_type_deleted", 'request_type', 'deleted'),                                   # 0012
-    ("ix_galaxy_user_username", 'galaxy_user', 'username'),                                   # 0014
-    ("ix_form_definition_type", 'form_definition', 'type'),                                   # 0019
-    ("ix_form_definition_layout", 'form_definition', 'layout'),                               # 0019
-    ("ix_job_library_folder_id", 'job', 'library_folder_id'),                                 # 0020
-    ("ix_page_published", 'page', 'published'),                                               # 0023
-    ("ix_page_deleted", 'page', 'deleted'),                                                   # 0023
-    ("ix_galaxy_user_form_values_id", 'galaxy_user', 'form_values_id'),                       # 0025
-    ("ix_lia_deleted", 'library_info_association', 'deleted'),                                # 0036
-    ("ix_lfia_deleted", 'library_folder_info_association', 'deleted'),                        # 0036
-    ("ix_lddia_deleted", 'library_dataset_dataset_info_association', 'deleted'),              # 0036
-    ("ix_sample_library_id", 'sample', 'library_id'),                                         # 0037
-    ("ix_sample_folder_id", 'sample', 'folder_id'),                                           # 0037
-    ("ix_lia_inheritable", 'library_info_association', 'inheritable'),                        # 0038
-    ("ix_lfia_inheritable", 'library_folder_info_association', 'inheritable'),                # 0038
-    ("ix_job_imported", 'job', 'imported'),                                                   # 0051
-    ("ix_request_notification", 'request', 'notification'),                                   # 0057
-    ("ix_sd_external_service_id", 'sample_dataset', 'external_service_id'),                   # 0068
-    ("ix_icda_ldda_parent_id", 'implicitly_converted_dataset_association', 'ldda_parent_id'),  # 0073
-    ("ix_library_dataset_purged", 'library_dataset', 'purged'),                               # 0074
-    ("ix_run_subindex", 'run', 'subindex'),                                                   # 0075
-    ("ix_history_dataset_association_purged", 'history_dataset_association', 'purged'),       # 0078
-    ("ix_galaxy_user_disk_usage", 'galaxy_user', 'disk_usage'),                               # 0078
-    ("ix_galaxy_session_disk_usage", 'galaxy_session', 'disk_usage'),                         # 0078
-    ("ix_icda_ldda_id", 'implicitly_converted_dataset_association', 'ldda_id'),               # 0084
-    ("ix_tsr_includes_datatypes", 'tool_shed_repository', 'includes_datatypes'),              # 0086
-    ("ix_dataset_object_store_id", 'dataset', 'object_store_id'),                             # 0089
-    ("ix_job_object_store_id", 'job', 'object_store_id'),                                     # 0089
-    ("ix_metadata_file_object_store_id", 'metadata_file', 'object_store_id'),                 # 0089
-    ("ix_job_handler", 'job', 'handler'),                                                     # 0094
-    ("ix_galaxy_user_email", 'galaxy_user', 'email')                                          # 0106
+    ("ix_metadata_file_lda_id", "metadata_file", "lda_id"),  # 0003
+    ("ix_history_importable", "history", "importable"),  # 0007
+    ("ix_sample_bar_code", "sample", "bar_code"),  # 0009
+    ("ix_request_type_deleted", "request_type", "deleted"),  # 0012
+    ("ix_galaxy_user_username", "galaxy_user", "username"),  # 0014
+    ("ix_form_definition_type", "form_definition", "type"),  # 0019
+    ("ix_form_definition_layout", "form_definition", "layout"),  # 0019
+    ("ix_job_library_folder_id", "job", "library_folder_id"),  # 0020
+    ("ix_page_published", "page", "published"),  # 0023
+    ("ix_page_deleted", "page", "deleted"),  # 0023
+    ("ix_galaxy_user_form_values_id", "galaxy_user", "form_values_id"),  # 0025
+    ("ix_lia_deleted", "library_info_association", "deleted"),  # 0036
+    ("ix_lfia_deleted", "library_folder_info_association", "deleted"),  # 0036
+    ("ix_lddia_deleted", "library_dataset_dataset_info_association", "deleted"),  # 0036
+    ("ix_sample_library_id", "sample", "library_id"),  # 0037
+    ("ix_sample_folder_id", "sample", "folder_id"),  # 0037
+    ("ix_lia_inheritable", "library_info_association", "inheritable"),  # 0038
+    ("ix_lfia_inheritable", "library_folder_info_association", "inheritable"),  # 0038
+    ("ix_job_imported", "job", "imported"),  # 0051
+    ("ix_request_notification", "request", "notification"),  # 0057
+    ("ix_sd_external_service_id", "sample_dataset", "external_service_id"),  # 0068
+    ("ix_icda_ldda_parent_id", "implicitly_converted_dataset_association", "ldda_parent_id"),  # 0073
+    ("ix_library_dataset_purged", "library_dataset", "purged"),  # 0074
+    ("ix_run_subindex", "run", "subindex"),  # 0075
+    ("ix_history_dataset_association_purged", "history_dataset_association", "purged"),  # 0078
+    ("ix_galaxy_user_disk_usage", "galaxy_user", "disk_usage"),  # 0078
+    ("ix_galaxy_session_disk_usage", "galaxy_session", "disk_usage"),  # 0078
+    ("ix_icda_ldda_id", "implicitly_converted_dataset_association", "ldda_id"),  # 0084
+    ("ix_tsr_includes_datatypes", "tool_shed_repository", "includes_datatypes"),  # 0086
+    ("ix_dataset_object_store_id", "dataset", "object_store_id"),  # 0089
+    ("ix_job_object_store_id", "job", "object_store_id"),  # 0089
+    ("ix_metadata_file_object_store_id", "metadata_file", "object_store_id"),  # 0089
+    ("ix_job_handler", "job", "handler"),  # 0094
+    ("ix_galaxy_user_email", "galaxy_user", "email"),  # 0106
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py b/lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
index 6b8b6433a0d..deb279fd518 100644
--- a/lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
+++ b/lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
@@ -4,7 +4,12 @@ Add the exit_code column to the Job and Task tables.
 
 import logging
 
-from sqlalchemy import Column, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
index e0b1701a8d0..8307074061d 100644
--- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
+++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
@@ -11,7 +11,7 @@ from sqlalchemy import (
     MetaData,
     String,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import JSONType
@@ -19,29 +19,31 @@ from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-ExtendedMetadata_table = Table("extended_metadata", metadata,
-                               Column("id", Integer, primary_key=True),
-                               Column("data", JSONType))
+ExtendedMetadata_table = Table(
+    "extended_metadata", metadata, Column("id", Integer, primary_key=True), Column("data", JSONType)
+)
 
-ExtendedMetadataIndex_table = Table("extended_metadata_index", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id",
-                                                                                       onupdate="CASCADE",
-                                                                                       ondelete="CASCADE"),
-                                           index=True),
-                                    Column("path", String(255)),
-                                    Column("value", TEXT))
+ExtendedMetadataIndex_table = Table(
+    "extended_metadata_index",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "extended_metadata_id",
+        Integer,
+        ForeignKey("extended_metadata.id", onupdate="CASCADE", ondelete="CASCADE"),
+        index=True,
+    ),
+    Column("path", String(255)),
+    Column("value", TEXT),
+)
 
-TABLES = [
-    ExtendedMetadata_table,
-    ExtendedMetadataIndex_table
-]
+TABLES = [ExtendedMetadata_table, ExtendedMetadataIndex_table]
 
 
 def upgrade(migrate_engine):
@@ -51,8 +53,10 @@ def upgrade(migrate_engine):
 
     for table in TABLES:
         create_table(table)
-    extended_metadata_ldda_col = Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), nullable=True)
-    add_column(extended_metadata_ldda_col, 'library_dataset_dataset_association', metadata)
+    extended_metadata_ldda_col = Column(
+        "extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), nullable=True
+    )
+    add_column(extended_metadata_ldda_col, "library_dataset_dataset_association", metadata)
 
 
 def downgrade(migrate_engine):
@@ -60,6 +64,6 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first.
-    drop_column('extended_metadata_id', 'library_dataset_dataset_association', metadata)
+    drop_column("extended_metadata_id", "library_dataset_dataset_association", metadata)
     for table in reversed(TABLES):
         drop_table(table)
diff --git a/lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py b/lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
index aeb6dfad721..8bd63e6ba1d 100644
--- a/lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
+++ b/lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
@@ -11,30 +11,36 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-RepositoryDependency_table = Table("repository_dependency", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("create_time", DateTime, default=now),
-                                   Column("update_time", DateTime, default=now, onupdate=now),
-                                   Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False))
+RepositoryDependency_table = Table(
+    "repository_dependency",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False),
+)
 
-RepositoryRepositoryDependencyAssociation_table = Table("repository_repository_dependency_association", metadata,
-                                                        Column("id", Integer, primary_key=True),
-                                                        Column("create_time", DateTime, default=now),
-                                                        Column("update_time", DateTime, default=now, onupdate=now),
-                                                        Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True),
-                                                        Column("repository_dependency_id", Integer, ForeignKey("repository_dependency.id"), index=True))
+RepositoryRepositoryDependencyAssociation_table = Table(
+    "repository_repository_dependency_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True),
+    Column("repository_dependency_id", Integer, ForeignKey("repository_dependency.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py b/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
index cb5c31b4b2a..8af310b03d2 100644
--- a/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
+++ b/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
@@ -4,7 +4,11 @@ Add UUID column to dataset table
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import UUIDType
 
diff --git a/lib/galaxy/model/migrate/versions/0111_add_job_destinations.py b/lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
index 18f2ea8ad5b..0cc3bda9049 100644
--- a/lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
+++ b/lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
@@ -4,7 +4,12 @@ Add support for job destinations to the job table
 
 import logging
 
-from sqlalchemy import Column, MetaData, String, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    String,
+    Table,
+)
 
 from galaxy.model.custom_types import JSONType
 
diff --git a/lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py b/lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
index 35189b1fd50..6451924d7d9 100644
--- a/lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
+++ b/lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
@@ -13,33 +13,37 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
 metadata = MetaData()
 
-DataManagerHistoryAssociation_table = Table("data_manager_history_association", metadata,
-                                            Column("id", Integer, primary_key=True),
-                                            Column("create_time", DateTime, default=now),
-                                            Column("update_time", DateTime, index=True, default=now, onupdate=now),
-                                            Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+DataManagerHistoryAssociation_table = Table(
+    "data_manager_history_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, index=True, default=now, onupdate=now),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 DataManagerJobAssociation_table = Table(
-    "data_manager_job_association", metadata,
+    "data_manager_job_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("update_time", DateTime, index=True, default=now, onupdate=now),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("data_manager_id", TEXT),
-    Index('ix_data_manager_job_association_data_manager_id', 'data_manager_id', mysql_length=200),
+    Index("ix_data_manager_job_association_data_manager_id", "data_manager_id", mysql_length=200),
 )
 
 TABLES = [DataManagerHistoryAssociation_table, DataManagerJobAssociation_table]
diff --git a/lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py b/lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
index 73e48f4a088..64f8ca530f2 100644
--- a/lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
+++ b/lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
@@ -14,7 +14,9 @@ def upgrade(migrate_engine):
         cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';"
         migrate_engine.execute(cmd)
     except Exception:
-        log.exception("Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed.")
+        log.exception(
+            "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed."
+        )
 
 
 def downgrade(migrate_engine):
@@ -22,4 +24,6 @@ def downgrade(migrate_engine):
         cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';"
         migrate_engine.execute(cmd)
     except Exception:
-        log.exception("Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed.")
+        log.exception(
+            "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed."
+        )
diff --git a/lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py b/lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
index b6abd06f97e..a8f25bd807d 100644
--- a/lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
+++ b/lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
@@ -14,7 +14,9 @@ def upgrade(migrate_engine):
         cmd = "UPDATE migrate_tools set repository_path='lib/tool_shed/galaxy_install/migrate';"
         migrate_engine.execute(cmd)
     except Exception:
-        log.exception("Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed.")
+        log.exception(
+            "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed."
+        )
 
 
 def downgrade(migrate_engine):
@@ -22,4 +24,6 @@ def downgrade(migrate_engine):
         cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';"
         migrate_engine.execute(cmd)
     except Exception:
-        log.exception("Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed.")
+        log.exception(
+            "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed."
+        )
diff --git a/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py b/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
index c30f63f7189..e5317271b57 100644
--- a/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
+++ b/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
@@ -3,14 +3,18 @@ Expand the length of the password fields in the galaxy_user table to allow for o
 """
 import logging
 
-from sqlalchemy import MetaData, String, Table
+from sqlalchemy import (
+    MetaData,
+    String,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 
 
 def upgrade(migrate_engine):
     meta = MetaData(bind=migrate_engine)
-    user = Table('galaxy_user', meta, autoload=True)
+    user = Table("galaxy_user", meta, autoload=True)
     try:
         user.c.password.alter(type=String(255))
     except Exception:
diff --git a/lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py b/lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
index aae01d769ed..fb6edb48384 100644
--- a/lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
+++ b/lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
@@ -8,14 +8,14 @@ from sqlalchemy import (
     Boolean,
     Column,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     add_column,
     drop_column,
-    engine_false
+    engine_false,
 )
 
 log = logging.getLogger(__name__)
@@ -29,8 +29,8 @@ def upgrade(migrate_engine):
 
     ToolShedRepository_table = Table("tool_shed_repository", metadata, autoload=True)
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
-        drop_column('update_available', ToolShedRepository_table)
+    if migrate_engine.name != "sqlite":
+        drop_column("update_available", ToolShedRepository_table)
     c = Column("tool_shed_status", JSONType, nullable=True)
     add_column(c, ToolShedRepository_table, metadata)
 
@@ -40,7 +40,7 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     ToolShedRepository_table = Table("tool_shed_repository", metadata, autoload=True)
-    drop_column('tool_shed_status', ToolShedRepository_table)
+    drop_column("tool_shed_status", ToolShedRepository_table)
     c = Column("update_available", Boolean, default=False)
     add_column(c, ToolShedRepository_table, metadata)
     try:
diff --git a/lib/galaxy/model/migrate/versions/0117_add_user_activation.py b/lib/galaxy/model/migrate/versions/0117_add_user_activation.py
index de67fa97157..dfb21022a20 100644
--- a/lib/galaxy/model/migrate/versions/0117_add_user_activation.py
+++ b/lib/galaxy/model/migrate/versions/0117_add_user_activation.py
@@ -4,7 +4,12 @@ Adds 'active' and 'activation_token' columns to the galaxy_user table.
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
@@ -39,7 +44,7 @@ def downgrade(migrate_engine):
     try:
         user_table = Table("galaxy_user", metadata, autoload=True)
         # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-        if migrate_engine.name != 'sqlite':
+        if migrate_engine.name != "sqlite":
             user_active = user_table.c.active
             user_active.drop()
         user_activation_token = user_table.c.activation_token
diff --git a/lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py b/lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
index 684c294dd95..e5b216759a9 100644
--- a/lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
+++ b/lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
@@ -4,7 +4,13 @@ Add link from history_dataset_association to the extended_metadata table
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0119_job_metrics.py b/lib/galaxy/model/migrate/versions/0119_job_metrics.py
index 340a2e82f9d..e2aee047ba9 100644
--- a/lib/galaxy/model/migrate/versions/0119_job_metrics.py
+++ b/lib/galaxy/model/migrate/versions/0119_job_metrics.py
@@ -11,12 +11,12 @@ from sqlalchemy import (
     MetaData,
     Numeric,
     Table,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -29,9 +29,18 @@ JobMetricText_table = Table(
     metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
-    Column("plugin", Unicode(255), ),
-    Column("metric_name", Unicode(255), ),
-    Column("metric_value", Unicode(TEXT_METRIC_MAX_LENGTH), ),
+    Column(
+        "plugin",
+        Unicode(255),
+    ),
+    Column(
+        "metric_name",
+        Unicode(255),
+    ),
+    Column(
+        "metric_value",
+        Unicode(TEXT_METRIC_MAX_LENGTH),
+    ),
 )
 
 
@@ -40,9 +49,18 @@ TaskMetricText_table = Table(
     metadata,
     Column("id", Integer, primary_key=True),
     Column("task_id", Integer, ForeignKey("task.id"), index=True),
-    Column("plugin", Unicode(255), ),
-    Column("metric_name", Unicode(255), ),
-    Column("metric_value", Unicode(TEXT_METRIC_MAX_LENGTH), ),
+    Column(
+        "plugin",
+        Unicode(255),
+    ),
+    Column(
+        "metric_name",
+        Unicode(255),
+    ),
+    Column(
+        "metric_value",
+        Unicode(TEXT_METRIC_MAX_LENGTH),
+    ),
 )
 
 
@@ -51,9 +69,18 @@ JobMetricNumeric_table = Table(
     metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
-    Column("plugin", Unicode(255), ),
-    Column("metric_name", Unicode(255), ),
-    Column("metric_value", Numeric(22, 7), ),
+    Column(
+        "plugin",
+        Unicode(255),
+    ),
+    Column(
+        "metric_name",
+        Unicode(255),
+    ),
+    Column(
+        "metric_value",
+        Numeric(22, 7),
+    ),
 )
 
 
@@ -62,9 +89,18 @@ TaskMetricNumeric_table = Table(
     metadata,
     Column("id", Integer, primary_key=True),
     Column("task_id", Integer, ForeignKey("task.id"), index=True),
-    Column("plugin", Unicode(255), ),
-    Column("metric_name", Unicode(255), ),
-    Column("metric_value", Numeric(22, 7), ),
+    Column(
+        "plugin",
+        Unicode(255),
+    ),
+    Column(
+        "metric_name",
+        Unicode(255),
+    ),
+    Column(
+        "metric_value",
+        Numeric(22, 7),
+    ),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0120_dataset_collections.py b/lib/galaxy/model/migrate/versions/0120_dataset_collections.py
index 12d854b46bc..fde673f78a4 100644
--- a/lib/galaxy/model/migrate/versions/0120_dataset_collections.py
+++ b/lib/galaxy/model/migrate/versions/0120_dataset_collections.py
@@ -14,7 +14,7 @@ from sqlalchemy import (
     MetaData,
     Table,
     TEXT,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -22,105 +22,165 @@ from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-DatasetCollection_table = Table("dataset_collection", metadata,
-                                Column("id", Integer, primary_key=True),
-                                Column("collection_type", Unicode(255), nullable=False, ),
-                                Column("create_time", DateTime, default=now),
-                                Column("update_time", DateTime, default=now, onupdate=now))
+DatasetCollection_table = Table(
+    "dataset_collection",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "collection_type",
+        Unicode(255),
+        nullable=False,
+    ),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-HistoryDatasetCollectionAssociation_table = Table("history_dataset_collection_association", metadata,
-                                                  Column("id", Integer, primary_key=True),
-                                                  Column("collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
-                                                  Column("history_id", Integer, ForeignKey("history.id"), index=True),
-                                                  Column("hid", Integer),
-                                                  Column("name", TrimmedString(255)),
-                                                  Column("deleted", Boolean, default=False),
-                                                  Column("visible", Boolean, default=True),
-                                                  Column("copied_from_history_dataset_collection_association_id", Integer, ForeignKey("history_dataset_collection_association.id"), nullable=True),
-                                                  Column("implicit_output_name", Unicode(255), nullable=True))
+HistoryDatasetCollectionAssociation_table = Table(
+    "history_dataset_collection_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
+    Column("history_id", Integer, ForeignKey("history.id"), index=True),
+    Column("hid", Integer),
+    Column("name", TrimmedString(255)),
+    Column("deleted", Boolean, default=False),
+    Column("visible", Boolean, default=True),
+    Column(
+        "copied_from_history_dataset_collection_association_id",
+        Integer,
+        ForeignKey("history_dataset_collection_association.id"),
+        nullable=True,
+    ),
+    Column("implicit_output_name", Unicode(255), nullable=True),
+)
 
-LibraryDatasetCollectionAssociation_table = Table("library_dataset_collection_association", metadata,
-                                                  Column("id", Integer, primary_key=True),
-                                                  Column("collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
-                                                  Column("name", TrimmedString(255)),
-                                                  Column("deleted", Boolean, default=False),
-                                                  Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True))
+LibraryDatasetCollectionAssociation_table = Table(
+    "library_dataset_collection_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
+    Column("name", TrimmedString(255)),
+    Column("deleted", Boolean, default=False),
+    Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True),
+)
 
-DatasetCollectionElement_table = Table("dataset_collection_element", metadata,
-                                       Column("id", Integer, primary_key=True),
-                                       Column("dataset_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True, nullable=False),
-                                       Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True),
-                                       Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True),
-                                       Column("child_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True, nullable=True),
-                                       Column("element_index", Integer, nullable=False),
-                                       Column("element_identifier", Unicode(255), nullable=False))
+DatasetCollectionElement_table = Table(
+    "dataset_collection_element",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("dataset_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True, nullable=False),
+    Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True),
+    Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True, nullable=True),
+    Column("child_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True, nullable=True),
+    Column("element_index", Integer, nullable=False),
+    Column("element_identifier", Unicode(255), nullable=False),
+)
 
-HistoryDatasetCollectionAnnotationAssociation_table = Table("history_dataset_collection_annotation_association", metadata,
-                                                            Column("id", Integer, primary_key=True),
-                                                            Column("history_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                            Column("annotation", TEXT))
+HistoryDatasetCollectionAnnotationAssociation_table = Table(
+    "history_dataset_collection_annotation_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "history_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    ),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("annotation", TEXT),
+)
 
-LibraryDatasetCollectionAnnotationAssociation_table = Table("library_dataset_collection_annotation_association", metadata,
-                                                            Column("id", Integer, primary_key=True),
-                                                            Column("library_dataset_collection_id", Integer, ForeignKey("library_dataset_collection_association.id"), index=True),
-                                                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                            Column("annotation", TEXT))
+LibraryDatasetCollectionAnnotationAssociation_table = Table(
+    "library_dataset_collection_annotation_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "library_dataset_collection_id", Integer, ForeignKey("library_dataset_collection_association.id"), index=True
+    ),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("annotation", TEXT),
+)
 
-HistoryDatasetCollectionRatingAssociation_table = Table("history_dataset_collection_rating_association", metadata,
-                                                        Column("id", Integer, primary_key=True),
-                                                        Column("history_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                        Column("rating", Integer, index=True))
+HistoryDatasetCollectionRatingAssociation_table = Table(
+    "history_dataset_collection_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "history_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    ),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
-LibraryDatasetCollectionRatingAssociation_table = Table("library_dataset_collection_rating_association", metadata,
-                                                        Column("id", Integer, primary_key=True),
-                                                        Column("library_dataset_collection_id", Integer, ForeignKey("library_dataset_collection_association.id"), index=True),
-                                                        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                        Column("rating", Integer, index=True))
+LibraryDatasetCollectionRatingAssociation_table = Table(
+    "library_dataset_collection_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "library_dataset_collection_id", Integer, ForeignKey("library_dataset_collection_association.id"), index=True
+    ),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+)
 
-HistoryDatasetCollectionTagAssociation_table = Table("history_dataset_collection_tag_association", metadata,
-                                                     Column("id", Integer, primary_key=True),
-                                                     Column("history_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                     Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                                     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                     Column("user_tname", Unicode(255), index=True),
-                                                     Column("value", Unicode(255), index=True),
-                                                     Column("user_value", Unicode(255), index=True))
+HistoryDatasetCollectionTagAssociation_table = Table(
+    "history_dataset_collection_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "history_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True
+    ),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", Unicode(255), index=True),
+    Column("value", Unicode(255), index=True),
+    Column("user_value", Unicode(255), index=True),
+)
 
-LibraryDatasetCollectionTagAssociation_table = Table("library_dataset_collection_tag_association", metadata,
-                                                     Column("id", Integer, primary_key=True),
-                                                     Column("library_dataset_collection_id", Integer, ForeignKey("library_dataset_collection_association.id"), index=True),
-                                                     Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                                     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                                     Column("user_tname", Unicode(255), index=True),
-                                                     Column("value", Unicode(255), index=True),
-                                                     Column("user_value", Unicode(255), index=True))
+LibraryDatasetCollectionTagAssociation_table = Table(
+    "library_dataset_collection_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column(
+        "library_dataset_collection_id", Integer, ForeignKey("library_dataset_collection_association.id"), index=True
+    ),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", Unicode(255), index=True),
+    Column("value", Unicode(255), index=True),
+    Column("user_value", Unicode(255), index=True),
+)
 
-JobToInputDatasetCollectionAssociation_table = Table("job_to_input_dataset_collection", metadata,
-                                                     Column("id", Integer, primary_key=True),
-                                                     Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                                                     Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                     Column("name", Unicode(255)))
+JobToInputDatasetCollectionAssociation_table = Table(
+    "job_to_input_dataset_collection",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("name", Unicode(255)),
+)
 
-JobToOutputDatasetCollectionAssociation_table = Table("job_to_output_dataset_collection", metadata,
-                                                      Column("id", Integer, primary_key=True),
-                                                      Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                                                      Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                      Column("name", Unicode(255)))
+JobToOutputDatasetCollectionAssociation_table = Table(
+    "job_to_output_dataset_collection",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("name", Unicode(255)),
+)
 
-ImplicitlyCreatedDatasetCollectionInput_table = Table("implicitly_created_dataset_collection_inputs", metadata,
-                                                      Column("id", Integer, primary_key=True),
-                                                      Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                      Column("input_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
-                                                      Column("name", Unicode(255)))
+ImplicitlyCreatedDatasetCollectionInput_table = Table(
+    "implicitly_created_dataset_collection_inputs",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("input_dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
+    Column("name", Unicode(255)),
+)
 
 
 TABLES = [
@@ -149,15 +209,20 @@ def upgrade(migrate_engine):
         create_table(table)
 
     # TODO: Find a better name for this column...
-    HiddenBeneathCollection_column = Column("hidden_beneath_collection_instance_id", Integer, ForeignKey("history_dataset_collection_association.id"), nullable=True)
-    add_column(HiddenBeneathCollection_column, 'history_dataset_association', metadata)
+    HiddenBeneathCollection_column = Column(
+        "hidden_beneath_collection_instance_id",
+        Integer,
+        ForeignKey("history_dataset_collection_association.id"),
+        nullable=True,
+    )
+    add_column(HiddenBeneathCollection_column, "history_dataset_association", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('hidden_beneath_collection_instance_id', 'history_dataset_association', metadata)
+    drop_column("hidden_beneath_collection_instance_id", "history_dataset_association", metadata)
 
     for table in reversed(TABLES):
         drop_table(table)
diff --git a/lib/galaxy/model/migrate/versions/0121_workflow_uuids.py b/lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
index 103331ffad0..c49982af39d 100644
--- a/lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
+++ b/lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
@@ -4,7 +4,11 @@ Add UUIDs to workflows
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import UUIDType
 
diff --git a/lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py b/lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
index 2c470ec18a6..62cc4b810fe 100644
--- a/lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
+++ b/lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
@@ -12,19 +12,19 @@ from sqlalchemy import (
     String,
     Table,
     TEXT,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.custom_types import (
     JSONType,
     TrimmedString,
-    UUIDType
+    UUIDType,
 )
 from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -32,9 +32,12 @@ metadata = MetaData()
 
 
 WorkflowRequestInputParameter_table = Table(
-    "workflow_request_input_parameters", metadata,
+    "workflow_request_input_parameters",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")),
+    Column(
+        "workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")
+    ),
     Column("name", Unicode(255)),
     Column("type", Unicode(255)),
     Column("value", TEXT),
@@ -42,16 +45,20 @@ WorkflowRequestInputParameter_table = Table(
 
 
 WorkflowRequestStepState_table = Table(
-    "workflow_request_step_states", metadata,
+    "workflow_request_step_states",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")),
+    Column(
+        "workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")
+    ),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
     Column("value", JSONType),
 )
 
 
 WorkflowRequestToInputDatasetAssociation_table = Table(
-    "workflow_request_to_input_dataset", metadata,
+    "workflow_request_to_input_dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("name", String(255)),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
@@ -61,7 +68,8 @@ WorkflowRequestToInputDatasetAssociation_table = Table(
 
 
 WorkflowRequestToInputDatasetCollectionAssociation_table = Table(
-    "workflow_request_to_input_collection_dataset", metadata,
+    "workflow_request_to_input_collection_dataset",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("name", String(255)),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
diff --git a/lib/galaxy/model/migrate/versions/0124_job_state_history.py b/lib/galaxy/model/migrate/versions/0124_job_state_history.py
index c256c51f580..ea9dcfc679c 100644
--- a/lib/galaxy/model/migrate/versions/0124_job_state_history.py
+++ b/lib/galaxy/model/migrate/versions/0124_job_state_history.py
@@ -5,22 +5,36 @@ Migration script for the job state history table
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-JobStateHistory_table = Table("job_state_history", metadata,
-                              Column("id", Integer, primary_key=True),
-                              Column("create_time", DateTime, default=now),
-                              Column("update_time", DateTime, default=now, onupdate=now),
-                              Column("job_id", Integer, ForeignKey("job.id"), index=True),
-                              Column("state", String(64), index=True),
-                              Column("info", TrimmedString(255)))
+JobStateHistory_table = Table(
+    "job_state_history",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("job_id", Integer, ForeignKey("job.id"), index=True),
+    Column("state", String(64), index=True),
+    Column("info", TrimmedString(255)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py b/lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
index b93c88765f8..155e0d60506 100644
--- a/lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
+++ b/lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
@@ -4,10 +4,19 @@ Migration script to enhance workflow step usability by adding labels and UUIDs.
 
 import logging
 
-from sqlalchemy import Column, MetaData
+from sqlalchemy import (
+    Column,
+    MetaData,
+)
 
-from galaxy.model.custom_types import TrimmedString, UUIDType
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.custom_types import (
+    TrimmedString,
+    UUIDType,
+)
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0126_password_reset.py b/lib/galaxy/model/migrate/versions/0126_password_reset.py
index ffc31ae7e6e..27124de1006 100644
--- a/lib/galaxy/model/migrate/versions/0126_password_reset.py
+++ b/lib/galaxy/model/migrate/versions/0126_password_reset.py
@@ -4,17 +4,31 @@ Migration script for the password reset table
 
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import create_table, drop_table
+from galaxy.model.migrate.versions.util import (
+    create_table,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-PasswordResetToken_table = Table("password_reset_token", metadata,
-                                 Column("token", String(32), primary_key=True, unique=True, index=True),
-                                 Column("expiration_time", DateTime),
-                                 Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+PasswordResetToken_table = Table(
+    "password_reset_token",
+    metadata,
+    Column("token", String(32), primary_key=True, unique=True, index=True),
+    Column("expiration_time", DateTime),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py b/lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
index c560f74493c..6346bff0d26 100644
--- a/lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
+++ b/lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
@@ -11,7 +11,7 @@ from sqlalchemy import (
     MetaData,
     Table,
     TEXT,
-    Unicode
+    Unicode,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -19,18 +19,19 @@ from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 JobToImplicitOutputDatasetCollectionAssociation_table = Table(
-    "job_to_implicit_output_dataset_collection", metadata,
+    "job_to_implicit_output_dataset_collection",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("dataset_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
-    Column("name", Unicode(255))
+    Column("name", Unicode(255)),
 )
 
 
@@ -43,10 +44,12 @@ def upgrade(migrate_engine):
 
     dataset_collection_table = Table("dataset_collection", metadata, autoload=True)
     # need server_default because column in non-null
-    populated_state_column = Column('populated_state', TrimmedString(64), default='ok', server_default="ok", nullable=False)
+    populated_state_column = Column(
+        "populated_state", TrimmedString(64), default="ok", server_default="ok", nullable=False
+    )
     add_column(populated_state_column, dataset_collection_table, metadata)
 
-    populated_message_column = Column('populated_state_message', TEXT, nullable=True)
+    populated_message_column = Column("populated_state_message", TEXT, nullable=True)
     add_column(populated_message_column, dataset_collection_table, metadata)
 
 
@@ -57,5 +60,5 @@ def downgrade(migrate_engine):
     drop_table(JobToImplicitOutputDatasetCollectionAssociation_table)
 
     dataset_collection_table = Table("dataset_collection", metadata, autoload=True)
-    drop_column('populated_state', dataset_collection_table)
-    drop_column('populated_state_message', dataset_collection_table)
+    drop_column("populated_state", dataset_collection_table)
+    drop_column("populated_state_message", dataset_collection_table)
diff --git a/lib/galaxy/model/migrate/versions/0128_session_timeout.py b/lib/galaxy/model/migrate/versions/0128_session_timeout.py
index 741d4e27e8c..062242585fc 100644
--- a/lib/galaxy/model/migrate/versions/0128_session_timeout.py
+++ b/lib/galaxy/model/migrate/versions/0128_session_timeout.py
@@ -4,9 +4,16 @@ Migration script to add session update time (used for timeouts)
 
 import logging
 
-from sqlalchemy import Column, DateTime, MetaData
+from sqlalchemy import (
+    Column,
+    DateTime,
+    MetaData,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py b/lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
index 99aeaf68e1c..2f6ad569bc2 100644
--- a/lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
+++ b/lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
@@ -4,9 +4,16 @@ Migration script to allow invalidation of job external output metadata temp file
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -25,5 +32,5 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
-    if migrate_engine.name != 'sqlite':
+    if migrate_engine.name != "sqlite":
         drop_column("is_valid", "job_external_output_metadata", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py b/lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
index 91ceadcb728..e5ed362792d 100644
--- a/lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
+++ b/lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
@@ -4,7 +4,11 @@ Migration script to change the 'value' column of 'user_preference' table from va
 
 import logging
 
-from sqlalchemy import MetaData, Table, Text
+from sqlalchemy import (
+    MetaData,
+    Table,
+    Text,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py b/lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
index 314d7395568..a75d820a66a 100644
--- a/lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
+++ b/lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
@@ -4,33 +4,53 @@ Migration script to support subworkflows and workflow request input parameters
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, ForeignKeyConstraint, Index, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    ForeignKeyConstraint,
+    Index,
+    Integer,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.custom_types import JSONType, TrimmedString, UUIDType
-from galaxy.model.migrate.versions.util import add_column, alter_column, create_table, drop_column, drop_table
+from galaxy.model.custom_types import (
+    JSONType,
+    TrimmedString,
+    UUIDType,
+)
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    alter_column,
+    create_table,
+    drop_column,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 WorkflowInvocationToSubworkflowInvocationAssociation_table = Table(
-    "workflow_invocation_to_subworkflow_invocation_association", metadata,
+    "workflow_invocation_to_subworkflow_invocation_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_id", Integer),
     Column("subworkflow_invocation_id", Integer),
     Column("workflow_step_id", Integer),
-    ForeignKeyConstraint(['workflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfi_swi_wfi'),
-    ForeignKeyConstraint(['subworkflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfi_swi_swi'),
-    ForeignKeyConstraint(['workflow_step_id'], ['workflow_step.id'], name='fk_wfi_swi_ws')
+    ForeignKeyConstraint(["workflow_invocation_id"], ["workflow_invocation.id"], name="fk_wfi_swi_wfi"),
+    ForeignKeyConstraint(["subworkflow_invocation_id"], ["workflow_invocation.id"], name="fk_wfi_swi_swi"),
+    ForeignKeyConstraint(["workflow_step_id"], ["workflow_step.id"], name="fk_wfi_swi_ws"),
 )
 
 WorkflowRequestInputStepParameter_table = Table(
-    "workflow_request_input_step_parameter", metadata,
+    "workflow_request_input_step_parameter",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_id", Integer),
     Column("workflow_step_id", Integer),
     Column("parameter_value", JSONType),
-    ForeignKeyConstraint(['workflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfreq_isp_wfi'),
-    ForeignKeyConstraint(['workflow_step_id'], ['workflow_step.id'], name='fk_wfreq_isp_ws')
+    ForeignKeyConstraint(["workflow_invocation_id"], ["workflow_invocation.id"], name="fk_wfreq_isp_wfi"),
+    ForeignKeyConstraint(["workflow_step_id"], ["workflow_step.id"], name="fk_wfreq_isp_ws"),
 )
 
 TABLES = [
@@ -40,8 +60,10 @@ TABLES = [
 
 INDEXES = [
     Index("ix_wfinv_swfinv_wfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.workflow_invocation_id),
-    Index("ix_wfinv_swfinv_swfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.subworkflow_invocation_id),
-    Index("ix_wfreq_inputstep_wfi", WorkflowRequestInputStepParameter_table.c.workflow_invocation_id)
+    Index(
+        "ix_wfinv_swfinv_swfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.subworkflow_invocation_id
+    ),
+    Index("ix_wfreq_inputstep_wfi", WorkflowRequestInputStepParameter_table.c.workflow_invocation_id),
 ]
 
 
@@ -50,9 +72,11 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    if migrate_engine.name in ['postgres', 'postgresql']:
+    if migrate_engine.name in ["postgres", "postgresql"]:
         subworkflow_id_column = Column("subworkflow_id", Integer, ForeignKey("workflow.id"), nullable=True)
-        input_subworkflow_step_id_column = Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), nullable=True)
+        input_subworkflow_step_id_column = Column(
+            "input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), nullable=True
+        )
         parent_workflow_id_column = Column("parent_workflow_id", Integer, ForeignKey("workflow.id"), nullable=True)
     else:
         subworkflow_id_column = Column("subworkflow_id", Integer, nullable=True)
diff --git a/lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py b/lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
index 0a81dfb8264..d1fe77793a3 100644
--- a/lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
+++ b/lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
@@ -2,17 +2,22 @@
 Migration script to add a last_password_change field to the user table
 """
 
-from sqlalchemy import Column, DateTime, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    MetaData,
+    Table,
+)
 
 
 def upgrade(migrate_engine):
     meta = MetaData(bind=migrate_engine)
-    account = Table('galaxy_user', meta, autoload=True)
-    lpc = Column('last_password_change', DateTime())
+    account = Table("galaxy_user", meta, autoload=True)
+    lpc = Column("last_password_change", DateTime())
     lpc.create(account)
 
 
 def downgrade(migrate_engine):
     meta = MetaData(bind=migrate_engine)
-    account = Table('galaxy_user', meta, autoload=True)
+    account = Table("galaxy_user", meta, autoload=True)
     account.c.last_password_change.drop()
diff --git a/lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py b/lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
index 65c5f83af22..9e264bfa2d5 100644
--- a/lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
+++ b/lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
@@ -4,7 +4,11 @@ Add dependencies column to jobs table
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import JSONType
 
diff --git a/lib/galaxy/model/migrate/versions/0135_add_library_tags.py b/lib/galaxy/model/migrate/versions/0135_add_library_tags.py
index 1275b60bf9e..9c5a68a883a 100644
--- a/lib/galaxy/model/migrate/versions/0135_add_library_tags.py
+++ b/lib/galaxy/model/migrate/versions/0135_add_library_tags.py
@@ -4,7 +4,13 @@ This migration script adds support for storing tags in the context of a dataset
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
@@ -14,14 +20,20 @@ metadata = MetaData()
 
 
 LibraryDatasetDatasetAssociationTagAssociation_table = Table(
-    "library_dataset_dataset_association_tag_association", metadata,
+    "library_dataset_dataset_association_tag_association",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True),
+    Column(
+        "library_dataset_dataset_association_id",
+        Integer,
+        ForeignKey("library_dataset_dataset_association.id"),
+        index=True,
+    ),
     Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
     Column("user_tname", TrimmedString(255), index=True),
     Column("value", TrimmedString(255), index=True),
     Column("user_value", TrimmedString(255), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True)
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py b/lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
index 1ef95341f06..be58fa9aa74 100644
--- a/lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
+++ b/lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
@@ -11,7 +11,7 @@ from sqlalchemy import (
     Integer,
     MetaData,
     String,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import TrimmedString
@@ -19,7 +19,7 @@ from galaxy.model.migrate.versions.util import (
     add_column,
     create_table,
     drop_column,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -27,7 +27,8 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 workflow_invocation_output_dataset_association_table = Table(
-    "workflow_invocation_output_dataset_association", metadata,
+    "workflow_invocation_output_dataset_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
@@ -36,16 +37,23 @@ workflow_invocation_output_dataset_association_table = Table(
 )
 
 workflow_invocation_output_dataset_collection_association_table = Table(
-    "workflow_invocation_output_dataset_collection_association", metadata,
+    "workflow_invocation_output_dataset_collection_association",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", name='fk_wiodca_wii'), index=True),
-    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wiodca_wsi')),
-    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id", name='fk_wiodca_dci'), index=True),
-    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id", name='fk_wiodca_woi')),
+    Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", name="fk_wiodca_wii"), index=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name="fk_wiodca_wsi")),
+    Column(
+        "dataset_collection_id",
+        Integer,
+        ForeignKey("history_dataset_collection_association.id", name="fk_wiodca_dci"),
+        index=True,
+    ),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id", name="fk_wiodca_woi")),
 )
 
 workflow_invocation_step_output_dataset_association_table = Table(
-    "workflow_invocation_step_output_dataset_association", metadata,
+    "workflow_invocation_step_output_dataset_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
     Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
@@ -53,22 +61,35 @@ workflow_invocation_step_output_dataset_association_table = Table(
 )
 
 workflow_invocation_step_output_dataset_collection_association_table = Table(
-    "workflow_invocation_step_output_dataset_collection_association", metadata,
+    "workflow_invocation_step_output_dataset_collection_association",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id", name='fk_wisodca_wisi'), index=True),
-    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wisodca_wsi')),
-    Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id", name='fk_wisodca_dci'), index=True),
+    Column(
+        "workflow_invocation_step_id",
+        Integer,
+        ForeignKey("workflow_invocation_step.id", name="fk_wisodca_wisi"),
+        index=True,
+    ),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name="fk_wisodca_wsi")),
+    Column(
+        "dataset_collection_id",
+        Integer,
+        ForeignKey("history_dataset_collection_association.id", name="fk_wisodca_dci"),
+        index=True,
+    ),
     Column("output_name", String(255), nullable=True),
 )
 
 implicit_collection_jobs_table = Table(
-    "implicit_collection_jobs", metadata,
+    "implicit_collection_jobs",
+    metadata,
     Column("id", Integer, primary_key=True),
-    Column("populated_state", TrimmedString(64), default='new', nullable=False),
+    Column("populated_state", TrimmedString(64), default="new", nullable=False),
 )
 
 implicit_collection_jobs_job_association_table = Table(
-    "implicit_collection_jobs_job_association", metadata,
+    "implicit_collection_jobs_job_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),  # Consider making this nullable...
@@ -86,7 +107,7 @@ def get_new_tables():
         workflow_invocation_step_output_dataset_association_table,
         workflow_invocation_step_output_dataset_collection_association_table,
         implicit_collection_jobs_table,
-        implicit_collection_jobs_job_association_table
+        implicit_collection_jobs_job_association_table,
     ]
 
 
@@ -100,8 +121,10 @@ def upgrade(migrate_engine):
 
     # Set default for creation to scheduled, actual mapping has new as default.
     workflow_invocation_step_state_column = Column("state", TrimmedString(64), default="scheduled")
-    if migrate_engine.name in ['postgres', 'postgresql']:
-        implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True)
+    if migrate_engine.name in ["postgres", "postgresql"]:
+        implicit_collection_jobs_id_column = Column(
+            "implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True
+        )
         job_id_column = Column("job_id", Integer, ForeignKey("job.id"), nullable=True)
     else:
         implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, nullable=True)
@@ -112,14 +135,17 @@ def upgrade(migrate_engine):
     add_column(job_id_column, "history_dataset_collection_association", metadata)
     add_column(dataset_collection_element_count_column, "dataset_collection", metadata)
 
-    implicit_collection_jobs_id_column = Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True)
+    implicit_collection_jobs_id_column = Column(
+        "implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), nullable=True
+    )
     add_column(implicit_collection_jobs_id_column, "workflow_invocation_step", metadata)
     add_column(workflow_invocation_step_state_column, "workflow_invocation_step", metadata)
 
-    cmd = \
-        "UPDATE dataset_collection SET element_count = " + \
-        "(SELECT (CASE WHEN count(*) > 0 THEN count(*) ELSE 0 END) FROM dataset_collection_element WHERE " + \
-        "dataset_collection_element.dataset_collection_id = dataset_collection.id)"
+    cmd = (
+        "UPDATE dataset_collection SET element_count = "
+        + "(SELECT (CASE WHEN count(*) > 0 THEN count(*) ELSE 0 END) FROM dataset_collection_element WHERE "
+        + "dataset_collection_element.dataset_collection_id = dataset_collection.id)"
+    )
     migrate_engine.execute(cmd)
 
 
diff --git a/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py b/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
index 03dd1f11681..5ed23b7dc6f 100644
--- a/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
+++ b/lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
@@ -4,7 +4,12 @@ Add copied_from_job_id column to jobs table
 
 import logging
 
-from sqlalchemy import Column, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 copied_from_job_id_column = Column("copied_from_job_id", Integer, nullable=True)
diff --git a/lib/galaxy/model/migrate/versions/0138_add_hda_version.py b/lib/galaxy/model/migrate/versions/0138_add_hda_version.py
index 01615304c22..f7aca943885 100644
--- a/lib/galaxy/model/migrate/versions/0138_add_hda_version.py
+++ b/lib/galaxy/model/migrate/versions/0138_add_hda_version.py
@@ -4,7 +4,12 @@ Add version column to  history_dataset_association table
 
 import logging
 
-from sqlalchemy import Column, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 version_column = Column("version", Integer, default=1)
diff --git a/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py b/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
index 4e71c5d0ba9..bd55c013a51 100644
--- a/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
+++ b/lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
@@ -11,16 +11,16 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.custom_types import (
     MetadataType,
-    TrimmedString
+    TrimmedString,
 )
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -28,14 +28,15 @@ now = datetime.datetime.utcnow
 metadata = MetaData()
 
 HistoryDatasetAssociationHistory_table = Table(
-    "history_dataset_association_history", metadata,
+    "history_dataset_association_history",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
     Column("update_time", DateTime, default=now),
     Column("version", Integer, index=True),
     Column("name", TrimmedString(255)),
     Column("extension", TrimmedString(64)),
-    Column("metadata", MetadataType, key='_metadata'),
+    Column("metadata", MetadataType, key="_metadata"),
     Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
 )
 
diff --git a/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py b/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py
index e8cad0626a7..d02febf1784 100644
--- a/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py
+++ b/lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py
@@ -4,7 +4,12 @@ Add dataset_version column to job_to_input_dataset table
 
 import logging
 
-from sqlalchemy import Column, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 dataset_version_column = Column("dataset_version", Integer)
diff --git a/lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py b/lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
index a582eece1f9..0bdc1a0cbe7 100644
--- a/lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
+++ b/lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
@@ -4,7 +4,15 @@ Migration script to add a new tables for an OpenID Connect authentication and au
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table, TEXT, VARCHAR
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+    VARCHAR,
+)
 
 from galaxy.model.custom_types import JSONType
 
@@ -12,49 +20,59 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 psa_association = Table(
-    "psa_association", metadata,
-    Column('id', Integer, primary_key=True),
-    Column('server_url', VARCHAR(255)),
-    Column('handle', VARCHAR(255)),
-    Column('secret', VARCHAR(255)),
-    Column('issued', Integer),
-    Column('lifetime', Integer),
-    Column('assoc_type', VARCHAR(64)))
+    "psa_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("server_url", VARCHAR(255)),
+    Column("handle", VARCHAR(255)),
+    Column("secret", VARCHAR(255)),
+    Column("issued", Integer),
+    Column("lifetime", Integer),
+    Column("assoc_type", VARCHAR(64)),
+)
 
 
 psa_code = Table(
-    "psa_code", metadata,
-    Column('id', Integer, primary_key=True),
-    Column('email', VARCHAR(200)),
-    Column('code', VARCHAR(32)))
+    "psa_code",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("email", VARCHAR(200)),
+    Column("code", VARCHAR(32)),
+)
 
 
 psa_nonce = Table(
-    "psa_nonce", metadata,
-    Column('id', Integer, primary_key=True),
-    Column('server_url', VARCHAR(255)),
-    Column('timestamp', Integer),
-    Column('salt', VARCHAR(40)))
+    "psa_nonce",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("server_url", VARCHAR(255)),
+    Column("timestamp", Integer),
+    Column("salt", VARCHAR(40)),
+)
 
 
 psa_partial = Table(
-    "psa_partial", metadata,
-    Column('id', Integer, primary_key=True),
-    Column('token', VARCHAR(32)),
-    Column('data', TEXT),
-    Column('next_step', Integer),
-    Column('backend', VARCHAR(32)))
+    "psa_partial",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("token", VARCHAR(32)),
+    Column("data", TEXT),
+    Column("next_step", Integer),
+    Column("backend", VARCHAR(32)),
+)
 
 
 oidc_user_authnz_tokens = Table(
-    "oidc_user_authnz_tokens", metadata,
-    Column('id', Integer, primary_key=True),
-    Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True),
-    Column('uid', VARCHAR(255)),
-    Column('provider', VARCHAR(32)),
-    Column('extra_data', JSONType, nullable=True),
-    Column('lifetime', Integer),
-    Column('assoc_type', VARCHAR(64)))
+    "oidc_user_authnz_tokens",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("uid", VARCHAR(255)),
+    Column("provider", VARCHAR(32)),
+    Column("extra_data", JSONType, nullable=True),
+    Column("lifetime", Integer),
+    Column("assoc_type", VARCHAR(64)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py b/lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
index 4fcd382a94e..4941abd8404 100644
--- a/lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
+++ b/lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
@@ -4,7 +4,11 @@ Migration script to change the 'value' column of 'user_preference' table from nu
 
 import logging
 
-from sqlalchemy import MetaData, Numeric, Table
+from sqlalchemy import (
+    MetaData,
+    Numeric,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
diff --git a/lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py b/lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
index 0bc2cba53ad..fc5b3ae3750 100644
--- a/lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
+++ b/lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
@@ -4,7 +4,16 @@ Migration script to add a new tables for CloudAuthz (tokens required to access c
 
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+    TEXT,
+)
 
 from galaxy.model.custom_types import JSONType
 
@@ -12,16 +21,18 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 cloudauthz = Table(
-    "cloudauthz", metadata,
-    Column('id', Integer, primary_key=True),
+    "cloudauthz",
+    metadata,
+    Column("id", Integer, primary_key=True),
     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-    Column('provider', String(255)),
-    Column('config', JSONType),
-    Column('authn_id', Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True),
-    Column('tokens', JSONType),
-    Column('last_update', DateTime),
-    Column('last_activity', DateTime),
-    Column('description', TEXT))
+    Column("provider", String(255)),
+    Column("config", JSONType),
+    Column("authn_id", Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True),
+    Column("tokens", JSONType),
+    Column("last_update", DateTime),
+    Column("last_activity", DateTime),
+    Column("description", TEXT),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py b/lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py
index ff42008929f..0e3facdbc26 100644
--- a/lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py
+++ b/lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py
@@ -11,12 +11,12 @@ from sqlalchemy import (
     ForeignKey,
     Integer,
     MetaData,
-    Table
+    Table,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 now = datetime.datetime.utcnow
@@ -25,11 +25,13 @@ metadata = MetaData()
 
 # New table to log cleanup events
 CleanupEventUserAssociation_table = Table(
-    "cleanup_event_user_association", metadata,
+    "cleanup_event_user_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("create_time", DateTime, default=now),
     Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py b/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
index 49f6f2d4aa2..bbcfd21b98d 100644
--- a/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
+++ b/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
@@ -20,14 +20,15 @@ from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     create_table,
     drop_index,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 WorkflowStepInput_table = Table(
-    "workflow_step_input", metadata,
+    "workflow_step_input",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
     Column("name", TEXT),
@@ -38,7 +39,13 @@ WorkflowStepInput_table = Table(
     Column("default_value", JSONType),
     Column("default_value_set", Boolean, default=False),
     Column("runtime_value", Boolean, default=False),
-    Index('ix_workflow_step_input_workflow_step_id_name_unique', "workflow_step_id", "name", unique=True, mysql_length={'name': 200}),
+    Index(
+        "ix_workflow_step_input_workflow_step_id_name_unique",
+        "workflow_step_id",
+        "name",
+        unique=True,
+        mysql_length={"name": 200},
+    ),
 )
 
 
@@ -49,11 +56,17 @@ def upgrade(migrate_engine):
 
     OldWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
     for fkc in OldWorkflowStepConnection_table.foreign_key_constraints:
-        mfkc = MigrateForeignKeyConstraint([_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name)
+        mfkc = MigrateForeignKeyConstraint(
+            [_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name
+        )
         try:
             mfkc.drop()
         except Exception:
-            log.exception("Dropping foreign key constraint '%s' from table '%s' failed", mfkc.name, OldWorkflowStepConnection_table)
+            log.exception(
+                "Dropping foreign key constraint '%s' from table '%s' failed",
+                mfkc.name,
+                OldWorkflowStepConnection_table,
+            )
 
     for index in OldWorkflowStepConnection_table.indexes:
         drop_index(index, OldWorkflowStepConnection_table)
@@ -64,7 +77,8 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     NewWorkflowStepConnection_table = Table(
-        "workflow_step_connection", metadata,
+        "workflow_step_connection",
+        metadata,
         Column("id", Integer, primary_key=True),
         Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
         Column("input_step_input_id", Integer, ForeignKey("workflow_step_input.id"), index=True),
@@ -74,15 +88,17 @@ def upgrade(migrate_engine):
     for table in (WorkflowStepInput_table, NewWorkflowStepConnection_table):
         create_table(table)
 
-    insert_step_inputs_cmd = \
-        "INSERT INTO workflow_step_input (workflow_step_id, name) " + \
-        "SELECT DISTINCT input_step_id, input_name FROM workflow_step_connection_preupgrade145"
+    insert_step_inputs_cmd = (
+        "INSERT INTO workflow_step_input (workflow_step_id, name) "
+        + "SELECT DISTINCT input_step_id, input_name FROM workflow_step_connection_preupgrade145"
+    )
     migrate_engine.execute(insert_step_inputs_cmd)
 
-    insert_step_connections_cmd = \
-        "INSERT INTO workflow_step_connection (output_step_id, input_step_input_id, output_name, input_subworkflow_step_id) " + \
-        "SELECT wsc.output_step_id, wsi.id, wsc.output_name, wsc.input_subworkflow_step_id " + \
-        "FROM workflow_step_connection_preupgrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_id = wsi.workflow_step_id AND wsc.input_name = wsi.name ORDER BY wsc.id"
+    insert_step_connections_cmd = (
+        "INSERT INTO workflow_step_connection (output_step_id, input_step_input_id, output_name, input_subworkflow_step_id) "
+        + "SELECT wsc.output_step_id, wsi.id, wsc.output_name, wsc.input_subworkflow_step_id "
+        + "FROM workflow_step_connection_preupgrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_id = wsi.workflow_step_id AND wsc.input_name = wsi.name ORDER BY wsc.id"
+    )
     migrate_engine.execute(insert_step_connections_cmd)
     drop_table(OldWorkflowStepConnection_table)
 
@@ -92,11 +108,17 @@ def downgrade(migrate_engine):
 
     NewWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
     for fkc in NewWorkflowStepConnection_table.foreign_key_constraints:
-        mfkc = MigrateForeignKeyConstraint([_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name)
+        mfkc = MigrateForeignKeyConstraint(
+            [_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name
+        )
         try:
             mfkc.drop()
         except Exception:
-            log.exception("Dropping foreign key constraint '%s' from table '%s' failed", mfkc.name, NewWorkflowStepConnection_table)
+            log.exception(
+                "Dropping foreign key constraint '%s' from table '%s' failed",
+                mfkc.name,
+                NewWorkflowStepConnection_table,
+            )
 
     for index in NewWorkflowStepConnection_table.indexes:
         drop_index(index, NewWorkflowStepConnection_table)
@@ -107,7 +129,8 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     OldWorkflowStepConnection_table = Table(
-        "workflow_step_connection", metadata,
+        "workflow_step_connection",
+        metadata,
         Column("id", Integer, primary_key=True),
         Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
         Column("input_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
@@ -117,10 +140,11 @@ def downgrade(migrate_engine):
     )
     create_table(OldWorkflowStepConnection_table)
 
-    insert_step_connections_cmd = \
-        "INSERT INTO workflow_step_connection (output_step_id, input_step_id, output_name, input_name, input_subworkflow_step_id) " + \
-        "SELECT wsc.output_step_id, wsi.workflow_step_id, wsc.output_name, wsi.name, wsc.input_subworkflow_step_id " + \
-        "FROM workflow_step_connection_predowngrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_input_id = wsi.id ORDER BY wsc.id"
+    insert_step_connections_cmd = (
+        "INSERT INTO workflow_step_connection (output_step_id, input_step_id, output_name, input_name, input_subworkflow_step_id) "
+        + "SELECT wsc.output_step_id, wsi.workflow_step_id, wsc.output_name, wsi.name, wsc.input_subworkflow_step_id "
+        + "FROM workflow_step_connection_predowngrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_input_id = wsi.id ORDER BY wsc.id"
+    )
     migrate_engine.execute(insert_step_connections_cmd)
 
     for table in (NewWorkflowStepConnection_table, WorkflowStepInput_table):
diff --git a/lib/galaxy/model/migrate/versions/0146_workflow_paths.py b/lib/galaxy/model/migrate/versions/0146_workflow_paths.py
index b0b182cdb48..5c267337377 100644
--- a/lib/galaxy/model/migrate/versions/0146_workflow_paths.py
+++ b/lib/galaxy/model/migrate/versions/0146_workflow_paths.py
@@ -12,7 +12,7 @@ from sqlalchemy import (
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/model/migrate/versions/0147_job_messages.py b/lib/galaxy/model/migrate/versions/0147_job_messages.py
index b022feb4cf3..74ea07dfe74 100644
--- a/lib/galaxy/model/migrate/versions/0147_job_messages.py
+++ b/lib/galaxy/model/migrate/versions/0147_job_messages.py
@@ -8,14 +8,14 @@ from sqlalchemy import (
     Column,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     add_column,
     alter_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -44,8 +44,8 @@ def upgrade(migrate_engine):
     add_column(task_job_stderr_column, tasks_table, metadata)
 
     for table in [jobs_table, tasks_table]:
-        alter_column('stdout', table, name='tool_stdout')
-        alter_column('stderr', table, name='tool_stderr')
+        alter_column("stdout", table, name="tool_stdout")
+        alter_column("stderr", table, name="tool_stderr")
 
 
 def downgrade(migrate_engine):
@@ -58,5 +58,5 @@ def downgrade(migrate_engine):
         drop_column(colname, jobs_table)
         drop_column(colname, tasks_table)
     for table in [jobs_table, tasks_table]:
-        alter_column('tool_stdout', table, name='stdout')
-        alter_column('tool_stderr', table, name='stderr')
+        alter_column("tool_stdout", table, name="stdout")
+        alter_column("tool_stderr", table, name="stderr")
diff --git a/lib/galaxy/model/migrate/versions/0148_add_checksum_table.py b/lib/galaxy/model/migrate/versions/0148_add_checksum_table.py
index b120711d8b5..7d865633f62 100644
--- a/lib/galaxy/model/migrate/versions/0148_add_checksum_table.py
+++ b/lib/galaxy/model/migrate/versions/0148_add_checksum_table.py
@@ -10,29 +10,31 @@ from sqlalchemy import (
     Integer,
     MetaData,
     Table,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.custom_types import JSONType
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 dataset_source_table = Table(
-    "dataset_source", metadata,
+    "dataset_source",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
     Column("source_uri", TEXT),
     Column("extra_files_path", TEXT),
-    Column("transform", JSONType)
+    Column("transform", JSONType),
 )
 
 dataset_hash_table = Table(
-    "dataset_hash", metadata,
+    "dataset_hash",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
     Column("hash_function", TEXT),
@@ -41,11 +43,12 @@ dataset_hash_table = Table(
 )
 
 dataset_source_hash_table = Table(
-    "dataset_source_hash", metadata,
+    "dataset_source_hash",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("dataset_source_id", Integer, ForeignKey("dataset_source.id"), index=True),
     Column("hash_function", TEXT),
-    Column("hash_value", TEXT)
+    Column("hash_value", TEXT),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0149_dynamic_tools.py b/lib/galaxy/model/migrate/versions/0149_dynamic_tools.py
index 2374b2b37bf..e1d4006fe58 100644
--- a/lib/galaxy/model/migrate/versions/0149_dynamic_tools.py
+++ b/lib/galaxy/model/migrate/versions/0149_dynamic_tools.py
@@ -4,10 +4,27 @@ Migration script to add the dynamic_tool table.
 import datetime
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, Unicode
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    Unicode,
+)
 
-from galaxy.model.custom_types import JSONType, UUIDType
-from galaxy.model.migrate.versions.util import add_column, create_table, drop_column, drop_table
+from galaxy.model.custom_types import (
+    JSONType,
+    UUIDType,
+)
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    create_table,
+    drop_column,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 now = datetime.datetime.utcnow
@@ -15,7 +32,8 @@ metadata = MetaData()
 
 
 DynamicTool_table = Table(
-    "dynamic_tool", metadata,
+    "dynamic_tool",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("uuid", UUIDType()),
     Column("create_time", DateTime, default=now),
@@ -40,7 +58,9 @@ def upgrade(migrate_engine):
 
     workflow_dynamic_tool_id_column = Column("dynamic_tool_id", Integer, ForeignKey("dynamic_tool.id"), nullable=True)
     add_column(workflow_dynamic_tool_id_column, "workflow_step", metadata)
-    job_workflow_dynamic_tool_id_column = Column("dynamic_tool_id", Integer, ForeignKey("dynamic_tool.id"), nullable=True)
+    job_workflow_dynamic_tool_id_column = Column(
+        "dynamic_tool_id", Integer, ForeignKey("dynamic_tool.id"), nullable=True
+    )
     add_column(job_workflow_dynamic_tool_id_column, "job", metadata)
 
 
diff --git a/lib/galaxy/model/migrate/versions/0150_add_create_time_field_for_cloudauthz.py b/lib/galaxy/model/migrate/versions/0150_add_create_time_field_for_cloudauthz.py
index 58e829db1a5..60fed37e4a9 100644
--- a/lib/galaxy/model/migrate/versions/0150_add_create_time_field_for_cloudauthz.py
+++ b/lib/galaxy/model/migrate/versions/0150_add_create_time_field_for_cloudauthz.py
@@ -5,9 +5,17 @@ Adds `create_time` columns to cloudauthz table.
 
 import logging
 
-from sqlalchemy import Column, DateTime, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -19,7 +27,7 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     cloudauthz_table = Table("cloudauthz", metadata, autoload=True)
-    create_time_column = Column('create_time', DateTime)
+    create_time_column = Column("create_time", DateTime)
     add_column(create_time_column, cloudauthz_table, metadata)
 
 
@@ -28,4 +36,4 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     cloudauthz_table = Table("cloudauthz", metadata, autoload=True)
-    drop_column('create_time', cloudauthz_table)
+    drop_column("create_time", cloudauthz_table)
diff --git a/lib/galaxy/model/migrate/versions/0151_add_worker_process.py b/lib/galaxy/model/migrate/versions/0151_add_worker_process.py
index 0b5e710deea..4a024ebbe61 100644
--- a/lib/galaxy/model/migrate/versions/0151_add_worker_process.py
+++ b/lib/galaxy/model/migrate/versions/0151_add_worker_process.py
@@ -16,7 +16,7 @@ from sqlalchemy import (
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 from galaxy.model.orm.now import now
 
@@ -25,13 +25,13 @@ metadata = MetaData()
 
 
 WorkerProcess_table = Table(
-    'worker_process',
+    "worker_process",
     metadata,
     Column("id", Integer, primary_key=True),
     Column("server_name", String(255), index=True),
     Column("hostname", String(255)),
     Column("update_time", DateTime, default=now, onupdate=now),
-    UniqueConstraint('server_name', 'hostname'),
+    UniqueConstraint("server_name", "hostname"),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py b/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py
index c1722e53cca..3e2e3c3ee73 100644
--- a/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py
+++ b/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py
@@ -7,13 +7,13 @@ import logging
 
 from sqlalchemy import (
     Column,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.custom_types import UUIDType
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -25,8 +25,8 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    uuid_column = Column('uuid', UUIDType())
-    add_column(uuid_column, 'metadata_file', metadata)
+    uuid_column = Column("uuid", UUIDType())
+    add_column(uuid_column, "metadata_file", metadata)
 
 
 def downgrade(migrate_engine):
@@ -34,4 +34,4 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('uuid', 'metadata_file', metadata)
+    drop_column("uuid", "metadata_file", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0153_add_custos_authnz_token_table.py b/lib/galaxy/model/migrate/versions/0153_add_custos_authnz_token_table.py
index 2b5f55a5aca..fa6de685a00 100644
--- a/lib/galaxy/model/migrate/versions/0153_add_custos_authnz_token_table.py
+++ b/lib/galaxy/model/migrate/versions/0153_add_custos_authnz_token_table.py
@@ -13,26 +13,27 @@ from sqlalchemy import (
     String,
     Table,
     Text,
-    UniqueConstraint
+    UniqueConstraint,
 )
 
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 CustosAuthnzToken_table = Table(
-    "custos_authnz_token", metadata,
-    Column('id', Integer, primary_key=True),
-    Column('user_id', Integer, ForeignKey("galaxy_user.id")),
-    Column('external_user_id', String(64)),
-    Column('provider', String(255)),
-    Column('access_token', Text),
-    Column('id_token', Text),
-    Column('refresh_token', Text),
+    "custos_authnz_token",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id")),
+    Column("external_user_id", String(64)),
+    Column("provider", String(255)),
+    Column("access_token", Text),
+    Column("id_token", Text),
+    Column("refresh_token", Text),
     Column("expiration_time", DateTime),
     Column("refresh_expiration_time", DateTime),
     UniqueConstraint("user_id", "external_user_id", "provider"),
diff --git a/lib/galaxy/model/migrate/versions/0154_created_from_basename.py b/lib/galaxy/model/migrate/versions/0154_created_from_basename.py
index d23701ec990..d998d45adf6 100644
--- a/lib/galaxy/model/migrate/versions/0154_created_from_basename.py
+++ b/lib/galaxy/model/migrate/versions/0154_created_from_basename.py
@@ -7,12 +7,12 @@ import logging
 from sqlalchemy import (
     Column,
     MetaData,
-    TEXT
+    TEXT,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -26,11 +26,11 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     created_from_basename_column = Column("created_from_basename", TEXT, default=None)
-    add_column(created_from_basename_column, 'dataset', metadata)
+    add_column(created_from_basename_column, "dataset", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('created_from_basename', 'dataset', metadata)
+    drop_column("created_from_basename", "dataset", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0155_job_galaxy_version.py b/lib/galaxy/model/migrate/versions/0155_job_galaxy_version.py
index ae7b10d4c1a..78b81fcf0c2 100644
--- a/lib/galaxy/model/migrate/versions/0155_job_galaxy_version.py
+++ b/lib/galaxy/model/migrate/versions/0155_job_galaxy_version.py
@@ -8,12 +8,12 @@ import logging
 from sqlalchemy import (
     Column,
     MetaData,
-    String
+    String,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -27,11 +27,11 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     created_from_basename_column = Column("galaxy_version", String(64), default=None)
-    add_column(created_from_basename_column, 'job', metadata)
+    add_column(created_from_basename_column, "job", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('galaxy_version', 'job', metadata)
+    drop_column("galaxy_version", "job", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0156_add_interactivetools.py b/lib/galaxy/model/migrate/versions/0156_add_interactivetools.py
index f6030a8a67c..23af62a7978 100644
--- a/lib/galaxy/model/migrate/versions/0156_add_interactivetools.py
+++ b/lib/galaxy/model/migrate/versions/0156_add_interactivetools.py
@@ -4,7 +4,16 @@ Migration script to add new tables for InteractiveTools.
 
 import logging
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 from galaxy.model.custom_types import JSONType
 from galaxy.model.orm.now import now
@@ -13,7 +22,8 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 interactivetool_entry_point = Table(
-    "interactivetool_entry_point", metadata,
+    "interactivetool_entry_point",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("name", TEXT),
@@ -27,17 +37,20 @@ interactivetool_entry_point = Table(
     Column("configured", Boolean, default=False),
     Column("deleted", Boolean, default=False),
     Column("created_time", DateTime, default=now),
-    Column("modified_time", DateTime, default=now, onupdate=now))
+    Column("modified_time", DateTime, default=now, onupdate=now),
+)
 
 job_container_association = Table(
-    "job_container_association", metadata,
+    "job_container_association",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("container_type", TEXT),
     Column("container_name", TEXT),
     Column("container_info", JSONType, nullable=True),
     Column("created_time", DateTime, default=now),
-    Column("modified_time", DateTime, default=now, onupdate=now))
+    Column("modified_time", DateTime, default=now, onupdate=now),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py b/lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py
index ea6441dd7cf..9675975e7c4 100644
--- a/lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py
+++ b/lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py
@@ -14,17 +14,25 @@ from sqlalchemy import (
 )
 
 from galaxy.model.custom_types import TrimmedString
-from galaxy.model.migrate.versions.util import add_column, create_table, drop_column, drop_table
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    create_table,
+    drop_column,
+    drop_table,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-validation_error_table = Table("validation_error", metadata,
+validation_error_table = Table(
+    "validation_error",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
     Column("message", TrimmedString(255)),
     Column("err_type", TrimmedString(64)),
-    Column("attributes", TEXT))
+    Column("attributes", TEXT),
+)
 
 
 def upgrade(migrate_engine):
@@ -37,10 +45,12 @@ def upgrade(migrate_engine):
     history_dataset_association_table = Table("history_dataset_association", metadata, autoload=True)
     library_dataset_dataset_association_table = Table("library_dataset_dataset_association", metadata, autoload=True)
     for dataset_instance_table in [history_dataset_association_table, library_dataset_dataset_association_table]:
-        validated_state_column = Column('validated_state', TrimmedString(64), default='unknown', server_default="unknown", nullable=False)
+        validated_state_column = Column(
+            "validated_state", TrimmedString(64), default="unknown", server_default="unknown", nullable=False
+        )
         add_column(validated_state_column, dataset_instance_table, metadata)
 
-        validated_state_message_column = Column('validated_state_message', TEXT)
+        validated_state_message_column = Column("validated_state_message", TEXT)
         add_column(validated_state_message_column, dataset_instance_table, metadata)
 
 
@@ -53,5 +63,5 @@ def downgrade(migrate_engine):
     history_dataset_association_table = Table("history_dataset_association", metadata, autoload=True)
     library_dataset_dataset_association_table = Table("library_dataset_dataset_association", metadata, autoload=True)
     for dataset_instance_table in [history_dataset_association_table, library_dataset_dataset_association_table]:
-        drop_column('validated_state', dataset_instance_table, metadata)
-        drop_column('validated_state_message', dataset_instance_table, metadata)
+        drop_column("validated_state", dataset_instance_table, metadata)
+        drop_column("validated_state_message", dataset_instance_table, metadata)
diff --git a/lib/galaxy/model/migrate/versions/0158_workflow_reports.py b/lib/galaxy/model/migrate/versions/0158_workflow_reports.py
index fcb231fc018..212c5368f66 100644
--- a/lib/galaxy/model/migrate/versions/0158_workflow_reports.py
+++ b/lib/galaxy/model/migrate/versions/0158_workflow_reports.py
@@ -4,10 +4,16 @@ Adds reports_config to workflow.
 import datetime
 import logging
 
-from sqlalchemy import Column, MetaData
+from sqlalchemy import (
+    Column,
+    MetaData,
+)
 
 from galaxy.model.custom_types import JSONType
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -19,12 +25,12 @@ def upgrade(migrate_engine):
     print(__doc__)
     metadata.reflect()
 
-    reports_config_column = Column('reports_config', JSONType, default=None)
-    add_column(reports_config_column, 'workflow', metadata)
+    reports_config_column = Column("reports_config", JSONType, default=None)
+    add_column(reports_config_column, "workflow", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('reports_config', 'workflow', metadata)
+    drop_column("reports_config", "workflow", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0159_add_job_external_id_index.py b/lib/galaxy/model/migrate/versions/0159_add_job_external_id_index.py
index c8086924ce4..d68e18ae5fd 100644
--- a/lib/galaxy/model/migrate/versions/0159_add_job_external_id_index.py
+++ b/lib/galaxy/model/migrate/versions/0159_add_job_external_id_index.py
@@ -8,7 +8,7 @@ from sqlalchemy import MetaData
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
@@ -19,10 +19,10 @@ def upgrade(migrate_engine):
     print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
-    add_index('ix_job_job_runner_external_id', 'job', 'job_runner_external_id', metadata)
+    add_index("ix_job_job_runner_external_id", "job", "job_runner_external_id", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
-    drop_index('ix_job_job_runner_external_id', 'job', 'job_runner_external_id', metadata)
+    drop_index("ix_job_job_runner_external_id", "job", "job_runner_external_id", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py b/lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py
index 45dc48954e8..7969c9e4c5a 100644
--- a/lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py
+++ b/lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py
@@ -12,7 +12,7 @@ log = logging.getLogger(__name__)
 
 def upgrade(migrate_engine):
     print(__doc__)
-    cmd = f'UPDATE history_dataset_association SET deleted={engine_true(migrate_engine)} WHERE purged AND NOT deleted;'
+    cmd = f"UPDATE history_dataset_association SET deleted={engine_true(migrate_engine)} WHERE purged AND NOT deleted;"
     try:
         migrate_engine.execute(cmd)
     except Exception:
diff --git a/lib/galaxy/model/migrate/versions/0161_add_workflow_invocation_output_table.py b/lib/galaxy/model/migrate/versions/0161_add_workflow_invocation_output_table.py
index 0cd7c0c8770..c60c103ec9b 100644
--- a/lib/galaxy/model/migrate/versions/0161_add_workflow_invocation_output_table.py
+++ b/lib/galaxy/model/migrate/versions/0161_add_workflow_invocation_output_table.py
@@ -4,7 +4,13 @@ Migration script to add a new workflow_invocation_output_parameter table to trac
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import JSONType
 
@@ -12,7 +18,8 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 workflow_invocation_output_parameter_table = Table(
-    "workflow_invocation_output_value", metadata,
+    "workflow_invocation_output_value",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
     Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
diff --git a/lib/galaxy/model/migrate/versions/0163_worker_process_pid.py b/lib/galaxy/model/migrate/versions/0163_worker_process_pid.py
index 525f002c073..7ae8578cba3 100644
--- a/lib/galaxy/model/migrate/versions/0163_worker_process_pid.py
+++ b/lib/galaxy/model/migrate/versions/0163_worker_process_pid.py
@@ -8,12 +8,12 @@ import logging
 from sqlalchemy import (
     Column,
     Integer,
-    MetaData
+    MetaData,
 )
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -25,8 +25,8 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    pid_column = Column('pid', Integer)
-    add_column(pid_column, 'worker_process', metadata)
+    pid_column = Column("pid", Integer)
+    add_column(pid_column, "worker_process", metadata)
 
 
 def downgrade(migrate_engine):
@@ -34,4 +34,4 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('pid', 'worker_process', metadata)
+    drop_column("pid", "worker_process", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0164_page_format.py b/lib/galaxy/model/migrate/versions/0164_page_format.py
index 4517939df02..5c791732e7e 100644
--- a/lib/galaxy/model/migrate/versions/0164_page_format.py
+++ b/lib/galaxy/model/migrate/versions/0164_page_format.py
@@ -4,10 +4,16 @@ Adds page content format.
 import datetime
 import logging
 
-from sqlalchemy import Column, MetaData
+from sqlalchemy import (
+    Column,
+    MetaData,
+)
 
 from galaxy.model.custom_types import TrimmedString
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -19,12 +25,14 @@ def upgrade(migrate_engine):
     print(__doc__)
     metadata.reflect()
 
-    content_format_column = Column('content_format', TrimmedString(32), default='html', server_default="html", nullable=False)
-    add_column(content_format_column, 'page_revision', metadata)
+    content_format_column = Column(
+        "content_format", TrimmedString(32), default="html", server_default="html", nullable=False
+    )
+    add_column(content_format_column, "page_revision", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('content_format', 'page_revision', metadata)
+    drop_column("content_format", "page_revision", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0165_add_content_update_time.py b/lib/galaxy/model/migrate/versions/0165_add_content_update_time.py
index 607dee1150d..cb369939ef3 100644
--- a/lib/galaxy/model/migrate/versions/0165_add_content_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0165_add_content_update_time.py
@@ -5,10 +5,21 @@ to update history.update_time when contents are changed.
 
 import logging
 
-from sqlalchemy import Column, DateTime, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    MetaData,
+    Table,
+)
 
-from galaxy.model.migrate.triggers.history_update_time_field import drop_timestamp_triggers, install_timestamp_triggers
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.triggers.history_update_time_field import (
+    drop_timestamp_triggers,
+    install_timestamp_triggers,
+)
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 from galaxy.model.orm.now import now
 
 log = logging.getLogger(__name__)
@@ -32,10 +43,10 @@ def downgrade(migrate_engine):
 
 def create_timestamps(metadata, table_name):
     target_table = Table(table_name, metadata, autoload=True)
-    if 'create_time' not in target_table.c:
+    if "create_time" not in target_table.c:
         create_time_column = Column("create_time", DateTime, default=now)
         add_column(create_time_column, target_table, metadata)
-    if 'update_time' not in target_table.c:
+    if "update_time" not in target_table.c:
         update_time_column = Column("update_time", DateTime, default=now, onupdate=now)
         add_column(update_time_column, target_table, metadata)
 
diff --git a/lib/galaxy/model/migrate/versions/0166_job_state_summary_view.py b/lib/galaxy/model/migrate/versions/0166_job_state_summary_view.py
index 062224e7abd..40b986408c6 100644
--- a/lib/galaxy/model/migrate/versions/0166_job_state_summary_view.py
+++ b/lib/galaxy/model/migrate/versions/0166_job_state_summary_view.py
@@ -6,7 +6,10 @@ Add job-state-summary view for hdca elements
 import logging
 
 from galaxy.model.view import HistoryDatasetCollectionJobStateSummary
-from galaxy.model.view.utils import CreateView, DropView
+from galaxy.model.view.utils import (
+    CreateView,
+    DropView,
+)
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/model/migrate/versions/0167_add_job_to_input_dataset_collection_element_association.py b/lib/galaxy/model/migrate/versions/0167_add_job_to_input_dataset_collection_element_association.py
index d218f487da3..681e1030959 100644
--- a/lib/galaxy/model/migrate/versions/0167_add_job_to_input_dataset_collection_element_association.py
+++ b/lib/galaxy/model/migrate/versions/0167_add_job_to_input_dataset_collection_element_association.py
@@ -4,17 +4,26 @@ Migration script to add a new job_to_input_dataset_collection_element table to t
 
 import logging
 
-from sqlalchemy import Column, ForeignKey, Integer, MetaData, Table, Unicode
+from sqlalchemy import (
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    Unicode,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 job_to_input_dataset_collection_element_table = Table(
-    "job_to_input_dataset_collection_element", metadata,
+    "job_to_input_dataset_collection_element",
+    metadata,
     Column("id", Integer, primary_key=True),
     Column("job_id", Integer, ForeignKey("job.id"), index=True),
     Column("dataset_collection_element_id", Integer, ForeignKey("dataset_collection_element.id"), index=True),
-    Column("name", Unicode(255)))
+    Column("name", Unicode(255)),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/galaxy/model/migrate/versions/0168_stored_workflow_hidden_col.py b/lib/galaxy/model/migrate/versions/0168_stored_workflow_hidden_col.py
index ad37a9ab436..5405c49bd90 100644
--- a/lib/galaxy/model/migrate/versions/0168_stored_workflow_hidden_col.py
+++ b/lib/galaxy/model/migrate/versions/0168_stored_workflow_hidden_col.py
@@ -4,9 +4,16 @@ Migration script to add a 'hidden' column to the 'StoredWorkflow' table.
 
 import logging
 
-from sqlalchemy import Boolean, Column, MetaData
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+)
 
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
@@ -20,11 +27,11 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    add_column(hidden_col, 'stored_workflow', metadata)
+    add_column(hidden_col, "stored_workflow", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('hidden', 'stored_workflow', metadata)
+    drop_column("hidden", "stored_workflow", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py b/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
index a9b56294e59..b3da46c043e 100644
--- a/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
+++ b/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
@@ -8,108 +8,44 @@ from sqlalchemy import MetaData
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 indexes = [
-    [
-        "ix_galaxy_user_activation_token",
-        "galaxy_user",
-        "activation_token"
-    ],
-    [
-        "ix_workflow_step_dynamic_tool_id",
-        "workflow_step",
-        "dynamic_tool_id"
-    ],
-    [
-        "ix_history_dataset_association_version",
-        "history_dataset_association",
-        "version"
-    ],
-    [
-        "ix_workflow_invocation_scheduler",
-        "workflow_invocation",
-        "scheduler"
-    ],
-    [
-        "ix_page_slug",
-        "page",
-        "slug"
-    ],
-    [
-        "ix_workflow_invocation_state",
-        "workflow_invocation",
-        "state"
-    ],
+    ["ix_galaxy_user_activation_token", "galaxy_user", "activation_token"],
+    ["ix_workflow_step_dynamic_tool_id", "workflow_step", "dynamic_tool_id"],
+    ["ix_history_dataset_association_version", "history_dataset_association", "version"],
+    ["ix_workflow_invocation_scheduler", "workflow_invocation", "scheduler"],
+    ["ix_page_slug", "page", "slug"],
+    ["ix_workflow_invocation_state", "workflow_invocation", "state"],
     [
         "ix_history_dataset_collection_association_implicit_collection_jobs_id",
         "history_dataset_collection_association",
-        "implicit_collection_jobs_id"
-    ],
-    [
-        "ix_workflow_step_subworkflow_id",
-        "workflow_step",
-        "subworkflow_id"
-    ],
-    [
-        "ix_dynamic_tool_update_time",
-        "dynamic_tool",
-        "update_time"
+        "implicit_collection_jobs_id",
     ],
+    ["ix_workflow_step_subworkflow_id", "workflow_step", "subworkflow_id"],
+    ["ix_dynamic_tool_update_time", "dynamic_tool", "update_time"],
     [
         "ix_library_dataset_dataset_association_extended_metadata_id",
         "library_dataset_dataset_association",
-        "extended_metadata_id"
+        "extended_metadata_id",
     ],
     [
         "ix_workflow_invocation_step_implicit_collection_jobs_id",
         "workflow_invocation_step",
-        "implicit_collection_jobs_id"
+        "implicit_collection_jobs_id",
     ],
-    [
-        "ix_workflow_invocation_step_state",
-        "workflow_invocation_step",
-        "state"
-    ],
-    [
-        "ix_workflow_invocation_history_id",
-        "workflow_invocation",
-        "history_id"
-    ],
-    [
-        "ix_workflow_parent_workflow_id",
-        "workflow",
-        "parent_workflow_id"
-    ],
-    [
-        "ix_metadata_file_uuid",
-        "metadata_file",
-        "uuid"
-    ],
-    [
-        "ix_history_dataset_collection_association_job_id",
-        "history_dataset_collection_association",
-        "job_id"
-    ],
-    [
-        "ix_galaxy_user_active",
-        "galaxy_user",
-        "active"
-    ],
-    [
-        "ix_job_dynamic_tool_id",
-        "job",
-        "dynamic_tool_id"
-    ],
-    [
-        "ix_history_dataset_association_extended_metadata_id",
-        "history_dataset_association",
-        "extended_metadata_id"
-    ]
+    ["ix_workflow_invocation_step_state", "workflow_invocation_step", "state"],
+    ["ix_workflow_invocation_history_id", "workflow_invocation", "history_id"],
+    ["ix_workflow_parent_workflow_id", "workflow", "parent_workflow_id"],
+    ["ix_metadata_file_uuid", "metadata_file", "uuid"],
+    ["ix_history_dataset_collection_association_job_id", "history_dataset_collection_association", "job_id"],
+    ["ix_galaxy_user_active", "galaxy_user", "active"],
+    ["ix_job_dynamic_tool_id", "job", "dynamic_tool_id"],
+    ["ix_history_dataset_association_extended_metadata_id", "history_dataset_association", "extended_metadata_id"],
 ]
 
 
diff --git a/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py b/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py
index d5f5fa54703..f2e8f331205 100644
--- a/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py
+++ b/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py
@@ -8,7 +8,7 @@ from sqlalchemy import MetaData
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
@@ -18,27 +18,27 @@ indexes = [
     [
         "ix_workflow_invocation_output_dataset_association_workflow_output_id",
         "workflow_invocation_output_dataset_association",
-        "workflow_output_id"
+        "workflow_output_id",
     ],
     [
         "ix_workflow_invocation_output_dataset_association_workflow_step_id",
         "workflow_invocation_output_dataset_association",
-        "workflow_step_id"
+        "workflow_step_id",
     ],
     [
         "ix_workflow_invocation_output_dataset_collection_association_workflow_output_id",
         "workflow_invocation_output_dataset_collection_association",
-        "workflow_output_id"
+        "workflow_output_id",
     ],
     [
         "ix_workflow_invocation_output_dataset_collection_association_workflow_step_id",
         "workflow_invocation_output_dataset_collection_association",
-        "workflow_step_id"
+        "workflow_step_id",
     ],
     [
         "ix_workflow_invocation_step_output_dataset_collection_association_workflow_step_id",
         "workflow_invocation_step_output_dataset_collection_association",
-        "workflow_step_id"
+        "workflow_step_id",
     ],
 ]
 
diff --git a/lib/galaxy/model/migrate/versions/0171_schemaorg_metadata.py b/lib/galaxy/model/migrate/versions/0171_schemaorg_metadata.py
index 4fb4d961192..c89af15f692 100644
--- a/lib/galaxy/model/migrate/versions/0171_schemaorg_metadata.py
+++ b/lib/galaxy/model/migrate/versions/0171_schemaorg_metadata.py
@@ -4,10 +4,17 @@ Adds license and creator metadata to workflow.
 import datetime
 import logging
 
-from sqlalchemy import Column, MetaData, TEXT
+from sqlalchemy import (
+    Column,
+    MetaData,
+    TEXT,
+)
 
 from galaxy.model.custom_types import JSONType
-from galaxy.model.migrate.versions.util import add_column, drop_column
+from galaxy.model.migrate.versions.util import (
+    add_column,
+    drop_column,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -23,11 +30,11 @@ def upgrade(migrate_engine):
     # person_metadata_column = Column('person_metadata', JSONType, default=None)
     # add_column(person_metadata_column, 'galaxy_user', metadata)
 
-    creator_metadata_column = Column('creator_metadata', JSONType, default=None)
-    add_column(creator_metadata_column, 'workflow', metadata)
+    creator_metadata_column = Column("creator_metadata", JSONType, default=None)
+    add_column(creator_metadata_column, "workflow", metadata)
 
-    license_column = Column('license', TEXT, default=None)
-    add_column(license_column, 'workflow', metadata)
+    license_column = Column("license", TEXT, default=None)
+    add_column(license_column, "workflow", metadata)
 
 
 def downgrade(migrate_engine):
@@ -35,5 +42,5 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     # drop_column('person_metadata', 'galaxy_user', metadata)
-    drop_column('creator_metadata', 'workflow', metadata)
-    drop_column('license', 'workflow', metadata)
+    drop_column("creator_metadata", "workflow", metadata)
+    drop_column("license", "workflow", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0172_it_entrypoint_requires_domain.py b/lib/galaxy/model/migrate/versions/0172_it_entrypoint_requires_domain.py
index bbc2a402add..6cb997b4005 100644
--- a/lib/galaxy/model/migrate/versions/0172_it_entrypoint_requires_domain.py
+++ b/lib/galaxy/model/migrate/versions/0172_it_entrypoint_requires_domain.py
@@ -12,7 +12,7 @@ from sqlalchemy import (
 
 from galaxy.model.migrate.versions.util import (
     add_column,
-    drop_column
+    drop_column,
 )
 
 log = logging.getLogger(__name__)
@@ -26,11 +26,11 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     requires_domain = Column("requires_domain", Boolean, default=None)
-    add_column(requires_domain, 'interactivetool_entry_point', metadata)
+    add_column(requires_domain, "interactivetool_entry_point", metadata)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('requires_domain', 'interactivetool_entry_point', metadata)
+    drop_column("requires_domain", "interactivetool_entry_point", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0173_add_job_id_to_dataset.py b/lib/galaxy/model/migrate/versions/0173_add_job_id_to_dataset.py
index 288e0e156c5..69ebfa8f067 100644
--- a/lib/galaxy/model/migrate/versions/0173_add_job_id_to_dataset.py
+++ b/lib/galaxy/model/migrate/versions/0173_add_job_id_to_dataset.py
@@ -25,12 +25,12 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    job_id_column = Column('job_id', Integer, ForeignKey('job.id'), index=True)
-    add_column(job_id_column, 'dataset', metadata, index_name='ix_dataset_job_id')
+    job_id_column = Column("job_id", Integer, ForeignKey("job.id"), index=True)
+    add_column(job_id_column, "dataset", metadata, index_name="ix_dataset_job_id")
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    drop_column('job_id', 'dataset', metadata)
+    drop_column("job_id", "dataset", metadata)
diff --git a/lib/galaxy/model/migrate/versions/0175_history_audit.py b/lib/galaxy/model/migrate/versions/0175_history_audit.py
index 521bb762396..ab47956bea6 100644
--- a/lib/galaxy/model/migrate/versions/0175_history_audit.py
+++ b/lib/galaxy/model/migrate/versions/0175_history_audit.py
@@ -5,15 +5,21 @@ Add history audit table and associated triggers
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, PrimaryKeyConstraint, Table
-
-from galaxy.model.migrate.triggers import (
-    history_update_time_field as old_triggers,  # rollback to old ones
-    update_audit_table as new_triggers,  # install me
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    PrimaryKeyConstraint,
+    Table,
 )
+
+from galaxy.model.migrate.triggers import history_update_time_field as old_triggers  # rollback to old ones
+from galaxy.model.migrate.triggers import update_audit_table as new_triggers  # install me
 from galaxy.model.migrate.versions.util import (
     create_table,
-    drop_table
+    drop_table,
 )
 
 log = logging.getLogger(__name__)
@@ -25,7 +31,7 @@ AuditTable = Table(
     metadata,
     Column("history_id", Integer, ForeignKey("history.id"), primary_key=True, nullable=False),
     Column("update_time", DateTime, default=now, primary_key=True, nullable=False),
-    PrimaryKeyConstraint(sqlite_on_conflict='IGNORE')
+    PrimaryKeyConstraint(sqlite_on_conflict="IGNORE"),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/0176_add_indexes_on_update_time.py b/lib/galaxy/model/migrate/versions/0176_add_indexes_on_update_time.py
index 87b77802ed4..12f3afe225c 100644
--- a/lib/galaxy/model/migrate/versions/0176_add_indexes_on_update_time.py
+++ b/lib/galaxy/model/migrate/versions/0176_add_indexes_on_update_time.py
@@ -8,43 +8,19 @@ from sqlalchemy import MetaData
 
 from galaxy.model.migrate.versions.util import (
     add_index,
-    drop_index
+    drop_index,
 )
 
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
 indexes = [
-    [
-        "ix_history_dataset_association_update_time",
-        "history_dataset_association",
-        "update_time"
-    ],
-    [
-        "ix_library_dataset_dataset_association_update_time",
-        "library_dataset_dataset_association",
-        "update_time"
-    ],
-    [
-        "ix_job_update_time",
-        "job",
-        "update_time"
-    ],
-    [
-        "ix_history_dataset_collection_association_update_time",
-        "history_dataset_collection_association",
-        "update_time"
-    ],
-    [
-        "ix_workflow_invocation_update_time",
-        "workflow_invocation",
-        "update_time"
-    ],
-    [
-        "ix_stored_workflow_update_time",
-        "stored_workflow",
-        "update_time"
-    ],
+    ["ix_history_dataset_association_update_time", "history_dataset_association", "update_time"],
+    ["ix_library_dataset_dataset_association_update_time", "library_dataset_dataset_association", "update_time"],
+    ["ix_job_update_time", "job", "update_time"],
+    ["ix_history_dataset_collection_association_update_time", "history_dataset_collection_association", "update_time"],
+    ["ix_workflow_invocation_update_time", "workflow_invocation", "update_time"],
+    ["ix_stored_workflow_update_time", "stored_workflow", "update_time"],
 ]
 
 
diff --git a/lib/galaxy/model/migrate/versions/0177_update_job_state_summary.py b/lib/galaxy/model/migrate/versions/0177_update_job_state_summary.py
index f8e279f833e..7823b7512ae 100644
--- a/lib/galaxy/model/migrate/versions/0177_update_job_state_summary.py
+++ b/lib/galaxy/model/migrate/versions/0177_update_job_state_summary.py
@@ -5,7 +5,10 @@ Update job-state-summary view for hdca elements to include job directly tied wit
 import logging
 
 from galaxy.model.view import HistoryDatasetCollectionJobStateSummary
-from galaxy.model.view.utils import CreateView, DropView
+from galaxy.model.view.utils import (
+    CreateView,
+    DropView,
+)
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/model/migrate/versions/0178_drop_deferredjob_table.py b/lib/galaxy/model/migrate/versions/0178_drop_deferredjob_table.py
index f3be5bd1491..1e94a7f7505 100644
--- a/lib/galaxy/model/migrate/versions/0178_drop_deferredjob_table.py
+++ b/lib/galaxy/model/migrate/versions/0178_drop_deferredjob_table.py
@@ -36,10 +36,10 @@ DeferredJob_table = Table(
     Column("state", String(64), index=True),
     Column("plugin", String(128), index=True),
     Column("params", JSONType),
-    Column("info", TEXT)
+    Column("info", TEXT),
 )
 
-deferred_job_id = Column('deferred_job_id', Integer, ForeignKey('deferred_job.id'), index=True)
+deferred_job_id = Column("deferred_job_id", Integer, ForeignKey("deferred_job.id"), index=True)
 
 
 def upgrade(migrate_engine):
@@ -48,7 +48,7 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     try:
-        drop_column(deferred_job_id.name, 'genome_index_tool_data', metadata)
+        drop_column(deferred_job_id.name, "genome_index_tool_data", metadata)
         drop_table(DeferredJob_table)
     except Exception:
         log.exception("Dropping deferred_job table failed")
@@ -60,6 +60,8 @@ def downgrade(migrate_engine):
 
     try:
         create_table(DeferredJob_table)
-        add_column(deferred_job_id, 'genome_index_tool_data', metadata, index_name='ix_genome_index_tool_data_deferred_job_id')
+        add_column(
+            deferred_job_id, "genome_index_tool_data", metadata, index_name="ix_genome_index_tool_data_deferred_job_id"
+        )
     except Exception:
         log.exception("Creating deferred_job table failed")
diff --git a/lib/galaxy/model/migrate/versions/0179_drop_transferjob_table.py b/lib/galaxy/model/migrate/versions/0179_drop_transferjob_table.py
index 26150ef0d29..acd6c76744b 100644
--- a/lib/galaxy/model/migrate/versions/0179_drop_transferjob_table.py
+++ b/lib/galaxy/model/migrate/versions/0179_drop_transferjob_table.py
@@ -36,9 +36,10 @@ TransferJob_table = Table(
     Column("path", String(1024)),
     Column("params", JSONType),
     Column("pid", Integer),
-    Column("socket", Integer))
+    Column("socket", Integer),
+)
 
-transfer_job_id = Column('transfer_job_id', Integer, ForeignKey('transfer_job.id'), index=True)
+transfer_job_id = Column("transfer_job_id", Integer, ForeignKey("transfer_job.id"), index=True)
 
 
 def upgrade(migrate_engine):
@@ -47,7 +48,7 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     try:
-        drop_column(transfer_job_id.name, 'genome_index_tool_data', metadata)
+        drop_column(transfer_job_id.name, "genome_index_tool_data", metadata)
         drop_table(TransferJob_table)
     except Exception:
         log.exception("Dropping transfer_job table failed")
@@ -59,6 +60,8 @@ def downgrade(migrate_engine):
 
     try:
         create_table(TransferJob_table)
-        add_column(transfer_job_id, 'genome_index_tool_data', metadata, index_name='ix_genome_index_tool_data_transfer_job_id')
+        add_column(
+            transfer_job_id, "genome_index_tool_data", metadata, index_name="ix_genome_index_tool_data_transfer_job_id"
+        )
     except Exception:
         log.exception("Creating transfer_job table failed")
diff --git a/lib/galaxy/model/migrate/versions/0180_add_vault_table.py b/lib/galaxy/model/migrate/versions/0180_add_vault_table.py
index d3671ccd559..7f18605b1b8 100644
--- a/lib/galaxy/model/migrate/versions/0180_add_vault_table.py
+++ b/lib/galaxy/model/migrate/versions/0180_add_vault_table.py
@@ -1,17 +1,25 @@
 import datetime
 
-from sqlalchemy import Column, DateTime, ForeignKey, MetaData, Table, Text
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    MetaData,
+    Table,
+    Text,
+)
 
 now = datetime.datetime.utcnow
 meta = MetaData()
 
 vault = Table(
-    'vault', meta,
-    Column('key', Text, primary_key=True),
-    Column('parent_key', Text, ForeignKey('vault.key'), index=True, nullable=True),
-    Column('value', Text, nullable=True),
+    "vault",
+    meta,
+    Column("key", Text, primary_key=True),
+    Column("parent_key", Text, ForeignKey("vault.key"), index=True, nullable=True),
+    Column("value", Text, nullable=True),
     Column("create_time", DateTime, default=now),
-    Column("update_time", DateTime, default=now, onupdate=now)
+    Column("update_time", DateTime, default=now, onupdate=now),
 )
 
 
diff --git a/lib/galaxy/model/migrate/versions/util.py b/lib/galaxy/model/migrate/versions/util.py
index f61ced8a927..5bc4ab61a72 100644
--- a/lib/galaxy/model/migrate/versions/util.py
+++ b/lib/galaxy/model/migrate/versions/util.py
@@ -6,7 +6,7 @@ from sqlalchemy import (
     DDL,
     Index,
     Table,
-    Text
+    Text,
 )
 from sqlalchemy.dialects.mysql import MEDIUMBLOB
 
@@ -14,46 +14,46 @@ log = logging.getLogger(__name__)
 
 
 def engine_false(migrate_engine):
-    if migrate_engine.name in ['postgres', 'postgresql']:
+    if migrate_engine.name in ["postgres", "postgresql"]:
         return "FALSE"
-    elif migrate_engine.name in ['mysql', 'sqlite']:
+    elif migrate_engine.name in ["mysql", "sqlite"]:
         return 0
     else:
-        raise Exception(f'Unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unknown database type: {migrate_engine.name}")
 
 
 def engine_true(migrate_engine):
-    if migrate_engine.name in ['postgres', 'postgresql']:
+    if migrate_engine.name in ["postgres", "postgresql"]:
         return "TRUE"
-    elif migrate_engine.name in ['mysql', 'sqlite']:
+    elif migrate_engine.name in ["mysql", "sqlite"]:
         return 1
     else:
-        raise Exception(f'Unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unknown database type: {migrate_engine.name}")
 
 
-def nextval(migrate_engine, table, col='id'):
-    if migrate_engine.name in ['postgres', 'postgresql']:
+def nextval(migrate_engine, table, col="id"):
+    if migrate_engine.name in ["postgres", "postgresql"]:
         return f"nextval('{table}_{col}_seq')"
-    elif migrate_engine.name in ['mysql', 'sqlite']:
+    elif migrate_engine.name in ["mysql", "sqlite"]:
         return "null"
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def localtimestamp(migrate_engine):
-    if migrate_engine.name in ['mysql', 'postgres', 'postgresql']:
+    if migrate_engine.name in ["mysql", "postgres", "postgresql"]:
         return "LOCALTIMESTAMP"
-    elif migrate_engine.name == 'sqlite':
+    elif migrate_engine.name == "sqlite":
         return "current_date || ' ' || current_time"
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def truncate_index_name(index_name, engine):
     # does what sqlalchemy does, see https://github.com/sqlalchemy/sqlalchemy/blob/8455a11bcc23e97afe666873cd872b0f204848d8/lib/sqlalchemy/sql/compiler.py#L4696
     max_index_name_length = engine.dialect.max_index_name_length or engine.dialect.max_identifier_length
     if len(index_name) > max_index_name_length:
-        suffix = hashlib.md5(index_name.encode('utf-8')).hexdigest()[-4:]
+        suffix = hashlib.md5(index_name.encode("utf-8")).hexdigest()[-4:]
         index_name = f"{index_name[0:max_index_name_length - 8]}_{suffix}"
     return index_name
 
@@ -91,13 +91,13 @@ def add_column(column, table, metadata, **kwds):
         migrate_engine = metadata.bind
         if not isinstance(table, Table):
             table = Table(table, metadata, autoload=True)
-        if migrate_engine.name == 'sqlite' and column.index and column.foreign_keys:
+        if migrate_engine.name == "sqlite" and column.index and column.foreign_keys:
             # SQLAlchemy Migrate has a bug when adding a column with both a
             # ForeignKey and an index in SQLite. Since SQLite creates an index
             # anyway, we can drop the explicit index creation.
             # TODO: this is hacky, but it solves this^ problem. Needs better solution.
-            index_to_create = (kwds['index_name'], table, column.name)
-            del kwds['index_name']
+            index_to_create = (kwds["index_name"], table, column.name)
+            del kwds["index_name"]
             column.index = False
         column.create(table, **kwds)
         assert column is table.c[column.name]
@@ -160,7 +160,7 @@ def add_index(index_name, table, column_name, metadata=None, **kwds):
             column = table.c[column_name]
             # MySQL cannot index a TEXT/BLOB column without specifying mysql_length
             if isinstance(column.type, (BLOB, MEDIUMBLOB, Text)):
-                kwds.setdefault('mysql_length', 200)
+                kwds.setdefault("mysql_length", 200)
             index = Index(index_name, column, **kwds)
             index.create()
         else:
diff --git a/lib/galaxy/model/none_like.py b/lib/galaxy/model/none_like.py
index f200f752926..549508d628a 100644
--- a/lib/galaxy/model/none_like.py
+++ b/lib/galaxy/model/none_like.py
@@ -19,11 +19,12 @@ class RecursiveNone:
 
     def __bool__(self):
         return False
+
     __nonzero__ = __bool__
 
 
 class NoneDataset(RecursiveNone):
-    def __init__(self, datatypes_registry=None, ext='data', dbkey='?'):
+    def __init__(self, datatypes_registry=None, ext="data", dbkey="?"):
         self.ext = self.extension = ext
         self.dbkey = dbkey
         assert datatypes_registry is not None
diff --git a/lib/galaxy/model/orm/engine_factory.py b/lib/galaxy/model/orm/engine_factory.py
index e84c796ba9d..d8def0560bd 100644
--- a/lib/galaxy/model/orm/engine_factory.py
+++ b/lib/galaxy/model/orm/engine_factory.py
@@ -25,7 +25,9 @@ def log_request_query_counts(req_id):
     try:
         times = QUERY_COUNT_LOCAL.times
         if times:
-            log.info(f"Executed [{len(times)}] SQL requests in for web request [{req_id}] ({sum(times) * 1000.0:0.3f} ms)")
+            log.info(
+                f"Executed [{len(times)}] SQL requests in for web request [{req_id}] ({sum(times) * 1000.0:0.3f} ms)"
+            )
     except AttributeError:
         # Didn't record anything so don't worry.
         pass
@@ -33,7 +35,7 @@ def log_request_query_counts(req_id):
 
 def stripwd(s):
     if s.startswith(WORKING_DIRECTORY):
-        return s[len(WORKING_DIRECTORY):]
+        return s[len(WORKING_DIRECTORY) :]
     return s
 
 
@@ -44,19 +46,27 @@ def pretty_stack():
     return rval
 
 
-def build_engine(url, engine_options, database_query_profiling_proxy=False, trace_logger=None, slow_query_log_threshold=0, thread_local_log=None, log_query_counts=False):
+def build_engine(
+    url,
+    engine_options,
+    database_query_profiling_proxy=False,
+    trace_logger=None,
+    slow_query_log_threshold=0,
+    thread_local_log=None,
+    log_query_counts=False,
+):
     if database_query_profiling_proxy or slow_query_log_threshold or thread_local_log or log_query_counts:
 
         @event.listens_for(Engine, "before_cursor_execute")
         def before_cursor_execute(conn, cursor, statement, parameters, context, executemany):
-            conn.info.setdefault('query_start_time', []).append(time.time())
+            conn.info.setdefault("query_start_time", []).append(time.time())
 
     if slow_query_log_threshold or thread_local_log or log_query_counts:
 
         @event.listens_for(Engine, "after_cursor_execute")
         def after_cursor_execute(conn, cursor, statement, parameters, context, executemany):
-            total = time.time() - conn.info['query_start_time'].pop(-1)
-            fragment = 'Slow query: '
+            total = time.time() - conn.info["query_start_time"].pop(-1)
+            fragment = "Slow query: "
             if total > slow_query_log_threshold:
                 log.debug(f"{fragment}{total:f}(s)\n{statement}\nParameters: {parameters}")
             if database_query_profiling_proxy:
@@ -67,12 +77,14 @@ def build_engine(url, engine_options, database_query_profiling_proxy=False, trac
                         statement=statement,
                         parameters=parameters,
                         executemany=executemany,
-                        duration=total
+                        duration=total,
                     )
                 else:
                     thread_ident = threading.get_ident()
                     stack = " > ".join(pretty_stack())
-                    log.debug(f"statement: {statement} parameters: {parameters} executemany: {executemany} duration: {total} stack: {stack} thread: {thread_ident}")
+                    log.debug(
+                        f"statement: {statement} parameters: {parameters} executemany: {executemany} duration: {total} stack: {stack} thread: {thread_ident}"
+                    )
             if log_query_counts:
                 try:
                     QUERY_COUNT_LOCAL.times.append(total)
@@ -89,8 +101,8 @@ def build_engine(url, engine_options, database_query_profiling_proxy=False, trac
     # Set check_same_thread to False for sqlite, handled by request-specific session
     # See https://fastapi.tiangolo.com/tutorial/sql-databases/#note
     connect_args = {}
-    if 'sqlite://' in url:
-        connect_args['check_same_thread'] = False
+    if "sqlite://" in url:
+        connect_args["check_same_thread"] = False
     # Create the database engine
     engine = create_engine(url, connect_args=connect_args, **engine_options)
     register_after_fork(engine, lambda e: e.dispose())
diff --git a/lib/galaxy/model/orm/now.py b/lib/galaxy/model/orm/now.py
index 1b90b5bff9a..d44fa59f6cd 100644
--- a/lib/galaxy/model/orm/now.py
+++ b/lib/galaxy/model/orm/now.py
@@ -10,4 +10,4 @@ from datetime import datetime
 # Return the current time in UTC without any timezone information
 now = datetime.utcnow
 
-__all__ = ('now', )
+__all__ = ("now",)
diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index 86ce5c03195..f62f4fb0e73 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -9,55 +9,58 @@ import sys
 from migrate.versioning.shell import main as migrate_main
 
 from galaxy.util.path import get_ext
-from galaxy.util.properties import find_config_file, get_data_dir, load_app_properties
+from galaxy.util.properties import (
+    find_config_file,
+    get_data_dir,
+    load_app_properties,
+)
 from galaxy.util.script import populate_config_args
 
-
 log = logging.getLogger(__name__)
 
-DEFAULT_CONFIG_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'config', 'sample'))
-DEFAULT_CONFIG_NAMES = ['galaxy', 'universe_wsgi']
-DEFAULT_CONFIG_PREFIX = ''
-DEFAULT_DATABASE = 'galaxy'
+DEFAULT_CONFIG_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "config", "sample"))
+DEFAULT_CONFIG_NAMES = ["galaxy", "universe_wsgi"]
+DEFAULT_CONFIG_PREFIX = ""
+DEFAULT_DATABASE = "galaxy"
 
 DATABASE = {
-    "galaxy":
-        {
-            'repo': 'galaxy/model/migrate',
-            'default_sqlite_file': 'universe.sqlite',
-            'config_override': 'GALAXY_CONFIG_',
-        },
-    "tools":
-        {
-            'repo': 'galaxy/model/tool_shed_install/migrate',
-            'default_sqlite_file': 'universe.sqlite',
-            'config_override': 'GALAXY_CONFIG_',
-        },
-    "tool_shed":
-        {
-            'repo': 'tool_shed/webapp/model/migrate',
-            'config_names': ['tool_shed', 'tool_shed_wsgi'],
-            'default_sqlite_file': 'community.sqlite',
-            'config_override': 'TOOL_SHED_CONFIG_',
-            'config_section': 'tool_shed',
-        },
-    "install":
-        {
-            'repo': 'galaxy/model/tool_shed_install/migrate',
-            'config_prefix': 'install_',
-            'default_sqlite_file': 'install.sqlite',
-            'config_override': 'GALAXY_INSTALL_CONFIG_',
-        },
+    "galaxy": {
+        "repo": "galaxy/model/migrate",
+        "default_sqlite_file": "universe.sqlite",
+        "config_override": "GALAXY_CONFIG_",
+    },
+    "tools": {
+        "repo": "galaxy/model/tool_shed_install/migrate",
+        "default_sqlite_file": "universe.sqlite",
+        "config_override": "GALAXY_CONFIG_",
+    },
+    "tool_shed": {
+        "repo": "tool_shed/webapp/model/migrate",
+        "config_names": ["tool_shed", "tool_shed_wsgi"],
+        "default_sqlite_file": "community.sqlite",
+        "config_override": "TOOL_SHED_CONFIG_",
+        "config_section": "tool_shed",
+    },
+    "install": {
+        "repo": "galaxy/model/tool_shed_install/migrate",
+        "config_prefix": "install_",
+        "default_sqlite_file": "install.sqlite",
+        "config_override": "GALAXY_INSTALL_CONFIG_",
+    },
 }
 
 
 def _read_model_arguments(argv, use_argparse=False):
     if use_argparse:
         parser = argparse.ArgumentParser()
-        parser.add_argument('database', metavar='DATABASE', type=str,
-                            default="galaxy",
-                            nargs='?',
-                            help='database to target (galaxy, tool_shed, install)')
+        parser.add_argument(
+            "database",
+            metavar="DATABASE",
+            type=str,
+            default="galaxy",
+            nargs="?",
+            help="database to target (galaxy, tool_shed, install)",
+        )
         populate_config_args(parser)
         args = parser.parse_args(argv[1:] if argv else [])
         return args.config_file, args.config_section, args.database
@@ -76,7 +79,7 @@ def _read_model_arguments(argv, use_argparse=False):
         if argv and (argv[-1] in DATABASE):
             database = argv.pop()  # database name tool_shed, galaxy, or install.
         else:
-            database = 'galaxy'
+            database = "galaxy"
         return config_file, config_section, database
 
 
@@ -113,35 +116,43 @@ def get_config(argv, use_argparse=True, cwd=None):
     config_file, config_section, database = _read_model_arguments(argv, use_argparse=use_argparse)
     database_defaults = DATABASE[database]
     if config_file is None:
-        config_names = database_defaults.get('config_names', DEFAULT_CONFIG_NAMES)
+        config_names = database_defaults.get("config_names", DEFAULT_CONFIG_NAMES)
         if cwd:
-            cwd = [cwd, os.path.join(cwd, 'config')]
+            cwd = [cwd, os.path.join(cwd, "config")]
         else:
             cwd = [DEFAULT_CONFIG_DIR]
         config_file = find_config_file(config_names, dirs=cwd)
 
-    repo = os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, database_defaults['repo'])
-    config_prefix = database_defaults.get('config_prefix', DEFAULT_CONFIG_PREFIX)
-    config_override = database_defaults.get('config_override', 'GALAXY_CONFIG_')
-    default_sqlite_file = database_defaults['default_sqlite_file']
+    repo = os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, database_defaults["repo"])
+    config_prefix = database_defaults.get("config_prefix", DEFAULT_CONFIG_PREFIX)
+    config_override = database_defaults.get("config_override", "GALAXY_CONFIG_")
+    default_sqlite_file = database_defaults["default_sqlite_file"]
     if config_section is None:
-        if not config_file or get_ext(config_file, ignore='sample') == 'yaml':
-            config_section = database_defaults.get('config_section', None)
+        if not config_file or get_ext(config_file, ignore="sample") == "yaml":
+            config_section = database_defaults.get("config_section", None)
         else:
             # Just use the default found by load_app_properties.
             config_section = None
-    properties = load_app_properties(config_file=config_file, config_prefix=config_override, config_section=config_section)
+    properties = load_app_properties(
+        config_file=config_file, config_prefix=config_override, config_section=config_section
+    )
 
     if (f"{config_prefix}database_connection") in properties:
         db_url = properties[f"{config_prefix}database_connection"]
     else:
         db_url = f"sqlite:///{os.path.join(get_data_dir(properties), default_sqlite_file)}?isolation_level=IMMEDIATE"
-    install_database_connection = properties.get('install_database_connection')
+    install_database_connection = properties.get("install_database_connection")
 
-    return dict(db_url=db_url, repo=repo, config_file=config_file, database=database, install_database_connection=install_database_connection)
+    return dict(
+        db_url=db_url,
+        repo=repo,
+        config_file=config_file,
+        database=database,
+        install_database_connection=install_database_connection,
+    )
 
 
 def manage_db():
     # Migrate has its own args, so cannot use argparse
     config = get_config(sys.argv, use_argparse=False, cwd=os.getcwd())
-    migrate_main(repository=config['repo'], url=config['db_url'])
+    migrate_main(repository=config["repo"], url=config["db_url"])
diff --git a/lib/galaxy/model/search.py b/lib/galaxy/model/search.py
index 19b59c459bb..4208677c970 100644
--- a/lib/galaxy/model/search.py
+++ b/lib/galaxy/model/search.py
@@ -53,7 +53,7 @@ from galaxy.model import (
     Page,
     PageRevision,
     StoredWorkflow,
-    StoredWorkflowTagAssociation
+    StoredWorkflowTagAssociation,
 )
 from galaxy.model.tool_shed_install import ToolVersion
 
@@ -100,22 +100,22 @@ class ViewQueryBaseClass:
         self.post_filter = []
 
     def decode_query_ids(self, trans, conditional):
-        if conditional.operator == 'and':
+        if conditional.operator == "and":
             self.decode_query_ids(trans, conditional.left)
             self.decode_query_ids(trans, conditional.right)
         else:
-            left_base = conditional.left.split('.')[0]
+            left_base = conditional.left.split(".")[0]
             if left_base in self.FIELDS:
                 field = self.FIELDS[left_base]
                 if field.id_decode:
                     conditional.right = trans.security.decode_id(conditional.right)
 
     def filter(self, left, operator, right):
-        if operator == 'and':
+        if operator == "and":
             self.filter(left.left, left.operator, left.right)
             self.filter(right.left, right.operator, right.right)
         else:
-            left_base = left.split('.')[0]
+            left_base = left.split(".")[0]
             if left_base in self.FIELDS:
                 self.do_query = True
                 field = self.FIELDS[left_base]
@@ -161,24 +161,20 @@ class ViewQueryBaseClass:
 
 def library_extended_metadata_filter(view, left, operator, right):
     view.do_query = True
-    if 'extended_metadata_joined' not in view.state:
+    if "extended_metadata_joined" not in view.state:
         view.query = view.query.join(ExtendedMetadata)
-        view.state['extended_metadata_joined'] = True
+        view.state["extended_metadata_joined"] = True
     alias = aliased(ExtendedMetadataIndex)
     field = f"/{'/'.join(left.split('.')[1:])}"
     view.query = view.query.filter(
-        and_(
-            ExtendedMetadata.id == alias.extended_metadata_id,
-            alias.path == field,
-            alias.value == str(right)
-        )
+        and_(ExtendedMetadata.id == alias.extended_metadata_id, alias.path == field, alias.value == str(right))
     )
 
 
 def ldda_parent_library_filter(item, left, operator, right):
-    if operator == '=':
+    if operator == "=":
         return right == item.library_dataset.folder.parent_library.id
-    elif operator == '!=':
+    elif operator == "!=":
         return right != item.library_dataset.folder.parent_library.id
     raise GalaxyParseError(f"Invalid comparison operator: {operator}")
 
@@ -186,12 +182,12 @@ def ldda_parent_library_filter(item, left, operator, right):
 class LibraryDatasetDatasetView(ViewQueryBaseClass):
     VIEW_NAME = "library_dataset_dataset"
     FIELDS = {
-        'extended_metadata': ViewField('extended_metadata', handler=library_extended_metadata_filter),
-        'name': ViewField('name', sqlalchemy_field=(LibraryDatasetDatasetAssociation, "name")),
-        'id': ViewField('id', sqlalchemy_field=(LibraryDatasetDatasetAssociation, 'id'), id_decode=True),
-        'deleted': ViewField('deleted', sqlalchemy_field=(LibraryDatasetDatasetAssociation, "deleted")),
-        'parent_library_id': ViewField('parent_library_id', id_decode=True, post_filter=ldda_parent_library_filter),
-        'data_type': ViewField('data_type', sqlalchemy_field=(LibraryDatasetDatasetAssociation, "extension")),
+        "extended_metadata": ViewField("extended_metadata", handler=library_extended_metadata_filter),
+        "name": ViewField("name", sqlalchemy_field=(LibraryDatasetDatasetAssociation, "name")),
+        "id": ViewField("id", sqlalchemy_field=(LibraryDatasetDatasetAssociation, "id"), id_decode=True),
+        "deleted": ViewField("deleted", sqlalchemy_field=(LibraryDatasetDatasetAssociation, "deleted")),
+        "parent_library_id": ViewField("parent_library_id", id_decode=True, post_filter=ldda_parent_library_filter),
+        "data_type": ViewField("data_type", sqlalchemy_field=(LibraryDatasetDatasetAssociation, "extension")),
     }
 
     def search(self, trans):
@@ -202,12 +198,13 @@ class LibraryDatasetDatasetView(ViewQueryBaseClass):
 # Library Searching
 ##################
 
+
 class LibraryView(ViewQueryBaseClass):
     VIEW_NAME = "library"
     FIELDS = {
-        'name': ViewField('name', sqlalchemy_field=(Library, "name")),
-        'id': ViewField('id', sqlalchemy_field=(Library, 'id'), id_decode=True),
-        'deleted': ViewField('deleted', sqlalchemy_field=(Library, "deleted")),
+        "name": ViewField("name", sqlalchemy_field=(Library, "name")),
+        "id": ViewField("id", sqlalchemy_field=(Library, "id"), id_decode=True),
+        "deleted": ViewField("deleted", sqlalchemy_field=(Library, "deleted")),
     }
 
     def search(self, trans):
@@ -218,18 +215,18 @@ class LibraryView(ViewQueryBaseClass):
 # Library Folder Searching
 ##################
 def library_folder_parent_library_id_filter(item, left, operator, right):
-    if operator == '=':
+    if operator == "=":
         return item.parent_library.id == right
-    if operator == '!=':
+    if operator == "!=":
         return item.parent_library.id != right
     raise GalaxyParseError(f"Invalid comparison operator: {operator}")
 
 
 def library_path_filter(item, left, operator, right):
     lpath = f"/{'/'.join(item.library_path)}"
-    if operator == '=':
+    if operator == "=":
         return lpath == right
-    if operator == '!=':
+    if operator == "!=":
         return lpath != right
     raise GalaxyParseError(f"Invalid comparison operator: {operator}")
 
@@ -237,11 +234,13 @@ def library_path_filter(item, left, operator, right):
 class LibraryFolderView(ViewQueryBaseClass):
     VIEW_NAME = "library_folder"
     FIELDS = {
-        'name': ViewField('name', sqlalchemy_field=(LibraryFolder, "name")),
-        'id': ViewField('id', sqlalchemy_field=(LibraryFolder, "id"), id_decode=True),
-        'parent_id': ViewField('parent_id', sqlalchemy_field=(LibraryFolder, "parent_id"), id_decode=True),
-        'parent_library_id': ViewField('parent_library_id', post_filter=library_folder_parent_library_id_filter, id_decode=True),
-        'library_path': ViewField('library_path', post_filter=library_path_filter)
+        "name": ViewField("name", sqlalchemy_field=(LibraryFolder, "name")),
+        "id": ViewField("id", sqlalchemy_field=(LibraryFolder, "id"), id_decode=True),
+        "parent_id": ViewField("parent_id", sqlalchemy_field=(LibraryFolder, "parent_id"), id_decode=True),
+        "parent_library_id": ViewField(
+            "parent_library_id", post_filter=library_folder_parent_library_id_filter, id_decode=True
+        ),
+        "library_path": ViewField("library_path", post_filter=library_path_filter),
     }
 
     def search(self, trans):
@@ -252,9 +251,9 @@ class LibraryFolderView(ViewQueryBaseClass):
 # Library Dataset Searching
 ##################
 def library_dataset_name_filter(item, left, operator, right):
-    if operator == '=':
+    if operator == "=":
         return item.name == right
-    if operator == '!=':
+    if operator == "!=":
         return item.name != right
     raise GalaxyParseError(f"Invalid comparison operator: {operator}")
 
@@ -262,9 +261,9 @@ def library_dataset_name_filter(item, left, operator, right):
 class LibraryDatasetView(ViewQueryBaseClass):
     VIEW_NAME = "library_dataset"
     FIELDS = {
-        'name': ViewField('name', post_filter=library_dataset_name_filter),
-        'id': ViewField('id', sqlalchemy_field=(LibraryDataset, "id"), id_decode=True),
-        'folder_id': ViewField('folder_id', sqlalchemy_field=(LibraryDataset, "folder_id"), id_decode=True)
+        "name": ViewField("name", post_filter=library_dataset_name_filter),
+        "id": ViewField("id", sqlalchemy_field=(LibraryDataset, "id"), id_decode=True),
+        "folder_id": ViewField("folder_id", sqlalchemy_field=(LibraryDataset, "folder_id"), id_decode=True),
     }
 
     def search(self, trans):
@@ -277,8 +276,8 @@ class LibraryDatasetView(ViewQueryBaseClass):
 class ToolView(ViewQueryBaseClass):
     VIEW_NAME = "tool"
     FIELDS = {
-        'tool_id': ViewField('name', sqlalchemy_field=(ToolVersion, "tool_id")),
-        'id': ViewField('id', sqlalchemy_field=(ToolVersion, "id")),
+        "tool_id": ViewField("name", sqlalchemy_field=(ToolVersion, "tool_id")),
+        "id": ViewField("id", sqlalchemy_field=(ToolVersion, "id")),
     }
 
     def search(self, trans):
@@ -294,9 +293,7 @@ def history_dataset_handle_tag(view, left, operator, right):
         # aliasing the tag association table, so multiple links to different tags can be formed during a single query
         tag_table = aliased(HistoryDatasetAssociationTagAssociation)
 
-        view.query = view.query.filter(
-            HistoryDatasetAssociation.id == tag_table.history_dataset_association_id
-        )
+        view.query = view.query.filter(HistoryDatasetAssociation.id == tag_table.history_dataset_association_id)
         tmp = right.split(":")
         view.query = view.query.filter(tag_table.user_tname == tmp[0])
         if len(tmp) > 1:
@@ -307,35 +304,37 @@ def history_dataset_handle_tag(view, left, operator, right):
 
 def history_dataset_extended_metadata_filter(view, left, operator, right):
     view.do_query = True
-    if 'extended_metadata_joined' not in view.state:
+    if "extended_metadata_joined" not in view.state:
         view.query = view.query.join(ExtendedMetadata)
-        view.state['extended_metadata_joined'] = True
+        view.state["extended_metadata_joined"] = True
     alias = aliased(ExtendedMetadataIndex)
     field = f"/{'/'.join(left.split('.')[1:])}"
     view.query = view.query.filter(
-        and_(
-            ExtendedMetadata.id == alias.extended_metadata_id,
-            alias.path == field,
-            alias.value == str(right)
-        )
+        and_(ExtendedMetadata.id == alias.extended_metadata_id, alias.path == field, alias.value == str(right))
     )
 
 
 class HistoryDatasetView(ViewQueryBaseClass):
     DOMAIN = "history_dataset"
     FIELDS = {
-        'name': ViewField('name', sqlalchemy_field=(HistoryDatasetAssociation, "name")),
-        'id': ViewField('id', sqlalchemy_field=(HistoryDatasetAssociation, "id"), id_decode=True),
-        'history_id': ViewField('history_id', sqlalchemy_field=(HistoryDatasetAssociation, "history_id"), id_decode=True),
-        'tag': ViewField("tag", handler=history_dataset_handle_tag),
-        'copied_from_ldda_id': ViewField("copied_from_ldda_id",
-                                         sqlalchemy_field=(HistoryDatasetAssociation, "copied_from_library_dataset_dataset_association_id"),
-                                         id_decode=True),
-        'copied_from_hda_id': ViewField("copied_from_hda_id",
-                                        sqlalchemy_field=(HistoryDatasetAssociation, "copied_from_history_dataset_association_id"),
-                                        id_decode=True),
-        'deleted': ViewField('deleted', sqlalchemy_field=(HistoryDatasetAssociation, "deleted")),
-        'extended_metadata': ViewField('extended_metadata', handler=history_dataset_extended_metadata_filter)
+        "name": ViewField("name", sqlalchemy_field=(HistoryDatasetAssociation, "name")),
+        "id": ViewField("id", sqlalchemy_field=(HistoryDatasetAssociation, "id"), id_decode=True),
+        "history_id": ViewField(
+            "history_id", sqlalchemy_field=(HistoryDatasetAssociation, "history_id"), id_decode=True
+        ),
+        "tag": ViewField("tag", handler=history_dataset_handle_tag),
+        "copied_from_ldda_id": ViewField(
+            "copied_from_ldda_id",
+            sqlalchemy_field=(HistoryDatasetAssociation, "copied_from_library_dataset_dataset_association_id"),
+            id_decode=True,
+        ),
+        "copied_from_hda_id": ViewField(
+            "copied_from_hda_id",
+            sqlalchemy_field=(HistoryDatasetAssociation, "copied_from_history_dataset_association_id"),
+            id_decode=True,
+        ),
+        "deleted": ViewField("deleted", sqlalchemy_field=(HistoryDatasetAssociation, "deleted")),
+        "extended_metadata": ViewField("extended_metadata", handler=history_dataset_extended_metadata_filter),
     }
 
     def search(self, trans):
@@ -351,9 +350,7 @@ def history_handle_tag(view, left, operator, right):
     if operator == "=":
         view.do_query = True
         tag_table = aliased(HistoryTagAssociation)
-        view.query = view.query.filter(
-            History.id == tag_table.history_id
-        )
+        view.query = view.query.filter(History.id == tag_table.history_id)
         tmp = right.split(":")
         view.query = view.query.filter(tag_table.user_tname == tmp[0])
         if len(tmp) > 1:
@@ -365,16 +362,19 @@ def history_handle_tag(view, left, operator, right):
 def history_handle_annotation(view, left, operator, right):
     if operator == "=":
         view.do_query = True
-        view.query = view.query.filter(and_(
-            HistoryAnnotationAssociation.history_id == History.id,
-            HistoryAnnotationAssociation.annotation == right
-        ))
+        view.query = view.query.filter(
+            and_(
+                HistoryAnnotationAssociation.history_id == History.id, HistoryAnnotationAssociation.annotation == right
+            )
+        )
     elif operator == "like":
         view.do_query = True
-        view.query = view.query.filter(and_(
-            HistoryAnnotationAssociation.history_id == History.id,
-            HistoryAnnotationAssociation.annotation.like(right)
-        ))
+        view.query = view.query.filter(
+            and_(
+                HistoryAnnotationAssociation.history_id == History.id,
+                HistoryAnnotationAssociation.annotation.like(right),
+            )
+        )
     else:
         raise GalaxyParseError(f"Invalid comparison operator: {operator}")
 
@@ -382,11 +382,11 @@ def history_handle_annotation(view, left, operator, right):
 class HistoryView(ViewQueryBaseClass):
     DOMAIN = "history"
     FIELDS = {
-        'name': ViewField('name', sqlalchemy_field=(History, "name")),
-        'id': ViewField('id', sqlalchemy_field=(History, "id"), id_decode=True),
-        'tag': ViewField("tag", handler=history_handle_tag),
-        'annotation': ViewField("annotation", handler=history_handle_annotation),
-        'deleted': ViewField('deleted', sqlalchemy_field=(History, "deleted"))
+        "name": ViewField("name", sqlalchemy_field=(History, "name")),
+        "id": ViewField("id", sqlalchemy_field=(History, "id"), id_decode=True),
+        "tag": ViewField("tag", handler=history_handle_tag),
+        "annotation": ViewField("annotation", handler=history_handle_annotation),
+        "deleted": ViewField("deleted", sqlalchemy_field=(History, "deleted")),
     }
 
     def search(self, trans):
@@ -401,9 +401,7 @@ class HistoryView(ViewQueryBaseClass):
 def workflow_tag_handler(view, left, operator, right):
     if operator == "=":
         view.do_query = True
-        view.query = view.query.filter(
-            StoredWorkflow.id == StoredWorkflowTagAssociation.stored_workflow_id
-        )
+        view.query = view.query.filter(StoredWorkflow.id == StoredWorkflowTagAssociation.stored_workflow_id)
         tmp = right.split(":")
         view.query = view.query.filter(StoredWorkflowTagAssociation.user_tname == tmp[0])
         if len(tmp) > 1:
@@ -415,10 +413,10 @@ def workflow_tag_handler(view, left, operator, right):
 class WorkflowView(ViewQueryBaseClass):
     DOMAIN = "workflow"
     FIELDS = {
-        'name': ViewField('name', sqlalchemy_field=(StoredWorkflow, "name")),
-        'id': ViewField('id', sqlalchemy_field=(StoredWorkflow, "id"), id_decode=True),
-        'tag': ViewField('tag', handler=workflow_tag_handler),
-        'deleted': ViewField('deleted', sqlalchemy_field=(StoredWorkflow, "deleted")),
+        "name": ViewField("name", sqlalchemy_field=(StoredWorkflow, "name")),
+        "id": ViewField("id", sqlalchemy_field=(StoredWorkflow, "id"), id_decode=True),
+        "tag": ViewField("tag", handler=workflow_tag_handler),
+        "deleted": ViewField("deleted", sqlalchemy_field=(StoredWorkflow, "deleted")),
     }
 
     def search(self, trans):
@@ -433,64 +431,40 @@ class WorkflowView(ViewQueryBaseClass):
 def job_param_filter(view, left, operator, right):
     view.do_query = True
     alias = aliased(JobParameter)
-    param_name = re.sub(r'^param.', '', left)
-    view.query = view.query.filter(
-        and_(
-            Job.id == alias.job_id,
-            alias.name == param_name,
-            alias.value == dumps(right)
-        )
-    )
+    param_name = re.sub(r"^param.", "", left)
+    view.query = view.query.filter(and_(Job.id == alias.job_id, alias.name == param_name, alias.value == dumps(right)))
 
 
 def job_input_hda_filter(view, left, operator, right):
     view.do_query = True
     alias = aliased(JobToInputDatasetAssociation)
-    param_name = re.sub(r'^input_hda.', '', left)
-    view.query = view.query.filter(
-        and_(
-            Job.id == alias.job_id,
-            alias.name == param_name,
-            alias.dataset_id == right
-        )
-    )
+    param_name = re.sub(r"^input_hda.", "", left)
+    view.query = view.query.filter(and_(Job.id == alias.job_id, alias.name == param_name, alias.dataset_id == right))
 
 
 def job_input_ldda_filter(view, left, operator, right):
     view.do_query = True
     alias = aliased(JobToInputLibraryDatasetAssociation)
-    param_name = re.sub(r'^input_ldda.', '', left)
-    view.query = view.query.filter(
-        and_(
-            Job.id == alias.job_id,
-            alias.name == param_name,
-            alias.ldda_id == right
-        )
-    )
+    param_name = re.sub(r"^input_ldda.", "", left)
+    view.query = view.query.filter(and_(Job.id == alias.job_id, alias.name == param_name, alias.ldda_id == right))
 
 
 def job_output_hda_filter(view, left, operator, right):
     view.do_query = True
     alias = aliased(JobToOutputDatasetAssociation)
-    param_name = re.sub(r'^output_hda.', '', left)
-    view.query = view.query.filter(
-        and_(
-            Job.id == alias.job_id,
-            alias.name == param_name,
-            alias.dataset_id == right
-        )
-    )
+    param_name = re.sub(r"^output_hda.", "", left)
+    view.query = view.query.filter(and_(Job.id == alias.job_id, alias.name == param_name, alias.dataset_id == right))
 
 
 class JobView(ViewQueryBaseClass):
     DOMAIN = "job"
     FIELDS = {
-        'tool_name': ViewField('tool_name', sqlalchemy_field=(Job, "tool_id")),
-        'state': ViewField('state', sqlalchemy_field=(Job, "state")),
-        'param': ViewField('param', handler=job_param_filter),
-        'input_ldda': ViewField('input_ldda', handler=job_input_ldda_filter, id_decode=True),
-        'input_hda': ViewField('input_hda', handler=job_input_hda_filter, id_decode=True),
-        'output_hda': ViewField('output_hda', handler=job_output_hda_filter, id_decode=True)
+        "tool_name": ViewField("tool_name", sqlalchemy_field=(Job, "tool_id")),
+        "state": ViewField("state", sqlalchemy_field=(Job, "state")),
+        "param": ViewField("param", handler=job_param_filter),
+        "input_ldda": ViewField("input_ldda", handler=job_input_ldda_filter, id_decode=True),
+        "input_hda": ViewField("input_hda", handler=job_input_hda_filter, id_decode=True),
+        "output_hda": ViewField("output_hda", handler=job_output_hda_filter, id_decode=True),
     }
 
     def search(self, trans):
@@ -505,10 +479,10 @@ class JobView(ViewQueryBaseClass):
 class PageView(ViewQueryBaseClass):
     DOMAIN = "page"
     FIELDS = {
-        'id': ViewField('id', sqlalchemy_field=(Page, "id"), id_decode=True),
-        'slug': ViewField('slug', sqlalchemy_field=(Page, "slug")),
-        'title': ViewField('title', sqlalchemy_field=(Page, "title")),
-        'deleted': ViewField('deleted', sqlalchemy_field=(Page, "deleted"))
+        "id": ViewField("id", sqlalchemy_field=(Page, "id"), id_decode=True),
+        "slug": ViewField("slug", sqlalchemy_field=(Page, "slug")),
+        "title": ViewField("title", sqlalchemy_field=(Page, "title")),
+        "deleted": ViewField("deleted", sqlalchemy_field=(Page, "deleted")),
     }
 
     def search(self, trans):
@@ -523,9 +497,9 @@ class PageView(ViewQueryBaseClass):
 class PageRevisionView(ViewQueryBaseClass):
     DOMAIN = "page_revision"
     FIELDS = {
-        'id': ViewField('id', sqlalchemy_field=(PageRevision, "id"), id_decode=True),
-        'title': ViewField('title', sqlalchemy_field=(PageRevision, "title")),
-        'page_id': ViewField('page_id', sqlalchemy_field=(PageRevision, "page_id"), id_decode=True),
+        "id": ViewField("id", sqlalchemy_field=(PageRevision, "id"), id_decode=True),
+        "title": ViewField("title", sqlalchemy_field=(PageRevision, "title")),
+        "page_id": ViewField("page_id", sqlalchemy_field=(PageRevision, "page_id"), id_decode=True),
     }
 
     def search(self, trans):
@@ -536,20 +510,20 @@ class PageRevisionView(ViewQueryBaseClass):
 # that will handle queries.
 
 view_mapping = {
-    'library': LibraryView,
-    'library_folder': LibraryFolderView,
-    'library_dataset_dataset': LibraryDatasetDatasetView,
-    'library_dataset': LibraryDatasetView,
-    'lda': LibraryDatasetView,
-    'ldda': LibraryDatasetDatasetView,
-    'history_dataset': HistoryDatasetView,
-    'hda': HistoryDatasetView,
-    'history': HistoryView,
-    'workflow': WorkflowView,
-    'tool': ToolView,
-    'job': JobView,
-    'page': PageView,
-    'page_revision': PageRevisionView,
+    "library": LibraryView,
+    "library_folder": LibraryFolderView,
+    "library_dataset_dataset": LibraryDatasetDatasetView,
+    "library_dataset": LibraryDatasetView,
+    "lda": LibraryDatasetView,
+    "ldda": LibraryDatasetDatasetView,
+    "history_dataset": HistoryDatasetView,
+    "hda": HistoryDatasetView,
+    "history": HistoryView,
+    "workflow": WorkflowView,
+    "tool": ToolView,
+    "job": JobView,
+    "page": PageView,
+    "page_revision": PageRevisionView,
 }
 
 # The GQL gramar is defined in Parsley syntax ( https://parsley.readthedocs.io/ )
@@ -629,7 +603,7 @@ class GalaxyQueryAnd:
 
     def __init__(self, left, right):
         self.left = left
-        self.operator = 'and'
+        self.operator = "and"
         self.right = right
 
 
@@ -649,15 +623,11 @@ class SearchQuery:
     def process(self, trans):
         self.view.search(trans)
         if self.query.conditional is not None:
-            self.view.filter(
-                self.query.conditional.left,
-                self.query.conditional.operator,
-                self.query.conditional.right
-            )
+            self.view.filter(self.query.conditional.left, self.query.conditional.operator, self.query.conditional.right)
         return self.view.get_results(True)
 
     def item_to_api_value(self, item):
-        r = item.to_dict(view='element')
+        r = item.to_dict(view="element")
         if self.query.field_list.count("*"):
             return r
         o = {}
@@ -673,12 +643,15 @@ class GalaxySearchEngine:
     """
 
     def __init__(self):
-        self.parser = parsley.makeGrammar(gqlGrammar, {
-            're': re,
-            'GalaxyQuery': GalaxyQuery,
-            'GalaxyQueryComparison': GalaxyQueryComparison,
-            'GalaxyQueryAnd': GalaxyQueryAnd
-        })
+        self.parser = parsley.makeGrammar(
+            gqlGrammar,
+            {
+                "re": re,
+                "GalaxyQuery": GalaxyQuery,
+                "GalaxyQueryComparison": GalaxyQueryComparison,
+                "GalaxyQueryAnd": GalaxyQueryAnd,
+            },
+        )
 
     def query(self, query_text):
         q = self.parser(query_text).expr()
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index ddad0310c0e..f2f04418aa4 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -1,16 +1,27 @@
 import logging
 import socket
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 
-from sqlalchemy import and_, false, not_, or_
+from sqlalchemy import (
+    and_,
+    false,
+    not_,
+    or_,
+)
 from sqlalchemy.orm import joinedload
 
 import galaxy.model
-from galaxy.security import Action, get_permitted_actions, RBACAgent
+from galaxy.security import (
+    Action,
+    get_permitted_actions,
+    RBACAgent,
+)
 from galaxy.util import listify
 from galaxy.util.bunch import Bunch
 
-
 log = logging.getLogger(__name__)
 
 
@@ -24,7 +35,8 @@ class GalaxyRBACAgent(RBACAgent):
             (self.model.Library, self.model.LibraryPermissions),
             (self.model.LibraryFolder, self.model.LibraryFolderPermissions),
             (self.model.LibraryDataset, self.model.LibraryDatasetPermissions),
-            (self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions))
+            (self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions),
+        )
 
     @property
     def sa_session(self):
@@ -51,22 +63,30 @@ class GalaxyRBACAgent(RBACAgent):
         """
         non-private, non-sharing roles
         """
-        return trans.sa_session.query(trans.app.model.Role) \
-                    .filter(and_(self.model.Role.deleted == false(),
-                        self.model.Role.type != self.model.Role.types.PRIVATE,
-                        self.model.Role.type != self.model.Role.types.SHARING)) \
-                    .order_by(self.model.Role.name)
+        return (
+            trans.sa_session.query(trans.app.model.Role)
+            .filter(
+                and_(
+                    self.model.Role.deleted == false(),
+                    self.model.Role.type != self.model.Role.types.PRIVATE,
+                    self.model.Role.type != self.model.Role.types.SHARING,
+                )
+            )
+            .order_by(self.model.Role.name)
+        )
 
     def get_all_roles(self, trans, cntrller):
-        admin_controller = cntrller in ['library_admin']
+        admin_controller = cntrller in ["library_admin"]
         roles = set()
         if not trans.user:
             return self._get_npns_roles(trans)
         if admin_controller:
             # The library is public and the user is an admin, so all roles are legitimate
-            for role in trans.sa_session.query(trans.app.model.Role) \
-                                        .filter(self.model.Role.deleted == false()) \
-                                        .order_by(self.model.Role.name):
+            for role in (
+                trans.sa_session.query(trans.app.model.Role)
+                .filter(self.model.Role.deleted == false())
+                .order_by(self.model.Role.name)
+            ):
                 roles.add(role)
         else:
             # Add the current user's private role
@@ -77,7 +97,7 @@ class GalaxyRBACAgent(RBACAgent):
             # Add all remaining non-private, non-sharing roles
             for role in self._get_npns_roles(trans):
                 roles.add(role)
-        return self.sort_by_attr([role for role in roles], 'name')
+        return self.sort_by_attr([role for role in roles], "name")
 
     def get_roles_for_action(self, item, action):
         """
@@ -102,8 +122,8 @@ class GalaxyRBACAgent(RBACAgent):
         sharing roles and any public role (not private and not sharing).
         """
         roles = []
-        if query not in [None, '']:
-            query = query.strip().replace('_', '/_').replace('%', '/%').replace('/', '//')
+        if query not in [None, ""]:
+            query = query.strip().replace("_", "/_").replace("%", "/%").replace("/", "//")
             search_query = f"{query}%"
         else:
             search_query = None
@@ -127,11 +147,11 @@ class GalaxyRBACAgent(RBACAgent):
                 db_query = trans.sa_session.query(trans.app.model.Role).filter(self.model.Role.deleted == false())
             else:
                 # User is not an admin but the configuration exposes all private roles to all users.
-                db_query = trans.sa_session.query(trans.app.model.Role) \
-                    .filter(and_(self.model.Role.deleted == false(),
-                                 self.model.Role.type == self.model.Role.types.PRIVATE))
+                db_query = trans.sa_session.query(trans.app.model.Role).filter(
+                    and_(self.model.Role.deleted == false(), self.model.Role.type == self.model.Role.types.PRIVATE)
+                )
             if search_query:
-                db_query = db_query.filter(self.model.Role.name.like(search_query, escape='/'))
+                db_query = db_query.filter(self.model.Role.name.like(search_query, escape="/"))
             total_count = db_query.count()
             if limit is not None:
                 # Takes the least number of results from beginning that includes the requested page
@@ -182,7 +202,7 @@ class GalaxyRBACAgent(RBACAgent):
         return_roles = set(roles)
         if total_count is None:
             total_count = len(return_roles)
-        return self.sort_by_attr([role for role in return_roles], 'name'), total_count
+        return self.sort_by_attr([role for role in return_roles], "name"), total_count
 
     def get_legitimate_roles(self, trans, item, cntrller):
         """
@@ -207,10 +227,11 @@ class GalaxyRBACAgent(RBACAgent):
               with each role that is associated with the access permission on item.  Private roles, except
               for the current user's private role, will be excluded.
         """
-        admin_controller = cntrller in ['library_admin']
+        admin_controller = cntrller in ["library_admin"]
         roles = set()
-        if (isinstance(item, self.model.Library) and self.library_is_public(item)) or \
-                (isinstance(item, self.model.Dataset) and self.dataset_is_public(item)):
+        if (isinstance(item, self.model.Library) and self.library_is_public(item)) or (
+            isinstance(item, self.model.Dataset) and self.dataset_is_public(item)
+        ):
             return self.get_all_roles(trans, cntrller)
         # If item has roles associated with the access permission, we need to start with them.
         access_roles = item.get_access_roles(self)
@@ -232,7 +253,7 @@ class GalaxyRBACAgent(RBACAgent):
                         for ura in user.roles:
                             if admin_controller or self.ok_to_display(trans.user, ura.role):
                                 roles.add(ura.role)
-        return self.sort_by_attr([role for role in roles], 'name')
+        return self.sort_by_attr([role for role in roles], "name")
 
     def ok_to_display(self, user, role):
         """
@@ -260,7 +281,7 @@ class GalaxyRBACAgent(RBACAgent):
         item_actions = self.get_item_actions(action, item)
 
         if not item_actions:
-            return action.model == 'restrict'
+            return action.model == "restrict"
         ret_val = False
         # For DATASET_ACCESS only, user must have ALL associated roles
         if action == self.permitted_actions.DATASET_ACCESS:
@@ -297,14 +318,20 @@ class GalaxyRBACAgent(RBACAgent):
         # If the dataset id has no corresponding action in its permissions,
         # then the returned permissions will not carry an entry for the dataset.
         ret_permissions = {}
-        if (len(permission_items) > 0):
+        if len(permission_items) > 0:
             # SM: NB: LibraryDatasets became Datasets for some odd reason.
-            if (isinstance(permission_items[0], trans.model.LibraryDataset)):
+            if isinstance(permission_items[0], trans.model.LibraryDataset):
                 ids = [item.library_dataset_id for item in permission_items]
-                permissions = trans.sa_session.query(trans.model.LibraryDatasetPermissions) \
-                                   .filter(and_(trans.model.LibraryDatasetPermissions.library_dataset_id.in_(ids),
-                                                trans.model.LibraryDatasetPermissions.action == action.action)) \
-                                   .all()
+                permissions = (
+                    trans.sa_session.query(trans.model.LibraryDatasetPermissions)
+                    .filter(
+                        and_(
+                            trans.model.LibraryDatasetPermissions.library_dataset_id.in_(ids),
+                            trans.model.LibraryDatasetPermissions.action == action.action,
+                        )
+                    )
+                    .all()
+                )
 
                 # Massage the return data. We will return a list of permissions
                 # for each library dataset. So we initialize the return list to
@@ -316,12 +343,18 @@ class GalaxyRBACAgent(RBACAgent):
                     ret_permissions[item.library_dataset_id] = []
                 for permission in permissions:
                     ret_permissions[permission.library_dataset_id].append(permission)
-            elif (isinstance(permission_items[0], trans.model.Dataset)):
+            elif isinstance(permission_items[0], trans.model.Dataset):
                 ids = [item.id for item in permission_items]
-                permissions = trans.sa_session.query(trans.model.DatasetPermissions) \
-                                   .filter(and_(trans.model.DatasetPermissions.dataset_id.in_(ids),
-                                                trans.model.DatasetPermissions.action == action.action)) \
-                                   .all()
+                permissions = (
+                    trans.sa_session.query(trans.model.DatasetPermissions)
+                    .filter(
+                        and_(
+                            trans.model.DatasetPermissions.dataset_id.in_(ids),
+                            trans.model.DatasetPermissions.action == action.action,
+                        )
+                    )
+                    .all()
+                )
 
                 # Massage the return data. We will return a list of permissions
                 # for each library dataset. So we initialize the return list to
@@ -347,17 +380,18 @@ class GalaxyRBACAgent(RBACAgent):
                     if len(base_result) == len(new_result):
                         common_result = set(base_result).intersection(new_result)
                         if len(common_result) == len(base_result):
-                            log.debug("Match on permissions for id %d" %
-                                      item.library_dataset_id)
+                            log.debug("Match on permissions for id %d" % item.library_dataset_id)
                         # TODO: Fix this failure message:
                         else:
-                            log.debug("Error: dataset %d; originally: %s; now: %s"
-                                      % (item.library_dataset_id,
-                                         base_result, new_result))
+                            log.debug(
+                                "Error: dataset %d; originally: %s; now: %s"
+                                % (item.library_dataset_id, base_result, new_result)
+                            )
                     else:
-                        log.debug("Error: dataset %d: had %d entries, now %d entries"
-                                  % (item.library_dataset_id, len(base_result),
-                                     len(new_result)))
+                        log.debug(
+                            "Error: dataset %d: had %d entries, now %d entries"
+                            % (item.library_dataset_id, len(base_result), len(new_result))
+                        )
                 log.debug("get_actions_for_items: Test end")
             except Exception as e:
                 log.debug(f"Exception in test code: {e}")
@@ -397,7 +431,7 @@ class GalaxyRBACAgent(RBACAgent):
                             break
 
             else:
-                if 'restrict' == action.model:
+                if "restrict" == action.model:
                     ret_allow_action[item.id] = True
                 else:
                     ret_allow_action[item.id] = False
@@ -412,27 +446,28 @@ class GalaxyRBACAgent(RBACAgent):
                 if orig_value == ret_allow_action[item.id]:
                     log.debug("Item %d: success" % item.id)
                 else:
-                    log.debug("Item %d: fail: original: %s; new: %s"
-                              % (item.id, orig_value, ret_allow_action[item.id]))
+                    log.debug("Item %d: fail: original: %s; new: %s" % (item.id, orig_value, ret_allow_action[item.id]))
             log.debug("allow_action_for_items: test end")
         return ret_allow_action
 
     # DELETEME: SM: DO NOT TOUCH! This actually works.
     def dataset_access_mapping(self, trans, user_roles, datasets):
-        '''
+        """
         For the given list of datasets, return a mapping of the datasets' ids
         to whether they can be accessed by the user or not. The datasets input
         is expected to be a simple list of Dataset objects.
-        '''
+        """
         datasets_public_map = self.datasets_are_public(trans, datasets)
-        datasets_allow_action_map = self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.DATASET_ACCESS, datasets)
+        datasets_allow_action_map = self.allow_action_on_libitems(
+            trans, user_roles, self.permitted_actions.DATASET_ACCESS, datasets
+        )
         can_access = {}
         for dataset in datasets:
             can_access[dataset.id] = datasets_public_map[dataset.id] or datasets_allow_action_map[dataset.id]
         return can_access
 
     def dataset_permission_map_for_access(self, trans, user_roles, libitems):
-        '''
+        """
         For a given list of library items (e.g., Datasets), return a map of the
         datasets' ids to whether they can have permission to use that action
         (e.g., "access" or "modify") on the dataset. The libitems input is
@@ -440,7 +475,7 @@ class GalaxyRBACAgent(RBACAgent):
         LibraryDatasets.
         NB: This is currently only usable for Datasets; it was intended to
         be used for any library item.
-        '''
+        """
         # Map the library items to whether they are publicly accessible or not.
         # Then determine what actions are allowed on the item (in case it's not
         # public). Finally, the item is accessible if it's publicly available
@@ -457,24 +492,20 @@ class GalaxyRBACAgent(RBACAgent):
         return can_access
 
     def item_permission_map_for_modify(self, trans, user_roles, libitems):
-        return self.allow_action_on_libitems(
-            trans, user_roles, self.permitted_actions.LIBRARY_MODIFY, libitems
-        )
+        return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_MODIFY, libitems)
 
     def item_permission_map_for_manage(self, trans, user_roles, libitems):
-        return self.allow_action_on_libitems(
-            trans, user_roles, self.permitted_actions.LIBRARY_MANAGE, libitems
-        )
+        return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_MANAGE, libitems)
 
     def item_permission_map_for_add(self, trans, user_roles, libitems):
-        return self.allow_action_on_libitems(
-            trans, user_roles, self.permitted_actions.LIBRARY_ADD, libitems
-        )
+        return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_ADD, libitems)
 
     def can_access_dataset(self, user_roles, dataset):
         # SM: dataset_is_public will access dataset.actions, which is a
         # backref that causes a query to be made to DatasetPermissions
-        retval = self.dataset_is_public(dataset) or self.allow_action(user_roles, self.permitted_actions.DATASET_ACCESS, dataset)
+        retval = self.dataset_is_public(dataset) or self.allow_action(
+            user_roles, self.permitted_actions.DATASET_ACCESS, dataset
+        )
         return retval
 
     def can_access_datasets(self, user_roles, action_tuples):
@@ -492,34 +523,57 @@ class GalaxyRBACAgent(RBACAgent):
         return self.allow_action(roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset)
 
     def can_access_library(self, roles, library):
-        return self.library_is_public(library) or self.allow_action(roles, self.permitted_actions.LIBRARY_ACCESS, library)
+        return self.library_is_public(library) or self.allow_action(
+            roles, self.permitted_actions.LIBRARY_ACCESS, library
+        )
 
     def get_accessible_libraries(self, trans, user):
         """Return all data libraries that the received user can access"""
         accessible_libraries = []
         current_user_role_ids = [role.id for role in user.all_roles()]
         library_access_action = self.permitted_actions.LIBRARY_ACCESS.action
-        restricted_library_ids = [lp.library_id for lp in trans.sa_session.query(trans.model.LibraryPermissions)
-                                  .filter(trans.model.LibraryPermissions.table.c.action == library_access_action).distinct()]
-        accessible_restricted_library_ids = [lp.library_id for lp in trans.sa_session.query(trans.model.LibraryPermissions)
-            .filter(and_(
-                trans.model.LibraryPermissions.table.c.action == library_access_action,
-                trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids)))]
+        restricted_library_ids = [
+            lp.library_id
+            for lp in trans.sa_session.query(trans.model.LibraryPermissions)
+            .filter(trans.model.LibraryPermissions.table.c.action == library_access_action)
+            .distinct()
+        ]
+        accessible_restricted_library_ids = [
+            lp.library_id
+            for lp in trans.sa_session.query(trans.model.LibraryPermissions).filter(
+                and_(
+                    trans.model.LibraryPermissions.table.c.action == library_access_action,
+                    trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids),
+                )
+            )
+        ]
         # Filter to get libraries accessible by the current user.  Get both
         # public libraries and restricted libraries accessible by the current user.
-        for library in trans.sa_session.query(trans.model.Library) \
-                                       .filter(and_(trans.model.Library.table.c.deleted == false(),
-                                                    (or_(not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
-                                                         trans.model.Library.table.c.id.in_(accessible_restricted_library_ids))))) \
-                                       .order_by(trans.app.model.Library.name):
+        for library in (
+            trans.sa_session.query(trans.model.Library)
+            .filter(
+                and_(
+                    trans.model.Library.table.c.deleted == false(),
+                    (
+                        or_(
+                            not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
+                            trans.model.Library.table.c.id.in_(accessible_restricted_library_ids),
+                        )
+                    ),
+                )
+            )
+            .order_by(trans.app.model.Library.name)
+        ):
             accessible_libraries.append(library)
         return accessible_libraries
 
     def has_accessible_folders(self, trans, folder, user, roles, search_downward=True):
-        if self.has_accessible_library_datasets(trans, folder, user, roles, search_downward=search_downward) or \
-                self.can_add_library_item(roles, folder) or \
-                self.can_modify_library_item(roles, folder) or \
-                self.can_manage_library_item(roles, folder):
+        if (
+            self.has_accessible_library_datasets(trans, folder, user, roles, search_downward=search_downward)
+            or self.can_add_library_item(roles, folder)
+            or self.can_modify_library_item(roles, folder)
+            or self.can_manage_library_item(roles, folder)
+        ):
             return True
         if search_downward:
             for folder in folder.active_folders:
@@ -527,9 +581,12 @@ class GalaxyRBACAgent(RBACAgent):
         return False
 
     def has_accessible_library_datasets(self, trans, folder, user, roles, search_downward=True):
-        for library_dataset in trans.sa_session.query(trans.model.LibraryDataset) \
-                .filter(and_(trans.model.LibraryDataset.table.c.deleted == false(),
-                             trans.app.model.LibraryDataset.table.c.folder_id == folder.id)):
+        for library_dataset in trans.sa_session.query(trans.model.LibraryDataset).filter(
+            and_(
+                trans.model.LibraryDataset.table.c.deleted == false(),
+                trans.app.model.LibraryDataset.table.c.folder_id == folder.id,
+            )
+        ):
             if self.can_access_library_item(roles, library_dataset, user):
                 return True
         if search_downward:
@@ -546,15 +603,21 @@ class GalaxyRBACAgent(RBACAgent):
         if type(item) == self.model.Library:
             return self.can_access_library(roles, item)
         elif type(item) == self.model.LibraryFolder:
-            return self.can_access_library(roles, item.parent_library) and self.check_folder_contents(user, roles, item)[0]
+            return (
+                self.can_access_library(roles, item.parent_library) and self.check_folder_contents(user, roles, item)[0]
+            )
         elif type(item) == self.model.LibraryDataset:
-            return self.can_access_library(roles, item.folder.parent_library) and self.can_access_dataset(roles, item.library_dataset_dataset_association.dataset)
+            return self.can_access_library(roles, item.folder.parent_library) and self.can_access_dataset(
+                roles, item.library_dataset_dataset_association.dataset
+            )
         elif type(item) == self.model.LibraryDatasetDatasetAssociation:
-            return self.can_access_library(roles, item.library_dataset.folder.parent_library) and self.can_access_dataset(roles, item.dataset)
+            return self.can_access_library(
+                roles, item.library_dataset.folder.parent_library
+            ) and self.can_access_dataset(roles, item.dataset)
         elif type(item) == self.model.LibraryDatasetCollectionAssociation:
             return self.can_access_library(roles, item.folder.parent_library)
         else:
-            log.warning(f'Unknown library item type: {type(item)}')
+            log.warning(f"Unknown library item type: {type(item)}")
             return False
 
     def can_add_library_item(self, roles, item):
@@ -591,10 +654,10 @@ class GalaxyRBACAgent(RBACAgent):
                 if action not in perms.keys():
                     perms[action] = roles
                 else:
-                    if action.model == 'grant':
+                    if action.model == "grant":
                         # intersect existing roles with new roles
                         perms[action] = [_ for _ in roles if _ in perms[action]]
-                    elif action.model == 'restrict':
+                    elif action.model == "restrict":
                         # join existing roles with new roles
                         perms[action].extend([_ for _ in roles if _ not in perms[action]])
         return perms
@@ -612,27 +675,27 @@ class GalaxyRBACAgent(RBACAgent):
             if action not in perms.keys():
                 perms[action] = list(role_ids)
             else:
-                if action.model == 'grant':
+                if action.model == "grant":
                     # intersect existing roles with new roles
                     perms[action] = [_ for _ in role_ids if _ in perms[action]]
-                elif action.model == 'restrict':
+                elif action.model == "restrict":
                     # join existing roles with new roles
                     perms[action].extend([_ for _ in role_ids if _ not in perms[action]])
         return perms
 
     def associate_components(self, **kwd):
-        if 'user' in kwd:
-            if 'group' in kwd:
-                return self.associate_user_group(kwd['user'], kwd['group'])
-            elif 'role' in kwd:
-                return self.associate_user_role(kwd['user'], kwd['role'])
-        elif 'role' in kwd:
-            if 'group' in kwd:
-                return self.associate_group_role(kwd['group'], kwd['role'])
-        if 'action' in kwd:
-            if 'dataset' in kwd and 'role' in kwd:
-                return self.associate_action_dataset_role(kwd['action'], kwd['dataset'], kwd['role'])
-        raise Exception(f'No valid method of associating provided components: {kwd}')
+        if "user" in kwd:
+            if "group" in kwd:
+                return self.associate_user_group(kwd["user"], kwd["group"])
+            elif "role" in kwd:
+                return self.associate_user_role(kwd["user"], kwd["role"])
+        elif "role" in kwd:
+            if "group" in kwd:
+                return self.associate_group_role(kwd["group"], kwd["role"])
+        if "action" in kwd:
+            if "dataset" in kwd and "role" in kwd:
+                return self.associate_action_dataset_role(kwd["action"], kwd["dataset"], kwd["role"])
+        raise Exception(f"No valid method of associating provided components: {kwd}")
 
     def associate_user_group(self, user, group):
         assoc = self.model.UserGroupAssociation(user, group)
@@ -674,11 +737,17 @@ class GalaxyRBACAgent(RBACAgent):
         return self.get_private_user_role(user)
 
     def get_private_user_role(self, user, auto_create=False):
-        role = self.sa_session.query(self.model.Role) \
-                              .filter(and_(self.model.UserRoleAssociation.table.c.user_id == user.id,
-                                           self.model.Role.id == self.model.UserRoleAssociation.table.c.role_id,
-                                           self.model.Role.type == self.model.Role.types.PRIVATE)) \
-                              .one_or_none()
+        role = (
+            self.sa_session.query(self.model.Role)
+            .filter(
+                and_(
+                    self.model.UserRoleAssociation.table.c.user_id == user.id,
+                    self.model.Role.id == self.model.UserRoleAssociation.table.c.role_id,
+                    self.model.Role.type == self.model.Role.types.PRIVATE,
+                )
+            )
+            .one_or_none()
+        )
         if not role:
             if auto_create:
                 return self.create_private_user_role(user)
@@ -689,10 +758,11 @@ class GalaxyRBACAgent(RBACAgent):
     def get_role(self, name, type=None):
         type = type or self.model.Role.types.SYSTEM
         # will raise exception if not found
-        return self.sa_session.query(self.model.Role) \
-            .filter(and_(self.model.Role.name == name,
-                     self.model.Role.type == type)) \
+        return (
+            self.sa_session.query(self.model.Role)
+            .filter(and_(self.model.Role.name == name, self.model.Role.type == type))
             .one()
+        )
 
     def create_role(self, name, description, in_users, in_groups, create_group_for_role=False, type=None):
         type = type or self.model.Role.types.SYSTEM
@@ -717,11 +787,22 @@ class GalaxyRBACAgent(RBACAgent):
         return role, num_in_groups
 
     def get_sharing_roles(self, user):
-        return self.sa_session.query(self.model.Role) \
-                              .filter(and_((self.model.Role.name).like(f"Sharing role for: %{user.email}%"),
-                                           self.model.Role.type == self.model.Role.types.SHARING))
+        return self.sa_session.query(self.model.Role).filter(
+            and_(
+                (self.model.Role.name).like(f"Sharing role for: %{user.email}%"),
+                self.model.Role.type == self.model.Role.types.SHARING,
+            )
+        )
 
-    def user_set_default_permissions(self, user, permissions=None, history=False, dataset=False, bypass_manage_permission=False, default_access_private=False):
+    def user_set_default_permissions(
+        self,
+        user,
+        permissions=None,
+        history=False,
+        dataset=False,
+        bypass_manage_permission=False,
+        default_access_private=False,
+    ):
         # bypass_manage_permission is used to change permissions of datasets in a userless history when logging in
         flush_needed = False
         permissions = permissions or {}
@@ -729,7 +810,9 @@ class GalaxyRBACAgent(RBACAgent):
             return None
         if not permissions:
             # default permissions
-            permissions = {self.permitted_actions.DATASET_MANAGE_PERMISSIONS: [self.get_private_user_role(user, auto_create=True)]}
+            permissions = {
+                self.permitted_actions.DATASET_MANAGE_PERMISSIONS: [self.get_private_user_role(user, auto_create=True)]
+            }
             # new_user_dataset_access_role_default_private is set as True in config file
             if default_access_private:
                 permissions[self.permitted_actions.DATASET_ACCESS] = next(iter(permissions.values()))
@@ -748,7 +831,9 @@ class GalaxyRBACAgent(RBACAgent):
             self.sa_session.flush()
         if history:
             for history in user.active_histories:
-                self.history_set_default_permissions(history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission)
+                self.history_set_default_permissions(
+                    history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission
+                )
 
     def user_get_default_permissions(self, user):
         permissions = {}
@@ -911,8 +996,9 @@ class GalaxyRBACAgent(RBACAgent):
                     sharing_role = role
                     break
         if sharing_role is None:
-            sharing_role = self.model.Role(name=f"Sharing role for: {', '.join(u.email for u in users)}",
-                                           type=self.model.Role.types.SHARING)
+            sharing_role = self.model.Role(
+                name=f"Sharing role for: {', '.join(u.email for u in users)}", type=self.model.Role.types.SHARING
+            )
             self.sa_session.add(sharing_role)
             self.sa_session.flush()
             for user in users:
@@ -943,7 +1029,9 @@ class GalaxyRBACAgent(RBACAgent):
                             # Well this looks like a bug, this should be looked at.
                             # Default permissions above is single hash that keeps getting reeditted here
                             # because permission is being defined instead of permissions. -John
-                            permissions[self.permitted_actions.DATASET_MANAGE_PERMISSIONS] = [trans.app.security_agent.get_private_user_role(library_item.user)]
+                            permissions[self.permitted_actions.DATASET_MANAGE_PERMISSIONS] = [
+                                trans.app.security_agent.get_private_user_role(library_item.user)
+                            ]
                             self.set_dataset_permission(library_item.dataset, permissions)
                         if action == self.permitted_actions.LIBRARY_MANAGE.action and roles:
                             # Handle the special case when we are setting the LIBRARY_MANAGE_PERMISSION on a
@@ -972,7 +1060,9 @@ class GalaxyRBACAgent(RBACAgent):
                     flush_needed = True
             # Add the new specific permission on the library item
             if isinstance(library_item, self.model.LibraryDataset):
-                for item_permission in [self.model.LibraryDatasetPermissions(action, library_item, role) for role in roles]:
+                for item_permission in [
+                    self.model.LibraryDatasetPermissions(action, library_item, role) for role in roles
+                ]:
                     self.sa_session.add(item_permission)
                     flush_needed = True
             elif isinstance(library_item, self.model.LibraryPermissions):
@@ -1065,11 +1155,11 @@ class GalaxyRBACAgent(RBACAgent):
                 return False
 
     def datasets_are_public(self, trans, datasets):
-        '''
+        """
         Given a transaction object and a list of Datasets, return
         a mapping from Dataset ids to whether the Dataset is public
         or not. All Dataset ids should be returned in the mapping's keys.
-        '''
+        """
         # We go the other way around from dataset_is_public: we start with
         # all datasets being marked as public. If there is an access action
         # associated with the dataset, then we mark it as nonpublic:
@@ -1079,10 +1169,16 @@ class GalaxyRBACAgent(RBACAgent):
             datasets_public[dataset_id] = True
 
         # Now get all datasets which have DATASET_ACCESS actions:
-        access_data_perms = trans.sa_session.query(trans.app.model.DatasetPermissions) \
-                                 .filter(and_(trans.app.model.DatasetPermissions.dataset_id.in_(dataset_ids),
-                                              trans.app.model.DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action)) \
-                                 .all()
+        access_data_perms = (
+            trans.sa_session.query(trans.app.model.DatasetPermissions)
+            .filter(
+                and_(
+                    trans.app.model.DatasetPermissions.dataset_id.in_(dataset_ids),
+                    trans.app.model.DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action,
+                )
+            )
+            .all()
+        )
         # Every dataset returned has "access" privileges associated with it,
         # so it's not public.
         for permission in access_data_perms:
@@ -1104,7 +1200,7 @@ class GalaxyRBACAgent(RBACAgent):
         # Check the access permission on a dataset.  If library is true, item_id refers to a library.  If library
         # is False, item_id refers to a dataset ( item_id must currently be decoded before being sent ).  The
         # cntrller param is the calling controller, which needs to be passed to get_legitimate_roles().
-        msg = ''
+        msg = ""
         permissions = {}
         # accessible will be True only if at least 1 user has every role in DATASET_ACCESS_in
         accessible = False
@@ -1115,7 +1211,7 @@ class GalaxyRBACAgent(RBACAgent):
         # permission on item, and at least 1 of the roles is private.
         private_role_found = False
         error = False
-        for k, v in get_permitted_actions(filter='DATASET').items():
+        for k, v in get_permitted_actions(filter="DATASET").items():
             # Change for removing the prefix '_in' from the roles select box
             in_roles = [self.sa_session.query(self.model.Role).get(x) for x in listify(kwd[k])]
             if not in_roles:
@@ -1216,8 +1312,10 @@ class GalaxyRBACAgent(RBACAgent):
                     found_permission_class = permission_class
                     break
             else:
-                raise Exception('Invalid class (%s) specified for target_library_item (%s)' %
-                                (target_library_item.__class__, target_library_item.__class__.__name__))
+                raise Exception(
+                    "Invalid class (%s) specified for target_library_item (%s)"
+                    % (target_library_item.__class__, target_library_item.__class__.__name__)
+                )
             # Make sure user's private role is included
             private_role = self.model.security_agent.get_private_user_role(user)
             for action in self.permitted_actions.values():
@@ -1238,9 +1336,11 @@ class GalaxyRBACAgent(RBACAgent):
             libraries = trans.app.security_agent.get_permitted_libraries( trans, user,
                 [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
         """
-        all_libraries = trans.sa_session.query(trans.app.model.Library) \
-                                        .filter(trans.app.model.Library.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.Library.name)
+        all_libraries = (
+            trans.sa_session.query(trans.app.model.Library)
+            .filter(trans.app.model.Library.table.c.deleted == false())
+            .order_by(trans.app.model.Library.name)
+        )
         roles = user.all_roles()
         actions_to_check = actions
         # The libraries dictionary looks like: { library : '1,2' }, library : '3' }
@@ -1256,7 +1356,7 @@ class GalaxyRBACAgent(RBACAgent):
                 libraries[library] = hidden_folder_ids
         return libraries
 
-    def show_library_item(self, user, roles, library_item, actions_to_check, hidden_folder_ids=''):
+    def show_library_item(self, user, roles, library_item, actions_to_check, hidden_folder_ids=""):
         """
         This method must be sent an instance of Library() or LibraryFolder().  Recursive execution produces a
         comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with
@@ -1269,19 +1369,23 @@ class GalaxyRBACAgent(RBACAgent):
             if self.allow_action(roles, action, library_item):
                 return True, hidden_folder_ids
         if isinstance(library_item, self.model.Library):
-            return self.show_library_item(user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids='')
+            return self.show_library_item(user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids="")
         if isinstance(library_item, self.model.LibraryFolder):
             for folder in library_item.active_folders:
-                can_show, hidden_folder_ids = self.show_library_item(user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids)
+                can_show, hidden_folder_ids = self.show_library_item(
+                    user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids
+                )
                 if can_show:
                     return True, hidden_folder_ids
                 if hidden_folder_ids:
-                    hidden_folder_ids = '%s,%d' % (hidden_folder_ids, folder.id)
+                    hidden_folder_ids = "%s,%d" % (hidden_folder_ids, folder.id)
                 else:
-                    hidden_folder_ids = '%d' % folder.id
+                    hidden_folder_ids = "%d" % folder.id
         return False, hidden_folder_ids
 
-    def get_showable_folders(self, user, roles, library_item, actions_to_check, hidden_folder_ids=None, showable_folders=None):
+    def get_showable_folders(
+        self, user, roles, library_item, actions_to_check, hidden_folder_ids=None, showable_folders=None
+    ):
         """
         This method must be sent an instance of Library(), all the folders of which are scanned to determine if
         user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should
@@ -1291,7 +1395,9 @@ class GalaxyRBACAgent(RBACAgent):
         hidden_folder_ids = hidden_folder_ids or []
         showable_folders = showable_folders or []
         if isinstance(library_item, self.model.Library):
-            return self.get_showable_folders(user, roles, library_item.root_folder, actions_to_check, showable_folders=[])
+            return self.get_showable_folders(
+                user, roles, library_item.root_folder, actions_to_check, showable_folders=[]
+            )
         if isinstance(library_item, self.model.LibraryFolder):
             if library_item.id not in hidden_folder_ids:
                 for action in actions_to_check:
@@ -1357,21 +1463,37 @@ class GalaxyRBACAgent(RBACAgent):
                 self.associate_components(group=group, role=role)
 
     def get_component_associations(self, **kwd):
-        assert len(kwd) == 2, 'You must specify exactly 2 Galaxy security components to check for associations.'
-        if 'dataset' in kwd:
-            if 'action' in kwd:
-                return self.sa_session.query(self.model.DatasetPermissions).filter_by(action=kwd['action'].action, dataset_id=kwd['dataset'].id).first()
-        elif 'user' in kwd:
-            if 'group' in kwd:
-                return self.sa_session.query(self.model.UserGroupAssociation).filter_by(group_id=kwd['group'].id, user_id=kwd['user'].id).first()
-            elif 'role' in kwd:
-                return self.sa_session.query(self.model.UserRoleAssociation).filter_by(role_id=kwd['role'].id, user_id=kwd['user'].id).first()
-        elif 'group' in kwd:
-            if 'role' in kwd:
-                return self.sa_session.query(self.model.GroupRoleAssociation).filter_by(role_id=kwd['role'].id, group_id=kwd['group'].id).first()
-        raise Exception(f'No valid method of associating provided components: {kwd}')
+        assert len(kwd) == 2, "You must specify exactly 2 Galaxy security components to check for associations."
+        if "dataset" in kwd:
+            if "action" in kwd:
+                return (
+                    self.sa_session.query(self.model.DatasetPermissions)
+                    .filter_by(action=kwd["action"].action, dataset_id=kwd["dataset"].id)
+                    .first()
+                )
+        elif "user" in kwd:
+            if "group" in kwd:
+                return (
+                    self.sa_session.query(self.model.UserGroupAssociation)
+                    .filter_by(group_id=kwd["group"].id, user_id=kwd["user"].id)
+                    .first()
+                )
+            elif "role" in kwd:
+                return (
+                    self.sa_session.query(self.model.UserRoleAssociation)
+                    .filter_by(role_id=kwd["role"].id, user_id=kwd["user"].id)
+                    .first()
+                )
+        elif "group" in kwd:
+            if "role" in kwd:
+                return (
+                    self.sa_session.query(self.model.GroupRoleAssociation)
+                    .filter_by(role_id=kwd["role"].id, group_id=kwd["group"].id)
+                    .first()
+                )
+        raise Exception(f"No valid method of associating provided components: {kwd}")
 
-    def check_folder_contents(self, user, roles, folder, hidden_folder_ids=''):
+    def check_folder_contents(self, user, roles, folder, hidden_folder_ids=""):
         """
         This method must always be sent an instance of LibraryFolder().  Recursive execution produces a
         comma-separated string of folder ids whose folders do NOT meet the criteria for showing.  Along
@@ -1382,15 +1504,17 @@ class GalaxyRBACAgent(RBACAgent):
         """
         # If a folder is writeable, it's accessable and we need not go further
         if self.can_add_library_item(roles, folder):
-            return True, ''
+            return True, ""
         action = self.permitted_actions.DATASET_ACCESS
 
-        lddas = self.sa_session.query(self.model.LibraryDatasetDatasetAssociation) \
-                               .join("library_dataset") \
-                               .filter(self.model.LibraryDataset.folder == folder) \
-                               .join("dataset") \
-                               .options(joinedload("dataset").joinedload("actions")) \
-                               .all()
+        lddas = (
+            self.sa_session.query(self.model.LibraryDatasetDatasetAssociation)
+            .join("library_dataset")
+            .filter(self.model.LibraryDataset.folder == folder)
+            .join("dataset")
+            .options(joinedload("dataset").joinedload("actions"))
+            .all()
+        )
 
         for ldda in lddas:
             ldda_access_permissions = self.get_item_actions(action, ldda.dataset)
@@ -1402,13 +1526,15 @@ class GalaxyRBACAgent(RBACAgent):
                     # The current user has access permission on the dataset
                     return True, hidden_folder_ids
         for sub_folder in folder.active_folders:
-            can_access, hidden_folder_ids = self.check_folder_contents(user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids)
+            can_access, hidden_folder_ids = self.check_folder_contents(
+                user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids
+            )
             if can_access:
                 return True, hidden_folder_ids
             if hidden_folder_ids:
-                hidden_folder_ids = '%s,%d' % (hidden_folder_ids, sub_folder.id)
+                hidden_folder_ids = "%s,%d" % (hidden_folder_ids, sub_folder.id)
             else:
-                hidden_folder_ids = '%d' % sub_folder.id
+                hidden_folder_ids = "%d" % sub_folder.id
         return False, hidden_folder_ids
 
 
@@ -1418,12 +1544,21 @@ class HostAgent(RBACAgent):
     This exists so that externals sites such as UCSC can gain access to
     datasets which have permissions which would normally prevent such access.
     """
+
     # TODO: Make sites user configurable
     sites = Bunch(
-        ucsc_main=('hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu',
-                   'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu'),
-        ucsc_test=('hgwdev.cse.ucsc.edu', ),
-        ucsc_archaea=('lowepub.cse.ucsc.edu', )
+        ucsc_main=(
+            "hgw1.cse.ucsc.edu",
+            "hgw2.cse.ucsc.edu",
+            "hgw3.cse.ucsc.edu",
+            "hgw4.cse.ucsc.edu",
+            "hgw5.cse.ucsc.edu",
+            "hgw6.cse.ucsc.edu",
+            "hgw7.cse.ucsc.edu",
+            "hgw8.cse.ucsc.edu",
+        ),
+        ucsc_test=("hgwdev.cse.ucsc.edu",),
+        ucsc_archaea=("lowepub.cse.ucsc.edu",),
     )
 
     def __init__(self, model, permitted_actions=None):
@@ -1437,15 +1572,22 @@ class HostAgent(RBACAgent):
         return self.model.context
 
     def allow_action(self, addr, action, **kwd):
-        if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS:
-            hda = kwd['dataset']
-            if action == self.permitted_actions.DATASET_ACCESS and action.action not in [dp.action for dp in hda.dataset.actions]:
-                log.debug('Allowing access to public dataset with hda: %i.' % hda.id)
+        if "dataset" in kwd and action == self.permitted_actions.DATASET_ACCESS:
+            hda = kwd["dataset"]
+            if action == self.permitted_actions.DATASET_ACCESS and action.action not in [
+                dp.action for dp in hda.dataset.actions
+            ]:
+                log.debug("Allowing access to public dataset with hda: %i." % hda.id)
                 return True  # dataset has no roles associated with the access permission, thus is already public
-            hdadaa = self.sa_session.query(self.model.HistoryDatasetAssociationDisplayAtAuthorization) \
-                                    .filter_by(history_dataset_association_id=hda.id).first()
+            hdadaa = (
+                self.sa_session.query(self.model.HistoryDatasetAssociationDisplayAtAuthorization)
+                .filter_by(history_dataset_association_id=hda.id)
+                .first()
+            )
             if not hdadaa:
-                log.debug('Denying access to private dataset with hda: %i.  No hdadaa record for this dataset.' % hda.id)
+                log.debug(
+                    "Denying access to private dataset with hda: %i.  No hdadaa record for this dataset." % hda.id
+                )
                 return False  # no auth
             # We could just look up the reverse of addr, but then we'd also
             # have to verify it with the forward address and special case any
@@ -1462,19 +1604,28 @@ class HostAgent(RBACAgent):
                 except (OSError, socket.gaierror):
                     pass  # can't resolve, try next
             else:
-                log.debug('Denying access to private dataset with hda: %i.  Remote addr is not a valid server for site: %s.' % (hda.id, hdadaa.site))
+                log.debug(
+                    "Denying access to private dataset with hda: %i.  Remote addr is not a valid server for site: %s."
+                    % (hda.id, hdadaa.site)
+                )
                 return False  # remote addr is not in the server list
             if (datetime.utcnow() - hdadaa.update_time) > timedelta(seconds=60):
-                log.debug('Denying access to private dataset with hda: %i.  Authorization was granted, but has expired.' % hda.id)
+                log.debug(
+                    "Denying access to private dataset with hda: %i.  Authorization was granted, but has expired."
+                    % hda.id
+                )
                 return False  # not authz'd in the last 60 seconds
-            log.debug('Allowing access to private dataset with hda: %i.  Remote server is: %s.' % (hda.id, server))
+            log.debug("Allowing access to private dataset with hda: %i.  Remote server is: %s." % (hda.id, server))
             return True
         else:
-            raise Exception('The dataset access permission is the only valid permission in the host security agent.')
+            raise Exception("The dataset access permission is the only valid permission in the host security agent.")
 
     def set_dataset_permissions(self, hda, user, site):
-        hdadaa = self.sa_session.query(self.model.HistoryDatasetAssociationDisplayAtAuthorization) \
-                                .filter_by(history_dataset_association_id=hda.id).first()
+        hdadaa = (
+            self.sa_session.query(self.model.HistoryDatasetAssociationDisplayAtAuthorization)
+            .filter_by(history_dataset_association_id=hda.id)
+            .first()
+        )
         if hdadaa:
             hdadaa.update_time = datetime.utcnow()
         else:
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 0153b1f7ca1..5235dd2a965 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -25,33 +25,39 @@ from boltons.iterutils import remap
 from sqlalchemy.orm import joinedload
 from sqlalchemy.sql import expression
 
-from galaxy.exceptions import MalformedContents, ObjectNotFound
+from galaxy.exceptions import (
+    MalformedContents,
+    ObjectNotFound,
+)
 from galaxy.model.metadata import MetadataCollection
 from galaxy.security.idencoding import IdEncodingHelper
-from galaxy.util import FILENAME_VALID_CHARS
-from galaxy.util import in_directory
+from galaxy.util import (
+    FILENAME_VALID_CHARS,
+    in_directory,
+)
 from galaxy.util.bunch import Bunch
 from galaxy.util.path import safe_walk
 from ..custom_types import json_encoder
-from ..item_attrs import add_item_annotation, get_item_annotation_str
+from ..item_attrs import (
+    add_item_annotation,
+    get_item_annotation_str,
+)
 from ... import model
 
-
 ObjectKeyType = Union[str, int]
 
-ATTRS_FILENAME_HISTORY = 'history_attrs.txt'
-ATTRS_FILENAME_DATASETS = 'datasets_attrs.txt'
-ATTRS_FILENAME_JOBS = 'jobs_attrs.txt'
-ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS = 'implicit_collection_jobs_attrs.txt'
-ATTRS_FILENAME_COLLECTIONS = 'collections_attrs.txt'
-ATTRS_FILENAME_EXPORT = 'export_attrs.txt'
-ATTRS_FILENAME_LIBRARIES = 'libraries_attrs.txt'
-TRACEBACK = 'traceback.txt'
+ATTRS_FILENAME_HISTORY = "history_attrs.txt"
+ATTRS_FILENAME_DATASETS = "datasets_attrs.txt"
+ATTRS_FILENAME_JOBS = "jobs_attrs.txt"
+ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS = "implicit_collection_jobs_attrs.txt"
+ATTRS_FILENAME_COLLECTIONS = "collections_attrs.txt"
+ATTRS_FILENAME_EXPORT = "export_attrs.txt"
+ATTRS_FILENAME_LIBRARIES = "libraries_attrs.txt"
+TRACEBACK = "traceback.txt"
 GALAXY_EXPORT_VERSION = "2"
 
 
 class ImportOptions:
-
     def __init__(self, allow_edit=False, allow_library_creation=False, allow_dataset_object_edit=None):
         self.allow_edit = allow_edit
         self.allow_library_creation = allow_library_creation
@@ -61,7 +67,6 @@ class ImportOptions:
 
 
 class SessionlessContext:
-
     def __init__(self):
         self.objects = defaultdict(dict)
 
@@ -72,7 +77,6 @@ class SessionlessContext:
         self.objects[obj.__class__][obj.id] = obj
 
     def query(self, model_class):
-
         def find(obj_id):
             return self.objects.get(model_class, {}).get(obj_id) or None
 
@@ -84,7 +88,6 @@ class SessionlessContext:
 
 
 def replace_metadata_file(metadata: Dict[str, Any], dataset_instance: model.DatasetInstance):
-
     def remap_objects(p, k, obj):
         if isinstance(obj, dict) and "model_class" in obj and obj["model_class"] == "MetadataFile":
             return (k, model.MetadataFile(dataset=dataset_instance, uuid=obj["uuid"]))
@@ -94,7 +97,6 @@ def replace_metadata_file(metadata: Dict[str, Any], dataset_instance: model.Data
 
 
 class ModelImportStore(metaclass=abc.ABCMeta):
-
     def __init__(self, import_options=None, app=None, user=None, object_store=None, tag_handler=None):
         if object_store is None:
             if app is not None:
@@ -158,18 +160,17 @@ class ModelImportStore(metaclass=abc.ABCMeta):
 
         if self.defines_new_history():
             history_properties = self.new_history_properties()
-            history_name = history_properties.get('name')
+            history_name = history_properties.get("name")
             if history_name:
-                history_name = f'imported from archive: {history_name}'
+                history_name = f"imported from archive: {history_name}"
             else:
-                history_name = 'unnamed imported history'
+                history_name = "unnamed imported history"
 
             # Create history.
-            new_history = model.History(name=history_name,
-                                        user=self.user)
+            new_history = model.History(name=history_name, user=self.user)
             new_history.importing = True
-            hid_counter = history_properties.get('hid_counter')
-            genome_build = history_properties.get('genome_build')
+            hid_counter = history_properties.get("hid_counter")
+            genome_build = history_properties.get("genome_build")
 
             # TODO: This seems like it shouldn't be imported, try to test and verify we can calculate this
             # and get away without it. -John
@@ -182,7 +183,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             self._flush()
 
             if self.user:
-                add_item_annotation(self.sa_session, self.user, new_history, history_properties.get('annotation'))
+                add_item_annotation(self.sa_session, self.user, new_history, history_properties.get("annotation"))
 
             history = new_history
         else:
@@ -241,7 +242,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
 
         for dataset_attrs in datasets_attrs:
 
-            if 'state' not in dataset_attrs:
+            if "state" not in dataset_attrs:
                 self.dataset_state_serialized = False
 
             def handle_dataset_object_edit(dataset_instance):
@@ -266,13 +267,15 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                     self._attach_dataset_hashes(dataset_attrs["dataset"], dataset_instance)
                     # TODO: Once we have a test...
                     #    self._attach_dataset_sources(dataset_attrs["dataset"], dataset_instance)
-                    if 'id' in dataset_attrs["dataset"] and self.import_options.allow_edit:
-                        dataset_instance.dataset.id = dataset_attrs["dataset"]['id']
+                    if "id" in dataset_attrs["dataset"] and self.import_options.allow_edit:
+                        dataset_instance.dataset.id = dataset_attrs["dataset"]["id"]
                     if job:
                         dataset_instance.dataset.job_id = job.id
 
-            if 'id' in dataset_attrs and self.import_options.allow_edit and not self.sessionless:
-                dataset_instance = self.sa_session.query(getattr(model, dataset_attrs['model_class'])).get(dataset_attrs["id"])
+            if "id" in dataset_attrs and self.import_options.allow_edit and not self.sessionless:
+                dataset_instance = self.sa_session.query(getattr(model, dataset_attrs["model_class"])).get(
+                    dataset_attrs["id"]
+                )
                 attributes = [
                     "name",
                     "extension",
@@ -295,55 +298,61 @@ class ModelImportStore(metaclass=abc.ABCMeta):
 
                 handle_dataset_object_edit(dataset_instance)
             else:
-                metadata = dataset_attrs['metadata']
+                metadata = dataset_attrs["metadata"]
 
                 model_class = dataset_attrs.get("model_class", "HistoryDatasetAssociation")
                 dataset_instance: model.DatasetInstance
                 if model_class == "HistoryDatasetAssociation":
                     # Create dataset and HDA.
-                    dataset_instance = model.HistoryDatasetAssociation(name=dataset_attrs['name'],
-                                                                       extension=dataset_attrs['extension'],
-                                                                       info=dataset_attrs['info'],
-                                                                       blurb=dataset_attrs['blurb'],
-                                                                       peek=dataset_attrs['peek'],
-                                                                       designation=dataset_attrs['designation'],
-                                                                       visible=dataset_attrs['visible'],
-                                                                       deleted=dataset_attrs.get('deleted', False),
-                                                                       dbkey=metadata['dbkey'],
-                                                                       tool_version=metadata.get('tool_version'),
-                                                                       history=history,
-                                                                       create_dataset=True,
-                                                                       flush=False,
-                                                                       sa_session=self.sa_session)
+                    dataset_instance = model.HistoryDatasetAssociation(
+                        name=dataset_attrs["name"],
+                        extension=dataset_attrs["extension"],
+                        info=dataset_attrs["info"],
+                        blurb=dataset_attrs["blurb"],
+                        peek=dataset_attrs["peek"],
+                        designation=dataset_attrs["designation"],
+                        visible=dataset_attrs["visible"],
+                        deleted=dataset_attrs.get("deleted", False),
+                        dbkey=metadata["dbkey"],
+                        tool_version=metadata.get("tool_version"),
+                        history=history,
+                        create_dataset=True,
+                        flush=False,
+                        sa_session=self.sa_session,
+                    )
                     dataset_instance._metadata = metadata
                 elif model_class == "LibraryDatasetDatasetAssociation":
                     # Create dataset and LDDA.
-                    dataset_instance = model.LibraryDatasetDatasetAssociation(name=dataset_attrs['name'],
-                                                                              extension=dataset_attrs['extension'],
-                                                                              info=dataset_attrs['info'],
-                                                                              blurb=dataset_attrs['blurb'],
-                                                                              peek=dataset_attrs['peek'],
-                                                                              designation=dataset_attrs['designation'],
-                                                                              visible=dataset_attrs['visible'],
-                                                                              deleted=dataset_attrs.get('deleted', False),
-                                                                              dbkey=metadata['dbkey'],
-                                                                              tool_version=metadata.get('tool_version'),
-                                                                              user=self.user,
-                                                                              create_dataset=True,
-                                                                              flush=False,
-                                                                              sa_session=self.sa_session)
+                    dataset_instance = model.LibraryDatasetDatasetAssociation(
+                        name=dataset_attrs["name"],
+                        extension=dataset_attrs["extension"],
+                        info=dataset_attrs["info"],
+                        blurb=dataset_attrs["blurb"],
+                        peek=dataset_attrs["peek"],
+                        designation=dataset_attrs["designation"],
+                        visible=dataset_attrs["visible"],
+                        deleted=dataset_attrs.get("deleted", False),
+                        dbkey=metadata["dbkey"],
+                        tool_version=metadata.get("tool_version"),
+                        user=self.user,
+                        create_dataset=True,
+                        flush=False,
+                        sa_session=self.sa_session,
+                    )
                 else:
                     raise Exception("Unknown dataset instance type encountered")
                 if self.sessionless:
-                    dataset_instance._metadata_collection = MetadataCollection(dataset_instance, session=self.sa_session)
+                    dataset_instance._metadata_collection = MetadataCollection(
+                        dataset_instance, session=self.sa_session
+                    )
                     metadata = replace_metadata_file(metadata, dataset_instance)
                 dataset_instance._metadata = metadata
                 self._attach_raw_id_if_editing(dataset_instance, dataset_attrs)
 
                 # Older style...
-                if 'uuid' in dataset_attrs:
+                if "uuid" in dataset_attrs:
                     dataset_instance.dataset.uuid = dataset_attrs["uuid"]
-                if 'dataset_uuid' in dataset_attrs:
+                if "dataset_uuid" in dataset_attrs:
                     dataset_instance.dataset.uuid = dataset_attrs["dataset_uuid"]
 
                 self._session_add(dataset_instance)
@@ -354,7 +363,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                     # HID structure.
                     hda.history = history
                     if new_history and self.trust_hid(dataset_attrs):
-                        hda.hid = dataset_attrs['hid']
+                        hda.hid = dataset_attrs["hid"]
                     else:
                         object_import_tracker.requires_hid.append(hda)
 
@@ -364,10 +373,10 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 # and the import options are configured for allowing editing the dataset (e.g. for metadata setting).
                 # Otherwise, we will check for "file" information instead of dataset information - currently this includes
                 # "file_name", "extra_files_path".
-                if 'dataset' in dataset_attrs:
+                if "dataset" in dataset_attrs:
                     handle_dataset_object_edit(dataset_instance)
                 else:
-                    file_name = dataset_attrs.get('file_name')
+                    file_name = dataset_attrs.get("file_name")
                     if file_name:
                         assert file_source_root
                         # Do security check and move/copy dataset data.
@@ -375,8 +384,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                         if os.path.islink(archive_path):
                             raise MalformedContents(f"Invalid dataset path: {archive_path}")
 
-                        temp_dataset_file_name = \
-                            os.path.realpath(archive_path)
+                        temp_dataset_file_name = os.path.realpath(archive_path)
 
                         if not in_directory(temp_dataset_file_name, file_source_root):
                             raise MalformedContents(f"Invalid dataset path: {temp_dataset_file_name}")
@@ -388,26 +396,33 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                         dataset_instance.dataset.deleted = True
                         dataset_instance.dataset.purged = True
                     else:
-                        dataset_instance.state = dataset_attrs.get('state', dataset_instance.states.OK)
-                        self.object_store.update_from_file(dataset_instance.dataset, file_name=temp_dataset_file_name, create=True)
+                        dataset_instance.state = dataset_attrs.get("state", dataset_instance.states.OK)
+                        self.object_store.update_from_file(
+                            dataset_instance.dataset, file_name=temp_dataset_file_name, create=True
+                        )
 
                         # Import additional files if present. Histories exported previously might not have this attribute set.
-                        dataset_extra_files_path = dataset_attrs.get('extra_files_path', None)
+                        dataset_extra_files_path = dataset_attrs.get("extra_files_path", None)
                         if dataset_extra_files_path:
                             assert file_source_root
                             dir_name = dataset_instance.dataset.extra_files_path_name
                             dataset_extra_files_path = os.path.join(file_source_root, dataset_extra_files_path)
                             for root, _dirs, files in safe_walk(dataset_extra_files_path):
-                                extra_dir = os.path.join(dir_name, root.replace(dataset_extra_files_path, '', 1).lstrip(os.path.sep))
+                                extra_dir = os.path.join(
+                                    dir_name, root.replace(dataset_extra_files_path, "", 1).lstrip(os.path.sep)
+                                )
                                 extra_dir = os.path.normpath(extra_dir)
                                 for extra_file in files:
                                     source = os.path.join(root, extra_file)
                                     if not in_directory(source, file_source_root):
                                         raise MalformedContents(f"Invalid dataset path: {source}")
                                     self.object_store.update_from_file(
-                                        dataset_instance.dataset, extra_dir=extra_dir,
-                                        alt_name=extra_file, file_name=source,
-                                        create=True)
+                                        dataset_instance.dataset,
+                                        extra_dir=extra_dir,
+                                        alt_name=extra_file,
+                                        file_name=source,
+                                        create=True,
+                                    )
                         dataset_instance.dataset.set_total_size()  # update the filesize record in the database
 
                     if dataset_instance.deleted:
@@ -419,10 +434,12 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                         dataset_instance.dataset.created_from_basename = file_metadata["created_from_basename"]
 
                 if model_class == "HistoryDatasetAssociation" and self.user:
-                    add_item_annotation(self.sa_session, self.user, dataset_instance, dataset_attrs['annotation'])
-                    tag_list = dataset_attrs.get('tags')
+                    add_item_annotation(self.sa_session, self.user, dataset_instance, dataset_attrs["annotation"])
+                    tag_list = dataset_attrs.get("tags")
                     if tag_list:
-                        self.tag_handler.set_tags_from_list(user=self.user, item=dataset_instance, new_tags_list=tag_list, flush=False)
+                        self.tag_handler.set_tags_from_list(
+                            user=self.user, item=dataset_instance, new_tags_list=tag_list, flush=False
+                        )
 
                 if self.app:
                     self.app.datatypes_registry.set_external_metadata_tool.regenerate_imported_metadata_if_needed(
@@ -433,14 +450,14 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                     if object_key in dataset_attrs:
                         object_import_tracker.hdas_by_key[dataset_attrs[object_key]] = dataset_instance
                     else:
-                        assert 'id' in dataset_attrs
-                        object_import_tracker.hdas_by_id[dataset_attrs['id']] = dataset_instance
+                        assert "id" in dataset_attrs
+                        object_import_tracker.hdas_by_id[dataset_attrs["id"]] = dataset_instance
                 else:
                     if object_key in dataset_attrs:
                         object_import_tracker.lddas_by_key[dataset_attrs[object_key]] = dataset_instance
                     else:
-                        assert 'id' in dataset_attrs
-                        object_import_tracker.lddas_by_key[dataset_attrs['id']] = dataset_instance
+                        assert "id" in dataset_attrs
+                        object_import_tracker.lddas_by_key[dataset_attrs["id"]] = dataset_instance
 
     def _import_libraries(self, object_import_tracker):
         object_key = self.object_key
@@ -449,15 +466,11 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             if root_folder:
                 library_folder = root_folder
             else:
-                name = folder_attrs['name']
-                description = folder_attrs['description']
-                genome_build = folder_attrs['genome_build']
-                deleted = folder_attrs['deleted']
-                library_folder = model.LibraryFolder(
-                    name=name,
-                    description=description,
-                    genome_build=genome_build
-                )
+                name = folder_attrs["name"]
+                description = folder_attrs["description"]
+                genome_build = folder_attrs["genome_build"]
+                deleted = folder_attrs["deleted"]
+                library_folder = model.LibraryFolder(name=name, description=description, genome_build=genome_build)
                 library_folder.deleted = deleted
 
             self._session_add(library_folder)
@@ -468,12 +481,9 @@ class ModelImportStore(metaclass=abc.ABCMeta):
 
             for ld_attrs in folder_attrs.get("datasets", []):
                 ld = model.LibraryDataset(
-                    folder=library_folder,
-                    name=ld_attrs['name'],
-                    info=ld_attrs['info'],
-                    order_id=ld_attrs['order_id']
+                    folder=library_folder, name=ld_attrs["name"], info=ld_attrs["info"], order_id=ld_attrs["order_id"]
                 )
-                if 'ldda' in ld_attrs:
+                if "ldda" in ld_attrs:
                     ldda = object_import_tracker.lddas_by_key[ld_attrs["ldda"][object_key]]
                     ld.library_dataset_dataset_association = ldda
                 self._session_add(ld)
@@ -483,20 +493,27 @@ class ModelImportStore(metaclass=abc.ABCMeta):
 
         libraries_attrs = self.library_properties()
         for library_attrs in libraries_attrs:
-            if library_attrs['model_class'] == 'LibraryFolder' and library_attrs.get('id') and not self.sessionless and self.import_options.allow_edit:
-                library_folder = self.sa_session.query(model.LibraryFolder).get(self.app.security.decode_id(library_attrs['id']))
+            if (
+                library_attrs["model_class"] == "LibraryFolder"
+                and library_attrs.get("id")
+                and not self.sessionless
+                and self.import_options.allow_edit
+            ):
+                library_folder = self.sa_session.query(model.LibraryFolder).get(
+                    self.app.security.decode_id(library_attrs["id"])
+                )
                 import_folder(library_attrs, root_folder=library_folder)
             else:
                 assert self.import_options.allow_library_creation
-                name = library_attrs['name']
-                description = library_attrs['description']
-                synopsis = library_attrs['synopsis']
+                name = library_attrs["name"]
+                description = library_attrs["description"]
+                synopsis = library_attrs["synopsis"]
                 library = model.Library(name=name, description=description, synopsis=synopsis)
                 self._session_add(library)
                 object_import_tracker.libraries_by_key[library_attrs[object_key]] = library
 
-            if 'root_folder' in library_attrs:
-                library.root_folder = import_folder(library_attrs['root_folder'])
+            if "root_folder" in library_attrs:
+                library.root_folder = import_folder(library_attrs["root_folder"])
 
     def _import_collection_instances(self, object_import_tracker, collections_attrs, history, new_history):
         object_key = self.object_key
@@ -506,23 +523,27 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 if "elements" not in collection_attrs:
                     return
 
-                elements_attrs = collection_attrs['elements']
+                elements_attrs = collection_attrs["elements"]
                 for element_attrs in elements_attrs:
-                    dce = model.DatasetCollectionElement(collection=dc,
-                                                         element=model.DatasetCollectionElement.UNINITIALIZED_ELEMENT,
-                                                         element_index=element_attrs['element_index'],
-                                                         element_identifier=element_attrs['element_identifier'])
-                    if 'encoded_id' in element_attrs:
-                        object_import_tracker.dces_by_key[element_attrs['encoded_id']] = dce
-                    if 'hda' in element_attrs:
-                        hda_attrs = element_attrs['hda']
+                    dce = model.DatasetCollectionElement(
+                        collection=dc,
+                        element=model.DatasetCollectionElement.UNINITIALIZED_ELEMENT,
+                        element_index=element_attrs["element_index"],
+                        element_identifier=element_attrs["element_identifier"],
+                    )
+                    if "encoded_id" in element_attrs:
+                        object_import_tracker.dces_by_key[element_attrs["encoded_id"]] = dce
+                    if "hda" in element_attrs:
+                        hda_attrs = element_attrs["hda"]
                         if object_key in hda_attrs:
                             hda_key = hda_attrs[object_key]
                             hdas_by_key = object_import_tracker.hdas_by_key
                             if hda_key in hdas_by_key:
                                 hda = hdas_by_key[hda_key]
                             else:
-                                raise KeyError(f"Failed to find exported hda with key [{hda_key}] of type [{object_key}] in [{hdas_by_key}]")
+                                raise KeyError(
+                                    f"Failed to find exported hda with key [{hda_key}] of type [{object_key}] in [{hdas_by_key}]"
+                                )
                         else:
                             hda_id = hda_attrs["id"]
                             hdas_by_id = object_import_tracker.hdas_by_id
@@ -530,8 +551,8 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                                 raise Exception(f"Failed to find HDA with id [{hda_id}] in [{hdas_by_id}]")
                             hda = hdas_by_id[hda_id]
                         dce.hda = hda
-                    elif 'child_collection' in element_attrs:
-                        dce.child_collection = import_collection(element_attrs['child_collection'])
+                    elif "child_collection" in element_attrs:
+                        dce.child_collection = import_collection(element_attrs["child_collection"])
                     else:
                         raise Exception("Unknown collection element type encountered.")
                 dc.element_count = len(elements_attrs)
@@ -550,9 +571,9 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 materialize_elements(dc)
             else:
                 # create collection
-                dc = model.DatasetCollection(collection_type=collection_attrs['type'])
+                dc = model.DatasetCollection(collection_type=collection_attrs["type"])
                 dc.populated_state = collection_attrs["populated_state"]
-                dc.populated_state_message = collection_attrs.get('populated_state_message')
+                dc.populated_state_message = collection_attrs.get("populated_state_message")
                 self._attach_raw_id_if_editing(dc, collection_attrs)
                 materialize_elements(dc)
 
@@ -560,21 +581,23 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             return dc
 
         for collection_attrs in collections_attrs:
-            if 'collection' in collection_attrs:
+            if "collection" in collection_attrs:
                 dc = import_collection(collection_attrs["collection"])
-                if 'id' in collection_attrs and self.import_options.allow_edit and not self.sessionless:
+                if "id" in collection_attrs and self.import_options.allow_edit and not self.sessionless:
                     hdca = self.sa_session.query(model.HistoryDatasetCollectionAssociation).get(collection_attrs["id"])
                     # TODO: edit attributes...
                 else:
-                    hdca = model.HistoryDatasetCollectionAssociation(collection=dc,
-                                                                     visible=True,
-                                                                     name=collection_attrs['display_name'],
-                                                                     implicit_output_name=collection_attrs.get("implicit_output_name"))
+                    hdca = model.HistoryDatasetCollectionAssociation(
+                        collection=dc,
+                        visible=True,
+                        name=collection_attrs["display_name"],
+                        implicit_output_name=collection_attrs.get("implicit_output_name"),
+                    )
                     self._attach_raw_id_if_editing(hdca, collection_attrs)
 
                     hdca.history = history
                     if new_history and self.trust_hid(collection_attrs):
-                        hdca.hid = collection_attrs['hid']
+                        hdca.hid = collection_attrs["hid"]
                     else:
                         object_import_tracker.requires_hid.append(hdca)
 
@@ -582,14 +605,14 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 if object_key in collection_attrs:
                     object_import_tracker.hdcas_by_key[collection_attrs[object_key]] = hdca
                 else:
-                    assert 'id' in collection_attrs
-                    object_import_tracker.hdcas_by_id[collection_attrs['id']] = hdca
+                    assert "id" in collection_attrs
+                    object_import_tracker.hdcas_by_id[collection_attrs["id"]] = hdca
             else:
                 import_collection(collection_attrs)
 
     def _attach_raw_id_if_editing(self, obj, attrs):
-        if self.sessionless and 'id' in attrs and self.import_options.allow_edit:
-            obj.id = attrs['id']
+        if self.sessionless and "id" in attrs and self.import_options.allow_edit:
+            obj.id = attrs["id"]
 
     def _import_collection_implicit_input_associations(self, object_import_tracker, collections_attrs):
         object_key = self.object_key
@@ -641,7 +664,9 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 # instance but I think it is fine to pretend in order to create a DAG here.
                 hda_copied_from_sinks = object_import_tracker.hda_copied_from_sinks
                 if copied_from_object_key in hda_copied_from_sinks:
-                    hda.copied_from_history_dataset_association = object_import_tracker.hdas_by_key[hda_copied_from_sinks[copied_from_object_key]]
+                    hda.copied_from_history_dataset_association = object_import_tracker.hdas_by_key[
+                        hda_copied_from_sinks[copied_from_object_key]
+                    ]
                 else:
                     hda_copied_from_sinks[copied_from_object_key] = dataset_key
 
@@ -670,10 +695,14 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             # sense.
             hdca_copied_from_sinks = object_import_tracker.hdca_copied_from_sinks
             if copied_from_object_key in object_import_tracker.hdcas_by_key:
-                hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[copied_from_object_key]
+                hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
+                    copied_from_object_key
+                ]
             else:
                 if copied_from_object_key in hdca_copied_from_sinks:
-                    hdca.copied_from_history_dataset_association = object_import_tracker.hdcas_by_key[hdca_copied_from_sinks[copied_from_object_key]]
+                    hdca.copied_from_history_dataset_association = object_import_tracker.hdcas_by_key[
+                        hdca_copied_from_sinks[copied_from_object_key]
+                    ]
                 else:
                     hdca_copied_from_sinks[copied_from_object_key] = dataset_collection_key
 
@@ -700,7 +729,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
         jobs_attrs = self.jobs_properties()
         # Create each job.
         for job_attrs in jobs_attrs:
-            if 'id' in job_attrs and not self.sessionless:
+            if "id" in job_attrs and not self.sessionless:
                 # only thing we allow editing currently is associations for incoming jobs.
                 assert self.import_options.allow_edit
                 job = self.sa_session.query(model.Job).get(job_attrs["id"])
@@ -710,12 +739,12 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 continue
 
             imported_job = model.Job()
-            imported_job.id = job_attrs.get('id')
+            imported_job.id = job_attrs.get("id")
             imported_job.user = self.user
             imported_job.history = history
             imported_job.imported = True
-            imported_job.tool_id = job_attrs['tool_id']
-            imported_job.tool_version = job_attrs['tool_version']
+            imported_job.tool_id = job_attrs["tool_id"]
+            imported_job.tool_version = job_attrs["tool_version"]
             self._set_job_attributes(imported_job, job_attrs, force_terminal=True)
 
             try:
@@ -788,6 +817,7 @@ class ObjectImportTracker:
 
     Needed to re-establish connections and such in multiple passes.
     """
+
     libraries_by_key: Dict[ObjectKeyType, model.Library]
     hdas_by_key: Dict[ObjectKeyType, model.HistoryDatasetAssociation]
     hdas_by_id: Dict[int, model.HistoryDatasetAssociation]
@@ -815,7 +845,9 @@ class ObjectImportTracker:
         self.jobs_by_key = {}
         self.requires_hid = []
 
-    def find_hda(self, input_key: ObjectKeyType, hda_id: Optional[int] = None) -> Optional[model.HistoryDatasetAssociation]:
+    def find_hda(
+        self, input_key: ObjectKeyType, hda_id: Optional[int] = None
+    ) -> Optional[model.HistoryDatasetAssociation]:
         hda = None
         if input_key in self.hdas_by_key:
             hda = self.hdas_by_key[input_key]
@@ -846,7 +878,6 @@ class ObjectImportTracker:
 
 
 class FileTracebackException(Exception):
-
     def __init__(self, traceback, *args, **kwargs):
         self.traceback = traceback
 
@@ -854,7 +885,9 @@ class FileTracebackException(Exception):
 def get_import_model_store_for_directory(archive_dir, **kwd):
     traceback_file = os.path.join(archive_dir, TRACEBACK)
     if not os.path.isdir(archive_dir):
-        raise Exception(f"Could not find import model store for directory [{archive_dir}] (full path [{os.path.abspath(archive_dir)}])")
+        raise Exception(
+            f"Could not find import model store for directory [{archive_dir}] (full path [{os.path.abspath(archive_dir)}])"
+        )
     if os.path.exists(os.path.join(archive_dir, ATTRS_FILENAME_EXPORT)):
         if os.path.exists(traceback_file):
             with open(traceback_file) as tb:
@@ -865,7 +898,6 @@ def get_import_model_store_for_directory(archive_dir, **kwd):
 
 
 class BaseDirectoryImportModelStore(ModelImportStore):
-
     @property
     def file_source_root(self):
         return self.archive_dir
@@ -914,7 +946,9 @@ class BaseDirectoryImportModelStore(ModelImportStore):
             return []
 
     def implicit_collection_jobs_properties(self):
-        implicit_collection_jobs_attrs_file_name = os.path.join(self.archive_dir, ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS)
+        implicit_collection_jobs_attrs_file_name = os.path.join(
+            self.archive_dir, ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS
+        )
         try:
             return load(open(implicit_collection_jobs_attrs_file_name))
         except FileNotFoundError:
@@ -922,30 +956,30 @@ class BaseDirectoryImportModelStore(ModelImportStore):
 
     def _set_job_attributes(self, imported_job, job_attrs, force_terminal=False):
         ATTRIBUTES = (
-            'info',
-            'exit_code',
-            'traceback',
-            'job_messages',
-            'tool_stdout',
-            'tool_stderr',
-            'job_stdout',
-            'job_stderr'
+            "info",
+            "exit_code",
+            "traceback",
+            "job_messages",
+            "tool_stdout",
+            "tool_stderr",
+            "job_stdout",
+            "job_stderr",
         )
         for attribute in ATTRIBUTES:
             value = job_attrs.get(attribute)
             if value is not None:
                 setattr(imported_job, attribute, value)
-        if 'stdout' in job_attrs:
-            imported_job.tool_stdout = job_attrs.get('stdout')
-            imported_job.tool_stderr = job_attrs.get('stderr')
-        raw_state = job_attrs.get('state')
+        if "stdout" in job_attrs:
+            imported_job.tool_stdout = job_attrs.get("stdout")
+            imported_job.tool_stderr = job_attrs.get("stderr")
+        raw_state = job_attrs.get("state")
         if force_terminal and raw_state and raw_state not in model.Job.terminal_states:
             raw_state = model.Job.states.ERROR
         imported_job.set_state(raw_state)
 
 
 class DirectoryImportModelStore1901(BaseDirectoryImportModelStore):
-    object_key = 'hid'
+    object_key = "hid"
 
     def __init__(self, archive_dir, **kwd):
         super().__init__(**kwd)
@@ -961,7 +995,7 @@ class DirectoryImportModelStore1901(BaseDirectoryImportModelStore):
         self.archive_dir = archive_dir
 
     def _connect_job_io(self, imported_job, job_attrs, _find_hda, _find_hdca, _find_dce):
-        for output_key in job_attrs['output_datasets']:
+        for output_key in job_attrs["output_datasets"]:
             output_hda = _find_hda(output_key)
             if output_hda:
                 if not self.dataset_state_serialized:
@@ -969,21 +1003,21 @@ class DirectoryImportModelStore1901(BaseDirectoryImportModelStore):
                     output_hda.state = imported_job.state
                 imported_job.add_output_dataset(output_hda.name, output_hda)
 
-        if 'input_mapping' in job_attrs:
-            for input_name, input_key in job_attrs['input_mapping'].items():
+        if "input_mapping" in job_attrs:
+            for input_name, input_key in job_attrs["input_mapping"].items():
                 input_hda = _find_hda(input_key)
                 if input_hda:
                     imported_job.add_input_dataset(input_name, input_hda)
 
     def _normalize_job_parameters(self, imported_job, job_attrs, _find_hda, _find_hdca, _find_dce):
         def remap_objects(p, k, obj):
-            if isinstance(obj, dict) and obj.get('__HistoryDatasetAssociation__', False):
+            if isinstance(obj, dict) and obj.get("__HistoryDatasetAssociation__", False):
                 imported_hda = _find_hda(obj[self.object_key])
                 if imported_hda:
                     return (k, {"src": "hda", "id": imported_hda.id})
             return (k, obj)
 
-        params = job_attrs['params']
+        params = job_attrs["params"]
         params = remap(params, remap_objects)
         return params
 
@@ -994,7 +1028,7 @@ class DirectoryImportModelStore1901(BaseDirectoryImportModelStore):
 
 
 class DirectoryImportModelStoreLatest(BaseDirectoryImportModelStore):
-    object_key = 'encoded_id'
+    object_key = "encoded_id"
 
     def __init__(self, archive_dir, **kwd):
         super().__init__(**kwd)
@@ -1007,34 +1041,34 @@ class DirectoryImportModelStoreLatest(BaseDirectoryImportModelStore):
 
     def _connect_job_io(self, imported_job, job_attrs, _find_hda, _find_hdca, _find_dce):
         if imported_job.command_line is None:
-            imported_job.command_line = job_attrs.get('command_line')
+            imported_job.command_line = job_attrs.get("command_line")
 
-        if 'input_dataset_mapping' in job_attrs:
-            for input_name, input_keys in job_attrs['input_dataset_mapping'].items():
+        if "input_dataset_mapping" in job_attrs:
+            for input_name, input_keys in job_attrs["input_dataset_mapping"].items():
                 input_keys = input_keys or []
                 for input_key in input_keys:
                     input_hda = _find_hda(input_key)
                     if input_hda:
                         imported_job.add_input_dataset(input_name, input_hda)
 
-        if 'input_dataset_collection_mapping' in job_attrs:
-            for input_name, input_keys in job_attrs['input_dataset_collection_mapping'].items():
+        if "input_dataset_collection_mapping" in job_attrs:
+            for input_name, input_keys in job_attrs["input_dataset_collection_mapping"].items():
                 input_keys = input_keys or []
                 for input_key in input_keys:
                     input_hdca = _find_hdca(input_key)
                     if input_hdca:
                         imported_job.add_input_dataset_collection(input_name, input_hdca)
 
-        if 'input_dataset_collection_element_mapping' in job_attrs:
-            for input_name, input_keys in job_attrs['input_dataset_collection_element_mapping'].items():
+        if "input_dataset_collection_element_mapping" in job_attrs:
+            for input_name, input_keys in job_attrs["input_dataset_collection_element_mapping"].items():
                 input_keys = input_keys or []
                 for input_key in input_keys:
                     input_dce = _find_dce(input_key)
                     if input_dce:
                         imported_job.add_input_dataset_collection_element(input_name, input_dce)
 
-        if 'output_dataset_mapping' in job_attrs:
-            for output_name, output_keys in job_attrs['output_dataset_mapping'].items():
+        if "output_dataset_mapping" in job_attrs:
+            for output_name, output_keys in job_attrs["output_dataset_mapping"].items():
                 output_keys = output_keys or []
                 for output_key in output_keys:
                     output_hda = _find_hda(output_key)
@@ -1044,8 +1078,8 @@ class DirectoryImportModelStoreLatest(BaseDirectoryImportModelStore):
                             output_hda.state = imported_job.state
                         imported_job.add_output_dataset(output_name, output_hda)
 
-        if 'output_dataset_collection_mapping' in job_attrs:
-            for output_name, output_keys in job_attrs['output_dataset_collection_mapping'].items():
+        if "output_dataset_collection_mapping" in job_attrs:
+            for output_name, output_keys in job_attrs["output_dataset_collection_mapping"].items():
                 output_keys = output_keys or []
                 for output_key in output_keys:
                     output_hdca = _find_hdca(output_key)
@@ -1084,13 +1118,12 @@ class DirectoryImportModelStoreLatest(BaseDirectoryImportModelStore):
 
             return (k, obj)
 
-        params = job_attrs['params']
+        params = job_attrs["params"]
         params = remap(params, remap_objects)
         return params
 
 
 class BagArchiveImportModelStore(DirectoryImportModelStoreLatest):
-
     def __init__(self, bag_archive, **kwd):
         archive_dir = tempfile.mkdtemp()
         bdb.extract_bag(bag_archive, output_path=archive_dir)
@@ -1101,13 +1134,14 @@ class BagArchiveImportModelStore(DirectoryImportModelStoreLatest):
 
 
 class ModelExportStore(metaclass=abc.ABCMeta):
-
     @abc.abstractmethod
     def export_history(self, history: model.History, include_hidden: bool = False, include_deleted: bool = False):
         """Export history to store."""
 
     @abc.abstractmethod
-    def add_dataset_collection(self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]):
+    def add_dataset_collection(
+        self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
+    ):
         """Add Dataset Collection or HDCA to export store."""
 
     @abc.abstractmethod
@@ -1128,8 +1162,16 @@ class ModelExportStore(metaclass=abc.ABCMeta):
 
 
 class DirectoryModelExportStore(ModelExportStore):
-
-    def __init__(self, export_directory, app=None, for_edit=False, serialize_dataset_objects=None, export_files=None, strip_metadata_files=True, serialize_jobs=True):
+    def __init__(
+        self,
+        export_directory,
+        app=None,
+        for_edit=False,
+        serialize_dataset_objects=None,
+        export_files=None,
+        strip_metadata_files=True,
+        serialize_jobs=True,
+    ):
         """
         :param export_directory: path to export directory. Will be created if it does not exist.
         :param app: Galaxy App or app-like object. Must be provided if `for_edit` and/or `serialize_dataset_objects` are True
@@ -1179,11 +1221,13 @@ class DirectoryModelExportStore(ModelExportStore):
         elif self.export_files == "symlink":
             add = os.symlink
         elif self.export_files == "copy":
+
             def add(src, dest):
                 if os.path.isdir(src):
                     shutil.copytree(src, dest)
                 else:
                     shutil.copyfile(src, dest)
+
         else:
             raise Exception(f"Unknown export_files parameter type encountered {self.export_files}")
 
@@ -1206,30 +1250,30 @@ class DirectoryModelExportStore(ModelExportStore):
         else:
             pass
 
-        dir_name = 'datasets'
+        dir_name = "datasets"
         dir_path = os.path.join(export_directory, dir_name)
-        dataset_hid = as_dict['hid']
+        dataset_hid = as_dict["hid"]
         assert dataset_hid, as_dict
 
         if dataset.dataset.id in self.dataset_id_to_path:
             file_name, extra_files_path = self.dataset_id_to_path[dataset.dataset.id]
             if file_name is not None:
-                as_dict['file_name'] = file_name
+                as_dict["file_name"] = file_name
             if extra_files_path is not None:
-                as_dict['extra_files_path'] = extra_files_path
+                as_dict["extra_files_path"] = extra_files_path
             return
 
         if file_name:
             if not os.path.exists(dir_path):
                 os.makedirs(dir_path)
 
-            target_filename = get_export_dataset_filename(as_dict['name'], as_dict['extension'], dataset_hid)
+            target_filename = get_export_dataset_filename(as_dict["name"], as_dict["extension"], dataset_hid)
             arcname = os.path.join(dir_name, target_filename)
 
             src = file_name
             dest = os.path.join(export_directory, arcname)
             add(src, dest)
-            as_dict['file_name'] = arcname
+            as_dict["file_name"] = arcname
 
         if extra_files_path:
             try:
@@ -1238,11 +1282,11 @@ class DirectoryModelExportStore(ModelExportStore):
                 file_list = []
 
             if len(file_list):
-                arcname = os.path.join(dir_name, f'extra_files_path_{dataset_hid}')
+                arcname = os.path.join(dir_name, f"extra_files_path_{dataset_hid}")
                 add(extra_files_path, os.path.join(export_directory, arcname))
-                as_dict['extra_files_path'] = arcname
+                as_dict["extra_files_path"] = arcname
             else:
-                as_dict['extra_files_path'] = ''
+                as_dict["extra_files_path"] = ""
 
         self.dataset_id_to_path[dataset.dataset.id] = (as_dict.get("file_name"), as_dict.get("extra_files_path"))
 
@@ -1254,9 +1298,9 @@ class DirectoryModelExportStore(ModelExportStore):
 
     def export_job(self, job: model.Job, tool=None, include_job_data=True):
         self.export_jobs([job], include_job_data=include_job_data)
-        tool_source = getattr(tool, 'tool_source', None)
+        tool_source = getattr(tool, "tool_source", None)
         if tool_source:
-            with open(os.path.join(self.export_directory, 'tool.xml'), 'w') as out:
+            with open(os.path.join(self.export_directory, "tool.xml"), "w") as out:
                 out.write(tool_source.to_string())
 
     def export_jobs(self, jobs: List[model.Job], jobs_attrs=None, include_job_data=True):
@@ -1320,7 +1364,9 @@ class DirectoryModelExportStore(ModelExportStore):
                         if name not in input_dataset_collection_element_mapping:
                             input_dataset_collection_element_mapping[name] = []
 
-                        input_dataset_collection_element_mapping[name].append(self.exported_key(assoc.dataset_collection_element))
+                        input_dataset_collection_element_mapping[name].append(
+                            self.exported_key(assoc.dataset_collection_element)
+                        )
                         if include_job_data:
                             if assoc.dataset_collection_element.is_collection:
                                 self.export_collection(assoc.dataset_collection_element.element_object)
@@ -1335,7 +1381,9 @@ class DirectoryModelExportStore(ModelExportStore):
                         if name not in output_dataset_collection_mapping:
                             output_dataset_collection_mapping[name] = []
 
-                        output_dataset_collection_mapping[name].append(self.exported_key(assoc.dataset_collection_instance))
+                        output_dataset_collection_mapping[name].append(
+                            self.exported_key(assoc.dataset_collection_instance)
+                        )
 
                 for assoc in job.output_dataset_collections:
                     if assoc.dataset_collection:
@@ -1344,21 +1392,23 @@ class DirectoryModelExportStore(ModelExportStore):
                         if name not in implicit_output_dataset_collection_mapping:
                             implicit_output_dataset_collection_mapping[name] = []
 
-                        implicit_output_dataset_collection_mapping[name].append(self.exported_key(assoc.dataset_collection))
+                        implicit_output_dataset_collection_mapping[name].append(
+                            self.exported_key(assoc.dataset_collection)
+                        )
                         if include_job_data:
                             self.export_collection(assoc.dataset_collection)
 
-                job_attrs['input_dataset_mapping'] = input_dataset_mapping
-                job_attrs['input_dataset_collection_mapping'] = input_dataset_collection_mapping
-                job_attrs['input_dataset_collection_element_mapping'] = input_dataset_collection_element_mapping
-                job_attrs['output_dataset_mapping'] = output_dataset_mapping
-                job_attrs['output_dataset_collection_mapping'] = output_dataset_collection_mapping
-                job_attrs['implicit_output_dataset_collection_mapping'] = implicit_output_dataset_collection_mapping
+                job_attrs["input_dataset_mapping"] = input_dataset_mapping
+                job_attrs["input_dataset_collection_mapping"] = input_dataset_collection_mapping
+                job_attrs["input_dataset_collection_element_mapping"] = input_dataset_collection_element_mapping
+                job_attrs["output_dataset_mapping"] = output_dataset_mapping
+                job_attrs["output_dataset_collection_mapping"] = output_dataset_collection_mapping
+                job_attrs["implicit_output_dataset_collection_mapping"] = implicit_output_dataset_collection_mapping
 
             jobs_attrs.append(job_attrs)
 
         jobs_attrs_filename = os.path.join(self.export_directory, ATTRS_FILENAME_JOBS)
-        with open(jobs_attrs_filename, 'w') as jobs_attrs_out:
+        with open(jobs_attrs_filename, "w") as jobs_attrs_out:
             jobs_attrs_out.write(json_encoder.encode(jobs_attrs))
         return jobs_attrs
 
@@ -1368,22 +1418,24 @@ class DirectoryModelExportStore(ModelExportStore):
 
         history_attrs = history.serialize(app.security, self.serialization_options)
         history_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_HISTORY)
-        with open(history_attrs_filename, 'w') as history_attrs_out:
+        with open(history_attrs_filename, "w") as history_attrs_out:
             dump(history_attrs, history_attrs_out)
 
         sa_session = app.model.session
 
         # Write collections' attributes (including datasets list) to file.
-        query = (sa_session.query(model.HistoryDatasetCollectionAssociation)
-                 .filter(model.HistoryDatasetCollectionAssociation.history == history)
-                 .filter(model.HistoryDatasetCollectionAssociation.deleted == expression.false()))
+        query = (
+            sa_session.query(model.HistoryDatasetCollectionAssociation)
+            .filter(model.HistoryDatasetCollectionAssociation.history == history)
+            .filter(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
+        )
         collections = query.all()
 
         for collection in collections:
             # filter this ?
             if not collection.populated:
                 break
-            if collection.state != 'ok':
+            if collection.state != "ok":
                 break
 
             self.add_dataset_collection(collection)
@@ -1399,12 +1451,14 @@ class DirectoryModelExportStore(ModelExportStore):
                 self.collection_datasets[collection_dataset.id] = True
 
         # Write datasets' attributes to file.
-        query = (sa_session.query(model.HistoryDatasetAssociation)
-                 .filter(model.HistoryDatasetAssociation.history == history)
-                 .join(model.Dataset)
-                 .options(joinedload("dataset").joinedload("actions"))
-                 .order_by(model.HistoryDatasetAssociation.hid)
-                 .filter(model.Dataset.purged == expression.false()))
+        query = (
+            sa_session.query(model.HistoryDatasetAssociation)
+            .filter(model.HistoryDatasetAssociation.history == history)
+            .join(model.Dataset)
+            .options(joinedload("dataset").joinedload("actions"))
+            .order_by(model.HistoryDatasetAssociation.hid)
+            .filter(model.Dataset.purged == expression.false())
+        )
         datasets = query.all()
         for dataset in datasets:
             dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
@@ -1417,7 +1471,7 @@ class DirectoryModelExportStore(ModelExportStore):
 
     def export_library(self, library, include_hidden=False, include_deleted=False):
         self.included_libraries.append(library)
-        root_folder = getattr(library, 'root_folder', library)
+        root_folder = getattr(library, "root_folder", library)
         self.included_library_folders.append(root_folder)
         self.export_library_folder(root_folder, include_hidden=include_hidden, include_deleted=include_deleted)
 
@@ -1435,11 +1489,17 @@ class DirectoryModelExportStore(ModelExportStore):
             job_output_dataset_associations[job_id] = {}
         job_output_dataset_associations[job_id][name] = dataset_instance
 
-    def export_collection(self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation], include_deleted: bool = False):
+    def export_collection(
+        self,
+        collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
+        include_deleted: bool = False,
+    ):
         self.add_dataset_collection(collection)
 
         # export datasets for this collection
-        has_collection = collection.collection if isinstance(collection, model.HistoryDatasetCollectionAssociation) else collection
+        has_collection = (
+            collection.collection if isinstance(collection, model.HistoryDatasetCollectionAssociation) else collection
+        )
         for collection_dataset in has_collection.dataset_instances:
             if collection_dataset.deleted and not include_deleted:
                 include_files = False
@@ -1449,7 +1509,9 @@ class DirectoryModelExportStore(ModelExportStore):
             self.add_dataset(collection_dataset, include_files=include_files)
             self.collection_datasets[collection_dataset.id] = True
 
-    def add_dataset_collection(self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]):
+    def add_dataset_collection(
+        self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
+    ):
         self.collections_attrs.append(collection)
         self.included_collections.append(collection)
 
@@ -1471,18 +1533,18 @@ class DirectoryModelExportStore(ModelExportStore):
             return json_encoder.encode([a.serialize(self.security, self.serialization_options) for a in attributes])
 
         datasets_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_DATASETS)
-        with open(datasets_attrs_filename, 'w') as datasets_attrs_out:
+        with open(datasets_attrs_filename, "w") as datasets_attrs_out:
             datasets_attrs_out.write(to_json(datasets_attrs))
 
-        with open(f"{datasets_attrs_filename}.provenance", 'w') as provenance_attrs_out:
+        with open(f"{datasets_attrs_filename}.provenance", "w") as provenance_attrs_out:
             provenance_attrs_out.write(to_json(provenance_attrs))
 
         libraries_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_LIBRARIES)
-        with open(libraries_attrs_filename, 'w') as libraries_attrs_out:
+        with open(libraries_attrs_filename, "w") as libraries_attrs_out:
             libraries_attrs_out.write(to_json(self.included_libraries))
 
         collections_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_COLLECTIONS)
-        with open(collections_attrs_filename, 'w') as collections_attrs_out:
+        with open(collections_attrs_filename, "w") as collections_attrs_out:
             collections_attrs_out.write(to_json(self.collections_attrs))
 
         jobs_attrs = []
@@ -1492,7 +1554,7 @@ class DirectoryModelExportStore(ModelExportStore):
                 if name not in output_dataset_mapping:
                     output_dataset_mapping[name] = []
                 output_dataset_mapping[name].append(self.exported_key(dataset))
-            jobs_attrs.append({"id": job_id, 'output_dataset_mapping': output_dataset_mapping})
+            jobs_attrs.append({"id": job_id, "output_dataset_mapping": output_dataset_mapping})
 
         if self.serialize_jobs:
 
@@ -1507,7 +1569,7 @@ class DirectoryModelExportStore(ModelExportStore):
             def record_associated_jobs(obj):
                 # Get the job object.
                 job = None
-                for assoc in getattr(obj, 'creating_job_associations', []):
+                for assoc in getattr(obj, "creating_job_associations", []):
                     # For mapped over jobs obj could be DatasetCollection, which has no creating_job_association
                     job = assoc.job
                     break
@@ -1545,11 +1607,11 @@ class DirectoryModelExportStore(ModelExportStore):
                 icjs_attrs.append(icj_attrs)
 
             icjs_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS)
-            with open(icjs_attrs_filename, 'w') as icjs_attrs_out:
+            with open(icjs_attrs_filename, "w") as icjs_attrs_out:
                 icjs_attrs_out.write(json_encoder.encode(icjs_attrs))
 
         export_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_EXPORT)
-        with open(export_attrs_filename, 'w') as export_attrs_out:
+        with open(export_attrs_filename, "w") as export_attrs_out:
             dump({"galaxy_export_version": GALAXY_EXPORT_VERSION}, export_attrs_out)
 
     def __exit__(self, exc_type, exc_val, exc_tb):
@@ -1561,7 +1623,6 @@ class DirectoryModelExportStore(ModelExportStore):
 
 
 class TarModelExportStore(DirectoryModelExportStore):
-
     def __init__(self, out_file, gzip=True, **kwds):
         self.gzip = gzip
         self.out_file = out_file
@@ -1575,7 +1636,6 @@ class TarModelExportStore(DirectoryModelExportStore):
 
 
 class BagDirectoryModelExportStore(DirectoryModelExportStore):
-
     def __init__(self, out_directory, **kwds):
         self.out_directory = out_directory
         super().__init__(out_directory, **kwds)
@@ -1586,7 +1646,6 @@ class BagDirectoryModelExportStore(DirectoryModelExportStore):
 
 
 class BagArchiveModelExportStore(BagDirectoryModelExportStore):
-
     def __init__(self, out_file, bag_archiver="tgz", **kwds):
         # bag_archiver in tgz, zip, tar
         self.bag_archiver = bag_archiver
@@ -1615,12 +1674,14 @@ def get_export_dataset_filename(name, ext, hid):
     """
     Builds a filename for a dataset using its name an extension.
     """
-    base = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in name)
+    base = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in name)
     return f"{base}_{hid}.{ext}"
 
 
 def imported_store_for_metadata(directory, object_store=None):
     import_options = ImportOptions(allow_dataset_object_edit=True, allow_edit=True)
-    import_model_store = get_import_model_store_for_directory(directory, import_options=import_options, object_store=object_store)
+    import_model_store = get_import_model_store_for_directory(
+        directory, import_options=import_options, object_store=object_store
+    )
     import_model_store.perform_import()
     return import_model_store
diff --git a/lib/galaxy/model/store/build_objects.py b/lib/galaxy/model/store/build_objects.py
index 6ed17529ff6..a0390d3d2f3 100644
--- a/lib/galaxy/model/store/build_objects.py
+++ b/lib/galaxy/model/store/build_objects.py
@@ -89,6 +89,7 @@ def main(argv=None):
     galaxy.model.Dataset.object_store = object_store
     galaxy.model.set_datatypes_registry(example_datatype_registry_for_sample())
     from galaxy.model import mapping
+
     mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=object_store)
 
     with open(args.objects) as f:
@@ -120,10 +121,10 @@ def main(argv=None):
 
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION, formatter_class=argparse.RawDescriptionHelpFormatter)
-    parser.add_argument('objects', metavar='OBJECT_CONFIG', help='config file describing files to build objects for')
-    parser.add_argument('--object-store-config', help="object store configuration file")
-    parser.add_argument('-e', '--export', default="export", help='export path')
-    parser.add_argument('--export-type', default=None, help='export type (if needed)')
+    parser.add_argument("objects", metavar="OBJECT_CONFIG", help="config file describing files to build objects for")
+    parser.add_argument("--object-store-config", help="object store configuration file")
+    parser.add_argument("-e", "--export", default="export", help="export path")
+    parser.add_argument("--export-type", default=None, help="export type (if needed)")
     return parser
 
 
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index f4da97d2509..a12d042f460 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -8,9 +8,7 @@ corresponding to files in other contexts.
 import abc
 import logging
 import os
-from collections import (
-    namedtuple,
-)
+from collections import namedtuple
 from typing import (
     Any,
     Callable,
@@ -26,20 +24,21 @@ from sqlalchemy.orm.scoping import ScopedSession
 
 import galaxy.model
 from galaxy import util
-from galaxy.exceptions import (
-    RequestParameterInvalidException
-)
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.model.dataset_collections import builder
 from galaxy.model.tags import GalaxySessionlessTagHandler
 from galaxy.objectstore import ObjectStore
 from galaxy.util import (
     chunk_iterable,
-    ExecutionTimer
+    ExecutionTimer,
 )
 from galaxy.util.hash_util import HASH_NAME_MAP
 
 if TYPE_CHECKING:
-    from galaxy.job_execution.output_collect import JobContext, SessionlessJobContext
+    from galaxy.job_execution.output_collect import (
+        JobContext,
+        SessionlessJobContext,
+    )
 
 
 log = logging.getLogger(__name__)
@@ -59,7 +58,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
     required for datasets and other potential model objects.
     """
 
-    max_discovered_files = float('inf')
+    max_discovered_files = float("inf")
     discovered_file_count: int
 
     def create_dataset(
@@ -82,7 +81,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         sources=None,
         hashes=None,
         created_from_basename=None,
-        final_job_state='ok',
+        final_job_state="ok",
         creating_job_id=None,
         storage_callbacks=None,
     ):
@@ -110,14 +109,16 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
             primary_data.dbkey = dbkey
         else:
             if not library_folder:
-                primary_data = galaxy.model.HistoryDatasetAssociation(extension=ext,
-                                                                      designation=designation,
-                                                                      visible=visible,
-                                                                      dbkey=dbkey,
-                                                                      create_dataset=True,
-                                                                      flush=False,
-                                                                      sa_session=sa_session,
-                                                                      creating_job_id=creating_job_id)
+                primary_data = galaxy.model.HistoryDatasetAssociation(
+                    extension=ext,
+                    designation=designation,
+                    visible=visible,
+                    dbkey=dbkey,
+                    create_dataset=True,
+                    flush=False,
+                    sa_session=sa_session,
+                    creating_job_id=creating_job_id,
+                )
                 self.persist_object(primary_data)
 
                 if init_from:
@@ -127,14 +128,16 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
                     self.permission_provider.set_default_hda_permissions(primary_data)
             else:
                 ld = galaxy.model.LibraryDataset(folder=library_folder, name=name)
-                ldda = galaxy.model.LibraryDatasetDatasetAssociation(name=name,
-                                                                     extension=ext,
-                                                                     dbkey=dbkey,
-                                                                     # library_dataset=ld,
-                                                                     user=self.user,
-                                                                     create_dataset=True,
-                                                                     flush=False,
-                                                                     sa_session=sa_session)
+                ldda = galaxy.model.LibraryDatasetDatasetAssociation(
+                    name=name,
+                    extension=ext,
+                    dbkey=dbkey,
+                    # library_dataset=ld,
+                    user=self.user,
+                    create_dataset=True,
+                    flush=False,
+                    sa_session=sa_session,
+                )
                 ld.library_dataset_dataset_association = ldda
 
                 self.add_library_dataset_to_folder(library_folder, ld)
@@ -183,9 +186,23 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
             primary_data.info = info
         if filename:
             if storage_callbacks is None:
-                self.finalize_storage(primary_data=primary_data, dataset_attributes=dataset_attributes, extra_files=extra_files, filename=filename, link_data=link_data)
+                self.finalize_storage(
+                    primary_data=primary_data,
+                    dataset_attributes=dataset_attributes,
+                    extra_files=extra_files,
+                    filename=filename,
+                    link_data=link_data,
+                )
             else:
-                storage_callbacks.append(lambda: self.finalize_storage(primary_data=primary_data, dataset_attributes=dataset_attributes, extra_files=extra_files, filename=filename, link_data=link_data))
+                storage_callbacks.append(
+                    lambda: self.finalize_storage(
+                        primary_data=primary_data,
+                        dataset_attributes=dataset_attributes,
+                        extra_files=extra_files,
+                        filename=filename,
+                        link_data=link_data,
+                    )
+                )
         return primary_data
 
     def finalize_storage(self, primary_data, dataset_attributes, extra_files, filename, link_data):
@@ -212,13 +229,17 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
                 # TODO: discover_files should produce a match that encorporates this -
                 # would simplify ToolProvidedMetadata interface and eliminate this
                 # crap path.
-                dataset_att_by_name = dict(ext='extension')
-                for att_set in ['name', 'info', 'ext', 'dbkey']:
+                dataset_att_by_name = dict(ext="extension")
+                for att_set in ["name", "info", "ext", "dbkey"]:
                     dataset_att_name = dataset_att_by_name.get(att_set, att_set)
-                    setattr(primary_data, dataset_att_name, dataset_attributes.get(att_set, getattr(primary_data, dataset_att_name)))
+                    setattr(
+                        primary_data,
+                        dataset_att_name,
+                        dataset_attributes.get(att_set, getattr(primary_data, dataset_att_name)),
+                    )
 
             try:
-                metadata_dict = dataset_attributes.get('metadata', None)
+                metadata_dict = dataset_attributes.get("metadata", None)
                 if metadata_dict:
                     if "dbkey" in dataset_attributes:
                         metadata_dict["dbkey"] = dataset_attributes["dbkey"]
@@ -236,7 +257,9 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
             except Exception:
                 log.exception("Exception occured while setting dataset peek")
 
-    def populate_collection_elements(self, collection, root_collection_builder, filenames, name=None, metadata_source_name=None, final_job_state='ok'):
+    def populate_collection_elements(
+        self, collection, root_collection_builder, filenames, name=None, metadata_source_name=None, final_job_state="ok"
+    ):
         # TODO: allow configurable sorting.
         #    <sort by="lexical" /> <!-- default -->
         #    <sort by="reverse_lexical" />
@@ -246,17 +269,35 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
             name = "unnamed output"
         if self.flush_per_n_datasets and self.flush_per_n_datasets > 0:
             for chunk in chunk_iterable(filenames.items(), size=self.flush_per_n_datasets):
-                self._populate_elements(chunk=chunk, name=name, root_collection_builder=root_collection_builder, metadata_source_name=metadata_source_name, final_job_state=final_job_state)
+                self._populate_elements(
+                    chunk=chunk,
+                    name=name,
+                    root_collection_builder=root_collection_builder,
+                    metadata_source_name=metadata_source_name,
+                    final_job_state=final_job_state,
+                )
                 if len(chunk) == self.flush_per_n_datasets:
                     # In most cases we don't need to flush, that happens in the caller.
                     # Only flush here for saving memory.
                     root_collection_builder.populate_partial()
                     self.flush()
         else:
-            self._populate_elements(chunk=filenames.items(), name=name, root_collection_builder=root_collection_builder, metadata_source_name=metadata_source_name, final_job_state=final_job_state)
+            self._populate_elements(
+                chunk=filenames.items(),
+                name=name,
+                root_collection_builder=root_collection_builder,
+                metadata_source_name=metadata_source_name,
+                final_job_state=final_job_state,
+            )
 
     def _populate_elements(self, chunk, name, root_collection_builder, metadata_source_name, final_job_state):
-        element_datasets: Dict[str, List[Any]] = {'element_identifiers': [], 'datasets': [], 'tag_lists': [], 'paths': [], 'extra_files': []}
+        element_datasets: Dict[str, List[Any]] = {
+            "element_identifiers": [],
+            "datasets": [],
+            "tag_lists": [],
+            "paths": [],
+            "extra_files": [],
+        }
         for filename, discovered_file in chunk:
             create_dataset_timer = ExecutionTimer()
             fields_match = discovered_file.match
@@ -302,14 +343,16 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
                 name,
                 create_dataset_timer,
             )
-            element_datasets['element_identifiers'].append(element_identifiers)
-            element_datasets['extra_files'].append(extra_files)
-            element_datasets['datasets'].append(dataset)
-            element_datasets['tag_lists'].append(discovered_file.match.tag_list)
-            element_datasets['paths'].append(filename)
+            element_datasets["element_identifiers"].append(element_identifiers)
+            element_datasets["extra_files"].append(extra_files)
+            element_datasets["datasets"].append(dataset)
+            element_datasets["tag_lists"].append(discovered_file.match.tag_list)
+            element_datasets["paths"].append(filename)
 
-        self.add_tags_to_datasets(datasets=element_datasets['datasets'], tag_lists=element_datasets['tag_lists'])
-        for (element_identifiers, dataset) in zip(element_datasets['element_identifiers'], element_datasets['datasets']):
+        self.add_tags_to_datasets(datasets=element_datasets["datasets"], tag_lists=element_datasets["tag_lists"])
+        for (element_identifiers, dataset) in zip(
+            element_datasets["element_identifiers"], element_datasets["datasets"]
+        ):
             current_builder = root_collection_builder
             for element_identifier in element_identifiers[:-1]:
                 current_builder = current_builder.get_level(element_identifier)
@@ -317,19 +360,23 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
 
             # Associate new dataset with job
             element_identifier_str = ":".join(element_identifiers)
-            association_name = f'__new_primary_file_{name}|{element_identifier_str}__'
+            association_name = f"__new_primary_file_{name}|{element_identifier_str}__"
             self.add_output_dataset_association(association_name, dataset)
 
         add_datasets_timer = ExecutionTimer()
-        self.add_datasets_to_history(element_datasets['datasets'])
-        self.update_object_store_with_datasets(datasets=element_datasets['datasets'], paths=element_datasets['paths'], extra_files=element_datasets['extra_files'])
+        self.add_datasets_to_history(element_datasets["datasets"])
+        self.update_object_store_with_datasets(
+            datasets=element_datasets["datasets"],
+            paths=element_datasets["paths"],
+            extra_files=element_datasets["extra_files"],
+        )
         log.debug(
             "(%s) Add dynamic collection datasets to history for output [%s] %s",
             self.job_id(),
             name,
             add_datasets_timer,
         )
-        self.set_datasets_metadata(datasets=element_datasets['datasets'])
+        self.set_datasets_metadata(datasets=element_datasets["datasets"])
 
     def add_tags_to_datasets(self, datasets, tag_lists):
         if any(tag_lists):
@@ -364,7 +411,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         """
 
     @abc.abstractproperty
-    def permission_provider(self) -> 'PermissionProvider':
+    def permission_provider(self) -> "PermissionProvider":
         """If bound to a database, return the SQL Alchemy session.
 
         Return None otherwise.
@@ -379,7 +426,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         """Return associated job object if bound to a job finish context connected to a database."""
 
     @abc.abstractproperty
-    def metadata_source_provider(self) -> 'MetadataSourceProvider':
+    def metadata_source_provider(self) -> "MetadataSourceProvider":
         """Return associated MetadataSourceProvider object."""
 
     @abc.abstractproperty
@@ -392,7 +439,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
 
     @property
     def input_dbkey(self) -> str:
-        return '?'
+        return "?"
 
     @abc.abstractmethod
     def add_library_dataset_to_folder(self, library_folder, ld):
@@ -410,7 +457,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         """Add datasets to the history this context points at."""
 
     def job_id(self):
-        return ''
+        return ""
 
     def persist_object(self, obj):
         """Add the target to the persistence layer."""
@@ -424,7 +471,9 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
     def increment_discovered_file_count(self):
         self.discovered_file_count += 1
         if self.discovered_file_count > self.max_discovered_files:
-            raise MaxDiscoveredFilesExceededError(f"Job generated more than maximum number ({self.max_discovered_files}) of output datasets")
+            raise MaxDiscoveredFilesExceededError(
+                f"Job generated more than maximum number ({self.max_discovered_files}) of output datasets"
+            )
 
 
 class PermissionProvider(metaclass=abc.ABCMeta):
@@ -443,7 +492,6 @@ class PermissionProvider(metaclass=abc.ABCMeta):
 
 
 class UnusedPermissionProvider(PermissionProvider):
-
     def copy_dataset_permissions(self, init_from, primary_data):
         """Throws NotImplementedError.
 
@@ -463,7 +511,6 @@ class MetadataSourceProvider(metaclass=abc.ABCMeta):
 
 
 class UnusedMetadataSourceProvider(MetadataSourceProvider):
-
     def get_metadata_source(self, input_name):
         """Throws NotImplementedError.
 
@@ -484,7 +531,7 @@ class SessionlessModelPersistenceContext(ModelPersistenceContext):
         self.export_store = export_store
         self._flush_per_n_datasets = None
         self.discovered_file_count = 0
-        self.max_discovered_files = float('inf')
+        self.max_discovered_files = float("inf")
 
         self.job_working_directory = working_directory  # TODO: rename...
 
@@ -540,11 +587,15 @@ class SessionlessModelPersistenceContext(ModelPersistenceContext):
         raise NotImplementedError()
 
     def create_hdca(self, name, structure):
-        collection = galaxy.model.DatasetCollection(collection_type=structure.collection_type_description.collection_type, populated=False)
+        collection = galaxy.model.DatasetCollection(
+            collection_type=structure.collection_type_description.collection_type, populated=False
+        )
         return galaxy.model.HistoryDatasetCollectionAssociation(name=name, collection=collection)
 
     def create_library_folder(self, parent_folder, name, description):
-        nested_folder = galaxy.model.LibraryFolder(name=name, description=description, order_id=parent_folder.item_count)
+        nested_folder = galaxy.model.LibraryFolder(
+            name=name, description=description, order_id=parent_folder.item_count
+        )
         parent_folder.item_count += 1
         parent_folder.folders.append(nested_folder)
         return nested_folder
@@ -580,7 +631,9 @@ def persist_extra_files(object_store, src_extra_files_path, primary_data):
         primary_data.dataset.create_extra_files_path()
         target_extra_files_path = primary_data.extra_files_path
         for root, _dirs, files in os.walk(src_extra_files_path):
-            extra_dir = os.path.join(target_extra_files_path, root.replace(src_extra_files_path, '', 1).lstrip(os.path.sep))
+            extra_dir = os.path.join(
+                target_extra_files_path, root.replace(src_extra_files_path, "", 1).lstrip(os.path.sep)
+            )
             extra_dir = os.path.normpath(extra_dir)
             for f in files:
                 object_store.update_from_file(
@@ -589,7 +642,7 @@ def persist_extra_files(object_store, src_extra_files_path, primary_data):
                     alt_name=f,
                     file_name=os.path.join(root, f),
                     create=True,
-                    preserve_symlinks=True
+                    preserve_symlinks=True,
                 )
 
 
@@ -610,7 +663,7 @@ def persist_target_to_export_store(target_dict, export_store, object_store, work
         name = get_required_item(destination, "name", "Must specify a library name")
         description = destination.get("description", "")
         synopsis = destination.get("synopsis", "")
-        root_folder = galaxy.model.LibraryFolder(name=name, description='')
+        root_folder = galaxy.model.LibraryFolder(name=name, description="")
         library = galaxy.model.Library(
             name=name,
             description=description,
@@ -635,7 +688,12 @@ def persist_target_to_export_store(target_dict, export_store, object_store, work
         export_store.add_dataset_collection(hdca)
 
 
-def persist_elements_to_hdca(model_persistence_context: Union['JobContext', 'SessionlessJobContext', SessionlessModelPersistenceContext], elements, hdca, collector=None):
+def persist_elements_to_hdca(
+    model_persistence_context: Union["JobContext", "SessionlessJobContext", SessionlessModelPersistenceContext],
+    elements,
+    hdca,
+    collector=None,
+):
     filenames = {}
 
     def add_to_discovered_files(elements, parent_identifiers=None):
@@ -644,7 +702,9 @@ def persist_elements_to_hdca(model_persistence_context: Union['JobContext', 'Ses
             if "elements" in element:
                 add_to_discovered_files(element["elements"], parent_identifiers + [element["name"]])
             else:
-                discovered_file = discovered_file_for_element(element, model_persistence_context, parent_identifiers, collector=collector)
+                discovered_file = discovered_file_for_element(
+                    element, model_persistence_context, parent_identifiers, collector=collector
+                )
                 filenames[discovered_file.path] = discovered_file
 
     add_to_discovered_files(elements)
@@ -683,7 +743,7 @@ def persist_elements_to_folder(model_persistence_context, elements, library_fold
             sources = fields_match.sources
             hashes = fields_match.hashes
             created_from_basename = fields_match.created_from_basename
-            state = 'ok'
+            state = "ok"
             if hasattr(discovered_file, "error_message"):
                 info = discovered_file.error_message
                 state = "error"
@@ -704,7 +764,7 @@ def persist_elements_to_folder(model_persistence_context, elements, library_fold
             )
 
 
-def persist_hdas(elements, model_persistence_context, final_job_state='ok'):
+def persist_hdas(elements, model_persistence_context, final_job_state="ok"):
     # discover files as individual datasets for the target history
     datasets = []
     storage_callbacks: List[Callable] = []
@@ -728,7 +788,9 @@ def persist_hdas(elements, model_persistence_context, final_job_state='ok'):
                 hda_id = discovered_file.match.object_id
                 primary_dataset = None
                 if hda_id:
-                    sa_session = model_persistence_context.sa_session or model_persistence_context.import_store.sa_session
+                    sa_session = (
+                        model_persistence_context.sa_session or model_persistence_context.import_store.sa_session
+                    )
                     primary_dataset = sa_session.query(galaxy.model.HistoryDatasetAssociation).get(hda_id)
 
                 sources = fields_match.sources
@@ -820,13 +882,20 @@ def replace_request_syntax_sugar(obj):
             obj["hashes"].extend(new_hashes)
 
 
-DiscoveredFile = namedtuple('DiscoveredFile', ['path', 'collector', 'match'])
+DiscoveredFile = namedtuple("DiscoveredFile", ["path", "collector", "match"])
 
 
-def discovered_file_for_element(dataset, model_persistence_context: Union['JobContext', 'SessionlessJobContext', SessionlessModelPersistenceContext], parent_identifiers=None, collector=None):
+def discovered_file_for_element(
+    dataset,
+    model_persistence_context: Union["JobContext", "SessionlessJobContext", SessionlessModelPersistenceContext],
+    parent_identifiers=None,
+    collector=None,
+):
     model_persistence_context.increment_discovered_file_count()
     parent_identifiers = parent_identifiers or []
-    target_directory = discover_target_directory(getattr(collector, "directory", None), model_persistence_context.job_working_directory)
+    target_directory = discover_target_directory(
+        getattr(collector, "directory", None), model_persistence_context.job_working_directory
+    )
     filename = dataset.get("filename")
     error_message = dataset.get("error_message")
     if error_message is None:
@@ -834,27 +903,38 @@ def discovered_file_for_element(dataset, model_persistence_context: Union['JobCo
         if not dataset.get("link_data_only"):
             path = os.path.join(target_directory, filename)
             if not util.in_directory(path, target_directory):
-                raise Exception("Problem with tool configuration, attempting to pull in datasets from outside working directory.")
+                raise Exception(
+                    "Problem with tool configuration, attempting to pull in datasets from outside working directory."
+                )
         else:
             path = filename
-        return DiscoveredFile(path, collector, JsonCollectedDatasetMatch(dataset, collector, filename, path=path, parent_identifiers=parent_identifiers))
+        return DiscoveredFile(
+            path,
+            collector,
+            JsonCollectedDatasetMatch(dataset, collector, filename, path=path, parent_identifiers=parent_identifiers),
+        )
     else:
         assert "error_message" in dataset
-        return DiscoveredFileError(dataset['error_message'], collector, JsonCollectedDatasetMatch(dataset, collector, None, parent_identifiers=parent_identifiers))
+        return DiscoveredFileError(
+            dataset["error_message"],
+            collector,
+            JsonCollectedDatasetMatch(dataset, collector, None, parent_identifiers=parent_identifiers),
+        )
 
 
 def discover_target_directory(dir_name, job_working_directory):
     if dir_name:
         directory = os.path.join(job_working_directory, dir_name)
         if not util.in_directory(directory, job_working_directory):
-            raise Exception("Problem with tool configuration, attempting to pull in datasets from outside working directory.")
+            raise Exception(
+                "Problem with tool configuration, attempting to pull in datasets from outside working directory."
+            )
         return directory
     else:
         return job_working_directory
 
 
 class JsonCollectedDatasetMatch:
-
     def __init__(self, as_dict, collector, filename, path=None, parent_identifiers=None):
         parent_identifiers = parent_identifiers or []
         self.as_dict = as_dict
@@ -897,8 +977,7 @@ class JsonCollectedDatasetMatch:
 
     @property
     def name(self):
-        """ Return name or None if not defined by the discovery pattern.
-        """
+        """Return name or None if not defined by the discovery pattern."""
         return self.as_dict.get("name")
 
     @property
@@ -946,15 +1025,12 @@ class JsonCollectedDatasetMatch:
 
 
 class RegexCollectedDatasetMatch(JsonCollectedDatasetMatch):
-
     def __init__(self, re_match, collector, filename, path=None):
-        super().__init__(
-            re_match.groupdict(), collector, filename, path=path
-        )
+        super().__init__(re_match.groupdict(), collector, filename, path=path)
 
 
 class DiscoveredFileError(NamedTuple):
     error_message: str
-    collector: Any   # TODO: setup interface for this
+    collector: Any  # TODO: setup interface for this
     match: JsonCollectedDatasetMatch
     path: Optional[str] = None
diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
index 6f77c1459ac..cd02f4d54c2 100644
--- a/lib/galaxy/model/tags.py
+++ b/lib/galaxy/model/tags.py
@@ -1,6 +1,11 @@
 import logging
 import re
-from typing import Dict, List, Optional, Tuple
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Tuple,
+)
 
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import sessionmaker
@@ -37,9 +42,9 @@ class TagHandler:
         # Maximum tag length.
         self.max_tag_len = 255
         # Tag separator.
-        self.tag_separators = ',;'
+        self.tag_separators = ",;"
         # Hierarchy separator.
-        self.hierarchy_separator = '.'
+        self.hierarchy_separator = "."
         # Key-value separator.
         self.key_value_separators = "=:"
         # Initialize with known classes - add to this in subclasses.
@@ -52,12 +57,12 @@ class TagHandler:
     def add_tags_from_list(self, user, item, new_tags_list, flush=True):
         new_tags_set = set(new_tags_list)
         if item.tags:
-            new_tags_set.update(self.get_tags_str(item.tags).split(','))
+            new_tags_set.update(self.get_tags_str(item.tags).split(","))
         return self.set_tags_from_list(user, item, new_tags_set, flush=flush)
 
     def remove_tags_from_list(self, user, item, tag_to_remove_list, flush=True):
         tag_to_remove_set = set(tag_to_remove_list)
-        tags_set = {_.strip() for _ in self.get_tags_str(item.tags).split(',')}
+        tags_set = {_.strip() for _ in self.get_tags_str(item.tags).split(",")}
         if item.tags:
             tags_set -= tag_to_remove_set
         return self.set_tags_from_list(user, item, tags_set, flush=flush)
@@ -66,8 +71,8 @@ class TagHandler:
         # precondition: item is already security checked against user
         # precondition: incoming tags is a list of sanitized/formatted strings
         self.delete_item_tags(user, item)
-        new_tags_str = ','.join(new_tags_list)
-        self.apply_item_tags(user, item, unicodify(new_tags_str, 'utf-8'), flush=flush)
+        new_tags_str = ",".join(new_tags_list)
+        self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush)
         if flush:
             self.sa_session.flush()
         return item.tags
@@ -88,18 +93,20 @@ class TagHandler:
         if not item_tag_assoc_class:
             return []
         # Build select statement.
-        cols_to_select = [item_tag_assoc_class.table.c.tag_id, func.count('*')]
+        cols_to_select = [item_tag_assoc_class.table.c.tag_id, func.count("*")]
         from_obj = item_tag_assoc_class.table.join(item_class.table).join(galaxy.model.Tag.table)
-        where_clause = (self.get_id_col_in_item_tag_assoc_table(item_class) == item.id)
+        where_clause = self.get_id_col_in_item_tag_assoc_table(item_class) == item.id
         order_by = [func.count("*").desc()]
         group_by = item_tag_assoc_class.table.c.tag_id
         # Do query and get result set.
-        query = select(columns=cols_to_select,
-                       from_obj=from_obj,
-                       whereclause=where_clause,
-                       group_by=group_by,
-                       order_by=order_by,
-                       limit=limit)
+        query = select(
+            columns=cols_to_select,
+            from_obj=from_obj,
+            whereclause=where_clause,
+            group_by=group_by,
+            order_by=order_by,
+            limit=limit,
+        )
         result_set = self.sa_session.execute(query)
         # Return community tags.
         community_tags = []
@@ -109,8 +116,9 @@ class TagHandler:
         return community_tags
 
     def get_tool_tags(self):
-        query = select(columns=[galaxy.model.ToolTagAssociation.table.c.tag_id],
-                       from_obj=galaxy.model.ToolTagAssociation.table).distinct()
+        query = select(
+            columns=[galaxy.model.ToolTagAssociation.table.c.tag_id], from_obj=galaxy.model.ToolTagAssociation.table
+        ).distinct()
         result_set = self.sa_session.execute(query)
 
         tags = []
@@ -327,7 +335,7 @@ class TagHandler:
         if not value:
             return None
         # Remove whitespace from value.
-        reg_exp = re.compile(r'\s')
+        reg_exp = re.compile(r"\s")
         scrubbed_value = re.sub(reg_exp, "", value)
         return scrubbed_value
 
@@ -337,7 +345,7 @@ class TagHandler:
         if not name:
             return None
         # Remove whitespace from name.
-        reg_exp = re.compile(r'\s')
+        reg_exp = re.compile(r"\s")
         scrubbed_name = re.sub(reg_exp, "", name)
         # Ignore starting ':' char.
         if scrubbed_name.startswith(self.hierarchy_separator):
@@ -357,7 +365,7 @@ class TagHandler:
     def _get_name_value_pair(self, tag_str) -> List[Optional[str]]:
         """Get name, value pair from a tag string."""
         # Use regular expression to parse name, value.
-        if tag_str.startswith('#'):
+        if tag_str.startswith("#"):
             tag_str = f"name:{tag_str[1:]}"
         reg_exp = re.compile(f"[{self.key_value_separators}]")
         name_value_pair: List[Optional[str]] = list(reg_exp.split(tag_str, 1))
@@ -370,31 +378,37 @@ class TagHandler:
 class GalaxyTagHandler(TagHandler):
     def __init__(self, sa_session: galaxy_scoped_session):
         from galaxy import model
+
         TagHandler.__init__(self, sa_session)
-        self.item_tag_assoc_info["History"] = ItemTagAssocInfo(model.History,
-                                                               model.HistoryTagAssociation,
-                                                               model.HistoryTagAssociation.history_id)
-        self.item_tag_assoc_info["HistoryDatasetAssociation"] = \
-            ItemTagAssocInfo(model.HistoryDatasetAssociation,
-                             model.HistoryDatasetAssociationTagAssociation,
-                             model.HistoryDatasetAssociationTagAssociation.history_dataset_association_id)
-        self.item_tag_assoc_info["HistoryDatasetCollectionAssociation"] = \
-            ItemTagAssocInfo(model.HistoryDatasetCollectionAssociation,
-                             model.HistoryDatasetCollectionTagAssociation,
-                             model.HistoryDatasetCollectionTagAssociation.history_dataset_collection_id)
-        self.item_tag_assoc_info["LibraryDatasetDatasetAssociation"] = \
-            ItemTagAssocInfo(model.LibraryDatasetDatasetAssociation,
-                             model.LibraryDatasetDatasetAssociationTagAssociation,
-                             model.LibraryDatasetDatasetAssociationTagAssociation.library_dataset_dataset_association_id)
-        self.item_tag_assoc_info["Page"] = ItemTagAssocInfo(model.Page,
-                                                            model.PageTagAssociation,
-                                                            model.PageTagAssociation.page_id)
-        self.item_tag_assoc_info["StoredWorkflow"] = ItemTagAssocInfo(model.StoredWorkflow,
-                                                                      model.StoredWorkflowTagAssociation,
-                                                                      model.StoredWorkflowTagAssociation.stored_workflow_id)
-        self.item_tag_assoc_info["Visualization"] = ItemTagAssocInfo(model.Visualization,
-                                                                     model.VisualizationTagAssociation,
-                                                                     model.VisualizationTagAssociation.visualization_id)
+        self.item_tag_assoc_info["History"] = ItemTagAssocInfo(
+            model.History, model.HistoryTagAssociation, model.HistoryTagAssociation.history_id
+        )
+        self.item_tag_assoc_info["HistoryDatasetAssociation"] = ItemTagAssocInfo(
+            model.HistoryDatasetAssociation,
+            model.HistoryDatasetAssociationTagAssociation,
+            model.HistoryDatasetAssociationTagAssociation.history_dataset_association_id,
+        )
+        self.item_tag_assoc_info["HistoryDatasetCollectionAssociation"] = ItemTagAssocInfo(
+            model.HistoryDatasetCollectionAssociation,
+            model.HistoryDatasetCollectionTagAssociation,
+            model.HistoryDatasetCollectionTagAssociation.history_dataset_collection_id,
+        )
+        self.item_tag_assoc_info["LibraryDatasetDatasetAssociation"] = ItemTagAssocInfo(
+            model.LibraryDatasetDatasetAssociation,
+            model.LibraryDatasetDatasetAssociationTagAssociation,
+            model.LibraryDatasetDatasetAssociationTagAssociation.library_dataset_dataset_association_id,
+        )
+        self.item_tag_assoc_info["Page"] = ItemTagAssocInfo(
+            model.Page, model.PageTagAssociation, model.PageTagAssociation.page_id
+        )
+        self.item_tag_assoc_info["StoredWorkflow"] = ItemTagAssocInfo(
+            model.StoredWorkflow,
+            model.StoredWorkflowTagAssociation,
+            model.StoredWorkflowTagAssociation.stored_workflow_id,
+        )
+        self.item_tag_assoc_info["Visualization"] = ItemTagAssocInfo(
+            model.Visualization, model.VisualizationTagAssociation, model.VisualizationTagAssociation.visualization_id
+        )
 
 
 class GalaxyTagHandlerSession(GalaxyTagHandler):
@@ -417,7 +431,6 @@ class GalaxyTagHandlerSession(GalaxyTagHandler):
 
 
 class GalaxySessionlessTagHandler(GalaxyTagHandlerSession):
-
     def _get_tag(self, tag_name):
         """Get tag from cache or database."""
         # Short-circuit session access
diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index 825e1e6900c..2cb34b7338a 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -21,7 +21,7 @@ from sqlalchemy.orm.decl_api import DeclarativeMeta
 
 from galaxy.model.custom_types import (
     MutableJSONType,
-    TrimmedString
+    TrimmedString,
 )
 from galaxy.model.orm.now import now
 from galaxy.util import asbool
@@ -34,8 +34,10 @@ log = logging.getLogger(__name__)
 mapper_registry = registry()
 
 if TYPE_CHECKING:
+
     class _HasTable:
         table: Table
+
 else:
     _HasTable = object
 
@@ -52,7 +54,7 @@ class Base(metaclass=DeclarativeMeta):
 
 
 class ToolShedRepository(Base, _HasTable):
-    __tablename__ = 'tool_shed_repository'
+    __tablename__ = "tool_shed_repository"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -64,7 +66,7 @@ class ToolShedRepository(Base, _HasTable):
     installed_changeset_revision = Column(TrimmedString(255))
     changeset_revision = Column(TrimmedString(255), index=True)
     ctx_rev = Column(TrimmedString(10))
-    metadata_ = Column('metadata', MutableJSONType, nullable=True)
+    metadata_ = Column("metadata", MutableJSONType, nullable=True)
     includes_datatypes = Column(Boolean, index=True, default=False)
     tool_shed_status = Column(MutableJSONType, nullable=True)
     deleted = Column(Boolean, index=True, default=False)
@@ -72,39 +74,86 @@ class ToolShedRepository(Base, _HasTable):
     dist_to_shed = Column(Boolean, default=False)
     status = Column(TrimmedString(255))
     error_message = Column(TEXT)
-    tool_versions = relationship('ToolVersion', back_populates='tool_shed_repository')
-    tool_dependencies = relationship('ToolDependency', order_by='ToolDependency.name',
-        back_populates='tool_shed_repository')
-    required_repositories = relationship('RepositoryRepositoryDependencyAssociation',
-        back_populates='repository')
+    tool_versions = relationship("ToolVersion", back_populates="tool_shed_repository")
+    tool_dependencies = relationship(
+        "ToolDependency", order_by="ToolDependency.name", back_populates="tool_shed_repository"
+    )
+    required_repositories = relationship("RepositoryRepositoryDependencyAssociation", back_populates="repository")
 
-    dict_collection_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
-                                    'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
-    dict_element_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
-                                 'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
+    dict_collection_visible_keys = [
+        "id",
+        "tool_shed",
+        "name",
+        "owner",
+        "installed_changeset_revision",
+        "changeset_revision",
+        "ctx_rev",
+        "includes_datatypes",
+        "tool_shed_status",
+        "deleted",
+        "uninstalled",
+        "dist_to_shed",
+        "status",
+        "error_message",
+        "description",
+    ]
+    dict_element_visible_keys = [
+        "id",
+        "tool_shed",
+        "name",
+        "owner",
+        "installed_changeset_revision",
+        "changeset_revision",
+        "ctx_rev",
+        "includes_datatypes",
+        "tool_shed_status",
+        "deleted",
+        "uninstalled",
+        "dist_to_shed",
+        "status",
+        "error_message",
+        "description",
+    ]
 
     class installation_status(str, Enum):
-        NEW = 'New'
-        CLONING = 'Cloning'
-        SETTING_TOOL_VERSIONS = 'Setting tool versions'
-        INSTALLING_REPOSITORY_DEPENDENCIES = 'Installing repository dependencies'
-        INSTALLING_TOOL_DEPENDENCIES = 'Installing tool dependencies'
-        LOADING_PROPRIETARY_DATATYPES = 'Loading proprietary datatypes'
-        INSTALLED = 'Installed'
-        DEACTIVATED = 'Deactivated'
-        ERROR = 'Error'
-        UNINSTALLED = 'Uninstalled'
+        NEW = "New"
+        CLONING = "Cloning"
+        SETTING_TOOL_VERSIONS = "Setting tool versions"
+        INSTALLING_REPOSITORY_DEPENDENCIES = "Installing repository dependencies"
+        INSTALLING_TOOL_DEPENDENCIES = "Installing tool dependencies"
+        LOADING_PROPRIETARY_DATATYPES = "Loading proprietary datatypes"
+        INSTALLED = "Installed"
+        DEACTIVATED = "Deactivated"
+        ERROR = "Error"
+        UNINSTALLED = "Uninstalled"
 
     class states(str, Enum):
-        INSTALLING = 'running'
-        OK = 'ok'
-        WARNING = 'queued'
-        ERROR = 'error'
-        UNINSTALLED = 'deleted_new'
+        INSTALLING = "running"
+        OK = "ok"
+        WARNING = "queued"
+        ERROR = "error"
+        UNINSTALLED = "deleted_new"
 
-    def __init__(self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None,
-                 changeset_revision=None, ctx_rev=None, metadata_=None, includes_datatypes=False, tool_shed_status=None, deleted=False,
-                 uninstalled=False, dist_to_shed=False, status=None, error_message=None):
+    def __init__(
+        self,
+        id=None,
+        create_time=None,
+        tool_shed=None,
+        name=None,
+        description=None,
+        owner=None,
+        installed_changeset_revision=None,
+        changeset_revision=None,
+        ctx_rev=None,
+        metadata_=None,
+        includes_datatypes=False,
+        tool_shed_status=None,
+        deleted=False,
+        uninstalled=False,
+        dist_to_shed=False,
+        status=None,
+        error_message=None,
+    ):
         self.id = id
         self.create_time = create_time
         self.tool_shed = tool_shed
@@ -124,7 +173,7 @@ class ToolShedRepository(Base, _HasTable):
         self.error_message = error_message
 
     def as_dict(self, value_mapper=None):
-        return self.to_dict(view='element', value_mapper=value_mapper)
+        return self.to_dict(view="element", value_mapper=value_mapper)
 
     @property
     def can_install(self):
@@ -140,9 +189,11 @@ class ToolShedRepository(Base, _HasTable):
 
     @property
     def can_deactivate(self):
-        return self.status not in [self.installation_status.DEACTIVATED,
-                                   self.installation_status.ERROR,
-                                   self.installation_status.UNINSTALLED]
+        return self.status not in [
+            self.installation_status.DEACTIVATED,
+            self.installation_status.ERROR,
+            self.installation_status.UNINSTALLED,
+        ]
 
     @property
     def can_reinstall_or_activate(self):
@@ -153,11 +204,11 @@ class ToolShedRepository(Base, _HasTable):
 
     @property
     def shed_config_filename(self):
-        return self.metadata_.get('shed_config_filename')
+        return self.metadata_.get("shed_config_filename")
 
     @shed_config_filename.setter
     def shed_config_filename(self, value):
-        self.metadata_['shed_config_filename'] = os.path.abspath(value)
+        self.metadata_["shed_config_filename"] = os.path.abspath(value)
 
     def get_shed_config_dict(self, app):
         """
@@ -176,26 +227,28 @@ class ToolShedRepository(Base, _HasTable):
         tool_path = None
         relative_path = None
         if shed_conf_dict:
-            tool_path = shed_conf_dict['tool_path']
-            relative_path = os.path.join(self.tool_shed_path_name, 'repos', self.owner, self.name, self.installed_changeset_revision)
+            tool_path = shed_conf_dict["tool_path"]
+            relative_path = os.path.join(
+                self.tool_shed_path_name, "repos", self.owner, self.name, self.installed_changeset_revision
+            )
         return tool_path, relative_path
 
     def guess_shed_config(self, app):
         tool_ids = []
-        for tool in self.metadata_.get('tools', []):
-            tool_ids.append(tool.get('guid'))
+        for tool in self.metadata_.get("tools", []):
+            tool_ids.append(tool.get("guid"))
         for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
-            name = shed_tool_conf_dict['config_filename']
-            for elem in shed_tool_conf_dict['config_elems']:
-                if elem.tag == 'tool':
-                    for sub_elem in elem.findall('id'):
+            name = shed_tool_conf_dict["config_filename"]
+            for elem in shed_tool_conf_dict["config_elems"]:
+                if elem.tag == "tool":
+                    for sub_elem in elem.findall("id"):
                         tool_id = sub_elem.text.strip()
                         if tool_id in tool_ids:
                             self.shed_config_filename = name
                             return shed_tool_conf_dict
                 elif elem.tag == "section":
-                    for tool_elem in elem.findall('tool'):
-                        for sub_elem in tool_elem.findall('id'):
+                    for tool_elem in elem.findall("tool"):
+                        for sub_elem in tool_elem.findall("id"):
                             tool_id = sub_elem.text.strip()
                             if tool_id in tool_ids:
                                 self.shed_config_filename = name
@@ -203,40 +256,52 @@ class ToolShedRepository(Base, _HasTable):
         # We need to search by file paths here, which is less desirable.
         tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(self.tool_shed)
         for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
-            tool_path = shed_tool_conf_dict['tool_path']
-            relative_path = os.path.join(tool_path, tool_shed, 'repos', self.owner, self.name)
+            tool_path = shed_tool_conf_dict["tool_path"]
+            relative_path = os.path.join(tool_path, tool_shed, "repos", self.owner, self.name)
             if os.path.exists(relative_path):
-                self.shed_config_filename = shed_tool_conf_dict['config_filename']
+                self.shed_config_filename = shed_tool_conf_dict["config_filename"]
                 return shed_tool_conf_dict
         # Very last resort, get default shed_tool_config file for this instance
         shed_tool_conf_dict = app.toolbox.default_shed_tool_conf_dict()
-        self.shed_config_filename = shed_tool_conf_dict['config_filename']
+        self.shed_config_filename = shed_tool_conf_dict["config_filename"]
         return shed_tool_conf_dict
 
     @property
     def has_readme_files(self):
-        return 'readme_files' in self.metadata_
+        return "readme_files" in self.metadata_
 
     @property
     def has_repository_dependencies(self):
-        repository_dependencies_dict = self.metadata_.get('repository_dependencies', {})
-        repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
+        repository_dependencies_dict = self.metadata_.get("repository_dependencies", {})
+        repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
         # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
         for rd_tup in repository_dependencies:
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                common_util.parse_repository_dependency_tuple(rd_tup)
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = common_util.parse_repository_dependency_tuple(rd_tup)
             if not asbool(only_if_compiling_contained_td):
                 return True
         return False
 
     @property
     def has_repository_dependencies_only_if_compiling_contained_td(self):
-        repository_dependencies_dict = self.metadata_.get('repository_dependencies', {})
-        repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
+        repository_dependencies_dict = self.metadata_.get("repository_dependencies", {})
+        repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
         # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
         for rd_tup in repository_dependencies:
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                common_util.parse_repository_dependency_tuple(rd_tup)
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = common_util.parse_repository_dependency_tuple(rd_tup)
             if not asbool(only_if_compiling_contained_td):
                 return False
         return True
@@ -247,28 +312,28 @@ class ToolShedRepository(Base, _HasTable):
 
     @property
     def includes_data_managers(self):
-        return bool(len(self.metadata_.get('data_manager', {}).get('data_managers', {})))
+        return bool(len(self.metadata_.get("data_manager", {}).get("data_managers", {})))
 
     @property
     def includes_tools(self):
-        return 'tools' in self.metadata_
+        return "tools" in self.metadata_
 
     @property
     def includes_tools_for_display_in_tool_panel(self):
         if self.includes_tools:
-            tool_dicts = self.metadata_['tools']
+            tool_dicts = self.metadata_["tools"]
             for tool_dict in tool_dicts:
-                if tool_dict.get('add_to_tool_panel', True):
+                if tool_dict.get("add_to_tool_panel", True):
                     return True
         return False
 
     @property
     def includes_tool_dependencies(self):
-        return 'tool_dependencies' in self.metadata_
+        return "tool_dependencies" in self.metadata_
 
     @property
     def includes_workflows(self):
-        return 'workflows' in self.metadata_
+        return "workflows" in self.metadata_
 
     @property
     def installed_repository_dependencies(self):
@@ -291,13 +356,12 @@ class ToolShedRepository(Base, _HasTable):
     @property
     def is_deprecated_in_tool_shed(self):
         if self.tool_shed_status:
-            return asbool(self.tool_shed_status.get('repository_deprecated', False))
+            return asbool(self.tool_shed_status.get("repository_deprecated", False))
         return False
 
     @property
     def is_deactivated_or_installed(self):
-        return self.status in [self.installation_status.DEACTIVATED,
-                               self.installation_status.INSTALLED]
+        return self.status in [self.installation_status.DEACTIVATED, self.installation_status.INSTALLED]
 
     @property
     def is_installed(self):
@@ -306,7 +370,7 @@ class ToolShedRepository(Base, _HasTable):
     @property
     def is_latest_installable_revision(self):
         if self.tool_shed_status:
-            return asbool(self.tool_shed_status.get('latest_installable_revision', False))
+            return asbool(self.tool_shed_status.get("latest_installable_revision", False))
         return False
 
     @property
@@ -340,8 +404,10 @@ class ToolShedRepository(Base, _HasTable):
     def repo_path(self, app):
         tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(self.tool_shed)
         for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
-            tool_path = shed_tool_conf_dict['tool_path']
-            relative_path = os.path.join(tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision)
+            tool_path = shed_tool_conf_dict["tool_path"]
+            relative_path = os.path.join(
+                tool_path, tool_shed, "repos", self.owner, self.name, self.installed_changeset_revision
+            )
             if os.path.exists(relative_path):
                 return relative_path
         return None
@@ -365,11 +431,13 @@ class ToolShedRepository(Base, _HasTable):
         """Return the repository's repository dependencies that are currently being installed."""
         required_repositories_being_installed = []
         for required_repository in self.repository_dependencies:
-            if required_repository.status in [self.installation_status.CLONING,
-                                              self.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
-                                              self.installation_status.INSTALLING_TOOL_DEPENDENCIES,
-                                              self.installation_status.LOADING_PROPRIETARY_DATATYPES,
-                                              self.installation_status.SETTING_TOOL_VERSIONS]:
+            if required_repository.status in [
+                self.installation_status.CLONING,
+                self.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
+                self.installation_status.INSTALLING_TOOL_DEPENDENCIES,
+                self.installation_status.LOADING_PROPRIETARY_DATATYPES,
+                self.installation_status.SETTING_TOOL_VERSIONS,
+            ]:
                 required_repositories_being_installed.append(required_repository)
         return required_repositories_being_installed
 
@@ -378,10 +446,12 @@ class ToolShedRepository(Base, _HasTable):
         """Return the repository's repository dependencies that are either missing or currently being installed."""
         required_repositories_missing_or_being_installed = []
         for required_repository in self.repository_dependencies:
-            if required_repository.status in [self.installation_status.ERROR,
-                                              self.installation_status.INSTALLING,
-                                              self.installation_status.NEVER_INSTALLED,
-                                              self.installation_status.UNINSTALLED]:
+            if required_repository.status in [
+                self.installation_status.ERROR,
+                self.installation_status.INSTALLING,
+                self.installation_status.NEVER_INSTALLED,
+                self.installation_status.UNINSTALLED,
+            ]:
                 required_repositories_missing_or_being_installed.append(required_repository)
         return required_repositories_missing_or_being_installed
 
@@ -407,22 +477,38 @@ class ToolShedRepository(Base, _HasTable):
         """
         required_rd_tups_that_must_be_installed = []
         if self.has_repository_dependencies:
-            rd_tups = self.metadata_['repository_dependencies']['repository_dependencies']
+            rd_tups = self.metadata_["repository_dependencies"]["repository_dependencies"]
             for rd_tup in rd_tups:
                 if len(rd_tup) == 5:
-                    tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                        common_util.parse_repository_dependency_tuple(rd_tup, contains_error=False)
+                    (
+                        tool_shed,
+                        name,
+                        owner,
+                        changeset_revision,
+                        prior_installation_required,
+                        only_if_compiling_contained_td,
+                    ) = common_util.parse_repository_dependency_tuple(rd_tup, contains_error=False)
                     if asbool(prior_installation_required):
-                        required_rd_tups_that_must_be_installed.append((tool_shed, name, owner, changeset_revision, 'True', 'False'))
+                        required_rd_tups_that_must_be_installed.append(
+                            (tool_shed, name, owner, changeset_revision, "True", "False")
+                        )
                 elif len(rd_tup) == 6:
-                    tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                        common_util.parse_repository_dependency_tuple(rd_tup, contains_error=False)
+                    (
+                        tool_shed,
+                        name,
+                        owner,
+                        changeset_revision,
+                        prior_installation_required,
+                        only_if_compiling_contained_td,
+                    ) = common_util.parse_repository_dependency_tuple(rd_tup, contains_error=False)
                     # The repository dependency will only be required to be previously installed if it does not fall into the category of
                     # a repository that must be installed only so that its contained tool dependency can be used for compiling the tool
                     # dependency of the dependent repository.
                     if not asbool(only_if_compiling_contained_td):
                         if asbool(prior_installation_required):
-                            required_rd_tups_that_must_be_installed.append((tool_shed, name, owner, changeset_revision, 'True', 'False'))
+                            required_rd_tups_that_must_be_installed.append(
+                                (tool_shed, name, owner, changeset_revision, "True", "False")
+                            )
         return required_rd_tups_that_must_be_installed
 
     @property
@@ -432,17 +518,17 @@ class ToolShedRepository(Base, _HasTable):
         # have to name it in such a way that it will not conflict with the eliminated tool_shed_repository.update_available column (which
         # cannot be eliminated if using the sqlite database).
         if self.tool_shed_status:
-            return asbool(self.tool_shed_status.get('revision_update', False))
+            return asbool(self.tool_shed_status.get("revision_update", False))
         return False
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         if value_mapper is None:
             value_mapper = {}
         rval = {}
         try:
             visible_keys = self.__getattribute__(f"dict_{view}_visible_keys")
         except AttributeError:
-            raise Exception(f'Unknown API view: {view}')
+            raise Exception(f"Unknown API view: {view}")
         for key in visible_keys:
             try:
                 rval[key] = self.__getattribute__(key)
@@ -465,8 +551,10 @@ class ToolShedRepository(Base, _HasTable):
         """Return the repository's tool dependencies that are currently installed, but possibly in an error state."""
         installed_dependencies = []
         for tool_dependency in self.tool_dependencies:
-            if tool_dependency.status in [ToolDependency.installation_status.INSTALLED,
-                                          ToolDependency.installation_status.ERROR]:
+            if tool_dependency.status in [
+                ToolDependency.installation_status.INSTALLED,
+                ToolDependency.installation_status.ERROR,
+            ]:
                 installed_dependencies.append(tool_dependency)
         return installed_dependencies
 
@@ -474,10 +562,12 @@ class ToolShedRepository(Base, _HasTable):
     def tool_dependencies_missing_or_being_installed(self):
         dependencies_missing_or_being_installed = []
         for tool_dependency in self.tool_dependencies:
-            if tool_dependency.status in [ToolDependency.installation_status.ERROR,
-                                          ToolDependency.installation_status.INSTALLING,
-                                          ToolDependency.installation_status.NEVER_INSTALLED,
-                                          ToolDependency.installation_status.UNINSTALLED]:
+            if tool_dependency.status in [
+                ToolDependency.installation_status.ERROR,
+                ToolDependency.installation_status.INSTALLING,
+                ToolDependency.installation_status.NEVER_INSTALLED,
+                ToolDependency.installation_status.UNINSTALLED,
+            ]:
                 dependencies_missing_or_being_installed.append(tool_dependency)
         return dependencies_missing_or_being_installed
 
@@ -492,10 +582,10 @@ class ToolShedRepository(Base, _HasTable):
     @property
     def tool_shed_path_name(self):
         tool_shed_url = self.tool_shed
-        if tool_shed_url.find(':') > 0:
+        if tool_shed_url.find(":") > 0:
             # Eliminate the port, if any, since it will result in an invalid directory name.
-            tool_shed_url = tool_shed_url.split(':')[0]
-        return tool_shed_url.rstrip('/')
+            tool_shed_url = tool_shed_url.split(":")[0]
+        return tool_shed_url.rstrip("/")
 
     @property
     def tuples_of_repository_dependencies_needed_for_compiling_td(self):
@@ -504,13 +594,22 @@ class ToolShedRepository(Base, _HasTable):
         dependencies.
         """
         rd_tups_of_repositories_needed_for_compiling_td = []
-        repository_dependencies = self.metadata_.get('repository_dependencies', {})
-        rd_tups = repository_dependencies.get('repository_dependencies', [])
+        repository_dependencies = self.metadata_.get("repository_dependencies", {})
+        rd_tups = repository_dependencies.get("repository_dependencies", [])
         for rd_tup in rd_tups:
             if len(rd_tup) == 6:
-                tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
+                (
+                    tool_shed,
+                    name,
+                    owner,
+                    changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                ) = rd_tup
                 if asbool(only_if_compiling_contained_td):
-                    rd_tups_of_repositories_needed_for_compiling_td.append((tool_shed, name, owner, changeset_revision, 'False', 'True'))
+                    rd_tups_of_repositories_needed_for_compiling_td.append(
+                        (tool_shed, name, owner, changeset_revision, "False", "True")
+                    )
         return rd_tups_of_repositories_needed_for_compiling_td
 
     @property
@@ -537,20 +636,20 @@ class ToolShedRepository(Base, _HasTable):
             if self.is_deprecated_in_tool_shed:
                 # Only allow revision upgrades if the repository is not deprecated in the tool shed.
                 return False
-            return asbool(self.tool_shed_status.get('revision_upgrade', False))
+            return asbool(self.tool_shed_status.get("revision_upgrade", False))
         return False
 
 
 class RepositoryRepositoryDependencyAssociation(Base, _HasTable):
-    __tablename__ = 'repository_repository_dependency_association'
+    __tablename__ = "repository_repository_dependency_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True)
-    repository_dependency_id = Column(ForeignKey('repository_dependency.id'), index=True)
-    repository = relationship('ToolShedRepository', back_populates='required_repositories')
-    repository_dependency = relationship('RepositoryDependency')
+    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True)
+    repository_dependency_id = Column(ForeignKey("repository_dependency.id"), index=True)
+    repository = relationship("ToolShedRepository", back_populates="required_repositories")
+    repository_dependency = relationship("RepositoryDependency")
 
     def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
         self.tool_shed_repository_id = tool_shed_repository_id
@@ -558,48 +657,52 @@ class RepositoryRepositoryDependencyAssociation(Base, _HasTable):
 
 
 class RepositoryDependency(Base, _HasTable):
-    __tablename__ = 'repository_dependency'
+    __tablename__ = "repository_dependency"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
-    repository = relationship('ToolShedRepository')
+    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True, nullable=False)
+    repository = relationship("ToolShedRepository")
 
     def __init__(self, tool_shed_repository_id=None):
         self.tool_shed_repository_id = tool_shed_repository_id
 
 
 class ToolDependency(Base, _HasTable):
-    __tablename__ = 'tool_dependency'
+    __tablename__ = "tool_dependency"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
+    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True, nullable=False)
     name = Column(TrimmedString(255))
     version = Column(TEXT)
     type = Column(TrimmedString(40))
     status = Column(TrimmedString(255), nullable=False)
     error_message = Column(TEXT)
-    tool_shed_repository = relationship('ToolShedRepository', back_populates='tool_dependencies')
+    tool_shed_repository = relationship("ToolShedRepository", back_populates="tool_dependencies")
 
     # converting this one to Enum breaks the tool shed tests,
     # don't know why though -John
-    installation_status = Bunch(NEVER_INSTALLED='Never installed',
-                                INSTALLING='Installing',
-                                INSTALLED='Installed',
-                                ERROR='Error',
-                                UNINSTALLED='Uninstalled')
+    installation_status = Bunch(
+        NEVER_INSTALLED="Never installed",
+        INSTALLING="Installing",
+        INSTALLED="Installed",
+        ERROR="Error",
+        UNINSTALLED="Uninstalled",
+    )
 
     class states(str, Enum):
-        INSTALLING = 'running'
-        OK = 'ok'
-        WARNING = 'queued'
-        ERROR = 'error'
-        UNINSTALLED = 'deleted_new'
+        INSTALLING = "running"
+        OK = "ok"
+        WARNING = "queued"
+        ERROR = "error"
+        UNINSTALLED = "deleted_new"
 
-    def __init__(self, tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None):
+    def __init__(
+        self, tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None
+    ):
         self.tool_shed_repository_id = tool_shed_repository_id
         self.name = name
         self.version = version
@@ -617,14 +720,16 @@ class ToolDependency(Base, _HasTable):
 
     @property
     def can_update(self):
-        return self.status in [self.installation_status.NEVER_INSTALLED,
-                               self.installation_status.INSTALLED,
-                               self.installation_status.ERROR,
-                               self.installation_status.UNINSTALLED]
+        return self.status in [
+            self.installation_status.NEVER_INSTALLED,
+            self.installation_status.INSTALLED,
+            self.installation_status.ERROR,
+            self.installation_status.UNINSTALLED,
+        ]
 
     def get_env_shell_file_path(self, app):
         installation_directory = self.installation_directory(app)
-        file_path = os.path.join(installation_directory, 'env.sh')
+        file_path = os.path.join(installation_directory, "env.sh")
         if os.path.exists(file_path):
             return file_path
         return None
@@ -634,20 +739,24 @@ class ToolDependency(Base, _HasTable):
         return self.status == self.installation_status.ERROR
 
     def installation_directory(self, app):
-        if self.type == 'package':
-            return os.path.join(app.tool_dependency_dir,
-                                self.name,
-                                self.version,
-                                self.tool_shed_repository.owner,
-                                self.tool_shed_repository.name,
-                                self.tool_shed_repository.installed_changeset_revision)
-        if self.type == 'set_environment':
-            return os.path.join(app.tool_dependency_dir,
-                                'environment_settings',
-                                self.name,
-                                self.tool_shed_repository.owner,
-                                self.tool_shed_repository.name,
-                                self.tool_shed_repository.installed_changeset_revision)
+        if self.type == "package":
+            return os.path.join(
+                app.tool_dependency_dir,
+                self.name,
+                self.version,
+                self.tool_shed_repository.owner,
+                self.tool_shed_repository.name,
+                self.tool_shed_repository.installed_changeset_revision,
+            )
+        if self.type == "set_environment":
+            return os.path.join(
+                app.tool_dependency_dir,
+                "environment_settings",
+                self.name,
+                self.tool_shed_repository.owner,
+                self.tool_shed_repository.name,
+                self.tool_shed_repository.installed_changeset_revision,
+            )
 
     @property
     def is_installed(self):
@@ -655,34 +764,36 @@ class ToolDependency(Base, _HasTable):
 
 
 class ToolVersion(Base, Dictifiable, _HasTable):
-    __tablename__ = 'tool_version'
+    __tablename__ = "tool_version"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     tool_id = Column(String(255))
-    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True, nullable=True)
-    parent_tool_association = relationship('ToolVersionAssociation',
-        primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id))
-    child_tool_association = relationship('ToolVersionAssociation',
-        primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.parent_id))
-    tool_shed_repository = relationship('ToolShedRepository', back_populates='tool_versions')
+    tool_shed_repository_id = Column(ForeignKey("tool_shed_repository.id"), index=True, nullable=True)
+    parent_tool_association = relationship(
+        "ToolVersionAssociation", primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id)
+    )
+    child_tool_association = relationship(
+        "ToolVersionAssociation", primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.parent_id)
+    )
+    tool_shed_repository = relationship("ToolShedRepository", back_populates="tool_versions")
 
-    dict_element_visible_keys = ['id', 'tool_shed_repository']
+    dict_element_visible_keys = ["id", "tool_shed_repository"]
 
-    def to_dict(self, view='element'):
+    def to_dict(self, view="element"):
         rval = super().to_dict(view=view)
-        rval['tool_name'] = self.tool_id
+        rval["tool_name"] = self.tool_id
         for a in self.parent_tool_association:
-            rval['parent_tool_id'] = a.parent_id
+            rval["parent_tool_id"] = a.parent_id
         for a in self.child_tool_association:
-            rval['child_tool_id'] = a.tool_id
+            rval["child_tool_id"] = a.tool_id
         return rval
 
 
 class ToolVersionAssociation(Base, _HasTable):
-    __tablename__ = 'tool_version_association'
+    __tablename__ = "tool_version_association"
 
     id = Column(Integer, primary_key=True)
-    tool_id = Column(ForeignKey('tool_version.id'), index=True, nullable=False)
-    parent_id = Column(ForeignKey('tool_version.id'), index=True, nullable=False)
+    tool_id = Column(ForeignKey("tool_version.id"), index=True, nullable=False)
+    parent_id = Column(ForeignKey("tool_version.id"), index=True, nullable=False)
diff --git a/lib/galaxy/model/tool_shed_install/migrate/check.py b/lib/galaxy/model/tool_shed_install/migrate/check.py
index bada20288ff..199b31b8bdf 100644
--- a/lib/galaxy/model/tool_shed_install/migrate/check.py
+++ b/lib/galaxy/model/tool_shed_install/migrate/check.py
@@ -4,29 +4,30 @@ import sys
 
 from migrate.versioning import (
     repository,
-    schema
+    schema,
 )
 from sqlalchemy import (
     create_engine,
     MetaData,
-    Table
+    Table,
 )
 from sqlalchemy.exc import NoSuchTableError
 
-from galaxy.model.database_utils import create_database, database_exists
+from galaxy.model.database_utils import (
+    create_database,
+    database_exists,
+)
 from galaxy.model.tool_shed_install import mapping
 
-
 log = logging.getLogger(__name__)
 
 # path relative to galaxy
-migrate_repository_directory = os.path.abspath(os.path.dirname(__file__)).replace(os.getcwd() + os.path.sep, '', 1)
+migrate_repository_directory = os.path.abspath(os.path.dirname(__file__)).replace(os.getcwd() + os.path.sep, "", 1)
 migrate_repository = repository.Repository(migrate_repository_directory)
 
 
 def create_or_verify_database(url, engine_options=None, app=None):
-    """
-    """
+    """ """
     # Create engine and metadata
     engine_options = engine_options or {}
     if not database_exists(url):
@@ -47,7 +48,7 @@ def create_or_verify_database(url, engine_options=None, app=None):
         migrate_to_current_version(engine, db_schema)
 
     meta = MetaData(bind=engine)
-    if app and getattr(app.config, 'database_auto_migrate', False):
+    if app and getattr(app.config, "database_auto_migrate", False):
         migrate()
         return
 
@@ -81,7 +82,10 @@ def create_or_verify_database(url, engine_options=None, app=None):
     # Verify that the code and the DB are in sync
     db_schema = schema.ControlledSchema(engine, migrate_repository)
     if migrate_repository.versions.latest != db_schema.version:
-        exception_msg = "Your database has version '%d' but this code expects version '%d'.  " % (db_schema.version, migrate_repository.versions.latest)
+        exception_msg = "Your database has version '%d' but this code expects version '%d'.  " % (
+            db_schema.version,
+            migrate_repository.versions.latest,
+        )
         exception_msg += "Back up your database and then migrate the schema by running the following from your Galaxy installation directory:"
         exception_msg += "\n\nsh manage_db.sh upgrade install\n"
 
@@ -94,7 +98,7 @@ def migrate_to_current_version(engine, schema):
     changeset = schema.changeset(None)
     for ver, change in changeset:
         nextver = ver + changeset.step
-        log.info(f'Migrating {ver} -> {nextver}... ')
+        log.info(f"Migrating {ver} -> {nextver}... ")
         old_stdout = sys.stdout
 
         class FakeStdout:
diff --git a/lib/galaxy/model/unittest_utils/__init__.py b/lib/galaxy/model/unittest_utils/__init__.py
index 788bdc9ef5f..790e54ae1f4 100644
--- a/lib/galaxy/model/unittest_utils/__init__.py
+++ b/lib/galaxy/model/unittest_utils/__init__.py
@@ -1,8 +1,10 @@
 """Interface provided by galaxy-data modules for unittest utilities for reuse by other modules."""
-from .data_app import GalaxyDataTestApp, GalaxyDataTestConfig
-
+from .data_app import (
+    GalaxyDataTestApp,
+    GalaxyDataTestConfig,
+)
 
 __all__ = [
-    'GalaxyDataTestApp',
-    'GalaxyDataTestConfig',
+    "GalaxyDataTestApp",
+    "GalaxyDataTestConfig",
 ]
diff --git a/lib/galaxy/model/unittest_utils/data_app.py b/lib/galaxy/model/unittest_utils/data_app.py
index a1c5552f830..5ff5dc3de92 100644
--- a/lib/galaxy/model/unittest_utils/data_app.py
+++ b/lib/galaxy/model/unittest_utils/data_app.py
@@ -9,20 +9,26 @@ import os
 import shutil
 import tempfile
 
-from galaxy import model, objectstore
+from galaxy import (
+    model,
+    objectstore,
+)
 from galaxy.datatypes import registry
-from galaxy.model.mapping import GalaxyModelMapping, init
+from galaxy.model.mapping import (
+    GalaxyModelMapping,
+    init,
+)
 from galaxy.model.security import GalaxyRBACAgent
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util.bunch import Bunch
 
-
-GALAXY_TEST_UNITTEST_SECRET = '6e46ed6483a833c100e68cc3f1d0dd76'
+GALAXY_TEST_UNITTEST_SECRET = "6e46ed6483a833c100e68cc3f1d0dd76"
 GALAXY_TEST_IN_MEMORY_DB_CONNECTION = "sqlite:///:memory:"
 
 
 class GalaxyDataTestConfig(Bunch):
     """Minimal Galaxy mock config object that exposes and uses only what is needed for the galaxy-data package."""
+
     security: IdEncodingHelper
     database_connection: str
     root: str
@@ -37,32 +43,33 @@ class GalaxyDataTestConfig(Bunch):
         else:
             self._remove_root = False
         self.root = root
-        self.data_dir = os.path.join(root, 'database')
+        self.data_dir = os.path.join(root, "database")
 
         self.security = IdEncodingHelper(id_secret=GALAXY_TEST_UNITTEST_SECRET)
-        self.database_connection = kwd.get('database_connection', GALAXY_TEST_IN_MEMORY_DB_CONNECTION)
+        self.database_connection = kwd.get("database_connection", GALAXY_TEST_IN_MEMORY_DB_CONNECTION)
 
         # objectstore config values...
-        self.object_store_config_file = ''
-        self.object_store = 'disk'
+        self.object_store_config_file = ""
+        self.object_store = "disk"
         self.object_store_check_old_style = False
-        self.object_store_cache_path = '/tmp/cache'
+        self.object_store_cache_path = "/tmp/cache"
         self.object_store_store_by = "uuid"
 
         self.umask = os.umask(0o77)
         self.gid = os.getgid()
         # objectstore config directories...
-        self.jobs_directory = os.path.join(self.data_dir, 'jobs_directory')
-        self.new_file_path = os.path.join(self.data_dir, 'tmp')
-        self.file_path = os.path.join(self.data_dir, 'files')
+        self.jobs_directory = os.path.join(self.data_dir, "jobs_directory")
+        self.new_file_path = os.path.join(self.data_dir, "tmp")
+        self.file_path = os.path.join(self.data_dir, "files")
 
     def __del__(self):
         if self._remove_root:
             shutil.rmtree(self.root)
 
 
-class GalaxyDataTestApp():
+class GalaxyDataTestApp:
     """Minimal Galaxy mock app object that exposes and uses only what is needed for the galaxy-data package."""
+
     security: IdEncodingHelper
     model: GalaxyModelMapping
     security_agent: GalaxyRBACAgent
@@ -85,6 +92,5 @@ class GalaxyDataTestApp():
 
 
 class MockSetExternalTool:
-
     def regenerate_imported_metadata_if_needed(self, *args, **kwds):
         pass
diff --git a/lib/galaxy/model/view/__init__.py b/lib/galaxy/model/view/__init__.py
index 5d0bd48a721..0bb5c2771a1 100644
--- a/lib/galaxy/model/view/__init__.py
+++ b/lib/galaxy/model/view/__init__.py
@@ -3,13 +3,16 @@ Galaxy sql view models
 """
 from sqlalchemy import Integer
 from sqlalchemy.orm import registry
-from sqlalchemy.sql import column, text
+from sqlalchemy.sql import (
+    column,
+    text,
+)
 
 from galaxy.model.view.utils import View
 
 
 class HistoryDatasetCollectionJobStateSummary(View):
-    name = 'collection_job_state_summary_view'
+    name = "collection_job_state_summary_view"
 
     aggregate_state_query = """
 SELECT
@@ -48,25 +51,26 @@ GROUP BY jobstates.hdca_id
 """
 
     __view__ = text(aggregate_state_query).columns(
-        column('hdca_id', Integer),
-        column('new', Integer),
-        column('resubmitted', Integer),
-        column('waiting', Integer),
-        column('queued', Integer),
-        column('running', Integer),
-        column('ok', Integer),
-        column('error', Integer),
-        column('failed', Integer),
-        column('paused', Integer),
-        column('deleted', Integer),
-        column('deleted_new', Integer),
-        column('upload', Integer),
-        column('all_jobs', Integer)
+        column("hdca_id", Integer),
+        column("new", Integer),
+        column("resubmitted", Integer),
+        column("waiting", Integer),
+        column("queued", Integer),
+        column("running", Integer),
+        column("ok", Integer),
+        column("error", Integer),
+        column("failed", Integer),
+        column("paused", Integer),
+        column("deleted", Integer),
+        column("deleted_new", Integer),
+        column("upload", Integer),
+        column("all_jobs", Integer),
     )
-    pkeys = {'hdca_id'}
+    pkeys = {"hdca_id"}
     __table__ = View._make_table(name, __view__, pkeys)
 
 
 mapper_registry = registry()
 mapper_registry.map_imperatively(
-    HistoryDatasetCollectionJobStateSummary, HistoryDatasetCollectionJobStateSummary.__table__)
+    HistoryDatasetCollectionJobStateSummary, HistoryDatasetCollectionJobStateSummary.__table__
+)
diff --git a/lib/galaxy/model/view/utils.py b/lib/galaxy/model/view/utils.py
index e5e0ac01804..14c4cbca8db 100644
--- a/lib/galaxy/model/view/utils.py
+++ b/lib/galaxy/model/view/utils.py
@@ -17,20 +17,13 @@ class View:
 
     @staticmethod
     def _make_table(name, selectable, pkeys):
-        """ Create a view.
+        """Create a view.
 
         :param name: The name of the view.
         :param selectable: SQLAlchemy selectable.
         :param pkeys: set of primary keys for the selectable.
         """
-        columns = [
-            Column(
-                c.name,
-                c.type,
-                primary_key=(c.name in pkeys)
-            )
-            for c in selectable.subquery().columns
-        ]
+        columns = [Column(c.name, c.type, primary_key=(c.name in pkeys)) for c in selectable.subquery().columns]
         # We do not use the metadata object from model.mapping.py that contains all the Table objects
         # because that would create a circular import (create_view is called from View objects
         # in model.view; but those View objects are imported into model.mapping.py where the
@@ -56,20 +49,21 @@ class DropView(DDLElement):
 @compiler.compiles(CreateView)
 def compile_create_view(element, compiler, **kw):
     compiled_selectable = compiler.sql_compiler.process(element.selectable, literal_binds=True)
-    return f'CREATE VIEW {element.name} AS {compiled_selectable}'
+    return f"CREATE VIEW {element.name} AS {compiled_selectable}"
 
 
 @compiler.compiles(DropView)
 def compile_drop_view(element, compiler, **kw):
-    return f'DROP VIEW IF EXISTS {element.name}'
+    return f"DROP VIEW IF EXISTS {element.name}"
 
 
 def is_view_model(o):
-    return hasattr(o, '__view__') and issubclass(o, View)
+    return hasattr(o, "__view__") and issubclass(o, View)
 
 
 def install_views(engine):
     import galaxy.model.view
+
     views = getmembers(galaxy.model.view, is_view_model)
     for _, view in views:
         # adding DropView here because our unit-testing calls this function when
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 2470d3591ca..69903c6020e 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -12,11 +12,19 @@ import random
 import shutil
 import threading
 import time
-from typing import Any, Dict, List, Type
+from typing import (
+    Any,
+    Dict,
+    List,
+    Type,
+)
 
 import yaml
 
-from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.exceptions import (
+    ObjectInvalid,
+    ObjectNotFound,
+)
 from galaxy.util import (
     directory_hash_id,
     force_symlink,
@@ -30,7 +38,9 @@ from galaxy.util.path import (
 )
 from galaxy.util.sleeper import Sleeper
 
-NO_SESSION_ERROR_MESSAGE = "Attempted to 'create' object store entity in configuration with no database session present."
+NO_SESSION_ERROR_MESSAGE = (
+    "Attempted to 'create' object store entity in configuration with no database session present."
+)
 
 log = logging.getLogger(__name__)
 
@@ -85,7 +95,9 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def create(
+        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+    ):
         """
         Mark the object (`obj`) as existing in the store, but with no content.
 
@@ -113,7 +125,16 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def delete(
+        self,
+        obj,
+        entire_dir=False,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+    ):
         """
         Delete the object identified by `obj`.
 
@@ -126,7 +147,17 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def get_data(
+        self,
+        obj,
+        start=0,
+        count=-1,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+    ):
         """
         Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
 
@@ -141,7 +172,9 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def get_filename(
+        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+    ):
         """
         Get the expected filename with absolute path for object with id `obj.id`.
 
@@ -150,7 +183,17 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False):
+    def update_from_file(
+        self,
+        obj,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        file_name=None,
+        create=False,
+    ):
         """
         Inform the store that the file associated with `obj.id` has been updated.
 
@@ -236,17 +279,18 @@ class BaseObjectStore(ObjectStore):
         self.config = config
         self.check_old_style = config.object_store_check_old_style
         extra_dirs = {}
-        extra_dirs['job_work'] = config.jobs_directory
-        extra_dirs['temp'] = config.new_file_path
-        extra_dirs.update({
-            e['type']: e['path'] for e in config_dict.get('extra_dirs', [])})
+        extra_dirs["job_work"] = config.jobs_directory
+        extra_dirs["temp"] = config.new_file_path
+        extra_dirs.update({e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])})
         self.extra_dirs = extra_dirs
 
     def shutdown(self):
         """Close any connections for this ObjectStore."""
         self.running = False
 
-    def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def file_ready(
+        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+    ):
         """
         Check if a file corresponding to a dataset is ready to be used.
 
@@ -273,9 +317,9 @@ class BaseObjectStore(ObjectStore):
         for extra_dir_type, extra_dir_path in self.extra_dirs.items():
             extra_dirs.append({"type": extra_dir_type, "path": extra_dir_path})
         return {
-            'config': config_to_dict(self.config),
-            'extra_dirs': extra_dirs,
-            'type': self.store_type,
+            "config": config_to_dict(self.config),
+            "extra_dirs": extra_dirs,
+            "type": self.store_type,
         }
 
     def _get_object_id(self, obj):
@@ -294,43 +338,43 @@ class BaseObjectStore(ObjectStore):
         return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
 
     def exists(self, obj, **kwargs):
-        return self._invoke('exists', obj, **kwargs)
+        return self._invoke("exists", obj, **kwargs)
 
     def create(self, obj, **kwargs):
-        return self._invoke('create', obj, **kwargs)
+        return self._invoke("create", obj, **kwargs)
 
     def empty(self, obj, **kwargs):
-        return self._invoke('empty', obj, **kwargs)
+        return self._invoke("empty", obj, **kwargs)
 
     def size(self, obj, **kwargs):
-        return self._invoke('size', obj, **kwargs)
+        return self._invoke("size", obj, **kwargs)
 
     def delete(self, obj, **kwargs):
-        return self._invoke('delete', obj, **kwargs)
+        return self._invoke("delete", obj, **kwargs)
 
     def get_data(self, obj, **kwargs):
-        return self._invoke('get_data', obj, **kwargs)
+        return self._invoke("get_data", obj, **kwargs)
 
     def get_filename(self, obj, **kwargs):
-        return self._invoke('get_filename', obj, **kwargs)
+        return self._invoke("get_filename", obj, **kwargs)
 
     def update_from_file(self, obj, **kwargs):
-        return self._invoke('update_from_file', obj, **kwargs)
+        return self._invoke("update_from_file", obj, **kwargs)
 
     def get_object_url(self, obj, **kwargs):
-        return self._invoke('get_object_url', obj, **kwargs)
+        return self._invoke("get_object_url", obj, **kwargs)
 
     def get_concrete_store_name(self, obj):
-        return self._invoke('get_concrete_store_name', obj)
+        return self._invoke("get_concrete_store_name", obj)
 
     def get_concrete_store_description_markdown(self, obj):
-        return self._invoke('get_concrete_store_description_markdown', obj)
+        return self._invoke("get_concrete_store_description_markdown", obj)
 
     def get_store_usage_percent(self):
-        return self._invoke('get_store_usage_percent')
+        return self._invoke("get_store_usage_percent")
 
     def get_store_by(self, obj, **kwargs):
-        return self._invoke('get_store_by', obj, **kwargs)
+        return self._invoke("get_store_by", obj, **kwargs)
 
 
 class ConcreteObjectStore(BaseObjectStore):
@@ -393,7 +437,8 @@ class DiskObjectStore(ConcreteObjectStore):
     True
     >>> assert s.get_filename(obj) == file_path + '/000/dataset_1.dat'
     """
-    store_type = 'disk'
+
+    store_type = "disk"
 
     def __init__(self, config, config_dict):
         """
@@ -419,19 +464,19 @@ class DiskObjectStore(ConcreteObjectStore):
         extra_dirs = []
         config_dict = {}
         if config_xml is not None:
-            store_by = config_xml.attrib.get('store_by', None)
+            store_by = config_xml.attrib.get("store_by", None)
             if store_by is not None:
-                config_dict['store_by'] = store_by
-            name = config_xml.attrib.get('name', None)
+                config_dict["store_by"] = store_by
+            name = config_xml.attrib.get("name", None)
             if name is not None:
-                config_dict['name'] = name
+                config_dict["name"] = name
             for e in config_xml:
-                if e.tag == 'files_dir':
-                    config_dict["files_dir"] = e.get('path')
-                elif e.tag == 'description':
+                if e.tag == "files_dir":
+                    config_dict["files_dir"] = e.get("path")
+                elif e.tag == "description":
                     config_dict["description"] = e.text
                 else:
-                    extra_dirs.append({"type": e.get('type'), "path": e.get('path')})
+                    extra_dirs.append({"type": e.get("type"), "path": e.get("path")})
 
         config_dict["extra_dirs"] = extra_dirs
         return config_dict
@@ -441,24 +486,50 @@ class DiskObjectStore(ConcreteObjectStore):
         as_dict["files_dir"] = self.file_path
         return as_dict
 
-    def __get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def __get_filename(
+        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+    ):
         """
         Return the absolute path for the file corresponding to the `obj.id`.
 
         This is regardless of whether or not the file exists.
         """
-        path = self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir,
-                                    extra_dir_at_root=extra_dir_at_root, alt_name=alt_name,
-                                    obj_dir=False, old_style=True)
+        path = self._construct_path(
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=False,
+            old_style=True,
+        )
         # For backward compatibility: check the old style root path first;
         # otherwise construct hashed path.
         if not os.path.exists(path):
-            return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir,
-                                        extra_dir_at_root=extra_dir_at_root, alt_name=alt_name)
+            return self._construct_path(
+                obj,
+                base_dir=base_dir,
+                dir_only=dir_only,
+                extra_dir=extra_dir,
+                extra_dir_at_root=extra_dir_at_root,
+                alt_name=alt_name,
+            )
 
     # TODO: rename to _disk_path or something like that to avoid conflicts with
     # children that'll use the local_extra_dirs decorator, e.g. S3
-    def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+    def _construct_path(
+        self,
+        obj,
+        old_style=False,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        **kwargs,
+    ):
         """
         Construct the absolute path for accessing the object identified by `obj.id`.
 
@@ -492,12 +563,12 @@ class DiskObjectStore(ConcreteObjectStore):
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning('extra_dir is not normalized: %s', extra_dir)
+            log.warning("extra_dir is not normalized: %s", extra_dir)
             raise ObjectInvalid("The requested object is invalid")
         # ensure that any parent directory references in alt_name would not
         # result in a path not contained in the directory path constructed here
         if alt_name and not safe_relpath(alt_name):
-            log.warning('alt_name would locate path outside dir: %s', alt_name)
+            log.warning("alt_name would locate path outside dir: %s", alt_name)
             raise ObjectInvalid("The requested object is invalid")
         obj_id = self._get_object_id(obj)
         if old_style:
@@ -519,7 +590,9 @@ class DiskObjectStore(ConcreteObjectStore):
                     rel_path = os.path.join(rel_path, extra_dir)
             path = os.path.join(base, rel_path)
         if not dir_only:
-            assert obj_id is not None, f"The effective dataset identifier consumed by object store [{self.store_by}] must be set before a path can be constructed."
+            assert (
+                obj_id is not None
+            ), f"The effective dataset identifier consumed by object store [{self.store_by}] must be set before a path can be constructed."
             path = os.path.join(path, alt_name if alt_name else f"dataset_{obj_id}.dat")
         return os.path.abspath(path)
 
@@ -537,13 +610,13 @@ class DiskObjectStore(ConcreteObjectStore):
         """Override `ObjectStore`'s stub by creating any files and folders on disk."""
         if not self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
-            dir_only = kwargs.get('dir_only', False)
+            dir_only = kwargs.get("dir_only", False)
             # Create directory if it does not exist
             dir = path if dir_only else os.path.dirname(path)
             safe_makedirs(dir)
             # Create the file if it does not exist
             if not dir_only:
-                open(path, 'w').close()  # Should be rb?
+                open(path, "w").close()  # Should be rb?
                 umask_fix_perms(path, self.config.umask, 0o666)
 
     def _empty(self, obj, **kwargs):
@@ -573,8 +646,8 @@ class DiskObjectStore(ConcreteObjectStore):
     def _delete(self, obj, entire_dir=False, **kwargs):
         """Override `ObjectStore`'s stub; delete the file or folder on disk."""
         path = self._get_filename(obj, **kwargs)
-        extra_dir = kwargs.get('extra_dir', None)
-        obj_dir = kwargs.get('obj_dir', False)
+        extra_dir = kwargs.get("extra_dir", None)
+        obj_dir = kwargs.get("obj_dir", False)
         try:
             if entire_dir and (extra_dir or obj_dir):
                 shutil.rmtree(path)
@@ -583,7 +656,7 @@ class DiskObjectStore(ConcreteObjectStore):
                 os.remove(path)
                 return True
         except OSError as ex:
-            log.critical(f'{self.__get_filename(obj, **kwargs)} delete error {ex}')
+            log.critical(f"{self.__get_filename(obj, **kwargs)} delete error {ex}")
         return False
 
     def _get_data(self, obj, start=0, count=-1, **kwargs):
@@ -614,7 +687,7 @@ class DiskObjectStore(ConcreteObjectStore):
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         """`create` parameter is not used in this implementation."""
-        preserve_symlinks = kwargs.pop('preserve_symlinks', False)
+        preserve_symlinks = kwargs.pop("preserve_symlinks", False)
         # FIXME: symlinks and the object store model may not play well together
         # these should be handled better, e.g. registering the symlink'd file
         # as an object
@@ -633,7 +706,7 @@ class DiskObjectStore(ConcreteObjectStore):
                 # the remote object from the cache file path
                 pass
             except OSError as ex:
-                log.critical(f'Error copying {file_name} to {self.__get_filename(obj, **kwargs)}: {ex}')
+                log.critical(f"Error copying {file_name} to {self.__get_filename(obj, **kwargs)}: {ex}")
                 raise ex
 
     def _get_object_url(self, obj, **kwargs):
@@ -671,11 +744,11 @@ class NestedObjectStore(BaseObjectStore):
 
     def _exists(self, obj, **kwargs):
         """Determine if the `obj` exists in any of the backends."""
-        return self._call_method('_exists', obj, False, False, **kwargs)
+        return self._call_method("_exists", obj, False, False, **kwargs)
 
     def file_ready(self, obj, **kwargs):
         """Determine if the file for `obj` is ready to be used by any of the backends."""
-        return self._call_method('file_ready', obj, False, False, **kwargs)
+        return self._call_method("file_ready", obj, False, False, **kwargs)
 
     def _create(self, obj, **kwargs):
         """Create a backing file in a random backend."""
@@ -683,61 +756,62 @@ class NestedObjectStore(BaseObjectStore):
 
     def _empty(self, obj, **kwargs):
         """For the first backend that has this `obj`, determine if it is empty."""
-        return self._call_method('_empty', obj, True, False, **kwargs)
+        return self._call_method("_empty", obj, True, False, **kwargs)
 
     def _size(self, obj, **kwargs):
         """For the first backend that has this `obj`, return its size."""
-        return self._call_method('_size', obj, 0, False, **kwargs)
+        return self._call_method("_size", obj, 0, False, **kwargs)
 
     def _delete(self, obj, **kwargs):
         """For the first backend that has this `obj`, delete it."""
-        return self._call_method('_delete', obj, False, False, **kwargs)
+        return self._call_method("_delete", obj, False, False, **kwargs)
 
     def _get_data(self, obj, **kwargs):
         """For the first backend that has this `obj`, get data from it."""
-        return self._call_method('_get_data', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method("_get_data", obj, ObjectNotFound, True, **kwargs)
 
     def _get_filename(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its filename."""
-        return self._call_method('_get_filename', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method("_get_filename", obj, ObjectNotFound, True, **kwargs)
 
     def _update_from_file(self, obj, **kwargs):
         """For the first backend that has this `obj`, update it from the given file."""
-        if kwargs.get('create', False):
+        if kwargs.get("create", False):
             self._create(obj, **kwargs)
-            kwargs['create'] = False
-        return self._call_method('_update_from_file', obj, ObjectNotFound, True, **kwargs)
+            kwargs["create"] = False
+        return self._call_method("_update_from_file", obj, ObjectNotFound, True, **kwargs)
 
     def _get_object_url(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its URL."""
-        return self._call_method('_get_object_url', obj, None, False, **kwargs)
+        return self._call_method("_get_object_url", obj, None, False, **kwargs)
 
     def _get_concrete_store_name(self, obj):
-        return self._call_method('_get_concrete_store_name', obj, None, False)
+        return self._call_method("_get_concrete_store_name", obj, None, False)
 
     def _get_concrete_store_description_markdown(self, obj):
-        return self._call_method('_get_concrete_store_description_markdown', obj, None, False)
+        return self._call_method("_get_concrete_store_description_markdown", obj, None, False)
 
     def _get_store_by(self, obj):
-        return self._call_method('_get_store_by', obj, None, False)
+        return self._call_method("_get_store_by", obj, None, False)
 
     def _repr_object_for_exception(self, obj):
         try:
             # there are a few objects in python that don't have __class__
             obj_id = self._get_object_id(obj)
-            return f'{obj.__class__.__name__}({self.store_by}={obj_id})'
+            return f"{obj.__class__.__name__}({self.store_by}={obj_id})"
         except AttributeError:
             return str(obj)
 
-    def _call_method(self, method, obj, default, default_is_exception,
-            **kwargs):
+    def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         """Check all children object stores for the first one with the dataset."""
         for store in self.backends.values():
             if store.exists(obj, **kwargs):
                 return store.__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
-            raise default('objectstore, _call_method failed: %s on %s, kwargs: %s'
-                          % (method, self._repr_object_for_exception(obj), str(kwargs)))
+            raise default(
+                "objectstore, _call_method failed: %s on %s, kwargs: %s"
+                % (method, self._repr_object_for_exception(obj), str(kwargs))
+            )
         else:
             return default
 
@@ -751,7 +825,8 @@ class DistributedObjectStore(NestedObjectStore):
     When creating objects they are created in a store selected randomly, but
     with weighting.
     """
-    store_type = 'distributed'
+
+    store_type = "distributed"
 
     def __init__(self, config, config_dict, fsmon=False):
         """
@@ -808,20 +883,20 @@ class DistributedObjectStore(NestedObjectStore):
         if legacy:
             backends_root = config_xml
         else:
-            backends_root = config_xml.find('backends')
+            backends_root = config_xml.find("backends")
 
         backends: List[Dict[str, Any]] = []
         config_dict = {
-            'global_max_percent_full': float(backends_root.get('maxpctfull', 0)),
-            'backends': backends,
+            "global_max_percent_full": float(backends_root.get("maxpctfull", 0)),
+            "backends": backends,
         }
 
-        for b in [e for e in backends_root if e.tag == 'backend']:
+        for b in [e for e in backends_root if e.tag == "backend"]:
             store_id = b.get("id")
             store_weight = int(b.get("weight", 1))
-            store_maxpctfull = float(b.get('maxpctfull', 0))
+            store_maxpctfull = float(b.get("maxpctfull", 0))
             store_type = b.get("type", "disk")
-            store_by = b.get('store_by', None)
+            store_by = b.get("store_by", None)
 
             objectstore_class, _ = type_to_object_store_class(store_type)
             backend_config_dict = objectstore_class.parse_xml(b)
@@ -840,16 +915,17 @@ class DistributedObjectStore(NestedObjectStore):
         legacy = False
         if config_xml is None:
             distributed_config = config.distributed_object_store_config_file
-            assert distributed_config is not None, \
-                "distributed object store ('object_store = distributed') " \
-                "requires a config file, please set one in " \
+            assert distributed_config is not None, (
+                "distributed object store ('object_store = distributed') "
+                "requires a config file, please set one in "
                 "'distributed_object_store_config_file')"
+            )
 
-            log.debug('Loading backends for distributed object store from %s', distributed_config)
+            log.debug("Loading backends for distributed object store from %s", distributed_config)
             config_xml = parse_xml(distributed_config).getroot()
             legacy = True
         else:
-            log.debug('Loading backends for distributed object store from %s', config_xml.get('id'))
+            log.debug("Loading backends for distributed object store from %s", config_xml.get("id"))
 
         config_dict = clazz.parse_xml(config_xml, legacy=legacy)
         return clazz(config, config_dict, fsmon=fsmon)
@@ -891,14 +967,19 @@ class DistributedObjectStore(NestedObjectStore):
                 try:
                     obj.object_store_id = random.choice(self.weighted_backend_ids)
                 except IndexError:
-                    raise ObjectInvalid('objectstore.create, could not generate '
-                                        'obj.object_store_id: %s, kwargs: %s'
-                                        % (str(obj), str(kwargs)))
-                log.debug("Selected backend '%s' for creation of %s %s"
-                          % (obj.object_store_id, obj.__class__.__name__, obj.id))
+                    raise ObjectInvalid(
+                        "objectstore.create, could not generate "
+                        "obj.object_store_id: %s, kwargs: %s" % (str(obj), str(kwargs))
+                    )
+                log.debug(
+                    "Selected backend '%s' for creation of %s %s"
+                    % (obj.object_store_id, obj.__class__.__name__, obj.id)
+                )
             else:
-                log.debug("Using preferred backend '%s' for creation of %s %s"
-                          % (obj.object_store_id, obj.__class__.__name__, obj.id))
+                log.debug(
+                    "Using preferred backend '%s' for creation of %s %s"
+                    % (obj.object_store_id, obj.__class__.__name__, obj.id)
+                )
             self.backends[obj.object_store_id].create(obj, **kwargs)
 
     def _call_method(self, method, obj, default, default_is_exception, **kwargs):
@@ -906,8 +987,10 @@ class DistributedObjectStore(NestedObjectStore):
         if object_store_id is not None:
             return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
-            raise default('objectstore, _call_method failed: %s on %s, kwargs: %s'
-                          % (method, self._repr_object_for_exception(obj), str(kwargs)))
+            raise default(
+                "objectstore, _call_method failed: %s on %s, kwargs: %s"
+                % (method, self._repr_object_for_exception(obj), str(kwargs))
+            )
         else:
             return default
 
@@ -916,15 +999,19 @@ class DistributedObjectStore(NestedObjectStore):
             if obj.object_store_id in self.backends:
                 return obj.object_store_id
             else:
-                log.warning('The backend object store ID (%s) for %s object with ID %s is invalid'
-                            % (obj.object_store_id, obj.__class__.__name__, obj.id))
+                log.warning(
+                    "The backend object store ID (%s) for %s object with ID %s is invalid"
+                    % (obj.object_store_id, obj.__class__.__name__, obj.id)
+                )
         # if this instance has been switched from a non-distributed to a
         # distributed object store, or if the object's store id is invalid,
         # try to locate the object
         for id, store in self.backends.items():
             if store.exists(obj, **kwargs):
-                log.warning('%s object with ID %s found in backend object store with ID %s'
-                            % (obj.__class__.__name__, obj.id, id))
+                log.warning(
+                    "%s object with ID %s found in backend object store with ID %s"
+                    % (obj.__class__.__name__, obj.id, id)
+                )
                 obj.object_store_id = id
                 return id
         return None
@@ -938,7 +1025,8 @@ class HierarchicalObjectStore(NestedObjectStore):
     When getting objects the first store where the object exists is used.
     When creating objects only the first store is used.
     """
-    store_type = 'hierarchical'
+
+    store_type = "hierarchical"
 
     def __init__(self, config, config_dict, fsmon=False):
         """The default constructor. Extends `NestedObjectStore`."""
@@ -953,7 +1041,7 @@ class HierarchicalObjectStore(NestedObjectStore):
     @classmethod
     def parse_xml(clazz, config_xml):
         backends_list = []
-        for b in sorted(config_xml.find('backends'), key=lambda b: int(b.get('order'))):
+        for b in sorted(config_xml.find("backends"), key=lambda b: int(b.get("order"))):
             store_type = b.get("type")
             objectstore_class, _ = type_to_object_store_class(store_type)
             backend_config_dict = objectstore_class.parse_xml(b)
@@ -986,31 +1074,37 @@ class HierarchicalObjectStore(NestedObjectStore):
 def type_to_object_store_class(store, fsmon=False):
     objectstore_class: Type[ObjectStore]
     objectstore_constructor_kwds = {}
-    if store == 'disk':
+    if store == "disk":
         objectstore_class = DiskObjectStore
-    elif store == 's3':
+    elif store == "s3":
         from .s3 import S3ObjectStore
+
         objectstore_class = S3ObjectStore
-    elif store == 'cloud':
+    elif store == "cloud":
         from .cloud import Cloud
+
         objectstore_class = Cloud
-    elif store == 'swift':
+    elif store == "swift":
         from .s3 import SwiftObjectStore
+
         objectstore_class = SwiftObjectStore
-    elif store == 'distributed':
+    elif store == "distributed":
         objectstore_class = DistributedObjectStore
         objectstore_constructor_kwds["fsmon"] = fsmon
-    elif store == 'hierarchical':
+    elif store == "hierarchical":
         objectstore_class = HierarchicalObjectStore
         objectstore_constructor_kwds["fsmon"] = fsmon
-    elif store == 'irods':
+    elif store == "irods":
         from .irods import IRODSObjectStore
+
         objectstore_class = IRODSObjectStore
-    elif store == 'azure_blob':
+    elif store == "azure_blob":
         from .azure_blob import AzureBlobObjectStore
+
         objectstore_class = AzureBlobObjectStore
-    elif store == 'pithos':
+    elif store == "pithos":
         from .pithos import PithosObjectStore
+
         objectstore_class = PithosObjectStore
     else:
         raise Exception(f"Unrecognized object store definition: {store}")
@@ -1033,13 +1127,15 @@ def build_object_store_from_config(config, fsmon=False, config_xml=None, config_
     the `config` object. Currently 'disk', 's3', 'swift', 'distributed',
     'hierarchical', 'irods', and 'pulsar' are supported values.
     """
-    from_object = 'xml'
+    from_object = "xml"
 
-    if config is None and config_dict is not None and 'config' in config_dict:
+    if config is None and config_dict is not None and "config" in config_dict:
         # Build a config object from to_dict of an ObjectStore.
         config = Bunch(**config_dict["config"])
     elif config is None:
-        raise Exception("build_object_store_from_config sent None as config parameter and one cannot be recovered from config_dict")
+        raise Exception(
+            "build_object_store_from_config sent None as config parameter and one cannot be recovered from config_dict"
+        )
 
     if config_xml is None and config_dict is None:
         config_file = config.object_store_config_file
@@ -1049,22 +1145,22 @@ def build_object_store_from_config(config, fsmon=False, config_xml=None, config_
                 # we have an object_store_conf.xml -- read the .xml and build
                 # accordingly
                 config_xml = parse_xml(config.object_store_config_file).getroot()
-                store = config_xml.get('type')
+                store = config_xml.get("type")
             else:
                 with open(config_file) as f:
                     config_dict = yaml.safe_load(f)
-                from_object = 'dict'
-                store = config_dict.get('type')
+                from_object = "dict"
+                store = config_dict.get("type")
         else:
             store = config.object_store
     elif config_xml is not None:
-        store = config_xml.get('type')
+        store = config_xml.get("type")
     elif config_dict is not None:
-        from_object = 'dict'
-        store = config_dict.get('type')
+        from_object = "dict"
+        store = config_dict.get("type")
 
     objectstore_class, objectstore_constructor_kwds = type_to_object_store_class(store, fsmon=fsmon)
-    if from_object == 'xml':
+    if from_object == "xml":
         return objectstore_class.from_xml(config=config, config_xml=config_xml, **objectstore_constructor_kwds)
     else:
         return objectstore_class(config=config, config_dict=config_dict, **objectstore_constructor_kwds)
@@ -1074,15 +1170,17 @@ def local_extra_dirs(func):
     """Non-local plugin decorator using local directories for the extra_dirs (job_work and temp)."""
 
     def wraps(self, *args, **kwargs):
-        if kwargs.get('base_dir', None) is None:
+        if kwargs.get("base_dir", None) is None:
             return func(self, *args, **kwargs)
         else:
             for c in self.__class__.__mro__:
-                if c.__name__ == 'DiskObjectStore':
+                if c.__name__ == "DiskObjectStore":
                     return getattr(c, func.__name__)(self, *args, **kwargs)
-            raise Exception("Could not call DiskObjectStore's %s method, does your "
-                            "Object Store plugin inherit from DiskObjectStore?"
-                            % func.__name__)
+            raise Exception(
+                "Could not call DiskObjectStore's %s method, does your "
+                "Object Store plugin inherit from DiskObjectStore?" % func.__name__
+            )
+
     return wraps
 
 
@@ -1094,37 +1192,36 @@ def convert_bytes(bytes):
 
     if bytes >= 1099511627776:
         terabytes = bytes / 1099511627776
-        size = f'{terabytes:.2f}TB'
+        size = f"{terabytes:.2f}TB"
     elif bytes >= 1073741824:
         gigabytes = bytes / 1073741824
-        size = f'{gigabytes:.2f}GB'
+        size = f"{gigabytes:.2f}GB"
     elif bytes >= 1048576:
         megabytes = bytes / 1048576
-        size = f'{megabytes:.2f}MB'
+        size = f"{megabytes:.2f}MB"
     elif bytes >= 1024:
         kilobytes = bytes / 1024
-        size = f'{kilobytes:.2f}KB'
+        size = f"{kilobytes:.2f}KB"
     else:
-        size = f'{bytes:.2f}b'
+        size = f"{bytes:.2f}b"
     return size
 
 
 def config_to_dict(config):
-    """Dict-ify the portion of a config object consumed by the ObjectStore class and its subclasses.
-    """
+    """Dict-ify the portion of a config object consumed by the ObjectStore class and its subclasses."""
     return {
-        'object_store_check_old_style': config.object_store_check_old_style,
-        'file_path': config.file_path,
-        'umask': config.umask,
-        'jobs_directory': config.jobs_directory,
-        'new_file_path': config.new_file_path,
-        'object_store_cache_path': config.object_store_cache_path,
-        'gid': config.gid,
+        "object_store_check_old_style": config.object_store_check_old_style,
+        "file_path": config.file_path,
+        "umask": config.umask,
+        "jobs_directory": config.jobs_directory,
+        "new_file_path": config.new_file_path,
+        "object_store_cache_path": config.object_store_cache_path,
+        "gid": config.gid,
     }
 
 
 class ObjectStorePopulator:
-    """ Small helper for interacting with the object store and making sure all
+    """Small helper for interacting with the object store and making sure all
     datasets from a job end up with the same object_store_id.
     """
 
@@ -1141,5 +1238,5 @@ class ObjectStorePopulator:
         try:
             self.object_store.create(data.dataset)
         except ObjectInvalid:
-            raise Exception('Unable to create output dataset: object store is full')
+            raise Exception("Unable to create output dataset: object store is full")
         self.object_store_id = data.dataset.object_store_id  # these will be the same thing after the first output
diff --git a/lib/galaxy/objectstore/azure_blob.py b/lib/galaxy/objectstore/azure_blob.py
index 51405dc4fa7..791e330c279 100644
--- a/lib/galaxy/objectstore/azure_blob.py
+++ b/lib/galaxy/objectstore/azure_blob.py
@@ -19,7 +19,7 @@ except ImportError:
 
 from galaxy.exceptions import (
     ObjectInvalid,
-    ObjectNotFound
+    ObjectNotFound,
 )
 from galaxy.util import (
     directory_hash_id,
@@ -33,48 +33,50 @@ from ..objectstore import (
     convert_bytes,
 )
 
-NO_BLOBSERVICE_ERROR_MESSAGE = ("ObjectStore configured, but no azure.storage.blob dependency available."
-                                "Please install and properly configure azure.storage.blob or modify Object Store configuration.")
+NO_BLOBSERVICE_ERROR_MESSAGE = (
+    "ObjectStore configured, but no azure.storage.blob dependency available."
+    "Please install and properly configure azure.storage.blob or modify Object Store configuration."
+)
 
 log = logging.getLogger(__name__)
 
 
 def parse_config_xml(config_xml):
     try:
-        auth_xml = config_xml.findall('auth')[0]
+        auth_xml = config_xml.findall("auth")[0]
 
-        account_name = auth_xml.get('account_name')
-        account_key = auth_xml.get('account_key')
+        account_name = auth_xml.get("account_name")
+        account_key = auth_xml.get("account_key")
 
-        container_xml = config_xml.find('container')
-        container_name = container_xml.get('name')
-        max_chunk_size = int(container_xml.get('max_chunk_size', 250))  # currently unused
+        container_xml = config_xml.find("container")
+        container_name = container_xml.get("name")
+        max_chunk_size = int(container_xml.get("max_chunk_size", 250))  # currently unused
 
-        c_xml = config_xml.findall('cache')[0]
-        cache_size = float(c_xml.get('size', -1))
-        staging_path = c_xml.get('path', None)
+        c_xml = config_xml.findall("cache")[0]
+        cache_size = float(c_xml.get("size", -1))
+        staging_path = c_xml.get("path", None)
 
-        tag, attrs = 'extra_dir', ('type', 'path')
+        tag, attrs = "extra_dir", ("type", "path")
         extra_dirs = config_xml.findall(tag)
         if not extra_dirs:
-            msg = f'No {tag} element in XML tree'
+            msg = f"No {tag} element in XML tree"
             log.error(msg)
             raise Exception(msg)
         extra_dirs = [{k: e.get(k) for k in attrs} for e in extra_dirs]
         return {
-            'auth': {
-                'account_name': account_name,
-                'account_key': account_key,
+            "auth": {
+                "account_name": account_name,
+                "account_key": account_key,
             },
-            'container': {
-                'name': container_name,
-                'max_chunk_size': max_chunk_size,
+            "container": {
+                "name": container_name,
+                "max_chunk_size": max_chunk_size,
             },
-            'cache': {
-                'size': cache_size,
-                'path': staging_path,
+            "cache": {
+                "size": cache_size,
+                "path": staging_path,
             },
-            'extra_dirs': extra_dirs,
+            "extra_dirs": extra_dirs,
         }
     except Exception:
         # Toss it back up after logging, we can't continue loading at this point.
@@ -88,7 +90,8 @@ class AzureBlobObjectStore(ConcreteObjectStore):
     cache exists that is used as an intermediate location for files between
     Galaxy and Azure.
     """
-    store_type = 'azure_blob'
+
+    store_type = "azure_blob"
 
     def __init__(self, config, config_dict):
         super().__init__(config, config_dict)
@@ -99,14 +102,14 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         container_dict = config_dict["container"]
         cache_dict = config_dict["cache"]
 
-        self.account_name = auth_dict.get('account_name')
-        self.account_key = auth_dict.get('account_key')
+        self.account_name = auth_dict.get("account_name")
+        self.account_key = auth_dict.get("account_key")
 
-        self.container_name = container_dict.get('name')
-        self.max_chunk_size = container_dict.get('max_chunk_size', 250)  # currently unused
+        self.container_name = container_dict.get("name")
+        self.max_chunk_size = container_dict.get("max_chunk_size", 250)  # currently unused
 
-        self.cache_size = cache_dict.get('size', -1)
-        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        self.cache_size = cache_dict.get("size", -1)
+        self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
 
         self._initialize()
 
@@ -128,20 +131,22 @@ class AzureBlobObjectStore(ConcreteObjectStore):
 
     def to_dict(self):
         as_dict = super().to_dict()
-        as_dict.update({
-            'auth': {
-                'account_name': self.account_name,
-                'account_key': self.account_key,
-            },
-            'container': {
-                'name': self.container_name,
-                'max_chunk_size': self.max_chunk_size,
-            },
-            'cache': {
-                'size': self.cache_size,
-                'path': self.staging_path,
+        as_dict.update(
+            {
+                "auth": {
+                    "account_name": self.account_name,
+                    "account_key": self.account_key,
+                },
+                "container": {
+                    "name": self.container_name,
+                    "max_chunk_size": self.max_chunk_size,
+                },
+                "cache": {
+                    "size": self.cache_size,
+                    "path": self.staging_path,
+                },
             }
-        })
+        )
         return as_dict
 
     ###################
@@ -158,17 +163,27 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         self.account = CloudStorageAccount(self.account_name, self.account_key)
         self.service = self.account.create_block_blob_service()
 
-    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+    def _construct_path(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        **kwargs,
+    ):
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning('extra_dir is not normalized: %s', extra_dir)
+            log.warning("extra_dir is not normalized: %s", extra_dir)
             raise ObjectInvalid("The requested object is invalid")
         # ensure that any parent directory references in alt_name would not
         # result in a path not contained in the directory path constructed here
         if alt_name:
             if not safe_relpath(alt_name):
-                log.warning('alt_name would locate path outside dir: %s', alt_name)
+                log.warning("alt_name would locate path outside dir: %s", alt_name)
                 raise ObjectInvalid("The requested object is invalid")
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
@@ -198,7 +213,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         return rel_path
 
     def _fix_permissions(self, rel_path):
-        """ Set permissions on rel_path"""
+        """Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
             umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
             for filename in files:
@@ -238,7 +253,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         return exists
 
     def _in_cache(self, rel_path):
-        """ Check if the given dataset is in the local cache. """
+        """Check if the given dataset is in the local cache."""
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
 
@@ -260,12 +275,18 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         try:
             log.debug("Pulling '%s' into cache to %s", rel_path, local_destination)
             if self.cache_size > 0 and self._get_size_in_azure(rel_path) > self.cache_size:
-                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
-                             rel_path, self._get_size_in_azure(rel_path), self.cache_size)
+                log.critical(
+                    "File %s is larger (%s) than the cache size (%s). Cannot download.",
+                    rel_path,
+                    self._get_size_in_azure(rel_path),
+                    self.cache_size,
+                )
                 return False
             else:
                 self.transfer_progress = 0  # Reset transfer progress counter
-                self.service.get_blob_to_path(self.container_name, rel_path, local_destination, progress_callback=self._transfer_cb)
+                self.service.get_blob_to_path(
+                    self.container_name, rel_path, local_destination, progress_callback=self._transfer_cb
+                )
                 return True
         except AzureHttpError:
             log.exception("Problem downloading '%s' from Azure", rel_path)
@@ -283,24 +304,44 @@ class AzureBlobObjectStore(ConcreteObjectStore):
             source_file = source_file or self._get_cache_path(rel_path)
 
             if not os.path.exists(source_file):
-                log.error("Tried updating blob '%s' from source file '%s', but source file does not exist.", rel_path, source_file)
+                log.error(
+                    "Tried updating blob '%s' from source file '%s', but source file does not exist.",
+                    rel_path,
+                    source_file,
+                )
                 return False
 
             if os.path.getsize(source_file) == 0:
-                log.debug("Wanted to push file '%s' to azure blob '%s' but its size is 0; skipping.", source_file, rel_path)
+                log.debug(
+                    "Wanted to push file '%s' to azure blob '%s' but its size is 0; skipping.", source_file, rel_path
+                )
                 return True
 
             if from_string:
-                self.service.create_blob_from_text(self.container_name, rel_path, from_string, progress_callback=self._transfer_cb)
+                self.service.create_blob_from_text(
+                    self.container_name, rel_path, from_string, progress_callback=self._transfer_cb
+                )
                 log.debug("Pushed data from string '%s' to blob '%s'", from_string, rel_path)
             else:
                 start_time = datetime.now()
-                log.debug("Pushing cache file '%s' of size %s bytes to '%s'", source_file, os.path.getsize(source_file), rel_path)
+                log.debug(
+                    "Pushing cache file '%s' of size %s bytes to '%s'",
+                    source_file,
+                    os.path.getsize(source_file),
+                    rel_path,
+                )
                 self.transfer_progress = 0  # Reset transfer progress counter
-                self.service.create_blob_from_path(self.container_name, rel_path, source_file, progress_callback=self._transfer_cb)
+                self.service.create_blob_from_path(
+                    self.container_name, rel_path, source_file, progress_callback=self._transfer_cb
+                )
                 end_time = datetime.now()
-                log.debug("Pushed cache file '%s' to blob '%s' (%s bytes transfered in %s sec)",
-                          source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
+                log.debug(
+                    "Pushed cache file '%s' to blob '%s' (%s bytes transfered in %s sec)",
+                    source_file,
+                    rel_path,
+                    os.path.getsize(source_file),
+                    end_time - start_time,
+                )
             return True
 
         except AzureHttpError:
@@ -319,8 +360,8 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         in_azure = self._in_azure(rel_path)
         # log.debug("~~~~~~ File '%s' exists in cache: %s; in azure: %s" % (rel_path, in_cache, in_azure))
         # dir_only does not get synced so shortcut the decision
-        dir_only = kwargs.get('dir_only', False)
-        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get("dir_only", False)
+        base_dir = kwargs.get("base_dir", None)
         if dir_only:
             if in_cache or in_azure:
                 return True
@@ -363,10 +404,10 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
-            extra_dir = kwargs.get('extra_dir', None)
-            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
-            dir_only = kwargs.get('dir_only', False)
-            alt_name = kwargs.get('alt_name', None)
+            extra_dir = kwargs.get("extra_dir", None)
+            extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+            dir_only = kwargs.get("dir_only", False)
+            alt_name = kwargs.get("alt_name", None)
 
             # Construct hashed path
             rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
@@ -391,14 +432,14 @@ class AzureBlobObjectStore(ConcreteObjectStore):
             # If instructed, create the dataset in cache & in S3
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
-                open(os.path.join(self.staging_path, rel_path), 'w').close()
-                self._push_to_os(rel_path, from_string='')
+                open(os.path.join(self.staging_path, rel_path), "w").close()
+                self._push_to_os(rel_path, from_string="")
 
     def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound(f'objectstore.empty, object does not exist: {str(obj)}, kwargs: {str(kwargs)}')
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {str(obj)}, kwargs: {str(kwargs)}")
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -414,10 +455,10 @@ class AzureBlobObjectStore(ConcreteObjectStore):
 
     def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
-        extra_dir = kwargs.get('extra_dir', None)
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        extra_dir = kwargs.get("extra_dir", None)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         try:
             if base_dir and dir_only and obj_dir:
                 # Remove temporary data in JOB_WORK directory
@@ -446,7 +487,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         except AzureHttpError:
             log.exception("Could not delete blob '%s' from Azure", rel_path)
         except OSError:
-            log.exception('%s delete error', self._get_filename(obj, **kwargs))
+            log.exception("%s delete error", self._get_filename(obj, **kwargs))
         return False
 
     def _get_data(self, obj, start=0, count=-1, **kwargs):
@@ -463,9 +504,9 @@ class AzureBlobObjectStore(ConcreteObjectStore):
 
     def _get_filename(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
 
         # for JOB_WORK directory
         if base_dir and dir_only and obj_dir:
@@ -494,7 +535,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound(f'objectstore.get_filename, no cache_path: {str(obj)}, kwargs: {str(kwargs)}')
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {str(obj)}, kwargs: {str(kwargs)}")
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create is True:
@@ -519,7 +560,9 @@ class AzureBlobObjectStore(ConcreteObjectStore):
             self._push_to_os(rel_path, source_file)
 
         else:
-            raise ObjectNotFound(f'objectstore.update_from_file, object does not exist: {str(obj)}, kwargs: {str(kwargs)}')
+            raise ObjectNotFound(
+                f"objectstore.update_from_file, object does not exist: {str(obj)}, kwargs: {str(kwargs)}"
+            )
 
     def _get_object_url(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
@@ -559,8 +602,11 @@ class AzureBlobObjectStore(ConcreteObjectStore):
             # Initiate cleaning once within 10% of the defined cache size?
             cache_limit = self.cache_size * 0.9
             if total_size > cache_limit:
-                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
-                         convert_bytes(total_size), convert_bytes(cache_limit))
+                log.info(
+                    "Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
+                    convert_bytes(total_size),
+                    convert_bytes(cache_limit),
+                )
                 # How much to delete? If simply deleting up to the cache-10% limit,
                 # is likely to be deleting frequently and may run the risk of hitting
                 # the limit - maybe delete additional #%?
diff --git a/lib/galaxy/objectstore/cloud.py b/lib/galaxy/objectstore/cloud.py
index 920f42d315e..d13cc390676 100644
--- a/lib/galaxy/objectstore/cloud.py
+++ b/lib/galaxy/objectstore/cloud.py
@@ -12,7 +12,10 @@ import threading
 import time
 from datetime import datetime
 
-from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.exceptions import (
+    ObjectInvalid,
+    ObjectNotFound,
+)
 from galaxy.util import (
     directory_hash_id,
     safe_relpath,
@@ -21,9 +24,16 @@ from galaxy.util import (
 )
 from galaxy.util.sleeper import Sleeper
 from .s3 import parse_config_xml
-from ..objectstore import ConcreteObjectStore, convert_bytes
+from ..objectstore import (
+    ConcreteObjectStore,
+    convert_bytes,
+)
+
 try:
-    from cloudbridge.factory import CloudProviderFactory, ProviderList
+    from cloudbridge.factory import (
+        CloudProviderFactory,
+        ProviderList,
+    )
     from cloudbridge.interfaces.exceptions import InvalidNameException
 except ImportError:
     CloudProviderFactory = None
@@ -38,7 +48,6 @@ NO_CLOUDBRIDGE_ERROR_MESSAGE = (
 
 
 class CloudConfigMixin:
-
     def _config_to_dict(self):
         return {
             "provider": self.provider,
@@ -58,7 +67,7 @@ class CloudConfigMixin:
                 "size": self.cache_size,
                 "path": self.staging_path,
             },
-            'enable_cache_monitor': False,
+            "enable_cache_monitor": False,
         }
 
 
@@ -68,31 +77,32 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
     cache exists that is used as an intermediate location for files between
     Galaxy and the cloud storage.
     """
-    store_type = 'cloud'
+
+    store_type = "cloud"
 
     def __init__(self, config, config_dict):
         super().__init__(config, config_dict)
         self.transfer_progress = 0
 
-        bucket_dict = config_dict['bucket']
-        connection_dict = config_dict.get('connection', {})
-        cache_dict = config_dict['cache']
-        self.enable_cache_monitor = config_dict.get('enable_cache_monitor', True)
+        bucket_dict = config_dict["bucket"]
+        connection_dict = config_dict.get("connection", {})
+        cache_dict = config_dict["cache"]
+        self.enable_cache_monitor = config_dict.get("enable_cache_monitor", True)
 
         self.provider = config_dict["provider"]
         self.credentials = config_dict["auth"]
-        self.bucket_name = bucket_dict.get('name')
-        self.use_rr = bucket_dict.get('use_reduced_redundancy', False)
-        self.max_chunk_size = bucket_dict.get('max_chunk_size', 250)
+        self.bucket_name = bucket_dict.get("name")
+        self.use_rr = bucket_dict.get("use_reduced_redundancy", False)
+        self.max_chunk_size = bucket_dict.get("max_chunk_size", 250)
 
-        self.host = connection_dict.get('host', None)
-        self.port = connection_dict.get('port', 6000)
-        self.multipart = connection_dict.get('multipart', True)
-        self.is_secure = connection_dict.get('is_secure', True)
-        self.conn_path = connection_dict.get('conn_path', '/')
+        self.host = connection_dict.get("host", None)
+        self.port = connection_dict.get("port", 6000)
+        self.multipart = connection_dict.get("multipart", True)
+        self.is_secure = connection_dict.get("is_secure", True)
+        self.conn_path = connection_dict.get("conn_path", "/")
 
-        self.cache_size = cache_dict.get('size', -1)
-        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        self.cache_size = cache_dict.get("size", -1)
+        self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
 
         self._initialize()
 
@@ -105,7 +115,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         self.start_cache_monitor()
         # Test if 'axel' is available for parallel download and pull the key into cache
         try:
-            subprocess.call('axel')
+            subprocess.call("axel")
             self.use_axel = True
         except OSError:
             self.use_axel = False
@@ -125,14 +135,15 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
     def _get_connection(provider, credentials):
         log.debug(f"Configuring `{provider}` Connection")
         if provider == "aws":
-            config = {"aws_access_key": credentials["access_key"],
-                      "aws_secret_key": credentials["secret_key"]}
+            config = {"aws_access_key": credentials["access_key"], "aws_secret_key": credentials["secret_key"]}
             connection = CloudProviderFactory().create_provider(ProviderList.AWS, config)
         elif provider == "azure":
-            config = {"azure_subscription_id": credentials["subscription_id"],
-                      "azure_client_id": credentials["client_id"],
-                      "azure_secret": credentials["secret"],
-                      "azure_tenant": credentials["tenant"]}
+            config = {
+                "azure_subscription_id": credentials["subscription_id"],
+                "azure_client_id": credentials["client_id"],
+                "azure_secret": credentials["secret"],
+                "azure_tenant": credentials["tenant"],
+            }
             connection = CloudProviderFactory().create_provider(ProviderList.AZURE, config)
         elif provider == "google":
             config = {"gcp_service_creds_file": credentials["credentials_file"]}
@@ -193,9 +204,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                 akey = auth_element.get("access_key")
                 skey = auth_element.get("secret_key")
 
-                config["auth"] = {
-                    "access_key": akey,
-                    "secret_key": skey}
+                config["auth"] = {"access_key": akey, "secret_key": skey}
             elif provider == "azure":
                 sid = auth_element.get("subscription_id")
                 if sid is None:
@@ -209,11 +218,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                 ten = auth_element.get("tenant")
                 if ten is None:
                     missing_config.append("tenant")
-                config["auth"] = {
-                    "subscription_id": sid,
-                    "client_id": cid,
-                    "secret": sec,
-                    "tenant": ten}
+                config["auth"] = {"subscription_id": sid, "client_id": cid, "secret": sec, "tenant": ten}
             elif provider == "google":
                 cre = auth_element.get("credentials_file")
                 if not os.path.isfile(cre):
@@ -222,16 +227,16 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                     raise OSError(msg)
                 if cre is None:
                     missing_config.append("credentials_file")
-                config["auth"] = {
-                    "credentials_file": cre}
+                config["auth"] = {"credentials_file": cre}
             else:
                 msg = f"Unsupported provider `{provider}`."
                 log.error(msg)
                 raise Exception(msg)
 
             if len(missing_config) > 0:
-                msg = "The following configuration required for {} cloud backend " \
-                      "are missing: {}".format(provider, missing_config)
+                msg = "The following configuration required for {} cloud backend " "are missing: {}".format(
+                    provider, missing_config
+                )
                 log.error(msg)
                 raise Exception(msg)
             else:
@@ -266,8 +271,11 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             # Initiate cleaning once within 10% of the defined cache size?
             cache_limit = self.cache_size * 0.9
             if total_size > cache_limit:
-                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
-                         convert_bytes(total_size), convert_bytes(cache_limit))
+                log.info(
+                    "Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
+                    convert_bytes(total_size),
+                    convert_bytes(cache_limit),
+                )
                 # How much to delete? If simply deleting up to the cache-10% limit,
                 # is likely to be deleting frequently and may run the risk of hitting
                 # the limit - maybe delete additional #%?
@@ -277,7 +285,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             self.sleeper.sleep(30)  # Test cache size every 30 seconds?
 
     def __clean_cache(self, file_list, delete_this_much):
-        """ Keep deleting files from the file_list until the size of the deleted
+        """Keep deleting files from the file_list until the size of the deleted
         files is greater than the value in delete_this_much parameter.
 
         :type file_list: list
@@ -327,7 +335,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         raise Exception
 
     def _fix_permissions(self, rel_path):
-        """ Set permissions on rel_path"""
+        """Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
             umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
             for filename in files:
@@ -337,18 +345,27 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                     continue
                 umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
 
-    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None,
-                        obj_dir=False, **kwargs):
+    def _construct_path(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        **kwargs,
+    ):
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning('extra_dir is not normalized: %s', extra_dir)
+            log.warning("extra_dir is not normalized: %s", extra_dir)
             raise ObjectInvalid("The requested object is invalid")
         # ensure that any parent directory references in alt_name would not
         # result in a path not contained in the directory path constructed here
         if alt_name:
             if not safe_relpath(alt_name):
-                log.warning('alt_name would locate path outside dir: %s', alt_name)
+                log.warning("alt_name would locate path outside dir: %s", alt_name)
                 raise ObjectInvalid("The requested object is invalid")
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
@@ -368,7 +385,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             return os.path.join(base, rel_path)
 
         # S3 folders are marked by having trailing '/' so add it now
-        rel_path = f'{rel_path}/'
+        rel_path = f"{rel_path}/"
 
         if not dir_only:
             rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
@@ -393,7 +410,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         exists = False
         try:
             # A hackish way of testing if the rel_path is a folder vs a file
-            is_dir = rel_path[-1] == '/'
+            is_dir = rel_path[-1] == "/"
             if is_dir:
                 keyresult = self.bucket.objects.list(prefix=rel_path)
                 if len(keyresult) > 0:
@@ -408,7 +425,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         return exists
 
     def _in_cache(self, rel_path):
-        """ Check if the given dataset is in the local cache and return True if so. """
+        """Check if the given dataset is in the local cache and return True if so."""
         # log.debug("------ Checking cache for rel_path %s" % rel_path)
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
@@ -432,8 +449,12 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             key = self.bucket.objects.get(rel_path)
             # Test if cache is large enough to hold the new file
             if self.cache_size > 0 and key.size > self.cache_size:
-                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
-                             rel_path, key.size, self.cache_size)
+                log.critical(
+                    "File %s is larger (%s) than the cache size (%s). Cannot download.",
+                    rel_path,
+                    key.size,
+                    self.cache_size,
+                )
                 return False
             if self.use_axel:
                 log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
@@ -464,8 +485,9 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             source_file = source_file if source_file else self._get_cache_path(rel_path)
             if os.path.exists(source_file):
                 if os.path.getsize(source_file) == 0 and (self.bucket.objects.get(rel_path) is not None):
-                    log.debug("Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file,
-                              rel_path)
+                    log.debug(
+                        "Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path
+                    )
                     return True
                 if from_string:
                     if not self.bucket.objects.get(rel_path):
@@ -476,8 +498,12 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                     log.debug("Pushed data from string '%s' to key '%s'", from_string, rel_path)
                 else:
                     start_time = datetime.now()
-                    log.debug("Pushing cache file '%s' of size %s bytes to key '%s'", source_file,
-                              os.path.getsize(source_file), rel_path)
+                    log.debug(
+                        "Pushing cache file '%s' of size %s bytes to key '%s'",
+                        source_file,
+                        os.path.getsize(source_file),
+                        rel_path,
+                    )
                     self.transfer_progress = 0  # Reset transfer progress counter
                     if not self.bucket.objects.get(rel_path):
                         created_obj = self.bucket.objects.create(rel_path)
@@ -486,12 +512,20 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                         self.bucket.objects.get(rel_path).upload_from_file(source_file)
 
                     end_time = datetime.now()
-                    log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
-                              source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
+                    log.debug(
+                        "Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
+                        source_file,
+                        rel_path,
+                        os.path.getsize(source_file),
+                        end_time - start_time,
+                    )
                 return True
             else:
-                log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
-                          rel_path, source_file)
+                log.error(
+                    "Tried updating key '%s' from source file '%s', but source file does not exist.",
+                    rel_path,
+                    source_file,
+                )
         except Exception:
             log.exception("Trouble pushing S3 key '%s' from file '%s'", rel_path, source_file)
         return False
@@ -506,8 +540,12 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_cloud(rel_path):
                 return True
-            log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
-                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_cloud(rel_path))
+            log.debug(
+                "Waiting for dataset %s to transfer from OS: %s/%s",
+                rel_path,
+                os.path.getsize(self._get_cache_path(rel_path)),
+                self._get_size_in_cloud(rel_path),
+            )
         return False
 
     def _exists(self, obj, **kwargs):
@@ -521,8 +559,8 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         in_cloud = self._key_exists(rel_path)
         # log.debug("~~~~~~ File '%s' exists in cache: %s; in s3: %s" % (rel_path, in_cache, in_s3))
         # dir_only does not get synced so shortcut the decision
-        dir_only = kwargs.get('dir_only', False)
-        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get("dir_only", False)
+        base_dir = kwargs.get("base_dir", None)
         if dir_only:
             if in_cache or in_cloud:
                 return True
@@ -547,10 +585,10 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
-            extra_dir = kwargs.get('extra_dir', None)
-            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
-            dir_only = kwargs.get('dir_only', False)
-            alt_name = kwargs.get('alt_name', None)
+            extra_dir = kwargs.get("extra_dir", None)
+            extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+            dir_only = kwargs.get("dir_only", False)
+            alt_name = kwargs.get("alt_name", None)
 
             # Construct hashed path
             rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
@@ -569,15 +607,14 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
 
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
-                open(os.path.join(self.staging_path, rel_path), 'w').close()
-                self._push_to_os(rel_path, from_string='')
+                open(os.path.join(self.staging_path, rel_path), "w").close()
+                self._push_to_os(rel_path, from_string="")
 
     def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
-                                 % (str(obj), str(kwargs)))
+            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -593,10 +630,10 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
 
     def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
-        extra_dir = kwargs.get('extra_dir', None)
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        extra_dir = kwargs.get("extra_dir", None)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         try:
             # Remove temparory data in JOB_WORK directory
             if base_dir and dir_only and obj_dir:
@@ -626,7 +663,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         except Exception:
             log.exception("Could not delete key '%s' from cloud", rel_path)
         except OSError:
-            log.exception('%s delete error', self._get_filename(obj, **kwargs))
+            log.exception("%s delete error", self._get_filename(obj, **kwargs))
         return False
 
     def _get_data(self, obj, start=0, count=-1, **kwargs):
@@ -642,9 +679,9 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         return content
 
     def _get_filename(self, obj, **kwargs):
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         rel_path = self._construct_path(obj, **kwargs)
 
         # for JOB_WORK directory
@@ -674,8 +711,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s'
-                             % (str(obj), str(kwargs)))
+        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -700,8 +736,9 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             # Update the file on cloud
             self._push_to_os(rel_path, source_file)
         else:
-            raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
-                                 % (str(obj), str(kwargs)))
+            raise ObjectNotFound(
+                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
+            )
 
     def _get_object_url(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
@@ -718,7 +755,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
 
     def shutdown(self):
         self.running = False
-        thread = getattr(self, 'cache_monitor_thread', None)
+        thread = getattr(self, "cache_monitor_thread", None)
         if thread:
             log.debug("Shutting down thread")
             self.sleeper.wake()
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 57cf93c082f..f5cb3955fce 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -10,13 +10,18 @@ from pathlib import Path
 try:
     import irods
     import irods.keywords as kw
-    from irods.exception import CollectionDoesNotExist
-    from irods.exception import DataObjectDoesNotExist
+    from irods.exception import (
+        CollectionDoesNotExist,
+        DataObjectDoesNotExist,
+    )
     from irods.session import iRODSSession
 except ImportError:
     irods = None
 
-from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.exceptions import (
+    ObjectInvalid,
+    ObjectNotFound,
+)
 from galaxy.util import (
     directory_hash_id,
     ExecutionTimer,
@@ -26,82 +31,82 @@ from galaxy.util import (
 from galaxy.util.path import safe_relpath
 from ..objectstore import DiskObjectStore
 
-IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
+IRODS_IMPORT_MESSAGE = "The Python irods package is required to use this feature, please install it"
 # 1 MB
 CHUNK_SIZE = 2**20
 log = logging.getLogger(__name__)
 
 
 def _config_xml_error(tag):
-    msg = f'No {tag} element in config XML tree'
+    msg = f"No {tag} element in config XML tree"
     raise Exception(msg)
 
 
 def _config_dict_error(key):
-    msg = 'No {key} key in config dictionary'.forma(key=key)
+    msg = "No {key} key in config dictionary".forma(key=key)
     raise Exception(msg)
 
 
 def parse_config_xml(config_xml):
     try:
-        a_xml = config_xml.findall('auth')
+        a_xml = config_xml.findall("auth")
         if not a_xml:
-            _config_xml_error('auth')
-        username = a_xml[0].get('username')
-        password = a_xml[0].get('password')
+            _config_xml_error("auth")
+        username = a_xml[0].get("username")
+        password = a_xml[0].get("password")
 
-        r_xml = config_xml.findall('resource')
+        r_xml = config_xml.findall("resource")
         if not r_xml:
-            _config_xml_error('resource')
-        resource_name = r_xml[0].get('name')
+            _config_xml_error("resource")
+        resource_name = r_xml[0].get("name")
 
-        z_xml = config_xml.findall('zone')
+        z_xml = config_xml.findall("zone")
         if not z_xml:
-            _config_xml_error('zone')
-        zone_name = z_xml[0].get('name')
+            _config_xml_error("zone")
+        zone_name = z_xml[0].get("name")
 
-        c_xml = config_xml.findall('connection')
+        c_xml = config_xml.findall("connection")
         if not c_xml:
-            _config_xml_error('connection')
-        host = c_xml[0].get('host', None)
-        port = int(c_xml[0].get('port', 0))
-        timeout = int(c_xml[0].get('timeout', 30))
-        refresh_time = int(c_xml[0].get('refresh_time', 300))
+            _config_xml_error("connection")
+        host = c_xml[0].get("host", None)
+        port = int(c_xml[0].get("port", 0))
+        timeout = int(c_xml[0].get("timeout", 30))
+        refresh_time = int(c_xml[0].get("refresh_time", 300))
 
-        c_xml = config_xml.findall('cache')
+        c_xml = config_xml.findall("cache")
         if not c_xml:
-            _config_xml_error('cache')
-        cache_size = float(c_xml[0].get('size', -1))
-        staging_path = c_xml[0].get('path', None)
+            _config_xml_error("cache")
+        cache_size = float(c_xml[0].get("size", -1))
+        staging_path = c_xml[0].get("path", None)
 
-        attrs = ('type', 'path')
-        e_xml = config_xml.findall('extra_dir')
+        attrs = ("type", "path")
+        e_xml = config_xml.findall("extra_dir")
         if not e_xml:
-            _config_xml_error('extra_dir')
+            _config_xml_error("extra_dir")
         extra_dirs = [{k: e.get(k) for k in attrs} for e in e_xml]
 
         return {
-            'auth': {
-                'username': username,
-                'password': password,
+            "auth": {
+                "username": username,
+                "password": password,
             },
-            'resource': {
-                'name': resource_name,
+            "resource": {
+                "name": resource_name,
             },
-            'zone': {
-                'name': zone_name,
+            "zone": {
+                "name": zone_name,
             },
-            'connection': {
-                'host': host,
-                'port': port,
-                'timeout': timeout,
-                'refresh_time': refresh_time,
+            "connection": {
+                "host": host,
+                "port": port,
+                "timeout": timeout,
+                "refresh_time": refresh_time,
             },
-            'cache': {
-                'size': cache_size,
-                'path': staging_path,
+            "cache": {
+                "size": cache_size,
+                "path": staging_path,
             },
-            'extra_dirs': extra_dirs,
+            "extra_dirs": extra_dirs,
         }
     except Exception:
         # Toss it back up after logging, we can't continue loading at this point.
@@ -110,29 +115,28 @@ def parse_config_xml(config_xml):
 
 
 class CloudConfigMixin:
-
     def _config_to_dict(self):
         return {
-            'auth': {
-                'username': self.username,
-                'password': self.password,
+            "auth": {
+                "username": self.username,
+                "password": self.password,
             },
-            'resource': {
-                'name': self.resource,
+            "resource": {
+                "name": self.resource,
             },
-            'zone': {
-                'name': self.zone,
+            "zone": {
+                "name": self.zone,
             },
-            'connection': {
-                'host': self.host,
-                'port': self.port,
-                'timeout': self.timeout,
-                'refresh_time': self.refresh_time,
+            "connection": {
+                "host": self.host,
+                "port": self.port,
+                "timeout": self.timeout,
+                "refresh_time": self.refresh_time,
+            },
+            "cache": {
+                "size": self.cache_size,
+                "path": self.staging_path,
             },
-            'cache': {
-                'size': self.cache_size,
-                'path': self.staging_path,
-            }
         }
 
 
@@ -142,66 +146,66 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     exists that is used as an intermediate location for files between Galaxy and iRODS.
     """
 
-    store_type = 'irods'
+    store_type = "irods"
 
     def __init__(self, config, config_dict):
         ipt_timer = ExecutionTimer()
         super().__init__(config, config_dict)
 
-        auth_dict = config_dict.get('auth')
+        auth_dict = config_dict.get("auth")
         if auth_dict is None:
-            _config_dict_error('auth')
+            _config_dict_error("auth")
 
-        self.username = auth_dict.get('username')
+        self.username = auth_dict.get("username")
         if self.username is None:
-            _config_dict_error('auth->username')
-        self.password = auth_dict.get('password')
+            _config_dict_error("auth->username")
+        self.password = auth_dict.get("password")
         if self.password is None:
-            _config_dict_error('auth->password')
+            _config_dict_error("auth->password")
 
-        resource_dict = config_dict['resource']
+        resource_dict = config_dict["resource"]
         if resource_dict is None:
-            _config_dict_error('resource')
-        self.resource = resource_dict.get('name')
+            _config_dict_error("resource")
+        self.resource = resource_dict.get("name")
         if self.resource is None:
-            _config_dict_error('resource->name')
+            _config_dict_error("resource->name")
 
-        zone_dict = config_dict['zone']
+        zone_dict = config_dict["zone"]
         if zone_dict is None:
-            _config_dict_error('zone')
-        self.zone = zone_dict.get('name')
+            _config_dict_error("zone")
+        self.zone = zone_dict.get("name")
         if self.zone is None:
-            _config_dict_error('zone->name')
+            _config_dict_error("zone->name")
 
-        connection_dict = config_dict['connection']
+        connection_dict = config_dict["connection"]
         if connection_dict is None:
-            _config_dict_error('connection')
-        self.host = connection_dict.get('host')
+            _config_dict_error("connection")
+        self.host = connection_dict.get("host")
         if self.host is None:
-            _config_dict_error('connection->host')
-        self.port = connection_dict.get('port')
+            _config_dict_error("connection->host")
+        self.port = connection_dict.get("port")
         if self.port is None:
-            _config_dict_error('connection->port')
-        self.timeout = connection_dict.get('timeout')
+            _config_dict_error("connection->port")
+        self.timeout = connection_dict.get("timeout")
         if self.timeout is None:
-            _config_dict_error('connection->timeout')
-        self.refresh_time = connection_dict.get('refresh_time')
+            _config_dict_error("connection->timeout")
+        self.refresh_time = connection_dict.get("refresh_time")
         if self.refresh_time is None:
-            _config_dict_error('connection->refresh_time')
+            _config_dict_error("connection->refresh_time")
 
-        cache_dict = config_dict['cache']
+        cache_dict = config_dict["cache"]
         if cache_dict is None:
-            _config_dict_error('cache')
-        self.cache_size = cache_dict.get('size', -1)
+            _config_dict_error("cache")
+        self.cache_size = cache_dict.get("size", -1)
         if self.cache_size is None:
-            _config_dict_error('cache->size')
-        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+            _config_dict_error("cache->size")
+        self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
         if self.staging_path is None:
-            _config_dict_error('cache->path')
+            _config_dict_error("cache->path")
 
-        extra_dirs = {e['type']: e['path'] for e in config_dict.get('extra_dirs', [])}
+        extra_dirs = {e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])}
         if not extra_dirs:
-            _config_dict_error('extra_dirs')
+            _config_dict_error("extra_dirs")
         self.extra_dirs.update(extra_dirs)
 
         if irods is None:
@@ -212,7 +216,14 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         if irods is None:
             raise Exception(IRODS_IMPORT_MESSAGE)
 
-        self.session = iRODSSession(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone, refresh_time=self.refresh_time)
+        self.session = iRODSSession(
+            host=self.host,
+            port=self.port,
+            user=self.username,
+            password=self.password,
+            zone=self.zone,
+            refresh_time=self.refresh_time,
+        )
         # Set connection timeout
         self.session.connection_timeout = self.timeout
         log.debug("irods_pt __init__: %s", ipt_timer)
@@ -237,7 +248,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         return as_dict
 
     def _fix_permissions(self, rel_path):
-        """ Set permissions on rel_path"""
+        """Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
             umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
             for filename in files:
@@ -247,18 +258,28 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                     continue
                 umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
 
-    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+    def _construct_path(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        **kwargs,
+    ):
         ipt_timer = ExecutionTimer()
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenanigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning('extra_dir is not normalized: %s', extra_dir)
+            log.warning("extra_dir is not normalized: %s", extra_dir)
             raise ObjectInvalid("The requested object is invalid")
         # ensure that any parent directory references in alt_name would not
         # result in a path not contained in the directory path constructed here
         if alt_name:
             if not safe_relpath(alt_name):
-                log.warning('alt_name would locate path outside dir: %s', alt_name)
+                log.warning("alt_name would locate path outside dir: %s", alt_name)
                 raise ObjectInvalid("The requested object is invalid")
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
@@ -327,7 +348,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             log.debug("irods_pt _data_object_exists: %s", ipt_timer)
 
     def _in_cache(self, rel_path):
-        """ Check if the given dataset is in the local cache and return True if so. """
+        """Check if the given dataset is in the local cache and return True if so."""
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
 
@@ -381,10 +402,12 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         subcollection_name = p.parent
 
         source_file = source_file if source_file else self._get_cache_path(rel_path)
-        options = {kw.FORCE_FLAG_KW: '', kw.DEST_RESC_NAME_KW: self.resource}
+        options = {kw.FORCE_FLAG_KW: "", kw.DEST_RESC_NAME_KW: self.resource}
 
         if not os.path.exists(source_file):
-            log.error("Tried updating key '%s' from source file '%s', but source file does not exist.", rel_path, source_file)
+            log.error(
+                "Tried updating key '%s' from source file '%s', but source file does not exist.", rel_path, source_file
+            )
             return False
 
         # Check if the data object exists in iRODS
@@ -396,7 +419,11 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             exists = self.session.data_objects.exists(data_object_path)
 
             if os.path.getsize(source_file) == 0 and exists:
-                log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
+                log.debug(
+                    "Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.",
+                    source_file,
+                    rel_path,
+                )
                 return True
 
             # Create sub-collection first
@@ -407,7 +434,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                 data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
 
                 # Save 'from_string' as a file
-                with data_obj.open('w') as data_obj_fp:
+                with data_obj.open("w") as data_obj_fp:
                     data_obj_fp.write(from_string)
 
                 # Add file containing 'from_string' to the irods collection, since
@@ -417,14 +444,24 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                 log.debug("Pushed data from string '%s' to collection '%s'", from_string, data_object_path)
             else:
                 start_time = datetime.now()
-                log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
+                log.debug(
+                    "Pushing cache file '%s' of size %s bytes to collection '%s'",
+                    source_file,
+                    os.path.getsize(source_file),
+                    rel_path,
+                )
 
                 # Add the source file to the irods collection
                 self.session.data_objects.put(source_file, data_object_path, **options)
 
                 end_time = datetime.now()
-                log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
-                        source_file, rel_path, os.path.getsize(source_file), (end_time - start_time).total_seconds())
+                log.debug(
+                    "Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
+                    source_file,
+                    rel_path,
+                    os.path.getsize(source_file),
+                    (end_time - start_time).total_seconds(),
+                )
             return True
         finally:
             log.debug("irods_pt _push_to_irods: %s", ipt_timer)
@@ -441,8 +478,12 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_irods(rel_path):
                 log.debug("irods_pt _file_ready: %s", ipt_timer)
                 return True
-            log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
-                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_irods(rel_path))
+            log.debug(
+                "Waiting for dataset %s to transfer from OS: %s/%s",
+                rel_path,
+                os.path.getsize(self._get_cache_path(rel_path)),
+                self._get_size_in_irods(rel_path),
+            )
         log.debug("irods_pt _file_ready: %s", ipt_timer)
         return False
 
@@ -456,8 +497,8 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             return True
 
         # dir_only does not get synced so shortcut the decision
-        dir_only = kwargs.get('dir_only', False)
-        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get("dir_only", False)
+        base_dir = kwargs.get("base_dir", None)
         if dir_only and base_dir:
             # for JOB_WORK directory
             if not os.path.exists(rel_path):
@@ -471,10 +512,10 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         ipt_timer = ExecutionTimer()
         if not self._exists(obj, **kwargs):
             # Pull out locally used fields
-            extra_dir = kwargs.get('extra_dir', None)
-            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
-            dir_only = kwargs.get('dir_only', False)
-            alt_name = kwargs.get('alt_name', None)
+            extra_dir = kwargs.get("extra_dir", None)
+            extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+            dir_only = kwargs.get("dir_only", False)
+            alt_name = kwargs.get("alt_name", None)
 
             # Construct hashed path
             rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
@@ -493,16 +534,15 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
 
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
-                open(os.path.join(self.staging_path, rel_path), 'w').close()
-                self._push_to_irods(rel_path, from_string='')
+                open(os.path.join(self.staging_path, rel_path), "w").close()
+                self._push_to_irods(rel_path, from_string="")
         log.debug("irods_pt _create: %s", ipt_timer)
 
     def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
-                                 % (str(obj), str(kwargs)))
+            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
 
     def _size(self, obj, **kwargs):
         ipt_timer = ExecutionTimer()
@@ -524,10 +564,10 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
     def _delete(self, obj, entire_dir=False, **kwargs):
         ipt_timer = ExecutionTimer()
         rel_path = self._construct_path(obj, **kwargs)
-        extra_dir = kwargs.get('extra_dir', None)
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        extra_dir = kwargs.get("extra_dir", None)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
 
         options = {kw.DEST_RESC_NAME_KW: self.resource}
 
@@ -584,7 +624,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                     log.info("Collection or data object (%s) does not exist", data_object_path)
                     return True
         except OSError:
-            log.exception('%s delete error', self._get_filename(obj, **kwargs))
+            log.exception("%s delete error", self._get_filename(obj, **kwargs))
         finally:
             log.debug("irods_pt _delete: %s", ipt_timer)
         return False
@@ -605,9 +645,9 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
 
     def _get_filename(self, obj, **kwargs):
         ipt_timer = ExecutionTimer()
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         rel_path = self._construct_path(obj, **kwargs)
 
         # for JOB_WORK directory
@@ -642,8 +682,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         # if dir_only:
         #     return cache_path
         log.debug("irods_pt _get_filename: %s", ipt_timer)
-        raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s'
-                             % (str(obj), str(kwargs)))
+        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -670,8 +709,9 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             self._push_to_irods(rel_path, source_file)
         else:
             log.debug("irods_pt _update_from_file: %s", ipt_timer)
-            raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
-                                 % (str(obj), str(kwargs)))
+            raise ObjectNotFound(
+                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
+            )
         log.debug("irods_pt _update_from_file: %s", ipt_timer)
 
     # Unlike S3, url is not really applicable to iRODS
diff --git a/lib/galaxy/objectstore/pithos.py b/lib/galaxy/objectstore/pithos.py
index 501e21afd17..88a0f9ff8aa 100644
--- a/lib/galaxy/objectstore/pithos.py
+++ b/lib/galaxy/objectstore/pithos.py
@@ -7,19 +7,19 @@ import os
 import shutil
 
 try:
+    from kamaki.clients import astakos
+    from kamaki.clients import Client as KamakiClient
     from kamaki.clients import (
-        astakos,
-        Client as KamakiClient,
         ClientError,
         pithos,
-        utils
+        utils,
     )
 except ImportError:
     KamakiClient = None
 
 from galaxy.exceptions import (
     ObjectInvalid,
-    ObjectNotFound
+    ObjectNotFound,
 )
 from galaxy.util import (
     directory_hash_id,
@@ -31,7 +31,8 @@ from ..objectstore import ConcreteObjectStore
 NO_KAMAKI_ERROR_MESSAGE = (
     "ObjectStore configured, but no kamaki.clients dependency available."
     "Please install and properly configure kamaki.clients or modify Object "
-    "Store configuration.")
+    "Store configuration."
+)
 
 log = logging.getLogger(__name__)
 
@@ -45,35 +46,43 @@ def parse_config_xml(config_xml):
     r = dict()
     try:
         for tag, required_attrs, optional_attrs in (
-                ('auth', ('url', 'token', ), ('ca_certs', 'ignore_ssl', )),
-                ('container', ('name', ), ('project', )), ):
+            (
+                "auth",
+                (
+                    "url",
+                    "token",
+                ),
+                (
+                    "ca_certs",
+                    "ignore_ssl",
+                ),
+            ),
+            ("container", ("name",), ("project",)),
+        ):
             element = config_xml.findall(tag)[0]
             required = tuple((k, element.get(k)) for k in required_attrs)
             for k, v in required:
                 if not v:
-                    msg = f'No value for {tag}:{k} in XML tree'
+                    msg = f"No value for {tag}:{k} in XML tree"
                     log.error(msg)
                     raise Exception(msg)
             optional = tuple((k, element.get(k)) for k in optional_attrs)
             r[tag] = dict(required + optional)
 
         # Extract extra_dir
-        tag, attrs = 'extra_dir', ('type', 'path')
+        tag, attrs = "extra_dir", ("type", "path")
         extra_dirs = config_xml.findall(tag)
         if not extra_dirs:
-            msg = f'No {tag} element in XML tree'
+            msg = f"No {tag} element in XML tree"
             log.error(msg)
             raise Exception(msg)
-        r['extra_dirs'] = [
-            {k: e.get(k) for k in attrs} for e in extra_dirs]
-        if 'job_work' not in (d['type'] for d in r['extra_dirs']):
+        r["extra_dirs"] = [{k: e.get(k) for k in attrs} for e in extra_dirs]
+        if "job_work" not in (d["type"] for d in r["extra_dirs"]):
             msg = f'No value for {tag}:type="job_work" in XML tree'
             log.error(msg)
             raise Exception(msg)
     except Exception:
-        log.exception(
-            "Malformed PithosObjectStore Configuration XML -- "
-            "unable to continue")
+        log.exception("Malformed PithosObjectStore Configuration XML -- " "unable to continue")
         raise
     return r
 
@@ -83,12 +92,13 @@ class PithosObjectStore(ConcreteObjectStore):
     Object store that stores objects as items in a Pithos+ container.
     Cache is ignored for the time being.
     """
-    store_type = 'pithos'
+
+    store_type = "pithos"
 
     def __init__(self, config, config_dict):
         super().__init__(config, config_dict)
         self.staging_path = self.config.file_path
-        log.info('Parse config_xml for pithos object store')
+        log.info("Parse config_xml for pithos object store")
         self.config_dict = config_dict
         log.debug(self.config_dict)
 
@@ -98,9 +108,9 @@ class PithosObjectStore(ConcreteObjectStore):
         if KamakiClient is None:
             raise Exception(NO_KAMAKI_ERROR_MESSAGE)
 
-        log.info('Authenticate Synnefo account')
+        log.info("Authenticate Synnefo account")
         self._authenticate()
-        log.info('Initialize Pithos+ client')
+        log.info("Initialize Pithos+ client")
         self._init_pithos()
 
     @classmethod
@@ -113,50 +123,56 @@ class PithosObjectStore(ConcreteObjectStore):
         return as_dict
 
     def _authenticate(self):
-        auth = self.config_dict['auth']
-        url, token = auth['url'], auth['token']
-        ca_certs = auth.get('ca_certs')
+        auth = self.config_dict["auth"]
+        url, token = auth["url"], auth["token"]
+        ca_certs = auth.get("ca_certs")
         if ca_certs:
             utils.https.patch_with_certs(ca_certs)
-        elif auth.get('ignore_ssl').lower() in ('true', 'yes', 'on'):
+        elif auth.get("ignore_ssl").lower() in ("true", "yes", "on"):
             utils.https.patch_ignore_ssl()
         self.astakos = astakos.AstakosClient(url, token)
 
     def _init_pithos(self):
-        uuid, token = self.astakos.user_term('id'), self.astakos.token
+        uuid, token = self.astakos.user_term("id"), self.astakos.token
         service_type = pithos.PithosClient.service_type
         pithos_url = self.astakos.get_endpoint_url(service_type)
-        container = self.config_dict['container']['name']
+        container = self.config_dict["container"]["name"]
         self.pithos = pithos.PithosClient(pithos_url, token, uuid, container)
 
         # Create container if not exist, or reassign to named project
-        project = self.config_dict['container'].get('project', None)
+        project = self.config_dict["container"].get("project", None)
         try:
             c = self.pithos.get_container_info()
         except ClientError as ce:
-            if ce.status not in (404, ):
+            if ce.status not in (404,):
                 raise
             c = self.pithos.create_container(project_id=project)
             return
-        if project and c.get('x-container-policy-project') != project:
+        if project and c.get("x-container-policy-project") != project:
             self.pithos.reassign_container(project)
 
     def _construct_path(
-            self, obj,
-            base_dir=None, dir_only=None, extra_dir=None,
-            extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+        self,
+        obj,
+        base_dir=None,
+        dir_only=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        **kwargs,
+    ):
         """Construct path from object and parameters"""
         # param extra_dir: should never be constructed from provided data but
         # just make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning(f'extra_dir is not normalized: {extra_dir}')
+            log.warning(f"extra_dir is not normalized: {extra_dir}")
             raise ObjectInvalid("The requested object is invalid")
         # ensure that any parent directory references in alt_name would not
         # result in a path not contained in the directory path constructed here
         if alt_name:
             if not safe_relpath(alt_name):
-                log.warning(
-                    f'alt_name would locate path outside dir: {alt_name}')
+                log.warning(f"alt_name would locate path outside dir: {alt_name}")
                 raise ObjectInvalid("The requested object is invalid")
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
@@ -176,10 +192,10 @@ class PithosObjectStore(ConcreteObjectStore):
             return os.path.join(base, rel_path)
 
         # Pithos+ folders are marked by having trailing '/' so add it now
-        rel_path = f'{rel_path}/'
+        rel_path = f"{rel_path}/"
 
         if not dir_only:
-            an = alt_name if alt_name else f'dataset_{self._get_object_id(obj)}.dat'
+            an = alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat"
             rel_path = os.path.join(rel_path, an)
         return rel_path
 
@@ -188,13 +204,13 @@ class PithosObjectStore(ConcreteObjectStore):
 
     def _in_cache(self, rel_path):
         """Check if the given dataset is in the local cache and return True if
-           so.
+        so.
         """
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
 
     def _fix_permissions(self, rel_path):
-        """ Set permissions on rel_path"""
+        """Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
             umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
             for filename in files:
@@ -202,8 +218,7 @@ class PithosObjectStore(ConcreteObjectStore):
                 # Ignore symlinks
                 if os.path.islink(path):
                     continue
-                umask_fix_perms(
-                    path, self.config.umask, 0o666, self.config.gid)
+                umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
 
     def _pull_into_cache(self, rel_path):
         # Ensure the cache directory structure exists (e.g., dataset_#_files/)
@@ -228,13 +243,13 @@ class PithosObjectStore(ConcreteObjectStore):
             self.pithos.get_object_info(path)
             return True
         except ClientError as ce:
-            if ce.status not in (404, ):
+            if ce.status not in (404,):
                 raise
 
         in_cache = self._in_cache(path)
-        dir_only = kwargs.get('dir_only', False)
+        dir_only = kwargs.get("dir_only", False)
         if dir_only:
-            base_dir = kwargs.get('base_dir', None)
+            base_dir = kwargs.get("base_dir", None)
             if in_cache:
                 return True
             elif base_dir:  # for JOB_WORK directory
@@ -255,10 +270,10 @@ class PithosObjectStore(ConcreteObjectStore):
         """Touch a file (aka create empty), if it doesn't exist"""
         if not self._exists(obj, **kwargs):
             # Pull out locally used fields
-            extra_dir = kwargs.get('extra_dir', None)
-            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
-            dir_only = kwargs.get('dir_only', False)
-            alt_name = kwargs.get('alt_name', None)
+            extra_dir = kwargs.get("extra_dir", None)
+            extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+            dir_only = kwargs.get("dir_only", False)
+            alt_name = kwargs.get("alt_name", None)
 
             # Construct hashed path
             rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
@@ -276,15 +291,12 @@ class PithosObjectStore(ConcreteObjectStore):
                 os.makedirs(cache_dir)
 
             if dir_only:
-                self.pithos.upload_from_string(
-                    rel_path, '', content_type='application/directory')
+                self.pithos.upload_from_string(rel_path, "", content_type="application/directory")
             else:
-                rel_path = os.path.join(
-                    rel_path,
-                    alt_name if alt_name else f'dataset_{self._get_object_id(obj)}.dat')
+                rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
                 new_file = os.path.join(self.staging_path, rel_path)
-                open(new_file, 'w').close()
-                self.pithos.upload_from_string(rel_path, '')
+                open(new_file, "w").close()
+                self.pithos.upload_from_string(rel_path, "")
 
     def _empty(self, obj, **kwargs):
         """
@@ -292,8 +304,7 @@ class PithosObjectStore(ConcreteObjectStore):
         :raises ObjectNotFound:
         """
         if not self._exists(obj, **kwargs):
-            raise ObjectNotFound(
-                f'objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}')
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
         return bool(self._size(obj, **kwargs))
 
     def _size(self, obj, **kwargs):
@@ -308,45 +319,45 @@ class PithosObjectStore(ConcreteObjectStore):
                 return os.path.getsize(self._get_cache_path(path))
             except OSError as ex:
                 log.warning(
-                    'Could not get size of file {path} in local cache,'
-                    'will try Pithos. Error: {err}'.format(path=path, err=ex))
+                    "Could not get size of file {path} in local cache,"
+                    "will try Pithos. Error: {err}".format(path=path, err=ex)
+                )
         try:
             file = self.pithos.get_object_info(path)
         except ClientError as ce:
-            if ce.status not in (404, ):
+            if ce.status not in (404,):
                 raise
             return 0
-        return int(file['content-length'])
+        return int(file["content-length"])
 
     def _delete(self, obj, **kwargs):
         """Delete the object
         :returns: weather the object was deleted
         """
         path = self._construct_path(obj, **kwargs)
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         try:
             if all((base_dir, dir_only, obj_dir)):
                 shutil.rmtree(os.path.abspath(path))
                 return True
             cache_path = self._get_cache_path(path)
 
-            entire_dir = kwargs.get('entire_dir', False)
-            extra_dir = kwargs.get('extra_dir', False)
+            entire_dir = kwargs.get("entire_dir", False)
+            extra_dir = kwargs.get("extra_dir", False)
             if entire_dir and extra_dir:
                 shutil.rmtree(cache_path)
-                log.debug(f'On Pithos: delete -r {path}/')
-                self.pithos.del_object(path, delimiter='/')
+                log.debug(f"On Pithos: delete -r {path}/")
+                self.pithos.del_object(path, delimiter="/")
                 return True
             else:
                 os.unlink(cache_path)
                 self.pithos.del_object(path)
         except OSError:
-            log.exception(
-                f'{self._get_filename(obj, **kwargs)} delete error')
+            log.exception(f"{self._get_filename(obj, **kwargs)} delete error")
         except ClientError as ce:
-            log.exception(f'Could not delete {path} from Pithos, {ce}')
+            log.exception(f"Could not delete {path} from Pithos, {ce}")
         return False
 
     def _get_data(self, obj, start=0, count=-1, **kwargs):
@@ -367,9 +378,9 @@ class PithosObjectStore(ConcreteObjectStore):
 
     def _get_filename(self, obj, **kwargs):
         """Get the expected filename with absolute path"""
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         path = self._construct_path(obj, **kwargs)
 
         # for JOB_WORK directory
@@ -386,21 +397,21 @@ class PithosObjectStore(ConcreteObjectStore):
             if not dir_only:
                 self._pull_into_cache(path)
                 return cache_path
-        raise ObjectNotFound(
-            f'objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}')
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
 
     def _update_from_file(self, obj, **kwargs):
         """Update the store when a file is updated"""
-        if kwargs.get('create'):
+        if kwargs.get("create"):
             self._create(obj, **kwargs)
         if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
-                'objectstore.update_from_file, object does not exist: {obj}, '
-                'kwargs: {kwargs}'.format(obj=obj, kwargs=kwargs))
+                "objectstore.update_from_file, object does not exist: {obj}, "
+                "kwargs: {kwargs}".format(obj=obj, kwargs=kwargs)
+            )
 
         path = self._construct_path(obj, **kwargs)
         cache_path = self._get_cache_path(path)
-        file_name = kwargs.get('file_name')
+        file_name = kwargs.get("file_name")
         if file_name:
             source_path = os.path.abspath(file_name)
             try:
@@ -410,7 +421,8 @@ class PithosObjectStore(ConcreteObjectStore):
             except OSError:
                 log.exception(
                     'Trouble copying source file "{source}" to cache "{cache}"'
-                    ''.format(source=source_path, cache=cache_path))
+                    "".format(source=source_path, cache=cache_path)
+                )
         else:
             with open(cache_path) as f:
                 self.pithos.upload_object(obj, f)
@@ -424,9 +436,8 @@ class PithosObjectStore(ConcreteObjectStore):
             try:
                 return self.pithos.publish_object(path)
             except ClientError as ce:
-                log.exception(
-                    f'Trouble generating URL for dataset "{path}"')
-                log.exception(f'Kamaki: {ce}')
+                log.exception(f'Trouble generating URL for dataset "{path}"')
+                log.exception(f"Kamaki: {ce}")
         return None
 
     def _get_store_usage_percent(self):
@@ -434,8 +445,8 @@ class PithosObjectStore(ConcreteObjectStore):
         :returns: percentage indicating how full the store is
         """
         quotas = self.astakos.get_quotas()
-        project = self.config_dict['container']['project']
-        pithos_quotas = quotas[project]['pithos.diskspace']
-        usage = pithos_quotas['usage']
-        limit = min(pithos_quotas['limit'], pithos_quotas['project_limit'])
+        project = self.config_dict["container"]["project"]
+        pithos_quotas = quotas[project]["pithos.diskspace"]
+        usage = pithos_quotas["usage"]
+        limit = min(pithos_quotas["limit"], pithos_quotas["project_limit"])
         return (100.0 * usage) / limit
diff --git a/lib/galaxy/objectstore/pulsar.py b/lib/galaxy/objectstore/pulsar.py
index 5473b8e3b82..39a54ca5650 100644
--- a/lib/galaxy/objectstore/pulsar.py
+++ b/lib/galaxy/objectstore/pulsar.py
@@ -59,7 +59,7 @@ class PulsarObjectStore(BaseObjectStore):
         return None
 
     def __build_kwds(self, obj, **kwds):
-        kwds['object_id'] = obj.id
+        kwds["object_id"] = obj.id
         return kwds
 
     def __build_pulsar_client(self, config_xml):
diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 40b91a567ce..41d18260c3c 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -19,7 +19,10 @@ try:
 except ImportError:
     boto = None  # type: ignore[assignment]
 
-from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.exceptions import (
+    ObjectInvalid,
+    ObjectNotFound,
+)
 from galaxy.util import (
     directory_hash_id,
     string_as_bool,
@@ -30,73 +33,78 @@ from galaxy.util import (
 from galaxy.util.path import safe_relpath
 from galaxy.util.sleeper import Sleeper
 from .s3_multipart_upload import multipart_upload
-from ..objectstore import ConcreteObjectStore, convert_bytes
+from ..objectstore import (
+    ConcreteObjectStore,
+    convert_bytes,
+)
 
-NO_BOTO_ERROR_MESSAGE = ("S3/Swift object store configured, but no boto dependency available."
-                         "Please install and properly configure boto or modify object store configuration.")
+NO_BOTO_ERROR_MESSAGE = (
+    "S3/Swift object store configured, but no boto dependency available."
+    "Please install and properly configure boto or modify object store configuration."
+)
 
 log = logging.getLogger(__name__)
-logging.getLogger('boto').setLevel(logging.INFO)  # Otherwise boto is quite noisy
+logging.getLogger("boto").setLevel(logging.INFO)  # Otherwise boto is quite noisy
 
 
 def parse_config_xml(config_xml):
     try:
-        a_xml = config_xml.findall('auth')[0]
-        access_key = a_xml.get('access_key')
-        secret_key = a_xml.get('secret_key')
+        a_xml = config_xml.findall("auth")[0]
+        access_key = a_xml.get("access_key")
+        secret_key = a_xml.get("secret_key")
 
-        b_xml = config_xml.findall('bucket')[0]
-        bucket_name = b_xml.get('name')
-        use_rr = string_as_bool(b_xml.get('use_reduced_redundancy', "False"))
-        max_chunk_size = int(b_xml.get('max_chunk_size', 250))
+        b_xml = config_xml.findall("bucket")[0]
+        bucket_name = b_xml.get("name")
+        use_rr = string_as_bool(b_xml.get("use_reduced_redundancy", "False"))
+        max_chunk_size = int(b_xml.get("max_chunk_size", 250))
 
-        cn_xml = config_xml.findall('connection')
+        cn_xml = config_xml.findall("connection")
         if not cn_xml:
             cn_xml = {}
         else:
             cn_xml = cn_xml[0]
 
-        host = cn_xml.get('host', None)
-        port = int(cn_xml.get('port', 6000))
-        multipart = string_as_bool(cn_xml.get('multipart', 'True'))
-        is_secure = string_as_bool(cn_xml.get('is_secure', 'True'))
-        conn_path = cn_xml.get('conn_path', '/')
+        host = cn_xml.get("host", None)
+        port = int(cn_xml.get("port", 6000))
+        multipart = string_as_bool(cn_xml.get("multipart", "True"))
+        is_secure = string_as_bool(cn_xml.get("is_secure", "True"))
+        conn_path = cn_xml.get("conn_path", "/")
 
-        c_xml = config_xml.findall('cache')[0]
-        cache_size = float(c_xml.get('size', -1))
+        c_xml = config_xml.findall("cache")[0]
+        cache_size = float(c_xml.get("size", -1))
 
-        staging_path = c_xml.get('path', None)
+        staging_path = c_xml.get("path", None)
 
-        tag, attrs = 'extra_dir', ('type', 'path')
+        tag, attrs = "extra_dir", ("type", "path")
         extra_dirs = config_xml.findall(tag)
         if not extra_dirs:
-            msg = f'No {tag} element in XML tree'
+            msg = f"No {tag} element in XML tree"
             log.error(msg)
             raise Exception(msg)
         extra_dirs = [{k: e.get(k) for k in attrs} for e in extra_dirs]
 
         return {
-            'auth': {
-                'access_key': access_key,
-                'secret_key': secret_key,
+            "auth": {
+                "access_key": access_key,
+                "secret_key": secret_key,
             },
-            'bucket': {
-                'name': bucket_name,
-                'use_reduced_redundancy': use_rr,
-                'max_chunk_size': max_chunk_size,
+            "bucket": {
+                "name": bucket_name,
+                "use_reduced_redundancy": use_rr,
+                "max_chunk_size": max_chunk_size,
             },
-            'connection': {
-                'host': host,
-                'port': port,
-                'multipart': multipart,
-                'is_secure': is_secure,
-                'conn_path': conn_path,
+            "connection": {
+                "host": host,
+                "port": port,
+                "multipart": multipart,
+                "is_secure": is_secure,
+                "conn_path": conn_path,
             },
-            'cache': {
-                'size': cache_size,
-                'path': staging_path,
+            "cache": {
+                "size": cache_size,
+                "path": staging_path,
             },
-            'extra_dirs': extra_dirs,
+            "extra_dirs": extra_dirs,
         }
     except Exception:
         # Toss it back up after logging, we can't continue loading at this point.
@@ -105,29 +113,28 @@ def parse_config_xml(config_xml):
 
 
 class CloudConfigMixin:
-
     def _config_to_dict(self):
         return {
-            'auth': {
-                'access_key': self.access_key,
-                'secret_key': self.secret_key,
+            "auth": {
+                "access_key": self.access_key,
+                "secret_key": self.secret_key,
             },
-            'bucket': {
-                'name': self.bucket,
-                'use_reduced_redundancy': self.use_rr,
+            "bucket": {
+                "name": self.bucket,
+                "use_reduced_redundancy": self.use_rr,
             },
-            'connection': {
-                'host': self.host,
-                'port': self.port,
-                'multipart': self.multipart,
-                'is_secure': self.is_secure,
-                'conn_path': self.conn_path,
+            "connection": {
+                "host": self.host,
+                "port": self.port,
+                "multipart": self.multipart,
+                "is_secure": self.is_secure,
+                "conn_path": self.conn_path,
             },
-            'cache': {
-                'size': self.cache_size,
-                'path': self.staging_path,
+            "cache": {
+                "size": self.cache_size,
+                "path": self.staging_path,
             },
-            'enable_cache_monitor': False,
+            "enable_cache_monitor": False,
         }
 
 
@@ -137,37 +144,37 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
     cache exists that is used as an intermediate location for files between
     Galaxy and S3.
     """
-    store_type = 's3'
+
+    store_type = "s3"
 
     def __init__(self, config, config_dict):
         super().__init__(config, config_dict)
 
         self.transfer_progress = 0
 
-        auth_dict = config_dict['auth']
-        bucket_dict = config_dict['bucket']
-        connection_dict = config_dict.get('connection', {})
-        cache_dict = config_dict['cache']
-        self.enable_cache_monitor = config_dict.get('enable_cache_monitor', True)
+        auth_dict = config_dict["auth"]
+        bucket_dict = config_dict["bucket"]
+        connection_dict = config_dict.get("connection", {})
+        cache_dict = config_dict["cache"]
+        self.enable_cache_monitor = config_dict.get("enable_cache_monitor", True)
 
-        self.access_key = auth_dict.get('access_key')
-        self.secret_key = auth_dict.get('secret_key')
+        self.access_key = auth_dict.get("access_key")
+        self.secret_key = auth_dict.get("secret_key")
 
-        self.bucket = bucket_dict.get('name')
-        self.use_rr = bucket_dict.get('use_reduced_redundancy', False)
-        self.max_chunk_size = bucket_dict.get('max_chunk_size', 250)
+        self.bucket = bucket_dict.get("name")
+        self.use_rr = bucket_dict.get("use_reduced_redundancy", False)
+        self.max_chunk_size = bucket_dict.get("max_chunk_size", 250)
 
-        self.host = connection_dict.get('host', None)
-        self.port = connection_dict.get('port', 6000)
-        self.multipart = connection_dict.get('multipart', True)
-        self.is_secure = connection_dict.get('is_secure', True)
-        self.conn_path = connection_dict.get('conn_path', '/')
+        self.host = connection_dict.get("host", None)
+        self.port = connection_dict.get("port", 6000)
+        self.multipart = connection_dict.get("multipart", True)
+        self.is_secure = connection_dict.get("is_secure", True)
+        self.conn_path = connection_dict.get("conn_path", "/")
 
-        self.cache_size = cache_dict.get('size', -1)
-        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        self.cache_size = cache_dict.get("size", -1)
+        self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
 
-        extra_dirs = {
-            e['type']: e['path'] for e in config_dict.get('extra_dirs', [])}
+        extra_dirs = {e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])}
         self.extra_dirs.update(extra_dirs)
 
         self._initialize()
@@ -177,20 +184,22 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             raise Exception(NO_BOTO_ERROR_MESSAGE)
 
         # for multipart upload
-        self.s3server = {'access_key': self.access_key,
-                         'secret_key': self.secret_key,
-                         'is_secure': self.is_secure,
-                         'max_chunk_size': self.max_chunk_size,
-                         'host': self.host,
-                         'port': self.port,
-                         'use_rr': self.use_rr,
-                         'conn_path': self.conn_path}
+        self.s3server = {
+            "access_key": self.access_key,
+            "secret_key": self.secret_key,
+            "is_secure": self.is_secure,
+            "max_chunk_size": self.max_chunk_size,
+            "host": self.host,
+            "port": self.port,
+            "use_rr": self.use_rr,
+            "conn_path": self.conn_path,
+        }
 
         self._configure_connection()
         self._bucket = self._get_bucket(self.bucket)
         self.start_cache_monitor()
         # Test if 'axel' is available for parallel download and pull the key into cache
-        if which('axel'):
+        if which("axel"):
             self.use_axel = True
         else:
             self.use_axel = False
@@ -244,8 +253,11 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # Initiate cleaning once within 10% of the defined cache size?
             cache_limit = self.cache_size * 0.9
             if total_size > cache_limit:
-                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
-                         convert_bytes(total_size), convert_bytes(cache_limit))
+                log.info(
+                    "Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
+                    convert_bytes(total_size),
+                    convert_bytes(cache_limit),
+                )
                 # How much to delete? If simply deleting up to the cache-10% limit,
                 # is likely to be deleting frequently and may run the risk of hitting
                 # the limit - maybe delete additional #%?
@@ -255,7 +267,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             self.sleeper.sleep(30)  # Test cache size every 30 seconds?
 
     def __clean_cache(self, file_list, delete_this_much):
-        """ Keep deleting files from the file_list until the size of the deleted
+        """Keep deleting files from the file_list until the size of the deleted
         files is greater than the value in delete_this_much parameter.
 
         :type file_list: list
@@ -288,8 +300,8 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 return
 
     def _get_bucket(self, bucket_name):
-        """ Sometimes a handle to a bucket is not established right away so try
-        it a few times. Raise error is connection is not established. """
+        """Sometimes a handle to a bucket is not established right away so try
+        it a few times. Raise error is connection is not established."""
         for i in range(5):
             try:
                 bucket = self.conn.get_bucket(bucket_name)
@@ -307,7 +319,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         raise S3ResponseError
 
     def _fix_permissions(self, rel_path):
-        """ Set permissions on rel_path"""
+        """Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
             umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
             for filename in files:
@@ -317,17 +329,27 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                     continue
                 umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
 
-    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+    def _construct_path(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir=False,
+        **kwargs,
+    ):
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning('extra_dir is not normalized: %s', extra_dir)
+            log.warning("extra_dir is not normalized: %s", extra_dir)
             raise ObjectInvalid("The requested object is invalid")
         # ensure that any parent directory references in alt_name would not
         # result in a path not contained in the directory path constructed here
         if alt_name:
             if not safe_relpath(alt_name):
-                log.warning('alt_name would locate path outside dir: %s', alt_name)
+                log.warning("alt_name would locate path outside dir: %s", alt_name)
                 raise ObjectInvalid("The requested object is invalid")
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
@@ -347,7 +369,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             return os.path.join(base, rel_path)
 
         # S3 folders are marked by having trailing '/' so add it now
-        rel_path = f'{rel_path}/'
+        rel_path = f"{rel_path}/"
 
         if not dir_only:
             rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
@@ -372,7 +394,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         exists = False
         try:
             # A hackish way of testing if the rel_path is a folder vs a file
-            is_dir = rel_path[-1] == '/'
+            is_dir = rel_path[-1] == "/"
             if is_dir:
                 keyresult = self._bucket.get_all_keys(prefix=rel_path)
                 if len(keyresult) > 0:
@@ -388,7 +410,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         return exists
 
     def _in_cache(self, rel_path):
-        """ Check if the given dataset is in the local cache and return True if so. """
+        """Check if the given dataset is in the local cache and return True if so."""
         # log.debug("------ Checking cache for rel_path %s" % rel_path)
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
@@ -435,14 +457,18 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             key = self._bucket.get_key(rel_path)
             # Test if cache is large enough to hold the new file
             if self.cache_size > 0 and key.size > self.cache_size:
-                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
-                             rel_path, key.size, self.cache_size)
+                log.critical(
+                    "File %s is larger (%s) than the cache size (%s). Cannot download.",
+                    rel_path,
+                    key.size,
+                    self.cache_size,
+                )
                 return False
             if self.use_axel:
                 log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
                 ncores = multiprocessing.cpu_count()
                 url = key.generate_url(7200)
-                ret_code = subprocess.call(['axel', '-a', '-n', str(ncores), url])
+                ret_code = subprocess.call(["axel", "-a", "-n", str(ncores), url])
                 if ret_code == 0:
                     return True
             else:
@@ -467,30 +493,44 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             if os.path.exists(source_file):
                 key = Key(self._bucket, rel_path)
                 if os.path.getsize(source_file) == 0 and key.exists():
-                    log.debug("Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path)
+                    log.debug(
+                        "Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path
+                    )
                     return True
                 if from_string:
                     key.set_contents_from_string(from_string, reduced_redundancy=self.use_rr)
                     log.debug("Pushed data from string '%s' to key '%s'", from_string, rel_path)
                 else:
                     start_time = datetime.now()
-                    log.debug("Pushing cache file '%s' of size %s bytes to key '%s'", source_file, os.path.getsize(source_file), rel_path)
+                    log.debug(
+                        "Pushing cache file '%s' of size %s bytes to key '%s'",
+                        source_file,
+                        os.path.getsize(source_file),
+                        rel_path,
+                    )
                     mb_size = os.path.getsize(source_file) / 1e6
                     if mb_size < 10 or (not self.multipart):
                         self.transfer_progress = 0  # Reset transfer progress counter
-                        key.set_contents_from_filename(source_file,
-                                                       reduced_redundancy=self.use_rr,
-                                                       cb=self._transfer_cb,
-                                                       num_cb=10)
+                        key.set_contents_from_filename(
+                            source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10
+                        )
                     else:
                         multipart_upload(self.s3server, self._bucket, key.name, source_file, mb_size)
                     end_time = datetime.now()
-                    log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
-                              source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
+                    log.debug(
+                        "Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
+                        source_file,
+                        rel_path,
+                        os.path.getsize(source_file),
+                        end_time - start_time,
+                    )
                 return True
             else:
-                log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
-                          rel_path, source_file)
+                log.error(
+                    "Tried updating key '%s' from source file '%s', but source file does not exist.",
+                    rel_path,
+                    source_file,
+                )
         except S3ResponseError:
             log.exception("Trouble pushing S3 key '%s' from file '%s'", rel_path, source_file)
             raise
@@ -506,8 +546,12 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
                 return True
-            log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
-                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
+            log.debug(
+                "Waiting for dataset %s to transfer from OS: %s/%s",
+                rel_path,
+                os.path.getsize(self._get_cache_path(rel_path)),
+                self._get_size_in_s3(rel_path),
+            )
         return False
 
     def _exists(self, obj, **kwargs):
@@ -521,8 +565,8 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         in_s3 = self._key_exists(rel_path)
         # log.debug("~~~~~~ File '%s' exists in cache: %s; in s3: %s" % (rel_path, in_cache, in_s3))
         # dir_only does not get synced so shortcut the decision
-        dir_only = kwargs.get('dir_only', False)
-        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get("dir_only", False)
+        base_dir = kwargs.get("base_dir", None)
         if dir_only:
             if in_cache or in_s3:
                 return True
@@ -547,10 +591,10 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
-            extra_dir = kwargs.get('extra_dir', None)
-            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
-            dir_only = kwargs.get('dir_only', False)
-            alt_name = kwargs.get('alt_name', None)
+            extra_dir = kwargs.get("extra_dir", None)
+            extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+            dir_only = kwargs.get("dir_only", False)
+            alt_name = kwargs.get("alt_name", None)
 
             # Construct hashed path
             rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
@@ -575,15 +619,14 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # If instructed, create the dataset in cache & in S3
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
-                open(os.path.join(self.staging_path, rel_path), 'w').close()
-                self._push_to_os(rel_path, from_string='')
+                open(os.path.join(self.staging_path, rel_path), "w").close()
+                self._push_to_os(rel_path, from_string="")
 
     def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
-                                 % (str(obj), str(kwargs)))
+            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -599,10 +642,10 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
 
     def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
-        extra_dir = kwargs.get('extra_dir', None)
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        extra_dir = kwargs.get("extra_dir", None)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         try:
             # Remove temparory data in JOB_WORK directory
             if base_dir and dir_only and obj_dir:
@@ -632,7 +675,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         except S3ResponseError:
             log.exception("Could not delete key '%s' from S3", rel_path)
         except OSError:
-            log.exception('%s delete error', self._get_filename(obj, **kwargs))
+            log.exception("%s delete error", self._get_filename(obj, **kwargs))
         return False
 
     def _get_data(self, obj, start=0, count=-1, **kwargs):
@@ -648,9 +691,9 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         return content
 
     def _get_filename(self, obj, **kwargs):
-        base_dir = kwargs.get('base_dir', None)
-        dir_only = kwargs.get('dir_only', False)
-        obj_dir = kwargs.get('obj_dir', False)
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        obj_dir = kwargs.get("obj_dir", False)
         rel_path = self._construct_path(obj, **kwargs)
 
         # for JOB_WORK directory
@@ -680,8 +723,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s'
-                             % (str(obj), str(kwargs)))
+        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -706,8 +748,9 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # Update the file on S3
             self._push_to_os(rel_path, source_file)
         else:
-            raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
-                                 % (str(obj), str(kwargs)))
+            raise ObjectNotFound(
+                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
+            )
 
     def _get_object_url(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
@@ -724,7 +767,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
 
     def shutdown(self):
         self.running = False
-        thread = getattr(self, 'cache_monitor_thread', None)
+        thread = getattr(self, "cache_monitor_thread", None)
         if thread:
             log.debug("Shutting down thread")
             self.sleeper.wake()
@@ -737,14 +780,17 @@ class SwiftObjectStore(S3ObjectStore):
     cache exists that is used as an intermediate location for files between
     Galaxy and Swift.
     """
-    store_type = 'swift'
+
+    store_type = "swift"
 
     def _configure_connection(self):
         log.debug("Configuring Swift Connection")
-        self.conn = boto.connect_s3(aws_access_key_id=self.access_key,
-                                    aws_secret_access_key=self.secret_key,
-                                    is_secure=self.is_secure,
-                                    host=self.host,
-                                    port=self.port,
-                                    calling_format=boto.s3.connection.OrdinaryCallingFormat(),
-                                    path=self.conn_path)
+        self.conn = boto.connect_s3(
+            aws_access_key_id=self.access_key,
+            aws_secret_access_key=self.secret_key,
+            is_secure=self.is_secure,
+            host=self.host,
+            port=self.port,
+            calling_format=boto.s3.connection.OrdinaryCallingFormat(),
+            path=self.conn_path,
+        )
diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py
index f90a4937ef6..3e9cd0e0b45 100644
--- a/lib/galaxy/objectstore/s3_multipart_upload.py
+++ b/lib/galaxy/objectstore/s3_multipart_upload.py
@@ -23,17 +23,19 @@ def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname):
     This allows us to reconstitute a connection to the upload
     from within multiprocessing functions.
     """
-    if s3server['host']:
-        conn = boto.connect_s3(aws_access_key_id=s3server['access_key'],
-                               aws_secret_access_key=s3server['secret_key'],
-                               is_secure=s3server['is_secure'],
-                               host=s3server['host'],
-                               port=s3server['port'],
-                               calling_format=boto.s3.connection.OrdinaryCallingFormat(),
-                               path=s3server['conn_path'])
+    if s3server["host"]:
+        conn = boto.connect_s3(
+            aws_access_key_id=s3server["access_key"],
+            aws_secret_access_key=s3server["secret_key"],
+            is_secure=s3server["is_secure"],
+            host=s3server["host"],
+            port=s3server["port"],
+            calling_format=boto.s3.connection.OrdinaryCallingFormat(),
+            path=s3server["conn_path"],
+        )
     else:
-        if s3server['access_key']:
-            conn = S3Connection(s3server['access_key'], s3server['secret_key'])
+        if s3server["access_key"]:
+            conn = S3Connection(s3server["access_key"], s3server["secret_key"])
         else:
             conn = S3Connection()
 
@@ -45,21 +47,19 @@ def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname):
 
 
 def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part):
-    """Transfer a part of a multipart upload. Designed to be run in parallel.
-    """
+    """Transfer a part of a multipart upload. Designed to be run in parallel."""
     mp = mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname)
-    with open(part, 'rb') as t_handle:
+    with open(part, "rb") as t_handle:
         mp.upload_part_from_file(t_handle, i + 1)
     os.remove(part)
 
 
 def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size):
-    """Upload large files using Amazon's multipart upload functionality.
-    """
+    """Upload large files using Amazon's multipart upload functionality."""
+
     def split_file(in_file, mb_size, split_num=5):
-        prefix = os.path.join(os.path.dirname(in_file),
-                              f"{os.path.basename(s3_key_name)}S3PART")
-        max_chunk = s3server['max_chunk_size']
+        prefix = os.path.join(os.path.dirname(in_file), f"{os.path.basename(s3_key_name)}S3PART")
+        max_chunk = s3server["max_chunk_size"]
         # Split chunks so they are 5MB < chunk < 250MB(max_chunk_size)
         split_size = int(max(min(mb_size / (split_num * 2.0), max_chunk), 5))
         if not os.path.exists(f"{prefix}aa"):
@@ -67,13 +67,10 @@ def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size):
             subprocess.check_call(cl)
         return sorted(glob.glob(f"{prefix}*"))
 
-    mp = bucket.initiate_multipart_upload(s3_key_name,
-                                          reduced_redundancy=s3server['use_rr'])
+    mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=s3server["use_rr"])
 
     for (i, part) in enumerate(split_file(tarball, mb_size)):
-        t = threading.Thread(
-            target=transfer_part,
-            args=(s3server, mp.id, mp.key_name, mp.bucket_name, i, part))
+        t = threading.Thread(target=transfer_part, args=(s3server, mp.id, mp.key_name, mp.bucket_name, i, part))
         t.start()
         t.join()
 
diff --git a/lib/galaxy/objectstore/unittest_utils/__init__.py b/lib/galaxy/objectstore/unittest_utils/__init__.py
index 938ff2c6917..6360426e6d1 100644
--- a/lib/galaxy/objectstore/unittest_utils/__init__.py
+++ b/lib/galaxy/objectstore/unittest_utils/__init__.py
@@ -31,7 +31,6 @@ extra_dirs:
 
 
 class Config:
-
     def __init__(self, config_str=DISK_TEST_CONFIG, clazz=None, store_by="id"):
         self.temp_directory = mkdtemp()
         if config_str.startswith("<"):
@@ -65,7 +64,6 @@ class Config:
 
 
 class MockConfig:
-
     def __init__(self, temp_directory, config_file, store_by="id"):
         self.file_path = temp_directory
         self.object_store_config_file = os.path.join(temp_directory, config_file)
@@ -79,8 +77,8 @@ class MockConfig:
 
 
 __all__ = [
-    'Config',
-    'MockConfig',
-    'DISK_TEST_CONFIG',
-    'DISK_TEST_CONFIG_YAML',
+    "Config",
+    "MockConfig",
+    "DISK_TEST_CONFIG",
+    "DISK_TEST_CONFIG_YAML",
 ]
diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py
index b0e28ca6d06..2ba2271d442 100644
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -18,15 +18,13 @@ from kombu import (
     uuid,
 )
 from kombu.mixins import ConsumerProducerMixin
-from kombu.pools import (
-    producers,
-)
+from kombu.pools import producers
 
 import galaxy.queues
 from galaxy import util
 from galaxy.config import reload_config_options
 
-logging.getLogger('kombu').setLevel(logging.WARNING)
+logging.getLogger("kombu").setLevel(logging.WARNING)
 log = logging.getLogger(__name__)
 
 
@@ -38,14 +36,13 @@ def send_local_control_task(app, task, get_response=False, kwargs=None):
     if kwargs is None:
         kwargs = {}
     log.info(f"Queuing {'sync' if get_response else 'async'} task {task} for {app.config.server_name}.")
-    payload = {'task': task,
-               'kwargs': kwargs}
-    routing_key = f'control.{app.config.server_name}@{socket.gethostname()}'
+    payload = {"task": task, "kwargs": kwargs}
+    routing_key = f"control.{app.config.server_name}@{socket.gethostname()}"
     control_task = ControlTask(app.queue_worker)
     return control_task.send_task(payload, routing_key, local=True, get_response=get_response)
 
 
-def send_control_task(app, task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None):
+def send_control_task(app, task, noop_self=False, get_response=False, routing_key="control.*", kwargs=None):
     """
     This sends a control task out to all processes, useful for things like
     reloading a data table, which needs to happen individually in all
@@ -57,16 +54,14 @@ def send_control_task(app, task, noop_self=False, get_response=False, routing_ke
     if kwargs is None:
         kwargs = {}
     log.info(f"Sending {task} control task.")
-    payload = {'task': task,
-               'kwargs': kwargs}
+    payload = {"task": task, "kwargs": kwargs}
     if noop_self:
-        payload['noop'] = app.config.server_name
+        payload["noop"] = app.config.server_name
     control_task = ControlTask(app.queue_worker)
     return control_task.send_task(payload=payload, routing_key=routing_key, get_response=get_response)
 
 
 class ControlTask:
-
     def __init__(self, queue_worker):
         self.queue_worker = queue_worker
         self.correlation_id = None
@@ -94,8 +89,8 @@ class ControlTask:
         return self.queue_worker.declare_queues
 
     def on_response(self, message):
-        if message.properties['correlation_id'] == self.correlation_id:
-            self.response = message.payload['result']
+        if message.properties["correlation_id"] == self.correlation_id:
+            self.response = message.payload["result"]
 
     def send_task(self, payload, routing_key, local=False, get_response=False, timeout=10):
         if local:
@@ -118,7 +113,7 @@ class ControlTask:
                     reply_to=reply_to,
                     correlation_id=self.correlation_id,
                     retry=True,
-                    headers={'epoch': time.time()},
+                    headers={"epoch": time.time()},
                 )
             if get_response:
                 with Consumer(self.connection, on_message=self.on_response, queues=callback_queue, no_ack=True):
@@ -136,6 +131,7 @@ class ControlTask:
 # where they're currently invoked, or elsewhere.  (potentially using a dispatch
 # decorator).
 
+
 def reconfigure_watcher(app, **kwargs):
     app.database_heartbeat.update_watcher_designation()
 
@@ -150,7 +146,7 @@ def create_panel_section(app, **kwargs):
 
 def reload_tool(app, **kwargs):
     params = util.Params(kwargs)
-    tool_id = params.get('tool_id', None)
+    tool_id = params.get("tool_id", None)
     log.debug(f"Executing reload tool task for {tool_id}")
     if tool_id:
         app.toolbox.reload_tool_by_id(tool_id)
@@ -162,11 +158,11 @@ def reload_toolbox(app, save_integrated_tool_panel=True, **kwargs):
     reload_timer = util.ExecutionTimer()
     log.debug("Executing toolbox reload on '%s'", app.config.server_name)
     reload_count = app.toolbox._reload_count
-    if hasattr(app, 'tool_cache'):
+    if hasattr(app, "tool_cache"):
         app.tool_cache.cleanup()
     _get_new_toolbox(app, save_integrated_tool_panel)
     app.toolbox._reload_count = reload_count + 1
-    send_local_control_task(app, 'rebuild_toolbox_search_index')
+    send_local_control_task(app, "rebuild_toolbox_search_index")
     log.debug("Toolbox reload %s", reload_timer)
 
 
@@ -177,9 +173,12 @@ def _get_new_toolbox(app, save_integrated_tool_panel=True):
     """
     from galaxy import tools
     from galaxy.tools.special_tools import load_lib_tools
+
     tool_configs = app.config.tool_configs
 
-    new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, save_integrated_tool_panel=save_integrated_tool_panel)
+    new_toolbox = tools.ToolBox(
+        tool_configs, app.config.tool_path, app, save_integrated_tool_panel=save_integrated_tool_panel
+    )
     new_toolbox.data_manager_tools = app.toolbox.data_manager_tools
     app.datatypes_registry.load_datatype_converters(new_toolbox, use_cached=True)
     app.datatypes_registry.load_external_metadata_tool(new_toolbox)
@@ -192,21 +191,22 @@ def _get_new_toolbox(app, save_integrated_tool_panel=True):
 def reload_data_managers(app, **kwargs):
     reload_timer = util.ExecutionTimer()
     from galaxy.tools.data_manager.manager import DataManagers
+
     log.debug("Executing data managers reload on '%s'", app.config.server_name)
     app._configure_tool_data_tables(from_shed_config=False)
     reload_tool_data_tables(app)
     reload_count = app.data_managers._reload_count
     app.data_managers = DataManagers(app)
     app.data_managers._reload_count = reload_count + 1
-    if hasattr(app, 'tool_cache'):
+    if hasattr(app, "tool_cache"):
         app.tool_cache.reset_status()
-    if hasattr(app, 'watchers'):
+    if hasattr(app, "watchers"):
         app.watchers.update_watch_data_table_paths()
     log.debug("Data managers reloaded %s", reload_timer)
 
 
 def reload_display_application(app, **kwargs):
-    display_application_ids = kwargs.get('display_application_ids', None)
+    display_application_ids = kwargs.get("display_application_ids", None)
     log.debug(f"Executing display application reload task for {display_application_ids}")
     app.datatypes_registry.reload_display_applications(display_application_ids)
 
@@ -217,7 +217,7 @@ def reload_sanitize_allowlist(app):
 
 
 def recalculate_user_disk_usage(app, **kwargs):
-    user_id = kwargs.get('user_id', None)
+    user_id = kwargs.get("user_id", None)
     sa_session = app.model.context
     if user_id:
         user = sa_session.query(app.model.User).get(app.security.decode_id(user_id))
@@ -230,9 +230,9 @@ def recalculate_user_disk_usage(app, **kwargs):
 
 
 def reload_tool_data_tables(app, **kwargs):
-    path = kwargs.get('path')
-    table_name = kwargs.get('table_name')
-    table_names = path or table_name or 'all tables'
+    path = kwargs.get("path")
+    table_name = kwargs.get("table_name")
+    table_names = path or table_name or "all tables"
     log.debug("Executing tool data table reload for %s", table_names)
     table_names = app.tool_data_tables.reload_tables(table_names=table_name, path=path)
     log.debug("Finished data table reload for %s", table_names)
@@ -251,8 +251,7 @@ def reload_job_rules(app, **kwargs):
     for module in job_rule_modules(app):
         rules_module_name = module.__name__
         for name, module in sys.modules.items():
-            if ((name == rules_module_name or name.startswith(f"{rules_module_name}."))
-                    and ismodule(module)):
+            if (name == rules_module_name or name.startswith(f"{rules_module_name}.")) and ismodule(module):
                 log.debug("Reloading job rules module: %s", name)
                 importlib.reload(module)
     log.debug("Job rules reloaded %s", reload_timer)
@@ -263,20 +262,20 @@ def reload_core_config(app, **kwargs):
 
 
 def reload_tour(app, **kwargs):
-    path = kwargs.get('path')
+    path = kwargs.get("path")
     app.tour_registry.reload_tour(path)
-    log.debug('Tour reloaded')
+    log.debug("Tour reloaded")
 
 
 def __job_rule_module_names(app):
-    rules_module_names = {'galaxy.jobs.rules'}
+    rules_module_names = {"galaxy.jobs.rules"}
     if app.job_config.dynamic_params is not None:
-        module_name = app.job_config.dynamic_params.get('rules_module')
+        module_name = app.job_config.dynamic_params.get("rules_module")
         if module_name:
             rules_module_names.add(module_name)
     # Also look for destination level rules_module overrides
     for dest_tuple in app.job_config.destinations.values():
-        module_name = dest_tuple[0].params.get('rules_module')
+        module_name = dest_tuple[0].params.get("rules_module")
         if module_name:
             rules_module_names.add(module_name)
     return rules_module_names
@@ -295,29 +294,30 @@ def job_rule_modules(app):
 
 
 def admin_job_lock(app, **kwargs):
-    job_lock = kwargs.get('job_lock', False)
+    job_lock = kwargs.get("job_lock", False)
     # job_queue is exposed in the root app, but this will be 'fixed' at some
     # point, so we're using the reference from the handler.
     app.job_manager.job_lock = job_lock
-    log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch."
-             % (job_lock, "not" if job_lock else "now"))
+    log.info(
+        "Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")
+    )
 
 
 control_message_to_task = {
-    'create_panel_section': create_panel_section,
-    'reload_tool': reload_tool,
-    'reload_toolbox': reload_toolbox,
-    'reload_data_managers': reload_data_managers,
-    'reload_display_application': reload_display_application,
-    'reload_tool_data_tables': reload_tool_data_tables,
-    'reload_job_rules': reload_job_rules,
-    'admin_job_lock': admin_job_lock,
-    'reload_sanitize_allowlist': reload_sanitize_allowlist,
-    'recalculate_user_disk_usage': recalculate_user_disk_usage,
-    'rebuild_toolbox_search_index': rebuild_toolbox_search_index,
-    'reconfigure_watcher': reconfigure_watcher,
-    'reload_tour': reload_tour,
-    'reload_core_config': reload_core_config,
+    "create_panel_section": create_panel_section,
+    "reload_tool": reload_tool,
+    "reload_toolbox": reload_toolbox,
+    "reload_data_managers": reload_data_managers,
+    "reload_display_application": reload_display_application,
+    "reload_tool_data_tables": reload_tool_data_tables,
+    "reload_job_rules": reload_job_rules,
+    "admin_job_lock": admin_job_lock,
+    "reload_sanitize_allowlist": reload_sanitize_allowlist,
+    "recalculate_user_disk_usage": recalculate_user_disk_usage,
+    "rebuild_toolbox_search_index": rebuild_toolbox_search_index,
+    "reconfigure_watcher": reconfigure_watcher,
+    "reload_tour": reload_tour,
+    "reload_core_config": reload_core_config,
 }
 
 
@@ -330,7 +330,11 @@ class GalaxyQueueWorker(ConsumerProducerMixin, threading.Thread):
 
     def __init__(self, app, task_mapping=None):
         super().__init__()
-        log.info("Initializing %s Galaxy Queue Worker on %s", app.config.server_name, util.mask_password_from_url(app.config.amqp_internal_connection))
+        log.info(
+            "Initializing %s Galaxy Queue Worker on %s",
+            app.config.server_name,
+            util.mask_password_from_url(app.config.amqp_internal_connection),
+        )
         self.daemon = True
         self.connection = app.amqp_internal_connection_obj
         # Force connection instead of lazy-connecting the first time it is required.
@@ -344,8 +348,15 @@ class GalaxyQueueWorker(ConsumerProducerMixin, threading.Thread):
         self.control_queues = []
         self.epoch = 0
 
-    def send_control_task(self, task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None):
-        return send_control_task(app=self.app, task=task, noop_self=noop_self, get_response=get_response, routing_key=routing_key, kwargs=kwargs)
+    def send_control_task(self, task, noop_self=False, get_response=False, routing_key="control.*", kwargs=None):
+        return send_control_task(
+            app=self.app,
+            task=task,
+            noop_self=noop_self,
+            get_response=get_response,
+            routing_key=routing_key,
+            kwargs=kwargs,
+        )
 
     def send_local_control_task(self, task, get_response=False, kwargs=None):
         return send_local_control_task(app=self.app, get_response=get_response, task=task, kwargs=kwargs)
@@ -364,38 +375,47 @@ class GalaxyQueueWorker(ConsumerProducerMixin, threading.Thread):
         self.start()
 
     def get_consumers(self, Consumer, channel):
-        return [Consumer(queues=[q],
-                         callbacks=[self.process_task],
-                         accept={'application/json'}) for q in self.control_queues]
+        return [
+            Consumer(queues=[q], callbacks=[self.process_task], accept={"application/json"})
+            for q in self.control_queues
+        ]
 
     def process_task(self, body, message):
-        result = 'NO_RESULT'
-        if body['task'] in self.task_mapping:
-            if body.get('noop', None) != self.app.config.server_name:
+        result = "NO_RESULT"
+        if body["task"] in self.task_mapping:
+            if body.get("noop", None) != self.app.config.server_name:
                 try:
-                    f = self.task_mapping[body['task']]
-                    if message.headers.get('epoch', math.inf) > self.epoch:
+                    f = self.task_mapping[body["task"]]
+                    if message.headers.get("epoch", math.inf) > self.epoch:
                         # Message was created after QueueWorker was started, execute
-                        log.info("Instance '%s' received '%s' task, executing now.", self.app.config.server_name, body['task'])
-                        result = f(self.app, **body['kwargs'])
+                        log.info(
+                            "Instance '%s' received '%s' task, executing now.",
+                            self.app.config.server_name,
+                            body["task"],
+                        )
+                        result = f(self.app, **body["kwargs"])
                     else:
                         # Message was created before QueueWorker was started, ack message but don't run task
-                        log.info("Instance '%s' received '%s' task from the past, discarding it", self.app.config.server_name, body['task'])
-                        result = 'NO_OP'
+                        log.info(
+                            "Instance '%s' received '%s' task from the past, discarding it",
+                            self.app.config.server_name,
+                            body["task"],
+                        )
+                        result = "NO_OP"
                 except Exception:
                     # this shouldn't ever throw an exception, but...
-                    log.exception("Error running control task type: %s", body['task'])
+                    log.exception("Error running control task type: %s", body["task"])
             else:
-                result = 'NO_OP'
+                result = "NO_OP"
         else:
             log.warning(f"Received a malformed task message:\n{body}")
-        if message.properties.get('reply_to'):
+        if message.properties.get("reply_to"):
             self.producer.publish(
-                {'result': result},
-                exchange='',
-                routing_key=message.properties['reply_to'],
-                correlation_id=message.properties['correlation_id'],
-                serializer='json',
+                {"result": result},
+                exchange="",
+                routing_key=message.properties["reply_to"],
+                correlation_id=message.properties["correlation_id"],
+                serializer="json",
                 retry=True,
             )
         message.ack()
diff --git a/lib/galaxy/queues.py b/lib/galaxy/queues.py
index ec654605981..75fd4fa5fb5 100644
--- a/lib/galaxy/queues.py
+++ b/lib/galaxy/queues.py
@@ -9,11 +9,11 @@ from typing import Optional
 from kombu import (
     Connection,
     Exchange,
-    Queue
+    Queue,
 )
 
 ALL_CONTROL = "control.*"
-galaxy_exchange = Exchange('galaxy_core_exchange', type='topic')
+galaxy_exchange = Exchange("galaxy_core_exchange", type="topic")
 
 
 def all_control_queues_for_declare(application_stack):
@@ -22,8 +22,11 @@ def all_control_queues_for_declare(application_stack):
     build the entire routing table in producers.
     """
     # Get all active processes and construct queues for each process
-    process_names = ("{p.server_name}@{p.hostname}".format(p=p) for p in application_stack.app.database_heartbeat.get_active_processes())
-    return [Queue(f"control.{server_name}", galaxy_exchange, routing_key='control.*') for server_name in process_names]
+    process_names = (
+        "{p.server_name}@{p.hostname}".format(p=p)
+        for p in application_stack.app.database_heartbeat.get_active_processes()
+    )
+    return [Queue(f"control.{server_name}", galaxy_exchange, routing_key="control.*") for server_name in process_names]
 
 
 def control_queues_from_config(config):
@@ -33,8 +36,8 @@ def control_queues_from_config(config):
     """
     hostname = socket.gethostname()
     process_name = f"{config.server_name}@{hostname}"
-    exchange_queue = Queue(f"control.{process_name}", galaxy_exchange, routing_key='control.*')
-    non_exchange_queue = Queue(f"control.{process_name}", routing_key=f'control.{process_name}')
+    exchange_queue = Queue(f"control.{process_name}", galaxy_exchange, routing_key="control.*")
+    non_exchange_queue = Queue(f"control.{process_name}", routing_key=f"control.{process_name}")
     return exchange_queue, non_exchange_queue
 
 
diff --git a/lib/galaxy/quota/__init__.py b/lib/galaxy/quota/__init__.py
index baa8101cb53..7c119f6bdc0 100644
--- a/lib/galaxy/quota/__init__.py
+++ b/lib/galaxy/quota/__init__.py
@@ -6,7 +6,7 @@ import galaxy.util
 log = logging.getLogger(__name__)
 
 
-class QuotaAgent():  # metaclass=abc.ABCMeta
+class QuotaAgent:  # metaclass=abc.ABCMeta
     """Abstraction around querying Galaxy for quota available and used.
 
     Certain parts of the app that deal directly with modifying the quota assume more than
@@ -30,7 +30,7 @@ class QuotaAgent():  # metaclass=abc.ABCMeta
         if quota_bytes is not None:
             quota_str = galaxy.util.nice_size(quota_bytes)
         else:
-            quota_str = 'unlimited'
+            quota_str = "unlimited"
         return quota_str
 
     # TODO: make abstractmethod after they work better with mypy
@@ -114,16 +114,16 @@ class DatabaseQuotaAgent(QuotaAgent):
         for quota in quotas:
             if quota.deleted:
                 continue
-            if quota.operation == '=' and quota.bytes == -1:
+            if quota.operation == "=" and quota.bytes == -1:
                 rval = None
                 break
-            elif quota.operation == '=':
+            elif quota.operation == "=":
                 use_default = False
                 if quota.bytes > max:
                     max = quota.bytes
-            elif quota.operation == '+':
+            elif quota.operation == "+":
                 adjustment += quota.bytes
-            elif quota.operation == '-':
+            elif quota.operation == "-":
                 adjustment -= quota.bytes
         if use_default:
             max = self.default_registered_quota
@@ -144,7 +144,11 @@ class DatabaseQuotaAgent(QuotaAgent):
         return self._default_quota(self.model.DefaultQuotaAssociation.types.REGISTERED)
 
     def _default_quota(self, default_type):
-        dqa = self.sa_session.query(self.model.DefaultQuotaAssociation).filter(self.model.DefaultQuotaAssociation.type == default_type).first()
+        dqa = (
+            self.sa_session.query(self.model.DefaultQuotaAssociation)
+            .filter(self.model.DefaultQuotaAssociation.type == default_type)
+            .first()
+        )
         if not dqa:
             return None
         if dqa.quota.bytes < 0:
@@ -161,7 +165,11 @@ class DatabaseQuotaAgent(QuotaAgent):
         for gqa in quota.groups:
             self.sa_session.delete(gqa)
         # Find the old default, assign the new quota if it exists
-        dqa = self.sa_session.query(self.model.DefaultQuotaAssociation).filter(self.model.DefaultQuotaAssociation.type == default_type).first()
+        dqa = (
+            self.sa_session.query(self.model.DefaultQuotaAssociation)
+            .filter(self.model.DefaultQuotaAssociation.type == default_type)
+            .first()
+        )
         if dqa:
             dqa.quota = quota
         # Or create if necessary
@@ -236,4 +244,4 @@ def get_quota_agent(config, model) -> QuotaAgent:
     return quota_agent
 
 
-__all__ = ('get_quota_agent', 'NoQuotaAgent')
+__all__ = ("get_quota_agent", "NoQuotaAgent")
diff --git a/lib/galaxy/quota/_schema.py b/lib/galaxy/quota/_schema.py
index 0300b806398..11d3b29e45b 100644
--- a/lib/galaxy/quota/_schema.py
+++ b/lib/galaxy/quota/_schema.py
@@ -30,14 +30,16 @@ class QuotaOperation(str, Enum):
     SUBTRACT = "-"
 
 
-class DefaultQuotaTypes(str, Enum):  # TODO: should this replace lib.galaxy.model.DefaultQuotaAssociation.types at some point?
-    UNREGISTERED = 'unregistered'
-    REGISTERED = 'registered'
+class DefaultQuotaTypes(
+    str, Enum
+):  # TODO: should this replace lib.galaxy.model.DefaultQuotaAssociation.types at some point?
+    UNREGISTERED = "unregistered"
+    REGISTERED = "registered"
 
 
 class DefaultQuotaValues(str, Enum):
-    UNREGISTERED = 'unregistered'
-    REGISTERED = 'registered'
+    UNREGISTERED = "unregistered"
+    REGISTERED = "registered"
     NO = "no"
 
 
@@ -61,7 +63,7 @@ QuotaOperationField = Field(
         "- `=` : The quota is exactly the amount specified"
         "- `+` : The amount specified will be added to the amounts of the user's other associated quota definitions"
         "- `-` : The amount specified will be subtracted from the amounts of the user's other associated quota definitions"
-    )
+    ),
 )
 
 
@@ -74,7 +76,7 @@ class DefaultQuota(BaseModel):  # TODO: should this replace lib.galaxy.model.Def
             "The type of the default quota. Either one of:\n"
             " - `registered`: the associated quota will affect registered users.\n"
             " - `unregistered`: the associated quota will affect unregistered users.\n"
-        )
+        ),
     )
 
 
@@ -98,6 +100,7 @@ class GroupQuota(BaseModel):
 
 class QuotaBase(BaseModel):
     """Base model containing common fields for Quotas."""
+
     model_class: str = ModelClassField(QUOTA_MODEL_CLASS_NAME)
     id: EncodedDatabaseIdField = Field(
         ...,
@@ -109,6 +112,7 @@ class QuotaBase(BaseModel):
 
 class QuotaSummary(QuotaBase):
     """Contains basic information about a Quota"""
+
     url: str = Field(
         ...,
         title="URL",
@@ -120,7 +124,7 @@ class QuotaSummary(QuotaBase):
 class QuotaSummaryList(BaseModel):
     __root__: List[QuotaSummary] = Field(
         default=[],
-        title='List with summary information of Quotas.',
+        title="List with summary information of Quotas.",
     )
 
 
@@ -214,7 +218,7 @@ class UpdateQuotaParams(BaseModel):
         description=(
             "One of (``+``, ``-``, ``=``). If you wish to change this value,"
             " you must also provide the ``amount``, otherwise it will not take effect."
-        )
+        ),
     )
     default: Optional[DefaultQuotaValues] = Field(
         default=None,
diff --git a/lib/galaxy/schema/__init__.py b/lib/galaxy/schema/__init__.py
index a87fbf2dce4..a177f27532b 100644
--- a/lib/galaxy/schema/__init__.py
+++ b/lib/galaxy/schema/__init__.py
@@ -61,27 +61,28 @@ class FilterQueryParams(BaseModel):
 
 class SerializationParams(BaseModel):
     """Contains common parameters for customizing model serialization."""
+
     view: Optional[str] = Field(
         default=None,
-        title='View',
+        title="View",
         description=(
-            'The name of the view used to serialize this item. '
-            'This will return a predefined set of attributes of the item.'
+            "The name of the view used to serialize this item. "
+            "This will return a predefined set of attributes of the item."
         ),
-        example="summary"
+        example="summary",
     )
     keys: Optional[List[str]] = Field(
         default=None,
-        title='Keys',
+        title="Keys",
         description=(
-            'List of keys (name of the attributes) that will be returned in addition '
-            'to the ones included in the `view`.'
+            "List of keys (name of the attributes) that will be returned in addition "
+            "to the ones included in the `view`."
         ),
     )
     default_view: Optional[str] = Field(
         default=None,
-        title='Default View',
-        description='The item view that will be used in case none was specified.',
+        title="Default View",
+        description="The item view that will be used in case none was specified.",
     )
 
 
diff --git a/lib/galaxy/schema/fields.py b/lib/galaxy/schema/fields.py
index 01f7ba8b868..488d8540b2a 100644
--- a/lib/galaxy/schema/fields.py
+++ b/lib/galaxy/schema/fields.py
@@ -9,7 +9,7 @@ from pydantic import (
 
 from galaxy.security.idencoding import IdEncodingHelper
 
-ENCODED_DATABASE_ID_PATTERN = re.compile('f?[0-9a-f]+')
+ENCODED_DATABASE_ID_PATTERN = re.compile("f?[0-9a-f]+")
 ENCODED_ID_LENGTH_MULTIPLE = 16
 
 
@@ -37,51 +37,49 @@ class BaseDatabaseIdField:
         # the returned value will be ignored
         field_schema.update(
             min_length=16,
-            pattern='[0-9a-fA-F]+',
-            examples=['0123456789ABCDEF'],
+            pattern="[0-9a-fA-F]+",
+            examples=["0123456789ABCDEF"],
             type="string",
         )
 
     def __repr__(self):
-        return f'DatabaseID ({super().__repr__()})'
+        return f"DatabaseID ({super().__repr__()})"
 
 
 class DecodedDatabaseIdField(int, BaseDatabaseIdField):
-
     @classmethod
     def validate(cls, v):
         if not isinstance(v, str):
-            raise TypeError('String required')
+            raise TypeError("String required")
         if v.startswith("F"):
             # Library Folder ids start with an additional "F"
             v = v[1:]
         len_v = len(v)
         if len_v % ENCODED_ID_LENGTH_MULTIPLE:
-            raise ValueError('Invalid id length, must be multiple of 16')
+            raise ValueError("Invalid id length, must be multiple of 16")
         m = ENCODED_DATABASE_ID_PATTERN.fullmatch(v.lower())
         if not m:
-            raise ValueError('Invalid characters in encoded ID')
+            raise ValueError("Invalid characters in encoded ID")
         return cls(cls.security.decode_id(v))
 
 
 class EncodedDatabaseIdField(str, BaseDatabaseIdField):
-
     @classmethod
     def validate(cls, v):
         if isinstance(v, int):
             return cls(cls.security.encode_id(v))
         if not isinstance(v, str):
-            raise TypeError('String required')
+            raise TypeError("String required")
         if v.startswith("F"):
             # Library Folder ids start with an additional "F"
             len_v = len(v) - 1
         else:
             len_v = len(v)
         if len_v % ENCODED_ID_LENGTH_MULTIPLE:
-            raise ValueError('Invalid id length, must be multiple of 16')
+            raise ValueError("Invalid id length, must be multiple of 16")
         m = ENCODED_DATABASE_ID_PATTERN.fullmatch(v.lower())
         if not m:
-            raise ValueError('Invalid characters in encoded ID')
+            raise ValueError("Invalid characters in encoded ID")
         return cls(v)
 
 
@@ -118,6 +116,7 @@ def optional(*fields):
     to the decorator.
     Taken from https://github.com/samuelcolvin/pydantic/issues/1223#issuecomment-775363074
     """
+
     def dec(_cls):
         for field in fields:
             _cls.__fields__[field].required = False
diff --git a/lib/galaxy/schema/remote_files.py b/lib/galaxy/schema/remote_files.py
index def79b125a5..942cd9bf92e 100644
--- a/lib/galaxy/schema/remote_files.py
+++ b/lib/galaxy/schema/remote_files.py
@@ -86,13 +86,15 @@ class FilesSourcePlugin(BaseModel):
 class FilesSourcePluginList(BaseModel):
     __root__: List[FilesSourcePlugin] = Field(
         default=[],
-        title='List of files source plugins',
-        example=[{
-            "id": "_import",
-            "type": "gximport",
-            "uri_root": "gximport://",
-            "label": "Library Import Directory",
-            "doc": "Galaxy's library import directory",
-            "writable": False
-        }]
+        title="List of files source plugins",
+        example=[
+            {
+                "id": "_import",
+                "type": "gximport",
+                "uri_root": "gximport://",
+                "label": "Library Import Directory",
+                "doc": "Galaxy's library import directory",
+                "writable": False,
+            }
+        ],
     )
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index e54e2f7f06b..448f7597da0 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -171,6 +171,7 @@ ContentsUrlField = Field(
 
 class Model(BaseModel):
     """Base model definition with common configuration used by all derived models."""
+
     class Config:
         use_enum_values = True  # when using .dict()
         allow_population_by_field_name = True
@@ -178,22 +179,24 @@ class Model(BaseModel):
 
 class UserModel(Model):
     """User in a transaction context."""
-    id: EncodedDatabaseIdField = Field(title='ID', description='User ID')
-    username: str = Field(title='Username', description='User username')
-    email: str = Field(title='Email', description='User email')
-    active: bool = Field(title='Active', description='User is active')
-    deleted: bool = Field(title='Deleted', description='User is deleted')
-    last_password_change: datetime = Field(title='Last password change', description='')
+
+    id: EncodedDatabaseIdField = Field(title="ID", description="User ID")
+    username: str = Field(title="Username", description="User username")
+    email: str = Field(title="Email", description="User email")
+    active: bool = Field(title="Active", description="User is active")
+    deleted: bool = Field(title="Deleted", description="User is deleted")
+    last_password_change: datetime = Field(title="Last password change", description="")
     model_class: str = ModelClassField(USER_MODEL_CLASS_NAME)
 
 
 class GroupModel(BaseModel):
     """User group model"""
+
     model_class: str = ModelClassField(GROUP_MODEL_CLASS_NAME)
     id: EncodedDatabaseIdField = Field(
         ...,  # Required
-        title='ID',
-        description='Encoded group ID',
+        title="ID",
+        description="Encoded group ID",
     )
     name: str = Field(
         ...,  # Required
@@ -204,6 +207,7 @@ class GroupModel(BaseModel):
 
 class JobSourceType(str, Enum):
     """Available types of job sources (model classes) that produce dataset collections."""
+
     Job = "Job"
     ImplicitCollectionJobs = "ImplicitCollectionJobs"
     WorkflowInvocation = "WorkflowInvocation"
@@ -211,18 +215,21 @@ class JobSourceType(str, Enum):
 
 class HistoryContentType(str, Enum):
     """Available types of History contents."""
+
     dataset = "dataset"
     dataset_collection = "dataset_collection"
 
 
 class HistoryImportArchiveSourceType(str, Enum):
     """Available types of History archive sources."""
+
     url = "url"
     file = "file"
 
 
 class DCEType(str, Enum):  # TODO: suspiciously similar to HistoryContentType
     """Available types of dataset collection elements."""
+
     hda = "hda"
     dataset_collection = "dataset_collection"
 
@@ -258,6 +265,7 @@ class TagItem(ConstrainedStr):
 
 class TagCollection(Model):
     """Represents the collection of tags associated with an item."""
+
     __root__: List[TagItem] = Field(
         default=...,
         title="Tags",
@@ -267,6 +275,7 @@ class TagCollection(Model):
 
 class MetadataFile(Model):
     """Metadata file associated with a dataset."""
+
     file_type: str = Field(
         ...,
         title="File Type",
@@ -277,6 +286,7 @@ class MetadataFile(Model):
 
 class DatasetPermissions(Model):
     """Role-based permissions for accessing and managing a dataset."""
+
     manage: List[EncodedDatabaseIdField] = Field(
         [],
         title="Management",
@@ -291,11 +301,9 @@ class DatasetPermissions(Model):
 
 class Hyperlink(Model):
     """Represents some text with an Hyperlink."""
+
     target: str = Field(
-        ...,
-        title="Target",
-        description="Specifies where to open the linked document.",
-        example="_blank"
+        ..., title="Target", description="Specifies where to open the linked document.", example="_blank"
     )
     href: AnyUrl = Field(
         ...,
@@ -311,6 +319,7 @@ class Hyperlink(Model):
 
 class DisplayApp(Model):
     """Basic linked information about an application that can display certain datatypes."""
+
     label: str = Field(
         ...,
         title="Label",
@@ -330,6 +339,7 @@ class Visualization(Model):  # TODO annotate this model
 
 class HistoryItemBase(Model):
     """Basic information provided by items contained in a History."""
+
     id: EncodedDatabaseIdField = EncodedEntityIdField
     name: Optional[str] = Field(
         title="Name",
@@ -360,6 +370,7 @@ class HistoryItemBase(Model):
 
 class HistoryItemCommon(HistoryItemBase):
     """Common information provided by items contained in a History."""
+
     class Config:
         extra = Extra.allow
 
@@ -382,6 +393,7 @@ class HistoryItemCommon(HistoryItemBase):
 
 class HDASummary(HistoryItemCommon):
     """History Dataset Association summary information."""
+
     dataset_id: EncodedDatabaseIdField = Field(
         ...,
         title="Dataset ID",
@@ -403,6 +415,7 @@ class HDASummary(HistoryItemCommon):
 
 class HDAInaccessible(HistoryItemBase):
     """History Dataset Association information when the user can not access it."""
+
     accessible: bool = AccessibleField
     state: Dataset.states = DatasetStateField
 
@@ -412,12 +425,13 @@ HdaLddaField = Field(
     const=True,
     title="HDA or LDDA",
     description="Whether this dataset belongs to a history (HDA) or a library (LDDA).",
-    deprecated=False  # TODO Should this field be deprecated in favor of model_class?
+    deprecated=False,  # TODO Should this field be deprecated in favor of model_class?
 )
 
 
 class HDADetailed(HDASummary):
     """History Dataset Association detailed information."""
+
     model_class: str = ModelClassField(HDA_MODEL_CLASS_NAME)
     hda_ldda: DatasetSourceType = HdaLddaField
     accessible: bool = AccessibleField
@@ -471,7 +485,7 @@ class HDADetailed(HDASummary):
         ...,
         title="Data Type",
         description="The fully qualified name of the class implementing the data type of this dataset.",
-        example="galaxy.datatypes.data.Text"
+        example="galaxy.datatypes.data.Text",
     )
     peek: Optional[str] = Field(
         default=None,
@@ -549,6 +563,7 @@ class HDADetailed(HDASummary):
 
 class HDAExtended(HDADetailed):
     """History Dataset Association extended information."""
+
     tool_version: str = Field(
         ...,
         title="Tool Version",
@@ -568,12 +583,14 @@ class HDAExtended(HDADetailed):
 
 class HDABeta(HDADetailed):  # TODO: change HDABeta name to a more appropriate one.
     """History Dataset Association information used in the new Beta History."""
+
     # Equivalent to `betawebclient` serialization view for HDAs
     pass
 
 
 class DCSummary(Model):
     """Dataset Collection summary information."""
+
     model_class: str = ModelClassField(DC_MODEL_CLASS_NAME)
     id: EncodedDatabaseIdField = EncodedEntityIdField
     create_time: datetime = CreateTimeField
@@ -586,6 +603,7 @@ class DCSummary(Model):
 
 class HDAObject(Model):
     """History Dataset Association Object"""
+
     id: EncodedDatabaseIdField = EncodedEntityIdField
     model_class: str = ModelClassField(HDA_MODEL_CLASS_NAME)
     state: Dataset.states = DatasetStateField
@@ -598,17 +616,19 @@ class HDAObject(Model):
 
 class DCObject(Model):
     """Dataset Collection Object"""
+
     id: EncodedDatabaseIdField = EncodedEntityIdField
     model_class: str = ModelClassField(DC_MODEL_CLASS_NAME)
     collection_type: CollectionType = CollectionTypeField
     populated: Optional[bool] = PopulatedField
     element_count: Optional[int] = ElementCountField
     contents_url: Optional[RelativeUrl] = ContentsUrlField
-    elements: List['DCESummary'] = ElementsField
+    elements: List["DCESummary"] = ElementsField
 
 
 class DCESummary(Model):
     """Dataset Collection Element summary information."""
+
     id: EncodedDatabaseIdField = EncodedEntityIdField
     model_class: str = ModelClassField(DCE_MODEL_CLASS_NAME)
     element_index: int = Field(
@@ -638,13 +658,17 @@ DCObject.update_forward_refs()
 
 class DCDetailed(DCSummary):
     """Dataset Collection detailed information."""
+
     populated: bool = PopulatedField
     elements: List[DCESummary] = ElementsField
 
 
 class HDCASummary(HistoryItemCommon):
     """History Dataset Collection Association summary information."""
-    model_class: str = ModelClassField(HDCA_MODEL_CLASS_NAME)  # TODO: inconsistency? HDASummary does not have model_class only the detailed view has it...
+
+    model_class: str = ModelClassField(
+        HDCA_MODEL_CLASS_NAME
+    )  # TODO: inconsistency? HDASummary does not have model_class only the detailed view has it...
     type: str = Field(
         "collection",
         const=True,
@@ -670,12 +694,14 @@ class HDCASummary(HistoryItemCommon):
 
 class HDCADetailed(HDCASummary):
     """History Dataset Collection Association detailed information."""
+
     populated: bool = PopulatedField
     elements: List[DCESummary] = ElementsField
 
 
 class HistoryBase(BaseModel):
     """Provides basic configuration for all the History models."""
+
     class Config:
         use_enum_values = True  # When using .dict()
         extra = Extra.allow  # Allow any other extra fields
@@ -683,6 +709,7 @@ class HistoryBase(BaseModel):
 
 class UpdateContentItem(HistoryBase):
     """Used for updating a particular HDA. All fields are optional."""
+
     history_content_type: HistoryContentType = Field(
         ...,
         title="Content Type",
@@ -703,12 +730,7 @@ class UpdateHistoryContentsBatchPayload(HistoryBase):
     class Config:
         schema_extra = {
             "example": {
-                "items": [
-                    {
-                        "history_content_type": "dataset",
-                        "id": "string"
-                    }
-                ],
+                "items": [{"history_content_type": "dataset", "id": "string"}],
                 "visible": False,
             }
         }
@@ -716,6 +738,7 @@ class UpdateHistoryContentsBatchPayload(HistoryBase):
 
 class UpdateHistoryContentsPayload(HistoryBase):
     """Contains arbitrary property values that will be updated for a particular history item."""
+
     class Config:
         schema_extra = {
             "example": {
@@ -727,6 +750,7 @@ class UpdateHistoryContentsPayload(HistoryBase):
 
 class HistorySummary(HistoryBase):
     """History summary information."""
+
     model_class: str = ModelClassField(HISTORY_MODEL_CLASS_NAME)
     id: EncodedDatabaseIdField = EncodedEntityIdField
     name: str = Field(
@@ -756,6 +780,7 @@ class HistorySummary(HistoryBase):
 
 class HistoryActiveContentCounts(Model):
     """Contains the number of active, deleted or hidden items in a History."""
+
     active: int = Field(
         ...,
         title="Active",
@@ -779,6 +804,7 @@ HistoryStateIds = Dict[Dataset.states, List[EncodedDatabaseIdField]]
 
 class HistoryDetailed(HistorySummary):  # Equivalent to 'dev-detailed' view, which seems the default
     """History detailed information."""
+
     contents_url: RelativeUrl = ContentsUrlField
     size: int = Field(
         ...,
@@ -833,6 +859,7 @@ class HistoryDetailed(HistorySummary):  # Equivalent to 'dev-detailed' view, whi
 
 class HistoryBeta(HistoryDetailed):
     """History detailed information used in the new Beta History."""
+
     annotation: Optional[str] = AnnotationField
     empty: bool = Field(
         ...,
@@ -840,10 +867,7 @@ class HistoryBeta(HistoryDetailed):
         description="Whether this History has any content.",
     )
     nice_size: str = Field(
-        ...,
-        title="Nice Size",
-        description="Human-readable size of the contents of this history.",
-        example="95.4 MB"
+        ..., title="Nice Size", description="Human-readable size of the contents of this history.", example="95.4 MB"
     )
     purged: bool = Field(
         ...,
@@ -864,7 +888,9 @@ class HistoryBeta(HistoryDetailed):
 
 
 AnyHistoryView = Union[
-    HistoryBeta, HistoryDetailed, HistorySummary,
+    HistoryBeta,
+    HistoryDetailed,
+    HistorySummary,
     # Any will cover those cases in which only specific `keys` are requested
     # otherwise the validation will fail because the required fields are not returned
     Any,
@@ -915,34 +941,27 @@ class SortByEnum(str, Enum):
 
 
 class InvocationIndexPayload(Model):
-    workflow_id: Optional[DecodedDatabaseIdField] = Field(title="Workflow ID", description="Return only invocations for this Workflow ID")
-    history_id: Optional[DecodedDatabaseIdField] = Field(title="History ID", description="Return only invocations for this History ID")
-    job_id: Optional[DecodedDatabaseIdField] = Field(title="Job ID", description="Return only invocations for this Job ID")
-    user_id: Optional[DecodedDatabaseIdField] = Field(title="User ID", description="Return invocations for this User ID")
-    sort_by: Optional[SortByEnum] = Field(
-        title="Sort By",
-        description="Sort Workflow Invocations by this attribute"
+    workflow_id: Optional[DecodedDatabaseIdField] = Field(
+        title="Workflow ID", description="Return only invocations for this Workflow ID"
     )
-    sort_desc: bool = Field(
-        default=False,
-        descritpion="Sort in descending order?"
+    history_id: Optional[DecodedDatabaseIdField] = Field(
+        title="History ID", description="Return only invocations for this History ID"
     )
-    include_terminal: bool = Field(
-        default=True,
-        description="Set to false to only include terminal Invocations."
+    job_id: Optional[DecodedDatabaseIdField] = Field(
+        title="Job ID", description="Return only invocations for this Job ID"
     )
+    user_id: Optional[DecodedDatabaseIdField] = Field(
+        title="User ID", description="Return invocations for this User ID"
+    )
+    sort_by: Optional[SortByEnum] = Field(title="Sort By", description="Sort Workflow Invocations by this attribute")
+    sort_desc: bool = Field(default=False, descritpion="Sort in descending order?")
+    include_terminal: bool = Field(default=True, description="Set to false to only include terminal Invocations.")
     limit: Optional[int] = Field(
         default=100,
         lt=1000,
     )
-    offset: Optional[int] = Field(
-        default=0,
-        description="Number of invocations to skip"
-    )
-    instance: bool = Field(
-        default=False,
-        description="Is provided workflow id for Workflow instead of StoredWorkflow?"
-    )
+    offset: Optional[int] = Field(default=0, description="Number of invocations to skip")
+    instance: bool = Field(default=False, description="Is provided workflow id for Workflow instead of StoredWorkflow?")
 
 
 class CreateHistoryPayload(Model):
@@ -955,24 +974,20 @@ class CreateHistoryPayload(Model):
         default=None,
         title="History ID",
         description=(
-            "The encoded ID of the history to copy. "
-            "Provide this value only if you want to copy an existing history."
+            "The encoded ID of the history to copy. " "Provide this value only if you want to copy an existing history."
         ),
     )
     all_datasets: Optional[bool] = Field(
         default=True,
         title="All Datasets",
         description=(
-            "Whether to copy also deleted HDAs/HDCAs. Only applies when "
-            "providing a `history_id` to copy from."
+            "Whether to copy also deleted HDAs/HDCAs. Only applies when " "providing a `history_id` to copy from."
         ),
     )
     archive_source: Optional[str] = Field(
         default=None,
         title="Archive Source",
-        description=(
-            "The URL that will generate the archive to import when `archive_type='url'`. "
-        ),
+        description=("The URL that will generate the archive to import when `archive_type='url'`. "),
     )
     archive_type: Optional[HistoryImportArchiveSourceType] = Field(
         default=HistoryImportArchiveSourceType.url,
@@ -1003,7 +1018,7 @@ class CollectionElementIdentifier(Model):
         description="The encoded ID of the element.",
     )
     collection_type: Optional[CollectionType] = CollectionTypeField
-    element_identifiers: Optional[List['CollectionElementIdentifier']] = Field(
+    element_identifiers: Optional[List["CollectionElementIdentifier"]] = Field(
         default=None,
         title="Element Identifiers",
         description="List of elements that should be in the new sub-collection.",
@@ -1106,6 +1121,7 @@ class JobExportHistoryArchiveCollection(Model):
 
 class LabelValuePair(BaseModel):
     """Generic Label/Value pair model."""
+
     label: str = Field(
         ...,
         title="Label",
@@ -1137,6 +1153,7 @@ class CustomBuildsMetadataResponse(BaseModel):
 
 class JobIdResponse(BaseModel):
     """Contains the ID of the job associated with a particular request."""
+
     job_id: EncodedDatabaseIdField = Field(
         ...,
         title="Job ID",
@@ -1146,6 +1163,7 @@ class JobIdResponse(BaseModel):
 
 class HDCJobStateSummary(Model):
     """Overview of the job states working inside a dataset collection."""
+
     all_jobs: int = Field(
         0,
         title="All jobs",
@@ -1215,6 +1233,7 @@ class HDCJobStateSummary(Model):
 
 class HDCABeta(HDCADetailed):  # TODO: change HDCABeta name to a more appropriate one.
     """History Dataset Collection Association information used in the new Beta History."""
+
     # Equivalent to `betawebclient` serialization view for HDCAs
     collection_id: EncodedDatabaseIdField = Field(
         # TODO: inconsistency? the equivalent counterpart for HDAs, `dataset_id`, is declared in `HDASummary` scope
@@ -1229,8 +1248,7 @@ class HDCABeta(HDCADetailed):  # TODO: change HDCABeta name to a more appropriat
         description="Overview of the job states working inside the dataset collection.",
     )
     elements_datatypes: Set[str] = Field(
-        ...,
-        description="A set containing all the different element datatypes in the collection."
+        ..., description="A set containing all the different element datatypes in the collection."
     )
 
 
@@ -1263,7 +1281,7 @@ class JobBaseModel(Model):
         ...,
         title="Galaxy Version",
         description="The (major) version of Galaxy used to create this job.",
-        example="21.05"
+        example="21.05",
     )
 
 
@@ -1280,11 +1298,7 @@ class JobStateSummary(Model):
     model: str = ModelClassField("Job")
     populated_state: DatasetCollection.populated_states = PopulatedStateField
     states: Dict[Job.states, int] = Field(
-        {},
-        title="States",
-        description=(
-            "A dictionary of job states and the number of jobs in that state."
-        )
+        {}, title="States", description=("A dictionary of job states and the number of jobs in that state.")
     )
 
 
@@ -1298,13 +1312,13 @@ class WorkflowInvocationStateSummary(JobStateSummary):
 
 class JobSummary(JobBaseModel):
     """Basic information about a job."""
+
     external_id: Optional[str] = Field(
         None,
         title="External ID",
         description=(
-            "The job id used by the external job runner (Condor, Pulsar, etc.)"
-            "Only administrator can see this value."
-        )
+            "The job id used by the external job runner (Condor, Pulsar, etc.)" "Only administrator can see this value."
+        ),
     )
     command_line: Optional[str] = Field(
         None,
@@ -1394,13 +1408,14 @@ class JobMetric(Model):
                 "value": "2021-02-25 14:55:40",
                 "plugin": "core",
                 "name": "start_epoch",
-                "raw_value": "1614261340.0000000"
+                "raw_value": "1614261340.0000000",
             }
         }
 
 
 class JobMetricCollection(Model):
     """Represents a collection of metrics associated with a Job."""
+
     __root__: List[JobMetric] = Field(
         [],
         title="Job Metrics",
@@ -1559,6 +1574,7 @@ class InputStep(BaseModel):
 
 class WorkflowModuleType(str, Enum):
     """Available types of modules that represent a step in a Workflow."""
+
     data_input = "data_input"
     data_collection_input = "data_collection_input"
     parameter_input = "parameter_input"
@@ -1571,104 +1587,69 @@ class WorkflowStepBase(BaseModel):
     id: int = Field(
         ...,
         title="ID",
-        description="The identifier of the step. It matches the index order of the step inside the workflow."
-    )
-    type: WorkflowModuleType = Field(
-        ...,
-        title="Type",
-        description="The type of workflow module."
+        description="The identifier of the step. It matches the index order of the step inside the workflow.",
     )
+    type: WorkflowModuleType = Field(..., title="Type", description="The type of workflow module.")
     annotation: Optional[str] = AnnotationField
     input_steps: Dict[str, InputStep] = Field(
         ...,
         title="Input Steps",
-        description="A dictionary containing information about the inputs connected to this workflow step."
+        description="A dictionary containing information about the inputs connected to this workflow step.",
     )
 
 
 class ToolBasedWorkflowStep(WorkflowStepBase):
     tool_id: Optional[str] = Field(
-        None,
-        title="Tool ID",
-        description="The unique name of the tool associated with this step."
+        None, title="Tool ID", description="The unique name of the tool associated with this step."
     )
     tool_version: Optional[str] = Field(
-        None,
-        title="Tool Version",
-        description="The version of the tool associated with this step."
-    )
-    tool_inputs: Any = Field(
-        ...,
-        title="Tool Inputs",
-        description="TODO"
+        None, title="Tool Version", description="The version of the tool associated with this step."
     )
+    tool_inputs: Any = Field(..., title="Tool Inputs", description="TODO")
 
 
 class InputDataStep(ToolBasedWorkflowStep):
     type: WorkflowModuleType = Field(
-        WorkflowModuleType.data_input, const=True,
-        title="Type",
-        description="The type of workflow module."
+        WorkflowModuleType.data_input, const=True, title="Type", description="The type of workflow module."
     )
 
 
 class InputDataCollectionStep(ToolBasedWorkflowStep):
     type: WorkflowModuleType = Field(
-        WorkflowModuleType.data_collection_input, const=True,
-        title="Type",
-        description="The type of workflow module."
+        WorkflowModuleType.data_collection_input, const=True, title="Type", description="The type of workflow module."
     )
 
 
 class InputParameterStep(ToolBasedWorkflowStep):
     type: WorkflowModuleType = Field(
-        WorkflowModuleType.parameter_input, const=True,
-        title="Type",
-        description="The type of workflow module."
+        WorkflowModuleType.parameter_input, const=True, title="Type", description="The type of workflow module."
     )
 
 
 class PauseStep(WorkflowStepBase):
     type: WorkflowModuleType = Field(
-        WorkflowModuleType.pause, const=True,
-        title="Type",
-        description="The type of workflow module."
+        WorkflowModuleType.pause, const=True, title="Type", description="The type of workflow module."
     )
 
 
 class ToolStep(ToolBasedWorkflowStep):
     type: WorkflowModuleType = Field(
-        WorkflowModuleType.tool, const=True,
-        title="Type",
-        description="The type of workflow module."
+        WorkflowModuleType.tool, const=True, title="Type", description="The type of workflow module."
     )
 
 
 class SubworkflowStep(WorkflowStepBase):
     type: WorkflowModuleType = Field(
-        WorkflowModuleType.subworkflow, const=True,
-        title="Type",
-        description="The type of workflow module."
+        WorkflowModuleType.subworkflow, const=True, title="Type", description="The type of workflow module."
     )
     workflow_id: EncodedDatabaseIdField = Field(
-        ...,
-        title="Workflow ID",
-        description="The encoded ID of the workflow that will be run on this step."
+        ..., title="Workflow ID", description="The encoded ID of the workflow that will be run on this step."
     )
 
 
 class Creator(BaseModel):
-    class_: str = Field(
-        ...,
-        alias="class",
-        title="Class",
-        description="The class representing this creator."
-    )
-    name: str = Field(
-        ...,
-        title="Name",
-        description="The name of the creator."
-    )
+    class_: str = Field(..., alias="class", title="Class", description="The class representing this creator.")
+    name: str = Field(..., title="Name", description="The name of the creator.")
     address: Optional[str] = Field(
         None,
         title="Address",
@@ -1687,11 +1668,7 @@ class Creator(BaseModel):
         alias="faxNumber",
         title="Fax Number",
     )
-    identifier: Optional[str] = Field(
-        None,
-        title="Identifier",
-        description="Identifier (typically an orcid.org ID)"
-    )
+    identifier: Optional[str] = Field(None, title="Identifier", description="Identifier (typically an orcid.org ID)")
     image: Optional[AnyHttpUrl] = Field(
         None,
         title="Image URL",
@@ -1737,10 +1714,7 @@ class Person(Creator):
         description="Honorific Prefix (e.g. Dr/Mrs/Mr)",
     )
     honorific_suffix: Optional[str] = Field(
-        None,
-        alias="honorificSuffix",
-        title="Honorific Suffix",
-        description="Honorific Suffix (e.g. M.D.)"
+        None, alias="honorificSuffix", title="Honorific Suffix", description="Honorific Suffix (e.g. M.D.)"
     )
     job_title: Optional[str] = Field(
         None,
@@ -1752,28 +1726,21 @@ class Person(Creator):
 class StoredWorkflowDetailed(StoredWorkflowSummary):
     annotation: Optional[str] = AnnotationField  # Inconsistency? See comment on StoredWorkflowSummary.annotations
     license: Optional[str] = Field(
-        None,
-        title="License",
-        description="SPDX Identifier of the license associated with this workflow."
+        None, title="License", description="SPDX Identifier of the license associated with this workflow."
     )
     version: int = Field(
-        ...,
-        title="Version",
-        description="The version of the workflow represented by an incremental number."
+        ..., title="Version", description="The version of the workflow represented by an incremental number."
     )
     inputs: Dict[int, WorkflowInput] = Field(
-        {},
-        title="Inputs",
-        description="A dictionary containing information about all the inputs of the workflow."
+        {}, title="Inputs", description="A dictionary containing information about all the inputs of the workflow."
     )
     creator: Optional[List[Union[Person, Organization]]] = Field(
         None,
         title="Creator",
-        description=(
-            "Additional information about the creator (or multiple creators) of this workflow."
-        )
+        description=("Additional information about the creator (or multiple creators) of this workflow."),
     )
-    steps: Dict[int,
+    steps: Dict[
+        int,
         Union[
             InputDataStep,
             InputDataCollectionStep,
@@ -1781,48 +1748,22 @@ class StoredWorkflowDetailed(StoredWorkflowSummary):
             PauseStep,
             ToolStep,
             SubworkflowStep,
-        ]
-    ] = Field(
-        {},
-        title="Steps",
-        description="A dictionary with information about all the steps of the workflow."
-    )
+        ],
+    ] = Field({}, title="Steps", description="A dictionary with information about all the steps of the workflow.")
 
 
 class Input(BaseModel):
-    name: str = Field(
-        ...,
-        title="Name",
-        description="The name of the input."
-    )
-    description: str = Field(
-        ...,
-        title="Description",
-        description="The annotation or description of the input."
-
-    )
+    name: str = Field(..., title="Name", description="The name of the input.")
+    description: str = Field(..., title="Description", description="The annotation or description of the input.")
 
 
 class Output(BaseModel):
-    name: str = Field(
-        ...,
-        title="Name",
-        description="The name of the output."
-    )
-    type: str = Field(
-        ...,
-        title="Type",
-        description="The extension or type of output."
-
-    )
+    name: str = Field(..., title="Name", description="The name of the output.")
+    type: str = Field(..., title="Type", description="The extension or type of output.")
 
 
 class InputConnection(BaseModel):
-    id: int = Field(
-        ...,
-        title="ID",
-        description="The identifier of the input."
-    )
+    id: int = Field(..., title="ID", description="The identifier of the input.")
     output_name: str = Field(
         ...,
         title="Output Name",
@@ -1837,69 +1778,28 @@ class InputConnection(BaseModel):
 
 class WorkflowStepLayoutPosition(BaseModel):
     """Position and dimensions of the workflow step represented by a box on the graph."""
-    bottom: int = Field(
-        ...,
-        title="Bottom",
-        description="Position in pixels of the bottom of the box."
-    )
-    top: int = Field(
-        ...,
-        title="Top",
-        description="Position in pixels of the top of the box."
-    )
-    left: int = Field(
-        ...,
-        title="Left",
-        description="Left margin or left-most position of the box."
-    )
-    right: int = Field(
-        ...,
-        title="Right",
-        description="Right margin or right-most position of the box."
-    )
-    x: int = Field(
-        ...,
-        title="X",
-        description="Horizontal pixel coordinate of the top right corner of the box."
-    )
-    y: int = Field(
-        ...,
-        title="Y",
-        description="Vertical pixel coordinate of the top right corner of the box."
-    )
-    height: int = Field(
-        ...,
-        title="Height",
-        description="Height of the box in pixels."
-    )
-    width: int = Field(
-        ...,
-        title="Width",
-        description="Width of the box in pixels."
-    )
+
+    bottom: int = Field(..., title="Bottom", description="Position in pixels of the bottom of the box.")
+    top: int = Field(..., title="Top", description="Position in pixels of the top of the box.")
+    left: int = Field(..., title="Left", description="Left margin or left-most position of the box.")
+    right: int = Field(..., title="Right", description="Right margin or right-most position of the box.")
+    x: int = Field(..., title="X", description="Horizontal pixel coordinate of the top right corner of the box.")
+    y: int = Field(..., title="Y", description="Vertical pixel coordinate of the top right corner of the box.")
+    height: int = Field(..., title="Height", description="Height of the box in pixels.")
+    width: int = Field(..., title="Width", description="Width of the box in pixels.")
 
 
 class WorkflowStepToExportBase(BaseModel):
     id: int = Field(
         ...,
         title="ID",
-        description="The identifier of the step. It matches the index order of the step inside the workflow."
-    )
-    type: str = Field(
-        ...,
-        title="Type",
-        description="The type of workflow module."
-    )
-    name: str = Field(
-        ...,
-        title="Name",
-        description="The descriptive name of the module or step."
+        description="The identifier of the step. It matches the index order of the step inside the workflow.",
     )
+    type: str = Field(..., title="Type", description="The type of workflow module.")
+    name: str = Field(..., title="Name", description="The descriptive name of the module or step.")
     annotation: Optional[str] = AnnotationField
     tool_id: Optional[str] = Field(  # Duplicate of `content_id` or viceversa?
-        None,
-        title="Tool ID",
-        description="The unique name of the tool associated with this step."
+        None, title="Tool ID", description="The unique name of the tool associated with this step."
     )
     uuid: UUID4 = Field(
         ...,
@@ -1931,22 +1831,16 @@ class WorkflowStepToExportBase(BaseModel):
         description="Layout position of this step in the graph",
     )
     workflow_outputs: List[WorkflowOutput] = Field(
-        [],
-        title="Workflow Outputs",
-        description="The version of the tool associated with this step."
+        [], title="Workflow Outputs", description="The version of the tool associated with this step."
     )
 
 
 class WorkflowStepToExport(WorkflowStepToExportBase):
     content_id: Optional[str] = Field(  # Duplicate of `tool_id` or viceversa?
-        None,
-        title="Content ID",
-        description="TODO"
+        None, title="Content ID", description="TODO"
     )
     tool_version: Optional[str] = Field(
-        None,
-        title="Tool Version",
-        description="The version of the tool associated with this step."
+        None, title="Tool Version", description="The version of the tool associated with this step."
     )
     tool_state: Json = Field(
         ...,
@@ -2003,42 +1897,30 @@ class PostJobAction(BaseModel):
 
 class WorkflowToolStepToExport(WorkflowStepToExportBase):
     tool_shed_repository: ToolShedRepositorySummary = Field(
-        ...,
-        title="Tool Shed Repository",
-        description="Information about the origin repository of this tool."
+        ..., title="Tool Shed Repository", description="Information about the origin repository of this tool."
     )
     post_job_actions: Dict[str, PostJobAction] = Field(
-        ...,
-        title="Post-job Actions",
-        description="Set of actions that will be run when the job finish."
+        ..., title="Post-job Actions", description="Set of actions that will be run when the job finish."
     )
 
 
 class SubworkflowStepToExport(WorkflowStepToExportBase):
-    subworkflow: 'WorkflowToExport' = Field(
-        ...,
-        title="Subworkflow",
-        description="Full information about the subworkflow associated with this step."
+    subworkflow: "WorkflowToExport" = Field(
+        ..., title="Subworkflow", description="Full information about the subworkflow associated with this step."
     )
 
 
 class WorkflowToExport(BaseModel):
     a_galaxy_workflow: str = Field(  # Is this meant to be a bool instead?
-        "true",
-        title="Galaxy Workflow",
-        description="Whether this workflow is a Galaxy Workflow."
+        "true", title="Galaxy Workflow", description="Whether this workflow is a Galaxy Workflow."
     )
     format_version: str = Field(
         "0.1",
         alias="format-version",  # why this field uses `-` instead of `_`?
         title="Galaxy Workflow",
-        description="Whether this workflow is a Galaxy Workflow."
-    )
-    name: str = Field(
-        ...,
-        title="Name",
-        description="The name of the workflow."
+        description="Whether this workflow is a Galaxy Workflow.",
     )
+    name: str = Field(..., title="Name", description="The name of the workflow.")
     annotation: Optional[str] = AnnotationField
     tags: TagCollection
     uuid: Optional[UUID4] = Field(
@@ -2049,24 +1931,16 @@ class WorkflowToExport(BaseModel):
     creator: Optional[List[Union[Person, Organization]]] = Field(
         None,
         title="Creator",
-        description=(
-            "Additional information about the creator (or multiple creators) of this workflow."
-        )
+        description=("Additional information about the creator (or multiple creators) of this workflow."),
     )
     license: Optional[str] = Field(
-        None,
-        title="License",
-        description="SPDX Identifier of the license associated with this workflow."
+        None, title="License", description="SPDX Identifier of the license associated with this workflow."
     )
     version: int = Field(
-        ...,
-        title="Version",
-        description="The version of the workflow represented by an incremental number."
+        ..., title="Version", description="The version of the workflow represented by an incremental number."
     )
     steps: Dict[int, Union[SubworkflowStepToExport, WorkflowToolStepToExport, WorkflowStepToExport]] = Field(
-        {},
-        title="Steps",
-        description="A dictionary with information about all the steps of the workflow."
+        {}, title="Steps", description="A dictionary with information about all the steps of the workflow."
     )
 
 
@@ -2117,6 +1991,7 @@ class GroupRoleModel(BaseModel):
 class GroupRoleListModel(BaseModel):
     __root__: List[GroupRoleModel]
 
+
 # Libraries -----------------------------------------------------------------
 
 
@@ -2196,7 +2071,7 @@ class LibrarySummary(LibraryLegacySummary):
 class LibrarySummaryList(BaseModel):
     __root__: List[LibrarySummary] = Field(
         default=[],
-        title='List with summary information of Libraries.',
+        title="List with summary information of Libraries.",
     )
 
 
@@ -2267,7 +2142,9 @@ class LibraryCurrentPermissions(BaseModel):
     )
 
 
-RoleIdList = Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]  # Should we support just List[EncodedDatabaseIdField] in the future?
+RoleIdList = Union[
+    List[EncodedDatabaseIdField], EncodedDatabaseIdField
+]  # Should we support just List[EncodedDatabaseIdField] in the future?
 
 
 class LegacyLibraryPermissionsPayload(BaseModel):
@@ -2341,6 +2218,7 @@ class LibraryPermissionsPayload(LibraryPermissionsPayloadBase):
 
 # Library Folders -----------------------------------------------------------------
 
+
 class LibraryFolderPermissionAction(str, Enum):
     set_permissions = "set_permissions"
 
@@ -2524,6 +2402,7 @@ class CustomHistoryItem(Model):
     Allows arbitrary custom keys to be specified in the serialization
     parameters without a particular view (predefined set of keys).
     """
+
     class Config:
         extra = Extra.allow
 
@@ -2563,6 +2442,7 @@ class DeleteHistoryContentResult(CustomHistoryItem):
     """Contains minimum information about the deletion state of a history item.
 
     Can also contain any other properties of the item."""
+
     id: EncodedDatabaseIdField = Field(
         ...,
         title="ID",
@@ -2589,12 +2469,14 @@ class HistoryContentsArchiveDryRunResult(BaseModel):
 
     This is used for debugging purposes.
     """
+
     # TODO: Use Tuple again when https://github.com/tiangolo/fastapi/issues/3665 is fixed upstream
     __root__: List[List[str]]  # List[Tuple[str, str]]
 
 
 class ContentsNearStats(BaseModel):
     """Stats used by the `contents_near` endpoint."""
+
     matches: int
     matches_up: int
     matches_down: int
@@ -2621,6 +2503,7 @@ class HistoryContentsResult(Model):
     """Collection of history content items.
     Can contain different views and kinds of items.
     """
+
     __root__: List[AnyHistoryContentItem]
 
 
@@ -2634,6 +2517,7 @@ class ContentsNearResult(BaseModel):
 
 class SharingOptions(str, Enum):
     """Options for sharing resources that may have restricted access to all or part of their contents."""
+
     make_public = "make_public"
     make_accessible_to_shared = "make_accessible_to_shared"
     no_changes = "no_changes"
@@ -2658,8 +2542,7 @@ class ShareWithPayload(BaseModel):
         ...,
         title="User Identifiers",
         description=(
-            "A collection of encoded IDs (or email addresses) of users "
-            "that this resource will be shared with."
+            "A collection of encoded IDs (or email addresses) of users " "that this resource will be shared with."
         ),
     )
     share_option: Optional[SharingOptions] = Field(
@@ -2770,11 +2653,10 @@ class ShareHistoryExtra(ShareWithExtra):
     accessible_count: int = Field(
         0,
         title="Accessible Count",
-        description=(
-            "The number of datasets in the history that are public or accessible by all the target users."
-        ),
+        description=("The number of datasets in the history that are public or accessible by all the target users."),
     )
 
+
 # Pages -------------------------------------------------------
 
 
@@ -2894,5 +2776,5 @@ class PageDetails(PageSummary):
 class PageSummaryList(BaseModel):
     __root__: List[PageSummary] = Field(
         default=[],
-        title='List with summary information of Pages.',
+        title="List with summary information of Pages.",
     )
diff --git a/lib/galaxy/security/__init__.py b/lib/galaxy/security/__init__.py
index b58d1e10aca..0beacd7c4ee 100644
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -14,13 +14,32 @@ class Action:
 
 class RBACAgent:
     """Class that handles galaxy security"""
+
     permitted_actions = Bunch(
-        DATASET_MANAGE_PERMISSIONS=Action("manage permissions", "Users having associated role can manage the roles associated with permissions on this dataset.", "grant"),
-        DATASET_ACCESS=Action("access", "Users having associated role can import this dataset into their history for analysis.", "restrict"),
-        LIBRARY_ACCESS=Action("access library", "Restrict access to this library to only users having associated role", "restrict"),
-        LIBRARY_ADD=Action("add library item", "Users having associated role can add library items to this library item", "grant"),
-        LIBRARY_MODIFY=Action("modify library item", "Users having associated role can modify this library item", "grant"),
-        LIBRARY_MANAGE=Action("manage library permissions", "Users having associated role can manage roles associated with permissions on this library item", "grant")
+        DATASET_MANAGE_PERMISSIONS=Action(
+            "manage permissions",
+            "Users having associated role can manage the roles associated with permissions on this dataset.",
+            "grant",
+        ),
+        DATASET_ACCESS=Action(
+            "access",
+            "Users having associated role can import this dataset into their history for analysis.",
+            "restrict",
+        ),
+        LIBRARY_ACCESS=Action(
+            "access library", "Restrict access to this library to only users having associated role", "restrict"
+        ),
+        LIBRARY_ADD=Action(
+            "add library item", "Users having associated role can add library items to this library item", "grant"
+        ),
+        LIBRARY_MODIFY=Action(
+            "modify library item", "Users having associated role can modify this library item", "grant"
+        ),
+        LIBRARY_MANAGE=Action(
+            "manage library permissions",
+            "Users having associated role can manage roles associated with permissions on this library item",
+            "grant",
+        ),
     )
 
     def get_action(self, name, default=None):
@@ -35,7 +54,7 @@ class RBACAgent:
         return list(self.permitted_actions.__dict__.values())
 
     def get_item_actions(self, action, item):
-        raise Exception(f'No valid method of retrieving action ({action}) for item {item}.')
+        raise Exception(f"No valid method of retrieving action ({action}) for item {item}.")
 
     def guess_derived_permissions_for_datasets(self, datasets=None):
         datasets = datasets or []
@@ -60,7 +79,7 @@ class RBACAgent:
         raise Exception("Unimplemented Method")
 
     def associate_components(self, **kwd):
-        raise Exception(f'No valid method of associating provided components: {kwd}')
+        raise Exception(f"No valid method of associating provided components: {kwd}")
 
     def create_private_user_role(self, user):
         raise Exception("Unimplemented Method")
@@ -134,11 +153,15 @@ class RBACAgent:
         When getting permitted actions from an untrusted source like a
         form, ensure that they match our actual permitted actions.
         """
-        return [_ for _ in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings] if _ is not None]
+        return [
+            _
+            for _ in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings]
+            if _ is not None
+        ]
 
 
 def get_permitted_actions(filter=None):
-    '''Utility method to return a subset of RBACAgent's permitted actions'''
+    """Utility method to return a subset of RBACAgent's permitted actions"""
     if filter is None:
         return RBACAgent.permitted_actions
     tmp_bunch = Bunch()
diff --git a/lib/galaxy/security/idencoding.py b/lib/galaxy/security/idencoding.py
index 027fea1814e..a4fc096ba03 100644
--- a/lib/galaxy/security/idencoding.py
+++ b/lib/galaxy/security/idencoding.py
@@ -9,24 +9,25 @@ from Crypto.Random import get_random_bytes
 import galaxy.exceptions
 from galaxy.util import (
     smart_str,
-    unicodify
+    unicodify,
 )
 
 log = logging.getLogger(__name__)
 
 MAXIMUM_ID_SECRET_BITS = 448
 MAXIMUM_ID_SECRET_LENGTH = int(MAXIMUM_ID_SECRET_BITS / 8)
-KIND_TOO_LONG_MESSAGE = "Galaxy coding error, keep encryption 'kinds' smaller to utilize more bites of randomness from id_secret values."
+KIND_TOO_LONG_MESSAGE = (
+    "Galaxy coding error, keep encryption 'kinds' smaller to utilize more bites of randomness from id_secret values."
+)
 
 
 class IdEncodingHelper:
-
     def __init__(self, **config):
-        id_secret = config['id_secret']
+        id_secret = config["id_secret"]
         self.id_secret = id_secret
         self.id_cipher = Blowfish.new(smart_str(self.id_secret), mode=Blowfish.MODE_ECB)
 
-        per_kind_id_secret_base = config.get('per_kind_id_secret_base', self.id_secret)
+        per_kind_id_secret_base = config.get("per_kind_id_secret_base", self.id_secret)
         self.id_ciphers_for_kind = _cipher_cache(per_kind_id_secret_base)
 
     def encode_id(self, obj_id, kind=None):
@@ -38,7 +39,7 @@ class IdEncodingHelper:
         # Pad to a multiple of 8 with leading "!"
         s = (b"!" * (8 - len(s) % 8)) + s
         # Encrypt
-        return unicodify(codecs.encode(id_cipher.encrypt(s), 'hex'))
+        return unicodify(codecs.encode(id_cipher.encrypt(s), "hex"))
 
     def encode_dict_ids(self, a_dict, kind=None, skip_startswith=None):
         """
@@ -46,7 +47,7 @@ class IdEncodingHelper:
         (b) a key that ends with '_id'
         """
         for key, val in a_dict.items():
-            if key == 'id' or key.endswith('_id') and (skip_startswith is None or not key.startswith(skip_startswith)):
+            if key == "id" or key.endswith("_id") and (skip_startswith is None or not key.startswith(skip_startswith)):
                 a_dict[key] = self.encode_id(val, kind=kind)
 
         return a_dict
@@ -60,12 +61,12 @@ class IdEncodingHelper:
         if not isinstance(rval, dict):
             return rval
         for k, v in rval.items():
-            if (k == 'id' or k.endswith('_id')) and v is not None and k not in ['tool_id', 'external_id']:
+            if (k == "id" or k.endswith("_id")) and v is not None and k not in ["tool_id", "external_id"]:
                 try:
                     rval[k] = self.encode_id(v)
                 except Exception:
                     pass  # probably already encoded
-            if (k.endswith("_ids") and isinstance(v, list)):
+            if k.endswith("_ids") and isinstance(v, list):
                 try:
                     o = []
                     for i in v:
@@ -83,11 +84,15 @@ class IdEncodingHelper:
     def decode_id(self, obj_id, kind=None, object_name: Optional[str] = None):
         try:
             id_cipher = self.__id_cipher(kind)
-            return int(unicodify(id_cipher.decrypt(codecs.decode(obj_id, 'hex'))).lstrip("!"))
+            return int(unicodify(id_cipher.decrypt(codecs.decode(obj_id, "hex"))).lstrip("!"))
         except TypeError:
-            raise galaxy.exceptions.MalformedId(f"Malformed {object_name if object_name is not None else ''} id ( {obj_id} ) specified, unable to decode.")
+            raise galaxy.exceptions.MalformedId(
+                f"Malformed {object_name if object_name is not None else ''} id ( {obj_id} ) specified, unable to decode."
+            )
         except ValueError:
-            raise galaxy.exceptions.MalformedId(f"Wrong {object_name if object_name is not None else ''} id ( {obj_id} ) specified, unable to decode.")
+            raise galaxy.exceptions.MalformedId(
+                f"Wrong {object_name if object_name is not None else ''} id ( {obj_id} ) specified, unable to decode."
+            )
 
     def encode_guid(self, session_key):
         # Session keys are strings
@@ -95,16 +100,16 @@ class IdEncodingHelper:
         session_key = smart_str(session_key)
         s = (b"!" * (8 - len(session_key) % 8)) + session_key
         # Encrypt
-        return codecs.encode(self.id_cipher.encrypt(s), 'hex')
+        return codecs.encode(self.id_cipher.encrypt(s), "hex")
 
     def decode_guid(self, session_key):
         # Session keys are strings
-        decoded_session_key = codecs.decode(session_key, 'hex')
-        return unicodify(self.id_cipher.decrypt(decoded_session_key)).lstrip('!')
+        decoded_session_key = codecs.decode(session_key, "hex")
+        return unicodify(self.id_cipher.decrypt(decoded_session_key)).lstrip("!")
 
     def get_new_guid(self):
         # Generate a unique, high entropy 128 bit random number
-        return unicodify(codecs.encode(get_random_bytes(16), 'hex'))
+        return unicodify(codecs.encode(get_random_bytes(16), "hex"))
 
     def __id_cipher(self, kind):
         if not kind:
@@ -115,7 +120,6 @@ class IdEncodingHelper:
 
 
 class _cipher_cache(collections.defaultdict):
-
     def __init__(self, secret_base):
         self.secret_base = secret_base
 
@@ -126,8 +130,7 @@ class _cipher_cache(collections.defaultdict):
 
 
 def _last_bits(secret):
-    """We append the kind at the end, so just use the bits at the end.
-    """
+    """We append the kind at the end, so just use the bits at the end."""
     last_bits = smart_str(secret)
     if len(last_bits) > MAXIMUM_ID_SECRET_LENGTH:
         last_bits = last_bits[-MAXIMUM_ID_SECRET_LENGTH:]
diff --git a/lib/galaxy/security/object_wrapper.py b/lib/galaxy/security/object_wrapper.py
index bec7d268710..359035aabbe 100644
--- a/lib/galaxy/security/object_wrapper.py
+++ b/lib/galaxy/security/object_wrapper.py
@@ -45,19 +45,51 @@ log = logging.getLogger(__name__)
 # Define different behaviors for different types, see also: https://docs.python.org/2/library/types.html
 
 # Known Callable types
-__CALLABLE_TYPES__ = (FunctionType, MethodType, GeneratorType, CodeType, BuiltinFunctionType, BuiltinMethodType, )
+__CALLABLE_TYPES__ = (
+    FunctionType,
+    MethodType,
+    GeneratorType,
+    CodeType,
+    BuiltinFunctionType,
+    BuiltinMethodType,
+)
 
 # Always wrap these types without attempting to subclass
-__WRAP_NO_SUBCLASS__ = (ModuleType, XRangeType, SliceType, BufferType, TracebackType, FrameType, DictProxyType,
-                        GetSetDescriptorType, MemberDescriptorType) + __CALLABLE_TYPES__
+__WRAP_NO_SUBCLASS__ = (
+    ModuleType,
+    XRangeType,
+    SliceType,
+    BufferType,
+    TracebackType,
+    FrameType,
+    DictProxyType,
+    GetSetDescriptorType,
+    MemberDescriptorType,
+) + __CALLABLE_TYPES__
 
 # Don't wrap or sanitize.
-__DONT_SANITIZE_TYPES__ = (Number, bool, NoneType, NotImplementedType, EllipsisType, bytearray, )
+__DONT_SANITIZE_TYPES__ = (
+    Number,
+    bool,
+    NoneType,
+    NotImplementedType,
+    EllipsisType,
+    bytearray,
+)
 
 # Wrap contents, but not the container
-__WRAP_SEQUENCES__ = (tuple, list, )
-__WRAP_SETS__ = (set, frozenset, )
-__WRAP_MAPPINGS__ = (dict, UserDict, )
+__WRAP_SEQUENCES__ = (
+    tuple,
+    list,
+)
+__WRAP_SETS__ = (
+    set,
+    frozenset,
+)
+__WRAP_MAPPINGS__ = (
+    dict,
+    UserDict,
+)
 
 
 # Define the set of characters that are not sanitized, and define a set of mappings for those that are.
@@ -65,18 +97,20 @@ __WRAP_MAPPINGS__ = (dict, UserDict, )
 VALID_CHARACTERS = set(f"{string.ascii_letters + string.digits} -=_.()/+*^,:?!@")
 
 # characters that are allowed but need to be escaped
-CHARACTER_MAP = {'>': '__gt__',
-                 '<': '__lt__',
-                 "'": '__sq__',
-                 '"': '__dq__',
-                 '[': '__ob__',
-                 ']': '__cb__',
-                 '{': '__oc__',
-                 '}': '__cc__',
-                 '\n': '__cn__',
-                 '\r': '__cr__',
-                 '\t': '__tc__',
-                 '#': '__pd__'}
+CHARACTER_MAP = {
+    ">": "__gt__",
+    "<": "__lt__",
+    "'": "__sq__",
+    '"': "__dq__",
+    "[": "__ob__",
+    "]": "__cb__",
+    "{": "__oc__",
+    "}": "__cc__",
+    "\n": "__cn__",
+    "\r": "__cr__",
+    "\t": "__tc__",
+    "#": "__pd__",
+}
 
 INVALID_CHARACTER = "X"
 
@@ -91,8 +125,12 @@ def cmp(x, y):
     return (x > y) - (x < y)
 
 
-def sanitize_lists_to_string(values, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP, invalid_character=INVALID_CHARACTER):
-    return _sanitize_lists_to_string(values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character)
+def sanitize_lists_to_string(
+    values, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP, invalid_character=INVALID_CHARACTER
+):
+    return _sanitize_lists_to_string(
+        values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character
+    )
 
 
 def wrap_with_safe_string(value, no_wrap_classes=None):
@@ -140,11 +178,18 @@ def wrap_with_safe_string(value, no_wrap_classes=None):
             do_wrap_func = global_dict.get(do_wrap_func_name, __do_wrap)
         else:
             try:
-                wrapped_class = type(wrapped_class_name, (safe_class, wrapped_class, ), {})
+                wrapped_class = type(
+                    wrapped_class_name,
+                    (
+                        safe_class,
+                        wrapped_class,
+                    ),
+                    {},
+                )
             except TypeError as e:
                 # Fail-safe for when a class cannot be dynamically subclassed.
                 log.warning(f"Unable to create dynamic subclass {wrapped_class_name} for {type(value)}, {value}: {e}")
-                wrapped_class = type(wrapped_class_name, (safe_class, ), {})
+                wrapped_class = type(wrapped_class_name, (safe_class,), {})
             if wrapped_class not in (SafeStringWrapper, CallableSafeStringWrapper):
                 # Save this wrapper for reuse and pickling/copying
                 global_dict[wrapped_class_name] = wrapped_class
@@ -152,7 +197,14 @@ def wrap_with_safe_string(value, no_wrap_classes=None):
                 global_dict[do_wrap_func_name] = do_wrap_func
 
                 def pickle_safe_object(safe_object):
-                    return (wrapped_class, (safe_object.unsanitized, do_wrap_func, ))
+                    return (
+                        wrapped_class,
+                        (
+                            safe_object.unsanitized,
+                            do_wrap_func,
+                        ),
+                    )
+
                 # Set pickle and copy properties
                 copyreg.pickle(wrapped_class, pickle_safe_object, do_wrap_func)
         return wrapped_class(value, safe_string_wrapper_function=do_wrap_func)
@@ -186,14 +238,17 @@ class SafeStringWrapper:
     is of a type found in __DONT_SANITIZE_TYPES__ + __DONT_WRAP_TYPES__, where e.g. ~(strings
     will still be sanitized, but not wrapped), and e.g. integers will have neither.
     """
-    __UNSANITIZED_ATTRIBUTE_NAME__ = 'unsanitized'
-    __NO_WRAP_NAMES__ = ['__safe_string_wrapper_function__', '__class__', __UNSANITIZED_ATTRIBUTE_NAME__]
+
+    __UNSANITIZED_ATTRIBUTE_NAME__ = "unsanitized"
+    __NO_WRAP_NAMES__ = ["__safe_string_wrapper_function__", "__class__", __UNSANITIZED_ATTRIBUTE_NAME__]
 
     def __new__(cls, *arg, **kwd):
         # We need to define a __new__ since, we are subclassing from e.g. immutable str, which internally sets data
         # that will be used when other + this (this + other is handled by __add__)
         try:
-            sanitized_value = sanitize_lists_to_string(arg[0], valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)
+            sanitized_value = sanitize_lists_to_string(
+                arg[0], valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP
+            )
             return super().__new__(cls, sanitized_value)
         except TypeError:
             # Class to be wrapped takes no parameters.
@@ -205,7 +260,9 @@ class SafeStringWrapper:
         self.__safe_string_wrapper_function__ = safe_string_wrapper_function
 
     def __str__(self):
-        return sanitize_lists_to_string(self.unsanitized, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)
+        return sanitize_lists_to_string(
+            self.unsanitized, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP
+        )
 
     def __repr__(self):
         return f"{sanitize_lists_to_string(self.__class__.__name__, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)} object at {id(self):x} on: {sanitize_lists_to_string(repr(self.unsanitized), valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)}"
@@ -252,6 +309,7 @@ class SafeStringWrapper:
 
     def __bool__(self):
         return bool(self.unsanitized)
+
     __nonzero__ = __bool__
 
     # Do not implement __unicode__, we will rely on __str__
@@ -283,7 +341,7 @@ class SafeStringWrapper:
     def __getattribute__(self, name):
         if name in SafeStringWrapper.__NO_WRAP_NAMES__:
             return object.__getattribute__(self, name)
-        return self.__safe_string_wrapper_function__(getattr(object.__getattribute__(self, 'unsanitized'), name))
+        return self.__safe_string_wrapper_function__(getattr(object.__getattribute__(self, "unsanitized"), name))
 
     # Skip Descriptors
 
@@ -458,14 +516,13 @@ class SafeStringWrapper:
 
 
 class CallableSafeStringWrapper(SafeStringWrapper):
-
     def __call__(self, *args, **kwds):
         return self.__safe_string_wrapper_function__(self.unsanitized(*args, **kwds))
 
 
 # Enable pickling/deepcopy
 def pickle_SafeStringWrapper(safe_object):
-    args = (safe_object.unsanitized, )
+    args = (safe_object.unsanitized,)
     cls = SafeStringWrapper
     if isinstance(safe_object, CallableSafeStringWrapper):
         cls = CallableSafeStringWrapper
diff --git a/lib/galaxy/security/passwords.py b/lib/galaxy/security/passwords.py
index ad673f01ab4..333a02756b1 100644
--- a/lib/galaxy/security/passwords.py
+++ b/lib/galaxy/security/passwords.py
@@ -5,12 +5,12 @@ from os import urandom
 from galaxy.util import (
     safe_str_cmp,
     smart_str,
-    unicodify
+    unicodify,
 )
 
 SALT_LENGTH = 12
 KEY_LENGTH = 24
-HASH_FUNCTION = 'sha256'
+HASH_FUNCTION = "sha256"
 COST_FACTOR = 100000
 
 
@@ -46,12 +46,12 @@ def hash_password_PBKDF2(password):
     hashed_password = pbkdf2_bin(password, salt, COST_FACTOR, KEY_LENGTH, HASH_FUNCTION)
     encoded_password = unicodify(b64encode(hashed_password))
     # Format
-    return f'PBKDF2${HASH_FUNCTION}${COST_FACTOR}${unicodify(salt)}${encoded_password}'
+    return f"PBKDF2${HASH_FUNCTION}${COST_FACTOR}${unicodify(salt)}${encoded_password}"
 
 
 def check_password_PBKDF2(guess, hashed):
     # Split the database representation to extract cost_factor and salt
-    name, hash_function, cost_factor, salt, encoded_original = hashed.split('$', 5)
+    name, hash_function, cost_factor, salt, encoded_original = hashed.split("$", 5)
     # Hash the guess using the same parameters
     hashed_guess = pbkdf2_bin(guess, salt, int(cost_factor), KEY_LENGTH, hash_function)
     encoded_guess = unicodify(b64encode(hashed_guess))
diff --git a/lib/galaxy/security/ssh_util.py b/lib/galaxy/security/ssh_util.py
index 77caacf6dd7..100b1b9f4cc 100644
--- a/lib/galaxy/security/ssh_util.py
+++ b/lib/galaxy/security/ssh_util.py
@@ -15,7 +15,7 @@ def generate_ssh_keys() -> SSHKeys:
     """Returns a named tuple with private and public key and their paths."""
     key = RSA.generate(2048)
     private_key = key.export_key()
-    public_key = key.publickey().export_key(format='OpenSSH')
+    public_key = key.publickey().export_key(format="OpenSSH")
     with tempfile.NamedTemporaryFile(delete=False) as f:
         f.write(private_key)
         private_key_file = f.name
diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index 4f20444b3e9..e49795c50ee 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -20,7 +20,7 @@ PUBLICNAME_MIN_LEN = 3
 PUBLICNAME_MAX_LEN = 255
 VALID_PUBLICNAME_RE = re.compile(r"^[a-z0-9._\-]+$")
 VALID_PUBLICNAME_SUB = re.compile(r"[^a-z0-9._\-]")
-FILL_CHAR = '-'
+FILL_CHAR = "-"
 
 # Password validity parameters
 PASSWORD_MIN_LEN = 6
@@ -30,7 +30,7 @@ def validate_email_str(email):
     """Validates a string containing an email address."""
     if not email:
         return "No email address was provided."
-    if not(VALID_EMAIL_RE.match(email)):
+    if not (VALID_EMAIL_RE.match(email)):
         return "The format of the email address is not correct."
     elif len(email) > EMAIL_MAX_LEN:
         return "Email address cannot be more than %d characters in length." % EMAIL_MAX_LEN
@@ -49,9 +49,9 @@ def validate_publicname_str(publicname):
         return "Public name must be at least %d characters in length." % (PUBLICNAME_MIN_LEN)
     if len(publicname) > PUBLICNAME_MAX_LEN:
         return "Public name cannot be more than %d characters in length." % (PUBLICNAME_MAX_LEN)
-    if not(VALID_PUBLICNAME_RE.match(publicname)):
+    if not (VALID_PUBLICNAME_RE.match(publicname)):
         return "Public name must contain only lower-case letters, numbers, '.', '_' and '-'."
-    return ''
+    return ""
 
 
 def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
@@ -59,11 +59,16 @@ def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
     Validates the email format, also checks whether the domain is blocklisted in the disposable domains configuration.
     """
     if (user and user.email == email) or (email == "" and allow_empty):
-        return ''
+        return ""
     message = validate_email_str(email)
     if message:
         pass
-    elif check_dup and trans.sa_session.query(trans.app.model.User).filter(func.lower(trans.app.model.User.table.c.email) == email.lower()).first():
+    elif (
+        check_dup
+        and trans.sa_session.query(trans.app.model.User)
+        .filter(func.lower(trans.app.model.User.table.c.email) == email.lower())
+        .first()
+    ):
         message = f"User with email '{email}' already exists."
     #  If the allowlist is not empty filter out any domain not in the list and ignore blocklist.
     elif trans.app.config.email_domain_allowlist_content is not None:
@@ -79,10 +84,10 @@ def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
 
 
 def extract_domain(email, base_only=False):
-    domain = email.split('@')[1]
-    parts = domain.split('.')
+    domain = email.split("@")[1]
+    parts = domain.split(".")
     if len(parts) > 2 and base_only:
-        return ('.').join(parts[-2:])
+        return (".").join(parts[-2:])
     return domain
 
 
@@ -92,13 +97,13 @@ def validate_publicname(trans, publicname, user=None):
     allowed characters, and that the username is not taken already.
     """
     if user and user.username == publicname:
-        return ''
+        return ""
     message = validate_publicname_str(publicname)
     if message:
         return message
     if trans.sa_session.query(trans.app.model.User).filter_by(username=publicname).first():
         return "Public name is taken; please choose another."
-    return ''
+    return ""
 
 
 def transform_publicname(publicname):
@@ -108,7 +113,7 @@ def transform_publicname(publicname):
     FILL_CHAR is used to extend or replace characters.
     """
     # TODO: Enhance to allow generation of semi-random publicnnames e.g., when valid but taken
-    if publicname not in ['None', None, '']:
+    if publicname not in ["None", None, ""]:
         publicname = publicname.lower()
         publicname = re.sub(VALID_PUBLICNAME_SUB, FILL_CHAR, publicname)
         publicname = publicname.ljust(PUBLICNAME_MIN_LEN + 1, FILL_CHAR)[:PUBLICNAME_MAX_LEN]
diff --git a/lib/galaxy/security/vault.py b/lib/galaxy/security/vault.py
index cf2e3a928de..104b90e2763 100644
--- a/lib/galaxy/security/vault.py
+++ b/lib/galaxy/security/vault.py
@@ -2,15 +2,22 @@ import abc
 import logging
 import os
 import re
-from typing import List, Optional
+from typing import (
+    List,
+    Optional,
+)
 
 import yaml
-from cryptography.fernet import Fernet, MultiFernet
+from cryptography.fernet import (
+    Fernet,
+    MultiFernet,
+)
 
 try:
     from custos.clients.resource_secret_management_client import ResourceSecretManagementClient
     from custos.clients.utils.exceptions.CustosExceptions import KeyDoesNotExist
     from custos.transport.settings import CustosServerClientSettings
+
     custos_sdk_available = True
 except ImportError:
     custos_sdk_available = False
@@ -75,46 +82,49 @@ class Vault(abc.ABC):
 
 
 class NullVault(Vault):
-
     def read_secret(self, key: str) -> Optional[str]:
-        raise InvalidVaultConfigException("No vault configured. Make sure the vault_config_file setting is defined in galaxy.yml")
+        raise InvalidVaultConfigException(
+            "No vault configured. Make sure the vault_config_file setting is defined in galaxy.yml"
+        )
 
     def write_secret(self, key: str, value: str) -> None:
-        raise InvalidVaultConfigException("No vault configured. Make sure the vault_config_file setting is defined in galaxy.yml")
+        raise InvalidVaultConfigException(
+            "No vault configured. Make sure the vault_config_file setting is defined in galaxy.yml"
+        )
 
     def list_secrets(self, key: str) -> List[str]:
         raise NotImplementedError()
 
 
 class HashicorpVault(Vault):
-
     def __init__(self, config):
         if not hvac:
-            raise InvalidVaultConfigException("Hashicorp vault library 'hvac' is not available. Make sure hvac is installed.")
-        self.vault_address = config.get('vault_address')
-        self.vault_token = config.get('vault_token')
+            raise InvalidVaultConfigException(
+                "Hashicorp vault library 'hvac' is not available. Make sure hvac is installed."
+            )
+        self.vault_address = config.get("vault_address")
+        self.vault_token = config.get("vault_token")
         self.client = hvac.Client(url=self.vault_address, token=self.vault_token)
 
     def read_secret(self, key: str) -> Optional[str]:
         try:
             response = self.client.secrets.kv.read_secret_version(path=key)
-            return response['data']['data'].get('value')
+            return response["data"]["data"].get("value")
         except hvac.exceptions.InvalidPath:
             return None
 
     def write_secret(self, key: str, value: str) -> None:
-        self.client.secrets.kv.v2.create_or_update_secret(path=key, secret={'value': value})
+        self.client.secrets.kv.v2.create_or_update_secret(path=key, secret={"value": value})
 
     def list_secrets(self, key: str) -> List[str]:
         raise NotImplementedError()
 
 
 class DatabaseVault(Vault):
-
     def __init__(self, sa_session, config):
         self.sa_session = sa_session
-        self.encryption_keys = config.get('encryption_keys')
-        self.fernet_keys = [Fernet(key.encode('utf-8')) for key in self.encryption_keys]
+        self.encryption_keys = config.get("encryption_keys")
+        self.fernet_keys = [Fernet(key.encode("utf-8")) for key in self.encryption_keys]
 
     def _get_multi_fernet(self) -> MultiFernet:
         return MultiFernet(self.fernet_keys)
@@ -140,33 +150,36 @@ class DatabaseVault(Vault):
         key_obj = self.sa_session.query(model.Vault).filter_by(key=key).first()
         if key_obj and key_obj.value:
             f = self._get_multi_fernet()
-            return f.decrypt(key_obj.value.encode('utf-8')).decode('utf-8')
+            return f.decrypt(key_obj.value.encode("utf-8")).decode("utf-8")
         return None
 
     def write_secret(self, key: str, value: str) -> None:
         f = self._get_multi_fernet()
-        token = f.encrypt(value.encode('utf-8'))
-        self._update_or_create(key=key, value=token.decode('utf-8'))
+        token = f.encrypt(value.encode("utf-8"))
+        self._update_or_create(key=key, value=token.decode("utf-8"))
 
     def list_secrets(self, key: str) -> List[str]:
         raise NotImplementedError()
 
 
 class CustosVault(Vault):
-
     def __init__(self, config):
         if not custos_sdk_available:
-            raise InvalidVaultConfigException("Custos sdk library 'custos-sdk' is not available. Make sure the custos-sdk is installed.")
-        custos_settings = CustosServerClientSettings(custos_host=config.get('custos_host'),
-                                                     custos_port=config.get('custos_port'),
-                                                     custos_client_id=config.get('custos_client_id'),
-                                                     custos_client_sec=config.get('custos_client_sec'))
+            raise InvalidVaultConfigException(
+                "Custos sdk library 'custos-sdk' is not available. Make sure the custos-sdk is installed."
+            )
+        custos_settings = CustosServerClientSettings(
+            custos_host=config.get("custos_host"),
+            custos_port=config.get("custos_port"),
+            custos_client_id=config.get("custos_client_id"),
+            custos_client_sec=config.get("custos_client_sec"),
+        )
         self.client = ResourceSecretManagementClient(custos_settings)
 
     def read_secret(self, key: str) -> Optional[str]:
         try:
             response = self.client.get_kv_credential(key=key)
-            return response.get('value')
+            return response.get("value")
         except KeyDoesNotExist:
             return None
 
@@ -178,7 +191,6 @@ class CustosVault(Vault):
 
 
 class UserVaultWrapper(Vault):
-
     def __init__(self, vault: Vault, user):
         self.vault = vault
         self.user = user
@@ -213,7 +225,8 @@ class VaultKeyValidationWrapper(Vault):
         if not self.validate_key(key):
             raise InvalidVaultKeyException(
                 f"Vault key: {key} is invalid. Make sure that it is not empty, contains double slashes or contains"
-                "whitespace before or after the separator.")
+                "whitespace before or after the separator."
+            )
         return key
 
     def read_secret(self, key: str) -> Optional[str]:
@@ -248,7 +261,6 @@ class VaultKeyPrefixWrapper(Vault):
 
 
 class VaultFactory(object):
-
     @staticmethod
     def load_vault_config(vault_conf_yml: str) -> Optional[dict]:
         if os.path.exists(vault_conf_yml):
@@ -267,13 +279,13 @@ class VaultFactory(object):
             vault = CustosVault(cfg)
         else:
             raise InvalidVaultConfigException(f"Unknown vault type: {vault_type}")
-        vault_prefix = cfg.get('path_prefix') or "/galaxy"
+        vault_prefix = cfg.get("path_prefix") or "/galaxy"
         return VaultKeyValidationWrapper(VaultKeyPrefixWrapper(vault, prefix=vault_prefix))
 
     @staticmethod
     def from_app(app) -> Vault:
         vault_config = VaultFactory.load_vault_config(app.config.vault_config_file)
         if vault_config:
-            return VaultFactory.from_vault_type(app, vault_config.get('type', None), vault_config)
+            return VaultFactory.from_vault_type(app, vault_config.get("type", None), vault_config)
         log.warning("No vault configured. We recommend defining the vault_config_file setting in galaxy.yml")
         return NullVault()
diff --git a/lib/galaxy/selenium/cli.py b/lib/galaxy/selenium/cli.py
index bf476c0be11..9445fa3ac65 100644
--- a/lib/galaxy/selenium/cli.py
+++ b/lib/galaxy/selenium/cli.py
@@ -19,34 +19,34 @@ def add_selenium_arguments(parser):
     """Add common selenium arguments for argparse driver utility."""
 
     parser.add_argument(
-        '--selenium-browser',
+        "--selenium-browser",
         default="auto",
         help=BROWSER_DESCRIPTION,
     )
     parser.add_argument(
-        '--selenium-headless',
+        "--selenium-headless",
         default=False,
         action="store_true",
         help=HEADLESS_DESCRIPTION,
     )
     parser.add_argument(
-        '--selenium-remote',
+        "--selenium-remote",
         default=False,
         action="store_true",
         help=REMOTE_DESCRIPTION,
     )
     parser.add_argument(
-        '--selenium-remote-host',
+        "--selenium-remote-host",
         default="127.0.0.1",
         help=REMOTE_HOST_DESCRIPTION,
     )
     parser.add_argument(
-        '--selenium-remote-port',
+        "--selenium-remote-port",
         default="4444",
         help=REMOTE_PORT_DESCRIPTION,
     )
     parser.add_argument(
-        '--galaxy_url',
+        "--galaxy_url",
         default="http://127.0.0.1:8080/",
         help=GALAXY_URL_DESCRIPTION,
     )
diff --git a/lib/galaxy/selenium/components.py b/lib/galaxy/selenium/components.py
index d99b1181a57..6c748af7e90 100644
--- a/lib/galaxy/selenium/components.py
+++ b/lib/galaxy/selenium/components.py
@@ -12,7 +12,6 @@ from galaxy.util.bunch import Bunch
 
 
 class Target(metaclass=ABCMeta):
-
     @abstractproperty
     def description(self):
         """Return a plain-text description of the browser target for logging/messages."""
@@ -23,7 +22,6 @@ class Target(metaclass=ABCMeta):
 
 
 class SelectorTemplate(Target):
-
     def __init__(self, selector: str, selector_type: str, children=None, kwds=None, with_classes=None, with_data=None):
         if selector_type == "data-description":
             selector_type = "css"
@@ -45,13 +43,27 @@ class SelectorTemplate(Target):
 
     def with_class(self, class_):
         assert self.selector_type == "css"
-        return SelectorTemplate(self._selector, self.selector_type, kwds=self.__kwds, with_classes=self.with_classes + [class_], with_data=self._with_data.copy(), children=self._children)
+        return SelectorTemplate(
+            self._selector,
+            self.selector_type,
+            kwds=self.__kwds,
+            with_classes=self.with_classes + [class_],
+            with_data=self._with_data.copy(),
+            children=self._children,
+        )
 
     def with_data(self, key, value):
         assert self.selector_type == "css"
         with_data = self._with_data.copy()
         with_data[key] = value
-        return SelectorTemplate(self._selector, self.selector_type, kwds=self.__kwds, with_classes=self.with_classes, with_data=with_data, children=self._children)
+        return SelectorTemplate(
+            self._selector,
+            self.selector_type,
+            kwds=self.__kwds,
+            with_classes=self.with_classes,
+            with_data=with_data,
+            children=self._children,
+        )
 
     def descendant(self, has_selector):
         assert self.selector_type == "css"
@@ -60,12 +72,16 @@ class SelectorTemplate(Target):
         else:
             selector = has_selector
 
-        return SelectorTemplate(f"{self.selector} {selector}", self.selector_type, kwds=self.__kwds, children=self._children)
+        return SelectorTemplate(
+            f"{self.selector} {selector}", self.selector_type, kwds=self.__kwds, children=self._children
+        )
 
     def __call__(self, **kwds):
         new_kwds = self.__kwds.copy()
         new_kwds.update(**kwds)
-        return SelectorTemplate(self._selector, self.selector_type, kwds=new_kwds, with_classes=self.with_classes, children=self._children)
+        return SelectorTemplate(
+            self._selector, self.selector_type, kwds=new_kwds, with_classes=self.with_classes, children=self._children
+        )
 
     @property
     def description(self):
@@ -116,7 +132,6 @@ class SelectorTemplate(Target):
 
 
 class Label(Target):
-
     def __init__(self, text):
         self.text = text
 
@@ -130,7 +145,6 @@ class Label(Target):
 
 
 class Text(Target):
-
     def __init__(self, text):
         self.text = text
 
@@ -147,7 +161,6 @@ HasText = Union[Label, Text]
 
 
 class Component:
-
     def __init__(self, name, sub_components, selectors, labels, text):
         self._name = name
         self._sub_components = sub_components
diff --git a/lib/galaxy/selenium/data.py b/lib/galaxy/selenium/data.py
index b59d6836a6c..80a8ea7f969 100644
--- a/lib/galaxy/selenium/data.py
+++ b/lib/galaxy/selenium/data.py
@@ -5,6 +5,6 @@ from .components import Component
 
 
 def load_root_component() -> Component:
-    new_data_yaml = resource_string(__name__, 'navigation.yml').decode("UTF-8")
+    new_data_yaml = resource_string(__name__, "navigation.yml").decode("UTF-8")
     navigation_raw = yaml.safe_load(new_data_yaml)
     return Component.from_dict("root", navigation_raw)
diff --git a/lib/galaxy/selenium/driver_factory.py b/lib/galaxy/selenium/driver_factory.py
index 6063c1c3b1e..118e6d12692 100644
--- a/lib/galaxy/selenium/driver_factory.py
+++ b/lib/galaxy/selenium/driver_factory.py
@@ -11,11 +11,11 @@ from selenium.webdriver.chrome.options import Options as ChromeOptions
 from selenium.webdriver.common.desired_capabilities import DesiredCapabilities
 from selenium.webdriver.remote.webdriver import WebDriver
 
-logger = logging.getLogger('selenium.webdriver.remote.remote_connection')
+logger = logging.getLogger("selenium.webdriver.remote.remote_connection")
 logger.setLevel(logging.WARNING)
 
 DEFAULT_BROWSER = "auto"
-DEFAULT_DOWNLOAD_PATH = '/tmp/'
+DEFAULT_DOWNLOAD_PATH = "/tmp/"
 LOGGING_PREFS = {
     "browser": "ALL",
 }
@@ -90,39 +90,34 @@ def get_local_driver(browser=DEFAULT_BROWSER, headless=False) -> WebDriver:
         "OPERA": webdriver.Opera,
     }
     driver_class = driver_to_class[browser]
-    if browser == 'CHROME':
+    if browser == "CHROME":
         options = ChromeOptions()
         if headless:
-            options.add_argument('--headless')
-        prefs = {'download.default_directory': DEFAULT_DOWNLOAD_PATH}
-        options.add_experimental_option('prefs', prefs)
+            options.add_argument("--headless")
+        prefs = {"download.default_directory": DEFAULT_DOWNLOAD_PATH}
+        options.add_experimental_option("prefs", prefs)
         return driver_class(desired_capabilities={"loggingPrefs": LOGGING_PREFS}, chrome_options=options)
-    elif browser == 'FIREFOX':
+    elif browser == "FIREFOX":
         fp = webdriver.FirefoxProfile()
-        fp.set_preference('network.proxy.type', 2)
-        fp.set_preference('network.proxy.autoconfig_url',
-                          "http://127.0.0.1:9675")
-        fp.set_preference('browser.download.folderList', 2)
-        fp.set_preference('browser.download.dir', DEFAULT_DOWNLOAD_PATH)
-        fp.set_preference("browser.helperApps.neverAsk.saveToDisk", 'application/octet-stream')
+        fp.set_preference("network.proxy.type", 2)
+        fp.set_preference("network.proxy.autoconfig_url", "http://127.0.0.1:9675")
+        fp.set_preference("browser.download.folderList", 2)
+        fp.set_preference("browser.download.dir", DEFAULT_DOWNLOAD_PATH)
+        fp.set_preference("browser.helperApps.neverAsk.saveToDisk", "application/octet-stream")
         return driver_class(firefox_profile=fp)
 
     else:
         return driver_class(desired_capabilities={"loggingPrefs": LOGGING_PREFS})
 
 
-def get_remote_driver(
-    host,
-    port,
-    browser=DEFAULT_BROWSER
-) -> WebDriver:
+def get_remote_driver(host, port, browser=DEFAULT_BROWSER) -> WebDriver:
     # docker run -d -p 4444:4444 -v /dev/shm:/dev/shm selenium/standalone-chrome:3.0.1-aluminum
     if browser == "auto":
         browser = "CHROME"
     assert browser in ["CHROME", "EDGE", "ANDROID", "FIREFOX", "INTERNETEXPLORER", "IPAD", "IPHONE", "OPERA", "SAFARI"]
     desired_capabilities = getattr(DesiredCapabilities, browser)
     desired_capabilities["loggingPrefs"] = LOGGING_PREFS
-    executor = f'http://{host}:{port}/wd/hub'
+    executor = f"http://{host}:{port}/wd/hub"
     driver = webdriver.Remote(
         command_executor=executor,
         desired_capabilities=desired_capabilities,
@@ -144,7 +139,6 @@ def virtual_display_if_enabled(enabled):
 
 
 class NoopDisplay:
-
     def stop(self):
         """No-op stop for consistent use with pyvirtualdisplay Display class."""
 
@@ -161,9 +155,9 @@ def _which(file):
 
 
 __all__ = (
-    'ConfiguredDriver',
-    'get_local_driver',
-    'get_remote_driver',
-    'is_virtual_display_available',
-    'virtual_display_if_enabled',
+    "ConfiguredDriver",
+    "get_local_driver",
+    "get_remote_driver",
+    "is_virtual_display_available",
+    "virtual_display_if_enabled",
 )
diff --git a/lib/galaxy/selenium/has_driver.py b/lib/galaxy/selenium/has_driver.py
index 6151f48afe2..edbedd6f33d 100644
--- a/lib/galaxy/selenium/has_driver.py
+++ b/lib/galaxy/selenium/has_driver.py
@@ -57,17 +57,13 @@ class HasDriver:
 
     def wait_for_xpath(self, xpath, **kwds):
         element = self._wait_on(
-            ec.presence_of_element_located((By.XPATH, xpath)),
-            f"XPATH selector [{xpath}] to become present",
-            **kwds
+            ec.presence_of_element_located((By.XPATH, xpath)), f"XPATH selector [{xpath}] to become present", **kwds
         )
         return element
 
     def wait_for_xpath_visible(self, xpath, **kwds):
         element = self._wait_on(
-            ec.visibility_of_element_located((By.XPATH, xpath)),
-            f"XPATH selector [{xpath}] to become visible",
-            **kwds
+            ec.visibility_of_element_located((By.XPATH, xpath)), f"XPATH selector [{xpath}] to become visible", **kwds
         )
         return element
 
@@ -75,7 +71,7 @@ class HasDriver:
         element = self._wait_on(
             ec.presence_of_element_located((By.CSS_SELECTOR, selector)),
             f"CSS selector [{selector}] to become present",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -83,7 +79,7 @@ class HasDriver:
         element = self._wait_on(
             ec.presence_of_element_located(selector_template.element_locator),
             f"{selector_template.description} to become present",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -91,7 +87,7 @@ class HasDriver:
         element = self._wait_on(
             ec.visibility_of_element_located(selector_template.element_locator),
             f"{selector_template.description} to become visible",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -99,7 +95,7 @@ class HasDriver:
         element = self._wait_on(
             ec.visibility_of_element_located((By.CSS_SELECTOR, selector)),
             f"CSS selector [{selector}] to become visible",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -107,7 +103,7 @@ class HasDriver:
         element = self._wait_on(
             ec.element_to_be_clickable((By.CSS_SELECTOR, selector)),
             f"CSS selector [{selector}] to become clickable",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -115,7 +111,7 @@ class HasDriver:
         element = self._wait_on(
             ec.element_to_be_clickable(selector_template.element_locator),
             f"{selector_template.description} to become clickable",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -123,7 +119,7 @@ class HasDriver:
         element = self._wait_on(
             ec.invisibility_of_element_located((By.CSS_SELECTOR, selector)),
             f"CSS selector [{selector}] to become absent or hidden",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -131,7 +127,7 @@ class HasDriver:
         element = self._wait_on(
             lambda driver: len(driver.find_elements_by_css_selector(selector)) == 0,
             f"CSS selector [{selector}] to become absent",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -139,7 +135,7 @@ class HasDriver:
         element = self._wait_on(
             lambda driver: len(driver.find_elements(*selector_template.element_locator)) == 0,
             f"{selector_template.description} to become absent",
-            **kwds
+            **kwds,
         )
         return element
 
@@ -147,16 +143,12 @@ class HasDriver:
         element = self._wait_on(
             ec.invisibility_of_element_located(selector_template.element_locator),
             f"{selector_template.description} to become absent or hidden",
-            **kwds
+            **kwds,
         )
         return element
 
     def wait_for_id(self, id, **kwds):
-        return self._wait_on(
-            ec.presence_of_element_located((By.ID, id)),
-            f"presence of DOM ID [{id}]",
-            **kwds
-        )
+        return self._wait_on(ec.presence_of_element_located((By.ID, id)), f"presence of DOM ID [{id}]", **kwds)
 
     def click(self, selector_template):
         element = self.driver.find_element(*selector_template.element_locator)
diff --git a/lib/galaxy/selenium/jupyter_context.py b/lib/galaxy/selenium/jupyter_context.py
index 850a4ba5b45..b22a5b0823c 100644
--- a/lib/galaxy/selenium/jupyter_context.py
+++ b/lib/galaxy/selenium/jupyter_context.py
@@ -1,4 +1,5 @@
-from .context import GalaxySeleniumContextImpl, init as c_init
+from .context import GalaxySeleniumContextImpl
+from .context import init as c_init
 
 
 def init(config=None):
@@ -6,8 +7,8 @@ def init(config=None):
 
 
 class JupyterContextImpl(GalaxySeleniumContextImpl):
-
     def screenshot(self, label):
         path = super().screenshot(label)
         from IPython.display import Image
+
         return Image(filename=path)
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index cdedba69a33..d03cb1aa3f3 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -9,8 +9,14 @@ import random
 import string
 import time
 from abc import abstractmethod
-from functools import partial, wraps
-from typing import cast, Union
+from functools import (
+    partial,
+    wraps,
+)
+from typing import (
+    cast,
+    Union,
+)
 
 import requests
 import yaml
@@ -19,10 +25,11 @@ from selenium.webdriver.remote.webdriver import WebDriver
 
 from galaxy.util import DEFAULT_SOCKET_TIMEOUT
 from . import sizzle
-from .components import Component, HasText
-from .data import (
-    load_root_component,
+from .components import (
+    Component,
+    HasText,
 )
+from .data import load_root_component
 from .has_driver import (
     exception_indicates_not_clickable,
     exception_indicates_stale_element,
@@ -32,9 +39,9 @@ from .has_driver import (
 from .smart_components import SmartComponent
 
 # Test case data
-DEFAULT_PASSWORD = '123456'
+DEFAULT_PASSWORD = "123456"
 
-RETRY_DURING_TRANSITIONS_SLEEP_DEFAULT = .1
+RETRY_DURING_TRANSITIONS_SLEEP_DEFAULT = 0.1
 RETRY_DURING_TRANSITIONS_ATTEMPTS_DEFAULT = 10
 
 GALAXY_MAIN_FRAME_ID = "galaxy_main"
@@ -58,9 +65,9 @@ class WAIT_TYPES:
     # Wait time for a GIE to spawn.
     GIE_SPAWN = WaitType("gie_spawn", 30)
     # Wait time for toolshed search
-    SHED_SEARCH = WaitType('shed_search', 30)
+    SHED_SEARCH = WaitType("shed_search", 30)
     # Wait time for repository installation
-    REPO_INSTALL = WaitType('repo_install', 60)
+    REPO_INSTALL = WaitType("repo_install", 60)
     # Beta history Polling Duration
     HISTORY_POLL = WaitType("history_poll", 3)
 
@@ -70,7 +77,6 @@ DEFAULT_WAIT_TYPE = WAIT_TYPES.DATABASE_OPERATION
 
 
 class NullTourCallback:
-
     def handle_step(self, step, step_index):
         pass
 
@@ -92,7 +98,12 @@ def exception_seems_to_indicate_transition(e):
     return exception_indicates_stale_element(e) or exception_indicates_not_clickable(e)
 
 
-def retry_call_during_transitions(f, attempts=RETRY_DURING_TRANSITIONS_ATTEMPTS_DEFAULT, sleep=RETRY_DURING_TRANSITIONS_SLEEP_DEFAULT, exception_check=exception_seems_to_indicate_transition):
+def retry_call_during_transitions(
+    f,
+    attempts=RETRY_DURING_TRANSITIONS_ATTEMPTS_DEFAULT,
+    sleep=RETRY_DURING_TRANSITIONS_SLEEP_DEFAULT,
+    exception_check=exception_seems_to_indicate_transition,
+):
     previous_attempts = 0
     while True:
         try:
@@ -108,11 +119,17 @@ def retry_call_during_transitions(f, attempts=RETRY_DURING_TRANSITIONS_ATTEMPTS_
             previous_attempts += 1
 
 
-def retry_during_transitions(f, attempts=RETRY_DURING_TRANSITIONS_ATTEMPTS_DEFAULT, sleep=RETRY_DURING_TRANSITIONS_SLEEP_DEFAULT, exception_check=exception_seems_to_indicate_transition):
-
+def retry_during_transitions(
+    f,
+    attempts=RETRY_DURING_TRANSITIONS_ATTEMPTS_DEFAULT,
+    sleep=RETRY_DURING_TRANSITIONS_SLEEP_DEFAULT,
+    exception_check=exception_seems_to_indicate_transition,
+):
     @wraps(f)
     def _retry(*args, **kwds):
-        return retry_call_during_transitions(partial(f, *args, **kwds), attempts=attempts, sleep=sleep, exception_check=exception_check)
+        return retry_call_during_transitions(
+            partial(f, *args, **kwds), attempts=attempts, sleep=sleep, exception_check=exception_check
+        )
 
     return _retry
 
@@ -129,7 +146,7 @@ def edit_details(f, scope=".beta.history"):
         result = f(self, *args, **kwds)
         # save edits
         if self.is_beta_history():
-            save_button = self.beta_history_element('editor save button')
+            save_button = self.beta_history_element("editor save button")
             save_button.wait_for_and_click()
         return result
 
@@ -152,6 +169,7 @@ class NavigatesGalaxy(HasDriver):
     class. For instance, the method for clicking an option in the workflow editor is
     workflow_editor_click_option instead of click_workflow_editor_option.
     """
+
     timeout_multiplier: float
     driver: WebDriver
 
@@ -214,11 +232,11 @@ class NavigatesGalaxy(HasDriver):
         self.components.masthead._.wait_for_visible()
 
     def trs_search(self) -> None:
-        self.driver.get(self.build_url('workflows/trs_search'))
+        self.driver.get(self.build_url("workflows/trs_search"))
         self.components.masthead._.wait_for_visible()
 
     def trs_by_id(self) -> None:
-        self.driver.get(self.build_url('workflows/trs_import'))
+        self.driver.get(self.build_url("workflows/trs_import"))
         self.components.masthead._.wait_for_visible()
 
     def switch_to_main_panel(self):
@@ -227,11 +245,11 @@ class NavigatesGalaxy(HasDriver):
     @contextlib.contextmanager
     def local_storage(self, key: str, value: Union[float, str]):
         """Method decorator to modify localStorage for the scope of the supplied context."""
-        self.driver.execute_script(f'''window.localStorage.setItem("{key}", {value});''')
+        self.driver.execute_script(f"""window.localStorage.setItem("{key}", {value});""")
         try:
             yield
         finally:
-            self.driver.execute_script(f'''window.localStorage.removeItem("{key}");''')
+            self.driver.execute_script(f"""window.localStorage.removeItem("{key}");""")
 
     @contextlib.contextmanager
     def main_panel(self):
@@ -245,7 +263,9 @@ class NavigatesGalaxy(HasDriver):
     def api_get(self, endpoint, data=None, raw=False):
         data = data or {}
         full_url = self.build_url(f"api/{endpoint}", for_selenium=False)
-        response = requests.get(full_url, data=data, cookies=self.selenium_to_requests_cookies(), timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.get(
+            full_url, data=data, cookies=self.selenium_to_requests_cookies(), timeout=DEFAULT_SOCKET_TIMEOUT
+        )
         if raw:
             return response
         else:
@@ -254,12 +274,16 @@ class NavigatesGalaxy(HasDriver):
     def api_post(self, endpoint, data=None):
         data = data or {}
         full_url = self.build_url(f"api/{endpoint}", for_selenium=False)
-        response = requests.post(full_url, data=data, cookies=self.selenium_to_requests_cookies(), timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.post(
+            full_url, data=data, cookies=self.selenium_to_requests_cookies(), timeout=DEFAULT_SOCKET_TIMEOUT
+        )
         return response.json()
 
     def api_delete(self, endpoint, raw=False):
         full_url = self.build_url(f"api/{endpoint}", for_selenium=False)
-        response = requests.delete(full_url, cookies=self.selenium_to_requests_cookies(), timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.delete(
+            full_url, cookies=self.selenium_to_requests_cookies(), timeout=DEFAULT_SOCKET_TIMEOUT
+        )
         if raw:
             return response
         else:
@@ -271,9 +295,7 @@ class NavigatesGalaxy(HasDriver):
                 return cookie["value"]
 
     def selenium_to_requests_cookies(self):
-        return {
-            'galaxysession': self.get_galaxy_session()
-        }
+        return {"galaxysession": self.get_galaxy_session()}
 
     def history_panel_name_element(self):
         if self.is_beta_history():
@@ -290,16 +312,16 @@ class NavigatesGalaxy(HasDriver):
         self.components.histories.sharing.make_accessible.wait_for_and_click()
         self.components.histories.sharing.make_publishable.wait_for_and_click()
 
-    def history_contents(self, history_id=None, view='summary', datasets_only=True):
+    def history_contents(self, history_id=None, view="summary", datasets_only=True):
         if history_id is None:
             history_id = self.current_history_id()
-        histories = self.api_get('histories?keys=id')
-        if history_id not in [h['id'] for h in histories]:
+        histories = self.api_get("histories?keys=id")
+        if history_id not in [h["id"] for h in histories]:
             return {}
         if datasets_only:
-            endpoint = f'histories/{history_id}/contents?view={view}'
+            endpoint = f"histories/{history_id}/contents?view={view}"
         else:
-            endpoint = f'histories/{history_id}?view={view}'
+            endpoint = f"histories/{history_id}?view={view}"
         return self.api_get(endpoint)
 
     def current_history(self):
@@ -340,7 +362,7 @@ class NavigatesGalaxy(HasDriver):
         self.sleep_for(WAIT_TYPES.UX_RENDER)
 
     def history_panel_wait_for_hid_ok(self, hid, allowed_force_refreshes=0):
-        return self.history_panel_wait_for_hid_state(hid, 'ok', allowed_force_refreshes=allowed_force_refreshes)
+        return self.history_panel_wait_for_hid_state(hid, "ok", allowed_force_refreshes=allowed_force_refreshes)
 
     def history_panel_item_component(self, history_item=None, hid=None, multi_history_panel=False):
         if self.is_beta_history():
@@ -352,13 +374,9 @@ class NavigatesGalaxy(HasDriver):
         item = self.components.history_panel.item.selector
         if multi_history_panel:
             item = self.components.multi_history_view.item
-        return item(
-            history_content_type=history_item["history_content_type"],
-            id=history_item["id"]
-        )
+        return item(history_content_type=history_item["history_content_type"], id=history_item["id"])
 
     def wait_for_history_to_have_hid(self, history_id, hid):
-
         def get_hids():
             contents = self.api_get(f"histories/{history_id}/contents")
             return [d["hid"] for d in contents]
@@ -382,7 +400,9 @@ class NavigatesGalaxy(HasDriver):
         # I think Mason thought the first was cleaner based on recent changes, but I think duplicated
         # HIDs due to conversions and such make using the actual history item ID more robust.
         history_item = self.hid_to_history_item(hid, current_history_id=current_history_id)
-        history_item_selector = self.history_panel_item_component(history_item, hid=hid, multi_history_panel=multi_history_panel)
+        history_item_selector = self.history_panel_item_component(
+            history_item, hid=hid, multi_history_panel=multi_history_panel
+        )
         try:
             self.history_item_wait_for(history_item_selector, allowed_force_refreshes)
         except self.TimeoutException as e:
@@ -427,7 +447,9 @@ class NavigatesGalaxy(HasDriver):
         return history_item_selector
 
     def history_panel_wait_for_hid_state(self, hid, state, allowed_force_refreshes=0, multi_history_panel=False):
-        history_item_selector = self.history_panel_wait_for_hid_visible(hid, allowed_force_refreshes=allowed_force_refreshes, multi_history_panel=multi_history_panel)
+        history_item_selector = self.history_panel_wait_for_hid_visible(
+            hid, allowed_force_refreshes=allowed_force_refreshes, multi_history_panel=multi_history_panel
+        )
         if self.is_beta_history():
             history_item_selector_state = self.content_item_by_attributes(hid=hid, state=state)
         else:
@@ -441,7 +463,7 @@ class NavigatesGalaxy(HasDriver):
             classes = history_item.get_attribute("class").split(" ")
             for clazz in classes:
                 if clazz.startswith("state-"):
-                    current_state = clazz[len("state-"):]
+                    current_state = clazz[len("state-") :]
             template = "Failed waiting on history item %d state to change to [%s] current state [%s]. "
             message = template % (hid, state, current_state)
             raise self.prepend_timeout_message(e, message)
@@ -450,16 +472,16 @@ class NavigatesGalaxy(HasDriver):
     def click_grid_popup_option(self, item_name, option_label):
         item_button = None
         grid = self.components.grids.body.wait_for_visible()
-        for row in grid.find_elements_by_tag_name('tr'):
-            name_cell = row.find_elements_by_tag_name('td')[1]
+        for row in grid.find_elements_by_tag_name("tr"):
+            name_cell = row.find_elements_by_tag_name("td")[1]
             if name_cell.text == item_name:
                 item_button = name_cell
                 break
 
         if item_button is None:
-            raise AssertionError(f'Failed to find item with name [{item_name}]')
+            raise AssertionError(f"Failed to find item with name [{item_name}]")
 
-        popup_menu_button = item_button.find_element_by_css_selector('.dropdown-toggle')
+        popup_menu_button = item_button.find_element_by_css_selector(".dropdown-toggle")
         popup_menu_button.click()
         popup_option = self.driver.find_element_by_link_text(option_label)
         popup_option.click()
@@ -499,29 +521,29 @@ class NavigatesGalaxy(HasDriver):
         return search_box
 
     def _get_random_name(self, prefix=None, suffix=None, len=10):
-        return '{}{}{}'.format(
-            prefix or '',
-            ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(len)),
-            suffix or '',
+        return "{}{}{}".format(
+            prefix or "",
+            "".join(random.choice(string.ascii_lowercase + string.digits) for _ in range(len)),
+            suffix or "",
         )
 
     def _get_random_email(self, username=None, domain=None):
-        username = username or 'test'
-        domain = domain or 'test.test'
+        username = username or "test"
+        domain = domain or "test.test"
         return self._get_random_name(prefix=username, suffix=f"@{domain}")
 
     # Creates a random password of length len by creating an array with all ASCII letters and the numbers 0 to 9,
     # then using the random number generator to pick one elemenent to concatinate it to the end of the password string until
     # we have a password of length len.
     def _get_random_password(self, len=6):
-        return ''.join(random.SystemRandom().choice(string.ascii_letters + string.digits) for _ in range(len))
+        return "".join(random.SystemRandom().choice(string.ascii_letters + string.digits) for _ in range(len))
 
     def submit_login(self, email, password=None, assert_valid=True, retries=0):
         if password is None:
             password = self.default_password
         login_info = {
-            'login': email,
-            'password': password,
+            "login": email,
+            "password": password,
         }
         self.components.masthead.register_or_login.wait_for_and_click()
         self.sleep_for(WAIT_TYPES.UX_RENDER)
@@ -555,12 +577,7 @@ class NavigatesGalaxy(HasDriver):
         self.components.masthead.register_or_login.wait_for_and_click()
         self.wait_for_and_click(self.navigation.registration.selectors.toggle)
         form = self.wait_for_visible(self.navigation.registration.selectors.form)
-        self.fill(form, dict(
-            email=email,
-            password=password,
-            username=username,
-            confirm=confirm
-        ))
+        self.fill(form, dict(email=email, password=password, username=username, confirm=confirm))
         self.wait_for_and_click(self.navigation.registration.selectors.submit)
         if assert_valid is False:
             self.assert_error_message()
@@ -596,7 +613,9 @@ class NavigatesGalaxy(HasDriver):
         except self.TimeoutException as e:
             ui_logged_out = self.components.masthead.logged_out_only.is_displayed
             if ui_logged_out:
-                dom_message = "Element a.loggedout-only is present in DOM, indicating Login or Register button still in masthead."
+                dom_message = (
+                    "Element a.loggedout-only is present in DOM, indicating Login or Register button still in masthead."
+                )
             else:
                 dom_message = "Element a.loggedout-only is *not* present in DOM."
             user_info = self.api_get("users/current")
@@ -632,11 +651,11 @@ class NavigatesGalaxy(HasDriver):
             self.upload_paste_data(paste_data)
 
         if ext is not None:
-            self.wait_for_selector_visible('.upload-extension')
+            self.wait_for_selector_visible(".upload-extension")
             self.select2_set_value(".upload-extension", ext)
 
         if genome is not None:
-            self.wait_for_selector_visible('.upload-genome')
+            self.wait_for_selector_visible(".upload-genome")
             self.select2_set_value(".upload-genome", genome)
 
         self.upload_start()
@@ -699,14 +718,14 @@ class NavigatesGalaxy(HasDriver):
     @retry_during_transitions
     def upload_set_footer_extension(self, ext, tab_id="regular"):
         if ext is not None:
-            selector = f'div#{tab_id} .upload-footer-extension'
+            selector = f"div#{tab_id} .upload-footer-extension"
             self.wait_for_selector_visible(selector)
             self.select2_set_value(selector, ext)
 
     @retry_during_transitions
     def upload_set_footer_genome(self, genome, tab_id="regular"):
         if genome is not None:
-            selector = f'div#{tab_id} .upload-footer-genome'
+            selector = f"div#{tab_id} .upload-footer-genome"
             self.wait_for_selector_visible(selector)
             self.select2_set_value(selector, genome)
 
@@ -722,7 +741,7 @@ class NavigatesGalaxy(HasDriver):
     def upload_build(self, tab="collection"):
         build_selector = f"div#{tab} button#btn-build"
         # Pause a bit to let the callback on the build button be registered.
-        time.sleep(.5)
+        time.sleep(0.5)
         # Click the Build button and make sure it disappears.
         self.wait_for_and_click_selector(build_selector)
         try:
@@ -1125,7 +1144,9 @@ class NavigatesGalaxy(HasDriver):
 
     def workflow_index_table_elements(self):
         self.wait_for_selector_visible("#workflow-table")
-        table_elements = self.driver.find_elements_by_css_selector("#workflow-table > tbody > tr:not([style*='display: none'])")
+        table_elements = self.driver.find_elements_by_css_selector(
+            "#workflow-table > tbody > tr:not([style*='display: none'])"
+        )
         return table_elements
 
     def workflow_index_table_row(self, workflow_index=0):
@@ -1303,7 +1324,9 @@ class NavigatesGalaxy(HasDriver):
             option_label = option_label_or_component
             # Click labelled option
             self.wait_for_visible(self.navigation.history_panel.options_menu)
-            menu_item_sizzle_selector = self.navigation.history_panel.options_menu_item(option_label=option_label).selector
+            menu_item_sizzle_selector = self.navigation.history_panel.options_menu_item(
+                option_label=option_label
+            ).selector
             menu_selection_element = self.wait_for_sizzle_selector_clickable(menu_item_sizzle_selector)
             menu_selection_element.click()
         else:
@@ -1355,17 +1378,17 @@ class NavigatesGalaxy(HasDriver):
 
     @retry_during_transitions
     def histories_click_advanced_search(self):
-        search_selector = '#standard-search .advanced-search-toggle'
+        search_selector = "#standard-search .advanced-search-toggle"
         self.wait_for_and_click_selector(search_selector)
 
     @retry_during_transitions
     def histories_get_history_names(self):
         self.sleep_for(self.wait_types.UX_RENDER)
         names = []
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            td = row.find_elements_by_tag_name('td')
-            name = td[1].text if td[0].text == '' else td[0].text
+        grid = self.wait_for_selector("#grid-table-body")
+        for row in grid.find_elements_by_tag_name("tr"):
+            td = row.find_elements_by_tag_name("td")
+            name = td[1].text if td[0].text == "" else td[0].text
             if name != "No items" and not name.startswith("No matching entries found"):
                 names.append(name)
         return names
@@ -1587,7 +1610,9 @@ class NavigatesGalaxy(HasDriver):
         except self.TimeoutException as e:
             message = "Clicked logout button but waiting for 'Login or Registration' button failed, perhaps the logout button was clicked before the handler was setup?"
             raise self.prepend_timeout_message(e, message)
-        assert not self.is_logged_in(), "Clicked to logged out and UI reflects a logout, but API still thinks a user is logged in."
+        assert (
+            not self.is_logged_in()
+        ), "Clicked to logged out and UI reflects a logout, but API still thinks a user is logged in."
 
     def run_tour(self, path, skip_steps=None, sleep_on_steps=None, tour_callback=None):
         skip_steps = skip_steps or []
@@ -1679,7 +1704,9 @@ class NavigatesGalaxy(HasDriver):
         text = self.get_tooltip_text(element, sleep=sleep, click_away=click_away)
         assert text == expected, f"Tooltip text [{text}] was not expected text [{expected}]."
 
-    def assert_tooltip_text_contains(self, element, expected: Union[str, HasText], sleep: int = 0, click_away: bool = True):
+    def assert_tooltip_text_contains(
+        self, element, expected: Union[str, HasText], sleep: int = 0, click_away: bool = True
+    ):
         if hasattr(expected, "text"):
             expected = cast(HasText, expected).text
         text = self.get_tooltip_text(element, sleep=sleep, click_away=click_away)
@@ -1698,8 +1725,9 @@ class NavigatesGalaxy(HasDriver):
         if contains is not None:
 
             if type(element) == list:
-                assert any(contains in el.text for el in element), \
-                    f"{contains} was not found in {[el.text for el in element]}"
+                assert any(
+                    contains in el.text for el in element
+                ), f"{contains} was not found in {[el.text for el in element]}"
                 return
 
             element = element.wait_for_visible()
@@ -1811,7 +1839,7 @@ class NavigatesGalaxy(HasDriver):
         # Wait for select2 options to load and then click to add this one.
         drop_elem = self.wait_for_selector_visible("#select2-drop")
         # Sleep seems to be needed - at least for send_enter.
-        time.sleep(.5)
+        time.sleep(0.5)
         if not with_click:
             # Wait for select2 options to load and then click to add this one.
             self.send_enter(text_element)
@@ -1841,12 +1869,7 @@ class NavigatesGalaxy(HasDriver):
 
 
 class NotLoggedInException(TimeoutException):
-
     def __init__(self, timeout_exception, user_info, dom_message):
         template = "Waiting for UI to reflect user logged in but it did not occur. API indicates no user is currently logged in. %s API response was [%s]. %s"
         msg = template % (dom_message, user_info, timeout_exception.msg)
-        super().__init__(
-            msg=msg,
-            screen=timeout_exception.screen,
-            stacktrace=timeout_exception.stacktrace
-        )
+        super().__init__(msg=msg, screen=timeout_exception.screen, stacktrace=timeout_exception.stacktrace)
diff --git a/lib/galaxy/selenium/scripts/dump_tour.py b/lib/galaxy/selenium/scripts/dump_tour.py
index 1ff2d0e69b3..cac64bf427d 100755
--- a/lib/galaxy/selenium/scripts/dump_tour.py
+++ b/lib/galaxy/selenium/scripts/dump_tour.py
@@ -28,21 +28,20 @@ def main(argv=None):
 
 
 class DumpTourCallback:
-
     def __init__(self, driver_wrapper, output):
         self.driver_wrapper = driver_wrapper
         self.output = output
 
     def handle_step(self, step, step_index):
-        time.sleep(.5)
+        time.sleep(0.5)
         self.driver_wrapper.driver.save_screenshot("%s/%i.png" % (self.output, step_index))
-        time.sleep(.5)
+        time.sleep(0.5)
 
 
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
-    parser.add_argument('tour', metavar='TOUR', help='tour to walk')
-    parser.add_argument('-o', '--output', default="tour_dump_TIMESTAMP", help='directory to dump tour to')
+    parser.add_argument("tour", metavar="TOUR", help="tour to walk")
+    parser.add_argument("-o", "--output", default="tour_dump_TIMESTAMP", help="directory to dump tour to")
     parser = cli.add_selenium_arguments(parser)
     return parser
 
diff --git a/lib/galaxy/selenium/sizzle.py b/lib/galaxy/selenium/sizzle.py
index 1e71e9e25f1..1282f016ee7 100644
--- a/lib/galaxy/selenium/sizzle.py
+++ b/lib/galaxy/selenium/sizzle.py
@@ -72,9 +72,7 @@ def find_element_by_sizzle(driver, sizzle_selector: str):
     if elements:
         return elements[0]
     else:
-        raise NoSuchElementException(
-            f"Unable to locate element by Sizzle: {sizzle_selector}"
-        )
+        raise NoSuchElementException(f"Unable to locate element by Sizzle: {sizzle_selector}")
 
 
 def find_elements_by_sizzle(driver, sizzle_selector: str):
@@ -90,7 +88,8 @@ def find_elements_by_sizzle(driver, sizzle_selector: str):
 
 
 def _inject_sizzle(driver, sizzle_url, timeout):
-    script = """
+    script = (
+        """
         if(typeof(window.$) != "undefined") {
             // Just reuse jQuery if it is available, avoids potential amd problems
             // that have cropped up with Galaxy for instance.
@@ -102,15 +101,16 @@ def _inject_sizzle(driver, sizzle_url, timeout):
             var _h = document.getElementsByTagName("head")[0];
             _h.appendChild(_s);
         }
-    """ % sizzle_url
+    """
+        % sizzle_url
+    )
     driver.execute_script(script)
     wait = WebDriverWait(driver, timeout)
-    wait.until(lambda d: _is_sizzle_loaded(d),
-               f"Can't inject Sizzle in {timeout} seconds")
+    wait.until(lambda d: _is_sizzle_loaded(d), f"Can't inject Sizzle in {timeout} seconds")
 
 
 def _is_sizzle_loaded(driver):
-    script = "return typeof(Sizzle) != \"undefined\";"
+    script = 'return typeof(Sizzle) != "undefined";'
     return driver.execute_script(script)
 
 
diff --git a/lib/galaxy/selenium/smart_components.py b/lib/galaxy/selenium/smart_components.py
index 58daeb5a277..48ff5f07148 100644
--- a/lib/galaxy/selenium/smart_components.py
+++ b/lib/galaxy/selenium/smart_components.py
@@ -31,8 +31,7 @@ class SmartComponent:
 
 
 class SmartTarget:
-    """Wrap a Target with driver aware methods.
-    """
+    """Wrap a Target with driver aware methods."""
 
     def __init__(self, target, has_driver):
         self._target = target
diff --git a/lib/galaxy/selenium/toolbox/filters.py b/lib/galaxy/selenium/toolbox/filters.py
index a1c28fbeb10..cbfc3a52aed 100644
--- a/lib/galaxy/selenium/toolbox/filters.py
+++ b/lib/galaxy/selenium/toolbox/filters.py
@@ -4,6 +4,6 @@ def restrict_test(context, section):
 
     This tool filter will disable the Test Section section.
     """
-    if section.name == 'Test Section':
+    if section.name == "Test Section":
         return False
     return True
diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index c3ff1e97531..31d98c0bce1 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -1,5 +1,10 @@
 """Typed description of Galaxy's app object."""
-from typing import Any, Optional, TYPE_CHECKING, Union
+from typing import (
+    Any,
+    Optional,
+    TYPE_CHECKING,
+    Union,
+)
 
 from kombu import Connection
 
@@ -8,11 +13,16 @@ from galaxy.datatypes.registry import Registry
 from galaxy.di import Container
 from galaxy.files import ConfiguredFileSources
 from galaxy.job_metrics import JobMetrics
-from galaxy.model.base import ModelMapping, SharedModelMapping
+from galaxy.model.base import (
+    ModelMapping,
+    SharedModelMapping,
+)
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.scoped_session import galaxy_scoped_session
-from galaxy.model.security import GalaxyRBACAgent
-from galaxy.model.security import HostAgent
+from galaxy.model.security import (
+    GalaxyRBACAgent,
+    HostAgent,
+)
 from galaxy.model.store import SessionlessContext
 from galaxy.model.tags import GalaxyTagHandler
 from galaxy.objectstore import ObjectStore
@@ -42,6 +52,7 @@ class BasicSharedApp(BasicApp):
     Code that is shared between Galaxy and the Tool Shed should be annotated as
     using BasicSharedApp instead of StructuredApp below.
     """
+
     application_stack: ApplicationStack
     model: SharedModelMapping
     security: IdEncodingHelper
@@ -55,7 +66,7 @@ class MinimalToolApp(BasicApp):
     sa_session: Union[galaxy_scoped_session, SessionlessContext]
     datatypes_registry: Registry
     object_store: ObjectStore
-    tool_data_table_manager: 'ToolDataTableManager'
+    tool_data_table_manager: "ToolDataTableManager"
     file_sources: ConfiguredFileSources
 
 
@@ -102,6 +113,7 @@ class StructuredApp(MinimalManagerApp):
     (cyclical imports), we're just setting the class attributes to
     Any.
     """
+
     is_webapp: bool  # is_webapp will be set to true when building WSGI app
     new_installation: bool
     tag_handler: GalaxyTagHandler
@@ -129,7 +141,7 @@ class StructuredApp(MinimalManagerApp):
     role_manager: Any  # 'galaxy.managers.roles.RoleManager'
     dynamic_tool_manager: Any  # 'galaxy.managers.tools.DynamicToolManager'
     data_provider_registry: Any  # 'galaxy.visualization.data_providers.registry.DataProviderRegistry'
-    tool_data_tables: 'ToolDataTableManager'
+    tool_data_tables: "ToolDataTableManager"
     genomes: Any  # 'galaxy.visualization.genomes.Genomes'
     error_reports: Any  # 'galaxy.tools.error_reports.ErrorReports'
     tool_cache: Any  # 'galaxy.tools.cache.ToolCache'
diff --git a/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py b/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
index a1350c3dedf..4ab8c2e6e32 100644
--- a/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
@@ -10,12 +10,12 @@ log = logging.getLogger(__name__)
 
 
 class CustomDatatypeLoader:
-
     def __init__(self, app):
         self.app = app
 
-    def alter_config_and_load_prorietary_datatypes(self, datatypes_config, relative_install_dir,
-                                                   deactivate=False, override=True):
+    def alter_config_and_load_prorietary_datatypes(
+        self, datatypes_config, relative_install_dir, deactivate=False, override=True
+    ):
         """
         Parse a custom datatypes config (a datatypes_conf.xml file included in an installed
         tool shed repository) and add information to appropriate element attributes that will
@@ -29,20 +29,19 @@ class CustomDatatypeLoader:
         if tree is None:
             return None, None
         datatypes_config_root = tree.getroot()
-        registration = datatypes_config_root.find('registration')
+        registration = datatypes_config_root.find("registration")
         if registration is None:
             # We have valid XML, but not a valid custom datatypes definition.
             return None, None
-        converter_path, display_path = self.get_converter_and_display_paths(registration,
-                                                                            relative_install_dir)
+        converter_path, display_path = self.get_converter_and_display_paths(registration, relative_install_dir)
         if converter_path:
             # Path to datatype converters
-            registration.attrib['proprietary_converter_path'] = converter_path
+            registration.attrib["proprietary_converter_path"] = converter_path
         if display_path:
             # Path to datatype display applications
-            registration.attrib['proprietary_display_path'] = display_path
+            registration.attrib["proprietary_display_path"] = display_path
         relative_path_to_datatype_file_name = None
-        datatype_files = datatypes_config_root.find('datatype_files')
+        datatype_files = datatypes_config_root.find("datatype_files")
         datatype_class_modules = []
         if datatype_files is not None:
             # The <datatype_files> tag set contains any number of <datatype_file> tags.
@@ -52,12 +51,12 @@ class CustomDatatypeLoader:
             # </datatype_files>
             # We'll add attributes to the datatype tag sets so that the modules can be properly imported
             # by the datatypes registry.
-            for elem in datatype_files.findall('datatype_file'):
-                datatype_file_name = elem.get('name', None)
+            for elem in datatype_files.findall("datatype_file"):
+                datatype_file_name = elem.get("name", None)
                 if datatype_file_name:
                     # Find the file in the installed repository.
                     for root, _dirs, files in os.walk(relative_install_dir):
-                        if root.find('.hg') < 0:
+                        if root.find(".hg") < 0:
                             for name in files:
                                 if name == datatype_file_name:
                                     datatype_class_modules.append(os.path.join(root, name))
@@ -66,36 +65,38 @@ class CustomDatatypeLoader:
             if datatype_class_modules:
                 for relative_path_to_datatype_file_name in datatype_class_modules:
                     datatype_file_name_path, datatype_file_name = os.path.split(relative_path_to_datatype_file_name)
-                    for elem in registration.findall('datatype'):
+                    for elem in registration.findall("datatype"):
                         # Handle 'type' attribute which should be something like one of the following:
                         # type="gmap:GmapDB"
                         # type="galaxy.datatypes.gmap:GmapDB"
-                        dtype = elem.get('type', None)
+                        dtype = elem.get("type", None)
                         if dtype:
-                            fields = dtype.split(':')
+                            fields = dtype.split(":")
                             proprietary_datatype_module = fields[0]
-                            if proprietary_datatype_module.find('.') >= 0:
+                            if proprietary_datatype_module.find(".") >= 0:
                                 # Handle the case where datatype_module is "galaxy.datatypes.gmap".
-                                proprietary_datatype_module = proprietary_datatype_module.split('.')[-1]
+                                proprietary_datatype_module = proprietary_datatype_module.split(".")[-1]
                             # The value of proprietary_path must be an absolute path due to job_working_directory.
-                            elem.attrib['proprietary_path'] = os.path.abspath(datatype_file_name_path)
-                            elem.attrib['proprietary_datatype_module'] = proprietary_datatype_module
+                            elem.attrib["proprietary_path"] = os.path.abspath(datatype_file_name_path)
+                            elem.attrib["proprietary_datatype_module"] = proprietary_datatype_module
         # Load custom datatypes
-        self.app.datatypes_registry.load_datatypes(root_dir=self.app.config.root,
-                                                   config=datatypes_config_root,
-                                                   deactivate=deactivate,
-                                                   override=override)
+        self.app.datatypes_registry.load_datatypes(
+            root_dir=self.app.config.root, config=datatypes_config_root, deactivate=deactivate, override=override
+        )
         return converter_path, display_path
 
-    def create_repository_dict_for_proprietary_datatypes(self, tool_shed, name, owner, installed_changeset_revision,
-                                                         tool_dicts, converter_path=None, display_path=None):
-        return dict(tool_shed=tool_shed,
-                    repository_name=name,
-                    repository_owner=owner,
-                    installed_changeset_revision=installed_changeset_revision,
-                    tool_dicts=tool_dicts,
-                    converter_path=converter_path,
-                    display_path=display_path)
+    def create_repository_dict_for_proprietary_datatypes(
+        self, tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None
+    ):
+        return dict(
+            tool_shed=tool_shed,
+            repository_name=name,
+            repository_owner=owner,
+            installed_changeset_revision=installed_changeset_revision,
+            tool_dicts=tool_dicts,
+            converter_path=converter_path,
+            display_path=display_path,
+        )
 
     def get_converter_and_display_paths(self, registration_elem, relative_install_dir):
         """
@@ -104,17 +105,17 @@ class CustomDatatypeLoader:
         """
         converter_path = None
         display_path = None
-        for elem in registration_elem.findall('datatype'):
+        for elem in registration_elem.findall("datatype"):
             if not converter_path:
                 # If any of the <datatype> tag sets contain <converter> tags, set the converter_path
                 # if it is not already set.  This requires developers to place all converters in the
                 # same subdirectory within the repository hierarchy.
-                for converter in elem.findall('converter'):
-                    converter_config = converter.get('file', None)
+                for converter in elem.findall("converter"):
+                    converter_config = converter.get("file", None)
                     if converter_config:
                         converter_config_file_name = strip_path(converter_config)
                         for root, _dirs, files in os.walk(relative_install_dir):
-                            if root.find('.hg') < 0:
+                            if root.find(".hg") < 0:
                                 for name in files:
                                     if name == converter_config_file_name:
                                         # The value of converter_path must be absolute due to job_working_directory.
@@ -126,12 +127,12 @@ class CustomDatatypeLoader:
                 # If any of the <datatype> tag sets contain <display> tags, set the display_path
                 # if it is not already set.  This requires developers to place all display acpplications
                 # in the same subdirectory within the repository hierarchy.
-                for display_app in elem.findall('display'):
-                    display_config = display_app.get('file', None)
+                for display_app in elem.findall("display"):
+                    display_config = display_app.get("file", None)
                     if display_config:
                         display_config_file_name = strip_path(display_config)
                         for root, _dirs, files in os.walk(relative_install_dir):
-                            if root.find('.hg') < 0:
+                            if root.find(".hg") < 0:
                                 for name in files:
                                     if name == display_config_file_name:
                                         # The value of display_path must be absolute due to job_working_directory.
@@ -145,9 +146,9 @@ class CustomDatatypeLoader:
 
     def load_installed_datatype_converters(self, installed_repository_dict, deactivate=False):
         """Load or deactivate proprietary datatype converters."""
-        self.app.datatypes_registry.load_datatype_converters(self.app.toolbox,
-                                                             installed_repository_dict=installed_repository_dict,
-                                                             deactivate=deactivate)
+        self.app.datatypes_registry.load_datatype_converters(
+            self.app.toolbox, installed_repository_dict=installed_repository_dict, deactivate=deactivate
+        )
 
     def load_installed_datatypes(self, repository, relative_install_dir, deactivate=False):
         """
@@ -158,23 +159,24 @@ class CustomDatatypeLoader:
         repository_dict = None
         datatypes_config = get_config_from_disk(DATATYPES_CONFIG_FILENAME, relative_install_dir)
         if datatypes_config:
-            converter_path, display_path = \
-                self.alter_config_and_load_prorietary_datatypes(datatypes_config,
-                                                                relative_install_dir,
-                                                                deactivate=deactivate)
+            converter_path, display_path = self.alter_config_and_load_prorietary_datatypes(
+                datatypes_config, relative_install_dir, deactivate=deactivate
+            )
             if converter_path or display_path:
                 # Create a dictionary of tool shed repository related information.
-                repository_dict = \
-                    self.create_repository_dict_for_proprietary_datatypes(tool_shed=repository.tool_shed,
-                                                                          name=repository.name,
-                                                                          owner=repository.owner,
-                                                                          installed_changeset_revision=repository.installed_changeset_revision,
-                                                                          tool_dicts=metadata.get('tools', []),
-                                                                          converter_path=converter_path,
-                                                                          display_path=display_path)
+                repository_dict = self.create_repository_dict_for_proprietary_datatypes(
+                    tool_shed=repository.tool_shed,
+                    name=repository.name,
+                    owner=repository.owner,
+                    installed_changeset_revision=repository.installed_changeset_revision,
+                    tool_dicts=metadata.get("tools", []),
+                    converter_path=converter_path,
+                    display_path=display_path,
+                )
         return repository_dict
 
     def load_installed_display_applications(self, installed_repository_dict, deactivate=False):
         """Load or deactivate custom datatype display applications."""
-        self.app.datatypes_registry.load_display_applications(self.app, installed_repository_dict=installed_repository_dict,
-                                                              deactivate=deactivate)
+        self.app.datatypes_registry.load_display_applications(
+            self.app, installed_repository_dict=installed_repository_dict, deactivate=deactivate
+        )
diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
index b909e457524..036d31c041b 100644
--- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
@@ -8,51 +8,73 @@ import traceback
 from fabric.api import lcd
 from sqlalchemy import or_
 
-from galaxy import exceptions, util
+from galaxy import (
+    exceptions,
+    util,
+)
 from galaxy.tool_shed.galaxy_install.datatypes import custom_datatype_manager
-from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
+from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import (
+    InstalledRepositoryMetadataManager,
+)
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment
-from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager
-from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager
-from galaxy.tool_shed.galaxy_install.tools import data_manager, tool_panel_manager
+from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import (
+    StepManager,
+    TagManager,
+)
+from galaxy.tool_shed.galaxy_install.tools import (
+    data_manager,
+    tool_panel_manager,
+)
 from galaxy.tool_shed.tools.data_table_manager import ShedToolDataTableManager
 from galaxy.tool_shed.util import (
     basic_util,
     hg_util,
     repository_util,
-    shed_util_common as suc,
+)
+from galaxy.tool_shed.util import shed_util_common as suc
+from galaxy.tool_shed.util import (
     tool_dependency_util,
-    tool_util
+    tool_util,
 )
 from galaxy.tool_util.deps import views
-from galaxy.util.tool_shed import common_util, encoding_util, xml_util
+from galaxy.util.tool_shed import (
+    common_util,
+    encoding_util,
+    xml_util,
+)
 
 log = logging.getLogger(__name__)
 
 
 class InstallToolDependencyManager:
-
     def __init__(self, app):
         self.app = app
         self.install_model = self.app.install_model
-        self.INSTALL_ACTIONS = ['download_binary', 'download_by_url', 'download_file',
-                                'setup_perl_environment', 'setup_python_environment',
-                                'setup_r_environment', 'setup_ruby_environment', 'shell_command']
+        self.INSTALL_ACTIONS = [
+            "download_binary",
+            "download_by_url",
+            "download_file",
+            "setup_perl_environment",
+            "setup_python_environment",
+            "setup_r_environment",
+            "setup_ruby_environment",
+            "shell_command",
+        ]
 
     def format_traceback(self):
         ex_type, ex, tb = sys.exc_info()
-        return ''.join(traceback.format_tb(tb))
+        return "".join(traceback.format_tb(tb))
 
     def get_tool_shed_repository_install_dir(self, tool_shed_repository):
         return os.path.abspath(tool_shed_repository.repo_files_directory(self.app))
 
     def install_and_build_package(self, install_environment, tool_dependency, actions_dict):
         """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
-        install_dir = actions_dict['install_dir']
-        package_name = actions_dict['package_name']
-        actions = actions_dict.get('actions', None)
+        install_dir = actions_dict["install_dir"]
+        package_name = actions_dict["package_name"]
+        actions = actions_dict.get("actions", None)
         filtered_actions = []
         env_file_builder = EnvFileBuilder(install_dir)
         step_manager = StepManager(self.app)
@@ -70,18 +92,19 @@ class InstallToolDependencyManager:
                         # but to allow for a standard method signature we'll pass them along.  We don't check the
                         # tool_dependency status in this stage because it should not have been changed based on a
                         # download.
-                        tool_dependency, filtered_actions, dir = \
-                            step_manager.execute_step(tool_dependency=tool_dependency,
-                                                      package_name=package_name,
-                                                      actions=actions,
-                                                      action_type=action_type,
-                                                      action_dict=action_dict,
-                                                      filtered_actions=filtered_actions,
-                                                      env_file_builder=env_file_builder,
-                                                      install_environment=install_environment,
-                                                      work_dir=work_dir,
-                                                      current_dir=None,
-                                                      initial_download=True)
+                        tool_dependency, filtered_actions, dir = step_manager.execute_step(
+                            tool_dependency=tool_dependency,
+                            package_name=package_name,
+                            actions=actions,
+                            action_type=action_type,
+                            action_dict=action_dict,
+                            filtered_actions=filtered_actions,
+                            env_file_builder=env_file_builder,
+                            install_environment=install_environment,
+                            work_dir=work_dir,
+                            current_dir=None,
+                            initial_download=True,
+                        )
                     else:
                         # We're handling a complex repository dependency where we only have a set_environment tag set.
                         # <action type="set_environment">
@@ -93,22 +116,23 @@ class InstallToolDependencyManager:
                     # now perform all of the actions defined for building it.
                     for action_tup in filtered_actions:
                         if dir is None:
-                            dir = ''
+                            dir = ""
                         current_dir = os.path.abspath(os.path.join(work_dir, dir))
                         with lcd(current_dir):
                             action_type, action_dict = action_tup
-                            tool_dependency, tmp_filtered_actions, tmp_dir = \
-                                step_manager.execute_step(tool_dependency=tool_dependency,
-                                                          package_name=package_name,
-                                                          actions=actions,
-                                                          action_type=action_type,
-                                                          action_dict=action_dict,
-                                                          filtered_actions=filtered_actions,
-                                                          env_file_builder=env_file_builder,
-                                                          install_environment=install_environment,
-                                                          work_dir=work_dir,
-                                                          current_dir=current_dir,
-                                                          initial_download=False)
+                            tool_dependency, tmp_filtered_actions, tmp_dir = step_manager.execute_step(
+                                tool_dependency=tool_dependency,
+                                package_name=package_name,
+                                actions=actions,
+                                action_type=action_type,
+                                action_dict=action_dict,
+                                filtered_actions=filtered_actions,
+                                env_file_builder=env_file_builder,
+                                install_environment=install_environment,
+                                work_dir=work_dir,
+                                current_dir=current_dir,
+                                initial_download=False,
+                            )
                             if tool_dependency.status in [self.install_model.ToolDependency.installation_status.ERROR]:
                                 # If the tool_dependency status is in an error state, return it with no additional
                                 # processing.
@@ -120,19 +144,25 @@ class InstallToolDependencyManager:
                                 dir = tmp_dir
         return tool_dependency
 
-    def install_and_build_package_via_fabric(self, install_environment, tool_shed_repository, tool_dependency, actions_dict):
+    def install_and_build_package_via_fabric(
+        self, install_environment, tool_shed_repository, tool_dependency, actions_dict
+    ):
         try:
             # There is currently only one fabric method.
             tool_dependency = self.install_and_build_package(install_environment, tool_dependency, actions_dict)
         except Exception as e:
-            log.exception('Error installing tool dependency %s version %s.', tool_dependency.name, tool_dependency.version)
+            log.exception(
+                "Error installing tool dependency %s version %s.", tool_dependency.name, tool_dependency.version
+            )
             # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must
             # be left False here.
-            error_message = f'{self.format_traceback()}\n{util.unicodify(e)}'
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency=tool_dependency,
-                                                                                  status=self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                                                  error_message=error_message)
+            error_message = f"{self.format_traceback()}\n{util.unicodify(e)}"
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app,
+                tool_dependency=tool_dependency,
+                status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                error_message=error_message,
+            )
         tool_dependency = self.mark_tool_dependency_installed(tool_dependency)
         return tool_dependency
 
@@ -156,24 +186,24 @@ class InstallToolDependencyManager:
         root = tree.getroot()
         elems = []
         for elem in root:
-            if elem.tag == 'set_environment':
-                version = elem.get('version', '1.0')
-                if version != '1.0':
-                    raise Exception('The <set_environment> tag must have a version attribute with value 1.0')
+            if elem.tag == "set_environment":
+                version = elem.get("version", "1.0")
+                if version != "1.0":
+                    raise Exception("The <set_environment> tag must have a version attribute with value 1.0")
                 for sub_elem in elem:
                     elems.append(sub_elem)
             else:
                 elems.append(elem)
         for elem in elems:
-            name = elem.get('name', None)
-            version = elem.get('version', None)
-            type = elem.get('type', None)
+            name = elem.get("name", None)
+            version = elem.get("version", None)
+            type = elem.get("type", None)
             if type is None:
-                if elem.tag in ['environment_variable', 'set_environment']:
-                    type = 'set_environment'
+                if elem.tag in ["environment_variable", "set_environment"]:
+                    type = "set_environment"
                 else:
-                    type = 'package'
-            if (name and type == 'set_environment') or (name and version):
+                    type = "package"
+            if (name and type == "set_environment") or (name and version):
                 # elem is a package set_environment tag set.
                 attr_tup = (name, version, type)
                 try:
@@ -184,37 +214,53 @@ class InstallToolDependencyManager:
                     tool_dependency = tool_dependencies[index]
                     # If the tool_dependency.type is 'set_environment', then the call to process_tag_set() will
                     # handle everything - no additional installation is necessary.
-                    tool_dependency, proceed_with_install, action_elem_tuples = \
-                        tag_manager.process_tag_set(tool_shed_repository,
-                                                    tool_dependency,
-                                                    elem,
-                                                    name,
-                                                    version,
-                                                    tool_dependency_db_records=tool_dependencies)
-                    if (tool_dependency.type == 'package' and proceed_with_install):
+                    tool_dependency, proceed_with_install, action_elem_tuples = tag_manager.process_tag_set(
+                        tool_shed_repository,
+                        tool_dependency,
+                        elem,
+                        name,
+                        version,
+                        tool_dependency_db_records=tool_dependencies,
+                    )
+                    if tool_dependency.type == "package" and proceed_with_install:
                         try:
-                            tool_dependency = self.install_package(elem,
-                                                                   tool_shed_repository,
-                                                                   tool_dependencies=tool_dependencies)
+                            tool_dependency = self.install_package(
+                                elem, tool_shed_repository, tool_dependencies=tool_dependencies
+                            )
                         except Exception as e:
-                            error_message = "Error installing tool dependency %s version %s: %s" % \
-                                (str(name), str(version), str(e))
+                            error_message = "Error installing tool dependency %s version %s: %s" % (
+                                str(name),
+                                str(version),
+                                str(e),
+                            )
                             log.exception(error_message)
                             if tool_dependency:
                                 # Since there was an installation error, update the tool dependency status to Error. The
                                 # remove_installation_path option must be left False here.
-                                tool_dependency = \
-                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                        tool_dependency=tool_dependency,
-                                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                                                        error_message=error_message)
-                        if tool_dependency and tool_dependency.status in [self.install_model.ToolDependency.installation_status.INSTALLED,
-                                                                          self.install_model.ToolDependency.installation_status.ERROR]:
+                                tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                                    self.app,
+                                    tool_dependency=tool_dependency,
+                                    status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                    error_message=error_message,
+                                )
+                        if tool_dependency and tool_dependency.status in [
+                            self.install_model.ToolDependency.installation_status.INSTALLED,
+                            self.install_model.ToolDependency.installation_status.ERROR,
+                        ]:
                             installed_packages.append(tool_dependency)
         return installed_packages
 
-    def install_via_fabric(self, tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None,
-                           actions_elem=None, action_elem=None, **kwd):
+    def install_via_fabric(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        install_dir,
+        package_name=None,
+        custom_fabfile_path=None,
+        actions_elem=None,
+        action_elem=None,
+        **kwd,
+    ):
         """
         Parse a tool_dependency.xml file's <actions> tag set to gather information for installation using
         self.install_and_build_package().  The use of fabric is being eliminated, so some of these functions
@@ -224,12 +270,12 @@ class InstallToolDependencyManager:
             os.makedirs(install_dir)
         actions_dict = dict(install_dir=install_dir)
         if package_name:
-            actions_dict['package_name'] = package_name
+            actions_dict["package_name"] = package_name
         actions = []
         is_binary_download = False
         if actions_elem is not None:
             elems = actions_elem
-            if elems.get('os') is not None and elems.get('architecture') is not None:
+            if elems.get("os") is not None and elems.get("architecture") is not None:
                 is_binary_download = True
         elif action_elem is not None:
             # We were provided with a single <action> element to perform certain actions after a platform-specific tarball was downloaded.
@@ -241,33 +287,34 @@ class InstallToolDependencyManager:
         install_environment = InstallEnvironment(self.app, tool_shed_repository_install_dir, install_dir)
         for action_elem in elems:
             # Make sure to skip all comments, since they are now included in the XML tree.
-            if action_elem.tag != 'action':
+            if action_elem.tag != "action":
                 continue
             action_dict = {}
-            action_type = action_elem.get('type', None)
+            action_type = action_elem.get("type", None)
             if action_type is not None:
-                action_dict = step_manager.prepare_step(tool_dependency=tool_dependency,
-                                                        action_type=action_type,
-                                                        action_elem=action_elem,
-                                                        action_dict=action_dict,
-                                                        install_environment=install_environment,
-                                                        is_binary_download=is_binary_download)
+                action_dict = step_manager.prepare_step(
+                    tool_dependency=tool_dependency,
+                    action_type=action_type,
+                    action_elem=action_elem,
+                    action_dict=action_dict,
+                    install_environment=install_environment,
+                    is_binary_download=is_binary_download,
+                )
                 action_tuple = (action_type, action_dict)
-                if action_type == 'set_environment':
+                if action_type == "set_environment":
                     if action_tuple not in actions:
                         actions.append(action_tuple)
                 else:
                     actions.append(action_tuple)
         if actions:
-            actions_dict['actions'] = actions
+            actions_dict["actions"] = actions
         if custom_fabfile_path is not None:
             # TODO: this is not yet supported or functional, but when it is handle it using the fabric api.
-            raise Exception('Tool dependency installation using proprietary fabric scripts is not yet supported.')
+            raise Exception("Tool dependency installation using proprietary fabric scripts is not yet supported.")
         else:
-            tool_dependency = self.install_and_build_package_via_fabric(install_environment,
-                                                                        tool_shed_repository,
-                                                                        tool_dependency,
-                                                                        actions_dict)
+            tool_dependency = self.install_and_build_package_via_fabric(
+                install_environment, tool_shed_repository, tool_dependency, actions_dict
+            )
         return tool_dependency
 
     def install_package(self, elem, tool_shed_repository, tool_dependencies=None):
@@ -278,8 +325,8 @@ class InstallToolDependencyManager:
         tag_manager = TagManager(self.app)
         # The value of package_name should match the value of the "package" type in the tool config's
         # <requirements> tag set, but it's not required.
-        package_name = elem.get('name', None)
-        package_version = elem.get('version', None)
+        package_name = elem.get("name", None)
+        package_version = elem.get("version", None)
         if tool_dependencies and package_name and package_version:
             tool_dependency = None
             for tool_dependency in tool_dependencies:
@@ -287,24 +334,26 @@ class InstallToolDependencyManager:
                     break
             if tool_dependency is not None:
                 for package_elem in elem:
-                    tool_dependency, proceed_with_install, actions_elem_tuples = \
-                        tag_manager.process_tag_set(tool_shed_repository,
-                                                    tool_dependency,
-                                                    package_elem,
-                                                    package_name,
-                                                    package_version,
-                                                    tool_dependency_db_records=None)
+                    tool_dependency, proceed_with_install, actions_elem_tuples = tag_manager.process_tag_set(
+                        tool_shed_repository,
+                        tool_dependency,
+                        package_elem,
+                        package_name,
+                        package_version,
+                        tool_dependency_db_records=None,
+                    )
                     if proceed_with_install and actions_elem_tuples:
                         # Get the installation directory for tool dependencies that will be installed for the received
                         # tool_shed_repository.
-                        install_dir = \
-                            tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
-                                                                                 repository_name=tool_shed_repository.name,
-                                                                                 repository_owner=tool_shed_repository.owner,
-                                                                                 repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                                 tool_dependency_type='package',
-                                                                                 tool_dependency_name=package_name,
-                                                                                 tool_dependency_version=package_version)
+                        install_dir = tool_dependency_util.get_tool_dependency_install_dir(
+                            app=self.app,
+                            repository_name=tool_shed_repository.name,
+                            repository_owner=tool_shed_repository.owner,
+                            repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+                            tool_dependency_type="package",
+                            tool_dependency_name=package_name,
+                            tool_dependency_version=package_version,
+                        )
                         # At this point we have a list of <actions> elems that are either defined within an <actions_group>
                         # tag set with <actions> sub-elements that contains os and architecture attributes filtered by the
                         # platform into which the appropriate compiled binary will be installed, or not defined within an
@@ -318,8 +367,8 @@ class InstallToolDependencyManager:
                                 # attributes are otherwise ignored.
                                 can_install_from_source = False
                                 for actions_elem in actions_elems:
-                                    system = actions_elem.get('os')
-                                    architecture = actions_elem.get('architecture')
+                                    system = actions_elem.get("os")
+                                    architecture = actions_elem.get("architecture")
                                     # If this <actions> element has the os and architecture attributes defined, then we only
                                     # want to process until a successful installation is achieved.
                                     if system and architecture:
@@ -331,13 +380,18 @@ class InstallToolDependencyManager:
                                         if binary_installed:
                                             continue
                                         # No platform-specific <actions> recipe has yet resulted in a successful installation.
-                                        tool_dependency = self.install_via_fabric(tool_shed_repository,
-                                                                                  tool_dependency,
-                                                                                  install_dir,
-                                                                                  package_name=package_name,
-                                                                                  actions_elem=actions_elem,
-                                                                                  action_elem=None)
-                                        if tool_dependency.status == self.install_model.ToolDependency.installation_status.INSTALLED:
+                                        tool_dependency = self.install_via_fabric(
+                                            tool_shed_repository,
+                                            tool_dependency,
+                                            install_dir,
+                                            package_name=package_name,
+                                            actions_elem=actions_elem,
+                                            action_elem=None,
+                                        )
+                                        if (
+                                            tool_dependency.status
+                                            == self.install_model.ToolDependency.installation_status.INSTALLED
+                                        ):
                                             # If an <actions> tag was found that matches the current platform, and
                                             # self.install_via_fabric() did not result in an error state, set binary_installed
                                             # to True in order to skip any remaining platform-specific <actions> tags.
@@ -345,25 +399,39 @@ class InstallToolDependencyManager:
                                         else:
                                             # Process the next matching <actions> tag, or any defined <actions> tags that do not
                                             # contain platform dependent recipes.
-                                            log.debug('Error downloading binary for tool dependency %s version %s: %s' %
-                                                      (str(package_name), str(package_version), str(tool_dependency.error_message)))
+                                            log.debug(
+                                                "Error downloading binary for tool dependency %s version %s: %s"
+                                                % (
+                                                    str(package_name),
+                                                    str(package_version),
+                                                    str(tool_dependency.error_message),
+                                                )
+                                            )
                                     else:
-                                        if actions_elem.tag == 'actions':
+                                        if actions_elem.tag == "actions":
                                             # We've reached an <actions> tag that defines the recipe for installing and compiling from
                                             # source.  If binary installation failed, we proceed with the recipe.
                                             if not binary_installed:
-                                                installation_directory = tool_dependency.installation_directory(self.app)
+                                                installation_directory = tool_dependency.installation_directory(
+                                                    self.app
+                                                )
                                                 if os.path.exists(installation_directory):
                                                     # Delete contents of installation directory if attempt at binary installation failed.
                                                     installation_directory_contents = os.listdir(installation_directory)
                                                     if installation_directory_contents:
-                                                        removed, error_message = \
-                                                            tool_dependency_util.remove_tool_dependency(self.app, tool_dependency)
+                                                        (
+                                                            removed,
+                                                            error_message,
+                                                        ) = tool_dependency_util.remove_tool_dependency(
+                                                            self.app, tool_dependency
+                                                        )
                                                         if removed:
                                                             can_install_from_source = True
                                                         else:
-                                                            log.debug('Error removing old files from installation directory %s: %s' %
-                                                                      (str(installation_directory, str(error_message))))
+                                                            log.debug(
+                                                                "Error removing old files from installation directory %s: %s"
+                                                                % (str(installation_directory, str(error_message)))
+                                                            )
                                                     else:
                                                         can_install_from_source = True
                                                 else:
@@ -371,58 +439,81 @@ class InstallToolDependencyManager:
                                             if can_install_from_source:
                                                 # We now know that binary installation was not successful, so proceed with the <actions>
                                                 # tag set that defines the recipe to install and compile from source.
-                                                log.debug('Proceeding with install and compile recipe for tool dependency %s.' %
-                                                          str(tool_dependency.name))
+                                                log.debug(
+                                                    "Proceeding with install and compile recipe for tool dependency %s."
+                                                    % str(tool_dependency.name)
+                                                )
                                                 # Reset above error to installing
-                                                tool_dependency.status = self.install_model.ToolDependency.installation_status.INSTALLING
-                                                tool_dependency = self.install_via_fabric(tool_shed_repository,
-                                                                                          tool_dependency,
-                                                                                          install_dir,
-                                                                                          package_name=package_name,
-                                                                                          actions_elem=actions_elem,
-                                                                                          action_elem=None)
-                                    if actions_elem.tag == 'action' and \
-                                            tool_dependency.status != self.install_model.ToolDependency.installation_status.ERROR:
+                                                tool_dependency.status = (
+                                                    self.install_model.ToolDependency.installation_status.INSTALLING
+                                                )
+                                                tool_dependency = self.install_via_fabric(
+                                                    tool_shed_repository,
+                                                    tool_dependency,
+                                                    install_dir,
+                                                    package_name=package_name,
+                                                    actions_elem=actions_elem,
+                                                    action_elem=None,
+                                                )
+                                    if (
+                                        actions_elem.tag == "action"
+                                        and tool_dependency.status
+                                        != self.install_model.ToolDependency.installation_status.ERROR
+                                    ):
                                         # If the tool dependency is not in an error state, perform any final actions that have been
                                         # defined within the actions_group tag set, but outside of an <actions> tag, which defines
                                         # the recipe for installing and compiling from source.
-                                        tool_dependency = self.install_via_fabric(tool_shed_repository,
-                                                                                  tool_dependency,
-                                                                                  install_dir,
-                                                                                  package_name=package_name,
-                                                                                  actions_elem=None,
-                                                                                  action_elem=actions_elem)
+                                        tool_dependency = self.install_via_fabric(
+                                            tool_shed_repository,
+                                            tool_dependency,
+                                            install_dir,
+                                            package_name=package_name,
+                                            actions_elem=None,
+                                            action_elem=actions_elem,
+                                        )
                             else:
                                 # Checks for "os" and "architecture" attributes  are not made for any <actions> tag sets outside of
                                 # an <actions_group> tag set.  If the attributes are defined, they will be ignored. All <actions> tags
                                 # outside of an <actions_group> tag set will always be processed.
-                                tool_dependency = self.install_via_fabric(tool_shed_repository,
-                                                                          tool_dependency,
-                                                                          install_dir,
-                                                                          package_name=package_name,
-                                                                          actions_elem=actions_elems,
-                                                                          action_elem=None)
-                                if tool_dependency.status != self.install_model.ToolDependency.installation_status.ERROR:
-                                    log.debug('Tool dependency %s version %s has been installed in %s.' %
-                                              (str(package_name), str(package_version), str(install_dir)))
+                                tool_dependency = self.install_via_fabric(
+                                    tool_shed_repository,
+                                    tool_dependency,
+                                    install_dir,
+                                    package_name=package_name,
+                                    actions_elem=actions_elems,
+                                    action_elem=None,
+                                )
+                                if (
+                                    tool_dependency.status
+                                    != self.install_model.ToolDependency.installation_status.ERROR
+                                ):
+                                    log.debug(
+                                        "Tool dependency %s version %s has been installed in %s."
+                                        % (str(package_name), str(package_version), str(install_dir))
+                                    )
         return tool_dependency
 
     def mark_tool_dependency_installed(self, tool_dependency):
-        if tool_dependency.status not in [self.install_model.ToolDependency.installation_status.ERROR,
-                                          self.install_model.ToolDependency.installation_status.INSTALLED]:
-            log.debug('Changing status for tool dependency %s from %s to %s.' %
-                      (str(tool_dependency.name),
-                       str(tool_dependency.status),
-                       str(self.install_model.ToolDependency.installation_status.INSTALLED)))
+        if tool_dependency.status not in [
+            self.install_model.ToolDependency.installation_status.ERROR,
+            self.install_model.ToolDependency.installation_status.INSTALLED,
+        ]:
+            log.debug(
+                "Changing status for tool dependency %s from %s to %s."
+                % (
+                    str(tool_dependency.name),
+                    str(tool_dependency.status),
+                    str(self.install_model.ToolDependency.installation_status.INSTALLED),
+                )
+            )
             status = self.install_model.ToolDependency.installation_status.INSTALLED
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency=tool_dependency,
-                                                                                  status=status)
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app, tool_dependency=tool_dependency, status=status
+            )
         return tool_dependency
 
 
 class InstallRepositoryManager:
-
     def __init__(self, app, tpm=None):
         self.app = app
         self.install_model = self.app.install_model
@@ -432,8 +523,9 @@ class InstallRepositoryManager:
         else:
             self.tpm = tpm
 
-    def get_repository_components_for_installation(self, encoded_tsr_id, encoded_tsr_ids, repo_info_dicts,
-                                                   tool_panel_section_keys):
+    def get_repository_components_for_installation(
+        self, encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys
+    ):
         """
         The received encoded_tsr_ids, repo_info_dicts, and
         tool_panel_section_keys are 3 lists that contain associated elements
@@ -442,24 +534,31 @@ class InstallRepositoryManager:
         received encoded_tsr_id by determining its location in the received
         encoded_tsr_ids list.
         """
-        for tsr_id, repo_info_dict, tool_panel_section_key in zip(encoded_tsr_ids,
-                                                                  repo_info_dicts,
-                                                                  tool_panel_section_keys):
+        for tsr_id, repo_info_dict, tool_panel_section_key in zip(
+            encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys
+        ):
             if tsr_id == encoded_tsr_id:
                 return repo_info_dict, tool_panel_section_key
         return None, None
 
     def __get_install_info_from_tool_shed(self, tool_shed_url, name, owner, changeset_revision):
-        params = dict(name=name,
-                      owner=owner,
-                      changeset_revision=changeset_revision)
-        pathspec = ['api', 'repositories', 'get_repository_revision_install_info']
+        params = dict(name=name, owner=owner, changeset_revision=changeset_revision)
+        pathspec = ["api", "repositories", "get_repository_revision_install_info"]
         try:
-            raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+            raw_text = util.url_get(
+                tool_shed_url,
+                auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                pathspec=pathspec,
+                params=params,
+            )
         except Exception:
             message = "Error attempting to retrieve installation information from tool shed "
-            message += "%s for revision %s of repository %s owned by %s" % \
-                (tool_shed_url, changeset_revision, name, owner)
+            message += "%s for revision %s of repository %s owned by %s" % (
+                tool_shed_url,
+                changeset_revision,
+                name,
+                owner,
+            )
             log.exception(message)
             raise exceptions.InternalServerError(message)
         if raw_text:
@@ -471,8 +570,10 @@ class InstallRepositoryManager:
             repository_revision_dict = items[1]
             repo_info_dict = items[2]
         else:
-            message = "Unable to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s" % \
-                (str(tool_shed_url), str(changeset_revision), str(name), str(owner))
+            message = (
+                "Unable to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s"
+                % (str(tool_shed_url), str(changeset_revision), str(name), str(owner))
+            )
             log.warning(message)
             raise exceptions.InternalServerError(message)
         # Make sure the tool shed returned everything we need for installing the repository.
@@ -487,9 +588,18 @@ class InstallRepositoryManager:
         repo_info_dicts = [repo_info_dict]
         return repository_revision_dict, repo_info_dicts
 
-    def __handle_repository_contents(self, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir,
-                                     tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False,
-                                     tool_panel_section_mapping=None):
+    def __handle_repository_contents(
+        self,
+        tool_shed_repository,
+        tool_path,
+        repository_clone_url,
+        relative_install_dir,
+        tool_shed=None,
+        tool_section=None,
+        shed_tool_conf=None,
+        reinstalling=False,
+        tool_panel_section_mapping=None,
+    ):
         """
         Generate the metadata for the installed tool shed repository, among other things.
         This method is called when an administrator is installing a new repository or
@@ -498,181 +608,214 @@ class InstallRepositoryManager:
         tool_panel_section_mapping = tool_panel_section_mapping or {}
         shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename(shed_tool_conf)
         stdtm = ShedToolDataTableManager(self.app)
-        irmm = InstalledRepositoryMetadataManager(app=self.app,
-                                                  tpm=self.tpm,
-                                                  repository=tool_shed_repository,
-                                                  changeset_revision=tool_shed_repository.changeset_revision,
-                                                  repository_clone_url=repository_clone_url,
-                                                  shed_config_dict=shed_config_dict,
-                                                  relative_install_dir=relative_install_dir,
-                                                  repository_files_dir=None,
-                                                  resetting_all_metadata_on_repository=False,
-                                                  updating_installed_repository=False,
-                                                  persist=True)
+        irmm = InstalledRepositoryMetadataManager(
+            app=self.app,
+            tpm=self.tpm,
+            repository=tool_shed_repository,
+            changeset_revision=tool_shed_repository.changeset_revision,
+            repository_clone_url=repository_clone_url,
+            shed_config_dict=shed_config_dict,
+            relative_install_dir=relative_install_dir,
+            repository_files_dir=None,
+            resetting_all_metadata_on_repository=False,
+            updating_installed_repository=False,
+            persist=True,
+        )
         irmm.generate_metadata_for_changeset_revision()
         irmm_metadata_dict = irmm.get_metadata_dict()
         tool_shed_repository.metadata_ = irmm_metadata_dict
         # Update the tool_shed_repository.tool_shed_status column in the database.
-        tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository(self.app, tool_shed_repository)
+        tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository(
+            self.app, tool_shed_repository
+        )
         if tool_shed_status_dict:
             tool_shed_repository.tool_shed_status = tool_shed_status_dict
         self.install_model.context.add(tool_shed_repository)
         self.install_model.context.flush()
-        if 'tool_dependencies' in irmm_metadata_dict and not reinstalling:
-            tool_dependency_util.create_tool_dependency_objects(self.app,
-                                                                tool_shed_repository,
-                                                                relative_install_dir,
-                                                                set_status=True)
-        if 'sample_files' in irmm_metadata_dict:
-            sample_files = irmm_metadata_dict.get('sample_files', [])
+        if "tool_dependencies" in irmm_metadata_dict and not reinstalling:
+            tool_dependency_util.create_tool_dependency_objects(
+                self.app, tool_shed_repository, relative_install_dir, set_status=True
+            )
+        if "sample_files" in irmm_metadata_dict:
+            sample_files = irmm_metadata_dict.get("sample_files", [])
             tool_index_sample_files = stdtm.get_tool_index_sample_files(sample_files)
-            tool_data_table_conf_filename, tool_data_table_elems = \
-                stdtm.install_tool_data_tables(tool_shed_repository, tool_index_sample_files)
+            tool_data_table_conf_filename, tool_data_table_elems = stdtm.install_tool_data_tables(
+                tool_shed_repository, tool_index_sample_files
+            )
             if tool_data_table_elems:
-                self.app.tool_data_tables.add_new_entries_from_config_file(tool_data_table_conf_filename,
-                                                                           None,
-                                                                           self.app.config.shed_tool_data_table_config,
-                                                                           persist=True)
-        if 'tools' in irmm_metadata_dict:
-            tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install(irmm_metadata_dict['tools'], tool_section)
-            sample_files = irmm_metadata_dict.get('sample_files', [])
+                self.app.tool_data_tables.add_new_entries_from_config_file(
+                    tool_data_table_conf_filename, None, self.app.config.shed_tool_data_table_config, persist=True
+                )
+        if "tools" in irmm_metadata_dict:
+            tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install(
+                irmm_metadata_dict["tools"], tool_section
+            )
+            sample_files = irmm_metadata_dict.get("sample_files", [])
             tool_index_sample_files = stdtm.get_tool_index_sample_files(sample_files)
             tool_util.copy_sample_files(self.app, tool_index_sample_files, tool_path=tool_path)
             sample_files_copied = [str(s) for s in tool_index_sample_files]
             repository_tools_tups = irmm.get_repository_tools_tups()
             if repository_tools_tups:
                 # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                repository_tools_tups = stdtm.handle_missing_data_table_entry(relative_install_dir,
-                                                                             tool_path,
-                                                                             repository_tools_tups)
+                repository_tools_tups = stdtm.handle_missing_data_table_entry(
+                    relative_install_dir, tool_path, repository_tools_tups
+                )
                 # Handle missing index files for tool parameters that are dynamically generated select lists.
-                repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file(self.app,
-                                                                                                 tool_path,
-                                                                                                 sample_files,
-                                                                                                 repository_tools_tups,
-                                                                                                 sample_files_copied)
+                repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file(
+                    self.app, tool_path, sample_files, repository_tools_tups, sample_files_copied
+                )
                 # Copy remaining sample files included in the repository to the ~/tool-data directory of the
                 # local Galaxy instance.
-                tool_util.copy_sample_files(self.app,
-                                            sample_files,
-                                            tool_path=tool_path,
-                                            sample_files_copied=sample_files_copied)
-                self.tpm.add_to_tool_panel(repository_name=tool_shed_repository.name,
-                                           repository_clone_url=repository_clone_url,
-                                           changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                           repository_tools_tups=repository_tools_tups,
-                                           owner=tool_shed_repository.owner,
-                                           shed_tool_conf=shed_tool_conf,
-                                           tool_panel_dict=tool_panel_dict,
-                                           new_install=True,
-                                           tool_panel_section_mapping=tool_panel_section_mapping)
-        if 'data_manager' in irmm_metadata_dict:
+                tool_util.copy_sample_files(
+                    self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied
+                )
+                self.tpm.add_to_tool_panel(
+                    repository_name=tool_shed_repository.name,
+                    repository_clone_url=repository_clone_url,
+                    changeset_revision=tool_shed_repository.installed_changeset_revision,
+                    repository_tools_tups=repository_tools_tups,
+                    owner=tool_shed_repository.owner,
+                    shed_tool_conf=shed_tool_conf,
+                    tool_panel_dict=tool_panel_dict,
+                    new_install=True,
+                    tool_panel_section_mapping=tool_panel_section_mapping,
+                )
+        if "data_manager" in irmm_metadata_dict:
             dmh = data_manager.DataManagerHandler(self.app)
-            dmh.install_data_managers(self.app.config.shed_data_manager_config_file,
-                                      irmm_metadata_dict,
-                                      shed_config_dict,
-                                      relative_install_dir,
-                                      tool_shed_repository,
-                                      repository_tools_tups)
-        if 'datatypes' in irmm_metadata_dict:
-            self.update_tool_shed_repository_status(tool_shed_repository,
-                                                    self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES)
+            dmh.install_data_managers(
+                self.app.config.shed_data_manager_config_file,
+                irmm_metadata_dict,
+                shed_config_dict,
+                relative_install_dir,
+                tool_shed_repository,
+                repository_tools_tups,
+            )
+        if "datatypes" in irmm_metadata_dict:
+            self.update_tool_shed_repository_status(
+                tool_shed_repository,
+                self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES,
+            )
             if not tool_shed_repository.includes_datatypes:
                 tool_shed_repository.includes_datatypes = True
             self.install_model.context.add(tool_shed_repository)
             self.install_model.context.flush()
             files_dir = relative_install_dir
-            if shed_config_dict.get('tool_path'):
-                files_dir = os.path.join(shed_config_dict['tool_path'], files_dir)
+            if shed_config_dict.get("tool_path"):
+                files_dir = os.path.join(shed_config_dict["tool_path"], files_dir)
             datatypes_config = hg_util.get_config_from_disk(suc.DATATYPES_CONFIG_FILENAME, files_dir)
             # Load data types required by tools.
             cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
-            converter_path, display_path = \
-                cdl.alter_config_and_load_prorietary_datatypes(datatypes_config, files_dir, override=False)
+            converter_path, display_path = cdl.alter_config_and_load_prorietary_datatypes(
+                datatypes_config, files_dir, override=False
+            )
             if converter_path or display_path:
                 # Create a dictionary of tool shed repository related information.
-                repository_dict = \
-                    cdl.create_repository_dict_for_proprietary_datatypes(tool_shed=tool_shed,
-                                                                         name=tool_shed_repository.name,
-                                                                         owner=tool_shed_repository.owner,
-                                                                         installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                         tool_dicts=irmm_metadata_dict.get('tools', []),
-                                                                         converter_path=converter_path,
-                                                                         display_path=display_path)
+                repository_dict = cdl.create_repository_dict_for_proprietary_datatypes(
+                    tool_shed=tool_shed,
+                    name=tool_shed_repository.name,
+                    owner=tool_shed_repository.owner,
+                    installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
+                    tool_dicts=irmm_metadata_dict.get("tools", []),
+                    converter_path=converter_path,
+                    display_path=display_path,
+                )
             if converter_path:
                 # Load proprietary datatype converters
-                self.app.datatypes_registry.load_datatype_converters(self.app.toolbox, installed_repository_dict=repository_dict, use_cached=True)
+                self.app.datatypes_registry.load_datatype_converters(
+                    self.app.toolbox, installed_repository_dict=repository_dict, use_cached=True
+                )
             if display_path:
                 # Load proprietary datatype display applications
-                self.app.datatypes_registry.load_display_applications(self.app, installed_repository_dict=repository_dict)
+                self.app.datatypes_registry.load_display_applications(
+                    self.app, installed_repository_dict=repository_dict
+                )
 
     def handle_tool_shed_repositories(self, installation_dict):
         # The following installation_dict entries are all required.
-        install_repository_dependencies = installation_dict['install_repository_dependencies']
-        new_tool_panel_section_label = installation_dict['new_tool_panel_section_label']
-        no_changes_checked = installation_dict['no_changes_checked']
-        repo_info_dicts = installation_dict['repo_info_dicts']
-        tool_panel_section_id = installation_dict['tool_panel_section_id']
-        tool_path = installation_dict['tool_path']
-        tool_shed_url = installation_dict['tool_shed_url']
+        install_repository_dependencies = installation_dict["install_repository_dependencies"]
+        new_tool_panel_section_label = installation_dict["new_tool_panel_section_label"]
+        no_changes_checked = installation_dict["no_changes_checked"]
+        repo_info_dicts = installation_dict["repo_info_dicts"]
+        tool_panel_section_id = installation_dict["tool_panel_section_id"]
+        tool_path = installation_dict["tool_path"]
+        tool_shed_url = installation_dict["tool_shed_url"]
         rdim = repository_dependency_manager.RepositoryDependencyInstallManager(self.app)
-        created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
-            rdim.create_repository_dependency_objects(tool_path=tool_path,
-                                                      tool_shed_url=tool_shed_url,
-                                                      repo_info_dicts=repo_info_dicts,
-                                                      install_repository_dependencies=install_repository_dependencies,
-                                                      no_changes_checked=no_changes_checked,
-                                                      tool_panel_section_id=tool_panel_section_id,
-                                                      new_tool_panel_section_label=new_tool_panel_section_label)
-        return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts
+        (
+            created_or_updated_tool_shed_repositories,
+            tool_panel_section_keys,
+            repo_info_dicts,
+            filtered_repo_info_dicts,
+        ) = rdim.create_repository_dependency_objects(
+            tool_path=tool_path,
+            tool_shed_url=tool_shed_url,
+            repo_info_dicts=repo_info_dicts,
+            install_repository_dependencies=install_repository_dependencies,
+            no_changes_checked=no_changes_checked,
+            tool_panel_section_id=tool_panel_section_id,
+            new_tool_panel_section_label=new_tool_panel_section_label,
+        )
+        return (
+            created_or_updated_tool_shed_repositories,
+            tool_panel_section_keys,
+            repo_info_dicts,
+            filtered_repo_info_dicts,
+        )
 
     def initiate_repository_installation(self, installation_dict):
         # The following installation_dict entries are all required.
-        created_or_updated_tool_shed_repositories = installation_dict['created_or_updated_tool_shed_repositories']
-        filtered_repo_info_dicts = installation_dict['filtered_repo_info_dicts']
-        has_repository_dependencies = installation_dict['has_repository_dependencies']
-        includes_tool_dependencies = installation_dict['includes_tool_dependencies']
-        includes_tools = installation_dict['includes_tools']
-        includes_tools_for_display_in_tool_panel = installation_dict['includes_tools_for_display_in_tool_panel']
-        install_repository_dependencies = installation_dict['install_repository_dependencies']
-        install_resolver_dependencies = installation_dict['install_resolver_dependencies']
-        install_tool_dependencies = installation_dict['install_tool_dependencies']
-        message = installation_dict['message']
-        new_tool_panel_section_label = installation_dict['new_tool_panel_section_label']
-        shed_tool_conf = installation_dict['shed_tool_conf']
-        status = installation_dict['status']
-        tool_panel_section_id = installation_dict['tool_panel_section_id']
-        tool_panel_section_keys = installation_dict['tool_panel_section_keys']
-        tool_panel_section_mapping = installation_dict.get('tool_panel_section_mapping', {})
-        tool_path = installation_dict['tool_path']
-        tool_shed_url = installation_dict['tool_shed_url']
+        created_or_updated_tool_shed_repositories = installation_dict["created_or_updated_tool_shed_repositories"]
+        filtered_repo_info_dicts = installation_dict["filtered_repo_info_dicts"]
+        has_repository_dependencies = installation_dict["has_repository_dependencies"]
+        includes_tool_dependencies = installation_dict["includes_tool_dependencies"]
+        includes_tools = installation_dict["includes_tools"]
+        includes_tools_for_display_in_tool_panel = installation_dict["includes_tools_for_display_in_tool_panel"]
+        install_repository_dependencies = installation_dict["install_repository_dependencies"]
+        install_resolver_dependencies = installation_dict["install_resolver_dependencies"]
+        install_tool_dependencies = installation_dict["install_tool_dependencies"]
+        message = installation_dict["message"]
+        new_tool_panel_section_label = installation_dict["new_tool_panel_section_label"]
+        shed_tool_conf = installation_dict["shed_tool_conf"]
+        status = installation_dict["status"]
+        tool_panel_section_id = installation_dict["tool_panel_section_id"]
+        tool_panel_section_keys = installation_dict["tool_panel_section_keys"]
+        tool_panel_section_mapping = installation_dict.get("tool_panel_section_mapping", {})
+        tool_path = installation_dict["tool_path"]
+        tool_shed_url = installation_dict["tool_shed_url"]
         # Handle contained tools.
         if includes_tools_for_display_in_tool_panel and (new_tool_panel_section_label or tool_panel_section_id):
-            self.tpm.handle_tool_panel_section(self.app.toolbox,
-                                               tool_panel_section_id=tool_panel_section_id,
-                                               new_tool_panel_section_label=new_tool_panel_section_label)
+            self.tpm.handle_tool_panel_section(
+                self.app.toolbox,
+                tool_panel_section_id=tool_panel_section_id,
+                new_tool_panel_section_label=new_tool_panel_section_label,
+            )
         if includes_tools_for_display_in_tool_panel and (tool_panel_section_mapping is not None):
             for tool_guid in tool_panel_section_mapping:
-                if tool_panel_section_mapping[tool_guid]['action'] == 'create':
-                    new_tool_panel_section_name = tool_panel_section_mapping[tool_guid]['tool_panel_section']
+                if tool_panel_section_mapping[tool_guid]["action"] == "create":
+                    new_tool_panel_section_name = tool_panel_section_mapping[tool_guid]["tool_panel_section"]
                     log.debug(f'Creating tool panel section "{new_tool_panel_section_name}" for tool {tool_guid}')
-                    self.tpm.handle_tool_panel_section(self.app.toolbox, None, tool_panel_section_mapping[tool_guid]['tool_panel_section'])
-        encoded_repository_ids = [self.app.security.encode_id(tsr.id) for tsr in created_or_updated_tool_shed_repositories]
-        new_kwd = dict(includes_tools=includes_tools,
-                       includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                       has_repository_dependencies=has_repository_dependencies,
-                       install_repository_dependencies=install_repository_dependencies,
-                       includes_tool_dependencies=includes_tool_dependencies,
-                       install_resolver_dependencies=install_resolver_dependencies,
-                       install_tool_dependencies=install_tool_dependencies,
-                       message=message,
-                       repo_info_dicts=filtered_repo_info_dicts,
-                       shed_tool_conf=shed_tool_conf,
-                       status=status,
-                       tool_path=tool_path,
-                       tool_panel_section_keys=tool_panel_section_keys,
-                       tool_shed_repository_ids=encoded_repository_ids,
-                       tool_shed_url=tool_shed_url)
+                    self.tpm.handle_tool_panel_section(
+                        self.app.toolbox, None, tool_panel_section_mapping[tool_guid]["tool_panel_section"]
+                    )
+        encoded_repository_ids = [
+            self.app.security.encode_id(tsr.id) for tsr in created_or_updated_tool_shed_repositories
+        ]
+        new_kwd = dict(
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            has_repository_dependencies=has_repository_dependencies,
+            install_repository_dependencies=install_repository_dependencies,
+            includes_tool_dependencies=includes_tool_dependencies,
+            install_resolver_dependencies=install_resolver_dependencies,
+            install_tool_dependencies=install_tool_dependencies,
+            message=message,
+            repo_info_dicts=filtered_repo_info_dicts,
+            shed_tool_conf=shed_tool_conf,
+            status=status,
+            tool_path=tool_path,
+            tool_panel_section_keys=tool_panel_section_keys,
+            tool_shed_repository_ids=encoded_repository_ids,
+            tool_shed_url=tool_shed_url,
+        )
         encoded_kwd = encoding_util.tool_shed_encode(new_kwd)
         tsr_ids = [r.id for r in created_or_updated_tool_shed_repositories]
         tool_shed_repositories = []
@@ -687,110 +830,129 @@ class InstallRepositoryManager:
 
     def install(self, tool_shed_url, name, owner, changeset_revision, install_options):
         # Get all of the information necessary for installing the repository from the specified tool shed.
-        repository_revision_dict, repo_info_dicts = self.__get_install_info_from_tool_shed(tool_shed_url,
-                                                                                           name,
-                                                                                           owner,
-                                                                                           changeset_revision)
-        if changeset_revision != repository_revision_dict['changeset_revision']:
+        repository_revision_dict, repo_info_dicts = self.__get_install_info_from_tool_shed(
+            tool_shed_url, name, owner, changeset_revision
+        )
+        if changeset_revision != repository_revision_dict["changeset_revision"]:
             # Demanded installation of a non-installable revision. Stop here if repository already installed.
             repo = repository_util.get_installed_repository(
                 app=self.app,
                 tool_shed=tool_shed_url,
                 name=name,
                 owner=owner,
-                changeset_revision=repository_revision_dict['changeset_revision'],
+                changeset_revision=repository_revision_dict["changeset_revision"],
             )
             if repo and repo.is_installed:
                 # Repo installed. Returning empty list indicated repo already installed.
                 return []
         installed_tool_shed_repositories = self.__initiate_and_install_repositories(
-            tool_shed_url,
-            repository_revision_dict,
-            repo_info_dicts,
-            install_options
+            tool_shed_url, repository_revision_dict, repo_info_dicts, install_options
         )
         return installed_tool_shed_repositories
 
-    def __initiate_and_install_repositories(self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options):
+    def __initiate_and_install_repositories(
+        self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options
+    ):
         try:
-            has_repository_dependencies = repository_revision_dict['has_repository_dependencies']
+            has_repository_dependencies = repository_revision_dict["has_repository_dependencies"]
         except KeyError:
-            raise exceptions.InternalServerError("Tool shed response missing required parameter 'has_repository_dependencies'.")
+            raise exceptions.InternalServerError(
+                "Tool shed response missing required parameter 'has_repository_dependencies'."
+            )
         try:
-            includes_tools = repository_revision_dict['includes_tools']
+            includes_tools = repository_revision_dict["includes_tools"]
         except KeyError:
             raise exceptions.InternalServerError("Tool shed response missing required parameter 'includes_tools'.")
         try:
-            includes_tool_dependencies = repository_revision_dict['includes_tool_dependencies']
+            includes_tool_dependencies = repository_revision_dict["includes_tool_dependencies"]
         except KeyError:
-            raise exceptions.InternalServerError("Tool shed response missing required parameter 'includes_tool_dependencies'.")
+            raise exceptions.InternalServerError(
+                "Tool shed response missing required parameter 'includes_tool_dependencies'."
+            )
         try:
-            includes_tools_for_display_in_tool_panel = repository_revision_dict['includes_tools_for_display_in_tool_panel']
+            includes_tools_for_display_in_tool_panel = repository_revision_dict[
+                "includes_tools_for_display_in_tool_panel"
+            ]
         except KeyError:
-            raise exceptions.InternalServerError("Tool shed response missing required parameter 'includes_tools_for_display_in_tool_panel'.")
+            raise exceptions.InternalServerError(
+                "Tool shed response missing required parameter 'includes_tools_for_display_in_tool_panel'."
+            )
         # Get the information about the Galaxy components (e.g., tool panel section, tool config file, etc) that will contain the repository information.
-        install_repository_dependencies = install_options.get('install_repository_dependencies', False)
-        install_resolver_dependencies = install_options.get('install_resolver_dependencies', False)
-        install_tool_dependencies = install_options.get('install_tool_dependencies', False)
-        new_tool_panel_section_label = install_options.get('new_tool_panel_section_label', '')
-        tool_panel_section_mapping = install_options.get('tool_panel_section_mapping', {})
-        shed_tool_conf = install_options.get('shed_tool_conf')
+        install_repository_dependencies = install_options.get("install_repository_dependencies", False)
+        install_resolver_dependencies = install_options.get("install_resolver_dependencies", False)
+        install_tool_dependencies = install_options.get("install_tool_dependencies", False)
+        new_tool_panel_section_label = install_options.get("new_tool_panel_section_label", "")
+        tool_panel_section_mapping = install_options.get("tool_panel_section_mapping", {})
+        shed_tool_conf = install_options.get("shed_tool_conf")
         if install_tool_dependencies and self.app.tool_dependency_dir is None:
-            raise exceptions.ConfigDoesNotAllowException("Tool dependency installation is disabled in your configuration files.")
+            raise exceptions.ConfigDoesNotAllowException(
+                "Tool dependency installation is disabled in your configuration files."
+            )
         if shed_tool_conf:
             # Get the tool_path setting.
             shed_config_dict = self.tpm.get_shed_tool_conf_dict(shed_tool_conf)
         else:
             shed_config_dict = self.app.toolbox.default_shed_tool_conf_dict()
-        shed_tool_conf = shed_config_dict['config_filename']
-        tool_path = shed_config_dict['tool_path']
-        tool_panel_section_id = self.app.toolbox.find_section_id(install_options.get('tool_panel_section_id', ''))
+        shed_tool_conf = shed_config_dict["config_filename"]
+        tool_path = shed_config_dict["tool_path"]
+        tool_panel_section_id = self.app.toolbox.find_section_id(install_options.get("tool_panel_section_id", ""))
         # Build the dictionary of information necessary for creating tool_shed_repository database records
         # for each repository being installed.
-        installation_dict = dict(install_repository_dependencies=install_repository_dependencies,
-                                 new_tool_panel_section_label=new_tool_panel_section_label,
-                                 tool_panel_section_mapping=tool_panel_section_mapping,
-                                 no_changes_checked=False,
-                                 repo_info_dicts=repo_info_dicts,
-                                 tool_panel_section_id=tool_panel_section_id,
-                                 tool_path=tool_path,
-                                 tool_shed_url=tool_shed_url)
+        installation_dict = dict(
+            install_repository_dependencies=install_repository_dependencies,
+            new_tool_panel_section_label=new_tool_panel_section_label,
+            tool_panel_section_mapping=tool_panel_section_mapping,
+            no_changes_checked=False,
+            repo_info_dicts=repo_info_dicts,
+            tool_panel_section_id=tool_panel_section_id,
+            tool_path=tool_path,
+            tool_shed_url=tool_shed_url,
+        )
         # Create the tool_shed_repository database records and gather additional information for repository installation.
-        created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
-            self.handle_tool_shed_repositories(installation_dict)
+        (
+            created_or_updated_tool_shed_repositories,
+            tool_panel_section_keys,
+            repo_info_dicts,
+            filtered_repo_info_dicts,
+        ) = self.handle_tool_shed_repositories(installation_dict)
         if created_or_updated_tool_shed_repositories:
             # Build the dictionary of information necessary for installing the repositories.
-            installation_dict = dict(created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
-                                     filtered_repo_info_dicts=filtered_repo_info_dicts,
-                                     has_repository_dependencies=has_repository_dependencies,
-                                     includes_tool_dependencies=includes_tool_dependencies,
-                                     includes_tools=includes_tools,
-                                     includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                                     install_repository_dependencies=install_repository_dependencies,
-                                     install_resolver_dependencies=install_resolver_dependencies,
-                                     install_tool_dependencies=install_tool_dependencies,
-                                     message='',
-                                     new_tool_panel_section_label=new_tool_panel_section_label,
-                                     shed_tool_conf=shed_tool_conf,
-                                     status='done',
-                                     tool_panel_section_id=tool_panel_section_id,
-                                     tool_panel_section_keys=tool_panel_section_keys,
-                                     tool_panel_section_mapping=tool_panel_section_mapping,
-                                     tool_path=tool_path,
-                                     tool_shed_url=tool_shed_url)
+            installation_dict = dict(
+                created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
+                filtered_repo_info_dicts=filtered_repo_info_dicts,
+                has_repository_dependencies=has_repository_dependencies,
+                includes_tool_dependencies=includes_tool_dependencies,
+                includes_tools=includes_tools,
+                includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+                install_repository_dependencies=install_repository_dependencies,
+                install_resolver_dependencies=install_resolver_dependencies,
+                install_tool_dependencies=install_tool_dependencies,
+                message="",
+                new_tool_panel_section_label=new_tool_panel_section_label,
+                shed_tool_conf=shed_tool_conf,
+                status="done",
+                tool_panel_section_id=tool_panel_section_id,
+                tool_panel_section_keys=tool_panel_section_keys,
+                tool_panel_section_mapping=tool_panel_section_mapping,
+                tool_path=tool_path,
+                tool_shed_url=tool_shed_url,
+            )
             # Prepare the repositories for installation.  Even though this
             # method receives a single combination of tool_shed_url, name,
             # owner and changeset_revision, there may be multiple repositories
             # for installation at this point because repository dependencies
             # may have added additional repositories for installation along
             # with the single specified repository.
-            encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
-                self.initiate_repository_installation(installation_dict)
+            encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = self.initiate_repository_installation(
+                installation_dict
+            )
             # Some repositories may have repository dependencies that are
             # required to be installed before the dependent repository, so
             # we'll order the list of tsr_ids to ensure all repositories
             # install in the required order.
-            tsr_ids = [self.app.security.encode_id(tool_shed_repository.id) for tool_shed_repository in tool_shed_repositories]
+            tsr_ids = [
+                self.app.security.encode_id(tool_shed_repository.id) for tool_shed_repository in tool_shed_repositories
+            ]
 
             decoded_kwd = dict(
                 shed_tool_conf=shed_tool_conf,
@@ -804,53 +966,59 @@ class InstallRepositoryManager:
             return self.install_repositories(tsr_ids, decoded_kwd, reinstalling=False, install_options=install_options)
 
     def install_repositories(self, tsr_ids, decoded_kwd, reinstalling, install_options=None):
-        shed_tool_conf = decoded_kwd.get('shed_tool_conf', '')
-        tool_path = decoded_kwd['tool_path']
-        tool_panel_section_keys = util.listify(decoded_kwd['tool_panel_section_keys'])
-        tool_panel_section_mapping = decoded_kwd.get('tool_panel_section_mapping', {})
-        repo_info_dicts = util.listify(decoded_kwd['repo_info_dicts'])
-        install_resolver_dependencies = decoded_kwd['install_resolver_dependencies']
-        install_tool_dependencies = decoded_kwd['install_tool_dependencies']
+        shed_tool_conf = decoded_kwd.get("shed_tool_conf", "")
+        tool_path = decoded_kwd["tool_path"]
+        tool_panel_section_keys = util.listify(decoded_kwd["tool_panel_section_keys"])
+        tool_panel_section_mapping = decoded_kwd.get("tool_panel_section_mapping", {})
+        repo_info_dicts = util.listify(decoded_kwd["repo_info_dicts"])
+        install_resolver_dependencies = decoded_kwd["install_resolver_dependencies"]
+        install_tool_dependencies = decoded_kwd["install_tool_dependencies"]
         filtered_repo_info_dicts = []
         filtered_tool_panel_section_keys = []
         repositories_for_installation = []
         # Some repositories may have repository dependencies that are required to be installed before the
         # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the
         # required order.
-        ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
-            self.order_components_for_installation(tsr_ids,
-                                                   repo_info_dicts,
-                                                   tool_panel_section_keys=tool_panel_section_keys)
+        (
+            ordered_tsr_ids,
+            ordered_repo_info_dicts,
+            ordered_tool_panel_section_keys,
+        ) = self.order_components_for_installation(
+            tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys
+        )
         for tsr_id in ordered_tsr_ids:
-            repository = self.install_model.context.query(self.install_model.ToolShedRepository) \
-                .get(self.app.security.decode_id(tsr_id))
-            if repository.status in [self.install_model.ToolShedRepository.installation_status.NEW,
-                                     self.install_model.ToolShedRepository.installation_status.UNINSTALLED]:
+            repository = self.install_model.context.query(self.install_model.ToolShedRepository).get(
+                self.app.security.decode_id(tsr_id)
+            )
+            if repository.status in [
+                self.install_model.ToolShedRepository.installation_status.NEW,
+                self.install_model.ToolShedRepository.installation_status.UNINSTALLED,
+            ]:
                 repositories_for_installation.append(repository)
-                repo_info_dict, tool_panel_section_key = \
-                    self.get_repository_components_for_installation(tsr_id,
-                                                                    ordered_tsr_ids,
-                                                                    ordered_repo_info_dicts,
-                                                                    ordered_tool_panel_section_keys)
+                repo_info_dict, tool_panel_section_key = self.get_repository_components_for_installation(
+                    tsr_id, ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys
+                )
                 filtered_repo_info_dicts.append(repo_info_dict)
                 filtered_tool_panel_section_keys.append(tool_panel_section_key)
 
         installed_tool_shed_repositories = []
         if repositories_for_installation:
-            for tool_shed_repository, repo_info_dict, tool_panel_section_key in zip(repositories_for_installation,
-                                                                                    filtered_repo_info_dicts,
-                                                                                    filtered_tool_panel_section_keys):
+            for tool_shed_repository, repo_info_dict, tool_panel_section_key in zip(
+                repositories_for_installation, filtered_repo_info_dicts, filtered_tool_panel_section_keys
+            ):
                 pre_install_state = tool_shed_repository.status
                 try:
-                    self.install_tool_shed_repository(tool_shed_repository,
-                                                      repo_info_dict=repo_info_dict,
-                                                      tool_panel_section_key=tool_panel_section_key,
-                                                      shed_tool_conf=shed_tool_conf,
-                                                      tool_path=tool_path,
-                                                      install_resolver_dependencies=install_resolver_dependencies,
-                                                      install_tool_dependencies=install_tool_dependencies,
-                                                      reinstalling=reinstalling,
-                                                      tool_panel_section_mapping=tool_panel_section_mapping)
+                    self.install_tool_shed_repository(
+                        tool_shed_repository,
+                        repo_info_dict=repo_info_dict,
+                        tool_panel_section_key=tool_panel_section_key,
+                        shed_tool_conf=shed_tool_conf,
+                        tool_path=tool_path,
+                        install_resolver_dependencies=install_resolver_dependencies,
+                        install_tool_dependencies=install_tool_dependencies,
+                        reinstalling=reinstalling,
+                        tool_panel_section_mapping=tool_panel_section_mapping,
+                    )
                 except Exception as e:
                     log.exception("Error installing repository '%s'", tool_shed_repository.name)
                     if pre_install_state != self.install_model.ToolShedRepository.states.OK:
@@ -871,38 +1039,62 @@ class InstallRepositoryManager:
             raise RepositoriesInstalledException()
         return installed_tool_shed_repositories
 
-    def install_tool_shed_repository(self, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path,
-                                     install_resolver_dependencies, install_tool_dependencies, reinstalling=False,
-                                     tool_panel_section_mapping=None, install_options=None):
+    def install_tool_shed_repository(
+        self,
+        tool_shed_repository,
+        repo_info_dict,
+        tool_panel_section_key,
+        shed_tool_conf,
+        tool_path,
+        install_resolver_dependencies,
+        install_tool_dependencies,
+        reinstalling=False,
+        tool_panel_section_mapping=None,
+        install_options=None,
+    ):
         tool_panel_section_mapping = tool_panel_section_mapping or {}
         self.app.install_model.context.flush()
         if tool_panel_section_key:
             _, tool_section = self.app.toolbox.get_section(tool_panel_section_key)
             if tool_section is None:
-                log.debug('Invalid tool_panel_section_key "%s" specified.  Tools will be loaded outside of sections in the tool panel.',
-                          str(tool_panel_section_key))
+                log.debug(
+                    'Invalid tool_panel_section_key "%s" specified.  Tools will be loaded outside of sections in the tool panel.',
+                    str(tool_panel_section_key),
+                )
         else:
             tool_section = None
         if isinstance(repo_info_dict, str):
             repo_info_dict = encoding_util.tool_shed_decode(repo_info_dict)
         repo_info_tuple = repo_info_dict[tool_shed_repository.name]
-        description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
+        (
+            description,
+            repository_clone_url,
+            changeset_revision,
+            ctx_rev,
+            repository_owner,
+            repository_dependencies,
+            tool_dependencies,
+        ) = repo_info_tuple
         if changeset_revision != tool_shed_repository.changeset_revision:
             # This is an update
-            tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_repository.tool_shed)
-            return self.update_tool_shed_repository(tool_shed_repository,
-                                                    tool_shed_url,
-                                                    ctx_rev,
-                                                    changeset_revision,
-                                                    install_options=install_options)
+            tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
+                self.app, tool_shed_repository.tool_shed
+            )
+            return self.update_tool_shed_repository(
+                tool_shed_repository, tool_shed_url, ctx_rev, changeset_revision, install_options=install_options
+            )
         # Clone the repository to the configured location.
-        self.update_tool_shed_repository_status(tool_shed_repository,
-                                                self.install_model.ToolShedRepository.installation_status.CLONING)
-        relative_clone_dir = repository_util.generate_tool_shed_repository_install_dir(repository_clone_url,
-                                                                                       tool_shed_repository.installed_changeset_revision)
+        self.update_tool_shed_repository_status(
+            tool_shed_repository, self.install_model.ToolShedRepository.installation_status.CLONING
+        )
+        relative_clone_dir = repository_util.generate_tool_shed_repository_install_dir(
+            repository_clone_url, tool_shed_repository.installed_changeset_revision
+        )
         relative_install_dir = os.path.join(relative_clone_dir, tool_shed_repository.name)
         install_dir = os.path.abspath(os.path.join(tool_path, relative_install_dir))
-        log.info("Cloning repository '%s' at %s:%s", repository_clone_url, ctx_rev, tool_shed_repository.changeset_revision)
+        log.info(
+            "Cloning repository '%s' at %s:%s", repository_clone_url, ctx_rev, tool_shed_repository.changeset_revision
+        )
         if os.path.exists(install_dir):
             # May exist from a previous failed install attempt, just try updating instead of cloning.
             hg_util.pull_repository(install_dir, repository_clone_url, ctx_rev)
@@ -914,67 +1106,92 @@ class InstallRepositoryManager:
         if reinstalling:
             # Since we're reinstalling the repository we need to find the latest changeset revision to
             # which it can be updated.
-            changeset_revision_dict = self.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(tool_shed_repository)
-            current_changeset_revision = changeset_revision_dict.get('changeset_revision', None)
-            current_ctx_rev = changeset_revision_dict.get('ctx_rev', None)
+            changeset_revision_dict = self.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(
+                tool_shed_repository
+            )
+            current_changeset_revision = changeset_revision_dict.get("changeset_revision", None)
+            current_ctx_rev = changeset_revision_dict.get("ctx_rev", None)
             if current_ctx_rev != ctx_rev:
                 repo_path = os.path.abspath(install_dir)
                 hg_util.pull_repository(repo_path, repository_clone_url, current_changeset_revision)
                 hg_util.update_repository(repo_path, ctx_rev=current_ctx_rev)
-        self.__handle_repository_contents(tool_shed_repository=tool_shed_repository,
-                                          tool_path=tool_path,
-                                          repository_clone_url=repository_clone_url,
-                                          relative_install_dir=relative_install_dir,
-                                          tool_shed=tool_shed_repository.tool_shed,
-                                          tool_section=tool_section,
-                                          shed_tool_conf=shed_tool_conf,
-                                          reinstalling=reinstalling,
-                                          tool_panel_section_mapping=tool_panel_section_mapping)
+        self.__handle_repository_contents(
+            tool_shed_repository=tool_shed_repository,
+            tool_path=tool_path,
+            repository_clone_url=repository_clone_url,
+            relative_install_dir=relative_install_dir,
+            tool_shed=tool_shed_repository.tool_shed,
+            tool_section=tool_section,
+            shed_tool_conf=shed_tool_conf,
+            reinstalling=reinstalling,
+            tool_panel_section_mapping=tool_panel_section_mapping,
+        )
         metadata = tool_shed_repository.metadata_
-        if 'tools' in metadata and install_resolver_dependencies:
-            self.update_tool_shed_repository_status(tool_shed_repository,
-                                                    self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
-            new_tools = [self.app.toolbox._tools_by_id.get(tool_d['guid'], None) for tool_d in metadata['tools']]
+        if "tools" in metadata and install_resolver_dependencies:
+            self.update_tool_shed_repository_status(
+                tool_shed_repository,
+                self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
+            )
+            new_tools = [self.app.toolbox._tools_by_id.get(tool_d["guid"], None) for tool_d in metadata["tools"]]
             new_requirements = {tool.requirements.packages for tool in new_tools if tool}
             [self._view.install_dependencies(r) for r in new_requirements]
             dependency_manager = self.app.toolbox.dependency_manager
             if dependency_manager.cached:
                 [dependency_manager.build_cache(r) for r in new_requirements]
 
-        if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:
+        if install_tool_dependencies and tool_shed_repository.tool_dependencies and "tool_dependencies" in metadata:
             work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-itsr")
             # Install tool dependencies.
-            self.update_tool_shed_repository_status(tool_shed_repository,
-                                                    self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
+            self.update_tool_shed_repository_status(
+                tool_shed_repository,
+                self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
+            )
             # Get the tool_dependencies.xml file from the repository.
-            tool_dependencies_config = hg_util.get_config_from_disk('tool_dependencies.xml', install_dir)
+            tool_dependencies_config = hg_util.get_config_from_disk("tool_dependencies.xml", install_dir)
             itdm = InstallToolDependencyManager(self.app)
-            itdm.install_specified_tool_dependencies(tool_shed_repository=tool_shed_repository,
-                                                     tool_dependencies_config=tool_dependencies_config,
-                                                     tool_dependencies=tool_shed_repository.tool_dependencies)
+            itdm.install_specified_tool_dependencies(
+                tool_shed_repository=tool_shed_repository,
+                tool_dependencies_config=tool_dependencies_config,
+                tool_dependencies=tool_shed_repository.tool_dependencies,
+            )
             basic_util.remove_dir(work_dir)
-        self.update_tool_shed_repository_status(tool_shed_repository,
-                                                self.install_model.ToolShedRepository.installation_status.INSTALLED)
+        self.update_tool_shed_repository_status(
+            tool_shed_repository, self.install_model.ToolShedRepository.installation_status.INSTALLED
+        )
 
-    def update_tool_shed_repository(self, repository, tool_shed_url, latest_ctx_rev, latest_changeset_revision,
-                                    install_new_dependencies=True, install_options=None):
+    def update_tool_shed_repository(
+        self,
+        repository,
+        tool_shed_url,
+        latest_ctx_rev,
+        latest_changeset_revision,
+        install_new_dependencies=True,
+        install_options=None,
+    ):
         install_options = install_options or {}
         original_metadata_dict = repository.metadata_
-        original_repository_dependencies_dict = original_metadata_dict.get('repository_dependencies', {})
-        original_repository_dependencies = original_repository_dependencies_dict.get('repository_dependencies', [])
-        original_tool_dependencies_dict = original_metadata_dict.get('tool_dependencies', {})
-        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(self.app, repository)
+        original_repository_dependencies_dict = original_metadata_dict.get("repository_dependencies", {})
+        original_repository_dependencies = original_repository_dependencies_dict.get("repository_dependencies", [])
+        original_tool_dependencies_dict = original_metadata_dict.get("tool_dependencies", {})
+        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
+            self.app, repository
+        )
         if tool_path:
             repo_files_dir = os.path.abspath(os.path.join(tool_path, relative_install_dir, repository.name))
         else:
             repo_files_dir = os.path.abspath(os.path.join(relative_install_dir, repository.name))
-        repository_clone_url = os.path.join(tool_shed_url, 'repos', repository.owner, repository.name)
+        repository_clone_url = os.path.join(tool_shed_url, "repos", repository.owner, repository.name)
         # Set a status, even though we're probably not cloning.
         self.update_tool_shed_repository_status(repository, status=repository.installation_status.CLONING)
         log.info("Updating repository '%s' to %s:%s", repository.name, latest_ctx_rev, latest_changeset_revision)
         if not os.path.exists(repo_files_dir):
-            log.debug("Repository directory '%s' does not exist, cloning repository instead of updating repository", repo_files_dir)
-            hg_util.clone_repository(repository_clone_url=repository_clone_url, repository_file_dir=repo_files_dir, ctx_rev=latest_ctx_rev)
+            log.debug(
+                "Repository directory '%s' does not exist, cloning repository instead of updating repository",
+                repo_files_dir,
+            )
+            hg_util.clone_repository(
+                repository_clone_url=repository_clone_url, repository_file_dir=repo_files_dir, ctx_rev=latest_ctx_rev
+            )
         hg_util.pull_repository(repo_files_dir, repository_clone_url, latest_ctx_rev)
         hg_util.update_repository(repo_files_dir, latest_ctx_rev)
         # Remove old Data Manager entries
@@ -983,46 +1200,52 @@ class InstallRepositoryManager:
             dmh.remove_from_data_manager(repository)
         # Update the repository metadata.
         tpm = tool_panel_manager.ToolPanelManager(self.app)
-        irmm = InstalledRepositoryMetadataManager(app=self.app,
-                                                  tpm=tpm,
-                                                  repository=repository,
-                                                  changeset_revision=latest_changeset_revision,
-                                                  repository_clone_url=repository_clone_url,
-                                                  shed_config_dict=repository.get_shed_config_dict(self.app),
-                                                  relative_install_dir=relative_install_dir,
-                                                  repository_files_dir=None,
-                                                  resetting_all_metadata_on_repository=False,
-                                                  updating_installed_repository=True,
-                                                  persist=True)
+        irmm = InstalledRepositoryMetadataManager(
+            app=self.app,
+            tpm=tpm,
+            repository=repository,
+            changeset_revision=latest_changeset_revision,
+            repository_clone_url=repository_clone_url,
+            shed_config_dict=repository.get_shed_config_dict(self.app),
+            relative_install_dir=relative_install_dir,
+            repository_files_dir=None,
+            resetting_all_metadata_on_repository=False,
+            updating_installed_repository=True,
+            persist=True,
+        )
         irmm.generate_metadata_for_changeset_revision()
         irmm_metadata_dict = irmm.get_metadata_dict()
         self.update_tool_shed_repository_status(repository, status=repository.installation_status.INSTALLED)
-        if 'tools' in irmm_metadata_dict:
-            tool_panel_dict = irmm_metadata_dict.get('tool_panel_section', None)
+        if "tools" in irmm_metadata_dict:
+            tool_panel_dict = irmm_metadata_dict.get("tool_panel_section", None)
             if tool_panel_dict is None:
                 tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries(repository)
             repository_tools_tups = irmm.get_repository_tools_tups()
-            tpm.add_to_tool_panel(repository_name=str(repository.name),
-                                  repository_clone_url=repository_clone_url,
-                                  changeset_revision=str(repository.installed_changeset_revision),
-                                  repository_tools_tups=repository_tools_tups,
-                                  owner=str(repository.owner),
-                                  shed_tool_conf=shed_tool_conf,
-                                  tool_panel_dict=tool_panel_dict,
-                                  new_install=False)
+            tpm.add_to_tool_panel(
+                repository_name=str(repository.name),
+                repository_clone_url=repository_clone_url,
+                changeset_revision=str(repository.installed_changeset_revision),
+                repository_tools_tups=repository_tools_tups,
+                owner=str(repository.owner),
+                shed_tool_conf=shed_tool_conf,
+                tool_panel_dict=tool_panel_dict,
+                new_install=False,
+            )
             # Add new Data Manager entries
-            if 'data_manager' in irmm_metadata_dict:
+            if "data_manager" in irmm_metadata_dict:
                 dmh = data_manager.DataManagerHandler(self.app)
-                dmh.install_data_managers(self.app.config.shed_data_manager_config_file,
-                                          irmm_metadata_dict,
-                                          repository.get_shed_config_dict(self.app),
-                                          os.path.join(relative_install_dir, repository.name),
-                                          repository,
-                                          repository_tools_tups)
-        if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict:
-            new_repository_dependencies_dict = irmm_metadata_dict.get('repository_dependencies', {})
-            new_repository_dependencies = new_repository_dependencies_dict.get('repository_dependencies', [])
-            new_tool_dependencies_dict = irmm_metadata_dict.get('tool_dependencies', {})
+                dmh.install_data_managers(
+                    self.app.config.shed_data_manager_config_file,
+                    irmm_metadata_dict,
+                    repository.get_shed_config_dict(self.app),
+                    os.path.join(relative_install_dir, repository.name),
+                    repository,
+                    repository_tools_tups,
+                )
+        if "repository_dependencies" in irmm_metadata_dict or "tool_dependencies" in irmm_metadata_dict:
+            new_repository_dependencies_dict = irmm_metadata_dict.get("repository_dependencies", {})
+            new_repository_dependencies = new_repository_dependencies_dict.get("repository_dependencies", [])
+            new_tool_dependencies_dict = irmm_metadata_dict.get("tool_dependencies", {})
             if new_repository_dependencies:
                 # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']]
                 if new_repository_dependencies == original_repository_dependencies:
@@ -1031,48 +1254,67 @@ class InstallRepositoryManager:
                         # TODO: Repository dependencies that are not installed should be displayed to the user,
                         # giving them the option to install them or not. This is the same behavior as when initially
                         # installing and when re-installing.
-                        new_tool_shed, new_name, new_owner, new_changeset_revision, new_pir, new_oicct = \
-                            common_util.parse_repository_dependency_tuple(new_repository_tup)
+                        (
+                            new_tool_shed,
+                            new_name,
+                            new_owner,
+                            new_changeset_revision,
+                            new_pir,
+                            new_oicct,
+                        ) = common_util.parse_repository_dependency_tuple(new_repository_tup)
                         # Mock up a repo_info_tupe that has the information needed to see if the repository dependency
                         # was previously installed.
-                        repo_info_tuple = ('', new_tool_shed, new_changeset_revision, '', new_owner, [], [])
+                        repo_info_tuple = ("", new_tool_shed, new_changeset_revision, "", new_owner, [], [])
                         # Since the value of new_changeset_revision came from a repository dependency
                         # definition, it may occur earlier in the Tool Shed's repository changelog than
                         # the Galaxy tool_shed_repository.installed_changeset_revision record value, so
                         # we set from_tip to True to make sure we get the entire set of changeset revisions
                         # from the Tool Shed.
-                        new_repository_db_record, installed_changeset_revision = \
-                            repository_util.repository_was_previously_installed(self.app,
-                                                                                tool_shed_url,
-                                                                                new_name,
-                                                                                repo_info_tuple,
-                                                                                from_tip=True)
-                        if ((new_repository_db_record and new_repository_db_record.status in [
+                        (
+                            new_repository_db_record,
+                            installed_changeset_revision,
+                        ) = repository_util.repository_was_previously_installed(
+                            self.app, tool_shed_url, new_name, repo_info_tuple, from_tip=True
+                        )
+                        if (
+                            new_repository_db_record
+                            and new_repository_db_record.status
+                            in [
                                 self.install_model.ToolShedRepository.installation_status.ERROR,
                                 self.install_model.ToolShedRepository.installation_status.NEW,
-                                self.install_model.ToolShedRepository.installation_status.UNINSTALLED]) or not new_repository_db_record):
-                            log.debug('Update to %s contains new repository dependency %s/%s', repository.name,
-                                      new_owner, new_name)
+                                self.install_model.ToolShedRepository.installation_status.UNINSTALLED,
+                            ]
+                        ) or not new_repository_db_record:
+                            log.debug(
+                                "Update to %s contains new repository dependency %s/%s",
+                                repository.name,
+                                new_owner,
+                                new_name,
+                            )
                             if not install_new_dependencies:
-                                return ('repository', irmm_metadata_dict)
+                                return ("repository", irmm_metadata_dict)
                             else:
-                                self.install(tool_shed_url, new_name, new_owner, new_changeset_revision, install_options)
+                                self.install(
+                                    tool_shed_url, new_name, new_owner, new_changeset_revision, install_options
+                                )
             # Updates received did not include any newly defined repository dependencies but did include
             # newly defined tool dependencies.  If the newly defined tool dependencies are not the same
             # as the originally defined tool dependencies, we need to install them.
             if not install_new_dependencies:
                 for new_key, new_val in new_tool_dependencies_dict.items():
                     if new_key not in original_tool_dependencies_dict:
-                        return ('tool', irmm_metadata_dict)
+                        return ("tool", irmm_metadata_dict)
                     original_val = original_tool_dependencies_dict[new_key]
                     if new_val != original_val:
-                        return ('tool', irmm_metadata_dict)
+                        return ("tool", irmm_metadata_dict)
         # Updates received did not include any newly defined repository dependencies or newly defined
         # tool dependencies that need to be installed.
-        repository = self.app.update_repository_manager.update_repository_record(repository=repository,
-                                                                                 updated_metadata_dict=irmm_metadata_dict,
-                                                                                 updated_changeset_revision=latest_changeset_revision,
-                                                                                 updated_ctx_rev=latest_ctx_rev)
+        repository = self.app.update_repository_manager.update_repository_record(
+            repository=repository,
+            updated_metadata_dict=irmm_metadata_dict,
+            updated_changeset_revision=latest_changeset_revision,
+            updated_ctx_rev=latest_ctx_rev,
+        )
         return (None, None)
 
     def order_components_for_installation(self, tsr_ids, repo_info_dicts, tool_panel_section_keys):
@@ -1092,13 +1334,14 @@ class InstallRepositoryManager:
         # Create a dictionary whose keys are the received tsr_ids and whose values are a list of
         # tsr_ids, each of which is contained in the received list of tsr_ids and whose associated
         # repository must be installed prior to the repository associated with the tsr_id key.
-        prior_install_required_dict = repository_util.get_prior_import_or_install_required_dict(self.app,
-                                                                                                tsr_ids,
-                                                                                                repo_info_dicts)
+        prior_install_required_dict = repository_util.get_prior_import_or_install_required_dict(
+            self.app, tsr_ids, repo_info_dicts
+        )
         processed_tsr_ids = []
         while len(processed_tsr_ids) != len(prior_install_required_dict.keys()):
-            tsr_id = suc.get_next_prior_import_or_install_required_dict_entry(prior_install_required_dict,
-                                                                              processed_tsr_ids)
+            tsr_id = suc.get_next_prior_import_or_install_required_dict_entry(
+                prior_install_required_dict, processed_tsr_ids
+            )
             processed_tsr_ids.append(tsr_id)
             # Create the ordered_tsr_ids, the ordered_repo_info_dicts and the ordered_tool_panel_section_keys lists.
             if tsr_id not in ordered_tsr_ids:
@@ -1106,19 +1349,21 @@ class InstallRepositoryManager:
                 for prior_install_required_id in prior_install_required_ids:
                     if prior_install_required_id not in ordered_tsr_ids:
                         # Install the associated repository dependency first.
-                        prior_repo_info_dict, prior_tool_panel_section_key = \
-                            self.get_repository_components_for_installation(prior_install_required_id,
-                                                                            tsr_ids,
-                                                                            repo_info_dicts,
-                                                                            tool_panel_section_keys=tool_panel_section_keys)
+                        (
+                            prior_repo_info_dict,
+                            prior_tool_panel_section_key,
+                        ) = self.get_repository_components_for_installation(
+                            prior_install_required_id,
+                            tsr_ids,
+                            repo_info_dicts,
+                            tool_panel_section_keys=tool_panel_section_keys,
+                        )
                         ordered_tsr_ids.append(prior_install_required_id)
                         ordered_repo_info_dicts.append(prior_repo_info_dict)
                         ordered_tool_panel_section_keys.append(prior_tool_panel_section_key)
-                repo_info_dict, tool_panel_section_key = \
-                    self.get_repository_components_for_installation(tsr_id,
-                                                                    tsr_ids,
-                                                                    repo_info_dicts,
-                                                                    tool_panel_section_keys=tool_panel_section_keys)
+                repo_info_dict, tool_panel_section_key = self.get_repository_components_for_installation(
+                    tsr_id, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys
+                )
                 if tsr_id not in ordered_tsr_ids:
                     ordered_tsr_ids.append(tsr_id)
                     ordered_repo_info_dicts.append(repo_info_dict)
@@ -1136,6 +1381,5 @@ class InstallRepositoryManager:
 
 
 class RepositoriesInstalledException(exceptions.RequestParameterInvalidException):
-
     def __init__(self):
-        super().__init__('All repositories that you are attempting to install have been previously installed.')
+        super().__init__("All repositories that you are attempting to install have been previously installed.")
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index d3e594d325e..88fe03c8c3b 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -6,14 +6,22 @@ import logging
 import os
 import shutil
 
-from sqlalchemy import and_, false, true
+from sqlalchemy import (
+    and_,
+    false,
+    true,
+)
 
 from galaxy import util
 from galaxy.tool_shed.galaxy_install.datatypes import custom_datatype_manager
-from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
+from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import (
+    InstalledRepositoryMetadataManager,
+)
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
-from galaxy.tool_shed.galaxy_install.tools import data_manager
-from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
+from galaxy.tool_shed.galaxy_install.tools import (
+    data_manager,
+    tool_panel_manager,
+)
 from galaxy.tool_shed.util import repository_util
 from galaxy.tool_shed.util import shed_util_common as suc
 from galaxy.tool_shed.util import tool_dependency_util
@@ -25,7 +33,6 @@ log = logging.getLogger(__name__)
 
 
 class InstalledRepositoryManager:
-
     def __init__(self, app):
         """
         Among other things, keep in in-memory sets of tuples defining installed repositories and tool dependencies along with
@@ -69,7 +76,7 @@ class InstalledRepositoryManager:
                 if error_message:
                     log.error(error_message)
                 else:
-                    tool_path = tree.getroot().get('tool_path')
+                    tool_path = tree.getroot().get("tool_path")
                     if tool_path:
                         tool_paths.append(tool_path)
             self._tool_paths = tool_paths
@@ -77,39 +84,47 @@ class InstalledRepositoryManager:
 
     def activate_repository(self, repository):
         """Activate an installed tool shed repository that has been marked as deactivated."""
-        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(self.app, repository)
+        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
+            self.app, repository
+        )
         repository.deleted = False
         repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED
         if repository.includes_tools_for_display_in_tool_panel:
             repository_clone_url = common_util.generate_clone_url_for_installed_repository(self.app, repository)
             tpm = tool_panel_manager.ToolPanelManager(self.app)
-            irmm = InstalledRepositoryMetadataManager(app=self.app,
-                                                      tpm=tpm,
-                                                      repository=repository,
-                                                      changeset_revision=repository.changeset_revision,
-                                                      metadata_dict=repository.metadata_)
+            irmm = InstalledRepositoryMetadataManager(
+                app=self.app,
+                tpm=tpm,
+                repository=repository,
+                changeset_revision=repository.changeset_revision,
+                metadata_dict=repository.metadata_,
+            )
             repository_tools_tups = irmm.get_repository_tools_tups()
             # Reload tools into the appropriate tool panel section.
-            tool_panel_dict = repository.metadata_['tool_panel_section']
-            tpm.add_to_tool_panel(repository.name,
-                                  repository_clone_url,
-                                  repository.installed_changeset_revision,
-                                  repository_tools_tups,
-                                  repository.owner,
-                                  shed_tool_conf,
-                                  tool_panel_dict,
-                                  new_install=False)
+            tool_panel_dict = repository.metadata_["tool_panel_section"]
+            tpm.add_to_tool_panel(
+                repository.name,
+                repository_clone_url,
+                repository.installed_changeset_revision,
+                repository_tools_tups,
+                repository.owner,
+                shed_tool_conf,
+                tool_panel_dict,
+                new_install=False,
+            )
             if repository.includes_data_managers:
                 tp, data_manager_relative_install_dir = repository.get_tool_relative_path(self.app)
                 # Hack to add repository.name here, which is actually the root of the installed repository
                 data_manager_relative_install_dir = os.path.join(data_manager_relative_install_dir, repository.name)
                 dmh = data_manager.DataManagerHandler(self.app)
-                dmh.install_data_managers(self.app.config.shed_data_manager_config_file,
-                                          repository.metadata_,
-                                          repository.get_shed_config_dict(self.app),
-                                          data_manager_relative_install_dir,
-                                          repository,
-                                          repository_tools_tups)
+                dmh.install_data_managers(
+                    self.app.config.shed_data_manager_config_file,
+                    repository.metadata_,
+                    repository.get_shed_config_dict(self.app),
+                    data_manager_relative_install_dir,
+                    repository,
+                    repository_tools_tups,
+                )
         self.install_model.session.add(repository)
         self.install_model.session.flush()
         if repository.includes_datatypes:
@@ -119,14 +134,14 @@ class InstalledRepositoryManager:
                 repository_install_dir = os.path.abspath(relative_install_dir)
             # Activate proprietary datatypes.
             cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
-            installed_repository_dict = cdl.load_installed_datatypes(repository,
-                                                                     repository_install_dir,
-                                                                     deactivate=False)
+            installed_repository_dict = cdl.load_installed_datatypes(
+                repository, repository_install_dir, deactivate=False
+            )
             if installed_repository_dict:
-                converter_path = installed_repository_dict.get('converter_path')
+                converter_path = installed_repository_dict.get("converter_path")
                 if converter_path is not None:
                     cdl.load_installed_datatype_converters(installed_repository_dict, deactivate=False)
-                display_path = installed_repository_dict.get('display_path')
+                display_path = installed_repository_dict.get("display_path")
                 if display_path is not None:
                     cdl.load_installed_display_applications(installed_repository_dict, deactivate=False)
 
@@ -140,13 +155,19 @@ class InstalledRepositoryManager:
         tool_shed, name, owner, installed_changeset_revision = repository_tup
         # Get the list of repository dependencies for this repository.
         status = self.install_model.ToolShedRepository.installation_status.INSTALLED
-        repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(repository, status=status)
+        repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(
+            repository, status=status
+        )
         # Add an entry to self.installed_repository_dependencies_of_installed_repositories.
         if repository_tup not in self.installed_repository_dependencies_of_installed_repositories:
-            debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            debug_msg = (
+                f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            )
             debug_msg += "to installed_repository_dependencies_of_installed_repositories."
             log.debug(debug_msg)
-            self.installed_repository_dependencies_of_installed_repositories[repository_tup] = repository_dependency_tups
+            self.installed_repository_dependencies_of_installed_repositories[
+                repository_tup
+            ] = repository_dependency_tups
         # Use the repository_dependency_tups to add entries to the reverse dictionary
         # self.installed_dependent_repositories_of_installed_repositories.
         for required_repository_tup in repository_dependency_tups:
@@ -154,26 +175,38 @@ class InstalledRepositoryManager:
             debug_msg += "to all dependent repositories in installed_dependent_repositories_of_installed_repositories."
             log.debug(debug_msg)
             if required_repository_tup in self.installed_dependent_repositories_of_installed_repositories:
-                self.installed_dependent_repositories_of_installed_repositories[required_repository_tup].append(repository_tup)
+                self.installed_dependent_repositories_of_installed_repositories[required_repository_tup].append(
+                    repository_tup
+                )
             else:
-                self.installed_dependent_repositories_of_installed_repositories[required_repository_tup] = [repository_tup]
+                self.installed_dependent_repositories_of_installed_repositories[required_repository_tup] = [
+                    repository_tup
+                ]
 
     def add_entry_to_repository_dependencies_of_installed_repositories(self, repository):
         """Add an entry to self.repository_dependencies_of_installed_repositories."""
         repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
         if repository_tup not in self.repository_dependencies_of_installed_repositories:
             tool_shed, name, owner, installed_changeset_revision = repository_tup
-            debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            debug_msg = (
+                f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            )
             debug_msg += "to repository_dependencies_of_installed_repositories."
             log.debug(debug_msg)
-            repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(repository, status=None)
+            repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(
+                repository, status=None
+            )
             self.repository_dependencies_of_installed_repositories[repository_tup] = repository_dependency_tups
 
     def get_containing_repository_for_tool_dependency(self, tool_dependency_tup):
         tool_shed_repository_id, name, version, type = tool_dependency_tup
-        return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).get(tool_shed_repository_id)
+        return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).get(
+            tool_shed_repository_id
+        )
 
-    def get_dependencies_for_repository(self, tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=False):
+    def get_dependencies_for_repository(
+        self, tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=False
+    ):
         """
         Return dictionaries containing the sets of installed and missing tool dependencies and repository
         dependencies associated with the repository defined by the received repo_info_dict.
@@ -186,54 +219,74 @@ class InstalledRepositoryManager:
         missing_td = {}
         name = next(iter(repo_info_dict))
         repo_info_tuple = repo_info_dict[name]
-        description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
-            repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+        (
+            description,
+            repository_clone_url,
+            changeset_revision,
+            ctx_rev,
+            repository_owner,
+            repository_dependencies,
+            tool_dependencies,
+        ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
         if tool_dependencies:
             if not includes_tool_dependencies:
                 includes_tool_dependencies = True
             # Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies.
             # We don't add to installed_td and missing_td here because at this point they are empty.
-            installed_td, missing_td = self.get_installed_and_missing_tool_dependencies_for_repository(tool_dependencies)
+            installed_td, missing_td = self.get_installed_and_missing_tool_dependencies_for_repository(
+                tool_dependencies
+            )
         # In cases where a repository dependency is required only for compiling a dependent repository's
         # tool dependency, the value of repository_dependencies will be an empty dictionary here.
         if repository_dependencies:
             # We have a repository with one or more defined repository dependencies.
             if not repository:
-                repository = repository_util.get_repository_for_dependency_relationship(self.app,
-                                                                                        tool_shed_url,
-                                                                                        name,
-                                                                                        repository_owner,
-                                                                                        changeset_revision)
+                repository = repository_util.get_repository_for_dependency_relationship(
+                    self.app, tool_shed_url, name, repository_owner, changeset_revision
+                )
             if not updating and repository and repository.metadata_:
                 installed_rd, missing_rd = self.get_installed_and_missing_repository_dependencies(repository)
             else:
-                installed_rd, missing_rd = \
-                    self.get_installed_and_missing_repository_dependencies_for_new_or_updated_install(repo_info_tuple)
+                (
+                    installed_rd,
+                    missing_rd,
+                ) = self.get_installed_and_missing_repository_dependencies_for_new_or_updated_install(repo_info_tuple)
             # Discover all repository dependencies and retrieve information for installing them.
             all_repo_info_dict = rdim.get_required_repo_info_dicts(tool_shed_url, util.listify(repo_info_dict))
-            has_repository_dependencies = all_repo_info_dict.get('has_repository_dependencies', False)
-            has_repository_dependencies_only_if_compiling_contained_td = \
-                all_repo_info_dict.get('has_repository_dependencies_only_if_compiling_contained_td', False)
-            includes_tools_for_display_in_tool_panel = all_repo_info_dict.get('includes_tools_for_display_in_tool_panel', False)
-            includes_tool_dependencies = all_repo_info_dict.get('includes_tool_dependencies', False)
-            includes_tools = all_repo_info_dict.get('includes_tools', False)
-            required_repo_info_dicts = all_repo_info_dict.get('all_repo_info_dicts', [])
+            has_repository_dependencies = all_repo_info_dict.get("has_repository_dependencies", False)
+            has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get(
+                "has_repository_dependencies_only_if_compiling_contained_td", False
+            )
+            includes_tools_for_display_in_tool_panel = all_repo_info_dict.get(
+                "includes_tools_for_display_in_tool_panel", False
+            )
+            includes_tool_dependencies = all_repo_info_dict.get("includes_tool_dependencies", False)
+            includes_tools = all_repo_info_dict.get("includes_tools", False)
+            required_repo_info_dicts = all_repo_info_dict.get("all_repo_info_dicts", [])
             # Display tool dependencies defined for each of the repository dependencies.
             if required_repo_info_dicts:
                 required_tool_dependencies = {}
                 for rid in required_repo_info_dicts:
                     for repo_info_tuple in rid.values():
-                        description, repository_clone_url, changeset_revision, ctx_rev, \
-                            repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
-                            repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+                        (
+                            description,
+                            repository_clone_url,
+                            changeset_revision,
+                            ctx_rev,
+                            repository_owner,
+                            rid_repository_dependencies,
+                            rid_tool_dependencies,
+                        ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
                         if rid_tool_dependencies:
                             for td_key, td_dict in rid_tool_dependencies.items():
                                 if td_key not in required_tool_dependencies:
                                     required_tool_dependencies[td_key] = td_dict
                 if required_tool_dependencies:
                     # Discover and categorize all tool dependencies defined for this repository's repository dependencies.
-                    required_installed_td, required_missing_td = \
-                        self.get_installed_and_missing_tool_dependencies_for_repository(required_tool_dependencies)
+                    (
+                        required_installed_td,
+                        required_missing_td,
+                    ) = self.get_installed_and_missing_tool_dependencies_for_repository(required_tool_dependencies)
                     if required_installed_td:
                         if not includes_tool_dependencies:
                             includes_tool_dependencies = True
@@ -249,26 +302,30 @@ class InstalledRepositoryManager:
         else:
             # We have a single repository with (possibly) no defined repository dependencies.
             all_repo_info_dict = rdim.get_required_repo_info_dicts(tool_shed_url, util.listify(repo_info_dict))
-            has_repository_dependencies = all_repo_info_dict.get('has_repository_dependencies', False)
-            has_repository_dependencies_only_if_compiling_contained_td = \
-                all_repo_info_dict.get('has_repository_dependencies_only_if_compiling_contained_td', False)
-            includes_tools_for_display_in_tool_panel = all_repo_info_dict.get('includes_tools_for_display_in_tool_panel', False)
-            includes_tool_dependencies = all_repo_info_dict.get('includes_tool_dependencies', False)
-            includes_tools = all_repo_info_dict.get('includes_tools', False)
-            required_repo_info_dicts = all_repo_info_dict.get('all_repo_info_dicts', [])
-        dependencies_for_repository_dict = \
-            dict(changeset_revision=changeset_revision,
-                 has_repository_dependencies=has_repository_dependencies,
-                 has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
-                 includes_tool_dependencies=includes_tool_dependencies,
-                 includes_tools=includes_tools,
-                 includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                 installed_repository_dependencies=installed_rd,
-                 installed_tool_dependencies=installed_td,
-                 missing_repository_dependencies=missing_rd,
-                 missing_tool_dependencies=missing_td,
-                 name=name,
-                 repository_owner=repository_owner)
+            has_repository_dependencies = all_repo_info_dict.get("has_repository_dependencies", False)
+            has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get(
+                "has_repository_dependencies_only_if_compiling_contained_td", False
+            )
+            includes_tools_for_display_in_tool_panel = all_repo_info_dict.get(
+                "includes_tools_for_display_in_tool_panel", False
+            )
+            includes_tool_dependencies = all_repo_info_dict.get("includes_tool_dependencies", False)
+            includes_tools = all_repo_info_dict.get("includes_tools", False)
+            required_repo_info_dicts = all_repo_info_dict.get("all_repo_info_dicts", [])
+        dependencies_for_repository_dict = dict(
+            changeset_revision=changeset_revision,
+            has_repository_dependencies=has_repository_dependencies,
+            has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
+            includes_tool_dependencies=includes_tool_dependencies,
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            installed_repository_dependencies=installed_rd,
+            installed_tool_dependencies=installed_td,
+            missing_repository_dependencies=missing_rd,
+            missing_tool_dependencies=missing_td,
+            name=name,
+            repository_owner=repository_owner,
+        )
         return dependencies_for_repository_dict
 
     def get_installed_and_missing_repository_dependencies(self, repository):
@@ -292,14 +349,16 @@ class InstalledRepositoryManager:
             for tsr in repository.repository_dependencies:
                 prior_installation_required = self.set_prior_installation_required(repository, tsr)
                 only_if_compiling_contained_td = self.set_only_if_compiling_contained_td(repository, tsr)
-                rd_tup = [tsr.tool_shed,
-                          tsr.name,
-                          tsr.owner,
-                          tsr.changeset_revision,
-                          prior_installation_required,
-                          only_if_compiling_contained_td,
-                          tsr.id,
-                          tsr.status]
+                rd_tup = [
+                    tsr.tool_shed,
+                    tsr.name,
+                    tsr.owner,
+                    tsr.changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                    tsr.id,
+                    tsr.status,
+                ]
                 if tsr.status == self.app.install_model.ToolShedRepository.installation_status.INSTALLED:
                     installed_rd_tups.append(rd_tup)
                 else:
@@ -315,24 +374,26 @@ class InstalledRepositoryManager:
                         missing_rd_tups.append(rd_tup)
             if installed_rd_tups or missing_rd_tups:
                 # Get the description from the metadata in case it has a value.
-                repository_dependencies = metadata.get('repository_dependencies', {})
-                description = repository_dependencies.get('description', None)
+                repository_dependencies = metadata.get("repository_dependencies", {})
+                description = repository_dependencies.get("description", None)
                 # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the
                 # missing_repository_dependencies dictionaries for proper display parsing.
-                root_key = generate_repository_dependencies_key_for_repository(repository.tool_shed,
-                                                                               repository.name,
-                                                                               repository.owner,
-                                                                               repository.installed_changeset_revision,
-                                                                               prior_installation_required,
-                                                                               only_if_compiling_contained_td)
+                root_key = generate_repository_dependencies_key_for_repository(
+                    repository.tool_shed,
+                    repository.name,
+                    repository.owner,
+                    repository.installed_changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                )
                 if installed_rd_tups:
-                    installed_repository_dependencies['root_key'] = root_key
+                    installed_repository_dependencies["root_key"] = root_key
                     installed_repository_dependencies[root_key] = installed_rd_tups
-                    installed_repository_dependencies['description'] = description
+                    installed_repository_dependencies["description"] = description
                 if missing_rd_tups:
-                    missing_repository_dependencies['root_key'] = root_key
+                    missing_repository_dependencies["root_key"] = root_key
                     missing_repository_dependencies[root_key] = missing_rd_tups
-                    missing_repository_dependencies['description'] = description
+                    missing_repository_dependencies["description"] = description
         return installed_repository_dependencies, missing_repository_dependencies
 
     def get_installed_and_missing_repository_dependencies_for_new_or_updated_install(self, repo_info_tuple):
@@ -345,19 +406,32 @@ class InstalledRepositoryManager:
         installed_repository_dependencies = {}
         missing_rd_tups = []
         installed_rd_tups = []
-        (description, repository_clone_url, changeset_revision, ctx_rev,
-         repository_owner, repository_dependencies, tool_dependencies) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+        (
+            description,
+            repository_clone_url,
+            changeset_revision,
+            ctx_rev,
+            repository_owner,
+            repository_dependencies,
+            tool_dependencies,
+        ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
         if repository_dependencies:
-            description = repository_dependencies['description']
-            root_key = repository_dependencies['root_key']
+            description = repository_dependencies["description"]
+            root_key = repository_dependencies["root_key"]
             # The repository dependencies container will include only the immediate repository dependencies of
             # this repository, so the container will be only a single level in depth.
             for key, rd_tups in repository_dependencies.items():
-                if key in ['description', 'root_key']:
+                if key in ["description", "root_key"]:
                     continue
                 for rd_tup in rd_tups:
-                    tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                        common_util.parse_repository_dependency_tuple(rd_tup)
+                    (
+                        tool_shed,
+                        name,
+                        owner,
+                        changeset_revision,
+                        prior_installation_required,
+                        only_if_compiling_contained_td,
+                    ) = common_util.parse_repository_dependency_tuple(rd_tup)
                     # Updates to installed repository revisions may have occurred, so make sure to locate the
                     # appropriate repository revision if one exists.  We need to create a temporary repo_info_tuple
                     # that includes the correct repository owner which we get from the current rd_tup.  The current
@@ -365,20 +439,20 @@ class InstalledRepositoryManager:
                     #                     repository_dependencies, installed_td )
                     tmp_clone_url = common_util.generate_clone_url_from_repo_info_tup(self.app, rd_tup)
                     tmp_repo_info_tuple = (None, tmp_clone_url, changeset_revision, None, owner, None, None)
-                    repository, installed_changeset_revision = repository_util.repository_was_previously_installed(self.app,
-                                                                                                                   tool_shed,
-                                                                                                                   name,
-                                                                                                                   tmp_repo_info_tuple,
-                                                                                                                   from_tip=False)
+                    repository, installed_changeset_revision = repository_util.repository_was_previously_installed(
+                        self.app, tool_shed, name, tmp_repo_info_tuple, from_tip=False
+                    )
                     if repository:
-                        new_rd_tup = [tool_shed,
-                                      name,
-                                      owner,
-                                      changeset_revision,
-                                      prior_installation_required,
-                                      only_if_compiling_contained_td,
-                                      repository.id,
-                                      repository.status]
+                        new_rd_tup = [
+                            tool_shed,
+                            name,
+                            owner,
+                            changeset_revision,
+                            prior_installation_required,
+                            only_if_compiling_contained_td,
+                            repository.id,
+                            repository.status,
+                        ]
                         if repository.status == self.install_model.ToolShedRepository.installation_status.INSTALLED:
                             if new_rd_tup not in installed_rd_tups:
                                 installed_rd_tups.append(new_rd_tup)
@@ -392,27 +466,29 @@ class InstalledRepositoryManager:
                                 if new_rd_tup not in missing_rd_tups:
                                     missing_rd_tups.append(new_rd_tup)
                     else:
-                        new_rd_tup = [tool_shed,
-                                      name,
-                                      owner,
-                                      changeset_revision,
-                                      prior_installation_required,
-                                      only_if_compiling_contained_td,
-                                      None,
-                                      'Never installed']
+                        new_rd_tup = [
+                            tool_shed,
+                            name,
+                            owner,
+                            changeset_revision,
+                            prior_installation_required,
+                            only_if_compiling_contained_td,
+                            None,
+                            "Never installed",
+                        ]
                         if not util.asbool(only_if_compiling_contained_td):
                             # A repository dependency that is not installed will not be considered missing if its value for
                             # only_if_compiling_contained_td is True - see above...
                             if new_rd_tup not in missing_rd_tups:
                                 missing_rd_tups.append(new_rd_tup)
         if installed_rd_tups:
-            installed_repository_dependencies['root_key'] = root_key
+            installed_repository_dependencies["root_key"] = root_key
             installed_repository_dependencies[root_key] = installed_rd_tups
-            installed_repository_dependencies['description'] = description
+            installed_repository_dependencies["description"] = description
         if missing_rd_tups:
-            missing_repository_dependencies['root_key'] = root_key
+            missing_repository_dependencies["root_key"] = root_key
             missing_repository_dependencies[root_key] = missing_rd_tups
-            missing_repository_dependencies['description'] = description
+            missing_repository_dependencies["description"] = description
         return installed_repository_dependencies, missing_repository_dependencies
 
     def get_installed_and_missing_tool_dependencies_for_repository(self, tool_dependencies_dict):
@@ -435,7 +511,7 @@ class InstalledRepositoryManager:
                 # Default the status to NEVER_INSTALLED.
                 tool_dependency_status = self.install_model.ToolDependency.installation_status.NEVER_INSTALLED
                 # Set environment tool dependencies are a list.
-                if td_key == 'set_environment':
+                if td_key == "set_environment":
                     new_val = []
                     for requirement_dict in val:
                         # {'repository_name': 'xx',
@@ -444,14 +520,15 @@ class InstalledRepositoryManager:
                         #  'repository_owner': 'yy',
                         #  'changeset_revision': 'zz',
                         #  'type': 'package'}
-                        tool_dependency = \
-                            tool_dependency_util.get_tool_dependency_by_name_version_type(self.app,
-                                                                                          requirement_dict.get('name', None),
-                                                                                          requirement_dict.get('version', None),
-                                                                                          requirement_dict.get('type', 'package'))
+                        tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type(
+                            self.app,
+                            requirement_dict.get("name", None),
+                            requirement_dict.get("version", None),
+                            requirement_dict.get("type", "package"),
+                        )
                         if tool_dependency:
                             tool_dependency_status = tool_dependency.status
-                        requirement_dict['status'] = tool_dependency_status
+                        requirement_dict["status"] = tool_dependency_status
                         new_val.append(requirement_dict)
                         if tool_dependency_status in [self.install_model.ToolDependency.installation_status.INSTALLED]:
                             if td_key in installed_tool_dependencies:
@@ -471,13 +548,12 @@ class InstalledRepositoryManager:
                     #  'repository_owner': 'yy',
                     #  'changeset_revision': 'zz',
                     #  'type': 'package'}
-                    tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type(self.app,
-                                                                                                    val.get('name', None),
-                                                                                                    val.get('version', None),
-                                                                                                    val.get('type', 'package'))
+                    tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type(
+                        self.app, val.get("name", None), val.get("version", None), val.get("type", "package")
+                    )
                     if tool_dependency:
                         tool_dependency_status = tool_dependency.status
-                    val['status'] = tool_dependency_status
+                    val["status"] = tool_dependency_status
                 if tool_dependency_status in [self.install_model.ToolDependency.installation_status.INSTALLED]:
                     installed_tool_dependencies[td_key] = val
                 else:
@@ -497,31 +573,38 @@ class InstalledRepositoryManager:
             repository_dependency = rrda.repository_dependency
             required_repository = repository_dependency.repository
             if status is None or required_repository.status == status:
-                required_repository_tup = self.get_repository_tuple_for_installed_repository_manager(required_repository)
+                required_repository_tup = self.get_repository_tuple_for_installed_repository_manager(
+                    required_repository
+                )
                 if required_repository_tup == repository_tup:
                     # We have a circular repository dependency relationship, skip this entry.
                     continue
                 if required_repository_tup not in dependency_tups:
                     dependency_tups.append(required_repository_tup)
-                    return self.get_repository_dependency_tups_for_installed_repository(required_repository,
-                                                                                        dependency_tups=dependency_tups)
+                    return self.get_repository_dependency_tups_for_installed_repository(
+                        required_repository, dependency_tups=dependency_tups
+                    )
         return dependency_tups
 
     def get_repository_tuple_for_installed_repository_manager(self, repository):
-        return (str(repository.tool_shed),
-                str(repository.name),
-                str(repository.owner),
-                str(repository.installed_changeset_revision))
+        return (
+            str(repository.tool_shed),
+            str(repository.name),
+            str(repository.owner),
+            str(repository.installed_changeset_revision),
+        )
 
     def get_repository_install_dir(self, tool_shed_repository):
         for tool_path in self.tool_paths:
             ts = common_util.remove_port_from_tool_shed_url(str(tool_shed_repository.tool_shed))
-            relative_path = os.path.join(tool_path,
-                                         ts,
-                                         'repos',
-                                         str(tool_shed_repository.owner),
-                                         str(tool_shed_repository.name),
-                                         str(tool_shed_repository.installed_changeset_revision))
+            relative_path = os.path.join(
+                tool_path,
+                ts,
+                "repos",
+                str(tool_shed_repository.owner),
+                str(tool_shed_repository.name),
+                str(tool_shed_repository.installed_changeset_revision),
+            )
             if os.path.exists(relative_path):
                 return relative_path
         return None
@@ -544,8 +627,10 @@ class InstalledRepositoryManager:
                             contents = open(env_shell_file_path).read()
                         except Exception as e:
                             contents = None
-                            log.debug('Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' %
-                                      (str(env_shell_file_path), str(td.name), str(tool_dependency.name), str(e)))
+                            log.debug(
+                                "Error reading file %s, so cannot determine if package %s requires package %s at run time: %s"
+                                % (str(env_shell_file_path), str(td.name), str(tool_dependency.name), str(e))
+                            )
                         if contents is not None and contents.find(required_env_shell_file_path) >= 0:
                             td_tuple = self.get_tool_dependency_tuple_for_installed_repository_manager(td)
                             runtime_dependent_tool_dependency_tups.append(td_tuple)
@@ -558,8 +643,9 @@ class InstalledRepositoryManager:
             type = str(tool_dependency.type)
         return (tool_dependency.tool_shed_repository_id, str(tool_dependency.name), str(tool_dependency.version), type)
 
-    def handle_existing_tool_dependencies_that_changed_in_update(self, repository, original_dependency_dict,
-                                                                 new_dependency_dict):
+    def handle_existing_tool_dependencies_that_changed_in_update(
+        self, repository, original_dependency_dict, new_dependency_dict
+    ):
         """
         This method is called when a Galaxy admin is getting updates for an installed tool shed
         repository in order to cover the case where an existing tool dependency was changed (e.g.,
@@ -573,21 +659,27 @@ class InstalledRepositoryManager:
         deleted_tool_dependency_names = []
         for original_dependency_key, original_dependency_val_dict in original_dependency_dict.items():
             if original_dependency_key not in new_dependency_dict:
-                updated_tool_dependency = self.update_existing_tool_dependency(repository,
-                                                                               original_dependency_val_dict,
-                                                                               new_dependency_dict)
+                updated_tool_dependency = self.update_existing_tool_dependency(
+                    repository, original_dependency_val_dict, new_dependency_dict
+                )
                 if updated_tool_dependency:
                     updated_tool_dependency_names.append(updated_tool_dependency.name)
                 else:
-                    deleted_tool_dependency_names.append(original_dependency_val_dict['name'])
+                    deleted_tool_dependency_names.append(original_dependency_val_dict["name"])
         return updated_tool_dependency_names, deleted_tool_dependency_names
 
     def load_proprietary_datatypes(self):
         cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
-        for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
-                                                .filter(and_(self.install_model.ToolShedRepository.table.c.includes_datatypes == true(),
-                                                             self.install_model.ToolShedRepository.table.c.deleted == false())) \
-                                                .order_by(self.install_model.ToolShedRepository.table.c.id):
+        for tool_shed_repository in (
+            self.context.query(self.install_model.ToolShedRepository)
+            .filter(
+                and_(
+                    self.install_model.ToolShedRepository.table.c.includes_datatypes == true(),
+                    self.install_model.ToolShedRepository.table.c.deleted == false(),
+                )
+            )
+            .order_by(self.install_model.ToolShedRepository.table.c.id)
+        ):
             relative_install_dir = self.get_repository_install_dir(tool_shed_repository)
             if relative_install_dir:
                 installed_repository_dict = cdl.load_installed_datatypes(tool_shed_repository, relative_install_dir)
@@ -597,15 +689,16 @@ class InstalledRepositoryManager:
     def load_proprietary_converters_and_display_applications(self, deactivate=False):
         cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
         for installed_repository_dict in self.installed_repository_dicts:
-            if installed_repository_dict['converter_path']:
+            if installed_repository_dict["converter_path"]:
                 cdl.load_installed_datatype_converters(installed_repository_dict, deactivate=deactivate)
-            if installed_repository_dict['display_path']:
+            if installed_repository_dict["display_path"]:
                 cdl.load_installed_display_applications(installed_repository_dict, deactivate=deactivate)
 
     def uninstall_repository(self, repository, remove_from_disk=True):
-        errors = ''
-        shed_tool_conf, tool_path, relative_install_dir = \
-            suc.get_tool_panel_config_tool_path_install_dir(app=self.app, repository=repository)
+        errors = ""
+        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
+            app=self.app, repository=repository
+        )
         if relative_install_dir:
             if tool_path:
                 relative_install_dir = os.path.join(tool_path, relative_install_dir)
@@ -615,23 +708,21 @@ class InstalledRepositoryManager:
         if repository.includes_tools_for_display_in_tool_panel:
             # Handle tool panel alterations.
             tpm = tool_panel_manager.ToolPanelManager(app=self.app)
-            tpm.remove_repository_contents(repository,
-                                           shed_tool_conf,
-                                           uninstall=remove_from_disk)
+            tpm.remove_repository_contents(repository, shed_tool_conf, uninstall=remove_from_disk)
         if repository.includes_data_managers:
             dmh = data_manager.DataManagerHandler(app=self.app)
             dmh.remove_from_data_manager(repository)
         if repository.includes_datatypes:
             # Deactivate proprietary datatypes.
             cdl = custom_datatype_manager.CustomDatatypeLoader(app=self.app)
-            installed_repository_dict = cdl.load_installed_datatypes(repository,
-                                                                     repository_install_dir,
-                                                                     deactivate=True)
+            installed_repository_dict = cdl.load_installed_datatypes(
+                repository, repository_install_dir, deactivate=True
+            )
             if installed_repository_dict:
-                converter_path = installed_repository_dict.get('converter_path')
+                converter_path = installed_repository_dict.get("converter_path")
                 if converter_path is not None:
                     cdl.load_installed_datatype_converters(installed_repository_dict, deactivate=True)
-                display_path = installed_repository_dict.get('display_path')
+                display_path = installed_repository_dict.get("display_path")
                 if display_path is not None:
                     cdl.load_installed_display_applications(installed_repository_dict, deactivate=True)
         if remove_from_disk:
@@ -656,7 +747,7 @@ class InstalledRepositoryManager:
                 for tool_dependency in tool_dependencies_to_uninstall:
                     uninstalled, error_message = tool_dependency_util.remove_tool_dependency(self.app, tool_dependency)
                     if error_message:
-                        errors = f'{errors}  {error_message}'
+                        errors = f"{errors}  {error_message}"
         repository.deleted = True
         if remove_from_disk:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
@@ -670,8 +761,8 @@ class InstalledRepositoryManager:
     def purge_repository(self, repository):
         """Purge a repository with status New (a white ghost) from the database."""
         sa_session = self.app.model.session
-        status = 'ok'
-        message = ''
+        status = "ok"
+        message = ""
         purged_tool_versions = 0
         purged_tool_dependencies = 0
         purged_required_repositories = 0
@@ -687,9 +778,11 @@ class InstalledRepositoryManager:
                                 sa_session.delete(tool_version_association)
                                 sa_session.flush()
                             except Exception as e:
-                                status = 'error'
-                                message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
-                                    (str(repository.name), str(repository.status), str(e))
+                                status = "error"
+                                message = (
+                                    "Error attempting to purge tool_versions for the repository named %s with status %s: %s."
+                                    % (str(repository.name), str(repository.status), str(e))
+                                )
                                 return status, message
                     if tool_version.child_tool_association:
                         for tool_version_association in tool_version.child_tool_association:
@@ -697,18 +790,22 @@ class InstalledRepositoryManager:
                                 sa_session.delete(tool_version_association)
                                 sa_session.flush()
                             except Exception as e:
-                                status = 'error'
-                                message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
-                                    (str(repository.name), str(repository.status), str(e))
+                                status = "error"
+                                message = (
+                                    "Error attempting to purge tool_versions for the repository named %s with status %s: %s."
+                                    % (str(repository.name), str(repository.status), str(e))
+                                )
                                 return status, message
                     try:
                         sa_session.delete(tool_version)
                         sa_session.flush()
                         purged_tool_versions += 1
                     except Exception as e:
-                        status = 'error'
-                        message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
-                            (str(repository.name), str(repository.status), str(e))
+                        status = "error"
+                        message = (
+                            "Error attempting to purge tool_versions for the repository named %s with status %s: %s."
+                            % (str(repository.name), str(repository.status), str(e))
+                        )
                         return status, message
             # Purge this repository's associated tool dependencies.
             if repository.tool_dependencies:
@@ -718,9 +815,11 @@ class InstalledRepositoryManager:
                         sa_session.flush()
                         purged_tool_dependencies += 1
                     except Exception as e:
-                        status = 'error'
-                        message = 'Error attempting to purge tool_dependencies for the repository named %s with status %s: %s.' % \
-                            (str(repository.name), str(repository.status), str(e))
+                        status = "error"
+                        message = (
+                            "Error attempting to purge tool_dependencies for the repository named %s with status %s: %s."
+                            % (str(repository.name), str(repository.status), str(e))
+                        )
                         return status, message
             # Purge this repository's associated required repositories.
             if repository.required_repositories:
@@ -730,54 +829,73 @@ class InstalledRepositoryManager:
                         sa_session.flush()
                         purged_required_repositories += 1
                     except Exception as e:
-                        status = 'error'
-                        message = 'Error attempting to purge required_repositories for the repository named %s with status %s: %s.' % \
-                            (str(repository.name), str(repository.status), str(e))
+                        status = "error"
+                        message = (
+                            "Error attempting to purge required_repositories for the repository named %s with status %s: %s."
+                            % (str(repository.name), str(repository.status), str(e))
+                        )
                         return status, message
             # Purge any "orphan" repository_dependency records associated with the repository, but not with any
             # repository_repository_dependency_association records.
-            for orphan_repository_dependency in \
-                sa_session.query(self.app.install_model.RepositoryDependency) \
-                          .filter(self.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id):
+            for orphan_repository_dependency in sa_session.query(self.app.install_model.RepositoryDependency).filter(
+                self.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id
+            ):
                 # Purge any repository_repository_dependency_association records whose repository_dependency_id is
                 # the id of the orphan repository_dependency record.
-                for orphan_rrda in \
-                    sa_session.query(self.app.install_model.RepositoryRepositoryDependencyAssociation) \
-                              .filter(self.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id):
+                for orphan_rrda in sa_session.query(
+                    self.app.install_model.RepositoryRepositoryDependencyAssociation
+                ).filter(
+                    self.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id
+                    == orphan_repository_dependency.id
+                ):
                     try:
                         sa_session.delete(orphan_rrda)
                         sa_session.flush()
                         purged_orphan_repository_repository_dependency_association_records += 1
                     except Exception as e:
-                        status = 'error'
-                        message = 'Error attempting to purge repository_repository_dependency_association records associated with '
-                        message += 'an orphan repository_dependency record for the repository named %s with status %s: %s.' % \
-                            (str(repository.name), str(repository.status), str(e))
+                        status = "error"
+                        message = "Error attempting to purge repository_repository_dependency_association records associated with "
+                        message += (
+                            "an orphan repository_dependency record for the repository named %s with status %s: %s."
+                            % (str(repository.name), str(repository.status), str(e))
+                        )
                         return status, message
                 try:
                     sa_session.delete(orphan_repository_dependency)
                     sa_session.flush()
                     purged_orphan_repository_dependency_records += 1
                 except Exception as e:
-                    status = 'error'
-                    message = 'Error attempting to purge orphan repository_dependency records for the repository named %s with status %s: %s.' % \
-                        (str(repository.name), str(repository.status), str(e))
+                    status = "error"
+                    message = (
+                        "Error attempting to purge orphan repository_dependency records for the repository named %s with status %s: %s."
+                        % (str(repository.name), str(repository.status), str(e))
+                    )
                     return status, message
             # Purge the repository.
             sa_session.delete(repository)
             sa_session.flush()
-            message = 'The repository named <b>%s</b> with status <b>%s</b> has been purged.<br/>' % \
-                (str(repository.name), str(repository.status))
-            message += 'Total associated tool_version records purged: %d<br/>' % purged_tool_versions
-            message += 'Total associated tool_dependency records purged: %d<br/>' % purged_tool_dependencies
-            message += 'Total associated repository_repository_dependency_association records purged: %d<br/>' % purged_required_repositories
-            message += 'Total associated orphan repository_repository_dependency_association records purged: %d<br/>' % \
-                purged_orphan_repository_repository_dependency_association_records
-            message += 'Total associated orphan repository_dependency records purged: %d<br/>' % purged_orphan_repository_dependency_records
+            message = "The repository named <b>%s</b> with status <b>%s</b> has been purged.<br/>" % (
+                str(repository.name),
+                str(repository.status),
+            )
+            message += "Total associated tool_version records purged: %d<br/>" % purged_tool_versions
+            message += "Total associated tool_dependency records purged: %d<br/>" % purged_tool_dependencies
+            message += (
+                "Total associated repository_repository_dependency_association records purged: %d<br/>"
+                % purged_required_repositories
+            )
+            message += (
+                "Total associated orphan repository_repository_dependency_association records purged: %d<br/>"
+                % purged_orphan_repository_repository_dependency_association_records
+            )
+            message += (
+                "Total associated orphan repository_dependency records purged: %d<br/>"
+                % purged_orphan_repository_dependency_records
+            )
         else:
-            status = 'error'
-            message = 'A repository must have the status <b>New</b> in order to be purged.  This repository has '
-            message += f' the status {str(repository.status)}.'
+            status = "error"
+            message = "A repository must have the status <b>New</b> in order to be purged.  This repository has "
+            message += f" the status {str(repository.status)}."
         return status, message
 
     def remove_entry_from_installed_repository_dependencies_of_installed_repositories(self, repository):
@@ -791,20 +909,29 @@ class InstalledRepositoryManager:
         altered_installed_dependent_repositories_of_installed_repositories = {}
         for r_tup, v_tups in self.installed_dependent_repositories_of_installed_repositories.items():
             if repository_tup in v_tups:
-                debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \
-                    (installed_changeset_revision, name, owner)
+                debug_msg = "Removing entry for revision %s of repository %s owned by %s " % (
+                    installed_changeset_revision,
+                    name,
+                    owner,
+                )
                 r_tool_shed, r_name, r_owner, r_installed_changeset_revision = r_tup
-                debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % \
-                    (r_installed_changeset_revision, r_name, r_owner)
+                debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % (
+                    r_installed_changeset_revision,
+                    r_name,
+                    r_owner,
+                )
                 debug_msg += "in installed_repository_dependencies_of_installed_repositories."
                 log.debug(debug_msg)
                 v_tups.remove(repository_tup)
             altered_installed_dependent_repositories_of_installed_repositories[r_tup] = v_tups
-        self.installed_dependent_repositories_of_installed_repositories = \
+        self.installed_dependent_repositories_of_installed_repositories = (
             altered_installed_dependent_repositories_of_installed_repositories
+        )
         # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories.
         if repository_tup in self.installed_repository_dependencies_of_installed_repositories:
-            debug_msg = f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            debug_msg = (
+                f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            )
             debug_msg += "from installed_repository_dependencies_of_installed_repositories."
             log.debug(debug_msg)
             del self.installed_repository_dependencies_of_installed_repositories[repository_tup]
@@ -814,24 +941,38 @@ class InstalledRepositoryManager:
         repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
         if repository_tup in self.repository_dependencies_of_installed_repositories:
             tool_shed, name, owner, installed_changeset_revision = repository_tup
-            debug_msg = f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            debug_msg = (
+                f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
+            )
             debug_msg += "from repository_dependencies_of_installed_repositories."
             log.debug(debug_msg)
             del self.repository_dependencies_of_installed_repositories[repository_tup]
 
     def repository_dependency_needed_only_for_compiling_tool_dependency(self, repository, repository_dependency):
         for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td:
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = rd_tup
             # TODO: we may discover that we need to check more than just installed_changeset_revision and changeset_revision here, in which
             # case we'll need to contact the tool shed to get the list of all possible changeset_revisions.
             cleaned_tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(tool_shed)
-            cleaned_repository_dependency_tool_shed = \
-                common_util.remove_protocol_and_port_from_tool_shed_url(str(repository_dependency.tool_shed))
-            if cleaned_repository_dependency_tool_shed == cleaned_tool_shed and \
-                repository_dependency.name == name and \
-                repository_dependency.owner == owner and \
-                (repository_dependency.installed_changeset_revision == changeset_revision
-                 or repository_dependency.changeset_revision == changeset_revision):
+            cleaned_repository_dependency_tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url(
+                str(repository_dependency.tool_shed)
+            )
+            if (
+                cleaned_repository_dependency_tool_shed == cleaned_tool_shed
+                and repository_dependency.name == name
+                and repository_dependency.owner == owner
+                and (
+                    repository_dependency.installed_changeset_revision == changeset_revision
+                    or repository_dependency.changeset_revision == changeset_revision
+                )
+            ):
                 return True
         return False
 
@@ -843,27 +984,32 @@ class InstalledRepositoryManager:
         # This method is called only from Galaxy when rendering repository dependencies
         # for an installed tool shed repository.
         # TODO: Do we need to check more than changeset_revision here?
-        required_repository_tup = [required_repository.tool_shed,
-                                   required_repository.name,
-                                   required_repository.owner,
-                                   required_repository.changeset_revision]
+        required_repository_tup = [
+            required_repository.tool_shed,
+            required_repository.name,
+            required_repository.owner,
+            required_repository.changeset_revision,
+        ]
         for tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td:
             partial_tup = tup[0:4]
             if partial_tup == required_repository_tup:
-                return 'True'
-        return 'False'
+                return "True"
+        return "False"
 
     def set_prior_installation_required(self, repository, required_repository):
         """
         Return True if the received required_repository must be installed before the
         received repository.
         """
-        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app,
-                                                                              str(required_repository.tool_shed))
-        required_repository_tup = [tool_shed_url,
-                                   str(required_repository.name),
-                                   str(required_repository.owner),
-                                   str(required_repository.changeset_revision)]
+        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
+            self.app, str(required_repository.tool_shed)
+        )
+        required_repository_tup = [
+            tool_shed_url,
+            str(required_repository.name),
+            str(required_repository.owner),
+            str(required_repository.changeset_revision),
+        ]
         # Get the list of repository dependency tuples associated with the received repository
         # where prior_installation_required is True.
         required_rd_tups_that_must_be_installed = repository.requires_prior_installation_of
@@ -874,7 +1020,7 @@ class InstalledRepositoryManager:
             if partial_required_rd_tup == required_repository_tup:
                 # Return the string value of prior_installation_required, which defaults to 'False'.
                 return str(required_rd_tup[4])
-        return 'False'
+        return "False"
 
     def update_existing_tool_dependency(self, repository, original_dependency_dict, new_dependencies_dict):
         """
@@ -891,20 +1037,23 @@ class InstalledRepositoryManager:
         The new_dependencies_dict is the dictionary generated by the metadata_util.generate_tool_dependency_metadata method.
         """
         new_tool_dependency = None
-        original_name = original_dependency_dict['name']
-        original_type = original_dependency_dict['type']
-        original_version = original_dependency_dict['version']
+        original_name = original_dependency_dict["name"]
+        original_type = original_dependency_dict["type"]
+        original_version = original_dependency_dict["version"]
         # Locate the appropriate tool_dependency associated with the repository.
         tool_dependency = None
         for tool_dependency in repository.tool_dependencies:
-            if tool_dependency.name == original_name and \
-                tool_dependency.type == original_type and \
-                    tool_dependency.version == original_version:
+            if (
+                tool_dependency.name == original_name
+                and tool_dependency.type == original_type
+                and tool_dependency.version == original_version
+            ):
                 break
         if tool_dependency and tool_dependency.can_update:
             dependency_install_dir = tool_dependency.installation_directory(self.app)
-            removed_from_disk, error_message = \
-                tool_dependency_util.remove_tool_dependency_installation_directory(dependency_install_dir)
+            removed_from_disk, error_message = tool_dependency_util.remove_tool_dependency_installation_directory(
+                dependency_install_dir
+            )
             if removed_from_disk:
                 context = self.app.install_model.context
                 new_dependency_name = None
@@ -912,19 +1061,23 @@ class InstalledRepositoryManager:
                 new_dependency_version = None
                 for new_dependency_val_dict in new_dependencies_dict.values():
                     # Match on name only, hopefully this will be enough!
-                    if original_name == new_dependency_val_dict['name']:
-                        new_dependency_name = new_dependency_val_dict['name']
-                        new_dependency_type = new_dependency_val_dict['type']
-                        new_dependency_version = new_dependency_val_dict['version']
+                    if original_name == new_dependency_val_dict["name"]:
+                        new_dependency_name = new_dependency_val_dict["name"]
+                        new_dependency_type = new_dependency_val_dict["type"]
+                        new_dependency_version = new_dependency_val_dict["version"]
                         break
                 if new_dependency_name and new_dependency_type and new_dependency_version:
                     # Update all attributes of the tool_dependency record in the database.
-                    log.debug("Updating version %s of tool dependency %s %s to have new version %s and type %s."
-                              % (str(tool_dependency.version),
-                                 str(tool_dependency.type),
-                                 str(tool_dependency.name),
-                                 str(new_dependency_version),
-                                 str(new_dependency_type)))
+                    log.debug(
+                        "Updating version %s of tool dependency %s %s to have new version %s and type %s."
+                        % (
+                            str(tool_dependency.version),
+                            str(tool_dependency.type),
+                            str(tool_dependency.name),
+                            str(new_dependency_version),
+                            str(new_dependency_type),
+                        )
+                    )
                     tool_dependency.type = new_dependency_type
                     tool_dependency.version = new_dependency_version
                     tool_dependency.status = self.app.install_model.ToolDependency.installation_status.UNINSTALLED
@@ -935,8 +1088,10 @@ class InstalledRepositoryManager:
                 else:
                     # We have no new tool dependency definition based on a matching dependency name, so remove
                     # the existing tool dependency record from the database.
-                    log.debug("Deleting version %s of tool dependency %s %s from the database since it is no longer defined."
-                              % (str(tool_dependency.version), str(tool_dependency.type), str(tool_dependency.name)))
+                    log.debug(
+                        "Deleting version %s of tool dependency %s %s from the database since it is no longer defined."
+                        % (str(tool_dependency.version), str(tool_dependency.type), str(tool_dependency.name))
+                    )
                     context.delete(tool_dependency)
                     context.flush()
         return new_tool_dependency
diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index 6578ccf90bc..db5717fe946 100644
--- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -6,41 +6,64 @@ from sqlalchemy import false
 from galaxy import util
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
 from galaxy.tool_shed.metadata.metadata_generator import MetadataGenerator
-from galaxy.tool_shed.util.repository_util import get_installed_tool_shed_repository, get_repository_owner
+from galaxy.tool_shed.util.repository_util import (
+    get_installed_tool_shed_repository,
+    get_repository_owner,
+)
 from galaxy.tool_shed.util.tool_util import generate_message_for_invalid_tools
 from galaxy.util import inflector
-from galaxy.util.tool_shed import common_util
-from galaxy.util.tool_shed import xml_util
+from galaxy.util.tool_shed import (
+    common_util,
+    xml_util,
+)
 from galaxy.web.form_builder import SelectField
 
 log = logging.getLogger(__name__)
 
 
 class InstalledRepositoryMetadataManager(MetadataGenerator):
-
-    def __init__(self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None,
-                 shed_config_dict=None, relative_install_dir=None, repository_files_dir=None,
-                 resetting_all_metadata_on_repository=False, updating_installed_repository=False,
-                 persist=False, metadata_dict=None):
-        super().__init__(app, repository, changeset_revision,
-                         repository_clone_url, shed_config_dict,
-                         relative_install_dir, repository_files_dir,
-                         resetting_all_metadata_on_repository,
-                         updating_installed_repository, persist,
-                         metadata_dict=metadata_dict, user=None)
+    def __init__(
+        self,
+        app,
+        tpm=None,
+        repository=None,
+        changeset_revision=None,
+        repository_clone_url=None,
+        shed_config_dict=None,
+        relative_install_dir=None,
+        repository_files_dir=None,
+        resetting_all_metadata_on_repository=False,
+        updating_installed_repository=False,
+        persist=False,
+        metadata_dict=None,
+    ):
+        super().__init__(
+            app,
+            repository,
+            changeset_revision,
+            repository_clone_url,
+            shed_config_dict,
+            relative_install_dir,
+            repository_files_dir,
+            resetting_all_metadata_on_repository,
+            updating_installed_repository,
+            persist,
+            metadata_dict=metadata_dict,
+            user=None,
+        )
         if tpm is None:
             self.tpm = tool_panel_manager.ToolPanelManager(self.app)
         else:
             self.tpm = tpm
 
-    def build_repository_ids_select_field(self, name='repository_ids', multiple=True, display='checkboxes'):
+    def build_repository_ids_select_field(self, name="repository_ids", multiple=True, display="checkboxes"):
         """Generate the current list of repositories for resetting metadata."""
         repositories_select_field = SelectField(name=name, multiple=multiple, display=display)
         query = self.get_query_for_setting_metadata_on_repositories(order=True)
         for repository in query:
             owner = str(repository.owner)
-            option_label = f'{str(repository.name)} ({owner})'
-            option_value = f'{self.app.security.encode_id(repository.id)}'
+            option_label = f"{str(repository.name)} ({owner})"
+            option_value = f"{self.app.security.encode_id(repository.id)}"
             repositories_select_field.add_option(option_label, option_value)
         return repositories_select_field
 
@@ -51,13 +74,18 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
         a page.  When called from the Galaxy API, order is False.
         """
         if order:
-            return self.app.install_model.context.query(self.app.install_model.ToolShedRepository) \
-                                                 .filter(self.app.install_model.ToolShedRepository.table.c.uninstalled == false()) \
-                                                 .order_by(self.app.install_model.ToolShedRepository.table.c.name,
-                                                           self.app.install_model.ToolShedRepository.table.c.owner)
+            return (
+                self.app.install_model.context.query(self.app.install_model.ToolShedRepository)
+                .filter(self.app.install_model.ToolShedRepository.table.c.uninstalled == false())
+                .order_by(
+                    self.app.install_model.ToolShedRepository.table.c.name,
+                    self.app.install_model.ToolShedRepository.table.c.owner,
+                )
+            )
         else:
-            return self.app.install_model.context.query(self.app.install_model.ToolShedRepository) \
-                                                 .filter(self.app.install_model.ToolShedRepository.table.c.uninstalled == false())
+            return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).filter(
+                self.app.install_model.ToolShedRepository.table.c.uninstalled == false()
+            )
 
     def get_repository_tools_tups(self):
         """
@@ -65,16 +93,18 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
         in the received tool shed repository metadata.
         """
         repository_tools_tups = []
-        shed_conf_dict = self.tpm.get_shed_tool_conf_dict(self.metadata_dict.get('shed_config_filename'))
-        if 'tools' in self.metadata_dict:
-            for tool_dict in self.metadata_dict['tools']:
-                load_relative_path = relative_path = tool_dict.get('tool_config', None)
-                if shed_conf_dict.get('tool_path'):
-                    load_relative_path = os.path.join(shed_conf_dict.get('tool_path'), relative_path)
-                guid = tool_dict.get('guid', None)
+        shed_conf_dict = self.tpm.get_shed_tool_conf_dict(self.metadata_dict.get("shed_config_filename"))
+        if "tools" in self.metadata_dict:
+            for tool_dict in self.metadata_dict["tools"]:
+                load_relative_path = relative_path = tool_dict.get("tool_config", None)
+                if shed_conf_dict.get("tool_path"):
+                    load_relative_path = os.path.join(shed_conf_dict.get("tool_path"), relative_path)
+                guid = tool_dict.get("guid", None)
                 if relative_path and guid:
                     try:
-                        tool = self.app.toolbox.load_tool(os.path.abspath(load_relative_path), guid=guid, use_cached=False)
+                        tool = self.app.toolbox.load_tool(
+                            os.path.abspath(load_relative_path), guid=guid, use_cached=False
+                        )
                     except Exception:
                         log.exception("Error while loading tool at path '%s'", load_relative_path)
                         tool = None
@@ -94,20 +124,20 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
                 self.update_in_shed_tool_config()
                 self.app.install_model.context.add(self.repository)
                 self.app.install_model.context.flush()
-                log.debug(f'Metadata has been reset on repository {self.repository.name}.')
+                log.debug(f"Metadata has been reset on repository {self.repository.name}.")
             else:
-                log.debug(f'Metadata did not need to be reset on repository {self.repository.name}.')
+                log.debug(f"Metadata did not need to be reset on repository {self.repository.name}.")
         else:
-            log.debug(f'Error locating installation directory for repository {self.repository.name}.')
+            log.debug(f"Error locating installation directory for repository {self.repository.name}.")
 
     def reset_metadata_on_selected_repositories(self, user, **kwd):
         """
         Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
         This method is called from both Galaxy and the Tool Shed.
         """
-        repository_ids = util.listify(kwd.get('repository_ids', None))
-        message = ''
-        status = 'done'
+        repository_ids = util.listify(kwd.get("repository_ids", None))
+        message = ""
+        status = "done"
         if repository_ids:
             successful_count = 0
             unsuccessful_count = 0
@@ -117,28 +147,32 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
                     self.set_repository(repository)
                     self.reset_all_metadata_on_installed_repository()
                     if self.invalid_file_tups:
-                        message = generate_message_for_invalid_tools(self.app,
-                                                                     self.invalid_file_tups,
-                                                                     repository,
-                                                                     None,
-                                                                     as_html=False)
+                        message = generate_message_for_invalid_tools(
+                            self.app, self.invalid_file_tups, repository, None, as_html=False
+                        )
                         log.debug(message)
                         unsuccessful_count += 1
                     else:
-                        log.debug("Successfully reset metadata on repository %s owned by %s" %
-                            (str(repository.name), str(repository.owner)))
+                        log.debug(
+                            "Successfully reset metadata on repository %s owned by %s"
+                            % (str(repository.name), str(repository.owner))
+                        )
                         successful_count += 1
                 except Exception:
                     log.exception("Error attempting to reset metadata on repository %s", str(repository.name))
                     unsuccessful_count += 1
-            message = "Successfully reset metadata on %d %s.  " % \
-                (successful_count, inflector.cond_plural(successful_count, "repository"))
+            message = "Successfully reset metadata on %d %s.  " % (
+                successful_count,
+                inflector.cond_plural(successful_count, "repository"),
+            )
             if unsuccessful_count:
-                message += "Error setting metadata on %d %s - see the paster log for details.  " % \
-                    (unsuccessful_count, inflector.cond_plural(unsuccessful_count, "repository"))
+                message += "Error setting metadata on %d %s - see the paster log for details.  " % (
+                    unsuccessful_count,
+                    inflector.cond_plural(unsuccessful_count, "repository"),
+                )
         else:
-            message = 'Select at least one repository to on which to reset all metadata.'
-            status = 'error'
+            message = "Select at least one repository to on which to reset all metadata."
+            status = "error"
         return message, status
 
     def set_repository(self, repository):
@@ -148,7 +182,11 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
     def tool_shed_from_repository_clone_url(self):
         """Given a repository clone URL, return the tool shed that contains the repository."""
         cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url(self.repository_clone_url)
-        return common_util.remove_protocol_and_user_from_clone_url(cleaned_repository_clone_url).split('/repos/')[0].rstrip('/')
+        return (
+            common_util.remove_protocol_and_user_from_clone_url(cleaned_repository_clone_url)
+            .split("/repos/")[0]
+            .rstrip("/")
+        )
 
     def update_in_shed_tool_config(self):
         """
@@ -156,8 +194,8 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
         file to generate the entire list of config_elems instead of using the in-memory list.
         """
         shed_conf_dict = self.shed_config_dict or self.repository.get_shed_config_dict(self.app)
-        shed_tool_conf = shed_conf_dict['config_filename']
-        tool_path = shed_conf_dict['tool_path']
+        shed_tool_conf = shed_conf_dict["config_filename"]
+        tool_path = shed_conf_dict["tool_path"]
         self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries(self.repository)
         repository_tools_tups = self.get_repository_tools_tups()
         clone_url = common_util.generate_clone_url_for_installed_repository(self.app, self.repository)
@@ -168,25 +206,27 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
             owner = get_repository_owner(cleaned_repository_clone_url)
         guid_to_tool_elem_dict = {}
         for tool_config_filename, guid, tool in repository_tools_tups:
-            guid_to_tool_elem_dict[guid] = self.tpm.generate_tool_elem(tool_shed,
-                                                                       self.repository.name,
-                                                                       self.repository.changeset_revision,
-                                                                       self.repository.owner or '',
-                                                                       tool_config_filename,
-                                                                       tool,
-                                                                       None)
+            guid_to_tool_elem_dict[guid] = self.tpm.generate_tool_elem(
+                tool_shed,
+                self.repository.name,
+                self.repository.changeset_revision,
+                self.repository.owner or "",
+                tool_config_filename,
+                tool,
+                None,
+            )
         config_elems = []
         tree, error_message = xml_util.parse_xml(shed_tool_conf)
         if tree:
             root = tree.getroot()
             for elem in root:
-                if elem.tag == 'section':
+                if elem.tag == "section":
                     for i, tool_elem in enumerate(elem):
-                        guid = tool_elem.attrib.get('guid')
+                        guid = tool_elem.attrib.get("guid")
                         if guid in guid_to_tool_elem_dict:
                             elem[i] = guid_to_tool_elem_dict[guid]
-                elif elem.tag == 'tool':
-                    guid = elem.attrib.get('guid')
+                elif elem.tag == "tool":
+                    guid = elem.attrib.get("guid")
                     if guid in guid_to_tool_elem_dict:
                         elem = guid_to_tool_elem_dict[guid]
                 config_elems.append(elem)
diff --git a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
index 3e552c203a3..9819fe44c40 100644
--- a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
@@ -27,14 +27,15 @@ from galaxy.util import (
     unicodify,
     url_get,
 )
-from galaxy.util.tool_shed import common_util
-from galaxy.util.tool_shed import encoding_util
+from galaxy.util.tool_shed import (
+    common_util,
+    encoding_util,
+)
 
 log = logging.getLogger(__name__)
 
 
 class RepositoryDependencyInstallManager:
-
     def __init__(self, app):
         self.app = app
 
@@ -50,17 +51,18 @@ class RepositoryDependencyInstallManager:
         log.debug("Building repository dependency relationships...")
         for repo_info_dict in repo_info_dicts:
             for repo_info_tuple in repo_info_dict.values():
-                description, \
-                    repository_clone_url, \
-                    changeset_revision, \
-                    ctx_rev, \
-                    repository_owner, \
-                    repository_dependencies, \
-                    tool_dependencies = \
-                    repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+                (
+                    description,
+                    repository_clone_url,
+                    changeset_revision,
+                    ctx_rev,
+                    repository_owner,
+                    repository_dependencies,
+                    tool_dependencies,
+                ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
                 if repository_dependencies:
                     for key, val in repository_dependencies.items():
-                        if key in ['root_key', 'description']:
+                        if key in ["root_key", "description"]:
                             continue
                         d_repository = None
                         repository_components_tuple = get_components_from_key(key)
@@ -71,38 +73,45 @@ class RepositoryDependencyInstallManager:
                             # the repository that will be dependent upon each of the tool shed repositories contained in
                             # val.  We'll need to check tool_shed_repository.tool_shed as well if/when repository dependencies
                             # across tool sheds is supported.
-                            if tsr.name == d_name and tsr.owner == d_owner and tsr.changeset_revision == d_changeset_revision:
+                            if (
+                                tsr.name == d_name
+                                and tsr.owner == d_owner
+                                and tsr.changeset_revision == d_changeset_revision
+                            ):
                                 d_repository = tsr
                                 break
                         if d_repository is None:
                             # The dependent repository is not in the received list so look in the database.
-                            d_repository = self.get_or_create_tool_shed_repository(d_toolshed,
-                                                                                   d_name,
-                                                                                   d_owner,
-                                                                                   d_changeset_revision)
+                            d_repository = self.get_or_create_tool_shed_repository(
+                                d_toolshed, d_name, d_owner, d_changeset_revision
+                            )
                         # Process each repository_dependency defined for the current dependent repository.
                         for repository_dependency_components_list in val:
                             required_repository = None
-                            rd_toolshed, \
-                                rd_name, \
-                                rd_owner, \
-                                rd_changeset_revision, \
-                                rd_prior_installation_required, \
-                                rd_only_if_compiling_contained_td = \
-                                common_util.parse_repository_dependency_tuple(repository_dependency_components_list)
+                            (
+                                rd_toolshed,
+                                rd_name,
+                                rd_owner,
+                                rd_changeset_revision,
+                                rd_prior_installation_required,
+                                rd_only_if_compiling_contained_td,
+                            ) = common_util.parse_repository_dependency_tuple(repository_dependency_components_list)
                             # Get the the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision.  This
                             # is the repository that will be required by the current d_repository.
                             # TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported.
                             for tsr in tool_shed_repositories:
-                                if tsr.name == rd_name and tsr.owner == rd_owner and tsr.changeset_revision == rd_changeset_revision:
+                                if (
+                                    tsr.name == rd_name
+                                    and tsr.owner == rd_owner
+                                    and tsr.changeset_revision == rd_changeset_revision
+                                ):
                                     required_repository = tsr
                                     break
                             if required_repository is None:
                                 # The required repository is not in the received list so look in the database.
-                                required_repository = self.get_or_create_tool_shed_repository(rd_toolshed,
-                                                                                              rd_name,
-                                                                                              rd_owner,
-                                                                                              rd_changeset_revision)
+                                required_repository = self.get_or_create_tool_shed_repository(
+                                    rd_toolshed, rd_name, rd_owner, rd_changeset_revision
+                                )
                             # Ensure there is a repository_dependency relationship between d_repository and required_repository.
                             rrda = None
                             for rd in d_repository.repository_dependencies:
@@ -111,24 +120,39 @@ class RepositoryDependencyInstallManager:
                                     break
                             if not rrda:
                                 # Make sure required_repository is in the repository_dependency table.
-                                repository_dependency = self.get_repository_dependency_by_repository_id(install_model,
-                                                                                                        required_repository.id)
+                                repository_dependency = self.get_repository_dependency_by_repository_id(
+                                    install_model, required_repository.id
+                                )
                                 if not repository_dependency:
-                                    log.debug('Creating new repository_dependency record for installed revision %s of repository: %s owned by %s.',
-                                              required_repository.installed_changeset_revision,
-                                              required_repository.name,
-                                              required_repository.owner)
-                                    repository_dependency = install_model.RepositoryDependency(tool_shed_repository_id=required_repository.id)
+                                    log.debug(
+                                        "Creating new repository_dependency record for installed revision %s of repository: %s owned by %s.",
+                                        required_repository.installed_changeset_revision,
+                                        required_repository.name,
+                                        required_repository.owner,
+                                    )
+                                    repository_dependency = install_model.RepositoryDependency(
+                                        tool_shed_repository_id=required_repository.id
+                                    )
                                     install_model.context.add(repository_dependency)
                                     install_model.context.flush()
                                 # Build the relationship between the d_repository and the required_repository.
-                                rrda = install_model.RepositoryRepositoryDependencyAssociation(tool_shed_repository_id=d_repository.id,
-                                                                                               repository_dependency_id=repository_dependency.id)
+                                rrda = install_model.RepositoryRepositoryDependencyAssociation(
+                                    tool_shed_repository_id=d_repository.id,
+                                    repository_dependency_id=repository_dependency.id,
+                                )
                                 install_model.context.add(rrda)
                                 install_model.context.flush()
 
-    def create_repository_dependency_objects(self, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False,
-                                             no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None):
+    def create_repository_dependency_objects(
+        self,
+        tool_path,
+        tool_shed_url,
+        repo_info_dicts,
+        install_repository_dependencies=False,
+        no_changes_checked=False,
+        tool_panel_section_id=None,
+        new_tool_panel_section_label=None,
+    ):
         """
         Discover all repository dependencies and make sure all tool_shed_repository and
         associated repository_dependency records exist as well as the dependency relationships
@@ -158,7 +182,7 @@ class RepositoryDependencyInstallManager:
         # to make sure all repository dependency objects exist so that the appropriate
         # repository dependency relationships can be built.
         all_required_repo_info_dict = self.get_required_repo_info_dicts(tool_shed_url, repo_info_dicts)
-        all_repo_info_dicts = all_required_repo_info_dict.get('all_repo_info_dicts', [])
+        all_repo_info_dicts = all_required_repo_info_dict.get("all_repo_info_dicts", [])
         if not all_repo_info_dicts:
             # No repository dependencies were discovered so process the received repositories.
             all_repo_info_dicts = [rid for rid in repo_info_dicts]
@@ -172,54 +196,79 @@ class RepositoryDependencyInstallManager:
                 for name, repo_info_tuple in repo_info_dict.items():
                     can_update_db_record = False
                     clear_metadata = True
-                    description, \
-                        repository_clone_url, \
-                        changeset_revision, \
-                        ctx_rev, \
-                        repository_owner, \
-                        repository_dependencies, \
-                        tool_dependencies = \
-                        repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+                    (
+                        description,
+                        repository_clone_url,
+                        changeset_revision,
+                        ctx_rev,
+                        repository_owner,
+                        repository_dependencies,
+                        tool_dependencies,
+                    ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
                     # See if the repository has an existing record in the database.
-                    repository_db_record, installed_changeset_revision = \
-                        repository_util.repository_was_previously_installed(self.app, tool_shed_url, name, repo_info_tuple, from_tip=False)
+                    (
+                        repository_db_record,
+                        installed_changeset_revision,
+                    ) = repository_util.repository_was_previously_installed(
+                        self.app, tool_shed_url, name, repo_info_tuple, from_tip=False
+                    )
                     if repository_db_record:
-                        if (installed_changeset_revision != changeset_revision
-                                and repository_db_record.status == install_model.ToolShedRepository.installation_status.INSTALLED):
+                        if (
+                            installed_changeset_revision != changeset_revision
+                            and repository_db_record.status
+                            == install_model.ToolShedRepository.installation_status.INSTALLED
+                        ):
                             log.info(
                                 "Repository '%s' already present at revision %s, will be updated to revision %s",
-                                repository_db_record.name, installed_changeset_revision, changeset_revision)
+                                repository_db_record.name,
+                                installed_changeset_revision,
+                                changeset_revision,
+                            )
                             can_update_db_record = True
                             clear_metadata = False
-                        elif repository_db_record.status in [install_model.ToolShedRepository.installation_status.INSTALLED,
-                                                           install_model.ToolShedRepository.installation_status.CLONING,
-                                                           install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
-                                                           install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
-                                                           install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
-                                                           install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
-                            info_msg = "Skipping installation of revision %s of repository '%s' because it was installed " % \
-                                (changeset_revision, repository_db_record.name)
-                            info_msg += "with the (possibly updated) revision %s and its current installation status is '%s'." % \
-                                (installed_changeset_revision, repository_db_record.status)
+                        elif repository_db_record.status in [
+                            install_model.ToolShedRepository.installation_status.INSTALLED,
+                            install_model.ToolShedRepository.installation_status.CLONING,
+                            install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
+                            install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
+                            install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
+                            install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES,
+                        ]:
+                            info_msg = (
+                                "Skipping installation of revision %s of repository '%s' because it was installed "
+                                % (changeset_revision, repository_db_record.name)
+                            )
+                            info_msg += (
+                                "with the (possibly updated) revision %s and its current installation status is '%s'."
+                                % (installed_changeset_revision, repository_db_record.status)
+                            )
                             log.info(info_msg)
                             can_update_db_record = False
                         else:
-                            if repository_db_record.status in [install_model.ToolShedRepository.installation_status.ERROR,
-                                                               install_model.ToolShedRepository.installation_status.NEW,
-                                                               install_model.ToolShedRepository.installation_status.UNINSTALLED]:
+                            if repository_db_record.status in [
+                                install_model.ToolShedRepository.installation_status.ERROR,
+                                install_model.ToolShedRepository.installation_status.NEW,
+                                install_model.ToolShedRepository.installation_status.UNINSTALLED,
+                            ]:
                                 # The current tool shed repository is not currently installed, so we can update its
                                 # record in the database.
                                 name = repository_db_record.name
                                 installed_changeset_revision = repository_db_record.installed_changeset_revision
                                 can_update_db_record = True
-                            elif repository_db_record.status in [install_model.ToolShedRepository.installation_status.DEACTIVATED]:
+                            elif repository_db_record.status in [
+                                install_model.ToolShedRepository.installation_status.DEACTIVATED
+                            ]:
                                 # The current tool shed repository is deactivated, so updating its database record
                                 # is not necessary - just activate it.
-                                log.info(f"Reactivating deactivated tool_shed_repository '{str(repository_db_record.name)}'.")
+                                log.info(
+                                    f"Reactivating deactivated tool_shed_repository '{str(repository_db_record.name)}'."
+                                )
                                 self.app.installed_repository_manager.activate_repository(repository_db_record)
                                 # No additional updates to the database record are necessary.
                                 can_update_db_record = False
-                            elif repository_db_record.status not in [install_model.ToolShedRepository.installation_status.NEW]:
+                            elif repository_db_record.status not in [
+                                install_model.ToolShedRepository.installation_status.NEW
+                            ]:
                                 # Set changeset_revision here so repository_util.create_or_update_tool_shed_repository will find
                                 # the previously installed and uninstalled repository instead of creating a new record.
                                 changeset_revision = repository_db_record.installed_changeset_revision
@@ -234,45 +283,57 @@ class RepositoryDependencyInstallManager:
                         # Get the repository metadata to see where it was previously located in the tool panel.
                         tpm = tool_panel_manager.ToolPanelManager(self.app)
                         if repository_db_record and repository_db_record.metadata_:
-                            _, tool_panel_section_key = \
-                                tpm.handle_tool_panel_selection(toolbox=self.app.toolbox,
-                                                                metadata=repository_db_record.metadata_,
-                                                                no_changes_checked=no_changes_checked,
-                                                                tool_panel_section_id=tool_panel_section_id,
-                                                                new_tool_panel_section_label=new_tool_panel_section_label)
+                            _, tool_panel_section_key = tpm.handle_tool_panel_selection(
+                                toolbox=self.app.toolbox,
+                                metadata=repository_db_record.metadata_,
+                                no_changes_checked=no_changes_checked,
+                                tool_panel_section_id=tool_panel_section_id,
+                                new_tool_panel_section_label=new_tool_panel_section_label,
+                            )
                         else:
                             # We're installing a new tool shed repository that does not yet have a database record.
-                            tool_panel_section_key, _ = \
-                                tpm.handle_tool_panel_section(self.app.toolbox,
-                                                              tool_panel_section_id=tool_panel_section_id,
-                                                              new_tool_panel_section_label=new_tool_panel_section_label)
+                            tool_panel_section_key, _ = tpm.handle_tool_panel_section(
+                                self.app.toolbox,
+                                tool_panel_section_id=tool_panel_section_id,
+                                new_tool_panel_section_label=new_tool_panel_section_label,
+                            )
                         metadata_dict = {} if clear_metadata else None
                         current_changeset_revision = changeset_revision if clear_metadata else None
-                        tool_shed_repository = \
-                            repository_util.create_or_update_tool_shed_repository(app=self.app,
-                                                                                  name=name,
-                                                                                  description=description,
-                                                                                  installed_changeset_revision=installed_changeset_revision,
-                                                                                  ctx_rev=ctx_rev,
-                                                                                  repository_clone_url=repository_clone_url,
-                                                                                  status=install_model.ToolShedRepository.installation_status.NEW,
-                                                                                  metadata_dict=metadata_dict,
-                                                                                  current_changeset_revision=current_changeset_revision,
-                                                                                  owner=repository_owner,
-                                                                                  dist_to_shed=False)
+                        tool_shed_repository = repository_util.create_or_update_tool_shed_repository(
+                            app=self.app,
+                            name=name,
+                            description=description,
+                            installed_changeset_revision=installed_changeset_revision,
+                            ctx_rev=ctx_rev,
+                            repository_clone_url=repository_clone_url,
+                            status=install_model.ToolShedRepository.installation_status.NEW,
+                            metadata_dict=metadata_dict,
+                            current_changeset_revision=current_changeset_revision,
+                            owner=repository_owner,
+                            dist_to_shed=False,
+                        )
                         if tool_shed_repository not in all_created_or_updated_tool_shed_repositories:
                             all_created_or_updated_tool_shed_repositories.append(tool_shed_repository)
                         # Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if
                         # it is supposed to be installed.
-                        if install_repository_dependencies or self.is_in_repo_info_dicts(repo_info_dict, repo_info_dicts):
+                        if install_repository_dependencies or self.is_in_repo_info_dicts(
+                            repo_info_dict, repo_info_dicts
+                        ):
                             if tool_shed_repository not in created_or_updated_tool_shed_repositories:
                                 # Keep the one-to-one mapping between items in 3 lists.
                                 created_or_updated_tool_shed_repositories.append(tool_shed_repository)
                                 tool_panel_section_keys.append(tool_panel_section_key)
                                 filtered_repo_info_dicts.append(repo_info_dict)
         # Build repository dependency relationships even if the user chose to not install repository dependencies.
-        self.build_repository_dependency_relationships(all_repo_info_dicts, all_created_or_updated_tool_shed_repositories)
-        return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
+        self.build_repository_dependency_relationships(
+            all_repo_info_dicts, all_created_or_updated_tool_shed_repositories
+        )
+        return (
+            created_or_updated_tool_shed_repositories,
+            tool_panel_section_keys,
+            all_repo_info_dicts,
+            filtered_repo_info_dicts,
+        )
 
     def get_or_create_tool_shed_repository(self, tool_shed, name, owner, changeset_revision):
         """
@@ -285,22 +346,26 @@ class RepositoryDependencyInstallManager:
         # We store the port in the database.
         tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed)
         # This method is used only in Galaxy, not the tool shed.
-        repository = repository_util.get_repository_for_dependency_relationship(self.app, tool_shed, name, owner, changeset_revision)
+        repository = repository_util.get_repository_for_dependency_relationship(
+            self.app, tool_shed, name, owner, changeset_revision
+        )
         if not repository:
             tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed)
-            repository_clone_url = os.path.join(tool_shed_url, 'repos', owner, name)
+            repository_clone_url = os.path.join(tool_shed_url, "repos", owner, name)
             ctx_rev = get_ctx_rev(self.app, tool_shed_url, name, owner, changeset_revision)
-            repository = repository_util.create_or_update_tool_shed_repository(app=self.app,
-                                                                               name=name,
-                                                                               description=None,
-                                                                               installed_changeset_revision=changeset_revision,
-                                                                               ctx_rev=ctx_rev,
-                                                                               repository_clone_url=repository_clone_url,
-                                                                               status=install_model.ToolShedRepository.installation_status.NEW,
-                                                                               metadata_dict={},
-                                                                               current_changeset_revision=None,
-                                                                               owner=owner,
-                                                                               dist_to_shed=False)
+            repository = repository_util.create_or_update_tool_shed_repository(
+                app=self.app,
+                name=name,
+                description=None,
+                installed_changeset_revision=changeset_revision,
+                ctx_rev=ctx_rev,
+                repository_clone_url=repository_clone_url,
+                status=install_model.ToolShedRepository.installation_status.NEW,
+                metadata_dict={},
+                current_changeset_revision=None,
+                owner=owner,
+                dist_to_shed=False,
+            )
         return repository
 
     def get_repository_dependencies_for_installed_tool_shed_repository(self, app, repository):
@@ -309,26 +374,34 @@ class RepositoryDependencyInstallManager:
         for the received repository which is installed into Galaxy.  This method is called only from Galaxy.
         """
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed))
-        params = dict(name=str(repository.name),
-                      owner=str(repository.owner),
-                      changeset_revision=str(repository.changeset_revision))
-        pathspec = ['repository', 'get_repository_dependencies']
+        params = dict(
+            name=str(repository.name),
+            owner=str(repository.owner),
+            changeset_revision=str(repository.changeset_revision),
+        )
+        pathspec = ["repository", "get_repository_dependencies"]
         try:
-            raw_text = url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+            raw_text = url_get(
+                tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+            )
         except Exception:
-            log.exception("Error while trying to get URL: %s", build_url(tool_shed_url, pathspec=pathspec, params=params))
-            return ''
+            log.exception(
+                "Error while trying to get URL: %s", build_url(tool_shed_url, pathspec=pathspec, params=params)
+            )
+            return ""
         if len(raw_text) > 2:
             encoded_text = json.loads(raw_text)
             text = encoding_util.tool_shed_decode(encoded_text)
         else:
-            text = ''
+            text = ""
         return text
 
     def get_repository_dependency_by_repository_id(self, install_model, decoded_repository_id):
-        return install_model.context.query(install_model.RepositoryDependency) \
-                                    .filter(install_model.RepositoryDependency.table.c.tool_shed_repository_id == decoded_repository_id) \
-                                    .first()
+        return (
+            install_model.context.query(install_model.RepositoryDependency)
+            .filter(install_model.RepositoryDependency.table.c.tool_shed_repository_id == decoded_repository_id)
+            .first()
+        )
 
     def get_required_repo_info_dicts(self, tool_shed_url, repo_info_dicts):
         """
@@ -347,17 +420,18 @@ class RepositoryDependencyInstallManager:
                 if repo_info_dict not in all_repo_info_dicts:
                     all_repo_info_dicts.append(repo_info_dict)
                 for repository_name, repo_info_tup in repo_info_dict.items():
-                    description, \
-                        repository_clone_url, \
-                        changeset_revision, \
-                        ctx_rev, \
-                        repository_owner, \
-                        repository_dependencies, \
-                        tool_dependencies = \
-                        repository_util.get_repo_info_tuple_contents(repo_info_tup)
+                    (
+                        description,
+                        repository_clone_url,
+                        changeset_revision,
+                        ctx_rev,
+                        repository_owner,
+                        repository_dependencies,
+                        tool_dependencies,
+                    ) = repository_util.get_repo_info_tuple_contents(repo_info_tup)
                     if repository_dependencies:
                         for key, val in repository_dependencies.items():
-                            if key in ['root_key', 'description']:
+                            if key in ["root_key", "description"]:
                                 continue
                             repository_components_tuple = get_components_from_key(key)
                             components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
@@ -366,11 +440,11 @@ class RepositoryDependencyInstallManager:
                             # a dependency of the dependent repository's contained tool dependency, and only if that
                             # tool dependency requires compilation.
                             # For backward compatibility to the 12/20/12 Galaxy release.
-                            only_if_compiling_contained_td = 'False'
+                            only_if_compiling_contained_td = "False"
                             if len(components_list) == 4:
-                                only_if_compiling_contained_td = 'False'
+                                only_if_compiling_contained_td = "False"
                             elif len(components_list) == 5:
-                                only_if_compiling_contained_td = 'False'
+                                only_if_compiling_contained_td = "False"
                             if not asbool(only_if_compiling_contained_td):
                                 if components_list not in required_repository_tups:
                                     required_repository_tups.append(components_list)
@@ -378,7 +452,7 @@ class RepositoryDependencyInstallManager:
                                 try:
                                     only_if_compiling_contained_td = components_list[5]
                                 except IndexError:
-                                    only_if_compiling_contained_td = 'False'
+                                    only_if_compiling_contained_td = "False"
                                 # Skip listing a repository dependency if it is required only to compile a tool dependency
                                 # defined for the dependent repository (see above comment).
                                 if not asbool(only_if_compiling_contained_td):
@@ -394,13 +468,15 @@ class RepositoryDependencyInstallManager:
                     for required_repository_tup in required_repository_tups:
                         # Convert every item in required_repository_tup to a string.
                         required_repository_tup = [str(item) for item in required_repository_tup]
-                        encoded_required_repository_tups.append(encoding_util.encoding_sep.join(required_repository_tup))
+                        encoded_required_repository_tups.append(
+                            encoding_util.encoding_sep.join(required_repository_tup)
+                        )
                     encoded_required_repository_str = encoding_util.encoding_sep2.join(encoded_required_repository_tups)
                     encoded_required_repository_str = encoding_util.tool_shed_encode(encoded_required_repository_str)
                     if repository_util.is_tool_shed_client(self.app):
                         # Handle secure / insecure Tool Shed URL protocol changes and port changes.
                         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
-                    pathspec = ['repository', 'get_required_repo_info_dict']
+                    pathspec = ["repository", "get_required_repo_info_dict"]
                     url = build_url(tool_shed_url, pathspec=pathspec)
                     # Fix for handling 307 redirect not being handled nicely by urlopen() when the Request() has data provided
                     try:
@@ -420,8 +496,8 @@ class RepositoryDependencyInstallManager:
                             return all_repo_info_dicts
                         required_repo_info_dicts = []
                         for k, v in required_repo_info_dict.items():
-                            if k == 'repo_info_dicts':
-                                encoded_dict_strings = required_repo_info_dict['repo_info_dicts']
+                            if k == "repo_info_dicts":
+                                encoded_dict_strings = required_repo_info_dict["repo_info_dicts"]
                                 for encoded_dict_str in encoded_dict_strings:
                                     decoded_dict = encoding_util.tool_shed_decode(encoded_dict_str)
                                     required_repo_info_dicts.append(decoded_dict)
@@ -460,7 +536,7 @@ class RepositoryDependencyInstallManager:
                                                         break
                                         if not is_present:
                                             all_repo_info_dicts.append(required_repo_info_dict)
-                        all_required_repo_info_dict['all_repo_info_dicts'] = all_repo_info_dicts
+                        all_required_repo_info_dict["all_repo_info_dicts"] = all_repo_info_dicts
         return all_required_repo_info_dict
 
     def is_in_repo_info_dicts(self, repo_info_dict, repo_info_dicts):
@@ -502,7 +578,7 @@ class RepositoryDependencyInstallManager:
 
 def _urlopen(url, data=None):
     scheme = urlparse(url).scheme
-    assert scheme in ('http', 'https', 'ftp'), f'Invalid URL scheme: {scheme}'
+    assert scheme in ("http", "https", "ftp"), f"Invalid URL scheme: {scheme}"
     if data is not None:
         data = smart_str(data)
     return urlopen(Request(url, data), timeout=DEFAULT_SOCKET_TIMEOUT)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/env_manager.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/env_manager.py
index d498592f451..15514739203 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/env_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/env_manager.py
@@ -8,29 +8,28 @@ log = logging.getLogger(__name__)
 
 
 class EnvManager:
-
     def __init__(self, app):
         self.app = app
 
     def create_env_var_dict(self, elem, install_environment):
-        env_var_name = elem.get('name', 'PATH')
-        env_var_action = elem.get('action', 'prepend_to')
+        env_var_name = elem.get("name", "PATH")
+        env_var_action = elem.get("action", "prepend_to")
         env_var_text = None
         tool_dependency_install_dir = install_environment.install_dir
         tool_shed_repository_install_dir = install_environment.tool_shed_repository_install_dir
-        if elem.text and elem.text.find('REPOSITORY_INSTALL_DIR') >= 0:
-            if tool_shed_repository_install_dir and elem.text.find('$REPOSITORY_INSTALL_DIR') != -1:
-                env_var_text = elem.text.replace('$REPOSITORY_INSTALL_DIR', tool_shed_repository_install_dir)
+        if elem.text and elem.text.find("REPOSITORY_INSTALL_DIR") >= 0:
+            if tool_shed_repository_install_dir and elem.text.find("$REPOSITORY_INSTALL_DIR") != -1:
+                env_var_text = elem.text.replace("$REPOSITORY_INSTALL_DIR", tool_shed_repository_install_dir)
                 return dict(name=env_var_name, action=env_var_action, value=env_var_text)
             else:
-                env_var_text = elem.text.replace('$REPOSITORY_INSTALL_DIR', tool_dependency_install_dir)
+                env_var_text = elem.text.replace("$REPOSITORY_INSTALL_DIR", tool_dependency_install_dir)
                 return dict(name=env_var_name, action=env_var_action, value=env_var_text)
-        if elem.text and elem.text.find('INSTALL_DIR') >= 0:
+        if elem.text and elem.text.find("INSTALL_DIR") >= 0:
             if tool_dependency_install_dir:
-                env_var_text = elem.text.replace('$INSTALL_DIR', tool_dependency_install_dir)
+                env_var_text = elem.text.replace("$INSTALL_DIR", tool_dependency_install_dir)
                 return dict(name=env_var_name, action=env_var_action, value=env_var_text)
             else:
-                env_var_text = elem.text.replace('$INSTALL_DIR', tool_shed_repository_install_dir)
+                env_var_text = elem.text.replace("$INSTALL_DIR", tool_shed_repository_install_dir)
                 return dict(name=env_var_name, action=env_var_action, value=env_var_text)
         # Allow for environment variables that contain neither REPOSITORY_INSTALL_DIR nor INSTALL_DIR
         # since there may be command line parameters that are tuned for a Galaxy instance.  Allowing them
@@ -42,11 +41,11 @@ class EnvManager:
         if elem.text is None:
             # Also allow for an empty value for the environment variable, which
             # may makes sense especially for the 'set_to' action
-            elem.text = ''
+            elem.text = ""
         return dict(name=env_var_name, action=env_var_action, value=elem.text)
 
     def get_env_shell_file_path(self, installation_directory):
-        env_shell_file_name = 'env.sh'
+        env_shell_file_name = "env.sh"
         default_location = os.path.abspath(os.path.join(installation_directory, env_shell_file_name))
         if os.path.exists(default_location):
             return default_location
@@ -62,30 +61,30 @@ class EnvManager:
         #        <package name="numpy" version="1.7.1" />
         #    </repository>
         env_shell_file_paths = []
-        toolshed = elem.get('toolshed', None)
-        repository_name = elem.get('name', None)
-        repository_owner = elem.get('owner', None)
-        changeset_revision = elem.get('changeset_revision', None)
+        toolshed = elem.get("toolshed", None)
+        repository_name = elem.get("name", None)
+        repository_owner = elem.get("owner", None)
+        changeset_revision = elem.get("changeset_revision", None)
         if toolshed and repository_name and repository_owner and changeset_revision:
             # The protocol is not stored, but the port is if it exists.
             toolshed = remove_protocol_from_tool_shed_url(toolshed)
-            repository = get_repository_for_dependency_relationship(self.app,
-                                                                    toolshed,
-                                                                    repository_name,
-                                                                    repository_owner,
-                                                                    changeset_revision)
+            repository = get_repository_for_dependency_relationship(
+                self.app, toolshed, repository_name, repository_owner, changeset_revision
+            )
             if repository:
                 for sub_elem in elem:
                     tool_dependency_type = sub_elem.tag
-                    tool_dependency_name = sub_elem.get('name')
-                    tool_dependency_version = sub_elem.get('version')
+                    tool_dependency_name = sub_elem.get("name")
+                    tool_dependency_version = sub_elem.get("version")
                     if tool_dependency_type and tool_dependency_name and tool_dependency_version:
                         # Get the tool_dependency so we can get its installation directory.
                         tool_dependency = None
                         for tool_dependency in repository.tool_dependencies:
-                            if tool_dependency.type == tool_dependency_type and \
-                                    tool_dependency.name == tool_dependency_name and \
-                                    tool_dependency.version == tool_dependency_version:
+                            if (
+                                tool_dependency.type == tool_dependency_type
+                                and tool_dependency.name == tool_dependency_name
+                                and tool_dependency.version == tool_dependency_version
+                            ):
                                 break
                         if tool_dependency:
                             installation_directory = tool_dependency.installation_directory(self.app)
@@ -94,29 +93,48 @@ class EnvManager:
                                 env_shell_file_paths.append(env_shell_file_path)
                             else:
                                 error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency "
-                                error_message += "type %s, name %s, version %s for repository %s" % \
-                                    (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version), str(repository.name))
+                                error_message += "type %s, name %s, version %s for repository %s" % (
+                                    str(tool_dependency_type),
+                                    str(tool_dependency_name),
+                                    str(tool_dependency_version),
+                                    str(repository.name),
+                                )
                                 log.debug(error_message)
                                 continue
                         else:
-                            error_message = "Skipping tool dependency definition because unable to locate tool dependency "
-                            error_message += "type %s, name %s, version %s for repository %s" % \
-                                (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version), str(repository.name))
+                            error_message = (
+                                "Skipping tool dependency definition because unable to locate tool dependency "
+                            )
+                            error_message += "type %s, name %s, version %s for repository %s" % (
+                                str(tool_dependency_type),
+                                str(tool_dependency_name),
+                                str(tool_dependency_version),
+                                str(repository.name),
+                            )
                             log.debug(error_message)
                             continue
                     else:
-                        error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % \
-                            (str(tool_dependency_type), str(tool_dependency_name), str(tool_dependency_version))
+                        error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % (
+                            str(tool_dependency_type),
+                            str(tool_dependency_name),
+                            str(tool_dependency_version),
+                        )
                         log.debug(error_message)
                         continue
             else:
                 error_message = "Skipping set_environment_for_install definition because unable to locate required installed tool shed repository: "
-                error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % \
-                    (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision))
+                error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % (
+                    str(toolshed),
+                    str(repository_name),
+                    str(repository_owner),
+                    str(changeset_revision),
+                )
                 log.debug(error_message)
         else:
-            error_message = "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s." % \
-                (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision))
+            error_message = (
+                "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s."
+                % (str(toolshed), str(repository_name), str(repository_owner), str(changeset_revision))
+            )
             log.debug(error_message)
         return env_shell_file_paths
 
@@ -139,10 +157,10 @@ class EnvManager:
         #     <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
         # </action>
         for action_elem in elem:
-            if action_elem.tag == 'repository':
+            if action_elem.tag == "repository":
                 env_shell_file_paths = self.get_env_shell_file_paths(action_elem)
                 all_env_shell_file_paths.extend(env_shell_file_paths)
         if all_env_shell_file_paths:
-            action_dict['env_shell_file_paths'] = all_env_shell_file_paths
-            action_dict['action_shell_file_paths'] = all_env_shell_file_paths
+            action_dict["env_shell_file_paths"] = all_env_shell_file_paths
+            action_dict["action_shell_file_paths"] = all_env_shell_file_paths
         return action_dict
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
index eff83c4d2d7..5e1d8c73127 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
@@ -22,7 +22,7 @@ class AsynchronousReader(threading.Thread):
         """Read lines and put them on the queue."""
         thread_lock = threading.Lock()
         thread_lock.acquire()
-        for line in iter(self._fd.readline, b''):
+        for line in iter(self._fd.readline, b""):
             stripped_line = unicodify(line).rstrip()
             self.lines.append(stripped_line)
             self._queue.put(stripped_line)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
index 96618935da9..f85cd23ecf5 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
@@ -2,12 +2,10 @@ import logging
 import os
 import stat
 
-
 log = logging.getLogger(__name__)
 
 
 class EnvFileBuilder:
-
     def __init__(self, install_dir):
         self.install_dir = install_dir
         self.return_code = 0
@@ -21,22 +19,22 @@ class EnvFileBuilder:
 
     @staticmethod
     def create_or_update_env_shell_file(install_dir, env_var_dict):
-        env_var_action = env_var_dict['action']
-        env_var_value = env_var_dict['value']
-        if env_var_action in ['prepend_to', 'set_to', 'append_to']:
-            env_var_name = env_var_dict['name']
-            if env_var_action == 'prepend_to':
-                changed_value = f'{env_var_value}:${env_var_name}'
-            elif env_var_action == 'set_to':
-                changed_value = f'{env_var_value}'
-            elif env_var_action == 'append_to':
-                changed_value = f'${env_var_name}:{env_var_value}'
+        env_var_action = env_var_dict["action"]
+        env_var_value = env_var_dict["value"]
+        if env_var_action in ["prepend_to", "set_to", "append_to"]:
+            env_var_name = env_var_dict["name"]
+            if env_var_action == "prepend_to":
+                changed_value = f"{env_var_value}:${env_var_name}"
+            elif env_var_action == "set_to":
+                changed_value = f"{env_var_value}"
+            elif env_var_action == "append_to":
+                changed_value = f"${env_var_name}:{env_var_value}"
             line = f"{env_var_name}={changed_value}; export {env_var_name}"
         elif env_var_action == "source":
             line = f"if [ -f {env_var_value} ] ; then . {env_var_value} ; fi"
         else:
             raise Exception(f"Unknown shell file action {env_var_action}")
-        env_shell_file_path = os.path.join(install_dir, 'env.sh')
+        env_shell_file_path = os.path.join(install_dir, "env.sh")
         return line, env_shell_file_path
 
     def file_append(self, text, file_path, make_executable=True):
@@ -66,7 +64,7 @@ class EnvFileBuilder:
                 log.exception(str(e))
                 return 1
         else:
-            env_file_handle = open(file_path, 'w')
+            env_file_handle = open(file_path, "w")
             env_file_handle.close()
             env_file_contents = []
         if make_executable:
@@ -84,13 +82,13 @@ class EnvFileBuilder:
             if line and line not in env_file_contents:
                 env_file_contents.append(line)
         try:
-            open(file_path, 'w').write('\n'.join(env_file_contents))
+            open(file_path, "w").write("\n".join(env_file_contents))
         except Exception as e:
             log.exception(str(e))
             return 1
         return 0
 
     def handle_action_shell_file_paths(self, action_dict):
-        shell_file_paths = action_dict.get('action_shell_file_paths', [])
+        shell_file_paths = action_dict.get("action_shell_file_paths", [])
         for shell_file_path in shell_file_paths:
             self.append_line(action="source", value=shell_file_path)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
index 03f1baebf64..6525e57ac2f 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
@@ -47,29 +47,29 @@ class InstallEnvironment:
         for path in paths:
             self.env_shell_file_paths.append(str(path))
 
-    def build_command(self, command, action_type='shell_command'):
+    def build_command(self, command, action_type="shell_command"):
         """
         Build command line for execution from simple command, but
         configuring environment described by this object.
         """
         env_cmds = self.environment_commands(action_type)
-        return '\n'.join(env_cmds + [command])
+        return "\n".join(env_cmds + [command])
 
     def close_file_descriptor(self, fd):
         """Attempt to close a file descriptor."""
         start_timer = time.time()
-        error = ''
+        error = ""
         while True:
             try:
                 fd.close()
                 break
             except OSError as e:
                 # Undoubtedly close() was called during a concurrent operation on the same file object.
-                log.debug(f'Error closing file descriptor: {str(e)}')
-                time.sleep(.5)
+                log.debug(f"Error closing file descriptor: {str(e)}")
+                time.sleep(0.5)
                 current_wait_time = time.time() - start_timer
                 if current_wait_time >= 600:
-                    error = f'Error closing file descriptor: {str(e)}'
+                    error = f"Error closing file descriptor: {str(e)}"
                     break
         return error
 
@@ -79,14 +79,14 @@ class InstallEnvironment:
         is printed and saved to that thread's queue. The calling thread can then retrieve the data using
         thread.stdout and thread.stderr.
         """
-        stdout_logger = logging.getLogger('install_environment.STDOUT')
-        stderr_logger = logging.getLogger('install_environment.STDERR')
-        for line in iter(stdout.readline, b''):
+        stdout_logger = logging.getLogger("install_environment.STDOUT")
+        stderr_logger = logging.getLogger("install_environment.STDERR")
+        for line in iter(stdout.readline, b""):
             output = unicodify(line).rstrip()
             stdout_logger.debug(output)
             stdout_queue.put(output)
         stdout_queue.put(None)
-        for line in iter(stderr.readline, b''):
+        for line in iter(stderr.readline, b""):
             output = unicodify(line).rstrip()
             stderr_logger.debug(output)
             stderr_queue.put(output)
@@ -98,21 +98,21 @@ class InstallEnvironment:
         for env_shell_file_path in self.env_shell_file_paths:
             if os.path.exists(env_shell_file_path):
                 for env_setting in open(env_shell_file_path):
-                    cmds.append(env_setting.strip('\n'))
+                    cmds.append(env_setting.strip("\n"))
             else:
-                log.debug(f'Invalid file {str(env_shell_file_path)} specified, ignoring {str(action_type)} action.')
+                log.debug(f"Invalid file {str(env_shell_file_path)} specified, ignoring {str(action_type)} action.")
         return cmds
 
-    def environment_dict(self, action_type='template_command'):
+    def environment_dict(self, action_type="template_command"):
         env_vars = dict()
         for env_shell_file_path in self.env_shell_file_paths:
             if os.path.exists(env_shell_file_path):
                 for env_setting in open(env_shell_file_path):
-                    env_string = env_setting.split(';')[0]
-                    env_name, env_path = env_string.split('=')
+                    env_string = env_setting.split(";")[0]
+                    env_name, env_path = env_string.split("=")
                     env_vars[env_name] = env_path
             else:
-                log.debug(f'Invalid file {str(env_shell_file_path)} specified, ignoring template_command action.')
+                log.debug(f"Invalid file {str(env_shell_file_path)} specified, ignoring template_command action.")
         return env_vars
 
     def handle_command(self, tool_dependency, cmd, return_output=False, job_name=""):
@@ -123,11 +123,19 @@ class InstallEnvironment:
         stdout = output.stdout
         stderr = output.stderr
         if len(stdout) > DATABASE_MAX_STRING_SIZE:
-            log.warning(f"Length of stdout > {str(DATABASE_MAX_STRING_SIZE_PRETTY)}, so only a portion will be saved in the database.")
-            stdout = shrink_string_by_size(stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
+            log.warning(
+                f"Length of stdout > {str(DATABASE_MAX_STRING_SIZE_PRETTY)}, so only a portion will be saved in the database."
+            )
+            stdout = shrink_string_by_size(
+                stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True
+            )
         if len(stderr) > DATABASE_MAX_STRING_SIZE:
-            log.warning(f"Length of stderr > {str(DATABASE_MAX_STRING_SIZE_PRETTY)}, so only a portion will be saved in the database.")
-            stderr = shrink_string_by_size(stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
+            log.warning(
+                f"Length of stderr > {str(DATABASE_MAX_STRING_SIZE_PRETTY)}, so only a portion will be saved in the database."
+            )
+            stderr = shrink_string_by_size(
+                stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True
+            )
         if output.return_code not in [0]:
             status = self.app.install_model.ToolDependency.installation_status.ERROR
             if stderr:
@@ -136,12 +144,13 @@ class InstallEnvironment:
                 error_message = unicodify(stdout)
             else:
                 # We have a problem if there was no stdout and no stderr.
-                error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \
-                    (str(cmd), str(output.return_code))
-            set_tool_dependency_attributes(self.app,
-                                           tool_dependency=tool_dependency,
-                                           status=status,
-                                           error_message=error_message)
+                error_message = "Unknown error occurred executing shell command %s, return_code: %s" % (
+                    str(cmd),
+                    str(output.return_code),
+                )
+            set_tool_dependency_attributes(
+                self.app, tool_dependency=tool_dependency, status=status, error_message=error_message
+            )
         if return_output:
             return output
         return output.return_code
@@ -164,13 +173,15 @@ class InstallEnvironment:
         # Print the command we're about to execute, ``set -x`` style.
         llog.debug(f"+ {str(command)}")
         # Launch the command as subprocess.  A bufsize of 1 means line buffered.
-        process_handle = subprocess.Popen(str(command),
-                                          stdout=subprocess.PIPE,
-                                          stderr=subprocess.PIPE,
-                                          bufsize=1,
-                                          close_fds=False,
-                                          shell=True,
-                                          cwd=state.env['lcwd'])
+        process_handle = subprocess.Popen(
+            str(command),
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            bufsize=1,
+            close_fds=False,
+            shell=True,
+            cwd=state.env["lcwd"],
+        )
         pid = process_handle.pid
         # Launch the asynchronous readers of the process' stdout and stderr.
         stdout_queue = queue.Queue()
@@ -181,11 +192,9 @@ class InstallEnvironment:
         stderr_reader.start()
         # Place streamed stdout and stderr into a threaded IPC queue target so it can
         # be printed and stored for later retrieval when generating the INSTALLATION.log.
-        stdio_thread = threading.Thread(target=self.enqueue_output,
-                                        args=(process_handle.stdout,
-                                              stdout_queue,
-                                              process_handle.stderr,
-                                              stderr_queue))
+        stdio_thread = threading.Thread(
+            target=self.enqueue_output, args=(process_handle.stdout, stdout_queue, process_handle.stderr, stderr_queue)
+        )
         thread_lock = threading.Lock()
         thread_lock.acquire()
         stdio_thread.start()
@@ -218,11 +227,13 @@ class InstallEnvironment:
                     stderr_queue.task_done()
                     break
             # Sleep a bit before asking the readers again.
-            time.sleep(.1)
+            time.sleep(0.1)
             current_wait_time = time.time() - start_timer
             if stdout_queue.empty() and stderr_queue.empty() and current_wait_time > NO_OUTPUT_TIMEOUT:
-                err_msg = "\nShutting down process id %s because it generated no output for the defined timeout period of %.1f seconds.\n" % \
-                          (pid, NO_OUTPUT_TIMEOUT)
+                err_msg = (
+                    "\nShutting down process id %s because it generated no output for the defined timeout period of %.1f seconds.\n"
+                    % (pid, NO_OUTPUT_TIMEOUT)
+                )
                 stderr_reader.lines.append(err_msg)
                 process_handle.kill()
                 break
@@ -235,8 +246,8 @@ class InstallEnvironment:
         # Close subprocess' file descriptors.
         self.close_file_descriptor(process_handle.stdout)
         self.close_file_descriptor(process_handle.stderr)
-        stdout = '\n'.join(stdout_reader.lines)
-        stderr = '\n'.join(stderr_reader.lines)
+        stdout = "\n".join(stdout_reader.lines)
+        stderr = "\n".join(stderr_reader.lines)
         # Handle error condition (deal with stdout being None, too)
         output = _AttributeString(stdout.strip() if stdout else "")
         errors = _AttributeString(stderr.strip() if stderr else "")
@@ -248,16 +259,16 @@ class InstallEnvironment:
 
     def log_results(self, command, fabric_AttributeString, file_path):
         """Write attributes of fabric.operations._AttributeString to a specified log file."""
-        mode = 'a' if os.path.exists(file_path) else 'w'
+        mode = "a" if os.path.exists(file_path) else "w"
         with open(file_path, mode) as logfile:
             logfile.write("\n#############################################\n")
             logfile.write(command)
-            logfile.write('\nSTDOUT\n')
+            logfile.write("\nSTDOUT\n")
             logfile.write(fabric_AttributeString.stdout)
             logfile.write("\n#############################################\n")
             logfile.write("\n#############################################\n")
             logfile.write(command)
-            logfile.write('\nSTDERR\n')
+            logfile.write("\nSTDERR\n")
             logfile.write(fabric_AttributeString.stderr)
             logfile.write("\n#############################################\n")
 
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
index 07e0607ca20..40d2a708418 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
@@ -1,13 +1,14 @@
 import logging
 
-from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe import step_handler
-from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe import tag_handler
+from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe import (
+    step_handler,
+    tag_handler,
+)
 
 log = logging.getLogger(__name__)
 
 
 class StepManager:
-
     def __init__(self, app):
         self.app = app
         self.step_handlers_by_type = self.load_step_handlers()
@@ -15,68 +16,87 @@ class StepManager:
     def get_step_handler_by_type(self, type):
         return self.step_handlers_by_type.get(type, None)
 
-    def execute_step(self, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions,
-                     env_file_builder, install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_type,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         if actions:
             step_handler = self.get_step_handler_by_type(action_type)
-            tool_dependency, filtered_actions, dir = step_handler.execute_step(tool_dependency=tool_dependency,
-                                                                               package_name=package_name,
-                                                                               actions=actions,
-                                                                               action_dict=action_dict,
-                                                                               filtered_actions=filtered_actions,
-                                                                               env_file_builder=env_file_builder,
-                                                                               install_environment=install_environment,
-                                                                               work_dir=work_dir,
-                                                                               current_dir=current_dir,
-                                                                               initial_download=initial_download)
+            tool_dependency, filtered_actions, dir = step_handler.execute_step(
+                tool_dependency=tool_dependency,
+                package_name=package_name,
+                actions=actions,
+                action_dict=action_dict,
+                filtered_actions=filtered_actions,
+                env_file_builder=env_file_builder,
+                install_environment=install_environment,
+                work_dir=work_dir,
+                current_dir=current_dir,
+                initial_download=initial_download,
+            )
         else:
             dir = None
         return tool_dependency, filtered_actions, dir
 
     def load_step_handlers(self):
-        step_handlers_by_type = dict(assert_directory_executable=step_handler.AssertDirectoryExecutable(self.app),
-                                     assert_directory_exists=step_handler.AssertDirectoryExists(self.app),
-                                     assert_file_executable=step_handler.AssertFileExecutable(self.app),
-                                     assert_file_exists=step_handler.AssertFileExists(self.app),
-                                     autoconf=step_handler.Autoconf(self.app),
-                                     change_directory=step_handler.ChangeDirectory(self.app),
-                                     chmod=step_handler.Chmod(self.app),
-                                     download_binary=step_handler.DownloadBinary(self.app),
-                                     download_by_url=step_handler.DownloadByUrl(self.app),
-                                     download_file=step_handler.DownloadFile(self.app),
-                                     make_directory=step_handler.MakeDirectory(self.app),
-                                     make_install=step_handler.MakeInstall(self.app),
-                                     move_directory_files=step_handler.MoveDirectoryFiles(self.app),
-                                     move_file=step_handler.MoveFile(self.app),
-                                     regex_replace=step_handler.RegexReplace(self.app),
-                                     set_environment=step_handler.SetEnvironment(self.app),
-                                     set_environment_for_install=step_handler.SetEnvironmentForInstall(self.app),
-                                     setup_perl_environment=step_handler.SetupPerlEnvironment(self.app),
-                                     setup_r_environment=step_handler.SetupREnvironment(self.app),
-                                     setup_ruby_environment=step_handler.SetupRubyEnvironment(self.app),
-                                     setup_python_environment=step_handler.SetupPythonEnvironment(self.app),
-                                     setup_virtualenv=step_handler.SetupVirtualEnv(self.app),
-                                     shell_command=step_handler.ShellCommand(self.app),
-                                     template_command=step_handler.TemplateCommand(self.app))
+        step_handlers_by_type = dict(
+            assert_directory_executable=step_handler.AssertDirectoryExecutable(self.app),
+            assert_directory_exists=step_handler.AssertDirectoryExists(self.app),
+            assert_file_executable=step_handler.AssertFileExecutable(self.app),
+            assert_file_exists=step_handler.AssertFileExists(self.app),
+            autoconf=step_handler.Autoconf(self.app),
+            change_directory=step_handler.ChangeDirectory(self.app),
+            chmod=step_handler.Chmod(self.app),
+            download_binary=step_handler.DownloadBinary(self.app),
+            download_by_url=step_handler.DownloadByUrl(self.app),
+            download_file=step_handler.DownloadFile(self.app),
+            make_directory=step_handler.MakeDirectory(self.app),
+            make_install=step_handler.MakeInstall(self.app),
+            move_directory_files=step_handler.MoveDirectoryFiles(self.app),
+            move_file=step_handler.MoveFile(self.app),
+            regex_replace=step_handler.RegexReplace(self.app),
+            set_environment=step_handler.SetEnvironment(self.app),
+            set_environment_for_install=step_handler.SetEnvironmentForInstall(self.app),
+            setup_perl_environment=step_handler.SetupPerlEnvironment(self.app),
+            setup_r_environment=step_handler.SetupREnvironment(self.app),
+            setup_ruby_environment=step_handler.SetupRubyEnvironment(self.app),
+            setup_python_environment=step_handler.SetupPythonEnvironment(self.app),
+            setup_virtualenv=step_handler.SetupVirtualEnv(self.app),
+            shell_command=step_handler.ShellCommand(self.app),
+            template_command=step_handler.TemplateCommand(self.app),
+        )
         return step_handlers_by_type
 
-    def prepare_step(self, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download):
+    def prepare_step(
+        self, tool_dependency, action_type, action_elem, action_dict, install_environment, is_binary_download
+    ):
         """
         Prepare the recipe step for later execution.  This generally alters the received action_dict
         with new information needed during this step's execution.
         """
         if action_elem is not None:
             step_handler = self.get_step_handler_by_type(action_type)
-            action_dict = step_handler.prepare_step(tool_dependency=tool_dependency,
-                                                    action_elem=action_elem,
-                                                    action_dict=action_dict,
-                                                    install_environment=install_environment,
-                                                    is_binary_download=is_binary_download)
+            action_dict = step_handler.prepare_step(
+                tool_dependency=tool_dependency,
+                action_elem=action_elem,
+                action_dict=action_dict,
+                install_environment=install_environment,
+                is_binary_download=is_binary_download,
+            )
         return action_dict
 
 
 class TagManager:
-
     def __init__(self, app):
         self.app = app
         self.tag_handlers = self.load_tag_handlers()
@@ -84,23 +104,33 @@ class TagManager:
     def get_tag_handler_by_tag(self, tag):
         return self.tag_handlers.get(tag, None)
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         tag_handler = self.get_tag_handler_by_tag(package_elem.tag)
-        tool_dependency, proceed_with_install, action_elem_tuples = \
-            tag_handler.process_tag_set(tool_shed_repository,
-                                        tool_dependency,
-                                        package_elem,
-                                        package_name,
-                                        package_version,
-                                        tool_dependency_db_records=tool_dependency_db_records)
+        tool_dependency, proceed_with_install, action_elem_tuples = tag_handler.process_tag_set(
+            tool_shed_repository,
+            tool_dependency,
+            package_elem,
+            package_name,
+            package_version,
+            tool_dependency_db_records=tool_dependency_db_records,
+        )
         return tool_dependency, proceed_with_install, action_elem_tuples
 
     def load_tag_handlers(self):
-        tag_handlers = dict(environment_variable=tag_handler.SetEnvironment(self.app),
-                            install=tag_handler.Install(self.app),
-                            package=tag_handler.Package(self.app),
-                            readme=tag_handler.ReadMe(self.app),
-                            repository=tag_handler.Repository(self.app),
-                            set_environment=tag_handler.SetEnvironment(self.app))
+        tag_handlers = dict(
+            environment_variable=tag_handler.SetEnvironment(self.app),
+            install=tag_handler.Install(self.app),
+            package=tag_handler.Package(self.app),
+            readme=tag_handler.ReadMe(self.app),
+            repository=tag_handler.Repository(self.app),
+            set_environment=tag_handler.SetEnvironment(self.app),
+        )
         return tag_handlers
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index ad04c547ac8..51f5eeebee9 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -10,24 +10,29 @@ import zipfile
 from string import Template
 
 # TODO: eliminate the use of fabric here.
-from fabric.api import lcd, settings
+from fabric.api import (
+    lcd,
+    settings,
+)
 
 from galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
-from galaxy.tool_shed.util import basic_util, tool_dependency_util
+from galaxy.tool_shed.util import (
+    basic_util,
+    tool_dependency_util,
+)
 from galaxy.util import (
     asbool,
-    download_to_file
+    download_to_file,
 )
 from galaxy.util.compression_utils import CompressedFile
 from galaxy.util.template import fill_template
 
 log = logging.getLogger(__name__)
 
-VIRTUALENV_URL = 'https://pypi.python.org/packages/d4/0c/9840c08189e030873387a73b90ada981885010dd9aea134d6de30cd24cb8/virtualenv-15.1.0.tar.gz'
+VIRTUALENV_URL = "https://pypi.python.org/packages/d4/0c/9840c08189e030873387a73b90ada981885010dd9aea134d6de30cd24cb8/virtualenv-15.1.0.tar.gz"
 
 
 class Download:
-
     def url_download(self, install_dir, downloaded_file_name, download_url, extract=True, checksums=None):
         """
         The given download_url can have an extension like #md5#, #sha256#, (or #md5= to support pypi defaults).
@@ -43,41 +48,45 @@ class Download:
         checksums = checksums or {}
         file_path = os.path.join(install_dir, downloaded_file_name)
         if download_url.startswith("file://"):
-            local_file_source = download_url[len('file://'):].split('#')[0]
+            local_file_source = download_url[len("file://") :].split("#")[0]
             shutil.copyfile(local_file_source, file_path)
         else:
             try:
                 download_to_file(download_url, file_path, chunk_size=basic_util.CHUNK_SIZE)
             except Exception as e:
-                err_msg = f'Error downloading from URL {str(download_url)} : {str(e)}'
+                err_msg = f"Error downloading from URL {str(download_url)} : {str(e)}"
                 raise Exception(err_msg)
 
-        if 'sha256sum' in checksums or '#sha256#' in download_url:
-            downloaded_checksum = hashlib.sha256(open(file_path, 'rb').read()).hexdigest().lower()
+        if "sha256sum" in checksums or "#sha256#" in download_url:
+            downloaded_checksum = hashlib.sha256(open(file_path, "rb").read()).hexdigest().lower()
 
             # Determine expected value
-            if 'sha256sum' in checksums:
-                expected = checksums['sha256sum'].lower()
+            if "sha256sum" in checksums:
+                expected = checksums["sha256sum"].lower()
             else:
-                expected = download_url.split('#sha256#')[1].lower()
+                expected = download_url.split("#sha256#")[1].lower()
 
             if downloaded_checksum != expected:
-                raise Exception(f'Given sha256 checksum does not match with the one from the downloaded file ({downloaded_checksum} != {expected}).')
+                raise Exception(
+                    f"Given sha256 checksum does not match with the one from the downloaded file ({downloaded_checksum} != {expected})."
+                )
 
-        if 'md5sum' in checksums or '#md5#' in download_url or '#md5=' in download_url:
-            downloaded_checksum = hashlib.md5(open(file_path, 'rb').read()).hexdigest().lower()
+        if "md5sum" in checksums or "#md5#" in download_url or "#md5=" in download_url:
+            downloaded_checksum = hashlib.md5(open(file_path, "rb").read()).hexdigest().lower()
 
             # Determine expected value
-            if 'md5sum' in checksums:
-                expected = checksums['md5sum'].lower()
+            if "md5sum" in checksums:
+                expected = checksums["md5sum"].lower()
             else:
-                expected = re.split('#md5[#=]', download_url)[1].lower()
+                expected = re.split("#md5[#=]", download_url)[1].lower()
 
             if downloaded_checksum != expected:
-                raise Exception(f'Given md5 checksum does not match with the one from the downloaded file ({downloaded_checksum} != {expected}).')
+                raise Exception(
+                    f"Given md5 checksum does not match with the one from the downloaded file ({downloaded_checksum} != {expected})."
+                )
 
         if extract:
-            if tarfile.is_tarfile(file_path) or (zipfile.is_zipfile(file_path) and not file_path.endswith('.jar')):
+            if tarfile.is_tarfile(file_path) or (zipfile.is_zipfile(file_path) and not file_path.endswith(".jar")):
                 archive = CompressedFile(file_path)
                 extraction_path = archive.extract(install_dir)
             else:
@@ -89,20 +98,31 @@ class Download:
 
     def get_elem_checksums(self, elem):
         rval = {}
-        for hash_type in ('md5sum', 'sha256sum'):
+        for hash_type in ("md5sum", "sha256sum"):
             if hash_type in elem.keys():
                 rval[hash_type] = elem.get(hash_type).lower()
         return rval
 
     def get_dict_checksums(self, dct):
-        return dict(i for i in dct.items() if i[0] in ['md5sum', 'sha256sum'])
+        return dict(i for i in dct.items() if i[0] in ["md5sum", "sha256sum"])
 
 
 class RecipeStep:
     """Abstract class that defines a standard format for handling recipe steps when installing packages."""
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         raise Exception("Unimplemented Method")
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
@@ -110,10 +130,9 @@ class RecipeStep:
 
 
 class AssertDirectoryExecutable(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'assert_directory_executable'
+        self.type = "assert_directory_executable"
 
     def assert_directory_executable(self, full_path):
         """
@@ -131,38 +150,47 @@ class AssertDirectoryExecutable(RecipeStep):
                 return True
         return False
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Make sure a symbolic link or directory on disk exists and is executable, but is not a file.
         Since this class is not used in the initial download stage, no recipe step filtering is
         performed here, and None values are always returned for filtered_actions and dir.
         """
-        if os.path.isabs(action_dict['full_path']):
-            full_path = action_dict['full_path']
+        if os.path.isabs(action_dict["full_path"]):
+            full_path = action_dict["full_path"]
         else:
-            full_path = os.path.join(current_dir, action_dict['full_path'])
+            full_path = os.path.join(current_dir, action_dict["full_path"])
         if not self.assert_directory_executable(full_path=full_path):
             status = self.app.install_model.ToolDependency.installation_status.ERROR
-            error_message = f'The path {str(full_path)} is not a directory or is not executable by the owner.'
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency,
-                                                                                  status=status,
-                                                                                  error_message=error_message)
+            error_message = f"The path {str(full_path)} is not a directory or is not executable by the owner."
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app, tool_dependency, status=status, error_message=error_message
+            )
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="assert_executable">$INSTALL_DIR/mira/my_file</action>
         if action_elem.text:
-            action_dict['full_path'] = basic_util.evaluate_template(action_elem.text, install_environment)
+            action_dict["full_path"] = basic_util.evaluate_template(action_elem.text, install_environment)
         return action_dict
 
 
 class AssertDirectoryExists(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'assert_directory_exists'
+        self.type = "assert_directory_exists"
 
     def assert_directory_exists(self, full_path):
         """
@@ -177,38 +205,47 @@ class AssertDirectoryExists(RecipeStep):
             return True
         return False
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Make sure a a symbolic link or directory on disk exists, but is not a file.  Since this
         class is not used in the initial download stage, no recipe step filtering is performed
         here, and None values are always returned for filtered_actions and dir.
         """
-        if os.path.isabs(action_dict['full_path']):
-            full_path = action_dict['full_path']
+        if os.path.isabs(action_dict["full_path"]):
+            full_path = action_dict["full_path"]
         else:
-            full_path = os.path.join(current_dir, action_dict['full_path'])
+            full_path = os.path.join(current_dir, action_dict["full_path"])
         if not self.assert_directory_exists(full_path=full_path):
             status = self.app.install_model.ToolDependency.installation_status.ERROR
-            error_message = f'The path {str(full_path)} is not a directory or does not exist.'
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency,
-                                                                                  status=status,
-                                                                                  error_message=error_message)
+            error_message = f"The path {str(full_path)} is not a directory or does not exist."
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app, tool_dependency, status=status, error_message=error_message
+            )
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="make_directory">$INSTALL_DIR/mira</action>
         if action_elem.text:
-            action_dict['full_path'] = basic_util.evaluate_template(action_elem.text, install_environment)
+            action_dict["full_path"] = basic_util.evaluate_template(action_elem.text, install_environment)
         return action_dict
 
 
 class AssertFileExecutable(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'assert_file_executable'
+        self.type = "assert_file_executable"
 
     def assert_file_executable(self, full_path):
         """
@@ -226,38 +263,47 @@ class AssertFileExecutable(RecipeStep):
                 return True
         return False
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Make sure a symbolic link or file on disk exists and is executable, but is not a directory.
         Since this class is not used in the initial download stage, no recipe step filtering is
         performed here, and None values are always returned for filtered_actions and dir.
         """
-        if os.path.isabs(action_dict['full_path']):
-            full_path = action_dict['full_path']
+        if os.path.isabs(action_dict["full_path"]):
+            full_path = action_dict["full_path"]
         else:
-            full_path = os.path.join(current_dir, action_dict['full_path'])
+            full_path = os.path.join(current_dir, action_dict["full_path"])
         if not self.assert_file_executable(full_path=full_path):
             status = self.app.install_model.ToolDependency.installation_status.ERROR
-            error_message = f'The path {str(full_path)} is not a file or is not executable by the owner.'
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency,
-                                                                                  status=status,
-                                                                                  error_message=error_message)
+            error_message = f"The path {str(full_path)} is not a file or is not executable by the owner."
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app, tool_dependency, status=status, error_message=error_message
+            )
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="assert_executable">$INSTALL_DIR/mira/my_file</action>
         if action_elem.text:
-            action_dict['full_path'] = basic_util.evaluate_template(action_elem.text, install_environment)
+            action_dict["full_path"] = basic_util.evaluate_template(action_elem.text, install_environment)
         return action_dict
 
 
 class AssertFileExists(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'assert_file_exists'
+        self.type = "assert_file_exists"
 
     def assert_file_exists(self, full_path):
         """
@@ -272,57 +318,76 @@ class AssertFileExists(RecipeStep):
             return True
         return False
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Make sure a symbolic link or file on disk exists, but is not a directory.  Since this
         class is not used in the initial download stage, no recipe step filtering is performed
         here, and None values are always returned for filtered_actions and dir.
         """
-        if os.path.isabs(action_dict['full_path']):
-            full_path = action_dict['full_path']
+        if os.path.isabs(action_dict["full_path"]):
+            full_path = action_dict["full_path"]
         else:
-            full_path = os.path.join(current_dir, action_dict['full_path'])
+            full_path = os.path.join(current_dir, action_dict["full_path"])
         if not self.assert_file_exists(full_path=full_path):
             status = self.app.install_model.ToolDependency.installation_status.ERROR
-            error_message = f'The path {str(full_path)} is not a file or does not exist.'
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency,
-                                                                                  status=status,
-                                                                                  error_message=error_message)
+            error_message = f"The path {str(full_path)} is not a file or does not exist."
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app, tool_dependency, status=status, error_message=error_message
+            )
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="assert_on_path">$INSTALL_DIR/mira/my_file</action>
         if action_elem.text:
-            action_dict['full_path'] = basic_util.evaluate_template(action_elem.text, install_environment)
+            action_dict["full_path"] = basic_util.evaluate_template(action_elem.text, install_environment)
         return action_dict
 
 
 class Autoconf(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'autoconf'
+        self.type = "autoconf"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Handle configure, make and make install in a shell, allowing for configuration options.  Since this
         class is not used in the initial download stage, no recipe step filtering is performed here, and None
         values are always returned for filtered_actions and dir.
         """
         with settings(warn_only=True):
-            configure_opts = action_dict.get('configure_opts', '')
-            if 'prefix=' in configure_opts:
-                pre_cmd = f'./configure {configure_opts} && make && make install'
+            configure_opts = action_dict.get("configure_opts", "")
+            if "prefix=" in configure_opts:
+                pre_cmd = f"./configure {configure_opts} && make && make install"
             else:
-                pre_cmd = f'./configure --prefix=$INSTALL_DIR {configure_opts} && make && make install'
+                pre_cmd = f"./configure --prefix=$INSTALL_DIR {configure_opts} && make && make install"
             cmd = install_environment.build_command(basic_util.evaluate_template(pre_cmd, install_environment))
-            install_environment.handle_command(tool_dependency=tool_dependency,
-                                               cmd=cmd,
-                                               return_output=False,
-                                               job_name=package_name)
+            install_environment.handle_command(
+                tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+            )
             # The caller should check the status of the returned tool_dependency since this function
             # does nothing with the return_code.
             return tool_dependency, None, None
@@ -331,18 +396,28 @@ class Autoconf(RecipeStep):
         # Handle configure, make and make install allow providing configuration options
         if action_elem.text:
             configure_opts = basic_util.evaluate_template(action_elem.text, install_environment)
-            action_dict['configure_opts'] = configure_opts
+            action_dict["configure_opts"] = configure_opts
         return action_dict
 
 
 class ChangeDirectory(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'change_directory'
+        self.type = "change_directory"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Change the working directory in a shell.  Since this class is not used in the initial download stage,
         no recipe step filtering is performed here and a None value is return for filtered_actions.  However,
@@ -358,44 +433,57 @@ class ChangeDirectory(RecipeStep):
                     return True
             return False
 
-        target_dir = os.path.realpath(os.path.normpath(action_dict['directory']))
+        target_dir = os.path.realpath(os.path.normpath(action_dict["directory"]))
         if dir_valid(target_dir):
             # We have a directory that includes a path.
             dir = target_dir
         else:
-            target_dir = os.path.realpath(os.path.normpath(os.path.join(current_dir, action_dict['directory'])))
+            target_dir = os.path.realpath(os.path.normpath(os.path.join(current_dir, action_dict["directory"])))
             if dir_valid(target_dir):
                 dir = target_dir
             else:
-                log.debug('Invalid or nonexistent directory %s specified, ignoring change_directory action.', str(action_dict['directory']))
+                log.debug(
+                    "Invalid or nonexistent directory %s specified, ignoring change_directory action.",
+                    str(action_dict["directory"]),
+                )
                 dir = current_dir
         return tool_dependency, None, dir
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="change_directory">PHYLIP-3.6b</action>
         if action_elem.text:
-            action_dict['directory'] = basic_util.evaluate_template(action_elem.text, install_environment)
+            action_dict["directory"] = basic_util.evaluate_template(action_elem.text, install_environment)
         return action_dict
 
 
 class Chmod(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'chmod'
+        self.type = "chmod"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Change the mode setting for certain files in the installation environment.  Since this class is not
         used in the initial download stage, no recipe step filtering is performed here, and None values are
         always returned for filtered_actions and dir.
         """
-        for target_file, mode in action_dict['change_modes']:
+        for target_file, mode in action_dict["change_modes"]:
             if os.path.exists(target_file):
                 os.chmod(target_file, mode)
             else:
-                log.debug('Invalid file %s specified, ignoring %s action.', target_file, self.type)
+                log.debug("Invalid file %s specified, ignoring %s action.", target_file, self.type)
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
@@ -403,7 +491,7 @@ class Chmod(RecipeStep):
         # <action type="chmod">
         #   <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file>
         # </action>
-        file_elems = action_elem.findall('file')
+        file_elems = action_elem.findall("file")
         chmod_actions = []
         # A unix octal mode is the sum of the following values:
         # Owner:
@@ -415,22 +503,21 @@ class Chmod(RecipeStep):
         for file_elem in file_elems:
             # So by the above table, owner read/write/execute and group read permission would be 740.
             # Python's os.chmod uses base 10 modes, convert received unix-style octal modes to base 10.
-            received_mode = int(file_elem.get('mode', 600), base=8)
+            received_mode = int(file_elem.get("mode", 600), base=8)
             # For added security, ensure that the setuid and setgid bits are not set.
             mode = received_mode & ~(stat.S_ISUID | stat.S_ISGID)
             file = basic_util.evaluate_template(file_elem.text, install_environment)
             chmod_tuple = (file, mode)
             chmod_actions.append(chmod_tuple)
         if chmod_actions:
-            action_dict['change_modes'] = chmod_actions
+            action_dict["change_modes"] = chmod_actions
         return action_dict
 
 
 class DownloadBinary(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'download_binary'
+        self.type = "download_binary"
 
     def download_binary(self, url, work_dir, checksums):
         """Download a pre-compiled binary from the specified URL."""
@@ -439,30 +526,41 @@ class DownloadBinary(Download, RecipeStep):
         return downloaded_filename
 
     def filter_actions_after_binary_installation(self, actions):
-        '''Filter out actions that should not be processed if a binary download succeeded.'''
+        """Filter out actions that should not be processed if a binary download succeeded."""
         filtered_actions = []
         for action in actions:
             action_type, action_dict = action
-            if action_type in ['set_environment', 'chmod', 'download_binary']:
+            if action_type in ["set_environment", "chmod", "download_binary"]:
                 filtered_actions.append(action)
         return filtered_actions
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Download a binary file.  If the value of initial_download is True, the recipe steps will be
         filtered and returned and the installation directory (i.e., dir) will be defined and returned.
         If we're not in the initial download stage, these actions will not occur, and None values will
         be returned for them.
         """
-        url = action_dict['url']
+        url = action_dict["url"]
         # Get the target directory for this download if the user has specified one. Default to the root of $INSTALL_DIR.
-        target_directory = action_dict.get('target_directory', None)
+        target_directory = action_dict.get("target_directory", None)
         # Attempt to download a binary from the specified URL.
         downloaded_filename = None
         try:
             checksums = self.get_dict_checksums(action_dict)
-            log.debug('Attempting to download from %s to %s', url, str(target_directory))
+            log.debug("Attempting to download from %s to %s", url, str(target_directory))
             downloaded_filename = self.download_binary(url, work_dir, checksums)
             if initial_download:
                 # Filter out any actions that are not download_binary, chmod, or set_environment.
@@ -481,8 +579,9 @@ class DownloadBinary(Download, RecipeStep):
         # any errors in the move step are correctly sent to the tool dependency error handler.
         if downloaded_filename and os.path.exists(os.path.join(work_dir, downloaded_filename)):
             if target_directory:
-                target_directory = os.path.realpath(os.path.normpath(os.path.join(install_environment.install_dir,
-                                                                                  target_directory)))
+                target_directory = os.path.realpath(
+                    os.path.normpath(os.path.join(install_environment.install_dir, target_directory))
+                )
                 # Make sure the target directory is not outside of $INSTALL_DIR.
                 if target_directory.startswith(os.path.realpath(install_environment.install_dir)):
                     full_path_to_dir = os.path.abspath(os.path.join(install_environment.install_dir, target_directory))
@@ -490,9 +589,7 @@ class DownloadBinary(Download, RecipeStep):
                     full_path_to_dir = os.path.abspath(install_environment.install_dir)
             else:
                 full_path_to_dir = os.path.abspath(install_environment.install_dir)
-            basic_util.move_file(current_dir=work_dir,
-                                 source=downloaded_filename,
-                                 destination=full_path_to_dir)
+            basic_util.move_file(current_dir=work_dir, source=downloaded_filename, destination=full_path_to_dir)
         # Not sure why dir is ignored in this method, need to investigate...
         dir = None
         if initial_download:
@@ -501,9 +598,9 @@ class DownloadBinary(Download, RecipeStep):
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         platform_info_dict = tool_dependency_util.get_platform_info_dict()
-        platform_info_dict['name'] = str(tool_dependency.name)
-        platform_info_dict['version'] = str(tool_dependency.version)
-        url_template_elems = action_elem.findall('url_template')
+        platform_info_dict["name"] = str(tool_dependency.name)
+        platform_info_dict["version"] = str(tool_dependency.version)
+        url_template_elems = action_elem.findall("url_template")
         # Check if there are multiple url_template elements, each with attrib entries for a specific platform.
         if len(url_template_elems) > 1:
             # <base_url os="darwin" extract="false">
@@ -512,23 +609,35 @@ class DownloadBinary(Download, RecipeStep):
             # This method returns the url_elem that best matches the current platform as received from os.uname().
             # Currently checked attributes are os and architecture.  These correspond to the values sysname and
             # processor from the Python documentation for os.uname().
-            url_template_elem = tool_dependency_util.get_download_url_for_platform(url_template_elems, platform_info_dict)
+            url_template_elem = tool_dependency_util.get_download_url_for_platform(
+                url_template_elems, platform_info_dict
+            )
         else:
             url_template_elem = url_template_elems[0]
-        action_dict['url'] = Template(url_template_elem.text.strip()).safe_substitute(platform_info_dict)
-        action_dict['target_directory'] = action_elem.get('target_directory', None)
+        action_dict["url"] = Template(url_template_elem.text.strip()).safe_substitute(platform_info_dict)
+        action_dict["target_directory"] = action_elem.get("target_directory", None)
         action_dict.update(self.get_elem_checksums(action_elem))
         return action_dict
 
 
 class DownloadByUrl(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'download_by_url'
+        self.type = "download_by_url"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Download a file via HTTP.  If the value of initial_download is True, the recipe steps will be
         filtered and returned and the installation directory (i.e., dir) will be defined and returned.
@@ -538,25 +647,25 @@ class DownloadByUrl(Download, RecipeStep):
         if initial_download:
             # Eliminate the download_by_url action so remaining actions can be processed correctly.
             filtered_actions = actions[1:]
-        url = action_dict['url']
-        is_binary = action_dict.get('is_binary', False)
-        if 'target_filename' in action_dict:
+        url = action_dict["url"]
+        is_binary = action_dict.get("is_binary", False)
+        if "target_filename" in action_dict:
             # Sometimes compressed archives extract their content to a folder other than the default
             # defined file name.  Using this attribute will ensure that the file name is set appropriately
             # and can be located after download, decompression and extraction.
-            downloaded_filename = action_dict['target_filename']
+            downloaded_filename = action_dict["target_filename"]
         else:
             downloaded_filename = os.path.split(url)[-1]
 
         checksums = self.get_dict_checksums(action_dict)
-        log.debug('Attempting to download via url: %s', url)
+        log.debug("Attempting to download via url: %s", url)
         dir = self.url_download(work_dir, downloaded_filename, url, extract=True, checksums=checksums)
         if is_binary:
             log_file = os.path.join(install_environment.install_dir, basic_util.INSTALLATION_LOG)
             if os.path.exists(log_file):
-                logfile = open(log_file, 'a')
+                logfile = open(log_file, "a")
             else:
-                logfile = open(log_file, 'w')
+                logfile = open(log_file, "w")
             logfile.write(f"Successfully downloaded from url: {action_dict['url']}\n")
             logfile.close()
         log.debug(f"Successfully downloaded from url: {action_dict['url']}")
@@ -573,24 +682,34 @@ class DownloadByUrl(Download, RecipeStep):
         #     http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2
         # </action>
         if is_binary_download:
-            action_dict['is_binary'] = True
+            action_dict["is_binary"] = True
         if action_elem.text:
-            action_dict['url'] = action_elem.text.strip()
-            target_filename = action_elem.get('target_filename', None)
+            action_dict["url"] = action_elem.text.strip()
+            target_filename = action_elem.get("target_filename", None)
             if target_filename:
-                action_dict['target_filename'] = target_filename
+                action_dict["target_filename"] = target_filename
         action_dict.update(self.get_elem_checksums(action_elem))
         return action_dict
 
 
 class DownloadFile(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'download_file'
+        self.type = "download_file"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Download a file.  If the value of initial_download is True, the recipe steps will be
         filtered and returned and the installation directory (i.e., dir) will be defined and returned.
@@ -601,19 +720,19 @@ class DownloadFile(Download, RecipeStep):
         # Download a single file to the working directory.
         if initial_download:
             filtered_actions = actions[1:]
-        url = action_dict['url']
-        if 'target_filename' in action_dict:
+        url = action_dict["url"]
+        if "target_filename" in action_dict:
             # Sometimes compressed archives extracts their content to a folder other than the default
             # defined file name.  Using this attribute will ensure that the file name is set appropriately
             # and can be located after download, decompression and extraction.
-            filename = action_dict['target_filename']
+            filename = action_dict["target_filename"]
         else:
-            filename = url.split('/')[-1]
+            filename = url.split("/")[-1]
         if current_dir is not None:
             work_dir = current_dir
         checksums = self.get_dict_checksums(action_dict)
-        log.debug('Attempting to download via url: %s', url)
-        self.url_download(work_dir, filename, url, extract=action_dict['extract'], checksums=checksums)
+        log.debug("Attempting to download via url: %s", url)
+        self.url_download(work_dir, filename, url, extract=action_dict["extract"], checksums=checksums)
         if initial_download:
             dir = os.path.curdir
             return tool_dependency, filtered_actions, dir
@@ -622,31 +741,41 @@ class DownloadFile(Download, RecipeStep):
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action>
         if action_elem.text:
-            action_dict['url'] = action_elem.text.strip()
-            target_filename = action_elem.get('target_filename', None)
+            action_dict["url"] = action_elem.text.strip()
+            target_filename = action_elem.get("target_filename", None)
             if target_filename:
-                action_dict['target_filename'] = target_filename
-            action_dict['extract'] = asbool(action_elem.get('extract', False))
+                action_dict["target_filename"] = target_filename
+            action_dict["extract"] = asbool(action_elem.get("extract", False))
         action_dict.update(self.get_elem_checksums(action_elem))
         return action_dict
 
 
 class MakeDirectory(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'make_directory'
+        self.type = "make_directory"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Make a directory on disk.  Since this class is not used in the initial download stage, no recipe step
         filtering is performed here, and None values are always returned for filtered_actions and dir.
         """
-        if os.path.isabs(action_dict['full_path']):
-            full_path = action_dict['full_path']
+        if os.path.isabs(action_dict["full_path"]):
+            full_path = action_dict["full_path"]
         else:
-            full_path = os.path.join(current_dir, action_dict['full_path'])
+            full_path = os.path.join(current_dir, action_dict["full_path"])
         self.make_directory(full_path=full_path)
         return tool_dependency, None, None
 
@@ -657,30 +786,39 @@ class MakeDirectory(RecipeStep):
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # <action type="make_directory">$INSTALL_DIR/lib/python</action>
         if action_elem.text:
-            action_dict['full_path'] = basic_util.evaluate_template(action_elem.text, install_environment)
+            action_dict["full_path"] = basic_util.evaluate_template(action_elem.text, install_environment)
         return action_dict
 
 
 class MakeInstall(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'make_install'
+        self.type = "make_install"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Execute a make_install command in a shell.  Since this class is not used in the initial download stage,
         no recipe step filtering is performed here, and None values are always returned for filtered_actions and dir.
         """
         # make; make install; allow providing make options
         with settings(warn_only=True):
-            make_opts = action_dict.get('make_opts', '')
-            cmd = install_environment.build_command(f'make {make_opts} && make install')
-            install_environment.handle_command(tool_dependency=tool_dependency,
-                                               cmd=cmd,
-                                               return_output=False,
-                                               job_name=package_name)
+            make_opts = action_dict.get("make_opts", "")
+            cmd = install_environment.build_command(f"make {make_opts} && make install")
+            install_environment.handle_command(
+                tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+            )
             # The caller should check the status of the returned tool_dependency since this function
             # does nothing with the return_code.
             return tool_dependency, None, None
@@ -689,25 +827,37 @@ class MakeInstall(RecipeStep):
         # make; make install; allow providing make options
         if action_elem.text:
             make_opts = basic_util.evaluate_template(action_elem.text, install_environment)
-            action_dict['make_opts'] = make_opts
+            action_dict["make_opts"] = make_opts
         return action_dict
 
 
 class MoveDirectoryFiles(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'move_directory_files'
+        self.type = "move_directory_files"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Move a directory of files.  Since this class is not used in the initial download stage, no recipe step
         filtering is performed here, and None values are always returned for filtered_actions and dir.
         """
-        self.move_directory_files(current_dir=current_dir,
-                                  source_dir=os.path.join(action_dict['source_directory']),
-                                  destination_dir=os.path.join(action_dict['destination_directory']))
+        self.move_directory_files(
+            current_dir=current_dir,
+            source_dir=os.path.join(action_dict["source_directory"]),
+            destination_dir=os.path.join(action_dict["destination_directory"]),
+        )
         return tool_dependency, None, None
 
     def move_directory_files(self, current_dir, source_dir, destination_dir):
@@ -737,21 +887,33 @@ class MoveDirectoryFiles(RecipeStep):
 
 
 class MoveFile(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'move_file'
+        self.type = "move_file"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Move a file on disk.  Since this class is not used in the initial download stage, no recipe step
         filtering is performed here, and None values are always returned for filtered_actions and dir.
         """
-        basic_util.move_file(current_dir=current_dir,
-                             source=os.path.join(action_dict['source']),
-                             destination=os.path.join(action_dict['destination']),
-                             rename_to=action_dict['rename_to'])
+        basic_util.move_file(
+            current_dir=current_dir,
+            source=os.path.join(action_dict["source"]),
+            destination=os.path.join(action_dict["destination"]),
+            rename_to=action_dict["rename_to"],
+        )
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
@@ -759,20 +921,32 @@ class MoveFile(RecipeStep):
         #     <source>misc/some_file</source>
         #     <destination>$INSTALL_DIR/bin</destination>
         # </action>
-        action_dict['source'] = basic_util.evaluate_template(action_elem.find('source').text, install_environment)
-        action_dict['destination'] = basic_util.evaluate_template(action_elem.find('destination').text, install_environment)
-        action_dict['rename_to'] = action_elem.get('rename_to')
+        action_dict["source"] = basic_util.evaluate_template(action_elem.find("source").text, install_environment)
+        action_dict["destination"] = basic_util.evaluate_template(
+            action_elem.find("destination").text, install_environment
+        )
+        action_dict["rename_to"] = action_elem.get("rename_to")
         return action_dict
 
 
 class RegexReplace(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'regex_replace'
+        self.type = "regex_replace"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         r"""
         Search and replace text in a file using regular expressions. Since this class is not used in the initial
         download stage, no recipe step filtering is performed here, and None values are always returned for
@@ -796,17 +970,17 @@ class RegexReplace(RecipeStep):
         """
         log_file = os.path.join(install_environment.install_dir, basic_util.INSTALLATION_LOG)
         if os.path.exists(log_file):
-            logfile = open(log_file, 'ab')
+            logfile = open(log_file, "ab")
         else:
-            logfile = open(log_file, 'wb')
-        if os.path.isabs(action_dict['filename']):
-            filename = action_dict['filename']
+            logfile = open(log_file, "wb")
+        if os.path.isabs(action_dict["filename"]):
+            filename = action_dict["filename"]
             if not (filename.startswith(current_dir) or filename.startswith(install_environment.install_dir)):
                 return tool_dependency, None, None
         else:
-            filename = os.path.abspath(os.path.join(current_dir, action_dict['filename']))
-        regex = re.compile(action_dict['regex'])
-        replacement = action_dict['replacement']
+            filename = os.path.abspath(os.path.join(current_dir, action_dict["filename"]))
+        regex = re.compile(action_dict["regex"])
+        replacement = action_dict["replacement"]
         temp_fh = tempfile.NamedTemporaryFile(dir=current_dir)
         ofh = temp_fh.file
         total_replacements = 0
@@ -820,56 +994,73 @@ class RegexReplace(RecipeStep):
                     ofh.write(line)
             ofh.flush()
         shutil.copyfile(temp_fh.name, filename)
-        log_text = 'Successfully replaced pattern %s with text %s in file %s: %s replacements made\n'
-        log_text = log_text % (action_dict['regex'], action_dict['replacement'], filename, total_replacements)
+        log_text = "Successfully replaced pattern %s with text %s in file %s: %s replacements made\n"
+        log_text = log_text % (action_dict["regex"], action_dict["replacement"], filename, total_replacements)
         log.debug(log_text)
         logfile.write(log_text)
         logfile.close()
         return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
-        '''
+        """
         Populate action_dict with the provided filename, regex, and replacement text.
-        '''
-        action_dict['filename'] = basic_util.evaluate_template(action_elem.get('filename'), install_environment)
-        action_dict['regex'] = basic_util.evaluate_template(action_elem.find('regex').text, install_environment)
-        action_dict['replacement'] = basic_util.evaluate_template(action_elem.find('replacement').text, install_environment)
+        """
+        action_dict["filename"] = basic_util.evaluate_template(action_elem.get("filename"), install_environment)
+        action_dict["regex"] = basic_util.evaluate_template(action_elem.find("regex").text, install_environment)
+        action_dict["replacement"] = basic_util.evaluate_template(
+            action_elem.find("replacement").text, install_environment
+        )
         return action_dict
 
 
 class SetEnvironment(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'set_environment'
+        self.type = "set_environment"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Configure an install environment.  Since this class is not used in the initial download stage,
         no recipe step filtering is performed here, and None values are always returned for filtered_actions
         and dir.
         """
         # Currently the only action supported in this category is "environment_variable".
-        cmds = install_environment.environment_commands('set_environment')
-        env_var_dicts = action_dict.get('environment_variable', [])
-        root_dir_dict = dict(action='set_to',
-                             name=f"{re.sub('[^A-Z0-9_]', '_', tool_dependency.name.upper())}_ROOT_DIR",
-                             value=install_environment.install_dir)
+        cmds = install_environment.environment_commands("set_environment")
+        env_var_dicts = action_dict.get("environment_variable", [])
+        root_dir_dict = dict(
+            action="set_to",
+            name=f"{re.sub('[^A-Z0-9_]', '_', tool_dependency.name.upper())}_ROOT_DIR",
+            value=install_environment.install_dir,
+        )
         env_var_dicts.append(root_dir_dict)
         for env_var_dict in env_var_dicts:
             # Check for the presence of the $ENV[] key string and populate it if possible.
-            env_var_dict = self.handle_environment_variables(install_environment=install_environment,
-                                                             tool_dependency=tool_dependency,
-                                                             env_var_dict=env_var_dict,
-                                                             set_prior_environment_commands=cmds)
+            env_var_dict = self.handle_environment_variables(
+                install_environment=install_environment,
+                tool_dependency=tool_dependency,
+                env_var_dict=env_var_dict,
+                set_prior_environment_commands=cmds,
+            )
             env_file_builder.append_line(**env_var_dict)
         # The caller should check the status of the returned tool_dependency since return_code is not
         # returned by this function.
         return tool_dependency, None, None
 
-    def handle_environment_variables(self, install_environment, tool_dependency, env_var_dict,
-                                     set_prior_environment_commands):
+    def handle_environment_variables(
+        self, install_environment, tool_dependency, env_var_dict, set_prior_environment_commands
+    ):
         """
         This method works with a combination of three tool dependency definition tag sets, which are defined in
         the tool_dependencies.xml file in the order discussed here.  The example for this discussion is the
@@ -937,31 +1128,31 @@ class SetEnvironment(RecipeStep):
             OSRA_DATA_FILES=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/share;
             export OSRA_DATA_FILES
         """
-        env_var_value = env_var_dict['value']
+        env_var_value = env_var_dict["value"]
         # env_var_value is the text of an environment variable tag like this:
         # <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">
         # Here is an example of what env_var_value could look like: $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/
-        if '$ENV[' in env_var_value and ']' in env_var_value:
+        if "$ENV[" in env_var_value and "]" in env_var_value:
             # Pull out the name of the environment variable to populate.
-            inherited_env_var_name = env_var_value.split('[')[1].split(']')[0]
-            to_replace = f'$ENV[{inherited_env_var_name}]'
+            inherited_env_var_name = env_var_value.split("[")[1].split("]")[0]
+            to_replace = f"$ENV[{inherited_env_var_name}]"
             found = False
             for env_cmd in set_prior_environment_commands:
                 # LD_LIBRARY_PATH=/<my configured tool dependency path>/<some path>; export LD_LIBRARY_PATH
                 if env_cmd.startswith(inherited_env_var_name):
-                    env_val = env_cmd.split('=')[1]
+                    env_val = env_cmd.split("=")[1]
                     # /<my configured tool dependency path>/<some path>; export LD_LIBRARY_PATH
-                    env_val = env_val.split(';')[0]
+                    env_val = env_val.split(";")[0]
                     # /<my configured tool dependency path>/<some path>
-                    log.info('Replacing %s with %s in env.sh for this repository.', to_replace, env_val)
+                    log.info("Replacing %s with %s in env.sh for this repository.", to_replace, env_val)
                     env_var_value = env_var_value.replace(to_replace, env_val)
                     found = True
                     break
             if not found:
                 # Replace the original $ENV[] with nothing, to avoid any shell misparsings later on.
-                log.debug('Environment variable %s not found, removing from set_environment.', inherited_env_var_name)
-                env_var_value = env_var_value.replace(to_replace, f'${inherited_env_var_name}')
-            env_var_dict['value'] = env_var_value
+                log.debug("Environment variable %s not found, removing from set_environment.", inherited_env_var_name)
+                env_var_value = env_var_value.replace(to_replace, f"${inherited_env_var_name}")
+            env_var_dict["value"] = env_var_value
         return env_var_dict
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
@@ -978,25 +1169,34 @@ class SetEnvironment(RecipeStep):
         env_manager = EnvManager(self.app)
         env_var_dicts = []
         for env_elem in action_elem:
-            if env_elem.tag == 'environment_variable':
-                env_var_dict = env_manager.create_env_var_dict(elem=env_elem,
-                                                               install_environment=install_environment)
+            if env_elem.tag == "environment_variable":
+                env_var_dict = env_manager.create_env_var_dict(elem=env_elem, install_environment=install_environment)
                 if env_var_dict:
                     env_var_dicts.append(env_var_dict)
         if env_var_dicts:
             # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'.
-            action_dict['environment_variable'] = env_var_dicts
+            action_dict["environment_variable"] = env_var_dicts
         return action_dict
 
 
 class SetEnvironmentForInstall(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'set_environment_for_install'
+        self.type = "set_environment_for_install"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Configure an environment for compiling a package.  Since this class is not used in the initial
         download stage, no recipe step filtering is performed here, and None values are always returned
@@ -1006,7 +1206,7 @@ class SetEnvironmentForInstall(RecipeStep):
         # dependency env.sh files, the environment setting in each of which will be injected into the
         # environment for all <action type="shell_command"> tags that follow this
         # <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file.
-        env_shell_file_paths = action_dict.get('env_shell_file_paths', [])
+        env_shell_file_paths = action_dict.get("env_shell_file_paths", [])
         install_environment.add_env_shell_file_paths(env_shell_file_paths)
         return tool_dependency, None, None
 
@@ -1025,22 +1225,32 @@ class SetEnvironmentForInstall(RecipeStep):
         all_env_shell_file_paths = []
         env_manager = EnvManager(self.app)
         for env_elem in action_elem:
-            if env_elem.tag == 'repository':
+            if env_elem.tag == "repository":
                 env_shell_file_paths = env_manager.get_env_shell_file_paths(env_elem)
                 if env_shell_file_paths:
                     all_env_shell_file_paths.extend(env_shell_file_paths)
-        action_dict['env_shell_file_paths'] = all_env_shell_file_paths
+        action_dict["env_shell_file_paths"] = all_env_shell_file_paths
         return action_dict
 
 
 class SetupPerlEnvironment(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'setup_perl_environment'
+        self.type = "setup_perl_environment"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Initialize the environment for installing Perl packages.  The class is called during the initial
         download stage when installing packages, so the value of initial_download will generally be True.
@@ -1060,53 +1270,58 @@ class SetupPerlEnvironment(Download, RecipeStep):
         dir = None
         if initial_download:
             filtered_actions = actions[1:]
-        env_shell_file_paths = action_dict.get('env_shell_file_paths', None)
+        env_shell_file_paths = action_dict.get("env_shell_file_paths", None)
         if env_shell_file_paths is None:
-            log.debug('Missing Perl environment, make sure your specified Perl installation exists.')
+            log.debug("Missing Perl environment, make sure your specified Perl installation exists.")
             if initial_download:
                 return tool_dependency, filtered_actions, dir
             return tool_dependency, None, None
         else:
             install_environment.add_env_shell_file_paths(env_shell_file_paths)
-        log.debug('Handling setup_perl_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' %
-                  (str(tool_dependency.name), str(install_environment.env_shell_file_paths)))
+        log.debug(
+            "Handling setup_perl_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"
+            % (str(tool_dependency.name), str(install_environment.env_shell_file_paths))
+        )
         dir = os.path.curdir
         current_dir = os.path.abspath(os.path.join(work_dir, dir))
         with lcd(current_dir):
             with settings(warn_only=True):
-                perl_packages = action_dict.get('perl_packages', [])
+                perl_packages = action_dict.get("perl_packages", [])
                 for perl_package_dict in perl_packages:
-                    perl_package = perl_package_dict['package']
+                    perl_package = perl_package_dict["package"]
                     # If set to a true value then MakeMaker's prompt function will always
                     # return the default without waiting for user input.
-                    cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; '''
-                    cmd += f'HOME={work_dir}; export HOME; '
-                    cmd += 'export PERL5LIB=$INSTALL_DIR/lib/perl5:$PERL5LIB;'
-                    cmd += 'export PATH=$INSTALL_DIR/bin:$PATH;'
-                    if perl_package.find('://') != -1:
+                    cmd = """PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; """
+                    cmd += f"HOME={work_dir}; export HOME; "
+                    cmd += "export PERL5LIB=$INSTALL_DIR/lib/perl5:$PERL5LIB;"
+                    cmd += "export PATH=$INSTALL_DIR/bin:$PATH;"
+                    if perl_package.find("://") != -1:
                         # We assume a URL to a gem file.
                         url = perl_package
-                        perl_package_name = url.split('/')[-1]
-                        checksums = perl_package_dict.get('checksums', {})
+                        perl_package_name = url.split("/")[-1]
+                        checksums = perl_package_dict.get("checksums", {})
                         dir = self.url_download(work_dir, perl_package_name, url, extract=True, checksums=checksums)
                         # Search for Build.PL or Makefile.PL (ExtUtils::MakeMaker vs. Module::Build).
                         tmp_work_dir = os.path.join(work_dir, dir)
-                        if os.path.exists(os.path.join(tmp_work_dir, 'Makefile.PL')):
-                            cmd += '''perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install'''
-                        elif os.path.exists(os.path.join(tmp_work_dir, 'Build.PL')):
-                            cmd += '''perl Build.PL --install_base $INSTALL_DIR && perl Build && perl Build install'''
+                        if os.path.exists(os.path.join(tmp_work_dir, "Makefile.PL")):
+                            cmd += """perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install"""
+                        elif os.path.exists(os.path.join(tmp_work_dir, "Build.PL")):
+                            cmd += """perl Build.PL --install_base $INSTALL_DIR && perl Build && perl Build install"""
                         else:
-                            log.debug('No Makefile.PL or Build.PL file found in %s. Skipping installation of %s.' %
-                                (url, perl_package_name))
+                            log.debug(
+                                "No Makefile.PL or Build.PL file found in %s. Skipping installation of %s."
+                                % (url, perl_package_name)
+                            )
                             if initial_download:
                                 return tool_dependency, filtered_actions, dir
                             return tool_dependency, None, None
                         with lcd(tmp_work_dir):
-                            cmd = install_environment.build_command(basic_util.evaluate_template(cmd, install_environment))
-                            return_code = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                                             cmd=cmd,
-                                                                             return_output=False,
-                                                                             job_name=package_name)
+                            cmd = install_environment.build_command(
+                                basic_util.evaluate_template(cmd, install_environment)
+                            )
+                            return_code = install_environment.handle_command(
+                                tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+                            )
                             if return_code:
                                 if initial_download:
                                     return tool_dependency, filtered_actions, dir
@@ -1114,12 +1329,11 @@ class SetupPerlEnvironment(Download, RecipeStep):
                     else:
                         # perl package from CPAN without version number.
                         # cpanm should be installed with the parent perl distribution, otherwise this will not work.
-                        cmd += f'''cpanm --local-lib=$INSTALL_DIR {perl_package}'''
+                        cmd += f"""cpanm --local-lib=$INSTALL_DIR {perl_package}"""
                         cmd = install_environment.build_command(basic_util.evaluate_template(cmd, install_environment))
-                        return_code = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                                         cmd=cmd,
-                                                                         return_output=False,
-                                                                         job_name=package_name)
+                        return_code = install_environment.handle_command(
+                            tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+                        )
                         if return_code:
                             if initial_download:
                                 return tool_dependency, filtered_actions, dir
@@ -1127,12 +1341,14 @@ class SetupPerlEnvironment(Download, RecipeStep):
                 # Pull in perl dependencies (runtime).
                 env_file_builder.handle_action_shell_file_paths(action_dict)
                 # Recursively add dependent PERL5LIB and PATH to env.sh & anything else needed.
-                env_file_builder.append_line(name="PERL5LIB",
-                                             action="prepend_to",
-                                             value=os.path.join(install_environment.install_dir, 'lib', 'perl5'))
-                env_file_builder.append_line(name="PATH",
-                                             action="prepend_to",
-                                             value=os.path.join(install_environment.install_dir, 'bin'))
+                env_file_builder.append_line(
+                    name="PERL5LIB",
+                    action="prepend_to",
+                    value=os.path.join(install_environment.install_dir, "lib", "perl5"),
+                )
+                env_file_builder.append_line(
+                    name="PATH", action="prepend_to", value=os.path.join(install_environment.install_dir, "bin")
+                )
                 return_code = env_file_builder.return_code
                 if return_code:
                     if initial_download:
@@ -1157,32 +1373,41 @@ class SetupPerlEnvironment(Download, RecipeStep):
         # in action_dict.
         all_env_shell_file_paths = []
         env_manager = EnvManager(self.app)
-        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(all_env_shell_file_paths,
-                                                                                       action_elem,
-                                                                                       action_dict)
+        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(
+            all_env_shell_file_paths, action_elem, action_dict
+        )
         perl_packages = []
         for env_elem in action_elem:
-            if env_elem.tag == 'package':
+            if env_elem.tag == "package":
                 # A valid package definition can be:
                 #    XML::Parser
                 #     http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz
                 # Unfortunately CPAN does not support versioning, so if you want real reproducibility you need to specify
                 # the tarball path and the right order of different tarballs manually.
-                perl_packages.append(dict(package=env_elem.text.strip(),
-                                          checksums=self.get_elem_checksums(env_elem)))
+                perl_packages.append(dict(package=env_elem.text.strip(), checksums=self.get_elem_checksums(env_elem)))
         if perl_packages:
-            action_dict['perl_packages'] = perl_packages
+            action_dict["perl_packages"] = perl_packages
         return action_dict
 
 
 class SetupREnvironment(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'setup_r_environment'
+        self.type = "setup_r_environment"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Initialize the environment for installing R packages.  The class is called during the initial
         download stage when installing packages, so the value of initial_download will generally be True.
@@ -1201,26 +1426,27 @@ class SetupREnvironment(Download, RecipeStep):
         dir = None
         if initial_download:
             filtered_actions = actions[1:]
-        env_shell_file_paths = action_dict.get('env_shell_file_paths', None)
+        env_shell_file_paths = action_dict.get("env_shell_file_paths", None)
         if env_shell_file_paths is None:
-            error_message = 'Missing R environment. Please check your specified R installation exists.'
+            error_message = "Missing R environment. Please check your specified R installation exists."
             log.error(error_message)
             status = self.app.install_model.ToolDependency.installation_status.ERROR
-            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                  tool_dependency,
-                                                                                  status=status,
-                                                                                  error_message=error_message)
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                self.app, tool_dependency, status=status, error_message=error_message
+            )
             return tool_dependency, [], None
         else:
             install_environment.add_env_shell_file_paths(env_shell_file_paths)
-        log.debug('Handling setup_r_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' %
-                  (str(tool_dependency.name), str(install_environment.env_shell_file_paths)))
+        log.debug(
+            "Handling setup_r_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"
+            % (str(tool_dependency.name), str(install_environment.env_shell_file_paths))
+        )
         tarball_names = []
-        for r_package_dict in action_dict['r_packages']:
-            url = r_package_dict['package']
-            filename = url.split('/')[-1]
+        for r_package_dict in action_dict["r_packages"]:
+            url = r_package_dict["package"]
+            filename = url.split("/")[-1]
             tarball_names.append(filename)
-            checksums = r_package_dict.get('checksums', {})
+            checksums = r_package_dict.get("checksums", {})
             self.url_download(work_dir, filename, url, extract=False, checksums=checksums)
         dir = os.path.curdir
         current_dir = os.path.abspath(os.path.join(work_dir, dir))
@@ -1230,13 +1456,13 @@ class SetupREnvironment(Download, RecipeStep):
                     # Use raw strings so that python won't automatically unescape the quotes before passing the command
                     # to subprocess.Popen.
                     cmd = r'''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR:$R_LIBS; export R_LIBS;
-                        Rscript -e "tryCatch( { install.packages(c('%s'), lib = '$INSTALL_DIR', repos = NULL, dependencies = FALSE) }, error = function(e) { print(e); quit(status = 1) }, warning = function(w) { if ( grepl('had non-zero exit status|is not writable|installation of one of more packages failed', as.character(w)) ) { print(w); quit(status = 1) } } )"''' % \
-                        (str(tarball_name))
+                        Rscript -e "tryCatch( { install.packages(c('%s'), lib = '$INSTALL_DIR', repos = NULL, dependencies = FALSE) }, error = function(e) { print(e); quit(status = 1) }, warning = function(w) { if ( grepl('had non-zero exit status|is not writable|installation of one of more packages failed', as.character(w)) ) { print(w); quit(status = 1) } } )"''' % (
+                        str(tarball_name)
+                    )
                     cmd = install_environment.build_command(basic_util.evaluate_template(cmd, install_environment))
-                    return_code = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                                     cmd=cmd,
-                                                                     return_output=False,
-                                                                     job_name=package_name)
+                    return_code = install_environment.handle_command(
+                        tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+                    )
                     if return_code:
                         if initial_download:
                             return tool_dependency, filtered_actions, dir
@@ -1268,27 +1494,36 @@ class SetupREnvironment(Download, RecipeStep):
         # 'env_shell_file_paths' entry in action_dict.
         all_env_shell_file_paths = []
         env_manager = EnvManager(self.app)
-        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(all_env_shell_file_paths,
-                                                                                       action_elem,
-                                                                                       action_dict)
+        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(
+            all_env_shell_file_paths, action_elem, action_dict
+        )
         r_packages = list()
         for env_elem in action_elem:
-            if env_elem.tag == 'package':
-                r_packages.append(dict(package=env_elem.text.strip(),
-                                       checksums=self.get_elem_checksums(env_elem)))
+            if env_elem.tag == "package":
+                r_packages.append(dict(package=env_elem.text.strip(), checksums=self.get_elem_checksums(env_elem)))
         if r_packages:
-            action_dict['r_packages'] = r_packages
+            action_dict["r_packages"] = r_packages
         return action_dict
 
 
 class SetupRubyEnvironment(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'setup_ruby_environment'
+        self.type = "setup_ruby_environment"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Initialize the environment for installing Ruby packages.  The class is called during the initial
         download stage when installing packages, so the value of initial_download will generally be True.
@@ -1309,69 +1544,78 @@ class SetupRubyEnvironment(Download, RecipeStep):
         dir = None
         if initial_download:
             filtered_actions = actions[1:]
-        env_shell_file_paths = action_dict.get('env_shell_file_paths', None)
+        env_shell_file_paths = action_dict.get("env_shell_file_paths", None)
         if env_shell_file_paths is None:
-            log.debug('Missing Ruby environment, make sure your specified Ruby installation exists.')
+            log.debug("Missing Ruby environment, make sure your specified Ruby installation exists.")
             if initial_download:
                 return tool_dependency, filtered_actions, dir
             return tool_dependency, None, None
         else:
             install_environment.add_env_shell_file_paths(env_shell_file_paths)
-        log.debug('Handling setup_ruby_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' %
-                  (str(tool_dependency.name), str(install_environment.env_shell_file_paths)))
+        log.debug(
+            "Handling setup_ruby_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"
+            % (str(tool_dependency.name), str(install_environment.env_shell_file_paths))
+        )
         dir = os.path.curdir
         current_dir = os.path.abspath(os.path.join(work_dir, dir))
         with lcd(current_dir):
             with settings(warn_only=True):
-                ruby_package_tups = action_dict.get('ruby_package_tups', [])
+                ruby_package_tups = action_dict.get("ruby_package_tups", [])
                 for ruby_package_tup_dict in ruby_package_tups:
-                    ruby_package_tup = ruby_package_tup_dict['package']
+                    ruby_package_tup = ruby_package_tup_dict["package"]
                     gem, gem_version, gem_parameters = ruby_package_tup
                     if gem_parameters:
-                        gem_parameters = f'-- {gem_parameters}'
+                        gem_parameters = f"-- {gem_parameters}"
                     else:
-                        gem_parameters = ''
+                        gem_parameters = ""
                     if os.path.isfile(gem):
                         # we assume a local shipped gem file
-                        cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
-                                gem install --local {} {}'''.format(gem, gem_parameters)
-                    elif gem.find('://') != -1:
+                        cmd = """PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
+                                gem install --local {} {}""".format(
+                            gem, gem_parameters
+                        )
+                    elif gem.find("://") != -1:
                         # We assume a URL to a gem file.
                         url = gem
-                        gem_name = url.split('/')[-1]
-                        checksums = ruby_package_tup_dict.get('checksums', {})
+                        gem_name = url.split("/")[-1]
+                        checksums = ruby_package_tup_dict.get("checksums", {})
                         self.url_download(work_dir, gem_name, url, extract=False, checksums=checksums)
-                        cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
-                                gem install --local {} {}'''.format(gem_name, gem_parameters)
+                        cmd = """PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
+                                gem install --local {} {}""".format(
+                            gem_name, gem_parameters
+                        )
                     else:
                         # gem file from rubygems.org with or without version number
                         if gem_version:
                             # Specific ruby gem version was requested.
                             # Use raw strings so that python won't automatically unescape the quotes before passing the command
                             # to subprocess.Popen.
-                            cmd = r'''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
-                                gem install {} --version "={}" {}'''.format(gem, gem_version, gem_parameters)
+                            cmd = r"""PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
+                                gem install {} --version "={}" {}""".format(
+                                gem, gem_version, gem_parameters
+                            )
                         else:
                             # no version number given
-                            cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
-                                gem install {} {}'''.format(gem, gem_parameters)
+                            cmd = """PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
+                                gem install {} {}""".format(
+                                gem, gem_parameters
+                            )
                     cmd = install_environment.build_command(basic_util.evaluate_template(cmd, install_environment))
-                    return_code = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                                     cmd=cmd,
-                                                                     return_output=False,
-                                                                     job_name=package_name)
+                    return_code = install_environment.handle_command(
+                        tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+                    )
                     if return_code:
                         if initial_download:
                             return tool_dependency, filtered_actions, dir
                         return tool_dependency, None, None
                 # Pull in ruby dependencies (runtime).
                 env_file_builder.handle_action_shell_file_paths(action_dict)
-                env_file_builder.append_line(name="GEM_PATH",
-                                             action="prepend_to",
-                                             value=install_environment.install_dir)
-                env_file_builder.append_line(name="PATH",
-                                             action="prepend_to",
-                                             value=os.path.join(install_environment.install_dir, 'bin'))
+                env_file_builder.append_line(
+                    name="GEM_PATH", action="prepend_to", value=install_environment.install_dir
+                )
+                env_file_builder.append_line(
+                    name="PATH", action="prepend_to", value=os.path.join(install_environment.install_dir, "bin")
+                )
                 return_code = env_file_builder.return_code
                 if return_code:
                     if initial_download:
@@ -1397,18 +1641,18 @@ class SetupRubyEnvironment(Download, RecipeStep):
         # 'env_shell_file_paths' entry in action_dict.
         all_env_shell_file_paths = []
         env_manager = EnvManager(self.app)
-        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(all_env_shell_file_paths,
-                                                                                       action_elem,
-                                                                                       action_dict)
+        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(
+            all_env_shell_file_paths, action_elem, action_dict
+        )
         ruby_package_tups = []
         for env_elem in action_elem:
-            if env_elem.tag == 'package':
+            if env_elem.tag == "package":
                 # A valid gem definition can be:
                 #    protk=1.2.4
                 #    protk
                 #    ftp://ftp.gruening.de/protk.gem
-                gem_token = env_elem.text.strip().split('=')
-                gem_parameters = env_elem.get('parameters', None)
+                gem_token = env_elem.text.strip().split("=")
+                gem_parameters = env_elem.get("parameters", None)
                 if len(gem_token) == 2:
                     # version string
                     gem_name = gem_token[0]
@@ -1418,21 +1662,30 @@ class SetupRubyEnvironment(Download, RecipeStep):
                     # gem name for rubygems.org without version number
                     gem = env_elem.text.strip()
                     tup = (gem, None, gem_parameters)
-                ruby_package_tups.append(dict(package=tup,
-                                              checksums=self.get_elem_checksums(env_elem)))
+                ruby_package_tups.append(dict(package=tup, checksums=self.get_elem_checksums(env_elem)))
         if ruby_package_tups:
-            action_dict['ruby_package_tups'] = ruby_package_tups
+            action_dict["ruby_package_tups"] = ruby_package_tups
         return action_dict
 
 
 class SetupPythonEnvironment(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'setup_python_environment'
+        self.type = "setup_python_environment"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Initialize the environment for installing Python packages.  The class is called during the initial
         download stage when installing packages, so the value of initial_download will generally be True.
@@ -1452,33 +1705,35 @@ class SetupPythonEnvironment(Download, RecipeStep):
         dir = None
         if initial_download:
             filtered_actions = actions[1:]
-        env_shell_file_paths = action_dict.get('env_shell_file_paths', None)
+        env_shell_file_paths = action_dict.get("env_shell_file_paths", None)
         if env_shell_file_paths is None:
-            log.debug('Missing Python environment, make sure your specified Python installation exists.')
+            log.debug("Missing Python environment, make sure your specified Python installation exists.")
             if initial_download:
                 return tool_dependency, filtered_actions, dir
             return tool_dependency, None, None
         else:
             install_environment.add_env_shell_file_paths(env_shell_file_paths)
-        log.debug('Handling setup_python_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' %
-                  (str(tool_dependency.name), str(install_environment.env_shell_file_paths)))
+        log.debug(
+            "Handling setup_python_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s"
+            % (str(tool_dependency.name), str(install_environment.env_shell_file_paths))
+        )
         dir = os.path.curdir
         current_dir = os.path.abspath(os.path.join(work_dir, dir))
         with lcd(current_dir):
             with settings(warn_only=True):
-                python_package_tups = action_dict.get('python_package_tups', [])
+                python_package_tups = action_dict.get("python_package_tups", [])
                 for python_package_tup_dict in python_package_tups:
-                    python_package_tup = python_package_tup_dict['package']
+                    python_package_tup = python_package_tup_dict["package"]
                     package, package_version = python_package_tup
                     package_path = os.path.join(install_environment.tool_shed_repository_install_dir, package)
                     if os.path.isfile(package_path):
                         # We assume a local shipped python package.
                         package_to_install = package_path
-                    elif package.find('://') != -1:
+                    elif package.find("://") != -1:
                         # We assume a URL to a python package.
                         url = package
-                        package_name = url.split('/')[-1]
-                        checksums = python_package_tup_dict.get('checksums', {})
+                        package_name = url.split("/")[-1]
+                        checksums = python_package_tup_dict.get("checksums", {})
                         self.url_download(work_dir, package_name, url, extract=False, checksums=checksums)
                         package_to_install = os.path.join(work_dir, package_name)
                     else:
@@ -1486,33 +1741,36 @@ class SetupPythonEnvironment(Download, RecipeStep):
                         pass
                     archive = CompressedFile(package_to_install)
                     uncompressed_path = archive.extract(work_dir)
-                    cmd = r'''PATH=$PYTHONHOME/bin:$PATH; export PATH;
+                    cmd = r"""PATH=$PYTHONHOME/bin:$PATH; export PATH;
                             mkdir -p $INSTALL_DIR/lib/python;
                             export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH;
                             cd %s;
                             python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
-                        ''' % (uncompressed_path)
+                        """ % (
+                        uncompressed_path
+                    )
 
                     cmd = install_environment.build_command(basic_util.evaluate_template(cmd, install_environment))
-                    return_code = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                                     cmd=cmd,
-                                                                     return_output=False,
-                                                                     job_name=package_name)
+                    return_code = install_environment.handle_command(
+                        tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+                    )
                     if return_code:
                         if initial_download:
                             return tool_dependency, filtered_actions, dir
                         return tool_dependency, None, None
                 # Pull in python dependencies (runtime).
                 env_file_builder.handle_action_shell_file_paths(action_dict)
-                env_file_builder.append_line(name="PYTHONPATH",
-                                             action="prepend_to",
-                                             value=os.path.join(install_environment.install_dir, 'lib', 'python'))
-                env_file_builder.append_line(name="PYTHONPATH",
-                                             action="prepend_to",
-                                             value=os.path.join(install_environment.install_dir))
-                env_file_builder.append_line(name="PATH",
-                                             action="prepend_to",
-                                             value=os.path.join(install_environment.install_dir, 'bin'))
+                env_file_builder.append_line(
+                    name="PYTHONPATH",
+                    action="prepend_to",
+                    value=os.path.join(install_environment.install_dir, "lib", "python"),
+                )
+                env_file_builder.append_line(
+                    name="PYTHONPATH", action="prepend_to", value=os.path.join(install_environment.install_dir)
+                )
+                env_file_builder.append_line(
+                    name="PATH", action="prepend_to", value=os.path.join(install_environment.install_dir, "bin")
+                )
                 return_code = env_file_builder.return_code
                 if return_code:
                     if initial_download:
@@ -1537,16 +1795,16 @@ class SetupPythonEnvironment(Download, RecipeStep):
         # 'env_shell_file_paths' entry in action_dict.
         all_env_shell_file_paths = []
         env_manager = EnvManager(self.app)
-        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(all_env_shell_file_paths,
-                                                                                       action_elem,
-                                                                                       action_dict)
+        action_dict = env_manager.get_env_shell_file_paths_from_setup_environment_elem(
+            all_env_shell_file_paths, action_elem, action_dict
+        )
         python_package_tups = []
         for env_elem in action_elem:
-            if env_elem.tag == 'package':
+            if env_elem.tag == "package":
                 # A valid package definitions can be:
                 #    pysam.tar.gz -> locally shipped tarball
                 #    ftp://ftp.gruening.de/pysam.tar.gz -> online tarball
-                python_token = env_elem.text.strip().split('=')
+                python_token = env_elem.text.strip().split("=")
                 if len(python_token) == 2:
                     # version string
                     package_name = python_token[0]
@@ -1556,22 +1814,31 @@ class SetupPythonEnvironment(Download, RecipeStep):
                     # package name for pypi.org without version number
                     package = env_elem.text.strip()
                     tup = (package, None)
-                python_package_tups.append(dict(package=tup,
-                                                checksums=self.get_elem_checksums(env_elem)))
+                python_package_tups.append(dict(package=tup, checksums=self.get_elem_checksums(env_elem)))
         if python_package_tups:
-            action_dict['python_package_tups'] = python_package_tups
+            action_dict["python_package_tups"] = python_package_tups
         action_dict.update(self.get_elem_checksums(action_elem))
         return action_dict
 
 
 class SetupVirtualEnv(Download, RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'setup_virtualenv'
+        self.type = "setup_virtualenv"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Initialize a virtual environment for installing packages.  If initial_download is True, the recipe
         steps will be filtered and returned and the installation directory (i.e., dir) will be defined and
@@ -1581,11 +1848,11 @@ class SetupVirtualEnv(Download, RecipeStep):
         # This class is not currently used during stage 1 of the installation process, so filter_actions
         # are not affected, and dir is not set.  Enhancements can easily be made to this function if this
         # class is needed in stage 1.
-        venv_src_directory = os.path.abspath(os.path.join(self.app.tool_dependency_dir, '__virtualenv_src'))
+        venv_src_directory = os.path.abspath(os.path.join(self.app.tool_dependency_dir, "__virtualenv_src"))
         if not self.install_virtualenv(install_environment, venv_src_directory):
-            log.debug('Unable to install virtualenv')
+            log.debug("Unable to install virtualenv")
             return tool_dependency, None, None
-        requirements = action_dict['requirements']
+        requirements = action_dict["requirements"]
         if os.path.exists(os.path.join(install_environment.install_dir, requirements)):
             # requirements specified as path to a file
             requirements_path = requirements
@@ -1595,19 +1862,20 @@ class SetupVirtualEnv(Download, RecipeStep):
             with open(requirements_path, "w") as f:
                 f.write(requirements)
         venv_directory = os.path.join(install_environment.install_dir, "venv")
-        python_cmd = action_dict['python']
+        python_cmd = action_dict["python"]
         # TODO: Consider making --no-site-packages optional.
         setup_command = f"{python_cmd} {venv_src_directory}/virtualenv.py --no-site-packages '{venv_directory}'"
         # POSIXLY_CORRECT forces shell commands . and source to have the same
         # and well defined behavior in bash/zsh.
         activate_command = f"POSIXLY_CORRECT=1; . {os.path.join(venv_directory, 'bin', 'activate')}"
-        if action_dict['use_requirements_file']:
-            install_command = "python '%s' install -r '%s' --log '%s'" % \
-                (os.path.join(venv_directory, "bin", "pip"),
-                 requirements_path,
-                 os.path.join(install_environment.install_dir, 'pip_install.log'))
+        if action_dict["use_requirements_file"]:
+            install_command = "python '%s' install -r '%s' --log '%s'" % (
+                os.path.join(venv_directory, "bin", "pip"),
+                requirements_path,
+                os.path.join(install_environment.install_dir, "pip_install.log"),
+            )
         else:
-            install_command = ''
+            install_command = ""
             with open(requirements_path, "rb") as f:
                 while True:
                     line = f.readline()
@@ -1615,29 +1883,26 @@ class SetupVirtualEnv(Download, RecipeStep):
                         break
                     line = line.strip()
                     if line:
-                        line_install_command = "python '%s' install %s --log '%s'" % \
-                            (os.path.join(venv_directory, "bin", "pip"),
-                             line,
-                             os.path.join(install_environment.install_dir, 'pip_install_%s.log' % (line)))
+                        line_install_command = "python '%s' install %s --log '%s'" % (
+                            os.path.join(venv_directory, "bin", "pip"),
+                            line,
+                            os.path.join(install_environment.install_dir, "pip_install_%s.log" % (line)),
+                        )
                         if not install_command:
                             install_command = line_install_command
                         else:
                             install_command = f"{install_command} && {line_install_command}"
         full_setup_command = f"{setup_command}; {activate_command}; {install_command}"
-        return_code = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                         cmd=full_setup_command,
-                                                         return_output=False,
-                                                         job_name=package_name)
+        return_code = install_environment.handle_command(
+            tool_dependency=tool_dependency, cmd=full_setup_command, return_output=False, job_name=package_name
+        )
         if return_code:
             log.error("Failed to do setup_virtualenv install, exit code='%s'", return_code)
             # would it be better to try to set env variables anway, instead of returning here?
             return tool_dependency, None, None
-        site_packages_directory, site_packages_directory_list = \
-            self.__get_site_packages_directory(install_environment,
-                                               self.app,
-                                               tool_dependency,
-                                               python_cmd,
-                                               venv_directory)
+        site_packages_directory, site_packages_directory_list = self.__get_site_packages_directory(
+            install_environment, self.app, tool_dependency, python_cmd, venv_directory
+        )
         env_file_builder.append_line(name="PATH", action="prepend_to", value=os.path.join(venv_directory, "bin"))
         if site_packages_directory is None:
             log.error("virtualenv's site-packages directory '%s' does not exist", site_packages_directory_list)
@@ -1651,12 +1916,16 @@ class SetupVirtualEnv(Download, RecipeStep):
     def install_virtualenv(self, install_environment, venv_dir):
         if not os.path.exists(venv_dir):
             with install_environment.use_tmp_dir() as work_dir:
-                downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1]
+                downloaded_filename = VIRTUALENV_URL.rsplit("/", 1)[-1]
                 try:
                     dir = self.url_download(work_dir, downloaded_filename, VIRTUALENV_URL)
                 except Exception:
-                    log.error("Failed to download virtualenv: url_download( '%s', '%s', '%s' ) threw an exception",
-                              work_dir, downloaded_filename, VIRTUALENV_URL)
+                    log.error(
+                        "Failed to download virtualenv: url_download( '%s', '%s', '%s' ) threw an exception",
+                        work_dir,
+                        downloaded_filename,
+                        VIRTUALENV_URL,
+                    )
                     return False
                 full_path_to_dir = os.path.abspath(os.path.join(work_dir, dir))
                 shutil.move(full_path_to_dir, venv_dir)
@@ -1670,20 +1939,22 @@ class SetupVirtualEnv(Download, RecipeStep):
         # <action type="setup_virtualenv">pyyaml==3.2.0
         # lxml==2.3.0</action>
         # Manually specify contents of requirements.txt file to create dynamically.
-        action_dict['use_requirements_file'] = asbool(action_elem.get('use_requirements_file', True))
-        action_dict['requirements'] = basic_util.evaluate_template(action_elem.text or 'requirements.txt', install_environment)
-        action_dict['python'] = action_elem.get('python', 'python')
+        action_dict["use_requirements_file"] = asbool(action_elem.get("use_requirements_file", True))
+        action_dict["requirements"] = basic_util.evaluate_template(
+            action_elem.text or "requirements.txt", install_environment
+        )
+        action_dict["python"] = action_elem.get("python", "python")
         return action_dict
 
     def __get_site_packages_directory(self, install_environment, app, tool_dependency, python_cmd, venv_directory):
         lib_dir = os.path.join(venv_directory, "lib")
-        rval = os.path.join(lib_dir, python_cmd, 'site-packages')
+        rval = os.path.join(lib_dir, python_cmd, "site-packages")
         site_packages_directory_list = [rval]
         if os.path.exists(rval):
             return (rval, site_packages_directory_list)
         for _dirpath, dirnames, _filenames in os.walk(lib_dir):
             for dirname in dirnames:
-                rval = os.path.join(lib_dir, dirname, 'site-packages')
+                rval = os.path.join(lib_dir, dirname, "site-packages")
                 site_packages_directory_list.append(rval)
                 if os.path.exists(rval):
                     return (rval, site_packages_directory_list)
@@ -1693,14 +1964,17 @@ class SetupVirtualEnv(Download, RecipeStep):
         # preventing the entire path from being included (it gets truncated)
         # Use raw strings so that python won't automatically unescape the quotes before passing the command
         # to subprocess.Popen.
-        for site_packages_command in [r"""%s -c 'import site; site.getsitepackages()[0]'""" %
-                                      os.path.join(venv_directory, "bin", "python"),
-                                      r"""%s -c 'from __future__ import print_function; import os, sys; print(os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages"))'""" %
-                                      os.path.join(venv_directory, "bin", "python")]:
-            output = install_environment.handle_command(tool_dependency=tool_dependency,
-                                                        cmd=site_packages_command,
-                                                        return_output=True,
-                                                        job_name='_get_site_packages')
+        for site_packages_command in [
+            r"""%s -c 'import site; site.getsitepackages()[0]'""" % os.path.join(venv_directory, "bin", "python"),
+            r"""%s -c 'from __future__ import print_function; import os, sys; print(os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages"))'"""
+            % os.path.join(venv_directory, "bin", "python"),
+        ]:
+            output = install_environment.handle_command(
+                tool_dependency=tool_dependency,
+                cmd=site_packages_command,
+                return_output=True,
+                job_name="_get_site_packages",
+            )
             site_packages_directory_list.append(output.stdout)
             if not output.return_code and os.path.exists(output.stdout):
                 return (output.stdout, site_packages_directory_list)
@@ -1708,13 +1982,23 @@ class SetupVirtualEnv(Download, RecipeStep):
 
 
 class ShellCommand(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'shell_command'
+        self.type = "shell_command"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Execute a command in a shell.  If the value of initial_download is True, the recipe steps will
         be filtered and returned and the installation directory (i.e., dir) will be defined and returned.
@@ -1728,16 +2012,15 @@ class ShellCommand(RecipeStep):
             # be the same no matter the stage?
             dir = package_name
             filtered_actions = actions[1:]
-            cmd = action_dict['command']
+            cmd = action_dict["command"]
         else:
-            cmd = install_environment.build_command(action_dict['command'])
+            cmd = install_environment.build_command(action_dict["command"])
         with settings(warn_only=True):
             # The caller should check the status of the returned tool_dependency since this function
             # does nothing with return_code.
-            install_environment.handle_command(tool_dependency=tool_dependency,
-                                               cmd=cmd,
-                                               return_output=False,
-                                               job_name=package_name)
+            install_environment.handle_command(
+                tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+            )
             if initial_download:
                 return tool_dependency, filtered_actions, dir
             return tool_dependency, None, None
@@ -1746,18 +2029,28 @@ class ShellCommand(RecipeStep):
         # <action type="shell_command">make</action>
         action_elem_text = basic_util.evaluate_template(action_elem.text, install_environment)
         if action_elem_text:
-            action_dict['command'] = action_elem_text
+            action_dict["command"] = action_elem_text
         return action_dict
 
 
 class TemplateCommand(RecipeStep):
-
     def __init__(self, app):
         self.app = app
-        self.type = 'template_command'
+        self.type = "template_command"
 
-    def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
-                     install_environment, work_dir, current_dir=None, initial_download=False):
+    def execute_step(
+        self,
+        tool_dependency,
+        package_name,
+        actions,
+        action_dict,
+        filtered_actions,
+        env_file_builder,
+        install_environment,
+        work_dir,
+        current_dir=None,
+        initial_download=False,
+    ):
         """
         Execute a template command in a shell.  If the value of initial_download is True, the recipe steps
         will be filtered and returned and the installation directory (i.e., dir) will be defined and returned.
@@ -1767,23 +2060,22 @@ class TemplateCommand(RecipeStep):
         env_vars = dict()
         env_vars = install_environment.environment_dict()
         env_vars.update(basic_util.get_env_var_values(install_environment))
-        language = action_dict['language']
+        language = action_dict["language"]
         with settings(warn_only=True, **env_vars):
-            if language == 'cheetah':
+            if language == "cheetah":
                 # We need to import fabric.api.env so that we can access all collected environment variables.
                 cmd = fill_template(f"#from fabric.api import env\n{action_dict['command']}", context=env_vars)
                 # The caller should check the status of the returned tool_dependency since this function
                 # does nothing with return_code.
-                install_environment.handle_command(tool_dependency=tool_dependency,
-                                                   cmd=cmd,
-                                                   return_output=False,
-                                                   job_name=package_name)
+                install_environment.handle_command(
+                    tool_dependency=tool_dependency, cmd=cmd, return_output=False, job_name=package_name
+                )
             return tool_dependency, None, None
 
     def prepare_step(self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download):
         # Default to Cheetah as it's the first template language supported.
-        language = action_elem.get('language', 'cheetah').lower()
-        if language == 'cheetah':
+        language = action_elem.get("language", "cheetah").lower()
+        if language == "cheetah":
             # Cheetah template syntax.
             # <action type="template_command" language="cheetah">
             #     #if env.PATH:
@@ -1792,8 +2084,8 @@ class TemplateCommand(RecipeStep):
             # </action>
             action_elem_text = action_elem.text.strip()
             if action_elem_text:
-                action_dict['language'] = language
-                action_dict['command'] = action_elem_text
+                action_dict["language"] = language
+                action_dict["command"] = action_elem_text
         else:
             log.debug(f"Unsupported template language '{str(language)}'. Not proceeding.")
             raise Exception(f"Unsupported template language '{str(language)}' in tool dependency definition.")
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
index 3eff81284cd..1a4be0d81e9 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -6,12 +6,24 @@ from galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager import EnvMan
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment
 from galaxy.tool_shed.util import tool_dependency_util
-from galaxy.tool_shed.util.basic_util import INSTALLATION_LOG, remove_dir
+from galaxy.tool_shed.util.basic_util import (
+    INSTALLATION_LOG,
+    remove_dir,
+)
 from galaxy.tool_shed.util.metadata_util import get_updated_changeset_revisions_from_tool_shed
-from galaxy.tool_shed.util.repository_util import get_absolute_path_to_file_in_repository, get_repository_for_dependency_relationship
+from galaxy.tool_shed.util.repository_util import (
+    get_absolute_path_to_file_in_repository,
+    get_repository_for_dependency_relationship,
+)
 from galaxy.tool_util.deps.resolvers import NullDependency
-from galaxy.util import listify, url_get
-from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry, remove_protocol_from_tool_shed_url
+from galaxy.util import (
+    listify,
+    url_get,
+)
+from galaxy.util.tool_shed.common_util import (
+    get_tool_shed_url_from_tool_shed_registry,
+    remove_protocol_from_tool_shed_url,
+)
 from galaxy.util.tool_shed.xml_util import parse_xml
 
 log = logging.getLogger(__name__)
@@ -20,15 +32,28 @@ log = logging.getLogger(__name__)
 class RecipeTag:
     """Abstract class that defines a standard format for handling recipe tags when installing packages."""
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         raise Exception("Unimplemented Method")
 
 
 class SyncDatabase:
-
-    def sync_database_with_file_system(self, app, tool_shed_repository, tool_dependency_name, tool_dependency_version,
-                                       tool_dependency_install_dir, tool_dependency_type='package'):
+    def sync_database_with_file_system(
+        self,
+        app,
+        tool_shed_repository,
+        tool_dependency_name,
+        tool_dependency_version,
+        tool_dependency_install_dir,
+        tool_dependency_type="package",
+    ):
         """
         The installation directory defined by the received tool_dependency_install_dir exists, so check for
         the presence of INSTALLATION_LOG.  If the files exists, we'll assume the tool dependency is installed,
@@ -42,25 +67,25 @@ class SyncDatabase:
         # followed by those containing valid tools and tool functional test components.
         log.debug("Synchronizing the database with the file system...")
         try:
-            log.debug("The value of app.config.running_functional_tests is: %s" %
-                str(app.config.running_functional_tests))
+            log.debug(
+                "The value of app.config.running_functional_tests is: %s" % str(app.config.running_functional_tests)
+            )
         except Exception:
             pass
         sa_session = app.install_model.context
         can_install_tool_dependency = False
-        tool_dependency = \
-            tool_dependency_util.get_tool_dependency_by_name_version_type_repository(app,
-                                                                                     tool_shed_repository,
-                                                                                     tool_dependency_name,
-                                                                                     tool_dependency_version,
-                                                                                     tool_dependency_type)
+        tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository(
+            app, tool_shed_repository, tool_dependency_name, tool_dependency_version, tool_dependency_type
+        )
         if tool_dependency.status == app.install_model.ToolDependency.installation_status.INSTALLING:
             # The tool dependency is in an Installing state, so we don't want to do anything to it.  If the tool
             # dependency is being installed by someone else, we don't want to interfere with that.  This assumes
             # the installation by "someone else" is not hung in an Installing state, which is a weakness if that
             # "someone else" never repaired it.
-            log.debug('Skipping installation of tool dependency %s version %s because it has a status of %s' %
-                (str(tool_dependency.name), str(tool_dependency.version), str(tool_dependency.status)))
+            log.debug(
+                "Skipping installation of tool dependency %s version %s because it has a status of %s"
+                % (str(tool_dependency.name), str(tool_dependency.version), str(tool_dependency.status))
+            )
         else:
             # We have a pre-existing installation directory on the file system, but our associated database record is
             # in a state that allowed us to arrive here.  At this point, we'll inspect the installation directory to
@@ -74,26 +99,34 @@ class SyncDatabase:
                 # the control of the Tool Shed.  Since a new record was created for it and we don't know the state of the
                 # files on disk, we will set it to an error state (unless we are running Tool Shed functional tests - see
                 # below).
-                log.debug('Skipping installation of tool dependency %s version %s because it is installed in %s' %
-                    (str(tool_dependency.name), str(tool_dependency.version), str(tool_dependency_install_dir)))
+                log.debug(
+                    "Skipping installation of tool dependency %s version %s because it is installed in %s"
+                    % (str(tool_dependency.name), str(tool_dependency.version), str(tool_dependency_install_dir))
+                )
                 if app.config.running_functional_tests:
                     # If we are running functional tests, the state will be set to Installed because previously compiled
                     # tool dependencies are not deleted by default, from the "install and test" framework..
                     tool_dependency.status = app.install_model.ToolDependency.installation_status.INSTALLED
                 else:
-                    error_message = 'The installation directory for this tool dependency had contents but the database had no record. '
-                    error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the '
-                    error_message += 'missing database record it is now being set to Error.'
+                    error_message = "The installation directory for this tool dependency had contents but the database had no record. "
+                    error_message += (
+                        "The installation log may show this tool dependency to be correctly installed, but due to the "
+                    )
+                    error_message += "missing database record it is now being set to Error."
                     tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR
                     tool_dependency.error_message = error_message
             else:
-                error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \
-                    (str(tool_dependency_install_dir),
-                     str(tool_dependency_name),
-                     str(tool_dependency_version),
-                     str(INSTALLATION_LOG))
-                error_message += ' is missing.  This indicates an installation error so the tool dependency is being'
-                error_message += ' prepared for re-installation.'
+                error_message = (
+                    "\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s"
+                    % (
+                        str(tool_dependency_install_dir),
+                        str(tool_dependency_name),
+                        str(tool_dependency_version),
+                        str(INSTALLATION_LOG),
+                    )
+                )
+                error_message += " is missing.  This indicates an installation error so the tool dependency is being"
+                error_message += " prepared for re-installation."
                 log.error(error_message)
                 tool_dependency.status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED
                 remove_dir(tool_dependency_install_dir)
@@ -101,90 +134,114 @@ class SyncDatabase:
             sa_session.add(tool_dependency)
             sa_session.flush()
         try:
-            log.debug("Returning from sync_database_with_file_system with tool_dependency %s, can_install_tool_dependency %s." %
-                (str(tool_dependency.name), str(can_install_tool_dependency)))
+            log.debug(
+                "Returning from sync_database_with_file_system with tool_dependency %s, can_install_tool_dependency %s."
+                % (str(tool_dependency.name), str(can_install_tool_dependency))
+            )
         except Exception as e:
             log.debug(str(e))
         return tool_dependency, can_install_tool_dependency
 
 
 class Install(RecipeTag, SyncDatabase):
-
     def __init__(self, app):
         self.app = app
-        self.tag = 'install'
+        self.tag = "install"
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         # <install version="1.0">
         # Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository.
         actions_elem_tuples = []
         proceed_with_install = False
-        install_dir = \
-            tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
-                                                                 repository_name=tool_shed_repository.name,
-                                                                 repository_owner=tool_shed_repository.owner,
-                                                                 repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                 tool_dependency_type='package',
-                                                                 tool_dependency_name=package_name,
-                                                                 tool_dependency_version=package_version)
+        install_dir = tool_dependency_util.get_tool_dependency_install_dir(
+            app=self.app,
+            repository_name=tool_shed_repository.name,
+            repository_owner=tool_shed_repository.owner,
+            repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+            tool_dependency_type="package",
+            tool_dependency_name=package_name,
+            tool_dependency_version=package_version,
+        )
         if os.path.exists(install_dir):
             # Notice that we'll throw away the following tool_dependency if it can be installed.
-            tool_dependency, proceed_with_install = self.sync_database_with_file_system(self.app,
-                                                                                        tool_shed_repository,
-                                                                                        package_name,
-                                                                                        package_version,
-                                                                                        install_dir,
-                                                                                        tool_dependency_type='package')
+            tool_dependency, proceed_with_install = self.sync_database_with_file_system(
+                self.app,
+                tool_shed_repository,
+                package_name,
+                package_version,
+                install_dir,
+                tool_dependency_type="package",
+            )
             if not proceed_with_install:
-                log.debug("Tool dependency %s version %s cannot be installed (it was probably previously installed), so returning it." %
-                    (str(tool_dependency.name), str(tool_dependency.version)))
+                log.debug(
+                    "Tool dependency %s version %s cannot be installed (it was probably previously installed), so returning it."
+                    % (str(tool_dependency.name), str(tool_dependency.version))
+                )
                 return tool_dependency, proceed_with_install, actions_elem_tuples
         else:
             proceed_with_install = True
         if proceed_with_install:
-            package_install_version = package_elem.get('version', '1.0')
+            package_install_version = package_elem.get("version", "1.0")
             status = self.app.install_model.ToolDependency.installation_status.INSTALLING
-            tool_dependency = \
-                tool_dependency_util.create_or_update_tool_dependency(app=self.app,
-                                                                      tool_shed_repository=tool_shed_repository,
-                                                                      name=package_name,
-                                                                      version=package_version,
-                                                                      type='package',
-                                                                      status=status,
-                                                                      set_status=True)
+            tool_dependency = tool_dependency_util.create_or_update_tool_dependency(
+                app=self.app,
+                tool_shed_repository=tool_shed_repository,
+                name=package_name,
+                version=package_version,
+                type="package",
+                status=status,
+                set_status=True,
+            )
             # Get the information about the current platform in case the tool dependency definition includes tag sets
             # for installing compiled binaries.
             platform_info_dict = tool_dependency_util.get_platform_info_dict()
-            if package_install_version == '1.0':
+            if package_install_version == "1.0":
                 # Handle tool dependency installation using a fabric method included in the Galaxy framework.
-                actions_elem_tuples = tool_dependency_util.parse_package_elem(package_elem,
-                                                                              platform_info_dict=platform_info_dict,
-                                                                              include_after_install_actions=True)
+                actions_elem_tuples = tool_dependency_util.parse_package_elem(
+                    package_elem, platform_info_dict=platform_info_dict, include_after_install_actions=True
+                )
                 if not actions_elem_tuples:
                     proceed_with_install = False
-                    error_message = f'Version {str(package_version)} of the {str(package_name)} package cannot be installed because '
-                    error_message += 'the recipe for installing the package is missing either an &lt;actions&gt; tag set or an &lt;actions_group&gt; '
-                    error_message += 'tag set.'
+                    error_message = f"Version {str(package_version)} of the {str(package_name)} package cannot be installed because "
+                    error_message += "the recipe for installing the package is missing either an &lt;actions&gt; tag set or an &lt;actions_group&gt; "
+                    error_message += "tag set."
                     # Since there was an installation error, update the tool dependency status to Error.
                     # The remove_installation_path option must be left False here.
-                    tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                          tool_dependency=tool_dependency,
-                                                                                          status=self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                                                          error_message=error_message)
+                    tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                        self.app,
+                        tool_dependency=tool_dependency,
+                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                        error_message=error_message,
+                    )
             else:
-                raise NotImplementedError('Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).')
+                raise NotImplementedError(
+                    'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).'
+                )
         return tool_dependency, proceed_with_install, actions_elem_tuples
 
 
 class Package(RecipeTag):
-
     def __init__(self, app):
         self.app = app
-        self.tag = 'package'
+        self.tag = "package"
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         action_elem_tuples = []
         proceed_with_install = False
         # Only install the tool_dependency if it is not already installed and it is associated with a database
@@ -192,30 +249,39 @@ class Package(RecipeTag):
         if package_name and package_version:
             dependencies_ignored = not self.app.toolbox.dependency_manager.uses_tool_shed_dependencies()
             if dependencies_ignored:
-                log.debug("Skipping installation of tool dependency package %s because tool shed dependency resolver not enabled." %
-                    str(package_name))
+                log.debug(
+                    "Skipping installation of tool dependency package %s because tool shed dependency resolver not enabled."
+                    % str(package_name)
+                )
                 # Tool dependency resolves have been configured and they do not include the tool shed. Do not install package.
-                dep = self.app.toolbox.dependency_manager.find_dep(package_name, package_version, type='package')
+                dep = self.app.toolbox.dependency_manager.find_dep(package_name, package_version, type="package")
                 if not isinstance(dep, NullDependency):
                     # TODO: Do something here such as marking it installed or configured externally.
                     pass
-                tool_dependency = \
-                    tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                        tool_dependency=tool_dependency,
-                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR)
+                tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                    self.app,
+                    tool_dependency=tool_dependency,
+                    status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                )
             else:
                 proceed_with_install = True
         return tool_dependency, proceed_with_install, action_elem_tuples
 
 
 class ReadMe(RecipeTag):
-
     def __init__(self, app):
         self.app = app
-        self.tag = 'readme'
+        self.tag = "readme"
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         # Nothing to be done.
         action_elem_tuples = []
         proceed_with_install = False
@@ -223,30 +289,33 @@ class ReadMe(RecipeTag):
 
 
 class Repository(RecipeTag, SyncDatabase):
-
     def __init__(self, app):
         self.app = app
-        self.tag = 'repository'
+        self.tag = "repository"
 
     def create_temporary_tool_dependencies_config(self, tool_shed_url, name, owner, changeset_revision):
         """Make a call to the tool shed to get the required repository's tool_dependencies.xml file."""
         tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
         if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
-            message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed because one or more of the "
-            message += "following required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
-                (str(tool_shed_url), str(name), str(owner), str(changeset_revision))
+            message = (
+                "Unable to retrieve required tool_dependencies.xml file from the Tool Shed because one or more of the "
+            )
+            message += (
+                "following required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s "
+                % (str(tool_shed_url), str(name), str(owner), str(changeset_revision))
+            )
             raise Exception(message)
-        params = dict(name=name,
-                      owner=owner,
-                      changeset_revision=changeset_revision)
-        pathspec = ['repository', 'get_tool_dependencies_config_contents']
-        text = url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        params = dict(name=name, owner=owner, changeset_revision=changeset_revision)
+        pathspec = ["repository", "get_tool_dependencies_config_contents"]
+        text = url_get(
+            tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         if text:
             # Write the contents to a temporary file on disk so it can be reloaded and parsed.
-            fh = tempfile.NamedTemporaryFile('w', prefix="tmp-toolshed-cttdc")
+            fh = tempfile.NamedTemporaryFile("w", prefix="tmp-toolshed-cttdc")
             tmp_filename = fh.name
             fh.close()
-            fh = open(tmp_filename, 'w')
+            fh = open(tmp_filename, "w")
             fh.write(text)
             fh.close()
             return tmp_filename
@@ -255,9 +324,15 @@ class Repository(RecipeTag, SyncDatabase):
             message += f"{str(changeset_revision)} of installed repository {str(name)} owned by {str(owner)}."
             raise Exception(message)
 
-    def create_tool_dependency_with_initialized_env_sh_file(self, dependent_install_dir, tool_shed_repository,
-                                                            required_repository, package_name, package_version,
-                                                            tool_dependencies_config):
+    def create_tool_dependency_with_initialized_env_sh_file(
+        self,
+        dependent_install_dir,
+        tool_shed_repository,
+        required_repository,
+        package_name,
+        package_version,
+        tool_dependencies_config,
+    ):
         """
         Create or get a tool_dependency record that is defined by the received package_name and package_version.
         An env.sh file will be created for the tool_dependency in the received dependent_install_dir.
@@ -279,76 +354,93 @@ class Repository(RecipeTag, SyncDatabase):
                 required_td_root = required_td_tree.getroot()
                 for required_td_elem in required_td_root:
                     # Find the appropriate package name and version.
-                    if required_td_elem.tag == 'package':
+                    if required_td_elem.tag == "package":
                         # <package name="bwa" version="0.5.9">
-                        required_td_package_name = required_td_elem.get('name', None)
-                        required_td_package_version = required_td_elem.get('version', None)
+                        required_td_package_name = required_td_elem.get("name", None)
+                        required_td_package_version = required_td_elem.get("version", None)
                         # Check the database to see if we have a record for the required tool dependency (we may not which is ok).  If we
                         # find a record, we need to see if it is in an error state and if so handle it appropriately.
-                        required_tool_dependency = \
-                            tool_dependency_util.get_tool_dependency_by_name_version_type_repository(self.app,
-                                                                                                     required_repository,
-                                                                                                     required_td_package_name,
-                                                                                                     required_td_package_version,
-                                                                                                     'package')
+                        required_tool_dependency = (
+                            tool_dependency_util.get_tool_dependency_by_name_version_type_repository(
+                                self.app,
+                                required_repository,
+                                required_td_package_name,
+                                required_td_package_version,
+                                "package",
+                            )
+                        )
                         if required_td_package_name == package_name and required_td_package_version == package_version:
                             # Get or create a database tool_dependency record with which the installed package on disk will be associated.
-                            tool_dependency = \
-                                tool_dependency_util.create_or_update_tool_dependency(app=self.app,
-                                                                                      tool_shed_repository=tool_shed_repository,
-                                                                                      name=package_name,
-                                                                                      version=package_version,
-                                                                                      type='package',
-                                                                                      status=self.app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                                                      set_status=True)
+                            tool_dependency = tool_dependency_util.create_or_update_tool_dependency(
+                                app=self.app,
+                                tool_shed_repository=tool_shed_repository,
+                                name=package_name,
+                                version=package_version,
+                                type="package",
+                                status=self.app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                set_status=True,
+                            )
                             # Create an env.sh file for the tool_dependency whose first line will source the env.sh file located in
                             # the path defined by required_tool_dependency_env_file_path.  It doesn't matter if the required env.sh
                             # file currently exists..
-                            required_tool_dependency_env_file_path = \
-                                self.get_required_repository_package_env_sh_path(package_name,
-                                                                                 package_version,
-                                                                                 required_repository)
+                            required_tool_dependency_env_file_path = self.get_required_repository_package_env_sh_path(
+                                package_name, package_version, required_repository
+                            )
                             env_file_builder = EnvFileBuilder(tool_dependency.installation_directory(self.app))
                             env_file_builder.append_line(action="source", value=required_tool_dependency_env_file_path)
                             return_code = env_file_builder.return_code
                             if return_code:
-                                error_message = 'Error defining env.sh file for package %s, return_code: %s' % \
-                                    (str(package_name), str(return_code))
-                                tool_dependency = \
-                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                        tool_dependency=tool_dependency,
-                                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                                                        error_message=error_message)
+                                error_message = "Error defining env.sh file for package %s, return_code: %s" % (
+                                    str(package_name),
+                                    str(return_code),
+                                )
+                                tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                                    self.app,
+                                    tool_dependency=tool_dependency,
+                                    status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                    error_message=error_message,
+                                )
                             elif required_tool_dependency is not None and required_tool_dependency.in_error_state:
-                                error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \
-                                    (str(required_tool_dependency.name), str(required_tool_dependency.version), str(required_tool_dependency.status))
-                                tool_dependency = \
-                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                        tool_dependency=tool_dependency,
-                                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                                                        error_message=error_message)
+                                error_message = (
+                                    "This tool dependency's required tool dependency %s version %s has status %s."
+                                    % (
+                                        str(required_tool_dependency.name),
+                                        str(required_tool_dependency.version),
+                                        str(required_tool_dependency.status),
+                                    )
+                                )
+                                tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                                    self.app,
+                                    tool_dependency=tool_dependency,
+                                    status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                    error_message=error_message,
+                                )
                             else:
-                                tool_dependency = \
-                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                        tool_dependency=tool_dependency,
-                                                                                        status=self.app.install_model.ToolDependency.installation_status.INSTALLED)
+                                tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                                    self.app,
+                                    tool_dependency=tool_dependency,
+                                    status=self.app.install_model.ToolDependency.installation_status.INSTALLED,
+                                )
                             tool_dependencies.append(tool_dependency)
         return tool_dependencies
 
     def get_required_repository_package_env_sh_path(self, package_name, package_version, required_repository):
         """Return path to env.sh file in required repository if the required repository has been installed."""
-        env_sh_file_dir = \
-            tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
-                                                                 repository_name=required_repository.name,
-                                                                 repository_owner=required_repository.owner,
-                                                                 repository_changeset_revision=required_repository.installed_changeset_revision,
-                                                                 tool_dependency_type='package',
-                                                                 tool_dependency_name=package_name,
-                                                                 tool_dependency_version=package_version)
-        env_sh_file_path = os.path.join(env_sh_file_dir, 'env.sh')
+        env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir(
+            app=self.app,
+            repository_name=required_repository.name,
+            repository_owner=required_repository.owner,
+            repository_changeset_revision=required_repository.installed_changeset_revision,
+            tool_dependency_type="package",
+            tool_dependency_name=package_name,
+            tool_dependency_version=package_version,
+        )
+        env_sh_file_path = os.path.join(env_sh_file_dir, "env.sh")
         return env_sh_file_path
 
-    def handle_complex_repository_dependency_for_package(self, elem, package_name, package_version, tool_shed_repository):
+    def handle_complex_repository_dependency_for_package(
+        self, elem, package_name, package_version, tool_shed_repository
+    ):
         """
         Inspect the repository defined by a complex repository dependency definition and take certain steps to
         enable installation of the received package name and version to proceed.  The received elem is the
@@ -357,49 +449,59 @@ class Repository(RecipeTag, SyncDatabase):
         and package_version is being installed.
         """
         handled_tool_dependencies = []
-        tool_shed_url = elem.attrib['toolshed']
-        required_repository_name = elem.attrib['name']
-        required_repository_owner = elem.attrib['owner']
-        default_required_repository_changeset_revision = elem.attrib['changeset_revision']
-        required_repository = get_repository_for_dependency_relationship(self.app, tool_shed_url,
-                                                                         required_repository_name,
-                                                                         required_repository_owner,
-                                                                         default_required_repository_changeset_revision)
+        tool_shed_url = elem.attrib["toolshed"]
+        required_repository_name = elem.attrib["name"]
+        required_repository_owner = elem.attrib["owner"]
+        default_required_repository_changeset_revision = elem.attrib["changeset_revision"]
+        required_repository = get_repository_for_dependency_relationship(
+            self.app,
+            tool_shed_url,
+            required_repository_name,
+            required_repository_owner,
+            default_required_repository_changeset_revision,
+        )
         tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url)
         tmp_filename = None
         if required_repository:
             required_repository_changeset_revision = required_repository.installed_changeset_revision
             # Define the installation directory for the required tool dependency package in the required repository.
-            required_repository_package_install_dir = \
-                tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
-                                                                     repository_name=required_repository_name,
-                                                                     repository_owner=required_repository_owner,
-                                                                     repository_changeset_revision=required_repository_changeset_revision,
-                                                                     tool_dependency_type='package',
-                                                                     tool_dependency_name=package_name,
-                                                                     tool_dependency_version=package_version)
+            required_repository_package_install_dir = tool_dependency_util.get_tool_dependency_install_dir(
+                app=self.app,
+                repository_name=required_repository_name,
+                repository_owner=required_repository_owner,
+                repository_changeset_revision=required_repository_changeset_revision,
+                tool_dependency_type="package",
+                tool_dependency_name=package_name,
+                tool_dependency_version=package_version,
+            )
             # Define this dependent repository's tool dependency installation directory that will contain
             # the env.sh file with a path to the required repository's installed tool dependency package.
-            dependent_install_dir = \
-                tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
-                                                                     repository_name=tool_shed_repository.name,
-                                                                     repository_owner=tool_shed_repository.owner,
-                                                                     repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                     tool_dependency_type='package',
-                                                                     tool_dependency_name=package_name,
-                                                                     tool_dependency_version=package_version)
+            dependent_install_dir = tool_dependency_util.get_tool_dependency_install_dir(
+                app=self.app,
+                repository_name=tool_shed_repository.name,
+                repository_owner=tool_shed_repository.owner,
+                repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+                tool_dependency_type="package",
+                tool_dependency_name=package_name,
+                tool_dependency_version=package_version,
+            )
             if os.path.exists(dependent_install_dir):
                 # Notice that we'll throw away the following tool_dependency if it can be installed.
-                tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system(self.app,
-                                                                                                   tool_shed_repository,
-                                                                                                   package_name,
-                                                                                                   package_version,
-                                                                                                   dependent_install_dir,
-                                                                                                   tool_dependency_type='package')
+                tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system(
+                    self.app,
+                    tool_shed_repository,
+                    package_name,
+                    package_version,
+                    dependent_install_dir,
+                    tool_dependency_type="package",
+                )
                 if not can_install_tool_dependency:
-                    log.debug("Tool dependency %s version %s cannot be installed (it was probably previously installed), "
-                              "so appending it to the list of handled tool dependencies.",
-                              str(tool_dependency.name), str(tool_dependency.version))
+                    log.debug(
+                        "Tool dependency %s version %s cannot be installed (it was probably previously installed), "
+                        "so appending it to the list of handled tool dependencies.",
+                        str(tool_dependency.name),
+                        str(tool_dependency.version),
+                    )
                     handled_tool_dependencies.append(tool_dependency)
             else:
                 can_install_tool_dependency = True
@@ -409,64 +511,96 @@ class Repository(RecipeTag, SyncDatabase):
                 # required_repository.
                 if required_repository.is_deactivated_or_installed:
                     if not os.path.exists(required_repository_package_install_dir):
-                        log.error(f'Missing required tool dependency directory {str(required_repository_package_install_dir)}')
+                        log.error(
+                            f"Missing required tool dependency directory {str(required_repository_package_install_dir)}"
+                        )
                     repo_files_dir = required_repository.repo_files_directory(self.app)
                     if not repo_files_dir:
-                        message = "Unable to locate the repository directory for revision %s of installed repository %s owned by %s." % \
-                            (str(required_repository.changeset_revision), str(required_repository.name), str(required_repository.owner))
+                        message = (
+                            "Unable to locate the repository directory for revision %s of installed repository %s owned by %s."
+                            % (
+                                str(required_repository.changeset_revision),
+                                str(required_repository.name),
+                                str(required_repository.owner),
+                            )
+                        )
                         raise Exception(message)
-                    tool_dependencies_config = get_absolute_path_to_file_in_repository(repo_files_dir, 'tool_dependencies.xml')
+                    tool_dependencies_config = get_absolute_path_to_file_in_repository(
+                        repo_files_dir, "tool_dependencies.xml"
+                    )
                     if tool_dependencies_config:
                         config_to_use = tool_dependencies_config
                     else:
-                        message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \
-                            (str(required_repository.changeset_revision), str(required_repository.name), str(required_repository.owner))
+                        message = (
+                            "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s."
+                            % (
+                                str(required_repository.changeset_revision),
+                                str(required_repository.name),
+                                str(required_repository.owner),
+                            )
+                        )
                         raise Exception(message)
                 else:
                     # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
                     # should be updated if it's not current.
-                    text = get_updated_changeset_revisions_from_tool_shed(app=self.app,
-                                                                          tool_shed_url=tool_shed,
-                                                                          name=required_repository_name,
-                                                                          owner=required_repository_owner,
-                                                                          changeset_revision=required_repository_changeset_revision)
+                    text = get_updated_changeset_revisions_from_tool_shed(
+                        app=self.app,
+                        tool_shed_url=tool_shed,
+                        name=required_repository_name,
+                        owner=required_repository_owner,
+                        changeset_revision=required_repository_changeset_revision,
+                    )
                     if text:
                         updated_changeset_revisions = listify(text)
                         # The list of changeset revisions is in reverse order, so the newest will be first.
                         required_repository_changeset_revision = updated_changeset_revisions[0]
                     # Make a call to the tool shed to get the required repository's tool_dependencies.xml file.
-                    tmp_filename = self.create_temporary_tool_dependencies_config(tool_shed,
-                                                                                  required_repository_name,
-                                                                                  required_repository_owner,
-                                                                                  required_repository_changeset_revision)
+                    tmp_filename = self.create_temporary_tool_dependencies_config(
+                        tool_shed,
+                        required_repository_name,
+                        required_repository_owner,
+                        required_repository_changeset_revision,
+                    )
                     config_to_use = tmp_filename
-                handled_tool_dependencies = \
-                    self.create_tool_dependency_with_initialized_env_sh_file(dependent_install_dir=dependent_install_dir,
-                                                                             tool_shed_repository=tool_shed_repository,
-                                                                             required_repository=required_repository,
-                                                                             package_name=package_name,
-                                                                             package_version=package_version,
-                                                                             tool_dependencies_config=config_to_use)
+                handled_tool_dependencies = self.create_tool_dependency_with_initialized_env_sh_file(
+                    dependent_install_dir=dependent_install_dir,
+                    tool_shed_repository=tool_shed_repository,
+                    required_repository=required_repository,
+                    package_name=package_name,
+                    package_version=package_version,
+                    tool_dependencies_config=config_to_use,
+                )
                 self.remove_file(tmp_filename)
         else:
-            message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
-                (str(required_repository_name), str(required_repository_owner), str(default_required_repository_changeset_revision))
+            message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % (
+                str(required_repository_name),
+                str(required_repository_owner),
+                str(default_required_repository_changeset_revision),
+            )
             raise Exception(message)
         return handled_tool_dependencies
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         # We have a complex repository dependency definition.
         action_elem_tuples = []
         proceed_with_install = False
-        rd_tool_dependencies = self.handle_complex_repository_dependency_for_package(package_elem,
-                                                                                     package_name,
-                                                                                     package_version,
-                                                                                     tool_shed_repository)
+        rd_tool_dependencies = self.handle_complex_repository_dependency_for_package(
+            package_elem, package_name, package_version, tool_shed_repository
+        )
         for rd_tool_dependency in rd_tool_dependencies:
             if rd_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
                 # We'll log the error here, but continue installing packages since some may not require this dependency.
-                log.error(f"Error installing tool dependency for required repository: {str(rd_tool_dependency.error_message)}")
+                log.error(
+                    f"Error installing tool dependency for required repository: {str(rd_tool_dependency.error_message)}"
+                )
         return tool_dependency, proceed_with_install, action_elem_tuples
 
     def remove_file(self, file_name):
@@ -480,13 +614,19 @@ class Repository(RecipeTag, SyncDatabase):
 
 
 class SetEnvironment(RecipeTag):
-
     def __init__(self, app):
         self.app = app
-        self.tag = 'set_environment'
+        self.tag = "set_environment"
 
-    def process_tag_set(self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
-                        tool_dependency_db_records=None):
+    def process_tag_set(
+        self,
+        tool_shed_repository,
+        tool_dependency,
+        package_elem,
+        package_name,
+        package_version,
+        tool_dependency_db_records=None,
+    ):
         # We need to handle two tag sets for package_elem here, this:
         # <set_environment version="1.0">
         #    <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
@@ -498,7 +638,9 @@ class SetEnvironment(RecipeTag):
         if tool_dependency_db_records is None:
             attr_tups_of_dependencies_for_install = []
         else:
-            attr_tups_of_dependencies_for_install = [(td.name, td.version, td.type) for td in tool_dependency_db_records]
+            attr_tups_of_dependencies_for_install = [
+                (td.name, td.version, td.type) for td in tool_dependency_db_records
+            ]
         try:
             self.set_environment(package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install)
         except Exception as e:
@@ -532,9 +674,9 @@ class SetEnvironment(RecipeTag):
         # </set_environment>
         env_manager = EnvManager(self.app)
         tool_dependencies = []
-        env_var_version = elem.get('version', '1.0')
+        env_var_version = elem.get("version", "1.0")
         tool_shed_repository_install_dir = os.path.abspath(tool_shed_repository.repo_files_directory(self.app))
-        if elem.tag == 'environment_variable':
+        if elem.tag == "environment_variable":
             # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
             elems = [elem]
         else:
@@ -543,73 +685,79 @@ class SetEnvironment(RecipeTag):
             # </set_environment>
             elems = [env_var_elem for env_var_elem in elem]
         for env_var_elem in elems:
-            env_var_name = env_var_elem.get('name')
+            env_var_name = env_var_elem.get("name")
             if not env_var_name:
-                raise Exception('The <environment_variable> tag must have a name attribute')
+                raise Exception("The <environment_variable> tag must have a name attribute")
             # The value of env_var_name must match the text value of at least 1 <requirement> tag in the
             # tool config's <requirements> tag set whose "type" attribute is "set_environment" (e.g.,
             # <requirement type="set_environment">R_SCRIPT_PATH</requirement>).
-            env_var_action = env_var_elem.get('action')
+            env_var_action = env_var_elem.get("action")
             if not env_var_action:
-                raise Exception('The <environment_variable> tag must have an action attribute')
+                raise Exception("The <environment_variable> tag must have an action attribute")
             # Tool dependencies of type "set_environment" always have the version attribute set to None.
-            attr_tup = (env_var_name, None, 'set_environment')
+            attr_tup = (env_var_name, None, "set_environment")
             if attr_tup in attr_tups_of_dependencies_for_install:
-                install_dir = \
-                    tool_dependency_util.get_tool_dependency_install_dir(app=self.app,
-                                                                         repository_name=tool_shed_repository.name,
-                                                                         repository_owner=tool_shed_repository.owner,
-                                                                         repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                         tool_dependency_type='set_environment',
-                                                                         tool_dependency_name=env_var_name,
-                                                                         tool_dependency_version=None)
-                install_environment = InstallEnvironment(app=self.app,
-                                                         tool_shed_repository_install_dir=tool_shed_repository_install_dir,
-                                                         install_dir=install_dir)
-                env_var_dict = env_manager.create_env_var_dict(elem=env_var_elem,
-                                                               install_environment=install_environment)
+                install_dir = tool_dependency_util.get_tool_dependency_install_dir(
+                    app=self.app,
+                    repository_name=tool_shed_repository.name,
+                    repository_owner=tool_shed_repository.owner,
+                    repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+                    tool_dependency_type="set_environment",
+                    tool_dependency_name=env_var_name,
+                    tool_dependency_version=None,
+                )
+                install_environment = InstallEnvironment(
+                    app=self.app,
+                    tool_shed_repository_install_dir=tool_shed_repository_install_dir,
+                    install_dir=install_dir,
+                )
+                env_var_dict = env_manager.create_env_var_dict(
+                    elem=env_var_elem, install_environment=install_environment
+                )
                 if not os.path.exists(install_dir):
                     os.makedirs(install_dir)
                 status = self.app.install_model.ToolDependency.installation_status.INSTALLING
-                tool_dependency = \
-                    tool_dependency_util.create_or_update_tool_dependency(app=self.app,
-                                                                          tool_shed_repository=tool_shed_repository,
-                                                                          name=env_var_name,
-                                                                          version=None,
-                                                                          type='set_environment',
-                                                                          status=status,
-                                                                          set_status=True)
-                if env_var_version == '1.0':
+                tool_dependency = tool_dependency_util.create_or_update_tool_dependency(
+                    app=self.app,
+                    tool_shed_repository=tool_shed_repository,
+                    name=env_var_name,
+                    version=None,
+                    type="set_environment",
+                    status=status,
+                    set_status=True,
+                )
+                if env_var_version == "1.0":
                     # Create this tool dependency's env.sh file.
                     env_file_builder = EnvFileBuilder(install_dir)
                     return_code = env_file_builder.append_line(make_executable=True, **env_var_dict)
                     if return_code:
-                        error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \
-                            (str(tool_dependency.name), str(return_code))
+                        error_message = "Error creating env.sh file for tool dependency %s, return_code: %s" % (
+                            str(tool_dependency.name),
+                            str(return_code),
+                        )
                         log.debug(error_message)
                         status = self.app.install_model.ToolDependency.installation_status.ERROR
-                        tool_dependency = \
-                            tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                tool_dependency=tool_dependency,
-                                                                                status=status,
-                                                                                error_message=error_message)
+                        tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                            self.app, tool_dependency=tool_dependency, status=status, error_message=error_message
+                        )
                     else:
-                        if tool_dependency.status not in [self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                          self.app.install_model.ToolDependency.installation_status.INSTALLED]:
+                        if tool_dependency.status not in [
+                            self.app.install_model.ToolDependency.installation_status.ERROR,
+                            self.app.install_model.ToolDependency.installation_status.INSTALLED,
+                        ]:
                             status = self.app.install_model.ToolDependency.installation_status.INSTALLED
-                            tool_dependency = \
-                                tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                                    tool_dependency=tool_dependency,
-                                                                                    status=status)
-                            log.debug('Environment variable %s set in %s for tool dependency %s.' %
-                                (str(env_var_name), str(install_dir), str(tool_dependency.name)))
+                            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                                self.app, tool_dependency=tool_dependency, status=status
+                            )
+                            log.debug(
+                                "Environment variable %s set in %s for tool dependency %s."
+                                % (str(env_var_name), str(install_dir), str(tool_dependency.name))
+                            )
                 else:
                     error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
                     status = self.app.install_model.ToolDependency.installation_status.ERROR
-                    tool_dependency = \
-                        tool_dependency_util.set_tool_dependency_attributes(self.app,
-                                                                            tool_dependency=tool_dependency,
-                                                                            status=status,
-                                                                            error_message=error_message)
+                    tool_dependency = tool_dependency_util.set_tool_dependency_attributes(
+                        self.app, tool_dependency=tool_dependency, status=status, error_message=error_message
+                    )
                 tool_dependencies.append(tool_dependency)
         return tool_dependencies
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
index eff5a432122..466a2743374 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
@@ -21,7 +21,6 @@ SHED_DATA_MANAGER_CONF_XML = """<?xml version="1.0"?>
 
 
 class DataManagerHandler:
-
     def __init__(self, app):
         self.app = app
 
@@ -30,7 +29,7 @@ class DataManagerHandler:
         tree, error_message = parse_xml(self.app.config.shed_data_manager_config_file)
         if tree:
             root = tree.getroot()
-            return root.get('tool_path', None)
+            return root.get("tool_path", None)
         return None
 
     def data_manager_config_elems_to_xml_file(self, config_elems, config_filename):
@@ -47,15 +46,22 @@ class DataManagerHandler:
         for elem in config_elems:
             root.append(elem)
         try:
-            with RenamedTemporaryFile(config_filename, mode='w') as fh:
+            with RenamedTemporaryFile(config_filename, mode="w") as fh:
                 fh.write(xml_to_string(root))
         except Exception:
             log.exception("Exception in DataManagerHandler.data_manager_config_elems_to_xml_file")
 
-    def install_data_managers(self, shed_data_manager_conf_filename, metadata_dict, shed_config_dict,
-                              relative_install_dir, repository, repository_tools_tups):
+    def install_data_managers(
+        self,
+        shed_data_manager_conf_filename,
+        metadata_dict,
+        shed_config_dict,
+        relative_install_dir,
+        repository,
+        repository_tools_tups,
+    ):
         rval = []
-        if 'data_manager' in metadata_dict:
+        if "data_manager" in metadata_dict:
             tpm = tool_panel_manager.ToolPanelManager(self.app)
             repository_tools_by_guid = {}
             for tool_tup in repository_tools_tups:
@@ -65,7 +71,7 @@ class DataManagerHandler:
                 tree, error_message = parse_xml(shed_data_manager_conf_filename, check_exists=False)
             except OSError as exc:
                 if exc.errno == errno.ENOENT:
-                    with open(shed_data_manager_conf_filename, 'w') as fh:
+                    with open(shed_data_manager_conf_filename, "w") as fh:
                         fh.write(SHED_DATA_MANAGER_CONF_XML)
                     tree, error_message = parse_xml(shed_data_manager_conf_filename)
                 else:
@@ -73,65 +79,79 @@ class DataManagerHandler:
             if tree is None:
                 return rval
             config_elems = [elem for elem in tree.getroot()]
-            repo_data_manager_conf_filename = metadata_dict['data_manager'].get('config_filename', None)
+            repo_data_manager_conf_filename = metadata_dict["data_manager"].get("config_filename", None)
             if repo_data_manager_conf_filename is None:
                 log.debug("No data_manager_conf.xml file has been defined.")
                 return rval
             data_manager_config_has_changes = False
-            relative_repo_data_manager_dir = os.path.join(shed_config_dict.get('tool_path', ''), relative_install_dir)
-            repo_data_manager_conf_filename = os.path.join(relative_repo_data_manager_dir, repo_data_manager_conf_filename)
+            relative_repo_data_manager_dir = os.path.join(shed_config_dict.get("tool_path", ""), relative_install_dir)
+            repo_data_manager_conf_filename = os.path.join(
+                relative_repo_data_manager_dir, repo_data_manager_conf_filename
+            )
             tree, error_message = parse_xml(repo_data_manager_conf_filename)
             if tree is None:
                 return rval
             root = tree.getroot()
             for elem in root:
-                if elem.tag == 'data_manager':
-                    data_manager_id = elem.get('id', None)
+                if elem.tag == "data_manager":
+                    data_manager_id = elem.get("id", None)
                     if data_manager_id is None:
-                        log.error("A data manager was defined that does not have an id and will not be installed:\n%s" %
-                                  xml_to_string(elem))
+                        log.error(
+                            "A data manager was defined that does not have an id and will not be installed:\n%s"
+                            % xml_to_string(elem)
+                        )
                         continue
-                    data_manager_dict = metadata_dict['data_manager'].get('data_managers', {}).get(data_manager_id, None)
+                    data_manager_dict = (
+                        metadata_dict["data_manager"].get("data_managers", {}).get(data_manager_id, None)
+                    )
                     if data_manager_dict is None:
                         log.error(f"Data manager metadata is not defined properly for '{data_manager_id}'.")
                         continue
-                    guid = data_manager_dict.get('guid', None)
+                    guid = data_manager_dict.get("guid", None)
                     if guid is None:
                         log.error(f"Data manager guid '{guid}' is not set in metadata for '{data_manager_id}'.")
                         continue
-                    elem.set('guid', guid)
-                    tool_guid = data_manager_dict.get('tool_guid', None)
+                    elem.set("guid", guid)
+                    tool_guid = data_manager_dict.get("tool_guid", None)
                     if tool_guid is None:
-                        log.error(f"Data manager tool guid '{tool_guid}' is not set in metadata for '{data_manager_id}'.")
+                        log.error(
+                            f"Data manager tool guid '{tool_guid}' is not set in metadata for '{data_manager_id}'."
+                        )
                         continue
                     tool_dict = repository_tools_by_guid.get(tool_guid, None)
                     if tool_dict is None:
-                        log.error("Data manager tool guid '%s' could not be found for '%s'. Perhaps the tool is invalid?" %
-                                  (tool_guid, data_manager_id))
+                        log.error(
+                            "Data manager tool guid '%s' could not be found for '%s'. Perhaps the tool is invalid?"
+                            % (tool_guid, data_manager_id)
+                        )
                         continue
-                    tool = tool_dict.get('tool', None)
+                    tool = tool_dict.get("tool", None)
                     if tool is None:
-                        log.error("Data manager tool with guid '%s' could not be found for '%s'. Perhaps the tool is invalid?" %
-                                  (tool_guid, data_manager_id))
+                        log.error(
+                            "Data manager tool with guid '%s' could not be found for '%s'. Perhaps the tool is invalid?"
+                            % (tool_guid, data_manager_id)
+                        )
                         continue
-                    tool_config_filename = tool_dict.get('tool_config_filename', None)
+                    tool_config_filename = tool_dict.get("tool_config_filename", None)
                     if tool_config_filename is None:
                         log.error(f"Data manager metadata is missing 'tool_config_file' for '{data_manager_id}'.")
                         continue
-                    elem.set('shed_conf_file', shed_config_dict['config_filename'])
-                    if elem.get('tool_file', None) is not None:
-                        del elem.attrib['tool_file']  # remove old tool_file info
-                    tool_elem = tpm.generate_tool_elem(repository.tool_shed,
-                                                       repository.name,
-                                                       repository.installed_changeset_revision,
-                                                       repository.owner,
-                                                       tool_config_filename,
-                                                       tool,
-                                                       None)
+                    elem.set("shed_conf_file", shed_config_dict["config_filename"])
+                    if elem.get("tool_file", None) is not None:
+                        del elem.attrib["tool_file"]  # remove old tool_file info
+                    tool_elem = tpm.generate_tool_elem(
+                        repository.tool_shed,
+                        repository.name,
+                        repository.installed_changeset_revision,
+                        repository.owner,
+                        tool_config_filename,
+                        tool,
+                        None,
+                    )
                     elem.insert(0, tool_elem)
-                    data_manager = \
-                        self.app.data_managers.load_manager_from_elem(elem,
-                                                                      tool_path=shed_config_dict.get('tool_path', ''))
+                    data_manager = self.app.data_managers.load_manager_from_elem(
+                        elem, tool_path=shed_config_dict.get("tool_path", "")
+                    )
                     if data_manager:
                         rval.append(data_manager)
                 elif elem.tag is etree.Comment:
@@ -150,27 +170,36 @@ class DataManagerHandler:
 
     def remove_from_data_manager(self, repository):
         metadata_dict = repository.metadata_
-        if metadata_dict and 'data_manager' in metadata_dict:
+        if metadata_dict and "data_manager" in metadata_dict:
             shed_data_manager_conf_filename = self.app.config.shed_data_manager_config_file
             tree, error_message = parse_xml(shed_data_manager_conf_filename)
             if tree:
                 root = tree.getroot()
-                assert root.tag == 'data_managers', f'The file provided ({shed_data_manager_conf_filename}) for removing data managers from is not a valid data manager xml file.'
-                guids = [data_manager_dict.get('guid') for data_manager_dict in metadata_dict.get('data_manager', {}).get('data_managers', {}).values() if 'guid' in data_manager_dict]
+                assert (
+                    root.tag == "data_managers"
+                ), f"The file provided ({shed_data_manager_conf_filename}) for removing data managers from is not a valid data manager xml file."
+                guids = [
+                    data_manager_dict.get("guid")
+                    for data_manager_dict in metadata_dict.get("data_manager", {}).get("data_managers", {}).values()
+                    if "guid" in data_manager_dict
+                ]
                 load_old_data_managers_by_guid = {}
                 data_manager_config_has_changes = False
                 config_elems = []
                 for elem in root:
                     # Match Data Manager elements by guid and installed_changeset_revision
                     elem_matches_removed_data_manager = False
-                    if elem.tag == 'data_manager':
-                        guid = elem.get('guid', None)
+                    if elem.tag == "data_manager":
+                        guid = elem.get("guid", None)
                         if guid in guids:
-                            tool_elem = elem.find('tool')
+                            tool_elem = elem.find("tool")
                             if tool_elem is not None:
-                                installed_changeset_revision_elem = tool_elem.find('installed_changeset_revision')
+                                installed_changeset_revision_elem = tool_elem.find("installed_changeset_revision")
                                 if installed_changeset_revision_elem is not None:
-                                    if installed_changeset_revision_elem.text == repository.installed_changeset_revision:
+                                    if (
+                                        installed_changeset_revision_elem.text
+                                        == repository.installed_changeset_revision
+                                    ):
                                         elem_matches_removed_data_manager = True
                                     else:
                                         # This is a different version, which had been previously overridden
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
index e97052a1709..9e2f0ce70e1 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
@@ -18,7 +18,6 @@ log = logging.getLogger(__name__)
 
 
 class ToolPanelManager:
-
     def __init__(self, app):
         self.app = app
 
@@ -33,22 +32,22 @@ class ToolPanelManager:
             # In that case we don't want to wait for a toolbox reload that will never happen.
             return
         old_toolbox = self.app.toolbox
-        shed_tool_conf = shed_tool_conf_dict['config_filename']
-        tool_cache_data_dir = shed_tool_conf_dict.get('tool_cache_data_dir')
-        tool_path = shed_tool_conf_dict['tool_path']
+        shed_tool_conf = shed_tool_conf_dict["config_filename"]
+        tool_cache_data_dir = shed_tool_conf_dict.get("tool_cache_data_dir")
+        tool_path = shed_tool_conf_dict["tool_path"]
         config_elems = []
         # Ideally shed_tool_conf.xml would be created before the repo is cloned and added to the DB, but this is called
         # from too many places to make it feasible at this time
         try:
             tree, error_message = parse_xml(shed_tool_conf, check_exists=False)
         except OSError as exc:
-            if (exc.errno == errno.ENOENT and shed_tool_conf_dict.get('create', None) is not None):
-                log.info('Creating shed tool config with default contents: %s', shed_tool_conf)
-                with open(shed_tool_conf, 'w') as fh:
-                    fh.write(shed_tool_conf_dict['create'])
+            if exc.errno == errno.ENOENT and shed_tool_conf_dict.get("create", None) is not None:
+                log.info("Creating shed tool config with default contents: %s", shed_tool_conf)
+                with open(shed_tool_conf, "w") as fh:
+                    fh.write(shed_tool_conf_dict["create"])
                 tree, error_message = parse_xml(shed_tool_conf)
             else:
-                log.error('Unable to load shed tool config: %s', shed_tool_conf)
+                log.error("Unable to load shed tool config: %s", shed_tool_conf)
                 raise
         if tree:
             root = tree.getroot()
@@ -56,11 +55,13 @@ class ToolPanelManager:
                 config_elems.append(elem)
             # Add the new elements to the in-memory list of config_elems.
             for elem_entry in elem_list:
-                if elem_entry.tag == 'section':
+                if elem_entry.tag == "section":
                     # Loop through section entries in the in-memory tool panel.
                     for existing_elem in config_elems:
                         # Compare the section ID for each one to the section ID for the tool being installed.
-                        if existing_elem.tag == 'section' and existing_elem.attrib.get('id', None) == elem_entry.attrib.get('id', None):
+                        if existing_elem.tag == "section" and existing_elem.attrib.get(
+                            "id", None
+                        ) == elem_entry.attrib.get("id", None):
                             # We've found a section, add the incoming tools to it.
                             for child in elem_entry:
                                 existing_elem.append(child)
@@ -78,24 +79,38 @@ class ToolPanelManager:
         else:
             log.error(error_message)
 
-    def add_to_tool_panel(self, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner,
-                          shed_tool_conf, tool_panel_dict, new_install=True, tool_panel_section_mapping=None):
+    def add_to_tool_panel(
+        self,
+        repository_name,
+        repository_clone_url,
+        changeset_revision,
+        repository_tools_tups,
+        owner,
+        shed_tool_conf,
+        tool_panel_dict,
+        new_install=True,
+        tool_panel_section_mapping=None,
+    ):
         """A tool shed repository is being installed or updated so handle tool panel alterations accordingly."""
         tool_panel_section_mapping = tool_panel_section_mapping or {}
         # We need to change the in-memory version and the file system version of the shed_tool_conf file.
         shed_tool_conf_dict = self.get_shed_tool_conf_dict(shed_tool_conf)
-        tool_panel_dict = self.update_tool_panel_dict(tool_panel_dict, tool_panel_section_mapping, repository_tools_tups)
+        tool_panel_dict = self.update_tool_panel_dict(
+            tool_panel_dict, tool_panel_section_mapping, repository_tools_tups
+        )
         # Generate the list of ElementTree Element objects for each section or tool.
-        elem_list = self.generate_tool_panel_elem_list(repository_name,
-                                                       repository_clone_url,
-                                                       changeset_revision,
-                                                       tool_panel_dict,
-                                                       repository_tools_tups,
-                                                       owner=owner)
+        elem_list = self.generate_tool_panel_elem_list(
+            repository_name,
+            repository_clone_url,
+            changeset_revision,
+            tool_panel_dict,
+            repository_tools_tups,
+            owner=owner,
+        )
         if new_install:
-            tool_path = shed_tool_conf_dict['tool_path']
+            tool_path = shed_tool_conf_dict["tool_path"]
             # Add the new elements to the shed_tool_conf file on disk.
-            config_elems = shed_tool_conf_dict['config_elems']
+            config_elems = shed_tool_conf_dict["config_elems"]
             for config_elem in elem_list:
                 # Add the new elements to the in-memory list of config_elems.
                 config_elems.append(config_elem)
@@ -104,10 +119,10 @@ class ToolPanelManager:
                     config_elem,
                     tool_path=tool_path,
                     load_panel_dict=True,
-                    guid=config_elem.get('guid'),
+                    guid=config_elem.get("guid"),
                 )
             # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict.
-            shed_tool_conf_dict['config_elems'] = config_elems
+            shed_tool_conf_dict["config_elems"] = config_elems
             self.app.toolbox.update_shed_config(shed_tool_conf_dict)
             self.add_to_shed_tool_config(shed_tool_conf_dict, elem_list)
 
@@ -117,37 +132,40 @@ class ToolPanelManager:
         value of config_filename.
         """
         try:
-            tool_cache_data_dir = f' tool_cache_data_dir="{tool_cache_data_dir}"' if tool_cache_data_dir else ''
-            root = parse_xml_string(f'<?xml version="1.0"?>\n<toolbox tool_path="{tool_path}"{tool_cache_data_dir}></toolbox>')
+            tool_cache_data_dir = f' tool_cache_data_dir="{tool_cache_data_dir}"' if tool_cache_data_dir else ""
+            root = parse_xml_string(
+                f'<?xml version="1.0"?>\n<toolbox tool_path="{tool_path}"{tool_cache_data_dir}></toolbox>'
+            )
             for elem in config_elems:
                 root.append(elem)
-            with RenamedTemporaryFile(config_filename, mode='w') as fh:
+            with RenamedTemporaryFile(config_filename, mode="w") as fh:
                 fh.write(xml_to_string(root, pretty=True))
         except Exception:
             log.exception("Exception in ToolPanelManager.config_elems_to_xml_file")
 
-    def generate_tool_elem(self, tool_shed, repository_name, changeset_revision, owner, tool_file_path,
-                           tool, tool_section):
+    def generate_tool_elem(
+        self, tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section
+    ):
         """Create and return an ElementTree tool Element."""
         if tool_section is not None:
-            tool_elem = etree.SubElement(tool_section, 'tool')
+            tool_elem = etree.SubElement(tool_section, "tool")
         else:
-            tool_elem = etree.Element('tool')
-        tool_elem.attrib['file'] = tool_file_path
+            tool_elem = etree.Element("tool")
+        tool_elem.attrib["file"] = tool_file_path
         if not tool.guid:
             raise ValueError("tool has no guid")
-        tool_elem.attrib['guid'] = tool.guid
-        tool_shed_elem = etree.SubElement(tool_elem, 'tool_shed')
+        tool_elem.attrib["guid"] = tool.guid
+        tool_shed_elem = etree.SubElement(tool_elem, "tool_shed")
         tool_shed_elem.text = tool_shed
-        repository_name_elem = etree.SubElement(tool_elem, 'repository_name')
+        repository_name_elem = etree.SubElement(tool_elem, "repository_name")
         repository_name_elem.text = repository_name
-        repository_owner_elem = etree.SubElement(tool_elem, 'repository_owner')
+        repository_owner_elem = etree.SubElement(tool_elem, "repository_owner")
         repository_owner_elem.text = owner
-        changeset_revision_elem = etree.SubElement(tool_elem, 'installed_changeset_revision')
+        changeset_revision_elem = etree.SubElement(tool_elem, "installed_changeset_revision")
         changeset_revision_elem.text = changeset_revision
-        id_elem = etree.SubElement(tool_elem, 'id')
+        id_elem = etree.SubElement(tool_elem, "id")
         id_elem.text = tool.id
-        version_elem = etree.SubElement(tool_elem, 'version')
+        version_elem = etree.SubElement(tool_elem, "version")
         version_elem.text = tool.version
         return tool_elem
 
@@ -161,16 +179,18 @@ class ToolPanelManager:
         if tool_section:
             section_id = tool_section.id
             section_name = tool_section.name
-            section_version = tool_section.version or ''
+            section_version = tool_section.version or ""
         else:
-            section_id = ''
-            section_name = ''
-            section_version = ''
+            section_id = ""
+            section_name = ""
+            section_version = ""
         for tool_dict in tool_dicts:
-            if tool_dict.get('add_to_tool_panel', True):
-                guid = tool_dict['guid']
-                tool_config = tool_dict['tool_config']
-                tool_section_dict = dict(tool_config=tool_config, id=section_id, name=section_name, version=section_version)
+            if tool_dict.get("add_to_tool_panel", True):
+                guid = tool_dict["guid"]
+                tool_config = tool_dict["tool_config"]
+                tool_section_dict = dict(
+                    tool_config=tool_config, id=section_id, name=section_name, version=section_version
+                )
                 if guid in tool_panel_dict:
                     tool_panel_dict[guid].append(tool_section_dict)
                 else:
@@ -195,8 +215,7 @@ class ToolPanelManager:
         """
         tool_panel_dict = {}
         file_name = strip_path(tool_config)
-        tool_section_dicts = self. generate_tool_section_dicts(tool_config=file_name,
-                                                               tool_sections=tool_sections)
+        tool_section_dicts = self.generate_tool_section_dicts(tool_config=file_name, tool_sections=tool_sections)
         tool_panel_dict[guid] = tool_section_dicts
         return tool_panel_dict
 
@@ -210,15 +229,16 @@ class ToolPanelManager:
         activation or re-installation using the original layout.
         """
         tool_panel_dict = {}
-        shed_tool_conf, tool_path, relative_install_dir = \
-            get_tool_panel_config_tool_path_install_dir(self.app, repository)
+        shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir(
+            self.app, repository
+        )
         metadata = repository.metadata_
         # Create a dictionary of tool guid and tool config file name for each tool in the repository.
         guids_and_configs = {}
-        if 'tools' in metadata:
-            for tool_dict in metadata['tools']:
-                guid = tool_dict['guid']
-                tool_config = tool_dict['tool_config']
+        if "tools" in metadata:
+            for tool_dict in metadata["tools"]:
+                guid = tool_dict["guid"]
+                tool_config = tool_dict["tool_config"]
                 file_name = strip_path(tool_config)
                 guids_and_configs[guid] = file_name
         # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict.
@@ -227,55 +247,64 @@ class ToolPanelManager:
             return tool_panel_dict
         root = tree.getroot()
         for elem in root:
-            if elem.tag == 'tool':
-                guid = elem.get('guid')
+            if elem.tag == "tool":
+                guid = elem.get("guid")
                 if guid in guids_and_configs:
                     # The tool is displayed in the tool panel outside of any tool sections.
-                    tool_section_dict = dict(tool_config=guids_and_configs[guid], id='', name='', version='')
+                    tool_section_dict = dict(tool_config=guids_and_configs[guid], id="", name="", version="")
                     if guid in tool_panel_dict:
                         tool_panel_dict[guid].append(tool_section_dict)
                     else:
                         tool_panel_dict[guid] = [tool_section_dict]
-            elif elem.tag == 'section':
-                section_id = elem.get('id') or ''
-                section_name = elem.get('name') or ''
-                section_version = elem.get('version') or ''
+            elif elem.tag == "section":
+                section_id = elem.get("id") or ""
+                section_name = elem.get("name") or ""
+                section_version = elem.get("version") or ""
                 for section_elem in elem:
-                    if section_elem.tag == 'tool':
-                        guid = section_elem.get('guid')
+                    if section_elem.tag == "tool":
+                        guid = section_elem.get("guid")
                         if guid in guids_and_configs:
                             # The tool is displayed in the tool panel inside the current tool section.
-                            tool_section_dict = dict(tool_config=guids_and_configs[guid],
-                                                     id=section_id,
-                                                     name=section_name,
-                                                     version=section_version)
+                            tool_section_dict = dict(
+                                tool_config=guids_and_configs[guid],
+                                id=section_id,
+                                name=section_name,
+                                version=section_version,
+                            )
                             if guid in tool_panel_dict:
                                 tool_panel_dict[guid].append(tool_section_dict)
                             else:
                                 tool_panel_dict[guid] = [tool_section_dict]
         return tool_panel_dict
 
-    def generate_tool_panel_elem_list(self, repository_name, repository_clone_url, changeset_revision,
-                                      tool_panel_dict, repository_tools_tups, owner=''):
+    def generate_tool_panel_elem_list(
+        self,
+        repository_name,
+        repository_clone_url,
+        changeset_revision,
+        tool_panel_dict,
+        repository_tools_tups,
+        owner="",
+    ):
         """Generate a list of ElementTree Element objects for each section or tool."""
         elem_list = []
         tool_elem = None
         cleaned_repository_clone_url = remove_protocol_and_user_from_clone_url(repository_clone_url)
         if not owner:
             owner = get_repository_owner(cleaned_repository_clone_url)
-        tool_shed = cleaned_repository_clone_url.split('/repos/')[0].rstrip('/')
+        tool_shed = cleaned_repository_clone_url.split("/repos/")[0].rstrip("/")
         for guid, tool_section_dicts in tool_panel_dict.items():
             for tool_section_dict in tool_section_dicts:
                 tool_section = None
                 inside_section = False
                 section_in_elem_list = None
-                if tool_section_dict['id']:
+                if tool_section_dict["id"]:
                     inside_section = True
                     # Create a new section element only if we haven't already created it.
                     for index, elem in enumerate(elem_list):
-                        if elem.tag == 'section':
-                            section_id = elem.get('id', None)
-                            if section_id == tool_section_dict['id']:
+                        if elem.tag == "section":
+                            section_id = elem.get("id", None)
+                            if section_id == tool_section_dict["id"]:
                                 section_in_elem_list = index
                                 tool_section = elem
                                 break
@@ -286,13 +315,15 @@ class ToolPanelManager:
                     tool_file_path, tup_guid, tool = repository_tool_tup
                     if tup_guid == guid:
                         break
-                tool_elem = self.generate_tool_elem(tool_shed,
-                                                    repository_name,
-                                                    changeset_revision,
-                                                    owner,
-                                                    tool_file_path,
-                                                    tool,
-                                                    tool_section if inside_section else None)
+                tool_elem = self.generate_tool_elem(
+                    tool_shed,
+                    repository_name,
+                    changeset_revision,
+                    owner,
+                    tool_file_path,
+                    tool,
+                    tool_section if inside_section else None,
+                )
                 if inside_section:
                     if section_in_elem_list is not None:
                         elem_list[section_in_elem_list] = tool_section
@@ -305,42 +336,43 @@ class ToolPanelManager:
     def generate_tool_section_dicts(self, tool_config=None, tool_sections=None):
         tool_section_dicts = []
         if tool_config is None:
-            tool_config = ''
+            tool_config = ""
         if tool_sections:
             for tool_section in tool_sections:
                 # The value of tool_section will be None if the tool is displayed outside
                 # of any sections in the tool panel.
                 if tool_section:
-                    section_id = tool_section.id or ''
-                    section_version = tool_section.version or ''
-                    section_name = tool_section.name or ''
+                    section_id = tool_section.id or ""
+                    section_version = tool_section.version or ""
+                    section_name = tool_section.name or ""
                 else:
-                    section_id = ''
-                    section_version = ''
-                    section_name = ''
-                tool_section_dicts.append(dict(tool_config=tool_config,
-                                               id=section_id,
-                                               version=section_version,
-                                               name=section_name))
+                    section_id = ""
+                    section_version = ""
+                    section_name = ""
+                tool_section_dicts.append(
+                    dict(tool_config=tool_config, id=section_id, version=section_version, name=section_name)
+                )
         else:
-            tool_section_dicts.append(dict(tool_config=tool_config, id='', version='', name=''))
+            tool_section_dicts.append(dict(tool_config=tool_config, id="", version="", name=""))
         return tool_section_dicts
 
     def generate_tool_section_element_from_dict(self, tool_section_dict):
         # The value of tool_section_dict looks like the following.
         # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}
-        if tool_section_dict['id']:
+        if tool_section_dict["id"]:
             # Create a new tool section.
-            tool_section = etree.Element('section')
-            tool_section.attrib['id'] = tool_section_dict['id']
-            tool_section.attrib['name'] = tool_section_dict['name']
-            tool_section.attrib['version'] = tool_section_dict['version']
+            tool_section = etree.Element("section")
+            tool_section.attrib["id"] = tool_section_dict["id"]
+            tool_section.attrib["name"] = tool_section_dict["name"]
+            tool_section.attrib["version"] = tool_section_dict["version"]
         else:
             tool_section = None
         return tool_section
 
     def get_or_create_tool_section(self, toolbox, tool_panel_section_id, new_tool_panel_section_label=None):
-        return toolbox.get_section(section_id=tool_panel_section_id, new_label=new_tool_panel_section_label, create_if_needed=True)
+        return toolbox.get_section(
+            section_id=tool_panel_section_id, new_label=new_tool_panel_section_label, create_if_needed=True
+        )
 
     def get_shed_tool_conf_dict(self, shed_tool_conf):
         """
@@ -348,13 +380,15 @@ class ToolPanelManager:
         the config_elems entry in the shed_tool_conf_dict associated with the file.
         """
         for shed_tool_conf_dict in self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
-            if shed_tool_conf == shed_tool_conf_dict['config_filename']:
+            if shed_tool_conf == shed_tool_conf_dict["config_filename"]:
                 return shed_tool_conf_dict
             else:
-                file_name = strip_path(shed_tool_conf_dict['config_filename'])
+                file_name = strip_path(shed_tool_conf_dict["config_filename"])
                 if shed_tool_conf == file_name:
                     return shed_tool_conf_dict
-        raise RequestParameterInvalidException(f"Requested shed_tool_conf '{shed_tool_conf}' is not an active shed_tool_config_file")
+        raise RequestParameterInvalidException(
+            f"Requested shed_tool_conf '{shed_tool_conf}' is not an active shed_tool_config_file"
+        )
 
     def handle_tool_panel_section(self, toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None):
         """Return a ToolSection object retrieved from the current in-memory tool_panel."""
@@ -363,19 +397,19 @@ class ToolPanelManager:
         # tool panel config (e.g., tool_conf.xml, which may have getext).  If new_tool_panel_section_label
         # is received, a new section will be added to the tool panel.
         if new_tool_panel_section_label:
-            section_id = str(new_tool_panel_section_label.lower().replace(' ', '_'))
-            tool_panel_section_key, tool_section = \
-                self.get_or_create_tool_section(toolbox,
-                                                tool_panel_section_id=section_id,
-                                                new_tool_panel_section_label=new_tool_panel_section_label)
+            section_id = str(new_tool_panel_section_label.lower().replace(" ", "_"))
+            tool_panel_section_key, tool_section = self.get_or_create_tool_section(
+                toolbox, tool_panel_section_id=section_id, new_tool_panel_section_label=new_tool_panel_section_label
+            )
         elif tool_panel_section_id:
             tool_panel_section_key, tool_section = toolbox.get_section(tool_panel_section_id)
         else:
             return None, None
         return tool_panel_section_key, tool_section
 
-    def handle_tool_panel_selection(self, toolbox, metadata, no_changes_checked, tool_panel_section_id,
-                                    new_tool_panel_section_label):
+    def handle_tool_panel_selection(
+        self, toolbox, metadata, no_changes_checked, tool_panel_section_id, new_tool_panel_section_label
+    ):
         """
         Handle the selected tool panel location for loading tools included in
         tool shed repositories when installing or reinstalling them.
@@ -383,35 +417,37 @@ class ToolPanelManager:
         # Get the location in the tool panel in which each tool was originally loaded.
         tool_section = None
         tool_panel_section_key = None
-        if 'tools' in metadata:
+        if "tools" in metadata:
             # This forces everything to be loaded into the same section (or no section)
             # in the tool panel.
             if no_changes_checked:
                 # Make sure the no_changes check box overrides the new_tool_panel_section_label
                 # if the user checked the check box and entered something into the field.
                 new_tool_panel_section_label = None
-                if 'tool_panel_section' in metadata:
-                    tool_panel_dict = metadata['tool_panel_section']
+                if "tool_panel_section" in metadata:
+                    tool_panel_dict = metadata["tool_panel_section"]
                     if not tool_panel_dict:
-                        tool_panel_dict = self.generate_tool_panel_dict_for_new_install(metadata['tools'])
+                        tool_panel_dict = self.generate_tool_panel_dict_for_new_install(metadata["tools"])
                 else:
-                    tool_panel_dict = self.generate_tool_panel_dict_for_new_install(metadata['tools'])
+                    tool_panel_dict = self.generate_tool_panel_dict_for_new_install(metadata["tools"])
                 if tool_panel_dict:
                     # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section.
                     tool_section_dicts = tool_panel_dict[next(iter(tool_panel_dict))]
                     tool_section_dict = tool_section_dicts[0]
-                    original_section_id = tool_section_dict['id']
+                    original_section_id = tool_section_dict["id"]
                     if original_section_id:
-                        tool_panel_section_key, tool_section = \
-                            self.get_or_create_tool_section(toolbox,
-                                                            tool_panel_section_id=original_section_id,
-                                                            new_tool_panel_section_label=new_tool_panel_section_label)
+                        tool_panel_section_key, tool_section = self.get_or_create_tool_section(
+                            toolbox,
+                            tool_panel_section_id=original_section_id,
+                            new_tool_panel_section_label=new_tool_panel_section_label,
+                        )
             else:
                 # The user elected to change the tool panel section to contain the tools.
-                tool_panel_section_key, tool_section = \
-                    self.handle_tool_panel_section(toolbox,
-                                                   tool_panel_section_id=tool_panel_section_id,
-                                                   new_tool_panel_section_label=new_tool_panel_section_label)
+                tool_panel_section_key, tool_section = self.handle_tool_panel_section(
+                    toolbox,
+                    tool_panel_section_id=tool_panel_section_id,
+                    new_tool_panel_section_label=new_tool_panel_section_label,
+                )
         return tool_section, tool_panel_section_key
 
     def remove_from_shed_tool_config(self, shed_tool_conf_dict, metadata):
@@ -422,15 +458,15 @@ class ToolPanelManager:
         subset of the entire list if one or more repositories have been
         deactivated.
         """
-        if 'tools' not in metadata:
+        if "tools" not in metadata:
             return
         # We need to use the tool path to uniquely identify the tools to remove,
         # since multiple installable revisions of a repository can provide the
         # same version of a tool (i.e. there may be another tool with the same
         # guid that we should not remove from shed_tool_conf).
-        guid_paths_to_remove = [(_['guid'], _['tool_config']) for _ in metadata['tools']]
-        shed_tool_conf = shed_tool_conf_dict['config_filename']
-        tool_path = shed_tool_conf_dict['tool_path']
+        guid_paths_to_remove = [(_["guid"], _["tool_config"]) for _ in metadata["tools"]]
+        shed_tool_conf = shed_tool_conf_dict["config_filename"]
+        tool_path = shed_tool_conf_dict["tool_path"]
         config_elems = []
         tree, error_message = parse_xml(shed_tool_conf)
         if tree:
@@ -439,10 +475,10 @@ class ToolPanelManager:
                 config_elems.append(elem)
             config_elems_to_remove = []
             for config_elem in config_elems:
-                if config_elem.tag == 'section':
+                if config_elem.tag == "section":
                     tool_elems_to_remove = []
                     for tool_elem in config_elem:
-                        if (tool_elem.get('guid'), tool_elem.get('file')) in guid_paths_to_remove:
+                        if (tool_elem.get("guid"), tool_elem.get("file")) in guid_paths_to_remove:
                             tool_elems_to_remove.append(tool_elem)
                     for tool_elem in tool_elems_to_remove:
                         # Remove all of the appropriate tool sub-elements from the section element.
@@ -450,8 +486,8 @@ class ToolPanelManager:
                     if len(config_elem) < 1:
                         # Keep a list of all empty section elements so they can be removed.
                         config_elems_to_remove.append(config_elem)
-                elif config_elem.tag == 'tool':
-                    if (config_elem.get('guid'), config_elem.get('file')) in guid_paths_to_remove:
+                elif config_elem.tag == "tool":
+                    if (config_elem.get("guid"), config_elem.get("file")) in guid_paths_to_remove:
                         config_elems_to_remove.append(config_elem)
             for config_elem in config_elems_to_remove:
                 config_elems.remove(config_elem)
@@ -467,7 +503,7 @@ class ToolPanelManager:
         # information so the tools can be displayed in the same way when the repository is
         # activated or reinstalled.
         tool_panel_dict = self.generate_tool_panel_dict_from_shed_tool_conf_entries(repository)
-        repository.metadata_['tool_panel_section'] = tool_panel_dict
+        repository.metadata_["tool_panel_section"] = tool_panel_dict
         self.app.install_model.context.add(repository)
         self.app.install_model.context.flush()
         # Create a list of guids for all tools that will be removed from the in-memory tool panel
@@ -488,8 +524,8 @@ class ToolPanelManager:
             if tool_guid not in tool_panel_section_mapping:
                 continue
             for tool in tool_panel_dict[tool_guid]:
-                section_name = tool_panel_section_mapping[tool_guid]['tool_panel_section']
-                section_id = str(tool_panel_section_mapping[tool_guid]['tool_panel_section'].lower().replace(' ', '_'))
-                tool['name'] = section_name
-                tool['id'] = section_id
+                section_name = tool_panel_section_mapping[tool_guid]["tool_panel_section"]
+                section_id = str(tool_panel_section_mapping[tool_guid]["tool_panel_section"].lower().replace(" ", "_"))
+                tool["name"] = section_name
+                tool["id"] = section_id
         return tool_panel_dict
diff --git a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
index 392628b51d2..64fdd140b8d 100644
--- a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
@@ -16,7 +16,6 @@ log = logging.getLogger(__name__)
 
 
 class UpdateRepositoryManager:
-
     def __init__(self, app):
         self.app = app
         self.context = self.app.install_model.context
@@ -33,58 +32,76 @@ class UpdateRepositoryManager:
         """Return the changeset revision hash to which the repository can be updated."""
         changeset_revision_dict = {}
         tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, str(repository.tool_shed))
-        params = dict(name=str(repository.name),
-                      owner=str(repository.owner),
-                      changeset_revision=str(repository.installed_changeset_revision))
-        pathspec = ['repository', 'get_changeset_revision_and_ctx_rev']
+        params = dict(
+            name=str(repository.name),
+            owner=str(repository.owner),
+            changeset_revision=str(repository.installed_changeset_revision),
+        )
+        pathspec = ["repository", "get_changeset_revision_and_ctx_rev"]
         try:
-            encoded_update_dict = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+            encoded_update_dict = util.url_get(
+                tool_shed_url,
+                auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                pathspec=pathspec,
+                params=params,
+            )
             if encoded_update_dict:
                 update_dict = tool_shed_decode(encoded_update_dict)
-                includes_data_managers = update_dict.get('includes_data_managers', False)
-                includes_datatypes = update_dict.get('includes_datatypes', False)
-                includes_tools = update_dict.get('includes_tools', False)
-                includes_tools_for_display_in_tool_panel = update_dict.get('includes_tools_for_display_in_tool_panel', False)
-                includes_tool_dependencies = update_dict.get('includes_tool_dependencies', False)
-                includes_workflows = update_dict.get('includes_workflows', False)
-                has_repository_dependencies = update_dict.get('has_repository_dependencies', False)
-                has_repository_dependencies_only_if_compiling_contained_td = update_dict.get('has_repository_dependencies_only_if_compiling_contained_td', False)
-                changeset_revision = update_dict.get('changeset_revision', None)
-                ctx_rev = update_dict.get('ctx_rev', None)
-            changeset_revision_dict['includes_data_managers'] = includes_data_managers
-            changeset_revision_dict['includes_datatypes'] = includes_datatypes
-            changeset_revision_dict['includes_tools'] = includes_tools
-            changeset_revision_dict['includes_tools_for_display_in_tool_panel'] = includes_tools_for_display_in_tool_panel
-            changeset_revision_dict['includes_tool_dependencies'] = includes_tool_dependencies
-            changeset_revision_dict['includes_workflows'] = includes_workflows
-            changeset_revision_dict['has_repository_dependencies'] = has_repository_dependencies
-            changeset_revision_dict['has_repository_dependencies_only_if_compiling_contained_td'] = has_repository_dependencies_only_if_compiling_contained_td
-            changeset_revision_dict['changeset_revision'] = changeset_revision
-            changeset_revision_dict['ctx_rev'] = ctx_rev
+                includes_data_managers = update_dict.get("includes_data_managers", False)
+                includes_datatypes = update_dict.get("includes_datatypes", False)
+                includes_tools = update_dict.get("includes_tools", False)
+                includes_tools_for_display_in_tool_panel = update_dict.get(
+                    "includes_tools_for_display_in_tool_panel", False
+                )
+                includes_tool_dependencies = update_dict.get("includes_tool_dependencies", False)
+                includes_workflows = update_dict.get("includes_workflows", False)
+                has_repository_dependencies = update_dict.get("has_repository_dependencies", False)
+                has_repository_dependencies_only_if_compiling_contained_td = update_dict.get(
+                    "has_repository_dependencies_only_if_compiling_contained_td", False
+                )
+                changeset_revision = update_dict.get("changeset_revision", None)
+                ctx_rev = update_dict.get("ctx_rev", None)
+            changeset_revision_dict["includes_data_managers"] = includes_data_managers
+            changeset_revision_dict["includes_datatypes"] = includes_datatypes
+            changeset_revision_dict["includes_tools"] = includes_tools
+            changeset_revision_dict[
+                "includes_tools_for_display_in_tool_panel"
+            ] = includes_tools_for_display_in_tool_panel
+            changeset_revision_dict["includes_tool_dependencies"] = includes_tool_dependencies
+            changeset_revision_dict["includes_workflows"] = includes_workflows
+            changeset_revision_dict["has_repository_dependencies"] = has_repository_dependencies
+            changeset_revision_dict[
+                "has_repository_dependencies_only_if_compiling_contained_td"
+            ] = has_repository_dependencies_only_if_compiling_contained_td
+            changeset_revision_dict["changeset_revision"] = changeset_revision
+            changeset_revision_dict["ctx_rev"] = ctx_rev
         except Exception as e:
-            log.debug(f"Error getting change set revision for update from the tool shed for repository '{repository.name}': {str(e)}")
-            changeset_revision_dict['includes_data_managers'] = False
-            changeset_revision_dict['includes_datatypes'] = False
-            changeset_revision_dict['includes_tools'] = False
-            changeset_revision_dict['includes_tools_for_display_in_tool_panel'] = False
-            changeset_revision_dict['includes_tool_dependencies'] = False
-            changeset_revision_dict['includes_workflows'] = False
-            changeset_revision_dict['has_repository_dependencies'] = False
-            changeset_revision_dict['has_repository_dependencies_only_if_compiling_contained_td'] = False
-            changeset_revision_dict['changeset_revision'] = None
-            changeset_revision_dict['ctx_rev'] = None
+            log.debug(
+                f"Error getting change set revision for update from the tool shed for repository '{repository.name}': {str(e)}"
+            )
+            changeset_revision_dict["includes_data_managers"] = False
+            changeset_revision_dict["includes_datatypes"] = False
+            changeset_revision_dict["includes_tools"] = False
+            changeset_revision_dict["includes_tools_for_display_in_tool_panel"] = False
+            changeset_revision_dict["includes_tool_dependencies"] = False
+            changeset_revision_dict["includes_workflows"] = False
+            changeset_revision_dict["has_repository_dependencies"] = False
+            changeset_revision_dict["has_repository_dependencies_only_if_compiling_contained_td"] = False
+            changeset_revision_dict["changeset_revision"] = None
+            changeset_revision_dict["ctx_rev"] = None
         return changeset_revision_dict
 
     def __restarter(self):
-        log.info('Update repository manager restarter starting up...')
+        log.info("Update repository manager restarter starting up...")
         while self.running:
             # Make a call to the Tool Shed for each installed repository to get the latest
             # status information in the Tool Shed for the repository.  This information includes
             # items like newer installable repository revisions, current revision updates, whether
             # the repository revision is the latest installable revision, and whether the repository
             # has been deprecated in the Tool Shed.
-            for repository in self.context.query(self.app.install_model.ToolShedRepository) \
-                                          .filter(self.app.install_model.ToolShedRepository.table.c.deleted == false()):
+            for repository in self.context.query(self.app.install_model.ToolShedRepository).filter(
+                self.app.install_model.ToolShedRepository.table.c.deleted == false()
+            ):
                 tool_shed_status_dict = get_tool_shed_status_for_installed_repository(self.app, repository)
                 if tool_shed_status_dict:
                     if tool_shed_status_dict != repository.tool_shed_status:
@@ -97,7 +114,7 @@ class UpdateRepositoryManager:
                         repository.tool_shed_status = tool_shed_status_dict
                         self.context.flush()
             self.sleeper.sleep(self.seconds_to_sleep)
-        log.info('Update repository manager restarter shutting down...')
+        log.info("Update repository manager restarter shutting down...")
 
     def shutdown(self):
         if self.app.config.enable_tool_shed_check:
diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index 906799c2ce0..f38866993e8 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -11,12 +11,15 @@ from galaxy.tool_shed.repository_type import (
     TOOL_DEPENDENCY_DEFINITION_FILENAME,
 )
 from galaxy.tool_shed.tools.tool_validator import ToolValidator
+from galaxy.tool_shed.util import shed_util_common as suc
 from galaxy.tool_shed.util import (
-    shed_util_common as suc,
     tool_dependency_util,
     tool_util,
 )
-from galaxy.tool_shed.util.basic_util import remove_dir, strip_path
+from galaxy.tool_shed.util.basic_util import (
+    remove_dir,
+    strip_path,
+)
 from galaxy.tool_shed.util.hg_util import get_config_from_disk
 from galaxy.tool_shed.util.metadata_util import get_updated_changeset_revisions_from_tool_shed
 from galaxy.tool_shed.util.repository_util import get_repository_for_dependency_relationship
@@ -37,15 +40,25 @@ log = logging.getLogger(__name__)
 
 
 class MetadataGenerator:
-
-    def __init__(self, app, repository=None, changeset_revision=None, repository_clone_url=None,
-                 shed_config_dict=None, relative_install_dir=None, repository_files_dir=None,
-                 resetting_all_metadata_on_repository=False, updating_installed_repository=False,
-                 persist=False, metadata_dict=None, user=None):
+    def __init__(
+        self,
+        app,
+        repository=None,
+        changeset_revision=None,
+        repository_clone_url=None,
+        shed_config_dict=None,
+        relative_install_dir=None,
+        repository_files_dir=None,
+        resetting_all_metadata_on_repository=False,
+        updating_installed_repository=False,
+        persist=False,
+        metadata_dict=None,
+        user=None,
+    ):
         self.app = app
         self.user = user
         self.repository = repository
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             if changeset_revision is None and self.repository is not None:
                 self.changeset_revision = self.repository.changeset_revision
             else:
@@ -68,7 +81,7 @@ class MetadataGenerator:
                 repository_files_dir = self.repository.repo_files_directory(self.app)
             if metadata_dict is None:
                 # Shed related tool panel configs are only relevant to Galaxy.
-                self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)}
+                self.metadata_dict = {"shed_config_filename": self.shed_config_dict.get("config_filename", None)}
             else:
                 self.metadata_dict = metadata_dict
         else:
@@ -78,8 +91,7 @@ class MetadataGenerator:
             else:
                 self.changeset_revision = changeset_revision
             if repository_clone_url is None and self.repository is not None:
-                self.repository_clone_url = \
-                    generate_clone_url_for_repository_in_tool_shed(self.user, self.repository)
+                self.repository_clone_url = generate_clone_url_for_repository_in_tool_shed(self.user, self.repository)
             else:
                 self.repository_clone_url = repository_clone_url
             if shed_config_dict is None:
@@ -101,13 +113,16 @@ class MetadataGenerator:
         self.persist = persist
         self.invalid_file_tups = []
         self.sa_session = app.model.session
-        self.NOT_TOOL_CONFIGS = [suc.DATATYPES_CONFIG_FILENAME,
-                                 REPOSITORY_DEPENDENCY_DEFINITION_FILENAME,
-                                 TOOL_DEPENDENCY_DEFINITION_FILENAME,
-                                 suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME]
+        self.NOT_TOOL_CONFIGS = [
+            suc.DATATYPES_CONFIG_FILENAME,
+            REPOSITORY_DEPENDENCY_DEFINITION_FILENAME,
+            TOOL_DEPENDENCY_DEFINITION_FILENAME,
+            suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME,
+        ]
 
-    def generate_data_manager_metadata(self, repo_dir, data_manager_config_filename, metadata_dict,
-                                       shed_config_dict=None):
+    def generate_data_manager_metadata(
+        self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None
+    ):
         """
         Update the received metadata_dict with information from the parsed data_manager_config_filename.
         """
@@ -122,59 +137,67 @@ class MetadataGenerator:
             # Tool Shed side.
             repo_files_directory = repo_path
         relative_data_manager_dir = util.relpath(os.path.split(data_manager_config_filename)[0], repo_dir)
-        rel_data_manager_config_filename = os.path.join(relative_data_manager_dir,
-                                                        os.path.split(data_manager_config_filename)[1])
+        rel_data_manager_config_filename = os.path.join(
+            relative_data_manager_dir, os.path.split(data_manager_config_filename)[1]
+        )
         data_managers = {}
         invalid_data_managers = []
-        data_manager_metadata = {'config_filename': rel_data_manager_config_filename,
-                                 'data_managers': data_managers,
-                                 'invalid_data_managers': invalid_data_managers,
-                                 'error_messages': []}
-        metadata_dict['data_manager'] = data_manager_metadata
+        data_manager_metadata = {
+            "config_filename": rel_data_manager_config_filename,
+            "data_managers": data_managers,
+            "invalid_data_managers": invalid_data_managers,
+            "error_messages": [],
+        }
+        metadata_dict["data_manager"] = data_manager_metadata
         tree, error_message = parse_xml(data_manager_config_filename)
         if tree is None:
             # We are not able to load any data managers.
-            data_manager_metadata['error_messages'].append(error_message)
+            data_manager_metadata["error_messages"].append(error_message)
             return metadata_dict
         tool_path = None
         if shed_config_dict:
-            tool_path = shed_config_dict.get('tool_path', None)
+            tool_path = shed_config_dict.get("tool_path", None)
         tools = {}
-        for tool in metadata_dict.get('tools', []):
-            tool_conf_name = tool['tool_config']
+        for tool in metadata_dict.get("tools", []):
+            tool_conf_name = tool["tool_config"]
             if tool_path:
                 tool_conf_name = os.path.join(tool_path, tool_conf_name)
             tools[tool_conf_name] = tool
         root = tree.getroot()
-        data_manager_tool_path = root.get('tool_path', None)
+        data_manager_tool_path = root.get("tool_path", None)
         if data_manager_tool_path:
             relative_data_manager_dir = os.path.join(relative_data_manager_dir, data_manager_tool_path)
-        for i, data_manager_elem in enumerate(root.findall('data_manager')):
-            tool_file = data_manager_elem.get('tool_file', None)
-            data_manager_id = data_manager_elem.get('id', None)
+        for i, data_manager_elem in enumerate(root.findall("data_manager")):
+            tool_file = data_manager_elem.get("tool_file", None)
+            data_manager_id = data_manager_elem.get("id", None)
             if data_manager_id is None:
                 log.error(f'Data Manager entry is missing id attribute in "{data_manager_config_filename}".')
-                invalid_data_managers.append({'index': i,
-                                              'error_message': 'Data Manager entry is missing id attribute'})
+                invalid_data_managers.append(
+                    {"index": i, "error_message": "Data Manager entry is missing id attribute"}
+                )
                 continue
             # FIXME: default behavior is to fall back to tool.name.
-            data_manager_name = data_manager_elem.get('name', data_manager_id)
-            version = data_manager_elem.get('version', DataManager.DEFAULT_VERSION)
+            data_manager_name = data_manager_elem.get("name", data_manager_id)
+            version = data_manager_elem.get("version", DataManager.DEFAULT_VERSION)
             guid = self.generate_guid_for_object(DataManager.GUID_TYPE, data_manager_id, version)
             data_tables = []
             if tool_file is None:
                 log.error(f'Data Manager entry is missing tool_file attribute in "{data_manager_config_filename}".')
-                invalid_data_managers.append({'index': i,
-                                              'error_message': 'Data Manager entry is missing tool_file attribute'})
+                invalid_data_managers.append(
+                    {"index": i, "error_message": "Data Manager entry is missing tool_file attribute"}
+                )
                 continue
             else:
                 bad_data_table = False
-                for data_table_elem in data_manager_elem.findall('data_table'):
-                    data_table_name = data_table_elem.get('name', None)
+                for data_table_elem in data_manager_elem.findall("data_table"):
+                    data_table_name = data_table_elem.get("name", None)
                     if data_table_name is None:
-                        log.error(f'Data Manager data_table entry is missing name attribute in "{data_manager_config_filename}".')
-                        invalid_data_managers.append({'index': i,
-                                                      'error_message': 'Data Manager entry is missing name attribute'})
+                        log.error(
+                            f'Data Manager data_table entry is missing name attribute in "{data_manager_config_filename}".'
+                        )
+                        invalid_data_managers.append(
+                            {"index": i, "error_message": "Data Manager entry is missing name attribute"}
+                        )
                         bad_data_table = True
                         break
                     else:
@@ -186,17 +209,18 @@ class MetadataGenerator:
             tool = tools.get(tool_metadata_tool_file, None)
             if tool is None:
                 log.error(f"Unable to determine tools metadata for '{data_manager_metadata_tool_file}'.")
-                invalid_data_managers.append({'index': i,
-                                              'error_message': 'Unable to determine tools metadata'})
+                invalid_data_managers.append({"index": i, "error_message": "Unable to determine tools metadata"})
                 continue
-            data_managers[data_manager_id] = {'id': data_manager_id,
-                                              'name': data_manager_name,
-                                              'guid': guid,
-                                              'version': version,
-                                              'tool_config_file': data_manager_metadata_tool_file,
-                                              'data_tables': data_tables,
-                                              'tool_guid': tool['guid']}
-            log.debug(f'Loaded Data Manager tool_files: {tool_file}')
+            data_managers[data_manager_id] = {
+                "id": data_manager_id,
+                "name": data_manager_name,
+                "guid": guid,
+                "version": version,
+                "tool_config_file": data_manager_metadata_tool_file,
+                "data_tables": data_tables,
+                "tool_guid": tool["guid"],
+            }
+            log.debug(f"Loaded Data Manager tool_files: {tool_file}")
         return metadata_dict
 
     def generate_datatypes_metadata(self, tv, repository_files_dir, datatypes_config, metadata_dict):
@@ -206,71 +230,70 @@ class MetadataGenerator:
             return metadata_dict
         root = tree.getroot()
         repository_datatype_code_files = []
-        datatype_files = root.find('datatype_files')
+        datatype_files = root.find("datatype_files")
         if datatype_files is not None:
-            for elem in datatype_files.findall('datatype_file'):
-                name = elem.get('name', None)
+            for elem in datatype_files.findall("datatype_file"):
+                name = elem.get("name", None)
                 repository_datatype_code_files.append(name)
-            metadata_dict['datatype_files'] = repository_datatype_code_files
+            metadata_dict["datatype_files"] = repository_datatype_code_files
         datatypes = []
-        registration = root.find('registration')
+        registration = root.find("registration")
         if registration is not None:
-            for elem in registration.findall('datatype'):
+            for elem in registration.findall("datatype"):
                 converters = []
                 display_app_containers = []
                 datatypes_dict = {}
                 # Handle defined datatype attributes.
-                display_in_upload = elem.get('display_in_upload', None)
+                display_in_upload = elem.get("display_in_upload", None)
                 if display_in_upload:
-                    datatypes_dict['display_in_upload'] = display_in_upload
-                dtype = elem.get('type', None)
+                    datatypes_dict["display_in_upload"] = display_in_upload
+                dtype = elem.get("type", None)
                 if dtype:
-                    datatypes_dict['dtype'] = dtype
-                extension = elem.get('extension', None)
+                    datatypes_dict["dtype"] = dtype
+                extension = elem.get("extension", None)
                 if extension:
-                    datatypes_dict['extension'] = extension
-                max_optional_metadata_filesize = elem.get('max_optional_metadata_filesize', None)
+                    datatypes_dict["extension"] = extension
+                max_optional_metadata_filesize = elem.get("max_optional_metadata_filesize", None)
                 if max_optional_metadata_filesize:
-                    datatypes_dict['max_optional_metadata_filesize'] = max_optional_metadata_filesize
-                mimetype = elem.get('mimetype', None)
+                    datatypes_dict["max_optional_metadata_filesize"] = max_optional_metadata_filesize
+                mimetype = elem.get("mimetype", None)
                 if mimetype:
-                    datatypes_dict['mimetype'] = mimetype
-                subclass = elem.get('subclass', None)
+                    datatypes_dict["mimetype"] = mimetype
+                subclass = elem.get("subclass", None)
                 if subclass:
-                    datatypes_dict['subclass'] = subclass
+                    datatypes_dict["subclass"] = subclass
                 # Handle defined datatype converters and display applications.
                 for sub_elem in elem:
-                    if sub_elem.tag == 'converter':
+                    if sub_elem.tag == "converter":
                         # <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
-                        tool_config = sub_elem.attrib['file']
-                        target_datatype = sub_elem.attrib['target_datatype']
+                        tool_config = sub_elem.attrib["file"]
+                        target_datatype = sub_elem.attrib["target_datatype"]
                         # Parse the tool_config to get the guid.
                         tool_config_path = get_config_from_disk(tool_config, repository_files_dir)
                         full_path = os.path.abspath(tool_config_path)
-                        tool, valid, error_message = \
-                            tv.load_tool_from_config(self.app.security.encode_id(self.repository.id), full_path)
+                        tool, valid, error_message = tv.load_tool_from_config(
+                            self.app.security.encode_id(self.repository.id), full_path
+                        )
                         if tool is None:
                             guid = None
                         else:
                             guid = suc.generate_tool_guid(self.repository_clone_url, tool)
-                        converter_dict = dict(tool_config=tool_config,
-                                              guid=guid,
-                                              target_datatype=target_datatype)
+                        converter_dict = dict(tool_config=tool_config, guid=guid, target_datatype=target_datatype)
                         converters.append(converter_dict)
-                    elif sub_elem.tag == 'display':
+                    elif sub_elem.tag == "display":
                         # <display file="ucsc/bigwig.xml" />
                         # Should we store more than this?
-                        display_file = sub_elem.attrib['file']
+                        display_file = sub_elem.attrib["file"]
                         display_app_dict = dict(display_file=display_file)
                         display_app_containers.append(display_app_dict)
                 if converters:
-                    datatypes_dict['converters'] = converters
+                    datatypes_dict["converters"] = converters
                 if display_app_containers:
-                    datatypes_dict['display_app_containers'] = display_app_containers
+                    datatypes_dict["display_app_containers"] = display_app_containers
                 if datatypes_dict:
                     datatypes.append(datatypes_dict)
             if datatypes:
-                metadata_dict['datatypes'] = datatypes
+                metadata_dict["datatypes"] = datatypes
         return metadata_dict
 
     def generate_environment_dependency_metadata(self, elem, valid_tool_dependencies_dict):
@@ -285,18 +308,18 @@ class MetadataGenerator:
         # </set_environment>
         for env_elem in elem:
             # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-            env_name = env_elem.get('name', None)
+            env_name = env_elem.get("name", None)
             if env_name:
-                requirements_dict = dict(name=env_name, type='set_environment')
-                if 'set_environment' in valid_tool_dependencies_dict:
-                    valid_tool_dependencies_dict['set_environment'].append(requirements_dict)
+                requirements_dict = dict(name=env_name, type="set_environment")
+                if "set_environment" in valid_tool_dependencies_dict:
+                    valid_tool_dependencies_dict["set_environment"].append(requirements_dict)
                 else:
-                    valid_tool_dependencies_dict['set_environment'] = [requirements_dict]
+                    valid_tool_dependencies_dict["set_environment"] = [requirements_dict]
         return valid_tool_dependencies_dict
 
     def generate_guid_for_object(self, guid_type, obj_id, version):
         tmp_url = remove_protocol_and_user_from_clone_url(self.repository_clone_url)
-        return f'{tmp_url}/{guid_type}/{obj_id}/{version}'
+        return f"{tmp_url}/{guid_type}/{obj_id}/{version}"
 
     def generate_metadata_for_changeset_revision(self):
         """
@@ -321,16 +344,18 @@ class MetadataGenerator:
         else:
             original_repository_metadata = None
         readme_file_names = _get_readme_file_names(str(self.repository.name))
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             # Shed related tool panel configs are only relevant to Galaxy.
-            metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename')}
+            metadata_dict = {"shed_config_filename": self.shed_config_dict.get("config_filename")}
         else:
             metadata_dict = {}
         readme_files = []
         invalid_tool_configs = []
         if self.resetting_all_metadata_on_repository:
             if not self.relative_install_dir:
-                raise Exception("The value of self.repository.repo_path must be set when resetting all metadata on a repository.")
+                raise Exception(
+                    "The value of self.repository.repo_path must be set when resetting all metadata on a repository."
+                )
             # Keep track of the location where the repository is temporarily cloned so that we can
             # strip the path when setting metadata.  The value of self.repository_files_dir is the
             # full path to the temporary directory to which self.repository was cloned.
@@ -344,26 +369,24 @@ class MetadataGenerator:
             # All other files are on disk in the repository's repo_path, which is the value of
             # self.relative_install_dir.
             files_dir = self.relative_install_dir
-            if self.shed_config_dict.get('tool_path'):
-                files_dir = os.path.join(self.shed_config_dict['tool_path'], files_dir)
+            if self.shed_config_dict.get("tool_path"):
+                files_dir = os.path.join(self.shed_config_dict["tool_path"], files_dir)
         # Create ValidationContext to load and validate tools, data tables and datatypes
         with ValidationContext.from_app(app=self.app, work_dir=work_dir) as validation_context:
             tv = ToolValidator(validation_context)
             # Handle proprietary datatypes, if any.
             datatypes_config = get_config_from_disk(suc.DATATYPES_CONFIG_FILENAME, files_dir)
             if datatypes_config:
-                metadata_dict = self.generate_datatypes_metadata(tv,
-                                                                 files_dir,
-                                                                 datatypes_config,
-                                                                 metadata_dict)
+                metadata_dict = self.generate_datatypes_metadata(tv, files_dir, datatypes_config, metadata_dict)
             # Get the relative path to all sample files included in the repository for storage in
             # the repository's metadata.
-            sample_file_metadata_paths, sample_file_copy_paths = \
-                self.get_sample_files_from_disk(repository_files_dir=files_dir,
-                                                tool_path=self.shed_config_dict.get('tool_path'),
-                                                relative_install_dir=self.relative_install_dir)
+            sample_file_metadata_paths, sample_file_copy_paths = self.get_sample_files_from_disk(
+                repository_files_dir=files_dir,
+                tool_path=self.shed_config_dict.get("tool_path"),
+                relative_install_dir=self.relative_install_dir,
+            )
             if sample_file_metadata_paths:
-                metadata_dict['sample_files'] = sample_file_metadata_paths
+                metadata_dict["sample_files"] = sample_file_metadata_paths
             # Copy all sample files included in the repository to a single directory location so we
             # can load tools that depend on them.
             data_table_conf_xml_sample_files = []
@@ -372,39 +395,38 @@ class MetadataGenerator:
                 # If the list of sample files includes a tool_data_table_conf.xml.sample file, load
                 # its table elements into memory.
                 relative_path, filename = os.path.split(sample_file)
-                if filename == 'tool_data_table_conf.xml.sample':
+                if filename == "tool_data_table_conf.xml.sample":
                     data_table_conf_xml_sample_files.append(sample_file)
 
             for data_table_conf_xml_sample_file in data_table_conf_xml_sample_files:
                 # We create a new ToolDataTableManager to avoid adding entries to the app-wide
                 # tool data tables. This is only used for checking that the data table is valid.
-                new_table_elems, error_message = \
-                    validation_context.tool_data_tables.add_new_entries_from_config_file(config_filename=data_table_conf_xml_sample_file,
-                                                                                         tool_data_path=work_dir,
-                                                                                         shed_tool_data_table_config=work_dir,
-                                                                                         persist=False)
+                new_table_elems, error_message = validation_context.tool_data_tables.add_new_entries_from_config_file(
+                    config_filename=data_table_conf_xml_sample_file,
+                    tool_data_path=work_dir,
+                    shed_tool_data_table_config=work_dir,
+                    persist=False,
+                )
                 if error_message:
                     self.invalid_file_tups.append((filename, error_message))
             for root, dirs, files in os.walk(files_dir):
-                if root.find('.hg') < 0 and root.find('hgrc') < 0:
-                    if '.hg' in dirs:
-                        dirs.remove('.hg')
+                if root.find(".hg") < 0 and root.find("hgrc") < 0:
+                    if ".hg" in dirs:
+                        dirs.remove(".hg")
                     for name in files:
                         # See if we have a repository dependencies defined.
                         if name == REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
                             path_to_repository_dependencies_config = os.path.join(root, name)
-                            metadata_dict, error_message = \
-                                self.generate_repository_dependency_metadata(path_to_repository_dependencies_config,
-                                                                             metadata_dict)
+                            metadata_dict, error_message = self.generate_repository_dependency_metadata(
+                                path_to_repository_dependencies_config, metadata_dict
+                            )
                             if error_message:
                                 self.invalid_file_tups.append((name, error_message))
                         # See if we have one or more READ_ME files.
                         elif name.lower() in readme_file_names:
-                            relative_path_to_readme = self.get_relative_path_to_repository_file(root,
-                                                                                                name,
-                                                                                                self.relative_install_dir,
-                                                                                                work_dir,
-                                                                                                self.shed_config_dict)
+                            relative_path_to_readme = self.get_relative_path_to_repository_file(
+                                root, name, self.relative_install_dir, work_dir, self.shed_config_dict
+                            )
                             readme_files.append(relative_path_to_readme)
                         # See if we have a tool config.
                         elif looks_like_a_tool(os.path.join(root, name), invalid_names=self.NOT_TOOL_CONFIGS):
@@ -414,21 +436,19 @@ class MetadataGenerator:
                                 is_tool = False
                             else:
                                 element_tree_root = element_tree.getroot()
-                                is_tool = element_tree_root.tag == 'tool'
+                                is_tool = element_tree_root.tag == "tool"
                             if is_tool:
-                                tool, valid, error_message = \
-                                    tv.load_tool_from_config(self.app.security.encode_id(self.repository.id),
-                                                             full_path)
+                                tool, valid, error_message = tv.load_tool_from_config(
+                                    self.app.security.encode_id(self.repository.id), full_path
+                                )
                                 if tool is None:
                                     if not valid:
                                         invalid_tool_configs.append(name)
                                         self.invalid_file_tups.append((name, error_message))
                                 else:
-                                    invalid_files_and_errors_tups = \
-                                        tv.check_tool_input_params(files_dir,
-                                                                   name,
-                                                                   tool,
-                                                                   sample_file_copy_paths)
+                                    invalid_files_and_errors_tups = tv.check_tool_input_params(
+                                        files_dir, name, tool, sample_file_copy_paths
+                                    )
                                     can_set_metadata = True
                                     for tup in invalid_files_and_errors_tups:
                                         if name in tup:
@@ -436,23 +456,20 @@ class MetadataGenerator:
                                             invalid_tool_configs.append(name)
                                             break
                                     if can_set_metadata:
-                                        relative_path_to_tool_config = \
-                                            self.get_relative_path_to_repository_file(root,
-                                                                                      name,
-                                                                                      self.relative_install_dir,
-                                                                                      work_dir,
-                                                                                      self.shed_config_dict)
-                                        metadata_dict = self.generate_tool_metadata(relative_path_to_tool_config,
-                                                                                    tool,
-                                                                                    metadata_dict)
+                                        relative_path_to_tool_config = self.get_relative_path_to_repository_file(
+                                            root, name, self.relative_install_dir, work_dir, self.shed_config_dict
+                                        )
+                                        metadata_dict = self.generate_tool_metadata(
+                                            relative_path_to_tool_config, tool, metadata_dict
+                                        )
                                     else:
                                         for tup in invalid_files_and_errors_tups:
                                             self.invalid_file_tups.append(tup)
                         # Find all exported workflows.
-                        elif name.endswith('.ga'):
+                        elif name.endswith(".ga"):
                             relative_path = os.path.join(root, name)
                             if os.path.getsize(os.path.abspath(relative_path)) > 0:
-                                fp = open(relative_path, 'rb')
+                                fp = open(relative_path, "rb")
                                 workflow_text = fp.read()
                                 fp.close()
                                 if workflow_text:
@@ -460,35 +477,37 @@ class MetadataGenerator:
                                     try:
                                         exported_workflow_dict = json.loads(workflow_text)
                                     except Exception:
-                                        log.exception("Skipping file %s since it does not seem to be a valid exported Galaxy workflow",
-                                                      str(relative_path))
+                                        log.exception(
+                                            "Skipping file %s since it does not seem to be a valid exported Galaxy workflow",
+                                            str(relative_path),
+                                        )
                                         valid_exported_galaxy_workflow = False
-                                if valid_exported_galaxy_workflow and \
-                                    'a_galaxy_workflow' in exported_workflow_dict and \
-                                        exported_workflow_dict['a_galaxy_workflow'] == 'true':
-                                    metadata_dict = self.generate_workflow_metadata(relative_path,
-                                                                                    exported_workflow_dict,
-                                                                                    metadata_dict)
+                                if (
+                                    valid_exported_galaxy_workflow
+                                    and "a_galaxy_workflow" in exported_workflow_dict
+                                    and exported_workflow_dict["a_galaxy_workflow"] == "true"
+                                ):
+                                    metadata_dict = self.generate_workflow_metadata(
+                                        relative_path, exported_workflow_dict, metadata_dict
+                                    )
         # Handle any data manager entries
         data_manager_config = get_config_from_disk(suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir)
-        metadata_dict = self.generate_data_manager_metadata(files_dir,
-                                                            data_manager_config,
-                                                            metadata_dict,
-                                                            shed_config_dict=self.shed_config_dict)
+        metadata_dict = self.generate_data_manager_metadata(
+            files_dir, data_manager_config, metadata_dict, shed_config_dict=self.shed_config_dict
+        )
 
         if readme_files:
-            metadata_dict['readme_files'] = readme_files
+            metadata_dict["readme_files"] = readme_files
         # This step must be done after metadata for tools has been defined.
         tool_dependencies_config = get_config_from_disk(TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir)
         if tool_dependencies_config:
-            metadata_dict, error_message = \
-                self.generate_tool_dependency_metadata(tool_dependencies_config,
-                                                       metadata_dict,
-                                                       original_repository_metadata=original_repository_metadata)
+            metadata_dict, error_message = self.generate_tool_dependency_metadata(
+                tool_dependencies_config, metadata_dict, original_repository_metadata=original_repository_metadata
+            )
             if error_message:
                 self.invalid_file_tups.append((TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message))
         if invalid_tool_configs:
-            metadata_dict['invalid_tools'] = invalid_tool_configs
+            metadata_dict["invalid_tools"] = invalid_tool_configs
         self.metadata_dict = metadata_dict
         remove_dir(work_dir)
 
@@ -502,32 +521,34 @@ class MetadataGenerator:
         repository_dependency_is_valid = True
         repository_dependency_tup = []
         requirements_dict = {}
-        error_message = ''
-        package_name = elem.get('name', None)
-        package_version = elem.get('version', None)
+        error_message = ""
+        package_name = elem.get("name", None)
+        package_version = elem.get("version", None)
         if package_name and package_version:
-            requirements_dict['name'] = package_name
-            requirements_dict['version'] = package_version
-            requirements_dict['type'] = 'package'
+            requirements_dict["name"] = package_name
+            requirements_dict["version"] = package_version
+            requirements_dict["type"] = "package"
             for sub_elem in elem:
-                if sub_elem.tag == 'readme':
-                    requirements_dict['readme'] = sub_elem.text
-                elif sub_elem.tag == 'repository':
+                if sub_elem.tag == "readme":
+                    requirements_dict["readme"] = sub_elem.text
+                elif sub_elem.tag == "repository":
                     # We have a complex repository dependency.  If the returned value of repository_dependency_is_valid
                     # is True, the tool dependency definition will be set as invalid.  This is currently the only case
                     # where a tool dependency definition is considered invalid.
-                    repository_dependency_tup, repository_dependency_is_valid, error_message = \
-                        self.handle_repository_elem(repository_elem=sub_elem,
-                                                    only_if_compiling_contained_td=False)
-                elif sub_elem.tag == 'install':
-                    package_install_version = sub_elem.get('version', '1.0')
-                    if package_install_version == '1.0':
+                    (
+                        repository_dependency_tup,
+                        repository_dependency_is_valid,
+                        error_message,
+                    ) = self.handle_repository_elem(repository_elem=sub_elem, only_if_compiling_contained_td=False)
+                elif sub_elem.tag == "install":
+                    package_install_version = sub_elem.get("version", "1.0")
+                    if package_install_version == "1.0":
                         # Complex repository dependencies can be defined within the last <actions> tag set contained in an
                         # <actions_group> tag set.  Comments, <repository> tag sets and <readme> tag sets will be skipped
                         # in tool_dependency_util.parse_package_elem().
-                        actions_elem_tuples = tool_dependency_util.parse_package_elem(sub_elem,
-                                                                                      platform_info_dict=None,
-                                                                                      include_after_install_actions=False)
+                        actions_elem_tuples = tool_dependency_util.parse_package_elem(
+                            sub_elem, platform_info_dict=None, include_after_install_actions=False
+                        )
                         if actions_elem_tuples:
                             # We now have a list of a single tuple that looks something like:
                             # [(True, <Element 'actions' at 0x104017850>)]
@@ -539,44 +560,55 @@ class MetadataGenerator:
                                 # contained within the last <actions> tag set within an <actions_group> tag set will have the
                                 # value of "only_if_compiling_contained_td" set to True in
                                 for action_elem in actions_elem:
-                                    if action_elem.tag == 'package':
+                                    if action_elem.tag == "package":
                                         # <package name="libgtextutils" version="0.6">
                                         #    <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" />
                                         # </package>
-                                        ae_package_name = action_elem.get('name', None)
-                                        ae_package_version = action_elem.get('version', None)
+                                        ae_package_name = action_elem.get("name", None)
+                                        ae_package_version = action_elem.get("version", None)
                                         if ae_package_name and ae_package_version:
                                             for sub_action_elem in action_elem:
-                                                if sub_action_elem.tag == 'repository':
+                                                if sub_action_elem.tag == "repository":
                                                     # We have a complex repository dependency.
-                                                    repository_dependency_tup, repository_dependency_is_valid, error_message = \
-                                                        self.handle_repository_elem(repository_elem=sub_action_elem,
-                                                                                    only_if_compiling_contained_td=True)
-                                    elif action_elem.tag == 'action':
+                                                    (
+                                                        repository_dependency_tup,
+                                                        repository_dependency_is_valid,
+                                                        error_message,
+                                                    ) = self.handle_repository_elem(
+                                                        repository_elem=sub_action_elem,
+                                                        only_if_compiling_contained_td=True,
+                                                    )
+                                    elif action_elem.tag == "action":
                                         # <action type="set_environment_for_install">
                                         #    <repository changeset_revision="b107b91b3574" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://localhost:9009">
                                         #        <package name="readline" version="6.2" />
                                         #    </repository>
                                         # </action>
                                         for sub_action_elem in action_elem:
-                                            if sub_action_elem.tag == 'repository':
+                                            if sub_action_elem.tag == "repository":
                                                 # We have a complex repository dependency.
-                                                repository_dependency_tup, repository_dependency_is_valid, error_message = \
-                                                    self.handle_repository_elem(repository_elem=sub_action_elem,
-                                                                                only_if_compiling_contained_td=True)
+                                                (
+                                                    repository_dependency_tup,
+                                                    repository_dependency_is_valid,
+                                                    error_message,
+                                                ) = self.handle_repository_elem(
+                                                    repository_elem=sub_action_elem, only_if_compiling_contained_td=True
+                                                )
         if requirements_dict:
-            dependency_key = f'{package_name}/{package_version}'
+            dependency_key = f"{package_name}/{package_version}"
             if repository_dependency_is_valid:
                 valid_tool_dependencies_dict[dependency_key] = requirements_dict
             else:
                 # Append the error message to the requirements_dict.
-                requirements_dict['error'] = error_message
+                requirements_dict["error"] = error_message
                 invalid_tool_dependencies_dict[dependency_key] = requirements_dict
-        return valid_tool_dependencies_dict, \
-            invalid_tool_dependencies_dict, \
-            repository_dependency_tup, \
-            repository_dependency_is_valid, \
-            error_message
+        return (
+            valid_tool_dependencies_dict,
+            invalid_tool_dependencies_dict,
+            repository_dependency_tup,
+            repository_dependency_is_valid,
+            error_message,
+        )
 
     def generate_repository_dependency_metadata(self, repository_dependencies_config, metadata_dict):
         """
@@ -589,37 +621,45 @@ class MetadataGenerator:
             xml_is_valid = False
         else:
             root = tree.getroot()
-            xml_is_valid = root.tag == 'repositories'
+            xml_is_valid = root.tag == "repositories"
         if xml_is_valid:
-            invalid_repository_dependencies_dict = dict(description=root.get('description'))
+            invalid_repository_dependencies_dict = dict(description=root.get("description"))
             invalid_repository_dependency_tups = []
-            valid_repository_dependencies_dict = dict(description=root.get('description'))
+            valid_repository_dependencies_dict = dict(description=root.get("description"))
             valid_repository_dependency_tups = []
-            for repository_elem in root.findall('repository'):
-                repository_dependency_tup, repository_dependency_is_valid, err_msg = \
-                    self.handle_repository_elem(repository_elem,
-                                                only_if_compiling_contained_td=False)
+            for repository_elem in root.findall("repository"):
+                repository_dependency_tup, repository_dependency_is_valid, err_msg = self.handle_repository_elem(
+                    repository_elem, only_if_compiling_contained_td=False
+                )
                 if repository_dependency_is_valid:
                     valid_repository_dependency_tups.append(repository_dependency_tup)
                 else:
                     # Append the error_message to the repository dependencies tuple.
-                    toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                        repository_dependency_tup
-                    repository_dependency_tup = (toolshed,
-                                                 name,
-                                                 owner,
-                                                 changeset_revision,
-                                                 prior_installation_required,
-                                                 only_if_compiling_contained_td,
-                                                 err_msg)
+                    (
+                        toolshed,
+                        name,
+                        owner,
+                        changeset_revision,
+                        prior_installation_required,
+                        only_if_compiling_contained_td,
+                    ) = repository_dependency_tup
+                    repository_dependency_tup = (
+                        toolshed,
+                        name,
+                        owner,
+                        changeset_revision,
+                        prior_installation_required,
+                        only_if_compiling_contained_td,
+                        err_msg,
+                    )
                     invalid_repository_dependency_tups.append(repository_dependency_tup)
                     error_message += err_msg
             if invalid_repository_dependency_tups:
-                invalid_repository_dependencies_dict['repository_dependencies'] = invalid_repository_dependency_tups
-                metadata_dict['invalid_repository_dependencies'] = invalid_repository_dependencies_dict
+                invalid_repository_dependencies_dict["repository_dependencies"] = invalid_repository_dependency_tups
+                metadata_dict["invalid_repository_dependencies"] = invalid_repository_dependencies_dict
             if valid_repository_dependency_tups:
-                valid_repository_dependencies_dict['repository_dependencies'] = valid_repository_dependency_tups
-                metadata_dict['repository_dependencies'] = valid_repository_dependencies_dict
+                valid_repository_dependencies_dict["repository_dependencies"] = valid_repository_dependency_tups
+                metadata_dict["repository_dependencies"] = valid_repository_dependencies_dict
         return metadata_dict, error_message
 
     def generate_tool_metadata(self, tool_config, tool, metadata_dict):
@@ -632,9 +672,7 @@ class MetadataGenerator:
             name = str(tool_requirement.name)
             tool_type = str(tool_requirement.type)
             version = str(tool_requirement.version) if tool_requirement.version else None
-            requirement_dict = dict(name=name,
-                                    type=tool_type,
-                                    version=version)
+            requirement_dict = dict(name=name, type=tool_type, version=version)
             tool_requirements.append(requirement_dict)
         # Handle tool.tests.
         tool_tests = []
@@ -671,7 +709,13 @@ class MetadataGenerator:
                                         inputs.append((param_name, values[0]))
                                         continue
                                 except TypeError:
-                                    log.exception('Expected a list of values for tool "%s" parameter "%s", got %s: %s', tool.id, param_name, type(values), values)
+                                    log.exception(
+                                        'Expected a list of values for tool "%s" parameter "%s", got %s: %s',
+                                        tool.id,
+                                        param_name,
+                                        type(values),
+                                        values,
+                                    )
                                 inputs.append((param_name, values))
                 outputs = []
                 for output in ttb.outputs:
@@ -679,47 +723,48 @@ class MetadataGenerator:
                     outputs.append((name, strip_path(file_name) if file_name else None))
                     if file_name not in required_files and file_name is not None:
                         required_files.append(file_name)
-                test_dict = dict(name=str(ttb.name),
-                                 required_files=required_files,
-                                 inputs=inputs,
-                                 outputs=outputs)
+                test_dict = dict(name=str(ttb.name), required_files=required_files, inputs=inputs, outputs=outputs)
                 tool_tests.append(test_dict)
         # Determine if the tool should be loaded into the tool panel.  Examples of valid tools that
         # should not be displayed in the tool panel are datatypes converters and DataManager tools
         # (which are of type 'manage_data').
-        datatypes = metadata_dict.get('datatypes', None)
-        add_to_tool_panel_attribute = self.set_add_to_tool_panel_attribute_for_tool(tool=tool,
-                                                                                    guid=guid,
-                                                                                    datatypes=datatypes)
-        tool_dict = dict(id=tool.id,
-                         guid=guid,
-                         name=tool.name,
-                         version=tool.version,
-                         profile=tool.profile,
-                         description=tool.description,
-                         version_string_cmd=tool.version_string_cmd,
-                         tool_config=tool_config,
-                         tool_type=tool.tool_type,
-                         requirements=tool_requirements,
-                         tests=tool_tests,
-                         add_to_tool_panel=add_to_tool_panel_attribute)
-        if 'tools' in metadata_dict:
-            metadata_dict['tools'].append(tool_dict)
+        datatypes = metadata_dict.get("datatypes", None)
+        add_to_tool_panel_attribute = self.set_add_to_tool_panel_attribute_for_tool(
+            tool=tool, guid=guid, datatypes=datatypes
+        )
+        tool_dict = dict(
+            id=tool.id,
+            guid=guid,
+            name=tool.name,
+            version=tool.version,
+            profile=tool.profile,
+            description=tool.description,
+            version_string_cmd=tool.version_string_cmd,
+            tool_config=tool_config,
+            tool_type=tool.tool_type,
+            requirements=tool_requirements,
+            tests=tool_tests,
+            add_to_tool_panel=add_to_tool_panel_attribute,
+        )
+        if "tools" in metadata_dict:
+            metadata_dict["tools"].append(tool_dict)
         else:
-            metadata_dict['tools'] = [tool_dict]
+            metadata_dict["tools"] = [tool_dict]
         return metadata_dict
 
-    def generate_tool_dependency_metadata(self, tool_dependencies_config, metadata_dict, original_repository_metadata=None):
+    def generate_tool_dependency_metadata(
+        self, tool_dependencies_config, metadata_dict, original_repository_metadata=None
+    ):
         """
         If the combination of name, version and type of each element is defined in the <requirement> tag for
         at least one tool in self.repository, then update the received metadata_dict with information from the
         parsed tool_dependencies_config.
         """
-        error_message = ''
+        error_message = ""
         if original_repository_metadata:
             # Keep a copy of the original tool dependencies dictionary and the list of tool
             # dictionaries in the metadata.
-            original_valid_tool_dependencies_dict = original_repository_metadata.get('tool_dependencies', None)
+            original_valid_tool_dependencies_dict = original_repository_metadata.get("tool_dependencies", None)
         else:
             original_valid_tool_dependencies_dict = None
         tree, error_message = parse_xml(tool_dependencies_config)
@@ -729,74 +774,96 @@ class MetadataGenerator:
 
         class RecurserValueStore:
             pass
+
         rvs = RecurserValueStore()
         rvs.valid_tool_dependencies_dict = {}
         rvs.invalid_tool_dependencies_dict = {}
         valid_repository_dependency_tups = []
         invalid_repository_dependency_tups = []
-        description = root.get('description')
+        description = root.get("description")
 
         def _check_elem_for_dep(elems):
             error_messages = []
             for elem in elems:
-                if elem.tag == 'package':
-                    rvs.valid_tool_dependencies_dict, rvs.invalid_tool_dependencies_dict, \
-                        repository_dependency_tup, repository_dependency_is_valid, \
-                        message = self.generate_package_dependency_metadata(elem,
-                                                                            rvs.valid_tool_dependencies_dict,
-                                                                            rvs.invalid_tool_dependencies_dict)
+                if elem.tag == "package":
+                    (
+                        rvs.valid_tool_dependencies_dict,
+                        rvs.invalid_tool_dependencies_dict,
+                        repository_dependency_tup,
+                        repository_dependency_is_valid,
+                        message,
+                    ) = self.generate_package_dependency_metadata(
+                        elem, rvs.valid_tool_dependencies_dict, rvs.invalid_tool_dependencies_dict
+                    )
                     if repository_dependency_is_valid:
-                        if repository_dependency_tup and repository_dependency_tup not in valid_repository_dependency_tups:
+                        if (
+                            repository_dependency_tup
+                            and repository_dependency_tup not in valid_repository_dependency_tups
+                        ):
                             # We have a valid complex repository dependency.
                             valid_repository_dependency_tups.append(repository_dependency_tup)
                     else:
-                        if repository_dependency_tup and repository_dependency_tup not in invalid_repository_dependency_tups:
+                        if (
+                            repository_dependency_tup
+                            and repository_dependency_tup not in invalid_repository_dependency_tups
+                        ):
                             # We have an invalid complex repository dependency, so mark the tool dependency as invalid.
                             # Append the error message to the invalid repository dependency tuple.
-                            toolshed, name, owner, changeset_revision, \
-                                prior_installation_required, \
-                                only_if_compiling_contained_td = \
-                                repository_dependency_tup
-                            repository_dependency_tup = \
-                                (toolshed,
-                                 name,
-                                 owner,
-                                 changeset_revision,
-                                 prior_installation_required,
-                                 only_if_compiling_contained_td,
-                                 message)
+                            (
+                                toolshed,
+                                name,
+                                owner,
+                                changeset_revision,
+                                prior_installation_required,
+                                only_if_compiling_contained_td,
+                            ) = repository_dependency_tup
+                            repository_dependency_tup = (
+                                toolshed,
+                                name,
+                                owner,
+                                changeset_revision,
+                                prior_installation_required,
+                                only_if_compiling_contained_td,
+                                message,
+                            )
                             invalid_repository_dependency_tups.append(repository_dependency_tup)
-                            error_messages.append(f'{error_message}  {message}')
-                elif elem.tag == 'set_environment':
-                    rvs.valid_tool_dependencies_dict = \
-                        self.generate_environment_dependency_metadata(elem, rvs.valid_tool_dependencies_dict)
+                            error_messages.append(f"{error_message}  {message}")
+                elif elem.tag == "set_environment":
+                    rvs.valid_tool_dependencies_dict = self.generate_environment_dependency_metadata(
+                        elem, rvs.valid_tool_dependencies_dict
+                    )
                 error_messages += _check_elem_for_dep(elem)
             return error_messages
+
         error_message = "\n".join([error_message] + _check_elem_for_dep(root))
         if rvs.valid_tool_dependencies_dict:
             if original_valid_tool_dependencies_dict:
                 # We're generating metadata on an update pulled to a tool shed repository installed
                 # into a Galaxy instance, so handle changes to tool dependencies appropriately.
                 irm = self.app.installed_repository_manager
-                updated_tool_dependency_names, deleted_tool_dependency_names = \
-                    irm.handle_existing_tool_dependencies_that_changed_in_update(self.repository,
-                                                                                 original_valid_tool_dependencies_dict,
-                                                                                 rvs.valid_tool_dependencies_dict)
-            metadata_dict['tool_dependencies'] = rvs.valid_tool_dependencies_dict
+                (
+                    updated_tool_dependency_names,
+                    deleted_tool_dependency_names,
+                ) = irm.handle_existing_tool_dependencies_that_changed_in_update(
+                    self.repository, original_valid_tool_dependencies_dict, rvs.valid_tool_dependencies_dict
+                )
+            metadata_dict["tool_dependencies"] = rvs.valid_tool_dependencies_dict
         if rvs.invalid_tool_dependencies_dict:
-            metadata_dict['invalid_tool_dependencies'] = rvs.invalid_tool_dependencies_dict
+            metadata_dict["invalid_tool_dependencies"] = rvs.invalid_tool_dependencies_dict
         if valid_repository_dependency_tups:
-            metadata_dict = \
-                self.update_repository_dependencies_metadata(metadata=metadata_dict,
-                                                             repository_dependency_tups=valid_repository_dependency_tups,
-                                                             is_valid=True,
-                                                             description=description)
+            metadata_dict = self.update_repository_dependencies_metadata(
+                metadata=metadata_dict,
+                repository_dependency_tups=valid_repository_dependency_tups,
+                is_valid=True,
+                description=description,
+            )
         if invalid_repository_dependency_tups:
-            metadata_dict = \
-                self.update_repository_dependencies_metadata(metadata=metadata_dict,
-                                                             repository_dependency_tups=invalid_repository_dependency_tups,
-                                                             is_valid=False,
-                                                             description=description)
+            metadata_dict = self.update_repository_dependencies_metadata(
+                metadata=metadata_dict,
+                repository_dependency_tups=invalid_repository_dependency_tups,
+                is_valid=False,
+                description=description,
+            )
         return metadata_dict, error_message
 
     def generate_workflow_metadata(self, relative_path, exported_workflow_dict, metadata_dict):
@@ -804,10 +871,10 @@ class MetadataGenerator:
         Update the received metadata_dict with changes that have been applied to the
         received exported_workflow_dict.
         """
-        if 'workflows' in metadata_dict:
-            metadata_dict['workflows'].append((relative_path, exported_workflow_dict))
+        if "workflows" in metadata_dict:
+            metadata_dict["workflows"].append((relative_path, exported_workflow_dict))
         else:
-            metadata_dict['workflows'] = [(relative_path, exported_workflow_dict)]
+            metadata_dict["workflows"] = [(relative_path, exported_workflow_dict)]
         return metadata_dict
 
     def get_invalid_file_tups(self):
@@ -819,20 +886,24 @@ class MetadataGenerator:
     def get_relative_path_to_repository_file(self, root, name, relative_install_dir, work_dir, shed_config_dict):
         if self.resetting_all_metadata_on_repository:
             full_path_to_file = os.path.join(root, name)
-            stripped_path_to_file = full_path_to_file.replace(work_dir, '')
-            if stripped_path_to_file.startswith('/'):
+            stripped_path_to_file = full_path_to_file.replace(work_dir, "")
+            if stripped_path_to_file.startswith("/"):
                 stripped_path_to_file = stripped_path_to_file[1:]
             relative_path_to_file = os.path.join(relative_install_dir, stripped_path_to_file)
         else:
             relative_path_to_file = os.path.join(root, name)
-            if relative_install_dir and \
-                shed_config_dict.get('tool_path') and \
-                    relative_path_to_file.startswith(os.path.join(shed_config_dict.get('tool_path'), relative_install_dir)):
-                relative_path_to_file = relative_path_to_file[len(shed_config_dict.get('tool_path')) + 1:]
+            if (
+                relative_install_dir
+                and shed_config_dict.get("tool_path")
+                and relative_path_to_file.startswith(
+                    os.path.join(shed_config_dict.get("tool_path"), relative_install_dir)
+                )
+            ):
+                relative_path_to_file = relative_path_to_file[len(shed_config_dict.get("tool_path")) + 1 :]
         return relative_path_to_file
 
     def get_sample_files_from_disk(self, repository_files_dir, tool_path=None, relative_install_dir=None):
-        work_dir = ''
+        work_dir = ""
         if self.resetting_all_metadata_on_repository:
             # Keep track of the location where the repository is temporarily cloned so that we can strip
             # it when setting metadata.
@@ -840,15 +911,17 @@ class MetadataGenerator:
         sample_file_metadata_paths = []
         sample_file_copy_paths = []
         for root, _dirs, files in os.walk(repository_files_dir):
-            if root.find('.hg') < 0:
+            if root.find(".hg") < 0:
                 for name in files:
-                    if name.endswith('.sample'):
+                    if name.endswith(".sample"):
                         if self.resetting_all_metadata_on_repository:
                             full_path_to_sample_file = os.path.join(root, name)
-                            stripped_path_to_sample_file = full_path_to_sample_file.replace(work_dir, '')
-                            if stripped_path_to_sample_file.startswith('/'):
+                            stripped_path_to_sample_file = full_path_to_sample_file.replace(work_dir, "")
+                            if stripped_path_to_sample_file.startswith("/"):
                                 stripped_path_to_sample_file = stripped_path_to_sample_file[1:]
-                            relative_path_to_sample_file = os.path.join(relative_install_dir, stripped_path_to_sample_file)
+                            relative_path_to_sample_file = os.path.join(
+                                relative_install_dir, stripped_path_to_sample_file
+                            )
                             if os.path.exists(relative_path_to_sample_file):
                                 sample_file_copy_paths.append(relative_path_to_sample_file)
                             else:
@@ -857,8 +930,10 @@ class MetadataGenerator:
                             relative_path_to_sample_file = os.path.join(root, name)
                             sample_file_copy_paths.append(relative_path_to_sample_file)
                             if tool_path and relative_install_dir:
-                                if relative_path_to_sample_file.startswith(os.path.join(tool_path, relative_install_dir)):
-                                    relative_path_to_sample_file = relative_path_to_sample_file[len(tool_path) + 1:]
+                                if relative_path_to_sample_file.startswith(
+                                    os.path.join(tool_path, relative_install_dir)
+                                ):
+                                    relative_path_to_sample_file = relative_path_to_sample_file[len(tool_path) + 1 :]
                         sample_file_metadata_paths.append(relative_path_to_sample_file)
         return sample_file_metadata_paths, sample_file_copy_paths
 
@@ -871,19 +946,21 @@ class MetadataGenerator:
         Tool Shed.
         """
         is_valid = True
-        error_message = ''
-        toolshed = repository_elem.get('toolshed', None)
-        name = repository_elem.get('name', None)
-        owner = repository_elem.get('owner', None)
-        changeset_revision = repository_elem.get('changeset_revision', None)
-        prior_installation_required = str(repository_elem.get('prior_installation_required', False))
-        repository_dependency_tup = [toolshed,
-                                     name,
-                                     owner,
-                                     changeset_revision,
-                                     prior_installation_required,
-                                     str(only_if_compiling_contained_td)]
-        if self.app.name == 'galaxy':
+        error_message = ""
+        toolshed = repository_elem.get("toolshed", None)
+        name = repository_elem.get("name", None)
+        owner = repository_elem.get("owner", None)
+        changeset_revision = repository_elem.get("changeset_revision", None)
+        prior_installation_required = str(repository_elem.get("prior_installation_required", False))
+        repository_dependency_tup = [
+            toolshed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            str(only_if_compiling_contained_td),
+        ]
+        if self.app.name == "galaxy":
             if self.updating_installed_repository:
                 pass
             else:
@@ -896,46 +973,38 @@ class MetadataGenerator:
                     # Raise an exception here instead of returning an error_message to keep the
                     # installation from proceeding.  Reaching here implies a bug in the Tool Shed
                     # framework.
-                    error_message = 'Installation encountered an invalid repository dependency definition:\n'
+                    error_message = "Installation encountered an invalid repository dependency definition:\n"
                     error_message += util.xml_to_string(repository_elem, pretty=True)
                     log.error(error_message)
                     return repository_dependency_tup, False, error_message
         if not toolshed:
             # Default to the current tool shed.
-            toolshed = str(url_for('/', qualified=True)).rstrip('/')
+            toolshed = str(url_for("/", qualified=True)).rstrip("/")
             repository_dependency_tup[0] = toolshed
         toolshed = remove_protocol_from_tool_shed_url(toolshed)
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             # We're in Galaxy.  We reach here when we're generating the metadata for a tool
             # dependencies package defined for a repository or when we're generating metadata
             # for an installed repository.  See if we can locate the installed repository via
             # the changeset_revision defined in the repository_elem (it may be outdated).  If
             # we're successful in locating an installed repository with the attributes defined
             # in the repository_elem, we know it is valid.
-            repository = get_repository_for_dependency_relationship(self.app,
-                                                                    toolshed,
-                                                                    name,
-                                                                    owner,
-                                                                    changeset_revision)
+            repository = get_repository_for_dependency_relationship(self.app, toolshed, name, owner, changeset_revision)
             if repository:
                 return repository_dependency_tup, is_valid, error_message
             else:
                 # Send a request to the tool shed to retrieve appropriate additional changeset
                 # revisions with which the repository
                 # may have been installed.
-                text = get_updated_changeset_revisions_from_tool_shed(self.app,
-                                                                      toolshed,
-                                                                      name,
-                                                                      owner,
-                                                                      changeset_revision)
+                text = get_updated_changeset_revisions_from_tool_shed(
+                    self.app, toolshed, name, owner, changeset_revision
+                )
                 if text:
                     updated_changeset_revisions = util.listify(text)
                     for updated_changeset_revision in updated_changeset_revisions:
-                        repository = get_repository_for_dependency_relationship(self.app,
-                                                                                toolshed,
-                                                                                name,
-                                                                                owner,
-                                                                                updated_changeset_revision)
+                        repository = get_repository_for_dependency_relationship(
+                            self.app, toolshed, name, owner, updated_changeset_revision
+                        )
                         if repository:
                             return repository_dependency_tup, is_valid, error_message
                         if self.updating_installed_repository:
@@ -954,8 +1023,10 @@ class MetadataGenerator:
                     # if an installed repository cannot be found.  This may not be ideal because the tool
                     # shed may have simply been inaccessible when metadata was being generated for the
                     # installed tool shed repository.
-                    error_message = "Ignoring invalid repository dependency definition for tool shed %s, name %s, owner %s, " % \
-                        (toolshed, name, owner)
+                    error_message = (
+                        "Ignoring invalid repository dependency definition for tool shed %s, name %s, owner %s, "
+                        % (toolshed, name, owner)
+                    )
                     error_message += f"changeset revision {changeset_revision}."
                     log.debug(error_message)
                     is_valid = False
@@ -964,24 +1035,36 @@ class MetadataGenerator:
             # We're in the tool shed.
             if suc.tool_shed_is_this_tool_shed(toolshed):
                 try:
-                    user = self.sa_session.query(self.app.model.User) \
-                                          .filter(self.app.model.User.table.c.username == owner) \
-                                          .one()
+                    user = (
+                        self.sa_session.query(self.app.model.User)
+                        .filter(self.app.model.User.table.c.username == owner)
+                        .one()
+                    )
                 except Exception:
-                    error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, " % \
-                        (toolshed, name, owner)
+                    error_message = (
+                        "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, "
+                        % (toolshed, name, owner)
+                    )
                     error_message += f"changeset revision {changeset_revision} because the owner is invalid."
                     log.debug(error_message)
                     is_valid = False
                     return repository_dependency_tup, is_valid, error_message
                 try:
-                    repository = self.sa_session.query(self.app.model.Repository) \
-                        .filter(and_(self.app.model.Repository.table.c.name == name,
-                                     self.app.model.Repository.table.c.user_id == user.id)) \
+                    repository = (
+                        self.sa_session.query(self.app.model.Repository)
+                        .filter(
+                            and_(
+                                self.app.model.Repository.table.c.name == name,
+                                self.app.model.Repository.table.c.user_id == user.id,
+                            )
+                        )
                         .one()
+                    )
                 except Exception:
-                    error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, " % \
-                        (toolshed, name, owner)
+                    error_message = (
+                        "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, "
+                        % (toolshed, name, owner)
+                    )
                     error_message += f"changeset revision {changeset_revision} because the name is invalid.  "
                     log.debug(error_message)
                     is_valid = False
@@ -995,12 +1078,14 @@ class MetadataGenerator:
                 # Make sure the repo.changlog includes at least 1 revision.
                 if changeset_revision is None and tip_ctx.rev() >= 0:
                     changeset_revision = str(tip_ctx)
-                    repository_dependency_tup = [toolshed,
-                                                 name,
-                                                 owner,
-                                                 changeset_revision,
-                                                 prior_installation_required,
-                                                 str(only_if_compiling_contained_td)]
+                    repository_dependency_tup = [
+                        toolshed,
+                        name,
+                        owner,
+                        changeset_revision,
+                        prior_installation_required,
+                        str(only_if_compiling_contained_td),
+                    ]
                     return repository_dependency_tup, is_valid, error_message
                 else:
                     # Find the specified changeset revision in the repository's changelog to see if it's valid.
@@ -1011,17 +1096,25 @@ class MetadataGenerator:
                             found = True
                             break
                     if not found:
-                        error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, " % \
-                            (toolshed, name, owner)
-                        error_message += f"changeset revision {changeset_revision} because the changeset revision is invalid.  "
+                        error_message = (
+                            "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, "
+                            % (toolshed, name, owner)
+                        )
+                        error_message += (
+                            f"changeset revision {changeset_revision} because the changeset revision is invalid.  "
+                        )
                         log.debug(error_message)
                         is_valid = False
                         return repository_dependency_tup, is_valid, error_message
             else:
                 # Repository dependencies are currently supported within a single tool shed.
-                error_message = "Repository dependencies are currently supported only within the same tool shed.  Ignoring "
-                error_message += "repository dependency definition  for tool shed %s, name %s, owner %s, changeset revision %s.  " % \
-                    (toolshed, name, owner, changeset_revision)
+                error_message = (
+                    "Repository dependencies are currently supported only within the same tool shed.  Ignoring "
+                )
+                error_message += (
+                    "repository dependency definition  for tool shed %s, name %s, owner %s, changeset revision %s.  "
+                    % (toolshed, name, owner, changeset_revision)
+                )
                 log.debug(error_message)
                 is_valid = False
                 return repository_dependency_tup, is_valid, error_message
@@ -1032,13 +1125,13 @@ class MetadataGenerator:
         Determine if a tool should be loaded into the Galaxy tool panel.  Examples of valid tools that
         should not be displayed in the tool panel are datatypes converters and DataManager tools.
         """
-        if hasattr(tool, 'tool_type'):
-            if tool.tool_type in ['manage_data']:
+        if hasattr(tool, "tool_type"):
+            if tool.tool_type in ["manage_data"]:
                 # We have a DataManager tool.
                 return False
         if datatypes:
             for datatype_dict in datatypes:
-                converters = datatype_dict.get('converters', None)
+                converters = datatype_dict.get("converters", None)
                 # [{"converters":
                 #    [{"target_datatype": "gff",
                 #      "tool_config": "bed_to_gff_converter.xml",
@@ -1048,7 +1141,7 @@ class MetadataGenerator:
                 #   "extension": "bed"}]
                 if converters:
                     for converter_dict in converters:
-                        converter_guid = converter_dict.get('guid', None)
+                        converter_guid = converter_dict.get("guid", None)
                         if converter_guid:
                             if converter_guid == guid:
                                 # We have a datatypes converter.
@@ -1064,7 +1157,7 @@ class MetadataGenerator:
     def set_repository(self, repository, relative_install_dir=None, changeset_revision=None):
         self.repository = repository
         # Shed related tool panel configs are only relevant to Galaxy.
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             if relative_install_dir is None and self.repository is not None:
                 tool_path, relative_install_dir = self.repository.get_tool_relative_path(self.app)
             if changeset_revision is None and self.repository is not None:
@@ -1072,7 +1165,7 @@ class MetadataGenerator:
             else:
                 self.set_changeset_revision(changeset_revision)
             self.shed_config_dict = repository.get_shed_config_dict(self.app)
-            self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)}
+            self.metadata_dict = {"shed_config_filename": self.shed_config_dict.get("config_filename", None)}
         else:
             if relative_install_dir is None and self.repository is not None:
                 relative_install_dir = repository.repo_path(self.app)
@@ -1097,33 +1190,34 @@ class MetadataGenerator:
 
     def update_repository_dependencies_metadata(self, metadata, repository_dependency_tups, is_valid, description):
         if is_valid:
-            repository_dependencies_dict = metadata.get('repository_dependencies', None)
+            repository_dependencies_dict = metadata.get("repository_dependencies", None)
         else:
-            repository_dependencies_dict = metadata.get('invalid_repository_dependencies', None)
+            repository_dependencies_dict = metadata.get("invalid_repository_dependencies", None)
         for repository_dependency_tup in repository_dependency_tups:
             if repository_dependencies_dict:
-                repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
+                repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
                 for repository_dependency_tup in repository_dependency_tups:
                     if repository_dependency_tup not in repository_dependencies:
                         repository_dependencies.append(repository_dependency_tup)
-                repository_dependencies_dict['repository_dependencies'] = repository_dependencies
+                repository_dependencies_dict["repository_dependencies"] = repository_dependencies
             else:
-                repository_dependencies_dict = dict(description=description,
-                                                    repository_dependencies=repository_dependency_tups)
+                repository_dependencies_dict = dict(
+                    description=description, repository_dependencies=repository_dependency_tups
+                )
         if repository_dependencies_dict:
             if is_valid:
-                metadata['repository_dependencies'] = repository_dependencies_dict
+                metadata["repository_dependencies"] = repository_dependencies_dict
             else:
-                metadata['invalid_repository_dependencies'] = repository_dependencies_dict
+                metadata["invalid_repository_dependencies"] = repository_dependencies_dict
         return metadata
 
 
 def _get_readme_file_names(repository_name):
     """Return a list of file names that will be categorized as README files for the received repository_name."""
-    readme_files = ['readme', 'read_me', 'install']
-    valid_filenames = [f'{f}.txt' for f in readme_files]
-    valid_filenames.extend([f'{f}.rst' for f in readme_files])
+    readme_files = ["readme", "read_me", "install"]
+    valid_filenames = [f"{f}.txt" for f in readme_files]
+    valid_filenames.extend([f"{f}.rst" for f in readme_files])
     valid_filenames.extend(readme_files)
-    valid_filenames.append(f'{repository_name}.txt')
-    valid_filenames.append(f'{repository_name}.rst')
+    valid_filenames.append(f"{repository_name}.txt")
+    valid_filenames.append(f"{repository_name}.rst")
     return valid_filenames
diff --git a/lib/galaxy/tool_shed/repository_type.py b/lib/galaxy/tool_shed/repository_type.py
index 909830c3171..a070b79dfc4 100644
--- a/lib/galaxy/tool_shed/repository_type.py
+++ b/lib/galaxy/tool_shed/repository_type.py
@@ -1,16 +1,16 @@
-REPOSITORY_DEPENDENCY_DEFINITION_FILENAME = 'repository_dependencies.xml'
-REPOSITORY_SUITE_DEFINITION = 'repository_suite_definition'
-TOOL_DEPENDENCY_DEFINITION = 'tool_dependency_definition'
-TOOL_DEPENDENCY_DEFINITION_FILENAME = 'tool_dependencies.xml'
-UNRESTRICTED = 'unrestricted'
+REPOSITORY_DEPENDENCY_DEFINITION_FILENAME = "repository_dependencies.xml"
+REPOSITORY_SUITE_DEFINITION = "repository_suite_definition"
+TOOL_DEPENDENCY_DEFINITION = "tool_dependency_definition"
+TOOL_DEPENDENCY_DEFINITION_FILENAME = "tool_dependencies.xml"
+UNRESTRICTED = "unrestricted"
 
 types = [UNRESTRICTED, TOOL_DEPENDENCY_DEFINITION, REPOSITORY_SUITE_DEFINITION]
 
 __all__ = (
-    'REPOSITORY_DEPENDENCY_DEFINITION_FILENAME',
-    'REPOSITORY_SUITE_DEFINITION',
-    'TOOL_DEPENDENCY_DEFINITION',
-    'TOOL_DEPENDENCY_DEFINITION_FILENAME',
-    'UNRESTRICTED',
-    'types',
+    "REPOSITORY_DEPENDENCY_DEFINITION_FILENAME",
+    "REPOSITORY_SUITE_DEFINITION",
+    "TOOL_DEPENDENCY_DEFINITION",
+    "TOOL_DEPENDENCY_DEFINITION_FILENAME",
+    "UNRESTRICTED",
+    "types",
 )
diff --git a/lib/galaxy/tool_shed/tool_shed_registry.py b/lib/galaxy/tool_shed/tool_shed_registry.py
index 3d927dc49c3..31799a931ea 100644
--- a/lib/galaxy/tool_shed/tool_shed_registry.py
+++ b/lib/galaxy/tool_shed/tool_shed_registry.py
@@ -20,7 +20,6 @@ class AUTH_TUPLE(NamedTuple):
 
 
 class Registry:
-
     def __init__(self, config=None):
         self.tool_sheds = {}
         self.tool_sheds_auth = {}
@@ -34,17 +33,17 @@ class Registry:
         else:
             root = parse_xml_string(DEFAULT_TOOL_SHEDS_CONF_XML)
             config = "internal default config"
-        log.debug(f'Loading references to tool sheds from {config}')
-        for elem in root.findall('tool_shed'):
+        log.debug(f"Loading references to tool sheds from {config}")
+        for elem in root.findall("tool_shed"):
             try:
-                name = elem.get('name', None)
-                url = elem.get('url', None)
-                username = elem.get('user', None)
-                password = elem.get('pass', None)
+                name = elem.get("name", None)
+                url = elem.get("url", None)
+                username = elem.get("user", None)
+                password = elem.get("pass", None)
                 if name and url:
                     self.tool_sheds[name] = url
                     self.tool_sheds_auth[name] = None
-                    log.debug(f'Loaded reference to tool shed: {name}')
+                    log.debug(f"Loaded reference to tool shed: {name}")
                 if name and url and username and password:
                     self.tool_sheds_auth[name] = AUTH_TUPLE(username, password)
             except Exception as e:
diff --git a/lib/galaxy/tool_shed/tools/data_table_manager.py b/lib/galaxy/tool_shed/tools/data_table_manager.py
index 8914325650b..cdf89ece2be 100644
--- a/lib/galaxy/tool_shed/tools/data_table_manager.py
+++ b/lib/galaxy/tool_shed/tools/data_table_manager.py
@@ -10,24 +10,24 @@ log = logging.getLogger(__name__)
 
 
 class ShedToolDataTableManager:
-
     def __init__(self, app):
         self.app = app
 
-    def generate_repository_info_elem(self, tool_shed, repository_name, changeset_revision, owner,
-                                      parent_elem=None, **kwd):
+    def generate_repository_info_elem(
+        self, tool_shed, repository_name, changeset_revision, owner, parent_elem=None, **kwd
+    ):
         """Create and return an ElementTree repository info Element."""
         if parent_elem is None:
-            elem = etree.Element('tool_shed_repository')
+            elem = etree.Element("tool_shed_repository")
         else:
-            elem = etree.SubElement(parent_elem, 'tool_shed_repository')
-        tool_shed_elem = etree.SubElement(elem, 'tool_shed')
+            elem = etree.SubElement(parent_elem, "tool_shed_repository")
+        tool_shed_elem = etree.SubElement(elem, "tool_shed")
         tool_shed_elem.text = tool_shed
-        repository_name_elem = etree.SubElement(elem, 'repository_name')
+        repository_name_elem = etree.SubElement(elem, "repository_name")
         repository_name_elem.text = repository_name
-        repository_owner_elem = etree.SubElement(elem, 'repository_owner')
+        repository_owner_elem = etree.SubElement(elem, "repository_owner")
         repository_owner_elem.text = owner
-        changeset_revision_elem = etree.SubElement(elem, 'installed_changeset_revision')
+        changeset_revision_elem = etree.SubElement(elem, "installed_changeset_revision")
         changeset_revision_elem.text = changeset_revision
         # add additional values
         # TODO: enhance additional values to allow e.g. use of dict values that will recurse
@@ -37,12 +37,14 @@ class ShedToolDataTableManager:
         return elem
 
     def generate_repository_info_elem_from_repository(self, tool_shed_repository, parent_elem=None, **kwd):
-        return self.generate_repository_info_elem(tool_shed_repository.tool_shed,
-                                                  tool_shed_repository.name,
-                                                  tool_shed_repository.installed_changeset_revision,
-                                                  tool_shed_repository.owner,
-                                                  parent_elem=parent_elem,
-                                                  **kwd)
+        return self.generate_repository_info_elem(
+            tool_shed_repository.tool_shed,
+            tool_shed_repository.name,
+            tool_shed_repository.installed_changeset_revision,
+            tool_shed_repository.owner,
+            parent_elem=parent_elem,
+            **kwd,
+        )
 
     def get_tool_index_sample_files(self, sample_files):
         """
@@ -53,7 +55,7 @@ class ShedToolDataTableManager:
         for s in sample_files:
             # The problem with this is that Galaxy does not follow a standard naming
             # convention for file names.
-            if s.endswith('.loc.sample') or s.endswith('.xml.sample') or s.endswith('.txt.sample'):
+            if s.endswith(".loc.sample") or s.endswith(".xml.sample") or s.endswith(".txt.sample"):
                 tool_index_sample_files.append(str(s))
         return tool_index_sample_files
 
@@ -73,12 +75,12 @@ class ShedToolDataTableManager:
         if missing_data_table_entry:
             # The repository must contain a tool_data_table_conf.xml.sample file that includes
             # all required entries for all tools in the repository.
-            sample_tool_data_table_conf = hg_util.get_config_from_disk('tool_data_table_conf.xml.sample',
-                                                                       relative_install_dir)
+            sample_tool_data_table_conf = hg_util.get_config_from_disk(
+                "tool_data_table_conf.xml.sample", relative_install_dir
+            )
             if sample_tool_data_table_conf:
                 # Add entries to the ToolDataTableManager's in-memory data_tables dictionary.
-                error, message = self.handle_sample_tool_data_table_conf_file(sample_tool_data_table_conf,
-                                                                              persist=True)
+                error, message = self.handle_sample_tool_data_table_conf_file(sample_tool_data_table_conf, persist=True)
                 if error:
                     # TODO: Do more here than logging an exception.
                     log.debug(message)
@@ -96,11 +98,12 @@ class ShedToolDataTableManager:
         """
         error = False
         try:
-            new_table_elems, message = self.app.tool_data_tables \
-                .add_new_entries_from_config_file(config_filename=filename,
-                                                  tool_data_path=self.app.config.shed_tool_data_path,
-                                                  shed_tool_data_table_config=self.app.config.shed_tool_data_table_config,
-                                                  persist=persist)
+            new_table_elems, message = self.app.tool_data_tables.add_new_entries_from_config_file(
+                config_filename=filename,
+                tool_data_path=self.app.config.shed_tool_data_path,
+                shed_tool_data_table_config=self.app.config.shed_tool_data_table_config,
+                persist=persist,
+            )
             if message:
                 error = True
         except Exception as e:
@@ -117,23 +120,27 @@ class ShedToolDataTableManager:
         return target_dir, tool_path, relative_target_dir
 
     def install_tool_data_tables(self, tool_shed_repository, tool_index_sample_files):
-        TOOL_DATA_TABLE_FILE_NAME = 'tool_data_table_conf.xml'
-        TOOL_DATA_TABLE_FILE_SAMPLE_NAME = f'{TOOL_DATA_TABLE_FILE_NAME}.sample'
-        SAMPLE_SUFFIX = '.sample'
+        TOOL_DATA_TABLE_FILE_NAME = "tool_data_table_conf.xml"
+        TOOL_DATA_TABLE_FILE_SAMPLE_NAME = f"{TOOL_DATA_TABLE_FILE_NAME}.sample"
+        SAMPLE_SUFFIX = ".sample"
         SAMPLE_SUFFIX_OFFSET = -len(SAMPLE_SUFFIX)
         target_dir, tool_path, relative_target_dir = self.get_target_install_dir(tool_shed_repository)
         for sample_file in tool_index_sample_files:
             path, filename = os.path.split(sample_file)
             target_filename = filename
             if target_filename.endswith(SAMPLE_SUFFIX):
-                target_filename = target_filename[: SAMPLE_SUFFIX_OFFSET]
+                target_filename = target_filename[:SAMPLE_SUFFIX_OFFSET]
             source_file = os.path.join(tool_path, sample_file)
             # We're not currently uninstalling index files, do not overwrite existing files.
             target_path_filename = os.path.join(target_dir, target_filename)
             if not os.path.exists(target_path_filename) or target_filename == TOOL_DATA_TABLE_FILE_NAME:
                 shutil.copy2(source_file, target_path_filename)
             else:
-                log.debug("Did not copy sample file '%s' to install directory '%s' because file already exists.", filename, target_dir)
+                log.debug(
+                    "Did not copy sample file '%s' to install directory '%s' because file already exists.",
+                    filename,
+                    target_dir,
+                )
             # For provenance and to simplify introspection, let's keep the original data table sample file around.
             if filename == TOOL_DATA_TABLE_FILE_SAMPLE_NAME:
                 shutil.copy2(source_file, os.path.join(target_dir, filename))
@@ -144,21 +151,24 @@ class ShedToolDataTableManager:
             if tree:
                 for elem in tree.getroot():
                     # Append individual table elems or other elemes, but not tables elems.
-                    if elem.tag == 'tables':
+                    if elem.tag == "tables":
                         # TODO: this code need to be revised
                         for _table_elem in elems:
                             elems.append(elem)
                     else:
                         elems.append(elem)
         else:
-            log.debug("The '%s' data table file was not found, but was expected to be copied from '%s' during repository installation.",
-                      tool_data_table_conf_filename, TOOL_DATA_TABLE_FILE_SAMPLE_NAME)
+            log.debug(
+                "The '%s' data table file was not found, but was expected to be copied from '%s' during repository installation.",
+                tool_data_table_conf_filename,
+                TOOL_DATA_TABLE_FILE_SAMPLE_NAME,
+            )
         for elem in elems:
-            if elem.tag == 'table':
-                for file_elem in elem.findall('file'):
-                    path = file_elem.get('path', None)
+            if elem.tag == "table":
+                for file_elem in elem.findall("file"):
+                    path = file_elem.get("path", None)
                     if path:
-                        file_elem.set('path', os.path.normpath(os.path.join(target_dir, os.path.split(path)[1])))
+                        file_elem.set("path", os.path.normpath(os.path.join(target_dir, os.path.split(path)[1])))
                 # Store repository info in the table tag set for trace-ability.
                 self.generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=elem)
         if elems:
diff --git a/lib/galaxy/tool_shed/tools/tool_validator.py b/lib/galaxy/tool_shed/tools/tool_validator.py
index 276de9b1919..4e4c2e71947 100644
--- a/lib/galaxy/tool_shed/tools/tool_validator.py
+++ b/lib/galaxy/tool_shed/tools/tool_validator.py
@@ -3,7 +3,7 @@ import logging
 from galaxy.tool_shed.tools.data_table_manager import ShedToolDataTableManager
 from galaxy.tool_shed.util import (
     basic_util,
-    hg_util
+    hg_util,
 )
 from galaxy.tool_util.fetcher import ToolLocationFetcher
 from galaxy.tools import (
@@ -17,7 +17,6 @@ log = logging.getLogger(__name__)
 
 
 class ToolValidator:
-
     def __init__(self, app):
         self.app = app
         self.stdtm = ShedToolDataTableManager(self.app)
@@ -36,13 +35,17 @@ class ToolValidator:
                 if options and isinstance(options, dynamic_options.DynamicOptions):
                     if options.tool_data_table or options.missing_tool_data_table_name:
                         # Make sure the repository contains a tool_data_table_conf.xml.sample file.
-                        sample_tool_data_table_conf = hg_util.get_config_from_disk('tool_data_table_conf.xml.sample', repo_dir)
+                        sample_tool_data_table_conf = hg_util.get_config_from_disk(
+                            "tool_data_table_conf.xml.sample", repo_dir
+                        )
                         if sample_tool_data_table_conf:
-                            error, correction_msg = \
-                                self.stdtm.handle_sample_tool_data_table_conf_file(sample_tool_data_table_conf,
-                                                                                  persist=False)
+                            error, correction_msg = self.stdtm.handle_sample_tool_data_table_conf_file(
+                                sample_tool_data_table_conf, persist=False
+                            )
                             if error:
-                                invalid_files_and_errors_tups.append(('tool_data_table_conf.xml.sample', correction_msg))
+                                invalid_files_and_errors_tups.append(
+                                    ("tool_data_table_conf.xml.sample", correction_msg)
+                                )
                         else:
                             correction_msg = "This file requires an entry in the tool_data_table_conf.xml file.  "
                             correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository "
@@ -57,7 +60,7 @@ class ToolValidator:
                         sample_found = False
                         for sample_file in sample_files:
                             sample_file_name = basic_util.strip_path(sample_file)
-                            if sample_file_name == f'{index_file_name}.sample':
+                            if sample_file_name == f"{index_file_name}.sample":
                                 options.index_file = index_file_name
                                 if options.tool_data_table:
                                     options.tool_data_table.missing_index_file = None
@@ -65,8 +68,10 @@ class ToolValidator:
                                 break
                         if not sample_found:
                             correction_msg = f"This file refers to a file named <b>{str(index_file_name)}</b>.  "
-                            correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % \
-                                str(index_file_name)
+                            correction_msg += (
+                                "Upload a file named <b>%s.sample</b> to the repository to correct this error."
+                                % str(index_file_name)
+                            )
                             invalid_files_and_errors_tups.append((tool_config_name, correction_msg))
         return invalid_files_and_errors_tups
 
@@ -77,20 +82,30 @@ class ToolValidator:
             tool_location_fetcher=ToolLocationFetcher(),
         )
         try:
-            tool = create_tool_from_source(config_file=full_path, app=self.app, tool_source=tool_source, repository_id=repository_id, allow_code_files=False)
+            tool = create_tool_from_source(
+                config_file=full_path,
+                app=self.app,
+                tool_source=tool_source,
+                repository_id=repository_id,
+                allow_code_files=False,
+            )
             tool.assert_finalized(raise_if_invalid=True)
             valid = True
             error_message = None
         except KeyError as e:
             tool = None
             valid = False
-            error_message = f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file.  Upload a file '
-            error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct '
-            error_message += 'this error.  '
+            error_message = (
+                f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file.  Upload a file '
+            )
+            error_message += (
+                "named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct "
+            )
+            error_message += "this error.  "
             log.exception(error_message)
         except Exception as e:
             tool = None
             valid = False
             error_message = str(e)
-            log.exception('Caught exception loading tool from %s:', full_path)
+            log.exception("Caught exception loading tool from %s:", full_path)
         return tool, valid, error_message
diff --git a/lib/galaxy/tool_shed/util/basic_util.py b/lib/galaxy/tool_shed/util/basic_util.py
index b3037315050..3a81420cf70 100644
--- a/lib/galaxy/tool_shed/util/basic_util.py
+++ b/lib/galaxy/tool_shed/util/basic_util.py
@@ -6,18 +6,21 @@ from string import Template
 
 import markupsafe
 
-from galaxy.util import nice_size, unicodify
+from galaxy.util import (
+    nice_size,
+    unicodify,
+)
 
 log = logging.getLogger(__name__)
 
-CHUNK_SIZE = 2 ** 20  # 1Mb
-INSTALLATION_LOG = 'INSTALLATION.log'
+CHUNK_SIZE = 2**20  # 1Mb
+INSTALLATION_LOG = "INSTALLATION.log"
 # Set no activity timeout to 20 minutes.
 NO_OUTPUT_TIMEOUT = 3600.0
 MAXDIFFSIZE = 8000
 MAX_DISPLAY_SIZE = 32768
 
-DOCKER_IMAGE_TEMPLATE = '''
+DOCKER_IMAGE_TEMPLATE = """
 # Galaxy Docker image
 
 FROM bgruening/galaxy-stable
@@ -39,11 +42,11 @@ EXPOSE :9001
 
 # Autostart script that is invoked during container start
 CMD ["/usr/bin/startup"]
-'''
+"""
 
-SELECTED_REPOSITORIES_TEMPLATE = '''
+SELECTED_REPOSITORIES_TEMPLATE = """
 RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}"
-'''
+"""
 
 
 def evaluate_template(text, install_environment):
@@ -66,24 +69,24 @@ def get_env_var_values(install_environment):
     temporary directory where the tool dependency compilation/installation is being processed.
     """
     env_var_dict = {}
-    env_var_dict['REPOSITORY_INSTALL_DIR'] = install_environment.tool_shed_repository_install_dir
-    env_var_dict['INSTALL_DIR'] = install_environment.install_dir
-    env_var_dict['TMP_WORK_DIR'] = install_environment.tmp_work_dir
-    env_var_dict['system_install'] = install_environment.install_dir
+    env_var_dict["REPOSITORY_INSTALL_DIR"] = install_environment.tool_shed_repository_install_dir
+    env_var_dict["INSTALL_DIR"] = install_environment.install_dir
+    env_var_dict["TMP_WORK_DIR"] = install_environment.tmp_work_dir
+    env_var_dict["system_install"] = install_environment.install_dir
     # If the Python interpreter is 64bit then we can safely assume that the underlying system is also 64bit.
-    env_var_dict['__is64bit__'] = sys.maxsize > 2 ** 32
+    env_var_dict["__is64bit__"] = sys.maxsize > 2**32
     return env_var_dict
 
 
 def get_file_type_str(changeset_revision, file_type):
-    if file_type == 'zip':
-        file_type_str = f'{changeset_revision}.zip'
-    elif file_type == 'bz2':
-        file_type_str = f'{changeset_revision}.tar.bz2'
-    elif file_type == 'gz':
-        file_type_str = f'{changeset_revision}.tar.gz'
+    if file_type == "zip":
+        file_type_str = f"{changeset_revision}.zip"
+    elif file_type == "bz2":
+        file_type_str = f"{changeset_revision}.tar.bz2"
+    elif file_type == "gz":
+        file_type_str = f"{changeset_revision}.tar.gz"
     else:
-        file_type_str = ''
+        file_type_str = ""
     return file_type_str
 
 
@@ -113,15 +116,17 @@ def remove_dir(dir):
 def size_string(raw_text, size=MAX_DISPLAY_SIZE):
     """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser."""
     if raw_text and len(raw_text) >= size:
-        large_str = f'\nFile contents truncated because file size is larger than maximum viewing size of {nice_size(size)}\n'
-        raw_text = f'{raw_text[0:size]}{large_str}'
-    return raw_text or ''
+        large_str = (
+            f"\nFile contents truncated because file size is larger than maximum viewing size of {nice_size(size)}\n"
+        )
+        raw_text = f"{raw_text[0:size]}{large_str}"
+    return raw_text or ""
 
 
 def stringify(list):
     if list:
-        return ','.join(list)
-    return ''
+        return ",".join(list)
+    return ""
 
 
 def strip_path(fpath):
@@ -143,7 +148,7 @@ def to_html_string(text):
         except UnicodeDecodeError as e:
             return f"Error decoding string: {str(e)}"
         text = str(markupsafe.escape(text))
-        text = text.replace('\n', '<br/>')
-        text = text.replace('    ', '&nbsp;&nbsp;&nbsp;&nbsp;')
-        text = text.replace(' ', '&nbsp;')
+        text = text.replace("\n", "<br/>")
+        text = text.replace("    ", "&nbsp;&nbsp;&nbsp;&nbsp;")
+        text = text.replace(" ", "&nbsp;")
     return text
diff --git a/lib/galaxy/tool_shed/util/container_util.py b/lib/galaxy/tool_shed/util/container_util.py
index 38db339ad81..e2798157218 100644
--- a/lib/galaxy/tool_shed/util/container_util.py
+++ b/lib/galaxy/tool_shed/util/container_util.py
@@ -5,12 +5,17 @@ from galaxy.util.tool_shed.common_util import remove_protocol_from_tool_shed_url
 log = logging.getLogger(__name__)
 
 # String separator
-STRSEP = '__ESEP__'
+STRSEP = "__ESEP__"
 
 
-def generate_repository_dependencies_key_for_repository(toolshed_base_url, repository_name, repository_owner,
-                                                        changeset_revision, prior_installation_required,
-                                                        only_if_compiling_contained_td):
+def generate_repository_dependencies_key_for_repository(
+    toolshed_base_url,
+    repository_name,
+    repository_owner,
+    changeset_revision,
+    prior_installation_required,
+    only_if_compiling_contained_td,
+):
     """
     Assumes tool shed is current tool shed since repository dependencies across tool sheds
     is not yet supported.
@@ -19,17 +24,19 @@ def generate_repository_dependencies_key_for_repository(toolshed_base_url, repos
     # of the Galaxy database for an installed repository.  This value does not include the protocol, but does include
     # the port if there is one.
     tool_shed = remove_protocol_from_tool_shed_url(toolshed_base_url)
-    return '{}{}{}{}{}{}{}{}{}{}{}'.format(tool_shed,
-                                       STRSEP,
-                                       str(repository_name),
-                                       STRSEP,
-                                       str(repository_owner),
-                                       STRSEP,
-                                       str(changeset_revision),
-                                       STRSEP,
-                                       str(prior_installation_required),
-                                       STRSEP,
-                                       str(only_if_compiling_contained_td))
+    return "{}{}{}{}{}{}{}{}{}{}{}".format(
+        tool_shed,
+        STRSEP,
+        str(repository_name),
+        STRSEP,
+        str(repository_owner),
+        STRSEP,
+        str(changeset_revision),
+        STRSEP,
+        str(prior_installation_required),
+        STRSEP,
+        str(only_if_compiling_contained_td),
+    )
 
 
 def get_components_from_key(key):
@@ -48,9 +55,14 @@ def get_components_from_key(key):
     elif len(items) == 6:
         prior_installation_required = items[4]
         only_if_compiling_contained_td = items[5]
-        return toolshed_base_url, repository_name, repository_owner, \
-            changeset_revision, prior_installation_required, \
-            only_if_compiling_contained_td
+        return (
+            toolshed_base_url,
+            repository_name,
+            repository_owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        )
     else:
         # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers
         # must handle exceptions.
diff --git a/lib/galaxy/tool_shed/util/hg_util.py b/lib/galaxy/tool_shed/util/hg_util.py
index 0e0218146ed..9f3e882e127 100644
--- a/lib/galaxy/tool_shed/util/hg_util.py
+++ b/lib/galaxy/tool_shed/util/hg_util.py
@@ -7,7 +7,7 @@ from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
-INITIAL_CHANGELOG_HASH = '000000000000'
+INITIAL_CHANGELOG_HASH = "000000000000"
 
 
 def clone_repository(repository_clone_url, repository_file_dir, ctx_rev=None):
@@ -15,9 +15,9 @@ def clone_repository(repository_clone_url, repository_file_dir, ctx_rev=None):
     Clone the repository up to the specified changeset_revision.  No subsequent revisions will be
     present in the cloned repository.
     """
-    cmd = ['hg', 'clone']
+    cmd = ["hg", "clone"]
     if ctx_rev:
-        cmd.extend(['-r', str(ctx_rev)])
+        cmd.extend(["-r", str(ctx_rev)])
     cmd.extend([repository_clone_url, repository_file_dir])
     # Make sure the destination path actually exists before attempting to clone
     if not os.path.exists(repository_file_dir):
@@ -26,7 +26,7 @@ def clone_repository(repository_clone_url, repository_file_dir, ctx_rev=None):
         subprocess.check_output(cmd, stderr=subprocess.STDOUT, stdin=subprocess.DEVNULL)
         return True, None
     except Exception as e:
-        error_message = f'Error cloning repository: {unicodify(e)}'
+        error_message = f"Error cloning repository: {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
             error_message += f"\nOutput was:\n{unicodify(e.output)}"
         log.error(error_message)
@@ -41,9 +41,9 @@ def copy_file_from_manifest(repo, changeset_revision, filename, dir):
     for changeset in reversed_upper_bounded_changelog(repo, changeset_revision):
         changeset_ctx = repo[changeset]
         fctx = get_file_context_from_ctx(changeset_ctx, filename)
-        if fctx and fctx not in ['DELETED']:
+        if fctx and fctx not in ["DELETED"]:
             file_path = os.path.join(dir, filename)
-            fh = open(file_path, 'wb')
+            fh = open(file_path, "wb")
             fh.write(fctx.data())
             fh.close()
             return file_path
@@ -61,7 +61,7 @@ def get_changectx_for_changeset(repo, changeset_revision, **kwd):
 
 def get_config_from_disk(config_file, relative_install_dir):
     for root, _dirs, files in os.walk(relative_install_dir):
-        if root.find('.hg') < 0:
+        if root.find(".hg") < 0:
             for name in files:
                 if name == config_file:
                     return os.path.abspath(os.path.join(root, name))
@@ -103,14 +103,16 @@ def get_file_context_from_ctx(ctx, filename):
                 # Set deleted for now, and continue looking in case the file was moved instead of deleted.
                 deleted = True
     if deleted:
-        return 'DELETED'
+        return "DELETED"
     return None
 
 
 def pull_repository(repo_path, repository_clone_url, ctx_rev):
     """Pull changes from a remote repository to a local one."""
     try:
-        subprocess.check_output(['hg', 'pull', '-r', ctx_rev, repository_clone_url], stderr=subprocess.STDOUT, cwd=repo_path)
+        subprocess.check_output(
+            ["hg", "pull", "-r", ctx_rev, repository_clone_url], stderr=subprocess.STDOUT, cwd=repo_path
+        )
     except Exception as e:
         error_message = f"Error pulling revision '{ctx_rev}': {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
@@ -118,7 +120,9 @@ def pull_repository(repo_path, repository_clone_url, ctx_rev):
         raise Exception(error_message)
 
 
-def reversed_lower_upper_bounded_changelog(repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision):
+def reversed_lower_upper_bounded_changelog(
+    repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision
+):
     """
     Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision,
     but up to and including the included_upper_bounds_changeset_revision.  The value of excluded_lower_bounds_changeset_revision
@@ -149,7 +153,9 @@ def reversed_upper_bounded_changelog(repo, included_upper_bounds_changeset_revis
     Return a reversed list of changesets in the repository changelog up to and including the
     included_upper_bounds_changeset_revision.
     """
-    return reversed_lower_upper_bounded_changelog(repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision)
+    return reversed_lower_upper_bounded_changelog(
+        repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision
+    )
 
 
 def update_repository(repo_path, ctx_rev=None):
@@ -168,27 +174,27 @@ def update_repository(repo_path, ctx_rev=None):
     # I = ignored
     # It would be nice if we could use mercurial's purge extension to remove untracked files.  The problem is that
     # purging is not supported by the mercurial API.
-    cmd = ['hg', 'update']
+    cmd = ["hg", "update"]
     if ctx_rev:
-        cmd.extend(['-r', ctx_rev])
+        cmd.extend(["-r", ctx_rev])
     try:
         subprocess.check_output(cmd, stderr=subprocess.STDOUT, cwd=repo_path)
     except Exception as e:
-        error_message = f'Error updating repository: {unicodify(e)}'
+        error_message = f"Error updating repository: {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
             error_message += f"\nOutput was:\n{unicodify(e.output)}"
         raise Exception(error_message)
 
 
 __all__ = (
-    'clone_repository',
-    'copy_file_from_manifest',
-    'get_changectx_for_changeset',
-    'get_config_from_disk',
-    'get_ctx_file_path_from_manifest',
-    'get_file_context_from_ctx',
-    'pull_repository',
-    'reversed_lower_upper_bounded_changelog',
-    'reversed_upper_bounded_changelog',
-    'update_repository',
+    "clone_repository",
+    "copy_file_from_manifest",
+    "get_changectx_for_changeset",
+    "get_config_from_disk",
+    "get_ctx_file_path_from_manifest",
+    "get_file_context_from_ctx",
+    "pull_repository",
+    "reversed_lower_upper_bounded_changelog",
+    "reversed_upper_bounded_changelog",
+    "update_repository",
 )
diff --git a/lib/galaxy/tool_shed/util/metadata_util.py b/lib/galaxy/tool_shed/util/metadata_util.py
index d25a458e01c..36387a28fba 100644
--- a/lib/galaxy/tool_shed/util/metadata_util.py
+++ b/lib/galaxy/tool_shed/util/metadata_util.py
@@ -10,10 +10,16 @@ def get_updated_changeset_revisions_from_tool_shed(app, tool_shed_url, name, own
     tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
     if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
         message = "Unable to get updated changeset revisions from the Tool Shed because one or more of the following "
-        message += "required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
-            (str(tool_shed_url), str(name), str(owner), str(changeset_revision))
+        message += "required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % (
+            str(tool_shed_url),
+            str(name),
+            str(owner),
+            str(changeset_revision),
+        )
         raise Exception(message)
     params = dict(name=name, owner=owner, changeset_revision=changeset_revision)
-    pathspec = ['repository', 'updated_changeset_revisions']
-    text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+    pathspec = ["repository", "updated_changeset_revisions"]
+    text = util.url_get(
+        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+    )
     return text
diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index f70ff38ed88..39d599c5e62 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -12,10 +12,15 @@ from sqlalchemy import (
 )
 from sqlalchemy.orm import joinedload
 
-from galaxy import util
-from galaxy import web
+from galaxy import (
+    util,
+    web,
+)
 from galaxy.tool_shed.util import basic_util
-from galaxy.util.tool_shed import common_util, encoding_util
+from galaxy.util.tool_shed import (
+    common_util,
+    encoding_util,
+)
 
 log = logging.getLogger(__name__)
 
@@ -23,20 +28,20 @@ VALID_REPOSITORYNAME_RE = re.compile(r"^[a-z0-9\_]+$")
 
 
 def check_for_updates(app, model, repository_id=None):
-    message = ''
-    status = 'ok'
+    message = ""
+    status = "ok"
     if repository_id is None:
         success_count = 0
         repository_names_not_updated = []
         updated_count = 0
-        for repository in model.context.query(model.ToolShedRepository) \
-                                       .filter(model.ToolShedRepository.table.c.deleted == false()):
-            ok, updated = \
-                check_or_update_tool_shed_status_for_installed_repository(app, repository)
+        for repository in model.context.query(model.ToolShedRepository).filter(
+            model.ToolShedRepository.table.c.deleted == false()
+        ):
+            ok, updated = check_or_update_tool_shed_status_for_installed_repository(app, repository)
             if ok:
                 success_count += 1
             else:
-                repository_names_not_updated.append(f'<b>{escape(str(repository.name))}</b>')
+                repository_names_not_updated.append(f"<b>{escape(str(repository.name))}</b>")
             if updated:
                 updated_count += 1
         message = "Checked the status in the tool shed for %d repositories.  " % success_count
@@ -46,16 +51,19 @@ def check_for_updates(app, model, repository_id=None):
             message += ", ".join(repository_names_not_updated)
     else:
         repository = get_tool_shed_repository_by_id(app, repository_id)
-        ok, updated = \
-            check_or_update_tool_shed_status_for_installed_repository(app, repository)
+        ok, updated = check_or_update_tool_shed_status_for_installed_repository(app, repository)
         if ok:
             if updated:
                 message = f"The tool shed status for repository <b>{escape(str(repository.name))}</b> has been updated."
             else:
-                message = f"The status has not changed in the tool shed for repository <b>{escape(str(repository.name))}</b>."
+                message = (
+                    f"The status has not changed in the tool shed for repository <b>{escape(str(repository.name))}</b>."
+                )
         else:
-            message = f"Unable to retrieve status from the tool shed for repository <b>{escape(str(repository.name))}</b>."
-            status = 'error'
+            message = (
+                f"Unable to retrieve status from the tool shed for repository <b>{escape(str(repository.name))}</b>."
+            )
+            status = "error"
     return message, status
 
 
@@ -74,8 +82,19 @@ def check_or_update_tool_shed_status_for_installed_repository(app, repository):
     return ok, updated
 
 
-def create_or_update_tool_shed_repository(app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url,
-                                          status, metadata_dict=None, current_changeset_revision=None, owner='', dist_to_shed=False):
+def create_or_update_tool_shed_repository(
+    app,
+    name,
+    description,
+    installed_changeset_revision,
+    ctx_rev,
+    repository_clone_url,
+    status,
+    metadata_dict=None,
+    current_changeset_revision=None,
+    owner="",
+    dist_to_shed=False,
+):
     """
     Update a tool shed repository record in the Galaxy database with the new information received.
     If a record defined by the received tool shed, repository name and owner does not exist, create
@@ -95,7 +114,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
     tool_shed = get_tool_shed_from_clone_url(repository_clone_url)
     if not owner:
         owner = get_repository_owner_from_clone_url(repository_clone_url)
-    includes_datatypes = 'datatypes' in metadata_dict
+    includes_datatypes = "datatypes" in metadata_dict
     if status in [app.install_model.ToolShedRepository.installation_status.DEACTIVATED]:
         deleted = True
         uninstalled = False
@@ -105,10 +124,15 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
     else:
         deleted = False
         uninstalled = False
-    tool_shed_repository = \
-        get_installed_repository(app, tool_shed=tool_shed, name=name, owner=owner, installed_changeset_revision=installed_changeset_revision)
+    tool_shed_repository = get_installed_repository(
+        app, tool_shed=tool_shed, name=name, owner=owner, installed_changeset_revision=installed_changeset_revision
+    )
     if tool_shed_repository:
-        log.debug("Updating an existing row for repository '%s' in the tool_shed_repository table, status set to '%s'.", name, status)
+        log.debug(
+            "Updating an existing row for repository '%s' in the tool_shed_repository table, status set to '%s'.",
+            name,
+            status,
+        )
         tool_shed_repository.description = description
         tool_shed_repository.changeset_revision = current_changeset_revision
         tool_shed_repository.ctx_rev = ctx_rev
@@ -118,28 +142,31 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
         tool_shed_repository.uninstalled = uninstalled
         tool_shed_repository.status = status
     else:
-        log.debug("Adding new row for repository '%s' in the tool_shed_repository table, status set to '%s'.", name, status)
-        tool_shed_repository = \
-            app.install_model.ToolShedRepository(tool_shed=tool_shed,
-                                                 name=name,
-                                                 description=description,
-                                                 owner=owner,
-                                                 installed_changeset_revision=installed_changeset_revision,
-                                                 changeset_revision=current_changeset_revision,
-                                                 ctx_rev=ctx_rev,
-                                                 metadata_=metadata_dict,
-                                                 includes_datatypes=includes_datatypes,
-                                                 dist_to_shed=dist_to_shed,
-                                                 deleted=deleted,
-                                                 uninstalled=uninstalled,
-                                                 status=status)
+        log.debug(
+            "Adding new row for repository '%s' in the tool_shed_repository table, status set to '%s'.", name, status
+        )
+        tool_shed_repository = app.install_model.ToolShedRepository(
+            tool_shed=tool_shed,
+            name=name,
+            description=description,
+            owner=owner,
+            installed_changeset_revision=installed_changeset_revision,
+            changeset_revision=current_changeset_revision,
+            ctx_rev=ctx_rev,
+            metadata_=metadata_dict,
+            includes_datatypes=includes_datatypes,
+            dist_to_shed=dist_to_shed,
+            deleted=deleted,
+            uninstalled=uninstalled,
+            status=status,
+        )
     context.add(tool_shed_repository)
     context.flush()
     return tool_shed_repository
 
 
 def extract_components_from_tuple(repository_components_tuple):
-    '''Extract the repository components from the provided tuple in a backward-compatible manner.'''
+    """Extract the repository components from the provided tuple in a backward-compatible manner."""
     toolshed = repository_components_tuple[0]
     name = repository_components_tuple[1]
     owner = repository_components_tuple[2]
@@ -149,8 +176,22 @@ def extract_components_from_tuple(repository_components_tuple):
         toolshed, name, owner, changeset_revision, prior_installation_required = repository_components_tuple
         components_list = [toolshed, name, owner, changeset_revision, prior_installation_required]
     elif len(repository_components_tuple) == 6:
-        toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_components_tuple
-        components_list = [toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td]
+        (
+            toolshed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = repository_components_tuple
+        components_list = [
+            toolshed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ]
     return components_list
 
 
@@ -162,11 +203,11 @@ def generate_tool_shed_repository_install_dir(repository_clone_url, changeset_re
     """
     tmp_url = common_util.remove_protocol_and_user_from_clone_url(repository_clone_url)
     # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
-    items = tmp_url.split('/repos/')
+    items = tmp_url.split("/repos/")
     tool_shed_url = items[0]
     repo_path = items[1]
     tool_shed_url = common_util.remove_port_from_tool_shed_url(tool_shed_url)
-    return '/'.join((tool_shed_url, 'repos', repo_path, changeset_revision))
+    return "/".join((tool_shed_url, "repos", repo_path, changeset_revision))
 
 
 def get_absolute_path_to_file_in_repository(repo_files_dir, file_name):
@@ -174,7 +215,7 @@ def get_absolute_path_to_file_in_repository(repo_files_dir, file_name):
     stripped_file_name = basic_util.strip_path(file_name)
     file_path = None
     for root, _, files in os.walk(repo_files_dir):
-        if root.find('.hg') < 0:
+        if root.find(".hg") < 0:
             for name in files:
                 if name == stripped_file_name:
                     return os.path.abspath(os.path.join(root, name))
@@ -186,22 +227,35 @@ def get_ids_of_tool_shed_repositories_being_installed(app, as_string=False):
     new_status = app.install_model.ToolShedRepository.installation_status.NEW
     cloning_status = app.install_model.ToolShedRepository.installation_status.CLONING
     setting_tool_versions_status = app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS
-    installing_dependencies_status = app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES
+    installing_dependencies_status = (
+        app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES
+    )
     loading_datatypes_status = app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
-    for tool_shed_repository in \
-        app.install_model.context.query(app.install_model.ToolShedRepository) \
-                                 .filter(or_(app.install_model.ToolShedRepository.status == new_status,
-                                             app.install_model.ToolShedRepository.status == cloning_status,
-                                             app.install_model.ToolShedRepository.status == setting_tool_versions_status,
-                                             app.install_model.ToolShedRepository.status == installing_dependencies_status,
-                                             app.install_model.ToolShedRepository.status == loading_datatypes_status)):
+    for tool_shed_repository in app.install_model.context.query(app.install_model.ToolShedRepository).filter(
+        or_(
+            app.install_model.ToolShedRepository.status == new_status,
+            app.install_model.ToolShedRepository.status == cloning_status,
+            app.install_model.ToolShedRepository.status == setting_tool_versions_status,
+            app.install_model.ToolShedRepository.status == installing_dependencies_status,
+            app.install_model.ToolShedRepository.status == loading_datatypes_status,
+        )
+    ):
         installing_repository_ids.append(app.security.encode_id(tool_shed_repository.id))
     if as_string:
-        return ','.join(installing_repository_ids)
+        return ",".join(installing_repository_ids)
     return installing_repository_ids
 
 
-def get_installed_repository(app, tool_shed=None, name=None, owner=None, changeset_revision=None, installed_changeset_revision=None, repository_id=None, from_cache=False):
+def get_installed_repository(
+    app,
+    tool_shed=None,
+    name=None,
+    owner=None,
+    changeset_revision=None,
+    installed_changeset_revision=None,
+    repository_id=None,
+    from_cache=False,
+):
     """
     Return a tool shed repository database record defined by the combination of a toolshed, repository name,
     repository owner and either current or originally installed changeset_revision.
@@ -209,7 +263,7 @@ def get_installed_repository(app, tool_shed=None, name=None, owner=None, changes
     # We store the port, if one exists, in the database.
     tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed)
     if from_cache:
-        tsr_cache = getattr(app, 'tool_shed_repository_cache', None)
+        tsr_cache = getattr(app, "tool_shed_repository_cache", None)
         if tsr_cache:
             return app.tool_shed_repository_cache.get_installed_repository(
                 tool_shed=tool_shed,
@@ -217,19 +271,23 @@ def get_installed_repository(app, tool_shed=None, name=None, owner=None, changes
                 owner=owner,
                 installed_changeset_revision=installed_changeset_revision,
                 changeset_revision=changeset_revision,
-                repository_id=repository_id
+                repository_id=repository_id,
             )
     query = app.install_model.context.query(app.install_model.ToolShedRepository)
     if repository_id:
         clause_list = [app.install_model.ToolShedRepository.table.c.id == repository_id]
     else:
-        clause_list = [app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                       app.install_model.ToolShedRepository.table.c.name == name,
-                       app.install_model.ToolShedRepository.table.c.owner == owner]
+        clause_list = [
+            app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
+            app.install_model.ToolShedRepository.table.c.name == name,
+            app.install_model.ToolShedRepository.table.c.owner == owner,
+        ]
     if changeset_revision is not None:
         clause_list.append(app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision)
     if installed_changeset_revision is not None:
-        clause_list.append(app.install_model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision)
+        clause_list.append(
+            app.install_model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision
+        )
     return query.filter(and_(*clause_list)).first()
 
 
@@ -262,13 +320,17 @@ def get_prior_import_or_install_required_dict(app, tsr_ids, repo_info_dicts):
         prior_import_or_install_required_dict[tsr_id] = []
     # Inspect the repository dependencies for each repository about to be installed and populate the dictionary.
     for repo_info_dict in repo_info_dicts:
-        repository, repository_dependencies = get_repository_and_repository_dependencies_from_repo_info_dict(app, repo_info_dict)
+        repository, repository_dependencies = get_repository_and_repository_dependencies_from_repo_info_dict(
+            app, repo_info_dict
+        )
         if repository:
             encoded_repository_id = app.security.encode_id(repository.id)
             if encoded_repository_id in tsr_ids:
                 # We've located the database table record for one of the repositories we're about to install, so find out if it has any repository
                 # dependencies that require prior installation.
-                prior_import_or_install_ids = get_repository_ids_requiring_prior_import_or_install(app, tsr_ids, repository_dependencies)
+                prior_import_or_install_ids = get_repository_ids_requiring_prior_import_or_install(
+                    app, tsr_ids, repository_dependencies
+                )
                 prior_import_or_install_required_dict[encoded_repository_id] = prior_import_or_install_ids
     return prior_import_or_install_required_dict
 
@@ -276,27 +338,59 @@ def get_prior_import_or_install_required_dict(app, tsr_ids, repo_info_dicts):
 def get_repo_info_tuple_contents(repo_info_tuple):
     """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced."""
     if len(repo_info_tuple) == 6:
-        description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+        (
+            description,
+            repository_clone_url,
+            changeset_revision,
+            ctx_rev,
+            repository_owner,
+            tool_dependencies,
+        ) = repo_info_tuple
         repository_dependencies = None
     elif len(repo_info_tuple) == 7:
-        description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
-    return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies
+        (
+            description,
+            repository_clone_url,
+            changeset_revision,
+            ctx_rev,
+            repository_owner,
+            repository_dependencies,
+            tool_dependencies,
+        ) = repo_info_tuple
+    return (
+        description,
+        repository_clone_url,
+        changeset_revision,
+        ctx_rev,
+        repository_owner,
+        repository_dependencies,
+        tool_dependencies,
+    )
 
 
 def get_repository_admin_role_name(repository_name, repository_owner):
-    return f'{str(repository_name)}_{str(repository_owner)}_admin'
+    return f"{str(repository_name)}_{str(repository_owner)}_admin"
 
 
 def get_repository_and_repository_dependencies_from_repo_info_dict(app, repo_info_dict):
     """Return a tool_shed_repository or repository record defined by the information in the received repo_info_dict."""
     repository_name = list(repo_info_dict.keys())[0]
     repo_info_tuple = repo_info_dict[repository_name]
-    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
-        get_repo_info_tuple_contents(repo_info_tuple)
+    (
+        description,
+        repository_clone_url,
+        changeset_revision,
+        ctx_rev,
+        repository_owner,
+        repository_dependencies,
+        tool_dependencies,
+    ) = get_repo_info_tuple_contents(repo_info_tuple)
     if hasattr(app, "install_model"):
         # In a tool shed client (Galaxy, or something install repositories like Galaxy)
         tool_shed = get_tool_shed_from_clone_url(repository_clone_url)
-        repository = get_repository_for_dependency_relationship(app, tool_shed, repository_name, repository_owner, changeset_revision)
+        repository = get_repository_for_dependency_relationship(
+            app, tool_shed, repository_name, repository_owner, changeset_revision
+        )
     else:
         # We're in the tool shed.
         repository = get_repository_by_name_and_owner(app, repository_name, repository_owner)
@@ -316,16 +410,18 @@ def get_repository_by_name_and_owner(app, name, owner, eagerload_columns=None):
     """Get a repository from the database via name and owner"""
     repository_query = get_repository_query(app)
     if is_tool_shed_client(app):
-        return repository_query \
-            .filter(and_(app.install_model.ToolShedRepository.table.c.name == name,
-                         app.install_model.ToolShedRepository.table.c.owner == owner)) \
-            .first()
+        return repository_query.filter(
+            and_(
+                app.install_model.ToolShedRepository.table.c.name == name,
+                app.install_model.ToolShedRepository.table.c.owner == owner,
+            )
+        ).first()
     # We're in the tool shed.
     q = repository_query.filter(
         and_(
             app.model.Repository.table.c.name == name,
             app.model.User.table.c.username == owner,
-            app.model.Repository.table.c.user_id == app.model.User.table.c.id
+            app.model.Repository.table.c.user_id == app.model.User.table.c.id,
         )
     )
     if eagerload_columns:
@@ -348,8 +444,14 @@ def get_repository_dependency_types(repository_dependencies):
     # only_if_compiling_contained_td as False.
     has_repository_dependencies = False
     for rd_tup in repository_dependencies:
-        tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(rd_tup)
+        (
+            tool_shed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(rd_tup)
         if not util.asbool(only_if_compiling_contained_td):
             has_repository_dependencies = True
             break
@@ -357,8 +459,14 @@ def get_repository_dependency_types(repository_dependencies):
     # least one repository_dependency is defined with the value of only_if_compiling_contained_td as True.
     has_repository_dependencies_only_if_compiling_contained_td = False
     for rd_tup in repository_dependencies:
-        tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(rd_tup)
+        (
+            tool_shed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(rd_tup)
         if util.asbool(only_if_compiling_contained_td):
             has_repository_dependencies_only_if_compiling_contained_td = True
             break
@@ -374,23 +482,23 @@ def get_repository_for_dependency_relationship(app, tool_shed, name, owner, chan
     tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed)
     if tool_shed is None or name is None or owner is None or changeset_revision is None:
         message = "Unable to retrieve the repository record from the database because one or more of the following "
-        message += "required parameters is None: tool_shed: %s, name: %s, owner: %s, changeset_revision: %s " % \
-            (str(tool_shed), str(name), str(owner), str(changeset_revision))
+        message += "required parameters is None: tool_shed: %s, name: %s, owner: %s, changeset_revision: %s " % (
+            str(tool_shed),
+            str(name),
+            str(owner),
+            str(changeset_revision),
+        )
         raise Exception(message)
-    repository = get_installed_repository(app=app,
-                                          tool_shed=tool_shed,
-                                          name=name,
-                                          owner=owner,
-                                          installed_changeset_revision=changeset_revision)
+    repository = get_installed_repository(
+        app=app, tool_shed=tool_shed, name=name, owner=owner, installed_changeset_revision=changeset_revision
+    )
     if not repository:
-        repository = get_installed_repository(app=app,
-                                              tool_shed=tool_shed,
-                                              name=name,
-                                              owner=owner,
-                                              changeset_revision=changeset_revision)
+        repository = get_installed_repository(
+            app=app, tool_shed=tool_shed, name=name, owner=owner, changeset_revision=changeset_revision
+        )
     if not repository:
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed)
-        repository_clone_url = os.path.join(tool_shed_url, 'repos', owner, name)
+        repository_clone_url = os.path.join(tool_shed_url, "repos", owner, name)
         repo_info_tuple = (None, repository_clone_url, changeset_revision, None, owner, None, None)
         repository, pcr = repository_was_previously_installed(app, tool_shed_url, name, repo_info_tuple)
     if not repository:
@@ -398,14 +506,14 @@ def get_repository_for_dependency_relationship(app, tool_shed, name, owner, chan
         # in the repository's changelog in the tool shed that is associated with repository_metadata.
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed)
         params = dict(name=name, owner=owner, changeset_revision=changeset_revision)
-        pathspec = ['repository', 'next_installable_changeset_revision']
-        text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        pathspec = ["repository", "next_installable_changeset_revision"]
+        text = util.url_get(
+            tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         if text:
-            repository = get_installed_repository(app=app,
-                                                  tool_shed=tool_shed,
-                                                  name=name,
-                                                  owner=owner,
-                                                  changeset_revision=text)
+            repository = get_installed_repository(
+                app=app, tool_shed=tool_shed, name=name, owner=owner, changeset_revision=text
+            )
     return repository
 
 
@@ -423,16 +531,17 @@ def get_repository_ids_requiring_prior_import_or_install(app, tsr_ids, repositor
     prior_tsr_ids = []
     if repository_dependencies:
         for key, rd_tups in repository_dependencies.items():
-            if key in ['description', 'root_key']:
+            if key in ["description", "root_key"]:
                 continue
             for rd_tup in rd_tups:
-                tool_shed, \
-                    name, \
-                    owner, \
-                    changeset_revision, \
-                    prior_installation_required, \
-                    only_if_compiling_contained_td = \
-                    common_util.parse_repository_dependency_tuple(rd_tup)
+                (
+                    tool_shed,
+                    name,
+                    owner,
+                    changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                ) = common_util.parse_repository_dependency_tuple(rd_tup)
                 # If only_if_compiling_contained_td is False, then the repository dependency
                 # is not required to be installed prior to the dependent repository even if
                 # prior_installation_required is True.  This is because the only meaningful
@@ -447,11 +556,9 @@ def get_repository_ids_requiring_prior_import_or_install(app, tsr_ids, repositor
                         if is_tool_shed_client(app):
                             # We store the port, if one exists, in the database.
                             tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed)
-                            repository = get_repository_for_dependency_relationship(app,
-                                                                                    tool_shed,
-                                                                                    name,
-                                                                                    owner,
-                                                                                    changeset_revision)
+                            repository = get_repository_for_dependency_relationship(
+                                app, tool_shed, name, owner, changeset_revision
+                            )
                         else:
                             repository = get_repository_by_name_and_owner(app, name, owner)
                         if repository:
@@ -471,11 +578,11 @@ def get_repository_in_tool_shed(app, id, eagerload_columns=None):
 
 def get_repository_owner(cleaned_repository_url):
     """Gvien a "cleaned" repository clone URL, return the owner of the repository."""
-    items = cleaned_repository_url.split('/repos/')
+    items = cleaned_repository_url.split("/repos/")
     repo_path = items[1]
-    if repo_path.startswith('/'):
-        repo_path = repo_path.replace('/', '', 1)
-    return repo_path.lstrip('/').split('/')[0]
+    if repo_path.startswith("/"):
+        repo_path = repo_path.replace("/", "", 1)
+    return repo_path.lstrip("/").split("/")[0]
 
 
 def get_repository_owner_from_clone_url(repository_clone_url):
@@ -500,15 +607,17 @@ def get_role_by_id(app, role_id):
 
 def get_tool_shed_from_clone_url(repository_clone_url):
     tmp_url = common_util.remove_protocol_and_user_from_clone_url(repository_clone_url)
-    return tmp_url.split('/repos/')[0].rstrip('/')
+    return tmp_url.split("/repos/")[0].rstrip("/")
 
 
 def get_tool_shed_repository_by_id(app, repository_id):
     """Return a tool shed repository database record defined by the id."""
     # This method is used only in Galaxy, not the tool shed.
-    return app.install_model.context.query(app.install_model.ToolShedRepository) \
-                                    .filter(app.install_model.ToolShedRepository.table.c.id == app.security.decode_id(repository_id)) \
-                                    .first()
+    return (
+        app.install_model.context.query(app.install_model.ToolShedRepository)
+        .filter(app.install_model.ToolShedRepository.table.c.id == app.security.decode_id(repository_id))
+        .first()
+    )
 
 
 def get_tool_shed_status_for_installed_repository(app, repository):
@@ -520,25 +629,31 @@ def get_tool_shed_status_for_installed_repository(app, repository):
     """
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed))
     params = dict(name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision)
-    pathspec = ['repository', 'status_for_installed_repository']
+    pathspec = ["repository", "status_for_installed_repository"]
     try:
-        encoded_tool_shed_status_dict = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        encoded_tool_shed_status_dict = util.url_get(
+            tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         tool_shed_status_dict = encoding_util.tool_shed_decode(encoded_tool_shed_status_dict)
         return tool_shed_status_dict
     except HTTPError as e:
         # This should handle backward compatility to the Galaxy 12/20/12 release.  We used to only handle updates for an installed revision
         # using a boolean value.
-        log.debug("Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n" %
-                  (str(repository.name), str(e)))
-        pathspec = ['repository', 'check_for_updates']
-        params['from_update_manager'] = True
+        log.debug(
+            "Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n"
+            % (str(repository.name), str(e))
+        )
+        pathspec = ["repository", "check_for_updates"]
+        params["from_update_manager"] = True
         try:
             # The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
-            text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+            text = util.url_get(
+                tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+            )
             return dict(revision_update=text)
         except Exception:
             # The required tool shed may be unavailable, so default the revision_update value to 'false'.
-            return dict(revision_update='false')
+            return dict(revision_update="false")
     except Exception:
         log.exception("Error attempting to get tool shed status for installed repository %s", str(repository.name))
         return {}
@@ -564,34 +679,49 @@ def repository_was_previously_installed(app, tool_shed_url, repository_name, rep
     the repository may be currently uninstalled.
     """
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
-    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
-        get_repo_info_tuple_contents(repo_info_tuple)
+    (
+        description,
+        repository_clone_url,
+        changeset_revision,
+        ctx_rev,
+        repository_owner,
+        repository_dependencies,
+        tool_dependencies,
+    ) = get_repo_info_tuple_contents(repo_info_tuple)
     tool_shed = get_tool_shed_from_clone_url(repository_clone_url)
     # See if we can locate the repository using the value of changeset_revision.
-    tool_shed_repository = get_installed_repository(app,
-                                                    tool_shed=tool_shed,
-                                                    name=repository_name,
-                                                    owner=repository_owner,
-                                                    installed_changeset_revision=changeset_revision)
+    tool_shed_repository = get_installed_repository(
+        app,
+        tool_shed=tool_shed,
+        name=repository_name,
+        owner=repository_owner,
+        installed_changeset_revision=changeset_revision,
+    )
     if tool_shed_repository:
         return tool_shed_repository, changeset_revision
     # Get all previous changeset revisions from the tool shed for the repository back to, but excluding,
     # the previous valid changeset revision to see if it was previously installed using one of them.
-    params = dict(galaxy_url=web.url_for('/', qualified=True),
-                  name=repository_name,
-                  owner=repository_owner,
-                  changeset_revision=changeset_revision,
-                  from_tip=str(from_tip))
-    pathspec = ['repository', 'previous_changeset_revisions']
-    text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+    params = dict(
+        galaxy_url=web.url_for("/", qualified=True),
+        name=repository_name,
+        owner=repository_owner,
+        changeset_revision=changeset_revision,
+        from_tip=str(from_tip),
+    )
+    pathspec = ["repository", "previous_changeset_revisions"]
+    text = util.url_get(
+        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+    )
     if text:
         changeset_revisions = util.listify(text)
         for previous_changeset_revision in changeset_revisions:
-            tool_shed_repository = get_installed_repository(app,
-                                                            tool_shed=tool_shed,
-                                                            name=repository_name,
-                                                            owner=repository_owner,
-                                                            installed_changeset_revision=previous_changeset_revision)
+            tool_shed_repository = get_installed_repository(
+                app,
+                tool_shed=tool_shed,
+                name=repository_name,
+                owner=repository_owner,
+                installed_changeset_revision=previous_changeset_revision,
+            )
             if tool_shed_repository:
                 return tool_shed_repository, previous_changeset_revision
     return None, None
@@ -616,34 +746,34 @@ def set_repository_attributes(app, repository, status, error_message, deleted, u
 
 
 __all__ = (
-    'check_for_updates',
-    'check_or_update_tool_shed_status_for_installed_repository',
-    'create_or_update_tool_shed_repository',
-    'extract_components_from_tuple',
-    'generate_tool_shed_repository_install_dir',
-    'get_absolute_path_to_file_in_repository',
-    'get_ids_of_tool_shed_repositories_being_installed',
-    'get_installed_repository',
-    'get_installed_tool_shed_repository',
-    'get_prior_import_or_install_required_dict',
-    'get_repo_info_tuple_contents',
-    'get_repository_admin_role_name',
-    'get_repository_and_repository_dependencies_from_repo_info_dict',
-    'get_repository_by_id',
-    'get_repository_by_name',
-    'get_repository_by_name_and_owner',
-    'get_repository_dependency_types',
-    'get_repository_for_dependency_relationship',
-    'get_repository_ids_requiring_prior_import_or_install',
-    'get_repository_in_tool_shed',
-    'get_repository_owner',
-    'get_repository_owner_from_clone_url',
-    'get_repository_query',
-    'get_role_by_id',
-    'get_tool_shed_from_clone_url',
-    'get_tool_shed_repository_by_id',
-    'get_tool_shed_status_for_installed_repository',
-    'is_tool_shed_client',
-    'repository_was_previously_installed',
-    'set_repository_attributes',
+    "check_for_updates",
+    "check_or_update_tool_shed_status_for_installed_repository",
+    "create_or_update_tool_shed_repository",
+    "extract_components_from_tuple",
+    "generate_tool_shed_repository_install_dir",
+    "get_absolute_path_to_file_in_repository",
+    "get_ids_of_tool_shed_repositories_being_installed",
+    "get_installed_repository",
+    "get_installed_tool_shed_repository",
+    "get_prior_import_or_install_required_dict",
+    "get_repo_info_tuple_contents",
+    "get_repository_admin_role_name",
+    "get_repository_and_repository_dependencies_from_repo_info_dict",
+    "get_repository_by_id",
+    "get_repository_by_name",
+    "get_repository_by_name_and_owner",
+    "get_repository_dependency_types",
+    "get_repository_for_dependency_relationship",
+    "get_repository_ids_requiring_prior_import_or_install",
+    "get_repository_in_tool_shed",
+    "get_repository_owner",
+    "get_repository_owner_from_clone_url",
+    "get_repository_query",
+    "get_role_by_id",
+    "get_tool_shed_from_clone_url",
+    "get_tool_shed_repository_by_id",
+    "get_tool_shed_status_for_installed_repository",
+    "is_tool_shed_client",
+    "repository_was_previously_installed",
+    "set_repository_attributes",
 )
diff --git a/lib/galaxy/tool_shed/util/shed_util_common.py b/lib/galaxy/tool_shed/util/shed_util_common.py
index bbd5d2e45a3..04a4450dd2f 100644
--- a/lib/galaxy/tool_shed/util/shed_util_common.py
+++ b/lib/galaxy/tool_shed/util/shed_util_common.py
@@ -6,12 +6,11 @@ from galaxy.tool_shed.util import repository_util
 from galaxy.util.tool_shed import common_util
 from galaxy.web import url_for
 
-
 log = logging.getLogger(__name__)
 
 MAX_CONTENT_SIZE = 1048576
-DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml'
-REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml'
+DATATYPES_CONFIG_FILENAME = "datatypes_conf.xml"
+REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = "data_manager_conf.xml"
 
 
 def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owner):
@@ -20,8 +19,8 @@ def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owne
     associated with a tool_shed_repository record on the Galaxy side
     can be eliminated.
     """
-    rd_dict = metadata_dict.get('repository_dependencies', {})
-    rd_tups = rd_dict.get('repository_dependencies', [])
+    rd_dict = metadata_dict.get("repository_dependencies", {})
+    rd_tups = rd_dict.get("repository_dependencies", [])
     for rd_tup in rd_tups:
         tsu, n, o, none1, none2, none3 = common_util.parse_repository_dependency_tuple(rd_tup)
         if tsu == tool_shed_url and n == name and o == owner:
@@ -36,19 +35,19 @@ def can_eliminate_tool_dependency(metadata_dict, name, dependency_type, version)
     associated with a tool_shed_repository record on the Galaxy side
     can be eliminated.
     """
-    td_dict = metadata_dict.get('tool_dependencies', {})
+    td_dict = metadata_dict.get("tool_dependencies", {})
     for td_key, td_val in td_dict.items():
-        if td_key == 'set_environment':
+        if td_key == "set_environment":
             for td in td_val:
-                n = td.get('name', None)
-                t = td.get('type', None)
+                n = td.get("name", None)
+                t = td.get("type", None)
                 if n == name and t == dependency_type:
                     # The tool dependency is current, so keep it.
                     return False
         else:
-            n = td_val.get('name', None)
-            t = td_val.get('type', None)
-            v = td_val.get('version', None)
+            n = td_val.get("name", None)
+            t = td_val.get("type", None)
+            v = td_val.get("version", None)
             if n == name and t == dependency_type and v == version:
                 # The tool dependency is current, so keep it.
                 return False
@@ -88,7 +87,7 @@ def generate_tool_guid(repository_clone_url, tool):
     <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
     """
     tmp_url = common_util.remove_protocol_and_user_from_clone_url(repository_clone_url)
-    return f'{tmp_url}/{tool.id}/{tool.version}'
+    return f"{tmp_url}/{tool.id}/{tool.version}"
 
 
 def get_ctx_rev(app, tool_shed_url, name, owner, changeset_revision):
@@ -98,8 +97,10 @@ def get_ctx_rev(app, tool_shed_url, name, owner, changeset_revision):
     """
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
     params = dict(name=name, owner=owner, changeset_revision=changeset_revision)
-    pathspec = ['repository', 'get_ctx_rev']
-    ctx_rev = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+    pathspec = ["repository", "get_ctx_rev"]
+    ctx_rev = util.url_get(
+        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+    )
     return ctx_rev
 
 
@@ -144,14 +145,13 @@ def get_tool_panel_config_tool_path_install_dir(app, repository):
     defined in a single shed-related tool panel config.
     """
     tool_shed = common_util.remove_port_from_tool_shed_url(str(repository.tool_shed))
-    relative_install_dir = '{}/repos/{}/{}/{}'.format(tool_shed,
-                                                  str(repository.owner),
-                                                  str(repository.name),
-                                                  str(repository.installed_changeset_revision))
+    relative_install_dir = "{}/repos/{}/{}/{}".format(
+        tool_shed, str(repository.owner), str(repository.name), str(repository.installed_changeset_revision)
+    )
     # Get the relative tool installation paths from each of the shed tool configs.
     shed_config_dict = repository.get_shed_config_dict(app)
-    shed_tool_conf = shed_config_dict['config_filename']
-    tool_path = shed_config_dict['tool_path']
+    shed_tool_conf = shed_config_dict["config_filename"]
+    tool_path = shed_config_dict["tool_path"]
     return shed_tool_conf, tool_path, relative_install_dir
 
 
@@ -174,12 +174,12 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
     """
     if text:
         if repository_util.is_tool_shed_client(app) and encoded_repository_id:
-            route_to_images = f'admin_toolshed/static/images/{encoded_repository_id}'
+            route_to_images = f"admin_toolshed/static/images/{encoded_repository_id}"
         elif encoded_repository_id:
             # We're in the tool shed.
-            route_to_images = f'/repository/static/images/{encoded_repository_id}'
+            route_to_images = f"/repository/static/images/{encoded_repository_id}"
         elif tool_shed_repository and tool_id and tool_version:
-            route_to_images = 'shed_tool_static/{shed}/{owner}/{repo}/{tool}/{version}'.format(
+            route_to_images = "shed_tool_static/{shed}/{owner}/{repo}/{tool}/{version}".format(
                 shed=tool_shed_repository.tool_shed,
                 owner=tool_shed_repository.owner,
                 repo=tool_shed_repository.name,
@@ -187,38 +187,40 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
                 version=tool_version,
             )
         else:
-            raise Exception("encoded_repository_id or tool_shed_repository and tool_id and tool_version must be provided")
+            raise Exception(
+                "encoded_repository_id or tool_shed_repository and tool_id and tool_version must be provided"
+            )
         # We used to require $PATH_TO_IMAGES and ${static_path}, but
         # we now eliminate it if it's used.
-        text = text.replace('$PATH_TO_IMAGES', '')
-        text = text.replace('${static_path}', '')
+        text = text.replace("$PATH_TO_IMAGES", "")
+        text = text.replace("${static_path}", "")
         # Use regex to instantiate routes into the defined image paths, but replace
         # paths that start with neither http:// nor https://, which will allow for
         # settings like .. images:: http_files/images/help.png
-        for match in re.findall('.. image:: (?!http)/?(.+)', text):
-            text = text.replace(match, match.replace('/', '%2F'))
-        text = re.sub(r'\.\. image:: (?!https?://)/?(.+)', r'.. image:: %s/\1' % route_to_images, text)
+        for match in re.findall(".. image:: (?!http)/?(.+)", text):
+            text = text.replace(match, match.replace("/", "%2F"))
+        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", r".. image:: %s/\1" % route_to_images, text)
     return text
 
 
 def tool_shed_is_this_tool_shed(toolshed_base_url):
     """Determine if a tool shed is the current tool shed."""
     cleaned_toolshed_base_url = common_util.remove_protocol_from_tool_shed_url(toolshed_base_url)
-    cleaned_tool_shed = common_util.remove_protocol_from_tool_shed_url(str(url_for('/', qualified=True)))
+    cleaned_tool_shed = common_util.remove_protocol_from_tool_shed_url(str(url_for("/", qualified=True)))
     return cleaned_toolshed_base_url == cleaned_tool_shed
 
 
 __all__ = (
-    'can_eliminate_repository_dependency',
-    'can_eliminate_tool_dependency',
-    'clean_dependency_relationships',
-    'DATATYPES_CONFIG_FILENAME',
-    'generate_tool_guid',
-    'get_ctx_rev',
-    'get_next_prior_import_or_install_required_dict_entry',
-    'get_tool_panel_config_tool_path_install_dir',
-    'get_user',
-    'have_shed_tool_conf_for_install',
-    'set_image_paths',
-    'tool_shed_is_this_tool_shed',
+    "can_eliminate_repository_dependency",
+    "can_eliminate_tool_dependency",
+    "clean_dependency_relationships",
+    "DATATYPES_CONFIG_FILENAME",
+    "generate_tool_guid",
+    "get_ctx_rev",
+    "get_next_prior_import_or_install_required_dict_entry",
+    "get_tool_panel_config_tool_path_install_dir",
+    "get_user",
+    "have_shed_tool_conf_for_install",
+    "set_image_paths",
+    "tool_shed_is_this_tool_shed",
 )
diff --git a/lib/galaxy/tool_shed/util/tool_dependency_util.py b/lib/galaxy/tool_shed/util/tool_dependency_util.py
index 318cec119c7..0ee1faefca7 100644
--- a/lib/galaxy/tool_shed/util/tool_dependency_util.py
+++ b/lib/galaxy/tool_shed/util/tool_dependency_util.py
@@ -12,8 +12,9 @@ from galaxy.web.form_builder import SelectField
 log = logging.getLogger(__name__)
 
 
-def build_tool_dependencies_select_field(app, tool_shed_repository, name, multiple=True, display='checkboxes',
-                                         uninstalled_only=False):
+def build_tool_dependencies_select_field(
+    app, tool_shed_repository, name, multiple=True, display="checkboxes", uninstalled_only=False
+):
     """
     Generate a SelectField consisting of the current list of tool dependency ids
     for an installed tool shed repository.
@@ -21,14 +22,18 @@ def build_tool_dependencies_select_field(app, tool_shed_repository, name, multip
     tool_dependencies_select_field = SelectField(name=name, multiple=multiple, display=display)
     for tool_dependency in tool_shed_repository.tool_dependencies:
         if uninstalled_only:
-            if tool_dependency.status not in [app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                              app.install_model.ToolDependency.installation_status.UNINSTALLED]:
+            if tool_dependency.status not in [
+                app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
+                app.install_model.ToolDependency.installation_status.UNINSTALLED,
+            ]:
                 continue
         else:
-            if tool_dependency.status in [app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                          app.install_model.ToolDependency.installation_status.UNINSTALLED]:
+            if tool_dependency.status in [
+                app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
+                app.install_model.ToolDependency.installation_status.UNINSTALLED,
+            ]:
                 continue
-        option_label = f'{str(tool_dependency.name)} version {str(tool_dependency.version)}'
+        option_label = f"{str(tool_dependency.name)} version {str(tool_dependency.version)}"
         option_value = app.security.encode_id(tool_dependency.id)
         tool_dependencies_select_field.add_option(option_label, option_value)
     return tool_dependencies_select_field
@@ -41,7 +46,9 @@ def create_or_update_tool_dependency(app, tool_shed_repository, name, version, t
     context = app.install_model.context
     # First see if an appropriate tool_dependency record exists for the received tool_shed_repository.
     if version:
-        tool_dependency = get_tool_dependency_by_name_version_type_repository(app, tool_shed_repository, name, version, type)
+        tool_dependency = get_tool_dependency_by_name_version_type_repository(
+            app, tool_shed_repository, name, version, type
+        )
     else:
         tool_dependency = get_tool_dependency_by_name_type_repository(app, tool_shed_repository, name, type)
     if tool_dependency:
@@ -51,9 +58,13 @@ def create_or_update_tool_dependency(app, tool_shed_repository, name, version, t
             set_tool_dependency_attributes(app, tool_dependency=tool_dependency, status=status)
     else:
         # Create a new tool_dependency record for the tool_shed_repository.
-        debug_msg = 'Creating a new record for version %s of tool dependency %s for revision %s of repository %s.  ' % \
-            (str(version), str(name), str(tool_shed_repository.changeset_revision), str(tool_shed_repository.name))
-        debug_msg += f'The status is being set to {str(status)}.'
+        debug_msg = "Creating a new record for version %s of tool dependency %s for revision %s of repository %s.  " % (
+            str(version),
+            str(name),
+            str(tool_shed_repository.changeset_revision),
+            str(tool_shed_repository.name),
+        )
+        debug_msg += f"The status is being set to {str(status)}."
         log.debug(debug_msg)
         tool_dependency = app.install_model.ToolDependency(tool_shed_repository.id, name, version, type, status)
         context.add(tool_dependency)
@@ -68,69 +79,73 @@ def create_tool_dependency_objects(app, tool_shed_repository, relative_install_d
     """
     tool_dependency_objects = []
     shed_config_dict = tool_shed_repository.get_shed_config_dict(app)
-    if shed_config_dict.get('tool_path'):
-        relative_install_dir = os.path.join(shed_config_dict.get('tool_path'), relative_install_dir)
+    if shed_config_dict.get("tool_path"):
+        relative_install_dir = os.path.join(shed_config_dict.get("tool_path"), relative_install_dir)
     # Get the tool_dependencies.xml file from the repository.
-    tool_dependencies_config = get_config_from_disk('tool_dependencies.xml', relative_install_dir)
+    tool_dependencies_config = get_config_from_disk("tool_dependencies.xml", relative_install_dir)
     tree, error_message = parse_xml(tool_dependencies_config)
     if tree is None:
         return tool_dependency_objects
     root = tree.getroot()
     for elem in root:
         tool_dependency_type = elem.tag
-        if tool_dependency_type == 'package':
-            name = elem.get('name', None)
-            version = elem.get('version', None)
+        if tool_dependency_type == "package":
+            name = elem.get("name", None)
+            version = elem.get("version", None)
             if name and version:
                 status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED
-                tool_dependency = create_or_update_tool_dependency(app,
-                                                                   tool_shed_repository,
-                                                                   name=name,
-                                                                   version=version,
-                                                                   type=tool_dependency_type,
-                                                                   status=status,
-                                                                   set_status=set_status)
+                tool_dependency = create_or_update_tool_dependency(
+                    app,
+                    tool_shed_repository,
+                    name=name,
+                    version=version,
+                    type=tool_dependency_type,
+                    status=status,
+                    set_status=set_status,
+                )
                 tool_dependency_objects.append(tool_dependency)
-        elif tool_dependency_type == 'set_environment':
+        elif tool_dependency_type == "set_environment":
             for env_elem in elem:
                 # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-                name = env_elem.get('name', None)
-                action = env_elem.get('action', None)
+                name = env_elem.get("name", None)
+                action = env_elem.get("action", None)
                 if name and action:
                     status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED
-                    tool_dependency = create_or_update_tool_dependency(app,
-                                                                       tool_shed_repository,
-                                                                       name=name,
-                                                                       version=None,
-                                                                       type=tool_dependency_type,
-                                                                       status=status,
-                                                                       set_status=set_status)
+                    tool_dependency = create_or_update_tool_dependency(
+                        app,
+                        tool_shed_repository,
+                        name=name,
+                        version=None,
+                        type=tool_dependency_type,
+                        status=status,
+                        set_status=set_status,
+                    )
                     tool_dependency_objects.append(tool_dependency)
     return tool_dependency_objects
 
 
 def get_download_url_for_platform(url_templates, platform_info_dict):
-    '''
+    """
     Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return
     true if and only if all defined attributes match the corresponding dict entries. If an entry is not
     defined in the url_template element, it is assumed to be irrelevant at this stage. For example,
     <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/faToTwoBit</url_template>
     where the OS must be 'darwin', but the architecture is filled in later using string.Template.
-    '''
+    """
     os_ok = False
     architecture_ok = False
     for url_template in url_templates:
-        os_name = url_template.get('os', None)
-        architecture = url_template.get('architecture', None)
+        os_name = url_template.get("os", None)
+        architecture = url_template.get("architecture", None)
         if os_name:
-            if os_name.lower() == platform_info_dict['os']:
+            if os_name.lower() == platform_info_dict["os"]:
                 os_ok = True
             else:
                 os_ok = False
         else:
             os_ok = True
         if architecture:
-            if architecture.lower() == platform_info_dict['architecture']:
+            if architecture.lower() == platform_info_dict["architecture"]:
                 architecture_ok = True
             else:
                 architecture_ok = False
@@ -142,11 +157,11 @@ def get_download_url_for_platform(url_templates, platform_info_dict):
 
 
 def get_platform_info_dict():
-    '''Return a dict with information about the current platform.'''
+    """Return a dict with information about the current platform."""
     platform_dict = {}
     sysname, nodename, release, version, machine = os.uname()
-    platform_dict['os'] = sysname.lower()
-    platform_dict['architecture'] = machine.lower()
+    platform_dict["os"] = sysname.lower()
+    platform_dict["architecture"] = machine.lower()
     return platform_dict
 
 
@@ -157,67 +172,100 @@ def get_tool_dependency(app, id):
 
 def get_tool_dependency_by_name_type_repository(app, repository, name, type):
     context = app.install_model.context
-    return context.query(app.install_model.ToolDependency) \
-                  .filter(and_(app.install_model.ToolDependency.table.c.tool_shed_repository_id == repository.id,
-                               app.install_model.ToolDependency.table.c.name == name,
-                               app.install_model.ToolDependency.table.c.type == type)) \
-                  .first()
+    return (
+        context.query(app.install_model.ToolDependency)
+        .filter(
+            and_(
+                app.install_model.ToolDependency.table.c.tool_shed_repository_id == repository.id,
+                app.install_model.ToolDependency.table.c.name == name,
+                app.install_model.ToolDependency.table.c.type == type,
+            )
+        )
+        .first()
+    )
 
 
 def get_tool_dependency_by_name_version_type(app, name, version, type):
     context = app.install_model.context
-    return context.query(app.install_model.ToolDependency) \
-                  .filter(and_(app.install_model.ToolDependency.table.c.name == name,
-                               app.install_model.ToolDependency.table.c.version == version,
-                               app.install_model.ToolDependency.table.c.type == type)) \
-                  .first()
+    return (
+        context.query(app.install_model.ToolDependency)
+        .filter(
+            and_(
+                app.install_model.ToolDependency.table.c.name == name,
+                app.install_model.ToolDependency.table.c.version == version,
+                app.install_model.ToolDependency.table.c.type == type,
+            )
+        )
+        .first()
+    )
 
 
 def get_tool_dependency_by_name_version_type_repository(app, repository, name, version, type):
     context = app.install_model.context
-    return context.query(app.install_model.ToolDependency) \
-                  .filter(and_(app.install_model.ToolDependency.table.c.tool_shed_repository_id == repository.id,
-                               app.install_model.ToolDependency.table.c.name == name,
-                               app.install_model.ToolDependency.table.c.version == version,
-                               app.install_model.ToolDependency.table.c.type == type)) \
-                  .first()
+    return (
+        context.query(app.install_model.ToolDependency)
+        .filter(
+            and_(
+                app.install_model.ToolDependency.table.c.tool_shed_repository_id == repository.id,
+                app.install_model.ToolDependency.table.c.name == name,
+                app.install_model.ToolDependency.table.c.version == version,
+                app.install_model.ToolDependency.table.c.type == type,
+            )
+        )
+        .first()
+    )
 
 
 def get_tool_dependency_ids(as_string=False, **kwd):
-    tool_dependency_id = kwd.get('tool_dependency_id', None)
-    if 'tool_dependency_ids' in kwd:
-        tool_dependency_ids = util.listify(kwd['tool_dependency_ids'])
-    elif 'id' in kwd:
-        tool_dependency_ids = util.listify(kwd['id'])
-    elif 'inst_td_ids' in kwd:
-        tool_dependency_ids = util.listify(kwd['inst_td_ids'])
-    elif 'uninstalled_tool_dependency_ids' in kwd:
-        tool_dependency_ids = util.listify(kwd['uninstalled_tool_dependency_ids'])
+    tool_dependency_id = kwd.get("tool_dependency_id", None)
+    if "tool_dependency_ids" in kwd:
+        tool_dependency_ids = util.listify(kwd["tool_dependency_ids"])
+    elif "id" in kwd:
+        tool_dependency_ids = util.listify(kwd["id"])
+    elif "inst_td_ids" in kwd:
+        tool_dependency_ids = util.listify(kwd["inst_td_ids"])
+    elif "uninstalled_tool_dependency_ids" in kwd:
+        tool_dependency_ids = util.listify(kwd["uninstalled_tool_dependency_ids"])
     else:
         tool_dependency_ids = []
     if tool_dependency_id and tool_dependency_id not in tool_dependency_ids:
         tool_dependency_ids.append(tool_dependency_id)
     if as_string:
-        return ','.join(tool_dependency_ids)
+        return ",".join(tool_dependency_ids)
     return tool_dependency_ids
 
 
-def get_tool_dependency_install_dir(app, repository_name, repository_owner, repository_changeset_revision, tool_dependency_type,
-                                    tool_dependency_name, tool_dependency_version):
-    if tool_dependency_type == 'package':
-        return os.path.abspath(os.path.join(app.tool_dependency_dir,
-                                            tool_dependency_name,
-                                            tool_dependency_version,
-                                            repository_owner,
-                                            repository_name,
-                                            repository_changeset_revision))
-    if tool_dependency_type == 'set_environment':
-        return os.path.abspath(os.path.join(app.tool_dependency_dir,
-                                            'environment_settings',
-                                            tool_dependency_name,
-                                            repository_owner,
-                                            repository_name,
-                                            repository_changeset_revision))
+def get_tool_dependency_install_dir(
+    app,
+    repository_name,
+    repository_owner,
+    repository_changeset_revision,
+    tool_dependency_type,
+    tool_dependency_name,
+    tool_dependency_version,
+):
+    if tool_dependency_type == "package":
+        return os.path.abspath(
+            os.path.join(
+                app.tool_dependency_dir,
+                tool_dependency_name,
+                tool_dependency_version,
+                repository_owner,
+                repository_name,
+                repository_changeset_revision,
+            )
+        )
+    if tool_dependency_type == "set_environment":
+        return os.path.abspath(
+            os.path.join(
+                app.tool_dependency_dir,
+                "environment_settings",
+                tool_dependency_name,
+                repository_owner,
+                repository_name,
+                repository_changeset_revision,
+            )
+        )
 
 
 def parse_package_elem(package_elem, platform_info_dict=None, include_after_install_actions=True):
@@ -237,25 +285,25 @@ def parse_package_elem(package_elem, platform_info_dict=None, include_after_inst
     # recipe for downloading and compiling source.
     actions_elem_list = []
     for elem in package_elem:
-        if elem.tag == 'actions':
+        if elem.tag == "actions":
             # We have an <actions> tag that should not be matched against a specific combination of
             # architecture and operating system.
             in_actions_group = False
             actions_elem_tuples.append((in_actions_group, elem))
-        elif elem.tag == 'actions_group':
+        elif elem.tag == "actions_group":
             # We have an actions_group element, and its child <actions> elements should therefore be compared
             # with the current operating system
             # and processor architecture.
             in_actions_group = True
             # Record the number of <actions> elements so we can filter out any <action> elements that precede
             # <actions> elements.
-            actions_elem_count = len(elem.findall('actions'))
+            actions_elem_count = len(elem.findall("actions"))
             # Record the number of <actions> elements that have both architecture and os specified, in order
             # to filter out any platform-independent <actions> elements that come before platform-specific
             # <actions> elements.
             platform_actions_elements = []
-            for actions_elem in elem.findall('actions'):
-                if actions_elem.get('architecture') is not None and actions_elem.get('os') is not None:
+            for actions_elem in elem.findall("actions"):
+                if actions_elem.get("architecture") is not None and actions_elem.get("os") is not None:
                     platform_actions_elements.append(actions_elem)
             platform_actions_element_count = len(platform_actions_elements)
             platform_actions_elements_processed = 0
@@ -266,14 +314,14 @@ def parse_package_elem(package_elem, platform_info_dict=None, include_after_inst
             after_install_actions = []
             # Inspect the <actions_group> element and build the actions_elem_list and the after_install_actions list.
             for child_element in elem:
-                if child_element.tag == 'actions':
+                if child_element.tag == "actions":
                     actions_elems_processed += 1
-                    system = child_element.get('os')
-                    architecture = child_element.get('architecture')
+                    system = child_element.get("os")
+                    architecture = child_element.get("architecture")
                     # Skip <actions> tags that have only one of architecture or os specified, in order for the
                     # count in platform_actions_elements_processed to remain accurate.
                     if (system and not architecture) or (architecture and not system):
-                        log.debug('Error: Both architecture and os attributes must be specified in an <actions> tag.')
+                        log.debug("Error: Both architecture and os attributes must be specified in an <actions> tag.")
                         continue
                     # Since we are inside an <actions_group> tag set, compare it with our current platform information
                     # and filter the <actions> tag sets that don't match. Require both the os and architecture attributes
@@ -283,7 +331,7 @@ def parse_package_elem(package_elem, platform_info_dict=None, include_after_inst
                         # If either the os or architecture do not match the platform, this <actions> tag will not be
                         # considered a match. Skip it and proceed with checking the next one.
                         if platform_info_dict:
-                            if platform_info_dict['os'] != system or platform_info_dict['architecture'] != architecture:
+                            if platform_info_dict["os"] != system or platform_info_dict["architecture"] != architecture:
                                 continue
                         else:
                             # We must not be installing a repository into Galaxy, so determining if we can install a
@@ -294,10 +342,16 @@ def parse_package_elem(package_elem, platform_info_dict=None, include_after_inst
                         # after platform-specific <actions> tags. If we find a platform-independent <actions> tag before
                         # all platform-specific <actions> tags have been processed.
                         if platform_actions_elements_processed < platform_actions_element_count:
-                            debug_msg = 'Error: <actions> tags without os and architecture attributes are only allowed '
-                            debug_msg += 'after all <actions> tags with os and architecture attributes have been defined.  '
-                            debug_msg += 'Skipping the <actions> tag set with no os or architecture attributes that has '
-                            debug_msg += 'been defined between two <actions> tag sets that have these attributes defined.  '
+                            debug_msg = "Error: <actions> tags without os and architecture attributes are only allowed "
+                            debug_msg += (
+                                "after all <actions> tags with os and architecture attributes have been defined.  "
+                            )
+                            debug_msg += (
+                                "Skipping the <actions> tag set with no os or architecture attributes that has "
+                            )
+                            debug_msg += (
+                                "been defined between two <actions> tag sets that have these attributes defined.  "
+                            )
                             log.debug(debug_msg)
                             continue
                     # If we reach this point, it means one of two things: 1) The system and architecture attributes are
@@ -305,7 +359,7 @@ def parse_package_elem(package_elem, platform_info_dict=None, include_after_inst
                     # they are an exact match for the current platform. Append the child element to the list of elements
                     # to process.
                     actions_elem_list.append(child_element)
-                elif child_element.tag == 'action':
+                elif child_element.tag == "action":
                     # Any <action> tags within an <actions_group> tag set must come after all <actions> tags.
                     if actions_elems_processed == actions_elem_count:
                         # If all <actions> elements have been processed, then this <action> element can be appended to the
@@ -314,9 +368,13 @@ def parse_package_elem(package_elem, platform_info_dict=None, include_after_inst
                     else:
                         # If any <actions> elements remain to be processed, then log a message stating that <action>
                         # elements are not allowed to precede any <actions> elements within an <actions_group> tag set.
-                        debug_msg = 'Error: <action> tags are only allowed at the end of an <actions_group> tag set after '
-                        debug_msg += 'all <actions> tags.  Skipping <%s> element with type %s.' % \
-                            (child_element.tag, child_element.get('type', 'unknown'))
+                        debug_msg = (
+                            "Error: <action> tags are only allowed at the end of an <actions_group> tag set after "
+                        )
+                        debug_msg += "all <actions> tags.  Skipping <%s> element with type %s." % (
+                            child_element.tag,
+                            child_element.get("type", "unknown"),
+                        )
                         log.debug(debug_msg)
                         continue
             if platform_info_dict is None and not include_after_install_actions:
@@ -361,15 +419,17 @@ def remove_tool_dependency_installation_directory(dependency_install_dir):
         try:
             shutil.rmtree(dependency_install_dir)
             removed = True
-            error_message = ''
+            error_message = ""
             log.debug(f"Removed tool dependency installation directory: {str(dependency_install_dir)}")
         except Exception as e:
             removed = False
-            error_message = f"Error removing tool dependency installation directory {str(dependency_install_dir)}: {str(e)}"
+            error_message = (
+                f"Error removing tool dependency installation directory {str(dependency_install_dir)}: {str(e)}"
+            )
             log.warning(error_message)
     else:
         removed = True
-        error_message = ''
+        error_message = ""
     return removed, error_message
 
 
@@ -381,9 +441,16 @@ def set_tool_dependency_attributes(app, tool_dependency, status, error_message=N
     tool_dependency.error_message = error_message
     if str(tool_dependency.status) != str(status):
         tool_shed_repository = tool_dependency.tool_shed_repository
-        debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \
-            (str(tool_dependency.version), str(tool_dependency.name), str(tool_shed_repository.changeset_revision), str(tool_shed_repository.name))
-        debug_msg += f'by updating the status from {str(tool_dependency.status)} to {str(status)}.'
+        debug_msg = (
+            "Updating an existing record for version %s of tool dependency %s for revision %s of repository %s "
+            % (
+                str(tool_dependency.version),
+                str(tool_dependency.name),
+                str(tool_shed_repository.changeset_revision),
+                str(tool_shed_repository.name),
+            )
+        )
+        debug_msg += f"by updating the status from {str(tool_dependency.status)} to {str(status)}."
         log.debug(debug_msg)
     tool_dependency.status = status
     sa_session.add(tool_dependency)
diff --git a/lib/galaxy/tool_shed/util/tool_util.py b/lib/galaxy/tool_shed/util/tool_util.py
index eb0091cf662..fe7ec9489a2 100644
--- a/lib/galaxy/tool_shed/util/tool_util.py
+++ b/lib/galaxy/tool_shed/util/tool_util.py
@@ -17,12 +17,12 @@ def build_shed_tool_conf_select_field(app):
     """Build a SelectField whose options are the keys in app.toolbox.shed_tool_confs."""
     options = []
     for dynamic_tool_conf_filename in app.toolbox.dynamic_conf_filenames():
-        if dynamic_tool_conf_filename.startswith('./'):
-            option_label = dynamic_tool_conf_filename.replace('./', '', 1)
+        if dynamic_tool_conf_filename.startswith("./"):
+            option_label = dynamic_tool_conf_filename.replace("./", "", 1)
         else:
             option_label = dynamic_tool_conf_filename
         options.append((option_label, dynamic_tool_conf_filename))
-    select_field = SelectField(name='shed_tool_conf')
+    select_field = SelectField(name="shed_tool_conf")
     for option_tup in options:
         select_field.add_option(option_tup[0], option_tup[1])
     return select_field
@@ -33,7 +33,7 @@ def build_tool_panel_section_select_field(app):
     options = []
     for section_id, section_name in app.toolbox.get_sections():
         options.append((section_name, section_id))
-    select_field = SelectField(name='tool_panel_section_id', field_id='tool_panel_section_select')
+    select_field = SelectField(name="tool_panel_section_id", field_id="tool_panel_section_select")
     for option_tup in options:
         select_field.add_option(option_tup[0], option_tup[1])
     return select_field
@@ -48,7 +48,7 @@ def copy_sample_file(app, filename, dest_path=None):
     if dest_path is None:
         dest_path = os.path.abspath(app.config.tool_data_path)
     sample_file_name = basic_util.strip_path(filename)
-    copied_file = sample_file_name.rsplit('.sample', 1)[0]
+    copied_file = sample_file_name.rsplit(".sample", 1)[0]
     full_source_path = os.path.abspath(filename)
     full_destination_path = os.path.join(dest_path, sample_file_name)
     # Don't copy a file to itself - not sure how this happens, but sometimes it does...
@@ -71,7 +71,7 @@ def copy_sample_files(app, sample_files, tool_path=None, sample_files_copied=Non
     appropriate files here because tool shed repositories can contain files ending in .sample
     that should not be copied to the ~/tool-data directory.
     """
-    filenames_not_to_copy = ['tool_data_table_conf.xml.sample']
+    filenames_not_to_copy = ["tool_data_table_conf.xml.sample"]
     sample_files_copied = util.listify(sample_files_copied)
     for filename in sample_files:
         filename_sans_path = os.path.split(filename)[1]
@@ -83,18 +83,19 @@ def copy_sample_files(app, sample_files, tool_path=None, sample_files_copied=Non
                 copy_sample_file(app, filename, dest_path=dest_path)
 
 
-def generate_message_for_invalid_tools(app, invalid_file_tups, repository, metadata_dict, as_html=True,
-                                       displaying_invalid_tool=False):
+def generate_message_for_invalid_tools(
+    app, invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False
+):
     if as_html:
-        new_line = '<br/>'
-        bold_start = '<b>'
-        bold_end = '</b>'
+        new_line = "<br/>"
+        bold_start = "<b>"
+        bold_end = "</b>"
     else:
-        new_line = '\n'
-        bold_start = ''
-        bold_end = ''
-    message = ''
-    if app.name == 'galaxy':
+        new_line = "\n"
+        bold_start = ""
+        bold_end = ""
+    message = ""
+    if app.name == "galaxy":
         tip_rev = str(repository.changeset_revision)
     else:
         tip_rev = str(repository.tip())
@@ -104,42 +105,48 @@ def generate_message_for_invalid_tools(app, invalid_file_tups, repository, metad
             message += f"Correct the following problems if necessary and reset metadata.{new_line}"
         else:
             message += f"Metadata cannot be defined for revision '{tip_rev}' so this revision cannot be automatically "
-            message += f"installed into a local Galaxy instance.  Correct the following problems and reset metadata.{new_line}"
+            message += (
+                f"installed into a local Galaxy instance.  Correct the following problems and reset metadata.{new_line}"
+            )
     for itc_tup in invalid_file_tups:
         tool_file, exception_msg = itc_tup
-        if exception_msg.find('No such file or directory') >= 0:
+        if exception_msg.find("No such file or directory") >= 0:
             exception_items = exception_msg.split()
-            missing_file_items = exception_items[7].split('/')
-            missing_file = missing_file_items[-1].rstrip('\'')
-            if missing_file.endswith('.loc'):
-                sample_ext = f'{missing_file}.sample'
+            missing_file_items = exception_items[7].split("/")
+            missing_file = missing_file_items[-1].rstrip("'")
+            if missing_file.endswith(".loc"):
+                sample_ext = f"{missing_file}.sample"
             else:
                 sample_ext = missing_file
-            correction_msg = "This file refers to a missing file %s%s%s.  " % \
-                (bold_start, str(missing_file), bold_end)
-            correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % \
-                (bold_start, sample_ext, bold_end)
+            correction_msg = "This file refers to a missing file %s%s%s.  " % (bold_start, str(missing_file), bold_end)
+            correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % (
+                bold_start,
+                sample_ext,
+                bold_end,
+            )
         else:
             if as_html:
                 correction_msg = exception_msg
             else:
-                correction_msg = exception_msg.replace('<br/>', new_line).replace('<b>', bold_start).replace('</b>', bold_end)
+                correction_msg = (
+                    exception_msg.replace("<br/>", new_line).replace("<b>", bold_start).replace("</b>", bold_end)
+                )
         message += f"{bold_start}{tool_file}{bold_end} - {correction_msg}{new_line}"
     return message
 
 
 def get_tool_path_install_dir(partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems):
     for elem in config_elems:
-        if elem.tag == 'tool':
-            if elem.get('guid') == tool_dict['guid']:
-                tool_path = shed_tool_conf_dict['tool_path']
+        if elem.tag == "tool":
+            if elem.get("guid") == tool_dict["guid"]:
+                tool_path = shed_tool_conf_dict["tool_path"]
                 relative_install_dir = os.path.join(tool_path, partial_install_dir)
                 return tool_path, relative_install_dir
-        elif elem.tag == 'section':
+        elif elem.tag == "section":
             for section_elem in elem:
-                if section_elem.tag == 'tool':
-                    if section_elem.get('guid') == tool_dict['guid']:
-                        tool_path = shed_tool_conf_dict['tool_path']
+                if section_elem.tag == "tool":
+                    if section_elem.get("guid") == tool_dict["guid"]:
+                        tool_path = shed_tool_conf_dict["tool_path"]
                         relative_install_dir = os.path.join(tool_path, partial_install_dir)
                         return tool_path, relative_install_dir
     return None, None
@@ -161,7 +168,7 @@ def handle_missing_index_file(app, tool_path, sample_files, repository_tools_tup
                 # The repository must contain the required xxx.loc.sample file.
                 for sample_file in sample_files:
                     sample_file_name = basic_util.strip_path(sample_file)
-                    if sample_file_name == f'{missing_file_name}.sample':
+                    if sample_file_name == f"{missing_file_name}.sample":
                         target_path = copy_sample_file(app, os.path.join(tool_path, sample_file))
                         if options.tool_data_table and options.tool_data_table.missing_index_file:
                             options.tool_data_table.handle_found_index_file(target_path)
@@ -208,7 +215,11 @@ def new_state(trans, tool, invalid=False):
         return tool.new_state(trans)
     except Exception as e:
         # Fall back to building tool state as below
-        log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e)
+        log.debug(
+            'Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s',
+            tool.id,
+            e,
+        )
     inputs = tool.inputs_by_page[0]
     context = ExpressionContext(state.inputs, parent=None)
     for input in inputs.values():
@@ -234,6 +245,6 @@ def panel_entry_per_tool(tool_section_dict):
     if len(tool_section_dict) != 3:
         return True
     for k in tool_section_dict.keys():
-        if k not in ['id', 'version', 'name']:
+        if k not in ["id", "version", "name"]:
             return True
     return False
diff --git a/lib/galaxy/tool_util/biotools/interface.py b/lib/galaxy/tool_util/biotools/interface.py
index 6b4a5a7cb4a..e0d7267f483 100644
--- a/lib/galaxy/tool_util/biotools/interface.py
+++ b/lib/galaxy/tool_util/biotools/interface.py
@@ -1,11 +1,17 @@
 import re
-from typing import Any, Dict, List, Optional
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+)
 
 TERM_PATTERN = re.compile(r"https?://edamontology.org/(.*)")
 
 
 class ParsedBiotoolsEntry:
     """Provide XML wrapper relevant entities from a bio.tool entry - topics and operations."""
+
     biotoolsID: str
     edam_topics: List[str]
     edam_operations: List[str]
@@ -13,12 +19,13 @@ class ParsedBiotoolsEntry:
 
 class BiotoolsEntry:
     """Parse the RAW entries of interest for Galaxy from a bio.tools entry."""
+
     biotoolsID: str
     topic: List[dict]
     function: List[dict]
 
     @staticmethod
-    def from_json(from_json: Dict[str, Any]) -> 'BiotoolsEntry':
+    def from_json(from_json: Dict[str, Any]) -> "BiotoolsEntry":
         entry = BiotoolsEntry()
         entry.biotoolsID = from_json["biotoolsID"]
         entry.topic = from_json["topic"]
diff --git a/lib/galaxy/tool_util/biotools/source.py b/lib/galaxy/tool_util/biotools/source.py
index af49b52c2c4..92c8b08a69b 100644
--- a/lib/galaxy/tool_util/biotools/source.py
+++ b/lib/galaxy/tool_util/biotools/source.py
@@ -1,7 +1,12 @@
 import functools
 import json
 import os
-from typing import Callable, Dict, List, Optional
+from typing import (
+    Callable,
+    Dict,
+    List,
+    Optional,
+)
 
 import requests
 
@@ -10,7 +15,6 @@ from .interface import BiotoolsEntry
 
 
 class BiotoolsMetadataSource:
-
     def get_biotools_metadata(self, biotools_reference: str) -> Optional[BiotoolsEntry]:
         """Return a BiotoolsEntry if available."""
 
@@ -67,7 +71,6 @@ class ApiBiotoolsMetadataSource(BiotoolsMetadataSource):
 
 
 class CascadingBiotoolsMetadataSource(BiotoolsMetadataSource):
-
     def __init__(self, use_api=False, cache=None, content_directory: Optional[str] = None):
         sources: List[BiotoolsMetadataSource] = []
         if content_directory:
diff --git a/lib/galaxy/tool_util/client/staging.py b/lib/galaxy/tool_util/client/staging.py
index be679c08e06..2e7669bcb9c 100644
--- a/lib/galaxy/tool_util/client/staging.py
+++ b/lib/galaxy/tool_util/client/staging.py
@@ -40,7 +40,7 @@ class StagingInterace(metaclass=abc.ABCMeta):
         """Make a post to the Galaxy API along supplied path."""
 
     def _attach_file(self, path):
-        return open(path, 'rb')
+        return open(path, "rb")
 
     def _tools_post(self, payload, files_attached=False):
         tool_response = self._post("tools", payload, files_attached=files_attached)
@@ -57,11 +57,19 @@ class StagingInterace(metaclass=abc.ABCMeta):
     def _handle_job(self, job_response):
         """Implementer can decide if to wait for job(s) individually or not here."""
 
-    def stage(self, tool_or_workflow, history_id, job=None, job_path=None, use_path_paste=LOAD_TOOLS_FROM_PATH, to_posix_lines=True, job_dir="."):
+    def stage(
+        self,
+        tool_or_workflow,
+        history_id,
+        job=None,
+        job_path=None,
+        use_path_paste=LOAD_TOOLS_FROM_PATH,
+        to_posix_lines=True,
+        job_dir=".",
+    ):
         files_attached = [False]
 
         def upload_func_fetch(upload_target):
-
             def _attach_file(upload_payload, uri, index=0):
                 uri = path_or_uri_to_uri(uri)
                 is_path = uri.startswith("file://")
@@ -69,15 +77,15 @@ class StagingInterace(metaclass=abc.ABCMeta):
                     return {"src": "url", "url": uri}
                 else:
                     files_attached[0] = True
-                    path = uri[len("file://"):]
+                    path = uri[len("file://") :]
                     upload_payload["__files"][f"files_{index}|file_data"] = self._attach_file(path)
                     return {"src": "files"}
 
             fetch_payload = None
             if isinstance(upload_target, FileUploadTarget):
                 file_path = upload_target.path
-                file_type = upload_target.properties.get('filetype', None) or DEFAULT_FILE_TYPE
-                dbkey = upload_target.properties.get('dbkey', None) or DEFAULT_DBKEY
+                file_type = upload_target.properties.get("filetype", None) or DEFAULT_FILE_TYPE
+                dbkey = upload_target.properties.get("dbkey", None) or DEFAULT_DBKEY
                 fetch_payload = _fetch_payload(
                     history_id,
                     file_type=file_type,
@@ -106,11 +114,13 @@ class StagingInterace(metaclass=abc.ABCMeta):
             elif isinstance(upload_target, FileLiteralTarget):
                 fetch_payload = _fetch_payload(history_id)
                 # For file literals - take them as is - never convert line endings.
-                fetch_payload["targets"][0]["elements"][0].update({
-                    "src": "pasted",
-                    "paste_content": upload_target.contents,
-                    "to_posix_lines": False,
-                })
+                fetch_payload["targets"][0]["elements"][0].update(
+                    {
+                        "src": "pasted",
+                        "paste_content": upload_target.contents,
+                        "to_posix_lines": False,
+                    }
+                )
                 tags = upload_target.properties.get("tags")
                 if tags:
                     fetch_payload["targets"][0]["elements"][0]["tags"] = tags
@@ -123,17 +133,18 @@ class StagingInterace(metaclass=abc.ABCMeta):
             else:
                 content = json.dumps(upload_target.object)
                 fetch_payload = _fetch_payload(history_id, file_type="expression.json")
-                fetch_payload["targets"][0]["elements"][0].update({
-                    "src": "pasted",
-                    "paste_content": content,
-                })
+                fetch_payload["targets"][0]["elements"][0].update(
+                    {
+                        "src": "pasted",
+                        "paste_content": content,
+                    }
+                )
                 tags = upload_target.properties.get("tags")
                 fetch_payload["targets"][0]["elements"][0]["tags"] = tags
             return self._fetch_post(fetch_payload, files_attached=files_attached[0])
 
         # Save legacy upload_func to target older Galaxy servers
         def upload_func(upload_target):
-
             def _attach_file(upload_payload, uri, index=0):
                 uri = path_or_uri_to_uri(uri)
                 is_path = uri.startswith("file://")
@@ -141,13 +152,13 @@ class StagingInterace(metaclass=abc.ABCMeta):
                     upload_payload["inputs"]["files_%d|url_paste" % index] = uri
                 else:
                     files_attached[0] = True
-                    path = uri[len("file://"):]
+                    path = uri[len("file://") :]
                     upload_payload["__files"]["files_%d|file_data" % index] = self._attach_file(path)
 
             if isinstance(upload_target, FileUploadTarget):
                 file_path = upload_target.path
-                file_type = upload_target.properties.get('filetype', None) or DEFAULT_FILE_TYPE
-                dbkey = upload_target.properties.get('dbkey', None) or DEFAULT_DBKEY
+                file_type = upload_target.properties.get("filetype", None) or DEFAULT_FILE_TYPE
+                dbkey = upload_target.properties.get("dbkey", None) or DEFAULT_DBKEY
                 upload_payload = _upload_payload(
                     history_id,
                     file_type=file_type,
@@ -249,7 +260,6 @@ class StagingInterace(metaclass=abc.ABCMeta):
 
 
 class InteractorStaging(StagingInterace):
-
     def __init__(self, galaxy_interactor, use_fetch_api=DEFAULT_USE_FETCH_API):
         self.galaxy_interactor = galaxy_interactor
         self._use_fetch_api = use_fetch_api
@@ -283,12 +293,12 @@ def _upload_payload(history_id, tool_id=UPLOAD_TOOL_ID, file_type=DEFAULT_FILE_T
     tool_input = {}
     tool_input["file_type"] = file_type
     tool_input["dbkey"] = dbkey
-    if not kwd.get('to_posix_lines', True):
-        tool_input['files_0|to_posix_lines'] = False
-    elif kwd.get('space_to_tab', False):
-        tool_input['files_0|space_to_tab'] = 'Yes'
-    if 'file_name' in kwd:
-        tool_input["files_0|NAME"] = kwd['file_name']
+    if not kwd.get("to_posix_lines", True):
+        tool_input["files_0|to_posix_lines"] = False
+    elif kwd.get("space_to_tab", False):
+        tool_input["files_0|space_to_tab"] = "Yes"
+    if "file_name" in kwd:
+        tool_input["files_0|NAME"] = kwd["file_name"]
     tool_input["files_0|type"] = "upload_dataset"
     payload["inputs"] = tool_input
     payload["__files"] = {}
@@ -300,20 +310,16 @@ def _fetch_payload(history_id, file_type=DEFAULT_FILE_TYPE, dbkey=DEFAULT_DBKEY,
         "ext": file_type,
         "dbkey": dbkey,
     }
-    for arg in ['to_posix_lines', 'space_to_tab']:
+    for arg in ["to_posix_lines", "space_to_tab"]:
         if arg in kwd:
             element[arg] = kwd[arg]
-    if 'file_name' in kwd:
-        element['name'] = kwd['file_name']
+    if "file_name" in kwd:
+        element["name"] = kwd["file_name"]
     target = {
         "destination": {"type": "hdas"},
         "elements": [element],
         "auto_decompress": False,
     }
     targets = [target]
-    payload = {
-        "history_id": history_id,
-        "targets": targets,
-        "__files": {}
-    }
+    payload = {"history_id": history_id, "targets": targets, "__files": {}}
     return payload
diff --git a/lib/galaxy/tool_util/cwl/__init__.py b/lib/galaxy/tool_util/cwl/__init__.py
index 70850b3b5a8..bb55b897519 100644
--- a/lib/galaxy/tool_util/cwl/__init__.py
+++ b/lib/galaxy/tool_util/cwl/__init__.py
@@ -2,18 +2,24 @@ from .cwltool_deps import (
     needs_shell_quoting,
     shellescape,
 )
-from .parser import tool_proxy, tool_proxy_from_persistent_representation, workflow_proxy
-from .representation import to_cwl_job, to_galaxy_parameters
+from .parser import (
+    tool_proxy,
+    tool_proxy_from_persistent_representation,
+    workflow_proxy,
+)
+from .representation import (
+    to_cwl_job,
+    to_galaxy_parameters,
+)
 from .runtime_actions import handle_outputs
 
-
 __all__ = (
-    'tool_proxy',
-    'tool_proxy_from_persistent_representation',
-    'workflow_proxy',
-    'handle_outputs',
-    'to_cwl_job',
-    'to_galaxy_parameters',
-    'needs_shell_quoting',
-    'shellescape',
+    "tool_proxy",
+    "tool_proxy_from_persistent_representation",
+    "workflow_proxy",
+    "handle_outputs",
+    "to_cwl_job",
+    "to_galaxy_parameters",
+    "needs_shell_quoting",
+    "shellescape",
 )
diff --git a/lib/galaxy/tool_util/cwl/cwltool_deps.py b/lib/galaxy/tool_util/cwl/cwltool_deps.py
index 02155e81dd9..f707477c13e 100644
--- a/lib/galaxy/tool_util/cwl/cwltool_deps.py
+++ b/lib/galaxy/tool_util/cwl/cwltool_deps.py
@@ -13,11 +13,11 @@ import requests
 
 try:
     from cwltool import (
-        main,
-        workflow,
         job,
-        process,
+        main,
         pathmapper,
+        process,
+        workflow,
     )
 except ImportError:
     main = None  # type: ignore[assignment]
@@ -106,22 +106,22 @@ def ensure_cwltool_available():
 
 
 __all__ = (
-    'default_loader',
-    'ensure_cwltool_available',
-    'getdefault',
-    'load_tool',
-    'LoadingContext',
-    'main',
-    'needs_shell_quoting',
-    'pathmapper',
-    'process',
-    'ref_resolver',
-    'relink_initialworkdir',
-    'resolve_and_validate_document',
-    'RuntimeContext',
-    'schema_salad',
-    'shellescape',
-    'sourceline',
-    'StdFsAccess',
-    'workflow',
+    "default_loader",
+    "ensure_cwltool_available",
+    "getdefault",
+    "load_tool",
+    "LoadingContext",
+    "main",
+    "needs_shell_quoting",
+    "pathmapper",
+    "process",
+    "ref_resolver",
+    "relink_initialworkdir",
+    "resolve_and_validate_document",
+    "RuntimeContext",
+    "schema_salad",
+    "shellescape",
+    "sourceline",
+    "StdFsAccess",
+    "workflow",
 )
diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index ceb519236b4..47d43f39487 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -10,11 +10,22 @@ import json
 import logging
 import os
 import pickle
-from abc import ABCMeta, abstractmethod
-from typing import Dict, List, overload, Union
+from abc import (
+    ABCMeta,
+    abstractmethod,
+)
+from typing import (
+    Dict,
+    List,
+    overload,
+    Union,
+)
 from uuid import uuid4
 
-from typing_extensions import Literal, TypedDict
+from typing_extensions import (
+    Literal,
+    TypedDict,
+)
 
 from galaxy.exceptions import MessageException
 from galaxy.util import (
@@ -70,8 +81,7 @@ SUPPORTED_TOOL_REQUIREMENTS = [
 ]
 
 
-SUPPORTED_WORKFLOW_REQUIREMENTS = SUPPORTED_TOOL_REQUIREMENTS + [
-]
+SUPPORTED_WORKFLOW_REQUIREMENTS = SUPPORTED_TOOL_REQUIREMENTS + []
 
 PERSISTED_REPRESENTATION = "cwl_tool_object"
 
@@ -98,7 +108,7 @@ InputInstanceArrayDict = TypedDict(
 
 
 def tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True, tool_directory=None, uuid=None):
-    """ Provide a proxy object to cwltool data structures to just
+    """Provide a proxy object to cwltool data structures to just
     grab relevant data.
     """
     ensure_cwltool_available()
@@ -107,7 +117,7 @@ def tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True, too
         tool_object=tool_object,
         strict_cwl_validation=strict_cwl_validation,
         tool_directory=tool_directory,
-        uuid=uuid
+        uuid=uuid,
     )
     return tool
 
@@ -121,7 +131,9 @@ def tool_proxy_from_persistent_representation(persisted_tool, strict_cwl_validat
         raw_process_reference = persisted_tool  # ???
         kwds = {"raw_process_reference": ToolProxy.from_persistent_representation(raw_process_reference)}
     uuid = persisted_tool["uuid"]
-    tool = _to_cwl_tool_object(uuid=uuid, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory, **kwds)
+    tool = _to_cwl_tool_object(
+        uuid=uuid, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory, **kwds
+    )
     return tool
 
 
@@ -143,12 +155,22 @@ def load_job_proxy(job_directory, strict_cwl_validation=True):
         cwl_tool = tool_proxy(tool_path, strict_cwl_validation=strict_cwl_validation)
     else:
         persisted_tool = job_objects["tool_representation"]
-        cwl_tool = tool_proxy_from_persistent_representation(persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation)
+        cwl_tool = tool_proxy_from_persistent_representation(
+            persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation
+        )
     cwl_job = cwl_tool.job_proxy(job_inputs, output_dict, job_directory=job_directory)
     return cwl_job
 
 
-def _to_cwl_tool_object(tool_path=None, tool_object=None, cwl_tool_object=None, raw_process_reference=None, strict_cwl_validation=False, tool_directory=None, uuid=None):
+def _to_cwl_tool_object(
+    tool_path=None,
+    tool_object=None,
+    cwl_tool_object=None,
+    raw_process_reference=None,
+    strict_cwl_validation=False,
+    tool_directory=None,
+    uuid=None,
+):
     if uuid is None:
         uuid = str(uuid4())
     schema_loader = _schema_loader(strict_cwl_validation)
@@ -166,6 +188,7 @@ def _to_cwl_tool_object(tool_path=None, tool_object=None, cwl_tool_object=None,
 
         # Allow loading tools from YAML...
         from ruamel import yaml as ryaml
+
         as_str = json.dumps(tool_object)
         tool_object = ryaml.round_trip_load(as_str)
         path = tool_directory
@@ -173,10 +196,7 @@ def _to_cwl_tool_object(tool_path=None, tool_object=None, cwl_tool_object=None,
             path = os.getcwd()
         uri = f"{ref_resolver.file_uri(path)}/"
         sourceline.add_lc_filename(tool_object, uri)
-        raw_process_reference = schema_loader.raw_process_reference_for_object(
-            tool_object,
-            uri=uri
-        )
+        raw_process_reference = schema_loader.raw_process_reference_for_object(tool_object, uri=uri)
         cwl_tool = schema_loader.tool(
             raw_process_reference=raw_process_reference,
         )
@@ -269,11 +289,11 @@ class ToolProxy(metaclass=ABCMeta):
         # remove input parameter formats from CWL files so that cwltool
         # does not complain they are missing in the input data
         for input_field in self._tool.inputs_record_schema["fields"]:
-            if 'format' in input_field:
-                del input_field['format']
+            if "format" in input_field:
+                del input_field["format"]
 
     def job_proxy(self, input_dict, output_dict, job_directory="."):
-        """ Build a cwltool.job.Job describing computation using a input_json
+        """Build a cwltool.job.Job describing computation using a input_json
         Galaxy will generate mapping the Galaxy description of the inputs into
         a cwltool compatible variant.
         """
@@ -299,23 +319,23 @@ class ToolProxy(metaclass=ABCMeta):
 
     @abstractmethod
     def input_instances(self):
-        """ Return InputInstance objects describing mapping to Galaxy inputs. """
+        """Return InputInstance objects describing mapping to Galaxy inputs."""
 
     @abstractmethod
     def output_instances(self):
-        """ Return OutputInstance objects describing mapping to Galaxy inputs. """
+        """Return OutputInstance objects describing mapping to Galaxy inputs."""
 
     @abstractmethod
     def docker_identifier(self):
-        """ Return docker identifier for embedding in tool description. """
+        """Return docker identifier for embedding in tool description."""
 
     @abstractmethod
     def description(self):
-        """ Return description to tool. """
+        """Return description to tool."""
 
     @abstractmethod
     def label(self):
-        """ Return label for tool. """
+        """Return label for tool."""
 
     def to_persistent_representation(self):
         """Return a JSON representation of this tool. Not for serialization
@@ -351,20 +371,20 @@ class CommandLineToolProxy(ToolProxy):
 
     def description(self):
         # Don't use description - typically too verbose.
-        return ''
+        return ""
 
     def doc(self):
         # TODO: parse multiple lines and merge - valid in cwl-1.1
-        doc = self._tool.tool.get('doc')
+        doc = self._tool.tool.get("doc")
         return doc
 
     def label(self):
-        label = self._tool.tool.get('label')
+        label = self._tool.tool.get("label")
 
         if label is not None:
             return label.partition(":")[0]  # return substring before ':'
         else:
-            return ''
+            return ""
 
     def input_fields(self):
         input_records_schema = self._eval_schema(self._tool.inputs_record_schema)
@@ -448,7 +468,6 @@ class ExpressionToolProxy(CommandLineToolProxy):
 
 
 class JobProxy:
-
     def __init__(self, tool_proxy, input_dict, output_dict, job_directory):
         self._tool_proxy = tool_proxy
         self._input_dict = input_dict
@@ -490,11 +509,7 @@ class JobProxy:
                 args.append(RuntimeContext(job_args))
             else:
                 kwargs = job_args
-            self._cwl_job = next(self._tool_proxy._tool.job(
-                self._input_dict,
-                self._output_callback,
-                *args, **kwargs
-            ))
+            self._cwl_job = next(self._tool_proxy._tool.job(self._input_dict, self._output_callback, *args, **kwargs))
             self._is_command_line_job = hasattr(self._cwl_job, "command_line")
 
     def _normalize_job(self):
@@ -552,6 +567,7 @@ class JobProxy:
                         stage_recursive(dict_value)
                 else:
                     log.info("skipping simple value...")
+
             stage_recursive(self._input_dict)
 
     def _select_resources(self, request, runtime_context=None):
@@ -614,9 +630,7 @@ class JobProxy:
         if not self.is_command_line_job:
             cwl_job = self.cwl_job()
             if RuntimeContext is not None:
-                cwl_job.run(
-                    RuntimeContext({})
-                )
+                cwl_job.run(RuntimeContext({}))
             else:
                 cwl_job.run()
             if not self._ok:
@@ -674,8 +688,9 @@ class JobProxy:
         if hasattr(cwl_job, "generatefiles"):
             outdir = os.path.join(self._job_directory, "working")
             # TODO: Why doesn't cwl_job.generatemapper work?
-            generate_mapper = pathmapper.PathMapper(cwl_job.generatefiles["listing"],
-                                                    outdir, outdir, separateDirs=False)
+            generate_mapper = pathmapper.PathMapper(
+                cwl_job.generatefiles["listing"], outdir, outdir, separateDirs=False
+            )
             # TODO: figure out what inplace_update should be.
             inplace_update = cwl_job.inplace_update
             process.stage_files(generate_mapper, stageFunc, ignore_writable=inplace_update, symlink=False)
@@ -688,7 +703,6 @@ class JobProxy:
 
 
 class WorkflowProxy:
-
     def __init__(self, workflow, workflow_path=None):
         self._workflow = workflow
         self._workflow_path = workflow_path
@@ -700,7 +714,7 @@ class WorkflowProxy:
 
     def get_outputs_for_label(self, label):
         outputs = []
-        for output in self._workflow.tool['outputs']:
+        for output in self._workflow.tool["outputs"]:
             step, output_name = split_step_references(
                 output["outputSource"],
                 multiple=False,
@@ -713,10 +727,12 @@ class WorkflowProxy:
                 else:
                     _, output_label = output_id.rsplit("/", 1)
 
-                outputs.append({
-                    "output_name": output_name,
-                    "label": output_label,
-                })
+                outputs.append(
+                    {
+                        "output_name": output_name,
+                        "label": output_label,
+                    }
+                )
         return outputs
 
     def tool_reference_proxies(self):
@@ -729,7 +745,7 @@ class WorkflowProxy:
     def step_proxies(self):
         if self._step_proxies is None:
             proxies = []
-            num_input_steps = len(self._workflow.tool['inputs'])
+            num_input_steps = len(self._workflow.tool["inputs"])
             for i, step in enumerate(self._workflow.steps):
                 proxies.append(build_step_proxy(self, step, i + num_input_steps))
             self._step_proxies = proxies
@@ -746,7 +762,7 @@ class WorkflowProxy:
     def cwl_ids_to_index(self, step_proxies):
         index = 0
         cwl_ids_to_index = {}
-        for input_dict in self._workflow.tool['inputs']:
+        for input_dict in self._workflow.tool["inputs"]:
             cwl_ids_to_index[input_dict["id"]] = index
             index += 1
 
@@ -758,7 +774,7 @@ class WorkflowProxy:
 
     @property
     def output_labels(self):
-        return [self.jsonld_id_to_label(o['id']) for o in self._workflow.tool['outputs']]
+        return [self.jsonld_id_to_label(o["id"]) for o in self._workflow.tool["outputs"]]
 
     def input_connections_by_step(self, step_proxies):
         cwl_ids_to_index = self.cwl_ids_to_index(step_proxies)
@@ -784,24 +800,24 @@ class WorkflowProxy:
                     if input_name not in input_connections_step:
                         input_connections_step[input_name] = []
 
-                    input_connections_step[input_name].append({
-                        "id": cwl_ids_to_index[output_step_id],
-                        "output_name": output_name,
-                        "input_type": "dataset"
-                    })
+                    input_connections_step[input_name].append(
+                        {"id": cwl_ids_to_index[output_step_id], "output_name": output_name, "input_type": "dataset"}
+                    )
 
             input_connections_by_step.append(input_connections_step)
 
         return input_connections_by_step
 
     def to_dict(self):
-        name = os.path.basename(self._workflow.tool.get('label') or self._workflow_path or 'TODO - derive a name from ID')
+        name = os.path.basename(
+            self._workflow.tool.get("label") or self._workflow_path or "TODO - derive a name from ID"
+        )
         steps = {}
 
         step_proxies = self.step_proxies()
         input_connections_by_step = self.input_connections_by_step(step_proxies)
         index = 0
-        for i, input_dict in enumerate(self._workflow.tool['inputs']):
+        for i, input_dict in enumerate(self._workflow.tool["inputs"]):
             steps[index] = self.cwl_input_to_galaxy_step(input_dict, i)
             index += 1
 
@@ -811,13 +827,13 @@ class WorkflowProxy:
             index += 1
 
         return {
-            'name': name,
-            'steps': steps,
-            'annotation': self.cwl_object_to_annotation(self._workflow.tool),
+            "name": name,
+            "steps": steps,
+            "annotation": self.cwl_object_to_annotation(self._workflow.tool),
         }
 
     def find_inputs_step_index(self, label):
-        for i, input in enumerate(self._workflow.tool['inputs']):
+        for i, input in enumerate(self._workflow.tool["inputs"]):
             if self.jsonld_id_to_label(input["id"]) == label:
                 return i
 
@@ -897,7 +913,7 @@ def split_step_references(step_references, workflow_id=None, multiple=True):
             expected_prefix = workflow_id + sep_on
             if not step_reference.startswith(expected_prefix):
                 raise AssertionError(f"step_reference [{step_reference}] doesn't start with {expected_prefix}")
-            step_reference = step_reference[len(expected_prefix):]
+            step_reference = step_reference[len(expected_prefix) :]
 
         # Now just grab the step name and input/output name.
         assert "#" not in step_reference
@@ -928,7 +944,6 @@ def build_step_proxy(workflow_proxy, step, index):
 
 
 class BaseStepProxy:
-
     def __init__(self, workflow_proxy, step, index):
         self._workflow_proxy = workflow_proxy
         self._step = step
@@ -986,7 +1001,6 @@ class BaseStepProxy:
 
 
 class InputProxy:
-
     def __init__(self, step_proxy, cwl_input):
         self._cwl_input = cwl_input
         self.step_proxy = step_proxy
@@ -1001,9 +1015,7 @@ class InputProxy:
 
         assert cwl_input_id
         step_name, input_name = split_step_references(
-            cwl_input_id,
-            multiple=False,
-            workflow_id=step_proxy.cwl_workflow_id
+            cwl_input_id, multiple=False, workflow_id=step_proxy.cwl_workflow_id
         )
         self.step_name = step_name
         self.input_name = input_name
@@ -1011,9 +1023,10 @@ class InputProxy:
         self.cwl_input_id = cwl_input_id
         self.cwl_source_id = cwl_source_id
 
-        scatter_inputs = [split_step_references(
-            i, multiple=False, workflow_id=step_proxy.cwl_workflow_id
-        )[1] for i in listify(step_proxy._step.tool.get("scatter", []))]
+        scatter_inputs = [
+            split_step_references(i, multiple=False, workflow_id=step_proxy.cwl_workflow_id)[1]
+            for i in listify(step_proxy._step.tool.get("scatter", []))
+        ]
         scatter = self.input_name in scatter_inputs
         self.scatter = scatter
 
@@ -1036,7 +1049,6 @@ class InputProxy:
 
 
 class ToolStepProxy(BaseStepProxy):
-
     def __init__(self, workflow_proxy, step, index):
         super().__init__(workflow_proxy, step, index)
         self._tool_proxy = None
@@ -1075,7 +1087,6 @@ class ToolStepProxy(BaseStepProxy):
 
 
 class SubworkflowStepProxy(BaseStepProxy):
-
     def __init__(self, workflow_proxy, step, index):
         super().__init__(workflow_proxy, step, index)
         self._subworkflow_proxy = None
@@ -1083,9 +1094,7 @@ class SubworkflowStepProxy(BaseStepProxy):
     def to_dict(self, input_connections):
         outputs = self.galaxy_workflow_outputs_list()
         for key, input_connection_list in input_connections.items():
-            input_subworkflow_step_id = self.subworkflow_proxy.find_inputs_step_index(
-                key
-            )
+            input_subworkflow_step_id = self.subworkflow_proxy.find_inputs_step_index(key)
             for input_connection in input_connection_list:
                 input_connection["input_subworkflow_step_id"] = input_subworkflow_step_id
 
@@ -1185,7 +1194,11 @@ def _outer_field_to_input_instance(field):
             only_type_description = type_descriptions[0]
 
         return InputInstance(
-            name, label, description, input_type=only_type_description.galaxy_param_type, collection_type=only_type_description.collection_type
+            name,
+            label,
+            description,
+            input_type=only_type_description.galaxy_param_type,
+            collection_type=only_type_description.collection_type,
         )
 
     # Older array to repeat handling, now we are just representing arrays as
@@ -1215,16 +1228,11 @@ def _field_metadata(field):
 def _simple_field_to_output(field):
     name = field["name"]
     output_data_class = field["type"]
-    output_instance = OutputInstance(
-        name,
-        output_data_type=output_data_class,
-        output_type=OUTPUT_TYPE.GLOB
-    )
+    output_instance = OutputInstance(name, output_data_type=output_data_class, output_type=OUTPUT_TYPE.GLOB)
     return output_instance
 
 
 class ConditionalInstance:
-
     def __init__(self, name, case, whens):
         self.input_type = INPUT_TYPE.CONDITIONAL
         self.name = name
@@ -1246,7 +1254,6 @@ class ConditionalInstance:
 
 
 class SelectInputInstance:
-
     def __init__(self, name, label, description, options):
         self.input_type = INPUT_TYPE.SELECT
         self.name = name
@@ -1267,7 +1274,6 @@ class SelectInputInstance:
 
 
 class InputInstance:
-
     def __init__(self, name, label, description, input_type, array=False, area=False, collection_type=None):
         self.input_type = input_type
         self.collection_type = collection_type
@@ -1283,22 +1289,13 @@ class InputInstance:
         ...
 
     @overload
-    def to_dict(
-        self, itemwise: Literal[True]
-    ) -> Union[InputInstanceDict, InputInstanceArrayDict]:
+    def to_dict(self, itemwise: Literal[True]) -> Union[InputInstanceDict, InputInstanceArrayDict]:
         ...
 
-    def to_dict(
-        self, itemwise: bool = True
-    ) -> Union[InputInstanceDict, InputInstanceArrayDict]:
+    def to_dict(self, itemwise: bool = True) -> Union[InputInstanceDict, InputInstanceArrayDict]:
         if itemwise and self.array:
             return InputInstanceArrayDict(
-                type="repeat",
-                name=f"{self.name}_repeat",
-                title=f"{self.name}",
-                blocks=[
-                    self.to_dict(itemwise=False)
-                ]
+                type="repeat", name=f"{self.name}_repeat", title=f"{self.name}", blocks=[self.to_dict(itemwise=False)]
             )
         else:
             as_dict = InputInstanceDict(
@@ -1328,7 +1325,6 @@ OUTPUT_TYPE = Bunch(
 
 # TODO: Different subclasses - this is representing different types of things.
 class OutputInstance:
-
     def __init__(self, name, output_data_type, output_type, path=None, fields=None):
         self.name = name
         self.output_data_type = output_data_type
@@ -1338,6 +1334,6 @@ class OutputInstance:
 
 
 __all__ = (
-    'tool_proxy',
-    'load_job_proxy',
+    "tool_proxy",
+    "load_job_proxy",
 )
diff --git a/lib/galaxy/tool_util/cwl/representation.py b/lib/galaxy/tool_util/cwl/representation.py
index a9870f78926..faea29894b3 100644
--- a/lib/galaxy/tool_util/cwl/representation.py
+++ b/lib/galaxy/tool_util/cwl/representation.py
@@ -5,13 +5,19 @@ import json
 import logging
 import os
 from enum import Enum
-from typing import Any, NamedTuple, Optional
+from typing import (
+    Any,
+    NamedTuple,
+    Optional,
+)
 
 from galaxy.exceptions import RequestParameterInvalidException
-from galaxy.util import safe_makedirs, string_as_bool
+from galaxy.util import (
+    safe_makedirs,
+    string_as_bool,
+)
 from .util import set_basename_and_derived_properties
 
-
 log = logging.getLogger(__name__)
 
 NOT_PRESENT = object()
@@ -179,7 +185,9 @@ def dataset_wrapper_to_file_json(inputs_dir, dataset_wrapper):
     if dataset_wrapper.unsanitized:
         raw_file_object["size"] = int(dataset_wrapper.get_size())
 
-    set_basename_and_derived_properties(raw_file_object, str(dataset_wrapper.created_from_basename or dataset_wrapper.name))
+    set_basename_and_derived_properties(
+        raw_file_object, str(dataset_wrapper.created_from_basename or dataset_wrapper.name)
+    )
     return raw_file_object
 
 
@@ -197,12 +205,14 @@ def dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper):
     except Exception:
         archive_location = None
 
-    directory_json = {"location": dataset_wrapper.extra_files_path,
-                      "class": "Directory",
-                      "name": directory_name,
-                      "archive_location": archive_location,
-                      "archive_nameext": nameext,
-                      "archive_nameroot": nameroot}
+    directory_json = {
+        "location": dataset_wrapper.extra_files_path,
+        "class": "Directory",
+        "name": directory_name,
+        "archive_location": archive_location,
+        "archive_nameext": nameext,
+        "archive_nameroot": nameroot,
+    }
 
     return directory_json
 
@@ -222,7 +232,7 @@ def collection_wrapper_to_record(inputs_dir, wrapped_value):
 
 
 def to_cwl_job(tool, param_dict, local_working_directory):
-    """ tool is Galaxy's representation of the tool and param_dict is the
+    """tool is Galaxy's representation of the tool and param_dict is the
     parameter dictionary with wrapped values.
     """
     tool_proxy = tool._cwl_tool_proxy
@@ -297,8 +307,8 @@ def to_cwl_job(tool, param_dict, local_working_directory):
             only_input = next(iter(input.inputs.values()))
             array_value = []
             for instance in param_dict[input_name]:
-                array_value.append(simple_value(only_input, instance[input_name[:-len("_repeat")]]))
-            input_json[input_name[:-len("_repeat")]] = array_value
+                array_value.append(simple_value(only_input, instance[input_name[: -len("_repeat")]]))
+            input_json[input_name[: -len("_repeat")]] = array_value
         elif input.type == "conditional":
             assert input_name in param_dict, f"No value for {input_name} in {param_dict}"
             current_case = param_dict[input_name]["_cwl__type_"]
@@ -327,7 +337,7 @@ def to_cwl_job(tool, param_dict, local_working_directory):
 
 
 def to_galaxy_parameters(tool, as_dict):
-    """ Tool is Galaxy's representation of the tool and as_dict is a Galaxified
+    """Tool is Galaxy's representation of the tool and as_dict is a Galaxified
     representation of the input json (no paths, HDA references for instance).
     """
     inputs = tool.inputs
@@ -357,7 +367,7 @@ def to_galaxy_parameters(tool, as_dict):
             # TODO: less crazy handling of defaults...
             if (as_dict_value is NOT_PRESENT or as_dict_value is None) and "null" in case_strings:
                 type_representation_name = "null"
-            elif (as_dict_value is NOT_PRESENT or as_dict_value is None):
+            elif as_dict_value is NOT_PRESENT or as_dict_value is None:
                 raise RequestParameterInvalidException(
                     "Cannot translate CWL datatype - value [{}] of type [{}] with case_strings [{}]. Non-null property must be set.".format(
                         as_dict_value, type(as_dict_value), case_strings
@@ -375,9 +385,19 @@ def to_galaxy_parameters(tool, as_dict):
                 type_representation_name = "double"
             elif isinstance(as_dict_value, str) and "string" in case_strings:
                 type_representation_name = "string"
-            elif isinstance(as_dict_value, dict) and "src" in as_dict_value and "id" in as_dict_value and "file" in case_strings:
+            elif (
+                isinstance(as_dict_value, dict)
+                and "src" in as_dict_value
+                and "id" in as_dict_value
+                and "file" in case_strings
+            ):
                 type_representation_name = "file"
-            elif isinstance(as_dict_value, dict) and "src" in as_dict_value and "id" in as_dict_value and "directory" in case_strings:
+            elif (
+                isinstance(as_dict_value, dict)
+                and "src" in as_dict_value
+                and "id" in as_dict_value
+                and "directory" in case_strings
+            ):
                 # TODO: can't disambiuate with above if both are available...
                 type_representation_name = "directory"
             elif "field" in case_strings:
diff --git a/lib/galaxy/tool_util/cwl/runnable.py b/lib/galaxy/tool_util/cwl/runnable.py
index d60853ef0ca..4ee7581d5fd 100644
--- a/lib/galaxy/tool_util/cwl/runnable.py
+++ b/lib/galaxy/tool_util/cwl/runnable.py
@@ -17,7 +17,6 @@ def get_outputs(path):
 
 
 class CwlWorkflowOutput:
-
     def __init__(self, label):
         self._label = label
 
@@ -26,7 +25,6 @@ class CwlWorkflowOutput:
 
 
 class ToolOutput:
-
     def __init__(self, tool_output):
         self._tool_output = tool_output
 
diff --git a/lib/galaxy/tool_util/cwl/runtime_actions.py b/lib/galaxy/tool_util/cwl/runtime_actions.py
index db20529a048..36c3946362a 100644
--- a/lib/galaxy/tool_util/cwl/runtime_actions.py
+++ b/lib/galaxy/tool_util/cwl/runtime_actions.py
@@ -32,7 +32,6 @@ class FileDescription:
 
 
 class PathFileDescription:
-
     def __init__(self, path):
         self.path = path
 
@@ -42,7 +41,6 @@ class PathFileDescription:
 
 
 class PathDirectoryDescription:
-
     def __init__(self, path):
         self.path = path
 
@@ -51,7 +49,6 @@ class PathDirectoryDescription:
 
 
 class LiteralFileDescription:
-
     def __init__(self, content):
         self.content = content
 
@@ -92,7 +89,11 @@ def handle_outputs(job_directory=None):
     tool_working_directory = os.path.join(job_directory, "working")
 
     job_id_tag = metadata_params["job_id_tag"]
-    from galaxy.job_execution.output_collect import default_exit_code_file, read_exit_code_from
+    from galaxy.job_execution.output_collect import (
+        default_exit_code_file,
+        read_exit_code_from,
+    )
+
     exit_code_file = default_exit_code_file(".", job_id_tag)
     tool_exit_code = read_exit_code_from(exit_code_file, job_id_tag)
 
@@ -127,9 +128,7 @@ def handle_outputs(job_directory=None):
         if secondary_files:
 
             order = []
-            index_contents = {
-                "order": order
-            }
+            index_contents = {"order": order}
 
             for secondary_file in secondary_files:
                 if output_name is None:
@@ -145,7 +144,7 @@ def handle_outputs(job_directory=None):
                     prefix = ""
                     while True:
                         if secondary_file_basename.startswith(output_basename):
-                            secondary_file_name = prefix + secondary_file_basename[len(output_basename):]
+                            secondary_file_name = prefix + secondary_file_basename[len(output_basename) :]
                             break
                         prefix = f"^{prefix}"
                         if "." not in output_basename:
@@ -156,9 +155,7 @@ def handle_outputs(job_directory=None):
                 else:
                     secondary_file_name = secondary_file_basename
                 # Convert to ^ format....
-                secondary_files_dir = job_proxy.output_secondary_files_dir(
-                    output_name, create=True
-                )
+                secondary_files_dir = job_proxy.output_secondary_files_dir(output_name, create=True)
                 extra_target = os.path.join(secondary_files_dir, secondary_file_name)
                 secondary_file_description.write_to(extra_target)
                 order.append(secondary_file_name)
@@ -214,7 +211,9 @@ def handle_outputs(job_directory=None):
             for index, el in enumerate(output):
                 if isinstance(el, dict) and el["class"] == "File":
                     output_path = _possible_uri_to_path(el["location"])
-                    elements.append({"name": str(index), "filename": output_path, "created_from_basename": el["basename"]})
+                    elements.append(
+                        {"name": str(index), "filename": output_path, "created_from_basename": el["basename"]}
+                    )
                 else:
                     target_path = f"{output_name}____{str(index)}"
                     with open(target_path, "w") as f:
@@ -233,6 +232,4 @@ def handle_outputs(job_directory=None):
         json.dump(provided_metadata, f)
 
 
-__all__ = (
-    'handle_outputs',
-)
+__all__ = ("handle_outputs",)
diff --git a/lib/galaxy/tool_util/cwl/schema.py b/lib/galaxy/tool_util/cwl/schema.py
index 5356a62d982..5bb2e036792 100644
--- a/lib/galaxy/tool_util/cwl/schema.py
+++ b/lib/galaxy/tool_util/cwl/schema.py
@@ -17,7 +17,6 @@ REWRITE_EXPRESSIONS = False
 
 
 class SchemaLoader:
-
     def __init__(self, strict=True, validate=True):
         self._strict = strict
         self._validate = validate
@@ -38,16 +37,17 @@ class SchemaLoader:
 
     def raw_process_reference(self, path, loading_context=None):
         with tempfile.TemporaryDirectory() as output_dir:
-            suffix = ''
-            if '#' in path:
-                path, suffix = path.split('#')
+            suffix = ""
+            if "#" in path:
+                path, suffix = path.split("#")
             processed_path = os.path.join(output_dir, os.path.basename(path))
             path = os.path.abspath(path)
             uri = f"file://{path}"
             loading_context = loading_context or self.loading_context()
             if REWRITE_EXPRESSIONS:
                 from cwl_utils import cwl_expression_refactor
-                exit_code = cwl_expression_refactor.main([output_dir, path, '--skip-some1', '--skip-some2'])
+
+                exit_code = cwl_expression_refactor.main([output_dir, path, "--skip-some1", "--skip-some2"])
                 if exit_code == 0:
                     uri = f"file://{processed_path}"
             if suffix:
diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index b4b5d9ad9b5..60890429619 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -10,7 +10,11 @@ import tarfile
 import tempfile
 import urllib.parse
 from collections import namedtuple
-from typing import Any, List, Optional
+from typing import (
+    Any,
+    List,
+    Optional,
+)
 
 import yaml
 from typing_extensions import TypedDict
@@ -87,8 +91,7 @@ def _handle_pseudo_location(properties, pseduo_location):
 
 
 def abs_path_or_uri(path_or_uri, relative_to):
-    """Return an absolute path if this isn't a URI, otherwise keep the URI the same.
-    """
+    """Return an absolute path if this isn't a URI, otherwise keep the URI the same."""
     is_uri = "://" in path_or_uri
     if not is_uri:
         if not os.path.isabs(path_or_uri):
@@ -100,7 +103,7 @@ def abs_path_or_uri(path_or_uri, relative_to):
 def abs_path(path_or_uri, relative_to):
     path_or_uri = abs_path_or_uri(path_or_uri, relative_to)
     if path_or_uri.startswith("file://"):
-        path_or_uri = path_or_uri[len("file://"):]
+        path_or_uri = path_or_uri[len("file://") :]
 
     return path_or_uri
 
@@ -112,9 +115,7 @@ def path_or_uri_to_uri(path_or_uri):
         return path_or_uri
 
 
-def galactic_job_json(
-    job, test_data_directory, upload_func, collection_create_func, tool_or_workflow="workflow"
-):
+def galactic_job_json(job, test_data_directory, upload_func, collection_create_func, tool_or_workflow="workflow"):
     """Adapt a CWL job object to the Galaxy API.
 
     CWL derived tools in Galaxy can consume a job description sort of like
@@ -200,8 +201,8 @@ def galactic_job_json(
             return replacement_record(value)
 
     def replacement_file(value):
-        if value.get('galaxy_id'):
-            return {"src": "hda", "id": str(value['galaxy_id'])}
+        if value.get("galaxy_id"):
+            return {"src": "hda", "id": str(value["galaxy_id"])}
         file_path = value.get("location", None) or value.get("path", None)
         # format to match output definitions in tool, where did filetype come from?
         filetype = value.get("filetype", None) or value.get("format", None)
@@ -234,11 +235,9 @@ def galactic_job_json(
         secondary_files_tar_path = None
         if secondary_files:
             tmp = tempfile.NamedTemporaryFile(delete=False)
-            tf = tarfile.open(fileobj=tmp, mode='w:')
+            tf = tarfile.open(fileobj=tmp, mode="w:")
             order: List[str] = []
-            index_contents = {
-                "order": order
-            }
+            index_contents = {"order": order}
             for secondary_file in secondary_files:
                 secondary_file_path = secondary_file.get("location", None) or secondary_file.get("path", None)
                 assert secondary_file_path, f"Invalid secondaryFile entry found [{secondary_file}]"
@@ -264,8 +263,8 @@ def galactic_job_json(
             file_path = os.path.join(test_data_directory, file_path)
 
         tmp = tempfile.NamedTemporaryFile(delete=False)
-        tf = tarfile.open(fileobj=tmp, mode='w:')
-        tf.add(file_path, '.')
+        tf = tarfile.open(fileobj=tmp, mode="w:")
+        tf.add(file_path, ".")
         tf.close()
 
         return upload_tar(tmp.name)
@@ -299,20 +298,20 @@ def galactic_job_json(
                 collection_element_identifiers.append(collection_element)
             else:
                 # nested collection
-                sub_collection_type = rank_collection_type[rank_collection_type.find(":") + 1:]
+                sub_collection_type = rank_collection_type[rank_collection_type.find(":") + 1 :]
                 collection_element = {
                     "name": element["identifier"],
                     "src": "new_collection",
                     "collection_type": sub_collection_type,
-                    "element_identifiers": to_elements(element, sub_collection_type)
+                    "element_identifiers": to_elements(element, sub_collection_type),
                 }
                 collection_element_identifiers.append(collection_element)
 
         return collection_element_identifiers
 
     def replacement_collection(value):
-        if value.get('galaxy_id'):
-            return {"src": "hdca", "id": str(value['galaxy_id'])}
+        if value.get("galaxy_id"):
+            return {"src": "hdca", "id": str(value["galaxy_id"])}
         assert "collection_type" in value
         collection_type = value["collection_type"]
         elements = to_elements(value, collection_type)
@@ -362,7 +361,6 @@ def _ensure_file_exists(file_path):
 
 
 class FileLiteralTarget:
-
     def __init__(self, contents, path=None, **kwargs):
         self.contents = contents
         self.properties = kwargs
@@ -373,7 +371,6 @@ class FileLiteralTarget:
 
 
 class FileUploadTarget:
-
     def __init__(self, path, secondary_files=None, **kwargs):
         self.path = path
         self.secondary_files = secondary_files
@@ -385,7 +382,6 @@ class FileUploadTarget:
 
 
 class ObjectUploadTarget:
-
     def __init__(self, the_object):
         self.object = the_object
         self.properties = {}
@@ -395,7 +391,6 @@ class ObjectUploadTarget:
 
 
 class DirectoryUploadTarget:
-
     def __init__(self, tar_path):
         self.tar_path = tar_path
 
@@ -435,13 +430,18 @@ def invocation_to_output(invocation, history_id, output_id):
 
 
 def output_to_cwl_json(
-    galaxy_output, get_metadata, get_dataset, get_extra_files, pseduo_location=False,
+    galaxy_output,
+    get_metadata,
+    get_dataset,
+    get_extra_files,
+    pseduo_location=False,
 ):
     """Convert objects in a Galaxy history into a CWL object.
 
     Useful in running conformance tests and implementing the cwl-runner
     interface via Galaxy.
     """
+
     def element_to_cwl_json(element):
         object = element["object"]
         content_type = object.get("history_content_type")
@@ -456,7 +456,9 @@ def output_to_cwl_json(
             object["id"],
             metadata,
         )
-        return output_to_cwl_json(element_output, get_metadata, get_dataset, get_extra_files, pseduo_location=pseduo_location)
+        return output_to_cwl_json(
+            element_output, get_metadata, get_dataset, get_extra_files, pseduo_location=pseduo_location
+        )
 
     output_metadata = galaxy_output.metadata
     if output_metadata is None:
@@ -522,9 +524,7 @@ def output_to_cwl_json(
                     for basename in index["order"]:
                         for extra_file in extra_files:
                             path = extra_file["path"]
-                            if path != os.path.join(
-                                SECONDARY_FILES_EXTRA_PREFIX, basename or ""
-                            ):
+                            if path != os.path.join(SECONDARY_FILES_EXTRA_PREFIX, basename or ""):
                                 continue
 
                             extra_file_class = extra_file["class"]
@@ -593,8 +593,8 @@ def output_to_cwl_json(
 def download_output(galaxy_output, get_metadata, get_dataset, get_extra_files, output_path):
     output_metadata = get_metadata(galaxy_output.history_content_type, galaxy_output.history_content_id)
     dataset_dict = get_dataset(output_metadata)
-    with open(output_path, 'wb') as fh:
-        fh.write(dataset_dict['content'])
+    with open(output_path, "wb") as fh:
+        fh.write(dataset_dict["content"])
 
 
 def guess_artifact_type(path):
@@ -603,15 +603,15 @@ def guess_artifact_type(path):
     with open(path) as f:
         document = yaml.safe_load(f)
 
-    if '$graph' in document:
+    if "$graph" in document:
         # Packed document without a process object at the root
-        objects = document['$graph']
+        objects = document["$graph"]
         if not object_id:
-            object_id = 'main'  # default object id
+            object_id = "main"  # default object id
 
         # Have to use str_removeprefix() instead of rstrip() because only the
         # first '#' should be removed from the object id
-        matching_objects = [o for o in objects if str_removeprefix(o['id'], '#') == object_id]
+        matching_objects = [o for o in objects if str_removeprefix(o["id"], "#") == object_id]
         if len(matching_objects) == 0:
             raise Exception(f"No process object with id [{object_id}]")
         if len(matching_objects) > 1:
diff --git a/lib/galaxy/tool_util/deps/__init__.py b/lib/galaxy/tool_util/deps/__init__.py
index 8dd0729e0c3..84c0723ea21 100644
--- a/lib/galaxy/tool_util/deps/__init__.py
+++ b/lib/galaxy/tool_util/deps/__init__.py
@@ -18,7 +18,7 @@ from .dependencies import ToolInfo
 from .requirements import (
     ContainerDescription,
     ToolRequirement,
-    ToolRequirements
+    ToolRequirements,
 )
 from .resolvers import (
     ContainerDependency,
@@ -31,7 +31,9 @@ log = logging.getLogger(__name__)
 CONFIG_VAL_NOT_FOUND = object()
 
 
-def build_dependency_manager(app_config_dict=None, resolution_config_dict=None, conf_file=None, default_tool_dependency_dir=None):
+def build_dependency_manager(
+    app_config_dict=None, resolution_config_dict=None, conf_file=None, default_tool_dependency_dir=None
+):
     """Build a DependencyManager object from app and/or resolution config.
 
     If app_config_dict is specified, it should be application configuration information
@@ -73,9 +75,11 @@ def build_dependency_manager(app_config_dict=None, resolution_config_dict=None,
     use_tool_dependencies = app_config_dict.get("use_tool_dependencies", None)
     # if we haven't set an explicit True or False, try to infer from config...
     if use_tool_dependencies is None:
-        use_tool_dependencies = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) is not None or \
-            app_config_dict.get("dependency_resolvers") or \
-            (conf_file and os.path.exists(conf_file))
+        use_tool_dependencies = (
+            app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) is not None
+            or app_config_dict.get("dependency_resolvers")
+            or (conf_file and os.path.exists(conf_file))
+        )
 
     if use_tool_dependencies:
         dependency_manager_kwds = {
@@ -104,6 +108,7 @@ class DependencyManager:
     and should each contain a file 'env.sh' which can be sourced to make the
     dependency available in the current shell environment.
     """
+
     cached = False
 
     def __init__(self, default_base_path, conf_file=None, app_config=None):
@@ -124,7 +129,7 @@ class DependencyManager:
         plugin_source = None
         dependency_resolver_dicts = app_config.get("dependency_resolvers")
         if dependency_resolver_dicts is not None:
-            plugin_source = plugin_config.PluginConfigSource('dict', dependency_resolver_dicts)
+            plugin_source = plugin_config.PluginConfigSource("dict", dependency_resolver_dicts)
         else:
             plugin_source = self.__build_dependency_resolvers_plugin_source(conf_file)
         self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source)
@@ -151,8 +156,7 @@ class DependencyManager:
         return self._enabled_container_types
 
     def get_resolver_option(self, resolver, key, explicit_resolver_options=None):
-        """Look in resolver-specific settings for option and then fallback to global settings.
-        """
+        """Look in resolver-specific settings for option and then fallback to global settings."""
         if explicit_resolver_options is None:
             explicit_resolver_options = {}
         default = resolver.config_options.get(key)
@@ -183,7 +187,11 @@ class DependencyManager:
     def dependency_shell_commands(self, requirements, **kwds):
         requirements_to_dependencies = self.requirements_to_dependencies(requirements, **kwds)
         ordered_dependencies = OrderedSet(requirements_to_dependencies.values())
-        return [dependency.shell_commands() for dependency in ordered_dependencies if not isinstance(dependency, ContainerDependency)]
+        return [
+            dependency.shell_commands()
+            for dependency in ordered_dependencies
+            if not isinstance(dependency, ContainerDependency)
+        ]
 
     def requirements_to_dependencies(self, requirements, **kwds):
         """
@@ -193,31 +201,31 @@ class DependencyManager:
         """
         requirement_to_dependency = self._requirements_to_dependencies_dict(requirements, **kwds)
 
-        if 'tool_instance' in kwds:
-            kwds['tool_instance'].dependencies = [dep.to_dict() for dep in requirement_to_dependency.values()]
+        if "tool_instance" in kwds:
+            kwds["tool_instance"].dependencies = [dep.to_dict() for dep in requirement_to_dependency.values()]
 
         return requirement_to_dependency
 
     def _requirements_to_dependencies_dict(self, requirements, search=False, **kwds):
         """Build simple requirements to dependencies dict for resolution."""
         requirement_to_dependency = {}
-        index = kwds.get('index')
-        install = kwds.get('install', False)
-        resolver_type = kwds.get('resolver_type')
-        include_containers = kwds.get('include_containers', False)
-        container_type = kwds.get('container_type')
-        require_exact = kwds.get('exact', False)
-        return_null_dependencies = kwds.get('return_null', False)
+        index = kwds.get("index")
+        install = kwds.get("install", False)
+        resolver_type = kwds.get("resolver_type")
+        include_containers = kwds.get("include_containers", False)
+        container_type = kwds.get("container_type")
+        require_exact = kwds.get("exact", False)
+        return_null_dependencies = kwds.get("return_null", False)
 
         resolvable_requirements = requirements.resolvable
 
         tool_info_kwds = dict(requirements=resolvable_requirements)
-        if 'tool_instance' in kwds:
-            tool = kwds['tool_instance']
-            tool_info_kwds['tool_id'] = tool.id
-            tool_info_kwds['tool_version'] = tool.version
-            tool_info_kwds['container_descriptions'] = tool.containers
-            tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment
+        if "tool_instance" in kwds:
+            tool = kwds["tool_instance"]
+            tool_info_kwds["tool_id"] = tool.id
+            tool_info_kwds["tool_version"] = tool.version
+            tool_info_kwds["container_descriptions"] = tool.containers
+            tool_info_kwds["requires_galaxy_python_environment"] = tool.requires_galaxy_python_environment
 
         tool_info = ToolInfo(**tool_info_kwds)
 
@@ -232,7 +240,9 @@ class DependencyManager:
             if container_type is not None and getattr(resolver, "container_type", None) != container_type:
                 continue
 
-            _requirement_to_dependency = {k: v for k, v in requirement_to_dependency.items() if not isinstance(v, NullDependency)}
+            _requirement_to_dependency = {
+                k: v for k, v in requirement_to_dependency.items() if not isinstance(v, NullDependency)
+            }
 
             if len(_requirement_to_dependency) == len(resolvable_requirements):
                 # Shortcut - resolution complete.
@@ -248,7 +258,9 @@ class DependencyManager:
                 if not install and resolver.builds_on_resolution:
                     # don't want to build images here
                     continue
-                if not resolver.resolver_type.startswith(('cached', 'explicit', 'fallback')) and not (search or install):
+                if not resolver.resolver_type.startswith(("cached", "explicit", "fallback")) and not (
+                    search or install
+                ):
                     # These would look up available containers using the quay API,
                     # we only want to do this if we search for containers
                     continue
@@ -257,14 +269,21 @@ class DependencyManager:
                 resolve = None
             if all_unmet and resolve is not None:
                 # TODO: Handle specs.
-                dependencies = resolve(requirements=resolvable_requirements,
-                                       enabled_container_types=self.enabled_container_types,
-                                       destination_for_container_type=self.get_destination_info_for_container_type,
-                                       tool_info=tool_info,
-                                       **kwds)
+                dependencies = resolve(
+                    requirements=resolvable_requirements,
+                    enabled_container_types=self.enabled_container_types,
+                    destination_for_container_type=self.get_destination_info_for_container_type,
+                    tool_info=tool_info,
+                    **kwds,
+                )
                 if dependencies:
                     if isinstance(dependencies, ContainerDescription):
-                        dependencies = [ContainerDependency(dependencies, name=r.name, version=r.version, container_resolver=resolver) for r in resolvable_requirements]
+                        dependencies = [
+                            ContainerDependency(
+                                dependencies, name=r.name, version=r.version, container_resolver=resolver
+                            )
+                            for r in resolvable_requirements
+                        ]
                     assert len(dependencies) == len(resolvable_requirements)
                     for requirement, dependency in zip(resolvable_requirements, dependencies):
                         log.debug(dependency.resolver_msg)
@@ -297,8 +316,8 @@ class DependencyManager:
     def uses_tool_shed_dependencies(self):
         return any(map(lambda r: isinstance(r, ToolShedPackageDependencyResolver), self.dependency_resolvers))
 
-    def find_dep(self, name, version=None, type='package', **kwds):
-        log.debug(f'Find dependency {name} version {version}')
+    def find_dep(self, name, version=None, type="package", **kwds):
+        log.debug(f"Find dependency {name} version {version}")
         requirements = ToolRequirements([ToolRequirement(name=name, version=version, type=type)])
         dep_dict = self._requirements_to_dependencies_dict(requirements, **kwds)
         if len(dep_dict) > 0:
@@ -316,24 +335,29 @@ class DependencyManager:
         return plugin_source
 
     def __default_dependency_resolvers_source(self):
-        return plugin_config.PluginConfigSource('dict', [
-            {"type": "tool_shed_packages"},
-            {"type": "galaxy_packages"},
-            {"type": "conda"},
-            {"type": "galaxy_packages", "versionless": True},
-            {"type": "conda", "versionless": True},
-        ])
+        return plugin_config.PluginConfigSource(
+            "dict",
+            [
+                {"type": "tool_shed_packages"},
+                {"type": "galaxy_packages"},
+                {"type": "conda"},
+                {"type": "galaxy_packages", "versionless": True},
+                {"type": "conda", "versionless": True},
+            ],
+        )
 
     def __parse_resolver_conf_plugins(self, plugin_source):
-        """
-        """
+        """ """
         extra_kwds = dict(dependency_manager=self)
         # Use either 'type' from YAML definition or 'resolver_type' from to_dict definition.
-        return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds, plugin_type_keys=['type', 'resolver_type'])
+        return plugin_config.load_plugins(
+            self.resolver_classes, plugin_source, extra_kwds, plugin_type_keys=["type", "resolver_type"]
+        )
 
     def __resolvers_dict(self):
         import galaxy.tool_util.deps.resolvers
-        return plugin_config.plugins_dict(galaxy.tool_util.deps.resolvers, 'resolver_type')
+
+        return plugin_config.plugins_dict(galaxy.tool_util.deps.resolvers, "resolver_type")
 
     def to_dict(self):
         return {
@@ -351,14 +375,16 @@ class CachedDependencyManager(DependencyManager):
 
     def __init__(self, default_base_path, **kwd):
         super().__init__(default_base_path=default_base_path, **kwd)
-        self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir") or os.path.join(default_base_path, "_cache")
+        self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir") or os.path.join(
+            default_base_path, "_cache"
+        )
 
     def build_cache(self, requirements, **kwds):
         resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
         cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable]
         hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies)
         if os.path.exists(hashed_dependencies_dir):
-            if kwds.get('force_rebuild', False):
+            if kwds.get("force_rebuild", False):
                 try:
                     shutil.rmtree(hashed_dependencies_dir)
                 except Exception:
@@ -390,7 +416,9 @@ class CachedDependencyManager(DependencyManager):
 
     def hash_dependencies(self, resolved_dependencies):
         """Return hash for dependencies"""
-        resolved_dependencies = [(dep.name, dep.version, dep.exact, dep.dependency_type) for dep in resolved_dependencies]
+        resolved_dependencies = [
+            (dep.name, dep.version, dep.exact, dep.dependency_type) for dep in resolved_dependencies
+        ]
         hash_str = json.dumps(sorted(resolved_dependencies))
         return hash_util.new_secure_hash(hash_str)[:8]  # short hash
 
@@ -427,7 +455,7 @@ class NullDependencyManager(DependencyManager):
     def dependency_shell_commands(self, requirements, **kwds):
         return []
 
-    def find_dep(self, name, version=None, type='package', **kwds):
+    def find_dep(self, name, version=None, type="package", **kwds):
         return NullDependency(version=version, name=name)
 
     def to_dict(self):
diff --git a/lib/galaxy/tool_util/deps/brew_exts.py b/lib/galaxy/tool_util/deps/brew_exts.py
index 82a275c7cdc..5c0acc66074 100755
--- a/lib/galaxy/tool_util/deps/brew_exts.py
+++ b/lib/galaxy/tool_util/deps/brew_exts.py
@@ -40,14 +40,15 @@ else:
     DEFAULT_HOMEBREW_ROOT = os.path.join(os.path.expanduser("~"), ".linuxbrew")
 
 NO_BREW_ERROR_MESSAGE = "Could not find brew on PATH, please place on path or pass to script with --brew argument."
-CANNOT_DETERMINE_TAP_ERROR_MESSAGE = "Cannot determine tap of specified recipe - please use fully qualified recipe (e.g. homebrew/science/samtools)."
+CANNOT_DETERMINE_TAP_ERROR_MESSAGE = (
+    "Cannot determine tap of specified recipe - please use fully qualified recipe (e.g. homebrew/science/samtools)."
+)
 VERBOSE = False
 RELAXED = False
 BREW_ARGS = []
 
 
 class BrewContext:
-
     def __init__(self, args=None):
         ensure_brew_on_path(args)
         raw_config = brew_execute(["config"])
@@ -61,7 +62,6 @@ class BrewContext:
 
 
 class RecipeContext:
-
     @staticmethod
     def from_args(args, brew_context=None):
         return RecipeContext(args.recipe, args.version, brew_context)
@@ -111,12 +111,18 @@ def main():
     actions = ["vinstall", "vuninstall", "vdeps", "vinfo", "env"]
     action = __action(sys)
     if not action:
-        parser.add_argument('action', metavar='action', help="Versioned action to perform.", choices=actions)
-    parser.add_argument('recipe', metavar='recipe', help="Recipe for action - should be absolute (e.g. homebrew/science/samtools).")
-    parser.add_argument('version', metavar='version', help="Version for action (e.g. 0.1.19).")
-    parser.add_argument('--relaxed', action='store_true', help="Relaxed processing - for instance allow use of env on non-vinstall-ed recipes.")
-    parser.add_argument('--verbose', action='store_true', help="Verbose output")
-    parser.add_argument('restargs', nargs=argparse.REMAINDER)
+        parser.add_argument("action", metavar="action", help="Versioned action to perform.", choices=actions)
+    parser.add_argument(
+        "recipe", metavar="recipe", help="Recipe for action - should be absolute (e.g. homebrew/science/samtools)."
+    )
+    parser.add_argument("version", metavar="version", help="Version for action (e.g. 0.1.19).")
+    parser.add_argument(
+        "--relaxed",
+        action="store_true",
+        help="Relaxed processing - for instance allow use of env on non-vinstall-ed recipes.",
+    )
+    parser.add_argument("--verbose", action="store_true", help="Verbose output")
+    parser.add_argument("restargs", nargs=argparse.REMAINDER)
     args = parser.parse_args()
     if args.verbose:
         VERBOSE = True
@@ -145,19 +151,19 @@ def main():
 
 
 class CommandLineException(Exception):
-
     def __init__(self, command, stdout, stderr):
         self.command = command
         self.stdout = stdout
         self.stderr = stderr
-        self.message = ("Failed to execute command-line %s, stderr was:\n"
-                        "-------->>begin stderr<<--------\n"
-                        "%s\n"
-                        "-------->>end stderr<<--------\n"
-                        "-------->>begin stdout<<--------\n"
-                        "%s\n"
-                        "-------->>end stdout<<--------\n"
-                        ) % (command, stderr, stdout)
+        self.message = (
+            "Failed to execute command-line %s, stderr was:\n"
+            "-------->>begin stderr<<--------\n"
+            "%s\n"
+            "-------->>end stderr<<--------\n"
+            "-------->>begin stdout<<--------\n"
+            "%s\n"
+            "-------->>end stdout<<--------\n"
+        ) % (command, stderr, stdout)
 
     def __str__(self):
         return self.message
@@ -202,11 +208,7 @@ def versioned_install(recipe_context, package=None, version=None, installed_deps
                 # dep_version obtained from brew versions doesn't
                 # include revision. This linked_keg attribute does.
                 keg_verion = brew_info(dep)["linked_keg"]
-                dep_metadata = {
-                    'name': dep,
-                    'version': keg_verion,
-                    'versioned': versioned
-                }
+                dep_metadata = {"name": dep, "version": keg_verion, "versioned": versioned}
                 deps_metadata.append(dep_metadata)
 
             cellar_root = recipe_context.brew_context.homebrew_cellar
@@ -221,9 +223,7 @@ def versioned_install(recipe_context, package=None, version=None, installed_deps
             brew_execute(args, env=env)
             deps = brew_execute(["deps", package])
             deps = [d.strip() for d in deps.split("\n") if d]
-            metadata = {
-                'deps': deps_metadata
-            }
+            metadata = {"deps": deps_metadata}
             cellar_root = recipe_context.brew_context.homebrew_cellar
             cellar_path = recipe_cellar_path(cellar_root, package, version)
             v_metadata_path = os.path.join(cellar_path, "INSTALL_RECEIPT_VERSIONED.json")
@@ -254,8 +254,8 @@ def commit_for_version(recipe_context, package, version):
 def print_versioned_deps(recipe_context, recipe, version):
     deps = load_versioned_deps(recipe_context.cellar_path)
     for dep in deps:
-        val = dep['name']
-        if dep['versioned']:
+        val = dep["name"]
+        if dep["versioned"]:
             val += f"@{dep['version']}"
         print(val)
 
@@ -271,7 +271,7 @@ def load_versioned_deps(cellar_path, relaxed=None):
             raise OSError(f"Could not locate versioned receipt file: {v_metadata_path}")
     with open(v_metadata_path) as f:
         metadata = json.load(f)
-    return metadata['deps']
+    return metadata["deps"]
 
 
 def unversioned_install(package):
@@ -337,33 +337,42 @@ def build_env_actions(deps, cellar_root, cellar_path, relaxed=None, custom_only=
             with open(env_path) as f:
                 env_metadata = json.load(f)
                 if "actions" in env_metadata:
+
                     def to_action(desc):
                         return EnvAction(cellar_path, desc)
+
                     actions.extend(map(to_action, env_metadata["actions"]))
 
     for dep in deps:
-        package = dep['name']
-        version = dep['version']
+        package = dep["name"]
+        version = dep["version"]
         dep_cellar_path = recipe_cellar_path(cellar_root, package, version)
         handle_keg(dep_cellar_path)
 
     handle_keg(cellar_path)
     if not custom_only:
         if path_appends:
-            actions.append(EnvAction(cellar_path, {"action": "prepend", "variable": "PATH", "value": ":".join(path_appends)}))
+            actions.append(
+                EnvAction(cellar_path, {"action": "prepend", "variable": "PATH", "value": ":".join(path_appends)})
+            )
         if ld_path_appends:
-            actions.append(EnvAction(cellar_path, {"action": "prepend", "variable": "LD_LIBRARY_PATH", "value": ":".join(path_appends)}))
+            actions.append(
+                EnvAction(
+                    cellar_path, {"action": "prepend", "variable": "LD_LIBRARY_PATH", "value": ":".join(path_appends)}
+                )
+            )
     return actions
 
 
 class EnvAction:
-
     def __init__(self, keg_root, action_description):
         self.variable = action_description["variable"]
         self.action = action_description["action"]
-        self.value = string.Template(action_description["value"]).safe_substitute({
-            'KEG_ROOT': keg_root,
-        })
+        self.value = string.Template(action_description["value"]).safe_substitute(
+            {
+                "KEG_ROOT": keg_root,
+            }
+        )
 
     @staticmethod
     def build_env(env_actions):
@@ -392,10 +401,7 @@ class EnvAction:
             template = '''${variable}="${value}:$$${variable}"'''
         else:
             template = '''${variable}="$$${variable}:${value}"'''
-        return [
-            self.__eval(template),
-            f"export {self.variable}"
-        ]
+        return [self.__eval(template), f"export {self.variable}"]
 
 
 @contextlib.contextmanager
@@ -475,17 +481,16 @@ def extended_brew_info(recipe):
 
     for line in raw_info.split("\n"):
         if line.startswith("From: "):
-            extra_info["from_url"] = line[len("From: "):].strip()
+            extra_info["from_url"] = line[len("From: ") :].strip()
         for dep_type in ["Build", "Required", "Recommended", "Optional"]:
             if line.startswith(f"{dep_type}: "):
                 key = f"{dep_type.lower()}_dependencies"
-                raw_val = line[len(f"{dep_type}: "):]
+                raw_val = line[len(f"{dep_type}: ") :]
                 extra_info[key].extend(raw_val.split(", "))
     return extra_info
 
 
 def brew_versions_info(package, tap_path):
-
     def versioned(recipe_path):
         if not os.path.isabs(recipe_path):
             recipe_path = os.path.join(os.getcwd(), recipe_path)
@@ -505,7 +510,7 @@ def brew_versions_info(package, tap_path):
 def __action(sys):
     script_name = os.path.basename(sys.argv[0])
     if script_name.startswith("brew-"):
-        return script_name[len("brew-"):]
+        return script_name[len("brew-") :]
     else:
         return None
 
diff --git a/lib/galaxy/tool_util/deps/brew_util.py b/lib/galaxy/tool_util/deps/brew_util.py
index c40976f37d5..d513a23461f 100644
--- a/lib/galaxy/tool_util/deps/brew_util.py
+++ b/lib/galaxy/tool_util/deps/brew_util.py
@@ -8,7 +8,6 @@ DEFAULT_TAP = "homebrew/science"
 
 
 class HomebrewRecipe:
-
     def __init__(self, recipe, version, tap):
         self.recipe = recipe
         self.version = version
@@ -31,9 +30,6 @@ def requirement_to_recipe(requirement):
 
 def requirements_to_recipe_contexts(requirements, brew_context):
     def to_recipe_context(homebrew_recipe):
-        return brew_exts.RecipeContext(
-            homebrew_recipe.recipe,
-            homebrew_recipe.version,
-            brew_context
-        )
+        return brew_exts.RecipeContext(homebrew_recipe.recipe, homebrew_recipe.version, brew_context)
+
     return map(to_recipe_context, requirements_to_recipes(requirements))
diff --git a/lib/galaxy/tool_util/deps/commands.py b/lib/galaxy/tool_util/deps/commands.py
index 7d79f18e225..821dafaffb1 100644
--- a/lib/galaxy/tool_util/deps/commands.py
+++ b/lib/galaxy/tool_util/deps/commands.py
@@ -12,5 +12,6 @@ from galaxy.util.commands import (  # noqa: F401
     which,
 )
 
-
-warnings.warn("Importing galaxy.tool_util.deps.commands is deprecated, use galaxy.util.commands instead", DeprecationWarning)
+warnings.warn(
+    "Importing galaxy.tool_util.deps.commands is deprecated, use galaxy.util.commands instead", DeprecationWarning
+)
diff --git a/lib/galaxy/tool_util/deps/conda_compat.py b/lib/galaxy/tool_util/deps/conda_compat.py
index 627ec63898a..8bc745e7cc0 100644
--- a/lib/galaxy/tool_util/deps/conda_compat.py
+++ b/lib/galaxy/tool_util/deps/conda_compat.py
@@ -15,14 +15,16 @@ except ImportError:
     MetaData = None
 
 try:
-    from anaconda_verify.recipe import parse, render_jinja2
+    from anaconda_verify.recipe import (
+        parse,
+        render_jinja2,
+    )
 except ImportError:
     render_jinja2 = None
     parse = None
 
 
 class _Memoized:
-
     def __init__(self, func):
         self.func = func
         self.cache = {}
@@ -55,7 +57,7 @@ def _render_jinja2(recipe_dir):
 
     loaders = [jinja2.FileSystemLoader(recipe_dir)]
     env = jinja2.Environment(loader=jinja2.ChoiceLoader(loaders))
-    template = env.get_or_select_template('meta.yaml')
+    template = env.get_or_select_template("meta.yaml")
     return template.render(environment=env)
 
 
@@ -77,23 +79,22 @@ if parse is None:
 
 def raw_metadata(recipe_dir):
     """Evaluate Conda template if needed and return raw metadata for supplied recipe directory."""
-    meta_path = os.path.join(recipe_dir, 'meta.yaml')
-    with open(meta_path, 'rb') as fi:
+    meta_path = os.path.join(recipe_dir, "meta.yaml")
+    with open(meta_path, "rb") as fi:
         data = fi.read()
-        if b'{{' in data:
+        if b"{{" in data:
             data = render_jinja2(recipe_dir)
     meta = parse(data, None)
     return meta
 
 
 class _MetaData:
-
     def __init__(self, input_dir):
         self.meta = raw_metadata(input_dir)
 
     def get_value(self, field, default=None):
         """Get nested field value or supplied default is not present."""
-        section, key = field.split('/')
+        section, key = field.split("/")
         submeta = self.meta.get(section)
         if submeta is None:
             submeta = {}
diff --git a/lib/galaxy/tool_util/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py
index bce8668c09d..feb74a45fe6 100644
--- a/lib/galaxy/tool_util/deps/conda_util.py
+++ b/lib/galaxy/tool_util/deps/conda_util.py
@@ -14,7 +14,7 @@ import packaging.version
 from galaxy.util import (
     commands,
     smart_str,
-    unicodify
+    unicodify,
 )
 from . import installable
 
@@ -48,7 +48,7 @@ def conda_link():
 
 
 def find_conda_prefix(conda_prefix=None):
-    """ If supplied conda_prefix is not set, default to the default location
+    """If supplied conda_prefix is not set, default to the default location
     for Miniconda installs.
     """
     if conda_prefix is None:
@@ -74,10 +74,18 @@ def find_conda_prefix(conda_prefix=None):
 class CondaContext(installable.InstallableContext):
     installable_description = "Conda"
 
-    def __init__(self, conda_prefix=None, conda_exec=None,
-                 shell_exec=None, debug=False, ensure_channels='',
-                 condarc_override=None, use_path_exec=USE_PATH_EXEC_DEFAULT,
-                 copy_dependencies=False, use_local=USE_LOCAL_DEFAULT):
+    def __init__(
+        self,
+        conda_prefix=None,
+        conda_exec=None,
+        shell_exec=None,
+        debug=False,
+        ensure_channels="",
+        condarc_override=None,
+        use_path_exec=USE_PATH_EXEC_DEFAULT,
+        copy_dependencies=False,
+        use_local=USE_LOCAL_DEFAULT,
+    ):
         self.condarc_override = condarc_override
         if not conda_exec and use_path_exec:
             conda_exec = commands.which("conda")
@@ -134,7 +142,7 @@ class CondaContext(installable.InstallableContext):
                 package_parts = package.split("-")
                 if len(package_parts) < 3:
                     continue
-                package = '-'.join(package_parts[:-2])
+                package = "-".join(package_parts[:-2])
                 version = package_parts[-2]
                 # build = package_parts[-1]
                 if package == "conda":
@@ -195,7 +203,7 @@ class CondaContext(installable.InstallableContext):
         does not exist or is empty.
         """
         conda_exec = os.path.abspath(self.conda_exec)
-        conda_prefix_plus_exec = os.path.abspath(os.path.join(self.conda_prefix, 'bin/conda'))
+        conda_prefix_plus_exec = os.path.abspath(os.path.join(self.conda_prefix, "bin/conda"))
         if conda_exec == conda_prefix_plus_exec:
             if not os.path.exists(self.conda_prefix):
                 return True
@@ -203,13 +211,17 @@ class CondaContext(installable.InstallableContext):
                 os.rmdir(self.conda_prefix)  # Conda's install script fails if path exists (even if empty).
                 return True
             else:
-                log.warning("Cannot install Conda because conda_prefix '%s' exists and is not empty.",
-                            self.conda_prefix)
+                log.warning(
+                    "Cannot install Conda because conda_prefix '%s' exists and is not empty.", self.conda_prefix
+                )
                 return False
         else:
-            log.warning("Skipping installation of Conda into conda_prefix '%s', "
-                        "since conda_exec '%s' is set to a path outside of conda_prefix.",
-                        self.conda_prefix, self.conda_exec)
+            log.warning(
+                "Skipping installation of Conda into conda_prefix '%s', "
+                "since conda_exec '%s' is set to a path outside of conda_prefix.",
+                self.conda_prefix,
+                self.conda_exec,
+            )
             return False
 
     def exec_command(self, operation, args, stdout_path=None):
@@ -226,21 +238,23 @@ class CondaContext(installable.InstallableContext):
         env = {}
         if self.condarc_override:
             env["CONDARC"] = self.condarc_override
-        cmd_string = ' '.join(map(shlex.quote, cmd))
+        cmd_string = " ".join(map(shlex.quote, cmd))
         kwds = dict()
         try:
             if stdout_path:
-                kwds['stdout'] = open(stdout_path, 'w')
+                kwds["stdout"] = open(stdout_path, "w")
                 cmd_string += f" > '{stdout_path}'"
-            conda_exec_home = env['HOME'] = tempfile.mkdtemp(prefix='conda_exec_home_')  # We don't want to pollute ~/.conda, which may not even be writable
+            conda_exec_home = env["HOME"] = tempfile.mkdtemp(
+                prefix="conda_exec_home_"
+            )  # We don't want to pollute ~/.conda, which may not even be writable
             log.debug("Executing command: %s", cmd_string)
             return self.shell_exec(cmd, env=env, **kwds)
         except Exception:
             log.exception("Failed to execute command: %s", cmd_string)
             return 1
         finally:
-            if kwds.get('stdout'):
-                kwds['stdout'].close()
+            if kwds.get("stdout"):
+                kwds["stdout"].close()
             if conda_exec_home:
                 shutil.rmtree(conda_exec_home, ignore_errors=True)
 
@@ -248,10 +262,7 @@ class CondaContext(installable.InstallableContext):
         """
         Return the process exit code (i.e. 0 in case of success).
         """
-        create_args = [
-            "-y",
-            "--quiet"
-        ]
+        create_args = ["-y", "--quiet"]
         if allow_local and self.use_local:
             create_args.extend(["--use-local"])
         create_args.extend(self._override_channels_args)
@@ -264,10 +275,7 @@ class CondaContext(installable.InstallableContext):
 
         Return the process exit code (i.e. 0 in case of success).
         """
-        remove_args = [
-            "-y",
-            "--name"
-        ]
+        remove_args = ["-y", "--name"]
         remove_args.extend(args)
         return self.exec_command("env remove", remove_args)
 
@@ -275,9 +283,7 @@ class CondaContext(installable.InstallableContext):
         """
         Return the process exit code (i.e. 0 in case of success).
         """
-        install_args = [
-            "-y"
-        ]
+        install_args = ["-y"]
         if allow_local and self.use_local:
             install_args.append("--use-local")
         install_args.extend(self._override_channels_args)
@@ -290,10 +296,7 @@ class CondaContext(installable.InstallableContext):
 
         Return the process exit code (i.e. 0 in case of success).
         """
-        clean_args = [
-            "--tarballs",
-            "-y"
-        ]
+        clean_args = ["--tarballs", "-y"]
         if args:
             clean_args.extend(args)
         stdout_path = None
@@ -305,10 +308,7 @@ class CondaContext(installable.InstallableContext):
         """
         Return the process exit code (i.e. 0 in case of success).
         """
-        return self.exec_command("list", [
-            "--name", name,
-            "--export"
-        ], stdout_path=path)
+        return self.exec_command("list", ["--name", name, "--export"], stdout_path=path)
 
     def env_path(self, env_name):
         return os.path.join(self.envs_path, env_name)
@@ -357,7 +357,6 @@ def installed_conda_targets(conda_context):
 
 
 class CondaTarget:
-
     def __init__(self, package, version=None, channel=None):
         if SHELL_UNSAFE_PATTERN.search(package) is not None:
             raise ValueError(f"Invalid package [{package}] encountered.")
@@ -385,8 +384,7 @@ class CondaTarget:
 
     @property
     def package_specifier(self):
-        """ Return a package specifier as consumed by conda install/create.
-        """
+        """Return a package specifier as consumed by conda install/create."""
         if self.version:
             return f"{self.package}={self.version}"
         else:
@@ -394,7 +392,7 @@ class CondaTarget:
 
     @property
     def install_environment(self):
-        """ The dependency resolution and installation frameworks will
+        """The dependency resolution and installation frameworks will
         expect each target to be installed it its own environment with
         a fixed and predictable name given package and version.
         """
@@ -412,14 +410,14 @@ class CondaTarget:
         return False
 
     def __ne__(self, other):
-        return not(self == other)
+        return not (self == other)
 
 
 def hash_conda_packages(conda_packages, conda_target=None):
-    """ Produce a unique hash on supplied packages.
+    """Produce a unique hash on supplied packages.
     TODO: Ideally we would do this in such a way that preserved environments.
     """
-    h = hashlib.new('sha256')
+    h = hashlib.new("sha256")
     for conda_package in conda_packages:
         h.update(smart_str(conda_package.install_environment))
     return h.hexdigest()
@@ -431,7 +429,7 @@ def install_conda(conda_context, force_conda_build=False):
     with tempfile.NamedTemporaryFile(suffix=".sh", prefix="conda_install", delete=False) as temp:
         script_path = temp.name
     download_cmd = commands.download_command(conda_link(), to=script_path)
-    install_cmd = ['bash', script_path, '-b', '-p', conda_context.conda_prefix]
+    install_cmd = ["bash", script_path, "-b", "-p", conda_context.conda_prefix]
     package_targets = [
         f"conda={CONDA_VERSION}",
     ]
@@ -444,7 +442,7 @@ def install_conda(conda_context, force_conda_build=False):
             return exit_code
         exit_code = conda_context.shell_exec(install_cmd)
     except Exception:
-        log.exception('Failed to install conda')
+        log.exception("Failed to install conda")
         return 1
     finally:
         if os.path.exists(script_path):
@@ -460,7 +458,8 @@ def install_conda_targets(conda_targets, conda_context, env_name=None, allow_loc
     """
     if env_name is not None:
         create_args = [
-            "--name", env_name,  # environment for package
+            "--name",
+            env_name,  # environment for package
         ]
         for conda_target in conda_targets:
             create_args.append(conda_target.package_specifier)
@@ -477,7 +476,8 @@ def install_conda_target(conda_target, conda_context, skip_environment=False):
     """
     if not skip_environment:
         create_args = [
-            "--name", conda_target.install_environment,  # environment for package
+            "--name",
+            conda_target.install_environment,  # environment for package
             conda_target.package_specifier,
         ]
         return conda_context.exec_create(create_args)
@@ -510,7 +510,7 @@ def best_search_result(conda_target, conda_context, channels_override=None, offl
     if offline:
         search_cmd.append("--offline")
     if platform:
-        search_cmd.extend(['--platform', platform])
+        search_cmd.extend(["--platform", platform])
     if channels_override:
         search_cmd.append("--override-channels")
         for channel in channels_override:
@@ -526,8 +526,8 @@ def best_search_result(conda_target, conda_context, channels_override=None, offl
         # then is the newest version with the newest build and
         # the latest update time.
         hits = json.loads(res).get(conda_target.package, [])[::-1]
-        hits = sorted(hits, key=lambda hit: hit['build_number'], reverse=True)
-        hits = sorted(hits, key=lambda hit: packaging.version.parse(hit['version']), reverse=True)
+        hits = sorted(hits, key=lambda hit: hit["build_number"], reverse=True)
+        hits = sorted(hits, key=lambda hit: packaging.version.parse(hit["version"]), reverse=True)
     except commands.CommandLineException:
         log.error("Could not execute: '%s'", search_cmd)
         hits = []
@@ -549,7 +549,7 @@ def is_search_hit_exact(conda_target, search_hit):
     target_version = conda_target.version
     # It'd be nice to make request verson of 1.0 match available
     # version of 1.0.3 or something like that.
-    return not target_version or search_hit['version'] == target_version
+    return not target_version or search_hit["version"] == target_version
 
 
 def is_conda_target_installed(conda_target, conda_context):
@@ -561,8 +561,7 @@ def is_conda_target_installed(conda_target, conda_context):
 
 
 def filter_installed_targets(conda_targets, conda_context):
-    installed = functools.partial(is_conda_target_installed,
-                                  conda_context=conda_context)
+    installed = functools.partial(is_conda_target_installed, conda_context=conda_context)
     return list(filter(installed, conda_targets))
 
 
@@ -573,7 +572,7 @@ def build_isolated_environment(
     copy=False,
     quiet=False,
 ):
-    """ Build a new environment (or reuse an existing one from hashes)
+    """Build a new environment (or reuse an existing one from hashes)
     for specified conda packages.
     """
     if not isinstance(conda_packages, list):
@@ -590,18 +589,16 @@ def build_isolated_environment(
         for conda_package in conda_packages:
             name = conda_package.install_environment
             export_path = os.path.join(tempdir, name)
-            conda_context.export_list(
-                name,
-                export_path
-            )
+            conda_context.export_list(name, export_path)
             export_paths.append(export_path)
         create_args = ["--unknown"]
         # Works in 3.19, 4.0 - 4.2 - not in 4.3.
         # Adjust fix if they fix Conda - xref
         # - https://github.com/galaxyproject/galaxy/issues/3635
         # - https://github.com/conda/conda/issues/2035
-        offline_works = (conda_context.conda_version < packaging.version.parse("4.3")) or \
-                        (conda_context.conda_version >= packaging.version.parse("4.4"))
+        offline_works = (conda_context.conda_version < packaging.version.parse("4.3")) or (
+            conda_context.conda_version >= packaging.version.parse("4.4")
+        )
         if offline_works:
             create_args.extend(["--offline"])
         else:
@@ -614,9 +611,7 @@ def build_isolated_environment(
         if copy:
             create_args.append("--copy")
         for export_path in export_paths:
-            create_args.extend([
-                "--file", export_path
-            ])
+            create_args.extend(["--file", export_path])
 
         stdout_path = None
         if quiet:
@@ -637,8 +632,7 @@ def build_isolated_environment(
 def requirement_to_conda_targets(requirement):
     conda_target = None
     if requirement.type == "package":
-        conda_target = CondaTarget(requirement.name,
-                                   version=requirement.version)
+        conda_target = CondaTarget(requirement.name, version=requirement.version)
     return conda_target
 
 
@@ -648,9 +642,9 @@ def requirements_to_conda_targets(requirements):
 
 
 __all__ = (
-    'CondaContext',
-    'CondaTarget',
-    'install_conda',
-    'install_conda_target',
-    'requirements_to_conda_targets',
+    "CondaContext",
+    "CondaTarget",
+    "install_conda",
+    "install_conda_target",
+    "requirements_to_conda_targets",
 )
diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index 6c79ea298c8..7eebea123a4 100644
--- a/lib/galaxy/tool_util/deps/container_classes.py
+++ b/lib/galaxy/tool_util/deps/container_classes.py
@@ -2,20 +2,19 @@ import os
 import string
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 from logging import getLogger
 from uuid import uuid4
 
-
 from galaxy.containers.docker_model import DockerVolume
 from galaxy.util import (
     asbool,
-    in_directory
+    in_directory,
 )
 from . import (
     docker_util,
-    singularity_util
+    singularity_util,
 )
 from .requirements import (
     DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES,
@@ -27,7 +26,7 @@ log = getLogger(__name__)
 DOCKER_CONTAINER_TYPE = "docker"
 SINGULARITY_CONTAINER_TYPE = "singularity"
 
-LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = r'''
+LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = r"""
 python << EOF
 from __future__ import print_function
 
@@ -54,7 +53,7 @@ if not found:
     cmd = "cat ${cached_image_file} | ${load_cmd}"
     subprocess.check_call(cmd, shell=True)
 EOF
-'''
+"""
 SOURCE_CONDA_ACTIVATE = """
 # Check if container was created by installing conda packages,
 # and if so, source scripts to populate environment variables
@@ -72,8 +71,9 @@ fi
 
 
 class Container(metaclass=ABCMeta):
-
-    def __init__(self, container_id, app_info, tool_info, destination_info, job_info, container_description, container_name=None):
+    def __init__(
+        self, container_id, app_info, tool_info, destination_info, job_info, container_description, container_name=None
+    ):
         self.container_id = container_id
         self.app_info = app_info
         self.tool_info = tool_info
@@ -89,7 +89,11 @@ class Container(metaclass=ABCMeta):
 
     @property
     def resolve_dependencies(self):
-        return DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES if not self.container_description else self.container_description.resolve_dependencies
+        return (
+            DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES
+            if not self.container_description
+            else self.container_description.resolve_dependencies
+        )
 
     @property
     def shell(self):
@@ -172,7 +176,7 @@ def preprocess_volumes(volumes_raw_str, container_type):
         # for a while singularity did not allow to specify the bind type rw
         # (which is the default). so we omit this default
         # see https://github.com/hpcng/singularity/pull/5487
-        if container_type == SINGULARITY_CONTAINER_TYPE and volume[1] == 'rw':
+        if container_type == SINGULARITY_CONTAINER_TYPE and volume[1] == "rw":
             del volume[1]
 
     return [":".join(v) for v in volumes]
@@ -205,8 +209,8 @@ class HasDockerLikeVolumes:
         add_var("galaxy_root", self.app_info.galaxy_root_dir)
         add_var("default_file_path", self.app_info.default_file_path)
         add_var("library_import_dir", self.app_info.library_import_dir)
-        add_var('tool_data_path', self.app_info.tool_data_path)
-        add_var('shed_tool_data_path', self.app_info.shed_tool_data_path)
+        add_var("tool_data_path", self.app_info.tool_data_path)
+        add_var("shed_tool_data_path", self.app_info.shed_tool_data_path)
 
         if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
             # We have a Pulsar job directory, so everything needed (excluding index
@@ -260,7 +264,7 @@ class HasDockerLikeVolumes:
             end_index = volumes_str.find(",", tool_directory_index)
             if end_index < 0:
                 end_index = len(volumes_str)
-            volumes_str = volumes_str[0:tool_directory_index] + volumes_str[end_index:len(volumes_str)]
+            volumes_str = volumes_str[0:tool_directory_index] + volumes_str[end_index : len(volumes_str)]
 
         return volumes_str
 
@@ -296,7 +300,7 @@ class DockerContainer(Container, HasDockerLikeVolumes):
         # pass through only what tool needs however. (See todo in ToolInfo.)
         for key, value in self.destination_info.items():
             if key.startswith("docker_env_"):
-                env = key[len("docker_env_"):]
+                env = key[len("docker_env_") :]
                 env_directives.append(f'"{env}={value}"')
 
         working_directory = self.job_info.working_directory
@@ -330,9 +334,11 @@ class DockerContainer(Container, HasDockerLikeVolumes):
             run_extra_arguments=self.prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS),
             guest_ports=self.tool_info.guest_ports,
             container_name=self.container_name,
-            **docker_host_props
+            **docker_host_props,
+        )
+        kill_command = docker_util.build_docker_simple_command(
+            "kill", container_name=self.container_name, **docker_host_props
         )
-        kill_command = docker_util.build_docker_simple_command("kill", container_name=self.container_name, **docker_host_props)
         # Suppress standard error below in the kill command because it can cause jobs that otherwise would work
         # to fail. Likely, in these cases the container has been stopped normally and so cannot be stopped again.
         # A less hacky approach might be to check if the container is running first before trying to kill.
@@ -352,9 +358,7 @@ trap _on_exit 0
         load_cmd = docker_util.build_docker_load_command(**docker_host_props)
 
         return string.Template(LOAD_CACHED_IMAGE_COMMAND_TEMPLATE).safe_substitute(
-            cached_image_file=cached_image_file,
-            images_cmd=images_cmd,
-            load_cmd=load_cmd
+            cached_image_file=cached_image_file, images_cmd=images_cmd, load_cmd=load_cmd
         )
 
     def __get_cached_image_file(self):
@@ -397,14 +401,12 @@ class SingularityContainer(Container, HasDockerLikeVolumes):
             docker_image_identifier=self.container_id,
             cache_directory=cache_directory,
             namespace=namespace,
-            **self.get_singularity_target_kwds()
+            **self.get_singularity_target_kwds(),
         )
 
     def build_singularity_pull_command(self, cache_path):
         return singularity_util.pull_singularity_command(
-            image_identifier=self.container_id,
-            cache_path=cache_path,
-            **self.get_singularity_target_kwds()
+            image_identifier=self.container_id, cache_path=cache_path, **self.get_singularity_target_kwds()
         )
 
     def containerize_command(self, command):
@@ -418,7 +420,7 @@ class SingularityContainer(Container, HasDockerLikeVolumes):
         # pass through only what tool needs however. (See todo in ToolInfo.)
         for key, value in self.destination_info.items():
             if key.startswith("singularity_env_"):
-                real_key = key[len("singularity_env_"):]
+                real_key = key[len("singularity_env_") :]
                 env.append((real_key, value))
 
         working_directory = self.job_info.working_directory
@@ -438,7 +440,7 @@ class SingularityContainer(Container, HasDockerLikeVolumes):
             run_extra_arguments=self.prop("run_extra_arguments", singularity_util.DEFAULT_RUN_EXTRA_ARGUMENTS),
             guest_ports=self.tool_info.guest_ports,
             container_name=self.container_name,
-            **self.get_singularity_target_kwds()
+            **self.get_singularity_target_kwds(),
         )
         return run_command
 
@@ -450,12 +452,12 @@ CONTAINER_CLASSES = dict(
 
 
 class NullContainer:
-
     def __init__(self):
         pass
 
     def __bool__(self):
         return False
+
     __nonzero__ = __bool__
 
 
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/__init__.py b/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
index 654f6b9d994..a470238f3cf 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
@@ -5,7 +5,6 @@ from abc import (
     abstractproperty,
 )
 
-
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
 
@@ -22,7 +21,7 @@ class ContainerResolver(Dictifiable, metaclass=ABCMeta):
     """Description of a technique for resolving container images for tool execution."""
 
     # Keys for dictification.
-    dict_collection_visible_keys = ['resolver_type', 'can_uninstall_dependencies', 'builds_on_resolution']
+    dict_collection_visible_keys = ["resolver_type", "can_uninstall_dependencies", "builds_on_resolution"]
     can_uninstall_dependencies = False
     builds_on_resolution = False
     read_only = True  # not used for containers, but set for when they are used like dependency resolvers
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/explicit.py b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
index 3ab776dce77..fbc43a2485c 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
@@ -34,8 +34,8 @@ class ExplicitContainerResolver(ContainerResolver):
 
 class ExplicitSingularityContainerResolver(ExplicitContainerResolver):
 
-    resolver_type = 'explicit_singularity'
-    container_type = 'singularity'
+    resolver_type = "explicit_singularity"
+    container_type = "singularity"
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
         """Find a container explicitly mentioned in tool description.
@@ -45,10 +45,10 @@ class ExplicitSingularityContainerResolver(ExplicitContainerResolver):
         hence the container_description hack here.
         """
         for container_description in tool_info.container_descriptions:
-            if container_description.type == 'docker':
+            if container_description.type == "docker":
                 desc_dict = container_description.to_dict()
-                desc_dict['type'] = self.container_type
-                desc_dict['identifier'] = f"docker://{container_description.identifier}"
+                desc_dict["type"] = self.container_type
+                desc_dict["identifier"] = f"docker://{container_description.identifier}"
                 container_description = container_description.from_dict(desc_dict)
             if self._container_type_enabled(container_description, enabled_container_types):
                 return container_description
@@ -57,13 +57,15 @@ class ExplicitSingularityContainerResolver(ExplicitContainerResolver):
 
 
 class CachedExplicitSingularityContainerResolver(CliContainerResolver):
-    resolver_type = 'cached_explicit_singularity'
-    container_type = 'singularity'
-    cli = 'singularity'
+    resolver_type = "cached_explicit_singularity"
+    container_type = "singularity"
+    cli = "singularity"
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.cache_directory_path = kwargs.get("cache_directory", os.path.join(kwargs['app_info'].container_image_cache_path, "singularity", "explicit"))
+        self.cache_directory_path = kwargs.get(
+            "cache_directory", os.path.join(kwargs["app_info"].container_image_cache_path, "singularity", "explicit")
+        )
         self._init_cache_directory()
 
     def _init_cache_directory(self):
@@ -77,10 +79,10 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
         hence the container_description hack here.
         """
         for container_description in tool_info.container_descriptions:  # type: ContainerDescription
-            if container_description.type == 'docker':
+            if container_description.type == "docker":
                 desc_dict = container_description.to_dict()
-                desc_dict['type'] = self.container_type
-                desc_dict['identifier'] = f"docker://{container_description.identifier}"
+                desc_dict["type"] = self.container_type
+                desc_dict["identifier"] = f"docker://{container_description.identifier}"
                 container_description = container_description.from_dict(desc_dict)
             if not self._container_type_enabled(container_description, enabled_container_types):
                 return None
@@ -90,18 +92,17 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
             cache_path = os.path.normpath(os.path.join(self.cache_directory_path, image_id))
             if install and not os.path.exists(cache_path):
                 destination_info = {}
-                destination_for_container_type = kwds.get(
-                    'destination_for_container_type')
+                destination_for_container_type = kwds.get("destination_for_container_type")
                 if destination_for_container_type:
-                    destination_info = destination_for_container_type(
-                        self.container_type)
+                    destination_info = destination_for_container_type(self.container_type)
                 container = SingularityContainer(
                     container_description.identifier,
                     self.app_info,
                     tool_info,
                     destination_info,
                     {},
-                    container_description)
+                    container_description,
+                )
                 command = container.build_singularity_pull_command(cache_path=cache_path)
                 shell(command)
             # Point to container in the cache in stead.
@@ -115,7 +116,6 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
 
 
 class BaseAdminConfiguredContainerResolver(ContainerResolver):
-
     def __init__(self, app_info=None, shell=DEFAULT_SHELL, **kwds):
         super().__init__(app_info, **kwds)
         self.shell = shell
@@ -133,7 +133,7 @@ class FallbackContainerResolver(BaseAdminConfiguredContainerResolver):
     """Specify an explicit, identified container as a Docker container resolver."""
 
     resolver_type = "fallback"
-    container_type = 'docker'
+    container_type = "docker"
 
     def __init__(self, app_info=None, identifier="", **kwds):
         super().__init__(app_info, **kwds)
@@ -155,7 +155,7 @@ class FallbackSingularityContainerResolver(FallbackContainerResolver):
     """Specify an explicit, identified container as a Singularity container resolver."""
 
     resolver_type = "fallback_singularity"
-    container_type = 'singularity'
+    container_type = "singularity"
 
 
 class FallbackNoRequirementsContainerResolver(FallbackContainerResolver):
@@ -170,7 +170,7 @@ class FallbackNoRequirementsContainerResolver(FallbackContainerResolver):
 class FallbackNoRequirementsSingularityContainerResolver(FallbackNoRequirementsContainerResolver):
 
     resolver_type = "fallback_no_requirements_singularity"
-    container_type = 'singularity'
+    container_type = "singularity"
 
 
 class RequiresGalaxyEnvironmentContainerResolver(FallbackContainerResolver):
@@ -185,7 +185,7 @@ class RequiresGalaxyEnvironmentContainerResolver(FallbackContainerResolver):
 class RequiresGalaxyEnvironmentSingularityContainerResolver(RequiresGalaxyEnvironmentContainerResolver):
 
     resolver_type = "requires_galaxy_environment_singularity"
-    container_type = 'singularity'
+    container_type = "singularity"
 
 
 class MappingContainerResolver(BaseAdminConfiguredContainerResolver):
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
index bbae6793514..ea932da9000 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
@@ -7,7 +7,10 @@ from abc import (
     ABCMeta,
     abstractmethod,
 )
-from typing import NamedTuple, Optional
+from typing import (
+    NamedTuple,
+    Optional,
+)
 
 from galaxy.util import (
     safe_makedirs,
@@ -17,9 +20,7 @@ from galaxy.util import (
 )
 from galaxy.util.commands import shell
 from ..container_classes import CONTAINER_CLASSES
-from ..container_resolvers import (
-    ContainerResolver,
-)
+from ..container_resolvers import ContainerResolver
 from ..docker_util import build_docker_images_command
 from ..mulled.mulled_build import (
     DEFAULT_CHANNELS,
@@ -128,8 +129,10 @@ class DirMtimeCacheDirectory(CacheDirectory):
         mtime = self.__get_mtime()
         if mtime != self.__mtime:
             if mtime < self.__mtime:
-                log.warning(f"Modification time '{mtime}' of cache directory '{self.path}' is older than previous "
-                            f"modification time '{self.__mtime}'! Cache directory will be recached")
+                log.warning(
+                    f"Modification time '{mtime}' of cache directory '{self.path}' is older than previous "
+                    f"modification time '{self.__mtime}'! Cache directory will be recached"
+                )
             self.__cache()
         return self.__contents
 
@@ -216,7 +219,7 @@ def identifier_to_cached_target(identifier, hash_func, namespace=None):
         if version and "--" in version:
             version, build = split_tag(version)
         if prefix and image_name.startswith(prefix):
-            image_name = image_name[len(prefix):]
+            image_name = image_name[len(prefix) :]
         image = CachedMulledImageSingleTarget(image_name, version, build, identifier)
     return image
 
@@ -275,7 +278,9 @@ def find_best_matching_cached_image(targets, cached_images, hash_func):
     return image
 
 
-def docker_cached_container_description(targets, namespace, hash_func="v2", shell=DEFAULT_CONTAINER_SHELL, resolution_cache=None):
+def docker_cached_container_description(
+    targets, namespace, hash_func="v2", shell=DEFAULT_CONTAINER_SHELL, resolution_cache=None
+):
     if len(targets) == 0:
         return None
 
@@ -324,7 +329,7 @@ def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None,
         unresolved_cache = set()
 
     mulled_resolution_cache = None
-    if resolution_cache and hasattr(resolution_cache, 'mulled_resolution_cache'):
+    if resolution_cache and hasattr(resolution_cache, "mulled_resolution_cache"):
         mulled_resolution_cache = resolution_cache.mulled_resolution_cache
 
     name = None
@@ -349,7 +354,7 @@ def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None,
 
         if tags:
             for tag in tags:
-                if '--' in tag:
+                if "--" in tag:
                     version, _ = split_tag(tag)
                 else:
                     version = tag
@@ -358,13 +363,16 @@ def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None,
                     break
 
     else:
+
         def first_tag_if_available(image_name):
             if ":" in image_name:
                 repo_name, tag_prefix = image_name.split(":", 2)
             else:
                 repo_name = image_name
                 tag_prefix = None
-            tags = mulled_tags_for(namespace, repo_name, tag_prefix=tag_prefix, resolution_cache=resolution_cache, session=session)
+            tags = mulled_tags_for(
+                namespace, repo_name, tag_prefix=tag_prefix, resolution_cache=resolution_cache, session=session
+            )
             return tags[0] if tags else None
 
         if hash_func == "v2":
@@ -404,8 +412,8 @@ def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None,
 
 class CliContainerResolver(ContainerResolver):
 
-    container_type = 'docker'
-    cli = 'docker'
+    container_type = "docker"
+    cli = "docker"
 
     def __init__(self, *args, **kwargs):
         self._cli_available = bool(which(self.cli))
@@ -418,18 +426,22 @@ class CliContainerResolver(ContainerResolver):
     @cli_available.setter
     def cli_available(self, value):
         if not value:
-            log.info(f'{self.cli} CLI not available, cannot list or pull images in Galaxy process. Does not impact kubernetes.')
+            log.info(
+                f"{self.cli} CLI not available, cannot list or pull images in Galaxy process. Does not impact kubernetes."
+            )
         self._cli_available = value
 
 
 class SingularityCliContainerResolver(CliContainerResolver):
 
-    container_type = 'singularity'
-    cli = 'singularity'
+    container_type = "singularity"
+    cli = "singularity"
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.cache_directory_path = kwargs.get("cache_directory", os.path.join(kwargs['app_info'].container_image_cache_path, "singularity", "mulled"))
+        self.cache_directory_path = kwargs.get(
+            "cache_directory", os.path.join(kwargs["app_info"].container_image_cache_path, "singularity", "mulled")
+        )
         self.cache_directory_cacher_type = kwargs.get("cache_directory_cacher_type", None)
         self.cache_directory = None
         self.hash_func = None
@@ -443,7 +455,7 @@ class SingularityCliContainerResolver(CliContainerResolver):
 class CachedMulledDockerContainerResolver(CliContainerResolver):
 
     resolver_type = "cached_mulled"
-    shell = '/bin/bash'
+    shell = "/bin/bash"
 
     def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", **kwds):
         super().__init__(app_info=app_info, **kwds)
@@ -451,13 +463,19 @@ class CachedMulledDockerContainerResolver(CliContainerResolver):
         self.hash_func = hash_func
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
-        if not self.cli_available or tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types:
+        if (
+            not self.cli_available
+            or tool_info.requires_galaxy_python_environment
+            or self.container_type not in enabled_container_types
+        ):
             return None
 
         targets = mulled_targets(tool_info)
         log.debug(f"Image name for tool {tool_info.tool_id}: {image_name(targets, self.hash_func)}")
         resolution_cache = kwds.get("resolution_cache")
-        return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func, shell=self.shell, resolution_cache=resolution_cache)
+        return docker_cached_container_description(
+            targets, self.namespace, hash_func=self.hash_func, shell=self.shell, resolution_cache=resolution_cache
+        )
 
     def __str__(self):
         return f"CachedMulledDockerContainerResolver[namespace={self.namespace}]"
@@ -466,7 +484,7 @@ class CachedMulledDockerContainerResolver(CliContainerResolver):
 class CachedMulledSingularityContainerResolver(SingularityCliContainerResolver):
 
     resolver_type = "cached_mulled_singularity"
-    shell = '/bin/bash'
+    shell = "/bin/bash"
 
     def __init__(self, app_info=None, hash_func="v2", **kwds):
         super().__init__(app_info=app_info, **kwds)
@@ -479,7 +497,9 @@ class CachedMulledSingularityContainerResolver(SingularityCliContainerResolver):
 
         targets = mulled_targets(tool_info)
         log.debug(f"Image name for tool {tool_info.tool_id}: {image_name(targets, self.hash_func)}")
-        return singularity_cached_container_description(targets, self.cache_directory, hash_func=self.hash_func, shell=self.shell)
+        return singularity_cached_container_description(
+            targets, self.cache_directory, hash_func=self.hash_func, shell=self.shell
+        )
 
     def __str__(self):
         return f"CachedMulledSingularityContainerResolver[cache_directory={self.cache_directory.path}]"
@@ -489,7 +509,7 @@ class MulledDockerContainerResolver(CliContainerResolver):
     """Look for mulled images matching tool dependencies."""
 
     resolver_type = "mulled"
-    shell = '/bin/bash'
+    shell = "/bin/bash"
     protocol: Optional[str] = None
 
     def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds):
@@ -504,7 +524,7 @@ class MulledDockerContainerResolver(CliContainerResolver):
         except subprocess.CalledProcessError:
             # We should only get here if a docker binary is available, but command quits with a non-zero exit code,
             # e.g if the docker daemon is not available
-            log.exception('An error occured while listing cached docker image. Docker daemon may need to be restarted.')
+            log.exception("An error occured while listing cached docker image. Docker daemon may need to be restarted.")
             return None
 
     def pull(self, container):
@@ -526,7 +546,13 @@ class MulledDockerContainerResolver(CliContainerResolver):
         if len(targets) == 0:
             return None
 
-        name = targets_to_mulled_name(targets=targets, hash_func=self.hash_func, namespace=self.namespace, resolution_cache=resolution_cache, session=session)
+        name = targets_to_mulled_name(
+            targets=targets,
+            hash_func=self.hash_func,
+            namespace=self.namespace,
+            resolution_cache=resolution_cache,
+            session=session,
+        )
         if name:
             container_id = f"quay.io/{self.namespace}/{name}"
             if self.protocol:
@@ -538,29 +564,34 @@ class MulledDockerContainerResolver(CliContainerResolver):
             )
             if self.can_list_containers:
                 if install and not self.cached_container_description(
-                        targets,
-                        namespace=self.namespace,
-                        hash_func=self.hash_func,
-                        resolution_cache=resolution_cache,
+                    targets,
+                    namespace=self.namespace,
+                    hash_func=self.hash_func,
+                    resolution_cache=resolution_cache,
                 ):
                     destination_info = {}
-                    destination_for_container_type = kwds.get('destination_for_container_type')
+                    destination_for_container_type = kwds.get("destination_for_container_type")
                     if destination_for_container_type:
                         destination_info = destination_for_container_type(self.container_type)
-                    container = CONTAINER_CLASSES[self.container_type](container_description.identifier,
-                                                                       self.app_info,
-                                                                       tool_info,
-                                                                       destination_info,
-                                                                       {},
-                                                                       container_description)
+                    container = CONTAINER_CLASSES[self.container_type](
+                        container_description.identifier,
+                        self.app_info,
+                        tool_info,
+                        destination_info,
+                        {},
+                        container_description,
+                    )
                     self.pull(container)
                 if not self.auto_install:
-                    container_description = self.cached_container_description(
-                        targets,
-                        namespace=self.namespace,
-                        hash_func=self.hash_func,
-                        resolution_cache=resolution_cache,
-                    ) or container_description
+                    container_description = (
+                        self.cached_container_description(
+                            targets,
+                            namespace=self.namespace,
+                            hash_func=self.hash_func,
+                            resolution_cache=resolution_cache,
+                        )
+                        or container_description
+                    )
             return container_description
 
     def __str__(self):
@@ -570,7 +601,7 @@ class MulledDockerContainerResolver(CliContainerResolver):
 class MulledSingularityContainerResolver(SingularityCliContainerResolver, MulledDockerContainerResolver):
 
     resolver_type = "mulled_singularity"
-    protocol = 'docker://'
+    protocol = "docker://"
 
     def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds):
         super().__init__(app_info=app_info, **kwds)
@@ -580,9 +611,9 @@ class MulledSingularityContainerResolver(SingularityCliContainerResolver, Mulled
         self.auto_install = string_as_bool(auto_install)
 
     def cached_container_description(self, targets, namespace, hash_func, resolution_cache):
-        return singularity_cached_container_description(targets,
-                                                        cache_directory=self.cache_directory,
-                                                        hash_func=hash_func)
+        return singularity_cached_container_description(
+            targets, cache_directory=self.cache_directory, hash_func=hash_func
+        )
 
     @property
     def can_list_containers(self):
@@ -591,7 +622,9 @@ class MulledSingularityContainerResolver(SingularityCliContainerResolver, Mulled
 
     def pull(self, container):
         if self.cli_available:
-            cmds = container.build_mulled_singularity_pull_command(cache_directory=self.cache_directory.path, namespace=self.namespace)
+            cmds = container.build_mulled_singularity_pull_command(
+                cache_directory=self.cache_directory.path, namespace=self.namespace
+            )
             shell(cmds=cmds)
             self.cache_directory.invalidate_cache()
 
@@ -603,22 +636,20 @@ class BuildMulledDockerContainerResolver(CliContainerResolver):
     """Build for Docker mulled images matching tool dependencies."""
 
     resolver_type = "build_mulled"
-    shell = '/bin/bash'
+    shell = "/bin/bash"
     builds_on_resolution = True
 
     def __init__(self, app_info=None, namespace="local", hash_func="v2", auto_install=True, **kwds):
         super().__init__(app_info=app_info, **kwds)
-        self._involucro_context_kwds = {
-            'involucro_bin': self._get_config_option("involucro_path", None)
-        }
+        self._involucro_context_kwds = {"involucro_bin": self._get_config_option("involucro_path", None)}
         self.namespace = namespace
         self.hash_func = hash_func
         self.auto_install = string_as_bool(auto_install)
         self._mulled_kwds = {
-            'namespace': namespace,
-            'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
-            'hash_func': self.hash_func,
-            'command': 'build-and-test',
+            "namespace": namespace,
+            "channels": self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
+            "hash_func": self.hash_func,
+            "command": "build-and-test",
         }
         self.auto_init = self._get_config_option("involucro_auto_init", True)
 
@@ -631,11 +662,7 @@ class BuildMulledDockerContainerResolver(CliContainerResolver):
         if len(targets) == 0:
             return None
         if self.auto_install or install:
-            mull_targets(
-                targets,
-                involucro_context=self._get_involucro_context(),
-                **self._mulled_kwds
-            )
+            mull_targets(targets, involucro_context=self._get_involucro_context(), **self._mulled_kwds)
         return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func, shell=self.shell)
 
     def _get_involucro_context(self):
@@ -651,23 +678,21 @@ class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver):
     """Build for Singularity mulled images matching tool dependencies."""
 
     resolver_type = "build_mulled_singularity"
-    shell = '/bin/bash'
+    shell = "/bin/bash"
     builds_on_resolution = True
 
     def __init__(self, app_info=None, hash_func="v2", auto_install=True, **kwds):
         super().__init__(app_info=app_info, **kwds)
-        self._involucro_context_kwds = {
-            'involucro_bin': self._get_config_option("involucro_path", None)
-        }
+        self._involucro_context_kwds = {"involucro_bin": self._get_config_option("involucro_path", None)}
         self.hash_func = hash_func
         self._init_cache_directory()
         self.auto_install = string_as_bool(auto_install)
         self._mulled_kwds = {
-            'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
-            'hash_func': self.hash_func,
-            'command': 'build-and-test',
-            'singularity': True,
-            'singularity_image_dir': self.cache_directory.path,
+            "channels": self._get_config_option("mulled_channels", DEFAULT_CHANNELS),
+            "hash_func": self.hash_func,
+            "command": "build-and-test",
+            "singularity": True,
+            "singularity_image_dir": self.cache_directory.path,
         }
         self.auto_init = self._get_config_option("involucro_auto_init", True)
 
@@ -681,12 +706,10 @@ class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver):
             return None
 
         if self.auto_install or install:
-            mull_targets(
-                targets,
-                involucro_context=self._get_involucro_context(),
-                **self._mulled_kwds
-            )
-        return singularity_cached_container_description(targets, self.cache_directory, hash_func=self.hash_func, shell=self.shell)
+            mull_targets(targets, involucro_context=self._get_involucro_context(), **self._mulled_kwds)
+        return singularity_cached_container_description(
+            targets, self.cache_directory, hash_func=self.hash_func, shell=self.shell
+        )
 
     def _get_involucro_context(self):
         involucro_context = InvolucroContext(**self._involucro_context_kwds)
diff --git a/lib/galaxy/tool_util/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
index 2d0d74ff409..ce7a28cb696 100644
--- a/lib/galaxy/tool_util/deps/containers.py
+++ b/lib/galaxy/tool_util/deps/containers.py
@@ -4,7 +4,7 @@ import os
 
 from galaxy.util import (
     asbool,
-    plugin_config
+    plugin_config,
 )
 from .container_classes import (
     CONTAINER_CLASSES,
@@ -25,9 +25,7 @@ from .container_resolvers.mulled import (
     MulledDockerContainerResolver,
     MulledSingularityContainerResolver,
 )
-from .requirements import (
-    ContainerDescription,
-)
+from .requirements import ContainerDescription
 
 log = logging.getLogger(__name__)
 
@@ -35,11 +33,12 @@ log = logging.getLogger(__name__)
 DEFAULT_CONTAINER_TYPE = DOCKER_CONTAINER_TYPE
 ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE, SINGULARITY_CONTAINER_TYPE]
 
-ResolvedContainerDescription = collections.namedtuple('ResolvedContainerDescription', ['container_resolver', 'container_description'])
+ResolvedContainerDescription = collections.namedtuple(
+    "ResolvedContainerDescription", ["container_resolver", "container_description"]
+)
 
 
 class ContainerFinder:
-
     def __init__(self, app_info, mulled_resolution_cache=None):
         self.app_info = app_info
         self.mulled_resolution_cache = mulled_resolution_cache
@@ -53,7 +52,9 @@ class ContainerFinder:
         """Regardless of destination properties - find best container for tool.
 
         Given container types and container.ToolInfo description of the tool."""
-        return self.default_container_registry.find_best_container_description(enabled_container_types, tool_info, **kwds)
+        return self.default_container_registry.find_best_container_description(
+            enabled_container_types, tool_info, **kwds
+        )
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
         """Regardless of destination properties - find ResolvedContainerDescription for tool."""
@@ -63,13 +64,23 @@ class ContainerFinder:
         destination_id = destination_info.get("id")  # Probably not the way to get the ID?
         destination_container_registry = None
         if destination_id and destination_id not in self.destination_container_registeries:
-            if 'container_resolvers' in destination_info:
-                destination_container_registry = ContainerRegistry(self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache)
+            if "container_resolvers" in destination_info:
+                destination_container_registry = ContainerRegistry(
+                    self.app_info,
+                    destination_info=destination_info,
+                    mulled_resolution_cache=self.mulled_resolution_cache,
+                )
                 self.destination_container_registeries[destination_id] = destination_container_registry
-        elif not destination_id and 'container_resolvers' in destination_info:
-            destination_container_registry = ContainerRegistry(self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache)
+        elif not destination_id and "container_resolvers" in destination_info:
+            destination_container_registry = ContainerRegistry(
+                self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache
+            )
 
-        if destination_container_registry is None and destination_id and destination_id in self.destination_container_registeries:
+        if (
+            destination_container_registry is None
+            and destination_id
+            and destination_id in self.destination_container_registeries
+        ):
             destination_container_registry = self.destination_container_registeries[destination_id]
 
         return destination_container_registry or self.default_container_registry
@@ -180,7 +191,9 @@ class ContainerFinder:
             return self.__build_container_id_from_parts(container_type, destination_info, mode="default")
         return None
 
-    def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info, container_description=None):
+    def __destination_container(
+        self, container_id, container_type, tool_info, destination_info, job_info, container_description=None
+    ):
         # TODO: ensure destination_info is dict-like
         if not self.__container_type_enabled(container_type, destination_info):
             return NULL_CONTAINER
@@ -189,14 +202,15 @@ class ContainerFinder:
         # container type is - there should be more thought put into this.
         # Checking which are available - settings policies for what can be
         # auto-fetched, etc....
-        return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info, container_description)
+        return CONTAINER_CLASSES[container_type](
+            container_id, self.app_info, tool_info, destination_info, job_info, container_description
+        )
 
     def __container_type_enabled(self, container_type, destination_info):
         return asbool(destination_info.get(f"{container_type}_enabled", False))
 
 
 class NullContainerFinder:
-
     def find_container(self, tool_info, destination_info, job_info):
         return []
 
@@ -212,12 +226,12 @@ class ContainerRegistry:
         self.mulled_resolution_cache = mulled_resolution_cache
 
     def __build_container_resolvers(self, app_info, destination_info):
-        app_conf_file = getattr(app_info, 'container_resolvers_config_file', None)
-        app_conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+        app_conf_file = getattr(app_info, "container_resolvers_config_file", None)
+        app_conf_dict = getattr(app_info, "container_resolvers_config_dict", None)
 
         if destination_info is not None:
-            conf_file = destination_info.get('container_resolvers_config_file', app_conf_file)
-            conf_dict = destination_info.get('container_resolvers', app_conf_dict)
+            conf_file = destination_info.get("container_resolvers_config_file", app_conf_file)
+            conf_dict = destination_info.get("container_resolvers", app_conf_dict)
         else:
             conf_file = app_conf_file
             conf_dict = app_conf_dict
@@ -236,9 +250,7 @@ class ContainerRegistry:
         return self.__default_container_resolvers()
 
     def _parse_resolver_conf(self, plugin_source):
-        extra_kwds = {
-            'app_info': self.app_info
-        }
+        extra_kwds = {"app_info": self.app_info}
         return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds)
 
     def __default_container_resolvers(self):
@@ -247,27 +259,32 @@ class ContainerRegistry:
             ExplicitSingularityContainerResolver(self.app_info),
         ]
         if self.enable_mulled_containers:
-            default_resolvers.extend([
-                CachedMulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
-                CachedMulledDockerContainerResolver(self.app_info, namespace="local"),
-                CachedMulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
-                CachedMulledSingularityContainerResolver(self.app_info, namespace="local"),
-                MulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
-                MulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
-            ])
+            default_resolvers.extend(
+                [
+                    CachedMulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
+                    CachedMulledDockerContainerResolver(self.app_info, namespace="local"),
+                    CachedMulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
+                    CachedMulledSingularityContainerResolver(self.app_info, namespace="local"),
+                    MulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
+                    MulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
+                ]
+            )
             # BuildMulledDockerContainerResolver and BuildMulledSingularityContainerResolver both need the docker daemon to build images.
             # If docker is not available, we don't load them.
             build_mulled_docker_container_resolver = BuildMulledDockerContainerResolver(self.app_info)
             if build_mulled_docker_container_resolver.cli_available:
-                default_resolvers.extend([
-                    build_mulled_docker_container_resolver,
-                    BuildMulledSingularityContainerResolver(self.app_info),
-                ])
+                default_resolvers.extend(
+                    [
+                        build_mulled_docker_container_resolver,
+                        BuildMulledSingularityContainerResolver(self.app_info),
+                    ]
+                )
         return default_resolvers
 
     def __resolvers_dict(self):
         import galaxy.tool_util.deps.container_resolvers
-        return plugin_config.plugins_dict(galaxy.tool_util.deps.container_resolvers, 'resolver_type')
+
+        return plugin_config.plugins_dict(galaxy.tool_util.deps.container_resolvers, "resolver_type")
 
     def get_resolution_cache(self):
         cache = ResolutionCache()
@@ -284,7 +301,16 @@ class ContainerRegistry:
             return None
         return None if resolved_container_description is None else resolved_container_description.container_description
 
-    def resolve(self, enabled_container_types, tool_info, index=None, resolver_type=None, install=True, resolution_cache=None, session=None):
+    def resolve(
+        self,
+        enabled_container_types,
+        tool_info,
+        index=None,
+        resolver_type=None,
+        install=True,
+        resolution_cache=None,
+        session=None,
+    ):
         resolution_cache = resolution_cache or self.get_resolution_cache()
         for i, container_resolver in enumerate(self.container_resolvers):
             if index is not None and i != index:
@@ -300,8 +326,12 @@ class ContainerRegistry:
             if not install and container_resolver.builds_on_resolution:
                 continue
 
-            container_description = container_resolver.resolve(enabled_container_types, tool_info, install=install, resolution_cache=resolution_cache, session=session)
-            log.info(f"Checking with container resolver [{container_resolver}] found description [{container_description}]")
+            container_description = container_resolver.resolve(
+                enabled_container_types, tool_info, install=install, resolution_cache=resolution_cache, session=session
+            )
+            log.info(
+                f"Checking with container resolver [{container_resolver}] found description [{container_description}]"
+            )
             if container_description:
                 assert container_description.type in enabled_container_types
                 return ResolvedContainerDescription(container_resolver, container_description)
diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
index ec22c43afe1..b519d9eff38 100644
--- a/lib/galaxy/tool_util/deps/dependencies.py
+++ b/lib/galaxy/tool_util/deps/dependencies.py
@@ -4,7 +4,6 @@ from .mulled.mulled_build import DEFAULT_CHANNELS
 
 
 class AppInfo:
-
     def __init__(
         self,
         galaxy_root_dir=None,
@@ -42,7 +41,17 @@ class ToolInfo:
     # variables they can consume (e.g. JVM options, license keys, etc..)
     # and add these to env_path_through
 
-    def __init__(self, container_descriptions=None, requirements=None, requires_galaxy_python_environment=False, env_pass_through=None, guest_ports=None, tool_id=None, tool_version=None, profile=-1):
+    def __init__(
+        self,
+        container_descriptions=None,
+        requirements=None,
+        requires_galaxy_python_environment=False,
+        env_pass_through=None,
+        guest_ports=None,
+        tool_id=None,
+        tool_version=None,
+        profile=-1,
+    ):
         if env_pass_through is None:
             env_pass_through = ["GALAXY_SLOTS", "GALAXY_MEMORY_MB", "GALAXY_MEMORY_MB_PER_SLOT"]
         if container_descriptions is None:
@@ -60,9 +69,14 @@ class ToolInfo:
 
 
 class JobInfo:
-
     def __init__(
-        self, working_directory, tool_directory, job_directory, tmp_directory, home_directory, job_directory_type,
+        self,
+        working_directory,
+        tool_directory,
+        job_directory,
+        tmp_directory,
+        home_directory,
+        job_directory_type,
     ):
         self.working_directory = working_directory
         # Tool files may be remote staged - so this is unintuitively a property
@@ -75,7 +89,7 @@ class JobInfo:
 
 
 class DependenciesDescription:
-    """ Capture (in a readily serializable way) context related a tool
+    """Capture (in a readily serializable way) context related a tool
     dependencies - both the tool's listed requirements and the tool shed
     related context required to resolve dependencies via the
     ToolShedPackageDependencyResolver.
@@ -95,7 +109,10 @@ class DependenciesDescription:
     def to_dict(self):
         return dict(
             requirements=[r.to_dict() for r in self.requirements],
-            installed_tool_dependencies=[DependenciesDescription._toolshed_install_dependency_to_dict(d) for d in self.installed_tool_dependencies]
+            installed_tool_dependencies=[
+                DependenciesDescription._toolshed_install_dependency_to_dict(d)
+                for d in self.installed_tool_dependencies
+            ],
         )
 
     @staticmethod
@@ -103,13 +120,14 @@ class DependenciesDescription:
         if as_dict is None:
             return None
 
-        requirements_dicts = as_dict.get('requirements', [])
+        requirements_dicts = as_dict.get("requirements", [])
         requirements = ToolRequirements.from_list(requirements_dicts)
-        installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', [])
-        installed_tool_dependencies = list(map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts))
+        installed_tool_dependencies_dicts = as_dict.get("installed_tool_dependencies", [])
+        installed_tool_dependencies = list(
+            map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts)
+        )
         return DependenciesDescription(
-            requirements=requirements,
-            installed_tool_dependencies=installed_tool_dependencies
+            requirements=requirements, installed_tool_dependencies=installed_tool_dependencies
         )
 
     @staticmethod
@@ -118,14 +136,14 @@ class DependenciesDescription:
         # containing only properties and associations used to resolve
         # dependencies for tool execution.
         repository_object = bunch.Bunch(
-            name=as_dict['repository_name'],
-            owner=as_dict['repository_owner'],
-            installed_changeset_revision=as_dict['repository_installed_changeset'],
+            name=as_dict["repository_name"],
+            owner=as_dict["repository_owner"],
+            installed_changeset_revision=as_dict["repository_installed_changeset"],
         )
         dependency_object = bunch.Bunch(
-            name=as_dict['dependency_name'],
-            version=as_dict['dependency_version'],
-            type=as_dict['dependency_type'],
+            name=as_dict["dependency_name"],
+            version=as_dict["dependency_version"],
+            type=as_dict["dependency_type"],
             tool_shed_repository=repository_object,
         )
         return dependency_object
diff --git a/lib/galaxy/tool_util/deps/docker_util.py b/lib/galaxy/tool_util/deps/docker_util.py
index b9b572aa199..dade02ba898 100644
--- a/lib/galaxy/tool_util/deps/docker_util.py
+++ b/lib/galaxy/tool_util/deps/docker_util.py
@@ -21,51 +21,30 @@ DEFAULT_SET_USER = "$UID"
 DEFAULT_RUN_EXTRA_ARGUMENTS = None
 
 
-def kill_command(
-    container,
-    signal=None,
-    **kwds
-):
+def kill_command(container, signal=None, **kwds):
     args = (["-s", signal] if signal else []) + [container]
     return command_list("kill", args, **kwds)
 
 
-def logs_command(
-    container,
-    **kwds
-):
+def logs_command(container, **kwds):
     return command_list("logs", [container], **kwds)
 
 
-def build_command(
-    image,
-    docker_build_path,
-    **kwds
-):
+def build_command(image, docker_build_path, **kwds):
     if os.path.isfile(docker_build_path):
         docker_build_path = os.path.dirname(os.path.abspath(docker_build_path))
     return command_list("build", ["-t", image, docker_build_path], **kwds)
 
 
-def build_save_image_command(
-    image,
-    destination,
-    **kwds
-):
+def build_save_image_command(image, destination, **kwds):
     return command_list("save", ["-o", destination, image], **kwds)
 
 
-def build_pull_command(
-    tag,
-    **kwds
-):
+def build_pull_command(tag, **kwds):
     return command_list("pull", [tag], **kwds)
 
 
-def build_docker_cache_command(
-    image,
-    **kwds
-):
+def build_docker_cache_command(image, **kwds):
     inspect_image_command = command_shell("inspect", [image], **kwds)
     pull_image_command = command_shell("pull", [image], **kwds)
     cache_command = f"{inspect_image_command} > /dev/null 2>&1\n[ $? -ne 0 ] && {pull_image_command} > /dev/null 2>&1\n"
@@ -73,7 +52,7 @@ def build_docker_cache_command(
 
 
 def build_docker_images_command(truncate=True, **kwds):
-    args = ["--no-trunc"] if not truncate else[]
+    args = ["--no-trunc"] if not truncate else []
     return command_shell("images", args, **kwds)
 
 
@@ -87,7 +66,7 @@ def build_docker_simple_command(
     sudo=DEFAULT_SUDO,
     sudo_cmd=DEFAULT_SUDO_COMMAND,
     container_name=None,
-    **kwd
+    **kwd,
 ):
     command_parts = _docker_prefix(
         docker_cmd=docker_cmd,
@@ -95,7 +74,7 @@ def build_docker_simple_command(
         sudo_cmd=sudo_cmd,
     )
     command_parts.append(command)
-    command_parts.append(container_name or '{CONTAINER_NAME}')
+    command_parts.append(container_name or "{CONTAINER_NAME}")
     return " ".join(command_parts)
 
 
@@ -120,16 +99,11 @@ def build_docker_run_command(
     set_user=DEFAULT_SET_USER,
     host=DEFAULT_HOST,
     guest_ports=False,
-    container_name=None
+    container_name=None,
 ):
     env_directives = env_directives or []
     volumes = volumes or []
-    command_parts = _docker_prefix(
-        docker_cmd=docker_cmd,
-        sudo=sudo,
-        sudo_cmd=sudo_cmd,
-        host=host
-    )
+    command_parts = _docker_prefix(docker_cmd=docker_cmd, sudo=sudo, sudo_cmd=sudo_cmd, host=host)
     command_parts.append("run")
     if interactive:
         command_parts.append("-i")
@@ -155,7 +129,7 @@ def build_docker_run_command(
         command_parts.extend(["--volumes-from", shlex.quote(str(volumes_from))])
     if memory:
         command_parts.extend(["-m", shlex.quote(memory)])
-    command_parts.extend(["--cpus", '${GALAXY_SLOTS:-1}'])
+    command_parts.extend(["--cpus", "${GALAXY_SLOTS:-1}"])
     if name:
         command_parts.extend(["--name", shlex.quote(name)])
     if working_directory:
@@ -205,11 +179,7 @@ def command_shell(command, command_args=None, **kwds):
 
 
 def _docker_prefix(
-    docker_cmd=DEFAULT_DOCKER_COMMAND,
-    sudo=DEFAULT_SUDO,
-    sudo_cmd=DEFAULT_SUDO_COMMAND,
-    host=DEFAULT_HOST,
-    **kwds
+    docker_cmd=DEFAULT_DOCKER_COMMAND, sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, host=DEFAULT_HOST, **kwds
 ):
     """Prefix to issue a docker command."""
     command_parts = []
@@ -232,12 +202,12 @@ def parse_port_text(port_text):
     ports = None
     if port_text is not None:
         ports = {}
-        for line in port_text.strip().split('\n'):
+        for line in port_text.strip().split("\n"):
             if " -> " not in line:
                 raise Exception(f"Cannot parse host and port from line [{line}]")
             tool, host = line.split(" -> ", 1)
-            hostname, port = host.rsplit(':', 1)
-            if hostname == '::':
+            hostname, port = host.rsplit(":", 1)
+            if hostname == "::":
                 # Skip unspecified IPv6 address, which is also specified as 0:0:0:0 in another line.
                 # This is brittle of course, but so is parsing the container ports like this.
                 continue
diff --git a/lib/galaxy/tool_util/deps/dockerfiles.py b/lib/galaxy/tool_util/deps/dockerfiles.py
index 47ccb567b58..4d2e1061c92 100644
--- a/lib/galaxy/tool_util/deps/dockerfiles.py
+++ b/lib/galaxy/tool_util/deps/dockerfiles.py
@@ -15,7 +15,7 @@ def docker_host_args(**kwds):
         docker_cmd=kwds["docker_cmd"],
         sudo=kwds["docker_sudo"],
         sudo_cmd=kwds["docker_sudo_cmd"],
-        host=kwds["docker_host"]
+        host=kwds["docker_host"],
     )
 
 
@@ -40,23 +40,17 @@ def dockerfile_build(path, dockerfile=None, error=log.error, **kwds):
 
     dockerfile = __find_dockerfile(dockerfile, tool_directories)
     if dockerfile is not None:
-        docker_command_parts = docker_util.build_command(
-            image_identifier,
-            dockerfile,
-            **docker_host_args(**kwds)
-        )
+        docker_command_parts = docker_util.build_command(image_identifier, dockerfile, **docker_host_args(**kwds))
     else:
         docker_command_parts = docker_util.build_pull_command(image_identifier, **docker_host_args(**kwds))
         commands.execute(docker_command_parts)
 
     commands.execute(docker_command_parts)
-    docker_image_cache = kwds['docker_image_cache']
+    docker_image_cache = kwds["docker_image_cache"]
     if docker_image_cache:
         destination = docker_cache_path(docker_image_cache, image_identifier)
         save_image_command_parts = docker_util.build_save_image_command(
-            image_identifier,
-            destination,
-            **docker_host_args(**kwds)
+            image_identifier, destination, **docker_host_args(**kwds)
         )
         commands.execute(save_image_command_parts)
 
diff --git a/lib/galaxy/tool_util/deps/installable.py b/lib/galaxy/tool_util/deps/installable.py
index c03503a4ee5..684ab058568 100644
--- a/lib/galaxy/tool_util/deps/installable.py
+++ b/lib/galaxy/tool_util/deps/installable.py
@@ -8,10 +8,9 @@ from abc import (
     abstractproperty,
 )
 
-
 from galaxy.util.filelock import (
     FileLock,
-    FileLockException
+    FileLockException,
 )
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/tool_util/deps/mulled/_cli.py b/lib/galaxy/tool_util/deps/mulled/_cli.py
index 067063d7bba..f5d49018e12 100644
--- a/lib/galaxy/tool_util/deps/mulled/_cli.py
+++ b/lib/galaxy/tool_util/deps/mulled/_cli.py
@@ -15,6 +15,4 @@ def arg_parser(argv, globals):
     return parser
 
 
-__all__ = (
-    "arg_parser",
-)
+__all__ = ("arg_parser",)
diff --git a/lib/galaxy/tool_util/deps/mulled/get_tests.py b/lib/galaxy/tool_util/deps/mulled/get_tests.py
index f2d05daf8b2..02df99661fe 100644
--- a/lib/galaxy/tool_util/deps/mulled/get_tests.py
+++ b/lib/galaxy/tool_util/deps/mulled/get_tests.py
@@ -13,6 +13,7 @@ from glob import glob
 
 import requests
 import yaml
+
 try:
     from jinja2 import Template
     from jinja2.exceptions import UndefinedError
@@ -26,7 +27,9 @@ from .util import (
     split_container_name,
 )
 
-INSTALL_JINJA_EXCEPTION = "This mulled functionality required jinja2 but it is unavailable, install condatesting extras."
+INSTALL_JINJA_EXCEPTION = (
+    "This mulled functionality required jinja2 but it is unavailable, install condatesting extras."
+)
 
 
 def get_commands_from_yaml(yaml_content):
@@ -39,38 +42,38 @@ def get_commands_from_yaml(yaml_content):
 
     try:
         # we expect to get an input in bytes, so first decode to string; run the file through the jinja processing; load as yaml
-        meta_yaml = yaml.safe_load(Template(yaml_content.decode('utf-8')).render())
+        meta_yaml = yaml.safe_load(Template(yaml_content.decode("utf-8")).render())
     except (yaml.scanner.ScannerError, UndefinedError) as e:  # what about things like {{ compiler('cxx') }}
         logging.info(e, exc_info=True)
         return None
     try:
-        if meta_yaml['test']['commands'] != [None] and meta_yaml['test']['commands'] is not None:
-            package_tests['commands'] = meta_yaml['test']['commands']
+        if meta_yaml["test"]["commands"] != [None] and meta_yaml["test"]["commands"] is not None:
+            package_tests["commands"] = meta_yaml["test"]["commands"]
     except (KeyError, TypeError):
-        logging.info('Error reading commands')
+        logging.info("Error reading commands")
     try:
-        if meta_yaml['test']['imports'] != [None] and meta_yaml['test']['imports'] is not None:
-            package_tests['imports'] = meta_yaml['test']['imports']
+        if meta_yaml["test"]["imports"] != [None] and meta_yaml["test"]["imports"] is not None:
+            package_tests["imports"] = meta_yaml["test"]["imports"]
     except (KeyError, TypeError):
-        logging.info('Error reading imports')
+        logging.info("Error reading imports")
 
-    if len(package_tests.get('commands', []) + package_tests.get('imports', [])) == 0:
+    if len(package_tests.get("commands", []) + package_tests.get("imports", [])) == 0:
         return None
 
     # need to know what scripting languages are needed to run the container
     try:
-        requirements = list(meta_yaml['requirements']['run'])
+        requirements = list(meta_yaml["requirements"]["run"])
     except (KeyError, TypeError):
-        logging.info('Error reading requirements', exc_info=True)
+        logging.info("Error reading requirements", exc_info=True)
     else:
         for requirement in requirements:
-            if requirement.split()[0] == 'perl':
-                package_tests['import_lang'] = 'perl -e'
+            if requirement.split()[0] == "perl":
+                package_tests["import_lang"] = "perl -e"
                 break
             # elif ... :
-                # other languages if necessary ... hopefully python and perl should suffice though
+            # other languages if necessary ... hopefully python and perl should suffice though
         else:  # python by default
-            package_tests['import_lang'] = 'python -c'
+            package_tests["import_lang"] = "python -c"
     return package_tests
 
 
@@ -79,11 +82,11 @@ def get_run_test(file):
     Get tests from a run_test.sh file
     """
     package_tests = {}
-    package_tests['commands'] = [file.replace('\n', ' && ')]
+    package_tests["commands"] = [file.replace("\n", " && ")]
     return package_tests
 
 
-def get_anaconda_url(container, anaconda_channel='bioconda'):
+def get_anaconda_url(container, anaconda_channel="bioconda"):
     """
     Download tarball from anaconda for test
     """
@@ -95,7 +98,7 @@ def prepend_anaconda_url(url):
     """
     Take a partial url and prepend 'https://anaconda.org'
     """
-    return f'https://anaconda.org{url}'
+    return f"https://anaconda.org{url}"
 
 
 def get_test_from_anaconda(url):
@@ -108,7 +111,7 @@ def get_test_from_anaconda(url):
         return None
 
     try:
-        metafile = tarball.extractfile('info/recipe/meta.yaml')
+        metafile = tarball.extractfile("info/recipe/meta.yaml")
     except (tarfile.ReadError, KeyError, TypeError):
         pass
     else:
@@ -118,7 +121,7 @@ def get_test_from_anaconda(url):
 
     # this part is perhaps unnecessary, but some of the older tarballs have a testfile with .yaml.template ext
     try:
-        metafile = tarball.extractfile('info/recipe/meta.yaml.template')
+        metafile = tarball.extractfile("info/recipe/meta.yaml.template")
     except (tarfile.ReadError, KeyError, TypeError):
         pass
     else:
@@ -128,51 +131,63 @@ def get_test_from_anaconda(url):
 
     # if meta.yaml was not present or there were no tests in it, try and get run_test.sh instead
     try:
-        run_test = tarball.extractfile('info/recipe/run_test.sh')
+        run_test = tarball.extractfile("info/recipe/run_test.sh")
         return get_run_test(run_test)
     except KeyError:
         logging.info("run_test.sh file not present.")
         return None
 
 
-def find_anaconda_versions(name, anaconda_channel='bioconda'):
+def find_anaconda_versions(name, anaconda_channel="bioconda"):
     """
     Find a list of available anaconda versions for a given container name
     """
     r = requests.get(f"https://anaconda.org/{anaconda_channel}/{name}/files", timeout=MULLED_SOCKET_TIMEOUT)
     urls = []
-    for line in r.text.split('\n'):
-        if 'download/linux' in line:
+    for line in r.text.split("\n"):
+        if "download/linux" in line:
             urls.append(line.split('"')[1])
     return urls
 
 
-def open_recipe_file(file, recipes_path=None, github_repo='bioconda/bioconda-recipes'):
+def open_recipe_file(file, recipes_path=None, github_repo="bioconda/bioconda-recipes"):
     """
     Open a file at a particular location and return contents as string
     """
     if recipes_path:
-        return open(f'{recipes_path}/{file}').read()
+        return open(f"{recipes_path}/{file}").read()
     else:  # if no clone of the repo is available locally, download from GitHub
-        r = requests.get(f'https://raw.githubusercontent.com/{github_repo}/master/{file}', timeout=MULLED_SOCKET_TIMEOUT)
+        r = requests.get(
+            f"https://raw.githubusercontent.com/{github_repo}/master/{file}", timeout=MULLED_SOCKET_TIMEOUT
+        )
         if r.status_code == 404:
             raise OSError
         else:
             return r.content
 
 
-def get_alternative_versions(filepath, filename, recipes_path=None, github_repo='bioconda/bioconda-recipes'):
+def get_alternative_versions(filepath, filename, recipes_path=None, github_repo="bioconda/bioconda-recipes"):
     """
     Return files that match ``filepath/*/filename`` in the bioconda-recipes repository
     """
     if recipes_path:
-        return [n.replace(f'{recipes_path}/', '') for n in glob(f'{recipes_path}/{filepath}/*/{filename}')]
+        return [n.replace(f"{recipes_path}/", "") for n in glob(f"{recipes_path}/{filepath}/*/{filename}")]
     # else use the GitHub API:
     versions = []
-    r = json.loads(requests.get(f'https://api.github.com/repos/{github_repo}/contents/{filepath}', timeout=MULLED_SOCKET_TIMEOUT).text)
+    r = json.loads(
+        requests.get(
+            f"https://api.github.com/repos/{github_repo}/contents/{filepath}", timeout=MULLED_SOCKET_TIMEOUT
+        ).text
+    )
     for subfile in r:
-        if subfile['type'] == 'dir':
-            if requests.get(f"https://raw.githubusercontent.com/{github_repo}/master/{subfile['path']}/{filename}", timeout=MULLED_SOCKET_TIMEOUT).status_code == 200:
+        if subfile["type"] == "dir":
+            if (
+                requests.get(
+                    f"https://raw.githubusercontent.com/{github_repo}/master/{subfile['path']}/{filename}",
+                    timeout=MULLED_SOCKET_TIMEOUT,
+                ).status_code
+                == 200
+            ):
                 versions.append(f"{subfile['path']}/{filename}")
     return versions
 
@@ -186,33 +201,50 @@ def try_a_func(func1, func2, param, container):
     except OSError:
         return None
     if result:
-        result['container'] = container
+        result["container"] = container
         return result
 
 
-def deep_test_search(container, recipes_path=None, anaconda_channel='bioconda', github_repo='bioconda/bioconda-recipes'):
+def deep_test_search(
+    container, recipes_path=None, anaconda_channel="bioconda", github_repo="bioconda/bioconda-recipes"
+):
     """
     Look in bioconda-recipes repo as well as anaconda for the tests, checking in multiple possible locations. If no test is found for the specified version, search if other package versions have a test available.
     """
     name = split_container_name(container)
     for f in [
-        (get_commands_from_yaml, open_recipe_file, (f'recipes/{name[0]}/{name[1]}/meta.yaml', recipes_path, github_repo), container),
-        (get_run_test, open_recipe_file, (f'recipes/{name[0]}/{name[1]}/run_test.sh', recipes_path, github_repo), container),
-        (get_commands_from_yaml, open_recipe_file, (f'recipes/{name[0]}/meta.yaml', recipes_path, github_repo), container),
-        (get_run_test, open_recipe_file, (f'recipes/{name[0]}/run_test.sh', recipes_path, github_repo), container),
+        (
+            get_commands_from_yaml,
+            open_recipe_file,
+            (f"recipes/{name[0]}/{name[1]}/meta.yaml", recipes_path, github_repo),
+            container,
+        ),
+        (
+            get_run_test,
+            open_recipe_file,
+            (f"recipes/{name[0]}/{name[1]}/run_test.sh", recipes_path, github_repo),
+            container,
+        ),
+        (
+            get_commands_from_yaml,
+            open_recipe_file,
+            (f"recipes/{name[0]}/meta.yaml", recipes_path, github_repo),
+            container,
+        ),
+        (get_run_test, open_recipe_file, (f"recipes/{name[0]}/run_test.sh", recipes_path, github_repo), container),
         (get_test_from_anaconda, get_anaconda_url, (container, anaconda_channel), container),
     ]:
         result = try_a_func(*f)
         if result:
             return result
 
-    versions = get_alternative_versions(f'recipes/{name[0]}', 'meta.yaml', recipes_path, github_repo)
+    versions = get_alternative_versions(f"recipes/{name[0]}", "meta.yaml", recipes_path, github_repo)
     for version in versions:
         result = try_a_func(get_commands_from_yaml, open_recipe_file, (version, recipes_path, github_repo), container)
         if result:
             return result
 
-    versions = get_alternative_versions(f'recipes/{name[0]}', 'run_test.sh', recipes_path, github_repo)
+    versions = get_alternative_versions(f"recipes/{name[0]}", "run_test.sh", recipes_path, github_repo)
     for version in versions:
         result = try_a_func(get_run_test, open_recipe_file, (version, recipes_path, github_repo), container)
         if result:
@@ -225,10 +257,12 @@ def deep_test_search(container, recipes_path=None, anaconda_channel='bioconda',
             return result
 
     # if everything fails
-    return {'container': container}
+    return {"container": container}
 
 
-def main_test_search(container, recipes_path=None, deep=False, anaconda_channel='bioconda', github_repo='bioconda/bioconda-recipes'):
+def main_test_search(
+    container, recipes_path=None, deep=False, anaconda_channel="bioconda", github_repo="bioconda/bioconda-recipes"
+):
     """
     Download tarball from anaconda for test
     """
@@ -238,39 +272,44 @@ def main_test_search(container, recipes_path=None, deep=False, anaconda_channel=
     result = try_a_func(get_test_from_anaconda, get_anaconda_url, (container, anaconda_channel), container)
     if result:
         return result
-    return {'container': container}
+    return {"container": container}
 
 
-def hashed_test_search(container, recipes_path=None, deep=False, anaconda_channel='bioconda', github_repo='bioconda/bioconda-recipes'):
+def hashed_test_search(
+    container, recipes_path=None, deep=False, anaconda_channel="bioconda", github_repo="bioconda/bioconda-recipes"
+):
     """
     Get test for hashed containers
     """
-    package_tests = {'commands': [], 'imports': [], 'container': container, 'import_lang': 'python -c'}
+    package_tests = {"commands": [], "imports": [], "container": container, "import_lang": "python -c"}
 
-    githubpage = requests.get(f'https://raw.githubusercontent.com/BioContainers/multi-package-containers/master/combinations/{container}.tsv', timeout=MULLED_SOCKET_TIMEOUT)
+    githubpage = requests.get(
+        f"https://raw.githubusercontent.com/BioContainers/multi-package-containers/master/combinations/{container}.tsv",
+        timeout=MULLED_SOCKET_TIMEOUT,
+    )
     if githubpage.status_code == 200:
-        packages = githubpage.text.split(',')  # get names of packages from github
-        packages = [package.split('=') for package in packages]
+        packages = githubpage.text.split(",")  # get names of packages from github
+        packages = [package.split("=") for package in packages]
     else:
         packages = []
 
     containers = []
     for package in packages:
         r = requests.get(f"https://anaconda.org/bioconda/{package[0]}/files", timeout=MULLED_SOCKET_TIMEOUT)
-        p = '-'.join(package)
-        for line in r.text.split('\n'):
+        p = "-".join(package)
+        for line in r.text.split("\n"):
             if p in line:
-                build = line.split(p)[1].split('.tar.bz2')[0]
+                build = line.split(p)[1].split(".tar.bz2")[0]
                 if build == "":
-                    containers.append(f'{package[0]}:{package[1]}')
+                    containers.append(f"{package[0]}:{package[1]}")
                 else:
-                    containers.append(f'{package[0]}:{package[1]}-{build}')
+                    containers.append(f"{package[0]}:{package[1]}-{build}")
                 break
 
     for container in containers:
         tests = main_test_search(container, recipes_path, deep, anaconda_channel, github_repo)
-        package_tests['commands'] += tests.get('commands', [])  # not a very nice solution but probably the simplest
-        for imp in tests.get('imports', []):
-            package_tests['imports'].append(f"{tests['import_lang']} 'import {imp}'")
+        package_tests["commands"] += tests.get("commands", [])  # not a very nice solution but probably the simplest
+        for imp in tests.get("imports", []):
+            package_tests["imports"].append(f"{tests['import_lang']} 'import {imp}'")
 
     return package_tests
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
index c9b4d266c58..054133fffe4 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -47,18 +47,20 @@ log = logging.getLogger(__name__)
 
 DIRNAME = os.path.dirname(__file__)
 DEFAULT_BASE_IMAGE = os.environ.get("DEFAULT_BASE_IMAGE", "quay.io/bioconda/base-glibc-busybox-bash:latest")
-DEFAULT_EXTENDED_BASE_IMAGE = os.environ.get("DEFAULT_EXTENDED_BASE_IMAGE", "quay.io/bioconda/base-glibc-debian-bash:latest")
-if 'DEFAULT_MULLED_CONDA_CHANNELS' in os.environ:
-    DEFAULT_CHANNELS = os.environ['DEFAULT_MULLED_CONDA_CHANNELS'].split(',')
+DEFAULT_EXTENDED_BASE_IMAGE = os.environ.get(
+    "DEFAULT_EXTENDED_BASE_IMAGE", "quay.io/bioconda/base-glibc-debian-bash:latest"
+)
+if "DEFAULT_MULLED_CONDA_CHANNELS" in os.environ:
+    DEFAULT_CHANNELS = os.environ["DEFAULT_MULLED_CONDA_CHANNELS"].split(",")
 else:
     DEFAULT_CHANNELS = ["conda-forge", "bioconda"]
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
-DEFAULT_WORKING_DIR = '/source/'
+DEFAULT_WORKING_DIR = "/source/"
 IS_OS_X = _platform == "darwin"
 INVOLUCRO_VERSION = "1.1.2"
-DEST_BASE_IMAGE = os.environ.get('DEST_BASE_IMAGE', None)
-CONDA_IMAGE = os.environ.get('CONDA_IMAGE', None)
+DEST_BASE_IMAGE = os.environ.get("DEST_BASE_IMAGE", None)
+CONDA_IMAGE = os.environ.get("CONDA_IMAGE", None)
 
 SINGULARITY_TEMPLATE = """Bootstrap: docker
 From: %(base_image)s
@@ -95,20 +97,20 @@ def get_tests(args, pkg_path):
     input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path))
     recipe_meta = MetaData(input_dir)
 
-    tests_commands = recipe_meta.get_value('test/commands')
-    tests_imports = recipe_meta.get_value('test/imports')
-    requirements = recipe_meta.get_value('requirements/run')
+    tests_commands = recipe_meta.get_value("test/commands")
+    tests_imports = recipe_meta.get_value("test/imports")
+    requirements = recipe_meta.get_value("requirements/run")
 
     if tests_imports or tests_commands:
         if tests_commands:
-            tests.append(' && '.join(tests_commands))
-        if tests_imports and 'python' in requirements:
-            tests.append(' && '.join(f'python -c "import {imp}"' for imp in tests_imports))
-        elif tests_imports and ('perl' in requirements or 'perl-threaded' in requirements):
-            tests.append(' && '.join(f'''perl -e "use {imp};\"''' for imp in tests_imports))
+            tests.append(" && ".join(tests_commands))
+        if tests_imports and "python" in requirements:
+            tests.append(" && ".join(f'python -c "import {imp}"' for imp in tests_imports))
+        elif tests_imports and ("perl" in requirements or "perl-threaded" in requirements):
+            tests.append(" && ".join(f'''perl -e "use {imp};\"''' for imp in tests_imports))
 
-    tests = ' && '.join(tests)
-    tests = tests.replace('$R ', 'Rscript ')
+    tests = " && ".join(tests)
+    tests = tests.replace("$R ", "Rscript ")
     return tests
 
 
@@ -118,7 +120,7 @@ def get_pkg_name(args, pkg_path):
 
     input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path))
     recipe_meta = MetaData(input_dir)
-    return recipe_meta.get_value('package/name')
+    return recipe_meta.get_value("package/name")
 
 
 def get_affected_packages(args):
@@ -128,9 +130,9 @@ def get_affected_packages(args):
     """
     recipes_dir = args.recipes_dir
     hours = args.diff_hours
-    cmd = ['git', 'log', '--diff-filter=ACMRTUXB', '--name-only', '--pretty=""', f'--since="{hours} hours ago"']
+    cmd = ["git", "log", "--diff-filter=ACMRTUXB", "--name-only", '--pretty=""', f'--since="{hours} hours ago"']
     changed_files = unicodify(subprocess.check_output(cmd, cwd=recipes_dir)).splitlines()
-    pkg_list = {x for x in changed_files if x.startswith('recipes/') and x.endswith('meta.yaml')}
+    pkg_list = {x for x in changed_files if x.startswith("recipes/") and x.endswith("meta.yaml")}
     for pkg in pkg_list:
         if pkg and os.path.exists(os.path.join(recipes_dir, pkg)):
             yield (get_pkg_name(args, pkg), get_tests(args, pkg))
@@ -140,14 +142,14 @@ def conda_versions(pkg_name, file_name):
     """Return all conda version strings for a specified package name."""
     j = json.load(open(file_name))
     ret = list()
-    for pkg in j['packages'].values():
-        if pkg['name'] == pkg_name:
+    for pkg in j["packages"].values():
+        if pkg["name"] == pkg_name:
             ret.append(f"{pkg['version']}--{pkg['build']}")
     return ret
 
 
 def get_conda_hits_for_targets(targets, conda_context):
-    search_results = (best_search_result(t, conda_context, platform='linux-64')[0] for t in targets)
+    search_results = (best_search_result(t, conda_context, platform="linux-64")[0] for t in targets)
     return [r for r in search_results if r]
 
 
@@ -155,14 +157,21 @@ def base_image_for_targets(targets, conda_context=None):
     hits = get_conda_hits_for_targets(targets, conda_context or CondaInDockerContext())
     for hit in hits:
         try:
-            tarball = get_file_from_recipe_url(hit['url'])
-            meta_content = unicodify(tarball.extractfile('info/about.json').read())
-            if json.loads(meta_content).get('extra', {}).get('container', {}).get('extended-base', False):
+            tarball = get_file_from_recipe_url(hit["url"])
+            meta_content = unicodify(tarball.extractfile("info/about.json").read())
+            if json.loads(meta_content).get("extra", {}).get("container", {}).get("extended-base", False):
                 return DEFAULT_EXTENDED_BASE_IMAGE
-            elif yaml.safe_load(unicodify(tarball.extractfile('info/recipe/meta.yaml').read())).get('extra', {}).get('container', {}).get('extended-base', False):
+            elif (
+                yaml.safe_load(unicodify(tarball.extractfile("info/recipe/meta.yaml").read()))
+                .get("extra", {})
+                .get("container", {})
+                .get("extended-base", False)
+            ):
                 return DEFAULT_EXTENDED_BASE_IMAGE
         except Exception:
-            log.warning("Could not load metadata.yaml for '%s', version '%s'", hit['name'], hit['version'], exc_info=True)
+            log.warning(
+                "Could not load metadata.yaml for '%s', version '%s'", hit["name"], hit["version"], exc_info=True
+            )
     return DEFAULT_BASE_IMAGE
 
 
@@ -175,13 +184,26 @@ class BuildExistsException(Exception):
 
 
 def mull_targets(
-    targets, involucro_context=None,
-    command="build", channels=DEFAULT_CHANNELS, namespace="biocontainers",
-    test='true', test_files=None, image_build=None, name_override=None,
-    repository_template=DEFAULT_REPOSITORY_TEMPLATE, dry_run=False,
-    conda_version=None, verbose=False, binds=DEFAULT_BINDS, rebuild=True,
-    oauth_token=None, hash_func="v2", singularity=False,
-    singularity_image_dir="singularity_import", base_image=None,
+    targets,
+    involucro_context=None,
+    command="build",
+    channels=DEFAULT_CHANNELS,
+    namespace="biocontainers",
+    test="true",
+    test_files=None,
+    image_build=None,
+    name_override=None,
+    repository_template=DEFAULT_REPOSITORY_TEMPLATE,
+    dry_run=False,
+    conda_version=None,
+    verbose=False,
+    binds=DEFAULT_BINDS,
+    rebuild=True,
+    oauth_token=None,
+    hash_func="v2",
+    singularity=False,
+    singularity_image_dir="singularity_import",
+    base_image=None,
     determine_base_image=True,
 ):
     targets = list(targets)
@@ -196,7 +218,7 @@ def mull_targets(
 
     repo_template_kwds = {
         "namespace": namespace,
-        "image": image_function(targets, image_build=image_build, name_override=name_override)
+        "image": image_function(targets, image_build=image_build, name_override=name_override),
     }
     repo = string.Template(repository_template).safe_substitute(repo_template_kwds)
 
@@ -219,19 +241,24 @@ def mull_targets(
             create_repository(repo_template_kwds["namespace"], repo_name, oauth_token)
 
     for channel in channels:
-        if channel.startswith('file://'):
+        if channel.startswith("file://"):
             bind_path = channel[7:]
-            binds.append(f'/{bind_path}:/{bind_path}')
+            binds.append(f"/{bind_path}:/{bind_path}")
 
     channels = ",".join(channels)
     target_str = ",".join(map(conda_build_target_str, targets))
     bind_str = ",".join(binds)
     involucro_args = [
-        '-f', f'{DIRNAME}/invfile.lua',
-        '-set', f"CHANNELS={channels}",
-        '-set', f"TARGETS={target_str}",
-        '-set', f"REPO={repo}",
-        '-set', f"BINDS={bind_str}",
+        "-f",
+        f"{DIRNAME}/invfile.lua",
+        "-set",
+        f"CHANNELS={channels}",
+        "-set",
+        f"TARGETS={target_str}",
+        "-set",
+        f"REPO={repo}",
+        "-set",
+        f"BINDS={bind_str}",
     ]
     dest_base_image = None
     if base_image:
@@ -248,7 +275,7 @@ def mull_targets(
     if verbose:
         involucro_args.extend(["-set", "VERBOSE=1"])
     if singularity:
-        singularity_image_name = repo_template_kwds['image']
+        singularity_image_name = repo_template_kwds["image"]
         involucro_args.extend(["-set", "SINGULARITY=1"])
         involucro_args.extend(["-set", f"SINGULARITY_IMAGE_NAME={singularity_image_name}"])
         involucro_args.extend(["-set", f"SINGULARITY_IMAGE_DIR={singularity_image_dir}"])
@@ -262,14 +289,14 @@ def mull_targets(
     if test_files:
         test_bind = []
         for test_file in test_files:
-            if ':' not in test_file:
+            if ":" not in test_file:
                 if os.path.exists(test_file):
                     test_bind.append(f"{test_file}:{DEFAULT_WORKING_DIR}/{test_file}")
             else:
-                if os.path.exists(test_file.split(':')[0]):
+                if os.path.exists(test_file.split(":")[0]):
                     test_bind.append(test_file)
         if test_bind:
-            involucro_args.insert(6, '-set')
+            involucro_args.insert(6, "-set")
             involucro_args.insert(7, f"TEST_BINDS={','.join(test_bind)}")
     cmd = involucro_context.build_command(involucro_args)
     print(f"Executing: {' '.join(shlex.quote(_) for _ in cmd)}")
@@ -279,8 +306,11 @@ def mull_targets(
     if singularity:
         if not os.path.exists(singularity_image_dir):
             safe_makedirs(singularity_image_dir)
-        with open(os.path.join(singularity_image_dir, 'Singularity.def'), 'w+') as sin_def:
-            fill_template = SINGULARITY_TEMPLATE % {'container_test': test, 'base_image': dest_base_image or DEFAULT_BASE_IMAGE}
+        with open(os.path.join(singularity_image_dir, "Singularity.def"), "w+") as sin_def:
+            fill_template = SINGULARITY_TEMPLATE % {
+                "container_test": test,
+                "base_image": dest_base_image or DEFAULT_BASE_IMAGE,
+            }
             sin_def.write(fill_template)
     with PrintProgress():
         ret = involucro_context.exec_command(involucro_args)
@@ -297,15 +327,14 @@ def context_from_args(args):
 
 
 class CondaInDockerContext:
-
     @property
     def conda_exec(self):
-        conda_image = CONDA_IMAGE or 'continuumio/miniconda3:latest'
-        return docker_command_list('run', [conda_image, 'conda'])
+        conda_image = CONDA_IMAGE or "continuumio/miniconda3:latest"
+        return docker_command_list("run", [conda_image, "conda"])
 
     @property
     def _override_channels_args(self):
-        override_channels_args = ['--override-channels']
+        override_channels_args = ["--override-channels"]
         for channel in DEFAULT_CHANNELS:
             override_channels_args.extend(["--channel", channel])
         return override_channels_args
@@ -333,15 +362,15 @@ class InvolucroContext(installable.InstallableContext):
         cmd = self.build_command(involucro_args)
         # Create ./build dir manually, otherwise Docker will do it as root
         created_build_dir = False
-        if not os.path.exists('build'):
+        if not os.path.exists("build"):
             created_build_dir = True
-            os.mkdir('./build')
+            os.mkdir("./build")
         try:
             res = self.shell_exec(cmd)
         finally:
             # delete build directory in any case
             if created_build_dir:
-                shutil.rmtree('./build')
+                shutil.rmtree("./build")
         return res
 
     def is_installed(self):
@@ -376,35 +405,61 @@ def install_involucro(involucro_context):
 
 def add_build_arguments(parser):
     """Base arguments describing how to 'mull'."""
-    parser.add_argument('--involucro-path', dest="involucro_path", default=None,
-                        help="Path to involucro (if not set will look in working directory and on PATH).")
-    parser.add_argument('--dry-run', dest='dry_run', action="store_true",
-                        help='Just print commands instead of executing them.')
-    parser.add_argument('--verbose', dest='verbose', action="store_true",
-                        help='Cause process to be verbose.')
-    parser.add_argument('--singularity', action="store_true",
-                        help='Additionally build a singularity image.')
-    parser.add_argument('--singularity-image-dir', dest="singularity_image_dir",
-                        help="Directory to write singularity images too.")
-    parser.add_argument('-n', '--namespace', dest='namespace', default="biocontainers",
-                        help='quay.io namespace.')
-    parser.add_argument('-r', '--repository_template', dest='repository_template', default=DEFAULT_REPOSITORY_TEMPLATE,
-                        help='Docker repository target for publication (only quay.io or compat. API is currently supported).')
-    parser.add_argument('-c', '--channels', dest='channels', default=",".join(DEFAULT_CHANNELS),
-                        help='Comma separated list of target conda channels.')
-    parser.add_argument('--conda-version', dest="conda_version", default=None,
-                        help="Change to specified version of Conda before installing packages.")
-    parser.add_argument('--oauth-token', dest="oauth_token", default=None,
-                        help="If set, use this token when communicating with quay.io API.")
-    parser.add_argument('--check-published', dest="rebuild", action='store_false')
-    parser.add_argument('--hash', dest="hash", choices=["v1", "v2"], default="v2")
+    parser.add_argument(
+        "--involucro-path",
+        dest="involucro_path",
+        default=None,
+        help="Path to involucro (if not set will look in working directory and on PATH).",
+    )
+    parser.add_argument(
+        "--dry-run", dest="dry_run", action="store_true", help="Just print commands instead of executing them."
+    )
+    parser.add_argument("--verbose", dest="verbose", action="store_true", help="Cause process to be verbose.")
+    parser.add_argument("--singularity", action="store_true", help="Additionally build a singularity image.")
+    parser.add_argument(
+        "--singularity-image-dir", dest="singularity_image_dir", help="Directory to write singularity images too."
+    )
+    parser.add_argument("-n", "--namespace", dest="namespace", default="biocontainers", help="quay.io namespace.")
+    parser.add_argument(
+        "-r",
+        "--repository_template",
+        dest="repository_template",
+        default=DEFAULT_REPOSITORY_TEMPLATE,
+        help="Docker repository target for publication (only quay.io or compat. API is currently supported).",
+    )
+    parser.add_argument(
+        "-c",
+        "--channels",
+        dest="channels",
+        default=",".join(DEFAULT_CHANNELS),
+        help="Comma separated list of target conda channels.",
+    )
+    parser.add_argument(
+        "--conda-version",
+        dest="conda_version",
+        default=None,
+        help="Change to specified version of Conda before installing packages.",
+    )
+    parser.add_argument(
+        "--oauth-token",
+        dest="oauth_token",
+        default=None,
+        help="If set, use this token when communicating with quay.io API.",
+    )
+    parser.add_argument("--check-published", dest="rebuild", action="store_false")
+    parser.add_argument("--hash", dest="hash", choices=["v1", "v2"], default="v2")
 
 
 def add_single_image_arguments(parser):
-    parser.add_argument("--name-override", dest="name_override", default=None,
-                        help="Override mulled image name - this is not recommended since metadata will not be detectable from the name of resulting images")
-    parser.add_argument("--image-build", dest="image_build", default=None,
-                        help="Build a versioned variant of this image.")
+    parser.add_argument(
+        "--name-override",
+        dest="name_override",
+        default=None,
+        help="Override mulled image name - this is not recommended since metadata will not be detectable from the name of resulting images",
+    )
+    parser.add_argument(
+        "--image-build", dest="image_build", default=None, help="Build a versioned variant of this image."
+    )
 
 
 def target_str_to_targets(targets_raw):
@@ -413,9 +468,9 @@ def target_str_to_targets(targets_raw):
             package_name, version = target_str.split("=", 1)
             build = None
             if "=" in version:
-                version, build = version.split('=')
+                version, build = version.split("=")
             elif "--" in version:
-                version, build = version.split('--')
+                version, build = version.split("--")
             target = build_target(package_name, version, build)
         else:
             target = build_target(target_str)
@@ -443,7 +498,7 @@ def args_to_mull_targets_kwds(args):
         if args.test_files:
             kwds["test_files"] = args.test_files.split(",")
     if hasattr(args, "channels"):
-        kwds["channels"] = args.channels.split(',')
+        kwds["channels"] = args.channels.split(",")
     if hasattr(args, "command"):
         kwds["command"] = args.command
     if hasattr(args, "repository_template"):
@@ -469,19 +524,29 @@ def main(argv=None):
     parser = arg_parser(argv, globals())
     add_build_arguments(parser)
     add_single_image_arguments(parser)
-    parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)')
-    parser.add_argument('targets', metavar="TARGETS", default=None, help="Build a single container with specific package(s).")
-    parser.add_argument('--repository-name', dest="repository_name", default=None, help="Name of mulled container (leave blank to auto-generate based on packages - recommended).")
-    parser.add_argument('--test', help='Provide a test command for the container.')
-    parser.add_argument('--test-files', help='Provide test-files that may be required to run the test command. Individual mounts are separated by comma.'
-                                             'The source:dest docker syntax is respected. If relative file paths are given, files will be mounted in /source/<relative_file_path>')
+    parser.add_argument("command", metavar="COMMAND", help="Command (build-and-test, build, all)")
+    parser.add_argument(
+        "targets", metavar="TARGETS", default=None, help="Build a single container with specific package(s)."
+    )
+    parser.add_argument(
+        "--repository-name",
+        dest="repository_name",
+        default=None,
+        help="Name of mulled container (leave blank to auto-generate based on packages - recommended).",
+    )
+    parser.add_argument("--test", help="Provide a test command for the container.")
+    parser.add_argument(
+        "--test-files",
+        help="Provide test-files that may be required to run the test command. Individual mounts are separated by comma."
+        "The source:dest docker syntax is respected. If relative file paths are given, files will be mounted in /source/<relative_file_path>",
+    )
     args = parser.parse_args()
     targets = target_str_to_targets(args.targets)
     sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))
 
 
-__all__ = ("main", )
+__all__ = ("main",)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py
index f610567feab..56a567dcf9f 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py
@@ -33,21 +33,27 @@ from .mulled_build import (
     get_affected_packages,
     mull_targets,
 )
-from .util import quay_versions, version_sorted
+from .util import (
+    quay_versions,
+    version_sorted,
+)
 
 
 def _fetch_repo_data(args):
     repo_data = args.repo_data
     channel = args.channel
     if not os.path.exists(repo_data):
-        platform_tag = 'osx-64' if sys.platform == 'darwin' else 'linux-64'
-        subprocess.check_call([
-            'wget', '--quiet', f'https://conda.anaconda.org/{channel}/{platform_tag}/repodata.json.bz2',
-            '-O', f'{repo_data}.bz2'
-        ])
-        subprocess.check_call([
-            'bzip2', '-d', f'{repo_data}.bz2'
-        ])
+        platform_tag = "osx-64" if sys.platform == "darwin" else "linux-64"
+        subprocess.check_call(
+            [
+                "wget",
+                "--quiet",
+                f"https://conda.anaconda.org/{channel}/{platform_tag}/repodata.json.bz2",
+                "-O",
+                f"{repo_data}.bz2",
+            ]
+        )
+        subprocess.check_call(["bzip2", "-d", f"{repo_data}.bz2"])
     return repo_data
 
 
@@ -82,18 +88,27 @@ def run_channel(args, build_last_n_versions=1):
 
 def get_pkg_names(args):
     """Print package names that would be affected."""
-    print('\n'.join(pkg_name for pkg_name, pkg_tests in get_affected_packages(args)))
+    print("\n".join(pkg_name for pkg_name, pkg_tests in get_affected_packages(args)))
 
 
 def add_channel_arguments(parser):
     """Add arguments only used if running mulled over a whole conda channel."""
-    parser.add_argument('--repo-data', dest='repo_data', required=True,
-                        help='Published repository data. If you want to build all containers for bioconda, this parameter needs to be set to "bioconda"')
-    parser.add_argument('--diff-hours', dest='diff_hours', default="25",
-                        help='If finding all recently changed recipes, use this number of hours.')
-    parser.add_argument('--recipes-dir', dest="recipes_dir", default="./bioconda-recipes")
-    parser.add_argument('--force-rebuild', dest="force_rebuild", action="store_true",
-                        help="Rebuild package even if already published.")
+    parser.add_argument(
+        "--repo-data",
+        dest="repo_data",
+        required=True,
+        help='Published repository data. If you want to build all containers for bioconda, this parameter needs to be set to "bioconda"',
+    )
+    parser.add_argument(
+        "--diff-hours",
+        dest="diff_hours",
+        default="25",
+        help="If finding all recently changed recipes, use this number of hours.",
+    )
+    parser.add_argument("--recipes-dir", dest="recipes_dir", default="./bioconda-recipes")
+    parser.add_argument(
+        "--force-rebuild", dest="force_rebuild", action="store_true", help="Rebuild package even if already published."
+    )
 
 
 def main(argv=None):
@@ -101,9 +116,16 @@ def main(argv=None):
     parser = arg_parser(argv, globals())
     add_channel_arguments(parser)
     add_build_arguments(parser)
-    parser.add_argument('command', metavar='COMMAND', help='Command (list, build-and-test, build, all)')
-    parser.add_argument('--targets', dest="targets", default=None, help="Build a single container with specific package(s).")
-    parser.add_argument('--repository-name', dest="repository_name", default=None, help="Name of a single container (leave blank to auto-generate based on packages).")
+    parser.add_argument("command", metavar="COMMAND", help="Command (list, build-and-test, build, all)")
+    parser.add_argument(
+        "--targets", dest="targets", default=None, help="Build a single container with specific package(s)."
+    )
+    parser.add_argument(
+        "--repository-name",
+        dest="repository_name",
+        default=None,
+        help="Name of a single container (leave blank to auto-generate based on packages).",
+    )
     args = parser.parse_args()
     if args.command == "list":
         get_pkg_names(args)
@@ -111,8 +133,8 @@ def main(argv=None):
         run_channel(args)
 
 
-__all__ = ("main", )
+__all__ = ("main",)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_files.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_files.py
index 8f436503f3a..9cbfff1c6df 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build_files.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_files.py
@@ -25,6 +25,7 @@ from .mulled_build import (
     mull_targets,
     target_str_to_targets,
 )
+
 KNOWN_FIELDS = ["targets", "image_build", "name_override", "base_image"]
 FALLBACK_LINE_TUPLE = collections.namedtuple("FALLBACK_LINE_TUPLE", "targets image_build name_override base_image")
 
@@ -33,9 +34,13 @@ def main(argv=None):
     """Main entry-point for the CLI tool."""
     parser = arg_parser(argv, globals())
     add_build_arguments(parser)
-    parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)')
-    parser.add_argument('files', metavar="FILES", default=".",
-                        help="Path to directory (or single file) of TSV files describing composite recipes.")
+    parser.add_argument("command", metavar="COMMAND", help="Command (build-and-test, build, all)")
+    parser.add_argument(
+        "files",
+        metavar="FILES",
+        default=".",
+        help="Path to directory (or single file) of TSV files describing composite recipes.",
+    )
     args = parser.parse_args()
     for target in generate_targets(args.files):
         try:
@@ -45,7 +50,7 @@ def main(argv=None):
                 name_override=target.name_override,
                 base_image=target.base_image,
                 determine_base_image=False,
-                **args_to_mull_targets_kwds(args)
+                **args_to_mull_targets_kwds(args),
             )
         except BuildExistsException:
             continue
@@ -69,7 +74,7 @@ def generate_targets(target_source):
             for line in f.readlines():
                 if line:
                     line = line.strip()
-                    if line.startswith('#'):
+                    if line.startswith("#"):
                         # headers can define a different column order
                         line_tuple = tuple_from_header(line)
                     else:
@@ -77,7 +82,7 @@ def generate_targets(target_source):
 
 
 def tuple_from_header(header):
-    fields = header[1:].split('\t')
+    fields = header[1:].split("\t")
     for field in fields:
         assert field in KNOWN_FIELDS, f"'{field}' is not one of {KNOWN_FIELDS}"
     # Make sure tuple contains all fields
@@ -91,15 +96,17 @@ def line_to_targets(line_str, line_tuple):
     """Parse a line so that some columns can remain unspecified."""
     line_parts = line_str.split("\t")
     n_fields = len(line_tuple._fields)
-    targets_column = line_tuple._fields.index('targets')
-    assert len(line_parts) <= n_fields, f"Too many fields in line [{line_str}], expect at most {n_fields} - targets, image build number, and name override."
+    targets_column = line_tuple._fields.index("targets")
+    assert (
+        len(line_parts) <= n_fields
+    ), f"Too many fields in line [{line_str}], expect at most {n_fields} - targets, image build number, and name override."
     line_parts += [None] * (n_fields - len(line_parts))
     line_parts[targets_column] = target_str_to_targets(line_parts[targets_column])
     return line_tuple(*line_parts)
 
 
-__all__ = ("main", )
+__all__ = ("main",)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
index a5fd21bf284..1c2d23a538a 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
@@ -25,8 +25,8 @@ def main(argv=None):
     parser = arg_parser(argv, globals())
     add_build_arguments(parser)
     add_single_image_arguments(parser)
-    parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)')
-    parser.add_argument('tool', metavar="TOOL", default=None, help="Path to tool to build mulled image for.")
+    parser.add_argument("command", metavar="COMMAND", help="Command (build-and-test, build, all)")
+    parser.add_argument("tool", metavar="TOOL", default=None, help="Path to tool to build mulled image for.")
     args = parser.parse_args()
     tool_source = get_tool_source(args.tool)
     requirements, _ = tool_source.parse_requirements_and_containers()
@@ -48,5 +48,5 @@ def requirements_to_mulled_targets(requirements):
 __all__ = ("main", "requirements_to_mulled_targets")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_hash.py b/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
index 186e8853aa3..691e4ab7e74 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
@@ -19,15 +19,17 @@ from .util import (
 def main(argv=None):
     """Main entry-point for the CLI tool."""
     parser = arg_parser(argv, globals())
-    parser.add_argument('targets', metavar="TARGETS", default=None, help="Comma-separated packages for calculating the mulled hash.")
-    parser.add_argument('--hash', dest="hash", choices=["v1", "v2"], default="v2")
+    parser.add_argument(
+        "targets", metavar="TARGETS", default=None, help="Comma-separated packages for calculating the mulled hash."
+    )
+    parser.add_argument("--hash", dest="hash", choices=["v1", "v2"], default="v2")
     args = parser.parse_args()
     targets = target_str_to_targets(args.targets)
-    image_name = v2_image_name if args.hash == 'v2' else v1_image_name
+    image_name = v2_image_name if args.hash == "v2" else v1_image_name
     print(image_name(targets))
 
 
-__all__ = ("main", )
+__all__ = ("main",)
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_list.py b/lib/galaxy/tool_util/deps/mulled/mulled_list.py
index c046d6530bf..00e892fbd64 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_list.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_list.py
@@ -9,28 +9,25 @@ import requests
 
 from .util import MULLED_SOCKET_TIMEOUT
 
-QUAY_API_ENDPOINT = 'https://quay.io/api/v1/repository'
+QUAY_API_ENDPOINT = "https://quay.io/api/v1/repository"
 
 
-def get_quay_containers(repository='biocontainers'):
+def get_quay_containers(repository="biocontainers"):
     """
     Get all quay containers in the biocontainers repo
     """
     containers = []
 
-    repos_parameters = {'public': 'true', 'namespace': repository}
-    repos_headers = {'Accept-encoding': 'gzip', 'Accept': 'application/json'}
-    repos_response = requests.get(
-        QUAY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=12)
+    repos_parameters = {"public": "true", "namespace": repository}
+    repos_headers = {"Accept-encoding": "gzip", "Accept": "application/json"}
+    repos_response = requests.get(QUAY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=12)
 
-    repos = repos_response.json()['repositories']
+    repos = repos_response.json()["repositories"]
 
     for repo in repos:
         logging.info(repo)
-        tags_response = requests.get(
-            f"{QUAY_API_ENDPOINT}/{repository}/{repo['name']}",
-            timeout=MULLED_SOCKET_TIMEOUT)
-        tags = tags_response.json()['tags']
+        tags_response = requests.get(f"{QUAY_API_ENDPOINT}/{repository}/{repo['name']}", timeout=MULLED_SOCKET_TIMEOUT)
+        tags = tags_response.json()["tags"]
         for tag in tags:
             containers.append(f"{repo['name']}:{tag}")
 
@@ -41,6 +38,7 @@ def get_singularity_containers():
     """
     Get all existing singularity containers from "https://depot.galaxyproject.org/singularity/"
     """
+
     class GetContainerNames(HTMLParser):  # small parser which gets list of containers
         def __init__(self):
             HTMLParser.__init__(self)
@@ -49,8 +47,8 @@ def get_singularity_containers():
         def handle_starttag(self, tag, attrs):
             try:
                 for attr in attrs:
-                    if attr[0] == 'href' and attr[1] != '../':
-                        self.containers.append(attr[1].replace('%3A', ':'))
+                    if attr[0] == "href" and attr[1] != "../":
+                        self.containers.append(attr[1].replace("%3A", ":"))
             except IndexError:
                 pass
 
@@ -64,7 +62,7 @@ def get_conda_envs(filepath):
     """
     Get list of already existing envs
     """
-    return [n.split('__')[-1].replace('@', ':') for n in glob(f'{filepath}/*')]
+    return [n.split("__")[-1].replace("@", ":") for n in glob(f"{filepath}/*")]
 
 
 def get_missing_containers(quay_list, singularity_list, blocklist_file=None):
@@ -74,7 +72,7 @@ def get_missing_containers(quay_list, singularity_list, blocklist_file=None):
     blocklist = []
     if blocklist_file:
         with open(blocklist_file) as fh:
-            blocklist = fh.read().split('\n')
+            blocklist = fh.read().split("\n")
     return [n for n in quay_list if n not in singularity_list and n not in blocklist]
 
 
@@ -85,52 +83,73 @@ def get_missing_envs(quay_list, conda_list, blocklist_file=None):
     blocklist = []
     if blocklist_file:
         with open(blocklist_file) as fh:
-            blocklist = fh.read().split('\n')
+            blocklist = fh.read().split("\n")
 
-    return [n for n in quay_list if n.split('--')[0] not in conda_list and n.split('--')[0] not in blocklist]
+    return [n for n in quay_list if n.split("--")[0] not in conda_list and n.split("--")[0] not in blocklist]
 
 
 def main():
     parser = argparse.ArgumentParser(
-        description='Returns list of Docker containers in the quay.io biocontainers repository.')
-    parser.add_argument('--source', '-s',
-                        help="Docker, Singularity or Conda.")
-    parser.add_argument('--not-singularity', dest='not_singularity', action="store_true",
-                        help="Exclude Docker containers from which Singularity containers have already been built.")
-    parser.add_argument('--not-conda', dest='not_conda', action="store_true",
-                        help="Exclude Docker containers from which Conda environments have already been extracted.")
-    parser.add_argument('--conda-filepath', dest='conda_filepath', default=None,
-                        help="If searching for conda environments or employing the --not-conda option, a filepath where the environments are located.")
-    parser.add_argument('-b', '--blocklist', '--blacklist', dest='blocklist', default=None,
-                        help="Provide a 'blocklist file' containing containers which should be excluded from the list.")
-    parser.add_argument('-f', '--file', dest='output', default=None,
-                        help="File to write list to. If not given output will be returned on the command line.")
+        description="Returns list of Docker containers in the quay.io biocontainers repository."
+    )
+    parser.add_argument("--source", "-s", help="Docker, Singularity or Conda.")
+    parser.add_argument(
+        "--not-singularity",
+        dest="not_singularity",
+        action="store_true",
+        help="Exclude Docker containers from which Singularity containers have already been built.",
+    )
+    parser.add_argument(
+        "--not-conda",
+        dest="not_conda",
+        action="store_true",
+        help="Exclude Docker containers from which Conda environments have already been extracted.",
+    )
+    parser.add_argument(
+        "--conda-filepath",
+        dest="conda_filepath",
+        default=None,
+        help="If searching for conda environments or employing the --not-conda option, a filepath where the environments are located.",
+    )
+    parser.add_argument(
+        "-b",
+        "--blocklist",
+        "--blacklist",
+        dest="blocklist",
+        default=None,
+        help="Provide a 'blocklist file' containing containers which should be excluded from the list.",
+    )
+    parser.add_argument(
+        "-f",
+        "--file",
+        dest="output",
+        default=None,
+        help="File to write list to. If not given output will be returned on the command line.",
+    )
 
     args = parser.parse_args()
 
-    if args.source == 'docker':
+    if args.source == "docker":
         containers = get_quay_containers()
         if args.not_singularity:
-            containers = get_missing_containers(
-                containers, get_singularity_containers(), args.blocklist)
+            containers = get_missing_containers(containers, get_singularity_containers(), args.blocklist)
         if args.not_conda:
-            containers = get_missing_envs(containers, get_conda_envs(
-                args.conda_filepath), args.blocklist)
-    elif args.source == 'singularity':
+            containers = get_missing_envs(containers, get_conda_envs(args.conda_filepath), args.blocklist)
+    elif args.source == "singularity":
         containers = get_singularity_containers()
-    elif args.source == 'conda':
+    elif args.source == "conda":
         containers = get_conda_envs(args.conda_filepath)
     else:
         print("The 'source' argument was not understood.")
         return
 
     if args.output:
-        with open(args.output, 'a') as f:
+        with open(args.output, "a") as f:
             for container in containers:
-                f.write(f'{container}\n')
+                f.write(f"{container}\n")
     else:
         print(containers)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_search.py b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
index dd9606d600e..e2c1ccc6880 100755
--- a/lib/galaxy/tool_util/deps/mulled/mulled_search.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
@@ -21,18 +21,20 @@ except ImportError:
     run_command = None
 
 try:
-    from whoosh.fields import Schema
-    from whoosh.fields import TEXT
-    from whoosh.fields import STORED
+    from whoosh.fields import (
+        Schema,
+        STORED,
+        TEXT,
+    )
     from whoosh.index import create_in
     from whoosh.qparser import QueryParser
 except ImportError:
     Schema = TEXT = STORED = create_in = QueryParser = None
 
-QUAY_API_URL = 'https://quay.io/api/v1/repository'
+QUAY_API_URL = "https://quay.io/api/v1/repository"
 
 
-class QuaySearch():
+class QuaySearch:
     """
     Tool to search within a quay organization for a given software name.
     """
@@ -48,9 +50,10 @@ class QuaySearch():
         # download all information about the repositories from the
         # given organization in self.organization
 
-        parameters = {'public': 'true', 'namespace': self.organization}
-        r = requests.get(QUAY_API_URL, headers={
-                         'Accept-encoding': 'gzip'}, params=parameters, timeout=MULLED_SOCKET_TIMEOUT)
+        parameters = {"public": "true", "namespace": self.organization}
+        r = requests.get(
+            QUAY_API_URL, headers={"Accept-encoding": "gzip"}, params=parameters, timeout=MULLED_SOCKET_TIMEOUT
+        )
         tmp_dir = tempfile.mkdtemp()
         schema = Schema(title=TEXT(stored=True), content=STORED)
         self.index = create_in(tmp_dir, schema)
@@ -58,9 +61,8 @@ class QuaySearch():
         json_decoder = json.JSONDecoder()
         decoded_request = json_decoder.decode(r.text)
         writer = self.index.writer()
-        for repository in decoded_request['repositories']:
-            writer.add_document(
-                title=repository['name'], content=repository['description'])
+        for repository in decoded_request["repositories"]:
+            writer.add_document(title=repository["name"], content=repository["description"])
         writer.commit()
 
     def search_repository(self, search_string, non_strict):
@@ -71,8 +73,7 @@ class QuaySearch():
         """
         # with statement closes searcher after usage.
         with self.index.searcher() as searcher:
-            query = QueryParser(
-                "title", self.index.schema).parse(search_string)
+            query = QueryParser("title", self.index.schema).parse(search_string)
             results = searcher.search(query)
             if non_strict:
                 # look for spelling errors and use suggestions as a search term too
@@ -82,17 +83,21 @@ class QuaySearch():
                 # get all repositories with suggested keywords
                 for suggestion in suggestions:
                     search_string = f"*{suggestion}*"
-                    query = QueryParser(
-                        "title", self.index.schema).parse(search_string)
+                    query = QueryParser("title", self.index.schema).parse(search_string)
                     results_tmp = searcher.search(query)
                     results.extend(results_tmp)
 
             out = list()
 
             for result in results:
-                title = result['title']
+                title = result["title"]
                 for version in self.get_additional_repository_information(title):
-                    out.append({'package': title, 'version': version, })
+                    out.append(
+                        {
+                            "package": title,
+                            "version": version,
+                        }
+                    )
 
             return out
 
@@ -102,14 +107,14 @@ class QuaySearch():
         get the tag-field which includes the version number.
         """
         url = f"{QUAY_API_URL}/{self.organization}/{repository_string}"
-        r = requests.get(url, headers={'Accept-encoding': 'gzip'}, timeout=MULLED_SOCKET_TIMEOUT)
+        r = requests.get(url, headers={"Accept-encoding": "gzip"}, timeout=MULLED_SOCKET_TIMEOUT)
 
         json_decoder = json.JSONDecoder()
         decoded_request = json_decoder.decode(r.text)
-        return decoded_request['tags']
+        return decoded_request["tags"]
 
 
-class CondaSearch():
+class CondaSearch:
     """
     Tool to search the bioconda channel
     """
@@ -124,18 +129,16 @@ class CondaSearch():
         """
         if run_command is None:
             raise Exception(f"Invalid search destination. {deps_error_message('conda')}")
-        raw_out, err, exit_code = run_command(
-            'search', '-c',
-            self.channel,
-            search_string,
-            use_exception_handler=True)
+        raw_out, err, exit_code = run_command("search", "-c", self.channel, search_string, use_exception_handler=True)
         if exit_code != 0:
-            logging.info(f'Search failed with: {err}')
+            logging.info(f"Search failed with: {err}")
             return []
-        return [{'package': n.split()[0], 'version': n.split()[1], 'build': n.split()[2]} for n in raw_out.split('\n')[2:-1]]
+        return [
+            {"package": n.split()[0], "version": n.split()[1], "build": n.split()[2]} for n in raw_out.split("\n")[2:-1]
+        ]
 
 
-class GitHubSearch():
+class GitHubSearch:
     """
     Tool to search the GitHub bioconda-recipes repo
     """
@@ -145,7 +148,9 @@ class GitHubSearch():
         Takes search_string variable and return results from the bioconda-recipes github repository in JSON format
         """
         response = requests.get(
-            f"https://api.github.com/search/code?q={search_string}+in:path+repo:bioconda/bioconda-recipes+path:recipes", timeout=MULLED_SOCKET_TIMEOUT)
+            f"https://api.github.com/search/code?q={search_string}+in:path+repo:bioconda/bioconda-recipes+path:recipes",
+            timeout=MULLED_SOCKET_TIMEOUT,
+        )
         response.raise_for_status()
         return response.json()
 
@@ -153,14 +158,17 @@ class GitHubSearch():
         """
         Take JSON input and process it, returning the required data
         """
-        top_10_items = json_response['items'][0:10]  # get top ten results
-        return [{'name': result['name'], 'path': result['path']} for result in top_10_items]
+        top_10_items = json_response["items"][0:10]  # get top ten results
+        return [{"name": result["name"], "path": result["path"]} for result in top_10_items]
 
     def recipe_present(self, search_string):
         """
         Check if a recipe exists in bioconda-recipes which matches search_string exactly
         """
-        response = requests.get(f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{search_string}", timeout=MULLED_SOCKET_TIMEOUT)
+        response = requests.get(
+            f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{search_string}",
+            timeout=MULLED_SOCKET_TIMEOUT,
+        )
         return response.status_code == 200
 
 
@@ -178,22 +186,24 @@ def get_package_hash(packages, versions):
             targets.append(build_target(p))
     # make the hash from the processed targets
     package_hash = v2_image_name(targets)
-    hash_results['package_hash'] = package_hash.split(':')[0]
+    hash_results["package_hash"] = package_hash.split(":")[0]
     if versions:
-        hash_results['version_hash'] = package_hash.split(':')[1]
+        hash_results["version_hash"] = package_hash.split(":")[1]
 
-    r = requests.get(f"https://quay.io/api/v1/repository/biocontainers/{hash_results['package_hash']}", timeout=MULLED_SOCKET_TIMEOUT)
+    r = requests.get(
+        f"https://quay.io/api/v1/repository/biocontainers/{hash_results['package_hash']}", timeout=MULLED_SOCKET_TIMEOUT
+    )
     if r.status_code == 200:
-        hash_results['container_present'] = True
+        hash_results["container_present"] = True
         if versions:  # now test if the version hash is listed in the repository tags
             # remove -0, -1, etc from end of the tag
-            tags = [n[:-2] for n in r.json()['tags']]
-            if hash_results['version_hash'] in tags:
-                hash_results['container_present_with_version'] = True
+            tags = [n[:-2] for n in r.json()["tags"]]
+            if hash_results["version_hash"] in tags:
+                hash_results["container_present_with_version"] = True
             else:
-                hash_results['container_present_with_version'] = False
+                hash_results["container_present_with_version"] = False
     else:
-        hash_results['container_present'] = False
+        hash_results["container_present"] = False
     return hash_results
 
 
@@ -207,78 +217,112 @@ def singularity_search(search_string):
 
     for container in containers:
         if search_string in container:
-            name = container.split(':')[0]
-            version = container.split(':')[1]
-            results.append({'package': name, 'version': version})
+            name = container.split(":")[0]
+            version = container.split(":")[1]
+            results.append({"package": name, "version": version})
 
     return results
 
 
-def readable_output(json, organization='biocontainers', channel='bioconda'):
+def readable_output(json, organization="biocontainers", channel="bioconda"):
 
     # if json is empty:
     if sum(len(json[destination][results]) for destination in json for results in json[destination]) == 0:
-        sys.stdout.write('No results found for that query.\n')
+        sys.stdout.write("No results found for that query.\n")
         return
 
     # return results for quay, conda and singularity together
-    if sum(len(json[destination][results]) for destination in ['quay', 'conda', 'singularity', ] for results in json.get(destination, [])) > 0:
+    if (
+        sum(
+            len(json[destination][results])
+            for destination in [
+                "quay",
+                "conda",
+                "singularity",
+            ]
+            for results in json.get(destination, [])
+        )
+        > 0
+    ):
         sys.stdout.write("The query returned the following result(s).\n")
         # put quay, conda etc results as lists in lines
-        lines = [['LOCATION', 'NAME', 'VERSION', 'COMMAND\n']]
-        for results in json.get('quay', {}).values():
+        lines = [["LOCATION", "NAME", "VERSION", "COMMAND\n"]]
+        for results in json.get("quay", {}).values():
             for result in results:
-                lines.append(['quay', result['package'], result['version'], 'docker pull quay.io/%s/%s:%s\n' %
-                              (organization, result['package'], result['version'])])  # NOT a real solution
-        for results in json.get('conda', {}).values():
+                lines.append(
+                    [
+                        "quay",
+                        result["package"],
+                        result["version"],
+                        "docker pull quay.io/%s/%s:%s\n" % (organization, result["package"], result["version"]),
+                    ]
+                )  # NOT a real solution
+        for results in json.get("conda", {}).values():
             for result in results:
-                lines.append(['conda', result['package'], f"{result['version']}--{result['build']}",
-                              f"conda install -c {channel} {result['package']}={result['version']}={result['build']}\n"])
-        for results in json.get('singularity', {}).values():
+                lines.append(
+                    [
+                        "conda",
+                        result["package"],
+                        f"{result['version']}--{result['build']}",
+                        f"conda install -c {channel} {result['package']}={result['version']}={result['build']}\n",
+                    ]
+                )
+        for results in json.get("singularity", {}).values():
             for result in results:
-                lines.append(['singularity', result['package'], result['version'],
-                              f"wget https://depot.galaxyproject.org/singularity/{result['package']}:{result['version']}\n"])
+                lines.append(
+                    [
+                        "singularity",
+                        result["package"],
+                        result["version"],
+                        f"wget https://depot.galaxyproject.org/singularity/{result['package']}:{result['version']}\n",
+                    ]
+                )
 
-        col_width0, col_width1, col_width2 = (max(len(
-            line[n]) for line in lines) + 2 for n in (0, 1, 2))  # def max col widths for the output
+        col_width0, col_width1, col_width2 = (
+            max(len(line[n]) for line in lines) + 2 for n in (0, 1, 2)
+        )  # def max col widths for the output
 
         # create table
         for line in lines:
-            sys.stdout.write("".join((line[0].ljust(col_width0), line[1].ljust(
-                col_width1), line[2].ljust(col_width2), line[3])))  # output
+            sys.stdout.write(
+                "".join((line[0].ljust(col_width0), line[1].ljust(col_width1), line[2].ljust(col_width2), line[3]))
+            )  # output
 
-    if json.get('github_recipe_present', False):
-        sys.stdout.write('\n' if 'lines' in locals() else '')
+    if json.get("github_recipe_present", False):
+        sys.stdout.write("\n" if "lines" in locals() else "")
         sys.stdout.write(
-            'The following recipes were found in the bioconda-recipes repository which exactly matched one of the search terms:\n')
-        lines = [['QUERY', 'LOCATION\n']]
-        for recipe in json['github_recipe_present']['recipes']:
+            "The following recipes were found in the bioconda-recipes repository which exactly matched one of the search terms:\n"
+        )
+        lines = [["QUERY", "LOCATION\n"]]
+        for recipe in json["github_recipe_present"]["recipes"]:
             lines.append(
-                [recipe, f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{recipe}\n"])
+                [recipe, f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{recipe}\n"]
+            )
 
         col_width0 = max(len(line[0]) for line in lines) + 2
 
         for line in lines:
-            sys.stdout.write(
-                "".join((line[0].ljust(col_width0), line[1])))  # output
+            sys.stdout.write("".join((line[0].ljust(col_width0), line[1])))  # output
 
-    if sum(len(json['github'][results]) for results in json.get('github', [])) > 0:
-        sys.stdout.write('\n' if 'lines' in locals() else '')
-        sys.stdout.write(
-            "Other result(s) on the bioconda-recipes GitHub repository:\n")
-        lines = [['QUERY', 'FILE', 'URL\n']]
-        for search_string, results in json.get('github', {}).items():
+    if sum(len(json["github"][results]) for results in json.get("github", [])) > 0:
+        sys.stdout.write("\n" if "lines" in locals() else "")
+        sys.stdout.write("Other result(s) on the bioconda-recipes GitHub repository:\n")
+        lines = [["QUERY", "FILE", "URL\n"]]
+        for search_string, results in json.get("github", {}).items():
             for result in results:
-                lines.append([search_string, result['name'],
-                              f"https://github.com/bioconda/bioconda-recipes/tree/master/{result['path']}\n"])
+                lines.append(
+                    [
+                        search_string,
+                        result["name"],
+                        f"https://github.com/bioconda/bioconda-recipes/tree/master/{result['path']}\n",
+                    ]
+                )
 
         # def max col widths for the output
-        col_width0, col_width1 = (
-            max(len(line[n]) for line in lines) + 2 for n in (0, 1))
+        col_width0, col_width1 = (max(len(line[n]) for line in lines) + 2 for n in (0, 1))
 
         for line in lines:
-            sys.stdout.write("".join(
-                (line[0].ljust(col_width0), line[1].ljust(col_width1), line[2])))  # output
+            sys.stdout.write("".join((line[0].ljust(col_width0), line[1].ljust(col_width1), line[2])))  # output
 
 
 def deps_error_message(package):
@@ -290,43 +334,59 @@ def main(argv=None):
         sys.stdout.write(deps_error_message("Whoosh"))
         return
 
-    destination_defaults = ['quay', 'singularity', 'github']
+    destination_defaults = ["quay", "singularity", "github"]
     if run_command is not None:
-        destination_defaults.append('conda')
+        destination_defaults.append("conda")
 
-    parser = argparse.ArgumentParser(
-        description='Searches in a given quay organization for a repository')
-    parser.add_argument('-d', '--destination', dest='search_dest', nargs='+', default=destination_defaults,
-                        help="Choose where to search. Options are 'conda', 'quay', 'singularity' and 'github'. If no option are given, all will be searched.")
-    parser.add_argument('-o', '--organization', dest='organization_string', default="biocontainers",
-                        help='Change quay organization to search; default is biocontainers.')
-    parser.add_argument('-c', '--channel', dest='channel_string', default="bioconda",
-                        help='Change conda channel to search; default is bioconda.')
-    parser.add_argument('--non-strict', dest='non_strict', action="store_true",
-                        help='Autocorrection of typos activated. Lists more results but can be confusing.\
-                        For too many queries quay.io blocks the request and the results can be incomplete.')
-    parser.add_argument('-j', '--json', dest='json',
-                        action="store_true", help='Returns results as JSON.')
-    parser.add_argument('-s', '--search', required=True, nargs='+',
-                        help='The name of the tool(s) to search for.')
+    parser = argparse.ArgumentParser(description="Searches in a given quay organization for a repository")
+    parser.add_argument(
+        "-d",
+        "--destination",
+        dest="search_dest",
+        nargs="+",
+        default=destination_defaults,
+        help="Choose where to search. Options are 'conda', 'quay', 'singularity' and 'github'. If no option are given, all will be searched.",
+    )
+    parser.add_argument(
+        "-o",
+        "--organization",
+        dest="organization_string",
+        default="biocontainers",
+        help="Change quay organization to search; default is biocontainers.",
+    )
+    parser.add_argument(
+        "-c",
+        "--channel",
+        dest="channel_string",
+        default="bioconda",
+        help="Change conda channel to search; default is bioconda.",
+    )
+    parser.add_argument(
+        "--non-strict",
+        dest="non_strict",
+        action="store_true",
+        help="Autocorrection of typos activated. Lists more results but can be confusing.\
+                        For too many queries quay.io blocks the request and the results can be incomplete.",
+    )
+    parser.add_argument("-j", "--json", dest="json", action="store_true", help="Returns results as JSON.")
+    parser.add_argument("-s", "--search", required=True, nargs="+", help="The name of the tool(s) to search for.")
 
     args = parser.parse_args()
     json_results = {dest: {} for dest in args.search_dest}
     versions = {}
 
     if len(args.search) > 1:  # get hash if multiple packages are searched
-        args.search.append(get_package_hash(
-            args.search, versions)['package_hash'])
+        args.search.append(get_package_hash(args.search, versions)["package_hash"])
 
-    if 'conda' in args.search_dest:
+    if "conda" in args.search_dest:
         conda_results = {}
         conda = CondaSearch(args.channel_string)
 
         for item in args.search:
             conda_results[item] = conda.get_json(item)
-        json_results['conda'] = conda_results
+        json_results["conda"] = conda_results
 
-    if 'github' in args.search_dest:
+    if "github" in args.search_dest:
         github_results = {}
         github_recipe_present = []
         github = GitHubSearch()
@@ -337,11 +397,10 @@ def main(argv=None):
             if github.recipe_present(item):
                 github_recipe_present.append(item)
 
-        json_results['github'] = github_results
-        json_results['github_recipe_present'] = {
-            'recipes': github_recipe_present}
+        json_results["github"] = github_results
+        json_results["github_recipe_present"] = {"recipes": github_recipe_present}
 
-    if 'quay' in args.search_dest:
+    if "quay" in args.search_dest:
         quay_results = {}
         quay = QuaySearch(args.organization_string)
         quay.build_index()
@@ -349,19 +408,18 @@ def main(argv=None):
         for item in args.search:
             quay_results[item] = quay.search_repository(item, args.non_strict)
 
-        json_results['quay'] = quay_results
+        json_results["quay"] = quay_results
 
-    if 'singularity' in args.search_dest:
+    if "singularity" in args.search_dest:
         singularity_results = {}
         for item in args.search:
             singularity_results[item] = singularity_search(item)
-        json_results['singularity'] = singularity_results
+        json_results["singularity"] = singularity_results
 
     if args.json:
         print(json_results)
     else:
-        readable_output(json_results, args.organization_string,
-                        args.channel_string)
+        readable_output(json_results, args.organization_string, args.channel_string)
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py b/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py
index 35ac039a60c..7fdacec2d14 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py
@@ -7,7 +7,10 @@ from glob import glob
 from subprocess import check_output
 
 from galaxy.util import unicodify
-from .get_tests import hashed_test_search, main_test_search
+from .get_tests import (
+    hashed_test_search,
+    main_test_search,
+)
 
 
 def get_list_from_file(filename):
@@ -22,13 +25,13 @@ def docker_to_singularity(container, installation, filepath, no_sudo=False):
     """
     Convert docker to singularity container.
     """
-    cmd = [installation, 'build', '/'.join((filepath, container)), f"docker://quay.io/biocontainers/{container}"]
+    cmd = [installation, "build", "/".join((filepath, container)), f"docker://quay.io/biocontainers/{container}"]
     try:
         if no_sudo:
             check_output(cmd, stderr=subprocess.STDOUT)
         else:
-            check_output(cmd.insert(0, 'sudo'), stderr=subprocess.STDOUT)
-            check_output(['sudo', 'rm', '-rf', '/root/.singularity/docker/'], stderr=subprocess.STDOUT)
+            check_output(cmd.insert(0, "sudo"), stderr=subprocess.STDOUT)
+            check_output(["sudo", "rm", "-rf", "/root/.singularity/docker/"], stderr=subprocess.STDOUT)
     except subprocess.CalledProcessError as e:
         raise Exception(f"Docker to Singularity conversion failed.\nOutput was:\n{unicodify(e.output)}")
 
@@ -37,65 +40,80 @@ def singularity_container_test(tests, installation, filepath):
     """
     Run tests, record if they pass or fail
     """
-    test_results = {'passed': [], 'failed': [], 'notest': []}
+    test_results = {"passed": [], "failed": [], "notest": []}
 
     # create a 'sanitised home' directory in which the containers may be mounted - see http://singularity.lbl.gov/faq#solution-1-specify-the-home-to-mount
     with tempfile.TemporaryDirectory() as tmpdirname:
         for container, test in tests.items():
-            if 'commands' not in test and 'imports' not in test:
-                test_results['notest'].append(container)
+            if "commands" not in test and "imports" not in test:
+                test_results["notest"].append(container)
 
             else:
-                exec_command = [installation, 'exec', '-H', tmpdirname, '/'.join((filepath, container))]
+                exec_command = [installation, "exec", "-H", tmpdirname, "/".join((filepath, container))]
                 test_passed = True
                 errors = []
-                if test.get('commands', False):
-                    for test_command in test['commands']:
-                        test_command = test_command.replace('$PREFIX', '/usr/local/')
-                        test_command = test_command.replace('${PREFIX}', '/usr/local/')
-                        test_command = test_command.replace('$R ', 'Rscript ')
+                if test.get("commands", False):
+                    for test_command in test["commands"]:
+                        test_command = test_command.replace("$PREFIX", "/usr/local/")
+                        test_command = test_command.replace("${PREFIX}", "/usr/local/")
+                        test_command = test_command.replace("$R ", "Rscript ")
 
                         try:
-                            check_output(exec_command.extend(['bash', '-c', test_command]), stderr=subprocess.STDOUT)
+                            check_output(exec_command.extend(["bash", "-c", test_command]), stderr=subprocess.STDOUT)
                         except subprocess.CalledProcessError:
                             try:
                                 check_output(exec_command.append(test_command), stderr=subprocess.STDOUT)
                             except subprocess.CalledProcessError as e:
-                                errors.append(
-                                    {'command': test_command, 'output': unicodify(e.output)})
+                                errors.append({"command": test_command, "output": unicodify(e.output)})
                                 test_passed = False
 
-                if test.get('imports', False):
-                    for imp in test['imports']:
+                if test.get("imports", False):
+                    for imp in test["imports"]:
                         try:
-                            check_output(exec_command.extend([test['import_lang'], f"import {imp}"]), stderr=subprocess.STDOUT)
+                            check_output(
+                                exec_command.extend([test["import_lang"], f"import {imp}"]), stderr=subprocess.STDOUT
+                            )
                         except subprocess.CalledProcessError as e:
-                            errors.append({'import': imp, 'output': unicodify(e.output)})
+                            errors.append({"import": imp, "output": unicodify(e.output)})
                             test_passed = False
 
                 if test_passed:
-                    test_results['passed'].append(container)
+                    test_results["passed"].append(container)
                 else:
-                    test['errors'] = errors
-                    test_results['failed'].append(test)
+                    test["errors"] = errors
+                    test_results["failed"].append(test)
     return test_results
 
 
 def main():
-    parser = argparse.ArgumentParser(
-        description='Updates index of singularity containers.')
-    parser.add_argument('-c', '--containers', dest='containers', nargs='+', default=None,
-                        help="Containers to be generated. If the number of containers is large, it may be simpler to use the --containers-list option.")
-    parser.add_argument('-l', '--container-list', dest='container_list', default=None,
-                        help="Name of file containing list of containers to be generated. Alternative to --containers.")
-    parser.add_argument('-f', '--filepath', dest='filepath',
-                        help="File path where newly-built Singularity containers are placed.")
-    parser.add_argument('-i', '--installation', dest='installation',
-                        help="File path of Singularity installation.")
-    parser.add_argument('--no-sudo', dest='no_sudo', action='store_true',
-                        help="Build containers without sudo.")
-    parser.add_argument('--testing', '-t', dest='testing', default=None,
-                        help="Performs testing automatically - a name for the output file should be provided. (Alternatively, testing may be done using the separate testing tool.")
+    parser = argparse.ArgumentParser(description="Updates index of singularity containers.")
+    parser.add_argument(
+        "-c",
+        "--containers",
+        dest="containers",
+        nargs="+",
+        default=None,
+        help="Containers to be generated. If the number of containers is large, it may be simpler to use the --containers-list option.",
+    )
+    parser.add_argument(
+        "-l",
+        "--container-list",
+        dest="container_list",
+        default=None,
+        help="Name of file containing list of containers to be generated. Alternative to --containers.",
+    )
+    parser.add_argument(
+        "-f", "--filepath", dest="filepath", help="File path where newly-built Singularity containers are placed."
+    )
+    parser.add_argument("-i", "--installation", dest="installation", help="File path of Singularity installation.")
+    parser.add_argument("--no-sudo", dest="no_sudo", action="store_true", help="Build containers without sudo.")
+    parser.add_argument(
+        "--testing",
+        "-t",
+        dest="testing",
+        default=None,
+        help="Performs testing automatically - a name for the output file should be provided. (Alternatively, testing may be done using the separate testing tool.",
+    )
 
     args = parser.parse_args()
 
@@ -108,70 +126,118 @@ def main():
         return
 
     for container in containers:
-        docker_to_singularity(container, args.installation,
-                              args.filepath, args.no_sudo)
+        docker_to_singularity(container, args.installation, args.filepath, args.no_sudo)
 
     if args.testing:
-        container_testing({'anaconda_channel': 'bioconda', 'installation': args.installation, 'filepath': args.filepath, 'github_repo': 'bioconda/bioconda-recipes',
-              'deep_search': False, 'github_local_path': None, 'logfile': args.testing, 'containers': containers})
+        container_testing(
+            {
+                "anaconda_channel": "bioconda",
+                "installation": args.installation,
+                "filepath": args.filepath,
+                "github_repo": "bioconda/bioconda-recipes",
+                "deep_search": False,
+                "github_local_path": None,
+                "logfile": args.testing,
+                "containers": containers,
+            }
+        )
 
 
 def container_testing(args=None):
     if not args:  # i.e. if testing is called directly from CLI and not via main()
-        parser = argparse.ArgumentParser(description='Tests.')
-        parser.add_argument('-c', '--containers', dest='containers', nargs='+', default=None,
-                            help="Containers to be tested. If the number of containers is large, it may be simpler to use the --containers-list option.")
-        parser.add_argument('-l', '--container-list', dest='container_list', default=None,
-                            help="Name of file containing list of containers to be tested. Alternative to --containers.")
-        parser.add_argument('-f', '--filepath', dest='filepath',
-                            help="File path where the containers to be tested are located.")
-        parser.add_argument('-o', '--logfile', dest='logfile', default='singularity.log',
-                            help="Filename for a log to be written to.")
-        parser.add_argument('-i', '--installation', dest='installation',
-                            help="File path of Singularity installation.")
-        parser.add_argument('--deep-search', dest='deep_search', action='store_true',
-                            help="Perform a more extensive, but probably slower, search for tests.")
-        parser.add_argument('--anaconda-channel', dest='anaconda_channel', default='bioconda',
-                            help="Anaconda channel to search for tests (default: bioconda).")
-        parser.add_argument('--github-repo', dest='github_repo', default='bioconda/bioconda-recipes',
-                            help="Github repository to search for tests - only relevant if --deep-search is activated (default: bioconda/bioconda-recipes")
-        parser.add_argument('--github-local-path', dest='github_local_path', default=None,
-                            help="If the bioconda-recipes repository (or other repository containing tests) is available locally, provide the path here. Only relevant if --deep-search is activated.")
+        parser = argparse.ArgumentParser(description="Tests.")
+        parser.add_argument(
+            "-c",
+            "--containers",
+            dest="containers",
+            nargs="+",
+            default=None,
+            help="Containers to be tested. If the number of containers is large, it may be simpler to use the --containers-list option.",
+        )
+        parser.add_argument(
+            "-l",
+            "--container-list",
+            dest="container_list",
+            default=None,
+            help="Name of file containing list of containers to be tested. Alternative to --containers.",
+        )
+        parser.add_argument(
+            "-f", "--filepath", dest="filepath", help="File path where the containers to be tested are located."
+        )
+        parser.add_argument(
+            "-o", "--logfile", dest="logfile", default="singularity.log", help="Filename for a log to be written to."
+        )
+        parser.add_argument("-i", "--installation", dest="installation", help="File path of Singularity installation.")
+        parser.add_argument(
+            "--deep-search",
+            dest="deep_search",
+            action="store_true",
+            help="Perform a more extensive, but probably slower, search for tests.",
+        )
+        parser.add_argument(
+            "--anaconda-channel",
+            dest="anaconda_channel",
+            default="bioconda",
+            help="Anaconda channel to search for tests (default: bioconda).",
+        )
+        parser.add_argument(
+            "--github-repo",
+            dest="github_repo",
+            default="bioconda/bioconda-recipes",
+            help="Github repository to search for tests - only relevant if --deep-search is activated (default: bioconda/bioconda-recipes",
+        )
+        parser.add_argument(
+            "--github-local-path",
+            dest="github_local_path",
+            default=None,
+            help="If the bioconda-recipes repository (or other repository containing tests) is available locally, provide the path here. Only relevant if --deep-search is activated.",
+        )
         args = vars(parser.parse_args())
 
-    if args['containers']:
-        containers = args['containers']
-    elif args['container_list']:
-        containers = get_list_from_file(args['container_list'])
+    if args["containers"]:
+        containers = args["containers"]
+    elif args["container_list"]:
+        containers = get_list_from_file(args["container_list"])
     else:  # if no containers are specified, test everything in the filepath
-        containers = [n.split(args['filepath'])[1]
-                      for n in glob(f"{args['filepath']}*")]
+        containers = [n.split(args["filepath"])[1] for n in glob(f"{args['filepath']}*")]
 
-    with open(args['logfile'], 'w') as f:
+    with open(args["logfile"], "w") as f:
         f.write("SINGULARITY CONTAINERS GENERATED:")
         tests = {}
         for container in containers:
-            if container[0:6] == 'mulled':  # if it is a 'hashed container'
+            if container[0:6] == "mulled":  # if it is a 'hashed container'
                 tests[container] = hashed_test_search(
-                    container, args['github_local_path'], args['deep_search'], args['anaconda_channel'], args['github_repo'])
+                    container,
+                    args["github_local_path"],
+                    args["deep_search"],
+                    args["anaconda_channel"],
+                    args["github_repo"],
+                )
             else:
                 tests[container] = main_test_search(
-                    container, args['github_local_path'], args['deep_search'], args['anaconda_channel'], args['github_repo'])
-        test_results = singularity_container_test(
-            tests, args['installation'], args['filepath'])
+                    container,
+                    args["github_local_path"],
+                    args["deep_search"],
+                    args["anaconda_channel"],
+                    args["github_repo"],
+                )
+        test_results = singularity_container_test(tests, args["installation"], args["filepath"])
 
-        f.write('\n\tTEST PASSED:')
-        for container in test_results['passed']:
-            f.write(f'\n\t\t{container}')
-        f.write('\n\tTEST FAILED:')
-        for container in test_results['failed']:
+        f.write("\n\tTEST PASSED:")
+        for container in test_results["passed"]:
+            f.write(f"\n\t\t{container}")
+        f.write("\n\tTEST FAILED:")
+        for container in test_results["failed"]:
             f.write(f"\n\t\t{container['container']}")
-            for error in container['errors']:
-                f.write('\n\t\t\tCOMMAND: {}\n\t\t\t\tERROR:{}'.format(error.get(
-                    'command', f"import{error.get('import', 'nothing found')}"), error['output']))
-        f.write('\n\tNO TEST AVAILABLE:')
-        for container in test_results['notest']:
-            f.write(f'\n\t\t{container}')
+            for error in container["errors"]:
+                f.write(
+                    "\n\t\t\tCOMMAND: {}\n\t\t\t\tERROR:{}".format(
+                        error.get("command", f"import{error.get('import', 'nothing found')}"), error["output"]
+                    )
+                )
+        f.write("\n\tNO TEST AVAILABLE:")
+        for container in test_results["notest"]:
+            f.write(f"\n\t\t{container}")
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
index 59328ccae5a..be3edad1923 100644
--- a/lib/galaxy/tool_util/deps/mulled/util.py
+++ b/lib/galaxy/tool_util/deps/mulled/util.py
@@ -14,15 +14,15 @@ import requests
 
 log = logging.getLogger(__name__)
 
-QUAY_REPOSITORY_API_ENDPOINT = 'https://quay.io/api/v1/repository'
-BUILD_NUMBER_REGEX = re.compile(r'\d+$')
-PARSED_TAG = collections.namedtuple('PARSED_TAG', 'tag version build_string build_number')
+QUAY_REPOSITORY_API_ENDPOINT = "https://quay.io/api/v1/repository"
+BUILD_NUMBER_REGEX = re.compile(r"\d+$")
+PARSED_TAG = collections.namedtuple("PARSED_TAG", "tag version build_string build_number")
 MULLED_SOCKET_TIMEOUT = 12
 
 
 def create_repository(namespace, repo_name, oauth_token):
     assert oauth_token
-    headers = {'Authorization': f'Bearer {oauth_token}'}
+    headers = {"Authorization": f"Bearer {oauth_token}"}
     data = {
         "repository": repo_name,
         "namespace": namespace,
@@ -36,19 +36,19 @@ def quay_versions(namespace, pkg_name, session=None):
     """Get all version tags for a Docker image stored on quay.io for supplied package name."""
     data = quay_repository(namespace, pkg_name, session=session)
 
-    if 'error_type' in data and data['error_type'] == "invalid_token":
+    if "error_type" in data and data["error_type"] == "invalid_token":
         return []
 
-    if 'tags' not in data:
+    if "tags" not in data:
         raise Exception(f"Unexpected response from quay.io - no tags description found [{data}]")
 
-    return [tag for tag in data['tags'].keys() if tag != 'latest']
+    return [tag for tag in data["tags"].keys() if tag != "latest"]
 
 
 def quay_repository(namespace, pkg_name, session=None):
     assert namespace is not None
     assert pkg_name is not None
-    url = f'https://quay.io/api/v1/repository/{namespace}/{pkg_name}'
+    url = f"https://quay.io/api/v1/repository/{namespace}/{pkg_name}"
     if not session:
         session = requests.session()
     response = session.get(url, timeout=MULLED_SOCKET_TIMEOUT)
@@ -64,12 +64,13 @@ def _namespace_has_repo_name(namespace, repo_name, resolution_cache):
     if resolution_cache is not None and cache_key in resolution_cache:
         repo_names = resolution_cache.get(cache_key)
     else:
-        repos_parameters = {'public': 'true', 'namespace': namespace}
-        repos_headers = {'Accept-encoding': 'gzip', 'Accept': 'application/json'}
+        repos_parameters = {"public": "true", "namespace": namespace}
+        repos_headers = {"Accept-encoding": "gzip", "Accept": "application/json"}
         repos_response = requests.get(
-            QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=MULLED_SOCKET_TIMEOUT)
+            QUAY_REPOSITORY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=MULLED_SOCKET_TIMEOUT
+        )
 
-        repos = repos_response.json()['repositories']
+        repos = repos_response.json()["repositories"]
         repo_names = [r["name"] for r in repos]
         if resolution_cache is not None:
             resolution_cache[cache_key] = repo_names
@@ -114,31 +115,33 @@ def mulled_tags_for(namespace, image, tag_prefix=None, resolution_cache=None, se
 
 def split_tag(tag):
     """Split mulled image tag into conda version and conda build."""
-    return tag.rsplit('--', 1)
+    return tag.rsplit("--", 1)
 
 
 def parse_tag(tag):
     """Decompose tag of mulled images into version, build string and build number."""
-    version = tag.rsplit(':')[-1]
+    version = tag.rsplit(":")[-1]
     build_string = "-1"
     build_number = -1
     match = BUILD_NUMBER_REGEX.search(version)
     if match:
         build_number = int(match.group(0))
-    if '--' in version:
-        version, build_string = version.rsplit('--', 1)
-    elif '-' in version:
+    if "--" in version:
+        version, build_string = version.rsplit("--", 1)
+    elif "-" in version:
         # Should be mulled multi-container image tag
-        version, build_string = version.rsplit('-', 1)
+        version, build_string = version.rsplit("-", 1)
     else:
         # We don't have a build number, and the BUILD_NUMBER_REGEX above is only accurate for build strings,
         # so set build number to -1. Any matching image:version combination with a build number
         # will be considered newer.
         build_number = -1
-    return PARSED_TAG(tag=tag,
-                      version=packaging.version.parse(version),
-                      build_string=packaging.version.parse(build_string),
-                      build_number=build_number)
+    return PARSED_TAG(
+        tag=tag,
+        version=packaging.version.parse(version),
+        build_string=packaging.version.parse(build_string),
+        build_number=build_number,
+    )
 
 
 def version_sorted(elements):
@@ -212,7 +215,9 @@ def v1_image_name(targets, image_build=None, name_override=None):
     'mulled-v1-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'
     """
     if name_override is not None:
-        print("WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result.")
+        print(
+            "WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result."
+        )
         return name_override
 
     targets = list(targets)
@@ -258,7 +263,9 @@ def v2_image_name(targets, image_build=None, name_override=None):
     'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'
     """
     if name_override is not None:
-        print("WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result.")
+        print(
+            "WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result."
+        )
         return name_override
 
     targets = list(targets)
@@ -306,7 +313,7 @@ def split_container_name(name):
     >>> split_container_name('samtools:1.7--1')
     ['samtools', '1.7', '1']
     """
-    return name.replace('--', ':').split(':')
+    return name.replace("--", ":").split(":")
 
 
 class PrintProgress:
diff --git a/lib/galaxy/tool_util/deps/requirements.py b/lib/galaxy/tool_util/deps/requirements.py
index b5a8dd439a3..b64d96faa38 100644
--- a/lib/galaxy/tool_util/deps/requirements.py
+++ b/lib/galaxy/tool_util/deps/requirements.py
@@ -1,13 +1,11 @@
 import copy
 
-
 from galaxy.util import (
     asbool,
     xml_text,
 )
 from galaxy.util.oset import OrderedSet
 
-
 DEFAULT_REQUIREMENT_TYPE = "package"
 DEFAULT_REQUIREMENT_VERSION = None
 
@@ -43,7 +41,12 @@ class ToolRequirement:
         return ToolRequirement(name=name, type=type, version=version, specs=specs)
 
     def __eq__(self, other):
-        return self.name == other.name and self.type == other.type and self.version == other.version and self.specs == other.specs
+        return (
+            self.name == other.name
+            and self.type == other.type
+            and self.version == other.version
+            and self.specs == other.specs
+        )
 
     def __ne__(self, other):
         return not self.__eq__(other)
@@ -99,8 +102,10 @@ class ToolRequirements:
     def __init__(self, tool_requirements=None):
         if tool_requirements:
             if not isinstance(tool_requirements, list):
-                raise ToolRequirementsException('ToolRequirements Constructor expects a list')
-            self.tool_requirements = OrderedSet([r if isinstance(r, ToolRequirement) else ToolRequirement.from_dict(r) for r in tool_requirements])
+                raise ToolRequirementsException("ToolRequirements Constructor expects a list")
+            self.tool_requirements = OrderedSet(
+                [r if isinstance(r, ToolRequirement) else ToolRequirement.from_dict(r) for r in tool_requirements]
+            )
         else:
             self.tool_requirements = OrderedSet()
 
@@ -110,11 +115,11 @@ class ToolRequirements:
 
     @property
     def resolvable(self):
-        return ToolRequirements([r for r in self.tool_requirements if r.type in {'package', 'set_environment'}])
+        return ToolRequirements([r for r in self.tool_requirements if r.type in {"package", "set_environment"}])
 
     @property
     def packages(self):
-        return ToolRequirements([r for r in self.tool_requirements if r.type == 'package'])
+        return ToolRequirements([r for r in self.tool_requirements if r.type == "package"])
 
     def to_list(self):
         return [r.to_dict() for r in self.tool_requirements]
@@ -125,7 +130,11 @@ class ToolRequirements:
         self.tool_requirements.add(requirement)
 
     def __eq__(self, other):
-        return len(self.tool_requirements & other.tool_requirements) == len(self.tool_requirements) == len(other.tool_requirements)
+        return (
+            len(self.tool_requirements & other.tool_requirements)
+            == len(self.tool_requirements)
+            == len(other.tool_requirements)
+        )
 
     def __ne__(self, other):
         return not self.__eq__(other)
@@ -156,7 +165,6 @@ DEFAULT_CONTAINER_SHELL = "/bin/sh"  # Galaxy assumes bash, but containers are u
 
 
 class ContainerDescription:
-
     def __init__(
         self,
         identifier=None,
@@ -229,7 +237,7 @@ def parse_requirements_from_xml(xml_root):
 
     requirement_elems = []
     if requirements_elem is not None:
-        requirement_elems = requirements_elem.findall('requirement')
+        requirement_elems = requirements_elem.findall("requirement")
 
     requirements = ToolRequirements()
     for requirement_elem in requirement_elems:
@@ -241,7 +249,7 @@ def parse_requirements_from_xml(xml_root):
 
     container_elems = []
     if requirements_elem is not None:
-        container_elems = requirements_elem.findall('container')
+        container_elems = requirements_elem.findall("container")
 
     containers = [container_from_element(c) for c in container_elems]
 
diff --git a/lib/galaxy/tool_util/deps/resolvers/__init__.py b/lib/galaxy/tool_util/deps/resolvers/__init__.py
index 1553e577f76..58f2bacc1e5 100644
--- a/lib/galaxy/tool_util/deps/resolvers/__init__.py
+++ b/lib/galaxy/tool_util/deps/resolvers/__init__.py
@@ -6,7 +6,10 @@ from abc import (
     abstractmethod,
     abstractproperty,
 )
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 import yaml
 
@@ -19,7 +22,12 @@ class DependencyResolver(Dictifiable, metaclass=ABCMeta):
     """Abstract description of a technique for resolving container images for tool execution."""
 
     # Keys for dictification.
-    dict_collection_visible_keys = ['resolver_type', 'resolves_simple_dependencies', 'can_uninstall_dependencies', 'read_only']
+    dict_collection_visible_keys = [
+        "resolver_type",
+        "resolves_simple_dependencies",
+        "can_uninstall_dependencies",
+        "read_only",
+    ]
     # A "simple" dependency is one that does not depend on the the tool
     # resolving the dependency. Classic tool shed dependencies are non-simple
     # because the repository install context is used in dependency resolution
@@ -50,7 +58,7 @@ class DependencyResolver(Dictifiable, metaclass=ABCMeta):
             return self._install_dependency(name, version, type, **kwds)
 
     def _install_dependency(self, name, version, type, **kwds):
-        """ Attempt to install this dependency if a recipe to do so
+        """Attempt to install this dependency if a recipe to do so
         has been registered in some way.
         """
         return False
@@ -79,14 +87,14 @@ class MultipleDependencyResolver:
 
 
 class ListableDependencyResolver(metaclass=ABCMeta):
-    """ Mix this into a ``DependencyResolver`` and implement to indicate
+    """Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can iterate over its dependencies and generate
     requirements.
     """
 
     @abstractmethod
     def list_dependencies(self):
-        """ List the "simple" requirements that may be resolved "exact"-ly
+        """List the "simple" requirements that may be resolved "exact"-ly
         by this dependency resolver.
         """
 
@@ -147,7 +155,6 @@ FROM_UNVERSIONED = object()
 
 
 class RequirementMapping:
-
     def __init__(self, from_name, from_version, to_name, to_version):
         self.from_name = from_name
         self.from_version = from_version
@@ -254,7 +261,7 @@ class SpecificationPatternDependencyResolver(SpecificationAwareDependencyResolve
 
 
 class Dependency(Dictifiable, metaclass=ABCMeta):
-    dict_collection_visible_keys = ['dependency_type', 'exact', 'name', 'version', 'cacheable']
+    dict_collection_visible_keys = ["dependency_type", "exact", "name", "version", "cacheable"]
     cacheable = False
 
     @abstractmethod
@@ -265,7 +272,7 @@ class Dependency(Dictifiable, metaclass=ABCMeta):
 
     @abstractproperty
     def exact(self):
-        """ Return true if version information wasn't discarded to resolve
+        """Return true if version information wasn't discarded to resolve
         the dependency.
         """
 
@@ -279,7 +286,11 @@ class Dependency(Dictifiable, metaclass=ABCMeta):
 
 class ContainerDependency(Dependency):
 
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'container_description', 'container_resolver']
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + [
+        "environment_path",
+        "container_description",
+        "container_resolver",
+    ]
 
     def __init__(self, container_description, name=None, version=None, container_resolver=None):
         self.container_description = container_description
diff --git a/lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py
index b4316894b08..7b0c52e7d97 100644
--- a/lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py
+++ b/lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py
@@ -9,7 +9,7 @@ import os
 from galaxy.util import parse_xml
 from . import (
     DependencyResolver,
-    NullDependency
+    NullDependency,
 )
 from .resolver_mixins import (
     UsesHomebrewMixin,
@@ -79,14 +79,13 @@ class HomebrewToolShedDependencyResolver(
             package_name=name,
             package_version=version,
             repository_owner=raw_dependency.repository_owner,
-            repository_name=raw_dependency.repository_name
+            repository_name=raw_dependency.repository_name,
         )
         dep = self._find_dep_default(recipe_name, None)
         return dep
 
 
 class RawDependencies:
-
     def __init__(self, dependencies_file):
         self.root = parse_xml(dependencies_file).getroot()
         dependencies = []
@@ -110,7 +109,6 @@ class RawDependencies:
 
 
 class RawDependency:
-
     def __init__(self, dependencies, package_el, repository_el):
         self.dependencies = dependencies
         self.package_el = package_el
@@ -121,7 +119,7 @@ class RawDependency:
         return temp % (
             self.package_el.attrib["name"],
             self.package_el.attrib["version"],
-            self.repository_el.attrib["name"]
+            self.repository_el.attrib["name"],
         )
 
     @property
@@ -150,4 +148,4 @@ def build_recipe_name(package_name, package_version, repository_owner, repositor
     return base
 
 
-__all__ = ('HomebrewToolShedDependencyResolver', )
+__all__ = ("HomebrewToolShedDependencyResolver",)
diff --git a/lib/galaxy/tool_util/deps/resolvers/conda.py b/lib/galaxy/tool_util/deps/resolvers/conda.py
index 3c035648adb..06370b00376 100644
--- a/lib/galaxy/tool_util/deps/resolvers/conda.py
+++ b/lib/galaxy/tool_util/deps/resolvers/conda.py
@@ -34,7 +34,6 @@ from ..conda_util import (
     USE_PATH_EXEC_DEFAULT,
 )
 
-
 DEFAULT_BASE_PATH_DIRECTORY = "_conda"
 DEFAULT_CONDARC_OVERRIDE = "_condarc"
 # Conda channel order from highest to lowest, following the one used in
@@ -63,26 +62,39 @@ done
 log = logging.getLogger(__name__)
 
 
-class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver):
-    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['prefix', 'versionless', 'ensure_channels', 'auto_install', 'auto_init', 'use_local']
+class CondaDependencyResolver(
+    DependencyResolver,
+    MultipleDependencyResolver,
+    ListableDependencyResolver,
+    SpecificationPatternDependencyResolver,
+    MappableDependencyResolver,
+):
+    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + [
+        "prefix",
+        "versionless",
+        "ensure_channels",
+        "auto_install",
+        "auto_init",
+        "use_local",
+    ]
     resolver_type = "conda"
     config_options = {
-        'prefix': None,
-        'exec': None,
-        'debug': None,
-        'ensure_channels': DEFAULT_ENSURE_CHANNELS,
-        'auto_install': False,
-        'auto_init': True,
-        'copy_dependencies': False,
-        'use_local': False,
+        "prefix": None,
+        "exec": None,
+        "debug": None,
+        "ensure_channels": DEFAULT_ENSURE_CHANNELS,
+        "auto_install": False,
+        "auto_init": True,
+        "copy_dependencies": False,
+        "use_local": False,
     }
     _specification_pattern = re.compile(r"https\:\/\/anaconda.org\/\w+\/\w+")
 
     def __init__(self, dependency_manager, **kwds):
-        read_only = _string_as_bool(kwds.get('read_only', 'false'))
+        read_only = _string_as_bool(kwds.get("read_only", "false"))
         self.read_only = read_only
         self._setup_mapping(dependency_manager, **kwds)
-        self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
+        self.versionless = _string_as_bool(kwds.get("versionless", "false"))
         self.dependency_manager = dependency_manager
 
         def get_option(name):
@@ -91,18 +103,14 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         # Conda context options (these define the environment)
         conda_prefix = get_option("prefix")
         if conda_prefix is None:
-            conda_prefix = os.path.join(
-                dependency_manager.default_base_path, DEFAULT_BASE_PATH_DIRECTORY
-            )
+            conda_prefix = os.path.join(dependency_manager.default_base_path, DEFAULT_BASE_PATH_DIRECTORY)
         conda_prefix = os.path.abspath(conda_prefix)
 
         self.conda_prefix_parent = os.path.dirname(conda_prefix)
 
         condarc_override = get_option("condarc_override")
         if condarc_override is None:
-            condarc_override = os.path.join(
-                dependency_manager.default_base_path, DEFAULT_CONDARC_OVERRIDE
-            )
+            condarc_override = os.path.join(dependency_manager.default_base_path, DEFAULT_CONDARC_OVERRIDE)
 
         copy_dependencies = _string_as_bool(get_option("copy_dependencies"))
         use_local = _string_as_bool(get_option("use_local"))
@@ -134,7 +142,9 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         auto_install = _string_as_bool(get_option("auto_install"))
         self.auto_init = _string_as_bool(get_option("auto_init"))
         self.conda_context = conda_context
-        self.disabled = not galaxy.tool_util.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
+        self.disabled = not galaxy.tool_util.deps.installable.ensure_installed(
+            conda_context, install_conda, self.auto_init
+        )
         if self.auto_init and not self.disabled:
             self.conda_context.ensure_conda_build_installed_if_needed()
         self.auto_install = auto_install
@@ -155,7 +165,9 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         return self.uninstall_environments(environments)
 
     def uninstall_environments(self, environments):
-        environments = [env if not env.startswith(self.conda_context.envs_path) else os.path.basename(env) for env in environments]
+        environments = [
+            env if not env.startswith(self.conda_context.envs_path) else os.path.basename(env) for env in environments
+        ]
         return_codes = [self.conda_context.exec_remove([env]) for env in environments]
         final_return_code = 0
         for env, return_code in zip(environments, return_codes):
@@ -223,7 +235,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         dependencies = []
 
         is_installed = self.conda_context.has_env(env)
-        install = kwds.get('install', None)
+        install = kwds.get("install", None)
         if install is None:
             # Default behavior, install dependencies if conda_auto_install is active.
             install = not is_installed and self.auto_install
@@ -273,14 +285,12 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
             version = None
 
         conda_target = CondaTarget(name, version=version)
-        is_installed = is_conda_target_installed(
-            conda_target, conda_context=self.conda_context
-        )
+        is_installed = is_conda_target_installed(conda_target, conda_context=self.conda_context)
 
         preserve_python_environment = kwds.get("preserve_python_environment", False)
 
         job_directory = kwds.get("job_directory", None)
-        install = kwds.get('install', None)
+        install = kwds.get("install", None)
         if install is None:
             install = not is_installed and self.auto_install
         elif install:
@@ -324,10 +334,12 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         used_paths = set()
         for dependencies in toolbox_requirements_status.values():
             for dependency in dependencies:
-                if dependency.get('dependency_type') == 'conda':
-                    path = os.path.basename(dependency['environment_path'])
+                if dependency.get("dependency_type") == "conda":
+                    path = os.path.basename(dependency["environment_path"])
                     used_paths.add(path)
-        dir_contents = set(os.listdir(self.conda_context.envs_path) if os.path.exists(self.conda_context.envs_path) else [])
+        dir_contents = set(
+            os.listdir(self.conda_context.envs_path) if os.path.exists(self.conda_context.envs_path) else []
+        )
         unused_paths = dir_contents.difference(used_paths)  # New set with paths in dir_contents but not in used_paths
         unused_paths = [os.path.join(self.conda_context.envs_path, p) for p in unused_paths]
         return unused_paths
@@ -352,9 +364,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
 
         conda_target = CondaTarget(name, version=version)
 
-        is_installed = is_conda_target_installed(
-            conda_target, conda_context=self.conda_context
-        )
+        is_installed = is_conda_target_installed(conda_target, conda_context=self.conda_context)
 
         if is_installed:
             return is_installed
@@ -364,9 +374,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
             is_installed = False
         else:
             # Recheck if installed
-            is_installed = is_conda_target_installed(
-                conda_target, conda_context=self.conda_context
-            )
+            is_installed = is_conda_target_installed(conda_target, conda_context=self.conda_context)
         if not is_installed:
             log.debug(f"Removing failed conda install of {name}, version '{version}'")
             cleanup_failed_install(conda_target, conda_context=self.conda_context)
@@ -379,10 +387,24 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
 
 
 class MergedCondaDependency(Dependency):
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version', 'dependency_resolver']
-    dependency_type = 'conda'
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + [
+        "environment_path",
+        "name",
+        "version",
+        "dependency_resolver",
+    ]
+    dependency_type = "conda"
 
-    def __init__(self, conda_context, environment_path, exact, name=None, version=None, preserve_python_environment=False, dependency_resolver=None):
+    def __init__(
+        self,
+        conda_context,
+        environment_path,
+        exact,
+        name=None,
+        version=None,
+        preserve_python_environment=False,
+        dependency_resolver=None,
+    ):
         self.activate = conda_context.activate
         self.conda_context = conda_context
         self.environment_path = environment_path
@@ -412,18 +434,29 @@ class MergedCondaDependency(Dependency):
             # variables in the future.
             return f"""export PATH=$PATH:'{self.environment_path}/bin' """
         else:
-            return CONDA_SOURCE_CMD.format(
-                activate_path=self.activate,
-                environment_path=self.environment_path
-            )
+            return CONDA_SOURCE_CMD.format(activate_path=self.activate, environment_path=self.environment_path)
 
 
 class CondaDependency(Dependency):
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version', 'dependency_resolver']
-    dependency_type = 'conda'
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + [
+        "environment_path",
+        "name",
+        "version",
+        "dependency_resolver",
+    ]
+    dependency_type = "conda"
     cacheable = True
 
-    def __init__(self, conda_context, environment_path, exact, name=None, version=None, preserve_python_environment=False, dependency_resolver=None):
+    def __init__(
+        self,
+        conda_context,
+        environment_path,
+        exact,
+        name=None,
+        version=None,
+        preserve_python_environment=False,
+        dependency_resolver=None,
+    ):
         self.activate = conda_context.activate
         self.conda_context = conda_context
         self.environment_path = environment_path
@@ -464,9 +497,11 @@ class CondaDependency(Dependency):
         if exit_code:
             if len(os.path.abspath(self.environment_path)) > 79:
                 # TODO: remove this once conda_build version 2 is released and packages have been rebuilt.
-                raise DependencyException("Conda dependency failed to build job environment. "
-                                          "This is most likely a limitation in conda. "
-                                          "You can try to shorten the path to the job_working_directory.")
+                raise DependencyException(
+                    "Conda dependency failed to build job environment. "
+                    "This is most likely a limitation in conda. "
+                    "You can try to shorten the path to the job_working_directory."
+                )
             raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")
 
     def shell_commands(self):
@@ -479,14 +514,11 @@ class CondaDependency(Dependency):
             # variables in the future.
             return f"""export PATH=$PATH:'{self.environment_path}/bin' """
         else:
-            return CONDA_SOURCE_CMD.format(
-                activate_path=self.activate,
-                environment_path=self.environment_path
-            )
+            return CONDA_SOURCE_CMD.format(activate_path=self.activate, environment_path=self.environment_path)
 
 
 def _string_as_bool(value):
     return str(value).lower() == "true"
 
 
-__all__ = ('CondaDependencyResolver', 'DEFAULT_ENSURE_CHANNELS')
+__all__ = ("CondaDependencyResolver", "DEFAULT_ENSURE_CHANNELS")
diff --git a/lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py b/lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py
index 7864f63f2d7..46b0a10f44f 100644
--- a/lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py
+++ b/lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py
@@ -22,8 +22,14 @@ log = logging.getLogger(__name__)
 
 
 class GalaxyPackageDependency(Dependency):
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['script', 'path', 'version', 'name', 'dependency_resolver']
-    dependency_type = 'galaxy_package'
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + [
+        "script",
+        "path",
+        "version",
+        "name",
+        "dependency_resolver",
+    ]
+    dependency_type = "galaxy_package"
 
     def __init__(self, script, path, name, type, version, exact=True, dependency_resolver=None):
         self.script = script
@@ -41,19 +47,19 @@ class GalaxyPackageDependency(Dependency):
 
     def shell_commands(self):
         base_path = self.path
-        if self.type == 'package' and self.script is None:
+        if self.type == "package" and self.script is None:
             commands = f'PACKAGE_BASE={base_path}; export PACKAGE_BASE; PATH="{base_path}/bin:$PATH"; export PATH'
         else:
-            commands = f'PACKAGE_BASE={base_path}; export PACKAGE_BASE; . {self.script}'
+            commands = f"PACKAGE_BASE={base_path}; export PACKAGE_BASE; . {self.script}"
         return commands
 
 
 class ToolShedDependency(GalaxyPackageDependency):
-    dependency_type = 'tool_shed_package'
+    dependency_type = "tool_shed_package"
 
 
 class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependencyDirMixin):
-    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'versionless']
+    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ["base_path", "versionless"]
     dependency_type = GalaxyPackageDependency
 
     def __init__(self, dependency_manager, **kwds):
@@ -62,7 +68,7 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
         # the tool shed so allow a fallback version of the Galaxy package
         # resolver that will just grab 'default' version of exact version
         # unavailable.
-        self.versionless = str(kwds.get('versionless', "false")).lower() == "true"
+        self.versionless = str(kwds.get("versionless", "false")).lower() == "true"
         self._init_base_path(dependency_manager, **kwds)
 
     def resolve(self, requirement, **kwds):
@@ -78,14 +84,14 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
         else:
             return self._find_dep_versioned(name, version, type=type, **kwds)
 
-    def _find_dep_versioned(self, name, version, type='package', **kwds):
+    def _find_dep_versioned(self, name, version, type="package", **kwds):
         base_path = self.base_path
         path = join(base_path, name, version)
         return self._galaxy_package_dep(path, version, name, type, True)
 
-    def _find_dep_default(self, name, type='package', exact=True, **kwds):
+    def _find_dep_default(self, name, type="package", exact=True, **kwds):
         base_path = self.base_path
-        path = join(base_path, name, 'default')
+        path = join(base_path, name, "default")
         if islink(path):
             real_path = realpath(path)
             real_version = basename(real_path)
@@ -94,15 +100,17 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
             return NullDependency(version=None, name=name)
 
     def _galaxy_package_dep(self, path, version, name, type, exact):
-        script = join(path, 'env.sh')
+        script = join(path, "env.sh")
         if exists(script):
             return self.dependency_type(script, path, name, type, version, exact, dependency_resolver=self)
-        elif exists(join(path, 'bin')):
+        elif exists(join(path, "bin")):
             return self.dependency_type(None, path, name, type, version, exact, dependency_resolver=self)
         return NullDependency(version=version, name=name)
 
 
-class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver, MappableDependencyResolver):
+class GalaxyPackageDependencyResolver(
+    BaseGalaxyPackageDependencyResolver, ListableDependencyResolver, MappableDependencyResolver
+):
     resolver_type = "galaxy_packages"
 
     def __init__(self, dependency_manager, **kwds):
@@ -128,11 +136,7 @@ class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Lista
 
 
 def _is_dependency_directory(directory):
-    return exists(join(directory, 'env.sh')) or exists(join(directory, 'bin'))
+    return exists(join(directory, "env.sh")) or exists(join(directory, "bin"))
 
 
-__all__ = (
-    'GalaxyPackageDependency',
-    'GalaxyPackageDependencyResolver',
-    'ToolShedDependency'
-)
+__all__ = ("GalaxyPackageDependency", "GalaxyPackageDependencyResolver", "ToolShedDependency")
diff --git a/lib/galaxy/tool_util/deps/resolvers/homebrew.py b/lib/galaxy/tool_util/deps/resolvers/homebrew.py
index 422dbe40513..1b4fe1191b1 100644
--- a/lib/galaxy/tool_util/deps/resolvers/homebrew.py
+++ b/lib/galaxy/tool_util/deps/resolvers/homebrew.py
@@ -14,13 +14,13 @@ incompatible changes coming.
 
 from . import (
     DependencyResolver,
-    NullDependency
+    NullDependency,
 )
 from .resolver_mixins import UsesHomebrewMixin
 
 # TODO: Implement prefer version linked...
-PREFER_VERSION_LINKED = 'linked'
-PREFER_VERSION_LATEST = 'latest'
+PREFER_VERSION_LINKED = "linked"
+PREFER_VERSION_LATEST = "latest"
 UNKNOWN_PREFER_VERSION_MESSAGE_TEMPLATE = "HomebrewDependencyResolver prefer_version must be %s"
 UNKNOWN_PREFER_VERSION_MESSAGE = UNKNOWN_PREFER_VERSION_MESSAGE_TEMPLATE % (PREFER_VERSION_LATEST)
 DEFAULT_PREFER_VERSION = PREFER_VERSION_LATEST
@@ -30,8 +30,8 @@ class HomebrewDependencyResolver(DependencyResolver, UsesHomebrewMixin):
     resolver_type = "homebrew"
 
     def __init__(self, dependency_manager, **kwds):
-        self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
-        self.prefer_version = kwds.get('prefer_version', None)
+        self.versionless = _string_as_bool(kwds.get("versionless", "false"))
+        self.prefer_version = kwds.get("prefer_version", None)
 
         if self.prefer_version is None:
             self.prefer_version = DEFAULT_PREFER_VERSION
@@ -57,4 +57,4 @@ def _string_as_bool(value):
     return str(value).lower() == "true"
 
 
-__all__ = ('HomebrewDependencyResolver', )
+__all__ = ("HomebrewDependencyResolver",)
diff --git a/lib/galaxy/tool_util/deps/resolvers/lmod.py b/lib/galaxy/tool_util/deps/resolvers/lmod.py
index 6779bfb84d3..082de0bbff0 100644
--- a/lib/galaxy/tool_util/deps/resolvers/lmod.py
+++ b/lib/galaxy/tool_util/deps/resolvers/lmod.py
@@ -12,7 +12,7 @@ from os import getenv
 from os.path import exists
 from subprocess import (
     PIPE,
-    Popen
+    Popen,
 )
 
 from . import (
@@ -24,10 +24,10 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-DEFAULT_LMOD_PATH = getenv('LMOD_CMD')
-DEFAULT_SETTARG_PATH = getenv('LMOD_SETTARG_CMD')
-DEFAULT_MODULEPATH = getenv('MODULEPATH')
-DEFAULT_MAPPING_FILE = 'config/lmod_modules_mapping.yml'
+DEFAULT_LMOD_PATH = getenv("LMOD_CMD")
+DEFAULT_SETTARG_PATH = getenv("LMOD_SETTARG_CMD")
+DEFAULT_MODULEPATH = getenv("MODULEPATH")
+DEFAULT_MAPPING_FILE = "config/lmod_modules_mapping.yml"
 INVALID_LMOD_PATH_MSG = "The following LMOD executable could not be found: %s. Either your LMOD Dependency Resolver is misconfigured or LMOD is improperly installed on your system !"
 EMPTY_MODULEPATH_MSG = "No valid LMOD MODULEPATH defined ! Either your LMOD Dependency Resolver is misconfigured or LMOD is improperly installed on your system !"
 
@@ -35,7 +35,7 @@ EMPTY_MODULEPATH_MSG = "No valid LMOD MODULEPATH defined ! Either your LMOD Depe
 class LmodDependencyResolver(DependencyResolver, MappableDependencyResolver):
     """Dependency resolver based on the LMOD environment modules system"""
 
-    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'modulepath']
+    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ["base_path", "modulepath"]
     resolver_type = "lmod"
 
     def __init__(self, dependency_manager, **kwds):
@@ -44,16 +44,16 @@ class LmodDependencyResolver(DependencyResolver, MappableDependencyResolver):
         self._setup_mapping(dependency_manager, **kwds)
 
         # Other attributes
-        self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
-        self.lmodexec = kwds.get('lmodexec', DEFAULT_LMOD_PATH)
-        self.settargexec = kwds.get('settargexec', DEFAULT_SETTARG_PATH)
-        self.modulepath = kwds.get('modulepath', DEFAULT_MODULEPATH)
+        self.versionless = _string_as_bool(kwds.get("versionless", "false"))
+        self.lmodexec = kwds.get("lmodexec", DEFAULT_LMOD_PATH)
+        self.settargexec = kwds.get("settargexec", DEFAULT_SETTARG_PATH)
+        self.modulepath = kwds.get("modulepath", DEFAULT_MODULEPATH)
         self.module_checker = AvailModuleChecker(self, self.modulepath)
 
     def _set_default_mapping_file(self, resolver_attributes):
-        if 'mapping_files' not in resolver_attributes:
+        if "mapping_files" not in resolver_attributes:
             if exists(DEFAULT_MAPPING_FILE):
-                resolver_attributes['mapping_files'] = DEFAULT_MAPPING_FILE
+                resolver_attributes["mapping_files"] = DEFAULT_MAPPING_FILE
 
     def resolve(self, requirement, **kwds):
         requirement = self._expand_mappings(requirement)
@@ -110,7 +110,7 @@ class AvailModuleChecker:
 
             # Split module lines by / to separate the module name from the module version
             # Module without version are discarded
-            module_parts = line.split('/')
+            module_parts = line.split("/")
             if len(module_parts) == 2:
                 yield module_parts[0], module_parts[1]
 
@@ -126,21 +126,29 @@ class AvailModuleChecker:
 
         # Build command line
         if default_version_only:
-            module_avail_command = [lmodexec, '-t', '-d', 'avail']
+            module_avail_command = [lmodexec, "-t", "-d", "avail"]
         else:
-            module_avail_command = [lmodexec, '-t', 'avail']
+            module_avail_command = [lmodexec, "-t", "avail"]
 
         # The list of avaialable modules is actually printed on stderr and not stdout for module commands
-        return Popen(module_avail_command, stdout=PIPE, stderr=PIPE, env={'MODULEPATH': self.modulepath}, close_fds=True).communicate()[1]
+        return Popen(
+            module_avail_command, stdout=PIPE, stderr=PIPE, env={"MODULEPATH": self.modulepath}, close_fds=True
+        ).communicate()[1]
 
 
 class LmodDependency(Dependency):
     """Prepare the commands required to solve the dependency and add them to the script used to run a tool in Galaxy."""
 
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['module_name', 'module_version', 'dependency_resolver']
-    dependency_type = 'lmod'
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + [
+        "module_name",
+        "module_version",
+        "dependency_resolver",
+    ]
+    dependency_type = "lmod"
 
-    def __init__(self, lmod_dependency_resolver, module_name, module_version=None, exact=True, dependency_resolver=None):
+    def __init__(
+        self, lmod_dependency_resolver, module_name, module_version=None, exact=True, dependency_resolver=None
+    ):
         self.lmod_dependency_resolver = lmod_dependency_resolver
         self.module_name = module_name
         self.module_version = module_version
@@ -163,18 +171,18 @@ class LmodDependency(Dependency):
         # Get the full module name in the form "tool_name/tool_version"
         module_to_load = self.module_name
         if self.module_version:
-            module_to_load = f'{self.module_name}/{self.module_version}'
+            module_to_load = f"{self.module_name}/{self.module_version}"
 
         # Build the list of command to add to run script
         # Note that since "module" is actually a bash function, we are directy executing the underlying executable instead
         # - Set the MODULEPATH environment variable
-        command = f'MODULEPATH={self.lmod_dependency_resolver.modulepath}; '
-        command += 'export MODULEPATH; '
+        command = f"MODULEPATH={self.lmod_dependency_resolver.modulepath}; "
+        command += "export MODULEPATH; "
         # - Execute the "module load" command (or rather the "/path/to/lmod load" command)
-        command += f'eval `{self.lmod_dependency_resolver.lmodexec} load {module_to_load}` '
+        command += f"eval `{self.lmod_dependency_resolver.lmodexec} load {module_to_load}` "
         # - Execute the "settarg" command in addition if needed
         if self.lmod_dependency_resolver.settargexec is not None:
-            command += f'&& eval `{self.lmod_dependency_resolver.settargexec} -s sh`'
+            command += f"&& eval `{self.lmod_dependency_resolver.settargexec} -s sh`"
 
         return command
 
@@ -183,4 +191,4 @@ def _string_as_bool(value):
     return str(value).lower() == "true"
 
 
-__all__ = ('LmodDependencyResolver', )
+__all__ = ("LmodDependencyResolver",)
diff --git a/lib/galaxy/tool_util/deps/resolvers/modules.py b/lib/galaxy/tool_util/deps/resolvers/modules.py
index c06d950fc54..3f7ce514bdb 100644
--- a/lib/galaxy/tool_util/deps/resolvers/modules.py
+++ b/lib/galaxy/tool_util/deps/resolvers/modules.py
@@ -10,16 +10,16 @@ import logging
 from io import StringIO
 from os import (
     environ,
-    pathsep
+    pathsep,
 )
 from os.path import (
     exists,
     isdir,
-    join
+    join,
 )
 from subprocess import (
     PIPE,
-    Popen
+    Popen,
 )
 
 from . import (
@@ -32,48 +32,57 @@ from . import (
 log = logging.getLogger(__name__)
 
 DEFAULT_MODULECMD_PATH = "modulecmd"  # Just check path
-DEFAULT_MODULE_PATH = '/usr/share/modules/modulefiles'
-DEFAULT_INDICATOR = '(default)'
+DEFAULT_MODULE_PATH = "/usr/share/modules/modulefiles"
+DEFAULT_INDICATOR = "(default)"
 DEFAULT_MODULE_PREFETCH = "true"
-DEFAULT_MAPPING_FILE = 'config/environment_modules_mapping.yml'
-UNKNOWN_FIND_BY_MESSAGE = "ModuleDependencyResolver does not know how to find modules by [%s], find_by should be one of %s"
+DEFAULT_MAPPING_FILE = "config/environment_modules_mapping.yml"
+UNKNOWN_FIND_BY_MESSAGE = (
+    "ModuleDependencyResolver does not know how to find modules by [%s], find_by should be one of %s"
+)
 
 
 class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver):
-    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'modulepath', 'modulecmd', 'prefetch', 'default_indicator', 'find_by']
+    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + [
+        "base_path",
+        "modulepath",
+        "modulecmd",
+        "prefetch",
+        "default_indicator",
+        "find_by",
+    ]
     resolver_type = "modules"
 
     def __init__(self, dependency_manager, **kwds):
         # Mapping file management
         self._set_default_mapping_file(kwds)
         self._setup_mapping(dependency_manager, **kwds)
-        self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
-        find_by = kwds.get('find_by', 'avail')
+        self.versionless = _string_as_bool(kwds.get("versionless", "false"))
+        find_by = kwds.get("find_by", "avail")
         self.find_by = find_by
-        prefetch = _string_as_bool(kwds.get('prefetch', DEFAULT_MODULE_PREFETCH))
-        self.modulecmd = kwds.get('modulecmd', DEFAULT_MODULECMD_PATH)
-        self.modulepath = kwds.get('modulepath', self.__default_modulespath())
-        self.default_indicator = kwds.get('default_indicator', DEFAULT_INDICATOR)
-        if find_by == 'directory':
+        prefetch = _string_as_bool(kwds.get("prefetch", DEFAULT_MODULE_PREFETCH))
+        self.modulecmd = kwds.get("modulecmd", DEFAULT_MODULECMD_PATH)
+        self.modulepath = kwds.get("modulepath", self.__default_modulespath())
+        self.default_indicator = kwds.get("default_indicator", DEFAULT_INDICATOR)
+        if find_by == "directory":
             self.module_checker = DirectoryModuleChecker(self, self.modulepath, prefetch)
-        elif find_by == 'avail':
+        elif find_by == "avail":
             self.module_checker = AvailModuleChecker(self, self.modulepath, prefetch, self.default_indicator)
         else:
             raise Exception(UNKNOWN_FIND_BY_MESSAGE % (find_by, ["avail", "directory"]))
 
     def __default_modulespath(self):
-        if 'MODULEPATH' in environ:
-            module_path = environ['MODULEPATH']
-        elif 'MODULESHOME' in environ:
-            module_path = join(environ['MODULESHOME'], 'modulefiles')
+        if "MODULEPATH" in environ:
+            module_path = environ["MODULEPATH"]
+        elif "MODULESHOME" in environ:
+            module_path = join(environ["MODULESHOME"], "modulefiles")
         else:
             module_path = DEFAULT_MODULE_PATH
         return module_path
 
     def _set_default_mapping_file(self, resolver_attributes):
-        if 'mapping_files' not in resolver_attributes:
+        if "mapping_files" not in resolver_attributes:
             if exists(DEFAULT_MAPPING_FILE):
-                resolver_attributes['mapping_files'] = DEFAULT_MAPPING_FILE
+                resolver_attributes["mapping_files"] = DEFAULT_MAPPING_FILE
 
     def resolve(self, requirement, **kwds):
         requirement = self._expand_mappings(requirement)
@@ -103,7 +112,9 @@ class DirectoryModuleChecker:
         self.module_dependency_resolver = module_dependency_resolver
         self.directories = modulepath.split(pathsep)
         if prefetch:
-            log.warning("Created module dependency resolver with prefetch enabled, but directory module checker does not support this.")
+            log.warning(
+                "Created module dependency resolver with prefetch enabled, but directory module checker does not support this."
+            )
 
     def has_module(self, module, version):
         has_module = False
@@ -163,8 +174,8 @@ class AvailModuleChecker:
             line_modules = line.split()
             for module in line_modules:
                 if module.endswith(self.default_indicator):
-                    module = module[0:-len(self.default_indicator)].strip()
-                module_parts = module.split('/')
+                    module = module[0 : -len(self.default_indicator)].strip()
+                module_parts = module.split("/")
                 module_version = None
                 if len(module_parts) == 2:
                     module_version = module_parts[1]
@@ -172,8 +183,8 @@ class AvailModuleChecker:
                 yield module_name, module_version
 
     def __module_avail_output(self):
-        avail_command = [self.module_dependency_resolver.modulecmd, 'sh', 'avail']
-        return Popen(avail_command, stderr=PIPE, env={'MODULEPATH': self.modulepath}).communicate()[1]
+        avail_command = [self.module_dependency_resolver.modulecmd, "sh", "avail"]
+        return Popen(avail_command, stderr=PIPE, env={"MODULEPATH": self.modulepath}).communicate()[1]
 
 
 class ModuleDependency(Dependency):
@@ -182,10 +193,17 @@ class ModuleDependency(Dependency):
     Using Environment Modules' 'modulecmd' (specifically 'modulecmd sh load') to
     convert module specifications into shell expressions for inclusion in
     the script used to run a tool in Galaxy."""
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['module_name', 'module_version', 'dependency_resolver']
-    dependency_type = 'module'
 
-    def __init__(self, module_dependency_resolver, module_name, module_version=None, exact=True, dependency_resolver=None):
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + [
+        "module_name",
+        "module_version",
+        "dependency_resolver",
+    ]
+    dependency_type = "module"
+
+    def __init__(
+        self, module_dependency_resolver, module_name, module_version=None, exact=True, dependency_resolver=None
+    ):
         self.module_dependency_resolver = module_dependency_resolver
         self.module_name = module_name
         self.module_version = module_version
@@ -207,10 +225,10 @@ class ModuleDependency(Dependency):
     def shell_commands(self):
         module_to_load = self.module_name
         if self.module_version:
-            module_to_load = f'{self.module_name}/{self.module_version}'
-        command = 'MODULEPATH={}; export MODULEPATH; eval `{} sh load {}`'.format(self.module_dependency_resolver.modulepath,
-                                                                              self.module_dependency_resolver.modulecmd,
-                                                                              module_to_load)
+            module_to_load = f"{self.module_name}/{self.module_version}"
+        command = "MODULEPATH={}; export MODULEPATH; eval `{} sh load {}`".format(
+            self.module_dependency_resolver.modulepath, self.module_dependency_resolver.modulecmd, module_to_load
+        )
         return command
 
 
@@ -218,4 +236,4 @@ def _string_as_bool(value):
     return str(value).lower() == "true"
 
 
-__all__ = ('ModuleDependencyResolver', )
+__all__ = ("ModuleDependencyResolver",)
diff --git a/lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py b/lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py
index 2f3d9b8d126..eec6207906a 100644
--- a/lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py
+++ b/lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py
@@ -2,7 +2,7 @@ import os
 
 from . import (
     Dependency,
-    NullDependency
+    NullDependency,
 )
 from ..brew_exts import (
     build_env_statements,
@@ -12,9 +12,8 @@ from ..brew_exts import (
 
 
 class UsesHomebrewMixin:
-
     def _init_homebrew(self, **kwds):
-        cellar_root = kwds.get('cellar', None)
+        cellar_root = kwds.get("cellar", None)
         if cellar_root is None:
             cellar_root = os.path.join(DEFAULT_HOMEBREW_ROOT, "Cellar")
 
@@ -48,13 +47,11 @@ class UsesHomebrewMixin:
 
 
 class UsesToolDependencyDirMixin:
-
     def _init_base_path(self, dependency_manager, **kwds):
-        self.base_path = os.path.abspath(kwds.get('base_path', dependency_manager.default_base_path))
+        self.base_path = os.path.abspath(kwds.get("base_path", dependency_manager.default_base_path))
 
 
 class UsesInstalledRepositoriesMixin:
-
     def _get_installed_dependency(self, name, type, version=None, **kwds):
         installed_tool_dependencies = kwds.get("installed_tool_dependencies") or []
         for installed_tool_dependency in installed_tool_dependencies:
@@ -65,7 +62,6 @@ class UsesInstalledRepositoriesMixin:
 
 
 class HomebrewDependency(Dependency):
-
     def __init__(self, commands, exact=True):
         self.commands = commands
         self._exact = exact
diff --git a/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
index 0816173ed68..30a8a1bcc39 100644
--- a/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
+++ b/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
@@ -1,9 +1,13 @@
-from os.path import abspath, exists, join
+from os.path import (
+    abspath,
+    exists,
+    join,
+)
 
 from . import NullDependency
 from .galaxy_packages import (
     BaseGalaxyPackageDependencyResolver,
-    ToolShedDependency
+    ToolShedDependency,
 )
 from .resolver_mixins import UsesInstalledRepositoriesMixin
 
@@ -19,7 +23,7 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
     def __init__(self, dependency_manager, **kwds):
         super().__init__(dependency_manager, **kwds)
 
-    def _find_dep_versioned(self, name, version, type='package', **kwds):
+    def _find_dep_versioned(self, name, version, type="package", **kwds):
         installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds)
         if installed_tool_dependency:
             path = self._get_package_installed_dependency_path(installed_tool_dependency, name, version)
@@ -27,8 +31,8 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
         else:
             return NullDependency(version=version, name=name)
 
-    def _find_dep_default(self, name, type='package', **kwds):
-        if type == 'set_environment' and kwds.get('installed_tool_dependencies', None):
+    def _find_dep_default(self, name, type="package", **kwds):
+        if type == "set_environment" and kwds.get("installed_tool_dependencies", None):
             installed_tool_dependency = self._get_installed_dependency(name, type, version=None, **kwds)
             if installed_tool_dependency:
                 dependency = self._get_set_environment_installed_dependency_script_path(installed_tool_dependency, name)
@@ -36,7 +40,15 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
                 has_script_dep = is_galaxy_dep and dependency.script and dependency.path
                 if has_script_dep:
                     # Environment settings do not use versions.
-                    return ToolShedDependency(dependency.script, dependency.path, name, 'set_environment', None, True, dependency_resolver=self)
+                    return ToolShedDependency(
+                        dependency.script,
+                        dependency.path,
+                        name,
+                        "set_environment",
+                        None,
+                        True,
+                        dependency_resolver=self,
+                    )
         return NullDependency(version=None, name=name)
 
     def _get_package_installed_dependency_path(self, installed_tool_dependency, name, version):
@@ -48,22 +60,26 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
             version,
             tool_shed_repository.owner,
             tool_shed_repository.name,
-            tool_shed_repository.installed_changeset_revision
+            tool_shed_repository.installed_changeset_revision,
         )
 
     def _get_set_environment_installed_dependency_script_path(self, installed_tool_dependency, name):
         tool_shed_repository = installed_tool_dependency.tool_shed_repository
         base_path = self.base_path
-        path = abspath(join(base_path,
-                            'environment_settings',
-                            name,
-                            tool_shed_repository.owner,
-                            tool_shed_repository.name,
-                            tool_shed_repository.installed_changeset_revision))
+        path = abspath(
+            join(
+                base_path,
+                "environment_settings",
+                name,
+                tool_shed_repository.owner,
+                tool_shed_repository.name,
+                tool_shed_repository.installed_changeset_revision,
+            )
+        )
         if exists(path):
-            script = join(path, 'env.sh')
-            return ToolShedDependency(script, path, name, 'set_environment', None, True, dependency_resolver=self)
+            script = join(path, "env.sh")
+            return ToolShedDependency(script, path, name, "set_environment", None, True, dependency_resolver=self)
         return NullDependency(version=None, name=name)
 
 
-__all__ = ('ToolShedPackageDependencyResolver', )
+__all__ = ("ToolShedPackageDependencyResolver",)
diff --git a/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
index 45685abb7b1..cb4593639e4 100644
--- a/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
+++ b/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
@@ -25,12 +25,12 @@ from os import listdir
 from os.path import (
     exists,
     getmtime,
-    join
+    join,
 )
 
 from . import (
     Dependency,
-    NullDependency
+    NullDependency,
 )
 from .galaxy_packages import BaseGalaxyPackageDependencyResolver
 
@@ -41,17 +41,20 @@ PREFERRED_OWNERS = f"{MANUAL},iuc,devteam"
 
 
 class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver):
-    dict_collection_visible_keys = BaseGalaxyPackageDependencyResolver.dict_collection_visible_keys + ['preferred_owners', 'select_by_owner']
+    dict_collection_visible_keys = BaseGalaxyPackageDependencyResolver.dict_collection_visible_keys + [
+        "preferred_owners",
+        "select_by_owner",
+    ]
     resolver_type = "unlinked_tool_shed_packages"
 
     def __init__(self, dependency_manager, **kwds):
         super().__init__(dependency_manager, **kwds)
         # Provide a list of preferred owners whose dependency to use
-        self.preferred_owners = kwds.get('preferred_owners', PREFERRED_OWNERS).split(",")
+        self.preferred_owners = kwds.get("preferred_owners", PREFERRED_OWNERS).split(",")
         # Option to ignore owner and just use last modified time
-        self.select_by_owner = str(kwds.get('select_by_owner', "true")).lower() != "false"
+        self.select_by_owner = str(kwds.get("select_by_owner", "true")).lower() != "false"
 
-    def _find_dep_versioned(self, name, version, type='package', **kwds):
+    def _find_dep_versioned(self, name, version, type="package", **kwds):
         try:
             possibles = self._find_possible_dependencies(name, version, type)
             if len(possibles) == 0:
@@ -90,7 +93,9 @@ class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResol
                                 revision_path = join(package_path, revision)
                                 package = self._galaxy_package_dep(revision_path, version, name, type, True)
                                 if not isinstance(package, NullDependency):
-                                    log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path)
+                                    log.debug(
+                                        "Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path
+                                    )
                                     possibles.append(CandidateDependency(package, package_path, owner))
         return possibles
 
@@ -122,8 +127,8 @@ class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResol
 
 
 class CandidateDependency(Dependency):
-    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['dependency', 'path', 'owner']
-    dependency_type = 'unlinked_tool_shed_package'
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ["dependency", "path", "owner"]
+    dependency_type = "unlinked_tool_shed_package"
 
     @property
     def exact(self):
@@ -141,7 +146,7 @@ class CandidateDependency(Dependency):
         return self.dependency.shell_commands()
 
 
-__all__ = ('UnlinkedToolShedPackageDependencyResolver', )
+__all__ = ("UnlinkedToolShedPackageDependencyResolver",)
 
 """
 At the time of writing July 3 2015 this resolver has to be plugged in.
diff --git a/lib/galaxy/tool_util/deps/singularity_util.py b/lib/galaxy/tool_util/deps/singularity_util.py
index 5117036873a..c783782c7d6 100644
--- a/lib/galaxy/tool_util/deps/singularity_util.py
+++ b/lib/galaxy/tool_util/deps/singularity_util.py
@@ -8,12 +8,14 @@ DEFAULT_SUDO_COMMAND = "sudo"
 DEFAULT_RUN_EXTRA_ARGUMENTS = None
 
 
-def pull_mulled_singularity_command(docker_image_identifier,
-                                    cache_directory,
-                                    namespace=None,
-                                    singularity_cmd=DEFAULT_SINGULARITY_COMMAND,
-                                    sudo=DEFAULT_SUDO,
-                                    sudo_cmd=DEFAULT_SUDO_COMMAND):
+def pull_mulled_singularity_command(
+    docker_image_identifier,
+    cache_directory,
+    namespace=None,
+    singularity_cmd=DEFAULT_SINGULARITY_COMMAND,
+    sudo=DEFAULT_SUDO,
+    sudo_cmd=DEFAULT_SUDO_COMMAND,
+):
     command_parts = []
     command_parts += _singularity_prefix(
         singularity_cmd=singularity_cmd,
@@ -24,16 +26,18 @@ def pull_mulled_singularity_command(docker_image_identifier,
     if namespace:
         prefix = f"docker://quay.io/{namespace}/"
         if docker_image_identifier.startswith(prefix):
-            save_path = docker_image_identifier[len(prefix):]
+            save_path = docker_image_identifier[len(prefix) :]
     command_parts.extend(["build", os.path.join(cache_directory, save_path), docker_image_identifier])
     return command_parts
 
 
-def pull_singularity_command(image_identifier: str,
-                             cache_path: str,
-                             singularity_cmd: str = DEFAULT_SINGULARITY_COMMAND,
-                             sudo: bool = DEFAULT_SUDO,
-                             sudo_cmd: str = DEFAULT_SUDO_COMMAND):
+def pull_singularity_command(
+    image_identifier: str,
+    cache_path: str,
+    singularity_cmd: str = DEFAULT_SINGULARITY_COMMAND,
+    sudo: bool = DEFAULT_SUDO,
+    sudo_cmd: str = DEFAULT_SUDO_COMMAND,
+):
     # Make sure cache dir exists
     dirname = os.path.dirname(os.path.normpath(cache_path))
     os.makedirs(dirname, exist_ok=True)
@@ -53,7 +57,7 @@ def build_singularity_run_command(
     sudo=DEFAULT_SUDO,
     sudo_cmd=DEFAULT_SUDO_COMMAND,
     guest_ports=False,
-    container_name=None
+    container_name=None,
 ):
     volumes = volumes or []
     env = env or []
@@ -61,7 +65,7 @@ def build_singularity_run_command(
     # http://singularity.lbl.gov/docs-environment-metadata
     home = None
     for (key, value) in env:
-        if key == 'HOME':
+        if key == "HOME":
             home = value
         command_parts.extend([f"SINGULARITYENV_{key}={value}"])
     command_parts += _singularity_prefix(
@@ -84,10 +88,7 @@ def build_singularity_run_command(
 
 
 def _singularity_prefix(
-    singularity_cmd=DEFAULT_SINGULARITY_COMMAND,
-    sudo=DEFAULT_SUDO,
-    sudo_cmd=DEFAULT_SUDO_COMMAND,
-    **kwds
+    singularity_cmd=DEFAULT_SINGULARITY_COMMAND, sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, **kwds
 ):
     """Prefix to issue a singularity command."""
     command_parts = []
@@ -97,5 +98,4 @@ def _singularity_prefix(
     return command_parts
 
 
-__all__ = ("build_singularity_run_command", "pull_mulled_singularity_command",
-           "pull_singularity_command")
+__all__ = ("build_singularity_run_command", "pull_mulled_singularity_command", "pull_singularity_command")
diff --git a/lib/galaxy/tool_util/deps/views.py b/lib/galaxy/tool_util/deps/views.py
index 4423c13b49b..5340adc181b 100644
--- a/lib/galaxy/tool_util/deps/views.py
+++ b/lib/galaxy/tool_util/deps/views.py
@@ -1,5 +1,8 @@
 from galaxy import exceptions
-from galaxy.util import asbool, listify
+from galaxy.util import (
+    asbool,
+    listify,
+)
 from .dependencies import ToolInfo
 from .resolvers import (
     ContainerDependency,
@@ -8,7 +11,7 @@ from .resolvers import (
 
 
 class DependencyResolversView:
-    """ Provide a RESTfulish/JSONy interface to a galaxy.tool_util.deps.DependencyResolver
+    """Provide a RESTfulish/JSONy interface to a galaxy.tool_util.deps.DependencyResolver
     object. This can be adapted by the Galaxy web framework or other web apps.
     """
 
@@ -53,19 +56,20 @@ class DependencyResolversView:
         Resolves dependencies to build a requirements status in the admin panel/API
         """
         to_deps_kwds = {
-            'install': False,
-            'return_null': True,
-            'installed_tool_dependencies': installed_tool_dependencies
+            "install": False,
+            "return_null": True,
+            "installed_tool_dependencies": installed_tool_dependencies,
         }
         to_deps_kwds.update(kwd)
-        dependencies_per_tool = {tool: self._dependency_manager.requirements_to_dependencies(requirements,
-                                                                                             **to_deps_kwds)
-                                 for tool, requirements in tool_requirements_d.items()}
+        dependencies_per_tool = {
+            tool: self._dependency_manager.requirements_to_dependencies(requirements, **to_deps_kwds)
+            for tool, requirements in tool_requirements_d.items()
+        }
         return dependencies_per_tool
 
     def uninstall_dependencies(self, index=None, resolver_type=None, container_type=None, **payload):
         """Attempt to uninstall requirements. Returns 0 if successfull, else None."""
-        requirements = payload.get('requirements')
+        requirements = payload.get("requirements")
         if not requirements:
             return None
         if index:
@@ -93,7 +97,7 @@ class DependencyResolversView:
         unused_dependencies = []
         toolbox_requirements_status = self.toolbox_requirements_status
         for resolver in self._dependency_resolvers:
-            if hasattr(resolver, 'unused_dependency_paths'):
+            if hasattr(resolver, "unused_dependency_paths"):
                 unused_dependencies.extend(resolver.unused_dependency_paths(toolbox_requirements_status))
         return set(unused_dependencies)
 
@@ -107,7 +111,7 @@ class DependencyResolversView:
         toolbox_requirements_status = self.toolbox_requirements_status
         removed_environments = set()
         for resolver in self._dependency_resolvers:
-            if hasattr(resolver, 'unused_dependency_paths') and hasattr(resolver, 'uninstall_environments'):
+            if hasattr(resolver, "unused_dependency_paths") and hasattr(resolver, "uninstall_environments"):
                 unused_dependencies = resolver.unused_dependency_paths(toolbox_requirements_status)
                 can_remove = envs_to_remove & set(unused_dependencies)
                 exit_code = resolver.uninstall_environments(can_remove)
@@ -117,7 +121,7 @@ class DependencyResolversView:
         return list(removed_environments)
 
     def install_dependencies(self, requirements, **kwds):
-        kwds['install'] = True
+        kwds["install"] = True
         return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds)
 
     def install_dependency(self, index=None, **payload):
@@ -145,31 +149,22 @@ class DependencyResolversView:
         """
         resolver = self._dependency_resolver(index)
         if resolver.read_only:
-            raise exceptions.RequestParameterInvalidException("Attempted to install on a read_only dependency resolver.")
+            raise exceptions.RequestParameterInvalidException(
+                "Attempted to install on a read_only dependency resolver."
+            )
         if resolver.disabled:
             raise exceptions.RequestParameterInvalidException("Attempted to install on a disabled dependency resolver.")
 
         name, version, type, extra_kwds = self._parse_dependency_info(payload)
-        return resolver.install_dependency(
-            name=name,
-            version=version,
-            type=type,
-            **extra_kwds
-        )
+        return resolver.install_dependency(name=name, version=version, type=type, **extra_kwds)
 
     def _dependency(self, index=None, **kwds):
         if index is not None:
             index = int(index)
 
         name, version, type, extra_kwds = self._parse_dependency_info(kwds)
-        resolve_kwds = dict(
-            job_directory=None,
-            index=index,
-            **extra_kwds
-        )
-        dependency = self._dependency_manager.find_dep(
-            name, version=version, type=type, **resolve_kwds
-        )
+        resolve_kwds = dict(job_directory=None, index=index, **extra_kwds)
+        dependency = self._dependency_manager.find_dep(name, version=version, type=type, **resolve_kwds)
         return dependency.to_dict()
 
     def _parse_dependency_info(self, kwds):
@@ -200,14 +195,22 @@ class DependencyResolversView:
         """
         List index for all active resolvers that have the 'install_dependency' attribute.
         """
-        return [index for index, resolver in enumerate(self._dependency_resolvers) if not resolver.read_only and not resolver.disabled]
+        return [
+            index
+            for index, resolver in enumerate(self._dependency_resolvers)
+            if not resolver.read_only and not resolver.disabled
+        ]
 
     @property
     def uninstallable_resolvers(self):
         """
         List index for all active resolvers that can uninstall dependencies that have been installed through this resolver.
         """
-        return [index for index, resolver in enumerate(self._dependency_resolvers) if resolver.can_uninstall_dependencies and not resolver.disabled]
+        return [
+            index
+            for index, resolver in enumerate(self._dependency_resolvers)
+            if resolver.can_uninstall_dependencies and not resolver.disabled
+        ]
 
     @property
     def tool_ids_by_requirements(self):
@@ -228,23 +231,28 @@ class DependencyResolversView:
 
     def summarize_requirements(self, **kwds):
         summary_kwds = {}
-        if 'index' in kwds:
-            summary_kwds['index'] = int(kwds['index'])
-        if 'include_containers' in kwds:
-            summary_kwds['include_containers'] = asbool(kwds['include_containers'])
-        if 'container_type' in kwds:
-            summary_kwds['container_type'] = kwds['container_type']
-        if 'resolver_type' in kwds:
-            summary_kwds['resolver_type'] = kwds['resolver_type']
-        if 'search' in kwds:
-            summary_kwds['search'] = asbool(kwds['search'])
-        if 'install' in kwds:
-            summary_kwds['install'] = asbool(kwds['install'])
+        if "index" in kwds:
+            summary_kwds["index"] = int(kwds["index"])
+        if "include_containers" in kwds:
+            summary_kwds["include_containers"] = asbool(kwds["include_containers"])
+        if "container_type" in kwds:
+            summary_kwds["container_type"] = kwds["container_type"]
+        if "resolver_type" in kwds:
+            summary_kwds["resolver_type"] = kwds["resolver_type"]
+        if "search" in kwds:
+            summary_kwds["search"] = asbool(kwds["search"])
+        if "install" in kwds:
+            summary_kwds["install"] = asbool(kwds["install"])
 
         tool_ids_by_requirements = self.tool_ids_by_requirements
-        statuses = {r: self.get_requirements_status(tool_requirements_d={tids[0]: r},
-                                                installed_tool_dependencies=self._app.toolbox.tools_by_id[tids[0]].installed_tool_dependencies, **summary_kwds)
-                for r, tids in tool_ids_by_requirements.items()}
+        statuses = {
+            r: self.get_requirements_status(
+                tool_requirements_d={tids[0]: r},
+                installed_tool_dependencies=self._app.toolbox.tools_by_id[tids[0]].installed_tool_dependencies,
+                **summary_kwds,
+            )
+            for r, tids in tool_ids_by_requirements.items()
+        }
         if kwds.get("for_json", False):
             # All public attributes of this class should be returning JSON - this is meant to mimic a restful API.
             rval = []
@@ -259,18 +267,18 @@ class DependencyResolversView:
 
     def summarize_tools(self, **kwds):
         summary_kwds = {}
-        if 'index' in kwds:
-            summary_kwds['index'] = int(kwds['index'])
-        if 'include_containers' in kwds:
-            summary_kwds['include_containers'] = asbool(kwds['include_containers'])
-        if 'container_type' in kwds:
-            summary_kwds['container_type'] = kwds['container_type']
-        if 'resolver_type' in kwds:
-            summary_kwds['resolver_type'] = kwds['resolver_type']
-        if 'search' in kwds:
-            summary_kwds['search'] = asbool(kwds['search'])
-        if 'install' in kwds:
-            summary_kwds['install'] = asbool(kwds['install'])
+        if "index" in kwds:
+            summary_kwds["index"] = int(kwds["index"])
+        if "include_containers" in kwds:
+            summary_kwds["include_containers"] = asbool(kwds["include_containers"])
+        if "container_type" in kwds:
+            summary_kwds["container_type"] = kwds["container_type"]
+        if "resolver_type" in kwds:
+            summary_kwds["resolver_type"] = kwds["resolver_type"]
+        if "search" in kwds:
+            summary_kwds["search"] = asbool(kwds["search"])
+        if "install" in kwds:
+            summary_kwds["install"] = asbool(kwds["install"])
 
         tool_ids = pop_tool_ids(kwds)
 
@@ -280,9 +288,12 @@ class DependencyResolversView:
                 continue
 
             requirements = tool.tool_requirements
-            status = self.get_requirements_status(tool_requirements_d={tid: requirements},
-                                                  installed_tool_dependencies=tool.installed_tool_dependencies,
-                                                  tool_instance=tool, **summary_kwds)
+            status = self.get_requirements_status(
+                tool_requirements_d={tid: requirements},
+                installed_tool_dependencies=tool.installed_tool_dependencies,
+                tool_instance=tool,
+                **summary_kwds,
+            )
             item = {}
             item["requirements"] = requirements.to_dict()
             item["status"] = status
@@ -313,13 +324,12 @@ class DependencyResolversView:
                 resolver.clean()
                 return "OK"
         else:
-            [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, 'clean')]
+            [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, "clean")]
             return "OK"
 
 
 class ContainerResolutionView:
-    """
-    """
+    """ """
 
     def __init__(self, app):
         self._app = app
@@ -332,20 +342,20 @@ class ContainerResolutionView:
 
     def resolve(self, **kwds):
         find_best_kwds = {
-            'install': False,
-            'enabled_container_types': ['docker', 'singularity'],
-            'resolution_cache': kwds.get("resolution_cache"),
-            'session': kwds.get('session'),
+            "install": False,
+            "enabled_container_types": ["docker", "singularity"],
+            "resolution_cache": kwds.get("resolution_cache"),
+            "session": kwds.get("session"),
         }
 
-        if 'index' in kwds:
-            find_best_kwds['index'] = int(kwds['index'])
-        if 'container_type' in kwds:
-            find_best_kwds['enabled_container_types'] = [kwds['container_type']]
-        if 'resolver_type' in kwds:
-            find_best_kwds['resolver_type'] = kwds['resolver_type']
-        if 'install' in kwds:
-            find_best_kwds['install'] = asbool(kwds['install'])
+        if "index" in kwds:
+            find_best_kwds["index"] = int(kwds["index"])
+        if "container_type" in kwds:
+            find_best_kwds["enabled_container_types"] = [kwds["container_type"]]
+        if "resolver_type" in kwds:
+            find_best_kwds["resolver_type"] = kwds["resolver_type"]
+        if "install" in kwds:
+            find_best_kwds["install"] = asbool(kwds["install"])
 
         tool_info_kwds = {}
         tool_id = kwds["tool_id"]
@@ -358,26 +368,23 @@ class ContainerResolutionView:
         # mimics the default behavior of searching for containers through the dependency resolution
         # component. Not useful for tool execution but perhaps when summarizing mulled containers for requirements.
         if not requirements_only:
-            tool_info_kwds['container_descriptions'] = tool.containers
-            tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment
-            tool_info_kwds['tool_id'] = tool.id
-            tool_info_kwds['tool_version'] = tool.version
+            tool_info_kwds["container_descriptions"] = tool.containers
+            tool_info_kwds["requires_galaxy_python_environment"] = tool.requires_galaxy_python_environment
+            tool_info_kwds["tool_id"] = tool.id
+            tool_info_kwds["tool_version"] = tool.version
 
         find_best_kwds["tool_info"] = ToolInfo(**tool_info_kwds)
 
         # Consider implementing 'search' to match dependency resolution API.
-        resolved_container_description = self._app.container_finder.resolve(
-            **find_best_kwds
-        )
+        resolved_container_description = self._app.container_finder.resolve(**find_best_kwds)
         if resolved_container_description:
-            status = ContainerDependency(resolved_container_description.container_description, container_resolver=resolved_container_description.container_resolver).to_dict()
+            status = ContainerDependency(
+                resolved_container_description.container_description,
+                container_resolver=resolved_container_description.container_resolver,
+            ).to_dict()
         else:
             status = NullDependency().to_dict()
-        return {
-            "tool_id": kwds["tool_id"],
-            "status": status,
-            "requirements": requirements.to_dict()
-        }
+        return {"tool_id": kwds["tool_id"], "status": status, "requirements": requirements.to_dict()}
 
     def resolve_toolbox(self, **kwds):
         rval = []
diff --git a/lib/galaxy/tool_util/edam_util.py b/lib/galaxy/tool_util/edam_util.py
index 3b85bb45635..26102b1ae37 100644
--- a/lib/galaxy/tool_util/edam_util.py
+++ b/lib/galaxy/tool_util/edam_util.py
@@ -1,15 +1,19 @@
 import os
-from typing import Dict, Optional, TextIO
+from typing import (
+    Dict,
+    Optional,
+    TextIO,
+)
 
 try:
     from edam_ontology.streams import tabular_stream
 except ImportError:
     tabular_stream = None
 
-EDAM_PREFIX = 'http://edamontology.org/'
+EDAM_PREFIX = "http://edamontology.org/"
 
-ROOT_OPERATION = 'operation_0004'
-ROOT_TOPIC = 'topic_0003'
+ROOT_OPERATION = "operation_0004"
+ROOT_TOPIC = "topic_0003"
 
 
 def load_edam_tree(path: Optional[str] = None):
@@ -17,7 +21,9 @@ def load_edam_tree(path: Optional[str] = None):
         assert os.path.exists(path), f"Failed to load EDAM tabular data at [{path}] path does not exist."
         handle = open(path)
     else:
-        assert tabular_stream is not None, "Failed to load optional import from edam-onotology package, install using [pip install edam-ontology]."
+        assert (
+            tabular_stream is not None
+        ), "Failed to load optional import from edam-onotology package, install using [pip install edam-ontology]."
         handle = tabular_stream()
     return load_edam_tree_from_tsv_stream(handle)
 
@@ -26,15 +32,15 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
     edam: Dict[str, Dict] = {}
 
     def _recurse_edam_parents(term, path=None):
-        if edam[term]['parents'] and len(edam[term]['parents']) > 0:
-            for parent in edam[term]['parents']:
+        if edam[term]["parents"] and len(edam[term]["parents"]) > 0:
+            for parent in edam[term]["parents"]:
                 yield from _recurse_edam_parents(parent, path + [parent])
         else:
             yield path
 
     is_first = True
     for line in tsv_stream.readlines():
-        fields = line.split('\t')
+        fields = line.split("\t")
         if is_first:
             columns = {}
             for i, field in enumerate(fields):
@@ -51,17 +57,17 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
         if not term.startswith(EDAM_PREFIX):
             continue
 
-        term_id = term[len(EDAM_PREFIX):]
+        term_id = term[len(EDAM_PREFIX) :]
 
         # Only care about formats and operations
-        if not (term_id.startswith('operation_') or term_id.startswith('topic_')):
+        if not (term_id.startswith("operation_") or term_id.startswith("topic_")):
             continue
 
-        parents = fields[parents_column].split('|')
+        parents = fields[parents_column].split("|")
         edam[term_id] = {
-            'label': fields[label_column],
-            'definition': fields[defintion_column].strip('"'),
-            'parents': [x[len(EDAM_PREFIX):] for x in parents if x.startswith(EDAM_PREFIX)],
+            "label": fields[label_column],
+            "definition": fields[defintion_column].strip('"'),
+            "parents": [x[len(EDAM_PREFIX) :] for x in parents if x.startswith(EDAM_PREFIX)],
         }
 
     for term in sorted(edam.keys()):
@@ -69,9 +75,9 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO):
         for x in _recurse_edam_parents(term, path=[]):
             if x[-2:] not in tails:
                 tails.append(x[-2:])
-        edam[term]['path'] = tails
+        edam[term]["path"] = tails
 
     return edam
 
 
-__all__ = ('load_edam_tree', 'ROOT_OPERATION', 'ROOT_TOPIC')
+__all__ = ("load_edam_tree", "ROOT_OPERATION", "ROOT_TOPIC")
diff --git a/lib/galaxy/tool_util/fetcher.py b/lib/galaxy/tool_util/fetcher.py
index 13d12d07a40..c9874e017f2 100644
--- a/lib/galaxy/tool_util/fetcher.py
+++ b/lib/galaxy/tool_util/fetcher.py
@@ -2,13 +2,13 @@ from galaxy.util import plugin_config
 
 
 class ToolLocationFetcher:
-
     def __init__(self):
         self.resolver_classes = self.__resolvers_dict()
 
     def __resolvers_dict(self):
         import galaxy.tool_util.locations
-        return plugin_config.plugins_dict(galaxy.tool_util.locations, 'scheme')
+
+        return plugin_config.plugins_dict(galaxy.tool_util.locations, "scheme")
 
     def to_tool_path(self, path_or_uri_like, **kwds):
         if "://" not in path_or_uri_like:
diff --git a/lib/galaxy/tool_util/lint.py b/lib/galaxy/tool_util/lint.py
index a16d19664ae..3d3e89fe32d 100644
--- a/lib/galaxy/tool_util/lint.py
+++ b/lib/galaxy/tool_util/lint.py
@@ -54,11 +54,14 @@ from typing import (
     Optional,
     Type,
     TypeVar,
-    Union
+    Union,
 )
 
 from galaxy.tool_util.parser import get_tool_source
-from galaxy.util import etree, submodules
+from galaxy.util import (
+    etree,
+    submodules,
+)
 
 
 class LintLevel(IntEnum):
@@ -74,6 +77,7 @@ class LintMessage:
     """
     a message from the linter
     """
+
     def __init__(self, level: str, message: str, **kwargs):
         self.level = level
         self.message = message
@@ -131,7 +135,7 @@ class XMLLintMessageXPath(LintMessage):
         return rval
 
 
-LintTargetType = TypeVar('LintTargetType')
+LintTargetType = TypeVar("LintTargetType")
 
 
 # TODO: Nothing inherently tool-y about LintContext and in fact
@@ -144,11 +148,13 @@ class LintContext:
     object_name: Optional[str]
     message_list: List[LintMessage]
 
-    def __init__(self,
-                 level: Union[LintLevel, str],
-                 lint_message_class: Type[LintMessage] = LintMessage,
-                 skip_types: Optional[List[str]] = None,
-                 object_name: Optional[str] = None):
+    def __init__(
+        self,
+        level: Union[LintLevel, str],
+        lint_message_class: Type[LintMessage] = LintMessage,
+        skip_types: Optional[List[str]] = None,
+        object_name: Optional[str] = None,
+    ):
         self.skip_types = skip_types or []
         if isinstance(level, str):
             self.level = LintLevel[level.upper()]
@@ -166,11 +172,8 @@ class LintContext:
     def found_warns(self) -> bool:
         return len(self.warn_messages) > 0
 
-    def lint(self,
-             name: str,
-             lint_func: Callable[[LintTargetType, 'LintContext'], None],
-             lint_target: LintTargetType):
-        name = name.replace("tsts", "tests")[len("lint_"):]
+    def lint(self, name: str, lint_func: Callable[[LintTargetType, "LintContext"], None], lint_target: LintTargetType):
+        name = name.replace("tsts", "tests")[len("lint_") :]
         if name in self.skip_types:
             return
 
@@ -261,13 +264,15 @@ class LintContext:
         found_warns = self.found_warns
         found_errors = self.found_errors
         if fail_level >= LintLevel.WARN:
-            lint_fail = (found_warns or found_errors)
+            lint_fail = found_warns or found_errors
         elif fail_level >= LintLevel.ERROR:
             lint_fail = found_errors
         return lint_fail
 
 
-def lint_tool_source(tool_source, level=LintLevel.ALL, fail_level=LintLevel.WARN, extra_modules=None, skip_types=None, name=None) -> bool:
+def lint_tool_source(
+    tool_source, level=LintLevel.ALL, fail_level=LintLevel.WARN, extra_modules=None, skip_types=None, name=None
+) -> bool:
     """
     apply all (applicable) linters from the linters submodule
     and the ones in extramodules
@@ -294,13 +299,23 @@ def get_lint_context_for_tool_source(tool_source, extra_modules=None, skip_types
     return lint_context
 
 
-def lint_xml(tool_xml, level=LintLevel.ALL, fail_level=LintLevel.WARN, lint_message_class=LintMessage, extra_modules=None, skip_types=None, name=None) -> bool:
+def lint_xml(
+    tool_xml,
+    level=LintLevel.ALL,
+    fail_level=LintLevel.WARN,
+    lint_message_class=LintMessage,
+    extra_modules=None,
+    skip_types=None,
+    name=None,
+) -> bool:
     """
     lint an xml tool
     """
     extra_modules = extra_modules or []
     skip_types = skip_types or []
-    lint_context = LintContext(level=level, lint_message_class=lint_message_class, skip_types=skip_types, object_name=name)
+    lint_context = LintContext(
+        level=level, lint_message_class=lint_message_class, skip_types=skip_types, object_name=name
+    )
     lint_xml_with(lint_context, tool_xml, extra_modules)
 
     return not lint_context.failed(fail_level)
@@ -309,6 +324,7 @@ def lint_xml(tool_xml, level=LintLevel.ALL, fail_level=LintLevel.WARN, lint_mess
 def lint_tool_source_with(lint_context, tool_source, extra_modules=None) -> LintContext:
     extra_modules = extra_modules or []
     import galaxy.tool_util.linters
+
     tool_xml = getattr(tool_source, "xml_tree", None)
     tool_type = tool_source.parse_tool_type() or "default"
     linter_modules = submodules.import_submodules(galaxy.tool_util.linters)
diff --git a/lib/galaxy/tool_util/linters/_util.py b/lib/galaxy/tool_util/linters/_util.py
index 3224150c792..1e12c82faa1 100644
--- a/lib/galaxy/tool_util/linters/_util.py
+++ b/lib/galaxy/tool_util/linters/_util.py
@@ -3,7 +3,7 @@ import re
 
 def is_datasource(tool_xml):
     """Returns true if the tool is a datasource tool"""
-    return tool_xml.getroot().attrib.get('tool_type', '') == 'data_source'
+    return tool_xml.getroot().attrib.get("tool_type", "") == "data_source"
 
 
 def is_valid_cheetah_placeholder(name):
diff --git a/lib/galaxy/tool_util/linters/citations.py b/lib/galaxy/tool_util/linters/citations.py
index b3940272ef9..562691c1521 100644
--- a/lib/galaxy/tool_util/linters/citations.py
+++ b/lib/galaxy/tool_util/linters/citations.py
@@ -23,14 +23,16 @@ def lint_citations(tool_xml, lint_ctx):
     valid_citations = 0
     for citation in citations[0]:
         if citation.tag != "citation":
-            lint_ctx.warn(f"Unknown tag discovered in citations block [{citation.tag}], will be ignored.", node=citation)
+            lint_ctx.warn(
+                f"Unknown tag discovered in citations block [{citation.tag}], will be ignored.", node=citation
+            )
             continue
         citation_type = citation.attrib.get("type")
-        if citation_type not in ('bibtex', 'doi'):
+        if citation_type not in ("bibtex", "doi"):
             lint_ctx.warn(f"Unknown citation type discovered [{citation_type}], will be ignored.", node=citation)
             continue
         if citation.text is None or not citation.text.strip():
-            lint_ctx.error(f'Empty {citation_type} citation.', node=citation)
+            lint_ctx.error(f"Empty {citation_type} citation.", node=citation)
             continue
         valid_citations += 1
 
diff --git a/lib/galaxy/tool_util/linters/general.py b/lib/galaxy/tool_util/linters/general.py
index a7e472544d9..086570a12f6 100644
--- a/lib/galaxy/tool_util/linters/general.py
+++ b/lib/galaxy/tool_util/linters/general.py
@@ -3,7 +3,6 @@ import re
 
 import packaging.version
 
-
 ERROR_VERSION_MSG = "Tool version is missing or empty."
 WARN_VERSION_MSG = "Tool version [%s] is not compliant with PEP 440."
 VALID_VERSION_MSG = "Tool defines a version [%s]."
@@ -21,8 +20,7 @@ PROFILE_INVALID_MSG = "Tool specifies an invalid profile version [%s]."
 
 WARN_WHITESPACE_MSG = "%s contains whitespace, this may cause errors: [%s]."
 WARN_WHITESPACE_PRESUFFIX = "%s is pre/suffixed by whitespace, this may cause errors: [%s]."
-WARN_ID_WHITESPACE_MSG = (
-    "Tool ID contains whitespace - this is discouraged: [%s].")
+WARN_ID_WHITESPACE_MSG = "Tool ID contains whitespace - this is discouraged: [%s]."
 
 lint_tool_types = ["*"]
 
@@ -35,14 +33,14 @@ def lint_general(tool_source, lint_ctx):
         tool_node = tool_xml.getroot()
     else:
         tool_node = None
-    version = tool_source.parse_version() or ''
+    version = tool_source.parse_version() or ""
     parsed_version = packaging.version.parse(version)
     if not version:
         lint_ctx.error(ERROR_VERSION_MSG, node=tool_node)
     elif isinstance(parsed_version, packaging.version.LegacyVersion):
         lint_ctx.warn(WARN_VERSION_MSG % version, node=tool_node)
     elif version != version.strip():
-        lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ('Tool version', version), node=tool_node)
+        lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ("Tool version", version), node=tool_node)
     else:
         lint_ctx.valid(VALID_VERSION_MSG % version, node=tool_node)
 
@@ -50,7 +48,7 @@ def lint_general(tool_source, lint_ctx):
     if not name:
         lint_ctx.error(ERROR_NAME_MSG, node=tool_node)
     elif name != name.strip():
-        lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ('Tool name', name), node=tool_node)
+        lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ("Tool name", name), node=tool_node)
     else:
         lint_ctx.valid(VALID_NAME_MSG % name, node=tool_node)
 
@@ -80,5 +78,4 @@ def lint_general(tool_source, lint_ctx):
                 lint_ctx.warn(f"Requirement {r.name} defines no version")
             # Warn requirement attributes with leading/trailing whitespace:
             elif r.version != r.version.strip():
-                lint_ctx.warn(
-                    WARN_WHITESPACE_MSG % ('Requirement version', r.version))
+                lint_ctx.warn(WARN_WHITESPACE_MSG % ("Requirement version", r.version))
diff --git a/lib/galaxy/tool_util/linters/help.py b/lib/galaxy/tool_util/linters/help.py
index 3d22accabdc..7d5a0ea9951 100644
--- a/lib/galaxy/tool_util/linters/help.py
+++ b/lib/galaxy/tool_util/linters/help.py
@@ -20,7 +20,7 @@ def lint_help(tool_xml, lint_ctx):
         lint_ctx.warn("No help section found, consider adding a help section to your tool.", node=root)
         return
 
-    help = helps[0].text or ''
+    help = helps[0].text or ""
     if not help.strip():
         lint_ctx.warn("Help section appears to be empty.", node=helps[0])
         return
diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py
index 39afa939ed8..1dfa95169be 100644
--- a/lib/galaxy/tool_util/linters/inputs.py
+++ b/lib/galaxy/tool_util/linters/inputs.py
@@ -4,48 +4,105 @@ import re
 from galaxy.util import string_as_bool
 from ._util import (
     is_datasource,
-    is_valid_cheetah_placeholder
+    is_valid_cheetah_placeholder,
 )
 from ..parser.util import _parse_name
 
 FILTER_TYPES = [
-    'data_meta',
-    'param_value',
-    'static_value',
-    'regexp',
-    'unique_value',
-    'multiple_splitter',
-    'attribute_value_splitter',
-    'add_value',
-    'remove_value',
-    'sort_by',
+    "data_meta",
+    "param_value",
+    "static_value",
+    "regexp",
+    "unique_value",
+    "multiple_splitter",
+    "attribute_value_splitter",
+    "add_value",
+    "remove_value",
+    "sort_by",
 ]
 
 ATTRIB_VALIDATOR_COMPATIBILITY = {
     "check": ["metadata"],
     "expression": ["substitute_value_in_message"],
-    "table_name": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "value_in_data_table", "value_not_in_data_table"],
+    "table_name": [
+        "dataset_metadata_in_data_table",
+        "dataset_metadata_not_in_data_table",
+        "value_in_data_table",
+        "value_not_in_data_table",
+    ],
     "filename": ["dataset_metadata_in_file"],
-    "metadata_name": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "dataset_metadata_in_file"],
-    "metadata_column": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "value_in_data_table", "value_not_in_data_table", "dataset_metadata_in_file"],
+    "metadata_name": [
+        "dataset_metadata_in_data_table",
+        "dataset_metadata_not_in_data_table",
+        "dataset_metadata_in_file",
+    ],
+    "metadata_column": [
+        "dataset_metadata_in_data_table",
+        "dataset_metadata_not_in_data_table",
+        "value_in_data_table",
+        "value_not_in_data_table",
+        "dataset_metadata_in_file",
+    ],
     "line_startswith": ["dataset_metadata_in_file"],
     "min": ["in_range", "length", "dataset_metadata_in_range"],
     "max": ["in_range", "length", "dataset_metadata_in_range"],
     "exclude_min": ["in_range", "dataset_metadata_in_range"],
     "exclude_max": ["in_range", "dataset_metadata_in_range"],
     "split": ["dataset_metadata_in_file"],
-    "skip": ["metadata"]
+    "skip": ["metadata"],
 }
 
 PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = {
     "integer": ["in_range", "expression"],
     "float": ["in_range", "expression"],
-    "data": ["metadata", "unspecified_build", "dataset_ok_validator", "dataset_metadata_in_range", "dataset_metadata_in_file", "dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "expression"],
-    "data_collection": ["metadata", "unspecified_build", "dataset_ok_validator", "dataset_metadata_in_range", "dataset_metadata_in_file", "dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "expression"],
+    "data": [
+        "metadata",
+        "unspecified_build",
+        "dataset_ok_validator",
+        "dataset_metadata_in_range",
+        "dataset_metadata_in_file",
+        "dataset_metadata_in_data_table",
+        "dataset_metadata_not_in_data_table",
+        "expression",
+    ],
+    "data_collection": [
+        "metadata",
+        "unspecified_build",
+        "dataset_ok_validator",
+        "dataset_metadata_in_range",
+        "dataset_metadata_in_file",
+        "dataset_metadata_in_data_table",
+        "dataset_metadata_not_in_data_table",
+        "expression",
+    ],
     "text": ["regex", "length", "empty_field", "value_in_data_table", "value_not_in_data_table", "expression"],
-    "select": ["no_options", "regex", "length", "empty_field", "value_in_data_table", "value_not_in_data_table", "expression"],
-    "drill_down": ["no_options", "regex", "length", "empty_field", "value_in_data_table", "value_not_in_data_table", "expression"],
-    "data_column": ["no_options", "regex", "length", "empty_field", "value_in_data_table", "value_not_in_data_table", "expression"]
+    "select": [
+        "no_options",
+        "regex",
+        "length",
+        "empty_field",
+        "value_in_data_table",
+        "value_not_in_data_table",
+        "expression",
+    ],
+    "drill_down": [
+        "no_options",
+        "regex",
+        "length",
+        "empty_field",
+        "value_in_data_table",
+        "value_not_in_data_table",
+        "expression",
+    ],
+    "data_column": [
+        "no_options",
+        "regex",
+        "length",
+        "empty_field",
+        "value_in_data_table",
+        "value_not_in_data_table",
+        "expression",
+    ],
 }
 
 
@@ -67,7 +124,10 @@ def lint_inputs(tool_xml, lint_ctx):
         param_name = _parse_name(param_attrib.get("name"), param_attrib.get("argument"))
         if "name" in param_attrib and "argument" in param_attrib:
             if param_attrib.get("name") == _parse_name(None, param_attrib.get("argument")):
-                lint_ctx.warn(f"Param input [{param_name}] 'name' attribute is redundant if argument implies the same name.", node=param)
+                lint_ctx.warn(
+                    f"Param input [{param_name}] 'name' attribute is redundant if argument implies the same name.",
+                    node=param,
+                )
         if param_name.strip() == "":
             lint_ctx.error("Param input with empty name.", node=param)
         elif not is_valid_cheetah_placeholder(param_name):
@@ -87,24 +147,34 @@ def lint_inputs(tool_xml, lint_ctx):
 
         if param_type == "data":
             if "format" not in param_attrib:
-                lint_ctx.warn(f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param)
+                lint_ctx.warn(
+                    f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param
+                )
         elif param_type == "select":
             # get dynamic/statically defined options
             dynamic_options = param.get("dynamic_options", None)
             options = param.findall("./options")
             filters = param.findall("./options/filter")
-            select_options = param.findall('./option')
+            select_options = param.findall("./option")
 
             if dynamic_options is not None:
-                lint_ctx.warn(f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.", node=param)
+                lint_ctx.warn(
+                    f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.", node=param
+                )
 
             # check if options are defined by exactly one possibility
             if param.getparent().tag != "conditional":
                 if (dynamic_options is not None) + (len(options) > 0) + (len(select_options) > 0) != 1:
-                    lint_ctx.error(f"Select parameter [{param_name}] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.", node=param)
+                    lint_ctx.error(
+                        f"Select parameter [{param_name}] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.",
+                        node=param,
+                    )
             else:
                 if len(select_options) == 0:
-                    lint_ctx.error(f"Select parameter of a conditional [{param_name}] options have to be defined by 'option' children elements.", node=param)
+                    lint_ctx.error(
+                        f"Select parameter of a conditional [{param_name}] options have to be defined by 'option' children elements.",
+                        node=param,
+                    )
 
             # lint dynamic options
             if len(options) == 1:
@@ -118,9 +188,11 @@ def lint_inputs(tool_xml, lint_ctx):
                         lint_ctx.error(f"Select parameter [{param_name}] contains filter without type.", node=f)
                         continue
                     if ftype not in FILTER_TYPES:
-                        lint_ctx.error(f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.", node=f)
+                        lint_ctx.error(
+                            f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.", node=f
+                        )
                         continue
-                    if ftype in ['add_value', 'data_meta']:
+                    if ftype in ["add_value", "data_meta"]:
                         filter_adds_options = True
                     # TODO more linting of filters
 
@@ -130,26 +202,42 @@ def lint_inputs(tool_xml, lint_ctx):
                 from_data_table = options[0].get("from_data_table", None)
                 # TODO check if input param is present for from_dataset
 
-                if (from_file is None and from_parameter is None
-                        and from_dataset is None and from_data_table is None
-                        and not filter_adds_options):
-                    lint_ctx.error(f"Select parameter [{param_name}] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values.", node=options[0])
+                if (
+                    from_file is None
+                    and from_parameter is None
+                    and from_dataset is None
+                    and from_data_table is None
+                    and not filter_adds_options
+                ):
+                    lint_ctx.error(
+                        f"Select parameter [{param_name}] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values.",
+                        node=options[0],
+                    )
 
                 for deprecated_attr in ["from_file", "from_parameter", "options_filter_attribute", "transform_lines"]:
                     if options[0].get(deprecated_attr) is not None:
-                        lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated '{deprecated_attr}' attribute.", node=options[0])
+                        lint_ctx.warn(
+                            f"Select parameter [{param_name}] options uses deprecated '{deprecated_attr}' attribute.",
+                            node=options[0],
+                        )
 
                 if from_dataset is not None and from_data_table is not None:
-                    lint_ctx.error(f"Select parameter [{param_name}] options uses 'from_dataset' and 'from_data_table' attribute.", node=options[0])
+                    lint_ctx.error(
+                        f"Select parameter [{param_name}] options uses 'from_dataset' and 'from_data_table' attribute.",
+                        node=options[0],
+                    )
 
                 if options[0].get("meta_file_key", None) is not None and from_dataset is None:
-                    lint_ctx.error(f"Select parameter [{param_name}] 'meta_file_key' is only compatible with 'from_dataset'.", node=options[0])
+                    lint_ctx.error(
+                        f"Select parameter [{param_name}] 'meta_file_key' is only compatible with 'from_dataset'.",
+                        node=options[0],
+                    )
 
             elif len(options) > 1:
                 lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements.", node=options[1])
 
             # lint statically defined options
-            if any('value' not in option.attrib for option in select_options):
+            if any("value" not in option.attrib for option in select_options):
                 lint_ctx.error(f"Select parameter [{param_name}] has option without value", node=param)
             if any(option.text is None for option in select_options):
                 lint_ctx.warn(f"Select parameter [{param_name}] has option without text", node=param)
@@ -165,7 +253,9 @@ def lint_inputs(tool_xml, lint_ctx):
                 select_options_texts.append((text, option.attrib.get("selected", "false")))
                 select_options_values.append((value, option.attrib.get("selected", "false")))
             if len(set(select_options_texts)) != len(select_options_texts):
-                lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content", node=param)
+                lint_ctx.error(
+                    f"Select parameter [{param_name}] has multiple options with the same text content", node=param
+                )
             if len(set(select_options_values)) != len(select_options_values):
                 lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value", node=param)
 
@@ -173,47 +263,90 @@ def lint_inputs(tool_xml, lint_ctx):
             optional = string_as_bool(param_attrib.get("optional", multiple))
             if param_attrib.get("display") == "checkboxes":
                 if not multiple:
-                    lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute', node=param)
+                    lint_ctx.error(
+                        f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute',
+                        node=param,
+                    )
                 if not optional:
-                    lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute', node=param)
+                    lint_ctx.error(
+                        f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute',
+                        node=param,
+                    )
             if param_attrib.get("display") == "radio":
                 if multiple:
-                    lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with multiple="true"', node=param)
+                    lint_ctx.error(
+                        f'Select [{param_name}] display="radio" is incompatible with multiple="true"', node=param
+                    )
                 if optional:
-                    lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with optional="true"', node=param)
+                    lint_ctx.error(
+                        f'Select [{param_name}] display="radio" is incompatible with optional="true"', node=param
+                    )
         # TODO: Validate type, much more...
 
         # lint validators
         # TODO check if dataset is available for validators referring other datasets
         validators = param.findall("./validator")
         for validator in validators:
-            vtype = validator.attrib['type']
+            vtype = validator.attrib["type"]
             if param_type in PARAMETER_VALIDATOR_TYPE_COMPATIBILITY:
                 if vtype not in PARAMETER_VALIDATOR_TYPE_COMPATIBILITY[param_type]:
-                    lint_ctx.error(f"Parameter [{param_name}]: validator with an incompatible type '{vtype}'", node=validator)
+                    lint_ctx.error(
+                        f"Parameter [{param_name}]: validator with an incompatible type '{vtype}'", node=validator
+                    )
             for attrib in ATTRIB_VALIDATOR_COMPATIBILITY:
                 if attrib in validator.attrib and vtype not in ATTRIB_VALIDATOR_COMPATIBILITY[attrib]:
-                    lint_ctx.error(f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'", node=validator)
+                    lint_ctx.error(
+                        f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'",
+                        node=validator,
+                    )
             if vtype == "expression":
                 if validator.text is None:
-                    lint_ctx.error(f"Parameter [{param_name}]: expression validators are expected to contain text", node=validator)
+                    lint_ctx.error(
+                        f"Parameter [{param_name}]: expression validators are expected to contain text", node=validator
+                    )
                 else:
                     try:
                         re.compile(validator.text)
                     except Exception as e:
-                        lint_ctx.error(f"Parameter [{param_name}]: '{validator.text}' is no valid regular expression: {str(e)}", node=validator)
+                        lint_ctx.error(
+                            f"Parameter [{param_name}]: '{validator.text}' is no valid regular expression: {str(e)}",
+                            node=validator,
+                        )
             if vtype not in ["expression", "regex"] and validator.text is not None:
-                lint_ctx.warn(f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')", node=validator)
-            if vtype in ["in_range", "length", "dataset_metadata_in_range"] and ("min" not in validator.attrib and "max" not in validator.attrib):
-                lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)", node=validator)
+                lint_ctx.warn(
+                    f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')",
+                    node=validator,
+                )
+            if vtype in ["in_range", "length", "dataset_metadata_in_range"] and (
+                "min" not in validator.attrib and "max" not in validator.attrib
+            ):
+                lint_ctx.error(
+                    f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)",
+                    node=validator,
+                )
             if vtype in ["metadata"] and ("check" not in validator.attrib and "skip" not in validator.attrib):
-                lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s)", node=validator)
-            if vtype in ["value_in_data_table", "value_not_in_data_table", "dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table"] and "table_name" not in validator.attrib:
-                lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute", node=validator)
+                lint_ctx.error(
+                    f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s)",
+                    node=validator,
+                )
+            if (
+                vtype
+                in [
+                    "value_in_data_table",
+                    "value_not_in_data_table",
+                    "dataset_metadata_in_data_table",
+                    "dataset_metadata_not_in_data_table",
+                ]
+                and "table_name" not in validator.attrib
+            ):
+                lint_ctx.error(
+                    f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute",
+                    node=validator,
+                )
 
     conditional_selects = tool_xml.findall("./inputs//conditional")
     for conditional in conditional_selects:
-        conditional_name = conditional.get('name')
+        conditional_name = conditional.get("name")
         if not conditional_name:
             lint_ctx.error("Conditional without a name", node=conditional)
         if conditional.get("value_from"):
@@ -221,49 +354,63 @@ def lint_inputs(tool_xml, lint_ctx):
             continue
         first_param = conditional.findall("param")
         if len(first_param) != 1:
-            lint_ctx.error(f"Conditional [{conditional_name}] needs exactly one child <param> found {len(first_param)}", node=conditional)
+            lint_ctx.error(
+                f"Conditional [{conditional_name}] needs exactly one child <param> found {len(first_param)}",
+                node=conditional,
+            )
             continue
         first_param = first_param[0]
-        first_param_type = first_param.get('type')
-        if first_param_type == 'boolean':
-            lint_ctx.warn(f'Conditional [{conditional_name}] first param of type="boolean" is discouraged, use a select', node=first_param)
-        elif first_param_type != 'select':
+        first_param_type = first_param.get("type")
+        if first_param_type == "boolean":
+            lint_ctx.warn(
+                f'Conditional [{conditional_name}] first param of type="boolean" is discouraged, use a select',
+                node=first_param,
+            )
+        elif first_param_type != "select":
             lint_ctx.error(f'Conditional [{conditional_name}] first param should have type="select"', node=first_param)
             continue
 
-        if first_param_type == 'select':
-            select_options = _find_with_attribute(first_param, 'option', 'value')
-            option_ids = [option.get('value') for option in select_options]
+        if first_param_type == "select":
+            select_options = _find_with_attribute(first_param, "option", "value")
+            option_ids = [option.get("value") for option in select_options]
         else:  # boolean
-            option_ids = [
-                first_param.get('truevalue', 'true'),
-                first_param.get('falsevalue', 'false')
-            ]
+            option_ids = [first_param.get("truevalue", "true"), first_param.get("falsevalue", "false")]
 
         for incomp in ["optional", "multiple"]:
             if string_as_bool(first_param.get(incomp, False)):
-                lint_ctx.warn(f'Conditional [{conditional_name}] test parameter cannot be {incomp}="true"', node=first_param)
+                lint_ctx.warn(
+                    f'Conditional [{conditional_name}] test parameter cannot be {incomp}="true"', node=first_param
+                )
 
-        whens = conditional.findall('./when')
-        if any('value' not in when.attrib for when in whens):
+        whens = conditional.findall("./when")
+        if any("value" not in when.attrib for when in whens):
             lint_ctx.error(f"Conditional [{conditional_name}] when without value", node=conditional)
 
-        when_ids = [w.get('value') for w in whens if w.get('value') is not None]
+        when_ids = [w.get("value") for w in whens if w.get("value") is not None]
 
         for option_id in option_ids:
             if option_id not in when_ids:
-                lint_ctx.warn(f"Conditional [{conditional_name}] no <when /> block found for {first_param_type} option '{option_id}'", node=conditional)
+                lint_ctx.warn(
+                    f"Conditional [{conditional_name}] no <when /> block found for {first_param_type} option '{option_id}'",
+                    node=conditional,
+                )
 
         for when_id in when_ids:
             if when_id not in option_ids:
-                if first_param_type == 'select':
-                    lint_ctx.warn(f"Conditional [{conditional_name}] no <option /> found for when block '{when_id}'", node=conditional)
+                if first_param_type == "select":
+                    lint_ctx.warn(
+                        f"Conditional [{conditional_name}] no <option /> found for when block '{when_id}'",
+                        node=conditional,
+                    )
                 else:
-                    lint_ctx.warn(f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'", node=conditional)
+                    lint_ctx.warn(
+                        f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'",
+                        node=conditional,
+                    )
 
     if datasource:
         # TODO only display is subtag of inputs, uihints is a separate top level tag (supporting only attrib minwidth)
-        for datasource_tag in ('display', 'uihints'):
+        for datasource_tag in ("display", "uihints"):
             if not any(param.tag == datasource_tag for param in inputs):
                 lint_ctx.info(f"{datasource_tag} tag usually present in data sources", node=tool_node)
 
@@ -288,7 +435,7 @@ def lint_repeats(tool_xml, lint_ctx):
 
 def _find_with_attribute(element, tag, attribute, test_value=None):
     rval = []
-    for el in (element.findall(f'./{tag}') or []):
+    for el in element.findall(f"./{tag}") or []:
         if attribute not in el.attrib:
             continue
         value = el.attrib[attribute]
diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index 2e8cd878e1a..e988edbc799 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -26,7 +26,9 @@ def lint_output(tool_xml, lint_ctx):
             lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.", node=output)
             # TODO make this an error if there is no discover_datasets / from_work_dir (is this then still a problem)
         elif not is_valid_cheetah_placeholder(output.attrib["name"]):
-            lint_ctx.warn(f'Tool output name [{output.attrib["name"]}] is not a valid Cheetah placeholder.', node=output)
+            lint_ctx.warn(
+                f'Tool output name [{output.attrib["name"]}] is not a valid Cheetah placeholder.', node=output
+            )
 
         format_set = False
         if __check_format(output, lint_ctx):
@@ -47,7 +49,10 @@ def lint_output(tool_xml, lint_ctx):
                 format_set = True
 
         if not format_set:
-            lint_ctx.warn(f"Tool {output.tag} output {output.attrib.get('name', 'with missing name')} doesn't define an output format.", node=output)
+            lint_ctx.warn(
+                f"Tool {output.tag} output {output.attrib.get('name', 'with missing name')} doesn't define an output format.",
+                node=output,
+            )
 
     # TODO: check for different labels in case of multiple outputs
     lint_ctx.info(f"{num_outputs} outputs found.", node=outputs[0])
@@ -60,7 +65,10 @@ def __check_format(node, lint_ctx, allow_ext=False):
     return true (node defines format/ext) / false (else)
     """
     if "format_source" in node.attrib and ("ext" in node.attrib or "format" in node.attrib):
-        lint_ctx.warn(f"Tool {node.tag} output '{node.attrib.get('name', 'with missing name')}' should use either format_source or format/ext", node=node)
+        lint_ctx.warn(
+            f"Tool {node.tag} output '{node.attrib.get('name', 'with missing name')}' should use either format_source or format/ext",
+            node=node,
+        )
     if "format_source" in node.attrib:
         return True
     # if allowed (e.g. for discover_datasets), ext takes precedence over format
@@ -70,7 +78,10 @@ def __check_format(node, lint_ctx, allow_ext=False):
     if fmt is None:
         fmt = node.attrib.get("format")
     if fmt == "input":
-        lint_ctx.warn(f"Using format='input' on {node.tag}, format_source attribute is less ambiguous and should be used instead.", node=node)
+        lint_ctx.warn(
+            f"Using format='input' on {node.tag}, format_source attribute is less ambiguous and should be used instead.",
+            node=node,
+        )
     return fmt is not None
 
 
@@ -82,7 +93,9 @@ def __check_pattern(node):
     """
     if node.tag != "discover_datasets":
         return False
-    if "from_tool_provided_metadata" in node.attrib and string_as_bool(node.attrib.get("from_tool_provided_metadata", "false")):
+    if "from_tool_provided_metadata" in node.attrib and string_as_bool(
+        node.attrib.get("from_tool_provided_metadata", "false")
+    ):
         return True
     if "pattern" not in node.attrib:
         return False
diff --git a/lib/galaxy/tool_util/linters/stdio.py b/lib/galaxy/tool_util/linters/stdio.py
index 1a7d5fc3003..de769e824ed 100644
--- a/lib/galaxy/tool_util/linters/stdio.py
+++ b/lib/galaxy/tool_util/linters/stdio.py
@@ -20,9 +20,15 @@ def lint_stdio(tool_source, lint_ctx):
         command = get_command(tool_xml) if tool_xml else None
         if command is None or not command.get("detect_errors"):
             if tool_source.parse_profile() <= "16.01":
-                lint_ctx.info("No stdio definition found, tool indicates error conditions with output written to stderr.", node=tool_node)
+                lint_ctx.info(
+                    "No stdio definition found, tool indicates error conditions with output written to stderr.",
+                    node=tool_node,
+                )
             else:
-                lint_ctx.info("No stdio definition found, tool indicates error conditions with non-zero exit codes.", node=tool_node)
+                lint_ctx.info(
+                    "No stdio definition found, tool indicates error conditions with non-zero exit codes.",
+                    node=tool_node,
+                )
         return
 
     if len(stdios) > 1:
diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index d2a4e48984d..70560824883 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -1,5 +1,8 @@
 """This module contains a linting functions for tool tests."""
-from inspect import Parameter, signature
+from inspect import (
+    Parameter,
+    signature,
+)
 
 from ._util import is_datasource
 from ..verify import asserts
@@ -46,13 +49,9 @@ def lint_tsts(tool_xml, lint_ctx):
                 lint_ctx.error(f"Test {test_idx}: Found test param tag without a name defined.", node=param)
                 continue
             name = name.split("|")[-1]
-            xpaths = [f"@name='{name}'",
-                      f"@argument='{name}'",
-                      f"@argument='-{name}'",
-                      f"@argument='--{name}'"]
+            xpaths = [f"@name='{name}'", f"@argument='{name}'", f"@argument='-{name}'", f"@argument='--{name}'"]
             if "_" in name:
-                xpaths += [f"@argument='-{name.replace('_', '-')}'",
-                           f"@argument='--{name.replace('_', '-')}'"]
+                xpaths += [f"@argument='-{name.replace('_', '-')}'", f"@argument='--{name.replace('_', '-')}'"]
             found = False
             for xp in xpaths:
                 inxpath = f".//inputs//param[{xp}]"
@@ -76,7 +75,10 @@ def lint_tsts(tool_xml, lint_ctx):
                 lint_ctx.error(f"Test {test_idx}: Found {output.tag} tag without a name defined.", node=output)
             else:
                 if name not in valid_names:
-                    lint_ctx.error(f"Test {test_idx}: Found {output.tag} tag with unknown name [{name}], valid names [{valid_names}]", node=output)
+                    lint_ctx.error(
+                        f"Test {test_idx}: Found {output.tag} tag with unknown name [{name}], valid names [{valid_names}]",
+                        node=output,
+                    )
 
         if "expect_failure" in test.attrib and found_output_test:
             lint_ctx.error(f"Test {test_idx}: Cannot specify outputs in a test expecting failure.", node=test)
@@ -84,7 +86,10 @@ def lint_tsts(tool_xml, lint_ctx):
 
         has_test = has_test or found_output_test
         if not has_test:
-            lint_ctx.warn(f"Test {test_idx}: No outputs or expectations defined for tests, this test is likely invalid.", node=test)
+            lint_ctx.warn(
+                f"Test {test_idx}: No outputs or expectations defined for tests, this test is likely invalid.",
+                node=test,
+            )
         else:
             num_valid_tests += 1
 
@@ -119,7 +124,8 @@ def _check_asserts(test_idx, assertions, lint_ctx):
                     except ValueError:
                         lint_ctx.error(
                             f"Test {test_idx}: attribute '{attrib}' for '{a.tag}' needs to be '{assert_function_sig.parameters[attrib].annotation.__name__}' got '{a.attrib[attrib]}'",
-                            node=a)
+                            node=a,
+                        )
             # check missing required attributes
             for p in assert_function_sig.parameters:
                 if p in ["output", "output_bytes", "verify_assertions_function", "children"]:
diff --git a/lib/galaxy/tool_util/linters/xml_order.py b/lib/galaxy/tool_util/linters/xml_order.py
index d9b136a679d..13cf74e413d 100644
--- a/lib/galaxy/tool_util/linters/xml_order.py
+++ b/lib/galaxy/tool_util/linters/xml_order.py
@@ -7,38 +7,38 @@ https://github.com/galaxy-iuc/standards.
 # https://github.com/galaxy-iuc/standards
 # https://github.com/galaxy-iuc/standards/pull/7/files
 TAG_ORDER = [
-    'description',
-    'macros',
-    'edam_topics',
-    'edam_operations',
-    'xrefs',
-    'parallelism',
-    'requirements',
-    'code',
-    'stdio',
-    'version_command',
-    'command',
-    'environment_variables',
-    'configfiles',
-    'inputs',
-    'outputs',
-    'tests',
-    'help',
-    'citations',
+    "description",
+    "macros",
+    "edam_topics",
+    "edam_operations",
+    "xrefs",
+    "parallelism",
+    "requirements",
+    "code",
+    "stdio",
+    "version_command",
+    "command",
+    "environment_variables",
+    "configfiles",
+    "inputs",
+    "outputs",
+    "tests",
+    "help",
+    "citations",
 ]
 
 DATASOURCE_TAG_ORDER = [
-    'description',
-    'macros',
-    'command',
-    'configfiles',
-    'inputs',
-    'request_param_translation',
-    'uihints',
-    'outputs',
-    'options',
-    'help',
-    'citations',
+    "description",
+    "macros",
+    "command",
+    "configfiles",
+    "inputs",
+    "request_param_translation",
+    "uihints",
+    "outputs",
+    "options",
+    "help",
+    "citations",
 ]
 
 
@@ -47,7 +47,7 @@ DATASOURCE_TAG_ORDER = [
 def lint_xml_order(tool_xml, lint_ctx):
     tool_root = tool_xml.getroot()
 
-    if tool_root.attrib.get('tool_type', '') == 'data_source':
+    if tool_root.attrib.get("tool_type", "") == "data_source":
         tag_ordering = DATASOURCE_TAG_ORDER
     else:
         tag_ordering = TAG_ORDER
@@ -60,7 +60,9 @@ def lint_xml_order(tool_xml, lint_ctx):
             key = tag_ordering.index(tag)
             if last_key:
                 if last_key > key:
-                    lint_ctx.warn(f"Best practice violation [{tag}] elements should come before [{last_tag}]", node=elem)
+                    lint_ctx.warn(
+                        f"Best practice violation [{tag}] elements should come before [{last_tag}]", node=elem
+                    )
             last_tag = tag
             last_key = key
         else:
diff --git a/lib/galaxy/tool_util/loader_directory.py b/lib/galaxy/tool_util/loader_directory.py
index 93cca0916a6..c3d22c0d12c 100644
--- a/lib/galaxy/tool_util/loader_directory.py
+++ b/lib/galaxy/tool_util/loader_directory.py
@@ -23,7 +23,7 @@ DATA_MANAGER_REGEX = re.compile(r"\stool_type=\"manage_data\"")
 
 YAML_EXTENSIONS = [".yaml", ".yml", ".json"]
 CWL_EXTENSIONS = YAML_EXTENSIONS + [".cwl"]
-EXCLUDE_WALK_DIRS = ['.hg', '.git', '.venv']
+EXCLUDE_WALK_DIRS = [".hg", ".git", ".venv"]
 
 
 def load_exception_handler(path, exc_info):
@@ -38,15 +38,9 @@ def find_possible_tools_from_path(
 ):
     """Walk a directory and find potential tool files."""
     possible_tool_files = []
-    for possible_tool_file in _find_tool_files(
-        path, recursive=recursive,
-        enable_beta_formats=enable_beta_formats
-    ):
+    for possible_tool_file in _find_tool_files(path, recursive=recursive, enable_beta_formats=enable_beta_formats):
         try:
-            does_look_like_a_tool = looks_like_a_tool(
-                possible_tool_file,
-                enable_beta_formats=enable_beta_formats
-            )
+            does_look_like_a_tool = looks_like_a_tool(possible_tool_file, enable_beta_formats=enable_beta_formats)
         except OSError:
             # Some problem reading the tool file, skip.
             continue
@@ -164,14 +158,16 @@ def looks_like_xml(path, regex=TOOL_REGEX):
     if not os.path.getsize(full_path):
         return False
 
-    if(checkers.check_binary(full_path)
-       or checkers.check_image(full_path)
-       or checkers.is_gzip(full_path)
-       or checkers.is_bz2(full_path)
-       or checkers.is_zip(full_path)):
+    if (
+        checkers.check_binary(full_path)
+        or checkers.check_image(full_path)
+        or checkers.is_gzip(full_path)
+        or checkers.is_bz2(full_path)
+        or checkers.is_zip(full_path)
+    ):
         return False
 
-    with open(path, encoding='utf-8') as f:
+    with open(path, encoding="utf-8") as f:
         try:
             start_contents = f.read(5 * 1024)
         except UnicodeDecodeError:
@@ -273,7 +269,7 @@ def _has_extension(path, extensions):
     return any(path.endswith(e) for e in extensions)
 
 
-def _find_files(directory, pattern='*'):
+def _find_files(directory, pattern="*"):
     if not os.path.exists(directory):
         raise ValueError(f"Directory not found {directory}")
 
@@ -296,14 +292,14 @@ def resolved_path(path_or_uri_like):
     if "://" not in path_or_uri_like:
         return path_or_uri_like
     elif path_or_uri_like.startswith("file://"):
-        return path_or_uri_like[len("file://"):]
+        return path_or_uri_like[len("file://") :]
     else:
         return UNRESOLVED_URI
 
 
 BETA_TOOL_CHECKERS = {
-    'yaml': looks_like_a_tool_yaml,
-    'cwl': looks_like_a_tool_cwl,
+    "yaml": looks_like_a_tool_yaml,
+    "cwl": looks_like_a_tool_cwl,
 }
 
 __all__ = (
diff --git a/lib/galaxy/tool_util/locations/dockstore.py b/lib/galaxy/tool_util/locations/dockstore.py
index ce919bfe489..991fbdc098b 100644
--- a/lib/galaxy/tool_util/locations/dockstore.py
+++ b/lib/galaxy/tool_util/locations/dockstore.py
@@ -4,9 +4,7 @@ import requests
 import yaml
 
 from galaxy.util import DEFAULT_SOCKET_TIMEOUT
-from ..locations import (
-    ToolLocationResolver,
-)
+from ..locations import ToolLocationResolver
 
 
 class DockStoreResolver(ToolLocationResolver):
@@ -15,7 +13,7 @@ class DockStoreResolver(ToolLocationResolver):
 
     def get_tool_source_path(self, uri_like):
         assert uri_like.startswith("dockstore://")
-        tool_id = uri_like[len("dockstore://"):]
+        tool_id = uri_like[len("dockstore://") :]
         if ":" in tool_id:
             tool_id, version = tool_id.split(":", 1)
         else:
@@ -28,7 +26,6 @@ class DockStoreResolver(ToolLocationResolver):
 
 
 class _Ga4ghToolClient:
-
     def __init__(self, base_url="https://www.dockstore.org:8443/api"):
         self.base_url = base_url
 
diff --git a/lib/galaxy/tool_util/locations/file.py b/lib/galaxy/tool_util/locations/file.py
index 3d25769783a..2d13ef2a7d4 100644
--- a/lib/galaxy/tool_util/locations/file.py
+++ b/lib/galaxy/tool_util/locations/file.py
@@ -1,6 +1,4 @@
-from ..locations import (
-    ToolLocationResolver,
-)
+from ..locations import ToolLocationResolver
 
 
 class HttpToolResolver(ToolLocationResolver):
@@ -9,4 +7,4 @@ class HttpToolResolver(ToolLocationResolver):
 
     def get_tool_source_path(self, uri_like):
         assert uri_like.startswith("file://")
-        return uri_like[len("file://"):]
+        return uri_like[len("file://") :]
diff --git a/lib/galaxy/tool_util/locations/http.py b/lib/galaxy/tool_util/locations/http.py
index 699df9200d2..dea0c868e42 100644
--- a/lib/galaxy/tool_util/locations/http.py
+++ b/lib/galaxy/tool_util/locations/http.py
@@ -1,7 +1,5 @@
 from galaxy.util import download_to_file
-from ..locations import (
-    ToolLocationResolver,
-)
+from ..locations import ToolLocationResolver
 
 
 class HttpToolResolver(ToolLocationResolver):
diff --git a/lib/galaxy/tool_util/output_checker.py b/lib/galaxy/tool_util/output_checker.py
index c5fcb9b81bf..8612737da7c 100644
--- a/lib/galaxy/tool_util/output_checker.py
+++ b/lib/galaxy/tool_util/output_checker.py
@@ -9,9 +9,9 @@ log = getLogger(__name__)
 
 
 class DETECTED_JOB_STATE(str, Enum):
-    OK = 'ok'
-    OUT_OF_MEMORY_ERROR = 'oom_error'
-    GENERIC_ERROR = 'generic_error'
+    OK = "ok"
+    OUT_OF_MEMORY_ERROR = "oom_error"
+    GENERIC_ERROR = "generic_error"
 
 
 ERROR_PEEK_SIZE = 2000
@@ -78,8 +78,7 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
             max_error_level = StdioErrorLevel.NO_ERROR
             if tool_exit_code is not None:
                 for stdio_exit_code in stdio_exit_codes:
-                    if (tool_exit_code >= stdio_exit_code.range_start
-                            and tool_exit_code <= stdio_exit_code.range_end):
+                    if tool_exit_code >= stdio_exit_code.range_start and tool_exit_code <= stdio_exit_code.range_end:
                         # Tack on a generic description of the code
                         # plus a specific code description. For example,
                         # this might prepend "Job 42: Warning (Out of Memory)\n".
@@ -89,17 +88,17 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
                         desc = "%s: Exit code %d (%s)" % (
                             StdioErrorLevel.desc(stdio_exit_code.error_level),
                             tool_exit_code,
-                            code_desc)
+                            code_desc,
+                        )
                         reason = {
-                            'type': 'exit_code',
-                            'desc': desc,
-                            'exit_code': tool_exit_code,
-                            'code_desc': code_desc,
-                            'error_level': stdio_exit_code.error_level,
+                            "type": "exit_code",
+                            "desc": desc,
+                            "exit_code": tool_exit_code,
+                            "code_desc": code_desc,
+                            "error_level": stdio_exit_code.error_level,
                         }
                         job_messages.append(reason)
-                        max_error_level = max(max_error_level,
-                                              stdio_exit_code.error_level)
+                        max_error_level = max(max_error_level, stdio_exit_code.error_level)
                         if max_error_level >= StdioErrorLevel.MAX:
                             break
 
@@ -119,12 +118,16 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
                     #   - If it matched, then determine the error level.
                     #       o If it was fatal, then we're done - break.
                     if regex.stderr_match:
-                        max_error_level = check_output_regex(job_id_tag, regex, stderr, 'stderr', job_messages, max_error_level)
+                        max_error_level = check_output_regex(
+                            job_id_tag, regex, stderr, "stderr", job_messages, max_error_level
+                        )
                         if max_error_level >= StdioErrorLevel.MAX:
                             break
 
                     if regex.stdout_match:
-                        max_error_level = check_output_regex(job_id_tag, regex, stdout, 'stdout', job_messages, max_error_level)
+                        max_error_level = check_output_regex(
+                            job_id_tag, regex, stdout, "stdout", job_messages, max_error_level
+                        )
                         if max_error_level >= StdioErrorLevel.MAX:
                             break
 
@@ -133,7 +136,7 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
             if max_error_level == StdioErrorLevel.FATAL_OOM:
                 state = DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR
             elif max_error_level >= StdioErrorLevel.FATAL:
-                reason = ''
+                reason = ""
                 if job_messages:
                     reason = f" Reasons are {job_messages}"
                 log.info(f"Job error detected, failing job.{reason}")
diff --git a/lib/galaxy/tool_util/parser/__init__.py b/lib/galaxy/tool_util/parser/__init__.py
index 2a215042946..27518c895be 100644
--- a/lib/galaxy/tool_util/parser/__init__.py
+++ b/lib/galaxy/tool_util/parser/__init__.py
@@ -1,10 +1,15 @@
 """ Package responsible for parsing tools from files/abstract tool sources.
 """
-from .factory import get_input_source, get_tool_source, get_tool_source_from_representation
-from .interface import RequiredFiles, ToolSource
-from .output_objects import (
-    ToolOutputCollectionPart,
+from .factory import (
+    get_input_source,
+    get_tool_source,
+    get_tool_source_from_representation,
 )
+from .interface import (
+    RequiredFiles,
+    ToolSource,
+)
+from .output_objects import ToolOutputCollectionPart
 
 __all__ = (
     "get_input_source",
diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index d5c6277f052..9f8d0a35d23 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -22,7 +22,7 @@ log = logging.getLogger(__name__)
 
 class CwlToolSource(ToolSource):
 
-    language = 'yaml'
+    language = "yaml"
 
     def __init__(self, tool_file, strict_cwl_validation=True, tool_id=None, tool_proxy=None):
         self._cwl_tool_file = tool_file
@@ -42,7 +42,7 @@ class CwlToolSource(ToolSource):
         return self._tool_proxy
 
     def parse_tool_type(self):
-        return 'cwl'
+        return "cwl"
 
     def parse_id(self):
         return self._id
@@ -149,14 +149,17 @@ class CwlToolSource(ToolSource):
         containers = []
         docker_identifier = self.tool_proxy.docker_identifier()
         if docker_identifier:
-            containers.append({"type": "docker",
-                               "identifier": docker_identifier})
+            containers.append({"type": "docker", "identifier": docker_identifier})
 
         software_requirements = self.tool_proxy.software_requirements()
-        return requirements.parse_requirements_from_dict(dict(
-            requirements=list(map(lambda r: {"name": r[0], "version": r[1], "type": "package"}, software_requirements)),
-            containers=containers,
-        ))
+        return requirements.parse_requirements_from_dict(
+            dict(
+                requirements=list(
+                    map(lambda r: {"name": r[0], "version": r[1], "type": "package"}, software_requirements)
+                ),
+                containers=containers,
+            )
+        )
 
     def parse_profile(self):
         return "16.04"
@@ -165,11 +168,10 @@ class CwlToolSource(ToolSource):
         return None
 
     def parse_python_template_version(self):
-        return '3.5'
+        return "3.5"
 
 
 class CwlPageSource(PageSource):
-
     def __init__(self, tool_proxy):
         cwl_instances = tool_proxy.input_instances()
         self._input_list = list(map(self._to_input_source, cwl_instances))
diff --git a/lib/galaxy/tool_util/parser/factory.py b/lib/galaxy/tool_util/parser/factory.py
index a0fb0130d61..e723793d6a5 100644
--- a/lib/galaxy/tool_util/parser/factory.py
+++ b/lib/galaxy/tool_util/parser/factory.py
@@ -7,10 +7,22 @@ from yaml import safe_load
 from galaxy.tool_util.loader import load_tool_with_refereces
 from galaxy.util import parse_xml_string_to_etree
 from galaxy.util.yaml_util import ordered_load
-from .cwl import CwlToolSource, tool_proxy
-from .interface import InputSource, ToolSource
-from .xml import XmlInputSource, XmlToolSource
-from .yaml import YamlInputSource, YamlToolSource
+from .cwl import (
+    CwlToolSource,
+    tool_proxy,
+)
+from .interface import (
+    InputSource,
+    ToolSource,
+)
+from .xml import (
+    XmlInputSource,
+    XmlToolSource,
+)
+from .yaml import (
+    YamlInputSource,
+    YamlToolSource,
+)
 from ..fetcher import ToolLocationFetcher
 
 log = logging.getLogger(__name__)
@@ -23,7 +35,7 @@ def build_xml_tool_source(xml_string):
 def build_cwl_tool_source(yaml_string):
     tool_proxy(tool_object=safe_load(yaml_string))
     # regular CwlToolSource sets basename as tool id, but that's not going to cut it in production
-    return CwlToolSource(tool_file=None, tool_id='serialized_cwl_tool', tool_proxy=tool_proxy)
+    return CwlToolSource(tool_file=None, tool_id="serialized_cwl_tool", tool_proxy=tool_proxy)
 
 
 def build_yaml_tool_source(yaml_string):
@@ -31,9 +43,9 @@ def build_yaml_tool_source(yaml_string):
 
 
 TOOL_SOURCE_FACTORIES = {
-    'XmlToolSource': build_xml_tool_source,
-    'YamlToolSource': build_yaml_tool_source,
-    'CwlToolSource': build_cwl_tool_source
+    "XmlToolSource": build_xml_tool_source,
+    "YamlToolSource": build_yaml_tool_source,
+    "CwlToolSource": build_cwl_tool_source,
 }
 
 
@@ -74,7 +86,9 @@ def get_tool_source(
             as_dict = ordered_load(f)
             return YamlToolSource(as_dict, source_path=config_file)
     elif config_file.endswith(".json") or config_file.endswith(".cwl"):
-        log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.")
+        log.info(
+            "Loading CWL tool - this is experimental - tool likely will not function in future at least in same way."
+        )
         return CwlToolSource(config_file)
     else:
         tree, macro_paths = load_tool_with_refereces(config_file)
diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
index 98173f44aec..957b8deb5ab 100644
--- a/lib/galaxy/tool_util/parser/interface.py
+++ b/lib/galaxy/tool_util/parser/interface.py
@@ -3,10 +3,14 @@ import os
 import re
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 from os.path import join
-from typing import Dict, List, Optional
+from typing import (
+    Dict,
+    List,
+    Optional,
+)
 
 from galaxy.util.path import safe_walk
 from .util import _parse_name
@@ -15,49 +19,48 @@ NOT_IMPLEMENTED_MESSAGE = "Galaxy tool format does not yet support this tool fea
 
 
 class ToolSource(metaclass=ABCMeta):
-    """ This interface represents an abstract source to parse tool
+    """This interface represents an abstract source to parse tool
     information from.
     """
+
     language: str
 
     @abstractmethod
     def parse_id(self):
-        """ Parse an ID describing the abstract tool. This is not the
+        """Parse an ID describing the abstract tool. This is not the
         GUID tracked by the tool shed but the simple id (there may be
         multiple tools loaded in Galaxy with this same simple id).
         """
 
     @abstractmethod
     def parse_version(self):
-        """ Parse a version describing the abstract tool.
-        """
+        """Parse a version describing the abstract tool."""
 
     def parse_tool_module(self):
-        """ Load Tool class from a custom module. (Optional).
+        """Load Tool class from a custom module. (Optional).
 
         If not None, return pair containing module and class (as strings).
         """
         return None
 
     def parse_action_module(self):
-        """ Load Tool class from a custom module. (Optional).
+        """Load Tool class from a custom module. (Optional).
 
         If not None, return pair containing module and class (as strings).
         """
         return None
 
     def parse_tool_type(self):
-        """ Load simple tool type string (e.g. 'data_source', 'default').
-        """
+        """Load simple tool type string (e.g. 'data_source', 'default')."""
         return None
 
     @abstractmethod
     def parse_name(self):
-        """ Parse a short name for tool (required). """
+        """Parse a short name for tool (required)."""
 
     @abstractmethod
     def parse_description(self):
-        """ Parse a description for tool. Longer than name, shorted than help. """
+        """Parse a description for tool. Longer than name, shorted than help."""
 
     def parse_edam_operations(self) -> List[str]:
         """Parse list of edam operation codes."""
@@ -71,18 +74,17 @@ class ToolSource(metaclass=ABCMeta):
         """Parse list of external resource URIs and types."""
 
     def parse_display_interface(self, default):
-        """ Parse display_interface - fallback to default for the tool type
+        """Parse display_interface - fallback to default for the tool type
         (supplied as default parameter) if not specified.
         """
         return default
 
     def parse_require_login(self, default):
-        """ Parse whether the tool requires login (as a bool).
-        """
+        """Parse whether the tool requires login (as a bool)."""
         return default
 
     def parse_request_param_translation_elem(self):
-        """ Return an XML element describing require parameter translation.
+        """Return an XML element describing require parameter translation.
 
         If we wish to support this feature for non-XML based tools this should
         be converted to return some sort of object interface instead of a RAW
@@ -92,27 +94,22 @@ class ToolSource(metaclass=ABCMeta):
 
     @abstractmethod
     def parse_command(self):
-        """ Return string contianing command to run.
-        """
+        """Return string contianing command to run."""
 
     def parse_expression(self):
-        """ Return string contianing command to run.
-        """
+        """Return string contianing command to run."""
         return None
 
     @abstractmethod
     def parse_environment_variables(self):
-        """ Return environment variable templates to expose.
-        """
+        """Return environment variable templates to expose."""
 
     def parse_home_target(self):
-        """Should be "job_home", "shared_home", "job_tmp", "pwd", or None.
-        """
+        """Should be "job_home", "shared_home", "job_tmp", "pwd", or None."""
         return "pwd"
 
     def parse_tmp_target(self):
-        """Should be "pwd", "shared_home", "job_tmp", "job_tmp_if_explicit", or None.
-        """
+        """Should be "pwd", "shared_home", "job_tmp", "job_tmp_if_explicit", or None."""
         return "job_tmp"
 
     def parse_tmp_directory_vars(self):
@@ -120,23 +117,28 @@ class ToolSource(metaclass=ABCMeta):
         return ["TMPDIR", "TMP", "TEMP"]
 
     def parse_docker_env_pass_through(self):
-        return ["GALAXY_SLOTS", "GALAXY_MEMORY_MB", "GALAXY_MEMORY_MB_PER_SLOT", "HOME",
-                "_GALAXY_JOB_HOME_DIR", "_GALAXY_JOB_TMP_DIR"] + self.parse_tmp_directory_vars()
+        return [
+            "GALAXY_SLOTS",
+            "GALAXY_MEMORY_MB",
+            "GALAXY_MEMORY_MB_PER_SLOT",
+            "HOME",
+            "_GALAXY_JOB_HOME_DIR",
+            "_GALAXY_JOB_TMP_DIR",
+        ] + self.parse_tmp_directory_vars()
 
     @abstractmethod
     def parse_interpreter(self):
-        """ Return string containing the interpreter to prepend to the command
+        """Return string containing the interpreter to prepend to the command
         (for instance this might be 'python' to run a Python wrapper located
         adjacent to the tool).
         """
 
     @abstractmethod
     def parse_interactivetool(self):
-        """ Return InteractiveTool entry point templates to expose.
-        """
+        """Return InteractiveTool entry point templates to expose."""
 
     def parse_redirect_url_params_elem(self):
-        """ Return an XML element describing redirect_url_params.
+        """Return an XML element describing redirect_url_params.
 
         If we wish to support this feature for non-XML based tools this should
         be converted to return some sort of object interface instead of a RAW
@@ -145,49 +147,46 @@ class ToolSource(metaclass=ABCMeta):
         return None
 
     def parse_version_command(self):
-        """ Parse command used to determine version of primary application
+        """Parse command used to determine version of primary application
         driving the tool. Return None to not generate or record such a command.
         """
         return None
 
     def parse_version_command_interpreter(self):
-        """ Parse command used to determine version of primary application
+        """Parse command used to determine version of primary application
         driving the tool. Return None to not generate or record such a command.
         """
         return None
 
     def parse_parallelism(self):
-        """ Return a galaxy.jobs.ParallismInfo object describing task splitting
+        """Return a galaxy.jobs.ParallismInfo object describing task splitting
         or None.
         """
         return None
 
     def parse_hidden(self):
-        """ Return boolean indicating whether tool should be hidden in the tool menu.
-        """
+        """Return boolean indicating whether tool should be hidden in the tool menu."""
         return False
 
     def parse_sanitize(self):
-        """ Return boolean indicating whether tool should be sanitized or not.
-        """
+        """Return boolean indicating whether tool should be sanitized or not."""
         return True
 
     def parse_refresh(self):
-        """ Return boolean indicating ... I have no clue...
-        """
+        """Return boolean indicating ... I have no clue..."""
         return False
 
-    def parse_required_files(self) -> Optional['RequiredFiles']:
-        """ Parse explicit RequiredFiles object or return None to let Galaxy decide implicit logic."""
+    def parse_required_files(self) -> Optional["RequiredFiles"]:
+        """Parse explicit RequiredFiles object or return None to let Galaxy decide implicit logic."""
         return None
 
     @abstractmethod
     def parse_requirements_and_containers(self):
-        """ Return pair of ToolRequirement and ContainerDescription lists. """
+        """Return pair of ToolRequirement and ContainerDescription lists."""
 
     @abstractmethod
     def parse_input_pages(self):
-        """ Return a PagesSource representing inputs by page for tool. """
+        """Return a PagesSource representing inputs by page for tool."""
 
     def parse_provided_metadata_style(self):
         """Return style of tool provided metadata file (e.g. galaxy.json).
@@ -207,33 +206,32 @@ class ToolSource(metaclass=ABCMeta):
 
     @abstractmethod
     def parse_outputs(self, tool):
-        """ Return a pair of output and output collections ordered
+        """Return a pair of output and output collections ordered
         dictionaries for use by Tool.
         """
 
     @abstractmethod
     def parse_strict_shell(self):
-        """ Return True if tool commands should be executed with
+        """Return True if tool commands should be executed with
         set -e.
         """
 
     @abstractmethod
     def parse_stdio(self):
-        """ Builds lists of ToolStdioExitCode and ToolStdioRegex objects
+        """Builds lists of ToolStdioExitCode and ToolStdioRegex objects
         to describe tool execution error conditions.
         """
         return [], []
 
     @abstractmethod
     def parse_help(self):
-        """ Return RST definition of help text for tool or None if the tool
+        """Return RST definition of help text for tool or None if the tool
         doesn't define help text.
         """
 
     @abstractmethod
     def parse_profile(self):
-        """ Return tool profile version as Galaxy major e.g. 16.01 or 16.04.
-        """
+        """Return tool profile version as Galaxy major e.g. 16.01 or 16.04."""
 
     @abstractmethod
     def parse_license(self):
@@ -267,19 +265,19 @@ class ToolSource(metaclass=ABCMeta):
         return paths_and_modtimes
 
     def parse_tests_to_dict(self):
-        return {'tests': []}
+        return {"tests": []}
 
     def __str__(self):
         source_path = self.source_path
         if source_path:
-            as_str = f'{self.__class__.__name__}[{source_path}]'
+            as_str = f"{self.__class__.__name__}[{source_path}]"
         else:
-            as_str = f'{self.__class__.__name__}[In-memory]'
+            as_str = f"{self.__class__.__name__}[In-memory]"
         return as_str
 
 
 class PagesSource:
-    """ Contains a list of Pages - each a list of InputSources -
+    """Contains a list of Pages - each a list of InputSources -
     each item in the outer list representing a page of inputs.
     Pages are deprecated so ideally this outer list will always
     be exactly a singleton.
@@ -294,13 +292,12 @@ class PagesSource:
 
 
 class PageSource(metaclass=ABCMeta):
-
     def parse_display(self):
         return None
 
     @abstractmethod
     def parse_input_sources(self) -> List:
-        """ Return a list of InputSource objects. """
+        """Return a list of InputSource objects."""
 
 
 class InputSource(metaclass=ABCMeta):
@@ -314,13 +311,13 @@ class InputSource(metaclass=ABCMeta):
 
     @abstractmethod
     def get(self, key, value=None):
-        """ Return simple named properties as string for this input source.
+        """Return simple named properties as string for this input source.
         keys to be supported depend on the parameter type.
         """
 
     @abstractmethod
     def get_bool(self, key, default):
-        """ Return simple named properties as boolean for this input source.
+        """Return simple named properties as boolean for this input source.
         keys to be supported depend on the parameter type.
         """
 
@@ -333,45 +330,43 @@ class InputSource(metaclass=ABCMeta):
         In the latter case, leading dashes are stripped and
         all remaining dashes are replaced by underscores.
         """
-        return _parse_name(self.get('name'), self.get('argument'))
+        return _parse_name(self.get("name"), self.get("argument"))
 
     def parse_help(self):
         return self.get("help")
 
     def parse_sanitizer_elem(self):
-        """ Return an XML description of sanitizers. This is a stop gap
+        """Return an XML description of sanitizers. This is a stop gap
         until we can rework galaxy.tools.parameters.sanitize to not
         explicitly depend on XML.
         """
         return None
 
     def parse_validator_elems(self):
-        """ Return an XML description of sanitizers. This is a stop gap
+        """Return an XML description of sanitizers. This is a stop gap
         until we can rework galaxy.tools.parameters.validation to not
         explicitly depend on XML.
         """
         return []
 
     def parse_optional(self, default=None):
-        """ Return boolean indicating wheter parameter is optional. """
+        """Return boolean indicating wheter parameter is optional."""
         if default is None:
             default = self.default_optional
         return self.get_bool("optional", default)
 
     def parse_dynamic_options_elem(self):
-        """ Return an XML elemnt describing dynamic options.
-        """
+        """Return an XML elemnt describing dynamic options."""
         return None
 
     def parse_static_options(self):
-        """ Return list of static options if this is a select type without
+        """Return list of static options if this is a select type without
         defining a dynamic options.
         """
         return []
 
     def parse_conversion_tuples(self):
-        """ Return list of (name, extension) to describe explicit conversions.
-        """
+        """Return list of (name, extension) to describe explicit conversions."""
         return []
 
     def parse_nested_inputs_source(self):
@@ -467,7 +462,6 @@ class TestCollectionDef:
 
 
 class RequiredFiles:
-
     def __init__(self, includes: List[Dict], excludes: List[Dict], extend_default_excludes: bool):
         self.includes = includes
         self.excludes = excludes
@@ -481,7 +475,6 @@ class RequiredFiles:
         return RequiredFiles(includes, excludes, extend_default_excludes)
 
     def find_required_files(self, tool_directory: str) -> List[str]:
-
         def matches(ie_list: List, rel_path: str):
             for ie_item in ie_list:
                 ie_item_path = ie_item["path"]
@@ -509,7 +502,7 @@ class RequiredFiles:
         files: List[str] = []
         for (dirpath, _, filenames) in safe_walk(tool_directory):
             for filename in filenames:
-                rel_path = join(dirpath, filename).replace(tool_directory + os.path.sep, '')
+                rel_path = join(dirpath, filename).replace(tool_directory + os.path.sep, "")
                 if matches(self.includes, rel_path) and not matches(self.excludes, rel_path):
                     files.append(rel_path)
         return files
@@ -535,8 +528,4 @@ class TestCollectionOutputDef:
         )
 
     def to_dict(self):
-        return dict(
-            name=self.name,
-            attributes=self.attrib,
-            element_tests=self.element_tests
-        )
+        return dict(name=self.name, attributes=self.attrib, element_tests=self.element_tests)
diff --git a/lib/galaxy/tool_util/parser/output_actions.py b/lib/galaxy/tool_util/parser/output_actions.py
index f58a8b6a817..dd04cfdb766 100644
--- a/lib/galaxy/tool_util/parser/output_actions.py
+++ b/lib/galaxy/tool_util/parser/output_actions.py
@@ -15,6 +15,7 @@ class ToolOutputActionGroup:
     """
     Manages a set of tool output dataset actions directives
     """
+
     tag = "group"
 
     def __init__(self, parent, config_elem):
@@ -100,11 +101,11 @@ class ToolOutputActionConditional:
 
     def __init__(self, parent, config_elem):
         self.parent = parent
-        self.name = config_elem.get('name', None)
+        self.name = config_elem.get("name", None)
         assert self.name is not None, "Required 'name' attribute missing from ToolOutputActionConditional"
-        self.name = self.name.split('.')
+        self.name = self.name.split(".")
         self.cases = []
-        for when_elem in config_elem.findall('when'):
+        for when_elem in config_elem.findall("when"):
             self.cases.append(ToolOutputActionConditionalWhen.from_elem(self, when_elem))
 
     def apply_action(self, output_dataset, other_values):
@@ -122,14 +123,14 @@ class ToolOutputAction:
     @classmethod
     def from_elem(cls, parent, elem):
         """Loads the proper action by the type attribute of elem"""
-        action_type = elem.get('type', None)
+        action_type = elem.get("type", None)
         assert action_type is not None, "Required 'type' attribute missing from ToolOutputAction"
         return action_types[action_type](parent, elem)
 
     def __init__(self, parent, elem):
         self.parent = parent
-        self.default = elem.get('default', None)
-        option_elem = elem.find('option')
+        self.default = elem.get("default", None)
+        option_elem = elem.find("option")
         self.option = ToolOutputActionOption.from_elem(self, option_elem)
 
     def apply_action(self, output_dataset, other_values):
@@ -147,9 +148,11 @@ class ToolOutputActionOption:
     def from_elem(cls, parent, elem):
         """Loads the proper action by the type attribute of elem"""
         if elem is None:
-            option_type = NullToolOutputActionOption.tag  # no ToolOutputActionOption's have been defined, use implicit NullToolOutputActionOption
+            option_type = (
+                NullToolOutputActionOption.tag
+            )  # no ToolOutputActionOption's have been defined, use implicit NullToolOutputActionOption
         else:
-            option_type = elem.get('type', None)
+            option_type = elem.get("type", None)
         assert option_type is not None, "Required 'type' attribute missing from ToolOutputActionOption"
         return option_types[option_type](parent, elem)
 
@@ -157,7 +160,7 @@ class ToolOutputActionOption:
         self.parent = parent
         self.filters = []
         if elem is not None:
-            for filter_elem in elem.findall('filter'):
+            for filter_elem in elem.findall("filter"):
                 self.filters.append(ToolOutputActionOptionFilter.from_elem(self, filter_elem))
 
     def get_value(self, other_values):
@@ -180,20 +183,20 @@ class FromFileToolOutputActionOption(ToolOutputActionOption):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.name = elem.get('name', None)
+        self.name = elem.get("name", None)
         assert self.name is not None, "Required 'name' attribute missing from FromFileToolOutputActionOption"
-        self.column = elem.get('column', None)
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from FromFileToolOutputActionOption"
         self.column = int(self.column)
-        self.offset = elem.get('offset', -1)
+        self.offset = elem.get("offset", -1)
         self.offset = int(self.offset)
-        self.separator = elem.get('separator', '\t')
+        self.separator = elem.get("separator", "\t")
         self.options = []
         data_file = self.name
         if not os.path.isabs(data_file):
             data_file = os.path.join(self.tool.app.config.tool_data_path, data_file)
         for line in open(data_file):
-            self.options.append(line.rstrip('\n\r').split(self.separator))
+            self.options.append(line.rstrip("\n\r").split(self.separator))
 
     def get_value(self, other_values):
         options = self.options
@@ -212,16 +215,16 @@ class FromParamToolOutputActionOption(ToolOutputActionOption):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.name = elem.get('name', None)
+        self.name = elem.get("name", None)
         assert self.name is not None, "Required 'name' attribute missing from FromFileToolOutputActionOption"
-        self.name = self.name.split('.')
-        self.column = elem.get('column', 0)
+        self.name = self.name.split(".")
+        self.column = elem.get("column", 0)
         self.column = int(self.column)
-        self.offset = elem.get('offset', -1)
+        self.offset = elem.get("offset", -1)
         self.offset = int(self.offset)
-        self.param_attribute = elem.get('param_attribute', [])
+        self.param_attribute = elem.get("param_attribute", [])
         if self.param_attribute:
-            self.param_attribute = self.param_attribute.split('.')
+            self.param_attribute = self.param_attribute.split(".")
 
     def get_value(self, other_values):
         value = other_values
@@ -231,7 +234,7 @@ class FromParamToolOutputActionOption(ToolOutputActionOption):
         for attr_name in self.param_attribute:
             # if the value is a list from a repeat tag you can access the first element of the repeat with
             # artifical 'first' attribute_name. For example: .. param_attribute="first.input_mate1.ext"
-            if isinstance(value, list) and attr_name == 'first':
+            if isinstance(value, list) and attr_name == "first":
                 value = value[0]
             elif isinstance(value, dict):
                 value = value[attr_name]
@@ -262,15 +265,15 @@ class FromDataTableOutputActionOption(ToolOutputActionOption):
     # TODO: allow accessing by column 'name' not just index
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.name = elem.get('name', None)
+        self.name = elem.get("name", None)
         assert self.name is not None, "Required 'name' attribute missing from FromDataTableOutputActionOption"
         self.missing_tool_data_table_name = None
         if self.name in self.tool.app.tool_data_tables:
             self.options = self.tool.app.tool_data_tables[self.name].get_fields()
-            self.column = elem.get('column', None)
+            self.column = elem.get("column", None)
             assert self.column is not None, "Required 'column' attribute missing from FromDataTableOutputActionOption"
             self.column = int(self.column)
-            self.offset = elem.get('offset', -1)
+            self.offset = elem.get("offset", -1)
             self.offset = int(self.offset)
         else:
             self.options = []
@@ -296,7 +299,7 @@ class MetadataToolOutputAction(ToolOutputAction):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.name = elem.get('name', None)
+        self.name = elem.get("name", None)
         assert self.name is not None, "Required 'name' attribute missing from MetadataToolOutputAction"
 
     def apply_action(self, output_dataset, other_values):
@@ -312,7 +315,7 @@ class FormatToolOutputAction(ToolOutputAction):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.default = elem.get('default', None)
+        self.default = elem.get("default", None)
 
     def apply_action(self, output_dataset, other_values):
         value = self.option.get_value(other_values)
@@ -328,7 +331,7 @@ class ToolOutputActionOptionFilter:
     @classmethod
     def from_elem(cls, parent, elem):
         """Loads the proper action by the type attribute of elem"""
-        filter_type = elem.get('type', None)
+        filter_type = elem.get("type", None)
         assert filter_type is not None, "Required 'type' attribute missing from ToolOutputActionOptionFilter"
         return filter_types[filter_type](parent, elem)
 
@@ -348,20 +351,24 @@ class ParamValueToolOutputActionOptionFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.ref = elem.get('ref', None)
+        self.ref = elem.get("ref", None)
         if self.ref:
-            self.ref = self.ref.split('.')
-        self.value = elem.get('value', None)
-        assert self.ref != self.value, "Required 'ref' or 'value' attribute missing from ParamValueToolOutputActionOptionFilter"
-        self.column = elem.get('column', None)
-        assert self.column is not None, "Required 'column' attribute missing from ParamValueToolOutputActionOptionFilter"
+            self.ref = self.ref.split(".")
+        self.value = elem.get("value", None)
+        assert (
+            self.ref != self.value
+        ), "Required 'ref' or 'value' attribute missing from ParamValueToolOutputActionOptionFilter"
+        self.column = elem.get("column", None)
+        assert (
+            self.column is not None
+        ), "Required 'column' attribute missing from ParamValueToolOutputActionOptionFilter"
         self.column = int(self.column)
-        self.keep = util.string_as_bool(elem.get("keep", 'True'))
-        self.compare = parse_compare_type(elem.get('compare', None))
+        self.keep = util.string_as_bool(elem.get("keep", "True"))
+        self.compare = parse_compare_type(elem.get("compare", None))
         self.cast = parse_cast_attribute(elem.get("cast", None))
-        self.param_attribute = elem.get('param_attribute', [])
+        self.param_attribute = elem.get("param_attribute", [])
         if self.param_attribute:
-            self.param_attribute = self.param_attribute.split('.')
+            self.param_attribute = self.param_attribute.split(".")
 
     def filter_options(self, options, other_values):
         if self.ref:
@@ -392,16 +399,18 @@ class InsertColumnToolOutputActionOptionFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.ref = elem.get('ref', None)
+        self.ref = elem.get("ref", None)
         if self.ref:
-            self.ref = self.ref.split('.')
-        self.value = elem.get('value', None)
-        assert self.ref != self.value, "Required 'ref' or 'value' attribute missing from InsertColumnToolOutputActionOptionFilter"
-        self.column = elem.get('column', None)  # None is append
+            self.ref = self.ref.split(".")
+        self.value = elem.get("value", None)
+        assert (
+            self.ref != self.value
+        ), "Required 'ref' or 'value' attribute missing from InsertColumnToolOutputActionOptionFilter"
+        self.column = elem.get("column", None)  # None is append
         if self.column:
             self.column = int(self.column)
         # TODO not supported in xsd
-        self.iterate = util.string_as_bool(elem.get("iterate", 'False'))
+        self.iterate = util.string_as_bool(elem.get("iterate", "False"))
 
     def filter_options(self, options, other_values):
         if self.ref:
@@ -433,7 +442,7 @@ class MultipleSplitterFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.column = elem.get('column', None)
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from MultipleSplitterFilter"
         self.column = int(self.column)
         self.separator = elem.get("separator", ",")
@@ -442,7 +451,7 @@ class MultipleSplitterFilter(ToolOutputActionOptionFilter):
         rval = []
         for fields in options:
             for field in fields[self.column].split(self.separator):
-                rval.append(fields[0:self.column] + [field] + fields[self.column + 1:])
+                rval.append(fields[0 : self.column] + [field] + fields[self.column + 1 :])
         return rval
 
 
@@ -451,7 +460,7 @@ class ColumnStripFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.column = elem.get('column', None)
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from ColumnStripFilter"
         self.column = int(self.column)
         self.strip = elem.get("strip", None)
@@ -459,7 +468,7 @@ class ColumnStripFilter(ToolOutputActionOptionFilter):
     def filter_options(self, options, other_values):
         rval = []
         for fields in options:
-            rval.append(fields[0:self.column] + [fields[self.column].strip(self.strip)] + fields[self.column + 1:])
+            rval.append(fields[0 : self.column] + [fields[self.column].strip(self.strip)] + fields[self.column + 1 :])
         return rval
 
 
@@ -468,12 +477,14 @@ class ColumnReplaceFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.old_column = elem.get('old_column', None)
+        self.old_column = elem.get("old_column", None)
         self.old_value = elem.get("old_value", None)
         self.new_value = elem.get("new_value", None)
-        self.new_column = elem.get('new_column', None)
-        assert (bool(self.old_column) ^ bool(self.old_value) and bool(self.new_column) ^ bool(self.new_value)), "Required 'old_column' or 'old_value' and 'new_column' or 'new_value' attribute missing from ColumnReplaceFilter"
-        self.column = elem.get('column', None)
+        self.new_column = elem.get("new_column", None)
+        assert bool(self.old_column) ^ bool(self.old_value) and bool(self.new_column) ^ bool(
+            self.new_value
+        ), "Required 'old_column' or 'old_value' and 'new_column' or 'new_value' attribute missing from ColumnReplaceFilter"
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from ColumnReplaceFilter"
         self.column = int(self.column)
         if self.old_column is not None:
@@ -492,7 +503,11 @@ class ColumnReplaceFilter(ToolOutputActionOptionFilter):
                 new_value = fields[self.new_column]
             else:
                 new_value = self.new_value
-            rval.append(fields[0:self.column] + [fields[self.column].replace(old_value, new_value)] + fields[self.column + 1:])
+            rval.append(
+                fields[0 : self.column]
+                + [fields[self.column].replace(old_value, new_value)]
+                + fields[self.column + 1 :]
+            )
         return rval
 
 
@@ -501,16 +516,16 @@ class MetadataValueFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.ref = elem.get('ref', None)
+        self.ref = elem.get("ref", None)
         assert self.ref is not None, "Required 'ref' attribute missing from MetadataValueFilter"
-        self.ref = self.ref.split('.')
-        self.name = elem.get('name', None)
+        self.ref = self.ref.split(".")
+        self.name = elem.get("name", None)
         assert self.name is not None, "Required 'name' attribute missing from MetadataValueFilter"
-        self.column = elem.get('column', None)
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from MetadataValueFilter"
         self.column = int(self.column)
-        self.keep = util.string_as_bool(elem.get("keep", 'True'))
-        self.compare = parse_compare_type(elem.get('compare', None))
+        self.keep = util.string_as_bool(elem.get("keep", "True"))
+        self.compare = parse_compare_type(elem.get("compare", None))
 
     def filter_options(self, options, other_values):
         ref = other_values
@@ -530,10 +545,10 @@ class BooleanFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.column = elem.get('column', None)
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from BooleanFilter"
         self.column = int(self.column)
-        self.keep = util.string_as_bool(elem.get("keep", 'True'))
+        self.keep = util.string_as_bool(elem.get("keep", "True"))
         self.cast = parse_cast_attribute(elem.get("cast", None))
 
     def filter_options(self, options, other_values):
@@ -554,17 +569,20 @@ class StringFunctionFilter(ToolOutputActionOptionFilter):
 
     def __init__(self, parent, elem):
         super().__init__(parent, elem)
-        self.column = elem.get('column', None)
+        self.column = elem.get("column", None)
         assert self.column is not None, "Required 'column' attribute missing from StringFunctionFilter"
         self.column = int(self.column)
         self.function = elem.get("name", None)
-        assert self.function in ['lower', 'upper'], "Required function 'name' missing or invalid from StringFunctionFilter"  # add function names as needed
+        assert self.function in [
+            "lower",
+            "upper",
+        ], "Required function 'name' missing or invalid from StringFunctionFilter"  # add function names as needed
         self.function = getattr(str, self.function)
 
     def filter_options(self, options, other_values):
         rval = []
         for fields in options:
-            rval.append(fields[0:self.column] + [self.function(fields[self.column])] + fields[self.column + 1:])
+            rval.append(fields[0 : self.column] + [self.function(fields[self.column])] + fields[self.column + 1 :])
         return rval
 
 
@@ -574,11 +592,25 @@ for action_type in [MetadataToolOutputAction, FormatToolOutputAction]:
     action_types[action_type.tag] = action_type
 
 option_types = {}
-for option_type in [NullToolOutputActionOption, FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption]:
+for option_type in [
+    NullToolOutputActionOption,
+    FromFileToolOutputActionOption,
+    FromParamToolOutputActionOption,
+    FromDataTableOutputActionOption,
+]:
     option_types[option_type.tag] = option_type
 
 filter_types = {}
-for filter_type in [ParamValueToolOutputActionOptionFilter, InsertColumnToolOutputActionOptionFilter, MultipleSplitterFilter, ColumnStripFilter, MetadataValueFilter, BooleanFilter, StringFunctionFilter, ColumnReplaceFilter]:
+for filter_type in [
+    ParamValueToolOutputActionOptionFilter,
+    InsertColumnToolOutputActionOptionFilter,
+    MultipleSplitterFilter,
+    ColumnStripFilter,
+    MetadataValueFilter,
+    BooleanFilter,
+    StringFunctionFilter,
+    ColumnReplaceFilter,
+]:
     filter_types[filter_type.tag] = filter_type
 
 
@@ -586,23 +618,24 @@ for filter_type in [ParamValueToolOutputActionOptionFilter, InsertColumnToolOutp
 # determine cast function
 # TODO add float
 def parse_cast_attribute(cast):
-    if cast == 'string_as_bool':
+    if cast == "string_as_bool":
         cast = util.string_as_bool
-    elif cast == 'int':
+    elif cast == "int":
         cast = int
-    elif cast == 'str':
+    elif cast == "str":
         cast = str
     else:
         # return value as-is
         def cast(x):
             return x
+
     return cast
 
 
 # comparison
 def parse_compare_type(compare):
     if compare is None:
-        compare = 'eq'
+        compare = "eq"
     assert compare in compare_types, f"Invalid compare type specified: {compare}"
     return compare_types[compare]
 
@@ -649,14 +682,14 @@ def compare_re_search(value1, value2):
 
 
 compare_types = {
-    'eq': compare_eq,
-    'neq': compare_neq,
-    'gt': compare_gt,
-    'gte': compare_gte,
-    'lt': compare_lt,
-    'lte': compare_lte,
-    'in': compare_in,
-    'startswith': compare_startswith,
-    'endswith': compare_endswith,
-    "re_search": compare_re_search
+    "eq": compare_eq,
+    "neq": compare_neq,
+    "gt": compare_gt,
+    "gte": compare_gte,
+    "lt": compare_lt,
+    "lte": compare_lte,
+    "in": compare_in,
+    "startswith": compare_startswith,
+    "endswith": compare_endswith,
+    "re_search": compare_re_search,
 }
diff --git a/lib/galaxy/tool_util/parser/output_collection_def.py b/lib/galaxy/tool_util/parser/output_collection_def.py
index 01bb7988eb2..8e5481feef2 100644
--- a/lib/galaxy/tool_util/parser/output_collection_def.py
+++ b/lib/galaxy/tool_util/parser/output_collection_def.py
@@ -6,7 +6,9 @@ from typing import List
 from galaxy.util import asbool
 from .util import is_dict
 
-DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
+DEFAULT_EXTRA_FILENAME_PATTERN = (
+    r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
+)
 DEFAULT_SORT_BY = "filename"
 DEFAULT_SORT_COMP = "lexical"
 
@@ -49,7 +51,9 @@ def _validate_collectors(collectors):
     if num_discover_dataset_blocks > 1:
         for collector in collectors:
             if collector.discover_via == "tool_provided_metadata":
-                raise Exception("Cannot specify more than one discover dataset condition if any of them specify tool_provided_metadata.")
+                raise Exception(
+                    "Cannot specify more than one discover dataset condition if any of them specify tool_provided_metadata."
+                )
 
     return collectors
 
@@ -71,28 +75,27 @@ def dataset_collection_description(**kwargs):
 
 
 class DatasetCollectionDescription:
-
     def __init__(self, **kwargs):
         self.default_dbkey = kwargs.get("dbkey", INPUT_DBKEY_TOKEN)
         self.default_ext = kwargs.get("ext", None)
         if self.default_ext is None and "format" in kwargs:
             self.default_ext = kwargs.get("format")
         self.default_visible = asbool(kwargs.get("visible", None))
-        self.assign_primary_output = asbool(kwargs.get('assign_primary_output', False))
+        self.assign_primary_output = asbool(kwargs.get("assign_primary_output", False))
         self.directory = kwargs.get("directory", None)
         self.recurse = False
         self.match_relative_path = kwargs.get("match_relative_path", False)
 
     def to_dict(self):
         return {
-            'discover_via': self.discover_via,
-            'dbkey': self.default_dbkey,
-            'format': self.default_ext,
-            'visible': self.default_visible,
-            'assign_primary_output': self.assign_primary_output,
-            'directory': self.directory,
-            'recurse': self.recurse,
-            'match_relative_path': self.match_relative_path,
+            "discover_via": self.discover_via,
+            "dbkey": self.default_dbkey,
+            "format": self.default_ext,
+            "visible": self.default_visible,
+            "assign_primary_output": self.assign_primary_output,
+            "directory": self.directory,
+            "recurse": self.recurse,
+            "match_relative_path": self.match_relative_path,
         }
 
     @property
@@ -120,7 +123,7 @@ class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
         self.sort_by = sort_by = kwargs.get("sort_by", DEFAULT_SORT_BY)
         if sort_by.startswith("reverse_"):
             self.sort_reverse = True
-            sort_by = sort_by[len("reverse_"):]
+            sort_by = sort_by[len("reverse_") :]
         else:
             self.sort_reverse = False
         if "_" in sort_by:
@@ -128,24 +131,21 @@ class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
             assert sort_comp in ["lexical", "numeric"]
         else:
             sort_comp = DEFAULT_SORT_COMP
-        assert sort_by in [
-            "filename",
-            "name",
-            "designation",
-            "dbkey"
-        ]
+        assert sort_by in ["filename", "name", "designation", "dbkey"]
         self.sort_key = sort_by
         self.sort_comp = sort_comp
 
     def to_dict(self):
         as_dict = super().to_dict()
-        as_dict.update({
-            "sort_key": self.sort_key,
-            "sort_comp": self.sort_comp,
-            "pattern": self.pattern,
-            "recurse": self.recurse,
-            "sort_by": self.sort_by,
-        })
+        as_dict.update(
+            {
+                "sort_key": self.sort_key,
+                "sort_comp": self.sort_comp,
+                "pattern": self.pattern,
+                "recurse": self.recurse,
+                "sort_by": self.sort_by,
+            }
+        )
         return as_dict
 
     @property
diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
index 4140be8f05d..64da29dcf97 100644
--- a/lib/galaxy/tool_util/parser/output_objects.py
+++ b/lib/galaxy/tool_util/parser/output_objects.py
@@ -2,11 +2,13 @@ from typing import List
 
 from galaxy.util.dictifiable import Dictifiable
 from .output_actions import ToolOutputActionGroup
-from .output_collection_def import dataset_collector_descriptions_from_output_dict, DatasetCollectionDescription
+from .output_collection_def import (
+    dataset_collector_descriptions_from_output_dict,
+    DatasetCollectionDescription,
+)
 
 
 class ToolOutputBase(Dictifiable):
-
     def __init__(self, name, label=None, filters=None, hidden=False, from_expression=None):
         super().__init__()
         self.name = name
@@ -16,7 +18,7 @@ class ToolOutputBase(Dictifiable):
         self.collection = False
         self.from_expression = from_expression
 
-    def to_dict(self, view='collection', value_mapper=None, app=None):
+    def to_dict(self, view="collection", value_mapper=None, app=None):
         return super().to_dict(view=view, value_mapper=value_mapper)
 
     @property
@@ -32,12 +34,34 @@ class ToolOutput(ToolOutputBase):
     (format, metadata_source, parent)
     """
 
-    dict_collection_visible_keys = ['name', 'format', 'label', 'hidden', 'output_type', 'format_source',
-                                    'default_identifier_source', 'metadata_source', 'parent', 'count', 'from_work_dir']
+    dict_collection_visible_keys = [
+        "name",
+        "format",
+        "label",
+        "hidden",
+        "output_type",
+        "format_source",
+        "default_identifier_source",
+        "metadata_source",
+        "parent",
+        "count",
+        "from_work_dir",
+    ]
 
-    def __init__(self, name, format=None, format_source=None, metadata_source=None,
-                 parent=None, label=None, filters=None, actions=None, hidden=False,
-                 implicit=False, from_expression=None):
+    def __init__(
+        self,
+        name,
+        format=None,
+        format_source=None,
+        metadata_source=None,
+        parent=None,
+        label=None,
+        filters=None,
+        actions=None,
+        hidden=False,
+        implicit=False,
+        from_expression=None,
+    ):
         super().__init__(name, label=label, filters=filters, hidden=hidden, from_expression=from_expression)
         self.output_type = "data"
         self.format = format
@@ -70,7 +94,7 @@ class ToolOutput(ToolOutputBase):
     def __iter__(self):
         return iter((self.format, self.metadata_source, self.parent))
 
-    def to_dict(self, view='collection', value_mapper=None, app=None):
+    def to_dict(self, view="collection", value_mapper=None, app=None):
         as_dict = super().to_dict(view=view, value_mapper=value_mapper, app=app)
         format = self.format
         if format and format != "input" and app:
@@ -78,7 +102,7 @@ class ToolOutput(ToolOutputBase):
             as_dict["edam_format"] = edam_format
             edam_data = app.datatypes_registry.edam_data.get(self.format)
             as_dict["edam_data"] = edam_data
-        as_dict['discover_datasets'] = list(map(lambda d: d.to_dict(), self.dataset_collector_descriptions))
+        as_dict["discover_datasets"] = list(map(lambda d: d.to_dict(), self.dataset_collector_descriptions))
         return as_dict
 
     @staticmethod
@@ -107,10 +131,9 @@ class ToolOutput(ToolOutputBase):
 
 
 class ToolExpressionOutput(ToolOutputBase):
-    dict_collection_visible_keys = ('name', 'format', 'label', 'hidden', 'output_type')
+    dict_collection_visible_keys = ("name", "format", "label", "hidden", "output_type")
 
-    def __init__(self, name, output_type, from_expression,
-                 label=None, filters=None, actions=None, hidden=False):
+    def __init__(self, name, output_type, from_expression, label=None, filters=None, actions=None, hidden=False):
         super().__init__(name, label=label, filters=filters, hidden=hidden)
         self.output_type = output_type  # JSON type...
         self.from_expression = from_expression
@@ -144,8 +167,19 @@ class ToolOutputCollection(ToolOutputBase):
         </collection>
         <outputs>
     """
-    dict_collection_visible_keys = ['name', 'format', 'label', 'hidden', 'output_type', 'default_format',
-                                    'default_format_source', 'default_metadata_source', 'inherit_format', 'inherit_metadata']
+
+    dict_collection_visible_keys = [
+        "name",
+        "format",
+        "label",
+        "hidden",
+        "output_type",
+        "default_format",
+        "default_format_source",
+        "default_metadata_source",
+        "inherit_format",
+        "inherit_metadata",
+    ]
 
     def __init__(
         self,
@@ -158,7 +192,7 @@ class ToolOutputCollection(ToolOutputBase):
         default_format_source=None,
         default_metadata_source=None,
         inherit_format=False,
-        inherit_metadata=False
+        inherit_metadata=False,
     ):
         super().__init__(name, label=label, filters=filters, hidden=hidden)
         self.output_type = "collection"
@@ -235,9 +269,9 @@ class ToolOutputCollection(ToolOutputBase):
             raise Exception("dataset_collector_descriptions called for output collection with static structure")
         return self.structure.dataset_collector_descriptions
 
-    def to_dict(self, view='collection', value_mapper=None, app=None):
+    def to_dict(self, view="collection", value_mapper=None, app=None):
         as_dict = super().to_dict(view=view, value_mapper=value_mapper, app=app)
-        as_dict['structure'] = self.structure.to_dict()
+        as_dict["structure"] = self.structure.to_dict()
         return as_dict
 
     @staticmethod
@@ -263,7 +297,6 @@ class ToolOutputCollection(ToolOutputBase):
 
 
 class ToolOutputCollectionStructure:
-
     def __init__(
         self,
         collection_type,
@@ -279,10 +312,20 @@ class ToolOutputCollectionStructure:
         self.dataset_collector_descriptions = dataset_collector_descriptions or []
         if collection_type and collection_type_source:
             raise ValueError("Cannot set both type and type_source on collection output.")
-        if collection_type is None and structured_like is None and dataset_collector_descriptions is None and collection_type_source is None and collection_type_from_rules is None:
-            raise ValueError("Output collection types must specify source of collection type information (e.g. structured_like or type_source).")
+        if (
+            collection_type is None
+            and structured_like is None
+            and dataset_collector_descriptions is None
+            and collection_type_source is None
+            and collection_type_from_rules is None
+        ):
+            raise ValueError(
+                "Output collection types must specify source of collection type information (e.g. structured_like or type_source)."
+            )
         if dataset_collector_descriptions and (structured_like or collection_type_from_rules):
-            raise ValueError("Cannot specify dynamic structure (discovered_datasets) and collection type attributes structured_like or collection_type_from_rules.")
+            raise ValueError(
+                "Cannot specify dynamic structure (discovered_datasets) and collection type attributes structured_like or collection_type_from_rules."
+            )
         self.dynamic = bool(dataset_collector_descriptions)
 
     def collection_prototype(self, inputs, type_registry):
@@ -298,20 +341,20 @@ class ToolOutputCollectionStructure:
 
     def to_dict(self):
         return {
-            'collection_type': self.collection_type,
-            'collection_type_source': self.collection_type_source,
-            'collection_type_from_rules': self.collection_type_from_rules,
-            'structured_like': self.structured_like,
-            'discover_datasets': [d.to_dict() for d in self.dataset_collector_descriptions],
+            "collection_type": self.collection_type,
+            "collection_type_source": self.collection_type_source,
+            "collection_type_from_rules": self.collection_type_from_rules,
+            "structured_like": self.structured_like,
+            "discover_datasets": [d.to_dict() for d in self.dataset_collector_descriptions],
         }
 
     @staticmethod
     def from_dict(as_dict):
         structure = ToolOutputCollectionStructure(
-            collection_type=as_dict['collection_type'],
-            collection_type_source=as_dict['collection_type_source'],
-            collection_type_from_rules=as_dict['collection_type_from_rules'],
-            structured_like=as_dict['structured_like'],
+            collection_type=as_dict["collection_type"],
+            collection_type_source=as_dict["collection_type_source"],
+            collection_type_from_rules=as_dict["collection_type_from_rules"],
+            structured_like=as_dict["structured_like"],
             dataset_collector_descriptions=dataset_collector_descriptions_from_output_dict(as_dict),
         )
         return structure
@@ -324,7 +367,9 @@ class ToolOutputCollectionStructure:
             return _merge_dataset_collector_descriptions_patterns(self.dataset_collector_descriptions)
 
 
-def _merge_dataset_collector_descriptions_patterns(dataset_collector_descriptions: List[DatasetCollectionDescription]) -> List[str]:
+def _merge_dataset_collector_descriptions_patterns(
+    dataset_collector_descriptions: List[DatasetCollectionDescription],
+) -> List[str]:
     patterns = []
     for description in dataset_collector_descriptions:
         patterns.extend(description.discover_patterns)
@@ -332,7 +377,6 @@ def _merge_dataset_collector_descriptions_patterns(dataset_collector_description
 
 
 class ToolOutputCollectionPart:
-
     def __init__(self, output_collection_def, element_identifier, output_def, parent_ids=None):
         parent_ids = parent_ids or []
         self.output_collection_def = output_collection_def
diff --git a/lib/galaxy/tool_util/parser/stdio.py b/lib/galaxy/tool_util/parser/stdio.py
index 31d5109216c..e51c942159f 100644
--- a/lib/galaxy/tool_util/parser/stdio.py
+++ b/lib/galaxy/tool_util/parser/stdio.py
@@ -7,6 +7,7 @@ class StdioErrorLevel:
     and exit codes. They are meant to be used comparatively, such as showing
     that warning < fatal. This is really meant to just be an enum.
     """
+
     NO_ERROR = 0
     LOG = 1
     QC = 1.1
@@ -15,12 +16,12 @@ class StdioErrorLevel:
     FATAL_OOM = 4
     MAX = 4
     descs = {
-        NO_ERROR: 'No error',
-        LOG: 'Log',
-        QC: 'QC',
-        WARNING: 'Warning',
-        FATAL: 'Fatal error',
-        FATAL_OOM: 'Out of memory error',
+        NO_ERROR: "No error",
+        LOG: "Log",
+        QC: "QC",
+        WARNING: "Warning",
+        FATAL: "Fatal error",
+        FATAL_OOM: "Out of memory error",
     }
 
     @staticmethod
@@ -113,7 +114,7 @@ def aggressive_error_checks():
         _oom_regex("java.lang.OutOfMemoryError"),
         _oom_regex("Out of memory"),
         _error_regex("exception:"),
-        _error_regex("error:")
+        _error_regex("error:"),
     ]
     return exit_codes, regexes
 
diff --git a/lib/galaxy/tool_util/parser/util.py b/lib/galaxy/tool_util/parser/util.py
index 74676e4bfba..2c43c51e5b4 100644
--- a/lib/galaxy/tool_util/parser/util.py
+++ b/lib/galaxy/tool_util/parser/util.py
@@ -17,5 +17,5 @@ def _parse_name(name, argument):
     if name is None:
         if not argument:
             raise ValueError("parameter must specify a 'name' or 'argument'.")
-        name = argument.lstrip('-').replace("-", "_")
+        name = argument.lstrip("-").replace("-", "_")
     return name
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 991016c3078..a07a565a85a 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -10,12 +10,12 @@ import packaging.version
 from galaxy.tool_util.deps import requirements
 from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA,
-    DEFAULT_DELTA_FRAC
+    DEFAULT_DELTA_FRAC,
 )
 from galaxy.util import (
     string_as_bool,
     xml_text,
-    xml_to_string
+    xml_to_string,
 )
 from .interface import (
     InputSource,
@@ -32,7 +32,7 @@ from .output_objects import (
     ToolExpressionOutput,
     ToolOutput,
     ToolOutputCollection,
-    ToolOutputCollectionStructure
+    ToolOutputCollectionStructure,
 )
 from .stdio import (
     aggressive_error_checks,
@@ -42,15 +42,13 @@ from .stdio import (
     ToolStdioRegex,
 )
 
-
 log = logging.getLogger(__name__)
 
 
 class XmlToolSource(ToolSource):
-    """ Responsible for parsing a tool from classic Galaxy representation.
-    """
+    """Responsible for parsing a tool from classic Galaxy representation."""
 
-    language = 'xml'
+    language = "xml"
 
     def __init__(self, xml_tree, source_path=None, macro_paths=None):
         self.xml_tree = xml_tree
@@ -72,8 +70,8 @@ class XmlToolSource(ToolSource):
         root = self.root
         if root.find("type") is not None:
             type_elem = root.find("type")
-            module = type_elem.get('module', 'galaxy.tools')
-            cls = type_elem.get('class')
+            module = type_elem.get("module", "galaxy.tools")
+            cls = type_elem.get("class")
             return module, cls
 
         return None
@@ -82,16 +80,16 @@ class XmlToolSource(ToolSource):
         root = self.root
         action_elem = root.find("action")
         if action_elem is not None:
-            module = action_elem.get('module')
-            cls = action_elem.get('class')
+            module = action_elem.get("module")
+            cls = action_elem.get("class")
             return module, cls
         else:
             return None
 
     def parse_tool_type(self):
         root = self.root
-        if root.get('tool_type', None) is not None:
-            return root.get('tool_type')
+        if root.get("tool_type", None) is not None:
+            return root.get("tool_type")
 
     def parse_name(self):
         return self.root.get("name")
@@ -112,7 +110,11 @@ class XmlToolSource(ToolSource):
         xrefs = self.root.find("xrefs")
         if xrefs is None:
             return []
-        return [dict(value=xref.text.strip(), reftype=xref.attrib['type']) for xref in xrefs.findall("xref") if xref.get("type")]
+        return [
+            dict(value=xref.text.strip(), reftype=xref.attrib["type"])
+            for xref in xrefs.findall("xref")
+            if xref.get("type")
+        ]
 
     def parse_description(self):
         return xml_text(self.root, "description")
@@ -131,8 +133,7 @@ class XmlToolSource(ToolSource):
         return ((command_el is not None) and command_el.text) or None
 
     def parse_expression(self):
-        """ Return string containing command to run.
-        """
+        """Return string containing command to run."""
         expression_el = self.root.find("expression")
         if expression_el is not None:
             expression_type = expression_el.get("type")
@@ -161,9 +162,7 @@ class XmlToolSource(ToolSource):
                 "inject": inject,
                 "strip": string_as_bool(environment_variable_el.get("strip", False)),
             }
-            environment_variables.append(
-                definition
-            )
+            environment_variables.append(definition)
         return environment_variables
 
     def parse_home_target(self):
@@ -219,12 +218,12 @@ class XmlToolSource(ToolSource):
             return rtt
         for ep_el in interactivetool_el.findall("entry_point"):
             port = ep_el.find("port")
-            assert port is not None, ValueError('A port is required for InteractiveTools')
+            assert port is not None, ValueError("A port is required for InteractiveTools")
             port = port.text.strip()
             url = ep_el.find("url")
             if url is not None:
                 url = url.text.strip()
-            name = ep_el.get('name', None)
+            name = ep_el.get("name", None)
             if name:
                 name = name.strip()
             requires_domain = string_as_bool(ep_el.attrib.get("requires_domain", False))
@@ -277,7 +276,9 @@ class XmlToolSource(ToolSource):
             return as_list
 
         as_dict = {}
-        as_dict["extend_default_excludes"] = self._get_attribute_as_bool("extend_default_excludes", True, elem=required_files)
+        as_dict["extend_default_excludes"] = self._get_attribute_as_bool(
+            "extend_default_excludes", True, elem=required_files
+        )
         as_dict["includes"] = parse_include_exclude_list("include")
         as_dict["excludes"] = parse_include_exclude_list("exclude")
         return RequiredFiles.from_dict(as_dict)
@@ -327,7 +328,7 @@ class XmlToolSource(ToolSource):
 
         def _parse_expression(output_elem, **kwds):
             output_def = self._parse_expression_output(output_elem, tool, **kwds)
-            output_def.filters = output_elem.findall('filter')
+            output_def.filters = output_elem.findall("filter")
             data_dict[output_def.name] = output_def
             return output_def
 
@@ -346,7 +347,7 @@ class XmlToolSource(ToolSource):
                 inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None))
             default_format_source = collection_elem.get("format_source", None)
             default_metadata_source = collection_elem.get("metadata_source", "")
-            filters = collection_elem.findall('filter')
+            filters = collection_elem.findall("filter")
 
             dataset_collector_descriptions = None
             if collection_elem.find("discover_datasets") is not None:
@@ -429,22 +430,24 @@ class XmlToolSource(ToolSource):
         output.format = output_format
         output.change_format = data_elem.findall("change_format")
         output.format_source = data_elem.get("format_source", default_format_source)
-        output.default_identifier_source = data_elem.get("default_identifier_source", 'None')
+        output.default_identifier_source = data_elem.get("default_identifier_source", "None")
         output.metadata_source = data_elem.get("metadata_source", default_metadata_source)
         output.parent = data_elem.get("parent", None)
         output.label = xml_text(data_elem, "label")
         output.count = int(data_elem.get("count", 1))
-        output.filters = data_elem.findall('filter')
+        output.filters = data_elem.findall("filter")
         output.tool = tool
         output.from_work_dir = data_elem.get("from_work_dir", None)
-        if output.from_work_dir and getattr(tool, 'profile', 0) < 21.09:
+        if output.from_work_dir and getattr(tool, "profile", 0) < 21.09:
             # We started quoting from_work_dir outputs in 21.09.
             # Prior to quoting, trailing spaces had no effect.
             # This ensures that old tools continue to work.
             output.from_work_dir = output.from_work_dir.strip()
         output.hidden = string_as_bool(data_elem.get("hidden", ""))
-        output.actions = ToolOutputActionGroup(output, data_elem.find('actions'))
-        output.dataset_collector_descriptions = dataset_collector_descriptions_from_elem(data_elem, legacy=self.legacy_defaults)
+        output.actions = ToolOutputActionGroup(output, data_elem.find("actions"))
+        output.dataset_collector_descriptions = dataset_collector_descriptions_from_elem(
+            data_elem, legacy=self.legacy_defaults
+        )
         return output
 
     def _parse_expression_output(self, output_elem, tool, **kwds):
@@ -459,7 +462,7 @@ class XmlToolSource(ToolSource):
         output.label = xml_text(output_elem, "label")
 
         output.hidden = string_as_bool(output_elem.get("hidden", ""))
-        output.actions = ToolOutputActionGroup(output, output_elem.find('actions'))
+        output.actions = ToolOutputActionGroup(output, output_elem.find("actions"))
         output.dataset_collector_descriptions = []
         return output
 
@@ -497,13 +500,13 @@ class XmlToolSource(ToolSource):
                 exit_codes, regexes = aggressive_error_checks()
             else:
                 raise ValueError(f"Unknown detect_errors value encountered [{detect_errors}]")
-        elif len(self.root.findall('stdio')) == 0 and not self.legacy_defaults:
+        elif len(self.root.findall("stdio")) == 0 and not self.legacy_defaults:
             exit_codes, regexes = error_on_exit_code()
         else:
             exit_codes = []
             regexes = []
 
-        if len(self.root.findall('stdio')) > 0:
+        if len(self.root.findall("stdio")) > 0:
             parser = StdioParser(self.root)
             exit_codes = parser.stdio_exit_codes + exit_codes
             regexes = parser.stdio_regexes + regexes
@@ -512,7 +515,7 @@ class XmlToolSource(ToolSource):
 
     def parse_strict_shell(self):
         command_el = self._command_el
-        if packaging.version.parse(self.parse_profile()) < packaging.version.parse('20.09'):
+        if packaging.version.parse(self.parse_profile()) < packaging.version.parse("20.09"):
             default = "False"
         else:
             default = "True"
@@ -522,7 +525,7 @@ class XmlToolSource(ToolSource):
             return string_as_bool(default)
 
     def parse_help(self):
-        help_elem = self.root.find('help')
+        help_elem = self.root.find("help")
         return help_elem.text if help_elem is not None else None
 
     @property
@@ -536,9 +539,7 @@ class XmlToolSource(ToolSource):
     def parse_tests_to_dict(self):
         tests_elem = self.root.find("tests")
         tests = []
-        rval = dict(
-            tests=tests
-        )
+        rval = dict(tests=tests)
 
         if tests_elem is not None:
             for i, test_elem in enumerate(tests_elem.findall("test")):
@@ -619,7 +620,7 @@ def __parse_output_elems(test_elem):
 
 def __parse_output_elem(output_elem):
     attrib = dict(output_elem.attrib)
-    name = attrib.pop('name', None)
+    name = attrib.pop("name", None)
     if name is None:
         raise Exception("Test output does not have a 'name'")
 
@@ -642,7 +643,7 @@ def __parse_output_collection_elems(test_elem, profile=None):
 
 def __parse_output_collection_elem(output_collection_elem, profile=None):
     attrib = dict(output_collection_elem.attrib)
-    name = attrib.pop('name', None)
+    name = attrib.pop("name", None)
     if name is None:
         raise Exception("Test output collection does not have a 'name'")
     element_tests = __parse_element_tests(output_collection_elem, profile=profile)
@@ -653,10 +654,12 @@ def __parse_element_tests(parent_element, profile=None):
     element_tests = {}
     for idx, element in enumerate(parent_element.findall("element")):
         element_attrib = dict(element.attrib)
-        identifier = element_attrib.pop('name', None)
+        identifier = element_attrib.pop("name", None)
         if identifier is None:
             raise Exception("Test primary dataset does not have a 'identifier'")
-        element_tests[identifier] = __parse_test_attributes(element, element_attrib, parse_elements=True, profile=profile)
+        element_tests[identifier] = __parse_test_attributes(
+            element, element_attrib, parse_elements=True, profile=profile
+        )
         if profile and profile >= "20.09":
             element_tests[identifier][1]["expected_sort_order"] = idx
 
@@ -668,31 +671,31 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
 
     # Allow either file or value to specify a target file to compare result with
     # file was traditionally used by outputs and value by extra files.
-    file = attrib.pop('file', attrib.pop('value', None))
+    file = attrib.pop("file", attrib.pop("value", None))
 
     # File no longer required if an list of assertions was present.
     attributes = {}
 
-    if 'value_json' in attrib:
-        attributes['object'] = json.loads(attrib.pop('value_json'))
+    if "value_json" in attrib:
+        attributes["object"] = json.loads(attrib.pop("value_json"))
 
     # Method of comparison
-    attributes['compare'] = attrib.pop('compare', 'diff').lower()
+    attributes["compare"] = attrib.pop("compare", "diff").lower()
     # Number of lines to allow to vary in logs (for dates, etc)
-    attributes['lines_diff'] = int(attrib.pop('lines_diff', '0'))
+    attributes["lines_diff"] = int(attrib.pop("lines_diff", "0"))
     # Allow a file size to vary if sim_size compare
-    attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA))
-    attributes['delta_frac'] = float(attrib['delta_frac']) if 'delta_frac' in attrib else DEFAULT_DELTA_FRAC
-    attributes['sort'] = string_as_bool(attrib.pop('sort', False))
-    attributes['decompress'] = string_as_bool(attrib.pop('decompress', False))
+    attributes["delta"] = int(attrib.pop("delta", DEFAULT_DELTA))
+    attributes["delta_frac"] = float(attrib["delta_frac"]) if "delta_frac" in attrib else DEFAULT_DELTA_FRAC
+    attributes["sort"] = string_as_bool(attrib.pop("sort", False))
+    attributes["decompress"] = string_as_bool(attrib.pop("decompress", False))
     extra_files = []
-    if 'ftype' in attrib:
-        attributes['ftype'] = attrib['ftype']
-    for extra in output_elem.findall('extra_files'):
+    if "ftype" in attrib:
+        attributes["ftype"] = attrib["ftype"]
+    for extra in output_elem.findall("extra_files"):
         extra_files.append(__parse_extra_files_elem(extra))
     metadata = {}
-    for metadata_elem in output_elem.findall('metadata'):
-        metadata[metadata_elem.get('name')] = metadata_elem.get('value')
+    for metadata_elem in output_elem.findall("metadata"):
+        metadata[metadata_elem.get("name")] = metadata_elem.get("value")
     md5sum = attrib.get("md5", None)
     checksum = attrib.get("checksum", None)
     element_tests = {}
@@ -701,25 +704,27 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
 
     primary_datasets = {}
     if parse_discovered_datasets:
-        for primary_elem in (output_elem.findall("discovered_dataset") or []):
+        for primary_elem in output_elem.findall("discovered_dataset") or []:
             primary_attrib = dict(primary_elem.attrib)
-            designation = primary_attrib.pop('designation', None)
+            designation = primary_attrib.pop("designation", None)
             if designation is None:
                 raise Exception("Test primary dataset does not have a 'designation'")
             primary_datasets[designation] = __parse_test_attributes(primary_elem, primary_attrib)
 
     has_checksum = md5sum or checksum
     has_nested_tests = extra_files or element_tests or primary_datasets
-    has_object = 'object' in attributes
+    has_object = "object" in attributes
     if not (assert_list or file or metadata or has_checksum or has_nested_tests or has_object):
-        raise Exception("Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)")
-    attributes['assert_list'] = assert_list
-    attributes['extra_files'] = extra_files
-    attributes['metadata'] = metadata
-    attributes['md5'] = md5sum
-    attributes['checksum'] = checksum
-    attributes['elements'] = element_tests
-    attributes['primary_datasets'] = primary_datasets
+        raise Exception(
+            "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)"
+        )
+    attributes["assert_list"] = assert_list
+    attributes["extra_files"] = extra_files
+    attributes["metadata"] = metadata
+    attributes["md5"] = md5sum
+    attributes["checksum"] = checksum
+    attributes["elements"] = element_tests
+    attributes["primary_datasets"] = primary_datasets
     return file, attributes
 
 
@@ -732,13 +737,14 @@ def __parse_assert_list_from_elem(assert_elem):
     assert_list = None
 
     def convert_elem(elem):
-        """ Converts and XML element to a dictionary format, used by assertion checking code. """
+        """Converts and XML element to a dictionary format, used by assertion checking code."""
         tag = elem.tag
         attributes = dict(elem.attrib)
         converted_children = []
         for child_elem in elem:
             converted_children.append(convert_elem(child_elem))
         return {"tag": tag, "attributes": attributes, "children": converted_children}
+
     if assert_elem is not None:
         assert_list = []
         for assert_child in list(assert_elem):
@@ -751,23 +757,19 @@ def __parse_extra_files_elem(extra):
     # File or directory, when directory, compare basename
     # by basename
     attrib = dict(extra.attrib)
-    extra_type = attrib.pop('type', 'file')
-    extra_name = attrib.pop('name', None)
-    assert extra_type == 'directory' or extra_name is not None, \
-        f'extra_files type ({extra_type}) requires a name attribute'
+    extra_type = attrib.pop("type", "file")
+    extra_name = attrib.pop("name", None)
+    assert (
+        extra_type == "directory" or extra_name is not None
+    ), f"extra_files type ({extra_type}) requires a name attribute"
     extra_value, extra_attributes = __parse_test_attributes(extra, attrib)
-    return {
-        "value": extra_value,
-        "name": extra_name,
-        "type": extra_type,
-        "attributes": extra_attributes
-    }
+    return {"value": extra_value, "name": extra_name, "type": extra_type, "attributes": extra_attributes}
 
 
 def __expand_input_elems(root_elem, prefix=""):
     __append_prefix_to_params(root_elem, prefix)
 
-    repeat_elems = root_elem.findall('repeat')
+    repeat_elems = root_elem.findall("repeat")
     indices = {}
     for repeat_elem in repeat_elems:
         name = repeat_elem.get("name")
@@ -782,13 +784,13 @@ def __expand_input_elems(root_elem, prefix=""):
         __expand_input_elems(repeat_elem, new_prefix)
         __pull_up_params(root_elem, repeat_elem)
 
-    cond_elems = root_elem.findall('conditional')
+    cond_elems = root_elem.findall("conditional")
     for cond_elem in cond_elems:
         new_prefix = __prefix_join(prefix, cond_elem.get("name"))
         __expand_input_elems(cond_elem, new_prefix)
         __pull_up_params(root_elem, cond_elem)
 
-    section_elems = root_elem.findall('section')
+    section_elems = root_elem.findall("section")
     for section_elem in section_elems:
         new_prefix = __prefix_join(prefix, section_elem.get("name"))
         __expand_input_elems(section_elem, new_prefix)
@@ -796,12 +798,12 @@ def __expand_input_elems(root_elem, prefix=""):
 
 
 def __append_prefix_to_params(elem, prefix):
-    for param_elem in elem.findall('param'):
+    for param_elem in elem.findall("param"):
         param_elem.set("name", __prefix_join(prefix, param_elem.get("name")))
 
 
 def __pull_up_params(parent_elem, child_elem):
-    for param_elem in child_elem.findall('param'):
+    for param_elem in child_elem.findall("param"):
         parent_elem.append(param_elem)
 
 
@@ -827,12 +829,12 @@ def __parse_inputs_elems(test_elem, i):
 
 def __parse_param_elem(param_elem, i=0):
     attrib = dict(param_elem.attrib)
-    if 'values' in attrib:
-        value = attrib['values'].split(',')
-    elif 'value' in attrib:
-        value = attrib['value']
-    elif 'value_json' in attrib:
-        value = json.loads(attrib['value_json'])
+    if "values" in attrib:
+        value = attrib["values"].split(",")
+    elif "value" in attrib:
+        value = attrib["value"]
+    elif "value_json" in attrib:
+        value = json.loads(attrib["value_json"])
     else:
         value = None
 
@@ -842,41 +844,35 @@ def __parse_param_elem(param_elem, i=0):
         # occurs on DataToolParameter test items but this could
         # change and would cause the below parsing to change
         # based upon differences in children items
-        attrib['metadata'] = {}
-        attrib['composite_data'] = []
-        attrib['edit_attributes'] = []
+        attrib["metadata"] = {}
+        attrib["composite_data"] = []
+        attrib["edit_attributes"] = []
         # Composite datasets need to be renamed uniquely
         composite_data_name = None
         for child in children_elem:
-            if child.tag == 'composite_data':
+            if child.tag == "composite_data":
                 file_name = child.get("value")
-                attrib['composite_data'].append(file_name)
+                attrib["composite_data"].append(file_name)
                 if composite_data_name is None:
                     # Generate a unique name; each test uses a
                     # fresh history.
-                    composite_data_name = '_COMPOSITE_RENAMED_t%d_%s' \
-                        % (i, uuid.uuid1().hex)
-            elif child.tag == 'metadata':
-                attrib['metadata'][child.get("name")] = child.get("value")
-            elif child.tag == 'edit_attributes':
-                attrib['edit_attributes'].append(child)
-            elif child.tag == 'collection':
-                attrib['collection'] = TestCollectionDef.from_xml(child, __parse_param_elem)
+                    composite_data_name = "_COMPOSITE_RENAMED_t%d_%s" % (i, uuid.uuid1().hex)
+            elif child.tag == "metadata":
+                attrib["metadata"][child.get("name")] = child.get("value")
+            elif child.tag == "edit_attributes":
+                attrib["edit_attributes"].append(child)
+            elif child.tag == "collection":
+                attrib["collection"] = TestCollectionDef.from_xml(child, __parse_param_elem)
         if composite_data_name:
             # Composite datasets need implicit renaming;
             # inserted at front of list so explicit declarations
             # take precedence
-            attrib['edit_attributes'].insert(0, {'type': 'name', 'value': composite_data_name})
-    name = attrib.pop('name')
-    return {
-        "name": name,
-        "value": value,
-        "attributes": attrib
-    }
+            attrib["edit_attributes"].insert(0, {"type": "name", "value": composite_data_name})
+    name = attrib.pop("name")
+    return {"name": name, "value": value, "attributes": attrib}
 
 
 class StdioParser:
-
     def __init__(self, root):
         try:
             self.stdio_exit_codes = list()
@@ -886,7 +882,7 @@ class StdioParser:
             # multiples.
             # For every stdio element, add all of the exit_code and regex
             # subelements that we find:
-            for stdio_elem in (root.findall('stdio')):
+            for stdio_elem in root.findall("stdio"):
                 self.parse_stdio_exit_codes(stdio_elem)
                 self.parse_stdio_regexes(stdio_elem)
         except Exception:
@@ -904,7 +900,7 @@ class StdioParser:
             # So if there are value and range attributes, we use the range
             # attribute. If there is neither a range nor a value, then print
             # a warning and skip to the next.
-            for exit_code_elem in (stdio_elem.findall("exit_code")):
+            for exit_code_elem in stdio_elem.findall("exit_code"):
                 exit_code = ToolStdioExitCode()
                 # Each exit code has an optional description that can be
                 # part of the "desc" or "description" attributes:
@@ -912,8 +908,7 @@ class StdioParser:
                 if exit_code.desc is None:
                     exit_code.desc = exit_code_elem.get("description")
                 # Parse the error level:
-                exit_code.error_level = (
-                    self.parse_error_level(exit_code_elem.get("level")))
+                exit_code.error_level = self.parse_error_level(exit_code_elem.get("level"))
                 code_range = exit_code_elem.get("range")
                 if code_range is None:
                     code_range = exit_code_elem.get("value")
@@ -930,17 +925,17 @@ class StdioParser:
                 # more efficient.
                 code_range = re.sub(r"\s", "", code_range)
                 code_ranges = re.split(r":", code_range)
-                if (len(code_ranges) == 2):
-                    if (code_ranges[0] is None or '' == code_ranges[0]):
+                if len(code_ranges) == 2:
+                    if code_ranges[0] is None or "" == code_ranges[0]:
                         exit_code.range_start = -math.inf
                     else:
                         exit_code.range_start = int(code_ranges[0])
-                    if (code_ranges[1] is None or '' == code_ranges[1]):
+                    if code_ranges[1] is None or "" == code_ranges[1]:
                         exit_code.range_end = math.inf
                     else:
                         exit_code.range_end = int(code_ranges[1])
                 # If we got more than one colon, then ignore the exit code.
-                elif (len(code_ranges) > 2):
+                elif len(code_ranges) > 2:
                     log.warning(f"Invalid tool exit_code range {code_range} - ignored")
                     continue
                 # Else we have a singular value. If it's not an integer, then
@@ -974,7 +969,7 @@ class StdioParser:
         try:
             # Look for every <regex> subelement. The regular expression
             # will have "match" and "source" (or "src") attributes.
-            for regex_elem in (stdio_elem.findall("regex")):
+            for regex_elem in stdio_elem.findall("regex"):
                 # TODO: Fill in ToolStdioRegex
                 regex = ToolStdioRegex()
                 # Each regex has an optional description that can be
@@ -983,12 +978,13 @@ class StdioParser:
                 if regex.desc is None:
                     regex.desc = regex_elem.get("description")
                 # Parse the error level
-                regex.error_level = (
-                    self.parse_error_level(regex_elem.get("level")))
+                regex.error_level = self.parse_error_level(regex_elem.get("level"))
                 regex.match = regex_elem.get("match")
                 if regex.match is None:
-                    log.warning(f"Ignoring tool's stdio regex element with attributes {regex_elem.attrib} - "
-                                "the 'match' attribute must exist")
+                    log.warning(
+                        f"Ignoring tool's stdio regex element with attributes {regex_elem.attrib} - "
+                        "the 'match' attribute must exist"
+                    )
                     continue
                 # Parse the output sources. We look for the "src", "source",
                 # and "sources" attributes, in that order. If there is no
@@ -1016,10 +1012,12 @@ class StdioParser:
                         regex.stdout_match = True
                     if re.search("err", src, re.IGNORECASE):
                         regex.stderr_match = True
-                    if (not regex.stdout_match and not regex.stderr_match):
-                        log.warning("Tool id %s: unable to determine if tool "
-                                    "stream source scanning is output, error, "
-                                    "or both. Defaulting to use both." % self.id)
+                    if not regex.stdout_match and not regex.stderr_match:
+                        log.warning(
+                            "Tool id %s: unable to determine if tool "
+                            "stream source scanning is output, error, "
+                            "or both. Defaulting to use both." % self.id
+                        )
                         regex.stdout_match = True
                         regex.stderr_match = True
                 self.stdio_regexes.append(regex)
@@ -1035,32 +1033,30 @@ class StdioParser:
         return_level = StdioErrorLevel.FATAL
         try:
             if err_level:
-                if (re.search("log", err_level, re.IGNORECASE)):
+                if re.search("log", err_level, re.IGNORECASE):
                     return_level = StdioErrorLevel.LOG
-                elif (re.search("qc", err_level, re.IGNORECASE)):
+                elif re.search("qc", err_level, re.IGNORECASE):
                     return_level = StdioErrorLevel.QC
-                elif (re.search("warning", err_level, re.IGNORECASE)):
+                elif re.search("warning", err_level, re.IGNORECASE):
                     return_level = StdioErrorLevel.WARNING
-                elif (re.search("fatal_oom", err_level, re.IGNORECASE)):
+                elif re.search("fatal_oom", err_level, re.IGNORECASE):
                     return_level = StdioErrorLevel.FATAL_OOM
-                elif (re.search("fatal", err_level, re.IGNORECASE)):
+                elif re.search("fatal", err_level, re.IGNORECASE):
                     return_level = StdioErrorLevel.FATAL
                 else:
-                    log.debug("Tool %s: error level %s did not match log/warning/fatal" %
-                              (self.id, err_level))
+                    log.debug("Tool %s: error level %s did not match log/warning/fatal" % (self.id, err_level))
         except Exception:
             log.exception("Exception in parse_error_level")
         return return_level
 
 
 class XmlPagesSource(PagesSource):
-
     def __init__(self, root):
         self.input_elem = root.find("inputs")
         page_sources = []
         if self.input_elem is not None:
             pages_elem = self.input_elem.findall("page")
-            for page in (pages_elem or [self.input_elem]):
+            for page in pages_elem or [self.input_elem]:
                 page_sources.append(XmlPageSource(page))
         super().__init__(page_sources)
 
@@ -1070,7 +1066,6 @@ class XmlPagesSource(PagesSource):
 
 
 class XmlPageSource(PageSource):
-
     def __init__(self, parent_elem):
         self.parent_elem = parent_elem
 
@@ -1087,7 +1082,6 @@ class XmlPageSource(PageSource):
 
 
 class XmlInputSource(InputSource):
-
     def __init__(self, input_elem):
         self.input_elem = input_elem
         self.input_type = self.input_elem.tag
@@ -1117,10 +1111,10 @@ class XmlInputSource(InputSource):
         return self.input_elem.findall("validator")
 
     def parse_dynamic_options_elem(self):
-        """ Return a galaxy.tools.parameters.dynamic_options.DynamicOptions
+        """Return a galaxy.tools.parameters.dynamic_options.DynamicOptions
         if appropriate.
         """
-        options_elem = self.input_elem.find('options')
+        options_elem = self.input_elem.find("options")
         return options_elem
 
     def parse_static_options(self):
@@ -1152,9 +1146,9 @@ class XmlInputSource(InputSource):
         return static_options
 
     def parse_optional(self, default=None):
-        """ Return boolean indicating whether parameter is optional. """
+        """Return boolean indicating whether parameter is optional."""
         elem = self.input_elem
-        if self.get('type') == "data_column":
+        if self.get("type") == "data_column":
             # Allow specifing force_select for backward compat., but probably
             # should use optional going forward for consistency with other
             # parameters.
@@ -1205,13 +1199,13 @@ class ParallelismInfo:
     """
 
     def __init__(self, tag):
-        self.method = tag.get('method')
+        self.method = tag.get("method")
         if isinstance(tag, dict):
             items = tag.items()
         else:
             items = tag.attrib.items()
-        self.attributes = dict([item for item in items if item[0] != 'method'])
+        self.attributes = dict([item for item in items if item[0] != "method"])
         if len(self.attributes) == 0:
             # legacy basic mode - provide compatible defaults
-            self.attributes['split_size'] = 20
-            self.attributes['split_mode'] = 'number_of_parts'
+            self.attributes["split_size"] = 20
+            self.attributes["split_mode"] = "number_of_parts"
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index b4ffa20473f..0e0a921261a 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -5,7 +5,7 @@ import packaging.version
 from galaxy.tool_util.deps import requirements
 from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA,
-    DEFAULT_DELTA_FRAC
+    DEFAULT_DELTA_FRAC,
 )
 from .interface import (
     InputSource,
@@ -25,7 +25,7 @@ from .util import is_dict
 
 class YamlToolSource(ToolSource):
 
-    language = 'yaml'
+    language = "yaml"
 
     def __init__(self, root_dict, source_path=None):
         self.root_dict = root_dict
@@ -65,10 +65,10 @@ class YamlToolSource(ToolSource):
         return self.root_dict.get("sanitize", True)
 
     def parse_display_interface(self, default):
-        return self.root_dict.get('display_interface', default)
+        return self.root_dict.get("display_interface", default)
 
     def parse_require_login(self, default):
-        return self.root_dict.get('require_login', default)
+        return self.root_dict.get("require_login", default)
 
     def parse_command(self):
         return self.root_dict.get("command")
@@ -170,9 +170,7 @@ class YamlToolSource(ToolSource):
 
     def parse_tests_to_dict(self):
         tests = []
-        rval = dict(
-            tests=tests
-        )
+        rval = dict(tests=tests)
 
         for i, test_dict in enumerate(self.root_dict.get("tests", [])):
             tests.append(_parse_test(i, test_dict))
@@ -218,11 +216,7 @@ def _parse_test(i, test_dict):
             else:
                 file = value
                 attributes = {}
-            new_outputs.append({
-                "name": key,
-                "value": file,
-                "attributes": attributes
-            })
+            new_outputs.append({"name": key, "value": file, "attributes": attributes})
     else:
         for output in outputs:
             name = output["name"]
@@ -233,11 +227,11 @@ def _parse_test(i, test_dict):
     for output in new_outputs:
         attributes = output["attributes"]
         defaults = {
-            'compare': 'diff',
-            'lines_diff': 0,
-            'delta': DEFAULT_DELTA,
-            'delta_frac': DEFAULT_DELTA_FRAC,
-            'sort': False,
+            "compare": "diff",
+            "lines_diff": 0,
+            "delta": DEFAULT_DELTA,
+            "delta_frac": DEFAULT_DELTA_FRAC,
+            "sort": False,
         }
         # TODO
         attributes["extra_files"] = []
@@ -290,7 +284,6 @@ def __to_test_assert_list(assertions):
 
 
 class YamlPageSource(PageSource):
-
     def __init__(self, inputs_list):
         self.inputs_list = inputs_list
 
@@ -299,7 +292,6 @@ class YamlPageSource(PageSource):
 
 
 class YamlInputSource(InputSource):
-
     def __init__(self, input_dict):
         self.input_dict = input_dict
 
diff --git a/lib/galaxy/tool_util/provided_metadata.py b/lib/galaxy/tool_util/provided_metadata.py
index e279b95c959..da899630b1a 100644
--- a/lib/galaxy/tool_util/provided_metadata.py
+++ b/lib/galaxy/tool_util/provided_metadata.py
@@ -40,7 +40,6 @@ def _guess_tool_provided_metadata_style(path):
 
 
 class BaseToolProvidedMetadata:
-
     def get_new_datasets(self, output_name):
         """Find new datasets for dataset discovery for specified output.
 
@@ -76,8 +75,7 @@ class BaseToolProvidedMetadata:
         return []
 
     def get_dataset_meta(self, output_name, dataset_id, dataset_uuid):
-        """Return primary dataset metadata for specified output.
-        """
+        """Return primary dataset metadata for specified output."""
         return {}
 
     def rewrite(self):
@@ -89,8 +87,7 @@ class BaseToolProvidedMetadata:
         return None
 
     def get_new_datasets_for_metadata_collection(self):
-        """Return all datasets tracked that are not explicit primary outputs.
-        """
+        """Return all datasets tracked that are not explicit primary outputs."""
         return []
 
 
@@ -99,7 +96,6 @@ class NullToolProvidedMetadata(BaseToolProvidedMetadata):
 
 
 class LegacyToolProvidedMetadata(BaseToolProvidedMetadata):
-
     def __init__(self, meta_file, job_wrapper=None):
         self.meta_file = meta_file
         self.tool_provided_job_metadata = []
@@ -108,46 +104,50 @@ class LegacyToolProvidedMetadata(BaseToolProvidedMetadata):
             for line in f:
                 try:
                     line = stringify_dictionary_keys(json.loads(line))
-                    assert 'type' in line
+                    assert "type" in line
                 except Exception as e:
-                    message = f"Got JSON data from tool, but line is improperly formatted or no \"type\" key in: [{line}]"
+                    message = f'Got JSON data from tool, but line is improperly formatted or no "type" key in: [{line}]'
                     raise ValueError(message) from e
                 # Set the dataset id if it's a dataset entry and isn't set.
                 # This isn't insecure.  We loop the job's output datasets in
                 # the finish method, so if a tool writes out metadata for a
                 # dataset id that it doesn't own, it'll just be ignored.
-                dataset_id_not_specified = line['type'] == 'dataset' and 'dataset_id' not in line
+                dataset_id_not_specified = line["type"] == "dataset" and "dataset_id" not in line
                 if dataset_id_not_specified:
-                    dataset_basename = line['dataset']
+                    dataset_basename = line["dataset"]
                     if job_wrapper:
                         try:
-                            line['dataset_id'] = job_wrapper.job_io.get_output_file_id(dataset_basename)
+                            line["dataset_id"] = job_wrapper.job_io.get_output_file_id(dataset_basename)
                         except KeyError:
-                            log.warning(f'({job_wrapper.job_id}) Tool provided job dataset-specific metadata without specifying a dataset')
+                            log.warning(
+                                f"({job_wrapper.job_id}) Tool provided job dataset-specific metadata without specifying a dataset"
+                            )
                             continue
                     else:
-                        match = re.match(r'(galaxy_)?dataset_(.*)\.dat', dataset_basename)
+                        match = re.match(r"(galaxy_)?dataset_(.*)\.dat", dataset_basename)
                         if match is None:
-                            raise Exception(f"processing tool_provided_metadata (e.g. galaxy.json) entry with invalid dataset name [{dataset_basename}]")
+                            raise Exception(
+                                f"processing tool_provided_metadata (e.g. galaxy.json) entry with invalid dataset name [{dataset_basename}]"
+                            )
                         dataset_id = match.group(2)
                         if dataset_id.isdigit():
-                            line['dataset_id'] = dataset_id
+                            line["dataset_id"] = dataset_id
                         else:
-                            line['dataset_uuid'] = dataset_id
+                            line["dataset_uuid"] = dataset_id
 
                 self.tool_provided_job_metadata.append(line)
 
     def get_dataset_meta(self, output_name, dataset_id, dataset_uuid):
         for meta in self.tool_provided_job_metadata:
-            if meta['type'] == 'dataset' and 'dataset_id' in meta and int(meta['dataset_id']) == dataset_id:
+            if meta["type"] == "dataset" and "dataset_id" in meta and int(meta["dataset_id"]) == dataset_id:
                 return meta
-            if meta['type'] == 'dataset' and 'dataset_uuid' in meta and meta['dataset_uuid'] == dataset_uuid:
+            if meta["type"] == "dataset" and "dataset_uuid" in meta and meta["dataset_uuid"] == dataset_uuid:
                 return meta
         return {}
 
     def get_new_dataset_meta_by_basename(self, output_name, basename):
         for meta in self.tool_provided_job_metadata:
-            if meta['type'] == 'new_primary_dataset' and meta['filename'] == basename:
+            if meta["type"] == "new_primary_dataset" and meta["filename"] == basename:
                 return meta
 
     def get_new_datasets(self, output_name):
@@ -167,18 +167,17 @@ class LegacyToolProvidedMetadata(BaseToolProvidedMetadata):
         return []
 
     def rewrite(self):
-        with open(self.meta_file, 'wt') as job_metadata_fh:
+        with open(self.meta_file, "wt") as job_metadata_fh:
             for meta in self.tool_provided_job_metadata:
                 job_metadata_fh.write(f"{json.dumps(meta)}\n")
 
     def get_new_datasets_for_metadata_collection(self):
         for meta in self.tool_provided_job_metadata:
-            if meta['type'] == 'new_primary_dataset':
+            if meta["type"] == "new_primary_dataset":
                 yield meta
 
 
 class ToolProvidedMetadata(BaseToolProvidedMetadata):
-
     def __init__(self, meta_file):
         self.meta_file = meta_file
         with open(meta_file) as f:
@@ -190,7 +189,7 @@ class ToolProvidedMetadata(BaseToolProvidedMetadata):
     def get_new_dataset_meta_by_basename(self, output_name, basename):
         datasets = self.tool_provided_job_metadata.get(output_name, {}).get("datasets", [])
         for meta in datasets:
-            if meta['filename'] == basename:
+            if meta["filename"] == basename:
                 return meta
 
     def get_new_datasets(self, output_name):
@@ -231,5 +230,5 @@ class ToolProvidedMetadata(BaseToolProvidedMetadata):
         return self.tool_provided_job_metadata.get("__unnamed_outputs", [])
 
     def rewrite(self):
-        with open(self.meta_file, 'wt') as job_metadata_fh:
+        with open(self.meta_file, "wt") as job_metadata_fh:
             json.dump(self.tool_provided_job_metadata, job_metadata_fh)
diff --git a/lib/galaxy/tool_util/toolbox/__init__.py b/lib/galaxy/tool_util/toolbox/__init__.py
index b4774ed8709..18b233672fb 100644
--- a/lib/galaxy/tool_util/toolbox/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/__init__.py
@@ -1,7 +1,14 @@
 """API for this module containing functionality related to the toolbox."""
 
-from .base import AbstractToolBox, BaseGalaxyToolBox
-from .panel import panel_item_types, ToolSection, ToolSectionLabel
+from .base import (
+    AbstractToolBox,
+    BaseGalaxyToolBox,
+)
+from .panel import (
+    panel_item_types,
+    ToolSection,
+    ToolSectionLabel,
+)
 
 __all__ = (
     "AbstractToolBox",
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 734971aea46..775c31210ee 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -5,7 +5,10 @@ import string
 import time
 from collections import namedtuple
 from errno import ENOENT
-from typing import Dict, List
+from typing import (
+    Dict,
+    List,
+)
 from urllib.parse import urlparse
 
 from markupsafe import escape
@@ -18,7 +21,7 @@ from galaxy.exceptions import (
 )
 from galaxy.tool_util.deps import (
     build_dependency_manager,
-    NullDependencyManager
+    NullDependencyManager,
 )
 from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.util import (
@@ -38,14 +41,17 @@ from .panel import (
     panel_item_types,
     ToolPanelElements,
     ToolSection,
-    ToolSectionLabel
+    ToolSectionLabel,
 )
 from .parser import (
     ensure_tool_conf_item,
-    get_toolbox_parser
+    get_toolbox_parser,
 )
 from .tags import tool_tag_manager
-from .views.edam import EdamPanelMode, EdamToolPanelView
+from .views.edam import (
+    EdamPanelMode,
+    EdamToolPanelView,
+)
 from .views.interface import (
     ToolBoxRegistry,
     ToolPanelView,
@@ -63,16 +69,21 @@ SHED_TOOL_CONF_XML = """<?xml version="1.0"?>
 
 # A fake ToolShedRepository constructed from a shed tool conf
 _ToolConfRepository = namedtuple(
-    '_ToolConfRepository',
+    "_ToolConfRepository",
     (
-        'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision',
-        'tool_dependencies_installed_or_in_error', 'repository_path', 'tool_path',
-    )
+        "tool_shed",
+        "name",
+        "owner",
+        "installed_changeset_revision",
+        "changeset_revision",
+        "tool_dependencies_installed_or_in_error",
+        "repository_path",
+        "tool_path",
+    ),
 )
 
 
 class ToolConfRepository(_ToolConfRepository):
-
     def get_tool_relative_path(self, *args, **kwargs):
         # This is a somewhat public function, used by data_manager_manual for instance
         return self.tool_path, self.repository_path
@@ -81,7 +92,7 @@ class ToolConfRepository(_ToolConfRepository):
 class ToolBoxRegistryImpl(ToolBoxRegistry):
     """View of ToolBox provided to ToolPanelView to reason about tools loaded."""
 
-    def __init__(self, toolbox: 'AbstractToolBox'):
+    def __init__(self, toolbox: "AbstractToolBox"):
         self.__toolbox = toolbox
 
     def has_tool(self, tool_id: str) -> bool:
@@ -103,7 +114,15 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
     workflows optionally in labelled sections.
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app, view_sources=None, default_panel_view="default", save_integrated_tool_panel=True):
+    def __init__(
+        self,
+        config_filenames,
+        tool_root_dir,
+        app,
+        view_sources=None,
+        default_panel_view="default",
+        save_integrated_tool_panel=True,
+    ):
         """
         Create a toolbox from the config files named by `config_filenames`, using
         `tool_root_dir` as the base directory for finding individual tool config files.
@@ -140,20 +159,23 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         self._tool_tag_manager = tool_tag_manager(app)
         self._init_tools_from_configs(config_filenames)
 
-        if self.app.name == 'galaxy' and self._integrated_tool_panel_config_has_contents:
+        if self.app.name == "galaxy" and self._integrated_tool_panel_config_has_contents:
             self._load_tool_panel()
 
         toolbox = self
 
         class DefaultToolPanelView(ToolPanelView):
-
-            def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
+            def apply_view(
+                self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry
+            ) -> ToolPanelElements:
                 return toolbox._tool_panel
 
             def to_model(self) -> ToolPanelViewModel:
                 model_id = "default"
                 name = "Full Tool Panel"
-                description = "Galaxy's fully configured toolbox panel with all sections, tools, and configured workflows loaded."
+                description = (
+                    "Galaxy's fully configured toolbox panel with all sections, tools, and configured workflows loaded."
+                )
                 view_type = ToolPanelViewModelType.default_type
                 model_class = DefaultToolPanelView.__class__.__name__
                 return ToolPanelViewModel(
@@ -181,7 +203,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         for tool_panel_view in tool_panel_views_list:
             self._tool_panel_views[tool_panel_view.to_model().id] = tool_panel_view
 
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             self._load_tool_panel_views()
         if save_integrated_tool_panel:
             self._save_integrated_tool_panel()
@@ -196,7 +218,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return True
 
     def _init_tools_from_configs(self, config_filenames):
-        """ Read through all tool config files and initialize tools in each
+        """Read through all tool config files and initialize tools in each
         with init_tools_from_config below.
         """
         execution_timer = ExecutionTimer()
@@ -205,7 +227,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         for config_filename in config_filenames:
             if os.path.isdir(config_filename):
                 directory_contents = sorted(os.listdir(config_filename))
-                directory_config_files = [config_file for config_file in directory_contents if config_file.endswith(".xml")]
+                directory_config_files = [
+                    config_file for config_file in directory_contents if config_file.endswith(".xml")
+                ]
                 config_filenames.remove(config_filename)
                 config_filenames.extend(directory_config_files)
         for config_filename in config_filenames:
@@ -251,12 +275,16 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         except OSError as exc:
             dynamic_confs = (self.app.config.shed_tool_config_file, self.app.config.migrated_tools_config)
             if config_filename in dynamic_confs and exc.errno == errno.ENOENT:
-                log.info("Shed-enabled tool configuration file does not exist, but will be created on demand: %s",
-                         config_filename)
-                stcd = dict(config_filename=config_filename,
-                            tool_path=self.app.config.shed_tools_dir,
-                            config_elems=[],
-                            create=SHED_TOOL_CONF_XML.format(shed_tools_dir=self.app.config.shed_tools_dir))
+                log.info(
+                    "Shed-enabled tool configuration file does not exist, but will be created on demand: %s",
+                    config_filename,
+                )
+                stcd = dict(
+                    config_filename=config_filename,
+                    tool_path=self.app.config.shed_tools_dir,
+                    config_elems=[],
+                    create=SHED_TOOL_CONF_XML.format(shed_tools_dir=self.app.config.shed_tools_dir),
+                )
                 self._dynamic_tool_confs.append(stcd)
                 return
             raise
@@ -266,7 +294,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if parsing_shed_tool_conf:
             # Keep an in-memory list of xml elements to enable persistence of the changing tool config.
             config_elems = []
-        tool_conf_type = 'shed tool' if parsing_shed_tool_conf else 'tool'
+        tool_conf_type = "shed tool" if parsing_shed_tool_conf else "tool"
         log.debug("Tool path for %s configuration %s is %s", tool_conf_type, config_filename, tool_path)
         tool_path = self.__resolve_tool_path(tool_path, config_filename)
         # Only load the panel_dict under certain conditions.
@@ -281,17 +309,19 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 tool_path=tool_path,
                 tool_cache_data_dir=tool_cache_data_dir,
                 load_panel_dict=load_panel_dict,
-                guid=item.get('guid'),
+                guid=item.get("guid"),
                 index=index,
             )
 
         if parsing_shed_tool_conf:
             # if read_only mode, (CVMFS consumer) don't add to dynamic_confs
             if os.access(config_filename, os.W_OK):
-                shed_tool_conf_dict = dict(config_filename=config_filename,
-                                           tool_path=tool_path,
-                                           tool_cache_data_dir=tool_cache_data_dir,
-                                           config_elems=config_elems)
+                shed_tool_conf_dict = dict(
+                    config_filename=config_filename,
+                    tool_path=tool_path,
+                    tool_cache_data_dir=tool_cache_data_dir,
+                    config_elems=config_elems,
+                )
                 self._dynamic_tool_confs.append(shed_tool_conf_dict)
 
     def _get_tool_by_uuid(self, tool_uuid):
@@ -323,7 +353,17 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         self._tools_by_uuid[dynamic_tool.uuid] = tool
         return tool
 
-    def load_item(self, item, tool_path, panel_dict=None, integrated_panel_dict=None, load_panel_dict=True, guid=None, index=None, tool_cache_data_dir=None):
+    def load_item(
+        self,
+        item,
+        tool_path,
+        panel_dict=None,
+        integrated_panel_dict=None,
+        load_panel_dict=True,
+        guid=None,
+        index=None,
+        tool_cache_data_dir=None,
+    ):
         with self.app._toolbox_lock:
             item = ensure_tool_conf_item(item)
             item_type = item.type
@@ -331,22 +371,56 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 panel_dict = self._tool_panel
             if integrated_panel_dict is None:
                 integrated_panel_dict = self._integrated_tool_panel
-            if item_type == 'tool':
-                self._load_tool_tag_set(item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, tool_path=tool_path, load_panel_dict=load_panel_dict, guid=guid, index=index, tool_cache_data_dir=tool_cache_data_dir)
-            elif item_type == 'workflow':
-                self._load_workflow_tag_set(item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, load_panel_dict=load_panel_dict, index=index)
-            elif item_type == 'section':
-                self._load_section_tag_set(item, tool_path=tool_path, load_panel_dict=load_panel_dict, index=index, tool_cache_data_dir=tool_cache_data_dir)
-            elif item_type == 'label':
-                self._load_label_tag_set(item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, load_panel_dict=load_panel_dict, index=index)
-            elif item_type == 'tool_dir':
-                self._load_tooldir_tag_set(item, panel_dict, tool_path, integrated_panel_dict, load_panel_dict=load_panel_dict, tool_cache_data_dir=tool_cache_data_dir)
+            if item_type == "tool":
+                self._load_tool_tag_set(
+                    item,
+                    panel_dict=panel_dict,
+                    integrated_panel_dict=integrated_panel_dict,
+                    tool_path=tool_path,
+                    load_panel_dict=load_panel_dict,
+                    guid=guid,
+                    index=index,
+                    tool_cache_data_dir=tool_cache_data_dir,
+                )
+            elif item_type == "workflow":
+                self._load_workflow_tag_set(
+                    item,
+                    panel_dict=panel_dict,
+                    integrated_panel_dict=integrated_panel_dict,
+                    load_panel_dict=load_panel_dict,
+                    index=index,
+                )
+            elif item_type == "section":
+                self._load_section_tag_set(
+                    item,
+                    tool_path=tool_path,
+                    load_panel_dict=load_panel_dict,
+                    index=index,
+                    tool_cache_data_dir=tool_cache_data_dir,
+                )
+            elif item_type == "label":
+                self._load_label_tag_set(
+                    item,
+                    panel_dict=panel_dict,
+                    integrated_panel_dict=integrated_panel_dict,
+                    load_panel_dict=load_panel_dict,
+                    index=index,
+                )
+            elif item_type == "tool_dir":
+                self._load_tooldir_tag_set(
+                    item,
+                    panel_dict,
+                    tool_path,
+                    integrated_panel_dict,
+                    load_panel_dict=load_panel_dict,
+                    tool_cache_data_dir=tool_cache_data_dir,
+                )
 
     def get_shed_config_dict_by_filename(self, filename):
         filename = os.path.abspath(filename)
         dynamic_tool_conf_paths = []
         for shed_config_dict in self._dynamic_tool_confs:
-            dynamic_tool_conf_path = os.path.abspath(shed_config_dict['config_filename'])
+            dynamic_tool_conf_path = os.path.abspath(shed_config_dict["config_filename"])
             dynamic_tool_conf_paths.append(dynamic_tool_conf_path)
             if dynamic_tool_conf_path == filename:
                 return shed_config_dict
@@ -354,12 +428,12 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return None
 
     def update_shed_config(self, shed_conf):
-        """  Update the in-memory descriptions of tools and write out the changes
-             to integrated tool panel unless we are just deactivating a tool (since
-             that doesn't affect that file).
+        """Update the in-memory descriptions of tools and write out the changes
+        to integrated tool panel unless we are just deactivating a tool (since
+        that doesn't affect that file).
         """
         for index, my_shed_tool_conf in enumerate(self._dynamic_tool_confs):
-            if shed_conf['config_filename'] == my_shed_tool_conf['config_filename']:
+            if shed_conf["config_filename"] == my_shed_tool_conf["config_filename"]:
                 self._dynamic_tool_confs[index] = shed_conf
         self._save_integrated_tool_panel()
 
@@ -378,9 +452,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 # This might add an ugly section label to the tool panel, but, oh well...
                 new_label = section_id
             section_dict = {
-                'name': new_label,
-                'id': section_id,
-                'version': '',
+                "name": new_label,
+                "id": section_id,
+                "version": "",
             }
             self.create_section(section_dict)
             tool_section = self._tool_panel[tool_panel_section_key]
@@ -479,7 +553,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                             # If the tool is not defined in integrated_tool_panel.xml, append it to the tool panel.
                             panel_dict.append_tool(tool)
                             log_msg = f"Loaded tool id: {tool.id}, version: {tool.version} into tool panel...."
-        if log_msg and (not hasattr(self.app, 'tool_cache') or tool_id in self.app.tool_cache._new_tool_ids):
+        if log_msg and (not hasattr(self.app, "tool_cache") or tool_id in self.app.tool_cache._new_tool_ids):
             log.debug(log_msg)
 
     def _load_tool_panel_views(self):
@@ -492,12 +566,12 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         execution_timer = ExecutionTimer()
         for key, item_type, val in self._integrated_tool_panel.panel_items_iter():
             if item_type == panel_item_types.TOOL:
-                tool_id = key.replace('tool_', '', 1)
+                tool_id = key.replace("tool_", "", 1)
                 if tool_id in self._tools_by_id:
                     self.__add_tool_to_tool_panel(val, self._tool_panel, section=False)
-                    self._tool_panel.record_section_for_tool_id(tool_id, '', '')
+                    self._tool_panel.record_section_for_tool_id(tool_id, "", "")
             elif item_type == panel_item_types.WORKFLOW:
-                workflow_id = key.replace('workflow_', '', 1)
+                workflow_id = key.replace("workflow_", "", 1)
                 if workflow_id in self._workflows_by_id:
                     workflow = self._workflows_by_id[workflow_id]
                     self._tool_panel[key] = workflow
@@ -506,20 +580,20 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 self._tool_panel[key] = val
             elif item_type == panel_item_types.SECTION:
                 section_dict = {
-                    'id': val.id or '',
-                    'name': val.name or '',
-                    'version': val.version or '',
+                    "id": val.id or "",
+                    "name": val.name or "",
+                    "version": val.version or "",
                 }
                 section = ToolSection(section_dict)
                 log.debug(f"Loading section: {section_dict.get('name')}")
                 for section_key, section_item_type, section_val in val.panel_items_iter():
                     if section_item_type == panel_item_types.TOOL:
-                        tool_id = section_key.replace('tool_', '', 1)
+                        tool_id = section_key.replace("tool_", "", 1)
                         if tool_id in self._tools_by_id:
                             self.__add_tool_to_tool_panel(section_val, section, section=True)
                             self._tool_panel.record_section_for_tool_id(tool_id, key, val.name)
                     elif section_item_type == panel_item_types.WORKFLOW:
-                        workflow_id = section_key.replace('workflow_', '', 1)
+                        workflow_id = section_key.replace("workflow_", "", 1)
                         if workflow_id in self._workflows_by_id:
                             workflow = self._workflows_by_id[workflow_id]
                             section.elems[section_key] = workflow
@@ -541,23 +615,23 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         tree = parse_xml(self._integrated_tool_panel_config)
         root = tree.getroot()
         for elem in root:
-            key = elem.get('id')
-            if elem.tag == 'tool':
+            key = elem.get("id")
+            if elem.tag == "tool":
                 self._integrated_tool_panel.stub_tool(key)
-            elif elem.tag == 'workflow':
+            elif elem.tag == "workflow":
                 self._integrated_tool_panel.stub_workflow(key)
-            elif elem.tag == 'section':
+            elif elem.tag == "section":
                 section = ToolSection(elem)
                 for section_elem in elem:
-                    section_id = section_elem.get('id')
-                    if section_elem.tag == 'tool':
+                    section_id = section_elem.get("id")
+                    if section_elem.tag == "tool":
                         section.elems.stub_tool(section_id)
-                    elif section_elem.tag == 'workflow':
+                    elif section_elem.tag == "workflow":
                         section.elems.stub_workflow(section_id)
-                    elif section_elem.tag == 'label':
+                    elif section_elem.tag == "label":
                         section.elems.stub_label(section_id)
                 self._integrated_tool_panel.append_section(key, section)
-            elif elem.tag == 'label':
+            elif elem.tag == "label":
                 self._integrated_tool_panel.stub_label(key)
 
     def get_tool(self, tool_id, tool_version=None, get_all_versions=False, exact=False, tool_uuid=None):
@@ -580,7 +654,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if "/repos/" in tool_id:  # test if tool came from a toolshed
             tool_id_without_tool_shed = tool_id.split("/repos/")[1]
             available_tool_sheds = [urlparse(_) for _ in self.app.tool_shed_registry.tool_sheds.values()]
-            available_tool_sheds = [url.geturl().replace(f"{url.scheme}://", '', 1) for url in available_tool_sheds]
+            available_tool_sheds = [url.geturl().replace(f"{url.scheme}://", "", 1) for url in available_tool_sheds]
             tool_ids = [f"{tool_shed}repos/{tool_id_without_tool_shed}" for tool_shed in available_tool_sheds]
             if tool_id in tool_ids:  # move original tool_id to the top of tool_ids
                 tool_ids.remove(tool_id)
@@ -649,7 +723,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if tool_id is None:
             # This is not a tool ID.
             return False
-        if 'repos' not in tool_id:
+        if "repos" not in tool_id:
             # This is not a shed tool.
             return False
         # This is a valid tool, and it is from a toolshed. Check if it's
@@ -681,7 +755,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
     def dynamic_confs(self, include_migrated_tool_conf=False):
         confs = []
         for dynamic_tool_conf_dict in self._dynamic_tool_confs:
-            dynamic_tool_conf_filename = dynamic_tool_conf_dict['config_filename']
+            dynamic_tool_conf_filename = dynamic_tool_conf_dict["config_filename"]
             if include_migrated_tool_conf or (dynamic_tool_conf_filename != self.app.config.migrated_tools_config):
                 confs.append(dynamic_tool_conf_dict)
         return confs
@@ -697,22 +771,32 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if self.app.config.shed_tool_config_file in self.app.config.tool_configs:
             # Use shed_tool_config_file if loaded
             for shed_config_dict in dynamic_confs:
-                if shed_config_dict.get('config_filename') == self.app.config.shed_tool_config_file:
+                if shed_config_dict.get("config_filename") == self.app.config.shed_tool_config_file:
                     break
         return shed_config_dict
 
     def dynamic_conf_filenames(self):
-        """ Return list of dynamic tool configuration filenames (shed_tools).
+        """Return list of dynamic tool configuration filenames (shed_tools).
         These must be used with various dynamic tool configuration update
         operations (e.g. with update_shed_config).
         """
         for dynamic_tool_conf_dict in self.dynamic_confs():
-            yield dynamic_tool_conf_dict['config_filename']
+            yield dynamic_tool_conf_dict["config_filename"]
 
     def _path_template_kwds(self):
         return {}
 
-    def _load_tool_tag_set(self, item, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None, tool_cache_data_dir=None):
+    def _load_tool_tag_set(
+        self,
+        item,
+        panel_dict,
+        integrated_panel_dict,
+        tool_path,
+        load_panel_dict,
+        guid=None,
+        index=None,
+        tool_cache_data_dir=None,
+    ):
         try:
             path_template = item.get("file")
             template_kwds = self._path_template_kwds()
@@ -734,16 +818,22 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if guid and not from_cache:  # tool was not in cache and is a tool shed tool
                 tool_shed_repository = self.get_tool_repository_from_xml_item(item.elem, concrete_path)
                 if tool_shed_repository:
-                    if hasattr(tool_shed_repository, 'deleted'):
+                    if hasattr(tool_shed_repository, "deleted"):
                         # The shed tool is in the install database
                         # Only load tools if the repository is not deactivated or uninstalled.
                         can_load_into_panel_dict = not tool_shed_repository.deleted
-                    tool = self.load_tool(concrete_path, guid=guid, tool_shed_repository=tool_shed_repository, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
+                    tool = self.load_tool(
+                        concrete_path,
+                        guid=guid,
+                        tool_shed_repository=tool_shed_repository,
+                        use_cached=False,
+                        tool_cache_data_dir=tool_cache_data_dir,
+                    )
             if not tool:  # tool was not in cache and is not a tool shed tool.
                 tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
-            if string_as_bool(item.get('hidden', False)):
+            if string_as_bool(item.get("hidden", False)):
                 tool.hidden = True
-            key = f'tool_{str(tool.id)}'
+            key = f"tool_{str(tool.id)}"
             if can_load_into_panel_dict:
                 if guid and not from_cache:
                     tool.tool_shed = tool_shed_repository.tool_shed
@@ -777,26 +867,34 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         repository_owner = elem.find("repository_owner").text
         # The definition of `installed_changeset_revision` for a repository is that it has been cloned at <tool_path/toolshed/repos/owner/name/installed_changeset_revision>
         # so if we load a tool it needs to be at a path that contains `installed_changeset_revision`.
-        path_to_installed_changeset_revision = os.path.join(tool_shed, 'repos', repository_owner, repository_name)
+        path_to_installed_changeset_revision = os.path.join(tool_shed, "repos", repository_owner, repository_name)
         if path_to_installed_changeset_revision in path:
-            installed_changeset_revision = path[path.index(path_to_installed_changeset_revision) + len(path_to_installed_changeset_revision):].split(os.path.sep)[1]
+            installed_changeset_revision = path[
+                path.index(path_to_installed_changeset_revision) + len(path_to_installed_changeset_revision) :
+            ].split(os.path.sep)[1]
         else:
             installed_changeset_revision_elem = elem.find("installed_changeset_revision")
             if installed_changeset_revision_elem is None:
                 # Backward compatibility issue - the tag used to be named 'changeset_revision'.
                 installed_changeset_revision_elem = elem.find("changeset_revision")
             installed_changeset_revision = installed_changeset_revision_elem.text
-        repository = self._get_tool_shed_repository(tool_shed=tool_shed,
-                                                    name=repository_name,
-                                                    owner=repository_owner,
-                                                    installed_changeset_revision=installed_changeset_revision)
+        repository = self._get_tool_shed_repository(
+            tool_shed=tool_shed,
+            name=repository_name,
+            owner=repository_owner,
+            installed_changeset_revision=installed_changeset_revision,
+        )
         if not repository:
-            msg = "Attempted to load tool shed tool, but the repository with name '%s' from owner '%s' was not found " \
-                  "in database. Tool will be loaded without install database."
+            msg = (
+                "Attempted to load tool shed tool, but the repository with name '%s' from owner '%s' was not found "
+                "in database. Tool will be loaded without install database."
+            )
             log.warning(msg, repository_name, repository_owner)
             # Figure out path to repository on disk given the tool shed info and the path to the tool contained in the repo
-            repository_path = os.path.join(tool_shed, 'repos', repository_owner, repository_name, installed_changeset_revision)
-            tool_path = path[:path.index(repository_path)]
+            repository_path = os.path.join(
+                tool_shed, "repos", repository_owner, repository_name, installed_changeset_revision
+            )
+            tool_path = path[: path.index(repository_path)]
             repository = ToolConfRepository(
                 tool_shed,
                 repository_name,
@@ -805,7 +903,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 installed_changeset_revision,
                 None,
                 repository_path,
-                tool_path
+                tool_path,
             )
             tsr_cache = self.app.tool_shed_repository_cache
             if tsr_cache:
@@ -834,7 +932,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
     def _load_workflow_tag_set(self, item, panel_dict, integrated_panel_dict, load_panel_dict, index=None):
         try:
             # TODO: should id be encoded?
-            workflow_id = item.get('id')
+            workflow_id = item.get("id")
             workflow = self._load_workflow(workflow_id)
             self._workflows_by_id[workflow_id] = workflow
             key = f"workflow_{workflow_id}"
@@ -873,7 +971,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 panel_dict=elems,
                 integrated_panel_dict=integrated_elems,
                 load_panel_dict=load_panel_dict,
-                guid=sub_item.get('guid'),
+                guid=sub_item.get("guid"),
                 index=sub_index,
                 tool_cache_data_dir=tool_cache_data_dir,
             )
@@ -882,7 +980,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         for section_key, section_item_type, section_item in integrated_elems.panel_items_iter():
             if section_item_type == panel_item_types.TOOL:
                 if section_item:
-                    tool_id = section_key.replace('tool_', '', 1)
+                    tool_id = section_key.replace("tool_", "", 1)
                     self._tool_panel.record_section_for_tool_id(tool_id, integrated_section.id, integrated_section.name)
 
         if load_panel_dict:
@@ -890,19 +988,37 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         # Always load sections into the integrated_tool_panel.
         self._integrated_tool_panel.update_or_append(index, key, integrated_section)
 
-    def _load_tooldir_tag_set(self, item, elems, tool_path, integrated_elems, load_panel_dict, tool_cache_data_dir=None):
+    def _load_tooldir_tag_set(
+        self, item, elems, tool_path, integrated_elems, load_panel_dict, tool_cache_data_dir=None
+    ):
         directory = os.path.join(tool_path, item.get("dir"))
         recursive = string_as_bool(item.get("recursive", True))
-        self.__watch_directory(directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=True, tool_cache_data_dir=tool_cache_data_dir)
-
-    def __watch_directory(self, directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=False, tool_cache_data_dir=None):
+        self.__watch_directory(
+            directory,
+            elems,
+            integrated_elems,
+            load_panel_dict,
+            recursive,
+            force_watch=True,
+            tool_cache_data_dir=tool_cache_data_dir,
+        )
 
+    def __watch_directory(
+        self,
+        directory,
+        elems,
+        integrated_elems,
+        load_panel_dict,
+        recursive,
+        force_watch=False,
+        tool_cache_data_dir=None,
+    ):
         def quick_load(tool_file, async_load=True):
             try:
                 tool = self.load_tool(tool_file, tool_cache_data_dir)
                 self.__add_tool(tool, load_panel_dict, elems)
                 # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file.
-                key = f'tool_{str(tool.id)}'
+                key = f"tool_{str(tool.id)}"
                 integrated_elems[key] = tool
 
                 if async_load:
@@ -919,7 +1035,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             log.error("Failed to read tool directory %s.", directory)
             return
         for name in os.listdir(directory):
-            if name.startswith(('.', '_')):
+            if name.startswith((".", "_")):
                 # Very unlikely that we want to load tools from a hidden or private folder
                 continue
             child_path = os.path.join(directory, name)
@@ -931,7 +1047,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if (tool_loaded or force_watch) and self._tool_watcher:
             self._tool_watcher.watch_directory(directory, quick_load)
 
-    def load_tool(self, config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds):
+    def load_tool(
+        self, config_file, guid=None, tool_shed_repository=None, use_cached=False, tool_cache_data_dir=None, **kwds
+    ):
         """Load a single tool from the file named by `config_file` and return an instance of `Tool`."""
         # Parse XML configuration file and get the root element
         tool = None
@@ -939,13 +1057,19 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             tool = self.load_tool_from_cache(config_file)
         if not tool or guid and guid != tool.guid:
             try:
-                tool = self.create_tool(config_file=config_file, tool_shed_repository=tool_shed_repository, guid=guid, tool_cache_data_dir=tool_cache_data_dir, **kwds)
+                tool = self.create_tool(
+                    config_file=config_file,
+                    tool_shed_repository=tool_shed_repository,
+                    guid=guid,
+                    tool_cache_data_dir=tool_cache_data_dir,
+                    **kwds,
+                )
             except Exception:
                 # If the tool is broken but still exists we can load it from the cache
                 tool = self.load_tool_from_cache(config_file, recover_tool=True)
                 if tool:
                     log.exception(f"Tool '{config_file}' is not valid:")
-                    tool.tool_errors = 'Current on-disk tool is not valid'
+                    tool.tool_errors = "Current on-disk tool is not valid"
                 else:
                     raise
             if tool.tool_shed_repository or not guid:
@@ -961,12 +1085,12 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 [self._tool_config_watcher.watch_file(macro_path) for macro_path in tool._macro_paths]
 
     def add_tool_to_cache(self, tool, config_file):
-        tool_cache = getattr(self.app, 'tool_cache', None)
+        tool_cache = getattr(self.app, "tool_cache", None)
         if tool_cache:
             self.app.tool_cache.cache_tool(config_file, tool)
 
     def load_tool_from_cache(self, config_file, recover_tool=False):
-        tool_cache = getattr(self.app, 'tool_cache', None)
+        tool_cache = getattr(self.app, "tool_cache", None)
         tool = None
         if tool_cache:
             if recover_tool:
@@ -980,7 +1104,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return self.load_hidden_tool(tool_xml)
 
     def load_hidden_tool(self, config_file, **kwds):
-        """ Load a hidden tool (in this context meaning one that does not
+        """Load a hidden tool (in this context meaning one that does not
         appear in the tool panel) and register it in _tools_by_id.
         """
         tool = self.load_tool(config_file, **kwds)
@@ -1024,7 +1148,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         """
         if tool_id not in self._tools_by_id:
             message = f"No tool with id '{escape(tool_id)}'."
-            status = 'error'
+            status = "error"
         else:
             old_tool = self._tools_by_id[tool_id]
             new_tool = self.load_tool(old_tool.config_file, use_cached=False)
@@ -1042,8 +1166,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             # (Re-)Register the reloaded tool, this will handle
             #  _tools_by_id and _tool_versions_by_id
             self.register_tool(new_tool)
-            message = {'name': old_tool.name, 'id': old_tool.id, 'version': old_tool.version}
-            status = 'done'
+            message = {"name": old_tool.name, "id": old_tool.id, "version": old_tool.version}
+            status = "done"
         return message, status
 
     def remove_tool_by_id(self, tool_id, remove_from_panel=True):
@@ -1056,11 +1180,11 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         """
         if tool_id not in self._tools_by_id:
             message = f"No tool with id {escape(tool_id)}"
-            status = 'error'
+            status = "error"
         else:
             tool = self._tools_by_id[tool_id]
             del self._tools_by_id[tool_id]
-            tool_cache = getattr(self.app, 'tool_cache', None)
+            tool_cache = getattr(self.app, "tool_cache", None)
             if tool_cache:
                 tool_cache.expire_tool(tool_id)
             if remove_from_panel:
@@ -1072,7 +1196,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             message += f"<b>name:</b> {escape(tool.name)}<br/>"
             message += f"<b>id:</b> {escape(tool.id)}<br/>"
             message += f"<b>version:</b> {escape(tool.version)}"
-            status = 'done'
+            status = "done"
         return message, status
 
     def get_sections(self):
@@ -1090,16 +1214,16 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         no such section id.
         """
         if not tool_panel_section_id:
-            tool_panel_section_id = ''
+            tool_panel_section_id = ""
         else:
             if tool_panel_section_id not in self._tool_panel:
                 # Hack introduced without comment in a29d54619813d5da992b897557162a360b8d610c-
                 # not sure why it is needed.
-                fixed_tool_panel_section_id = f'section_{tool_panel_section_id}'
+                fixed_tool_panel_section_id = f"section_{tool_panel_section_id}"
                 if fixed_tool_panel_section_id in self._tool_panel:
                     tool_panel_section_id = fixed_tool_panel_section_id
                 else:
-                    tool_panel_section_id = ''
+                    tool_panel_section_id = ""
         return tool_panel_section_id
 
     def _load_workflow(self, workflow_id):
@@ -1112,8 +1236,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return stored.latest_workflow
 
     def tool_panel_contents(self, trans, view=None, **kwds):
-        """ Filter tool_panel contents for displaying for user.
-        """
+        """Filter tool_panel contents for displaying for user."""
         if view is None:
             view = self._default_panel_view
         if view not in self._tool_panel_view_rendered:
@@ -1172,7 +1295,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return rval
 
     def _lineage_in_panel(self, panel_dict, tool=None, tool_lineage=None):
-        """ If tool with same lineage already in panel (or section) - find
+        """If tool with same lineage already in panel (or section) - find
         and return it. Otherwise return None.
         """
         if tool_lineage is None:
@@ -1190,7 +1313,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         return None
 
     def _newer_tool(self, tool1, tool2):
-        """ Return True if tool1 is considered "newer" given its own lineage
+        """Return True if tool1 is considered "newer" given its own lineage
         description.
         """
         return tool1.version_object > tool2.version_object
@@ -1212,6 +1335,7 @@ def _filter_for_panel(item, item_type, filters, context):
     Filters tool panel elements so that only those that are compatible
     with provided filters are kept.
     """
+
     def _apply_filter(filter_item, filter_list):
         for filter_method in filter_list:
             try:
@@ -1220,31 +1344,32 @@ def _filter_for_panel(item, item_type, filters, context):
             except Exception as e:
                 raise MessageException(f"Toolbox filter exception from '{filter_method.__name__}': {unicodify(e)}.")
         return True
+
     if item_type == panel_item_types.TOOL:
-        if _apply_filter(item, filters['tool']):
+        if _apply_filter(item, filters["tool"]):
             return item
     elif item_type == panel_item_types.LABEL:
-        if _apply_filter(item, filters['label']):
+        if _apply_filter(item, filters["label"]):
             return item
     elif item_type == panel_item_types.SECTION:
         # Filter section item-by-item. Only show a label if there are
         # non-filtered tools below it.
 
-        if _apply_filter(item, filters['section']):
+        if _apply_filter(item, filters["section"]):
             cur_label_key = None
             tools_under_label = False
             filtered_elems = item.elems.copy()
             for key, section_item_type, section_item in item.panel_items_iter():
                 if section_item_type == panel_item_types.TOOL:
                     # Filter tool.
-                    if _apply_filter(section_item, filters['tool']):
+                    if _apply_filter(section_item, filters["tool"]):
                         tools_under_label = True
                     else:
                         del filtered_elems[key]
                 elif section_item_type == panel_item_types.LABEL:
                     # If there is a label and it does not have tools,
                     # remove it.
-                    if cur_label_key and (not tools_under_label or not _apply_filter(section_item, filters['label'])):
+                    if cur_label_key and (not tools_under_label or not _apply_filter(section_item, filters["label"])):
                         del filtered_elems[cur_label_key]
 
                     # Reset attributes for new label.
@@ -1272,9 +1397,19 @@ class BaseGalaxyToolBox(AbstractToolBox):
     shouldn't really depend on.
     """
 
-    def __init__(self, config_filenames, tool_root_dir, app, view_sources=None, default_panel_view=None, save_integrated_tool_panel=True):
-        super().__init__(config_filenames, tool_root_dir, app, view_sources, default_panel_view, save_integrated_tool_panel)
-        old_toolbox = getattr(app, 'toolbox', None)
+    def __init__(
+        self,
+        config_filenames,
+        tool_root_dir,
+        app,
+        view_sources=None,
+        default_panel_view=None,
+        save_integrated_tool_panel=True,
+    ):
+        super().__init__(
+            config_filenames, tool_root_dir, app, view_sources, default_panel_view, save_integrated_tool_panel
+        )
+        old_toolbox = getattr(app, "toolbox", None)
         if old_toolbox:
             self.dependency_manager = old_toolbox.dependency_manager
         else:
@@ -1298,9 +1433,13 @@ class BaseGalaxyToolBox(AbstractToolBox):
         app_config_dict = self.app.config.config_dict
         conf_file = app_config_dict.get("dependency_resolvers_config_file")
         default_tool_dependency_dir = os.path.join(
-            self.app.config.data_dir, self.app.config.schema.defaults['tool_dependency_dir'])
+            self.app.config.data_dir, self.app.config.schema.defaults["tool_dependency_dir"]
+        )
         self.dependency_manager = build_dependency_manager(
-            app_config_dict=app_config_dict, conf_file=conf_file, default_tool_dependency_dir=default_tool_dependency_dir)
+            app_config_dict=app_config_dict,
+            conf_file=conf_file,
+            default_tool_dependency_dir=default_tool_dependency_dir,
+        )
 
     def reload_dependency_manager(self):
         self._init_dependency_manager()
diff --git a/lib/galaxy/tool_util/toolbox/filters/__init__.py b/lib/galaxy/tool_util/toolbox/filters/__init__.py
index 922323b5733..aa2a73f631d 100644
--- a/lib/galaxy/tool_util/toolbox/filters/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/filters/__init__.py
@@ -22,7 +22,9 @@ class FilterFactory:
         self.default_filters = dict(tool=[_not_hidden, _handle_authorization], section=[], label=[])
         # Add dynamic filters to these default filters.
         config = toolbox.app.config
-        self.__base_modules = listify(getattr(config, "toolbox_filter_base_modules", "galaxy.tool_util.toolbox.filters"))
+        self.__base_modules = listify(
+            getattr(config, "toolbox_filter_base_modules", "galaxy.tool_util.toolbox.filters")
+        )
         self.__init_filters("tool", getattr(config, "tool_filters", ""), self.default_filters)
         self.__init_filters("section", getattr(config, "tool_section_filters", ""), self.default_filters)
         self.__init_filters("label", getattr(config, "tool_label_filters", ""), self.default_filters)
@@ -36,15 +38,15 @@ class FilterFactory:
             for name, value in trans.user.preferences.items():
                 if value and value.strip():
                     user_filters = listify(value, do_strip=True)
-                    category = ''
-                    if name == 'toolbox_tool_filters':
+                    category = ""
+                    if name == "toolbox_tool_filters":
                         category = "tool"
-                    elif name == 'toolbox_section_filters':
+                    elif name == "toolbox_section_filters":
                         category = "section"
-                    elif name == 'toolbox_label_filters':
+                    elif name == "toolbox_label_filters":
                         category = "label"
                     if category:
-                        validate = getattr(trans.app.config, f'user_tool_{category}_filters', [])
+                        validate = getattr(trans.app.config, f"user_tool_{category}_filters", [])
                         self.__init_filters(category, user_filters, filters, validate=validate)
         if kwds.get("trackster", False):
             filters["tool"].append(_has_trackster_conf)
diff --git a/lib/galaxy/tool_util/toolbox/integrated_panel.py b/lib/galaxy/tool_util/toolbox/integrated_panel.py
index 4646896cbb8..4ceb8a5ae24 100644
--- a/lib/galaxy/tool_util/toolbox/integrated_panel.py
+++ b/lib/galaxy/tool_util/toolbox/integrated_panel.py
@@ -10,7 +10,7 @@ from galaxy.util import RW_R__R__
 from galaxy.util.renamed_temporary_file import RenamedTemporaryFile
 from .panel import (
     panel_item_types,
-    ToolPanelElements
+    ToolPanelElements,
 )
 
 log = logging.getLogger(__name__)
@@ -31,14 +31,18 @@ its section) modify that file and restart Galaxy.
 
 
 class ManagesIntegratedToolPanelMixin:
-
     def _init_integrated_tool_panel(self, config):
         self.update_integrated_tool_panel = config.update_integrated_tool_panel
         self._integrated_tool_panel_config = config.integrated_tool_panel_config
-        self._integrated_tool_panel_tracking_directory = getattr(config, "integrated_tool_panel_tracking_directory", None)
+        self._integrated_tool_panel_tracking_directory = getattr(
+            config, "integrated_tool_panel_tracking_directory", None
+        )
         # In-memory dictionary that defines the layout of the tool_panel.xml file on disk.
         self._integrated_tool_panel = ToolPanelElements()
-        self._integrated_tool_panel_config_has_contents = os.path.exists(self._integrated_tool_panel_config) and os.stat(self._integrated_tool_panel_config).st_size > 0
+        self._integrated_tool_panel_config_has_contents = (
+            os.path.exists(self._integrated_tool_panel_config)
+            and os.stat(self._integrated_tool_panel_config).st_size > 0
+        )
         if self._integrated_tool_panel_config_has_contents:
             self._load_integrated_tool_panel_keys()
 
@@ -65,14 +69,16 @@ class ManagesIntegratedToolPanelMixin:
             filename = os.path.join(tracking_directory, name)
         else:
             filename = destination
-        template = string.Template("""<?xml version="1.0"?>
+        template = string.Template(
+            """<?xml version="1.0"?>
 <toolbox>
     <!--
     $INTEGRATED_TOOL_PANEL_DESCRIPTION
     -->
 $INTEGRATED_TOOL_PANEL
 </toolbox>
-""")
+"""
+        )
         integrated_tool_panel = []
         for _, item_type, item in self._integrated_tool_panel.panel_items_iter():
             if item:
@@ -81,15 +87,19 @@ $INTEGRATED_TOOL_PANEL
                 elif item_type == panel_item_types.WORKFLOW:
                     integrated_tool_panel.append(f'    <workflow id="{item.id}" />\n')
                 elif item_type == panel_item_types.LABEL:
-                    label_id = item.id or ''
-                    label_text = item.text or ''
-                    label_version = item.version or ''
-                    integrated_tool_panel.append(f'    <label id="{label_id}" text="{label_text}" version="{label_version}" />\n')
+                    label_id = item.id or ""
+                    label_text = item.text or ""
+                    label_version = item.version or ""
+                    integrated_tool_panel.append(
+                        f'    <label id="{label_id}" text="{label_text}" version="{label_version}" />\n'
+                    )
                 elif item_type == panel_item_types.SECTION:
-                    section_id = item.id or ''
-                    section_name = item.name or ''
-                    section_version = item.version or ''
-                    integrated_tool_panel.append(f'    <section id="{escape(section_id)}" name="{escape(section_name)}" version="{section_version}">\n')
+                    section_id = item.id or ""
+                    section_name = item.name or ""
+                    section_version = item.version or ""
+                    integrated_tool_panel.append(
+                        f'    <section id="{escape(section_id)}" name="{escape(section_name)}" version="{section_version}">\n'
+                    )
                     for _section_key, section_item_type, section_item in item.panel_items_iter():
                         if section_item_type == panel_item_types.TOOL:
                             if section_item:
@@ -99,19 +109,23 @@ $INTEGRATED_TOOL_PANEL
                                 integrated_tool_panel.append(f'        <workflow id="{section_item.id}" />\n')
                         elif section_item_type == panel_item_types.LABEL:
                             if section_item:
-                                label_id = section_item.id or ''
-                                label_text = section_item.text or ''
-                                label_version = section_item.version or ''
-                                integrated_tool_panel.append(f'        <label id="{label_id}" text="{label_text}" version="{label_version}" />\n')
-                    integrated_tool_panel.append('    </section>\n')
-        tool_panel_description = '\n    '.join(line for line in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if line)
-        tp_string = template.substitute(INTEGRATED_TOOL_PANEL_DESCRIPTION=tool_panel_description,
-                                        INTEGRATED_TOOL_PANEL='\n'.join(integrated_tool_panel))
-        with RenamedTemporaryFile(filename, mode='w') as f:
+                                label_id = section_item.id or ""
+                                label_text = section_item.text or ""
+                                label_version = section_item.version or ""
+                                integrated_tool_panel.append(
+                                    f'        <label id="{label_id}" text="{label_text}" version="{label_version}" />\n'
+                                )
+                    integrated_tool_panel.append("    </section>\n")
+        tool_panel_description = "\n    ".join(line for line in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if line)
+        tp_string = template.substitute(
+            INTEGRATED_TOOL_PANEL_DESCRIPTION=tool_panel_description,
+            INTEGRATED_TOOL_PANEL="\n".join(integrated_tool_panel),
+        )
+        with RenamedTemporaryFile(filename, mode="w") as f:
             f.write(tp_string)
         if tracking_directory:
             with open(f"{filename}.stack", "w") as f:
-                f.write(''.join(traceback.format_stack()))
+                f.write("".join(traceback.format_stack()))
             shutil.copy(filename, f"{filename}.copy")
             shutil.move(f"{filename}.copy", destination)
         try:
diff --git a/lib/galaxy/tool_util/toolbox/lineages/__init__.py b/lib/galaxy/tool_util/toolbox/lineages/__init__.py
index d4e823400de..5b2cdc3e5b5 100644
--- a/lib/galaxy/tool_util/toolbox/lineages/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/lineages/__init__.py
@@ -1,5 +1,4 @@
 from .factory import LineageMap
 from .interface import ToolLineage
 
-
 __all__ = ("LineageMap", "ToolLineage")
diff --git a/lib/galaxy/tool_util/toolbox/lineages/factory.py b/lib/galaxy/tool_util/toolbox/lineages/factory.py
index e7053e5c6b3..96efb51d77d 100644
--- a/lib/galaxy/tool_util/toolbox/lineages/factory.py
+++ b/lib/galaxy/tool_util/toolbox/lineages/factory.py
@@ -1,12 +1,14 @@
-from typing import Dict, Optional
+from typing import (
+    Dict,
+    Optional,
+)
 
 from galaxy.util.tool_version import remove_version_from_guid
 from .interface import ToolLineage
 
 
 class LineageMap:
-    """ Map each unique tool id to a lineage object.
-    """
+    """Map each unique tool id to a lineage object."""
 
     def __init__(self, app):
         self.lineage_map: Dict[str, ToolLineage] = {}
@@ -54,4 +56,4 @@ class LineageMap:
         return self.lineage_map.get(versionless_tool_id, None)
 
 
-__all__ = ("LineageMap", )
+__all__ = ("LineageMap",)
diff --git a/lib/galaxy/tool_util/toolbox/lineages/interface.py b/lib/galaxy/tool_util/toolbox/lineages/interface.py
index b8f48657bac..3722148e3b1 100644
--- a/lib/galaxy/tool_util/toolbox/lineages/interface.py
+++ b/lib/galaxy/tool_util/toolbox/lineages/interface.py
@@ -1,5 +1,9 @@
 import threading
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 
 import packaging.version
 from sortedcontainers import SortedSet
@@ -8,9 +12,9 @@ from galaxy.util.tool_version import remove_version_from_guid
 
 
 class ToolLineageVersion:
-    """ Represents a single tool in a lineage. If lineage is based
+    """Represents a single tool in a lineage. If lineage is based
     around GUIDs that somehow encode the version (either using GUID
-    or a simple tool id and a version). """
+    or a simple tool id and a version)."""
 
     def __init__(self, id, version):
         self.id = id
@@ -18,7 +22,7 @@ class ToolLineageVersion:
 
     @property
     def id_based(self):
-        """ Return True if the lineage is defined by GUIDs (in this
+        """Return True if the lineage is defined by GUIDs (in this
         case the indexer of the tools (i.e. the ToolBox) should ignore
         the tool_version (because it is encoded in the GUID and managed
         externally).
@@ -33,10 +37,11 @@ class ToolLineageVersion:
 
 
 class ToolLineage:
-    """ Simple tool's loaded directly from file system with lineage
+    """Simple tool's loaded directly from file system with lineage
     determined solely by PEP 440 versioning scheme.
     """
-    lineages_by_id: Dict[str, 'ToolLineage'] = {}
+
+    lineages_by_id: Dict[str, "ToolLineage"] = {}
     lock = threading.Lock()
 
     def __init__(self, tool_id, **kwds):
@@ -50,7 +55,7 @@ class ToolLineage:
         return [f"{tool_id}/{version}" for version in self.tool_versions]
 
     @staticmethod
-    def from_tool(tool) -> 'ToolLineage':
+    def from_tool(tool) -> "ToolLineage":
         tool_id = tool.id
         lineages_by_id = ToolLineage.lineages_by_id
         with ToolLineage.lock:
@@ -69,7 +74,10 @@ class ToolLineage:
         Return an ordered list of lineages (ToolLineageVersion) in this
         chain, from oldest to newest.
         """
-        return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)]
+        return [
+            ToolLineageVersion(tool_id, tool_version)
+            for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)
+        ]
 
     def get_version_ids(self, reverse=False) -> List[str]:
         if reverse:
@@ -80,5 +88,5 @@ class ToolLineage:
         return dict(
             tool_id=self.tool_id,
             tool_versions=list(self.tool_versions),
-            lineage_type='stock',
+            lineage_type="stock",
         )
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 0b2770e78ea..4e30bc27bf9 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -1,6 +1,10 @@
 from abc import abstractmethod
 from enum import Enum
-from typing import Dict, Optional, Tuple
+from typing import (
+    Dict,
+    Optional,
+    Tuple,
+)
 
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.odict import odict
@@ -15,17 +19,16 @@ class panel_item_types(str, Enum):
 
 
 class HasPanelItems:
-    """
-    """
+    """ """
 
     @abstractmethod
     def panel_items(self):
-        """ Return an ordered dictionary-like object describing tool panel
+        """Return an ordered dictionary-like object describing tool panel
         items (such as workflows, tools, labels, and sections).
         """
 
     def panel_items_iter(self):
-        """ Iterate through panel items each represented as a tuple of
+        """Iterate through panel items each represented as a tuple of
         (panel_key, panel_type, panel_content).
         """
         for panel_key, panel_value in self.panel_items().items():
@@ -47,18 +50,17 @@ class ToolSection(Dictifiable, HasPanelItems):
     group in the user interface.
     """
 
-    dict_collection_visible_keys = ['id', 'name', 'version', 'description', 'links']
+    dict_collection_visible_keys = ["id", "name", "version", "description", "links"]
 
     def __init__(self, item=None):
-        """ Build a ToolSection from an ElementTree element or a dictionary.
-        """
+        """Build a ToolSection from an ElementTree element or a dictionary."""
         if item is None:
             item = dict()
-        self.name = item.get('name') or ''
-        self.id = item.get('id') or ''
-        self.version = item.get('version') or ''
-        self.description = item.get('description') or None
-        self.links = item.get('links') or None
+        self.name = item.get("name") or ""
+        self.id = item.get("id") or ""
+        self.version = item.get("version") or ""
+        self.description = item.get("description") or None
+        self.links = item.get("links") or None
         self.elems = ToolPanelElements()
 
     def copy(self):
@@ -72,21 +74,17 @@ class ToolSection(Dictifiable, HasPanelItems):
         return copy
 
     def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None):
-        """ Return a dict that includes section's attributes. """
+        """Return a dict that includes section's attributes."""
 
         section_dict = super().to_dict()
         section_elts = []
-        kwargs = dict(
-            trans=trans,
-            link_details=link_details,
-            tool_help=tool_help
-        )
+        kwargs = dict(trans=trans, link_details=link_details, tool_help=tool_help)
         for elt in self.elems.values():
             if hasattr(elt, "tool_type") and toolbox:
                 section_elts.append(toolbox.get_tool_to_dict(trans, elt, tool_help=tool_help))
             else:
                 section_elts.append(elt.to_dict(**kwargs))
-        section_dict['elems'] = section_elts
+        section_dict["elems"] = section_elts
 
         return section_dict
 
@@ -99,27 +97,29 @@ class ToolSectionLabel(Dictifiable):
     A label for a set of tools that can be displayed above groups of tools
     and sections in the user interface
     """
-    dict_collection_visible_keys = ['id', 'text', 'version', 'description', 'links']
+
+    dict_collection_visible_keys = ["id", "text", "version", "description", "links"]
 
     def __init__(self, item):
-        """ Build a ToolSectionLabel from an ElementTree element or a
+        """Build a ToolSectionLabel from an ElementTree element or a
         dictionary.
         """
         item = ensure_tool_conf_item(item)
         self.text = item.get("text")
         self.id = item.get("id")
-        self.version = item.get("version") or ''
-        self.description = item.get('description') or None
-        self.links = item.get('links', None)
+        self.version = item.get("version") or ""
+        self.description = item.get("description") or None
+        self.links = item.get("links", None)
 
     def to_dict(self, **kwds):
         return super().to_dict()
 
 
 class ToolPanelElements(odict, HasPanelItems):
-    """ Represents an ordered dictionary of tool entries - abstraction
+    """Represents an ordered dictionary of tool entries - abstraction
     used both by tool panel itself (normal and integrated) and its sections.
     """
+
     _section_by_tool: Dict[str, Tuple[str, str]] = {}
 
     def record_section_for_tool_id(self, tool_id: str, key: str, val: str):
@@ -136,14 +136,18 @@ class ToolPanelElements(odict, HasPanelItems):
             if key == tool_key:
                 self[key] = new_tool
                 break
-            elif key.startswith('section'):
+            elif key.startswith("section"):
                 if tool_key in val.elems:
                     self[key].elems[tool_key] = new_tool
                     break
 
-    def get_or_create_section(self, sec_id: str, sec_nm: str, description: Optional[str] = None, links: Optional[Dict[str, str]] = None) -> ToolSection:
+    def get_or_create_section(
+        self, sec_id: str, sec_nm: str, description: Optional[str] = None, links: Optional[Dict[str, str]] = None
+    ) -> ToolSection:
         if sec_id not in self:
-            section = ToolSection({'id': sec_id, 'name': sec_nm, 'description': description, 'version': '', 'links': links})
+            section = ToolSection(
+                {"id": sec_id, "name": sec_nm, "description": description, "version": "", "links": links}
+            )
             self[sec_id] = section
         else:
             section = self[sec_id]
@@ -155,7 +159,7 @@ class ToolPanelElements(odict, HasPanelItems):
             if key == tool_key:
                 del self[key]
                 break
-            elif key.startswith('section'):
+            elif key.startswith("section"):
                 if tool_key in val.elems:
                     del self[key].elems[tool_key]
                     break
@@ -173,18 +177,18 @@ class ToolPanelElements(odict, HasPanelItems):
         return None
 
     def has_tool_with_id(self, tool_id: str) -> bool:
-        key = f'tool_{tool_id}'
+        key = f"tool_{tool_id}"
         return key in self
 
     def replace_tool(self, previous_tool_id: str, new_tool_id: str, tool) -> None:
-        previous_key = f'tool_{previous_tool_id}'
-        new_key = f'tool_{new_tool_id}'
+        previous_key = f"tool_{previous_tool_id}"
+        new_key = f"tool_{new_tool_id}"
         index = self.keys().index(previous_key)
         del self[previous_key]
         self.insert(index, new_key, tool)
 
     def index_of_tool_id(self, tool_id: str) -> Optional[int]:
-        query_key = f'tool_{tool_id}'
+        query_key = f"tool_{tool_id}"
         for index, target_key in enumerate(self.keys()):
             if query_key == target_key:
                 return index
@@ -207,11 +211,11 @@ class ToolPanelElements(odict, HasPanelItems):
         self[key] = None
 
     def stub_workflow(self, key: str) -> None:
-        key = f'workflow_{key}'
+        key = f"workflow_{key}"
         self[key] = None
 
     def stub_label(self, key: str) -> None:
-        key = f'label_{key}'
+        key = f"label_{key}"
         self[key] = None
 
     def append_section(self, key: str, section: ToolSection) -> None:
@@ -246,7 +250,7 @@ class ToolPanelElements(odict, HasPanelItems):
         for key in to_remove:
             del self[key]
 
-    def copy(self) -> 'ToolPanelElements':
+    def copy(self) -> "ToolPanelElements":
         the_copy = ToolPanelElements()
         the_copy.update(self)
         return the_copy
diff --git a/lib/galaxy/tool_util/toolbox/parser.py b/lib/galaxy/tool_util/toolbox/parser.py
index e4df9ff5492..b0b5aaa67f5 100644
--- a/lib/galaxy/tool_util/toolbox/parser.py
+++ b/lib/galaxy/tool_util/toolbox/parser.py
@@ -3,11 +3,17 @@
 These files define tool lists, sections, labels, etc... the elements of the
 Galaxy tool panel.
 """
-from abc import ABCMeta, abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod,
+)
 
 import yaml
 
-from galaxy.util import parse_xml, string_as_bool
+from galaxy.util import (
+    parse_xml,
+    string_as_bool,
+)
 
 DEFAULT_MONITOR = False
 
@@ -33,16 +39,15 @@ class ToolConfSource(metaclass=ABCMeta):
 
 
 class XmlToolConfSource(ToolConfSource):
-
     def __init__(self, config_filename):
         tree = parse_xml(config_filename)
         self.root = tree.getroot()
 
     def parse_tool_path(self):
-        return self.root.get('tool_path')
+        return self.root.get("tool_path")
 
     def parse_tool_cache_data_dir(self):
-        return self.root.get('tool_cache_data_dir')
+        return self.root.get("tool_cache_data_dir")
 
     def parse_items(self):
         return [ensure_tool_conf_item(_) for _ in self.root]
@@ -53,27 +58,26 @@ class XmlToolConfSource(ToolConfSource):
         return has_tool_path and is_shed_conf
 
     def parse_monitor(self):
-        return string_as_bool(self.root.get('monitor', DEFAULT_MONITOR))
+        return string_as_bool(self.root.get("monitor", DEFAULT_MONITOR))
 
 
 class YamlToolConfSource(ToolConfSource):
-
     def __init__(self, config_filename):
         with open(config_filename) as f:
             as_dict = yaml.safe_load(f)
         self.as_dict = as_dict
 
     def parse_tool_path(self):
-        return self.as_dict.get('tool_path')
+        return self.as_dict.get("tool_path")
 
     def parse_tool_cache_data_dir(self):
-        return self.as_dict.get('tool_cache_data_dir')
+        return self.as_dict.get("tool_cache_data_dir")
 
     def parse_items(self):
-        return [ToolConfItem.from_dict(_) for _ in self.as_dict.get('items')]
+        return [ToolConfItem.from_dict(_) for _ in self.as_dict.get("items")]
 
     def parse_monitor(self):
-        return self.as_dict.get('monitor', DEFAULT_MONITOR)
+        return self.as_dict.get("monitor", DEFAULT_MONITOR)
 
     def is_shed_tool_conf(self):
         return False
@@ -93,12 +97,12 @@ class ToolConfItem:
     @classmethod
     def from_dict(cls, _as_dict):
         as_dict = _as_dict.copy()
-        type = as_dict.get('type')
-        del as_dict['type']
+        type = as_dict.get("type")
+        del as_dict["type"]
         attributes = as_dict
-        if type == 'section':
-            items = [cls.from_dict(_) for _ in as_dict['items']]
-            del as_dict['items']
+        if type == "section":
+            items = [cls.from_dict(_) for _ in as_dict["items"]]
+            del as_dict["items"]
             item = ToolConfSection(attributes, items)
         else:
             item = ToolConfItem(type, attributes)
@@ -126,9 +130,8 @@ class ToolConfItem:
 
 
 class ToolConfSection(ToolConfItem):
-
     def __init__(self, attributes, items, elem=None):
-        super().__init__('section', attributes, elem)
+        super().__init__("section", attributes, elem)
         self.items = items
 
 
diff --git a/lib/galaxy/tool_util/toolbox/tags.py b/lib/galaxy/tool_util/toolbox/tags.py
index 88f25557543..d7b7790183c 100644
--- a/lib/galaxy/tool_util/toolbox/tags.py
+++ b/lib/galaxy/tool_util/toolbox/tags.py
@@ -3,38 +3,33 @@
 import logging
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
-
 log = logging.getLogger(__name__)
 
 
 def tool_tag_manager(app):
-    """ Build a tool tag manager according to app's configuration
+    """Build a tool tag manager according to app's configuration
     and return it.
     """
-    if hasattr(app.config, "get_bool") and app.config.get_bool('enable_tool_tags', False):
+    if hasattr(app.config, "get_bool") and app.config.get_bool("enable_tool_tags", False):
         return PersistentToolTagManager(app)
     else:
         return NullToolTagManager()
 
 
 class AbstractToolTagManager(metaclass=ABCMeta):
-
     @abstractmethod
     def reset_tags(self):
-        """ Starting to load tool panels, reset all tags.
-        """
+        """Starting to load tool panels, reset all tags."""
 
     @abstractmethod
     def handle_tags(self, tool_id, tool_definition_source):
-        """ Parse out tags and persist them.
-        """
+        """Parse out tags and persist them."""
 
 
 class NullToolTagManager(AbstractToolTagManager):
-
     def reset_tags(self):
         return None
 
@@ -43,22 +38,23 @@ class NullToolTagManager(AbstractToolTagManager):
 
 
 class PersistentToolTagManager(AbstractToolTagManager):
-
     def __init__(self, app):
         self.app = app
         self.sa_session = app.model.context
 
     def reset_tags(self):
-        log.info(f"removing all tool tag associations ({str(self.sa_session.query(self.app.model.ToolTagAssociation).count())})")
+        log.info(
+            f"removing all tool tag associations ({str(self.sa_session.query(self.app.model.ToolTagAssociation).count())})"
+        )
         self.sa_session.query(self.app.model.ToolTagAssociation).delete()
         self.sa_session.flush()
 
     def handle_tags(self, tool_id, tool_definition_source):
         elem = tool_definition_source
-        if self.app.config.get_bool('enable_tool_tags', False):
+        if self.app.config.get_bool("enable_tool_tags", False):
             tag_names = elem.get("tags", "").split(",")
             for tag_name in tag_names:
-                if tag_name == '':
+                if tag_name == "":
                     continue
                 tag = self.sa_session.query(self.app.model.Tag).filter_by(name=tag_name).first()
                 if not tag:
diff --git a/lib/galaxy/tool_util/toolbox/views/definitions.py b/lib/galaxy/tool_util/toolbox/views/definitions.py
index 735bcd9286b..084c471b5e4 100644
--- a/lib/galaxy/tool_util/toolbox/views/definitions.py
+++ b/lib/galaxy/tool_util/toolbox/views/definitions.py
@@ -1,15 +1,24 @@
 from enum import Enum
-from typing import Any, cast, List, Optional, Union
+from typing import (
+    Any,
+    cast,
+    List,
+    Optional,
+    Union,
+)
 
-from pydantic import BaseModel, Field
+from pydantic import (
+    BaseModel,
+    Field,
+)
 from typing_extensions import Literal
 
 
 class StaticToolBoxViewTypeEnum(str, Enum):
-    generic = 'generic'
-    activity = 'activity'
-    publication = 'publication'
-    training = 'training'
+    generic = "generic"
+    activity = "activity"
+    publication = "publication"
+    training = "training"
 
 
 class ExcludeTool(BaseModel):
@@ -33,7 +42,7 @@ OptionalExclusionList = Optional[List[Exclusions]]
 
 
 class Tool(BaseModel):
-    content_type: Literal['tool'] = Field("tool", alias="type")
+    content_type: Literal["tool"] = Field("tool", alias="type")
     id: str
 
     class Config:
@@ -41,7 +50,7 @@ class Tool(BaseModel):
 
 
 class Label(BaseModel):
-    content_type: Literal['label'] = Field(alias="type")
+    content_type: Literal["label"] = Field(alias="type")
     id: Optional[str]
     text: str
 
@@ -55,7 +64,7 @@ class LabelShortcut(BaseModel):
 
 
 class Workflow(BaseModel):
-    content_type: Literal['workflow'] = Field(alias="type")
+    content_type: Literal["workflow"] = Field(alias="type")
     id: str
 
     class Config:
@@ -81,7 +90,7 @@ class HasItems:
     items: Optional[List[Any]]
 
     @property
-    def items_expanded(self) -> Optional[List['ExpandedRootContent']]:
+    def items_expanded(self) -> Optional[List["ExpandedRootContent"]]:
         if self.items is None:
             return None
 
@@ -110,7 +119,7 @@ class HasItems:
 
 
 class Section(BaseModel, HasItems):
-    content_type: Literal['section'] = Field(alias="type")
+    content_type: Literal["section"] = Field(alias="type")
     id: Optional[str]
     name: Optional[str]
     items: Optional[List[SectionContent]]
diff --git a/lib/galaxy/tool_util/toolbox/views/edam.py b/lib/galaxy/tool_util/toolbox/views/edam.py
index 3dcf909f532..22a2ee210f9 100644
--- a/lib/galaxy/tool_util/toolbox/views/edam.py
+++ b/lib/galaxy/tool_util/toolbox/views/edam.py
@@ -1,16 +1,19 @@
 import logging
 import os
 from enum import Enum
-from typing import Dict, List, Optional, Tuple
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Tuple,
+)
 
 from galaxy.tool_util.edam_util import (
     load_edam_tree,
     ROOT_OPERATION,
     ROOT_TOPIC,
 )
-from galaxy.util import (
-    ExecutionTimer,
-)
+from galaxy.util import ExecutionTimer
 from .interface import (
     ToolBoxRegistry,
     ToolPanelView,
@@ -33,9 +36,10 @@ class EdamPanelMode(str, Enum):
 
 
 class EdamToolPanelView(ToolPanelView):
-
     def __init__(self, edam_ontology_path: Optional[str], mode: EdamPanelMode = EdamPanelMode.merged):
-        edam = load_edam_tree(None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path)
+        edam = load_edam_tree(
+            None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path
+        )
         self.edam = edam
         self.mode = mode
         self.include_topics = mode in [EdamPanelMode.merged, EdamPanelMode.topics]
@@ -53,22 +57,16 @@ class EdamToolPanelView(ToolPanelView):
         # topics = sorted(topics, key=lambda x: self.edam[x]['label'])
 
         # Convert these to list of dicts, wherein we'll add our tools/etc.
-        operations: Dict[str, Dict] = {
-            x: {}
-            for x in operations_list
-        }
-        topics: Dict[str, Dict] = {
-            x: {}
-            for x in topics_list
-        }
+        operations: Dict[str, Dict] = {x: {} for x in operations_list}
+        topics: Dict[str, Dict] = {x: {} for x in topics_list}
         uncategorized: List[Tuple] = []
 
         for tool_id, key, val, val_name in walk_loaded_tools(base_tool_panel, toolbox_registry):
             for term in self._get_edam_sec(val):
-                if term == 'uncategorized' or term not in self.edam:
+                if term == "uncategorized" or term not in self.edam:
                     uncategorized.append((tool_id, key, val, val_name))
                 else:
-                    for path in self.edam[term]['path']:
+                    for path in self.edam[term]["path"]:
                         if len(path) == 1:
                             t = term
                         elif len(path) == 0:
@@ -76,19 +74,19 @@ class EdamToolPanelView(ToolPanelView):
                         else:
                             t = path[0]
 
-                        if path[0].startswith('operation_'):
+                        if path[0].startswith("operation_"):
                             operations[t][tool_id] = (term, tool_id, key, val, val_name)
-                        elif path[0].startswith('topic_'):
+                        elif path[0].startswith("topic_"):
                             topics[t][tool_id] = (term, tool_id, key, val, val_name)
 
         new_panel = ToolPanelElements()
 
         def populate_section(term, tool_id, key, val, val_name):
             edam_def = self.edam[term]
-            description = edam_def['definition']
-            label = edam_def['label']
+            description = edam_def["definition"]
+            label = edam_def["label"]
             links = {
-                'edam_browser': f"https://edamontology.github.io/edam-browser/#{term}",
+                "edam_browser": f"https://edamontology.github.io/edam-browser/#{term}",
             }
             section = new_panel.get_or_create_section(term, label, description=description, links=links)
             toolbox_registry.add_tool_to_tool_panel_view(val, section)
@@ -99,13 +97,13 @@ class EdamToolPanelView(ToolPanelView):
                 continue
 
             label_dict = {
-                'type': 'label',
-                'text': self.edam[term]['label'],
-                'description': self.edam[term]['definition'],
-                'links': {
-                    'edam_browser': f"https://edamontology.github.io/edam-browser/#{term}",
+                "type": "label",
+                "text": self.edam[term]["label"],
+                "description": self.edam[term]["definition"],
+                "links": {
+                    "edam_browser": f"https://edamontology.github.io/edam-browser/#{term}",
                 },
-                'id': term,
+                "id": term,
             }
             new_panel[f"label_{term}"] = ToolSectionLabel(label_dict)
 
@@ -117,20 +115,20 @@ class EdamToolPanelView(ToolPanelView):
                 continue
 
             label_dict = {
-                'type': 'label',
-                'text': self.edam[term]['label'],
-                'description': self.edam[term]['definition'],
-                'links': {
-                    'edam_browser': f"https://edamontology.github.io/edam-browser/#{term}",
+                "type": "label",
+                "text": self.edam[term]["label"],
+                "description": self.edam[term]["definition"],
+                "links": {
+                    "edam_browser": f"https://edamontology.github.io/edam-browser/#{term}",
                 },
-                'id': term,
+                "id": term,
             }
             new_panel[f"label_{term}"] = ToolSectionLabel(label_dict)
 
             for (term, tool_id, key, val, val_name) in topics[term].values():
                 populate_section(term, tool_id, key, val, val_name)
 
-        section = new_panel.get_or_create_section('uncategorized', 'Uncategorized')
+        section = new_panel.get_or_create_section("uncategorized", "Uncategorized")
         for (tool_id, key, val, val_name) in uncategorized:
             toolbox_registry.add_tool_to_tool_panel_view(val, section)
             new_panel.record_section_for_tool_id(tool_id, key, val_name)
@@ -146,17 +144,17 @@ class EdamToolPanelView(ToolPanelView):
         if len(edam) > 0:
             yield from edam
         else:
-            yield 'uncategorized'
+            yield "uncategorized"
 
     def _sort_edam_key(self, x):
         if x in (ROOT_OPERATION, ROOT_TOPIC):
             return f"!{x}"
         else:
-            return self.edam[x]['label']
+            return self.edam[x]["label"]
 
     def _edam_children_of(self, parentTerm):
         for term in self.edam.keys():
-            if parentTerm in self.edam[term]['parents']:
+            if parentTerm in self.edam[term]["parents"]:
                 yield term
 
     def to_model(self) -> ToolPanelViewModel:
diff --git a/lib/galaxy/tool_util/toolbox/views/interface.py b/lib/galaxy/tool_util/toolbox/views/interface.py
index e7bea38174e..c0153527369 100644
--- a/lib/galaxy/tool_util/toolbox/views/interface.py
+++ b/lib/galaxy/tool_util/toolbox/views/interface.py
@@ -12,16 +12,17 @@ from ..panel import (
 
 
 class ToolPanelViewModelType(str, Enum):
-    default_type = 'default'
-    generic = 'generic'
-    activity = 'activity'
-    ontology = 'ontology'
-    publication = 'publication'
-    training = 'training'
+    default_type = "default"
+    generic = "generic"
+    activity = "activity"
+    ontology = "ontology"
+    publication = "publication"
+    training = "training"
 
 
 class ToolPanelViewModel(BaseModel):
     """A view of ToolPanelView objects serialized for the API."""
+
     id: str
     model_class: str
     name: str
@@ -51,7 +52,6 @@ class ToolBoxRegistry:
 
 
 class ToolPanelView:
-
     @abstractmethod
     def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
         """Consume tool panel state and return custom tool panel view."""
@@ -64,12 +64,12 @@ class ToolPanelView:
 def walk_loaded_tools(tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry):
     for key, item_type, val in tool_panel.panel_items_iter():
         if item_type == panel_item_types.TOOL:
-            tool_id = key.replace('tool_', '', 1)
+            tool_id = key.replace("tool_", "", 1)
             if toolbox_registry.has_tool(tool_id):
                 yield (tool_id, key, val, val.name)
         elif item_type == panel_item_types.SECTION:
             for section_key, section_item_type, section_val in val.panel_items_iter():
                 if section_item_type == panel_item_types.TOOL:
-                    tool_id = section_key.replace('tool_', '', 1)
+                    tool_id = section_key.replace("tool_", "", 1)
                     if toolbox_registry.has_tool(tool_id):
                         yield (tool_id, key, section_val, val.name)
diff --git a/lib/galaxy/tool_util/toolbox/views/sources.py b/lib/galaxy/tool_util/toolbox/views/sources.py
index 286a46a07ee..c78b7889a50 100644
--- a/lib/galaxy/tool_util/toolbox/views/sources.py
+++ b/lib/galaxy/tool_util/toolbox/views/sources.py
@@ -1,6 +1,9 @@
 import logging
 import os
-from typing import Dict, List
+from typing import (
+    Dict,
+    List,
+)
 
 import yaml
 
diff --git a/lib/galaxy/tool_util/toolbox/views/static.py b/lib/galaxy/tool_util/toolbox/views/static.py
index 7bf5612ba76..35dfe8db446 100644
--- a/lib/galaxy/tool_util/toolbox/views/static.py
+++ b/lib/galaxy/tool_util/toolbox/views/static.py
@@ -27,7 +27,6 @@ from ..panel import (
     ToolSectionLabel,
 )
 
-
 log = logging.getLogger(__name__)
 
 
@@ -69,7 +68,6 @@ class StaticToolPanelView(ToolPanelView):
         self._definition = definition
 
     def apply_view(self, base_tool_panel: ToolPanelElements, toolbox_registry: ToolBoxRegistry) -> ToolPanelElements:
-
         def apply_filter(definition, elems):
             excludes = self._all_excludes(definition)
             if excludes:
@@ -103,7 +101,9 @@ class StaticToolPanelView(ToolPanelView):
                     else:
                         closest_section = base_tool_panel.closest_section(section_def.id, section_def.name)
                         if closest_section is None:
-                            log.warning(f"Failed to find matching section for (id, name) = ({section_def.id}, {section_def.name})")
+                            log.warning(
+                                f"Failed to find matching section for (id, name) = ({section_def.id}, {section_def.name})"
+                            )
                             continue
                         section = closest_section.copy()
                         if section_def.id is not None:
@@ -116,7 +116,9 @@ class StaticToolPanelView(ToolPanelView):
                     assert allow_sections
                     closest_section = base_tool_panel.closest_section(element.section, element.section)
                     if closest_section is None:
-                        log.warning(f"Failed to find matching section for (id, name) = ({element.section}, {element.section})")
+                        log.warning(
+                            f"Failed to find matching section for (id, name) = ({element.section}, {element.section})"
+                        )
                         continue
                     section = closest_section.copy()
                     apply_filter(element, section.elems)
@@ -133,7 +135,9 @@ class StaticToolPanelView(ToolPanelView):
                 elif element.content_type == "tool":
                     tool_id = element.id
                     if not toolbox_registry.has_tool(tool_id):
-                        log.warning(f"Failed to find tool_id {tool_id} from parent toolbox, cannot load into panel view")
+                        log.warning(
+                            f"Failed to find tool_id {tool_id} from parent toolbox, cannot load into panel view"
+                        )
                         continue
                     tool = toolbox_registry.get_tool(tool_id)
                     toolbox_registry.add_tool_to_tool_panel_view(tool, new_panel)
diff --git a/lib/galaxy/tool_util/toolbox/watcher.py b/lib/galaxy/tool_util/toolbox/watcher.py
index b807b2c2b76..b91751e0ac0 100644
--- a/lib/galaxy/tool_util/toolbox/watcher.py
+++ b/lib/galaxy/tool_util/toolbox/watcher.py
@@ -6,6 +6,7 @@ try:
     from watchdog.events import FileSystemEventHandler
     from watchdog.observers import Observer
     from watchdog.observers.polling import PollingObserver
+
     can_watch = True
 except ImportError:
     Observer = None
@@ -38,7 +39,6 @@ def get_tool_watcher(toolbox, config):
 
 
 class ToolFileEventHandler(FileSystemEventHandler):
-
     def __init__(self, tool_watcher):
         self.tool_watcher = tool_watcher
 
@@ -49,7 +49,7 @@ class ToolFileEventHandler(FileSystemEventHandler):
         # modified events will only have src path, move events will
         # have dest_path and src_path but we only care about dest. So
         # look at dest if it exists else use src.
-        path = getattr(event, 'dest_path', None) or event.src_path
+        path = getattr(event, "dest_path", None) or event.src_path
         path = os.path.abspath(path)
         tool_id = self.tool_watcher.tool_file_ids.get(path, None)
         if tool_id:
@@ -68,7 +68,6 @@ class ToolFileEventHandler(FileSystemEventHandler):
 
 
 class ToolConfWatcher:
-
     def __init__(self, reload_callback, tool_cache=None):
         self.paths = {}
         self.cache = tool_cache
@@ -168,7 +167,6 @@ class ToolConfWatcher:
 
 
 class ToolWatcher(BaseWatcher):
-
     def __init__(self, observer_class, event_handler_class, toolbox):
         super().__init__(observer_class, event_handler_class)
         self.toolbox = toolbox
diff --git a/lib/galaxy/tool_util/unittest_utils/sample_data.py b/lib/galaxy/tool_util/unittest_utils/sample_data.py
index dc0bcb02093..d4b6ddb6f02 100644
--- a/lib/galaxy/tool_util/unittest_utils/sample_data.py
+++ b/lib/galaxy/tool_util/unittest_utils/sample_data.py
@@ -7,11 +7,13 @@ SIMPLE_TOOL_WITH_MACRO = """<tool id="tool_with_macro" name="macro_annotation" v
     </macros>
 </tool>"""
 
-SIMPLE_MACRO = Template("""
+SIMPLE_MACRO = Template(
+    """
 <macros>
     <token name="@WRAPPER_VERSION@">$tool_version</token>
     <macro name="inputs">
         <inputs/>
     </macro>
 </macros>
-""")
+"""
+)
diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index 8fb1b5abd71..4838e125db5 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -18,7 +18,7 @@ except ImportError:
 
 from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA,
-    DEFAULT_DELTA_FRAC
+    DEFAULT_DELTA_FRAC,
 )
 from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
@@ -39,7 +39,7 @@ def verify(
     get_filename=None,
     keep_outputs_dir=None,
     verify_extra_files=None,
-    mode='file',
+    mode="file",
 ):
     """Verify the content of a test output using test definitions described by attributes.
 
@@ -52,7 +52,7 @@ def verify(
         def get_filename(filename):
             file_content = get_filecontent(filename)
             local_name = make_temp_fname(fname=filename)
-            with open(local_name, 'wb') as f:
+            with open(local_name, "wb") as f:
                 f.write(file_content)
             return local_name
 
@@ -62,7 +62,7 @@ def verify(
         try:
             verify_assertions(output_content, attributes["assert_list"])
         except AssertionError as err:
-            errmsg = f'{item_label} different than expected\n'
+            errmsg = f"{item_label} different than expected\n"
             errmsg += unicodify(err)
             raise AssertionError(errmsg)
 
@@ -82,7 +82,7 @@ def verify(
         try:
             _verify_checksum(output_content, expected_checksum_type, expected_checksum)
         except AssertionError as err:
-            errmsg = f'{item_label} different than expected\n'
+            errmsg = f"{item_label} different than expected\n"
             errmsg += unicodify(err)
             raise AssertionError(errmsg)
 
@@ -90,10 +90,10 @@ def verify(
         attributes = {}
 
     # expected object might be None, so don't pull unless available
-    has_expected_object = 'object' in attributes
+    has_expected_object = "object" in attributes
     if has_expected_object:
         assert filename is None
-        expected_object = attributes.get('object')
+        expected_object = attributes.get("object")
         actual_object = json.loads(output_content)
 
         expected_object_type = type(expected_object)
@@ -109,7 +109,7 @@ def verify(
 
     elif filename is not None:
         temp_name = make_temp_fname(fname=filename)
-        with open(temp_name, 'wb') as f:
+        with open(temp_name, "wb") as f:
             f.write(output_content)
 
         # If the server's env has GALAXY_TEST_SAVE, save the output file to that
@@ -123,52 +123,58 @@ def verify(
             out_dir = os.path.dirname(ofn)
             if not os.path.exists(out_dir):
                 os.makedirs(out_dir)
-            log.debug('keep_outputs_dir: %s, ofn: %s', keep_outputs_dir, ofn)
+            log.debug("keep_outputs_dir: %s, ofn: %s", keep_outputs_dir, ofn)
             try:
                 shutil.copy(temp_name, ofn)
             except Exception:
-                log.exception('Could not save output file %s to %s', temp_name, ofn)
+                log.exception("Could not save output file %s to %s", temp_name, ofn)
             else:
-                log.debug('## GALAXY_TEST_SAVE=%s. saved %s', keep_outputs_dir, ofn)
+                log.debug("## GALAXY_TEST_SAVE=%s. saved %s", keep_outputs_dir, ofn)
 
-        if mode == 'directory':
+        if mode == "directory":
             # if verifying a file inside a extra_files_path directory
             # filename already point to a file that exists on disk
             local_name = filename
         else:
             local_name = get_filename(filename)
 
-        compare = attributes.get('compare', 'diff')
+        compare = attributes.get("compare", "diff")
         try:
-            if attributes.get('ftype', None) in ['bam', 'qname_sorted.bam', 'qname_input_sorted.bam', 'unsorted.bam', 'cram']:
+            if attributes.get("ftype", None) in [
+                "bam",
+                "qname_sorted.bam",
+                "qname_input_sorted.bam",
+                "unsorted.bam",
+                "cram",
+            ]:
                 try:
                     local_fh, temp_name = _bam_to_sam(local_name, temp_name)
                     local_name = local_fh.name
                 except Exception as e:
                     log.warning("%s. Will compare BAM files", unicodify(e))
-            if compare == 'diff':
+            if compare == "diff":
                 files_diff(local_name, temp_name, attributes=attributes)
-            elif compare == 're_match':
+            elif compare == "re_match":
                 files_re_match(local_name, temp_name, attributes=attributes)
-            elif compare == 're_match_multiline':
+            elif compare == "re_match_multiline":
                 files_re_match_multiline(local_name, temp_name, attributes=attributes)
-            elif compare == 'sim_size':
+            elif compare == "sim_size":
                 files_delta(local_name, temp_name, attributes=attributes)
             elif compare == "contains":
                 files_contains(local_name, temp_name, attributes=attributes)
             else:
-                raise Exception(f'Unimplemented Compare type: {compare}')
+                raise Exception(f"Unimplemented Compare type: {compare}")
         except AssertionError as err:
-            errmsg = f'{item_label} different than expected, difference (using {compare}):\n'
+            errmsg = f"{item_label} different than expected, difference (using {compare}):\n"
             errmsg += f"( {local_name} v. {temp_name} )\n"
             errmsg += unicodify(err)
             raise AssertionError(errmsg)
         finally:
-            if 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
+            if "GALAXY_TEST_NO_CLEANUP" not in os.environ:
                 os.remove(temp_name)
 
     if verify_extra_files:
-        extra_files = attributes.get('extra_files', None)
+        extra_files = attributes.get("extra_files", None)
         if extra_files:
             verify_extra_files(extra_files)
 
@@ -176,20 +182,20 @@ def verify(
 def make_temp_fname(fname=None):
     """Safe temp name - preserve the file extension for tools that interpret it."""
     suffix = os.path.split(fname)[-1]  # ignore full path
-    with tempfile.NamedTemporaryFile(prefix='tmp', suffix=suffix, delete=False) as temp:
+    with tempfile.NamedTemporaryFile(prefix="tmp", suffix=suffix, delete=False) as temp:
         return temp.name
 
 
 def _bam_to_sam(local_name, temp_name):
-    temp_local = tempfile.NamedTemporaryFile(suffix='.sam', prefix='local_bam_converted_to_sam_')
-    with tempfile.NamedTemporaryFile(suffix='.sam', prefix='history_bam_converted_to_sam_', delete=False) as temp:
+    temp_local = tempfile.NamedTemporaryFile(suffix=".sam", prefix="local_bam_converted_to_sam_")
+    with tempfile.NamedTemporaryFile(suffix=".sam", prefix="history_bam_converted_to_sam_", delete=False) as temp:
         try:
-            pysam.view('-h', '--no-PG', '-o', temp_local.name, local_name, catch_stdout=False)
+            pysam.view("-h", "--no-PG", "-o", temp_local.name, local_name, catch_stdout=False)
         except Exception as e:
             msg = f"Converting local (test-data) BAM to SAM failed: {unicodify(e)}"
             raise Exception(msg)
         try:
-            pysam.view('-h', '--no-PG', '-o', temp.name, temp_name, catch_stdout=False)
+            pysam.view("-h", "--no-PG", "-o", temp.name, temp_name, catch_stdout=False)
         except Exception as e:
             msg = f"Converting history BAM to SAM failed: {unicodify(e)}"
             raise Exception(msg)
@@ -214,14 +220,18 @@ def files_delta(file1, file2, attributes=None):
     """Check the contents of 2 files for size differences."""
     if attributes is None:
         attributes = {}
-    delta = attributes.get('delta', DEFAULT_DELTA)
-    delta_frac = attributes.get('delta_frac', DEFAULT_DELTA_FRAC)
+    delta = attributes.get("delta", DEFAULT_DELTA)
+    delta_frac = attributes.get("delta_frac", DEFAULT_DELTA_FRAC)
     s1 = os.path.getsize(file1)
     s2 = os.path.getsize(file2)
     if abs(s1 - s2) > delta:
-        raise AssertionError('Files %s=%db but %s=%db - compare by size (delta=%s) failed' % (file1, s1, file2, s2, delta))
+        raise AssertionError(
+            "Files %s=%db but %s=%db - compare by size (delta=%s) failed" % (file1, s1, file2, s2, delta)
+        )
     if delta_frac is not None and not (s1 - (s1 * delta_frac) <= s2 <= s1 + (s1 * delta_frac)):
-        raise AssertionError('Files %s=%db but %s=%db - compare by size (delta_frac=%s) failed' % (file1, s1, file2, s2, delta_frac))
+        raise AssertionError(
+            "Files %s=%db but %s=%db - compare by size (delta_frac=%s) failed" % (file1, s1, file2, s2, delta_frac)
+        )
 
 
 def get_compressed_formats(attributes):
@@ -238,7 +248,9 @@ def files_diff(file1, file2, attributes=None):
     def get_lines_diff(diff):
         count = 0
         for line in diff:
-            if (line.startswith('+') and not line.startswith('+++')) or (line.startswith('-') and not line.startswith('---')):
+            if (line.startswith("+") and not line.startswith("+++")) or (
+                line.startswith("-") and not line.startswith("---")
+            ):
                 count += 1
         return count
 
@@ -251,22 +263,26 @@ def files_diff(file1, file2, attributes=None):
             with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
                 local_file = fh.readlines()
         except UnicodeDecodeError:
-            if file1.endswith('.pdf') or file2.endswith('.pdf'):
+            if file1.endswith(".pdf") or file2.endswith(".pdf"):
                 is_pdf = True
                 # Replace non-Unicode characters using unicodify(),
                 # difflib.unified_diff doesn't work on list of bytes
-                history_data = [unicodify(line) for line in get_fileobj(file2, mode='rb', compressed_formats=compressed_formats)]
-                local_file = [unicodify(line) for line in get_fileobj(file1, mode='rb', compressed_formats=compressed_formats)]
+                history_data = [
+                    unicodify(line) for line in get_fileobj(file2, mode="rb", compressed_formats=compressed_formats)
+                ]
+                local_file = [
+                    unicodify(line) for line in get_fileobj(file1, mode="rb", compressed_formats=compressed_formats)
+                ]
             else:
                 raise AssertionError("Binary data detected, not displaying diff")
-        if attributes.get('sort', False):
+        if attributes.get("sort", False):
             local_file.sort()
             history_data.sort()
-        allowed_diff_count = int(attributes.get('lines_diff', 0))
+        allowed_diff_count = int(attributes.get("lines_diff", 0))
         diff = list(difflib.unified_diff(local_file, history_data, "local_file", "history_data"))
         diff_lines = get_lines_diff(diff)
         if diff_lines > allowed_diff_count:
-            if 'GALAXY_TEST_RAW_DIFF' in os.environ:
+            if "GALAXY_TEST_RAW_DIFF" in os.environ:
                 diff_slice = diff
             else:
                 if len(diff) < 60:
@@ -282,14 +298,18 @@ def files_diff(file1, file2, attributes=None):
                 # PDF files contain creation dates, modification dates, ids and descriptions that change with each
                 # new file, so we need to handle these differences.  As long as the rest of the PDF file does
                 # not differ we're ok.
-                valid_diff_strs = ['description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator']
+                valid_diff_strs = ["description", "createdate", "creationdate", "moddate", "id", "producer", "creator"]
                 valid_diff = False
                 invalid_diff_lines = 0
                 for line in diff_slice:
                     # Make sure to lower case strings before checking.
                     line = line.lower()
                     # Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n'
-                    if (line.startswith('+') or line.startswith('-')) and line.find('local_file') < 0 and line.find('history_data') < 0:
+                    if (
+                        (line.startswith("+") or line.startswith("-"))
+                        and line.find("local_file") < 0
+                        and line.find("history_data") < 0
+                    ):
                         for vdf in valid_diff_strs:
                             if line.find(vdf) < 0:
                                 valid_diff = False
@@ -299,20 +319,26 @@ def files_diff(file1, file2, attributes=None):
                                 break
                         if not valid_diff:
                             invalid_diff_lines += 1
-                log.info("## files diff on '%s' and '%s': lines_diff = %d, found diff = %d, found pdf invalid diff = %d" % (file1, file2, allowed_diff_count, diff_lines, invalid_diff_lines))
+                log.info(
+                    "## files diff on '%s' and '%s': lines_diff = %d, found diff = %d, found pdf invalid diff = %d"
+                    % (file1, file2, allowed_diff_count, diff_lines, invalid_diff_lines)
+                )
                 if invalid_diff_lines > allowed_diff_count:
                     # Print out diff_slice so we can see what failed
                     log.info("###### diff_slice ######")
                     raise AssertionError("".join(diff_slice))
             else:
-                log.info("## files diff on '%s' and '%s': lines_diff = %d, found diff = %d" % (file1, file2, allowed_diff_count, diff_lines))
+                log.info(
+                    "## files diff on '%s' and '%s': lines_diff = %d, found diff = %d"
+                    % (file1, file2, allowed_diff_count, diff_lines)
+                )
                 raise AssertionError("".join(diff_slice))
 
 
 def files_re_match(file1, file2, attributes=None):
     """Check the contents of 2 files for differences using re.match."""
     attributes = attributes or {}
-    join_char = ''
+    join_char = ""
     to_strip = os.linesep
     compressed_formats = get_compressed_formats(attributes)
     try:
@@ -321,16 +347,19 @@ def files_re_match(file1, file2, attributes=None):
         with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
             local_file = fh.readlines()
     except UnicodeDecodeError:
-        join_char = b''
-        to_strip = os.linesep.encode('utf-8')
-        with open(file2, 'rb') as fh:
+        join_char = b""
+        to_strip = os.linesep.encode("utf-8")
+        with open(file2, "rb") as fh:
             history_data = fh.readlines()
-        with open(file1, 'rb') as fh:
+        with open(file1, "rb") as fh:
             local_file = fh.readlines()
-    assert len(local_file) == len(history_data), 'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), join_char.join(history_data[:40]))
-    if attributes.get('sort', False):
+    assert len(local_file) == len(history_data), (
+        "Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s"
+        % (len(local_file), len(history_data), join_char.join(history_data[:40]))
+    )
+    if attributes.get("sort", False):
         history_data.sort()
-    lines_diff = int(attributes.get('lines_diff', 0))
+    lines_diff = int(attributes.get("lines_diff", 0))
     line_diff_count = 0
     diffs = []
     for regex_line, data_line in zip(local_file, history_data):
@@ -338,15 +367,17 @@ def files_re_match(file1, file2, attributes=None):
         data_line = data_line.rstrip(to_strip)
         if not re.match(regex_line, data_line):
             line_diff_count += 1
-            diffs.append(f'Regular Expression: {regex_line}, Data file: {data_line}\n')
+            diffs.append(f"Regular Expression: {regex_line}, Data file: {data_line}\n")
     if line_diff_count > lines_diff:
-        raise AssertionError("Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs)))
+        raise AssertionError(
+            "Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs))
+        )
 
 
 def files_re_match_multiline(file1, file2, attributes=None):
     """Check the contents of 2 files for differences using re.match in multiline mode."""
     attributes = attributes or {}
-    join_char = ''
+    join_char = ""
     compressed_formats = get_compressed_formats(attributes)
     try:
         with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
@@ -354,12 +385,12 @@ def files_re_match_multiline(file1, file2, attributes=None):
         with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
             local_file = fh.read()
     except UnicodeDecodeError:
-        join_char = b''
-        with open(file2, 'rb') as fh:
+        join_char = b""
+        with open(file2, "rb") as fh:
             history_data = fh.readlines()
-        with open(file1, 'rb') as fh:
+        with open(file1, "rb") as fh:
             local_file = fh.read()
-    if attributes.get('sort', False):
+    if attributes.get("sort", False):
         history_data.sort()
     history_data = join_char.join(history_data)
     # lines_diff not applicable to multiline matching
@@ -378,12 +409,12 @@ def files_contains(file1, file2, attributes=None):
         with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
             local_file = fh.readlines()
     except UnicodeDecodeError:
-        to_strip = os.linesep.encode('utf-8')
-        with open(file2, 'rb') as fh:
+        to_strip = os.linesep.encode("utf-8")
+        with open(file2, "rb") as fh:
             history_data = fh.read()
-        with open(file1, 'rb') as fh:
+        with open(file1, "rb") as fh:
             local_file = fh.readlines()
-    lines_diff = int(attributes.get('lines_diff', 0))
+    lines_diff = int(attributes.get("lines_diff", 0))
     line_diff_count = 0
     for contains in local_file:
         contains = contains.rstrip(to_strip)
diff --git a/lib/galaxy/tool_util/verify/asserts/__init__.py b/lib/galaxy/tool_util/verify/asserts/__init__.py
index df54c4cdbbf..58b38debbf0 100644
--- a/lib/galaxy/tool_util/verify/asserts/__init__.py
+++ b/lib/galaxy/tool_util/verify/asserts/__init__.py
@@ -1,12 +1,15 @@
 import logging
 import sys
-from inspect import getfullargspec, getmembers
+from inspect import (
+    getfullargspec,
+    getmembers,
+)
 
 from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
-assertion_module_names = ['text', 'tabular', 'xml', 'hdf5', 'archive', 'size']
+assertion_module_names = ["text", "tabular", "xml", "hdf5", "archive", "size"]
 
 # Code for loading modules containing assertion checking functions, to
 # create a new module of assertion functions, create the needed python
@@ -20,7 +23,7 @@ for assertion_module_name in assertion_module_names:
         __import__(full_assertion_module_name)
         assertion_module = sys.modules[full_assertion_module_name]
     except Exception:
-        log.exception('Failed to load assertion module: %s', assertion_module_name)
+        log.exception("Failed to load assertion module: %s", assertion_module_name)
         continue
     for member, value in getmembers(assertion_module):
         if member.startswith("assert_"):
@@ -28,8 +31,8 @@ for assertion_module_name in assertion_module_names:
 
 
 def verify_assertions(data, assertion_description_list):
-    """ This function takes a list of assertions and a string to check
-    these assertions against. """
+    """This function takes a list of assertions and a string to check
+    these assertions against."""
     for assertion_description in assertion_description_list:
         verify_assertion(data, assertion_description)
 
diff --git a/lib/galaxy/tool_util/verify/asserts/_util.py b/lib/galaxy/tool_util/verify/asserts/_util.py
index 98d63e74a5b..c8f6281c760 100644
--- a/lib/galaxy/tool_util/verify/asserts/_util.py
+++ b/lib/galaxy/tool_util/verify/asserts/_util.py
@@ -21,7 +21,9 @@ def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text):
     if n is not None:
         n_bytes = parse_bytesize(n)
         delta_bytes = parse_bytesize(delta)
-        assert (not negate) == (abs(count - n_bytes) <= delta_bytes), n_text.format(expected=expected, n=n, delta=delta, text="{text}", output="{output}") + f" found {count}"
+        assert (not negate) == (abs(count - n_bytes) <= delta_bytes), (
+            n_text.format(expected=expected, n=n, delta=delta, text="{text}", output="{output}") + f" found {count}"
+        )
     if min is not None or max is not None:
         if min is None:
             min = -inf  # also replacing min/max for output
@@ -33,10 +35,15 @@ def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text):
             max_bytes = inf
         else:
             max_bytes = parse_bytesize(max)
-        assert (not negate) == (min_bytes <= count <= max_bytes), min_max_text.format(expected=expected, min=min, max=max, text="{text}", output="{output}") + f" found {count}"
+        assert (not negate) == (min_bytes <= count <= max_bytes), (
+            min_max_text.format(expected=expected, min=min, max=max, text="{text}", output="{output}")
+            + f" found {count}"
+        )
 
 
-def _assert_presence_number(output, text, n, delta, min, max, negate, check_presence_foo, count_foo, presence_text, n_text, min_max_text):
+def _assert_presence_number(
+    output, text, n, delta, min, max, negate, check_presence_foo, count_foo, presence_text, n_text, min_max_text
+):
     """
     helper function to assert that
     - text is present in output using check_presence_foo
@@ -51,7 +58,9 @@ def _assert_presence_number(output, text, n, delta, min, max, negate, check_pres
     negate = asbool(negate)
     expected = "Expected" if not negate else "Did not expect"
     if n is None and min is None and max is None:
-        assert (not negate) == check_presence_foo(output, text), presence_text.format(expected=expected, output=output, text=text)
+        assert (not negate) == check_presence_foo(output, text), presence_text.format(
+            expected=expected, output=output, text=text
+        )
     try:
         _assert_number(count_foo(output, text), n, delta, min, max, negate, n_text, min_max_text)
     except AssertionError as e:
diff --git a/lib/galaxy/tool_util/verify/asserts/archive.py b/lib/galaxy/tool_util/verify/asserts/archive.py
index fd5caa58f77..e119ce5a3b4 100644
--- a/lib/galaxy/tool_util/verify/asserts/archive.py
+++ b/lib/galaxy/tool_util/verify/asserts/archive.py
@@ -10,7 +10,7 @@ from ._util import _assert_presence_number
 
 def _extract_from_tar(bytes, fn):
     with io.BytesIO(bytes) as temp:
-        with tarfile.open(fileobj=temp, mode='r') as tar_temp:
+        with tarfile.open(fileobj=temp, mode="r") as tar_temp:
             ti = tar_temp.getmember(fn)
             # zip treats directories like empty files.
             # so make this consistent for tar
@@ -23,7 +23,7 @@ def _extract_from_tar(bytes, fn):
 def _list_from_tar(bytes, path):
     lst = list()
     with io.BytesIO(bytes) as temp:
-        with tarfile.open(fileobj=temp, mode='r') as tar_temp:
+        with tarfile.open(fileobj=temp, mode="r") as tar_temp:
             for fn in tar_temp.getnames():
                 if not re.match(path, fn):
                     continue
@@ -33,7 +33,7 @@ def _list_from_tar(bytes, path):
 
 def _extract_from_zip(bytes, fn):
     with io.BytesIO(bytes) as temp:
-        with zipfile.ZipFile(temp, mode='r') as zip_temp:
+        with zipfile.ZipFile(temp, mode="r") as zip_temp:
             with zip_temp.open(fn) as member_fh:
                 return member_fh.read()
 
@@ -41,7 +41,7 @@ def _extract_from_zip(bytes, fn):
 def _list_from_zip(bytes, path):
     lst = list()
     with io.BytesIO(bytes) as temp:
-        with zipfile.ZipFile(temp, mode='r') as zip_temp:
+        with zipfile.ZipFile(temp, mode="r") as zip_temp:
             for fn in zip_temp.namelist():
                 if not re.match(path, fn):
                     continue
@@ -49,8 +49,19 @@ def _list_from_zip(bytes, path):
     return sorted(lst)
 
 
-def assert_has_archive_member(output_bytes, path, verify_assertions_function, children, all="false", n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
-    """ Recursively checks the specified children assertions against the text of
+def assert_has_archive_member(
+    output_bytes,
+    path,
+    verify_assertions_function,
+    children,
+    all="false",
+    n: int = None,
+    delta: int = 0,
+    min: int = None,
+    max: int = None,
+    negate: bool = False,
+):
+    """Recursively checks the specified children assertions against the text of
     the first element matching the specified path found within the archive.
     Currently supported formats: .zip, .tar, .tar.gz."""
     all = asbool(all)
@@ -72,12 +83,20 @@ def assert_has_archive_member(output_bytes, path, verify_assertions_function, ch
     # min, max (slightly abusing the output and text as well as the function
     # parameters)
     fns = list_foo(output_bytes, path)
-    _assert_presence_number(None, path, n, delta, min, max, negate,
+    _assert_presence_number(
+        None,
+        path,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         lambda o, t: len(fns) > 0,
         lambda o, t: len(fns),
         "{expected} path '{text}' in archive",
         "{expected} {n}+-{delta} matches for path '{text}' in archive",
-        "{expected} that the number of matches for path '{text}' in archive is in [{min}:{max}]")
+        "{expected} that the number of matches for path '{text}' in archive is in [{min}:{max}]",
+    )
 
     # check sub-assertions on members matching path
     for fn in fns:
diff --git a/lib/galaxy/tool_util/verify/asserts/hdf5.py b/lib/galaxy/tool_util/verify/asserts/hdf5.py
index e273aa1ae53..8eab9f74794 100644
--- a/lib/galaxy/tool_util/verify/asserts/hdf5.py
+++ b/lib/galaxy/tool_util/verify/asserts/hdf5.py
@@ -18,16 +18,17 @@ def assert_has_h5_attribute(output_bytes, key, value):
     attribute"""
     _assert_h5py()
     output_temp = io.BytesIO(output_bytes)
-    local_attrs = h5py.File(output_temp, 'r').attrs
-    assert key in local_attrs and str(local_attrs[key]) == value, (
-        f"Not a HDF5 file or H5 attributes do not match:\n\t{list(local_attrs.items())}\n\n\t({key} : {value})")
+    local_attrs = h5py.File(output_temp, "r").attrs
+    assert (
+        key in local_attrs and str(local_attrs[key]) == value
+    ), f"Not a HDF5 file or H5 attributes do not match:\n\t{list(local_attrs.items())}\n\n\t({key} : {value})"
 
 
 # TODO the function actually queries groups. so the function and argument name are misleading
 def assert_has_h5_keys(output_bytes, keys):
-    """ Asserts the specified HDF5 output has the given keys."""
+    """Asserts the specified HDF5 output has the given keys."""
     _assert_h5py()
-    keys = [k.strip() for k in keys.strip().split(',')]
+    keys = [k.strip() for k in keys.strip().split(",")]
     h5_keys = sorted(keys)
     output_temp = io.BytesIO(output_bytes)
     local_keys = []
@@ -35,7 +36,8 @@ def assert_has_h5_keys(output_bytes, keys):
     def append_keys(key):
         local_keys.append(key)
         return None
-    h5py.File(output_temp, 'r').visit(append_keys)
+
+    h5py.File(output_temp, "r").visit(append_keys)
     missing = 0
     for key in h5_keys:
         if key not in local_keys:
diff --git a/lib/galaxy/tool_util/verify/asserts/size.py b/lib/galaxy/tool_util/verify/asserts/size.py
index 2e16d041f37..f40afee9558 100644
--- a/lib/galaxy/tool_util/verify/asserts/size.py
+++ b/lib/galaxy/tool_util/verify/asserts/size.py
@@ -1,12 +1,21 @@
 from ._util import _assert_number
 
 
-def assert_has_size(output_bytes, value: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
+def assert_has_size(
+    output_bytes, value: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+):
     """
     Asserts the specified output has a size of the specified value,
     allowing for absolute (delta) and relative (delta_frac) difference.
     """
     output_size = len(output_bytes)
-    _assert_number(output_size, value, delta, min, max, negate,
+    _assert_number(
+        output_size,
+        value,
+        delta,
+        min,
+        max,
+        negate,
         "{expected} file size of {n}+-{delta}",
-        "{expected} file size to be in [{min}:{max}]")
+        "{expected} file size to be in [{min}:{max}]",
+    )
diff --git a/lib/galaxy/tool_util/verify/asserts/tabular.py b/lib/galaxy/tool_util/verify/asserts/tabular.py
index c16fe6f4732..9c686a10945 100644
--- a/lib/galaxy/tool_util/verify/asserts/tabular.py
+++ b/lib/galaxy/tool_util/verify/asserts/tabular.py
@@ -17,13 +17,22 @@ def get_first_line(output, comment):
         return match.group(1)
 
 
-def assert_has_n_columns(output, n: int = None, delta: int = 0, min: int = None, max: int = None, sep='\t', comment="", negate: bool = False):
-    """ Asserts the tabular output contains n columns. The optional
+def assert_has_n_columns(
+    output, n: int = None, delta: int = 0, min: int = None, max: int = None, sep="\t", comment="", negate: bool = False
+):
+    """Asserts the tabular output contains n columns. The optional
     sep argument specifies the column seperator used to determine the
     number of columns. The optional comment argument specifies
     comment characters"""
     first_line = get_first_line(output, comment)
     n_columns = len(first_line.split(sep))
-    _assert_number(n_columns, n, delta, min, max, negate,
+    _assert_number(
+        n_columns,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         "{expected} {n}+-{delta} columns in output",
-        "{expected} the number of columns in output to be in [{min}:{max}]")
+        "{expected} the number of columns in output to be in [{min}:{max}]",
+    )
diff --git a/lib/galaxy/tool_util/verify/asserts/text.py b/lib/galaxy/tool_util/verify/asserts/text.py
index 6215fa26bc5..155df596498 100644
--- a/lib/galaxy/tool_util/verify/asserts/text.py
+++ b/lib/galaxy/tool_util/verify/asserts/text.py
@@ -1,39 +1,62 @@
 import re
 
-from ._util import _assert_number, _assert_presence_number
+from ._util import (
+    _assert_number,
+    _assert_presence_number,
+)
 
 
-def assert_has_text(output, text, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
-    """ Asserts specified output contains the substring specified by
+def assert_has_text(
+    output, text, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+):
+    """Asserts specified output contains the substring specified by
     the argument text. The exact number of occurrences can be
     optionally specified by the argument n"""
     assert output is not None, "Checking has_text assertion on empty output (None)"
-    _assert_presence_number(output, text, n, delta, min, max, negate,
+    _assert_presence_number(
+        output,
+        text,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         lambda o, t: o.find(t) >= 0,
         lambda o, t: len(re.findall(re.escape(t), o)),
         "{expected} text '{text}' in output ('{output}')",
         "{expected} {n}+-{delta} occurences of '{text}' in output ('{output}')",
-        "{expected} that the number of occurences of '{text}' in output is in [{min}:{max}] ('{output}')")
+        "{expected} that the number of occurences of '{text}' in output is in [{min}:{max}] ('{output}')",
+    )
 
 
 def assert_not_has_text(output, text):
-    """ Asserts specified output does not contain the substring
+    """Asserts specified output does not contain the substring
     specified by the argument text"""
     assert output is not None, "Checking not_has_text assertion on empty output (None)"
     assert output.find(text) < 0, f"Output file contains unexpected text '{text}'"
 
 
-def assert_has_line(output, line, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
-    """ Asserts the specified output contains the line specified by the
+def assert_has_line(
+    output, line, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+):
+    """Asserts the specified output contains the line specified by the
     argument line. The exact number of occurrences can be optionally
     specified by the argument n"""
     assert output is not None, "Checking has_line assertion on empty output (None)"
-    _assert_presence_number(output, line, n, delta, min, max, negate,
+    _assert_presence_number(
+        output,
+        line,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         lambda o, l: re.search(f"^{re.escape(l)}$", o, flags=re.MULTILINE) is not None,
         lambda o, l: len(re.findall(f"^{re.escape(l)}$", o, flags=re.MULTILINE)),
         "{expected} line '{text}' in output ('{output}')",
         "{expected} {n}+-{delta} lines '{text}' in output ('{output}')",
-        "{expected} that the number of lines '{text}' in output is in [{min}:{max}] ('{output}')")
+        "{expected} that the number of lines '{text}' in output is in [{min}:{max}] ('{output}')",
+    )
 
 
 def assert_has_n_lines(output, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
@@ -42,32 +65,59 @@ def assert_has_n_lines(output, n: int = None, delta: int = 0, min: int = None, m
     or relative differebce in the number of lines"""
     assert output is not None, "Checking has_n_lines assertion on empty output (None)"
     count = len(output.splitlines())
-    _assert_number(count, n, delta, min, max, negate,
+    _assert_number(
+        count,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         "{expected} {n}+-{delta} lines in the output",
-        "{expected} the number of line to be in [{min}:{max}]")
+        "{expected} the number of line to be in [{min}:{max}]",
+    )
 
 
-def assert_has_text_matching(output, expression, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
-    """ Asserts the specified output contains text matching the
+def assert_has_text_matching(
+    output, expression, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+):
+    """Asserts the specified output contains text matching the
     regular expression specified by the argument expression.
     If n is given the assertion checks for exacly n (nonoverlapping)
     occurences.
     """
-    _assert_presence_number(output, expression, n, delta, min, max, negate,
+    _assert_presence_number(
+        output,
+        expression,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         lambda o, e: re.search(e, o) is not None,
         lambda o, e: len(re.findall(e, o)),
         "{expected} text matching expression '{text}' in output ('{output}')",
         "{expected} {n}+-{delta} (non-overlapping) matches for '{text}' in output ('{output}')",
-        "{expected} that the number of (non-overlapping) matches for '{text}' in output is in [{min}:{max}] ('{output}')")
+        "{expected} that the number of (non-overlapping) matches for '{text}' in output is in [{min}:{max}] ('{output}')",
+    )
 
 
-def assert_has_line_matching(output, expression, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
-    """ Asserts the specified output contains a line matching the
+def assert_has_line_matching(
+    output, expression, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+):
+    """Asserts the specified output contains a line matching the
     regular expression specified by the argument expression. If n is given
     the assertion checks for exactly n occurences."""
-    _assert_presence_number(output, expression, n, delta, min, max, negate,
+    _assert_presence_number(
+        output,
+        expression,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         lambda o, e: re.search(f"^{e}$", o, flags=re.MULTILINE) is not None,
         lambda o, e: len(re.findall(f"^{e}$", o, flags=re.MULTILINE)),
         "{expected} line matching expression '{text}' in output ('{output}')",
         "{expected} {n}+-{delta} lines matching for '{text}' in output ('{output}')",
-        "{expected} that the number of lines matching for '{text}' in output is in [{min}:{max}] ('{output}')")
+        "{expected} that the number of lines matching for '{text}' in output is in [{min}:{max}] ('{output}')",
+    )
diff --git a/lib/galaxy/tool_util/verify/asserts/xml.py b/lib/galaxy/tool_util/verify/asserts/xml.py
index b8842384b4f..26acacd6bee 100644
--- a/lib/galaxy/tool_util/verify/asserts/xml.py
+++ b/lib/galaxy/tool_util/verify/asserts/xml.py
@@ -11,7 +11,7 @@ from galaxy.util import (
 
 
 def assert_is_valid_xml(output):
-    """ Simple assertion that just verifies the specified output
+    """Simple assertion that just verifies the specified output
     is valid XML."""
     try:
         parse_xml_string(output)
@@ -20,52 +20,66 @@ def assert_is_valid_xml(output):
 
 
 def assert_has_element_with_path(output, path, negate: bool = False):
-    """ Asserts the specified output has at least one XML element with a
+    """Asserts the specified output has at least one XML element with a
     path matching the specified path argument. Valid paths are the
     simplified subsets of XPath implemented by lxml.etree;
     https://lxml.de/xpathxslt.html for more information."""
     assert_xml_element(output, path, negate=negate)
 
 
-def assert_has_n_elements_with_path(output, path, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
-    """ Asserts the specified output has exactly n elements matching the
+def assert_has_n_elements_with_path(
+    output, path, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+):
+    """Asserts the specified output has exactly n elements matching the
     path specified."""
     assert_xml_element(output, path, n=n, delta=delta, min=min, max=max, negate=negate)
 
 
 def assert_element_text_matches(output, path, expression, negate: bool = False):
-    """ Asserts the text of the first element matching the specified
+    """Asserts the text of the first element matching the specified
     path matches the specified regular expression."""
-    sub = {"tag": "has_text_matching", 'attributes': {'expression': expression, 'negate': negate}}
+    sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub])
 
 
 def assert_element_text_is(output, path, text, negate: bool = False):
-    """ Asserts the text of the first element matching the specified
-    path matches exactly the specified text. """
+    """Asserts the text of the first element matching the specified
+    path matches exactly the specified text."""
     assert_element_text_matches(output, path, re.escape(text) + "$", negate=negate)
 
 
 def assert_attribute_matches(output, path, attribute, expression, negate: bool = False):
-    """ Asserts the specified attribute of the first element matching
+    """Asserts the specified attribute of the first element matching
     the specified path matches the specified regular expression."""
-    sub = {"tag": "has_text_matching", 'attributes': {'expression': expression, 'negate': negate}}
+    sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub], attribute=attribute)
 
 
 def assert_attribute_is(output, path, attribute, text, negate: bool = False):
-    """ Asserts the specified attribute of the first element matching
+    """Asserts the specified attribute of the first element matching
     the specified path matches exactly the specified text."""
     assert_attribute_matches(output, path, attribute, re.escape(text) + "$", negate=negate)
 
 
 def assert_element_text(output, path, verify_assertions_function, children, negate: bool = False):
-    """ Recursively checks the specified assertions against the text of
+    """Recursively checks the specified assertions against the text of
     the first element matching the specified path."""
     assert_xml_element(output, path, verify_assertions_function, children, negate=negate)
 
 
-def assert_xml_element(output, path, verify_assertions_function=None, children=None, attribute=None, all=False, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
+def assert_xml_element(
+    output,
+    path,
+    verify_assertions_function=None,
+    children=None,
+    attribute=None,
+    all=False,
+    n: int = None,
+    delta: int = 0,
+    min: int = None,
+    max: int = None,
+    negate: bool = False,
+):
     """
     Check if path occurs in the xml. If n and delta or min and max are given
     also the number of occurences is checked.
@@ -79,12 +93,20 @@ def assert_xml_element(output, path, verify_assertions_function=None, children=N
     # assert that path is in output (the specified number of times)
 
     xml = parse_xml_string(output)
-    asserts._util._assert_presence_number(xml, path, n, delta, min, max, negate,
+    asserts._util._assert_presence_number(
+        xml,
+        path,
+        n,
+        delta,
+        min,
+        max,
+        negate,
         lambda x, p: x.find(p) is not None,
         lambda x, p: len(x.findall(p)),
         "{expected} path '{text}' in xml",
         "{expected} {n}+-{delta} occurrences of path '{text}' in xml",
-        "{expected} that the number of occurences of path '{text}' in xml is in [{min}:{max}]")
+        "{expected} that the number of occurences of path '{text}' in xml is in [{min}:{max}]",
+    )
 
     # check sub-assertions
     if len(children) == 0 or verify_assertions_function is None:
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 035f50cfd3f..9673081ba3c 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -13,15 +13,22 @@ from json import dumps
 from logging import getLogger
 
 import requests
-from packaging.version import parse as parse_version, Version
+from packaging.version import parse as parse_version
+from packaging.version import Version
+
 try:
     from nose.tools import nottest
 except ImportError:
+
     def nottest(x):
         return x
 
+
 from galaxy import util
-from galaxy.tool_util.parser.interface import TestCollectionDef, TestCollectionOutputDef
+from galaxy.tool_util.parser.interface import (
+    TestCollectionDef,
+    TestCollectionOutputDef,
+)
 from galaxy.util.bunch import Bunch
 from . import verify
 from .asserts import verify_assertions
@@ -37,7 +44,7 @@ UPLOAD_ASYNC = util.asbool(os.environ.get("GALAXY_TEST_UPLOAD_ASYNC", True))
 ERROR_MESSAGE_DATASET_SEP = "--------------------------------------"
 DEFAULT_TOOL_TEST_WAIT = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400))
 
-DEFAULT_FTYPE = 'auto'
+DEFAULT_FTYPE = "auto"
 # This following default dbkey was traditionally hg17 before Galaxy 18.05,
 # restore this behavior by setting GALAXY_TEST_DEFAULT_DBKEY to hg17.
 DEFAULT_DBKEY = os.environ.get("GALAXY_TEST_DEFAULT_DBKEY", "?")
@@ -60,7 +67,15 @@ class OutputsDict(dict):
             return super().__getitem__(item)
 
 
-def stage_data_in_history(galaxy_interactor, tool_id, all_test_data, history=None, force_path_paste=False, maxseconds=DEFAULT_TOOL_TEST_WAIT, tool_version=None):
+def stage_data_in_history(
+    galaxy_interactor,
+    tool_id,
+    all_test_data,
+    history=None,
+    force_path_paste=False,
+    maxseconds=DEFAULT_TOOL_TEST_WAIT,
+    tool_version=None,
+):
     # Upload any needed files
     upload_waits = []
 
@@ -68,33 +83,40 @@ def stage_data_in_history(galaxy_interactor, tool_id, all_test_data, history=Non
 
     if UPLOAD_ASYNC:
         for test_data in all_test_data:
-            upload_waits.append(galaxy_interactor.stage_data_async(test_data,
-                                                                   history,
-                                                                   tool_id,
-                                                                   force_path_paste=force_path_paste,
-                                                                   maxseconds=maxseconds,
-                                                                   tool_version=tool_version))
+            upload_waits.append(
+                galaxy_interactor.stage_data_async(
+                    test_data,
+                    history,
+                    tool_id,
+                    force_path_paste=force_path_paste,
+                    maxseconds=maxseconds,
+                    tool_version=tool_version,
+                )
+            )
         for upload_wait in upload_waits:
             upload_wait()
     else:
         for test_data in all_test_data:
-            upload_wait = galaxy_interactor.stage_data_async(test_data,
-                                                             history,
-                                                             tool_id,
-                                                             force_path_paste=force_path_paste,
-                                                             maxseconds=maxseconds,
-                                                             tool_version=tool_version)
+            upload_wait = galaxy_interactor.stage_data_async(
+                test_data,
+                history,
+                tool_id,
+                force_path_paste=force_path_paste,
+                maxseconds=maxseconds,
+                tool_version=tool_version,
+            )
             upload_wait()
 
 
 class GalaxyInteractorApi:
-
     def __init__(self, **kwds):
         self.api_url = f"{kwds['galaxy_url'].rstrip('/')}/api"
         self.cookies = None
         self.master_api_key = kwds["master_api_key"]
-        self.api_key = self.__get_user_key(kwds.get("api_key"), kwds.get("master_api_key"), test_user=kwds.get("test_user"))
-        if kwds.get('user_api_key_is_admin_key', False):
+        self.api_key = self.__get_user_key(
+            kwds.get("api_key"), kwds.get("master_api_key"), test_user=kwds.get("test_user")
+        )
+        if kwds.get("user_api_key_is_admin_key", False):
             self.master_api_key = self.api_key
         self.keep_outputs_dir = kwds["keep_outputs_dir"]
         self.download_attempts = kwds.get("download_attempts", 1)
@@ -109,7 +131,7 @@ class GalaxyInteractorApi:
     @property
     def target_galaxy_version(self):
         if self._target_galaxy_version is None:
-            self._target_galaxy_version = parse_version(self._get('version').json()['version_major'])
+            self._target_galaxy_version = parse_version(self._get("version").json()["version_major"])
         return self._target_galaxy_version
 
     @property
@@ -136,13 +158,17 @@ class GalaxyInteractorApi:
 
     def get_tool_tests(self, tool_id, tool_version=None):
         url = f"tools/{tool_id}/test_data"
-        params = {'tool_version': tool_version} if tool_version else None
+        params = {"tool_version": tool_version} if tool_version else None
         response = self._get(url, data=params)
         assert response.status_code == 200, f"Non 200 response from tool test API. [{response.content}]"
         return response.json()
 
-    def verify_output_collection(self, output_collection_def, output_collection_id, history, tool_id, tool_version=None):
-        data_collection = self._get(f"dataset_collections/{output_collection_id}", data={"instance_type": "history"}).json()
+    def verify_output_collection(
+        self, output_collection_def, output_collection_id, history, tool_id, tool_version=None
+    ):
+        data_collection = self._get(
+            f"dataset_collections/{output_collection_id}", data={"instance_type": "history"}
+        ).json()
 
         def verify_dataset(element, element_attrib, element_outfile):
             hda = element["object"]
@@ -156,7 +182,9 @@ class GalaxyInteractorApi:
                     tool_version=tool_version,
                 )
             except AssertionError as e:
-                raise AssertionError(f"Collection element {element.get('element_identifier', '')} of collection {output_collection_def.name}: {e}")
+                raise AssertionError(
+                    f"Collection element {element.get('element_identifier', '')} of collection {output_collection_def.name}: {e}"
+                )
 
         verify_collection(output_collection_def, data_collection, verify_dataset)
 
@@ -169,11 +197,18 @@ class GalaxyInteractorApi:
         hid = self.__output_id(output_data)
         # TODO: Twill version verifies dataset is 'ok' in here.
         try:
-            self.verify_output_dataset(history_id=history_id, hda_id=hid, outfile=outfile, attributes=attributes, tool_id=tool_id, tool_version=tool_version)
+            self.verify_output_dataset(
+                history_id=history_id,
+                hda_id=hid,
+                outfile=outfile,
+                attributes=attributes,
+                tool_id=tool_id,
+                tool_version=tool_version,
+            )
         except AssertionError as e:
             raise AssertionError(f"Output {name}: {str(e)}")
 
-        primary_datasets = attributes.get('primary_datasets', {})
+        primary_datasets = attributes.get("primary_datasets", {})
         if primary_datasets:
             job_id = self._dataset_provenance(history_id, hid)["job_id"]
             outputs = self._get(f"jobs/{job_id}/outputs").json()
@@ -181,22 +216,31 @@ class GalaxyInteractorApi:
         for designation, (primary_outfile, primary_attributes) in primary_datasets.items():
             primary_output = None
             for output in outputs:
-                if output["name"] == f'__new_primary_file_{name}|{designation}__':
+                if output["name"] == f"__new_primary_file_{name}|{designation}__":
                     primary_output = output
                     break
 
             if not primary_output:
-                raise Exception(f"Failed to find primary dataset with designation [{designation}] for output with name [{name}]")
+                raise Exception(
+                    f"Failed to find primary dataset with designation [{designation}] for output with name [{name}]"
+                )
 
             primary_hda_id = primary_output["dataset"]["id"]
             try:
-                self.verify_output_dataset(history_id, primary_hda_id, primary_outfile, primary_attributes, tool_id=tool_id, tool_version=tool_version)
+                self.verify_output_dataset(
+                    history_id,
+                    primary_hda_id,
+                    primary_outfile,
+                    primary_attributes,
+                    tool_id=tool_id,
+                    tool_version=tool_version,
+                )
             except AssertionError as e:
                 raise AssertionError(f"Primary output {name}: {str(e)}")
 
     def wait_for_jobs(self, history_id, jobs, maxseconds):
         for job in jobs:
-            self.wait_for_job(job['id'], history_id, maxseconds)
+            self.wait_for_job(job["id"], history_id, maxseconds)
 
     def verify_output_dataset(self, history_id, hda_id, outfile, attributes, tool_id, tool_version=None):
         fetcher = self.__dataset_fetcher(history_id)
@@ -207,7 +251,7 @@ class GalaxyInteractorApi:
             attributes=attributes,
             dataset_fetcher=fetcher,
             test_data_downloader=test_data_downloader,
-            keep_outputs_dir=self.keep_outputs_dir
+            keep_outputs_dir=self.keep_outputs_dir,
         )
         self._verify_metadata(history_id, hda_id, attributes)
 
@@ -218,16 +262,16 @@ class GalaxyInteractorApi:
         `dbkey` and `tags` all map to the API description directly. Other metadata attributes
         are assumed to be datatype-specific and mapped with a prefix of `metadata_`.
         """
-        metadata = attributes.get('metadata', {}).copy()
+        metadata = attributes.get("metadata", {}).copy()
         for key in metadata.copy().keys():
-            if key not in ['name', 'info', 'tags', 'created_from_basename']:
+            if key not in ["name", "info", "tags", "created_from_basename"]:
                 new_key = f"metadata_{key}"
                 metadata[new_key] = metadata[key]
                 del metadata[key]
             elif key == "info":
                 metadata["misc_info"] = metadata["info"]
                 del metadata["info"]
-        expected_file_type = attributes.get('ftype', None)
+        expected_file_type = attributes.get("ftype", None)
         if expected_file_type:
             metadata["file_ext"] = expected_file_type
 
@@ -241,7 +285,7 @@ class GalaxyInteractorApi:
                 except requests.exceptions.HTTPError:
                     return None
 
-            dataset = wait_on(wait_for_content, desc='dataset metadata', timeout=10)
+            dataset = wait_on(wait_for_content, desc="dataset metadata", timeout=10)
 
             for key, value in metadata.items():
                 try:
@@ -268,7 +312,7 @@ class GalaxyInteractorApi:
     def wait_for_job(self, job_id, history_id=None, maxseconds=DEFAULT_TOOL_TEST_WAIT):
         self.wait_for(lambda: self.__job_ready(job_id, history_id), maxseconds=maxseconds)
 
-    def wait_for(self, func, what='tool test run', **kwd):
+    def wait_for(self, func, what="tool test run", **kwd):
         walltime_exceeded = int(kwd.get("maxseconds", DEFAULT_TOOL_TEST_WAIT))
         wait_on(func, what, walltime_exceeded)
 
@@ -277,12 +321,12 @@ class GalaxyInteractorApi:
         return job_stdio
 
     def __get_job(self, job_id):
-        return self._get(f'jobs/{job_id}')
+        return self._get(f"jobs/{job_id}")
 
     def __get_job_stdio(self, job_id):
-        return self._get(f'jobs/{job_id}?full=true')
+        return self._get(f"jobs/{job_id}?full=true")
 
-    def get_history(self, history_name='test_history'):
+    def get_history(self, history_name="test_history"):
         # Return the most recent non-deleted history matching the provided name
         response = self._get(f"histories?q=name&qv={history_name}&order=update_time")
         try:
@@ -290,39 +334,41 @@ class GalaxyInteractorApi:
         except IndexError:
             return None
 
-    def new_history(self, history_name='test_history', publish_history=False):
+    def new_history(self, history_name="test_history", publish_history=False):
         create_response = self._post("histories", {"name": history_name})
         try:
             create_response.raise_for_status()
         except Exception as e:
             raise Exception(f"Error occured while creating history with name '{history_name}': {e}")
-        history_id = create_response.json()['id']
+        history_id = create_response.json()["id"]
         if publish_history:
             self.publish_history(history_id)
         return history_id
 
     def publish_history(self, history_id):
-        response = self._put(f'histories/{history_id}', json.dumps({'published': True}))
+        response = self._put(f"histories/{history_id}", json.dumps({"published": True}))
         response.raise_for_status()
 
     @nottest
     def test_data_path(self, tool_id, filename, tool_version=None):
-        version_fragment = f'&tool_version={tool_version}' if tool_version else ''
+        version_fragment = f"&tool_version={tool_version}" if tool_version else ""
         response = self._get(f"tools/{tool_id}/test_data_path?filename={filename}{version_fragment}", admin=True)
         return response.json()
 
     @nottest
-    def test_data_download(self, tool_id, filename, mode='file', is_output=True, tool_version=None):
+    def test_data_download(self, tool_id, filename, mode="file", is_output=True, tool_version=None):
         result = None
         local_path = None
 
         if self.supports_test_data_download:
-            version_fragment = f'&tool_version={tool_version}' if tool_version else ''
-            response = self._get(f"tools/{tool_id}/test_data_download?filename={filename}{version_fragment}", admin=True)
+            version_fragment = f"&tool_version={tool_version}" if tool_version else ""
+            response = self._get(
+                f"tools/{tool_id}/test_data_download?filename={filename}{version_fragment}", admin=True
+            )
             if response.status_code == 200:
-                if mode == 'file':
+                if mode == "file":
                     result = response.content
-                elif mode == 'directory':
+                elif mode == "directory":
                     prefix = os.path.basename(filename)
                     path = tempfile.mkdtemp(prefix=prefix)
                     fileobj = io.BytesIO(response.content)
@@ -345,10 +391,10 @@ class GalaxyInteractorApi:
                     break
 
         if result is None and local_path is not None and os.path.exists(local_path):
-            if mode == 'file':
-                with open(local_path, mode='rb') as f:
+            if mode == "file":
+                with open(local_path, mode="rb") as f:
                     result = f.read()
-            elif mode == 'directory':
+            elif mode == "directory":
                 # Make a copy, since we are going to clean up the returned path
                 path = tempfile.mkdtemp()
                 shutil.copytree(local_path, path)
@@ -356,7 +402,9 @@ class GalaxyInteractorApi:
 
         if result is None:
             if is_output:
-                raise AssertionError(f"Test output file ({filename}) is missing. If you are using planemo, try adding --update_test_data to generate it.")
+                raise AssertionError(
+                    f"Test output file ({filename}) is missing. If you are using planemo, try adding --update_test_data to generate it."
+                )
             else:
                 raise AssertionError(f"Test input file ({filename}) cannot be found.")
 
@@ -366,65 +414,79 @@ class GalaxyInteractorApi:
         # Allow data structure coming out of tools API - {id: <id>, output_name: <name>, etc...}
         # or simple id as comes out of workflow API.
         try:
-            output_id = output_data.get('id')
+            output_id = output_data.get("id")
         except AttributeError:
             output_id = output_data
         return output_id
 
-    def stage_data_async(self, test_data, history_id, tool_id, force_path_paste=False, maxseconds=DEFAULT_TOOL_TEST_WAIT, tool_version=None):
-        fname = test_data['fname']
+    def stage_data_async(
+        self,
+        test_data,
+        history_id,
+        tool_id,
+        force_path_paste=False,
+        maxseconds=DEFAULT_TOOL_TEST_WAIT,
+        tool_version=None,
+    ):
+        fname = test_data["fname"]
         tool_input = {
-            "file_type": test_data['ftype'],
-            "dbkey": test_data['dbkey'],
+            "file_type": test_data["ftype"],
+            "dbkey": test_data["dbkey"],
         }
         metadata = test_data.get("metadata", {})
         if not hasattr(metadata, "items"):
             raise Exception(f"Invalid metadata description found for input [{fname}] - [{metadata}]")
-        for name, value in test_data.get('metadata', {}).items():
+        for name, value in test_data.get("metadata", {}).items():
             tool_input[f"files_metadata|{name}"] = value
 
-        composite_data = test_data['composite_data']
+        composite_data = test_data["composite_data"]
         if composite_data:
             files = {}
             for i, file_name in enumerate(composite_data):
                 if force_path_paste:
                     file_path = self.test_data_path(tool_id, file_name, tool_version=tool_version)
-                    tool_input.update({
-                        f"files_{i}|url_paste": f"file://{file_path}"
-                    })
+                    tool_input.update({f"files_{i}|url_paste": f"file://{file_path}"})
                 else:
-                    file_content = self.test_data_download(tool_id, file_name, is_output=False, tool_version=tool_version)
+                    file_content = self.test_data_download(
+                        tool_id, file_name, is_output=False, tool_version=tool_version
+                    )
                     files[f"files_{i}|file_data"] = file_content
-                tool_input.update({
-                    f"files_{i}|type": "upload_dataset",
-                })
-            name = test_data['name']
+                tool_input.update(
+                    {
+                        f"files_{i}|type": "upload_dataset",
+                    }
+                )
+            name = test_data["name"]
         else:
             name = os.path.basename(fname)
-            tool_input.update({
-                "files_0|NAME": name,
-                "files_0|type": "upload_dataset",
-            })
+            tool_input.update(
+                {
+                    "files_0|NAME": name,
+                    "files_0|type": "upload_dataset",
+                }
+            )
             files = {}
             if force_path_paste:
                 file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
-                tool_input.update({
-                    "files_0|url_paste": f"file://{file_name}"
-                })
+                tool_input.update({"files_0|url_paste": f"file://{file_name}"})
             else:
                 file_content = self.test_data_download(tool_id, fname, is_output=False, tool_version=tool_version)
-                files = {
-                    "files_0|file_data": file_content
-                }
-        submit_response_object = self.__submit_tool(history_id, "upload1", tool_input, extra_data={"type": "upload_dataset"}, files=files)
+                files = {"files_0|file_data": file_content}
+        submit_response_object = self.__submit_tool(
+            history_id, "upload1", tool_input, extra_data={"type": "upload_dataset"}, files=files
+        )
         submit_response = ensure_tool_run_response_okay(submit_response_object, f"upload dataset {name}")
-        assert "outputs" in submit_response, f"Invalid response from server [{submit_response}], expecting outputs in response."
+        assert (
+            "outputs" in submit_response
+        ), f"Invalid response from server [{submit_response}], expecting outputs in response."
         outputs = submit_response["outputs"]
         assert len(outputs) > 0, f"Invalid response from server [{submit_response}], expecting an output dataset."
         dataset = outputs[0]
-        hid = dataset['id']
+        hid = dataset["id"]
         self.uploads[os.path.basename(fname)] = self.uploads[fname] = self.uploads[name] = {"src": "hda", "id": hid}
-        assert "jobs" in submit_response, f"Invalid response from server [{submit_response}], expecting jobs in response."
+        assert (
+            "jobs" in submit_response
+        ), f"Invalid response from server [{submit_response}], expecting jobs in response."
         jobs = submit_response["jobs"]
         assert len(jobs) > 0, f"Invalid response from server [{submit_response}], expecting a job."
         return lambda: self.wait_for_job(jobs[0]["id"], history_id, maxseconds=maxseconds)
@@ -459,7 +521,9 @@ class GalaxyInteractorApi:
 
         submit_response = None
         for _ in range(DEFAULT_TOOL_TEST_WAIT):
-            submit_response = self.__submit_tool(history_id, tool_id=testdef.tool_id, tool_input=inputs_tree, tool_version=testdef.tool_version)
+            submit_response = self.__submit_tool(
+                history_id, tool_id=testdef.tool_id, tool_input=inputs_tree, tool_version=testdef.tool_version
+            )
             if _are_tool_inputs_not_ready(submit_response):
                 print("Tool inputs not ready yet")
                 time.sleep(1)
@@ -472,7 +536,7 @@ class GalaxyInteractorApi:
                 inputs=inputs_tree,
                 outputs=self.__dictify_outputs(submit_response_object),
                 output_collections=self.__dictify_output_collections(submit_response_object),
-                jobs=submit_response_object['jobs'],
+                jobs=submit_response_object["jobs"],
             )
         except KeyError:
             message = f"Error creating a job for these tool inputs - {submit_response_object['err_msg']}"
@@ -498,7 +562,7 @@ class GalaxyInteractorApi:
                     name=element_identifier,
                     src="new_collection",
                     collection_type=element_def.collection_type,
-                    element_identifiers=subelement_identifiers
+                    element_identifiers=subelement_identifiers,
                 )
             else:
                 element = self.uploads[element_def["value"]].copy()
@@ -511,7 +575,7 @@ class GalaxyInteractorApi:
 
     def __dictify_output_collections(self, submit_response):
         output_collections_dict = {}
-        for output_collection in submit_response['output_collections']:
+        for output_collection in submit_response["output_collections"]:
             output_collections_dict[output_collection.get("output_name")] = output_collection
         return output_collections_dict
 
@@ -521,12 +585,12 @@ class GalaxyInteractorApi:
         # but also allows fallback to legacy access as list mode.
         outputs_dict = OutputsDict()
 
-        for output in datasets_object['outputs']:
+        for output in datasets_object["outputs"]:
             outputs_dict[output.get("output_name")] = output
         return outputs_dict
 
     def output_hid(self, output_data):
-        return output_data['id']
+        return output_data["id"]
 
     def delete_history(self, history):
         self._delete(f"histories/{history}")
@@ -556,10 +620,12 @@ class GalaxyInteractorApi:
             dataset = history_content
 
             print(ERROR_MESSAGE_DATASET_SEP)
-            dataset_id = dataset.get('id', None)
+            dataset_id = dataset.get("id", None)
             print(f"| {dataset['hid']} - {dataset['name']} (HID - NAME) ")
-            if history_content['history_content_type'] == 'dataset_collection':
-                history_contents_json = self._get(f"histories/{history_id}/contents/dataset_collections/{history_content['id']}").json()
+            if history_content["history_content_type"] == "dataset_collection":
+                history_contents_json = self._get(
+                    f"histories/{history_id}/contents/dataset_collections/{history_content['id']}"
+                ).json()
                 print(f"| Dataset Collection: {history_contents_json}")
                 print("|")
                 continue
@@ -621,38 +687,38 @@ class GalaxyInteractorApi:
         return history_contents_response.json()
 
     def _state_ready(self, job_id, error_msg):
-        state_str = self.__get_job(job_id).json()['state']
-        if state_str == 'ok':
+        state_str = self.__get_job(job_id).json()["state"]
+        if state_str == "ok":
             return True
-        elif state_str == 'error':
+        elif state_str == "error":
             job_json = self.get_job_stdio(job_id)
-            raise Exception(f"{error_msg}. tool_id: {job_json['tool_id']}, exit_code: {job_json['exit_code']}, stderr: {job_json['stderr']}.")
+            raise Exception(
+                f"{error_msg}. tool_id: {job_json['tool_id']}, exit_code: {job_json['exit_code']}, stderr: {job_json['stderr']}."
+            )
         return None
 
     def __submit_tool(self, history_id, tool_id, tool_input, extra_data=None, files=None, tool_version=None):
         extra_data = extra_data or {}
         data = dict(
-            history_id=history_id,
-            tool_id=tool_id,
-            inputs=dumps(tool_input),
-            tool_version=tool_version,
-            **extra_data
+            history_id=history_id, tool_id=tool_id, inputs=dumps(tool_input), tool_version=tool_version, **extra_data
         )
         return self._post("tools", files=files, data=data)
 
     def ensure_user_with_email(self, email, password=None):
         admin_key = self.master_api_key
-        all_users_response = self._get('users', key=admin_key)
+        all_users_response = self._get("users", key=admin_key)
         try:
             all_users_response.raise_for_status()
         except requests.exceptions.HTTPError as e:
-            raise Exception(f"Failed to verify user with email [{email}] exists - perhaps you're targetting the wrong Galaxy server or using an incorrect admin API key. HTTP error: {e}")
+            raise Exception(
+                f"Failed to verify user with email [{email}] exists - perhaps you're targetting the wrong Galaxy server or using an incorrect admin API key. HTTP error: {e}"
+            )
         all_users = all_users_response.json()
         try:
             test_user = [user for user in all_users if user["email"] == email][0]
         except IndexError:
-            username = re.sub(r"[^a-z-\d]", '--', email.lower())
-            password = password or 'testpass'
+            username = re.sub(r"[^a-z-\d]", "--", email.lower())
+            password = password or "testpass"
             # If remote user middleware is enabled - this endpoint consumes
             # ``remote_user_email`` otherwise it requires ``email``, ``password``
             # and ``username``.
@@ -662,12 +728,13 @@ class GalaxyInteractorApi:
                 password=password,
                 username=username,
             )
-            test_user = self._post('users', data, key=admin_key).json()
+            test_user = self._post("users", data, key=admin_key).json()
         return test_user
 
     def __test_data_downloader(self, tool_id, tool_version=None):
-        def test_data_download(filename, mode='file'):
+        def test_data_download(filename, mode="file"):
             return self.test_data_download(tool_id, filename, mode=mode, tool_version=tool_version)
+
         return test_data_download
 
     def __dataset_fetcher(self, history_id):
@@ -695,35 +762,35 @@ class GalaxyInteractorApi:
         if not anon:
             if not key:
                 key = self.api_key if not admin else self.master_api_key
-            header['x-api-key'] = key
+            header["x-api-key"] = key
         return header
 
     def _post(self, path, data=None, files=None, key=None, headers=None, admin=False, anon=False, json=False):
         headers = self.api_key_header(key=key, admin=admin, anon=anon, headers=headers)
         url = self.get_api_url(path)
         kwd = self._prepare_request_params(data=data, files=files, as_json=json, headers=headers)
-        kwd['timeout'] = kwd.pop('timeout', util.DEFAULT_SOCKET_TIMEOUT)
+        kwd["timeout"] = kwd.pop("timeout", util.DEFAULT_SOCKET_TIMEOUT)
         return requests.post(url, **kwd)
 
     def _delete(self, path, data=None, key=None, headers=None, admin=False, anon=False, json=False):
         headers = self.api_key_header(key=key, admin=admin, anon=anon, headers=headers)
         url = self.get_api_url(path)
         kwd = self._prepare_request_params(data=data, as_json=json, headers=headers)
-        kwd['timeout'] = kwd.pop('timeout', util.DEFAULT_SOCKET_TIMEOUT)
+        kwd["timeout"] = kwd.pop("timeout", util.DEFAULT_SOCKET_TIMEOUT)
         return requests.delete(url, **kwd)
 
     def _patch(self, path, data=None, key=None, headers=None, admin=False, anon=False, json=False):
         headers = self.api_key_header(key=key, admin=admin, anon=anon, headers=headers)
         url = self.get_api_url(path)
         kwd = self._prepare_request_params(data=data, as_json=json, headers=headers)
-        kwd['timeout'] = kwd.pop('timeout', util.DEFAULT_SOCKET_TIMEOUT)
+        kwd["timeout"] = kwd.pop("timeout", util.DEFAULT_SOCKET_TIMEOUT)
         return requests.patch(url, **kwd)
 
     def _put(self, path, data=None, key=None, headers=None, admin=False, anon=False, json=False):
         headers = self.api_key_header(key=key, admin=admin, anon=anon, headers=headers)
         url = self.get_api_url(path)
         kwd = self._prepare_request_params(data=data, as_json=json, headers=headers)
-        kwd['timeout'] = kwd.pop('timeout', util.DEFAULT_SOCKET_TIMEOUT)
+        kwd["timeout"] = kwd.pop("timeout", util.DEFAULT_SOCKET_TIMEOUT)
         return requests.put(url, **kwd)
 
     def _get(self, path, data=None, key=None, headers=None, admin=False, anon=False):
@@ -731,7 +798,7 @@ class GalaxyInteractorApi:
         url = self.get_api_url(path)
         kwargs = {}
         if self.cookies:
-            kwargs['cookies'] = self.cookies
+            kwargs["cookies"] = self.cookies
         # no data for GET
         return requests.get(url, params=data, headers=headers, timeout=util.DEFAULT_SOCKET_TIMEOUT, **kwargs)
 
@@ -739,10 +806,12 @@ class GalaxyInteractorApi:
         if path.startswith("http"):
             return path
         elif path.startswith("/api/"):
-            path = path[len("/api/"):]
+            path = path[len("/api/") :]
         return urllib.parse.urljoin(f"{self.api_url}/", path)
 
-    def _prepare_request_params(self, data=None, files=None, as_json: bool = False, params: dict = None, headers: dict = None):
+    def _prepare_request_params(
+        self, data=None, files=None, as_json: bool = False, params: dict = None, headers: dict = None
+    ):
         """Handle some Galaxy conventions and work around requests issues.
 
         This is admittedly kind of hacky, so the interface may change frequently - be
@@ -776,18 +845,18 @@ class GalaxyInteractorApi:
             data.update(new_items)
 
         kwd = {
-            'files': files,
+            "files": files,
         }
         if headers:
-            kwd['headers'] = headers
+            kwd["headers"] = headers
         if as_json:
-            kwd['json'] = data or None
-            kwd['params'] = params
+            kwd["json"] = data or None
+            kwd["params"] = params
         else:
             data.update(params)
-            kwd['data'] = data
+            kwd["data"] = data
         if self.cookies:
-            kwd['cookies'] = self.cookies
+            kwd["cookies"] = self.cookies
 
         return kwd
 
@@ -830,7 +899,6 @@ def _are_tool_inputs_not_ready(submit_response):
 
 
 class RunToolException(Exception):
-
     def __init__(self, message, inputs=None, dynamic_param_error=False):
         super().__init__(message)
         self.inputs = inputs
@@ -838,11 +906,19 @@ class RunToolException(Exception):
 
 
 # Galaxy specific methods - rest of this can be used with arbitrary files and such.
-def verify_hid(filename, hda_id, attributes, test_data_downloader, hid="", dataset_fetcher=None, keep_outputs_dir=False):
+def verify_hid(
+    filename, hda_id, attributes, test_data_downloader, hid="", dataset_fetcher=None, keep_outputs_dir=False
+):
     assert dataset_fetcher is not None
 
     def verify_extra_files(extra_files):
-        _verify_extra_files_content(extra_files, hda_id, dataset_fetcher=dataset_fetcher, test_data_downloader=test_data_downloader, keep_outputs_dir=keep_outputs_dir)
+        _verify_extra_files_content(
+            extra_files,
+            hda_id,
+            dataset_fetcher=dataset_fetcher,
+            test_data_downloader=test_data_downloader,
+            keep_outputs_dir=keep_outputs_dir,
+        )
 
     data = dataset_fetcher(hda_id)
     item_label = ""
@@ -889,8 +965,8 @@ def verify_collection(output_collection_def, data_collection, verify_dataset):
                 element_outfile, element_attrib = None, element_test
             else:
                 element_outfile, element_attrib = element_test
-            if 'expected_sort_order' in element_attrib:
-                expected_sort_order[element_attrib['expected_sort_order']] = element_identifier
+            if "expected_sort_order" in element_attrib:
+                expected_sort_order[element_attrib["expected_sort_order"]] = element_identifier
 
             element = get_element(element_objects, element_identifier)
             if not element:
@@ -918,7 +994,16 @@ def verify_collection(output_collection_def, data_collection, verify_dataset):
     verify_elements(data_collection["elements"], output_collection_def.element_tests)
 
 
-def _verify_composite_datatype_file_content(file_name, hda_id, base_name=None, attributes=None, dataset_fetcher=None, test_data_downloader=None, keep_outputs_dir=False, mode='file'):
+def _verify_composite_datatype_file_content(
+    file_name,
+    hda_id,
+    base_name=None,
+    attributes=None,
+    dataset_fetcher=None,
+    test_data_downloader=None,
+    keep_outputs_dir=False,
+    mode="file",
+):
     assert dataset_fetcher is not None
 
     data = dataset_fetcher(hda_id, base_name)
@@ -934,7 +1019,7 @@ def _verify_composite_datatype_file_content(file_name, hda_id, base_name=None, a
             mode=mode,
         )
     except AssertionError as err:
-        errmsg = f'Composite file ({base_name}) of {item_label} different than expected, difference:\n'
+        errmsg = f"Composite file ({base_name}) of {item_label} different than expected, difference:\n"
         errmsg += util.unicodify(err)
         raise AssertionError(errmsg)
 
@@ -948,34 +1033,43 @@ def _verify_extra_files_content(extra_files, hda_id, dataset_fetcher, test_data_
         extra_file_attributes = extra_file_dict["attributes"]
         extra_file_value = extra_file_dict["value"]
 
-        if extra_file_type == 'file':
+        if extra_file_type == "file":
             files_list.append((extra_file_name, extra_file_value, extra_file_attributes, extra_file_type))
-        elif extra_file_type == 'directory':
-            extracted_path = test_data_downloader(extra_file_value, mode='directory')
+        elif extra_file_type == "directory":
+            extracted_path = test_data_downloader(extra_file_value, mode="directory")
             cleanup_directories.append(extracted_path)
             for root, _directories, files in util.path.safe_walk(extracted_path):
                 for filename in files:
                     filename = os.path.join(root, filename)
                     filename = os.path.relpath(filename, extracted_path)
-                    files_list.append((filename, os.path.join(extracted_path, filename), extra_file_attributes, extra_file_type))
+                    files_list.append(
+                        (filename, os.path.join(extracted_path, filename), extra_file_attributes, extra_file_type)
+                    )
         else:
-            raise ValueError(f'unknown extra_files type: {extra_file_type}')
+            raise ValueError(f"unknown extra_files type: {extra_file_type}")
     try:
         for filename, filepath, attributes, extra_file_type in files_list:
-            _verify_composite_datatype_file_content(filepath, hda_id, base_name=filename, attributes=attributes, dataset_fetcher=dataset_fetcher, test_data_downloader=test_data_downloader, keep_outputs_dir=keep_outputs_dir, mode=extra_file_type)
+            _verify_composite_datatype_file_content(
+                filepath,
+                hda_id,
+                base_name=filename,
+                attributes=attributes,
+                dataset_fetcher=dataset_fetcher,
+                test_data_downloader=test_data_downloader,
+                keep_outputs_dir=keep_outputs_dir,
+                mode=extra_file_type,
+            )
     finally:
         for path in cleanup_directories:
             shutil.rmtree(path)
 
 
 class NullClientTestConfig:
-
     def get_test_config(self, job_data):
         return None
 
 
 class DictClientTestConfig:
-
     def __init__(self, tools):
         self._tools = tools or {}
 
@@ -1005,29 +1099,31 @@ class DictClientTestConfig:
                 return tool_version_test_config[test_index]
             elif str(test_index) in tool_version_test_config:
                 return tool_version_test_config[str(test_index)]
-            if 'default' in tool_version_test_config:
-                return tool_version_test_config['default']
+            if "default" in tool_version_test_config:
+                return tool_version_test_config["default"]
             elif is_default:
                 return tool_version_test_config
         return None
 
 
-def verify_tool(tool_id,
-                galaxy_interactor,
-                resource_parameters=None,
-                register_job_data=None,
-                test_index=0,
-                tool_version=None,
-                quiet=False,
-                test_history=None,
-                no_history_cleanup=False,
-                publish_history=False,
-                force_path_paste=False,
-                maxseconds=DEFAULT_TOOL_TEST_WAIT,
-                tool_test_dicts=None,
-                client_test_config=None,
-                skip_with_reference_data=False,
-                skip_on_dynamic_param_errors=False):
+def verify_tool(
+    tool_id,
+    galaxy_interactor,
+    resource_parameters=None,
+    register_job_data=None,
+    test_index=0,
+    tool_version=None,
+    quiet=False,
+    test_history=None,
+    no_history_cleanup=False,
+    publish_history=False,
+    force_path_paste=False,
+    maxseconds=DEFAULT_TOOL_TEST_WAIT,
+    tool_test_dicts=None,
+    client_test_config=None,
+    skip_with_reference_data=False,
+    skip_on_dynamic_param_errors=False,
+):
     if resource_parameters is None:
         resource_parameters = {}
     if client_test_config is None:
@@ -1066,7 +1162,7 @@ def verify_tool(tool_id,
         register_job_data(job_data)
         return
 
-    tool_test_dict.setdefault('maxseconds', maxseconds)
+    tool_test_dict.setdefault("maxseconds", maxseconds)
     testdef = ToolTestDescription(tool_test_dict)
     _handle_def_errors(testdef)
 
@@ -1120,7 +1216,9 @@ def verify_tool(tool_id,
             assert data_list or data_collection_list
 
             try:
-                job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
+                job_stdio = _verify_outputs(
+                    testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet
+                )
             except JobOutputsError as e:
                 job_stdio = e.job_stdio
                 job_output_exceptions = e.output_exceptions
@@ -1176,7 +1274,7 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
     def register_exception(e):
         if not found_exceptions and not quiet:
             # Only print this stuff out once.
-            for stream in ['stdout', 'stderr']:
+            for stream in ["stdout", "stderr"]:
                 if stream in job_stdio:
                     print(_format_stream(job_stdio[stream], stream=stream, format=True), file=sys.stderr)
         found_exceptions.append(e)
@@ -1190,13 +1288,13 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
     # status was not what test was expecting.
     job_failed = False
     try:
-        galaxy_interactor.wait_for_job(job['id'], history, maxseconds)
+        galaxy_interactor.wait_for_job(job["id"], history, maxseconds)
     except Exception as e:
         job_failed = True
         if not testdef.expect_failure:
             found_exceptions.append(e)
 
-    job_stdio = galaxy_interactor.get_job_stdio(job['id'])
+    job_stdio = galaxy_interactor.get_job_stdio(job["id"])
 
     if testdef.num_outputs is not None:
         expected = testdef.num_outputs
@@ -1235,7 +1333,15 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
                 output_data = data_list[len(data_list) - len(testdef.outputs) + output_index]
         assert output_data is not None
         try:
-            galaxy_interactor.verify_output(history, jobs, output_data, output_testdef=output_testdef, tool_id=job['tool_id'], maxseconds=maxseconds, tool_version=testdef.tool_version)
+            galaxy_interactor.verify_output(
+                history,
+                jobs,
+                output_data,
+                output_testdef=output_testdef,
+                tool_id=job["tool_id"],
+                maxseconds=maxseconds,
+                tool_version=testdef.tool_version,
+            )
         except Exception as e:
             register_exception(e)
 
@@ -1276,7 +1382,7 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
                     data = raw_data
                 verify_assertions(data, assertions)
             except AssertionError as err:
-                errmsg = f'{description} different than expected\n'
+                errmsg = f"{description} different than expected\n"
                 errmsg += util.unicodify(err)
                 register_exception(AssertionError(errmsg))
 
@@ -1285,13 +1391,17 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
             name = output_collection_def.name
             # TODO: data_collection_list is clearly a bad name for dictionary.
             if name not in data_collection_list:
-                message = f"Failed to find output [{name}], tool outputs include [{','.join(data_collection_list.keys())}]"
+                message = (
+                    f"Failed to find output [{name}], tool outputs include [{','.join(data_collection_list.keys())}]"
+                )
                 raise AssertionError(message)
 
             # Data collection returned from submission, elements may have been populated after
             # the job completed so re-hit the API for more information.
             data_collection_id = data_collection_list[name]["id"]
-            galaxy_interactor.verify_output_collection(output_collection_def, data_collection_id, history, job['tool_id'])
+            galaxy_interactor.verify_output_collection(
+                output_collection_def, data_collection_id, history, job["tool_id"]
+            )
         except Exception as e:
             register_exception(e)
 
@@ -1302,7 +1412,7 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
 
 
 def _format_stream(output, stream, format):
-    output = output or ''
+    output = output or ""
     if format:
         msg = f"---------------------- >> begin tool {stream} << -----------------------\n"
         msg += f"{output}\n"
@@ -1313,7 +1423,6 @@ def _format_stream(output, stream, format):
 
 
 class JobOutputsError(AssertionError):
-
     def __init__(self, output_exceptions, job_stdio):
         big_message = "\n".join(map(util.unicodify, output_exceptions))
         super().__init__(big_message)
@@ -1329,15 +1438,19 @@ class ToolTestDescription:
     """
 
     def __init__(self, processed_test_dict):
-        assert "test_index" in processed_test_dict, "Invalid processed test description, must have a 'test_index' for naming, etc.."
+        assert (
+            "test_index" in processed_test_dict
+        ), "Invalid processed test description, must have a 'test_index' for naming, etc.."
         test_index = processed_test_dict["test_index"]
-        name = processed_test_dict.get('name', f'Test-{test_index + 1}')
-        maxseconds = processed_test_dict.get('maxseconds', DEFAULT_TOOL_TEST_WAIT)
+        name = processed_test_dict.get("name", f"Test-{test_index + 1}")
+        maxseconds = processed_test_dict.get("maxseconds", DEFAULT_TOOL_TEST_WAIT)
         if maxseconds is not None:
             maxseconds = int(maxseconds)
 
         self.test_index = test_index
-        assert "tool_id" in processed_test_dict, "Invalid processed test description, must have a 'tool_id' for naming, etc.."
+        assert (
+            "tool_id" in processed_test_dict
+        ), "Invalid processed test description, must have a 'tool_id' for naming, etc.."
         self.tool_id = processed_test_dict["tool_id"]
         self.tool_version = processed_test_dict.get("tool_version")
         self.name = name
@@ -1361,7 +1474,9 @@ class ToolTestDescription:
         self.error = processed_test_dict.get("error", False)
         self.exception = processed_test_dict.get("exception", None)
 
-        self.output_collections = [TestCollectionOutputDef.from_dict(d) for d in processed_test_dict.get("output_collections", [])]
+        self.output_collections = [
+            TestCollectionOutputDef.from_dict(d) for d in processed_test_dict.get("output_collections", [])
+        ]
         self.command_line = processed_test_dict.get("command_line", None)
         self.command_version = processed_test_dict.get("command_version", None)
         self.stdout = processed_test_dict.get("stdout", None)
@@ -1413,19 +1528,19 @@ def test_data_iter(required_files):
     for fname, extra in required_files:
         data_dict = dict(
             fname=fname,
-            metadata=extra.get('metadata', {}),
-            composite_data=extra.get('composite_data', []),
-            ftype=extra.get('ftype', DEFAULT_FTYPE),
-            dbkey=extra.get('dbkey', DEFAULT_DBKEY),
+            metadata=extra.get("metadata", {}),
+            composite_data=extra.get("composite_data", []),
+            ftype=extra.get("ftype", DEFAULT_FTYPE),
+            dbkey=extra.get("dbkey", DEFAULT_DBKEY),
         )
-        edit_attributes = extra.get('edit_attributes', [])
+        edit_attributes = extra.get("edit_attributes", [])
 
         # currently only renaming is supported
         for edit_att in edit_attributes:
-            if edit_att.get('type', None) == 'name':
-                new_name = edit_att.get('value', None)
-                assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag'
-                data_dict['name'] = new_name
+            if edit_att.get("type", None) == "name":
+                new_name = edit_att.get("value", None)
+                assert new_name, "You must supply the new dataset name as the value tag of the edit_attributes tag"
+                data_dict["name"] = new_name
             else:
                 raise Exception(f"edit_attributes type ({edit_att.get('type', None)}) is unimplemented")
 
diff --git a/lib/galaxy/tool_util/verify/script.py b/lib/galaxy/tool_util/verify/script.py
index 12e9b634881..976aec1438e 100644
--- a/lib/galaxy/tool_util/verify/script.py
+++ b/lib/galaxy/tool_util/verify/script.py
@@ -8,7 +8,10 @@ import os
 import sys
 import tempfile
 from collections import namedtuple
-from concurrent.futures import thread, ThreadPoolExecutor
+from concurrent.futures import (
+    thread,
+    ThreadPoolExecutor,
+)
 
 import yaml
 
@@ -31,7 +34,6 @@ TestException = namedtuple("TestException", ["tool_id", "exception", "was_record
 
 
 class Results:
-
     def __init__(self, default_suitename, test_json, append=False, galaxy_url=None):
         self.test_json = test_json or "-"
         self.galaxy_url = galaxy_url
@@ -58,7 +60,7 @@ class Results:
     def already_successful(self, test_reference):
         test_data = self._previous_test_data(test_reference)
         if test_data:
-            if 'status' in test_data and test_data['status'] == 'success':
+            if "status" in test_data and test_data["status"] == "success":
                 return True
 
         return False
@@ -66,7 +68,7 @@ class Results:
     def already_executed(self, test_reference):
         test_data = self._previous_test_data(test_reference)
         if test_data:
-            if 'status' in test_data and test_data['status'] != 'skipped':
+            if "status" in test_data and test_data["status"] != "skipped":
                 return True
 
         return False
@@ -74,10 +76,10 @@ class Results:
     def _previous_test_data(self, test_reference):
         test_id = _test_id_for_reference(test_reference)
         for test_result in self.test_results:
-            if test_result.get('id') != test_id:
+            if test_result.get("id") != test_id:
                 continue
 
-            has_data = test_result.get('has_data', False)
+            has_data = test_result.get("has_data", False)
             if has_data:
                 test_data = test_result.get("data", {})
                 return test_data
@@ -85,16 +87,16 @@ class Results:
         return None
 
     def write(self):
-        tests = sorted(self.test_results, key=lambda el: el['id'])
+        tests = sorted(self.test_results, key=lambda el: el["id"])
         n_passed, n_failures, n_skips = 0, 0, 0
         n_errors = len([e for e in self.test_exceptions if not e.was_recorded])
         for test in tests:
-            has_data = test.get('has_data', False)
+            has_data = test.get("has_data", False)
             if has_data:
                 test_data = test.get("data", {})
-                if 'status' not in test_data:
+                if "status" not in test_data:
                     raise Exception(f"Test result data {test_data} doesn't contain a status key.")
-                status = test_data['status']
+                status = test_data["status"]
                 if status == "success":
                     n_passed += 1
                 elif status == "error":
@@ -104,18 +106,18 @@ class Results:
                 elif status == "failure":
                     n_failures += 1
         report_obj = {
-            'version': '0.1',
-            'suitename': self.suitename,
-            'results': {
-                'total': n_passed + n_failures + n_skips + n_errors,
-                'errors': n_errors,
-                'failures': n_failures,
-                'skips': n_skips,
+            "version": "0.1",
+            "suitename": self.suitename,
+            "results": {
+                "total": n_passed + n_failures + n_skips + n_errors,
+                "errors": n_errors,
+                "failures": n_failures,
+                "skips": n_skips,
             },
-            'tests': tests,
+            "tests": tests,
         }
         if self.galaxy_url:
-            report_obj['galaxy_url'] = self.galaxy_url
+            report_obj["galaxy_url"] = self.galaxy_url
         if self.test_json == "-":
             print(json.dumps(report_obj))
         else:
@@ -124,43 +126,31 @@ class Results:
 
     def info_message(self):
         messages = []
-        passed_tests = self._tests_with_status('success')
-        messages.append("Passed tool tests ({}): {}".format(
-            len(passed_tests),
-            [t["id"] for t in passed_tests]
-        ))
-        failed_tests = self._tests_with_status('failure')
-        messages.append("Failed tool tests ({}): {}".format(
-            len(failed_tests),
-            [t["id"] for t in failed_tests]
-        ))
-        skiped_tests = self._tests_with_status('skip')
-        messages.append("Skipped tool tests ({}): {}".format(
-            len(skiped_tests),
-            [t["id"] for t in skiped_tests]
-        ))
-        errored_tests = self._tests_with_status('error')
-        messages.append("Errored tool tests ({}): {}".format(
-            len(errored_tests),
-            [t["id"] for t in errored_tests]
-        ))
+        passed_tests = self._tests_with_status("success")
+        messages.append("Passed tool tests ({}): {}".format(len(passed_tests), [t["id"] for t in passed_tests]))
+        failed_tests = self._tests_with_status("failure")
+        messages.append("Failed tool tests ({}): {}".format(len(failed_tests), [t["id"] for t in failed_tests]))
+        skiped_tests = self._tests_with_status("skip")
+        messages.append("Skipped tool tests ({}): {}".format(len(skiped_tests), [t["id"] for t in skiped_tests]))
+        errored_tests = self._tests_with_status("error")
+        messages.append("Errored tool tests ({}): {}".format(len(errored_tests), [t["id"] for t in errored_tests]))
         return "\n".join(messages)
 
     @property
     def success_count(self):
-        self._tests_with_status('success')
+        self._tests_with_status("success")
 
     @property
     def skip_count(self):
-        self._tests_with_status('skip')
+        self._tests_with_status("skip")
 
     @property
     def error_count(self):
-        return self._tests_with_status('error') + len(self.test_exceptions)
+        return self._tests_with_status("error") + len(self.test_exceptions)
 
     @property
     def failure_count(self):
-        return self._tests_with_status('failure')
+        return self._tests_with_status("failure")
 
     def _tests_with_status(self, status):
         return [t for t in self.test_results if t.get("data", {}).get("status") == status]
@@ -196,7 +186,7 @@ def test_tools(
         if not no_history_reuse:
             history = galaxy_interactor.get_history(history_name=history_name)
             if history:
-                test_history = history['id']
+                test_history = history["id"]
                 if log:
                     log.info(f"Using existing history with id '{test_history}', last updated: {history['update_time']}")
         if not test_history:
@@ -204,10 +194,12 @@ def test_tools(
             test_history = galaxy_interactor.new_history(history_name=history_name, publish_history=publish_history)
             if log:
                 log.info(f"History created with id '{test_history}'")
-    verify_kwds.update({
-        "no_history_cleanup": no_history_cleanup,
-        "test_history": test_history,
-    })
+    verify_kwds.update(
+        {
+            "no_history_cleanup": no_history_cleanup,
+            "test_history": test_history,
+        }
+    )
     with ThreadPoolExecutor(max_workers=parallel_tests) as executor:
         try:
             for test_reference in test_references:
@@ -231,7 +223,7 @@ def test_tools(
             results.write()
             if log:
                 if results.test_json == "-":
-                    destination = 'standard output'
+                    destination = "standard output"
                 else:
                     destination = os.path.abspath(results.test_json)
                 log.info(f"Report written to '{destination}'")
@@ -247,7 +239,7 @@ def _test_id_for_reference(test_reference):
     test_index = test_reference.test_index
 
     if tool_version and tool_id.endswith(f"/{tool_version}"):
-        tool_id = tool_id[:-len(f"/{tool_version}")]
+        tool_id = tool_id[: -len(f"/{tool_version}")]
 
     label_base = tool_id
     if tool_version:
@@ -273,7 +265,7 @@ def _test_tool(
     # If given a tool_id with a version suffix, strip it off so we can treat tool_version
     # correctly at least in client_test_config.
     if tool_version and tool_id.endswith(f"/{tool_version}"):
-        tool_id = tool_id[:-len(f"/{tool_version}")]
+        tool_id = tool_id[: -len(f"/{tool_version}")]
 
     test_id = _test_id_for_reference(test_reference)
 
@@ -293,8 +285,13 @@ def _test_tool(
                     if log:
                         log.info("Executing test '%s'", test_id)
                     verify_tool(
-                        tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version,
-                        register_job_data=register, publish_history=publish_history, **verify_kwds
+                        tool_id,
+                        galaxy_interactor,
+                        test_index=test_index,
+                        tool_version=tool_version,
+                        register_job_data=register,
+                        publish_history=publish_history,
+                        **verify_kwds,
                     )
                     if log:
                         log.info("Test '%s' passed", test_id)
@@ -307,11 +304,13 @@ def _test_tool(
                     run_retries -= 1
         finally:
             if job_data is not None:
-                results.register_result({
-                    "id": test_id,
-                    "has_data": True,
-                    "data": job_data,
-                })
+                results.register_result(
+                    {
+                        "id": test_id,
+                        "has_data": True,
+                        "data": job_data,
+                    }
+                )
             if job_exception is not None:
                 was_recorded = job_data is not None
                 test_exception = TestException(tool_id, job_exception, was_recorded)
@@ -464,7 +463,7 @@ def run_tests(args, test_filters=None, log=None):
 
 
 def setup_global_logger(name, log_file=None, verbose=False):
-    formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s')
+    formatter = logging.Formatter("%(asctime)s %(levelname)-5s - %(message)s")
     console = logging.StreamHandler()
     console.setFormatter(formatter)
 
@@ -486,38 +485,111 @@ def setup_global_logger(name, log_file=None, verbose=False):
 
 def arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
-    parser.add_argument('-u', '--galaxy-url', default="http://localhost:8080", help='Galaxy URL')
-    parser.add_argument('-k', '--key', default=None, help='Galaxy User API Key')
-    parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key')
-    parser.add_argument('--force_path_paste', default=False, action="store_true", help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.')
-    parser.add_argument('-t', '--tool-id', default=ALL_TOOLS, help='Tool ID')
-    parser.add_argument('--tool-version', default=None, help='Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions')
-    parser.add_argument('-i', '--test-index', default=ALL_TESTS, type=int, help='Tool Test Index (starting at 0) - by default all tests will run.')
-    parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to')
-    parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.")
+    parser.add_argument("-u", "--galaxy-url", default="http://localhost:8080", help="Galaxy URL")
+    parser.add_argument("-k", "--key", default=None, help="Galaxy User API Key")
+    parser.add_argument("-a", "--admin-key", default=None, help="Galaxy Admin API Key")
+    parser.add_argument(
+        "--force_path_paste",
+        default=False,
+        action="store_true",
+        help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.',
+    )
+    parser.add_argument("-t", "--tool-id", default=ALL_TOOLS, help="Tool ID")
+    parser.add_argument(
+        "--tool-version",
+        default=None,
+        help="Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions",
+    )
+    parser.add_argument(
+        "-i",
+        "--test-index",
+        default=ALL_TESTS,
+        type=int,
+        help="Tool Test Index (starting at 0) - by default all tests will run.",
+    )
+    parser.add_argument("-o", "--output", default=None, help="directory to dump outputs to")
+    parser.add_argument(
+        "--append",
+        default=False,
+        action="store_true",
+        help="Extend a test record json (created with --output-json) with additional tests.",
+    )
     skip_group = parser.add_mutually_exclusive_group()
-    skip_group.add_argument('--skip-previously-executed', dest="skip", default="no", action="store_const", const="executed", help="When used with --append, skip any test previously executed.")
-    skip_group.add_argument('--skip-previously-successful', dest="skip", default="no", action="store_const", const="successful", help="When used with --append, skip any test previously executed successfully.")
-    parser.add_argument('-j', '--output-json', default=None, help='output metadata json')
-    parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
-    parser.add_argument('-c', '--client-test-config', default=None, help="Test config YAML to help with client testing")
-    parser.add_argument('--suite-name', default=DEFAULT_SUITE_NAME, help="Suite name for tool test output")
-    parser.add_argument('--with-reference-data', dest="with_reference_data", default=False, action="store_true")
-    parser.add_argument('--skip-with-reference-data', dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.")
+    skip_group.add_argument(
+        "--skip-previously-executed",
+        dest="skip",
+        default="no",
+        action="store_const",
+        const="executed",
+        help="When used with --append, skip any test previously executed.",
+    )
+    skip_group.add_argument(
+        "--skip-previously-successful",
+        dest="skip",
+        default="no",
+        action="store_const",
+        const="successful",
+        help="When used with --append, skip any test previously executed successfully.",
+    )
+    parser.add_argument("-j", "--output-json", default=None, help="output metadata json")
+    parser.add_argument("--verbose", default=False, action="store_true", help="Verbose logging.")
+    parser.add_argument("-c", "--client-test-config", default=None, help="Test config YAML to help with client testing")
+    parser.add_argument("--suite-name", default=DEFAULT_SUITE_NAME, help="Suite name for tool test output")
+    parser.add_argument("--with-reference-data", dest="with_reference_data", default=False, action="store_true")
+    parser.add_argument(
+        "--skip-with-reference-data",
+        dest="with_reference_data",
+        action="store_false",
+        help="Skip tests the Galaxy server believes use data tables or loc files.",
+    )
     history_per_group = parser.add_mutually_exclusive_group()
-    history_per_group.add_argument('--history-per-suite', dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).")
-    history_per_group.add_argument('--history-per-test-case', dest="history_per_test_case", action="store_true", help="Create new history per test case.")
-    history_per_group.add_argument('--history-name', default=None, help="Override default history name")
-    parser.add_argument('--no-history-reuse', default=False, action="store_true", help="Do not reuse histories if a matching one already exists.")
-    parser.add_argument('--no-history-cleanup', default=False, action="store_true", help="Perserve histories created for testing.")
-    parser.add_argument('--publish-history', default=False, action="store_true", help="Publish test history. Useful for CI testing.")
-    parser.add_argument('--parallel-tests', default=1, type=int, help="Parallel tests.")
-    parser.add_argument('--retries', default=0, type=int, help="Retry failed tests.")
-    parser.add_argument('--page-size', default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests.")
-    parser.add_argument('--page-number', default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0.")
-    parser.add_argument('--download-attempts', default=1, type=int, help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.")
-    parser.add_argument('--download-sleep', default=1, type=int, help="If download attempts is greater than 1, the amount to sleep between download attempts.")
-    parser.add_argument('--test-data', action='append', help='Add local test data path to search for missing test data')
+    history_per_group.add_argument(
+        "--history-per-suite",
+        dest="history_per_test_case",
+        default=False,
+        action="store_false",
+        help="Create new history per test suite (all tests in same history).",
+    )
+    history_per_group.add_argument(
+        "--history-per-test-case",
+        dest="history_per_test_case",
+        action="store_true",
+        help="Create new history per test case.",
+    )
+    history_per_group.add_argument("--history-name", default=None, help="Override default history name")
+    parser.add_argument(
+        "--no-history-reuse",
+        default=False,
+        action="store_true",
+        help="Do not reuse histories if a matching one already exists.",
+    )
+    parser.add_argument(
+        "--no-history-cleanup", default=False, action="store_true", help="Perserve histories created for testing."
+    )
+    parser.add_argument(
+        "--publish-history", default=False, action="store_true", help="Publish test history. Useful for CI testing."
+    )
+    parser.add_argument("--parallel-tests", default=1, type=int, help="Parallel tests.")
+    parser.add_argument("--retries", default=0, type=int, help="Retry failed tests.")
+    parser.add_argument(
+        "--page-size", default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests."
+    )
+    parser.add_argument(
+        "--page-number", default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0."
+    )
+    parser.add_argument(
+        "--download-attempts",
+        default=1,
+        type=int,
+        help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.",
+    )
+    parser.add_argument(
+        "--download-sleep",
+        default=1,
+        type=int,
+        help="If download attempts is greater than 1, the amount to sleep between download attempts.",
+    )
+    parser.add_argument("--test-data", action="append", help="Add local test data path to search for missing test data")
     return parser
 
 
diff --git a/lib/galaxy/tool_util/verify/test_data.py b/lib/galaxy/tool_util/verify/test_data.py
index de1a3f51401..0b81eba6759 100644
--- a/lib/galaxy/tool_util/verify/test_data.py
+++ b/lib/galaxy/tool_util/verify/test_data.py
@@ -7,17 +7,15 @@ from string import Template
 from galaxy.util import (
     asbool,
     in_directory,
-    smart_str
+    smart_str,
 )
 
 UPDATE_TEMPLATE = Template(
-    "git --work-tree $dir --git-dir $dir/.git fetch && "
-    "git --work-tree $dir --git-dir $dir/.git merge origin/master"
+    "git --work-tree $dir --git-dir $dir/.git fetch && " "git --work-tree $dir --git-dir $dir/.git merge origin/master"
 )
 
 UPDATE_FAILED_TEMPLATE = Template(
-    "Warning failed to update test repository $dir - "
-    "update stdout was [$stdout] and stderr was [$stderr]."
+    "Warning failed to update test repository $dir - " "update stdout was [$stdout] and stderr was [$stderr]."
 )
 
 
@@ -27,7 +25,7 @@ LIST_SEP = re.compile(r"\s*,\s*")
 class TestDataResolver:
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
 
-    def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ):
+    def __init__(self, file_dirs=None, env_var="GALAXY_TEST_FILE_DIR", environ=os.environ):
         if file_dirs is None:
             file_dirs = environ.get(env_var, None)
         if file_dirs is None:
@@ -47,7 +45,7 @@ class TestDataResolver:
 
     def get_filecontent(self, name):
         filename = self.get_filename(name=name)
-        with open(filename, mode='rb') as f:
+        with open(filename, mode="rb") as f:
             return f.read()
 
     def get_directory(self, name):
@@ -62,7 +60,6 @@ def build_resolver(uri, environ):
 
 
 class FileDataResolver:
-
     def __init__(self, file_dir):
         self.file_dir = file_dir
 
@@ -75,7 +72,6 @@ class FileDataResolver:
 
 
 class GitDataResolver(FileDataResolver):
-
     def __init__(self, repository, environ):
         self.repository = repository
         self.updated = False
@@ -116,8 +112,8 @@ class GitDataResolver(FileDataResolver):
         stdout, stderr = p.communicate()
         if p.returncode != 0:
             kwds = {
-                'dir': self.file_dir,
-                'stdout': stdout,
-                'stderr': stderr,
+                "dir": self.file_dir,
+                "stdout": stdout,
+                "stderr": stderr,
             }
             print(UPDATE_FAILED_TEMPLATE.substitute(**kwds))
diff --git a/lib/galaxy/tool_util/verify/wait.py b/lib/galaxy/tool_util/verify/wait.py
index 0ef1f5d57b1..4fbe6ad3373 100644
--- a/lib/galaxy/tool_util/verify/wait.py
+++ b/lib/galaxy/tool_util/verify/wait.py
@@ -1,7 +1,11 @@
 """Abstraction for waiting on API conditions to become true."""
 
 import time
-from typing import Callable, Optional, Union
+from typing import (
+    Callable,
+    Optional,
+    Union,
+)
 
 DEFAULT_POLLING_BACKOFF = 0
 DEFAULT_POLLING_DELTA = 0.25
@@ -10,7 +14,14 @@ TIMEOUT_MESSAGE_TEMPLATE = "Timed out after {} seconds waiting on {}."
 timeout_type = Union[int, float]
 
 
-def wait_on(function: Callable, desc: str, timeout: timeout_type, delta: timeout_type = DEFAULT_POLLING_DELTA, polling_backoff: timeout_type = DEFAULT_POLLING_BACKOFF, sleep_: Optional[Callable] = None):
+def wait_on(
+    function: Callable,
+    desc: str,
+    timeout: timeout_type,
+    delta: timeout_type = DEFAULT_POLLING_DELTA,
+    polling_backoff: timeout_type = DEFAULT_POLLING_BACKOFF,
+    sleep_: Optional[Callable] = None,
+):
     """Wait for function to return non-None value.
 
     Grow the polling interval (initially ``delta`` defaulting to 0.25 seconds)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 088696a853e..9f79340a6df 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -35,35 +35,36 @@ from webob.compat import cgi_FieldStorage
 
 from galaxy import (
     exceptions,
-    model
+    model,
 )
 from galaxy.exceptions import ToolInputsNotReadyException
 from galaxy.job_execution import output_collect
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.tool_shed.util.repository_util import get_installed_repository
 from galaxy.tool_shed.util.shed_util_common import set_image_paths
-from galaxy.tool_util.deps import (
-    CachedDependencyManager,
-)
+from galaxy.tool_util.deps import CachedDependencyManager
 from galaxy.tool_util.fetcher import ToolLocationFetcher
 from galaxy.tool_util.loader import (
     imported_macro_paths,
     raw_tool_xml_tree,
-    template_macro_params
+    template_macro_params,
 )
 from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
 from galaxy.tool_util.parser import (
     get_tool_source,
     get_tool_source_from_representation,
     RequiredFiles,
-    ToolOutputCollectionPart
+    ToolOutputCollectionPart,
 )
 from galaxy.tool_util.parser.xml import XmlPageSource
 from galaxy.tool_util.provided_metadata import parse_tool_provided_metadata
 from galaxy.tool_util.toolbox import BaseGalaxyToolBox
 from galaxy.tool_util.toolbox.views.sources import StaticToolBoxViewSources
 from galaxy.tools import expressions
-from galaxy.tools.actions import DefaultToolAction, ToolAction
+from galaxy.tools.actions import (
+    DefaultToolAction,
+    ToolAction,
+)
 from galaxy.tools.actions.data_manager import DataManagerToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
 from galaxy.tools.actions.model_operations import ModelOperationToolAction
@@ -76,7 +77,7 @@ from galaxy.tools.parameters import (
     params_to_incoming,
     params_to_strings,
     populate_state,
-    visit_input_values
+    visit_input_values,
 )
 from galaxy.tools.parameters.basic import (
     BaseURLToolParameter,
@@ -92,7 +93,13 @@ from galaxy.tools.parameters.dataset_matcher import (
     set_dataset_matcher_factory,
     unset_dataset_matcher_factory,
 )
-from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, Section, UploadDataset
+from galaxy.tools.parameters.grouping import (
+    Conditional,
+    ConditionalWhen,
+    Repeat,
+    Section,
+    UploadDataset,
+)
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
 from galaxy.tools.parameters.wrapped_json import json_wrap
@@ -123,19 +130,19 @@ from galaxy.util.tool_shed.common_util import (
 )
 from galaxy.version import VERSION_MAJOR
 from galaxy.work.context import proxy_work_context_for_history
-from .execute import (
-    execute as execute_job,
-    MappingParameters,
-)
+from .execute import execute as execute_job
+from .execute import MappingParameters
 
 if TYPE_CHECKING:
-    from galaxy.tools.actions.metadata import SetMetadataToolAction
     from galaxy.managers.jobs import JobSearch
+    from galaxy.tools.actions.metadata import SetMetadataToolAction
 
 log = logging.getLogger(__name__)
 
-REQUIRES_JS_RUNTIME_MESSAGE = ("The tool [%s] requires a nodejs runtime to execute "
-                               "but node or nodejs could not be found. Please contact the Galaxy adminstrator")
+REQUIRES_JS_RUNTIME_MESSAGE = (
+    "The tool [%s] requires a nodejs runtime to execute "
+    "but node or nodejs could not be found. Please contact the Galaxy adminstrator"
+)
 
 HELP_UNINITIALIZED = threading.Lock()
 MODEL_TOOLS_PATH = os.path.abspath(os.path.dirname(__file__))
@@ -210,14 +217,23 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "winSplitter": packaging.version.parse("1.0.1"),
 }
 
-BIOTOOLS_MAPPING_CONTENT = resource_string(__name__, 'biotools_mappings.tsv').decode("UTF-8")
-BIOTOOLS_MAPPING: Dict[str, str] = dict([cast(Tuple[str, str], tuple(x.split("\t"))) for x in BIOTOOLS_MAPPING_CONTENT.splitlines() if not x.startswith("#")])
+BIOTOOLS_MAPPING_CONTENT = resource_string(__name__, "biotools_mappings.tsv").decode("UTF-8")
+BIOTOOLS_MAPPING: Dict[str, str] = dict(
+    [
+        cast(Tuple[str, str], tuple(x.split("\t")))
+        for x in BIOTOOLS_MAPPING_CONTENT.splitlines()
+        if not x.startswith("#")
+    ]
+)
 
 REQUIRE_FULL_DIRECTORY = {
     "includes": [{"path": "**", "path_type": "glob"}],
 }
 IMPLICITLY_REQUIRED_TOOL_FILES: Dict[str, Dict] = {
-    "deseq2": {"version": packaging.version.parse("2.11.40.6"), "required": {"includes": [{"path": "*.R", "path_type": "glob"}]}},
+    "deseq2": {
+        "version": packaging.version.parse("2.11.40.6"),
+        "required": {"includes": [{"path": "*.R", "path_type": "glob"}]},
+    },
     # minimum example:
     # "foobar": {"required": REQUIRE_FULL_DIRECTORY}
     # if no version is specified, all versions without explicit RequiredFiles will be selected
@@ -246,14 +262,14 @@ class safe_update(NamedTuple):
 
 # Tool updates that did not change parameters in a way that requires rebuilding workflows
 WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
-    'Filter1': safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.1.1")),
-    '__BUILD_LIST__': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
-    '__APPLY_RULES__': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
-    '__EXTRACT_DATASET__': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
-    'Grep1': safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.3")),
-    'Show beginning1': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
-    'Show tail1': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
-    'sort1': safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.2.0")),
+    "Filter1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.1.1")),
+    "__BUILD_LIST__": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
+    "__APPLY_RULES__": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
+    "__EXTRACT_DATASET__": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
+    "Grep1": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.3")),
+    "Show beginning1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
+    "Show tail1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
+    "sort1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.2.0")),
 }
 
 
@@ -273,14 +289,14 @@ def create_tool_from_source(app, tool_source, config_file=None, **kwds):
         ToolClass = tool_types.get(tool_type)
     else:
         # Normal tool
-        root = getattr(tool_source, 'root', None)
+        root = getattr(tool_source, "root", None)
         ToolClass = Tool
     tool = ToolClass(config_file, tool_source, app, **kwds)
     return tool
 
 
 class ToolBox(BaseGalaxyToolBox):
-    """ A derivative of AbstractToolBox with knowledge about Tool internals -
+    """A derivative of AbstractToolBox with knowledge about Tool internals -
     how to construct them, action types, dependency management, etc....
     """
 
@@ -291,8 +307,8 @@ class ToolBox(BaseGalaxyToolBox):
         # This is here to deal with the old default value, which doesn't make
         # sense in an "installed Galaxy" world.
         # FIXME: ./
-        if tool_root_dir == './tools':
-            tool_root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'bundled'))
+        if tool_root_dir == "./tools":
+            tool_root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "bundled"))
         view_sources = StaticToolBoxViewSources(
             view_directories=app.config.panel_views_dir,
             view_dicts=app.config.panel_views,
@@ -323,15 +339,18 @@ class ToolBox(BaseGalaxyToolBox):
                     self.app.application_stack.register_postfork_function(region.reopen_ro)
 
     def can_load_config_file(self, config_filename):
-        if config_filename == self.app.config.shed_tool_config_file and not self.app.config.is_set('shed_tool_config_file'):
+        if config_filename == self.app.config.shed_tool_config_file and not self.app.config.is_set(
+            "shed_tool_config_file"
+        ):
             if self.dynamic_confs():
                 # Do not load or create a default shed_tool_config_file if another shed_tool_config file has already been loaded
                 return False
-        elif self.app.config.is_set('tool_config_file'):
+        elif self.app.config.is_set("tool_config_file"):
             log.warning(
                 "The default shed tool config file (%s) has been added to the tool_config_file option, if this is "
                 "not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool "
-                "config file", self.app.config.shed_tool_config_file
+                "config file",
+                self.app.config.shed_tool_config_file,
             )
         return True
 
@@ -356,13 +375,13 @@ class ToolBox(BaseGalaxyToolBox):
 
     def create_tool(self, config_file, tool_cache_data_dir=None, **kwds):
         cache = self.get_cache_region(tool_cache_data_dir or self.app.config.tool_cache_data_dir)
-        if config_file.endswith('.xml') and cache and not cache.disabled:
+        if config_file.endswith(".xml") and cache and not cache.disabled:
             tool_document = cache.get(config_file)
             if tool_document:
                 tool_source = self.get_expanded_tool_source(
                     config_file=config_file,
-                    xml_tree=etree.ElementTree(etree.fromstring(tool_document['document'].encode('utf-8'))),
-                    macro_paths=tool_document['macro_paths']
+                    xml_tree=etree.ElementTree(etree.fromstring(tool_document["document"].encode("utf-8"))),
+                    macro_paths=tool_document["macro_paths"],
                 )
             else:
                 tool_source = self.get_expanded_tool_source(config_file)
@@ -420,7 +439,7 @@ class ToolBox(BaseGalaxyToolBox):
         # are now using only GALAXY_URL.
         tool_ids = listify(tool_id)
         for tool_id in tool_ids:
-            if tool_id.endswith('/'):
+            if tool_id.endswith("/"):
                 # Some data sources send back redirects ending with `/`, this takes care of that case
                 tool_id = tool_id[:-1]
             if get_loaded_tools_by_lineage:
@@ -457,13 +476,13 @@ class ToolBox(BaseGalaxyToolBox):
         options: List[Tuple[str, str]] = []
         for tool in tools:
             options.insert(0, (tool.version, tool.id))
-        select_field = SelectField(name='tool_id')
+        select_field = SelectField(name="tool_id")
         for option_tup in options:
             selected = set_selected and option_tup[1] == tool_id
             if selected:
-                select_field.add_option(f'version {option_tup[0]}', option_tup[1], selected=True)
+                select_field.add_option(f"version {option_tup[0]}", option_tup[1], selected=True)
             else:
-                select_field.add_option(f'version {option_tup[0]}', option_tup[1])
+                select_field.add_option(f"version {option_tup[0]}", option_tup[1])
         return select_field
 
 
@@ -527,19 +546,30 @@ class Tool(Dictifiable):
     Represents a computational tool that can be executed through Galaxy.
     """
 
-    tool_type = 'default'
+    tool_type = "default"
     requires_setting_metadata = True
     produces_entry_points = False
     default_tool_action = DefaultToolAction
     tool_action: ToolAction
     tool_type_local = False
-    dict_collection_visible_keys = ['id', 'name', 'version', 'description', 'labels']
+    dict_collection_visible_keys = ["id", "name", "version", "description", "labels"]
     __help: Optional[threading.Lock]
     __help_by_page: Union[threading.Lock, List[str]]
-    job_search: 'JobSearch'
+    job_search: "JobSearch"
     version: str
 
-    def __init__(self, config_file, tool_source, app, guid=None, repository_id=None, tool_shed_repository=None, allow_code_files=True, dynamic=False, tool_dir=None):
+    def __init__(
+        self,
+        config_file,
+        tool_source,
+        app,
+        guid=None,
+        repository_id=None,
+        tool_shed_repository=None,
+        allow_code_files=True,
+        dynamic=False,
+        tool_dir=None,
+    ):
         """Load a tool from the config named by `config_file`"""
         # Determine the full path of the directory where the tool config is
         if config_file is not None:
@@ -606,26 +636,26 @@ class Tool(Dictifiable):
             raise e
         # The job search is only relevant in a galaxy context, and breaks
         # loading tools into the toolshed for validation.
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             self.job_search = self.app.job_search
 
     def __getattr__(self, name):
         lazy_attributes = {
-            'action',
-            'check_values',
-            'display_by_page',
-            'enctype',
-            'has_multiple_pages',
-            'inputs',
-            'inputs_by_page',
-            'last_page',
-            'method',
-            'npages',
-            'nginx_upload',
-            'target',
-            'template_macro_params',
-            'outputs',
-            'output_collections'
+            "action",
+            "check_values",
+            "display_by_page",
+            "enctype",
+            "has_multiple_pages",
+            "inputs",
+            "inputs_by_page",
+            "last_page",
+            "method",
+            "npages",
+            "nginx_upload",
+            "target",
+            "template_macro_params",
+            "outputs",
+            "output_collections",
         }
         if name in lazy_attributes:
             self.assert_finalized()
@@ -639,13 +669,15 @@ class Tool(Dictifiable):
                 self.parse_outputs(self.tool_source)
                 self.finalized = True
             except Exception:
-                toolbox = getattr(self.app, 'toolbox', None)
+                toolbox = getattr(self.app, "toolbox", None)
                 if toolbox:
                     toolbox.remove_tool_by_id(self.id)
                 if raise_if_invalid:
                     raise
                 else:
-                    log.warning("An error occured while parsing the tool wrapper xml, the tool is not functional", exc_info=True)
+                    log.warning(
+                        "An error occured while parsing the tool wrapper xml, the tool is not functional", exc_info=True
+                    )
 
     def remove_from_cache(self):
         source_path = self.tool_source._source_path
@@ -703,16 +735,17 @@ class Tool(Dictifiable):
     def tool_shed_repository(self):
         # If this tool is included in an installed tool shed repository, return it.
         if self.tool_shed:
-            return get_installed_repository(self.app,
-                                            tool_shed=self.tool_shed,
-                                            name=self.repository_name,
-                                            owner=self.repository_owner,
-                                            installed_changeset_revision=self.installed_changeset_revision,
-                                            from_cache=True)
+            return get_installed_repository(
+                self.app,
+                tool_shed=self.tool_shed,
+                name=self.repository_name,
+                owner=self.repository_owner,
+                installed_changeset_revision=self.installed_changeset_revision,
+                from_cache=True,
+            )
 
     @property
     def produces_collections_with_unknown_structure(self):
-
         def output_is_dynamic(output):
             if not output.collection:
                 return False
@@ -750,9 +783,7 @@ class Tool(Dictifiable):
             unversioned_legacy_tool = self.old_id in GALAXY_LIB_TOOLS_UNVERSIONED
             versioned_legacy_tool = self.old_id in GALAXY_LIB_TOOLS_VERSIONED
             legacy_tool = unversioned_legacy_tool or (
-                versioned_legacy_tool
-                and self.old_id
-                and self.version_object < GALAXY_LIB_TOOLS_VERSIONED[self.old_id]
+                versioned_legacy_tool and self.old_id and self.version_object < GALAXY_LIB_TOOLS_VERSIONED[self.old_id]
             )
             return legacy_tool
 
@@ -784,7 +815,9 @@ class Tool(Dictifiable):
                         break
                 else:
                     rval = job_tool_config
-        assert rval is not None, f'Could not get a job tool configuration for Tool {self.id} with job_params {job_params}, this is a bug'
+        assert (
+            rval is not None
+        ), f"Could not get a job tool configuration for Tool {self.id} with job_params {job_params}, this is a bug"
         return rval
 
     def get_configured_job_handler(self, job_params=None):
@@ -833,7 +866,11 @@ class Tool(Dictifiable):
             raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
 
         profile = packaging.version.parse(str(self.profile))
-        if self.app.name == 'galaxy' and profile >= packaging.version.parse("16.04") and packaging.version.parse(VERSION_MAJOR) < profile:
+        if (
+            self.app.name == "galaxy"
+            and profile >= packaging.version.parse("16.04")
+            and packaging.version.parse(VERSION_MAJOR) < profile
+        ):
             message = f"The tool [{self.id}] targets version {self.profile} of Galaxy, you should upgrade Galaxy to ensure proper functioning of this tool."
             raise Exception(message)
 
@@ -841,9 +878,9 @@ class Tool(Dictifiable):
         if self.python_template_version is None:
             # If python_template_version not specified we assume tools with profile versions >= 19.05 are python 3 ready
             if self.profile >= 19.05:
-                self.python_template_version = packaging.version.parse('3.5')
+                self.python_template_version = packaging.version.parse("3.5")
             else:
-                self.python_template_version = packaging.version.parse('2.7')
+                self.python_template_version = packaging.version.parse("2.7")
 
         # Get the (user visible) name of the tool
         self.name = tool_source.parse_name()
@@ -896,7 +933,7 @@ class Tool(Dictifiable):
         if self.environment_variables:
             if not self.docker_env_pass_through:
                 self.docker_env_pass_through = []
-            self.docker_env_pass_through.extend(map(lambda x: x['name'], self.environment_variables))
+            self.docker_env_pass_through.extend(map(lambda x: x["name"], self.environment_variables))
 
         # Parameters used to build URL for redirection to external app
         redirect_url_params = tool_source.parse_redirect_url_params_elem()
@@ -905,9 +942,9 @@ class Tool(Dictifiable):
             redirect_url_params = redirect_url_params.text.strip()
             # Replace remaining white space with something we can safely split on later
             # when we are building the params
-            self.redirect_url_params = redirect_url_params.replace(' ', '**^**')
+            self.redirect_url_params = redirect_url_params.replace(" ", "**^**")
         else:
-            self.redirect_url_params = ''
+            self.redirect_url_params = ""
 
         # Short description of the tool
         self.description = tool_source.parse_description()
@@ -936,18 +973,18 @@ class Tool(Dictifiable):
             self_ids = [self.id.lower()]
             if self.old_id != self.id:
                 # Handle toolshed guids
-                self_ids = [self.id.lower(), self.id.lower().rsplit('/', 1)[0], self.old_id.lower()]
+                self_ids = [self.id.lower(), self.id.lower().rsplit("/", 1)[0], self.old_id.lower()]
         else:
             self_ids = []
         self.all_ids = self_ids
 
         # In the toolshed context, there is no job config.
-        if hasattr(self.app, 'job_config'):
+        if hasattr(self.app, "job_config"):
             # Order of this list must match documentation in job_conf.sample_advanced.yml
             tool_classes = []
             if self.tool_type_local:
                 tool_classes.append("local")
-            elif self.old_id in ['upload1', '__DATA_FETCH__']:
+            elif self.old_id in ["upload1", "__DATA_FETCH__"]:
                 tool_classes.append("local")
             if self.requires_galaxy_python_environment:
                 tool_classes.append("requires_galaxy")
@@ -1052,7 +1089,7 @@ class Tool(Dictifiable):
         self.hook_map: Dict[str, str] = {}
         self.uihints: Dict[str, str] = {}
 
-        if not hasattr(tool_source, 'root'):
+        if not hasattr(tool_source, "root"):
             return
 
         # TODO: Move following logic into XmlToolSource.
@@ -1071,7 +1108,7 @@ class Tool(Dictifiable):
                 with open(code_path) as f:
                     code_string = f.read()
                 try:
-                    compiled_code = compile(code_string, code_path, 'exec')
+                    compiled_code = compile(code_string, code_path, "exec")
                     exec(compiled_code, self.code_namespace)
                 except Exception:
                     if (
@@ -1080,8 +1117,10 @@ class Tool(Dictifiable):
                         and self.python_template_version.release[0] < 3
                     ):
                         # Could be a code file that uses python 2 syntax
-                        translated_code = str(refactoring_tool.refactor_string(code_string, name='auto_translated_code_file'))
-                        compiled_code = compile(translated_code, f"futurized_{code_path}", 'exec')
+                        translated_code = str(
+                            refactoring_tool.refactor_string(code_string, name="auto_translated_code_file")
+                        )
+                        compiled_code = compile(translated_code, f"futurized_{code_path}", "exec")
                         exec(compiled_code, self.code_namespace)
                     else:
                         raise
@@ -1098,7 +1137,7 @@ class Tool(Dictifiable):
 
     def __parse_config_files(self, tool_source):
         self.config_files = []
-        if not hasattr(tool_source, 'root'):
+        if not hasattr(tool_source, "root"):
             return
 
         root = tool_source.root
@@ -1126,7 +1165,7 @@ class Tool(Dictifiable):
 
     def __parse_trackster_conf(self, tool_source):
         self.trackster_conf = None
-        if not hasattr(tool_source, 'root'):
+        if not hasattr(tool_source, "root"):
             return
 
         # Trackster configuration.
@@ -1155,7 +1194,7 @@ class Tool(Dictifiable):
         """If tool shed installed tool, the base directory of the repository installed."""
         repository_base_dir = None
 
-        if getattr(self, 'tool_shed', None):
+        if getattr(self, "tool_shed", None):
             tool_dir = Path(self.tool_dir)
             for repo_dir in itertools.chain([tool_dir], tool_dir.parents):
                 if repo_dir.name == self.repository_name:
@@ -1185,10 +1224,10 @@ class Tool(Dictifiable):
 
     def __walk_test_data(self, dir, filename):
         for root, dirs, _ in os.walk(dir):
-            if '.hg' in dirs:
-                dirs.remove('.hg')
-            if 'test-data' in dirs:
-                test_data_dir = os.path.join(root, 'test-data')
+            if ".hg" in dirs:
+                dirs.remove(".hg")
+            if "test-data" in dirs:
+                test_data_dir = os.path.join(root, "test-data")
                 result = os.path.abspath(os.path.join(test_data_dir, filename))
                 if not in_directory(result, test_data_dir):
                     # Don't raise an explicit exception and reveal details about what
@@ -1201,11 +1240,12 @@ class Tool(Dictifiable):
 
     def tool_provided_metadata(self, job_wrapper):
         meta_file = os.path.join(job_wrapper.tool_working_directory, self.provided_metadata_file)
-        return parse_tool_provided_metadata(meta_file, provided_metadata_style=self.provided_metadata_style, job_wrapper=job_wrapper)
+        return parse_tool_provided_metadata(
+            meta_file, provided_metadata_style=self.provided_metadata_style, job_wrapper=job_wrapper
+        )
 
     def parse_command(self, tool_source):
-        """
-        """
+        """ """
         # Command line (template). Optional for tools that do not invoke a local program
         command = tool_source.parse_command()
         if command is not None:
@@ -1213,7 +1253,7 @@ class Tool(Dictifiable):
             # Must pre-pend this AFTER processing the cheetah command template
             self.interpreter = tool_source.parse_interpreter()
         else:
-            self.command = ''
+            self.command = ""
             self.interpreter = None
 
     def parse_environment_variables(self, tool_source):
@@ -1234,16 +1274,12 @@ class Tool(Dictifiable):
                 # Handle properties of the input form
                 self.check_values = string_as_bool(input_elem.get("check_values", self.check_values))
                 self.nginx_upload = string_as_bool(input_elem.get("nginx_upload", self.nginx_upload))
-                self.action = input_elem.get('action', self.action)
+                self.action = input_elem.get("action", self.action)
                 # If we have an nginx upload, save the action as a tuple instead of
                 # a string. The actual action needs to get url_for run to add any
                 # prefixes, and we want to avoid adding the prefix to the
                 # nginx_upload_path.
-                if (
-                    self.nginx_upload
-                    and self.app.config.nginx_upload_path
-                    and not isinstance(self.action, tuple)
-                ):
+                if self.nginx_upload and self.app.config.nginx_upload_path and not isinstance(self.action, tuple):
                     if "?" in unquote_plus(self.action):
                         raise Exception(
                             "URL parameters in a non-default tool action can not be used "
@@ -1283,7 +1319,7 @@ class Tool(Dictifiable):
         # parameters at all really, and should be passed in a different
         # way, making this check easier.
         template_macros = {}
-        if hasattr(tool_source, 'root'):
+        if hasattr(tool_source, "root"):
             template_macros = template_macro_params(tool_source.root)
         self.template_macro_params = template_macros
         for param in self.inputs.values():
@@ -1322,7 +1358,7 @@ class Tool(Dictifiable):
 
     def _parse_citations(self, tool_source):
         # TODO: Move following logic into ToolSource abstraction.
-        if not hasattr(tool_source, 'root'):
+        if not hasattr(tool_source, "root"):
             return []
 
         root = tool_source.root
@@ -1334,7 +1370,7 @@ class Tool(Dictifiable):
         for citation_elem in citations_elem:
             if citation_elem.tag != "citation":
                 pass
-            if hasattr(self.app, 'citations_manager'):
+            if hasattr(self.app, "citations_manager"):
                 citation = self.app.citations_manager.parse_citation(citation_elem)
                 if citation:
                     citations.append(citation)
@@ -1366,31 +1402,25 @@ class Tool(Dictifiable):
                     f"Tool with id '{self.id}': min repeat count must be less-than-or-equal to the max."
                 )
                 # Force default to be within min-max range
-                group_r.default = cast(
-                    int, min(max(group_r.default, group_r.min), group_r.max)
-                )
+                group_r.default = cast(int, min(max(group_r.default, group_r.min), group_r.max))
                 rval[group_r.name] = group_r
             elif input_type == "conditional":
                 group_c = Conditional()
                 group_c.name = input_source.get("name")
                 group_c.value_ref = input_source.get("value_ref", None)
-                group_c.value_ref_in_group = input_source.get_bool(
-                    "value_ref_in_group", True
-                )
+                group_c.value_ref_in_group = input_source.get_bool("value_ref_in_group", True)
                 value_from = input_source.get("value_from", None)
                 if value_from:
-                    value_from = value_from.split(':')
+                    value_from = value_from.split(":")
                     temp_value_from = locals().get(value_from[0])
                     group_c.test_param = rval[group_c.value_ref]
                     group_c.test_param.refresh_on_change = True
-                    for attr in value_from[1].split('.'):
+                    for attr in value_from[1].split("."):
                         temp_value_from = getattr(temp_value_from, attr)
                     group_c.value_from = temp_value_from  # type: ignore[assignment]
                     # ^^ due to https://github.com/python/mypy/issues/2427
                     assert group_c.value_from
-                    for case_value, case_inputs in group_c.value_from(
-                        context, group_c, self
-                    ).items():
+                    for case_value, case_inputs in group_c.value_from(context, group_c, self).items():
                         case = ConditionalWhen()
                         case.value = case_value
                         if case_inputs:
@@ -1402,11 +1432,11 @@ class Tool(Dictifiable):
                 else:
                     # Should have one child "input" which determines the case
                     test_param_input_source = input_source.parse_test_input_source()
-                    group_c.test_param = self.parse_param_elem(
-                        test_param_input_source, enctypes, context
-                    )
+                    group_c.test_param = self.parse_param_elem(test_param_input_source, enctypes, context)
                     if group_c.test_param.optional:
-                        log.debug(f"Tool with id '{self.id}': declares a conditional test parameter as optional, this is invalid and will be ignored.")
+                        log.debug(
+                            f"Tool with id '{self.id}': declares a conditional test parameter as optional, this is invalid and will be ignored."
+                        )
                         group_c.test_param.optional = False
                     possible_cases = list(
                         group_c.test_param.legal_values
@@ -1460,26 +1490,20 @@ class Tool(Dictifiable):
                 group_u = UploadDataset()
                 group_u.name = elem.get("name")
                 group_u.title = elem.get("title")
-                group_u.file_type_name = elem.get(
-                    "file_type_name", group_u.file_type_name
-                )
-                group_u.default_file_type = elem.get(
-                    "default_file_type", group_u.default_file_type
-                )
+                group_u.file_type_name = elem.get("file_type_name", group_u.file_type_name)
+                group_u.default_file_type = elem.get("default_file_type", group_u.default_file_type)
                 group_u.metadata_ref = elem.get("metadata_ref", group_u.metadata_ref)
                 try:
                     rval[group_u.file_type_name].refresh_on_change = True
                 except KeyError:
                     pass
                 group_page_source = XmlPageSource(elem)
-                group_u.inputs = self.parse_input_elem(
-                    group_page_source, enctypes, context
-                )
+                group_u.inputs = self.parse_input_elem(group_page_source, enctypes, context)
                 rval[group_u.name] = group_u
             elif input_type == "param":
                 param = self.parse_param_elem(input_source, enctypes, context)
                 rval[param.name] = param
-                if hasattr(param, 'data_ref'):
+                if hasattr(param, "data_ref"):
                     param.ref_input = context[param.data_ref]
                 self.input_params.append(param)
         return rval
@@ -1504,13 +1528,17 @@ class Tool(Dictifiable):
         return param
 
     def populate_resource_parameters(self, tool_source):
-        root = getattr(tool_source, 'root', None)
-        if root is not None and hasattr(self.app, 'job_config') and hasattr(self.app.job_config, 'get_tool_resource_xml'):
-            resource_xml = self.app.job_config.get_tool_resource_xml(root.get('id', '').lower(), self.tool_type)
+        root = getattr(tool_source, "root", None)
+        if (
+            root is not None
+            and hasattr(self.app, "job_config")
+            and hasattr(self.app.job_config, "get_tool_resource_xml")
+        ):
+            resource_xml = self.app.job_config.get_tool_resource_xml(root.get("id", "").lower(), self.tool_type)
             if resource_xml is not None:
-                inputs = root.find('inputs')
+                inputs = root.find("inputs")
                 if inputs is None:
-                    inputs = parse_xml_string('<inputs/>')
+                    inputs = parse_xml_string("<inputs/>")
                     root.append(inputs)
                 inputs.append(resource_xml)
 
@@ -1576,16 +1604,26 @@ class Tool(Dictifiable):
         help_text = tool_source.parse_help()
         if help_text is not None:
             try:
-                if help_text.find('.. image:: ') >= 0 and (self.tool_shed_repository or self.repository_id):
+                if help_text.find(".. image:: ") >= 0 and (self.tool_shed_repository or self.repository_id):
                     help_text = set_image_paths(
-                        self.app, help_text, encoded_repository_id=self.repository_id, tool_shed_repository=self.tool_shed_repository, tool_id=self.old_id, tool_version=self.version
+                        self.app,
+                        help_text,
+                        encoded_repository_id=self.repository_id,
+                        tool_shed_repository=self.tool_shed_repository,
+                        tool_id=self.old_id,
+                        tool_version=self.version,
                     )
             except Exception:
-                log.exception("Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id)
+                log.exception(
+                    "Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id
+                )
             try:
-                self.__help = Template(rst_to_html(help_text), input_encoding='utf-8',
-                                       default_filters=['decode.utf8'],
-                                       encoding_errors='replace')
+                self.__help = Template(
+                    rst_to_html(help_text),
+                    input_encoding="utf-8",
+                    default_filters=["decode.utf8"],
+                    encoding_errors="replace",
+                )
             except Exception:
                 log.exception("Exception while parsing help for tool with id '%s'", self.id)
 
@@ -1650,7 +1688,7 @@ class Tool(Dictifiable):
             return False
         # This is probably the best bet for detecting external web tools
         # right now
-        if self.tool_type.startswith('data_source'):
+        if self.tool_type.startswith("data_source"):
             return False
 
         if hasattr(tool_source, "root"):
@@ -1703,14 +1741,16 @@ class Tool(Dictifiable):
         if self.check_values:
             visit_input_values(self.inputs, values, callback)
 
-    def expand_incoming(self, trans, incoming, request_context, input_format='legacy'):
+    def expand_incoming(self, trans, incoming, request_context, input_format="legacy"):
         rerun_remap_job_id = None
-        if 'rerun_remap_job_id' in incoming:
+        if "rerun_remap_job_id" in incoming:
             try:
-                rerun_remap_job_id = trans.app.security.decode_id(incoming['rerun_remap_job_id'])
+                rerun_remap_job_id = trans.app.security.decode_id(incoming["rerun_remap_job_id"])
             except Exception as exception:
                 log.error(str(exception))
-                raise exceptions.MessageException("Failure executing tool with id '%s' (attempting to rerun invalid job).", self.id)
+                raise exceptions.MessageException(
+                    "Failure executing tool with id '%s' (attempting to rerun invalid job).", self.id
+                )
 
         set_dataset_matcher_factory(request_context, self)
 
@@ -1722,12 +1762,14 @@ class Tool(Dictifiable):
         # remap if multi-runs of tools are being used.
         if rerun_remap_job_id and len(expanded_incomings) > 1:
             raise exceptions.MessageException(
-                "Failure executing tool with id '%s' (cannot create multiple jobs when remapping existing job).", self.id)
+                "Failure executing tool with id '%s' (cannot create multiple jobs when remapping existing job).",
+                self.id,
+            )
 
         # Process incoming data
         validation_timer = self.app.execution_timer_factory.get_timer(
-            'internals.galaxy.tools.validation',
-            'Validated and populated state for tool request',
+            "internals.galaxy.tools.validation",
+            "Validated and populated state for tool request",
         )
         all_errors = []
         all_params = []
@@ -1744,9 +1786,17 @@ class Tool(Dictifiable):
             else:
                 # Update state for all inputs on the current page taking new
                 # values from `incoming`.
-                populate_state(request_context, self.inputs, expanded_incoming, params, errors, simple_errors=False, input_format=input_format)
+                populate_state(
+                    request_context,
+                    self.inputs,
+                    expanded_incoming,
+                    params,
+                    errors,
+                    simple_errors=False,
+                    input_format=input_format,
+                )
                 # If the tool provides a `validate_input` hook, call it.
-                validate_input = self.get_hook('validate_input')
+                validate_input = self.get_hook("validate_input")
                 if validate_input:
                     validate_input(request_context, errors, params, self.inputs)
             all_errors.append(errors)
@@ -1756,7 +1806,7 @@ class Tool(Dictifiable):
         log.info(validation_timer)
         return all_params, all_errors, rerun_remap_job_id, collection_info
 
-    def handle_input(self, trans, incoming, history=None, use_cached_job=False, input_format='legacy'):
+    def handle_input(self, trans, incoming, history=None, use_cached_job=False, input_format="legacy"):
         """
         Process incoming parameters for this tool from the dict `incoming`,
         update the tool state (or create if none existed), and either return
@@ -1764,7 +1814,9 @@ class Tool(Dictifiable):
         there were no errors).
         """
         request_context = proxy_work_context_for_history(trans, history=history)
-        all_params, all_errors, rerun_remap_job_id, collection_info = self.expand_incoming(trans=trans, incoming=incoming, request_context=request_context, input_format=input_format)
+        all_params, all_errors, rerun_remap_job_id, collection_info = self.expand_incoming(
+            trans=trans, incoming=incoming, request_context=request_context, input_format=input_format
+        )
         # If there were errors, we stay on the same page and display them
         if any(all_errors):
             # simple param_key -> message string for tool form.
@@ -1772,12 +1824,14 @@ class Tool(Dictifiable):
             param_errors = {}
             for d in all_errors:
                 for key, value in d.items():
-                    if hasattr(value, 'to_dict'):
+                    if hasattr(value, "to_dict"):
                         value_obj = value.to_dict()
                     else:
                         value_obj = {"message": unicodify(value)}
                     param_errors[key] = value_obj
-            raise exceptions.RequestParameterInvalidException(', '.join(msg for msg in err_data.values()), err_data=err_data, param_errors=param_errors)
+            raise exceptions.RequestParameterInvalidException(
+                ", ".join(msg for msg in err_data.values()), err_data=err_data, param_errors=param_errors
+            )
         else:
             mapping_params = MappingParameters(incoming, all_params)
             completed_jobs = {}
@@ -1793,7 +1847,15 @@ class Tool(Dictifiable):
                     )
                 else:
                     completed_jobs[i] = None
-            execution_tracker = execute_job(trans, self, mapping_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info, completed_jobs=completed_jobs)
+            execution_tracker = execute_job(
+                trans,
+                self,
+                mapping_params,
+                history=request_context.history,
+                rerun_remap_job_id=rerun_remap_job_id,
+                collection_info=collection_info,
+                completed_jobs=completed_jobs,
+            )
             # Raise an exception if there were jobs to execute and none of them were submitted,
             # if at least one is submitted or there are no jobs to execute - return aggregate
             # information including per-job errors. Arguably we should just always return the
@@ -1803,14 +1865,27 @@ class Tool(Dictifiable):
             if raise_execution_exception:
                 raise exceptions.MessageException(execution_tracker.execution_errors[0])
 
-            return dict(out_data=execution_tracker.output_datasets,
-                        num_jobs=len(execution_tracker.successful_jobs),
-                        job_errors=execution_tracker.execution_errors,
-                        jobs=execution_tracker.successful_jobs,
-                        output_collections=execution_tracker.output_collections,
-                        implicit_collections=execution_tracker.implicit_collections)
+            return dict(
+                out_data=execution_tracker.output_datasets,
+                num_jobs=len(execution_tracker.successful_jobs),
+                job_errors=execution_tracker.execution_errors,
+                jobs=execution_tracker.successful_jobs,
+                output_collections=execution_tracker.output_collections,
+                implicit_collections=execution_tracker.implicit_collections,
+            )
 
-    def handle_single_execution(self, trans, rerun_remap_job_id, execution_slice, history, execution_cache=None, completed_job=None, collection_info=None, job_callback=None, flush_job=True):
+    def handle_single_execution(
+        self,
+        trans,
+        rerun_remap_job_id,
+        execution_slice,
+        history,
+        execution_cache=None,
+        completed_job=None,
+        collection_info=None,
+        job_callback=None,
+        flush_job=True,
+    ):
         """
         Return a pair with whether execution is successful as well as either
         resulting output data or an error message indicating the problem.
@@ -1882,7 +1957,12 @@ class Tool(Dictifiable):
         for input_param in self.input_params:
             if isinstance(input_param, SelectToolParameter) and input_param.is_dynamic:
                 options = input_param.options
-                if options and options.tool_data_table and options.tool_data_table.missing_index_file and input_param not in params:
+                if (
+                    options
+                    and options.tool_data_table
+                    and options.tool_data_table.missing_index_file
+                    and input_param not in params
+                ):
                     params.append(input_param)
         return params
 
@@ -1914,10 +1994,12 @@ class Tool(Dictifiable):
         if incoming is None:
             incoming = {}
         try:
-            return self.tool_action.execute(self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs)
+            return self.tool_action.execute(
+                self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs
+            )
         except exceptions.ToolExecutionError as exc:
             job = exc.job
-            job_id = 'unknown'
+            job_id = "unknown"
             if job is not None:
                 job.mark_failed(info=exc.err_msg, blurb=exc.err_code.default_error_message)
                 job_id = job.id
@@ -1943,15 +2025,17 @@ class Tool(Dictifiable):
             if not error:
                 value, error = check_param(request_context, input, value, context)
             if error:
-                if update_values and not hasattr(input, 'data_ref'):
+                if update_values and not hasattr(input, "data_ref"):
                     try:
                         previous_value = value
                         value = input.get_initial_value(request_context, context)
-                        if not prefixed_name.startswith('__'):
-                            messages[prefixed_name] = error if previous_value == value else f'{error} Using default: \'{value}\'.'
+                        if not prefixed_name.startswith("__"):
+                            messages[prefixed_name] = (
+                                error if previous_value == value else f"{error} Using default: '{value}'."
+                            )
                         parent[input.name] = value
                     except Exception:
-                        messages[prefixed_name] = 'Attempt to replace invalid value for \'%s\' failed.' % (prefixed_label)
+                        messages[prefixed_name] = "Attempt to replace invalid value for '%s' failed." % (prefixed_label)
                 else:
                     messages[prefixed_name] = error
 
@@ -1967,7 +2051,7 @@ class Tool(Dictifiable):
                 job_directory=None,
                 metadata=False,
                 tool_instance=self,
-                **kwds
+                **kwds,
             )
 
     def build_dependency_shell_commands(self, job_directory=None, metadata=False):
@@ -1981,7 +2065,7 @@ class Tool(Dictifiable):
             job_directory=job_directory,
             preserve_python_environment=self.requires_galaxy_python_environment,
             metadata=metadata,
-            tool_instance=self
+            tool_instance=self,
         )
 
     @property
@@ -2040,19 +2124,19 @@ class Tool(Dictifiable):
         3) GALAXY_URL - the url to which the external application may post
            data as a response
         """
-        redirect_url = param_dict.get('REDIRECT_URL')
+        redirect_url = param_dict.get("REDIRECT_URL")
         redirect_url_params = self.build_redirect_url_params(param_dict)
         # Add the parameters to the redirect url.  We're splitting the param
         # string on '**^**' because the self.parse() method replaced white
         # space with that separator.
-        params = redirect_url_params.split('**^**')
+        params = redirect_url_params.split("**^**")
         rup_dict = {}
         for param in params:
-            p_list = param.split('=')
+            p_list = param.split("=")
             p_name = p_list[0]
             p_val = p_list[1]
             rup_dict[p_name] = p_val
-        DATA_URL = param_dict.get('DATA_URL', None)
+        DATA_URL = param_dict.get("DATA_URL", None)
         assert DATA_URL is not None, "DATA_URL parameter missing in tool config."
         DATA_URL += f"/{str(data.id)}/display"
         redirect_url += f"?DATA_URL={DATA_URL}"
@@ -2063,7 +2147,7 @@ class Tool(Dictifiable):
         if data.history.user:
             USERNAME = str(data.history.user.email)
         else:
-            USERNAME = 'Anonymous'
+            USERNAME = "Anonymous"
         redirect_url += f"&USERNAME={USERNAME}"
         return redirect_url
 
@@ -2077,10 +2161,10 @@ class Tool(Dictifiable):
             if code:
                 return code(*args, **kwargs)
         except Exception as e:
-            original_message = ''
+            original_message = ""
             if len(e.args):
                 original_message = e.args[0]
-            e.args = (f"Error in '{self.name}' hook '{hook_name}', original message: {original_message}", )
+            e.args = (f"Error in '{self.name}' hook '{hook_name}', original message: {original_message}",)
             raise
 
     def exec_before_job(self, app, inp_data, out_data, param_dict=None):
@@ -2094,7 +2178,18 @@ class Tool(Dictifiable):
         Called when a job has failed
         """
 
-    def discover_outputs(self, out_data, out_collections, tool_provided_metadata, tool_working_directory, job, input_ext, input_dbkey, inp_data=None, final_job_state='ok'):
+    def discover_outputs(
+        self,
+        out_data,
+        out_collections,
+        tool_provided_metadata,
+        tool_working_directory,
+        job,
+        input_ext,
+        input_dbkey,
+        inp_data=None,
+        final_job_state="ok",
+    ):
         """
         Find any additional datasets generated by a tool and attach (for
         cases where number of outputs is not known in advance).
@@ -2142,22 +2237,20 @@ class Tool(Dictifiable):
         if tool.help is not None:
             tool_help = tool.help._source
             # Check each line of the rendered tool help for an image tag that points to a location under static/
-            for help_line in tool_help.split('\n'):
+            for help_line in tool_help.split("\n"):
                 image_regex = re.compile(r'img alt="[^"]+" src="\${static_path}/([^"]+)"')
                 matches = re.search(image_regex, help_line)
                 if matches is not None:
                     tool_help_image = matches.group(1)
                     tarball_path = tool_help_image
-                    filesystem_path = os.path.abspath(os.path.join(self.app.config.root, 'static', tool_help_image))
+                    filesystem_path = os.path.abspath(os.path.join(self.app.config.root, "static", tool_help_image))
                     if os.path.exists(filesystem_path):
                         tarball_files.append((filesystem_path, tarball_path))
                         image_found = True
-                        tool_xml = tool_xml.replace('${static_path}/%s' % tarball_path, tarball_path)
+                        tool_xml = tool_xml.replace("${static_path}/%s" % tarball_path, tarball_path)
         # If one or more tool help images were found, add the modified tool XML to the tarball instead of the original.
         if image_found:
-            with tempfile.NamedTemporaryFile(
-                mode="w", suffix=".xml", delete=False
-            ) as fh2:
+            with tempfile.NamedTemporaryFile(mode="w", suffix=".xml", delete=False) as fh2:
                 new_tool_config = fh2.name
                 fh2.write(tool_xml)
             tool_tup = (new_tool_config, os.path.split(tool.config_file)[-1])
@@ -2185,52 +2278,51 @@ class Tool(Dictifiable):
                 for input in test.inputs:
                     for input_value in test.inputs[input]:
                         input_filename = str(input_value)
-                        input_path = os.path.abspath(os.path.join('test-data', input_filename))
+                        input_path = os.path.abspath(os.path.join("test-data", input_filename))
                         if os.path.exists(input_path):
-                            td_tup = (input_path, os.path.join('test-data', input_filename))
+                            td_tup = (input_path, os.path.join("test-data", input_filename))
                             tarball_files.append(td_tup)
                 # And add output file tuples to the list.
                 for _, filename, _ in test.outputs:
-                    output_filepath = os.path.abspath(os.path.join('test-data', filename))
+                    output_filepath = os.path.abspath(os.path.join("test-data", filename))
                     if os.path.exists(output_filepath):
-                        td_tup = (output_filepath, os.path.join('test-data', filename))
+                        td_tup = (output_filepath, os.path.join("test-data", filename))
                         tarball_files.append(td_tup)
         for param in tool.input_params:
             # Check for tool data table definitions.
-            if hasattr(param, 'options'):
-                if hasattr(param.options, 'tool_data_table'):
+            if hasattr(param, "options"):
+                if hasattr(param.options, "tool_data_table"):
                     data_table = param.options.tool_data_table
-                    if hasattr(data_table, 'filenames'):
+                    if hasattr(data_table, "filenames"):
                         data_table_definitions = []
                         for data_table_filename in data_table.filenames:
                             # FIXME: from_shed_config seems to always be False.
-                            if not data_table.filenames[data_table_filename]['from_shed_config']:
+                            if not data_table.filenames[data_table_filename]["from_shed_config"]:
                                 tar_file = f"{data_table.filenames[data_table_filename]['filename']}.sample"
-                                sample_file = os.path.join(data_table.filenames[data_table_filename]['tool_data_path'],
-                                                           tar_file)
+                                sample_file = os.path.join(
+                                    data_table.filenames[data_table_filename]["tool_data_path"], tar_file
+                                )
                                 # Use the .sample file, if one exists. If not, skip this data table.
                                 if os.path.exists(sample_file):
                                     tarfile_path, tarfile_name = os.path.split(tar_file)
-                                    tarfile_path = os.path.join('tool-data', tarfile_name)
+                                    tarfile_path = os.path.join("tool-data", tarfile_name)
                                     tarball_files.append((sample_file, tarfile_path))
                                 data_table_definitions.append(data_table.xml_string)
                         if len(data_table_definitions) > 0:
                             # Put the data table definition XML in a temporary file.
                             table_definition = '<?xml version="1.0" encoding="utf-8"?>\n<tables>\n    %s</tables>'
-                            table_definition = table_definition % "\n".join(
-                                data_table_definitions
-                            )
-                            with tempfile.NamedTemporaryFile(
-                                mode="w", delete=False
-                            ) as fh3:
+                            table_definition = table_definition % "\n".join(data_table_definitions)
+                            with tempfile.NamedTemporaryFile(mode="w", delete=False) as fh3:
                                 table_conf = fh3.name
                                 fh3.write(table_definition)
-                            tarball_files.append((table_conf, os.path.join('tool-data', 'tool_data_table_conf.xml.sample')))
+                            tarball_files.append(
+                                (table_conf, os.path.join("tool-data", "tool_data_table_conf.xml.sample"))
+                            )
                             temp_files.append(table_conf)
         # Create the tarball.
         with tempfile.NamedTemporaryFile(suffix=".tgz", delete=False) as fh4:
             tarball_archive = fh4.name
-        tarball = tarfile.open(name=tarball_archive, mode='w:gz')
+        tarball = tarfile.open(name=tarball_archive, mode="w:gz")
         # Add the files from the previously generated list.
         for fspath, tarpath in tarball_files:
             tarball.add(fspath, arcname=tarpath)
@@ -2241,7 +2333,7 @@ class Tool(Dictifiable):
         return tarball_archive
 
     def to_dict(self, trans, link_details=False, io_details=False, tool_help=False):
-        """ Returns dict of tool. """
+        """Returns dict of tool."""
 
         # Basic information
         tool_dict = super().to_dict()
@@ -2253,38 +2345,36 @@ class Tool(Dictifiable):
         tool_dict["xrefs"] = self.xrefs
 
         # Fill in ToolShedRepository info
-        if hasattr(self, 'tool_shed') and self.tool_shed:
-            tool_dict['tool_shed_repository'] = {
-                'name': self.repository_name,
-                'owner': self.repository_owner,
-                'changeset_revision': self.changeset_revision,
-                'tool_shed': self.tool_shed
+        if hasattr(self, "tool_shed") and self.tool_shed:
+            tool_dict["tool_shed_repository"] = {
+                "name": self.repository_name,
+                "owner": self.repository_owner,
+                "changeset_revision": self.changeset_revision,
+                "tool_shed": self.tool_shed,
             }
 
         # If an admin user, expose the path to the actual tool config XML file.
         if trans.user_is_admin:
             config_file = None if not self.config_file else os.path.abspath(self.config_file)
-            tool_dict['config_file'] = config_file
+            tool_dict["config_file"] = config_file
 
         # Add link details.
         if link_details:
             # Add details for creating a hyperlink to the tool.
             if not isinstance(self, DataSourceTool):
-                link = self.app.url_for(controller='tool_runner', tool_id=self.id)
+                link = self.app.url_for(controller="tool_runner", tool_id=self.id)
             else:
-                link = self.app.url_for(controller='tool_runner', action='data_source_redirect', tool_id=self.id)
+                link = self.app.url_for(controller="tool_runner", action="data_source_redirect", tool_id=self.id)
 
             # Basic information
-            tool_dict.update({'link': link,
-                              'min_width': self.uihints.get('minwidth', -1),
-                              'target': self.target})
+            tool_dict.update({"link": link, "min_width": self.uihints.get("minwidth", -1), "target": self.target})
 
         # Add input and output details.
         if io_details:
-            tool_dict['inputs'] = [input.to_dict(trans) for input in self.inputs.values()]
-            tool_dict['outputs'] = [output.to_dict(app=self.app) for output in self.outputs.values()]
+            tool_dict["inputs"] = [input.to_dict(trans) for input in self.inputs.values()]
+            tool_dict["outputs"] = [output.to_dict(app=self.app) for output in self.outputs.values()]
 
-        tool_dict['panel_section_id'], tool_dict['panel_section_name'] = self.get_panel_section()
+        tool_dict["panel_section_id"], tool_dict["panel_section_name"] = self.get_panel_section()
 
         tool_class = self.__class__
         # FIXME: the Tool class should declare directly, instead of ad hoc inspection
@@ -2292,11 +2382,13 @@ class Tool(Dictifiable):
         tool_dict["form_style"] = "regular" if regular_form else "special"
         if tool_help:
             # create tool help
-            help_txt = ''
+            help_txt = ""
             if self.help:
-                help_txt = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
+                help_txt = self.help.render(
+                    static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
+                )
                 help_txt = unicodify(help_txt)
-            tool_dict['help'] = help_txt
+            tool_dict["help"] = help_txt
 
         return tool_dict
 
@@ -2306,20 +2398,23 @@ class Tool(Dictifiable):
         """
         if kwd is None:
             kwd = {}
-        if workflow_building_mode is workflow_building_modes.USE_HISTORY or workflow_building_mode is workflow_building_modes.DISABLED:
+        if (
+            workflow_building_mode is workflow_building_modes.USE_HISTORY
+            or workflow_building_mode is workflow_building_modes.DISABLED
+        ):
             # We don't need a history when exporting a workflow for the workflow editor or when downloading a workflow
             history = history or trans.get_history()
             if history is None and job is not None:
                 history = self.history_manager.get_owned(job.history.id, trans.user, current_history=trans.history)
             if history is None:
-                raise exceptions.MessageException('History unavailable. Please specify a valid history id')
+                raise exceptions.MessageException("History unavailable. Please specify a valid history id")
 
         # build request context
         request_context = proxy_work_context_for_history(trans, history, workflow_building_mode=workflow_building_mode)
 
         # load job parameters into incoming
-        tool_message = ''
-        tool_warnings = ''
+        tool_message = ""
+        tool_warnings = ""
         if job:
             try:
                 job_params = job.get_param_values(self.app, ignore_errors=True)
@@ -2351,15 +2446,17 @@ class Tool(Dictifiable):
 
         # create tool model
         tool_model = self.to_dict(request_context)
-        tool_model['inputs'] = []
-        self.populate_model(request_context, self.inputs, state_inputs, tool_model['inputs'])
+        tool_model["inputs"] = []
+        self.populate_model(request_context, self.inputs, state_inputs, tool_model["inputs"])
         unset_dataset_matcher_factory(request_context)
 
         # create tool help
-        tool_help = ''
+        tool_help = ""
         if self.help:
-            tool_help = self.help.render(static_path=self.app.url_for('/static'), host_url=self.app.url_for('/', qualified=True))
-            tool_help = unicodify(tool_help, 'utf-8')
+            tool_help = self.help.render(
+                static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
+            )
+            tool_help = unicodify(tool_help, "utf-8")
 
         if isinstance(self.action, tuple):
             action = self.action[0] + self.app.url_for(self.action[1])
@@ -2367,28 +2464,30 @@ class Tool(Dictifiable):
             action = self.app.url_for(self.action)
 
         # update tool model
-        tool_model.update({
-            'id': self.id,
-            'help': tool_help,
-            'citations': bool(self.citations),
-            'sharable_url': self.sharable_url,
-            'message': tool_message,
-            'warnings': tool_warnings,
-            'versions': self.tool_versions,
-            'requirements': [{'name': r.name, 'version': r.version} for r in self.requirements],
-            'errors': state_errors,
-            'tool_errors': self.tool_errors,
-            'state_inputs': params_to_strings(self.inputs, state_inputs, self.app, use_security=True, nested=True),
-            'job_id': trans.security.encode_id(job.id) if job else None,
-            'job_remap': job.remappable() if job else None,
-            'history_id': trans.security.encode_id(history.id) if history else None,
-            'display': self.display_interface,
-            'action': action,
-            'license': self.license,
-            'creator': self.creator,
-            'method': self.method,
-            'enctype': self.enctype
-        })
+        tool_model.update(
+            {
+                "id": self.id,
+                "help": tool_help,
+                "citations": bool(self.citations),
+                "sharable_url": self.sharable_url,
+                "message": tool_message,
+                "warnings": tool_warnings,
+                "versions": self.tool_versions,
+                "requirements": [{"name": r.name, "version": r.version} for r in self.requirements],
+                "errors": state_errors,
+                "tool_errors": self.tool_errors,
+                "state_inputs": params_to_strings(self.inputs, state_inputs, self.app, use_security=True, nested=True),
+                "job_id": trans.security.encode_id(job.id) if job else None,
+                "job_remap": job.remappable() if job else None,
+                "history_id": trans.security.encode_id(history.id) if history else None,
+                "display": self.display_interface,
+                "action": action,
+                "license": self.license,
+                "creator": self.creator,
+                "method": self.method,
+                "enctype": self.enctype,
+            }
+        )
         return tool_model
 
     def populate_model(self, request_context, inputs, state_inputs, group_inputs, other_values=None):
@@ -2399,7 +2498,7 @@ class Tool(Dictifiable):
         for input_index, input in enumerate(inputs.values()):
             tool_dict = None
             group_state = state_inputs.get(input.name, {})
-            if input.type == 'repeat':
+            if input.type == "repeat":
                 tool_dict = input.to_dict(request_context)
                 group_size = len(group_state)
                 tool_dict["cache"] = [None] * group_size
@@ -2407,31 +2506,44 @@ class Tool(Dictifiable):
                 for i in range(group_size):
                     group_cache[i] = []
                     self.populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
-            elif input.type == 'conditional':
+            elif input.type == "conditional":
                 tool_dict = input.to_dict(request_context)
-                if 'test_param' in tool_dict:
-                    test_param = tool_dict['test_param']
-                    test_param['value'] = input.test_param.value_to_basic(group_state.get(test_param['name'], input.test_param.get_initial_value(request_context, other_values)), self.app)
-                    test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'])
-                    for i in range(len(tool_dict['cases'])):
+                if "test_param" in tool_dict:
+                    test_param = tool_dict["test_param"]
+                    test_param["value"] = input.test_param.value_to_basic(
+                        group_state.get(
+                            test_param["name"], input.test_param.get_initial_value(request_context, other_values)
+                        ),
+                        self.app,
+                    )
+                    test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
+                    for i in range(len(tool_dict["cases"])):
                         current_state = {}
-                        if i == group_state.get('__current_case__'):
+                        if i == group_state.get("__current_case__"):
                             current_state = group_state
-                        self.populate_model(request_context, input.cases[i].inputs, current_state, tool_dict['cases'][i]['inputs'], other_values)
-            elif input.type == 'section':
+                        self.populate_model(
+                            request_context,
+                            input.cases[i].inputs,
+                            current_state,
+                            tool_dict["cases"][i]["inputs"],
+                            other_values,
+                        )
+            elif input.type == "section":
                 tool_dict = input.to_dict(request_context)
-                self.populate_model(request_context, input.inputs, group_state, tool_dict['inputs'], other_values)
+                self.populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
             else:
                 try:
                     initial_value = input.get_initial_value(request_context, other_values)
                     tool_dict = input.to_dict(request_context, other_values=other_values)
-                    tool_dict['value'] = input.value_to_basic(state_inputs.get(input.name, initial_value), self.app, use_security=True)
-                    tool_dict['default_value'] = input.value_to_basic(initial_value, self.app, use_security=True)
-                    tool_dict['text_value'] = input.value_to_display_text(tool_dict['value'])
+                    tool_dict["value"] = input.value_to_basic(
+                        state_inputs.get(input.name, initial_value), self.app, use_security=True
+                    )
+                    tool_dict["default_value"] = input.value_to_basic(initial_value, self.app, use_security=True)
+                    tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
                 except ImplicitConversionRequired:
                     tool_dict = input.to_dict(request_context)
                     # This hack leads client to display a text field
-                    tool_dict['textable'] = True
+                    tool_dict["textable"] = True
                 except Exception:
                     tool_dict = input.to_dict(request_context)
                     log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
@@ -2449,13 +2561,13 @@ class Tool(Dictifiable):
         # Create index for hdas.
         hda_source_dict = {}
         for hda in history.datasets:
-            key = f'{hda.hid}_{hda.dataset.id}'
+            key = f"{hda.hid}_{hda.dataset.id}"
             hda_source_dict[hda.dataset.id] = hda_source_dict[key] = hda
 
         # Ditto for dataset collections.
         hdca_source_dict = {}
         for hdca in history.dataset_collections:
-            key = f'{hdca.hid}_{hdca.collection.id}'
+            key = f"{hdca.hid}_{hdca.collection.id}"
             hdca_source_dict[hdca.collection.id] = hdca_source_dict[key] = hdca
 
         # Map dataset or collection to current history
@@ -2470,7 +2582,7 @@ class Tool(Dictifiable):
                 source = hdca_source_dict
             else:
                 return None
-            key = f'{value.hid}_{id}'
+            key = f"{value.hid}_{id}"
             if key in source:
                 return source[key]
             elif id in source:
@@ -2493,6 +2605,7 @@ class Tool(Dictifiable):
                     return map_to_history(value)
             elif isinstance(input, DataCollectionToolParameter):
                 return map_to_history(value)
+
         visit_input_values(tool_inputs, params, mapping_callback)
 
     def _compare_tool_version(self, job):
@@ -2501,30 +2614,36 @@ class Tool(Dictifiable):
         """
         tool_id = job.tool_id
         tool_version = job.tool_version
-        message = ''
+        message = ""
         try:
-            select_field, tools, tool = self.app.toolbox.get_tool_components(tool_id, tool_version=tool_version, get_loaded_tools_by_lineage=False, set_selected=True)
+            select_field, tools, tool = self.app.toolbox.get_tool_components(
+                tool_id, tool_version=tool_version, get_loaded_tools_by_lineage=False, set_selected=True
+            )
             if tool is None:
-                raise exceptions.MessageException('This dataset was created by an obsolete tool (%s). Can\'t re-run.' % tool_id)
+                raise exceptions.MessageException(
+                    "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id
+                )
             if (self.id != tool_id and self.old_id != tool_id) or self.version != tool_version:
                 if self.id == tool_id:
                     if tool_version:
                         message = f'This job was run with tool version "{tool_version}", which is not available. '
                         if len(tools) > 1:
-                            message += 'You can re-run the job with the selected tool or choose another version of the tool. '
+                            message += (
+                                "You can re-run the job with the selected tool or choose another version of the tool. "
+                            )
                         else:
-                            message += 'You can re-run the job with this tool version, which is a different version of the original tool. '
+                            message += "You can re-run the job with this tool version, which is a different version of the original tool. "
                 else:
-                    new_tool_shed_url = f'{tool.sharable_url}/{tool.changeset_revision}/'
-                    old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_id.split('/repos/')[0])
-                    old_tool_shed_url = f'{old_tool_shed_url}/view/{tool.repository_owner}/{tool.repository_name}/'
-                    message = f'This job was run with <a href=\"{old_tool_shed_url}\" target=\"_blank\">tool id \"{tool_id}\"</a>, version "{tool_version}", which is not available. '
+                    new_tool_shed_url = f"{tool.sharable_url}/{tool.changeset_revision}/"
+                    old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_id.split("/repos/")[0])
+                    old_tool_shed_url = f"{old_tool_shed_url}/view/{tool.repository_owner}/{tool.repository_name}/"
+                    message = f'This job was run with <a href="{old_tool_shed_url}" target="_blank">tool id "{tool_id}"</a>, version "{tool_version}", which is not available. '
                     if len(tools) > 1:
-                        message += f'You can re-run the job with the selected <a href=\"{new_tool_shed_url}\" target=\"_blank\">tool id \"{self.id}\"</a> or choose another derivation of the tool. '
+                        message += f'You can re-run the job with the selected <a href="{new_tool_shed_url}" target="_blank">tool id "{self.id}"</a> or choose another derivation of the tool. '
                     else:
-                        message += f'You can re-run the job with <a href=\"{new_tool_shed_url}\" target=\"_blank\">tool id \"{self.id}\"</a>, which is a derivation of the original tool. '
+                        message += f'You can re-run the job with <a href="{new_tool_shed_url}" target="_blank">tool id "{self.id}"</a>, which is a derivation of the original tool. '
             if not self.is_latest_version:
-                message += 'There is a newer version of this tool available.'
+                message += "There is a newer version of this tool available."
         except Exception as e:
             raise exceptions.MessageException(unicodify(e))
         return message
@@ -2534,15 +2653,15 @@ class Tool(Dictifiable):
 
     @classmethod
     def get_externally_referenced_paths(self, path):
-        """ Return relative paths to externally referenced files by the tool
+        """Return relative paths to externally referenced files by the tool
         described by file at `path`. External components should not assume things
         about the structure of tool xml files (this is the tool's responsibility).
         """
         tree = raw_tool_xml_tree(path)
         root = tree.getroot()
         external_paths = []
-        for code_elem in root.findall('code'):
-            external_path = code_elem.get('file')
+        for code_elem in root.findall("code"):
+            external_path = code_elem.get("file")
             if external_path:
                 external_paths.append(external_path)
         external_paths.extend(imported_macro_paths(root))
@@ -2555,7 +2674,8 @@ class OutputParameterJSONTool(Tool):
     Alternate implementation of Tool that provides parameters and other values
     JSONified within the contents of an output dataset
     """
-    tool_type = 'output_parameter_json'
+
+    tool_type = "output_parameter_json"
 
     def _prepare_json_list(self, param_list):
         rval = []
@@ -2583,9 +2703,15 @@ class OutputParameterJSONTool(Tool):
         if param_dict is None:
             param_dict = {}
         json_params = {}
-        json_params['param_dict'] = self._prepare_json_param_dict(param_dict)  # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones?
-        json_params['output_data'] = []
-        json_params['job_config'] = dict(GALAXY_DATATYPES_CONF_FILE=param_dict.get('GALAXY_DATATYPES_CONF_FILE'), GALAXY_ROOT_DIR=param_dict.get('GALAXY_ROOT_DIR'), TOOL_PROVIDED_JOB_METADATA_FILE=self.provided_metadata_file)
+        json_params["param_dict"] = self._prepare_json_param_dict(
+            param_dict
+        )  # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones?
+        json_params["output_data"] = []
+        json_params["job_config"] = dict(
+            GALAXY_DATATYPES_CONF_FILE=param_dict.get("GALAXY_DATATYPES_CONF_FILE"),
+            GALAXY_ROOT_DIR=param_dict.get("GALAXY_ROOT_DIR"),
+            TOOL_PROVIDED_JOB_METADATA_FILE=self.provided_metadata_file,
+        )
         json_filename = None
         for out_name, data in out_data.items():
             # use wrapped dataset to access certain values
@@ -2593,26 +2719,26 @@ class OutputParameterJSONTool(Tool):
             # allow multiple files to be created
             file_name = str(wrapped_data)
             extra_files_path = str(wrapped_data.files_path)
-            data_dict = dict(out_data_name=out_name,
-                             ext=data.ext,
-                             dataset_id=data.dataset.id,
-                             hda_id=data.id,
-                             file_name=file_name,
-                             extra_files_path=extra_files_path)
-            json_params['output_data'].append(data_dict)
+            data_dict = dict(
+                out_data_name=out_name,
+                ext=data.ext,
+                dataset_id=data.dataset.id,
+                hda_id=data.id,
+                file_name=file_name,
+                extra_files_path=extra_files_path,
+            )
+            json_params["output_data"].append(data_dict)
             if json_filename is None:
                 json_filename = file_name
         if json_filename is None:
-            raise Exception(
-                "Must call 'exec_before_job' with 'out_data' containing at least one entry."
-            )
+            raise Exception("Must call 'exec_before_job' with 'out_data' containing at least one entry.")
         with open(json_filename, "w") as out:
             out.write(json.dumps(json_params))
 
 
 class ExpressionTool(Tool):
     requires_js_runtime = True
-    tool_type = 'expression'
+    tool_type = "expression"
     tool_type_local = True
     EXPRESSION_INPUTS_NAME = "_expression_inputs_.json"
 
@@ -2645,21 +2771,23 @@ class ExpressionTool(Tool):
             wrapped_data = param_dict.get(out_name)
             file_name = str(wrapped_data)
 
-            outputs.append(dict(
-                name=out_name,
-                from_expression=output_def.from_expression,
-                path=file_name,
-            ))
+            outputs.append(
+                dict(
+                    name=out_name,
+                    from_expression=output_def.from_expression,
+                    path=file_name,
+                )
+            )
 
         if param_dict is None:
             raise Exception("Internal error - param_dict is empty.")
 
         job: Dict[str, str] = {}
-        json_wrap(self.inputs, param_dict, self.profile, job, handle_files='OBJECT')
+        json_wrap(self.inputs, param_dict, self.profile, job, handle_files="OBJECT")
         expression_inputs = {
-            'job': job,
-            'script': self._expression,
-            'outputs': outputs,
+            "job": job,
+            "script": self._expression,
+            "outputs": outputs,
         }
         expressions.write_evalute_script(os.path.join(local_working_directory))
         with open(expression_inputs_path, "w") as f:
@@ -2686,8 +2814,7 @@ class ExpressionTool(Tool):
                 out_data[key].copy_from(copy_object)
 
     def parse_environment_variables(self, tool_source):
-        """ Setup environment variable for inputs file.
-        """
+        """Setup environment variable for inputs file."""
         environmnt_variables_raw = super().parse_environment_variables(tool_source)
         expression_script_inputs = dict(
             name="GALAXY_EXPRESSION_INPUTS",
@@ -2702,38 +2829,47 @@ class DataSourceTool(OutputParameterJSONTool):
     Alternate implementation of Tool for data_source tools -- those that
     allow the user to query and extract data from another web site.
     """
-    tool_type = 'data_source'
+
+    tool_type = "data_source"
     default_tool_action = DataSourceToolAction
 
     def _build_GALAXY_URL_parameter(self):
-        return ToolParameter.build(self, XML(f'<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id={self.id}" />'))
+        return ToolParameter.build(
+            self, XML(f'<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id={self.id}" />')
+        )
 
     def parse_inputs(self, tool_source):
         super().parse_inputs(tool_source)
         # Open all data_source tools in _top.
-        self.target = '_top'
-        if 'GALAXY_URL' not in self.inputs:
-            self.inputs['GALAXY_URL'] = self._build_GALAXY_URL_parameter()
-            self.inputs_by_page[0]['GALAXY_URL'] = self.inputs['GALAXY_URL']
+        self.target = "_top"
+        if "GALAXY_URL" not in self.inputs:
+            self.inputs["GALAXY_URL"] = self._build_GALAXY_URL_parameter()
+            self.inputs_by_page[0]["GALAXY_URL"] = self.inputs["GALAXY_URL"]
 
     def exec_before_job(self, app, inp_data, out_data, param_dict=None):
         if param_dict is None:
             param_dict = {}
-        dbkey = param_dict.get('dbkey')
-        info = param_dict.get('info')
-        data_type = param_dict.get('data_type')
-        name = param_dict.get('name')
+        dbkey = param_dict.get("dbkey")
+        info = param_dict.get("info")
+        data_type = param_dict.get("data_type")
+        name = param_dict.get("name")
 
         json_params = {}
-        json_params['param_dict'] = self._prepare_json_param_dict(param_dict)  # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones?
-        json_params['output_data'] = []
-        json_params['job_config'] = dict(GALAXY_DATATYPES_CONF_FILE=param_dict.get('GALAXY_DATATYPES_CONF_FILE'), GALAXY_ROOT_DIR=param_dict.get('GALAXY_ROOT_DIR'), TOOL_PROVIDED_JOB_METADATA_FILE=self.provided_metadata_file)
+        json_params["param_dict"] = self._prepare_json_param_dict(
+            param_dict
+        )  # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones?
+        json_params["output_data"] = []
+        json_params["job_config"] = dict(
+            GALAXY_DATATYPES_CONF_FILE=param_dict.get("GALAXY_DATATYPES_CONF_FILE"),
+            GALAXY_ROOT_DIR=param_dict.get("GALAXY_ROOT_DIR"),
+            TOOL_PROVIDED_JOB_METADATA_FILE=self.provided_metadata_file,
+        )
         json_filename = None
         for out_name, data in out_data.items():
             # use wrapped dataset to access certain values
             wrapped_data = param_dict.get(out_name)
             # allow multiple files to be created
-            cur_base_param_name = f'GALAXY|{out_name}|'
+            cur_base_param_name = f"GALAXY|{out_name}|"
             cur_name = param_dict.get(f"{cur_base_param_name}name", name)
             cur_dbkey = param_dict.get(f"{cur_base_param_name}dkey", dbkey)
             cur_info = param_dict.get(f"{cur_base_param_name}info", info)
@@ -2748,32 +2884,32 @@ class DataSourceTool(OutputParameterJSONTool):
                 data.extension = cur_data_type
             file_name = str(wrapped_data)
             extra_files_path = str(wrapped_data.files_path)
-            data_dict = dict(out_data_name=out_name,
-                             ext=data.ext,
-                             dataset_id=data.dataset.id,
-                             hda_id=data.id,
-                             file_name=file_name,
-                             extra_files_path=extra_files_path)
-            json_params['output_data'].append(data_dict)
+            data_dict = dict(
+                out_data_name=out_name,
+                ext=data.ext,
+                dataset_id=data.dataset.id,
+                hda_id=data.id,
+                file_name=file_name,
+                extra_files_path=extra_files_path,
+            )
+            json_params["output_data"].append(data_dict)
             if json_filename is None:
                 json_filename = file_name
         if json_filename is None:
-            raise Exception(
-                "Must call 'exec_before_job' with 'out_data' containing at least one entry."
-            )
+            raise Exception("Must call 'exec_before_job' with 'out_data' containing at least one entry.")
         with open(json_filename, "w") as out:
             out.write(json.dumps(json_params))
 
 
 class AsyncDataSourceTool(DataSourceTool):
-    tool_type = 'data_source_async'
+    tool_type = "data_source_async"
 
     def _build_GALAXY_URL_parameter(self):
         return ToolParameter.build(self, XML(f'<param name="GALAXY_URL" type="baseurl" value="/async/{self.id}" />'))
 
 
 class DataDestinationTool(Tool):
-    tool_type = 'data_destination'
+    tool_type = "data_destination"
 
 
 class SetMetadataTool(Tool):
@@ -2781,26 +2917,26 @@ class SetMetadataTool(Tool):
     Tool implementation for special tool that sets metadata on an existing
     dataset.
     """
-    tool_type = 'set_metadata'
+
+    tool_type = "set_metadata"
     requires_setting_metadata = False
     tool_action: "SetMetadataToolAction"
 
     def regenerate_imported_metadata_if_needed(self, hda, history, job):
         if hda.has_metadata_files:
             job, *_ = self.tool_action.execute_via_app(
-                self, self.app, job.session_id,
-                history.id, job.user, incoming={'input1': hda}, overwrite=False
+                self, self.app, job.session_id, history.id, job.user, incoming={"input1": hda}, overwrite=False
             )
             self.app.job_manager.enqueue(job=job, tool=self)
 
     def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
-        working_directory = app.object_store.get_filename(
-            job, base_dir='job_work', dir_only=True, obj_dir=True
-        )
+        working_directory = app.object_store.get_filename(job, base_dir="job_work", dir_only=True, obj_dir=True)
         for name, dataset in inp_data.items():
             external_metadata = get_metadata_compute_strategy(app.config, job.id, tool_id=self.id)
             sa_session = app.model.context
-            metadata_set_successfully = external_metadata.external_metadata_set_successfully(dataset, name, sa_session, working_directory=working_directory)
+            metadata_set_successfully = external_metadata.external_metadata_set_successfully(
+                dataset, name, sa_session, working_directory=working_directory
+            )
             if metadata_set_successfully:
                 try:
                     # external_metadata_set_successfully is only an approximation (the metadata json file exists),
@@ -2818,8 +2954,8 @@ class SetMetadataTool(Tool):
             # user? For now, we'll leave the default metadata and set the state
             # back to its original.
             dataset.datatype.after_setting_metadata(dataset)
-            if job and job.tool_id == '1.0.0':
-                dataset.state = param_dict.get('__ORIGINAL_DATASET_STATE__')
+            if job and job.tool_id == "1.0.0":
+                dataset.state = param_dict.get("__ORIGINAL_DATASET_STATE__")
             else:
                 # Revert dataset.state to fall back to dataset.dataset.state
                 dataset._state = None
@@ -2843,11 +2979,11 @@ class SetMetadataTool(Tool):
 
 
 class ExportHistoryTool(Tool):
-    tool_type = 'export_history'
+    tool_type = "export_history"
 
 
 class ImportHistoryTool(Tool):
-    tool_type = 'import_history'
+    tool_type = "import_history"
 
     def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None, **kwds):
         super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
@@ -2857,17 +2993,19 @@ class ImportHistoryTool(Tool):
 
 
 class InteractiveTool(Tool):
-    tool_type = 'interactive'
+    tool_type = "interactive"
     produces_entry_points = True
 
     def __init__(self, config_file, tool_source, app, **kwd):
-        assert app.config.interactivetools_enable, ValueError('Trying to load an InteractiveTool, but InteractiveTools are not enabled.')
+        assert app.config.interactivetools_enable, ValueError(
+            "Trying to load an InteractiveTool, but InteractiveTools are not enabled."
+        )
         super().__init__(config_file, tool_source, app, **kwd)
 
     def __remove_interactivetool_by_job(self, job):
         if job:
             eps = job.interactivetool_entry_points
-            log.debug('__remove_interactivetool_by_job: %s', eps)
+            log.debug("__remove_interactivetool_by_job: %s", eps)
             self.app.interactivetool_manager.remove_entry_points(eps)
         else:
             log.warning("Could not determine job to stop InteractiveTool: %s", job)
@@ -2884,7 +3022,7 @@ class InteractiveTool(Tool):
 
 
 class DataManagerTool(OutputParameterJSONTool):
-    tool_type = 'manage_data'
+    tool_type = "manage_data"
     default_tool_action = DataManagerToolAction
 
     def __init__(self, config_file, root, app, guid=None, data_manager_id=None, **kwds):
@@ -2902,18 +3040,21 @@ class DataManagerTool(OutputParameterJSONTool):
         # process results of tool
         data_manager_id = job.data_manager_association.data_manager_id
         data_manager = self.app.data_managers.get_manager(data_manager_id, None)
-        assert data_manager is not None, f"Invalid data manager ({data_manager_id}) requested. It may have been removed before the job completed."
+        assert (
+            data_manager is not None
+        ), f"Invalid data manager ({data_manager_id}) requested. It may have been removed before the job completed."
         data_manager.process_result(out_data)
 
     def get_default_history_by_trans(self, trans, create=False):
         def _create_data_manager_history(user):
-            history = trans.app.model.History(name='Data Manager History (automatically created)', user=user)
+            history = trans.app.model.History(name="Data Manager History (automatically created)", user=user)
             data_manager_association = trans.app.model.DataManagerHistoryAssociation(user=user, history=history)
             trans.sa_session.add_all((history, data_manager_association))
             trans.sa_session.flush()
             return history
+
         user = trans.user
-        assert user, 'You must be logged in to use this tool.'
+        assert user, "You must be logged in to use this tool."
         assert self.allow_user_access(user), "You must be an admin to access this tool."
         dm_history_associations = user.data_manager_histories
         if not dm_history_associations:
@@ -2981,7 +3122,9 @@ class DatabaseOperationTool(Tool):
 
             if self.require_dataset_ok:
                 if state != model.Dataset.states.OK:
-                    raise ValueError(f"Tool requires inputs to be in valid state, but dataset {input_dataset} is in state '{input_dataset.state}'")
+                    raise ValueError(
+                        f"Tool requires inputs to be in valid state, but dataset {input_dataset} is in state '{input_dataset.state}'"
+                    )
 
         for input_dataset in input_datasets.values():
             check_dataset_state(input_dataset.state)
@@ -3009,7 +3152,7 @@ class DatabaseOperationTool(Tool):
 
 
 class UnzipCollectionTool(DatabaseOperationTool):
-    tool_type = 'unzip_collection'
+    tool_type = "unzip_collection"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         has_collection = incoming["input"]
@@ -3030,7 +3173,7 @@ class UnzipCollectionTool(DatabaseOperationTool):
 
 
 class ZipCollectionTool(DatabaseOperationTool):
-    tool_type = 'zip_collection'
+    tool_type = "zip_collection"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         forward_o = incoming["input_forward"]
@@ -3047,7 +3190,7 @@ class ZipCollectionTool(DatabaseOperationTool):
 
 
 class BuildListCollectionTool(DatabaseOperationTool):
-    tool_type = 'build_list'
+    tool_type = "build_list"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         new_elements = {}
@@ -3058,12 +3201,12 @@ class BuildListCollectionTool(DatabaseOperationTool):
                     id_select = incoming_repeat["id_cond"]["id_select"]
                 except KeyError:
                     # Prior to tool version 1.2.0
-                    id_select = 'idx'
-                if id_select == 'idx':
+                    id_select = "idx"
+                if id_select == "idx":
                     identifier = str(i)
-                elif id_select == 'identifier':
-                    identifier = getattr(incoming_repeat["input"], 'element_identifier', incoming_repeat["input"].name)
-                elif id_select == 'manual':
+                elif id_select == "identifier":
+                    identifier = getattr(incoming_repeat["input"], "element_identifier", incoming_repeat["input"].name)
+                elif id_select == "manual":
                     identifier = incoming_repeat["id_cond"]["identifier"]
                 new_elements[identifier] = incoming_repeat["input"].copy(copy_tags=incoming_repeat["input"].tags)
 
@@ -3074,7 +3217,7 @@ class BuildListCollectionTool(DatabaseOperationTool):
 
 
 class ExtractDatasetCollectionTool(DatabaseOperationTool):
-    tool_type = 'extract_dataset'
+    tool_type = "extract_dataset"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, tags=None, **kwds):
         has_collection = incoming["input"]
@@ -3104,7 +3247,7 @@ class ExtractDatasetCollectionTool(DatabaseOperationTool):
 
 
 class MergeCollectionTool(DatabaseOperationTool):
-    tool_type = 'merge_collection'
+    tool_type = "merge_collection"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         input_lists = []
@@ -3116,10 +3259,10 @@ class MergeCollectionTool(DatabaseOperationTool):
         dupl_actions = "keep_first"
         suffix_pattern = None
         if advanced is not None:
-            dupl_actions = advanced["conflict"]['duplicate_options']
+            dupl_actions = advanced["conflict"]["duplicate_options"]
 
-            if dupl_actions in ['suffix_conflict', 'suffix_every', 'suffix_conflict_rest']:
-                suffix_pattern = advanced['conflict']['suffix_pattern']
+            if dupl_actions in ["suffix_conflict", "suffix_every", "suffix_conflict_rest"]:
+                suffix_pattern = advanced["conflict"]["suffix_pattern"]
 
         new_element_structure = {}
 
@@ -3188,7 +3331,6 @@ class MergeCollectionTool(DatabaseOperationTool):
 
 
 class FilterDatasetsTool(DatabaseOperationTool):
-
     def _get_new_elements(self, history, elements_to_copy):
         new_elements = {}
         for dce in elements_to_copy:
@@ -3203,7 +3345,7 @@ class FilterDatasetsTool(DatabaseOperationTool):
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         collection = incoming["input"]
 
-        if hasattr(collection, 'element_object'):
+        if hasattr(collection, "element_object"):
             # A list
             elements = collection.element_object.elements
             collection_type = collection.element_object.collection_type
@@ -3216,7 +3358,7 @@ class FilterDatasetsTool(DatabaseOperationTool):
 
         elements_to_copy = []
         for element in elements:
-            if collection_type == 'list':
+            if collection_type == "list":
                 if self.element_is_valid(element):
                     elements_to_copy.append(element)
             else:
@@ -3230,15 +3372,12 @@ class FilterDatasetsTool(DatabaseOperationTool):
         new_elements = self._get_new_elements(history=history, elements_to_copy=elements_to_copy)
         self._add_datasets_to_history(history, new_elements.values())
         output_collections.create_collection(
-            next(iter(self.outputs.values())),
-            "output",
-            elements=new_elements,
-            propagate_hda_tags=False
+            next(iter(self.outputs.values())), "output", elements=new_elements, propagate_hda_tags=False
         )
 
 
 class FilterFailedDatasetsTool(FilterDatasetsTool):
-    tool_type = 'filter_failed_datasets_collection'
+    tool_type = "filter_failed_datasets_collection"
     require_dataset_ok = False
 
     def element_is_valid(self, element):
@@ -3246,7 +3385,7 @@ class FilterFailedDatasetsTool(FilterDatasetsTool):
 
 
 class FilterEmptyDatasetsTool(FilterDatasetsTool):
-    tool_type = 'filter_empty_datasets_collection'
+    tool_type = "filter_empty_datasets_collection"
     require_dataset_ok = False
 
     def element_is_valid(self, element):
@@ -3254,7 +3393,7 @@ class FilterEmptyDatasetsTool(FilterDatasetsTool):
 
 
 class FlattenTool(DatabaseOperationTool):
-    tool_type = 'flatten_collection'
+    tool_type = "flatten_collection"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
@@ -3282,7 +3421,7 @@ class FlattenTool(DatabaseOperationTool):
 
 
 class SortTool(DatabaseOperationTool):
-    tool_type = 'sort_collection'
+    tool_type = "sort_collection"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
@@ -3290,15 +3429,15 @@ class SortTool(DatabaseOperationTool):
         new_elements = {}
         elements = hdca.collection.elements
         presort_elements = []
-        if sorttype == 'alpha':
+        if sorttype == "alpha":
             presort_elements = [(dce.element_identifier, dce) for dce in elements]
-        elif sorttype == 'numeric':
-            presort_elements = [(int(re.sub('[^0-9]', '', dce.element_identifier)), dce) for dce in elements]
+        elif sorttype == "numeric":
+            presort_elements = [(int(re.sub("[^0-9]", "", dce.element_identifier)), dce) for dce in elements]
         if presort_elements:
             sorted_elements = [x[1] for x in sorted(presort_elements, key=lambda x: x[0])]
-        if sorttype == 'file':
+        if sorttype == "file":
             hda = incoming["sort_type"]["sort_file"]
-            data_lines = hda.metadata.get('data_lines', 0)
+            data_lines = hda.metadata.get("data_lines", 0)
             if data_lines == len(elements):
                 old_elements_dict = {}
                 for element in elements:
@@ -3329,7 +3468,7 @@ class SortTool(DatabaseOperationTool):
 
 
 class RelabelFromFileTool(DatabaseOperationTool):
-    tool_type = 'relabel_from_file'
+    tool_type = "relabel_from_file"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
@@ -3341,7 +3480,9 @@ class RelabelFromFileTool(DatabaseOperationTool):
         def add_copied_value_to_new_elements(new_label, dce_object):
             new_label = new_label.strip()
             if new_label in new_elements:
-                raise Exception(f"New identifier [{new_label}] appears twice in resulting collection, these values must be unique.")
+                raise Exception(
+                    f"New identifier [{new_label}] appears twice in resulting collection, these values must be unique."
+                )
             if getattr(dce_object, "history_content_type", None) == "dataset":
                 copied_value = dce_object.copy(copy_tags=dce_object.tags, flush=False)
             else:
@@ -3356,7 +3497,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
         if how_type == "tabular":
             # We have a tabular file, where the first column is an existing element identifier,
             # and the second column is the new element identifier.
-            source_new_label = (line.strip().split('\t') for line in new_labels)
+            source_new_label = (line.strip().split("\t") for line in new_labels)
             new_labels_dict = {source: new_label for source, new_label in source_new_label}
             for dce in hdca.collection.elements:
                 dce_object = dce.element_object
@@ -3381,7 +3522,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
 
 
 class ApplyRulesTool(DatabaseOperationTool):
-    tool_type = 'apply_rules'
+    tool_type = "apply_rules"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
         hdca = incoming["input"]
@@ -3396,21 +3537,23 @@ class ApplyRulesTool(DatabaseOperationTool):
             copied_datasets.append(copied_dataset)
             return copied_dataset
 
-        new_elements = self.app.dataset_collection_manager.apply_rules(
-            hdca, rule_set, copy_dataset
-        )
+        new_elements = self.app.dataset_collection_manager.apply_rules(hdca, rule_set, copy_dataset)
         self._add_datasets_to_history(history, copied_datasets)
         output_collections.create_collection(
-            next(iter(self.outputs.values())), "output", collection_type=rule_set.collection_type, elements=new_elements, propagate_hda_tags=False
+            next(iter(self.outputs.values())),
+            "output",
+            collection_type=rule_set.collection_type,
+            elements=new_elements,
+            propagate_hda_tags=False,
         )
 
 
 class TagFromFileTool(DatabaseOperationTool):
-    tool_type = 'tag_from_file'
+    tool_type = "tag_from_file"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
         hdca = incoming["input"]
-        how = incoming['how']
+        how = incoming["how"]
         new_tags_dataset_assoc = incoming["tags"]
         new_elements = {}
         new_datasets = []
@@ -3423,15 +3566,17 @@ class TagFromFileTool(DatabaseOperationTool):
                 new_datasets.append(copied_value)
                 new_tags = new_tags_dict.get(dce.element_identifier)
                 if new_tags:
-                    if how in ('add', 'remove') and dce.element_object.tags:
+                    if how in ("add", "remove") and dce.element_object.tags:
                         # We need get the original tags and update them with the new tags
-                        old_tags = {tag for tag in tag_handler.get_tags_str(dce.element_object.tags).split(',') if tag}
-                        if how == 'add':
+                        old_tags = {tag for tag in tag_handler.get_tags_str(dce.element_object.tags).split(",") if tag}
+                        if how == "add":
                             old_tags.update(set(new_tags))
-                        elif how == 'remove':
+                        elif how == "remove":
                             old_tags = old_tags - set(new_tags)
                         new_tags = old_tags
-                    tag_handler.add_tags_from_list(user=history.user, item=copied_value, new_tags_list=new_tags, flush=False)
+                    tag_handler.add_tags_from_list(
+                        user=history.user, item=copied_value, new_tags_list=new_tags, flush=False
+                    )
             else:
                 # We have a collection, and we copy the elements so that we don't manipulate the original tags
                 copied_value = dce.element_object.copy(element_destination=history)
@@ -3440,15 +3585,19 @@ class TagFromFileTool(DatabaseOperationTool):
                     # don't set `visible` to `False` if you don't hide the original elements.
                     new_element.element_object.visible = False
                     new_tags = new_tags_dict.get(new_element.element_identifier)
-                    if how in ('add', 'remove'):
-                        old_tags = {tag for tag in tag_handler.get_tags_str(old_element.element_object.tags).split(',') if tag}
+                    if how in ("add", "remove"):
+                        old_tags = {
+                            tag for tag in tag_handler.get_tags_str(old_element.element_object.tags).split(",") if tag
+                        }
                         if new_tags:
-                            if how == 'add':
+                            if how == "add":
                                 old_tags.update(set(new_tags))
-                            elif how == 'remove':
+                            elif how == "remove":
                                 old_tags = old_tags - set(new_tags)
                         new_tags = old_tags
-                    tag_handler.add_tags_from_list(user=history.user, item=new_element.element_object, new_tags_list=new_tags, flush=False)
+                    tag_handler.add_tags_from_list(
+                        user=history.user, item=new_element.element_object, new_tags_list=new_tags, flush=False
+                    )
             new_elements[dce.element_identifier] = copied_value
 
         new_tags_path = new_tags_dataset_assoc.file_name
@@ -3456,7 +3605,7 @@ class TagFromFileTool(DatabaseOperationTool):
             new_tags = fh.readlines(1024 * 1000000)
         # We have a tabular file, where the first column is an existing element identifier,
         # and the remaining columns represent new tags.
-        source_new_tags = (line.strip().split('\t') for line in new_tags)
+        source_new_tags = (line.strip().split("\t") for line in new_tags)
         new_tags_dict = {item[0]: item[1:] for item in source_new_tags}
         for dce in hdca.collection.elements:
             add_copied_value_to_new_elements(new_tags_dict, dce)
@@ -3467,7 +3616,7 @@ class TagFromFileTool(DatabaseOperationTool):
 
 
 class FilterFromFileTool(DatabaseOperationTool):
-    tool_type = 'filter_from_file'
+    tool_type = "filter_from_file"
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
@@ -3525,7 +3674,7 @@ TOOL_CLASSES: List[Type[Tool]] = [
     FilterFromFileTool,
     BuildListCollectionTool,
     ExtractDatasetCollectionTool,
-    DataDestinationTool
+    DataDestinationTool,
 ]
 for tool_class in TOOL_CLASSES:
     tool_types[tool_class.tool_type] = tool_class
@@ -3533,7 +3682,7 @@ for tool_class in TOOL_CLASSES:
 
 # ---- Utility classes to be factored out -----------------------------------
 class TracksterConfig:
-    """ Trackster configuration encapsulation. """
+    """Trackster configuration encapsulation."""
 
     def __init__(self, actions):
         self.actions = actions
@@ -3547,7 +3696,7 @@ class TracksterConfig:
 
 
 class SetParamAction:
-    """ Set parameter action. """
+    """Set parameter action."""
 
     def __init__(self, name, output_name):
         self.name = name
@@ -3555,7 +3704,7 @@ class SetParamAction:
 
     @staticmethod
     def parse(elt):
-        """ Parse action from element. """
+        """Parse action from element."""
         return SetParamAction(elt.get("name"), elt.get("output_name"))
 
 
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 6ee80c94bca..29d9271ab8c 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -4,16 +4,30 @@ import os
 import re
 from abc import abstractmethod
 from json import dumps
-from typing import Any, cast, Dict, List, Set, Union
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Set,
+    Union,
+)
 
 from galaxy import model
 from galaxy.exceptions import ItemAccessibilityException
 from galaxy.job_execution.actions.post import ActionBox
-from galaxy.model import LibraryDatasetDatasetAssociation, WorkflowRequestInputParameter
+from galaxy.model import (
+    LibraryDatasetDatasetAssociation,
+    WorkflowRequestInputParameter,
+)
 from galaxy.model.dataset_collections.builder import CollectionBuilder
 from galaxy.model.none_like import NoneDataset
 from galaxy.tools.parameters import update_dataset_ids
-from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue
+from galaxy.tools.parameters.basic import (
+    DataCollectionToolParameter,
+    DataToolParameter,
+    RuntimeValue,
+)
 from galaxy.tools.parameters.wrapped import WrappedParameters
 from galaxy.util import ExecutionTimer
 from galaxy.util.template import fill_template
@@ -23,7 +37,7 @@ log = logging.getLogger(__name__)
 
 
 class ToolExecutionCache:
-    """ An object mean to cache calculation caused by repeatedly evaluting
+    """An object mean to cache calculation caused by repeatedly evaluting
     the same tool by the same user with slightly different parameters.
     """
 
@@ -35,11 +49,15 @@ class ToolExecutionCache:
 
     def get_chrom_info(self, tool_id, input_dbkey):
         genome_builds = self.trans.app.genome_builds
-        custom_build_hack_get_len_from_fasta_conversion = tool_id != 'CONVERTER_fasta_to_len'
+        custom_build_hack_get_len_from_fasta_conversion = tool_id != "CONVERTER_fasta_to_len"
         if custom_build_hack_get_len_from_fasta_conversion and input_dbkey in self.chrom_info:
             return self.chrom_info[input_dbkey]
 
-        chrom_info_pair = genome_builds.get_chrom_info(input_dbkey, trans=self.trans, custom_build_hack_get_len_from_fasta_conversion=custom_build_hack_get_len_from_fasta_conversion)
+        chrom_info_pair = genome_builds.get_chrom_info(
+            input_dbkey,
+            trans=self.trans,
+            custom_build_hack_get_len_from_fasta_conversion=custom_build_hack_get_len_from_fasta_conversion,
+        )
         if custom_build_hack_get_len_from_fasta_conversion:
             self.chrom_info[input_dbkey] = chrom_info_pair
 
@@ -59,9 +77,19 @@ class ToolAction:
 
 class DefaultToolAction(ToolAction):
     """Default tool action is to run an external command"""
+
     produces_real_jobs = True
 
-    def _collect_input_datasets(self, tool, param_values, trans, history, current_user_roles=None, dataset_collection_elements=None, collection_info=None):
+    def _collect_input_datasets(
+        self,
+        tool,
+        param_values,
+        trans,
+        history,
+        current_user_roles=None,
+        dataset_collection_elements=None,
+        collection_info=None,
+    ):
         """
         Collect any dataset inputs from incoming. Returns a mapping from
         parameter name to Dataset instance for each tool parameter that is
@@ -78,7 +106,6 @@ class DefaultToolAction(ToolAction):
             all_permissions[action].add(role_id)
 
         def visitor(input, value, prefix, parent=None, **kwargs):
-
             def process_dataset(data, formats=None):
                 if not data or isinstance(data, RuntimeValue):
                     return None
@@ -98,17 +125,22 @@ class DefaultToolAction(ToolAction):
                 if collection_info and collection_info.is_mapped_over(input_name):
                     action_tuples = collection_info.map_over_action_tuples(input_name)
                     if not trans.app.security_agent.can_access_datasets(current_user_roles, action_tuples):
-                        raise ItemAccessibilityException("User does not have permission to use a dataset provided for input.")
+                        raise ItemAccessibilityException(
+                            "User does not have permission to use a dataset provided for input."
+                        )
                     for action, role_id in action_tuples:
                         record_permission(action, role_id)
                 else:
                     if not trans.app.security_agent.can_access_dataset(current_user_roles, data.dataset):
-                        raise ItemAccessibilityException(f"User does not have permission to use a dataset ({data.id}) provided for input.")
+                        raise ItemAccessibilityException(
+                            f"User does not have permission to use a dataset ({data.id}) provided for input."
+                        )
                     permissions = trans.app.security_agent.get_permissions(data.dataset)
                     for action, roles in permissions.items():
                         for role in roles:
                             record_permission(action.action, model.cached_id(role))
                 return data
+
             if isinstance(input, DataToolParameter):
                 if isinstance(value, list):
                     # If there are multiple inputs with the same name, they
@@ -121,22 +153,30 @@ class DefaultToolAction(ToolAction):
                         input_datasets[prefix + input.name + str(i + 1)] = processed_dataset
                         conversions = []
                         for conversion_name, conversion_extensions, conversion_datatypes in input.conversions:
-                            new_data = process_dataset(input_datasets[prefix + input.name + str(i + 1)], conversion_datatypes)
+                            new_data = process_dataset(
+                                input_datasets[prefix + input.name + str(i + 1)], conversion_datatypes
+                            )
                             if not new_data or new_data.datatype.matches_any(conversion_datatypes):
                                 input_datasets[prefix + conversion_name + str(i + 1)] = new_data
                                 conversions.append((conversion_name, new_data))
                             else:
-                                raise Exception(f'A path for explicit datatype conversion has not been found: {input_datasets[prefix + input.name + str(i + 1)].extension} --/--> {conversion_extensions}')
+                                raise Exception(
+                                    f"A path for explicit datatype conversion has not been found: {input_datasets[prefix + input.name + str(i + 1)].extension} --/--> {conversion_extensions}"
+                                )
                         if parent:
                             parent[input.name][i] = input_datasets[prefix + input.name + str(i + 1)]
                             for conversion_name, conversion_data in conversions:
                                 # allow explicit conversion to be stored in job_parameter table
-                                parent[conversion_name][i] = conversion_data.id  # a more robust way to determine JSONable value is desired
+                                parent[conversion_name][
+                                    i
+                                ] = conversion_data.id  # a more robust way to determine JSONable value is desired
                         else:
                             param_values[input.name][i] = input_datasets[prefix + input.name + str(i + 1)]
                             for conversion_name, conversion_data in conversions:
                                 # allow explicit conversion to be stored in job_parameter table
-                                param_values[conversion_name][i] = conversion_data.id  # a more robust way to determine JSONable value is desired
+                                param_values[conversion_name][
+                                    i
+                                ] = conversion_data.id  # a more robust way to determine JSONable value is desired
                 else:
                     input_datasets[prefix + input.name] = process_dataset(value)
                     conversions = []
@@ -146,21 +186,25 @@ class DefaultToolAction(ToolAction):
                             input_datasets[prefix + conversion_name] = new_data
                             conversions.append((conversion_name, new_data))
                         else:
-                            raise Exception(f'A path for explicit datatype conversion has not been found: {input_datasets[prefix + input.name].extension} --/--> {conversion_extensions}')
+                            raise Exception(
+                                f"A path for explicit datatype conversion has not been found: {input_datasets[prefix + input.name].extension} --/--> {conversion_extensions}"
+                            )
                     target_dict = parent
                     if not target_dict:
                         target_dict = param_values
                     target_dict[input.name] = input_datasets[prefix + input.name]
                     for conversion_name, conversion_data in conversions:
                         # allow explicit conversion to be stored in job_parameter table
-                        target_dict[conversion_name] = conversion_data.id  # a more robust way to determine JSONable value is desired
+                        target_dict[
+                            conversion_name
+                        ] = conversion_data.id  # a more robust way to determine JSONable value is desired
             elif isinstance(input, DataCollectionToolParameter):
                 if not value:
                     return
 
                 collection = None
                 child_collection = False
-                if hasattr(value, 'child_collection'):
+                if hasattr(value, "child_collection"):
                     # if we are mapping a collection over a tool, we only require the child_collection
                     child_collection = True
                     collection = value.child_collection
@@ -170,7 +214,9 @@ class DefaultToolAction(ToolAction):
 
                 action_tuples = collection.dataset_action_tuples
                 if not trans.app.security_agent.can_access_datasets(current_user_roles, action_tuples):
-                    raise ItemAccessibilityException("User does not have permission to use a dataset provided for input.")
+                    raise ItemAccessibilityException(
+                        "User does not have permission to use a dataset provided for input."
+                    )
                 for action, role_id in action_tuples:
                     record_permission(action, role_id)
 
@@ -191,7 +237,11 @@ class DefaultToolAction(ToolAction):
                             processed_dataset_dict[v] = processed_dataset
                     input_datasets[prefix + input.name + str(i + 1)] = processed_dataset or v
                 if conversion_required:
-                    collection_type_description = trans.app.dataset_collection_manager.collection_type_descriptions.for_collection_type(collection.collection_type)
+                    collection_type_description = (
+                        trans.app.dataset_collection_manager.collection_type_descriptions.for_collection_type(
+                            collection.collection_type
+                        )
+                    )
                     collection_builder = CollectionBuilder(collection_type_description)
                     collection_builder.replace_elements_in_collection(
                         template_collection=collection,
@@ -220,7 +270,9 @@ class DefaultToolAction(ToolAction):
                 if not isinstance(values, list):
                     values = [value]
                 for i, value in enumerate(values):
-                    if isinstance(value, model.HistoryDatasetCollectionAssociation) or isinstance(value, model.DatasetCollectionElement):
+                    if isinstance(value, model.HistoryDatasetCollectionAssociation) or isinstance(
+                        value, model.DatasetCollectionElement
+                    ):
                         append_to_key(input_dataset_collections, prefixed_name, (value, True))
                         target_dict = parent
                         if not target_dict:
@@ -248,7 +300,7 @@ class DefaultToolAction(ToolAction):
         assert tool.allow_user_access(trans.user), f"User ({trans.user}) is not allowed to access this tool."
 
     def _collect_inputs(self, tool, trans, incoming, history, current_user_roles, collection_info):
-        """ Collect history as well as input datasets and collections. """
+        """Collect history as well as input datasets and collections."""
         # Set history.
         if not history:
             history = tool.get_default_history_by_trans(trans, create=True)
@@ -257,7 +309,14 @@ class DefaultToolAction(ToolAction):
         # input datasets can process these normally.
         inp_dataset_collections = self.collect_input_dataset_collections(tool, incoming)
         # Collect any input datasets from the incoming parameters
-        inp_data, all_permissions = self._collect_input_datasets(tool, incoming, trans, history=history, current_user_roles=current_user_roles, collection_info=collection_info)
+        inp_data, all_permissions = self._collect_input_datasets(
+            tool,
+            incoming,
+            trans,
+            history=history,
+            current_user_roles=current_user_roles,
+            collection_info=collection_info,
+        )
 
         preserved_tags = {}
         preserved_hdca_tags = {}
@@ -278,22 +337,23 @@ class DefaultToolAction(ToolAction):
         preserved_tags.update(preserved_hdca_tags)
         return history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions
 
-    def execute(self,
-                tool,
-                trans,
-                incoming=None,
-                return_job=False,
-                set_output_hid=True,
-                history=None,
-                job_params=None,
-                rerun_remap_job_id=None,
-                execution_cache=None,
-                dataset_collection_elements=None,
-                completed_job=None,
-                collection_info=None,
-                job_callback=None,
-                flush_job=True
-                ):
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming=None,
+        return_job=False,
+        set_output_hid=True,
+        history=None,
+        job_params=None,
+        rerun_remap_job_id=None,
+        execution_cache=None,
+        dataset_collection_elements=None,
+        completed_job=None,
+        collection_info=None,
+        job_callback=None,
+        flush_job=True,
+    ):
         """
         Executes a tool, creating job and tool outputs, associating them, and
         submitting the job to the job queue. If history is not specified, use
@@ -306,14 +366,21 @@ class DefaultToolAction(ToolAction):
         if execution_cache is None:
             execution_cache = ToolExecutionCache(trans)
         current_user_roles = execution_cache.current_user_roles
-        history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
+        (
+            history,
+            inp_data,
+            inp_dataset_collections,
+            preserved_tags,
+            preserved_hdca_tags,
+            all_permissions,
+        ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
         # Build name for output datasets based on tool name and input names
         on_text = self._get_on_text(inp_data)
 
         # format='input" previously would give you a random extension from
         # the input extensions, now it should just give "input" as the output
         # format.
-        input_ext = 'data' if tool.profile < 16.04 else "input"
+        input_ext = "data" if tool.profile < 16.04 else "input"
         input_dbkey = incoming.get("dbkey", "?")
         for name, data in reversed(list(inp_data.items())):
             if not data:
@@ -328,7 +395,7 @@ class DefaultToolAction(ToolAction):
             if tool.profile < 16.04:
                 input_ext = data.ext
 
-            if data.dbkey not in [None, '?']:
+            if data.dbkey not in [None, "?"]:
                 input_dbkey = data.dbkey
 
             identifier = getattr(data, "element_identifier", None)
@@ -377,7 +444,7 @@ class DefaultToolAction(ToolAction):
         # datasets first, then create the associations
         parent_to_child_pairs = []
         child_dataset_names = set()
-        async_tool = tool.tool_type == 'data_source_async'
+        async_tool = tool.tool_type == "data_source_async"
 
         def handle_output(name, output, hidden=None):
             if output.parent:
@@ -410,7 +477,9 @@ class DefaultToolAction(ToolAction):
                             dataset = output_dataset.dataset.dataset
                             break
 
-                data = app.model.HistoryDatasetAssociation(extension=ext, dataset=dataset, create_dataset=create_datasets, flush=False)
+                data = app.model.HistoryDatasetAssociation(
+                    extension=ext, dataset=dataset, create_dataset=create_datasets, flush=False
+                )
                 if create_datasets:
                     from_work_dir = output.from_work_dir
                     if from_work_dir is not None:
@@ -425,7 +494,9 @@ class DefaultToolAction(ToolAction):
                     dataset_collection_elements[name].hda = data
                 trans.sa_session.add(data)
                 if not completed_job:
-                    trans.app.security_agent.set_all_dataset_permissions(data.dataset, output_permissions, new=True, flush=False)
+                    trans.app.security_agent.set_all_dataset_permissions(
+                        data.dataset, output_permissions, new=True, flush=False
+                    )
             data.copy_tags_to(preserved_tags.values())
 
             # This may not be neccesary with the new parent/child associations
@@ -453,7 +524,9 @@ class DefaultToolAction(ToolAction):
             else:
                 data.blurb = "queued"
             # Set output label
-            data.name = self.get_output_name(output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params)
+            data.name = self.get_output_name(
+                output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params
+            )
             # Store output
             out_data[name] = data
             if output.actions:
@@ -462,7 +535,9 @@ class DefaultToolAction(ToolAction):
                 output_action_params.update(incoming)
                 output.actions.apply_action(data, output_action_params)
             # Also set the default values of actions of type metadata
-            self.set_metadata_defaults(output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params)
+            self.set_metadata_defaults(
+                output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params
+            )
             # Flush all datasets at once.
             return data
 
@@ -474,9 +549,7 @@ class DefaultToolAction(ToolAction):
                         # Output collection is mapped over and has already been copied from original job
                         continue
                     collections_manager = app.dataset_collection_manager
-                    element_identifiers: List[
-                        Dict[str, Union[str, List[Dict[str, Union[str, List[Any]]]]]]
-                    ] = []
+                    element_identifiers: List[Dict[str, Union[str, List[Dict[str, Union[str, List[Any]]]]]]] = []
                     # mypy doesn't yet support recursive type definitions
                     known_outputs = output.known_outputs(input_collections, collections_manager.type_registry)
                     # Just to echo TODO elsewhere - this should be restructured to allow
@@ -486,33 +559,33 @@ class DefaultToolAction(ToolAction):
                         current_element_identifiers = element_identifiers
                         current_collection_type = output.structure.collection_type
 
-                        for parent_id in (output_part_def.parent_ids or []):
+                        for parent_id in output_part_def.parent_ids or []:
                             # TODO: replace following line with formal abstractions for doing this.
                             current_collection_type = ":".join(current_collection_type.split(":")[1:])
-                            name_to_index = {value["name"]: index for (index, value) in enumerate(current_element_identifiers)}
+                            name_to_index = {
+                                value["name"]: index for (index, value) in enumerate(current_element_identifiers)
+                            }
                             if parent_id not in name_to_index:
                                 if parent_id not in current_element_identifiers:
                                     index = len(current_element_identifiers)
-                                    current_element_identifiers.append(dict(
-                                        name=parent_id,
-                                        collection_type=current_collection_type,
-                                        src="new_collection",
-                                        element_identifiers=[],
-                                    ))
+                                    current_element_identifiers.append(
+                                        dict(
+                                            name=parent_id,
+                                            collection_type=current_collection_type,
+                                            src="new_collection",
+                                            element_identifiers=[],
+                                        )
+                                    )
                                 else:
                                     index = name_to_index[parent_id]
                             current_element_identifiers = cast(
                                 List[
                                     Dict[
                                         str,
-                                        Union[
-                                            str, List[Dict[str, Union[str, List[Any]]]]
-                                        ],
+                                        Union[str, List[Dict[str, Union[str, List[Any]]]]],
                                     ]
                                 ],
-                                current_element_identifiers[index][
-                                    "element_identifiers"
-                                ],
+                                current_element_identifiers[index]["element_identifiers"],
                             )
 
                         effective_output_name = output_part_def.effective_output_name
@@ -524,10 +597,12 @@ class DefaultToolAction(ToolAction):
                         # Following hack causes dataset to no be added to history...
                         child_dataset_names.add(effective_output_name)
                         trans.sa_session.add(element)
-                        current_element_identifiers.append({
-                            "__object__": element,
-                            "name": output_part_def.element_identifier,
-                        })
+                        current_element_identifiers.append(
+                            {
+                                "__object__": element,
+                                "name": output_part_def.element_identifier,
+                            }
+                        )
 
                     if output.dynamic_structure:
                         assert not element_identifiers  # known_outputs must have been empty
@@ -535,10 +610,7 @@ class DefaultToolAction(ToolAction):
                     else:
                         element_kwds = dict(element_identifiers=element_identifiers)
                     output_collections.create_collection(
-                        output=output,
-                        name=name,
-                        completed_job=completed_job,
-                        **element_kwds
+                        output=output, name=name, completed_job=completed_job, **element_kwds
                     )
                     log.info(f"Handled collection output named {name} for tool {tool.id} {handle_output_timer}")
                 else:
@@ -546,12 +618,14 @@ class DefaultToolAction(ToolAction):
                     log.info(f"Handled output named {name} for tool {tool.id} {handle_output_timer}")
 
         add_datasets_timer = tool.app.execution_timer_factory.get_timer(
-            'internals.galaxy.tools.actions.add_datasets',
-            'Added output datasets to history',
+            "internals.galaxy.tools.actions.add_datasets",
+            "Added output datasets to history",
         )
         # Add all the top-level (non-child) datasets to the history unless otherwise specified
         for name, data in out_data.items():
-            if name not in child_dataset_names and name not in incoming:  # don't add children; or already existing datasets, i.e. async created
+            if (
+                name not in child_dataset_names and name not in incoming
+            ):  # don't add children; or already existing datasets, i.e. async created
                 history.stage_addition(data)
         history.add_pending_items(set_output_hid=set_output_hid)
 
@@ -585,25 +659,27 @@ class DefaultToolAction(ToolAction):
                 session.flush()
             finally:
                 session.expire_on_commit = True
-            self._remap_job_on_rerun(trans=trans,
-                                     galaxy_session=galaxy_session,
-                                     rerun_remap_job_id=rerun_remap_job_id,
-                                     current_job=job,
-                                     out_data=out_data)
+            self._remap_job_on_rerun(
+                trans=trans,
+                galaxy_session=galaxy_session,
+                rerun_remap_job_id=rerun_remap_job_id,
+                current_job=job,
+                out_data=out_data,
+            )
         log.info(f"Setup for job {job.log_str()} complete, ready to be enqueued {job_setup_timer}")
 
         # Some tools are not really executable, but jobs are still created for them ( for record keeping ).
         # Examples include tools that redirect to other applications ( epigraph ).  These special tools must
         # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job
         # from being queued.
-        if 'REDIRECT_URL' in incoming:
+        if "REDIRECT_URL" in incoming:
             # Get the dataset - there should only be 1
             for name in inp_data.keys():
                 dataset = inp_data[name]
             redirect_url = tool.parse_redirect_url(dataset, incoming)
             # GALAXY_URL should be include in the tool params to enable the external application
             # to send back to the current Galaxy instance
-            GALAXY_URL = incoming.get('GALAXY_URL', None)
+            GALAXY_URL = incoming.get("GALAXY_URL", None)
             assert GALAXY_URL is not None, "GALAXY_URL parameter missing in tool config."
             redirect_url += f"&GALAXY_URL={GALAXY_URL}"
             # Job should not be queued, so set state to ok
@@ -611,7 +687,9 @@ class DefaultToolAction(ToolAction):
             job.info = f"Redirected to: {redirect_url}"
             trans.sa_session.add(job)
             trans.sa_session.flush()
-            trans.response.send_redirect(url_for(controller='tool_runner', action='redirect', redirect_url=redirect_url))
+            trans.response.send_redirect(
+                url_for(controller="tool_runner", action="redirect", redirect_url=redirect_url)
+            )
         else:
             if flush_job:
                 # Set HID and add to history.
@@ -631,14 +709,20 @@ class DefaultToolAction(ToolAction):
         """
         try:
             old_job = trans.sa_session.query(trans.app.model.Job).get(rerun_remap_job_id)
-            assert old_job is not None, f'({rerun_remap_job_id}/{current_job.id}): Old job id is invalid'
-            assert old_job.tool_id == current_job.tool_id, f'({old_job.id}/{current_job.id}): Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})'
+            assert old_job is not None, f"({rerun_remap_job_id}/{current_job.id}): Old job id is invalid"
+            assert (
+                old_job.tool_id == current_job.tool_id
+            ), f"({old_job.id}/{current_job.id}): Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})"
             if trans.user is not None:
-                assert old_job.user_id == trans.user.id, f'({old_job.id}/{current_job.id}): Old user id ({old_job.user_id}) does not match rerun user id ({trans.user.id})'
+                assert (
+                    old_job.user_id == trans.user.id
+                ), f"({old_job.id}/{current_job.id}): Old user id ({old_job.user_id}) does not match rerun user id ({trans.user.id})"
             elif trans.user is None and type(galaxy_session) == trans.model.GalaxySession:
-                assert old_job.session_id == galaxy_session.id, f'({old_job.id}/{current_job.id}): Old session id ({old_job.session_id}) does not match rerun session id ({galaxy_session.id})'
+                assert (
+                    old_job.session_id == galaxy_session.id
+                ), f"({old_job.id}/{current_job.id}): Old session id ({old_job.session_id}) does not match rerun session id ({galaxy_session.id})"
             else:
-                raise Exception(f'({old_job.id}/{current_job.id}): Remapping via the API is not (yet) supported')
+                raise Exception(f"({old_job.id}/{current_job.id}): Remapping via the API is not (yet) supported")
             # Start by hiding current job outputs before taking over the old job's (implicit) outputs.
             current_job.hide_outputs(flush=False)
             # Duplicate PJAs before remap.
@@ -654,13 +738,14 @@ class DefaultToolAction(ToolAction):
                     if pja.action_type in ActionBox.immediate_actions:
                         ActionBox.execute(trans.app, trans.sa_session, pja, current_job, replacement_dict)
             for p in old_job.parameters:
-                if p.name.endswith('|__identifier__'):
+                if p.name.endswith("|__identifier__"):
                     current_job.parameters.append(p.copy())
             remapped_hdas = self.__remap_data_inputs(old_job=old_job, current_job=current_job)
             for jtod in old_job.output_datasets:
                 for (job_to_remap, jtid) in [(jtid.job, jtid) for jtid in jtod.dataset.dependent_jobs]:
                     if (trans.user is not None and job_to_remap.user_id == trans.user.id) or (
-                            trans.user is None and job_to_remap.session_id == galaxy_session.id):
+                        trans.user is None and job_to_remap.session_id == galaxy_session.id
+                    ):
                         self.__remap_parameters(job_to_remap, jtid, jtod, out_data)
                         trans.sa_session.add(job_to_remap)
                         trans.sa_session.add(jtid)
@@ -680,7 +765,7 @@ class DefaultToolAction(ToolAction):
             for jtoidca in old_job.output_dataset_collections:
                 jtoidca.dataset_collection.replace_failed_elements(remapped_hdas)
         except Exception:
-            log.exception('Cannot remap rerun dependencies.')
+            log.exception("Cannot remap rerun dependencies.")
 
     def __remap_data_inputs(self, old_job, current_job):
         """Record output datasets from old_job and build a dictionary that maps the old output HDAs to the new output HDAs."""
@@ -694,12 +779,12 @@ class DefaultToolAction(ToolAction):
         input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
         old_dataset_id = jtod.dataset_id
         new_dataset_id = out_data[jtod.name].id
-        input_values = update_dataset_ids(input_values, {old_dataset_id: new_dataset_id}, src='hda')
+        input_values = update_dataset_ids(input_values, {old_dataset_id: new_dataset_id}, src="hda")
         for p in job_to_remap.parameters:
             p.value = json.dumps(input_values[p.name])
         jtid.dataset = out_data[jtod.name]
         jtid.dataset.hid = jtod.dataset.hid
-        log.info(f'Job {job_to_remap.id} input HDA {jtod.dataset.id} remapped to new HDA {jtid.dataset.id}')
+        log.info(f"Job {job_to_remap.id} input HDA {jtod.dataset.id} remapped to new HDA {jtid.dataset.id}")
 
     def _wrapped_params(self, trans, tool, incoming, input_datasets=None):
         wrapped_params = WrappedParameters(trans, tool, incoming, input_datasets=input_datasets)
@@ -709,7 +794,7 @@ class DefaultToolAction(ToolAction):
         input_names = []
         for data in reversed(list(inp_data.values())):
             if getattr(data, "hid", None):
-                input_names.append(f'data {data.hid}')
+                input_names.append(f"data {data.hid}")
 
         return on_text_for_names(input_names)
 
@@ -766,9 +851,9 @@ class DefaultToolAction(ToolAction):
                 target_dict[input.name] = []
                 for reduced_collection in reductions[prefixed_name]:
                     if hasattr(reduced_collection, "child_collection"):
-                        target_dict[input.name].append({'id': model.cached_id(reduced_collection), 'src': 'dce'})
+                        target_dict[input.name].append({"id": model.cached_id(reduced_collection), "src": "dce"})
                     else:
-                        target_dict[input.name].append({'id': model.cached_id(reduced_collection), 'src': 'hdca'})
+                        target_dict[input.name].append({"id": model.cached_id(reduced_collection), "src": "hdca"})
 
         if reductions:
             tool.visit_inputs(incoming, restore_reduction_visitor)
@@ -793,13 +878,33 @@ class DefaultToolAction(ToolAction):
             # TODO: figure out why can't pass dataset_id here.
             job.add_input_dataset(name, dataset=dataset)
 
-    def get_output_name(self, output, dataset=None, tool=None, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None):
+    def get_output_name(
+        self,
+        output,
+        dataset=None,
+        tool=None,
+        on_text=None,
+        trans=None,
+        incoming=None,
+        history=None,
+        params=None,
+        job_params=None,
+    ):
         if output.label:
-            params['tool'] = tool
-            params['on_string'] = on_text
+            params["tool"] = tool
+            params["on_string"] = on_text
             return fill_template(output.label, context=params, python_template_version=tool.python_template_version)
         else:
-            return self._get_default_data_name(dataset, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params)
+            return self._get_default_data_name(
+                dataset,
+                tool,
+                on_text=on_text,
+                trans=trans,
+                incoming=incoming,
+                history=history,
+                params=params,
+                job_params=job_params,
+            )
 
     def set_metadata_defaults(self, output, dataset, tool, on_text, trans, incoming, history, params, job_params):
         """
@@ -816,10 +921,14 @@ class DefaultToolAction(ToolAction):
         if output.actions:
             for action in output.actions.actions:
                 if action.tag == "metadata" and action.default:
-                    metadata_new_value = fill_template(action.default, context=params, python_template_version=tool.python_template_version).split(",")
+                    metadata_new_value = fill_template(
+                        action.default, context=params, python_template_version=tool.python_template_version
+                    ).split(",")
                     dataset.metadata.__setattr__(str(action.name), metadata_new_value)
 
-    def _get_default_data_name(self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd):
+    def _get_default_data_name(
+        self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd
+    ):
         name = tool.name
         if on_text:
             name += f" on {on_text}"
@@ -827,14 +936,28 @@ class DefaultToolAction(ToolAction):
 
 
 class OutputCollections:
-    """ Keeps track of collections (DC or HDCA) created by actions.
+    """Keeps track of collections (DC or HDCA) created by actions.
 
     Actions do fairly different things depending on whether we are creating
     just part of an collection or a whole output collection (mapping_over_collection
     parameter).
     """
 
-    def __init__(self, trans, history, tool, tool_action, input_collections, dataset_collection_elements, on_text, incoming, params, job_params, tags, hdca_tags):
+    def __init__(
+        self,
+        trans,
+        history,
+        tool,
+        tool_action,
+        input_collections,
+        dataset_collection_elements,
+        on_text,
+        incoming,
+        params,
+        job_params,
+        tags,
+        hdca_tags,
+    ):
         self.trans = trans
         self.tag_handler = trans.app.tag_handler.create_tag_handler_session()
         self.history = history
@@ -851,7 +974,9 @@ class OutputCollections:
         self.tags = tags  # all inherited tags
         self.hdca_tags = hdca_tags  # only tags inherited from input HDCAs
 
-    def create_collection(self, output, name, collection_type=None, completed_job=None, propagate_hda_tags=True, **element_kwds):
+    def create_collection(
+        self, output, name, collection_type=None, completed_job=None, propagate_hda_tags=True, **element_kwds
+    ):
         input_collections = self.input_collections
         collections_manager = self.trans.app.dataset_collection_manager
         collection_type = collection_type or output.structure.collection_type
@@ -866,11 +991,11 @@ class OutputCollections:
 
             # Using the collection_type_source string we get the DataCollectionToolParameter
             data_param = self.tool.inputs
-            groups = collection_type_source.split('|')
+            groups = collection_type_source.split("|")
             for group in groups:
-                values = group.split('_')
+                values = group.split("_")
                 if values[-1].isdigit():
-                    key = ("_".join(values[0:-1]))
+                    key = "_".join(values[0:-1])
                     # We don't care about the repeat index, we just need to find the correct DataCollectionToolParameter
                 else:
                     key = group
@@ -878,13 +1003,16 @@ class OutputCollections:
                     data_param = data_param.get(key)
                 else:
                     data_param = data_param.inputs.get(key)
-            collection_type_description = data_param._history_query(self.trans).can_map_over(input_collections[collection_type_source])
+            collection_type_description = data_param._history_query(self.trans).can_map_over(
+                input_collections[collection_type_source]
+            )
             if collection_type_description:
                 collection_type = collection_type_description.collection_type
             else:
                 collection_type = input_collections[collection_type_source].collection.collection_type
 
         if "elements" in element_kwds:
+
             def check_elements(elements):
                 if hasattr(elements, "items"):  # else it is ELEMENTS_UNINITIALIZED object.
                     for value in elements.values():
@@ -903,9 +1031,7 @@ class OutputCollections:
 
         if self.dataset_collection_elements is not None:
             dc = collections_manager.create_dataset_collection(
-                self.trans,
-                collection_type=collection_type,
-                **element_kwds
+                self.trans, collection_type=collection_type, **element_kwds
             )
             if name in self.dataset_collection_elements:
                 self.dataset_collection_elements[name].child_collection = dc
@@ -934,7 +1060,7 @@ class OutputCollections:
                 flush=False,
                 completed_job=completed_job,
                 output_name=name,
-                **element_kwds
+                **element_kwds,
             )
             # name here is name of the output element - not name
             # of the hdca.
@@ -956,11 +1082,11 @@ def on_text_for_names(input_names):
     if len(input_names) == 1:
         on_text = input_names[0]
     elif len(input_names) == 2:
-        on_text = '%s and %s' % tuple(input_names[0:2])
+        on_text = "%s and %s" % tuple(input_names[0:2])
     elif len(input_names) == 3:
-        on_text = '%s, %s, and %s' % tuple(input_names[0:3])
+        on_text = "%s, %s, and %s" % tuple(input_names[0:3])
     elif len(input_names) > 3:
-        on_text = '%s, %s, and others' % tuple(input_names[0:2])
+        on_text = "%s, %s, and others" % tuple(input_names[0:2])
     else:
         on_text = ""
     return on_text
@@ -972,7 +1098,7 @@ def filter_output(tool, output, incoming):
             if not eval(filter.text.strip(), globals(), incoming):
                 return True  # do not create this dataset
         except Exception as e:
-            log.debug(f'Tool {tool.id} output {output.name}: dataset output filter ({filter.text}) failed: {e}')
+            log.debug(f"Tool {tool.id} output {output.name}: dataset output filter ({filter.text}) failed: {e}")
     return False
 
 
@@ -986,8 +1112,16 @@ def get_ext_or_implicit_ext(hda):
     return hda.ext
 
 
-def determine_output_format(output, parameter_context, input_datasets, input_dataset_collections, random_input_ext, python_template_version='3', execution_cache=None):
-    """ Determines the output format for a dataset based on an abstract
+def determine_output_format(
+    output,
+    parameter_context,
+    input_datasets,
+    input_dataset_collections,
+    random_input_ext,
+    python_template_version="3",
+    execution_cache=None,
+):
+    """Determines the output format for a dataset based on an abstract
     description of the output (galaxy.tool_util.parser.ToolOutput), the parameter
     wrappers, a map of the input datasets (name => HDA), and the last input
     extensions in the tool form.
@@ -998,7 +1132,7 @@ def determine_output_format(output, parameter_context, input_datasets, input_dat
     # the type should match the input
     ext = output.format
     if ext == "input":
-        if input_datasets and random_input_ext in {'data', 'auto'}:
+        if input_datasets and random_input_ext in {"data", "auto"}:
             # Probably dealing with an implicitly converted dataset
             try:
                 first_input_dataset = next(iter(input_datasets.values()))
@@ -1035,9 +1169,13 @@ def determine_output_format(output, parameter_context, input_datasets, input_dat
                         input_element = input_collection_collection[element_index]
                     except KeyError:
                         if execution_cache:
-                            dataset_elements = execution_cache.cached_collection_elements.get(input_collection_collection.id)
+                            dataset_elements = execution_cache.cached_collection_elements.get(
+                                input_collection_collection.id
+                            )
                             if dataset_elements is None:
-                                dataset_elements = execution_cache.cached_collection_elements[input_collection_collection.id] = input_collection_collection.dataset_elements
+                                dataset_elements = execution_cache.cached_collection_elements[
+                                    input_collection_collection.id
+                                ] = input_collection_collection.dataset_elements
                         else:
                             dataset_elements = input_collection_collection.dataset_elements
                         for element in dataset_elements:
@@ -1053,25 +1191,27 @@ def determine_output_format(output, parameter_context, input_datasets, input_dat
     if output.change_format is not None:
         new_format_set = False
         for change_elem in output.change_format:
-            for when_elem in change_elem.findall('when'):
-                check = when_elem.get('input', None)
+            for when_elem in change_elem.findall("when"):
+                check = when_elem.get("input", None)
                 if check is not None:
                     try:
-                        if '$' not in check:
+                        if "$" not in check:
                             # allow a simple name or more complex specifications
-                            check = '${%s}' % check
-                        if fill_template(check, context=parameter_context, python_template_version=python_template_version) == when_elem.get('value', None):
-                            ext = when_elem.get('format', ext)
+                            check = "${%s}" % check
+                        if fill_template(
+                            check, context=parameter_context, python_template_version=python_template_version
+                        ) == when_elem.get("value", None):
+                            ext = when_elem.get("format", ext)
                     except Exception:  # bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct
                         continue
                 else:
-                    check = when_elem.get('input_dataset', None)
+                    check = when_elem.get("input_dataset", None)
                     if check is not None:
                         check = input_datasets.get(check, None)
                         # At this point check is a HistoryDatasetAssociation object.
-                        check_format = when_elem.get('format', ext)
-                        check_value = when_elem.get('value', None)
-                        check_attribute = when_elem.get('attribute', None)
+                        check_format = when_elem.get("format", ext)
+                        check_value = when_elem.get("value", None)
+                        check_attribute = when_elem.get("attribute", None)
                         if check is not None and check_value is not None and check_attribute is not None:
                             # See if the attribute to be checked belongs to the HistoryDatasetAssociation object.
                             if hasattr(check, check_attribute):
diff --git a/lib/galaxy/tools/actions/data_source.py b/lib/galaxy/tools/actions/data_source.py
index eb02c994ff4..14f3a1b1044 100644
--- a/lib/galaxy/tools/actions/data_source.py
+++ b/lib/galaxy/tools/actions/data_source.py
@@ -8,7 +8,18 @@ log = logging.getLogger(__name__)
 class DataSourceToolAction(DefaultToolAction):
     """Tool action used for Data Source Tools"""
 
-    def _get_default_data_name(self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd):
-        if incoming and 'name' in incoming:
-            return incoming['name']
-        return super()._get_default_data_name(dataset, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params)
+    def _get_default_data_name(
+        self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd
+    ):
+        if incoming and "name" in incoming:
+            return incoming["name"]
+        return super()._get_default_data_name(
+            dataset,
+            tool,
+            on_text=on_text,
+            trans=trans,
+            incoming=incoming,
+            history=history,
+            params=params,
+            job_params=job_params,
+        )
diff --git a/lib/galaxy/tools/actions/history_imp_exp.py b/lib/galaxy/tools/actions/history_imp_exp.py
index c0a7afd11fd..efd8a851d47 100644
--- a/lib/galaxy/tools/actions/history_imp_exp.py
+++ b/lib/galaxy/tools/actions/history_imp_exp.py
@@ -7,7 +7,7 @@ from galaxy.job_execution.setup import create_working_directory_for_job
 from galaxy.tools.actions import ToolAction
 from galaxy.tools.imp_exp import (
     JobExportHistoryArchiveWrapper,
-    JobImportHistoryArchiveWrapper
+    JobImportHistoryArchiveWrapper,
 )
 from galaxy.util import ready_name_for_url
 
@@ -15,7 +15,8 @@ log = logging.getLogger(__name__)
 
 
 class ImportHistoryToolAction(ToolAction):
-    """Tool action used for importing a history to an archive. """
+    """Tool action used for importing a history to an archive."""
+
     produces_real_jobs = True
 
     def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs):
@@ -38,7 +39,9 @@ class ImportHistoryToolAction(ToolAction):
         job.tool_id = tool.id
         job.user_id = trans.user.id
         start_job_state = job.state  # should be job.states.NEW
-        job.state = job.states.WAITING  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
+        job.state = (
+            job.states.WAITING
+        )  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
         trans.sa_session.add(job)
         trans.sa_session.flush()  # ensure job.id are available
 
@@ -55,14 +58,14 @@ class ImportHistoryToolAction(ToolAction):
         trans.sa_session.add(jiha)
 
         job_wrapper = JobImportHistoryArchiveWrapper(trans.app, job)
-        job_wrapper.setup_job(jiha, incoming['__ARCHIVE_SOURCE__'], incoming["__ARCHIVE_TYPE__"])
+        job_wrapper.setup_job(jiha, incoming["__ARCHIVE_SOURCE__"], incoming["__ARCHIVE_TYPE__"])
 
         #
         # Add parameters to job_parameter table.
         #
 
         # Set additional parameters.
-        incoming['__DEST_DIR__'] = jiha.archive_dir
+        incoming["__DEST_DIR__"] = jiha.archive_dir
         for name, value in tool.params_to_strings(incoming, trans.app).items():
             job.add_parameter(name, value)
 
@@ -71,7 +74,8 @@ class ImportHistoryToolAction(ToolAction):
 
 
 class ExportHistoryToolAction(ToolAction):
-    """Tool action used for exporting a history to an archive. """
+    """Tool action used for exporting a history to an archive."""
+
     produces_real_jobs = True
 
     def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs):
@@ -89,7 +93,7 @@ class ExportHistoryToolAction(ToolAction):
                 break
 
         if not history:
-            raise Exception('There is no history to export.')
+            raise Exception("There is no history to export.")
 
         #
         # Create the job and output dataset objects
@@ -104,10 +108,12 @@ class ExportHistoryToolAction(ToolAction):
         if trans.user:
             # If this is an actual user, run the job as that individual.  Otherwise we're running as guest.
             job.user_id = trans.user.id
-        job.state = job.states.WAITING  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
+        job.state = (
+            job.states.WAITING
+        )  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
         trans.sa_session.add(job)
 
-        compressed = incoming['compress']
+        compressed = incoming["compress"]
         exporting_to_uri = "directory_uri" in incoming
         if not exporting_to_uri:
             # see comment below about how this should be transitioned to occuring in a
@@ -139,8 +145,8 @@ class ExportHistoryToolAction(ToolAction):
         #
 
         # Set additional parameters.
-        incoming['__HISTORY_TO_EXPORT__'] = history.id
-        incoming['__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__'] = cmd_line
+        incoming["__HISTORY_TO_EXPORT__"] = history.id
+        incoming["__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__"] = cmd_line
         if exporting_to_uri:
             directory_uri = incoming["directory_uri"]
             file_name = incoming.get("file_name")
@@ -155,7 +161,7 @@ class ExportHistoryToolAction(ToolAction):
 
             file_name = os.path.basename(os.path.abspath(file_name))
             sep = "" if directory_uri.endswith("/") else "/"
-            incoming['__EXPORT_TO_URI__'] = f"{directory_uri}{sep}{file_name}"
+            incoming["__EXPORT_TO_URI__"] = f"{directory_uri}{sep}{file_name}"
 
         for name, value in tool.params_to_strings(incoming, trans.app).items():
             job.add_parameter(name, value)
@@ -165,8 +171,9 @@ class ExportHistoryToolAction(ToolAction):
         job_wrapper.setup_job(
             history,
             store_directory,
-            include_hidden=incoming['include_hidden'],
-            include_deleted=incoming['include_deleted'],
-            compressed=compressed)
+            include_hidden=incoming["include_hidden"],
+            include_deleted=incoming["include_deleted"],
+            compressed=compressed,
+        )
 
         return job, {}
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index 2c7cb1e925c..8c44032ca5d 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -12,9 +12,12 @@ log = logging.getLogger(__name__)
 
 class SetMetadataToolAction(ToolAction):
     """Tool action used for setting external metadata on an existing dataset"""
+
     produces_real_jobs = False
 
-    def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs):
+    def execute(
+        self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs
+    ):
         """
         Execute using a web transaction.
         """
@@ -23,16 +26,35 @@ class SetMetadataToolAction(ToolAction):
         session_id = session and session.id
         history_id = trans.history and trans.history.id
         incoming = incoming or {}
-        job, odict = self.execute_via_app(tool, trans.app, session_id,
-                                          history_id, trans.user, incoming, set_output_hid,
-                                          overwrite, history, job_params)
+        job, odict = self.execute_via_app(
+            tool,
+            trans.app,
+            session_id,
+            history_id,
+            trans.user,
+            incoming,
+            set_output_hid,
+            overwrite,
+            history,
+            job_params,
+        )
         # FIXME: can remove this when logging in execute_via_app method.
         trans.log_event(f"Added set external metadata job to the job queue, id: {str(job.id)}", tool_id=job.tool_id)
         return job, odict
 
-    def execute_via_app(self, tool, app, session_id, history_id, user=None,
-                        incoming=None, set_output_hid=False, overwrite=True,
-                        history=None, job_params=None):
+    def execute_via_app(
+        self,
+        tool,
+        app,
+        session_id,
+        history_id,
+        user=None,
+        incoming=None,
+        set_output_hid=False,
+        overwrite=True,
+        history=None,
+        job_params=None,
+    ):
         """
         Execute using application.
         """
@@ -44,15 +66,15 @@ class SetMetadataToolAction(ToolAction):
             if isinstance(value, app.model.HistoryDatasetAssociation):
                 dataset = value
                 dataset_name = name
-                type = 'hda'
+                type = "hda"
                 break
             elif isinstance(value, app.model.LibraryDatasetDatasetAssociation):
                 dataset = value
                 dataset_name = name
-                type = 'ldda'
+                type = "ldda"
                 break
             else:
-                raise Exception('The dataset to set metadata on could not be determined.')
+                raise Exception("The dataset to set metadata on could not be determined.")
 
         sa_session = app.model.context
 
@@ -73,47 +95,51 @@ class SetMetadataToolAction(ToolAction):
         except AttributeError:
             job.tool_version = "1.0.1"
         job.dynamic_tool = tool.dynamic_tool
-        job.state = job.states.WAITING  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
+        job.state = (
+            job.states.WAITING
+        )  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
         sa_session.add(job)
         sa_session.flush()  # ensure job.id is available
 
         # add parameters to job_parameter table
         # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)?
-        incoming['__ORIGINAL_DATASET_STATE__'] = dataset.state
+        incoming["__ORIGINAL_DATASET_STATE__"] = dataset.state
         input_paths = [DatasetPath(dataset.id, real_path=dataset.file_name, mutable=False)]
-        app.object_store.create(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
-        job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
-        datatypes_config = os.path.join(job_working_dir, 'registry.xml')
+        app.object_store.create(job, base_dir="job_work", dir_only=True, extra_dir=str(job.id))
+        job_working_dir = app.object_store.get_filename(job, base_dir="job_work", dir_only=True, extra_dir=str(job.id))
+        datatypes_config = os.path.join(job_working_dir, "registry.xml")
         app.datatypes_registry.to_xml_file(path=datatypes_config)
         external_metadata_wrapper = get_metadata_compute_strategy(app.config, job.id, tool_id=tool.id)
         output_datatasets_dict = {
             dataset_name: dataset,
         }
         validate_outputs = asbool(incoming.get("validate", False))
-        cmd_line = external_metadata_wrapper.setup_external_metadata(output_datatasets_dict,
-                                                                     {},
-                                                                     sa_session,
-                                                                     exec_dir=None,
-                                                                     tmp_dir=job_working_dir,
-                                                                     dataset_files_path=app.model.Dataset.file_path,
-                                                                     output_fnames=input_paths,
-                                                                     config_root=app.config.root,
-                                                                     config_file=app.config.config_file,
-                                                                     datatypes_config=datatypes_config,
-                                                                     job_metadata=os.path.join(job_working_dir, 'working', tool.provided_metadata_file),
-                                                                     include_command=False,
-                                                                     max_metadata_value_size=app.config.max_metadata_value_size,
-                                                                     max_discovered_files=app.config.max_discovered_files,
-                                                                     validate_outputs=validate_outputs,
-                                                                     job=job,
-                                                                     kwds={'overwrite': overwrite})
-        incoming['__SET_EXTERNAL_METADATA_COMMAND_LINE__'] = cmd_line
+        cmd_line = external_metadata_wrapper.setup_external_metadata(
+            output_datatasets_dict,
+            {},
+            sa_session,
+            exec_dir=None,
+            tmp_dir=job_working_dir,
+            dataset_files_path=app.model.Dataset.file_path,
+            output_fnames=input_paths,
+            config_root=app.config.root,
+            config_file=app.config.config_file,
+            datatypes_config=datatypes_config,
+            job_metadata=os.path.join(job_working_dir, "working", tool.provided_metadata_file),
+            include_command=False,
+            max_metadata_value_size=app.config.max_metadata_value_size,
+            max_discovered_files=app.config.max_discovered_files,
+            validate_outputs=validate_outputs,
+            job=job,
+            kwds={"overwrite": overwrite},
+        )
+        incoming["__SET_EXTERNAL_METADATA_COMMAND_LINE__"] = cmd_line
         for name, value in tool.params_to_strings(incoming, app).items():
             job.add_parameter(name, value)
         # add the dataset to job_to_input_dataset table
-        if type == 'hda':
+        if type == "hda":
             job.add_input_dataset(dataset_name, dataset)
-        elif type == 'ldda':
+        elif type == "ldda":
             job.add_input_library_dataset(dataset_name, dataset)
         # Need a special state here to show that metadata is being set and also allow the job to run
         # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state
diff --git a/lib/galaxy/tools/actions/model_operations.py b/lib/galaxy/tools/actions/model_operations.py
index 3f7d3fa451d..f963321283c 100644
--- a/lib/galaxy/tools/actions/model_operations.py
+++ b/lib/galaxy/tools/actions/model_operations.py
@@ -17,11 +17,26 @@ class ModelOperationToolAction(DefaultToolAction):
             execution_cache = ToolExecutionCache(trans)
 
         current_user_roles = execution_cache.current_user_roles
-        history, inp_data, inp_dataset_collections, _, _, _ = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
+        history, inp_data, inp_dataset_collections, _, _, _ = self._collect_inputs(
+            tool, trans, incoming, history, current_user_roles, collection_info
+        )
 
         tool.check_inputs_ready(inp_data, inp_dataset_collections)
 
-    def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, execution_cache=None, collection_info=None, job_callback=None, **kwargs):
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming=None,
+        set_output_hid=False,
+        overwrite=True,
+        history=None,
+        job_params=None,
+        execution_cache=None,
+        collection_info=None,
+        job_callback=None,
+        **kwargs,
+    ):
         incoming = incoming or {}
         trans.check_user_activation()
 
@@ -29,7 +44,14 @@ class ModelOperationToolAction(DefaultToolAction):
             execution_cache = ToolExecutionCache(trans)
 
         current_user_roles = execution_cache.current_user_roles
-        history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
+        (
+            history,
+            inp_data,
+            inp_dataset_collections,
+            preserved_tags,
+            preserved_hdca_tags,
+            all_permissions,
+        ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
 
         # Build name for output datasets based on tool name and input names
         on_text = self._get_on_text(inp_data)
@@ -58,7 +80,16 @@ class ModelOperationToolAction(DefaultToolAction):
         # Create job.
         #
         job, galaxy_session = self._new_job_for_session(trans, tool, history)
-        self._produce_outputs(trans, tool, out_data, output_collections, incoming=incoming, history=history, tags=preserved_tags, hdca_tags=preserved_hdca_tags)
+        self._produce_outputs(
+            trans,
+            tool,
+            out_data,
+            output_collections,
+            incoming=incoming,
+            history=history,
+            tags=preserved_tags,
+            hdca_tags=preserved_hdca_tags,
+        )
         self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections)
         self._record_outputs(job, out_data, output_collections)
         if job_callback:
@@ -74,7 +105,16 @@ class ModelOperationToolAction(DefaultToolAction):
 
     def _produce_outputs(self, trans, tool, out_data, output_collections, incoming, history, tags, hdca_tags):
         tag_handler = trans.app.tag_handler.create_tag_handler_session()
-        tool.produce_outputs(trans, out_data, output_collections, incoming, history=history, tags=tags, hdca_tags=hdca_tags, tag_handler=tag_handler)
+        tool.produce_outputs(
+            trans,
+            out_data,
+            output_collections,
+            incoming,
+            history=history,
+            tags=tags,
+            hdca_tags=hdca_tags,
+            tag_handler=tag_handler,
+        )
         mapped_over_elements = output_collections.dataset_collection_elements
         if mapped_over_elements:
             for name, value in out_data.items():
diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py
index 0ae13887a1d..8294af59f1b 100644
--- a/lib/galaxy/tools/actions/upload.py
+++ b/lib/galaxy/tools/actions/upload.py
@@ -42,24 +42,22 @@ class BaseUploadToolAction(ToolAction):
 
 
 class UploadToolAction(BaseUploadToolAction):
-
     def _setup_job(self, tool, trans, incoming, dataset_upload_inputs, history):
         check_timer = ExecutionTimer()
-        uploaded_datasets = upload_common.get_uploaded_datasets(trans, '', incoming, dataset_upload_inputs, history=history)
+        uploaded_datasets = upload_common.get_uploaded_datasets(
+            trans, "", incoming, dataset_upload_inputs, history=history
+        )
 
         if not uploaded_datasets:
-            return None, 'No data was entered in the upload form, please go back and choose data to upload.'
+            return None, "No data was entered in the upload form, please go back and choose data to upload."
 
         json_file_path = upload_common.create_paramfile(trans, uploaded_datasets)
         data_list = [ud.data for ud in uploaded_datasets]
         log.debug(f"Checked uploads {check_timer}")
-        return self._create_job(
-            trans, incoming, tool, json_file_path, data_list, history=history
-        )
+        return self._create_job(trans, incoming, tool, json_file_path, data_list, history=history)
 
 
 class FetchUploadToolAction(BaseUploadToolAction):
-
     def _setup_job(self, tool, trans, incoming, dataset_upload_inputs, history):
         # Now replace references in requests with these.
         files = incoming.get("files", [])
@@ -74,7 +72,9 @@ class FetchUploadToolAction(BaseUploadToolAction):
                     except StopIteration:
                         path_def = None
                     if path_def is None or path_def["file_data"] is None:
-                        raise RequestParameterMissingException("Failed to find uploaded file matching target with src='files'")
+                        raise RequestParameterMissingException(
+                            "Failed to find uploaded file matching target with src='files'"
+                        )
                     request_part["path"] = path_def["file_data"]["local_filename"]
                     if "name" not in request_part:
                         request_part["name"] = path_def["file_data"]["filename"]
@@ -103,9 +103,7 @@ class FetchUploadToolAction(BaseUploadToolAction):
                 _precreate_fetched_collection_instance(trans, history, target, outputs)
 
         incoming["request_json"] = json.dumps(request)
-        return self._create_job(
-            trans, incoming, tool, None, outputs, history=history
-        )
+        return self._create_job(trans, incoming, tool, None, outputs, history=history)
 
 
 def _precreate_fetched_hdas(trans, history, target, outputs):
@@ -124,11 +122,11 @@ def _precreate_fetched_hdas(trans, history, target, outputs):
 
         file_type = item.get("ext", "auto")
         dbkey = item.get("dbkey", "?")
-        uploaded_dataset = Bunch(
-            type='file', name=name, file_type=file_type, dbkey=dbkey
-        )
+        uploaded_dataset = Bunch(type="file", name=name, file_type=file_type, dbkey=dbkey)
         tag_list = item.get("tags", [])
-        data = upload_common.new_upload(trans, '', uploaded_dataset, library_bunch=None, history=history, tag_list=tag_list)
+        data = upload_common.new_upload(
+            trans, "", uploaded_dataset, library_bunch=None, history=history, tag_list=tag_list
+        )
         outputs.append(data)
         item["object_id"] = data.id
 
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index 6690701cd32..ac9cb3e3086 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -5,8 +5,15 @@ import socket
 import tempfile
 from dataclasses import dataclass
 from io import StringIO
-from json import dump, dumps
-from typing import Dict, List, Optional
+from json import (
+    dump,
+    dumps,
+)
+from typing import (
+    Dict,
+    List,
+    Optional,
+)
 from urllib.parse import urlparse
 
 from sqlalchemy.orm import joinedload
@@ -27,7 +34,7 @@ from galaxy.model import (
 )
 from galaxy.util import (
     is_url,
-    unicodify
+    unicodify,
 )
 from galaxy.util.path import external_chown
 
@@ -35,13 +42,13 @@ log = logging.getLogger(__name__)
 
 
 def validate_datatype_extension(datatypes_registry, ext):
-    if ext and ext not in ('auto', 'data') and not datatypes_registry.get_datatype_by_extension(ext):
+    if ext and ext not in ("auto", "data") and not datatypes_registry.get_datatype_by_extension(ext):
         raise RequestParameterInvalidException(f"Requested extension '{ext}' unknown, cannot upload dataset.")
 
 
 def validate_url(url, ip_allowlist):
     # If it doesn't look like a URL, ignore it.
-    if not (url.lstrip().startswith('http://') or url.lstrip().startswith('https://')):
+    if not (url.lstrip().startswith("http://") or url.lstrip().startswith("https://")):
         return url
 
     # Strip leading whitespace before passing url to urlparse()
@@ -49,9 +56,9 @@ def validate_url(url, ip_allowlist):
     # Extract hostname component
     parsed_url = urlparse(url).netloc
     # If credentials are in this URL, we need to strip those.
-    if parsed_url.count('@') > 0:
+    if parsed_url.count("@") > 0:
         # credentials.
-        parsed_url = parsed_url[parsed_url.rindex('@') + 1:]
+        parsed_url = parsed_url[parsed_url.rindex("@") + 1 :]
     # Percent encoded colons and other characters will not be resolved as such
     # so we don't have to either.
 
@@ -59,20 +66,20 @@ def validate_url(url, ip_allowlist):
     # need to extract that.
     port = None
     # However, it could ALSO be an IPv6 address they've supplied.
-    if ':' in parsed_url:
+    if ":" in parsed_url:
         # IPv6 addresses have colons in them already (it seems like always more than two)
-        if parsed_url.count(':') >= 2:
+        if parsed_url.count(":") >= 2:
             # Since IPv6 already use colons extensively, they wrap it in
             # brackets when there is a port, e.g. http://[2001:db8:1f70::999:de8:7648:6e8]:100/
             # However if it ends with a ']' then there is no port after it and
             # they've wrapped it in brackets just for fun.
-            if ']' in parsed_url and not parsed_url.endswith(']'):
+            if "]" in parsed_url and not parsed_url.endswith("]"):
                 # If this +1 throws a range error, we don't care, their url
                 # shouldn't end with a colon.
-                idx = parsed_url.rindex(':')
+                idx = parsed_url.rindex(":")
                 # We parse as an int and let this fail ungracefully if parsing
                 # fails because we desire to fail closed rather than open.
-                port = int(parsed_url[idx + 1:])
+                port = int(parsed_url[idx + 1 :])
                 parsed_url = parsed_url[:idx]
             else:
                 # Plain ipv6 without port
@@ -80,8 +87,8 @@ def validate_url(url, ip_allowlist):
         else:
             # This should finally be ipv4 with port. It cannot be IPv6 as that
             # was caught by earlier cases, and it cannot be due to credentials.
-            idx = parsed_url.rindex(':')
-            port = int(parsed_url[idx + 1:])
+            idx = parsed_url.rindex(":")
+            port = int(parsed_url[idx + 1 :])
             parsed_url = parsed_url[:idx]
 
     # safe to log out, no credentials/request path, just an IP + port
@@ -106,7 +113,7 @@ def validate_url(url, ip_allowlist):
             # If this IP is not anywhere in the allowlist
             for allowlisted in ip_allowlist:
                 # If it's an IP address range (rather than a single one...)
-                if hasattr(allowlisted, 'subnets'):
+                if hasattr(allowlisted, "subnets"):
                     results.append(ip in allowlisted)
                 else:
                     results.append(ip == allowlisted)
@@ -127,28 +134,31 @@ def persist_uploads(params, trans):
     """
     Turn any uploads in the submitted form to persisted files.
     """
-    if 'files' in params:
+    if "files" in params:
         new_files = []
-        for upload_dataset in params['files']:
-            f = upload_dataset['file_data']
+        for upload_dataset in params["files"]:
+            f = upload_dataset["file_data"]
             if isinstance(f, cgi_FieldStorage):
                 assert not isinstance(f.file, StringIO)
-                assert f.file.name != '<fdopen>'
-                local_filename = util.mkstemp_ln(f.file.name, 'upload_file_data_')
+                assert f.file.name != "<fdopen>"
+                local_filename = util.mkstemp_ln(f.file.name, "upload_file_data_")
                 f.file.close()
-                upload_dataset['file_data'] = dict(filename=f.filename,
-                                                   local_filename=local_filename)
-            elif type(f) == dict and 'local_filename' not in f:
-                raise Exception('Uploaded file was encoded in a way not understood by Galaxy.')
-            if 'url_paste' in upload_dataset and upload_dataset['url_paste'] and upload_dataset['url_paste'].strip() != '':
-                upload_dataset['url_paste'] = stream_to_file(
-                    StringIO(validate_url(upload_dataset['url_paste'], trans.app.config.fetch_url_allowlist_ips)),
-                    prefix="strio_url_paste_"
+                upload_dataset["file_data"] = dict(filename=f.filename, local_filename=local_filename)
+            elif type(f) == dict and "local_filename" not in f:
+                raise Exception("Uploaded file was encoded in a way not understood by Galaxy.")
+            if (
+                "url_paste" in upload_dataset
+                and upload_dataset["url_paste"]
+                and upload_dataset["url_paste"].strip() != ""
+            ):
+                upload_dataset["url_paste"] = stream_to_file(
+                    StringIO(validate_url(upload_dataset["url_paste"], trans.app.config.fetch_url_allowlist_ips)),
+                    prefix="strio_url_paste_",
                 )
             else:
-                upload_dataset['url_paste'] = None
+                upload_dataset["url_paste"] = None
             new_files.append(upload_dataset)
-        params['files'] = new_files
+        params["files"] = new_files
     return params
 
 
@@ -163,31 +173,33 @@ class LibraryParams:
     replace_dataset: Optional[LibraryDataset]
 
 
-def handle_library_params(trans, params, folder_id: str, replace_dataset: Optional[LibraryDataset] = None) -> LibraryParams:
+def handle_library_params(
+    trans, params, folder_id: str, replace_dataset: Optional[LibraryDataset] = None
+) -> LibraryParams:
     # FIXME: the received params has already been parsed by util.Params() by the time it reaches here,
     # so no complex objects remain.  This is not good because it does not allow for those objects to be
     # manipulated here.  The received params should be the original kwd from the initial request.
-    message = params.get('ldda_message', '')
+    message = params.get("ldda_message", "")
     # See if we have any template field contents
     template_field_contents = {}
-    template_id = params.get('template_id', None)
+    template_id = params.get("template_id", None)
     folder = trans.sa_session.query(LibraryFolder).get(trans.security.decode_id(folder_id))
     # We are inheriting the folder's info_association, so we may have received inherited contents or we may have redirected
     # here after the user entered template contents ( due to errors ).
     template: Optional[FormDefinition] = None
-    if template_id not in [None, 'None']:
+    if template_id not in [None, "None"]:
         template = trans.sa_session.query(FormDefinition).get(template_id)
         assert template
         for field in template.fields:
-            field_name = field['name']
+            field_name = field["name"]
             if params.get(field_name, False):
-                field_value = util.restore_text(params.get(field_name, ''))
+                field_value = util.restore_text(params.get(field_name, ""))
                 template_field_contents[field_name] = field_value
     roles: List[Role] = []
-    for role_id in util.listify(params.get('roles', [])):
+    for role_id in util.listify(params.get("roles", [])):
         role = trans.sa_session.query(Role).get(role_id)
         roles.append(role)
-    tags = params.get('tags', None)
+    tags = params.get("tags", None)
     return LibraryParams(
         folder=folder,
         message=message,
@@ -202,12 +214,14 @@ def handle_library_params(trans, params, folder_id: str, replace_dataset: Option
 def __new_history_upload(trans, uploaded_dataset, history=None, state=None):
     if not history:
         history = trans.history
-    hda = trans.app.model.HistoryDatasetAssociation(name=uploaded_dataset.name,
-                                                    extension=uploaded_dataset.file_type,
-                                                    dbkey=uploaded_dataset.dbkey,
-                                                    history=history,
-                                                    create_dataset=True,
-                                                    sa_session=trans.sa_session)
+    hda = trans.app.model.HistoryDatasetAssociation(
+        name=uploaded_dataset.name,
+        extension=uploaded_dataset.file_type,
+        dbkey=uploaded_dataset.dbkey,
+        history=history,
+        create_dataset=True,
+        sa_session=trans.sa_session,
+    )
     trans.sa_session.add(hda)
     if state:
         hda.state = state
@@ -223,11 +237,14 @@ def __new_history_upload(trans, uploaded_dataset, history=None, state=None):
 
 def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_handler, state=None):
     current_user_roles = trans.get_current_user_roles()
-    if not ((trans.user_is_admin and cntrller in ['library_admin', 'api']) or trans.app.security_agent.can_add_library_item(current_user_roles, library_bunch.folder)):
+    if not (
+        (trans.user_is_admin and cntrller in ["library_admin", "api"])
+        or trans.app.security_agent.can_add_library_item(current_user_roles, library_bunch.folder)
+    ):
         # This doesn't have to be pretty - the only time this should happen is if someone's being malicious.
         raise Exception("User is not authorized to add datasets to this library.")
     folder = library_bunch.folder
-    if uploaded_dataset.get('in_folder', False):
+    if uploaded_dataset.get("in_folder", False):
         # Create subfolders if desired
         for name in uploaded_dataset.in_folder.split(os.path.sep):
             trans.sa_session.refresh(folder)
@@ -235,7 +252,7 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_h
             if matches:
                 folder = matches[0]
             else:
-                new_folder = LibraryFolder(name=name, description='Automatically created by upload tool')
+                new_folder = LibraryFolder(name=name, description="Automatically created by upload tool")
                 new_folder.genome_build = trans.app.genome_builds.default_value
                 folder.add_folder(new_folder)
                 trans.sa_session.add(new_folder)
@@ -249,21 +266,23 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_h
         trans.sa_session.add(ld)
         trans.sa_session.flush()
         trans.app.security_agent.copy_library_permissions(trans, folder, ld)
-    ldda = trans.app.model.LibraryDatasetDatasetAssociation(name=uploaded_dataset.name,
-                                                            extension=uploaded_dataset.file_type,
-                                                            dbkey=uploaded_dataset.dbkey,
-                                                            library_dataset=ld,
-                                                            user=trans.user,
-                                                            create_dataset=True,
-                                                            sa_session=trans.sa_session)
-    if uploaded_dataset.get('tag_using_filenames', False):
+    ldda = trans.app.model.LibraryDatasetDatasetAssociation(
+        name=uploaded_dataset.name,
+        extension=uploaded_dataset.file_type,
+        dbkey=uploaded_dataset.dbkey,
+        library_dataset=ld,
+        user=trans.user,
+        create_dataset=True,
+        sa_session=trans.sa_session,
+    )
+    if uploaded_dataset.get("tag_using_filenames", False):
         tag_from_filename = os.path.splitext(os.path.basename(uploaded_dataset.name))[0]
-        tag_handler.apply_item_tag(item=ldda, user=trans.user, name='name', value=tag_from_filename, flush=False)
+        tag_handler.apply_item_tag(item=ldda, user=trans.user, name="name", value=tag_from_filename, flush=False)
 
-    tags_list = uploaded_dataset.get('tags', False)
+    tags_list = uploaded_dataset.get("tags", False)
     if tags_list:
         for tag in tags_list:
-            tag_handler.apply_item_tag(item=ldda, user=trans.user, name='name', value=tag, flush=False)
+            tag_handler.apply_item_tag(item=ldda, user=trans.user, name="name", value=tag, flush=False)
 
     trans.sa_session.add(ldda)
     if state:
@@ -276,10 +295,14 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_h
     trans.app.security_agent.copy_library_permissions(trans, ld, ldda)
     if library_bunch.replace_dataset:
         # Copy the Dataset level permissions from replace_dataset to the new LibraryDatasetDatasetAssociation.dataset
-        trans.app.security_agent.copy_dataset_permissions(library_bunch.replace_dataset.library_dataset_dataset_association.dataset, ldda.dataset)
+        trans.app.security_agent.copy_dataset_permissions(
+            library_bunch.replace_dataset.library_dataset_dataset_association.dataset, ldda.dataset
+        )
     else:
         # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset
-        trans.app.security_agent.set_all_dataset_permissions(ldda.dataset, trans.app.security_agent.user_get_default_permissions(trans.user))
+        trans.app.security_agent.set_all_dataset_permissions(
+            ldda.dataset, trans.app.security_agent.user_get_default_permissions(trans.user)
+        )
         folder.add_library_dataset(ld, genome_build=uploaded_dataset.dbkey)
         trans.sa_session.add(folder)
         trans.sa_session.flush()
@@ -301,13 +324,17 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_h
         # Create a new info_association between the current ldda and form_values
         # TODO: Currently info_associations at the ldda level are not inheritable to the associated LibraryDataset,
         # we need to figure out if this is optimal
-        info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation(ldda, library_bunch.template, form_values)
+        info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation(
+            ldda, library_bunch.template, form_values
+        )
         trans.sa_session.add(info_association)
         trans.sa_session.flush()
     # If roles were selected upon upload, restrict access to the Dataset to those roles
     if library_bunch.roles:
         for role in library_bunch.roles:
-            dp = trans.app.model.DatasetPermissions(trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, ldda.dataset, role)
+            dp = trans.app.model.DatasetPermissions(
+                trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, ldda.dataset, role
+            )
             trans.sa_session.add(dp)
             trans.sa_session.flush()
     return ldda
@@ -316,11 +343,15 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_h
 def new_upload(trans, cntrller, uploaded_dataset, library_bunch=None, history=None, state=None, tag_list=None):
     tag_handler = tags.GalaxyTagHandlerSession(trans.sa_session)
     if library_bunch:
-        upload_target_dataset_instance = __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_handler, state)
+        upload_target_dataset_instance = __new_library_upload(
+            trans, cntrller, uploaded_dataset, library_bunch, tag_handler, state
+        )
         if library_bunch.tags and not uploaded_dataset.tags:
             new_tags = tag_handler.parse_tags_list(library_bunch.tags)
             for tag in new_tags:
-                tag_handler.apply_item_tag(user=trans.user, item=upload_target_dataset_instance, name=tag[0], value=tag[1], flush=False)
+                tag_handler.apply_item_tag(
+                    user=trans.user, item=upload_target_dataset_instance, name=tag[0], value=tag[1], flush=False
+                )
     else:
         upload_target_dataset_instance = __new_history_upload(trans, uploaded_dataset, history=history, state=state)
 
@@ -348,21 +379,23 @@ def create_paramfile(trans, uploaded_datasets):
     json_file_path = None
     for uploaded_dataset in uploaded_datasets:
         data = uploaded_dataset.data
-        if uploaded_dataset.type == 'composite':
+        if uploaded_dataset.type == "composite":
             # we need to init metadata before the job is dispatched
             data.init_meta()
             for meta_name, meta_value in uploaded_dataset.metadata.items():
                 setattr(data.metadata, meta_name, meta_value)
             trans.sa_session.add(data)
             trans.sa_session.flush()
-            params = dict(file_type=uploaded_dataset.file_type,
-                          dataset_id=data.dataset.id,
-                          dbkey=uploaded_dataset.dbkey,
-                          type=uploaded_dataset.type,
-                          metadata=uploaded_dataset.metadata,
-                          primary_file=uploaded_dataset.primary_file,
-                          composite_file_paths=uploaded_dataset.composite_files,
-                          composite_files={k: v.__dict__ for k, v in data.datatype.get_composite_files(data).items()})
+            params = dict(
+                file_type=uploaded_dataset.file_type,
+                dataset_id=data.dataset.id,
+                dbkey=uploaded_dataset.dbkey,
+                type=uploaded_dataset.type,
+                metadata=uploaded_dataset.metadata,
+                primary_file=uploaded_dataset.primary_file,
+                composite_file_paths=uploaded_dataset.composite_files,
+                composite_files={k: v.__dict__ for k, v in data.datatype.get_composite_files(data).items()},
+            )
         else:
             try:
                 is_binary = uploaded_dataset.datatype.is_binary
@@ -371,7 +404,7 @@ def create_paramfile(trans, uploaded_datasets):
             try:
                 link_data_only = uploaded_dataset.link_data_only
             except Exception:
-                link_data_only = 'copy_files'
+                link_data_only = "copy_files"
             try:
                 uuid_str = uploaded_dataset.uuid
             except Exception:
@@ -385,32 +418,42 @@ def create_paramfile(trans, uploaded_datasets):
             except Exception:
                 user_ftp_dir = None
             if user_ftp_dir and uploaded_dataset.path.startswith(user_ftp_dir):
-                uploaded_dataset.type = 'ftp_import'
-            params = dict(file_type=uploaded_dataset.file_type,
-                          ext=uploaded_dataset.ext,
-                          name=uploaded_dataset.name,
-                          dataset_id=data.dataset.id,
-                          dbkey=uploaded_dataset.dbkey,
-                          type=uploaded_dataset.type,
-                          is_binary=is_binary,
-                          link_data_only=link_data_only,
-                          uuid=uuid_str,
-                          to_posix_lines=getattr(uploaded_dataset, "to_posix_lines", True),
-                          auto_decompress=getattr(uploaded_dataset, "auto_decompress", True),
-                          purge_source=purge_source,
-                          space_to_tab=uploaded_dataset.space_to_tab,
-                          run_as_real_user=trans.app.config.external_chown_script is not None,
-                          check_content=trans.app.config.check_upload_content,
-                          path=uploaded_dataset.path)
+                uploaded_dataset.type = "ftp_import"
+            params = dict(
+                file_type=uploaded_dataset.file_type,
+                ext=uploaded_dataset.ext,
+                name=uploaded_dataset.name,
+                dataset_id=data.dataset.id,
+                dbkey=uploaded_dataset.dbkey,
+                type=uploaded_dataset.type,
+                is_binary=is_binary,
+                link_data_only=link_data_only,
+                uuid=uuid_str,
+                to_posix_lines=getattr(uploaded_dataset, "to_posix_lines", True),
+                auto_decompress=getattr(uploaded_dataset, "auto_decompress", True),
+                purge_source=purge_source,
+                space_to_tab=uploaded_dataset.space_to_tab,
+                run_as_real_user=trans.app.config.external_chown_script is not None,
+                check_content=trans.app.config.check_upload_content,
+                path=uploaded_dataset.path,
+            )
             # TODO: This will have to change when we start bundling inputs.
             # Also, in_place above causes the file to be left behind since the
             # user cannot remove it unless the parent directory is writable.
-            if link_data_only == 'copy_files' and trans.user and trans.app.config.external_chown_script and not is_url(uploaded_dataset.path):
-                external_chown(uploaded_dataset.path,
-                               trans.user.system_user_pwent(trans.app.config.real_system_username),
-                               trans.app.config.external_chown_script, description="uploaded file")
+            if (
+                link_data_only == "copy_files"
+                and trans.user
+                and trans.app.config.external_chown_script
+                and not is_url(uploaded_dataset.path)
+            ):
+                external_chown(
+                    uploaded_dataset.path,
+                    trans.user.system_user_pwent(trans.app.config.real_system_username),
+                    trans.app.config.external_chown_script,
+                    description="uploaded file",
+                )
         tool_params.append(params)
-    with tempfile.NamedTemporaryFile(mode="w", prefix='upload_params_', delete=False) as fh:
+    with tempfile.NamedTemporaryFile(mode="w", prefix="upload_params_", delete=False) as fh:
         json_file_path = fh.name
         dump(tool_params, fh)
     return json_file_path
@@ -440,7 +483,7 @@ def create_job(trans, params, tool, json_file_path, outputs, folder=None, histor
 
     for name, value in tool.params_to_strings(params, trans.app).items():
         job.add_parameter(name, value)
-    job.add_parameter('paramfile', dumps(json_file_path))
+    job.add_parameter("paramfile", dumps(json_file_path))
     for i, output_object in enumerate(outputs):
         output_name = "output%i" % i
         if hasattr(output_object, "collection"):
@@ -461,7 +504,7 @@ def create_job(trans, params, tool, json_file_path, outputs, folder=None, histor
     output = {}
     for i, v in enumerate(outputs):
         if not hasattr(output_object, "collection_type"):
-            output['output%i' % i] = v
+            output["output%i" % i] = v
     return job, output
 
 
@@ -469,8 +512,10 @@ def active_folders(trans, folder):
     # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues).
     # Much faster way of retrieving all active sub-folders within a given folder than the
     # performance of the mapper.  This query also eagerloads the permissions on each folder.
-    return trans.sa_session.query(LibraryFolder) \
-                           .filter_by(parent=folder, deleted=False) \
-                           .options(joinedload("actions")) \
-                           .order_by(LibraryFolder.table.c.name) \
-                           .all()
+    return (
+        trans.sa_session.query(LibraryFolder)
+        .filter_by(parent=folder, deleted=False)
+        .options(joinedload("actions"))
+        .order_by(LibraryFolder.table.c.name)
+        .all()
+    )
diff --git a/lib/galaxy/tools/biotools.py b/lib/galaxy/tools/biotools.py
index 774a7257899..d396037b138 100644
--- a/lib/galaxy/tools/biotools.py
+++ b/lib/galaxy/tools/biotools.py
@@ -16,10 +16,10 @@ def get_galaxy_biotools_metadata_source(config) -> BiotoolsMetadataSource:
     biotools_metadata_source_config.content_directory = config.biotools_content_directory
     biotools_metadata_source_config.use_api = config.biotools_use_api
     cache_opts = {
-        'cache.type': getattr(config, 'biotools_service_cache_type', 'file'),
-        'cache.data_dir': getattr(config, 'biotools_service_cache_data_dir', None),
-        'cache.lock_dir': getattr(config, 'biotools_service_cache_lock_dir', None),
+        "cache.type": getattr(config, "biotools_service_cache_type", "file"),
+        "cache.data_dir": getattr(config, "biotools_service_cache_data_dir", None),
+        "cache.lock_dir": getattr(config, "biotools_service_cache_lock_dir", None),
     }
-    cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('doi')
+    cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache("doi")
     biotools_metadata_source_config.cache = cache
     return get_biotools_metadata_source(biotools_metadata_source_config)
diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index 780dae71491..69036f486b3 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -7,7 +7,11 @@ import tempfile
 import zlib
 from collections import defaultdict
 from threading import Lock
-from typing import Dict, List, Tuple
+from typing import (
+    Dict,
+    List,
+    Tuple,
+)
 
 from sqlalchemy.orm import defer
 from sqlitedict import SqliteDict
@@ -18,27 +22,25 @@ from galaxy.tool_util.toolbox.base import ToolConfRepository
 from galaxy.util import unicodify
 from galaxy.util.hash_util import md5_hash_file
 
-
 log = logging.getLogger(__name__)
 
 CURRENT_TOOL_CACHE_VERSION = 0
 
 
 def encoder(obj):
-    return sqlite3.Binary(zlib.compress(json.dumps(obj).encode('utf-8')))
+    return sqlite3.Binary(zlib.compress(json.dumps(obj).encode("utf-8")))
 
 
 def decoder(obj):
-    return json.loads(zlib.decompress(bytes(obj)).decode('utf-8'))
+    return json.loads(zlib.decompress(bytes(obj)).decode("utf-8"))
 
 
 class ToolDocumentCache:
-
     def __init__(self, cache_dir):
         self.cache_dir = cache_dir
         if not os.path.exists(self.cache_dir):
             os.makedirs(self.cache_dir)
-        self.cache_file = os.path.join(self.cache_dir, 'cache.sqlite')
+        self.cache_file = os.path.join(self.cache_dir, "cache.sqlite")
         self.writeable_cache_file = None
         self._cache = None
         self.disabled = False
@@ -47,18 +49,18 @@ class ToolDocumentCache:
     def close(self):
         self._cache and self._cache.close()
 
-    def _get_cache(self, flag='r', create_if_necessary=False):
+    def _get_cache(self, flag="r", create_if_necessary=False):
         try:
             if create_if_necessary and not os.path.exists(self.cache_file):
                 # Create database if necessary using 'c' flag
-                self._cache = SqliteDict(self.cache_file, flag='c', encode=encoder, decode=decoder, autocommit=False)
-                if flag == 'r':
+                self._cache = SqliteDict(self.cache_file, flag="c", encode=encoder, decode=decoder, autocommit=False)
+                if flag == "r":
                     self._cache.flag = flag
             else:
                 cache_file = self.writeable_cache_file.name if self.writeable_cache_file else self.cache_file
                 self._cache = SqliteDict(cache_file, flag=flag, encode=encoder, decode=decoder, autocommit=False)
         except sqlite3.OperationalError:
-            log.warning('Tool document cache unavailable')
+            log.warning("Tool document cache unavailable")
             self._cache = None
             self.disabled = True
 
@@ -67,7 +69,7 @@ class ToolDocumentCache:
         return os.access(self.cache_file, os.W_OK)
 
     def reopen_ro(self):
-        self._get_cache(flag='r')
+        self._get_cache(flag="r")
         self.writeable_cache_file = None
 
     def get(self, config_file):
@@ -78,20 +80,22 @@ class ToolDocumentCache:
             return None
         if not tool_document:
             return None
-        if tool_document.get('tool_cache_version') != CURRENT_TOOL_CACHE_VERSION:
+        if tool_document.get("tool_cache_version") != CURRENT_TOOL_CACHE_VERSION:
             return None
         if self.cache_file_is_writeable:
-            for path, modtime in tool_document['paths_and_modtimes'].items():
+            for path, modtime in tool_document["paths_and_modtimes"].items():
                 if os.path.getmtime(path) != modtime:
                     return None
         return tool_document
 
     def _make_writable(self):
         if not self.writeable_cache_file:
-            self.writeable_cache_file = tempfile.NamedTemporaryFile(dir=self.cache_dir, suffix='cache.sqlite.tmp', delete=False)
+            self.writeable_cache_file = tempfile.NamedTemporaryFile(
+                dir=self.cache_dir, suffix="cache.sqlite.tmp", delete=False
+            )
             if os.path.exists(self.cache_file):
                 shutil.copy(self.cache_file, self.writeable_cache_file.name)
-            self._get_cache(flag='c')
+            self._get_cache(flag="c")
 
     def persist(self):
         if self.writeable_cache_file:
@@ -104,10 +108,10 @@ class ToolDocumentCache:
             if self.cache_file_is_writeable:
                 self._make_writable()
                 to_persist = {
-                    'document': tool_source.to_string(),
-                    'macro_paths': tool_source.macro_paths,
-                    'paths_and_modtimes': tool_source.paths_and_modtimes(),
-                    'tool_cache_version': CURRENT_TOOL_CACHE_VERSION,
+                    "document": tool_source.to_string(),
+                    "macro_paths": tool_source.macro_paths,
+                    "paths_and_modtimes": tool_source.paths_and_modtimes(),
+                    "tool_cache_version": CURRENT_TOOL_CACHE_VERSION,
                 }
                 try:
                     self._cache[config_file] = to_persist
@@ -165,7 +169,9 @@ class ToolCache:
         try:
             with self._lock:
                 persist_tool_document_cache = False
-                paths_to_cleanup = {(path, tool) for path, tool in self._tools_by_path.items() if self._should_cleanup(path)}
+                paths_to_cleanup = {
+                    (path, tool) for path, tool in self._tools_by_path.items() if self._should_cleanup(path)
+                }
                 for config_filename, tool in paths_to_cleanup:
                     tool.remove_from_cache()
                     persist_tool_document_cache = True
@@ -219,7 +225,7 @@ class ToolCache:
         return self._removed_tools_by_path.get(config_filename)
 
     def get_tool_by_id(self, tool_id):
-        """Get the tool with the id `tool_id` from the cache if the tool is up to date. """
+        """Get the tool with the id `tool_id` from the cache if the tool is up to date."""
         return self.get_tool(self._tool_paths_by_id.get(tool_id))
 
     def expire_tool(self, tool_id):
@@ -260,7 +266,6 @@ class ToolCache:
 
 
 class ToolHash:
-
     def __init__(self, path, modtime=None, lazy_hash=False):
         self.path = path
         self.modtime = modtime or os.path.getmtime(path)
@@ -279,6 +284,7 @@ class ToolShedRepositoryCache:
     """
     Cache installed ToolShedRepository objects.
     """
+
     local_repositories: List[ToolConfRepository]
     repositories: List[ToolShedRepository]
     repos_by_tuple: Dict[Tuple[str, str, str], List[ToolConfRepository]]
@@ -298,15 +304,21 @@ class ToolShedRepositoryCache:
         self.repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
 
     def _build(self):
-        self.repositories = self.session.query(ToolShedRepository).options(
-            defer(ToolShedRepository.metadata_)
-        ).all()
+        self.repositories = self.session.query(ToolShedRepository).options(defer(ToolShedRepository.metadata_)).all()
         repos_by_tuple = defaultdict(list)
         for repository in self.repositories + self.local_repositories:
             repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
         self.repos_by_tuple = repos_by_tuple
 
-    def get_installed_repository(self, tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None):
+    def get_installed_repository(
+        self,
+        tool_shed=None,
+        name=None,
+        owner=None,
+        installed_changeset_revision=None,
+        changeset_revision=None,
+        repository_id=None,
+    ):
         if repository_id:
             repos = [repo for repo in self.repositories if repo.id == repository_id]
             if repos:
diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py
index e81895c67c8..a2eb2cca077 100644
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -32,7 +32,7 @@ from galaxy.util.template import fill_template
 
 log = logging.getLogger(__name__)
 
-DEFAULT_TABLE_TYPE = 'tabular'
+DEFAULT_TABLE_TYPE = "tabular"
 
 TOOL_DATA_TABLE_CONF_XML = """<?xml version="1.0"?>
 <tables>
@@ -41,7 +41,6 @@ TOOL_DATA_TABLE_CONF_XML = """<?xml version="1.0"?>
 
 
 class ToolDataPathFiles:
-
     def __init__(self, tool_data_path):
         self.tool_data_path = os.path.abspath(tool_data_path)
         self.update_time = 0
@@ -55,7 +54,17 @@ class ToolDataPathFiles:
     def update_files(self):
         try:
             content = os.walk(self.tool_data_path)
-            self._tool_data_path_files = set(filter(os.path.exists, [os.path.join(dirpath, fn) for dirpath, _, fn_list in content for fn in fn_list if fn and fn.endswith('.loc') or fn.endswith('.loc.sample')]))
+            self._tool_data_path_files = set(
+                filter(
+                    os.path.exists,
+                    [
+                        os.path.join(dirpath, fn)
+                        for dirpath, _, fn_list in content
+                        for fn in fn_list
+                        if fn and fn.endswith(".loc") or fn.endswith(".loc.sample")
+                    ],
+                )
+            )
             self.update_time = time.time()
         except Exception:
             log.exception()
@@ -72,7 +81,9 @@ class ToolDataPathFiles:
 class ToolDataTableManager(Dictifiable):
     """Manages a collection of tool data tables"""
 
-    def __init__(self, tool_data_path, config_filename=None, tool_data_table_config_path_set=None, other_config_dict=None):
+    def __init__(
+        self, tool_data_path, config_filename=None, tool_data_table_config_path_set=None, other_config_dict=None
+    ):
         self.tool_data_path = tool_data_path
         # This stores all defined data table entries from both the tool_data_table_conf.xml file and the shed_tool_data_table_conf.xml file
         # at server startup. If tool shed repositories are installed that contain a valid file named tool_data_table_conf.xml.sample, entries
@@ -107,10 +118,10 @@ class ToolDataTableManager(Dictifiable):
         return self.data_tables
 
     def to_dict(self):
-        return {name: data_table.to_dict(view='export') for name, data_table in self.data_tables.items()}
+        return {name: data_table.to_dict(view="export") for name, data_table in self.data_tables.items()}
 
     def to_json(self, path):
-        with open(path, 'w') as out:
+        with open(path, "w") as out:
             out.write(json.dumps(self.to_dict()))
 
     @classmethod
@@ -135,19 +146,34 @@ class ToolDataTableManager(Dictifiable):
         for filename in config_filename:
             tree = util.parse_xml(filename)
             root = tree.getroot()
-            for table_elem in root.findall('table'):
-                table = ToolDataTable.from_elem(table_elem, tool_data_path, from_shed_config, filename=filename, tool_data_path_files=self.tool_data_path_files, other_config_dict=self.other_config_dict)
+            for table_elem in root.findall("table"):
+                table = ToolDataTable.from_elem(
+                    table_elem,
+                    tool_data_path,
+                    from_shed_config,
+                    filename=filename,
+                    tool_data_path_files=self.tool_data_path_files,
+                    other_config_dict=self.other_config_dict,
+                )
                 table_elems.append(table_elem)
                 if table.name not in self.data_tables:
                     self.data_tables[table.name] = table
                     log.debug("Loaded tool data table '%s' from file '%s'", table.name, filename)
                 else:
-                    log.debug("Loading another instance of data table '%s' from file '%s', attempting to merge content.", table.name, filename)
-                    self.data_tables[table.name].merge_tool_data_table(table, allow_duplicates=False)  # only merge content, do not persist to disk, do not allow duplicate rows when merging
+                    log.debug(
+                        "Loading another instance of data table '%s' from file '%s', attempting to merge content.",
+                        table.name,
+                        filename,
+                    )
+                    self.data_tables[table.name].merge_tool_data_table(
+                        table, allow_duplicates=False
+                    )  # only merge content, do not persist to disk, do not allow duplicate rows when merging
                     # FIXME: This does not account for an entry with the same unique build ID, but a different path.
         return table_elems
 
-    def add_new_entries_from_config_file(self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False):
+    def add_new_entries_from_config_file(
+        self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False
+    ):
         """
         This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being
         installed into a local galaxy instance.  We have 2 cases to handle, files whose root tag is <tables>, for example::
@@ -169,13 +195,15 @@ class ToolDataTableManager(Dictifiable):
             </table>
 
         """
-        error_message = ''
+        error_message = ""
         try:
-            table_elems = self.load_from_config_file(config_filename=config_filename,
-                                                     tool_data_path=tool_data_path,
-                                                     from_shed_config=True)
+            table_elems = self.load_from_config_file(
+                config_filename=config_filename, tool_data_path=tool_data_path, from_shed_config=True
+            )
         except Exception as e:
-            error_message = f'Error attempting to parse file {str(os.path.split(config_filename)[1])}: {util.unicodify(e)}'
+            error_message = (
+                f"Error attempting to parse file {str(os.path.split(config_filename)[1])}: {util.unicodify(e)}"
+            )
             log.debug(error_message, exc_info=True)
             table_elems = []
         if persist:
@@ -189,7 +217,7 @@ class ToolDataTableManager(Dictifiable):
         remove_elems are removed before new_elems are added.
         """
         if not (new_elems or remove_elems):
-            log.debug('ToolDataTableManager.to_xml_file called without any elements to add or remove.')
+            log.debug("ToolDataTableManager.to_xml_file called without any elements to add or remove.")
             return  # no changes provided, no need to persist any changes
         if not new_elems:
             new_elems = []
@@ -202,7 +230,7 @@ class ToolDataTableManager(Dictifiable):
                 tree = util.parse_xml(full_path)
             except OSError as e:
                 if e.errno == errno.ENOENT:
-                    with open(full_path, 'w') as fh:
+                    with open(full_path, "w") as fh:
                         fh.write(TOOL_DATA_TABLE_CONF_XML)
                     tree = util.parse_xml(full_path)
                 else:
@@ -211,7 +239,7 @@ class ToolDataTableManager(Dictifiable):
             out_elems = [elem for elem in root]
         except Exception as e:
             out_elems = []
-            log.debug('Could not parse existing tool data table config, assume no existing elements: %s', e)
+            log.debug("Could not parse existing tool data table config, assume no existing elements: %s", e)
         for elem in remove_elems:
             # handle multiple occurrences of remove elem in existing elems
             while elem in out_elems:
@@ -223,7 +251,7 @@ class ToolDataTableManager(Dictifiable):
         root = util.parse_xml_string('<?xml version="1.0"?>\n<tables></tables>')
         for elem in out_elems:
             root.append(elem)
-        with RenamedTemporaryFile(full_path, mode='w') as out:
+        with RenamedTemporaryFile(full_path, mode="w") as out:
             out.write(util.xml_to_string(root, pretty=True))
         os.chmod(full_path, RW_R__R__)
         if out_path_is_new:
@@ -259,27 +287,44 @@ class ToolDataTable:
     type_key: str
 
     @classmethod
-    def from_elem(cls, table_elem, tool_data_path, from_shed_config, filename, tool_data_path_files, other_config_dict=None):
-        table_type = table_elem.get('type', 'tabular')
+    def from_elem(
+        cls, table_elem, tool_data_path, from_shed_config, filename, tool_data_path_files, other_config_dict=None
+    ):
+        table_type = table_elem.get("type", "tabular")
         assert table_type in tool_data_table_types, f"Unknown data table type '{table_type}'"
-        return tool_data_table_types[table_type](table_elem, tool_data_path, from_shed_config=from_shed_config, filename=filename, tool_data_path_files=tool_data_path_files, other_config_dict=other_config_dict)
+        return tool_data_table_types[table_type](
+            table_elem,
+            tool_data_path,
+            from_shed_config=from_shed_config,
+            filename=filename,
+            tool_data_path_files=tool_data_path_files,
+            other_config_dict=other_config_dict,
+        )
 
     @classmethod
     def from_dict(cls, d):
-        data_table_class = globals()[d['model_class']]
+        data_table_class = globals()[d["model_class"]]
         data_table = data_table_class.__new__(data_table_class)
         for attr, val in d.items():
-            if not attr == 'model_class':
+            if not attr == "model_class":
                 setattr(data_table, attr, val)
         data_table._loaded_content_version = 1
         return data_table
 
-    def __init__(self, config_element, tool_data_path, from_shed_config=False, filename=None, tool_data_path_files=None, other_config_dict=None):
-        self.name = config_element.get('name')
-        self.comment_char = config_element.get('comment_char')
-        self.empty_field_value = config_element.get('empty_field_value', '')
+    def __init__(
+        self,
+        config_element,
+        tool_data_path,
+        from_shed_config=False,
+        filename=None,
+        tool_data_path_files=None,
+        other_config_dict=None,
+    ):
+        self.name = config_element.get("name")
+        self.comment_char = config_element.get("comment_char")
+        self.empty_field_value = config_element.get("empty_field_value", "")
         self.empty_field_values = {}
-        self.allow_duplicate_entries = util.asbool(config_element.get('allow_duplicate_entries', True))
+        self.allow_duplicate_entries = util.asbool(config_element.get("allow_duplicate_entries", True))
         self.here = filename and os.path.dirname(filename)
         self.filenames = {}
         self.tool_data_path = tool_data_path
@@ -289,7 +334,15 @@ class ToolDataTable:
         # increment this variable any time a new entry is added, or when the table is totally reloaded
         # This value has no external meaning, and does not represent an abstract version of the underlying data
         self._loaded_content_version = 1
-        self._load_info = ([config_element, tool_data_path], {'from_shed_config': from_shed_config, 'tool_data_path_files': self.tool_data_path_files, 'other_config_dict': other_config_dict, 'filename': filename})
+        self._load_info = (
+            [config_element, tool_data_path],
+            {
+                "from_shed_config": from_shed_config,
+                "tool_data_path_files": self.tool_data_path_files,
+                "other_config_dict": other_config_dict,
+                "filename": filename,
+            },
+        )
         self._merged_load_info = []
 
     def _update_version(self, version=None):
@@ -312,7 +365,9 @@ class ToolDataTable:
     def add_entries(self, entries, allow_duplicates=True, persist=False, entry_source=None, **kwd):
         for entry in entries:
             try:
-                self.add_entry(entry, allow_duplicates=allow_duplicates, persist=persist, entry_source=entry_source, **kwd)
+                self.add_entry(
+                    entry, allow_duplicates=allow_duplicates, persist=persist, entry_source=entry_source, **kwd
+                )
             except Exception as e:
                 log.error(str(e))
         return self._loaded_content_version
@@ -354,14 +409,30 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
         </table>
 
     """
-    dict_collection_visible_keys = ['name']
-    dict_element_visible_keys = ['name', 'fields']
-    dict_export_visible_keys = ['name', 'data', 'largest_index', 'columns', 'missing_index_file']
 
-    type_key = 'tabular'
+    dict_collection_visible_keys = ["name"]
+    dict_element_visible_keys = ["name", "fields"]
+    dict_export_visible_keys = ["name", "data", "largest_index", "columns", "missing_index_file"]
 
-    def __init__(self, config_element, tool_data_path, from_shed_config=False, filename=None, tool_data_path_files=None, other_config_dict=None):
-        super().__init__(config_element, tool_data_path, from_shed_config, filename, tool_data_path_files, other_config_dict=other_config_dict)
+    type_key = "tabular"
+
+    def __init__(
+        self,
+        config_element,
+        tool_data_path,
+        from_shed_config=False,
+        filename=None,
+        tool_data_path_files=None,
+        other_config_dict=None,
+    ):
+        super().__init__(
+            config_element,
+            tool_data_path,
+            from_shed_config,
+            filename,
+            tool_data_path_files,
+            other_config_dict=other_config_dict,
+        )
         self.config_element = config_element
         self.data = []
         self.configure_and_load(config_element, tool_data_path, from_shed_config)
@@ -370,27 +441,31 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
         """
         Configure and load table from an XML element.
         """
-        self.separator = config_element.get('separator', '\t')
-        self.comment_char = config_element.get('comment_char', '#')
+        self.separator = config_element.get("separator", "\t")
+        self.comment_char = config_element.get("comment_char", "#")
         # Configure columns
         self.parse_column_spec(config_element)
 
         # store repo info if available:
-        repo_elem = config_element.find('tool_shed_repository')
+        repo_elem = config_element.find("tool_shed_repository")
         if repo_elem is not None:
-            repo_info = dict(tool_shed=repo_elem.find('tool_shed').text, name=repo_elem.find('repository_name').text,
-                             owner=repo_elem.find('repository_owner').text, installed_changeset_revision=repo_elem.find('installed_changeset_revision').text)
+            repo_info = dict(
+                tool_shed=repo_elem.find("tool_shed").text,
+                name=repo_elem.find("repository_name").text,
+                owner=repo_elem.find("repository_owner").text,
+                installed_changeset_revision=repo_elem.find("installed_changeset_revision").text,
+            )
         else:
             repo_info = None
         # Read every file
-        for file_element in config_element.findall('file'):
+        for file_element in config_element.findall("file"):
             tmp_file = None
-            filename = file_element.get('path', None)
+            filename = file_element.get("path", None)
             if filename is None:
                 # Handle URLs as files
-                filename = file_element.get('url', None)
+                filename = file_element.get("url", None)
                 if filename:
-                    tmp_file = NamedTemporaryFile(prefix=f'TTDT_URL_{self.name}-', mode='w')
+                    tmp_file = NamedTemporaryFile(prefix=f"TTDT_URL_{self.name}-", mode="w")
                     try:
                         tmp_file.write(requests.get(filename, timeout=url_timeout).text)
                     except Exception as e:
@@ -401,13 +476,17 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
                     tmp_file.flush()
                 else:
                     # Pull the filename from a global config
-                    filename = file_element.get('from_config', None) or None
+                    filename = file_element.get("from_config", None) or None
                     if filename:
                         filename = self.other_config_dict.get(filename, None)
             filename = file_path = expand_here_template(filename, here=self.here)
             found = False
             if file_path is None:
-                log.debug("Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string(file_element), self.name)
+                log.debug(
+                    "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.",
+                    util.xml_to_string(file_element),
+                    self.name,
+                )
                 continue
 
             # FIXME: splitting on and merging paths from a configuration file when loading is wonky
@@ -455,17 +534,28 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
                 # populate them.
                 log.warning(f"Cannot find index file '{filename}' for tool data table '{self.name}'")
 
-            if filename not in self.filenames or not self.filenames[filename]['found']:
-                self.filenames[filename] = dict(found=found, filename=filename, from_shed_config=from_shed_config, tool_data_path=tool_data_path,
-                                                config_element=config_element, tool_shed_repository=repo_info, errors=errors)
+            if filename not in self.filenames or not self.filenames[filename]["found"]:
+                self.filenames[filename] = dict(
+                    found=found,
+                    filename=filename,
+                    from_shed_config=from_shed_config,
+                    tool_data_path=tool_data_path,
+                    config_element=config_element,
+                    tool_shed_repository=repo_info,
+                    errors=errors,
+                )
             else:
-                log.debug("Filename '%s' already exists in filenames (%s), not adding", filename, list(self.filenames.keys()))
+                log.debug(
+                    "Filename '%s' already exists in filenames (%s), not adding", filename, list(self.filenames.keys())
+                )
             # Remove URL tmp file
             if tmp_file is not None:
                 tmp_file.close()
 
     def merge_tool_data_table(self, other_table, allow_duplicates=True, persist=False, entry_source=None, **kwd):
-        assert self.columns == other_table.columns, f"Merging tabular data tables with non matching columns is not allowed: {self.name}:{self.columns} != {other_table.name}:{other_table.columns}"
+        assert (
+            self.columns == other_table.columns
+        ), f"Merging tabular data tables with non matching columns is not allowed: {self.name}:{self.columns} != {other_table.name}:{other_table.columns}"
         # merge filename info
         for filename, info in other_table.filenames.items():
             if filename not in self.filenames:
@@ -474,11 +564,16 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
         self._merged_load_info.append((other_table.__class__, other_table._load_info))
         # If we are merging in a data table that does not allow duplicates, enforce that upon the data table
         if self.allow_duplicate_entries and not other_table.allow_duplicate_entries:
-            log.debug('While attempting to merge tool data table "%s", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries.', self.name)
+            log.debug(
+                'While attempting to merge tool data table "%s", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries.',
+                self.name,
+            )
             self.allow_duplicate_entries = False
             self._deduplicate_data()
         # add data entries and return current data table version
-        return self.add_entries(other_table.data, allow_duplicates=allow_duplicates, persist=persist, entry_source=entry_source, **kwd)
+        return self.add_entries(
+            other_table.data, allow_duplicates=allow_duplicates, persist=persist, entry_source=entry_source, **kwd
+        )
 
     def handle_found_index_file(self, filename):
         self.missing_index_file = None
@@ -490,7 +585,7 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
     def get_field(self, value):
         rval = None
         for i in self.get_named_fields_list():
-            if i['value'] == value:
+            if i["value"] == value:
                 rval = TabularToolDataField(i)
         return rval
 
@@ -522,29 +617,29 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
         A column named 'value' is required.
         """
         self.columns = {}
-        if config_element.find('columns') is not None:
-            column_names = util.xml_text(config_element.find('columns'))
-            column_names = [n.strip() for n in column_names.split(',')]
+        if config_element.find("columns") is not None:
+            column_names = util.xml_text(config_element.find("columns"))
+            column_names = [n.strip() for n in column_names.split(",")]
             for index, name in enumerate(column_names):
                 self.columns[name] = index
                 self.largest_index = index
         else:
             self.largest_index = 0
-            for column_elem in config_element.findall('column'):
-                name = column_elem.get('name', None)
+            for column_elem in config_element.findall("column"):
+                name = column_elem.get("name", None)
                 assert name is not None, "Required 'name' attribute missing from column def"
-                index = column_elem.get('index', None)
+                index = column_elem.get("index", None)
                 assert index is not None, "Required 'index' attribute missing from column def"
                 index = int(index)
                 self.columns[name] = index
                 if index > self.largest_index:
                     self.largest_index = index
-                empty_field_value = column_elem.get('empty_field_value', None)
+                empty_field_value = column_elem.get("empty_field_value", None)
                 if empty_field_value is not None:
                     self.empty_field_values[name] = empty_field_value
-        assert 'value' in self.columns, "Required 'value' column missing from column def"
-        if 'name' not in self.columns:
-            self.columns['name'] = self.columns['value']
+        assert "value" in self.columns, "Required 'value' column missing from column def"
+        if "name" not in self.columns:
+            self.columns["name"] = self.columns["value"]
 
     def extend_data_with(self, filename, errors=None):
         here = os.path.dirname(os.path.abspath(filename))
@@ -571,7 +666,10 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
                     if self.largest_index < len(fields):
                         rval.append(fields)
                     else:
-                        line_error = "Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s" % ((i + 1), self.name, separator_char, line)
+                        line_error = (
+                            "Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s"
+                            % ((i + 1), self.name, separator_char, line)
+                        )
                         if errors is not None:
                             errors.append(line_error)
                         log.warning(line_error)
@@ -586,7 +684,7 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
                 if index == i:
                     if not found_column:
                         rval.append(name)
-                    elif name == 'value':
+                    elif name == "value":
                         # the column named 'value' always has priority over other named columns
                         rval[-1] = name
                     found_column = True
@@ -640,8 +738,10 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
             source_repo_info = None
         filename = default
         for name, value in self.filenames.items():
-            repo_info = value.get('tool_shed_repository', None)
-            if (not source_repo_info and not repo_info) or (source_repo_info and repo_info and source_repo_info == repo_info):
+            repo_info = value.get("tool_shed_repository", None)
+            if (not source_repo_info and not repo_info) or (
+                source_repo_info and repo_info and source_repo_info == repo_info
+            ):
                 filename = name
                 break
         return filename
@@ -652,7 +752,12 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
             fields = []
             for column_name in self.get_column_name_list():
                 if column_name not in entry:
-                    log.debug("Using default column value for column '%s' when adding data table entry (%s) to table '%s'.", column_name, entry, self.name)
+                    log.debug(
+                        "Using default column value for column '%s' when adding data table entry (%s) to table '%s'.",
+                        column_name,
+                        entry,
+                        self.name,
+                    )
                     field_value = self.get_empty_field_by_name(column_name)
                 else:
                     field_value = entry[column_name]
@@ -664,35 +769,41 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
             if (allow_duplicates and self.allow_duplicate_entries) or fields not in self.get_fields():
                 self.data.append(fields)
             else:
-                raise MessageException(f"Attempted to add fields ({fields}) to data table '{self.name}', but this entry already exists and allow_duplicates is False.")
+                raise MessageException(
+                    f"Attempted to add fields ({fields}) to data table '{self.name}', but this entry already exists and allow_duplicates is False."
+                )
         else:
-            raise MessageException(f"Attempted to add fields ({fields}) to data table '{self.name}', but there were not enough fields specified ( {len(fields)} < {self.largest_index + 1} ).")
+            raise MessageException(
+                f"Attempted to add fields ({fields}) to data table '{self.name}', but there were not enough fields specified ( {len(fields)} < {self.largest_index + 1} )."
+            )
         filename = None
 
         if persist:
             filename = self.get_filename_for_source(entry_source)
             if filename is None:
                 # If we reach this point, there is no data table with a corresponding .loc file.
-                raise MessageException(f"Unable to determine filename for persisting data table '{self.name}' values: '{self.fields}'.")
+                raise MessageException(
+                    f"Unable to determine filename for persisting data table '{self.name}' values: '{self.fields}'."
+                )
             else:
                 log.debug("Persisting changes to file: %s", filename)
                 with FileLock(filename):
                     try:
                         if os.path.exists(filename):
-                            data_table_fh = open(filename, 'r+b')
+                            data_table_fh = open(filename, "r+b")
                             if os.stat(filename).st_size > 0:
                                 # ensure last existing line ends with new line
                                 data_table_fh.seek(-1, 2)  # last char in file
                                 last_char = data_table_fh.read(1)
-                                if last_char not in [b'\n', b'\r']:
-                                    data_table_fh.write(b'\n')
+                                if last_char not in [b"\n", b"\r"]:
+                                    data_table_fh.write(b"\n")
                         else:
-                            data_table_fh = open(filename, 'wb')
+                            data_table_fh = open(filename, "wb")
                     except OSError as e:
-                        log.exception('Error opening data table file (%s): %s', filename, e)
+                        log.exception("Error opening data table file (%s): %s", filename, e)
                         raise
                 fields = f"{self.separator.join(fields)}\n"
-                data_table_fh.write(fields.encode('utf-8'))
+                data_table_fh.write(fields.encode("utf-8"))
 
     def _remove_entry(self, values):
 
@@ -723,7 +834,7 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
                         if fields != values:
                             rval += line
 
-        with open(loc_file, 'w') as writer:
+        with open(loc_file, "w") as writer:
             writer.write(rval)
 
         return rval
@@ -755,7 +866,11 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
             fields_hash = hash(self.separator.join(fields))
             if fields_hash in hash_set:
                 dup_lines.append(i)
-                log.debug('Found duplicate entry in tool data table "%s", but duplicates are not allowed, removing additional entry for: "%s"', self.name, fields)
+                log.debug(
+                    'Found duplicate entry in tool data table "%s", but duplicates are not allowed, removing additional entry for: "%s"',
+                    self.name,
+                    fields,
+                )
             else:
                 hash_set.add(fields_hash)
         for i in reversed(dup_lines):
@@ -765,11 +880,11 @@ class TabularToolDataTable(ToolDataTable, Dictifiable):
     def xml_string(self):
         return util.xml_to_string(self.config_element)
 
-    def to_dict(self, view='collection'):
+    def to_dict(self, view="collection"):
         rval = super().to_dict(view=view)
-        if view == 'element':
-            rval['columns'] = sorted(self.columns.keys(), key=lambda x: self.columns[x])
-            rval['fields'] = self.get_fields()
+        if view == "element":
+            rval["columns"] = sorted(self.columns.keys(), key=lambda x: self.columns[x])
+            rval["fields"] = self.get_fields()
         return rval
 
 
@@ -784,7 +899,7 @@ class TabularToolDataField(Dictifiable):
         return self.data[key]
 
     def get_base_path(self):
-        return os.path.normpath(os.path.abspath(self.data['path']))
+        return os.path.normpath(os.path.abspath(self.data["path"]))
 
     def get_base_dir(self):
         path = self.get_base_path()
@@ -817,11 +932,11 @@ class TabularToolDataField(Dictifiable):
 
     def to_dict(self):
         rval = super().to_dict()
-        rval['name'] = self.data['value']
-        rval['fields'] = self.data
-        rval['base_dir'] = self.get_base_dir(),
-        rval['files'] = self.get_filesize_map(True)
-        rval['fingerprint'] = self.get_fingerprint()
+        rval["name"] = self.data["value"]
+        rval["fields"] = self.data
+        rval["base_dir"] = (self.get_base_dir(),)
+        rval["files"] = self.get_filesize_map(True)
+        rval["fingerprint"] = self.get_fingerprint()
         return rval
 
 
@@ -839,22 +954,40 @@ class RefgenieToolDataTable(TabularToolDataTable):
             <field name="path" template="true">${__REFGENIE_ASSET__}</field>
         </table>
     """
-    dict_collection_visible_keys = ['name']
-    dict_element_visible_keys = ['name', 'fields']
-    dict_export_visible_keys = ['name', 'data', 'rg_asset', 'largest_index', 'columns', 'missing_index_file']
 
-    type_key = 'refgenie'
+    dict_collection_visible_keys = ["name"]
+    dict_element_visible_keys = ["name", "fields"]
+    dict_export_visible_keys = ["name", "data", "rg_asset", "largest_index", "columns", "missing_index_file"]
 
-    def __init__(self, config_element, tool_data_path, from_shed_config=False, filename=None, tool_data_path_files=None, other_config_dict=None):
-        super().__init__(config_element, tool_data_path, from_shed_config, filename, tool_data_path_files, other_config_dict=other_config_dict)
+    type_key = "refgenie"
+
+    def __init__(
+        self,
+        config_element,
+        tool_data_path,
+        from_shed_config=False,
+        filename=None,
+        tool_data_path_files=None,
+        other_config_dict=None,
+    ):
+        super().__init__(
+            config_element,
+            tool_data_path,
+            from_shed_config,
+            filename,
+            tool_data_path_files,
+            other_config_dict=other_config_dict,
+        )
         self.config_element = config_element
         self.data = []
         self.configure_and_load(config_element, tool_data_path, from_shed_config)
 
     def configure_and_load(self, config_element, tool_data_path, from_shed_config=False, url_timeout=10):
-        self.rg_asset = config_element.get('asset', None)
-        assert self.rg_asset, ValueError('You must specify an asset attribute.')
-        super().configure_and_load(config_element, tool_data_path, from_shed_config=from_shed_config, url_timeout=url_timeout)
+        self.rg_asset = config_element.get("asset", None)
+        assert self.rg_asset, ValueError("You must specify an asset attribute.")
+        super().configure_and_load(
+            config_element, tool_data_path, from_shed_config=from_shed_config, url_timeout=url_timeout
+        )
 
     def parse_column_spec(self, config_element):
         self.columns = {}
@@ -862,24 +995,24 @@ class RefgenieToolDataTable(TabularToolDataTable):
         self.template_for_column = {}
         self.strip_for_column = {}
         self.largest_index = 0
-        for i, elem in enumerate(config_element.findall('field')):
-            name = elem.get('name', None)
-            assert name, ValueError('You must provide a name refgenie field element.')
+        for i, elem in enumerate(config_element.findall("field")):
+            name = elem.get("name", None)
+            assert name, ValueError("You must provide a name refgenie field element.")
             value = elem.text
             self.key_map[name] = value
-            column_index = int(elem.get('column_index', i))
+            column_index = int(elem.get("column_index", i))
 
-            empty_field_value = elem.get('empty_field_value', None)
+            empty_field_value = elem.get("empty_field_value", None)
             if empty_field_value is not None:
                 self.empty_field_values[name] = empty_field_value
 
-            self.template_for_column[name] = util.asbool(elem.get('template', False))
-            self.strip_for_column[name] = util.asbool(elem.get('strip', False))
+            self.template_for_column[name] = util.asbool(elem.get("template", False))
+            self.strip_for_column[name] = util.asbool(elem.get("strip", False))
 
             self.columns[name] = column_index
             self.largest_index = max(self.largest_index, column_index)
-        if 'name' not in self.columns:
-            self.columns['name'] = self.columns['value']
+        if "name" not in self.columns:
+            self.columns["name"] = self.columns["value"]
 
     def parse_file_fields(self, filename, errors=None, here="__HERE__"):
         try:
@@ -892,33 +1025,34 @@ class RefgenieToolDataTable(TabularToolDataTable):
         rval = []
         for genome in rgc.list_genomes_by_asset(self.rg_asset):
             genome_attributes = rgc.get_genome_attributes(genome)
-            description = genome_attributes.get('genome_description', None)
+            description = genome_attributes.get("genome_description", None)
             if description:
-                description = f'{description} (refgenie: {genome})'
+                description = f"{description} (refgenie: {genome})"
             asset_list = rgc.list(genome, include_tags=True)[genome]
             for tagged_asset in asset_list:
-                asset, tag = tagged_asset.rsplit(':', 1)
+                asset, tag = tagged_asset.rsplit(":", 1)
                 if asset != self.rg_asset:
                     continue
                 digest = rgc.id(genome, asset, tag=tag)
-                uuid = f'refgenie:{genome}/{self.rg_asset}:{tag}@{digest}'
-                display_name = description or f'{genome}/{tagged_asset}'
+                uuid = f"refgenie:{genome}/{self.rg_asset}:{tag}@{digest}"
+                display_name = description or f"{genome}/{tagged_asset}"
 
                 def _seek_key(key):
                     return rgc.seek(genome, asset, tag_name=tag, seek_key=key)
+
                 template_dict = {
-                    '__REFGENIE_UUID__': uuid,
-                    '__REFGENIE_GENOME__': genome,
-                    '__REFGENIE_TAG__': tag,
-                    '__REFGENIE_DISPLAY_NAME__': display_name,
-                    '__REFGENIE_ASSET__': rgc.seek(genome, asset, tag_name=tag),
-                    '__REFGENIE_ASSET_NAME__': asset,
-                    '__REFGENIE_DIGEST__': digest,
-                    '__REFGENIE_GENOME_ATTRIBUTES__': genome_attributes,
-                    '__REFGENIE__': rgc,
-                    '__REFGENIE_SEEK_KEY__': _seek_key,
+                    "__REFGENIE_UUID__": uuid,
+                    "__REFGENIE_GENOME__": genome,
+                    "__REFGENIE_TAG__": tag,
+                    "__REFGENIE_DISPLAY_NAME__": display_name,
+                    "__REFGENIE_ASSET__": rgc.seek(genome, asset, tag_name=tag),
+                    "__REFGENIE_ASSET_NAME__": asset,
+                    "__REFGENIE_DIGEST__": digest,
+                    "__REFGENIE_GENOME_ATTRIBUTES__": genome_attributes,
+                    "__REFGENIE__": rgc,
+                    "__REFGENIE_SEEK_KEY__": _seek_key,
                 }
-                fields = [''] * (self.largest_index + 1)
+                fields = [""] * (self.largest_index + 1)
                 for name, index in self.columns.items():
                     rg_value = self.key_map[name]
                     # Default is hard-coded value
@@ -928,12 +1062,17 @@ class RefgenieToolDataTable(TabularToolDataTable):
                         rg_value = rg_value.strip()
                     fields[index] = rg_value
                 rval.append(fields)
-        log.debug("Loaded %i entries from refgenie '%s' asset '%s' for '%s'", len(rval), filename, self.rg_asset, self.name)
+        log.debug(
+            "Loaded %i entries from refgenie '%s' asset '%s' for '%s'", len(rval), filename, self.rg_asset, self.name
+        )
         return rval
 
     def _remove_entry(self, values):
 
-        log.warning("Deletion from refgenie-backed '%s' data table is not supported, will only try to delete from .loc files", self.name)
+        log.warning(
+            "Deletion from refgenie-backed '%s' data table is not supported, will only try to delete from .loc files",
+            self.name,
+        )
 
         # Update every non-refgenie files
         super()._remove_entry(values)
diff --git a/lib/galaxy/tools/data/_schema.py b/lib/galaxy/tools/data/_schema.py
index f9eed32570d..35805e4fe94 100644
--- a/lib/galaxy/tools/data/_schema.py
+++ b/lib/galaxy/tools/data/_schema.py
@@ -35,17 +35,12 @@ class ToolDataDetails(ToolDataEntry):
         ...,  # Mark this field as required
         title="Columns",
         description="A list of column names",
-        example=[
-            "value",
-            "dbkey",
-            "name",
-            "path"
-        ],
+        example=["value", "dbkey", "name", "path"],
     )
     # We must use an alias since the name 'fields'
     # shadows a BaseModel attribute
     fields_value: List[List[str]] = Field(
-        alias='fields',
+        alias="fields",
         default=[],
         title="Fields",
         description="",  # TODO add documentation
@@ -68,7 +63,7 @@ class ToolDataField(BaseModel):
     # shadows a BaseModel attribute
     fields_value: Dict[str, str] = Field(
         ...,  # Mark this field as required
-        alias='fields',
+        alias="fields",
         title="Fields",
         description="",  # TODO add documentation
     )
@@ -95,7 +90,9 @@ class ToolDataItem(BaseModel):
     values: str = Field(
         ...,  # Mark this field as required
         title="Values",
-        description=("A `\\t` (TAB) separated list of column __contents__."
-        " You must specify a value for each of the columns of the data table."),
+        description=(
+            "A `\\t` (TAB) separated list of column __contents__."
+            " You must specify a value for each of the columns of the data table."
+        ),
         example="value\tdbkey\tname\tpath",
     )
diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index 8ac78877589..57996890055 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -6,7 +6,12 @@ import shutil
 import sys
 import tempfile
 from io import StringIO
-from typing import Any, Dict, List, Tuple
+from typing import (
+    Any,
+    Dict,
+    List,
+    Tuple,
+)
 
 import bdbag.bdbag_api
 
@@ -16,10 +21,16 @@ from galaxy.datatypes.upload_util import (
     handle_upload,
     UploadProblemException,
 )
-from galaxy.util import in_directory, safe_makedirs
+from galaxy.util import (
+    in_directory,
+    safe_makedirs,
+)
 from galaxy.util.bunch import Bunch
 from galaxy.util.compression_utils import CompressedFile
-from galaxy.util.hash_util import HASH_NAMES, memory_bound_hexdigest
+from galaxy.util.hash_util import (
+    HASH_NAMES,
+    memory_bound_hexdigest,
+)
 
 DESCRIPTION = """Data Import Script"""
 
@@ -139,11 +150,13 @@ def _fetch_target(upload_config, target):
             # get_composite_dataset_name finds dataset name from basename of contents
             # and such but we're not implementing that here yet. yagni?
             # also need name...
-            name = item.get("name") or 'Composite Dataset'
+            name = item.get("name") or "Composite Dataset"
             dataset_bunch = Bunch(
                 name=name,
             )
-            primary_file = sniff.stream_to_file(StringIO(datatype.generate_primary_file(dataset_bunch)), prefix='upload_auto_primary_file', dir=".")
+            primary_file = sniff.stream_to_file(
+                StringIO(datatype.generate_primary_file(dataset_bunch)), prefix="upload_auto_primary_file", dir="."
+            )
             extra_files_path = f"{primary_file}_extra"
             os.mkdir(extra_files_path)
             rval: Dict[str, Any] = {
@@ -238,7 +251,7 @@ def _fetch_target(upload_config, target):
                 path=path,
                 requested_ext=requested_ext,
                 name=name,
-                tmp_prefix='data_fetch_upload_',
+                tmp_prefix="data_fetch_upload_",
                 tmp_dir=".",
                 check_content=check_content,
                 link_data_only=link_data_only,
@@ -255,8 +268,10 @@ def _fetch_target(upload_config, target):
             if link_data_only:
                 # Never alter a file that will not be copied to Galaxy's local file store.
                 if datatype.dataset_content_needs_grooming(path):
-                    err_msg = 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be ' + \
-                        '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.'
+                    err_msg = (
+                        "The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be "
+                        + "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
+                    )
                     raise UploadProblemException(err_msg)
 
             # If this file is not in the workdir make sure it gets there.
@@ -294,6 +309,7 @@ def _fetch_target(upload_config, target):
                             if not os.path.exists(parent_dir):
                                 safe_makedirs(parent_dir)
                             shutil.move(src_path, file_output_path)
+
                 walk_extra_files(extra_files.get("elements", []))
 
             # TODO:
@@ -302,17 +318,24 @@ def _fetch_target(upload_config, target):
             needs_grooming = not link_data_only and datatype and datatype.dataset_content_needs_grooming(path)
             if needs_grooming:
                 # Groom the dataset content if necessary
-                transform.append({
-                    "action": "datatype_groom",
-                    "datatype_ext": ext,
-                    "datatype_class": datatype.__class__.__name__
-                })
+                transform.append(
+                    {"action": "datatype_groom", "datatype_ext": ext, "datatype_class": datatype.__class__.__name__}
+                )
                 datatype.groom_dataset_content(path)
 
             if len(transform) > 0:
                 source_dict["transform"] = transform
 
-        rval = {"name": name, "filename": path, "dbkey": dbkey, "ext": ext, "link_data_only": link_data_only, "sources": sources, "hashes": hashes, "info": f"uploaded {ext} file"}
+        rval = {
+            "name": name,
+            "filename": path,
+            "dbkey": dbkey,
+            "ext": ext,
+            "link_data_only": link_data_only,
+            "sources": sources,
+            "hashes": hashes,
+            "info": f"uploaded {ext} file",
+        }
         if staged_extra_files:
             rval["extra_files"] = os.path.abspath(staged_extra_files)
         return _copy_and_validate_simple_attributes(item, rval)
@@ -428,7 +451,9 @@ def _handle_hash_validation(upload_config, hash_function, hash_value, path):
     if upload_config.validate_hashes:
         calculated_hash_value = memory_bound_hexdigest(hash_func_name=hash_function, path=path)
         if calculated_hash_value != hash_value:
-            raise Exception(f"Failed to validate upload with [{hash_function}] - expected [{hash_value}] got [{calculated_hash_value}]")
+            raise Exception(
+                f"Failed to validate upload with [{hash_function}] - expected [{hash_value}] got [{calculated_hash_value}]"
+            )
 
 
 def _arg_parser():
@@ -448,6 +473,7 @@ def get_file_sources(working_directory):
     global _file_sources
     if _file_sources is None:
         from galaxy.files import ConfiguredFileSources
+
         file_sources = None
         file_sources_path = os.path.join(working_directory, "file_sources.json")
         if os.path.exists(file_sources_path):
@@ -463,7 +489,6 @@ def get_file_sources(working_directory):
 
 
 class UploadConfig:
-
     def __init__(self, request, registry, working_directory, allow_failed_collections):
         self.registry = registry
         self.working_directory = working_directory
diff --git a/lib/galaxy/tools/data_manager/manager.py b/lib/galaxy/tools/data_manager/manager.py
index e26425d10b5..92ed7aee725 100644
--- a/lib/galaxy/tools/data_manager/manager.py
+++ b/lib/galaxy/tools/data_manager/manager.py
@@ -11,14 +11,14 @@ from galaxy.util.template import fill_template
 
 log = logging.getLogger(__name__)
 
-SUPPORTED_DATA_TABLE_TYPES = (TabularToolDataTable)
+SUPPORTED_DATA_TABLE_TYPES = TabularToolDataTable
 VALUE_TRANSLATION_FUNCTIONS = dict(abspath=os.path.abspath)
-DEFAULT_VALUE_TRANSLATION_TYPE = 'template'
+DEFAULT_VALUE_TRANSLATION_TYPE = "template"
 
 
 class DataManagers:
-    data_managers: Dict[str, 'DataManager']
-    managed_data_tables: Dict[str, 'DataManager']
+    data_managers: Dict[str, "DataManager"]
+    managed_data_tables: Dict[str, "DataManager"]
 
     def __init__(self, app: MinimalManagerApp, xml_filename=None):
         self.app = app
@@ -35,31 +35,33 @@ class DataManagers:
             try:
                 self.load_from_xml(self.app.config.shed_data_manager_config_file, store_tool_path=True)
             except OSError as exc:
-                if exc.errno != errno.ENOENT or self.app.config.is_set('shed_data_manager_config_file'):
+                if exc.errno != errno.ENOENT or self.app.config.is_set("shed_data_manager_config_file"):
                     raise
 
     def load_from_xml(self, xml_filename, store_tool_path=True):
         try:
             tree = util.parse_xml(xml_filename)
         except OSError as e:
-            if e.errno != errno.ENOENT or self.app.config.is_set('data_manager_config_file'):
+            if e.errno != errno.ENOENT or self.app.config.is_set("data_manager_config_file"):
                 raise
             return  # default config option and it doesn't exist, which is fine
         except Exception as e:
             log.error(f'There was an error parsing your Data Manager config file "{xml_filename}": {e}')
             return  # we are not able to load any data managers
         root = tree.getroot()
-        if root.tag != 'data_managers':
-            log.error(f'A data managers configuration must have a "data_managers" tag as the root. "{root.tag}" is present')
+        if root.tag != "data_managers":
+            log.error(
+                f'A data managers configuration must have a "data_managers" tag as the root. "{root.tag}" is present'
+            )
             return
         if store_tool_path:
-            tool_path = root.get('tool_path', None)
+            tool_path = root.get("tool_path", None)
             if tool_path is None:
                 tool_path = self.app.config.tool_path
             if not tool_path:
-                tool_path = '.'
+                tool_path = "."
             self.tool_path = tool_path
-        for data_manager_elem in root.findall('data_manager'):
+        for data_manager_elem in root.findall("data_manager"):
             if not self.load_manager_from_elem(data_manager_elem, tool_path=self.tool_path):
                 # Wasn't able to load manager, could happen when galaxy is managed by planemo.
                 # Fall back to loading relative to the data_manager_conf.xml file
@@ -78,7 +80,7 @@ class DataManagers:
             return None
         if add_manager:
             self.add_manager(data_manager)
-        log.debug(f'Loaded Data Manager: {data_manager.id}')
+        log.debug(f"Loaded Data Manager: {data_manager.id}")
         return data_manager
 
     def add_manager(self, data_manager):
@@ -115,7 +117,7 @@ class DataManagers:
 
 
 class DataManager:
-    GUID_TYPE = 'data_manager'
+    GUID_TYPE = "data_manager"
     DEFAULT_VERSION = "0.0.1"
 
     def __init__(self, data_managers, elem=None, tool_path=None):
@@ -136,24 +138,30 @@ class DataManager:
             self.load_from_element(elem, tool_path or self.data_managers.tool_path)
 
     def load_from_element(self, elem, tool_path):
-        assert elem.tag == 'data_manager', f'A data manager configuration must have a "data_manager" tag as the root. "{elem.tag}" is present'
-        self.declared_id = elem.get('id')
-        self.guid = elem.get('guid')
-        path = elem.get('tool_file')
+        assert (
+            elem.tag == "data_manager"
+        ), f'A data manager configuration must have a "data_manager" tag as the root. "{elem.tag}" is present'
+        self.declared_id = elem.get("id")
+        self.guid = elem.get("guid")
+        path = elem.get("tool_file")
         tool_shed_repository = None
         tool_guid = None
 
         if path is None:
-            tool_elem = elem.find('tool')
-            assert tool_elem is not None, f"Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n{util.xml_to_string(elem)}"
+            tool_elem = elem.find("tool")
+            assert (
+                tool_elem is not None
+            ), f"Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n{util.xml_to_string(elem)}"
             path = tool_elem.get("file")
             tool_guid = tool_elem.get("guid")
             # need to determine repository info so that dependencies will work correctly
             tool_shed_repository = self.data_managers.app.toolbox.get_tool_repository_from_xml_item(tool_elem, path)
-            self.tool_shed_repository_info_dict = dict(tool_shed=tool_shed_repository.tool_shed,
-                                                       name=tool_shed_repository.name,
-                                                       owner=tool_shed_repository.owner,
-                                                       installed_changeset_revision=tool_shed_repository.installed_changeset_revision)
+            self.tool_shed_repository_info_dict = dict(
+                tool_shed=tool_shed_repository.tool_shed,
+                name=tool_shed_repository.name,
+                owner=tool_shed_repository.owner,
+                installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
+            )
             # use shed_conf_file to determine tool_path
             shed_conf_file = elem.get("shed_conf_file")
             if shed_conf_file:
@@ -161,90 +169,112 @@ class DataManager:
                 if shed_conf:
                     tool_path = shed_conf.get("tool_path", tool_path)
         assert path is not None, f"A tool file path could not be determined:\n{util.xml_to_string(elem)}"
-        self.load_tool(os.path.join(tool_path, path),
-                       guid=tool_guid,
-                       data_manager_id=self.id,
-                       tool_shed_repository=tool_shed_repository)
-        self.name = elem.get('name', self.tool.name)
-        self.description = elem.get('description', self.tool.description)
-        self.undeclared_tables = util.asbool(elem.get('undeclared_tables', self.undeclared_tables))
-        self.version = elem.get('version', self.tool.version)
+        self.load_tool(
+            os.path.join(tool_path, path),
+            guid=tool_guid,
+            data_manager_id=self.id,
+            tool_shed_repository=tool_shed_repository,
+        )
+        self.name = elem.get("name", self.tool.name)
+        self.description = elem.get("description", self.tool.description)
+        self.undeclared_tables = util.asbool(elem.get("undeclared_tables", self.undeclared_tables))
+        self.version = elem.get("version", self.tool.version)
 
-        for data_table_elem in elem.findall('data_table'):
+        for data_table_elem in elem.findall("data_table"):
             data_table_name = data_table_elem.get("name")
             assert data_table_name is not None, "A name is required for a data table entry"
             if data_table_name not in self.data_tables:
                 self.data_tables[data_table_name] = {}
-            output_elem = data_table_elem.find('output')
+            output_elem = data_table_elem.find("output")
             if output_elem is not None:
-                for column_elem in output_elem.findall('column'):
-                    column_name = column_elem.get('name', None)
+                for column_elem in output_elem.findall("column"):
+                    column_name = column_elem.get("name", None)
                     assert column_name is not None, "Name is required for column entry"
-                    data_table_coumn_name = column_elem.get('data_table_name', column_name)
+                    data_table_coumn_name = column_elem.get("data_table_name", column_name)
                     self.data_tables[data_table_name][data_table_coumn_name] = column_name
-                    output_ref = column_elem.get('output_ref', None)
+                    output_ref = column_elem.get("output_ref", None)
                     if output_ref is not None:
                         if data_table_name not in self.output_ref_by_data_table:
                             self.output_ref_by_data_table[data_table_name] = {}
                         self.output_ref_by_data_table[data_table_name][data_table_coumn_name] = output_ref
-                    value_translation_elems = column_elem.findall('value_translation')
+                    value_translation_elems = column_elem.findall("value_translation")
                     if value_translation_elems is not None:
                         for value_translation_elem in value_translation_elems:
                             value_translation = value_translation_elem.text
                             if value_translation is not None:
-                                value_translation_type = value_translation_elem.get('type', DEFAULT_VALUE_TRANSLATION_TYPE)
+                                value_translation_type = value_translation_elem.get(
+                                    "type", DEFAULT_VALUE_TRANSLATION_TYPE
+                                )
                                 if data_table_name not in self.value_translation_by_data_table_column:
                                     self.value_translation_by_data_table_column[data_table_name] = {}
-                                if data_table_coumn_name not in self.value_translation_by_data_table_column[data_table_name]:
-                                    self.value_translation_by_data_table_column[data_table_name][data_table_coumn_name] = []
-                                if value_translation_type == 'function':
+                                if (
+                                    data_table_coumn_name
+                                    not in self.value_translation_by_data_table_column[data_table_name]
+                                ):
+                                    self.value_translation_by_data_table_column[data_table_name][
+                                        data_table_coumn_name
+                                    ] = []
+                                if value_translation_type == "function":
                                     if value_translation in VALUE_TRANSLATION_FUNCTIONS:
                                         value_translation = VALUE_TRANSLATION_FUNCTIONS[value_translation]
                                     else:
-                                        raise ValueError(f"Unsupported value translation function: '{value_translation}'")
+                                        raise ValueError(
+                                            f"Unsupported value translation function: '{value_translation}'"
+                                        )
                                 else:
-                                    assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError(f"Unsupported value translation type: '{value_translation_type}'")
-                                self.value_translation_by_data_table_column[data_table_name][data_table_coumn_name].append(value_translation)
+                                    assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError(
+                                        f"Unsupported value translation type: '{value_translation_type}'"
+                                    )
+                                self.value_translation_by_data_table_column[data_table_name][
+                                    data_table_coumn_name
+                                ].append(value_translation)
 
-                    for move_elem in column_elem.findall('move'):
-                        move_type = move_elem.get('type', 'directory')
-                        relativize_symlinks = move_elem.get('relativize_symlinks', False)  # TODO: should we instead always relativize links?
-                        source_elem = move_elem.find('source')
+                    for move_elem in column_elem.findall("move"):
+                        move_type = move_elem.get("type", "directory")
+                        relativize_symlinks = move_elem.get(
+                            "relativize_symlinks", False
+                        )  # TODO: should we instead always relativize links?
+                        source_elem = move_elem.find("source")
                         if source_elem is None:
                             source_base = None
-                            source_value = ''
+                            source_value = ""
                         else:
-                            source_base = source_elem.get('base', None)
+                            source_base = source_elem.get("base", None)
                             source_value = source_elem.text
-                        target_elem = move_elem.find('target')
+                        target_elem = move_elem.find("target")
                         if target_elem is None:
                             target_base = None
-                            target_value = ''
+                            target_value = ""
                         else:
-                            target_base = target_elem.get('base', None)
+                            target_base = target_elem.get("base", None)
                             target_value = target_elem.text
                         if data_table_name not in self.move_by_data_table_column:
                             self.move_by_data_table_column[data_table_name] = {}
-                        self.move_by_data_table_column[data_table_name][data_table_coumn_name] = \
-                            dict(type=move_type,
-                                 source_base=source_base,
-                                 source_value=source_value,
-                                 target_base=target_base,
-                                 target_value=target_value,
-                                 relativize_symlinks=relativize_symlinks)
+                        self.move_by_data_table_column[data_table_name][data_table_coumn_name] = dict(
+                            type=move_type,
+                            source_base=source_base,
+                            source_value=source_value,
+                            target_base=target_base,
+                            target_value=target_value,
+                            relativize_symlinks=relativize_symlinks,
+                        )
 
     @property
     def id(self):
         return self.guid or self.declared_id  # if we have a guid, we will use that as the data_manager id
 
-    def load_tool(self, tool_filename, guid=None, data_manager_id=None, tool_shed_repository_id=None, tool_shed_repository=None):
+    def load_tool(
+        self, tool_filename, guid=None, data_manager_id=None, tool_shed_repository_id=None, tool_shed_repository=None
+    ):
         toolbox = self.data_managers.app.toolbox
-        tool = toolbox.load_hidden_tool(tool_filename,
-                                        guid=guid,
-                                        data_manager_id=data_manager_id,
-                                        repository_id=tool_shed_repository_id,
-                                        tool_shed_repository=tool_shed_repository,
-                                        use_cached=True)
+        tool = toolbox.load_hidden_tool(
+            tool_filename,
+            guid=guid,
+            data_manager_id=data_manager_id,
+            repository_id=tool_shed_repository_id,
+            tool_shed_repository=tool_shed_repository,
+            use_cached=True,
+        )
         self.data_managers.app.toolbox.data_manager_tools[tool.id] = tool
         self.tool = tool
         return tool
@@ -266,26 +296,32 @@ class DataManager:
                 data_manager_dict[key].update(value)
             data_manager_dict.update(output_dict)
 
-        data_tables_dict = data_manager_dict.get('data_tables', {})
+        data_tables_dict = data_manager_dict.get("data_tables", {})
         for data_table_name in self.data_tables.keys():
             data_table_values = data_tables_dict.pop(data_table_name, None)
             if not data_table_values:
-                log.warning(f'No values for data table "{data_table_name}" were returned by the data manager "{self.id}".')
+                log.warning(
+                    f'No values for data table "{data_table_name}" were returned by the data manager "{self.id}".'
+                )
                 continue  # next data table
             data_table_remove_values = None
             if isinstance(data_table_values, dict):
-                values_to_add = data_table_values.get('add')
-                data_table_remove_values = data_table_values.get('remove')
+                values_to_add = data_table_values.get("add")
+                data_table_remove_values = data_table_values.get("remove")
                 if values_to_add or data_table_remove_values:
                     # We don't have an old style data table definition
                     data_table_values = values_to_add
 
             data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None)
             if data_table is None:
-                log.error(f"The data manager \"{self.id}\" returned an unknown data table \"{data_table_name}\" with new entries \"{data_table_values}\". These entries will not be created. Please confirm that an entry for \"{data_table_name}\" exists in your \"tool_data_table_conf.xml\" file.")
+                log.error(
+                    f'The data manager "{self.id}" returned an unknown data table "{data_table_name}" with new entries "{data_table_values}". These entries will not be created. Please confirm that an entry for "{data_table_name}" exists in your "tool_data_table_conf.xml" file.'
+                )
                 continue  # next table name
             if not isinstance(data_table, SUPPORTED_DATA_TABLE_TYPES):
-                log.error(f'The data manager "{self.id}" returned an unsupported data table "{data_table_name}" with type "{type(data_table)}" with new entries "{data_table_values}". These entries will not be created. Please confirm that the data table is of a supported type ({SUPPORTED_DATA_TABLE_TYPES}).')
+                log.error(
+                    f'The data manager "{self.id}" returned an unsupported data table "{data_table_name}" with type "{type(data_table)}" with new entries "{data_table_values}". These entries will not be created. Please confirm that the data table is of a supported type ({SUPPORTED_DATA_TABLE_TYPES}).'
+                )
                 continue  # next table name
             output_ref_values = {}
             if data_table_name in self.output_ref_by_data_table:
@@ -300,10 +336,18 @@ class DataManager:
                 data_table_remove_values = [data_table_remove_values] if data_table_remove_values else []
             for data_table_row in data_table_values:
                 data_table_value = dict(**data_table_row)  # keep original values here
-                for name in data_table_row.keys():  # FIXME: need to loop through here based upon order listed in data_manager config
+                for (
+                    name
+                ) in (
+                    data_table_row.keys()
+                ):  # FIXME: need to loop through here based upon order listed in data_manager config
                     if name in output_ref_values:
-                        self.process_move(data_table_name, name, output_ref_values[name].extra_files_path, **data_table_value)
-                        data_table_value[name] = self.process_value_translation(data_table_name, name, **data_table_value)
+                        self.process_move(
+                            data_table_name, name, output_ref_values[name].extra_files_path, **data_table_value
+                        )
+                        data_table_value[name] = self.process_value_translation(
+                            data_table_name, name, **data_table_value
+                        )
                 data_table.add_entry(data_table_value, persist=True, entry_source=self)
             # Removes data table entries
             for data_table_row in data_table_remove_values:
@@ -311,18 +355,18 @@ class DataManager:
                 data_table.remove_entry(list(data_table_value.values()))
 
             self.data_managers.app.queue_worker.send_control_task(
-                'reload_tool_data_tables',
-                noop_self=True,
-                kwargs={'table_name': data_table_name}
+                "reload_tool_data_tables", noop_self=True, kwargs={"table_name": data_table_name}
             )
         if self.undeclared_tables and data_tables_dict:
             # We handle the data move, by just moving all the data out of the extra files path
             # moving a directory and the target already exists, we move the contents instead
-            log.debug('Attempting to add entries for undeclared tables: %s.', ', '.join(data_tables_dict.keys()))
+            log.debug("Attempting to add entries for undeclared tables: %s.", ", ".join(data_tables_dict.keys()))
             for ref_file in out_data.values():
                 if ref_file.extra_files_path_exists():
-                    util.move_merge(ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path)
-            path_column_names = ['path']
+                    util.move_merge(
+                        ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path
+                    )
+            path_column_names = ["path"]
             for data_table_name, data_table_values in data_tables_dict.items():
                 data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None)
                 if not isinstance(data_table_values, list):
@@ -331,38 +375,65 @@ class DataManager:
                     data_table_value = dict(**data_table_row)  # keep original values here
                     for name, value in data_table_row.items():
                         if name in path_column_names:
-                            data_table_value[name] = os.path.abspath(os.path.join(self.data_managers.app.config.galaxy_data_manager_data_path, value))
+                            data_table_value[name] = os.path.abspath(
+                                os.path.join(self.data_managers.app.config.galaxy_data_manager_data_path, value)
+                            )
                     data_table.add_entry(data_table_value, persist=True, entry_source=self)
                 self.data_managers.app.queue_worker.send_control_task(
-                    'reload_tool_data_tables',
-                    noop_self=True,
-                    kwargs={'table_name': data_table_name}
+                    "reload_tool_data_tables", noop_self=True, kwargs={"table_name": data_table_name}
                 )
         else:
             for data_table_name, data_table_values in data_tables_dict.items():
                 # tool returned extra data table entries, but data table was not declared in data manager
                 # do not add these values, but do provide messages
-                log.warning(f'The data manager "{self.id}" returned an undeclared data table "{data_table_name}" with new entries "{data_table_values}". These entries will not be created. Please confirm that an entry for "{data_table_name}" exists in your "{self.data_managers.filename}" file.')
+                log.warning(
+                    f'The data manager "{self.id}" returned an undeclared data table "{data_table_name}" with new entries "{data_table_values}". These entries will not be created. Please confirm that an entry for "{data_table_name}" exists in your "{self.data_managers.filename}" file.'
+                )
 
     def process_move(self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd):
-        if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[data_table_name]:
+        if (
+            data_table_name in self.move_by_data_table_column
+            and column_name in self.move_by_data_table_column[data_table_name]
+        ):
             move_dict = self.move_by_data_table_column[data_table_name][column_name]
-            source = move_dict['source_base']
+            source = move_dict["source_base"]
             if source is None:
                 source = source_base_path
             else:
-                source = fill_template(source, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
-            if move_dict['source_value']:
-                source = os.path.join(source, fill_template(move_dict['source_value'], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip())
-            target = move_dict['target_base']
+                source = fill_template(
+                    source,
+                    GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
+                    **kwd,
+                ).strip()
+            if move_dict["source_value"]:
+                source = os.path.join(
+                    source,
+                    fill_template(
+                        move_dict["source_value"],
+                        GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
+                        **kwd,
+                    ).strip(),
+                )
+            target = move_dict["target_base"]
             if target is None:
                 target = self.data_managers.app.config.galaxy_data_manager_data_path
             else:
-                target = fill_template(target, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
-            if move_dict['target_value']:
-                target = os.path.join(target, fill_template(move_dict['target_value'], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip())
+                target = fill_template(
+                    target,
+                    GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
+                    **kwd,
+                ).strip()
+            if move_dict["target_value"]:
+                target = os.path.join(
+                    target,
+                    fill_template(
+                        move_dict["target_value"],
+                        GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
+                        **kwd,
+                    ).strip(),
+                )
 
-            if move_dict['type'] == 'file':
+            if move_dict["type"] == "file":
                 dirs = os.path.split(target)[0]
                 try:
                     os.makedirs(dirs)
@@ -373,7 +444,7 @@ class DataManager:
             if os.path.exists(source):
                 util.move_merge(source, target)
 
-            if move_dict.get('relativize_symlinks', False):
+            if move_dict.get("relativize_symlinks", False):
                 util.relativize_symlinks(target)
 
             return True
@@ -381,10 +452,17 @@ class DataManager:
 
     def process_value_translation(self, data_table_name, column_name, **kwd):
         value = kwd.get(column_name)
-        if data_table_name in self.value_translation_by_data_table_column and column_name in self.value_translation_by_data_table_column[data_table_name]:
+        if (
+            data_table_name in self.value_translation_by_data_table_column
+            and column_name in self.value_translation_by_data_table_column[data_table_name]
+        ):
             for value_translation in self.value_translation_by_data_table_column[data_table_name][column_name]:
                 if isinstance(value_translation, str):
-                    value = fill_template(value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
+                    value = fill_template(
+                        value_translation,
+                        GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
+                        **kwd,
+                    ).strip()
                 else:
                     value = value_translation(value)
         return value
diff --git a/lib/galaxy/tools/error_reports/__init__.py b/lib/galaxy/tools/error_reports/__init__.py
index 490e762f3c9..83762ac5c96 100644
--- a/lib/galaxy/tools/error_reports/__init__.py
+++ b/lib/galaxy/tools/error_reports/__init__.py
@@ -10,12 +10,12 @@ log = logging.getLogger(__name__)
 
 DEFAULT_CONFIG = [
     {
-        'type': 'email',
-        'verbose': True,
-        'user_submission': True,
+        "type": "email",
+        "verbose": True,
+        "user_submission": True,
     },
 ]
-DEFAULT_PLUGINS_SOURCE = plugin_config.PluginConfigSource('dict', DEFAULT_CONFIG)
+DEFAULT_PLUGINS_SOURCE = plugin_config.PluginConfigSource("dict", DEFAULT_CONFIG)
 
 
 class ErrorReports:
@@ -29,11 +29,11 @@ class ErrorReports:
 
     def __plugins_dict(self):
         import galaxy.tools.error_reports.plugins
-        return plugin_config.plugins_dict(galaxy.tools.error_reports.plugins, 'plugin_type')
+
+        return plugin_config.plugins_dict(galaxy.tools.error_reports.plugins, "plugin_type")
 
 
 class NullErrorPlugin:
-
     def submit_report(self, dataset, job, tool, **kwargs):
         log.warning("Bug report for dataset %s, job %s submitted to NullErrorPlugin", dataset, job)
         return [("Error reporting is not configured for this Galaxy instance", "danger")]
@@ -43,10 +43,9 @@ NULL_ERROR_PLUGIN = NullErrorPlugin()
 
 
 class ErrorPlugin:
-
     def __init__(self, plugin_classes, plugins_source, **kwargs):
         self.extra_kwargs = kwargs
-        self.app = kwargs['app']
+        self.app = kwargs["app"]
         self.plugin_classes = plugin_classes
         self.plugins = self.__plugins_from_source(plugins_source)
 
diff --git a/lib/galaxy/tools/error_reports/plugins/__init__.py b/lib/galaxy/tools/error_reports/plugins/__init__.py
index 625537a68fd..04fed72a165 100644
--- a/lib/galaxy/tools/error_reports/plugins/__init__.py
+++ b/lib/galaxy/tools/error_reports/plugins/__init__.py
@@ -4,7 +4,7 @@ These are responsible for collecting and formatting a coherent set of metrics.
 """
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
 
@@ -14,9 +14,8 @@ class ErrorPlugin(metaclass=ABCMeta):
     @property
     @abstractmethod
     def plugin_type(self):
-        """Short string providing labelling this plugin """
+        """Short string providing labelling this plugin"""
 
     def submit_report(self, dataset, job, tool, user_submission=False, **kwargs):
-        """Submit the bug report and render a string to be displayed to the user.
-        """
+        """Submit the bug report and render a string to be displayed to the user."""
         return None
diff --git a/lib/galaxy/tools/error_reports/plugins/base_git.py b/lib/galaxy/tools/error_reports/plugins/base_git.py
index ca5630634cc..b0e6e1e793a 100644
--- a/lib/galaxy/tools/error_reports/plugins/base_git.py
+++ b/lib/galaxy/tools/error_reports/plugins/base_git.py
@@ -5,7 +5,7 @@
 import logging
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 from typing import Dict
 
@@ -22,8 +22,8 @@ log = logging.getLogger(__name__)
 
 
 class BaseGitPlugin(ErrorPlugin, metaclass=ABCMeta):
-    """Base definition to send error reports to a Git repository provider
-    """
+    """Base definition to send error reports to a Git repository provider"""
+
     issue_cache: Dict[str, Dict] = {}
     ts_urls: Dict[str, str] = {}
     ts_repo_cache: Dict[str, Dict] = {}
@@ -52,11 +52,15 @@ class BaseGitPlugin(ErrorPlugin, metaclass=ABCMeta):
             return None
         try:
             if job.tool_id not in self.ts_repo_cache:
-                ts_repo_request_data = requests.get(f"{ts_url}/api/repositories?tool_ids={str(job.tool_id)}", timeout=DEFAULT_SOCKET_TIMEOUT).json()
+                ts_repo_request_data = requests.get(
+                    f"{ts_url}/api/repositories?tool_ids={str(job.tool_id)}", timeout=DEFAULT_SOCKET_TIMEOUT
+                ).json()
 
                 for repoinfo in ts_repo_request_data.values():
                     if isinstance(repoinfo, dict):
-                        self.ts_repo_cache[job.tool_id] = repoinfo.get('repository', {}).get('remote_repository_url', None)
+                        self.ts_repo_cache[job.tool_id] = repoinfo.get("repository", {}).get(
+                            "remote_repository_url", None
+                        )
             return self.ts_repo_cache[job.tool_id]
         except Exception:
             return None
@@ -67,14 +71,17 @@ class BaseGitPlugin(ErrorPlugin, metaclass=ABCMeta):
     def _generate_error_message(self, dataset, job, kwargs):
         # We'll re-use the email error reporter's template since most Git providers supports HTML
         error_reporter = EmailErrorReporter(dataset.id, self.app)
-        error_reporter.create_report(job.get_user(), email=kwargs.get('email', None),
-                                     message=kwargs.get('message', None),
-                                     redact_user_details_in_bugreport=self.redact_user_details_in_bugreport)
+        error_reporter.create_report(
+            job.get_user(),
+            email=kwargs.get("email", None),
+            message=kwargs.get("message", None),
+            redact_user_details_in_bugreport=self.redact_user_details_in_bugreport,
+        )
         # Return the HTML report
         return error_reporter.html_report
 
     def _generate_error_title(self, job):
-        tool_kw = {'tool_id': unicodify(job.tool_id), 'tool_version': unicodify(job.tool_version)}
+        tool_kw = {"tool_id": unicodify(job.tool_id), "tool_version": unicodify(job.tool_version)}
         return """Galaxy Job Error: {tool_id} v{tool_version}""".format(**tool_kw)
 
     @abstractmethod
diff --git a/lib/galaxy/tools/error_reports/plugins/email.py b/lib/galaxy/tools/error_reports/plugins/email.py
index f1debbf93d7..42446c2ecb3 100644
--- a/lib/galaxy/tools/error_reports/plugins/email.py
+++ b/lib/galaxy/tools/error_reports/plugins/email.py
@@ -13,25 +13,29 @@ log = logging.getLogger(__name__)
 
 
 class EmailPlugin(ErrorPlugin):
-    """Send error report as an email
-    """
+    """Send error report as an email"""
+
     plugin_type = "email"
 
     def __init__(self, **kwargs):
-        self.app = kwargs['app']
+        self.app = kwargs["app"]
         self.redact_user_details_in_bugreport = self.app.config.redact_user_details_in_bugreport
-        self.verbose = string_as_bool(kwargs.get('verbose', True))
-        self.user_submission = string_as_bool(kwargs.get('user_submission', True))
+        self.verbose = string_as_bool(kwargs.get("verbose", True))
+        self.user_submission = string_as_bool(kwargs.get("user_submission", True))
 
     def submit_report(self, dataset, job, tool, **kwargs):
-        """Send report as an email
-        """
+        """Send report as an email"""
         try:
             error_reporter = EmailErrorReporter(dataset.id, self.app)
-            error_reporter.send_report(user=job.get_user(), email=kwargs.get('email', None), message=kwargs.get('message', None), redact_user_details_in_bugreport=self.redact_user_details_in_bugreport)
+            error_reporter.send_report(
+                user=job.get_user(),
+                email=kwargs.get("email", None),
+                message=kwargs.get("message", None),
+                redact_user_details_in_bugreport=self.redact_user_details_in_bugreport,
+            )
             return ("Your error report has been sent", "success")
         except Exception as e:
             return (f"An error occurred sending the report by email: {unicodify(e)}", "danger")
 
 
-__all__ = ('EmailPlugin', )
+__all__ = ("EmailPlugin",)
diff --git a/lib/galaxy/tools/error_reports/plugins/github.py b/lib/galaxy/tools/error_reports/plugins/github.py
index a7f93f17294..e3de97a91b8 100644
--- a/lib/galaxy/tools/error_reports/plugins/github.py
+++ b/lib/galaxy/tools/error_reports/plugins/github.py
@@ -3,40 +3,43 @@
 import logging
 from urllib.parse import urlparse
 
-from galaxy.util import string_as_bool, unicodify
+from galaxy.util import (
+    string_as_bool,
+    unicodify,
+)
 from .base_git import BaseGitPlugin
 
 log = logging.getLogger(__name__)
 
 
 class GithubPlugin(BaseGitPlugin):
-    """Send error report to Github.
-    """
+    """Send error report to Github."""
+
     plugin_type = "github"
 
     def __init__(self, **kwargs):
-        self.app = kwargs['app']
+        self.app = kwargs["app"]
         self.redact_user_details_in_bugreport = self.app.config.redact_user_details_in_bugreport
-        self.verbose = string_as_bool(kwargs.get('verbose', False))
-        self.user_submission = string_as_bool(kwargs.get('user_submission', False))
+        self.verbose = string_as_bool(kwargs.get("verbose", False))
+        self.user_submission = string_as_bool(kwargs.get("user_submission", False))
 
         # Github settings
-        self.github_base_url = kwargs.get('github_base_url', 'https://github.com')
-        self.github_api_url = kwargs.get('github_api_url', 'https://api.github.com')
-        self.git_default_repo_owner = kwargs.get('github_default_repo_owner', False)
-        self.git_default_repo_name = kwargs.get('github_default_repo_name', False)
-        self.git_default_repo_only = string_as_bool(kwargs.get('github_default_repo_only', True))
+        self.github_base_url = kwargs.get("github_base_url", "https://github.com")
+        self.github_api_url = kwargs.get("github_api_url", "https://api.github.com")
+        self.git_default_repo_owner = kwargs.get("github_default_repo_owner", False)
+        self.git_default_repo_name = kwargs.get("github_default_repo_name", False)
+        self.git_default_repo_only = string_as_bool(kwargs.get("github_default_repo_only", True))
 
         try:
             import github
 
             self.github = github.Github(
-                kwargs['github_oauth_token'],
+                kwargs["github_oauth_token"],
                 # Allow running against GH enterprise deployments.
-                base_url=self.github_api_url
+                base_url=self.github_api_url,
             )
             # Connect to the default repository and fill up the issue cache for it
-            repo = self.github.get_repo(f'{self.git_default_repo_owner}/{self.git_default_repo_name}')
+            repo = self.github.get_repo(f"{self.git_default_repo_owner}/{self.git_default_repo_name}")
             self._fill_issue_cache(repo, "default")
 
             # We'll also cache labels which we'll use for tagging issues.
@@ -47,8 +50,7 @@ class GithubPlugin(BaseGitPlugin):
             self.github = None
 
     def submit_report(self, dataset, job, tool, **kwargs):
-        """Submit the error report to sentry
-        """
+        """Submit the error report to sentry"""
         log.info(self.github)
 
         if self.github:
@@ -64,13 +66,16 @@ class GithubPlugin(BaseGitPlugin):
             ts_repourl = self._get_gitrepo_from_ts(job, ts_url)
 
             # Determine the GitLab project URL and the issue cache key
-            github_projecturl = urlparse(ts_repourl).path[1:] if (ts_repourl and not self.git_default_repo_only) \
+            github_projecturl = (
+                urlparse(ts_repourl).path[1:]
+                if (ts_repourl and not self.git_default_repo_only)
                 else "/".join((self.git_default_repo_owner, self.git_default_repo_name))
+            )
             issue_cache_key = self._get_issue_cache_key(job, ts_repourl)
 
             # Connect to the repo
             if github_projecturl not in self.git_project_cache:
-                self.git_project_cache[github_projecturl] = self.github.get_repo(f'{github_projecturl}')
+                self.git_project_cache[github_projecturl] = self.github.get_repo(f"{github_projecturl}")
             gh_project = self.git_project_cache[github_projecturl]
 
             # Make sure we keep a cache of the issues, per tool in this case
@@ -78,7 +83,9 @@ class GithubPlugin(BaseGitPlugin):
                 self._fill_issue_cache(gh_project, issue_cache_key)
 
             # Retrieve label
-            label = self.get_label(f'{unicodify(job.tool_id)}/{unicodify(job.tool_version)}', gh_project, issue_cache_key)
+            label = self.get_label(
+                f"{unicodify(job.tool_id)}/{unicodify(job.tool_version)}", gh_project, issue_cache_key
+            )
 
             # Generate information for the tool
             error_title = self._generate_error_title(job)
@@ -92,10 +99,17 @@ class GithubPlugin(BaseGitPlugin):
                 self._create_issue(issue_cache_key, error_title, error_message, gh_project, label=label)
             else:
                 self._append_issue(issue_cache_key, error_title, error_message)
-            return ('Submitted error report to Github. Your issue number is <a href="%s/%s/issues/%s" '
-                    'target="_blank">#%s</a>.' % (self.github_base_url, github_projecturl,
-                                                  self.issue_cache[issue_cache_key][error_title].number,
-                                                  self.issue_cache[issue_cache_key][error_title].number), 'success')
+            return (
+                'Submitted error report to Github. Your issue number is <a href="%s/%s/issues/%s" '
+                'target="_blank">#%s</a>.'
+                % (
+                    self.github_base_url,
+                    github_projecturl,
+                    self.issue_cache[issue_cache_key][error_title].number,
+                    self.issue_cache[issue_cache_key][error_title].number,
+                ),
+                "success",
+            )
 
     def _create_issue(self, issue_cache_key, error_title, error_mesage, project, **kwargs):
         # Create a new issue.
@@ -103,7 +117,7 @@ class GithubPlugin(BaseGitPlugin):
             title=error_title,
             body=error_mesage,
             # Label it with a tag: tool_id/tool_version
-            labels=[kwargs.get('label')]
+            labels=[kwargs.get("label")],
         )
 
     def _append_issue(self, issue_cache_key, error_title, error_message, **kwargs):
@@ -117,7 +131,7 @@ class GithubPlugin(BaseGitPlugin):
         # a cache of open issues and just add to it whenever we create a
         # new one.
         self.issue_cache[issue_cache_key] = {}
-        for issue in git_project.get_issues(state='open'):
+        for issue in git_project.get_issues(state="open"):
             log.info(issue)
             self.issue_cache[issue_cache_key][issue.title] = issue
         log.info(self.issue_cache)
@@ -135,9 +149,9 @@ class GithubPlugin(BaseGitPlugin):
             self._fill_label_cache(git_project, issue_cache_key)
 
         if label not in self.label_cache[issue_cache_key]:
-            self.label_cache[issue_cache_key][label] = git_project.create_label(name=label, color='ffffff')
+            self.label_cache[issue_cache_key][label] = git_project.create_label(name=label, color="ffffff")
 
         return self.label_cache[issue_cache_key][label]
 
 
-__all__ = ('GithubPlugin', )
+__all__ = ("GithubPlugin",)
diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index ae40c51c520..881d47320c2 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -17,30 +17,32 @@ log = logging.getLogger(__name__)
 
 
 class GitLabPlugin(BaseGitPlugin):
-    """Send error report to GitLab.
-    """
+    """Send error report to GitLab."""
+
     plugin_type = "gitlab"
 
     def __init__(self, **kwargs):
-        self.app = kwargs['app']
+        self.app = kwargs["app"]
         self.redact_user_details_in_bugreport = self.app.config.redact_user_details_in_bugreport
-        self.verbose = string_as_bool(kwargs.get('verbose', False))
-        self.user_submission = string_as_bool(kwargs.get('user_submission', False))
+        self.verbose = string_as_bool(kwargs.get("verbose", False))
+        self.user_submission = string_as_bool(kwargs.get("user_submission", False))
 
         # GitLab settings
-        self.gitlab_base_url = kwargs.get('gitlab_base_url', 'https://gitlab.com')
-        self.gitlab_private_token = kwargs.get('gitlab_private_token', "")
-        self.git_default_repo_owner = kwargs.get('gitlab_default_repo_owner', False)
-        self.git_default_repo_name = kwargs.get('gitlab_default_repo_name', False)
-        self.git_default_repo_only = string_as_bool(kwargs.get('gitlab_default_repo_only', True))
-        self.gitlab_use_proxy = string_as_bool(kwargs.get('gitlab_allow_proxy', True))
+        self.gitlab_base_url = kwargs.get("gitlab_base_url", "https://gitlab.com")
+        self.gitlab_private_token = kwargs.get("gitlab_private_token", "")
+        self.git_default_repo_owner = kwargs.get("gitlab_default_repo_owner", False)
+        self.git_default_repo_name = kwargs.get("gitlab_default_repo_name", False)
+        self.git_default_repo_only = string_as_bool(kwargs.get("gitlab_default_repo_only", True))
+        self.gitlab_use_proxy = string_as_bool(kwargs.get("gitlab_allow_proxy", True))
         self.gitlab_new_issue_on_closed = string_as_bool(kwargs.get("gitlab_new_issue_on_closed", False))
         self.gitlab_labels = kwargs.get("gitlab_labels", [])
 
         try:
             if gitlab is None:
-                raise Exception("GitLab error reporting plugin is configured, but gitlab is not installed. "
-                                "Please install python-gitlab v2.10.0 or higher.")
+                raise Exception(
+                    "GitLab error reporting plugin is configured, but gitlab is not installed. "
+                    "Please install python-gitlab v2.10.0 or higher."
+                )
             self.gitlab = self.gitlab_connect()
             self.gitlab.auth()
 
@@ -59,23 +61,23 @@ class GitLabPlugin(BaseGitPlugin):
 
     def gitlab_connect(self):
         import gitlab
+
         session = requests.Session()
         if self.gitlab_use_proxy:
             session.proxies = {
-                'https': os.environ.get('https_proxy'),
-                'http': os.environ.get('http_proxy'),
+                "https": os.environ.get("https_proxy"),
+                "http": os.environ.get("http_proxy"),
             }
 
         return gitlab.Gitlab(
             # Allow running against GL enterprise deployments
             self.gitlab_base_url,
             private_token=self.gitlab_private_token,
-            session=session
+            session=session,
         )
 
     def submit_report(self, dataset, job, tool, **kwargs):
-        """Submit the error report to GitLab
-        """
+        """Submit the error report to GitLab"""
         log.info(self.gitlab)
 
         # Try to connect beforehand, as we might lose connection
@@ -87,8 +89,11 @@ class GitLabPlugin(BaseGitPlugin):
         if self.gitlab:
             # Import GitLab here for the error handling
             import gitlab
+
             try:
-                log.info(f"GitLab error reporting - submit report - job tool id: {job.tool_id} - job tool version: {job.tool_version} - tool tool_shed: {tool.tool_shed}")
+                log.info(
+                    f"GitLab error reporting - submit report - job tool id: {job.tool_id} - job tool version: {job.tool_version} - tool tool_shed: {tool.tool_shed}"
+                )
 
                 # Determine the ToolShed url, initially we connect with HTTP and if redirect to HTTPS is set up,
                 # this will be detected by requests and used further down the line. Also cache this so everything is
@@ -106,8 +111,11 @@ class GitLabPlugin(BaseGitPlugin):
                 log.info(f"GitLab error reporting - Determine ToolShed Repository URL: {ts_repourl}")
 
                 # Determine the GitLab project URL and the issue cache key
-                gitlab_projecturl = urllib.parse.urlparse(ts_repourl).path[1:] if (ts_repourl and not self.git_default_repo_only)\
+                gitlab_projecturl = (
+                    urllib.parse.urlparse(ts_repourl).path[1:]
+                    if (ts_repourl and not self.git_default_repo_only)
                     else "/".join((self.git_default_repo_owner, self.git_default_repo_name))
+                )
                 issue_cache_key = self._get_issue_cache_key(job, ts_repourl)
 
                 # Make sure we are always logged in, then retrieve the GitLab project if it isn't cached.
@@ -117,7 +125,9 @@ class GitLabPlugin(BaseGitPlugin):
                         self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_projecturl)
                 except gitlab.GitlabGetError:
                     # Handle scenario where the repository doesn't exist so we can still continue
-                    log.warning(f"GitLab error reporting - Repository '{gitlab_projecturl}' doesn't exist, using default repository.")
+                    log.warning(
+                        f"GitLab error reporting - Repository '{gitlab_projecturl}' doesn't exist, using default repository."
+                    )
                     # Redo some of the previous steps to recover from such an issue but continue issue creation
                     gitlab_projecturl = "/".join((self.git_default_repo_owner, self.git_default_repo_name))
                     if gitlab_projecturl not in self.git_project_cache:
@@ -137,7 +147,7 @@ class GitLabPlugin(BaseGitPlugin):
                 # Determine the user to assign to the issue
                 gl_userid = None
                 if len(gl_project.commits.list()) > 0:
-                    gl_useremail = gl_project.commits.list()[0].attributes['author_email']
+                    gl_useremail = gl_project.commits.list()[0].attributes["author_email"]
                     if not self.redact_user_details_in_bugreport:
                         log.debug(f"GitLab error reporting - Last author email: {gl_useremail}")
                     if gl_useremail not in self.git_username_id_cache:
@@ -150,63 +160,79 @@ class GitLabPlugin(BaseGitPlugin):
 
                 log.info(error_title in self.issue_cache[issue_cache_key])
                 if error_title not in self.issue_cache[issue_cache_key]:
-                    self._open_issue(error_message, error_title, gitlab_projecturl, gl_project, gl_userid,
-                                     issue_cache_key)
+                    self._open_issue(
+                        error_message, error_title, gitlab_projecturl, gl_project, gl_userid, issue_cache_key
+                    )
                 else:
                     if not self.gitlab_new_issue_on_closed:
                         # Check if issue is closed, otherwise reopen it
                         issue_id = self.issue_cache[issue_cache_key][error_title]
                         issue = gl_project.issues.get(issue_id)
                         log.info(f"GitLab error reporting - Issue state is {issue.state}")
-                        if issue.state == 'closed':
+                        if issue.state == "closed":
                             # Reopen issue
-                            issue.state_event = 'reopen'
+                            issue.state_event = "reopen"
                             issue.save()
                             log.info(f"GitLab error reporting - Reopened issue {issue_id}")
 
                         # Add a comment to an issue...
-                        self._append_issue(issue_cache_key, error_title, error_message,
-                                           gitlab_projecturl=gitlab_projecturl)
+                        self._append_issue(
+                            issue_cache_key, error_title, error_message, gitlab_projecturl=gitlab_projecturl
+                        )
                     else:
-                        self._open_issue(error_message, error_title, gitlab_projecturl, gl_project, gl_userid,
-                                         issue_cache_key)
+                        self._open_issue(
+                            error_message, error_title, gitlab_projecturl, gl_project, gl_userid, issue_cache_key
+                        )
 
-                return ('Submitted error report to GitLab. Your issue number is <a href="%s/%s/issues/%s" '
-                        'target="_blank">#%s</a>.' % (self.gitlab_base_url, gitlab_projecturl,
-                                                      self.issue_cache[issue_cache_key][error_title],
-                                                      self.issue_cache[issue_cache_key][error_title]), 'success')
+                return (
+                    'Submitted error report to GitLab. Your issue number is <a href="%s/%s/issues/%s" '
+                    'target="_blank">#%s</a>.'
+                    % (
+                        self.gitlab_base_url,
+                        gitlab_projecturl,
+                        self.issue_cache[issue_cache_key][error_title],
+                        self.issue_cache[issue_cache_key][error_title],
+                    ),
+                    "success",
+                )
 
             except gitlab.GitlabCreateError:
                 log.error("GitLab error reporting - Could not create the issue on GitLab.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                return ("Internal Error.", "danger")
             except gitlab.GitlabOwnershipError:
-                log.error("GitLab error reporting - Could not create the issue on GitLab due to ownership issues.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                log.error(
+                    "GitLab error reporting - Could not create the issue on GitLab due to ownership issues.",
+                    exc_info=True,
+                )
+                return ("Internal Error.", "danger")
             except gitlab.GitlabSearchError:
                 log.error("GitLab error reporting - Could not find repository on GitLab.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                return ("Internal Error.", "danger")
             except gitlab.GitlabAuthenticationError:
                 log.error("GitLab error reporting - Could not authenticate with GitLab.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                return ("Internal Error.", "danger")
             except gitlab.GitlabParsingError:
                 log.error("GitLab error reporting - Could not parse GitLab message.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                return ("Internal Error.", "danger")
             except (gitlab.GitlabConnectionError, gitlab.GitlabHttpError):
                 log.error("GitLab error reporting - Could not connect to GitLab.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                return ("Internal Error.", "danger")
             except gitlab.GitlabError:
                 log.error("GitLab error reporting - General error communicating with GitLab.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                return ("Internal Error.", "danger")
             except Exception:
-                log.error("GitLab error reporting - Error reporting to GitLab had an exception that could not be "
-                          "determined.", exc_info=True)
-                return ('Internal Error.', 'danger')
+                log.error(
+                    "GitLab error reporting - Error reporting to GitLab had an exception that could not be "
+                    "determined.",
+                    exc_info=True,
+                )
+                return ("Internal Error.", "danger")
         else:
             log.error("GitLab error reporting - No connection to GitLab. Cannot report error to GitLab.")
-            return ('Internal Error.', 'danger')
+            return ("Internal Error.", "danger")
 
     def _open_issue(self, error_message, error_title, gitlab_projecturl, gl_project, gl_userid, issue_cache_key):
-        """ Open an issue """
+        """Open an issue"""
         try:
             # Create a new issue.
             self._create_issue(issue_cache_key, error_title, error_message, gl_project, gl_userid=gl_userid)
@@ -225,15 +251,12 @@ class GitLabPlugin(BaseGitPlugin):
 
     def _create_issue(self, issue_cache_key, error_title, error_message, project, **kwargs):
         # Set payload for the issue
-        issue_data = {
-            'title': error_title,
-            'description': error_message
-        }
+        issue_data = {"title": error_title, "description": error_message}
 
         # Assign the user to the issue
         gl_userid = kwargs.get("gl_userid", None)
         if gl_userid is not None:
-            issue_data['assignee_ids'] = [gl_userid]
+            issue_data["assignee_ids"] = [gl_userid]
 
         # Create the issue on GitLab
         issue = project.issues.create(issue_data)
@@ -247,25 +270,27 @@ class GitLabPlugin(BaseGitPlugin):
 
     def _append_issue(self, issue_cache_key, error_title, error_message, **kwargs):
         # Add a comment to an existing issue
-        gl_url = "/".join((
-            self.gitlab_base_url,
-            "api",
-            "v4",
-            "projects",
-            kwargs.get('gitlab_projecturl'),
-            "issues",
-            str(self.issue_cache[issue_cache_key][error_title]),
-            "notes"
-        ))
-        self.gitlab.http_post(gl_url, post_data={'body': error_message})
+        gl_url = "/".join(
+            (
+                self.gitlab_base_url,
+                "api",
+                "v4",
+                "projects",
+                kwargs.get("gitlab_projecturl"),
+                "issues",
+                str(self.issue_cache[issue_cache_key][error_title]),
+                "notes",
+            )
+        )
+        self.gitlab.http_post(gl_url, post_data={"body": error_message})
 
     def _fill_issue_cache(self, git_project, issue_cache_key):
         self.issue_cache[issue_cache_key] = {}
         # Loop over all open issues and add the issue iid to the cache
         for issue in git_project.issues.list():
-            if issue.state != 'closed':
+            if issue.state != "closed":
                 log.info("GitLab error reporting - Repo issue: %s", str(issue.iid))
                 self.issue_cache[issue_cache_key][issue.title] = issue.iid
 
 
-__all__ = ('GitLabPlugin', )
+__all__ = ("GitLabPlugin",)
diff --git a/lib/galaxy/tools/error_reports/plugins/influxdb.py b/lib/galaxy/tools/error_reports/plugins/influxdb.py
index 6842ff8fda6..925d2aafda2 100644
--- a/lib/galaxy/tools/error_reports/plugins/influxdb.py
+++ b/lib/galaxy/tools/error_reports/plugins/influxdb.py
@@ -16,47 +16,45 @@ log = logging.getLogger(__name__)
 
 
 class InfluxDBPlugin(ErrorPlugin):
-    """Send error report to InfluxDB
-    """
+    """Send error report to InfluxDB"""
+
     plugin_type = "influxdb"
 
     def __init__(self, **kwargs):
         if not influxdb:
-            raise ImportError("Could not find InfluxDB Client, this error reporter will be disabled; please pip install influxdb")
+            raise ImportError(
+                "Could not find InfluxDB Client, this error reporter will be disabled; please pip install influxdb"
+            )
 
-        self.app = kwargs['app']
+        self.app = kwargs["app"]
         # Neither of these matter
         self.verbose = False
         self.user_submission = False
         # Anything with influxdb_ gets sent to the client initialization
-        influx_args = {
-            k[len('influxdb_'):]: v
-            for (k, v)
-            in kwargs.items()
-            if k.startswith('influxdb_')
-        }
+        influx_args = {k[len("influxdb_") :]: v for (k, v) in kwargs.items() if k.startswith("influxdb_")}
         print(influx_args)
         self.client = influxdb.InfluxDBClient(**influx_args)
 
     def submit_report(self, dataset, job, tool, **kwargs):
-        """Submit the error report to sentry
-        """
-        self.client.write_points([{
-            'measurement': 'galaxy_tool_error',
-            'time': datetime.datetime.utcnow().strftime('%Y-%m-%dT%H:%M:%SZ'),
-            'fields': {
-                'value': 1
-            },
-            'tags': {
-                'exit_code': job.exit_code,
-                'tool_id': unicodify(job.tool_id),
-                'tool_version': unicodify(job.tool_version),
-                'tool_xml': unicodify(tool.config_file) if tool else None,
-                'destination_id': unicodify(job.destination_id),
-                'handler': unicodify(job.handler),
-            }
-        }])
-        return ('Submitted to InfluxDB', 'success')
+        """Submit the error report to sentry"""
+        self.client.write_points(
+            [
+                {
+                    "measurement": "galaxy_tool_error",
+                    "time": datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ"),
+                    "fields": {"value": 1},
+                    "tags": {
+                        "exit_code": job.exit_code,
+                        "tool_id": unicodify(job.tool_id),
+                        "tool_version": unicodify(job.tool_version),
+                        "tool_xml": unicodify(tool.config_file) if tool else None,
+                        "destination_id": unicodify(job.destination_id),
+                        "handler": unicodify(job.handler),
+                    },
+                }
+            ]
+        )
+        return ("Submitted to InfluxDB", "success")
 
 
-__all__ = ('InfluxDBPlugin', )
+__all__ = ("InfluxDBPlugin",)
diff --git a/lib/galaxy/tools/error_reports/plugins/json.py b/lib/galaxy/tools/error_reports/plugins/json.py
index 5cf959c721c..e4709c30db1 100644
--- a/lib/galaxy/tools/error_reports/plugins/json.py
+++ b/lib/galaxy/tools/error_reports/plugins/json.py
@@ -12,51 +12,48 @@ log = logging.getLogger(__name__)
 
 
 class JsonPlugin(ErrorPlugin):
-    """Write error report to a JSON file.
-    """
+    """Write error report to a JSON file."""
+
     plugin_type = "json"
 
     def __init__(self, **kwargs):
-        self.app = kwargs['app']
-        self.verbose = string_as_bool(kwargs.get('verbose', False))
+        self.app = kwargs["app"]
+        self.verbose = string_as_bool(kwargs.get("verbose", False))
         self.redact_user_details_in_bugreport = self.app.config.redact_user_details_in_bugreport
-        self.user_submission = string_as_bool(kwargs.get('user_submission', False))
+        self.user_submission = string_as_bool(kwargs.get("user_submission", False))
         self.report_directory = kwargs.get("directory", tempfile.gettempdir())
         if not os.path.exists(self.report_directory):
             os.makedirs(self.report_directory)
 
     def submit_report(self, dataset, job, tool, **kwargs):
-        """Write the report to a json file.
-        """
+        """Write the report to a json file."""
         path = os.path.join(self.report_directory, str(dataset.id))
-        with open(path, 'w') as handle:
+        with open(path, "w") as handle:
             data = {
-                'info': job.info,
-                'id': job.id,
-                'command_line': job.command_line,
-                'destination_id': job.destination_id,
-                'stderr': job.stderr,
-                'traceback': job.traceback,
-                'exit_code': job.exit_code,
-                'stdout': job.stdout,
-                'handler': job.handler,
-                'tool_version': job.tool_version,
-                'tool_xml': str(tool.config_file) if tool else None
+                "info": job.info,
+                "id": job.id,
+                "command_line": job.command_line,
+                "destination_id": job.destination_id,
+                "stderr": job.stderr,
+                "traceback": job.traceback,
+                "exit_code": job.exit_code,
+                "stdout": job.stdout,
+                "handler": job.handler,
+                "tool_version": job.tool_version,
+                "tool_xml": str(tool.config_file) if tool else None,
             }
             if self.redact_user_details_in_bugreport:
-                data['user'] = {
-                    'id': job.get_user().id
-                }
+                data["user"] = {"id": job.get_user().id}
             else:
-                data['user'] = job.get_user().to_dict()
-                if 'email' in kwargs:
-                    data['email'] = kwargs['email']
+                data["user"] = job.get_user().to_dict()
+                if "email" in kwargs:
+                    data["email"] = kwargs["email"]
 
-            if 'message' in kwargs:
-                data['message'] = kwargs['message']
+            if "message" in kwargs:
+                data["message"] = kwargs["message"]
 
             json.dump(data, handle, indent=2)
-        return (f'Wrote error report to {path}', 'success')
+        return (f"Wrote error report to {path}", "success")
 
 
-__all__ = ('JsonPlugin', )
+__all__ = ("JsonPlugin",)
diff --git a/lib/galaxy/tools/error_reports/plugins/sentry.py b/lib/galaxy/tools/error_reports/plugins/sentry.py
index f99ea963fc0..96622b9361f 100644
--- a/lib/galaxy/tools/error_reports/plugins/sentry.py
+++ b/lib/galaxy/tools/error_reports/plugins/sentry.py
@@ -12,7 +12,7 @@ from . import ErrorPlugin
 
 log = logging.getLogger(__name__)
 
-SENTRY_SDK_IMPORT_MESSAGE = 'The Python sentry-sdk package is required to use this feature, please install it'
+SENTRY_SDK_IMPORT_MESSAGE = "The Python sentry-sdk package is required to use this feature, please install it"
 ERROR_TEMPLATE = """Galaxy Job Error: {tool_id} v{tool_version}
 
 Command Line:
@@ -29,42 +29,41 @@ The user provided the following information:
 
 
 class SentryPlugin(ErrorPlugin):
-    """Send error report to Sentry.
-    """
+    """Send error report to Sentry."""
+
     plugin_type = "sentry"
 
     def __init__(self, **kwargs):
-        self.app = kwargs['app']
+        self.app = kwargs["app"]
         self.redact_user_details_in_bugreport = self.app.config.redact_user_details_in_bugreport
-        self.verbose = string_as_bool(kwargs.get('verbose', False))
-        self.user_submission = string_as_bool(kwargs.get('user_submission', False))
+        self.verbose = string_as_bool(kwargs.get("verbose", False))
+        self.user_submission = string_as_bool(kwargs.get("user_submission", False))
         assert sentry_sdk, SENTRY_SDK_IMPORT_MESSAGE
 
     def submit_report(self, dataset, job, tool, **kwargs):
-        """Submit the error report to sentry
-        """
+        """Submit the error report to sentry"""
         extra = {
-            'info': job.info,
-            'id': job.id,
-            'command_line': job.command_line,
-            'destination_id': job.destination_id,
-            'stderr': job.stderr,
-            'traceback': job.traceback,
-            'exit_code': job.exit_code,
-            'stdout': job.stdout,
-            'handler': job.handler,
-            'tool_id': job.tool_id,
-            'tool_version': job.tool_version,
-            'tool_xml': tool.config_file if tool else None
+            "info": job.info,
+            "id": job.id,
+            "command_line": job.command_line,
+            "destination_id": job.destination_id,
+            "stderr": job.stderr,
+            "traceback": job.traceback,
+            "exit_code": job.exit_code,
+            "stdout": job.stdout,
+            "handler": job.handler,
+            "tool_id": job.tool_id,
+            "tool_version": job.tool_version,
+            "tool_xml": tool.config_file if tool else None,
         }
         if self.redact_user_details_in_bugreport:
-            extra['email'] = 'redacted'
+            extra["email"] = "redacted"
         else:
-            if 'email' in kwargs:
-                extra['email'] = kwargs['email']
+            if "email" in kwargs:
+                extra["email"] = kwargs["email"]
 
         # User submitted message
-        extra['message'] = kwargs.get('message', '')
+        extra["message"] = kwargs.get("message", "")
 
         # Construct the error message to send to sentry. The first line
         # will be the issue title, everything after that becomes the
@@ -77,10 +76,12 @@ class SentryPlugin(ErrorPlugin):
         # Getting the url allows us to link to the dataset info page in case
         # anything is missing from this report.
         try:
-            url = web.url_for(controller="dataset",
-                              action="show_params",
-                              dataset_id=self.app.security.encode_id(dataset.id),
-                              qualified=True)
+            url = web.url_for(
+                controller="dataset",
+                action="show_params",
+                dataset_id=self.app.security.encode_id(dataset.id),
+                qualified=True,
+            )
         except AttributeError:
             # The above does not work when handlers are separate from the web handlers
             url = None
@@ -89,29 +90,27 @@ class SentryPlugin(ErrorPlugin):
         if self.redact_user_details_in_bugreport:
             if user:
                 # Opaque identifier
-                context['user'] = {
-                    'id': user.id
-                }
+                context["user"] = {"id": user.id}
         else:
             if user:
                 # User information here also places email links + allows seeing
                 # a list of affected users in the tags/filtering.
-                context['user'] = {
-                    'name': user.username,
-                    'email': user.email,
+                context["user"] = {
+                    "name": user.username,
+                    "email": user.email,
                 }
 
-        context['request'] = {'url': url}
+        context["request"] = {"url": url}
 
         for key, value in context.items():
             sentry_sdk.set_context(key, value)
-        sentry_sdk.set_context('job', extra)
-        sentry_sdk.set_tag('tool_id', job.tool_id)
-        sentry_sdk.set_tag('tool_version', job.tool_version)
+        sentry_sdk.set_context("job", extra)
+        sentry_sdk.set_tag("tool_id", job.tool_id)
+        sentry_sdk.set_tag("tool_version", job.tool_version)
 
         # Send the message, using message because
         response = sentry_sdk.capture_message(error_message)
-        return (f'Submitted bug report to Sentry. Your guru meditation number is {response}', 'success')
+        return (f"Submitted bug report to Sentry. Your guru meditation number is {response}", "success")
 
 
-__all__ = ('SentryPlugin', )
+__all__ = ("SentryPlugin",)
diff --git a/lib/galaxy/tools/errors.py b/lib/galaxy/tools/errors.py
index b4eaf8047bf..c406a952c26 100644
--- a/lib/galaxy/tools/errors.py
+++ b/lib/galaxy/tools/errors.py
@@ -8,7 +8,7 @@ import markupsafe
 from galaxy import (
     model,
     util,
-    web
+    web,
 )
 from galaxy.security.validate_user_input import validate_email_str
 from galaxy.util import unicodify
@@ -156,14 +156,16 @@ class ErrorReporter:
             roles = []
         return self.app.security_agent.can_access_dataset(roles, self.hda.dataset)
 
-    def create_report(self, user, email='', message='', redact_user_details_in_bugreport=False, **kwd):
+    def create_report(self, user, email="", message="", redact_user_details_in_bugreport=False, **kwd):
         hda = self.hda
         job = self.job
-        host = web.url_for('/', qualified=True)
+        host = web.url_for("/", qualified=True)
         history_id_encoded = self.app.security.encode_id(hda.history_id)
         history_view_link = web.url_for("/histories/view", id=history_id_encoded, qualified=True)
         hda_id_encoded = self.app.security.encode_id(hda.id)
-        hda_show_params_link = web.url_for(controller="dataset", action="details", dataset_id=hda_id_encoded, qualified=True)
+        hda_show_params_link = web.url_for(
+            controller="dataset", action="details", dataset_id=hda_id_encoded, qualified=True
+        )
         # Build the email message
         if redact_user_details_in_bugreport:
             # This is sub-optimal but it is hard to solve fully. This affects
@@ -179,16 +181,16 @@ class ErrorReporter:
             # the bug reporter (and preventing information about the bug
             # reporter from leaving the EU until it hits email directly to the
             # user.)
-            email_str = 'redacted'
+            email_str = "redacted"
             if user:
-                email_str += f' (user: {user.id})'
+                email_str += f" (user: {user.id})"
         else:
             if user:
                 email_str = f"'{user.email}'"
                 if email and user.email != email:
                     email_str += f" (providing preferred contact email '{email}')"
             else:
-                email_str = "'%s'" % (email or 'anonymous')
+                email_str = "'%s'" % (email or "anonymous")
 
         report_variables = dict(
             host=host,
@@ -213,7 +215,7 @@ class ErrorReporter:
             job_info=util.unicodify(job.info),
             job_traceback=util.unicodify(job.traceback),
             email_str=email_str,
-            message=util.unicodify(message)
+            message=util.unicodify(message),
         )
 
         self.report = string.Template(error_report_template).safe_substitute(report_variables)
@@ -248,7 +250,8 @@ class EmailErrorReporter(ErrorReporter):
         subject = f"Galaxy tool error report from {email}"
         try:
             subject = "{} ({})".format(
-                subject, self.app.toolbox.get_tool(self.job.tool_id, self.job.tool_version).old_id)
+                subject, self.app.toolbox.get_tool(self.job.tool_id, self.job.tool_version).old_id
+            )
         except Exception:
             pass
 
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 6f4eed1fa99..eb0daba297b 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -5,7 +5,13 @@ import shlex
 import string
 import tempfile
 from datetime import datetime
-from typing import Any, Callable, Dict, List, Optional
+from typing import (
+    Any,
+    Callable,
+    Dict,
+    List,
+    Optional,
+)
 
 from galaxy import model
 from galaxy.job_execution.compute_environment import ComputeEnvironment
@@ -24,7 +30,7 @@ from galaxy.tools.parameters.basic import (
 from galaxy.tools.parameters.grouping import (
     Conditional,
     Repeat,
-    Section
+    Section,
 )
 from galaxy.tools.wrappers import (
     DatasetCollectionWrapper,
@@ -55,12 +61,9 @@ class ToolErrorLog:
         self.max_errors = 100
 
     def add_error(self, file, phase, exception):
-        self.error_stack.insert(0, {
-            "file": file,
-            "time": str(datetime.now()),
-            "phase": phase,
-            "error": unicodify(exception)
-        })
+        self.error_stack.insert(
+            0, {"file": file, "time": str(datetime.now()), "phase": phase, "error": unicodify(exception)}
+        )
         if len(self.error_stack) > self.max_errors:
             self.error_stack.pop()
 
@@ -78,7 +81,7 @@ def global_tool_logs(func, config_file, action_str):
 
 
 class ToolEvaluator:
-    """ An abstraction linking together a tool and a job runtime to evaluate
+    """An abstraction linking together a tool and a job runtime to evaluate
     tool inputs in an isolated, testable manner.
     """
 
@@ -111,6 +114,7 @@ class ToolEvaluator:
         def validate_inputs(input, value, context, **kwargs):
             value = input.from_json(value, request_context, context)
             input.validate(value, request_context)
+
         visit_input_values(self.tool.inputs, incoming, validate_inputs)
 
         # Restore input / output data lists
@@ -138,8 +142,9 @@ class ToolEvaluator:
         # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ).
         self.tool.exec_before_job(self.app, inp_data, out_data, self.param_dict)
         # Run the before queue ("exec_before_job") hook
-        self.tool.call_hook('exec_before_job', self.app, inp_data=inp_data,
-                            out_data=out_data, tool=self.tool, param_dict=incoming)
+        self.tool.call_hook(
+            "exec_before_job", self.app, inp_data=inp_data, out_data=out_data, tool=self.tool, param_dict=incoming
+        )
 
     def build_param_dict(self, incoming, input_datasets, output_datasets, output_collections):
         """
@@ -158,12 +163,14 @@ class ToolEvaluator:
             raise SyntaxError("Unbound variable input.")  # Don't let $input hang Python evaluation process.
 
         param_dict["input"] = input
-        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.join(job_working_directory, 'registry.xml')
-        if self.job.tool_id == 'upload1':
-            param_dict['paramfile'] = os.path.join(job_working_directory, 'upload_params.json')
+        param_dict["__datatypes_config__"] = param_dict["GALAXY_DATATYPES_CONF_FILE"] = os.path.join(
+            job_working_directory, "registry.xml"
+        )
+        if self.job.tool_id == "upload1":
+            param_dict["paramfile"] = os.path.join(job_working_directory, "upload_params.json")
         if self._history:
-            param_dict['__history_id__'] = self.app.security.encode_id(self._history.id)
-        param_dict['__galaxy_url__'] = self.compute_environment.galaxy_url()
+            param_dict["__history_id__"] = self.app.security.encode_id(self._history.id)
+        param_dict["__galaxy_url__"] = self.compute_environment.galaxy_url()
         param_dict.update(self.tool.template_macro_params)
         # All parameters go into the param_dict
         param_dict.update(incoming)
@@ -182,7 +189,6 @@ class ToolEvaluator:
         return param_dict
 
     def __walk_inputs(self, inputs, input_values, func):
-
         def do_walk(inputs, input_values):
             """
             Wraps parameters as neccesary.
@@ -205,19 +211,19 @@ class ToolEvaluator:
         do_walk(inputs, input_values)
 
     def __populate_wrappers(self, param_dict, input_datasets, job_working_directory):
-
         def wrap_input(input_values, input):
             value = input_values[input.name]
             if isinstance(input, DataToolParameter) and input.multiple:
                 dataset_instances = DatasetListWrapper.to_dataset_instances(value)
-                input_values[input.name] = \
-                    DatasetListWrapper(job_working_directory,
-                                       dataset_instances,
-                                       compute_environment=self.compute_environment,
-                                       datatypes_registry=self.app.datatypes_registry,
-                                       tool=self.tool,
-                                       name=input.name,
-                                       formats=input.formats)
+                input_values[input.name] = DatasetListWrapper(
+                    job_working_directory,
+                    dataset_instances,
+                    compute_environment=self.compute_environment,
+                    datatypes_registry=self.app.datatypes_registry,
+                    tool=self.tool,
+                    name=input.name,
+                    formats=input.formats,
+                )
 
             elif isinstance(input, DataToolParameter):
                 dataset = input_values[input.name]
@@ -225,35 +231,30 @@ class ToolEvaluator:
                     datatypes_registry=self.app.datatypes_registry,
                     tool=self,
                     name=input.name,
-                    compute_environment=self.compute_environment
+                    compute_environment=self.compute_environment,
                 )
                 element_identifier = element_identifier_mapper.identifier(dataset, param_dict)
                 if element_identifier:
                     wrapper_kwds["identifier"] = element_identifier
-                input_values[input.name] = \
-                    DatasetFilenameWrapper(dataset, **wrapper_kwds)
+                input_values[input.name] = DatasetFilenameWrapper(dataset, **wrapper_kwds)
             elif isinstance(input, DataCollectionToolParameter):
                 dataset_collection = value
                 wrapper_kwds = dict(
                     datatypes_registry=self.app.datatypes_registry,
                     compute_environment=self.compute_environment,
                     tool=self,
-                    name=input.name
-                )
-                wrapper = DatasetCollectionWrapper(
-                    job_working_directory,
-                    dataset_collection,
-                    **wrapper_kwds
+                    name=input.name,
                 )
+                wrapper = DatasetCollectionWrapper(job_working_directory, dataset_collection, **wrapper_kwds)
                 input_values[input.name] = wrapper
             elif isinstance(input, SelectToolParameter):
                 if input.multiple:
                     value = listify(value)
                 input_values[input.name] = SelectToolParameterWrapper(
-                    input, value, other_values=param_dict, compute_environment=self.compute_environment)
+                    input, value, other_values=param_dict, compute_environment=self.compute_environment
+                )
             else:
-                input_values[input.name] = InputValueWrapper(
-                    input, value, param_dict)
+                input_values[input.name] = InputValueWrapper(input, value, param_dict)
 
         # HACK: only wrap if check_values is not false, this deals with external
         #       tools where the inputs don't even get passed through. These
@@ -308,15 +309,11 @@ class ToolEvaluator:
             wrapper_kwds = dict(
                 datatypes_registry=self.app.datatypes_registry,
                 compute_environment=self.compute_environment,
-                io_type='output',
+                io_type="output",
                 tool=tool,
-                name=name
-            )
-            wrapper = DatasetCollectionWrapper(
-                job_working_directory,
-                out_collection,
-                **wrapper_kwds
+                name=name,
             )
+            wrapper = DatasetCollectionWrapper(job_working_directory, out_collection, **wrapper_kwds)
             param_dict[name] = wrapper
             # TODO: Handle nested collections...
             output_def = tool.output_collections[name]
@@ -330,9 +327,11 @@ class ToolEvaluator:
         for name, hda in output_datasets.items():
             # Write outputs to the working directory (for security purposes)
             # if desired.
-            param_dict[name] = DatasetFilenameWrapper(hda, compute_environment=self.compute_environment, io_type="output")
-            if '|__part__|' in name:
-                unqualified_name = name.split('|__part__|')[-1]
+            param_dict[name] = DatasetFilenameWrapper(
+                hda, compute_environment=self.compute_environment, io_type="output"
+            )
+            if "|__part__|" in name:
+                unqualified_name = name.split("|__part__|")[-1]
                 if unqualified_name not in param_dict:
                     param_dict[unqualified_name] = param_dict[name]
             output_path = str(param_dict[name])
@@ -340,7 +339,7 @@ class ToolEvaluator:
             # - may already exist (e.g. symlink output)
             # - parent directory might not exist (e.g. Pulsar)
             if not os.path.exists(output_path) and os.path.exists(os.path.dirname(output_path)):
-                open(output_path, 'w').close()
+                open(output_path, "w").close()
 
             # Provide access to a path to store additional files
             # TODO: move compute path logic into compute environment, move setting files_path
@@ -367,30 +366,33 @@ class ToolEvaluator:
             if table_name in self.app.tool_data_tables:
                 return self.app.tool_data_tables[table_name].get_entry(query_attr, query_val, return_attr)
 
-        param_dict['__tool_directory__'] = self.compute_environment.tool_directory()
-        param_dict['__get_data_table_entry__'] = get_data_table_entry
-        param_dict['__local_working_directory__'] = self.local_working_directory
+        param_dict["__tool_directory__"] = self.compute_environment.tool_directory()
+        param_dict["__get_data_table_entry__"] = get_data_table_entry
+        param_dict["__local_working_directory__"] = self.local_working_directory
         # We add access to app here, this allows access to app.config, etc
-        param_dict['__app__'] = RawObjectWrapper(self.app)
+        param_dict["__app__"] = RawObjectWrapper(self.app)
         # More convienent access to app.config.new_file_path; we don't need to
         # wrap a string, but this method of generating additional datasets
         # should be considered DEPRECATED
-        param_dict['__new_file_path__'] = self.compute_environment.new_file_path()
+        param_dict["__new_file_path__"] = self.compute_environment.new_file_path()
         # The following points to location (xxx.loc) files which are pointers
         # to locally cached data
-        param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path
+        param_dict["__tool_data_path__"] = param_dict["GALAXY_DATA_INDEX_DIR"] = self.app.config.tool_data_path
         # For the upload tool, we need to know the root directory and the
         # datatypes conf path, so we can load the datatypes registry
-        param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath(self.app.config.root)
-        param_dict['__admin_users__'] = self.app.config.admin_users
-        param_dict['__user__'] = RawObjectWrapper(param_dict.get('__user__', None))
+        param_dict["__root_dir__"] = param_dict["GALAXY_ROOT_DIR"] = os.path.abspath(self.app.config.root)
+        param_dict["__admin_users__"] = self.app.config.admin_users
+        param_dict["__user__"] = RawObjectWrapper(param_dict.get("__user__", None))
 
     def __populate_unstructured_path_rewrites(self, param_dict):
-
         def rewrite_unstructured_paths(input_values, input):
             if isinstance(input, SelectToolParameter):
                 input_values[input.name] = SelectToolParameterWrapper(
-                    input, input_values[input.name], other_values=param_dict, compute_environment=self.compute_environment)
+                    input,
+                    input_values[input.name],
+                    other_values=param_dict,
+                    compute_environment=self.compute_environment,
+                )
 
         if not self.tool.check_values and self.compute_environment:
             # The tools weren't "wrapped" yet, but need to be in order to get
@@ -402,16 +404,18 @@ class ToolEvaluator:
         Populate InteractiveTools templated values.
         """
         it = []
-        for ep in getattr(self.tool, 'ports', []):
+        for ep in getattr(self.tool, "ports", []):
             ep_dict = {}
-            for key in 'port', 'name', 'url', 'requires_domain':
+            for key in "port", "name", "url", "requires_domain":
                 val = ep.get(key, None)
                 if val is not None and not isinstance(val, bool):
-                    val = fill_template(val, context=self.param_dict, python_template_version=self.tool.python_template_version)
+                    val = fill_template(
+                        val, context=self.param_dict, python_template_version=self.tool.python_template_version
+                    )
                     clean_val = []
-                    for line in val.split('\n'):
+                    for line in val.split("\n"):
                         clean_val.append(line.strip())
-                    val = '\n'.join(clean_val)
+                    val = "\n".join(clean_val)
                     val = val.replace("\n", " ").replace("\r", " ").strip()
                 ep_dict[key] = val
             it.append(ep_dict)
@@ -426,14 +430,16 @@ class ToolEvaluator:
         Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place.
         """
         # chromInfo is a filename, do not sanitize it.
-        skip = ['chromInfo'] + list(self.tool.template_macro_params.keys())
+        skip = ["chromInfo"] + list(self.tool.template_macro_params.keys())
         if not self.tool or not self.tool.options or self.tool.options.sanitize:
             for key, value in list(param_dict.items()):
                 if key not in skip:
                     # Remove key so that new wrapped object will occupy key slot
                     del param_dict[key]
                     # And replace with new wrapped key
-                    param_dict[wrap_with_safe_string(key, no_wrap_classes=ToolParameterValueWrapper)] = wrap_with_safe_string(value, no_wrap_classes=ToolParameterValueWrapper)
+                    param_dict[
+                        wrap_with_safe_string(key, no_wrap_classes=ToolParameterValueWrapper)
+                    ] = wrap_with_safe_string(value, no_wrap_classes=ToolParameterValueWrapper)
 
     def build(self):
         """
@@ -443,7 +449,7 @@ class ToolEvaluator:
         """
         config_file = self.tool.config_file
         global_tool_logs(self._build_config_files, config_file, "Building Config Files")
-        global_tool_logs(self._build_param_file, config_file, 'Building Param File')
+        global_tool_logs(self._build_param_file, config_file, "Building Param File")
         global_tool_logs(self._build_command_line, config_file, "Building Command Line")
         global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
         return self.command_line, self.extra_filenames, self.environment_variables
@@ -452,7 +458,7 @@ class ToolEvaluator:
         """
         Build command line to invoke this tool given a populated param_dict
         """
-        command = self.tool.command or ''
+        command = self.tool.command or ""
         param_dict = self.param_dict
         interpreter = self.tool.interpreter
         version_string_cmd_raw = self.tool.version_string_cmd
@@ -461,12 +467,14 @@ class ToolEvaluator:
             return
         try:
             # Substituting parameters into the command
-            command_line = fill_template(command, context=param_dict, python_template_version=self.tool.python_template_version)
+            command_line = fill_template(
+                command, context=param_dict, python_template_version=self.tool.python_template_version
+            )
             cleaned_command_line = []
             # Remove leading and trailing whitespace from each line for readability.
-            for line in command_line.split('\n'):
+            for line in command_line.split("\n"):
                 cleaned_command_line.append(line.strip())
-            command_line = '\n'.join(cleaned_command_line)
+            command_line = "\n".join(cleaned_command_line)
             # Remove newlines from command line, and any leading/trailing white space
             command_line = command_line.replace("\n", " ").replace("\r", " ").strip()
         except Exception:
@@ -481,7 +489,9 @@ class ToolEvaluator:
             command_line = command_line.replace(executable, f"{interpreter} {shlex.quote(abs_executable)}", 1)
         if version_string_cmd_raw:
             version_command_template = string.Template(version_string_cmd_raw)
-            version_string_cmd = version_command_template.safe_substitute({"__tool_directory__": self.compute_environment.tool_directory()})
+            version_string_cmd = version_command_template.safe_substitute(
+                {"__tool_directory__": self.compute_environment.tool_directory()}
+            )
             command_line = f"{version_string_cmd} > {self.compute_environment.version_path()} 2>&1;\n{command_line}"
         self.command_line = command_line
 
@@ -518,6 +528,7 @@ class ToolEvaluator:
             if inject == "api_key":
                 if self._user:
                     from galaxy.managers import api_keys
+
                     environment_variable_template = api_keys.ApiKeyManager(self.app).get_or_create_api_key(self._user)
                 else:
                     environment_variable_template = ""
@@ -526,10 +537,18 @@ class ToolEvaluator:
                 is_template = True
             with tempfile.NamedTemporaryFile(dir=directory, prefix="tool_env_", delete=False) as temp:
                 config_filename = temp.name
-            self.__write_workdir_file(config_filename, environment_variable_template, param_dict, is_template=is_template, strip=environment_variable_def.get("strip", False))
+            self.__write_workdir_file(
+                config_filename,
+                environment_variable_template,
+                param_dict,
+                is_template=is_template,
+                strip=environment_variable_def.get("strip", False),
+            )
             config_file_basename = os.path.basename(config_filename)
             # environment setup in job file template happens before `cd $working_directory`
-            environment_variable["value"] = f'`cat "{self.compute_environment.env_config_directory()}/{config_file_basename}"`'
+            environment_variable[
+                "value"
+            ] = f'`cat "{self.compute_environment.env_config_directory()}/{config_file_basename}"`'
             environment_variable["raw"] = True
             environment_variable["job_directory_path"] = config_filename
             environment_variables.append(environment_variable)
@@ -552,14 +571,14 @@ class ToolEvaluator:
         directory = self.local_working_directory
         command = self.tool.command
         if self.tool.profile < 16.04 and command and "$param_file" in command:
-            with tempfile.NamedTemporaryFile(mode='w', dir=directory, delete=False) as param:
+            with tempfile.NamedTemporaryFile(mode="w", dir=directory, delete=False) as param:
                 for key, value in param_dict.items():
                     # parameters can be strings or lists of strings, coerce to list
                     if not isinstance(value, list):
                         value = [value]
                     for elem in value:
-                        param.write(f'{key}={elem}\n')
-            self.__register_extra_file('param_file', param.name)
+                        param.write(f"{key}={elem}\n")
+            self.__register_extra_file("param_file", param.name)
             return param.name
         else:
             return None
@@ -583,10 +602,12 @@ class ToolEvaluator:
         else:
             raise Exception(f"Unknown config file type {config_type}")
 
-        return json.dumps(wrapped_json.json_wrap(self.tool.inputs,
-                                                 self.param_dict,
-                                                 self.tool.profile,
-                                                 handle_files=handle_files)), False
+        return (
+            json.dumps(
+                wrapped_json.json_wrap(self.tool.inputs, self.param_dict, self.tool.profile, handle_files=handle_files)
+            ),
+            False,
+        )
 
     def __write_workdir_file(self, config_filename, content, context, is_template=True, strip=False):
         parent_dir = os.path.dirname(config_filename)
@@ -598,7 +619,7 @@ class ToolEvaluator:
             value = unicodify(content)
         if strip:
             value = value.strip()
-        with open(config_filename, "w", encoding='utf-8') as f:
+        with open(config_filename, "w", encoding="utf-8") as f:
             f.write(value)
         # For running jobs as the actual user, ensure the config file is globally readable
         os.chmod(config_filename, RW_R__R__)
@@ -654,6 +675,6 @@ class RemoteToolEvaluator(ToolEvaluator):
     def build(self):
         config_file = self.tool.config_file
         global_tool_logs(self._build_config_files, config_file, "Building Config Files")
-        global_tool_logs(self._build_param_file, config_file, 'Building Param File')
+        global_tool_logs(self._build_param_file, config_file, "Building Param File")
         global_tool_logs(self._build_command_line, config_file, "Building Command Line")
         return self.command_line, self.extra_filenames, self.environment_variables
diff --git a/lib/galaxy/tools/exception_handling.py b/lib/galaxy/tools/exception_handling.py
index 0c161622e8c..d05f3dd3fdd 100644
--- a/lib/galaxy/tools/exception_handling.py
+++ b/lib/galaxy/tools/exception_handling.py
@@ -1,6 +1,9 @@
 # We put a tool that references this package into the tool shed
 # so we have to provide this legacy location for import indefinitely
 # it seems.
-from galaxy.util.ucsc import UCSCLimitException, UCSCOutWrapper
+from galaxy.util.ucsc import (
+    UCSCLimitException,
+    UCSCOutWrapper,
+)
 
-__all__ = ('UCSCOutWrapper', 'UCSCLimitException')
+__all__ = ("UCSCOutWrapper", "UCSCLimitException")
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index 69eb89ae804..ae2305f6dce 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -6,14 +6,24 @@ collections from matched collections.
 import collections
 import logging
 from abc import abstractmethod
-from typing import Dict, List
+from typing import (
+    Dict,
+    List,
+)
 
 from boltons.iterutils import remap
 
 from galaxy import model
-from galaxy.model.dataset_collections.structure import get_structure, tool_output_to_structure
+from galaxy.model.dataset_collections.structure import (
+    get_structure,
+    tool_output_to_structure,
+)
 from galaxy.tool_util.parser import ToolOutputCollectionPart
-from galaxy.tools.actions import filter_output, on_text_for_names, ToolExecutionCache
+from galaxy.tools.actions import (
+    filter_output,
+    on_text_for_names,
+    ToolExecutionCache,
+)
 from galaxy.tools.parameters.basic import is_runtime_value
 
 log = logging.getLogger(__name__)
@@ -23,7 +33,6 @@ BATCH_EXECUTION_MESSAGE = "Executed ${job_count} job(s) for tool ${tool_id} requ
 
 
 class PartialJobExecution(Exception):
-
     def __init__(self, execution_tracker):
         self.execution_tracker = execution_tracker
 
@@ -31,7 +40,21 @@ class PartialJobExecution(Exception):
 MappingParameters = collections.namedtuple("MappingParameters", ["param_template", "param_combinations"])
 
 
-def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, collection_info=None, workflow_invocation_uuid=None, invocation_step=None, max_num_jobs=None, job_callback=None, completed_jobs=None, workflow_resource_parameters=None, validate_outputs=False):
+def execute(
+    trans,
+    tool,
+    mapping_params,
+    history,
+    rerun_remap_job_id=None,
+    collection_info=None,
+    workflow_invocation_uuid=None,
+    invocation_step=None,
+    max_num_jobs=None,
+    job_callback=None,
+    completed_jobs=None,
+    workflow_resource_parameters=None,
+    validate_outputs=False,
+):
     """
     Execute a tool and return object containing summary (output data, number of
     failures, etc...).
@@ -42,7 +65,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
         assert invocation_step is None
 
     all_jobs_timer = tool.app.execution_timer_factory.get_timer(
-        'internals.galaxy.tools.execute.job_batch', BATCH_EXECUTION_MESSAGE
+        "internals.galaxy.tools.execute.job_batch", BATCH_EXECUTION_MESSAGE
     )
 
     if invocation_step is None:
@@ -50,29 +73,41 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
             trans, tool, mapping_params, collection_info, completed_jobs=completed_jobs
         )
     else:
-        execution_tracker = WorkflowStepExecutionTracker(trans, tool, mapping_params, collection_info, invocation_step, completed_jobs=completed_jobs)
+        execution_tracker = WorkflowStepExecutionTracker(
+            trans, tool, mapping_params, collection_info, invocation_step, completed_jobs=completed_jobs
+        )
     execution_cache = ToolExecutionCache(trans)
 
     def execute_single_job(execution_slice, completed_job):
         job_timer = tool.app.execution_timer_factory.get_timer(
-            'internals.galaxy.tools.execute.job_single', SINGLE_EXECUTION_SUCCESS_MESSAGE
+            "internals.galaxy.tools.execute.job_single", SINGLE_EXECUTION_SUCCESS_MESSAGE
         )
         params = execution_slice.param_combination
         if workflow_invocation_uuid:
-            params['__workflow_invocation_uuid__'] = workflow_invocation_uuid
-        elif '__workflow_invocation_uuid__' in params:
+            params["__workflow_invocation_uuid__"] = workflow_invocation_uuid
+        elif "__workflow_invocation_uuid__" in params:
             # Only workflow invocation code gets to set this, ignore user supplied
             # values or rerun parameters.
-            del params['__workflow_invocation_uuid__']
+            del params["__workflow_invocation_uuid__"]
         if workflow_resource_parameters:
-            params['__workflow_resource_params__'] = workflow_resource_parameters
-        elif '__workflow_resource_params__' in params:
+            params["__workflow_resource_params__"] = workflow_resource_parameters
+        elif "__workflow_resource_params__" in params:
             # Only workflow invocation code gets to set this, ignore user supplied
             # values or rerun parameters.
-            del params['__workflow_resource_params__']
+            del params["__workflow_resource_params__"]
         if validate_outputs:
-            params['__validate_outputs__'] = True
-        job, result = tool.handle_single_execution(trans, rerun_remap_job_id, execution_slice, history, execution_cache, completed_job, collection_info, job_callback=job_callback, flush_job=False)
+            params["__validate_outputs__"] = True
+        job, result = tool.handle_single_execution(
+            trans,
+            rerun_remap_job_id,
+            execution_slice,
+            history,
+            execution_cache,
+            completed_job,
+            collection_info,
+            job_callback=job_callback,
+            flush_job=False,
+        )
         if job:
             log.debug(job_timer.to_str(tool_id=tool.id, job_id=job.id))
             execution_tracker.record_success(execution_slice, job, result)
@@ -104,9 +139,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
     jobs_executed = 0
     has_remaining_jobs = False
     execution_slice = None
-    job_datasets: Dict[
-        str, List[model.DatasetInstance]
-    ] = {}  # job: list of dataset instances created by job
+    job_datasets: Dict[str, List[model.DatasetInstance]] = {}  # job: list of dataset instances created by job
 
     for i, execution_slice in enumerate(execution_tracker.new_execution_slices()):
         if max_num_jobs is not None and jobs_executed >= max_num_jobs:
@@ -131,9 +164,7 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
     for job2 in execution_tracker.successful_jobs:
         # Put the job in the queue if tracking in memory
         tool.app.job_manager.enqueue(job2, tool=tool, flush=False)
-        trans.log_event(
-            f"Added job to the job queue, id: {str(job2.id)}", tool_id=tool_id
-        )
+        trans.log_event(f"Added job to the job queue, id: {str(job2.id)}", tool_id=tool_id)
     trans.sa_session.flush()
 
     if has_remaining_jobs:
@@ -146,7 +177,6 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
 
 
 class ExecutionSlice:
-
     def __init__(self, job_index, param_combination, dataset_collection_elements=None):
         self.job_index = job_index
         self.param_combination = param_combination
@@ -155,7 +185,6 @@ class ExecutionSlice:
 
 
 class ExecutionTracker:
-
     def __init__(self, trans, tool, mapping_params, collection_info, completed_jobs=None):
         # Known ahead of time...
         self.trans = trans
@@ -254,12 +283,18 @@ class ExecutionTracker:
         if not hasattr(input_collection, "collection"):
             raise Exception("Referenced input parameter is not a collection.")
 
-        collection_type_description = self.trans.app.dataset_collection_manager.collection_type_descriptions.for_collection_type(input_collection.collection.collection_type)
+        collection_type_description = (
+            self.trans.app.dataset_collection_manager.collection_type_descriptions.for_collection_type(
+                input_collection.collection.collection_type
+            )
+        )
         subcollection_mapping_type = None
         if self.is_implicit_input(input_name):
             subcollection_mapping_type = self.collection_info.subcollection_mapping_type(input_name)
 
-        return get_structure(input_collection, collection_type_description, leaf_subcollection_type=subcollection_mapping_type)
+        return get_structure(
+            input_collection, collection_type_description, leaf_subcollection_type=subcollection_mapping_type
+        )
 
     def _structure_for_output(self, trans, tool_output):
         structure = self.collection_info.structure
@@ -269,8 +304,12 @@ class ExecutionTracker:
 
             source_collection = self.collection_info.collections.get(tool_output.default_identifier_source)
             if source_collection:
-                collection_type_description = collection_type_descriptions.for_collection_type(source_collection.collection.collection_type)
-                _structure = structure.for_dataset_collection(source_collection.collection, collection_type_description=collection_type_description)
+                collection_type_description = collection_type_descriptions.for_collection_type(
+                    source_collection.collection.collection_type
+                )
+                _structure = structure.for_dataset_collection(
+                    source_collection.collection, collection_type_description=collection_type_description
+                )
                 if structure.can_match(_structure):
                     structure = _structure
 
@@ -278,7 +317,9 @@ class ExecutionTracker:
 
     def _mapped_output_structure(self, trans, tool_output):
         collections_manager = trans.app.dataset_collection_manager
-        output_structure = tool_output_to_structure(self.sliced_input_collection_structure, tool_output, collections_manager)
+        output_structure = tool_output_to_structure(
+            self.sliced_input_collection_structure, tool_output, collections_manager
+        )
         # self.collection_info.structure - the mapping structure with default_identifier_source
         # used to determine the identifiers to use.
         mapping_structure = self._structure_for_output(trans, tool_output)
@@ -302,7 +343,9 @@ class ExecutionTracker:
         # with the collection and wrap everything up so can evaluate output
         # label.
         trans = self.trans
-        params.update(self.collection_info.collections)  # Replace datasets with source collections for labelling outputs.
+        params.update(
+            self.collection_info.collections
+        )  # Replace datasets with source collections for labelling outputs.
 
         collection_instances = {}
         implicit_inputs = self.implicit_inputs
@@ -366,7 +409,9 @@ class ExecutionTracker:
                     implicit_collection_jobs = implicit_collection.implicit_collection_jobs
                     implicit_collection_jobs.populated_state = "failed"
                     trans.sa_session.add(implicit_collection_jobs)
-                implicit_collection.collection.handle_population_failed("One or more jobs failed during dataset initialization.")
+                implicit_collection.collection.handle_population_failed(
+                    "One or more jobs failed during dataset initialization."
+                )
                 trans.sa_session.add(implicit_collection.collection)
         else:
             for i, implicit_collection in enumerate(self.implicit_collections.values()):
@@ -425,7 +470,6 @@ class ExecutionTracker:
 # Seperate these because workflows need to track their jobs belong to the invocation
 # in the database immediately and they can be recovered.
 class ToolExecutionTracker(ExecutionTracker):
-
     def __init__(self, trans, tool, mapping_params, collection_info, completed_jobs=None):
         super().__init__(trans, tool, mapping_params, collection_info, completed_jobs=completed_jobs)
 
@@ -446,7 +490,9 @@ class ToolExecutionTracker(ExecutionTracker):
             self.outputs_by_output_name[job_output.name].append(job_output.dataset_collection)
 
     def new_collection_execution_slices(self):
-        for job_index, (param_combination, dataset_collection_elements) in enumerate(zip(self.param_combinations, self.walk_implicit_collections())):
+        for job_index, (param_combination, dataset_collection_elements) in enumerate(
+            zip(self.param_combinations, self.walk_implicit_collections())
+        ):
             completed_job = self.completed_jobs and self.completed_jobs[job_index]
             if not completed_job:
                 for dataset_collection_element in dataset_collection_elements.values():
@@ -456,7 +502,6 @@ class ToolExecutionTracker(ExecutionTracker):
 
 
 class WorkflowStepExecutionTracker(ExecutionTracker):
-
     def __init__(self, trans, tool, mapping_params, collection_info, invocation_step, completed_jobs=None):
         super().__init__(trans, tool, mapping_params, collection_info, completed_jobs=completed_jobs)
         self.invocation_step = invocation_step
@@ -469,7 +514,9 @@ class WorkflowStepExecutionTracker(ExecutionTracker):
             self.invocation_step.job = job
 
     def new_collection_execution_slices(self):
-        for job_index, (param_combination, dataset_collection_elements) in enumerate(zip(self.param_combinations, self.walk_implicit_collections())):
+        for job_index, (param_combination, dataset_collection_elements) in enumerate(
+            zip(self.param_combinations, self.walk_implicit_collections())
+        ):
             completed_job = self.completed_jobs and self.completed_jobs[job_index]
             if not completed_job:
                 found_result = False
@@ -501,4 +548,4 @@ class WorkflowStepExecutionTracker(ExecutionTracker):
         self.invocation_step.implicit_collection_jobs = self.implicit_collection_jobs
 
 
-__all__ = ('execute', )
+__all__ = ("execute",)
diff --git a/lib/galaxy/tools/expressions/__init__.py b/lib/galaxy/tools/expressions/__init__.py
index bf20411a392..7509b33b947 100644
--- a/lib/galaxy/tools/expressions/__init__.py
+++ b/lib/galaxy/tools/expressions/__init__.py
@@ -6,11 +6,10 @@ from .script import (
 )
 from .util import find_engine
 
-
 __all__ = (
-    'evaluate',
-    'EXPRESSION_SCRIPT_CALL',
-    'EXPRESSION_SCRIPT_NAME',
-    'find_engine',
-    'write_evalute_script',
+    "evaluate",
+    "EXPRESSION_SCRIPT_CALL",
+    "EXPRESSION_SCRIPT_NAME",
+    "find_engine",
+    "write_evalute_script",
 )
diff --git a/lib/galaxy/tools/expressions/evaluation.py b/lib/galaxy/tools/expressions/evaluation.py
index 204e771ca60..6ba878274ae 100644
--- a/lib/galaxy/tools/expressions/evaluation.py
+++ b/lib/galaxy/tools/expressions/evaluation.py
@@ -22,11 +22,9 @@ def evaluate(config, input):
     new_input = default_context
     new_input.update(input)
 
-    sp = subprocess.Popen([application, NODE_ENGINE],
-                          shell=False,
-                          close_fds=True,
-                          stdin=subprocess.PIPE,
-                          stdout=subprocess.PIPE)
+    sp = subprocess.Popen(
+        [application, NODE_ENGINE], shell=False, close_fds=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE
+    )
     input_str = f"{json.dumps(new_input)}\n\n"
     input_bytes = input_str.encode("utf-8")
     (stdoutdata, stderrdata) = sp.communicate(input_bytes)
diff --git a/lib/galaxy/tools/expressions/script.py b/lib/galaxy/tools/expressions/script.py
index f19bd697b6e..ef79dbd2acf 100644
--- a/lib/galaxy/tools/expressions/script.py
+++ b/lib/galaxy/tools/expressions/script.py
@@ -5,11 +5,11 @@ EXPRESSION_SCRIPT_CALL = f"python {EXPRESSION_SCRIPT_NAME}"
 
 
 def write_evalute_script(in_directory):
-    """ Responsible for writing the script that evaluates expressions
+    """Responsible for writing the script that evaluates expressions
     in Galaxy jobs.
     """
     script = os.path.join(in_directory, EXPRESSION_SCRIPT_NAME)
     with open(script, "w") as f:
-        f.write('from galaxy_ext.expressions.handle_job import run; run()')
+        f.write("from galaxy_ext.expressions.handle_job import run; run()")
 
     return script
diff --git a/lib/galaxy/tools/imp_exp/__init__.py b/lib/galaxy/tools/imp_exp/__init__.py
index bced4bfee0f..df125fc5dda 100644
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -12,8 +12,8 @@ log = logging.getLogger(__name__)
 
 class JobImportHistoryArchiveWrapper:
     """
-        Class provides support for performing jobs that import a history from
-        an archive.
+    Class provides support for performing jobs that import a history from
+    an archive.
     """
 
     def __init__(self, app, job_id):
@@ -28,18 +28,18 @@ class JobImportHistoryArchiveWrapper:
                     archive_source,
                     jiha.job.user.system_user_pwent(self.app.config.real_system_username),
                     self.app.config.external_chown_script,
-                    "history import archive"
+                    "history import archive",
                 )
             external_chown(
                 jiha.archive_dir,
                 jiha.job.user.system_user_pwent(self.app.config.real_system_username),
                 self.app.config.external_chown_script,
-                "history import archive directory"
+                "history import archive directory",
             )
 
     def cleanup_after_job(self):
-        """ Set history, datasets, collections and jobs' attributes
-            and clean up archive directory.
+        """Set history, datasets, collections and jobs' attributes
+        and clean up archive directory.
         """
 
         #
@@ -59,9 +59,11 @@ class JobImportHistoryArchiveWrapper:
                     archive_dir,
                     jiha.job.user.system_user_pwent(getpass.getuser()),
                     self.app.config.external_chown_script,
-                    "history import archive directory"
+                    "history import archive directory",
                 )
-            model_store = store.get_import_model_store_for_directory(archive_dir, app=self.app, user=user, tag_handler=self.app.tag_handler.create_tag_handler_session())
+            model_store = store.get_import_model_store_for_directory(
+                archive_dir, app=self.app, user=user, tag_handler=self.app.tag_handler.create_tag_handler_session()
+            )
             job = jiha.job
             with model_store.target_history(default_history=job.history) as new_history:
 
@@ -98,8 +100,21 @@ class JobExportHistoryArchiveWrapper:
         app = self.app
 
         from galaxy.celery.tasks import export_history
+
         if app.config.enable_celery_tasks:
             # symlink files on export, on worker files will tarred up in a dereferenced manner.
-            export_history.delay(store_directory=store_directory, history_id=history.id, job_id=self.job_id, include_hidden=include_hidden, include_deleted=include_deleted)
+            export_history.delay(
+                store_directory=store_directory,
+                history_id=history.id,
+                job_id=self.job_id,
+                include_hidden=include_hidden,
+                include_deleted=include_deleted,
+            )
         else:
-            export_history(store_directory=store_directory, history_id=history.id, job_id=self.job_id, include_hidden=include_hidden, include_deleted=include_deleted)
+            export_history(
+                store_directory=store_directory,
+                history_id=history.id,
+                job_id=self.job_id,
+                include_hidden=include_hidden,
+                include_deleted=include_deleted,
+            )
diff --git a/lib/galaxy/tools/imp_exp/export_history.py b/lib/galaxy/tools/imp_exp/export_history.py
index 7cd45abf0a7..75241b2d0c3 100644
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -21,10 +21,10 @@ def create_archive(export_directory, out_file, gzip=False):
     try:
         tar_export_directory(export_directory, out_file, gzip)
         # Status.
-        print('Created history archive.')
+        print("Created history archive.")
         return 0
     except Exception as e:
-        print(f'Error creating history archive: {unicodify(e)}', file=sys.stderr)
+        print(f"Error creating history archive: {unicodify(e)}", file=sys.stderr)
         return 1
     finally:
         shutil.rmtree(export_directory, ignore_errors=True)
@@ -33,9 +33,11 @@ def create_archive(export_directory, out_file, gzip=False):
 def main(argv=None):
     # Parse command line.
     parser = optparse.OptionParser()
-    parser.add_option('-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.')
-    parser.add_option('--galaxy-version', dest='galaxy_version', help='Galaxy version that initiated the command.', default=None)
-    parser.add_option('--file-sources', type=str, help='file sources json')
+    parser.add_option("-G", "--gzip", dest="gzip", action="store_true", help="Compress archive using gzip.")
+    parser.add_option(
+        "--galaxy-version", dest="galaxy_version", help="Galaxy version that initiated the command.", default=None
+    )
+    parser.add_option("--file-sources", type=str, help="file sources json")
     (options, args) = parser.parse_args(argv)
     galaxy_version = options.galaxy_version
     if galaxy_version is None:
@@ -71,6 +73,7 @@ def _write_to_destination(file_sources_path, out_file, destination_uri):
 def get_file_sources(file_sources_path):
     assert os.path.exists(file_sources_path), f"file sources path [{file_sources_path}] does not exist"
     from galaxy.files import ConfiguredFileSources
+
     with open(file_sources_path) as f:
         file_sources_as_dict = json.load(f)
     file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict)
diff --git a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
index e39fd240f91..cfc5bc23110 100644
--- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
+++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
@@ -23,6 +23,7 @@ MAX_SIZE = 100 * math.pow(2, 30)
 def get_file_sources(file_sources_path):
     assert os.path.exists(file_sources_path), f"file sources path [{file_sources_path}] does not exist"
     from galaxy.files import ConfiguredFileSources
+
     with open(file_sources_path) as f:
         file_sources_as_dict = json.load(f)
     file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict)
@@ -34,14 +35,11 @@ def check_archive(archive_file, dest_dir):
     Ensure that a tar archive has no absolute paths or relative paths outside
     the archive.
     """
-    with tarfile.open(archive_file, mode='r') as archive_fp:
+    with tarfile.open(archive_file, mode="r") as archive_fp:
         for arc_path in archive_fp.getnames():
-            assert os.path.normpath(
-                os.path.join(
-                    dest_dir,
-                    arc_path
-                )).startswith(dest_dir.rstrip(os.sep) + os.sep), \
-                f"Archive member would extract outside target directory: {arc_path}"
+            assert os.path.normpath(os.path.join(dest_dir, arc_path)).startswith(
+                dest_dir.rstrip(os.sep) + os.sep
+            ), f"Archive member would extract outside target directory: {arc_path}"
     return True
 
 
@@ -49,7 +47,7 @@ def unpack_archive(archive_file, dest_dir):
     """
     Unpack a tar and/or gzipped archive into a destination directory.
     """
-    archive_fp = tarfile.open(archive_file, mode='r')
+    archive_fp = tarfile.open(archive_file, mode="r")
     archive_fp.extractall(path=dest_dir)
     archive_fp.close()
 
@@ -60,8 +58,8 @@ def main(options, args):
     archive_source, dest_dir = args
 
     if options.is_b64encoded:
-        archive_source = b64decode(archive_source).decode('utf-8')
-        dest_dir = b64decode(dest_dir).decode('utf-8')
+        archive_source = b64decode(archive_source).decode("utf-8")
+        dest_dir = b64decode(dest_dir).decode("utf-8")
 
     # Get archive from URL.
     if is_url:
@@ -77,9 +75,16 @@ def main(options, args):
 if __name__ == "__main__":
     # Parse command line.
     parser = optparse.OptionParser()
-    parser.add_option('-U', '--url', dest='is_url', action="store_true", help='Source is a URL.')
-    parser.add_option('-F', '--file', dest='is_file', action="store_true", help='Source is a file.')
-    parser.add_option('-e', '--encoded', dest='is_b64encoded', action="store_true", default=False, help='Source and destination dir values are base64 encoded.')
-    parser.add_option('--file-sources', type=str, help='file sources json')
+    parser.add_option("-U", "--url", dest="is_url", action="store_true", help="Source is a URL.")
+    parser.add_option("-F", "--file", dest="is_file", action="store_true", help="Source is a file.")
+    parser.add_option(
+        "-e",
+        "--encoded",
+        dest="is_b64encoded",
+        action="store_true",
+        default=False,
+        help="Source and destination dir values are base64 encoded.",
+    )
+    parser.add_option("--file-sources", type=str, help="file sources json")
     (options, args) = parser.parse_args()
     main(options, args)
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 03fd992ad40..904fd948139 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -17,15 +17,30 @@ from .basic import (
     runtime_to_json,
     SelectToolParameter,
 )
-from .grouping import Conditional, Repeat, Section, UploadDataset
+from .grouping import (
+    Conditional,
+    Repeat,
+    Section,
+    UploadDataset,
+)
 
 REPLACE_ON_TRUTHY = object()
 
 # Some tools use the code tag and access the code base, expecting certain tool parameters to be available here.
-__all__ = ('DataCollectionToolParameter', 'DataToolParameter', 'SelectToolParameter')
+__all__ = ("DataCollectionToolParameter", "DataToolParameter", "SelectToolParameter")
 
 
-def visit_input_values(inputs, input_values, callback, name_prefix='', label_prefix='', parent_prefix='', context=None, no_replacement_value=REPLACE_ON_TRUTHY, replace_optional_connections=False):
+def visit_input_values(
+    inputs,
+    input_values,
+    callback,
+    name_prefix="",
+    label_prefix="",
+    parent_prefix="",
+    context=None,
+    no_replacement_value=REPLACE_ON_TRUTHY,
+    replace_optional_connections=False,
+):
     """
     Given a tools parameter definition (`inputs`) and a specific set of
     parameter `values`, call `callback` for each non-grouping parameter,
@@ -120,20 +135,21 @@ def visit_input_values(inputs, input_values, callback, name_prefix='', label_pre
     name=j, prefix=b_0|d_0|, prefixed_name=b_0|d_0|f_1|j, prefixed_label=b 1 > d 1 > j, value=None
     No value found for 'b 1 > d 1 > j'.
     """
+
     def callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix, context=None, error=None):
         value = input_values.get(input.name)
         args = {
-            'input': input,
-            'parent': input_values,
-            'value': value,
-            'prefixed_name': f'{name_prefix}{input.name}',
-            'prefixed_label': f'{label_prefix}{input.label or input.name}',
-            'prefix': parent_prefix,
-            'context': context,
-            'error': error
+            "input": input,
+            "parent": input_values,
+            "value": value,
+            "prefixed_name": f"{name_prefix}{input.name}",
+            "prefixed_label": f"{label_prefix}{input.label or input.name}",
+            "prefix": parent_prefix,
+            "context": context,
+            "error": error,
         }
         if input.name not in input_values:
-            args['error'] = f"No value found for '{args.get('prefixed_label')}'."
+            args["error"] = f"No value found for '{args.get('prefixed_label')}'."
         new_value = callback(**args)
         if no_replacement_value is REPLACE_ON_TRUTHY:
             replace = bool(new_value)
@@ -141,7 +157,7 @@ def visit_input_values(inputs, input_values, callback, name_prefix='', label_pre
             replace = new_value != no_replacement_value
         if replace:
             input_values[input.name] = new_value
-        elif replace_optional_connections and is_runtime_value(value) and hasattr(input, 'value'):
+        elif replace_optional_connections and is_runtime_value(value) and hasattr(input, "value"):
             input_values[input.name] = input.value
 
     def get_current_case(input, input_values):
@@ -151,29 +167,57 @@ def visit_input_values(inputs, input_values, callback, name_prefix='', label_pre
             return -1
 
     context = ExpressionContext(input_values, context)
-    payload = {'context': context, 'no_replacement_value': no_replacement_value}
+    payload = {"context": context, "no_replacement_value": no_replacement_value}
     for input in inputs.values():
         if isinstance(input, Repeat) or isinstance(input, UploadDataset):
             values = input_values[input.name] = input_values.get(input.name, [])
             for i, d in enumerate(values):
-                d['__index__'] = i
-                new_name_prefix = name_prefix + '%s_%d|' % (input.name, i)
-                new_label_prefix = label_prefix + '%s %d > ' % (input.title, i + 1)
-                visit_input_values(input.inputs, d, callback, new_name_prefix, new_label_prefix, parent_prefix=new_name_prefix, **payload)
+                d["__index__"] = i
+                new_name_prefix = name_prefix + "%s_%d|" % (input.name, i)
+                new_label_prefix = label_prefix + "%s %d > " % (input.title, i + 1)
+                visit_input_values(
+                    input.inputs,
+                    d,
+                    callback,
+                    new_name_prefix,
+                    new_label_prefix,
+                    parent_prefix=new_name_prefix,
+                    **payload,
+                )
         elif isinstance(input, Conditional):
             values = input_values[input.name] = input_values.get(input.name, {})
             new_name_prefix = f"{name_prefix + input.name}|"
-            case_error = None if get_current_case(input, values) >= 0 else 'The selected case is unavailable/invalid.'
-            callback_helper(input.test_param, values, new_name_prefix, label_prefix, parent_prefix=name_prefix, context=context, error=case_error)
-            values['__current_case__'] = get_current_case(input, values)
-            if values['__current_case__'] >= 0:
-                visit_input_values(input.cases[values['__current_case__']].inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload)
+            case_error = None if get_current_case(input, values) >= 0 else "The selected case is unavailable/invalid."
+            callback_helper(
+                input.test_param,
+                values,
+                new_name_prefix,
+                label_prefix,
+                parent_prefix=name_prefix,
+                context=context,
+                error=case_error,
+            )
+            values["__current_case__"] = get_current_case(input, values)
+            if values["__current_case__"] >= 0:
+                visit_input_values(
+                    input.cases[values["__current_case__"]].inputs,
+                    values,
+                    callback,
+                    new_name_prefix,
+                    label_prefix,
+                    parent_prefix=name_prefix,
+                    **payload,
+                )
         elif isinstance(input, Section):
             values = input_values[input.name] = input_values.get(input.name, {})
             new_name_prefix = f"{name_prefix + input.name}|"
-            visit_input_values(input.inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload)
+            visit_input_values(
+                input.inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload
+            )
         else:
-            callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context)
+            callback_helper(
+                input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context
+            )
 
 
 def check_param(trans, param, incoming_value, param_values, simple_errors=True):
@@ -227,7 +271,7 @@ def params_from_strings(params, param_values, app, ignore_errors=False):
     param_values = param_values or {}
     for key, value in param_values.items():
         param = params.get(key)
-        if not param or not (param.type == 'text' and value == 'null'):
+        if not param or not (param.type == "text" and value == "null"):
             # safe_loads attempts to handle some, but not all divergent handling
             # between JSON types and python types. TODO: We should let the
             # parameters handle all conversion, since they know what is an
@@ -254,12 +298,12 @@ def params_to_incoming(incoming, inputs, input_values, app, name_prefix=""):
     for input in inputs.values():
         if isinstance(input, Repeat) or isinstance(input, UploadDataset):
             for d in input_values[input.name]:
-                index = d['__index__']
-                new_name_prefix = name_prefix + '%s_%d|' % (input.name, index)
+                index = d["__index__"]
+                new_name_prefix = name_prefix + "%s_%d|" % (input.name, index)
                 params_to_incoming(incoming, input.inputs, d, app, new_name_prefix)
         elif isinstance(input, Conditional):
             values = input_values[input.name]
-            current = values['__current_case__']
+            current = values["__current_case__"]
             new_name_prefix = f"{name_prefix + input.name}|"
             incoming[new_name_prefix + input.test_param.name] = values[input.test_param.name]
             params_to_incoming(incoming, input.cases[current].inputs, values, app, new_name_prefix)
@@ -273,22 +317,31 @@ def params_to_incoming(incoming, inputs, input_values, app, name_prefix=""):
 
 
 def update_dataset_ids(input_values, translate_values, src):
-
     def replace_dataset_ids(path, key, value):
         """Exchanges dataset_ids (HDA, LDA, HDCA, not Dataset) in input_values with dataset ids used in job."""
         current_case = input_values
-        if key == 'id':
+        if key == "id":
             for p in path:
                 if isinstance(current_case, (list, dict)):
                     current_case = current_case[p]
-            if src == current_case.get('src'):
-                return key, translate_values.get(current_case['id'], value)
+            if src == current_case.get("src"):
+                return key, translate_values.get(current_case["id"], value)
         return key, value
 
     return remap(input_values, visit=replace_dataset_ids)
 
 
-def populate_state(request_context, inputs, incoming, state, errors=None, context=None, check=True, simple_errors=True, input_format='legacy'):
+def populate_state(
+    request_context,
+    inputs,
+    incoming,
+    state,
+    errors=None,
+    context=None,
+    check=True,
+    simple_errors=True,
+    input_format="legacy",
+):
     """
     Populates nested state dict from incoming parameter values.
     >>> from galaxy.util import XML
@@ -344,30 +397,55 @@ def populate_state(request_context, inputs, incoming, state, errors=None, contex
     """
     if errors is None:
         errors = {}
-    if input_format == 'legacy':
-        _populate_state_legacy(request_context, inputs, incoming, state, errors=errors, context=context, check=check, simple_errors=simple_errors)
+    if input_format == "legacy":
+        _populate_state_legacy(
+            request_context,
+            inputs,
+            incoming,
+            state,
+            errors=errors,
+            context=context,
+            check=check,
+            simple_errors=simple_errors,
+        )
         return
-    elif input_format == '21.01':
+    elif input_format == "21.01":
         context = ExpressionContext(state, context)
         for input in inputs.values():
             state[input.name] = input.get_initial_value(request_context, context)
             group_state = state[input.name]
-            if input.type == 'repeat':
+            if input.type == "repeat":
                 if len(incoming[input.name]) > input.max or len(incoming[input.name]) < input.min:
-                    errors[input.name] = 'The number of repeat elements is outside the range specified by the tool.'
+                    errors[input.name] = "The number of repeat elements is outside the range specified by the tool."
                 else:
                     del group_state[:]
                     for rep in incoming[input.name]:
                         new_state = {}
                         group_state.append(new_state)
                         new_errors = {}
-                        populate_state(request_context, input.inputs, rep, new_state, new_errors, context=context, check=check, simple_errors=simple_errors, input_format=input_format)
+                        populate_state(
+                            request_context,
+                            input.inputs,
+                            rep,
+                            new_state,
+                            new_errors,
+                            context=context,
+                            check=check,
+                            simple_errors=simple_errors,
+                            input_format=input_format,
+                        )
                         if new_errors:
                             errors[input.name] = new_errors
 
-            elif input.type == 'conditional':
+            elif input.type == "conditional":
                 test_param_value = incoming.get(input.name, {}).get(input.test_param.name)
-                value, error = check_param(request_context, input.test_param, test_param_value, context, simple_errors=simple_errors) if check else [test_param_value, None]
+                value, error = (
+                    check_param(
+                        request_context, input.test_param, test_param_value, context, simple_errors=simple_errors
+                    )
+                    if check
+                    else [test_param_value, None]
+                )
                 if error:
                     errors[input.test_param.name] = error
                 else:
@@ -375,88 +453,165 @@ def populate_state(request_context, inputs, incoming, state, errors=None, contex
                         current_case = input.get_current_case(value)
                         group_state = state[input.name] = {}
                         new_errors = {}
-                        populate_state(request_context, input.cases[current_case].inputs, incoming.get(input.name), group_state, new_errors, context=context, check=check, simple_errors=simple_errors, input_format=input_format)
+                        populate_state(
+                            request_context,
+                            input.cases[current_case].inputs,
+                            incoming.get(input.name),
+                            group_state,
+                            new_errors,
+                            context=context,
+                            check=check,
+                            simple_errors=simple_errors,
+                            input_format=input_format,
+                        )
                         if new_errors:
                             errors[input.name] = new_errors
-                        group_state['__current_case__'] = current_case
+                        group_state["__current_case__"] = current_case
                     except Exception:
-                        errors[input.test_param.name] = 'The selected case is unavailable/invalid.'
+                        errors[input.test_param.name] = "The selected case is unavailable/invalid."
                 group_state[input.test_param.name] = value
 
-            elif input.type == 'section':
+            elif input.type == "section":
                 new_errors = {}
-                populate_state(request_context, input.inputs, incoming.get(input.name), group_state, new_errors, context=context, check=check, simple_errors=simple_errors, input_format=input_format)
+                populate_state(
+                    request_context,
+                    input.inputs,
+                    incoming.get(input.name),
+                    group_state,
+                    new_errors,
+                    context=context,
+                    check=check,
+                    simple_errors=simple_errors,
+                    input_format=input_format,
+                )
                 if new_errors:
                     errors[input.name] = new_errors
 
-            elif input.type == 'upload_dataset':
+            elif input.type == "upload_dataset":
                 raise NotImplementedError
 
             else:
                 param_value = _get_incoming_value(incoming, input.name, state.get(input.name))
-                value, error = check_param(request_context, input, param_value, context, simple_errors=simple_errors) if check else [param_value, None]
+                value, error = (
+                    check_param(request_context, input, param_value, context, simple_errors=simple_errors)
+                    if check
+                    else [param_value, None]
+                )
                 if error:
                     errors[input.name] = error
                 state[input.name] = value
     else:
-        raise Exception(f'Input format {input_format} not recognized; input_format must be either legacy or 21.01.')
+        raise Exception(f"Input format {input_format} not recognized; input_format must be either legacy or 21.01.")
 
 
-def _populate_state_legacy(request_context, inputs, incoming, state, errors, prefix='', context=None, check=True, simple_errors=True):
+def _populate_state_legacy(
+    request_context, inputs, incoming, state, errors, prefix="", context=None, check=True, simple_errors=True
+):
     context = ExpressionContext(state, context)
     for input in inputs.values():
         state[input.name] = input.get_initial_value(request_context, context)
         key = prefix + input.name
         group_state = state[input.name]
-        group_prefix = f'{key}|'
-        if input.type == 'repeat':
+        group_prefix = f"{key}|"
+        if input.type == "repeat":
             rep_index = 0
             del group_state[:]
             while True:
-                rep_prefix = '%s_%d' % (key, rep_index)
-                if not any(incoming_key.startswith(rep_prefix) for incoming_key in incoming.keys()) and rep_index >= input.min:
+                rep_prefix = "%s_%d" % (key, rep_index)
+                if (
+                    not any(incoming_key.startswith(rep_prefix) for incoming_key in incoming.keys())
+                    and rep_index >= input.min
+                ):
                     break
                 if rep_index < input.max:
-                    new_state = {'__index__': rep_index}
+                    new_state = {"__index__": rep_index}
                     group_state.append(new_state)
-                    _populate_state_legacy(request_context, input.inputs, incoming, new_state, errors, prefix=f"{rep_prefix}|", context=context, check=check, simple_errors=simple_errors)
+                    _populate_state_legacy(
+                        request_context,
+                        input.inputs,
+                        incoming,
+                        new_state,
+                        errors,
+                        prefix=f"{rep_prefix}|",
+                        context=context,
+                        check=check,
+                        simple_errors=simple_errors,
+                    )
                 rep_index += 1
-        elif input.type == 'conditional':
+        elif input.type == "conditional":
             if input.value_ref and not input.value_ref_in_group:
                 test_param_key = prefix + input.test_param.name
             else:
                 test_param_key = group_prefix + input.test_param.name
             test_param_value = incoming.get(test_param_key, group_state.get(input.test_param.name))
-            value, error = check_param(request_context, input.test_param, test_param_value, context, simple_errors=simple_errors) if check else [test_param_value, None]
+            value, error = (
+                check_param(request_context, input.test_param, test_param_value, context, simple_errors=simple_errors)
+                if check
+                else [test_param_value, None]
+            )
             if error:
                 errors[test_param_key] = error
             else:
                 try:
                     current_case = input.get_current_case(value)
                     group_state = state[input.name] = {}
-                    _populate_state_legacy(request_context, input.cases[current_case].inputs, incoming, group_state, errors, prefix=group_prefix, context=context, check=check, simple_errors=simple_errors)
-                    group_state['__current_case__'] = current_case
+                    _populate_state_legacy(
+                        request_context,
+                        input.cases[current_case].inputs,
+                        incoming,
+                        group_state,
+                        errors,
+                        prefix=group_prefix,
+                        context=context,
+                        check=check,
+                        simple_errors=simple_errors,
+                    )
+                    group_state["__current_case__"] = current_case
                 except Exception:
-                    errors[test_param_key] = 'The selected case is unavailable/invalid.'
+                    errors[test_param_key] = "The selected case is unavailable/invalid."
             group_state[input.test_param.name] = value
-        elif input.type == 'section':
-            _populate_state_legacy(request_context, input.inputs, incoming, group_state, errors, prefix=group_prefix, context=context, check=check, simple_errors=simple_errors)
-        elif input.type == 'upload_dataset':
+        elif input.type == "section":
+            _populate_state_legacy(
+                request_context,
+                input.inputs,
+                incoming,
+                group_state,
+                errors,
+                prefix=group_prefix,
+                context=context,
+                check=check,
+                simple_errors=simple_errors,
+            )
+        elif input.type == "upload_dataset":
             file_count = input.get_file_count(request_context, context)
             while len(group_state) > file_count:
                 del group_state[-1]
             while file_count > len(group_state):
-                new_state = {'__index__': len(group_state)}
+                new_state = {"__index__": len(group_state)}
                 for upload_item in input.inputs.values():
                     new_state[upload_item.name] = upload_item.get_initial_value(request_context, context)
                 group_state.append(new_state)
             for rep_state in group_state:
-                rep_index = rep_state['__index__']
-                rep_prefix = '%s_%d|' % (key, rep_index)
-                _populate_state_legacy(request_context, input.inputs, incoming, rep_state, errors, prefix=rep_prefix, context=context, check=check, simple_errors=simple_errors)
+                rep_index = rep_state["__index__"]
+                rep_prefix = "%s_%d|" % (key, rep_index)
+                _populate_state_legacy(
+                    request_context,
+                    input.inputs,
+                    incoming,
+                    rep_state,
+                    errors,
+                    prefix=rep_prefix,
+                    context=context,
+                    check=check,
+                    simple_errors=simple_errors,
+                )
         else:
             param_value = _get_incoming_value(incoming, key, state.get(input.name))
-            value, error = check_param(request_context, input, param_value, context, simple_errors=simple_errors) if check else [param_value, None]
+            value, error = (
+                check_param(request_context, input, param_value, context, simple_errors=simple_errors)
+                if check
+                else [param_value, None]
+            )
             if error:
                 errors[key] = error
             state[input.name] = value
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 4dbfbcafa56..b8255575979 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -8,7 +8,14 @@ import logging
 import os
 import os.path
 import re
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
 
 from webob.compat import cgi_FieldStorage
 
@@ -38,11 +45,9 @@ from galaxy.util.rules_dsl import RuleSet
 from . import (
     dynamic_options,
     history_query,
-    validation
-)
-from .dataset_matcher import (
-    get_dataset_matcher_factory,
+    validation,
 )
+from .dataset_matcher import get_dataset_matcher_factory
 from .sanitize import ToolParameterSanitizer
 
 log = logging.getLogger(__name__)
@@ -54,7 +59,7 @@ class workflow_building_modes:
     USE_HISTORY = 1
 
 
-WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile(r'\$\{.+?\}')
+WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile(r"\$\{.+?\}")
 
 
 class ImplicitConversionRequired(Exception):
@@ -72,8 +77,9 @@ def contains_workflow_parameter(value, search=False):
 
 
 def is_runtime_value(value):
-    return isinstance(value, RuntimeValue) or (isinstance(value, dict)
-        and value.get("__class__") in ["RuntimeValue", "ConnectedValue"])
+    return isinstance(value, RuntimeValue) or (
+        isinstance(value, dict) and value.get("__class__") in ["RuntimeValue", "ConnectedValue"]
+    )
 
 
 def is_runtime_context(trans, other_values):
@@ -83,9 +89,9 @@ def is_runtime_context(trans, other_values):
         if is_runtime_value(context_value):
             return True
         for v in util.listify(context_value):
-            if isinstance(v, HistoryDatasetAssociation) and \
-                    ((hasattr(v, 'state') and v.state != Dataset.states.OK)
-                    or hasattr(v, 'implicit_conversion')):
+            if isinstance(v, HistoryDatasetAssociation) and (
+                (hasattr(v, "state") and v.state != Dataset.states.OK) or hasattr(v, "implicit_conversion")
+            ):
                 return True
     return False
 
@@ -114,7 +120,6 @@ def assert_throws_param_value_error(message):
 
 
 class ParameterValueError(ValueError):
-
     def __init__(self, message_suffix, parameter_name, parameter_value=NO_PARAMETER_VALUE, is_dynamic=None):
         message = f"parameter '{parameter_name}': {message_suffix}"
         super().__init__(message)
@@ -146,7 +151,8 @@ class ToolParameter(Dictifiable):
     >>> assert p.name == 'parameter_name'
     >>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
     """
-    dict_collection_visible_keys = ['name', 'argument', 'type', 'label', 'help', 'refresh_on_change']
+
+    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "refresh_on_change"]
 
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
@@ -222,10 +228,10 @@ class ToolParameter(Dictifiable):
         # Handle Runtime and Unvalidated values
         if is_runtime_value(value):
             if isinstance(self, HiddenToolParameter):
-                raise ParameterValueError(message_suffix='Runtime Parameter not valid', parameter_name=self.name)
+                raise ParameterValueError(message_suffix="Runtime Parameter not valid", parameter_name=self.name)
             return runtime_to_object(value)
-        elif isinstance(value, dict) and value.get('__class__') == 'UnvalidatedValue':
-            return value['value']
+        elif isinstance(value, dict) and value.get("__class__") == "UnvalidatedValue":
+            return value["value"]
         # Delegate to the 'to_python' method
         if ignore_errors:
             try:
@@ -285,14 +291,16 @@ class ToolParameter(Dictifiable):
             validator.validate(value, trans)
 
     def to_dict(self, trans, other_values=None):
-        """ to_dict tool parameter. This can be overridden by subclasses. """
+        """to_dict tool parameter. This can be overridden by subclasses."""
         other_values = other_values or {}
         tool_dict = super().to_dict()
-        tool_dict['model_class'] = self.__class__.__name__
-        tool_dict['optional'] = self.optional
-        tool_dict['hidden'] = self.hidden
-        tool_dict['is_dynamic'] = self.is_dynamic
-        tool_dict['value'] = self.value_to_basic(self.get_initial_value(trans, other_values), trans.app, use_security=True)
+        tool_dict["model_class"] = self.__class__.__name__
+        tool_dict["optional"] = self.optional
+        tool_dict["hidden"] = self.hidden
+        tool_dict["is_dynamic"] = self.is_dynamic
+        tool_dict["value"] = self.value_to_basic(
+            self.get_initial_value(trans, other_values), trans.app, use_security=True
+        )
         return tool_dict
 
     @classmethod
@@ -300,7 +308,7 @@ class ToolParameter(Dictifiable):
         """Factory method to create parameter of correct type"""
         input_source = ensure_input_source(input_source)
         param_name = cls.parse_name(input_source)
-        param_type = input_source.get('type')
+        param_type = input_source.get("type")
         if not param_type:
             raise ValueError(f"parameter '{param_name}' requires a 'type'")
         elif param_type not in parameter_types:
@@ -314,20 +322,19 @@ class ToolParameter(Dictifiable):
 
 
 class SimpleTextToolParameter(ToolParameter):
-
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.optional = input_source.get_bool('optional', False)
+        self.optional = input_source.get_bool("optional", False)
         if self.optional:
             self.value = None
         else:
-            self.value = ''
+            self.value = ""
 
     def to_json(self, value, app, use_security):
         """Convert a value to a string representation suitable for persisting"""
         if value is None:
-            rval = '' if not self.optional else None
+            rval = "" if not self.optional else None
         else:
             rval = unicodify(value)
         return rval
@@ -353,21 +360,25 @@ class TextToolParameter(SimpleTextToolParameter):
         super().__init__(tool, input_source)
         self.datalist = []
         for (title, value, _) in input_source.parse_static_options():
-            self.datalist.append({'label': title, 'value': value})
-        self.value = input_source.get('value')
-        self.area = input_source.get_bool('area', False)
+            self.datalist.append({"label": title, "value": value})
+        self.value = input_source.get("value")
+        self.area = input_source.get_bool("area", False)
 
     def validate(self, value, trans=None):
         search = self.type == "text"
-        if not (trans and trans.workflow_building_mode is workflow_building_modes.ENABLED and contains_workflow_parameter(value, search=search)):
+        if not (
+            trans
+            and trans.workflow_building_mode is workflow_building_modes.ENABLED
+            and contains_workflow_parameter(value, search=search)
+        ):
             return super().validate(value, trans)
 
     def to_dict(self, trans, other_values=None):
         d = super().to_dict(trans)
         other_values = other_values or {}
-        d['area'] = self.area
-        d['datalist'] = self.datalist
-        d['optional'] = self.optional
+        d["area"] = self.area
+        d["datalist"] = self.datalist
+        d["optional"] = self.optional
         return d
 
 
@@ -386,7 +397,7 @@ class IntegerToolParameter(TextToolParameter):
     ...     p.from_json("_string", trans)
     """
 
-    dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ['min', 'max']
+    dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ["min", "max"]
 
     def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
@@ -397,8 +408,8 @@ class IntegerToolParameter(TextToolParameter):
                 raise ParameterValueError("the attribute 'value' must be an integer", self.name)
         elif self.value is None and not self.optional:
             raise ParameterValueError("the attribute 'value' must be set for non optional parameters", self.name, None)
-        self.min = input_source.get('min')
-        self.max = input_source.get('max')
+        self.min = input_source.get("min")
+        self.max = input_source.get("max")
         if self.min:
             try:
                 self.min = int(self.min)
@@ -424,7 +435,9 @@ class IntegerToolParameter(TextToolParameter):
             if trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 raise ParameterValueError("an integer or workflow parameter is required", self.name, value)
             else:
-                raise ParameterValueError("the attribute 'value' must be set for non optional parameters", self.name, value)
+                raise ParameterValueError(
+                    "the attribute 'value' must be set for non optional parameters", self.name, value
+                )
 
     def to_python(self, value, app):
         try:
@@ -458,12 +471,12 @@ class FloatToolParameter(TextToolParameter):
     ...     p.from_json("_string", trans)
     """
 
-    dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ['min', 'max']
+    dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ["min", "max"]
 
     def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
-        self.min = input_source.get('min')
-        self.max = input_source.get('max')
+        self.min = input_source.get("min")
+        self.max = input_source.get("max")
         if self.value:
             try:
                 float(self.value)
@@ -496,7 +509,9 @@ class FloatToolParameter(TextToolParameter):
             if trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 raise ParameterValueError("an integer or workflow parameter is required", self.name, value)
             else:
-                raise ParameterValueError("the attribute 'value' must be set for non optional parameters", self.name, value)
+                raise ParameterValueError(
+                    "the attribute 'value' must be set for non optional parameters", self.name, value
+                )
 
     def to_python(self, value, app):
         try:
@@ -540,11 +555,11 @@ class BooleanToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.truevalue = input_source.get('truevalue', 'true')
-        self.falsevalue = input_source.get('falsevalue', 'false')
-        nullable = input_source.get_bool('optional', False)
+        self.truevalue = input_source.get("truevalue", "true")
+        self.falsevalue = input_source.get("falsevalue", "false")
+        nullable = input_source.get_bool("optional", False)
         self.optional = nullable
-        self.checked = input_source.get_bool('checked', None if nullable else False)
+        self.checked = input_source.get_bool("checked", None if nullable else False)
 
     def from_json(self, value, trans=None, other_values=None):
         return self.to_python(value)
@@ -571,9 +586,9 @@ class BooleanToolParameter(ToolParameter):
 
     def to_dict(self, trans, other_values=None):
         d = super().to_dict(trans)
-        d['truevalue'] = self.truevalue
-        d['falsevalue'] = self.falsevalue
-        d['optional'] = self.optional
+        d["truevalue"] = self.truevalue
+        d["falsevalue"] = self.falsevalue
+        d["optional"] = self.optional
         return d
 
     @property
@@ -601,19 +616,23 @@ class FileToolParameter(ToolParameter):
         # Middleware or proxies may encode files in special ways (TODO: this
         # should be pluggable)
         if type(value) == dict:
-            if 'session_id' in value:
+            if "session_id" in value:
                 # handle api upload
                 session_id = value["session_id"]
                 upload_store = trans.app.config.new_file_path
-                if re.match(r'^[\w-]+$', session_id) is None:
+                if re.match(r"^[\w-]+$", session_id) is None:
                     raise ValueError("Invalid session id format.")
                 local_filename = os.path.abspath(os.path.join(upload_store, session_id))
             else:
                 # handle nginx upload
                 upload_store = trans.app.config.nginx_upload_store
-                assert upload_store, "Request appears to have been processed by nginx_upload_module but Galaxy is not configured to recognize it."
-                local_filename = os.path.abspath(value['path'])
-                assert local_filename.startswith(upload_store), f"Filename provided by nginx ({local_filename}) is not in correct directory ({upload_store})."
+                assert (
+                    upload_store
+                ), "Request appears to have been processed by nginx_upload_module but Galaxy is not configured to recognize it."
+                local_filename = os.path.abspath(value["path"])
+                assert local_filename.startswith(
+                    upload_store
+                ), f"Filename provided by nginx ({local_filename}) is not in correct directory ({upload_store})."
             value = dict(filename=value["name"], local_filename=local_filename)
         return value
 
@@ -624,14 +643,14 @@ class FileToolParameter(ToolParameter):
         return "multipart/form-data"
 
     def to_json(self, value, app, use_security):
-        if value in [None, '']:
+        if value in [None, ""]:
             return None
         elif isinstance(value, str):
             return value
         elif isinstance(value, dict):
             # or should we jsonify?
             try:
-                return value['local_filename']
+                return value["local_filename"]
             except KeyError:
                 return None
         elif isinstance(value, cgi_FieldStorage):
@@ -663,9 +682,9 @@ class FTPFileToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.multiple = input_source.get_bool('multiple', True)
+        self.multiple = input_source.get_bool("multiple", True)
         self.optional = input_source.parse_optional(True)
-        self.user_ftp_dir = ''
+        self.user_ftp_dir = ""
 
     def get_initial_value(self, trans, other_values):
         if trans is not None:
@@ -680,9 +699,9 @@ class FTPFileToolParameter(ToolParameter):
         return True
 
     def to_param_dict_string(self, value, other_values=None):
-        if value == '':
-            return 'None'
-        lst = [f'{self.user_ftp_dir}{dataset}' for dataset in value]
+        if value == "":
+            return "None"
+        lst = [f"{self.user_ftp_dir}{dataset}" for dataset in value]
         if self.multiple:
             return lst
         else:
@@ -699,11 +718,11 @@ class FTPFileToolParameter(ToolParameter):
             value = [value]
         lst: List[str] = []
         for val in value:
-            if val in [None, '']:
+            if val in [None, ""]:
                 lst = []
                 break
             if isinstance(val, dict):
-                lst.append(val['name'])
+                lst.append(val["name"])
             else:
                 lst.append(val)
         if len(lst) == 0:
@@ -716,7 +735,7 @@ class FTPFileToolParameter(ToolParameter):
 
     def to_dict(self, trans, other_values=None):
         d = super().to_dict(trans)
-        d['multiple'] = self.multiple
+        d["multiple"] = self.multiple
         return d
 
 
@@ -734,7 +753,7 @@ class HiddenToolParameter(ToolParameter):
 
     def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
-        self.value = input_source.get('value')
+        self.value = input_source.get("value")
         self.hidden = True
 
     def get_initial_value(self, trans, other_values):
@@ -769,8 +788,8 @@ class ColorToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.value = input_source.get('value', '#000000')
-        self.rgb = input_source.get('rgb', False)
+        self.value = input_source.get("value", "#000000")
+        self.rgb = input_source.get("rgb", False)
 
     def get_initial_value(self, trans, other_values):
         if self.value is not None:
@@ -779,7 +798,7 @@ class ColorToolParameter(ToolParameter):
     def to_param_dict_string(self, value, other_values=None):
         if self.rgb:
             try:
-                return str(tuple(int(value.lstrip('#')[i: i + 2], 16) for i in (0, 2, 4)))
+                return str(tuple(int(value.lstrip("#")[i : i + 2], 16) for i in (0, 2, 4)))
             except Exception:
                 raise ParameterValueError(f"Failed to convert '{value}' to RGB.", self.name)
         return str(value)
@@ -800,7 +819,7 @@ class BaseURLToolParameter(HiddenToolParameter):
 
     def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
-        self.value = input_source.get('value', '')
+        self.value = input_source.get("value", "")
 
     def get_initial_value(self, trans, other_values):
         return self._get_value(trans)
@@ -861,13 +880,13 @@ class SelectToolParameter(ToolParameter):
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.multiple = input_source.get_bool('multiple', False)
+        self.multiple = input_source.get_bool("multiple", False)
         # Multiple selects are optional by default, single selection is the inverse.
         self.optional = input_source.parse_optional(self.multiple)
-        self.display = input_source.get('display', None)
-        self.separator = input_source.get('separator', ',')
+        self.display = input_source.get("display", None)
+        self.separator = input_source.get("separator", ",")
         self.legal_values = set()
-        self.dynamic_options = input_source.get('dynamic_options', None)
+        self.dynamic_options = input_source.get("dynamic_options", None)
         self.options = parse_dynamic_options(self, input_source)
         if self.options is not None:
             for validator in self.options.validators:
@@ -876,10 +895,10 @@ class SelectToolParameter(ToolParameter):
             self.static_options = input_source.parse_static_options()
             for (_, value, _) in self.static_options:
                 self.legal_values.add(value)
-        self.is_dynamic = ((self.dynamic_options is not None) or (self.options is not None))
+        self.is_dynamic = (self.dynamic_options is not None) or (self.options is not None)
 
     def _get_dynamic_options_call_other_values(self, trans, other_values):
-        call_other_values = ExpressionContext({'__trans__': trans})
+        call_other_values = ExpressionContext({"__trans__": trans})
         if other_values:
             call_other_values.parent = other_values.parent
             call_other_values.update(other_values.dict)
@@ -893,7 +912,12 @@ class SelectToolParameter(ToolParameter):
             try:
                 return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
             except Exception as e:
-                log.debug("Error determining dynamic options for parameter '%s' in tool '%s':", self.name, self.tool.id, exc_info=e)
+                log.debug(
+                    "Error determining dynamic options for parameter '%s' in tool '%s':",
+                    self.name,
+                    self.tool.id,
+                    exc_info=e,
+                )
                 return []
         else:
             return self.static_options
@@ -927,7 +951,7 @@ class SelectToolParameter(ToolParameter):
                 # we do not allow this to be the case in a dynamically
                 # generated multiple select list being set in workflow building
                 # mode we instead treat '' as 'No option Selected' (None)
-                if value == '':
+                if value == "":
                     value = None
                 else:
                     if isinstance(value, str):
@@ -939,31 +963,45 @@ class SelectToolParameter(ToolParameter):
         elif value is None:
             if self.optional:
                 return None
-            raise ParameterValueError("an invalid option (None) was selected, please verify", self.name, None, is_dynamic=self.is_dynamic)
+            raise ParameterValueError(
+                "an invalid option (None) was selected, please verify", self.name, None, is_dynamic=self.is_dynamic
+            )
         elif not legal_values:
             if self.optional and self.tool.profile < 18.09:
                 # Covers optional parameters with default values that reference other optional parameters.
                 # These will have a value but no legal_values.
                 # See https://github.com/galaxyproject/tools-iuc/pull/1842#issuecomment-394083768 for context.
                 return None
-            raise ParameterValueError("requires a value, but no legal values defined", self.name, is_dynamic=self.is_dynamic)
+            raise ParameterValueError(
+                "requires a value, but no legal values defined", self.name, is_dynamic=self.is_dynamic
+            )
         if isinstance(value, list):
             if not self.multiple:
-                raise ParameterValueError("multiple values provided but parameter is not expecting multiple values", self.name, is_dynamic=self.is_dynamic)
+                raise ParameterValueError(
+                    "multiple values provided but parameter is not expecting multiple values",
+                    self.name,
+                    is_dynamic=self.is_dynamic,
+                )
             if set(value).issubset(legal_values):
                 return value
             elif set(value).issubset(set(fallback_values.keys())):
                 return [fallback_values[v] for v in value]
             else:
-                raise ParameterValueError(f"invalid options ({','.join(set(value) - set(legal_values))!r}) were selected (valid options: {','.join(legal_values)})", self.name, is_dynamic=self.is_dynamic)
+                raise ParameterValueError(
+                    f"invalid options ({','.join(set(value) - set(legal_values))!r}) were selected (valid options: {','.join(legal_values)})",
+                    self.name,
+                    is_dynamic=self.is_dynamic,
+                )
         else:
-            value_is_none = (value == "None" and "None" not in legal_values)
+            value_is_none = value == "None" and "None" not in legal_values
             if value_is_none or not value:
                 if self.multiple:
                     if self.optional:
                         return []
                     else:
-                        raise ParameterValueError("no option was selected for non optional parameter", self.name, is_dynamic=self.is_dynamic)
+                        raise ParameterValueError(
+                            "no option was selected for non optional parameter", self.name, is_dynamic=self.is_dynamic
+                        )
             if is_runtime_value(value):
                 return None
             if value in legal_values:
@@ -973,14 +1011,23 @@ class SelectToolParameter(ToolParameter):
             elif not require_legal_value:
                 return value
             else:
-                raise ParameterValueError(f"an invalid option ({value!r}) was selected (valid options: {','.join(legal_values)})", self.name, value, is_dynamic=self.is_dynamic)
+                raise ParameterValueError(
+                    f"an invalid option ({value!r}) was selected (valid options: {','.join(legal_values)})",
+                    self.name,
+                    value,
+                    is_dynamic=self.is_dynamic,
+                )
 
     def to_param_dict_string(self, value, other_values=None):
         if value in (None, []):
             return "None"
         if isinstance(value, list):
             if not self.multiple:
-                raise ParameterValueError("multiple values provided but parameter is not expecting multiple values", self.name, is_dynamic=self.is_dynamic)
+                raise ParameterValueError(
+                    "multiple values provided but parameter is not expecting multiple values",
+                    self.name,
+                    is_dynamic=self.is_dynamic,
+                )
             value = list(map(str, value))
         else:
             value = str(value)
@@ -1049,10 +1096,10 @@ class SelectToolParameter(ToolParameter):
 
         # Get options, value.
         options = self.get_options(trans, other_values)
-        d['options'] = options
-        d['display'] = self.display
-        d['multiple'] = self.multiple
-        d['textable'] = is_runtime_context(trans, other_values)
+        d["options"] = options
+        d["display"] = self.display
+        d["multiple"] = self.multiple
+        d["textable"] = is_runtime_context(trans, other_values)
         return d
 
     def validate(self, value, trans=None):
@@ -1115,12 +1162,14 @@ class GenomeBuildParameter(SelectToolParameter):
                 # Found selected option.
                 value = option[1]
 
-        d.update({
-            'options': options,
-            'value': value,
-            'display': self.display,
-            'multiple': self.multiple,
-        })
+        d.update(
+            {
+                "options": options,
+                "value": value,
+                "display": self.display,
+                "multiple": self.multiple,
+            }
+        )
 
         return d
 
@@ -1162,9 +1211,9 @@ class SelectTagParameter(SelectToolParameter):
             # split on newline and ,
             if isinstance(value, list) or isinstance(value, str):
                 if not isinstance(value, list):
-                    value = value.split('\n')
+                    value = value.split("\n")
                 for tag_str in value:
-                    for tag in str(tag_str).split(','):
+                    for tag in str(tag_str).split(","):
                         tag = tag.strip()
                         if tag:
                             tag_list.append(tag)
@@ -1192,14 +1241,14 @@ class SelectTagParameter(SelectToolParameter):
             return []
         tags = set()
         for history_item in util.listify(history_items):
-            if hasattr(history_item, 'dataset_instances'):
+            if hasattr(history_item, "dataset_instances"):
                 for dataset in history_item.dataset_instances:
                     for tag in dataset.tags:
-                        if tag.user_tname == 'group':
+                        if tag.user_tname == "group":
                             tags.add(tag.user_value)
             else:
                 for tag in history_item.tags:
-                    if tag.user_tname == 'group':
+                    if tag.user_tname == "group":
                         tags.add(tag.user_value)
         return list(tags)
 
@@ -1228,7 +1277,7 @@ class SelectTagParameter(SelectToolParameter):
     def to_dict(self, trans, other_values=None):
         other_values = other_values or {}
         d = super().to_dict(trans, other_values=other_values)
-        d['data_ref'] = self.data_ref
+        d["data_ref"] = self.data_ref
         return d
 
 
@@ -1288,9 +1337,9 @@ class ColumnListParameter(SelectToolParameter):
             if isinstance(value, list) or isinstance(value, str):
                 column_list = []
                 if not isinstance(value, list):
-                    value = value.split('\n')
+                    value = value.split("\n")
                 for column in value:
-                    for column2 in str(column).split(','):
+                    for column2 in str(column).split(","):
                         column2 = column2.strip()
                         if column2:
                             column_list.append(column2)
@@ -1306,14 +1355,14 @@ class ColumnListParameter(SelectToolParameter):
             else:
                 value = None
         if not value and self.accept_default:
-            value = self.default_value or '1'
+            value = self.default_value or "1"
             return [value] if self.multiple else value
         return super().from_json(value, trans, other_values)
 
     @staticmethod
     def _strip_c(column):
         if isinstance(column, str):
-            if column.startswith('c') and len(column) > 1 and all(c.isdigit() for c in column[1:]):
+            if column.startswith("c") and len(column) > 1 and all(c.isdigit() for c in column[1:]):
                 column = column.strip().lower()[1:]
         return column
 
@@ -1333,23 +1382,27 @@ class ColumnListParameter(SelectToolParameter):
             if isinstance(dataset, HistoryDatasetCollectionAssociation):
                 dataset = dataset.to_hda_representative()
             if isinstance(dataset, HistoryDatasetAssociation) and self.ref_input and self.ref_input.formats:
-                direct_match, target_ext, converted_dataset = dataset.find_conversion_destination(self.ref_input.formats)
+                direct_match, target_ext, converted_dataset = dataset.find_conversion_destination(
+                    self.ref_input.formats
+                )
                 if not direct_match and target_ext:
                     if not converted_dataset:
                         raise ImplicitConversionRequired
                     else:
                         dataset = converted_dataset
             # Columns can only be identified if the dataset is ready and metadata is available
-            if not hasattr(dataset, 'metadata') or \
-                    not hasattr(dataset.metadata, 'columns') or \
-                    not dataset.metadata.columns:
+            if (
+                not hasattr(dataset, "metadata")
+                or not hasattr(dataset.metadata, "columns")
+                or not dataset.metadata.columns
+            ):
                 return []
             # Build up possible columns for this dataset
             this_column_list = []
             if self.numerical:
                 # If numerical was requested, filter columns based on metadata
                 for i, col in enumerate(dataset.metadata.column_types):
-                    if col == 'int' or col == 'float':
+                    if col == "int" or col == "float":
                         this_column_list.append(str(i + 1))
             else:
                 this_column_list = [str(i) for i in range(1, dataset.metadata.columns + 1)]
@@ -1370,12 +1423,12 @@ class ColumnListParameter(SelectToolParameter):
             try:
                 with open(dataset.get_file_name()) as f:
                     head = f.readline()
-                cnames = head.rstrip("\n\r ").split('\t')
-                column_list = [('%d' % (i + 1), 'c%d: %s' % (i + 1, x)) for i, x in enumerate(cnames)]
+                cnames = head.rstrip("\n\r ").split("\t")
+                column_list = [("%d" % (i + 1), "c%d: %s" % (i + 1, x)) for i, x in enumerate(cnames)]
                 if self.numerical:  # If numerical was requested, filter columns based on metadata
-                    if hasattr(dataset, 'metadata') and hasattr(dataset.metadata, 'column_types'):
+                    if hasattr(dataset, "metadata") and hasattr(dataset.metadata, "column_types"):
                         if len(dataset.metadata.column_types) >= len(cnames):
-                            numerics = [i for i, x in enumerate(dataset.metadata.column_types) if x in ['int', 'float']]
+                            numerics = [i for i, x in enumerate(dataset.metadata.column_types) if x in ["int", "float"]]
                             column_list = [column_list[i] for i in numerics]
             except Exception:
                 column_list = self.get_column_list(trans, other_values)
@@ -1428,8 +1481,8 @@ class ColumnListParameter(SelectToolParameter):
     def to_dict(self, trans, other_values=None):
         other_values = other_values or {}
         d = super().to_dict(trans, other_values=other_values)
-        d['data_ref'] = self.data_ref
-        d['numerical'] = self.numerical
+        d["data_ref"] = self.data_ref
+        d["numerical"] = self.numerical
         return d
 
 
@@ -1480,47 +1533,57 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     def __init__(self, tool, input_source, context=None):
         def recurse_option_elems(cur_options, option_elems):
             for option_elem in option_elems:
-                selected = string_as_bool(option_elem.get('selected', False))
-                cur_options.append({'name': option_elem.get('name'), 'value': option_elem.get('value'), 'options': [], 'selected': selected})
-                recurse_option_elems(cur_options[-1]['options'], option_elem.findall('option'))
+                selected = string_as_bool(option_elem.get("selected", False))
+                cur_options.append(
+                    {
+                        "name": option_elem.get("name"),
+                        "value": option_elem.get("value"),
+                        "options": [],
+                        "selected": selected,
+                    }
+                )
+                recurse_option_elems(cur_options[-1]["options"], option_elem.findall("option"))
 
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
         # TODO: abstract XML out of here - so non-XML InputSources can
         # specify DrillDown parameters.
         elem = input_source.elem()
-        self.multiple = string_as_bool(elem.get('multiple', False))
-        self.display = elem.get('display', None)
-        self.hierarchy = elem.get('hierarchy', 'exact')  # exact or recurse
-        self.separator = elem.get('separator', ',')
-        from_file = elem.get('from_file', None)
+        self.multiple = string_as_bool(elem.get("multiple", False))
+        self.display = elem.get("display", None)
+        self.hierarchy = elem.get("hierarchy", "exact")  # exact or recurse
+        self.separator = elem.get("separator", ",")
+        from_file = elem.get("from_file", None)
         if from_file:
             if not os.path.isabs(from_file):
                 from_file = os.path.join(tool.app.config.tool_data_path, from_file)
             elem = XML(f"<root>{open(from_file).read()}</root>")
-        self.dynamic_options = elem.get('dynamic_options', None)
+        self.dynamic_options = elem.get("dynamic_options", None)
         if self.dynamic_options:
             self.is_dynamic = True
         self.options = []
         self.filtered: Dict[str, Any] = {}
-        if elem.find('filter'):
+        if elem.find("filter"):
             self.is_dynamic = True
-            for filter in elem.findall('filter'):
+            for filter in elem.findall("filter"):
                 # currently only filtering by metadata key matching input file is allowed
-                if filter.get('type') == 'data_meta':
-                    if filter.get('data_ref') not in self.filtered:
-                        self.filtered[filter.get('data_ref')] = {}
-                    if filter.get('meta_key') not in self.filtered[filter.get('data_ref')]:
-                        self.filtered[filter.get('data_ref')][filter.get('meta_key')] = {}
-                    if filter.get('value') not in self.filtered[filter.get('data_ref')][filter.get('meta_key')]:
-                        self.filtered[filter.get('data_ref')][filter.get('meta_key')][filter.get('value')] = []
-                    recurse_option_elems(self.filtered[filter.get('data_ref')][filter.get('meta_key')][filter.get('value')], filter.find('options').findall('option'))
+                if filter.get("type") == "data_meta":
+                    if filter.get("data_ref") not in self.filtered:
+                        self.filtered[filter.get("data_ref")] = {}
+                    if filter.get("meta_key") not in self.filtered[filter.get("data_ref")]:
+                        self.filtered[filter.get("data_ref")][filter.get("meta_key")] = {}
+                    if filter.get("value") not in self.filtered[filter.get("data_ref")][filter.get("meta_key")]:
+                        self.filtered[filter.get("data_ref")][filter.get("meta_key")][filter.get("value")] = []
+                    recurse_option_elems(
+                        self.filtered[filter.get("data_ref")][filter.get("meta_key")][filter.get("value")],
+                        filter.find("options").findall("option"),
+                    )
         elif not self.dynamic_options:
-            recurse_option_elems(self.options, elem.find('options').findall('option'))
+            recurse_option_elems(self.options, elem.find("options").findall("option"))
 
     def _get_options_from_code(self, trans=None, value=None, other_values=None):
         assert self.dynamic_options, Exception("dynamic_options was not specifed")
-        call_other_values = ExpressionContext({'__trans__': trans, '__value__': value})
+        call_other_values = ExpressionContext({"__trans__": trans, "__value__": value})
         if other_values:
             call_other_values.parent = other_values.parent
             call_other_values.update(other_values.dict)
@@ -1538,12 +1601,16 @@ class DrillDownSelectToolParameter(SelectToolParameter):
                 options = []
             for filter_key, filter_value in self.filtered.items():
                 dataset = other_values.get(filter_key)
-                if dataset.__class__.__name__.endswith("DatasetFilenameWrapper"):  # this is a bad way to check for this, but problems importing class (due to circular imports?)
+                if dataset.__class__.__name__.endswith(
+                    "DatasetFilenameWrapper"
+                ):  # this is a bad way to check for this, but problems importing class (due to circular imports?)
                     dataset = dataset.dataset
                 if dataset:
                     for meta_key, meta_dict in filter_value.items():
-                        if hasattr(dataset, 'metadata') and hasattr(dataset.metadata, 'spec'):
-                            check_meta_val = dataset.metadata.spec[meta_key].param.to_string(dataset.metadata.get(meta_key))
+                        if hasattr(dataset, "metadata") and hasattr(dataset.metadata, "spec"):
+                            check_meta_val = dataset.metadata.spec[meta_key].param.to_string(
+                                dataset.metadata.get(meta_key)
+                            )
                             if check_meta_val in meta_dict:
                                 options.extend(meta_dict[check_meta_val])
             return options
@@ -1552,8 +1619,9 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     def get_legal_values(self, trans, other_values, value):
         def recurse_options(legal_values, options):
             for option in options:
-                legal_values.append(option['value'])
-                recurse_options(legal_values, option['options'])
+                legal_values.append(option["value"])
+                recurse_options(legal_values, option["options"])
+
         legal_values: List[str] = []
         recurse_options(legal_values, self.get_options(trans=trans, other_values=other_values))
         return legal_values
@@ -1563,7 +1631,7 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         legal_values = self.get_legal_values(trans, other_values, value)
         if not legal_values and trans.workflow_building_mode:
             if self.multiple:
-                if value == '':  # No option selected
+                if value == "":  # No option selected
                     value = None
                 else:
                     value = value.split("\n")
@@ -1577,11 +1645,17 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         if not isinstance(value, list):
             value = [value]
         if len(value) > 1 and not self.multiple:
-            raise ParameterValueError("multiple values provided but parameter is not expecting multiple values", self.name)
+            raise ParameterValueError(
+                "multiple values provided but parameter is not expecting multiple values", self.name
+            )
         rval = []
         for val in value:
             if val not in legal_values:
-                raise ParameterValueError(f"an invalid option ({val!r}) was selected (valid options: {','.join(legal_values)})", self.name, val)
+                raise ParameterValueError(
+                    f"an invalid option ({val!r}) was selected (valid options: {','.join(legal_values)})",
+                    self.name,
+                    val,
+                )
             rval.append(val)
         return rval
 
@@ -1591,18 +1665,18 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         def get_options_list(value):
             def get_base_option(value, options):
                 for option in options:
-                    if value == option['value']:
+                    if value == option["value"]:
                         return option
-                    rval = get_base_option(value, option['options'])
+                    rval = get_base_option(value, option["options"])
                     if rval:
                         return rval
                 return None  # not found
 
             def recurse_option(option_list, option):
-                if not option['options']:
-                    option_list.append(option['value'])
+                if not option["options"]:
+                    option_list.append(option["value"])
                 else:
-                    for opt in option['options']:
+                    for opt in option["options"]:
                         recurse_option(option_list, opt)
 
             rval: List[str] = []
@@ -1619,7 +1693,9 @@ class DrillDownSelectToolParameter(SelectToolParameter):
                 options = get_options_list(val)
                 rval.extend(options)
         if len(rval) > 1 and not self.multiple:
-            raise ParameterValueError("multiple values provided but parameter is not expecting multiple values", self.name)
+            raise ParameterValueError(
+                "multiple values provided but parameter is not expecting multiple values", self.name
+            )
         rval = self.separator.join(rval)
         if self.tool is None or self.tool.options.sanitize:
             if self.sanitizer:
@@ -1631,9 +1707,10 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     def get_initial_value(self, trans, other_values):
         def recurse_options(initial_values, options):
             for option in options:
-                if option['selected']:
-                    initial_values.append(option['value'])
-                recurse_options(initial_values, option['options'])
+                if option["selected"]:
+                    initial_values.append(option["value"])
+                recurse_options(initial_values, option["options"])
+
         # More working around dynamic options for workflow
         options = self.get_options(trans=trans, other_values=other_values)
         if not options:
@@ -1647,12 +1724,13 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     def to_text(self, value):
         def get_option_display(value, options):
             for option in options:
-                if value == option['value']:
-                    return option['name']
-                rval = get_option_display(value, option['options'])
+                if value == option["value"]:
+                    return option["name"]
+                rval = get_option_display(value, option["options"])
                 if rval:
                     return rval
             return None  # not found
+
         if not value:
             value = []
         elif not isinstance(value, list):
@@ -1685,9 +1763,9 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         other_values = other_values or {}
         # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
         d = ToolParameter.to_dict(self, trans)
-        d['options'] = self.get_options(trans=trans, other_values=other_values)
-        d['display'] = self.display
-        d['multiple'] = self.multiple
+        d["options"] = self.get_options(trans=trans, other_values=other_values)
+        d["display"] = self.display
+        d["multiple"] = self.multiple
         return d
 
 
@@ -1697,8 +1775,8 @@ class BaseDataToolParameter(ToolParameter):
 
     def __init__(self, tool, input_source, trans):
         super().__init__(tool, input_source)
-        self.min = input_source.get('min')
-        self.max = input_source.get('max')
+        self.min = input_source.get("min")
+        self.max = input_source.get("max")
         if self.min:
             try:
                 self.min = int(self.min)
@@ -1719,16 +1797,19 @@ class BaseDataToolParameter(ToolParameter):
             else:
                 # This occurs for things such as unit tests
                 import galaxy.datatypes.registry
+
                 self.datatypes_registry = galaxy.datatypes.registry.Registry()
                 self.datatypes_registry.load_datatypes()
         else:
-            self.datatypes_registry = self.tool.app.datatypes_registry  # can be None if self.tool.app is a ValidationContext
+            self.datatypes_registry = (
+                self.tool.app.datatypes_registry
+            )  # can be None if self.tool.app is a ValidationContext
 
     def _parse_formats(self, trans, input_source):
         """
         Build list of classes for supported data formats
         """
-        self.extensions = input_source.get('format', 'data').split(",")
+        self.extensions = input_source.get("format", "data").split(",")
         formats = []
         if self.datatypes_registry:  # This may be None when self.tool.app is a ValidationContext
             normalized_extensions = [extension.strip().lower() for extension in self.extensions]
@@ -1737,7 +1818,9 @@ class BaseDataToolParameter(ToolParameter):
                 if datatype is not None:
                     formats.append(datatype)
                 else:
-                    log.warning(f"Datatype class not found for extension '{extension}', which is used in the 'format' attribute of parameter '{self.name}'")
+                    log.warning(
+                        f"Datatype class not found for extension '{extension}', which is used in the 'format' attribute of parameter '{self.name}'"
+                    )
         self.formats = formats
 
     def _parse_options(self, input_source):
@@ -1748,12 +1831,12 @@ class BaseDataToolParameter(ToolParameter):
         self.options = parse_dynamic_options(self, input_source)
         if self.options:
             # TODO: Abstract away XML handling here.
-            options_elem = input_source.elem().find('options')
-            self.options_filter_attribute = options_elem.get('options_filter_attribute', None)
+            options_elem = input_source.elem().find("options")
+            self.options_filter_attribute = options_elem.get("options_filter_attribute", None)
         self.is_dynamic = self.options is not None
 
     def get_initial_value(self, trans, other_values):
-        if trans.workflow_building_mode is workflow_building_modes.ENABLED or trans.app.name == 'tool_shed':
+        if trans.workflow_building_mode is workflow_building_modes.ENABLED or trans.app.name == "tool_shed":
             return RuntimeValue()
         if self.optional:
             return None
@@ -1775,73 +1858,81 @@ class BaseDataToolParameter(ToolParameter):
     def to_json(self, value, app, use_security):
         def single_to_json(value):
             src = None
-            if isinstance(value, dict) and 'src' in value and 'id' in value:
+            if isinstance(value, dict) and "src" in value and "id" in value:
                 return value
             elif isinstance(value, DatasetCollectionElement):
-                src = 'dce'
+                src = "dce"
             elif isinstance(value, HistoryDatasetCollectionAssociation):
-                src = 'hdca'
+                src = "hdca"
             elif isinstance(value, LibraryDatasetDatasetAssociation):
-                src = 'ldda'
-            elif isinstance(value, HistoryDatasetAssociation) or hasattr(value, 'id'):
+                src = "ldda"
+            elif isinstance(value, HistoryDatasetAssociation) or hasattr(value, "id"):
                 # hasattr 'id' fires a query on persistent objects after a flush so better
                 # to do the isinstance check. Not sure we need the hasattr check anymore - it'd be
                 # nice to drop it.
-                src = 'hda'
+                src = "hda"
             if src is not None:
                 object_id = cached_id(value)
-                return {'id': app.security.encode_id(object_id) if use_security else object_id, 'src': src}
+                return {"id": app.security.encode_id(object_id) if use_security else object_id, "src": src}
 
-        if value not in [None, '', 'None']:
+        if value not in [None, "", "None"]:
             if isinstance(value, list) and len(value) > 0:
                 values = [single_to_json(v) for v in value]
             else:
                 values = [single_to_json(value)]
-            return {'values': values}
+            return {"values": values}
         return None
 
     def to_python(self, value, app):
         def single_to_python(value):
-            if isinstance(value, dict) and 'src' in value:
-                id = value['id'] if isinstance(value['id'], int) else app.security.decode_id(value['id'])
-                if value['src'] == 'dce':
+            if isinstance(value, dict) and "src" in value:
+                id = value["id"] if isinstance(value["id"], int) else app.security.decode_id(value["id"])
+                if value["src"] == "dce":
                     return app.model.context.query(DatasetCollectionElement).get(id)
-                elif value['src'] == 'hdca':
+                elif value["src"] == "hdca":
                     return app.model.context.query(HistoryDatasetCollectionAssociation).get(id)
-                elif value['src'] == 'ldda':
+                elif value["src"] == "ldda":
                     return app.model.context.query(LibraryDatasetDatasetAssociation).get(id)
                 else:
                     return app.model.context.query(HistoryDatasetAssociation).get(id)
 
-        if isinstance(value, dict) and 'values' in value:
-            if hasattr(self, 'multiple') and self.multiple is True:
-                return [single_to_python(v) for v in value['values']]
-            elif len(value['values']) > 0:
-                return single_to_python(value['values'][0])
+        if isinstance(value, dict) and "values" in value:
+            if hasattr(self, "multiple") and self.multiple is True:
+                return [single_to_python(v) for v in value["values"]]
+            elif len(value["values"]) > 0:
+                return single_to_python(value["values"][0])
 
         # Handle legacy string values potentially stored in databases
-        none_values = [None, '', 'None']
+        none_values = [None, "", "None"]
         if value in none_values:
             return None
-        if isinstance(value, str) and value.find(',') > -1:
-            return [app.model.context.query(HistoryDatasetAssociation).get(int(v)) for v in value.split(',') if v not in none_values]
+        if isinstance(value, str) and value.find(",") > -1:
+            return [
+                app.model.context.query(HistoryDatasetAssociation).get(int(v))
+                for v in value.split(",")
+                if v not in none_values
+            ]
         elif str(value).startswith("__collection_reduce__|"):
-            decoded_id = str(value)[len("__collection_reduce__|"):]
+            decoded_id = str(value)[len("__collection_reduce__|") :]
             if not decoded_id.isdigit():
                 decoded_id = app.security.decode_id(decoded_id)
             return app.model.context.query(HistoryDatasetCollectionAssociation).get(int(decoded_id))
         elif str(value).startswith("dce:"):
-            return app.model.context.query(DatasetCollectionElement).get(int(value[len("dce:"):]))
+            return app.model.context.query(DatasetCollectionElement).get(int(value[len("dce:") :]))
         elif str(value).startswith("hdca:"):
-            return app.model.context.query(HistoryDatasetCollectionAssociation).get(int(value[len("hdca:"):]))
+            return app.model.context.query(HistoryDatasetCollectionAssociation).get(int(value[len("hdca:") :]))
         else:
             return app.model.context.query(HistoryDatasetAssociation).get(int(value))
 
     def validate(self, value, trans=None):
-
         def do_validate(v):
             for validator in self.validators:
-                if validator.requires_dataset_metadata and v and hasattr(v, 'dataset') and v.dataset.state != Dataset.states.OK:
+                if (
+                    validator.requires_dataset_metadata
+                    and v
+                    and hasattr(v, "dataset")
+                    and v.dataset.state != Dataset.states.OK
+                ):
                     return
                 else:
                     validator.validate(v, trans)
@@ -1894,26 +1985,38 @@ class DataToolParameter(BaseDataToolParameter):
         super().__init__(tool, input_source, trans)
         self.load_contents = int(input_source.get("load_contents", 0))
         # Add metadata validator
-        if not input_source.get_bool('no_validation', False):
+        if not input_source.get_bool("no_validation", False):
             self.validators.append(validation.MetadataValidator())
         self._parse_formats(trans, input_source)
         tag = input_source.get("tag")
-        self.multiple = input_source.get_bool('multiple', False)
+        self.multiple = input_source.get_bool("multiple", False)
         if not self.multiple and (self.min is not None):
-            raise ParameterValueError("cannot specify 'min' property on single data parameter. Set multiple=\"true\" to enable this option", self.name)
+            raise ParameterValueError(
+                "cannot specify 'min' property on single data parameter. Set multiple=\"true\" to enable this option",
+                self.name,
+            )
         if not self.multiple and (self.max is not None):
-            raise ParameterValueError("cannot specify 'max' property on single data parameter. Set multiple=\"true\" to enable this option", self.name)
+            raise ParameterValueError(
+                "cannot specify 'max' property on single data parameter. Set multiple=\"true\" to enable this option",
+                self.name,
+            )
         self.tag = tag
         self.is_dynamic = True
         self._parse_options(input_source)
         # Load conversions required for the dataset input
         self.conversions = []
         for name, conv_extension in input_source.parse_conversion_tuples():
-            assert None not in [name, conv_extension], f'A name ({name}) and type ({conv_extension}) are required for explicit conversion'
+            assert None not in [
+                name,
+                conv_extension,
+            ], f"A name ({name}) and type ({conv_extension}) are required for explicit conversion"
             if self.datatypes_registry:
                 conv_type = self.datatypes_registry.get_datatype_by_extension(conv_extension.lower())
                 if conv_type is None:
-                    raise ParameterValueError(f"datatype class not found for extension '{conv_type}', which is used as 'type' attribute in conversion of data parameter", self.name)
+                    raise ParameterValueError(
+                        f"datatype class not found for extension '{conv_type}', which is used as 'type' attribute in conversion of data parameter",
+                        self.name,
+                    )
                 self.conversions.append((name, conv_extension, [conv_type]))
 
     def from_json(self, value, trans, other_values=None):
@@ -1922,9 +2025,9 @@ class DataToolParameter(BaseDataToolParameter):
             return None
         if not value and not self.optional:
             raise ParameterValueError("specify a dataset of the required format / build for parameter", self.name)
-        if value in [None, "None", '']:
+        if value in [None, "None", ""]:
             return None
-        if isinstance(value, dict) and 'values' in value:
+        if isinstance(value, dict) and "values" in value:
             value = self.to_python(value, trans.app)
         if isinstance(value, str) and value.find(",") > 0:
             value = [int(value_part) for value_part in value.split(",")]
@@ -1932,25 +2035,28 @@ class DataToolParameter(BaseDataToolParameter):
         if isinstance(value, list):
             found_hdca = False
             for single_value in value:
-                if isinstance(single_value, dict) and 'src' in single_value and 'id' in single_value:
-                    if single_value['src'] == 'hda':
-                        decoded_id = trans.security.decode_id(single_value['id'])
+                if isinstance(single_value, dict) and "src" in single_value and "id" in single_value:
+                    if single_value["src"] == "hda":
+                        decoded_id = trans.security.decode_id(single_value["id"])
                         rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(decoded_id))
-                    elif single_value['src'] == 'hdca':
+                    elif single_value["src"] == "hdca":
                         found_hdca = True
-                        decoded_id = trans.security.decode_id(single_value['id'])
+                        decoded_id = trans.security.decode_id(single_value["id"])
                         rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
-                    elif single_value['src'] == 'ldda':
-                        decoded_id = trans.security.decode_id(single_value['id'])
+                    elif single_value["src"] == "ldda":
+                        decoded_id = trans.security.decode_id(single_value["id"])
                         rval.append(trans.sa_session.query(LibraryDatasetDatasetAssociation).get(decoded_id))
                     else:
                         raise ValueError(f"Unknown input source {single_value['src']} passed to job submission API.")
-                elif isinstance(single_value, (
+                elif isinstance(
+                    single_value,
+                    (
                         HistoryDatasetCollectionAssociation,
                         DatasetCollectionElement,
                         HistoryDatasetAssociation,
-                        LibraryDatasetDatasetAssociation
-                )):
+                        LibraryDatasetDatasetAssociation,
+                    ),
+                ):
                     rval.append(single_value)
                 else:
                     if len(str(single_value)) == 16:
@@ -1962,20 +2068,23 @@ class DataToolParameter(BaseDataToolParameter):
             if found_hdca:
                 for val in rval:
                     if not isinstance(val, HistoryDatasetCollectionAssociation):
-                        raise ParameterValueError("if collections are supplied to multiple data input parameter, only collections may be used", self.name)
+                        raise ParameterValueError(
+                            "if collections are supplied to multiple data input parameter, only collections may be used",
+                            self.name,
+                        )
         elif isinstance(value, (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation)):
             rval.append(value)
-        elif isinstance(value, dict) and 'src' in value and 'id' in value:
-            if value['src'] == 'hda':
-                decoded_id = trans.security.decode_id(value['id'])
+        elif isinstance(value, dict) and "src" in value and "id" in value:
+            if value["src"] == "hda":
+                decoded_id = trans.security.decode_id(value["id"])
                 rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(decoded_id))
-            elif value['src'] == 'hdca':
-                decoded_id = trans.security.decode_id(value['id'])
+            elif value["src"] == "hdca":
+                decoded_id = trans.security.decode_id(value["id"])
                 rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
             else:
                 raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
         elif str(value).startswith("__collection_reduce__|"):
-            encoded_ids = [v[len("__collection_reduce__|"):] for v in str(value).split(",")]
+            encoded_ids = [v[len("__collection_reduce__|") :] for v in str(value).split(",")]
             decoded_ids = map(trans.security.decode_id, encoded_ids)
             rval = []
             for decoded_id in decoded_ids:
@@ -1992,7 +2101,9 @@ class DataToolParameter(BaseDataToolParameter):
                 if hasattr(v, "deleted") and v.deleted:
                     raise ParameterValueError("the previously selected dataset has been deleted.", self.name)
                 elif hasattr(v, "dataset") and v.dataset.state in [Dataset.states.ERROR, Dataset.states.DISCARDED]:
-                    raise ParameterValueError("the previously selected dataset has entered an unusable state", self.name)
+                    raise ParameterValueError(
+                        "the previously selected dataset has entered an unusable state", self.name
+                    )
                 elif hasattr(v, "dataset"):
                     match = dataset_matcher.hda_match(v)
                     if match and match.implicit_conversion:
@@ -2031,7 +2142,12 @@ class DataToolParameter(BaseDataToolParameter):
             return []
 
     def converter_safe(self, other_values, trans):
-        if self.tool is None or self.tool.has_multiple_pages or not hasattr(trans, 'workflow_building_mode') or trans.workflow_building_mode:
+        if (
+            self.tool is None
+            or self.tool.has_multiple_pages
+            or not hasattr(trans, "workflow_building_mode")
+            or trans.workflow_building_mode
+        ):
             return False
         if other_values is None:
             return True  # we don't know other values, so we can't check, assume ok
@@ -2039,8 +2155,15 @@ class DataToolParameter(BaseDataToolParameter):
 
         def visitor(prefix, input, value, parent=None):
             if isinstance(input, SelectToolParameter) and self.name in input.get_dependencies():
-                if input.is_dynamic and (input.dynamic_options or (not input.dynamic_options and not input.options) or not input.options.converter_safe):
-                    converter_safe[0] = False  # This option does not allow for conversion, i.e. uses contents of dataset file to generate options
+                if input.is_dynamic and (
+                    input.dynamic_options
+                    or (not input.dynamic_options and not input.options)
+                    or not input.options.converter_safe
+                ):
+                    converter_safe[
+                        0
+                    ] = False  # This option does not allow for conversion, i.e. uses contents of dataset file to generate options
+
         self.tool.visit_inputs(other_values, visitor)
         return False not in converter_safe
 
@@ -2057,7 +2180,7 @@ class DataToolParameter(BaseDataToolParameter):
         else:
             call_attribute = False
         ref = value
-        for attribute in options_filter_attribute.split('.'):
+        for attribute in options_filter_attribute.split("."):
             ref = getattr(ref, attribute)
         if call_attribute:
             ref = ref()
@@ -2068,20 +2191,22 @@ class DataToolParameter(BaseDataToolParameter):
         # create dictionary and fill default parameters
         d = super().to_dict(trans)
         extensions = self.extensions
-        all_edam_formats = self.datatypes_registry.edam_formats if hasattr(self.datatypes_registry, 'edam_formats') else {}
-        all_edam_data = self.datatypes_registry.edam_data if hasattr(self.datatypes_registry, 'edam_formats') else {}
+        all_edam_formats = (
+            self.datatypes_registry.edam_formats if hasattr(self.datatypes_registry, "edam_formats") else {}
+        )
+        all_edam_data = self.datatypes_registry.edam_data if hasattr(self.datatypes_registry, "edam_formats") else {}
         edam_formats = [all_edam_formats.get(ext, None) for ext in extensions]
         edam_data = [all_edam_data.get(ext, None) for ext in extensions]
 
-        d['extensions'] = extensions
-        d['edam'] = {'edam_formats': edam_formats, 'edam_data': edam_data}
-        d['multiple'] = self.multiple
+        d["extensions"] = extensions
+        d["edam"] = {"edam_formats": edam_formats, "edam_data": edam_data}
+        d["multiple"] = self.multiple
         if self.multiple:
             # For consistency, should these just always be in the dict?
-            d['min'] = self.min
-            d['max'] = self.max
-        d['options'] = {'hda': [], 'hdca': []}
-        d['tag'] = self.tag
+            d["min"] = self.min
+            d["max"] = self.max
+        d["options"] = {"hda": [], "hdca": []}
+        d["tag"] = self.tag
 
         # return dictionary without options if context is unavailable
         history = trans.history
@@ -2096,12 +2221,12 @@ class DataToolParameter(BaseDataToolParameter):
         # build and append a new select option
         def append(list, hda, name, src, keep=False, subcollection_type=None):
             value = {
-                'id': trans.security.encode_id(hda.id),
-                'hid': hda.hid if hda.hid is not None else -1,
-                'name': name,
-                'tags': [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hda.tags],
-                'src': src,
-                'keep': keep
+                "id": trans.security.encode_id(hda.id),
+                "hid": hda.hid if hda.hid is not None else -1,
+                "name": name,
+                "tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hda.tags],
+                "src": src,
+                "keep": keep,
             }
             if subcollection_type:
                 value["map_over_type"] = subcollection_type
@@ -2115,17 +2240,17 @@ class DataToolParameter(BaseDataToolParameter):
             if match:
                 m = match.hda
                 hda_list = [h for h in hda_list if h != m and h != hda]
-                m_name = f'{match.original_hda.name} (as {match.target_ext})' if match.implicit_conversion else m.name
-                append(d['options']['hda'], m, m_name, 'hda')
+                m_name = f"{match.original_hda.name} (as {match.target_ext})" if match.implicit_conversion else m.name
+                append(d["options"]["hda"], m, m_name, "hda")
         for hda in hda_list:
-            if hasattr(hda, 'hid'):
+            if hasattr(hda, "hid"):
                 if hda.deleted:
-                    hda_state = 'deleted'
+                    hda_state = "deleted"
                 elif not hda.visible:
-                    hda_state = 'hidden'
+                    hda_state = "hidden"
                 else:
-                    hda_state = 'unavailable'
-                append(d['options']['hda'], hda, f'({hda_state}) {hda.name}', 'hda', True)
+                    hda_state = "unavailable"
+                append(d["options"]["hda"], hda, f"({hda_state}) {hda.name}", "hda", True)
 
         # add dataset collections
         dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
@@ -2133,7 +2258,7 @@ class DataToolParameter(BaseDataToolParameter):
             match = dataset_collection_matcher.hdca_match(hdca)
             if match:
                 subcollection_type = None
-                if multiple and hdca.collection.collection_type != 'list':
+                if multiple and hdca.collection.collection_type != "list":
                     collection_type_description = self._history_query(trans).can_map_over(hdca)
                     if collection_type_description:
                         subcollection_type = collection_type_description.collection_type
@@ -2143,12 +2268,12 @@ class DataToolParameter(BaseDataToolParameter):
                 name = hdca.name
                 if match.implicit_conversion:
                     name = f"{name} (with implicit datatype conversion)"
-                append(d['options']['hdca'], hdca, name, 'hdca', subcollection_type=subcollection_type)
+                append(d["options"]["hdca"], hdca, name, "hdca", subcollection_type=subcollection_type)
                 continue
 
         # sort both lists
-        d['options']['hda'] = sorted(d['options']['hda'], key=lambda k: k.get('hid', -1), reverse=True)
-        d['options']['hdca'] = sorted(d['options']['hdca'], key=lambda k: k.get('hid', -1), reverse=True)
+        d["options"]["hda"] = sorted(d["options"]["hda"], key=lambda k: k.get("hid", -1), reverse=True)
+        d["options"]["hdca"] = sorted(d["options"]["hdca"], key=lambda k: k.get("hid", -1), reverse=True)
 
         # return final dictionary
         return d
@@ -2161,8 +2286,7 @@ class DataToolParameter(BaseDataToolParameter):
 
 
 class DataCollectionToolParameter(BaseDataToolParameter):
-    """
-    """
+    """ """
 
     def __init__(self, tool, input_source, trans=None):
         input_source = ensure_input_source(input_source)
@@ -2187,7 +2311,9 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         return history_query.HistoryQuery.from_parameter(self, dataset_collection_type_descriptions)
 
     def match_collections(self, trans, history, dataset_collection_matcher):
-        dataset_collections = trans.app.dataset_collection_manager.history_dataset_collections(history, self._history_query(trans))
+        dataset_collections = trans.app.dataset_collection_manager.history_dataset_collections(
+            history, self._history_query(trans)
+        )
 
         for dataset_collection_instance in dataset_collections:
             match = dataset_collection_matcher.hdca_match(dataset_collection_instance)
@@ -2213,7 +2339,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
             raise ParameterValueError("specify a dataset collection of the correct type", self.name)
         if value in [None, "None"]:
             return None
-        if isinstance(value, dict) and 'values' in value:
+        if isinstance(value, dict) and "values" in value:
             value = self.to_python(value, trans.app)
         if isinstance(value, str) and value.find(",") > 0:
             value = [int(value_part) for value_part in value.split(",")]
@@ -2224,22 +2350,28 @@ class DataCollectionToolParameter(BaseDataToolParameter):
             # a DatasetCollectionElement instead of a
             # HistoryDatasetCollectionAssociation.
             rval = value
-        elif isinstance(value, dict) and 'src' in value and 'id' in value:
-            if value['src'] == 'hdca':
-                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(trans.security.decode_id(value['id']))
+        elif isinstance(value, dict) and "src" in value and "id" in value:
+            if value["src"] == "hdca":
+                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(
+                    trans.security.decode_id(value["id"])
+                )
         elif isinstance(value, list):
             if len(value) > 0:
                 value = value[0]
-                if isinstance(value, dict) and 'src' in value and 'id' in value:
-                    if value['src'] == 'hdca':
-                        rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(trans.security.decode_id(value['id']))
-                    elif value['src'] == 'dce':
-                        rval = trans.sa_session.query(DatasetCollectionElement).get(trans.security.decode_id(value['id']))
+                if isinstance(value, dict) and "src" in value and "id" in value:
+                    if value["src"] == "hdca":
+                        rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(
+                            trans.security.decode_id(value["id"])
+                        )
+                    elif value["src"] == "dce":
+                        rval = trans.sa_session.query(DatasetCollectionElement).get(
+                            trans.security.decode_id(value["id"])
+                        )
         elif isinstance(value, str):
             if value.startswith("dce:"):
-                rval = trans.sa_session.query(DatasetCollectionElement).get(value[len("dce:"):])
+                rval = trans.sa_session.query(DatasetCollectionElement).get(value[len("dce:") :])
             elif value.startswith("hdca:"):
-                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(value[len("hdca:"):])
+                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(value[len("hdca:") :])
             else:
                 rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(value)
         if rval and isinstance(rval, HistoryDatasetCollectionAssociation):
@@ -2262,10 +2394,10 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         # create dictionary and fill default parameters
         other_values = other_values or {}
         d = super().to_dict(trans)
-        d['extensions'] = self.extensions
-        d['multiple'] = self.multiple
-        d['options'] = {'hda': [], 'hdca': [], 'dce': []}
-        d['tag'] = self.tag
+        d["extensions"] = self.extensions
+        d["multiple"] = self.multiple
+        d["options"] = {"hda": [], "hdca": [], "dce": []}
+        d["tag"] = self.tag
 
         # return dictionary without options if context is unavailable
         history = trans.history
@@ -2280,26 +2412,30 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         # append DCE
         if isinstance(other_values.get(self.name), DatasetCollectionElement):
             dce = other_values[self.name]
-            d['options']['dce'].append({
-                'id': trans.security.encode_id(dce.id),
-                'hid': None,
-                'name': dce.element_identifier,
-                'src': 'dce',
-                'tags': []
-            })
+            d["options"]["dce"].append(
+                {
+                    "id": trans.security.encode_id(dce.id),
+                    "hid": None,
+                    "name": dce.element_identifier,
+                    "src": "dce",
+                    "tags": [],
+                }
+            )
 
         # append directly matched collections
         for hdca, implicit_conversion in self.match_collections(trans, history, dataset_collection_matcher):
             name = hdca.name
             if implicit_conversion:
                 name = f"{name} (with implicit datatype conversion)"
-            d['options']['hdca'].append({
-                'id': trans.security.encode_id(hdca.id),
-                'hid': hdca.hid,
-                'name': name,
-                'src': 'hdca',
-                'tags': [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags]
-            })
+            d["options"]["hdca"].append(
+                {
+                    "id": trans.security.encode_id(hdca.id),
+                    "hid": hdca.hid,
+                    "name": name,
+                    "src": "hdca",
+                    "tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags],
+                }
+            )
 
         # append matching subcollections
         for hdca, implicit_conversion in self.match_multirun_collections(trans, history, dataset_collection_matcher):
@@ -2307,17 +2443,19 @@ class DataCollectionToolParameter(BaseDataToolParameter):
             name = hdca.name
             if implicit_conversion:
                 name = f"{name} (with implicit datatype conversion)"
-            d['options']['hdca'].append({
-                'id': trans.security.encode_id(hdca.id),
-                'hid': hdca.hid,
-                'name': name,
-                'src': 'hdca',
-                'tags': [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags],
-                'map_over_type': subcollection_type
-            })
+            d["options"]["hdca"].append(
+                {
+                    "id": trans.security.encode_id(hdca.id),
+                    "hid": hdca.hid,
+                    "name": name,
+                    "src": "hdca",
+                    "tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags],
+                    "map_over_type": subcollection_type,
+                }
+            )
 
         # sort both lists
-        d['options']['hdca'] = sorted(d['options']['hdca'], key=lambda k: k.get('hid', -1), reverse=True)
+        d["options"]["hdca"] = sorted(d["options"]["hdca"], key=lambda k: k.get("hid", -1), reverse=True)
 
         # return final dictionary
         return d
@@ -2344,7 +2482,7 @@ class LibraryDatasetToolParameter(ToolParameter):
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.multiple = input_source.get_bool('multiple', True)
+        self.multiple = input_source.get_bool("multiple", True)
 
     def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
@@ -2352,7 +2490,7 @@ class LibraryDatasetToolParameter(ToolParameter):
 
     def to_param_dict_string(self, value, other_values=None):
         if value is None:
-            return 'None'
+            return "None"
         elif self.multiple:
             return [dataset.get_file_name() for dataset in value]
         else:
@@ -2370,17 +2508,13 @@ class LibraryDatasetToolParameter(ToolParameter):
                 lda_id = app.security.encode_id(item.id) if use_security else item.id
                 lda_name = item.name
             elif isinstance(item, dict):
-                lda_id = item.get('id')
-                lda_name = item.get('name')
+                lda_id = item.get("id")
+                lda_name = item.get("name")
             else:
                 lst = []
                 break
             if lda_id is not None:
-                lst.append({
-                    'id': lda_id,
-                    'name': lda_name,
-                    'src': 'ldda'
-                })
+                lst.append({"id": lda_id, "name": lda_name, "src": "ldda"})
         if len(lst) == 0:
             return None
         else:
@@ -2403,17 +2537,21 @@ class LibraryDatasetToolParameter(ToolParameter):
             else:
                 lda_id = None
                 if isinstance(item, dict):
-                    lda_id = item.get('id')
+                    lda_id = item.get("id")
                 elif isinstance(item, str):
                     lda_id = item
                 else:
                     lst = []
                     break
-                lda = app.model.context.query(LibraryDatasetDatasetAssociation).get(lda_id if isinstance(lda_id, int) else app.security.decode_id(lda_id))
+                lda = app.model.context.query(LibraryDatasetDatasetAssociation).get(
+                    lda_id if isinstance(lda_id, int) else app.security.decode_id(lda_id)
+                )
                 if lda is not None:
                     lst.append(lda)
                 elif validate:
-                    raise ParameterValueError("one of the selected library datasets is invalid or not available anymore", self.name)
+                    raise ParameterValueError(
+                        "one of the selected library datasets is invalid or not available anymore", self.name
+                    )
         if len(lst) == 0:
             if not self.optional and validate:
                 raise ParameterValueError("invalid library dataset selected", self.name)
@@ -2423,7 +2561,7 @@ class LibraryDatasetToolParameter(ToolParameter):
 
     def to_dict(self, trans, other_values=None):
         d = super().to_dict(trans)
-        d['multiple'] = self.multiple
+        d["multiple"] = self.multiple
         return d
 
 
@@ -2531,19 +2669,23 @@ parameter_types = dict(
     library_data=LibraryDatasetToolParameter,
     rules=RulesListToolParameter,
     directory_uri=DirectoryUriToolParameter,
-    drill_down=DrillDownSelectToolParameter
+    drill_down=DrillDownSelectToolParameter,
 )
 
 
 def runtime_to_json(runtime_value):
-    if isinstance(runtime_value, ConnectedValue) or (isinstance(runtime_value, dict) and runtime_value["__class__"] == "ConnectedValue"):
+    if isinstance(runtime_value, ConnectedValue) or (
+        isinstance(runtime_value, dict) and runtime_value["__class__"] == "ConnectedValue"
+    ):
         return {"__class__": "ConnectedValue"}
     else:
         return {"__class__": "RuntimeValue"}
 
 
 def runtime_to_object(runtime_value):
-    if isinstance(runtime_value, ConnectedValue) or (isinstance(runtime_value, dict) and runtime_value["__class__"] == "ConnectedValue"):
+    if isinstance(runtime_value, ConnectedValue) or (
+        isinstance(runtime_value, dict) and runtime_value["__class__"] == "ConnectedValue"
+    ):
         return ConnectedValue()
     else:
         return RuntimeValue()
diff --git a/lib/galaxy/tools/parameters/dataset_matcher.py b/lib/galaxy/tools/parameters/dataset_matcher.py
index 9a704d25733..c7fcf12fc75 100644
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -36,7 +36,7 @@ class DatasetMatcherFactory:
             for input in tool.inputs.values():
                 self._collect_data_inputs(input)
 
-            require_public = self._tool and self._tool.tool_type == 'data_destination'
+            require_public = self._tool and self._tool.tool_type == "data_destination"
             if not require_public and self._data_inputs:
                 can_process_summary = True
                 for data_input in self._data_inputs:
@@ -58,7 +58,9 @@ class DatasetMatcherFactory:
 
         formats = self._matches_format_cache[hda_extension]
         if format not in formats:
-            datatype = galaxy.model.datatype_for_extension(hda_extension, datatypes_registry=self._trans.app.datatypes_registry)
+            datatype = galaxy.model.datatype_for_extension(
+                hda_extension, datatypes_registry=self._trans.app.datatypes_registry
+            )
             formats[format] = datatype.matches_any([format])
 
         return formats[format]
@@ -86,7 +88,7 @@ class DatasetMatcherFactory:
 
 
 class DatasetMatcher:
-    """ Utility class to aid DataToolParameter and similar classes in reasoning
+    """Utility class to aid DataToolParameter and similar classes in reasoning
     about what HDAs could match or are selected for a parameter and value.
 
     Goal here is to both encapsulate and reuse logic related to filtering,
@@ -109,7 +111,7 @@ class DatasetMatcher:
         self.filter_values = filter_values
 
     def valid_hda_match(self, hda, check_implicit_conversions=True):
-        """ Return False if this parameter can not be matched to the supplied
+        """Return False if this parameter can not be matched to the supplied
         HDA, otherwise return a description of the match (either a
         HdaDirectMatch describing a direct match or a HdaImplicitMatch
         describing an implicit conversion.)
@@ -134,7 +136,7 @@ class DatasetMatcher:
         return rval
 
     def hda_match(self, hda, check_implicit_conversions=True, ensure_visible=True):
-        """ If HDA is accessible, return information about whether it could
+        """If HDA is accessible, return information about whether it could
         match this parameter and if so how. See valid_hda_match for more
         information.
         """
@@ -143,13 +145,13 @@ class DatasetMatcher:
         if valid_state and (not ensure_visible or hda.visible):
             # If we are sending data to an external application, then we need to make sure there are no roles
             # associated with the dataset that restrict its access from "public".
-            require_public = self.tool and self.tool.tool_type == 'data_destination'
+            require_public = self.tool and self.tool.tool_type == "data_destination"
             if require_public and not self.trans.app.security_agent.dataset_is_public(dataset):
                 return False
             return self.valid_hda_match(hda, check_implicit_conversions=check_implicit_conversions)
 
     def filter(self, hda):
-        """ Filter out this value based on other values for job (if
+        """Filter out this value based on other values for job (if
         applicable).
         """
         param = self.param
@@ -157,7 +159,7 @@ class DatasetMatcher:
 
 
 class HdaDirectMatch:
-    """ Supplied HDA was a valid option directly (did not need to find implicit
+    """Supplied HDA was a valid option directly (did not need to find implicit
     conversion).
     """
 
@@ -170,7 +172,7 @@ class HdaDirectMatch:
 
 
 class HdaImplicitMatch:
-    """ Supplied HDA was a valid option directly (did not need to find implicit
+    """Supplied HDA was a valid option directly (did not need to find implicit
     conversion).
     """
 
@@ -199,7 +201,6 @@ class HdcaImplicitMatch:
 
 
 class SummaryDatasetCollectionMatcher:
-
     def __init__(self, dataset_matcher_factory, trans, dataset_matcher):
         self.dataset_matcher_factory = dataset_matcher_factory
         self._trans = trans
@@ -220,7 +221,9 @@ class SummaryDatasetCollectionMatcher:
         uses_implicit_conversion = False
         for extension in extensions:
             datatypes_registry = self._trans.app.datatypes_registry
-            direct_match, converted_ext, _ = datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension, formats)
+            direct_match, converted_ext, _ = datatypes_registry.find_conversion_destination_for_dataset_by_extensions(
+                extension, formats
+            )
             if direct_match:
                 continue
             if not converted_ext:
@@ -232,7 +235,6 @@ class SummaryDatasetCollectionMatcher:
 
 
 class DatasetCollectionMatcher:
-
     def __init__(self, trans, dataset_matcher):
         self.dataset_matcher = dataset_matcher
         self._trans = trans
@@ -277,4 +279,4 @@ class DatasetCollectionMatcher:
         return valid and (HdcaImplicitMatch() if uses_implicit_conversion else HdcaDirectMatch())
 
 
-__all__ = ('get_dataset_matcher_factory', 'set_dataset_matcher_factory', 'unset_dataset_matcher_factory')
+__all__ = ("get_dataset_matcher_factory", "set_dataset_matcher_factory", "unset_dataset_matcher_factory")
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index b10af39e191..fcd6794cc8e 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -12,11 +12,11 @@ from galaxy.model import (
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,
     MetadataFile,
-    User
+    User,
 )
 from galaxy.tools.wrappers import (
     DatasetFilenameWrapper,
-    DatasetListWrapper
+    DatasetListWrapper,
 )
 from galaxy.util import string_as_bool
 from . import validation
@@ -28,10 +28,11 @@ class Filter:
     """
     A filter takes the current options list and modifies it.
     """
+
     @classmethod
     def from_element(cls, d_option, elem):
         """Loads the proper filter by the type attribute of elem"""
-        type = elem.get('type', None)
+        type = elem.get("type", None)
         assert type is not None, "Required 'type' attribute missing from filter"
         return filter_types[type.strip()](d_option, elem)
 
@@ -69,7 +70,7 @@ class StaticValueFilter(Filter):
         column = elem.get("column", None)
         assert column is not None, "Required 'column' attribute missing from filter, when loading from file"
         self.column = d_option.column_spec_to_index(column)
-        self.keep = string_as_bool(elem.get("keep", 'True'))
+        self.keep = string_as_bool(elem.get("keep", "True"))
 
     def filter_options(self, options, trans, other_values):
         rval = []
@@ -105,7 +106,7 @@ class RegexpFilter(Filter):
         column = elem.get("column", None)
         assert column is not None, "Required 'column' attribute missing from filter, when loading from file"
         self.column = d_option.column_spec_to_index(column)
-        self.keep = string_as_bool(elem.get("keep", 'True'))
+        self.keep = string_as_bool(elem.get("keep", "True"))
 
     def filter_options(self, options, trans, other_values):
         rval = []
@@ -152,12 +153,16 @@ class DataMetaFilter(Filter):
         assert self.key is not None, "Required 'key' attribute missing from filter"
         self.column = elem.get("column", None)
         if self.column is None:
-            assert self.dynamic_option.file_fields is None and self.dynamic_option.dataset_ref_name is None, "Required 'column' attribute missing from filter, when loading from file"
+            assert (
+                self.dynamic_option.file_fields is None and self.dynamic_option.dataset_ref_name is None
+            ), "Required 'column' attribute missing from filter, when loading from file"
         else:
             self.column = d_option.column_spec_to_index(self.column)
         self.multiple = string_as_bool(elem.get("multiple", "False"))
         self.separator = elem.get("separator", ",")
-        log.error(f"data_meta.init: ref_name {self.ref_name} key {self.key} column {self.column} multiple {self.multiple} separator {self.separator}")
+        log.error(
+            f"data_meta.init: ref_name {self.ref_name} key {self.key} column {self.column} multiple {self.multiple} separator {self.separator}"
+        )
 
     def get_dependency_name(self):
         return self.ref_name
@@ -221,11 +226,7 @@ class DataMetaFilter(Filter):
             return rval
         else:
             if not self.dynamic_option.columns:
-                self.dynamic_option.columns = {
-                    "name": 0,
-                    "value": 1,
-                    "selected": 2
-                }
+                self.dynamic_option.columns = {"name": 0, "value": 1, "selected": 2}
                 self.dynamic_option.largest_index = 2
             for value in meta_value:
                 options.append((value, value, False))
@@ -258,10 +259,10 @@ class ParamValueFilter(Filter):
         column = elem.get("column", None)
         assert column is not None, "Required 'column' attribute missing from filter"
         self.column = d_option.column_spec_to_index(column)
-        self.keep = string_as_bool(elem.get("keep", 'True'))
+        self.keep = string_as_bool(elem.get("keep", "True"))
         self.ref_attribute = elem.get("ref_attribute", None)
         if self.ref_attribute:
-            self.ref_attribute = self.ref_attribute.split('.')
+            self.ref_attribute = self.ref_attribute.split(".")
         else:
             self.ref_attribute = []
 
@@ -354,7 +355,7 @@ class MultipleSplitterFilter(Filter):
         for fields in options:
             for column in self.columns:
                 for field in fields[column].split(self.separator):
-                    rval.append(fields[0:column] + [field] + fields[column + 1:])
+                    rval.append(fields[0:column] + [field] + fields[column + 1 :])
         return rval
 
 
@@ -425,8 +426,8 @@ class AdditionalValueFilter(Filter):
         add_value = []
         for _ in range(self.dynamic_option.largest_index + 1):
             add_value.append("")
-        value_col = self.dynamic_option.columns.get('value', 0)
-        name_col = self.dynamic_option.columns.get('name', value_col)
+        value_col = self.dynamic_option.columns.get("value", 0)
+        name_col = self.dynamic_option.columns.get("name", value_col)
         # Set name first, then value, in case they are the same column
         add_value[name_col] = self.name
         add_value[value_col] = self.value
@@ -460,7 +461,11 @@ class RemoveValueFilter(Filter):
         self.ref_name = elem.get("ref", None)
         self.meta_ref = elem.get("meta_ref", None)
         self.metadata_key = elem.get("key", None)
-        assert self.value is not None or self.ref_name is not None or (self.meta_ref is not None and self.metadata_key is not None), ValueError("Required 'value', or 'ref', or 'meta_ref' and 'key' attributes missing from filter")
+        assert (
+            self.value is not None
+            or self.ref_name is not None
+            or (self.meta_ref is not None and self.metadata_key is not None)
+        ), ValueError("Required 'value', or 'ref', or 'meta_ref' and 'key' attributes missing from filter")
         self.multiple = string_as_bool(elem.get("multiple", "False"))
         self.separator = elem.get("separator", ",")
 
@@ -489,11 +494,13 @@ class RemoveValueFilter(Filter):
                 data_ref = other_values.get(self.meta_ref)
                 if isinstance(data_ref, HistoryDatasetCollectionAssociation):
                     data_ref = data_ref.to_hda_representative()
-                if not isinstance(data_ref, HistoryDatasetAssociation) and not isinstance(data_ref, DatasetFilenameWrapper):
+                if not isinstance(data_ref, HistoryDatasetAssociation) and not isinstance(
+                    data_ref, DatasetFilenameWrapper
+                ):
                     return options  # cannot modify options
                 value = data_ref.metadata.get(self.metadata_key, None)
         # Default to the second column (i.e. 1) since this used to work only on options produced by the data_meta filter
-        value_col = self.dynamic_option.columns.get('value', 1)
+        value_col = self.dynamic_option.columns.get("value", 1)
         return [option for option in options if not compare_value(option[value_col], value)]
 
 
@@ -517,16 +524,18 @@ class SortByColumnFilter(Filter):
         return sorted(options, key=lambda x: x[self.column])
 
 
-filter_types = dict(data_meta=DataMetaFilter,
-                    param_value=ParamValueFilter,
-                    static_value=StaticValueFilter,
-                    regexp=RegexpFilter,
-                    unique_value=UniqueValueFilter,
-                    multiple_splitter=MultipleSplitterFilter,
-                    attribute_value_splitter=AttributeValueSplitterFilter,
-                    add_value=AdditionalValueFilter,
-                    remove_value=RemoveValueFilter,
-                    sort_by=SortByColumnFilter)
+filter_types = dict(
+    data_meta=DataMetaFilter,
+    param_value=ParamValueFilter,
+    static_value=StaticValueFilter,
+    regexp=RegexpFilter,
+    unique_value=UniqueValueFilter,
+    multiple_splitter=MultipleSplitterFilter,
+    attribute_value_splitter=AttributeValueSplitterFilter,
+    add_value=AdditionalValueFilter,
+    remove_value=RemoveValueFilter,
+    sort_by=SortByColumnFilter,
+)
 
 
 class DynamicOptions:
@@ -535,11 +544,12 @@ class DynamicOptions:
     def __init__(self, elem, tool_param):
         def load_from_parameter(from_parameter, transform_lines=None):
             obj = self.tool_param
-            for field in from_parameter.split('.'):
+            for field in from_parameter.split("."):
                 obj = getattr(obj, field)
             if transform_lines:
-                obj = eval(transform_lines, {'self': self, 'obj': obj})
+                obj = eval(transform_lines, {"self": self, "obj": obj})
             return self.parse_file_fields(obj)
+
         self.tool_param = tool_param
         self.columns = {}
         self.filters = []
@@ -553,14 +563,14 @@ class DynamicOptions:
         self.converter_safe = True
 
         # Parse the <options> tag
-        self.separator = elem.get('separator', '\t')
-        self.line_startswith = elem.get('startswith', None)
-        data_file = elem.get('from_file', None)
+        self.separator = elem.get("separator", "\t")
+        self.line_startswith = elem.get("startswith", None)
+        data_file = elem.get("from_file", None)
         self.index_file = None
         self.missing_index_file = None
-        dataset_file = elem.get('from_dataset', None)
-        from_parameter = elem.get('from_parameter', None)
-        self.tool_data_table_name = elem.get('from_data_table', None)
+        dataset_file = elem.get("from_dataset", None)
+        from_parameter = elem.get("from_parameter", None)
+        self.tool_data_table_name = elem.get("from_data_table", None)
         # Options are defined from a data table loaded by the app
         self._tool_data_table = None
         self.elem = elem
@@ -569,7 +579,9 @@ class DynamicOptions:
 
         # Options are defined by parsing tabular text data from a data file
         # on disk, a dataset, or the value of another parameter
-        if not self.tool_data_table_name and (data_file is not None or dataset_file is not None or from_parameter is not None):
+        if not self.tool_data_table_name and (
+            data_file is not None or dataset_file is not None or from_parameter is not None
+        ):
             self.parse_column_definitions(elem)
             if data_file is not None:
                 data_file = data_file.strip()
@@ -582,20 +594,20 @@ class DynamicOptions:
                     else:
                         self.missing_index_file = data_file
             elif dataset_file is not None:
-                self.meta_file_key = elem.get('meta_file_key', None)
+                self.meta_file_key = elem.get("meta_file_key", None)
                 self.dataset_ref_name = dataset_file
                 self.has_dataset_dependencies = True
                 self.converter_safe = False
             elif from_parameter is not None:
-                transform_lines = elem.get('transform_lines', None)
+                transform_lines = elem.get("transform_lines", None)
                 self.file_fields = list(load_from_parameter(from_parameter, transform_lines))
 
         # Load filters
-        for filter_elem in elem.findall('filter'):
+        for filter_elem in elem.findall("filter"):
             self.filters.append(Filter.from_element(self, filter_elem))
 
         # Load Validators
-        for validator in elem.findall('validator'):
+        for validator in elem.findall("validator"):
             self.validators.append(validation.Validator.from_element(self.tool_param, validator))
 
         if self.dataset_ref_name:
@@ -629,24 +641,24 @@ class DynamicOptions:
         return None
 
     def parse_column_definitions(self, elem):
-        for column_elem in elem.findall('column'):
-            name = column_elem.get('name', None)
+        for column_elem in elem.findall("column"):
+            name = column_elem.get("name", None)
             assert name is not None, "Required 'name' attribute missing from column def"
-            index = column_elem.get('index', None)
+            index = column_elem.get("index", None)
             assert index is not None, "Required 'index' attribute missing from column def"
             index = int(index)
             self.columns[name] = index
             if index > self.largest_index:
                 self.largest_index = index
-        assert 'value' in self.columns, "Required 'value' column missing from column def"
-        if 'name' not in self.columns:
-            self.columns['name'] = self.columns['value']
+        assert "value" in self.columns, "Required 'value' column missing from column def"
+        if "name" not in self.columns:
+            self.columns["name"] = self.columns["value"]
 
     def parse_file_fields(self, reader):
         rval = []
         field_count = None
         for line in reader:
-            if line.startswith('#') or (self.line_startswith and not line.startswith(self.line_startswith)):
+            if line.startswith("#") or (self.line_startswith and not line.startswith(self.line_startswith)):
                 continue
             line = line.rstrip("\n\r")
             if line:
@@ -660,8 +672,10 @@ class DynamicOptions:
                         except AttributeError:
                             name = "a configuration file"
                         # Perhaps this should be an error, but even a warning is useful.
-                        log.warning("Inconsistent number of fields (%i vs %i) in %s using separator %r, check line: %r" %
-                                    (field_count, len(fields), name, self.separator, line))
+                        log.warning(
+                            "Inconsistent number of fields (%i vs %i) in %s using separator %r, check line: %r"
+                            % (field_count, len(fields), name, self.separator, line)
+                        )
                     rval.append(fields)
         return rval
 
@@ -684,10 +698,14 @@ class DynamicOptions:
             try:
                 datasets = _get_ref_data(other_values, self.dataset_ref_name)
             except KeyError:  # no such dataset
-                log.warning(f"Parameter {self.tool_param.name}: could not create dynamic options from_dataset: {self.dataset_ref_name} unknown")
+                log.warning(
+                    f"Parameter {self.tool_param.name}: could not create dynamic options from_dataset: {self.dataset_ref_name} unknown"
+                )
                 return []
             except ValueError:  # not a valid dataset
-                log.warning(f"Parameter {self.tool_param.name}: could not create dynamic options from_dataset: {self.dataset_ref_name} not a data or collection parameter")
+                log.warning(
+                    f"Parameter {self.tool_param.name}: could not create dynamic options from_dataset: {self.dataset_ref_name} not a data or collection parameter"
+                )
                 return []
 
             options = []
@@ -696,12 +714,14 @@ class DynamicOptions:
                 if meta_file_key:
                     dataset = getattr(dataset.metadata, meta_file_key, None)
                     if not isinstance(dataset, MetadataFile):
-                        log.warning(f"The meta_file_key `{meta_file_key}` was invalid or the referred object was not a valid file type metadata!")
+                        log.warning(
+                            f"The meta_file_key `{meta_file_key}` was invalid or the referred object was not a valid file type metadata!"
+                        )
                         continue
-                    if getattr(dataset, 'purged', False) or getattr(dataset, 'deleted', False):
+                    if getattr(dataset, "purged", False) or getattr(dataset, "deleted", False):
                         log.warning(f"The metadata file inferred from key `{meta_file_key}` was deleted!")
                         continue
-                if not hasattr(dataset, 'file_name'):
+                if not hasattr(dataset, "file_name"):
                     continue
                 # Ensure parsing dynamic options does not consume more than a megabyte worth memory.
                 path = dataset.file_name
@@ -729,7 +749,7 @@ class DynamicOptions:
         Return a list of fields with column 'value' matching provided value.
         """
         rval = []
-        val_index = self.columns['value']
+        val_index = self.columns["value"]
         for fields in self.get_fields(trans, other_values):
             if fields[val_index] == value:
                 rval.append(fields)
@@ -754,10 +774,15 @@ class DynamicOptions:
 
     def get_options(self, trans, other_values):
         rval = []
-        if self.file_fields is not None or self.tool_data_table is not None or self.dataset_ref_name is not None or self.missing_index_file:
+        if (
+            self.file_fields is not None
+            or self.tool_data_table is not None
+            or self.dataset_ref_name is not None
+            or self.missing_index_file
+        ):
             options = self.get_fields(trans, other_values)
             for fields in options:
-                rval.append((fields[self.columns['name']], fields[self.columns['value']], False))
+                rval.append((fields[self.columns["name"]], fields[self.columns["value"]], False))
         else:
             for filter in self.filters:
                 rval = filter.filter_options(rval, trans, other_values)
@@ -783,7 +808,16 @@ def _get_ref_data(other_values, ref_name):
     - a ValueError is raised if the element is not of the type DatasetFilenameWrapper, HistoryDatasetAssociation, DatasetListWrapper, HistoryDatasetCollectionAssociation, list
     """
     ref = other_values[ref_name]
-    if not isinstance(ref, (DatasetFilenameWrapper, HistoryDatasetAssociation, DatasetListWrapper, HistoryDatasetCollectionAssociation, list)):
+    if not isinstance(
+        ref,
+        (
+            DatasetFilenameWrapper,
+            HistoryDatasetAssociation,
+            DatasetListWrapper,
+            HistoryDatasetCollectionAssociation,
+            list,
+        ),
+    ):
         raise ValueError
     if isinstance(ref, (DatasetFilenameWrapper, HistoryDatasetAssociation)):
         ref = [ref]
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 9eff77a0365..3ef9eac064a 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -5,9 +5,20 @@ import io
 import logging
 import os
 import unicodedata
-from typing import Any, Callable, Dict, List, Mapping, Optional, TYPE_CHECKING
+from typing import (
+    Any,
+    Callable,
+    Dict,
+    List,
+    Mapping,
+    Optional,
+    TYPE_CHECKING,
+)
 
-from galaxy.datatypes import data, sniff
+from galaxy.datatypes import (
+    data,
+    sniff,
+)
 from galaxy.exceptions import (
     AdminRequiredException,
     ConfigDoesNotAllowException,
@@ -16,15 +27,15 @@ from galaxy.util import (
     asbool,
     inflector,
     relpath,
-    sanitize_for_filename
+    sanitize_for_filename,
 )
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.expressions import ExpressionContext
 
 if TYPE_CHECKING:
-    from galaxy.tools.parameter.basic import ToolParameter
     from galaxy.tools import Tool
+    from galaxy.tools.parameter.basic import ToolParameter
 
 log = logging.getLogger(__name__)
 URI_PREFIXES = [f"{x}://" for x in ["http", "https", "ftp", "file", "gxfiles", "gximport", "gxuserimport", "gxftp"]]
@@ -32,7 +43,7 @@ URI_PREFIXES = [f"{x}://" for x in ["http", "https", "ftp", "file", "gxfiles", "
 
 class Group(Dictifiable):
 
-    dict_collection_visible_keys = ['name', 'type']
+    dict_collection_visible_keys = ["name", "type"]
 
     def __init__(self):
         self.name = None
@@ -68,7 +79,7 @@ class Group(Dictifiable):
 
 class Repeat(Group):
 
-    dict_collection_visible_keys = ['name', 'type', 'title', 'help', 'default', 'min', 'max']
+    dict_collection_visible_keys = ["name", "type", "title", "help", "default", "min", "max"]
     type = "repeat"
 
     def __init__(self):
@@ -102,8 +113,8 @@ class Repeat(Group):
         for d in value:
             rval_dict = {}
             # Propogate __index__
-            if '__index__' in d:
-                rval_dict['__index__'] = d['__index__']
+            if "__index__" in d:
+                rval_dict["__index__"] = d["__index__"]
             for input in self.inputs.values():
                 if input.name in d:
                     rval_dict[input.name] = input.value_to_basic(d[input.name], app, use_security)
@@ -119,7 +130,7 @@ class Repeat(Group):
                 rval_dict = {}
                 # If the special __index__ key is not set, create it (for backward
                 # compatibility)
-                rval_dict['__index__'] = d.get('__index__', i)
+                rval_dict["__index__"] = d.get("__index__", i)
                 # Restore child inputs
                 for input in self.inputs.values():
                     if ignore_errors and input.name not in d:
@@ -140,7 +151,7 @@ class Repeat(Group):
             raise Exception("Must set 'inputs' attribute to use.")
         rval = []
         for i in range(self.default):
-            rval_dict = {'__index__': i}
+            rval_dict = {"__index__": i}
             for input in self.inputs.values():
                 rval_dict[input.name] = input.get_initial_value(trans, context)
             rval.append(rval_dict)
@@ -160,7 +171,7 @@ class Repeat(Group):
 
 class Section(Group):
 
-    dict_collection_visible_keys = ['name', 'type', 'title', 'help', 'expanded']
+    dict_collection_visible_keys = ["name", "type", "title", "help", "expanded"]
     type = "section"
 
     def __init__(self):
@@ -246,33 +257,33 @@ class UploadDataset(Group):
         Group.__init__(self)
         self.title = None
         self.inputs = None
-        self.file_type_name = 'file_type'
-        self.default_file_type = 'txt'
-        self.file_type_to_ext = {'auto': self.default_file_type}
-        self.metadata_ref = 'files_metadata'
+        self.file_type_name = "file_type"
+        self.default_file_type = "txt"
+        self.file_type_to_ext = {"auto": self.default_file_type}
+        self.metadata_ref = "files_metadata"
 
     def get_composite_dataset_name(self, context):
         # FIXME: HACK
         # Special case of using 'base_name' metadata for use as Dataset name needs to be done in a General Fashion, as defined within a particular Datatype.
 
         # We get two different types of contexts here, one straight from submitted parameters, the other after being parsed into tool inputs
-        dataset_name = context.get('files_metadata|base_name', None)
+        dataset_name = context.get("files_metadata|base_name", None)
         if dataset_name is None:
-            dataset_name = context.get('files_metadata', {}).get('base_name', None)
+            dataset_name = context.get("files_metadata", {}).get("base_name", None)
         if dataset_name is None:
             filenames = list()
-            for composite_file in context.get('files', []):
-                if not composite_file.get('ftp_files', ''):
-                    filenames.append((composite_file.get('file_data') or {}).get('filename', ''))
+            for composite_file in context.get("files", []):
+                if not composite_file.get("ftp_files", ""):
+                    filenames.append((composite_file.get("file_data") or {}).get("filename", ""))
                 else:
-                    filenames.append(composite_file.get('ftp_files', [])[0])
-            dataset_name = os.path.commonprefix(filenames).rstrip('.') or None
+                    filenames.append(composite_file.get("ftp_files", [])[0])
+            dataset_name = os.path.commonprefix(filenames).rstrip(".") or None
         if dataset_name is None:
-            dataset_name = f'Uploaded Composite Dataset ({self.get_file_type(context)})'
+            dataset_name = f"Uploaded Composite Dataset ({self.get_file_type(context)})"
         return dataset_name
 
     def get_file_base_name(self, context):
-        fd = context.get('files_metadata|base_name', 'Galaxy_Composite_file')
+        fd = context.get("files_metadata|base_name", "Galaxy_Composite_file")
         return fd
 
     def get_file_type(self, context, parent_context=None):
@@ -294,7 +305,9 @@ class UploadDataset(Group):
     def get_datatype_ext(self, trans, context, parent_context=None):
         ext = self.get_file_type(context, parent_context=parent_context)
         if ext in self.file_type_to_ext:
-            ext = self.file_type_to_ext[ext]  # when using autodetect, we will use composite info from 'text', i.e. only the main file
+            ext = self.file_type_to_ext[
+                ext
+            ]  # when using autodetect, we will use composite info from 'text', i.e. only the main file
         return ext
 
     def get_datatype(self, trans, context, parent_context=None):
@@ -329,8 +342,8 @@ class UploadDataset(Group):
         for d in value:
             rval_dict = {}
             # Propogate __index__
-            if '__index__' in d:
-                rval_dict['__index__'] = d['__index__']
+            if "__index__" in d:
+                rval_dict["__index__"] = d["__index__"]
             for input in self.inputs.values():
                 if input.name in d:
                     rval_dict[input.name] = input.value_to_basic(d[input.name], app, use_security)
@@ -346,7 +359,7 @@ class UploadDataset(Group):
                 rval_dict = {}
                 # If the special __index__ key is not set, create it (for backward
                 # compatibility)
-                rval_dict['__index__'] = d.get('__index__', i)
+                rval_dict["__index__"] = d.get("__index__", i)
                 # Restore child inputs
                 for input in self.inputs.values():
                     if ignore_errors and input.name not in d:  # this wasn't tested
@@ -374,7 +387,7 @@ class UploadDataset(Group):
         rval = []
         for i in range(file_count):
             rval_dict = {}
-            rval_dict['__index__'] = i  # create __index__
+            rval_dict["__index__"] = i  # create __index__
             for input in self.inputs.values():
                 rval_dict[input.name] = input.get_initial_value(trans, context)
             rval.append(rval_dict)
@@ -385,20 +398,21 @@ class UploadDataset(Group):
             dataset_name = override_name
 
             def get_file_name(file_name):
-                file_name = file_name.split('\\')[-1]
-                file_name = file_name.split('/')[-1]
+                file_name = file_name.split("\\")[-1]
+                file_name = file_name.split("/")[-1]
                 return file_name
+
             try:
                 # Use the existing file
-                if not dataset_name and 'filename' in data_file:
-                    dataset_name = get_file_name(data_file['filename'])
-                return Bunch(type='file', path=data_file['local_filename'], name=dataset_name, purge_source=purge)
+                if not dataset_name and "filename" in data_file:
+                    dataset_name = get_file_name(data_file["filename"])
+                return Bunch(type="file", path=data_file["local_filename"], name=dataset_name, purge_source=purge)
             except Exception:
                 # The uploaded file should've been persisted by the upload tool action
                 return Bunch(type=None, path=None, name=None)
 
         def get_url_paste_urls_or_filename(group_incoming, override_name=None, override_info=None):
-            url_paste_file = group_incoming.get('url_paste', None)
+            url_paste_file = group_incoming.get("url_paste", None)
             if url_paste_file is not None:
                 url_paste = open(url_paste_file).read()
 
@@ -424,38 +438,38 @@ class UploadDataset(Group):
                                     raise AdminRequiredException()
                                 elif not trans.app.config.allow_path_paste:
                                     raise ConfigDoesNotAllowException()
-                                upload_path = line[len("file://"):]
+                                upload_path = line[len("file://") :]
                                 dataset_name = os.path.basename(upload_path)
                             else:
                                 dataset_name = line
 
                             if override_name:
                                 dataset_name = override_name
-                            yield Bunch(type='url', path=line, name=dataset_name)
+                            yield Bunch(type="url", path=line, name=dataset_name)
                 else:
-                    dataset_name = 'Pasted Entry'  # we need to differentiate between various url pastes here
+                    dataset_name = "Pasted Entry"  # we need to differentiate between various url pastes here
                     if override_name:
                         dataset_name = override_name
-                    yield Bunch(type='file', path=url_paste_file, name=dataset_name)
+                    yield Bunch(type="file", path=url_paste_file, name=dataset_name)
 
         def get_one_filename(context):
-            data_file = context['file_data']
-            url_paste = context['url_paste']
-            ftp_files = context['ftp_files']
-            name = context.get('NAME', None)
-            info = context.get('INFO', None)
-            uuid = context.get('uuid', None) or None  # Turn '' to None
-            file_type = context.get('file_type', None)
+            data_file = context["file_data"]
+            url_paste = context["url_paste"]
+            ftp_files = context["ftp_files"]
+            name = context.get("NAME", None)
+            info = context.get("INFO", None)
+            uuid = context.get("uuid", None) or None  # Turn '' to None
+            file_type = context.get("file_type", None)
             dbkey = self.get_dbkey(context)
             warnings = []
             to_posix_lines = False
-            if context.get('to_posix_lines', None) not in ["None", None, False]:
+            if context.get("to_posix_lines", None) not in ["None", None, False]:
                 to_posix_lines = True
             auto_decompress = False
-            if context.get('auto_decompress', None) not in ["None", None, False]:
+            if context.get("auto_decompress", None) not in ["None", None, False]:
                 auto_decompress = True
             space_to_tab = False
-            if context.get('space_to_tab', None) not in ["None", None, False]:
+            if context.get("space_to_tab", None) not in ["None", None, False]:
                 space_to_tab = True
             file_bunch = get_data_file_filename(data_file, override_name=name, override_info=info)
             if file_bunch.path:
@@ -478,9 +492,11 @@ class UploadDataset(Group):
                             if ftp_filename == filename:
                                 path = relpath(os.path.join(dirpath, filename), user_ftp_dir)
                                 if not os.path.islink(os.path.join(dirpath, filename)):
-                                    ftp_data_file = {'local_filename': os.path.abspath(os.path.join(user_ftp_dir, path)),
-                                                     'filename': os.path.basename(path)}
-                                    purge = getattr(trans.app.config, 'ftp_upload_purge', True)
+                                    ftp_data_file = {
+                                        "local_filename": os.path.abspath(os.path.join(user_ftp_dir, path)),
+                                        "filename": os.path.basename(path),
+                                    }
+                                    purge = getattr(trans.app.config, "ftp_upload_purge", True)
                                     file_bunch = get_data_file_filename(
                                         ftp_data_file,
                                         override_name=name,
@@ -505,21 +521,21 @@ class UploadDataset(Group):
 
         def get_filenames(context):
             rval = []
-            data_file = context['file_data']
-            ftp_files = context['ftp_files']
-            uuid = context.get('uuid', None) or None  # Turn '' to None
-            name = context.get('NAME', None)
-            info = context.get('INFO', None)
-            file_type = context.get('file_type', None)
+            data_file = context["file_data"]
+            ftp_files = context["ftp_files"]
+            uuid = context.get("uuid", None) or None  # Turn '' to None
+            name = context.get("NAME", None)
+            info = context.get("INFO", None)
+            file_type = context.get("file_type", None)
             dbkey = self.get_dbkey(context)
             to_posix_lines = False
-            if context.get('to_posix_lines', None) not in ["None", None, False]:
+            if context.get("to_posix_lines", None) not in ["None", None, False]:
                 to_posix_lines = True
             auto_decompress = False
-            if context.get('auto_decompress', None) not in ["None", None, False]:
+            if context.get("auto_decompress", None) not in ["None", None, False]:
                 auto_decompress = True
             space_to_tab = False
-            if context.get('space_to_tab', None) not in ["None", None, False]:
+            if context.get("space_to_tab", None) not in ["None", None, False]:
                 space_to_tab = True
             file_bunch = get_data_file_filename(data_file, override_name=name, override_info=info)
             file_bunch.uuid = uuid
@@ -550,9 +566,9 @@ class UploadDataset(Group):
             if ftp_files is not None:
                 # Normalize input paths to ensure utf-8 encoding is normal form c.
                 # This allows for comparison when the filesystem uses a different encoding than the browser.
-                ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files if isinstance(f, str)]
+                ftp_files = [unicodedata.normalize("NFC", f) for f in ftp_files if isinstance(f, str)]
                 if trans.user is None:
-                    log.warning(f'Anonymous user passed values in ftp_files: {ftp_files}')
+                    log.warning(f"Anonymous user passed values in ftp_files: {ftp_files}")
                     ftp_files = []
                     # TODO: warning to the user (could happen if session has become invalid)
                 else:
@@ -564,7 +580,7 @@ class UploadDataset(Group):
                             if not os.path.islink(os.path.join(dirpath, filename)):
                                 # Normalize filesystem paths
                                 if isinstance(path, str):
-                                    valid_files.append(unicodedata.normalize('NFC', path))
+                                    valid_files.append(unicodedata.normalize("NFC", path))
                                 else:
                                     valid_files.append(path)
 
@@ -572,12 +588,14 @@ class UploadDataset(Group):
                 ftp_files = []
             for ftp_file in ftp_files:
                 if ftp_file not in valid_files:
-                    log.warning(f'User passed an invalid file path in ftp_files: {ftp_file}')
+                    log.warning(f"User passed an invalid file path in ftp_files: {ftp_file}")
                     continue
                     # TODO: warning to the user (could happen if file is already imported)
-                ftp_data_file = {'local_filename': os.path.abspath(os.path.join(user_ftp_dir, ftp_file)),
-                                 'filename': os.path.basename(ftp_file)}
-                purge = getattr(trans.app.config, 'ftp_upload_purge', True)
+                ftp_data_file = {
+                    "local_filename": os.path.abspath(os.path.join(user_ftp_dir, ftp_file)),
+                    "filename": os.path.basename(ftp_file),
+                }
+                purge = getattr(trans.app.config, "ftp_upload_purge", True)
                 file_bunch = get_data_file_filename(ftp_data_file, override_name=name, override_info=info, purge=purge)
                 if file_bunch.path:
                     file_bunch.to_posix_lines = to_posix_lines
@@ -589,24 +607,25 @@ class UploadDataset(Group):
                         file_bunch.dbkey = dbkey
                     rval.append(file_bunch)
             return rval
+
         file_type = self.get_file_type(context)
         file_count = self.get_file_count(trans, context)
         d_type = self.get_datatype(trans, context)
         dbkey = self.get_dbkey(context)
-        tag_using_filenames = context.get('tag_using_filenames', False)
-        tags = context.get('tags', False)
-        force_composite = asbool(context.get('force_composite', 'False'))
+        tag_using_filenames = context.get("tag_using_filenames", False)
+        tags = context.get("tags", False)
+        force_composite = asbool(context.get("force_composite", "False"))
         writable_files = d_type.writable_files
         writable_files_offset = 0
         groups_incoming = [None for _ in range(file_count)]
         for group_incoming in context.get(self.name, []):
-            i = int(group_incoming['__index__'])
+            i = int(group_incoming["__index__"])
             groups_incoming[i] = group_incoming
         if d_type.composite_type is not None or force_composite:
             # handle uploading of composite datatypes
             # Only one Dataset can be created
             dataset = Dataset()
-            dataset.type = 'composite'
+            dataset.type = "composite"
             dataset.file_type = file_type
             dataset.dbkey = dbkey
             dataset.datatype = d_type
@@ -618,18 +637,28 @@ class UploadDataset(Group):
             dataset.tags = None
             # load metadata
             files_metadata = context.get(self.metadata_ref, {})
-            metadata_name_substition_default_dict = {composite_file.substitute_name_with_metadata: d_type.metadata_spec[composite_file.substitute_name_with_metadata].default for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata}
+            metadata_name_substition_default_dict = {
+                composite_file.substitute_name_with_metadata: d_type.metadata_spec[
+                    composite_file.substitute_name_with_metadata
+                ].default
+                for composite_file in d_type.composite_files.values()
+                if composite_file.substitute_name_with_metadata
+            }
             for meta_name, meta_spec in d_type.metadata_spec.items():
                 if meta_spec.set_in_upload:
                     if meta_name in files_metadata:
                         meta_value = files_metadata[meta_name]
                         if meta_name in metadata_name_substition_default_dict:
-                            meta_value = sanitize_for_filename(meta_value, default=metadata_name_substition_default_dict[meta_name])
+                            meta_value = sanitize_for_filename(
+                                meta_value, default=metadata_name_substition_default_dict[meta_name]
+                            )
                         dataset.metadata[meta_name] = meta_value
             dataset.name = self.get_composite_dataset_name(context)
-            if dataset.datatype.composite_type == 'auto_primary_file':
+            if dataset.datatype.composite_type == "auto_primary_file":
                 # replace sniff here with just creating an empty file
-                temp_name = sniff.stream_to_file(io.StringIO(d_type.generate_primary_file(dataset)), prefix='upload_auto_primary_file')
+                temp_name = sniff.stream_to_file(
+                    io.StringIO(d_type.generate_primary_file(dataset)), prefix="upload_auto_primary_file"
+                )
                 dataset.primary_file = temp_name
                 dataset.to_posix_lines = True
                 dataset.auto_decompress = True
@@ -647,14 +676,18 @@ class UploadDataset(Group):
                     dataset.dbkey = dbkey
                 dataset.warnings.extend(warnings)
             if dataset.primary_file is None:  # remove this before finish, this should create an empty dataset
-                raise Exception('No primary dataset file was available for composite upload')
+                raise Exception("No primary dataset file was available for composite upload")
             if not force_composite:
                 keys = [value.name for value in writable_files.values()]
             else:
                 keys = [str(index) for index in range(file_count)]
             for i, group_incoming in enumerate(groups_incoming[writable_files_offset:]):
                 key = keys[i + writable_files_offset]
-                if not force_composite and group_incoming is None and not writable_files[list(writable_files.keys())[keys.index(key)]].optional:
+                if (
+                    not force_composite
+                    and group_incoming is None
+                    and not writable_files[list(writable_files.keys())[keys.index(key)]].optional
+                ):
                     dataset.warnings.append(f"A required composite file ({key}) was not specified.")
                     dataset.composite_files[key] = None
                 else:
@@ -688,9 +721,7 @@ class UploadDataset(Group):
 
 class Conditional(Group):
     type = "conditional"
-    value_from: Callable[
-        ["Conditional", ExpressionContext, "Conditional", "Tool"], Mapping[str, str]
-    ]
+    value_from: Callable[["Conditional", ExpressionContext, "Conditional", "Tool"], Mapping[str, str]]
 
     def __init__(self):
         Group.__init__(self)
@@ -719,7 +750,7 @@ class Conditional(Group):
             raise Exception("Must set 'test_param' attribute to use.")
         rval = dict()
         rval[self.test_param.name] = self.test_param.value_to_basic(value[self.test_param.name], app)
-        current_case = rval['__current_case__'] = self.get_current_case(value[self.test_param.name])
+        current_case = rval["__current_case__"] = self.get_current_case(value[self.test_param.name])
         for input in self.cases[current_case].inputs.values():
             if input.name in value:  # parameter might be absent in unverified workflow
                 rval[input.name] = input.value_to_basic(value[input.name], app, use_security=use_security)
@@ -730,8 +761,10 @@ class Conditional(Group):
             raise Exception("Must set 'test_param' attribute to use.")
         rval = dict()
         try:
-            rval[self.test_param.name] = self.test_param.value_from_basic(value.get(self.test_param.name), app, ignore_errors)
-            current_case = rval['__current_case__'] = self.get_current_case(rval[self.test_param.name])
+            rval[self.test_param.name] = self.test_param.value_from_basic(
+                value.get(self.test_param.name), app, ignore_errors
+            )
+            current_case = rval["__current_case__"] = self.get_current_case(rval[self.test_param.name])
             # Inputs associated with current case
             for input in self.cases[current_case].inputs.values():
                 # If we do not have a value, and are ignoring errors, we simply
@@ -754,7 +787,7 @@ class Conditional(Group):
         test_value = self.test_param.get_initial_value(trans, context)
         current_case = self.get_current_case(test_value)
         # Store the current case in a special value
-        rval['__current_case__'] = current_case
+        rval["__current_case__"] = current_case
         # Store the value of the test element
         rval[self.test_param.name] = test_value
         # Fill in state for selected case
@@ -777,7 +810,7 @@ class Conditional(Group):
 
 
 class ConditionalWhen(Dictifiable):
-    dict_collection_visible_keys = ['value']
+    dict_collection_visible_keys = ["value"]
 
     def __init__(self):
         self.value = None
diff --git a/lib/galaxy/tools/parameters/history_query.py b/lib/galaxy/tools/parameters/history_query.py
index f13766d7f49..4e6ebf11c02 100644
--- a/lib/galaxy/tools/parameters/history_query.py
+++ b/lib/galaxy/tools/parameters/history_query.py
@@ -1,9 +1,10 @@
 import logging
+
 log = logging.getLogger(__name__)
 
 
 class HistoryQuery:
-    """ An object for describing the collections to pull out of a history,
+    """An object for describing the collections to pull out of a history,
     used by DataCollectionToolParameter.
     """
 
@@ -18,7 +19,9 @@ class HistoryQuery:
     @staticmethod
     def from_collection_types(collection_types, collection_type_descriptions):
         if collection_types:
-            collection_type_descriptions = [collection_type_descriptions.for_collection_type(t) for t in collection_types]
+            collection_type_descriptions = [
+                collection_type_descriptions.for_collection_type(t) for t in collection_types
+            ]
             # Place higher dimension descriptions first so subcollection mapping
             # (until we expose it to the user) will default to providing tool as much
             # data as possible. So a list:list:paired mapped to a tool that takes
@@ -31,8 +34,7 @@ class HistoryQuery:
 
     @staticmethod
     def from_parameter(param, collection_type_descriptions):
-        """ Take in a tool parameter element.
-        """
+        """Take in a tool parameter element."""
         collection_types = param.collection_types
         return HistoryQuery.from_collection_types(collection_types, collection_type_descriptions)
 
diff --git a/lib/galaxy/tools/parameters/input_translation.py b/lib/galaxy/tools/parameters/input_translation.py
index 158a54371ca..035a2c30ceb 100644
--- a/lib/galaxy/tools/parameters/input_translation.py
+++ b/lib/galaxy/tools/parameters/input_translation.py
@@ -48,6 +48,7 @@ class ToolInputTranslator:
     >>> params.get('URL', None) in ['URL_value?GALAXY_URL=0&_export=1', 'URL_value?_export=1&GALAXY_URL=0']
     True
     """
+
     @classmethod
     def from_element(cls, elem):
         """Loads the proper filter by the type attribute of elem"""
@@ -61,9 +62,9 @@ class ToolInputTranslator:
             value_trans = {}
             append_param = None
 
-            value_trans_elem = req_param.find('value_translation')
+            value_trans_elem = req_param.find("value_translation")
             if value_trans_elem is not None:
-                for value_elem in value_trans_elem.findall('value'):
+                for value_elem in value_trans_elem.findall("value"):
                     remote_value = value_elem.get("remote_value")
                     galaxy_value = value_elem.get("galaxy_value")
                     if None not in [remote_value, galaxy_value]:
@@ -71,18 +72,22 @@ class ToolInputTranslator:
 
             append_param_elem = req_param.find("append_param")
             if append_param_elem is not None:
-                separator = append_param_elem.get('separator', ',')
-                first_separator = append_param_elem.get('first_separator', None)
-                join_str = append_param_elem.get('join', '=')
+                separator = append_param_elem.get("separator", ",")
+                first_separator = append_param_elem.get("first_separator", None)
+                join_str = append_param_elem.get("join", "=")
                 append_dict = {}
-                for value_elem in append_param_elem.findall('value'):
-                    value_name = value_elem.get('name')
-                    value_missing = value_elem.get('missing')
+                for value_elem in append_param_elem.findall("value"):
+                    value_name = value_elem.get("name")
+                    value_missing = value_elem.get("missing")
                     if None not in [value_name, value_missing]:
                         append_dict[value_name] = value_missing
-                append_param = Bunch(separator=separator, first_separator=first_separator, join_str=join_str, append_dict=append_dict)
+                append_param = Bunch(
+                    separator=separator, first_separator=first_separator, join_str=join_str, append_dict=append_dict
+                )
 
-            rval.param_trans_dict[remote_name] = Bunch(galaxy_name=galaxy_name, missing=missing, value_trans=value_trans, append_param=append_param)
+            rval.param_trans_dict[remote_name] = Bunch(
+                galaxy_name=galaxy_name, missing=missing, value_trans=value_trans, append_param=append_param
+            )
 
         return rval
 
@@ -94,8 +99,12 @@ class ToolInputTranslator:
         update params in-place
         """
         for remote_name, translator in self.param_trans_dict.items():
-            galaxy_name = translator.galaxy_name  # NB: if a param by name galaxy_name is provided, it is always thrown away unless galaxy_name == remote_name
-            value = params.get(remote_name, translator.missing)  # get value from input params, or use default value specified in tool config
+            galaxy_name = (
+                translator.galaxy_name
+            )  # NB: if a param by name galaxy_name is provided, it is always thrown away unless galaxy_name == remote_name
+            value = params.get(
+                remote_name, translator.missing
+            )  # get value from input params, or use default value specified in tool config
             if translator.value_trans and value in translator.value_trans:
                 value = translator.value_trans[value]
             if translator.append_param:
@@ -105,5 +114,5 @@ class ToolInputTranslator:
                         sep = translator.append_param.first_separator
                     else:
                         sep = translator.append_param.separator
-                    value += f'{sep}{param_name}{translator.append_param.join_str}{param_value}'
+                    value += f"{sep}{param_name}{translator.append_param.join_str}{param_value}"
             params.update({galaxy_name: value})
diff --git a/lib/galaxy/tools/parameters/meta.py b/lib/galaxy/tools/parameters/meta.py
index 7d834d29596..b403bde3641 100644
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -6,26 +6,29 @@ from collections import namedtuple
 from galaxy import (
     exceptions,
     model,
-    util
+    util,
+)
+from galaxy.model.dataset_collections import (
+    matching,
+    subcollections,
 )
-from galaxy.model.dataset_collections import matching, subcollections
 from galaxy.util import permutations
 from . import visit_input_values
 
 log = logging.getLogger(__name__)
 
-WorkflowParameterExpansion = namedtuple('WorkflowParameterExpansion', ['param_combinations', 'param_keys', 'input_combinations'])
+WorkflowParameterExpansion = namedtuple(
+    "WorkflowParameterExpansion", ["param_combinations", "param_keys", "input_combinations"]
+)
 
 
 class ParamKey:
-
     def __init__(self, step_id, key):
         self.step_id = step_id
         self.key = key
 
 
 class InputKey:
-
     def __init__(self, input_id):
         self.input_id = input_id
 
@@ -62,42 +65,52 @@ def expand_workflow_inputs(param_inputs, inputs=None):
     product_keys = []
 
     def is_batch(value):
-        return isinstance(value, dict) and 'batch' in value and value['batch'] is True and 'values' in value and isinstance(value['values'], list)
+        return (
+            isinstance(value, dict)
+            and "batch" in value
+            and value["batch"] is True
+            and "values" in value
+            and isinstance(value["values"], list)
+        )
 
     for step_id, step in sorted(param_inputs.items()):
         for key, value in sorted(step.items()):
             if is_batch(value):
-                nval = len(value['values'])
-                if 'product' in value and value['product'] is True:
-                    product.append(value['values'])
+                nval = len(value["values"])
+                if "product" in value and value["product"] is True:
+                    product.append(value["values"])
                     product_keys.append(ParamKey(step_id, key))
                 else:
                     if linked_n is None:
                         linked_n = nval
                     elif linked_n != nval or nval == 0:
-                        raise exceptions.RequestParameterInvalidException('Failed to match linked batch selections. Please select equal number of data files.')
-                    linked.append(value['values'])
+                        raise exceptions.RequestParameterInvalidException(
+                            "Failed to match linked batch selections. Please select equal number of data files."
+                        )
+                    linked.append(value["values"])
                     linked_keys.append(ParamKey(step_id, key))
 
     # Force it to a list to allow modification...
     input_items = list(inputs.items())
     for input_id, value in input_items:
         if is_batch(value):
-            nval = len(value['values'])
-            if 'product' in value and value['product'] is True:
-                product.append(value['values'])
+            nval = len(value["values"])
+            if "product" in value and value["product"] is True:
+                product.append(value["values"])
                 product_keys.append(InputKey(input_id))
             else:
                 if linked_n is None:
                     linked_n = nval
                 elif linked_n != nval or nval == 0:
-                    raise exceptions.RequestParameterInvalidException('Failed to match linked batch selections. Please select equal number of data files.')
-                linked.append(value['values'])
+                    raise exceptions.RequestParameterInvalidException(
+                        "Failed to match linked batch selections. Please select equal number of data files."
+                    )
+                linked.append(value["values"])
                 linked_keys.append(InputKey(input_id))
-        elif isinstance(value, dict) and 'batch' in value:
+        elif isinstance(value, dict) and "batch" in value:
             # remove batch wrapper and render simplified input form rest of workflow
             # code expects
-            inputs[input_id] = value['values'][0]
+            inputs[input_id] = value["values"][0]
 
     param_combinations = []
     input_combinations = []
@@ -117,14 +130,14 @@ def expand_workflow_inputs(param_inputs, inputs=None):
                     key = input_key.key
                     assert step_id is not None
                     new_params[step_id][key] = value
-                    if 'hid' in value:
-                        new_keys.append(str(value['hid']))
+                    if "hid" in value:
+                        new_keys.append(str(value["hid"]))
                 else:
                     input_id = input_key.input_id
                     assert input_id is not None
                     new_inputs[input_id] = value
-                    if 'hid' in value:
-                        new_keys.append(str(value['hid']))
+                    if "hid" in value:
+                        new_keys.append(str(value["hid"]))
 
         params_keys.append(new_keys)
         param_combinations.append(new_params)
@@ -134,20 +147,20 @@ def expand_workflow_inputs(param_inputs, inputs=None):
 
 
 def process_key(incoming_key, incoming_value, d):
-    key_parts = incoming_key.split('|')
+    key_parts = incoming_key.split("|")
     if len(key_parts) == 1:
         # Regular parameter
         if incoming_key in d and not incoming_value:
             # In case we get an empty repeat after we already filled in a repeat element
             return
         d[incoming_key] = incoming_value
-    elif key_parts[0].rsplit('_', 1)[-1].isdigit():
+    elif key_parts[0].rsplit("_", 1)[-1].isdigit():
         # Repeat
-        input_name, index = key_parts[0].rsplit('_', 1)
+        input_name, index = key_parts[0].rsplit("_", 1)
         index = int(index)
         d.setdefault(input_name, [])
         newlist = [{} for _ in range(index + 1)]
-        d[input_name].extend(newlist[len(d[input_name]):])
+        d[input_name].extend(newlist[len(d[input_name]) :])
         subdict = d[input_name][index]
         process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)
     else:
@@ -175,7 +188,7 @@ def expand_meta_parameters(trans, tool, incoming):
     incoming_copy = incoming.copy()
     nested_dict = {}
     for incoming_key, incoming_value in incoming_copy.items():
-        if not incoming_key.startswith('__'):
+        if not incoming_key.startswith("__"):
             process_key(incoming_key, incoming_value=incoming_value, d=nested_dict)
 
     reordered_incoming = {}
@@ -190,10 +203,10 @@ def expand_meta_parameters(trans, tool, incoming):
 
     def classifier(input_key):
         value = incoming[input_key]
-        if isinstance(value, dict) and 'values' in value:
+        if isinstance(value, dict) and "values" in value:
             # Explicit meta wrapper for inputs...
-            is_batch = value.get('batch', False)
-            is_linked = value.get('linked', True)
+            is_batch = value.get("batch", False)
+            is_linked = value.get("linked", True)
             if is_batch and is_linked:
                 classification = permutations.input_classification.MATCHED
             elif is_batch:
@@ -201,10 +214,12 @@ def expand_meta_parameters(trans, tool, incoming):
             else:
                 classification = permutations.input_classification.SINGLE
             if __collection_multirun_parameter(value):
-                collection_value = value['values'][0]
-                values = __expand_collection_parameter(trans, input_key, collection_value, collections_to_match, linked=is_linked)
+                collection_value = value["values"][0]
+                values = __expand_collection_parameter(
+                    trans, input_key, collection_value, collections_to_match, linked=is_linked
+                )
             else:
-                values = value['values']
+                values = value["values"]
         else:
             classification = permutations.input_classification.SINGLE
             values = value
@@ -235,7 +250,7 @@ def __expand_collection_parameter(trans, input_key, incoming_val, collections_to
             if src != "hdca":
                 raise exceptions.ToolMetaParameterException(f"Invalid dataset collection source type {src}")
             encoded_hdc_id = incoming_val["id"]
-            subcollection_type = incoming_val.get('map_over_type', None)
+            subcollection_type = incoming_val.get("map_over_type", None)
         except TypeError:
             encoded_hdc_id = incoming_val
             subcollection_type = None
@@ -255,13 +270,13 @@ def __expand_collection_parameter(trans, input_key, incoming_val, collections_to
 
 
 def __collection_multirun_parameter(value):
-    is_batch = value.get('batch', False)
+    is_batch = value.get("batch", False)
     if not is_batch:
         return False
 
-    batch_values = util.listify(value['values'])
+    batch_values = util.listify(value["values"])
     if len(batch_values) == 1:
         batch_over = batch_values[0]
-        if isinstance(batch_over, dict) and ('src' in batch_over) and (batch_over['src'] in {'hdca', 'dce'}):
+        if isinstance(batch_over, dict) and ("src" in batch_over) and (batch_over["src"] in {"hdca", "dce"}):
             return True
     return False
diff --git a/lib/galaxy/tools/parameters/sanitize.py b/lib/galaxy/tools/parameters/sanitize.py
index 79c498db340..9a576b5c9d8 100644
--- a/lib/galaxy/tools/parameters/sanitize.py
+++ b/lib/galaxy/tools/parameters/sanitize.py
@@ -4,7 +4,6 @@ Tool Parameter specific sanitizing.
 import logging
 import string
 
-
 import galaxy.util
 
 log = logging.getLogger(__name__)
@@ -43,9 +42,9 @@ class ToolParameterSanitizer:
     True
     """
 
-    VALID_PRESET = {'default': (f"{string.ascii_letters + string.digits} -=_.()/+*^,:?!"), 'none': ''}
-    MAPPING_PRESET = {'default': galaxy.util.mapped_chars, 'none': {}}
-    DEFAULT_INVALID_CHAR = 'X'
+    VALID_PRESET = {"default": (f"{string.ascii_letters + string.digits} -=_.()/+*^,:?!"), "none": ""}
+    MAPPING_PRESET = {"default": galaxy.util.mapped_chars, "none": {}}
+    DEFAULT_INVALID_CHAR = "X"
 
     # class methods
     @classmethod
@@ -53,76 +52,77 @@ class ToolParameterSanitizer:
         """Loads the proper filter by the type attribute of elem"""
         # TODO: Add ability to generically specify a method to use for sanitizing input via specification in tool XML
         rval = ToolParameterSanitizer()
-        rval._invalid_char = elem.get('invalid_char', cls.DEFAULT_INVALID_CHAR)
-        rval.sanitize = galaxy.util.string_as_bool(elem.get('sanitize', 'True'))
-        for valid_elem in elem.findall('valid'):
-            rval._valid_chars = rval.get_valid_by_name(valid_elem.get('initial', 'default'))
+        rval._invalid_char = elem.get("invalid_char", cls.DEFAULT_INVALID_CHAR)
+        rval.sanitize = galaxy.util.string_as_bool(elem.get("sanitize", "True"))
+        for valid_elem in elem.findall("valid"):
+            rval._valid_chars = rval.get_valid_by_name(valid_elem.get("initial", "default"))
             for action_elem in valid_elem:
-                preset = rval.get_valid_by_name(action_elem.get('preset', 'none'))
-                valid_value = [val for val in action_elem.get('value', [])]
-                if action_elem.tag.lower() == 'add':
+                preset = rval.get_valid_by_name(action_elem.get("preset", "none"))
+                valid_value = [val for val in action_elem.get("value", [])]
+                if action_elem.tag.lower() == "add":
                     for val in preset + valid_value:
                         if val not in rval._valid_chars:
                             rval._valid_chars.append(val)
-                elif action_elem.tag.lower() == 'remove':
+                elif action_elem.tag.lower() == "remove":
                     for val in preset + valid_value:
                         while val in rval._valid_chars:
                             rval._valid_chars.remove(val)
                 else:
-                    log.debug(f'Invalid action tag in valid: {action_elem.tag}')
-        for mapping_elem in elem.findall('mapping'):
-            rval._mapped_chars = rval.get_mapping_by_name(mapping_elem.get('initial', 'default'))
+                    log.debug(f"Invalid action tag in valid: {action_elem.tag}")
+        for mapping_elem in elem.findall("mapping"):
+            rval._mapped_chars = rval.get_mapping_by_name(mapping_elem.get("initial", "default"))
             for action_elem in mapping_elem:
-                map_source = action_elem.get('source', None)
-                map_target = action_elem.get('target', None)
-                preset = rval.get_mapping_by_name(action_elem.get('preset', 'none'))
-                if action_elem.tag.lower() == 'add':
+                map_source = action_elem.get("source", None)
+                map_target = action_elem.get("target", None)
+                preset = rval.get_mapping_by_name(action_elem.get("preset", "none"))
+                if action_elem.tag.lower() == "add":
                     rval._mapped_chars.update(preset)
                     if None not in [map_source, map_target]:
                         rval._mapped_chars[map_source] = map_target
-                elif action_elem.tag.lower() == 'remove':
+                elif action_elem.tag.lower() == "remove":
                     for map_key in preset.keys():
                         if map_key in rval._mapped_chars:
                             del rval._mapped_chars[map_key]
                     if map_source is not None and map_key in rval._mapped_chars:
                         del rval._mapped_chars[map_key]
                 else:
-                    log.debug(f'Invalid action tag in mapping: {action_elem.tag}')
+                    log.debug(f"Invalid action tag in mapping: {action_elem.tag}")
         return rval
 
     @classmethod
     def get_valid_by_name(cls, name):
         rval = []
-        for split_name in name.split(','):
+        for split_name in name.split(","):
             # Remove ';' (if present) and everything after it
-            split_name = split_name.split(';', 1)[0]
+            split_name = split_name.split(";", 1)[0]
             split_name = split_name.strip()
             value = []
-            if split_name.startswith('string.'):
+            if split_name.startswith("string."):
                 string_constant = split_name[7:]
-                if string_constant in ('letters', 'lowercase', 'uppercase'):
+                if string_constant in ("letters", "lowercase", "uppercase"):
                     split_name = f"string.ascii_{string_constant}"
                 try:
                     value = eval(split_name)
                 except NameError as e:
-                    log.debug(f'Invalid string preset specified: {e}')
+                    log.debug(f"Invalid string preset specified: {e}")
             elif split_name in cls.VALID_PRESET:
                 value = cls.VALID_PRESET[split_name]
             else:
-                log.debug(f'Invalid preset name specified: {split_name}')
+                log.debug(f"Invalid preset name specified: {split_name}")
             rval.extend([val for val in value if val not in rval])
         return rval
 
     @classmethod
     def get_mapping_by_name(cls, name):
         rval = {}
-        for split_name in name.split(','):
+        for split_name in name.split(","):
             split_name = split_name.strip()
             if split_name in cls.MAPPING_PRESET:
                 rval.update(cls.MAPPING_PRESET[split_name])
             else:
-                log.debug(f'Invalid preset name specified: {split_name}')
+                log.debug(f"Invalid preset name specified: {split_name}")
         return rval
+
     # end class methods
 
     def __init__(self):
@@ -150,7 +150,7 @@ class ToolParameterSanitizer:
                 rval.append(self._mapped_chars[c])
             else:
                 rval.append(self._invalid_char)
-        return ''.join(rval)
+        return "".join(rval)
 
     def sanitize_param(self, value):
         """Clean incoming parameters (strings or lists)"""
@@ -161,4 +161,4 @@ class ToolParameterSanitizer:
         elif isinstance(value, list):
             return list(map(self.sanitize_text, value))
         else:
-            raise Exception(f'Unknown parameter type ({type(value)}:{value})')
+            raise Exception(f"Unknown parameter type ({type(value)}:{value})")
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index becd7e6e74e..f907bde7857 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -6,10 +6,9 @@ import logging
 import os.path
 import re
 
-
 from galaxy import (
     model,
-    util
+    util,
 )
 
 log = logging.getLogger(__name__)
@@ -18,7 +17,7 @@ log = logging.getLogger(__name__)
 def get_test_fname(fname):
     """Returns test data filename"""
     path, name = os.path.split(__file__)
-    full_path = os.path.join(path, 'test', fname)
+    full_path = os.path.join(path, "test", fname)
     return full_path
 
 
@@ -26,6 +25,7 @@ class Validator(abc.ABC):
     """
     A validator checks that a value meets some conditions OR raises ValueError
     """
+
     requires_dataset_metadata = False
 
     @classmethod
@@ -44,7 +44,7 @@ class Validator(abc.ABC):
         param elem the validator element
         return an object of a Validator subclass that corresponds to the type attribute of the validator element
         """
-        _type = elem.get('type', None)
+        _type = elem.get("type", None)
         assert _type is not None, "Required 'type' attribute missing from validator"
         return validator_types[_type].from_element(param, elem)
 
@@ -72,7 +72,7 @@ class Validator(abc.ABC):
 
         return None if positive validation, otherwise a ValueError is raised
         """
-        assert isinstance(value, bool), 'value must be boolean'
+        assert isinstance(value, bool), "value must be boolean"
         if message is None:
             message = self.message
         if value_to_show and "%s" in message:
@@ -129,7 +129,7 @@ class RegexValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        return cls(elem.get('message', None), elem.text, elem.get('negate', 'false'))
+        return cls(elem.get("message", None), elem.text, elem.get("negate", "false"))
 
     def __init__(self, message, expression, negate):
         if message is None:
@@ -143,7 +143,7 @@ class RegexValidator(Validator):
         if not isinstance(value, list):
             value = [value]
         for val in value:
-            match = re.match(self.expression, val or '')
+            match = re.match(self.expression, val or "")
             super().validate(match is not None, value_to_show=val)
 
 
@@ -193,14 +193,14 @@ class ExpressionValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        return cls(elem.get('message', None), elem.text, elem.get('negate', 'false'))
+        return cls(elem.get("message", None), elem.text, elem.get("negate", "false"))
 
     def __init__(self, message, expression, negate):
         if message is None:
             message = f"Value '%s' does not evaluate to {'True' if negate == 'false' else 'False'} for '{expression}'"
         super().__init__(message, negate)
         # Save compiled expression, code objects are thread safe (right?)
-        self.expression = compile(expression, '<string>', 'eval')
+        self.expression = compile(expression, "<string>", "eval")
 
     def validate(self, value, trans=None):
         try:
@@ -251,10 +251,14 @@ class InRangeValidator(ExpressionValidator):
 
     @classmethod
     def from_element(cls, param, elem):
-        return cls(elem.get('message', None), elem.get('min'),
-                   elem.get('max'), elem.get('exclude_min', 'false'),
-                   elem.get('exclude_max', 'false'),
-                   elem.get('negate', 'false'))
+        return cls(
+            elem.get("message", None),
+            elem.get("min"),
+            elem.get("max"),
+            elem.get("exclude_min", "false"),
+            elem.get("exclude_max", "false"),
+            elem.get("negate", "false"),
+        )
 
     def __init__(self, message, range_min, range_max, exclude_min=False, exclude_max=False, negate=False):
         """
@@ -264,18 +268,18 @@ class InRangeValidator(ExpressionValidator):
         (1.e., min <= value <= max).  Combinations of exclude_min and exclude_max
         values are allowed.
         """
-        self.min = range_min if range_min is not None else '-inf'
+        self.min = range_min if range_min is not None else "-inf"
         self.exclude_min = util.asbool(exclude_min)
-        self.max = range_max if range_max is not None else 'inf'
+        self.max = range_max if range_max is not None else "inf"
         self.exclude_max = util.asbool(exclude_max)
-        assert float(self.min) <= float(self.max), 'min must be less than or equal to max'
+        assert float(self.min) <= float(self.max), "min must be less than or equal to max"
         # Remove unneeded 0s and decimal from floats to make message pretty.
-        op1 = '<='
-        op2 = '<='
+        op1 = "<="
+        op2 = "<="
         if self.exclude_min:
-            op1 = '<'
+            op1 = "<"
         if self.exclude_max:
-            op2 = '<'
+            op2 = "<"
         expression = f"float('{self.min}') {op1} value {op2} float('{self.max}')"
         if message is None:
             message = f"Value ('%s') must {'not ' if negate == 'true' else ''}fulfill {expression}"
@@ -323,7 +327,7 @@ class LengthValidator(InRangeValidator):
 
     @classmethod
     def from_element(cls, param, elem):
-        return cls(elem.get('message', None), elem.get('min', None), elem.get('max', None), elem.get('negate', 'false'))
+        return cls(elem.get("message", None), elem.get("min", None), elem.get("max", None), elem.get("negate", "false"))
 
     def __init__(self, message, length_min, length_max, negate):
         if message is None:
@@ -379,10 +383,10 @@ class DatasetOkValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        negate = elem.get('negate', 'false')
-        message = elem.get('message', None)
+        negate = elem.get("negate", "false")
+        message = elem.get("message", None)
         if message is None:
-            if negate == 'false':
+            if negate == "false":
                 message = "The selected dataset is still being generated, select another dataset or wait until it is completed"
             else:
                 message = "The selected dataset must not be in state OK"
@@ -438,8 +442,8 @@ class DatasetEmptyValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        message = elem.get('message', None)
-        negate = elem.get('negate', 'false')
+        message = elem.get("message", None)
+        negate = elem.get("negate", "false")
         if not message:
             message = f"The selected dataset is {'non-' if negate == 'true' else ''}empty, this tool expects {'non-' if negate=='false' else ''}empty files."
         return cls(message, negate)
@@ -496,8 +500,8 @@ class DatasetExtraFilesPathEmptyValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        message = elem.get('message', None)
-        negate = elem.get('negate', 'false')
+        message = elem.get("message", None)
+        negate = elem.get("negate", "false")
         if not message:
             message = f"The selected dataset's extra_files_path directory is {'non-' if negate == 'true' else ''}empty or does {'not ' if negate == 'false' else ''}exist, this tool expects {'non-' if negate == 'false' else ''}empty extra_files_path directories associated with the selected input."
         return cls(message, negate)
@@ -563,24 +567,24 @@ class MetadataValidator(Validator):
         ...
     ValueError: At least one of the non skipped metadata 'dbkey,comment_lines,column_names,strandCol' is set, click the pencil icon in the history item to edit / save the metadata attributes
     """
+
     requires_dataset_metadata = True
 
     @classmethod
     def from_element(cls, param, elem):
-        message = elem.get('message', None)
-        return cls(message=message,
-                   check=elem.get('check', ""),
-                   skip=elem.get('skip', ""),
-                   negate=elem.get('negate', 'false'))
+        message = elem.get("message", None)
+        return cls(
+            message=message, check=elem.get("check", ""), skip=elem.get("skip", ""), negate=elem.get("negate", "false")
+        )
 
-    def __init__(self, message=None, check="", skip="", negate='false'):
+    def __init__(self, message=None, check="", skip="", negate="false"):
         if not message:
             if not util.asbool(negate):
                 message = "Metadata '%s' missing, click the pencil icon in the history item to edit / save the metadata attributes"
             else:
-                if check != '':
+                if check != "":
                     message = f"At least one of the checked metadata '{check}' is set, click the pencil icon in the history item to edit / save the metadata attributes"
-                elif skip != '':
+                elif skip != "":
                     message = f"At least one of the non skipped metadata '{skip}' is set, click the pencil icon in the history item to edit / save the metadata attributes"
         super().__init__(message, negate)
         self.check = check.split(",") if check else None
@@ -636,12 +640,13 @@ class UnspecifiedBuildValidator(Validator):
     ValueError: Specified genome build, click the pencil icon in the history item to remove the genome build
     >>> t = p.validate(has_no_dbkey_hda)
     """
+
     requires_dataset_metadata = True
 
     @classmethod
     def from_element(cls, param, elem):
-        message = elem.get('message', None)
-        negate = elem.get('negate', 'false')
+        message = elem.get("message", None)
+        negate = elem.get("negate", "false")
         if not message:
             message = f"{'Unspecified' if negate == 'false' else 'Specified'} genome build, click the pencil icon in the history item to {'set' if negate == 'false' else 'remove'} the genome build"
         return cls(message, negate)
@@ -653,7 +658,7 @@ class UnspecifiedBuildValidator(Validator):
             # TODO can dbkey really be a list?
             if isinstance(dbkey, list):
                 dbkey = dbkey[0]
-            super().validate(dbkey != '?')
+            super().validate(dbkey != "?")
 
 
 class NoOptionsValidator(Validator):
@@ -688,8 +693,8 @@ class NoOptionsValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        message = elem.get('message', None)
-        negate = elem.get('negate', 'false')
+        message = elem.get("message", None)
+        negate = elem.get("negate", "false")
         if not message:
             message = f"{'No options' if negate == 'false' else 'Options'} available for selection"
         return cls(message, negate)
@@ -727,17 +732,17 @@ class EmptyTextfieldValidator(Validator):
 
     @classmethod
     def from_element(cls, param, elem):
-        message = elem.get('message', None)
-        negate = elem.get('negate', 'false')
+        message = elem.get("message", None)
+        negate = elem.get("negate", "false")
         if not message:
-            if negate == 'false':
-                message = elem.get('message', "Field requires a value")
+            if negate == "false":
+                message = elem.get("message", "Field requires a value")
             else:
-                message = elem.get('message', "Field must not set a value")
+                message = elem.get("message", "Field must not set a value")
         return cls(message, negate)
 
     def validate(self, value, trans=None):
-        super().validate(value != '')
+        super().validate(value != "")
 
 
 class MetadataInFileColumnValidator(Validator):
@@ -748,6 +753,7 @@ class MetadataInFileColumnValidator(Validator):
 
     note: this is covered in a framework test (validation_dataset_metadata_in_file)
     """
+
     requires_dataset_metadata = True
 
     @classmethod
@@ -764,10 +770,19 @@ class MetadataInFileColumnValidator(Validator):
         line_startswith = elem.get("line_startswith", None)
         if line_startswith:
             line_startswith = line_startswith.strip()
-        negate = elem.get('negate', 'false')
+        negate = elem.get("negate", "false")
         return cls(filename, metadata_name, metadata_column, message, line_startswith, split, negate)
 
-    def __init__(self, filename, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None, split="\t", negate="false"):
+    def __init__(
+        self,
+        filename,
+        metadata_name,
+        metadata_column,
+        message="Value for metadata not found.",
+        line_startswith=None,
+        split="\t",
+        negate="false",
+    ):
         super().__init__(message, negate)
         self.metadata_name = metadata_name
         self.valid_values = set()
@@ -780,7 +795,10 @@ class MetadataInFileColumnValidator(Validator):
     def validate(self, value, trans=None):
         if not value:
             return
-        super().validate(value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)) in self.valid_values)
+        super().validate(
+            value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name))
+            in self.valid_values
+        )
 
 
 class ValueInDataTableColumnValidator(Validator):
@@ -793,7 +811,7 @@ class ValueInDataTableColumnValidator(Validator):
     @classmethod
     def from_element(cls, param, elem):
         table_name = elem.get("table_name", None)
-        assert table_name, 'You must specify a table_name.'
+        assert table_name, "You must specify a table_name."
         tool_data_table = param.tool.app.tool_data_tables[table_name]
         column = elem.get("metadata_column", 0)
         try:
@@ -801,10 +819,10 @@ class ValueInDataTableColumnValidator(Validator):
         except ValueError:
             pass
         message = elem.get("message", f"Value was not found in {table_name}.")
-        negate = elem.get('negate', 'false')
+        negate = elem.get("negate", "false")
         return cls(tool_data_table, column, message, negate)
 
-    def __init__(self, tool_data_table, column, message="Value not found.", negate='false'):
+    def __init__(self, tool_data_table, column, message="Value not found.", negate="false"):
         super().__init__(message, negate)
         self.valid_values = []
         self._data_table_content_version = None
@@ -825,7 +843,10 @@ class ValueInDataTableColumnValidator(Validator):
         if not value:
             return
         if not self._tool_data_table.is_current_version(self._data_table_content_version):
-            log.debug('ValueInDataTableColumnValidator: values are out of sync with data table (%s), updating validator.', self._tool_data_table.name)
+            log.debug(
+                "ValueInDataTableColumnValidator: values are out of sync with data table (%s), updating validator.",
+                self._tool_data_table.name,
+            )
             self._load_values()
         super().validate(value in self.valid_values)
 
@@ -838,7 +859,7 @@ class ValueNotInDataTableColumnValidator(ValueInDataTableColumnValidator):
     note: this is covered in a framework test (validation_value_in_datatable)
     """
 
-    def __init__(self, tool_data_table, metadata_column, message="Value already present.", negate='false'):
+    def __init__(self, tool_data_table, metadata_column, message="Value already present.", negate="false"):
         super().__init__(tool_data_table, metadata_column, message, negate)
 
     def validate(self, value, trans=None):
@@ -856,12 +877,13 @@ class MetadataInDataTableColumnValidator(ValueInDataTableColumnValidator):
 
     note: this is covered in a framework test (validation_metadata_in_datatable)
     """
+
     requires_dataset_metadata = True
 
     @classmethod
     def from_element(cls, param, elem):
         table_name = elem.get("table_name", None)
-        assert table_name, 'You must specify a table_name.'
+        assert table_name, "You must specify a table_name."
         tool_data_table = param.tool.app.tool_data_tables[table_name]
         metadata_name = elem.get("metadata_name", None)
         if metadata_name:
@@ -873,15 +895,19 @@ class MetadataInDataTableColumnValidator(ValueInDataTableColumnValidator):
         except ValueError:
             pass
         message = elem.get("message", f"Value for metadata {metadata_name} was not found in {table_name}.")
-        negate = elem.get('negate', 'false')
+        negate = elem.get("negate", "false")
         return cls(tool_data_table, metadata_name, metadata_column, message, negate)
 
-    def __init__(self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"):
+    def __init__(
+        self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"
+    ):
         super().__init__(tool_data_table, metadata_column, message, negate)
         self.metadata_name = metadata_name
 
     def validate(self, value, trans=None):
-        super().validate(value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)), trans)
+        super().validate(
+            value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)), trans
+        )
 
 
 class MetadataNotInDataTableColumnValidator(MetadataInDataTableColumnValidator):
@@ -891,9 +917,12 @@ class MetadataNotInDataTableColumnValidator(MetadataInDataTableColumnValidator):
 
     note: this is covered in a framework test (validation_metadata_in_datatable)
     """
+
     requires_dataset_metadata = True
 
-    def __init__(self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"):
+    def __init__(
+        self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"
+    ):
         super().__init__(tool_data_table, metadata_name, metadata_column, message, negate)
 
     def validate(self, value, trans=None):
@@ -911,17 +940,23 @@ class MetadataInRangeValidator(InRangeValidator):
 
     note: this is covered in a framework test (validation_metadata_in_range)
     """
+
     requires_dataset_metadata = True
 
     @classmethod
     def from_element(cls, param, elem):
-        metadata_name = elem.get('metadata_name', None)
+        metadata_name = elem.get("metadata_name", None)
         assert metadata_name, "dataset_metadata_in_range validator requires metadata_name attribute."
         metadata_name = metadata_name.strip()
-        ret = cls(metadata_name, elem.get('message', None),
-                  elem.get('min'), elem.get('max'),
-                  elem.get('exclude_min', 'false'), elem.get('exclude_max', 'false'),
-                  elem.get('negate', 'false'))
+        ret = cls(
+            metadata_name,
+            elem.get("message", None),
+            elem.get("min"),
+            elem.get("max"),
+            elem.get("exclude_min", "false"),
+            elem.get("exclude_max", "false"),
+            elem.get("negate", "false"),
+        )
         ret.message = "Metadata: " + ret.message
         return ret
 
@@ -932,13 +967,15 @@ class MetadataInRangeValidator(InRangeValidator):
     def validate(self, value, trans=None):
         if value:
             if not isinstance(value, model.DatasetInstance):
-                raise ValueError('A non-dataset value was provided.')
+                raise ValueError("A non-dataset value was provided.")
             try:
-                value_to_check = float(value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)))
+                value_to_check = float(
+                    value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name))
+                )
             except KeyError:
-                raise ValueError(f'{self.metadata_name} Metadata missing')
+                raise ValueError(f"{self.metadata_name} Metadata missing")
             except ValueError:
-                raise ValueError(f'{self.metadata_name} must be a float or an integer')
+                raise ValueError(f"{self.metadata_name} must be a float or an integer")
             log.error(f"MetadataInRangeValidato.validate value_to_check {value_to_check}")
             super().validate(value_to_check, trans)
 
@@ -962,9 +999,7 @@ validator_types = dict(
     dataset_ok_validator=DatasetOkValidator,
 )
 
-deprecated_validator_types = dict(
-    dataset_metadata_in_file=MetadataInFileColumnValidator
-)
+deprecated_validator_types = dict(dataset_metadata_in_file=MetadataInFileColumnValidator)
 validator_types.update(deprecated_validator_types)
 
 
@@ -972,4 +1007,5 @@ def get_suite():
     """Get unittest suite for this module"""
     import doctest
     import sys
+
     return doctest.DocTestSuite(sys.modules[__name__])
diff --git a/lib/galaxy/tools/parameters/wrapped.py b/lib/galaxy/tools/parameters/wrapped.py
index 912ee26dd83..71a81c8f245 100644
--- a/lib/galaxy/tools/parameters/wrapped.py
+++ b/lib/galaxy/tools/parameters/wrapped.py
@@ -1,12 +1,12 @@
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     DataToolParameter,
-    SelectToolParameter
+    SelectToolParameter,
 )
 from galaxy.tools.parameters.grouping import (
     Conditional,
     Repeat,
-    Section
+    Section,
 )
 from galaxy.tools.wrappers import (
     DatasetCollectionWrapper,
@@ -14,7 +14,7 @@ from galaxy.tools.wrappers import (
     DatasetListWrapper,
     ElementIdentifierMapper,
     InputValueWrapper,
-    SelectToolParameterWrapper
+    SelectToolParameterWrapper,
 )
 
 PARAMS_UNWRAPPED = object()
@@ -23,13 +23,12 @@ PARAMS_UNWRAPPED = object()
 def copy_identifiers(source, destination):
     if isinstance(source, dict):
         for k, v in source.items():
-            if k.endswith('|__identifier__'):
+            if k.endswith("|__identifier__"):
                 if isinstance(destination, dict):
                     destination[k] = v
 
 
 class WrappedParameters:
-
     def __init__(self, trans, tool, incoming, input_datasets=None):
         self.trans = trans
         self.tool = tool
@@ -71,19 +70,17 @@ class WrappedParameters:
                 self.wrap_values(input.inputs, values, skip_missing_values=skip_missing_values)
             elif isinstance(input, DataToolParameter) and input.multiple:
                 dataset_instances = DatasetListWrapper.to_dataset_instances(value)
-                input_values[input.name] = \
-                    DatasetListWrapper(None,
-                                       dataset_instances,
-                                       datatypes_registry=trans.app.datatypes_registry,
-                                       tool=tool,
-                                       name=input.name,
-                                       formats=input.formats)
-            elif isinstance(input, DataToolParameter):
-                wrapper_kwds = dict(
+                input_values[input.name] = DatasetListWrapper(
+                    None,
+                    dataset_instances,
                     datatypes_registry=trans.app.datatypes_registry,
                     tool=tool,
                     name=input.name,
-                    formats=input.formats
+                    formats=input.formats,
+                )
+            elif isinstance(input, DataToolParameter):
+                wrapper_kwds = dict(
+                    datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name, formats=input.formats
                 )
                 element_identifier = element_identifier_mapper.identifier(value, input_values)
                 if element_identifier:
@@ -113,7 +110,7 @@ def make_dict_copy(from_dict):
     """
     copy_from_dict = {}
     for key, value in from_dict.items():
-        if type(value).__name__ == 'dict':
+        if type(value).__name__ == "dict":
             copy_from_dict[key] = make_dict_copy(value)
         elif isinstance(value, list):
             copy_from_dict[key] = make_list_copy(value)
@@ -134,4 +131,4 @@ def make_list_copy(from_list):
     return new_list
 
 
-__all__ = ('WrappedParameters', 'make_dict_copy')
+__all__ = ("WrappedParameters", "make_dict_copy")
diff --git a/lib/galaxy/tools/parameters/wrapped_json.py b/lib/galaxy/tools/parameters/wrapped_json.py
index 82c37e8dccb..1cac8c2e2e5 100644
--- a/lib/galaxy/tools/parameters/wrapped_json.py
+++ b/lib/galaxy/tools/parameters/wrapped_json.py
@@ -1,5 +1,10 @@
 import logging
-from typing import Any, Dict, List, Sequence
+from typing import (
+    Any,
+    Dict,
+    List,
+    Sequence,
+)
 
 import packaging.version
 
@@ -15,8 +20,7 @@ def json_wrap(inputs, input_values, profile, as_dict=None, handle_files="skip"):
     for input in inputs.values():
         input_name = input.name
         value_wrapper = input_values[input_name]
-        json_value = _json_wrap_input(input, value_wrapper, profile,
-                                      handle_files=handle_files)
+        json_value = _json_wrap_input(input, value_wrapper, profile, handle_files=handle_files)
         if json_value is SKIP_INPUT:
             continue
         as_dict[input_name] = json_value
@@ -43,20 +47,25 @@ def data_collection_input_to_staging_path_and_source_path(
     source_paths = v.all_paths
     metadata_files = v.all_metadata_files
     return [
-        {'staging_path': staging_path,
-         'source_path': source_path,
-         'metadata_files': [{'staging_path': f"{staging_path}.{mf[0]}", 'source_path': mf[1]} for mf in metadata_files]
-         } for staging_path, source_path, metadata_files in zip(staging_paths, source_paths, metadata_files)]
+        {
+            "staging_path": staging_path,
+            "source_path": source_path,
+            "metadata_files": [
+                {"staging_path": f"{staging_path}.{mf[0]}", "source_path": mf[1]} for mf in metadata_files
+            ],
+        }
+        for staging_path, source_path, metadata_files in zip(staging_paths, source_paths, metadata_files)
+    ]
 
 
-def data_input_to_staging_path_and_source_path(
-    v, invalid_chars: Sequence[str] = ("/",)
-) -> Dict[str, Any]:
+def data_input_to_staging_path_and_source_path(v, invalid_chars: Sequence[str] = ("/",)) -> Dict[str, Any]:
     staging_path = v.get_staging_path(invalid_chars=invalid_chars)
     return {
-        'staging_path': staging_path,
-        'source_path': data_input_to_path(v),
-        'metadata_files': [{'staging_path': f"{staging_path}.{mf[0]}", 'source_path': mf[1]} for mf in v.all_metadata_files]
+        "staging_path": staging_path,
+        "source_path": data_input_to_path(v),
+        "metadata_files": [
+            {"staging_path": f"{staging_path}.{mf[0]}", "source_path": mf[1]} for mf in v.all_metadata_files
+        ],
     }
 
 
@@ -67,20 +76,17 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
         repeat_job_value = []
         for d in value_wrapper:
             repeat_instance_job_value = {}
-            json_wrap(input.inputs, d, profile, repeat_instance_job_value,
-                      handle_files=handle_files)
+            json_wrap(input.inputs, d, profile, repeat_instance_job_value, handle_files=handle_files)
             repeat_job_value.append(repeat_instance_job_value)
         json_value = repeat_job_value
     elif input_type == "conditional":
         values = value_wrapper
         current = values["__current_case__"]
         conditional_job_value = {}
-        json_wrap(input.cases[current].inputs, values, profile,
-                  conditional_job_value, handle_files=handle_files)
+        json_wrap(input.cases[current].inputs, values, profile, conditional_job_value, handle_files=handle_files)
         test_param = input.test_param
         test_param_name = test_param.name
-        test_value = _json_wrap_input(test_param, values[test_param_name],
-                                      profile, handle_files=handle_files)
+        test_value = _json_wrap_input(test_param, values[test_param_name], profile, handle_files=handle_files)
         conditional_job_value[test_param_name] = test_value
         json_value = conditional_job_value
     elif input_type == "section":
@@ -91,7 +97,7 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
     elif input_type == "data" and input.multiple:
         if handle_files == "paths":
             json_value = [data_input_to_path(v) for v in value_wrapper]
-        elif handle_files == 'staging_path_and_source_path':
+        elif handle_files == "staging_path_and_source_path":
             json_value = [data_input_to_staging_path_and_source_path(v) for v in value_wrapper]
         elif handle_files == "skip":
             return SKIP_INPUT
@@ -100,7 +106,7 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
     elif input_type == "data":
         if handle_files == "paths":
             json_value = data_input_to_path(value_wrapper)
-        elif handle_files == 'staging_path_and_source_path':
+        elif handle_files == "staging_path_and_source_path":
             json_value = data_input_to_staging_path_and_source_path(value_wrapper)
         elif handle_files == "skip":
             return SKIP_INPUT
@@ -110,8 +116,8 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
                     value_wrapper = value_wrapper[0]
                 json_value = _hda_to_object(value_wrapper)
                 if input.load_contents:
-                    with open(str(value_wrapper), mode='rb') as fh:
-                        json_value['contents'] = fh.read(input.load_contents).decode('utf-8', errors='replace')
+                    with open(str(value_wrapper), mode="rb") as fh:
+                        json_value["contents"] = fh.read(input.load_contents).decode("utf-8", errors="replace")
                 return json_value
             else:
                 return None
@@ -140,7 +146,7 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
         else:
             json_value = _cast_if_not_none(value_wrapper, bool, empty_to_none=input.optional)
     elif input_type == "select":
-        if packaging.version.parse(str(profile)) < packaging.version.parse('20.05'):
+        if packaging.version.parse(str(profile)) < packaging.version.parse("20.05"):
             json_value = _cast_if_not_none(value_wrapper, str)
         else:
             if input.multiple:
@@ -167,23 +173,23 @@ def _hda_to_object(hda):
 
     for key, value in hda_dict.items():
         if key.startswith("metadata_"):
-            metadata_dict[key[len("metadata_"):]] = value
+            metadata_dict[key[len("metadata_") :]] = value
 
     return {
-        'file_ext': hda_dict['file_ext'],
-        'file_size': hda_dict['file_size'],
-        'name': hda_dict['name'],
-        'metadata': metadata_dict,
-        'src': {'src': 'hda', 'id': hda.id},
+        "file_ext": hda_dict["file_ext"],
+        "file_size": hda_dict["file_size"],
+        "name": hda_dict["name"],
+        "metadata": metadata_dict,
+        "src": {"src": "hda", "id": hda.id},
     }
 
 
 def _cast_if_not_none(value, cast_to, empty_to_none=False):
     # log.debug("value [%s], type[%s]" % (value, type(value)))
-    if value is None or (empty_to_none and str(value) == ''):
+    if value is None or (empty_to_none and str(value) == ""):
         return None
     else:
         return cast_to(value)
 
 
-__all__ = ('json_wrap', )
+__all__ = ("json_wrap",)
diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index b95d2b88371..7eb612d9d11 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -17,8 +17,7 @@ from galaxy.workflow.modules import module_factory
 log = logging.getLogger(__name__)
 
 
-class ToolRecommendations():
-
+class ToolRecommendations:
     def __init__(self):
         self.tool_recommendation_model_path = None
         self.admin_tool_recommendations_path = None
@@ -58,6 +57,7 @@ class ToolRecommendations():
             # keras is not downloaded because of conditional requirement and Galaxy does not build
             try:
                 import tensorflow as tf
+
                 tf.compat.v1.disable_v2_behavior()
             except Exception:
                 trans.response.status = 400
@@ -70,8 +70,8 @@ class ToolRecommendations():
             counter_layer_weights = 0
             self.tool_recommendation_model_path = self.__download_model(remote_model_url)
             # read the hdf5 attributes
-            trained_model = h5py.File(self.tool_recommendation_model_path, 'r')
-            model_config = json.loads(trained_model['model_config'][()])
+            trained_model = h5py.File(self.tool_recommendation_model_path, "r")
+            model_config = json.loads(trained_model["model_config"][()])
             # set tensorflow's graph and session to maintain
             # consistency between model load and predict methods
             with self.graph.as_default():
@@ -90,12 +90,12 @@ class ToolRecommendations():
                         trans.response.status = 400
                         return False
             # set the dictionary of tools
-            self.model_data_dictionary = json.loads(trained_model['data_dictionary'][()])
+            self.model_data_dictionary = json.loads(trained_model["data_dictionary"][()])
             self.reverse_dictionary = {v: k for k, v in self.model_data_dictionary.items()}
             # set the list of compatible tools
-            self.compatible_tools = json.loads(trained_model['compatible_tools'][()])
-            tool_weights = json.loads(trained_model['class_weights'][()])
-            self.standard_connections = json.loads(trained_model['standard_connections'][()])
+            self.compatible_tools = json.loads(trained_model["compatible_tools"][()])
+            tool_weights = json.loads(trained_model["class_weights"][()])
+            self.standard_connections = json.loads(trained_model["standard_connections"][()])
             # sort the tools' usage dictionary
             tool_pos_sorted = [int(key) for key in tool_weights.keys()]
             for k in tool_pos_sorted:
@@ -122,21 +122,21 @@ class ToolRecommendations():
                     if admin_recommendation_preferences:
                         for tool_id in admin_recommendation_preferences:
                             tool_info = admin_recommendation_preferences[tool_id]
-                            if 'is_deprecated' in tool_info[0]:
+                            if "is_deprecated" in tool_info[0]:
                                 self.deprecated_tools[tool_id] = tool_info[0]["text_message"]
                             else:
                                 if tool_id not in self.admin_recommendations:
                                     self.admin_recommendations[tool_id] = tool_info
 
-    def __download_model(self, model_url, download_local='database/'):
+    def __download_model(self, model_url, download_local="database/"):
         """
         Download the model from remote server
         """
-        local_dir = os.path.join(os.getcwd(), download_local, 'tool_recommendation_model.hdf5')
+        local_dir = os.path.join(os.getcwd(), download_local, "tool_recommendation_model.hdf5")
         # read model from remote
         model_binary = requests.get(model_url, timeout=DEFAULT_SOCKET_TIMEOUT)
         # save model to a local directory
-        with open(local_dir, 'wb') as model_file:
+        with open(local_dir, "wb") as model_file:
             model_file.write(model_binary.content)
             return local_dir
 
@@ -144,11 +144,11 @@ class ToolRecommendations():
         """
         Get the input and output extensions of a tool
         """
-        payload = {'type': 'tool', 'tool_id': tool_id, '_': 'true'}
-        inputs = payload.get('inputs', {})
+        payload = {"type": "tool", "tool_id": tool_id, "_": "true"}
+        inputs = payload.get("inputs", {})
         trans.workflow_building_mode = workflow_building_modes.ENABLED
         module = module_factory.from_dict(trans, payload)
-        if 'tool_state' not in payload:
+        if "tool_state" not in payload:
             module_state = {}
             populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
             module.recover_state(module_state)
@@ -157,9 +157,9 @@ class ToolRecommendations():
         input_extensions = list()
         output_extensions = list()
         for i_ext in inputs:
-            input_extensions.extend(i_ext['extensions'])
+            input_extensions.extend(i_ext["extensions"])
         for o_ext in outputs:
-            output_extensions.extend(o_ext['extensions'])
+            output_extensions.extend(o_ext["extensions"])
         return input_extensions, output_extensions
 
     def __filter_tool_predictions(self, trans, prediction_data, tool_ids, tool_scores, last_tool_name):
@@ -180,7 +180,12 @@ class ToolRecommendations():
             c_dict = dict()
             for t_id in self.all_tools:
                 # select the name and tool id if it is installed in Galaxy
-                if t_id == child and score > 0.0 and child in last_compatible_tools and child not in self.deprecated_tools:
+                if (
+                    t_id == child
+                    and score > 0.0
+                    and child in last_compatible_tools
+                    and child not in self.deprecated_tools
+                ):
                     full_tool_id = self.all_tools[t_id][0]
                     pred_input_extensions, _ = self.__get_tool_extensions(trans, full_tool_id)
                     c_dict["name"] = self.all_tools[t_id][1]
@@ -191,7 +196,9 @@ class ToolRecommendations():
         # incorporate preferences set by admins
         if self.admin_tool_recommendations_path:
             # filter out deprecated tools
-            t_ids_scores = [(tid, score) for tid, score in zip(tool_ids, tool_scores) if tid not in self.deprecated_tools]
+            t_ids_scores = [
+                (tid, score) for tid, score in zip(tool_ids, tool_scores) if tid not in self.deprecated_tools
+            ]
             # set the property if the last tool of the sequence is deprecated
             if last_tool_name in self.deprecated_tools:
                 prediction_data["is_deprecated"] = True
@@ -291,9 +298,13 @@ class ToolRecommendations():
             prediction = np.reshape(prediction, (nw_dimension,))
             half_len = int(nw_dimension / 2)
             # get recommended tools from published workflows
-            pub_t, pub_v = self.__separate_predictions(self.standard_connections, prediction[:half_len], last_tool_name, weight_values, topk)
+            pub_t, pub_v = self.__separate_predictions(
+                self.standard_connections, prediction[:half_len], last_tool_name, weight_values, topk
+            )
             # get recommended tools from normal workflows
-            c_t, c_v = self.__separate_predictions(self.compatible_tools, prediction[half_len:], last_tool_name, weight_values, topk)
+            c_t, c_v = self.__separate_predictions(
+                self.compatible_tools, prediction[half_len:], last_tool_name, weight_values, topk
+            )
             # combine predictions coming from different workflows
             # promote recommended tools coming from published workflows
             # to the top and then show other recommendations
diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py
index 8ffef968398..d7c67391929 100644
--- a/lib/galaxy/tools/remote_tool_eval.py
+++ b/lib/galaxy/tools/remote_tool_eval.py
@@ -45,7 +45,8 @@ class ToolAppConfig(NamedTuple):
 
 class ToolApp(MinimalToolApp):
     """Dummy App that allows loading tools"""
-    name = 'tool_app'
+
+    name = "tool_app"
 
     def __init__(
         self,
@@ -70,22 +71,23 @@ def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):
     metadata_params = get_metadata_params(WORKING_DIRECTORY)
     datatypes_config = metadata_params["datatypes_config"]
     if not os.path.exists(datatypes_config):
-        datatypes_config = os.path.join(WORKING_DIRECTORY, 'configs', datatypes_config)
+        datatypes_config = os.path.join(WORKING_DIRECTORY, "configs", datatypes_config)
     datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
     object_store = get_object_store(WORKING_DIRECTORY)
     import_store = store.imported_store_for_metadata(IMPORT_STORE_DIRECTORY)
     # TODO: clean up random places from which we read files in the working directory
-    job_io = JobIO.from_json(os.path.join(IMPORT_STORE_DIRECTORY, 'job_io.json'), sa_session=import_store.sa_session)
+    job_io = JobIO.from_json(os.path.join(IMPORT_STORE_DIRECTORY, "job_io.json"), sa_session=import_store.sa_session)
     tool_app_config = ToolAppConfig(
-        name='tool_app',
+        name="tool_app",
         tool_data_path=job_io.tool_data_path,
         galaxy_data_manager_data_path=job_io.galaxy_data_manager_data_path,
         nginx_upload_path=TMPDIR,
         len_file_path=job_io.len_file_path,
         builds_file_path=job_io.builds_file_path,
         root=TMPDIR,
-        is_admin_user=lambda _: job_io.user_context.is_admin)
-    with open(os.path.join(IMPORT_STORE_DIRECTORY, 'tool_data_tables.json')) as data_tables_json:
+        is_admin_user=lambda _: job_io.user_context.is_admin,
+    )
+    with open(os.path.join(IMPORT_STORE_DIRECTORY, "tool_data_tables.json")) as data_tables_json:
         tdtm = ToolDataTableManager.from_dict(json.load(data_tables_json))
     app = ToolApp(
         sa_session=import_store.sa_session,
@@ -98,9 +100,11 @@ def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):
     # TODO: could try to serialize just a minimal tool variant instead of the whole thing ?
     tool_source = get_tool_source(tool_source_class=job_io.tool_source_class, raw_tool_source=job_io.tool_source)
     tool = create_tool_from_source(app, tool_source=tool_source, tool_dir=job_io.tool_dir)
-    tool_evaluator = evaluation.RemoteToolEvaluator(app=app, tool=tool, job=job_io.job, local_working_directory=WORKING_DIRECTORY)
+    tool_evaluator = evaluation.RemoteToolEvaluator(
+        app=app, tool=tool, job=job_io.job, local_working_directory=WORKING_DIRECTORY
+    )
     tool_evaluator.set_compute_environment(compute_environment=SharedComputeEnvironment(job_io=job_io, job=job_io.job))
-    with open(os.path.join(WORKING_DIRECTORY, 'tool_script.sh'), 'a') as out:
+    with open(os.path.join(WORKING_DIRECTORY, "tool_script.sh"), "a") as out:
         command_line, extra_filenames, environment_variables = tool_evaluator.build()
         out.write(command_line)
 
@@ -109,17 +113,17 @@ if __name__ == "__main__":
     TMPDIR = tempfile.mkdtemp()
     WORKING_DIRECTORY = os.getcwd()
     WORKING_PARENT = os.path.join(WORKING_DIRECTORY, os.path.pardir)
-    if not os.path.isdir("working") and os.path.isdir(os.path.join(WORKING_PARENT, 'working')):
+    if not os.path.isdir("working") and os.path.isdir(os.path.join(WORKING_PARENT, "working")):
         # We're probably in pulsar
         WORKING_DIRECTORY = WORKING_PARENT
-    METADATA_DIRECTORY = os.path.join(WORKING_DIRECTORY, 'metadata')
-    IMPORT_STORE_DIRECTORY = os.path.join(METADATA_DIRECTORY, 'outputs_new')
-    EXPORT_STORE_DIRECTORY = os.path.join(METADATA_DIRECTORY, 'outputs_populated')
+    METADATA_DIRECTORY = os.path.join(WORKING_DIRECTORY, "metadata")
+    IMPORT_STORE_DIRECTORY = os.path.join(METADATA_DIRECTORY, "outputs_new")
+    EXPORT_STORE_DIRECTORY = os.path.join(METADATA_DIRECTORY, "outputs_populated")
     try:
         main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY)
     except Exception:
         os.makedirs(EXPORT_STORE_DIRECTORY, exist_ok=True)
-        with open(os.path.join(EXPORT_STORE_DIRECTORY, 'traceback.txt'), 'w') as out:
+        with open(os.path.join(EXPORT_STORE_DIRECTORY, "traceback.txt"), "w") as out:
             out.write(traceback.format_exc())
         raise
     finally:
diff --git a/lib/galaxy/tools/repositories.py b/lib/galaxy/tools/repositories.py
index cedb4c4c8d2..bb4a3f43635 100644
--- a/lib/galaxy/tools/repositories.py
+++ b/lib/galaxy/tools/repositories.py
@@ -30,16 +30,16 @@ class ValidationContext:
         self.config = Bunch()
         self.config.tool_data_path = tool_data_path
         self.config.shed_tool_data_path = shed_tool_data_path
-        self.temporary_path = tempfile.mkdtemp(prefix='tool_validation_')
-        self.config.tool_data_table_config = os.path.join(self.temporary_path, 'tool_data_table_conf.xml')
-        self.config.shed_tool_data_table_config = os.path.join(self.temporary_path, 'shed_tool_data_table_conf.xml')
+        self.temporary_path = tempfile.mkdtemp(prefix="tool_validation_")
+        self.config.tool_data_table_config = os.path.join(self.temporary_path, "tool_data_table_conf.xml")
+        self.config.shed_tool_data_table_config = os.path.join(self.temporary_path, "shed_tool_data_table_conf.xml")
         self.config.interactivetools_enable = True
         self.tool_data_tables = tool_data_tables
         self.tool_shed_registry = Bunch(tool_sheds={})
         self.datatypes_registry = registry
         self.hgweb_config_manager = hgweb_config_manager
         self.biotools_metadata_source = biotools_metadata_source
-        self.config.len_file_path = os.path.join(self.temporary_path, 'chromlen.txt')
+        self.config.len_file_path = os.path.join(self.temporary_path, "chromlen.txt")
         # If the builds file path is set to None, tools/__init__.py will load the default.
         # Otherwise it will attempt to load a nonexistent file and log an error. This does
         # not appear to be an issue with the len_file_path config option.
@@ -70,8 +70,8 @@ class ValidationContext:
                 shed_tool_data_path=work_dir,
                 tool_data_tables=tool_data_tables,
                 registry=app.datatypes_registry,
-                hgweb_config_manager=getattr(app, 'hgweb_config_manager', None),
-                biotools_metadata_source=getattr(app, 'biotools_metadata_source', None),
+                hgweb_config_manager=getattr(app, "hgweb_config_manager", None),
+                biotools_metadata_source=getattr(app, "biotools_metadata_source", None),
             ) as app:
                 yield app
         finally:
diff --git a/lib/galaxy/tools/search/__init__.py b/lib/galaxy/tools/search/__init__.py
index a324321e9e9..46e853199e8 100644
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -7,7 +7,12 @@ through the library docs at https://whoosh.readthedocs.io.
 import logging
 import os
 import re
-from typing import Dict, List, Tuple, Union
+from typing import (
+    Dict,
+    List,
+    Tuple,
+    Union,
+)
 
 from whoosh import (
     analysis,
@@ -18,7 +23,7 @@ from whoosh.fields import (
     ID,
     KEYWORD,
     Schema,
-    TEXT
+    TEXT,
 )
 from whoosh.qparser import (
     MultifieldParser,
@@ -63,7 +68,9 @@ class ToolBoxSearch:
         for panel_view in toolbox.panel_views():
             panel_view_id = panel_view.id
             panel_index_dir = os.path.join(index_dir, panel_view_id)
-            panel_searches[panel_view_id] = ToolPanelViewSearch(toolbox, panel_view_id, panel_index_dir, index_help=index_help)
+            panel_searches[panel_view_id] = ToolPanelViewSearch(
+                toolbox, panel_view_id, panel_index_dir, index_help=index_help
+            )
         self.panel_searches = panel_searches
         # We keep track of how many times the tool index has been rebuilt.
         # We start at -1, so that after the first index the count is at 0,
@@ -91,14 +98,16 @@ class ToolPanelViewSearch:
     """
 
     def __init__(self, toolbox, panel_view_id: str, index_dir: str, index_help: bool = True):
-        self.schema = Schema(id=ID(stored=True, unique=True),
-                             old_id=ID,
-                             stub=KEYWORD,
-                             name=TEXT(analyzer=analysis.SimpleAnalyzer()),
-                             description=TEXT,
-                             section=TEXT,
-                             help=TEXT,
-                             labels=KEYWORD)
+        self.schema = Schema(
+            id=ID(stored=True, unique=True),
+            old_id=ID,
+            stub=KEYWORD,
+            name=TEXT(analyzer=analysis.SimpleAnalyzer()),
+            description=TEXT,
+            section=TEXT,
+            help=TEXT,
+            labels=KEYWORD,
+        )
         self.rex = analysis.RegexTokenizer()
         self.index_dir = index_dir
         self.toolbox = toolbox
@@ -117,8 +126,10 @@ class ToolPanelViewSearch:
         execution_timer = ExecutionTimer()
         with self.index.reader() as reader:
             # Index ocasionally contains empty stored fields
-            indexed_tool_ids = {f['id'] for f in reader.all_stored_fields() if f}
-        tool_ids_to_remove = (indexed_tool_ids - set(tool_cache._tool_paths_by_id.keys())).union(tool_cache._removed_tool_ids)
+            indexed_tool_ids = {f["id"] for f in reader.all_stored_fields() if f}
+        tool_ids_to_remove = (indexed_tool_ids - set(tool_cache._tool_paths_by_id.keys())).union(
+            tool_cache._removed_tool_ids
+        )
         for indexed_tool_id in indexed_tool_ids:
             indexed_tool = tool_cache.get_tool_by_id(indexed_tool_id)
             if indexed_tool:
@@ -130,7 +141,7 @@ class ToolPanelViewSearch:
             tool_ids_to_remove.add(indexed_tool_id)
         with AsyncWriter(self.index) as writer:
             for tool_id in tool_ids_to_remove:
-                writer.delete_by_term('id', tool_id)
+                writer.delete_by_term("id", tool_id)
             for tool_id in tool_cache._new_tool_ids - indexed_tool_ids:
                 tool = self.toolbox.get_tool(tool_id)
                 if tool and tool.is_latest_version and self.toolbox.panel_has_tool(tool, self.panel_view_id):
@@ -152,40 +163,41 @@ class ToolPanelViewSearch:
 
     def _create_doc(self, tool_id: str, tool, index_help: bool = True) -> Dict[str, str]:
         #  Do not add data managers to the public index
-        if tool.tool_type == 'manage_data':
+        if tool.tool_type == "manage_data":
             return {}
         add_doc_kwds = {
             "id": tool_id,
             "description": to_unicode(tool.description),
-            "section": to_unicode(tool.get_panel_section()[1] if len(tool.get_panel_section()) == 2 else ''),
-            "help": to_unicode("")
+            "section": to_unicode(tool.get_panel_section()[1] if len(tool.get_panel_section()) == 2 else ""),
+            "help": to_unicode(""),
         }
-        if tool.name.find('-') != -1:
+        if tool.name.find("-") != -1:
             # Replace hyphens, since they are wildcards in Whoosh causing false positives
-            add_doc_kwds['name'] = (' ').join(token.text for token in self.rex(to_unicode(tool.name)))
+            add_doc_kwds["name"] = (" ").join(token.text for token in self.rex(to_unicode(tool.name)))
         else:
-            add_doc_kwds['name'] = to_unicode(tool.name)
+            add_doc_kwds["name"] = to_unicode(tool.name)
         if tool.guid:
             # Create a stub consisting of owner, repo, and tool from guid
-            slash_indexes = [m.start() for m in re.finditer('/', tool.guid)]
-            id_stub = tool.guid[(slash_indexes[1] + 1): slash_indexes[4]]
-            add_doc_kwds['stub'] = (' ').join(token.text for token in self.rex(to_unicode(id_stub)))
+            slash_indexes = [m.start() for m in re.finditer("/", tool.guid)]
+            id_stub = tool.guid[(slash_indexes[1] + 1) : slash_indexes[4]]
+            add_doc_kwds["stub"] = (" ").join(token.text for token in self.rex(to_unicode(id_stub)))
         else:
-            add_doc_kwds['stub'] = to_unicode(id)
+            add_doc_kwds["stub"] = to_unicode(id)
         if tool.labels:
-            add_doc_kwds['labels'] = to_unicode(" ".join(tool.labels))
+            add_doc_kwds["labels"] = to_unicode(" ".join(tool.labels))
         if index_help:
             raw_help = tool.raw_help
             if raw_help:
                 try:
-                    add_doc_kwds['help'] = to_unicode(raw_help)
+                    add_doc_kwds["help"] = to_unicode(raw_help)
                 except Exception:
                     # Don't fail to build index just because help can't be converted.
                     pass
         return add_doc_kwds
 
     def search(
-        self, q: str,
+        self,
+        q: str,
         tool_name_boost: CanConvertToFloat,
         tool_id_boost: CanConvertToFloat,
         tool_section_boost: CanConvertToFloat,
@@ -196,22 +208,23 @@ class ToolPanelViewSearch:
         tool_search_limit: CanConvertToFloat,
         tool_enable_ngram_search: bool,
         tool_ngram_minsize: CanConvertToInt,
-        tool_ngram_maxsize: CanConvertToInt
+        tool_ngram_maxsize: CanConvertToInt,
     ) -> List[str]:
         """
         Perform search on the in-memory index. Weight in the given boosts.
         """
         # Change field boosts for searcher
         self.searcher = self.index.searcher(
-            weighting=MultiWeighting(BM25F(),
-                                     old_id=BM25F(old_id_B=float(tool_id_boost)),
-                                     name=BM25F(name_B=float(tool_name_boost)),
-                                     section=BM25F(section_B=float(tool_section_boost)),
-                                     description=BM25F(description_B=float(tool_description_boost)),
-                                     labels=BM25F(labels_B=float(tool_label_boost)),
-                                     stub=BM25F(stub_B=float(tool_stub_boost)),
-                                     help=BM25F(help_B=float(tool_help_boost))
-                                     )
+            weighting=MultiWeighting(
+                BM25F(),
+                old_id=BM25F(old_id_B=float(tool_id_boost)),
+                name=BM25F(name_B=float(tool_name_boost)),
+                section=BM25F(section_B=float(tool_section_boost)),
+                description=BM25F(description_B=float(tool_description_boost)),
+                labels=BM25F(labels_B=float(tool_label_boost)),
+                stub=BM25F(stub_B=float(tool_stub_boost)),
+                help=BM25F(help_B=float(tool_help_boost)),
+            )
         )
         # Use OrGroup to change the default operation for joining multiple terms to logical OR.
         # This means e.g. for search 'bowtie of king arthur' a document that only has 'bowtie' will be a match.
@@ -222,27 +235,37 @@ class ToolPanelViewSearch:
         # https://whoosh.readthedocs.io/en/latest/parsing.html#searching-for-any-terms-instead-of-all-terms-by-default
         # Adding the FuzzyTermPlugin to account for misspellings and typos, using a max distance of 2
         og = OrGroup.factory(0.9)
-        self.parser = MultifieldParser(['name', 'old_id', 'description', 'section', 'help', 'labels', 'stub'], schema=self.schema, group=og)
+        self.parser = MultifieldParser(
+            ["name", "old_id", "description", "section", "help", "labels", "stub"], schema=self.schema, group=og
+        )
 
         cleaned_query = q.lower()
         if tool_enable_ngram_search is True:
             rval = self._search_ngrams(cleaned_query, tool_ngram_minsize, tool_ngram_maxsize, tool_search_limit)
             return rval
         else:
-            cleaned_query = ' '.join(token.text for token in self.rex(cleaned_query))
+            cleaned_query = " ".join(token.text for token in self.rex(cleaned_query))
             # Use asterisk Whoosh wildcard so e.g. 'bow' easily matches 'bowtie'
             parsed_query = self.parser.parse(f"*{cleaned_query}*")
-            hits = self.searcher.search(parsed_query, limit=float(tool_search_limit), sortedby='')
-            return [hit['id'] for hit in hits]
+            hits = self.searcher.search(parsed_query, limit=float(tool_search_limit), sortedby="")
+            return [hit["id"] for hit in hits]
 
-    def _search_ngrams(self, cleaned_query: str, tool_ngram_minsize: CanConvertToInt, tool_ngram_maxsize: CanConvertToInt, tool_search_limit: CanConvertToFloat) -> List[str]:
+    def _search_ngrams(
+        self,
+        cleaned_query: str,
+        tool_ngram_minsize: CanConvertToInt,
+        tool_ngram_maxsize: CanConvertToInt,
+        tool_search_limit: CanConvertToFloat,
+    ) -> List[str]:
         """
         Break tokens into ngrams and search on those instead.
         This should make searching more resistant to typos and unfinished words.
         See docs at https://whoosh.readthedocs.io/en/latest/ngrams.html
         """
         hits_with_score: Dict[str, float] = {}
-        token_analyzer = StandardAnalyzer() | analysis.NgramFilter(minsize=int(tool_ngram_minsize), maxsize=int(tool_ngram_maxsize))
+        token_analyzer = StandardAnalyzer() | analysis.NgramFilter(
+            minsize=int(tool_ngram_minsize), maxsize=int(tool_ngram_maxsize)
+        )
         ngrams = [token.text for token in token_analyzer(cleaned_query)]
         for query in ngrams:
             # Get the tool list with respective scores for each qgram
@@ -251,15 +274,17 @@ class ToolPanelViewSearch:
                 is_present = False
                 for prev_hit in hits_with_score:
                     # Check if the tool appears again for the next qgram search
-                    if curr_hit['id'] == prev_hit:
+                    if curr_hit["id"] == prev_hit:
                         is_present = True
                         # Add the current score with the previous one if the
                         # tool appears again for the next qgram
                         hits_with_score[prev_hit] = curr_hits.score(i) + hits_with_score[prev_hit]
                 # Add the tool if not present to the collection with its score
                 if not is_present:
-                    hits_with_score[curr_hit['id']] = curr_hits.score(i)
+                    hits_with_score[curr_hit["id"]] = curr_hits.score(i)
         # Sort the results based on aggregated BM25 score in decreasing order of scores
-        hits_with_score_list: List[Tuple[str, float]] = sorted(hits_with_score.items(), key=lambda x: x[1], reverse=True)
+        hits_with_score_list: List[Tuple[str, float]] = sorted(
+            hits_with_score.items(), key=lambda x: x[1], reverse=True
+        )
         # Return the tool ids
-        return [item[0] for item in hits_with_score_list[0:int(tool_search_limit)]]
+        return [item[0] for item in hits_with_score_list[0 : int(tool_search_limit)]]
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index 8920b1d2a2e..e90df90a485 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -1,7 +1,10 @@
 import logging
 import os
 import os.path
-from typing import List, Tuple
+from typing import (
+    List,
+    Tuple,
+)
 
 import galaxy.tools.parameters.basic
 import galaxy.tools.parameters.grouping
@@ -15,9 +18,11 @@ from galaxy.util import (
 try:
     from nose.tools import nottest
 except ImportError:
+
     def nottest(x):
         return x
 
+
 log = logging.getLogger(__name__)
 
 
@@ -29,7 +34,7 @@ def parse_tests(tool, tests_source):
     """
     raw_tests_dict = tests_source.parse_tests_to_dict()
     tests = []
-    for i, raw_test_dict in enumerate(raw_tests_dict.get('tests', [])):
+    for i, raw_test_dict in enumerate(raw_tests_dict.get("tests", [])):
         test = description_from_tool_object(tool, i, raw_test_dict)
         tests.append(test)
     return tests
@@ -40,12 +45,14 @@ def description_from_tool_object(tool, test_index, raw_test_dict):
     required_data_tables: List[str] = []
     required_loc_files: List[str] = []
 
-    num_outputs = raw_test_dict.get('expect_num_outputs', None)
+    num_outputs = raw_test_dict.get("expect_num_outputs", None)
     if num_outputs:
         num_outputs = int(num_outputs)
 
     try:
-        processed_inputs = _process_raw_inputs(tool, tool.inputs, raw_test_dict["inputs"], required_files, required_data_tables, required_loc_files)
+        processed_inputs = _process_raw_inputs(
+            tool, tool.inputs, raw_test_dict["inputs"], required_files, required_data_tables, required_loc_files
+        )
         processed_test_dict = {
             "inputs": processed_inputs,
             "outputs": raw_test_dict["outputs"],
@@ -80,7 +87,9 @@ def description_from_tool_object(tool, test_index, raw_test_dict):
     return ToolTestDescription(processed_test_dict)
 
 
-def _process_raw_inputs(tool, tool_inputs, raw_inputs, required_files, required_data_tables, required_loc_files, parent_context=None):
+def _process_raw_inputs(
+    tool, tool_inputs, raw_inputs, required_files, required_data_tables, required_loc_files, parent_context=None
+):
     """
     Recursively expand flat list of inputs into "tree" form of flat list
     (| using to nest to new levels) structure and expand dataset
@@ -98,7 +107,15 @@ def _process_raw_inputs(tool, tool_inputs, raw_inputs, required_files, required_
             case = _matching_case_for_value(tool, value, case_value)
             if case:
                 for input_name, input_value in case.inputs.items():
-                    case_inputs = _process_raw_inputs(tool, {input_name: input_value}, raw_inputs, required_files, required_data_tables, required_loc_files, parent_context=cond_context)
+                    case_inputs = _process_raw_inputs(
+                        tool,
+                        {input_name: input_value},
+                        raw_inputs,
+                        required_files,
+                        required_data_tables,
+                        required_loc_files,
+                        parent_context=cond_context,
+                    )
                     expanded_inputs.update(case_inputs)
                 if not value.type == "text":
                     expanded_case_value = _split_if_str(case.value)
@@ -110,13 +127,23 @@ def _process_raw_inputs(tool, tool_inputs, raw_inputs, required_files, required_
                     # as a new instance with value defined and hence enter
                     # an infinite loop - hence the "case_value is not None"
                     # check.
-                    processed_value = _process_simple_value(value.test_param, expanded_case_value, required_data_tables, required_loc_files)
+                    processed_value = _process_simple_value(
+                        value.test_param, expanded_case_value, required_data_tables, required_loc_files
+                    )
                     expanded_inputs[case_context.for_state()] = processed_value
         elif isinstance(value, galaxy.tools.parameters.grouping.Section):
             context = ParamContext(name=value.name, parent_context=parent_context)
             assert value.inputs
             for r_value in value.inputs.values():
-                expanded_input = _process_raw_inputs(tool, {context.for_state(): r_value}, raw_inputs, required_files, required_data_tables, required_loc_files, parent_context=context)
+                expanded_input = _process_raw_inputs(
+                    tool,
+                    {context.for_state(): r_value},
+                    raw_inputs,
+                    required_files,
+                    required_data_tables,
+                    required_loc_files,
+                    parent_context=context,
+                )
                 if expanded_input:
                     expanded_inputs.update(expanded_input)
         elif isinstance(value, galaxy.tools.parameters.grouping.Repeat):
@@ -126,7 +153,15 @@ def _process_raw_inputs(tool, tool_inputs, raw_inputs, required_files, required_
                 updated = False
                 assert value.inputs
                 for r_value in value.inputs.values():
-                    expanded_input = _process_raw_inputs(tool, {context.for_state(): r_value}, raw_inputs, required_files, required_data_tables, required_loc_files, parent_context=context)
+                    expanded_input = _process_raw_inputs(
+                        tool,
+                        {context.for_state(): r_value},
+                        raw_inputs,
+                        required_files,
+                        required_data_tables,
+                        required_loc_files,
+                        parent_context=context,
+                    )
                     if expanded_input:
                         expanded_inputs.update(expanded_input)
                         updated = True
@@ -149,8 +184,8 @@ def _process_raw_inputs(tool, tool_inputs, raw_inputs, required_files, required_
                         _add_uploaded_dataset(context.for_state(), v, param_extra, value, required_files)
                     processed_value = param_value
                 elif isinstance(value, galaxy.tools.parameters.basic.DataCollectionToolParameter):
-                    assert 'collection' in param_extra
-                    collection_def = param_extra['collection']
+                    assert "collection" in param_extra
+                    collection_def = param_extra["collection"]
                     for input_dict in collection_def.collect_inputs():
                         name = input_dict["name"]
                         value = input_dict["value"]
@@ -158,7 +193,9 @@ def _process_raw_inputs(tool, tool_inputs, raw_inputs, required_files, required_
                         require_file(name, value, attributes, required_files)
                     processed_value = collection_def
                 else:
-                    processed_value = _process_simple_value(value, param_value, required_data_tables, required_loc_files)
+                    processed_value = _process_simple_value(
+                        value, param_value, required_data_tables, required_loc_files
+                    )
                 expanded_inputs[context.for_state()] = processed_value
     return expanded_inputs
 
@@ -172,7 +209,7 @@ def _process_simple_value(param, param_value, required_data_tables, required_loc
         def process_param_value(param_value):
             found_value = False
             value_for_text = None
-            for (text, opt_value, _) in getattr(param, 'static_options', []):
+            for (text, opt_value, _) in getattr(param, "static_options", []):
                 if param_value == opt_value:
                     found_value = True
                 if value_for_text is None and param_value == text:
@@ -187,6 +224,7 @@ def _process_simple_value(param, param_value, required_data_tables, required_loc
             else:
                 processed_value = param_value
             return processed_value
+
         # Do replacement described above for lists or singleton
         # values.
         if isinstance(param_value, list):
@@ -213,12 +251,14 @@ def _matching_case_for_value(tool, cond, declared_value):
 
         def matches_declared_value(case_value):
             return _process_bool_param_value(test_param, case_value) == query_value
+
     elif isinstance(test_param, galaxy.tools.parameters.basic.SelectToolParameter):
         if declared_value is not None:
             # Test case supplied explicit value to check against.
 
             def matches_declared_value(case_value):
                 return case_value == declared_value
+
         elif test_param.static_options:
             # No explicit value in test case, not much to do if options are dynamic but
             # if static options are available can find the one specified as default or
@@ -233,6 +273,7 @@ def _matching_case_for_value(tool, cond, declared_value):
 
             def matches_declared_value(case_value):
                 return case_value == default_option
+
         else:
             # No explicit value for this param and cannot determine a
             # default - give up. Previously this would just result in a key
@@ -253,7 +294,7 @@ def _matching_case_for_value(tool, cond, declared_value):
 
 def _add_uploaded_dataset(name, value, extra, input_parameter, required_files):
     if value is None:
-        assert input_parameter.optional, f'{name} is not optional. You must provide a valid filename.'
+        assert input_parameter.optional, f"{name} is not optional. You must provide a valid filename."
         return value
     return require_file(name, value, extra, required_files)
 
@@ -286,21 +327,20 @@ def _process_bool_param_value(param, param_value):
 def require_file(name, value, extra, required_files):
     if (value, extra) not in required_files:
         required_files.append((value, extra))  # these files will be uploaded
-    name_change = [att for att in extra.get('edit_attributes', []) if att.get('type') == 'name']
+    name_change = [att for att in extra.get("edit_attributes", []) if att.get("type") == "name"]
     if name_change:
-        name_change = name_change[-1].get('value')  # only the last name change really matters
+        name_change = name_change[-1].get("value")  # only the last name change really matters
         value = name_change  # change value for select to renamed uploaded file for e.g. composite dataset
     else:
-        for end in ['.zip', '.gz']:
+        for end in [".zip", ".gz"]:
             if value.endswith(end):
-                value = value[:-len(end)]
+                value = value[: -len(end)]
                 break
         value = os.path.basename(value)  # if uploading a file in a path other than root of test-data
     return value
 
 
 class ParamContext:
-
     def __init__(self, name, index=None, parent_context=None):
         self.parent_context = parent_context
         self.name = name
@@ -349,7 +389,6 @@ class ParamContext:
 
 
 class RootParamContext:
-
     def __init__(self):
         pass
 
diff --git a/lib/galaxy/tools/util/galaxyops/__init__.py b/lib/galaxy/tools/util/galaxyops/__init__.py
index 70839468ab2..3dc2537d640 100644
--- a/lib/galaxy/tools/util/galaxyops/__init__.py
+++ b/lib/galaxy/tools/util/galaxyops/__init__.py
@@ -26,8 +26,8 @@ def parse_cols_arg(cols):
     if cols:
         # Handle case where no strand column included - in this case, cols
         # looks something like 1,2,3,
-        if cols.endswith(','):
-            cols += '0'
+        if cols.endswith(","):
+            cols += "0"
         col_list = [int(x) - 1 for x in cols.split(",")]
         return col_list
     else:
@@ -41,4 +41,10 @@ def default_printer(stream, exc, obj):
 
 def skipped(reader, filedesc=""):
     first_line, line_contents, problem = reader.skipped_lines[0]
-    return 'Skipped %d invalid lines%s, 1st line #%d: "%s", problem: %s' % (reader.skipped, filedesc, first_line, line_contents, problem)
+    return 'Skipped %d invalid lines%s, 1st line #%d: "%s", problem: %s' % (
+        reader.skipped,
+        filedesc,
+        first_line,
+        line_contents,
+        problem,
+    )
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index f84f926f0cf..f7abc1b7f1f 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -36,11 +36,14 @@ from galaxy.tools.parameters.wrapped_json import (
 from galaxy.util import filesystem_safe_string
 
 if TYPE_CHECKING:
-    from galaxy.tools import Tool
-    from galaxy.tools.parameters.basic import SelectToolParameter, ToolParameter
     from galaxy.datatypes.registry import Registry
     from galaxy.job_execution.compute_environment import ComputeEnvironment
     from galaxy.model.metadata import MetadataCollection
+    from galaxy.tools import Tool
+    from galaxy.tools.parameters.basic import (
+        SelectToolParameter,
+        ToolParameter,
+    )
 
 log = logging.getLogger(__name__)
 
@@ -61,6 +64,7 @@ class ToolParameterValueWrapper:
 
     def __bool__(self) -> bool:
         return bool(self.value)
+
     __nonzero__ = __bool__
 
     def get_display_text(self, quote: bool = True) -> str:
@@ -68,7 +72,7 @@ class ToolParameterValueWrapper:
         Returns a string containing the value that would be displayed to the user in the tool interface.
         When quote is True (default), the string is escaped for e.g. command-line usage.
         """
-        rval = self.input.value_to_display_text(self.value) or ''
+        rval = self.input.value_to_display_text(self.value) or ""
         if quote:
             return shlex.quote(rval)
         return rval
@@ -83,7 +87,10 @@ class RawObjectWrapper(ToolParameterValueWrapper):
         self.obj = obj
 
     def __bool__(self) -> bool:
-        return bool(self.obj)  # FIXME: would it be safe/backwards compatible to rename .obj to .value, so that we can just inherit this method?
+        return bool(
+            self.obj
+        )  # FIXME: would it be safe/backwards compatible to rename .obj to .value, so that we can just inherit this method?
+
     __nonzero__ = __bool__
 
     def __str__(self) -> str:
@@ -114,7 +121,7 @@ class InputValueWrapper(ToolParameterValueWrapper):
         self._other_values: Dict[str, str] = other_values or {}
 
     def _get_cast_value(self, other: Any) -> Union[str, int, float, bool, None]:
-        if self.input.type == 'boolean' and isinstance(other, str):
+        if self.input.type == "boolean" and isinstance(other, str):
             return str(self)
         # For backward compatibility, allow `$wrapper != ""` for optional non-text param
         if self.input.optional and self.value is None:
@@ -123,14 +130,12 @@ class InputValueWrapper(ToolParameterValueWrapper):
             else:
                 return None
         cast_table = {
-            'text': str,
-            'integer': int,
-            'float': float,
-            'boolean': bool,
+            "text": str,
+            "integer": int,
+            "float": float,
+            "boolean": bool,
         }
-        return cast(
-            Union[str, int, float, bool], cast_table.get(self.input.type, str)(self)
-        )
+        return cast(Union[str, int, float, bool], cast_table.get(self.input.type, str)(self))
 
     def __eq__(self, other: Any) -> bool:
         return bool(self._get_cast_value(other) == other)
@@ -141,7 +146,7 @@ class InputValueWrapper(ToolParameterValueWrapper):
     def __str__(self) -> str:
         to_param_dict_string = self.input.to_param_dict_string(self.value, self._other_values)
         if isinstance(to_param_dict_string, list):
-            return ','.join(to_param_dict_string)
+            return ",".join(to_param_dict_string)
         else:
             return to_param_dict_string
 
@@ -194,7 +199,9 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
 
         def __getattr__(self, name: str) -> Any:
             if name not in self._fields:
-                self._fields[name] = self._input.options.get_field_by_name_for_value(name, self._value, None, self._other_values)
+                self._fields[name] = self._input.options.get_field_by_name_for_value(
+                    name, self._value, None, self._other_values
+                )
             values = map(str, self._fields[name])
             if name in PATH_ATTRIBUTES and self._compute_environment:
                 # If we infer this is a path, rewrite it if needed.
@@ -225,7 +232,7 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
 
     def __eq__(self, other: Any) -> bool:
         if isinstance(other, str):
-            if other == '' and self.value in (None, []):
+            if other == "" and self.value in (None, []):
                 # Allow $wrapper == '' for select (self.value is None) and multiple select (self.value is []) params
                 return True
             return str(self) == other
@@ -238,12 +245,10 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
     def __str__(self) -> str:
         # Assuming value is never a path - otherwise would need to pass
         # along following argument value_map=self._path_rewriter.
-        return str(
-            self.input.to_param_dict_string(self.value, other_values=self._other_values)
-        )
+        return str(self.input.to_param_dict_string(self.value, other_values=self._other_values))
 
     def __add__(self, x: Any) -> str:
-        return f'{self}{x}'
+        return f"{self}{x}"
 
     def __getattr__(self, key: Any) -> Any:
         return getattr(self.input, key)
@@ -285,6 +290,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
                     rval = self.metadata.spec[name].no_value
                 metadata_param = self.metadata.spec[name].param
                 from galaxy.model.metadata import FileParameter
+
                 rval = metadata_param.to_safe_string(rval)
                 if isinstance(metadata_param, FileParameter) and self.compute_environment:
                     rewrite = self.compute_environment.input_metadata_rewrite(self.dataset, rval)
@@ -301,6 +307,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
 
         def __bool__(self) -> bool:
             return bool(self.metadata.__nonzero__())
+
         __nonzero__ = __bool__
 
         def __iter__(self) -> Iterator[Any]:
@@ -355,7 +362,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
             assert dataset
             self.metadata = self.MetadataWrapper(dataset, compute_environment)
             if isinstance(dataset, HasTags):
-                self.groups = {tag.user_value.lower() for tag in dataset.tags if tag.user_tname == 'group'}
+                self.groups = {tag.user_value.lower() for tag in dataset.tags if tag.user_tname == "group"}
             else:
                 # May be a 'FakeDatasetAssociation'
                 self.groups = set()
@@ -405,7 +412,9 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         Not safe for commandline use, would need additional sanitization.
         """
         max_len = 254 - len(self.file_ext)
-        safe_element_identifier = filesystem_safe_string(self.element_identifier, max_len=max_len, invalid_chars=invalid_chars)
+        safe_element_identifier = filesystem_safe_string(
+            self.element_identifier, max_len=max_len, invalid_chars=invalid_chars
+        )
         return f"{safe_element_identifier}.{self.file_ext}"
 
     @property
@@ -413,13 +422,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         return self.unsanitized.get_metadata_file_paths_and_extensions() if self else []
 
     def serialize(self, invalid_chars: Sequence[str] = ("/",)) -> Dict[str, Any]:
-        return (
-            data_input_to_staging_path_and_source_path(
-                self, invalid_chars=invalid_chars
-            )
-            if self
-            else {}
-        )
+        return data_input_to_staging_path_and_source_path(self, invalid_chars=invalid_chars) if self else {}
 
     @property
     def is_collection(self) -> bool:
@@ -434,7 +437,9 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
             if datatype is not None:
                 datatypes.append(datatype)
             else:
-                log.warning(f"Datatype class not found for extension '{e}', which is used as parameter of 'is_of_type()' method")
+                log.warning(
+                    f"Datatype class not found for extension '{e}', which is used as parameter of 'is_of_type()' method"
+                )
         return self.dataset.datatype.matches_any(datatypes)
 
     def __str__(self) -> str:
@@ -444,14 +449,18 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
             return str(self.unsanitized.file_name)
 
     def __getattr__(self, key: Any) -> Any:
-        if self.false_path is not None and key == 'file_name':
+        if self.false_path is not None and key == "file_name":
             # Path to dataset was rewritten for this job.
             return self.false_path
-        elif key == 'extra_files_path':
+        elif key == "extra_files_path":
             if self.__io_type == "input":
-                path_rewrite = self.compute_environment and self.compute_environment.input_extra_files_rewrite(self.unsanitized)
+                path_rewrite = self.compute_environment and self.compute_environment.input_extra_files_rewrite(
+                    self.unsanitized
+                )
             else:
-                path_rewrite = self.compute_environment and self.compute_environment.output_extra_files_rewrite(self.unsanitized)
+                path_rewrite = self.compute_environment and self.compute_environment.output_extra_files_rewrite(
+                    self.unsanitized
+                )
             if path_rewrite:
                 return path_rewrite
             else:
@@ -471,13 +480,14 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
                         # instead of just returning a non-existent
                         # path like DiskObjectStore.
                         raise
-        elif key == 'serialize':
+        elif key == "serialize":
             return self.serialize
         else:
             return getattr(self.dataset, key)
 
     def __bool__(self) -> bool:
         return bool(self.dataset)
+
     __nonzero__ = __bool__
 
 
@@ -488,22 +498,20 @@ class HasDatasets:
     def __iter__(self) -> Iterator[Any]:
         pass
 
-    def _dataset_wrapper(
-        self, dataset: DatasetInstance, **kwargs: Any
-    ) -> DatasetFilenameWrapper:
+    def _dataset_wrapper(self, dataset: DatasetInstance, **kwargs: Any) -> DatasetFilenameWrapper:
         return DatasetFilenameWrapper(dataset, **kwargs)
 
     def paths_as_file(self, sep: str = "\n") -> str:
         contents = sep.join(map(str, self))
-        with tempfile.NamedTemporaryFile(mode='w+', prefix="gx_file_list", dir=self.job_working_directory, delete=False) as fh:
+        with tempfile.NamedTemporaryFile(
+            mode="w+", prefix="gx_file_list", dir=self.job_working_directory, delete=False
+        ) as fh:
             fh.write(contents)
             filepath = fh.name
         return filepath
 
 
-class DatasetListWrapper(
-    List[DatasetFilenameWrapper], ToolParameterValueWrapper, HasDatasets
-):
+class DatasetListWrapper(List[DatasetFilenameWrapper], ToolParameterValueWrapper, HasDatasets):
     """ """
 
     def __init__(
@@ -567,7 +575,7 @@ class DatasetListWrapper(
         if not self._dataset_elements_cache.get(group):
             wrappers = []
             for element in self:
-                if any(t for t in element.tags if t.user_tname.lower() == 'group' and t.value.lower() == group):
+                if any(t for t in element.tags if t.user_tname.lower() == "group" and t.value.lower() == group):
                     wrappers.append(element)
             self._dataset_elements_cache[group] = wrappers
         return self._dataset_elements_cache[group]
@@ -576,11 +584,12 @@ class DatasetListWrapper(
         return [v.serialize(invalid_chars) for v in self]
 
     def __str__(self) -> str:
-        return ','.join(map(str, self))
+        return ",".join(map(str, self))
 
     def __bool__(self) -> bool:
         # Fail `#if $param` checks in cheetah if optional input is not provided
         return any(self)
+
     __nonzero__ = __bool__
 
 
@@ -591,20 +600,16 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
     def __init__(
         self,
         job_working_directory: Optional[str],
-        has_collection: Union[
-            None, DatasetCollectionElement, HistoryDatasetCollectionAssociation
-        ],
+        has_collection: Union[None, DatasetCollectionElement, HistoryDatasetCollectionAssociation],
         datatypes_registry: "Registry",
         **kwargs: Any,
     ) -> None:
         super().__init__()
         self.job_working_directory = job_working_directory
         self._dataset_elements_cache: Dict[str, List[DatasetFilenameWrapper]] = {}
-        self._element_identifiers_extensions_paths_and_metadata_files: Optional[
-            List[List[Any]]
-        ] = None
+        self._element_identifiers_extensions_paths_and_metadata_files: Optional[List[List[Any]]] = None
         self.datatypes_registry = datatypes_registry
-        kwargs['datatypes_registry'] = datatypes_registry
+        kwargs["datatypes_registry"] = datatypes_registry
         self.kwargs = kwargs
 
         if has_collection is None:
@@ -633,9 +638,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
             element_identifier = dataset_collection_element.element_identifier
 
             if dataset_collection_element.is_collection:
-                element_wrapper: Union[
-                    DatasetCollectionWrapper, DatasetFilenameWrapper
-                ] = DatasetCollectionWrapper(
+                element_wrapper: Union[DatasetCollectionWrapper, DatasetFilenameWrapper] = DatasetCollectionWrapper(
                     job_working_directory, dataset_collection_element, **kwargs
                 )
             else:
@@ -652,8 +655,16 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         if not self._dataset_elements_cache.get(group):
             wrappers = []
             for element in self.collection.dataset_elements:
-                if any(t for t in element.dataset_instance.tags if t.user_tname.lower() == 'group' and t.value.lower() == group):
-                    wrappers.append(self._dataset_wrapper(element.element_object, identifier=element.element_identifier, **self.kwargs))
+                if any(
+                    t
+                    for t in element.dataset_instance.tags
+                    if t.user_tname.lower() == "group" and t.value.lower() == group
+                ):
+                    wrappers.append(
+                        self._dataset_wrapper(
+                            element.element_object, identifier=element.element_identifier, **self.kwargs
+                        )
+                    )
             self._dataset_elements_cache[group] = wrappers
         return self._dataset_elements_cache[group]
 
@@ -676,7 +687,9 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
 
     @property
     def all_metadata_files(self) -> List[List[str]]:
-        return [metadata_files for _, _, _, metadata_files in self.element_identifiers_extensions_paths_and_metadata_files]
+        return [
+            metadata_files for _, _, _, metadata_files in self.element_identifiers_extensions_paths_and_metadata_files
+        ]
 
     @property
     def element_identifiers_extensions_paths_and_metadata_files(
@@ -684,9 +697,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
     ) -> List[List[Any]]:
         if self._element_identifiers_extensions_paths_and_metadata_files is None:
             if self.collection:
-                result = (
-                    self.collection.element_identifiers_extensions_paths_and_metadata_files
-                )
+                result = self.collection.element_identifiers_extensions_paths_and_metadata_files
                 self._element_identifiers_extensions_paths_and_metadata_files = result
                 return result
             else:
@@ -702,19 +713,21 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         for element_identifiers, extension, *_ in self.element_identifiers_extensions_paths_and_metadata_files:
             datatype = self.datatypes_registry.get_datatype_by_extension(extension)
             if datatype:
-                extension = getattr(datatype, 'file_ext_export_alias', extension)
+                extension = getattr(datatype, "file_ext_export_alias", extension)
             current_element_identifiers = []
             for element_identifier in element_identifiers:
                 max_len = 254 - len(extension)
                 if include_collection_name:
                     max_len = max_len - (len(self.name or "") + 1)
-                    assert max_len >= 1, 'Could not stage element, element identifier is too long'
-                current_element_identifier = filesystem_safe_string(element_identifier, max_len=max_len, invalid_chars=invalid_chars)
+                    assert max_len >= 1, "Could not stage element, element identifier is too long"
+                current_element_identifier = filesystem_safe_string(
+                    element_identifier, max_len=max_len, invalid_chars=invalid_chars
+                )
                 if include_collection_name and self.name:
                     current_element_identifier = f"{filesystem_safe_string(self.name, invalid_chars=invalid_chars)}{os.path.sep}{current_element_identifier}"
                 current_element_identifiers.append(current_element_identifier)
 
-            safe_element_identifiers.append(f'{os.path.sep.join(current_element_identifiers)}.{extension}')
+            safe_element_identifiers.append(f"{os.path.sep.join(current_element_identifiers)}.{extension}")
         return safe_element_identifiers
 
     def serialize(
@@ -732,9 +745,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
     def is_input_supplied(self) -> bool:
         return self.__input_supplied
 
-    def __getitem__(
-        self, key: Union[str, int]
-    ) -> Union[None, "DatasetCollectionWrapper", DatasetFilenameWrapper]:
+    def __getitem__(self, key: Union[str, int]) -> Union[None, "DatasetCollectionWrapper", DatasetFilenameWrapper]:
         if not self.__input_supplied:
             return None
         if isinstance(key, int):
@@ -742,9 +753,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         else:
             return self.__element_instances[key]
 
-    def __getattr__(
-        self, key: str
-    ) -> Union[None, "DatasetCollectionWrapper", DatasetFilenameWrapper]:
+    def __getattr__(self, key: str) -> Union[None, "DatasetCollectionWrapper", DatasetFilenameWrapper]:
         if not self.__input_supplied:
             return None
         try:
@@ -763,6 +772,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         # Fail `#if $param` checks in cheetah is optional input
         # not specified or if resulting collection is empty.
         return self.__input_supplied and bool(self.__element_instance_list)
+
     __nonzero__ = __bool__
 
 
@@ -775,9 +785,7 @@ class ElementIdentifierMapper:
         else:
             self.identifier_key_dict = {}
 
-    def identifier(
-        self, dataset_value: str, input_values: Dict[str, str]
-    ) -> Optional[str]:
+    def identifier(self, dataset_value: str, input_values: Dict[str, str]) -> Optional[str]:
         identifier_key = self.identifier_key_dict.get(dataset_value, None)
         element_identifier = None
         if identifier_key:
diff --git a/lib/galaxy/tours/__init__.py b/lib/galaxy/tours/__init__.py
index b8549dc9a45..0074f981b72 100644
--- a/lib/galaxy/tours/__init__.py
+++ b/lib/galaxy/tours/__init__.py
@@ -1,17 +1,11 @@
 from ._impl import build_tours_registry
 from ._interface import ToursRegistry
-from ._schema import Tour
-from ._schema import TourCore
-from ._schema import TourDetails
-from ._schema import TourList
-from ._schema import TourStep
+from ._schema import (
+    Tour,
+    TourCore,
+    TourDetails,
+    TourList,
+    TourStep,
+)
 
-__all__ = [
-    'build_tours_registry',
-    'ToursRegistry',
-    'Tour',
-    'TourCore',
-    'TourDetails',
-    'TourList',
-    'TourStep'
-]
+__all__ = ["build_tours_registry", "ToursRegistry", "Tour", "TourCore", "TourDetails", "TourList", "TourStep"]
diff --git a/lib/galaxy/tours/_impl.py b/lib/galaxy/tours/_impl.py
index 68f4b692c83..fb3071bd1c6 100644
--- a/lib/galaxy/tours/_impl.py
+++ b/lib/galaxy/tours/_impl.py
@@ -11,7 +11,6 @@ from galaxy.util import config_directories_from_setting
 from ._interface import ToursRegistry
 from ._schema import TourList
 
-
 log = logging.getLogger(__name__)
 
 
@@ -21,24 +20,23 @@ def build_tours_registry(tour_directories: str):
 
 def load_tour_steps(contents_dict):
     #  Some of this can be done on the clientside.  Maybe even should?
-    title_default = contents_dict.get('title_default')
-    for step in contents_dict['steps']:
-        if 'intro' in step:
-            step['content'] = step.pop('intro')
-        if 'position' in step:
-            step['placement'] = step.pop('position')
-        if 'element' not in step:
-            step['orphan'] = True
-        if title_default and 'title' not in step:
-            step['title'] = title_default
+    title_default = contents_dict.get("title_default")
+    for step in contents_dict["steps"]:
+        if "intro" in step:
+            step["content"] = step.pop("intro")
+        if "position" in step:
+            step["placement"] = step.pop("position")
+        if "element" not in step:
+            step["orphan"] = True
+        if title_default and "title" not in step:
+            step["title"] = title_default
 
 
 @ToursRegistry.register
 class ToursRegistryImpl:
-
     def __init__(self, tour_directories):
         self.tour_directories = config_directories_from_setting(tour_directories)
-        self._extensions = ('.yml', '.yaml')
+        self._extensions = (".yml", ".yaml")
         self._load_tours()
 
     def get_tours(self):
@@ -46,10 +44,10 @@ class ToursRegistryImpl:
         tours = []
         for k in self.tours.keys():
             tourdata = {
-                'id': k,
-                'name': self.tours[k].get('name'),
-                'description': self.tours[k].get('description'),
-                'tags': self.tours[k].get('tags')
+                "id": k,
+                "name": self.tours[k].get("name"),
+                "description": self.tours[k].get("description"),
+                "tags": self.tours[k].get("tags"),
             }
             tours.append(tourdata)
         return parse_obj_as(TourList, tours)
@@ -97,11 +95,14 @@ class ToursRegistryImpl:
         except OSError:
             log.exception(f"Tour '{tour_id}' could not be loaded, error reading file.")
         except yaml.error.YAMLError:
-            log.exception("Tour '%s' could not be loaded, error within file."
-                " Please check your yaml syntax." % tour_id)
+            log.exception(
+                "Tour '%s' could not be loaded, error within file." " Please check your yaml syntax." % tour_id
+            )
         except TypeError:
-            log.exception("Tour '%s' could not be loaded, error within file."
-                " Possibly spacing related. Please check your yaml syntax." % tour_id)
+            log.exception(
+                "Tour '%s' could not be loaded, error within file."
+                " Possibly spacing related. Please check your yaml syntax." % tour_id
+            )
 
     def _get_tour_id_from_path(self, tour_path):
         filename = os.path.basename(tour_path)
diff --git a/lib/galaxy/tours/_interface.py b/lib/galaxy/tours/_interface.py
index 33cd2f76168..86c33a9b858 100644
--- a/lib/galaxy/tours/_interface.py
+++ b/lib/galaxy/tours/_interface.py
@@ -1,4 +1,7 @@
-from abc import ABC, abstractmethod
+from abc import (
+    ABC,
+    abstractmethod,
+)
 
 from ._schema import (
     TourDetails,
@@ -7,7 +10,6 @@ from ._schema import (
 
 
 class ToursRegistry(ABC):
-
     @abstractmethod
     def get_tours(self) -> TourList:
         """Return list of tours."""
diff --git a/lib/galaxy/tours/_schema.py b/lib/galaxy/tours/_schema.py
index bf5d1274fef..056223e216d 100644
--- a/lib/galaxy/tours/_schema.py
+++ b/lib/galaxy/tours/_schema.py
@@ -3,80 +3,50 @@ from typing import (
     Optional,
 )
 
-from pydantic import BaseModel, Field
+from pydantic import (
+    BaseModel,
+    Field,
+)
 
 
 class TourCore(BaseModel):
-    name: str = Field(
-        title='Name',
-        description='Name of tour'
-    )
-    description: str = Field(
-        title='Description',
-        description='Tour description'
-    )
-    tags: List[str] = Field(
-        title='Tags',
-        description='Topic topic tags'
-    )
+    name: str = Field(title="Name", description="Name of tour")
+    description: str = Field(title="Description", description="Tour description")
+    tags: List[str] = Field(title="Tags", description="Topic topic tags")
 
 
 class Tour(TourCore):
-    id: str = Field(
-        title='Identifier',
-        description='Tour identifier'
-    )
+    id: str = Field(title="Identifier", description="Tour identifier")
 
 
 class TourList(BaseModel):
-    __root__: List[Tour] = Field(
-        title='List of tours',
-        default=[]
-    )
+    __root__: List[Tour] = Field(title="List of tours", default=[])
 
 
 class TourStep(BaseModel):
-    title: Optional[str] = Field(
-        title='Title',
-        description='Title displayed in the header of the step container'
-    )
-    content: Optional[str] = Field(
-        title='Content',
-        description='Text shown to the user'
-    )
+    title: Optional[str] = Field(title="Title", description="Title displayed in the header of the step container")
+    content: Optional[str] = Field(title="Content", description="Text shown to the user")
     element: Optional[str] = Field(
-        title='Element',
-        description='JQuery selector for the element to be described/clicked'
+        title="Element", description="JQuery selector for the element to be described/clicked"
     )
     placement: Optional[str] = Field(
-        title='Placement',
-        description='Placement of the text box relative to the selected element'
+        title="Placement", description="Placement of the text box relative to the selected element"
     )
     preclick: Optional[list] = Field(
-        title='Pre-click',
-        description='Elements that receive a click() event before the step is shown'
+        title="Pre-click", description="Elements that receive a click() event before the step is shown"
     )
     postclick: Optional[list] = Field(
-        title='Post-click',
-        description='Elements that receive a click() event after the step is shown'
+        title="Post-click", description="Elements that receive a click() event after the step is shown"
     )
     textinsert: Optional[str] = Field(
-        title='Text-insert',
-        description='Text to insert if element is a text box (e.g. tool search or upload)'
+        title="Text-insert", description="Text to insert if element is a text box (e.g. tool search or upload)"
     )
     backdrop: Optional[bool] = Field(
-        title='Backdrop',
-        description=('Show a dark backdrop behind the popover and its element,'
-            'highlighting the current step')
+        title="Backdrop",
+        description=("Show a dark backdrop behind the popover and its element," "highlighting the current step"),
     )
 
 
 class TourDetails(TourCore):
-    title_default: Optional[str] = Field(
-        title='Default title',
-        description='Default title for each step'
-    )
-    steps: List[TourStep] = Field(
-        title='Steps',
-        description='Tour steps'
-    )
+    title_default: Optional[str] = Field(title="Default title", description="Default title for each step")
+    steps: List[TourStep] = Field(title="Steps", description="Tour steps")
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index a259fbb4f52..ec2b61cd186 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -44,6 +44,7 @@ from boltons.iterutils import (
 )
 from requests.adapters import HTTPAdapter
 from requests.packages.urllib3.util.retry import Retry
+
 try:
     import grp
 except ImportError:
@@ -68,7 +69,11 @@ except ImportError:
 
 from .custom_logging import get_logger
 from .inflection import Inflector
-from .path import safe_contains, safe_makedirs, safe_relpath  # noqa: F401
+from .path import (  # noqa: F401
+    safe_contains,
+    safe_makedirs,
+    safe_relpath,
+)
 
 inflector = Inflector()
 
@@ -80,16 +85,16 @@ namedtuple = collections.namedtuple
 CHUNK_SIZE = 65536  # 64k
 
 DATABASE_MAX_STRING_SIZE = 32768
-DATABASE_MAX_STRING_SIZE_PRETTY = '32K'
+DATABASE_MAX_STRING_SIZE_PRETTY = "32K"
 
 DEFAULT_SOCKET_TIMEOUT = 600
 
-gzip_magic = b'\x1f\x8b'
-bz2_magic = b'BZh'
-DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8')
-NULL_CHAR = b'\x00'
+gzip_magic = b"\x1f\x8b"
+bz2_magic = b"BZh"
+DEFAULT_ENCODING = os.environ.get("GALAXY_DEFAULT_ENCODING", "utf-8")
+NULL_CHAR = b"\x00"
 BINARY_CHARS = [NULL_CHAR]
-FILENAME_VALID_CHARS = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
+FILENAME_VALID_CHARS = ".,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
 
 RW_R__R__ = stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IROTH
 RWXR_XR_X = stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH
@@ -107,23 +112,23 @@ def str_removeprefix(s: str, prefix: str):
     if sys.version_info >= (3, 9):
         return s.removeprefix(prefix)
     if s.startswith(prefix):
-        return s[len(prefix):]
+        return s[len(prefix) :]
     return s
 
 
 def remove_protocol_from_url(url):
-    """ Supplied URL may be null, if not ensure http:// or https://
+    """Supplied URL may be null, if not ensure http:// or https://
     etc... is stripped off.
     """
     if url is None:
         return url
 
     # We have a URL
-    if url.find('://') > 0:
-        new_url = url.split('://')[1]
+    if url.find("://") > 0:
+        new_url = url.split("://")[1]
     else:
         new_url = url
-    return new_url.rstrip('/')
+    return new_url.rstrip("/")
 
 
 def is_binary(value):
@@ -182,16 +187,16 @@ def directory_hash_id(id):
         # Drop the last three digits -- 1000 files per directory
         padded = padded[:-3]
         # Break into chunks of three
-        return [padded[i * 3:(i + 1) * 3] for i in range(len(padded) // 3)]
+        return [padded[i * 3 : (i + 1) * 3] for i in range(len(padded) // 3)]
     else:
         # assume it is a UUID
         return list(iter(s[0:3]))
 
 
 def get_charset_from_http_headers(headers, default=None):
-    rval = headers.get('content-type', None)
-    if rval and 'charset=' in rval:
-        rval = rval.split('charset=')[-1].split(';')[0].strip()
+    rval = headers.get("content-type", None)
+    if rval and "charset=" in rval:
+        rval = rval.split("charset=")[-1].split(";")[0].strip()
         if rval:
             return rval
     return default
@@ -199,12 +204,14 @@ def get_charset_from_http_headers(headers, default=None):
 
 def synchronized(func):
     """This wrapper will serialize access to 'func' to a single thread. Use it as a decorator."""
+
     def caller(*params, **kparams):
         _lock.acquire(True)  # Wait
         try:
             return func(*params, **kparams)
         finally:
             _lock.release()
+
     return caller
 
 
@@ -267,7 +274,7 @@ def parse_xml(fname, strip_whitespace=True, remove_comments=True):
         tree = etree.parse(fname, parser=parser)
         root = tree.getroot()
         if strip_whitespace:
-            for elem in root.iter('*'):
+            for elem in root.iter("*"):
                 if elem.text is not None:
                     elem.text = elem.text.strip()
                 if elem.tail is not None:
@@ -287,12 +294,12 @@ def parse_xml_string(xml_string, strip_whitespace=True):
     try:
         tree = etree.fromstring(xml_string)
     except ValueError as e:
-        if 'strings with encoding declaration are not supported' in unicodify(e):
-            tree = etree.fromstring(xml_string.encode('utf-8'))
+        if "strings with encoding declaration are not supported" in unicodify(e):
+            tree = etree.fromstring(xml_string.encode("utf-8"))
         else:
             raise e
     if strip_whitespace:
-        for elem in tree.iter('*'):
+        for elem in tree.iter("*"):
             if elem.text is not None:
                 elem.text = elem.text.strip()
             if elem.tail is not None:
@@ -310,18 +317,18 @@ def xml_to_string(elem, pretty=False):
     """
     try:
         if elem is not None:
-            xml_str = etree.tostring(elem, encoding='unicode')
+            xml_str = etree.tostring(elem, encoding="unicode")
         else:
-            xml_str = ''
+            xml_str = ""
     except TypeError as e:
         # we assume this is a comment
-        if hasattr(elem, 'text'):
+        if hasattr(elem, "text"):
             return f"<!-- {elem.text} -->\n"
         else:
             raise e
     if xml_str and pretty:
-        pretty_string = xml.dom.minidom.parseString(xml_str).toprettyxml(indent='    ')
-        return "\n".join(line for line in pretty_string.split('\n') if not re.match(r'^[\s\\nb\']*$', line))
+        pretty_string = xml.dom.minidom.parseString(xml_str).toprettyxml(indent="    ")
+        return "\n".join(line for line in pretty_string.split("\n") if not re.match(r"^[\s\\nb\']*$", line))
     return xml_str
 
 
@@ -364,7 +371,7 @@ def xml_element_to_dict(elem):
     if elem.text:
         text = elem.text.strip()
         if text and sub_elems or elem.attrib:
-            rval[elem.tag]['#text'] = text
+            rval[elem.tag]["#text"] = text
         else:
             rval[elem.tag] = text
 
@@ -372,7 +379,7 @@ def xml_element_to_dict(elem):
 
 
 def pretty_print_xml(elem, level=0):
-    pad = '    '
+    pad = "    "
     i = "\n" + level * pad
     if len(elem):
         if not elem.text or not elem.text.strip():
@@ -410,14 +417,16 @@ def get_file_size(value, default=None):
                 return default
 
 
-def shrink_stream_by_size(value, size, join_by=b"..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False):
+def shrink_stream_by_size(
+    value, size, join_by=b"..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False
+):
     """
     Shrinks bytes read from `value` to `size`.
 
     `value` needs to implement tell/seek, so files need to be opened in binary mode.
     Returns unicode text with invalid characters replaced.
     """
-    rval = b''
+    rval = b""
     join_by = smart_str(join_by)
     if get_file_size(value) > size:
         start = value.tell()
@@ -433,7 +442,9 @@ def shrink_stream_by_size(value, size, join_by=b"..", left_larger=True, beginnin
                 rval = value.read(size)
                 value.seek(start)
                 return rval
-            raise ValueError('With the provided join_by value (%s), the minimum size value is %i.' % (join_by, min_size))
+            raise ValueError(
+                "With the provided join_by value (%s), the minimum size value is %i." % (join_by, min_size)
+            )
         left_index = right_index = int((size - len_join_by) / 2)
         if left_index + right_index + len_join_by < size:
             if left_larger:
@@ -453,17 +464,17 @@ def shrink_stream_by_size(value, size, join_by=b"..", left_larger=True, beginnin
 
 
 def shrink_and_unicodify(stream):
-    stream = unicodify(stream, strip_null=True) or ''
-    if (len(stream) > DATABASE_MAX_STRING_SIZE):
-        stream = shrink_string_by_size(stream,
-                                       DATABASE_MAX_STRING_SIZE,
-                                       join_by="\n..\n",
-                                       left_larger=True,
-                                       beginning_on_size_error=True)
+    stream = unicodify(stream, strip_null=True) or ""
+    if len(stream) > DATABASE_MAX_STRING_SIZE:
+        stream = shrink_string_by_size(
+            stream, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True
+        )
     return stream
 
 
-def shrink_string_by_size(value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False):
+def shrink_string_by_size(
+    value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False
+):
     if len(value) > size:
         len_join_by = len(join_by)
         min_size = len_join_by + 2
@@ -472,7 +483,9 @@ def shrink_string_by_size(value, size, join_by="..", left_larger=True, beginning
                 return value[:size]
             elif end_on_size_error:
                 return value[-size:]
-            raise ValueError('With the provided join_by value (%s), the minimum size value is %i.' % (join_by, min_size))
+            raise ValueError(
+                "With the provided join_by value (%s), the minimum size value is %i." % (join_by, min_size)
+            )
         left_index = right_index = int((size - len_join_by) / 2)
         if left_index + right_index + len_join_by < size:
             if left_larger:
@@ -511,7 +524,7 @@ def pretty_print_time_interval(time=False, precise=False, utc=False):
     day_diff = diff.days
 
     if day_diff < 0:
-        return ''
+        return ""
 
     if precise:
         if day_diff == 0:
@@ -560,19 +573,21 @@ def pretty_print_json(json_data, is_json_string=False):
 valid_chars = set(string.ascii_letters + string.digits + " -=_.()/+*^,:?!")
 
 # characters that are allowed but need to be escaped
-mapped_chars = {'>': '__gt__',
-                '<': '__lt__',
-                "'": '__sq__',
-                '"': '__dq__',
-                '[': '__ob__',
-                ']': '__cb__',
-                '{': '__oc__',
-                '}': '__cc__',
-                '@': '__at__',
-                '\n': '__cn__',
-                '\r': '__cr__',
-                '\t': '__tc__',
-                '#': '__pd__'}
+mapped_chars = {
+    ">": "__gt__",
+    "<": "__lt__",
+    "'": "__sq__",
+    '"': "__dq__",
+    "[": "__ob__",
+    "]": "__cb__",
+    "{": "__oc__",
+    "}": "__cc__",
+    "@": "__at__",
+    "\n": "__cn__",
+    "\r": "__cr__",
+    "\t": "__tc__",
+    "#": "__pd__",
+}
 
 
 def restore_text(text, character_map=mapped_chars):
@@ -584,19 +599,24 @@ def restore_text(text, character_map=mapped_chars):
     return text
 
 
-def sanitize_text(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
+def sanitize_text(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character="X"):
     """
     Restricts the characters that are allowed in text; accepts both strings
     and lists of strings; non-string entities will be cast to strings.
     """
     if isinstance(text, list):
-        return [sanitize_text(x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) for x in text]
+        return [
+            sanitize_text(
+                x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character
+            )
+            for x in text
+        ]
     if not isinstance(text, str):
         text = smart_str(text)
     return _sanitize_text_helper(text, valid_characters=valid_characters, character_map=character_map)
 
 
-def _sanitize_text_helper(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
+def _sanitize_text_helper(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character="X"):
     """Restricts the characters that are allowed in a string"""
 
     out = []
@@ -607,35 +627,48 @@ def _sanitize_text_helper(text, valid_characters=valid_chars, character_map=mapp
             out.append(character_map[c])
         else:
             out.append(invalid_character)  # makes debugging easier
-    return ''.join(out)
+    return "".join(out)
 
 
-def sanitize_lists_to_string(values, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
+def sanitize_lists_to_string(values, valid_characters=valid_chars, character_map=mapped_chars, invalid_character="X"):
     if isinstance(values, list):
         rval = []
         for value in values:
-            rval.append(sanitize_lists_to_string(value,
-                                                 valid_characters=valid_characters,
-                                                 character_map=character_map,
-                                                 invalid_character=invalid_character))
+            rval.append(
+                sanitize_lists_to_string(
+                    value,
+                    valid_characters=valid_characters,
+                    character_map=character_map,
+                    invalid_character=invalid_character,
+                )
+            )
         values = ",".join(rval)
     else:
-        values = sanitize_text(values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character)
+        values = sanitize_text(
+            values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character
+        )
     return values
 
 
-def sanitize_param(value, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
+def sanitize_param(value, valid_characters=valid_chars, character_map=mapped_chars, invalid_character="X"):
     """Clean incoming parameters (strings or lists)"""
     if isinstance(value, str):
-        return sanitize_text(value, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character)
+        return sanitize_text(
+            value, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character
+        )
     elif isinstance(value, list):
-        return [sanitize_text(x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) for x in value]
+        return [
+            sanitize_text(
+                x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character
+            )
+            for x in value
+        ]
     else:
-        raise Exception(f'Unknown parameter type ({type(value)})')
+        raise Exception(f"Unknown parameter type ({type(value)})")
 
 
-valid_filename_chars = set(string.ascii_letters + string.digits + '_.')
-invalid_filenames = ['', '.', '..']
+valid_filename_chars = set(string.ascii_letters + string.digits + "_.")
+invalid_filenames = ["", ".", ".."]
 
 
 def sanitize_for_filename(text, default=None):
@@ -648,8 +681,8 @@ def sanitize_for_filename(text, default=None):
         if c in valid_filename_chars:
             out.append(c)
         else:
-            out.append('_')
-    out = ''.join(out)
+            out.append("_")
+    out = "".join(out)
     if out in invalid_filenames:
         if default is None:
             return sanitize_for_filename(str(unique_id()))
@@ -703,13 +736,15 @@ def mask_password_from_url(url):
             # This can manipulate the input other than just masking password,
             # so the previous string replace method is preferred when the
             # password doesn't appear twice in the url
-            split = split._replace(netloc=split.netloc.replace(f"{split.username}:{split.password}", f'{split.username}:********'))
+            split = split._replace(
+                netloc=split.netloc.replace(f"{split.username}:{split.password}", f"{split.username}:********")
+            )
             url = urlunsplit(split)
     return url
 
 
 def ready_name_for_url(raw_name):
-    """ General method to convert a string (i.e. object name) to a URL-ready
+    """General method to convert a string (i.e. object name) to a URL-ready
     slug.
 
     >>> ready_name_for_url( "My Cool Object" )
@@ -725,7 +760,7 @@ def ready_name_for_url(raw_name):
     # Remove all non-alphanumeric characters.
     slug_base = re.sub(r"[^a-zA-Z0-9\-]", "", slug_base)
     # Remove trailing '-'.
-    if slug_base.endswith('-'):
+    if slug_base.endswith("-"):
         slug_base = slug_base[:-1]
     return slug_base
 
@@ -766,7 +801,7 @@ def in_directory(file, directory, local_path_module=os.path):
     False
     """
     if local_path_module != os.path:
-        _safe_contains = importlib.import_module(f'galaxy.util.path.{local_path_module.__name__}').safe_contains
+        _safe_contains = importlib.import_module(f"galaxy.util.path.{local_path_module.__name__}").safe_contains
     else:
         directory = os.path.realpath(directory)
         _safe_contains = safe_contains
@@ -789,9 +824,7 @@ def merge_sorted_iterables(operator, *iterables):
         yield from first_iterable
     else:
         yield from __merge_two_sorted_iterables(
-            operator,
-            iter(first_iterable),
-            merge_sorted_iterables(operator, *iterables[1:])
+            operator, iter(first_iterable), merge_sorted_iterables(operator, *iterables[1:])
         )
 
 
@@ -846,7 +879,7 @@ class Params:
     """
 
     # is NEVER_SANITIZE required now that sanitizing for tool parameters can be controlled on a per parameter basis and occurs via InputValueWrappers?
-    NEVER_SANITIZE = ['file_data', 'url_paste', 'URL', 'filesystem_paths']
+    NEVER_SANITIZE = ["file_data", "url_paste", "URL", "filesystem_paths"]
 
     def __init__(self, params, sanitize=True):
         if sanitize:
@@ -855,9 +888,12 @@ class Params:
                 # name. Anything relying on NEVER_SANITIZE should be
                 # changed to not require this and NEVER_SANITIZE should be
                 # removed.
-                if (value is not None and key not in self.NEVER_SANITIZE
-                        and True not in [key.endswith(f"|{nonsanitize_parameter}") for
-                                         nonsanitize_parameter in self.NEVER_SANITIZE]):
+                if (
+                    value is not None
+                    and key not in self.NEVER_SANITIZE
+                    and True
+                    not in [key.endswith(f"|{nonsanitize_parameter}") for nonsanitize_parameter in self.NEVER_SANITIZE]
+                ):
                     self.__dict__[key] = sanitize_param(value)
                 else:
                     self.__dict__[key] = value
@@ -885,7 +921,7 @@ class Params:
         return self.__dict__.get(key, default)
 
     def __str__(self):
-        return f'{self.__dict__}'
+        return f"{self.__dict__}"
 
     def __len__(self):
         return len(self.__dict__)
@@ -916,12 +952,12 @@ def rst_to_html(s, error=False):
         "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"),
         "warning_stream": FakeStream(),
         "doctitle_xform": False,  # without option, very different rendering depending on
-                                  # number of sections in help content.
+        # number of sections in help content.
     }
 
-    return unicodify(docutils_core.publish_string(
-        s, writer=docutils_html4css1.Writer(),
-        settings_overrides=settings_overrides))
+    return unicodify(
+        docutils_core.publish_string(s, writer=docutils_html4css1.Writer(), settings_overrides=settings_overrides)
+    )
 
 
 def xml_text(root, name=None):
@@ -936,10 +972,10 @@ def xml_text(root, name=None):
     else:
         elem = root
     if elem is not None and elem.text:
-        text = ''.join(elem.text.splitlines())
+        text = "".join(elem.text.splitlines())
         return text.strip()
     # No luck, return empty string
-    return ''
+    return ""
 
 
 def parse_resource_parameters(resource_param_file):
@@ -959,8 +995,8 @@ def parse_resource_parameters(resource_param_file):
 
 
 # asbool implementation pulled from PasteDeploy
-truthy = frozenset({'true', 'yes', 'on', 'y', 't', '1'})
-falsy = frozenset({'false', 'no', 'off', 'n', 'f', '0'})
+truthy = frozenset({"true", "yes", "on", "y", "t", "1"})
+falsy = frozenset({"false", "no", "off", "n", "f", "0"})
 
 
 def asbool(obj):
@@ -976,7 +1012,7 @@ def asbool(obj):
 
 
 def string_as_bool(string: str) -> bool:
-    if str(string).lower() in ('true', 'yes', 'on', '1'):
+    if str(string).lower() in ("true", "yes", "on", "1"):
         return True
     else:
         return False
@@ -993,9 +1029,9 @@ def string_as_bool_or_none(string):
     function equivalently.
     """
     string = str(string).lower()
-    if string in ('true', 'yes', 'on'):
+    if string in ("true", "yes", "on"):
         return True
-    elif string in ['none', 'null']:
+    elif string in ["none", "null"]:
         return None
     else:
         return False
@@ -1024,18 +1060,18 @@ def listify(item, do_strip=False) -> typing.List[typing.Any]:
         return item
     elif isinstance(item, tuple):
         return list(item)
-    elif isinstance(item, str) and item.count(','):
+    elif isinstance(item, str) and item.count(","):
         if do_strip:
-            return [token.strip() for token in item.split(',')]
+            return [token.strip() for token in item.split(",")]
         else:
-            return item.split(',')
+            return item.split(",")
     else:
         return [item]
 
 
 def commaify(amount):
     orig = amount
-    new = re.sub(r"^(-?\d+)(\d{3})", r'\g<1>,\g<2>', amount)
+    new = re.sub(r"^(-?\d+)(\d{3})", r"\g<1>,\g<2>", amount)
     if orig == new:
         return new
     else:
@@ -1049,10 +1085,10 @@ def roundify(amount, sfs=2):
     if len(amount) <= sfs:
         return amount
     else:
-        return amount[0:sfs] + '0' * (len(amount) - sfs)
+        return amount[0:sfs] + "0" * (len(amount) - sfs)
 
 
-def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', strip_null=False, log_exception=True):
+def unicodify(value, encoding=DEFAULT_ENCODING, error="replace", strip_null=False, log_exception=True):
     """
     Returns a Unicode string or None.
 
@@ -1083,11 +1119,13 @@ def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', strip_null=Fals
             log.exception(msg)
         raise
     if strip_null:
-        return value.replace('\0', '')
+        return value.replace("\0", "")
     return value
 
 
-def filesystem_safe_string(s, max_len=255, truncation_chars='..', strip_leading_dot=True, invalid_chars=('/',), replacement_char='_'):
+def filesystem_safe_string(
+    s, max_len=255, truncation_chars="..", strip_leading_dot=True, invalid_chars=("/",), replacement_char="_"
+):
     """
     Strip unicode null chars, truncate at 255 characters.
     Optionally replace additional ``invalid_chars`` with `replacement_char` .
@@ -1097,16 +1135,16 @@ def filesystem_safe_string(s, max_len=255, truncation_chars='..', strip_leading_
     """
     sanitized_string = unicodify(s, strip_null=True)
     if strip_leading_dot:
-        sanitized_string = sanitized_string.lstrip('.')
+        sanitized_string = sanitized_string.lstrip(".")
     for invalid_char in invalid_chars:
         sanitized_string = sanitized_string.replace(invalid_char, replacement_char)
     if len(sanitized_string) > max_len:
-        sanitized_string = sanitized_string[:max_len - len(truncation_chars)]
+        sanitized_string = sanitized_string[: max_len - len(truncation_chars)]
         sanitized_string = f"{sanitized_string}{truncation_chars}"
     return sanitized_string
 
 
-def smart_str(s, encoding=DEFAULT_ENCODING, strings_only=False, errors='strict'):
+def smart_str(s, encoding=DEFAULT_ENCODING, strings_only=False, errors="strict"):
     """
     Returns a bytestring version of 's', encoded as specified in 'encoding'.
 
@@ -1151,7 +1189,7 @@ def string_to_object(s):
     return binascii.unhexlify(s)
 
 
-def clean_multiline_string(multiline_string, sep='\n'):
+def clean_multiline_string(multiline_string, sep="\n"):
     """
     Dedent, split, remove first and last empty lines, rejoin.
     """
@@ -1161,12 +1199,11 @@ def clean_multiline_string(multiline_string, sep='\n'):
         string_list = string_list[1:]
     if not string_list[-1]:
         string_list = string_list[:-1]
-    return '\n'.join(string_list) + '\n'
+    return "\n".join(string_list) + "\n"
 
 
 class ParamsWithSpecs(collections.defaultdict):
-    """
-    """
+    """ """
 
     def __init__(self, specs=None, params=None):
         self.specs = specs or dict()
@@ -1174,19 +1211,19 @@ class ParamsWithSpecs(collections.defaultdict):
         for name, value in self.params.items():
             if name not in self.specs:
                 self._param_unknown_error(name)
-            if 'map' in self.specs[name]:
+            if "map" in self.specs[name]:
                 try:
-                    self.params[name] = self.specs[name]['map'](value)
+                    self.params[name] = self.specs[name]["map"](value)
                 except Exception:
                     self._param_map_error(name, value)
-            if 'valid' in self.specs[name]:
-                if not self.specs[name]['valid'](value):
+            if "valid" in self.specs[name]:
+                if not self.specs[name]["valid"](value):
                     self._param_vaildation_error(name, value)
 
         self.update(self.params)
 
     def __missing__(self, name):
-        return self.specs[name]['default']
+        return self.specs[name]["default"]
 
     def __getattr__(self, name):
         return self[name]
@@ -1214,7 +1251,7 @@ def compare_urls(url1, url2, compare_scheme=True, compare_hostname=True, compare
 
 
 def read_build_sites(filename, check_builds=True):
-    """ read db names to ucsc mappings from file, this file should probably be merged with the one above """
+    """read db names to ucsc mappings from file, this file should probably be merged with the one above"""
     build_sites = []
     try:
         for line in open(filename):
@@ -1226,9 +1263,9 @@ def read_build_sites(filename, check_builds=True):
                 site = fields[1]
                 if check_builds:
                     site_builds = fields[2].split(",")
-                    site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
+                    site_dict = {"name": site_name, "url": site, "builds": site_builds}
                 else:
-                    site_dict = {'name': site_name, 'url': site}
+                    site_dict = {"name": site_name, "url": site}
                 build_sites.append(site_dict)
             except Exception:
                 continue
@@ -1264,7 +1301,7 @@ def stringify_dictionary_keys(in_dict):
     return out_dict
 
 
-def mkstemp_ln(src, prefix='mkstemp_ln_'):
+def mkstemp_ln(src, prefix="mkstemp_ln_"):
     """
     From tempfile._mkstemp_inner, generate a hard link in the same dir with a
     random name.  Created so we can persist the underlying file of a
@@ -1277,7 +1314,7 @@ def mkstemp_ln(src, prefix='mkstemp_ln_'):
         file = os.path.join(dir, prefix + name)
         try:
             os.link(src, file)
-            return (os.path.abspath(file))
+            return os.path.abspath(file)
         except OSError as e:
             if e.errno == errno.EEXIST:
                 continue  # try again
@@ -1293,18 +1330,18 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
     try:
         st = os.stat(path)
     except OSError:
-        log.exception('Unable to set permissions or group on %s', path)
+        log.exception("Unable to set permissions or group on %s", path)
         return
     # fix modes
     if stat.S_IMODE(st.st_mode) != perms:
         try:
             os.chmod(path, perms)
         except Exception as e:
-            log.warning('Unable to honor umask ({}) for {}, tried to set: {} but mode remains {}, error was: {}'.format(oct(umask),
-                                                                                                                    path,
-                                                                                                                    oct(perms),
-                                                                                                                    oct(stat.S_IMODE(st.st_mode)),
-                                                                                                                    unicodify(e)))
+            log.warning(
+                "Unable to honor umask ({}) for {}, tried to set: {} but mode remains {}, error was: {}".format(
+                    oct(umask), path, oct(perms), oct(stat.S_IMODE(st.st_mode)), unicodify(e)
+                )
+            )
     # fix group
     if gid is not None and st.st_gid != gid:
         try:
@@ -1316,16 +1353,17 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
             except Exception:
                 desired_group = gid
                 current_group = st.st_gid
-            log.warning('Unable to honor primary group ({}) for {}, group remains {}, error was: {}'.format(desired_group,
-                                                                                                        path,
-                                                                                                        current_group,
-                                                                                                        unicodify(e)))
+            log.warning(
+                "Unable to honor primary group ({}) for {}, group remains {}, error was: {}".format(
+                    desired_group, path, current_group, unicodify(e)
+                )
+            )
 
 
 def docstring_trim(docstring):
     """Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/"""
     if not docstring:
-        return ''
+        return ""
     # Convert tabs to spaces (following the normal Python rules)
     # and split into a list of lines:
     lines = docstring.expandtabs().splitlines()
@@ -1346,7 +1384,7 @@ def docstring_trim(docstring):
     while trimmed and not trimmed[0]:
         trimmed.pop(0)
     # Return a single string:
-    return '\n'.join(trimmed)
+    return "\n".join(trimmed)
 
 
 def nice_size(size):
@@ -1362,23 +1400,23 @@ def nice_size(size):
     >>> nice_size(100000000)
     '95.4 MB'
     """
-    words = ['bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB']
-    prefix = ''
+    words = ["bytes", "KB", "MB", "GB", "TB", "PB", "EB"]
+    prefix = ""
     try:
         size = float(size)
         if size < 0:
             size = abs(size)
-            prefix = '-'
+            prefix = "-"
     except Exception:
-        return '??? bytes'
+        return "??? bytes"
     for ind, word in enumerate(words):
         step = 1024 ** (ind + 1)
         if step > size:
-            size = size / float(1024 ** ind)
-            if word == 'bytes':  # No decimals for bytes
+            size = size / float(1024**ind)
+            if word == "bytes":  # No decimals for bytes
                 return "%s%d bytes" % (prefix, size)
             return f"{prefix}{size:.1f} {word}"
-    return '??? bytes'
+    return "??? bytes"
 
 
 def size_to_bytes(size):
@@ -1403,26 +1441,26 @@ def size_to_bytes(size):
     122880
     """
     # The following number regexp is based on https://stackoverflow.com/questions/385558/extract-float-double-value/385597#385597
-    size_re = re.compile(r'(?P<number>(\d+(\.\d*)?|\.\d+)(e[+-]?\d+)?)\s*(?P<multiple>[eptgmk]?(b|bytes?)?)?$')
+    size_re = re.compile(r"(?P<number>(\d+(\.\d*)?|\.\d+)(e[+-]?\d+)?)\s*(?P<multiple>[eptgmk]?(b|bytes?)?)?$")
     size_match = size_re.match(size.lower())
     if size_match is None:
         raise ValueError(f"Could not parse string '{size}'")
     number = float(size_match.group("number"))
     multiple = size_match.group("multiple")
-    if multiple == "" or multiple.startswith('b'):
+    if multiple == "" or multiple.startswith("b"):
         return int(number)
-    elif multiple.startswith('k'):
+    elif multiple.startswith("k"):
         return int(number * 1024)
-    elif multiple.startswith('m'):
-        return int(number * 1024 ** 2)
-    elif multiple.startswith('g'):
-        return int(number * 1024 ** 3)
-    elif multiple.startswith('t'):
-        return int(number * 1024 ** 4)
-    elif multiple.startswith('p'):
-        return int(number * 1024 ** 5)
-    elif multiple.startswith('e'):
-        return int(number * 1024 ** 6)
+    elif multiple.startswith("m"):
+        return int(number * 1024**2)
+    elif multiple.startswith("g"):
+        return int(number * 1024**3)
+    elif multiple.startswith("t"):
+        return int(number * 1024**4)
+    elif multiple.startswith("p"):
+        return int(number * 1024**5)
+    elif multiple.startswith("e"):
+        return int(number * 1024**6)
     else:
         raise ValueError(f"Unknown multiplier '{multiple}' in '{size}'")
 
@@ -1453,13 +1491,13 @@ def send_mail(frm, to, subject, body, config, html=None):
 
     to = listify(to)
     if html:
-        msg = MIMEMultipart('alternative')
+        msg = MIMEMultipart("alternative")
     else:
-        msg = MIMEText(body, 'plain', 'utf-8')
+        msg = MIMEText(body, "plain", "utf-8")
 
-    msg['To'] = ', '.join(to)
-    msg['From'] = frm
-    msg['Subject'] = subject
+    msg["To"] = ", ".join(to)
+    msg["From"] = frm
+    msg["Subject"] = subject
 
     if config.smtp_server is None:
         log.error("Mail is not configured for this Galaxy instance.")
@@ -1467,12 +1505,12 @@ def send_mail(frm, to, subject, body, config, html=None):
         return
 
     if html:
-        mp_text = MIMEText(body, 'plain', 'utf-8')
-        mp_html = MIMEText(html, 'html', 'utf-8')
+        mp_text = MIMEText(body, "plain", "utf-8")
+        mp_html = MIMEText(html, "html", "utf-8")
         msg.attach(mp_text)
         msg.attach(mp_html)
 
-    smtp_ssl = asbool(getattr(config, 'smtp_ssl', False))
+    smtp_ssl = asbool(getattr(config, "smtp_ssl", False))
     if smtp_ssl:
         s = smtplib.SMTP_SSL(config.smtp_server)
     else:
@@ -1480,15 +1518,15 @@ def send_mail(frm, to, subject, body, config, html=None):
     if not smtp_ssl:
         try:
             s.starttls()
-            log.debug('Initiated SSL/TLS connection to SMTP server: %s', config.smtp_server)
+            log.debug("Initiated SSL/TLS connection to SMTP server: %s", config.smtp_server)
         except RuntimeError as e:
-            log.warning('SSL/TLS support is not available to your Python interpreter: %s', unicodify(e))
+            log.warning("SSL/TLS support is not available to your Python interpreter: %s", unicodify(e))
         except smtplib.SMTPHeloError as e:
             log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
             s.close()
             raise
         except smtplib.SMTPException as e:
-            log.warning('The server does not support the STARTTLS extension: %s', unicodify(e))
+            log.warning("The server does not support the STARTTLS extension: %s", unicodify(e))
     if config.smtp_username and config.smtp_password:
         try:
             s.login(config.smtp_username, config.smtp_password)
@@ -1544,8 +1582,7 @@ def move_merge(source, target):
 
 
 def safe_str_cmp(a, b):
-    """safely compare two strings in a timing-attack-resistant manner
-    """
+    """safely compare two strings in a timing-attack-resistant manner"""
     if len(a) != len(b):
         return False
     rv = 0
@@ -1556,7 +1593,7 @@ def safe_str_cmp(a, b):
 
 #  Don't use these two directly, prefer method version that "works" with packaged Galaxy.
 galaxy_root_path = os.path.join(__path__[0], os.pardir, os.pardir, os.pardir)  # type: ignore[name-defined]
-galaxy_samples_path = os.path.join(__path__[0], os.pardir, 'config', 'sample')  # type: ignore[name-defined]
+galaxy_samples_path = os.path.join(__path__[0], os.pardir, "config", "sample")  # type: ignore[name-defined]
 
 
 def galaxy_directory():
@@ -1567,7 +1604,7 @@ def galaxy_directory():
 
 
 def galaxy_samples_directory():
-    return os.path.join(galaxy_directory(), 'lib', 'galaxy', 'config', 'sample')
+    return os.path.join(galaxy_directory(), "lib", "galaxy", "config", "sample")
 
 
 def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root_path):
@@ -1590,10 +1627,10 @@ def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root
 
     for directory in listify(directories_setting):
         directory = directory.strip()
-        if not directory.startswith('/'):
+        if not directory.startswith("/"):
             directory = os.path.join(galaxy_root, directory)
         if not os.path.exists(directory):
-            log.warning('directory not found: %s', directory)
+            log.warning("directory not found: %s", directory)
             continue
         directories.append(directory)
     return directories
@@ -1638,32 +1675,32 @@ def parse_non_hex_float(s):
     """
     f = float(s)
     # successfully parsed as float if here - check for format in original string
-    if 'e' in s and not ('+' in s or '-' in s):
-        raise ValueError('could not convert string to float: ' + s)
+    if "e" in s and not ("+" in s or "-" in s):
+        raise ValueError("could not convert string to float: " + s)
     return f
 
 
-def build_url(base_url, port=80, scheme='http', pathspec=None, params=None, doseq=False):
+def build_url(base_url, port=80, scheme="http", pathspec=None, params=None, doseq=False):
     if params is None:
         params = dict()
     if pathspec is None:
         pathspec = []
     parsed_url = urlparse(base_url)
-    if scheme != 'http':
+    if scheme != "http":
         parsed_url.scheme = scheme
-    assert parsed_url.scheme in ('http', 'https', 'ftp'), f'Invalid URL scheme: {scheme}'
+    assert parsed_url.scheme in ("http", "https", "ftp"), f"Invalid URL scheme: {scheme}"
     if port != 80:
-        url = '%s://%s:%d/%s' % (parsed_url.scheme, parsed_url.netloc.rstrip('/'), int(port), parsed_url.path)
+        url = "%s://%s:%d/%s" % (parsed_url.scheme, parsed_url.netloc.rstrip("/"), int(port), parsed_url.path)
     else:
         url = f"{parsed_url.scheme}://{parsed_url.netloc.rstrip('/')}/{parsed_url.path.lstrip('/')}"
     if len(pathspec) > 0:
         url = f"{url.rstrip('/')}/{'/'.join(pathspec)}"
     if parsed_url.query:
-        for query_parameter in parsed_url.query.split('&'):
-            key, value = query_parameter.split('=')
+        for query_parameter in parsed_url.query.split("&"):
+            key, value = query_parameter.split("=")
             params[key] = value
     if params:
-        url += f'?{urlencode(params, doseq=doseq)}'
+        url += f"?{urlencode(params, doseq=doseq)}"
     return url
 
 
@@ -1695,15 +1732,17 @@ def is_url(uri, allow_list=None):
     return any(uri.startswith(scheme) for scheme in allow_list)
 
 
-def download_to_file(url, dest_file_path, timeout=30, chunk_size=2 ** 20):
+def download_to_file(url, dest_file_path, timeout=30, chunk_size=2**20):
     """Download a URL to a file in chunks."""
-    with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, 'wb') as f:
+    with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, "wb") as f:
         for chunk in r.iter_content(chunk_size):
             if chunk:
                 f.write(chunk)
 
 
-def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source_error='strict', target_encoding=None, target_error='strict'):
+def stream_to_open_named_file(
+    stream, fd, filename, source_encoding=None, source_error="strict", target_encoding=None, target_error="strict"
+):
     """Writes a stream to the provided file descriptor, returns the file name. Closes file descriptor"""
     # signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better
     CHUNK_SIZE = 1048576
@@ -1738,7 +1777,6 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
 
 
 class classproperty:
-
     def __init__(self, f):
         self.f = f
 
@@ -1747,7 +1785,6 @@ class classproperty:
 
 
 class ExecutionTimer:
-
     def __init__(self):
         self.begin = time.time()
 
@@ -1756,11 +1793,10 @@ class ExecutionTimer:
 
     @property
     def elapsed(self):
-        return (time.time() - self.begin)
+        return time.time() - self.begin
 
 
 class StructuredExecutionTimer:
-
     def __init__(self, timer_id, template, **tags):
         self.begin = time.time()
         self.timer_id = timer_id
@@ -1780,9 +1816,10 @@ class StructuredExecutionTimer:
 
     @property
     def elapsed(self):
-        return (time.time() - self.begin)
+        return time.time() - self.begin
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     doctest.testmod(sys.modules[__name__], verbose=False)
diff --git a/lib/galaxy/util/bool_expressions.py b/lib/galaxy/util/bool_expressions.py
index 488e8687849..c33ef7d9304 100644
--- a/lib/galaxy/util/bool_expressions.py
+++ b/lib/galaxy/util/bool_expressions.py
@@ -50,6 +50,7 @@ class BoolOperand:
     """Represents a boolean operand that has a label and a value.
 
     The value is determined by a custom TokenEvaluator."""
+
     evaluator: TokenEvaluator
 
     def __init__(self, token):
@@ -67,6 +68,7 @@ class BoolOperand:
 
 class BoolBinaryOperation:
     """Base representation of a boolean binary operation."""
+
     reprsymbol: str
     evalop: Callable[[Iterable[object]], bool]
 
@@ -85,12 +87,14 @@ class BoolBinaryOperation:
 
 class BoolAnd(BoolBinaryOperation):
     """Represents the `AND` boolean operation."""
+
     reprsymbol = "&"
     evalop = all
 
 
 class BoolOr(BoolBinaryOperation):
     """Represents the `OR` boolean operation."""
+
     reprsymbol = "|"
     evalop = any
 
@@ -147,7 +151,7 @@ class BooleanExpressionEvaluator:
             res = self.boolExpr.parseString(expr, parseAll=True)[0]
             return bool(res)
         except ParseException as e:
-            log.error(f'BooleanExpressionEvaluator unable to evaluate expression => {expr}', exc_info=e)
+            log.error(f"BooleanExpressionEvaluator unable to evaluate expression => {expr}", exc_info=e)
             raise e
 
     @classmethod
diff --git a/lib/galaxy/util/bunch.py b/lib/galaxy/util/bunch.py
index 7a15a5c3461..1a8d9785b7d 100644
--- a/lib/galaxy/util/bunch.py
+++ b/lib/galaxy/util/bunch.py
@@ -31,10 +31,11 @@ class Bunch(HasDynamicProperties):
         return self.__dict__.values()
 
     def __str__(self):
-        return f'{self.__dict__}'
+        return f"{self.__dict__}"
 
     def __bool__(self):
         return bool(self.__dict__)
+
     __nonzero__ = __bool__
 
     def __setitem__(self, k, v):
diff --git a/lib/galaxy/util/bytesize.py b/lib/galaxy/util/bytesize.py
index aa33020497c..35f06809f30 100644
--- a/lib/galaxy/util/bytesize.py
+++ b/lib/galaxy/util/bytesize.py
@@ -1,16 +1,16 @@
 SUFFIX_TO_BYTES = {
-    'KI': 1024,
-    'MI': 1024**2,
-    'GI': 1024**3,
-    'TI': 1024**4,
-    'PI': 1024**5,
-    'EI': 1024**6,
-    'K': 1000,
-    'M': 1000**2,
-    'G': 1000**3,
-    'T': 1000**4,
-    'P': 1000**5,
-    'E': 1000**6,
+    "KI": 1024,
+    "MI": 1024**2,
+    "GI": 1024**3,
+    "TI": 1024**4,
+    "PI": 1024**5,
+    "EI": 1024**6,
+    "K": 1000,
+    "M": 1000**2,
+    "G": 1000**3,
+    "T": 1000**4,
+    "P": 1000**5,
+    "E": 1000**6,
 }
 
 
@@ -55,7 +55,7 @@ def parse_bytesize(value):
             found_suffix = suffix
             break
     if found_suffix:
-        value = value[:-len(found_suffix)]
+        value = value[: -len(found_suffix)]
     try:
         value = int(value)
     except ValueError:
diff --git a/lib/galaxy/util/checkers.py b/lib/galaxy/util/checkers.py
index 3265cf8086f..a400fdb87fe 100644
--- a/lib/galaxy/util/checkers.py
+++ b/lib/galaxy/util/checkers.py
@@ -6,7 +6,7 @@ import tarfile
 import zipfile
 from io import (
     BytesIO,
-    StringIO
+    StringIO,
 )
 from typing import (
     IO,
@@ -20,7 +20,7 @@ from galaxy import util
 from galaxy.util.image_util import image_type
 
 HTML_CHECK_LINES = 100
-CHUNK_SIZE = 2 ** 15  # 32Kb
+CHUNK_SIZE = 2**15  # 32Kb
 HTML_REGEXPS = (
     re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I),
     re.compile(r"<IFRAME[^>]*>", re.I),
@@ -31,7 +31,6 @@ HTML_REGEXPS = (
 
 
 class CompressionChecker(Protocol):
-
     def __call__(self, file_path: str, check_content: bool = True) -> Tuple[bool, bool]:
         ...
 
@@ -43,7 +42,7 @@ def check_html(name, file_path: bool = True) -> bool:
     # Handles files if file_path is True or text if file_path is False
     temp: IO[str]
     if file_path:
-        temp = open(name, encoding='utf-8')
+        temp = open(name, encoding="utf-8")
     else:
         temp = StringIO(util.unicodify(name))
     try:
@@ -101,17 +100,17 @@ def check_gzip(file_path: str, check_content: bool = True) -> Tuple[bool, bool]:
     # If the file is Bam, it should already have been detected as such, so we'll just check
     # for sff format.
     try:
-        with gzip.open(file_path, 'rb') as fh:
+        with gzip.open(file_path, "rb") as fh:
             header = fh.read(4)
-        if header == b'.sff':
+        if header == b".sff":
             return (True, True)
     except Exception:
-        return(False, False)
+        return (False, False)
 
     if not check_content:
         return (True, True)
 
-    with gzip.open(file_path, mode='rb') as gzipped_file:
+    with gzip.open(file_path, mode="rb") as gzipped_file:
         chunk = gzipped_file.read(CHUNK_SIZE)
     # See if we have a compressed HTML file
     if check_html(chunk, file_path=False):
@@ -131,7 +130,7 @@ def check_bz2(file_path: str, check_content: bool = True) -> Tuple[bool, bool]:
     if not check_content:
         return (True, True)
 
-    with bz2.BZ2File(file_path, mode='rb') as bzipped_file:
+    with bz2.BZ2File(file_path, mode="rb") as bzipped_file:
         chunk = bzipped_file.read(CHUNK_SIZE)
     # See if we have a compressed HTML file
     if check_html(chunk, file_path=False):
@@ -185,29 +184,33 @@ def is_tar(file_path: str) -> bool:
 
 def iter_zip(file_path: str):
     with zipfile.ZipFile(file_path) as z:
-        for f in filter(lambda x: not x.endswith('/'), z.namelist()):
+        for f in filter(lambda x: not x.endswith("/"), z.namelist()):
             yield (z.open(f), f)
 
 
 def check_image(file_path: str):
-    """ Simple wrapper around image_type to yield a True/False verdict """
+    """Simple wrapper around image_type to yield a True/False verdict"""
     if image_type(file_path):
         return True
     return False
 
 
-COMPRESSION_CHECK_FUNCTIONS: List[Tuple[str, CompressionChecker]] = [('gz', check_gzip), ('bz2', check_bz2), ('zip', check_zip)]
+COMPRESSION_CHECK_FUNCTIONS: List[Tuple[str, CompressionChecker]] = [
+    ("gz", check_gzip),
+    ("bz2", check_bz2),
+    ("zip", check_zip),
+]
 
 
 __all__ = (
-    'check_binary',
-    'check_bz2',
-    'check_gzip',
-    'check_html',
-    'check_image',
-    'check_zip',
-    'COMPRESSION_CHECK_FUNCTIONS',
-    'is_gzip',
-    'is_bz2',
-    'is_zip',
+    "check_binary",
+    "check_bz2",
+    "check_gzip",
+    "check_html",
+    "check_image",
+    "check_zip",
+    "COMPRESSION_CHECK_FUNCTIONS",
+    "is_gzip",
+    "is_bz2",
+    "is_zip",
 )
diff --git a/lib/galaxy/util/commands.py b/lib/galaxy/util/commands.py
index c4ac1668793..75ee2db7cb3 100644
--- a/lib/galaxy/util/commands.py
+++ b/lib/galaxy/util/commands.py
@@ -8,7 +8,7 @@ import tempfile
 
 from galaxy.util import (
     unicodify,
-    which
+    which,
 )
 
 log = logging.getLogger(__name__)
@@ -71,7 +71,7 @@ def shell_process(cmds, env=None, **kwds):
     popen_kwds = dict()
     if isinstance(cmds, str):
         log.warning("Passing program arguments as a string may be a security hazard if combined with untrusted input")
-        popen_kwds['shell'] = True
+        popen_kwds["shell"] = True
     if kwds.get("stdout", None) is None and redirecting_io(sys=sys):
         popen_kwds["stdout"] = subprocess.PIPE
     if kwds.get("stderr", None) is None and redirecting_io(sys=sys):
@@ -145,14 +145,15 @@ class CommandLineException(Exception):
         self.stdout = stdout
         self.stderr = stderr
         self.returncode = returncode
-        self.message = ("Failed to execute command-line %s, stderr was:\n"
-                        "-------->>begin stderr<<--------\n"
-                        "%s\n"
-                        "-------->>end stderr<<--------\n"
-                        "-------->>begin stdout<<--------\n"
-                        "%s\n"
-                        "-------->>end stdout<<--------\n"
-                        ) % (command, stderr, stdout)
+        self.message = (
+            "Failed to execute command-line %s, stderr was:\n"
+            "-------->>begin stderr<<--------\n"
+            "%s\n"
+            "-------->>end stderr<<--------\n"
+            "-------->>begin stdout<<--------\n"
+            "%s\n"
+            "-------->>end stdout<<--------\n"
+        ) % (command, stderr, stdout)
 
     def __str__(self):
         """Return a verbose error message indicating the command problem."""
@@ -178,14 +179,14 @@ def new_clean_env():
 
 
 __all__ = (
-    'argv_to_str',
-    'CommandLineException',
-    'download_command',
-    'execute',
-    'new_clean_env',
-    'redirect_aware_commmunicate',
-    'redirecting_io',
-    'shell',
-    'shell_process',
-    'which',
+    "argv_to_str",
+    "CommandLineException",
+    "download_command",
+    "execute",
+    "new_clean_env",
+    "redirect_aware_commmunicate",
+    "redirecting_io",
+    "shell",
+    "shell_process",
+    "which",
 )
diff --git a/lib/galaxy/util/compression_utils.py b/lib/galaxy/util/compression_utils.py
index e102ff91e54..9c115c16240 100644
--- a/lib/galaxy/util/compression_utils.py
+++ b/lib/galaxy/util/compression_utils.py
@@ -23,7 +23,7 @@ from typing_extensions import Literal
 from galaxy.util.path import safe_relpath
 from .checkers import (
     is_bz2,
-    is_gzip
+    is_gzip,
 )
 
 log = logging.getLogger(__name__)
@@ -34,16 +34,12 @@ FileObjType = Union[FileObjTypeStr, FileObjTypeBytes]
 
 
 @overload
-def get_fileobj(
-    filename: str, mode: Literal["r"], compressed_formats: Optional[List[str]] = None
-) -> FileObjTypeStr:
+def get_fileobj(filename: str, mode: Literal["r"], compressed_formats: Optional[List[str]] = None) -> FileObjTypeStr:
     ...
 
 
 @overload
-def get_fileobj(
-    filename: str, mode: Literal["rb"], compressed_formats: Optional[List[str]] = None
-) -> FileObjTypeBytes:
+def get_fileobj(filename: str, mode: Literal["rb"], compressed_formats: Optional[List[str]] = None) -> FileObjTypeBytes:
     ...
 
 
@@ -53,15 +49,11 @@ def get_fileobj(filename: str) -> FileObjTypeStr:
 
 
 @overload
-def get_fileobj(
-    filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None
-) -> FileObjType:
+def get_fileobj(filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None) -> FileObjType:
     ...
 
 
-def get_fileobj(
-    filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None
-) -> FileObjType:
+def get_fileobj(filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None) -> FileObjType:
     """
     Returns a fileobj. If the file is compressed, return an appropriate file
     reader. In text mode, always use 'utf-8' encoding.
@@ -104,44 +96,40 @@ def get_fileobj_raw(
     filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None
 ) -> Tuple[Optional[str], FileObjType]:
     if compressed_formats is None:
-        compressed_formats = ['bz2', 'gzip', 'zip']
+        compressed_formats = ["bz2", "gzip", "zip"]
     # Remove 't' from mode, which may cause an error for compressed files
-    mode = mode.replace('t', '')
+    mode = mode.replace("t", "")
     # 'U' mode is deprecated, we open in 'r'.
-    if mode == 'U':
-        mode = 'r'
+    if mode == "U":
+        mode = "r"
     compressed_format = None
-    if 'gzip' in compressed_formats and is_gzip(filename):
+    if "gzip" in compressed_formats and is_gzip(filename):
         fh: Union[gzip.GzipFile, bz2.BZ2File, IO[bytes]] = gzip.GzipFile(filename, mode)
-        compressed_format = 'gzip'
-    elif 'bz2' in compressed_formats and is_bz2(filename):
+        compressed_format = "gzip"
+    elif "bz2" in compressed_formats and is_bz2(filename):
         fh = bz2.BZ2File(filename, mode)
-        compressed_format = 'bz2'
-    elif 'zip' in compressed_formats and zipfile.is_zipfile(filename):
+        compressed_format = "bz2"
+    elif "zip" in compressed_formats and zipfile.is_zipfile(filename):
         # Return fileobj for the first file in a zip file.
         # 'b' is not allowed in the ZipFile mode argument
         # since it always opens files in binary mode.
         # For emulating text mode, we will be returning the binary fh in a
         # TextIOWrapper.
-        zf_mode = mode.replace('b', '')
+        zf_mode = mode.replace("b", "")
         with zipfile.ZipFile(filename, zf_mode) as zh:
             fh = zh.open(zh.namelist()[0], zf_mode)
-        compressed_format = 'zip'
-    elif 'b' in mode:
+        compressed_format = "zip"
+    elif "b" in mode:
         return compressed_format, open(filename, mode)
     else:
         return compressed_format, open(filename, mode, encoding="utf-8")
     if "b" not in mode:
-        return compressed_format, io.TextIOWrapper(
-            cast(IO[bytes], fh), encoding="utf-8"
-        )
+        return compressed_format, io.TextIOWrapper(cast(IO[bytes], fh), encoding="utf-8")
     else:
         return compressed_format, fh
 
 
-def file_iter(
-    fname: str, sep: Optional[Any] = None
-) -> Generator[Union[List[bytes], Any, List[str]], None, None]:
+def file_iter(fname: str, sep: Optional[Any] = None) -> Generator[Union[List[bytes], Any, List[str]], None, None]:
     """
     This generator iterates over a file and yields its lines
     splitted via the C{sep} parameter. Skips empty lines and lines starting with
@@ -153,7 +141,7 @@ def file_iter(
     """
     with get_fileobj(fname) as fh:
         for line in fh:
-            if line and line[0] != '#':
+            if line and line[0] != "#":
                 yield line.split(sep)
 
 
@@ -170,18 +158,18 @@ class CompressedFile:
 
     def __init__(self, file_path: str, mode: str = "r") -> None:
         if tarfile.is_tarfile(file_path):
-            self.file_type = 'tar'
-        elif zipfile.is_zipfile(file_path) and not file_path.endswith('.jar'):
-            self.file_type = 'zip'
+            self.file_type = "tar"
+        elif zipfile.is_zipfile(file_path) and not file_path.endswith(".jar"):
+            self.file_type = "zip"
         self.file_name = os.path.splitext(os.path.basename(file_path))[0]
-        if self.file_name.endswith('.tar'):
+        if self.file_name.endswith(".tar"):
             self.file_name = os.path.splitext(self.file_name)[0]
         self.type = self.file_type
-        method = f'open_{self.file_type}'
+        method = f"open_{self.file_type}"
         if hasattr(self, method):
             self.archive = getattr(self, method)(file_path, mode)
         else:
-            raise NameError(f'File type {self.file_type} specified, no open method found.')
+            raise NameError(f"File type {self.file_type} specified, no open method found.")
 
     @property
     def common_prefix_dir(self) -> str:
@@ -192,7 +180,7 @@ class CompressedFile:
         the root of the archive.
         """
         contents = self.getmembers()
-        common_prefix = ''
+        common_prefix = ""
         if len(contents) > 1:
             common_prefix = os.path.commonprefix([self.getname(item) for item in contents])
             # If the common_prefix does not end with a slash, check that is a
@@ -203,19 +191,15 @@ class CompressedFile:
                 and not common_prefix.endswith(os.sep)
                 and common_prefix_member
                 and self.isdir(common_prefix_member)
-                and all(
-                    self.getname(item).startswith(common_prefix + os.sep)
-                    for item in contents
-                    if self.isfile(item)
-                )
+                and all(self.getname(item).startswith(common_prefix + os.sep) for item in contents if self.isfile(item))
             ):
                 common_prefix += os.sep
             if not common_prefix.endswith(os.sep):
-                common_prefix = ''
+                common_prefix = ""
         return common_prefix
 
     def extract(self, path: str) -> str:
-        '''Determine the path to which the archive should be extracted.'''
+        """Determine the path to which the archive should be extracted."""
         contents = self.getmembers()
         extraction_path = path
         common_prefix_dir = self.common_prefix_dir
@@ -244,7 +228,7 @@ class CompressedFile:
                 self.archive.extractall(extraction_path, members=members_z)
         # Since .zip files store unix permissions separately, we need to iterate through the zip file
         # and set permissions on extracted members.
-        if self.file_type == 'zip':
+        if self.file_type == "zip":
             assert isinstance(self.archive, zipfile.ZipFile)
             for zipped_file in contents:
                 filename = self.getname(zipped_file)
@@ -256,7 +240,9 @@ class CompressedFile:
                     if os.path.exists(absolute_filepath):
                         os.chmod(absolute_filepath, unix_permissions)
                     else:
-                        log.warning(f"Unable to change permission on extracted file '{absolute_filepath}' as it does not exist")
+                        log.warning(
+                            f"Unable to change permission on extracted file '{absolute_filepath}' as it does not exist"
+                        )
         return os.path.abspath(os.path.join(extraction_path, common_prefix_dir))
 
     def safemembers(self) -> Union[Iterable[tarfile.TarInfo], Iterable[str]]:
diff --git a/lib/galaxy/util/custom_logging/fluent_log.py b/lib/galaxy/util/custom_logging/fluent_log.py
index 2b00a417b51..ed9ede536e9 100644
--- a/lib/galaxy/util/custom_logging/fluent_log.py
+++ b/lib/galaxy/util/custom_logging/fluent_log.py
@@ -12,12 +12,11 @@ except ImportError:
     FluentSender = None
 
 
-FLUENT_IMPORT_MESSAGE = ('The Python fluent package is required to use this '
-                         'feature, please install it')
+FLUENT_IMPORT_MESSAGE = "The Python fluent package is required to use this " "feature, please install it"
 
 
 class FluentTraceLogger:
-    def __init__(self, name, host='localhost', port=24224):
+    def __init__(self, name, host="localhost", port=24224):
         assert FluentSender is not None, FLUENT_IMPORT_MESSAGE
         self.lock = threading.Lock()
         self.thread_local = threading.local()
@@ -26,7 +25,7 @@ class FluentTraceLogger:
 
     def context_set(self, key, value):
         self.lock.acquire()
-        if not hasattr(self.thread_local, 'context'):
+        if not hasattr(self.thread_local, "context"):
             self.thread_local.context = {}
         self.thread_local.context[key] = value
         self.lock.release()
@@ -38,7 +37,7 @@ class FluentTraceLogger:
 
     def log(self, label, event_time=None, **kwargs):
         self.lock.acquire()
-        if hasattr(self.thread_local, 'context'):
+        if hasattr(self.thread_local, "context"):
             kwargs.update(self.thread_local.context)
         self.lock.release()
         event_time = event_time or time.time()
diff --git a/lib/galaxy/util/dbkeys.py b/lib/galaxy/util/dbkeys.py
index 1e788501fbc..a9da14f4d4a 100644
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -16,7 +16,7 @@ log = logging.getLogger(__name__)
 
 
 def read_dbnames(filename):
-    """ Read build names from file """
+    """Read build names from file"""
     db_names = []
     try:
         ucsc_builds = {}
@@ -24,7 +24,7 @@ def read_dbnames(filename):
         name_to_db_base = {}
         if filename is None:
             # Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test
-            filename = os.path.join(galaxy_directory(), 'tool-data', 'shared', 'ucsc', 'builds.txt.sample')
+            filename = os.path.join(galaxy_directory(), "tool-data", "shared", "ucsc", "builds.txt.sample")
         for line in open(filename):
             try:
                 if line[0:1] == "#":
@@ -38,12 +38,12 @@ def read_dbnames(filename):
                     int(fields[0])
                     man_builds.append((fields[1], fields[0]))
                 except Exception:  # UCSC build
-                    db_base = fields[0].rstrip('0123456789')
+                    db_base = fields[0].rstrip("0123456789")
                     if db_base not in ucsc_builds:
                         ucsc_builds[db_base] = []
                         name_to_db_base[fields[1]] = db_base
                     # we want to sort within a species numerically by revision number
-                    build_rev = re.compile(r'\d+$')
+                    build_rev = re.compile(r"\d+$")
                     try:
                         build_rev = int(build_rev.findall(fields[0])[0])
                     except Exception:
@@ -91,13 +91,14 @@ class GenomeBuilds:
                 # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering,
                 # so a len file will be listed twice (as the build name and again as dataset name),
                 # if custom dbkey creation/conversion occurred within the current history.
-                datasets = trans.sa_session.query(self._app.model.HistoryDatasetAssociation) \
-                                .filter_by(deleted=False, history_id=trans.history.id, extension="len")
+                datasets = trans.sa_session.query(self._app.model.HistoryDatasetAssociation).filter_by(
+                    deleted=False, history_id=trans.history.id, extension="len"
+                )
                 for dataset in datasets:
                     rval.append((dataset.dbkey, f"{dataset.name} ({dataset.dbkey}) [History]"))
             user = trans.user
-            if user and hasattr(user, 'preferences') and 'dbkeys' in user.preferences:
-                user_keys = loads(user.preferences['dbkeys'])
+            if user and hasattr(user, "preferences") and "dbkeys" in user.preferences:
+                user_keys = loads(user.preferences["dbkeys"])
                 for key, chrom_dict in user_keys.items():
                     rval.append((key, f"{chrom_dict['name']} ({key}) [Custom]"))
         # Load old builds.txt static keys
@@ -106,7 +107,7 @@ class GenomeBuilds:
         dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None)
         if dbkey_table is not None:
             for field_dict in dbkey_table.get_named_fields_list():
-                rval.append((field_dict['value'], field_dict['name']))
+                rval.append((field_dict["value"], field_dict["name"]))
         return rval
 
     def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True):
@@ -120,26 +121,36 @@ class GenomeBuilds:
                 chrom_info = db_dataset.file_name
             else:
                 # Do Custom Build handling
-                if trans.user and ('dbkeys' in trans.user.preferences) and (dbkey in loads(trans.user.preferences['dbkeys'])):
-                    custom_build_dict = loads(trans.user.preferences['dbkeys'])[dbkey]
+                if (
+                    trans.user
+                    and ("dbkeys" in trans.user.preferences)
+                    and (dbkey in loads(trans.user.preferences["dbkeys"]))
+                ):
+                    custom_build_dict = loads(trans.user.preferences["dbkeys"])[dbkey]
                     # HACK: the attempt to get chrom_info below will trigger the
                     # fasta-to-len converter if the dataset is not available or,
                     # which will in turn create a recursive loop when
                     # running the fasta-to-len tool. So, use a hack in the second
                     # condition below to avoid getting chrom_info when running the
                     # fasta-to-len converter.
-                    if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
+                    if "fasta" in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
                         # Build is defined by fasta; get len file, which is obtained from converting fasta.
-                        build_fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['fasta'])
-                        chrom_info = build_fasta_dataset.get_converted_dataset(trans, 'len').file_name
-                    elif 'len' in custom_build_dict:
+                        build_fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(
+                            custom_build_dict["fasta"]
+                        )
+                        chrom_info = build_fasta_dataset.get_converted_dataset(trans, "len").file_name
+                    elif "len" in custom_build_dict:
                         # Build is defined by len file, so use it.
-                        chrom_info = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['len']).file_name
+                        chrom_info = (
+                            trans.sa_session.query(trans.app.model.HistoryDatasetAssociation)
+                            .get(custom_build_dict["len"])
+                            .file_name
+                        )
         # Check Data table
         if not chrom_info:
             dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None)
             if dbkey_table is not None:
-                chrom_info = dbkey_table.get_entry('value', dbkey, 'len_path', default=None)
+                chrom_info = dbkey_table.get_entry("value", dbkey, "len_path", default=None)
         # use configured server len path
         if not chrom_info:
             # Default to built-in build.
diff --git a/lib/galaxy/util/dictifiable.py b/lib/galaxy/util/dictifiable.py
index acd6a5eaefb..551638dc3a1 100644
--- a/lib/galaxy/util/dictifiable.py
+++ b/lib/galaxy/util/dictifiable.py
@@ -4,18 +4,15 @@ import uuid
 
 def dict_for(obj, **kwds):
     # Create dict to represent item.
-    return dict(
-        model_class=obj.__class__.__name__,
-        **kwds
-    )
+    return dict(model_class=obj.__class__.__name__, **kwds)
 
 
 class Dictifiable:
-    """ Mixin that enables objects to be converted to dictionaries. This is useful
-        when for sharing objects across boundaries, such as the API, tool scripts,
-        and JavaScript code. """
+    """Mixin that enables objects to be converted to dictionaries. This is useful
+    when for sharing objects across boundaries, such as the API, tool scripts,
+    and JavaScript code."""
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         """
         Return item dictionary.
         """
@@ -52,7 +49,7 @@ class Dictifiable:
         try:
             visible_keys = self.__getattribute__(f"dict_{view}_visible_keys")
         except AttributeError:
-            raise Exception(f'Unknown Dictifiable view: {view}')
+            raise Exception(f"Unknown Dictifiable view: {view}")
         for key in visible_keys:
             try:
                 item = self.__getattribute__(key)
diff --git a/lib/galaxy/util/dynamic.py b/lib/galaxy/util/dynamic.py
index b0ae04de1b2..573db58924e 100644
--- a/lib/galaxy/util/dynamic.py
+++ b/lib/galaxy/util/dynamic.py
@@ -1,9 +1,11 @@
-from typing import Any, TYPE_CHECKING
-
+from typing import (
+    Any,
+    TYPE_CHECKING,
+)
 
 if TYPE_CHECKING:
-    class HasDynamicProperties:
 
+    class HasDynamicProperties:
         def __getattr__(self, property: str) -> Any:
             return object()
 
diff --git a/lib/galaxy/util/expressions.py b/lib/galaxy/util/expressions.py
index 0170d90c2ae..f5a58eec2fc 100644
--- a/lib/galaxy/util/expressions.py
+++ b/lib/galaxy/util/expressions.py
@@ -54,4 +54,5 @@ class ExpressionContext(MutableMapping):
         if not self.dict and not self.parent:
             return False
         return True
+
     __nonzero__ = __bool__
diff --git a/lib/galaxy/util/facts.py b/lib/galaxy/util/facts.py
index a00f597c11f..00ca0ff09f1 100644
--- a/lib/galaxy/util/facts.py
+++ b/lib/galaxy/util/facts.py
@@ -17,19 +17,19 @@ class Facts(MutableMapping):
     def __set_defaults(self, config):
         # config here may be a Galaxy config object, or it may just be a dict
         defaults = {
-            'server_name': lambda: config.get('base_server_name', 'main'),
-            'server_id': None,
-            'instance_id': None,
-            'pool_name': None,
-            'fqdn': lambda: socket.getfqdn(),
-            'hostname': lambda: socket.gethostname().split('.', 1)[0],
+            "server_name": lambda: config.get("base_server_name", "main"),
+            "server_id": None,
+            "instance_id": None,
+            "pool_name": None,
+            "fqdn": lambda: socket.getfqdn(),
+            "hostname": lambda: socket.gethostname().split(".", 1)[0],
         }
         self.__dict__.update(defaults)
 
     def __set_config(self, config):
         if config is not None:
             for name in dir(config):
-                if not name.startswith('_') and isinstance(getattr(config, name), str):
+                if not name.startswith("_") and isinstance(getattr(config, name), str):
                     self.__dict__[f"config_{name}"] = lambda name=name: getattr(config, name)
 
     def __getitem__(self, key):
diff --git a/lib/galaxy/util/filelock.py b/lib/galaxy/util/filelock.py
index 03d0261735e..860a9d8a701 100644
--- a/lib/galaxy/util/filelock.py
+++ b/lib/galaxy/util/filelock.py
@@ -15,14 +15,14 @@ class FileLockException(Exception):
 
 
 class FileLock:
-    """ A file locking mechanism that has context-manager support so
-        you can use it in a with statement. This should be relatively cross
-        compatible as it doesn't rely on msvcrt or fcntl for the locking.
+    """A file locking mechanism that has context-manager support so
+    you can use it in a with statement. This should be relatively cross
+    compatible as it doesn't rely on msvcrt or fcntl for the locking.
     """
 
-    def __init__(self, file_name, timeout=10, delay=.05):
-        """ Prepare the file locker. Specify the file to lock and optionally
-            the maximum timeout and the delay between each attempt to lock.
+    def __init__(self, file_name, timeout=10, delay=0.05):
+        """Prepare the file locker. Specify the file to lock and optionally
+        the maximum timeout and the delay between each attempt to lock.
         """
         self.is_locked = False
         full_path = os.path.abspath(file_name)
@@ -32,10 +32,10 @@ class FileLock:
         self.delay = delay
 
     def acquire(self):
-        """ Acquire the lock, if possible. If the lock is in use, it check again
-            every `wait` seconds. It does this until it either gets the lock or
-            exceeds `timeout` number of seconds, in which case it throws
-            an exception.
+        """Acquire the lock, if possible. If the lock is in use, it check again
+        every `wait` seconds. It does this until it either gets the lock or
+        exceeds `timeout` number of seconds, in which case it throws
+        an exception.
         """
         start_time = time.time()
         while True:
@@ -51,9 +51,9 @@ class FileLock:
         self.is_locked = True
 
     def release(self):
-        """ Get rid of the lock by deleting the lockfile.
-            When working in a `with` statement, this gets automatically
-            called at the end.
+        """Get rid of the lock by deleting the lockfile.
+        When working in a `with` statement, this gets automatically
+        called at the end.
         """
         if self.is_locked:
             os.close(self.fd)
@@ -61,22 +61,22 @@ class FileLock:
             self.is_locked = False
 
     def __enter__(self):
-        """ Activated when used in the with statement.
-            Should automatically acquire a lock to be used in the with block.
+        """Activated when used in the with statement.
+        Should automatically acquire a lock to be used in the with block.
         """
         if not self.is_locked:
             self.acquire()
         return self
 
     def __exit__(self, type, value, traceback):
-        """ Activated at the end of the with statement.
-            It automatically releases the lock if it isn't locked.
+        """Activated at the end of the with statement.
+        It automatically releases the lock if it isn't locked.
         """
         if self.is_locked:
             self.release()
 
     def __del__(self):
-        """ Make sure that the FileLock instance doesn't leave a lockfile
-            lying around.
+        """Make sure that the FileLock instance doesn't leave a lockfile
+        lying around.
         """
         self.release()
diff --git a/lib/galaxy/util/form_builder.py b/lib/galaxy/util/form_builder.py
index c2478beb6dd..010ce5ef29c 100644
--- a/lib/galaxy/util/form_builder.py
+++ b/lib/galaxy/util/form_builder.py
@@ -4,9 +4,7 @@ Classes for generating HTML forms
 
 import logging
 
-from galaxy.util import (
-    asbool
-)
+from galaxy.util import asbool
 
 log = logging.getLogger(__name__)
 
@@ -16,21 +14,21 @@ class BaseField:
         self.name = name
         self.label = label
         self.value = value
-        self.disabled = kwds.get('disabled', False)
-        if 'optional' in kwds:
-            self.optional = asbool(kwds.get('optional'))
+        self.disabled = kwds.get("disabled", False)
+        if "optional" in kwds:
+            self.optional = asbool(kwds.get("optional"))
         else:
-            self.optional = kwds.get('required', 'optional') == 'optional'
-        self.help = kwds.get('helptext')
+            self.optional = kwds.get("required", "optional") == "optional"
+        self.help = kwds.get("helptext")
 
     def to_dict(self):
         return {
-            'name': self.name,
-            'label': self.label,
-            'disabled': self.disabled,
-            'optional': self.optional,
-            'value': self.value,
-            'help': self.help
+            "name": self.name,
+            "label": self.label,
+            "disabled": self.disabled,
+            "optional": self.optional,
+            "value": self.value,
+            "help": self.help,
         }
 
 
@@ -38,9 +36,10 @@ class TextField(BaseField):
     """
     A standard text input box.
     """
+
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'text'
+        d["type"] = "text"
         return d
 
 
@@ -48,9 +47,10 @@ class PasswordField(BaseField):
     """
     A password input box. text appears as "******"
     """
+
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'password'
+        d["type"] = "password"
         return d
 
 
@@ -58,10 +58,11 @@ class TextArea(BaseField):
     """
     A standard text area box.
     """
+
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'text'
-        d['area'] = True
+        d["type"] = "text"
+        d["area"] = True
         return d
 
 
@@ -69,6 +70,7 @@ class CheckboxField(BaseField):
     """
     A checkbox (boolean input)
     """
+
     @staticmethod
     def is_checked(value):
         if value in [True, "True", "true"]:
@@ -77,7 +79,7 @@ class CheckboxField(BaseField):
 
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'boolean'
+        d["type"] = "boolean"
         return d
 
 
@@ -86,7 +88,17 @@ class SelectField(BaseField):
     A select field.
     """
 
-    def __init__(self, name, multiple=None, display=None, field_id=None, value=None, selectlist=None, refresh_on_change=False, **kwds):
+    def __init__(
+        self,
+        name,
+        multiple=None,
+        display=None,
+        field_id=None,
+        value=None,
+        selectlist=None,
+        refresh_on_change=False,
+        **kwds,
+    ):
         super().__init__(name, value, **kwds)
         self.field_id = field_id
         self.multiple = multiple or False
@@ -96,7 +108,7 @@ class SelectField(BaseField):
         if display == "checkboxes":
             assert multiple, "Checkbox display only supported for multiple select"
         elif display == "radio":
-            assert not(multiple), "Radio display only supported for single select"
+            assert not (multiple), "Radio display only supported for single select"
         elif display is not None:
             raise Exception(f"Unknown display type: {display}")
         self.display = display
@@ -106,28 +118,30 @@ class SelectField(BaseField):
 
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'select'
-        d['display'] = self.display
-        d['multiple'] = self.multiple
-        d['data'] = []
+        d["type"] = "select"
+        d["display"] = self.display
+        d["multiple"] = self.multiple
+        d["data"] = []
         for value in self.selectlist:
-            d['data'].append({'label': value, 'value': value})
-        d['options'] = [{'label': t[0], 'value': t[1]} for t in self.options]
+            d["data"].append({"label": value, "value": value})
+        d["options"] = [{"label": t[0], "value": t[1]} for t in self.options]
         return d
 
 
 class AddressField(BaseField):
     @staticmethod
     def fields():
-        return [("desc", "Short address description", "Required"),
-                ("name", "Name", ""),
-                ("institution", "Institution", ""),
-                ("address", "Address", ""),
-                ("city", "City", ""),
-                ("state", "State/Province/Region", ""),
-                ("postal_code", "Postal Code", ""),
-                ("country", "Country", ""),
-                ("phone", "Phone", "")]
+        return [
+            ("desc", "Short address description", "Required"),
+            ("name", "Name", ""),
+            ("institution", "Institution", ""),
+            ("address", "Address", ""),
+            ("city", "City", ""),
+            ("state", "State/Province/Region", ""),
+            ("postal_code", "Postal Code", ""),
+            ("country", "Country", ""),
+            ("phone", "Phone", ""),
+        ]
 
     def __init__(self, name, user=None, value=None, security=None, **kwds):
         super().__init__(name, value, **kwds)
@@ -136,12 +150,12 @@ class AddressField(BaseField):
 
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'select'
-        d['data'] = []
+        d["type"] = "select"
+        d["data"] = []
         if self.user and self.security:
             for a in self.user.addresses:
                 if not a.deleted:
-                    d['data'].append({'label': a.desc, 'value': self.security.encode_id(a.id)})
+                    d["data"].append({"label": a.desc, "value": self.security.encode_id(a.id)})
         return d
 
 
@@ -154,12 +168,12 @@ class WorkflowField(BaseField):
 
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'select'
-        d['data'] = []
+        d["type"] = "select"
+        d["data"] = []
         if self.user and self.security:
             for a in self.user.stored_workflows:
                 if not a.deleted:
-                    d['data'].append({'label': a.name, 'value': self.security.encode_id(a.id)})
+                    d["data"].append({"label": a.name, "value": self.security.encode_id(a.id)})
         return d
 
 
@@ -178,12 +192,12 @@ class HistoryField(BaseField):
 
     def to_dict(self):
         d = super().to_dict()
-        d['type'] = 'select'
-        d['data'] = [{'label': 'New History', 'value': 'new'}]
+        d["type"] = "select"
+        d["data"] = [{"label": "New History", "value": "new"}]
         if self.user and self.security:
             for a in self.user.histories:
                 if not a.deleted:
-                    d['data'].append({'label': a.name, 'value': self.security.encode_id(a.id)})
+                    d["data"].append({"label": a.name, "value": self.security.encode_id(a.id)})
         return d
 
 
@@ -191,4 +205,5 @@ def get_suite():
     """Get unittest suite for this module"""
     import doctest
     import sys
+
     return doctest.DocTestSuite(sys.modules[__name__])
diff --git a/lib/galaxy/util/hash_util.py b/lib/galaxy/util/hash_util.py
index 7513ddcf1f1..427a8eccf81 100644
--- a/lib/galaxy/util/hash_util.py
+++ b/lib/galaxy/util/hash_util.py
@@ -9,7 +9,6 @@ import logging
 
 from . import smart_str
 
-
 log = logging.getLogger(__name__)
 
 BLOCK_SIZE = 1024 * 1024
@@ -42,7 +41,7 @@ def memory_bound_hexdigest(hash_func=None, hash_func_name=None, path=None, file=
         assert path is None, "Cannot specify path and path keyword arguments."
 
     try:
-        for block in iter(lambda: file.read(BLOCK_SIZE), b''):
+        for block in iter(lambda: file.read(BLOCK_SIZE), b""):
             hasher.update(block)
         return hasher.hexdigest()
     finally:
@@ -55,7 +54,7 @@ def md5_hash_file(path):
     """
     hasher = hashlib.md5()
     try:
-        with open(path, 'rb') as afile:
+        with open(path, "rb") as afile:
             buf = afile.read()
             hasher.update(buf)
             return hasher.hexdigest()
@@ -84,4 +83,4 @@ def is_hashable(value):
     return True
 
 
-__all__ = ('md5', 'hashlib', 'sha1', 'sha', 'new_secure_hash', 'hmac_new', 'is_hashable')
+__all__ = ("md5", "hashlib", "sha1", "sha", "new_secure_hash", "hmac_new", "is_hashable")
diff --git a/lib/galaxy/util/heartbeat.py b/lib/galaxy/util/heartbeat.py
index baf8623486c..48bf6d5ea72 100644
--- a/lib/galaxy/util/heartbeat.py
+++ b/lib/galaxy/util/heartbeat.py
@@ -48,10 +48,7 @@ class Heartbeat(threading.Thread):
 
     def run(self):
         self.pid = os.getpid()
-        self.fname = self.fname.format(
-            server_name=self.config.server_name,
-            pid=self.pid
-        )
+        self.fname = self.fname.format(server_name=self.config.server_name, pid=self.pid)
         fname, ext = os.path.splitext(self.fname)
         self.fname_nonsleeping = f"{fname}.nonsleeping{ext}"
         wait = self.period
@@ -67,12 +64,16 @@ class Heartbeat(threading.Thread):
             self.file = open(self.fname, "a")
             self.file_nonsleeping = open(self.fname_nonsleeping, "a")
             self.file.write("Heartbeat for pid %d thread started at %s\n\n" % (self.pid, time.asctime()))
-            self.file_nonsleeping.write("Non-Sleeping-threads for pid %d thread started at %s\n\n" % (self.pid, time.asctime()))
+            self.file_nonsleeping.write(
+                "Non-Sleeping-threads for pid %d thread started at %s\n\n" % (self.pid, time.asctime())
+            )
 
     def close_logs(self):
         if self.file is not None and not self.file.closed:
             self.file.write("Heartbeat for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()))
-            self.file_nonsleeping.write("Non-Sleeping-threads for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()))
+            self.file_nonsleeping.write(
+                "Non-Sleeping-threads for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime())
+            )
             self.file.close()
             self.file_nonsleeping.close()
 
@@ -124,8 +125,11 @@ class Heartbeat(threading.Thread):
             return True
         if _funcname == "accept" and _text[-14:] == "_sock.accept()":
             return True
-        if _funcname in ("monitor", "__monitor", "app_loop", "check") \
-                and _text.startswith("time.sleep(") and _text.endswith(")"):
+        if (
+            _funcname in ("monitor", "__monitor", "app_loop", "check")
+            and _text.startswith("time.sleep(")
+            and _text.endswith(")")
+        ):
             return True
         if _funcname == "drain_events" and _text == "sleep(polling_interval)":
             return True
@@ -178,8 +182,18 @@ class Heartbeat(threading.Thread):
                 self.nonsleeping_heartbeats[thread_id] = 1
 
             good_frame = self.get_interesting_stack_frame(tb)
-            self.file_nonsleeping.write("Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n  File %s:%d\n    Function \"%s\"\n      %s\n" %
-                (thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3]))
+            self.file_nonsleeping.write(
+                'Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n  File %s:%d\n    Function "%s"\n      %s\n'
+                % (
+                    thread_id,
+                    object,
+                    self.nonsleeping_heartbeats[thread_id],
+                    good_frame[0],
+                    good_frame[1],
+                    good_frame[2],
+                    good_frame[3],
+                )
+            )
             all_threads_are_sleeping = False
 
         if all_threads_are_sleeping:
diff --git a/lib/galaxy/util/inflection.py b/lib/galaxy/util/inflection.py
index 3f5a5ca7b01..286537ed25f 100644
--- a/lib/galaxy/util/inflection.py
+++ b/lib/galaxy/util/inflection.py
@@ -14,89 +14,95 @@ class Inflector:
     """
     Inflector for pluralizing and singularizing English nouns.
     """
+
     # This is a small subset of words that either have the same singular and plural form, or have no singular form
     NONCHANGING_WORDS = {
-        'equipment',
-        'information',
-        'rice',
-        'money',
-        'species',
-        'series',
-        'sheep',
-        'sms',
+        "equipment",
+        "information",
+        "rice",
+        "money",
+        "species",
+        "series",
+        "sheep",
+        "sms",
     }
 
     IRREGULAR_WORDS = {
-        'person': 'people',
-        'man': 'men',
-        'child': 'children',
-        'sex': 'sexes',
-        'move': 'moves',
-        'octopus': 'octopi',
+        "person": "people",
+        "man": "men",
+        "child": "children",
+        "sex": "sexes",
+        "move": "moves",
+        "octopus": "octopi",
     }
 
     PLURALIZE_RULES = (
-        ('(?i)(quiz)$', '\\1zes'),
-        ('(?i)^(ox)$', '\\1en'),
-        ('(?i)([m|l])ouse$', '\\1ice'),
-        ('(?i)(matr|vert|ind)ix|ex$', '\\1ices'),
-        ('(?i)(x|ch|ss|sh)$', '\\1es'),
-        ('(?i)([^aeiouy]|qu)ies$', '\\1y'),
-        ('(?i)([^aeiouy]|qu)y$', '\\1ies'),
-        ('(?i)(hive)$', '\\1s'),
-        ('(?i)(?:([^f])fe|([lr])f)$', '\\1\\2ves'),
-        ('(?i)sis$', 'ses'),
-        ('(?i)([ti])um$', '\\1a'),
-        ('(?i)(buffal|tomat)o$', '\\1oes'),
-        ('(?i)(bu)s$', '\\1ses'),
-        ('(?i)(alias|status|virus)', '\\1es'),
-        ('(?i)(ax|test)is$', '\\1es'),
-        ('(?i)s$', 's'),
-        ('(?i)$', 's')
+        ("(?i)(quiz)$", "\\1zes"),
+        ("(?i)^(ox)$", "\\1en"),
+        ("(?i)([m|l])ouse$", "\\1ice"),
+        ("(?i)(matr|vert|ind)ix|ex$", "\\1ices"),
+        ("(?i)(x|ch|ss|sh)$", "\\1es"),
+        ("(?i)([^aeiouy]|qu)ies$", "\\1y"),
+        ("(?i)([^aeiouy]|qu)y$", "\\1ies"),
+        ("(?i)(hive)$", "\\1s"),
+        ("(?i)(?:([^f])fe|([lr])f)$", "\\1\\2ves"),
+        ("(?i)sis$", "ses"),
+        ("(?i)([ti])um$", "\\1a"),
+        ("(?i)(buffal|tomat)o$", "\\1oes"),
+        ("(?i)(bu)s$", "\\1ses"),
+        ("(?i)(alias|status|virus)", "\\1es"),
+        ("(?i)(ax|test)is$", "\\1es"),
+        ("(?i)s$", "s"),
+        ("(?i)$", "s"),
     )
 
     SINGULARIZE_RULES = (
-        ('(?i)(quiz)zes$', '\\1'),
-        ('(?i)(matr)ices$', '\\1ix'),
-        ('(?i)(vert|ind)ices$', '\\1ex'),
-        ('(?i)^(ox)en', '\\1'),
-        ('(?i)(alias|status|virus)es$', '\\1'),
-        ('(?i)(cris|ax|test)es$', '\\1is'),
-        ('(?i)(shoe)s$', '\\1'),
-        ('(?i)(o)es$', '\\1'),
-        ('(?i)(bus)es$', '\\1'),
-        ('(?i)([m|l])ice$', '\\1ouse'),
-        ('(?i)(x|ch|ss|sh)es$', '\\1'),
-        ('(?i)(m)ovies$', '\\1ovie'),
-        ('(?i)(s)eries$', '\\1eries'),
-        ('(?i)([^aeiouy]|qu)ies$', '\\1y'),
-        ('(?i)([lr])ves$', '\\1f'),
-        ('(?i)(tive)s$', '\\1'),
-        ('(?i)(hive)s$', '\\1'),
-        ('(?i)([^f])ves$', '\\1fe'),
-        ('(?i)(^analy)ses$', '\\1sis'),
-        ('(?i)((a)naly|(b)a|(d)iagno|(p)arenthe|(p)rogno|(s)ynop|(t)he)ses$', '\\1\\2sis'),
-        ('(?i)([ti])a$', '\\1um'),
-        ('(?i)(n)ews$', '\\1ews'),
-        ('(?i)s$', ''),
+        ("(?i)(quiz)zes$", "\\1"),
+        ("(?i)(matr)ices$", "\\1ix"),
+        ("(?i)(vert|ind)ices$", "\\1ex"),
+        ("(?i)^(ox)en", "\\1"),
+        ("(?i)(alias|status|virus)es$", "\\1"),
+        ("(?i)(cris|ax|test)es$", "\\1is"),
+        ("(?i)(shoe)s$", "\\1"),
+        ("(?i)(o)es$", "\\1"),
+        ("(?i)(bus)es$", "\\1"),
+        ("(?i)([m|l])ice$", "\\1ouse"),
+        ("(?i)(x|ch|ss|sh)es$", "\\1"),
+        ("(?i)(m)ovies$", "\\1ovie"),
+        ("(?i)(s)eries$", "\\1eries"),
+        ("(?i)([^aeiouy]|qu)ies$", "\\1y"),
+        ("(?i)([lr])ves$", "\\1f"),
+        ("(?i)(tive)s$", "\\1"),
+        ("(?i)(hive)s$", "\\1"),
+        ("(?i)([^f])ves$", "\\1fe"),
+        ("(?i)(^analy)ses$", "\\1sis"),
+        ("(?i)((a)naly|(b)a|(d)iagno|(p)arenthe|(p)rogno|(s)ynop|(t)he)ses$", "\\1\\2sis"),
+        ("(?i)([ti])a$", "\\1um"),
+        ("(?i)(n)ews$", "\\1ews"),
+        ("(?i)s$", ""),
     )
 
     def pluralize(self, word):
-        '''Pluralizes nouns.'''
+        """Pluralizes nouns."""
         return self._transform(self.PLURALIZE_RULES, word)
 
     def singularize(self, word):
-        '''Singularizes nouns.'''
+        """Singularizes nouns."""
         return self._transform(self.SINGULARIZE_RULES, word, pluralize=False)
 
     def cond_plural(self, number_of_records, word):
-        '''Returns the plural form of a word if first parameter is greater than 1'''
+        """Returns the plural form of a word if first parameter is greater than 1"""
         if number_of_records != 1:
             return self.pluralize(word)
         return word
 
     def _transform(self, rules, word, pluralize=True):
-        return self._handle_nonchanging(word) or self._handle_irregular(word, pluralize=pluralize) or self._apply_rules(rules, word) or word
+        return (
+            self._handle_nonchanging(word)
+            or self._handle_irregular(word, pluralize=pluralize)
+            or self._apply_rules(rules, word)
+            or word
+        )
 
     def _handle_nonchanging(self, word):
         lower_cased_word = word.lower()
@@ -111,7 +117,7 @@ class Inflector:
                 form_a, form_b = form_b, form_a
             match = re.search(f"({form_a})$", word, re.IGNORECASE)
             if match:
-                return re.sub(f"(?i){form_a}$", match.expand('\\1')[0] + form_b[1:], word)
+                return re.sub(f"(?i){form_a}$", match.expand("\\1")[0] + form_b[1:], word)
 
     def _apply_rules(self, rules, word):
         for pattern, replacement in rules:
diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py
index 090588746ae..b15a8788df5 100644
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -10,7 +10,6 @@ from collections.abc import (
     Sequence,
 )
 
-
 from ..util import unicodify
 
 __all__ = ("safe_dumps", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response")
@@ -72,8 +71,8 @@ def safe_dumps(*args, **kwargs):
     except ValueError:
         obj = swap_inf_nan(args[0])
         dumped = json.dumps(obj, allow_nan=False, **kwargs)
-    if kwargs.get('escape_closing_tags', True):
-        return dumped.replace('</', '<\\/')
+    if kwargs.get("escape_closing_tags", True):
+        return dumped.replace("</", "<\\/")
     return dumped
 
 
@@ -83,7 +82,7 @@ def safe_dumps_formatted(obj):
     If serialization fails, the object's string representation will be returned instead.
     """
     try:
-        return safe_dumps(obj, sort_keys=True, indent=4, separators=(',', ': '))
+        return safe_dumps(obj, sort_keys=True, indent=4, separators=(",", ": "))
     except TypeError:
         log.warning("JSON serialization failed for object: %s", str(obj))
         return str(obj)
@@ -91,40 +90,56 @@ def safe_dumps_formatted(obj):
 
 # Methods for handling JSON-RPC
 
+
 def validate_jsonrpc_request(request, regular_methods, notification_methods):
     try:
         request = json.loads(request)
     except Exception as e:
-        return False, request, jsonrpc_response(id=None,
-                                                error=dict(code=-32700,
-                                                           message='Parse error',
-                                                           data=unicodify(e)))
+        return (
+            False,
+            request,
+            jsonrpc_response(id=None, error=dict(code=-32700, message="Parse error", data=unicodify(e))),
+        )
     try:
-        assert 'jsonrpc' in request, \
-            'This server requires JSON-RPC 2.0 and no "jsonrpc" member was sent with the Request object as per the JSON-RPC 2.0 Specification.'
-        assert request['jsonrpc'] == '2.0', \
-            f"Requested JSON-RPC version \"{request['jsonrpc']}\" != required version \"2.0\"."
-        assert 'method' in request, 'No "method" member was sent with the Request object'
+        assert (
+            "jsonrpc" in request
+        ), 'This server requires JSON-RPC 2.0 and no "jsonrpc" member was sent with the Request object as per the JSON-RPC 2.0 Specification.'
+        assert (
+            request["jsonrpc"] == "2.0"
+        ), f"Requested JSON-RPC version \"{request['jsonrpc']}\" != required version \"2.0\"."
+        assert "method" in request, 'No "method" member was sent with the Request object'
     except AssertionError as e:
-        return False, request, jsonrpc_response(request=request,
-                                                error=dict(code=-32600,
-                                                           message='Invalid Request',
-                                                           data=unicodify(e)))
+        return (
+            False,
+            request,
+            jsonrpc_response(request=request, error=dict(code=-32600, message="Invalid Request", data=unicodify(e))),
+        )
     try:
-        assert request['method'] in (regular_methods + notification_methods)
+        assert request["method"] in (regular_methods + notification_methods)
     except AssertionError:
-        return False, request, jsonrpc_response(request=request,
-                                                error=dict(code=-32601,
-                                                           message='Method not found',
-                                                           data=f"Valid methods are: {', '.join(regular_methods + notification_methods)}"))
+        return (
+            False,
+            request,
+            jsonrpc_response(
+                request=request,
+                error=dict(
+                    code=-32601,
+                    message="Method not found",
+                    data=f"Valid methods are: {', '.join(regular_methods + notification_methods)}",
+                ),
+            ),
+        )
     try:
-        if request['method'] in regular_methods:
-            assert 'id' in request, f"No \"id\" member was sent with the Request object and the requested method \"{request['method']}\" is not a notification method"
+        if request["method"] in regular_methods:
+            assert (
+                "id" in request
+            ), f"No \"id\" member was sent with the Request object and the requested method \"{request['method']}\" is not a notification method"
     except AssertionError as e:
-        return False, request, jsonrpc_response(request=request,
-                                                error=dict(code=-32600,
-                                                           message='Invalid Request',
-                                                           data=unicodify(e)))
+        return (
+            False,
+            request,
+            jsonrpc_response(request=request, error=dict(code=-32600, message="Invalid Request", data=unicodify(e))),
+        )
     return True, request, None
 
 
@@ -132,47 +147,49 @@ def validate_jsonrpc_response(response, id=None):
     try:
         response = json.loads(response)
     except Exception as e:
-        log.error('Response was not valid JSON: %s', unicodify(e))
-        log.debug('Response was: %s', response)
+        log.error("Response was not valid JSON: %s", unicodify(e))
+        log.debug("Response was: %s", response)
         return False, response
     try:
-        assert 'jsonrpc' in response, \
-            'This server requires JSON-RPC 2.0 and no "jsonrpc" member was sent with the Response object as per the JSON-RPC 2.0 Specification.'
-        assert ('result' in response or 'error' in response), \
-            'Neither of "result" or "error" members were sent with the Response object.'
-        if 'error' in response:
-            assert int(response['error']['code']), \
-                'The "code" member of the "error" object in the Response is missing or not an integer.'
-            assert 'message' in response, \
-                'The "message" member of the "error" object in the Response is missing.'
+        assert (
+            "jsonrpc" in response
+        ), 'This server requires JSON-RPC 2.0 and no "jsonrpc" member was sent with the Response object as per the JSON-RPC 2.0 Specification.'
+        assert (
+            "result" in response or "error" in response
+        ), 'Neither of "result" or "error" members were sent with the Response object.'
+        if "error" in response:
+            assert int(
+                response["error"]["code"]
+            ), 'The "code" member of the "error" object in the Response is missing or not an integer.'
+            assert "message" in response, 'The "message" member of the "error" object in the Response is missing.'
     except Exception:
-        log.exception('Response was not valid JSON-RPC')
-        log.debug(f'Response was: {response}')
+        log.exception("Response was not valid JSON-RPC")
+        log.debug(f"Response was: {response}")
         return False, response
     if id is not None:
         try:
-            assert 'id' in response and response['id'] == id
+            assert "id" in response and response["id"] == id
         except Exception:
             log.error(f"The response id \"{response['id']}\" does not match the request id \"{id}\"")
             return False, response
     return True, response
 
 
-def jsonrpc_request(method, params=None, id=None, jsonrpc='2.0'):
+def jsonrpc_request(method, params=None, id=None, jsonrpc="2.0"):
     if method is None:
         log.error('jsonrpc_request(): "method" parameter cannot be None')
         return None
     request = dict(jsonrpc=jsonrpc, method=method)
     if params:
-        request['params'] = params
+        request["params"] = params
     if id is not None and id is True:
-        request['id'] = ''.join(random.choice(string.hexdigits) for i in range(16))
+        request["id"] = "".join(random.choice(string.hexdigits) for i in range(16))
     elif id is not None:
-        request['id'] = id
+        request["id"] = id
     return request
 
 
-def jsonrpc_response(request=None, id=None, result=None, error=None, jsonrpc='2.0'):
+def jsonrpc_response(request=None, id=None, result=None, error=None, jsonrpc="2.0"):
     if result:
         rval = dict(jsonrpc=jsonrpc, result=result)
     elif error:
@@ -182,7 +199,7 @@ def jsonrpc_response(request=None, id=None, result=None, error=None, jsonrpc='2.
         log.error(msg)
         rval = dict(jsonrpc=jsonrpc, error=msg)
     if id is not None:
-        rval['id'] = id
-    elif request is not None and 'id' in request:
-        rval['id'] = request['id']
+        rval["id"] = id
+    elif request is not None and "id" in request:
+        rval["id"] = request["id"]
     return rval
diff --git a/lib/galaxy/util/lazy_process.py b/lib/galaxy/util/lazy_process.py
index 4565296c572..ef0365fe8c9 100644
--- a/lib/galaxy/util/lazy_process.py
+++ b/lib/galaxy/util/lazy_process.py
@@ -4,7 +4,7 @@ import time
 
 
 class LazyProcess:
-    """ Abstraction describing a command line launching a service - probably
+    """Abstraction describing a command line launching a service - probably
     as needed as functionality is accessed in Galaxy.
     """
 
@@ -32,7 +32,7 @@ class LazyProcess:
         if self.running:
             assert self.process  # tell type checker it can not be None if self.running
             self.process.terminate()
-            time.sleep(.01)
+            time.sleep(0.01)
             if self.running:
                 self.process.kill()
 
@@ -42,7 +42,7 @@ class LazyProcess:
 
 
 class NoOpLazyProcess:
-    """ LazyProcess abstraction meant to describe potentially optional
+    """LazyProcess abstraction meant to describe potentially optional
     services, in those cases where one is not configured or valid, this
     class can be used in place of LazyProcess.
     """
diff --git a/lib/galaxy/util/monitors.py b/lib/galaxy/util/monitors.py
index 4b885e056ea..0128c9ddba2 100644
--- a/lib/galaxy/util/monitors.py
+++ b/lib/galaxy/util/monitors.py
@@ -9,7 +9,6 @@ DEFAULT_MONITOR_THREAD_JOIN_TIMEOUT = 5
 
 
 class Monitors:
-
     def _init_monitor_thread(self, name, target_name=None, target=None, start=False, config=None):
         self.monitor_join_sleep = getattr(config, "monitor_thread_join_timeout", DEFAULT_MONITOR_THREAD_JOIN_TIMEOUT)
         self.monitor_join = self.monitor_join_sleep > 0
diff --git a/lib/galaxy/util/odict.py b/lib/galaxy/util/odict.py
index ca284dfb459..b485ba3025b 100644
--- a/lib/galaxy/util/odict.py
+++ b/lib/galaxy/util/odict.py
@@ -61,7 +61,7 @@ class odict(UserDict):
         try:
             key = self._keys[-1]
         except IndexError:
-            raise KeyError('dictionary is empty')
+            raise KeyError("dictionary is empty")
         val = self[key]
         del self[key]
         return (key, val)
diff --git a/lib/galaxy/util/oset.py b/lib/galaxy/util/oset.py
index c3e3c873267..eb8d5d0a828 100644
--- a/lib/galaxy/util/oset.py
+++ b/lib/galaxy/util/oset.py
@@ -7,8 +7,8 @@ from collections.abc import MutableSet
 class OrderedSet(MutableSet):
     def __init__(self, iterable=None):
         self.end = end = []
-        end += [None, end, end]         # sentinel node for doubly linked list
-        self.map = {}                   # key --> [key, prev, next]
+        end += [None, end, end]  # sentinel node for doubly linked list
+        self.map = {}  # key --> [key, prev, next]
         if iterable is not None:
             self |= iterable
 
@@ -46,15 +46,15 @@ class OrderedSet(MutableSet):
 
     def pop(self, last=True):
         if not self:
-            raise KeyError('set is empty')
+            raise KeyError("set is empty")
         key = self.end[1][0] if last else self.end[2][0]
         self.discard(key)
         return key
 
     def __repr__(self):
         if not self:
-            return f'{self.__class__.__name__}()'
-        return f'{self.__class__.__name__}({list(self)!r})'
+            return f"{self.__class__.__name__}()"
+        return f"{self.__class__.__name__}({list(self)!r})"
 
     def __eq__(self, other):
         if isinstance(other, OrderedSet):
diff --git a/lib/galaxy/util/pastescript/loadwsgi.py b/lib/galaxy/util/pastescript/loadwsgi.py
index c2dc4e346f3..7bd7f9986e3 100644
--- a/lib/galaxy/util/pastescript/loadwsgi.py
+++ b/lib/galaxy/util/pastescript/loadwsgi.py
@@ -8,15 +8,20 @@ import os
 import re
 import sys
 from inspect import getfullargspec
-from typing import Callable, Dict, List, Optional, Union
+from typing import (
+    Callable,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
 from urllib.parse import unquote
 
 import pkg_resources
 
 from galaxy.util.properties import NicerConfigParser
 
-
-__all__ = ('loadapp', 'loadserver', 'loadfilter', 'appconfig')
+__all__ = ("loadapp", "loadserver", "loadfilter", "appconfig")
 
 # ---- from paste.deploy.compat --------------------------------------
 
@@ -33,7 +38,8 @@ def print_(template, *args, **kwargs):
 
 
 def reraise(t, e, tb):
-    exec('raise e from tb', dict(e=e, tb=tb))
+    exec("raise e from tb", dict(e=e, tb=tb))
+
 
 # ---- from paste.deploy.util ----------------------------------------
 
@@ -54,20 +60,22 @@ def fix_type_error(exc_info, callable, varargs, kwargs):
     """
     if exc_info is None:
         exc_info = sys.exc_info()
-    if (exc_info[0] != TypeError
-            or str(exc_info[1]).find('argument') == -1
-            or getattr(exc_info[1], '_type_error_fixed', False)):
+    if (
+        exc_info[0] != TypeError
+        or str(exc_info[1]).find("argument") == -1
+        or getattr(exc_info[1], "_type_error_fixed", False)
+    ):
         return exc_info
     exc_info[1]._type_error_fixed = True
     argspec = inspect.formatargspec(*getfullargspec(callable))
-    args = ', '.join(map(_short_repr, varargs))
+    args = ", ".join(map(_short_repr, varargs))
     if kwargs and args:
-        args += ', '
+        args += ", "
     if kwargs:
         kwargs = sorted(kwargs.keys())
-        args += ', '.join(f'{n}=...' for n in kwargs)
-    gotspec = f'({args})'
-    msg = f'{exc_info[1]}; got {gotspec}, wanted {argspec}'
+        args += ", ".join(f"{n}=..." for n in kwargs)
+    gotspec = f"({args})"
+    msg = f"{exc_info[1]}; got {gotspec}, wanted {argspec}"
     exc_info[1].args = (msg,)
     return exc_info
 
@@ -96,14 +104,15 @@ def lookup_object(spec):
     Looks up a module or object from a some.module:func_name specification.
     To just look up a module, omit the colon and everything after it.
     """
-    parts, target = spec.split(':') if ':' in spec else (spec, None)
+    parts, target = spec.split(":") if ":" in spec else (spec, None)
     module = __import__(parts)
 
-    for part in parts.split('.')[1:] + ([target] if target else []):
+    for part in parts.split(".")[1:] + ([target] if target else []):
         module = getattr(module, part)
 
     return module
 
+
 # ---- from paste.deploy.loadwsgi ------------------------------------
 
 ############################################################
@@ -157,30 +166,23 @@ class _ObjectType:
         self.config_prefixes = [_aslist(p) for p in _aslist(self.config_prefixes)]
 
     def __repr__(self):
-        return '<{} protocols={!r} prefixes={!r}>'.format(
-            self.name, self.egg_protocols, self.config_prefixes)
+        return "<{} protocols={!r} prefixes={!r}>".format(self.name, self.egg_protocols, self.config_prefixes)
 
     def invoke(self, context):
         assert context.protocol in _flatten(self.egg_protocols)
-        return fix_call(context.object,
-                        context.global_conf, **context.local_conf)
+        return fix_call(context.object, context.global_conf, **context.local_conf)
 
 
 class _App(_ObjectType):
 
-    name = 'application'
-    egg_protocols = ['paste.app_factory', 'paste.composite_factory',
-                     'paste.composit_factory']
-    config_prefixes = [['app', 'application'], ['composite', 'composit'],
-                       'pipeline', 'filter-app']
+    name = "application"
+    egg_protocols = ["paste.app_factory", "paste.composite_factory", "paste.composit_factory"]
+    config_prefixes = [["app", "application"], ["composite", "composit"], "pipeline", "filter-app"]
 
     def invoke(self, context):
-        if context.protocol in ('paste.composit_factory',
-                                'paste.composite_factory'):
-            return fix_call(context.object,
-                            context.loader, context.global_conf,
-                            **context.local_conf)
-        elif context.protocol == 'paste.app_factory':
+        if context.protocol in ("paste.composit_factory", "paste.composite_factory"):
+            return fix_call(context.object, context.loader, context.global_conf, **context.local_conf)
+        elif context.protocol == "paste.app_factory":
             return fix_call(context.object, context.global_conf, **context.local_conf)
         else:
             assert 0, f"Protocol {context.protocol!r} unknown"
@@ -190,20 +192,19 @@ APP = _App()
 
 
 class _Filter(_ObjectType):
-    name = 'filter'
-    egg_protocols = [['paste.filter_factory', 'paste.filter_app_factory']]
-    config_prefixes = ['filter']
+    name = "filter"
+    egg_protocols = [["paste.filter_factory", "paste.filter_app_factory"]]
+    config_prefixes = ["filter"]
 
     def invoke(self, context):
-        if context.protocol == 'paste.filter_factory':
-            return fix_call(context.object,
-                            context.global_conf, **context.local_conf)
-        elif context.protocol == 'paste.filter_app_factory':
+        if context.protocol == "paste.filter_factory":
+            return fix_call(context.object, context.global_conf, **context.local_conf)
+        elif context.protocol == "paste.filter_app_factory":
+
             def filter_wrapper(wsgi_app):
                 # This should be an object, so it has a nicer __repr__
-                return fix_call(context.object,
-                                wsgi_app, context.global_conf,
-                                **context.local_conf)
+                return fix_call(context.object, wsgi_app, context.global_conf, **context.local_conf)
+
             return filter_wrapper
         else:
             assert 0, f"Protocol {context.protocol!r} unknown"
@@ -213,20 +214,19 @@ FILTER = _Filter()
 
 
 class _Server(_ObjectType):
-    name = 'server'
-    egg_protocols = [['paste.server_factory', 'paste.server_runner']]
-    config_prefixes = ['server']
+    name = "server"
+    egg_protocols = [["paste.server_factory", "paste.server_runner"]]
+    config_prefixes = ["server"]
 
     def invoke(self, context):
-        if context.protocol == 'paste.server_factory':
-            return fix_call(context.object,
-                            context.global_conf, **context.local_conf)
-        elif context.protocol == 'paste.server_runner':
+        if context.protocol == "paste.server_factory":
+            return fix_call(context.object, context.global_conf, **context.local_conf)
+        elif context.protocol == "paste.server_runner":
+
             def server_wrapper(wsgi_app):
                 # This should be an object, so it has a nicer __repr__
-                return fix_call(context.object,
-                                wsgi_app, context.global_conf,
-                                **context.local_conf)
+                return fix_call(context.object, wsgi_app, context.global_conf, **context.local_conf)
+
             return server_wrapper
         else:
             assert 0, f"Protocol {context.protocol!r} unknown"
@@ -238,7 +238,7 @@ SERVER = _Server()
 # Virtual type: (@@: There's clearly something crufty here;
 # this probably could be more elegant)
 class _PipeLine(_ObjectType):
-    name = 'pipeline'
+    name = "pipeline"
 
     def invoke(self, context):
         app = context.app_context.create()
@@ -253,7 +253,7 @@ PIPELINE = _PipeLine()
 
 
 class _FilterApp(_ObjectType):
-    name = 'filter_app'
+    name = "filter_app"
 
     def invoke(self, context):
         next_app = context.next_context.create()
@@ -265,7 +265,7 @@ FILTER_APP = _FilterApp()
 
 
 class _FilterWith(_App):
-    name = 'filtered_with'
+    name = "filtered_with"
 
     def invoke(self, context):
         filter_ = context.filter_context.create()
@@ -276,6 +276,7 @@ class _FilterWith(_App):
             # filtering a filter
             def composed(app):
                 return filter_(filtered(app))
+
             return composed
 
 
@@ -299,62 +300,49 @@ def loadserver(uri, name=None, **kw):
 
 
 def appconfig(uri, name=None, relative_to=None, global_conf=None):
-    context = loadcontext(APP, uri, name=name,
-                          relative_to=relative_to,
-                          global_conf=global_conf)
+    context = loadcontext(APP, uri, name=name, relative_to=relative_to, global_conf=global_conf)
     return context.config()
 
 
 _loaders: Dict[str, Callable] = {}
 
 
-def loadobj(object_type, uri, name=None, relative_to=None,
-            global_conf=None):
-    context = loadcontext(
-        object_type, uri, name=name, relative_to=relative_to,
-        global_conf=global_conf)
+def loadobj(object_type, uri, name=None, relative_to=None, global_conf=None):
+    context = loadcontext(object_type, uri, name=name, relative_to=relative_to, global_conf=global_conf)
     return context.create()
 
 
-def loadcontext(object_type, uri, name=None, relative_to=None,
-                global_conf=None):
-    if '#' in uri:
+def loadcontext(object_type, uri, name=None, relative_to=None, global_conf=None):
+    if "#" in uri:
         if name is None:
-            uri, name = uri.split('#', 1)
+            uri, name = uri.split("#", 1)
         else:
             # @@: Ignore fragment or error?
-            uri = uri.split('#', 1)[0]
+            uri = uri.split("#", 1)[0]
     if name is None:
-        name = 'main'
-    if ':' not in uri:
+        name = "main"
+    if ":" not in uri:
         raise LookupError(f"URI has no scheme: {uri!r}")
-    scheme, path = uri.split(':', 1)
+    scheme, path = uri.split(":", 1)
     scheme = scheme.lower()
     if scheme not in _loaders:
-        raise LookupError(
-            f"URI scheme not known: {scheme!r} (from {', '.join(_loaders.keys())})")
-    return _loaders[scheme](
-        object_type,
-        uri, path, name=name, relative_to=relative_to,
-        global_conf=global_conf)
+        raise LookupError(f"URI scheme not known: {scheme!r} (from {', '.join(_loaders.keys())})")
+    return _loaders[scheme](object_type, uri, path, name=name, relative_to=relative_to, global_conf=global_conf)
 
 
-def _loadconfig(object_type, uri, path, name, relative_to,
-                global_conf):
+def _loadconfig(object_type, uri, path, name, relative_to, global_conf):
     isabs = os.path.isabs(path)
     # De-Windowsify the paths:
-    path = path.replace('\\', '/')
+    path = path.replace("\\", "/")
     if not isabs:
         if not relative_to:
-            raise ValueError(
-                "Cannot resolve relative uri %r; no relative_to keyword "
-                "argument given" % uri)
-        relative_to = relative_to.replace('\\', '/')
-        if relative_to.endswith('/'):
+            raise ValueError("Cannot resolve relative uri %r; no relative_to keyword " "argument given" % uri)
+        relative_to = relative_to.replace("\\", "/")
+        if relative_to.endswith("/"):
             path = relative_to + path
         else:
             path = f"{relative_to}/{path}"
-    if path.startswith('///'):
+    if path.startswith("///"):
         path = path[2:]
     path = unquote(path)
     loader = ConfigLoader(path)
@@ -363,26 +351,24 @@ def _loadconfig(object_type, uri, path, name, relative_to,
     return loader.get_context(object_type, name, global_conf)
 
 
-_loaders['config'] = _loadconfig
+_loaders["config"] = _loadconfig
 
 
-def _loadegg(object_type, uri, spec, name, relative_to,
-             global_conf):
+def _loadegg(object_type, uri, spec, name, relative_to, global_conf):
     loader = EggLoader(spec)
     return loader.get_context(object_type, name, global_conf)
 
 
-_loaders['egg'] = _loadegg
+_loaders["egg"] = _loadegg
 
 
-def _loadfunc(object_type, uri, spec, name, relative_to,
-              global_conf):
+def _loadfunc(object_type, uri, spec, name, relative_to, global_conf):
 
     loader = FuncLoader(spec)
     return loader.get_context(object_type, name, global_conf)
 
 
-_loaders['call'] = _loadfunc
+_loaders["call"] = _loadfunc
 
 ############################################################
 # Loaders
@@ -390,32 +376,25 @@ _loaders['call'] = _loadfunc
 
 
 class _Loader:
-
     def get_app(self, name=None, global_conf=None):
-        return self.app_context(
-            name=name, global_conf=global_conf).create()
+        return self.app_context(name=name, global_conf=global_conf).create()
 
     def get_filter(self, name=None, global_conf=None):
-        return self.filter_context(
-            name=name, global_conf=global_conf).create()
+        return self.filter_context(name=name, global_conf=global_conf).create()
 
     def get_server(self, name=None, global_conf=None):
-        return self.server_context(
-            name=name, global_conf=global_conf).create()
+        return self.server_context(name=name, global_conf=global_conf).create()
 
     def app_context(self, name=None, global_conf=None):
-        return self.get_context(
-            APP, name=name, global_conf=global_conf)
+        return self.get_context(APP, name=name, global_conf=global_conf)
 
     def filter_context(self, name=None, global_conf=None):
-        return self.get_context(
-            FILTER, name=name, global_conf=global_conf)
+        return self.get_context(FILTER, name=name, global_conf=global_conf)
 
     def server_context(self, name=None, global_conf=None):
-        return self.get_context(
-            SERVER, name=name, global_conf=global_conf)
+        return self.get_context(SERVER, name=name, global_conf=global_conf)
 
-    _absolute_re = re.compile(r'^[a-zA-Z]+:')
+    _absolute_re = re.compile(r"^[a-zA-Z]+:")
 
     def absolute_name(self, name):
         """
@@ -427,13 +406,9 @@ class _Loader:
 
 
 class ConfigLoader(_Loader):
-
     def __init__(self, filename):
         self.filename = filename = filename.strip()
-        defaults = {
-            'here': os.path.dirname(os.path.abspath(filename)),
-            '__file__': os.path.abspath(filename)
-        }
+        defaults = {"here": os.path.dirname(os.path.abspath(filename)), "__file__": os.path.abspath(filename)}
         self.parser = NicerConfigParser(filename, defaults=defaults)
         self.parser.optionxform = str  # Don't lower-case keys
         with open(filename) as f:
@@ -447,11 +422,8 @@ class ConfigLoader(_Loader):
 
     def get_context(self, object_type, name=None, global_conf=None):
         if self.absolute_name(name):
-            return loadcontext(object_type, name,
-                               relative_to=os.path.dirname(self.filename),
-                               global_conf=global_conf)
-        section = self.find_config_section(
-            object_type, name=name)
+            return loadcontext(object_type, name, relative_to=os.path.dirname(self.filename), global_conf=global_conf)
+        section = self.find_config_section(object_type, name=name)
         if global_conf is None:
             global_conf = {}
         else:
@@ -462,11 +434,10 @@ class ConfigLoader(_Loader):
         global_additions = {}
         get_from_globals = {}
         for option in self.parser.options(section):
-            if option.startswith('set '):
+            if option.startswith("set "):
                 name = option[4:].strip()
-                global_additions[name] = global_conf[name] = (
-                    self.parser.get(section, option))
-            elif option.startswith('get '):
+                global_additions[name] = global_conf[name] = self.parser.get(section, option)
+            elif option.startswith("get "):
                 name = option[4:].strip()
                 get_from_globals[name] = self.parser.get(section, option)
             else:
@@ -476,75 +447,77 @@ class ConfigLoader(_Loader):
                 local_conf[option] = self.parser.get(section, option)
         for local_var, glob_var in get_from_globals.items():
             local_conf[local_var] = global_conf[glob_var]
-        if object_type in (APP, FILTER) and 'filter-with' in local_conf:
-            filter_with = local_conf.pop('filter-with')
+        if object_type in (APP, FILTER) and "filter-with" in local_conf:
+            filter_with = local_conf.pop("filter-with")
         else:
             filter_with = None
-        if 'require' in local_conf:
-            for spec in local_conf['require'].split():
+        if "require" in local_conf:
+            for spec in local_conf["require"].split():
                 pkg_resources.require(spec)
-            del local_conf['require']
-        if section.startswith('filter-app:'):
+            del local_conf["require"]
+        if section.startswith("filter-app:"):
             context = self._filter_app_context(
-                object_type, section, name=name,
-                global_conf=global_conf, local_conf=local_conf,
-                global_additions=global_additions)
-        elif section.startswith('pipeline:'):
+                object_type,
+                section,
+                name=name,
+                global_conf=global_conf,
+                local_conf=local_conf,
+                global_additions=global_additions,
+            )
+        elif section.startswith("pipeline:"):
             context = self._pipeline_app_context(
-                object_type, section, name=name,
-                global_conf=global_conf, local_conf=local_conf,
-                global_additions=global_additions)
-        elif 'use' in local_conf:
-            context = self._context_from_use(
-                object_type, local_conf, global_conf, global_additions,
-                section)
+                object_type,
+                section,
+                name=name,
+                global_conf=global_conf,
+                local_conf=local_conf,
+                global_additions=global_additions,
+            )
+        elif "use" in local_conf:
+            context = self._context_from_use(object_type, local_conf, global_conf, global_additions, section)
         else:
-            context = self._context_from_explicit(
-                object_type, local_conf, global_conf, global_additions,
-                section)
+            context = self._context_from_explicit(object_type, local_conf, global_conf, global_additions, section)
         if filter_with is not None:
             filter_with_context = LoaderContext(
                 obj=None,
                 object_type=FILTER_WITH,
                 protocol=None,
-                global_conf=global_conf, local_conf=local_conf,
-                loader=self)
-            filter_with_context.filter_context = self.filter_context(
-                name=filter_with, global_conf=global_conf)
+                global_conf=global_conf,
+                local_conf=local_conf,
+                loader=self,
+            )
+            filter_with_context.filter_context = self.filter_context(name=filter_with, global_conf=global_conf)
             filter_with_context.next_context = context
             return filter_with_context
         return context
 
-    def _context_from_use(self, object_type, local_conf, global_conf,
-                          global_additions, section):
-        use = local_conf.pop('use')
-        context = self.get_context(
-            object_type, name=use, global_conf=global_conf)
+    def _context_from_use(self, object_type, local_conf, global_conf, global_additions, section):
+        use = local_conf.pop("use")
+        context = self.get_context(object_type, name=use, global_conf=global_conf)
         context.global_conf.update(global_additions)
         context.local_conf.update(local_conf)
-        if '__file__' in global_conf:
+        if "__file__" in global_conf:
             # use sections shouldn't overwrite the original __file__
-            context.global_conf['__file__'] = global_conf['__file__']
+            context.global_conf["__file__"] = global_conf["__file__"]
         # @@: Should loader be overwritten?
         context.loader = self
 
         if context.protocol is None:
             # Determine protocol from section type
-            section_protocol = section.split(':', 1)[0]
-            if section_protocol in ('application', 'app'):
-                context.protocol = 'paste.app_factory'
-            elif section_protocol in ('composit', 'composite'):
-                context.protocol = 'paste.composit_factory'
+            section_protocol = section.split(":", 1)[0]
+            if section_protocol in ("application", "app"):
+                context.protocol = "paste.app_factory"
+            elif section_protocol in ("composit", "composite"):
+                context.protocol = "paste.composit_factory"
             else:
                 # This will work with 'server' and 'filter', otherwise it
                 # could fail but there is an error message already for
                 # bad protocols
-                context.protocol = f'paste.{section_protocol}_factory'
+                context.protocol = f"paste.{section_protocol}_factory"
 
         return context
 
-    def _context_from_explicit(self, object_type, local_conf, global_conf,
-                               global_addition, section):
+    def _context_from_explicit(self, object_type, local_conf, global_conf, global_addition, section):
         possible = []
         for protocol_options in object_type.egg_protocols:
             for protocol in protocol_options:
@@ -552,59 +525,41 @@ class ConfigLoader(_Loader):
                     possible.append((protocol, local_conf[protocol]))
                     break
         if len(possible) > 1:
-            raise LookupError(
-                f"Multiple protocols given in section {section!r}: {possible}")
+            raise LookupError(f"Multiple protocols given in section {section!r}: {possible}")
         if not possible:
-            raise LookupError(
-                f"No loader given in section {section!r}")
+            raise LookupError(f"No loader given in section {section!r}")
         found_protocol, found_expr = possible[0]
         del local_conf[found_protocol]
         value = import_string(found_expr)
-        context = LoaderContext(
-            value, object_type, found_protocol,
-            global_conf, local_conf, self)
+        context = LoaderContext(value, object_type, found_protocol, global_conf, local_conf, self)
         return context
 
-    def _filter_app_context(self, object_type, section, name,
-                            global_conf, local_conf, global_additions):
-        if 'next' not in local_conf:
-            raise LookupError(
-                "The [%s] section in %s is missing a 'next' setting"
-                % (section, self.filename))
-        next_name = local_conf.pop('next')
-        context = LoaderContext(None, FILTER_APP, None, global_conf,
-                                local_conf, self)
-        context.next_context = self.get_context(
-            APP, next_name, global_conf)
-        if 'use' in local_conf:
-            context.filter_context = self._context_from_use(
-                FILTER, local_conf, global_conf, global_additions,
-                section)
+    def _filter_app_context(self, object_type, section, name, global_conf, local_conf, global_additions):
+        if "next" not in local_conf:
+            raise LookupError("The [%s] section in %s is missing a 'next' setting" % (section, self.filename))
+        next_name = local_conf.pop("next")
+        context = LoaderContext(None, FILTER_APP, None, global_conf, local_conf, self)
+        context.next_context = self.get_context(APP, next_name, global_conf)
+        if "use" in local_conf:
+            context.filter_context = self._context_from_use(FILTER, local_conf, global_conf, global_additions, section)
         else:
             context.filter_context = self._context_from_explicit(
-                FILTER, local_conf, global_conf, global_additions,
-                section)
+                FILTER, local_conf, global_conf, global_additions, section
+            )
         return context
 
-    def _pipeline_app_context(self, object_type, section, name,
-                              global_conf, local_conf, global_additions):
-        if 'pipeline' not in local_conf:
-            raise LookupError(
-                "The [%s] section in %s is missing a 'pipeline' setting"
-                % (section, self.filename))
-        pipeline = local_conf.pop('pipeline').split()
+    def _pipeline_app_context(self, object_type, section, name, global_conf, local_conf, global_additions):
+        if "pipeline" not in local_conf:
+            raise LookupError("The [%s] section in %s is missing a 'pipeline' setting" % (section, self.filename))
+        pipeline = local_conf.pop("pipeline").split()
         if local_conf:
             raise LookupError(
                 "The [%s] pipeline section in %s has extra "
-                "(disallowed) settings: %s"
-                % (', '.join(local_conf.keys())))
-        context = LoaderContext(None, PIPELINE, None, global_conf,
-                                local_conf, self)
-        context.app_context = self.get_context(
-            APP, pipeline[-1], global_conf)
-        context.filter_contexts = [
-            self.get_context(FILTER, pname, global_conf)
-            for pname in pipeline[:-1]]
+                "(disallowed) settings: %s" % (", ".join(local_conf.keys()))
+            )
+        context = LoaderContext(None, PIPELINE, None, global_conf, local_conf, self)
+        context.app_context = self.get_context(APP, pipeline[-1], global_conf)
+        context.filter_contexts = [self.get_context(FILTER, pname, global_conf) for pname in pipeline[:-1]]
         return context
 
     def find_config_section(self, object_type, name=None):
@@ -619,24 +574,21 @@ class ConfigLoader(_Loader):
         possible = []
         for name_options in object_type.config_prefixes:
             for name_prefix in name_options:
-                found = self._find_sections(
-                    self.parser.sections(), name_prefix, name)
+                found = self._find_sections(self.parser.sections(), name_prefix, name)
                 if found:
                     possible.extend(found)
                     break
         if not possible:
             raise LookupError(
                 "No section %r (prefixed by %s) found in config %s"
-                % (name,
-                   ' or '.join(map(repr, _flatten(object_type.config_prefixes))),
-                   self.filename))
+                % (name, " or ".join(map(repr, _flatten(object_type.config_prefixes))), self.filename)
+            )
         if len(possible) > 1:
             raise LookupError(
                 "Ambiguous section names %r for section %r (prefixed by %s) "
                 "found in config %s"
-                % (possible, name,
-                   ' or '.join(map(repr, _flatten(object_type.config_prefixes))),
-                   self.filename))
+                % (possible, name, " or ".join(map(repr, _flatten(object_type.config_prefixes))), self.filename)
+            )
         return possible[0]
 
     def _find_sections(self, sections, name_prefix, name):
@@ -644,33 +596,32 @@ class ConfigLoader(_Loader):
         if name is None:
             if name_prefix in sections:
                 found.append(name_prefix)
-            name = 'main'
+            name = "main"
         for section in sections:
             if section.startswith(f"{name_prefix}:"):
-                if section[len(name_prefix) + 1:].strip() == name:
+                if section[len(name_prefix) + 1 :].strip() == name:
                     found.append(section)
         return found
 
 
 class EggLoader(_Loader):
-
     def __init__(self, spec):
         self.spec = spec
 
     def get_context(self, object_type, name=None, global_conf=None):
         if self.absolute_name(name):
-            return loadcontext(object_type, name,
-                               global_conf=global_conf)
-        entry_point, protocol, ep_name = self.find_egg_entry_point(
-            object_type, name=name)
+            return loadcontext(object_type, name, global_conf=global_conf)
+        entry_point, protocol, ep_name = self.find_egg_entry_point(object_type, name=name)
         return LoaderContext(
             entry_point,
             object_type,
             protocol,
-            global_conf or {}, {},
+            global_conf or {},
+            {},
             self,
             distribution=pkg_resources.get_distribution(self.spec),
-            entry_point_name=ep_name)
+            entry_point_name=ep_name,
+        )
 
     def find_egg_entry_point(self, object_type, name=None):
         """
@@ -678,15 +629,12 @@ class EggLoader(_Loader):
         ``name``.
         """
         if name is None:
-            name = 'main'
+            name = "main"
         possible = []
         for protocol_options in object_type.egg_protocols:
             for protocol in protocol_options:
                 pkg_resources.require(self.spec)
-                entry = pkg_resources.get_entry_info(
-                    self.spec,
-                    protocol,
-                    name)
+                entry = pkg_resources.get_entry_info(self.spec, protocol, name)
                 if entry is not None:
                     possible.append((entry.load(), protocol, entry.name))
                     break
@@ -696,21 +644,32 @@ class EggLoader(_Loader):
             raise LookupError(
                 "Entry point %r not found in egg %r (dir: %s; protocols: %s; "
                 "entry_points: %s)"
-                % (name, self.spec,
+                % (
+                    name,
+                    self.spec,
                     dist.location,
-                    ', '.join(_flatten(object_type.egg_protocols)),
-                    ', '.join(_flatten([
-                        list((pkg_resources.get_entry_info(self.spec, prot, name) or {}).keys())
-                        for prot in protocol_options] or '(no entry points)'))))
+                    ", ".join(_flatten(object_type.egg_protocols)),
+                    ", ".join(
+                        _flatten(
+                            [
+                                list((pkg_resources.get_entry_info(self.spec, prot, name) or {}).keys())
+                                for prot in protocol_options
+                            ]
+                            or "(no entry points)"
+                        )
+                    ),
+                )
+            )
         if len(possible) > 1:
             raise LookupError(
                 "Ambiguous entry points for %r in egg %r (protocols: %s)"
-                % (name, self.spec, ', '.join(_flatten(protocol_options))))
+                % (name, self.spec, ", ".join(_flatten(protocol_options)))
+            )
         return possible[0]
 
 
 class FuncLoader(_Loader):
-    """ Loader that supports specifying functions inside modules, without
+    """Loader that supports specifying functions inside modules, without
     using eggs at all. Configuration should be in the format:
         use = call:my.module.path:function_name
 
@@ -720,7 +679,7 @@ class FuncLoader(_Loader):
 
     def __init__(self, spec):
         self.spec = spec
-        if ':' not in spec:
+        if ":" not in spec:
             raise LookupError("Configuration not in format module:function")
 
     def get_context(self, object_type, name=None, global_conf=None):
@@ -736,10 +695,9 @@ class FuncLoader(_Loader):
 
 
 class LoaderContext:
-
-    def __init__(self, obj, object_type, protocol,
-                 global_conf, local_conf, loader,
-                 distribution=None, entry_point_name=None):
+    def __init__(
+        self, obj, object_type, protocol, global_conf, local_conf, loader, distribution=None, entry_point_name=None
+    ):
         self.object = obj
         self.object_type = object_type
         self.protocol = protocol
diff --git a/lib/galaxy/util/pastescript/serve.py b/lib/galaxy/util/pastescript/serve.py
index 56ebe6c090c..42cdf4c26fb 100644
--- a/lib/galaxy/util/pastescript/serve.py
+++ b/lib/galaxy/util/pastescript/serve.py
@@ -38,8 +38,10 @@ from gettext import gettext as _
 from logging.config import fileConfig
 from typing import Optional
 
-from .loadwsgi import loadapp, loadserver
-
+from .loadwsgi import (
+    loadapp,
+    loadserver,
+)
 
 difflib = None
 
@@ -53,7 +55,6 @@ options (like ``--verbose``) to also take arguments (like
 
 
 class BoolOptionParser(optparse.OptionParser):
-
     def _process_long_opt(self, rargs, values):
         arg = rargs.pop(0)
 
@@ -75,8 +76,7 @@ class BoolOptionParser(optparse.OptionParser):
                 if nargs == 1:
                     self.error(_("%s option requires an argument") % opt)
                 else:
-                    self.error(_("%s option requires %d arguments")
-                               % (opt, nargs))
+                    self.error(_("%s option requires %d arguments") % (opt, nargs))
             elif nargs == 1:
                 value = rargs.pop(0)
             else:
@@ -86,19 +86,20 @@ class BoolOptionParser(optparse.OptionParser):
         elif had_explicit_value:
             value = rargs[0].lower().strip()
             del rargs[0:1]
-            if value in ('true', 'yes', 'on', '1', 'y', 't'):
+            if value in ("true", "yes", "on", "1", "y", "t"):
                 value = None
-            elif value in ('false', 'no', 'off', '0', 'n', 'f'):
+            elif value in ("false", "no", "off", "0", "n", "f"):
                 # Don't process
                 return
             else:
-                self.error(_('%s option takes a boolean value only (true/false)') % opt)
+                self.error(_("%s option takes a boolean value only (true/false)") % opt)
 
         else:
             value = None
 
         option.process(opt, value, values, self)
 
+
 # ---- from paste.script.command --------------------------------------
 
 # (c) 2005 Ian Bicking and contributors; written for Paste (http://pythonpaste.org)
@@ -106,7 +107,6 @@ class BoolOptionParser(optparse.OptionParser):
 
 
 class BadCommand(Exception):
-
     def __init__(self, message, exit_code=2):
         self.message = message
         self.exit_code = exit_code
@@ -135,14 +135,13 @@ class NoDefault:
 
 # run and invoke methods moved below ServeCommand
 class Command:
-
     def __init__(self, name):
         self.command_name = name
 
     max_args = None
-    max_args_error = 'You must provide no more than %(max_args)s arguments'
+    max_args_error = "You must provide no more than %(max_args)s arguments"
     min_args: Optional[int] = None
-    min_args_error = 'You must provide at least %(min_args)s arguments'
+    min_args_error = "You must provide at least %(min_args)s arguments"
     required_args = None
     # If this command takes a configuration file, set this to 1 or -1
     # Then if invoked through #! the config file will be put into the positional
@@ -150,11 +149,11 @@ class Command:
     takes_config_file: Optional[int] = None
 
     # Grouped in help messages by this:
-    group_name = ''
+    group_name = ""
 
     required_args = ()
     description: Optional[str] = None
-    usage = ''
+    usage = ""
     hidden = False
     # This is the default verbosity level; --quiet subtracts,
     # --verbose adds:
@@ -174,52 +173,43 @@ class Command:
         self.parse_args(args)
 
         # Setup defaults:
-        for name, default in [('verbose', 0),
-                              ('quiet', 0),
-                              ('interactive', False),
-                              ('overwrite', False)]:
+        for name, default in [("verbose", 0), ("quiet", 0), ("interactive", False), ("overwrite", False)]:
             if not hasattr(self.options, name):
                 setattr(self.options, name, default)
-        if getattr(self.options, 'simulate', False):
+        if getattr(self.options, "simulate", False):
             self.options.verbose = max(self.options.verbose, 1)
         self.interactive = self.default_interactive
-        if getattr(self.options, 'interactive', False):
+        if getattr(self.options, "interactive", False):
             self.interactive += self.options.interactive
-        if getattr(self.options, 'no_interactive', False):
+        if getattr(self.options, "no_interactive", False):
             self.interactive = False
         self.verbose = self.default_verbosity
         self.verbose += self.options.verbose
         self.verbose -= self.options.quiet
-        self.simulate = getattr(self.options, 'simulate', False)
+        self.simulate = getattr(self.options, "simulate", False)
 
         # For #! situations:
-        if os.environ.get('PASTE_CONFIG_FILE') and self.takes_config_file is not None:
+        if os.environ.get("PASTE_CONFIG_FILE") and self.takes_config_file is not None:
             take = self.takes_config_file
-            filename = os.environ.get('PASTE_CONFIG_FILE')
+            filename = os.environ.get("PASTE_CONFIG_FILE")
             if take == 1:
                 self.args.insert(0, filename)
             elif take == -1:
                 self.args.append(filename)
             else:
-                assert 0, (
-                    f"Value takes_config_file must be None, 1, or -1 (not {take!r})")
+                assert 0, f"Value takes_config_file must be None, 1, or -1 (not {take!r})"
 
-        if os.environ.get('PASTE_DEFAULT_QUIET'):
+        if os.environ.get("PASTE_DEFAULT_QUIET"):
             self.verbose = 0
 
         # Validate:
         if self.min_args is not None and len(self.args) < self.min_args:
-            raise BadCommand(
-                self.min_args_error % {'min_args': self.min_args,
-                                       'actual_args': len(self.args)})
+            raise BadCommand(self.min_args_error % {"min_args": self.min_args, "actual_args": len(self.args)})
         if self.max_args is not None and len(self.args) > self.max_args:
-            raise BadCommand(
-                self.max_args_error % {'max_args': self.max_args,
-                                       'actual_args': len(self.args)})
+            raise BadCommand(self.max_args_error % {"max_args": self.max_args, "actual_args": len(self.args)})
         for var_name, option_name in self.required_args:
             if not getattr(self.options, var_name, None):
-                raise BadCommand(
-                    f'You must provide the option {option_name}')
+                raise BadCommand(f"You must provide the option {option_name}")
         result = self.command()
         if result is None:
             return self.return_code
@@ -230,7 +220,7 @@ class Command:
         if self.usage:
             usage = f" {self.usage}"
         else:
-            usage = ''
+            usage = ""
         self.parser.usage = f"%prog [options]{usage}\n{self.summary}"
         self.parser.prog = self._prog_name()
         if self.description:
@@ -240,26 +230,23 @@ class Command:
         self.options, self.args = self.parser.parse_args(args)
 
     def _prog_name(self):
-        return f'{os.path.basename(sys.argv[0])} {self.command_name}'
+        return f"{os.path.basename(sys.argv[0])} {self.command_name}"
 
     ########################################
     # Utility methods
     ########################################
 
-    def pad(self, s, length, dir='left'):
+    def pad(self, s, length, dir="left"):
         if len(s) >= length:
             return s
-        if dir == 'left':
-            return s + ' ' * (length - len(s))
+        if dir == "left":
+            return s + " " * (length - len(s))
         else:
-            return ' ' * (length - len(s)) + s
+            return " " * (length - len(s)) + s
 
-    def _standard_parser(cls, verbose=True,
-                        interactive=False,
-                        no_interactive=False,
-                        simulate=False,
-                        quiet=False,
-                        overwrite=False):
+    def _standard_parser(
+        cls, verbose=True, interactive=False, no_interactive=False, simulate=False, quiet=False, overwrite=False
+    ):
         """
         Create a standard ``OptionParser`` instance.
 
@@ -273,35 +260,23 @@ class Command:
         """
         parser = BoolOptionParser()
         if verbose:
-            parser.add_option('-v', '--verbose',
-                              action='count',
-                              dest='verbose',
-                              default=0)
+            parser.add_option("-v", "--verbose", action="count", dest="verbose", default=0)
         if quiet:
-            parser.add_option('-q', '--quiet',
-                              action='count',
-                              dest='quiet',
-                              default=0)
+            parser.add_option("-q", "--quiet", action="count", dest="quiet", default=0)
         if no_interactive:
-            parser.add_option('--no-interactive',
-                              action="count",
-                              dest="no_interactive",
-                              default=0)
+            parser.add_option("--no-interactive", action="count", dest="no_interactive", default=0)
         if interactive:
-            parser.add_option('-i', '--interactive',
-                              action='count',
-                              dest='interactive',
-                              default=0)
+            parser.add_option("-i", "--interactive", action="count", dest="interactive", default=0)
         if simulate:
-            parser.add_option('-n', '--simulate',
-                              action='store_true',
-                              dest='simulate',
-                              default=False)
+            parser.add_option("-n", "--simulate", action="store_true", dest="simulate", default=False)
         if overwrite:
-            parser.add_option('-f', '--overwrite',
-                              dest="overwrite",
-                              action="store_true",
-                              help="Overwrite files (warnings will be emitted for non-matching files otherwise)")
+            parser.add_option(
+                "-f",
+                "--overwrite",
+                dest="overwrite",
+                action="store_true",
+                help="Overwrite files (warnings will be emitted for non-matching files otherwise)",
+            )
         return parser
 
     standard_parser = classmethod(_standard_parser)
@@ -313,7 +288,7 @@ class Command:
         that case, or on non-Windows systems or an executable with no
         spaces, it just leaves well enough alone.
         """
-        if sys.platform != 'win32' or ' ' not in arg:
+        if sys.platform != "win32" or " " not in arg:
             # Problem does not apply:
             return arg
         try:
@@ -322,7 +297,8 @@ class Command:
             raise ValueError(
                 "The executable %r contains a space, and in order to "
                 "handle this issue you must have the win32api module "
-                "installed" % arg)
+                "installed" % arg
+            )
         arg = win32api.GetShortPathName(arg)
         return arg
 
@@ -333,10 +309,9 @@ class Command:
         """
         result = {}
         for arg in args:
-            if '=' not in arg:
-                raise BadCommand(
-                    f'Variable assignment {arg!r} invalid (no "=")')
-            name, value = arg.split('=', 1)
+            if "=" not in arg:
+                raise BadCommand(f'Variable assignment {arg!r} invalid (no "=")')
+            name, value = arg.split("=", 1)
             result[name] = value
         return result
 
@@ -350,28 +325,25 @@ class Command:
         """
         parser = configparser.ConfigParser()
         parser.read([config_file])
-        if parser.has_section('loggers'):
+        if parser.has_section("loggers"):
             config_file = os.path.abspath(config_file)
-            fileConfig(config_file, dict(__file__=config_file,
-                                         here=os.path.dirname(config_file)))
+            fileConfig(config_file, dict(__file__=config_file, here=os.path.dirname(config_file)))
 
 
 class NotFoundCommand(Command):
-
     def run(self, args):
-        print('Command %r not known (you may need to run setup.py egg_info)'
-              % self.command_name)
+        print("Command %r not known (you may need to run setup.py egg_info)" % self.command_name)
         commands = list()
         commands.sort()
         if not commands:
-            print('No commands registered.')
-            print('Have you installed Paste Script?')
-            print('(try running python setup.py develop)')
+            print("No commands registered.")
+            print("Have you installed Paste Script?")
+            print("(try running python setup.py develop)")
             return 2
-        print('Known commands:')
+        print("Known commands:")
         longest = max(len(n) for n, c in commands)
         for name, command in commands:
-            print(f'  {self.pad(name, length=longest)}  {command.load().summary}')
+            print(f"  {self.pad(name, length=longest)}  {command.load().summary}")
         return 2
 
 
@@ -379,7 +351,7 @@ class NotFoundCommand(Command):
 
 MAXFD = 1024
 
-jython = sys.platform.startswith('java')
+jython = sys.platform.startswith("java")
 
 
 class DaemonizeException(Exception):
@@ -389,10 +361,12 @@ class DaemonizeException(Exception):
 class ServeCommand(Command):
 
     min_args = 0
-    usage = 'CONFIG_FILE [start|stop|restart|status] [var=value]'
+    usage = "CONFIG_FILE [start|stop|restart|status] [var=value]"
     takes_config_file = 1
     summary = "Serve the described application"
-    description: Optional[str] = """\
+    description: Optional[
+        str
+    ] = """\
     This command serves a web application that uses a paste.deploy
     configuration file for the server and application.
 
@@ -407,93 +381,90 @@ class ServeCommand(Command):
     requires_config_file = True
 
     parser = Command.standard_parser(quiet=True)
-    parser.add_option('-n', '--app-name',
-                      dest='app_name',
-                      metavar='NAME',
-                      help="Load the named application (default main)")
-    parser.add_option('-s', '--server',
-                      dest='server',
-                      metavar='SERVER_TYPE',
-                      help="Use the named server.")
-    parser.add_option('--server-name',
-                      dest='server_name',
-                      metavar='SECTION_NAME',
-                      help="Use the named server as defined in the configuration file (default: main)")
-    if hasattr(os, 'fork'):
-        parser.add_option('--daemon',
-                          dest="daemon",
-                          action="store_true",
-                          help="Run in daemon (background) mode")
-    parser.add_option('--pid-file',
-                      dest='pid_file',
-                      metavar='FILENAME',
-                      help="Save PID to file (default to paster.pid if running in daemon mode)")
-    parser.add_option('--log-file',
-                      dest='log_file',
-                      metavar='LOG_FILE',
-                      help="Save output to the given log file (redirects stdout)")
-    parser.add_option('--reload',
-                      dest='reload',
-                      action='store_true',
-                      help="Use auto-restart file monitor")
-    parser.add_option('--reload-interval',
-                      dest='reload_interval',
-                      default=1,
-                      help="Seconds between checking files (low number can cause significant CPU usage)")
-    parser.add_option('--monitor-restart',
-                      dest='monitor_restart',
-                      action='store_true',
-                      help="Auto-restart server if it dies")
-    parser.add_option('--status',
-                      action='store_true',
-                      dest='show_status',
-                      help="Show the status of the (presumably daemonized) server")
+    parser.add_option(
+        "-n", "--app-name", dest="app_name", metavar="NAME", help="Load the named application (default main)"
+    )
+    parser.add_option("-s", "--server", dest="server", metavar="SERVER_TYPE", help="Use the named server.")
+    parser.add_option(
+        "--server-name",
+        dest="server_name",
+        metavar="SECTION_NAME",
+        help="Use the named server as defined in the configuration file (default: main)",
+    )
+    if hasattr(os, "fork"):
+        parser.add_option("--daemon", dest="daemon", action="store_true", help="Run in daemon (background) mode")
+    parser.add_option(
+        "--pid-file",
+        dest="pid_file",
+        metavar="FILENAME",
+        help="Save PID to file (default to paster.pid if running in daemon mode)",
+    )
+    parser.add_option(
+        "--log-file", dest="log_file", metavar="LOG_FILE", help="Save output to the given log file (redirects stdout)"
+    )
+    parser.add_option("--reload", dest="reload", action="store_true", help="Use auto-restart file monitor")
+    parser.add_option(
+        "--reload-interval",
+        dest="reload_interval",
+        default=1,
+        help="Seconds between checking files (low number can cause significant CPU usage)",
+    )
+    parser.add_option(
+        "--monitor-restart", dest="monitor_restart", action="store_true", help="Auto-restart server if it dies"
+    )
+    parser.add_option(
+        "--status",
+        action="store_true",
+        dest="show_status",
+        help="Show the status of the (presumably daemonized) server",
+    )
 
-    if hasattr(os, 'setuid'):
+    if hasattr(os, "setuid"):
         # I don't think these are available on Windows
-        parser.add_option('--user',
-                          dest='set_user',
-                          metavar="USERNAME",
-                          help="Set the user (usually only possible when run as root)")
-        parser.add_option('--group',
-                          dest='set_group',
-                          metavar="GROUP",
-                          help="Set the group (usually only possible when run as root)")
+        parser.add_option(
+            "--user", dest="set_user", metavar="USERNAME", help="Set the user (usually only possible when run as root)"
+        )
+        parser.add_option(
+            "--group", dest="set_group", metavar="GROUP", help="Set the group (usually only possible when run as root)"
+        )
 
-    parser.add_option('--stop-daemon',
-                      dest='stop_daemon',
-                      action='store_true',
-                      help='Stop a daemonized server (given a PID file, or default paster.pid file)')
+    parser.add_option(
+        "--stop-daemon",
+        dest="stop_daemon",
+        action="store_true",
+        help="Stop a daemonized server (given a PID file, or default paster.pid file)",
+    )
 
     if jython:
-        parser.add_option('--disable-jython-reloader',
-                          action='store_true',
-                          dest='disable_jython_reloader',
-                          help="Disable the Jython reloader")
+        parser.add_option(
+            "--disable-jython-reloader",
+            action="store_true",
+            dest="disable_jython_reloader",
+            help="Disable the Jython reloader",
+        )
 
-    _scheme_re = re.compile(r'^[a-z][a-z]+:', re.I)
+    _scheme_re = re.compile(r"^[a-z][a-z]+:", re.I)
 
     default_verbosity = 1
 
-    _reloader_environ_key = 'PYTHON_RELOADER_SHOULD_RUN'
-    _monitor_environ_key = 'PASTE_MONITOR_SHOULD_RUN'
+    _reloader_environ_key = "PYTHON_RELOADER_SHOULD_RUN"
+    _monitor_environ_key = "PASTE_MONITOR_SHOULD_RUN"
 
-    possible_subcommands = ('start', 'stop', 'restart', 'status')
+    possible_subcommands = ("start", "stop", "restart", "status")
 
     def command(self):
         if self.options.stop_daemon:
             return self.stop_daemon()
 
-        if not hasattr(self.options, 'set_user'):
+        if not hasattr(self.options, "set_user"):
             # Windows case:
             self.options.set_user = self.options.set_group = None
         # @@: Is this the right stage to set the user at?
-        self.change_user_group(
-            self.options.set_user, self.options.set_group)
+        self.change_user_group(self.options.set_user, self.options.set_group)
 
         if self.requires_config_file:
             if not self.args:
-                raise BadCommand('You must give a config file')
+                raise BadCommand("You must give a config file")
             app_spec = self.args[0]
             if len(self.args) > 1 and self.args[1] in self.possible_subcommands:
                 cmd = self.args[1]
@@ -510,9 +481,8 @@ class ServeCommand(Command):
                 cmd = None
                 restvars = self.args[:]
 
-        if (getattr(self.options, 'daemon', False)
-                and getattr(self.options, 'reload', False)):
-            raise BadCommand('The --daemon and --reload options may not be used together')
+        if getattr(self.options, "daemon", False) and getattr(self.options, "reload", False):
+            raise BadCommand("The --daemon and --reload options may not be used together")
 
         jython_monitor = False
         if self.options.reload:
@@ -526,42 +496,41 @@ class ServeCommand(Command):
                 except ImportError:
                     pass
                 else:
-                    jython_monitor = JythonMonitor(poll_interval=int(
-                        self.options.reload_interval))
+                    jython_monitor = JythonMonitor(poll_interval=int(self.options.reload_interval))
                     if self.requires_config_file:
                         jython_monitor.watch_file(self.args[0])
 
             if not jython_monitor:
                 if os.environ.get(self._reloader_environ_key):
                     from paste import reloader
+
                     if self.verbose > 1:
-                        print('Running reloading file monitor')
+                        print("Running reloading file monitor")
                     reloader.install(int(self.options.reload_interval))
                     if self.requires_config_file:
                         reloader.watch_file(self.args[0])
                 else:
                     return self.restart_with_reloader()
 
-        if cmd not in (None, 'start', 'stop', 'restart', 'status'):
-            raise BadCommand(
-                f'Error: must give start|stop|restart (not {cmd})')
+        if cmd not in (None, "start", "stop", "restart", "status"):
+            raise BadCommand(f"Error: must give start|stop|restart (not {cmd})")
 
-        if cmd == 'status' or self.options.show_status:
+        if cmd == "status" or self.options.show_status:
             return self.show_status()
 
-        if cmd == 'restart' or cmd == 'stop':
+        if cmd == "restart" or cmd == "stop":
             result = self.stop_daemon()
             if result:
                 print("Could not stop daemon")
                 # It's ok to continue trying to restart if stop_daemon returns
                 # a 1, otherwise shortcut and return.
-                if cmd == 'restart' and result != 1:
+                if cmd == "restart" and result != 1:
                     return result
-            if cmd == 'stop':
+            if cmd == "stop":
                 return result
             self.options.daemon = True
 
-        if cmd == 'start':
+        if cmd == "start":
             self.options.daemon = True
 
         app_name = self.options.app_name
@@ -570,38 +539,38 @@ class ServeCommand(Command):
             app_spec = f"config:{app_spec}"
         server_name = self.options.server_name
         if self.options.server:
-            server_spec = 'egg:PasteScript'
+            server_spec = "egg:PasteScript"
             assert server_name is None
             server_name = self.options.server
         else:
             server_spec = app_spec
         base = os.getcwd()
 
-        if getattr(self.options, 'daemon', False):
+        if getattr(self.options, "daemon", False):
             if not self.options.pid_file:
-                self.options.pid_file = 'paster.pid'
+                self.options.pid_file = "paster.pid"
             if not self.options.log_file:
-                self.options.log_file = 'paster.log'
+                self.options.log_file = "paster.log"
 
         # Ensure the log file is writeable
         if self.options.log_file:
             try:
-                writeable_log_file = open(self.options.log_file, 'a')
+                writeable_log_file = open(self.options.log_file, "a")
             except OSError as ioe:
-                msg = f'Error: Unable to write to log file: {ioe}'
+                msg = f"Error: Unable to write to log file: {ioe}"
                 raise BadCommand(msg)
             writeable_log_file.close()
 
         # Ensure the pid file is writeable
         if self.options.pid_file:
             try:
-                writeable_pid_file = open(self.options.pid_file, 'a')
+                writeable_pid_file = open(self.options.pid_file, "a")
             except OSError as ioe:
-                msg = f'Error: Unable to write to pid file: {ioe}'
+                msg = f"Error: Unable to write to pid file: {ioe}"
                 raise BadCommand(msg)
             writeable_pid_file.close()
 
-        if getattr(self.options, 'daemon', False):
+        if getattr(self.options, "daemon", False):
             try:
                 self.daemonize()
             except DaemonizeException as ex:
@@ -609,23 +578,22 @@ class ServeCommand(Command):
                     print(str(ex))
                 return
 
-        if (self.options.monitor_restart and not
-                os.environ.get(self._monitor_environ_key)):
+        if self.options.monitor_restart and not os.environ.get(self._monitor_environ_key):
             return self.restart_with_monitor()
 
         if self.options.pid_file:
             self.record_pid(self.options.pid_file)
 
         if self.options.log_file:
-            stdout_log = LazyWriter(self.options.log_file, 'a')
+            stdout_log = LazyWriter(self.options.log_file, "a")
             sys.stdout = stdout_log
             sys.stderr = stdout_log
             logging.basicConfig(stream=stdout_log)
 
         log_fn = app_spec
-        if log_fn.startswith('config:'):
-            log_fn = app_spec[len('config:'):]
-        elif log_fn.startswith('egg:'):
+        if log_fn.startswith("config:"):
+            log_fn = app_spec[len("config:") :]
+        elif log_fn.startswith("egg:"):
             log_fn = None
         if log_fn:
             log_fn = os.path.join(base, log_fn)
@@ -636,10 +604,10 @@ class ServeCommand(Command):
         app = loadapp(app_spec, name=app_name, relative_to=base, global_conf=vars)
 
         if self.verbose > 0:
-            if hasattr(os, 'getpid'):
-                msg = 'Starting server in PID %i.' % os.getpid()
+            if hasattr(os, "getpid"):
+                msg = "Starting server in PID %i." % os.getpid()
             else:
-                msg = 'Starting server.'
+                msg = "Starting server."
             print(msg)
 
         def serve():
@@ -651,19 +619,19 @@ class ServeCommand(Command):
                 if str(e):
                     msg = f" {str(e)}"
                 else:
-                    msg = ''
-                print(f'Exiting{msg} (-v to see traceback)')
+                    msg = ""
+                print(f"Exiting{msg} (-v to see traceback)")
             except AttributeError as e:
                 # Capturing bad error response from paste
                 if str(e) == "'WSGIThreadPoolServer' object has no attribute 'thread_pool'":
-                    raise OSError(98, 'Address already in use')
+                    raise OSError(98, "Address already in use")
                 else:
                     raise AttributeError(e)
 
         if jython_monitor:
             # JythonMonitor has to be ran from the main thread
             threading.Thread(target=serve).start()
-            print('Starting Jython file monitor')
+            print("Starting Jython file monitor")
             jython_monitor.periodic_reload()
         else:
             serve()
@@ -672,11 +640,11 @@ class ServeCommand(Command):
         pid = live_pidfile(self.options.pid_file)
         if pid:
             raise DaemonizeException(
-                "Daemon is already running (PID: %s from PID file %s)"
-                % (pid, self.options.pid_file))
+                "Daemon is already running (PID: %s from PID file %s)" % (pid, self.options.pid_file)
+            )
 
         if self.verbose > 0:
-            print('Entering daemon mode')
+            print("Entering daemon mode")
         pid = os.fork()
         if pid:
             # The forked process also has a handle on resources, so we
@@ -714,16 +682,16 @@ class ServeCommand(Command):
     def record_pid(self, pid_file):
         pid = os.getpid()
         if self.verbose > 1:
-            print(f'Writing PID {pid} to {pid_file}')
-        f = open(pid_file, 'w')
+            print(f"Writing PID {pid} to {pid_file}")
+        f = open(pid_file, "w")
         f.write(str(pid))
         f.close()
         atexit.register(_remove_pid_file, pid, pid_file, self.verbose)
 
     def stop_daemon(self):
-        pid_file = self.options.pid_file or 'paster.pid'
+        pid_file = self.options.pid_file or "paster.pid"
         if not os.path.exists(pid_file):
-            print(f'No PID file exists in {pid_file}')
+            print(f"No PID file exists in {pid_file}")
             return 1
         pid = read_pidfile(pid_file)
         if not pid:
@@ -751,19 +719,19 @@ class ServeCommand(Command):
         return 0
 
     def show_status(self):
-        pid_file = self.options.pid_file or 'paster.pid'
+        pid_file = self.options.pid_file or "paster.pid"
         if not os.path.exists(pid_file):
-            print(f'No PID file {pid_file}')
+            print(f"No PID file {pid_file}")
             return 1
         pid = read_pidfile(pid_file)
         if not pid:
-            print(f'No PID in file {pid_file}')
+            print(f"No PID in file {pid_file}")
             return 1
         pid = live_pidfile(pid_file)
         if not pid:
-            print(f'PID {pid} in {pid_file} is not running')
+            print(f"PID {pid} in {pid_file} is not running")
             return 1
-        print(f'Server running in PID {pid}')
+        print(f"Server running in PID {pid}")
         return 0
 
     def restart_with_reloader(self):
@@ -772,16 +740,16 @@ class ServeCommand(Command):
     def restart_with_monitor(self, reloader=False):
         if self.verbose > 0:
             if reloader:
-                print('Starting subprocess with file monitor')
+                print("Starting subprocess with file monitor")
             else:
-                print('Starting subprocess with monitor parent')
+                print("Starting subprocess with monitor parent")
         while 1:
             args = [self.quote_first_command_arg(sys.executable)] + sys.argv
             new_environ = os.environ.copy()
             if reloader:
-                new_environ[self._reloader_environ_key] = 'true'
+                new_environ[self._reloader_environ_key] = "true"
             else:
-                new_environ[self._monitor_environ_key] = 'true'
+                new_environ[self._monitor_environ_key] = "true"
             proc = None
             try:
                 try:
@@ -790,12 +758,12 @@ class ServeCommand(Command):
                     exit_code = proc.wait()
                     proc = None
                 except KeyboardInterrupt:
-                    print('^C caught in monitor process')
+                    print("^C caught in monitor process")
                     if self.verbose > 1:
                         raise
                     return 1
             finally:
-                if proc is not None and hasattr(os, 'kill'):
+                if proc is not None and hasattr(os, "kill"):
                     try:
                         os.kill(proc.pid, signal.SIGTERM)
                     except OSError:
@@ -807,7 +775,7 @@ class ServeCommand(Command):
                 if exit_code != 3:
                     return exit_code
             if self.verbose > 0:
-                print('-' * 20, 'Restarting', '-' * 20)
+                print("-" * 20, "Restarting", "-" * 20)
 
     def change_user_group(self, user, group):
         if not user and not group:
@@ -821,8 +789,7 @@ class ServeCommand(Command):
                 try:
                     entry = grp.getgrnam(group)
                 except KeyError:
-                    raise BadCommand(
-                        f"Bad group: {group!r}; no such group exists")
+                    raise BadCommand(f"Bad group: {group!r}; no such group exists")
                 gid = entry.gr_gid
         try:
             uid = int(user)
@@ -831,19 +798,16 @@ class ServeCommand(Command):
             try:
                 entry = pwd.getpwnam(user)
             except KeyError:
-                raise BadCommand(
-                    f"Bad username: {user!r}; no such user exists")
+                raise BadCommand(f"Bad username: {user!r}; no such user exists")
             if not gid:
                 gid = entry.pw_gid
             uid = entry.pw_uid
         if self.verbose > 0:
-            print('Changing user to {}:{} ({}:{})'.format(
-                user, group or '(unknown)', uid, gid))
-        if hasattr(os, 'initgroups'):
+            print("Changing user to {}:{} ({}:{})".format(user, group or "(unknown)", uid, gid))
+        if hasattr(os, "initgroups"):
             os.initgroups(user, gid)
         else:
-            os.setgroups([e.gr_gid for e in grp.getgrall()
-                          if user in e.gr_mem] + [gid])
+            os.setgroups([e.gr_gid for e in grp.getgrall() if user in e.gr_mem] + [gid])
         if gid:
             os.setgid(gid)
         if uid:
@@ -857,7 +821,7 @@ class LazyWriter:
     to.
     """
 
-    def __init__(self, filename, mode='w'):
+    def __init__(self, filename, mode="w"):
         self.filename = filename
         self.fileobj = None
         self.lock = threading.Lock()
@@ -934,8 +898,7 @@ def _remove_pid_file(written_pid, filename, verbosity):
         pass
     else:
         if pid_in_file != current_pid:
-            print("PID file {} contains {}, not expected PID {}".format(
-                filename, pid_in_file, current_pid))
+            print("PID file {} contains {}, not expected PID {}".format(filename, pid_in_file, current_pid))
             return
     if verbosity > 0:
         print(f"Removing PID file {filename}")
@@ -947,13 +910,13 @@ def _remove_pid_file(written_pid, filename, verbosity):
         print(f"Cannot remove PID file: {e}")
     # well, at least lets not leave the invalid PID around...
     try:
-        f = open(filename, 'w')
-        f.write('')
+        f = open(filename, "w")
+        f.write("")
         f.close()
     except OSError as e:
-        print(f'Stale PID left in file: {filename} ({e:e})')
+        print(f"Stale PID left in file: {filename} ({e:e})")
     else:
-        print('Stale PID removed')
+        print("Stale PID removed")
 
 
 def ensure_port_cleanup(bound_addresses, maxtries=30, sleeptime=2):
@@ -966,8 +929,7 @@ def ensure_port_cleanup(bound_addresses, maxtries=30, sleeptime=2):
         import paste.script
         ensure_port_cleanup([80, 443])
     """
-    atexit.register(_cleanup_ports, bound_addresses, maxtries=maxtries,
-                    sleeptime=sleeptime)
+    atexit.register(_cleanup_ports, bound_addresses, maxtries=maxtries, sleeptime=sleeptime)
 
 
 def _cleanup_ports(bound_addresses, maxtries=30, sleeptime=2):
@@ -984,7 +946,7 @@ def _cleanup_ports(bound_addresses, maxtries=30, sleeptime=2):
             else:
                 time.sleep(sleeptime)
         else:
-            raise SystemExit('Timeout waiting for port.')
+            raise SystemExit("Timeout waiting for port.")
         sock.close()
 
 
@@ -995,45 +957,47 @@ def _turn_sigterm_into_systemexit():
 
     def handle_term(signo, frame):
         raise SystemExit
+
     signal.signal(signal.SIGTERM, handle_term)
 
 
 # ---- from paste.script.command --------------------------------------
 python_version = sys.version.splitlines()[0].strip()
 
-parser = optparse.OptionParser(add_help_option=False,
-                               # version='%s from %s (python %s)'
-                               # % (dist, dist.location, python_version),
-                               usage='%prog [paster_options] COMMAND [command_options]')
+parser = optparse.OptionParser(
+    add_help_option=False,
+    # version='%s from %s (python %s)'
+    # % (dist, dist.location, python_version),
+    usage="%prog [paster_options] COMMAND [command_options]",
+)
 
-parser.add_option(
-    '-h', '--help',
-    action='store_true',
-    dest='do_help',
-    help="Show this help message")
+parser.add_option("-h", "--help", action="store_true", dest="do_help", help="Show this help message")
 parser.disable_interspersed_args()
 
 # @@: Add an option to run this in another Python interpreter
 
-commands = {
-    'serve': ServeCommand
-}
+commands = {"serve": ServeCommand}
 
 
 def run(args=None):
-    if (not args and len(sys.argv) >= 2 and os.environ.get('_')
-            and sys.argv[0] != os.environ['_'] and os.environ['_'] == sys.argv[1]):
+    if (
+        not args
+        and len(sys.argv) >= 2
+        and os.environ.get("_")
+        and sys.argv[0] != os.environ["_"]
+        and os.environ["_"] == sys.argv[1]
+    ):
         # probably it's an exe execution
-        args = ['exe', os.environ['_']] + sys.argv[2:]
+        args = ["exe", os.environ["_"]] + sys.argv[2:]
     if args is None:
         args = sys.argv[1:]
     options, args = parser.parse_args(args)
     options.base_parser = parser
     if options.do_help:
-        args = ['help'] + args
+        args = ["help"] + args
     if not args:
-        print(f'Usage: {sys.argv[0]} COMMAND')
-        args = ['help']
+        print(f"Usage: {sys.argv[0]} COMMAND")
+        args = ["help"]
     command_name = args[0]
     if command_name not in commands:
         command = NotFoundCommand
diff --git a/lib/galaxy/util/path/__init__.py b/lib/galaxy/util/path/__init__.py
index d77854448df..c53f028a472 100644
--- a/lib/galaxy/util/path/__init__.py
+++ b/lib/galaxy/util/path/__init__.py
@@ -12,7 +12,7 @@ from os import (
     extsep,
     makedirs,
     stat,
-    walk
+    walk,
 )
 from os.path import (
     abspath,
@@ -26,9 +26,10 @@ from os.path import (
     pardir,
     realpath,
     relpath,
-    sep as separator,
 )
+from os.path import sep as separator
 from pathlib import Path
+
 try:
     from grp import getgrgid
 except ImportError:
@@ -86,7 +87,6 @@ def safe_contains(prefix, path, allowlist=None, real=None):
 
 
 class _SafeContainsDirectoryChecker:
-
     def __init__(self, dirpath, prefix, allowlist=None):
         self.allowlist = allowlist
         self.dirpath = dirpath
@@ -151,8 +151,9 @@ def safe_walk(path, allowlist=None):
 
         if allowlist and i % WALK_MAX_DIRS == 0:
             raise RuntimeError(
-                'Breaking out of walk of %s after %s iterations (most likely infinite symlink recursion) at: %s' %
-                (path, WALK_MAX_DIRS, dirpath))
+                "Breaking out of walk of %s after %s iterations (most likely infinite symlink recursion) at: %s"
+                % (path, WALK_MAX_DIRS, dirpath)
+            )
         _prefix = partial(join, dirpath)
 
         prune = False
@@ -216,9 +217,11 @@ def __path_permission_for_user(path, username):
     owner_permissions = int(oct_mode[-3])
     group_permissions = int(oct_mode[-2])
     other_permissions = int(oct_mode[-1])
-    if other_permissions >= 4 or \
-            (file_owner == username and owner_permissions >= 4) or \
-            (username in group_members and group_permissions >= 4):
+    if (
+        other_permissions >= 4
+        or (file_owner == username and owner_permissions >= 4)
+        or (username in group_members and group_permissions >= 4)
+    ):
         return True
     return False
 
@@ -323,6 +326,7 @@ class Extensions(dict):
 
     The first item in the sequence should match the key and is the "canonicalization".
     """
+
     def __missing__(self, key):
         for v in self.values():
             if key in v:
@@ -335,11 +339,13 @@ class Extensions(dict):
         return self[ext][0]
 
 
-extensions = Extensions({
-    'ini': ['ini'],
-    'json': ['json'],
-    'yaml': ['yaml', 'yml'],
-})
+extensions = Extensions(
+    {
+        "ini": ["ini"],
+        "json": ["json"],
+        "yaml": ["yaml", "yml"],
+    }
+)
 
 
 def external_chown(path, pwent, external_chown_script, description="file"):
@@ -352,7 +358,7 @@ def external_chown(path, pwent, external_chown_script, description="file"):
     """
     try:
         if not external_chown_script:
-            raise ValueError('external_chown_script is not defined')
+            raise ValueError("external_chown_script is not defined")
         if Path(path).owner() == pwent[0]:
             return True
 
@@ -362,13 +368,12 @@ def external_chown(path, pwent, external_chown_script, description="file"):
         galaxy.util.commands.execute(cmd)
         return True
     except galaxy.util.commands.CommandLineException as e:
-        log.warning(f'Changing ownership of {description} {path} failed: {galaxy.util.unicodify(e)}')
+        log.warning(f"Changing ownership of {description} {path} failed: {galaxy.util.unicodify(e)}")
         return False
 
 
 def __listify(item):
-    """A non-splitting version of :func:`galaxy.util.listify`.
-    """
+    """A non-splitting version of :func:`galaxy.util.listify`."""
     if not item:
         return []
     elif isinstance(item, list) or isinstance(item, tuple):
@@ -402,7 +407,7 @@ def __ext_strip_sep(ext):
 
 def __splitext_no_sep(path):
     path = galaxy.util.unicodify(path)
-    return (path.rsplit(extsep, 1) + [''])[0:2]
+    return (path.rsplit(extsep, 1) + [""])[0:2]
 
 
 def __splitext_ignore(path, ignore=None):
@@ -410,7 +415,7 @@ def __splitext_ignore(path, ignore=None):
     ignore = map(__ext_strip_sep, __listify(ignore))
     root, ext = __splitext_no_sep(path)
     if ext in ignore:
-        new_path = path[0:(-len(ext) - 1)]
+        new_path = path[0 : (-len(ext) - 1)]
         root, ext = __splitext_no_sep(new_path)
 
     return (root, ext)
@@ -431,10 +436,9 @@ def _build_self(target, path_module):
 
 
 def __copy_self(names=__name__, parent=None):
-    """Returns a copy of this module that can be modified without modifying `galaxy.util.path`` in ``sys.modules``.
-    """
+    """Returns a copy of this module that can be modified without modifying `galaxy.util.path`` in ``sys.modules``."""
     if isinstance(names, str):
-        names = iter(names.split('.'))
+        names = iter(names.split("."))
     try:
         name = next(names)
     except StopIteration:
@@ -459,25 +463,25 @@ def __set_fxns_on(target, path_module):
 
 
 __pathfxns__ = (
-    'abspath',
-    'basename',
-    'exists',
-    'isabs',
-    'join',
-    'normpath',
-    'pardir',
-    'realpath',
-    'relpath',
+    "abspath",
+    "basename",
+    "exists",
+    "isabs",
+    "join",
+    "normpath",
+    "pardir",
+    "realpath",
+    "relpath",
 )
 
 __all__ = (
-    'extensions',
-    'get_ext',
-    'has_ext',
-    'joinext',
-    'safe_contains',
-    'safe_makedirs',
-    'safe_relpath',
-    'safe_walk',
-    'unsafe_walk',
+    "extensions",
+    "get_ext",
+    "has_ext",
+    "joinext",
+    "safe_contains",
+    "safe_makedirs",
+    "safe_relpath",
+    "safe_walk",
+    "unsafe_walk",
 )
diff --git a/lib/galaxy/util/path/ntpath.py b/lib/galaxy/util/path/ntpath.py
index f14d933eadb..90b89275332 100644
--- a/lib/galaxy/util/path/ntpath.py
+++ b/lib/galaxy/util/path/ntpath.py
@@ -6,5 +6,4 @@ import sys
 
 from . import _build_self
 
-
 _build_self(sys.modules[__name__], ntpath)
diff --git a/lib/galaxy/util/path/posixpath.py b/lib/galaxy/util/path/posixpath.py
index 7e2e049f617..2a5b5b4809b 100644
--- a/lib/galaxy/util/path/posixpath.py
+++ b/lib/galaxy/util/path/posixpath.py
@@ -6,5 +6,4 @@ import sys
 
 from . import _build_self
 
-
 _build_self(sys.modules[__name__], posixpath)
diff --git a/lib/galaxy/util/permutations.py b/lib/galaxy/util/permutations.py
index 8b3314580a4..da71f7966e5 100644
--- a/lib/galaxy/util/permutations.py
+++ b/lib/galaxy/util/permutations.py
@@ -18,18 +18,14 @@ input_classification = Bunch(
 
 
 class InputMatchedException(MessageException):
-    """ Indicates problem matching inputs while building up inputs
-    permutations. """
+    """Indicates problem matching inputs while building up inputs
+    permutations."""
 
 
 def expand_multi_inputs(inputs, classifier, key_filter=None):
     key_filter = key_filter or (lambda x: True)
 
-    single_inputs, matched_multi_inputs, multiplied_multi_inputs = __split_inputs(
-        inputs,
-        classifier,
-        key_filter
-    )
+    single_inputs, matched_multi_inputs, multiplied_multi_inputs = __split_inputs(inputs, classifier, key_filter)
 
     # Build up every combination of inputs to be run together.
     input_combos = __extend_with_matched_combos(single_inputs, matched_multi_inputs)
@@ -84,8 +80,10 @@ def __extend_with_matched_combos(single_inputs, multi_inputs):
         if multi_input_key == first_multi_input_key:
             continue
         if len(multi_input_values) != len(first_multi_value):
-            raise InputMatchedException("Received %d inputs for '%s' and %d inputs for '%s', these should be of equal length" %
-                                        (len(multi_input_values), multi_input_key, len(first_multi_value), first_multi_input_key))
+            raise InputMatchedException(
+                "Received %d inputs for '%s' and %d inputs for '%s', these should be of equal length"
+                % (len(multi_input_values), multi_input_key, len(first_multi_value), first_multi_input_key)
+            )
 
         for index, value in enumerate(multi_input_values):
             matched_multi_inputs[index][multi_input_key] = value
diff --git a/lib/galaxy/util/plugin_config.py b/lib/galaxy/util/plugin_config.py
index aec2a2a1856..fd33488a3ce 100644
--- a/lib/galaxy/util/plugin_config.py
+++ b/lib/galaxy/util/plugin_config.py
@@ -5,12 +5,11 @@ import yaml
 from galaxy.util import parse_xml
 from galaxy.util.submodules import import_submodules
 
-
-PluginConfigSource = collections.namedtuple('PluginConfigSource', ['type', 'source'])
+PluginConfigSource = collections.namedtuple("PluginConfigSource", ["type", "source"])
 
 
 def plugins_dict(module, plugin_type_identifier):
-    """ Walk through all classes in submodules of module and find ones labelled
+    """Walk through all classes in submodules of module and find ones labelled
     with specified plugin_type_identifier and throw in a dictionary to allow
     constructions from plugins by these types later on.
     """
@@ -25,7 +24,7 @@ def plugins_dict(module, plugin_type_identifier):
     return plugin_dict
 
 
-def load_plugins(plugins_dict, plugin_source, extra_kwds=None, plugin_type_keys=('type',), dict_to_list_key=None):
+def load_plugins(plugins_dict, plugin_source, extra_kwds=None, plugin_type_keys=("type",), dict_to_list_key=None):
     if extra_kwds is None:
         extra_kwds = {}
     if plugin_source.type == "xml":
@@ -100,13 +99,13 @@ def __load_plugins_from_dicts(plugins_dict, configs, extra_kwds, plugin_type_key
 
 def plugin_source_from_path(path):
     if path.endswith(".yaml") or path.endswith(".yml") or path.endswith(".yaml.sample") or path.endswith(".yml.sample"):
-        return PluginConfigSource('dict', __read_yaml(path))
+        return PluginConfigSource("dict", __read_yaml(path))
     else:
-        return PluginConfigSource('xml', parse_xml(path, remove_comments=True).getroot())
+        return PluginConfigSource("xml", parse_xml(path, remove_comments=True).getroot())
 
 
 def plugin_source_from_dict(as_dict):
-    return PluginConfigSource('dict', as_dict)
+    return PluginConfigSource("dict", as_dict)
 
 
 def __read_yaml(path):
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index 64638a46199..13fb5aa2f9d 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -7,12 +7,19 @@ import os.path
 import sys
 from configparser import ConfigParser
 from functools import partial
-from itertools import product, starmap
+from itertools import (
+    product,
+    starmap,
+)
 
 import yaml
 
 from galaxy.exceptions import InvalidFileFormatError
-from galaxy.util.path import extensions, has_ext, joinext
+from galaxy.util.path import (
+    extensions,
+    has_ext,
+    joinext,
+)
 
 
 def find_config_file(names, exts=None, dirs=None, include_samples=False):
@@ -51,8 +58,8 @@ def find_config_file(names, exts=None, dirs=None, include_samples=False):
     """
     found = __find_config_files(
         names,
-        exts=exts or extensions['yaml'] + extensions['ini'],
-        dirs=dirs or [os.getcwd(), os.path.join(os.getcwd(), 'config')],
+        exts=exts or extensions["yaml"] + extensions["ini"],
+        dirs=dirs or [os.getcwd(), os.path.join(os.getcwd(), "config")],
         include_samples=include_samples,
     )
     if not found:
@@ -63,12 +70,7 @@ def find_config_file(names, exts=None, dirs=None, include_samples=False):
 
 
 def load_app_properties(
-    kwds=None,
-    ini_file=None,
-    ini_section=None,
-    config_file=None,
-    config_section=None,
-    config_prefix="GALAXY_CONFIG_"
+    kwds=None, ini_file=None, ini_section=None, config_file=None, config_section=None, config_prefix="GALAXY_CONFIG_"
 ):
     if config_file is None:
         config_file = ini_file
@@ -78,7 +80,7 @@ def load_app_properties(
     if config_file:
         properties = read_properties_from_file(config_file, config_section)
     else:
-        properties = {'__file__': None}
+        properties = {"__file__": None}
 
     # update from kwds
     if kwds:
@@ -88,10 +90,10 @@ def load_app_properties(
     override_prefix = f"{config_prefix}OVERRIDE_"
     for key in os.environ:
         if key.startswith(override_prefix):
-            config_key = key[len(override_prefix):].lower()
+            config_key = key[len(override_prefix) :].lower()
             properties[config_key] = os.environ[key]
         elif key.startswith(config_prefix):
-            config_key = key[len(config_prefix):].lower()
+            config_key = key[len(config_prefix) :].lower()
             if config_key not in properties:
                 properties[config_key] = os.environ[key]
 
@@ -100,14 +102,14 @@ def load_app_properties(
 
 def read_properties_from_file(config_file, config_section=None):
     properties = {}
-    if has_ext(config_file, 'yaml', aliases=True, ignore='sample'):
+    if has_ext(config_file, "yaml", aliases=True, ignore="sample"):
         if config_section is None:
             config_section = "galaxy"
         properties.update(__default_properties(config_file))
         raw_properties = _read_from_yaml_file(config_file)
         if raw_properties:
             properties.update(raw_properties.get(config_section) or {})
-    elif has_ext(config_file, 'ini', aliases=True, ignore='sample'):
+    elif has_ext(config_file, "ini", aliases=True, ignore="sample"):
         if config_section is None:
             config_section = "app:main"
         parser = nice_config_parser(config_file)  # default properties loaded w/parser
@@ -134,14 +136,13 @@ def nice_config_parser(path):
 
 
 class NicerConfigParser(ConfigParser):
-
     def __init__(self, filename, *args, **kw):
         ConfigParser.__init__(self, *args, **kw)
         self.filename = filename
-        if hasattr(self, '_interpolation'):
+        if hasattr(self, "_interpolation"):
             self._interpolation = self.InterpolateWrapper(self._interpolation)
 
-    read_file = getattr(ConfigParser, 'read_file', ConfigParser.readfp)
+    read_file = getattr(ConfigParser, "read_file", ConfigParser.readfp)
     read_file.__doc__ = ""
 
     def defaults(self):
@@ -152,18 +153,17 @@ class NicerConfigParser(ConfigParser):
         """
         defaults = ConfigParser.defaults(self).copy()
         for key, val in defaults.items():
-            defaults[key] = self.get('DEFAULT', key) or val
+            defaults[key] = self.get("DEFAULT", key) or val
         return defaults
 
     def _interpolate(self, section, option, rawval, vars):
         # Python < 3.2
         try:
-            return ConfigParser._interpolate(
-                self, section, option, rawval, vars)
+            return ConfigParser._interpolate(self, section, option, rawval, vars)
         except Exception:
             e = sys.exc_info()[1]
             args = list(e.args)
-            args[0] = f'Error in file {self.filename}: {e}'
+            args[0] = f"Error in file {self.filename}: {e}"
             e.args = tuple(args)
             e.message = args[0]
             raise
@@ -178,19 +178,18 @@ class NicerConfigParser(ConfigParser):
 
         def before_get(self, parser, section, option, value, defaults):
             try:
-                return self._original.before_get(parser, section, option,
-                                                 value, defaults)
+                return self._original.before_get(parser, section, option, value, defaults)
             except Exception:
                 e = sys.exc_info()[1]
                 args = list(e.args)
-                args[0] = f'Error in file {parser.filename}: {e}'
+                args[0] = f"Error in file {parser.filename}: {e}"
                 e.args = tuple(args)
                 e.message = args[0]
                 raise
 
 
 def _running_from_source():
-    paths = ['run.sh', 'lib/galaxy/__init__.py', 'scripts/common_startup.sh']
+    paths = ["run.sh", "lib/galaxy/__init__.py", "scripts/common_startup.sh"]
     return all(map(os.path.exists, paths))
 
 
@@ -198,13 +197,13 @@ running_from_source = _running_from_source()
 
 
 def get_data_dir(properties):
-    data_dir = properties.get('data_dir', None)
+    data_dir = properties.get("data_dir", None)
     if data_dir is None:
         if running_from_source:
-            data_dir = './database'
+            data_dir = "./database"
         else:
-            config_dir = properties.get('config_dir', os.path.dirname(properties['__file__']))
-            data_dir = os.path.join(config_dir, 'data')
+            config_dir = properties.get("config_dir", os.path.dirname(properties["__file__"]))
+            data_dir = os.path.join(config_dir, "data")
     return data_dir
 
 
@@ -222,17 +221,14 @@ def __find_config_files(names, exts=None, dirs=None, include_samples=False):
         # add exts to names, converts back into a list because it's going to be small and we might consume names twice
         names = list(starmap(joinext, product(names, exts)))
     if include_samples:
-        sample_names = map(partial(joinext, ext='sample'), names)
+        sample_names = map(partial(joinext, ext="sample"), names)
     # check for all names in each dir before moving to the next dir. could do it the other way around but that makes
     # less sense to me.
     return __get_all_configs(dirs, names) or __get_all_configs(dirs, sample_names)
 
 
 def __default_properties(path):
-    return {
-        'here': os.path.dirname(os.path.abspath(path)),
-        '__file__': os.path.abspath(path)
-    }
+    return {"here": os.path.dirname(os.path.abspath(path)), "__file__": os.path.abspath(path)}
 
 
-__all__ = ('find_config_file', 'get_data_dir', 'load_app_properties', 'NicerConfigParser', 'running_from_source')
+__all__ = ("find_config_file", "get_data_dir", "load_app_properties", "NicerConfigParser", "running_from_source")
diff --git a/lib/galaxy/util/renamed_temporary_file.py b/lib/galaxy/util/renamed_temporary_file.py
index af490073261..ff4052faa5d 100644
--- a/lib/galaxy/util/renamed_temporary_file.py
+++ b/lib/galaxy/util/renamed_temporary_file.py
@@ -9,13 +9,14 @@ class RenamedTemporaryFile:
     A temporary file object which will be renamed to the specified
     path on exit.
     """
+
     def __init__(self, final_path, **kwargs):
         """
         >>> dir = tempfile.mkdtemp()
         >>> with RenamedTemporaryFile(os.path.join(dir, 'test.txt'), mode="w") as out:
         ...     _ = out.write('bla')
         """
-        tmpfile_dir = kwargs.pop('dir', None)
+        tmpfile_dir = kwargs.pop("dir", None)
 
         # Put temporary file in the same directory as the location for the
         # final file so that an atomic move into place can occur.
diff --git a/lib/galaxy/util/rules_dsl.py b/lib/galaxy/util/rules_dsl.py
index 47a94a759da..122a6841444 100644
--- a/lib/galaxy/util/rules_dsl.py
+++ b/lib/galaxy/util/rules_dsl.py
@@ -1,14 +1,17 @@
 import abc
 import itertools
 import re
-from typing import List, Type
+from typing import (
+    List,
+    Type,
+)
 
 import yaml
 from pkg_resources import resource_stream
 
 
 def get_rules_specification():
-    return yaml.safe_load(resource_stream(__name__, 'rules_dsl_spec.yml'))
+    return yaml.safe_load(resource_stream(__name__, "rules_dsl_spec.yml"))
 
 
 def _ensure_rule_contains_keys(rule, keys):
@@ -57,7 +60,6 @@ def apply_regex(regex, target, data, replacement=None, group_count=None):
 
 
 class BaseRuleDefinition(metaclass=abc.ABCMeta):
-
     @abc.abstractproperty
     def rule_type(self):
         """Short string describing type of rule (plugin class) to use."""
@@ -80,7 +82,7 @@ class AddColumnMetadataRuleDefinition(BaseRuleDefinition):
     def apply(self, rule, data, sources):
         rule_value = rule["value"]
         if rule_value.startswith("identifier"):
-            identifier_index = int(rule_value[len("identifier"):])
+            identifier_index = int(rule_value[len("identifier") :])
 
             new_rows = []
             for index, row in enumerate(data):
@@ -116,7 +118,7 @@ class AddColumnGroupTagValueRuleDefinition(BaseRuleDefinition):
             tags = source["tags"]
             for tag in sorted(tags):
                 if tag.startswith(tag_prefix):
-                    group_tag_value = tag[len(tag_prefix):]
+                    group_tag_value = tag[len(tag_prefix) :]
                     break
 
             if group_tag_value is None:
@@ -208,11 +210,14 @@ class AddColumnSubstrRuleDefinition(BaseRuleDefinition):
     rule_type = "add_column_substr"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column": int,
-            "length": int,
-            "substr_type": str,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_column": int,
+                "length": int,
+                "substr_type": str,
+            },
+        )
         _ensure_key_value_in(rule, "substr_type", ["keep_prefix", "drop_prefix", "keep_suffix", "drop_suffix"])
 
     def apply(self, rule, data, sources):
@@ -247,9 +252,12 @@ class RemoveColumnsRuleDefinition(BaseRuleDefinition):
     rule_type = "remove_columns"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_columns": list,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_columns": list,
+            },
+        )
 
     def apply(self, rule, data, sources):
         target_columns = rule["target_columns"]
@@ -277,11 +285,14 @@ class AddFilterRegexRuleDefinition(BaseRuleDefinition):
     rule_type = "add_filter_regex"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column": int,
-            "invert": bool,
-            "expression": str,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_column": int,
+                "invert": bool,
+                "expression": str,
+            },
+        )
         _ensure_valid_pattern(rule["expression"])
 
     def apply(self, rule, data, sources):
@@ -302,11 +313,14 @@ class AddFilterCountRuleDefinition(BaseRuleDefinition):
     rule_type = "add_filter_count"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "count": int,
-            "invert": bool,
-            "which": str,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "count": int,
+                "invert": bool,
+                "which": str,
+            },
+        )
         _ensure_key_value_in(rule, "which", ["first", "last"])
 
     def apply(self, rule, data, sources):
@@ -329,10 +343,7 @@ class AddFilterEmptyRuleDefinition(BaseRuleDefinition):
     rule_type = "add_filter_empty"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column": int,
-            "invert": bool
-        })
+        _ensure_rule_contains_keys(rule, {"target_column": int, "invert": bool})
 
     def apply(self, rule, data, sources):
         invert = rule["invert"]
@@ -349,11 +360,14 @@ class AddFilterMatchesRuleDefinition(BaseRuleDefinition):
     rule_type = "add_filter_matches"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column": int,
-            "invert": bool,
-            "value": str,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_column": int,
+                "invert": bool,
+                "value": str,
+            },
+        )
 
     def apply(self, rule, data, sources):
         invert = rule["invert"]
@@ -372,12 +386,17 @@ class AddFilterCompareRuleDefinition(BaseRuleDefinition):
     rule_type = "add_filter_compare"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column": int,
-            "value": int,
-            "compare_type": str,
-        })
-        _ensure_key_value_in(rule, "compare_type", ["less_than", "less_than_equal", "greater_than", "greater_than_equal"])
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_column": int,
+                "value": int,
+                "compare_type": str,
+            },
+        )
+        _ensure_key_value_in(
+            rule, "compare_type", ["less_than", "less_than_equal", "greater_than", "greater_than_equal"]
+        )
 
     def apply(self, rule, data, sources):
         target_column = rule["target_column"]
@@ -405,10 +424,13 @@ class SortRuleDefinition(BaseRuleDefinition):
     rule_type = "sort"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column": int,
-            "numeric": bool,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_column": int,
+                "numeric": bool,
+            },
+        )
 
     def apply(self, rule, data, sources):
         target = rule["target_column"]
@@ -438,10 +460,13 @@ class SwapColumnsRuleDefinition(BaseRuleDefinition):
     rule_type = "swap_columns"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_column_0": int,
-            "target_column_1": int,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_column_0": int,
+                "target_column_1": int,
+            },
+        )
 
     def apply(self, rule, data, sources):
         target_column_0 = rule["target_column_0"]
@@ -460,10 +485,13 @@ class SplitColumnsRuleDefinition(BaseRuleDefinition):
     rule_type = "split_columns"
 
     def validate_rule(self, rule):
-        _ensure_rule_contains_keys(rule, {
-            "target_columns_0": list,
-            "target_columns_1": list,
-        })
+        _ensure_rule_contains_keys(
+            rule,
+            {
+                "target_columns_0": list,
+                "target_columns_1": list,
+            },
+        )
 
     def apply(self, rule, data, sources):
         target_columns_0 = rule["target_columns_0"]
@@ -494,7 +522,6 @@ def flat_map(f, items):
 
 
 class RuleSet:
-
     def __init__(self, rule_set_as_dict):
         self.raw_rules = rule_set_as_dict["rules"]
         self.raw_mapping = rule_set_as_dict.get("mapping", [])
diff --git a/lib/galaxy/util/sanitize_html.py b/lib/galaxy/util/sanitize_html.py
index 1ff4b8c2ec4..cdfe5229168 100644
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -5,43 +5,248 @@ import bleach
 
 from galaxy.util import unicodify
 
+_acceptable_elements = [
+    "a",
+    "abbr",
+    "acronym",
+    "address",
+    "area",
+    "article",
+    "aside",
+    "audio",
+    "b",
+    "big",
+    "blockquote",
+    "br",
+    "button",
+    "canvas",
+    "caption",
+    "center",
+    "cite",
+    "code",
+    "col",
+    "colgroup",
+    "command",
+    "datagrid",
+    "datalist",
+    "dd",
+    "del",
+    "details",
+    "dfn",
+    "dialog",
+    "dir",
+    "div",
+    "dl",
+    "dt",
+    "em",
+    "event-source",
+    "fieldset",
+    "figure",
+    "footer",
+    "font",
+    "form",
+    "header",
+    "h1",
+    "h2",
+    "h3",
+    "h4",
+    "h5",
+    "h6",
+    "hr",
+    "i",
+    "img",
+    "input",
+    "ins",
+    "keygen",
+    "kbd",
+    "label",
+    "legend",
+    "li",
+    "m",
+    "map",
+    "menu",
+    "meter",
+    "multicol",
+    "nav",
+    "nextid",
+    "ol",
+    "output",
+    "optgroup",
+    "option",
+    "p",
+    "pre",
+    "progress",
+    "q",
+    "s",
+    "samp",
+    "section",
+    "select",
+    "small",
+    "sound",
+    "source",
+    "spacer",
+    "span",
+    "strike",
+    "strong",
+    "sub",
+    "sup",
+    "table",
+    "tbody",
+    "td",
+    "textarea",
+    "time",
+    "tfoot",
+    "th",
+    "thead",
+    "tr",
+    "tt",
+    "u",
+    "ul",
+    "var",
+    "video",
+    "noscript",
+]
 
-_acceptable_elements = ['a', 'abbr', 'acronym', 'address', 'area', 'article',
-        'aside', 'audio', 'b', 'big', 'blockquote', 'br', 'button', 'canvas',
-        'caption', 'center', 'cite', 'code', 'col', 'colgroup', 'command',
-        'datagrid', 'datalist', 'dd', 'del', 'details', 'dfn', 'dialog', 'dir',
-        'div', 'dl', 'dt', 'em', 'event-source', 'fieldset', 'figure',
-        'footer', 'font', 'form', 'header', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6',
-        'hr', 'i', 'img', 'input', 'ins', 'keygen', 'kbd', 'label', 'legend',
-        'li', 'm', 'map', 'menu', 'meter', 'multicol', 'nav', 'nextid', 'ol',
-        'output', 'optgroup', 'option', 'p', 'pre', 'progress', 'q', 's',
-        'samp', 'section', 'select', 'small', 'sound', 'source', 'spacer',
-        'span', 'strike', 'strong', 'sub', 'sup', 'table', 'tbody', 'td',
-        'textarea', 'time', 'tfoot', 'th', 'thead', 'tr', 'tt', 'u', 'ul',
-        'var', 'video', 'noscript']
-
-_acceptable_attributes = ['abbr', 'accept', 'accept-charset', 'accesskey',
-        'action', 'align', 'alt', 'autocomplete', 'autofocus', 'axis',
-        'background', 'balance', 'bgcolor', 'bgproperties', 'border',
-        'bordercolor', 'bordercolordark', 'bordercolorlight', 'bottompadding',
-        'cellpadding', 'cellspacing', 'ch', 'challenge', 'char', 'charoff',
-        'choff', 'charset', 'checked', 'cite', 'class', 'clear', 'color',
-        'cols', 'colspan', 'compact', 'contenteditable', 'controls', 'coords',
-        'data', 'datafld', 'datapagesize', 'datasrc', 'datetime', 'default',
-        'delay', 'dir', 'disabled', 'draggable', 'dynsrc', 'enctype', 'end',
-        'face', 'for', 'form', 'frame', 'galleryimg', 'gutter', 'headers',
-        'height', 'hidefocus', 'hidden', 'high', 'href', 'hreflang', 'hspace',
-        'icon', 'id', 'inputmode', 'ismap', 'keytype', 'label', 'leftspacing',
-        'lang', 'list', 'longdesc', 'loop', 'loopcount', 'loopend',
-        'loopstart', 'low', 'lowsrc', 'max', 'maxlength', 'media', 'method',
-        'min', 'multiple', 'name', 'nohref', 'noshade', 'nowrap', 'open',
-        'optimum', 'pattern', 'ping', 'point-size', 'prompt', 'pqg',
-        'radiogroup', 'readonly', 'rel', 'repeat-max', 'repeat-min', 'replace',
-        'required', 'rev', 'rightspacing', 'rows', 'rowspan', 'rules', 'scope',
-        'selected', 'shape', 'size', 'span', 'src', 'start', 'step', 'summary',
-        'suppress', 'tabindex', 'target', 'template', 'title', 'toppadding',
-        'type', 'unselectable', 'usemap', 'urn', 'valign', 'value', 'variable',
-        'volume', 'vspace', 'vrml', 'width', 'wrap', 'xml:lang']
+_acceptable_attributes = [
+    "abbr",
+    "accept",
+    "accept-charset",
+    "accesskey",
+    "action",
+    "align",
+    "alt",
+    "autocomplete",
+    "autofocus",
+    "axis",
+    "background",
+    "balance",
+    "bgcolor",
+    "bgproperties",
+    "border",
+    "bordercolor",
+    "bordercolordark",
+    "bordercolorlight",
+    "bottompadding",
+    "cellpadding",
+    "cellspacing",
+    "ch",
+    "challenge",
+    "char",
+    "charoff",
+    "choff",
+    "charset",
+    "checked",
+    "cite",
+    "class",
+    "clear",
+    "color",
+    "cols",
+    "colspan",
+    "compact",
+    "contenteditable",
+    "controls",
+    "coords",
+    "data",
+    "datafld",
+    "datapagesize",
+    "datasrc",
+    "datetime",
+    "default",
+    "delay",
+    "dir",
+    "disabled",
+    "draggable",
+    "dynsrc",
+    "enctype",
+    "end",
+    "face",
+    "for",
+    "form",
+    "frame",
+    "galleryimg",
+    "gutter",
+    "headers",
+    "height",
+    "hidefocus",
+    "hidden",
+    "high",
+    "href",
+    "hreflang",
+    "hspace",
+    "icon",
+    "id",
+    "inputmode",
+    "ismap",
+    "keytype",
+    "label",
+    "leftspacing",
+    "lang",
+    "list",
+    "longdesc",
+    "loop",
+    "loopcount",
+    "loopend",
+    "loopstart",
+    "low",
+    "lowsrc",
+    "max",
+    "maxlength",
+    "media",
+    "method",
+    "min",
+    "multiple",
+    "name",
+    "nohref",
+    "noshade",
+    "nowrap",
+    "open",
+    "optimum",
+    "pattern",
+    "ping",
+    "point-size",
+    "prompt",
+    "pqg",
+    "radiogroup",
+    "readonly",
+    "rel",
+    "repeat-max",
+    "repeat-min",
+    "replace",
+    "required",
+    "rev",
+    "rightspacing",
+    "rows",
+    "rowspan",
+    "rules",
+    "scope",
+    "selected",
+    "shape",
+    "size",
+    "span",
+    "src",
+    "start",
+    "step",
+    "summary",
+    "suppress",
+    "tabindex",
+    "target",
+    "template",
+    "title",
+    "toppadding",
+    "type",
+    "unselectable",
+    "usemap",
+    "urn",
+    "valign",
+    "value",
+    "variable",
+    "volume",
+    "vspace",
+    "vrml",
+    "width",
+    "wrap",
+    "xml:lang",
+]
 
 
 def sanitize_html(htmlSource, allow_data_urls=False):
diff --git a/lib/galaxy/util/script.py b/lib/galaxy/util/script.py
index a56eb67f20f..9b0e0e5dc0d 100644
--- a/lib/galaxy/util/script.py
+++ b/lib/galaxy/util/script.py
@@ -5,7 +5,10 @@ import logging
 import os
 import sys
 
-from galaxy.util.properties import find_config_file, load_app_properties
+from galaxy.util.properties import (
+    find_config_file,
+    load_app_properties,
+)
 
 DESCRIPTION = None
 ACTIONS = None
@@ -67,24 +70,27 @@ def populate_config_args(parser):
     # set setting GALAXY_CONFIG_OPTION_NAME where OPTION_NAME is option_name converted to upper case.
     # Options specified in that file can be overridden for this program set setting
     # GALAXY_CONFIG_OVERRIDE_OPTION_NAME to a new value.
-    parser.add_argument("-c", "--config-file", "--config",
-                        default=os.environ.get('GALAXY_CONFIG_FILE', None),
-                        help=ARG_HELP_CONFIG_FILE)
-    parser.add_argument("--config-section",
-                        default=os.environ.get('GALAXY_CONFIG_SECTION', None),
-                        help=argparse.SUPPRESS)  # See ARG_HELP_CONFIG_SECTION comment above for unsuppressed details.
+    parser.add_argument(
+        "-c", "--config-file", "--config", default=os.environ.get("GALAXY_CONFIG_FILE", None), help=ARG_HELP_CONFIG_FILE
+    )
+    parser.add_argument(
+        "--config-section", default=os.environ.get("GALAXY_CONFIG_SECTION", None), help=argparse.SUPPRESS
+    )  # See ARG_HELP_CONFIG_SECTION comment above for unsuppressed details.
 
 
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
-    parser.add_argument('action', metavar='ACTION', type=str,
-                        choices=list(ACTIONS.keys()),
-                        default=DEFAULT_ACTION,
-                        nargs='?' if DEFAULT_ACTION is not None else None,
-                        help='action to perform')
+    parser.add_argument(
+        "action",
+        metavar="ACTION",
+        type=str,
+        choices=list(ACTIONS.keys()),
+        default=DEFAULT_ACTION,
+        nargs="?" if DEFAULT_ACTION is not None else None,
+        help="action to perform",
+    )
     populate_config_args(parser)
-    parser.add_argument("--app",
-                        default=os.environ.get('GALAXY_APP', 'galaxy'))
+    parser.add_argument("--app", default=os.environ.get("GALAXY_APP", "galaxy"))
     for argument in ARGUMENTS:
         parser.add_argument(*argument[0], **argument[1])
     return parser
diff --git a/lib/galaxy/util/search.py b/lib/galaxy/util/search.py
index 2a4257a03c1..d862d83bff0 100644
--- a/lib/galaxy/util/search.py
+++ b/lib/galaxy/util/search.py
@@ -17,17 +17,17 @@ def parse_filters(search_term, filters):
     search_term_without_filters = None
     search_space = search_term.replace('"', "'")
     filter_keys = "|".join(list(filters.keys()))
-    pattern = fr"({filter_keys}):(?:\s+)?([\w-]+|\'.*?\')"
+    pattern = rf"({filter_keys}):(?:\s+)?([\w-]+|\'.*?\')"
     reserved = re.compile(pattern)
     while True:
         match = reserved.search(search_space)
         if match is None:
-            search_term_without_filters = ' '.join(search_space.split())
+            search_term_without_filters = " ".join(search_space.split())
             break
         first_group = match.groups()[0]
         if first_group in filters:
             filter_as = filters[first_group]
             allow_terms.append((filter_as, match.groups()[1].strip().replace("'", "")))
-        search_space = search_space[0:match.start()] + search_space[match.end():]
+        search_space = search_space[0 : match.start()] + search_space[match.end() :]
     allow_query = allow_terms if len(allow_terms) > 0 else None
     return allow_query, search_term_without_filters
diff --git a/lib/galaxy/util/simplegraph.py b/lib/galaxy/util/simplegraph.py
index 936e36a1936..fe7fd3b03ae 100644
--- a/lib/galaxy/util/simplegraph.py
+++ b/lib/galaxy/util/simplegraph.py
@@ -106,7 +106,7 @@ class SimpleGraph:
             { 'id': <the nodes unique id>, 'data': <any additional node data> }
         """
         for node_id, node in self.nodes.items():
-            yield {'id': node_id, 'data': node.data}
+            yield {"id": node_id, "data": node.data}
 
     def gen_edge_dicts(self):
         """
@@ -119,7 +119,7 @@ class SimpleGraph:
             }
         """
         for edge in self.edges:
-            yield {'source': edge.source_index, 'target': edge.target_index, 'data': edge.data}
+            yield {"source": edge.source_index, "target": edge.target_index, "data": edge.data}
 
     def as_dict(self):
         """
@@ -127,4 +127,4 @@ class SimpleGraph:
 
             { 'nodes': <a list of node dictionaries>, 'edges': <a list of node dictionaries> }
         """
-        return {'nodes': list(self.gen_node_dicts()), 'edges': list(self.gen_edge_dicts())}
+        return {"nodes": list(self.gen_node_dicts()), "edges": list(self.gen_edge_dicts())}
diff --git a/lib/galaxy/util/sockets.py b/lib/galaxy/util/sockets.py
index a1c1c329844..7b864ab9ecd 100644
--- a/lib/galaxy/util/sockets.py
+++ b/lib/galaxy/util/sockets.py
@@ -8,7 +8,7 @@ def get_ip():
     s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
     try:
         # doesn't even have to be reachable
-        s.connect(('10.255.255.255', 1))
+        s.connect(("10.255.255.255", 1))
         ip = s.getsockname()[0]
     except Exception:
         ip = None
@@ -27,7 +27,7 @@ def unused_port(range=None):
 def __unused_port_rangeless():
     # TODO: Allow ranges (though then need to guess and check)...
     s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-    s.bind(('localhost', 0))
+    s.bind(("localhost", 0))
     addr, port = s.getsockname()
     s.close()
     return port
@@ -41,11 +41,11 @@ def __unused_port_on_range(range):
     stdout = commands.execute(cmd_netstat)
 
     occupied_ports = set()
-    for line in stdout.split('\n'):
-        if line.startswith('tcp') or line.startswith('tcp6'):
+    for line in stdout.split("\n"):
+        if line.startswith("tcp") or line.startswith("tcp6"):
             col = line.split()
             local_address = col[3]
-            local_port = local_address.split(':')[1]
+            local_port = local_address.split(":")[1]
             occupied_ports.add(int(local_port))
 
     # Generate random free port number.
diff --git a/lib/galaxy/util/sqlite.py b/lib/galaxy/util/sqlite.py
index 7c275ae833e..95c185c2a8c 100644
--- a/lib/galaxy/util/sqlite.py
+++ b/lib/galaxy/util/sqlite.py
@@ -15,7 +15,7 @@ except ImportError:
     # Without sqlparse we use a very weak regex check
     def is_read_only_query(query):
         if re.match("select ", query, re.IGNORECASE):
-            if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query):
+            if re.search('^([^"]|"[^"]*")*?;', query) or re.search("^([^']|'[^']*')*?;", query):
                 return False
             else:
                 return True
diff --git a/lib/galaxy/util/submodules.py b/lib/galaxy/util/submodules.py
index d0544e7489a..f328f8b01ce 100644
--- a/lib/galaxy/util/submodules.py
+++ b/lib/galaxy/util/submodules.py
@@ -6,7 +6,7 @@ log = logging.getLogger(__name__)
 
 
 def import_submodules(module, ordered=True, recursive=False):
-    """ Import all submodules of a module
+    """Import all submodules of a module
 
     :param module: module (package name or actual module)
     :type module: str | module
@@ -29,7 +29,7 @@ def import_submodules(module, ordered=True, recursive=False):
 
 
 def __import_submodules_impl(module, recursive=False):
-    """ Implementation of import only, without sorting.
+    """Implementation of import only, without sorting.
 
     :param module: module (package name or actual module)
     :type module: str | module
diff --git a/lib/galaxy/util/task.py b/lib/galaxy/util/task.py
index df718e261b0..8b23237d77e 100644
--- a/lib/galaxy/util/task.py
+++ b/lib/galaxy/util/task.py
@@ -10,7 +10,6 @@ log = logging.getLogger(__name__)
 
 
 class IntervalTask:
-
     def __init__(self, func, name="Periodic task", interval=3600, immediate_start=False, time_execution=False):
         """
         Run an arbitrary function `func` every `interval` seconds.
diff --git a/lib/galaxy/util/template.py b/lib/galaxy/util/template.py
index 25890fe572b..665bda39788 100644
--- a/lib/galaxy/util/template.py
+++ b/lib/galaxy/util/template.py
@@ -14,8 +14,8 @@ from . import unicodify
 
 # Skip libpasteurize fixers, which make sure code is py2 and py3 compatible.
 # This is not needed, we only translate code on py3.
-myfixes = [f for f in myfixes if not f.startswith('libpasteurize')]
-refactoring_tool = RefactoringTool(myfixes, {'print_function': True})
+myfixes = [f for f in myfixes if not f.startswith("libpasteurize")]
+refactoring_tool = RefactoringTool(myfixes, {"print_function": True})
 
 
 class FixedModuleCodeCompiler(Compiler):
@@ -28,7 +28,6 @@ class FixedModuleCodeCompiler(Compiler):
 
 
 def create_compiler_class(module_code):
-
     class CustomCompilerClass(FixedModuleCodeCompiler):
         pass
 
@@ -36,14 +35,16 @@ def create_compiler_class(module_code):
     return CustomCompilerClass
 
 
-def fill_template(template_text,
-                  context=None,
-                  retry=10,
-                  compiler_class=Compiler,
-                  first_exception=None,
-                  futurized=False,
-                  python_template_version='3',
-                  **kwargs):
+def fill_template(
+    template_text,
+    context=None,
+    retry=10,
+    compiler_class=Compiler,
+    first_exception=None,
+    futurized=False,
+    python_template_version="3",
+    **kwargs,
+):
     """Fill a cheetah template out for specified context.
 
     If template_text is None, an exception will be thrown, if context
@@ -63,7 +64,9 @@ def fill_template(template_text,
         if first_exception is None:
             first_exception = e
         if python_template_version.release[0] < 3 and retry > 0:
-            module_code = Template.compile(source=template_text, compilerClass=compiler_class, returnAClass=False).decode('utf-8')
+            module_code = Template.compile(
+                source=template_text, compilerClass=compiler_class, returnAClass=False
+            ).decode("utf-8")
             module_code = futurize_preprocessor(module_code)
             compiler_class = create_compiler_class(module_code)
             return fill_template(
@@ -84,7 +87,7 @@ def fill_template(template_text,
         if python_template_version.release[0] < 3 and retry > 0:
             tb = e.__traceback__
             last_stack = traceback.extract_tb(tb)[-1]
-            if last_stack.name == '<listcomp>':
+            if last_stack.name == "<listcomp>":
                 # On python 3 list, dict and set comprehensions as well as generator expressions
                 # have their own local scope, which prevents accessing frame variables in cheetah.
                 # We can work around this by replacing `$var` with `var`, but we only do this for
@@ -97,13 +100,14 @@ def fill_template(template_text,
                 module_code[lineno] = module_code[lineno].replace(replace_str, var_not_found)
                 module_code = "\n".join(module_code)
                 compiler_class = create_compiler_class(module_code)
-                return fill_template(template_text=template_text,
-                                     context=context,
-                                     retry=retry - 1,
-                                     compiler_class=compiler_class,
-                                     first_exception=first_exception,
-                                     python_template_version=python_template_version,
-                                     )
+                return fill_template(
+                    template_text=template_text,
+                    context=context,
+                    retry=retry - 1,
+                    compiler_class=compiler_class,
+                    first_exception=first_exception,
+                    python_template_version=python_template_version,
+                )
         raise first_exception or e
     except Exception as e:
         if first_exception is None:
@@ -115,19 +119,20 @@ def fill_template(template_text,
             module_code = t._CHEETAH_generatedModuleCode
             module_code = futurize_preprocessor(module_code)
             compiler_class = create_compiler_class(module_code)
-            return fill_template(template_text=template_text,
-                                 context=context,
-                                 retry=retry,
-                                 compiler_class=compiler_class,
-                                 first_exception=first_exception,
-                                 futurized=True,
-                                 python_template_version=python_template_version,
-                                 )
+            return fill_template(
+                template_text=template_text,
+                context=context,
+                retry=retry,
+                compiler_class=compiler_class,
+                first_exception=first_exception,
+                futurized=True,
+                python_template_version=python_template_version,
+            )
         raise first_exception or e
 
 
 def futurize_preprocessor(source):
-    source = str(refactoring_tool.refactor_string(source, name='auto_translate_cheetah'))
+    source = str(refactoring_tool.refactor_string(source, name="auto_translate_cheetah"))
     # libfuturize.fixes.fix_unicode_keep_u' breaks from Cheetah.compat import unicode
-    source = source.replace('from Cheetah.compat import str', 'from Cheetah.compat import unicode')
+    source = source.replace("from Cheetah.compat import str", "from Cheetah.compat import unicode")
     return source
diff --git a/lib/galaxy/util/tool_shed/common_util.py b/lib/galaxy/util/tool_shed/common_util.py
index 23d593c0062..224b590c3b6 100644
--- a/lib/galaxy/util/tool_shed/common_util.py
+++ b/lib/galaxy/util/tool_shed/common_util.py
@@ -7,11 +7,14 @@ from urllib.parse import urljoin
 from routes import url_for
 
 from galaxy import util
-from galaxy.util.tool_shed import encoding_util, xml_util
+from galaxy.util.tool_shed import (
+    encoding_util,
+    xml_util,
+)
 
 log = logging.getLogger(__name__)
 
-REPOSITORY_OWNER = 'devteam'
+REPOSITORY_OWNER = "devteam"
 
 
 def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies):
@@ -25,61 +28,72 @@ def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_to
 
 def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number):
     # Get the 000x_tools.xml file associated with the current migrate_tools version number.
-    tools_xml_file_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
-                                                       os.pardir, 'galaxy_install',
-                                                       'migrate', 'scripts',
-                                                       '%04d_tools.xml' % latest_tool_migration_script_number))
+    tools_xml_file_path = os.path.abspath(
+        os.path.join(
+            os.path.dirname(__file__),
+            os.pardir,
+            "galaxy_install",
+            "migrate",
+            "scripts",
+            "%04d_tools.xml" % latest_tool_migration_script_number,
+        )
+    )
     # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config.
     migrated_tool_configs_dict = {}
     tree, error_message = xml_util.parse_xml(tools_xml_file_path)
     if tree is None:
         return False, {}
     root = tree.getroot()
-    tool_shed = root.get('name')
+    tool_shed = root.get("name")
     tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed)
     # The default behavior is that the tool shed is down.
     tool_shed_accessible = False
     missing_tool_configs_dict = {}
     if tool_shed_url:
         for elem in root:
-            if elem.tag == 'repository':
+            if elem.tag == "repository":
                 repository_dependencies = []
                 all_tool_dependencies = []
-                repository_name = elem.get('name')
-                changeset_revision = elem.get('changeset_revision')
-                tool_shed_accessible, repository_dependencies_dict = get_repository_dependencies(app,
-                                                                                                 tool_shed_url,
-                                                                                                 repository_name,
-                                                                                                 REPOSITORY_OWNER,
-                                                                                                 changeset_revision)
+                repository_name = elem.get("name")
+                changeset_revision = elem.get("changeset_revision")
+                tool_shed_accessible, repository_dependencies_dict = get_repository_dependencies(
+                    app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision
+                )
                 if tool_shed_accessible:
                     # Accumulate all tool dependencies defined for repository dependencies for display to the user.
                     for rd_key, rd_tups in repository_dependencies_dict.items():
-                        if rd_key in ['root_key', 'description']:
+                        if rd_key in ["root_key", "description"]:
                             continue
                         for rd_tup in rd_tups:
-                            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                                parse_repository_dependency_tuple(rd_tup)
-                        tool_shed_accessible, tool_dependencies = get_tool_dependencies(app,
-                                                                                        tool_shed_url,
-                                                                                        name,
-                                                                                        owner,
-                                                                                        changeset_revision)
-                        all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies)
-                    tool_shed_accessible, tool_dependencies = get_tool_dependencies(app,
-                                                                                    tool_shed_url,
-                                                                                    repository_name,
-                                                                                    REPOSITORY_OWNER,
-                                                                                    changeset_revision)
-                    all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies)
-                    for tool_elem in elem.findall('tool'):
-                        tool_config_file_name = tool_elem.get('file')
+                            (
+                                tool_shed,
+                                name,
+                                owner,
+                                changeset_revision,
+                                prior_installation_required,
+                                only_if_compiling_contained_td,
+                            ) = parse_repository_dependency_tuple(rd_tup)
+                        tool_shed_accessible, tool_dependencies = get_tool_dependencies(
+                            app, tool_shed_url, name, owner, changeset_revision
+                        )
+                        all_tool_dependencies = accumulate_tool_dependencies(
+                            tool_shed_accessible, tool_dependencies, all_tool_dependencies
+                        )
+                    tool_shed_accessible, tool_dependencies = get_tool_dependencies(
+                        app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision
+                    )
+                    all_tool_dependencies = accumulate_tool_dependencies(
+                        tool_shed_accessible, tool_dependencies, all_tool_dependencies
+                    )
+                    for tool_elem in elem.findall("tool"):
+                        tool_config_file_name = tool_elem.get("file")
                         if tool_config_file_name:
                             # We currently do nothing with repository dependencies except install them (we do not display repositories that will be
                             # installed to the user).  However, we'll store them in the following dictionary in case we choose to display them in the
                             # future.
-                            dependencies_dict = dict(tool_dependencies=all_tool_dependencies,
-                                                     repository_dependencies=repository_dependencies)
+                            dependencies_dict = dict(
+                                tool_dependencies=all_tool_dependencies, repository_dependencies=repository_dependencies
+                            )
                             migrated_tool_configs_dict[tool_config_file_name] = dependencies_dict
                 else:
                     break
@@ -90,21 +104,25 @@ def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_scrip
                 if tree:
                     root = tree.getroot()
                     for elem in root:
-                        if elem.tag == 'tool':
-                            missing_tool_configs_dict = check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict)
-                        elif elem.tag == 'section':
+                        if elem.tag == "tool":
+                            missing_tool_configs_dict = check_tool_tag_set(
+                                elem, migrated_tool_configs_dict, missing_tool_configs_dict
+                            )
+                        elif elem.tag == "section":
                             for section_elem in elem:
-                                if section_elem.tag == 'tool':
-                                    missing_tool_configs_dict = check_tool_tag_set(section_elem, migrated_tool_configs_dict, missing_tool_configs_dict)
+                                if section_elem.tag == "tool":
+                                    missing_tool_configs_dict = check_tool_tag_set(
+                                        section_elem, migrated_tool_configs_dict, missing_tool_configs_dict
+                                    )
     else:
-        exception_msg = f'\n\nThe entry for the main Galaxy tool shed at {tool_shed} is missing from the {app.config.tool_sheds_config} file.  '
-        exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n'
+        exception_msg = f"\n\nThe entry for the main Galaxy tool shed at {tool_shed} is missing from the {app.config.tool_sheds_config} file.  "
+        exception_msg += "The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n"
         raise Exception(exception_msg)
     return tool_shed_accessible, missing_tool_configs_dict
 
 
 def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict):
-    file_path = elem.get('file', None)
+    file_path = elem.get("file", None)
     if file_path:
         name = os.path.basename(file_path)
         for migrated_tool_config in migrated_tool_configs_dict.keys():
@@ -116,28 +134,34 @@ def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_di
 def generate_clone_url_for_installed_repository(app, repository):
     """Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
     tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed))
-    return util.build_url(tool_shed_url, pathspec=['repos', str(repository.owner), str(repository.name)])
+    return util.build_url(tool_shed_url, pathspec=["repos", str(repository.owner), str(repository.name)])
 
 
 def generate_clone_url_for_repository_in_tool_shed(user, repository):
     """Generate the URL for cloning a repository that is in the tool shed."""
-    base_url = url_for('/', qualified=True).rstrip('/')
+    base_url = url_for("/", qualified=True).rstrip("/")
     if user:
-        protocol, base = base_url.split('://')
-        username = f'{user.username}@'
-        return f'{protocol}://{username}{base}/repos/{repository.user.username}/{repository.name}'
+        protocol, base = base_url.split("://")
+        username = f"{user.username}@"
+        return f"{protocol}://{username}{base}/repos/{repository.user.username}/{repository.name}"
     else:
-        return f'{base_url}/repos/{repository.user.username}/{repository.name}'
+        return f"{base_url}/repos/{repository.user.username}/{repository.name}"
 
 
 def generate_clone_url_from_repo_info_tup(app, repo_info_tup):
     """Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision."""
     # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab', False]
-    toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-        parse_repository_dependency_tuple(repo_info_tup)
+    (
+        toolshed,
+        name,
+        owner,
+        changeset_revision,
+        prior_installation_required,
+        only_if_compiling_contained_td,
+    ) = parse_repository_dependency_tuple(repo_info_tup)
     tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, toolshed)
     # Don't include the changeset_revision in clone urls.
-    return util.build_url(tool_shed_url, pathspec=['repos', owner, name])
+    return util.build_url(tool_shed_url, pathspec=["repos", owner, name])
 
 
 def get_non_shed_tool_panel_configs(app):
@@ -149,15 +173,17 @@ def get_non_shed_tool_panel_configs(app):
         try:
             tree, error_message = xml_util.parse_xml(config_filename)
         except OSError as exc:
-            if (config_filename == app.config.shed_tool_conf
-                    and not app.config.shed_tool_conf_set
-                    and exc.errno == errno.ENOENT):
+            if (
+                config_filename == app.config.shed_tool_conf
+                and not app.config.shed_tool_conf_set
+                and exc.errno == errno.ENOENT
+            ):
                 continue
             raise
         if tree is None:
             continue
         root = tree.getroot()
-        tool_path = root.get('tool_path', None)
+        tool_path = root.get("tool_path", None)
         if tool_path is None:
             config_filenames.append(config_filename)
     return config_filenames
@@ -167,13 +193,19 @@ def get_repository_dependencies(app, tool_shed_url, repository_name, repository_
     repository_dependencies_dict = {}
     tool_shed_accessible = True
     params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision)
-    pathspec = ['repository', 'get_repository_dependencies']
+    pathspec = ["repository", "get_repository_dependencies"]
     try:
-        raw_text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        raw_text = util.url_get(
+            tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         tool_shed_accessible = True
     except Exception as e:
         tool_shed_accessible = False
-        log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e)
+        log.warning(
+            "The URL\n%s\nraised the exception:\n%s\n",
+            util.build_url(tool_shed_url, pathspec=pathspec, params=params),
+            e,
+        )
     if tool_shed_accessible:
         if len(raw_text) > 2:
             encoded_text = json.loads(util.unicodify(raw_text))
@@ -184,58 +216,64 @@ def get_repository_dependencies(app, tool_shed_url, repository_name, repository_
 def get_protocol_from_tool_shed_url(tool_shed_url):
     """Return the protocol from the received tool_shed_url if it exists."""
     try:
-        if tool_shed_url.find('://') > 0:
-            return tool_shed_url.split('://')[0].lower()
+        if tool_shed_url.find("://") > 0:
+            return tool_shed_url.split("://")[0].lower()
     except Exception:
         # We receive a lot of calls here where the tool_shed_url is None.  The container_util uses
         # that value when creating a header row.  If the tool_shed_url is not None, we have a problem.
         if tool_shed_url is not None:
             log.exception("Handled exception getting the protocol from Tool Shed URL %s", str(tool_shed_url))
         # Default to HTTP protocol.
-        return 'http'
+        return "http"
 
 
 def get_tool_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision):
     tool_dependencies = []
     tool_shed_accessible = True
     params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision)
-    pathspec = ['repository', 'get_tool_dependencies']
+    pathspec = ["repository", "get_tool_dependencies"]
     try:
-        text = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        text = util.url_get(
+            tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         tool_shed_accessible = True
     except Exception as e:
         tool_shed_accessible = False
-        log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e)
+        log.warning(
+            "The URL\n%s\nraised the exception:\n%s\n",
+            util.build_url(tool_shed_url, pathspec=pathspec, params=params),
+            e,
+        )
     if tool_shed_accessible:
         if text:
             tool_dependencies_dict = encoding_util.tool_shed_decode(text)
             for requirements_dict in tool_dependencies_dict.values():
-                tool_dependency_name = requirements_dict['name']
-                tool_dependency_version = requirements_dict['version']
-                tool_dependency_type = requirements_dict['type']
+                tool_dependency_name = requirements_dict["name"]
+                tool_dependency_version = requirements_dict["version"]
+                tool_dependency_type = requirements_dict["type"]
                 tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type))
     return tool_shed_accessible, tool_dependencies
 
 
 def get_tool_shed_repository_ids(as_string=False, **kwd):
-    tsrid = kwd.get('tool_shed_repository_id', None)
-    tsridslist = util.listify(kwd.get('tool_shed_repository_ids', None))
+    tsrid = kwd.get("tool_shed_repository_id", None)
+    tsridslist = util.listify(kwd.get("tool_shed_repository_ids", None))
     if not tsridslist:
-        tsridslist = util.listify(kwd.get('id', None))
+        tsridslist = util.listify(kwd.get("id", None))
     if tsridslist is not None:
         if tsrid is not None and tsrid not in tsridslist:
             tsridslist.append(tsrid)
         if as_string:
-            return ','.join(tsridslist)
+            return ",".join(tsridslist)
         return tsridslist
     else:
-        tsridslist = util.listify(kwd.get('ordered_tsr_ids', None))
+        tsridslist = util.listify(kwd.get("ordered_tsr_ids", None))
         if tsridslist is not None:
             if as_string:
-                return ','.join(tsridslist)
+                return ",".join(tsridslist)
             return tsridslist
     if as_string:
-        return ''
+        return ""
     return []
 
 
@@ -247,8 +285,8 @@ def get_tool_shed_url_from_tool_shed_registry(app, tool_shed):
     cleaned_tool_shed = remove_protocol_from_tool_shed_url(tool_shed)
     for shed_url in app.tool_shed_registry.tool_sheds.values():
         if shed_url.find(cleaned_tool_shed) >= 0:
-            if shed_url.endswith('/'):
-                shed_url = shed_url.rstrip('/')
+            if shed_url.endswith("/"):
+                shed_url = shed_url.rstrip("/")
             return shed_url
     # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml.
     return None
@@ -259,8 +297,8 @@ def get_tool_shed_repository_url(app, tool_shed, owner, name):
     if tool_shed_url:
         # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate
         # the last part of a URL if it does not end with a forward slash.
-        tool_shed_url = f'{tool_shed_url}/'
-        return urljoin(tool_shed_url, f'view/{owner}/{name}')
+        tool_shed_url = f"{tool_shed_url}/"
+        return urljoin(tool_shed_url, f"view/{owner}/{name}")
     return tool_shed_url
 
 
@@ -268,31 +306,29 @@ def get_user_by_username(app, username):
     """Get a user from the database by username."""
     sa_session = app.model.session
     try:
-        user = sa_session.query(app.model.User) \
-                         .filter(app.model.User.table.c.username == username) \
-                         .one()
+        user = sa_session.query(app.model.User).filter(app.model.User.table.c.username == username).one()
         return user
     except Exception:
         return None
 
 
 def handle_galaxy_url(trans, **kwd):
-    galaxy_url = kwd.get('galaxy_url', None)
+    galaxy_url = kwd.get("galaxy_url", None)
     if galaxy_url:
-        trans.set_cookie(galaxy_url, name='toolshedgalaxyurl')
+        trans.set_cookie(galaxy_url, name="toolshedgalaxyurl")
     else:
-        galaxy_url = trans.get_cookie(name='toolshedgalaxyurl')
+        galaxy_url = trans.get_cookie(name="toolshedgalaxyurl")
     return galaxy_url
 
 
 def handle_tool_shed_url_protocol(app, shed_url):
     """Handle secure and insecure HTTP protocol since they may change over time."""
     try:
-        if app.name == 'galaxy':
+        if app.name == "galaxy":
             url = remove_protocol_from_tool_shed_url(shed_url)
             tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, url)
         else:
-            tool_shed_url = str(url_for('/', qualified=True)).rstrip('/')
+            tool_shed_url = str(url_for("/", qualified=True)).rstrip("/")
         return tool_shed_url
     except Exception:
         # We receive a lot of calls here where the tool_shed_url is None.  The container_util uses
@@ -305,36 +341,58 @@ def handle_tool_shed_url_protocol(app, shed_url):
 def parse_repository_dependency_tuple(repository_dependency_tuple, contains_error=False):
     # Default both prior_installation_required and only_if_compiling_contained_td to False in cases where metadata should be reset on the
     # repository containing the repository_dependency definition.
-    prior_installation_required = 'False'
-    only_if_compiling_contained_td = 'False'
+    prior_installation_required = "False"
+    only_if_compiling_contained_td = "False"
     if contains_error:
         if len(repository_dependency_tuple) == 5:
             tool_shed, name, owner, changeset_revision, error = repository_dependency_tuple
         elif len(repository_dependency_tuple) == 6:
             tool_shed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple
         elif len(repository_dependency_tuple) == 7:
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
-                repository_dependency_tuple
-        return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+                error,
+            ) = repository_dependency_tuple
+        return (
+            tool_shed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+            error,
+        )
     else:
         if len(repository_dependency_tuple) == 4:
             tool_shed, name, owner, changeset_revision = repository_dependency_tuple
         elif len(repository_dependency_tuple) == 5:
             tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tuple
         elif len(repository_dependency_tuple) == 6:
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_dependency_tuple
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = repository_dependency_tuple
         return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td
 
 
 def remove_port_from_tool_shed_url(tool_shed_url):
     """Return a partial Tool Shed URL, eliminating the port if it exists."""
     try:
-        if tool_shed_url.find(':') > 0:
+        if tool_shed_url.find(":") > 0:
             # Eliminate the port, if any, since it will result in an invalid directory name.
-            new_tool_shed_url = tool_shed_url.split(':')[0]
+            new_tool_shed_url = tool_shed_url.split(":")[0]
         else:
             new_tool_shed_url = tool_shed_url
-        return new_tool_shed_url.rstrip('/')
+        return new_tool_shed_url.rstrip("/")
     except Exception:
         # We receive a lot of calls here where the tool_shed_url is None.  The container_util uses
         # that value when creating a header row.  If the tool_shed_url is not None, we have a problem.
@@ -352,19 +410,19 @@ def remove_protocol_and_port_from_tool_shed_url(tool_shed_url):
 
 def remove_protocol_and_user_from_clone_url(repository_clone_url):
     """Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists."""
-    if repository_clone_url.find('@') > 0:
+    if repository_clone_url.find("@") > 0:
         # We have an url that includes an authenticated user, something like:
         # http://test@bx.psu.edu:9009/repos/some_username/column
-        items = repository_clone_url.split('@')
+        items = repository_clone_url.split("@")
         tmp_url = items[1]
-    elif repository_clone_url.find('//') > 0:
+    elif repository_clone_url.find("//") > 0:
         # We have an url that includes only a protocol, something like:
         # http://bx.psu.edu:9009/repos/some_username/column
-        items = repository_clone_url.split('//')
+        items = repository_clone_url.split("//")
         tmp_url = items[1]
     else:
         tmp_url = repository_clone_url
-    return tmp_url.rstrip('/')
+    return tmp_url.rstrip("/")
 
 
 def remove_protocol_from_tool_shed_url(tool_shed_url):
diff --git a/lib/galaxy/util/tool_shed/encoding_util.py b/lib/galaxy/util/tool_shed/encoding_util.py
index 78ec66a3386..d24e1ab5e99 100644
--- a/lib/galaxy/util/tool_shed/encoding_util.py
+++ b/lib/galaxy/util/tool_shed/encoding_util.py
@@ -3,13 +3,12 @@ import json
 
 from galaxy.util import (
     smart_str,
-    unicodify
+    unicodify,
 )
 from galaxy.util.hash_util import hmac_new
 
-
-encoding_sep = '__esep__'
-encoding_sep2 = '__esepii__'
+encoding_sep = "__esep__"
+encoding_sep2 = "__esepii__"
 
 
 def tool_shed_decode(value):
@@ -17,7 +16,7 @@ def tool_shed_decode(value):
     value = unicodify(value)
     a, b = value.split(":")
     value = binascii.unhexlify(b)
-    test = hmac_new(b'ToolShedAndGalaxyMustHaveThisSameKey', value)
+    test = hmac_new(b"ToolShedAndGalaxyMustHaveThisSameKey", value)
     assert a == test
     # Restore from string
     values = None
@@ -36,6 +35,6 @@ def tool_shed_encode(val):
         value = json.dumps(val)
     else:
         value = val
-    a = hmac_new(b'ToolShedAndGalaxyMustHaveThisSameKey', value)
+    a = hmac_new(b"ToolShedAndGalaxyMustHaveThisSameKey", value)
     b = unicodify(binascii.hexlify(smart_str(value)))
     return f"{a}:{b}"
diff --git a/lib/galaxy/util/tool_shed/xml_util.py b/lib/galaxy/util/tool_shed/xml_util.py
index 699d7cf34cf..b82d41df951 100644
--- a/lib/galaxy/util/tool_shed/xml_util.py
+++ b/lib/galaxy/util/tool_shed/xml_util.py
@@ -2,9 +2,9 @@ import logging
 import os
 import tempfile
 
+from galaxy.util import etree
+from galaxy.util import parse_xml as galaxy_parse_xml
 from galaxy.util import (
-    etree,
-    parse_xml as galaxy_parse_xml,
     unicodify,
     xml_to_string,
 )
@@ -16,7 +16,7 @@ def create_and_write_tmp_file(elem):
     tmp_str = xml_to_string(elem, pretty=True)
     with tempfile.NamedTemporaryFile(prefix="tmp-toolshed-cawrf", delete=False) as fh:
         tmp_filename = fh.name
-    with open(tmp_filename, mode='w', encoding='utf-8') as fh:
+    with open(tmp_filename, mode="w", encoding="utf-8") as fh:
         fh.write(tmp_str)
     return tmp_filename
 
@@ -38,14 +38,14 @@ def create_element(tag, attributes=None, sub_elements=None):
             for k, v in sub_elements.items():
                 # Don't include fields that are blank.
                 if v:
-                    if k == 'packages':
+                    if k == "packages":
                         # The received sub_elements is an odict whose key is 'packages' and whose
                         # value is a list of ( name, version ) tuples.
                         for v_tuple in v:
-                            sub_elem = etree.SubElement(elem, 'package')
+                            sub_elem = etree.SubElement(elem, "package")
                             sub_elem_name, sub_elem_version = v_tuple
-                            sub_elem.set('name', sub_elem_name)
-                            sub_elem.set('version', sub_elem_version)
+                            sub_elem.set("name", sub_elem_name)
+                            sub_elem.set("version", sub_elem_version)
                     elif isinstance(v, list):
                         sub_elem = etree.SubElement(elem, k)
                         # If v is a list, then it must be a list of tuples where the first
@@ -67,7 +67,7 @@ def create_element(tag, attributes=None, sub_elements=None):
 
 def parse_xml(file_name, check_exists=True):
     """Returns a parsed xml tree with comments intact."""
-    error_message = ''
+    error_message = ""
     if check_exists and not os.path.exists(file_name):
         return None, f"File does not exist {str(file_name)}"
     try:
diff --git a/lib/galaxy/util/tool_version.py b/lib/galaxy/util/tool_version.py
index 03ef6c7a3b3..2cb22be093e 100644
--- a/lib/galaxy/util/tool_version.py
+++ b/lib/galaxy/util/tool_version.py
@@ -4,5 +4,5 @@ def remove_version_from_guid(guid):
     """
     if "/" not in guid:
         return None
-    last_slash = guid.rfind('/')
+    last_slash = guid.rfind("/")
     return guid[:last_slash]
diff --git a/lib/galaxy/util/topsort.py b/lib/galaxy/util/topsort.py
index a0bd490deac..64a1338fa1a 100644
--- a/lib/galaxy/util/topsort.py
+++ b/lib/galaxy/util/topsort.py
@@ -40,8 +40,7 @@ a good deal more code than topsort itself!
 
 class CycleError(Exception):
     def __init__(self, sofar, numpreds, succs):
-        Exception.__init__(self, "cycle in constraints",
-                           sofar, numpreds, succs)
+        Exception.__init__(self, "cycle in constraints", sofar, numpreds, succs)
         self.preds = None
 
     # return as much of the total ordering as topsort was able to
@@ -114,6 +113,7 @@ class CycleError(Exception):
         # reverse the path.
         preds = self.get_preds()
         from random import choice
+
         x = choice(remaining_elts)
         answer = []
         index = {}
@@ -123,13 +123,13 @@ class CycleError(Exception):
             answer.append(x)
             x = choice(preds[x])
         answer.append(x)
-        answer = answer[index[x]:]
+        answer = answer[index[x] :]
         answer.reverse()
         return answer
 
 
 def _numpreds_and_successors_from_pairlist(pairlist):
-    numpreds = {}   # elt -> # of predecessors
+    numpreds = {}  # elt -> # of predecessors
     successors = {}  # elt -> list of successors
     for first, second in pairlist:
         # make sure every elt is a key in numpreds
diff --git a/lib/galaxy/util/validation.py b/lib/galaxy/util/validation.py
index ec4d1f0ee56..c8ba7fef107 100644
--- a/lib/galaxy/util/validation.py
+++ b/lib/galaxy/util/validation.py
@@ -9,8 +9,7 @@ from galaxy.util.sanitize_html import sanitize_html
 
 def validate_and_sanitize_basestring(key, val):
     if not isinstance(val, str):
-        raise exceptions.RequestParameterInvalidException('%s must be a string or unicode: %s'
-                                                          % (key, str(type(val))))
+        raise exceptions.RequestParameterInvalidException("%s must be a string or unicode: %s" % (key, str(type(val))))
     return sanitize_html(val)
 
 
@@ -19,14 +18,12 @@ def validate_and_sanitize_basestring_list(key, val):
         assert isinstance(val, list)
         return [sanitize_html(t) for t in val]
     except (AssertionError, TypeError):
-        raise exceptions.RequestParameterInvalidException('%s must be a list of strings: %s'
-                                                          % (key, str(type(val))))
+        raise exceptions.RequestParameterInvalidException("%s must be a list of strings: %s" % (key, str(type(val))))
 
 
 def validate_boolean(key, val):
     if not isinstance(val, bool):
-        raise exceptions.RequestParameterInvalidException('%s must be a boolean: %s'
-                                                          % (key, str(type(val))))
+        raise exceptions.RequestParameterInvalidException("%s must be a boolean: %s" % (key, str(type(val))))
     return val
 
 
diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py
index 3a2c56a67d5..6bfc5861bd3 100644
--- a/lib/galaxy/util/watcher.py
+++ b/lib/galaxy/util/watcher.py
@@ -6,11 +6,11 @@ import logging
 import os.path
 import time
 
-
 try:
     from watchdog.events import FileSystemEventHandler
     from watchdog.observers import Observer
     from watchdog.observers.polling import PollingObserver
+
     can_watch = True
 except ImportError:
     Observer = None
@@ -24,8 +24,7 @@ log = logging.getLogger(__name__)
 
 
 def get_observer_class(config_name, config_value, default, monitor_what_str):
-    """
-    """
+    """ """
     config_value = config_value or default
     config_value = str(config_value).lower()
     if config_value in ("true", "yes", "on", "auto"):
@@ -34,7 +33,7 @@ def get_observer_class(config_name, config_value, default, monitor_what_str):
     elif config_value == "polling":
         expect_observer = True
         observer_class = PollingObserver
-    elif config_value in ('false', 'no', 'off'):
+    elif config_value in ("false", "no", "off"):
         expect_observer = False
         observer_class = None
     else:
@@ -51,8 +50,9 @@ def get_observer_class(config_name, config_value, default, monitor_what_str):
     return observer_class
 
 
-def get_watcher(config, config_name, default="False", monitor_what_str=None, watcher_class=None,
-                event_handler_class=None, **kwargs):
+def get_watcher(
+    config, config_name, default="False", monitor_what_str=None, watcher_class=None, event_handler_class=None, **kwargs
+):
     config_value = getattr(config, config_name, None)
     observer_class = get_observer_class(config_name, config_value, default=default, monitor_what_str=monitor_what_str)
     if observer_class is not None:
@@ -64,7 +64,6 @@ def get_watcher(config, config_name, default="False", monitor_what_str=None, wat
 
 
 class BaseWatcher:
-
     def __init__(self, observer_class, event_handler_class, **kwargs):
         self.observer = None
         self.observer_class = observer_class
@@ -94,7 +93,6 @@ class BaseWatcher:
 
 
 class Watcher(BaseWatcher):
-
     def __init__(self, observer_class, event_handler_class, **kwargs):
         super().__init__(observer_class, event_handler_class, **kwargs)
         self.path_hash = {}
@@ -113,7 +111,9 @@ class Watcher(BaseWatcher):
             self.monitor(dir_path)
             log.debug("Watching for changes to file: %s", file_path)
 
-    def watch_directory(self, dir_path, callback=None, recursive=False, ignore_extensions=None, require_extensions=None):
+    def watch_directory(
+        self, dir_path, callback=None, recursive=False, ignore_extensions=None, require_extensions=None
+    ):
         dir_path = os.path.abspath(dir_path)
         if dir_path not in self.monitored_dirs:
             if callback is not None:
@@ -123,11 +123,10 @@ class Watcher(BaseWatcher):
             if require_extensions:
                 self.require_extensions[dir_path] = require_extensions
             self.monitor(dir_path, recursive=recursive)
-            log.debug("Watching for changes in directory%s: %s", ' (recursively)' if recursive else '', dir_path)
+            log.debug("Watching for changes in directory%s: %s", " (recursively)" if recursive else "", dir_path)
 
 
 class EventHandler(FileSystemEventHandler):
-
     def __init__(self, watcher):
         self.watcher = watcher
 
@@ -144,10 +143,10 @@ class EventHandler(FileSystemEventHandler):
         # modified events will only have src path, move events will
         # have dest_path and src_path but we only care about dest. So
         # look at dest if it exists else use src.
-        path = getattr(event, 'dest_path', None) or event.src_path
+        path = getattr(event, "dest_path", None) or event.src_path
         path = os.path.abspath(path)
         callback = self.watcher.file_callbacks.get(path)
-        if os.path.basename(path).startswith('.'):
+        if os.path.basename(path).startswith("."):
             return
         if callback:
             ext_ok = self._extension_check(path, path)
@@ -174,7 +173,6 @@ class EventHandler(FileSystemEventHandler):
 
 
 class NullWatcher:
-
     def start(self):
         pass
 
diff --git a/lib/galaxy/util/web_compat.py b/lib/galaxy/util/web_compat.py
index e3a98359f3d..8d99a8792d8 100644
--- a/lib/galaxy/util/web_compat.py
+++ b/lib/galaxy/util/web_compat.py
@@ -6,5 +6,6 @@ otherwise.
 try:
     from galaxy.web_stack import register_postfork_function
 except ImportError:
+
     def register_postfork_function(f, *args, **kwargs):
         f(*args, **kwargs)
diff --git a/lib/galaxy/util/xml_macros.py b/lib/galaxy/util/xml_macros.py
index 2b662981db8..bf608a2e0e2 100644
--- a/lib/galaxy/util/xml_macros.py
+++ b/lib/galaxy/util/xml_macros.py
@@ -1,5 +1,8 @@
 import os
-from copy import copy, deepcopy
+from copy import (
+    copy,
+    deepcopy,
+)
 
 from galaxy.util import parse_xml
 
@@ -29,11 +32,11 @@ def load_with_references(path):
         macros_copy = None
 
     # Collect tokens
-    tokens = _macros_of_type(macros_copy, 'token', lambda el: el.text or '')
+    tokens = _macros_of_type(macros_copy, "token", lambda el: el.text or "")
     tokens = expand_nested_tokens(tokens)
 
     # Expand xml macros
-    macro_dict = _macros_of_type(macros_copy, 'xml', lambda el: XmlMacroDef(el))
+    macro_dict = _macros_of_type(macros_copy, "xml", lambda el: XmlMacroDef(el))
     _expand_macros([root], macro_dict, tokens)
 
     # readd the stashed children of the macros node
@@ -41,8 +44,8 @@ def load_with_references(path):
     if macros_copy is not None:
         _xml_set_children(macros_el, list(macros_copy))
 
-    for el in root.xpath('//macro'):
-        if el.get('type') != 'template':
+    for el in root.xpath("//macro"):
+        if el.get("type") != "template":
             # Only keep template macros
             el.getparent().remove(el)
     _expand_tokens_for_el(root, tokens)
@@ -61,14 +64,14 @@ def template_macro_params(root):
     """
     param_dict = {}
     macros_el = _macros_el(root)
-    macro_dict = _macros_of_type(macros_el, 'template', lambda el: el.text)
+    macro_dict = _macros_of_type(macros_el, "template", lambda el: el.text)
     for key, value in macro_dict.items():
         param_dict[key] = value
     return param_dict
 
 
 def raw_xml_tree(path):
-    """ Load raw (no macro expansion) tree representation of XML represented
+    """Load raw (no macro expansion) tree representation of XML represented
     at the specified path.
     """
     tree = parse_xml(path, strip_whitespace=False, remove_comments=True)
@@ -94,16 +97,14 @@ def _import_macros(root, path):
 
 
 def _macros_el(root):
-    return root.find('macros')
+    return root.find("macros")
 
 
 def _macros_of_type(macros_el, type, el_func):
     if macros_el is None:
         return {}
-    macro_els = macros_el.findall('macro')
-    filtered_els = [(macro_el.get("name"), el_func(macro_el))
-                    for macro_el in macro_els
-                    if macro_el.get('type') == type]
+    macro_els = macros_el.findall("macro")
+    filtered_els = [(macro_el.get("name"), el_func(macro_el)) for macro_el in macro_els if macro_el.get("type") == type]
     return dict(filtered_els)
 
 
@@ -161,7 +162,7 @@ def _expand_macros(elements, macros, tokens, visited=None):
 
     for element in elements:
         while True:
-            expand_el = element.find('.//expand')
+            expand_el = element.find(".//expand")
             if expand_el is None:
                 break
             if visited is None:
@@ -172,11 +173,13 @@ def _expand_macros(elements, macros, tokens, visited=None):
 
 
 def _expand_macro(expand_el, macros, tokens, visited):
-    macro_name = expand_el.get('macro')
+    macro_name = expand_el.get("macro")
     assert macro_name is not None, "Attempted to expand macro with no 'macro' attribute defined."
 
     # check for cycles in the nested macro expansion
-    assert macro_name not in visited, f"Cycle in nested macros: already expanded {visited} can't expand '{macro_name}' again"
+    assert (
+        macro_name not in visited
+    ), f"Cycle in nested macros: already expanded {visited} can't expand '{macro_name}' again"
     visited.append(macro_name)
 
     assert macro_name in macros, f"No macro named {macro_name} found, known macros are {', '.join(macros.keys())}."
@@ -203,7 +206,7 @@ def _expand_yield_statements(macro_def, expand_el):
     2. all unnamed yield tags by the non-token children of the expand tag
     """
     # replace named yields
-    for token_el in expand_el.findall('./token'):
+    for token_el in expand_el.findall("./token"):
         name = token_el.attrib.get("name", None)
         assert name is not None, "Found unnamed token" + str(token_el.attrib)
         yield_els = [yield_el for yield_el in macro_def.findall(f".//yield[@name='{name}']")]
@@ -213,7 +216,7 @@ def _expand_yield_statements(macro_def, expand_el):
             _xml_replace(yield_el, token_el_children)
 
     # replace unnamed yields
-    yield_els = [yield_el for yield_el in macro_def.findall('.//yield')]
+    yield_els = [yield_el for yield_el in macro_def.findall(".//yield")]
     expand_el_children = [c for c in expand_el if c.tag != "token"]
     for yield_el in yield_els:
         _xml_replace(yield_el, expand_el_children)
@@ -237,20 +240,20 @@ def _load_embedded_macros(macros_el, xml_base_dir):
     if macros_el is not None:
         macro_els = macros_el.findall("macro")
     for macro in macro_els:
-        if 'type' not in macro.attrib:
-            macro.attrib['type'] = 'xml'
+        if "type" not in macro.attrib:
+            macro.attrib["type"] = "xml"
         macros.append(macro)
 
     # type shortcuts (<xml> is a shortcut for <macro type="xml",
     # likewise for <template>.
-    typed_tag = ['template', 'xml', 'token']
+    typed_tag = ["template", "xml", "token"]
     for tag in typed_tag:
         macro_els = []
         if macros_el is not None:
             macro_els = macros_el.findall(tag)
         for macro_el in macro_els:
-            macro_el.attrib['type'] = tag
-            macro_el.tag = 'macro'
+            macro_el.attrib["type"] = tag
+            macro_el.tag = "macro"
             macros.append(macro_el)
 
     return macros
@@ -261,8 +264,7 @@ def _load_imported_macros(macros_el, xml_base_dir):
     macro_paths = []
 
     for tool_relative_import_path in _imported_macro_paths_from_el(macros_el):
-        import_path = \
-            os.path.join(xml_base_dir, tool_relative_import_path)
+        import_path = os.path.join(xml_base_dir, tool_relative_import_path)
         macro_paths.append(import_path)
         file_macros, current_macro_paths = _load_macro_file(import_path, xml_base_dir)
         macros.extend(file_macros)
@@ -304,7 +306,7 @@ def _xml_set_children(element, new_children):
 
 
 def _xml_replace(query, targets):
-    parent_el = query.find('..')
+    parent_el = query.find("..")
     matching_index = -1
     # for index, el in enumerate(parent_el.iter('.')):  ## Something like this for newer implementation
     for index, el in enumerate(list(parent_el)):
@@ -337,6 +339,7 @@ class XmlMacroDef:
     TODO: `token_quote` forbids `"quote"` as character name of optional
     parameters
     """
+
     def __init__(self, el):
         self.element = el
         parameters = {}
@@ -349,7 +352,7 @@ class XmlMacroDef:
                 for token in value.split(","):
                     tokens.append((token, REQUIRED_PARAMETER))
             elif key.startswith("token_"):
-                token = key[len("token_"):]
+                token = key[len("token_") :]
                 tokens.append((token, value))
         for name, default in tokens:
             parameters[name] = (token_quote, default)
diff --git a/lib/galaxy/util/yaml_util.py b/lib/galaxy/util/yaml_util.py
index 60b02f736b4..a9bbabdc30f 100644
--- a/lib/galaxy/util/yaml_util.py
+++ b/lib/galaxy/util/yaml_util.py
@@ -4,6 +4,7 @@ from collections import OrderedDict
 
 import yaml
 from yaml.constructor import ConstructorError
+
 try:
     from yaml import CSafeLoader as SafeLoader
 except ImportError:
@@ -36,6 +37,7 @@ def ordered_load(stream, merge_duplicate_keys=False):
     Otherwise, following YAML 1.2 specification which says that "each key is
     unique in the association", raise a ConstructionError exception.
     """
+
     def construct_mapping(loader, node, deep=False):
         loader.flatten_mapping(node)
         mapping = {}
@@ -45,8 +47,12 @@ def ordered_load(stream, merge_duplicate_keys=False):
             value = loader.construct_object(value_node, deep=deep)
             if key in mapping:
                 if not merge_duplicate_keys:
-                    raise ConstructorError("while constructing a mapping", node.start_mark,
-                        f"found duplicated key ({key})", key_node.start_mark)
+                    raise ConstructorError(
+                        "while constructing a mapping",
+                        node.start_mark,
+                        f"found duplicated key ({key})",
+                        key_node.start_mark,
+                    )
                 log.debug("Merging values for duplicate key '%s' into a list", key)
                 if merged_duplicate.get(key):
                     mapping[key].append(value)
@@ -57,10 +63,8 @@ def ordered_load(stream, merge_duplicate_keys=False):
                 mapping[key] = value
         return mapping
 
-    OrderedLoader.add_constructor(
-        yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
-        construct_mapping)
-    OrderedLoader.add_constructor('!include', OrderedLoader.include)
+    OrderedLoader.add_constructor(yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, construct_mapping)
+    OrderedLoader.add_constructor("!include", OrderedLoader.include)
 
     return yaml.load(stream, OrderedLoader)
 
@@ -70,8 +74,7 @@ def ordered_dump(data, stream=None, Dumper=yaml.Dumper, **kwds):
         pass
 
     def _dict_representer(dumper, data):
-        return dumper.represent_mapping(
-            yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
-            list(data.items()))
+        return dumper.represent_mapping(yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, list(data.items()))
+
     OrderedDumper.add_representer(OrderedDict, _dict_representer)
     return yaml.dump(data, stream, OrderedDumper, **kwds)
diff --git a/lib/galaxy/util/zipstream.py b/lib/galaxy/util/zipstream.py
index e467d5ab586..2ca66162591 100644
--- a/lib/galaxy/util/zipstream.py
+++ b/lib/galaxy/util/zipstream.py
@@ -7,12 +7,13 @@ from .path import safe_walk
 
 
 class ZipstreamWrapper:
-
     def __init__(self, archive_name=None, upstream_mod_zip=False, upstream_gzip=False):
         self.upstream_mod_zip = upstream_mod_zip
         self.archive_name = archive_name
         if not self.upstream_mod_zip:
-            self.archive = zipstream.ZipFile(allowZip64=True, compression=zipstream.ZIP_STORED if upstream_gzip else zipstream.ZIP_DEFLATED)
+            self.archive = zipstream.ZipFile(
+                allowZip64=True, compression=zipstream.ZIP_STORED if upstream_gzip else zipstream.ZIP_DEFLATED
+            )
         self.files = []
         self.size = 0
 
@@ -28,11 +29,11 @@ class ZipstreamWrapper:
     def get_headers(self):
         headers = {}
         if self.archive_name:
-            headers['Content-Disposition'] = f'attachment; filename="{self.archive_name}.zip"'
+            headers["Content-Disposition"] = f'attachment; filename="{self.archive_name}.zip"'
         if self.upstream_mod_zip:
-            headers['X-Archive-Files'] = 'zip'
+            headers["X-Archive-Files"] = "zip"
         else:
-            headers['Content-Type'] = 'application/x-zip-compressed'
+            headers["Content-Type"] = "application/x-zip-compressed"
         return headers
 
     def add_path(self, path, archive_name):
diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index 79769b43d65..129af6925aa 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
 VERSION_MAJOR = "22.05"
 VERSION_MINOR = "dev0"
-VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else '')
+VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
diff --git a/lib/galaxy/visualization/data_providers/basic.py b/lib/galaxy/visualization/data_providers/basic.py
index dfbcbdec324..7f2caa74bee 100644
--- a/lib/galaxy/visualization/data_providers/basic.py
+++ b/lib/galaxy/visualization/data_providers/basic.py
@@ -14,11 +14,17 @@ class BaseDataProvider:
     - write subsets of data to new datasets
 
     """
+
     original_dataset: DatasetInstance
 
-    def __init__(self, converted_dataset=None, original_dataset=None, dependencies=None,
-                 error_max_vals="Only the first %i values are returned."):
-        """ Create basic data provider. """
+    def __init__(
+        self,
+        converted_dataset=None,
+        original_dataset=None,
+        dependencies=None,
+        error_max_vals="Only the first %i values are returned.",
+    ):
+        """Create basic data provider."""
         self.converted_dataset = converted_dataset
         self.original_dataset = original_dataset
         self.dependencies = dependencies
@@ -62,7 +68,8 @@ class BaseDataProvider:
 
 
 class ColumnDataProvider(BaseDataProvider):
-    """ Data provider for columnar data """
+    """Data provider for columnar data"""
+
     MAX_LINES_RETURNED = 30000
 
     def __init__(self, original_dataset, max_lines_returned=MAX_LINES_RETURNED):
@@ -81,7 +88,7 @@ class ColumnDataProvider(BaseDataProvider):
         where each list is a line of data.
         """
         if not columns:
-            raise TypeError('parameter required: columns')
+            raise TypeError("parameter required: columns")
 
         # TODO: validate kwargs
         try:
@@ -98,40 +105,38 @@ class ColumnDataProvider(BaseDataProvider):
 
         # skip comment lines (if any/avail)
         # pre: should have original_dataset and
-        if(skip_comments
-                and self.original_dataset.metadata.comment_lines
-                and start_val < self.original_dataset.metadata.comment_lines):
+        if (
+            skip_comments
+            and self.original_dataset.metadata.comment_lines
+            and start_val < self.original_dataset.metadata.comment_lines
+        ):
             start_val = int(self.original_dataset.metadata.comment_lines)
 
         # columns is an array of ints for now (should handle column names later)
         columns = loads(columns)
         for column in columns:
-            assert((column < self.original_dataset.metadata.columns)
-                   and (column >= 0)), (
-                "column index (%d) must be positive and less" % (column)
-                + " than the number of columns: %d" % (self.original_dataset.metadata.columns))
+            assert (column < self.original_dataset.metadata.columns) and (
+                column >= 0
+            ), "column index (%d) must be positive and less" % (column) + " than the number of columns: %d" % (
+                self.original_dataset.metadata.columns
+            )
 
         # set up the response, column lists
         response = {}
-        response['data'] = data = [[] for column in columns]
-        response['meta'] = meta = [{
-            'min': None,
-            'max': None,
-            'count': 0,
-            'sum': 0
-        } for column in columns]
+        response["data"] = data = [[] for column in columns]
+        response["meta"] = meta = [{"min": None, "max": None, "count": 0, "sum": 0} for column in columns]
 
         column_types = [self.original_dataset.metadata.column_types[column] for column in columns]
 
         # function for casting by column_types
         def cast_val(val, type):
-            """ Cast value based on type. Return None if can't be cast """
-            if type == 'int':
+            """Cast value based on type. Return None if can't be cast"""
+            if type == "int":
                 try:
                     val = int(val)
                 except ValueError:
                     return None
-            elif type == 'float':
+            elif type == "float":
                 try:
                     val = float(val)
                 except ValueError:
@@ -162,39 +167,39 @@ class ColumnDataProvider(BaseDataProvider):
                     if column_val is not None:
 
                         # if numeric, maintain min, max, sum
-                        if(column_type == 'float' or column_type == 'int'):
-                            if((meta[index]['min'] is None) or (column_val < meta[index]['min'])):
-                                meta[index]['min'] = column_val
+                        if column_type == "float" or column_type == "int":
+                            if (meta[index]["min"] is None) or (column_val < meta[index]["min"]):
+                                meta[index]["min"] = column_val
 
-                            if((meta[index]['max'] is None) or (column_val > meta[index]['max'])):
-                                meta[index]['max'] = column_val
+                            if (meta[index]["max"] is None) or (column_val > meta[index]["max"]):
+                                meta[index]["max"] = column_val
 
-                            meta[index]['sum'] += column_val
+                            meta[index]["sum"] += column_val
 
                 # maintain a count - for other stats
-                meta[index]['count'] += 1
+                meta[index]["count"] += 1
                 data[index].append(column_val)
 
-        response['endpoint'] = dict(last_line=(count - 1), file_ptr=f.tell())
+        response["endpoint"] = dict(last_line=(count - 1), file_ptr=f.tell())
         f.close()
 
         if not returning_data:
             return None
 
-        for index, meta in enumerate(response['meta']):
+        for index, meta in enumerate(response["meta"]):
             column_type = column_types[index]
-            count = meta['count']
+            count = meta["count"]
 
-            if((column_type == 'float' or column_type == 'int') and count):
-                meta['mean'] = float(meta['sum']) / count
+            if (column_type == "float" or column_type == "int") and count:
+                meta["mean"] = float(meta["sum"]) / count
 
-                sorted_data = sorted(response['data'][index])
+                sorted_data = sorted(response["data"][index])
                 middle_index = (count / 2) - 1
                 if count % 2 == 0:
-                    meta['median'] = ((sorted_data[middle_index] + sorted_data[(middle_index + 1)]) / 2.0)
+                    meta["median"] = (sorted_data[middle_index] + sorted_data[(middle_index + 1)]) / 2.0
 
                 else:
-                    meta['median'] = sorted_data[middle_index]
+                    meta["median"] = sorted_data[middle_index]
 
         # ugh ... metadata_data_lines is not a reliable source; hafta have an EOF
         return response
diff --git a/lib/galaxy/visualization/data_providers/cigar.py b/lib/galaxy/visualization/data_providers/cigar.py
index b65072c77fb..41d5e943596 100644
--- a/lib/galaxy/visualization/data_providers/cigar.py
+++ b/lib/galaxy/visualization/data_providers/cigar.py
@@ -1,19 +1,19 @@
-'''
+"""
 Functions for working with SAM/BAM CIGAR representation.
-'''
+"""
 
 import operator
 
 
 def get_ref_based_read_seq_and_cigar(read_seq, read_start, ref_seq, ref_seq_start, cigar):
-    '''
+    """
     Returns a ( new_read_seq, new_cigar ) that can be used with reference
     sequence to reconstruct the read. The new read sequence includes only
     bases that cannot be recovered from the reference: mismatches and
     insertions (soft clipped bases are not included). The new cigar replaces
     Ms with =s and Xs because the M operation can denote a sequence match or
     mismatch.
-    '''
+    """
 
     if not ref_seq:
         return read_seq, cigar
@@ -23,63 +23,63 @@ def get_ref_based_read_seq_and_cigar(read_seq, read_start, ref_seq, ref_seq_star
     read_pos = 0
 
     # Create new read sequence, cigar.
-    new_read_seq = ''
-    new_cigar = ''
-    cigar_ops = 'MIDNSHP=X'
+    new_read_seq = ""
+    new_cigar = ""
+    cigar_ops = "MIDNSHP=X"
     for op_tuple in cigar:
         op, op_len = op_tuple
         # Op is index into string 'MIDNSHP=X'
         if op == 0:  # Match
             # Transform Ms to =s and Xs using reference.
-            new_op = ''
+            new_op = ""
             total_count = 0
             while total_count < op_len and ref_seq_pos < len(ref_seq):
                 match, count = _match_mismatch_counter(read_seq, read_pos, ref_seq, ref_seq_pos)
                 # Use min because count cannot exceed remainder of operation.
                 count = min(count, op_len - total_count)
                 if match:
-                    new_op = '='
+                    new_op = "="
                 else:
-                    new_op = 'X'
+                    new_op = "X"
                     # Include mismatched bases in new read sequence.
-                    new_read_seq += read_seq[read_pos:read_pos + count]
-                new_cigar += '%i%s' % (count, new_op)
+                    new_read_seq += read_seq[read_pos : read_pos + count]
+                new_cigar += "%i%s" % (count, new_op)
                 total_count += count
                 read_pos += count
                 ref_seq_pos += count
 
             # If end of read falls outside of ref_seq data, leave as M.
             if total_count < op_len:
-                new_cigar += '%iM' % (op_len - total_count)
+                new_cigar += "%iM" % (op_len - total_count)
         elif op == 1:  # Insertion
-            new_cigar += '%i%s' % (op_len, cigar_ops[op])
+            new_cigar += "%i%s" % (op_len, cigar_ops[op])
             # Include insertion bases in new read sequence.
-            new_read_seq += read_seq[read_pos:read_pos + op_len]
+            new_read_seq += read_seq[read_pos : read_pos + op_len]
             read_pos += op_len
         elif op in [2, 3, 6]:  # Deletion, Skip, or Padding
             ref_seq_pos += op_len
-            new_cigar += '%i%s' % (op_len, cigar_ops[op])
+            new_cigar += "%i%s" % (op_len, cigar_ops[op])
         elif op == 4:  # Soft clipping
             read_pos += op_len
-            new_cigar += '%i%s' % (op_len, cigar_ops[op])
+            new_cigar += "%i%s" % (op_len, cigar_ops[op])
         elif op == 5:  # Hard clipping
-            new_cigar += '%i%s' % (op_len, cigar_ops[op])
+            new_cigar += "%i%s" % (op_len, cigar_ops[op])
         elif op in [7, 8]:  # Match or mismatch
             if op == 8:
                 # Include mismatched bases in new read sequence.
-                new_read_seq += read_seq[read_pos:read_pos + op_len]
+                new_read_seq += read_seq[read_pos : read_pos + op_len]
             read_pos += op_len
             ref_seq_pos += op_len
-            new_cigar += '%i%s' % (op_len, cigar_ops[op])
+            new_cigar += "%i%s" % (op_len, cigar_ops[op])
 
     return (new_read_seq, new_cigar)
 
 
 def _match_mismatch_counter(s1, p1, s2, p2):
-    '''
+    """
     Count consecutive matches/mismatches between strings s1 and s2
     starting at p1 and p2, respectively.
-    '''
+    """
 
     # Do initial comparison to determine whether to count matches or
     # mismatches.
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index cd0d0993508..5de9fed137e 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -10,15 +10,34 @@ import re
 import sys
 from contextlib import contextmanager
 from json import loads
-from typing import Any, Dict, IO, Iterator, List, Optional, Tuple, Union
+from typing import (
+    Any,
+    Dict,
+    IO,
+    Iterator,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
 
 import pysam
 from bx.bbi.bigbed_file import BigBedFile
 from bx.bbi.bigwig_file import BigWigFile
 from bx.interval_index_file import Indexes
 
-from galaxy.datatypes.interval import Bed, Gff, Gtf
-from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFFeature, GFFInterval, GFFReaderWrapper, parse_gff_attributes
+from galaxy.datatypes.interval import (
+    Bed,
+    Gff,
+    Gtf,
+)
+from galaxy.datatypes.util.gff_util import (
+    convert_gff_coords_to_bed,
+    GFFFeature,
+    GFFInterval,
+    GFFReaderWrapper,
+    parse_gff_attributes,
+)
 from galaxy.model import DatasetInstance
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
@@ -35,9 +54,9 @@ PAYLOAD_LIST_TYPE = List[Optional[Union[str, int, float, List[Tuple[int, int]]]]
 
 
 def float_nan(n):
-    '''
+    """
     Return None instead of NaN to pass jQuery 1.4's strict JSON
-    '''
+    """
     if n != n:  # NaN != NaN
         return None
     else:
@@ -45,9 +64,9 @@ def float_nan(n):
 
 
 def get_bounds(reads, start_pos_index, end_pos_index):
-    '''
+    """
     Returns the minimum and maximum position for a set of reads.
-    '''
+    """
     max_low = sys.maxsize
     max_high = -sys.maxsize
     for read in reads:
@@ -59,20 +78,22 @@ def get_bounds(reads, start_pos_index, end_pos_index):
 
 
 def _convert_between_ucsc_and_ensemble_naming(chrom):
-    '''
+    """
     Convert between UCSC chromosome ('chr1') naming conventions and Ensembl
     naming conventions ('1')
-    '''
-    if chrom.startswith('chr'):
+    """
+    if chrom.startswith("chr"):
         # Convert from UCSC to Ensembl
         return chrom[3:]
     else:
         # Convert from Ensembl to UCSC
-        return 'chr' + chrom
+        return "chr" + chrom
 
 
 def _chrom_naming_matches(chrom1, chrom2):
-    return (chrom1.startswith('chr') and chrom2.startswith('chr')) or (not chrom1.startswith('chr') and not chrom2.startswith('chr'))
+    return (chrom1.startswith("chr") and chrom2.startswith("chr")) or (
+        not chrom1.startswith("chr") and not chrom2.startswith("chr")
+    )
 
 
 class FeatureLocationIndexDataProvider(BaseDataProvider):
@@ -116,7 +137,7 @@ class FeatureLocationIndexDataProvider(BaseDataProvider):
             line = textloc_file.readline()
             if not line.startswith(query):
                 break
-            if line[-1:] == '\n':
+            if line[-1:] == "\n":
                 line = line[:-1]
             result.append(line.split()[1:])
 
@@ -138,12 +159,19 @@ class GenomeDataProvider(BaseDataProvider):
     # col_name_data_attr_mapping = {4 : { index: 5, name: 'Score' } }
     col_name_data_attr_mapping: Dict[Union[str, int], Dict] = {}
 
-    def __init__(self, converted_dataset=None, original_dataset=None, dependencies=None,
-                 error_max_vals="Only the first %i %s in this region are displayed."):
-        super().__init__(converted_dataset=converted_dataset,
-                         original_dataset=original_dataset,
-                         dependencies=dependencies,
-                         error_max_vals=error_max_vals)
+    def __init__(
+        self,
+        converted_dataset=None,
+        original_dataset=None,
+        dependencies=None,
+        error_max_vals="Only the first %i %s in this region are displayed.",
+    ):
+        super().__init__(
+            converted_dataset=converted_dataset,
+            original_dataset=original_dataset,
+            dependencies=dependencies,
+            error_max_vals=error_max_vals,
+        )
 
     def write_data_to_file(self, regions, filename):
         """
@@ -203,24 +231,19 @@ class GenomeDataProvider(BaseDataProvider):
         Returns data for complete genome.
         """
         genome_data = []
-        for chrom_info in chroms_info['chrom_info']:
-            chrom = chrom_info['chrom']
-            chrom_len = chrom_info['len']
+        for chrom_info in chroms_info["chrom_info"]:
+            chrom = chrom_info["chrom"]
+            chrom_len = chrom_info["len"]
             chrom_data = self.get_data(chrom, 0, chrom_len, **kwargs)
             # FIXME: data providers probably should never return None.
             # Some data providers return None when there's no data, so
             # create a dummy dict if necessary.
             if not chrom_data:
-                chrom_data = {
-                    'data': None
-                }
-            chrom_data['region'] = "%s:%i-%i" % (chrom, 0, chrom_len)
+                chrom_data = {"data": None}
+            chrom_data["region"] = "%s:%i-%i" % (chrom, 0, chrom_len)
             genome_data.append(chrom_data)
 
-        return {
-            'data': genome_data,
-            'dataset_type': self.dataset_type
-        }
+        return {"data": genome_data, "dataset_type": self.dataset_type}
 
     def get_filters(self):
         """
@@ -258,14 +281,13 @@ class GenomeDataProvider(BaseDataProvider):
                     attrs = self.col_name_data_attr_mapping[col_name]
                 except KeyError:
                     continue
-                filters.append({'name': attrs['name'],
-                                'type': column_types[viz_col_index],
-                                'index': attrs['index']})
+                filters.append({"name": attrs["name"], "type": column_types[viz_col_index], "index": attrs["index"]})
         return filters
 
     def get_default_max_vals(self):
         return 5000
 
+
 #
 # -- Base mixins and providers --
 #
@@ -275,7 +297,7 @@ class FilterableMixin:
     original_dataset: DatasetInstance
 
     def get_filters(self):
-        """ Returns a dataset's filters. """
+        """Returns a dataset's filters."""
         # Get filters.
         # TODOs:
         # (a) might be useful to move this into each datatype's set_meta method;
@@ -286,30 +308,29 @@ class FilterableMixin:
         filter_col = 8
         if isinstance(self.original_dataset.datatype, Gff):
             # Can filter by score and GTF attributes.
-            filters = [{'name': 'Score',
-                        'type': 'number',
-                        'index': filter_col,
-                        'tool_id': 'Filter1',
-                        'tool_exp_name': 'c6'}]
+            filters = [
+                {"name": "Score", "type": "number", "index": filter_col, "tool_id": "Filter1", "tool_exp_name": "c6"}
+            ]
             filter_col += 1
             if isinstance(self.original_dataset.datatype, Gtf):
                 # Create filters based on dataset metadata.
                 for name, a_type in self.original_dataset.metadata.attribute_types.items():
-                    if a_type in ['int', 'float']:
+                    if a_type in ["int", "float"]:
                         filters.append(
-                            {'name': name,
-                             'type': 'number',
-                             'index': filter_col,
-                             'tool_id': 'gff_filter_by_attribute',
-                             'tool_exp_name': name})
+                            {
+                                "name": name,
+                                "type": "number",
+                                "index": filter_col,
+                                "tool_id": "gff_filter_by_attribute",
+                                "tool_exp_name": name,
+                            }
+                        )
                         filter_col += 1
         elif isinstance(self.original_dataset.datatype, Bed):
             # Can filter by score column only.
-            filters = [{'name': 'Score',
-                        'type': 'number',
-                        'index': filter_col,
-                        'tool_id': 'Filter1',
-                        'tool_exp_name': 'c5'}]
+            filters = [
+                {"name": "Score", "type": "number", "index": filter_col, "tool_id": "Filter1", "tool_exp_name": "c5"}
+            ]
 
         return filters
 
@@ -318,16 +339,17 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
     """
     Tabix index data provider for the Galaxy track browser.
     """
-    dataset_type = 'tabix'
 
-    col_name_data_attr_mapping: Dict[Union[str, int], Dict] = {4: {'index': 4, 'name': 'Score'}}
+    dataset_type = "tabix"
+
+    col_name_data_attr_mapping: Dict[Union[str, int], Dict] = {4: {"index": 4, "name": "Score"}}
 
     @contextmanager
     def open_data_file(self):
         # We create a symlink to the index file. This is
         # required until https://github.com/pysam-developers/pysam/pull/586 is merged.
         index_path = self.converted_dataset.file_name
-        with pysam.TabixFile(self.dependencies['bgzip'].file_name, index=index_path) as f:
+        with pysam.TabixFile(self.dependencies["bgzip"].file_name, index=index_path) as f:
             yield f
 
     def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
@@ -337,7 +359,7 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
         start = int(start)
         end = int(end)
         if end >= (2 << 29):
-            end = (2 << 29 - 1)  # Tabix-enforced maximum
+            end = 2 << 29 - 1  # Tabix-enforced maximum
         # Get iterator using either naming scheme.
         iterator: Iterator[str] = iter([])
         if chrom in data_file.contigs:
@@ -351,13 +373,14 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
         return iterator
 
     def write_data_to_file(self, regions, filename):
-        with self.open_data_file() as data_file, open(filename, 'w') as out:
+        with self.open_data_file() as data_file, open(filename, "w") as out:
             for region in regions:
                 # Write data in region.
                 iterator = self.get_iterator(data_file, region.chrom, region.start, region.end)
                 for line in iterator:
                     out.write(f"{line}\n")
 
+
 #
 # -- Interval data providers --
 #
@@ -369,7 +392,8 @@ class IntervalDataProvider(GenomeDataProvider):
 
     Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]
     """
-    dataset_type = 'interval_index'
+
+    dataset_type = "interval_index"
 
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         raise Exception("Unimplemented Function")
@@ -384,7 +408,7 @@ class IntervalDataProvider(GenomeDataProvider):
         # First three entries are mandatory, others are optional.
         #
         filter_cols = loads(kwargs.get("filter_cols", "[]"))
-        no_detail = ("no_detail" in kwargs)
+        no_detail = "no_detail" in kwargs
         rval = []
         message = None
 
@@ -430,7 +454,7 @@ class IntervalDataProvider(GenomeDataProvider):
 
             rval.append(payload)
 
-        return {'data': rval, 'message': message}
+        return {"data": rval, "message": message}
 
     def write_data_to_file(self, regions, filename):
         raise Exception("Unimplemented Function")
@@ -446,6 +470,7 @@ class IntervalTabixDataProvider(TabixDataProvider, IntervalDataProvider):
 # -- BED data providers --
 #
 
+
 class BedDataProvider(GenomeDataProvider):
     """
     Processes BED data from native format to payload format.
@@ -453,7 +478,7 @@ class BedDataProvider(GenomeDataProvider):
     Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]
     """
 
-    dataset_type = 'interval_index'
+    dataset_type = "interval_index"
 
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         raise Exception("Unimplemented Method")
@@ -469,7 +494,7 @@ class BedDataProvider(GenomeDataProvider):
         # First three entries are mandatory, others are optional.
         #
         filter_cols = loads(kwargs.get("filter_cols", "[]"))
-        no_detail = ("no_detail" in kwargs)
+        no_detail = "no_detail" in kwargs
         rval = []
         message = None
         for count, line in enumerate(iterator):
@@ -501,10 +526,12 @@ class BedDataProvider(GenomeDataProvider):
 
             # Blocks.
             if length >= 12:
-                block_sizes = [int(n) for n in feature[10].split(',') if n != '']
-                block_starts = [int(n) for n in feature[11].split(',') if n != '']
+                block_sizes = [int(n) for n in feature[10].split(",") if n != ""]
+                block_starts = [int(n) for n in feature[11].split(",") if n != ""]
                 blocks = list(zip(block_sizes, block_starts))
-                payload.append([(int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0]) for block in blocks])
+                payload.append(
+                    [(int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0]) for block in blocks]
+                )
 
             # Score (filter data)
             if length >= 5 and filter_cols and filter_cols[0] == "Score":
@@ -520,7 +547,7 @@ class BedDataProvider(GenomeDataProvider):
 
             rval.append(payload)
 
-        return {'data': rval, 'dataset_type': self.dataset_type, 'message': message}
+        return {"data": rval, "dataset_type": self.dataset_type, "message": message}
 
     def write_data_to_file(self, regions, filename):
         with open(filename, "w") as out:
@@ -567,14 +594,17 @@ class RawBedDataProvider(BedDataProvider):
                     feature_chrom = feature[0]
                     feature_start = int(feature[1])
                     feature_end = int(feature[2])
-                    if (chrom is not None and feature_chrom != chrom) \
-                            or (start is not None and feature_start > end) \
-                            or (end is not None and feature_end < start):
+                    if (
+                        (chrom is not None and feature_chrom != chrom)
+                        or (start is not None and feature_start > end)
+                        or (end is not None and feature_end < start)
+                    ):
                         continue
                     yield line
 
         return line_filter_iter()
 
+
 #
 # -- VCF data providers --
 #
@@ -599,9 +629,9 @@ class VcfDataProvider(GenomeDataProvider):
 
     """
 
-    col_name_data_attr_mapping: Dict[Union[str, int], Dict] = {'Qual': {'index': 6, 'name': 'Qual'}}
+    col_name_data_attr_mapping: Dict[Union[str, int], Dict] = {"Qual": {"index": 6, "name": "Qual"}}
 
-    dataset_type = 'variant'
+    dataset_type = "variant"
 
     def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
         """
@@ -638,15 +668,15 @@ class VcfDataProvider(GenomeDataProvider):
             # Deletions?
             alt_in_ref_index = ref.find(alt)
             if alt_in_ref_index != -1:
-                return alt_in_ref_index, ref[alt_in_ref_index + 1:], [[cig_ops.find("D"), ref_len - alt_len]]
+                return alt_in_ref_index, ref[alt_in_ref_index + 1 :], [[cig_ops.find("D"), ref_len - alt_len]]
 
             # Insertions?
             ref_in_alt_index = alt.find(ref)
             if ref_in_alt_index != -1:
-                return ref_in_alt_index, alt[ref_in_alt_index + 1:], [[cig_ops.find("I"), alt_len - ref_len]]
+                return ref_in_alt_index, alt[ref_in_alt_index + 1 :], [[cig_ops.find("I"), alt_len - ref_len]]
 
         # Pack data.
-        genotype_re = re.compile(r'/|\|')
+        genotype_re = re.compile(r"/|\|")
         for count, line in enumerate(iterator):
             if count < start_val:
                 continue
@@ -667,12 +697,12 @@ class VcfDataProvider(GenomeDataProvider):
             pos = int(pos) - 1
 
             # FIXME: OK to skip?
-            if alt == '.':
+            if alt == ".":
                 count -= 1
                 continue
 
             # Set up array to track allele counts.
-            allele_counts = [0 for i in range(alt.count(',') + 1)]
+            allele_counts = [0 for i in range(alt.count(",") + 1)]
             sample_gts = []
 
             if samples_data:
@@ -682,7 +712,7 @@ class VcfDataProvider(GenomeDataProvider):
 
                 for sample in samples_data:
                     # Parse and count alleles.
-                    genotype = sample.split(':')[0]
+                    genotype = sample.split(":")[0]
                     has_alleles = False
                     alleles_seen.clear()
                     for allele_str in genotype_re.split(genotype):
@@ -700,29 +730,20 @@ class VcfDataProvider(GenomeDataProvider):
 
                     # If no alleles, use empty string as proxy.
                     if not has_alleles:
-                        genotype = ''
+                        genotype = ""
 
                     sample_gts.append(genotype)
             else:
                 # No samples, so set allele count and sample genotype manually.
                 allele_counts = [1]
-                sample_gts = ['1/1']
+                sample_gts = ["1/1"]
 
             # Add locus data.
-            locus_data = [
-                -1,
-                pos,
-                c_id,
-                ref,
-                alt,
-                qual,
-                c_filter,
-                ','.join(sample_gts)
-            ]
+            locus_data = [-1, pos, c_id, ref, alt, qual, c_filter, ",".join(sample_gts)]
             locus_data.extend(allele_counts)
             data.append(locus_data)
 
-        return {'data': data, 'message': message}
+        return {"data": data, "message": message}
 
     def write_data_to_file(self, regions, filename):
         out = open(filename, "w")
@@ -739,7 +760,7 @@ class VcfTabixDataProvider(TabixDataProvider, VcfDataProvider):
     Provides data from a VCF file indexed via tabix.
     """
 
-    dataset_type = 'variant'
+    dataset_type = "variant"
 
 
 class RawVcfDataProvider(VcfDataProvider):
@@ -773,14 +794,14 @@ class RawVcfDataProvider(VcfDataProvider):
                 chrom = _convert_between_ucsc_and_ensemble_naming(chrom)
 
         def line_in_region(vcf_line, chrom, start, end):
-            """ Returns true if line is in region. """
+            """Returns true if line is in region."""
             variant_chrom, variant_start = vcf_line.split()[0:2]
             # VCF format is 1-based.
             variant_start = int(variant_start) - 1
             return variant_chrom == chrom and variant_start >= start and variant_start <= end
 
         def line_filter_iter():
-            """ Yields lines in data that are in region chrom:start-end """
+            """Yields lines in data that are in region chrom:start-end"""
             # Yield data line read above.
             if line_in_region(line, chrom, start, end):
                 yield line
@@ -799,7 +820,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
     data is reported in BED format: 0-based, half-open.
     """
 
-    dataset_type = 'bai'
+    dataset_type = "bai"
 
     def get_filters(self):
         """
@@ -808,9 +829,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         # HACK: first 7 fields are for drawing, so start filter column index at 7.
         filter_col = 7
         filters = []
-        filters.append({'name': 'Mapping Quality',
-                        'type': 'number',
-                        'index': filter_col})
+        filters.append({"name": "Mapping Quality", "type": "number", "index": filter_col})
         return filters
 
     def write_data_to_file(self, regions, filename):
@@ -819,11 +838,12 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         """
 
         # Open current BAM file using index.
-        bamfile = pysam.AlignmentFile(self.original_dataset.file_name, mode='rb',
-                                      index_filename=self.converted_dataset.file_name)
+        bamfile = pysam.AlignmentFile(
+            self.original_dataset.file_name, mode="rb", index_filename=self.converted_dataset.file_name
+        )
 
         # TODO: write headers as well?
-        new_bamfile = pysam.AlignmentFile(filename, template=bamfile, mode='wb')
+        new_bamfile = pysam.AlignmentFile(filename, template=bamfile, mode="wb")
 
         for region in regions:
             # Write data from region.
@@ -852,8 +872,9 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
     @contextmanager
     def open_data_file(self):
         # Attempt to open the BAM file with index
-        with pysam.AlignmentFile(self.original_dataset.file_name, mode='rb',
-                                 index_filename=self.converted_dataset.file_name) as f:
+        with pysam.AlignmentFile(
+            self.original_dataset.file_name, mode="rb", index_filename=self.converted_dataset.file_name
+        ) as f:
             yield f
 
     def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
@@ -876,8 +897,18 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
                 return iter([])
         return data
 
-    def process_data(self, iterator, start_val=0, max_vals=None, ref_seq=None,
-                     iterator_type='nth', mean_depth=None, start=0, end=0, **kwargs):
+    def process_data(
+        self,
+        iterator,
+        start_val=0,
+        max_vals=None,
+        ref_seq=None,
+        iterator_type="nth",
+        mean_depth=None,
+        start=0,
+        end=0,
+        **kwargs,
+    ):
         """
         Returns a dict with the following attributes::
 
@@ -903,16 +934,16 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         """
         # No iterator indicates no reads.
         if iterator is None:
-            return {'data': [], 'message': None}
+            return {"data": [], "message": None}
 
         #
         # Helper functions.
         #
 
         def decode_strand(read_flag, mask):
-            """ Decode strand from read flag. """
+            """Decode strand from read flag."""
 
-            strand_flag = (read_flag & mask == 0)
+            strand_flag = read_flag & mask == 0
             if strand_flag:
                 return "+"
             else:
@@ -945,7 +976,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
             first_read = next(iterator)
         except StopIteration:
             # no reads.
-            return {'data': [], 'message': None, 'max_low': start, 'max_high': start}
+            return {"data": [], "message": None, "max_low": start, "max_high": start}
 
         read_len = len(first_read.seq)
         num_reads = max((end - start) * mean_depth / float(read_len), 1)
@@ -955,11 +986,11 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         # Use specified iterator type, save for when threshold is >= 1.
         # A threshold of >= 1 indicates all reads are to be returned, so no
         # sampling needed and seqential iterator will be used.
-        if iterator_type == 'sequential' or threshold >= 1:
+        if iterator_type == "sequential" or threshold >= 1:
             read_iterator = iterator
-        elif iterator_type == 'random':
+        elif iterator_type == "random":
             read_iterator = _random_read_iterator(iterator, threshold)
-        elif iterator_type == 'nth':
+        elif iterator_type == "nth":
             read_iterator = _nth_read_iterator(iterator, threshold)
 
         #
@@ -978,7 +1009,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
                 break
 
             # If not mapped, skip read.
-            is_mapped = (read.flag & 0x0004 == 0)
+            is_mapped = read.flag & 0x0004 == 0
             if not is_mapped:
                 unmapped += 1
                 continue
@@ -995,69 +1026,91 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
                 if qname in paired_pending:
                     # Found pair.
                     pair = paired_pending[qname]
-                    results.append([hash("%i_%s" % (pair['start'], qname)),
-                                    pair['start'],
-                                    read.pos + read_len,
-                                    qname,
-                                    [pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq']],
-                                    [read.pos, read.pos + read_len, read.cigar, strand, seq],
-                                    None, [pair['mapq'], read.mapq]])
+                    results.append(
+                        [
+                            hash("%i_%s" % (pair["start"], qname)),
+                            pair["start"],
+                            read.pos + read_len,
+                            qname,
+                            [pair["start"], pair["end"], pair["cigar"], pair["strand"], pair["seq"]],
+                            [read.pos, read.pos + read_len, read.cigar, strand, seq],
+                            None,
+                            [pair["mapq"], read.mapq],
+                        ]
+                    )
                     del paired_pending[qname]
                 else:
                     # Insert first of pair.
-                    paired_pending[qname] = {'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos,
-                                             'rlen': read_len, 'strand': strand, 'cigar': read.cigar, 'mapq': read.mapq}
+                    paired_pending[qname] = {
+                        "start": read.pos,
+                        "end": read.pos + read_len,
+                        "seq": seq,
+                        "mate_start": read.mpos,
+                        "rlen": read_len,
+                        "strand": strand,
+                        "cigar": read.cigar,
+                        "mapq": read.mapq,
+                    }
                     count += 1
             else:
-                results.append([hash("%i_%s" % (read.pos, qname)),
-                                read.pos, read.pos + read_len, qname,
-                                read.cigar, strand, read.seq, read.mapq])
+                results.append(
+                    [
+                        hash("%i_%s" % (read.pos, qname)),
+                        read.pos,
+                        read.pos + read_len,
+                        qname,
+                        read.cigar,
+                        strand,
+                        read.seq,
+                        read.mapq,
+                    ]
+                )
                 count += 1
 
         # Take care of reads whose mates are out of range.
         for qname, read in paired_pending.items():
-            if read['mate_start'] < read['start']:
+            if read["mate_start"] < read["start"]:
                 # Mate is before read.
-                read_start = read['mate_start']
-                read_end = read['end']
+                read_start = read["mate_start"]
+                read_end = read["end"]
                 # Make read_1 start=end so that length is 0 b/c we don't know
                 # read length.
-                r1 = [read['mate_start'], read['mate_start']]
-                r2 = [read['start'], read['end'], read['cigar'], read['strand'], read['seq']]
+                r1 = [read["mate_start"], read["mate_start"]]
+                r2 = [read["start"], read["end"], read["cigar"], read["strand"], read["seq"]]
             else:
                 # Mate is after read.
-                read_start = read['start']
+                read_start = read["start"]
                 # Make read_2 start=end so that length is 0 b/c we don't know
                 # read length. Hence, end of read is start of read_2.
-                read_end = read['mate_start']
-                r1 = [read['start'], read['end'], read['cigar'], read['strand'], read['seq']]
-                r2 = [read['mate_start'], read['mate_start']]
+                read_end = read["mate_start"]
+                r1 = [read["start"], read["end"], read["cigar"], read["strand"], read["seq"]]
+                r2 = [read["mate_start"], read["mate_start"]]
 
-            results.append([hash("%i_%s" % (read_start, qname)), read_start, read_end, qname, r1, r2, [read['mapq'], 125]])
+            results.append(
+                [hash("%i_%s" % (read_start, qname)), read_start, read_end, qname, r1, r2, [read["mapq"], 125]]
+            )
 
         # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data.
         # bamfile.close()
 
         def compress_seq_and_cigar(read, start_field, cigar_field, seq_field):
-            '''
+            """
             Use reference-based compression to compress read sequence and cigar.
-            '''
-            read_seq, read_cigar = get_ref_based_read_seq_and_cigar(read[seq_field].upper(),
-                                                                    read[start_field],
-                                                                    ref_seq.sequence,
-                                                                    ref_seq.start,
-                                                                    read[cigar_field])
+            """
+            read_seq, read_cigar = get_ref_based_read_seq_and_cigar(
+                read[seq_field].upper(), read[start_field], ref_seq.sequence, ref_seq.start, read[cigar_field]
+            )
             read[seq_field] = read_seq
             read[cigar_field] = read_cigar
 
         def convert_cigar(read, start_field, cigar_field, seq_field):
-            '''
+            """
             Convert read cigar from pysam format to string format.
-            '''
-            cigar_ops = 'MIDNSHP=X'
-            read_cigar = ''
+            """
+            cigar_ops = "MIDNSHP=X"
+            read_cigar = ""
             for op_tuple in read[cigar_field]:
-                read_cigar += '%i%s' % (op_tuple[1], cigar_ops[op_tuple[0]])
+                read_cigar += "%i%s" % (op_tuple[1], cigar_ops[op_tuple[0]])
             read[cigar_field] = read_cigar
 
         # Choose method for processing reads. Use reference-based compression
@@ -1083,18 +1136,18 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
 
         max_low, max_high = get_bounds(results, 1, 2)
 
-        return {'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high}
+        return {"data": results, "message": message, "max_low": max_low, "max_high": max_high}
 
 
 class SamDataProvider(BamDataProvider):
 
-    dataset_type = 'bai'
+    dataset_type = "bai"
 
     def __init__(self, converted_dataset=None, original_dataset=None, dependencies=None):
-        """ Create SamDataProvider. """
-        super().__init__(converted_dataset=converted_dataset,
-                         original_dataset=original_dataset,
-                         dependencies=dependencies)
+        """Create SamDataProvider."""
+        super().__init__(
+            converted_dataset=converted_dataset, original_dataset=original_dataset, dependencies=dependencies
+        )
 
         # To use BamDataProvider, original dataset must be BAM and
         # converted dataset must be BAI. Use BAI from BAM metadata.
@@ -1108,7 +1161,7 @@ class BBIDataProvider(GenomeDataProvider):
     BBI data provider for the Galaxy track browser.
     """
 
-    dataset_type = 'bigwig'
+    dataset_type = "bigwig"
 
     def _get_dataset(self) -> Tuple[IO[bytes], Union[BigBedFile, BigWigFile]]:
         ...
@@ -1119,8 +1172,9 @@ class BBIDataProvider(GenomeDataProvider):
 
     def has_data(self, chrom):
         f, bbi = self._get_dataset()
-        all_dat = bbi.query(chrom, 0, 2147483647, 1) or \
-            bbi.query(_convert_between_ucsc_and_ensemble_naming(chrom), 0, 2147483647, 1)
+        all_dat = bbi.query(chrom, 0, 2147483647, 1) or bbi.query(
+            _convert_between_ucsc_and_ensemble_naming(chrom), 0, 2147483647, 1
+        )
         f.close()
         return all_dat is not None
 
@@ -1131,8 +1185,9 @@ class BBIDataProvider(GenomeDataProvider):
         # Helper function for getting summary data regardless of chromosome
         # naming convention.
         def _summarize_bbi(bbi, chrom, start, end, num_points):
-            return bbi.summarize(chrom, start, end, num_points) or \
-                bbi.summarize(_convert_between_ucsc_and_ensemble_naming(chrom), start, end, num_points)
+            return bbi.summarize(chrom, start, end, num_points) or bbi.summarize(
+                _convert_between_ucsc_and_ensemble_naming(chrom), start, end, num_points
+            )
 
         # Bigwig can be a standalone bigwig file, in which case we use
         # original_dataset, or coming from wig->bigwig conversion in
@@ -1142,7 +1197,7 @@ class BBIDataProvider(GenomeDataProvider):
         # If stats requested, compute overall summary data for the range
         # start:endbut no reduced data. This is currently used by client
         # to determine the default range.
-        if 'stats' in kwargs:
+        if "stats" in kwargs:
             summary = _summarize_bbi(bbi, chrom, start, end, 1)
             f.close()
 
@@ -1167,11 +1222,11 @@ class BBIDataProvider(GenomeDataProvider):
             return dict(data=dict(min=min_val, max=max_val, mean=mean, sd=sd))
 
         def summarize_region(bbi, chrom, start, end, num_points):
-            '''
+            """
             Returns results from summarizing a region using num_points.
             NOTE: num_points cannot be greater than end - start or BBI
             will return None for all positions.
-            '''
+            """
             result = []
 
             # Get summary; this samples at intervals of length
@@ -1230,16 +1285,13 @@ class BBIDataProvider(GenomeDataProvider):
 
         # Cleanup and return.
         f.close()
-        return {
-            'data': result,
-            'dataset_type': self.dataset_type
-        }
+        return {"data": result, "dataset_type": self.dataset_type}
 
 
 class BigBedDataProvider(BBIDataProvider):
     def _get_dataset(self):
         # Nothing converts to bigBed so we don't consider converted dataset
-        f = open(self.original_dataset.file_name, 'rb')
+        f = open(self.original_dataset.file_name, "rb")
         return f, BigBedFile(file=f)
 
 
@@ -1251,9 +1303,9 @@ class BigWigDataProvider(BBIDataProvider):
 
     def _get_dataset(self):
         if self.converted_dataset is not None:
-            f = open(self.converted_dataset.file_name, 'rb')
+            f = open(self.converted_dataset.file_name, "rb")
         else:
-            f = open(self.original_dataset.file_name, 'rb')
+            f = open(self.original_dataset.file_name, "rb")
         return f, BigWigFile(file=f)
 
 
@@ -1261,13 +1313,14 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
     """
     Interval index files used for GFF, Pileup files.
     """
-    col_name_data_attr_mapping = {4: {'index': 4, 'name': 'Score'}}
 
-    dataset_type = 'interval_index'
+    col_name_data_attr_mapping = {4: {"index": 4, "name": "Score"}}
+
+    dataset_type = "interval_index"
 
     def write_data_to_file(self, regions, filename):
         index = Indexes(self.converted_dataset.file_name)
-        with open(self.original_dataset.file_name) as source, open(filename, 'w') as out:
+        with open(self.original_dataset.file_name) as source, open(filename, "w") as out:
             for region in regions:
                 # Write data from region.
                 chrom = region.chrom
@@ -1277,14 +1330,14 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
                     source.seek(offset)
 
                     # HACK: write differently depending on original dataset format.
-                    if self.original_dataset.ext not in ['gff', 'gff3', 'gtf']:
+                    if self.original_dataset.ext not in ["gff", "gff3", "gtf"]:
                         line = source.readline()
                         out.write(line)
                     else:
                         reader = GFFReaderWrapper(source, fix_strand=True)
                         feature = next(reader)
                         for interval in feature.intervals:
-                            out.write('\t'.join(interval.fields) + '\n')
+                            out.write("\t".join(interval.fields) + "\n")
 
     @contextmanager
     def open_data_file(self):
@@ -1311,7 +1364,7 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
             #
             # First three entries are mandatory, others are optional.
             filter_cols = loads(kwargs.get("filter_cols", "[]"))
-            no_detail = ("no_detail" in kwargs)
+            no_detail = "no_detail" in kwargs
             for count, val in enumerate(iterator):
                 offset = val[2]
                 if count < start_val:
@@ -1330,7 +1383,7 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
 
                 results.append(payload)
 
-        return {'data': results, 'message': message}
+        return {"data": results, "message": message}
 
 
 class RawGFFDataProvider(GenomeDataProvider):
@@ -1341,7 +1394,7 @@ class RawGFFDataProvider(GenomeDataProvider):
     for large datasets.
     """
 
-    dataset_type = 'interval_index'
+    dataset_type = "interval_index"
 
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         """
@@ -1380,7 +1433,7 @@ class RawGFFDataProvider(GenomeDataProvider):
         Process data from an iterator to a format that can be provided to client.
         """
         filter_cols = loads(kwargs.get("filter_cols", "[]"))
-        no_detail = ("no_detail" in kwargs)
+        no_detail = "no_detail" in kwargs
         results = []
         message = None
 
@@ -1395,7 +1448,7 @@ class RawGFFDataProvider(GenomeDataProvider):
             payload.insert(0, offset)
             results.append(payload)
 
-        return {'data': results, 'dataset_type': self.dataset_type, 'message': message}
+        return {"data": results, "dataset_type": self.dataset_type, "message": message}
 
 
 class GtfTabixDataProvider(TabixDataProvider):
@@ -1412,19 +1465,19 @@ class GtfTabixDataProvider(TabixDataProvider):
         features: Dict[str, List[GFFInterval]] = {}
 
         for line in iterator:
-            line_attrs = parse_gff_attributes(line.split('\t')[8])
-            transcript_id = line_attrs['transcript_id']
+            line_attrs = parse_gff_attributes(line.split("\t")[8])
+            transcript_id = line_attrs["transcript_id"]
             feature_list: List[GFFInterval]
             if transcript_id in features:
                 feature_list = features[transcript_id]
             else:
                 feature_list = []
                 features[transcript_id] = feature_list
-            feature_list.append(GFFInterval(None, line.split('\t')))
+            feature_list.append(GFFInterval(None, line.split("\t")))
 
         # Process data.
         filter_cols = loads(kwargs.get("filter_cols", "[]"))
-        no_detail = ("no_detail" in kwargs)
+        no_detail = "no_detail" in kwargs
         results = []
         message = None
 
@@ -1437,10 +1490,11 @@ class GtfTabixDataProvider(TabixDataProvider):
 
             feature = GFFFeature(None, intervals=intervals)
             payload = package_gff_feature(feature, no_detail=no_detail, filter_cols=filter_cols)
-            payload.insert(0, feature.intervals[0].attributes['transcript_id'])
+            payload.insert(0, feature.intervals[0].attributes["transcript_id"])
             results.append(payload)
 
-        return {'data': results, 'message': message}
+        return {"data": results, "message": message}
+
 
 #
 # -- ENCODE Peak data providers.
@@ -1472,7 +1526,7 @@ class ENCODEPeakDataProvider(GenomeDataProvider):
         #
         # First three entries are mandatory, others are optional.
         #
-        no_detail = ("no_detail" in kwargs)
+        no_detail = "no_detail" in kwargs
         rval = []
         message = None
         for count, line in enumerate(iterator):
@@ -1490,7 +1544,7 @@ class ENCODEPeakDataProvider(GenomeDataProvider):
                 hash(line),
                 # Add start, end.
                 int(feature[1]),
-                int(feature[2])
+                int(feature[2]),
             ]
 
             if no_detail:
@@ -1498,25 +1552,27 @@ class ENCODEPeakDataProvider(GenomeDataProvider):
                 continue
 
             # Extend with additional data.
-            payload.extend([
-                # Add name, strand.
-                feature[3],
-                feature[5],
-                # Thick start, end are feature start, end for now.
-                int(feature[1]),
-                int(feature[2]),
-                # No blocks.
-                None,
-                # Filtering data: Score, signalValue, pValue, qValue.
-                float(feature[4]),
-                float(feature[6]),
-                float(feature[7]),
-                float(feature[8])
-            ])
+            payload.extend(
+                [
+                    # Add name, strand.
+                    feature[3],
+                    feature[5],
+                    # Thick start, end are feature start, end for now.
+                    int(feature[1]),
+                    int(feature[2]),
+                    # No blocks.
+                    None,
+                    # Filtering data: Score, signalValue, pValue, qValue.
+                    float(feature[4]),
+                    float(feature[6]),
+                    float(feature[7]),
+                    float(feature[8]),
+                ]
+            )
 
             rval.append(payload)
 
-        return {'data': rval, 'message': message}
+        return {"data": rval, "message": message}
 
 
 class ENCODEPeakTabixDataProvider(TabixDataProvider, ENCODEPeakDataProvider):
@@ -1531,31 +1587,24 @@ class ENCODEPeakTabixDataProvider(TabixDataProvider, ENCODEPeakDataProvider):
         # HACK: first 8 fields are for drawing, so start filter column index at 9.
         filter_col = 8
         filters = []
-        filters.append({'name': 'Score',
-                        'type': 'number',
-                        'index': filter_col,
-                        'tool_id': 'Filter1',
-                        'tool_exp_name': 'c6'})
+        filters.append(
+            {"name": "Score", "type": "number", "index": filter_col, "tool_id": "Filter1", "tool_exp_name": "c6"}
+        )
         filter_col += 1
-        filters.append({'name': 'Signal Value',
-                        'type': 'number',
-                        'index': filter_col,
-                        'tool_id': 'Filter1',
-                        'tool_exp_name': 'c7'})
+        filters.append(
+            {"name": "Signal Value", "type": "number", "index": filter_col, "tool_id": "Filter1", "tool_exp_name": "c7"}
+        )
         filter_col += 1
-        filters.append({'name': 'pValue',
-                        'type': 'number',
-                        'index': filter_col,
-                        'tool_id': 'Filter1',
-                        'tool_exp_name': 'c8'})
+        filters.append(
+            {"name": "pValue", "type": "number", "index": filter_col, "tool_id": "Filter1", "tool_exp_name": "c8"}
+        )
         filter_col += 1
-        filters.append({'name': 'qValue',
-                        'type': 'number',
-                        'index': filter_col,
-                        'tool_id': 'Filter1',
-                        'tool_exp_name': 'c9'})
+        filters.append(
+            {"name": "qValue", "type": "number", "index": filter_col, "tool_id": "Filter1", "tool_exp_name": "c9"}
+        )
         return filters
 
+
 #
 # -- ChromatinInteraction data providers --
 #
@@ -1590,21 +1639,27 @@ class ChromatinInteractionsDataProvider(GenomeDataProvider):
                 # GUID is just a hash of the line
                 hash(line),
                 # Add start1, end1, chr2, start2, end2, value.
-                s1, e1, c, s2, e2, v
+                s1,
+                e1,
+                c,
+                s2,
+                e2,
+                v,
             ]
 
             rval.append(payload)
 
-        return {'data': rval, 'message': message}
+        return {"data": rval, "message": message}
 
     def get_default_max_vals(self):
         return 100000
 
 
 class ChromatinInteractionsTabixDataProvider(TabixDataProvider, ChromatinInteractionsDataProvider):
-    def get_iterator(self, data_file, chrom, start=0, end=sys.maxsize, interchromosomal=False, **kwargs) -> Iterator[str]:
-        """
-        """
+    def get_iterator(
+        self, data_file, chrom, start=0, end=sys.maxsize, interchromosomal=False, **kwargs
+    ) -> Iterator[str]:
+        """ """
         # Modify start as needed to get earlier interactions with start region.
         span = int(end) - int(start)
         filter_start = max(0, int(start) - span - span / 2)
@@ -1623,15 +1678,17 @@ class ChromatinInteractionsTabixDataProvider(TabixDataProvider, ChromatinInterac
                 # Check for interchromosal interactions.
                 if interchromosomal and c != chrom:
                     yield line
+
         return filter(TabixDataProvider.get_iterator(self, data_file, chrom, filter_start, end))
 
+
 #
 # -- Helper methods. --
 #
 
 
 def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_LIST_TYPE:
-    """ Package a GFF feature in an array for data providers. """
+    """Package a GFF feature in an array for data providers."""
     filter_cols = filter_cols or []
     feature = convert_gff_coords_to_bed(feature)
 
@@ -1640,14 +1697,16 @@ def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_L
         return [feature.start, feature.end]
 
     # Return full feature.
-    payload = [feature.start,
-               feature.end,
-               feature.name(),
-               feature.strand,
-               # No notion of thick start, end in GFF, so make everything
-               # thick.
-               feature.start,
-               feature.end]
+    payload = [
+        feature.start,
+        feature.end,
+        feature.name(),
+        feature.strand,
+        # No notion of thick start, end in GFF, so make everything
+        # thick.
+        feature.start,
+        feature.end,
+    ]
 
     # HACK: ignore interval with name 'transcript' from feature.
     # Cufflinks puts this interval in each of its transcripts,
@@ -1655,7 +1714,7 @@ def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_L
     # This interval will always be a feature's first interval,
     # and the GFF's third column is its feature name.
     feature_intervals = feature.intervals
-    if feature.intervals[0].fields[2] == 'transcript':
+    if feature.intervals[0].fields[2] == "transcript":
         feature_intervals = feature.intervals[1:]
     # Add blocks.
     block_sizes = [(interval.end - interval.start) for interval in feature_intervals]
@@ -1666,7 +1725,7 @@ def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_L
     # Add filter data to payload.
     for col in filter_cols:
         if col == "Score":
-            if feature.score == 'nan':
+            if feature.score == "nan":
                 payload.append(feature.score)
             else:
                 try:
@@ -1675,7 +1734,7 @@ def package_gff_feature(feature, no_detail=False, filter_cols=None) -> PAYLOAD_L
                 except Exception:
                     payload.append(feature.score)
         elif col in feature.attributes:
-            if feature.attributes[col] == 'nan':
+            if feature.attributes[col] == "nan":
                 payload.append(feature.attributes[col])
             else:
                 try:
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/__init__.py b/lib/galaxy/visualization/data_providers/phyloviz/__init__.py
index d869c5a6e7e..95726d69fa3 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/__init__.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/__init__.py
@@ -1,5 +1,8 @@
 """ Data providers code for PhyloViz """
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.phyloviz.newickparser import Newick_Parser
@@ -24,7 +27,7 @@ class PhylovizDataProvider(BaseDataProvider):
         file_name = self.original_dataset.file_name
         parseMsg = None
         jsonDicts = []
-        rval: Dict[str, Any] = {'dataset_type': self.dataset_type}
+        rval: Dict[str, Any] = {"dataset_type": self.dataset_type}
 
         if file_ext in ["newick", "nhx"]:  # parses newick files
             newickParser = Newick_Parser()
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
index 162a20c90b3..a552e0921b4 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
@@ -1,5 +1,8 @@
 import json
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 
 class Node:
@@ -33,19 +36,14 @@ class Node:
 
     def toJson(self) -> Dict[str, Any]:
         """Converts the data in the node to a dict representation of json"""
-        thisJson = {
-            "name": self.name,
-            "id": self.id,
-            "depth": self.depth,
-            "dist": self.length
-        }
+        thisJson = {"name": self.name, "id": self.id, "depth": self.depth, "dist": self.length}
         thisJson = self.addChildrenToJson(thisJson)
         thisJson = self.addMiscToJson(thisJson)
         return thisJson
 
     def addChildrenToJson(self, jsonDict):
         """Needs a special method to addChildren, such that the key does not appear in the Jsondict when the children is empty
-        this requirement is due to the layout algorithm used by d3 layout for hiding subtree """
+        this requirement is due to the layout algorithm used by d3 layout for hiding subtree"""
         if len(self.children) > 0:
             children = [node.toJson() for node in self.children]
             jsonDict["children"] = children
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
index 1328884805c..1c091d527d4 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
@@ -1,6 +1,9 @@
 import re
 
-from .baseparser import Base_Parser, PhyloTree
+from .baseparser import (
+    Base_Parser,
+    PhyloTree,
+)
 
 
 class Newick_Parser(Base_Parser):
@@ -37,7 +40,7 @@ class Newick_Parser(Base_Parser):
 
     def cleanNewickString(self, rawNewick):
         r"""removing semi colon, and illegal json characters (\,',") and white spaces"""
-        return re.sub(r'\s|;|\"|\'|\\', r'', rawNewick)
+        return re.sub(r"\s|;|\"|\'|\\", r"", rawNewick)
 
     def _makeNodesFromString(self, string, depth):
         """elements separated by comma could be empty"""
@@ -57,7 +60,7 @@ class Newick_Parser(Base_Parser):
                 length = nodeInfo[1]
                 # checking for bootstap values
                 name = nodeInfo[0]
-                try:    # Nexus may bootstrap in names position
+                try:  # Nexus may bootstrap in names position
                     name_as_float = float(name)
                     if 0 <= name_as_float <= 1:
                         bootstrap = name_as_float
@@ -67,7 +70,7 @@ class Newick_Parser(Base_Parser):
                 except ValueError:
                     name = nodeInfo[0]
             else:
-                name = nodeInfo[0]      # string only contains name
+                name = nodeInfo[0]  # string only contains name
             node = self.phyloTree.makeNode(name, length=length, depth=depth, bootstrap=bootstrap)
             childrenNodes += [node]
         return childrenNodes
@@ -83,14 +86,16 @@ class Newick_Parser(Base_Parser):
 
         for i in range(len(newickString)):
             if newickString[i] == "(" or newickString[i] == ",":
-                if re.match(r"[,(]", newickString[i + 1:]):
+                if re.match(r"[,(]", newickString[i + 1 :]):
                     continue
                 else:
                     end = i + 1
                     # i now refers to the starting position of the term to be replaced,
                     # we will next find j which is the ending pos of the term
                     for j in range(i + 1, len(newickString)):
-                        enclosingSymbol = newickString[j]   # the immediate symbol after a common or left bracket which denotes the end of a term
+                        enclosingSymbol = newickString[
+                            j
+                        ]  # the immediate symbol after a common or left bracket which denotes the end of a term
                         if enclosingSymbol == ")" or enclosingSymbol == ":" or enclosingSymbol == ",":
                             termToReplace = newickString[end:j]
 
@@ -119,16 +124,16 @@ class Newick_Parser(Base_Parser):
         if string.find("(") == -1:
             return self._makeNodesFromString(string, depth)
 
-        nodes = []      # nodes refer to the nodes on this level
+        nodes = []  # nodes refer to the nodes on this level
         start = 0
         lenOfPreceedingInternalNodeString = 0
         bracketStack = []
 
         for j in range(len(string)):
-            if string[j] == "(":    # finding the positions of all the open brackets
+            if string[j] == "(":  # finding the positions of all the open brackets
                 bracketStack.append(j)
                 continue
-            if string[j] == ")":    # finding the positions of all the closed brackets to extract claude
+            if string[j] == ")":  # finding the positions of all the closed brackets to extract claude
                 i = bracketStack.pop()
 
                 if len(bracketStack) == 0:  # is child of current node
@@ -136,13 +141,13 @@ class Newick_Parser(Base_Parser):
                     InternalNode = None
 
                     # First flat call to make nodes of the same depth but from the preceeding string.
-                    startSubstring = string[start + lenOfPreceedingInternalNodeString: i]
+                    startSubstring = string[start + lenOfPreceedingInternalNodeString : i]
                     preceedingNodes = self._makeNodesFromString(startSubstring, depth)
                     nodes += preceedingNodes
 
                     # Then We will try to see if the substring has any internal nodes first, make it then make nodes preceeding it and succeeding it.
                     if j + 1 < len(string):
-                        stringRightOfBracket = string[j + 1:]      # Eg. '(b:0.4,a:0.3)c:0.3, stringRightOfBracket = c:0.3
+                        stringRightOfBracket = string[j + 1 :]  # Eg. '(b:0.4,a:0.3)c:0.3, stringRightOfBracket = c:0.3
                         match = re.search(r"[\)\,\(]", stringRightOfBracket)
                         if match:
                             indexOfNextSymbol = match.start()
@@ -151,15 +156,17 @@ class Newick_Parser(Base_Parser):
                             if len(internalNodes) > 0:
                                 InternalNode = internalNodes[0]
                             lenOfPreceedingInternalNodeString = len(stringRepOfInternalNode)
-                        else:   # sometimes the node can be the last element of a string
-                            InternalNode = self._makeNodesFromString(string[j + 1:], depth)[0]
+                        else:  # sometimes the node can be the last element of a string
+                            InternalNode = self._makeNodesFromString(string[j + 1 :], depth)[0]
                             lenOfPreceedingInternalNodeString = len(string) - j
-                    if InternalNode is None:       # creating a generic node if it is unnamed
-                        InternalNode = self.phyloTree.makeNode("", depth=depth, isInternal=True)  # "internal-" + str(depth)
+                    if InternalNode is None:  # creating a generic node if it is unnamed
+                        InternalNode = self.phyloTree.makeNode(
+                            "", depth=depth, isInternal=True
+                        )  # "internal-" + str(depth)
                         lenOfPreceedingInternalNodeString = 0
 
                     # recussive call to make the internal claude
-                    childSubString = string[i + 1:j]
+                    childSubString = string[i + 1 : j]
                     InternalNode.addChildNode(self.parseNode(childSubString, depth + 1))
 
                     nodes.append(InternalNode)  # we append the internal node later to preserve order
@@ -167,12 +174,14 @@ class Newick_Parser(Base_Parser):
                     start = j + 1
                 continue
 
-        if depth == 0:    # if it's the root node, we do nothing about it and return
+        if depth == 0:  # if it's the root node, we do nothing about it and return
             return nodes[0]
 
         # Adding last most set of children
         endString = string[start:]
-        if string[start - 1] == ")":  # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse
+        if (
+            string[start - 1] == ")"
+        ):  # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse
             match = re.search(r"[\)\,\(]", endString)
             if match:
                 endOfNodeName = start + match.start() + 1
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
index 2fac57800f2..6d409fbb131 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
@@ -6,7 +6,6 @@ MAX_READLINES = 200000
 
 
 class Nexus_Parser(Newick_Parser):
-
     def __init__(self):
         super().__init__()
 
@@ -15,7 +14,7 @@ class Nexus_Parser(Newick_Parser):
         return self.parseNexus(filePath)
 
     def parseNexus(self, filename):
-        """ Nexus data is stored in blocks between a line starting with begin and another line starting with end;
+        """Nexus data is stored in blocks between a line starting with begin and another line starting with end;
         Commends inside square brackets are to be ignored,
         For more information: http://wiki.christophchamp.com/index.php/NEXUS_file_format
         Nexus can store multiple trees
@@ -25,10 +24,12 @@ class Nexus_Parser(Newick_Parser):
             nexlines = nex_file.readlines()
 
         rowCount = 0
-        inTreeBlock = False         # sentinel to check if we are in a tree block
-        intranslateBlock = False    # sentinel to check if we are in the translate region of the tree. Stores synonyms of the labellings
+        inTreeBlock = False  # sentinel to check if we are in a tree block
+        intranslateBlock = (
+            False  # sentinel to check if we are in the translate region of the tree. Stores synonyms of the labellings
+        )
         self.inCommentBlock = False
-        self.nameMapping = None       # stores mapping representation used in nexus format
+        self.nameMapping = None  # stores mapping representation used in nexus format
         treeNames = []
 
         for line in nexlines:
@@ -48,7 +49,7 @@ class Nexus_Parser(Newick_Parser):
 
             if inTreeBlock:
 
-                if "title" in lline:        # Adding title to the tree
+                if "title" in lline:  # Adding title to the tree
                     continue
 
                 if "translate" in lline:
@@ -58,7 +59,9 @@ class Nexus_Parser(Newick_Parser):
 
                 if intranslateBlock:
                     mappingLine = self.splitLinebyWhitespaces(line)
-                    key, value = mappingLine[1], mappingLine[2].replace(",", "").replace("'", "")    # replacing illegal json characters
+                    key, value = mappingLine[1], mappingLine[2].replace(",", "").replace(
+                        "'", ""
+                    )  # replacing illegal json characters
                     self.nameMapping[key] = value
 
                 # Extracting newick Trees
@@ -68,14 +71,14 @@ class Nexus_Parser(Newick_Parser):
                     treeLineCols = self.splitLinebyWhitespaces(line)
                     treeName, newick = treeLineCols[2], treeLineCols[-1]
 
-                    if newick == "":    # Empty lines can be found in tree blocks
+                    if newick == "":  # Empty lines can be found in tree blocks
                         continue
 
                     currPhyloTree = self._parseNewickToJson(newick, treeName, nameMap=self.nameMapping)
 
                     self.phyloTrees.append(currPhyloTree)
                     treeIndex = len(self.phyloTrees) - 1
-                    treeNames.append((treeName, treeIndex))    # appending name of tree, and its index
+                    treeNames.append((treeName, treeIndex))  # appending name of tree, and its index
                     continue
 
         return self.phyloTrees, treeNames
@@ -91,12 +94,12 @@ class Nexus_Parser(Newick_Parser):
                 if "]" not in line:
                     self.inCommentBlock = True
                 else:
-                    return "Nextline"   # need to move on to the nextline after getting out of comment
+                    return "Nextline"  # need to move on to the nextline after getting out of comment
         else:
             if "]" in line:
                 if line.rfind("[") > line.rfind("]"):
-                    pass                # a comment block is closed but another is open.
+                    pass  # a comment block is closed but another is open.
                 else:
                     self.inCommentBlock = False
-                    return "Nextline"   # need to move on to the nextline after getting out of comment
+                    return "Nextline"  # need to move on to the nextline after getting out of comment
         return ""
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
index 84ee9303597..1b7693d70bc 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
@@ -2,7 +2,7 @@ from galaxy.util import parse_xml
 from .baseparser import (
     Base_Parser,
     Node,
-    PhyloTree
+    PhyloTree,
 )
 
 
@@ -17,14 +17,16 @@ class Phyloxml_Parser(Base_Parser):
             "name": "name",
             "branch_length": "length",
             "confidence": "bootstrap",
-            "events": "events"
+            "events": "events",
         }
 
     def parseFile(self, filePath):
         """passes a file and extracts its Phylogeny Tree content."""
         xmlTree = parse_xml(filePath)
         xmlRoot = xmlTree.getroot()[0]
-        self.nameSpaceIndex = xmlRoot.tag.rfind("}") + 1  # used later by the clean tag method to remove the name space in every element.tag
+        self.nameSpaceIndex = (
+            xmlRoot.tag.rfind("}") + 1
+        )  # used later by the clean tag method to remove the name space in every element.tag
 
         phyloRoot = None
         for child in xmlRoot:
@@ -54,14 +56,14 @@ class Phyloxml_Parser(Base_Parser):
                 hasInnerClade = True
                 break
 
-        if hasInnerClade:       # this node is an internal node
+        if hasInnerClade:  # this node is an internal node
             currentNode = self._makeInternalNode(node, depth=depth)
             for child in node:
                 child = self.parseNode(child, depth + 1)
                 if isinstance(child, Node):
                     currentNode.addChildNode(child)
 
-        else:                   # this node is a leaf node
+        else:  # this node is a leaf node
             currentNode = self._makeLeafNode(node, depth=depth + 1)
 
         return currentNode
@@ -72,7 +74,7 @@ class Phyloxml_Parser(Base_Parser):
         for child in leafNode:
             childTag = self.cleanTag(child.tag)
             if childTag in self.tagsOfInterest:
-                key = self.tagsOfInterest[childTag]    # need to map phyloxml terms to ours
+                key = self.tagsOfInterest[childTag]  # need to map phyloxml terms to ours
                 node[key] = child.text
 
         node["depth"] = depth
@@ -84,11 +86,7 @@ class Phyloxml_Parser(Base_Parser):
         def getTagFromTaxonomyNode(node):
             """Returns the name of a taxonomy node. A taxonomy node have to be treated differently as the name
             is embedded one level deeper"""
-            phyloxmlTaxoNames = {
-                "common_name": "",
-                "scientific_name": "",
-                "code": ""
-            }
+            phyloxmlTaxoNames = {"common_name": "", "scientific_name": "", "code": ""}
             for child in node:
                 childTag = self.cleanTag(child.tag)
                 if childTag in phyloxmlTaxoNames:
@@ -108,7 +106,7 @@ class Phyloxml_Parser(Base_Parser):
         return nodeName
 
     def _makeInternalNode(self, internalNode, depth=0):
-        """ Makes an internal node from an element object that is guranteed to be a parent node.
+        """Makes an internal node from an element object that is guranteed to be a parent node.
         Gets the value of interests like events and appends it to a custom node object that will be passed to PhyloTree to make nodes
         """
         node = {}
@@ -117,7 +115,7 @@ class Phyloxml_Parser(Base_Parser):
             if childTag == "clade":
                 continue
             elif childTag in self.tagsOfInterest:
-                if childTag == "events":    # events is nested 1 more level deeper than others
+                if childTag == "events":  # events is nested 1 more level deeper than others
                     key, text = "events", self.cleanTag(child[0].tag)
                 else:
                     key = self.tagsOfInterest[childTag]
@@ -127,4 +125,4 @@ class Phyloxml_Parser(Base_Parser):
         return self.phyloTree.makeNode(self._getNodeName(internalNode, depth), **node)
 
     def cleanTag(self, tagString):
-        return tagString[self.nameSpaceIndex:]
+        return tagString[self.nameSpaceIndex :]
diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py
index c9caa10c80f..21ce1a6a970 100644
--- a/lib/galaxy/visualization/data_providers/registry.py
+++ b/lib/galaxy/visualization/data_providers/registry.py
@@ -1,24 +1,38 @@
-from typing import Dict, Optional, Type, Union
+from typing import (
+    Dict,
+    Optional,
+    Type,
+    Union,
+)
 
 from typing_extensions import Literal
 
-from galaxy.datatypes.data import Data, Newick, Nexus
+from galaxy.datatypes.data import (
+    Data,
+    Newick,
+    Nexus,
+)
 from galaxy.datatypes.interval import (
     Bed,
     ChromatinInteractions,
     ENCODEPeak,
     Gff,
     Gtf,
-    Interval
+    Interval,
+)
+from galaxy.datatypes.tabular import (
+    Tabular,
+    Vcf,
 )
-from galaxy.datatypes.tabular import Tabular, Vcf
 from galaxy.datatypes.xml import Phyloxml
 from galaxy.model import NoConverterException
 from galaxy.visualization.data_providers import genome
-from galaxy.visualization.data_providers.basic import BaseDataProvider, ColumnDataProvider
+from galaxy.visualization.data_providers.basic import (
+    BaseDataProvider,
+    ColumnDataProvider,
+)
 from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
 
-
 # a dict keyed on datatype with a 'default' string key.
 PROVIDER_BY_DATATYPE_CLASS_DICT = Dict[Union[Literal["default"], Type[Data]], Type[BaseDataProvider]]
 DATA_PROVIDER_BY_TYPE_NAME_DICT = Dict[str, Union[Type[BaseDataProvider], PROVIDER_BY_DATATYPE_CLASS_DICT]]
@@ -41,17 +55,17 @@ class DataProviderRegistry:
                 ENCODEPeak: genome.ENCODEPeakTabixDataProvider,
                 Interval: genome.IntervalTabixDataProvider,
                 ChromatinInteractions: genome.ChromatinInteractionsTabixDataProvider,
-                "default": genome.TabixDataProvider
+                "default": genome.TabixDataProvider,
             },
             "interval_index": genome.IntervalIndexDataProvider,
             "bai": genome.BamDataProvider,
             "bam": genome.SamDataProvider,
             "bigwig": genome.BigWigDataProvider,
             "bigbed": genome.BigBedDataProvider,
-            "column_with_stats": ColumnDataProvider
+            "column_with_stats": ColumnDataProvider,
         }
 
-    def get_data_provider(self, trans, name=None, source='data', raw=False, original_dataset=None):
+    def get_data_provider(self, trans, name=None, source="data", raw=False, original_dataset=None):
         """
         Returns data provider matching parameter values. For standalone data
         sources, source parameter is ignored.
@@ -100,9 +114,9 @@ class DataProviderRegistry:
                 else:
                     converted_dataset = original_dataset.get_converted_dataset(trans, name)
                     deps = original_dataset.get_converted_dataset_deps(trans, name)
-                    data_provider = data_provider_class(original_dataset=original_dataset,
-                                                        converted_dataset=converted_dataset,
-                                                        dependencies=deps)
+                    data_provider = data_provider_class(
+                        original_dataset=original_dataset, converted_dataset=converted_dataset, dependencies=deps
+                    )
 
             elif original_dataset:
                 # No name, so look up a provider name from datatype's information.
@@ -113,10 +127,10 @@ class DataProviderRegistry:
 
                 # Get data provider mapping and data provider.
                 data_provider_mapping = original_dataset.datatype.data_sources
-                if 'data_standalone' in data_provider_mapping:
-                    data_provider = self.get_data_provider(trans,
-                                                           name=data_provider_mapping['data_standalone'],
-                                                           original_dataset=original_dataset)
+                if "data_standalone" in data_provider_mapping:
+                    data_provider = self.get_data_provider(
+                        trans, name=data_provider_mapping["data_standalone"], original_dataset=original_dataset
+                    )
                 else:
                     source_list = data_provider_mapping[source]
                     if isinstance(source_list, str):
@@ -125,7 +139,9 @@ class DataProviderRegistry:
                     # Find a valid data provider in the source list.
                     for source in source_list:
                         try:
-                            data_provider = self.get_data_provider(trans, name=source, original_dataset=original_dataset)
+                            data_provider = self.get_data_provider(
+                                trans, name=source, original_dataset=original_dataset
+                            )
                             break
                         except NoConverterException:
                             pass
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 3624f087e3b..9931b889ddf 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -26,14 +26,14 @@ messages = Bunch(
     NO_TOOL="no tool",
     DATA="data",
     ERROR="error",
-    OK="ok"
+    OK="ok",
 )
 
 
 def decode_dbkey(dbkey):
-    """ Decodes dbkey and returns tuple ( username, dbkey )"""
-    if isinstance(dbkey, str) and ':' in dbkey:
-        return dbkey.split(':')
+    """Decodes dbkey and returns tuple ( username, dbkey )"""
+    if isinstance(dbkey, str) and ":" in dbkey:
+        return dbkey.split(":")
     else:
         return None, dbkey
 
@@ -54,24 +54,20 @@ class GenomeRegion:
 
     @staticmethod
     def from_dict(obj_dict):
-        return GenomeRegion(chrom=obj_dict['chrom'],
-                            start=obj_dict['start'],
-                            end=obj_dict['end'])
+        return GenomeRegion(chrom=obj_dict["chrom"], start=obj_dict["start"], end=obj_dict["end"])
 
     @staticmethod
     def from_str(obj_str):
         # check for gene region
-        gene_region = obj_str.split(':')
+        gene_region = obj_str.split(":")
 
         # split gene region into components
-        if (len(gene_region) == 2):
-            gene_interval = gene_region[1].split('-')
+        if len(gene_region) == 2:
+            gene_interval = gene_region[1].split("-")
 
             # check length
-            if (len(gene_interval) == 2):
-                return GenomeRegion(chrom=gene_region[0],
-                                    start=gene_interval[0],
-                                    end=gene_interval[1])
+            if len(gene_interval) == 2:
+                return GenomeRegion(chrom=gene_region[0], start=gene_interval[0], end=gene_interval[1])
 
         # return genome region instance
         return GenomeRegion()
@@ -94,7 +90,7 @@ class Genome:
         """
         # if there's no len_file, there's nothing to return
         if not self.len_file:
-            raise ReferenceDataError(f'len_file not set for {self.key}')
+            raise ReferenceDataError(f"len_file not set for {self.key}")
 
         def check_int(s):
             if s.isdigit():
@@ -103,7 +99,7 @@ class Genome:
                 return s
 
         def split_by_number(s):
-            return [check_int(c) for c in re.split('([0-9]+)', s)]
+            return [check_int(c) for c in re.split("([0-9]+)", s)]
 
         #
         # Parameter check, setting.
@@ -155,7 +151,7 @@ class Genome:
             else:
                 # Use low to start list.
                 high = low + int(num)
-                prev_chroms = (low != 0)
+                prev_chroms = low != 0
                 start_index = low
 
                 # Read chrom data from len file.
@@ -180,15 +176,15 @@ class Genome:
                 # No more chroms to read.
                 pass
 
-            to_sort = [{'chrom': chrm, 'len': length} for chrm, length in chroms.items()]
-            to_sort.sort(key=lambda _: split_by_number(_['chrom']))
+            to_sort = [{"chrom": chrm, "len": length} for chrm, length in chroms.items()]
+            to_sort.sort(key=lambda _: split_by_number(_["chrom"]))
             return {
-                'id': self.key,
-                'reference': self.twobit_file is not None,
-                'chrom_info': to_sort,
-                'prev_chroms': prev_chroms,
-                'next_chroms': next_chroms,
-                'start_index': start_index
+                "id": self.key,
+                "reference": self.twobit_file is not None,
+                "chrom_info": to_sort,
+                "prev_chroms": prev_chroms,
+                "next_chroms": next_chroms,
+                "start_index": start_index,
             }
 
 
@@ -202,7 +198,7 @@ class Genomes:
         # Create list of genomes from app.genome_builds
         self.genomes: Dict[str, Genome] = {}
         # Store internal versions of data tables for twobit and __dbkey__
-        self._table_versions = {'twobit': None, '__dbkeys__': None}
+        self._table_versions = {"twobit": None, "__dbkeys__": None}
         self.reload_genomes()
 
     def reload_genomes(self):
@@ -213,7 +209,7 @@ class Genomes:
             if table is not None:
                 self._table_versions[table_name] = table._loaded_content_version
 
-        twobit_table = self.app.tool_data_tables.get('twobit', None)
+        twobit_table = self.app.tool_data_tables.get("twobit", None)
         twobit_fields = {}
         if twobit_table is None:
             # Add genome data (twobit files) to genomes, directly from twobit.loc
@@ -239,7 +235,7 @@ class Genomes:
                     self.genomes[key].len_file = None
             # Add genome data (twobit files) to genomes.
             if twobit_table is not None:
-                self.genomes[key].twobit_file = twobit_table.get_entry('value', key, 'path', default=None)
+                self.genomes[key].twobit_file = twobit_table.get_entry("value", key, "path", default=None)
             elif key in twobit_fields:
                 self.genomes[key].twobit_file = twobit_fields[key]
 
@@ -251,7 +247,7 @@ class Genomes:
                 return self.reload_genomes()
 
     def get_build(self, dbkey):
-        """ Returns build for the given key. """
+        """Returns build for the given key."""
         self.check_and_reload()
         rval = None
         if dbkey in self.genomes:
@@ -259,23 +255,26 @@ class Genomes:
         return rval
 
     def get_dbkeys(self, user, chrom_info=False):
-        """ Returns all known dbkeys. If chrom_info is True, only dbkeys with
-            chromosome lengths are returned. """
+        """Returns all known dbkeys. If chrom_info is True, only dbkeys with
+        chromosome lengths are returned."""
         self.check_and_reload()
         dbkeys = []
 
         # Add user's custom keys to dbkeys.
-        if user and 'dbkeys' in user.preferences:
-            user_keys_dict = loads(user.preferences['dbkeys'])
-            dbkeys.extend([(attributes['name'], key) for key, attributes in user_keys_dict.items()])
+        if user and "dbkeys" in user.preferences:
+            user_keys_dict = loads(user.preferences["dbkeys"])
+            dbkeys.extend([(attributes["name"], key) for key, attributes in user_keys_dict.items()])
 
         # Add app keys to dbkeys.
 
         # If chrom_info is True, only include keys with len files (which contain chromosome info).
         if chrom_info:
+
             def filter_fn(b):
                 return b.len_file is not None
+
         else:
+
             def filter_fn(b):
                 return True
 
@@ -303,24 +302,30 @@ class Genomes:
         twobit_file = None
 
         # Look first in user's custom builds.
-        if dbkey_user and 'dbkeys' in dbkey_user.preferences:
-            user_keys = loads(dbkey_user.preferences['dbkeys'])
+        if dbkey_user and "dbkeys" in dbkey_user.preferences:
+            user_keys = loads(dbkey_user.preferences["dbkeys"])
             if dbkey in user_keys:
                 dbkey_attributes = user_keys[dbkey]
-                dbkey_name = dbkey_attributes['name']
+                dbkey_name = dbkey_attributes["name"]
 
                 # If there's a fasta for genome, convert to 2bit for later use.
-                if 'fasta' in dbkey_attributes:
-                    build_fasta = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dbkey_attributes['fasta'])
-                    len_file = build_fasta.get_converted_dataset(trans, 'len').file_name
-                    build_fasta.get_converted_dataset(trans, 'twobit')
+                if "fasta" in dbkey_attributes:
+                    build_fasta = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(
+                        dbkey_attributes["fasta"]
+                    )
+                    len_file = build_fasta.get_converted_dataset(trans, "len").file_name
+                    build_fasta.get_converted_dataset(trans, "twobit")
                     # HACK: set twobit_file to True rather than a file name because
                     # get_converted_dataset returns null during conversion even though
                     # there will eventually be a twobit file available for genome.
                     twobit_file = True
                 # Backwards compatibility: look for len file directly.
-                elif 'len' in dbkey_attributes:
-                    len_file = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(user_keys[dbkey]['len']).file_name
+                elif "len" in dbkey_attributes:
+                    len_file = (
+                        trans.sa_session.query(trans.app.model.HistoryDatasetAssociation)
+                        .get(user_keys[dbkey]["len"])
+                        .file_name
+                    )
                 if len_file:
                     genome = Genome(dbkey, dbkey_name, len_file=len_file, twobit_file=twobit_file)
 
@@ -335,7 +340,7 @@ class Genomes:
                 genome = self.genomes[dbkey]
 
         if not genome:
-            raise ObjectNotFound(f'genome not found for key {dbkey}')
+            raise ObjectNotFound(f"genome not found for key {dbkey}")
 
         return genome.to_dict(num=num, chrom=chrom, low=low)
 
@@ -351,11 +356,11 @@ class Genomes:
             return True
 
         # Look for key in owner's custom builds.
-        if dbkey_owner and 'dbkeys' in dbkey_owner.preferences:
-            user_keys = loads(dbkey_owner.preferences['dbkeys'])
+        if dbkey_owner and "dbkeys" in dbkey_owner.preferences:
+            user_keys = loads(dbkey_owner.preferences["dbkeys"])
             if dbkey in user_keys:
                 dbkey_attributes = user_keys[dbkey]
-                if 'fasta' in dbkey_attributes:
+                if "fasta" in dbkey_attributes:
                     # Fasta + converted datasets can provide reference data.
                     return True
 
@@ -384,14 +389,16 @@ class Genomes:
             # Built-in twobit.
             twobit_file_name = self.genomes[dbkey].twobit_file
         else:
-            user_keys = loads(dbkey_user.preferences['dbkeys'])
+            user_keys = loads(dbkey_user.preferences["dbkeys"])
             dbkey_attributes = user_keys[dbkey]
-            fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dbkey_attributes['fasta'])
-            msg = fasta_dataset.convert_dataset(trans, 'twobit')
+            fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(
+                dbkey_attributes["fasta"]
+            )
+            msg = fasta_dataset.convert_dataset(trans, "twobit")
             if msg:
                 return msg
             else:
-                twobit_dataset = fasta_dataset.get_converted_dataset(trans, 'twobit')
+                twobit_dataset = fasta_dataset.get_converted_dataset(trans, "twobit")
                 twobit_file_name = twobit_dataset.file_name
 
         return self._get_reference_data(twobit_file_name, chrom, low, high)
@@ -399,7 +406,7 @@ class Genomes:
     @staticmethod
     def _get_reference_data(twobit_file_name, chrom, low, high):
         # Read and return reference data.
-        with open(twobit_file_name, 'rb') as f:
+        with open(twobit_file_name, "rb") as f:
             twobit = TwoBitFile(f)
             if chrom in twobit:
                 seq_data = twobit[chrom].get(int(low), int(high))
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index 29b345fc65c..240cf3eca11 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -1,5 +1,9 @@
 import logging
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 
 import galaxy.model
 from galaxy.util import asbool
@@ -27,10 +31,11 @@ class VisualizationsConfigParser:
             -- what provides the data
             -- what information needs to be added to the query string
     """
+
     #: what are the allowed 'entry_point_type' for entry_point elements
-    ALLOWED_ENTRY_POINT_TYPES = ['mako', 'html', 'script', 'chart']
+    ALLOWED_ENTRY_POINT_TYPES = ["mako", "html", "script", "chart"]
     #: what are the allowed href targets when clicking on a visualization anchor
-    VALID_RENDER_TARGETS = ['galaxy_main', '_top', '_blank']
+    VALID_RENDER_TARGETS = ["galaxy_main", "_top", "_blank"]
 
     def __init__(self):
         # what parsers should be used for sub-components
@@ -56,64 +61,64 @@ class VisualizationsConfigParser:
 
         # main tag specifies plugin type (visualization or
         # interactive_enviornment).
-        returned['plugin_type'] = xml_tree.tag
+        returned["plugin_type"] = xml_tree.tag
 
         # a text display name for end user links
-        returned['name'] = xml_tree.attrib.get('name', None)
-        if not returned['name']:
-            raise ParsingException('Visualization needs a name attribute.')
+        returned["name"] = xml_tree.attrib.get("name", None)
+        if not returned["name"]:
+            raise ParsingException("Visualization needs a name attribute.")
 
         # allow manually turning off a vis by checking for a disabled property
-        if 'disabled' in xml_tree.attrib:
-            log.info('Visualizations plugin disabled: %s. Skipping...', returned['name'])
+        if "disabled" in xml_tree.attrib:
+            log.info("Visualizations plugin disabled: %s. Skipping...", returned["name"])
             return None
 
         # record the embeddable flag - defaults to true
-        returned['embeddable'] = True
-        if 'embeddable' in xml_tree.attrib:
-            returned['embeddable'] = asbool(xml_tree.attrib.get('embeddable'))
+        returned["embeddable"] = True
+        if "embeddable" in xml_tree.attrib:
+            returned["embeddable"] = asbool(xml_tree.attrib.get("embeddable"))
 
         # a (for now) text description of what the visualization does
-        description = xml_tree.find('description')
-        returned['description'] = description.text.strip() if description is not None else None
+        description = xml_tree.find("description")
+        returned["description"] = description.text.strip() if description is not None else None
 
         # data_sources are the kinds of objects/data associated with the visualization
         #   e.g. views on HDAs can use this to find out what visualizations are applicable to them
         data_sources = []
-        data_sources_confs = xml_tree.find('data_sources')
-        for data_source_conf in data_sources_confs.findall('data_source'):
+        data_sources_confs = xml_tree.find("data_sources")
+        for data_source_conf in data_sources_confs.findall("data_source"):
             data_source = self.data_source_parser.parse(data_source_conf)
             if data_source:
                 data_sources.append(data_source)
         # data_sources are not required
         if not data_sources:
-            raise ParsingException('No valid data_sources for visualization')
-        returned['data_sources'] = data_sources
+            raise ParsingException("No valid data_sources for visualization")
+        returned["data_sources"] = data_sources
 
         # TODO: this is effectively required due to param_confs.findall( 'param' )
         # parameters spell out how to convert query string params into resources and data
         #   that will be parsed, fetched, etc. and passed to the template
         # list or dict? ordered or not?
         params = {}
-        param_confs = xml_tree.find('params')
-        param_elements = param_confs.findall('param') if param_confs is not None else []
+        param_confs = xml_tree.find("params")
+        param_elements = param_confs.findall("param") if param_confs is not None else []
         for param_conf in param_elements:
             param = self.param_parser.parse(param_conf)
             if param:
                 params[param_conf.text] = param
         # params are not required
         if params:
-            returned['params'] = params
+            returned["params"] = params
 
         # param modifiers provide extra information for other params (e.g. hda_ldda='hda' -> dataset_id is an hda id)
         # store these modifiers in a 2-level dictionary { target_param: { param_modifier_key: { param_mod_data }
         # ugh - wish we didn't need these
         param_modifiers: Dict[str, Any] = {}
-        param_modifier_elements = param_confs.findall('param_modifier') if param_confs is not None else []
+        param_modifier_elements = param_confs.findall("param_modifier") if param_confs is not None else []
         for param_modifier_conf in param_modifier_elements:
             param_modifier = self.param_modifier_parser.parse(param_modifier_conf)
             # param modifiers map accrd. to the params they modify (for faster lookup)
-            target_param = param_modifier_conf.get('modifies')
+            target_param = param_modifier_conf.get("modifies")
             param_modifier_key = param_modifier_conf.text
             if param_modifier and target_param in params:
                 # multiple params can modify a single, other param,
@@ -124,40 +129,39 @@ class VisualizationsConfigParser:
 
         # not required
         if param_modifiers:
-            returned['param_modifiers'] = param_modifiers
+            returned["param_modifiers"] = param_modifiers
 
         # entry_point: how will this plugin render/load? mako, script tag, or static html file?
-        returned['entry_point'] = self.parse_entry_point(xml_tree)
+        returned["entry_point"] = self.parse_entry_point(xml_tree)
 
         # link_text: the string to use for the text of any links/anchors to this visualization
-        link_text = xml_tree.find('link_text')
+        link_text = xml_tree.find("link_text")
         if link_text is not None and link_text.text:
-            returned['link_text'] = link_text
+            returned["link_text"] = link_text
 
         # render_target: where in the browser to open the rendered visualization
         # defaults to: galaxy_main
-        render_target = xml_tree.find('render_target')
-        if((render_target is not None and render_target.text)
-                and (render_target.text in self.VALID_RENDER_TARGETS)):
-            returned['render_target'] = render_target.text
+        render_target = xml_tree.find("render_target")
+        if (render_target is not None and render_target.text) and (render_target.text in self.VALID_RENDER_TARGETS):
+            returned["render_target"] = render_target.text
         else:
-            returned['render_target'] = 'galaxy_main'
+            returned["render_target"] = "galaxy_main"
         # consider unifying the above into its own element and parsing method
 
         # load optional custom configuration specifiers
-        specs_section = xml_tree.find('specs')
+        specs_section = xml_tree.find("specs")
         if specs_section is not None:
-            returned['specs'] = DictParser(specs_section)
+            returned["specs"] = DictParser(specs_section)
 
         # load group specifiers
-        groups_section = xml_tree.find('groups')
+        groups_section = xml_tree.find("groups")
         if groups_section is not None:
-            returned['groups'] = ListParser(groups_section)
+            returned["groups"] = ListParser(groups_section)
 
         # load settings specifiers
-        settings_section = xml_tree.find('settings')
+        settings_section = xml_tree.find("settings")
         if settings_section is not None:
-            returned['settings'] = ListParser(settings_section)
+            returned["settings"] = ListParser(settings_section)
 
         return returned
 
@@ -168,30 +172,22 @@ class VisualizationsConfigParser:
         the element.
         """
         # (older) mako-only syntax: the template to use in rendering the visualization
-        template = xml_tree.find('template')
+        template = xml_tree.find("template")
         if template is not None and template.text:
-            log.info('template syntax is deprecated: use entry_point instead')
-            return {
-                'type': 'mako',
-                'file': template.text,
-                'attr': {}
-            }
+            log.info("template syntax is deprecated: use entry_point instead")
+            return {"type": "mako", "file": template.text, "attr": {}}
 
         # need one of the two: (the deprecated) template or entry_point
-        entry_point = xml_tree.find('entry_point')
+        entry_point = xml_tree.find("entry_point")
         if entry_point is None:
-            raise ParsingException('template or entry_point required')
+            raise ParsingException("template or entry_point required")
 
         # parse by returning a sub-object and simply copying any attributes unused here
         entry_point_attrib = dict(entry_point.attrib)
-        entry_point_type = entry_point_attrib.pop('entry_point_type', 'mako')
+        entry_point_type = entry_point_attrib.pop("entry_point_type", "mako")
         if entry_point_type not in self.ALLOWED_ENTRY_POINT_TYPES:
             raise ParsingException(f"Unknown entry_point type: {entry_point_type}")
-        return {
-            'type': entry_point_type,
-            'file': entry_point.text,
-            'attr': entry_point_attrib
-        }
+        return {"type": entry_point_type, "file": entry_point.text, "attr": entry_point_attrib}
 
 
 # -------------------------------------------------------------------
@@ -204,19 +200,14 @@ class DataSourceParser:
     data for the visualization to consume (e.g. HDAs, LDDAs, Jobs, Users, etc.).
     There can be more than one data_source associated with a visualization.
     """
+
     # these are the allowed classes to associate visualizations with (as strings)
     #   any model_class element not in this list will throw a parsing ParsingExcepion
-    ALLOWED_MODEL_CLASSES = [
-        'Visualization',
-        'HistoryDatasetAssociation',
-        'LibraryDatasetDatasetAssociation'
-    ]
-    ATTRIBUTE_SPLIT_CHAR = '.'
+    ALLOWED_MODEL_CLASSES = ["Visualization", "HistoryDatasetAssociation", "LibraryDatasetDatasetAssociation"]
+    ATTRIBUTE_SPLIT_CHAR = "."
     # these are the allowed object attributes to use in data source tests
     #   any attribute element not in this list will throw a parsing ParsingExcepion
-    ALLOWED_DATA_SOURCE_ATTRIBUTES = [
-        'datatype'
-    ]
+    ALLOWED_DATA_SOURCE_ATTRIBUTES = ["datatype"]
 
     def parse(self, xml_tree):
         """
@@ -225,20 +216,20 @@ class DataSourceParser:
         """
         returned = {}
         # model_class (required, only one) - look up and convert model_class to actual galaxy model class
-        model_class = self.parse_model_class(xml_tree.find('model_class'))
+        model_class = self.parse_model_class(xml_tree.find("model_class"))
         if not model_class:
-            raise ParsingException('data_source needs a model class')
-        returned['model_class'] = model_class
+            raise ParsingException("data_source needs a model class")
+        returned["model_class"] = model_class
 
         # tests (optional, 0 or more) - data for boolean test: 'is the visualization usable by this object?'
         # when no tests are given, default to isinstance( object, model_class )
-        returned['tests'] = self.parse_tests(xml_tree.findall('test'))
+        returned["tests"] = self.parse_tests(xml_tree.findall("test"))
 
         # to_params (optional, 0 or more) - tells the registry to set certain params based on the model_clas, tests
-        returned['to_params'] = {}
-        to_params = self.parse_to_params(xml_tree.findall('to_param'))
+        returned["to_params"] = {}
+        to_params = self.parse_to_params(xml_tree.findall("to_param"))
         if to_params:
-            returned['to_params'] = to_params
+            returned["to_params"] = to_params
 
         return returned
 
@@ -251,11 +242,11 @@ class DataSourceParser:
         The model_class string must be in ALLOWED_MODEL_CLASSES.
         """
         if xml_tree is None or not xml_tree.text:
-            raise ParsingException('data_source entry requires a model_class')
+            raise ParsingException("data_source entry requires a model_class")
 
         if xml_tree.text not in self.ALLOWED_MODEL_CLASSES:
             # log.debug( 'available data_source model_classes: %s' %( str( self.ALLOWED_MODEL_CLASSES ) ) )
-            raise ParsingException(f'Invalid data_source model_class: {xml_tree.text}')
+            raise ParsingException(f"Invalid data_source model_class: {xml_tree.text}")
 
         # look up the model from the model module returning an empty data_source if not found
         model_class = getattr(galaxy.model, xml_tree.text, None)
@@ -292,45 +283,47 @@ class DataSourceParser:
             return tests
 
         for test_elem in xml_tree_list:
-            test_type = test_elem.get('type', 'eq')
+            test_type = test_elem.get("type", "eq")
             test_result = test_elem.text.strip() if test_elem.text else None
             if not test_type or not test_result:
-                log.warning('Skipping test. Needs both type attribute and text node to be parsed: '
-                          + f'{test_type}, {test_elem.text}')
+                log.warning(
+                    "Skipping test. Needs both type attribute and text node to be parsed: "
+                    + f"{test_type}, {test_elem.text}"
+                )
                 continue
             test_result = test_result.strip()
 
             # test_attr can be a dot separated chain of object attributes (e.g. dataset.datatype) - convert to list
             # TODO: too dangerous - constrain these to some allowed list
             # TODO: does this err if no test_attr - it should...
-            test_attr = test_elem.get('test_attr')
+            test_attr = test_elem.get("test_attr")
             test_attr = test_attr.split(self.ATTRIBUTE_SPLIT_CHAR) if isinstance(test_attr, str) else []
             # log.debug( 'test_type: %s, test_attr: %s, test_result: %s', test_type, test_attr, test_result )
 
             # build a lambda function that gets the desired attribute to test
             getter = self._build_getattr_lambda(test_attr)
             # result type should tell the registry how to convert the result before the test
-            test_result_type = test_elem.get('result_type', 'string')
+            test_result_type = test_elem.get("result_type", "string")
 
             # test functions should be sent an object to test, and the parsed result expected from the test
-            if test_type == 'isinstance':
+            if test_type == "isinstance":
                 # is test_attr attribute an instance of result
                 # TODO: wish we could take this further but it would mean passing in the datatypes_registry
                 def test_fn(o, result):
                     return isinstance(getter(o), result)
 
-            elif test_type == 'has_dataprovider':
+            elif test_type == "has_dataprovider":
                 # does the object itself have a datatype attr and does that datatype have the given dataprovider
                 def test_fn(o, result):
-                    return (hasattr(getter(o), 'has_dataprovider')
-                            and getter(o).has_dataprovider(result))
+                    return hasattr(getter(o), "has_dataprovider") and getter(o).has_dataprovider(result)
 
-            elif test_type == 'has_attribute':
+            elif test_type == "has_attribute":
                 # does the object itself have attr in 'result' (no equivalence checking)
                 def test_fn(o, result):
                     return hasattr(getter(o), result)
 
-            elif test_type == 'not_eq':
+            elif test_type == "not_eq":
+
                 def test_fn(o, result):
                     return str(getter(o)) != result
 
@@ -339,12 +332,7 @@ class DataSourceParser:
                 def test_fn(o, result):
                     return str(getter(o)) == result
 
-            tests.append({
-                'type': test_type,
-                'result': test_result,
-                'result_type': test_result_type,
-                'fn': test_fn
-            })
+            tests.append({"type": test_type, "result": test_result, "result_type": test_result_type, "fn": test_fn})
 
         return tests
 
@@ -362,24 +350,24 @@ class DataSourceParser:
             # param_name required
             param_name = element.text
             if not param_name:
-                raise ParsingException('to_param requires text (the param name)')
+                raise ParsingException("to_param requires text (the param name)")
 
             param = {}
             # assign is a shortcut param_attr that assigns a value to a param (as text)
-            assign = element.get('assign')
+            assign = element.get("assign")
             if assign is not None:
-                param['assign'] = assign
+                param["assign"] = assign
 
             # param_attr is the attribute of the object (that the visualization will be applied to)
             #   that should be converted into a query param (e.g. param_attr="id" -> dataset_id)
             # TODO:?? use the build attr getter here?
             # simple (1 lvl) attrs for now
-            param_attr = element.get('param_attr')
+            param_attr = element.get("param_attr")
             if param_attr is not None:
-                param['param_attr'] = param_attr
+                param["param_attr"] = param_attr
             # element must have either param_attr or assign? what about no params (the object itself)
             if not param_attr and not assign:
-                raise ParsingException('to_param requires either assign or param_attr attributes: %s', param_name)
+                raise ParsingException("to_param requires either assign or param_attr attributes: %s", param_name)
 
             # TODO: consider making the to_param name an attribute (param="hda_ldda") and the text what would
             #           be used for the conversion - this would allow CDATA values to be passed
@@ -396,6 +384,7 @@ class ListParser(list):
     Converts a xml structure into an array
     See: http://code.activestate.com/recipes/410469-xml-as-dictionary/
     """
+
     def __init__(self, aList):
         for element in aList:
             if len(element) > 0:
@@ -414,6 +403,7 @@ class DictParser(dict):
     Converts a xml structure into a dictionary
     See: http://code.activestate.com/recipes/410469-xml-as-dictionary/
     """
+
     def __init__(self, parent_element):
         if parent_element.items():
             self.update(dict(parent_element.items()))
@@ -442,7 +432,8 @@ class ParamParser:
     params are parameters that will be parsed (based on their `type`, etc.)
     and sent to the visualization template by controllers.visualization.render.
     """
-    DEFAULT_PARAM_TYPE = 'str'
+
+    DEFAULT_PARAM_TYPE = "str"
 
     def parse(self, xml_tree):
         """
@@ -453,37 +444,37 @@ class ParamParser:
         # don't store key, just check it
         param_key = xml_tree.text
         if not param_key:
-            raise ParsingException('Param entry requires text')
+            raise ParsingException("Param entry requires text")
 
-        returned['type'] = self.parse_param_type(xml_tree)
+        returned["type"] = self.parse_param_type(xml_tree)
 
         # is the parameter required in the template and,
         #   if not, what is the default value?
-        required = xml_tree.get('required') == "true"
-        returned['required'] = required
+        required = xml_tree.get("required") == "true"
+        returned["required"] = required
         if not required:
             # default defaults to None
             default = None
-            if 'default' in xml_tree.attrib:
-                default = xml_tree.get('default')
+            if "default" in xml_tree.attrib:
+                default = xml_tree.get("default")
                 # convert default based on param_type here
-            returned['default'] = default
+            returned["default"] = default
 
         # does the param have to be within a list of certain values
         # NOTE: the interpretation of this list is deferred till parsing and based on param type
         #   e.g. it could be 'val in constrain_to', or 'constrain_to is min, max for number', etc.
         # TODO: currently unused
-        constrain_to = xml_tree.get('constrain_to')
+        constrain_to = xml_tree.get("constrain_to")
         if constrain_to:
-            returned['constrain_to'] = constrain_to.split(',')
+            returned["constrain_to"] = constrain_to.split(",")
 
         # is the param a comma-separated-value list?
-        returned['csv'] = xml_tree.get('csv') == "true"
+        returned["csv"] = xml_tree.get("csv") == "true"
 
         # remap keys in the params/query string to the var names used in the template
-        var_name_in_template = xml_tree.get('var_name_in_template')
+        var_name_in_template = xml_tree.get("var_name_in_template")
         if var_name_in_template:
-            returned['var_name_in_template'] = var_name_in_template
+            returned["var_name_in_template"] = var_name_in_template
 
         return returned
 
@@ -492,7 +483,7 @@ class ParamParser:
         Parse a param type from the given `xml_tree`.
         """
         # default to string as param_type
-        param_type = xml_tree.get('type') or self.DEFAULT_PARAM_TYPE
+        param_type = xml_tree.get("type") or self.DEFAULT_PARAM_TYPE
         # TODO: set parsers and validaters, convert here
         return param_type
 
@@ -510,7 +501,7 @@ class ParamModifierParser(ParamParser):
 
     def parse(self, element):
         # modifies is required
-        modifies = element.get('modifies')
+        modifies = element.get("modifies")
         if not modifies:
             raise ParsingException('param_modifier entry requires a target param key (attribute "modifies")')
         returned = super().parse(element)
diff --git a/lib/galaxy/visualization/plugins/interactive_environments.py b/lib/galaxy/visualization/plugins/interactive_environments.py
index 713d679ac2f..db11ead565b 100644
--- a/lib/galaxy/visualization/plugins/interactive_environments.py
+++ b/lib/galaxy/visualization/plugins/interactive_environments.py
@@ -9,37 +9,43 @@ import stat
 import tempfile
 import uuid
 from itertools import product
-from subprocess import PIPE, Popen
+from subprocess import (
+    PIPE,
+    Popen,
+)
 from sys import platform as _platform
 
 import yaml
 
-from galaxy import model, web
+from galaxy import (
+    model,
+    web,
+)
 from galaxy.containers import ContainerPort
 from galaxy.containers.docker_model import DockerVolume
 from galaxy.managers import api_keys
 from galaxy.util import (
     string_as_bool_or_none,
-    unicodify
+    unicodify,
 )
 from galaxy.util.bunch import Bunch
 
-
 IS_OS_X = _platform == "darwin"
-CONTAINER_NAME_PREFIX = 'gie_'
-ENV_OVERRIDE_CAPITALIZE = frozenset({
-    'notebook_username',
-    'notebook_password',
-    'dataset_hid',
-    'dataset_filename',
-    'additional_ids',
-})
+CONTAINER_NAME_PREFIX = "gie_"
+ENV_OVERRIDE_CAPITALIZE = frozenset(
+    {
+        "notebook_username",
+        "notebook_password",
+        "dataset_hid",
+        "dataset_filename",
+        "additional_ids",
+    }
+)
 
 log = logging.getLogger(__name__)
 
 
 class InteractiveEnvironmentRequest:
-
     def __init__(self, trans, plugin):
         self.trans = trans
         self.log = log
@@ -59,7 +65,7 @@ class InteractiveEnvironmentRequest:
         # Store our template and configuration path
         self.attr.our_config_dir = os.path.join(plugin_path, "config")
         self.attr.our_template_dir = os.path.join(plugin_path, "templates")
-        self.attr.HOST = trans.request.host.rsplit(':', 1)[0]
+        self.attr.HOST = trans.request.host.rsplit(":", 1)[0]
 
         self.load_deploy_config()
         self.load_allowed_images()
@@ -87,44 +93,49 @@ class InteractiveEnvironmentRequest:
 
         # This duplicates the logic in the proxy manager
         if self.attr.galaxy_config.dynamic_proxy_external_proxy:
-            self.attr.proxy_prefix = '/'.join(
+            self.attr.proxy_prefix = "/".join(
                 (
-                    '',
-                    trans.cookie_path.strip('/'),
-                    self.attr.galaxy_config.dynamic_proxy_prefix.strip('/'),
+                    "",
+                    trans.cookie_path.strip("/"),
+                    self.attr.galaxy_config.dynamic_proxy_prefix.strip("/"),
                     self.attr.viz_id,
                 )
             )
         else:
-            self.attr.proxy_prefix = ''
+            self.attr.proxy_prefix = ""
         # If cookie_path is unset (thus '/'), the proxy prefix ends up with
         # multiple leading '/' characters, which will cause the client to
         # request resources from http://dynamic_proxy_prefix
-        if self.attr.proxy_prefix.startswith('/'):
+        if self.attr.proxy_prefix.startswith("/"):
             self.attr.proxy_prefix = f"/{self.attr.proxy_prefix.lstrip('/')}"
 
-        assert not self.attr.container_interface \
-            or not self.attr.container_interface.publish_port_list_required \
-            or (self.attr.container_interface.publish_port_list_required and self.attr.docker_connect_port is not None), \
-            "Error: Container interface requires publish port list but docker_connect_port is not set"
+        assert (
+            not self.attr.container_interface
+            or not self.attr.container_interface.publish_port_list_required
+            or (self.attr.container_interface.publish_port_list_required and self.attr.docker_connect_port is not None)
+        ), "Error: Container interface requires publish port list but docker_connect_port is not set"
 
     def load_allowed_images(self):
-        if os.path.exists(os.path.join(self.attr.our_config_dir, 'allowed_images.yml')):
-            fn = os.path.join(self.attr.our_config_dir, 'allowed_images.yml')
-        elif os.path.exists(os.path.join(self.attr.our_config_dir, 'allowed_images.yml.sample')):
-            fn = os.path.join(self.attr.our_config_dir, 'allowed_images.yml.sample')
+        if os.path.exists(os.path.join(self.attr.our_config_dir, "allowed_images.yml")):
+            fn = os.path.join(self.attr.our_config_dir, "allowed_images.yml")
+        elif os.path.exists(os.path.join(self.attr.our_config_dir, "allowed_images.yml.sample")):
+            fn = os.path.join(self.attr.our_config_dir, "allowed_images.yml.sample")
         else:
             # If we don't have an allowed images, then we fall back to image
             # name specified in the .ini file
             try:
-                self.allowed_images = [self.attr.viz_config.get('docker', 'image')]
-                self.default_image = self.attr.viz_config.get('docker', 'image')
+                self.allowed_images = [self.attr.viz_config.get("docker", "image")]
+                self.default_image = self.attr.viz_config.get("docker", "image")
                 return
             except AttributeError:
-                raise Exception("[{0}] Could not find allowed_images.yml, or image tag in {0}.ini file for ".format(self.attr.viz_id))
+                raise Exception(
+                    "[{0}] Could not find allowed_images.yml, or image tag in {0}.ini file for ".format(
+                        self.attr.viz_id
+                    )
+                )
 
         with open(fn) as handle:
-            self.allowed_images = [x['image'] for x in yaml.safe_load(handle)]
+            self.allowed_images = [x["image"] for x in yaml.safe_load(handle)]
 
             if len(self.allowed_images) == 0:
                 raise Exception(f"No allowed images specified for {self.attr.viz_id}")
@@ -137,13 +148,13 @@ class InteractiveEnvironmentRequest:
         # .get() that will ignore missing sections, so we must make use of
         # their defaults dictionary instead.
         default_dict = {
-            'container_interface': None,
-            'command': 'docker',
-            'command_inject': '-e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120',
-            'docker_hostname': 'localhost',
-            'wx_tempdir': 'False',
-            'docker_galaxy_temp_dir': None,
-            'docker_connect_port': None,
+            "container_interface": None,
+            "command": "docker",
+            "command_inject": "-e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120",
+            "docker_hostname": "localhost",
+            "wx_tempdir": "False",
+            "docker_galaxy_temp_dir": None,
+            "docker_connect_port": None,
         }
         viz_config = configparser.ConfigParser(default_dict)
         conf_path = os.path.join(self.attr.our_config_dir, f"{self.attr.viz_id}.ini")
@@ -171,7 +182,7 @@ class InteractiveEnvironmentRequest:
             key = self.attr.viz_config.get("main", "container_interface")
         elif self.attr.galaxy_config.enable_beta_containers_interface:
             # TODO: don't hardcode this, and allow for mapping
-            key = '_default_'
+            key = "_default_"
         if key:
             try:
                 self.attr.container_interface = self.trans.app.containers[key]
@@ -180,49 +191,49 @@ class InteractiveEnvironmentRequest:
 
     def get_conf_dict(self):
         """
-            Build up a configuration dictionary that is standard for ALL IEs.
+        Build up a configuration dictionary that is standard for ALL IEs.
 
-            TODO: replace hashed password with plaintext.
+        TODO: replace hashed password with plaintext.
         """
         trans = self.trans
         request = trans.request
         api_key = api_keys.ApiKeyManager(trans.app).get_or_create_api_key(trans.user)
         conf_file = {
-            'history_id': self.attr.history_id,
-            'api_key': api_key,
-            'remote_host': request.remote_addr,
+            "history_id": self.attr.history_id,
+            "api_key": api_key,
+            "remote_host": request.remote_addr,
             # DOCKER_PORT is NO LONGER AVAILABLE. All IEs must update.
-            'cors_origin': request.host_url,
-            'user_email': self.trans.user.email,
-            'proxy_prefix': self.attr.proxy_prefix,
+            "cors_origin": request.host_url,
+            "user_email": self.trans.user.email,
+            "proxy_prefix": self.attr.proxy_prefix,
         }
 
         web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port
-        conf_file['galaxy_web_port'] = web_port
+        conf_file["galaxy_web_port"] = web_port
 
         if self.attr.viz_config.has_option("docker", "galaxy_url"):
-            conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url")
+            conf_file["galaxy_url"] = self.attr.viz_config.get("docker", "galaxy_url")
         elif self.attr.galaxy_config.galaxy_infrastructure_url_set:
-            conf_file['galaxy_url'] = f"{self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/')}/"
+            conf_file["galaxy_url"] = f"{self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/')}/"
         else:
-            conf_file['galaxy_url'] = f"{request.application_url.rstrip('/')}/"
+            conf_file["galaxy_url"] = f"{request.application_url.rstrip('/')}/"
             # Galaxy paster port is deprecated
-            conf_file['galaxy_paster_port'] = conf_file['galaxy_web_port']
+            conf_file["galaxy_paster_port"] = conf_file["galaxy_web_port"]
 
         return conf_file
 
     def generate_hex(self, length):
-        return ''.join(random.choice('0123456789abcdef') for _ in range(length))
+        return "".join(random.choice("0123456789abcdef") for _ in range(length))
 
     def generate_password(self, length):
         """
-            Generate a random alphanumeric password
+        Generate a random alphanumeric password
         """
-        return ''.join(random.choice('0123456789abcdefghijklmnopqrstuvwxyz') for _ in range(length))
+        return "".join(random.choice("0123456789abcdefghijklmnopqrstuvwxyz") for _ in range(length))
 
     def javascript_boolean(self, python_boolean):
         """
-            Convenience function to convert boolean for use in JS
+        Convenience function to convert boolean for use in JS
         """
         if python_boolean:
             return "true"
@@ -240,17 +251,17 @@ class InteractiveEnvironmentRequest:
         # Next several lines for older style replacements (not used with Galaxy dynamic
         # proxy)
         if self.attr.SSL_URLS:
-            protocol = 'https'
+            protocol = "https"
         else:
-            protocol = 'http'
+            protocol = "http"
 
-        url_template = url_template.replace('${PROTO}', protocol) \
-            .replace('${HOST}', self.attr.HOST)
+        url_template = url_template.replace("${PROTO}", protocol).replace("${HOST}", self.attr.HOST)
 
         # Only the following replacements are used with Galaxy dynamic proxy
         # URLs
-        url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) \
-            .replace('${PROXY_PREFIX}', str(self.attr.proxy_prefix.replace('/', '%2F')))
+        url = url_template.replace("${PROXY_URL}", str(self.attr.proxy_url)).replace(
+            "${PROXY_PREFIX}", str(self.attr.proxy_prefix.replace("/", "%2F"))
+        )
         return url
 
     def volume(self, container_path, host_path, **kwds):
@@ -258,9 +269,8 @@ class InteractiveEnvironmentRequest:
             return DockerVolume(container_path, host_path, **kwds)
         else:
             return self.attr.container_interface.volume_class(
-                container_path,
-                host_path=host_path,
-                mode=kwds.get('mode', 'ro'))
+                container_path, host_path=host_path, mode=kwds.get("mode", "ro")
+            )
 
     def _get_env_for_run(self, env_override=None):
         if env_override is None:
@@ -275,8 +285,8 @@ class InteractiveEnvironmentRequest:
 
     def _get_import_volume_for_run(self):
         if self.use_volumes and self.attr.import_volume:
-            return f'{self.temp_dir}:/import/'
-        return ''
+            return f"{self.temp_dir}:/import/"
+        return ""
 
     def _get_name_for_run(self):
         return CONTAINER_NAME_PREFIX + uuid.uuid4().hex
@@ -284,15 +294,16 @@ class InteractiveEnvironmentRequest:
     def base_docker_cmd(self, subcmd=None):
         # This is the basic docker command such as "sudo -u docker docker" or just "docker"
         # Previously, {docker_args} was required to be in the string, this is no longer the case
-        base = shlex.split(self.attr.viz_config.get("docker", "command").format(docker_args='').strip())
+        base = shlex.split(self.attr.viz_config.get("docker", "command").format(docker_args="").strip())
         if subcmd:
             base.append(subcmd)
         return base
 
     def docker_cmd(self, image, env_override=None, volumes=None):
         """
-            Generate and return the docker command to execute
+        Generate and return the docker command to execute
         """
+
         def _flag_opts(flag, opts):
             return [arg for pair in product((flag,), opts) for arg in pair]
 
@@ -306,14 +317,14 @@ class InteractiveEnvironmentRequest:
             # -e USER_UID=$(id -u) -e USER_GID=$(id -g)
             uid_gid_subs = {"$(id -u)": f"{os.geteuid()}", "$(id -g)": f"{os.getgid()}"}
             subs = sorted(uid_gid_subs)
-            regex = re.compile('|'.join(map(re.escape, subs)))
+            regex = re.compile("|".join(map(re.escape, subs)))
             return regex.sub(lambda match: uid_gid_subs[match.group(0)], cmd_inject)
 
         command_inject = self.attr.viz_config.get("docker", "command_inject")
         command_inject = _check_uid_and_gid(command_inject)
 
         # --name should really not be set, but we'll try to honor it anyway
-        name = [f'--name={self._get_name_for_run()}'] if '--name' not in command_inject else []
+        name = [f"--name={self._get_name_for_run()}"] if "--name" not in command_inject else []
         env = self._get_env_for_run(env_override)
         import_volume_def = self._get_import_volume_for_run()
         if volumes is None:
@@ -322,12 +333,12 @@ class InteractiveEnvironmentRequest:
             volumes.insert(0, import_volume_def)
 
         return (
-            self.base_docker_cmd('run')
+            self.base_docker_cmd("run")
             + shlex.split(command_inject)
             + name
-            + _flag_opts('-e', ['='.join(map(str, t)) for t in env.items()])
-            + ['-d', '-P']
-            + _flag_opts('-v', map(str, volumes))
+            + _flag_opts("-e", ["=".join(map(str, t)) for t in env.items()])
+            + ["-d", "-P"]
+            + _flag_opts("-v", map(str, volumes))
             + [image]
         )
 
@@ -341,22 +352,21 @@ class InteractiveEnvironmentRequest:
             return True
 
     def _get_command_inject_env(self):
-        """For the containers interface, parse any -e/--env flags from `command_inject`.
-        """
+        """For the containers interface, parse any -e/--env flags from `command_inject`."""
         # using a list ensures that later vars override earlier ones with the
         # same name, which is how `docker run` works on the command line
         envsets = []
         command_inject = self.attr.viz_config.get("docker", "command_inject").strip().split()
         for i, item in enumerate(command_inject):
-            if item.startswith('-e=') or item.startswith('--env='):
-                envsets.append(item.split('=', 1)[1])
-            elif item == ('-e') or item == ('--env'):
+            if item.startswith("-e=") or item.startswith("--env="):
+                envsets.append(item.split("=", 1)[1])
+            elif item == ("-e") or item == ("--env"):
                 envsets.append(command_inject[i + 1])
-            elif item.startswith('-e'):
+            elif item.startswith("-e"):
                 envsets.append(item[2:])
-            elif item.startswith('--env'):
+            elif item.startswith("--env"):
                 envsets.append(item[5:])
-        return dict(_.split('=', 1) for _ in envsets)
+        return dict(_.split("=", 1) for _ in envsets)
 
     def container_run_args(self, image, env_override=None, volumes=None):
         if volumes is None:
@@ -367,17 +377,17 @@ class InteractiveEnvironmentRequest:
         env = self._get_command_inject_env()
         env.update(self._get_env_for_run(env_override))
         args = {
-            'image': image,
-            'environment': env,
-            'volumes': volumes,
-            'name': self._get_name_for_run(),
-            'detach': True,
-            'publish_all_ports': True,
+            "image": image,
+            "environment": env,
+            "volumes": volumes,
+            "name": self._get_name_for_run(),
+            "detach": True,
+            "publish_all_ports": True,
         }
         if self.attr.docker_connect_port:
             # TODO: we can inspect the image for this, and if it's not pulled
             # yet we can query the registry for it
-            args['publish_port_random'] = self.attr.docker_connect_port
+            args["publish_port_random"] = self.attr.docker_connect_port
         return args
 
     def _ids_to_volumes(self, ids):
@@ -385,7 +395,7 @@ class InteractiveEnvironmentRequest:
             return []
 
         # They come as a comma separated list
-        ids = ids.split(',')
+        ids = ids.split(",")
 
         # Next we need to turn these into volumes
         volumes = []
@@ -393,7 +403,7 @@ class InteractiveEnvironmentRequest:
             decoded_id = self.trans.security.decode_id(id)
             dataset = self.trans.sa_session.query(model.HistoryDatasetAssociation).get(decoded_id)
             # TODO: do we need to check if the user has access?
-            volumes.append(self.volume(f'/import/[{dataset.id}] {dataset.name}.{dataset.ext}', dataset.get_file_name()))
+            volumes.append(self.volume(f"/import/[{dataset.id}] {dataset.name}.{dataset.ext}", dataset.get_file_name()))
         return volumes
 
     def _find_port_mapping(self, port_mappings):
@@ -405,7 +415,9 @@ class InteractiveEnvironmentRequest:
                         port_mapping = _port_mapping
                         break
             else:
-                log.warning("Don't know how to handle proxies to containers with multiple exposed ports. Arbitrarily choosing first. Please set 'docker_connect_port' in your config file to be more specific.")
+                log.warning(
+                    "Don't know how to handle proxies to containers with multiple exposed ports. Arbitrarily choosing first. Please set 'docker_connect_port' in your config file to be more specific."
+                )
         elif len(port_mappings) == 0:
             log.warning("No exposed ports to map! Images MUST EXPOSE")
             return None
@@ -415,23 +427,24 @@ class InteractiveEnvironmentRequest:
         return port_mapping
 
     def _launch_legacy(self, image, env_override, volumes):
-        """Legacy launch method for use when the container interface is not enabled
-        """
+        """Legacy launch method for use when the container interface is not enabled"""
         raw_cmd = self.docker_cmd(image, env_override=env_override, volumes=volumes)
         redacted_command = raw_cmd
         if self.attr.redact_username_in_logs:
+
             def make_safe(param):
-                if 'USER_EMAIL' in param:
-                    return re.sub('USER_EMAIL=[^ ]*', 'USER_EMAIL=*********', param)
+                if "USER_EMAIL" in param:
+                    return re.sub("USER_EMAIL=[^ ]*", "USER_EMAIL=*********", param)
                 else:
                     return param
 
             redacted_command = [make_safe(x) for x in raw_cmd]
 
-        log.info("Starting docker container for IE {} with command [{}]".format(
-            self.attr.viz_id,
-            ' '.join(shlex.quote(x) for x in redacted_command)
-        ))
+        log.info(
+            "Starting docker container for IE {} with command [{}]".format(
+                self.attr.viz_id, " ".join(shlex.quote(x) for x in redacted_command)
+            )
+        )
         p = Popen(raw_cmd, stdout=PIPE, stderr=PIPE, close_fds=True)
         stdout, stderr = p.communicate()
         stdout = unicodify(stdout)
@@ -459,7 +472,7 @@ class InteractiveEnvironmentRequest:
                 container_ids=[container_id],
             )
             # These variables then become available for use in templating URLs
-            self.attr.proxy_url = self.attr.proxy_request['proxy_url']
+            self.attr.proxy_url = self.attr.proxy_request["proxy_url"]
             # Commented out because it needs to be documented and visible that
             # this variable was moved here. Usually would remove commented
             # code, but again, needs to be clear where this went. Remove at a
@@ -470,19 +483,27 @@ class InteractiveEnvironmentRequest:
             # self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ]
 
     def _launch_container_interface(self, image, env_override, volumes):
-        """Launch method for use when the container interface is enabled
-        """
+        """Launch method for use when the container interface is enabled"""
         run_args = self.container_run_args(image, env_override, volumes)
         container = self.attr.container_interface.run_in_container(None, **run_args)
         container_port = container.map_port(self.attr.docker_connect_port)
         if not container_port:
-            log.warning("Container %s (%s) created but no port information available, readiness check will determine "
-                        "ports", container.name, container.id)
+            log.warning(
+                "Container %s (%s) created but no port information available, readiness check will determine " "ports",
+                container.name,
+                container.id,
+            )
             container_port = ContainerPort(self.attr.docker_connect_port, None, None, None)
             # a negated docker_connect_port will be stored in the proxy to indicate that the readiness check should
             # attempt to determine the port
-        log.debug("Container %s (%s) port %s accessible at: %s:%s", container.name, container.id, container_port.port,
-                  container_port.hostaddr, container_port.hostport)
+        log.debug(
+            "Container %s (%s) port %s accessible at: %s:%s",
+            container.name,
+            container.id,
+            container_port.port,
+            container_port.hostaddr,
+            container_port.hostport,
+        )
         self.attr.proxy_request = self.trans.app.proxy_manager.setup_proxy(
             self.trans,
             host=container_port.hostaddr,
@@ -490,9 +511,9 @@ class InteractiveEnvironmentRequest:
             proxy_prefix=self.attr.proxy_prefix,
             route_name=self.attr.viz_id,
             container_ids=[container.id],
-            container_interface=self.attr.container_interface.key
+            container_interface=self.attr.container_interface.key,
         )
-        self.attr.proxy_url = self.attr.proxy_request['proxy_url']
+        self.attr.proxy_url = self.attr.proxy_request["proxy_url"]
 
     def launch(self, image=None, additional_ids=None, env_override=None, volumes=None):
         """Launch a docker image.
@@ -522,8 +543,10 @@ class InteractiveEnvironmentRequest:
         if image not in self.allowed_images:
             # Now that we're allowing users to specify images, we need to ensure that they aren't
             # requesting images we have not specifically allowed.
-            raise Exception("Attempting to launch disallowed image! %s not in list of allowed images [%s]"
-                            % (image, ', '.join(self.allowed_images)))
+            raise Exception(
+                "Attempting to launch disallowed image! %s not in list of allowed images [%s]"
+                % (image, ", ".join(self.allowed_images))
+            )
 
         if additional_ids is not None:
             volumes += self._ids_to_volumes(additional_ids)
@@ -541,11 +564,12 @@ class InteractiveEnvironmentRequest:
 
         :returns: inspect_data, a dict of docker inspect output
         """
-        raw_cmd = self.base_docker_cmd('inspect') + [container_id]
-        log.info("Inspecting docker container {} with command [{}]".format(
-            container_id,
-            ' '.join(shlex.quote(x) for x in raw_cmd)
-        ))
+        raw_cmd = self.base_docker_cmd("inspect") + [container_id]
+        log.info(
+            "Inspecting docker container {} with command [{}]".format(
+                container_id, " ".join(shlex.quote(x) for x in raw_cmd)
+            )
+        )
 
         p = Popen(raw_cmd, stdout=PIPE, stderr=PIPE, close_fds=True)
         stdout, stderr = p.communicate()
@@ -569,13 +593,13 @@ class InteractiveEnvironmentRequest:
                   running on.
         """
         inspect_data = inspect_data[0]
-        if 'Node' in inspect_data:
-            return inspect_data['Node']['IP']
+        if "Node" in inspect_data:
+            return inspect_data["Node"]["IP"]
         elif self.attr.docker_hostname == "localhost" and not IS_OS_X:
             # If this is on Docker of Mac OS X that Gateway will be an
             # IP address only available in the Docker host VM - so we
             # stick with localhost.
-            return inspect_data['NetworkSettings']['Gateway']
+            return inspect_data["NetworkSettings"]["Gateway"]
         else:
             return self.attr.docker_hostname
 
@@ -600,12 +624,14 @@ class InteractiveEnvironmentRequest:
         #                 }
         #             ]
         mappings = []
-        port_mappings = inspect_data[0]['NetworkSettings']['Ports']
+        port_mappings = inspect_data[0]["NetworkSettings"]["Ports"]
         for port_name in port_mappings:
             for binding in port_mappings[port_name]:
-                mappings.append((
-                    int(port_name.replace('/tcp', '').replace('/udp', '')),
-                    binding['HostIp'],
-                    int(binding['HostPort'])
-                ))
+                mappings.append(
+                    (
+                        int(port_name.replace("/tcp", "").replace("/udp", "")),
+                        binding["HostIp"],
+                        int(binding["HostPort"]),
+                    )
+                )
         return mappings
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index 64d5b1439ef..f598713e67f 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -5,7 +5,10 @@ from a query string and render a webpage based on those data.
 import copy
 import logging
 import os
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 import mako.lookup
 
@@ -13,7 +16,7 @@ from galaxy.managers import api_keys
 from galaxy.visualization.plugins import (
     interactive_environments,
     resource_parser,
-    utils
+    utils,
 )
 from galaxy.web import url_for
 
@@ -24,6 +27,7 @@ class ServesTemplatesPluginMixin:
     """
     An object that renders (mako) template files from the server.
     """
+
     path: str
 
     #: default number of templates to search for plugin template lookup
@@ -36,8 +40,9 @@ class ServesTemplatesPluginMixin:
         self.serves_templates = False
         if self._is_template_plugin():
             self.template_path = self._build_template_path()
-            self.template_lookup = self._build_template_lookup(template_cache_dir,
-                                                               additional_template_paths=additional_template_paths)
+            self.template_lookup = self._build_template_lookup(
+                template_cache_dir, additional_template_paths=additional_template_paths
+            )
             self.serves_templates = True
         return self.serves_templates
 
@@ -45,10 +50,11 @@ class ServesTemplatesPluginMixin:
         return os.path.isdir(self._build_template_path())
 
     def _build_template_path(self):
-        return os.path.join(self.path, 'templates')
+        return os.path.join(self.path, "templates")
 
-    def _build_template_lookup(self, template_cache_dir, additional_template_paths=None,
-                               collection_size=DEFAULT_TEMPLATE_COLLECTION_SIZE):
+    def _build_template_lookup(
+        self, template_cache_dir, additional_template_paths=None, collection_size=DEFAULT_TEMPLATE_COLLECTION_SIZE
+    ):
         """
         Build a mako template filename lookup for the plugin.
         """
@@ -56,9 +62,8 @@ class ServesTemplatesPluginMixin:
         if additional_template_paths:
             template_lookup_paths = [template_lookup_paths] + additional_template_paths
         return mako.lookup.TemplateLookup(
-            directories=template_lookup_paths,
-            module_directory=template_cache_dir,
-            collection_size=collection_size)
+            directories=template_lookup_paths, module_directory=template_cache_dir, collection_size=collection_size
+        )
 
 
 class VisualizationPlugin(ServesTemplatesPluginMixin):
@@ -66,19 +71,20 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
     A plugin that instantiates resources, serves static files, and uses mako
     templates to render web pages.
     """
+
     def __init__(self, app, path, name, config, context=None, **kwargs):
         context = context or {}
         self.app = app
         self.path = path
         self.name = name
         self.config = config
-        base_url = context.get('base_url', '')
-        self.base_url = '/'.join((base_url, self.name)) if base_url else self.name
+        base_url = context.get("base_url", "")
+        self.base_url = "/".join((base_url, self.name)) if base_url else self.name
         self.static_path = self._get_static_path(self.path)
-        if self.static_path and os.path.exists(os.path.join(self.static_path, 'logo.png')):
-            self.config['logo'] = f"{self.static_path}/logo.png"
-        template_cache_dir = context.get('template_cache_dir', None)
-        additional_template_paths = context.get('additional_template_paths', [])
+        if self.static_path and os.path.exists(os.path.join(self.static_path, "logo.png")):
+            self.config["logo"] = f"{self.static_path}/logo.png"
+        template_cache_dir = context.get("template_cache_dir", None)
+        additional_template_paths = context.get("additional_template_paths", [])
         self._set_up_template_plugin(template_cache_dir, additional_template_paths=additional_template_paths)
         self.resource_parser = resource_parser.ResourceParser(app)
 
@@ -100,40 +106,42 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         # pass the saved visualization config for parsing into render vars
         render_vars = self._build_render_vars(config, trans=trans, **kwargs)
         # update any values that were loaded from the saved Visualization
-        render_vars.update(dict(
-            title=visualization.latest_revision.title,
-            saved_visualization=visualization,
-            visualization_id=trans.security.encode_id(visualization.id),
-        ))
+        render_vars.update(
+            dict(
+                title=visualization.latest_revision.title,
+                saved_visualization=visualization,
+                visualization_id=trans.security.encode_id(visualization.id),
+            )
+        )
         return self._render(render_vars, trans=trans, embedded=embedded)
 
     def to_dict(self):
         return {
-            'name': self.name,
-            'html': self.config.get('name'),
-            'description': self.config.get('description'),
-            'logo': self.config.get('logo'),
-            'title': self.config.get('title'),
-            'target': self.config.get('render_target', 'galaxy_main'),
-            'embeddable': self.config.get('embeddable'),
-            'entry_point': self.config.get('entry_point'),
-            'settings': self.config.get('settings'),
-            'groups': self.config.get('groups'),
-            'specs': self.config.get('specs'),
-            'href': self._get_url()
+            "name": self.name,
+            "html": self.config.get("name"),
+            "description": self.config.get("description"),
+            "logo": self.config.get("logo"),
+            "title": self.config.get("title"),
+            "target": self.config.get("render_target", "galaxy_main"),
+            "embeddable": self.config.get("embeddable"),
+            "entry_point": self.config.get("entry_point"),
+            "settings": self.config.get("settings"),
+            "groups": self.config.get("groups"),
+            "specs": self.config.get("specs"),
+            "href": self._get_url(),
         }
 
     def _get_url(self):
         if self.name in self.app.visualizations_registry.BUILT_IN_VISUALIZATIONS:
-            return url_for(controller='visualization', action=self.name)
-        return url_for('visualization_plugin', visualization_name=self.name)
+            return url_for(controller="visualization", action=self.name)
+        return url_for("visualization_plugin", visualization_name=self.name)
 
     def _get_static_path(self, path):
-        if '/config/' in path:
-            match = path.split('/config/')[-1]
-            return os.path.join('./static', match, 'static')
+        if "/config/" in path:
+            match = path.split("/config/")[-1]
+            return os.path.join("./static", match, "static")
         else:
-            log.debug(f'Visualization has no static path: {path}.')
+            log.debug(f"Visualization has no static path: {path}.")
 
     def _get_saved_visualization_config(self, visualization, revision=None, **kwargs) -> Dict[str, Any]:
         """
@@ -153,8 +161,8 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         # Meta variables passed to the template/renderer to describe the visualization being rendered.
         render_vars.update(
             visualization_name=self.name,
-            visualization_display_name=self.config['name'],
-            title=kwargs.get('title', None),
+            visualization_display_name=self.config["name"],
+            title=kwargs.get("title", None),
             saved_visualization=None,
             visualization_id=None,
             visualization_plugin=self.to_dict(),
@@ -163,7 +171,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         )
         # config based on existing or kwargs
         render_config = self._build_config(config, trans=trans, **kwargs)
-        render_vars['config'] = render_config
+        render_vars["config"] = render_config
         # further parse config to resources (models, etc.) used in template based on registry config
         resources = self._config_to_resources(trans, render_config)
         render_vars.update(resources)
@@ -192,7 +200,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         Given a kwargs dict (gen. a query string dict from a controller action), parse
         and return any key/value pairs found in the plugin's `params` section.
         """
-        expected_params = self.config.get('params', {})
+        expected_params = self.config.get("params", {})
         config = self.resource_parser.parse_config(trans, expected_params, kwargs)
         return config
 
@@ -201,8 +209,8 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         Instantiate/deserialize the resources (HDAs, LDDAs, etc.) given in a
         visualization config into models/variables a visualization renderer can use.
         """
-        expected_params = self.config.get('params', {})
-        param_modifiers = self.config.get('param_modifiers', {})
+        expected_params = self.config.get("params", {})
+        param_modifiers = self.config.get("param_modifiers", {})
         resources = self.resource_parser.parse_parameter_dictionary(trans, expected_params, config, param_modifiers)
         return resources
 
@@ -210,12 +218,12 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         """
         Render the visualization via Mako and the plugin's template file.
         """
-        render_vars['embedded'] = self._parse_embedded(embedded)
+        render_vars["embedded"] = self._parse_embedded(embedded)
         # NOTE: (mako specific) vars is a dictionary for shared data in the template
         #   this feels hacky to me but it's what mako recommends:
         #   http://docs.makotemplates.org/en/latest/runtime.html
         render_vars.update(vars={})
-        template_filename = self.config['entry_point']['file']
+        template_filename = self.config["entry_point"]["file"]
         return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
 
     def _parse_embedded(self, embedded):
@@ -230,26 +238,32 @@ class InteractiveEnvironmentPlugin(VisualizationPlugin):
     """
     Serves web-based REPLs such as Jupyter and RStudio.
     """
+
     INTENV_REQUEST_FACTORY = interactive_environments.InteractiveEnvironmentRequest
 
     def __init__(self, app, path, name, config, context=None, **kwargs):
         # TODO: this is a hack until we can get int envs seperated from the vis reg and into their own framework
-        context['base_url'] = 'interactive_environments'
+        context["base_url"] = "interactive_environments"
         super().__init__(app, path, name, config, context=context, **kwargs)
 
     def _error_template(self, trans):
-        return trans.fill_template('message.mako',
-            message='Loading the interactive environment failed, please contact the {admin_tag} for assistance'.format(
+        return trans.fill_template(
+            "message.mako",
+            message="Loading the interactive environment failed, please contact the {admin_tag} for assistance".format(
                 admin_tag='<a href="mailto:{admin_mail}">Galaxy administrator</a>'.format(
-                    admin_mail=trans.app.config.error_email_to)
-                if trans.app.config.error_email_to else 'Galaxy administrator'),
-            status='error')
+                    admin_mail=trans.app.config.error_email_to
+                )
+                if trans.app.config.error_email_to
+                else "Galaxy administrator"
+            ),
+            status="error",
+        )
 
     def _render(self, render_vars, trans=None, embedded=None, **kwargs):
         """
         Override to add interactive environment specific template vars.
         """
-        render_vars['embedded'] = self._parse_embedded(embedded)
+        render_vars["embedded"] = self._parse_embedded(embedded)
         # NOTE: (mako specific) vars is a dictionary for shared data in the template
         #   this feels hacky to me but it's what mako recommends:
         #   http://docs.makotemplates.org/en/latest/runtime.html
@@ -257,15 +271,17 @@ class InteractiveEnvironmentPlugin(VisualizationPlugin):
         # No longer needed but being left around for a few releases as jupyter-galaxy
         # as an external visualization plugin is deprecated in favor of core interactive
         # environment plugin.
-        if 'get_api_key' not in render_vars:
+        if "get_api_key" not in render_vars:
+
             def get_api_key():
                 return api_keys.ApiKeyManager(trans.app).get_or_create_api_key(trans.user)
-            render_vars['get_api_key'] = get_api_key
 
-        if 'plugin_path' not in render_vars:
-            render_vars['plugin_path'] = os.path.abspath(self.path)
+            render_vars["get_api_key"] = get_api_key
 
-        if self.config.get('plugin_type', 'visualization') == "interactive_environment":
+        if "plugin_path" not in render_vars:
+            render_vars["plugin_path"] = os.path.abspath(self.path)
+
+        if self.config.get("plugin_type", "visualization") == "interactive_environment":
             try:
                 request = self.INTENV_REQUEST_FACTORY(trans, self)
             except Exception:
@@ -273,7 +289,7 @@ class InteractiveEnvironmentPlugin(VisualizationPlugin):
                 return self._error_template(trans)
             render_vars["ie_request"] = request
 
-        template_filename = self.config['entry_point']['file']
+        template_filename = self.config["entry_point"]["file"]
         try:
             return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
         except Exception:
@@ -281,7 +297,7 @@ class InteractiveEnvironmentPlugin(VisualizationPlugin):
             return self._error_template(trans)
 
     def _get_url(self):
-        return url_for('interactive_environment_plugin', visualization_name=self.name)
+        return url_for("interactive_environment_plugin", visualization_name=self.name)
 
 
 class ScriptVisualizationPlugin(VisualizationPlugin):
@@ -291,7 +307,8 @@ class ScriptVisualizationPlugin(VisualizationPlugin):
     The script is loaded into a pre-defined mako template:
         `config/plugins/visualizations/common/templates/script_entry_point.mako`
     """
-    MAKO_TEMPLATE = 'script_entry_point.mako'
+
+    MAKO_TEMPLATE = "script_entry_point.mako"
 
     def _is_template_plugin(self):
         """
@@ -305,18 +322,16 @@ class ScriptVisualizationPlugin(VisualizationPlugin):
         Override to add script attributes and point mako at the script entry point
         template.
         """
-        render_vars['embedded'] = self._parse_embedded(embedded)
-        render_vars['static_url'] = url_for(f'/{self.static_path}/')
+        render_vars["embedded"] = self._parse_embedded(embedded)
+        render_vars["static_url"] = url_for(f"/{self.static_path}/")
         render_vars.update(vars={})
-        render_vars.update({
-            "script_attributes": self.config['entry_point']['attr']
-        })
+        render_vars.update({"script_attributes": self.config["entry_point"]["attr"]})
         template_filename = os.path.join(self.MAKO_TEMPLATE)
         return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
 
 
 class ChartVisualizationPlugin(ScriptVisualizationPlugin):
-    MAKO_TEMPLATE = 'chart_entry_point.mako'
+    MAKO_TEMPLATE = "chart_entry_point.mako"
 
 
 class StaticFileVisualizationPlugin(VisualizationPlugin):
@@ -324,6 +339,7 @@ class StaticFileVisualizationPlugin(VisualizationPlugin):
     A visualization plugin that starts by loading a static html file defined in
     the visualization's config file.
     """
+
     # TODO: these are not embeddable by their nature - update config
     # TODO: should do render/render_saved here since most of the calc done there is unneeded in this case
 
@@ -331,10 +347,10 @@ class StaticFileVisualizationPlugin(VisualizationPlugin):
         """
         Render the static file simply by reading and returning it.
         """
-        render_vars['embedded'] = self._parse_embedded(embedded)
+        render_vars["embedded"] = self._parse_embedded(embedded)
         render_vars.update(vars={})
 
-        static_file_path = self.config['entry_point']['file']
+        static_file_path = self.config["entry_point"]["file"]
         static_file_path = os.path.join(self.path, static_file_path)
         with open(static_file_path) as outfile:
             return outfile.read()
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index be1112778a5..82ffe781e34 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -11,12 +11,10 @@ import weakref
 from galaxy.exceptions import ObjectNotFound
 from galaxy.util import (
     config_directories_from_setting,
-    parse_xml
-)
-from galaxy.visualization.plugins import (
-    config_parser,
-    plugin as vis_plugins
+    parse_xml,
 )
+from galaxy.visualization.plugins import config_parser
+from galaxy.visualization.plugins import plugin as vis_plugins
 
 log = logging.getLogger(__name__)
 
@@ -31,17 +29,13 @@ class VisualizationsRegistry:
         - validating and parsing params into resources (based on a context)
             used in the visualization template
     """
+
     #: base url to controller endpoint
-    BASE_URL = 'visualizations'
+    BASE_URL = "visualizations"
     #: name of files to search for additional template lookup directories
-    TEMPLATE_PATHS_CONFIG = 'additional_template_paths.xml'
+    TEMPLATE_PATHS_CONFIG = "additional_template_paths.xml"
     #: built-in visualizations
-    BUILT_IN_VISUALIZATIONS = [
-        'trackster',
-        'circster',
-        'sweepster',
-        'phyloviz'
-    ]
+    BUILT_IN_VISUALIZATIONS = ["trackster", "circster", "sweepster", "phyloviz"]
 
     def __str__(self):
         return self.__class__.__name__
@@ -97,7 +91,7 @@ class VisualizationsRegistry:
         additional_paths = []
         xml_tree = parse_xml(config_filepath)
         paths_list = xml_tree.getroot()
-        for rel_path_elem in paths_list.findall('path'):
+        for rel_path_elem in paths_list.findall("path"):
             if rel_path_elem.text is not None:
                 additional_paths.append(os.path.join(base_directory, rel_path_elem.text))
         return additional_paths
@@ -112,13 +106,13 @@ class VisualizationsRegistry:
                 plugin = self._load_plugin(plugin_path)
                 if plugin and plugin.name not in self.plugins:
                     self.plugins[plugin.name] = plugin
-                    log.info('%s, loaded plugin: %s', self, plugin.name)
+                    log.info("%s, loaded plugin: %s", self, plugin.name)
                 elif plugin and plugin.name in self.plugins:
-                    log.warning('%s, plugin with name already exists: %s. Skipping...', self, plugin.name)
+                    log.warning("%s, plugin with name already exists: %s. Skipping...", self, plugin.name)
             except Exception:
                 if not self.skip_bad_plugins:
                     raise
-                log.exception('Plugin loading raised exception: %s. Skipping...', plugin_path)
+                log.exception("Plugin loading raised exception: %s. Skipping...", plugin_path)
         return self.plugins
 
     def _find_plugins(self):
@@ -161,10 +155,10 @@ class VisualizationsRegistry:
         if not os.path.isdir(plugin_path):
             # super won't work here - different criteria
             return False
-        if 'config' not in os.listdir(plugin_path):
+        if "config" not in os.listdir(plugin_path):
             return False
-        expected_config_filename = f'{os.path.split(plugin_path)[1]}.xml'
-        if not os.path.isfile(os.path.join(plugin_path, 'config', expected_config_filename)):
+        expected_config_filename = f"{os.path.split(plugin_path)[1]}.xml"
+        if not os.path.isfile(os.path.join(plugin_path, "config", expected_config_filename)):
             return False
         return True
 
@@ -180,7 +174,7 @@ class VisualizationsRegistry:
         """
         plugin_name = os.path.split(plugin_path)[1]
         # TODO: this is the standard/older way to config
-        config_file = os.path.join(plugin_path, 'config', (f"{plugin_name}.xml"))
+        config_file = os.path.join(plugin_path, "config", (f"{plugin_name}.xml"))
         if os.path.exists(config_file):
             config = self.config_parser.parse_file(config_file)
             if config is not None:
@@ -188,7 +182,7 @@ class VisualizationsRegistry:
                 plugin = self._build_plugin(plugin_name, plugin_path, config)
                 return plugin
         else:
-            raise ObjectNotFound(f'Visualization XML not found: {config_file}.')
+            raise ObjectNotFound(f"Visualization XML not found: {config_file}.")
 
     def _build_plugin(self, plugin_name, plugin_path, config):
         # TODO: as builder not factory
@@ -196,22 +190,28 @@ class VisualizationsRegistry:
         # default class
         plugin_class = vis_plugins.VisualizationPlugin
         # jupyter, etc
-        if config['plugin_type'] == 'interactive_environment':
+        if config["plugin_type"] == "interactive_environment":
             plugin_class = vis_plugins.InteractiveEnvironmentPlugin
         # js only
-        elif config['entry_point']['type'] == 'script':
+        elif config["entry_point"]["type"] == "script":
             plugin_class = vis_plugins.ScriptVisualizationPlugin
         # js only using charts environment
-        elif config['entry_point']['type'] == 'chart':
+        elif config["entry_point"]["type"] == "chart":
             plugin_class = vis_plugins.ChartVisualizationPlugin
         # from a static file (html, etc)
-        elif config['entry_point']['type'] == 'html':
+        elif config["entry_point"]["type"] == "html":
             plugin_class = vis_plugins.StaticFileVisualizationPlugin
-        return plugin_class(self.app(), plugin_path, plugin_name, config, context=dict(
-            base_url=self.base_url,
-            template_cache_dir=self.template_cache_dir,
-            additional_template_paths=self.additional_template_paths
-        ))
+        return plugin_class(
+            self.app(),
+            plugin_path,
+            plugin_name,
+            config,
+            context=dict(
+                base_url=self.base_url,
+                template_cache_dir=self.template_cache_dir,
+                additional_template_paths=self.additional_template_paths,
+            ),
+        )
 
     def get_plugin(self, key):
         """
@@ -224,10 +224,10 @@ class VisualizationsRegistry:
     def get_plugins(self, embeddable=None):
         result = []
         for plugin in self.plugins.values():
-            if embeddable and not plugin.config.get('embeddable'):
+            if embeddable and not plugin.config.get("embeddable"):
                 continue
             result.append(plugin.to_dict())
-        return sorted(result, key=lambda k: k.get('html'))
+        return sorted(result, key=lambda k: k.get("html"))
 
     # -- building links to visualizations from objects --
     def get_visualizations(self, trans, target_object):
@@ -240,7 +240,7 @@ class VisualizationsRegistry:
             url_data = self.get_visualization(trans, vis_name, target_object)
             if url_data:
                 applicable_visualizations.append(url_data)
-        return sorted(applicable_visualizations, key=lambda k: k.get('html'))
+        return sorted(applicable_visualizations, key=lambda k: k.get("html"))
 
     def get_visualization(self, trans, visualization_name, target_object):
         """
@@ -250,11 +250,11 @@ class VisualizationsRegistry:
         """
         visualization = self.plugins.get(visualization_name, None)
         if visualization is not None:
-            data_sources = visualization.config['data_sources']
+            data_sources = visualization.config["data_sources"]
             for data_source in data_sources:
-                model_class = data_source['model_class']
+                model_class = data_source["model_class"]
                 if isinstance(target_object, model_class):
-                    tests = data_source['tests']
+                    tests = data_source["tests"]
                     if tests is None or self.is_object_applicable(trans, target_object, tests):
                         return visualization.to_dict()
 
@@ -265,16 +265,16 @@ class VisualizationsRegistry:
         """
         # log.debug( 'is_object_applicable( self, trans, %s, %s )', target_object, data_source_tests )
         for test in data_source_tests:
-            test_type = test['type']
-            result_type = test['result_type']
-            test_result = test['result']
-            test_fn = test['fn']
+            test_type = test["type"]
+            result_type = test["result_type"]
+            test_result = test["result"]
+            test_fn = test["fn"]
             # log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
             #           test_type, result_type, test_result, test_fn )
 
-            if test_type == 'isinstance':
+            if test_type == "isinstance":
                 # parse test_result based on result_type (curr: only datatype has to do this)
-                if result_type == 'datatype':
+                if result_type == "datatype":
                     # convert datatypes to their actual classes (for use with isinstance)
                     datatype_class_name = test_result
                     test_result = trans.app.datatypes_registry.get_datatype_class_by_name(datatype_class_name)
diff --git a/lib/galaxy/visualization/plugins/resource_parser.py b/lib/galaxy/visualization/plugins/resource_parser.py
index b1f33bf2d6c..1e8b13e241a 100644
--- a/lib/galaxy/visualization/plugins/resource_parser.py
+++ b/lib/galaxy/visualization/plugins/resource_parser.py
@@ -5,22 +5,31 @@ a dictionary of string data/ids (often from a query string).
 import json
 import logging
 import weakref
-from typing import Callable, Dict, Optional, Union
+from typing import (
+    Callable,
+    Dict,
+    Optional,
+    Union,
+)
 
 import galaxy.exceptions
 import galaxy.util
-from galaxy.managers import (
-    hdas as hda_manager,
-    visualizations as visualization_manager
+from galaxy.managers import hdas as hda_manager
+from galaxy.managers import visualizations as visualization_manager
+from galaxy.model import (
+    HistoryDatasetAssociation,
+    LibraryDatasetDatasetAssociation,
+    Visualization,
 )
-from galaxy.model import HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, Visualization
 from galaxy.util import bunch
 
 log = logging.getLogger(__name__)
 
 
 ParameterPrimitiveType = Union[int, float, str]
-ParameterType = Union[ParameterPrimitiveType, HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, Visualization]
+ParameterType = Union[
+    ParameterPrimitiveType, HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, Visualization
+]
 
 
 class ResourceParser:
@@ -34,14 +43,14 @@ class ResourceParser:
     The keys used to store the new values can optionally be re-mapped to
     new keys (e.g. dataset_id="NNN" -> hda=<HistoryDatasetAssociation>).
     """
+
     primitive_parsers: Dict[str, Callable[[str], ParameterPrimitiveType]] = {
-        'str': lambda param: galaxy.util.sanitize_html.sanitize_html(param),
-        'bool': lambda param: galaxy.util.string_as_bool(param),
-        'int': int,
-        'float': float,
+        "str": lambda param: galaxy.util.sanitize_html.sanitize_html(param),
+        "bool": lambda param: galaxy.util.string_as_bool(param),
+        "int": int,
+        "float": float,
         # 'date'  : lambda param: ,
-        'json': (lambda param: json.loads(
-            galaxy.util.sanitize_html.sanitize_html(param))),
+        "json": (lambda param: json.loads(galaxy.util.sanitize_html.sanitize_html(param))),
     }
 
     def __init__(self, app, *args, **kwargs):
@@ -64,13 +73,12 @@ class ResourceParser:
 
         # parse the modifiers first since they modify the params coming next
         # TODO: this is all really for hda_ldda - which we could replace with model polymorphism
-        params_that_modify_other_params = self.parse_parameter_modifiers(
-            trans, param_modifiers, query_params)
+        params_that_modify_other_params = self.parse_parameter_modifiers(trans, param_modifiers, query_params)
 
         resources = {}
         for param_name, param_config in param_config_dict.items():
             # optionally rename the variable returned, defaulting to the original name
-            var_name_in_template = param_config.get('var_name_in_template', param_name)
+            var_name_in_template = param_config.get("var_name_in_template", param_name)
 
             # if the param is present, get its value, any param modifiers for that param, and parse it into a resource
             # use try catch here and not caller to fall back on the default value or re-raise if required
@@ -79,22 +87,28 @@ class ResourceParser:
             if query_val is not None:
                 try:
                     target_param_modifiers = params_that_modify_other_params.get(param_name, None)
-                    resource = self.parse_parameter(trans, param_config,
-                                                    query_val, param_modifiers=target_param_modifiers)
+                    resource = self.parse_parameter(
+                        trans, param_config, query_val, param_modifiers=target_param_modifiers
+                    )
 
                 except Exception as exception:
                     if trans.debug:
                         raise
                     else:
-                        log.warning('Exception parsing visualization param from query: %s, %s, (%s) %s',
-                                  param_name, query_val, str(type(exception)), str(exception))
+                        log.warning(
+                            "Exception parsing visualization param from query: %s, %s, (%s) %s",
+                            param_name,
+                            query_val,
+                            str(type(exception)),
+                            str(exception),
+                        )
                     resource = None
 
             # here - we've either had no value in the query_params or there was a failure to parse
             #   so: error if required, otherwise get a default (which itself defaults to None)
             if resource is None:
-                if param_config['required']:
-                    raise KeyError(f'required param {param_name} not found in URL')
+                if param_config["required"]:
+                    raise KeyError(f"required param {param_name} not found in URL")
                 resource = self.parse_parameter_default(trans, param_config)
 
             resources[var_name_in_template] = resource
@@ -112,19 +126,21 @@ class ResourceParser:
         config = {}
         for param_name, param_config in param_config_dict.items():
             config_val = query_params.get(param_name, None)
-            if config_val is not None and param_config['type'] in self.primitive_parsers:
+            if config_val is not None and param_config["type"] in self.primitive_parsers:
                 try:
                     config_val = self.parse_parameter(trans, param_config, config_val)
 
                 except Exception as exception:
-                    log.warning('Exception parsing visualization param from query: '
-                              + f'{param_name}, {config_val}, ({str(type(exception))}) {str(exception)}')
+                    log.warning(
+                        "Exception parsing visualization param from query: "
+                        + f"{param_name}, {config_val}, ({str(type(exception))}) {str(exception)}"
+                    )
                     config_val = None
 
             # here - we've either had no value in the query_params or there was a failure to parse
             #   so: if there's a default and it's not None, add it to the config
             if config_val is None:
-                if param_config.get('default', None) is None:
+                if param_config.get("default", None) is None:
                     continue
                 config_val = self.parse_parameter_default(trans, param_config)
 
@@ -133,7 +149,9 @@ class ResourceParser:
         return config
 
     # TODO: I would LOVE to rip modifiers out completely
-    def parse_parameter_modifiers(self, trans, param_modifiers, query_params) -> Dict[str, Dict[str, Optional[ParameterType]]]:
+    def parse_parameter_modifiers(
+        self, trans, param_modifiers, query_params
+    ) -> Dict[str, Dict[str, Optional[ParameterType]]]:
         """
         Parse and return parameters that are meant to modify other parameters,
         be grouped with them, or are needed to successfully parse other parameters.
@@ -166,7 +184,7 @@ class ResourceParser:
         to `None`.
         """
         # currently, *default* default is None, so this is quaranteed to be part of the dictionary
-        default = param_config['default']
+        default = param_config["default"]
         # if default is None, do not attempt to parse it
         if default is None:
             return default
@@ -175,13 +193,12 @@ class ResourceParser:
         #   (and adding this code to the xml parser)
         return self.parse_parameter(trans, param_config, default)
 
-    def parse_parameter(self, trans, expected_param_data, query_param,
-                        recurse=True, param_modifiers=None):
+    def parse_parameter(self, trans, expected_param_data, query_param, recurse=True, param_modifiers=None):
         """
         Use data in `expected_param_data` to parse `query_param` from a string into
         a resource usable directly by a template.
         """
-        param_type = expected_param_data.get('type')
+        param_type = expected_param_data.get("type")
         parsed_param: Optional[ParameterType] = None
 
         if param_type in self.primitive_parsers:
@@ -191,27 +208,27 @@ class ResourceParser:
         # TODO: constrain_to: this gets complicated - remove?
 
         # db models
-        elif param_type == 'visualization':
+        elif param_type == "visualization":
             # ?: is this even used anymore/anywhere?
             decoded_visualization_id = trans.security.decode_id(query_param, object_name=param_type)
             parsed_param = self.managers.visualization.get_accessible(decoded_visualization_id, trans.user)
 
-        elif param_type == 'dataset':
+        elif param_type == "dataset":
             decoded_dataset_id = trans.security.decode_id(query_param, object_name=param_type)
             parsed_param = self.managers.hda.get_accessible(decoded_dataset_id, trans.user)
 
-        elif param_type == 'hda_or_ldda':
+        elif param_type == "hda_or_ldda":
             encoded_dataset_id = query_param
             # needs info from another param...
-            hda_ldda = param_modifiers.get('hda_ldda')
-            if hda_ldda == 'hda':
+            hda_ldda = param_modifiers.get("hda_ldda")
+            if hda_ldda == "hda":
                 decoded_dataset_id = trans.security.decode_id(query_param, object_name="dataset")
                 parsed_param = self.managers.hda.get_accessible(decoded_dataset_id, trans.user)
             else:
                 parsed_param = self.managers.ldda.get(trans, encoded_dataset_id)
 
         # TODO: ideally this would check v. a list of valid dbkeys
-        elif param_type == 'dbkey':
+        elif param_type == "dbkey":
             dbkey = query_param
             parsed_param = galaxy.util.sanitize_html.sanitize_html(dbkey)
 
diff --git a/lib/galaxy/visualization/plugins/utils.py b/lib/galaxy/visualization/plugins/utils.py
index 371d0fe4ec4..ebbc6f7466a 100644
--- a/lib/galaxy/visualization/plugins/utils.py
+++ b/lib/galaxy/visualization/plugins/utils.py
@@ -36,7 +36,7 @@ def getattr_recursive(item, attr_key, *args):
     using_default = len(args) >= 1
     default = args[0] if using_default else None
 
-    for attr_key in attr_key.split('.'):
+    for attr_key in attr_key.split("."):
         try:
             if isinstance(item, dict):
                 item = item.__getitem__(attr_key)
@@ -57,8 +57,8 @@ def hasattr_recursive(item, attr_key):
 
     NOTE: also searches dictionaries
     """
-    if '.' in attr_key:
-        attr_key, last_key = attr_key.rsplit('.', 1)
+    if "." in attr_key:
+        attr_key, last_key = attr_key.rsplit(".", 1)
         item = getattr_recursive(item, attr_key, None)
         if item is None:
             return False
diff --git a/lib/galaxy/web/__init__.py b/lib/galaxy/web/__init__.py
index 696fd07f2b3..78e9b77ac7d 100644
--- a/lib/galaxy/web/__init__.py
+++ b/lib/galaxy/web/__init__.py
@@ -25,11 +25,25 @@ from .framework.decorators import (
     require_login,
 )
 
-__all__ = ('do_not_cache', 'error', 'expose', 'expose_api',
-        'expose_api_anonymous', 'expose_api_anonymous_and_sessionless',
-        'expose_api_raw', 'expose_api_raw_anonymous',
-        'expose_api_raw_anonymous_and_sessionless',
-        'format_return_as_json', 'httpexceptions', 'json', 'json_pretty',
-        'legacy_expose_api', 'legacy_expose_api_anonymous',
-        'legacy_expose_api_raw', 'legacy_expose_api_raw_anonymous',
-        'require_admin', 'require_login', 'url_for')
+__all__ = (
+    "do_not_cache",
+    "error",
+    "expose",
+    "expose_api",
+    "expose_api_anonymous",
+    "expose_api_anonymous_and_sessionless",
+    "expose_api_raw",
+    "expose_api_raw_anonymous",
+    "expose_api_raw_anonymous_and_sessionless",
+    "format_return_as_json",
+    "httpexceptions",
+    "json",
+    "json_pretty",
+    "legacy_expose_api",
+    "legacy_expose_api_anonymous",
+    "legacy_expose_api_raw",
+    "legacy_expose_api_raw_anonymous",
+    "require_admin",
+    "require_login",
+    "url_for",
+)
diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py
index 2641c01dde7..ef953ccd1ba 100644
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -7,4 +7,4 @@ except ImportError:
     # is fine - we shouldn't be using this entry point anyway.
     app_factory = None  # type: ignore[misc, assignment]
 
-__all__ = ('app_factory', )
+__all__ = ("app_factory",)
diff --git a/lib/galaxy/web/formatting.py b/lib/galaxy/web/formatting.py
index d7b2151b566..1233fb8b9e6 100644
--- a/lib/galaxy/web/formatting.py
+++ b/lib/galaxy/web/formatting.py
@@ -1,7 +1,7 @@
 import locale
 from string import Template
 
-DEFAULT_LOCALE_FORMAT = '%a %b %e %H:%M:%S %Y'
+DEFAULT_LOCALE_FORMAT = "%a %b %e %H:%M:%S %Y"
 ISO_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
 
 
diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index 81a88d16643..b8020ebf9d8 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -9,7 +9,10 @@ import tarfile
 import tempfile
 import time
 import types
-from http.cookies import CookieError, SimpleCookie
+from http.cookies import (
+    CookieError,
+    SimpleCookie,
+)
 from importlib import import_module
 
 import routes
@@ -17,6 +20,7 @@ import webob.compat
 import webob.cookies
 import webob.exc
 import webob.exc as httpexceptions  # noqa: F401
+
 # We will use some very basic HTTP/wsgi utilities from the paste library
 from paste.response import HeaderDict
 
@@ -36,10 +40,29 @@ def __resource_with_deleted(self, member_name, collection_name, **kwargs):
     """
     collection_path = f"{kwargs.get('path_prefix', '')}/{collection_name}/deleted"
     member_path = f"{collection_path}/{{id}}"
-    self.connect(f"deleted_{collection_name}", collection_path, controller=collection_name, action='index', deleted=True, conditions=dict(method=['GET']))
-    self.connect(f"deleted_{member_name}", member_path, controller=collection_name, action='show', deleted=True, conditions=dict(method=['GET']))
-    self.connect(f"undelete_deleted_{member_name}", f"{member_path}/undelete", controller=collection_name, action='undelete',
-                 conditions=dict(method=['POST']))
+    self.connect(
+        f"deleted_{collection_name}",
+        collection_path,
+        controller=collection_name,
+        action="index",
+        deleted=True,
+        conditions=dict(method=["GET"]),
+    )
+    self.connect(
+        f"deleted_{member_name}",
+        member_path,
+        controller=collection_name,
+        action="show",
+        deleted=True,
+        conditions=dict(method=["GET"]),
+    )
+    self.connect(
+        f"undelete_deleted_{member_name}",
+        f"{member_path}/undelete",
+        controller=collection_name,
+        action="undelete",
+        conditions=dict(method=["POST"]),
+    )
     self.resource(member_name, collection_name, **kwargs)
 
 
@@ -79,13 +102,11 @@ class WebApplication:
         methods which handle web requests. To connect a URL to a controller's
         method use `add_route`.
         """
-        log.debug("Enabling '%s' controller, class: %s",
-                  controller_name, controller.__class__.__name__)
+        log.debug("Enabling '%s' controller, class: %s", controller_name, controller.__class__.__name__)
         self.controllers[controller_name] = controller
 
     def add_api_controller(self, controller_name, controller):
-        log.debug("Enabling '%s' API controller, class: %s",
-                  controller_name, controller.__class__.__name__)
+        log.debug("Enabling '%s' API controller, class: %s", controller_name, controller.__class__.__name__)
         self.api_controllers[controller_name] = controller
 
     def add_route(self, route, **kwargs):
@@ -100,8 +121,8 @@ class WebApplication:
         """
         self.mapper.connect(route, **kwargs)
 
-    def add_client_route(self, route, controller='root'):
-        self.clientside_routes.connect(route, controller=controller, action='client')
+    def add_client_route(self, route, controller="root"):
+        self.clientside_routes.connect(route, controller=controller, action="client")
 
     def set_transaction_factory(self, transaction_factory):
         """
@@ -130,7 +151,7 @@ class WebApplication:
         and calls it.
         """
         # Immediately create request_id which we will use for logging
-        request_id = environ.get('request_id', 'unknown')
+        request_id = environ.get("request_id", "unknown")
         if self.trace_logger:
             self.trace_logger.context_set("request_id", request_id)
         self.trace(message="Starting request")
@@ -143,14 +164,14 @@ class WebApplication:
 
     def _resolve_map_match(self, map_match, path_info, controllers, use_default=True):
         # Get the controller class
-        controller_name = map_match.pop('controller', None)
+        controller_name = map_match.pop("controller", None)
         controller = controllers.get(controller_name, None)
         if controller is None:
             raise webob.exc.HTTPNotFound(f"No controller for {path_info}")
         # Resolve action method on controller
         # This is the easiest way to make the controller/action accessible for
         # url_for invocations.  Specifically, grids.
-        action = map_match.pop('action', 'index')
+        action = map_match.pop("action", "index")
         method = getattr(controller, action, None)
         if method is None and not use_default:
             # Skip default, we do this, for example, when we want to fail
@@ -158,11 +179,11 @@ class WebApplication:
             raise webob.exc.HTTPNotFound(f"No action for {path_info}")
         if method is None:
             # no matching method, we try for a default
-            method = getattr(controller, 'default', None)
+            method = getattr(controller, "default", None)
         if method is None:
             raise webob.exc.HTTPNotFound(f"No action for {path_info}")
         # Is the method exposed
-        if not getattr(method, 'exposed', False):
+        if not getattr(method, "exposed", False):
             raise webob.exc.HTTPNotFound(f"Action not exposed for {path_info}")
         # Is the method callable
         if not callable(method):
@@ -171,16 +192,16 @@ class WebApplication:
 
     def handle_request(self, environ, start_response, body_renderer=None):
         # Grab the request_id (should have been set by middleware)
-        request_id = environ.get('request_id', 'unknown')
+        request_id = environ.get("request_id", "unknown")
         # Map url using routes
-        path_info = environ.get('PATH_INFO', '')
+        path_info = environ.get("PATH_INFO", "")
         client_match = self.clientside_routes.match(path_info, environ)
         map_match = self.mapper.match(path_info, environ) or client_match
-        if path_info.startswith('/api'):
-            environ['is_api_request'] = True
+        if path_info.startswith("/api"):
+            environ["is_api_request"] = True
             controllers = self.api_controllers
         else:
-            environ['is_api_request'] = False
+            environ["is_api_request"] = False
             controllers = self.controllers
         if map_match is None:
             raise webob.exc.HTTPNotFound(f"No route for {path_info}")
@@ -198,21 +219,27 @@ class WebApplication:
         try:
             # We don't use default methods if there's a clientside match for this route.
             use_default = client_match is None
-            controller_name, controller, action, method = self._resolve_map_match(map_match, path_info, controllers, use_default=use_default)
+            controller_name, controller, action, method = self._resolve_map_match(
+                map_match, path_info, controllers, use_default=use_default
+            )
         except webob.exc.HTTPNotFound:
             # Failed, let's check client routes
-            if not environ['is_api_request'] and client_match is not None:
-                controller_name, controller, action, method = self._resolve_map_match(client_match, path_info, controllers)
+            if not environ["is_api_request"] and client_match is not None:
+                controller_name, controller, action, method = self._resolve_map_match(
+                    client_match, path_info, controllers
+                )
             else:
                 raise
         trans.controller = controller_name
         trans.action = action
-        environ['controller_action_key'] = f"{'api' if environ['is_api_request'] else 'web'}.{controller_name}.{action or 'default'}"
+        environ[
+            "controller_action_key"
+        ] = f"{'api' if environ['is_api_request'] else 'web'}.{controller_name}.{action or 'default'}"
         # Combine mapper args and query string / form args and call
         kwargs = trans.request.params.mixed()
         kwargs.update(map_match)
         # Special key for AJAX debugging, remove to avoid confusing methods
-        kwargs.pop('_', None)
+        kwargs.pop("_", None)
         try:
             body = method(trans, **kwargs)
         except Exception as e:
@@ -231,15 +258,13 @@ class WebApplication:
         elif isinstance(body, tarfile.ExFileObject):
             # Stream the tarfile member back to the browser
             body = iterate_file(body)
-            start_response(trans.response.wsgi_status(),
-                           trans.response.wsgi_headeritems())
+            start_response(trans.response.wsgi_status(), trans.response.wsgi_headeritems())
             return body
         elif isinstance(body, io.IOBase):
             # Stream the file back to the browser
             return send_file(start_response, trans, body)
         else:
-            start_response(trans.response.wsgi_status(),
-                           trans.response.wsgi_headeritems())
+            start_response(trans.response.wsgi_status(), trans.response.wsgi_headeritems())
             return self.make_body_iterable(trans, body)
 
     def make_body_iterable(self, trans, body):
@@ -267,7 +292,7 @@ class WSGIEnvironmentProperty:
     environment)
     """
 
-    def __init__(self, key, default=''):
+    def __init__(self, key, default=""):
         self.key = key
         self.default = default
 
@@ -316,10 +341,10 @@ class DefaultWebTransaction:
         Get the user's session state. This is laze since we rarely use it
         and the creation/serialization cost is high.
         """
-        if 'com.saddi.service.session' in self.environ:
-            return self.environ['com.saddi.service.session'].session
-        elif 'beaker.session' in self.environ:
-            return self.environ['beaker.session']
+        if "com.saddi.service.session" in self.environ:
+            return self.environ["com.saddi.service.session"].session
+        elif "beaker.session" in self.environ:
+            return self.environ["beaker.session"]
         else:
             return None
 
@@ -332,7 +357,7 @@ def _make_file(self, binary=None):
     if self._binary_file or self.length >= 0:
         return tempfile.NamedTemporaryFile("wb+", delete=False)
     else:
-        return tempfile.NamedTemporaryFile("w+", encoding=self.encoding, newline='\n', delete=False)
+        return tempfile.NamedTemporaryFile("w+", encoding=self.encoding, newline="\n", delete=False)
 
 
 def _read_lines(self):
@@ -362,7 +387,8 @@ class Request(webob.Request):
         Create a new request wrapping the WSGI environment `environ`
         """
         #  self.environ = environ
-        webob.Request.__init__(self, environ, charset='utf-8')
+        webob.Request.__init__(self, environ, charset="utf-8")
+
     # Properties that are computed and cached on first use
 
     @lazy_property
@@ -385,7 +411,7 @@ class Request(webob.Request):
         cookie_header = self.environ.get("HTTP_COOKIE")
         if cookie_header:
             all_cookies = webob.cookies.parse_cookie(cookie_header)
-            galaxy_cookies = {k.decode(): v.decode() for k, v in all_cookies if k.startswith(b'galaxy')}
+            galaxy_cookies = {k.decode(): v.decode() for k, v in all_cookies if k.startswith(b"galaxy")}
             if galaxy_cookies:
                 try:
                     cookies.load(galaxy_cookies)
@@ -395,7 +421,7 @@ class Request(webob.Request):
 
     @lazy_property
     def base(self):
-        return (f"{self.scheme}://{self.host}")
+        return f"{self.scheme}://{self.host}"
 
     # @lazy_property
     # def params( self ):
@@ -403,7 +429,7 @@ class Request(webob.Request):
 
     @lazy_property
     def path(self):
-        return self.environ.get('SCRIPT_NAME', '') + self.environ['PATH_INFO']
+        return self.environ.get("SCRIPT_NAME", "") + self.environ["PATH_INFO"]
 
     @lazy_property
     def browser_url(self):
@@ -414,12 +440,12 @@ class Request(webob.Request):
     # scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' )
     # remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' )
 
-    remote_port = WSGIEnvironmentProperty('REMOTE_PORT')
+    remote_port = WSGIEnvironmentProperty("REMOTE_PORT")
 
     # method = WSGIEnvironmentProperty( 'REQUEST_METHOD' )
     # script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' )
 
-    protocol = WSGIEnvironmentProperty('SERVER_PROTOCOL')
+    protocol = WSGIEnvironmentProperty("SERVER_PROTOCOL")
 
     # query_string = WSGIEnvironmentProperty( 'QUERY_STRING' )
     # path_info = WSGIEnvironmentProperty( 'PATH_INFO' )
@@ -463,7 +489,7 @@ class Response:
         result = self.headers.headeritems()
         # Add cookie to header
         for crumb in self.cookies.values():
-            header, value = str(crumb).split(': ', 1)
+            header, value = str(crumb).split(": ", 1)
             result.append((header, value))
         return result
 
@@ -480,7 +506,7 @@ class Response:
 
 # ---- Utilities ------------------------------------------------------------
 
-CHUNK_SIZE = 2 ** 16
+CHUNK_SIZE = 2**16
 
 
 def send_file(start_response, trans, body):
@@ -488,19 +514,17 @@ def send_file(start_response, trans, body):
     base = trans.app.config.nginx_x_accel_redirect_base
     apache_xsendfile = trans.app.config.apache_xsendfile
     if base:
-        trans.response.headers.pop('content-length', None)
-        trans.response.headers['X-Accel-Redirect'] = \
-            base + os.path.abspath(body.name)
+        trans.response.headers.pop("content-length", None)
+        trans.response.headers["X-Accel-Redirect"] = base + os.path.abspath(body.name)
         body = [b""]
     elif apache_xsendfile:
-        trans.response.headers.pop('content-length', None)
-        trans.response.headers['X-Sendfile'] = os.path.abspath(body.name)
+        trans.response.headers.pop("content-length", None)
+        trans.response.headers["X-Sendfile"] = os.path.abspath(body.name)
         body = [b""]
     # Fall back on sending the file in chunks
     else:
         body = iterate_file(body)
-    start_response(trans.response.wsgi_status(),
-                   trans.response.wsgi_headeritems())
+    start_response(trans.response.wsgi_status(), trans.response.wsgi_headeritems())
     return body
 
 
@@ -531,7 +555,7 @@ def walk_controller_modules(package_name):
     package = import_module(package_name)
     controller_dir = package.__path__[0]
     for fname in os.listdir(controller_dir):
-        if not(fname.startswith("_")) and fname.endswith(".py"):
+        if not (fname.startswith("_")) and fname.endswith(".py"):
             name = fname[:-3]
             module_name = f"{package_name}.{name}"
             module = import_module(module_name)
diff --git a/lib/galaxy/web/framework/decorators.py b/lib/galaxy/web/framework/decorators.py
index 35ef8d15c6b..ab1ab7c201b 100644
--- a/lib/galaxy/web/framework/decorators.py
+++ b/lib/galaxy/web/framework/decorators.py
@@ -16,7 +16,7 @@ from galaxy.exceptions import (
 )
 from galaxy.util import (
     parse_non_hex_float,
-    unicodify
+    unicodify,
 )
 from galaxy.util.json import safe_dumps
 from galaxy.web.framework import url_for
@@ -25,16 +25,16 @@ log = logging.getLogger(__name__)
 
 JSON_CONTENT_TYPE = "application/json; charset=UTF-8"
 JSONP_CONTENT_TYPE = "application/javascript"
-JSONP_CALLBACK_KEY = 'callback'
+JSONP_CALLBACK_KEY = "callback"
 
 
 def error(message):
-    raise MessageException(message, type='error')
+    raise MessageException(message, type="error")
 
 
 # ----------------------------------------------------------------------------- web controller decorators
 def _save_orig_fn(wrapped, orig):
-    if not hasattr(orig, '_orig'):
+    if not hasattr(orig, "_orig"):
         wrapped._orig = orig
     return wrapped
 
@@ -52,6 +52,7 @@ def json(func, pretty=False):
     Format the response as JSON and set the response content type to
     JSON_CONTENT_TYPE.
     """
+
     @wraps(func)
     def call_and_format(self, trans, *args, **kwargs):
         # pull out any callback argument to the api endpoint and set the content type to json or javascript
@@ -63,7 +64,7 @@ def json(func, pretty=False):
         rval = func(self, trans, *args, **kwargs)
         return format_return_as_json(rval, jsonp_callback, pretty=(pretty or trans.debug))
 
-    if not hasattr(func, '_orig'):
+    if not hasattr(func, "_orig"):
         call_and_format._orig = func
     return expose(_save_orig_fn(call_and_format, func))
 
@@ -83,15 +84,16 @@ def require_login(verb="perform this action", use_panels=False):
                 return func(self, trans, *args, **kwargs)
             else:
                 redirect_url = url_for(controller=trans.controller, action=trans.action)
-                query_string = trans.environ.get('QUERY_STRING', '')
+                query_string = trans.environ.get("QUERY_STRING", "")
                 if query_string:
                     redirect_url = f"{redirect_url}?{query_string}"
-                href = url_for(controller='login', redirect=redirect_url)
+                href = url_for(controller="login", redirect=redirect_url)
                 return trans.show_error_message(
-                    f'You must be <a target="galaxy_main" href="{href}">logged in</a> to {verb}.',
-                    use_panels=use_panels
+                    f'You must be <a target="galaxy_main" href="{href}">logged in</a> to {verb}.', use_panels=use_panels
                 )
+
         return decorator
+
     return argcatcher
 
 
@@ -103,13 +105,12 @@ def require_admin(func):
             trans.response.status = 403
             content_type = trans.response.get_content_type()
             # content_type for instance may be... application/json; charset=UTF-8
-            if 'application/json' in content_type:
-                return __api_error_dict(
-                    trans, status_code=403, err_code=error_codes.ADMIN_REQUIRED, err_msg=msg
-                )
+            if "application/json" in content_type:
+                return __api_error_dict(trans, status_code=403, err_code=error_codes.ADMIN_REQUIRED, err_msg=msg)
             else:
                 return trans.show_error_message(msg)
         return func(self, trans, *args, **kwargs)
+
     return decorator
 
 
@@ -127,12 +128,14 @@ def do_not_cache(func):
     """
     Sets cache-prevention headers for the request.
     """
+
     @wraps(func)
     def set_nocache_headers(self, trans, *args, **kwargs):
-        trans.response.headers['Cache-Control'] = ['no-cache', 'no-store', 'must-revalidate']
-        trans.response.headers['Pragma'] = 'no-cache'
-        trans.response.headers['Expires'] = '0'
+        trans.response.headers["Cache-Control"] = ["no-cache", "no-store", "must-revalidate"]
+        trans.response.headers["Pragma"] = "no-cache"
+        trans.response.headers["Expires"] = "0"
         return func(self, trans, *args, **kwargs)
+
     return set_nocache_headers
 
 
@@ -141,12 +144,14 @@ def legacy_expose_api(func, to_json=True, user_required=True):
     """
     Expose this function via the API.
     """
+
     @wraps(func)
     def decorator(self, trans, *args, **kwargs):
         def error(environ, start_response):
-            start_response(error_status, [('Content-type', 'text/plain')])
+            start_response(error_status, [("Content-type", "text/plain")])
             return error_message
-        error_status = '403 Forbidden'
+
+        error_status = "403 Forbidden"
         if trans.error_message:
             return trans.error_message
         if user_required and trans.anonymous:
@@ -154,10 +159,10 @@ def legacy_expose_api(func, to_json=True, user_required=True):
             return error
         if trans.request.body:
             try:
-                kwargs['payload'] = __extract_payload_from_request(trans, func, kwargs)
+                kwargs["payload"] = __extract_payload_from_request(trans, func, kwargs)
             except ValueError:
-                error_status = '400 Bad Request'
-                error_message = 'Your request did not appear to be valid JSON, please consult the API documentation'
+                error_status = "400 Bad Request"
+                error_message = "Your request did not appear to be valid JSON, please consult the API documentation"
                 return error
 
         # pull out any callback argument to the api endpoint and set the content type to json or javascript
@@ -168,15 +173,15 @@ def legacy_expose_api(func, to_json=True, user_required=True):
             trans.response.set_content_type(JSON_CONTENT_TYPE)
 
         # send 'do not cache' headers to handle IE's caching of ajax get responses
-        trans.response.headers['Cache-Control'] = "max-age=0,no-cache,no-store"
+        trans.response.headers["Cache-Control"] = "max-age=0,no-cache,no-store"
 
         # Perform api_run_as processing, possibly changing identity
-        if 'payload' in kwargs and isinstance(kwargs['payload'], dict) and 'run_as' in kwargs['payload']:
+        if "payload" in kwargs and isinstance(kwargs["payload"], dict) and "run_as" in kwargs["payload"]:
             if not trans.user_can_do_run_as:
-                error_message = 'User does not have permissions to run jobs as another user'
+                error_message = "User does not have permissions to run jobs as another user"
                 return error
             try:
-                decoded_user_id = trans.security.decode_id(kwargs['payload']['run_as'])
+                decoded_user_id = trans.security.decode_id(kwargs["payload"]["run_as"])
             except TypeError:
                 trans.response.status = 400
                 return f"Malformed user id ( {str(kwargs['payload']['run_as'])} ) specified, unable to decode."
@@ -194,14 +199,15 @@ def legacy_expose_api(func, to_json=True, user_required=True):
         except paste.httpexceptions.HTTPException:
             raise  # handled
         except Exception:
-            log.exception('Uncaught exception in exposed API method:')
+            log.exception("Uncaught exception in exposed API method:")
             raise paste.httpexceptions.HTTPServerError()
+
     return expose(_save_orig_fn(decorator, func))
 
 
 def __extract_payload_from_request(trans, func, kwargs):
-    content_type = trans.request.headers.get('content-type', '')
-    if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'):
+    content_type = trans.request.headers.get("content-type", "")
+    if content_type.startswith("application/x-www-form-urlencoded") or content_type.startswith("multipart/form-data"):
         # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body
         # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which
         # are not a part of the request body. This is a problem because it's not possible to differentiate between values
@@ -222,16 +228,16 @@ def __extract_payload_from_request(trans, func, kwargs):
                 except Exception:
                     # may not actually be json, just continue
                     pass
-    elif content_type == 'application/offset+octet-stream':
+    elif content_type == "application/offset+octet-stream":
         return unicodify(trans.request.body)
     else:
         # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check
         # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding
         # such as multipart/form-data. Leaving it as is for backward compatibility, just in case.
         payload = loads(unicodify(trans.request.body))
-    run_as = trans.request.headers.get('run-as')
+    run_as = trans.request.headers.get("run-as")
     if run_as:
-        payload['run_as'] = run_as
+        payload["run_as"] = run_as
     return payload
 
 
@@ -263,25 +269,35 @@ def expose_api(func, to_json=True, user_required=True, user_or_session_required=
     """
     Expose this function via the API.
     """
+
     @wraps(func)
     def decorator(self, trans, *args, **kwargs):
         # errors passed in from trans._authenicate_api
         if trans.error_message:
-            return __api_error_response(trans, status_code=403, err_code=error_codes.USER_NO_API_KEY,
-                                        err_msg=trans.error_message)
+            return __api_error_response(
+                trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, err_msg=trans.error_message
+            )
         if trans.anonymous:
             # error if anon and user required
             if user_required:
-                return __api_error_response(trans, status_code=403, err_code=error_codes.USER_NO_API_KEY,
-                                            err_msg="API authentication required for this request")
+                return __api_error_response(
+                    trans,
+                    status_code=403,
+                    err_code=error_codes.USER_NO_API_KEY,
+                    err_msg="API authentication required for this request",
+                )
             # error if anon and no session
             if not trans.galaxy_session and user_or_session_required:
-                return __api_error_response(trans, status_code=403, err_code=error_codes.USER_NO_API_KEY,
-                                            err_msg="API authentication or Galaxy session required for this request")
+                return __api_error_response(
+                    trans,
+                    status_code=403,
+                    err_code=error_codes.USER_NO_API_KEY,
+                    err_msg="API authentication or Galaxy session required for this request",
+                )
 
         if trans.request.body:
             try:
-                kwargs['payload'] = __extract_payload_from_request(trans, func, kwargs)
+                kwargs["payload"] = __extract_payload_from_request(trans, func, kwargs)
             except ValueError:
                 error_code = error_codes.USER_INVALID_JSON
                 return __api_error_response(trans, status_code=400, err_code=error_code)
@@ -295,16 +311,16 @@ def expose_api(func, to_json=True, user_required=True, user_or_session_required=
             trans.response.set_content_type(JSON_CONTENT_TYPE)
 
         # send 'do not cache' headers to handle IE's caching of ajax get responses
-        trans.response.headers['Cache-Control'] = "max-age=0,no-cache,no-store"
+        trans.response.headers["Cache-Control"] = "max-age=0,no-cache,no-store"
 
         # TODO: Refactor next block out into a helper procedure.
         # Perform api_run_as processing, possibly changing identity
-        if 'payload' in kwargs and 'run_as' in kwargs['payload']:
+        if "payload" in kwargs and "run_as" in kwargs["payload"]:
             if not trans.user_can_do_run_as:
                 error_code = error_codes.USER_CANNOT_RUN_AS
                 return __api_error_response(trans, err_code=error_code, status_code=403)
             try:
-                decoded_user_id = trans.security.decode_id(kwargs['payload']['run_as'])
+                decoded_user_id = trans.security.decode_id(kwargs["payload"]["run_as"])
             except (TypeError, ValueError):
                 error_message = f"Malformed user id ( {str(kwargs['payload']['run_as'])} ) specified, unable to decode."
                 error_code = error_codes.USER_INVALID_RUN_AS
@@ -331,7 +347,7 @@ def expose_api(func, to_json=True, user_required=True, user_or_session_required=
             raise  # handled
         except Exception as e:
             traceback_string = format_exc()
-            error_message = 'Uncaught exception in exposed API method:'
+            error_message = "Uncaught exception in exposed API method:"
             log.exception(error_message)
             return __api_error_response(
                 trans,
@@ -339,9 +355,10 @@ def expose_api(func, to_json=True, user_required=True, user_or_session_required=
                 exception=e,
                 traceback=traceback_string,
                 err_msg=error_message,
-                err_code=error_codes.UNKNOWN
+                err_code=error_codes.UNKNOWN,
             )
-    if not hasattr(func, '_orig'):
+
+    if not hasattr(func, "_orig"):
         decorator._orig = func
     decorator.exposed = True
     return decorator
@@ -383,7 +400,7 @@ def api_error_message(trans, **kwds):
         # If we are passed a MessageException use err_msg.
         default_error_code = getattr(exception, "err_code", error_codes.UNKNOWN)
         default_error_message = getattr(exception, "err_msg", default_error_code.default_error_message)
-        extra_error_info = getattr(exception, 'extra_error_info', {})
+        extra_error_info = getattr(exception, "extra_error_info", {})
         if not isinstance(extra_error_info, dict):
             extra_error_info = {}
     else:
@@ -457,10 +474,4 @@ def expose_api_raw_anonymous(func):
 
 def expose_api_raw_anonymous_and_sessionless(func):
     # TODO: tool_shed api implemented JSONP first on a method-by-method basis, don't overwrite that for now
-    return expose_api(
-        func,
-        to_json=False,
-        user_required=False,
-        user_or_session_required=False,
-        handle_jsonp=False
-    )
+    return expose_api(func, to_json=False, user_required=False, user_or_session_required=False, handle_jsonp=False)
diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index e89b438f5b8..9c75b88e976 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -5,7 +5,10 @@ The functions in this module should be considered part of the API used by
 visualizations in their mako files through the `$h` object, see
 GalaxyWebTransaction in galaxy/webapps/base/webapp.py
 """
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 
 from babel import default_locale
 from babel.dates import format_timedelta
@@ -19,7 +22,7 @@ from galaxy.util import (
 from galaxy.util.json import safe_dumps as dumps  # noqa: F401
 from .tags import (
     javascript_link,
-    stylesheet_link
+    stylesheet_link,
 )
 from ..base import server_starttime
 
@@ -34,8 +37,8 @@ def time_ago(x):
     else:
         # Workaround https://github.com/python-babel/babel/issues/137
         kwargs = dict()
-        if not default_locale('LC_TIME'):
-            kwargs['locale'] = 'en_US_POSIX'
+        if not default_locale("LC_TIME"):
+            kwargs["locale"] = "en_US_POSIX"
         return format_timedelta(x - datetime.utcnow(), threshold=1, add_direction=True, **kwargs)
 
 
@@ -49,14 +52,14 @@ def iff(a, b, c):
         return c
 
 
-def truncate(content, length=100, suffix='...'):
+def truncate(content, length=100, suffix="..."):
     """
     Smart string truncation
     """
     if len(content) <= length:
         return content
     else:
-        return content[:length].rsplit(' ', 1)[0] + suffix
+        return content[:length].rsplit(" ", 1)[0] + suffix
 
 
 # Quick helpers for static content
@@ -96,7 +99,7 @@ def dist_js(*args):
     Take a prefix and list of javascript names and return appropriate
     string of script tags.
     """
-    return js_helper('static/dist/', *args)
+    return js_helper("static/dist/", *args)
 
 
 # Hashes
@@ -115,14 +118,14 @@ def to_unicode(a_string):
     Convert a string to unicode in utf-8 format; if string is already unicode,
     does nothing because string's encoding cannot be determined by introspection.
     """
-    return unicodify(a_string, 'utf-8')
+    return unicodify(a_string, "utf-8")
 
 
 def is_true(val):
     """
     Returns true if input is a boolean and true or is a string and looks like a true value.
     """
-    return val is True or val in ['True', 'true', 'T', 't']
+    return val is True or val in ["True", "true", "T", "t"]
 
 
 def to_js_bool(val):
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index be220f00577..96e7114786c 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -1,25 +1,62 @@
 import logging
 import math
-from json import dumps, loads
-from typing import Dict, List, Optional
+from json import (
+    dumps,
+    loads,
+)
+from typing import (
+    Dict,
+    List,
+    Optional,
+)
 
 from markupsafe import escape
-from sqlalchemy.sql.expression import and_, false, func, null, or_, true
-
-from galaxy.model.item_attrs import get_foreign_key, UsesAnnotations, UsesItemRatings
-from galaxy.util import restore_text, sanitize_text, unicodify
-from galaxy.web.framework import decorators, url_for
+from sqlalchemy.sql.expression import (
+    and_,
+    false,
+    func,
+    null,
+    or_,
+    true,
+)
 
+from galaxy.model.item_attrs import (
+    get_foreign_key,
+    UsesAnnotations,
+    UsesItemRatings,
+)
+from galaxy.util import (
+    restore_text,
+    sanitize_text,
+    unicodify,
+)
+from galaxy.web.framework import (
+    decorators,
+    url_for,
+)
 
 log = logging.getLogger(__name__)
 
 
 class GridColumn:
-    def __init__(self, label, key=None, model_class=None, method=None, format=None,
-                 link=None, attach_popup=False, visible=True, nowrap=False,
-                 # Valid values for filterable are ['standard', 'advanced', None]
-                 filterable=None, sortable=True, label_id_prefix=None, target=None,
-                 delayed=False):
+    def __init__(
+        self,
+        label,
+        key=None,
+        model_class=None,
+        method=None,
+        format=None,
+        link=None,
+        attach_popup=False,
+        visible=True,
+        nowrap=False,
+        # Valid values for filterable are ['standard', 'advanced', None]
+        filterable=None,
+        sortable=True,
+        label_id_prefix=None,
+        target=None,
+        delayed=False,
+    ):
         """Create a grid column."""
         self.label = label
         self.key = key
@@ -34,8 +71,8 @@ class GridColumn:
         self.filterable = filterable
         self.delayed = delayed
         # Column must have a key to be sortable.
-        self.sortable = (self.key is not None and sortable)
-        self.label_id_prefix = label_id_prefix or ''
+        self.sortable = self.key is not None and sortable
+        self.label_id_prefix = label_id_prefix or ""
 
     def get_value(self, trans, grid, item):
         if self.method:
@@ -54,7 +91,7 @@ class GridColumn:
         return None
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to reflect the column filter. """
+        """Modify query to reflect the column filter."""
         if column_filter == "All":
             pass
         if column_filter == "True":
@@ -64,7 +101,7 @@ class GridColumn:
         return query
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filters_vals = ["False", "True", "All"]
         accepted_filters = []
         for val in accepted_filters_vals:
@@ -87,17 +124,17 @@ class GridColumn:
 
 
 class ReverseSortColumn(GridColumn):
-    """ Column that reverses sorting; this is useful when the natural sort is descending. """
+    """Column that reverses sorting; this is useful when the natural sort is descending."""
 
     def sort(self, trans, query, ascending, column_name=None):
         return GridColumn.sort(self, trans, query, (not ascending), column_name=column_name)
 
 
 class TextColumn(GridColumn):
-    """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """
+    """Generic column that employs freetext and, hence, supports freetext, case-independent filtering."""
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter using free text, case independence. """
+        """Modify query to filter using free text, case independence."""
         if column_filter == "All":
             pass
         elif column_filter:
@@ -105,7 +142,7 @@ class TextColumn(GridColumn):
         return query
 
     def get_filter(self, trans, user, column_filter):
-        """ Returns a SQLAlchemy criterion derived from column_filter. """
+        """Returns a SQLAlchemy criterion derived from column_filter."""
         if isinstance(column_filter, str):
             return self.get_single_filter(user, column_filter)
         elif isinstance(column_filter, list):
@@ -121,8 +158,8 @@ class TextColumn(GridColumn):
         """
         # Queries that include table joins cannot guarantee that table column names will be
         # unique, so check to see if a_filter is of type <TableName>.<ColumnName>.
-        if self.key.find('.') > -1:
-            a_key = self.key.split('.')[1]
+        if self.key.find(".") > -1:
+            a_key = self.key.split(".")[1]
         else:
             a_key = self.key
         model_class_key_field = getattr(self.model_class, a_key)
@@ -151,8 +188,8 @@ class BooleanColumn(TextColumn):
         return GridColumn.sort(self, trans, query, ascending, column_name=column_name)
 
     def get_single_filter(self, user, a_filter):
-        if self.key.find('.') > -1:
-            a_key = self.key.split('.')[1]
+        if self.key.find(".") > -1:
+            a_key = self.key.split(".")[1]
         else:
             a_key = self.key
         model_class_key_field = getattr(self.model_class, a_key)
@@ -188,37 +225,45 @@ class IntegerColumn(TextColumn):
 
 
 class CommunityRatingColumn(GridColumn, UsesItemRatings):
-    """ Column that displays community ratings for an item. """
+    """Column that displays community ratings for an item."""
 
     def get_value(self, trans, grid, item):
         if not hasattr(item, "average_rating"):
             # No prefetched column property, generate it on the fly.
-            ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, item, webapp_model=trans.model)
+            ave_item_rating, num_ratings = self.get_ave_item_rating_data(
+                trans.sa_session, item, webapp_model=trans.model
+            )
         else:
             ave_item_rating = item.average_rating
             num_ratings = 2  # just used for pluralization
         if not ave_item_rating:
             ave_item_rating = 0
-        return trans.fill_template("tool_shed_rating.mako",
-                                   ave_item_rating=ave_item_rating,
-                                   num_ratings=num_ratings,
-                                   item_id=trans.security.encode_id(item.id))
+        return trans.fill_template(
+            "tool_shed_rating.mako",
+            ave_item_rating=ave_item_rating,
+            num_ratings=num_ratings,
+            item_id=trans.security.encode_id(item.id),
+        )
 
     def sort(self, trans, query, ascending, column_name=None):
         # Get the columns that connect item's table and item's rating association table.
-        item_rating_assoc_class = getattr(trans.model, f'{self.model_class.__name__}RatingAssociation')
+        item_rating_assoc_class = getattr(trans.model, f"{self.model_class.__name__}RatingAssociation")
         foreign_key = get_foreign_key(item_rating_assoc_class, self.model_class)
         fk_col = foreign_key.parent
         referent_col = foreign_key.get_referent(self.model_class.table)
         # Do sorting using a subquery.
         # Subquery to get average rating for each item.
-        ave_rating_subquery = trans.sa_session.query(fk_col,
-                                                     func.avg(item_rating_assoc_class.table.c.rating).label('avg_rating')) \
-            .group_by(fk_col).subquery()
+        ave_rating_subquery = (
+            trans.sa_session.query(fk_col, func.avg(item_rating_assoc_class.table.c.rating).label("avg_rating"))
+            .group_by(fk_col)
+            .subquery()
+        )
         # Integrate subquery into main query.
         query = query.outerjoin((ave_rating_subquery, referent_col == ave_rating_subquery.columns[fk_col.name]))
         # Sort using subquery results; use coalesce to avoid null values.
-        if not ascending:  # TODO: for now, reverse sorting b/c first sort is ascending, and that should be the natural sort.
+        if (
+            not ascending
+        ):  # TODO: for now, reverse sorting b/c first sort is ascending, and that should be the natural sort.
             query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).asc())
         else:
             query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).desc())
@@ -226,7 +271,7 @@ class CommunityRatingColumn(GridColumn, UsesItemRatings):
 
 
 class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
-    """ Column that displays and filters item owner's annotations. """
+    """Column that displays and filters item owner's annotations."""
 
     def __init__(self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None):
         GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
@@ -234,41 +279,56 @@ class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
         self.model_annotation_association_class = model_annotation_association_class
 
     def get_value(self, trans, grid, item):
-        """ Returns first 150 characters of annotation. """
+        """Returns first 150 characters of annotation."""
         annotation = self.get_item_annotation_str(trans.sa_session, item.user, item)
         if annotation:
             ann_snippet = annotation[:155]
             if len(annotation) > 155:
-                ann_snippet = ann_snippet[:ann_snippet.rfind(' ')]
+                ann_snippet = ann_snippet[: ann_snippet.rfind(" ")]
                 ann_snippet += "..."
         else:
             ann_snippet = ""
         return escape(ann_snippet)
 
     def get_single_filter(self, user, a_filter):
-        """ Filter by annotation and annotation owner. """
+        """Filter by annotation and annotation owner."""
         return self.model_class.annotations.any(
-            and_(func.lower(self.model_annotation_association_class.annotation).like(f"%{a_filter.lower()}%"),
-               # TODO: not sure why, to filter by owner's annotations, we have to do this rather than
-               # 'self.model_class.user==self.model_annotation_association_class.user'
-               self.model_annotation_association_class.table.c.user_id == self.model_class.table.c.user_id))
+            and_(
+                func.lower(self.model_annotation_association_class.annotation).like(f"%{a_filter.lower()}%"),
+                # TODO: not sure why, to filter by owner's annotations, we have to do this rather than
+                # 'self.model_class.user==self.model_annotation_association_class.user'
+                self.model_annotation_association_class.table.c.user_id == self.model_class.table.c.user_id,
+            )
+        )
 
 
 class CommunityTagsColumn(TextColumn):
-    """ Column that supports community tags. """
+    """Column that supports community tags."""
 
-    def __init__(self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None):
-        GridColumn.__init__(self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False)
+    def __init__(
+        self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None
+    ):
+        GridColumn.__init__(
+            self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False
+        )
         self.model_tag_association_class = model_tag_association_class
         # Column-specific attributes.
         self.grid_name = grid_name
 
     def get_value(self, trans, grid, item):
-        return trans.fill_template("/tagging_common.mako", tag_type="community", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name,
-                                   tag_click_fn="add_tag_to_grid_filter", use_toggle_link=True)
+        return trans.fill_template(
+            "/tagging_common.mako",
+            tag_type="community",
+            trans=trans,
+            user=trans.get_user(),
+            tagged_item=item,
+            elt_context=self.grid_name,
+            tag_click_fn="add_tag_to_grid_filter",
+            use_toggle_link=True,
+        )
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter model_class by tag. Multiple filters are ANDed. """
+        """Modify query to filter model_class by tag. Multiple filters are ANDed."""
         if column_filter == "All":
             pass
         elif column_filter:
@@ -285,24 +345,34 @@ class CommunityTagsColumn(TextColumn):
         for name, value in raw_tags:
             if name:
                 # Filter by all tags.
-                clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%")))
+                clause_list.append(
+                    self.model_class.tags.any(
+                        func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%")
+                    )
+                )
                 if value:
                     # Filter by all values.
-                    clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%")))
+                    clause_list.append(
+                        self.model_class.tags.any(
+                            func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%")
+                        )
+                    )
         return and_(*clause_list)
 
 
 class IndividualTagsColumn(CommunityTagsColumn):
-    """ Column that supports individual tags. """
+    """Column that supports individual tags."""
 
     def get_value(self, trans, grid, item):
-        return trans.fill_template("/tagging_common.mako",
-                                   tag_type="individual",
-                                   user=trans.user,
-                                   tagged_item=item,
-                                   elt_context=self.grid_name,
-                                   tag_click_fn="add_tag_to_grid_filter",
-                                   use_toggle_link=True)
+        return trans.fill_template(
+            "/tagging_common.mako",
+            tag_type="individual",
+            user=trans.user,
+            tagged_item=item,
+            elt_context=self.grid_name,
+            tag_click_fn="add_tag_to_grid_filter",
+            use_toggle_link=True,
+        )
 
     def get_filter(self, trans, user, column_filter):
         # Parse filter to extract multiple tags.
@@ -314,22 +384,36 @@ class IndividualTagsColumn(CommunityTagsColumn):
         for name, value in raw_tags:
             if name:
                 # Filter by individual's tag names.
-                clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%"), self.model_tag_association_class.user == user)))
+                clause_list.append(
+                    self.model_class.tags.any(
+                        and_(
+                            func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%"),
+                            self.model_tag_association_class.user == user,
+                        )
+                    )
+                )
                 if value:
                     # Filter by individual's tag values.
-                    clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%"), self.model_tag_association_class.user == user)))
+                    clause_list.append(
+                        self.model_class.tags.any(
+                            and_(
+                                func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%"),
+                                self.model_tag_association_class.user == user,
+                            )
+                        )
+                    )
         return and_(*clause_list)
 
 
 class MulticolFilterColumn(TextColumn):
-    """ Column that performs multicolumn filtering. """
+    """Column that performs multicolumn filtering."""
 
     def __init__(self, col_name, cols_to_filter, key, visible, filterable="default"):
         GridColumn.__init__(self, col_name, key=key, visible=visible, filterable=filterable)
         self.cols_to_filter = cols_to_filter
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter model_class by tag. Multiple filters are ANDed. """
+        """Modify query to filter model_class by tag. Multiple filters are ANDed."""
         if column_filter == "All":
             return query
         if isinstance(column_filter, list):
@@ -349,13 +433,13 @@ class MulticolFilterColumn(TextColumn):
 
 
 class OwnerColumn(TextColumn):
-    """ Column that lists item's owner. """
+    """Column that lists item's owner."""
 
     def get_value(self, trans, grid, item):
         return item.user.username
 
     def sort(self, trans, query, ascending, column_name=None):
-        """ Sort column using case-insensitive alphabetical sorting on item's username. """
+        """Sort column using case-insensitive alphabetical sorting on item's username."""
         if ascending:
             query = query.order_by(func.lower(self.model_class.username).asc())
         else:
@@ -364,11 +448,11 @@ class OwnerColumn(TextColumn):
 
 
 class PublicURLColumn(TextColumn):
-    """ Column displays item's public URL based on username and slug. """
+    """Column displays item's public URL based on username and slug."""
 
     def get_link(self, trans, grid, item):
         if item.user.username and item.slug:
-            return dict(action='display_by_username_and_slug', username=item.user.username, slug=item.slug)
+            return dict(action="display_by_username_and_slug", username=item.user.username, slug=item.slug)
         elif not item.user.username:
             # TODO: provide link to set username.
             return None
@@ -378,10 +462,10 @@ class PublicURLColumn(TextColumn):
 
 
 class DeletedColumn(GridColumn):
-    """ Column that tracks and filters for items with deleted attribute. """
+    """Column that tracks and filters for items with deleted attribute."""
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filter_labels_and_vals = {"active": "False", "deleted": "True", "all": "All"}
         accepted_filters = []
         for label, val in accepted_filter_labels_and_vals.items():
@@ -399,10 +483,10 @@ class DeletedColumn(GridColumn):
 
 
 class PurgedColumn(GridColumn):
-    """ Column that tracks and filters for items with purged attribute. """
+    """Column that tracks and filters for items with purged attribute."""
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filter_labels_and_vals = {"nonpurged": "False", "purged": "True", "all": "All"}
         accepted_filters = []
         for label, val in accepted_filter_labels_and_vals.items():
@@ -440,7 +524,7 @@ class StateColumn(GridColumn):
 
     def get_accepted_filters(self):
         """Returns a list of accepted filters for this column."""
-        all = GridColumnFilter('all', {self.key: 'All'})
+        all = GridColumnFilter("all", {self.key: "All"})
         accepted_filters = [all]
         for v in self.model_class.states.values():
             args = {self.key: v}
@@ -449,7 +533,7 @@ class StateColumn(GridColumn):
 
 
 class SharingStatusColumn(GridColumn):
-    """ Grid column to indicate sharing status. """
+    """Grid column to indicate sharing status."""
 
     def __init__(self, *args, **kwargs):
         self.use_shared_with_count = kwargs.pop("use_shared_with_count", False)
@@ -477,7 +561,7 @@ class SharingStatusColumn(GridColumn):
         return item.users_shared_with
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter histories by sharing status. """
+        """Modify query to filter histories by sharing status."""
         if column_filter == "All":
             pass
         elif column_filter:
@@ -493,7 +577,7 @@ class SharingStatusColumn(GridColumn):
         return query
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filter_labels_and_vals = {}
         accepted_filter_labels_and_vals["private"] = "private"
         accepted_filter_labels_and_vals["shared"] = "shared"
@@ -508,9 +592,19 @@ class SharingStatusColumn(GridColumn):
 
 
 class GridOperation:
-    def __init__(self, label, key=None, condition=None, allow_multiple=True, allow_popup=True,
-                 target=None, url_args=None, async_compatible=False, confirm=None,
-                 global_operation=None):
+    def __init__(
+        self,
+        label,
+        key=None,
+        condition=None,
+        allow_multiple=True,
+        allow_popup=True,
+        target=None,
+        url_args=None,
+        async_compatible=False,
+        confirm=None,
+        global_operation=None,
+    ):
         self.label = label
         self.key = key
         self.allow_multiple = allow_multiple
@@ -533,7 +627,7 @@ class GridOperation:
                 url_args = self.url_args(item)
             else:
                 url_args = dict(self.url_args)
-            url_args['id'] = item.id
+            url_args["id"] = item.id
             return url_args
         else:
             return dict(operation=self.label, id=item.id)
@@ -546,10 +640,10 @@ class GridOperation:
 
 
 class DisplayByUsernameAndSlugGridOperation(GridOperation):
-    """ Operation to display an item by username and slug. """
+    """Operation to display an item by username and slug."""
 
     def get_url_args(self, item):
-        return {'action': 'display_by_username_and_slug', 'username': item.user.username, 'slug': item.slug}
+        return {"action": "display_by_username_and_slug", "username": item.user.username, "slug": item.slug}
 
 
 class GridAction:
@@ -575,6 +669,7 @@ class Grid:
     """
     Specifies the content and format of a grid (data table).
     """
+
     title = ""
     model_class: Optional[type] = None
     show_item_checkboxes = False
@@ -612,8 +707,8 @@ class Grid:
     def __call__(self, trans, **kwargs):
         # Get basics.
         # FIXME: pretty sure this is only here to pass along, can likely be eliminated
-        status = kwargs.get('status', None)
-        message = kwargs.get('message', None)
+        status = kwargs.get("status", None)
+        message = kwargs.get("message", None)
         # Build a base filter and sort key that is the combination of the saved state and defaults.
         # Saved state takes preference over defaults.
         base_filter = {}
@@ -627,10 +722,10 @@ class Grid:
         # Maintain sort state in generated urls
         extra_url_args = {}
         # Determine whether use_default_filter flag is set.
-        use_default_filter_str = kwargs.get('use_default_filter')
+        use_default_filter_str = kwargs.get("use_default_filter")
         use_default_filter = False
         if use_default_filter_str:
-            use_default_filter = (use_default_filter_str.lower() == 'true')
+            use_default_filter = use_default_filter_str.lower() == "true"
         # Process filtering arguments to (a) build a query that represents the filter and (b) build a
         # dictionary that denotes the current filter.
         cur_filter_dict = {}
@@ -669,6 +764,7 @@ class Grid:
                             a_list = loads_recurse(element)
                             decoded_list = decoded_list + a_list
                     return decoded_list
+
                 # If column filter found, apply it.
                 if column_filter is not None:
                     # TextColumns may have a mix of json and strings.
@@ -677,18 +773,18 @@ class Grid:
                         if len(column_filter) == 1:
                             column_filter = column_filter[0]
                     # Interpret ',' as a separator for multiple terms.
-                    if isinstance(column_filter, str) and column_filter.find(',') != -1:
-                        column_filter = column_filter.split(',')
+                    if isinstance(column_filter, str) and column_filter.find(",") != -1:
+                        column_filter = column_filter.split(",")
 
                     # Check if filter is empty
                     if isinstance(column_filter, list):
                         # Remove empty strings from filter list
-                        column_filter = [x for x in column_filter if x != '']
+                        column_filter = [x for x in column_filter if x != ""]
                         if len(column_filter) == 0:
                             continue
                     elif isinstance(column_filter, str):
                         # If filter criterion is empty, do nothing.
-                        if column_filter == '':
+                        if column_filter == "":
                             continue
 
                     # Update query.
@@ -706,17 +802,17 @@ class Grid:
                         extra_url_args[f"f-{column.key}"] = column_filter
         # Process sort arguments.
         sort_key = None
-        if 'sort' in kwargs:
-            sort_key = kwargs['sort']
+        if "sort" in kwargs:
+            sort_key = kwargs["sort"]
         elif base_sort_key:
             sort_key = base_sort_key
         if sort_key:
-            ascending = not(sort_key.startswith("-"))
+            ascending = not (sort_key.startswith("-"))
             # Queries that include table joins cannot guarantee unique column names.  This problem is
             # handled by setting the column_filter value to <TableName>.<ColumnName>.
             table_name = None
-            if sort_key.find('.') > -1:
-                a_list = sort_key.split('.')
+            if sort_key.find(".") > -1:
+                a_list = sort_key.split(".")
                 if ascending:
                     table_name = a_list[0]
                 else:
@@ -728,25 +824,25 @@ class Grid:
                 column_name = sort_key[1:]
             # Sort key is a column key.
             for column in self.columns:
-                if column.key and column.key.find('.') > -1:
-                    column_key = column.key.split('.')[1]
+                if column.key and column.key.find(".") > -1:
+                    column_key = column.key.split(".")[1]
                 else:
                     column_key = column.key
                 if (table_name is None or table_name == column.model_class.__name__) and column_key == column_name:
                     query = column.sort(trans, query, ascending, column_name=column_name)
                     break
-            extra_url_args['sort'] = sort_key
+            extra_url_args["sort"] = sort_key
         # There might be a current row
         current_item = self.get_current_item(trans, **kwargs)
         # Process page number.
         num_pages = None
         total_row_count_query = query  # query without limit applied to get total number of rows.
         if self.use_paging:
-            if 'page' in kwargs:
-                if kwargs['page'] == 'all':
+            if "page" in kwargs:
+                if kwargs["page"] == "all":
                     page_num = 0
                 else:
-                    page_num = int(kwargs['page'])
+                    page_num = int(kwargs["page"])
             else:
                 page_num = 1
             if page_num == 0:
@@ -764,14 +860,14 @@ class Grid:
         # Log grid view.
         context = str(self.__class__.__name__)
         params = cur_filter_dict.copy()
-        params['sort'] = sort_key
+        params["sort"] = sort_key
 
         # Render grid.
         def url(*args, **kwargs):
-            route_name = kwargs.pop('__route_name__', None)
+            route_name = kwargs.pop("__route_name__", None)
             # Only include sort/filter arguments if not linking to another
             # page. This is a bit of a hack.
-            if 'action' in kwargs:
+            if "action" in kwargs:
                 new_kwargs = dict()
             else:
                 new_kwargs = dict(extra_url_args)
@@ -780,111 +876,116 @@ class Grid:
                 new_kwargs.update(args[0])
             new_kwargs.update(kwargs)
             # We need to encode item ids
-            if 'id' in new_kwargs:
-                id = new_kwargs['id']
+            if "id" in new_kwargs:
+                id = new_kwargs["id"]
                 if isinstance(id, list):
-                    new_kwargs['id'] = [trans.security.encode_id(i) for i in id]
+                    new_kwargs["id"] = [trans.security.encode_id(i) for i in id]
                 else:
-                    new_kwargs['id'] = trans.security.encode_id(id)
+                    new_kwargs["id"] = trans.security.encode_id(id)
             # The url_for invocation *must* include a controller and action.
-            if 'controller' not in new_kwargs:
-                new_kwargs['controller'] = trans.controller
-            if 'action' not in new_kwargs:
-                new_kwargs['action'] = trans.action
+            if "controller" not in new_kwargs:
+                new_kwargs["controller"] = trans.controller
+            if "action" not in new_kwargs:
+                new_kwargs["action"] = trans.action
             if route_name:
                 return url_for(route_name, **new_kwargs)
             return url_for(**new_kwargs)
 
-        self.use_panels = (kwargs.get('use_panels', False) in [True, 'True', 'true'])
-        self.advanced_search = (kwargs.get('advanced_search', False) in [True, 'True', 'true'])
+        self.use_panels = kwargs.get("use_panels", False) in [True, "True", "true"]
+        self.advanced_search = kwargs.get("advanced_search", False) in [True, "True", "true"]
         # Currently, filling the template returns a str object; this requires decoding the string into a
         # unicode object within mako templates. What probably should be done is to return the template as
         # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
         # results via a controller method, which is require substantial changes. Hence, for now, return grid
         # as str.
         grid_config = {
-            'title': self.title,
-            'title_id': getattr(self, "title_id", None),
-            'url_base': trans.request.path_url,
-            'async_ops': [],
-            'categorical_filters': {},
-            'filters': cur_filter_dict,
-            'sort_key': sort_key,
-            'show_item_checkboxes': self.show_item_checkboxes or kwargs.get('show_item_checkboxes', '') in ['True', 'true'],
-            'cur_page_num': page_num,
-            'num_page_links': self.num_page_links,
-            'status': status,
-            'message': restore_text(message),
-            'global_actions': [],
-            'operations': [],
-            'items': [],
-            'columns': [],
-            'model_class': str(self.model_class),
-            'use_paging': self.use_paging,
-            'legend': self.legend,
-            'current_item_id': False,
-            'use_hide_message': self.use_hide_message,
-            'default_filter_dict': self.default_filter,
-            'advanced_search': self.advanced_search,
-            'info_text': self.info_text,
-            'url': url(dict()),
-            'refresh_frames': kwargs.get('refresh_frames', [])
+            "title": self.title,
+            "title_id": getattr(self, "title_id", None),
+            "url_base": trans.request.path_url,
+            "async_ops": [],
+            "categorical_filters": {},
+            "filters": cur_filter_dict,
+            "sort_key": sort_key,
+            "show_item_checkboxes": self.show_item_checkboxes
+            or kwargs.get("show_item_checkboxes", "") in ["True", "true"],
+            "cur_page_num": page_num,
+            "num_page_links": self.num_page_links,
+            "status": status,
+            "message": restore_text(message),
+            "global_actions": [],
+            "operations": [],
+            "items": [],
+            "columns": [],
+            "model_class": str(self.model_class),
+            "use_paging": self.use_paging,
+            "legend": self.legend,
+            "current_item_id": False,
+            "use_hide_message": self.use_hide_message,
+            "default_filter_dict": self.default_filter,
+            "advanced_search": self.advanced_search,
+            "info_text": self.info_text,
+            "url": url(dict()),
+            "refresh_frames": kwargs.get("refresh_frames", []),
         }
         if current_item:
-            grid_config['current_item_id'] = current_item.id
+            grid_config["current_item_id"] = current_item.id
         for column in self.columns:
-            extra = ''
+            extra = ""
             if column.sortable:
                 if sort_key.endswith(column.key):
                     if not sort_key.startswith("-"):
                         extra = "&darr;"
                     else:
                         extra = "&uarr;"
-            grid_config['columns'].append({
-                'key': column.key,
-                'visible': column.visible,
-                'nowrap': column.nowrap,
-                'attach_popup': column.attach_popup,
-                'label_id_prefix': column.label_id_prefix,
-                'sortable': column.sortable,
-                'label': column.label,
-                'filterable': column.filterable,
-                'delayed': column.delayed,
-                'is_text': isinstance(column, TextColumn),
-                'extra': extra
-            })
+            grid_config["columns"].append(
+                {
+                    "key": column.key,
+                    "visible": column.visible,
+                    "nowrap": column.nowrap,
+                    "attach_popup": column.attach_popup,
+                    "label_id_prefix": column.label_id_prefix,
+                    "sortable": column.sortable,
+                    "label": column.label,
+                    "filterable": column.filterable,
+                    "delayed": column.delayed,
+                    "is_text": isinstance(column, TextColumn),
+                    "extra": extra,
+                }
+            )
         for operation in self.operations:
-            grid_config['operations'].append({
-                'allow_multiple': operation.allow_multiple,
-                'allow_popup': operation.allow_popup,
-                'target': operation.target,
-                'label': operation.label,
-                'confirm': operation.confirm,
-                'href': url(**operation.url_args) if isinstance(operation.url_args, dict) else None,
-                'global_operation': False
-            })
+            grid_config["operations"].append(
+                {
+                    "allow_multiple": operation.allow_multiple,
+                    "allow_popup": operation.allow_popup,
+                    "target": operation.target,
+                    "label": operation.label,
+                    "confirm": operation.confirm,
+                    "href": url(**operation.url_args) if isinstance(operation.url_args, dict) else None,
+                    "global_operation": False,
+                }
+            )
             if operation.allow_multiple:
-                grid_config['show_item_checkboxes'] = True
+                grid_config["show_item_checkboxes"] = True
             if operation.global_operation:
-                grid_config['global_operation'] = url(** (operation.global_operation()))
+                grid_config["global_operation"] = url(**(operation.global_operation()))
         for action in self.global_actions:
-            grid_config['global_actions'].append({
-                'url_args': url(**action.url_args),
-                'label': action.label,
-                'target': action.target
-            })
+            grid_config["global_actions"].append(
+                {"url_args": url(**action.url_args), "label": action.label, "target": action.target}
+            )
         for operation in [op for op in self.operations if op.async_compatible]:
-            grid_config['async_ops'].append(operation.label.lower())
+            grid_config["async_ops"].append(operation.label.lower())
         for column in self.columns:
             if column.filterable is not None and not isinstance(column, TextColumn):
-                grid_config['categorical_filters'][column.key] = {filter.label: filter.args for filter in column.get_accepted_filters()}
+                grid_config["categorical_filters"][column.key] = {
+                    filter.label: filter.args for filter in column.get_accepted_filters()
+                }
         for item in query:
             item_dict = {
-                'id': item.id,
-                'encode_id': trans.security.encode_id(item.id),
-                'link': [],
-                'operation_config': {},
-                'column_config': {}
+                "id": item.id,
+                "encode_id": trans.security.encode_id(item.id),
+                "link": [],
+                "operation_config": {},
+                "column_config": {},
             }
             for column in self.columns:
                 if column.visible:
@@ -896,19 +997,15 @@ class Grid:
                     target = column.target
                     value = unicodify(column.get_value(trans, self, item))
                     if value:
-                        value = value.replace('/', '//')
-                    item_dict['column_config'][column.label] = {
-                        'link': link,
-                        'value': value,
-                        'target': target
-                    }
+                        value = value.replace("/", "//")
+                    item_dict["column_config"][column.label] = {"link": link, "value": value, "target": target}
             for operation in self.operations:
-                item_dict['operation_config'][operation.label] = {
-                    'allowed': operation.allowed(item),
-                    'url_args': url(**operation.get_url_args(item)),
-                    'target': operation.target
+                item_dict["operation_config"][operation.label] = {
+                    "allowed": operation.allowed(item),
+                    "url_args": url(**operation.get_url_args(item)),
+                    "target": operation.target,
                 }
-            grid_config['items'].append(item_dict)
+            grid_config["items"].append(item_dict)
 
         if self.use_paging and num_pages is None:
             # TODO: it would be better to just return this as None, render, and fire
@@ -923,8 +1020,8 @@ class Grid:
 
     def get_ids(self, **kwargs):
         id = []
-        if 'id' in kwargs:
-            id = kwargs['id']
+        if "id" in kwargs:
+            id = kwargs["id"]
             # Coerce ids to list
             if not isinstance(id, list):
                 id = id.split(",")
diff --git a/lib/galaxy/web/framework/helpers/tags.py b/lib/galaxy/web/framework/helpers/tags.py
index 255460bba8f..7afed6843ba 100644
--- a/lib/galaxy/web/framework/helpers/tags.py
+++ b/lib/galaxy/web/framework/helpers/tags.py
@@ -22,10 +22,8 @@ def format_attrs(**attrs):
     >>> format_attrs(p=None) == u''
     True
     """
-    strings = [f' {attr}="{escape_silent(value)}"'
-        for attr, value in sorted(attrs.items())
-        if value is not None]
-    return ''.join(strings)
+    strings = [f' {attr}="{escape_silent(value)}"' for attr, value in sorted(attrs.items()) if value is not None]
+    return "".join(strings)
 
 
 def javascript_link(*urls, **attrs):
@@ -47,16 +45,16 @@ def javascript_link(*urls, **attrs):
         <script src="/app.js" type="text/javascript"></script>
         <script src="/test/test.1.js" type="text/javascript"></script>
     """
-    if 'defer' in attrs:
-        if attrs['defer']:
-            attrs['defer'] = 'defer'
+    if "defer" in attrs:
+        if attrs["defer"]:
+            attrs["defer"] = "defer"
         else:
-            del attrs['defer']
-    attrs['type'] = 'text/javascript'
-    tag_template = '<script%s></script>'
+            del attrs["defer"]
+    attrs["type"] = "text/javascript"
+    tag_template = "<script%s></script>"
     tags = []
     for url in urls:
-        attrs['src'] = url
+        attrs["src"] = url
         tag = tag_template % format_attrs(**attrs)
         tags.append(tag)
     return "\n".join(tags)
@@ -81,10 +79,10 @@ def stylesheet_link(*urls, **attrs):
     attrs.setdefault("rel", "stylesheet")
     attrs.setdefault("type", "text/css")
     attrs.setdefault("media", "screen")
-    tag_template = '<link%s />'
+    tag_template = "<link%s />"
     tags = []
     for url in urls:
-        attrs['href'] = url
+        attrs["href"] = url
         tag = tag_template % format_attrs(**attrs)
         tags.append(tag)
     return "\n".join(tags)
diff --git a/lib/galaxy/web/framework/middleware/batch.py b/lib/galaxy/web/framework/middleware/batch.py
index 468a57f5143..4d7ad739d97 100644
--- a/lib/galaxy/web/framework/middleware/batch.py
+++ b/lib/galaxy/web/framework/middleware/batch.py
@@ -31,7 +31,7 @@ import webob.exc
 
 from galaxy.util import (
     smart_str,
-    unicodify
+    unicodify,
 )
 
 log = logging.getLogger(__name__)
@@ -60,13 +60,14 @@ class BatchMiddleware:
       * `body` is the text body of the request (optional)
       * `contentType` content-type request header (defaults to application/json)
     """
+
     DEFAULT_CONFIG = {
-        'route': '/api/batch',
-        'allowed_routes': [
-            r'^api\/users.*',
-            r'^api\/histories.*',
-            r'^api\/jobs.*',
-        ]
+        "route": "/api/batch",
+        "allowed_routes": [
+            r"^api\/users.*",
+            r"^api\/histories.*",
+            r"^api\/jobs.*",
+        ],
     }
 
     def __init__(self, application, galaxy, config=None):
@@ -76,11 +77,11 @@ class BatchMiddleware:
         self.galaxy = galaxy
         self.config = self.DEFAULT_CONFIG.copy()
         self.config.update(config)
-        self.base_url = routes.url_for('/')
+        self.base_url = routes.url_for("/")
         self.handle_request = self.galaxy.handle_request
 
     def __call__(self, environ, start_response):
-        if environ['PATH_INFO'] == self.config['route']:
+        if environ["PATH_INFO"] == self.config["route"]:
             return self.process_batch_requests(environ, start_response)
         return self.application(environ, start_response)
 
@@ -90,12 +91,12 @@ class BatchMiddleware:
         JSON responses, and wraps them in the batch call response.
         """
         payload = self._read_post_payload(batch_environ)
-        requests = payload.get('batch', [])
+        requests = payload.get("batch", [])
 
         responses = []
         for request in requests:
-            if not self._is_allowed_route(request['url']):
-                responses.append(self._disallowed_route_response(request['url']))
+            if not self._is_allowed_route(request["url"]):
+                responses.append(self._disallowed_route_response(request["url"]))
                 continue
 
             request_environ = self._build_request_environ(batch_environ, request)
@@ -103,33 +104,40 @@ class BatchMiddleware:
             responses.append(response)
 
         batch_response_body = smart_str(json.dumps(responses))
-        start_response('200 OK', [
-            ('Content-Length', str(len(batch_response_body))),
-            ('Content-Type', 'application/json'),
-        ])
+        start_response(
+            "200 OK",
+            [
+                ("Content-Length", str(len(batch_response_body))),
+                ("Content-Type", "application/json"),
+            ],
+        )
         return [batch_response_body]
 
     def _read_post_payload(self, environ):
-        request_body_size = int(environ.get('CONTENT_LENGTH', 0))
-        request_body = environ['wsgi.input'].read(request_body_size) or '{}'
+        request_body_size = int(environ.get("CONTENT_LENGTH", 0))
+        request_body = environ["wsgi.input"].read(request_body_size) or "{}"
         # TODO: json decode error handling
         # log.debug( 'request_body: (%s)\n%s', type( request_body ), request_body )
         payload = json.loads(unicodify(request_body))
         return payload
 
     def _is_allowed_route(self, route):
-        if self.config.get('allowed_routes', None):
-            shortened_route = route.replace(self.base_url, '', 1)
-            matches = [re.match(allowed, shortened_route) for allowed in self.config['allowed_routes']]
+        if self.config.get("allowed_routes", None):
+            shortened_route = route.replace(self.base_url, "", 1)
+            matches = [re.match(allowed, shortened_route) for allowed in self.config["allowed_routes"]]
             return any(matches)
         return True
 
     def _disallowed_route_response(self, route):
-        return dict(status=403, headers=self._default_headers(), body={
-            'err_msg': 'Disallowed route used for batch operation',
-            'route': route,
-            'allowed': self.config['allowed_routes']
-        })
+        return dict(
+            status=403,
+            headers=self._default_headers(),
+            body={
+                "err_msg": "Disallowed route used for batch operation",
+                "route": route,
+                "allowed": self.config["allowed_routes"],
+            },
+        )
 
     def _build_request_environ(self, original_environ, request):
         """
@@ -140,20 +148,20 @@ class BatchMiddleware:
         # copy the original environ and reconstruct a fake version for each batched request
         request_environ = original_environ.copy()
         # TODO: for now, do not overwrite the other headers used in the main api/batch request
-        request_environ['CONTENT_TYPE'] = request.get('contentType', 'application/json')
-        request_environ['REQUEST_METHOD'] = request.get('method', request.get('type', 'GET'))
-        url = '{}://{}{}'.format(request_environ.get('wsgi.url_scheme'),
-                                 request_environ.get('HTTP_HOST'),
-                                 request['url'])
+        request_environ["CONTENT_TYPE"] = request.get("contentType", "application/json")
+        request_environ["REQUEST_METHOD"] = request.get("method", request.get("type", "GET"))
+        url = "{}://{}{}".format(
+            request_environ.get("wsgi.url_scheme"), request_environ.get("HTTP_HOST"), request["url"]
+        )
         parsed = urlparse(url)
-        request_environ['PATH_INFO'] = parsed.path
-        request_environ['QUERY_STRING'] = parsed.query
+        request_environ["PATH_INFO"] = parsed.path
+        request_environ["QUERY_STRING"] = parsed.query
 
-        request_body = request.get('body', '')
-        request_body = request_body.encode('utf8')
-        request_environ['CONTENT_LENGTH'] = len(request_body)
+        request_body = request.get("body", "")
+        request_body = request_body.encode("utf8")
+        request_environ["CONTENT_LENGTH"] = len(request_body)
         request_body = io.BytesIO(request_body)
-        request_environ['wsgi.input'] = request_body
+        request_environ["wsgi.input"] = request_body
 
         return request_environ
 
@@ -178,14 +186,14 @@ class BatchMiddleware:
         return dict(
             status=trans.response.status,
             headers=trans.response.headers,
-            body=json.loads(unicodify(self.galaxy.make_body_iterable(trans, body)[0]))
+            body=json.loads(unicodify(self.galaxy.make_body_iterable(trans, body)[0])),
         )
 
     def _default_headers(self):
         return {
-            'x-frame-options': 'SAMEORIGIN',
-            'content-type': 'application/json',
-            'cache-control': 'max-age=0,no-cache,no-store'
+            "x-frame-options": "SAMEORIGIN",
+            "content-type": "application/json",
+            "cache-control": "max-age=0,no-cache,no-store",
         }
 
     def handle_exception(self, environ):
diff --git a/lib/galaxy/web/framework/middleware/error.py b/lib/galaxy/web/framework/middleware/error.py
index 9c9bdf9b39a..cb6ccfb8d99 100644
--- a/lib/galaxy/web/framework/middleware/error.py
+++ b/lib/galaxy/web/framework/middleware/error.py
@@ -17,16 +17,20 @@ from typing import cast
 import markupsafe
 from paste import (
     request,
-    wsgilib
+    wsgilib,
+)
+from paste.exceptions import (
+    collector,
+    formatter,
+    reporter,
 )
-from paste.exceptions import collector, formatter, reporter
 
-__all__ = ('ErrorMiddleware', 'handle_exception')
+__all__ = ("ErrorMiddleware", "handle_exception")
 
 
 class _NoDefault:
     def __repr__(self):
-        return '<NoDefault>'
+        return "<NoDefault>"
 
 
 NoDefault = _NoDefault()
@@ -88,53 +92,60 @@ class ErrorMiddleware:
 
     """
 
-    def __init__(self, application, global_conf=None,
-                 debug=NoDefault,
-                 error_email=None,
-                 error_log=None,
-                 show_exceptions_in_wsgi_errors=NoDefault,
-                 from_address=None,
-                 smtp_server=None,
-                 smtp_username=None,
-                 smtp_password=None,
-                 smtp_use_tls=False,
-                 error_subject_prefix=None,
-                 error_message=None,
-                 xmlhttp_key=None):
+    def __init__(
+        self,
+        application,
+        global_conf=None,
+        debug=NoDefault,
+        error_email=None,
+        error_log=None,
+        show_exceptions_in_wsgi_errors=NoDefault,
+        from_address=None,
+        smtp_server=None,
+        smtp_username=None,
+        smtp_password=None,
+        smtp_use_tls=False,
+        error_subject_prefix=None,
+        error_message=None,
+        xmlhttp_key=None,
+    ):
         from paste.util import converters
+
         self.application = application
         # @@: global_conf should be handled elsewhere in a separate
         # function for the entry point
         if global_conf is None:
             global_conf = {}
         if debug is NoDefault:
-            debug = converters.asbool(global_conf.get('debug'))
+            debug = converters.asbool(global_conf.get("debug"))
         if show_exceptions_in_wsgi_errors is NoDefault:
-            show_exceptions_in_wsgi_errors = converters.asbool(global_conf.get('show_exceptions_in_wsgi_errors'))
+            show_exceptions_in_wsgi_errors = converters.asbool(global_conf.get("show_exceptions_in_wsgi_errors"))
         self.debug_mode = converters.asbool(debug)
         if error_email is None:
-            error_email = (global_conf.get('error_email')
-                           or global_conf.get('admin_email')
-                           or global_conf.get('webmaster_email')
-                           or global_conf.get('sysadmin_email'))
+            error_email = (
+                global_conf.get("error_email")
+                or global_conf.get("admin_email")
+                or global_conf.get("webmaster_email")
+                or global_conf.get("sysadmin_email")
+            )
         self.error_email = converters.aslist(error_email)
         self.error_log = error_log
         self.show_exceptions_in_wsgi_errors = show_exceptions_in_wsgi_errors
         if from_address is None:
-            from_address = global_conf.get('error_from_address', 'errors@localhost')
+            from_address = global_conf.get("error_from_address", "errors@localhost")
         self.from_address = from_address
         if smtp_server is None:
-            smtp_server = global_conf.get('smtp_server', 'localhost')
+            smtp_server = global_conf.get("smtp_server", "localhost")
         self.smtp_server = smtp_server
-        self.smtp_username = smtp_username or global_conf.get('smtp_username')
-        self.smtp_password = smtp_password or global_conf.get('smtp_password')
-        self.smtp_use_tls = smtp_use_tls or converters.asbool(global_conf.get('smtp_use_tls'))
-        self.error_subject_prefix = error_subject_prefix or ''
+        self.smtp_username = smtp_username or global_conf.get("smtp_username")
+        self.smtp_password = smtp_password or global_conf.get("smtp_password")
+        self.smtp_use_tls = smtp_use_tls or converters.asbool(global_conf.get("smtp_use_tls"))
+        self.error_subject_prefix = error_subject_prefix or ""
         if error_message is None:
-            error_message = global_conf.get('error_message')
+            error_message = global_conf.get("error_message")
         self.error_message = error_message
         if xmlhttp_key is None:
-            xmlhttp_key = global_conf.get('xmlhttp_key', '_')
+            xmlhttp_key = global_conf.get("xmlhttp_key", "_")
         self.xmlhttp_key = xmlhttp_key
 
     def __call__(self, environ, start_response):
@@ -144,9 +155,9 @@ class ErrorMiddleware:
         # We want to be careful about not sending headers twice,
         # and the content type that the app has committed to (if there
         # is an exception in the iterator body of the response)
-        if environ.get('paste.throw_errors'):
+        if environ.get("paste.throw_errors"):
             return self.application(environ, start_response)
-        environ['paste.throw_errors'] = True
+        environ["paste.throw_errors"] = True
 
         try:
             __traceback_supplement__ = Supplement, self, environ
@@ -156,12 +167,10 @@ class ErrorMiddleware:
         except Exception:
             exc_info = sys.exc_info()
             try:
-                for expect in environ.get('paste.expected_exceptions', []):
+                for expect in environ.get("paste.expected_exceptions", []):
                     if isinstance(exc_info[1], expect):
                         raise
-                start_response('500 Internal Server Error',
-                               [('content-type', 'text/html')],
-                               exc_info)
+                start_response("500 Internal Server Error", [("content-type", "text/html")], exc_info)
                 # @@: it would be nice to deal with bad content types here
                 response = self.exception_handler(exc_info, environ)
                 return [response]
@@ -182,7 +191,8 @@ class ErrorMiddleware:
             if dict(get_vars).get(self.xmlhttp_key):
                 simple_html_error = True
         return handle_exception(
-            exc_info, environ['wsgi.errors'],
+            exc_info,
+            environ["wsgi.errors"],
             html=True,
             debug_mode=self.debug_mode,
             error_email=self.error_email,
@@ -196,7 +206,8 @@ class ErrorMiddleware:
             error_subject_prefix=self.error_subject_prefix,
             error_message=self.error_message,
             simple_html_error=simple_html_error,
-            environ=environ)
+            environ=environ,
+        )
 
 
 class ResponseStartChecker:
@@ -231,8 +242,7 @@ class CatchingIter:
         return self
 
     def __next__(self):
-        __traceback_supplement__ = (
-            Supplement, self.error_middleware, self.environ)
+        __traceback_supplement__ = (Supplement, self.error_middleware, self.environ)
         if self.closed:
             raise StopIteration
         try:
@@ -248,16 +258,12 @@ class CatchingIter:
             self.closed = True
             close_response = self._close()
             exc_info = sys.exc_info()
-            response = self.error_middleware.exception_handler(
-                exc_info, self.environ)
+            response = self.error_middleware.exception_handler(exc_info, self.environ)
             if close_response is not None:
-                response += (
-                    f'<hr noshade>Error in .close():<br>{close_response}')
+                response += f"<hr noshade>Error in .close():<br>{close_response}"
 
             if not self.start_checker.response_started:
-                self.start_checker('500 Internal Server Error',
-                                   [('content-type', 'text/html')],
-                                   exc_info)
+                self.start_checker("500 Internal Server Error", [("content-type", "text/html")], exc_info)
 
             return response
 
@@ -269,14 +275,13 @@ class CatchingIter:
 
     def _close(self):
         """Close and return any error message"""
-        if not hasattr(self.app_iterable, 'close'):
+        if not hasattr(self.app_iterable, "close"):
             return None
         try:
             self.app_iterable.close()
             return None
         except Exception:
-            close_response = self.error_middleware.exception_handler(
-                sys.exc_info(), self.environ)
+            close_response = self.error_middleware.exception_handler(sys.exc_info(), self.environ)
             return close_response
 
 
@@ -294,59 +299,66 @@ class Supplement:
 
     def extraData(self):
         data = {}
-        cgi_vars = data[('extra', 'CGI Variables')] = {}
-        wsgi_vars = data[('extra', 'WSGI Variables')] = {}
-        hide_vars = ['paste.config', 'wsgi.errors', 'wsgi.input',
-                     'wsgi.multithread', 'wsgi.multiprocess',
-                     'wsgi.run_once', 'wsgi.version',
-                     'wsgi.url_scheme']
+        cgi_vars = data[("extra", "CGI Variables")] = {}
+        wsgi_vars = data[("extra", "WSGI Variables")] = {}
+        hide_vars = [
+            "paste.config",
+            "wsgi.errors",
+            "wsgi.input",
+            "wsgi.multithread",
+            "wsgi.multiprocess",
+            "wsgi.run_once",
+            "wsgi.version",
+            "wsgi.url_scheme",
+        ]
         for name, value in self.environ.items():
             if name.upper() == name:
                 if value:
                     cgi_vars[name] = value
             elif name not in hide_vars:
                 wsgi_vars[name] = value
-        if self.environ['wsgi.version'] != (1, 0):
-            wsgi_vars['wsgi.version'] = self.environ['wsgi.version']
-        proc_desc = tuple(int(bool(self.environ[key])) for key in (
-            'wsgi.multiprocess',
-            'wsgi.multithread',
-            'wsgi.run_once'
-        ))
-        wsgi_vars['wsgi process'] = self.process_combos[proc_desc]
-        wsgi_vars['application'] = self.middleware.application
-        if 'paste.config' in self.environ:
-            data[('extra', 'Configuration')] = dict(self.environ['paste.config'])
+        if self.environ["wsgi.version"] != (1, 0):
+            wsgi_vars["wsgi.version"] = self.environ["wsgi.version"]
+        proc_desc = tuple(
+            int(bool(self.environ[key])) for key in ("wsgi.multiprocess", "wsgi.multithread", "wsgi.run_once")
+        )
+        wsgi_vars["wsgi process"] = self.process_combos[proc_desc]
+        wsgi_vars["application"] = self.middleware.application
+        if "paste.config" in self.environ:
+            data[("extra", "Configuration")] = dict(self.environ["paste.config"])
         return data
 
     process_combos = {
         # multiprocess, multithread, run_once
-        (0, 0, 0): 'Non-concurrent server',
-        (0, 1, 0): 'Multithreaded',
-        (1, 0, 0): 'Multiprocess',
-        (1, 1, 0): 'Multi process AND threads (?)',
-        (0, 0, 1): 'Non-concurrent CGI',
-        (0, 1, 1): 'Multithread CGI (?)',
-        (1, 0, 1): 'CGI',
-        (1, 1, 1): 'Multi thread/process CGI (?)',
+        (0, 0, 0): "Non-concurrent server",
+        (0, 1, 0): "Multithreaded",
+        (1, 0, 0): "Multiprocess",
+        (1, 1, 0): "Multi process AND threads (?)",
+        (0, 0, 1): "Non-concurrent CGI",
+        (0, 1, 1): "Multithread CGI (?)",
+        (1, 0, 1): "CGI",
+        (1, 1, 1): "Multi thread/process CGI (?)",
     }
 
 
-def handle_exception(exc_info, error_stream, html=True,
-                     debug_mode=False,
-                     error_email=None,
-                     error_log=None,
-                     show_exceptions_in_wsgi_errors=False,
-                     error_email_from='errors@localhost',
-                     smtp_server='localhost',
-                     smtp_username=None,
-                     smtp_password=None,
-                     smtp_use_tls=False,
-                     error_subject_prefix='',
-                     error_message=None,
-                     simple_html_error=False,
-                     environ=None
-                     ):
+def handle_exception(
+    exc_info,
+    error_stream,
+    html=True,
+    debug_mode=False,
+    error_email=None,
+    error_log=None,
+    show_exceptions_in_wsgi_errors=False,
+    error_email_from="errors@localhost",
+    smtp_server="localhost",
+    smtp_username=None,
+    smtp_password=None,
+    smtp_use_tls=False,
+    error_subject_prefix="",
+    error_message=None,
+    simple_html_error=False,
+    environ=None,
+):
     """
     For exception handling outside of a web context
 
@@ -366,7 +378,7 @@ def handle_exception(exc_info, error_stream, html=True,
     """
     reported = False
     exc_data = collector.collect_exception(*exc_info)
-    extra_data = ''
+    extra_data = ""
     if error_email:
         rep = reporter.EmailReporter(
             to_addresses=error_email,
@@ -375,57 +387,54 @@ def handle_exception(exc_info, error_stream, html=True,
             smtp_username=smtp_username,
             smtp_password=smtp_password,
             smtp_use_tls=smtp_use_tls,
-            subject_prefix=error_subject_prefix)
+            subject_prefix=error_subject_prefix,
+        )
         rep_err = send_report(rep, exc_data, html=html)
         if rep_err:
             extra_data += rep_err
         else:
             reported = True
     if error_log:
-        rep = reporter.LogReporter(
-            filename=error_log)
+        rep = reporter.LogReporter(filename=error_log)
         rep_err = send_report(rep, exc_data, html=html)
         if rep_err:
             extra_data += rep_err
         else:
             reported = True
     if show_exceptions_in_wsgi_errors:
-        rep = reporter.FileReporter(
-            file=error_stream)
+        rep = reporter.FileReporter(file=error_stream)
         rep_err = send_report(rep, exc_data, html=html)
         if rep_err:
             extra_data += rep_err
         else:
             reported = True
     else:
-        error_stream.write('Error - {}: {}\n'.format(
-            exc_data.exception_type, exc_data.exception_value))
+        error_stream.write("Error - {}: {}\n".format(exc_data.exception_type, exc_data.exception_value))
     if html:
         if debug_mode and simple_html_error:
             return_error = formatter.format_html(
-                exc_data, include_hidden_frames=False,
-                include_reusable=False, show_extra_data=False)
+                exc_data, include_hidden_frames=False, include_reusable=False, show_extra_data=False
+            )
             reported = True
         elif debug_mode and not simple_html_error:
-            error_html = formatter.format_html(
-                exc_data,
-                include_hidden_frames=True,
-                include_reusable=False)
+            error_html = formatter.format_html(exc_data, include_hidden_frames=True, include_reusable=False)
             head_html = formatter.error_css + formatter.hide_display_js
-            return_error = error_template(
-                head_html, error_html, extra_data)
-            extra_data = ''
+            return_error = error_template(head_html, error_html, extra_data)
+            extra_data = ""
             reported = True
         else:
-            msg = error_message or '''
+            msg = (
+                error_message
+                or """
             An error occurred.
-            '''
+            """
+            )
             extra = "<p><b>The error has been logged to our team.</b>"
-            if 'sentry_event_id' in environ:
+            if "sentry_event_id" in environ:
                 extra += " If you want to contact us about this error, please reference the following<br><br>"
                 extra += f"<b><large>GURU MEDITATION: #{environ['sentry_event_id']}</large></b>"
             extra += "</p>"
-            return_error = error_template('', msg, extra)
+            return_error = error_template("", msg, extra)
     else:
         return_error = None
     if not reported and error_stream:
@@ -449,17 +458,16 @@ def send_report(rep, exc_data, html=True):
 
             <pre>{}</pre>
             </p>""".format(
-                markupsafe.escape(str(rep)), output.getvalue())
+                markupsafe.escape(str(rep)), output.getvalue()
+            )
         else:
-            return (
-                "Additionally an error occurred while sending the "
-                "%s report:\n%s" % (str(rep), output.getvalue()))
+            return "Additionally an error occurred while sending the " "%s report:\n%s" % (str(rep), output.getvalue())
     else:
-        return ''
+        return ""
 
 
 def error_template(head_html, exception, extra):
-    return '''
+    return """
     <!DOCTYPE HTML>
     <html>
     <head>
@@ -483,7 +491,9 @@ def error_template(head_html, exception, extra):
     {}
     </div>
     </body>
-    </html>'''.format(head_html, exception, extra)
+    </html>""".format(
+        head_html, exception, extra
+    )
 
 
 def make_error_middleware(app, global_conf, **kw):
@@ -492,7 +502,7 @@ def make_error_middleware(app, global_conf, **kw):
 
 doc_lines = cast(str, ErrorMiddleware.__doc__).splitlines(True)
 for i in range(len(doc_lines)):
-    if doc_lines[i].strip().startswith('Settings'):
-        make_error_middleware.__doc__ = ''.join(doc_lines[i:])
+    if doc_lines[i].strip().startswith("Settings"):
+        make_error_middleware.__doc__ = "".join(doc_lines[i:])
         break
 del i, doc_lines
diff --git a/lib/galaxy/web/framework/middleware/profile.py b/lib/galaxy/web/framework/middleware/profile.py
index f3cfd09bc47..6e9d3d597e7 100644
--- a/lib/galaxy/web/framework/middleware/profile.py
+++ b/lib/galaxy/web/framework/middleware/profile.py
@@ -9,7 +9,6 @@ import threading
 import markupsafe
 from paste import response
 
-
 template = """
 <script>
 function show_profile_output()
@@ -63,19 +62,20 @@ class ProfileMiddleware:
 
         def run_app():
             body.extend(self.app(environ, replace_start_response))
+
         # Run in profiler
         prof = cProfile.Profile()
         prof.runctx("run_app()", globals(), locals())
         # Build up body with stats
-        body = ''.join(body)
+        body = "".join(body)
         headers = catch_response[1]
-        content_type = response.header_value(headers, 'content-type')
-        if not content_type.startswith('text/html'):
+        content_type = response.header_value(headers, "content-type")
+        if not content_type.startswith("text/html"):
             # We can't add info to non-HTML output
             return [body]
         stats = pstats.Stats(prof)
         stats.strip_dirs()
-        stats.sort_stats('time', 'calls')
+        stats.sort_stats("time", "calls")
         output = pstats_as_html(stats, self.limit)
         body += template % output
         return [body]
@@ -87,8 +87,10 @@ def pstats_as_html(stats, *sel_list):
     """
     rval = []
     # Number of function calls, primitive calls, total time
-    rval.append("<div>%d function calls (%d primitive) in %0.3f CPU seconds</div>"
-                % (stats.total_calls, stats.prim_calls, stats.total_tt))
+    rval.append(
+        "<div>%d function calls (%d primitive) in %0.3f CPU seconds</div>"
+        % (stats.total_calls, stats.prim_calls, stats.total_tt)
+    )
     # Extract functions that match 'sel_list'
     funcs, order_message, select_message = get_func_list(stats, sel_list)
     # Deal with any ordering or selection messages
@@ -100,12 +102,14 @@ def pstats_as_html(stats, *sel_list):
     if list:
         rval.append("<table>")
         # Header
-        rval.append("<tr><th>ncalls</th>"
-                    "<th>tottime</th>"
-                    "<th>percall</th>"
-                    "<th>cumtime</th>"
-                    "<th>percall</th>"
-                    "<th>filename:lineno(function)</th></tr>")
+        rval.append(
+            "<tr><th>ncalls</th>"
+            "<th>tottime</th>"
+            "<th>percall</th>"
+            "<th>cumtime</th>"
+            "<th>percall</th>"
+            "<th>filename:lineno(function)</th></tr>"
+        )
         for func in funcs:
             rval.append("<tr>")
             # Calculate each field
@@ -163,11 +167,11 @@ def func_std_string(func_name):
     """
     Match what old profile produced
     """
-    if func_name[:2] == ('~', 0):
+    if func_name[:2] == ("~", 0):
         # special case for built-in functions
         name = func_name[2]
-        if name.startswith('<') and name.endswith('>'):
-            return '{%s}' % name[1:-1]
+        if name.startswith("<") and name.endswith(">"):
+            return "{%s}" % name[1:-1]
         else:
             return name
     else:
diff --git a/lib/galaxy/web/framework/middleware/remoteuser.py b/lib/galaxy/web/framework/middleware/remoteuser.py
index e1e07d37e8e..a0d1909460a 100644
--- a/lib/galaxy/web/framework/middleware/remoteuser.py
+++ b/lib/galaxy/web/framework/middleware/remoteuser.py
@@ -41,54 +41,65 @@ errorpage = """
 
 
 class RemoteUser:
-
-    def __init__(self, app, maildomain=None, display_servers=None, admin_users=None,
-                 single_user=None, remote_user_header=None, remote_user_secret_header=None,
-                 normalize_remote_user_email=False):
+    def __init__(
+        self,
+        app,
+        maildomain=None,
+        display_servers=None,
+        admin_users=None,
+        single_user=None,
+        remote_user_header=None,
+        remote_user_secret_header=None,
+        normalize_remote_user_email=False,
+    ):
         self.app = app
         self.maildomain = maildomain
         self.display_servers = display_servers or []
         self.admin_users = admin_users or []
-        self.remote_user_header = remote_user_header or 'HTTP_REMOTE_USER'
+        self.remote_user_header = remote_user_header or "HTTP_REMOTE_USER"
         self.single_user = single_user
         self.config_secret_header = remote_user_secret_header
         self.normalize_remote_user_email = normalize_remote_user_email
 
     def __call__(self, environ, start_response):
         # Allow display servers
-        if self.display_servers and 'REMOTE_ADDR' in environ:
+        if self.display_servers and "REMOTE_ADDR" in environ:
             try:
-                host = socket.gethostbyaddr(environ['REMOTE_ADDR'])[0]
-            except(OSError, socket.herror, socket.gaierror, socket.timeout):
+                host = socket.gethostbyaddr(environ["REMOTE_ADDR"])[0]
+            except (OSError, socket.herror, socket.gaierror, socket.timeout):
                 # in the event of a lookup failure, deny access
                 host = None
             if host in self.display_servers:
-                environ[self.remote_user_header] = 'remote_display_server@%s' % (self.maildomain or 'example.org')
+                environ[self.remote_user_header] = "remote_display_server@%s" % (self.maildomain or "example.org")
                 return self.app(environ, start_response)
 
         if self.single_user:
             assert self.remote_user_header not in environ
             environ[self.remote_user_header] = self.single_user
 
-        if environ.get(self.remote_user_header, '').startswith('(null)'):
+        if environ.get(self.remote_user_header, "").startswith("(null)"):
             # Throw away garbage headers.
             # Apache sets REMOTE_USER to the string '(null)' when using the
             # Rewrite* method for passing REMOTE_USER and a user is not authenticated.
             # Any other possible values need to go here as well.
-            log.debug("Discarding invalid remote user header %s:%s.", self.remote_user_header, environ.get(self.remote_user_header, None))
+            log.debug(
+                "Discarding invalid remote user header %s:%s.",
+                self.remote_user_header,
+                environ.get(self.remote_user_header, None),
+            )
             environ.pop(self.remote_user_header)
         if self.remote_user_header in environ:
             # process remote user with configuration options.
             if self.normalize_remote_user_email:
                 environ[self.remote_user_header] = environ[self.remote_user_header].lower()
-            if self.maildomain and '@' not in environ[self.remote_user_header]:
+            if self.maildomain and "@" not in environ[self.remote_user_header]:
                 environ[self.remote_user_header] = f"{environ[self.remote_user_header]}@{self.maildomain}"
 
-        path_info = environ.get('PATH_INFO', '')
+        path_info = environ.get("PATH_INFO", "")
 
         # The API handles its own authentication via keys
         # Check for API key before checking for header
-        if path_info.startswith('/api/'):
+        if path_info.startswith("/api/"):
             return self.app(environ, start_response)
 
         # If the secret header is enabled, we expect upstream to send along some key
@@ -104,7 +115,7 @@ class RemoteUser:
         # Galaxy would not have access to Galaxy itself, and be attempting to
         # attack the system
         if self.config_secret_header is not None:
-            if environ.get('HTTP_GX_SECRET') is None:
+            if environ.get("HTTP_GX_SECRET") is None:
                 title = "Access to Galaxy is denied"
                 message = """
                 Galaxy is configured to authenticate users via an external
@@ -117,7 +128,7 @@ class RemoteUser:
                 access Galaxy.
                 """
                 return self.error(start_response, title, message)
-            if not safe_str_cmp(environ.get('HTTP_GX_SECRET', ''), self.config_secret_header):
+            if not safe_str_cmp(environ.get("HTTP_GX_SECRET", ""), self.config_secret_header):
                 title = "Access to Galaxy is denied"
                 message = """
                 Galaxy is configured to authenticate users via an external
@@ -132,7 +143,7 @@ class RemoteUser:
                 return self.error(start_response, title, message)
 
         if environ.get(self.remote_user_header, None):
-            if not environ[self.remote_user_header].count('@'):
+            if not environ[self.remote_user_header].count("@"):
                 if self.maildomain is not None:
                     environ[self.remote_user_header] += f"@{self.maildomain}"
                 else:
@@ -149,38 +160,39 @@ class RemoteUser:
                     """
                     return self.error(start_response, title, message)
             user_accessible_paths = (
-                '/users',
-                '/user/api_key',
-                '/user/edit_username',
-                '/user/dbkeys',
-                '/user/logout',
-                '/user/toolbox_filters',
-                '/user/set_default_permissions',
+                "/users",
+                "/user/api_key",
+                "/user/edit_username",
+                "/user/dbkeys",
+                "/user/logout",
+                "/user/toolbox_filters",
+                "/user/set_default_permissions",
             )
 
             admin_accessible_paths = (
-                '/user/create',
-                '/user/logout',
-                '/user/manage_user_info',
-                '/user/edit_info',
-                '/userskeys/all_users',
-                '/userskeys/admin_api_keys',
+                "/user/create",
+                "/user/logout",
+                "/user/manage_user_info",
+                "/user/edit_info",
+                "/userskeys/all_users",
+                "/userskeys/admin_api_keys",
             )
 
-            if not path_info.startswith('/user'):
+            if not path_info.startswith("/user"):
                 # shortcut the following allowlist for non-user-controller
                 # requests.
                 pass
-            elif environ[self.remote_user_header] in self.admin_users and \
-                    any(path_info.startswith(prefix) for prefix in admin_accessible_paths):
+            elif environ[self.remote_user_header] in self.admin_users and any(
+                path_info.startswith(prefix) for prefix in admin_accessible_paths
+            ):
                 # If the user is an admin user, and any of the admin accessible paths match..., allow them to execute that action.
                 pass
             elif any(path_info.startswith(prefix) for prefix in user_accessible_paths):
                 # If the user is allowed to access the path, pass
                 pass
-            elif path_info == '/user' or path_info == '/user/':
+            elif path_info == "/user" or path_info == "/user/":
                 pass  # We do allow access to the root user preferences page.
-            elif path_info.startswith('/user'):
+            elif path_info.startswith("/user"):
                 # Any other endpoint in the user controller is off limits
                 title = "Access to Galaxy user controls is disabled"
                 message = """
@@ -205,5 +217,5 @@ class RemoteUser:
             return self.error(start_response, title, message)
 
     def error(self, start_response, title="Access denied", message="Please contact your local Galaxy administrator."):
-        start_response('403 Forbidden', [('Content-type', 'text/html')])
+        start_response("403 Forbidden", [("Content-type", "text/html")])
         return [errorpage % (title, message)]
diff --git a/lib/galaxy/web/framework/middleware/request_id.py b/lib/galaxy/web/framework/middleware/request_id.py
index ad10c7985f3..a7639724314 100644
--- a/lib/galaxy/web/framework/middleware/request_id.py
+++ b/lib/galaxy/web/framework/middleware/request_id.py
@@ -11,5 +11,5 @@ class RequestIDMiddleware:
         self.app = app
 
     def __call__(self, environ, start_response):
-        environ['request_id'] = uuid.uuid1().hex
+        environ["request_id"] = uuid.uuid1().hex
         return self.app(environ, start_response)
diff --git a/lib/galaxy/web/framework/middleware/sqldebug.py b/lib/galaxy/web/framework/middleware/sqldebug.py
index 687a84ccddd..d4828aaeb98 100644
--- a/lib/galaxy/web/framework/middleware/sqldebug.py
+++ b/lib/galaxy/web/framework/middleware/sqldebug.py
@@ -3,21 +3,24 @@ Per-request SQL debugging middleware.
 """
 import logging
 
-from galaxy.model.orm.engine_factory import log_request_query_counts, reset_request_query_counts
+from galaxy.model.orm.engine_factory import (
+    log_request_query_counts,
+    reset_request_query_counts,
+)
 
 log = logging.getLogger(__name__)
 
 
 class SQLDebugMiddleware:
-
     def __init__(self, application, galaxy, config=None):
         #: the wrapped webapp
         self.application = application
 
     def __call__(self, environ, start_response):
-        query_string = environ.get('QUERY_STRING')
+        query_string = environ.get("QUERY_STRING")
         if "sql_debug=1" in query_string:
             import galaxy.app
+
             if galaxy.app.app.model.thread_local_log:
                 galaxy.app.app.model.thread_local_log.log = True
 
diff --git a/lib/galaxy/web/framework/middleware/static.py b/lib/galaxy/web/framework/middleware/static.py
index fcc878f16ff..100b2336589 100644
--- a/lib/galaxy/web/framework/middleware/static.py
+++ b/lib/galaxy/web/framework/middleware/static.py
@@ -1,5 +1,8 @@
 import os
-from typing import List, Tuple
+from typing import (
+    List,
+    Tuple,
+)
 
 from paste import request
 from paste.fileapp import FileApp
@@ -8,14 +11,13 @@ from paste.urlparser import StaticURLParser
 
 
 class CacheableStaticURLParser(StaticURLParser):
-
     def __init__(self, directory, cache_seconds=None, directory_per_host=None):
         StaticURLParser.__init__(self, directory)
         self.cache_seconds = cache_seconds
         self.directory_per_host = directory_per_host
 
     def __call__(self, environ, start_response):
-        path_info = environ.get('PATH_INFO', '')
+        path_info = environ.get("PATH_INFO", "")
         if not path_info:
             # See if this is a static file hackishly mapped.
             if os.path.exists(self.directory) and os.path.isfile(self.directory):
@@ -24,14 +26,14 @@ class CacheableStaticURLParser(StaticURLParser):
                     app.cache_control(max_age=int(self.cache_seconds))
                 return app(environ, start_response)
             return self.add_slash(environ, start_response)
-        if path_info == '/':
+        if path_info == "/":
             # @@: This should obviously be configurable
-            filename = 'index.html'
+            filename = "index.html"
         else:
             filename = request.path_info_pop(environ)
 
         directory = self.directory
-        host = environ.get('HTTP_HOST')
+        host = environ.get("HTTP_HOST")
         if self.directory_per_host and host:
             for host_key, host_val in self.directory_per_host.items():
                 if host_key in host:
@@ -44,16 +46,16 @@ class CacheableStaticURLParser(StaticURLParser):
         if os.path.isdir(full):
             # @@: Cache?
             return self.__class__(full)(environ, start_response)
-        if environ.get('PATH_INFO') and environ.get('PATH_INFO') != '/':
+        if environ.get("PATH_INFO") and environ.get("PATH_INFO") != "/":
             return self.error_extra_path(environ, start_response)
-        if_none_match = environ.get('HTTP_IF_NONE_MATCH')
+        if_none_match = environ.get("HTTP_IF_NONE_MATCH")
         if if_none_match:
             mytime = os.stat(full).st_mtime
             if str(mytime) == if_none_match:
                 headers: List[Tuple[str, str]] = []
                 ETAG.update(headers, mytime)
-                start_response('304 Not Modified', headers)
-                return ['']  # empty body
+                start_response("304 Not Modified", headers)
+                return [""]  # empty body
         app = FileApp(full)
         if self.cache_seconds:
             app.cache_control(max_age=int(self.cache_seconds))
diff --git a/lib/galaxy/web/framework/middleware/statsd.py b/lib/galaxy/web/framework/middleware/statsd.py
index 40814988ca3..1b017f71565 100644
--- a/lib/galaxy/web/framework/middleware/statsd.py
+++ b/lib/galaxy/web/framework/middleware/statsd.py
@@ -14,13 +14,7 @@ class StatsdMiddleware:
     instance.
     """
 
-    def __init__(self,
-                 application,
-                 statsd_host,
-                 statsd_port,
-                 statsd_prefix,
-                 statsd_influxdb,
-                 statsd_mock_calls):
+    def __init__(self, application, statsd_host, statsd_port, statsd_prefix, statsd_influxdb, statsd_mock_calls):
         self.application = application
         self.galaxy_stasd_client = GalaxyStatsdClient(
             statsd_host,
@@ -34,11 +28,13 @@ class StatsdMiddleware:
         start_time = time.time()
         req = self.application(environ, start_response)
         dt = int((time.time() - start_time) * 1000)
-        page = environ.get('controller_action_key', None) or environ.get('PATH_INFO', "NOPATH").strip('/').replace('/', '.')
+        page = environ.get("controller_action_key", None) or environ.get("PATH_INFO", "NOPATH").strip("/").replace(
+            "/", "."
+        )
         self.galaxy_stasd_client.timing(page, dt)
         try:
             times = QUERY_COUNT_LOCAL.times
-            self.galaxy_stasd_client.timing(f"sql.{page}", sum(times) * 1000.)
+            self.galaxy_stasd_client.timing(f"sql.{page}", sum(times) * 1000.0)
             self.galaxy_stasd_client.incr(f"sqlqueries.{page}", len(times))
         except AttributeError:
             # Not logging query counts, skip
diff --git a/lib/galaxy/web/framework/middleware/translogger.py b/lib/galaxy/web/framework/middleware/translogger.py
index b567b2c9d1f..aedfb83c622 100644
--- a/lib/galaxy/web/framework/middleware/translogger.py
+++ b/lib/galaxy/web/framework/middleware/translogger.py
@@ -18,17 +18,22 @@ class TransLogger:
     logger will be sent to the console.
     """
 
-    format = ('%(REMOTE_ADDR)s - %(REMOTE_USER)s [%(time)s] '
-              '"%(REQUEST_METHOD)s %(REQUEST_URI)s %(HTTP_VERSION)s" '
-              '%(status)s %(bytes)s "%(HTTP_REFERER)s" "%(HTTP_USER_AGENT)s"')
+    format = (
+        "%(REMOTE_ADDR)s - %(REMOTE_USER)s [%(time)s] "
+        '"%(REQUEST_METHOD)s %(REQUEST_URI)s %(HTTP_VERSION)s" '
+        '%(status)s %(bytes)s "%(HTTP_REFERER)s" "%(HTTP_USER_AGENT)s"'
+    )
 
-    def __init__(self, application,
-                 logger=None,
-                 format=None,
-                 logging_level=logging.INFO,
-                 logger_name='wsgi',
-                 setup_console_handler=True,
-                 set_logger_level=logging.DEBUG):
+    def __init__(
+        self,
+        application,
+        logger=None,
+        format=None,
+        logging_level=logging.INFO,
+        logger_name="wsgi",
+        setup_console_handler=True,
+        set_logger_level=logging.DEBUG,
+    ):
         if format is not None:
             self.format = format
         self.application = application
@@ -40,7 +45,7 @@ class TransLogger:
                 console = logging.StreamHandler()
                 console.setLevel(logging.DEBUG)
                 # We need to control the exact format:
-                console.setFormatter(logging.Formatter('%(message)s'))
+                console.setFormatter(logging.Formatter("%(message)s"))
                 self.logger.addHandler(console)
                 self.logger.propagate = False
             if set_logger_level is not None:
@@ -50,11 +55,10 @@ class TransLogger:
 
     def __call__(self, environ, start_response):
         start = time.localtime()
-        req_uri = quote(environ.get('SCRIPT_NAME', '')
-                        + environ.get('PATH_INFO', ''))
-        if environ.get('QUERY_STRING'):
+        req_uri = quote(environ.get("SCRIPT_NAME", "") + environ.get("PATH_INFO", ""))
+        if environ.get("QUERY_STRING"):
             req_uri += f"?{environ['QUERY_STRING']}"
-        method = environ['REQUEST_METHOD']
+        method = environ["REQUEST_METHOD"]
 
         def replacement_start_response(status, headers, exc_info=None):
             # @@: Ideally we would count the bytes going by if no
@@ -62,15 +66,16 @@ class TransLogger:
             # some overhead, so at least for now we'll be lazy.
             bytes = None
             for name, value in headers:
-                if name.lower() == 'content-length':
+                if name.lower() == "content-length":
                     bytes = value
             self.write_log(environ, method, req_uri, start, status, bytes)
             return start_response(status, headers, exc_info)
+
         return self.application(environ, replacement_start_response)
 
     def write_log(self, environ, method, req_uri, start, status, bytes):
         if bytes is None:
-            bytes = '-'
+            bytes = "-"
         if time.daylight:
             offset = time.altzone / 60 / 60 * -100
         else:
@@ -80,29 +85,32 @@ class TransLogger:
         elif offset < 0:
             offset = "%0.4d" % (offset)
         d = {
-            'REMOTE_ADDR': environ.get('REMOTE_ADDR') or '-',
-            'REMOTE_USER': environ.get('REMOTE_USER') or '-',
-            'REQUEST_METHOD': method,
-            'REQUEST_URI': req_uri,
-            'HTTP_VERSION': environ.get('SERVER_PROTOCOL'),
-            'time': time.strftime('%d/%b/%Y:%H:%M:%S ', start) + offset,
-            'status': status.split(None, 1)[0],
-            'bytes': bytes,
-            'HTTP_REFERER': environ.get('HTTP_REFERER', '-'),
-            'HTTP_USER_AGENT': environ.get('HTTP_USER_AGENT', '-'),
+            "REMOTE_ADDR": environ.get("REMOTE_ADDR") or "-",
+            "REMOTE_USER": environ.get("REMOTE_USER") or "-",
+            "REQUEST_METHOD": method,
+            "REQUEST_URI": req_uri,
+            "HTTP_VERSION": environ.get("SERVER_PROTOCOL"),
+            "time": time.strftime("%d/%b/%Y:%H:%M:%S ", start) + offset,
+            "status": status.split(None, 1)[0],
+            "bytes": bytes,
+            "HTTP_REFERER": environ.get("HTTP_REFERER", "-"),
+            "HTTP_USER_AGENT": environ.get("HTTP_USER_AGENT", "-"),
         }
         message = self.format % d
         self.logger.log(self.logging_level, message)
 
 
 def make_filter(
-        app, global_conf,
-        logger_name='wsgi',
-        format=None,
-        logging_level=logging.INFO,
-        setup_console_handler=True,
-        set_logger_level=logging.DEBUG):
+    app,
+    global_conf,
+    logger_name="wsgi",
+    format=None,
+    logging_level=logging.INFO,
+    setup_console_handler=True,
+    set_logger_level=logging.DEBUG,
+):
     from paste.util.converters import asbool
+
     if isinstance(logging_level, str):
         logging_level = logging._levelNames[logging_level]
     if isinstance(set_logger_level, str):
@@ -113,7 +121,8 @@ def make_filter(
         logging_level=logging_level,
         logger_name=logger_name,
         setup_console_handler=asbool(setup_console_handler),
-        set_logger_level=set_logger_level)
+        set_logger_level=set_logger_level,
+    )
 
 
 make_filter.__doc__ = TransLogger.__doc__
diff --git a/lib/galaxy/web/framework/middleware/xforwardedhost.py b/lib/galaxy/web/framework/middleware/xforwardedhost.py
index 8494cccae36..8542a804eec 100644
--- a/lib/galaxy/web/framework/middleware/xforwardedhost.py
+++ b/lib/galaxy/web/framework/middleware/xforwardedhost.py
@@ -8,16 +8,16 @@ class XForwardedHostMiddleware:
         self.app = app
 
     def __call__(self, environ, start_response):
-        x_forwarded_host = environ.get('HTTP_X_FORWARDED_HOST', None)
+        x_forwarded_host = environ.get("HTTP_X_FORWARDED_HOST", None)
         if x_forwarded_host:
-            environ['ORGINAL_HTTP_HOST'] = environ['HTTP_HOST']
-            environ['HTTP_HOST'] = x_forwarded_host.split(', ', 1)[0]
-        x_forwarded_for = environ.get('HTTP_X_FORWARDED_FOR', None)
+            environ["ORGINAL_HTTP_HOST"] = environ["HTTP_HOST"]
+            environ["HTTP_HOST"] = x_forwarded_host.split(", ", 1)[0]
+        x_forwarded_for = environ.get("HTTP_X_FORWARDED_FOR", None)
         if x_forwarded_for:
-            environ['ORGINAL_REMOTE_ADDR'] = environ['REMOTE_ADDR']
-            environ['REMOTE_ADDR'] = x_forwarded_for.split(', ', 1)[0]
-        x_url_scheme = environ.get('HTTP_X_URL_SCHEME', None)
+            environ["ORGINAL_REMOTE_ADDR"] = environ["REMOTE_ADDR"]
+            environ["REMOTE_ADDR"] = x_forwarded_for.split(", ", 1)[0]
+        x_url_scheme = environ.get("HTTP_X_URL_SCHEME", None)
         if x_url_scheme:
-            environ['original_wsgi.url_scheme'] = environ['wsgi.url_scheme']
-            environ['wsgi.url_scheme'] = x_url_scheme
+            environ["original_wsgi.url_scheme"] = environ["wsgi.url_scheme"]
+            environ["wsgi.url_scheme"] = x_url_scheme
         return self.app(environ, start_response)
diff --git a/lib/galaxy/web/legacy_framework/grids.py b/lib/galaxy/web/legacy_framework/grids.py
index 15e3522a13f..8b4fca1f8c5 100644
--- a/lib/galaxy/web/legacy_framework/grids.py
+++ b/lib/galaxy/web/legacy_framework/grids.py
@@ -1,25 +1,61 @@
 import logging
 import math
-from json import dumps, loads
-from typing import Dict, List, Optional
+from json import (
+    dumps,
+    loads,
+)
+from typing import (
+    Dict,
+    List,
+    Optional,
+)
 
 from markupsafe import escape
-from sqlalchemy.sql.expression import and_, false, func, null, or_, true
+from sqlalchemy.sql.expression import (
+    and_,
+    false,
+    func,
+    null,
+    or_,
+    true,
+)
 
-from galaxy.model.item_attrs import get_foreign_key, UsesAnnotations, UsesItemRatings
-from galaxy.util import sanitize_text, unicodify
-from galaxy.web.framework import decorators, url_for
+from galaxy.model.item_attrs import (
+    get_foreign_key,
+    UsesAnnotations,
+    UsesItemRatings,
+)
+from galaxy.util import (
+    sanitize_text,
+    unicodify,
+)
+from galaxy.web.framework import (
+    decorators,
+    url_for,
+)
 from galaxy.web.framework.helpers import iff
 
-
 log = logging.getLogger(__name__)
 
 
 class GridColumn:
-    def __init__(self, label, key=None, model_class=None, method=None, format=None,
-                 link=None, attach_popup=False, visible=True, nowrap=False,
-                 # Valid values for filterable are ['standard', 'advanced', None]
-                 filterable=None, sortable=True, label_id_prefix=None, target=None):
+    def __init__(
+        self,
+        label,
+        key=None,
+        model_class=None,
+        method=None,
+        format=None,
+        link=None,
+        attach_popup=False,
+        visible=True,
+        nowrap=False,
+        # Valid values for filterable are ['standard', 'advanced', None]
+        filterable=None,
+        sortable=True,
+        label_id_prefix=None,
+        target=None,
+    ):
         """Create a grid column."""
         self.label = label
         self.key = key
@@ -33,8 +69,8 @@ class GridColumn:
         self.visible = visible
         self.filterable = filterable
         # Column must have a key to be sortable.
-        self.sortable = (self.key is not None and sortable)
-        self.label_id_prefix = label_id_prefix or ''
+        self.sortable = self.key is not None and sortable
+        self.label_id_prefix = label_id_prefix or ""
 
     def get_value(self, trans, grid, item):
         if self.method:
@@ -53,7 +89,7 @@ class GridColumn:
         return None
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to reflect the column filter. """
+        """Modify query to reflect the column filter."""
         if column_filter == "All":
             pass
         if column_filter == "True":
@@ -63,7 +99,7 @@ class GridColumn:
         return query
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filters_vals = ["False", "True", "All"]
         accepted_filters = []
         for val in accepted_filters_vals:
@@ -83,17 +119,17 @@ class GridColumn:
 
 
 class ReverseSortColumn(GridColumn):
-    """ Column that reverses sorting; this is useful when the natural sort is descending. """
+    """Column that reverses sorting; this is useful when the natural sort is descending."""
 
     def sort(self, trans, query, ascending, column_name=None):
         return GridColumn.sort(self, trans, query, (not ascending), column_name=column_name)
 
 
 class TextColumn(GridColumn):
-    """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """
+    """Generic column that employs freetext and, hence, supports freetext, case-independent filtering."""
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter using free text, case independence. """
+        """Modify query to filter using free text, case independence."""
         if column_filter == "All":
             pass
         elif column_filter:
@@ -101,7 +137,7 @@ class TextColumn(GridColumn):
         return query
 
     def get_filter(self, trans, user, column_filter):
-        """ Returns a SQLAlchemy criterion derived from column_filter. """
+        """Returns a SQLAlchemy criterion derived from column_filter."""
         if isinstance(column_filter, str):
             return self.get_single_filter(user, column_filter)
         elif isinstance(column_filter, list):
@@ -117,8 +153,8 @@ class TextColumn(GridColumn):
         """
         # Queries that include table joins cannot guarantee that table column names will be
         # unique, so check to see if a_filter is of type <TableName>.<ColumnName>.
-        if self.key.find('.') > -1:
-            a_key = self.key.split('.')[1]
+        if self.key.find(".") > -1:
+            a_key = self.key.split(".")[1]
         else:
             a_key = self.key
         model_class_key_field = getattr(self.model_class, a_key)
@@ -147,8 +183,8 @@ class BooleanColumn(TextColumn):
         return GridColumn.sort(self, trans, query, ascending, column_name=column_name)
 
     def get_single_filter(self, user, a_filter):
-        if self.key.find('.') > -1:
-            a_key = self.key.split('.')[1]
+        if self.key.find(".") > -1:
+            a_key = self.key.split(".")[1]
         else:
             a_key = self.key
         model_class_key_field = getattr(self.model_class, a_key)
@@ -184,30 +220,36 @@ class IntegerColumn(TextColumn):
 
 
 class CommunityRatingColumn(GridColumn, UsesItemRatings):
-    """ Column that displays community ratings for an item. """
+    """Column that displays community ratings for an item."""
 
     def get_value(self, trans, grid, item):
         ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, item, webapp_model=trans.model)
-        return trans.fill_template("tool_shed_rating.mako",
-                                   ave_item_rating=ave_item_rating,
-                                   num_ratings=num_ratings,
-                                   item_id=trans.security.encode_id(item.id))
+        return trans.fill_template(
+            "tool_shed_rating.mako",
+            ave_item_rating=ave_item_rating,
+            num_ratings=num_ratings,
+            item_id=trans.security.encode_id(item.id),
+        )
 
     def sort(self, trans, query, ascending, column_name=None):
         # Get the columns that connect item's table and item's rating association table.
-        item_rating_assoc_class = getattr(trans.model, f'{self.model_class.__name__}RatingAssociation')
+        item_rating_assoc_class = getattr(trans.model, f"{self.model_class.__name__}RatingAssociation")
         foreign_key = get_foreign_key(item_rating_assoc_class, self.model_class)
         fk_col = foreign_key.parent
         referent_col = foreign_key.get_referent(self.model_class.table)
         # Do sorting using a subquery.
         # Subquery to get average rating for each item.
-        ave_rating_subquery = trans.sa_session.query(fk_col,
-                                                     func.avg(item_rating_assoc_class.table.c.rating).label('avg_rating')) \
-            .group_by(fk_col).subquery()
+        ave_rating_subquery = (
+            trans.sa_session.query(fk_col, func.avg(item_rating_assoc_class.table.c.rating).label("avg_rating"))
+            .group_by(fk_col)
+            .subquery()
+        )
         # Integrate subquery into main query.
         query = query.outerjoin((ave_rating_subquery, referent_col == ave_rating_subquery.columns[fk_col.name]))
         # Sort using subquery results; use coalesce to avoid null values.
-        if not ascending:  # TODO: for now, reverse sorting b/c first sort is ascending, and that should be the natural sort.
+        if (
+            not ascending
+        ):  # TODO: for now, reverse sorting b/c first sort is ascending, and that should be the natural sort.
             query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).asc())
         else:
             query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).desc())
@@ -215,7 +257,7 @@ class CommunityRatingColumn(GridColumn, UsesItemRatings):
 
 
 class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
-    """ Column that displays and filters item owner's annotations. """
+    """Column that displays and filters item owner's annotations."""
 
     def __init__(self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None):
         GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
@@ -223,41 +265,56 @@ class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
         self.model_annotation_association_class = model_annotation_association_class
 
     def get_value(self, trans, grid, item):
-        """ Returns first 150 characters of annotation. """
+        """Returns first 150 characters of annotation."""
         annotation = self.get_item_annotation_str(trans.sa_session, item.user, item)
         if annotation:
             ann_snippet = annotation[:155]
             if len(annotation) > 155:
-                ann_snippet = ann_snippet[:ann_snippet.rfind(' ')]
+                ann_snippet = ann_snippet[: ann_snippet.rfind(" ")]
                 ann_snippet += "..."
         else:
             ann_snippet = ""
         return escape(ann_snippet)
 
     def get_single_filter(self, user, a_filter):
-        """ Filter by annotation and annotation owner. """
+        """Filter by annotation and annotation owner."""
         return self.model_class.annotations.any(
-            and_(func.lower(self.model_annotation_association_class.annotation).like(f"%{a_filter.lower()}%"),
-               # TODO: not sure why, to filter by owner's annotations, we have to do this rather than
-               # 'self.model_class.user==self.model_annotation_association_class.user'
-               self.model_annotation_association_class.table.c.user_id == self.model_class.table.c.user_id))
+            and_(
+                func.lower(self.model_annotation_association_class.annotation).like(f"%{a_filter.lower()}%"),
+                # TODO: not sure why, to filter by owner's annotations, we have to do this rather than
+                # 'self.model_class.user==self.model_annotation_association_class.user'
+                self.model_annotation_association_class.table.c.user_id == self.model_class.table.c.user_id,
+            )
+        )
 
 
 class CommunityTagsColumn(TextColumn):
-    """ Column that supports community tags. """
+    """Column that supports community tags."""
 
-    def __init__(self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None):
-        GridColumn.__init__(self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False)
+    def __init__(
+        self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None
+    ):
+        GridColumn.__init__(
+            self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False
+        )
         self.model_tag_association_class = model_tag_association_class
         # Column-specific attributes.
         self.grid_name = grid_name
 
     def get_value(self, trans, grid, item):
-        return trans.fill_template("/tagging_common.mako", tag_type="community", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name,
-                                   tag_click_fn="add_tag_to_grid_filter", use_toggle_link=True)
+        return trans.fill_template(
+            "/tagging_common.mako",
+            tag_type="community",
+            trans=trans,
+            user=trans.get_user(),
+            tagged_item=item,
+            elt_context=self.grid_name,
+            tag_click_fn="add_tag_to_grid_filter",
+            use_toggle_link=True,
+        )
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter model_class by tag. Multiple filters are ANDed. """
+        """Modify query to filter model_class by tag. Multiple filters are ANDed."""
         if column_filter == "All":
             pass
         elif column_filter:
@@ -274,24 +331,34 @@ class CommunityTagsColumn(TextColumn):
         for name, value in raw_tags:
             if name:
                 # Filter by all tags.
-                clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%")))
+                clause_list.append(
+                    self.model_class.tags.any(
+                        func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%")
+                    )
+                )
                 if value:
                     # Filter by all values.
-                    clause_list.append(self.model_class.tags.any(func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%")))
+                    clause_list.append(
+                        self.model_class.tags.any(
+                            func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%")
+                        )
+                    )
         return and_(*clause_list)
 
 
 class IndividualTagsColumn(CommunityTagsColumn):
-    """ Column that supports individual tags. """
+    """Column that supports individual tags."""
 
     def get_value(self, trans, grid, item):
-        return trans.fill_template("/tagging_common.mako",
-                                   tag_type="individual",
-                                   user=trans.user,
-                                   tagged_item=item,
-                                   elt_context=self.grid_name,
-                                   tag_click_fn="add_tag_to_grid_filter",
-                                   use_toggle_link=True)
+        return trans.fill_template(
+            "/tagging_common.mako",
+            tag_type="individual",
+            user=trans.user,
+            tagged_item=item,
+            elt_context=self.grid_name,
+            tag_click_fn="add_tag_to_grid_filter",
+            use_toggle_link=True,
+        )
 
     def get_filter(self, trans, user, column_filter):
         # Parse filter to extract multiple tags.
@@ -303,22 +370,36 @@ class IndividualTagsColumn(CommunityTagsColumn):
         for name, value in raw_tags:
             if name:
                 # Filter by individual's tag names.
-                clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%"), self.model_tag_association_class.user == user)))
+                clause_list.append(
+                    self.model_class.tags.any(
+                        and_(
+                            func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%"),
+                            self.model_tag_association_class.user == user,
+                        )
+                    )
+                )
                 if value:
                     # Filter by individual's tag values.
-                    clause_list.append(self.model_class.tags.any(and_(func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%"), self.model_tag_association_class.user == user)))
+                    clause_list.append(
+                        self.model_class.tags.any(
+                            and_(
+                                func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%"),
+                                self.model_tag_association_class.user == user,
+                            )
+                        )
+                    )
         return and_(*clause_list)
 
 
 class MulticolFilterColumn(TextColumn):
-    """ Column that performs multicolumn filtering. """
+    """Column that performs multicolumn filtering."""
 
     def __init__(self, col_name, cols_to_filter, key, visible, filterable="default"):
         GridColumn.__init__(self, col_name, key=key, visible=visible, filterable=filterable)
         self.cols_to_filter = cols_to_filter
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter model_class by tag. Multiple filters are ANDed. """
+        """Modify query to filter model_class by tag. Multiple filters are ANDed."""
         if column_filter == "All":
             return query
         if isinstance(column_filter, list):
@@ -338,13 +419,13 @@ class MulticolFilterColumn(TextColumn):
 
 
 class OwnerColumn(TextColumn):
-    """ Column that lists item's owner. """
+    """Column that lists item's owner."""
 
     def get_value(self, trans, grid, item):
         return item.user.username
 
     def sort(self, trans, query, ascending, column_name=None):
-        """ Sort column using case-insensitive alphabetical sorting on item's username. """
+        """Sort column using case-insensitive alphabetical sorting on item's username."""
         if ascending:
             query = query.order_by(func.lower(self.model_class.username).asc())
         else:
@@ -353,11 +434,11 @@ class OwnerColumn(TextColumn):
 
 
 class PublicURLColumn(TextColumn):
-    """ Column displays item's public URL based on username and slug. """
+    """Column displays item's public URL based on username and slug."""
 
     def get_link(self, trans, grid, item):
         if item.user.username and item.slug:
-            return dict(action='display_by_username_and_slug', username=item.user.username, slug=item.slug)
+            return dict(action="display_by_username_and_slug", username=item.user.username, slug=item.slug)
         elif not item.user.username:
             # TODO: provide link to set username.
             return None
@@ -367,10 +448,10 @@ class PublicURLColumn(TextColumn):
 
 
 class DeletedColumn(GridColumn):
-    """ Column that tracks and filters for items with deleted attribute. """
+    """Column that tracks and filters for items with deleted attribute."""
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filter_labels_and_vals = {"active": "False", "deleted": "True", "all": "All"}
         accepted_filters = []
         for label, val in accepted_filter_labels_and_vals.items():
@@ -405,7 +486,7 @@ class StateColumn(GridColumn):
 
     def get_accepted_filters(self):
         """Returns a list of accepted filters for this column."""
-        all = GridColumnFilter('all', {self.key: 'All'})
+        all = GridColumnFilter("all", {self.key: "All"})
         accepted_filters = [all]
         for state in self.model_class.states:
             args = {self.key: state.value}
@@ -414,7 +495,7 @@ class StateColumn(GridColumn):
 
 
 class SharingStatusColumn(GridColumn):
-    """ Grid column to indicate sharing status. """
+    """Grid column to indicate sharing status."""
 
     def get_value(self, trans, grid, item):
         # Delete items cannot be shared.
@@ -436,7 +517,7 @@ class SharingStatusColumn(GridColumn):
         return None
 
     def filter(self, trans, user, query, column_filter):
-        """ Modify query to filter histories by sharing status. """
+        """Modify query to filter histories by sharing status."""
         if column_filter == "All":
             pass
         elif column_filter:
@@ -452,7 +533,7 @@ class SharingStatusColumn(GridColumn):
         return query
 
     def get_accepted_filters(self):
-        """ Returns a list of accepted filters for this column. """
+        """Returns a list of accepted filters for this column."""
         accepted_filter_labels_and_vals = {}
         accepted_filter_labels_and_vals["private"] = "private"
         accepted_filter_labels_and_vals["shared"] = "shared"
@@ -467,9 +548,19 @@ class SharingStatusColumn(GridColumn):
 
 
 class GridOperation:
-    def __init__(self, label, key=None, condition=None, allow_multiple=True, allow_popup=True,
-                 target=None, url_args=None, async_compatible=False, confirm=None,
-                 global_operation=None):
+    def __init__(
+        self,
+        label,
+        key=None,
+        condition=None,
+        allow_multiple=True,
+        allow_popup=True,
+        target=None,
+        url_args=None,
+        async_compatible=False,
+        confirm=None,
+        global_operation=None,
+    ):
         self.label = label
         self.key = key
         self.allow_multiple = allow_multiple
@@ -492,7 +583,7 @@ class GridOperation:
                 url_args = self.url_args(item)
             else:
                 url_args = dict(self.url_args)
-            url_args['id'] = item.id
+            url_args["id"] = item.id
             return url_args
         else:
             return dict(operation=self.label, id=item.id)
@@ -505,10 +596,10 @@ class GridOperation:
 
 
 class DisplayByUsernameAndSlugGridOperation(GridOperation):
-    """ Operation to display an item by username and slug. """
+    """Operation to display an item by username and slug."""
 
     def get_url_args(self, item):
-        return {'action': 'display_by_username_and_slug', 'username': item.user.username, 'slug': item.slug}
+        return {"action": "display_by_username_and_slug", "username": item.user.username, "slug": item.slug}
 
 
 class GridAction:
@@ -534,6 +625,7 @@ class Grid:
     """
     Specifies the content and format of a grid (data table).
     """
+
     title = ""
     model_class: Optional[type] = None
     show_item_checkboxes = False
@@ -575,8 +667,8 @@ class Grid:
     def __call__(self, trans, **kwargs):
         # Get basics.
         # FIXME: pretty sure this is only here to pass along, can likely be eliminated
-        status = kwargs.get('status', None)
-        message = kwargs.get('message', None)
+        status = kwargs.get("status", None)
+        message = kwargs.get("message", None)
         # Build a base filter and sort key that is the combination of the saved state and defaults.
         # Saved state takes preference over defaults.
         base_filter = {}
@@ -590,10 +682,10 @@ class Grid:
         # Maintain sort state in generated urls
         extra_url_args = {}
         # Determine whether use_default_filter flag is set.
-        use_default_filter_str = kwargs.get('use_default_filter')
+        use_default_filter_str = kwargs.get("use_default_filter")
         use_default_filter = False
         if use_default_filter_str:
-            use_default_filter = (use_default_filter_str.lower() == 'true')
+            use_default_filter = use_default_filter_str.lower() == "true"
         # Process filtering arguments to (a) build a query that represents the filter and (b) build a
         # dictionary that denotes the current filter.
         cur_filter_dict = {}
@@ -632,6 +724,7 @@ class Grid:
                             a_list = loads_recurse(element)
                             decoded_list = decoded_list + a_list
                     return decoded_list
+
                 # If column filter found, apply it.
                 if column_filter is not None:
                     # TextColumns may have a mix of json and strings.
@@ -640,18 +733,18 @@ class Grid:
                         if len(column_filter) == 1:
                             column_filter = column_filter[0]
                     # Interpret ',' as a separator for multiple terms.
-                    if isinstance(column_filter, str) and column_filter.find(',') != -1:
-                        column_filter = column_filter.split(',')
+                    if isinstance(column_filter, str) and column_filter.find(",") != -1:
+                        column_filter = column_filter.split(",")
 
                     # Check if filter is empty
                     if isinstance(column_filter, list):
                         # Remove empty strings from filter list
-                        column_filter = [x for x in column_filter if x != '']
+                        column_filter = [x for x in column_filter if x != ""]
                         if len(column_filter) == 0:
                             continue
                     elif isinstance(column_filter, str):
                         # If filter criterion is empty, do nothing.
-                        if column_filter == '':
+                        if column_filter == "":
                             continue
 
                     # Update query.
@@ -663,7 +756,7 @@ class Grid:
                     # that we can encode to UTF-8 and thus handle user input to filters.
                     if isinstance(column_filter, list):
                         # Filter is a list; process each item.
-                        column_filter = [str(_).encode('utf-8') if not isinstance(_, str) else _ for _ in column_filter]
+                        column_filter = [str(_).encode("utf-8") if not isinstance(_, str) else _ for _ in column_filter]
                         extra_url_args[f"f-{column.key}"] = dumps(column_filter)
                     else:
                         # Process singleton filter.
@@ -672,17 +765,17 @@ class Grid:
                         extra_url_args[f"f-{column.key}"] = column_filter.encode("utf-8")
         # Process sort arguments.
         sort_key = None
-        if 'sort' in kwargs:
-            sort_key = kwargs['sort']
+        if "sort" in kwargs:
+            sort_key = kwargs["sort"]
         elif base_sort_key:
             sort_key = base_sort_key
         if sort_key:
-            ascending = not(sort_key.startswith("-"))
+            ascending = not (sort_key.startswith("-"))
             # Queries that include table joins cannot guarantee unique column names.  This problem is
             # handled by setting the column_filter value to <TableName>.<ColumnName>.
             table_name = None
-            if sort_key.find('.') > -1:
-                a_list = sort_key.split('.')
+            if sort_key.find(".") > -1:
+                a_list = sort_key.split(".")
                 if ascending:
                     table_name = a_list[0]
                 else:
@@ -694,20 +787,20 @@ class Grid:
                 column_name = sort_key[1:]
             # Sort key is a column key.
             for column in self.columns:
-                if column.key and column.key.find('.') > -1:
-                    column_key = column.key.split('.')[1]
+                if column.key and column.key.find(".") > -1:
+                    column_key = column.key.split(".")[1]
                 else:
                     column_key = column.key
                 if (table_name is None or table_name == column.model_class.__name__) and column_key == column_name:
                     query = column.sort(trans, query, ascending, column_name=column_name)
                     break
-            extra_url_args['sort'] = sort_key
+            extra_url_args["sort"] = sort_key
         # There might be a current row
         current_item = self.get_current_item(trans, **kwargs)
         # Process page number.
         if self.use_paging:
-            if 'page' in kwargs:
-                if kwargs['page'] == 'all':
+            if "page" in kwargs:
+                if kwargs["page"] == "all":
                     page_num = 0
                     if self.allow_fetching_all_results:
                         page_num = 0
@@ -715,7 +808,7 @@ class Grid:
                         # Should make it harder to return all results at once
                         page_num = 1
                 else:
-                    page_num = int(kwargs['page'])
+                    page_num = int(kwargs["page"])
             else:
                 page_num = 1
             if page_num == 0:
@@ -740,8 +833,8 @@ class Grid:
         # Log grid view.
         context = str(self.__class__.__name__)
         params = cur_filter_dict.copy()
-        params['sort'] = sort_key
-        params['async'] = ('async' in kwargs)
+        params["sort"] = sort_key
+        params["async"] = "async" in kwargs
 
         # TODO:??
         # commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn
@@ -752,10 +845,10 @@ class Grid:
 
         # Render grid.
         def url(*args, **kwargs):
-            route_name = kwargs.pop('__route_name__', None)
+            route_name = kwargs.pop("__route_name__", None)
             # Only include sort/filter arguments if not linking to another
             # page. This is a bit of a hack.
-            if 'action' in kwargs:
+            if "action" in kwargs:
                 new_kwargs = dict()
             else:
                 new_kwargs = dict(extra_url_args)
@@ -764,60 +857,63 @@ class Grid:
                 new_kwargs.update(args[0])
             new_kwargs.update(kwargs)
             # We need to encode item ids
-            if 'id' in new_kwargs:
-                id = new_kwargs['id']
+            if "id" in new_kwargs:
+                id = new_kwargs["id"]
                 if isinstance(id, list):
-                    new_kwargs['id'] = [trans.security.encode_id(i) for i in id]
+                    new_kwargs["id"] = [trans.security.encode_id(i) for i in id]
                 else:
-                    new_kwargs['id'] = trans.security.encode_id(id)
+                    new_kwargs["id"] = trans.security.encode_id(id)
             # The url_for invocation *must* include a controller and action.
-            if 'controller' not in new_kwargs:
-                new_kwargs['controller'] = trans.controller
-            if 'action' not in new_kwargs:
-                new_kwargs['action'] = trans.action
+            if "controller" not in new_kwargs:
+                new_kwargs["controller"] = trans.controller
+            if "action" not in new_kwargs:
+                new_kwargs["action"] = trans.action
             if route_name:
                 return url_for(route_name, **new_kwargs)
             return url_for(**new_kwargs)
 
-        self.use_panels = (kwargs.get('use_panels', False) in [True, 'True', 'true'])
-        self.advanced_search = (kwargs.get('advanced_search', False) in [True, 'True', 'true'])
-        async_request = ((self.use_async) and (kwargs.get('async', False) in [True, 'True', 'true']))
+        self.use_panels = kwargs.get("use_panels", False) in [True, "True", "true"]
+        self.advanced_search = kwargs.get("advanced_search", False) in [True, "True", "true"]
+        async_request = (self.use_async) and (kwargs.get("async", False) in [True, "True", "true"])
         # Currently, filling the template returns a str object; this requires decoding the string into a
         # unicode object within mako templates. What probably should be done is to return the template as
         # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
         # results via a controller method, which is require substantial changes. Hence, for now, return grid
         # as str.
-        page = trans.fill_template(iff(async_request, self.async_template, self.template),
-                                   grid=self,
-                                   query=query,
-                                   cur_page_num=page_num,
-                                   num_pages=num_pages,
-                                   num_page_links=self.num_page_links,
-                                   allow_fetching_all_results=self.allow_fetching_all_results,
-                                   default_filter_dict=self.default_filter,
-                                   cur_filter_dict=cur_filter_dict,
-                                   sort_key=sort_key,
-                                   current_item=current_item,
-                                   ids=kwargs.get('id', []),
-                                   url=url,
-                                   status=status,
-                                   message=message,
-                                   info_text=self.info_text,
-                                   use_panels=self.use_panels,
-                                   use_hide_message=self.use_hide_message,
-                                   advanced_search=self.advanced_search,
-                                   show_item_checkboxes=(self.show_item_checkboxes
-                                                         or kwargs.get('show_item_checkboxes', '') in ['True', 'true']),
-                                   # Pass back kwargs so that grid template can set and use args without
-                                   # grid explicitly having to pass them.
-                                   kwargs=kwargs)
+        page = trans.fill_template(
+            iff(async_request, self.async_template, self.template),
+            grid=self,
+            query=query,
+            cur_page_num=page_num,
+            num_pages=num_pages,
+            num_page_links=self.num_page_links,
+            allow_fetching_all_results=self.allow_fetching_all_results,
+            default_filter_dict=self.default_filter,
+            cur_filter_dict=cur_filter_dict,
+            sort_key=sort_key,
+            current_item=current_item,
+            ids=kwargs.get("id", []),
+            url=url,
+            status=status,
+            message=message,
+            info_text=self.info_text,
+            use_panels=self.use_panels,
+            use_hide_message=self.use_hide_message,
+            advanced_search=self.advanced_search,
+            show_item_checkboxes=(
+                self.show_item_checkboxes or kwargs.get("show_item_checkboxes", "") in ["True", "true"]
+            ),
+            # Pass back kwargs so that grid template can set and use args without
+            # grid explicitly having to pass them.
+            kwargs=kwargs,
+        )
         trans.log_action(trans.get_user(), "grid.view", context, params)
         return page
 
     def get_ids(self, **kwargs):
         id = []
-        if 'id' in kwargs:
-            id = kwargs['id']
+        if "id" in kwargs:
+            id = kwargs["id"]
             # Coerce ids to list
             if not isinstance(id, list):
                 id = id.split(",")
diff --git a/lib/galaxy/web/proxy/__init__.py b/lib/galaxy/web/proxy/__init__.py
index 9d15b550f1d..3cfbb3efd55 100644
--- a/lib/galaxy/web/proxy/__init__.py
+++ b/lib/galaxy/web/proxy/__init__.py
@@ -9,10 +9,13 @@ import requests
 from galaxy.util import (
     sockets,
     sqlite,
-    unique_id
+    unique_id,
 )
 from galaxy.util.filelock import FileLock
-from galaxy.util.lazy_process import LazyProcess, NoOpLazyProcess
+from galaxy.util.lazy_process import (
+    LazyProcess,
+    NoOpLazyProcess,
+)
 from galaxy.web.framework import url_for
 
 log = logging.getLogger(__name__)
@@ -26,20 +29,26 @@ SECURE_COOKIE = "galaxysession"
 class ProxyManager:
 
     valid_update_keys = (
-        'host',
-        'port',
+        "host",
+        "port",
     )
 
     def __init__(self, config):
-        for option in ["manage_dynamic_proxy", "dynamic_proxy_bind_port",
-                       "dynamic_proxy_bind_ip", "dynamic_proxy_debug",
-                       "dynamic_proxy_external_proxy", "dynamic_proxy_prefix",
-                       "proxy_session_map",
-                       "dynamic_proxy", "cookie_path",
-                       "dynamic_proxy_golang_noaccess",
-                       "dynamic_proxy_golang_clean_interval",
-                       "dynamic_proxy_golang_docker_address",
-                       "dynamic_proxy_golang_api_key"]:
+        for option in [
+            "manage_dynamic_proxy",
+            "dynamic_proxy_bind_port",
+            "dynamic_proxy_bind_ip",
+            "dynamic_proxy_debug",
+            "dynamic_proxy_external_proxy",
+            "dynamic_proxy_prefix",
+            "proxy_session_map",
+            "dynamic_proxy",
+            "cookie_path",
+            "dynamic_proxy_golang_noaccess",
+            "dynamic_proxy_golang_clean_interval",
+            "dynamic_proxy_golang_docker_address",
+            "dynamic_proxy_golang_api_key",
+        ]:
 
             setattr(self, option, getattr(config, option))
 
@@ -56,7 +65,16 @@ class ProxyManager:
     def shutdown(self):
         self.lazy_process.shutdown()
 
-    def setup_proxy(self, trans, host=DEFAULT_PROXY_TO_HOST, port=None, proxy_prefix="", route_name="", container_ids=None, container_interface=None):
+    def setup_proxy(
+        self,
+        trans,
+        host=DEFAULT_PROXY_TO_HOST,
+        port=None,
+        proxy_prefix="",
+        route_name="",
+        container_ids=None,
+        container_interface=None,
+    ):
         if self.manage_dynamic_proxy:
             log.info("Attempting to start dynamic proxy process")
             log.debug(f"Cmd: {' '.join(self.lazy_process.command_and_args)}")
@@ -70,24 +88,24 @@ class ProxyManager:
         self.proxy_ipc.handle_requests(
             authentication,
             proxy_requests,
-            f'/{route_name}',
+            f"/{route_name}",
             container_ids,
             container_interface,
         )
         # TODO: These shouldn't need to be request.host and request.scheme -
         # though they are reasonable defaults.
         host = trans.request.host
-        if ':' in host:
-            host = host[0:host.index(':')]
+        if ":" in host:
+            host = host[0 : host.index(":")]
         scheme = trans.request.scheme
         if not self.dynamic_proxy_external_proxy:
-            proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port)
+            proxy_url = "%s://%s:%d" % (scheme, host, self.dynamic_proxy_bind_port)
         else:
-            proxy_url = f'{scheme}://{host}{proxy_prefix}'
+            proxy_url = f"{scheme}://{host}{proxy_prefix}"
         return {
-            'proxy_url': proxy_url,
-            'proxied_port': proxy_requests.port,
-            'proxied_host': proxy_requests.host,
+            "proxy_url": proxy_url,
+            "proxied_port": proxy_requests.port,
+            "proxied_host": proxy_requests.host,
         }
 
     def update_proxy(self, trans, **kwargs):
@@ -116,18 +134,19 @@ class ProxyManager:
 
 
 class ProxyLauncher:
-
     def launch_proxy_command(self, config):
         raise NotImplementedError()
 
 
 class NodeProxyLauncher:
-
     def launch_proxy_command(self, config):
         args = [
-            "--sessions", config.proxy_session_map,
-            "--ip", config.dynamic_proxy_bind_ip,
-            "--port", str(config.dynamic_proxy_bind_port),
+            "--sessions",
+            config.proxy_session_map,
+            "--ip",
+            config.dynamic_proxy_bind_ip,
+            "--port",
+            str(config.dynamic_proxy_bind_port),
             "--reverseProxy",
         ]
         if config.dynamic_proxy_debug:
@@ -140,24 +159,29 @@ class NodeProxyLauncher:
 
 
 class GolangProxyLauncher:
-
     def launch_proxy_command(self, config):
         args = [
             "gxproxy",  # Must be on path. TODO: wheel?
-            "--listenAddr", '%s:%d' % (
+            "--listenAddr",
+            "%s:%d"
+            % (
                 config.dynamic_proxy_bind_ip,
                 config.dynamic_proxy_bind_port,
             ),
-            "--listenPath", "/".join((
-                (config.cookie_path or url_for('/')),
-                config.dynamic_proxy_prefix
-            )),
-            "--cookieName", "galaxysession",
-            "--storage", config.proxy_session_map.replace('.sqlite', '.xml'),  # just in case.
-            "--apiKey", config.dynamic_proxy_golang_api_key,
-            "--noAccess", config.dynamic_proxy_golang_noaccess,
-            "--cleanInterval", config.dynamic_proxy_golang_clean_interval,
-            "--dockerAddr", config.dynamic_proxy_golang_docker_address,
+            "--listenPath",
+            "/".join(((config.cookie_path or url_for("/")), config.dynamic_proxy_prefix)),
+            "--cookieName",
+            "galaxysession",
+            "--storage",
+            config.proxy_session_map.replace(".sqlite", ".xml"),  # just in case.
+            "--apiKey",
+            config.dynamic_proxy_golang_api_key,
+            "--noAccess",
+            config.dynamic_proxy_golang_noaccess,
+            "--cleanInterval",
+            config.dynamic_proxy_golang_clean_interval,
+            "--dockerAddr",
+            config.dynamic_proxy_golang_docker_address,
         ]
         if config.dynamic_proxy_debug:
             args.append("--verbose")
@@ -165,14 +189,12 @@ class GolangProxyLauncher:
 
 
 class AuthenticationToken:
-
     def __init__(self, trans):
         self.cookie_name = SECURE_COOKIE
         self.cookie_value = trans.get_cookie(self.cookie_name)
 
 
 class ProxyRequests:
-
     def __init__(self, host=None, port=None):
         if host is None:
             host = DEFAULT_PROXY_TO_HOST
@@ -195,7 +217,6 @@ def proxy_ipc(config):
 
 
 class ProxyIpc:
-
     def handle_requests(self, authentication, proxy_requests, route_name, container_ids, container_interface):
         raise NotImplementedError()
 
@@ -204,7 +225,6 @@ class ProxyIpc:
 
 
 class JsonFileProxyIpc:
-
     def __init__(self, proxy_session_map):
         self.proxy_session_map = proxy_session_map
 
@@ -216,10 +236,10 @@ class JsonFileProxyIpc:
             json_data = open(self.proxy_session_map).read()
             session_map = json.loads(json_data)
             session_map[key] = {
-                'host': proxy_requests.host,
-                'port': proxy_requests.port,
-                'container_ids': container_ids,
-                'container_interface': container_interface,
+                "host": proxy_requests.host,
+                "port": proxy_requests.port,
+                "container_ids": container_ids,
+                "container_interface": container_interface,
             }
             new_json_data = json.dumps(session_map)
             open(self.proxy_session_map, "w").write(new_json_data)
@@ -228,8 +248,8 @@ class JsonFileProxyIpc:
         key = authentication.cookie_value
         with FileLock(self.proxy_session_map):
             session_map = json.load(open(self.proxy_session_map))
-            session_map[key]['host'] = host
-            session_map[key]['port'] = port
+            session_map[key]["host"] = host
+            session_map[key]["port"] = port
             new_json_data = json.dumps(session_map)
             open(self.proxy_session_map, "w").write(new_json_data)
 
@@ -240,18 +260,17 @@ class JsonFileProxyIpc:
                 session_map = json.load(fh)
                 m = session_map[key]
                 return ProxyMapping(
-                    host=m['host'],
-                    port=m['port'],
-                    container_ids=m['container_ids'],
-                    container_interface=m['container_interface'],
+                    host=m["host"],
+                    port=m["port"],
+                    container_ids=m["container_ids"],
+                    container_interface=m["container_interface"],
                 )
         except (TypeError, KeyError):
-            log.warning('fetch_requests(): invalid key: %s', key)
+            log.warning("fetch_requests(): invalid key: %s", key)
             return None
 
 
 class SqliteProxyIpc:
-
     def __init__(self, proxy_session_map):
         self.proxy_session_map = proxy_session_map
 
@@ -263,25 +282,25 @@ class SqliteProxyIpc:
                 c = conn.cursor()
                 try:
                     # Create table
-                    c.execute('''CREATE TABLE gxproxy2
+                    c.execute(
+                        """CREATE TABLE gxproxy2
                                  (key text PRIMARY KEY,
                                   host text,
                                   port integer,
                                   container_ids text,
-                                  container_interface text)''')
+                                  container_interface text)"""
+                    )
                 except Exception:
                     pass
-                delete = '''DELETE FROM gxproxy2 WHERE key=?'''
+                delete = """DELETE FROM gxproxy2 WHERE key=?"""
                 c.execute(delete, (key,))
-                insert = '''INSERT INTO gxproxy2
+                insert = """INSERT INTO gxproxy2
                             (key, host, port, container_ids, container_interface)
-                            VALUES (?, ?, ?, ?, ?)'''
-                c.execute(insert,
-                          (key,
-                           proxy_requests.host,
-                           proxy_requests.port,
-                           json.dumps(container_ids),
-                           container_interface))
+                            VALUES (?, ?, ?, ?, ?)"""
+                c.execute(
+                    insert,
+                    (key, proxy_requests.host, proxy_requests.port, json.dumps(container_ids), container_interface),
+                )
                 conn.commit()
             finally:
                 conn.close()
@@ -292,9 +311,9 @@ class SqliteProxyIpc:
             conn = sqlite.connect(self.proxy_session_map)
             try:
                 c = conn.cursor()
-                update = '''UPDATE gxproxy2
+                update = """UPDATE gxproxy2
                             SET host = ?, port = ?
-                            WHERE key = ?'''
+                            WHERE key = ?"""
                 c.execute(update, (host, port, key))
                 conn.commit()
             finally:
@@ -306,54 +325,55 @@ class SqliteProxyIpc:
             conn = sqlite.connect(self.proxy_session_map)
             try:
                 c = conn.cursor()
-                select = '''SELECT host, port, container_ids, container_interface
+                select = """SELECT host, port, container_ids, container_interface
                             FROM gxproxy2
-                            WHERE key=?'''
+                            WHERE key=?"""
                 c.execute(select, (key,))
                 try:
                     host, port, container_ids, container_interface = c.fetchone()
                 except TypeError:
-                    log.warning('fetch_requests(): invalid key: %s', key)
+                    log.warning("fetch_requests(): invalid key: %s", key)
                     return None
                 return ProxyMapping(
                     host=host,
                     port=port,
                     container_ids=json.loads(container_ids),
-                    container_interface=container_interface)
+                    container_interface=container_interface,
+                )
             finally:
                 conn.close()
 
 
 class RestGolangProxyIpc:
-
     def __init__(self, config):
         self.config = config
-        self.api_url = f'http://127.0.0.1:{self.config.dynamic_proxy_bind_port}/api?api_key={self.config.dynamic_proxy_golang_api_key}'
+        self.api_url = f"http://127.0.0.1:{self.config.dynamic_proxy_bind_port}/api?api_key={self.config.dynamic_proxy_golang_api_key}"
 
     def handle_requests(self, authentication, proxy_requests, route_name, container_ids, container_interface, sleep=1):
-        """Make a POST request to the GO proxy to register a route
-        """
+        """Make a POST request to the GO proxy to register a route"""
         values = {
-            'FrontendPath': route_name,
-            'BackendAddr': f"{proxy_requests.host}:{proxy_requests.port}",
-            'AuthorizedCookie': authentication.cookie_value,
-            'ContainerIds': container_ids,
+            "FrontendPath": route_name,
+            "BackendAddr": f"{proxy_requests.host}:{proxy_requests.port}",
+            "AuthorizedCookie": authentication.cookie_value,
+            "ContainerIds": container_ids,
         }
 
         # Sometimes it takes our poor little proxy a second or two to get
         # going, so if this fails, re-call ourselves with an increased timeout.
         try:
-            requests.get(self.api_url, headers={'Content-Type': 'application/json'}, data=json.dumps(values))
+            requests.get(self.api_url, headers={"Content-Type": "application/json"}, data=json.dumps(values))
         except requests.exceptions.ConnectionError as err:
             log.exception(err)
             if sleep > 5:
                 excp = f"Could not contact proxy after {sum(range(sleep + 1))} seconds"
                 raise Exception(excp)
             time.sleep(sleep)
-            self.handle_requests(authentication, proxy_requests, route_name, container_ids, container_interface, sleep=sleep + 1)
+            self.handle_requests(
+                authentication, proxy_requests, route_name, container_ids, container_interface, sleep=sleep + 1
+            )
 
 
-ProxyMapping = namedtuple('ProxyMapping', ['host', 'port', 'container_ids', 'container_interface'])
+ProxyMapping = namedtuple("ProxyMapping", ["host", "port", "container_ids", "container_interface"])
 
 
 # TODO: MQ diven proxy?
diff --git a/lib/galaxy/web/statsd_client.py b/lib/galaxy/web/statsd_client.py
index 193a6d9177f..df681ca7905 100644
--- a/lib/galaxy/web/statsd_client.py
+++ b/lib/galaxy/web/statsd_client.py
@@ -1,5 +1,9 @@
 import sys
-from typing import Dict, Optional, Type
+from typing import (
+    Dict,
+    Optional,
+    Type,
+)
 
 try:
     import statsd
@@ -11,21 +15,17 @@ from galaxy.util import asbool
 
 # TODO: optimize with two separate implementations around statsd_influxdb?
 class VanillaGalaxyStatsdClient:
-
-    def __init__(self,
-                 statsd_host,
-                 statsd_port,
-                 statsd_prefix,
-                 statsd_influxdb,
-                 statsd_mock_calls=False):
+    def __init__(self, statsd_host, statsd_port, statsd_prefix, statsd_influxdb, statsd_mock_calls=False):
         if not statsd:
-            raise ImportError("Statsd logging configured, but no statsd python module found. "
-                           "Please install the python statsd module to use this functionality.")
+            raise ImportError(
+                "Statsd logging configured, but no statsd python module found. "
+                "Please install the python statsd module to use this functionality."
+            )
 
-        self.metric_infix = ''
+        self.metric_infix = ""
         self.statsd_influxdb = asbool(statsd_influxdb)
         if self.statsd_influxdb:
-            statsd_prefix = statsd_prefix.strip(',')
+            statsd_prefix = statsd_prefix.strip(",")
         if statsd_mock_calls:
             self.statsd_client = MockStatsClient()
         else:
@@ -42,11 +42,11 @@ class VanillaGalaxyStatsdClient:
     def _effective_infix(self, path, tags):
         tags = tags or {}
         if self.statsd_influxdb and tags:
-            return f",{','.join(f'{k}={v}' for k, v in tags.items())}" + ',path='
+            return f",{','.join(f'{k}={v}' for k, v in tags.items())}" + ",path="
         if self.statsd_influxdb:
-            return ',path='
+            return ",path="
         else:
-            return ''
+            return ""
 
 
 CURRENT_TEST: Optional[str] = None
@@ -54,7 +54,6 @@ CURRENT_TEST_METRICS: Optional[Dict[str, Dict]] = None
 
 
 class PyTestGalaxyStatsdClient(VanillaGalaxyStatsdClient):
-
     def timing(self, path, time, tags=None):
         metrics = CURRENT_TEST_METRICS
         if metrics is not None:
@@ -82,7 +81,6 @@ class PyTestGalaxyStatsdClient(VanillaGalaxyStatsdClient):
 
 
 class MockStatsClient:
-
     def timing(self, path, time, tags=None):
         pass
 
@@ -92,10 +90,10 @@ class MockStatsClient:
 
 GalaxyStatsdClient: Type[VanillaGalaxyStatsdClient]
 # Replace stats collector if in pytest environment
-if 'pytest' in sys.modules:
+if "pytest" in sys.modules:
     GalaxyStatsdClient = PyTestGalaxyStatsdClient
 else:
     GalaxyStatsdClient = VanillaGalaxyStatsdClient
 
 
-__all__ = ('GalaxyStatsdClient',)
+__all__ = ("GalaxyStatsdClient",)
diff --git a/lib/galaxy/web_stack/__init__.py b/lib/galaxy/web_stack/__init__.py
index 5993d40d075..f26d01d805b 100644
--- a/lib/galaxy/web_stack/__init__.py
+++ b/lib/galaxy/web_stack/__init__.py
@@ -5,7 +5,15 @@ import json
 import logging
 import multiprocessing
 import os
-from typing import Callable, Dict, FrozenSet, List, Optional, Tuple, Type
+from typing import (
+    Callable,
+    Dict,
+    FrozenSet,
+    List,
+    Optional,
+    Tuple,
+    Type,
+)
 from urllib.request import install_opener
 
 # The uwsgi module is automatically injected by the parent uwsgi process and only exists that way.  If anything works,
@@ -22,9 +30,14 @@ from galaxy.util.facts import get_facts
 from galaxy.util.path import has_ext
 from galaxy.util.properties import nice_config_parser
 from .handlers import HANDLER_ASSIGNMENT_METHODS
-from .message import ApplicationStackMessage, ApplicationStackMessageDispatcher
-from .transport import ApplicationStackTransport, UWSGIFarmMessageTransport
-
+from .message import (
+    ApplicationStackMessage,
+    ApplicationStackMessageDispatcher,
+)
+from .transport import (
+    ApplicationStackTransport,
+    UWSGIFarmMessageTransport,
+)
 
 log = logging.getLogger(__name__)
 
@@ -48,10 +61,10 @@ class ApplicationStack:
     prohibited_middleware: FrozenSet[str] = frozenset()
     transport_class = ApplicationStackTransport
     log_filter_class: Type[logging.Filter] = ApplicationStackLogFilter
-    log_format = '%(name)s %(levelname)s %(asctime)s [pN:%(processName)s,p:%(process)d,tN:%(threadName)s] %(message)s'
+    log_format = "%(name)s %(levelname)s %(asctime)s [pN:%(processName)s,p:%(process)d,tN:%(threadName)s] %(message)s"
     # TODO: this belongs in the pool configuration
-    server_name_template = '{server_name}'
-    default_app_name = 'main'
+    server_name_template = "{server_name}"
+    default_app_name = "main"
 
     @classmethod
     def log_filter(cls):
@@ -72,7 +85,7 @@ class ApplicationStack:
         self._supports_returning = None
         self._supports_skip_locked = None
         self._preferred_handler_assignment_method = None
-        multiprocessing.current_process().name = getattr(self.config, 'server_name', 'main')
+        multiprocessing.current_process().name = getattr(self.config, "server_name", "main")
         if app:
             log.debug("%s initialized", self.__class__.__name__)
 
@@ -103,7 +116,9 @@ class ApplicationStack:
             if self.app.application_stack.supports_skip_locked():
                 self._preferred_handler_assignment_method = HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED
             else:
-                log.debug("Database does not support WITH FOR UPDATE statement, cannot use DB-SKIP-LOCKED handler assignment")
+                log.debug(
+                    "Database does not support WITH FOR UPDATE statement, cannot use DB-SKIP-LOCKED handler assignment"
+                )
                 self._preferred_handler_assignment_method = HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION
         return self._preferred_handler_assignment_method
 
@@ -118,13 +133,12 @@ class ApplicationStack:
             self._set_default_job_handler_assignment_methods(job_config, base_pool)
 
     def _init_job_handler_subpools(self, job_config, base_pool):
-        """Set up members of "subpools" ("base_pool.*") as handlers (including the base pool itself, if it exists).
-        """
+        """Set up members of "subpools" ("base_pool.*") as handlers (including the base pool itself, if it exists)."""
         for pool_name in self.configured_pools:
             if pool_name == base_pool:
                 tag = job_config.DEFAULT_HANDLER_TAG
             elif pool_name.startswith(f"{base_pool}."):
-                tag = pool_name.replace(f"{base_pool}.", '', 1)
+                tag = pool_name.replace(f"{base_pool}.", "", 1)
             else:
                 continue
             # Pools are hierarchical (so that you can have e.g. workflow schedulers use the job handlers pool if no
@@ -163,7 +177,7 @@ class ApplicationStack:
         pass
 
     def allowed_middleware(self, middleware):
-        if hasattr(middleware, '__name__'):
+        if hasattr(middleware, "__name__"):
             middleware = middleware.__name__
         return middleware not in self.prohibited_middleware
 
@@ -194,13 +208,13 @@ class ApplicationStack:
     @property
     def facts(self):
         facts = get_facts(config=self.config)
-        facts.update({'pool_name': self.pool_name})
+        facts.update({"pool_name": self.pool_name})
         return facts
 
     def set_postfork_server_name(self, app):
         new_server_name = self.server_name_template.format(**self.facts)
         multiprocessing.current_process().name = app.config.server_name = new_server_name
-        log.debug('server_name set to: %s', new_server_name)
+        log.debug("server_name set to: %s", new_server_name)
 
     def register_message_handler(self, func, name=None):
         pass
@@ -242,16 +256,12 @@ class MessageApplicationStack(ApplicationStack):
     def send_message(self, dest, msg=None, target=None, params=None, **kwargs):
         assert msg is not None or target is not None, "Either 'msg' or 'target' parameters must be set"
         if not msg:
-            msg = ApplicationStackMessage(
-                target=target,
-                params=params,
-                **kwargs
-            )
+            msg = ApplicationStackMessage(target=target, params=params, **kwargs)
         self.transport.send_message(msg.encode(), dest)
 
     def shutdown(self):
         if self.use_messaging and self.running:
-            log.info('Application stack interface shutting down')
+            log.info("Application stack interface shutting down")
             self.transport.shutdown()
             self.running = False
 
@@ -262,36 +272,38 @@ class UWSGIApplicationStack(MessageApplicationStack):
 
     Note that mules will use this as their stack class even though they start with the "webless" loading point.
     """
-    name = 'uWSGI'
-    prohibited_middleware = frozenset({
-        'wrap_in_static',
-        'EvalException',
-    })
+
+    name = "uWSGI"
+    prohibited_middleware = frozenset(
+        {
+            "wrap_in_static",
+            "EvalException",
+        }
+    )
     transport_class = UWSGIFarmMessageTransport
     log_filter_class = UWSGILogFilter
-    log_format = '%(name)s %(levelname)s %(asctime)s [pN:%(processName)s,p:%(process)d,w:%(worker_id)s,m:%(mule_id)s,tN:%(threadName)s] %(message)s'
-    server_name_template = '{server_name}.{pool_name}.{instance_id}'
+    log_format = "%(name)s %(levelname)s %(asctime)s [pN:%(processName)s,p:%(process)d,w:%(worker_id)s,m:%(mule_id)s,tN:%(threadName)s] %(message)s"
+    server_name_template = "{server_name}.{pool_name}.{instance_id}"
 
     postfork_functions: List[Tuple[Callable, List, Dict]] = []
 
-    localhost_addrs = ('127.0.0.1', '[::1]')
-    bind_all_addrs = ('', '0.0.0.0', '[::]')
+    localhost_addrs = ("127.0.0.1", "[::1]")
+    bind_all_addrs = ("", "0.0.0.0", "[::]")
 
     @staticmethod
     def _get_config_file(confs, loader, section):
-        """uWSGI allows config merging, in which case the corresponding config file option will be a list.
-        """
+        """uWSGI allows config merging, in which case the corresponding config file option will be a list."""
         conf = None
         if isinstance(confs, list):
             gconfs = [_ for _ in confs if os.path.exists(_) and section in loader(open(_))]
             if len(gconfs) == 1:
                 conf = gconfs[0]
             elif len(gconfs) == 0:
-                log.warning('Could not locate a config file containing a Galaxy config from: %s',
-                            ', '.join(confs))
+                log.warning("Could not locate a config file containing a Galaxy config from: %s", ", ".join(confs))
             else:
-                log.warning('Multiple config files contain Galaxy configs, merging is not supported: %s',
-                            ', '.join(gconfs))
+                log.warning(
+                    "Multiple config files contain Galaxy configs, merging is not supported: %s", ", ".join(gconfs)
+                )
         else:
             conf = confs
         return conf
@@ -301,24 +313,24 @@ class UWSGIApplicationStack(MessageApplicationStack):
         try:
             opt = unicodify(opt)
             val = unicodify(val)
-            if val.startswith('='):
-                val = unicodify(uwsgi.opt.get('shared-socket', [])[int(val.split('=')[1])])
-            proto = opt if opt != 'socket' else 'uwsgi'
-            if proto == 'uwsgi' and ':' not in val:
+            if val.startswith("="):
+                val = unicodify(uwsgi.opt.get("shared-socket", [])[int(val.split("=")[1])])
+            proto = opt if opt != "socket" else "uwsgi"
+            if proto == "uwsgi" and ":" not in val:
                 return f"uwsgi://{val}"
             else:
                 proto = f"{proto}://"
-                host, port = val.rsplit(':', 1)
+                host, port = val.rsplit(":", 1)
                 port = f":{port.split(',', 1)[0]}"
             if host in UWSGIApplicationStack.bind_all_addrs:
                 host = UWSGIApplicationStack.localhost_addrs[0]
             return proto + host + port
         except (IndexError, AttributeError):
-            return f'{opt} {val}'
+            return f"{opt} {val}"
 
     @staticmethod
     def _socket_opts():
-        for opt in ('https', 'http', 'socket'):
+        for opt in ("https", "http", "socket"):
             if opt in uwsgi.opt:
                 val = uwsgi.opt[opt]
                 if isinstance(val, list):
@@ -335,8 +347,8 @@ class UWSGIApplicationStack(MessageApplicationStack):
     @classmethod
     def get_app_kwds(cls, config_section, app_name=None):
         kwds = {
-            'config_file': None,
-            'config_section': config_section,
+            "config_file": None,
+            "config_section": config_section,
         }
         uwsgi_opt = uwsgi.opt
         config_file = None
@@ -346,8 +358,9 @@ class UWSGIApplicationStack(MessageApplicationStack):
             config_file = uwsgi_opt.get("galaxy_config_file")
         # check for --yaml or --json uWSGI config options next
         if config_file is None:
-            config_file = (UWSGIApplicationStack._get_config_file(uwsgi_opt.get("yaml"), yaml.safe_load, config_section)
-                           or UWSGIApplicationStack._get_config_file(uwsgi_opt.get("json"), json.load, config_section))
+            config_file = UWSGIApplicationStack._get_config_file(
+                uwsgi_opt.get("yaml"), yaml.safe_load, config_section
+            ) or UWSGIApplicationStack._get_config_file(uwsgi_opt.get("json"), json.load, config_section)
         # --ini and --ini-paste don't behave the same way, but this method will only be called by mules if the main
         # application was loaded with --ini-paste, so we can make some assumptions, most notably, uWSGI does not have
         # any way to set the app name when loading with paste.deploy:loadapp(), so hardcoding the alternate section
@@ -357,9 +370,9 @@ class UWSGIApplicationStack(MessageApplicationStack):
         if has_ini_config:
             config_file = config_file or uwsgi_opt.get("ini") or uwsgi_opt.get("ini-paste")
             parser = nice_config_parser(config_file)
-            if not parser.has_section(config_section) and parser.has_section('app:main'):
-                kwds['config_section'] = 'app:main'
-        kwds['config_file'] = unicodify(config_file)
+            if not parser.has_section(config_section) and parser.has_section("app:main"):
+                kwds["config_section"] = "app:main"
+        kwds["config_file"] = unicodify(config_file)
         return kwds
 
     @classmethod
@@ -391,13 +404,18 @@ class UWSGIApplicationStack(MessageApplicationStack):
         # remove DB_SELF
         conf_class_name = job_config.__class__.__name__
         remove_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF]
-        if (HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE not in job_config.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS):
+        if HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE not in job_config.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS:
             add_method = HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE
         else:
             add_method = self.get_preferred_handler_assignment_method()
             remove_methods.append(HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE)
-        log.debug("%s: No job handler assignment methods were configured but a uWSGI farm named '%s' exists,"
-                  " automatically enabling the '%s' assignment method", conf_class_name, base_pool, add_method)
+        log.debug(
+            "%s: No job handler assignment methods were configured but a uWSGI farm named '%s' exists,"
+            " automatically enabling the '%s' assignment method",
+            conf_class_name,
+            base_pool,
+            add_method,
+        )
         for m in remove_methods:
             try:
                 job_config.handler_assignment_methods.remove(m)
@@ -406,8 +424,11 @@ class UWSGIApplicationStack(MessageApplicationStack):
                 pass
         if add_method not in job_config.handler_assignment_methods:
             job_config.handler_assignment_methods.insert(0, add_method)
-        log.debug("%s: handler assignment methods updated to: %s", conf_class_name,
-                  ', '.join(job_config.handler_assignment_methods))
+        log.debug(
+            "%s: handler assignment methods updated to: %s",
+            conf_class_name,
+            ", ".join(job_config.handler_assignment_methods),
+        )
 
     def _init_job_handler_assignment_methods(self, job_config, base_pool):
         super()._init_job_handler_assignment_methods(job_config, base_pool)
@@ -420,7 +441,7 @@ class UWSGIApplicationStack(MessageApplicationStack):
         # Count the required number of uWSGI locks
         if job_config.use_messaging:
             for pool_name in self.configured_pools:
-                if (pool_name == base_pool or pool_name.startswith(f"{base_pool}.")):
+                if pool_name == base_pool or pool_name.startswith(f"{base_pool}."):
                     self._lock_farms.add(pool_name)
 
     @property
@@ -437,12 +458,12 @@ class UWSGIApplicationStack(MessageApplicationStack):
     def configured_pools(self):
         if self._farms_dict is None:
             self._farms_dict = {}
-            farms = uwsgi.opt.get('farm', [])
+            farms = uwsgi.opt.get("farm", [])
             farms = farms if isinstance(farms, list) else [farms]
             for farm in farms:
                 farm = unicodify(farm)
-                name, mules = farm.split(':', 1)
-                self._farms_dict[name] = [int(m) for m in mules.split(',')]
+                name, mules = farm.split(":", 1)
+                self._farms_dict[name] = [int(m) for m in mules.split(",")]
         return self._farms_dict
 
     @property
@@ -477,11 +498,13 @@ class UWSGIApplicationStack(MessageApplicationStack):
                 server_names = []
                 facts = self.facts
                 for mule in mules:
-                    facts.update({
-                        'pool_name': farm_name,
-                        'server_id': mule,
-                        'instance_id': self._mule_index_in_farm(farm_name, mule) + 1,
-                    })
+                    facts.update(
+                        {
+                            "pool_name": farm_name,
+                            "server_id": mule,
+                            "instance_id": self._mule_index_in_farm(farm_name, mule) + 1,
+                        }
+                    )
                     server_names.append(self.server_name_template.format(**facts))
                 self._farm_server_names_dict[farm_name] = server_names
         return self._farm_server_names_dict
@@ -507,18 +530,18 @@ class UWSGIApplicationStack(MessageApplicationStack):
             # grepping for this line. Here root_pid is the same that gets
             # written to file when using the --pidfile option of uwsgi
             root_pid = uwsgi.masterpid() or os.getpid()
-            msg.append('Starting server in PID %d.' % root_pid)
+            msg.append("Starting server in PID %d." % root_pid)
             for s in UWSGIApplicationStack._serving_on():
                 msg.append(f"serving on {s}")
             if len(msg) == 1:
-                msg.append('serving on unknown URL')
-        log.info('\n'.join(msg))
+                msg.append("serving on unknown URL")
+        log.info("\n".join(msg))
 
     def start(self):
         # Does a generalized `is_worker` attribute make sense? Hard to say w/o other stack paradigms.
         if self._is_mule and self._farm_name:
             # used by main.py to send a shutdown message on termination
-            os.environ['_GALAXY_UWSGI_FARM_NAMES'] = ','.join(self._farms)
+            os.environ["_GALAXY_UWSGI_FARM_NAMES"] = ",".join(self._farms)
         super().start()
 
     def in_pool(self, pool_name):
@@ -537,16 +560,20 @@ class UWSGIApplicationStack(MessageApplicationStack):
     def facts(self):
         facts = super().facts
         if not self._is_mule:
-            facts.update({
-                'pool_name': 'web',
-                'server_id': uwsgi.worker_id(),
-            })
+            facts.update(
+                {
+                    "pool_name": "web",
+                    "server_id": uwsgi.worker_id(),
+                }
+            )
         else:
-            facts.update({
-                'pool_name': self._farm_name,
-                'server_id': uwsgi.mule_id(),
-            })
-        facts['instance_id'] = self.instance_id
+            facts.update(
+                {
+                    "pool_name": self._farm_name,
+                    "server_id": uwsgi.mule_id(),
+                }
+            )
+        facts["instance_id"] = self.instance_id
         return facts
 
     def shutdown(self):
@@ -554,11 +581,11 @@ class UWSGIApplicationStack(MessageApplicationStack):
 
 
 class PasteApplicationStack(ApplicationStack):
-    name = 'Python Paste'
+    name = "Python Paste"
 
 
 class WeblessApplicationStack(ApplicationStack):
-    name = 'Webless'
+    name = "Webless"
 
     def _set_default_job_handler_assignment_methods(self, job_config, base_pool):
         # We will only get here if --attach-to-pool has been set so it is safe to assume that this handler is dynamic
@@ -569,23 +596,35 @@ class WeblessApplicationStack(ApplicationStack):
         conf_class_name = job_config.__class__.__name__
         remove_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF]
         add_method = self.get_preferred_handler_assignment_method()
-        log.debug("%s: No job handler assignment methods were configured but this server is configured to attach to the"
-                  " '%s' pool, automatically enabling the '%s' assignment method", conf_class_name, base_pool, add_method)
+        log.debug(
+            "%s: No job handler assignment methods were configured but this server is configured to attach to the"
+            " '%s' pool, automatically enabling the '%s' assignment method",
+            conf_class_name,
+            base_pool,
+            add_method,
+        )
         for m in remove_methods:
             try:
                 job_config.handler_assignment_methods.remove(m)
-                log.debug("%s: Removed '%s' from handler assignment methods due to use of --attach-to-pool", conf_class_name, m)
+                log.debug(
+                    "%s: Removed '%s' from handler assignment methods due to use of --attach-to-pool",
+                    conf_class_name,
+                    m,
+                )
             except ValueError:
                 pass
         if add_method not in job_config.handler_assignment_methods:
             job_config.handler_assignment_methods.insert(0, add_method)
-        log.debug("%s: handler assignment methods updated to: %s", conf_class_name,
-                  ', '.join(job_config.handler_assignment_methods))
+        log.debug(
+            "%s: handler assignment methods updated to: %s",
+            conf_class_name,
+            ", ".join(job_config.handler_assignment_methods),
+        )
 
     def __init__(self, app=None, config=None):
         super().__init__(app=app, config=config)
         if self.app and self.config and self.config.attach_to_pools:
-            log.debug("Will attach to pool(s): %s", ', '.join(self.config.attach_to_pools))
+            log.debug("Will attach to pool(s): %s", ", ".join(self.config.attach_to_pools))
 
     @property
     def configured_pools(self):
@@ -602,12 +641,12 @@ def application_stack_class() -> Type[ApplicationStack]:
     """Returns the correct ApplicationStack class for the stack under which
     this Galaxy process is running.
     """
-    if uwsgi is not None and hasattr(uwsgi, 'numproc'):
+    if uwsgi is not None and hasattr(uwsgi, "numproc"):
         return UWSGIApplicationStack
     else:
         # cleverer ideas welcome
         for frame in inspect.stack():
-            if frame[1].endswith(os.path.join('pastescript', 'loadwsgi.py')):
+            if frame[1].endswith(os.path.join("pastescript", "loadwsgi.py")):
                 return PasteApplicationStack
     return WeblessApplicationStack
 
@@ -638,7 +677,7 @@ def get_stack_facts(config=None):
 
 
 def _uwsgi_configured_mules():
-    mules = uwsgi.opt.get('mule', [])
+    mules = uwsgi.opt.get("mule", [])
     return [mules] if isinstance(mules, str) or mules is True else mules
 
 
@@ -649,7 +688,7 @@ def _do_uwsgi_postfork():
             # should not do that (they will call the postfork functions in-place as they start up after exec())
             UWSGIApplicationStack.postfork_functions = [(_mule_fixup, (), {})]
     for f, args, kwargs in [t for t in UWSGIApplicationStack.postfork_functions]:
-        log.debug('Calling postfork function: %s', f)
+        log.debug("Calling postfork function: %s", f)
         f(*args, **kwargs)
 
 
diff --git a/lib/galaxy/web_stack/handlers.py b/lib/galaxy/web_stack/handlers.py
index d69460bfea2..1487800f85f 100644
--- a/lib/galaxy/web_stack/handlers.py
+++ b/lib/galaxy/web_stack/handlers.py
@@ -8,26 +8,29 @@ import logging
 import os
 import random
 from enum import Enum
-from typing import Set, Tuple
+from typing import (
+    Set,
+    Tuple,
+)
 
 from sqlalchemy.orm import object_session
 
 from galaxy.exceptions import HandlerAssignmentError
 from galaxy.util import (
     ExecutionTimer,
-    listify
+    listify,
 )
 
 log = logging.getLogger(__name__)
 
 
 class HANDLER_ASSIGNMENT_METHODS(str, Enum):
-    MEM_SELF = 'mem-self'
-    DB_SELF = 'db-self'
-    DB_PREASSIGN = 'db-preassign'
-    DB_TRANSACTION_ISOLATION = 'db-transaction-isolation'
-    DB_SKIP_LOCKED = 'db-skip-locked'
-    UWSGI_MULE_MESSAGE = 'uwsgi-mule-message'
+    MEM_SELF = "mem-self"
+    DB_SELF = "db-self"
+    DB_PREASSIGN = "db-preassign"
+    DB_TRANSACTION_ISOLATION = "db-transaction-isolation"
+    DB_SKIP_LOCKED = "db-skip-locked"
+    UWSGI_MULE_MESSAGE = "uwsgi-mule-message"
 
     @classmethod
     def has_value(cls, value):
@@ -35,12 +38,11 @@ class HANDLER_ASSIGNMENT_METHODS(str, Enum):
 
 
 class HandlerAssignmentSkip(Exception):
-    """Exception for handler assignment methods to raise if the next method should be tried.
-    """
+    """Exception for handler assignment methods to raise if the next method should be tried."""
 
 
 class ConfiguresHandlers:
-    DEFAULT_HANDLER_TAG = '_default_'
+    DEFAULT_HANDLER_TAG = "_default_"
     DEFAULT_BASE_HANDLER_POOLS: Tuple[str, ...] = ()
     UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS: Set[str] = set()
 
@@ -62,16 +64,16 @@ class ConfiguresHandlers:
 
         # Parse handlers
         if config_element is not None:
-            for handler in ConfiguresHandlers._findall_with_required(config_element, 'handler'):
-                handler_id = handler.get('id')
+            for handler in ConfiguresHandlers._findall_with_required(config_element, "handler"):
+                handler_id = handler.get("id")
                 if handler_id in processes:
                     log.error("Handler '%s' overlaps handler with the same name, ignoring", handler_id)
                 else:
                     log.debug("Read definition for handler '%s'", handler_id)
                     plugins = []
-                    for plugin in ConfiguresHandlers._findall_with_required(handler, 'plugin', ['id']):
+                    for plugin in ConfiguresHandlers._findall_with_required(handler, "plugin", ["id"]):
                         plugins.append(plugin.get("id"))
-                    tags = [x.strip() for x in handler.get('tags', ConfiguresHandlers.DEFAULT_HANDLER_TAG).split(',')]
+                    tags = [x.strip() for x in handler.get("tags", ConfiguresHandlers.DEFAULT_HANDLER_TAG).split(",")]
                     handler_def = {"tags": tags}
                     if plugins:
                         handler_def["plugins"] = plugins
@@ -80,10 +82,10 @@ class ConfiguresHandlers:
             if default_handler:
                 handling_config_dict["default"] = default_handler
 
-            assign = listify(config_element.attrib.get('assign_with', []), do_strip=True)
+            assign = listify(config_element.attrib.get("assign_with", []), do_strip=True)
             if len(assign) > 0:
                 handling_config_dict["assign"] = assign
-            max_grab_str = config_element.attrib.get('max_grab', None)
+            max_grab_str = config_element.attrib.get("max_grab", None)
             if max_grab_str:
                 handling_config_dict["max_grab"] = int(max_grab_str)
             ready_window_size_str = config_element.attrib.get("ready_window_size", None)
@@ -103,7 +105,9 @@ class ConfiguresHandlers:
                 self._parse_handler(handler_id, process)
                 self.add_handler(handler_id, process.get("tags") or [self.DEFAULT_HANDLER_TAG])
 
-        self.default_handler_id = self._ensure_default_set(handling_config_dict.get("default"), list(self.handlers.keys()), required=False)
+        self.default_handler_id = self._ensure_default_set(
+            handling_config_dict.get("default"), list(self.handlers.keys()), required=False
+        )
 
     def _init_handler_assignment_methods(self, handling_config_dict=None):
         handling_config_dict = handling_config_dict or {}
@@ -122,9 +126,11 @@ class ConfiguresHandlers:
         if handling_config_dict:
             for method in handling_config_dict.get("assign", []):
                 method = method.lower()
-                assert HANDLER_ASSIGNMENT_METHODS.has_value(method), \
-                    "Invalid job handler assignment method '{}', must be one of: {}".format(
-                        method, ', '.join(h.value for h in HANDLER_ASSIGNMENT_METHODS))
+                assert HANDLER_ASSIGNMENT_METHODS.has_value(
+                    method
+                ), "Invalid job handler assignment method '{}', must be one of: {}".format(
+                    method, ", ".join(h.value for h in HANDLER_ASSIGNMENT_METHODS)
+                )
                 try:
                     self.handler_assignment_methods.append(method)
                 except AttributeError:
@@ -132,38 +138,45 @@ class ConfiguresHandlers:
                     self.handler_assignment_methods = [method]
             if self.handler_assignment_methods == [HANDLER_ASSIGNMENT_METHODS.MEM_SELF]:
                 self.app.config.track_jobs_in_database = False
-            self.handler_max_grab = handling_config_dict.get('max_grab', self.handler_max_grab)
+            self.handler_max_grab = handling_config_dict.get("max_grab", self.handler_max_grab)
             if self.handler_max_grab is not None:
                 self.handler_max_grab = int(self.handler_max_grab)
 
     def _set_default_handler_assignment_methods(self):
         if not self.handler_assignment_methods_configured:
-            if not self.app.config.track_jobs_in_database and \
-                    HANDLER_ASSIGNMENT_METHODS.MEM_SELF not in self.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS:
+            if (
+                not self.app.config.track_jobs_in_database
+                and HANDLER_ASSIGNMENT_METHODS.MEM_SELF not in self.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS
+            ):
                 # DEPRECATED: You should just set mem_self as the only method if you want this
-                log.warning("The `track_jobs_in_database` option is deprecated, please set `%s` as the job"
-                            " handler assignment method in the job handler configuration",
-                            HANDLER_ASSIGNMENT_METHODS.MEM_SELF)
+                log.warning(
+                    "The `track_jobs_in_database` option is deprecated, please set `%s` as the job"
+                    " handler assignment method in the job handler configuration",
+                    HANDLER_ASSIGNMENT_METHODS.MEM_SELF,
+                )
                 self.handler_assignment_methods = [HANDLER_ASSIGNMENT_METHODS.MEM_SELF]
             else:
                 self.handler_assignment_methods = [self.app.application_stack.get_preferred_handler_assignment_method()]
             # If the stack has handler pools it can override these defaults
             self.app.application_stack.init_job_handling(self)
-            log.info("%s: No job handler assignment method is set, defaulting to '%s', set the `assign_with` attribute"
-                     " on <handlers> to override the default", self.__class__.__name__,
-                     self.handler_assignment_methods[0])
+            log.info(
+                "%s: No job handler assignment method is set, defaulting to '%s', set the `assign_with` attribute"
+                " on <handlers> to override the default",
+                self.__class__.__name__,
+                self.handler_assignment_methods[0],
+            )
 
     def _parse_handler(self, handler_id, handler_def):
         pass
 
     @staticmethod
     def get_xml_default(config, parent):
-        rval = parent.get('default')
-        if 'default_from_environ' in parent.attrib:
-            environ_var = parent.attrib['default_from_environ']
+        rval = parent.get("default")
+        if "default_from_environ" in parent.attrib:
+            environ_var = parent.attrib["default_from_environ"]
             rval = os.environ.get(environ_var, rval)
-        elif 'default_from_config' in parent.attrib:
-            config_val = parent.attrib['default_from_config']
+        elif "default_from_config" in parent.attrib:
+            config_val = parent.attrib["default_from_config"]
             rval = config.config_dict.get(config_val, rval)
         return rval
 
@@ -215,7 +228,7 @@ class ConfiguresHandlers:
         """
         rval = []
         if attribs is None:
-            attribs = ('id',)
+            attribs = ("id",)
         for elem in parent.findall(match):
             for attrib in attribs:
                 if attrib not in elem.attrib:
@@ -233,10 +246,15 @@ class ConfiguresHandlers:
     @property
     def deterministic_handler_assignment(self):
         return self.handler_assignment_methods and any(
-            filter(lambda x: x in (
-                HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE,
-                HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN,
-            ), self.handler_assignment_methods))
+            filter(
+                lambda x: x
+                in (
+                    HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE,
+                    HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN,
+                ),
+                self.handler_assignment_methods,
+            )
+        )
 
     def _get_is_handler(self):
         """Indicate whether the current server is configured as a handler.
@@ -245,15 +263,22 @@ class ConfiguresHandlers:
         """
         if self.__is_handler is not None:
             return self.__is_handler
-        if (HANDLER_ASSIGNMENT_METHODS.DB_SELF in self.handler_assignment_methods
-                or HANDLER_ASSIGNMENT_METHODS.MEM_SELF in self.handler_assignment_methods):
+        if (
+            HANDLER_ASSIGNMENT_METHODS.DB_SELF in self.handler_assignment_methods
+            or HANDLER_ASSIGNMENT_METHODS.MEM_SELF in self.handler_assignment_methods
+        ):
             return True
         for collection in self.handlers.values():
             if self.app.config.server_name in collection:
                 return True
-        if not self.handlers and not self.handler_assignment_methods_configured \
-                and (HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION in self.handler_assignment_methods
-                or HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED in self.handler_assignment_methods):
+        if (
+            not self.handlers
+            and not self.handler_assignment_methods_configured
+            and (
+                HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION in self.handler_assignment_methods
+                or HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED in self.handler_assignment_methods
+            )
+        ):
             return True
         return False
 
@@ -263,8 +288,7 @@ class ConfiguresHandlers:
     is_handler = property(_get_is_handler, _set_is_handler)
 
     def _get_single_item(self, collection, index=None):
-        """Given a collection of handlers or destinations, return one item from the collection at random.
-        """
+        """Given a collection of handlers or destinations, return one item from the collection at random."""
         # Done like this to avoid random under the assumption it's faster to avoid it
         if len(collection) == 1:
             return collection[0]
@@ -275,15 +299,15 @@ class ConfiguresHandlers:
 
     @property
     def handler_tags(self):
-        """Get an iterable of all configured handler tags.
-        """
+        """Get an iterable of all configured handler tags."""
         return filter(lambda k: isinstance(self.handlers[k], list), self.handlers.keys())
 
     @property
     def self_handler_tags(self):
-        """Get an iterable of the current process's configured handler tags.
-        """
-        return [k for k in self.handler_tags if self.app.config.server_name in self.handlers[k]] or [self.DEFAULT_HANDLER_TAG]
+        """Get an iterable of the current process's configured handler tags."""
+        return [k for k in self.handler_tags if self.app.config.server_name in self.handlers[k]] or [
+            self.DEFAULT_HANDLER_TAG
+        ]
 
     # If these get to be any more complex we should probably modularize them, or at least move to a separate class
 
@@ -321,12 +345,17 @@ class ConfiguresHandlers:
 
         :returns: str -- This process's server name (handler ID).
         """
-        assert queue_callback is not None, \
-            f"Cannot perform '{HANDLER_ASSIGNMENT_METHODS.MEM_SELF}' handler assignment: `queue_callback` is None"
+        assert (
+            queue_callback is not None
+        ), f"Cannot perform '{HANDLER_ASSIGNMENT_METHODS.MEM_SELF}' handler assignment: `queue_callback` is None"
         if configured:
-            log.warning("(%s) Ignoring handler assignment to '%s' because configured handler assignment method"
-                        " '' overrides per-tool handler assignment", obj.log_str(),
-                        HANDLER_ASSIGNMENT_METHODS.MEM_SELF, configured)
+            log.warning(
+                "(%s) Ignoring handler assignment to '%s' because configured handler assignment method"
+                " '' overrides per-tool handler assignment",
+                obj.log_str(),
+                HANDLER_ASSIGNMENT_METHODS.MEM_SELF,
+                configured,
+            )
         if flush():
             _timed_flush_obj(obj)
         queue_callback()
@@ -379,8 +408,9 @@ class ConfiguresHandlers:
         # HandlerAssigmentError.
         handler_id = self._get_single_item(self.handlers[handler], index=index)
         if handler != handler_id:
-            log.debug("(%s) Selected handler '%s' by random choice from handler tag '%s'", obj.log_str(),
-                      handler_id, handler)
+            log.debug(
+                "(%s) Selected handler '%s' by random choice from handler tag '%s'", obj.log_str(), handler_id, handler
+            )
         obj.set_handler(handler_id)
         if flush:
             _timed_flush_obj(obj)
@@ -418,9 +448,10 @@ class ConfiguresHandlers:
         :raises HandlerAssignmentSkip: if the configured or default handler is not a known handler pool (farm)
         :returns: str -- The assigned handler pool.
         """
-        assert message_callback is not None, \
-            "Cannot perform '%s' handler assignment: `message_callback` is None" \
+        assert message_callback is not None, (
+            "Cannot perform '%s' handler assignment: `message_callback` is None"
             % HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE
+        )
         tag = configured or self.DEFAULT_HANDLER_TAG
         pool = self.pool_for_tag.get(tag)
         if pool is None:
@@ -451,19 +482,24 @@ class ConfiguresHandlers:
         # that's currently the best place for it. It's worth noting that this method is also part of the
         # WorkflowSchedulingManager, which acts like a combined JobConfiguration and JobManager. Combining those two
         # classes would probably be reasonable (and would remove the need for the queue callback).
-        if self._assign_handler_direct(obj, configured, flush=kwargs.get('flush', True)):
-            log.info("(%s) Skipped handler assignment logic due to explicit configuration` to a single handler: %s",
-                     obj.log_str(), configured)
+        if self._assign_handler_direct(obj, configured, flush=kwargs.get("flush", True)):
+            log.info(
+                "(%s) Skipped handler assignment logic due to explicit configuration` to a single handler: %s",
+                obj.log_str(),
+                configured,
+            )
             return True
         for method in self.handler_assignment_methods:
             try:
-                handler = self._handler_assignment_method_methods[method](
-                    obj, method, configured=configured, **kwargs)
+                handler = self._handler_assignment_method_methods[method](obj, method, configured=configured, **kwargs)
                 log.info("(%s) Handler '%s' assigned using '%s' assignment method", obj.log_str(), handler, method)
                 return handler
             except HandlerAssignmentSkip:
-                log.debug("(%s) Handler assignment method '%s' did not assign a handler, trying next method",
-                          obj.log_str(), method)
+                log.debug(
+                    "(%s) Handler assignment method '%s' did not assign a handler, trying next method",
+                    obj.log_str(),
+                    method,
+                )
             except Exception:
                 log.exception("Caught exception in handler assignment method: %s", method)
         else:
diff --git a/lib/galaxy/web_stack/message.py b/lib/galaxy/web_stack/message.py
index 1e1266bd927..d71f86100f8 100644
--- a/lib/galaxy/web_stack/message.py
+++ b/lib/galaxy/web_stack/message.py
@@ -3,7 +3,10 @@
 import json
 import logging
 import types
-from typing import Optional, Tuple
+from typing import (
+    Optional,
+    Tuple,
+)
 
 log = logging.getLogger(__name__)
 
@@ -37,20 +40,24 @@ class ApplicationStackMessageDispatcher:
         try:
             msg.validate()
         except AssertionError as exc:
-            log.error('Invalid message received: %s, error: %s', msg_str, exc)
+            log.error("Invalid message received: %s, error: %s", msg_str, exc)
             return
         if msg.target not in self.__funcs:
-            log.error("Received message with target '%s' but no functions were registered with that name. Params were: %s", msg.target, msg.params)
+            log.error(
+                "Received message with target '%s' but no functions were registered with that name. Params were: %s",
+                msg.target,
+                msg.params,
+            )
         else:
             self.__funcs[msg.target](msg)
 
 
 class ApplicationStackMessage(dict):
     default_handler = None
-    _validate_kwargs = ('target',)
+    _validate_kwargs = ("target",)
 
     def __init__(self, target=None, **kwargs):
-        self['target'] = target
+        self["target"] = target
         self._merge_class_tuples()
 
     def _merge_class_tuples(self):
@@ -60,13 +67,14 @@ class ApplicationStackMessage(dict):
         """
         names = set()
         for cls in reversed(self.__class__.mro()):
-            names.update([x for x in dir(cls) if x.startswith('_') and not x.startswith('__') and type(getattr(cls, x)) == tuple])
+            names.update(
+                [x for x in dir(cls) if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple]
+            )
         for name in names:
-            setattr(self.__class__, name.lstrip('_'), property(lambda self, name=name: self._get_list_from_mro(name)))
+            setattr(self.__class__, name.lstrip("_"), property(lambda self, name=name: self._get_list_from_mro(name)))
 
     def _get_list_from_mro(self, name):
-        """Locate all class-level tuples with the given `name` in the MRO and return their union.
-        """
+        """Locate all class-level tuples with the given `name` in the MRO and return their union."""
         r = set()
         for cls in reversed(self.__class__.mro()):
             r.update(getattr(cls, name, []))
@@ -77,10 +85,10 @@ class ApplicationStackMessage(dict):
             assert item in obj, f"Missing '{item}' message {name}"
 
     def validate(self):
-        self._validate_items(self, self.validate_kwargs, 'argument')
+        self._validate_items(self, self.validate_kwargs, "argument")
 
     def encode(self):
-        self['__classname__'] = self.__class__.__name__
+        self["__classname__"] = self.__class__.__name__
         return json.dumps(self)
 
     def bind_default_handler(self, obj, name):
@@ -88,78 +96,80 @@ class ApplicationStackMessage(dict):
 
         This could also be implemented as a mixin class.
         """
-        assert self.default_handler is not None, f'{self.__class__.__name__} has no default handler method, cannot bind'
+        assert self.default_handler is not None, f"{self.__class__.__name__} has no default handler method, cannot bind"
         setattr(obj, name, types.MethodType(self.default_handler, obj))
-        log.debug("Bound default message handler '%s.%s' to %s", self.__class__.__name__, self.default_handler.__name__,
-                  getattr(obj, name))
+        log.debug(
+            "Bound default message handler '%s.%s' to %s",
+            self.__class__.__name__,
+            self.default_handler.__name__,
+            getattr(obj, name),
+        )
 
     @property
     def target(self) -> Optional[str]:
-        return self['target']
+        return self["target"]
 
     @target.setter  # type: ignore[attr-defined]
     def set_target(self, target):
-        self['target'] = target
+        self["target"] = target
 
 
 class ParamMessage(ApplicationStackMessage):
-    _validate_kwargs = ('params',)
+    _validate_kwargs = ("params",)
     _validate_params: Tuple[str, ...] = ()
     _exclude_params: Tuple[str, ...] = ()
 
     def __init__(self, target=None, params=None, **kwargs):
         super().__init__(target=target)
-        self['params'] = params or {}
+        self["params"] = params or {}
         for k, v in kwargs.items():
-            self['params'][k] = v
+            self["params"][k] = v
 
     def validate(self):
         super().validate()
-        self._validate_items(self['params'], self.validate_params, 'parameters')
+        self._validate_items(self["params"], self.validate_params, "parameters")
 
     @property
     def params(self):
-        d = self['params'].copy()
+        d = self["params"].copy()
         for key in self.exclude_params:
             d.pop(key, None)
         return d
 
     @params.setter
     def params(self, params):
-        self['params'] = params
+        self["params"] = params
 
 
 class TaskMessage(ParamMessage):
-    _validate_params = ('task',)
-    _exclude_params = ('task',)
+    _validate_params = ("task",)
+    _exclude_params = ("task",)
 
     @staticmethod
     def default_handler(self, msg):
-        """Can be bound to an instance of any class that has message handling methods named like `_handle_{task}_method`
-        """
-        name = f'_handle_{msg.task}_msg'
+        """Can be bound to an instance of any class that has message handling methods named like `_handle_{task}_method`"""
+        name = f"_handle_{msg.task}_msg"
         assert name in dir(self), "{cls} has no method _handle_{task}_msg, cannot handle message: {msg}".format(
-            cls=self.__class__.__name__,
-            task=msg.task,
-            msg=msg)
-        getattr(self, f'_handle_{msg.task}_msg')(**msg.params)
+            cls=self.__class__.__name__, task=msg.task, msg=msg
+        )
+        getattr(self, f"_handle_{msg.task}_msg")(**msg.params)
 
     @property
     def task(self):
-        return self['params']['task']
+        return self["params"]["task"]
 
 
 class JobHandlerMessage(TaskMessage):
-    target = 'job_handler'
-    _validate_params = ('job_id',)
+    target = "job_handler"
+    _validate_params = ("job_id",)
 
 
 class WorkflowSchedulingMessage(TaskMessage):
-    target = 'workflow_scheduling'
-    _validate_params = ('workflow_invocation_id',)
+    target = "workflow_scheduling"
+    _validate_params = ("workflow_invocation_id",)
 
 
 def decode(msg_str):
     d = json.loads(msg_str)
-    cls = d.pop('__classname__')
+    cls = d.pop("__classname__")
     return globals()[cls](**d)
diff --git a/lib/galaxy/web_stack/transport.py b/lib/galaxy/web_stack/transport.py
index 95d8ecf93ac..2420cc94b84 100644
--- a/lib/galaxy/web_stack/transport.py
+++ b/lib/galaxy/web_stack/transport.py
@@ -17,11 +17,10 @@ log = logging.getLogger(__name__)
 
 
 class ApplicationStackTransport:
-    SHUTDOWN_MSG = '__SHUTDOWN__'
+    SHUTDOWN_MSG = "__SHUTDOWN__"
 
     def __init__(self, app, stack, dispatcher=None):
-        """ Pre-fork initialization.
-        """
+        """Pre-fork initialization."""
         self.app = app
         self.stack = stack
         self.can_run = False
@@ -37,22 +36,35 @@ class ApplicationStackTransport:
 
     def start_if_needed(self):
         # Don't unnecessarily start a thread that we don't need.
-        if self.can_run and not self.running and not self.dispatcher_thread and self.dispatcher and self.dispatcher.handler_count:
+        if (
+            self.can_run
+            and not self.running
+            and not self.dispatcher_thread
+            and self.dispatcher
+            and self.dispatcher.handler_count
+        ):
             self.running = True
-            self.dispatcher_thread = threading.Thread(name=f"{self.__class__.__name__}.dispatcher_thread", target=self._dispatch_messages)
+            self.dispatcher_thread = threading.Thread(
+                name=f"{self.__class__.__name__}.dispatcher_thread", target=self._dispatch_messages
+            )
             self.dispatcher_thread.start()
-            log.info('%s dispatcher started', self.__class__.__name__)
+            log.info("%s dispatcher started", self.__class__.__name__)
 
     def stop_if_unneeded(self):
-        if self.can_run and self.running and self.dispatcher_thread and self.dispatcher and not self.dispatcher.handler_count:
+        if (
+            self.can_run
+            and self.running
+            and self.dispatcher_thread
+            and self.dispatcher
+            and not self.dispatcher.handler_count
+        ):
             self.running = False
             self.dispatcher_thread.join()
             self.dispatcher_thread = None
-            log.info('%s dispatcher stopped', self.__class__.__name__)
+            log.info("%s dispatcher stopped", self.__class__.__name__)
 
     def start(self):
-        """ Post-fork initialization.
-        """
+        """Post-fork initialization."""
         self.can_run = True
         self.start_if_needed()
 
@@ -62,22 +74,25 @@ class ApplicationStackTransport:
     def shutdown(self):
         self.running = False
         if self.dispatcher_thread:
-            log.info('Joining application stack transport dispatcher thread')
+            log.info("Joining application stack transport dispatcher thread")
             self.dispatcher_thread.join()
             self.dispatcher_thread = None
 
 
 class UWSGIFarmMessageTransport(ApplicationStackTransport):
-    """ Communication via uWSGI Mule Farm messages. Communication is unidirectional (workers -> mules).
-    """
+    """Communication via uWSGI Mule Farm messages. Communication is unidirectional (workers -> mules)."""
+
     # Define any static lock names here, additional locks will be appended for each configured farm's message handler
     _locks: List[str] = []
 
     def init_late_prefork(self):
-        num = int(uwsgi.opt.get('locks', 0)) + 1
+        num = int(uwsgi.opt.get("locks", 0)) + 1
         need = len(self.stack._lock_farms)
         if num < need:
-            raise RuntimeError('Need %i uWSGI locks but only %i exist(s): Set `locks = %i` in uWSGI configuration' % (need, num, need - 1))
+            raise RuntimeError(
+                "Need %i uWSGI locks but only %i exist(s): Set `locks = %i` in uWSGI configuration"
+                % (need, num, need - 1)
+            )
         self._locks.extend([f"RECV_MSG_FARM_{x}" for x in sorted(self.stack._lock_farms)])
         # this would be nice, but in my 2.0.15 uWSGI, the uwsgi module has no set_option function, and I don't know if it'd work even if the function existed as documented
         # if len(self.lock_map) > 1:
@@ -104,42 +119,56 @@ class UWSGIFarmMessageTransport(ApplicationStackTransport):
 
     def _dispatch_messages(self):
         # this could be moved to the base class if locking was abstracted and a get_message method was added
-        log.info('Application stack message dispatcher thread starting up')
+        log.info("Application stack message dispatcher thread starting up")
         # we are going to do this a lot, so cache the lock number
         lock = self._farm_recv_msg_lock_num()
         while self.running:
             msg = None
             self.__lock(lock)
             try:
-                log.debug('Acquired message lock, waiting for new message')
+                log.debug("Acquired message lock, waiting for new message")
                 msg = unicodify(uwsgi.farm_get_msg())
-                log.debug('Received message: %s', msg)
+                log.debug("Received message: %s", msg)
                 if msg == self.SHUTDOWN_MSG:
                     self.running = False
                 else:
                     self.dispatcher.dispatch(msg)
             except Exception:
-                log.exception('Exception in mule message handling')
+                log.exception("Exception in mule message handling")
             finally:
                 self.__unlock(lock)
-                log.debug('Released lock')
-        log.info('Application stack message dispatcher thread exiting')
+                log.debug("Released lock")
+        log.info("Application stack message dispatcher thread exiting")
 
     # TODO: start_if_needed would be called on a web worker by the stack's register_message_handler function if a
     # function were registered in a web handler, that should probably be prevented.
 
     def start(self):
-        """ Post-fork initialization.
+        """Post-fork initialization.
 
         This is mainly done here for the future possibility that we'll be able to run mules post-fork without exec()ing. In a programmed mule it could be done at __init__ time.
         """
         if self.stack._is_mule:
             if not uwsgi.in_farm():
-                raise RuntimeError('Mule %s is not in a farm! Set `farm = <pool_name>:%s` in uWSGI configuration'
-                                   % (uwsgi.mule_id(),
-                                      ','.join(map(str, range(1, len([x for x in self.stack._configured_mules if x.endswith('galaxy/main.py')]) + 1)))))
+                raise RuntimeError(
+                    "Mule %s is not in a farm! Set `farm = <pool_name>:%s` in uWSGI configuration"
+                    % (
+                        uwsgi.mule_id(),
+                        ",".join(
+                            map(
+                                str,
+                                range(
+                                    1,
+                                    len([x for x in self.stack._configured_mules if x.endswith("galaxy/main.py")]) + 1,
+                                ),
+                            )
+                        ),
+                    )
+                )
             elif len(self.stack._farms) > 1:
-                raise RuntimeError(f'Mule {uwsgi.mule_id()} is in multiple farms! This configuration is not supported due to locking issues')
+                raise RuntimeError(
+                    f"Mule {uwsgi.mule_id()} is in multiple farms! This configuration is not supported due to locking issues"
+                )
             # only mules receive messages so don't bother starting the dispatcher if we're not a mule (although
             # currently it doesn't have any registered handlers and so wouldn't start anyway)
             super().start()
@@ -149,5 +178,5 @@ class UWSGIFarmMessageTransport(ApplicationStackTransport):
             super().shutdown()
 
     def send_message(self, msg, dest):
-        log.debug('Sending message to farm %s: %s', dest, msg)
+        log.debug("Sending message to farm %s: %s", dest, msg)
         uwsgi.farm_msg(dest, msg)
diff --git a/lib/galaxy/webapps/base/api.py b/lib/galaxy/webapps/base/api.py
index 06d9fb98bd8..59edb2b4f64 100644
--- a/lib/galaxy/webapps/base/api.py
+++ b/lib/galaxy/webapps/base/api.py
@@ -1,7 +1,11 @@
-from fastapi import FastAPI, Request
+from fastapi import (
+    FastAPI,
+    Request,
+)
 from fastapi.exceptions import RequestValidationError
 from fastapi.responses import JSONResponse
 from starlette.responses import Response
+
 try:
     from starlette_context.middleware import RawContextMiddleware
     from starlette_context.plugins import RequestIdPlugin
@@ -12,30 +16,21 @@ from galaxy.exceptions import MessageException
 from galaxy.web.framework.base import walk_controller_modules
 from galaxy.web.framework.decorators import (
     api_error_message,
-    validation_error_to_message_exception
+    validation_error_to_message_exception,
 )
 
 
-def add_exception_handler(
-    app: FastAPI
-) -> None:
-
+def add_exception_handler(app: FastAPI) -> None:
     @app.exception_handler(RequestValidationError)
     async def validate_exception_middleware(request: Request, exc: RequestValidationError) -> Response:
         exc = validation_error_to_message_exception(exc)
         error_dict = api_error_message(None, exception=exc)
-        return JSONResponse(
-            status_code=400,
-            content=error_dict
-        )
+        return JSONResponse(status_code=400, content=error_dict)
 
     @app.exception_handler(MessageException)
     async def message_exception_middleware(request: Request, exc: MessageException) -> Response:
         error_dict = api_error_message(None, exception=exc)
-        return JSONResponse(
-            status_code=exc.status_code,
-            content=error_dict
-        )
+        return JSONResponse(status_code=exc.status_code, content=error_dict)
 
 
 def add_request_id_middleware(app: FastAPI):
diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
index 0af1743f842..383e2cefe2d 100644
--- a/lib/galaxy/webapps/base/controller.py
+++ b/lib/galaxy/webapps/base/controller.py
@@ -2,13 +2,16 @@
 Contains functionality needed in every web interface
 """
 import logging
-from typing import Any, Optional
+from typing import (
+    Any,
+    Optional,
+)
 
 from sqlalchemy import true
 from webob.exc import (
     HTTPBadRequest,
     HTTPInternalServerError,
-    HTTPNotImplemented
+    HTTPNotImplemented,
 )
 
 from galaxy import (
@@ -16,15 +19,15 @@ from galaxy import (
     model,
     security,
     util,
-    web
+    web,
 )
 from galaxy.datatypes.interval import ChromatinInteractions
+from galaxy.managers import api_keys
+from galaxy.managers import base as managers_base
 from galaxy.managers import (
-    api_keys,
-    base as managers_base,
     configuration,
     users,
-    workflows
+    workflows,
 )
 from galaxy.managers.sharable import SlugBuilder
 from galaxy.model import (
@@ -39,12 +42,12 @@ from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import (
     error,
-    url_for
+    url_for,
 )
 from galaxy.web.form_builder import (
     AddressField,
     CheckboxField,
-    PasswordField
+    PasswordField,
 )
 from galaxy.workflow.modules import WorkflowModuleInjector
 
@@ -70,14 +73,16 @@ class BaseController:
         return self.app.toolbox
 
     def get_class(self, class_name):
-        """ Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>). """
+        """Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>)."""
         return managers_base.get_class(class_name)
 
     def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
         """
         Convenience method to get a model object with the specified checks.
         """
-        return managers_base.get_object(trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
+        return managers_base.get_object(
+            trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted
+        )
 
     # this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin
     #   but *don't* then becomes difficult
@@ -87,13 +92,13 @@ class BaseController:
     #    return item
 
     def get_user(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
-        return self.get_object(trans, id, 'User', check_ownership=False, check_accessible=False, deleted=deleted)
+        return self.get_object(trans, id, "User", check_ownership=False, check_accessible=False, deleted=deleted)
 
     def get_group(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
-        return self.get_object(trans, id, 'Group', check_ownership=False, check_accessible=False, deleted=deleted)
+        return self.get_object(trans, id, "Group", check_ownership=False, check_accessible=False, deleted=deleted)
 
     def get_role(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
-        return self.get_object(trans, id, 'Role', check_ownership=False, check_accessible=False, deleted=deleted)
+        return self.get_object(trans, id, "Role", check_ownership=False, check_accessible=False, deleted=deleted)
 
     # ---- parsing query params
     def decode_id(self, id):
@@ -108,11 +113,10 @@ class BaseController:
         return trans.security.encode_all_ids(rval, recursive=recursive)
 
     # TODO this will be replaced by lib.galaxy.managers.base.ModelFilterParser.build_filter_params
-    def parse_filter_params(self, qdict, filter_attr_key='q', filter_value_key='qv', attr_op_split_char='-'):
-        """
-        """
+    def parse_filter_params(self, qdict, filter_attr_key="q", filter_value_key="qv", attr_op_split_char="-"):
+        """ """
         # TODO: import DEFAULT_OP from FilterParser
-        DEFAULT_OP = 'eq'
+        DEFAULT_OP = "eq"
         if filter_attr_key not in qdict:
             return []
         # precondition: attrs/value pairs are in-order in the qstring
@@ -140,8 +144,8 @@ class BaseController:
         return list(zip(attrs, ops, values))
 
     def parse_limit_offset(self, qdict):
-        """
-        """
+        """ """
+
         def _parse_pos_int(i):
             try:
                 new_val = int(i)
@@ -151,8 +155,8 @@ class BaseController:
                 pass
             return None
 
-        limit = _parse_pos_int(qdict.get('limit', None))
-        offset = _parse_pos_int(qdict.get('offset', None))
+        limit = _parse_pos_int(qdict.get("limit", None))
+        offset = _parse_pos_int(qdict.get("offset", None))
         return (limit, offset)
 
 
@@ -160,28 +164,40 @@ Root = BaseController
 
 
 class BaseUIController(BaseController):
-
     def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
         try:
-            return BaseController.get_object(self, trans, id, class_name,
-                                             check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
+            return BaseController.get_object(
+                self,
+                trans,
+                id,
+                class_name,
+                check_ownership=check_ownership,
+                check_accessible=check_accessible,
+                deleted=deleted,
+            )
         except exceptions.MessageException:
-            raise       # handled in the caller
+            raise  # handled in the caller
         except Exception:
             log.exception("Exception in get_object check for %s %s:", class_name, str(id))
-            raise Exception(f'Server error retrieving {class_name} id ( {str(id)} ).')
+            raise Exception(f"Server error retrieving {class_name} id ( {str(id)} ).")
 
     def message_exception(self, trans, message, sanitize=True):
         trans.response.status = 400
-        return {'err_msg': util.sanitize_text(message) if sanitize else message}
+        return {"err_msg": util.sanitize_text(message) if sanitize else message}
 
 
 class BaseAPIController(BaseController):
-
     def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
         try:
-            return BaseController.get_object(self, trans, id, class_name,
-                                             check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
+            return BaseController.get_object(
+                self,
+                trans,
+                id,
+                class_name,
+                check_ownership=check_ownership,
+                check_accessible=check_accessible,
+                deleted=deleted,
+            )
 
         except exceptions.ItemDeletionException as e:
             raise HTTPBadRequest(detail=f"Invalid {class_name} id ( {str(id)} ) specified: {util.unicodify(e)}")
@@ -195,15 +211,15 @@ class BaseAPIController(BaseController):
         raise HTTPNotImplemented()
 
     def _parse_serialization_params(self, kwd, default_view):
-        view = kwd.get('view', None)
-        keys = kwd.get('keys')
+        view = kwd.get("view", None)
+        keys = kwd.get("keys")
         if isinstance(keys, str):
-            keys = keys.split(',')
+            keys = keys.split(",")
         return dict(view=view, keys=keys, default_view=default_view)
 
     # TODO: this will be replaced by lib.galaxy.schema.FilterQueryParams.build_order_by
     def _parse_order_by(self, manager, order_by_string):
-        ORDER_BY_SEP_CHAR = ','
+        ORDER_BY_SEP_CHAR = ","
         if ORDER_BY_SEP_CHAR in order_by_string:
             return [manager.parse_order_by(o) for o in order_by_string.split(ORDER_BY_SEP_CHAR)]
         return manager.parse_order_by(order_by_string)
@@ -219,8 +235,17 @@ class JSAppLauncher(BaseUIController):
     #: window-scoped js function to call to start the app (will be passed options, bootstrapped)
     DEFAULT_ENTRY_FN = "app"
     #: keys used when serializing current user for bootstrapped data
-    USER_BOOTSTRAP_KEYS = ('id', 'email', 'username', 'is_admin', 'tags_used',
-                           'total_disk_usage', 'nice_total_disk_usage', 'quota_percent', 'preferences')
+    USER_BOOTSTRAP_KEYS = (
+        "id",
+        "email",
+        "username",
+        "is_admin",
+        "tags_used",
+        "total_disk_usage",
+        "nice_total_disk_usage",
+        "quota_percent",
+        "preferences",
+    )
 
     def __init__(self, app):
         super().__init__(app)
@@ -250,9 +275,9 @@ class JSAppLauncher(BaseUIController):
     # This includes contextualized user options in the bootstrapped data; we
     # don't want to cache it.
     @web.do_not_cache
-    def _bootstrapped_client(self, trans, app_name='analysis', **kwd):
+    def _bootstrapped_client(self, trans, app_name="analysis", **kwd):
         js_options = self._get_js_options(trans)
-        js_options['config'].update(self._get_extended_config(trans))
+        js_options["config"].update(self._get_extended_config(trans))
         return self.template(trans, app_name, options=js_options, **kwd)
 
     def _get_js_options(self, trans, root=None):
@@ -262,38 +287,39 @@ class JSAppLauncher(BaseUIController):
 
         Defaults to `config`, `user`, and the root url. Pass kwargs to update further.
         """
-        root = root or web.url_for('/')
+        root = root or web.url_for("/")
         js_options = {
-            'root': root,
-            'user': self.user_serializer.serialize(trans.user, self.USER_BOOTSTRAP_KEYS, trans=trans),
-            'config': self._get_site_configuration(trans),
-            'params': dict(trans.request.params),
-            'session_csrf_token': trans.session_csrf_token,
+            "root": root,
+            "user": self.user_serializer.serialize(trans.user, self.USER_BOOTSTRAP_KEYS, trans=trans),
+            "config": self._get_site_configuration(trans),
+            "params": dict(trans.request.params),
+            "session_csrf_token": trans.session_csrf_token,
         }
         return js_options
 
     def _get_extended_config(self, trans):
         config = {
-            'active_view': 'analysis',
-            'enable_webhooks': True if trans.app.webhooks_registry.webhooks else False,
-            'message_box_visible': trans.app.config.message_box_visible,
-            'show_inactivity_warning': trans.app.config.user_activation_on and trans.user and not trans.user.active,
-            'tool_shed_urls': list(trans.app.tool_shed_registry.tool_sheds.values()) if trans.app.tool_shed_registry else [],
-            'tool_dynamic_configs': list(trans.app.toolbox.dynamic_conf_filenames())
+            "active_view": "analysis",
+            "enable_webhooks": True if trans.app.webhooks_registry.webhooks else False,
+            "message_box_visible": trans.app.config.message_box_visible,
+            "show_inactivity_warning": trans.app.config.user_activation_on and trans.user and not trans.user.active,
+            "tool_shed_urls": list(trans.app.tool_shed_registry.tool_sheds.values())
+            if trans.app.tool_shed_registry
+            else [],
+            "tool_dynamic_configs": list(trans.app.toolbox.dynamic_conf_filenames()),
         }
 
         # TODO: move to user
         stored_workflow_menu_index = {}
         stored_workflow_menu_entries = []
-        for menu_item in getattr(trans.user, 'stored_workflow_menu_entries', []):
+        for menu_item in getattr(trans.user, "stored_workflow_menu_entries", []):
             encoded_stored_workflow_id = trans.security.encode_id(menu_item.stored_workflow_id)
             if encoded_stored_workflow_id not in stored_workflow_menu_index:
                 stored_workflow_menu_index[encoded_stored_workflow_id] = True
-                stored_workflow_menu_entries.append({
-                    'id': encoded_stored_workflow_id,
-                    'name': util.unicodify(menu_item.stored_workflow.name)
-                })
-        config['stored_workflow_menu_entries'] = stored_workflow_menu_entries
+                stored_workflow_menu_entries.append(
+                    {"id": encoded_stored_workflow_id, "name": util.unicodify(menu_item.stored_workflow.name)}
+                )
+        config["stored_workflow_menu_entries"] = stored_workflow_menu_entries
         return config
 
     def _get_site_configuration(self, trans):
@@ -304,12 +330,21 @@ class JSAppLauncher(BaseUIController):
             serializer = self.config_serializer
             if self.user_manager.is_admin(trans.user, trans=trans):
                 serializer = self.admin_config_serializer
-            return serializer.serialize_to_view(self.app.config, view='all', host=trans.host)
+            return serializer.serialize_to_view(self.app.config, view="all", host=trans.host)
         except Exception as exc:
             log.exception(exc)
             return {}
 
-    def template(self, trans, app_name: str, entry_fn: str = 'app', options=None, bootstrapped_data: Optional[dict] = None, masthead: Optional[bool] = True, **additional_options):
+    def template(
+        self,
+        trans,
+        app_name: str,
+        entry_fn: str = "app",
+        options=None,
+        bootstrapped_data: Optional[dict] = None,
+        masthead: Optional[bool] = True,
+        **additional_options,
+    ):
         """
         Render and return the single page mako template that starts the app.
 
@@ -329,7 +364,7 @@ class JSAppLauncher(BaseUIController):
             js_app_entry_fn=(entry_fn or self.DEFAULT_ENTRY_FN),
             options=options,
             bootstrapped=(bootstrapped_data or {}),
-            masthead=masthead
+            masthead=masthead,
         )
 
 
@@ -343,6 +378,7 @@ class Datatype:
         self.mimetype = mimetype
         self.display_in_upload = display_in_upload
 
+
 #
 # -- Mixins for working with Galaxy objects. --
 #
@@ -360,29 +396,29 @@ class CreatesApiKeysMixin:
 
 
 class SharableItemSecurityMixin:
-    """ Mixin for handling security for sharable items. """
+    """Mixin for handling security for sharable items."""
 
     def security_check(self, trans, item, check_ownership=False, check_accessible=False):
-        """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """
-        return managers_base.security_check(trans, item, check_ownership=check_ownership, check_accessible=check_accessible)
+        """Security checks for an item: checks if (a) user owns item or (b) item is accessible to user."""
+        return managers_base.security_check(
+            trans, item, check_ownership=check_ownership, check_accessible=check_accessible
+        )
 
 
 class UsesLibraryMixinItems(SharableItemSecurityMixin):
-
     def get_library_folder(self, trans, id, check_ownership=False, check_accessible=True):
-        return self.get_object(trans, id, 'LibraryFolder',
-                               check_ownership=False, check_accessible=check_accessible)
+        return self.get_object(trans, id, "LibraryFolder", check_ownership=False, check_accessible=check_accessible)
 
     def get_library_dataset_dataset_association(self, trans, id, check_ownership=False, check_accessible=True):
         # Deprecated in lieu to galaxy.managers.lddas.LDDAManager.get() but not
         # reusing that exactly because of subtle differences in exception handling
         # logic (API controller override get_object to be slightly different).
-        return self.get_object(trans, id, 'LibraryDatasetDatasetAssociation',
-                               check_ownership=False, check_accessible=check_accessible)
+        return self.get_object(
+            trans, id, "LibraryDatasetDatasetAssociation", check_ownership=False, check_accessible=check_accessible
+        )
 
     def get_library_dataset(self, trans, id, check_ownership=False, check_accessible=True):
-        return self.get_object(trans, id, 'LibraryDataset',
-                               check_ownership=False, check_accessible=check_accessible)
+        return self.get_object(trans, id, "LibraryDataset", check_ownership=False, check_accessible=check_accessible)
 
     # TODO: it makes no sense that I can get roles from a user but not user.is_admin()
     # def can_user_add_to_library_item( self, trans, user, item ):
@@ -393,8 +429,9 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
     def can_current_user_add_to_library_item(self, trans, item):
         if not trans.user:
             return False
-        return (trans.user_is_admin
-                or trans.app.security_agent.can_add_library_item(trans.get_current_user_roles(), item))
+        return trans.user_is_admin or trans.app.security_agent.can_add_library_item(
+            trans.get_current_user_roles(), item
+        )
 
     def check_user_can_add_to_library_item(self, trans, item, check_accessible=True):
         """
@@ -411,31 +448,40 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
 
         if check_accessible:
             if not trans.app.security_agent.can_access_library_item(current_user_roles, item, trans.user):
-                raise exceptions.ItemAccessibilityException('You do not have access to the requested item')
+                raise exceptions.ItemAccessibilityException("You do not have access to the requested item")
 
         if not trans.app.security_agent.can_add_library_item(trans.get_current_user_roles(), item):
             # Slight misuse of ItemOwnershipException?
             raise exceptions.ItemOwnershipException("User cannot add to library item.")
 
-    def _copy_hdca_to_library_folder(self, trans, hda_manager, from_hdca_id, folder_id, ldda_message=''):
+    def _copy_hdca_to_library_folder(self, trans, hda_manager, from_hdca_id, folder_id, ldda_message=""):
         """
         Fetches the collection identified by `from_hcda_id` and dispatches individual collection elements to
         _copy_hda_to_library_folder
         """
         hdca = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(from_hdca_id)
-        if hdca.collection.collection_type != 'list':
-            raise exceptions.NotImplemented('Cannot add nested collections to library. Please flatten your collection first.')
+        if hdca.collection.collection_type != "list":
+            raise exceptions.NotImplemented(
+                "Cannot add nested collections to library. Please flatten your collection first."
+            )
         hdas = []
         for element in hdca.collection.elements:
             hdas.append((element.element_identifier, element.dataset_instance.id))
-        return [self._copy_hda_to_library_folder(trans,
-                                                 hda_manager=hda_manager,
-                                                 from_hda_id=hda_id,
-                                                 folder_id=folder_id,
-                                                 ldda_message=ldda_message,
-                                                 element_identifier=element_identifier) for (element_identifier, hda_id) in hdas]
+        return [
+            self._copy_hda_to_library_folder(
+                trans,
+                hda_manager=hda_manager,
+                from_hda_id=hda_id,
+                folder_id=folder_id,
+                ldda_message=ldda_message,
+                element_identifier=element_identifier,
+            )
+            for (element_identifier, hda_id) in hdas
+        ]
 
-    def _copy_hda_to_library_folder(self, trans, hda_manager, from_hda_id, folder_id, ldda_message='', element_identifier=None):
+    def _copy_hda_to_library_folder(
+        self, trans, hda_manager, from_hda_id, folder_id, ldda_message="", element_identifier=None
+    ):
         """
         Copies hda ``from_hda_id`` to library folder ``folder_id``, optionally
         adding ``ldda_message`` to the new ldda's ``message``.
@@ -443,7 +489,7 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
         ``library_contents.create`` will branch to this if called with 'from_hda_id'
         in its payload.
         """
-        log.debug(f'_copy_hda_to_library_folder: {str((from_hda_id, folder_id, ldda_message))}')
+        log.debug(f"_copy_hda_to_library_folder: {str((from_hda_id, folder_id, ldda_message))}")
         # PRECONDITION: folder_id has already been altered to remove the folder prefix ('F')
         # TODO: allow name and other, editable ldda attrs?
         if ldda_message:
@@ -458,11 +504,17 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
         # TOOD: refactor to use check_user_can_add_to_library_item, eliminate boolean
         # can_current_user_add_to_library_item.
         if folder.parent_library.deleted:
-            raise exceptions.ObjectAttributeInvalidException('You cannot add datasets into deleted library. Undelete it first.')
+            raise exceptions.ObjectAttributeInvalidException(
+                "You cannot add datasets into deleted library. Undelete it first."
+            )
         if not self.can_current_user_add_to_library_item(trans, folder):
-            raise exceptions.InsufficientPermissionsException('You do not have proper permissions to add a dataset to this folder,')
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permissions to add a dataset to this folder,"
+            )
 
-        ldda = self.copy_hda_to_library_folder(trans, hda, folder, ldda_message=ldda_message, element_identifier=element_identifier)
+        ldda = self.copy_hda_to_library_folder(
+            trans, hda, folder, ldda_message=ldda_message, element_identifier=element_identifier
+        )
         # I don't see a reason why hdas copied into libraries should not be visible.
         # If there is, refactor `ldda.visible = True` to do this only when adding HDCAs.
         ldda.visible = True
@@ -471,10 +523,12 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
         ldda_dict = ldda.to_dict()
         rval = trans.security.encode_dict_ids(ldda_dict)
         update_time = ldda.update_time.strftime("%Y-%m-%d %I:%M %p")
-        rval['update_time'] = update_time
+        rval["update_time"] = update_time
         return rval
 
-    def copy_hda_to_library_folder(self, trans, hda, library_folder, roles=None, ldda_message='', element_identifier=None):
+    def copy_hda_to_library_folder(
+        self, trans, hda, library_folder, roles=None, ldda_message="", element_identifier=None
+    ):
         # PRECONDITION: permissions for this action on hda and library_folder have been checked
         roles = roles or []
 
@@ -482,8 +536,13 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
         # TODO: refactor library_common.add_history_datasets_to_library to use this for each hda to copy
 
         # create the new ldda and apply the folder perms to it
-        ldda = hda.to_library_dataset_dataset_association(trans, target_folder=library_folder,
-                                                          roles=roles, ldda_message=ldda_message, element_identifier=element_identifier)
+        ldda = hda.to_library_dataset_dataset_association(
+            trans,
+            target_folder=library_folder,
+            roles=roles,
+            ldda_message=ldda_message,
+            element_identifier=element_identifier,
+        )
         self._apply_library_folder_permissions_to_ldda(trans, library_folder, ldda)
         self._apply_hda_permissions_to_ldda(trans, hda, ldda)
         # TODO:?? not really clear on how permissions are being traded here
@@ -517,8 +576,8 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
 
         # except that: if DATASET_MANAGE_PERMISSIONS exists in the hda.dataset permissions,
         #   we need to instead apply those roles to the LIBRARY_MANAGE permission to the library dataset
-        dataset_manage_permissions_action = security_agent.get_action('DATASET_MANAGE_PERMISSIONS').action
-        library_manage_permissions_action = security_agent.get_action('LIBRARY_MANAGE').action
+        dataset_manage_permissions_action = security_agent.get_action("DATASET_MANAGE_PERMISSIONS").action
+        library_manage_permissions_action = security_agent.get_action("LIBRARY_MANAGE").action
         # TODO: test this and remove if in loop below
         # TODO: doesn't handle action.action
         # if dataset_manage_permissions_action in dataset_permissions_dict:
@@ -557,6 +616,7 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
     """
     Mixin for controllers that use Visualization objects.
     """
+
     slug_builder = SlugBuilder()
 
     def get_visualization(self, trans, id, check_ownership=True, check_accessible=False):
@@ -654,10 +714,10 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         # TODO: deleted
         # TODO: importable
         return {
-            'id': visualization.id,
-            'title': visualization.title,
-            'type': visualization.type,
-            'dbkey': visualization.dbkey,
+            "id": visualization.id,
+            "title": visualization.title,
+            "type": visualization.type,
+            "dbkey": visualization.dbkey,
         }
 
     def get_visualization_dict(self, visualization):
@@ -667,16 +727,16 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         NOTE: that encoding ids isn't done here should happen at the caller level.
         """
         return {
-            'model_class': 'Visualization',
-            'id': visualization.id,
-            'title': visualization.title,
-            'type': visualization.type,
-            'user_id': visualization.user.id,
-            'dbkey': visualization.dbkey,
-            'slug': visualization.slug,
+            "model_class": "Visualization",
+            "id": visualization.id,
+            "title": visualization.title,
+            "type": visualization.type,
+            "user_id": visualization.user.id,
+            "dbkey": visualization.dbkey,
+            "slug": visualization.slug,
             # to_dict only the latest revision (allow older to be fetched elsewhere)
-            'latest_revision': self.get_visualization_revision_dict(visualization.latest_revision),
-            'revisions': [r.id for r in visualization.revisions],
+            "latest_revision": self.get_visualization_revision_dict(visualization.latest_revision),
+            "revisions": [r.id for r in visualization.revisions],
         }
 
     def get_visualization_revision_dict(self, revision):
@@ -685,12 +745,12 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         NOTE: that encoding ids isn't done here should happen at the caller level.
         """
         return {
-            'model_class': 'VisualizationRevision',
-            'id': revision.id,
-            'visualization_id': revision.visualization.id,
-            'title': revision.title,
-            'dbkey': revision.dbkey,
-            'config': revision.config,
+            "model_class": "VisualizationRevision",
+            "id": revision.id,
+            "visualization_id": revision.visualization.id,
+            "title": revision.title,
+            "dbkey": revision.dbkey,
+            "config": revision.config,
         }
 
     def import_visualization(self, trans, id, user=None):
@@ -711,7 +771,9 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         # check accessibility
         visualization = self.get_visualization(trans, id, check_ownership=False)
         if not visualization.importable:
-            raise exceptions.ItemAccessibilityException("The owner of this visualization has disabled imports via this link.")
+            raise exceptions.ItemAccessibilityException(
+                "The owner of this visualization has disabled imports via this link."
+            )
         if visualization.deleted:
             raise exceptions.ItemDeletionException("You can't import this visualization because it has been deleted.")
 
@@ -722,8 +784,17 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         trans.sa_session.flush()
         return imported_visualization
 
-    def create_visualization(self, trans, type, title="Untitled Visualization", slug=None,
-                             dbkey=None, annotation=None, config=None, save=True):
+    def create_visualization(
+        self,
+        trans,
+        type,
+        title="Untitled Visualization",
+        slug=None,
+        dbkey=None,
+        annotation=None,
+        config=None,
+        save=True,
+    ):
         """
         Create visualiation and first revision.
         """
@@ -732,11 +803,12 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         # TODO: handle this error structure better either in _create or here
         if isinstance(visualization, dict):
             err_dict = visualization
-            raise ValueError(err_dict['title_err'] or err_dict['slug_err'])
+            raise ValueError(err_dict["title_err"] or err_dict["slug_err"])
 
         # Create and save first visualization revision
-        revision = trans.model.VisualizationRevision(visualization=visualization, title=title,
-                                                     config=config, dbkey=dbkey)
+        revision = trans.model.VisualizationRevision(
+            visualization=visualization, title=title, config=config, dbkey=dbkey
+        )
         visualization.latest_revision = revision
 
         if save:
@@ -754,7 +826,9 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         """
         # precondition: only add new revision on owned vis's
         # TODO:?? should we default title, dbkey, config? to which: visualization or latest_revision?
-        revision = trans.model.VisualizationRevision(visualization=visualization, title=title, dbkey=dbkey, config=config)
+        revision = trans.model.VisualizationRevision(
+            visualization=visualization, title=title, dbkey=dbkey, config=config
+        )
 
         visualization.latest_revision = revision
         # TODO:?? does this automatically add revision to visualzation.revisions?
@@ -784,35 +858,36 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
 
         # -- Validate config. --
 
-        if vis.type == 'trackster':
+        if vis.type == "trackster":
+
             def unpack_track(track_dict):
-                """ Unpack a track from its json. """
-                dataset_dict = track_dict['dataset']
+                """Unpack a track from its json."""
+                dataset_dict = track_dict["dataset"]
                 return {
-                    "dataset_id": trans.security.decode_id(dataset_dict['id']),
-                    "hda_ldda": dataset_dict.get('hda_ldda', 'hda'),
-                    "track_type": track_dict['track_type'],
-                    "prefs": track_dict['prefs'],
-                    "mode": track_dict['mode'],
-                    "filters": track_dict['filters'],
-                    "tool_state": track_dict['tool_state']
+                    "dataset_id": trans.security.decode_id(dataset_dict["id"]),
+                    "hda_ldda": dataset_dict.get("hda_ldda", "hda"),
+                    "track_type": track_dict["track_type"],
+                    "prefs": track_dict["prefs"],
+                    "mode": track_dict["mode"],
+                    "filters": track_dict["filters"],
+                    "tool_state": track_dict["tool_state"],
                 }
 
             def unpack_collection(collection_json):
-                """ Unpack a collection from its json. """
+                """Unpack a collection from its json."""
                 unpacked_drawables = []
-                drawables = collection_json['drawables']
+                drawables = collection_json["drawables"]
                 for drawable_json in drawables:
-                    if 'track_type' in drawable_json:
+                    if "track_type" in drawable_json:
                         drawable = unpack_track(drawable_json)
                     else:
                         drawable = unpack_collection(drawable_json)
                     unpacked_drawables.append(drawable)
                 return {
-                    "obj_type": collection_json['obj_type'],
+                    "obj_type": collection_json["obj_type"],
                     "drawables": unpacked_drawables,
-                    "prefs": collection_json.get('prefs', []),
-                    "filters": collection_json.get('filters', None)
+                    "prefs": collection_json.get("prefs", []),
+                    "filters": collection_json.get("filters", None),
                 }
 
             # TODO: unpack and validate bookmarks:
@@ -820,17 +895,17 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                 return bookmarks_json
 
             # Unpack and validate view content.
-            view_content = unpack_collection(config['view'])
-            bookmarks = unpack_bookmarks(config['bookmarks'])
+            view_content = unpack_collection(config["view"])
+            bookmarks = unpack_bookmarks(config["bookmarks"])
             vis_rev.config = {"view": view_content, "bookmarks": bookmarks}
             # Viewport from payload
-            viewport = config.get('viewport')
+            viewport = config.get("viewport")
             if viewport:
-                chrom = viewport['chrom']
-                start = viewport['start']
-                end = viewport['end']
-                overview = viewport['overview']
-                vis_rev.config["viewport"] = {'chrom': chrom, 'start': start, 'end': end, 'overview': overview}
+                chrom = viewport["chrom"]
+                start = viewport["start"]
+                end = viewport["end"]
+                overview = viewport["overview"]
+                vis_rev.config["viewport"] = {"chrom": chrom, "start": start, "end": end, "overview": overview}
         else:
             # Default action is to save the config as is with no validation.
             vis_rev.config = config
@@ -839,10 +914,10 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         session.add(vis_rev)
         session.flush()
         encoded_id = trans.security.encode_id(vis.id)
-        return {"vis_id": encoded_id, "url": url_for(controller='visualization', action=vis.type, id=encoded_id)}
+        return {"vis_id": encoded_id, "url": url_for(controller="visualization", action=vis.type, id=encoded_id)}
 
     def get_tool_def(self, trans, hda):
-        """ Returns definition of an interactive tool for an HDA. """
+        """Returns definition of an interactive tool for an HDA."""
 
         # Get dataset's job.
         job = None
@@ -866,61 +941,61 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         tool_param_values = tool.params_from_strings(tool_param_values, trans.app, ignore_errors=True)
 
         # Only get values for simple inputs for now.
-        inputs_dict = [i for i in tool_dict['inputs'] if i['type'] not in ['data', 'hidden_data', 'conditional']]
+        inputs_dict = [i for i in tool_dict["inputs"] if i["type"] not in ["data", "hidden_data", "conditional"]]
         for t_input in inputs_dict:
             # Add value to tool.
-            if 'name' in t_input:
-                name = t_input['name']
+            if "name" in t_input:
+                name = t_input["name"]
                 if name in tool_param_values:
                     value = tool_param_values[name]
                     if isinstance(value, Dictifiable):
                         value = value.to_dict()
-                    t_input['value'] = value
+                    t_input["value"] = value
 
         return tool_dict
 
     def get_visualization_config(self, trans, visualization):
-        """ Returns a visualization's configuration. Only works for trackster visualizations right now. """
+        """Returns a visualization's configuration. Only works for trackster visualizations right now."""
         config = None
-        if visualization.type in ['trackster', 'genome']:
+        if visualization.type in ["trackster", "genome"]:
             # Unpack Trackster config.
             latest_revision = visualization.latest_revision
-            bookmarks = latest_revision.config.get('bookmarks', [])
+            bookmarks = latest_revision.config.get("bookmarks", [])
 
             def pack_track(track_dict):
-                dataset_id = track_dict['dataset_id']
-                hda_ldda = track_dict.get('hda_ldda', 'hda')
+                dataset_id = track_dict["dataset_id"]
+                hda_ldda = track_dict.get("hda_ldda", "hda")
                 dataset_id = trans.security.encode_id(dataset_id)
                 dataset = self.get_hda_or_ldda(trans, hda_ldda, dataset_id)
                 try:
-                    prefs = track_dict['prefs']
+                    prefs = track_dict["prefs"]
                 except KeyError:
                     prefs = {}
-                track_data_provider = trans.app.data_provider_registry.get_data_provider(trans,
-                                                                                         original_dataset=dataset,
-                                                                                         source='data')
+                track_data_provider = trans.app.data_provider_registry.get_data_provider(
+                    trans, original_dataset=dataset, source="data"
+                )
                 return {
                     "track_type": dataset.datatype.track_type,
                     "dataset": trans.security.encode_dict_ids(dataset.to_dict()),
                     "prefs": prefs,
-                    "mode": track_dict.get('mode', 'Auto'),
-                    "filters": track_dict.get('filters', {'filters': track_data_provider.get_filters()}),
+                    "mode": track_dict.get("mode", "Auto"),
+                    "filters": track_dict.get("filters", {"filters": track_data_provider.get_filters()}),
                     "tool": self.get_tool_def(trans, dataset),
-                    "tool_state": track_dict.get('tool_state', {})
+                    "tool_state": track_dict.get("tool_state", {}),
                 }
 
             def pack_collection(collection_dict):
                 drawables = []
-                for drawable_dict in collection_dict['drawables']:
-                    if 'track_type' in drawable_dict:
+                for drawable_dict in collection_dict["drawables"]:
+                    if "track_type" in drawable_dict:
                         drawables.append(pack_track(drawable_dict))
                     else:
                         drawables.append(pack_collection(drawable_dict))
                 return {
-                    'obj_type': collection_dict['obj_type'],
-                    'drawables': drawables,
-                    'prefs': collection_dict.get('prefs', []),
-                    'filters': collection_dict.get('filters', {})
+                    "obj_type": collection_dict["obj_type"],
+                    "drawables": drawables,
+                    "prefs": collection_dict.get("prefs", []),
+                    "filters": collection_dict.get("filters", {}),
                 }
 
             def encode_dbkey(dbkey):
@@ -930,32 +1005,34 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                 """
                 encoded_dbkey = dbkey
                 user = visualization.user
-                if 'dbkeys' in user.preferences and str(dbkey) in user.preferences['dbkeys']:
+                if "dbkeys" in user.preferences and str(dbkey) in user.preferences["dbkeys"]:
                     encoded_dbkey = f"{user.username}:{dbkey}"
                 return encoded_dbkey
 
             # Set tracks.
             tracks = []
-            if 'tracks' in latest_revision.config:
+            if "tracks" in latest_revision.config:
                 # Legacy code.
-                for track_dict in visualization.latest_revision.config['tracks']:
+                for track_dict in visualization.latest_revision.config["tracks"]:
                     tracks.append(pack_track(track_dict))
-            elif 'view' in latest_revision.config:
-                for drawable_dict in visualization.latest_revision.config['view']['drawables']:
-                    if 'track_type' in drawable_dict:
+            elif "view" in latest_revision.config:
+                for drawable_dict in visualization.latest_revision.config["view"]["drawables"]:
+                    if "track_type" in drawable_dict:
                         tracks.append(pack_track(drawable_dict))
                     else:
                         tracks.append(pack_collection(drawable_dict))
 
-            config = {"title": visualization.title,
-                      "vis_id": trans.security.encode_id(visualization.id) if visualization.id is not None else None,
-                      "tracks": tracks,
-                      "bookmarks": bookmarks,
-                      "chrom": "",
-                      "dbkey": encode_dbkey(visualization.dbkey)}
+            config = {
+                "title": visualization.title,
+                "vis_id": trans.security.encode_id(visualization.id) if visualization.id is not None else None,
+                "tracks": tracks,
+                "bookmarks": bookmarks,
+                "chrom": "",
+                "dbkey": encode_dbkey(visualization.dbkey),
+            }
 
-            if 'viewport' in latest_revision.config:
-                config['viewport'] = latest_revision.config['viewport']
+            if "viewport" in latest_revision.config:
+                config["viewport"] = latest_revision.config["viewport"]
         else:
             # Default action is to return config unaltered.
             latest_revision = visualization.latest_revision
@@ -976,13 +1053,13 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
             "name": dataset.name,
             "dataset": trans.security.encode_dict_ids(dataset.to_dict()),
             "prefs": {},
-            "filters": {'filters': track_data_provider.get_filters()},
+            "filters": {"filters": track_data_provider.get_filters()},
             "tool": self.get_tool_def(trans, dataset),
-            "tool_state": {}
+            "tool_state": {},
         }
 
     def get_hda_or_ldda(self, trans, hda_ldda, dataset_id):
-        """ Returns either HDA or LDDA for hda/ldda and id combination. """
+        """Returns either HDA or LDDA for hda/ldda and id combination."""
         if hda_ldda == "hda":
             return self.get_hda(trans, dataset_id, check_ownership=False, check_accessible=True)
         else:
@@ -1023,14 +1100,15 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                 error("You are not allowed to access this dataset")
 
             if check_state and data.state == trans.model.Dataset.states.UPLOAD:
-                return trans.show_error_message("Please wait until this dataset finishes uploading "
-                                                + "before attempting to view it.")
+                return trans.show_error_message(
+                    "Please wait until this dataset finishes uploading " + "before attempting to view it."
+                )
         return data
 
     # -- Helper functions --
 
     def _create_visualization(self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True):
-        """ Create visualization but not first revision. Returns Visualization object. """
+        """Create visualization but not first revision. Returns Visualization object."""
         user = trans.get_user()
 
         # Error checking.
@@ -1039,11 +1117,14 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
             title_err = "visualization name is required"
         elif slug and not managers_base.is_valid_slug(slug):
             slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
-        elif slug and trans.sa_session.query(trans.model.Visualization).filter_by(user=user, slug=slug, deleted=False).first():
+        elif (
+            slug
+            and trans.sa_session.query(trans.model.Visualization).filter_by(user=user, slug=slug, deleted=False).first()
+        ):
             slug_err = "visualization identifier must be unique"
 
         if title_err or slug_err:
-            return {'title_err': title_err, 'slug_err': slug_err}
+            return {"title_err": title_err, "slug_err": slug_err}
 
         # Create visualization
         visualization = trans.model.Visualization(user=user, title=title, dbkey=dbkey, type=type)
@@ -1078,26 +1159,25 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         chroms_info = self.app.genomes.chroms(trans, dbkey=query_dbkey)
 
         # If there are no messages (messages indicate data is not ready/available), get data.
-        messages_list = [data_source_dict['message'] for data_source_dict in data_sources.values()]
+        messages_list = [data_source_dict["message"] for data_source_dict in data_sources.values()]
         message = self._get_highest_priority_msg(messages_list)
         if message:
             rval = message
         else:
             # HACK: chromatin interactions tracks use data as source.
-            source = 'index'
+            source = "index"
             if isinstance(dataset.datatype, ChromatinInteractions):
-                source = 'data'
+                source = "data"
 
-            data_provider = trans.app.data_provider_registry.get_data_provider(trans,
-                                                                               original_dataset=dataset,
-                                                                               source=source)
+            data_provider = trans.app.data_provider_registry.get_data_provider(
+                trans, original_dataset=dataset, source=source
+            )
             # HACK: pass in additional params which are used for only some
             # types of data providers; level, cutoffs used for summary tree,
             # num_samples for BBI, and interchromosomal used for chromatin interactions.
-            rval = data_provider.get_genome_data(chroms_info,
-                                                 level=4, detail_cutoff=0, draw_cutoff=0,
-                                                 num_samples=150,
-                                                 interchromosomal=True)
+            rval = data_provider.get_genome_data(
+                chroms_info, level=4, detail_cutoff=0, draw_cutoff=0, num_samples=150, interchromosomal=True
+            )
 
         return rval
 
@@ -1122,11 +1202,12 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
 
 
 class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
-    """ Mixin for controllers that use StoredWorkflow objects. """
+    """Mixin for controllers that use StoredWorkflow objects."""
+
     slug_builder = SlugBuilder()
 
     def get_stored_workflow(self, trans, id, check_ownership=True, check_accessible=False):
-        """ Get a StoredWorkflow from the database by id, verifying ownership. """
+        """Get a StoredWorkflow from the database by id, verifying ownership."""
         # Load workflow from database
         workflow_contents_manager = workflows.WorkflowsManager(self.app)
         workflow = workflow_contents_manager.get_stored_workflow(trans=trans, workflow_id=id)
@@ -1144,7 +1225,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
         return workflow
 
     def get_stored_workflow_steps(self, trans, stored_workflow):
-        """ Restores states for a stored workflow's steps. """
+        """Restores states for a stored workflow's steps."""
         module_injector = WorkflowModuleInjector(trans)
         for step in stored_workflow.latest_workflow.steps:
             try:
@@ -1153,7 +1234,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
                 pass
 
     def _import_shared_workflow(self, trans, stored):
-        """ Imports a shared workflow """
+        """Imports a shared workflow"""
         # Copy workflow.
         imported_stored = model.StoredWorkflow()
         imported_stored.name = f"imported: {stored.name}"
@@ -1170,8 +1251,9 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
         # Copy annotations.
         self.copy_item_annotation(session, stored.user, stored, imported_stored.user, imported_stored)
         for order_index, step in enumerate(stored.latest_workflow.steps):
-            self.copy_item_annotation(session, stored.user, step,
-                                      imported_stored.user, imported_stored.latest_workflow.steps[order_index])
+            self.copy_item_annotation(
+                session, stored.user, step, imported_stored.user, imported_stored.latest_workflow.steps[order_index]
+            )
         session.flush()
         return imported_stored
 
@@ -1189,7 +1271,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
 class UsesFormDefinitionsMixin:
     """Mixin for controllers that use Galaxy form objects."""
 
-    def get_all_forms(self, trans, all_versions=False, filter=None, form_type='All'):
+    def get_all_forms(self, trans, all_versions=False, filter=None, form_type="All"):
         """
         Return all the latest forms from the form_definition_current table
         if all_versions is set to True. Otherwise return all the versions
@@ -1201,7 +1283,7 @@ class UsesFormDefinitionsMixin:
             fdc_list = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).filter_by(**filter)
         else:
             fdc_list = trans.sa_session.query(trans.app.model.FormDefinitionCurrent)
-        if form_type == 'All':
+        if form_type == "All":
             return [fdc.latest_form for fdc in fdc_list]
         else:
             return [fdc.latest_form for fdc in fdc_list if fdc.latest_form.type == form_type]
@@ -1210,44 +1292,44 @@ class UsesFormDefinitionsMixin:
         # Save a form_builder field object
         params = util.Params(kwd)
         if isinstance(field_obj, trans.model.UserAddress):
-            field_obj.desc = util.restore_text(params.get(f'{widget_name}_short_desc', ''))
-            field_obj.name = util.restore_text(params.get(f'{widget_name}_name', ''))
-            field_obj.institution = util.restore_text(params.get(f'{widget_name}_institution', ''))
-            field_obj.address = util.restore_text(params.get(f'{widget_name}_address', ''))
-            field_obj.city = util.restore_text(params.get(f'{widget_name}_city', ''))
-            field_obj.state = util.restore_text(params.get(f'{widget_name}_state', ''))
-            field_obj.postal_code = util.restore_text(params.get(f'{widget_name}_postal_code', ''))
-            field_obj.country = util.restore_text(params.get(f'{widget_name}_country', ''))
-            field_obj.phone = util.restore_text(params.get(f'{widget_name}_phone', ''))
+            field_obj.desc = util.restore_text(params.get(f"{widget_name}_short_desc", ""))
+            field_obj.name = util.restore_text(params.get(f"{widget_name}_name", ""))
+            field_obj.institution = util.restore_text(params.get(f"{widget_name}_institution", ""))
+            field_obj.address = util.restore_text(params.get(f"{widget_name}_address", ""))
+            field_obj.city = util.restore_text(params.get(f"{widget_name}_city", ""))
+            field_obj.state = util.restore_text(params.get(f"{widget_name}_state", ""))
+            field_obj.postal_code = util.restore_text(params.get(f"{widget_name}_postal_code", ""))
+            field_obj.country = util.restore_text(params.get(f"{widget_name}_country", ""))
+            field_obj.phone = util.restore_text(params.get(f"{widget_name}_phone", ""))
             trans.sa_session.add(field_obj)
             trans.sa_session.flush()
 
     def get_form_values(self, trans, user, form_definition, **kwd):
-        '''
+        """
         Returns the name:value dictionary containing all the form values
-        '''
+        """
         params = util.Params(kwd)
         values = {}
         for field in form_definition.fields:
-            field_type = field['type']
-            field_name = field['name']
-            input_value = params.get(field_name, '')
+            field_type = field["type"]
+            field_name = field["name"]
+            input_value = params.get(field_name, "")
             if field_type == AddressField.__name__:
                 input_text_value = util.restore_text(input_value)
-                if input_text_value == 'new':
+                if input_text_value == "new":
                     # Save this new address in the list of this user's addresses
                     user_address = trans.model.UserAddress(user=user)
                     self.save_widget_field(trans, user_address, field_name, **kwd)
                     trans.sa_session.refresh(user)
                     field_value = int(user_address.id)
-                elif input_text_value in ['', 'none', 'None', None]:
-                    field_value = ''
+                elif input_text_value in ["", "none", "None", None]:
+                    field_value = ""
                 else:
                     field_value = int(input_text_value)
             elif field_type == CheckboxField.__name__:
                 field_value = CheckboxField.is_checked(input_value)
             elif field_type == PasswordField.__name__:
-                field_value = kwd.get(field_name, '')
+                field_value = kwd.get(field_name, "")
             else:
                 field_value = util.restore_text(input_value)
             values[field_name] = field_value
@@ -1255,7 +1337,7 @@ class UsesFormDefinitionsMixin:
 
 
 class SharableMixin:
-    """ Mixin for a controller that manages an item that can be shared. """
+    """Mixin for a controller that manages an item that can be shared."""
 
     manager: Any = None
     serializer: Any = None
@@ -1264,7 +1346,7 @@ class SharableMixin:
     # -- Implemented methods. --
 
     def _is_valid_slug(self, slug):
-        """ Returns true if slug is valid. """
+        """Returns true if slug is valid."""
         return managers_base.is_valid_slug(slug)
 
     @web.expose
@@ -1280,9 +1362,9 @@ class SharableMixin:
         return item.slug
 
     def _make_item_accessible(self, sa_session, item):
-        """ Makes item accessible--viewable and importable--and sets item's slug.
-            Does not flush/commit changes, however. Item must have name, user,
-            importable, and slug attributes. """
+        """Makes item accessible--viewable and importable--and sets item's slug.
+        Does not flush/commit changes, however. Item must have name, user,
+        importable, and slug attributes."""
         item.importable = True
         self.slug_builder.create_item_slug(sa_session, item)
 
@@ -1291,33 +1373,32 @@ class SharableMixin:
     @web.expose
     @web.require_login("share Galaxy items")
     def share(self, trans, id=None, email="", **kwd):
-        """ Handle sharing an item with a particular user. """
+        """Handle sharing an item with a particular user."""
         raise NotImplementedError()
 
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug):
-        """ Display item by username and slug. """
+        """Display item by username and slug."""
         raise NotImplementedError()
 
     @web.json
     @web.require_login("get item name and link")
     def get_name_and_link_async(self, trans, id=None):
-        """ Returns item's name and link. """
+        """Returns item's name and link."""
         raise NotImplementedError()
 
     @web.expose
     @web.require_login("get item content asynchronously")
     def get_item_content_async(self, trans, id):
-        """ Returns item content in HTML format. """
+        """Returns item content in HTML format."""
         raise NotImplementedError()
 
     def get_item(self, trans, id):
-        """ Return item based on id. """
+        """Return item based on id."""
         raise NotImplementedError()
 
 
 class UsesTagsMixin(SharableItemSecurityMixin):
-
     def get_tag_handler(self, trans) -> tags.GalaxyTagHandler:
         return trans.app.tag_handler
 
@@ -1327,7 +1408,9 @@ class UsesTagsMixin(SharableItemSecurityMixin):
         return [tag for tag in tagged_item.tags if tag.user == user]
 
     def _get_tagged_item(self, trans, item_class_name, id, check_ownership=True):
-        tagged_item = self.get_object(trans, id, item_class_name, check_ownership=check_ownership, check_accessible=True)
+        tagged_item = self.get_object(
+            trans, id, item_class_name, check_ownership=check_ownership, check_accessible=True
+        )
         return tagged_item
 
     def _remove_items_tag(self, trans, item_class_name, id, tag_name):
@@ -1373,8 +1456,9 @@ class UsesTagsMixin(SharableItemSecurityMixin):
         # create a union of subqueries for each for this user - getting only the tname and user_value
         all_tags_query = None
         for tag_model in tag_models:
-            subq = (trans.sa_session.query(tag_model.user_tname, tag_model.user_value)
-                    .filter(tag_model.user == trans.user))
+            subq = trans.sa_session.query(tag_model.user_tname, tag_model.user_value).filter(
+                tag_model.user == trans.user
+            )
             all_tags_query = subq if all_tags_query is None else all_tags_query.union(subq)
 
         # if nothing init'd the query, bail
@@ -1388,7 +1472,7 @@ class UsesTagsMixin(SharableItemSecurityMixin):
 
 
 class UsesExtendedMetadataMixin(SharableItemSecurityMixin):
-    """ Mixin for getting and setting item extended metadata. """
+    """Mixin for getting and setting item extended metadata."""
 
     def get_item_extended_metadata_obj(self, trans, item):
         """
@@ -1401,7 +1485,9 @@ class UsesExtendedMetadataMixin(SharableItemSecurityMixin):
 
     def set_item_extended_metadata_obj(self, trans, item, extmeta_obj, check_writable=False):
         if item.__class__ == LibraryDatasetDatasetAssociation:
-            if not check_writable or trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item, trans.user):
+            if not check_writable or trans.app.security_agent.can_modify_library_item(
+                trans.get_current_user_roles(), item, trans.user
+            ):
                 item.extended_metadata = extmeta_obj
                 trans.sa_session.flush()
         if item.__class__ == HistoryDatasetAssociation:
@@ -1416,7 +1502,9 @@ class UsesExtendedMetadataMixin(SharableItemSecurityMixin):
 
     def unset_item_extended_metadata_obj(self, trans, item, check_writable=False):
         if item.__class__ == LibraryDatasetDatasetAssociation:
-            if not check_writable or trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item, trans.user):
+            if not check_writable or trans.app.security_agent.can_modify_library_item(
+                trans.get_current_user_roles(), item, trans.user
+            ):
                 item.extended_metadata = None
                 trans.sa_session.flush()
         if item.__class__ == HistoryDatasetAssociation:
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 9a99007f1af..efa7dc4f0a3 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -9,14 +9,20 @@ import socket
 import string
 import time
 from http.cookies import CookieError
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 from urllib.parse import urlparse
 
 import mako.lookup
 import mako.runtime
 from babel import Locale
 from babel.support import Translations
-from sqlalchemy import and_, true
+from sqlalchemy import (
+    and_,
+    true,
+)
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import util
@@ -31,13 +37,13 @@ from galaxy.managers.users import UserManager
 from galaxy.util import (
     asbool,
     safe_makedirs,
-    unicodify
+    unicodify,
 )
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web.framework import (
     base,
     helpers,
-    url_for
+    url_for,
 )
 from galaxy.web_stack import get_app_kwds
 
@@ -51,22 +57,22 @@ log = logging.getLogger(__name__)
 
 
 UCSC_SERVERS = (
-    'hgw1.cse.ucsc.edu',
-    'hgw2.cse.ucsc.edu',
-    'hgw3.cse.ucsc.edu',
-    'hgw4.cse.ucsc.edu',
-    'hgw5.cse.ucsc.edu',
-    'hgw6.cse.ucsc.edu',
-    'hgw7.cse.ucsc.edu',
-    'hgw8.cse.ucsc.edu',
-    'hgw1.soe.ucsc.edu',
-    'hgw2.soe.ucsc.edu',
-    'hgw3.soe.ucsc.edu',
-    'hgw4.soe.ucsc.edu',
-    'hgw5.soe.ucsc.edu',
-    'hgw6.soe.ucsc.edu',
-    'hgw7.soe.ucsc.edu',
-    'hgw8.soe.ucsc.edu',
+    "hgw1.cse.ucsc.edu",
+    "hgw2.cse.ucsc.edu",
+    "hgw3.cse.ucsc.edu",
+    "hgw4.cse.ucsc.edu",
+    "hgw5.cse.ucsc.edu",
+    "hgw6.cse.ucsc.edu",
+    "hgw7.cse.ucsc.edu",
+    "hgw8.cse.ucsc.edu",
+    "hgw1.soe.ucsc.edu",
+    "hgw2.soe.ucsc.edu",
+    "hgw3.soe.ucsc.edu",
+    "hgw4.soe.ucsc.edu",
+    "hgw5.soe.ucsc.edu",
+    "hgw6.soe.ucsc.edu",
+    "hgw7.soe.ucsc.edu",
+    "hgw8.soe.ucsc.edu",
 )
 
 
@@ -82,9 +88,10 @@ class WebApplication(base.WebApplication):
         * builds mako template lookups.
         * generates GalaxyWebTransactions.
     """
+
     injection_aware: bool = False
 
-    def __init__(self, galaxy_app, session_cookie='galaxysession', name=None):
+    def __init__(self, galaxy_app, session_cookie="galaxysession", name=None):
         super().__init__()
         self.name = name
         galaxy_app.is_webapp = True
@@ -96,17 +103,19 @@ class WebApplication(base.WebApplication):
 
     def create_mako_template_lookup(self, galaxy_app, name):
         paths = []
-        base_package = 'tool_shed.webapp' if galaxy_app.name == 'tool_shed' else 'galaxy.webapps.base'  # reports has templates in galaxy package
-        base_template_path = files(base_package) / 'templates'
+        base_package = (
+            "tool_shed.webapp" if galaxy_app.name == "tool_shed" else "galaxy.webapps.base"
+        )  # reports has templates in galaxy package
+        base_template_path = files(base_package) / "templates"
         # First look in webapp specific directory
         if name is not None:
-            paths.append(base_template_path / 'webapps' / name)
+            paths.append(base_template_path / "webapps" / name)
         # Then look in root directory
         paths.append(base_template_path)
         # Create TemplateLookup with a small cache
-        return mako.lookup.TemplateLookup(directories=paths,
-                                          module_directory=galaxy_app.config.template_cache_path,
-                                          collection_size=500)
+        return mako.lookup.TemplateLookup(
+            directories=paths, module_directory=galaxy_app.config.template_cache_path, collection_size=500
+        )
 
     def handle_controller_exception(self, e, trans, **kwargs):
         if isinstance(e, MessageException):
@@ -127,6 +136,7 @@ class WebApplication(base.WebApplication):
         them to the webapp.
         """
         from galaxy.webapps.base.controller import BaseUIController
+
         for name, module in base.walk_controller_modules(package_name):
             # Look for a controller inside the modules
             for key in dir(module):
@@ -141,6 +151,7 @@ class WebApplication(base.WebApplication):
         them to the webapp.
         """
         from galaxy.webapps.base.controller import BaseAPIController
+
         for name, module in base.walk_controller_modules(package_name):
             for key in dir(module):
                 T = getattr(module, key)
@@ -152,7 +163,7 @@ class WebApplication(base.WebApplication):
                     self.add_api_controller(controller_name, controller)
 
     def _instantiate_controller(self, T, app):
-        """ Extension point, allow apps to construct controllers differently,
+        """Extension point, allow apps to construct controllers differently,
         really just used to stub out actual controllers for routes testing.
         """
         controller = None
@@ -185,7 +196,7 @@ def config_allows_origin(origin_raw, config):
 
     # check for '*' or compare to list of allowed
     for allowed_origin in config.allowed_origin_hostnames:
-        if allowed_origin == '*' or matches_allowed_origin(origin, allowed_origin):
+        if allowed_origin == "*" or matches_allowed_origin(origin, allowed_origin):
             return True
 
     return False
@@ -211,10 +222,10 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         self.setup_i18n()
         self.expunge_all()
         config = self.app.config
-        self.debug = asbool(config.get('debug', False))
-        x_frame_options = getattr(config, 'x_frame_options', None)
+        self.debug = asbool(config.get("debug", False))
+        x_frame_options = getattr(config, "x_frame_options", None)
         if x_frame_options:
-            self.response.headers['X-Frame-Options'] = x_frame_options
+            self.response.headers["X-Frame-Options"] = x_frame_options
         # Flag indicating whether we are in workflow building mode (means
         # that the current history should not be used for parameter values
         # and such).
@@ -227,7 +238,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         # set any cross origin resource sharing headers if configured to do so
         self.set_cors_headers()
 
-        if self.environ.get('is_api_request', False):
+        if self.environ.get("is_api_request", False):
             # With API requests, if there's a key, use it and associate the
             # user with the transaction.
             # If not, check for an active session but do not create one.
@@ -244,7 +255,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             # following.
             # Prevent deleted users from accessing Galaxy
             if config.use_remote_user and self.galaxy_session.user.deleted:
-                self.response.send_redirect(url_for('/static/user_disabled.html'))
+                self.response.send_redirect(url_for("/static/user_disabled.html"))
             if config.require_login:
                 self._ensure_logged_in_user(environ, session_cookie)
             if config.session_duration:
@@ -258,7 +269,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
                 # update timestamp.
                 now = datetime.datetime.now()
                 if self.galaxy_session.last_action:
-                    expiration_time = self.galaxy_session.last_action + datetime.timedelta(minutes=config.session_duration)
+                    expiration_time = self.galaxy_session.last_action + datetime.timedelta(
+                        minutes=config.session_duration
+                    )
                 else:
                     expiration_time = now
                     self.galaxy_session.last_action = now - datetime.timedelta(seconds=1)
@@ -267,16 +280,20 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
                 if expiration_time < now:
                     # Expiration time has passed.
                     self.handle_user_logout()
-                    if self.environ.get('is_api_request', False):
+                    if self.environ.get("is_api_request", False):
                         self.response.status = 401
                         self.user = None
                         self.galaxy_session = None
                     else:
-                        self.response.send_redirect(url_for(controller='root',
-                                                     action='login',
-                                                     message="You have been logged out due to inactivity.  Please log in again to continue using Galaxy.",
-                                                     status='info',
-                                                     use_panels=True))
+                        self.response.send_redirect(
+                            url_for(
+                                controller="root",
+                                action="login",
+                                message="You have been logged out due to inactivity.  Please log in again to continue using Galaxy.",
+                                status="info",
+                                use_panels=True,
+                            )
+                        )
                 else:
                     self.galaxy_session.last_action = now
                     self.sa_session.add(self.galaxy_session)
@@ -292,28 +309,28 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
 
     def setup_i18n(self):
         locales = []
-        if 'HTTP_ACCEPT_LANGUAGE' in self.environ:
+        if "HTTP_ACCEPT_LANGUAGE" in self.environ:
             # locales looks something like: ['en', 'en-us;q=0.7', 'ja;q=0.3']
-            client_locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split(',')
+            client_locales = self.environ["HTTP_ACCEPT_LANGUAGE"].split(",")
             for locale in client_locales:
                 try:
-                    locales.append(Locale.parse(locale.split(';')[0].strip(), sep='-').language)
+                    locales.append(Locale.parse(locale.split(";")[0].strip(), sep="-").language)
                 except Exception as e:
                     log.debug("Error parsing locale '%s'. %s: %s", locale, type(e), e)
         if not locales:
             # Default to English
-            locales = 'en'
-        t = Translations.load(dirname='locale', locales=locales, domain='ginga')
+            locales = "en"
+        t = Translations.load(dirname="locale", locales=locales, domain="ginga")
         self.template_context.update(dict(_=t.ugettext, n_=t.ugettext, N_=t.ungettext))
 
     def set_cors_allow(self, name=None, value=None):
-        acr = 'Access-Control-Request-'
+        acr = "Access-Control-Request-"
         if name is None:
             for key in self.request.headers.keys():
                 if key.startswith(acr):
-                    self.set_cors_allow(name=key[len(acr):], value=value)
+                    self.set_cors_allow(name=key[len(acr) :], value=value)
         else:
-            resp_name = f'Access-Control-Allow-{name}'
+            resp_name = f"Access-Control-Allow-{name}"
             if value is None:
                 value = self.request.headers.get(acr + name, None)
             if value:
@@ -325,9 +342,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         if origin is None:
             origin = self.request.headers.get("Origin", None)
         if origin:
-            self.response.headers['Access-Control-Allow-Origin'] = origin
-        elif 'Access-Control-Allow-Origin' in self.response.headers:
-            del self.response.headers['Access-Control-Allow-Origin']
+            self.response.headers["Access-Control-Allow-Origin"] = origin
+        elif "Access-Control-Allow-Origin" in self.response.headers:
+            del self.response.headers["Access-Control-Allow-Origin"]
 
     def set_cors_headers(self):
         """Allow CORS requests if configured to do so by echoing back the
@@ -343,7 +360,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         """
 
         # do not set any access control headers if not configured for it (common case)
-        if not self.app.config.get('allowed_origin_hostnames', None):
+        if not self.app.config.get("allowed_origin_hostnames", None):
             return
         # do not set any access control headers if there's no origin header on the request
         origin_header = self.request.headers.get("Origin", None)
@@ -375,7 +392,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
 
     user = property(get_user, set_user)
 
-    def get_cookie(self, name='galaxysession'):
+    def get_cookie(self, name="galaxysession"):
         """Convenience method for getting a session cookie"""
         try:
             # If we've changed the cookie during the request return the new value
@@ -386,33 +403,33 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         except Exception:
             return None
 
-    def set_cookie(self, value, name='galaxysession', path='/', age=90, version='1'):
+    def set_cookie(self, value, name="galaxysession", path="/", age=90, version="1"):
         """Convenience method for setting a session cookie"""
         # The galaxysession cookie value must be a high entropy 128 bit random number encrypted
         # using a server secret key.  Any other value is invalid and could pose security issues.
         self.response.cookies[name] = unicodify(value)
-        self.response.cookies[name]['path'] = path
-        self.response.cookies[name]['max-age'] = 3600 * 24 * age  # 90 days
+        self.response.cookies[name]["path"] = path
+        self.response.cookies[name]["max-age"] = 3600 * 24 * age  # 90 days
         tstamp = time.localtime(time.time() + 3600 * 24 * age)
-        self.response.cookies[name]['expires'] = time.strftime('%a, %d-%b-%Y %H:%M:%S GMT', tstamp)
-        self.response.cookies[name]['version'] = version
+        self.response.cookies[name]["expires"] = time.strftime("%a, %d-%b-%Y %H:%M:%S GMT", tstamp)
+        self.response.cookies[name]["version"] = version
         https = self.request.environ["wsgi.url_scheme"] == "https"
         if https:
-            self.response.cookies[name]['secure'] = True
+            self.response.cookies[name]["secure"] = True
         try:
-            self.response.cookies[name]['httponly'] = True
+            self.response.cookies[name]["httponly"] = True
         except CookieError as e:
             log.warning(f"Error setting httponly attribute in cookie '{name}': {e}")
         if self.app.config.cookie_domain is not None:
-            self.response.cookies[name]['domain'] = self.app.config.cookie_domain
+            self.response.cookies[name]["domain"] = self.app.config.cookie_domain
 
     def _authenticate_api(self, session_cookie):
         """
         Authenticate for the API via key or session (if available).
         """
-        api_key = self.request.params.get('key', None) or self.request.headers.get('x-api-key', None)
+        api_key = self.request.params.get("key", None) or self.request.headers.get("x-api-key", None)
         secure_id = self.get_cookie(name=session_cookie)
-        api_key_supplied = self.environ.get('is_api_request', False) and api_key
+        api_key_supplied = self.environ.get("is_api_request", False) and api_key
         if api_key_supplied:
             # Sessionless API transaction, we just need to associate a user.
             try:
@@ -427,7 +444,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             try:
                 self._ensure_valid_session(session_cookie)
             except Exception:
-                log.exception("Exception during Session-based API authentication, this was most likely an attempt to use an anonymous cookie under remote authentication (so, no user), which we don't support.")
+                log.exception(
+                    "Exception during Session-based API authentication, this was most likely an attempt to use an anonymous cookie under remote authentication (so, no user), which we don't support."
+                )
                 self.user = None
                 self.galaxy_session = None
         else:
@@ -468,29 +487,38 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
                     # No user, associate
                     galaxy_session.user = self.get_or_create_remote_user(remote_user_email)
                     galaxy_session_requires_flush = True
-                elif (remote_user_email
-                      and galaxy_session.user.email != remote_user_email
-                      and (not self.app.config.allow_user_impersonation
-                           or remote_user_email not in self.app.config.admin_users_list)):
+                elif (
+                    remote_user_email
+                    and galaxy_session.user.email != remote_user_email
+                    and (
+                        not self.app.config.allow_user_impersonation
+                        or remote_user_email not in self.app.config.admin_users_list
+                    )
+                ):
                     # Session exists but is not associated with the correct
                     # remote user, and the currently set remote_user is not a
                     # potentially impersonating admin.
                     invalidate_existing_session = True
                     user_for_new_session = self.get_or_create_remote_user(remote_user_email)
-                    log.warning("User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
-                                remote_user_email, galaxy_session.user.email)
+                    log.warning(
+                        "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
+                        remote_user_email,
+                        galaxy_session.user.email,
+                    )
             elif remote_user_email:
                 # No session exists, get/create user for new session
                 user_for_new_session = self.get_or_create_remote_user(remote_user_email)
-            if ((galaxy_session and galaxy_session.user is None) and user_for_new_session is None):
+            if (galaxy_session and galaxy_session.user is None) and user_for_new_session is None:
                 raise Exception("Remote Authentication Failure - user is unknown and/or not supplied.")
         else:
             if galaxy_session is not None and galaxy_session.user and galaxy_session.user.external:
                 # Remote user support is not enabled, but there is an existing
                 # session with an external user, invalidate
                 invalidate_existing_session = True
-                log.warning("User '%s' is an external user with an existing session, invalidating session since external auth is disabled",
-                            galaxy_session.user.email)
+                log.warning(
+                    "User '%s' is an external user with an existing session, invalidating session since external auth is disabled",
+                    galaxy_session.user.email,
+                )
             elif galaxy_session is not None and galaxy_session.user is not None and galaxy_session.user.deleted:
                 invalidate_existing_session = True
                 log.warning(f"User '{galaxy_session.user.email}' is marked deleted, invalidating session")
@@ -524,56 +552,59 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         # The value of session_cookie can be one of
         # 'galaxysession' or 'galaxycommunitysession'
         # Currently this method does nothing unless session_cookie is 'galaxysession'
-        if session_cookie == 'galaxysession' and self.galaxy_session.user is None:
+        if session_cookie == "galaxysession" and self.galaxy_session.user is None:
             # TODO: re-engineer to eliminate the use of allowed_paths
             # as maintenance overhead is far too high.
             allowed_paths = [
                 # client app route
                 # TODO: might be better as '/:username/login', '/:username/logout'
-                url_for(controller='root', action='login'),
+                url_for(controller="root", action="login"),
                 # mako app routes
-                url_for(controller='user', action='login'),
-                url_for(controller='user', action='logout'),
-                url_for(controller='user', action='reset_password'),
-                url_for(controller='user', action='change_password'),
+                url_for(controller="user", action="login"),
+                url_for(controller="user", action="logout"),
+                url_for(controller="user", action="reset_password"),
+                url_for(controller="user", action="change_password"),
                 # TODO: do any of these still need to bypass require login?
-                url_for(controller='user', action='api_keys'),
-                url_for(controller='user', action='create'),
-                url_for(controller='user', action='index'),
-                url_for(controller='user', action='manage_user_info'),
-                url_for(controller='user', action='set_default_permissions'),
+                url_for(controller="user", action="api_keys"),
+                url_for(controller="user", action="create"),
+                url_for(controller="user", action="index"),
+                url_for(controller="user", action="manage_user_info"),
+                url_for(controller="user", action="set_default_permissions"),
             ]
             # append the welcome url to allowed paths if we'll show it at the login screen
             if self.app.config.show_welcome_with_login:
-                allowed_paths.append(url_for(controller='root', action='welcome'))
+                allowed_paths.append(url_for(controller="root", action="welcome"))
 
             # prevent redirect when UCSC server attempts to get dataset contents as 'anon' user
-            display_as = url_for(controller='root', action='display_as')
-            if self.app.datatypes_registry.get_display_sites('ucsc') and self.request.path == display_as:
+            display_as = url_for(controller="root", action="display_as")
+            if self.app.datatypes_registry.get_display_sites("ucsc") and self.request.path == display_as:
                 try:
-                    host = socket.gethostbyaddr(self.environ['REMOTE_ADDR'])[0]
-                except(OSError, socket.herror, socket.gaierror, socket.timeout):
+                    host = socket.gethostbyaddr(self.environ["REMOTE_ADDR"])[0]
+                except (OSError, socket.herror, socket.gaierror, socket.timeout):
                     host = None
                 if host in UCSC_SERVERS:
                     return
             # prevent redirect for external, enabled display applications getting dataset contents
-            external_display_path = url_for(controller='', action='display_application')
+            external_display_path = url_for(controller="", action="display_application")
             if self.request.path.startswith(external_display_path):
-                request_path_split = self.request.path.split('/')
+                request_path_split = self.request.path.split("/")
                 try:
-                    if (self.app.datatypes_registry.display_applications.get(request_path_split[-5])
-                            and request_path_split[-4] in self.app.datatypes_registry.display_applications.get(request_path_split[-5]).links
-                            and request_path_split[-3] != 'None'):
+                    if (
+                        self.app.datatypes_registry.display_applications.get(request_path_split[-5])
+                        and request_path_split[-4]
+                        in self.app.datatypes_registry.display_applications.get(request_path_split[-5]).links
+                        and request_path_split[-3] != "None"
+                    ):
                         return
                 except IndexError:
                     pass
-            authnz_controller_base = url_for(controller='authnz', action='index')
+            authnz_controller_base = url_for(controller="authnz", action="index")
             if self.request.path.startswith(authnz_controller_base):
                 #  All authnz requests pass through
                 return
             # redirect to root if the path is not in the list above
             if self.request.path not in allowed_paths:
-                login_url = url_for(controller='root', action='login', redirect=self.request.path)
+                login_url = url_for(controller="root", action="login", redirect=self.request.path)
                 self.response.send_redirect(login_url)
 
     def __create_new_session(self, prev_galaxy_session=None, user_for_new_session=None):
@@ -590,7 +621,8 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             is_valid=True,
             remote_host=self.request.remote_host,
             remote_addr=self.request.remote_addr,
-            referer=self.request.headers.get('Referer', None))
+            referer=self.request.headers.get("Referer", None),
+        )
         if prev_galaxy_session:
             # Invalidated an existing session for some reason, keep track
             galaxy_session.prev_session_id = prev_galaxy_session.id
@@ -607,26 +639,30 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             return None
         if getattr(self.app.config, "normalize_remote_user_email", False):
             remote_user_email = remote_user_email.lower()
-        user = self.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == remote_user_email).first()
+        user = (
+            self.sa_session.query(self.app.model.User)
+            .filter(self.app.model.User.table.c.email == remote_user_email)
+            .first()
+        )
         if user:
             # GVK: June 29, 2009 - This is to correct the behavior of a previous bug where a private
             # role and default user / history permissions were not set for remote users.  When a
             # remote user authenticates, we'll look for this information, and if missing, create it.
             if not self.app.security_agent.get_private_user_role(user):
                 self.app.security_agent.create_private_user_role(user)
-            if 'webapp' not in self.environ or self.environ['webapp'] != 'tool_shed':
+            if "webapp" not in self.environ or self.environ["webapp"] != "tool_shed":
                 if not user.default_permissions:
                     self.app.security_agent.user_set_default_permissions(user)
                     self.app.security_agent.user_set_default_permissions(user, history=True, dataset=True)
         elif user is None:
-            username = remote_user_email.split('@', 1)[0].lower()
+            username = remote_user_email.split("@", 1)[0].lower()
             random.seed()
             user = self.app.model.User(email=remote_user_email)
             user.set_random_password(length=12)
             user.external = True
             # Replace invalid characters in the username
             for char in [x for x in username if x not in f"{string.ascii_lowercase + string.digits}-."]:
-                username = username.replace(char, '-')
+                username = username.replace(char, "-")
             # Find a unique username - user can change it later
             if self.sa_session.query(self.app.model.User).filter_by(username=username).first():
                 i = 1
@@ -638,7 +674,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             self.sa_session.flush()
             self.app.security_agent.create_private_user_role(user)
             # We set default user permissions, before we log in and set the default history permissions
-            if 'webapp' not in self.environ or self.environ['webapp'] != 'tool_shed':
+            if "webapp" not in self.environ or self.environ["webapp"] != "tool_shed":
                 self.app.security_agent.user_set_default_permissions(user)
             # self.log_event( "Automatically created account '%s'", user.email )
         return user
@@ -646,14 +682,13 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
     @property
     def cookie_path(self):
         # Cookies for non-root paths should not end with `/` -> https://stackoverflow.com/questions/36131023/setting-a-slash-on-cookie-path
-        return (self.app.config.cookie_path or url_for('/')).rstrip('/') or '/'
+        return (self.app.config.cookie_path or url_for("/")).rstrip("/") or "/"
 
-    def __update_session_cookie(self, name='galaxysession'):
+    def __update_session_cookie(self, name="galaxysession"):
         """
         Update the session cookie to match the current session.
         """
-        self.set_cookie(self.security.encode_guid(self.galaxy_session.session_key),
-                        name=name, path=self.cookie_path)
+        self.set_cookie(self.security.encode_guid(self.galaxy_session.session_key), name=name, path=self.cookie_path)
 
     def check_user_library_import_dir(self, user):
         if getattr(self.app.config, "user_library_import_dir_auto_creation", False):
@@ -679,12 +714,13 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             users_last_session = user.galaxy_sessions[0]
         except Exception:
             users_last_session = None
-        if (prev_galaxy_session
-                and prev_galaxy_session.current_history
-                and not prev_galaxy_session.current_history.deleted
-                and prev_galaxy_session.current_history.datasets
-                and (prev_galaxy_session.current_history.user is None
-                     or prev_galaxy_session.current_history.user == user)):
+        if (
+            prev_galaxy_session
+            and prev_galaxy_session.current_history
+            and not prev_galaxy_session.current_history.deleted
+            and prev_galaxy_session.current_history.datasets
+            and (prev_galaxy_session.current_history.user is None or prev_galaxy_session.current_history.user == user)
+        ):
             # If the previous galaxy session had a history, associate it with the new session, but only if it didn't
             # belong to a different user.
             history = prev_galaxy_session.current_history
@@ -697,9 +733,12 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
                 set_permissions = True
         elif self.galaxy_session.current_history:
             history = self.galaxy_session.current_history
-        if (not history and users_last_session
-                and users_last_session.current_history and not
-                users_last_session.current_history.deleted):
+        if (
+            not history
+            and users_last_session
+            and users_last_session.current_history
+            and not users_last_session.current_history.deleted
+        ):
             history = users_last_session.current_history
         elif not history:
             history = self.get_history(create=True, most_recent=True)
@@ -709,7 +748,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             history.user = user
         self.galaxy_session.current_history = history
         if set_permissions:
-            self.app.security_agent.history_set_default_permissions(history, dataset=True, bypass_manage_permission=True)
+            self.app.security_agent.history_set_default_permissions(
+                history, dataset=True, bypass_manage_permission=True
+            )
         self.sa_session.add_all((prev_galaxy_session, self.galaxy_session, history))
 
     def handle_user_login(self, user):
@@ -729,11 +770,11 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         prev_galaxy_session.is_valid = False
         # Define a new current_session
         self.galaxy_session = self.__create_new_session(prev_galaxy_session, user)
-        if self.webapp.name == 'galaxy':
-            cookie_name = 'galaxysession'
+        if self.webapp.name == "galaxy":
+            cookie_name = "galaxysession"
             self._associate_user_history(user, prev_galaxy_session)
         else:
-            cookie_name = 'galaxycommunitysession'
+            cookie_name = "galaxycommunitysession"
             self.sa_session.add_all((prev_galaxy_session, self.galaxy_session))
         self.sa_session.flush()
         # This method is not called from the Galaxy reports, so the cookie will always be galaxysession
@@ -751,18 +792,21 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         self.sa_session.add_all((prev_galaxy_session, self.galaxy_session))
         galaxy_user_id = prev_galaxy_session.user_id
         if logout_all and galaxy_user_id is not None:
-            for other_galaxy_session in (self.sa_session.query(self.app.model.GalaxySession)
-                                         .filter(and_(self.app.model.GalaxySession.table.c.user_id == galaxy_user_id,
-                                                      self.app.model.GalaxySession.table.c.is_valid == true(),
-                                                      self.app.model.GalaxySession.table.c.id != prev_galaxy_session.id))):
+            for other_galaxy_session in self.sa_session.query(self.app.model.GalaxySession).filter(
+                and_(
+                    self.app.model.GalaxySession.table.c.user_id == galaxy_user_id,
+                    self.app.model.GalaxySession.table.c.is_valid == true(),
+                    self.app.model.GalaxySession.table.c.id != prev_galaxy_session.id,
+                )
+            ):
                 other_galaxy_session.is_valid = False
                 self.sa_session.add(other_galaxy_session)
         self.sa_session.flush()
-        if self.webapp.name == 'galaxy':
+        if self.webapp.name == "galaxy":
             # This method is not called from the Galaxy reports, so the cookie will always be galaxysession
-            self.__update_session_cookie(name='galaxysession')
-        elif self.webapp.name == 'tool_shed':
-            self.__update_session_cookie(name='galaxycommunitysession')
+            self.__update_session_cookie(name="galaxysession")
+        elif self.webapp.name == "tool_shed":
+            self.__update_session_cookie(name="galaxycommunitysession")
 
     def get_galaxy_session(self):
         """
@@ -782,7 +826,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         """
         history = None
         if self.galaxy_session:
-            if hasattr(self.galaxy_session, 'current_history'):
+            if hasattr(self.galaxy_session, "current_history"):
                 history = self.galaxy_session.current_history
         if not history and most_recent:
             history = self.get_most_recent_history()
@@ -814,9 +858,8 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         # (b) has no datasets. If suitable history found, use it; otherwise, create
         # new history.
         unnamed_histories = self.sa_session.query(self.app.model.History).filter_by(
-            user=self.galaxy_session.user,
-            name=self.app.model.History.default_name,
-            deleted=False)
+            user=self.galaxy_session.user, name=self.app.model.History.default_name, deleted=False
+        )
         default_history = None
         for history in unnamed_histories:
             if len(history.datasets) == 0:
@@ -842,9 +885,12 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         if not self.galaxy_session.user:
             return None
         try:
-            recent_history = self.sa_session.query(self.app.model.History).filter_by(
-                user=self.galaxy_session.user,
-                deleted=False).order_by(self.app.model.History.update_time.desc()).first()
+            recent_history = (
+                self.sa_session.query(self.app.model.History)
+                .filter_by(user=self.galaxy_session.user, deleted=False)
+                .order_by(self.app.model.History.update_time.desc())
+                .first()
+            )
         except NoResultFound:
             return None
         self.set_history(recent_history)
@@ -884,18 +930,18 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         Convenience method for setting the 'message' and 'message_type'
         element of the template context.
         """
-        self.template_context['message'] = message
+        self.template_context["message"] = message
         if type:
-            self.template_context['status'] = type
+            self.template_context["status"] = type
 
     def get_message(self):
         """
         Convenience method for getting the 'message' element of the template
         context.
         """
-        return self.template_context['message']
+        return self.template_context["message"]
 
-    def show_message(self, message, type='info', refresh_frames=None, cont=None, use_panels=False, active_view=""):
+    def show_message(self, message, type="info", refresh_frames=None, cont=None, use_panels=False, active_view=""):
         """
         Convenience method for displaying a simple page with a single message.
 
@@ -906,36 +952,42 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
                           refreshed when the message is displayed
         """
         refresh_frames = refresh_frames or []
-        return self.fill_template("message.mako", status=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view)
+        return self.fill_template(
+            "message.mako",
+            status=type,
+            message=message,
+            refresh_frames=refresh_frames,
+            cont=cont,
+            use_panels=use_panels,
+            active_view=active_view,
+        )
 
     def show_error_message(self, message, refresh_frames=None, use_panels=False, active_view=""):
         """
         Convenience method for displaying an error message. See `show_message`.
         """
         refresh_frames = refresh_frames or []
-        return self.show_message(message, 'error', refresh_frames, use_panels=use_panels, active_view=active_view)
+        return self.show_message(message, "error", refresh_frames, use_panels=use_panels, active_view=active_view)
 
     def show_ok_message(self, message, refresh_frames=None, use_panels=False, active_view=""):
         """
         Convenience method for displaying an ok message. See `show_message`.
         """
         refresh_frames = refresh_frames or []
-        return self.show_message(message, 'done', refresh_frames, use_panels=use_panels, active_view=active_view)
+        return self.show_message(message, "done", refresh_frames, use_panels=use_panels, active_view=active_view)
 
     def show_warn_message(self, message, refresh_frames=None, use_panels=False, active_view=""):
         """
         Convenience method for displaying an warn message. See `show_message`.
         """
         refresh_frames = refresh_frames or []
-        return self.show_message(message, 'warning', refresh_frames, use_panels=use_panels, active_view=active_view)
+        return self.show_message(message, "warning", refresh_frames, use_panels=use_panels, active_view=active_view)
 
     @property
     def session_csrf_token(self):
-        token = ''
+        token = ""
         if self.galaxy_session:
-            token = self.security.encode_id(
-                self.galaxy_session.id, kind="csrf"
-            )
+            token = self.security.encode_id(self.galaxy_session.id, kind="csrf")
         return token
 
     def check_csrf_token(self, payload):
@@ -959,7 +1011,16 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         template_lookup = template_lookup or self.webapp.mako_template_lookup
         template = template_lookup.get_template(filename)
 
-        data = dict(caller=self, t=self, trans=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app)
+        data = dict(
+            caller=self,
+            t=self,
+            trans=self,
+            h=helpers,
+            util=util,
+            request=self.request,
+            response=self.response,
+            app=self.app,
+        )
         data.update(self.template_context)
         data.update(kwargs)
         return template.render(**data)
@@ -984,7 +1045,9 @@ def build_native_uwsgi_app(paste_factory, config_section):
 
 def build_url_map(app, global_conf, local_conf):
     from paste.urlmap import URLMap
+
     from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
+
     urlmap = URLMap()
     # Merge the global and local configurations
     conf = global_conf.copy()
@@ -1010,6 +1073,6 @@ def build_url_map(app, global_conf, local_conf):
     urlmap["/favicon.ico"] = get_static_from_config("static_favicon_dir", "static/favicon.ico")
     urlmap["/robots.txt"] = get_static_from_config("static_robots_txt", "static/robots.txt")
 
-    if 'static_local_dir' in conf:
+    if "static_local_dir" in conf:
         urlmap["/static_local"] = Static(conf["static_local_dir"], cache_time)
     return urlmap, cache_time
diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index bc08740bc52..c27c236a61c 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -24,13 +24,14 @@ from fastapi_utils.cbv import cbv
 from fastapi_utils.inferring_router import InferringRouter
 from pydantic.main import BaseModel
 from starlette.routing import NoMatchFound
+
 try:
     from starlette_context import context as request_context
 except ImportError:
     request_context = None  # type: ignore[assignment]
 
+from galaxy import app as galaxy_app
 from galaxy import (
-    app as galaxy_app,
     model,
     web,
 )
@@ -60,7 +61,7 @@ def get_app() -> StructuredApp:
 
 async def get_app_with_request_session() -> AsyncGenerator[StructuredApp, None]:
     app = get_app()
-    request_id = request_context.data['X-Request-ID']
+    request_id = request_context.data["X-Request-ID"]
     app.model.set_request_id(request_id)
     try:
         yield app
@@ -83,7 +84,6 @@ class GalaxyTypeDepends(Depends):
 
 
 def depends(dep_type: Type[T]) -> Any:
-
     def _do_resolve(request: Request):
         return get_app().resolve(dep_type)
 
@@ -95,9 +95,11 @@ def get_session_manager(app: StructuredApp = DependsOnApp) -> GalaxySessionManag
     return GalaxySessionManager(app.model)
 
 
-def get_session(session_manager: GalaxySessionManager = Depends(get_session_manager),
-                security: IdEncodingHelper = depends(IdEncodingHelper),
-                galaxysession: Optional[str] = Cookie(None)) -> Optional[model.GalaxySession]:
+def get_session(
+    session_manager: GalaxySessionManager = Depends(get_session_manager),
+    security: IdEncodingHelper = depends(IdEncodingHelper),
+    galaxysession: Optional[str] = Cookie(None),
+) -> Optional[model.GalaxySession]:
     if galaxysession:
         session_key = security.decode_guid(galaxysession)
         if session_key:
@@ -107,18 +109,18 @@ def get_session(session_manager: GalaxySessionManager = Depends(get_session_mana
 
 
 def get_api_user(
-        security: IdEncodingHelper = depends(IdEncodingHelper),
-        user_manager: UserManager = depends(UserManager),
-        key: Optional[str] = Query(None),
-        x_api_key: Optional[str] = Header(None),
-        run_as: Optional[EncodedDatabaseIdField] = Header(
-            default=None,
-            title='Run as User',
-            description=(
-                'The user ID that will be used to effectively make this API call. '
-                'Only admins and designated users can make API calls on behalf of other users.'
-            )
-        )
+    security: IdEncodingHelper = depends(IdEncodingHelper),
+    user_manager: UserManager = depends(UserManager),
+    key: Optional[str] = Query(None),
+    x_api_key: Optional[str] = Header(None),
+    run_as: Optional[EncodedDatabaseIdField] = Header(
+        default=None,
+        title="Run as User",
+        description=(
+            "The user ID that will be used to effectively make this API call. "
+            "Only admins and designated users can make API calls on behalf of other users."
+        ),
+    ),
 ) -> Optional[User]:
     api_key = key or x_api_key
     if not api_key:
@@ -136,14 +138,16 @@ def get_api_user(
     return user
 
 
-def get_user(galaxy_session: Optional[model.GalaxySession] = Depends(get_session), api_user: Optional[User] = Depends(get_api_user)) -> Optional[User]:
+def get_user(
+    galaxy_session: Optional[model.GalaxySession] = Depends(get_session),
+    api_user: Optional[User] = Depends(get_api_user),
+) -> Optional[User]:
     if galaxy_session:
         return galaxy_session.user
     return api_user
 
 
 class UrlBuilder:
-
     def __init__(self, request: Request):
         self.request = request
 
@@ -199,14 +203,19 @@ def get_current_history_from_session(galaxy_session: Optional[model.GalaxySessio
     return None
 
 
-def get_trans(request: Request, response: Response, app: StructuredApp = DependsOnApp, user: Optional[User] = Depends(get_user),
-              galaxy_session: Optional[model.GalaxySession] = Depends(get_session),
-              ) -> SessionRequestContext:
+def get_trans(
+    request: Request,
+    response: Response,
+    app: StructuredApp = DependsOnApp,
+    user: Optional[User] = Depends(get_user),
+    galaxy_session: Optional[model.GalaxySession] = Depends(get_session),
+) -> SessionRequestContext:
     url_builder = UrlBuilder(request)
     galaxy_request = GalaxyASGIRequest(request)
     galaxy_response = GalaxyASGIResponse(response)
     return SessionRequestContext(
-        app=app, user=user,
+        app=app,
+        user=user,
         galaxy_session=galaxy_session,
         url_builder=url_builder,
         request=galaxy_request,
@@ -228,14 +237,12 @@ AdminUserRequired = Depends(get_admin_user)
 
 
 class BaseGalaxyAPIController(BaseAPIController):
-
     def __init__(self, app: StructuredApp):
         super().__init__(app)
 
 
 class Router(InferringRouter):
-    """A FastAPI Inferring Router tailored to Galaxy.
-    """
+    """A FastAPI Inferring Router tailored to Galaxy."""
 
     def get(self, *args, **kwd):
         """Extend FastAPI.get to accept a require_admin Galaxy flag."""
@@ -293,8 +300,8 @@ def as_form(cls: Type[BaseModel]):
 
     sig = inspect.signature(_as_form)
     sig = sig.replace(parameters=new_params)
-    _as_form.__signature__ = sig    # type: ignore[attr-defined]
-    cls.as_form = _as_form          # type: ignore[attr-defined]
+    _as_form.__signature__ = sig  # type: ignore[attr-defined]
+    cls.as_form = _as_form  # type: ignore[attr-defined]
     return cls
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/_fetch_util.py b/lib/galaxy/webapps/galaxy/api/_fetch_util.py
index 9135e8cab4c..9da35e4b1ca 100644
--- a/lib/galaxy/webapps/galaxy/api/_fetch_util.py
+++ b/lib/galaxy/webapps/galaxy/api/_fetch_util.py
@@ -5,9 +5,7 @@ from galaxy.actions.library import (
     validate_path_upload,
     validate_server_directory_upload,
 )
-from galaxy.exceptions import (
-    RequestParameterInvalidException
-)
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.model.store.discover import (
     get_required_item,
     replace_request_syntax_sugar,
@@ -16,9 +14,7 @@ from galaxy.tools.actions.upload_common import (
     validate_datatype_extension,
     validate_url,
 )
-from galaxy.util import (
-    relpath,
-)
+from galaxy.util import relpath
 
 log = logging.getLogger(__name__)
 
@@ -55,9 +51,7 @@ def validate_and_normalize_targets(trans, payload):
             library_name = get_required_item(destination, "name", "Must specify a library name")
             description = destination.get("description", "")
             synopsis = destination.get("synopsis", "")
-            library = trans.app.library_manager.create(
-                trans, library_name, description=description, synopsis=synopsis
-            )
+            library = trans.app.library_manager.create(trans, library_name, description=description, synopsis=synopsis)
             destination["type"] = "library_folder"
             for key in ["name", "description", "synopsis"]:
                 if key in destination:
@@ -68,7 +62,7 @@ def validate_and_normalize_targets(trans, payload):
     # in_place and purge_source are set on the individual upload fetch sources as needed based
     # on this.
     run_as_real_user = trans.app.config.external_chown_script is not None  # See comment in upload.py
-    purge_ftp_source = getattr(trans.app.config, 'ftp_upload_purge', True) and not run_as_real_user
+    purge_ftp_source = getattr(trans.app.config, "ftp_upload_purge", True) and not run_as_real_user
 
     payload["check_content"] = trans.app.config.check_upload_content
 
@@ -76,7 +70,7 @@ def validate_and_normalize_targets(trans, payload):
         if "object_id" in item:
             raise RequestParameterInvalidException("object_id not allowed to appear in the request.")
 
-        validate_datatype_extension(datatypes_registry=trans.app.datatypes_registry, ext=item.get('ext'))
+        validate_datatype_extension(datatypes_registry=trans.app.datatypes_registry, ext=item.get("ext"))
 
         # Normalize file:// URLs into paths.
         if item["src"] == "url":
@@ -86,7 +80,7 @@ def validate_and_normalize_targets(trans, payload):
             url = item["url"]
             if url.startswith("file://"):
                 item["src"] = "path"
-                item["path"] = url[len("file://"):]
+                item["path"] = url[len("file://") :]
                 del item["url"]
 
         if "in_place" in item:
@@ -154,7 +148,9 @@ def validate_and_normalize_targets(trans, payload):
                                 break
 
             if not full_path:
-                raise RequestParameterInvalidException("Failed to find referenced ftp_path or symbolic link was enountered")
+                raise RequestParameterInvalidException(
+                    "Failed to find referenced ftp_path or symbolic link was enountered"
+                )
 
             item["src"] = "path"
             item["path"] = full_path
@@ -197,7 +193,9 @@ def _handle_invalid_link_data_only_type(item):
 def _handle_invalid_link_data_only_elements_type(item):
     link_data_only = item.get("link_data_only", False)
     if link_data_only and item.get("elements_from", False) in ELEMENTS_FROM_TRANSIENT_TYPES:
-        raise RequestParameterInvalidException(f"link_data_only is invalid for derived elements from [{item.get('elements_from')}]")
+        raise RequestParameterInvalidException(
+            f"link_data_only is invalid for derived elements from [{item.get('elements_from')}]"
+        )
 
 
 def _for_each_src(f, obj):
diff --git a/lib/galaxy/webapps/galaxy/api/annotations.py b/lib/galaxy/webapps/galaxy/api/annotations.py
index 5f93f54db51..bacfc79f034 100644
--- a/lib/galaxy/webapps/galaxy/api/annotations.py
+++ b/lib/galaxy/webapps/galaxy/api/annotations.py
@@ -6,16 +6,17 @@ from abc import abstractmethod
 
 from galaxy import (
     exceptions,
-    managers
+    managers,
 )
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import expose_api
-from galaxy.webapps.base.controller import (
-    UsesStoredWorkflowMixin
+from galaxy.webapps.base.controller import UsesStoredWorkflowMixin
+from . import (
+    BaseGalaxyAPIController,
+    depends,
 )
-from . import BaseGalaxyAPIController, depends
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py
index b8b96fe0dc5..b35060acbde 100644
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -22,7 +22,7 @@ from urllib.parse import unquote
 from galaxy import exceptions
 from galaxy.util import (
     smart_str,
-    unicodify
+    unicodify,
 )
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.webapps.base.webapp import GalaxyWebTransaction
@@ -32,7 +32,6 @@ log = logging.getLogger(__name__)
 
 
 class AuthenticationController(BaseGalaxyAPIController):
-
     @expose_api_anonymous_and_sessionless
     def options(self, trans: GalaxyWebTransaction, **kwd):
         """
@@ -41,8 +40,8 @@ class AuthenticationController(BaseGalaxyAPIController):
         Right now this is solely to inform preflight CORS checks, which are API wide.
         Might be better placed elsewhere, but for now this is the initial entrypoint for relevant consumers.
         """
-        trans.response.headers['Access-Control-Allow-Headers'] = '*'
-        trans.response.headers['Access-Control-Max-Age'] = 600
+        trans.response.headers["Access-Control-Allow-Headers"] = "*"
+        trans.response.headers["Access-Control-Max-Age"] = 600
         # No need to set allow-methods for preflight cors check, I don't think.
         # When this is actually granular, endpoints should *probably* respond appropriately.
         # trans.response.headers['Access-Control-Allow-Methods'] = 'POST, PUT, GET, OPTIONS, DELETE'
@@ -58,17 +57,17 @@ class AuthenticationController(BaseGalaxyAPIController):
 
         :raises: ObjectNotFound, HTTPBadRequest
         """
-        identity, password = self._decode_baseauth(trans.environ.get('HTTP_AUTHORIZATION'))
+        identity, password = self._decode_baseauth(trans.environ.get("HTTP_AUTHORIZATION"))
         # check if this is an email address or username
         user = self.app.user_manager.get_user_by_identity(identity)
         if not user:
-            raise exceptions.ObjectNotFound('The user does not exist.')
+            raise exceptions.ObjectNotFound("The user does not exist.")
         is_valid_user = self.app.auth_manager.check_password(user, password)
         if is_valid_user:
             key = self.app.api_keys_manager.get_or_create_api_key(user)
             return dict(api_key=key)
         else:
-            raise exceptions.AuthenticationFailed('Invalid password.')
+            raise exceptions.AuthenticationFailed("Invalid password.")
 
     def _decode_baseauth(self, encoded_str):
         """
@@ -87,15 +86,15 @@ class AuthenticationController(BaseGalaxyAPIController):
         :raises: HTTPBadRequest
         """
         try:
-            split = encoded_str.strip().split(' ')
+            split = encoded_str.strip().split(" ")
         except AttributeError:
-            raise exceptions.RequestParameterInvalidException('Authentication is missing')
+            raise exceptions.RequestParameterInvalidException("Authentication is missing")
 
         # If split is only one element, try to decode the email and password
         # directly.
         if len(split) == 1:
             try:
-                email, password = unicodify(b64decode(smart_str(split[0]))).split(':')
+                email, password = unicodify(b64decode(smart_str(split[0]))).split(":")
             except Exception as e:
                 raise exceptions.ActionInputError(e)
 
@@ -103,9 +102,9 @@ class AuthenticationController(BaseGalaxyAPIController):
         # 'basic' so that we know we're about to decode the right thing. If not,
         # bail out.
         elif len(split) == 2:
-            if split[0].strip().lower() == 'basic':
+            if split[0].strip().lower() == "basic":
                 try:
-                    email, password = unicodify(b64decode(smart_str(split[1]))).split(':')
+                    email, password = unicodify(b64decode(smart_str(split[1]))).split(":")
                 except Exception:
                     raise exceptions.ActionInputError()
             else:
diff --git a/lib/galaxy/webapps/galaxy/api/cloud.py b/lib/galaxy/webapps/galaxy/api/cloud.py
index fd81b6654b2..2d1c2c1a580 100644
--- a/lib/galaxy/webapps/galaxy/api/cloud.py
+++ b/lib/galaxy/webapps/galaxy/api/cloud.py
@@ -8,7 +8,7 @@ from galaxy import exceptions
 from galaxy.exceptions import ActionInputError
 from galaxy.managers import (
     cloud,
-    datasets
+    datasets,
 )
 from galaxy.structured_app import StructuredApp
 from galaxy.web import expose_api
@@ -22,7 +22,9 @@ class CloudController(BaseGalaxyAPIController):
     RESTfull controller for interaction with Amazon S3.
     """
 
-    def __init__(self, app: StructuredApp, cloud_manager: cloud.CloudManager, datasets_serializer: datasets.DatasetSerializer):
+    def __init__(
+        self, app: StructuredApp, cloud_manager: cloud.CloudManager, datasets_serializer: datasets.DatasetSerializer
+    ):
         super().__init__(app)
         self.cloud_manager = cloud_manager
         self.datasets_serializer = datasets_serializer
@@ -38,7 +40,7 @@ class CloudController(BaseGalaxyAPIController):
         """
         # TODO: This can be implemented leveraging PluggedMedia objects (part of the user-based object store project)
         trans.response.status = 501
-        return 'Not Implemented'
+        return "Not Implemented"
 
     @expose_api
     def get(self, trans, payload, **kwargs):
@@ -91,8 +93,10 @@ class CloudController(BaseGalaxyAPIController):
 
         """
         if not isinstance(payload, dict):
-            raise ActionInputError('Invalid payload data type. The payload is expected to be a dictionary, '
-                                   'but received data of type `{}`.'.format(str(type(payload))))
+            raise ActionInputError(
+                "Invalid payload data type. The payload is expected to be a dictionary, "
+                "but received data of type `{}`.".format(str(type(payload)))
+            )
 
         missing_arguments = []
         encoded_history_id = payload.get("history_id", None)
@@ -117,26 +121,29 @@ class CloudController(BaseGalaxyAPIController):
         try:
             history_id = self.decode_id(encoded_history_id)
         except exceptions.MalformedId as e:
-            raise ActionInputError(f'Invalid history ID. {e}')
+            raise ActionInputError(f"Invalid history ID. {e}")
 
         try:
             authz_id = self.decode_id(encoded_authz_id)
         except exceptions.MalformedId as e:
-            raise ActionInputError(f'Invalid authz ID. {e}')
+            raise ActionInputError(f"Invalid authz ID. {e}")
 
         if not isinstance(objects, list):
-            raise ActionInputError('The `objects` should be a list, but received an object of type {} instead.'.format(
-                type(objects)))
+            raise ActionInputError(
+                "The `objects` should be a list, but received an object of type {} instead.".format(type(objects))
+            )
 
-        datasets = self.cloud_manager.get(trans=trans,
-                                          history_id=history_id,
-                                          bucket_name=bucket,
-                                          objects=objects,
-                                          authz_id=authz_id,
-                                          input_args=payload.get("input_args", None))
+        datasets = self.cloud_manager.get(
+            trans=trans,
+            history_id=history_id,
+            bucket_name=bucket,
+            objects=objects,
+            authz_id=authz_id,
+            input_args=payload.get("input_args", None),
+        )
         rtv = []
         for dataset in datasets:
-            rtv.append(self.datasets_serializer.serialize_to_view(dataset, view='summary'))
+            rtv.append(self.datasets_serializer.serialize_to_view(dataset, view="summary"))
         return rtv
 
     @expose_api
@@ -208,12 +215,12 @@ class CloudController(BaseGalaxyAPIController):
         try:
             history_id = self.decode_id(encoded_history_id)
         except exceptions.MalformedId as e:
-            raise ActionInputError(f'Invalid history ID. {e}')
+            raise ActionInputError(f"Invalid history ID. {e}")
 
         try:
             authz_id = self.decode_id(encoded_authz_id)
         except exceptions.MalformedId as e:
-            raise ActionInputError(f'Invalid authz ID. {e}')
+            raise ActionInputError(f"Invalid authz ID. {e}")
 
         encoded_dataset_ids = payload.get("dataset_ids", None)
         if encoded_dataset_ids is None:
@@ -227,20 +234,24 @@ class CloudController(BaseGalaxyAPIController):
                 except exceptions.MalformedId:
                     invalid_dataset_ids.append(encoded_id)
             if len(invalid_dataset_ids) > 0:
-                raise ActionInputError("The following provided dataset IDs are invalid, please correct them and retry. "
-                                       "{}".format(invalid_dataset_ids))
+                raise ActionInputError(
+                    "The following provided dataset IDs are invalid, please correct them and retry. "
+                    "{}".format(invalid_dataset_ids)
+                )
 
-        log.info(msg="Received api/send request for `{}` datasets using authnz with id `{}`, and history `{}`."
-                     "".format("all the dataset in the given history" if not dataset_ids else len(dataset_ids),
-                               authz_id,
-                               history_id))
+        log.info(
+            msg="Received api/send request for `{}` datasets using authnz with id `{}`, and history `{}`."
+            "".format(
+                "all the dataset in the given history" if not dataset_ids else len(dataset_ids), authz_id, history_id
+            )
+        )
 
-        sent, failed = self.cloud_manager.send(trans=trans,
-                                               history_id=history_id,
-                                               bucket_name=bucket,
-                                               authz_id=authz_id,
-                                               dataset_ids=dataset_ids,
-                                               overwrite_existing=payload.get("overwrite_existing", False))
-        return {'sent_dataset_labels': sent,
-                'failed_dataset_labels': failed,
-                'bucket_name': bucket}
+        sent, failed = self.cloud_manager.send(
+            trans=trans,
+            history_id=history_id,
+            bucket_name=bucket,
+            authz_id=authz_id,
+            dataset_ids=dataset_ids,
+            overwrite_existing=payload.get("overwrite_existing", False),
+        )
+        return {"sent_dataset_labels": sent, "failed_dataset_labels": failed, "bucket_name": bucket}
diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
index a14469a6fe3..a9573c17f14 100644
--- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py
+++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
@@ -15,14 +15,12 @@ from galaxy.exceptions import (
     InternalServerError,
     MalformedId,
     RequestParameterInvalidException,
-    RequestParameterMissingException
+    RequestParameterMissingException,
 )
 from galaxy.managers import cloudauthzs
 from galaxy.structured_app import StructuredApp
 from galaxy.util import unicodify
-from galaxy.web import (
-    expose_api
-)
+from galaxy.web import expose_api
 from . import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
@@ -56,8 +54,11 @@ class CloudAuthzController(BaseGalaxyAPIController):
         """
         rtv = []
         for cloudauthz in trans.user.cloudauthz:
-            rtv.append(self.cloudauthz_serializer.serialize_to_view(
-                cloudauthz, user=trans.user, trans=trans, **self._parse_serialization_params(kwargs, 'summary')))
+            rtv.append(
+                self.cloudauthz_serializer.serialize_to_view(
+                    cloudauthz, user=trans.user, trans=trans, **self._parse_serialization_params(kwargs, "summary")
+                )
+            )
         return rtv
 
     @expose_api
@@ -93,33 +94,38 @@ class CloudAuthzController(BaseGalaxyAPIController):
         """
         msg_template = f"Rejected user `{str(trans.user.id)}`'s request to create cloudauthz config because of {{}}."
         if not isinstance(payload, dict):
-            raise ActionInputError('Invalid payload data type. The payload is expected to be a dictionary, but '
-                                   'received data of type `{}`.'.format(str(type(payload))))
+            raise ActionInputError(
+                "Invalid payload data type. The payload is expected to be a dictionary, but "
+                "received data of type `{}`.".format(str(type(payload)))
+            )
 
         missing_arguments = []
-        provider = payload.get('provider', None)
+        provider = payload.get("provider", None)
         if provider is None:
-            missing_arguments.append('provider')
+            missing_arguments.append("provider")
 
-        config = payload.get('config', None)
+        config = payload.get("config", None)
         if config is None:
-            missing_arguments.append('config')
+            missing_arguments.append("config")
 
-        authn_id = payload.get('authn_id', None)
+        authn_id = payload.get("authn_id", None)
         if authn_id is None and provider.lower() not in ["azure", "gcp"]:
-            missing_arguments.append('authn_id')
+            missing_arguments.append("authn_id")
 
         if len(missing_arguments) > 0:
             log.debug(msg_template.format(f"missing required config {missing_arguments}"))
-            raise RequestParameterMissingException('The following required arguments are missing in the payload: '
-                                                   '{}'.format(missing_arguments))
+            raise RequestParameterMissingException(
+                "The following required arguments are missing in the payload: " "{}".format(missing_arguments)
+            )
 
         description = payload.get("description", "")
 
         if not isinstance(config, dict):
             log.debug(msg_template.format(f"invalid config type `{type(config)}`, expect `dict`"))
-            raise RequestParameterInvalidException('Invalid type for the required `config` variable; expect `dict` '
-                                                   'but received `{}`.'.format(type(config)))
+            raise RequestParameterInvalidException(
+                "Invalid type for the required `config` variable; expect `dict` "
+                "but received `{}`.".format(type(config))
+            )
         if authn_id:
             try:
                 decoded_authn_id = self.decode_id(authn_id)
@@ -136,25 +142,27 @@ class CloudAuthzController(BaseGalaxyAPIController):
         # exact same key/value should exist.
         for ca in trans.user.cloudauthz:
             if ca.equals(trans.user.id, provider, authn_id, config):
-                log.debug("Rejected user `{}`'s request to create cloud authorization because a similar config "
-                          "already exists.".format(trans.user.id))
+                log.debug(
+                    "Rejected user `{}`'s request to create cloud authorization because a similar config "
+                    "already exists.".format(trans.user.id)
+                )
                 raise ActionInputError("A similar cloud authorization configuration is already defined.")
 
         try:
             new_cloudauthz = self.cloudauthz_manager.create(
-                user_id=trans.user.id,
-                provider=provider,
-                config=config,
-                authn_id=authn_id,
-                description=description
+                user_id=trans.user.id, provider=provider, config=config, authn_id=authn_id, description=description
             )
-            view = self.cloudauthz_serializer.serialize_to_view(new_cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, 'summary'))
-            log.debug(f'Created a new cloudauthz record for the user id `{str(trans.user.id)}` ')
+            view = self.cloudauthz_serializer.serialize_to_view(
+                new_cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, "summary")
+            )
+            log.debug(f"Created a new cloudauthz record for the user id `{str(trans.user.id)}` ")
             return view
         except Exception as e:
             log.exception(msg_template.format("exception while creating the new cloudauthz record"))
-            raise InternalServerError('An unexpected error has occurred while responding to the create request of the '
-                                      'cloudauthz API.' + unicodify(e))
+            raise InternalServerError(
+                "An unexpected error has occurred while responding to the create request of the "
+                "cloudauthz API." + unicodify(e)
+            )
 
     @expose_api
     def delete(self, trans, encoded_authz_id, **kwargs):
@@ -183,15 +191,22 @@ class CloudAuthzController(BaseGalaxyAPIController):
             cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
             trans.sa_session.delete(cloudauthz)
             trans.sa_session.flush()
-            log.debug(f'Deleted a cloudauthz record with id `{authz_id}` for the user id `{str(trans.user.id)}` ')
-            view = self.cloudauthz_serializer.serialize_to_view(cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, 'summary'))
-            trans.response.status = '200'
+            log.debug(f"Deleted a cloudauthz record with id `{authz_id}` for the user id `{str(trans.user.id)}` ")
+            view = self.cloudauthz_serializer.serialize_to_view(
+                cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, "summary")
+            )
+            trans.response.status = "200"
             return view
         except Exception as e:
-            log.exception(msg_template.format("exception while deleting the cloudauthz record with "
-                                              "ID: `{}`.".format(encoded_authz_id)))
-            raise InternalServerError('An unexpected error has occurred while responding to the DELETE request of the '
-                                      'cloudauthz API.' + unicodify(e))
+            log.exception(
+                msg_template.format(
+                    "exception while deleting the cloudauthz record with " "ID: `{}`.".format(encoded_authz_id)
+                )
+            )
+            raise InternalServerError(
+                "An unexpected error has occurred while responding to the DELETE request of the "
+                "cloudauthz API." + unicodify(e)
+            )
 
     @expose_api
     def update(self, trans, encoded_authz_id, payload, **kwargs):
@@ -244,14 +259,21 @@ class CloudAuthzController(BaseGalaxyAPIController):
             raise e
 
         try:
-            cloudauthz_to_update = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
+            cloudauthz_to_update = trans.app.authnz_manager.try_get_authz_config(
+                trans.sa_session, trans.user.id, authz_id
+            )
             self.cloudauthz_deserializer.deserialize(cloudauthz_to_update, payload, trans=trans)
-            self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view='summary')
-            return self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view='summary')
+            self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view="summary")
+            return self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view="summary")
         except MalformedId as e:
             raise e
         except Exception as e:
-            log.exception(msg_template.format("exception while updating the cloudauthz record with "
-                                              "ID: `{}`.".format(encoded_authz_id)))
-            raise InternalServerError('An unexpected error has occurred while responding to the PUT request of the '
-                                      'cloudauthz API.' + unicodify(e))
+            log.exception(
+                msg_template.format(
+                    "exception while updating the cloudauthz record with " "ID: `{}`.".format(encoded_authz_id)
+                )
+            )
+            raise InternalServerError(
+                "An unexpected error has occurred while responding to the PUT request of the "
+                "cloudauthz API." + unicodify(e)
+            )
diff --git a/lib/galaxy/webapps/galaxy/api/common.py b/lib/galaxy/webapps/galaxy/api/common.py
index be66dddedff..ae651fb0ea5 100644
--- a/lib/galaxy/webapps/galaxy/api/common.py
+++ b/lib/galaxy/webapps/galaxy/api/common.py
@@ -20,20 +20,20 @@ from galaxy.schema.schema import UpdateDatasetPermissionsPayload
 
 SerializationViewQueryParam: Optional[str] = Query(
     None,
-    title='View',
-    description='View to be passed to the serializer',
+    title="View",
+    description="View to be passed to the serializer",
 )
 
 SerializationKeysQueryParam: Optional[str] = Query(
     None,
-    title='Keys',
-    description='Comma-separated list of keys to be passed to the serializer',
+    title="Keys",
+    description="Comma-separated list of keys to be passed to the serializer",
 )
 
 SerializationDefaultViewQueryParam: Optional[str] = Query(
     None,
-    title='Default View',
-    description='The item view that will be used in case no particular view was specified.',
+    title="Default View",
+    description="The item view that will be used in case no particular view was specified.",
 )
 
 
@@ -45,7 +45,7 @@ def parse_serialization_params(
 ) -> SerializationParams:
     key_list = None
     if keys:
-        key_list = keys.split(',')
+        key_list = keys.split(",")
     return SerializationParams(view=view, keys=key_list, default_view=default_view)
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py
index 439a31f35e2..714808f5f44 100644
--- a/lib/galaxy/webapps/galaxy/api/configuration.py
+++ b/lib/galaxy/webapps/galaxy/api/configuration.py
@@ -7,24 +7,20 @@ from typing import (
     Any,
     Dict,
     List,
-    Optional
+    Optional,
 )
 
 from fastapi import Path
 
 from galaxy.managers.configuration import ConfigurationManager
-from galaxy.managers.context import (
-    ProvidesUserContext,
-)
-from galaxy.managers.users import (
-    UserManager,
-)
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.users import UserManager
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.schema.schema import UserModel
 from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
-    require_admin
+    require_admin,
 )
 from . import (
     BaseGalaxyAPIController,
@@ -40,13 +36,13 @@ from .common import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['configuration'])
+router = Router(tags=["configuration"])
 
 
 EncodedIdPathParam: EncodedDatabaseIdField = Path(
     ...,
-    title='Encoded id',
-    description='Encoded id to be decoded',
+    title="Encoded id",
+    description="Encoded id to be decoded",
 )
 
 
@@ -55,18 +51,18 @@ class FastAPIConfiguration:
     configuration_manager: ConfigurationManager = depends(ConfigurationManager)
 
     @router.get(
-        '/api/whoami',
+        "/api/whoami",
         summary="Return information about the current authenticated user",
-        response_description="Information about the current authenticated user"
+        response_description="Information about the current authenticated user",
     )
     def whoami(self, trans: ProvidesUserContext = DependsOnTrans) -> Optional[UserModel]:
         """Return information about the current authenticated user."""
         return _user_to_model(trans.user, trans.security)
 
     @router.get(
-        '/api/configuration',
+        "/api/configuration",
         summary="Return an object containing exposable configuration settings",
-        response_description="Object containing exposable configuration settings"
+        response_description="Object containing exposable configuration settings",
     )
     def index(
         self,
@@ -84,51 +80,46 @@ class FastAPIConfiguration:
         return _index(self.configuration_manager, trans, view, keys)
 
     @router.get(
-        '/api/version',
+        "/api/version",
         summary="Return Galaxy version information: major/minor version, optional extra info",
-        response_description="Galaxy version information: major/minor version, optional extra info"
+        response_description="Galaxy version information: major/minor version, optional extra info",
     )
     def version(self) -> Dict[str, Any]:
         """Return Galaxy version information: major/minor version, optional extra info."""
         return self.configuration_manager.version()
 
     @router.get(
-        '/api/configuration/dynamic_tool_confs',
+        "/api/configuration/dynamic_tool_confs",
         require_admin=True,
         summary="Return dynamic tool configuration files",
-        response_description="Dynamic tool configuration files"
+        response_description="Dynamic tool configuration files",
     )
     def dynamic_tool_confs(self) -> List[Dict[str, str]]:
         """Return dynamic tool configuration files."""
         return self.configuration_manager.dynamic_tool_confs()
 
     @router.get(
-        '/api/configuration/decode/{encoded_id}',
+        "/api/configuration/decode/{encoded_id}",
         require_admin=True,
         summary="Decode a given id",
-        response_description="Decoded id"
+        response_description="Decoded id",
     )
-    def decode_id(
-        self,
-        encoded_id: EncodedDatabaseIdField = EncodedIdPathParam
-    ) -> Dict[str, int]:
+    def decode_id(self, encoded_id: EncodedDatabaseIdField = EncodedIdPathParam) -> Dict[str, int]:
         """Decode a given id."""
         return self.configuration_manager.decode_id(encoded_id)
 
     @router.get(
-        '/api/configuration/tool_lineages',
+        "/api/configuration/tool_lineages",
         require_admin=True,
         summary="Return tool lineages for tools that have them",
-        response_description="Tool lineages for tools that have them"
+        response_description="Tool lineages for tools that have them",
     )
     def tool_lineages(self) -> List[Dict[str, Dict]]:
         """Return tool lineages for tools that have them."""
         return self.configuration_manager.tool_lineages()
 
     @router.put(
-        '/api/configuration/toolbox',
-        require_admin=True,
-        summary="Reload the Galaxy toolbox (but not individual tools)"
+        "/api/configuration/toolbox", require_admin=True, summary="Reload the Galaxy toolbox (but not individual tools)"
     )
     def reload_toolbox(self):
         """Reload the Galaxy toolbox (but not individual tools)."""
@@ -201,14 +192,14 @@ class ConfigurationController(BaseGalaxyAPIController):
 
     def get_config_dict(self, trans, **kwd):
         """Return an object containing exposable configuration settings."""
-        view, keys = kwd.get('view'), kwd.get('keys')
+        view, keys = kwd.get("view"), kwd.get("keys")
         return _index(self.configuration_manager, trans, view, keys)
 
 
 def _user_to_model(user, security):
-    return UserModel(**user.to_dict(view='element', value_mapper={'id': security.encode_id})) if user else None
+    return UserModel(**user.to_dict(view="element", value_mapper={"id": security.encode_id})) if user else None
 
 
 def _index(manager: ConfigurationManager, trans, view, keys):
-    serialization_params = parse_serialization_params(view, keys, 'all')
+    serialization_params = parse_serialization_params(view, keys, "all")
     return manager.get_configuration(trans, serialization_params)
diff --git a/lib/galaxy/webapps/galaxy/api/container_resolution.py b/lib/galaxy/webapps/galaxy/api/container_resolution.py
index 208c1195505..07b9a9edaa3 100644
--- a/lib/galaxy/webapps/galaxy/api/container_resolution.py
+++ b/lib/galaxy/webapps/galaxy/api/container_resolution.py
@@ -9,7 +9,7 @@ from galaxy.structured_app import StructuredApp
 from galaxy.tool_util.deps import views
 from galaxy.web import (
     expose_api,
-    require_admin
+    require_admin,
 )
 from . import BaseGalaxyAPIController
 
@@ -17,7 +17,6 @@ log = logging.getLogger(__name__)
 
 
 class ContainerResolutionAPIController(BaseGalaxyAPIController):
-
     def __init__(self, app: StructuredApp):
         super().__init__(app)
         self._view = views.ContainerResolutionView(app)
@@ -65,7 +64,7 @@ class ContainerResolutionAPIController(BaseGalaxyAPIController):
         :returns:   a dictified description of the container dependency, with attribute
                     ``dependency_type: None`` if no match was found.
         """
-        kwds['session'] = requests.session()
+        kwds["session"] = requests.session()
         return self._view.resolve(index=index, **kwds)
 
     @expose_api
@@ -85,7 +84,7 @@ class ContainerResolutionAPIController(BaseGalaxyAPIController):
         :rtype:     list
         :returns:   list of items returned from resolve()
         """
-        kwds['session'] = requests.session()
+        kwds["session"] = requests.session()
         return self._view.resolve_toolbox(**kwds)
 
     @expose_api
@@ -104,7 +103,7 @@ class ContainerResolutionAPIController(BaseGalaxyAPIController):
         """
         kwds.update(payload)
         kwds["install"] = True
-        kwds['session'] = requests.session()
+        kwds["session"] = requests.session()
         return self._view.resolve_toolbox(**kwds)
 
     @expose_api
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index b817ca85461..c9c4ee8bf42 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -1,7 +1,11 @@
 from logging import getLogger
 from typing import Optional
 
-from fastapi import Body, Path, Query
+from fastapi import (
+    Body,
+    Path,
+    Query,
+)
 
 from galaxy import exceptions
 from galaxy.managers.context import ProvidesHistoryContext
@@ -24,21 +28,20 @@ from . import (
     BaseGalaxyAPIController,
     depends,
     DependsOnTrans,
-    Router
+    Router,
 )
 
 log = getLogger(__name__)
 
-router = Router(tags=['dataset collections'])
+router = Router(tags=["dataset collections"])
 
 DatasetCollectionIdPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    description="The encoded identifier of the dataset collection."
+    ..., description="The encoded identifier of the dataset collection."
 )
 
 InstanceTypeQueryParam: DatasetCollectionInstanceType = Query(
     default=DatasetCollectionInstanceType.history,
-    description="The type of collection instance. Either `history` (default) or `library`."
+    description="The type of collection instance. Either `history` (default) or `library`.",
 )
 
 
@@ -47,7 +50,7 @@ class FastAPIDatasetCollections:
     service: DatasetCollectionsService = depends(DatasetCollectionsService)
 
     @router.post(
-        '/api/dataset_collections',
+        "/api/dataset_collections",
         summary="Create a new dataset collection instance.",
     )
     def create(
@@ -58,7 +61,7 @@ class FastAPIDatasetCollections:
         return self.service.create(trans, payload)
 
     @router.post(
-        '/api/dataset_collections/{id}/copy',
+        "/api/dataset_collections/{id}/copy",
         summary="Copy the given collection datasets to a new collection using a new `dbkey` attribute.",
     )
     def copy(
@@ -70,7 +73,7 @@ class FastAPIDatasetCollections:
         self.service.copy(trans, id, payload)
 
     @router.get(
-        '/api/dataset_collections/{id}/attributes',
+        "/api/dataset_collections/{id}/attributes",
         summary="Returns `dbkey`/`extension` attributes for all the collection elements.",
     )
     def attributes(
@@ -82,7 +85,7 @@ class FastAPIDatasetCollections:
         return self.service.attributes(trans, id, instance_type)
 
     @router.get(
-        '/api/dataset_collections/{id}/suitable_converters',
+        "/api/dataset_collections/{id}/suitable_converters",
         summary="Returns a list of applicable converters for all datatypes in the given collection.",
     )
     def suitable_converters(
@@ -94,7 +97,7 @@ class FastAPIDatasetCollections:
         return self.service.suitable_converters(trans, id, instance_type)
 
     @router.get(
-        '/api/dataset_collections/{id}',
+        "/api/dataset_collections/{id}",
         summary="Returns detailed information about the given collection.",
     )
     def show(
@@ -106,7 +109,7 @@ class FastAPIDatasetCollections:
         return self.service.show(trans, id, instance_type)
 
     @router.get(
-        '/api/dataset_collections/{hdca_id}/contents/{parent_id}',
+        "/api/dataset_collections/{hdca_id}/contents/{parent_id}",
         name="contents_dataset_collection",
         summary="Returns direct child contents of indicated dataset collection parent ID.",
     )
@@ -169,7 +172,7 @@ class DatasetCollectionsController(BaseGalaxyAPIController):
         self.service.copy(trans, id, update_payload)
 
     @expose_api
-    def attributes(self, trans: ProvidesHistoryContext, id, instance_type='history'):
+    def attributes(self, trans: ProvidesHistoryContext, id, instance_type="history"):
         """
         GET /api/dataset_collections/{hdca_id}/attributes
 
@@ -178,7 +181,7 @@ class DatasetCollectionsController(BaseGalaxyAPIController):
         return self.service.attributes(trans, id, instance_type)
 
     @expose_api
-    def suitable_converters(self, trans: ProvidesHistoryContext, id, instance_type='history', **kwds):
+    def suitable_converters(self, trans: ProvidesHistoryContext, id, instance_type="history", **kwds):
         """
         GET /api/dataset_collections/{hdca_id}/suitable_converters
 
@@ -187,7 +190,7 @@ class DatasetCollectionsController(BaseGalaxyAPIController):
         return self.service.suitable_converters(trans, id, instance_type)
 
     @expose_api
-    def show(self, trans: ProvidesHistoryContext, id, instance_type='history', **kwds):
+    def show(self, trans: ProvidesHistoryContext, id, instance_type="history", **kwds):
         """
         GET /api/dataset_collections/{hdca_id}
         GET /api/dataset_collections/{ldca_id}?instance_type=library
@@ -195,7 +198,16 @@ class DatasetCollectionsController(BaseGalaxyAPIController):
         return self.service.show(trans, id, instance_type)
 
     @expose_api
-    def contents(self, trans: ProvidesHistoryContext, hdca_id, parent_id, instance_type='history', limit=None, offset=None, **kwds):
+    def contents(
+        self,
+        trans: ProvidesHistoryContext,
+        hdca_id,
+        parent_id,
+        instance_type="history",
+        limit=None,
+        offset=None,
+        **kwds,
+    ):
         """
         GET /api/dataset_collection/{hdca_id}/contents/{parent_id}?limit=100&offset=0
 
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 2ef05428573..d159ae96110 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -62,17 +62,11 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['datasets'])
+router = Router(tags=["datasets"])
 
-DatasetIDPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    description="The encoded database identifier of the dataset."
-)
+DatasetIDPathParam: EncodedDatabaseIdField = Path(..., description="The encoded database identifier of the dataset.")
 
-HistoryIDPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    description="The encoded database identifier of the History."
-)
+HistoryIDPathParam: EncodedDatabaseIdField = Path(..., description="The encoded database identifier of the History.")
 
 DatasetSourceQueryParam: DatasetSourceType = Query(
     default=DatasetSourceType.hda,
@@ -85,15 +79,15 @@ class FastAPIDatasets:
     service: DatasetsService = depends(DatasetsService)
 
     @router.get(
-        '/api/datasets',
-        summary='Search datasets or collections using a query system.',
+        "/api/datasets",
+        summary="Search datasets or collections using a query system.",
     )
     def index(
         self,
         trans=DependsOnTrans,
         history_id: Optional[EncodedDatabaseIdField] = Query(
             default=None,
-            description="Optional identifier of a History. Use it to restrict the search whithin a particular History."
+            description="Optional identifier of a History. Use it to restrict the search whithin a particular History.",
         ),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
@@ -101,8 +95,8 @@ class FastAPIDatasets:
         return self.service.index(trans, history_id, serialization_params, filter_query_params)
 
     @router.get(
-        '/api/datasets/{dataset_id}/storage',
-        summary='Display user-facing storage details related to the objectstore a dataset resides in.',
+        "/api/datasets/{dataset_id}/storage",
+        summary="Display user-facing storage details related to the objectstore a dataset resides in.",
     )
     def show_storage(
         self,
@@ -113,8 +107,8 @@ class FastAPIDatasets:
         return self.service.show_storage(trans, dataset_id, hda_ldda)
 
     @router.get(
-        '/api/datasets/{dataset_id}/inheritance_chain',
-        summary='For internal use, this endpoint may change without warning.',
+        "/api/datasets/{dataset_id}/inheritance_chain",
+        summary="For internal use, this endpoint may change without warning.",
         include_in_schema=True,  # Can be changed to False if we don't really want to expose this
     )
     def show_inheritance_chain(
@@ -126,8 +120,8 @@ class FastAPIDatasets:
         return self.service.show_inheritance_chain(trans, dataset_id, hda_ldda)
 
     @router.get(
-        '/api/datasets/{dataset_id}/get_content_as_text',
-        summary='Returns dataset content as Text.',
+        "/api/datasets/{dataset_id}/get_content_as_text",
+        summary="Returns dataset content as Text.",
     )
     def get_content_as_text(
         self,
@@ -137,8 +131,8 @@ class FastAPIDatasets:
         return self.service.get_content_as_text(trans, dataset_id)
 
     @router.get(
-        '/api/datasets/{dataset_id}/converted/{ext}',
-        summary='Return information about datasets made by converting this dataset to a new format.',
+        "/api/datasets/{dataset_id}/converted/{ext}",
+        summary="Return information about datasets made by converting this dataset to a new format.",
     )
     def converted_ext(
         self,
@@ -160,10 +154,8 @@ class FastAPIDatasets:
         return self.service.converted_ext(trans, dataset_id, ext, serialization_params)
 
     @router.get(
-        '/api/datasets/{dataset_id}/converted',
-        summary=(
-            "Return a a map with all the existing converted datasets associated with this instance."
-        ),
+        "/api/datasets/{dataset_id}/converted",
+        summary=("Return a a map with all the existing converted datasets associated with this instance."),
     )
     def converted(
         self,
@@ -176,8 +168,8 @@ class FastAPIDatasets:
         return self.service.converted(trans, dataset_id)
 
     @router.put(
-        '/api/datasets/{dataset_id}/permissions',
-        summary='Set permissions of the given history dataset to the given role ids.',
+        "/api/datasets/{dataset_id}/permissions",
+        summary="Set permissions of the given history dataset to the given role ids.",
     )
     def update_permissions(
         self,
@@ -194,8 +186,8 @@ class FastAPIDatasets:
         return self.service.update_permissions(trans, dataset_id, update_payload)
 
     @router.get(
-        '/api/histories/{history_id}/contents/{history_content_id}/extra_files',
-        summary='Generate list of extra files.',
+        "/api/histories/{history_id}/contents/{history_content_id}/extra_files",
+        summary="Generate list of extra files.",
         tags=["histories"],
     )
     def extra_files(
@@ -207,9 +199,9 @@ class FastAPIDatasets:
         return self.service.extra_files(trans, history_content_id)
 
     @router.get(
-        '/api/histories/{history_id}/contents/{history_content_id}/display',
+        "/api/histories/{history_id}/contents/{history_content_id}/display",
         name="history_contents_display",
-        summary='Displays dataset (preview) content.',
+        summary="Displays dataset (preview) content.",
         tags=["histories"],
         response_class=StreamingResponse,
     )
@@ -235,7 +227,7 @@ class FastAPIDatasets:
             description=(
                 "The file extension when downloading the display data. Use the value `data` to "
                 "let the server infer it from the data type."
-            )
+            ),
         ),
         raw: bool = Query(
             default=False,
@@ -248,12 +240,14 @@ class FastAPIDatasets:
     ):
         """Streams the preview contents of a dataset to be displayed in a browser."""
         extra_params = get_query_parameters_from_request_excluding(request, {"preview", "filename", "to_ext", "raw"})
-        display_data, headers = self.service.display(trans, history_content_id, history_id, preview, filename, to_ext, raw, **extra_params)
+        display_data, headers = self.service.display(
+            trans, history_content_id, history_id, preview, filename, to_ext, raw, **extra_params
+        )
         return StreamingResponse(display_data, headers=headers)
 
     @router.get(
-        '/api/histories/{history_id}/contents/{history_content_id}/metadata_file',
-        summary='Returns the metadata file associated with this history item.',
+        "/api/histories/{history_id}/contents/{history_content_id}/metadata_file",
+        summary="Returns the metadata file associated with this history item.",
         tags=["histories"],
         response_class=FileResponse,
     )
@@ -271,7 +265,7 @@ class FastAPIDatasets:
         return FileResponse(path=cast(str, metadata_file_path), headers=headers)
 
     @router.get(
-        '/api/datasets/{dataset_id}',
+        "/api/datasets/{dataset_id}",
         summary="Displays information about and/or content of a dataset.",
     )
     def show(
@@ -281,9 +275,7 @@ class FastAPIDatasets:
         dataset_id: EncodedDatabaseIdField = DatasetIDPathParam,
         hda_ldda: DatasetSourceType = Query(
             default=DatasetSourceType.hda,
-            description=(
-                "The type of information about the dataset to be requested."
-            ),
+            description=("The type of information about the dataset to be requested."),
         ),
         data_type: Optional[RequestDataType] = Query(
             default=None,
@@ -368,25 +360,25 @@ class DatasetsController(BaseGalaxyAPIController):
         filter_parameters = FilterQueryParams(**kwd)
         filter_parameters.limit = filter_parameters.limit or limit
         filter_parameters.offset = filter_parameters.offset or offset
-        return self.service.index(
-            trans, history_id, serialization_params, filter_parameters
-        )
+        return self.service.index(trans, history_id, serialization_params, filter_parameters)
 
     @web.expose_api_anonymous_and_sessionless
-    def show(self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd):
+    def show(self, trans, id, hda_ldda="hda", data_type=None, provider=None, **kwd):
         """
         GET /api/datasets/{encoded_dataset_id}
         Displays information about and/or content of a dataset.
         """
         serialization_params = parse_serialization_params(**kwd)
-        kwd.update({
-            "provider": provider,
-        })
+        kwd.update(
+            {
+                "provider": provider,
+            }
+        )
         rval = self.service.show(trans, id, hda_ldda, serialization_params, data_type, **kwd)
         return rval
 
     @web.expose_api_anonymous
-    def show_storage(self, trans, dataset_id, hda_ldda='hda', **kwd):
+    def show_storage(self, trans, dataset_id, hda_ldda="hda", **kwd):
         """
         GET /api/datasets/{encoded_dataset_id}/storage
 
@@ -396,7 +388,7 @@ class DatasetsController(BaseGalaxyAPIController):
         return self.service.show_storage(trans, dataset_id, hda_ldda)
 
     @web.expose_api_anonymous
-    def show_inheritance_chain(self, trans, dataset_id, hda_ldda='hda', **kwd):
+    def show_inheritance_chain(self, trans, dataset_id, hda_ldda="hda", **kwd):
         """
         GET /api/datasets/{dataset_id}/inheritance_chain
 
@@ -415,7 +407,7 @@ class DatasetsController(BaseGalaxyAPIController):
         :rtype:     dict
         :returns:   dictionary containing new permissions
         """
-        hda_ldda = kwd.pop('hda_ldda', DatasetSourceType.hda)
+        hda_ldda = kwd.pop("hda_ldda", DatasetSourceType.hda)
         if payload:
             kwd.update(payload)
         update_payload = get_update_permission_payload(kwd)
@@ -430,8 +422,9 @@ class DatasetsController(BaseGalaxyAPIController):
         return self.service.extra_files(trans, history_content_id)
 
     @web.expose_api_raw_anonymous_and_sessionless
-    def display(self, trans, history_content_id, history_id,
-                preview=False, filename=None, to_ext=None, raw=False, **kwd):
+    def display(
+        self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, raw=False, **kwd
+    ):
         """
         GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display
         Displays history content (dataset).
@@ -449,7 +442,7 @@ class DatasetsController(BaseGalaxyAPIController):
 
     @web.expose_api
     def get_content_as_text(self, trans, dataset_id):
-        """ Returns item content as Text. """
+        """Returns item content as Text."""
         return self.service.get_content_as_text(trans, dataset_id)
 
     @web.expose_api_raw_anonymous_and_sessionless
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index e9f4031c007..43f83f777b2 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -23,7 +23,7 @@ from galaxy.managers.datatypes import (
     view_index,
     view_mapping,
     view_sniffers,
-    view_types_and_mapping
+    view_types_and_mapping,
 )
 from galaxy.util import asbool
 from galaxy.web import expose_api_anonymous_and_sessionless
@@ -35,7 +35,7 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['datatypes'])
+router = Router(tags=["datatypes"])
 
 ExtensionOnlyQueryParam: Optional[bool] = Query(
     default=True,
@@ -55,76 +55,76 @@ class FastAPIDatatypes:
     datatypes_registry: Registry = depends(Registry)
 
     @router.get(
-        '/api/datatypes',
+        "/api/datatypes",
         summary="Lists all available data types",
         response_description="List of data types",
     )
     async def index(
         self,
         extension_only: Optional[bool] = ExtensionOnlyQueryParam,
-        upload_only: Optional[bool] = UploadOnlyQueryParam
+        upload_only: Optional[bool] = UploadOnlyQueryParam,
     ) -> Union[List[DatatypeDetails], List[str]]:
         """Gets the list of all available data types."""
         return view_index(self.datatypes_registry, extension_only, upload_only)
 
     @router.get(
-        '/api/datatypes/mapping',
+        "/api/datatypes/mapping",
         summary="Returns mappings for data types and their implementing classes",
-        response_description="Dictionary to map data types with their classes"
+        response_description="Dictionary to map data types with their classes",
     )
     async def mapping(self) -> DatatypesMap:
         """Gets mappings for data types."""
         return view_mapping(self.datatypes_registry)
 
     @router.get(
-        '/api/datatypes/types_and_mapping',
+        "/api/datatypes/types_and_mapping",
         summary="Returns all the data types extensions and their mappings",
-        response_description="Dictionary to map data types with their classes"
+        response_description="Dictionary to map data types with their classes",
     )
     async def types_and_mapping(
         self,
         extension_only: Optional[bool] = ExtensionOnlyQueryParam,
-        upload_only: Optional[bool] = UploadOnlyQueryParam
+        upload_only: Optional[bool] = UploadOnlyQueryParam,
     ) -> DatatypesCombinedMap:
         """Combines the datatype information from (/api/datatypes) and the
         mapping information from (/api/datatypes/mapping) into a single
         response."""
         return DatatypesCombinedMap(
             datatypes=view_index(self.datatypes_registry, extension_only, upload_only),
-            datatypes_mapping=view_mapping(self.datatypes_registry)
+            datatypes_mapping=view_mapping(self.datatypes_registry),
         )
 
     @router.get(
-        '/api/datatypes/sniffers',
+        "/api/datatypes/sniffers",
         summary="Returns the list of all installed sniffers",
-        response_description="List of datatype sniffers"
+        response_description="List of datatype sniffers",
     )
     async def sniffers(self) -> List[str]:
         """Gets the list of all installed data type sniffers."""
         return view_sniffers(self.datatypes_registry)
 
     @router.get(
-        '/api/datatypes/converters',
+        "/api/datatypes/converters",
         summary="Returns the list of all installed converters",
-        response_description="List of all datatype converters"
+        response_description="List of all datatype converters",
     )
     async def converters(self) -> DatatypeConverterList:
         """Gets the list of all installed converters."""
         return view_converters(self.datatypes_registry)
 
     @router.get(
-        '/api/datatypes/edam_formats',
+        "/api/datatypes/edam_formats",
         summary="Returns a dictionary/map of datatypes and EDAM formats",
-        response_description="Dictionary/map of datatypes and EDAM formats"
+        response_description="Dictionary/map of datatypes and EDAM formats",
     )
     async def edam_formats(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM formats."""
         return self.datatypes_registry.edam_formats
 
     @router.get(
-        '/api/datatypes/edam_data',
+        "/api/datatypes/edam_data",
         summary="Returns a dictionary/map of datatypes and EDAM data",
-        response_description="Dictionary/map of datatypes and EDAM data"
+        response_description="Dictionary/map of datatypes and EDAM data",
     )
     async def edam_data(self) -> Dict[str, str]:
         """Gets a map of datatypes and their corresponding EDAM data."""
@@ -140,16 +140,16 @@ class DatatypesController(BaseGalaxyAPIController):
         GET /api/datatypes
         Return an object containing upload datatypes.
         """
-        extension_only = asbool(kwd.get('extension_only', True))
-        upload_only = asbool(kwd.get('upload_only', True))
+        extension_only = asbool(kwd.get("extension_only", True))
+        upload_only = asbool(kwd.get("upload_only", True))
         return view_index(self.datatypes_registry, extension_only, upload_only)
 
     @expose_api_anonymous_and_sessionless
     def mapping(self, trans, **kwd):
-        '''
+        """
         GET /api/datatypes/mapping
         Return a dictionary of class to class mappings.
-        '''
+        """
         return view_mapping(self.datatypes_registry)
 
     @expose_api_anonymous_and_sessionless
@@ -161,16 +161,16 @@ class DatatypesController(BaseGalaxyAPIController):
         mapping information from (/api/datatypes/mapping) into a single
         response.
         """
-        extension_only = asbool(kwd.get('extension_only', True))
-        upload_only = asbool(kwd.get('upload_only', True))
+        extension_only = asbool(kwd.get("extension_only", True))
+        upload_only = asbool(kwd.get("upload_only", True))
         return view_types_and_mapping(self.datatypes_registry, extension_only, upload_only)
 
     @expose_api_anonymous_and_sessionless
     def sniffers(self, trans, **kwd):
-        '''
+        """
         GET /api/datatypes/sniffers
         Return a list of sniffers.
-        '''
+        """
         return view_sniffers(self.datatypes_registry)
 
     @expose_api_anonymous_and_sessionless
diff --git a/lib/galaxy/webapps/galaxy/api/display_applications.py b/lib/galaxy/webapps/galaxy/api/display_applications.py
index 94cb0957d9b..e0540cd91f6 100644
--- a/lib/galaxy/webapps/galaxy/api/display_applications.py
+++ b/lib/galaxy/webapps/galaxy/api/display_applications.py
@@ -8,7 +8,10 @@ from galaxy.web import (
     expose_api,
     require_admin,
 )
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
@@ -40,5 +43,5 @@ class DisplayApplicationsController(BaseGalaxyAPIController):
         :type   ids:  list
         """
         payload = payload or {}
-        ids = payload.get('ids', [])
+        ids = payload.get("ids", [])
         return self.manager.reload(ids)
diff --git a/lib/galaxy/webapps/galaxy/api/dynamic_tools.py b/lib/galaxy/webapps/galaxy/api/dynamic_tools.py
index 037a0e47fe5..6731bf51131 100644
--- a/lib/galaxy/webapps/galaxy/api/dynamic_tools.py
+++ b/lib/galaxy/webapps/galaxy/api/dynamic_tools.py
@@ -1,9 +1,14 @@
 import logging
 
-from galaxy import util, web
+from galaxy import (
+    util,
+    web,
+)
 from galaxy.exceptions import ObjectNotFound
-from galaxy.web import expose_api
-from galaxy.web import expose_api_anonymous_and_sessionless
+from galaxy.web import (
+    expose_api,
+    expose_api_anonymous_and_sessionless,
+)
 from galaxy.webapps.base.controller import BaseAPIController
 
 log = logging.getLogger(__name__)
@@ -28,9 +33,7 @@ class DynamicToolsController(BaseAPIController):
         ID (and optionally version) returned from this endpoint.
         """
         manager = self.app.dynamic_tools_manager
-        return list(
-            map(lambda t: t.to_dict(), manager.list_tools())
-        )
+        return list(map(lambda t: t.to_dict(), manager.list_tools()))
 
     @expose_api_anonymous_and_sessionless
     def show(self, trans, id, **kwd):
diff --git a/lib/galaxy/webapps/galaxy/api/extended_metadata.py b/lib/galaxy/webapps/galaxy/api/extended_metadata.py
index c4a4dc9fcca..7565c9a38af 100644
--- a/lib/galaxy/webapps/galaxy/api/extended_metadata.py
+++ b/lib/galaxy/webapps/galaxy/api/extended_metadata.py
@@ -2,7 +2,11 @@
 API operations on annotations.
 """
 import logging
-from typing import Generic, Optional, TypeVar
+from typing import (
+    Generic,
+    Optional,
+    TypeVar,
+)
 
 from galaxy import (
     managers,
@@ -12,16 +16,21 @@ from galaxy import (
 from galaxy.webapps.base.controller import (
     UsesExtendedMetadataMixin,
     UsesLibraryMixinItems,
-    UsesStoredWorkflowMixin
+    UsesStoredWorkflowMixin,
+)
+from . import (
+    BaseGalaxyAPIController,
+    depends,
 )
-from . import BaseGalaxyAPIController, depends
 
 log = logging.getLogger(__name__)
 
-T = TypeVar('T')
+T = TypeVar("T")
 
 
-class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin, Generic[T]):
+class BaseExtendedMetadataController(
+    BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin, Generic[T]
+):
     exmeta_item_id: str
 
     def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[T]:
diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py
index 6ee8277d62a..46224d6b5b5 100644
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -3,15 +3,16 @@ API operations on the contents of a library folder.
 """
 import logging
 
-from galaxy import (
-    util
-)
+from galaxy import util
 from galaxy.web import (
     expose_api,
-    expose_api_anonymous
+    expose_api_anonymous,
 )
 from galaxy.webapps.galaxy.services.library_folder_contents import LibraryFolderContentsService
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
@@ -20,6 +21,7 @@ class FolderContentsController(BaseGalaxyAPIController):
     """
     Class controls retrieval, creation and updating of folder contents.
     """
+
     service: LibraryFolderContentsService = depends(LibraryFolderContentsService)
 
     @expose_api_anonymous
@@ -58,7 +60,7 @@ class FolderContentsController(BaseGalaxyAPIController):
         :raises: MalformedId, InconsistentDatabase, ObjectNotFound,
              InternalServerError
         """
-        include_deleted = util.asbool(kwd.get('include_deleted', False))
+        include_deleted = util.asbool(kwd.get("include_deleted", False))
         return self.service.index(trans, folder_id, limit, offset, search_text, include_deleted)
 
     @expose_api
diff --git a/lib/galaxy/webapps/galaxy/api/folders.py b/lib/galaxy/webapps/galaxy/api/folders.py
index e5377781f30..8f58bd2f3ec 100644
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -15,7 +15,7 @@ from fastapi import (
 
 from galaxy import (
     exceptions,
-    util
+    util,
 )
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.schema.fields import EncodedDatabaseIdField
@@ -40,18 +40,14 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['folders'])
+router = Router(tags=["folders"])
 
 FolderIdPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title="Folder ID",
-    description="The encoded identifier of the library folder."
+    ..., title="Folder ID", description="The encoded identifier of the library folder."
 )
 
 UndeleteQueryParam: Optional[bool] = Query(
-    default=None,
-    title="Undelete",
-    description="Whether to restore a deleted library folder."
+    default=None, title="Undelete", description="Whether to restore a deleted library folder."
 )
 
 
@@ -60,7 +56,7 @@ class FastAPILibraryFolders:
     service: LibraryFoldersService = depends(LibraryFoldersService)
 
     @router.get(
-        '/api/folders/{id}',
+        "/api/folders/{id}",
         summary="Displays information about a particular library folder.",
     )
     def show(
@@ -72,24 +68,23 @@ class FastAPILibraryFolders:
         return self.service.show(trans, id)
 
     @router.post(
-        '/api/folders/{id}',
+        "/api/folders/{id}",
         summary="Create a new library folder underneath the one specified by the ID.",
     )
     def create(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         id: EncodedDatabaseIdField = FolderIdPathParam,
-        payload: CreateLibraryFolderPayload = Body(...)
-
+        payload: CreateLibraryFolderPayload = Body(...),
     ) -> LibraryFolderDetails:
         """Returns detailed information about the newly created library folder."""
         return self.service.create(trans, id, payload)
 
     @router.put(
-        '/api/folders/{id}',
+        "/api/folders/{id}",
         summary="Updates the information of an existing library folder.",
     )
-    @router.patch('/api/folders/{id}')
+    @router.patch("/api/folders/{id}")
     def update(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -100,7 +95,7 @@ class FastAPILibraryFolders:
         return self.service.update(trans, id, payload)
 
     @router.delete(
-        '/api/folders/{id}',
+        "/api/folders/{id}",
         summary="Marks the specified library folder as deleted (or undeleted).",
     )
     def delete(
@@ -113,7 +108,7 @@ class FastAPILibraryFolders:
         return self.service.delete(trans, id, undelete)
 
     @router.get(
-        '/api/folders/{id}/permissions',
+        "/api/folders/{id}/permissions",
         summary="Gets the current or available permissions of a particular library folder.",
     )
     def get_permissions(
@@ -121,22 +116,18 @@ class FastAPILibraryFolders:
         trans: ProvidesUserContext = DependsOnTrans,
         id: EncodedDatabaseIdField = FolderIdPathParam,
         scope: Optional[LibraryPermissionScope] = Query(
-            None, title="Scope",
-            description="The scope of the permissions to retrieve. Either the `current` permissions or the `available`."
+            None,
+            title="Scope",
+            description="The scope of the permissions to retrieve. Either the `current` permissions or the `available`.",
         ),
         page: Optional[int] = Query(
-            default=1,
-            title="Page",
-            description="The page number to retrieve when paginating the available roles."
+            default=1, title="Page", description="The page number to retrieve when paginating the available roles."
         ),
         page_limit: Optional[int] = Query(
-            default=10,
-            title="Page Limit",
-            description="The maximum number of permissions per page when paginating."
+            default=10, title="Page Limit", description="The maximum number of permissions per page when paginating."
         ),
         q: Optional[str] = Query(
-            None, title="Query",
-            description="Optional search text to retrieve only the roles matching this query."
+            None, title="Query", description="Optional search text to retrieve only the roles matching this query."
         ),
     ) -> Union[LibraryFolderCurrentPermissions, LibraryAvailablePermissions]:
         """Gets the current or available permissions of a particular library.
@@ -151,7 +142,7 @@ class FastAPILibraryFolders:
         )
 
     @router.post(
-        '/api/folders/{id}/permissions',
+        "/api/folders/{id}/permissions",
         summary="Sets the permissions to manage a library folder.",
     )
     def set_permissions(
@@ -187,7 +178,7 @@ class FoldersController(BaseGalaxyAPIController):
         This would normally display a list of folders. However, that would
         be across multiple libraries, so it's not implemented.
         """
-        raise exceptions.NotImplemented('Listing all accessible library folders is not implemented.')
+        raise exceptions.NotImplemented("Listing all accessible library folders is not implemented.")
 
     @expose_api
     def show(self, trans, id, **kwd):
@@ -246,14 +237,14 @@ class FoldersController(BaseGalaxyAPIController):
 
         :raises: InsufficientPermissionsException
         """
-        scope = kwd.get('scope')
-        page = kwd.get('page')
+        scope = kwd.get("scope")
+        page = kwd.get("page")
         if isinstance(page, str):
             page = int(page)
-        page_limit = kwd.get('page_limit')
+        page_limit = kwd.get("page_limit")
         if isinstance(page_limit, str):
             page_limit = int(page_limit)
-        query = kwd.get('q')
+        query = kwd.get("q")
         return self.service.get_permissions(trans, encoded_folder_id, scope, page, page_limit, query)
 
     @expose_api
@@ -305,31 +296,31 @@ class FoldersController(BaseGalaxyAPIController):
         :rtype:     dictionary
 
         """
-        undelete = util.string_as_bool(kwd.get('undelete', False))
+        undelete = util.string_as_bool(kwd.get("undelete", False))
         return self.service.delete(trans, encoded_folder_id, undelete)
 
     @expose_api
     def update(self, trans, encoded_folder_id, payload, **kwd):
         """
-        PATCH /api/folders/{encoded_folder_id}
+         PATCH /api/folders/{encoded_folder_id}
 
-        Update the folder defined by an ``encoded_folder_id``
-        with the data in the payload.
+         Update the folder defined by an ``encoded_folder_id``
+         with the data in the payload.
 
-       .. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
+        .. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
 
-        :param  id:      the encoded id of the folder
-        :type   id:      an encoded id string
+         :param  id:      the encoded id of the folder
+         :type   id:      an encoded id string
 
-        :param  payload: (required) dictionary structure containing::
-            'name':         new folder's name, cannot be empty
-            'description':  new folder's description
-        :type   payload: dict
+         :param  payload: (required) dictionary structure containing::
+             'name':         new folder's name, cannot be empty
+             'description':  new folder's description
+         :type   payload: dict
 
-        :returns:   detailed folder information
-        :rtype:     dict
+         :returns:   detailed folder information
+         :rtype:     dict
 
-        :raises: RequestParameterMissingException
+         :raises: RequestParameterMissingException
         """
         update_payload = UpdateLibraryFolderPayload(**payload)
         return self.service.update(trans, encoded_folder_id, update_payload)
diff --git a/lib/galaxy/webapps/galaxy/api/forms.py b/lib/galaxy/webapps/galaxy/api/forms.py
index a105d86642f..90277054e59 100644
--- a/lib/galaxy/webapps/galaxy/api/forms.py
+++ b/lib/galaxy/webapps/galaxy/api/forms.py
@@ -8,11 +8,11 @@ from galaxy.forms.forms import form_factory
 from galaxy.util import XML
 from galaxy.webapps.base.controller import url_for
 from . import BaseGalaxyAPIController
+
 log = logging.getLogger(__name__)
 
 
 class FormDefinitionAPIController(BaseGalaxyAPIController):
-
     @web.legacy_expose_api
     def index(self, trans, **kwd):
         """
@@ -25,8 +25,10 @@ class FormDefinitionAPIController(BaseGalaxyAPIController):
         query = trans.sa_session.query(trans.app.model.FormDefinition)
         rval = []
         for form_definition in query:
-            item = form_definition.to_dict(value_mapper={'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id})
-            item['url'] = url_for('form', id=trans.security.encode_id(form_definition.id))
+            item = form_definition.to_dict(
+                value_mapper={"id": trans.security.encode_id, "form_definition_current_id": trans.security.encode_id}
+            )
+            item["url"] = url_for("form", id=trans.security.encode_id(form_definition.id))
             rval.append(item)
         return rval
 
@@ -49,8 +51,11 @@ class FormDefinitionAPIController(BaseGalaxyAPIController):
         if not form_definition or not trans.user_is_admin:
             trans.response.status = 400
             return f"Invalid form definition id ( {str(form_definition_id)} ) specified."
-        item = form_definition.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id})
-        item['url'] = url_for('form', id=form_definition_id)
+        item = form_definition.to_dict(
+            view="element",
+            value_mapper={"id": trans.security.encode_id, "form_definition_current_id": trans.security.encode_id},
+        )
+        item["url"] = url_for("form", id=form_definition_id)
         return item
 
     @web.legacy_expose_api
@@ -62,7 +67,7 @@ class FormDefinitionAPIController(BaseGalaxyAPIController):
         if not trans.user_is_admin:
             trans.response.status = 403
             return "You are not authorized to create a new form."
-        xml_text = payload.get('xml_text', None)
+        xml_text = payload.get("xml_text", None)
         if xml_text is None:
             trans.response.status = 400
             return "Missing required parameter 'xml_text'."
@@ -71,6 +76,9 @@ class FormDefinitionAPIController(BaseGalaxyAPIController):
         trans.sa_session.add(form_definition)
         trans.sa_session.flush()
         encoded_id = trans.security.encode_id(form_definition.id)
-        item = form_definition.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'form_definition_current_id': trans.security.encode_id})
-        item['url'] = url_for('form', id=encoded_id)
+        item = form_definition.to_dict(
+            view="element",
+            value_mapper={"id": trans.security.encode_id, "form_definition_current_id": trans.security.encode_id},
+        )
+        item["url"] = url_for("form", id=encoded_id)
         return [item]
diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index 5550d405f53..dc693936690 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -23,61 +23,44 @@ from . import (
     Router,
 )
 
+router = Router(tags=["genomes"])
 
-router = Router(tags=['genomes'])
-
-IdPathParam: str = Path(
-    ...,
-    title='Genome ID',
-    description='Genome ID'
-)
+IdPathParam: str = Path(..., title="Genome ID", description="Genome ID")
 
 ChromInfoQueryParam: bool = Query(
-    None,
-    title='ChromInfo',
-    description='If true, return genome keys with chromosome lengths'
+    None, title="ChromInfo", description="If true, return genome keys with chromosome lengths"
 )
 
 NumQueryParam: int = Query(
     None,
-    title='Number',
-    description='Limits size of returned data',
+    title="Number",
+    description="Limits size of returned data",
 )
 
 ChromQueryParam: Any = Query(
     None,
-    title='Chrom',
-    description='Limits size of returned data',
+    title="Chrom",
+    description="Limits size of returned data",
 )
 
 LowQueryParam: int = Query(
     None,
-    title='Low',
-    description='Limits size of returned data',
+    title="Low",
+    description="Limits size of returned data",
 )
 
 HighQueryParam: int = Query(
     None,
-    title='High',
-    description='Limits size of returned data',
+    title="High",
+    description="Limits size of returned data",
 )
 
-FormatQueryParam: str = Query(
-    None,
-    title='Format',
-    description='Format'
-)
+FormatQueryParam: str = Query(None, title="Format", description="Format")
 
-ReferenceQueryParam: bool = Query(
-    None,
-    title='Reference',
-    description='If true, return reference data'
-)
+ReferenceQueryParam: bool = Query(None, title="Reference", description="If true, return reference data")
 
 IndexTypeQueryParam: str = Query(
-    'fasta_indexes',  # currently this is the only supported index type
-    title='Index type',
-    description='Index type'
+    "fasta_indexes", title="Index type", description="Index type"  # currently this is the only supported index type
 )
 
 
@@ -91,22 +74,16 @@ def get_id(base, format):
 class FastAPIGenomes:
     manager: GenomesManager = depends(GenomesManager)
 
-    @router.get(
-        '/api/genomes',
-        summary='Return a list of installed genomes',
-        response_description='Installed genomes'
-    )
+    @router.get("/api/genomes", summary="Return a list of installed genomes", response_description="Installed genomes")
     def index(
-        self,
-        trans: ProvidesUserContext = DependsOnTrans,
-        chrom_info: bool = ChromInfoQueryParam
+        self, trans: ProvidesUserContext = DependsOnTrans, chrom_info: bool = ChromInfoQueryParam
     ) -> List[List[str]]:
         return self.manager.get_dbkeys(trans.user, chrom_info)
 
     @router.get(
-        '/api/genomes/{id}',
-        summary='Return information about build <id>',
-        response_description='Information about genome build <id>'
+        "/api/genomes/{id}",
+        summary="Return information about build <id>",
+        response_description="Information about genome build <id>",
     )
     def show(
         self,
@@ -123,9 +100,9 @@ class FastAPIGenomes:
         return self.manager.get_genome(trans, id, num, chrom, low, high, reference)
 
     @router.get(
-        '/api/genomes/{id}/indexes',
-        summary='Return all available indexes for a genome id for provided type',
-        response_description='Indexes for a genome id for provided type'
+        "/api/genomes/{id}/indexes",
+        summary="Return all available indexes for a genome id for provided type",
+        response_description="Indexes for a genome id for provided type",
     )
     def indexes(
         self,
@@ -138,9 +115,7 @@ class FastAPIGenomes:
         return Response(rval)
 
     @router.get(
-        '/api/genomes/{id}/sequences',
-        summary='Return raw sequence data',
-        response_description='Raw sequence data'
+        "/api/genomes/{id}/sequences", summary="Return raw sequence data", response_description="Raw sequence data"
     )
     def sequences(
         self,
@@ -161,6 +136,7 @@ class GenomesController(BaseGalaxyAPIController):
     """
     RESTful controller for interactions with genome data.
     """
+
     manager: GenomesManager = depends(GenomesManager)
 
     @expose_api_anonymous_and_sessionless
@@ -168,7 +144,7 @@ class GenomesController(BaseGalaxyAPIController):
         """
         GET /api/genomes: returns a list of installed genomes
         """
-        chrom_info = kwd.get('chrom_info')
+        chrom_info = kwd.get("chrom_info")
         return self.manager.get_dbkeys(trans.user, chrom_info)
 
     @expose_api_anonymous_and_sessionless
@@ -178,8 +154,8 @@ class GenomesController(BaseGalaxyAPIController):
 
         Returns information about build <id>
         """
-        id = get_id(id, kwd.get('format'))
-        reference = is_true(kwd.get('reference', False))
+        id = get_id(id, kwd.get("format"))
+        reference = is_true(kwd.get("reference", False))
         return self.manager.get_genome(trans, id, num, chrom, low, high, reference)
 
     @expose_api_raw_anonymous_and_sessionless
@@ -190,8 +166,8 @@ class GenomesController(BaseGalaxyAPIController):
         Returns all available indexes for a genome id for type={table name}
         For instance, /api/genomes/hg19/indexes?type=fasta_indexes
         """
-        id = get_id(id, kwd.get('format'))
-        index_type = kwd.get('type')
+        id = get_id(id, kwd.get("format"))
+        index_type = kwd.get("type")
         return self.manager.get_indexes(id, index_type)
 
     @expose_api_raw_anonymous_and_sessionless
@@ -202,5 +178,5 @@ class GenomesController(BaseGalaxyAPIController):
         This is a wrapper for accepting sequence requests that
         want a raw return, not json
         """
-        id = get_id(id, kwd.get('format'))
+        id = get_id(id, kwd.get("format"))
         return self.manager.get_sequence(trans, id, chrom, low, high)
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index f9980effb94..bef5f7ba106 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -9,7 +9,10 @@ from fastapi import Path
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.managers.group_roles import GroupRolesManager
 from galaxy.schema.fields import EncodedDatabaseIdField
-from galaxy.schema.schema import GroupRoleListModel, GroupRoleModel
+from galaxy.schema.schema import (
+    GroupRoleListModel,
+    GroupRoleModel,
+)
 from galaxy.web import (
     expose_api,
     require_admin,
@@ -18,74 +21,67 @@ from . import (
     BaseGalaxyAPIController,
     depends,
     DependsOnTrans,
-    Router
+    Router,
 )
 
-
 log = logging.getLogger(__name__)
 
-router = Router(tags=['group_roles'])
+router = Router(tags=["group_roles"])
 
-GroupIDParam: EncodedDatabaseIdField = Path(
-    ...,
-    title='GroupID',
-    description='The ID of the group'
-)
+GroupIDParam: EncodedDatabaseIdField = Path(..., title="GroupID", description="The ID of the group")
 
-RoleIDParam: EncodedDatabaseIdField = Path(
-    ...,
-    title='RoleID',
-    description='The ID of the role'
-)
+RoleIDParam: EncodedDatabaseIdField = Path(..., title="RoleID", description="The ID of the role")
 
 
 def group_role_to_model(trans, encoded_group_id, role):
     encoded_role_id = trans.security.encode_id(role.id)
-    url = trans.url_builder('group_role', group_id=encoded_group_id, id=encoded_role_id)
-    return GroupRoleModel(
-        id=encoded_role_id,
-        name=role.name,
-        url=url
-    )
+    url = trans.url_builder("group_role", group_id=encoded_group_id, id=encoded_role_id)
+    return GroupRoleModel(id=encoded_role_id, name=role.name, url=url)
 
 
 @router.cbv
 class FastAPIGroupRoles:
     manager: GroupRolesManager = depends(GroupRolesManager)
 
-    @router.get('/api/groups/{group_id}/roles',
-                require_admin=True,
-                summary='Displays a collection (list) of groups.')
-    def index(self, trans: ProvidesAppContext = DependsOnTrans,
-              group_id: EncodedDatabaseIdField = GroupIDParam) -> GroupRoleListModel:
+    @router.get("/api/groups/{group_id}/roles", require_admin=True, summary="Displays a collection (list) of groups.")
+    def index(
+        self, trans: ProvidesAppContext = DependsOnTrans, group_id: EncodedDatabaseIdField = GroupIDParam
+    ) -> GroupRoleListModel:
         group_roles = self.manager.index(trans, group_id)
         return GroupRoleListModel(__root__=[group_role_to_model(trans, group_id, gr.role) for gr in group_roles])
 
-    @router.get('/api/groups/{group_id}/roles/{id}',
-                name="group_role",
-                require_admin=True,
-                summary='Displays information about a group role.')
-    def show(self, trans: ProvidesAppContext = DependsOnTrans,
-             group_id: EncodedDatabaseIdField = GroupIDParam,
-             id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    @router.get(
+        "/api/groups/{group_id}/roles/{id}",
+        name="group_role",
+        require_admin=True,
+        summary="Displays information about a group role.",
+    )
+    def show(
+        self,
+        trans: ProvidesAppContext = DependsOnTrans,
+        group_id: EncodedDatabaseIdField = GroupIDParam,
+        id: EncodedDatabaseIdField = RoleIDParam,
+    ) -> GroupRoleModel:
         role = self.manager.show(trans, id, group_id)
         return group_role_to_model(trans, group_id, role)
 
-    @router.put('/api/groups/{group_id}/roles/{role_id}',
-                require_admin=True,
-                summary='Adds a role to a group')
-    def update(self, trans: ProvidesAppContext = DependsOnTrans,
-               group_id: EncodedDatabaseIdField = GroupIDParam,
-               role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    @router.put("/api/groups/{group_id}/roles/{role_id}", require_admin=True, summary="Adds a role to a group")
+    def update(
+        self,
+        trans: ProvidesAppContext = DependsOnTrans,
+        group_id: EncodedDatabaseIdField = GroupIDParam,
+        role_id: EncodedDatabaseIdField = RoleIDParam,
+    ) -> GroupRoleModel:
         role = self.manager.update(trans, role_id, group_id)
         return group_role_to_model(trans, group_id, role)
 
-    @router.delete('/api/groups/{group_id}/roles/{role_id}',
-                   require_admin=True,
-                   summary='Removes a role from a group')
-    def delete(self, trans: ProvidesAppContext = DependsOnTrans,
-               group_id: EncodedDatabaseIdField = GroupIDParam,
-               role_id: EncodedDatabaseIdField = RoleIDParam) -> GroupRoleModel:
+    @router.delete("/api/groups/{group_id}/roles/{role_id}", require_admin=True, summary="Removes a role from a group")
+    def delete(
+        self,
+        trans: ProvidesAppContext = DependsOnTrans,
+        group_id: EncodedDatabaseIdField = GroupIDParam,
+        role_id: EncodedDatabaseIdField = RoleIDParam,
+    ) -> GroupRoleModel:
         role = self.manager.delete(trans, role_id, group_id)
         return group_role_to_model(trans, group_id, role)
 
diff --git a/lib/galaxy/webapps/galaxy/api/group_users.py b/lib/galaxy/webapps/galaxy/api/group_users.py
index ec75947701d..57b534cdbd2 100644
--- a/lib/galaxy/webapps/galaxy/api/group_users.py
+++ b/lib/galaxy/webapps/galaxy/api/group_users.py
@@ -10,7 +10,10 @@ from galaxy.web import (
     expose_api,
     require_admin,
 )
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/webapps/galaxy/api/groups.py b/lib/galaxy/webapps/galaxy/api/groups.py
index 5e18a0f8c44..6e2c543a8c2 100644
--- a/lib/galaxy/webapps/galaxy/api/groups.py
+++ b/lib/galaxy/webapps/galaxy/api/groups.py
@@ -14,7 +14,10 @@ from galaxy.web import (
     expose_api,
     require_admin,
 )
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 2628d6a5f95..6a460b1f5db 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -23,9 +23,7 @@ from pydantic.fields import Field
 from pydantic.main import BaseModel
 from starlette.responses import FileResponse
 
-from galaxy import (
-    util
-)
+from galaxy import util
 from galaxy.managers.context import (
     ProvidesHistoryContext,
     ProvidesUserContext,
@@ -52,9 +50,7 @@ from galaxy.schema.schema import (
     SharingStatus,
 )
 from galaxy.schema.types import LatestLiteral
-from galaxy.util import (
-    string_as_bool
-)
+from galaxy.util import string_as_bool
 from galaxy.web import (
     expose_api,
     expose_api_anonymous,
@@ -72,27 +68,25 @@ from . import (
     depends,
     DependsOnTrans,
     Router,
-    try_get_request_body_as_json
+    try_get_request_body_as_json,
 )
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['histories'])
+router = Router(tags=["histories"])
 
 HistoryIDPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title="History ID",
-    description="The encoded database identifier of the History."
+    ..., title="History ID", description="The encoded database identifier of the History."
 )
 
 JehaIDPathParam: Union[EncodedDatabaseIdField, LatestLiteral] = Path(
     default="latest",
-    title='Job Export History ID',
+    title="Job Export History ID",
     description=(
-        'The ID of the specific Job Export History Association or '
-        '`latest` (default) to download the last generated archive.'
+        "The ID of the specific Job Export History Association or "
+        "`latest` (default) to download the last generated archive."
     ),
-    example="latest"
+    example="latest",
 )
 
 
@@ -106,9 +100,7 @@ class HistoryIndexParams(HistoryFilterQueryParams):
 
 class DeleteHistoryPayload(BaseModel):
     purge: bool = Field(
-        default=False,
-        title="Purge",
-        description="Whether to definitely remove this history from disk."
+        default=False, title="Purge", description="Whether to definitely remove this history from disk."
     )
 
 
@@ -122,8 +114,8 @@ class FastAPIHistories:
     service: HistoriesService = depends(HistoriesService)
 
     @router.get(
-        '/api/histories',
-        summary='Returns histories for the current user.',
+        "/api/histories",
+        summary="Returns histories for the current user.",
     )
     def index(
         self,
@@ -135,13 +127,13 @@ class FastAPIHistories:
             title="Deleted Only",
             description="Whether to return only deleted items.",
             deprecated=True,  # Marked as deprecated as it seems just like '/api/histories/deleted'
-        )
+        ),
     ) -> List[AnyHistoryView]:
         return self.service.index(trans, serialization_params, params, deleted_only=deleted, all_histories=params.all)
 
     @router.get(
-        '/api/histories/deleted',
-        summary='Returns deleted histories for the current user.',
+        "/api/histories/deleted",
+        summary="Returns deleted histories for the current user.",
     )
     def index_deleted(
         self,
@@ -152,8 +144,8 @@ class FastAPIHistories:
         return self.service.index(trans, serialization_params, params, deleted_only=True, all_histories=params.all)
 
     @router.get(
-        '/api/histories/published',
-        summary='Return all histories that are published.',
+        "/api/histories/published",
+        summary="Return all histories that are published.",
     )
     def published(
         self,
@@ -164,8 +156,8 @@ class FastAPIHistories:
         return self.service.published(trans, serialization_params, filter_params)
 
     @router.get(
-        '/api/histories/shared_with_me',
-        summary='Return all histories that are shared with the current user.',
+        "/api/histories/shared_with_me",
+        summary="Return all histories that are shared with the current user.",
     )
     def shared_with_me(
         self,
@@ -176,8 +168,8 @@ class FastAPIHistories:
         return self.service.shared_with_me(trans, serialization_params, filter_params)
 
     @router.get(
-        '/api/histories/most_recently_used',
-        summary='Returns the most recently used history of the user.',
+        "/api/histories/most_recently_used",
+        summary="Returns the most recently used history of the user.",
     )
     def show_recent(
         self,
@@ -187,8 +179,8 @@ class FastAPIHistories:
         return self.service.show(trans, serialization_params)
 
     @router.get(
-        '/api/histories/{id}',
-        summary='Returns the history with the given ID.',
+        "/api/histories/{id}",
+        summary="Returns the history with the given ID.",
     )
     def show(
         self,
@@ -199,8 +191,8 @@ class FastAPIHistories:
         return self.service.show(trans, serialization_params, id)
 
     @router.get(
-        '/api/histories/{id}/citations',
-        summary='Return all the citations for the tools used to produce the datasets in the history.',
+        "/api/histories/{id}/citations",
+        summary="Return all the citations for the tools used to produce the datasets in the history.",
     )
     def citations(
         self,
@@ -210,8 +202,8 @@ class FastAPIHistories:
         return self.service.citations(trans, id)
 
     @router.post(
-        '/api/histories',
-        summary='Creates a new history.',
+        "/api/histories",
+        summary="Creates a new history.",
     )
     def create(
         self,
@@ -232,8 +224,8 @@ class FastAPIHistories:
         return self.service.create(trans, payload, serialization_params)
 
     @router.delete(
-        '/api/histories/{id}',
-        summary='Marks the history with the given ID as deleted.',
+        "/api/histories/{id}",
+        summary="Marks the history with the given ID as deleted.",
     )
     def delete(
         self,
@@ -241,14 +233,14 @@ class FastAPIHistories:
         id: EncodedDatabaseIdField = HistoryIDPathParam,
         serialization_params: SerializationParams = Depends(query_serialization_params),
         purge: bool = Query(default=False),
-        payload: Optional[DeleteHistoryPayload] = Body(default=None)
+        payload: Optional[DeleteHistoryPayload] = Body(default=None),
     ) -> AnyHistoryView:
         if payload:
             purge = payload.purge
         return self.service.delete(trans, id, serialization_params, purge)
 
     @router.post(
-        '/api/histories/deleted/{id}/undelete',
+        "/api/histories/deleted/{id}/undelete",
         summary="Restores a deleted history with the given ID (that hasn't been purged).",
     )
     def undelete(
@@ -260,7 +252,7 @@ class FastAPIHistories:
         return self.service.undelete(trans, id, serialization_params)
 
     @router.put(
-        '/api/histories/{id}',
+        "/api/histories/{id}",
         summary="Updates the values for the history with the given ID.",
     )
     def update(
@@ -276,10 +268,8 @@ class FastAPIHistories:
         return self.service.update(trans, id, payload, serialization_params)
 
     @router.get(
-        '/api/histories/{id}/exports',
-        summary=(
-            "Get previous history exports (to links). Effectively returns serialized JEHA objects."
-        ),
+        "/api/histories/{id}/exports",
+        summary=("Get previous history exports (to links). Effectively returns serialized JEHA objects."),
     )
     def index_exports(
         self,
@@ -290,17 +280,15 @@ class FastAPIHistories:
         return JobExportHistoryArchiveCollection.parse_obj(exports)
 
     @router.put(  # PUT instead of POST because multiple requests should just result in one object being created.
-        '/api/histories/{id}/exports',
-        summary=(
-            "Start job (if needed) to create history export for corresponding history."
-        ),
+        "/api/histories/{id}/exports",
+        summary=("Start job (if needed) to create history export for corresponding history."),
         responses={
             200: {
                 "description": "Object containing url to fetch export from.",
             },
             202: {
                 "description": "The exported archive file is not ready yet.",
-            }
+            },
         },
     )
     def archive_export(
@@ -326,11 +314,9 @@ class FastAPIHistories:
         return export_result
 
     @router.get(
-        '/api/histories/{id}/exports/{jeha_id}',
+        "/api/histories/{id}/exports/{jeha_id}",
         name="history_archive_download",
-        summary=(
-            "If ready and available, return raw contents of exported history as a downloadable archive."
-        ),
+        summary=("If ready and available, return raw contents of exported history as a downloadable archive."),
         response_class=FileResponse,
         responses={
             200: {
@@ -359,7 +345,7 @@ class FastAPIHistories:
         )
 
     @router.get(
-        '/api/histories/{id}/custom_builds_metadata',
+        "/api/histories/{id}/custom_builds_metadata",
         summary="Returns meta data for custom builds.",
     )
     def get_custom_builds_metadata(
@@ -370,7 +356,7 @@ class FastAPIHistories:
         return self.service.get_custom_builds_metadata(trans, id)
 
     @router.get(
-        '/api/histories/{id}/sharing',
+        "/api/histories/{id}/sharing",
         summary="Get the current sharing status of the given item.",
     )
     def sharing(
@@ -382,7 +368,7 @@ class FastAPIHistories:
         return self.service.shareable_service.sharing(trans, id)
 
     @router.put(
-        '/api/histories/{id}/enable_link_access',
+        "/api/histories/{id}/enable_link_access",
         summary="Makes this item accessible by a URL link.",
     )
     def enable_link_access(
@@ -394,7 +380,7 @@ class FastAPIHistories:
         return self.service.shareable_service.enable_link_access(trans, id)
 
     @router.put(
-        '/api/histories/{id}/disable_link_access',
+        "/api/histories/{id}/disable_link_access",
         summary="Makes this item inaccessible by a URL link.",
     )
     def disable_link_access(
@@ -406,7 +392,7 @@ class FastAPIHistories:
         return self.service.shareable_service.disable_link_access(trans, id)
 
     @router.put(
-        '/api/histories/{id}/publish',
+        "/api/histories/{id}/publish",
         summary="Makes this item public and accessible by a URL link.",
     )
     def publish(
@@ -418,7 +404,7 @@ class FastAPIHistories:
         return self.service.shareable_service.publish(trans, id)
 
     @router.put(
-        '/api/histories/{id}/unpublish',
+        "/api/histories/{id}/unpublish",
         summary="Removes this item from the published list.",
     )
     def unpublish(
@@ -430,20 +416,20 @@ class FastAPIHistories:
         return self.service.shareable_service.unpublish(trans, id)
 
     @router.put(
-        '/api/histories/{id}/share_with_users',
+        "/api/histories/{id}/share_with_users",
         summary="Share this item with specific users.",
     )
     def share_with_users(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         id: EncodedDatabaseIdField = HistoryIDPathParam,
-        payload: ShareWithPayload = Body(...)
+        payload: ShareWithPayload = Body(...),
     ) -> ShareWithStatus:
         """Shares this item with specific users and return the current sharing status."""
         return self.service.shareable_service.share_with_users(trans, id, payload)
 
     @router.put(
-        '/api/histories/{id}/slug',
+        "/api/histories/{id}/slug",
         summary="Set a new slug for this shared item.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
@@ -462,7 +448,7 @@ class HistoriesController(BaseGalaxyAPIController):
     service: HistoriesService = depends(HistoriesService)
 
     @expose_api_anonymous
-    def index(self, trans, deleted='False', **kwd):
+    def index(self, trans, deleted="False", **kwd):
         """
         GET /api/histories
 
@@ -554,13 +540,13 @@ class HistoriesController(BaseGalaxyAPIController):
         'order' defaults to 'create_time-dsc'
         """
         deleted_only = util.string_as_bool(deleted)
-        all_histories = util.string_as_bool(kwd.get('all', False))
+        all_histories = util.string_as_bool(kwd.get("all", False))
         serialization_params = parse_serialization_params(**kwd)
         filter_parameters = HistoryFilterQueryParams(**kwd)
         return self.service.index(trans, serialization_params, filter_parameters, deleted_only, all_histories)
 
     @expose_api_anonymous
-    def show(self, trans, id, deleted='False', **kwd):
+    def show(self, trans, id, deleted="False", **kwd):
         """
         show( trans, id, deleted='False' )
         * GET /api/histories/{id}:
@@ -678,10 +664,10 @@ class HistoriesController(BaseGalaxyAPIController):
         """
         history_id = id
         # a request body is optional here
-        purge = string_as_bool(kwd.get('purge', False))
+        purge = string_as_bool(kwd.get("purge", False))
         # for backwards compat, keep the payload sub-dictionary
-        if kwd.get('payload', None):
-            purge = string_as_bool(kwd['payload'].get('purge', purge))
+        if kwd.get("payload", None):
+            purge = string_as_bool(kwd["payload"].get("purge", purge))
 
         serialization_params = parse_serialization_params(**kwd)
         return self.service.delete(trans, history_id, serialization_params, purge)
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index a9c9ff61277..21427c08089 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -20,7 +20,10 @@ from fastapi import (
     Request,
 )
 from starlette import status
-from starlette.responses import Response, StreamingResponse
+from starlette.responses import (
+    Response,
+    StreamingResponse,
+)
 
 from galaxy import util
 from galaxy.managers.context import ProvidesHistoryContext
@@ -77,24 +80,16 @@ from . import (
 log = logging.getLogger(__name__)
 
 
-router = Router(tags=['histories'])
+router = Router(tags=["histories"])
 
-HistoryIDPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title='History ID',
-    description='The ID of the History.'
-)
+HistoryIDPathParam: EncodedDatabaseIdField = Path(..., title="History ID", description="The ID of the History.")
 
 HistoryItemIDPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title='History Item ID',
-    description='The ID of the item (`HDA`/`HDCA`) contained in the history.'
+    ..., title="History Item ID", description="The ID of the item (`HDA`/`HDCA`) contained in the history."
 )
 
 HistoryHDCAIDPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title='History Dataset Collection ID',
-    description='The ID of the `HDCA` contained in the history.'
+    ..., title="History Dataset Collection ID", description="The ID of the `HDCA` contained in the history."
 )
 
 ContentTypeQueryParam = Query(
@@ -173,9 +168,7 @@ def get_legacy_index_query_params(
     details: Optional[str] = Query(
         default=None,
         title="Details",
-        description=(
-            "Legacy name for the `dataset_details` parameter."
-        ),
+        description=("Legacy name for the `dataset_details` parameter."),
         deprecated=True,
     ),
     deleted: Optional[bool] = Query(
@@ -224,7 +217,7 @@ def parse_legacy_index_query_params(
     if ids:
         id_list = util.listify(ids)
         # If explicit ids given, always used detailed result.
-        dataset_details = 'all'
+        dataset_details = "all"
     else:
         dataset_details = parse_dataset_details(details)
 
@@ -241,7 +234,7 @@ def parse_dataset_details(details: Optional[str]):
     """Parses the different values that the `dataset_details` parameter
     can have from a string."""
     dataset_details: Optional[DatasetDetailsType] = None
-    if details and details != 'all':
+    if details and details != "all":
         dataset_details = set(util.listify(details))
     else:  # either None or 'all'
         dataset_details = details  # type: ignore
@@ -281,10 +274,7 @@ def parse_index_jobs_summary_params(
 ) -> HistoryContentsIndexJobsSummaryParams:
     """Parses query parameters for the history contents `index_jobs_summary` operation
     and returns a model containing the values in the correct type."""
-    return HistoryContentsIndexJobsSummaryParams(
-        ids=util.listify(ids),
-        types=util.listify(types)
-    )
+    return HistoryContentsIndexJobsSummaryParams(ids=util.listify(ids), types=util.listify(types))
 
 
 def parse_content_filter_params(
@@ -299,8 +289,8 @@ def parse_content_filter_params(
     Currently used by the `contents_near` endpoint. The `exclude` set can contain
     names of parameters that will be ignored and not added to the filters.
     """
-    DEFAULT_OP = 'eq'
-    splitchar = '-'
+    DEFAULT_OP = "eq"
+    splitchar = "-"
 
     exclude = exclude or set()
     result = []
@@ -321,13 +311,13 @@ class FastAPIHistoryContents:
     service: HistoriesContentsService = depends(HistoriesContentsService)
 
     @router.get(
-        '/api/histories/{history_id}/contents/{type}s',
-        summary='Returns the contents of the given history filtered by type.',
+        "/api/histories/{history_id}/contents/{type}s",
+        summary="Returns the contents of the given history filtered by type.",
     )
     @router.get(
-        '/api/histories/{history_id}/contents',
-        name='history_contents',
-        summary='Returns the contents of the given history.',
+        "/api/histories/{history_id}/contents",
+        name="history_contents",
+        summary="Returns the contents of the given history.",
     )
     def index(
         self,
@@ -357,8 +347,8 @@ class FastAPIHistoryContents:
         return items
 
     @router.get(
-        '/api/histories/{history_id}/contents/{type}s/{id}/jobs_summary',
-        summary='Return detailed information about an `HDA` or `HDCAs` jobs.',
+        "/api/histories/{history_id}/contents/{type}s/{id}/jobs_summary",
+        summary="Return detailed information about an `HDA` or `HDCAs` jobs.",
     )
     def show_jobs_summary(
         self,
@@ -377,15 +367,15 @@ class FastAPIHistoryContents:
         return self.service.show_jobs_summary(trans, id, contents_type=type)
 
     @router.get(
-        '/api/histories/{history_id}/contents/{type}s/{id}',
-        name='history_content_typed',
-        summary='Return detailed information about a specific HDA or HDCA with the given `ID` within a history.',
+        "/api/histories/{history_id}/contents/{type}s/{id}",
+        name="history_content_typed",
+        summary="Return detailed information about a specific HDA or HDCA with the given `ID` within a history.",
         response_model_exclude_unset=True,
     )
     @router.get(
-        '/api/histories/{history_id}/contents/{id}',
-        name='history_content',
-        summary='Return detailed information about an HDA within a history.',
+        "/api/histories/{history_id}/contents/{id}",
+        name="history_content",
+        summary="Return detailed information about an HDA within a history.",
         response_model_exclude_unset=True,
         deprecated=True,
     )
@@ -399,20 +389,20 @@ class FastAPIHistoryContents:
             default=None,
             title="Fuzzy Count",
             description=(
-                'This value can be used to broadly restrict the magnitude '
-                'of the number of elements returned via the API for large '
-                'collections. The number of actual elements returned may '
+                "This value can be used to broadly restrict the magnitude "
+                "of the number of elements returned via the API for large "
+                "collections. The number of actual elements returned may "
                 'be "a bit" more than this number or "a lot" less - varying '
-                'on the depth of nesting, balance of nesting at each level, '
-                'and size of target collection. The consumer of this API should '
-                'not expect a stable number or pre-calculable number of '
-                'elements to be produced given this parameter - the only '
-                'promise is that this API will not respond with an order '
-                'of magnitude more elements estimated with this value. '
+                "on the depth of nesting, balance of nesting at each level, "
+                "and size of target collection. The consumer of this API should "
+                "not expect a stable number or pre-calculable number of "
+                "elements to be produced given this parameter - the only "
+                "promise is that this API will not respond with an order "
+                "of magnitude more elements estimated with this value. "
                 'The UI uses this parameter to fetch a "balanced" concept of '
                 'the "start" of large collections at every depth of the '
-                'collection.'
-            )
+                "collection."
+            ),
         ),
         serialization_params: SerializationParams = Depends(query_serialization_params),
     ) -> AnyHistoryContentItem:
@@ -430,8 +420,8 @@ class FastAPIHistoryContents:
         )
 
     @router.get(
-        '/api/histories/{history_id}/jobs_summary',
-        summary='Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.',
+        "/api/histories/{history_id}/jobs_summary",
+        summary="Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.",
     )
     def index_jobs_summary(
         self,
@@ -449,13 +439,13 @@ class FastAPIHistoryContents:
         return self.service.index_jobs_summary(trans, params)
 
     @router.get(
-        '/api/histories/{history_id}/contents/dataset_collections/{id}/download',
-        summary='Download the content of a dataset collection as a `zip` archive.',
+        "/api/histories/{history_id}/contents/dataset_collections/{id}/download",
+        summary="Download the content of a dataset collection as a `zip` archive.",
         response_class=StreamingResponse,
     )
     @router.get(
-        '/api/dataset_collection/{id}/download',
-        summary='Download the content of a dataset collection as a `zip` archive.',
+        "/api/dataset_collection/{id}/download",
+        summary="Download the content of a dataset collection as a `zip` archive.",
         response_class=StreamingResponse,
         tags=["dataset collections"],
     )
@@ -472,13 +462,13 @@ class FastAPIHistoryContents:
         return StreamingResponse(archive.get_iterator(), headers=archive.get_headers())
 
     @router.post(
-        '/api/histories/{history_id}/contents/{type}s',
-        summary='Create a new `HDA` or `HDCA` in the given History.',
+        "/api/histories/{history_id}/contents/{type}s",
+        summary="Create a new `HDA` or `HDCA` in the given History.",
         response_model_exclude_unset=True,
     )
     @router.post(
-        '/api/histories/{history_id}/contents',
-        summary='Create a new `HDA` or `HDCA` in the given History.',
+        "/api/histories/{history_id}/contents",
+        summary="Create a new `HDA` or `HDCA` in the given History.",
         response_model_exclude_unset=True,
         deprecated=True,
     )
@@ -500,8 +490,8 @@ class FastAPIHistoryContents:
         return self.service.create(trans, history_id, payload, serialization_params)
 
     @router.put(
-        '/api/histories/{history_id}/contents/{dataset_id}/permissions',
-        summary='Set permissions of the given history dataset to the given role ids.',
+        "/api/histories/{history_id}/contents/{dataset_id}/permissions",
+        summary="Set permissions of the given history dataset to the given role ids.",
     )
     def update_permissions(
         self,
@@ -519,8 +509,8 @@ class FastAPIHistoryContents:
         return self.service.update_permissions(trans, dataset_id, update_payload)
 
     @router.put(
-        '/api/histories/{history_id}/contents',
-        summary='Batch update specific properties of a set items contained in the given History.',
+        "/api/histories/{history_id}/contents",
+        summary="Batch update specific properties of a set items contained in the given History.",
     )
     def update_batch(
         self,
@@ -538,8 +528,8 @@ class FastAPIHistoryContents:
         return HistoryContentsResult.parse_obj(result)
 
     @router.put(
-        '/api/histories/{history_id}/contents/{id}/validate',
-        summary='Validates the metadata associated with a dataset within a History.',
+        "/api/histories/{history_id}/contents/{id}/validate",
+        summary="Validates the metadata associated with a dataset within a History.",
     )
     def validate(
         self,
@@ -551,13 +541,13 @@ class FastAPIHistoryContents:
         return self.service.validate(trans, history_id, id)
 
     @router.put(
-        '/api/histories/{history_id}/contents/{type}s/{id}',
-        summary='Updates the values for the history content item with the given ``ID``.',
+        "/api/histories/{history_id}/contents/{type}s/{id}",
+        summary="Updates the values for the history content item with the given ``ID``.",
         response_model_exclude_unset=True,
     )
     @router.put(
-        '/api/histories/{history_id}/contents/{id}',
-        summary='Updates the values for the history content item with the given ``ID``.',
+        "/api/histories/{history_id}/contents/{id}",
+        summary="Updates the values for the history content item with the given ``ID``.",
         response_model_exclude_unset=True,
         deprecated=True,
     )
@@ -574,12 +564,12 @@ class FastAPIHistoryContents:
         return self.service.update(trans, history_id, id, payload.dict(), serialization_params, contents_type=type)
 
     @router.delete(
-        '/api/histories/{history_id}/contents/{type}s/{id}',
-        summary='Delete the history content with the given ``ID`` and specified type.',
+        "/api/histories/{history_id}/contents/{type}s/{id}",
+        summary="Delete the history content with the given ``ID`` and specified type.",
     )
     @router.delete(
-        '/api/histories/{history_id}/contents/{id}',
-        summary='Delete the history dataset with the given ``ID``.',
+        "/api/histories/{history_id}/contents/{id}",
+        summary="Delete the history dataset with the given ``ID``.",
     )
     def delete(
         self,
@@ -622,12 +612,12 @@ class FastAPIHistoryContents:
         return rval
 
     @router.get(
-        '/api/histories/{history_id}/contents/archive/{filename}.{format}',
-        summary='Build and return a compressed archive of the selected history contents.',
+        "/api/histories/{history_id}/contents/archive/{filename}.{format}",
+        summary="Build and return a compressed archive of the selected history contents.",
     )
     @router.get(
-        '/api/histories/{history_id}/contents/archive/{id}',
-        summary='Build and return a compressed archive of the selected history contents.',
+        "/api/histories/{history_id}/contents/archive/{id}",
+        summary="Build and return a compressed archive of the selected history contents.",
     )
     def archive(
         self,
@@ -659,8 +649,8 @@ class FastAPIHistoryContents:
         return StreamingResponse(archive.get_iterator(), headers=archive.get_headers(), media_type="application/zip")
 
     @router.get(
-        '/api/histories/{history_id}/contents/{direction}/{hid}/{limit}',
-        summary='Get content items around a particular `HID`.',
+        "/api/histories/{history_id}/contents/{direction}/{hid}/{limit}",
+        summary="Get content items around a particular `HID`.",
     )
     def contents_near(
         self,
@@ -731,7 +721,14 @@ class FastAPIHistoryContents:
         filter_params = parse_content_filter_params(request.query_params._dict, exclude=exclude_params)
 
         result = self.service.contents_near(
-            trans, history_id, serialization_params, filter_params, direction, hid, limit, since,
+            trans,
+            history_id,
+            serialization_params,
+            filter_params,
+            direction,
+            hid,
+            limit,
+            since,
         )
         if result is None:
             return Response(status_code=status.HTTP_204_NO_CONTENT)
@@ -776,10 +773,7 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         serialization_params = parse_serialization_params(**kwd)
         filter_parameters = FilterQueryParams(**kwd)
         return self.service.index(
-            trans, history_id,
-            index_params,
-            legacy_params,
-            serialization_params, filter_parameters
+            trans, history_id, index_params, legacy_params, serialization_params, filter_parameters
         )
 
     @expose_api_anonymous
@@ -880,7 +874,7 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         return self.service.show_jobs_summary(trans, id, contents_type)
 
     def __get_contents_type(self, kwd: dict) -> HistoryContentType:
-        contents_type = kwd.get('type', 'dataset')
+        contents_type = kwd.get("type", "dataset")
         return HistoryContentType(contents_type)
 
     @expose_api_raw_anonymous
@@ -1082,9 +1076,7 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         """
         serialization_params = parse_serialization_params(**kwd)
         contents_type = self.__get_contents_type(kwd)
-        return self.service.update(
-            trans, history_id, id, payload, serialization_params, contents_type
-        )
+        return self.service.update(trans, history_id, id, payload, serialization_params, contents_type)
 
     @expose_api_anonymous
     def validate(self, trans, history_id, history_content_id, payload=None, **kwd):
@@ -1139,15 +1131,15 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         contents_type = self.__get_contents_type(kwd)
         purge = util.string_as_bool(purge)
         recursive = util.string_as_bool(recursive)
-        if kwd.get('payload', None):
+        if kwd.get("payload", None):
             # payload takes priority
-            purge = util.string_as_bool(kwd['payload'].get('purge', purge))
-            recursive = util.string_as_bool(kwd['payload'].get('recursive', recursive))
+            purge = util.string_as_bool(kwd["payload"].get("purge", purge))
+            recursive = util.string_as_bool(kwd["payload"].get("recursive", recursive))
         delete_payload = DeleteHistoryContentPayload(purge=purge, recursive=recursive)
         return self.service.delete(trans, id, serialization_params, contents_type, delete_payload)
 
     @expose_api
-    def archive(self, trans, history_id, filename='', format='zip', dry_run=True, **kwd):
+    def archive(self, trans, history_id, filename="", format="zip", dry_run=True, **kwd):
         """
         archive( self, trans, history_id, filename='', format='zip', dry_run=True, **kwd )
         * GET /api/histories/{history_id}/contents/archive/{id}
@@ -1194,9 +1186,9 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
 
         GET /api/histories/{history_id}/contents/{direction:near|before|after}/{hid}/{limit}
         """
-        serialization_params = parse_serialization_params(default_view='betawebclient', **kwd)
+        serialization_params = parse_serialization_params(default_view="betawebclient", **kwd)
 
-        since_str = kwd.pop('since', None)
+        since_str = kwd.pop("since", None)
         if since_str:
             since = dateutil.parser.isoparse(since_str)
         else:
@@ -1207,7 +1199,14 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         limit = int(limit)
 
         result = self.service.contents_near(
-            trans, history_id, serialization_params, filter_params, direction, hid, limit, since,
+            trans,
+            history_id,
+            serialization_params,
+            filter_params,
+            direction,
+            hid,
+            limit,
+            since,
         )
         if result is None:
             trans.response.status = 204
diff --git a/lib/galaxy/webapps/galaxy/api/item_tags.py b/lib/galaxy/webapps/galaxy/api/item_tags.py
index 63fae9ddb21..4ab80440390 100644
--- a/lib/galaxy/webapps/galaxy/api/item_tags.py
+++ b/lib/galaxy/webapps/galaxy/api/item_tags.py
@@ -5,28 +5,24 @@ import logging
 
 from galaxy import exceptions
 from galaxy.web import expose_api
-from galaxy.webapps.base.controller import (
-    UsesTagsMixin
-)
+from galaxy.webapps.base.controller import UsesTagsMixin
 from . import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
 
 
 class BaseItemTagsController(BaseGalaxyAPIController, UsesTagsMixin):
-    """
-    """
+    """ """
+
     @expose_api
     def index(self, trans, **kwd):
-        """
-        """
+        """ """
         tags = self._get_user_tags(trans, self.tagged_item_class, kwd[self.tagged_item_id])
-        return [self._api_value(tag, trans, view='collection') for tag in tags]
+        return [self._api_value(tag, trans, view="collection") for tag in tags]
 
     @expose_api
     def show(self, trans, tag_name, **kwd):
-        """
-        """
+        """ """
         tag = self._get_item_tag_assoc(trans, self.tagged_item_class, kwd[self.tagged_item_id], tag_name)
         if not tag:
             raise exceptions.ObjectNotFound("Failed to retrieve specified tag.")
@@ -34,8 +30,7 @@ class BaseItemTagsController(BaseGalaxyAPIController, UsesTagsMixin):
 
     @expose_api
     def create(self, trans, tag_name, payload=None, **kwd):
-        """
-        """
+        """ """
         payload = payload or {}
         value = payload.get("value", None)
         tag = self._apply_item_tag(trans, self.tagged_item_class, kwd[self.tagged_item_id], tag_name, value)
@@ -46,16 +41,15 @@ class BaseItemTagsController(BaseGalaxyAPIController, UsesTagsMixin):
 
     @expose_api
     def delete(self, trans, tag_name, **kwd):
-        """
-        """
+        """ """
         deleted = self._remove_items_tag(trans, self.tagged_item_class, kwd[self.tagged_item_id], tag_name)
         if not deleted:
             raise exceptions.RequestParameterInvalidException("Failed to delete specified tag.")
         # TODO: ugh - 204 would be better
-        return 'OK'
+        return "OK"
 
-    def _api_value(self, tag, trans, view='element'):
-        return tag.to_dict(view=view, value_mapper={'id': trans.security.encode_id})
+    def _api_value(self, tag, trans, view="element"):
+        return tag.to_dict(view=view, value_mapper={"id": trans.security.encode_id})
 
 
 class HistoryContentTagsController(BaseItemTagsController):
@@ -75,4 +69,5 @@ class WorkflowTagsController(BaseItemTagsController):
     tagged_item_class = "StoredWorkflow"
     tagged_item_id = "workflow_id"
 
+
 # TODO: Visualization and Pages once APIs for those are available
diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index 1376de16918..c182afbdb8e 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -8,7 +8,7 @@ import shutil
 from galaxy import (
     exceptions,
     model,
-    util
+    util,
 )
 from galaxy.web import (
     expose_api_anonymous_and_sessionless,
@@ -20,7 +20,7 @@ log = logging.getLogger(__name__)
 
 
 class JobFilesAPIController(BaseGalaxyAPIController):
-    """ This job files controller allows remote job running mechanisms to
+    """This job files controller allows remote job running mechanisms to
     read and modify the current state of files for queued and running jobs.
     It is certainly not meant to represent part of Galaxy's stable, user
     facing API.
@@ -56,7 +56,7 @@ class JobFilesAPIController(BaseGalaxyAPIController):
         """
         self.__authorize_job_access(trans, job_id, **kwargs)
         path = kwargs.get("path", None)
-        return open(path, 'rb')
+        return open(path, "rb")
 
     @expose_api_anonymous_and_sessionless
     def create(self, trans, job_id, payload, **kwargs):
@@ -87,19 +87,20 @@ class JobFilesAPIController(BaseGalaxyAPIController):
         self.__check_job_can_write_to_path(trans, job, path)
 
         # Is this writing an unneeded file? Should this just copy in Python?
-        if '__file_path' in payload:
-            file_path = payload.get('__file_path')
+        if "__file_path" in payload:
+            file_path = payload.get("__file_path")
             upload_store = trans.app.config.nginx_upload_job_files_store
-            assert upload_store, ("Request appears to have been processed by"
-                                  " nginx_upload_module but Galaxy is not"
-                                  " configured to recognize it")
-            assert file_path.startswith(upload_store), \
-                ("Filename provided by nginx (%s) is not in correct"
-                 " directory (%s)" % (file_path, upload_store))
+            assert upload_store, (
+                "Request appears to have been processed by"
+                " nginx_upload_module but Galaxy is not"
+                " configured to recognize it"
+            )
+            assert file_path.startswith(
+                upload_store
+            ), "Filename provided by nginx (%s) is not in correct" " directory (%s)" % (file_path, upload_store)
             input_file = open(file_path)
         else:
-            input_file = payload.get("file",
-                                     payload.get("__file", None)).file
+            input_file = payload.get("file", payload.get("__file", None)).file
         target_dir = os.path.dirname(path)
         util.safe_makedirs(target_dir)
         try:
@@ -132,7 +133,7 @@ class JobFilesAPIController(BaseGalaxyAPIController):
         return job
 
     def __check_job_can_write_to_path(self, trans, job, path):
-        """ Verify an idealized job runner should actually be able to write to
+        """Verify an idealized job runner should actually be able to write to
         the specified path - it must be a dataset output, a dataset "extra
         file", or a some place in the working directory of this job.
 
@@ -152,7 +153,7 @@ class JobFilesAPIController(BaseGalaxyAPIController):
         return in_temp_dir and os.path.split(path)[-1].startswith("GALAXY_VERSION_")
 
     def __is_output_dataset_path(self, job, path):
-        """ Check if is an output path for this job or a file in the an
+        """Check if is an output path for this job or a file in the an
         output's extra files path.
         """
         da_lists = [job.output_datasets, job.output_library_datasets]
@@ -168,5 +169,7 @@ class JobFilesAPIController(BaseGalaxyAPIController):
         return False
 
     def __in_working_directory(self, job, path, app):
-        working_directory = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
+        working_directory = app.object_store.get_filename(
+            job, base_dir="job_work", dir_only=True, extra_dir=str(job.id)
+        )
         return util.in_directory(path, working_directory)
diff --git a/lib/galaxy/webapps/galaxy/api/job_lock.py b/lib/galaxy/webapps/galaxy/api/job_lock.py
index bce2b9adf2e..2d68747fe99 100644
--- a/lib/galaxy/webapps/galaxy/api/job_lock.py
+++ b/lib/galaxy/webapps/galaxy/api/job_lock.py
@@ -1,20 +1,24 @@
-from fastapi import (
-    Body,
+from fastapi import Body
+
+from galaxy.managers.jobs import (
+    JobLock,
+    JobManager,
+)
+from . import (
+    depends,
+    Router,
 )
 
-from galaxy.managers.jobs import JobLock, JobManager
-from . import depends, Router
-
-router = Router(tags=['job_lock'])
+router = Router(tags=["job_lock"])
 
 
-@router.get('/api/job_lock', require_admin=True)
+@router.get("/api/job_lock", require_admin=True)
 def job_lock_status(job_manager: JobManager = depends(JobManager)) -> JobLock:
     """Get job lock status."""
     return job_manager.job_lock()
 
 
-@router.put('/api/job_lock', require_admin=True)
+@router.put("/api/job_lock", require_admin=True)
 def update_job_lock(job_manager: JobManager = depends(JobManager), job_lock: JobLock = Body(...)) -> JobLock:
     """Set job lock status."""
     return job_manager.update_job_lock(job_lock)
diff --git a/lib/galaxy/webapps/galaxy/api/job_ports.py b/lib/galaxy/webapps/galaxy/api/job_ports.py
index 76054cda133..bf63f84f89a 100644
--- a/lib/galaxy/webapps/galaxy/api/job_ports.py
+++ b/lib/galaxy/webapps/galaxy/api/job_ports.py
@@ -8,7 +8,7 @@ from . import BaseGalaxyAPIController
 
 
 class JobPortsAPIController(BaseGalaxyAPIController):
-    """ This job files controller allows remote job running mechanisms to
+    """This job files controller allows remote job running mechanisms to
     modify the current state of ports for queued and running jobs.
     It is certainly not meant to represent part of Galaxy's stable, user
     facing API.
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index b70837c8012..5b76d4682ed 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -7,9 +7,7 @@ API operations on a jobs.
 import logging
 import typing
 
-from sqlalchemy import (
-    or_,
-)
+from sqlalchemy import or_
 
 from galaxy import (
     exceptions,
@@ -17,7 +15,10 @@ from galaxy import (
     util,
 )
 from galaxy.managers import hdas
-from galaxy.managers.context import ProvidesHistoryContext, ProvidesUserContext
+from galaxy.managers.context import (
+    ProvidesHistoryContext,
+    ProvidesUserContext,
+)
 from galaxy.managers.jobs import (
     JobLock,
     JobManager,
@@ -33,12 +34,8 @@ from galaxy.web import (
     expose_api_anonymous,
     require_admin,
 )
-from galaxy.webapps.base.controller import (
-    UsesVisualizationMixin
-)
-from galaxy.work.context import (
-    WorkRequestContext,
-)
+from galaxy.webapps.base.controller import UsesVisualizationMixin
+from galaxy.work.context import WorkRequestContext
 from . import (
     BaseGalaxyAPIController,
     depends,
@@ -58,7 +55,12 @@ class FastAPIJobs:
     hda_manager: hdas.HDAManager = depends(hdas.HDAManager)
 
     @router.get("/api/job/{id}")
-    def show(self, id: EncodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans, full: typing.Optional[bool] = False) -> typing.Dict:
+    def show(
+        self,
+        id: EncodedDatabaseIdField,
+        trans: ProvidesUserContext = DependsOnTrans,
+        full: typing.Optional[bool] = False,
+    ) -> typing.Dict:
         """
         Return dictionary containing description of job data
 
@@ -127,14 +129,14 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :rtype:     list
         :returns:   list of dictionaries containing summary job information
         """
-        state = kwd.get('state', None)
+        state = kwd.get("state", None)
         is_admin = trans.user_is_admin
-        user_details = kwd.get('user_details', False)
-        user_id = kwd.get('user_id', None)
-        view = kwd.get('view', 'collection')
-        if view not in ('collection', 'admin_job_list'):
+        user_details = kwd.get("user_details", False)
+        user_id = kwd.get("user_id", None)
+        view = kwd.get("view", "collection")
+        if view not in ("collection", "admin_job_list"):
             raise exceptions.RequestParameterInvalidException(f"view parameter '{view} is invalid")
-        if view == 'admin_job_list' and not is_admin:
+        if view == "admin_job_list" and not is_admin:
             raise exceptions.AdminRequiredException("Only admins can use the admin_job_list view")
 
         if user_id:
@@ -164,37 +166,50 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
         query = build_and_apply_filters(query, state, lambda s: model.Job.state == s)
 
-        query = build_and_apply_filters(query, kwd.get('tool_id', None), lambda t: model.Job.tool_id == t)
-        query = build_and_apply_filters(query, kwd.get('tool_id_like', None), lambda t: model.Job.tool_id.like(t))
+        query = build_and_apply_filters(query, kwd.get("tool_id", None), lambda t: model.Job.tool_id == t)
+        query = build_and_apply_filters(query, kwd.get("tool_id_like", None), lambda t: model.Job.tool_id.like(t))
 
-        query = build_and_apply_filters(query, kwd.get('date_range_min', None), lambda dmin: model.Job.update_time >= dmin)
-        query = build_and_apply_filters(query, kwd.get('date_range_max', None), lambda dmax: model.Job.update_time <= dmax)
+        query = build_and_apply_filters(
+            query, kwd.get("date_range_min", None), lambda dmin: model.Job.update_time >= dmin
+        )
+        query = build_and_apply_filters(
+            query, kwd.get("date_range_max", None), lambda dmax: model.Job.update_time <= dmax
+        )
 
-        history_id = kwd.get('history_id', None)
-        workflow_id = kwd.get('workflow_id', None)
-        invocation_id = kwd.get('invocation_id', None)
+        history_id = kwd.get("history_id", None)
+        workflow_id = kwd.get("workflow_id", None)
+        invocation_id = kwd.get("invocation_id", None)
         if history_id is not None:
             decoded_history_id = self.decode_id(history_id)
             query = query.filter(model.Job.history_id == decoded_history_id)
         if workflow_id or invocation_id:
             if workflow_id is not None:
                 decoded_workflow_id = self.decode_id(workflow_id)
-                wfi_step = trans.sa_session.query(model.WorkflowInvocationStep).join(model.WorkflowInvocation).join(model.Workflow).filter(
-                    model.Workflow.stored_workflow_id == decoded_workflow_id,
-                ).subquery()
+                wfi_step = (
+                    trans.sa_session.query(model.WorkflowInvocationStep)
+                    .join(model.WorkflowInvocation)
+                    .join(model.Workflow)
+                    .filter(
+                        model.Workflow.stored_workflow_id == decoded_workflow_id,
+                    )
+                    .subquery()
+                )
             elif invocation_id is not None:
                 decoded_invocation_id = self.decode_id(invocation_id)
-                wfi_step = trans.sa_session.query(model.WorkflowInvocationStep).filter(
-                    model.WorkflowInvocationStep.workflow_invocation_id == decoded_invocation_id
-                ).subquery()
+                wfi_step = (
+                    trans.sa_session.query(model.WorkflowInvocationStep)
+                    .filter(model.WorkflowInvocationStep.workflow_invocation_id == decoded_invocation_id)
+                    .subquery()
+                )
             query1 = query.join(wfi_step)
             query2 = query.join(model.ImplicitCollectionJobsJobAssociation).join(
                 wfi_step,
-                model.ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id == wfi_step.c.implicit_collection_jobs_id
+                model.ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id
+                == wfi_step.c.implicit_collection_jobs_id,
             )
             query = query1.union(query2)
 
-        if kwd.get('order_by') == 'create_time':
+        if kwd.get("order_by") == "create_time":
             order_by = model.Job.create_time.desc()
         else:
             order_by = model.Job.update_time.desc()
@@ -207,10 +222,10 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         for job in query.yield_per(model.YIELD_PER_ROWS):
             job_dict = job.to_dict(view, system_details=is_admin)
             j = self.encode_all_ids(trans, job_dict, True)
-            if view == 'admin_job_list':
-                j['decoded_job_id'] = job.id
+            if view == "admin_job_list":
+                j["decoded_job_id"] = job.id
             if user_details:
-                j['user_email'] = job.get_user_email()
+                j["user_email"] = job.get_user_email()
             out.append(j)
 
         return out
@@ -232,7 +247,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :returns:   dictionary containing full description of job data
         """
         job = self.__get_job(trans, id)
-        full_output = util.asbool(kwd.get('full', 'false'))
+        full_output = util.asbool(kwd.get("full", "false"))
         return view_show_job(trans, job, full_output)
 
     @expose_api
@@ -420,7 +435,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         job = self.__get_job(trans, id)
         if not job:
             raise exceptions.ObjectNotFound(f"Could not access job with id '{id}'")
-        tool = self.app.toolbox.get_tool(job.tool_id, kwd.get('tool_version') or job.tool_version)
+        tool = self.app.toolbox.get_tool(job.tool_id, kwd.get("tool_version") or job.tool_version)
         if tool is None:
             raise exceptions.ObjectNotFound("Requested tool not found")
         if not tool.is_workflow_compatible:
@@ -455,8 +470,8 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
     @expose_api
     def create(self, trans: ProvidesUserContext, payload, **kwd):
-        """ See the create method in tools.py in order to submit a job. """
-        raise exceptions.NotImplemented('Please POST to /api/tools instead.')
+        """See the create method in tools.py in order to submit a job."""
+        raise exceptions.NotImplemented("Please POST to /api/tools instead.")
 
     @expose_api
     def search(self, trans: ProvidesHistoryContext, payload: dict, **kwd):
@@ -476,35 +491,39 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply
         recycle the old results.
         """
-        tool_id = payload.get('tool_id')
+        tool_id = payload.get("tool_id")
         if tool_id is None:
             raise exceptions.RequestParameterMissingException("No tool id")
         tool = trans.app.toolbox.get_tool(tool_id)
         if tool is None:
             raise exceptions.ObjectNotFound("Requested tool not found")
-        if 'inputs' not in payload:
+        if "inputs" not in payload:
             raise exceptions.RequestParameterMissingException("No inputs defined")
-        inputs = payload.get('inputs', {})
+        inputs = payload.get("inputs", {})
         # Find files coming in as multipart file data and add to inputs.
         for k, v in payload.items():
-            if k.startswith('files_') or k.startswith('__files_'):
+            if k.startswith("files_") or k.startswith("__files_"):
                 inputs[k] = v
         request_context = WorkRequestContext(app=trans.app, user=trans.user, history=trans.history)
-        all_params, all_errors, _, _ = tool.expand_incoming(trans=trans, incoming=inputs, request_context=request_context)
+        all_params, all_errors, _, _ = tool.expand_incoming(
+            trans=trans, incoming=inputs, request_context=request_context
+        )
         if any(all_errors):
             return []
         params_dump = [tool.params_to_strings(param, self.app, nested=True) for param in all_params]
         jobs = []
         for param_dump, param in zip(params_dump, all_params):
-            job = self.job_search.by_tool_input(trans=trans,
-                                                tool_id=tool_id,
-                                                tool_version=tool.version,
-                                                param=param,
-                                                param_dump=param_dump,
-                                                job_state=payload.get('state'))
+            job = self.job_search.by_tool_input(
+                trans=trans,
+                tool_id=tool_id,
+                tool_version=tool.version,
+                param=param,
+                param_dump=param_dump,
+                job_state=payload.get("state"),
+            )
             if job:
                 jobs.append(job)
-        return [self.encode_all_ids(trans, single_job.to_dict('element'), True) for single_job in jobs]
+        return [self.encode_all_ids(trans, single_job.to_dict("element"), True) for single_job in jobs]
 
     @expose_api_anonymous
     def error(self, trans: ProvidesUserContext, id, payload, **kwd):
@@ -520,18 +539,18 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :returns:   dictionary containing information regarding where the error report was sent.
         """
         # Get dataset on which this error was triggered
-        dataset_id = payload.get('dataset_id')
+        dataset_id = payload.get("dataset_id")
         if not dataset_id:
-            raise exceptions.RequestParameterMissingException('No dataset_id')
+            raise exceptions.RequestParameterMissingException("No dataset_id")
         decoded_dataset_id = self.decode_id(dataset_id)
         dataset = self.hda_manager.get_accessible(decoded_dataset_id, trans.user)
 
         # Get job
         job = self.__get_job(trans, id)
         if dataset.creating_job.id != job.id:
-            raise exceptions.RequestParameterInvalidException('dataset_id was not created by job_id')
+            raise exceptions.RequestParameterInvalidException("dataset_id was not created by job_id")
         tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version) or None
-        email = payload.get('email')
+        email = payload.get("email")
         if not email and not trans.anonymous:
             email = trans.user.email
         messages = trans.app.error_reports.default_error_plugin.submit_report(
@@ -541,10 +560,10 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
             user_submission=True,
             user=trans.user,
             email=email,
-            message=payload.get('message')
+            message=payload.get("message"),
         )
 
-        return {'messages': messages}
+        return {"messages": messages}
 
     @require_admin
     @expose_api
diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py
index ebb4f0dc49e..d4a0abdbdcb 100644
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -46,24 +46,18 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['libraries'])
+router = Router(tags=["libraries"])
 
 DeletedQueryParam: Optional[bool] = Query(
-    default=None,
-    title="Display deleted",
-    description="Whether to include deleted libraries in the result."
+    default=None, title="Display deleted", description="Whether to include deleted libraries in the result."
 )
 
 LibraryIdPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title="Library ID",
-    description="The encoded identifier of the Library."
+    ..., title="Library ID", description="The encoded identifier of the Library."
 )
 
 UndeleteQueryParam: Optional[bool] = Query(
-    default=None,
-    title="Undelete",
-    description="Whether to restore a deleted library."
+    default=None, title="Undelete", description="Whether to restore a deleted library."
 )
 
 
@@ -72,7 +66,7 @@ class FastAPILibraries:
     service: LibrariesService = depends(LibrariesService)
 
     @router.get(
-        '/api/libraries',
+        "/api/libraries",
         summary="Returns a list of summary data for all libraries.",
     )
     def index(
@@ -84,7 +78,7 @@ class FastAPILibraries:
         return self.service.index(trans, deleted)
 
     @router.get(
-        '/api/libraries/deleted',
+        "/api/libraries/deleted",
         summary="Returns a list of summary data for all libraries marked as deleted.",
     )
     def index_deleted(
@@ -95,7 +89,7 @@ class FastAPILibraries:
         return self.service.index(trans, True)
 
     @router.get(
-        '/api/libraries/{id}',
+        "/api/libraries/{id}",
         summary="Returns summary information about a particular library.",
     )
     def show(
@@ -107,7 +101,7 @@ class FastAPILibraries:
         return self.service.show(trans, id)
 
     @router.post(
-        '/api/libraries',
+        "/api/libraries",
         summary="Creates a new library and returns its summary information.",
         require_admin=True,
     )
@@ -120,7 +114,7 @@ class FastAPILibraries:
         return self.service.create(trans, payload)
 
     @router.put(
-        '/api/libraries/{id}',
+        "/api/libraries/{id}",
         summary="Updates the information of an existing library.",
         require_admin=True,
     )
@@ -135,7 +129,7 @@ class FastAPILibraries:
         return self.service.update(trans, id, payload)
 
     @router.delete(
-        '/api/libraries/{id}',
+        "/api/libraries/{id}",
         summary="Marks the specified library as deleted (or undeleted).",
         require_admin=True,
     )
@@ -153,7 +147,7 @@ class FastAPILibraries:
         return self.service.delete(trans, id, undelete)
 
     @router.get(
-        '/api/libraries/{id}/permissions',
+        "/api/libraries/{id}/permissions",
         summary="Gets the current or available permissions of a particular library.",
     )
     def get_permissions(
@@ -161,26 +155,23 @@ class FastAPILibraries:
         trans: ProvidesUserContext = DependsOnTrans,
         id: EncodedDatabaseIdField = LibraryIdPathParam,
         scope: Optional[LibraryPermissionScope] = Query(
-            None, title="Scope",
-            description="The scope of the permissions to retrieve. Either the `current` permissions or the `available`."
+            None,
+            title="Scope",
+            description="The scope of the permissions to retrieve. Either the `current` permissions or the `available`.",
         ),
         is_library_access: Optional[bool] = Query(
-            None, title="Is Library Access",
-            description="Indicates whether the roles available for the library access are requested."
+            None,
+            title="Is Library Access",
+            description="Indicates whether the roles available for the library access are requested.",
         ),
         page: Optional[int] = Query(
-            default=1,
-            title="Page",
-            description="The page number to retrieve when paginating the available roles."
+            default=1, title="Page", description="The page number to retrieve when paginating the available roles."
         ),
         page_limit: Optional[int] = Query(
-            default=10,
-            title="Page Limit",
-            description="The maximum number of permissions per page when paginating."
+            default=10, title="Page Limit", description="The maximum number of permissions per page when paginating."
         ),
         q: Optional[str] = Query(
-            None, title="Query",
-            description="Optional search text to retrieve only the roles matching this query."
+            None, title="Query", description="Optional search text to retrieve only the roles matching this query."
         ),
     ) -> Union[LibraryCurrentPermissions, LibraryAvailablePermissions]:
         """Gets the current or available permissions of a particular library.
@@ -196,7 +187,7 @@ class FastAPILibraries:
         )
 
     @router.post(
-        '/api/libraries/{id}/permissions',
+        "/api/libraries/{id}/permissions",
         summary="Sets the permissions to access and manipulate a library.",
     )
     def set_permissions(
@@ -212,10 +203,7 @@ class FastAPILibraries:
             LibraryPermissionsPayload,
             LegacyLibraryPermissionsPayload,
         ] = Body(...),
-    ) -> Union[
-        LibraryLegacySummary,  # Old legacy response
-        LibraryCurrentPermissions,
-    ]:
+    ) -> Union[LibraryLegacySummary, LibraryCurrentPermissions,]:  # Old legacy response
         """Sets the permissions to access and manipulate a library."""
         payload_dict = payload.dict(by_alias=True)
         if isinstance(payload, LibraryPermissionsPayload) and action is not None:
@@ -242,7 +230,7 @@ class LibrariesController(BaseGalaxyAPIController):
         .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys`
 
         """
-        deleted = util.string_as_bool_or_none(kwd.get('deleted', None))
+        deleted = util.string_as_bool_or_none(kwd.get("deleted", None))
         return self.service.index(trans, deleted)
 
     @expose_api_anonymous
@@ -292,24 +280,24 @@ class LibrariesController(BaseGalaxyAPIController):
     @expose_api
     def update(self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, payload: Dict[str, str], **kwd):
         """
-        * PATCH /api/libraries/{encoded_id}
-           Updates the library defined by an ``encoded_id`` with the data in the payload.
+         * PATCH /api/libraries/{encoded_id}
+            Updates the library defined by an ``encoded_id`` with the data in the payload.
 
-       .. note:: Currently, only admin users can update libraries. Also the library must not be `deleted`.
+        .. note:: Currently, only admin users can update libraries. Also the library must not be `deleted`.
 
-        :param  id:      the encoded id of the library
-        :type   id:      an encoded id string
-        :param  payload: dictionary structure containing::
-            :param name:         new library's name, cannot be empty
-            :type  name:         str
-            :param description:  new library's description
-            :type  description:  str
-            :param synopsis:     new library's synopsis
-            :type  synopsis:     str
-        :type   payload: dict
-        :returns:   detailed library information
-        :rtype:     dict
-        :raises: RequestParameterMissingException
+         :param  id:      the encoded id of the library
+         :type   id:      an encoded id string
+         :param  payload: dictionary structure containing::
+             :param name:         new library's name, cannot be empty
+             :type  name:         str
+             :param description:  new library's description
+             :type  description:  str
+             :param synopsis:     new library's synopsis
+             :type  synopsis:     str
+         :type   payload: dict
+         :returns:   detailed library information
+         :rtype:     dict
+         :raises: RequestParameterMissingException
         """
         update_payload = UpdateLibraryPayload(**payload)
         return self.service.update(trans, id, update_payload)
@@ -336,7 +324,7 @@ class LibrariesController(BaseGalaxyAPIController):
         """
         if payload:
             kwd.update(payload)
-        undelete = util.string_as_bool(kwd.get('undelete', False))
+        undelete = util.string_as_bool(kwd.get("undelete", False))
         return self.service.delete(trans, id, undelete)
 
     @expose_api
@@ -360,26 +348,30 @@ class LibrariesController(BaseGalaxyAPIController):
 
         :raises: InsufficientPermissionsException
         """
-        scope = kwd.get('scope', None)
-        is_library_access = util.string_as_bool(kwd.get('is_library_access', False))
-        page = kwd.get('page', None)
+        scope = kwd.get("scope", None)
+        is_library_access = util.string_as_bool(kwd.get("is_library_access", False))
+        page = kwd.get("page", None)
         if page is not None:
             page = int(page)
         else:
             page = 1
 
-        page_limit = kwd.get('page_limit', None)
+        page_limit = kwd.get("page_limit", None)
         if page_limit is not None:
             page_limit = int(page_limit)
         else:
             page_limit = 10
 
-        query = kwd.get('q', None)
+        query = kwd.get("q", None)
 
-        return self.service.get_permissions(trans, encoded_library_id, scope, is_library_access, page, page_limit, query)
+        return self.service.get_permissions(
+            trans, encoded_library_id, scope, is_library_access, page, page_limit, query
+        )
 
     @expose_api
-    def set_permissions(self, trans: ProvidesUserContext, encoded_library_id: EncodedDatabaseIdField, payload: Dict[str, Any], **kwd):
+    def set_permissions(
+        self, trans: ProvidesUserContext, encoded_library_id: EncodedDatabaseIdField, payload: Dict[str, Any], **kwd
+    ):
         """
         POST /api/libraries/{encoded_library_id}/permissions
 
diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py
index af8a68c92ee..aeb9d3d6595 100644
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -14,16 +14,19 @@ from galaxy import (
     managers,
     util,
 )
-from galaxy.actions.library import LibraryActions, validate_path_upload
+from galaxy.actions.library import (
+    LibraryActions,
+    validate_path_upload,
+)
 from galaxy.managers.collections_util import (
     api_payload_to_create_params,
-    dictify_dataset_collection_instance
+    dictify_dataset_collection_instance,
 )
 from galaxy.model import (
     ExtendedMetadata,
     ExtendedMetadataIndex,
     LibraryDataset,
-    tags
+    tags,
 )
 from galaxy.structured_app import StructuredApp
 from galaxy.web import expose_api
@@ -31,15 +34,16 @@ from galaxy.webapps.base.controller import (
     HTTPBadRequest,
     url_for,
     UsesFormDefinitionsMixin,
-    UsesLibraryMixinItems
+    UsesLibraryMixinItems,
 )
 from . import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
 
 
-class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems, UsesFormDefinitionsMixin, LibraryActions):
-
+class LibraryContentsController(
+    BaseGalaxyAPIController, UsesLibraryMixinItems, UsesFormDefinitionsMixin, LibraryActions
+):
     def __init__(self, app: StructuredApp, hda_manager: managers.hdas.HDAManager):
         super().__init__(app)
         self.hda_manager = hda_manager
@@ -77,51 +81,68 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
             rval = []
             for subfolder in folder.active_folders:
                 if not admin:
-                    can_access, folder_ids = trans.app.security_agent.check_folder_contents(trans.user, current_user_roles, subfolder)
+                    can_access, folder_ids = trans.app.security_agent.check_folder_contents(
+                        trans.user, current_user_roles, subfolder
+                    )
                 if (admin or can_access) and not subfolder.deleted:
                     subfolder.api_path = f"{folder.api_path}/{subfolder.name}"
-                    subfolder.api_type = 'folder'
+                    subfolder.api_type = "folder"
                     rval.append(subfolder)
                     rval.extend(traverse(subfolder))
             for ld in folder.datasets:
                 if not admin:
                     can_access = trans.app.security_agent.can_access_dataset(
-                        current_user_roles,
-                        ld.library_dataset_dataset_association.dataset
+                        current_user_roles, ld.library_dataset_dataset_association.dataset
                     )
                 if (admin or can_access) and not ld.deleted:
                     ld.api_path = f"{folder.api_path}/{ld.name}"
-                    ld.api_type = 'file'
+                    ld.api_type = "file"
                     rval.append(ld)
             return rval
 
         decoded_library_id = self.decode_id(library_id)
         try:
-            library = trans.sa_session.query(trans.app.model.Library).filter(trans.app.model.Library.table.c.id == decoded_library_id).one()
+            library = (
+                trans.sa_session.query(trans.app.model.Library)
+                .filter(trans.app.model.Library.table.c.id == decoded_library_id)
+                .one()
+            )
         except MultipleResultsFound:
-            raise exceptions.InconsistentDatabase('Multiple libraries found with the same id.')
+            raise exceptions.InconsistentDatabase("Multiple libraries found with the same id.")
         except NoResultFound:
-            raise exceptions.RequestParameterInvalidException('No library found with the id provided.')
+            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
         except Exception as e:
             raise exceptions.InternalServerError(f"Error loading from the database.{util.unicodify(e)}")
         if not (trans.user_is_admin or trans.app.security_agent.can_access_library(current_user_roles, library)):
-            raise exceptions.RequestParameterInvalidException('No library found with the id provided.')
+            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
         encoded_id = f"F{trans.security.encode_id(library.root_folder.id)}"
         # appending root folder
-        rval.append(dict(id=encoded_id,
-                         type='folder',
-                         name='/',
-                         url=url_for('library_content', library_id=library_id, id=encoded_id)))
-        library.root_folder.api_path = ''
+        rval.append(
+            dict(
+                id=encoded_id,
+                type="folder",
+                name="/",
+                url=url_for("library_content", library_id=library_id, id=encoded_id),
+            )
+        )
+        library.root_folder.api_path = ""
         # appending all other items in the library recursively
         for content in traverse(library.root_folder):
             encoded_id = trans.security.encode_id(content.id)
-            if content.api_type == 'folder':
+            if content.api_type == "folder":
                 encoded_id = f"F{encoded_id}"
-            rval.append(dict(id=encoded_id,
-                             type=content.api_type,
-                             name=content.api_path,
-                             url=url_for('library_content', library_id=library_id, id=encoded_id, )))
+            rval.append(
+                dict(
+                    id=encoded_id,
+                    type=content.api_type,
+                    name=content.api_path,
+                    url=url_for(
+                        "library_content",
+                        library_id=library_id,
+                        id=encoded_id,
+                    ),
+                )
+            )
         return rval
 
     @expose_api
@@ -145,23 +166,23 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
             :attr:`galaxy.model.LibraryFolder.dict_element_visible_keys`
         """
         class_name, content_id = self._decode_library_content_id(id)
-        if class_name == 'LibraryFolder':
+        if class_name == "LibraryFolder":
             content = self.get_library_folder(trans, content_id, check_ownership=False, check_accessible=True)
-            rval = content.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
-            rval['id'] = f"F{str(rval['id'])}"
-            if rval['parent_id'] is not None:  # This can happen for root folders.
-                rval['parent_id'] = f"F{str(trans.security.encode_id(rval['parent_id']))}"
-            rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id'])
+            rval = content.to_dict(view="element", value_mapper={"id": trans.security.encode_id})
+            rval["id"] = f"F{str(rval['id'])}"
+            if rval["parent_id"] is not None:  # This can happen for root folders.
+                rval["parent_id"] = f"F{str(trans.security.encode_id(rval['parent_id']))}"
+            rval["parent_library_id"] = trans.security.encode_id(rval["parent_library_id"])
         else:
             content = self.get_library_dataset(trans, content_id, check_ownership=False, check_accessible=True)
-            rval = content.to_dict(view='element')
-            rval['id'] = trans.security.encode_id(rval['id'])
-            rval['ldda_id'] = trans.security.encode_id(rval['ldda_id'])
-            rval['folder_id'] = f"F{str(trans.security.encode_id(rval['folder_id']))}"
-            rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id'])
+            rval = content.to_dict(view="element")
+            rval["id"] = trans.security.encode_id(rval["id"])
+            rval["ldda_id"] = trans.security.encode_id(rval["ldda_id"])
+            rval["folder_id"] = f"F{str(trans.security.encode_id(rval['folder_id']))}"
+            rval["parent_library_id"] = trans.security.encode_id(rval["parent_library_id"])
 
             tag_manager = tags.GalaxyTagHandler(trans.sa_session)
-            rval['tags'] = tag_manager.get_tags_str(content.library_dataset_dataset_association.tags)
+            rval["tags"] = tag_manager.get_tags_str(content.library_dataset_dataset_association.tags)
         return rval
 
     @expose_api
@@ -218,54 +239,72 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         """
         if trans.user_is_bootstrap_admin:
             raise exceptions.RealUserRequiredException("Only real users can create a new library file or folder.")
-        if 'create_type' not in payload:
+        if "create_type" not in payload:
             raise exceptions.RequestParameterMissingException("Missing required 'create_type' parameter.")
-        create_type = payload.pop('create_type')
-        if create_type not in ('file', 'folder', 'collection'):
-            raise exceptions.RequestParameterInvalidException(f"Invalid value for 'create_type' parameter ( {create_type} ) specified.")
-        if 'upload_option' in payload and payload['upload_option'] not in ('upload_file', 'upload_directory', 'upload_paths'):
-            raise exceptions.RequestParameterInvalidException(f"Invalid value for 'upload_option' parameter ( {payload['upload_option']} ) specified.")
-        if 'folder_id' not in payload:
+        create_type = payload.pop("create_type")
+        if create_type not in ("file", "folder", "collection"):
+            raise exceptions.RequestParameterInvalidException(
+                f"Invalid value for 'create_type' parameter ( {create_type} ) specified."
+            )
+        if "upload_option" in payload and payload["upload_option"] not in (
+            "upload_file",
+            "upload_directory",
+            "upload_paths",
+        ):
+            raise exceptions.RequestParameterInvalidException(
+                f"Invalid value for 'upload_option' parameter ( {payload['upload_option']} ) specified."
+            )
+        if "folder_id" not in payload:
             raise exceptions.RequestParameterMissingException("Missing required 'folder_id' parameter.")
-        folder_id = payload.pop('folder_id')
+        folder_id = payload.pop("folder_id")
         _, folder_id = self._decode_library_content_id(folder_id)
         # security is checked in the downstream controller
         parent = self.get_library_folder(trans, folder_id, check_ownership=False, check_accessible=False)
         # The rest of the security happens in the library_common controller.
         real_folder_id = trans.security.encode_id(parent.id)
 
-        payload['tag_using_filenames'] = util.string_as_bool(payload.get('tag_using_filenames', None))
-        payload['tags'] = util.listify(payload.get('tags', None))
+        payload["tag_using_filenames"] = util.string_as_bool(payload.get("tag_using_filenames", None))
+        payload["tags"] = util.listify(payload.get("tags", None))
 
         # are we copying an HDA to the library folder?
         #   we'll need the id and any message to attach, then branch to that private function
-        from_hda_id, from_hdca_id, ldda_message = (payload.pop('from_hda_id', None), payload.pop('from_hdca_id', None), payload.pop('ldda_message', ''))
-        if create_type == 'file':
+        from_hda_id, from_hdca_id, ldda_message = (
+            payload.pop("from_hda_id", None),
+            payload.pop("from_hdca_id", None),
+            payload.pop("ldda_message", ""),
+        )
+        if create_type == "file":
             if from_hda_id:
-                return self._copy_hda_to_library_folder(trans, self.hda_manager, self.decode_id(from_hda_id), real_folder_id, ldda_message)
+                return self._copy_hda_to_library_folder(
+                    trans, self.hda_manager, self.decode_id(from_hda_id), real_folder_id, ldda_message
+                )
             if from_hdca_id:
-                return self._copy_hdca_to_library_folder(trans, self.hda_manager, self.decode_id(from_hdca_id), real_folder_id, ldda_message)
+                return self._copy_hdca_to_library_folder(
+                    trans, self.hda_manager, self.decode_id(from_hdca_id), real_folder_id, ldda_message
+                )
 
         # check for extended metadata, store it and pop it out of the param
         # otherwise sanitize_param will have a fit
-        ex_meta_payload = payload.pop('extended_metadata', None)
+        ex_meta_payload = payload.pop("extended_metadata", None)
 
         # Now create the desired content object, either file or folder.
-        if create_type == 'file':
+        if create_type == "file":
             status, output = self._upload_library_dataset(trans, library_id, real_folder_id, **payload)
-        elif create_type == 'folder':
+        elif create_type == "folder":
             status, output = self._create_folder(trans, real_folder_id, library_id, **payload)
-        elif create_type == 'collection':
+        elif create_type == "collection":
             # Not delegating to library_common, so need to check access to parent
             # folder here.
             self.check_user_can_add_to_library_item(trans, parent, check_accessible=True)
             create_params = api_payload_to_create_params(payload)
-            create_params['parent'] = parent
+            create_params["parent"] = parent
             dataset_collection_manager = trans.app.dataset_collection_manager
             dataset_collection_instance = dataset_collection_manager.create(**create_params)
-            return [dictify_dataset_collection_instance(
-                dataset_collection_instance, security=trans.security, url_builder=trans.url_builder, parent=parent
-            )]
+            return [
+                dictify_dataset_collection_instance(
+                    dataset_collection_instance, security=trans.security, url_builder=trans.url_builder, parent=parent
+                )
+            ]
         if status != 200:
             trans.response.status = status
             return output
@@ -286,26 +325,28 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
                 if type(v) == trans.app.model.LibraryDatasetDatasetAssociation:
                     v = v.library_dataset
                 encoded_id = trans.security.encode_id(v.id)
-                if create_type == 'folder':
+                if create_type == "folder":
                     encoded_id = f"F{encoded_id}"
-                rval.append(dict(id=encoded_id,
-                                 name=v.name,
-                                 url=url_for('library_content', library_id=library_id, id=encoded_id)))
+                rval.append(
+                    dict(
+                        id=encoded_id, name=v.name, url=url_for("library_content", library_id=library_id, id=encoded_id)
+                    )
+                )
             return rval
 
     def _upload_library_dataset(self, trans, library_id, folder_id, **kwd):
-        replace_id = kwd.get('replace_id', None)
+        replace_id = kwd.get("replace_id", None)
         replace_dataset: Optional[LibraryDataset] = None
-        upload_option = kwd.get('upload_option', 'upload_file')
-        dbkey = kwd.get('dbkey', '?')
+        upload_option = kwd.get("upload_option", "upload_file")
+        dbkey = kwd.get("dbkey", "?")
         if isinstance(dbkey, list):
             last_used_build = dbkey[0]
         else:
             last_used_build = dbkey
-        roles = kwd.get('roles', '')
+        roles = kwd.get("roles", "")
         is_admin = trans.user_is_admin
         current_user_roles = trans.get_current_user_roles()
-        if replace_id not in ['', None, 'None']:
+        if replace_id not in ["", None, "None"]:
             replace_dataset = trans.sa_session.query(LibraryDataset).get(trans.security.decode_id(replace_id))
             self._check_access(trans, is_admin, replace_dataset, current_user_roles)
             self._check_modify(trans, is_admin, replace_dataset, current_user_roles)
@@ -320,24 +361,24 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
             self._check_access(trans, is_admin, folder, current_user_roles)
             self._check_add(trans, is_admin, folder, current_user_roles)
             library = folder.parent_library
-        if folder and last_used_build in ['None', None, '?']:
+        if folder and last_used_build in ["None", None, "?"]:
             last_used_build = folder.genome_build
         error = False
-        if upload_option == 'upload_paths':
+        if upload_option == "upload_paths":
             validate_path_upload(trans)  # Duplicate check made in _upload_dataset.
         elif roles:
             # Check to see if the user selected roles to associate with the DATASET_ACCESS permission
             # on the dataset that would cause accessibility issues.
             vars = dict(DATASET_ACCESS_in=roles)
-            permissions, in_roles, error, message = \
-                trans.app.security_agent.derive_roles_from_access(trans, library.id, 'api', library=True, **vars)
+            permissions, in_roles, error, message = trans.app.security_agent.derive_roles_from_access(
+                trans, library.id, "api", library=True, **vars
+            )
         if error:
             return 400, message
         else:
-            created_outputs_dict = self._upload_dataset(trans,
-                                                        folder_id=trans.security.encode_id(folder.id),
-                                                        replace_dataset=replace_dataset,
-                                                        **kwd)
+            created_outputs_dict = self._upload_dataset(
+                trans, folder_id=trans.security.encode_id(folder.id), replace_dataset=replace_dataset, **kwd
+            )
             if created_outputs_dict:
                 if type(created_outputs_dict) == str:
                     return 400, created_outputs_dict
@@ -392,24 +433,26 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         :rtype:     None
         :returns:   None
         """
-        if 'converted_dataset_id' in payload:
-            converted_id = payload.pop('converted_dataset_id')
+        if "converted_dataset_id" in payload:
+            converted_id = payload.pop("converted_dataset_id")
             content = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=False)
             content_conv = self.get_library_dataset(trans, converted_id, check_ownership=False, check_accessible=False)
-            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(parent=content.library_dataset_dataset_association,
-                                                                          dataset=content_conv.library_dataset_dataset_association,
-                                                                          file_type=content_conv.library_dataset_dataset_association.extension,
-                                                                          metadata_safe=True)
+            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
+                parent=content.library_dataset_dataset_association,
+                dataset=content_conv.library_dataset_dataset_association,
+                file_type=content_conv.library_dataset_dataset_association.extension,
+                metadata_safe=True,
+            )
             trans.sa_session.add(assoc)
             trans.sa_session.flush()
 
     def _decode_library_content_id(self, content_id):
         if len(content_id) % 16 == 0:
-            return 'LibraryDataset', content_id
-        elif content_id.startswith('F'):
-            return 'LibraryFolder', content_id[1:]
+            return "LibraryDataset", content_id
+        elif content_id.startswith("F"):
+            return "LibraryFolder", content_id[1:]
         else:
-            raise HTTPBadRequest(f'Malformed library content id ( {str(content_id)} ) specified, unable to decode.')
+            raise HTTPBadRequest(f"Malformed library content id ( {str(content_id)} ) specified, unable to decode.")
 
     @expose_api
     def delete(self, trans, library_id, id, **kwd):
@@ -433,18 +476,18 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
             * purged:     if the library dataset was purged
         """
         purge = False
-        if kwd.get('payload', None):
-            purge = util.string_as_bool(kwd['payload'].get('purge', False))
+        if kwd.get("payload", None):
+            purge = util.string_as_bool(kwd["payload"].get("purge", False))
 
-        rval = {'id': id}
+        rval = {"id": id}
         try:
             ld = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=True)
             user_is_admin = trans.user_is_admin
             can_modify = trans.app.security_agent.can_modify_library_item(trans.user.all_roles(), ld)
-            log.debug('is_admin: %s, can_modify: %s', user_is_admin, can_modify)
+            log.debug("is_admin: %s, can_modify: %s", user_is_admin, can_modify)
             if not (user_is_admin or can_modify):
                 trans.response.status = 403
-                rval.update({'error': 'Unauthorized to delete or purge this library dataset'})
+                rval.update({"error": "Unauthorized to delete or purge this library dataset"})
                 return rval
 
             ld.deleted = True
@@ -467,19 +510,17 @@ class LibraryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
                         pass
                     # flush now to preserve deleted state in case of later interruption
                     trans.sa_session.flush()
-                rval['purged'] = True
+                rval["purged"] = True
             trans.sa_session.flush()
-            rval['deleted'] = True
+            rval["deleted"] = True
 
         except exceptions.httpexceptions.HTTPInternalServerError:
-            log.exception('Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s',
-                          id, str(kwd))
+            log.exception("Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s", id, str(kwd))
             raise
         except exceptions.httpexceptions.HTTPException:
             raise
         except Exception as exc:
-            log.exception('library_contents API, delete: uncaught exception: %s, %s',
-                          id, str(kwd))
+            log.exception("library_contents API, delete: uncaught exception: %s, %s", id, str(kwd))
             trans.response.status = 500
-            rval.update({'error': util.unicodify(exc)})
+            rval.update({"error": util.unicodify(exc)})
         return rval
diff --git a/lib/galaxy/webapps/galaxy/api/library_datasets.py b/lib/galaxy/webapps/galaxy/api/library_datasets.py
index 9da03f23366..2bff35929a1 100644
--- a/lib/galaxy/webapps/galaxy/api/library_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/library_datasets.py
@@ -6,21 +6,24 @@ import os.path
 import string
 from json import dumps
 
-from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
+from paste.httpexceptions import (
+    HTTPBadRequest,
+    HTTPInternalServerError,
+)
 
 from galaxy import (
     exceptions,
     util,
-    web
+    web,
 )
 from galaxy.actions.library import LibraryActions
 from galaxy.exceptions import ObjectNotFound
+from galaxy.managers import base as managers_base
 from galaxy.managers import (
-    base as managers_base,
     folders,
     lddas,
     library_datasets,
-    roles
+    roles,
 )
 from galaxy.structured_app import StructuredApp
 from galaxy.tools.actions import upload_common
@@ -36,16 +39,13 @@ from galaxy.web import (
     expose_api,
     expose_api_anonymous,
 )
-from galaxy.webapps.base.controller import (
-    UsesVisualizationMixin,
-)
+from galaxy.webapps.base.controller import UsesVisualizationMixin
 from . import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
 
 
 class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin, LibraryActions):
-
     def __init__(self, app: StructuredApp):
         super().__init__(app)
         self.app = app
@@ -92,12 +92,14 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
 
         try:
-            ldda = self.get_library_dataset_dataset_association(trans, id=encoded_ldda_id, check_ownership=False, check_accessible=False)
+            ldda = self.get_library_dataset_dataset_association(
+                trans, id=encoded_ldda_id, check_ownership=False, check_accessible=False
+            )
         except Exception as e:
             raise exceptions.ObjectNotFound(f"Requested version of library dataset was not found.{util.unicodify(e)}")
 
         if ldda not in library_dataset.expired_datasets:
-            raise exceptions.ObjectNotFound('Given library dataset does not have the requested version.')
+            raise exceptions.ObjectNotFound("Given library dataset does not have the requested version.")
 
         rval = trans.security.encode_all_ids(ldda.to_dict())
         return rval
@@ -127,22 +129,24 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         # User has to have manage permissions permission in order to see the roles.
         can_manage = trans.app.security_agent.can_manage_dataset(current_user_roles, dataset) or trans.user_is_admin
         if not can_manage:
-            raise exceptions.InsufficientPermissionsException('You do not have proper permission to access permissions.')
-        scope = kwd.get('scope', None)
-        if scope in ['current', None]:
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permission to access permissions."
+            )
+        scope = kwd.get("scope", None)
+        if scope in ["current", None]:
             return self._get_current_roles(trans, library_dataset)
-        elif scope in ['available']:
-            page = kwd.get('page', None)
+        elif scope in ["available"]:
+            page = kwd.get("page", None)
             if page is not None:
                 page = int(page)
             else:
                 page = 1
-            page_limit = kwd.get('page_limit', None)
+            page_limit = kwd.get("page_limit", None)
             if page_limit is not None:
                 page_limit = int(page_limit)
             else:
                 page_limit = 10
-            query = kwd.get('q', None)
+            query = kwd.get("q", None)
             roles, total_roles = trans.app.security_agent.get_valid_roles(trans, dataset, query, page, page_limit)
             return_roles = []
             for role in roles:
@@ -150,7 +154,9 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 return_roles.append(dict(id=role_id, name=role.name, type=role.type))
             return dict(roles=return_roles, page=page, page_limit=page_limit, total=total_roles)
         else:
-            raise exceptions.RequestParameterInvalidException("The value of 'scope' parameter is invalid. Alllowed values: current, available")
+            raise exceptions.RequestParameterInvalidException(
+                "The value of 'scope' parameter is invalid. Alllowed values: current, available"
+            )
 
     def _get_current_roles(self, trans, library_dataset):
         """
@@ -226,34 +232,40 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         """
         if payload:
             kwd.update(payload)
-        action = kwd.get('action', None)
-        if action not in ['remove_restrictions', 'make_private', 'set_permissions']:
-            raise exceptions.RequestParameterInvalidException('The mandatory parameter "action" has an invalid value. '
-                                                              'Allowed values are: "remove_restrictions", "make_private", "set_permissions"')
+        action = kwd.get("action", None)
+        if action not in ["remove_restrictions", "make_private", "set_permissions"]:
+            raise exceptions.RequestParameterInvalidException(
+                'The mandatory parameter "action" has an invalid value. '
+                'Allowed values are: "remove_restrictions", "make_private", "set_permissions"'
+            )
         library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
         # Some permissions are attached directly to the underlying dataset.
         dataset = library_dataset.library_dataset_dataset_association.dataset
         current_user_roles = trans.get_current_user_roles()
         can_manage = trans.app.security_agent.can_manage_dataset(current_user_roles, dataset) or trans.user_is_admin
         if not can_manage:
-            raise exceptions.InsufficientPermissionsException('You do not have proper permissions to manage permissions on this dataset.')
-        new_access_roles_ids = util.listify(kwd.get('access_ids[]', None))
-        new_manage_roles_ids = util.listify(kwd.get('manage_ids[]', None))
-        new_modify_roles_ids = util.listify(kwd.get('modify_ids[]', None))
-        if action == 'remove_restrictions':
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permissions to manage permissions on this dataset."
+            )
+        new_access_roles_ids = util.listify(kwd.get("access_ids[]", None))
+        new_manage_roles_ids = util.listify(kwd.get("manage_ids[]", None))
+        new_modify_roles_ids = util.listify(kwd.get("modify_ids[]", None))
+        if action == "remove_restrictions":
             trans.app.security_agent.make_dataset_public(dataset)
             if not trans.app.security_agent.dataset_is_public(dataset):
-                raise exceptions.InternalServerError('An error occurred while making dataset public.')
-        elif action == 'make_private':
+                raise exceptions.InternalServerError("An error occurred while making dataset public.")
+        elif action == "make_private":
             if not trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
                 private_role = trans.app.security_agent.get_private_user_role(trans.user)
-                dp = trans.app.model.DatasetPermissions(trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role)
+                dp = trans.app.model.DatasetPermissions(
+                    trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role
+                )
                 trans.sa_session.add(dp)
                 trans.sa_session.flush()
             if not trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
                 # Check again and inform the user if dataset is not private.
-                raise exceptions.InternalServerError('An error occurred and the dataset is NOT private.')
-        elif action == 'set_permissions':
+                raise exceptions.InternalServerError("An error occurred and the dataset is NOT private.")
+        elif action == "set_permissions":
             # ACCESS DATASET ROLES
             valid_access_roles = []
             invalid_access_roles_ids = []
@@ -268,7 +280,9 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                     else:
                         invalid_access_roles_ids.append(role_id)
                 if len(invalid_access_roles_ids) > 0:
-                    log.warning(f"The following roles could not be added to the dataset access permission: {str(invalid_access_roles_ids)}")
+                    log.warning(
+                        f"The following roles could not be added to the dataset access permission: {str(invalid_access_roles_ids)}"
+                    )
 
                 access_permission = dict(access=valid_access_roles)
                 trans.app.security_agent.set_dataset_permission(dataset, access_permission)
@@ -284,8 +298,12 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 else:
                     invalid_manage_roles_ids.append(role_id)
             if len(invalid_manage_roles_ids) > 0:
-                log.warning(f"The following roles could not be added to the dataset manage permission: {str(invalid_manage_roles_ids)}")
-            manage_permission = {trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS: valid_manage_roles}
+                log.warning(
+                    f"The following roles could not be added to the dataset manage permission: {str(invalid_manage_roles_ids)}"
+                )
+            manage_permission = {
+                trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS: valid_manage_roles
+            }
             trans.app.security_agent.set_dataset_permission(dataset, manage_permission)
 
             # MODIFY LIBRARY ITEM ROLES
@@ -299,7 +317,9 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 else:
                     invalid_modify_roles_ids.append(role_id)
             if len(invalid_modify_roles_ids) > 0:
-                log.warning(f"The following roles could not be added to the dataset modify permission: {str(invalid_modify_roles_ids)}")
+                log.warning(
+                    f"The following roles could not be added to the dataset modify permission: {str(invalid_modify_roles_ids)}"
+                )
             modify_permission = {trans.app.security_agent.permitted_actions.LIBRARY_MODIFY: valid_modify_roles}
             trans.app.security_agent.set_library_item_permission(library_dataset, modify_permission)
         return self._get_current_roles(trans, library_dataset)
@@ -319,12 +339,14 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         :returns:   dict containing information about the dataset
         :rtype:     dictionary
         """
-        undelete = util.string_as_bool(kwd.get('undelete', False))
+        undelete = util.string_as_bool(kwd.get("undelete", False))
         library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
         current_user_roles = trans.get_current_user_roles()
         allowed = trans.app.security_agent.can_modify_library_item(current_user_roles, library_dataset)
         if (not allowed) and (not trans.user_is_admin):
-            raise exceptions.InsufficientPermissionsException('You do not have proper permissions to delete this dataset.')
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permissions to delete this dataset."
+            )
 
         if undelete:
             library_dataset.deleted = False
@@ -336,10 +358,10 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
 
         rval = trans.security.encode_all_ids(library_dataset.to_dict())
         nice_size = util.nice_size(int(library_dataset.library_dataset_dataset_association.get_size()))
-        rval['file_size'] = nice_size
-        rval['update_time'] = library_dataset.update_time.strftime("%Y-%m-%d %I:%M %p")
-        rval['deleted'] = library_dataset.deleted
-        rval['folder_id'] = f"F{rval['folder_id']}"
+        rval["file_size"] = nice_size
+        rval["update_time"] = library_dataset.update_time.strftime("%Y-%m-%d %I:%M %p")
+        rval["deleted"] = library_dataset.deleted
+        rval["folder_id"] = f"F{rval['folder_id']}"
         return rval
 
     @expose_api
@@ -401,80 +423,102 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         """
         if payload:
             kwd.update(payload)
-        kwd['space_to_tab'] = False
-        kwd['to_posix_lines'] = True
-        kwd['dbkey'] = kwd.get('dbkey', '?')
-        kwd['file_type'] = kwd.get('file_type', 'auto')
-        kwd['link_data_only'] = 'link_to_files' if util.string_as_bool(kwd.get('link_data', False)) else 'copy_files'
-        kwd['tag_using_filenames'] = util.string_as_bool(kwd.get('tag_using_filenames', None))
-        encoded_folder_id = kwd.get('encoded_folder_id', None)
+        kwd["space_to_tab"] = False
+        kwd["to_posix_lines"] = True
+        kwd["dbkey"] = kwd.get("dbkey", "?")
+        kwd["file_type"] = kwd.get("file_type", "auto")
+        kwd["link_data_only"] = "link_to_files" if util.string_as_bool(kwd.get("link_data", False)) else "copy_files"
+        kwd["tag_using_filenames"] = util.string_as_bool(kwd.get("tag_using_filenames", None))
+        encoded_folder_id = kwd.get("encoded_folder_id", None)
         if encoded_folder_id is not None:
             folder_id = self.folder_manager.cut_and_decode(trans, encoded_folder_id)
         else:
-            raise exceptions.RequestParameterMissingException('The required attribute encoded_folder_id is missing.')
-        path = kwd.get('path', None)
+            raise exceptions.RequestParameterMissingException("The required attribute encoded_folder_id is missing.")
+        path = kwd.get("path", None)
         if path is None:
-            raise exceptions.RequestParameterMissingException('The required attribute path is missing.')
+            raise exceptions.RequestParameterMissingException("The required attribute path is missing.")
         if not isinstance(path, str):
-            raise exceptions.RequestParameterInvalidException('The required attribute path is not String.')
+            raise exceptions.RequestParameterInvalidException("The required attribute path is not String.")
 
         folder = self.folder_manager.get(trans, folder_id)
 
-        source = kwd.get('source', None)
-        if source not in ['userdir_file', 'userdir_folder', 'importdir_file', 'importdir_folder', 'admin_path']:
-            raise exceptions.RequestParameterMissingException('You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder", "admin_path", "importdir_file" and "importdir_folder". ')
-        elif source in ['importdir_file', 'importdir_folder']:
+        source = kwd.get("source", None)
+        if source not in ["userdir_file", "userdir_folder", "importdir_file", "importdir_folder", "admin_path"]:
+            raise exceptions.RequestParameterMissingException(
+                'You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder", "admin_path", "importdir_file" and "importdir_folder". '
+            )
+        elif source in ["importdir_file", "importdir_folder"]:
             if not trans.user_is_admin:
-                raise exceptions.AdminRequiredException('Only admins can import from importdir.')
+                raise exceptions.AdminRequiredException("Only admins can import from importdir.")
             if not trans.app.config.library_import_dir:
-                raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow admins to import into library from importdir.')
+                raise exceptions.ConfigDoesNotAllowException(
+                    "The configuration of this Galaxy instance does not allow admins to import into library from importdir."
+                )
             import_base_dir = trans.app.config.library_import_dir
             if not safe_relpath(path):
                 # admins shouldn't be able to explicitly specify a path outside server_dir, but symlinks are allowed.
                 # the reasoning here is that galaxy admins may not have direct filesystem access or can only access
                 # library_import_dir via FTP (which cannot create symlinks), and may rely on sysadmins to set up the
                 # import directory. if they have filesystem access, all bets are off.
-                raise exceptions.RequestParameterInvalidException('The given path is invalid.')
+                raise exceptions.RequestParameterInvalidException("The given path is invalid.")
             path = os.path.join(import_base_dir, path)
-        elif source in ['userdir_file', 'userdir_folder']:
+        elif source in ["userdir_file", "userdir_folder"]:
             username = trans.user.username if trans.app.config.user_library_import_check_permissions else None
             user_login = trans.user.email
             user_base_dir = trans.app.config.user_library_import_dir
             if user_base_dir is None:
-                raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow upload from user directories.')
+                raise exceptions.ConfigDoesNotAllowException(
+                    "The configuration of this Galaxy instance does not allow upload from user directories."
+                )
             full_dir = os.path.join(user_base_dir, user_login)
 
             if not safe_contains(full_dir, path, allowlist=trans.app.config.user_library_import_symlink_allowlist):
                 # the path is a symlink outside the user dir
                 path = os.path.join(full_dir, path)
-                log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', path, os.path.realpath(path))
-                raise exceptions.RequestParameterInvalidException('The given path is invalid.')
-            if trans.app.config.user_library_import_check_permissions and not full_path_permission_for_user(full_dir, path, username):
-                log.error('User attempted to import a path that resolves to a path outside of their import dir: '
-                        '%s -> %s and cannot be read by them.', path, os.path.realpath(path))
-                raise exceptions.RequestParameterInvalidException('The given path is invalid.')
+                log.error(
+                    "User attempted to import a path that resolves to a path outside of their import dir: %s -> %s",
+                    path,
+                    os.path.realpath(path),
+                )
+                raise exceptions.RequestParameterInvalidException("The given path is invalid.")
+            if trans.app.config.user_library_import_check_permissions and not full_path_permission_for_user(
+                full_dir, path, username
+            ):
+                log.error(
+                    "User attempted to import a path that resolves to a path outside of their import dir: "
+                    "%s -> %s and cannot be read by them.",
+                    path,
+                    os.path.realpath(path),
+                )
+                raise exceptions.RequestParameterInvalidException("The given path is invalid.")
             path = os.path.join(full_dir, path)
-            if unsafe_walk(path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username):
+            if unsafe_walk(
+                path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username
+            ):
                 # the path is a dir and contains files that symlink outside the user dir
-                error = 'User attempted to import a path that resolves to a path outside of their import dir: {} -> {}'.format(
+                error = "User attempted to import a path that resolves to a path outside of their import dir: {} -> {}".format(
                     path, os.path.realpath(path)
                 )
                 if trans.app.config.user_library_import_check_permissions:
-                    error += ' or is not readable for them.'
+                    error += " or is not readable for them."
                 log.error(error)
-                raise exceptions.RequestParameterInvalidException('The given path is invalid.')
+                raise exceptions.RequestParameterInvalidException("The given path is invalid.")
             if not os.path.exists(path):
-                raise exceptions.RequestParameterInvalidException('Given path does not exist on the host.')
+                raise exceptions.RequestParameterInvalidException("Given path does not exist on the host.")
             if not self.folder_manager.can_add_item(trans, folder):
-                raise exceptions.InsufficientPermissionsException('You do not have proper permission to add items to the given folder.')
-        elif source == 'admin_path':
+                raise exceptions.InsufficientPermissionsException(
+                    "You do not have proper permission to add items to the given folder."
+                )
+        elif source == "admin_path":
             if not trans.app.config.allow_library_path_paste:
-                raise exceptions.ConfigDoesNotAllowException('The configuration of this Galaxy instance does not allow admins to import into library from path.')
+                raise exceptions.ConfigDoesNotAllowException(
+                    "The configuration of this Galaxy instance does not allow admins to import into library from path."
+                )
             if not trans.user_is_admin:
-                raise exceptions.AdminRequiredException('Only admins can import from path.')
+                raise exceptions.AdminRequiredException("Only admins can import from path.")
 
         # Set up the traditional tool state/params
-        tool_id = 'upload1'
+        tool_id = "upload1"
         tool = trans.app.toolbox.get_tool(tool_id)
         state = tool.new_state(trans)
         populate_state(trans, tool.inputs, kwd, state.inputs)
@@ -485,44 +529,47 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 dataset_upload_inputs.append(input)
         library_bunch = upload_common.handle_library_params(trans, {}, trans.security.encode_id(folder.id))
         abspath_datasets = []
-        kwd['filesystem_paths'] = path
-        if source in ['importdir_folder']:
-            kwd['filesystem_paths'] = os.path.join(import_base_dir, path)
+        kwd["filesystem_paths"] = path
+        if source in ["importdir_folder"]:
+            kwd["filesystem_paths"] = os.path.join(import_base_dir, path)
         # user wants to import one file only
         elif source in ["userdir_file", "importdir_file"]:
             file = os.path.abspath(path)
-            abspath_datasets.append(self._make_library_uploaded_dataset(
-                trans, kwd, os.path.basename(file), file, 'server_dir', library_bunch))
+            abspath_datasets.append(
+                self._make_library_uploaded_dataset(
+                    trans, kwd, os.path.basename(file), file, "server_dir", library_bunch
+                )
+            )
         # user wants to import whole folder
         elif source == "userdir_folder":
-            uploaded_datasets_bunch = self._get_path_paste_uploaded_datasets(
-                trans, kwd, library_bunch, 200, '')
+            uploaded_datasets_bunch = self._get_path_paste_uploaded_datasets(trans, kwd, library_bunch, 200, "")
             uploaded_datasets = uploaded_datasets_bunch[0]
             if uploaded_datasets is None:
-                raise exceptions.ObjectNotFound('Given folder does not contain any datasets.')
+                raise exceptions.ObjectNotFound("Given folder does not contain any datasets.")
             for ud in uploaded_datasets:
                 ud.path = os.path.abspath(ud.path)
                 abspath_datasets.append(ud)
         #  user wants to import from path
         if source in ["admin_path", "importdir_folder"]:
             # validate the path is within root
-            uploaded_datasets_bunch = self._get_path_paste_uploaded_datasets(
-                trans, kwd, library_bunch, 200, '')
+            uploaded_datasets_bunch = self._get_path_paste_uploaded_datasets(trans, kwd, library_bunch, 200, "")
             uploaded_datasets = uploaded_datasets_bunch[0]
             if uploaded_datasets is None:
-                raise exceptions.ObjectNotFound('Given folder does not contain any datasets.')
+                raise exceptions.ObjectNotFound("Given folder does not contain any datasets.")
             for ud in uploaded_datasets:
                 ud.path = os.path.abspath(ud.path)
                 abspath_datasets.append(ud)
         json_file_path = upload_common.create_paramfile(trans, abspath_datasets)
         data_list = [ud.data for ud in abspath_datasets]
         job_params = {}
-        job_params['link_data_only'] = dumps(kwd.get('link_data_only', 'copy_files'))
-        job_params['uuid'] = dumps(kwd.get('uuid', None))
-        job, output = upload_common.create_job(trans, tool_params, tool, json_file_path, data_list, folder=folder, job_params=job_params)
+        job_params["link_data_only"] = dumps(kwd.get("link_data_only", "copy_files"))
+        job_params["uuid"] = dumps(kwd.get("uuid", None))
+        job, output = upload_common.create_job(
+            trans, tool_params, tool, json_file_path, data_list, folder=folder, job_params=job_params
+        )
         trans.app.job_manager.enqueue(job, tool=tool)
         job_dict = job.to_dict()
-        job_dict['id'] = trans.security.encode_id(job_dict['id'])
+        job_dict["id"] = trans.security.encode_id(job_dict["id"])
         return job_dict
 
     @web.expose
@@ -551,25 +598,27 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound
         """
         library_datasets = []
-        datasets_to_download = kwd.get('ld_ids%5B%5D', None)
+        datasets_to_download = kwd.get("ld_ids%5B%5D", None)
         if datasets_to_download is None:
-            datasets_to_download = kwd.get('ld_ids', None)
+            datasets_to_download = kwd.get("ld_ids", None)
         if datasets_to_download is not None:
             datasets_to_download = util.listify(datasets_to_download)
             for dataset_id in datasets_to_download:
                 try:
-                    library_dataset = self.get_library_dataset(trans, id=dataset_id, check_ownership=False, check_accessible=True)
+                    library_dataset = self.get_library_dataset(
+                        trans, id=dataset_id, check_ownership=False, check_accessible=True
+                    )
                     library_datasets.append(library_dataset)
                 except HTTPBadRequest:
-                    raise exceptions.RequestParameterInvalidException('Bad Request.')
+                    raise exceptions.RequestParameterInvalidException("Bad Request.")
                 except HTTPInternalServerError:
-                    raise exceptions.InternalServerError('Internal error.')
+                    raise exceptions.InternalServerError("Internal error.")
                 except Exception as e:
                     raise exceptions.InternalServerError(f"Unknown error.{util.unicodify(e)}")
 
-        folders_to_download = kwd.get('folder_ids%5B%5D', None)
+        folders_to_download = kwd.get("folder_ids%5B%5D", None)
         if folders_to_download is None:
-            folders_to_download = kwd.get('folder_ids', None)
+            folders_to_download = kwd.get("folder_ids", None)
         if folders_to_download is not None:
             folders_to_download = util.listify(folders_to_download)
 
@@ -580,14 +629,15 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 rval = []
                 for subfolder in folder.active_folders:
                     if not admin:
-                        can_access, folder_ids = trans.app.security_agent.check_folder_contents(trans.user, current_user_roles, subfolder)
+                        can_access, folder_ids = trans.app.security_agent.check_folder_contents(
+                            trans.user, current_user_roles, subfolder
+                        )
                     if (admin or can_access) and not subfolder.deleted:
                         rval.extend(traverse(subfolder))
                 for ld in folder.datasets:
                     if not admin:
                         can_access = trans.app.security_agent.can_access_dataset(
-                            current_user_roles,
-                            ld.library_dataset_dataset_association.dataset
+                            current_user_roles, ld.library_dataset_dataset_association.dataset
                         )
                     if (admin or can_access) and not ld.deleted:
                         rval.append(ld)
@@ -599,16 +649,18 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 library_datasets.extend(traverse(folder))
 
         if not library_datasets:
-            raise exceptions.RequestParameterMissingException('Request has to contain a list of dataset ids or folder ids to download.')
+            raise exceptions.RequestParameterMissingException(
+                "Request has to contain a list of dataset ids or folder ids to download."
+            )
 
-        if archive_format == 'zip':
+        if archive_format == "zip":
             archive = ZipstreamWrapper(
                 archive_name="selected_library_files",
                 upstream_mod_zip=self.app.config.upstream_mod_zip,
                 upstream_gzip=self.app.config.upstream_gzip,
             )
             killme = string.punctuation + string.whitespace
-            trantab = str.maketrans(killme, '_' * len(killme))
+            trantab = str.maketrans(killme, "_" * len(killme))
             seen = []
             for ld in library_datasets:
                 ldda = ld.library_dataset_dataset_association
@@ -624,7 +676,7 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                     parent_folder = parent_folder.parent
                 path += ldda.name
                 while path in seen:
-                    path += '_'
+                    path += "_"
                 path = f"{path}.{ldda.extension}"
                 seen.append(path)
                 zpath = os.path.split(path)[-1]  # comes as base_name/fname
@@ -632,27 +684,35 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
 
                 if is_composite:
                     # need to add all the components from the extra_files_path to the zip
-                    if zpathext == '':
-                        zpath = f'{zpath}.html'  # fake the real nature of the html file
+                    if zpathext == "":
+                        zpath = f"{zpath}.html"  # fake the real nature of the html file
                     try:
-                        if archive_format == 'zip':
+                        if archive_format == "zip":
                             archive.write(ldda.dataset.file_name, zpath)  # add the primary of a composite set
                         else:
                             archive.write(ldda.dataset.file_name, zpath)  # add the primary of a composite set
                     except OSError:
-                        log.exception("Unable to add composite parent %s to temporary library download archive", ldda.dataset.file_name)
+                        log.exception(
+                            "Unable to add composite parent %s to temporary library download archive",
+                            ldda.dataset.file_name,
+                        )
                         raise exceptions.InternalServerError("Unable to create archive for download.")
                     except ObjectNotFound:
                         log.exception("Requested dataset %s does not exist on the host.", ldda.dataset.file_name)
                         raise exceptions.ObjectNotFound("Requested dataset not found. ")
                     except Exception as e:
-                        log.exception("Unable to add composite parent %s to temporary library download archive", ldda.dataset.file_name)
-                        raise exceptions.InternalServerError(f"Unable to add composite parent to temporary library download archive. {util.unicodify(e)}")
+                        log.exception(
+                            "Unable to add composite parent %s to temporary library download archive",
+                            ldda.dataset.file_name,
+                        )
+                        raise exceptions.InternalServerError(
+                            f"Unable to add composite parent to temporary library download archive. {util.unicodify(e)}"
+                        )
 
-                    flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, '*.*'))  # glob returns full paths
+                    flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, "*.*"))  # glob returns full paths
                     for fpath in flist:
                         efp, fname = os.path.split(fpath)
-                        if fname > '':
+                        if fname > "":
                             fname = fname.translate(trantab)
                         try:
                             archive.write(fpath, fname)
@@ -664,36 +724,46 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                             raise exceptions.ObjectNotFound("Requested dataset not found.")
                         except Exception as e:
                             log.exception("Unable to add %s to temporary library download archive %s", fname, outfname)
-                            raise exceptions.InternalServerError(f"Unable to add dataset to temporary library download archive . {util.unicodify(e)}")
+                            raise exceptions.InternalServerError(
+                                f"Unable to add dataset to temporary library download archive . {util.unicodify(e)}"
+                            )
                 else:
                     try:
                         archive.write(ldda.dataset.file_name, path)
                     except OSError:
-                        log.exception("Unable to write %s to temporary library download archive", ldda.dataset.file_name)
+                        log.exception(
+                            "Unable to write %s to temporary library download archive", ldda.dataset.file_name
+                        )
                         raise exceptions.InternalServerError("Unable to create archive for download")
                     except ObjectNotFound:
                         log.exception("Requested dataset %s does not exist on the host.", ldda.dataset.file_name)
                         raise exceptions.ObjectNotFound("Requested dataset not found.")
                     except Exception as e:
-                        log.exception("Unable to add %s to temporary library download archive %s", ldda.dataset.file_name, outfname)
+                        log.exception(
+                            "Unable to add %s to temporary library download archive %s",
+                            ldda.dataset.file_name,
+                            outfname,
+                        )
                         raise exceptions.InternalServerError(f"Unknown error. {util.unicodify(e)}")
             trans.response.headers.update(archive.get_headers())
             return archive.response()
-        elif archive_format == 'uncompressed':
+        elif archive_format == "uncompressed":
             if len(library_datasets) != 1:
-                raise exceptions.RequestParameterInvalidException("You can download only one uncompressed file at once.")
+                raise exceptions.RequestParameterInvalidException(
+                    "You can download only one uncompressed file at once."
+                )
             else:
                 single_ld = library_datasets[0]
                 ldda = single_ld.library_dataset_dataset_association
                 dataset = ldda.dataset
                 fStat = os.stat(dataset.file_name)
                 trans.response.set_content_type(ldda.get_mime())
-                trans.response.headers['Content-Length'] = str(fStat.st_size)
+                trans.response.headers["Content-Length"] = str(fStat.st_size)
                 fname = f"{ldda.name}.{ldda.extension}"
-                fname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in fname)[0:150]
+                fname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in fname)[0:150]
                 trans.response.headers["Content-Disposition"] = f'attachment; filename="{fname}"'
                 try:
-                    return open(dataset.file_name, 'rb')
+                    return open(dataset.file_name, "rb")
                 except Exception:
                     raise exceptions.InternalServerError("This dataset contains no content.")
         else:
diff --git a/lib/galaxy/webapps/galaxy/api/licenses.py b/lib/galaxy/webapps/galaxy/api/licenses.py
index 1ce73186ce5..270d379ec4f 100644
--- a/lib/galaxy/webapps/galaxy/api/licenses.py
+++ b/lib/galaxy/webapps/galaxy/api/licenses.py
@@ -1,12 +1,10 @@
 from typing import List
 
-from fastapi import (
-    Path
-)
+from fastapi import Path
 
 from galaxy.managers.licenses import (
     LicenseMetadataModel,
-    LicensesManager
+    LicensesManager,
 )
 from galaxy.web import expose_api_anonymous_and_sessionless
 from . import (
@@ -15,13 +13,13 @@ from . import (
     Router,
 )
 
-router = Router(tags=['licenses'])
+router = Router(tags=["licenses"])
 
 LicenseIdPath: str = Path(
     ...,  # Mark this Path parameter as required
     title="SPDX license short ID",
     description="The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/)",
-    example="Apache-2.0"
+    example="Apache-2.0",
 )
 
 
@@ -29,16 +27,18 @@ LicenseIdPath: str = Path(
 class FastAPILicenses:
     licenses_manager: LicensesManager = depends(LicensesManager)
 
-    @router.get('/api/licenses',
-        summary="Lists all available SPDX licenses",
-        response_description="List of SPDX licenses")
+    @router.get(
+        "/api/licenses", summary="Lists all available SPDX licenses", response_description="List of SPDX licenses"
+    )
     async def index(self) -> List[LicenseMetadataModel]:
         """Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/)."""
         return self.licenses_manager.get_licenses()
 
-    @router.get('/api/licenses/{id}',
+    @router.get(
+        "/api/licenses/{id}",
         summary="Gets the SPDX license metadata associated with the short identifier",
-        response_description="SPDX license metadata")
+        response_description="SPDX license metadata",
+    )
     async def get(self, id=LicenseIdPath) -> LicenseMetadataModel:
         """Returns the license metadata associated with the given
         [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/)."""
diff --git a/lib/galaxy/webapps/galaxy/api/metrics.py b/lib/galaxy/webapps/galaxy/api/metrics.py
index a2542f1bb73..fcfba047a37 100644
--- a/lib/galaxy/webapps/galaxy/api/metrics.py
+++ b/lib/galaxy/webapps/galaxy/api/metrics.py
@@ -25,7 +25,7 @@ from . import (
 log = logging.getLogger(__name__)
 
 
-router = Router(tags=['metrics'])
+router = Router(tags=["metrics"])
 
 
 @router.cbv
@@ -33,7 +33,7 @@ class FastAPIMetrics:
     manager: MetricsManager = depends(MetricsManager)
 
     @router.post(
-        '/api/metrics',
+        "/api/metrics",
         summary="Records a collection of metrics.",
     )
     def create(
diff --git a/lib/galaxy/webapps/galaxy/api/page_revisions.py b/lib/galaxy/webapps/galaxy/api/page_revisions.py
index 2ef7ba8d2a7..85121077e53 100644
--- a/lib/galaxy/webapps/galaxy/api/page_revisions.py
+++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py
@@ -6,7 +6,10 @@ import logging
 from galaxy.managers.base import get_object
 from galaxy.managers.pages import PageManager
 from galaxy.web import expose_api
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
@@ -26,7 +29,7 @@ class PageRevisionsController(BaseGalaxyAPIController):
         :rtype:     list
         :returns:   dictionaries containing different revisions of the page
         """
-        page = get_object(trans, page_id, 'Page', check_ownership=False, check_accessible=True)
+        page = get_object(trans, page_id, "Page", check_ownership=False, check_accessible=True)
         r = trans.sa_session.query(trans.app.model.PageRevision).filter_by(page_id=page.id)
         out = []
         for page in r:
@@ -49,7 +52,7 @@ class PageRevisionsController(BaseGalaxyAPIController):
         :rtype:     dictionary
         :returns:   Dictionary with 'success' or 'error' element to indicate the result of the request
         """
-        page = get_object(trans, page_id, 'Page', check_ownership=True)
+        page = get_object(trans, page_id, "Page", check_ownership=True)
         page_revision = self.manager.save_new_revision(trans, page, payload)
         rval = self.encode_all_ids(trans, page_revision.to_dict(view="element"), True)
         self.manager.rewrite_content_for_export(trans, rval)
diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py
index 02c04ac57bb..3326a27652f 100644
--- a/lib/galaxy/webapps/galaxy/api/pages.py
+++ b/lib/galaxy/webapps/galaxy/api/pages.py
@@ -28,7 +28,7 @@ from galaxy.schema.schema import (
 from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
-    expose_api_raw_anonymous_and_sessionless
+    expose_api_raw_anonymous_and_sessionless,
 )
 from galaxy.webapps.galaxy.services.pages import PagesService
 from . import (
@@ -40,18 +40,14 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['pages'])
+router = Router(tags=["pages"])
 
 DeletedQueryParam: bool = Query(
-    default=False,
-    title="Display deleted",
-    description="Whether to include deleted pages in the result."
+    default=False, title="Display deleted", description="Whether to include deleted pages in the result."
 )
 
 PageIdPathParam: EncodedDatabaseIdField = Path(
-    ...,  # Required
-    title="Page ID",
-    description="The encoded database identifier of the Page."
+    ..., title="Page ID", description="The encoded database identifier of the Page."  # Required
 )
 
 
@@ -60,7 +56,7 @@ class FastAPIPages:
     service: PagesService = depends(PagesService)
 
     @router.get(
-        '/api/pages',
+        "/api/pages",
         summary="Lists all Pages viewable by the user.",
         response_description="A list with summary page information.",
     )
@@ -73,7 +69,7 @@ class FastAPIPages:
         return self.service.index(trans, deleted)
 
     @router.post(
-        '/api/pages',
+        "/api/pages",
         summary="Create a page and return summary information.",
         response_description="The page summary information.",
     )
@@ -86,7 +82,7 @@ class FastAPIPages:
         return self.service.create(trans, payload)
 
     @router.delete(
-        '/api/pages/{id}',
+        "/api/pages/{id}",
         summary="Marks the specific Page as deleted.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
@@ -100,7 +96,7 @@ class FastAPIPages:
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.get(
-        '/api/pages/{id}.pdf',
+        "/api/pages/{id}.pdf",
         summary="Return a PDF document of the last revision of the Page.",
         response_class=StreamingResponse,
         responses={
@@ -108,9 +104,7 @@ class FastAPIPages:
                 "description": "PDF document with the last revision of the page.",
                 "content": {"application/pdf": {}},
             },
-            501: {
-                "description": "PDF conversion service not available."
-            }
+            501: {"description": "PDF conversion service not available."},
         },
     )
     async def show_pdf(
@@ -126,7 +120,7 @@ class FastAPIPages:
         return StreamingResponse(io.BytesIO(pdf_bytes), media_type="application/pdf")
 
     @router.get(
-        '/api/pages/{id}',
+        "/api/pages/{id}",
         summary="Return a page summary and the content of the last revision.",
         response_description="The page summary information.",
     )
@@ -139,7 +133,7 @@ class FastAPIPages:
         return self.service.show(trans, id)
 
     @router.get(
-        '/api/pages/{id}/sharing',
+        "/api/pages/{id}/sharing",
         summary="Get the current sharing status of the given Page.",
     )
     def sharing(
@@ -151,7 +145,7 @@ class FastAPIPages:
         return self.service.shareable_service.sharing(trans, id)
 
     @router.put(
-        '/api/pages/{id}/enable_link_access',
+        "/api/pages/{id}/enable_link_access",
         summary="Makes this item accessible by a URL link.",
     )
     def enable_link_access(
@@ -163,7 +157,7 @@ class FastAPIPages:
         return self.service.shareable_service.enable_link_access(trans, id)
 
     @router.put(
-        '/api/pages/{id}/disable_link_access',
+        "/api/pages/{id}/disable_link_access",
         summary="Makes this item inaccessible by a URL link.",
     )
     def disable_link_access(
@@ -175,7 +169,7 @@ class FastAPIPages:
         return self.service.shareable_service.disable_link_access(trans, id)
 
     @router.put(
-        '/api/pages/{id}/publish',
+        "/api/pages/{id}/publish",
         summary="Makes this item public and accessible by a URL link.",
     )
     def publish(
@@ -187,7 +181,7 @@ class FastAPIPages:
         return self.service.shareable_service.publish(trans, id)
 
     @router.put(
-        '/api/pages/{id}/unpublish',
+        "/api/pages/{id}/unpublish",
         summary="Removes this item from the published list.",
     )
     def unpublish(
@@ -199,20 +193,20 @@ class FastAPIPages:
         return self.service.shareable_service.unpublish(trans, id)
 
     @router.put(
-        '/api/pages/{id}/share_with_users',
+        "/api/pages/{id}/share_with_users",
         summary="Share this item with specific users.",
     )
     def share_with_users(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         id: EncodedDatabaseIdField = PageIdPathParam,
-        payload: ShareWithPayload = Body(...)
+        payload: ShareWithPayload = Body(...),
     ) -> ShareWithStatus:
         """Shares this item with specific users and return the current sharing status."""
         return self.service.shareable_service.share_with_users(trans, id, payload)
 
     @router.put(
-        '/api/pages/{id}/slug',
+        "/api/pages/{id}/slug",
         summary="Set a new slug for this shared item.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
@@ -231,6 +225,7 @@ class PagesController(BaseGalaxyAPIController):
     """
     RESTful controller for interactions with pages.
     """
+
     service: PagesService = depends(PagesService)
 
     @expose_api_anonymous_and_sessionless
diff --git a/lib/galaxy/webapps/galaxy/api/plugins.py b/lib/galaxy/webapps/galaxy/api/plugins.py
index e69276a96fb..fff097727dd 100644
--- a/lib/galaxy/webapps/galaxy/api/plugins.py
+++ b/lib/galaxy/webapps/galaxy/api/plugins.py
@@ -4,10 +4,16 @@ Plugins resource control over the API.
 import logging
 
 from galaxy import exceptions
-from galaxy.managers import hdas, histories
+from galaxy.managers import (
+    hdas,
+    histories,
+)
 from galaxy.util import asbool
 from galaxy.web import expose_api
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
@@ -16,6 +22,7 @@ class PluginsController(BaseGalaxyAPIController):
     """
     RESTful controller for interactions with plugins.
     """
+
     hda_manager: hdas.HDAManager = depends(hdas.HDAManager)
     history_manager: histories.HistoryManager = depends(histories.HistoryManager)
 
@@ -41,14 +48,13 @@ class PluginsController(BaseGalaxyAPIController):
         registry = self._get_registry(trans)
         history_id = kwargs.get("history_id")
         if history_id is not None:
-            history = self.history_manager.get_owned(trans.security.decode_id(history_id), trans.user, current_history=trans.history)
+            history = self.history_manager.get_owned(
+                trans.security.decode_id(history_id), trans.user, current_history=trans.history
+            )
             result = {"hdas": []}
             for hda in history.contents_iter(types=["dataset"], deleted=False, visible=True):
                 if registry.get_visualization(trans, id, hda):
-                    result["hdas"].append({
-                        "id": trans.security.encode_id(hda.id),
-                        "name": hda.name
-                    })
+                    result["hdas"].append({"id": trans.security.encode_id(hda.id), "name": hda.name})
         else:
             result = registry.get_plugin(id).to_dict()
         return result
diff --git a/lib/galaxy/webapps/galaxy/api/provenance.py b/lib/galaxy/webapps/galaxy/api/provenance.py
index 187db11fff3..adbb79c75ca 100644
--- a/lib/galaxy/webapps/galaxy/api/provenance.py
+++ b/lib/galaxy/webapps/galaxy/api/provenance.py
@@ -5,31 +5,31 @@ import logging
 
 from paste.httpexceptions import (
     HTTPBadRequest,
-    HTTPNotImplemented
+    HTTPNotImplemented,
 )
 
-from galaxy import (
-    web
-)
+from galaxy import web
 from galaxy.managers.hdas import HDAManager
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
 
 class BaseProvenanceController(BaseGalaxyAPIController):
-    """
-    """
+    """ """
 
     @web.legacy_expose_api
     def index(self, trans, **kwd):
-        follow = kwd.get('follow', False)
+        follow = kwd.get("follow", False)
         value = self._get_provenance(trans, self.provenance_item_class, kwd[self.provenance_item_id], follow)
         return value
 
     @web.legacy_expose_api
     def show(self, trans, elem_name, **kwd):
-        follow = kwd.get('follow', False)
+        follow = kwd.get("follow", False)
         value = self._get_provenance(trans, self.provenance_item_class, kwd[self.provenance_item_id], follow)
         return value
 
@@ -43,7 +43,9 @@ class BaseProvenanceController(BaseGalaxyAPIController):
         raise HTTPBadRequest("Cannot Delete Provenance")
 
     def _get_provenance(self, trans, item_class_name, item_id, follow=True):
-        provenance_item = self.get_object(trans, item_id, item_class_name, check_ownership=False, check_accessible=False)
+        provenance_item = self.get_object(
+            trans, item_id, item_class_name, check_ownership=False, check_accessible=False
+        )
         if item_class_name == "HistoryDatasetAssociation":
             self.hda_manager.error_unless_accessible(provenance_item, trans.user)
         else:
@@ -69,7 +71,7 @@ class BaseProvenanceController(BaseGalaxyAPIController):
             else:
                 return {
                     "id": trans.security.encode_id(item.id),
-                    "uuid": (lambda uuid: str(uuid) if uuid else None)(item.dataset.uuid)
+                    "uuid": (lambda uuid: str(uuid) if uuid else None)(item.dataset.uuid),
                 }
         return None
 
diff --git a/lib/galaxy/webapps/galaxy/api/quotas.py b/lib/galaxy/webapps/galaxy/api/quotas.py
index 8eaa3b49944..bc54aba40fd 100644
--- a/lib/galaxy/webapps/galaxy/api/quotas.py
+++ b/lib/galaxy/webapps/galaxy/api/quotas.py
@@ -31,13 +31,11 @@ from . import (
 log = logging.getLogger(__name__)
 
 
-router = Router(tags=['quotas'])
+router = Router(tags=["quotas"])
 
 
 QuotaIdPathParam: EncodedDatabaseIdField = Path(
-    ...,  # Required
-    title="Quota ID",
-    description="The encoded identifier of the Quota."
+    ..., title="Quota ID", description="The encoded identifier of the Quota."  # Required
 )
 
 
@@ -46,7 +44,7 @@ class FastAPIQuota:
     service: QuotasService = depends(QuotasService)
 
     @router.get(
-        '/api/quotas',
+        "/api/quotas",
         summary="Displays a list with information of quotas that are currently active.",
         require_admin=True,
     )
@@ -58,7 +56,7 @@ class FastAPIQuota:
         return self.service.index(trans)
 
     @router.get(
-        '/api/quotas/deleted',
+        "/api/quotas/deleted",
         summary="Displays a list with information of quotas that have been deleted.",
         require_admin=True,
     )
@@ -70,20 +68,18 @@ class FastAPIQuota:
         return self.service.index(trans, deleted=True)
 
     @router.get(
-        '/api/quotas/{id}',
+        "/api/quotas/{id}",
         summary="Displays details on a particular active quota.",
         require_admin=True,
     )
     def show(
-        self,
-        trans: ProvidesUserContext = DependsOnTrans,
-        id: EncodedDatabaseIdField = QuotaIdPathParam
+        self, trans: ProvidesUserContext = DependsOnTrans, id: EncodedDatabaseIdField = QuotaIdPathParam
     ) -> QuotaDetails:
         """Displays details on a particular active quota."""
         return self.service.show(trans, id)
 
     @router.get(
-        '/api/quotas/deleted/{id}',
+        "/api/quotas/deleted/{id}",
         summary="Displays details on a particular quota that has been deleted.",
         require_admin=True,
     )
@@ -96,7 +92,7 @@ class FastAPIQuota:
         return self.service.show(trans, id, deleted=True)
 
     @router.post(
-        '/api/quotas',
+        "/api/quotas",
         summary="Creates a new quota.",
         require_admin=True,
     )
@@ -109,7 +105,7 @@ class FastAPIQuota:
         return self.service.create(trans, payload)
 
     @router.put(
-        '/api/quotas/{id}',
+        "/api/quotas/{id}",
         summary="Updates an existing quota.",
         require_admin=True,
     )
@@ -123,7 +119,7 @@ class FastAPIQuota:
         return self.service.update(trans, id, payload)
 
     @router.delete(
-        '/api/quotas/{id}',
+        "/api/quotas/{id}",
         summary="Deletes an existing quota.",
         require_admin=True,
     )
@@ -137,7 +133,7 @@ class FastAPIQuota:
         return self.service.delete(trans, id, payload)
 
     @router.post(
-        '/api/quotas/deleted/{id}/undelete',
+        "/api/quotas/deleted/{id}/undelete",
         summary="Restores a previously deleted quota.",
         require_admin=True,
     )
@@ -156,7 +152,7 @@ class QuotaAPIController(BaseGalaxyAPIController):
 
     @web.require_admin
     @web.expose_api
-    def index(self, trans, deleted='False', **kwd):
+    def index(self, trans, deleted="False", **kwd):
         """
         GET /api/quotas
         GET /api/quotas/deleted
@@ -167,7 +163,7 @@ class QuotaAPIController(BaseGalaxyAPIController):
 
     @web.require_admin
     @web.expose_api
-    def show(self, trans, id, deleted='False', **kwd):
+    def show(self, trans, id, deleted="False", **kwd):
         """
         GET /api/quotas/{encoded_quota_id}
         GET /api/quotas/deleted/{encoded_quota_id}
@@ -204,7 +200,7 @@ class QuotaAPIController(BaseGalaxyAPIController):
         Deletes a quota
         """
         # a request body is optional here
-        payload = DeleteQuotaPayload(**kwd.get('payload', {}))
+        payload = DeleteQuotaPayload(**kwd.get("payload", {}))
         return self.service.delete(trans, id, payload)
 
     @web.require_admin
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 9f0b2bd16c8..ba96899a06e 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -2,7 +2,12 @@
 API operations on remote files.
 """
 import logging
-from typing import Any, Dict, List, Optional
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+)
 
 from fastapi.param_functions import Query
 
@@ -24,15 +29,12 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['remote files'])
+router = Router(tags=["remote files"])
 
 TargetQueryParam: str = Query(
     default=RemoteFilesTarget.ftpdir,
     title="Target source",
-    description=(
-        "The source to load datasets from."
-        " Possible values: ftpdir, userdir, importdir"
-    ),
+    description=("The source to load datasets from." " Possible values: ftpdir, userdir, importdir"),
 )
 
 FormatQueryParam: Optional[RemoteFilesFormat] = Query(
@@ -49,8 +51,7 @@ RecursiveQueryParam: Optional[bool] = Query(
     default=None,
     title="Recursive",
     description=(
-        "Wether to recursively lists all sub-directories."
-        " This will be `True` by default depending on the `target`."
+        "Wether to recursively lists all sub-directories." " This will be `True` by default depending on the `target`."
     ),
 )
 
@@ -70,7 +71,7 @@ class FastAPIRemoteFiles:
     manager: RemoteFilesManager = depends(RemoteFilesManager)
 
     @router.get(
-        '/api/remote_files',
+        "/api/remote_files",
         summary="Displays remote files available to the user.",
         response_description="A list with details about the remote files available to the user.",
     )
@@ -80,13 +81,13 @@ class FastAPIRemoteFiles:
         target: str = TargetQueryParam,
         format: Optional[RemoteFilesFormat] = FormatQueryParam,
         recursive: Optional[bool] = RecursiveQueryParam,
-        disable: Optional[RemoteFilesDisableMode] = DisableModeQueryParam
+        disable: Optional[RemoteFilesDisableMode] = DisableModeQueryParam,
     ) -> List[Dict[str, Any]]:
         """Lists all remote files available to the user from different sources."""
         return self.manager.index(user_ctx, target, format, recursive, disable)
 
     @router.get(
-        '/api/remote_files/plugins',
+        "/api/remote_files/plugins",
         summary="Display plugin information for each of the gxfiles:// URI targets available.",
         response_description="A list with details about each plugin.",
     )
@@ -119,10 +120,10 @@ class RemoteFilesAPIController(BaseGalaxyAPIController):
         :rtype:     list
         """
         # If set, target must be one of 'ftpdir' (default), 'userdir', 'importdir'
-        target = kwd.get('target', 'ftpdir')
-        format = kwd.get('format', None)
-        recursive = kwd.get('recursive', None)
-        disable = kwd.get('disable', None)
+        target = kwd.get("target", "ftpdir")
+        format = kwd.get("format", None)
+        recursive = kwd.get("recursive", None)
+        disable = kwd.get("disable", None)
 
         return self.manager.index(trans, target, format, recursive, disable)
 
diff --git a/lib/galaxy/webapps/galaxy/api/roles.py b/lib/galaxy/webapps/galaxy/api/roles.py
index e3dbb545723..93a8b0d76bd 100644
--- a/lib/galaxy/webapps/galaxy/api/roles.py
+++ b/lib/galaxy/webapps/galaxy/api/roles.py
@@ -4,9 +4,7 @@ API operations on Role objects.
 import json
 import logging
 
-from fastapi import (
-    Body,
-)
+from fastapi import Body
 
 from galaxy import web
 from galaxy.managers.base import decode_id
@@ -35,9 +33,9 @@ router = Router(tags=["roles"])
 
 
 def role_to_model(trans, role):
-    item = role.to_dict(view='element', value_mapper={'id': trans.security.encode_id})
+    item = role.to_dict(view="element", value_mapper={"id": trans.security.encode_id})
     role_id = trans.security.encode_id(role.id)
-    item['url'] = url_for('role', id=role_id)
+    item["url"] = url_for("role", id=role_id)
     return RoleModel(**item)
 
 
@@ -45,19 +43,21 @@ def role_to_model(trans, role):
 class FastAPIRoles:
     role_manager: RoleManager = depends(RoleManager)
 
-    @router.get('/api/roles')
+    @router.get("/api/roles")
     def index(self, trans: ProvidesUserContext = DependsOnTrans) -> RoleListModel:
         roles = self.role_manager.list_displayable_roles(trans)
         return RoleListModel(__root__=[role_to_model(trans, r) for r in roles])
 
-    @router.get('/api/roles/{id}')
+    @router.get("/api/roles/{id}")
     def show(self, id: EncodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans) -> RoleModel:
         role_id = trans.app.security.decode_id(id)
         role = self.role_manager.get(trans, role_id)
         return role_to_model(trans, role)
 
     @router.post("/api/roles", require_admin=True)
-    def create(self, trans: ProvidesUserContext = DependsOnTrans, role_definition_model: RoleDefinitionModel = Body(...)) -> RoleModel:
+    def create(
+        self, trans: ProvidesUserContext = DependsOnTrans, role_definition_model: RoleDefinitionModel = Body(...)
+    ) -> RoleModel:
         role = self.role_manager.create_role(trans, role_definition_model)
         return role_to_model(trans, role)
 
diff --git a/lib/galaxy/webapps/galaxy/api/sanitize_allow.py b/lib/galaxy/webapps/galaxy/api/sanitize_allow.py
index f3c36dcbee3..0ecb709d696 100755
--- a/lib/galaxy/webapps/galaxy/api/sanitize_allow.py
+++ b/lib/galaxy/webapps/galaxy/api/sanitize_allow.py
@@ -2,7 +2,10 @@
 API operations allowing clients to retrieve and modify the HTML sanitization allow list.
 """
 import logging
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 from galaxy import web
 from galaxy.webapps.base.controller import BaseAPIController
@@ -11,7 +14,6 @@ log = logging.getLogger(__name__)
 
 
 class SanitizeAllowController(BaseAPIController):
-
     @web.require_admin
     @web.expose_api
     def index(self, trans, **kwd):
@@ -47,46 +49,56 @@ class SanitizeAllowController(BaseAPIController):
 
     def _save_allowlist(self, trans):
         trans.app.config.sanitize_allowlist = sorted(trans.app.config.sanitize_allowlist)
-        with open(trans.app.config.sanitize_allowlist_file, 'w') as f:
+        with open(trans.app.config.sanitize_allowlist_file, "w") as f:
             f.write("\n".join(trans.app.config.sanitize_allowlist))
-        trans.app.queue_worker.send_control_task('reload_sanitize_allowlist', noop_self=True)
+        trans.app.queue_worker.send_control_task("reload_sanitize_allowlist", noop_self=True)
 
     def _generate_allowlist(self, trans):
-        sanitize_dict: Dict[str, Any] = dict(blocked_toolshed=[], allowed_toolshed=[], blocked_local=[], allowed_local=[])
+        sanitize_dict: Dict[str, Any] = dict(
+            blocked_toolshed=[], allowed_toolshed=[], blocked_local=[], allowed_local=[]
+        )
         ids = None
         for tool_id in trans.app.config.sanitize_allowlist:
             installed_name = ""
-            installed_ids = {'full': '',
-                             'allowed': tool_id,
-                             'owner': '',
-                             'repository': '',
-                             'tool': ''}
+            installed_ids = {"full": "", "allowed": tool_id, "owner": "", "repository": "", "tool": ""}
             for toolbox_id in trans.app.toolbox.tools_by_id:
                 if toolbox_id.startswith(tool_id):
                     tool = trans.app.toolbox.tools_by_id[toolbox_id]
                     installed_name = tool.name
                     full_id = tool.id
-                    installed_ids = {'full': full_id,
-                                     'allowed': tool_id,
-                                     'owner': '/'.join(full_id.split('/')[:3]),
-                                     'repository': '/'.join(full_id.split('/')[:4]),
-                                     'tool': '/'.join(full_id.split('/')[:5])}
+                    installed_ids = {
+                        "full": full_id,
+                        "allowed": tool_id,
+                        "owner": "/".join(full_id.split("/")[:3]),
+                        "repository": "/".join(full_id.split("/")[:4]),
+                        "tool": "/".join(full_id.split("/")[:5]),
+                    }
                     break
-            tool_dict = dict(tool_name=installed_name, tool_id=tool_id.split('/'), ids=installed_ids, allowed=True, toolshed='/' in tool_id)
-            if '/' in tool_id:
-                sanitize_dict['allowed_toolshed'].append(tool_dict)
+            tool_dict = dict(
+                tool_name=installed_name,
+                tool_id=tool_id.split("/"),
+                ids=installed_ids,
+                allowed=True,
+                toolshed="/" in tool_id,
+            )
+            if "/" in tool_id:
+                sanitize_dict["allowed_toolshed"].append(tool_dict)
             else:
-                sanitize_dict['allowed_local'].append(tool_dict)
+                sanitize_dict["allowed_local"].append(tool_dict)
         for tool_id in sorted(trans.app.toolbox.tools_by_id):
             if not tool_id.startswith(tuple(trans.app.config.sanitize_allowlist)):
                 tool = trans.app.toolbox.tools_by_id[tool_id]
-                ids = {'full': tool_id,
-                       'owner': '/'.join(tool_id.split('/')[:3]),
-                       'repository': '/'.join(tool_id.split('/')[:4]),
-                       'tool': '/'.join(tool_id.split('/')[:5])}
-                tool_dict = dict(tool_name=tool.name, tool_id=tool_id.split('/'), ids=ids, allowed=False, toolshed='/' in tool_id)
-                if '/' in tool_id:
-                    sanitize_dict['blocked_toolshed'].append(tool_dict)
+                ids = {
+                    "full": tool_id,
+                    "owner": "/".join(tool_id.split("/")[:3]),
+                    "repository": "/".join(tool_id.split("/")[:4]),
+                    "tool": "/".join(tool_id.split("/")[:5]),
+                }
+                tool_dict = dict(
+                    tool_name=tool.name, tool_id=tool_id.split("/"), ids=ids, allowed=False, toolshed="/" in tool_id
+                )
+                if "/" in tool_id:
+                    sanitize_dict["blocked_toolshed"].append(tool_dict)
                 else:
-                    sanitize_dict['blocked_local'].append(tool_dict)
+                    sanitize_dict["blocked_local"].append(tool_dict)
         return sanitize_dict
diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py
index a12be20b22c..940e42b647e 100644
--- a/lib/galaxy/webapps/galaxy/api/search.py
+++ b/lib/galaxy/webapps/galaxy/api/search.py
@@ -3,7 +3,10 @@ API for searching Galaxy Datasets
 """
 import logging
 
-from galaxy import model, web
+from galaxy import (
+    model,
+    web,
+)
 from galaxy.exceptions import ItemAccessibilityException
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model.search import GalaxySearchEngine
@@ -15,7 +18,6 @@ log = logging.getLogger(__name__)
 
 
 class SearchController(BaseGalaxyAPIController, SharableItemSecurityMixin):
-
     @web.legacy_expose_api
     def create(self, trans: ProvidesUserContext, payload: dict, **kwd):
         """
@@ -29,21 +31,27 @@ class SearchController(BaseGalaxyAPIController, SharableItemSecurityMixin):
             try:
                 query = se.query(query_txt)
             except Exception as e:
-                return {'error': unicodify(e)}
+                return {"error": unicodify(e)}
             if query is not None:
                 query.decode_query_ids(trans)
                 current_user_roles = trans.get_current_user_roles()
                 try:
                     results = query.process(trans)
                 except Exception as e:
-                    return {'error': unicodify(e)}
+                    return {"error": unicodify(e)}
                 for item in results:
                     append = False
                     if trans.user_is_admin:
                         append = True
                     if not append:
-                        if type(item) in [model.LibraryFolder, model.LibraryDatasetDatasetAssociation, model.LibraryDataset]:
-                            if (trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), item, trans.user)):
+                        if type(item) in [
+                            model.LibraryFolder,
+                            model.LibraryDatasetDatasetAssociation,
+                            model.LibraryDataset,
+                        ]:
+                            if trans.app.security_agent.can_access_library_item(
+                                trans.get_current_user_roles(), item, trans.user
+                            ):
                                 append = True
                         elif type(item) in [model.Job]:
                             if item.used_id == trans.user or trans.user_is_admin:
@@ -60,11 +68,11 @@ class SearchController(BaseGalaxyAPIController, SharableItemSecurityMixin):
                                     append = True
                             except ItemAccessibilityException:
                                 append = False
-                        elif hasattr(item, 'dataset'):
+                        elif hasattr(item, "dataset"):
                             if trans.app.security_agent.can_access_dataset(current_user_roles, item.dataset):
                                 append = True
 
                     if append:
                         row = query.item_to_api_value(item)
                         out.append(self.encode_all_ids(trans, row, True))
-        return {'results': out}
+        return {"results": out}
diff --git a/lib/galaxy/webapps/galaxy/api/tags.py b/lib/galaxy/webapps/galaxy/api/tags.py
index bcfa479fdbb..2a5d7d943d5 100644
--- a/lib/galaxy/webapps/galaxy/api/tags.py
+++ b/lib/galaxy/webapps/galaxy/api/tags.py
@@ -24,7 +24,7 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['tags'])
+router = Router(tags=["tags"])
 
 
 @router.cbv
@@ -32,7 +32,7 @@ class FastAPITags:
     manager: TagsManager = depends(TagsManager)
 
     @router.put(
-        '/api/tags',
+        "/api/tags",
         summary="Apply a new set of tags to an item.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py
index aae40ae42af..6edf7c1a399 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -1,8 +1,6 @@
 from typing import Optional
 
-from fastapi import (
-    Path,
-)
+from fastapi import Path
 from fastapi.responses import FileResponse
 
 from galaxy import web
@@ -21,10 +19,10 @@ from galaxy.web import (
 from . import (
     BaseGalaxyAPIController,
     depends,
-    Router
+    Router,
 )
 
-router = Router(tags=['tool data tables'])
+router = Router(tags=["tool data tables"])
 
 ToolDataTableName = Path(
     ...,  # Mark this field as required
@@ -45,7 +43,7 @@ class FastAPIToolData:
     tool_data_manager: ToolDataManager = depends(ToolDataManager)
 
     @router.get(
-        '/api/tool_data',
+        "/api/tool_data",
         summary="Lists all available data tables",
         response_description="A list with details on individual data tables.",
         require_admin=True,
@@ -55,7 +53,7 @@ class FastAPIToolData:
         return self.tool_data_manager.index()
 
     @router.get(
-        '/api/tool_data/{table_name}',
+        "/api/tool_data/{table_name}",
         summary="Get details of a given data table",
         response_description="A description of the given data table and its content",
         require_admin=True,
@@ -65,7 +63,7 @@ class FastAPIToolData:
         return self.tool_data_manager.show(table_name)
 
     @router.get(
-        '/api/tool_data/{table_name}/reload',
+        "/api/tool_data/{table_name}/reload",
         summary="Reloads a tool data table",
         response_description="A description of the reloaded data table and its content",
         require_admin=True,
@@ -75,7 +73,7 @@ class FastAPIToolData:
         return self.tool_data_manager.reload(table_name)
 
     @router.get(
-        '/api/tool_data/{table_name}/fields/{field_name}',
+        "/api/tool_data/{table_name}/fields/{field_name}",
         summary="Get information about a particular field in a tool data table",
         response_description="Information about a data table field",
         require_admin=True,
@@ -89,7 +87,7 @@ class FastAPIToolData:
         return self.tool_data_manager.show_field(table_name, field_name)
 
     @router.get(
-        '/api/tool_data/{table_name}/fields/{field_name}/files/{file_name}',
+        "/api/tool_data/{table_name}/fields/{field_name}/files/{file_name}",
         summary="Get information about a particular field in a tool data table",
         response_description="Information about a data table field",
         response_class=FileResponse,
@@ -110,7 +108,7 @@ class FastAPIToolData:
         return FileResponse(str(path))
 
     @router.delete(
-        '/api/tool_data/{table_name}',
+        "/api/tool_data/{table_name}",
         summary="Removes an item from a data table",
         response_description="A description of the affected data table and its content",
         require_admin=True,
@@ -128,6 +126,7 @@ class ToolData(BaseGalaxyAPIController):
     """
     RESTful controller for interactions with tool data
     """
+
     tool_data_manager: ToolDataManager = depends(ToolDataManager)
 
     @web.require_admin
@@ -181,8 +180,8 @@ class ToolData(BaseGalaxyAPIController):
                 * values:   <TAB> separated list of column contents, there must be a value for all the columns of the data table
         """
         values: Optional[str] = None
-        if kwd.get('payload', None):
-            values = kwd['payload'].get('values', '')
+        if kwd.get("payload", None):
+            values = kwd["payload"].get("values", "")
         # Here dict(by_alias=True) is required to return
         # `field_value` as `field` since `field` can not be directly
         # used in the pydantic BaseModel and needs to be aliased
diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
index 62ccbe92015..bb9989222b1 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
@@ -9,7 +9,7 @@ from galaxy.structured_app import StructuredApp
 from galaxy.tool_util.deps import views
 from galaxy.web import (
     expose_api,
-    require_admin
+    require_admin,
 )
 from . import BaseGalaxyAPIController
 
@@ -17,7 +17,6 @@ log = logging.getLogger(__name__)
 
 
 class ToolDependenciesAPIController(BaseGalaxyAPIController):
-
     def __init__(self, app: StructuredApp):
         super().__init__(app)
         self._view = views.DependencyResolversView(app)
@@ -252,12 +251,12 @@ class ToolDependenciesAPIController(BaseGalaxyAPIController):
         requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids}
         install_kwds = {}
         for source in [payload, kwds]:
-            if 'include_containers' in source:
-                install_kwds['include_containers'] = source['container_type']
-            if 'container_type' in kwds:
-                install_kwds['container_type'] = source['container_type']
-            if 'resolver_type' in source:
-                install_kwds['resolver_type'] = source['resolver_type']
+            if "include_containers" in source:
+                install_kwds["include_containers"] = source["container_type"]
+            if "container_type" in kwds:
+                install_kwds["container_type"] = source["container_type"]
+            if "resolver_type" in source:
+                install_kwds["resolver_type"] = source["resolver_type"]
         [self._view.install_dependencies(requirements=r, index=index, **install_kwds) for r in requirements]
 
     @expose_api
@@ -286,12 +285,12 @@ class ToolDependenciesAPIController(BaseGalaxyAPIController):
         requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids}
         install_kwds = {}
         for source in [payload, kwds]:
-            if 'include_containers' in source:
-                install_kwds['include_containers'] = source['container_type']
-            if 'container_type' in kwds:
-                install_kwds['container_type'] = source['container_type']
-            if 'resolver_type' in source:
-                install_kwds['resolver_type'] = source['resolver_type']
+            if "include_containers" in source:
+                install_kwds["include_containers"] = source["container_type"]
+            if "container_type" in kwds:
+                install_kwds["container_type"] = source["container_type"]
+            if "resolver_type" in source:
+                install_kwds["resolver_type"] = source["resolver_type"]
 
         [self._view.uninstall_dependencies(index=index, requirements=r, **install_kwds) for r in requirements]
 
diff --git a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
index d339c95212e..832124c9397 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
@@ -3,7 +3,10 @@ related to running and queued jobs.
 """
 import logging
 
-from galaxy import exceptions, util
+from galaxy import (
+    exceptions,
+    util,
+)
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import (
     InteractiveToolEntryPoint,
@@ -17,7 +20,6 @@ log = logging.getLogger(__name__)
 
 
 class ToolEntryPointsAPIController(BaseGalaxyAPIController):
-
     def __init__(self, app: StructuredApp):
         self.app = app
         self.interactivetool_manager = app.interactivetool_manager
@@ -44,7 +46,9 @@ class ToolEntryPointsAPIController(BaseGalaxyAPIController):
             raise exceptions.RequestParameterInvalidException("Currently this API must passed a job id or running=true")
 
         if job_id is not None and running:
-            raise exceptions.RequestParameterInvalidException("Currently this API must passed only a job id or running=true")
+            raise exceptions.RequestParameterInvalidException(
+                "Currently this API must passed only a job id or running=true"
+            )
 
         if job_id is not None:
             job = trans.sa_session.query(Job).get(self.decode_id(job_id))
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index b9434eae382..7ea6515e1c7 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -4,7 +4,7 @@ from time import strftime
 
 from paste.httpexceptions import (
     HTTPBadRequest,
-    HTTPForbidden
+    HTTPForbidden,
 )
 from sqlalchemy import (
     and_,
@@ -14,13 +14,15 @@ from sqlalchemy import (
 
 from galaxy import (
     exceptions,
-    util
+    util,
 )
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model.tool_shed_install import ToolShedRepository
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
-from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
+from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import (
+    InstalledRepositoryMetadataManager,
+)
 from galaxy.tool_shed.util.repository_util import (
     check_for_updates,
     get_installed_repository,
@@ -32,19 +34,18 @@ from galaxy.tool_shed.util.tool_util import generate_message_for_invalid_tools
 from galaxy.web import (
     expose_api,
     require_admin,
-    url_for
+    url_for,
 )
 from . import BaseGalaxyAPIController
 
-
 log = logging.getLogger(__name__)
 
 
 def get_message_for_no_shed_tool_config():
     # This Galaxy instance is not configured with a shed-related tool panel configuration file.
-    message = 'The tool_config_file setting in galaxy.ini must include at least one shed tool configuration file name with a <toolbox> '
-    message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to '
-    message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is '
+    message = "The tool_config_file setting in galaxy.ini must include at least one shed tool configuration file name with a <toolbox> "
+    message += "tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to "
+    message += "automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is "
     message += '<toolbox tool_path="database/shed_tools">).  For details, see the "Installation of Galaxy tool shed repository tools into a '
     message += 'local Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/'
     return message
@@ -58,14 +59,18 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
         if not have_shed_tool_conf_for_install(self.app):
             message = get_message_for_no_shed_tool_config()
             log.debug(message)
-            return dict(status='error', error=message)
+            return dict(status="error", error=message)
         # Make sure the current user's API key proves he is an admin user in this Galaxy instance.
         if not trans.user_is_admin:
-            raise exceptions.AdminRequiredException('You are not authorized to request the latest installable revision for a repository in this Galaxy instance.')
+            raise exceptions.AdminRequiredException(
+                "You are not authorized to request the latest installable revision for a repository in this Galaxy instance."
+            )
 
     def __get_value_mapper(self, trans, tool_shed_repository):
-        value_mapper = {'id': trans.security.encode_id(tool_shed_repository.id),
-                        'error_message': tool_shed_repository.error_message or ''}
+        value_mapper = {
+            "id": trans.security.encode_id(tool_shed_repository.id),
+            "error_message": tool_shed_repository.error_message or "",
+        }
         return value_mapper
 
     @expose_api
@@ -76,28 +81,31 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
         """
         # Example URL: http://localhost:8763/api/tool_shed_repositories
         clause_list = []
-        if 'name' in kwd:
-            clause_list.append(ToolShedRepository.table.c.name == kwd.get('name'))
-        if 'owner' in kwd:
-            clause_list.append(ToolShedRepository.table.c.owner == kwd.get('owner'))
-        if 'changeset' in kwd:
-            clause_list.append(ToolShedRepository.table.c.changeset_revision == kwd.get('changeset'))
-        if 'deleted' in kwd:
-            clause_list.append(ToolShedRepository.table.c.deleted == util.asbool(kwd.get('deleted')))
-        if 'uninstalled' in kwd:
-            clause_list.append(ToolShedRepository.table.c.uninstalled == util.asbool(kwd.get('uninstalled')))
+        if "name" in kwd:
+            clause_list.append(ToolShedRepository.table.c.name == kwd.get("name"))
+        if "owner" in kwd:
+            clause_list.append(ToolShedRepository.table.c.owner == kwd.get("owner"))
+        if "changeset" in kwd:
+            clause_list.append(ToolShedRepository.table.c.changeset_revision == kwd.get("changeset"))
+        if "deleted" in kwd:
+            clause_list.append(ToolShedRepository.table.c.deleted == util.asbool(kwd.get("deleted")))
+        if "uninstalled" in kwd:
+            clause_list.append(ToolShedRepository.table.c.uninstalled == util.asbool(kwd.get("uninstalled")))
         tool_shed_repository_dicts = []
-        query = trans.install_model.context.query(ToolShedRepository) \
-                                           .order_by(ToolShedRepository.table.c.name) \
-                                           .order_by(cast(ToolShedRepository.ctx_rev, Integer).desc())
+        query = (
+            trans.install_model.context.query(ToolShedRepository)
+            .order_by(ToolShedRepository.table.c.name)
+            .order_by(cast(ToolShedRepository.ctx_rev, Integer).desc())
+        )
         if len(clause_list) > 0:
             query = query.filter(and_(*clause_list))
         for tool_shed_repository in query.all():
-            tool_shed_repository_dict = \
-                tool_shed_repository.to_dict(value_mapper=self.__get_value_mapper(trans, tool_shed_repository))
-            tool_shed_repository_dict['url'] = url_for(controller='tool_shed_repositories',
-                                                       action='show',
-                                                       id=trans.security.encode_id(tool_shed_repository.id))
+            tool_shed_repository_dict = tool_shed_repository.to_dict(
+                value_mapper=self.__get_value_mapper(trans, tool_shed_repository)
+            )
+            tool_shed_repository_dict["url"] = url_for(
+                controller="tool_shed_repositories", action="show", id=trans.security.encode_id(tool_shed_repository.id)
+            )
             tool_shed_repository_dicts.append(tool_shed_repository_dict)
         return tool_shed_repository_dicts
 
@@ -151,21 +159,22 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
 
         """
         # Get the information about the repository to be installed from the payload.
-        tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload(payload, include_changeset=True)
+        tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload(
+            payload, include_changeset=True
+        )
         self.__ensure_can_install_repos(trans)
         irm = InstallRepositoryManager(self.app)
-        installed_tool_shed_repositories = irm.install(tool_shed_url,
-                                                       name,
-                                                       owner,
-                                                       changeset_revision,
-                                                       payload)
+        installed_tool_shed_repositories = irm.install(tool_shed_url, name, owner, changeset_revision, payload)
 
         def to_dict(tool_shed_repository):
-            tool_shed_repository_dict = tool_shed_repository.as_dict(value_mapper=self.__get_value_mapper(trans, tool_shed_repository))
-            tool_shed_repository_dict['url'] = url_for(controller='tool_shed_repositories',
-                                                       action='show',
-                                                       id=trans.security.encode_id(tool_shed_repository.id))
+            tool_shed_repository_dict = tool_shed_repository.as_dict(
+                value_mapper=self.__get_value_mapper(trans, tool_shed_repository)
+            )
+            tool_shed_repository_dict["url"] = url_for(
+                controller="tool_shed_repositories", action="show", id=trans.security.encode_id(tool_shed_repository.id)
+            )
             return tool_shed_repository_dict
+
         if installed_tool_shed_repositories:
             return list(map(to_dict, installed_tool_shed_repositories))
         message = "No repositories were installed, possibly because the selected repository has already been installed."
@@ -224,40 +233,44 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
         """
         self.__ensure_can_install_repos(trans)
         # Get the information about all of the repositories to be installed.
-        tool_shed_urls = util.listify(payload.get('tool_shed_urls', ''))
-        names = util.listify(payload.get('names', ''))
-        owners = util.listify(payload.get('owners', ''))
-        changeset_revisions = util.listify(payload.get('changeset_revisions', ''))
+        tool_shed_urls = util.listify(payload.get("tool_shed_urls", ""))
+        names = util.listify(payload.get("names", ""))
+        owners = util.listify(payload.get("owners", ""))
+        changeset_revisions = util.listify(payload.get("changeset_revisions", ""))
         num_specified_repositories = len(tool_shed_urls)
-        if len(names) != num_specified_repositories or \
-                len(owners) != num_specified_repositories or \
-                len(changeset_revisions) != num_specified_repositories:
-            message = 'Error in tool_shed_repositories API in install_repository_revisions: the received parameters must be ordered '
-            message += 'lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated.'
+        if (
+            len(names) != num_specified_repositories
+            or len(owners) != num_specified_repositories
+            or len(changeset_revisions) != num_specified_repositories
+        ):
+            message = "Error in tool_shed_repositories API in install_repository_revisions: the received parameters must be ordered "
+            message += "lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated."
             log.debug(message)
-            return dict(status='error', error=message)
+            return dict(status="error", error=message)
         # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain information
         # about each of the repositories being installed.
         # TODO: we may want to enhance this method to allow for each of the following to be associated with each repository instead of
         # forcing all repositories to use the same settings.
-        install_repository_dependencies = payload.get('install_repository_dependencies', False)
-        install_resolver_dependencies = payload.get('install_resolver_dependencies', False)
-        install_tool_dependencies = payload.get('install_tool_dependencies', False)
-        new_tool_panel_section_label = payload.get('new_tool_panel_section_label', '')
-        shed_tool_conf = payload.get('shed_tool_conf', None)
-        tool_panel_section_id = payload.get('tool_panel_section_id', '')
+        install_repository_dependencies = payload.get("install_repository_dependencies", False)
+        install_resolver_dependencies = payload.get("install_resolver_dependencies", False)
+        install_tool_dependencies = payload.get("install_tool_dependencies", False)
+        new_tool_panel_section_label = payload.get("new_tool_panel_section_label", "")
+        shed_tool_conf = payload.get("shed_tool_conf", None)
+        tool_panel_section_id = payload.get("tool_panel_section_id", "")
         all_installed_tool_shed_repositories = []
         for tool_shed_url, name, owner, changeset_revision in zip(tool_shed_urls, names, owners, changeset_revisions):
-            current_payload = dict(tool_shed_url=tool_shed_url,
-                                   name=name,
-                                   owner=owner,
-                                   changeset_revision=changeset_revision,
-                                   new_tool_panel_section_label=new_tool_panel_section_label,
-                                   tool_panel_section_id=tool_panel_section_id,
-                                   install_repository_dependencies=install_repository_dependencies,
-                                   install_resolver_dependencies=install_resolver_dependencies,
-                                   install_tool_dependencies=install_tool_dependencies,
-                                   shed_tool_conf=shed_tool_conf)
+            current_payload = dict(
+                tool_shed_url=tool_shed_url,
+                name=name,
+                owner=owner,
+                changeset_revision=changeset_revision,
+                new_tool_panel_section_label=new_tool_panel_section_label,
+                tool_panel_section_id=tool_panel_section_id,
+                install_repository_dependencies=install_repository_dependencies,
+                install_resolver_dependencies=install_resolver_dependencies,
+                install_tool_dependencies=install_tool_dependencies,
+                shed_tool_conf=shed_tool_conf,
+            )
             installed_tool_shed_repositories = self.install_repository_revision(trans, **current_payload)
             if isinstance(installed_tool_shed_repositories, dict):
                 # We encountered an error.
@@ -283,48 +296,52 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
             'tool_shed_url': Tool Shed URL
 
         """
-        remove_from_disk = util.asbool(kwd.get('remove_from_disk', True))
+        remove_from_disk = util.asbool(kwd.get("remove_from_disk", True))
         if id:
             try:
                 repository = get_tool_shed_repository_by_id(self.app, id)
             except ValueError:
                 raise HTTPBadRequest(detail=f"No repository with id '{id}' found")
         else:
-            tsr_arguments = ['name', 'owner', 'changeset_revision', 'tool_shed_url']
+            tsr_arguments = ["name", "owner", "changeset_revision", "tool_shed_url"]
             try:
                 tsr_arguments = {key: kwd[key] for key in tsr_arguments}
             except KeyError as e:
                 raise HTTPBadRequest(detail=f"Missing required parameter '{e.args[0]}'")
-            repository = get_installed_repository(app=self.app,
-                                                  tool_shed=tsr_arguments['tool_shed_url'],
-                                                  name=tsr_arguments['name'],
-                                                  owner=tsr_arguments['owner'],
-                                                  changeset_revision=tsr_arguments['changeset_revision'])
+            repository = get_installed_repository(
+                app=self.app,
+                tool_shed=tsr_arguments["tool_shed_url"],
+                name=tsr_arguments["name"],
+                owner=tsr_arguments["owner"],
+                changeset_revision=tsr_arguments["changeset_revision"],
+            )
             if not repository:
                 raise HTTPBadRequest(detail="Repository not found")
         irm = InstalledRepositoryManager(app=self.app)
         errors = irm.uninstall_repository(repository=repository, remove_from_disk=remove_from_disk)
         if not errors:
-            action = 'removed' if remove_from_disk else 'deactivated'
-            return {'message': f'The repository named {repository.name} has been {action}.'}
+            action = "removed" if remove_from_disk else "deactivated"
+            return {"message": f"The repository named {repository.name} has been {action}."}
         else:
-            raise Exception(f'Attempting to uninstall tool dependencies for repository named {repository.name} resulted in errors: {errors}')
+            raise Exception(
+                f"Attempting to uninstall tool dependencies for repository named {repository.name} resulted in errors: {errors}"
+            )
 
     def __parse_repository_from_payload(self, payload, include_changeset=False):
         # Get the information about the repository to be installed from the payload.
-        tool_shed_url = payload.get('tool_shed_url', '')
+        tool_shed_url = payload.get("tool_shed_url", "")
         if not tool_shed_url:
             raise exceptions.RequestParameterMissingException("Missing required parameter 'tool_shed_url'.")
-        name = payload.get('name', '')
+        name = payload.get("name", "")
         if not name:
             raise exceptions.RequestParameterMissingException("Missing required parameter 'name'.")
-        owner = payload.get('owner', '')
+        owner = payload.get("owner", "")
         if not owner:
             raise exceptions.RequestParameterMissingException("Missing required parameter 'owner'.")
         if not include_changeset:
             return tool_shed_url, name, owner
 
-        changeset_revision = payload.get('changeset_revision', '')
+        changeset_revision = payload.get("changeset_revision", "")
         if not changeset_revision:
             raise HTTPBadRequest(detail="Missing required parameter 'changeset_revision'.")
 
@@ -333,15 +350,15 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
     @require_admin
     @expose_api
     def check_for_updates(self, trans, **kwd):
-        '''
+        """
         GET /api/tool_shed_repositories/check_for_updates
         Check for updates to the specified repository, or all installed repositories.
 
         :param id: the encoded repository id
-        '''
-        repository_id = kwd.get('id', None)
+        """
+        repository_id = kwd.get("id", None)
         message, status = check_for_updates(self.app, trans.install_model, repository_id)
-        return {'status': status, 'message': message}
+        return {"status": status, "message": message}
 
     @require_admin
     @expose_api
@@ -382,13 +399,12 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
         :param key: the API key of the Galaxy admin user.
         """
         start_time = strftime("%Y-%m-%d %H:%M:%S")
-        results = dict(start_time=start_time,
-                       successful_count=0,
-                       unsuccessful_count=0,
-                       repository_status=[])
+        results = dict(start_time=start_time, successful_count=0, unsuccessful_count=0, repository_status=[])
         # Make sure the current user's API key proves he is an admin user in this Galaxy instance.
         if not trans.user_is_admin:
-            raise HTTPForbidden(detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.')
+            raise HTTPForbidden(
+                detail="You are not authorized to reset metadata on repositories installed into this Galaxy instance."
+            )
         irmm = InstalledRepositoryMetadataManager(self.app)
         query = irmm.get_query_for_setting_metadata_on_repositories(order=False)
         # Now reset metadata on all remaining repositories.
@@ -398,23 +414,26 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
                 irmm.reset_all_metadata_on_installed_repository()
                 irmm_invalid_file_tups = irmm.get_invalid_file_tups()
                 if irmm_invalid_file_tups:
-                    message = generate_message_for_invalid_tools(self.app,
-                                                                 irmm_invalid_file_tups,
-                                                                 repository,
-                                                                 None,
-                                                                 as_html=False)
-                    results['unsuccessful_count'] += 1
+                    message = generate_message_for_invalid_tools(
+                        self.app, irmm_invalid_file_tups, repository, None, as_html=False
+                    )
+                    results["unsuccessful_count"] += 1
                 else:
-                    message = "Successfully reset metadata on repository %s owned by %s" % \
-                        (str(repository.name), str(repository.owner))
-                    results['successful_count'] += 1
+                    message = "Successfully reset metadata on repository %s owned by %s" % (
+                        str(repository.name),
+                        str(repository.owner),
+                    )
+                    results["successful_count"] += 1
             except Exception as e:
-                message = "Error resetting metadata on repository %s owned by %s: %s" % \
-                    (str(repository.name), str(repository.owner), util.unicodify(e))
-                results['unsuccessful_count'] += 1
-            results['repository_status'].append(message)
+                message = "Error resetting metadata on repository %s owned by %s: %s" % (
+                    str(repository.name),
+                    str(repository.owner),
+                    util.unicodify(e),
+                )
+                results["unsuccessful_count"] += 1
+            results["repository_status"].append(message)
         stop_time = strftime("%Y-%m-%d %H:%M:%S")
-        results['stop_time'] = stop_time
+        results["stop_time"] = stop_time
         return json.dumps(results, sort_keys=True, indent=4)
 
     @expose_api
@@ -455,8 +474,10 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
         if tool_shed_repository is None:
             log.debug(f"Unable to locate tool_shed_repository record for id {str(id)}.")
             return {}
-        tool_shed_repository_dict = tool_shed_repository.as_dict(value_mapper=self.__get_value_mapper(trans, tool_shed_repository))
-        tool_shed_repository_dict['url'] = url_for(controller='tool_shed_repositories',
-                                                   action='show',
-                                                   id=trans.security.encode_id(tool_shed_repository.id))
+        tool_shed_repository_dict = tool_shed_repository.as_dict(
+            value_mapper=self.__get_value_mapper(trans, tool_shed_repository)
+        )
+        tool_shed_repository_dict["url"] = url_for(
+            controller="tool_shed_repositories", action="show", id=trans.security.encode_id(tool_shed_repository.id)
+        )
         return tool_shed_repository_dict
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 47fe01229e4..61c63a62537 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -1,9 +1,21 @@
 import logging
 import os
-from json import dumps, loads
-from typing import Any, cast, Dict, Optional
+from json import (
+    dumps,
+    loads,
+)
+from typing import (
+    Any,
+    cast,
+    Dict,
+    Optional,
+)
 
-from galaxy import exceptions, util, web
+from galaxy import (
+    exceptions,
+    util,
+    web,
+)
 from galaxy.datatypes.data import get_params_and_input_name
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
@@ -21,7 +33,10 @@ from galaxy.web import (
 from galaxy.web.framework.decorators import expose_api_raw
 from galaxy.webapps.base.controller import UsesVisualizationMixin
 from galaxy.webapps.base.webapp import GalaxyWebTransaction
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 from ._fetch_util import validate_and_normalize_targets
 
 log = logging.getLogger(__name__)
@@ -30,13 +45,14 @@ log = logging.getLogger(__name__)
 # provides access via a different API endpoint.
 PROTECTED_TOOLS = ["__DATA_FETCH__"]
 # Tool search bypasses the fulltext for the following list of terms
-SEARCH_RESERVED_TERMS_FAVORITES = ['#favs', '#favorites', '#favourites']
+SEARCH_RESERVED_TERMS_FAVORITES = ["#favs", "#favorites", "#favourites"]
 
 
 class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
     """
     RESTful controller for interactions with tools.
     """
+
     history_manager: HistoryManager = depends(HistoryManager)
     hda_manager: HDAManager = depends(HDAManager)
     hdca_manager: DatasetCollectionManager = depends(DatasetCollectionManager)
@@ -59,19 +75,19 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         """
 
         # Read params.
-        in_panel = util.string_as_bool(kwds.get('in_panel', 'True'))
-        trackster = util.string_as_bool(kwds.get('trackster', 'False'))
-        q = kwds.get('q', '')
-        tool_id = kwds.get('tool_id', '')
-        tool_help = util.string_as_bool(kwds.get('tool_help', 'False'))
+        in_panel = util.string_as_bool(kwds.get("in_panel", "True"))
+        trackster = util.string_as_bool(kwds.get("trackster", "False"))
+        q = kwds.get("q", "")
+        tool_id = kwds.get("tool_id", "")
+        tool_help = util.string_as_bool(kwds.get("tool_help", "False"))
         view = kwds.get("view", None)
 
         # Find whether to search.
         if q:
             if trans.user and q in SEARCH_RESERVED_TERMS_FAVORITES:
-                if 'favorites' in trans.user.preferences:
-                    favorites = loads(trans.user.preferences['favorites'])
-                    hits = favorites['tools']
+                if "favorites" in trans.user.preferences:
+                    favorites = loads(trans.user.preferences["favorites"])
+                    hits = favorites["tools"]
                 else:
                     hits = None
             else:
@@ -96,7 +112,9 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
         # Return everything.
         try:
-            return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help, view=view)
+            return self.app.toolbox.to_dict(
+                trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help, view=view
+            )
         except exceptions.MessageException:
             raise
         except Exception:
@@ -115,9 +133,9 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
                 link_details - if true, hyperlink to the tool is returned
                 tool_version - if provided return this tool version
         """
-        io_details = util.string_as_bool(kwd.get('io_details', False))
-        link_details = util.string_as_bool(kwd.get('link_details', False))
-        tool_version = kwd.get('tool_version')
+        io_details = util.string_as_bool(kwd.get("io_details", False))
+        link_details = util.string_as_bool(kwd.get("link_details", False))
+        tool_version = kwd.get("tool_version")
         tool = self._get_tool(id, user=trans.user, tool_version=tool_version)
         return tool.to_dict(trans, io_details=io_details, link_details=link_details)
 
@@ -128,13 +146,15 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         Returns a tool model including dynamic parameters and updated values, repeats block etc.
         """
         kwd = _kwd_or_payload(kwd)
-        tool_version = kwd.get('tool_version')
-        history_id = kwd.pop('history_id', None)
+        tool_version = kwd.get("tool_version")
+        history_id = kwd.pop("history_id", None)
         history = None
         if history_id:
-            history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
+            history = self.history_manager.get_owned(
+                self.decode_id(history_id), trans.user, current_history=trans.history
+            )
         tool = self._get_tool(id, tool_version=tool_version, user=trans.user)
-        return tool.to_json(trans, kwd.get('inputs', kwd), history=history)
+        return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
 
     @web.require_admin
     @expose_api
@@ -143,7 +163,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         GET /api/tools/{tool_id}/test_data_path?tool_version={tool_version}
         """
         kwd = _kwd_or_payload(kwd)
-        tool_version = kwd.get('tool_version', None)
+        tool_version = kwd.get("tool_version", None)
         tool = self._get_tool(id, tool_version=tool_version, user=trans.user)
         path = tool.test_data_path(kwd.get("filename"))
         if path:
@@ -156,7 +176,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         """
         GET /api/tools/{tool_id}/test_data_download?tool_version={tool_version}&filename={filename}
         """
-        tool_version = kwd.get('tool_version', None)
+        tool_version = kwd.get("tool_version", None)
         tool = self._get_tool(id, tool_version=tool_version, user=trans.user)
         filename = kwd.get("filename")
         if filename is None:
@@ -165,7 +185,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         if path:
             if os.path.isfile(path):
                 trans.response.headers["Content-Disposition"] = f'attachment; filename="{filename}"'
-                return open(path, mode='rb')
+                return open(path, mode="rb")
             elif os.path.isdir(path):
                 # Set upstream_mod_zip to false, otherwise tool data must be among allowed internal routes
                 archive = ZipstreamWrapper(
@@ -218,7 +238,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         set as '*' to get tests for all configured versions.
         """
         kwd = _kwd_or_payload(kwd)
-        tool_version = kwd.get('tool_version', None)
+        tool_version = kwd.get("tool_version", None)
         if tool_version == "*":
             tools = self.app.toolbox.get_tool(id, get_all_versions=True)
             for tool in tools:
@@ -239,11 +259,11 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         GET /api/tools/{tool_id}/reload
         Reload specified tool.
         """
-        trans.app.queue_worker.send_control_task('reload_tool', noop_self=True, kwargs={'tool_id': id})
+        trans.app.queue_worker.send_control_task("reload_tool", noop_self=True, kwargs={"tool_id": id})
         message, status = trans.app.toolbox.reload_tool_by_id(id)
-        if status == 'error':
+        if status == "error":
             raise exceptions.MessageException(message)
-        return {'message': message}
+        return {"message": message}
 
     @web.require_admin
     @expose_api
@@ -288,7 +308,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         """
         tool = self._get_tool(id, user=trans.user)
         tool._view.install_dependencies(tool.requirements, **kwds)
-        if kwds.get('build_dependency_cache'):
+        if kwds.get("build_dependency_cache"):
             tool.build_dependency_cache(**kwds)
         # TODO: rework resolver install system to log and report what has been done.
         # _view.install_dependencies should return a dict with stdout, stderr and success status
@@ -344,7 +364,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
             return x.to_dict()
 
         tool = self._get_tool(id, user=trans.user)
-        if hasattr(tool, 'lineage'):
+        if hasattr(tool, "lineage"):
             lineage_dict = tool.lineage.to_dict()
         else:
             lineage_dict = None
@@ -397,31 +417,33 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :return type: dict
         """
         panel_view = view or self.app.config.default_panel_view
-        tool_name_boost = self.app.config.get('tool_name_boost', 9)
-        tool_id_boost = self.app.config.get('tool_id_boost', 9)
-        tool_section_boost = self.app.config.get('tool_section_boost', 3)
-        tool_description_boost = self.app.config.get('tool_description_boost', 2)
-        tool_label_boost = self.app.config.get('tool_label_boost', 1)
-        tool_stub_boost = self.app.config.get('tool_stub_boost', 5)
-        tool_help_boost = self.app.config.get('tool_help_boost', 0.5)
-        tool_search_limit = self.app.config.get('tool_search_limit', 20)
-        tool_enable_ngram_search = self.app.config.get('tool_enable_ngram_search', False)
-        tool_ngram_minsize = self.app.config.get('tool_ngram_minsize', 3)
-        tool_ngram_maxsize = self.app.config.get('tool_ngram_maxsize', 4)
+        tool_name_boost = self.app.config.get("tool_name_boost", 9)
+        tool_id_boost = self.app.config.get("tool_id_boost", 9)
+        tool_section_boost = self.app.config.get("tool_section_boost", 3)
+        tool_description_boost = self.app.config.get("tool_description_boost", 2)
+        tool_label_boost = self.app.config.get("tool_label_boost", 1)
+        tool_stub_boost = self.app.config.get("tool_stub_boost", 5)
+        tool_help_boost = self.app.config.get("tool_help_boost", 0.5)
+        tool_search_limit = self.app.config.get("tool_search_limit", 20)
+        tool_enable_ngram_search = self.app.config.get("tool_enable_ngram_search", False)
+        tool_ngram_minsize = self.app.config.get("tool_ngram_minsize", 3)
+        tool_ngram_maxsize = self.app.config.get("tool_ngram_maxsize", 4)
 
-        results = self.app.toolbox_search.search(q=q,
-                                                 panel_view=panel_view,
-                                                 tool_name_boost=tool_name_boost,
-                                                 tool_id_boost=tool_id_boost,
-                                                 tool_section_boost=tool_section_boost,
-                                                 tool_description_boost=tool_description_boost,
-                                                 tool_label_boost=tool_label_boost,
-                                                 tool_stub_boost=tool_stub_boost,
-                                                 tool_help_boost=tool_help_boost,
-                                                 tool_search_limit=tool_search_limit,
-                                                 tool_enable_ngram_search=tool_enable_ngram_search,
-                                                 tool_ngram_minsize=tool_ngram_minsize,
-                                                 tool_ngram_maxsize=tool_ngram_maxsize)
+        results = self.app.toolbox_search.search(
+            q=q,
+            panel_view=panel_view,
+            tool_name_boost=tool_name_boost,
+            tool_id_boost=tool_id_boost,
+            tool_section_boost=tool_section_boost,
+            tool_description_boost=tool_description_boost,
+            tool_label_boost=tool_label_boost,
+            tool_stub_boost=tool_stub_boost,
+            tool_help_boost=tool_help_boost,
+            tool_search_limit=tool_search_limit,
+            tool_enable_ngram_search=tool_enable_ngram_search,
+            tool_ngram_minsize=tool_ngram_minsize,
+            tool_ngram_maxsize=tool_ngram_maxsize,
+        )
         return results
 
     @expose_api_anonymous_and_sessionless
@@ -429,7 +451,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         tool = self._get_tool(id, user=trans.user)
         rval = []
         for citation in tool.citations:
-            rval.append(citation.to_dict('bibtex'))
+            rval.append(citation.to_dict("bibtex"))
         return rval
 
     @expose_api
@@ -458,13 +480,15 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
             ],
             "batch": input_src == "hdca",
         }
-        history_id = payload.get('history_id')
+        history_id = payload.get("history_id")
         if history_id:
             decoded_id = self.decode_id(history_id)
             target_history = self.history_manager.get_owned(decoded_id, trans.user, current_history=trans.history)
         else:
             if input_src == "hdca":
-                target_history = self.hdca_manager.get_dataset_collection_instance(trans, instance_type='history', id=input_id).history
+                target_history = self.hdca_manager.get_dataset_collection_instance(
+                    trans, instance_type="history", id=input_id
+                ).history
             elif input_src == "hda":
                 decoded_id = trans.app.security.decode_id(input_id)
                 target_history = self.hda_manager.get_accessible(decoded_id, trans.user).history
@@ -473,7 +497,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
                 raise exceptions.RequestParameterInvalidException("Must run conversion on either hdca or hda.")
 
         # Make the target datatype available to the converter
-        params['__target_datatype__'] = target_type
+        params["__target_datatype__"] = target_type
         vars = converter.handle_input(trans, params, history=target_history)
         return self._handle_inputs_output_to_api_response(trans, converter, target_history, vars)
 
@@ -486,7 +510,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
     @web.legacy_expose_api_raw
     def download(self, trans: GalaxyWebTransaction, id, **kwds):
         tool_tarball = trans.app.toolbox.package_tool(trans, id)
-        trans.response.set_content_type('application/x-gzip')
+        trans.response.set_content_type("application/x-gzip")
         download_file = open(tool_tarball, "rb")
         trans.response.headers["Content-Disposition"] = f'attachment; filename="{id}.tgz"'
         return download_file
@@ -495,16 +519,17 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
     def raw_tool_source(self, trans: GalaxyWebTransaction, id, **kwds):
         """Returns tool source. ``language`` is included in the response header."""
         if not trans.app.config.enable_tool_source_display and not trans.user_is_admin:
-            raise exceptions.InsufficientPermissionsException("Only administrators may display tool sources on this Galaxy server.")
-        tool = self._get_tool(id, user=trans.user, tool_version=kwds.get('tool_version'))
-        trans.response.headers['language'] = tool.tool_source.language
+            raise exceptions.InsufficientPermissionsException(
+                "Only administrators may display tool sources on this Galaxy server."
+            )
+        tool = self._get_tool(id, user=trans.user, tool_version=kwds.get("tool_version"))
+        trans.response.headers["language"] = tool.tool_source.language
         return tool.tool_source.to_string()
 
     @expose_api_anonymous
     def fetch(self, trans: GalaxyWebTransaction, payload, **kwd):
-        """Adapt clean API to tool-constrained API.
-        """
-        request_version = '1'
+        """Adapt clean API to tool-constrained API."""
+        request_version = "1"
         if "history_id" not in payload:
             raise exceptions.RequestParameterMissingException("history_id must be specified")
         history_id = payload.pop("history_id")
@@ -513,7 +538,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         for key, value in payload.items():
             if key == "key":
                 continue
-            if key.startswith('files_') or key.startswith('__files_'):
+            if key.startswith("files_") or key.startswith("__files_"):
                 files_payload[key] = value
                 continue
             clean_payload[key] = value
@@ -521,12 +546,12 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         clean_payload["check_content"] = trans.app.config.check_upload_content
         request = dumps(clean_payload)
         create_payload = {
-            'tool_id': "__DATA_FETCH__",
-            'history_id': history_id,
-            'inputs': {
-                'request_version': request_version,
-                'request_json': request,
-                'file_count': str(len(files_payload))
+            "tool_id": "__DATA_FETCH__",
+            "history_id": history_id,
+            "inputs": {
+                "request_version": request_version,
+                "request_json": request,
+                "file_count": str(len(files_payload)),
             },
         }
         create_payload.update(files_payload)
@@ -557,7 +582,9 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         tool_id = payload.get("tool_id")
         tool_uuid = payload.get("tool_uuid")
         if tool_id in PROTECTED_TOOLS:
-            raise exceptions.RequestParameterInvalidException(f"Cannot execute tool [{tool_id}] directly, must use alternative endpoint.")
+            raise exceptions.RequestParameterInvalidException(
+                f"Cannot execute tool [{tool_id}] directly, must use alternative endpoint."
+            )
         if tool_id is None and tool_uuid is None:
             raise exceptions.RequestParameterInvalidException("Must specify a valid tool_id to use this endpoint.")
         return self._create(trans, payload, **kwd)
@@ -565,14 +592,14 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
     def _create(self, trans: GalaxyWebTransaction, payload, **kwd):
         if trans.user_is_bootstrap_admin:
             raise exceptions.RealUserRequiredException("Only real users can execute tools or run jobs.")
-        action = payload.get('action')
-        if action == 'rerun':
+        action = payload.get("action")
+        if action == "rerun":
             raise Exception("'rerun' action has been deprecated")
 
         # Get tool.
-        tool_version = payload.get('tool_version')
-        tool_id = payload.get('tool_id')
-        tool_uuid = payload.get('tool_uuid')
+        tool_version = payload.get("tool_version")
+        tool_id = payload.get("tool_id")
+        tool_uuid = payload.get("tool_uuid")
         get_kwds = dict(
             tool_id=tool_id,
             tool_uuid=tool_uuid,
@@ -584,19 +611,21 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         tool = trans.app.toolbox.get_tool(**get_kwds)
         if not tool:
             log.debug(f"Not found tool with kwds [{get_kwds}]")
-            raise exceptions.ToolMissingException('Tool not found.')
+            raise exceptions.ToolMissingException("Tool not found.")
         if not tool.allow_user_access(trans.user):
-            raise exceptions.ItemAccessibilityException('Tool not accessible.')
+            raise exceptions.ItemAccessibilityException("Tool not accessible.")
         if trans.app.config.user_activation_on:
             if not trans.user:
                 log.warning("Anonymous user attempts to execute tool, but account activation is turned on.")
             elif not trans.user.active:
-                log.warning(f"User \"{trans.user.email}\" attempts to execute tool, but account activation is turned on and user account is not active.")
+                log.warning(
+                    f'User "{trans.user.email}" attempts to execute tool, but account activation is turned on and user account is not active.'
+                )
 
         # Set running history from payload parameters.
         # History not set correctly as part of this API call for
         # dataset upload.
-        history_id = payload.get('history_id')
+        history_id = payload.get("history_id")
         if history_id:
             decoded_id = self.decode_id(history_id)
             target_history = self.history_manager.get_owned(decoded_id, trans.user, current_history=trans.history)
@@ -604,13 +633,13 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
             target_history = None
 
         # Set up inputs.
-        inputs = payload.get('inputs', {})
+        inputs = payload.get("inputs", {})
         if not isinstance(inputs, dict):
             raise exceptions.RequestParameterInvalidException(f"inputs invalid {inputs}")
 
         # Find files coming in as multipart file data and add to inputs.
         for k, v in payload.items():
-            if k.startswith('files_') or k.startswith('__files_'):
+            if k.startswith("files_") or k.startswith("__files_"):
                 inputs[k] = v
 
         # for inputs that are coming from the Library, copy them into the history
@@ -624,21 +653,25 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         # use_cached_job can be passed in via the top-level payload or among the tool inputs.
         # I think it should be a top-level parameter, but because the selector is implemented
         # as a regular tool parameter we accept both.
-        use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false'))
+        use_cached_job = payload.get("use_cached_job", False) or util.string_as_bool(
+            inputs.get("use_cached_job", "false")
+        )
 
-        input_format = str(payload.get('input_format', 'legacy'))
+        input_format = str(payload.get("input_format", "legacy"))
 
-        vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)
+        vars = tool.handle_input(
+            trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format
+        )
 
         new_pja_flush = False
-        for job in vars.get('jobs', []):
-            if inputs.get('send_email_notification', False):
+        for job in vars.get("jobs", []):
+            if inputs.get("send_email_notification", False):
                 # Unless an anonymous user is invoking this via the API it
                 # should never be an option, but check and enforce that here
                 if trans.user is None:
                     raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.")
                 else:
-                    job_email_action = PostJobAction('EmailAction')
+                    job_email_action = PostJobAction("EmailAction")
                     job.add_post_job_action(job_email_action)
                     new_pja_flush = True
 
@@ -649,42 +682,48 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
     def _handle_inputs_output_to_api_response(self, trans, tool, target_history, vars):
         # TODO: check for errors and ensure that output dataset(s) are available.
-        output_datasets = vars.get('out_data', [])
-        rval: Dict[str, Any] = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []}
-        rval['produces_entry_points'] = tool.produces_entry_points
-        job_errors = vars.get('job_errors', [])
+        output_datasets = vars.get("out_data", [])
+        rval: Dict[str, Any] = {"outputs": [], "output_collections": [], "jobs": [], "implicit_collections": []}
+        rval["produces_entry_points"] = tool.produces_entry_points
+        job_errors = vars.get("job_errors", [])
         if job_errors:
             # If we are here - some jobs were successfully executed but some failed.
-            rval['errors'] = job_errors
+            rval["errors"] = job_errors
 
-        outputs = rval['outputs']
+        outputs = rval["outputs"]
         # TODO:?? poss. only return ids?
         for output_name, output in output_datasets:
             output_dict = output.to_dict()
             # add the output name back into the output data structure
             # so it's possible to figure out which newly created elements
             # correspond with which tool file outputs
-            output_dict['output_name'] = output_name
+            output_dict["output_name"] = output_name
             outputs.append(trans.security.encode_dict_ids(output_dict, skip_startswith="metadata_"))
 
-        for job in vars.get('jobs', []):
-            rval['jobs'].append(self.encode_all_ids(trans, job.to_dict(view='collection'), recursive=True))
+        for job in vars.get("jobs", []):
+            rval["jobs"].append(self.encode_all_ids(trans, job.to_dict(view="collection"), recursive=True))
 
-        for output_name, collection_instance in vars.get('output_collections', []):
+        for output_name, collection_instance in vars.get("output_collections", []):
             history = target_history or trans.history
             output_dict = dictify_dataset_collection_instance(
-                collection_instance, security=trans.security, url_builder=trans.url_builder, parent=history,
+                collection_instance,
+                security=trans.security,
+                url_builder=trans.url_builder,
+                parent=history,
             )
-            output_dict['output_name'] = output_name
-            rval['output_collections'].append(output_dict)
+            output_dict["output_name"] = output_name
+            rval["output_collections"].append(output_dict)
 
-        for output_name, collection_instance in vars.get('implicit_collections', {}).items():
+        for output_name, collection_instance in vars.get("implicit_collections", {}).items():
             history = target_history or trans.history
             output_dict = dictify_dataset_collection_instance(
-                collection_instance, security=trans.security, url_builder=trans.url_builder, parent=history,
+                collection_instance,
+                security=trans.security,
+                url_builder=trans.url_builder,
+                parent=history,
             )
-            output_dict['output_name'] = output_name
-            rval['implicit_collections'].append(output_dict)
+            output_dict["output_name"] = output_name
+            rval["implicit_collections"].append(output_dict)
 
         return rval
 
@@ -696,17 +735,19 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
             new_value = self._patch_library_dataset(trans, v, target_history)
             if new_value:
                 v = new_value
-            elif isinstance(v, dict) and 'values' in v:
-                for index, value in enumerate(v['values']):
+            elif isinstance(v, dict) and "values" in v:
+                for index, value in enumerate(v["values"]):
                     patched = self._patch_library_dataset(trans, value, target_history)
                     if patched:
-                        v['values'][index] = patched
+                        v["values"][index] = patched
             inputs[k] = v
 
     def _patch_library_dataset(self, trans: GalaxyWebTransaction, v, target_history):
-        if isinstance(v, dict) and 'id' in v and v.get('src') == 'ldda':
-            ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id']))
-            if trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset):
+        if isinstance(v, dict) and "id" in v and v.get("src") == "ldda":
+            ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v["id"]))
+            if trans.user_is_admin or trans.app.security_agent.can_access_dataset(
+                trans.get_current_user_roles(), ldda.dataset
+            ):
                 return ldda.to_history_dataset_association(target_history, add_to_history=True)
 
     #
@@ -722,6 +763,6 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
 
 
 def _kwd_or_payload(kwd: Dict[str, Any]) -> Dict[str, Any]:
-    if 'payload' in kwd:
-        kwd = cast(Dict[str, Any], kwd.get('payload'))
+    if "payload" in kwd:
+        kwd = cast(Dict[str, Any], kwd.get("payload"))
     return kwd
diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py
index 6a0fec3ad88..7cf739116bc 100644
--- a/lib/galaxy/webapps/galaxy/api/toolshed.py
+++ b/lib/galaxy/webapps/galaxy/api/toolshed.py
@@ -4,7 +4,10 @@ from urllib.parse import quote
 
 from galaxy.exceptions import MessageException
 from galaxy.util import url_get
-from galaxy.web import expose_api, require_admin
+from galaxy.web import (
+    expose_api,
+    require_admin,
+)
 from . import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
@@ -21,7 +24,7 @@ class ToolShedController(BaseGalaxyAPIController):
         """
         tool_sheds = []
         for name, url in trans.app.tool_shed_registry.tool_sheds.items():
-            tool_sheds.append(dict(name=name, url=quote(url, '')))
+            tool_sheds.append(dict(name=name, url=quote(url, "")))
         return tool_sheds
 
     @require_admin
diff --git a/lib/galaxy/webapps/galaxy/api/tours.py b/lib/galaxy/webapps/galaxy/api/tours.py
index d1cc0c1afd4..17e4765e919 100644
--- a/lib/galaxy/webapps/galaxy/api/tours.py
+++ b/lib/galaxy/webapps/galaxy/api/tours.py
@@ -11,7 +11,7 @@ from galaxy.tours import (
 from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
-    require_admin
+    require_admin,
 )
 from . import (
     BaseGalaxyAPIController,
@@ -22,7 +22,7 @@ from . import (
 log = logging.getLogger(__name__)
 
 
-router = Router(tags=['tours'])
+router = Router(tags=["tours"])
 
 
 @router.cbv
@@ -30,17 +30,17 @@ class FastAPITours:
     # ugh - mypy https://github.com/python/mypy/issues/5374
     registry: ToursRegistry = depends(ToursRegistry)  # type: ignore[misc]
 
-    @router.get('/api/tours')
+    @router.get("/api/tours")
     def index(self) -> TourList:
         """Return list of available tours."""
         return self.registry.get_tours()
 
-    @router.get('/api/tours/{tour_id}')
+    @router.get("/api/tours/{tour_id}")
     def show(self, tour_id: str) -> TourDetails:
         """Return a tour definition."""
         return self.registry.tour_contents(tour_id)
 
-    @router.post('/api/tours/{tour_id}', require_admin=True)
+    @router.post("/api/tours/{tour_id}", require_admin=True)
     def update_tour(self, tour_id: str) -> TourDetails:
         """Return a tour definition."""
         return self.registry.load_tour(tour_id)
diff --git a/lib/galaxy/webapps/galaxy/api/trs_consumer.py b/lib/galaxy/webapps/galaxy/api/trs_consumer.py
index 3e0043fbd8c..d226d89f428 100644
--- a/lib/galaxy/webapps/galaxy/api/trs_consumer.py
+++ b/lib/galaxy/webapps/galaxy/api/trs_consumer.py
@@ -4,11 +4,15 @@ Information on TRS can be found at https://github.com/ga4gh/tool-registry-servic
 """
 from galaxy.web import expose_api
 from galaxy.workflow.trs_proxy import TrsProxy
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 
 class TrsConsumeAPIController(BaseGalaxyAPIController):
     """Controller for TRS proxying."""
+
     _trs_proxy: TrsProxy = depends(TrsProxy)
 
     @expose_api
diff --git a/lib/galaxy/webapps/galaxy/api/trs_search.py b/lib/galaxy/webapps/galaxy/api/trs_search.py
index ce2db31f4ae..2c06c9a27dc 100644
--- a/lib/galaxy/webapps/galaxy/api/trs_search.py
+++ b/lib/galaxy/webapps/galaxy/api/trs_search.py
@@ -5,8 +5,14 @@ Information on TRS can be found at https://github.com/ga4gh/tool-registry-servic
 import logging
 
 from galaxy.web import expose_api
-from galaxy.workflow.trs_proxy import parse_search_kwds, TrsProxy
-from . import BaseGalaxyAPIController, depends
+from galaxy.workflow.trs_proxy import (
+    parse_search_kwds,
+    TrsProxy,
+)
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
@@ -17,6 +23,7 @@ class TrsSearchAPIController(BaseGalaxyAPIController):
     Not trying to emulate the actual underlying GA4GH API interface so throwing
     the search functionality into a different controller than the trs_consumer.
     """
+
     _trs_proxy: TrsProxy = depends(TrsProxy)
 
     @expose_api
diff --git a/lib/galaxy/webapps/galaxy/api/uploads.py b/lib/galaxy/webapps/galaxy/api/uploads.py
index 43d0b6208ce..e432fc3f819 100644
--- a/lib/galaxy/webapps/galaxy/api/uploads.py
+++ b/lib/galaxy/webapps/galaxy/api/uploads.py
@@ -10,16 +10,14 @@ from galaxy.web.framework.decorators import (
     expose_api_raw_anonymous,
     legacy_expose_api_anonymous,
 )
-from . import (
-    BaseGalaxyAPIController,
-)
+from . import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
 
 
 class UploadsAPIController(BaseGalaxyAPIController):
 
-    READ_CHUNK_SIZE = 2 ** 16
+    READ_CHUNK_SIZE = 2**16
 
     @expose_api_raw_anonymous
     def hooks(self, trans, **kwds):
@@ -41,7 +39,7 @@ class UploadsAPIController(BaseGalaxyAPIController):
         session_id = payload.get("session_id")
         session_start = payload.get("session_start")
         session_chunk = payload.get("session_chunk")
-        if re.match(r'^[\w-]+$', session_id) is None:
+        if re.match(r"^[\w-]+$", session_id) is None:
             raise exceptions.MessageException("Requires a session id.")
         if session_start is None:
             raise exceptions.MessageException("Requires a session start.")
diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py
index 88d842a81bc..e5bfde0ed4c 100644
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -10,44 +10,50 @@ from markupsafe import escape
 from sqlalchemy import (
     false,
     or_,
-    true
+    true,
 )
 
 from galaxy import (
     exceptions,
     util,
-    web
+    web,
 )
 from galaxy.exceptions import ObjectInvalid
 from galaxy.managers import (
     api_keys,
-    users
+    users,
 )
 from galaxy.managers.context import ProvidesUserContext
-from galaxy.model import User, UserAddress
+from galaxy.model import (
+    User,
+    UserAddress,
+)
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_password,
-    validate_publicname
+    validate_publicname,
 )
 from galaxy.security.vault import UserVaultWrapper
 from galaxy.tool_util.toolbox.filters import FilterFactory
 from galaxy.util import (
     docstring_trim,
-    listify
+    listify,
 )
 from galaxy.web import (
     expose_api,
-    expose_api_anonymous
+    expose_api_anonymous,
 )
 from galaxy.web.form_builder import AddressField
 from galaxy.webapps.base.controller import (
     BaseUIController,
     UsesFormDefinitionsMixin,
-    UsesTagsMixin
+    UsesTagsMixin,
 )
 from galaxy.webapps.base.webapp import GalaxyWebTransaction
-from . import BaseGalaxyAPIController, depends
+from . import (
+    BaseGalaxyAPIController,
+    depends,
+)
 
 log = logging.getLogger(__name__)
 
@@ -59,7 +65,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
     api_key_manager: api_keys.ApiKeyManager = depends(api_keys.ApiKeyManager)
 
     @expose_api
-    def index(self, trans: ProvidesUserContext, deleted='False', f_email=None, f_name=None, f_any=None, **kwd):
+    def index(self, trans: ProvidesUserContext, deleted="False", f_email=None, f_name=None, f_any=None, **kwd):
         """
         GET /api/users
         GET /api/users/deleted
@@ -96,16 +102,10 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
 
         if f_any:
             if trans.user_is_admin:
-                query = query.filter(or_(
-                    User.email.like(f"%{f_any}%"),
-                    User.username.like(f"%{f_any}%")
-                ))
+                query = query.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%")))
             else:
                 if trans.app.config.expose_user_email and trans.app.config.expose_user_name:
-                    query = query.filter(or_(
-                        User.email.like(f"%{f_any}%"),
-                        User.username.like(f"%{f_any}%")
-                    ))
+                    query = query.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%")))
                 elif trans.app.config.expose_user_email:
                     query = query.filter(User.email.like(f"%{f_any}%"))
                 elif trans.app.config.expose_user_name:
@@ -120,12 +120,16 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
             # special case: user can see only their own user
             # special case2: if the galaxy admin has specified that other user email/names are
             #   exposed, we don't want special case #1
-            if not trans.user_is_admin and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email:
-                item = trans.user.to_dict(value_mapper={'id': trans.security.encode_id})
+            if (
+                not trans.user_is_admin
+                and not trans.app.config.expose_user_name
+                and not trans.app.config.expose_user_email
+            ):
+                item = trans.user.to_dict(value_mapper={"id": trans.security.encode_id})
                 return [item]
             query = query.filter(User.table.c.deleted == false())
         for user in query:
-            item = user.to_dict(value_mapper={'id': trans.security.encode_id})
+            item = user.to_dict(value_mapper={"id": trans.security.encode_id})
             # If NOT configured to expose_email, do not expose email UNLESS the user is self, or
             # the user is an admin
             if user is not trans.user and not trans.user_is_admin:
@@ -145,7 +149,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         return rval
 
     @expose_api_anonymous
-    def show(self, trans: ProvidesUserContext, id, deleted='False', **kwd):
+    def show(self, trans: ProvidesUserContext, id, deleted="False", **kwd):
         """
         GET /api/users/{encoded_id}
         GET /api/users/deleted/{encoded_id}
@@ -173,8 +177,8 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         except exceptions.ItemDeletionException:
             raise
         except Exception:
-            raise exceptions.RequestParameterInvalidException('Invalid user id specified', id=id)
-        return self.user_serializer.serialize_to_view(user, view='detailed')
+            raise exceptions.RequestParameterInvalidException("Invalid user id specified", id=id)
+        return self.user_serializer.serialize_to_view(user, view="detailed")
 
     @expose_api
     def create(self, trans: GalaxyWebTransaction, payload: dict, **kwd):
@@ -183,24 +187,27 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         Creates a new Galaxy user.
         """
         if not trans.app.config.allow_user_creation and not trans.user_is_admin:
-            raise exceptions.ConfigDoesNotAllowException('User creation is not allowed in this Galaxy instance')
+            raise exceptions.ConfigDoesNotAllowException("User creation is not allowed in this Galaxy instance")
         if trans.app.config.use_remote_user and trans.user_is_admin:
-            user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email'])
+            user = trans.get_or_create_remote_user(remote_user_email=payload["remote_user_email"])
         elif trans.user_is_admin:
-            username = payload['username']
-            email = payload['email']
-            password = payload['password']
-            message = "\n".join((validate_email(trans, email),
-                                 validate_password(trans, password, password),
-                                 validate_publicname(trans, username))).rstrip()
+            username = payload["username"]
+            email = payload["email"]
+            password = payload["password"]
+            message = "\n".join(
+                (
+                    validate_email(trans, email),
+                    validate_password(trans, password, password),
+                    validate_publicname(trans, username),
+                )
+            ).rstrip()
             if message:
                 raise exceptions.RequestParameterInvalidException(message)
             else:
                 user = self.user_manager.create(email=email, username=username, password=password)
         else:
             raise exceptions.NotImplemented()
-        item = user.to_dict(view='element', value_mapper={'id': trans.security.encode_id,
-                                                          'total_disk_usage': float})
+        item = user.to_dict(view="element", value_mapper={"id": trans.security.encode_id, "total_disk_usage": float})
         return item
 
     @expose_api
@@ -226,10 +233,10 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         editing_someone_else = current_user != user_to_update
         is_admin = self.user_manager.is_admin(current_user)
         if editing_someone_else and not is_admin:
-            raise exceptions.InsufficientPermissionsException('You are not allowed to update that user', id=id)
+            raise exceptions.InsufficientPermissionsException("You are not allowed to update that user", id=id)
 
         self.user_deserializer.deserialize(user_to_update, payload, user=current_user, trans=trans)
-        return self.user_serializer.serialize_to_view(user_to_update, view='detailed')
+        return self.user_serializer.serialize_to_view(user_to_update, view="detailed")
 
     @expose_api
     def delete(self, trans, id, **kwd):
@@ -246,7 +253,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         """
         user_to_update = self.user_manager.by_id(self.decode_id(id))
         if trans.user_is_admin:
-            purge = util.string_as_bool(kwd.get('purge', False))
+            purge = util.string_as_bool(kwd.get("purge", False))
             if purge:
                 log.debug("Purging user %s", user_to_update)
                 self.user_manager.purge(user_to_update)
@@ -256,8 +263,8 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
             if trans.user == user_to_update:
                 self.user_manager.delete(user_to_update)
             else:
-                raise exceptions.InsufficientPermissionsException('You may only delete your own account.', id=id)
-        return self.user_serializer.serialize_to_view(user_to_update, view='detailed')
+                raise exceptions.InsufficientPermissionsException("You may only delete your own account.", id=id)
+        return self.user_serializer.serialize_to_view(user_to_update, view="detailed")
 
     @web.require_admin
     @expose_api
@@ -271,7 +278,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         """
         user = self.get_user(trans, id)
         self.user_manager.undelete(user)
-        return self.user_serializer.serialize_to_view(user, view='detailed')
+        return self.user_serializer.serialize_to_view(user, view="detailed")
 
     # TODO: move to more basal, common resource than this
     def anon_user_api_value(self, trans):
@@ -281,16 +288,18 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
             return {}
         usage = trans.app.quota_agent.get_usage(trans)
         percent = trans.app.quota_agent.get_percent(trans=trans, usage=usage)
-        return {'total_disk_usage': int(usage),
-                'nice_total_disk_usage': util.nice_size(usage),
-                'quota_percent': percent}
+        return {
+            "total_disk_usage": int(usage),
+            "nice_total_disk_usage": util.nice_size(usage),
+            "quota_percent": percent,
+        }
 
     def _get_extra_user_preferences(self, trans):
         """
         Reads the file user_preferences_extra_conf.yml to display
         admin defined user informations
         """
-        return trans.app.config.user_preferences_extra['preferences']
+        return trans.app.config.user_preferences_extra["preferences"]
 
     def _build_extra_user_pref_inputs(self, trans, preferences, user):
         """
@@ -306,26 +315,34 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
             if value is not None:
                 input_fields = copy.deepcopy(value["inputs"])
                 for input in input_fields:
-                    help = input.get('help', '')
-                    required = 'Required' if util.string_as_bool(input.get('required')) else ''
+                    help = input.get("help", "")
+                    required = "Required" if util.string_as_bool(input.get("required")) else ""
                     if help:
-                        input['help'] = f"{help} {required}"
+                        input["help"] = f"{help} {required}"
                     else:
-                        input['help'] = required
-                    if input.get('store') == 'vault':
+                        input["help"] = required
+                    if input.get("store") == "vault":
                         field = f"{item}/{input['name']}"
-                        input['value'] = user_vault.read_secret(f'preferences/{field}')
+                        input["value"] = user_vault.read_secret(f"preferences/{field}")
                     else:
                         field = f"{item}|{input['name']}"
                         for data_item in user.extra_preferences:
                             if field in data_item:
-                                input['value'] = user.extra_preferences[data_item]
+                                input["value"] = user.extra_preferences[data_item]
                     # regardless of the store, do not send secret type values to client
-                    if input.get('type') == 'secret':
-                        input['value'] = "__SECRET_PLACEHOLDER__"
+                    if input.get("type") == "secret":
+                        input["value"] = "__SECRET_PLACEHOLDER__"
                         # let the client treat it as a password field
-                        input['type'] = "password"
-                extra_pref_inputs.append({'type': 'section', 'title': value['description'], 'name': item, 'expanded': True, 'inputs': input_fields})
+                        input["type"] = "password"
+                extra_pref_inputs.append(
+                    {
+                        "type": "section",
+                        "title": value["description"],
+                        "name": item,
+                        "expanded": True,
+                        "inputs": input_fields,
+                    }
+                )
         return extra_pref_inputs
 
     @expose_api
@@ -341,58 +358,72 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         email = user.email
         username = user.username
         inputs = list()
-        inputs.append({
-            'id': 'email_input',
-            'name': 'email',
-            'type': 'text',
-            'label': 'Email address',
-            'value': email,
-            'help': 'If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it.'})
-        if trans.webapp.name == 'galaxy':
-            inputs.append({
-                'id': 'name_input',
-                'name': 'username',
-                'type': 'text',
-                'label': 'Public name',
-                'value': username,
-                'help': 'Your public name is an identifier that will be used to generate addresses for information you share publicly. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the "-" character.'})
-            info_form_models = self.get_all_forms(trans, filter=dict(deleted=False), form_type=trans.app.model.FormDefinition.types.USER_INFO)
+        inputs.append(
+            {
+                "id": "email_input",
+                "name": "email",
+                "type": "text",
+                "label": "Email address",
+                "value": email,
+                "help": "If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it.",
+            }
+        )
+        if trans.webapp.name == "galaxy":
+            inputs.append(
+                {
+                    "id": "name_input",
+                    "name": "username",
+                    "type": "text",
+                    "label": "Public name",
+                    "value": username,
+                    "help": 'Your public name is an identifier that will be used to generate addresses for information you share publicly. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the "-" character.',
+                }
+            )
+            info_form_models = self.get_all_forms(
+                trans, filter=dict(deleted=False), form_type=trans.app.model.FormDefinition.types.USER_INFO
+            )
             if info_form_models:
                 info_form_id = trans.security.encode_id(user.values.form_definition.id) if user.values else None
                 info_field = {
-                    'type': 'conditional',
-                    'name': 'info',
-                    'cases': [],
-                    'test_param': {
-                        'name': 'form_id',
-                        'label': 'User type',
-                        'type': 'select',
-                        'value': info_form_id,
-                        'help': '',
-                        'data': []
-                    }
+                    "type": "conditional",
+                    "name": "info",
+                    "cases": [],
+                    "test_param": {
+                        "name": "form_id",
+                        "label": "User type",
+                        "type": "select",
+                        "value": info_form_id,
+                        "help": "",
+                        "data": [],
+                    },
                 }
                 for f in info_form_models:
                     values = None
                     if info_form_id == trans.security.encode_id(f.id) and user.values:
                         values = user.values.content
                     info_form = f.to_dict(user=user, values=values, security=trans.security)
-                    info_field['test_param']['data'].append({'label': info_form['name'], 'value': info_form['id']})
-                    info_field['cases'].append({'value': info_form['id'], 'inputs': info_form['inputs']})
+                    info_field["test_param"]["data"].append({"label": info_form["name"], "value": info_form["id"]})
+                    info_field["cases"].append({"value": info_form["id"], "inputs": info_form["inputs"]})
                 inputs.append(info_field)
 
-            address_inputs = [{'type': 'hidden', 'name': 'id', 'hidden': True}]
+            address_inputs = [{"type": "hidden", "name": "id", "hidden": True}]
             for field in AddressField.fields():
-                address_inputs.append({'type': 'text', 'name': field[0], 'label': field[1], 'help': field[2]})
-            address_repeat = {'title': 'Address', 'name': 'address', 'type': 'repeat', 'inputs': address_inputs, 'cache': []}
+                address_inputs.append({"type": "text", "name": field[0], "label": field[1], "help": field[2]})
+            address_repeat = {
+                "title": "Address",
+                "name": "address",
+                "type": "repeat",
+                "inputs": address_inputs,
+                "cache": [],
+            }
             address_values = [address.to_dict(trans) for address in user.addresses]
             for address in address_values:
                 address_cache = []
                 for input in address_inputs:
                     input_copy = input.copy()
-                    input_copy['value'] = address.get(input['name'])
+                    input_copy["value"] = address.get(input["name"])
                     address_cache.append(input_copy)
-                address_repeat['cache'].append(address_cache)
+                address_repeat["cache"].append(address_cache)
             inputs.append(address_repeat)
 
             # Build input sections for extra user preferences
@@ -401,14 +432,32 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                 inputs.append(item)
         else:
             if user.active_repositories:
-                inputs.append(dict(id='name_input', name='username', label='Public name:', type='hidden', value=username, help='You cannot change your public name after you have created a repository in this tool shed.'))
+                inputs.append(
+                    dict(
+                        id="name_input",
+                        name="username",
+                        label="Public name:",
+                        type="hidden",
+                        value=username,
+                        help="You cannot change your public name after you have created a repository in this tool shed.",
+                    )
+                )
             else:
-                inputs.append(dict(id='name_input', name='username', label='Public name:', type='text', value=username, help='Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the "-" character. You cannot change your public name after you have created a repository in this tool shed.'))
+                inputs.append(
+                    dict(
+                        id="name_input",
+                        name="username",
+                        label="Public name:",
+                        type="text",
+                        value=username,
+                        help='Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the "-" character. You cannot change your public name after you have created a repository in this tool shed.',
+                    )
+                )
         return {
-            'email': email,
-            'username': username,
-            'addresses': [address.to_dict(trans) for address in user.addresses],
-            'inputs': inputs,
+            "email": email,
+            "username": username,
+            "addresses": [address.to_dict(trans) for address in user.addresses],
+            "inputs": inputs,
         }
 
     @expose_api
@@ -426,8 +475,8 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         payload = payload or {}
         user = self._get_user(trans, id)
         # Update email
-        if 'email' in payload:
-            email = payload.get('email')
+        if "email" in payload:
+            email = payload.get("email")
             message = validate_email(trans, email, user)
             if message:
                 raise exceptions.RequestParameterInvalidException(message)
@@ -444,29 +493,31 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                     # Deactivate the user if email was changed and activation is on.
                     user.active = False
                     if self.user_manager.send_activation_email(trans, user.email, user.username):
-                        message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.'
+                        message = "The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message."
                     else:
-                        message = 'Unable to send activation email, please contact your local Galaxy administrator.'
+                        message = "Unable to send activation email, please contact your local Galaxy administrator."
                         if trans.app.config.error_email_to is not None:
-                            message += f' Contact: {trans.app.config.error_email_to}'
+                            message += f" Contact: {trans.app.config.error_email_to}"
                         raise exceptions.InternalServerError(message)
         # Update public name
-        if 'username' in payload:
-            username = payload.get('username')
+        if "username" in payload:
+            username = payload.get("username")
             message = validate_publicname(trans, username, user)
             if message:
                 raise exceptions.RequestParameterInvalidException(message)
             if user.username != username:
                 user.username = username
         # Update user custom form
-        user_info_form_id = payload.get('info|form_id')
+        user_info_form_id = payload.get("info|form_id")
         if user_info_form_id:
-            prefix = 'info|'
-            user_info_form = trans.sa_session.query(trans.app.model.FormDefinition).get(trans.security.decode_id(user_info_form_id))
+            prefix = "info|"
+            user_info_form = trans.sa_session.query(trans.app.model.FormDefinition).get(
+                trans.security.decode_id(user_info_form_id)
+            )
             user_info_values = {}
             for item in payload:
                 if item.startswith(prefix):
-                    user_info_values[item[len(prefix):]] = payload[item]
+                    user_info_values[item[len(prefix) :]] = payload[item]
             form_values = trans.model.FormValues(user_info_form, user_info_values)
             trans.sa_session.add(form_values)
             user.values = form_values
@@ -482,14 +533,14 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                     if item.startswith(key_prefix):
                         keys = item.split("|")
                         section = extra_pref_keys[keys[0]]
-                        matching_input = [input for input in section['inputs'] if input['name'] == keys[1]]
+                        matching_input = [input for input in section["inputs"] if input["name"] == keys[1]]
                         if matching_input:
                             input = matching_input[0]
-                            if input.get('required') and payload[item] == "":
+                            if input.get("required") and payload[item] == "":
                                 raise exceptions.ObjectAttributeMissingException("Please fill the required field")
-                            if not (input.get('type') == 'secret' and payload[item] == "__SECRET_PLACEHOLDER__"):
-                                if input.get('store') == 'vault':
-                                    user_vault.write_secret(f'preferences/{keys[0]}/{keys[1]}', str(payload[item]))
+                            if not (input.get("type") == "secret" and payload[item] == "__SECRET_PLACEHOLDER__"):
+                                if input.get("store") == "vault":
+                                    user_vault.write_secret(f"preferences/{keys[0]}/{keys[1]}", str(payload[item]))
                                 else:
                                     extra_user_pref_data[item] = payload[item]
                         else:
@@ -500,36 +551,38 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         address_dicts = {}
         address_count = 0
         for item in payload:
-            match = re.match(r'^address_(?P<index>\d+)\|(?P<attribute>\S+)', item)
+            match = re.match(r"^address_(?P<index>\d+)\|(?P<attribute>\S+)", item)
             if match:
                 groups = match.groupdict()
-                index = int(groups['index'])
-                attribute = groups['attribute']
+                index = int(groups["index"])
+                attribute = groups["attribute"]
                 address_dicts[index] = address_dicts.get(index) or {}
                 address_dicts[index][attribute] = payload[item]
                 address_count = max(address_count, index + 1)
         user.addresses = []
         for index in range(0, address_count):
             d = address_dicts[index]
-            if d.get('id'):
+            if d.get("id"):
                 try:
-                    user_address = trans.sa_session.query(UserAddress).get(trans.security.decode_id(d['id']))
+                    user_address = trans.sa_session.query(UserAddress).get(trans.security.decode_id(d["id"]))
                 except Exception as e:
                     raise exceptions.ObjectNotFound(f"Failed to access user address ({d['id']}). {e}")
             else:
                 user_address = UserAddress()
-                trans.log_event('User address added')
+                trans.log_event("User address added")
             for field in AddressField.fields():
-                if str(field[2]).lower() == 'required' and not d.get(field[0]):
-                    raise exceptions.ObjectAttributeMissingException(f'Address {index + 1}: {field[1]} ({field[0]}) required.')
-                setattr(user_address, field[0], str(d.get(field[0], '')))
+                if str(field[2]).lower() == "required" and not d.get(field[0]):
+                    raise exceptions.ObjectAttributeMissingException(
+                        f"Address {index + 1}: {field[1]} ({field[0]}) required."
+                    )
+                setattr(user_address, field[0], str(d.get(field[0], "")))
             user_address.user = user
             user.addresses.append(user_address)
             trans.sa_session.add(user_address)
         trans.sa_session.add(user)
         trans.sa_session.flush()
-        trans.log_event('User information added')
-        return {'message': 'User information has been saved.'}
+        trans.log_event("User information added")
+        return {"message": "User information has been saved."}
 
     @expose_api
     def set_favorite(self, trans, id, object_type, payload=None, **kwd):
@@ -546,22 +599,22 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         payload = payload or {}
         self._validate_favorite_object_type(object_type)
         user = self._get_user(trans, id)
-        favorites = json.loads(user.preferences['favorites']) if 'favorites' in user.preferences else {}
-        if object_type == 'tools':
-            tool_id = payload.get('object_id')
+        favorites = json.loads(user.preferences["favorites"]) if "favorites" in user.preferences else {}
+        if object_type == "tools":
+            tool_id = payload.get("object_id")
             tool = self.app.toolbox.get_tool(tool_id)
             if not tool:
                 raise exceptions.ObjectNotFound(f"Could not find tool with id '{tool_id}'.")
             if not tool.allow_user_access(user):
                 raise exceptions.AuthenticationFailed(f"Access denied for tool with id '{tool_id}'.")
-            if 'tools' in favorites:
-                favorite_tools = favorites['tools']
+            if "tools" in favorites:
+                favorite_tools = favorites["tools"]
             else:
                 favorite_tools = []
             if tool_id not in favorite_tools:
                 favorite_tools.append(tool_id)
-                favorites['tools'] = favorite_tools
-                user.preferences['favorites'] = json.dumps(favorites)
+                favorites["tools"] = favorite_tools
+                user.preferences["favorites"] = json.dumps(favorites)
                 trans.sa_session.flush()
         return favorites
 
@@ -580,24 +633,26 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         payload = payload or {}
         self._validate_favorite_object_type(object_type)
         user = self._get_user(trans, id)
-        favorites = json.loads(user.preferences['favorites']) if 'favorites' in user.preferences else {}
-        if object_type == 'tools':
-            if 'tools' in favorites:
-                favorite_tools = favorites['tools']
+        favorites = json.loads(user.preferences["favorites"]) if "favorites" in user.preferences else {}
+        if object_type == "tools":
+            if "tools" in favorites:
+                favorite_tools = favorites["tools"]
                 if object_id in favorite_tools:
                     del favorite_tools[favorite_tools.index(object_id)]
-                    favorites['tools'] = favorite_tools
-                    user.preferences['favorites'] = json.dumps(favorites)
+                    favorites["tools"] = favorite_tools
+                    user.preferences["favorites"] = json.dumps(favorites)
                     trans.sa_session.flush()
                 else:
-                    raise exceptions.ObjectNotFound('Given object is not in the list of favorites')
+                    raise exceptions.ObjectNotFound("Given object is not in the list of favorites")
         return favorites
 
     def _validate_favorite_object_type(self, object_type):
-        if object_type in ['tools']:
+        if object_type in ["tools"]:
             pass
         else:
-            raise exceptions.ObjectAttributeInvalidException(f"This type is not supported. Given object_type: {object_type}")
+            raise exceptions.ObjectAttributeInvalidException(
+                f"This type is not supported. Given object_type: {object_type}"
+            )
 
     @expose_api
     def get_password(self, trans, id, payload=None, **kwd):
@@ -605,9 +660,13 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         Return available password inputs.
         """
         payload = payload or {}
-        return {'inputs': [{'name': 'current', 'type': 'password', 'label': 'Current password'},
-                           {'name': 'password', 'type': 'password', 'label': 'New password'},
-                           {'name': 'confirm', 'type': 'password', 'label': 'Confirm password'}]}
+        return {
+            "inputs": [
+                {"name": "current", "type": "password", "label": "Current password"},
+                {"name": "password", "type": "password", "label": "New password"},
+                {"name": "confirm", "type": "password", "label": "Confirm password"},
+            ]
+        }
 
     @expose_api
     def set_password(self, trans, id, payload=None, **kwd):
@@ -630,15 +689,19 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         roles = user.all_roles()
         inputs = []
         for index, action in trans.app.model.Dataset.permitted_actions.items():
-            inputs.append({'type': 'select',
-                           'multiple': True,
-                           'optional': True,
-                           'name': index,
-                           'label': action.action,
-                           'help': action.description,
-                           'options': list({(r.name, r.id) for r in roles}),
-                           'value': [a.role.id for a in user.default_permissions if a.action == action.action]})
-        return {'inputs': inputs}
+            inputs.append(
+                {
+                    "type": "select",
+                    "multiple": True,
+                    "optional": True,
+                    "name": index,
+                    "label": action.action,
+                    "help": action.description,
+                    "options": list({(r.name, r.id) for r in roles}),
+                    "value": [a.role.id for a in user.default_permissions if a.action == action.action],
+                }
+            )
+        return {"inputs": inputs}
 
     @expose_api
     def set_permissions(self, trans, id, payload=None, **kwd):
@@ -650,9 +713,11 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         permissions = {}
         for index, action in trans.app.model.Dataset.permitted_actions.items():
             action_id = trans.app.security_agent.get_action(action.action).action
-            permissions[action_id] = [trans.sa_session.query(trans.app.model.Role).get(x) for x in (payload.get(index) or [])]
+            permissions[action_id] = [
+                trans.sa_session.query(trans.app.model.Role).get(x) for x in (payload.get(index) or [])
+            ]
         trans.app.security_agent.user_set_default_permissions(user, permissions)
-        return {'message': 'Permissions have been saved.'}
+        return {"message": "Permissions have been saved."}
 
     @expose_api
     def get_toolbox_filters(self, trans, id, payload=None, **kwd):
@@ -667,16 +732,18 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         for name, value in user.preferences.items():
             if name in filter_types:
                 saved_values[name] = listify(value, do_strip=True)
-        inputs = [{
-            'type': 'hidden',
-            'name': 'helptext',
-            'label': 'In this section you may enable or disable Toolbox filters. Please contact your admin to configure filters as necessary.'
-        }]
+        inputs = [
+            {
+                "type": "hidden",
+                "name": "helptext",
+                "label": "In this section you may enable or disable Toolbox filters. Please contact your admin to configure filters as necessary.",
+            }
+        ]
         errors = {}
         factory = FilterFactory(trans.app.toolbox)
         for filter_type in filter_types:
             self._add_filter_inputs(factory, filter_types, inputs, errors, filter_type, saved_values)
-        return {'inputs': inputs, 'errors': errors}
+        return {"inputs": inputs, "errors": errors}
 
     @expose_api
     def set_toolbox_filters(self, trans, id, payload=None, **kwd):
@@ -692,49 +759,63 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                 if prefixed_name.startswith(filter_type):
                     filter_selection = payload.get(prefixed_name)
                     if type(filter_selection) != bool:
-                        raise exceptions.RequestParameterInvalidException('Please specify the filter selection as boolean value.')
+                        raise exceptions.RequestParameterInvalidException(
+                            "Please specify the filter selection as boolean value."
+                        )
                     if filter_selection:
                         prefix = f"{filter_type}|"
-                        new_filters.append(prefixed_name[len(prefix):])
-            user.preferences[filter_type] = ','.join(new_filters)
+                        new_filters.append(prefixed_name[len(prefix) :])
+            user.preferences[filter_type] = ",".join(new_filters)
         trans.sa_session.add(user)
         trans.sa_session.flush()
-        return {'message': 'Toolbox filters have been saved.'}
+        return {"message": "Toolbox filters have been saved."}
 
     def _add_filter_inputs(self, factory, filter_types, inputs, errors, filter_type, saved_values):
         filter_inputs = list()
         filter_values = saved_values.get(filter_type, [])
-        filter_config = filter_types[filter_type]['config']
-        filter_title = filter_types[filter_type]['title']
+        filter_config = filter_types[filter_type]["config"]
+        filter_title = filter_types[filter_type]["title"]
         for filter_name in filter_config:
             function = factory.build_filter_function(filter_name)
             if function is None:
-                errors[f'{filter_type}|{filter_name}'] = 'Filter function not found.'
+                errors[f"{filter_type}|{filter_name}"] = "Filter function not found."
 
             short_description, description = None, None
             doc_string = docstring_trim(function.__doc__)
-            split = doc_string.split('\n\n')
+            split = doc_string.split("\n\n")
             if split:
                 short_description = split[0]
                 if len(split) > 1:
                     description = split[1]
             else:
-                log.warning(f'No description specified in the __doc__ string for {filter_name}.')
+                log.warning(f"No description specified in the __doc__ string for {filter_name}.")
 
-            filter_inputs.append({
-                'type': 'boolean',
-                'name': filter_name,
-                'label': short_description or filter_name,
-                'help': description or 'No description available.',
-                'value': True if filter_name in filter_values else False
-            })
+            filter_inputs.append(
+                {
+                    "type": "boolean",
+                    "name": filter_name,
+                    "label": short_description or filter_name,
+                    "help": description or "No description available.",
+                    "value": True if filter_name in filter_values else False,
+                }
+            )
         if filter_inputs:
-            inputs.append({'type': 'section', 'title': filter_title, 'name': filter_type, 'expanded': True, 'inputs': filter_inputs})
+            inputs.append(
+                {
+                    "type": "section",
+                    "title": filter_title,
+                    "name": filter_type,
+                    "expanded": True,
+                    "inputs": filter_inputs,
+                }
+            )
 
     def _get_filter_types(self, trans):
-        return {'toolbox_tool_filters': {'title': 'Tools', 'config': trans.app.config.user_tool_filters},
-                'toolbox_section_filters': {'title': 'Sections', 'config': trans.app.config.user_tool_section_filters},
-                'toolbox_label_filters': {'title': 'Labels', 'config': trans.app.config.user_tool_label_filters}}
+        return {
+            "toolbox_tool_filters": {"title": "Tools", "config": trans.app.config.user_tool_filters},
+            "toolbox_section_filters": {"title": "Sections", "config": trans.app.config.user_tool_section_filters},
+            "toolbox_label_filters": {"title": "Labels", "config": trans.app.config.user_tool_label_filters},
+        }
 
     @expose_api
     def api_key(self, trans, id, payload=None, **kwd):
@@ -771,19 +852,23 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         payload = payload or {}
         user = self._get_user(trans, id)
         self.api_key_manager.create_api_key(user)
-        return self._build_inputs_api_key(user, message='Generated a new web API key.')
+        return self._build_inputs_api_key(user, message="Generated a new web API key.")
 
-    def _build_inputs_api_key(self, user, message=''):
+    def _build_inputs_api_key(self, user, message=""):
         """
         Build API key inputs.
         """
-        inputs = [{'name': 'api-key',
-                   'type': 'text',
-                   'label': 'Current API key:',
-                   'value': user.api_keys[0].key if user.api_keys else 'Not available.',
-                   'readonly': True,
-                   'help': ' An API key will allow you to access via web API. Please note that this key acts as an alternate means to access your account and should be treated with the same care as your login password.'}]
-        return {'message': message, 'inputs': inputs}
+        inputs = [
+            {
+                "name": "api-key",
+                "type": "text",
+                "label": "Current API key:",
+                "value": user.api_keys[0].key if user.api_keys else "Not available.",
+                "readonly": True,
+                "help": " An API key will allow you to access via web API. Please note that this key acts as an alternate means to access your account and should be treated with the same care as your login password.",
+            }
+        ]
+        return {"message": message, "inputs": inputs}
 
     @expose_api
     def get_custom_builds(self, trans, id, payload=None, **kwd):
@@ -796,24 +881,30 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         """
         payload = payload or {}
         user = self._get_user(trans, id)
-        dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {}
+        dbkeys = json.loads(user.preferences["dbkeys"]) if "dbkeys" in user.preferences else {}
         valid_dbkeys = {}
         update = False
         for key, dbkey in dbkeys.items():
-            if 'count' not in dbkey and 'linecount' in dbkey:
-                chrom_count_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dbkey['linecount'])
-                if chrom_count_dataset and not chrom_count_dataset.deleted and chrom_count_dataset.state == trans.app.model.HistoryDatasetAssociation.states.OK:
+            if "count" not in dbkey and "linecount" in dbkey:
+                chrom_count_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(
+                    dbkey["linecount"]
+                )
+                if (
+                    chrom_count_dataset
+                    and not chrom_count_dataset.deleted
+                    and chrom_count_dataset.state == trans.app.model.HistoryDatasetAssociation.states.OK
+                ):
                     chrom_count = int(open(chrom_count_dataset.file_name).readline())
-                    dbkey['count'] = chrom_count
+                    dbkey["count"] = chrom_count
                     valid_dbkeys[key] = dbkey
                     update = True
             else:
                 valid_dbkeys[key] = dbkey
         if update:
-            user.preferences['dbkeys'] = json.dumps(valid_dbkeys)
+            user.preferences["dbkeys"] = json.dumps(valid_dbkeys)
         dbkey_collection = []
         for key, attributes in valid_dbkeys.items():
-            attributes['id'] = key
+            attributes["id"] = key
             dbkey_collection.append(attributes)
         return dbkey_collection
 
@@ -834,38 +925,42 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         """
         payload = payload or {}
         user = self._get_user(trans, id)
-        dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {}
-        name = payload.get('name')
-        len_type = payload.get('len|type')
-        len_value = payload.get('len|value')
-        if len_type not in ['file', 'fasta', 'text'] or not len_value:
-            raise exceptions.RequestParameterInvalidException('Please specify a valid data source type.')
+        dbkeys = json.loads(user.preferences["dbkeys"]) if "dbkeys" in user.preferences else {}
+        name = payload.get("name")
+        len_type = payload.get("len|type")
+        len_value = payload.get("len|value")
+        if len_type not in ["file", "fasta", "text"] or not len_value:
+            raise exceptions.RequestParameterInvalidException("Please specify a valid data source type.")
         if not name or not key:
-            raise exceptions.RequestParameterMissingException('You must specify values for all the fields.')
+            raise exceptions.RequestParameterMissingException("You must specify values for all the fields.")
         elif key in dbkeys:
-            raise exceptions.DuplicatedIdentifierException('There is already a custom build with that key. Delete it first if you want to replace it.')
+            raise exceptions.DuplicatedIdentifierException(
+                "There is already a custom build with that key. Delete it first if you want to replace it."
+            )
         else:
             # Have everything needed; create new build.
-            build_dict = {'name': name}
-            if len_type in ['text', 'file']:
+            build_dict = {"name": name}
+            if len_type in ["text", "file"]:
                 # Create new len file
-                new_len = trans.app.model.HistoryDatasetAssociation(extension='len', create_dataset=True, sa_session=trans.sa_session)
+                new_len = trans.app.model.HistoryDatasetAssociation(
+                    extension="len", create_dataset=True, sa_session=trans.sa_session
+                )
                 trans.sa_session.add(new_len)
                 new_len.name = name
                 new_len.visible = False
                 new_len.state = trans.app.model.Job.states.OK
-                new_len.info = 'custom build .len file'
+                new_len.info = "custom build .len file"
                 try:
                     trans.app.object_store.create(new_len.dataset)
                 except ObjectInvalid:
-                    raise exceptions.InternalServerError('Unable to create output dataset: object store is full.')
+                    raise exceptions.InternalServerError("Unable to create output dataset: object store is full.")
                 trans.sa_session.flush()
                 counter = 0
                 lines_skipped = 0
-                with open(new_len.file_name, 'w') as f:
+                with open(new_len.file_name, "w") as f:
                     # LEN files have format:
                     #   <chrom_name><tab><chrom_length>
-                    for line in len_value.split('\n'):
+                    for line in len_value.split("\n"):
                         # Splits at the last whitespace in the line
                         lst = line.strip().rsplit(None, 1)
                         if not lst or len(lst) < 2:
@@ -878,25 +973,25 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                             lines_skipped += 1
                             continue
                         if chrom != escape(chrom):
-                            build_dict['message'] = 'Invalid chromosome(s) with HTML detected and skipped.'
+                            build_dict["message"] = "Invalid chromosome(s) with HTML detected and skipped."
                             lines_skipped += 1
                             continue
                         counter += 1
-                        f.write(f'{chrom}\t{length}\n')
-                build_dict['len'] = new_len.id
-                build_dict['count'] = counter
+                        f.write(f"{chrom}\t{length}\n")
+                build_dict["len"] = new_len.id
+                build_dict["count"] = counter
             else:
-                build_dict['fasta'] = trans.security.decode_id(len_value)
-                dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(build_dict['fasta'])
+                build_dict["fasta"] = trans.security.decode_id(len_value)
+                dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(build_dict["fasta"])
                 try:
-                    new_len = dataset.get_converted_dataset(trans, 'len')
-                    new_linecount = new_len.get_converted_dataset(trans, 'linecount')
-                    build_dict['len'] = new_len.id
-                    build_dict['linecount'] = new_linecount.id
+                    new_len = dataset.get_converted_dataset(trans, "len")
+                    new_linecount = new_len.get_converted_dataset(trans, "linecount")
+                    build_dict["len"] = new_len.id
+                    build_dict["linecount"] = new_linecount.id
                 except Exception:
-                    raise exceptions.ToolExecutionError('Failed to convert dataset.')
+                    raise exceptions.ToolExecutionError("Failed to convert dataset.")
             dbkeys[key] = build_dict
-            user.preferences['dbkeys'] = json.dumps(dbkeys)
+            user.preferences["dbkeys"] = json.dumps(dbkeys)
             trans.sa_session.flush()
             return build_dict
 
@@ -914,19 +1009,19 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         """
         payload = payload or {}
         user = self._get_user(trans, id)
-        dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {}
+        dbkeys = json.loads(user.preferences["dbkeys"]) if "dbkeys" in user.preferences else {}
         if key and key in dbkeys:
             del dbkeys[key]
-            user.preferences['dbkeys'] = json.dumps(dbkeys)
+            user.preferences["dbkeys"] = json.dumps(dbkeys)
             trans.sa_session.flush()
-            return {'message': f'Deleted {key}.'}
+            return {"message": f"Deleted {key}."}
         else:
-            raise exceptions.ObjectNotFound(f'Could not find and delete build ({key}).')
+            raise exceptions.ObjectNotFound(f"Could not find and delete build ({key}).")
 
     def _get_user(self, trans, id):
         user = self.get_user(trans, id)
         if not user:
-            raise exceptions.RequestParameterInvalidException(f'Invalid user ({id}).')
+            raise exceptions.RequestParameterInvalidException(f"Invalid user ({id}).")
         if user != trans.user and not trans.user_is_admin:
-            raise exceptions.InsufficientPermissionsException('Access denied.')
+            raise exceptions.InsufficientPermissionsException("Access denied.")
         return user
diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py
index edc889b1d09..b1156928e58 100644
--- a/lib/galaxy/webapps/galaxy/api/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/api/visualizations.py
@@ -17,16 +17,19 @@ from fastapi import (
 from galaxy import (
     exceptions,
     util,
-    web
+    web,
 )
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.schema.fields import EncodedDatabaseIdField
-from galaxy.schema.schema import SetSlugPayload, ShareWithPayload, ShareWithStatus, SharingStatus
-from galaxy.web import expose_api
-from galaxy.webapps.base.controller import (
-    UsesVisualizationMixin
+from galaxy.schema.schema import (
+    SetSlugPayload,
+    ShareWithPayload,
+    ShareWithStatus,
+    SharingStatus,
 )
+from galaxy.web import expose_api
+from galaxy.webapps.base.controller import UsesVisualizationMixin
 from galaxy.webapps.base.webapp import GalaxyWebTransaction
 from galaxy.webapps.galaxy.services.visualizations import VisualizationsService
 from . import (
@@ -38,12 +41,10 @@ from . import (
 
 log = logging.getLogger(__name__)
 
-router = Router(tags=['visualizations'])
+router = Router(tags=["visualizations"])
 
 VisualizationIdPathParam: EncodedDatabaseIdField = Path(
-    ...,
-    title="Visualization ID",
-    description="The encoded database identifier of the Visualization."
+    ..., title="Visualization ID", description="The encoded database identifier of the Visualization."
 )
 
 
@@ -52,7 +53,7 @@ class FastAPIVisualizations:
     service: VisualizationsService = depends(VisualizationsService)
 
     @router.get(
-        '/api/visualizations/{id}/sharing',
+        "/api/visualizations/{id}/sharing",
         summary="Get the current sharing status of the given Page.",
     )
     def sharing(
@@ -64,7 +65,7 @@ class FastAPIVisualizations:
         return self.service.shareable_service.sharing(trans, id)
 
     @router.put(
-        '/api/visualizations/{id}/enable_link_access',
+        "/api/visualizations/{id}/enable_link_access",
         summary="Makes this item accessible by a URL link.",
     )
     def enable_link_access(
@@ -76,7 +77,7 @@ class FastAPIVisualizations:
         return self.service.shareable_service.enable_link_access(trans, id)
 
     @router.put(
-        '/api/visualizations/{id}/disable_link_access',
+        "/api/visualizations/{id}/disable_link_access",
         summary="Makes this item inaccessible by a URL link.",
     )
     def disable_link_access(
@@ -88,7 +89,7 @@ class FastAPIVisualizations:
         return self.service.shareable_service.disable_link_access(trans, id)
 
     @router.put(
-        '/api/visualizations/{id}/publish',
+        "/api/visualizations/{id}/publish",
         summary="Makes this item public and accessible by a URL link.",
     )
     def publish(
@@ -100,7 +101,7 @@ class FastAPIVisualizations:
         return self.service.shareable_service.publish(trans, id)
 
     @router.put(
-        '/api/visualizations/{id}/unpublish',
+        "/api/visualizations/{id}/unpublish",
         summary="Removes this item from the published list.",
     )
     def unpublish(
@@ -112,20 +113,20 @@ class FastAPIVisualizations:
         return self.service.shareable_service.unpublish(trans, id)
 
     @router.put(
-        '/api/visualizations/{id}/share_with_users',
+        "/api/visualizations/{id}/share_with_users",
         summary="Share this item with specific users.",
     )
     def share_with_users(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         id: EncodedDatabaseIdField = VisualizationIdPathParam,
-        payload: ShareWithPayload = Body(...)
+        payload: ShareWithPayload = Body(...),
     ) -> ShareWithStatus:
         """Shares this item with specific users and return the current sharing status."""
         return self.service.shareable_service.share_with_users(trans, id, payload)
 
     @router.put(
-        '/api/visualizations/{id}/slug',
+        "/api/visualizations/{id}/slug",
         summary="Set a new slug for this shared item.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
@@ -144,6 +145,7 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
     """
     RESTful controller for interactions with visualizations.
     """
+
     service: VisualizationsService = depends(VisualizationsService)
 
     @expose_api
@@ -167,7 +169,7 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         for visualization in visualizations:
             item = self.get_visualization_summary_dict(visualization)
             item = trans.security.encode_dict_ids(item)
-            item['url'] = web.url_for('visualization', id=item['id'])
+            item["url"] = web.url_for("visualization", id=item["id"])
             rval.append(item)
 
         return rval
@@ -182,19 +184,23 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         # TODO:?? /api/visualizations/registry -> json of registry.listings?
         visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
         dictionary = trans.security.encode_dict_ids(self.get_visualization_dict(visualization))
-        dictionary['url'] = web.url_for(controller='visualization',
-                                        action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug)
-        dictionary['annotation'] = self.get_item_annotation_str(trans.sa_session, trans.user, visualization)
+        dictionary["url"] = web.url_for(
+            controller="visualization",
+            action="display_by_username_and_slug",
+            username=visualization.user.username,
+            slug=visualization.slug,
+        )
+        dictionary["annotation"] = self.get_item_annotation_str(trans.sa_session, trans.user, visualization)
         # need to encode ids in revisions as well
         encoded_revisions = []
-        for revision in dictionary['revisions']:
+        for revision in dictionary["revisions"]:
             # NOTE: does not encode ids inside the configs
             encoded_revisions.append(trans.security.encode_id(revision))
-        dictionary['revisions'] = encoded_revisions
-        dictionary['latest_revision'] = trans.security.encode_dict_ids(dictionary['latest_revision'])
+        dictionary["revisions"] = encoded_revisions
+        dictionary["latest_revision"] = trans.security.encode_dict_ids(dictionary["latest_revision"])
         if trans.app.visualizations_registry:
-            visualization = trans.app.visualizations_registry.get_plugin(dictionary['type'])
-            dictionary['plugin'] = visualization.to_dict()
+            visualization = trans.app.visualizations_registry.get_plugin(dictionary["type"])
+            dictionary["plugin"] = visualization.to_dict()
         return dictionary
 
     @expose_api
@@ -208,25 +214,25 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         """
         rval = None
 
-        if 'import_id' in payload:
-            import_id = payload['import_id']
+        if "import_id" in payload:
+            import_id = payload["import_id"]
             visualization = self.import_visualization(trans, import_id, user=trans.user)
 
         else:
             payload = self._validate_and_parse_payload(payload)
             # must have a type (I've taken this to be the visualization name)
-            if 'type' not in payload:
+            if "type" not in payload:
                 raise exceptions.RequestParameterMissingException("key/value 'type' is required")
-            vis_type = payload.pop('type', False)
+            vis_type = payload.pop("type", False)
 
-            payload['save'] = True
+            payload["save"] = True
             try:
                 # generate defaults - this will err if given a weird key?
                 visualization = self.create_visualization(trans, vis_type, **payload)
             except ValueError as val_err:
                 raise exceptions.RequestParameterMissingException(str(val_err))
 
-        rval = {'id': trans.security.encode_id(visualization.id)}
+        rval = {"id": trans.security.encode_id(visualization.id)}
 
         return rval
 
@@ -248,16 +254,18 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
 
         # only update owned visualizations
         visualization = self.get_visualization(trans, id, check_ownership=True)
-        title = payload.get('title', visualization.latest_revision.title)
-        dbkey = payload.get('dbkey', visualization.latest_revision.dbkey)
-        config = payload.get('config', visualization.latest_revision.config)
+        title = payload.get("title", visualization.latest_revision.title)
+        dbkey = payload.get("dbkey", visualization.latest_revision.dbkey)
+        config = payload.get("config", visualization.latest_revision.config)
 
         latest_config = visualization.latest_revision.config
-        if((title != visualization.latest_revision.title)
-                or (dbkey != visualization.latest_revision.dbkey)
-                or (json.dumps(config) != json.dumps(latest_config))):
+        if (
+            (title != visualization.latest_revision.title)
+            or (dbkey != visualization.latest_revision.dbkey)
+            or (json.dumps(config) != json.dumps(latest_config))
+        ):
             revision = self.add_visualization_revision(trans, visualization, config, title, dbkey)
-            rval = {'id': id, 'revision': revision.id}
+            rval = {"id": id, "revision": revision.id}
 
         # allow updating vis title
         visualization.title = title
@@ -330,7 +338,8 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         # keys listed here don't error when attempting to set, but fail silently
         #   this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs
         valid_but_uneditable_keys = (
-            'id', 'model_class'
+            "id",
+            "model_class"
             # TODO: fill out when we create to_dict, get_dict, whatevs
         )
         # TODO: deleted
@@ -340,32 +349,32 @@ class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         validated_payload = {}
         for key, val in payload.items():
             # TODO: validate types in VALID_TYPES/registry names at the mixin/model level?
-            if key == 'type':
+            if key == "type":
                 if not isinstance(val, str):
-                    raise ValidationError(f'{key} must be a string or unicode: {str(type(val))}')
+                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
                 val = util.sanitize_html.sanitize_html(val)
-            elif key == 'config':
+            elif key == "config":
                 if not isinstance(val, dict):
-                    raise ValidationError(f'{key} must be a dictionary: {str(type(val))}')
+                    raise ValidationError(f"{key} must be a dictionary: {str(type(val))}")
 
-            elif key == 'annotation':
+            elif key == "annotation":
                 if not isinstance(val, str):
-                    raise ValidationError(f'{key} must be a string or unicode: {str(type(val))}')
+                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
                 val = util.sanitize_html.sanitize_html(val)
 
             # these are keys that actually only be *updated* at the revision level and not here
             #   (they are still valid for create, tho)
-            elif key == 'title':
+            elif key == "title":
                 if not isinstance(val, str):
-                    raise ValidationError(f'{key} must be a string or unicode: {str(type(val))}')
+                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
                 val = util.sanitize_html.sanitize_html(val)
-            elif key == 'slug':
+            elif key == "slug":
                 if not isinstance(val, str):
-                    raise ValidationError(f'{key} must be a string: {str(type(val))}')
+                    raise ValidationError(f"{key} must be a string: {str(type(val))}")
                 val = util.sanitize_html.sanitize_html(val)
-            elif key == 'dbkey':
+            elif key == "dbkey":
                 if not isinstance(val, str):
-                    raise ValidationError(f'{key} must be a string or unicode: {str(type(val))}')
+                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
                 val = util.sanitize_html.sanitize_html(val)
 
             elif key not in valid_but_uneditable_keys:
diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py
index 27d28c8d0f0..033f65cc00f 100644
--- a/lib/galaxy/webapps/galaxy/api/webhooks.py
+++ b/lib/galaxy/webapps/galaxy/api/webhooks.py
@@ -13,7 +13,6 @@ log = logging.getLogger(__name__)
 
 
 class WebhooksController(BaseGalaxyAPIController):
-
     @expose_api_anonymous_and_sessionless
     def all_webhooks(self, trans: GalaxyWebTransaction, **kwd):
         """
@@ -21,10 +20,7 @@ class WebhooksController(BaseGalaxyAPIController):
 
         Return all webhooks.
         """
-        return [
-            webhook.to_dict()
-            for webhook in self.app.webhooks_registry.webhooks
-        ]
+        return [webhook.to_dict() for webhook in self.app.webhooks_registry.webhooks]
 
     @expose_api_anonymous_and_sessionless
     def webhook_data(self, trans: Any, webhook_id, **kwd):
@@ -38,15 +34,13 @@ class WebhooksController(BaseGalaxyAPIController):
         for key, value in kwd.items():
             params[key] = value
 
-        webhook = next(
-            webhook
-            for webhook in self.app.webhooks_registry.webhooks
-            if webhook.id == webhook_id
-        )
+        webhook = next(webhook for webhook in self.app.webhooks_registry.webhooks if webhook.id == webhook_id)
 
-        if webhook and webhook.helper != '':
+        if webhook and webhook.helper != "":
             return imp.load_source(webhook.path, webhook.helper).main(  # type: ignore[attr-defined]
-                trans, webhook, params,
+                trans,
+                webhook,
+                params,
             )
         else:
             return {}
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 5e06952caea..7382f476577 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -6,21 +6,33 @@ import hashlib
 import json
 import logging
 import os
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 import requests
 from gxformat2._yaml import ordered_dump
 from markupsafe import escape
-from sqlalchemy import desc, false, or_, true
+from sqlalchemy import (
+    desc,
+    false,
+    or_,
+    true,
+)
 from sqlalchemy.orm import joinedload
 
 from galaxy import (
     exceptions,
     model,
-    util
+    util,
 )
 from galaxy.managers.context import ProvidesUserContext
-from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter, summarize_job_metrics
+from galaxy.managers.jobs import (
+    fetch_job_states,
+    invocation_job_source_iter,
+    summarize_job_metrics,
+)
 from galaxy.managers.workflows import (
     MissingToolsException,
     RefactorRequest,
@@ -46,7 +58,7 @@ from galaxy.web import (
 from galaxy.webapps.base.controller import (
     SharableMixin,
     url_for,
-    UsesStoredWorkflowMixin
+    UsesStoredWorkflowMixin,
 )
 from galaxy.webapps.base.webapp import GalaxyWebTransaction
 from galaxy.workflow.extract import extract_workflow
@@ -59,7 +71,6 @@ log = logging.getLogger(__name__)
 
 
 class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, UsesAnnotations, SharableMixin):
-
     def __init__(self, app: StructuredApp):
         super().__init__(app)
         self.history_manager = app.history_manager
@@ -88,10 +99,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         """
         user = trans.user
         ids_in_menu = [x.stored_workflow_id for x in user.stored_workflow_menu_entries]
-        return {
-            'ids_in_menu': ids_in_menu,
-            'workflows': self.get_workflows_list(trans, **kwd)
-        }
+        return {"ids_in_menu": ids_in_menu, "workflows": self.get_workflows_list(trans, **kwd)}
 
     @expose_api
     def set_workflow_menu(self, trans: GalaxyWebTransaction, payload=None, **kwd):
@@ -101,7 +109,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         """
         payload = payload or {}
         user = trans.user
-        workflow_ids = payload.get('workflow_ids')
+        workflow_ids = payload.get("workflow_ids")
         if workflow_ids is None:
             workflow_ids = []
         elif type(workflow_ids) != list:
@@ -130,9 +138,17 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         sess.flush()
         message = "Menu updated."
         trans.set_message(message)
-        return {'message': message, 'status': 'done'}
+        return {"message": message, "status": "done"}
 
-    def get_workflows_list(self, trans: ProvidesUserContext, missing_tools=False, show_published=None, show_hidden=False, show_deleted=False, **kwd):
+    def get_workflows_list(
+        self,
+        trans: ProvidesUserContext,
+        missing_tools=False,
+        show_published=None,
+        show_hidden=False,
+        show_deleted=False,
+        **kwd,
+    ):
         """
         Displays a collection of workflows.
 
@@ -150,64 +166,80 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         user = trans.user
         if show_published or user is None and show_published is None:
             filter1 = or_(filter1, (model.StoredWorkflow.published == true()))
-        query = trans.sa_session.query(model.StoredWorkflow).options(
-            joinedload("annotations")).options(
-            joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
-            joinedload("tags")
-        ).filter(filter1)
+        query = (
+            trans.sa_session.query(model.StoredWorkflow)
+            .options(joinedload("annotations"))
+            .options(joinedload("latest_workflow").undefer("step_count").lazyload("steps"))
+            .options(joinedload("tags"))
+            .filter(filter1)
+        )
         query = query.filter_by(hidden=true() if show_hidden else false(), deleted=true() if show_deleted else false())
         for wf in query.order_by(desc(model.StoredWorkflow.table.c.update_time)).all():
-            item = wf.to_dict(value_mapper={'id': trans.security.encode_id})
+            item = wf.to_dict(value_mapper={"id": trans.security.encode_id})
             encoded_id = trans.security.encode_id(wf.id)
-            item['annotations'] = [x.annotation for x in wf.annotations]
-            item['url'] = url_for('workflow', id=encoded_id)
-            item['owner'] = wf.user.username
-            item['number_of_steps'] = wf.latest_workflow.step_count
-            item['show_in_tool_panel'] = False
+            item["annotations"] = [x.annotation for x in wf.annotations]
+            item["url"] = url_for("workflow", id=encoded_id)
+            item["owner"] = wf.user.username
+            item["number_of_steps"] = wf.latest_workflow.step_count
+            item["show_in_tool_panel"] = False
             if user is not None:
-                item['show_in_tool_panel'] = wf.show_in_tool_panel(user_id=user.id)
+                item["show_in_tool_panel"] = wf.show_in_tool_panel(user_id=user.id)
             rval.append(item)
-        for wf_sa in trans.sa_session.query(model.StoredWorkflowUserShareAssociation).join(
-                model.StoredWorkflowUserShareAssociation.stored_workflow).options(
-                joinedload("stored_workflow").joinedload("annotations")).options(
-                joinedload("stored_workflow").joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
-                joinedload("stored_workflow").joinedload("user")).options(
-                joinedload("stored_workflow").joinedload("tags")).filter(model.StoredWorkflowUserShareAssociation.user == trans.user).filter(
-                model.StoredWorkflow.table.c.deleted == false()).order_by(
-                desc(model.StoredWorkflow.update_time)).all():
-            item = wf_sa.stored_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
+        for wf_sa in (
+            trans.sa_session.query(model.StoredWorkflowUserShareAssociation)
+            .join(model.StoredWorkflowUserShareAssociation.stored_workflow)
+            .options(joinedload("stored_workflow").joinedload("annotations"))
+            .options(
+                joinedload("stored_workflow").joinedload("latest_workflow").undefer("step_count").lazyload("steps")
+            )
+            .options(joinedload("stored_workflow").joinedload("user"))
+            .options(joinedload("stored_workflow").joinedload("tags"))
+            .filter(model.StoredWorkflowUserShareAssociation.user == trans.user)
+            .filter(model.StoredWorkflow.table.c.deleted == false())
+            .order_by(desc(model.StoredWorkflow.update_time))
+            .all()
+        ):
+            item = wf_sa.stored_workflow.to_dict(value_mapper={"id": trans.security.encode_id})
             encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
-            item['annotations'] = [x.annotation for x in wf_sa.stored_workflow.annotations]
-            item['url'] = url_for('workflow', id=encoded_id)
-            item['slug'] = wf_sa.stored_workflow.slug
-            item['owner'] = wf_sa.stored_workflow.user.username
-            item['number_of_steps'] = wf_sa.stored_workflow.latest_workflow.step_count
-            item['show_in_tool_panel'] = False
+            item["annotations"] = [x.annotation for x in wf_sa.stored_workflow.annotations]
+            item["url"] = url_for("workflow", id=encoded_id)
+            item["slug"] = wf_sa.stored_workflow.slug
+            item["owner"] = wf_sa.stored_workflow.user.username
+            item["number_of_steps"] = wf_sa.stored_workflow.latest_workflow.step_count
+            item["show_in_tool_panel"] = False
             if user is not None:
-                item['show_in_tool_panel'] = wf_sa.stored_workflow.show_in_tool_panel(user_id=user.id)
+                item["show_in_tool_panel"] = wf_sa.stored_workflow.show_in_tool_panel(user_id=user.id)
             rval.append(item)
         if missing_tools:
             workflows_missing_tools = []
             workflows = []
             workflows_by_toolshed = dict()
             for value in rval:
-                tool_ids = self.workflow_contents_manager.get_all_tool_ids(self.__get_stored_workflow(trans, value['id']).latest_workflow)
+                tool_ids = self.workflow_contents_manager.get_all_tool_ids(
+                    self.__get_stored_workflow(trans, value["id"]).latest_workflow
+                )
                 missing_tool_ids = [tool_id for tool_id in tool_ids if self.app.toolbox.is_missing_shed_tool(tool_id)]
                 if len(missing_tool_ids) > 0:
-                    value['missing_tools'] = missing_tool_ids
+                    value["missing_tools"] = missing_tool_ids
                     workflows_missing_tools.append(value)
             for workflow in workflows_missing_tools:
-                for tool_id in workflow['missing_tools']:
-                    toolshed, _, owner, name, tool, version = tool_id.split('/')
+                for tool_id in workflow["missing_tools"]:
+                    toolshed, _, owner, name, tool, version = tool_id.split("/")
                     shed_url = self.__get_full_shed_url(toolshed)
-                    repo_identifier = '/'.join((toolshed, owner, name))
+                    repo_identifier = "/".join((toolshed, owner, name))
                     if repo_identifier not in workflows_by_toolshed:
-                        workflows_by_toolshed[repo_identifier] = dict(shed=shed_url.rstrip('/'), repository=name, owner=owner, tools=[tool_id], workflows=[workflow['name']])
+                        workflows_by_toolshed[repo_identifier] = dict(
+                            shed=shed_url.rstrip("/"),
+                            repository=name,
+                            owner=owner,
+                            tools=[tool_id],
+                            workflows=[workflow["name"]],
+                        )
                     else:
-                        if tool_id not in workflows_by_toolshed[repo_identifier]['tools']:
-                            workflows_by_toolshed[repo_identifier]['tools'].append(tool_id)
-                        if workflow['name'] not in workflows_by_toolshed[repo_identifier]['workflows']:
-                            workflows_by_toolshed[repo_identifier]['workflows'].append(workflow['name'])
+                        if tool_id not in workflows_by_toolshed[repo_identifier]["tools"]:
+                            workflows_by_toolshed[repo_identifier]["tools"].append(tool_id)
+                        if workflow["name"] not in workflows_by_toolshed[repo_identifier]["workflows"]:
+                            workflows_by_toolshed[repo_identifier]["workflows"].append(workflow["name"])
             for repo_tag in workflows_by_toolshed:
                 workflows.append(workflows_by_toolshed[repo_tag])
             return workflows
@@ -226,14 +258,19 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         """
         stored_workflow = self.__get_stored_workflow(trans, id, **kwd)
         if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin:
-            if trans.sa_session.query(model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
+            if (
+                trans.sa_session.query(model.StoredWorkflowUserShareAssociation)
+                .filter_by(user=trans.user, stored_workflow=stored_workflow)
+                .count()
+                == 0
+            ):
                 message = "Workflow is neither importable, nor owned by or shared with current user"
                 raise exceptions.ItemAccessibilityException(message)
         if kwd.get("legacy", False):
             style = "legacy"
         else:
             style = "instance"
-        version = kwd.get('version')
+        version = kwd.get("version")
         if version is None and util.string_as_bool(kwd.get("instance", "false")):
             # A Workflow instance may not be the latest workflow version attached to StoredWorkflow.
             # This figures out the correct version so that we return the correct Workflow and version.
@@ -256,8 +293,13 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         Lists all versions of this workflow.
         """
         instance = util.string_as_bool(kwds.get("instance", "false"))
-        stored_workflow = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, by_stored_id=not instance)
-        return [{'version': i, 'update_time': str(w.update_time), 'steps': len(w.steps)} for i, w in enumerate(reversed(stored_workflow.workflows))]
+        stored_workflow = self.workflow_manager.get_stored_accessible_workflow(
+            trans, workflow_id, by_stored_id=not instance
+        )
+        return [
+            {"version": i, "update_time": str(w.update_time), "steps": len(w.steps)}
+            for i, w in enumerate(reversed(stored_workflow.workflows))
+        ]
 
     @expose_api
     def create(self, trans: GalaxyWebTransaction, payload=None, **kwd):
@@ -283,11 +325,11 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
 
         """
         ways_to_create = {
-            'archive_source',
-            'from_history_id',
-            'from_path',
-            'shared_workflow_id',
-            'workflow',
+            "archive_source",
+            "from_history_id",
+            "from_path",
+            "shared_workflow_id",
+            "workflow",
         }
 
         if trans.user_is_bootstrap_admin:
@@ -301,15 +343,15 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             message = f"Only one parameter among - {', '.join(ways_to_create)} - must be specified"
             raise exceptions.RequestParameterInvalidException(message)
 
-        if 'archive_source' in payload:
-            archive_source = payload['archive_source']
-            archive_file = payload.get('archive_file')
+        if "archive_source" in payload:
+            archive_source = payload["archive_source"]
+            archive_file = payload.get("archive_file")
             archive_data = None
             if archive_source:
                 if archive_source.startswith("file://"):
                     if not trans.user_is_admin:
                         raise exceptions.AdminRequiredException()
-                    workflow_src = {"src": "from_path", "path": archive_source[len("file://"):]}
+                    workflow_src = {"src": "from_path", "path": archive_source[len("file://") :]}
                     payload["workflow"] = workflow_src
                     return self.__api_import_new_workflow(trans, payload, **kwd)
                 elif archive_source == "trs_tool":
@@ -322,7 +364,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
                         archive_data = requests.get(archive_source, timeout=util.DEFAULT_SOCKET_TIMEOUT).text
                     except Exception:
                         raise exceptions.MessageException(f"Failed to open URL '{escape(archive_source)}'.")
-            elif hasattr(archive_file, 'file'):
+            elif hasattr(archive_file, "file"):
                 uploaded_file = archive_file.file
                 uploaded_file_name = uploaded_file.name
                 if os.path.getsize(os.path.abspath(uploaded_file_name)) > 0:
@@ -333,15 +375,15 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
                 raise exceptions.MessageException("Please provide a URL or file.")
             return self.__api_import_from_archive(trans, archive_data, "uploaded file", payload=payload)
 
-        if 'from_history_id' in payload:
-            from_history_id = payload.get('from_history_id')
+        if "from_history_id" in payload:
+            from_history_id = payload.get("from_history_id")
             from_history_id = self.decode_id(from_history_id)
             history = self.history_manager.get_accessible(from_history_id, trans.user, current_history=trans.history)
 
-            job_ids = [self.decode_id(_) for _ in payload.get('job_ids', [])]
-            dataset_ids = payload.get('dataset_ids', [])
-            dataset_collection_ids = payload.get('dataset_collection_ids', [])
-            workflow_name = payload['workflow_name']
+            job_ids = [self.decode_id(_) for _ in payload.get("job_ids", [])]
+            dataset_ids = payload.get("dataset_ids", [])
+            dataset_collection_ids = payload.get("dataset_collection_ids", [])
+            workflow_name = payload["workflow_name"]
             stored_workflow = extract_workflow(
                 trans=trans,
                 user=trans.user,
@@ -351,12 +393,12 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
                 dataset_collection_ids=dataset_collection_ids,
                 workflow_name=workflow_name,
             )
-            item = stored_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
-            item['url'] = url_for('workflow', id=item['id'])
+            item = stored_workflow.to_dict(value_mapper={"id": trans.security.encode_id})
+            item["url"] = url_for("workflow", id=item["id"])
             return item
 
-        if 'from_path' in payload:
-            from_path = payload.get('from_path')
+        if "from_path" in payload:
+            from_path = payload.get("from_path")
             object_id = payload.get("object_id")
             workflow_src = {"src": "from_path", "path": from_path}
             if object_id is not None:
@@ -364,11 +406,11 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             payload["workflow"] = workflow_src
             return self.__api_import_new_workflow(trans, payload, **kwd)
 
-        if 'shared_workflow_id' in payload:
-            workflow_id = payload['shared_workflow_id']
+        if "shared_workflow_id" in payload:
+            workflow_id = payload["shared_workflow_id"]
             return self.__api_import_shared_workflow(trans, workflow_id, payload)
 
-        if 'workflow' in payload:
+        if "workflow" in payload:
             return self.__api_import_new_workflow(trans, payload, **kwd)
 
         # This was already raised above, but just in case...
@@ -397,24 +439,30 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id, **kwd)
 
         style = kwd.get("style", "export")
-        download_format = kwd.get('format')
-        version = kwd.get('version')
-        history_id = kwd.get('history_id')
+        download_format = kwd.get("format")
+        version = kwd.get("version")
+        history_id = kwd.get("history_id")
         history = None
         if history_id:
-            history = self.history_manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history)
-        ret_dict = self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version, history=history)
-        if download_format == 'json-download':
+            history = self.history_manager.get_accessible(
+                self.decode_id(history_id), trans.user, current_history=trans.history
+            )
+        ret_dict = self.workflow_contents_manager.workflow_to_dict(
+            trans, stored_workflow, style=style, version=version, history=history
+        )
+        if download_format == "json-download":
             sname = stored_workflow.name
-            sname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in sname)[0:150]
+            sname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in sname)[0:150]
             if ret_dict.get("format-version", None) == "0.1":
                 extension = "ga"
             else:
                 extension = "gxwf.json"
-            trans.response.headers["Content-Disposition"] = f'attachment; filename="Galaxy-Workflow-{sname}.{extension}"'
-            trans.response.set_content_type('application/galaxy-archive')
+            trans.response.headers[
+                "Content-Disposition"
+            ] = f'attachment; filename="Galaxy-Workflow-{sname}.{extension}"'
+            trans.response.set_content_type("application/galaxy-archive")
 
-        if style == "format2" and download_format != 'json-download':
+        if style == "format2" and download_format != "json-download":
             return ordered_dump(ret_dict)
         else:
             return format_return_as_json(ret_dict, pretty=True)
@@ -439,7 +487,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         trans.sa_session.flush()
 
         # TODO: Unsure of response message to let api know that a workflow was successfully deleted
-        return (f"Workflow '{stored_workflow.name}' successfully deleted")
+        return f"Workflow '{stored_workflow.name}' successfully deleted"
 
     @expose_api
     def import_new_workflow_deprecated(self, trans: GalaxyWebTransaction, payload, **kwd):
@@ -506,15 +554,15 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         :returns:   serialized version of the workflow
         """
         stored_workflow = self.__get_stored_workflow(trans, id, **kwds)
-        workflow_dict = payload.get('workflow', {})
+        workflow_dict = payload.get("workflow", {})
         workflow_dict.update({k: v for k, v in payload.items() if k not in workflow_dict})
         if workflow_dict:
             raw_workflow_description = self.__normalize_workflow(trans, workflow_dict)
             workflow_dict = raw_workflow_description.as_dict
-            new_workflow_name = workflow_dict.get('name')
+            new_workflow_name = workflow_dict.get("name")
             old_workflow = stored_workflow.latest_workflow
-            name_updated = (new_workflow_name and new_workflow_name != stored_workflow.name)
-            steps_updated = 'steps' in workflow_dict
+            name_updated = new_workflow_name and new_workflow_name != stored_workflow.name
+            steps_updated = "steps" in workflow_dict
             if name_updated and not steps_updated:
                 sanitized_name = sanitize_html(new_workflow_name or old_workflow.name)
                 workflow = old_workflow.copy(user=trans.user)
@@ -525,21 +573,21 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
                 trans.sa_session.add(workflow, stored_workflow)
                 trans.sa_session.flush()
 
-            if 'hidden' in workflow_dict and stored_workflow.hidden != workflow_dict['hidden']:
-                stored_workflow.hidden = workflow_dict['hidden']
+            if "hidden" in workflow_dict and stored_workflow.hidden != workflow_dict["hidden"]:
+                stored_workflow.hidden = workflow_dict["hidden"]
                 trans.sa_session.flush()
 
-            if 'published' in workflow_dict and stored_workflow.published != workflow_dict['published']:
-                stored_workflow.published = workflow_dict['published']
+            if "published" in workflow_dict and stored_workflow.published != workflow_dict["published"]:
+                stored_workflow.published = workflow_dict["published"]
                 trans.sa_session.flush()
 
-            if 'annotation' in workflow_dict and not steps_updated:
-                newAnnotation = sanitize_html(workflow_dict['annotation'])
+            if "annotation" in workflow_dict and not steps_updated:
+                newAnnotation = sanitize_html(workflow_dict["annotation"])
                 self.add_item_annotation(trans.sa_session, trans.user, stored_workflow, newAnnotation)
                 trans.sa_session.flush()
 
-            if 'menu_entry' in workflow_dict or 'show_in_tool_panel' in workflow_dict:
-                if workflow_dict.get('menu_entry') or workflow_dict.get('show_in_tool_panel'):
+            if "menu_entry" in workflow_dict or "show_in_tool_panel" in workflow_dict:
+                if workflow_dict.get("menu_entry") or workflow_dict.get("show_in_tool_panel"):
                     workflow_ids = [wf.stored_workflow_id for wf in trans.user.stored_workflow_menu_entries]
                     if trans.security.decode_id(id) not in workflow_ids:
                         menuEntry = model.StoredWorkflowMenuEntry()
@@ -551,10 +599,12 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
                     if trans.security.decode_id(id) in entries:
                         trans.user.stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
             # set tags
-            if 'tags' in workflow_dict:
-                trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict['tags'])
+            if "tags" in workflow_dict:
+                trans.app.tag_handler.set_tags_from_list(
+                    user=trans.user, item=stored_workflow, new_tags_list=workflow_dict["tags"]
+                )
 
-            if 'steps' in workflow_dict:
+            if "steps" in workflow_dict:
                 try:
                     workflow_update_options = WorkflowUpdateOptions(**payload)
                     workflow, errors = self.workflow_contents_manager.update_workflow_from_raw_description(
@@ -564,7 +614,9 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
                         workflow_update_options,
                     )
                 except MissingToolsException:
-                    raise exceptions.MessageException("This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed.")
+                    raise exceptions.MessageException(
+                        "This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed."
+                    )
 
         else:
             message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
@@ -589,9 +641,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         """
         stored_workflow = self.__get_stored_workflow(trans, id, **kwds)
         refactor_request = RefactorRequest(**payload)
-        return self.workflow_contents_manager.refactor(
-            trans, stored_workflow, refactor_request
-        )
+        return self.workflow_contents_manager.refactor(trans, stored_workflow, refactor_request)
 
     @expose_api
     def build_module(self, trans: GalaxyWebTransaction, payload=None):
@@ -601,23 +651,23 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         """
         if payload is None:
             payload = {}
-        inputs = payload.get('inputs', {})
+        inputs = payload.get("inputs", {})
         trans.workflow_building_mode = workflow_building_modes.ENABLED
         module = module_factory.from_dict(trans, payload, from_tool_form=True)
-        if 'tool_state' not in payload:
+        if "tool_state" not in payload:
             module_state: Dict[str, Any] = {}
             populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
             module.recover_state(module_state, from_tool_form=True)
         return {
-            'label': inputs.get('__label', ''),
-            'annotation': inputs.get('__annotation', ''),
-            'name': module.get_name(),
-            'tool_state': module.get_state(),
-            'content_id': module.get_content_id(),
-            'inputs': module.get_all_inputs(connectable_only=True),
-            'outputs': module.get_all_outputs(),
-            'config_form': module.get_config_form(),
-            'post_job_actions': module.get_post_job_actions(inputs)
+            "label": inputs.get("__label", ""),
+            "annotation": inputs.get("__annotation", ""),
+            "name": module.get_name(),
+            "tool_state": module.get_state(),
+            "content_id": module.get_content_id(),
+            "inputs": module.get_all_inputs(connectable_only=True),
+            "outputs": module.get_all_outputs(),
+            "config_form": module.get_config_form(),
+            "post_job_actions": module.get_post_job_actions(inputs),
         }
 
     @expose_api
@@ -634,15 +684,14 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             'tool_sequence' - comma separated sequence of tool ids
             'remote_model_url' - (optional) path to the deep learning model
         """
-        remote_model_url = payload.get('remote_model_url', trans.app.config.tool_recommendation_model_path)
-        tool_sequence = payload.get('tool_sequence', "")
-        if 'tool_sequence' not in payload or remote_model_url is None:
+        remote_model_url = payload.get("remote_model_url", trans.app.config.tool_recommendation_model_path)
+        tool_sequence = payload.get("tool_sequence", "")
+        if "tool_sequence" not in payload or remote_model_url is None:
             return
-        tool_sequence, recommended_tools = self.tool_recommendations.get_predictions(trans, tool_sequence, remote_model_url)
-        return {
-            "current_tool": tool_sequence,
-            "predicted_data": recommended_tools
-        }
+        tool_sequence, recommended_tools = self.tool_recommendations.get_predictions(
+            trans, tool_sequence, remote_model_url
+        )
+        return {"current_tool": tool_sequence, "predicted_data": recommended_tools}
 
     #
     # -- Helper methods --
@@ -660,12 +709,17 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             raise exceptions.MessageException("The data content is missing.")
         raw_workflow_description = self.__normalize_workflow(trans, data)
         workflow_create_options = WorkflowCreateOptions(**payload)
-        workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, workflow_create_options, source=source)
+        workflow, missing_tool_tups = self._workflow_from_dict(
+            trans, raw_workflow_description, workflow_create_options, source=source
+        )
         workflow_id = workflow.id
         workflow = workflow.latest_workflow
 
-        response = {"message": f"Workflow '{escape(workflow.name)}' imported successfully.", "status": "success",
-                    "id": trans.security.encode_id(workflow_id)}
+        response = {
+            "message": f"Workflow '{escape(workflow.name)}' imported successfully.",
+            "status": "success",
+            "id": trans.security.encode_id(workflow_id),
+        }
         if workflow.has_errors:
             response["message"] = "Imported, but some steps in this workflow have validation errors."
             response["status"] = "error"
@@ -678,7 +732,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         return response
 
     def __api_import_new_workflow(self, trans: GalaxyWebTransaction, payload, **kwd):
-        data = payload['workflow']
+        data = payload["workflow"]
         raw_workflow_description = self.__normalize_workflow(trans, data)
         workflow_create_options = WorkflowCreateOptions(**payload)
         workflow, missing_tool_tups = self._workflow_from_dict(
@@ -690,11 +744,11 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         workflow_id = workflow.id
         # api encoded, id
         encoded_id = trans.security.encode_id(workflow_id)
-        item = workflow.to_dict(value_mapper={'id': trans.security.encode_id})
-        item['annotations'] = [x.annotation for x in workflow.annotations]
-        item['url'] = url_for('workflow', id=encoded_id)
-        item['owner'] = workflow.user.username
-        item['number_of_steps'] = len(workflow.latest_workflow.steps)
+        item = workflow.to_dict(value_mapper={"id": trans.security.encode_id})
+        item["annotations"] = [x.annotation for x in workflow.annotations]
+        item["url"] = url_for("workflow", id=encoded_id)
+        item["owner"] = workflow.user.username
+        item["number_of_steps"] = len(workflow.latest_workflow.steps)
         return item
 
     def __normalize_workflow(self, trans: GalaxyWebTransaction, as_dict):
@@ -712,7 +766,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         :raises: exceptions.MessageException, exceptions.ObjectNotFound
         """
         # Pull parameters out of payload.
-        workflow_id = payload.get('workflow_id', None)
+        workflow_id = payload.get("workflow_id", None)
         if workflow_id is None:
             raise exceptions.ObjectAttributeMissingException("Missing required parameter 'workflow_id'.")
         self.__api_import_shared_workflow(trans, workflow_id, payload)
@@ -723,13 +777,15 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         except Exception:
             raise exceptions.ObjectNotFound(f"Malformed workflow id ( {workflow_id} ) specified.")
         if stored_workflow.importable is False:
-            raise exceptions.ItemAccessibilityException('The owner of this workflow has disabled imports via this link.')
+            raise exceptions.ItemAccessibilityException(
+                "The owner of this workflow has disabled imports via this link."
+            )
         elif stored_workflow.deleted:
             raise exceptions.ItemDeletionException("You can't import this workflow because it has been deleted.")
         imported_workflow = self._import_shared_workflow(trans, stored_workflow)
-        item = imported_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
+        item = imported_workflow.to_dict(value_mapper={"id": trans.security.encode_id})
         encoded_id = trans.security.encode_id(imported_workflow.id)
-        item['url'] = url_for('workflow', id=encoded_id)
+        item["url"] = url_for("workflow", id=encoded_id)
         return item
 
     @expose_api
@@ -745,21 +801,23 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         :raises: exceptions.MessageException, exceptions.RequestParameterInvalidException
         """
         # Get workflow + accessibility check.
-        stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id, instance=kwd.get('instance', False))
+        stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id, instance=kwd.get("instance", False))
         workflow = stored_workflow.latest_workflow
         run_configs = build_workflow_run_configs(trans, workflow, payload)
-        is_batch = payload.get('batch')
+        is_batch = payload.get("batch")
         if not is_batch and len(run_configs) != 1:
             raise exceptions.RequestParameterInvalidException("Must specify 'batch' to use batch parameters.")
 
         tool_ids = self.workflow_contents_manager.get_all_tool_ids(workflow)
         missing_tool_ids = [tool_id for tool_id in tool_ids if not self.app.toolbox.has_tool(tool_id)]
         if missing_tool_ids:
-            raise exceptions.MessageException(f"Workflow was not invoked; the following required tools are not installed: {', '.join(missing_tool_ids)}")
+            raise exceptions.MessageException(
+                f"Workflow was not invoked; the following required tools are not installed: {', '.join(missing_tool_ids)}"
+            )
 
         invocations = []
         for run_config in run_configs:
-            workflow_scheduler_id = payload.get('scheduler', None)
+            workflow_scheduler_id = payload.get("scheduler", None)
             # TODO: workflow scheduler hints
             work_request_params = dict(scheduler=workflow_scheduler_id)
             workflow_invocation = queue_invoke(
@@ -819,10 +877,14 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         invocation_payload = InvocationIndexPayload(**kwd)
         workflow_id = invocation_payload.workflow_id
         if invocation_payload.instance:
-            invocation_payload.workflow_id = self.__get_stored_workflow(trans, trans.security.encode_id(workflow_id), instance=True).id
+            invocation_payload.workflow_id = self.__get_stored_workflow(
+                trans, trans.security.encode_id(workflow_id), instance=True
+            ).id
         if invocation_payload.history_id:
             # access check
-            self.history_manager.get_accessible(invocation_payload.history_id, trans.user, current_history=trans.history)
+            self.history_manager.get_accessible(
+                invocation_payload.history_id, trans.user, current_history=trans.history
+            )
         if not trans.user_is_admin:
             # We restrict the query to the current users' invocations
             # Endpoint requires user login, so trans.user.id is never None
@@ -845,7 +907,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             sort_by=invocation_payload.sort_by,
             sort_desc=invocation_payload.sort_desc,
         )
-        trans.response.headers['total_matches'] = total_matches
+        trans.response.headers["total_matches"] = total_matches
         return self.workflow_manager.serialize_workflow_invocations(invocations, **kwd)
 
     @expose_api
@@ -880,9 +942,11 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         decoded_workflow_invocation_id = self.decode_id(invocation_id)
         workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id, eager=True)
         if workflow_invocation:
-            step_details = util.string_as_bool(kwd.pop('step_details', 'False'))
-            legacy_job_state = util.string_as_bool(kwd.pop('legacy_job_state', 'False'))
-            return self.__encode_invocation(workflow_invocation, step_details=step_details, legacy_job_state=legacy_job_state, **kwd)
+            step_details = util.string_as_bool(kwd.pop("step_details", "False"))
+            legacy_job_state = util.string_as_bool(kwd.pop("legacy_job_state", "False"))
+            return self.__encode_invocation(
+                workflow_invocation, step_details=step_details, legacy_job_state=legacy_job_state, **kwd
+            )
         return None
 
     @expose_api
@@ -940,7 +1004,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         encoded_history_id = trans.security.encode_id(history.id)
         dict_workflow = json.loads(self.workflow_dict(trans, encoded_workflow_id))
 
-        spec_version = kwd.get('spec_version', 'https://w3id.org/ieee/ieee-2791-schema/2791object.json')
+        spec_version = kwd.get("spec_version", "https://w3id.org/ieee/ieee-2791-schema/2791object.json")
 
         for i, w in enumerate(reversed(stored_workflow.workflows)):
             if workflow == w:
@@ -949,39 +1013,39 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         contributors = []
         for contributing_user in contributing_users:
             contributor = {
-                'orcid': kwd.get('xref', []),
-                'name': contributing_user.username,
-                'affiliation': "",
-                'contribution': ['authoredBy'],
-                'email': contributing_user.email,
+                "orcid": kwd.get("xref", []),
+                "name": contributing_user.username,
+                "affiliation": "",
+                "contribution": ["authoredBy"],
+                "email": contributing_user.email,
             }
             contributors.append(contributor)
 
         reviewers = []
         for reviewer in reviewing_users:
             reviewer = {
-                'status': 'approved',
-                'reviewer_comment': '',
-                'date': workflow_invocation.update_time.isoformat(),
-                'reviewer': {
-                    'orcid': kwd.get('orcid', []),
-                    'name': contributing_user.username,
-                    'affiliation': "",
-                    'contribution': 'curatedBy',
-                    'email': contributing_user.email
-                }
+                "status": "approved",
+                "reviewer_comment": "",
+                "date": workflow_invocation.update_time.isoformat(),
+                "reviewer": {
+                    "orcid": kwd.get("orcid", []),
+                    "name": contributing_user.username,
+                    "affiliation": "",
+                    "contribution": "curatedBy",
+                    "email": contributing_user.email,
+                },
             }
             reviewers.append(reviewer)
 
         provenance_domain = {
-            'name': workflow.name,
-            'version': current_version,
-            'review': reviewers,
-            'derived_from': url_for('workflow', id=encoded_workflow_id, qualified=True),
-            'created': workflow_invocation.create_time.isoformat(),
-            'modified': workflow_invocation.update_time.isoformat(),
-            'contributors': contributors,
-            'license': 'https://spdx.org/licenses/CC-BY-4.0.html',
+            "name": workflow.name,
+            "version": current_version,
+            "review": reviewers,
+            "derived_from": url_for("workflow", id=encoded_workflow_id, qualified=True),
+            "created": workflow_invocation.create_time.isoformat(),
+            "modified": workflow_invocation.update_time.isoformat(),
+            "contributors": contributors,
+            "license": "https://spdx.org/licenses/CC-BY-4.0.html",
         }
 
         keywords = []
@@ -994,88 +1058,110 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         metrics = {}
         tools, input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], [], []
         for step in workflow_invocation.steps:
-            if step.workflow_step.type == 'tool':
+            if step.workflow_step.type == "tool":
                 workflow_outputs_list, output_list, input_list = set(), [], []
                 for wo in step.workflow_step.workflow_outputs:
                     workflow_outputs_list.add(wo.output_name)
                 for job in step.jobs:
                     metrics[i] = summarize_job_metrics(trans, job)
                     for job_input in job.input_datasets:
-                        if hasattr(job_input.dataset, 'dataset_id'):
+                        if hasattr(job_input.dataset, "dataset_id"):
                             encoded_dataset_id = trans.security.encode_id(job_input.dataset.dataset_id)
                             input_obj = {
                                 # TODO: that should maybe be a step prefix + element identifier where appropriate.
-                                'filename': job_input.dataset.name,
-                                'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
-                                'access_time': job_input.dataset.create_time.isoformat(),
+                                "filename": job_input.dataset.name,
+                                "uri": url_for(
+                                    "history_content",
+                                    history_id=encoded_history_id,
+                                    id=encoded_dataset_id,
+                                    qualified=True,
+                                ),
+                                "access_time": job_input.dataset.create_time.isoformat(),
                             }
                             input_list.append(input_obj)
 
                     for job_output in job.output_datasets:
-                        if hasattr(job_output.dataset, 'dataset_id'):
+                        if hasattr(job_output.dataset, "dataset_id"):
                             encoded_dataset_id = trans.security.encode_id(job_output.dataset.dataset_id)
                             output_obj = {
-                                'filename': job_output.dataset.name,
-                                'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
-                                'access_time': job_output.dataset.create_time.isoformat(),
+                                "filename": job_output.dataset.name,
+                                "uri": url_for(
+                                    "history_content",
+                                    history_id=encoded_history_id,
+                                    id=encoded_dataset_id,
+                                    qualified=True,
+                                ),
+                                "access_time": job_output.dataset.create_time.isoformat(),
                             }
                             output_list.append(output_obj)
 
                             if job_output.name in workflow_outputs_list:
                                 output = {
-                                    'mediatype': job_output.dataset.extension,
-                                    'uri': {
-                                        'filename': job_output.dataset.name,
-                                        'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
-                                        'access_time': job_output.dataset.create_time.isoformat(),
-                                    }
+                                    "mediatype": job_output.dataset.extension,
+                                    "uri": {
+                                        "filename": job_output.dataset.name,
+                                        "uri": url_for(
+                                            "history_content",
+                                            history_id=encoded_history_id,
+                                            id=encoded_dataset_id,
+                                            qualified=True,
+                                        ),
+                                        "access_time": job_output.dataset.create_time.isoformat(),
+                                    },
                                 }
                                 output_subdomain.append(output)
                 workflow_step = step.workflow_step
                 step_index = workflow_step.order_index
-                current_step = dict_workflow['steps'][str(step_index)]
+                current_step = dict_workflow["steps"][str(step_index)]
                 pipeline_step = {
-                    'step_number': step_index,
-                    'name': current_step['name'],
-                    'description': current_step['annotation'],
-                    'version': current_step['tool_version'],
-                    'prerequisite': kwd.get('prerequisite', []),
-                    'input_list': input_list,
-                    'output_list': output_list
+                    "step_number": step_index,
+                    "name": current_step["name"],
+                    "description": current_step["annotation"],
+                    "version": current_step["tool_version"],
+                    "prerequisite": kwd.get("prerequisite", []),
+                    "input_list": input_list,
+                    "output_list": output_list,
                 }
                 pipeline_steps.append(pipeline_step)
                 try:
                     software_prerequisite = {
-                        'name': current_step['content_id'],
-                        'version': current_step['tool_version'],
-                        'uri': {
-                            'uri': current_step['content_id'],
-                            'access_time': current_step['uuid']
-                        }
+                        "name": current_step["content_id"],
+                        "version": current_step["tool_version"],
+                        "uri": {"uri": current_step["content_id"], "access_time": current_step["uuid"]},
                     }
-                    if software_prerequisite['uri']['uri'] not in tools:
+                    if software_prerequisite["uri"]["uri"] not in tools:
                         software_prerequisites.append(software_prerequisite)
-                        tools.append(software_prerequisite['uri']['uri'])
+                        tools.append(software_prerequisite["uri"]["uri"])
                 except Exception:
                     continue
 
-            if step.workflow_step.type == 'data_input' and step.output_datasets:
+            if step.workflow_step.type == "data_input" and step.output_datasets:
                 for output_assoc in step.output_datasets:
                     encoded_dataset_id = trans.security.encode_id(output_assoc.dataset_id)
                     input_obj = {
-                        'filename': step.workflow_step.label,
-                        'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True),
-                        'access_time': step.workflow_step.update_time.isoformat(),
+                        "filename": step.workflow_step.label,
+                        "uri": url_for(
+                            "history_content", history_id=encoded_history_id, id=encoded_dataset_id, qualified=True
+                        ),
+                        "access_time": step.workflow_step.update_time.isoformat(),
                     }
                     input_subdomain.append(input_obj)
 
-            if step.workflow_step.type == 'data_collection_input' and step.output_dataset_collections:
+            if step.workflow_step.type == "data_collection_input" and step.output_dataset_collections:
                 for output_dataset_collection_association in step.output_dataset_collections:
-                    encoded_dataset_id = trans.security.encode_id(output_dataset_collection_association.dataset_collection_id)
+                    encoded_dataset_id = trans.security.encode_id(
+                        output_dataset_collection_association.dataset_collection_id
+                    )
                     input_obj = {
-                        'filename': step.workflow_step.label,
-                        'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, type="dataset_collection", qualified=True),
-                        'access_time': step.workflow_step.update_time.isoformat(),
+                        "filename": step.workflow_step.label,
+                        "uri": url_for(
+                            "history_content",
+                            history_id=encoded_history_id,
+                            id=encoded_dataset_id,
+                            type="dataset_collection",
+                            qualified=True,
+                        ),
+                        "access_time": step.workflow_step.update_time.isoformat(),
                     }
                     input_subdomain.append(input_obj)
 
@@ -1090,74 +1176,75 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
             try:
                 for k, v in inv_step.workflow_step.tool_inputs.items():
                     param, value, step = k, v, inv_step.workflow_step.order_index
-                    parametric_domain.append({'param': param, 'value': value, 'step': step})
+                    parametric_domain.append({"param": param, "value": value, "step": step})
             except Exception:
                 continue
 
         execution_domain = {
-            'script_access_type': 'a_galaxy_workflow',
-            'script': [url_for('workflows', encoded_workflow_id=encoded_workflow_id, qualified=True)],
-            'script_driver': 'Galaxy',
-            'software_prerequisites': software_prerequisites,
-            'external_data_endpoints': [
-                {
-                    'name': 'Access to Galaxy',
-                    'url': url_for('/', qualified=True)
-                },
-                kwd.get('external_data_endpoints')
+            "script_access_type": "a_galaxy_workflow",
+            "script": [url_for("workflows", encoded_workflow_id=encoded_workflow_id, qualified=True)],
+            "script_driver": "Galaxy",
+            "software_prerequisites": software_prerequisites,
+            "external_data_endpoints": [
+                {"name": "Access to Galaxy", "url": url_for("/", qualified=True)},
+                kwd.get("external_data_endpoints"),
             ],
-            'environment_variables': kwd.get('environment_variables', {})
+            "environment_variables": kwd.get("environment_variables", {}),
         }
 
         extension = [
             {
-                'extension_schema': 'https://raw.githubusercontent.com/biocompute-objects/extension_domain/6d2cd8482e6075746984662edcf78b57d3d38065/galaxy/galaxy_extension.json',
-                'galaxy_extension': {
-                    'galaxy_url': url_for('/', qualified=True),
-                    'galaxy_version': VERSION,
+                "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/6d2cd8482e6075746984662edcf78b57d3d38065/galaxy/galaxy_extension.json",
+                "galaxy_extension": {
+                    "galaxy_url": url_for("/", qualified=True),
+                    "galaxy_version": VERSION,
                     # TODO:
                     # 'aws_estimate': aws_estimate,
                     # 'job_metrics': metrics
-                }
+                },
             }
         ]
 
         error_domain = {
-            'empirical_error': kwd.get('empirical_error', []),
-            'algorithmic_error': kwd.get('algorithmic_error', [])
+            "empirical_error": kwd.get("empirical_error", []),
+            "algorithmic_error": kwd.get("algorithmic_error", []),
         }
 
         bco_dict = {
-            'provenance_domain': provenance_domain,
-            'usability_domain': usability_domain,
-            'extension_domain': extension,
-            'description_domain': {
-                'keywords': keywords,
-                'xref': kwd.get('xref', []),
-                'platform': ['Galaxy'],
-                'pipeline_steps': pipeline_steps,
+            "provenance_domain": provenance_domain,
+            "usability_domain": usability_domain,
+            "extension_domain": extension,
+            "description_domain": {
+                "keywords": keywords,
+                "xref": kwd.get("xref", []),
+                "platform": ["Galaxy"],
+                "pipeline_steps": pipeline_steps,
             },
-            'execution_domain': execution_domain,
-            'parametric_domain': parametric_domain,
-            'io_domain': {
-                'input_subdomain': input_subdomain,
-                'output_subdomain': output_subdomain,
+            "execution_domain": execution_domain,
+            "parametric_domain": parametric_domain,
+            "io_domain": {
+                "input_subdomain": input_subdomain,
+                "output_subdomain": output_subdomain,
             },
-            'error_domain': error_domain,
+            "error_domain": error_domain,
         }
         # Generate etag from the BCO excluding object_id and spec_version, as
         # specified in https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/top-level.md#203-etag-etag
         etag = hashlib.sha256(json.dumps(bco_dict, sort_keys=True).encode()).hexdigest()
-        bco_dict.update({
-            'object_id': url_for(controller=f"api/invocations/{invocation_id}", action='biocompute', qualified=True),
-            'spec_version': spec_version,
-            'etag': etag,
-        })
+        bco_dict.update(
+            {
+                "object_id": url_for(
+                    controller=f"api/invocations/{invocation_id}", action="biocompute", qualified=True
+                ),
+                "spec_version": spec_version,
+                "etag": etag,
+            }
+        )
         return bco_dict
 
     @expose_api
     def export_invocation_bco(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
-        '''
+        """
         GET /api/invocations/{invocations_id}/biocompute
 
         Return a BioCompute Object for the workflow invocation.
@@ -1166,7 +1253,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         as how inputs and outputs are represented, how the workflow is encoded,
         and how author and version information is encoded, and how URLs are
         generated will very likely change in important ways over time.
-        '''
+        """
         return self._generate_invocation_bco(trans, invocation_id, **kwd)
 
     @expose_api_raw
@@ -1205,10 +1292,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         :raises: exceptions.MessageException, exceptions.ObjectNotFound
         """
         decoded_invocation_step_id = self.decode_id(step_id)
-        invocation_step = self.workflow_manager.get_invocation_step(
-            trans,
-            decoded_invocation_step_id
-        )
+        invocation_step = self.workflow_manager.get_invocation_step(trans, decoded_invocation_step_id)
         return self.__encode_invocation_step(trans, invocation_step)
 
     @expose_api_anonymous_and_sessionless
@@ -1324,16 +1408,23 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         data = raw_workflow_description.as_dict
 
         tools = {}
-        for key in data['steps']:
-            item = data['steps'][key]
+        for key in data["steps"]:
+            item = data["steps"][key]
             if item is not None:
-                if 'tool_shed_repository' in item:
-                    tool_shed_repository = item['tool_shed_repository']
-                    if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository:
-                        toolstr = tool_shed_repository['owner'] \
-                            + tool_shed_repository['changeset_revision'] \
-                            + tool_shed_repository['name'] \
-                            + tool_shed_repository['tool_shed']
+                if "tool_shed_repository" in item:
+                    tool_shed_repository = item["tool_shed_repository"]
+                    if (
+                        "owner" in tool_shed_repository
+                        and "changeset_revision" in tool_shed_repository
+                        and "name" in tool_shed_repository
+                        and "tool_shed" in tool_shed_repository
+                    ):
+                        toolstr = (
+                            tool_shed_repository["owner"]
+                            + tool_shed_repository["changeset_revision"]
+                            + tool_shed_repository["name"]
+                            + tool_shed_repository["tool_shed"]
+                        )
                         tools[toolstr] = tool_shed_repository
 
         irm = InstallRepositoryManager(self.app)
@@ -1341,21 +1432,13 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U
         for k in tools:
             item = tools[k]
             tool_shed_url = f"https://{item['tool_shed']}/"
-            name = item['name']
-            owner = item['owner']
-            changeset_revision = item['changeset_revision']
-            irm.install(tool_shed_url,
-                        name,
-                        owner,
-                        changeset_revision,
-                        install_options)
+            name = item["name"]
+            owner = item["owner"]
+            changeset_revision = item["changeset_revision"]
+            irm.install(tool_shed_url, name, owner, changeset_revision, install_options)
 
     def __encode_invocation_step(self, trans: ProvidesUserContext, invocation_step):
-        return self.encode_all_ids(
-            trans,
-            invocation_step.to_dict('element'),
-            True
-        )
+        return self.encode_all_ids(trans, invocation_step.to_dict("element"), True)
 
     def __get_stored_accessible_workflow(self, trans, workflow_id, **kwd):
         instance = util.string_as_bool(kwd.get("instance", "false"))
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index be5ba193ab6..2dbb96d3a56 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -49,13 +49,10 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     middleware to handle CORS options, etc..
     """
     load_app_kwds = load_app_kwds or {}
-    kwargs = load_app_properties(
-        kwds=kwargs,
-        **load_app_kwds
-    )
+    kwargs = load_app_properties(kwds=kwargs, **load_app_kwds)
     # Create the Galaxy application unless passed in
-    if 'app' in kwargs:
-        app = kwargs.pop('app')
+    if "app" in kwargs:
+        app = kwargs.pop("app")
         galaxy.app.app = app
     else:
         try:
@@ -65,52 +62,110 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
             traceback.print_exc()
             sys.exit(1)
 
-    if kwargs.get('register_shutdown_at_exit', True):
+    if kwargs.get("register_shutdown_at_exit", True):
         # Call app's shutdown method when the interpeter exits, this cleanly stops
         # the various Galaxy application daemon threads
         app.application_stack.register_postfork_function(atexit.register, app.shutdown)
     # Create the universe WSGI application
-    webapp = GalaxyWebApplication(app, session_cookie='galaxysession', name='galaxy')
+    webapp = GalaxyWebApplication(app, session_cookie="galaxysession", name="galaxy")
 
     # STANDARD CONTROLLER ROUTES
-    webapp.add_ui_controllers('galaxy.webapps.galaxy.controllers', app)
+    webapp.add_ui_controllers("galaxy.webapps.galaxy.controllers", app)
     # Force /history to go to view of current
-    webapp.add_route('/history', controller='history', action='view')
-    webapp.add_route('/history/view/{id}', controller='history', action='view')
+    webapp.add_route("/history", controller="history", action="view")
+    webapp.add_route("/history/view/{id}", controller="history", action="view")
 
     # Force /activate to go to the controller
-    webapp.add_route('/activate', controller='user', action='activate')
+    webapp.add_route("/activate", controller="user", action="activate")
 
     # Authentication endpoints.
-    webapp.add_route('/authnz/', controller='authnz', action='index', provider=None)
-    webapp.add_route('/authnz/{provider}/login', controller='authnz', action='login', provider=None)
-    webapp.add_route('/authnz/{provider}/callback', controller='authnz', action='callback', provider=None)
-    webapp.add_route('/authnz/{provider}/disconnect/{email}', controller='authnz', action='disconnect', provider=None, email=None)
-    webapp.add_route('/authnz/{provider}/logout', controller='authnz', action='logout', provider=None)
-    webapp.add_route('/authnz/{provider}/create_user', controller='authnz', action='create_user')
+    webapp.add_route("/authnz/", controller="authnz", action="index", provider=None)
+    webapp.add_route("/authnz/{provider}/login", controller="authnz", action="login", provider=None)
+    webapp.add_route("/authnz/{provider}/callback", controller="authnz", action="callback", provider=None)
+    webapp.add_route(
+        "/authnz/{provider}/disconnect/{email}", controller="authnz", action="disconnect", provider=None, email=None
+    )
+    webapp.add_route("/authnz/{provider}/logout", controller="authnz", action="logout", provider=None)
+    webapp.add_route("/authnz/{provider}/create_user", controller="authnz", action="create_user")
     # Returns the provider specific logout url for currently logged in provider
-    webapp.add_route('/authnz/logout', controller='authnz', action='get_logout_url')
-    webapp.add_route('/authnz/get_cilogon_idps', controller='authnz', action='get_cilogon_idps')
+    webapp.add_route("/authnz/logout", controller="authnz", action="get_logout_url")
+    webapp.add_route("/authnz/get_cilogon_idps", controller="authnz", action="get_cilogon_idps")
 
     # These two routes handle our simple needs at the moment
-    webapp.add_route('/async/{tool_id}/{data_id}/{data_secret}', controller='async', action='index', tool_id=None, data_id=None, data_secret=None)
-    webapp.add_route('/{controller}/{action}', action='index')
-    webapp.add_route('/{action}', controller='root', action='index')
+    webapp.add_route(
+        "/async/{tool_id}/{data_id}/{data_secret}",
+        controller="async",
+        action="index",
+        tool_id=None,
+        data_id=None,
+        data_secret=None,
+    )
+    webapp.add_route("/{controller}/{action}", action="index")
+    webapp.add_route("/{action}", controller="root", action="index")
 
     # allow for subdirectories in extra_files_path
-    webapp.add_route('/datasets/{dataset_id}/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
-    webapp.add_route('/datasets/{dataset_id}/{action}/{filename}', controller='dataset', action='index', dataset_id=None, filename=None)
-    webapp.add_route('/display_application/{dataset_id}/{app_name}/{link_name}/{user_id}/{app_action}/{action_param}/{action_param_extra:.+?}',
-                     controller='dataset', action='display_application', dataset_id=None, user_id=None,
-                     app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None)
+    webapp.add_route(
+        "/datasets/{dataset_id}/display/{filename:.+?}",
+        controller="dataset",
+        action="display",
+        dataset_id=None,
+        filename=None,
+    )
+    webapp.add_route(
+        "/datasets/{dataset_id}/{action}/{filename}",
+        controller="dataset",
+        action="index",
+        dataset_id=None,
+        filename=None,
+    )
+    webapp.add_route(
+        "/display_application/{dataset_id}/{app_name}/{link_name}/{user_id}/{app_action}/{action_param}/{action_param_extra:.+?}",
+        controller="dataset",
+        action="display_application",
+        dataset_id=None,
+        user_id=None,
+        app_name=None,
+        link_name=None,
+        app_action=None,
+        action_param=None,
+        action_param_extra=None,
+    )
 
-    USERNAME_REQS = {'username': VALID_PUBLICNAME_RE.pattern.strip("^$")}
-    webapp.add_route('/u/{username}/d/{slug}/{filename}', controller='dataset', action='display_by_username_and_slug', filename=None, requirements=USERNAME_REQS)
-    webapp.add_route('/u/{username}/p/{slug}', controller='page', action='display_by_username_and_slug', requirements=USERNAME_REQS)
-    webapp.add_route('/u/{username}/h/{slug}', controller='history', action='display_by_username_and_slug', requirements=USERNAME_REQS)
-    webapp.add_route('/u/{username}/w/{slug}', controller='workflow', action='display_by_username_and_slug', requirements=USERNAME_REQS)
-    webapp.add_route('/u/{username}/w/{slug}/{format}', controller='workflow', action='display_by_username_and_slug', requirements=USERNAME_REQS)
-    webapp.add_route('/u/{username}/v/{slug}', controller='visualization', action='display_by_username_and_slug', requirements=USERNAME_REQS)
+    USERNAME_REQS = {"username": VALID_PUBLICNAME_RE.pattern.strip("^$")}
+    webapp.add_route(
+        "/u/{username}/d/{slug}/{filename}",
+        controller="dataset",
+        action="display_by_username_and_slug",
+        filename=None,
+        requirements=USERNAME_REQS,
+    )
+    webapp.add_route(
+        "/u/{username}/p/{slug}", controller="page", action="display_by_username_and_slug", requirements=USERNAME_REQS
+    )
+    webapp.add_route(
+        "/u/{username}/h/{slug}",
+        controller="history",
+        action="display_by_username_and_slug",
+        requirements=USERNAME_REQS,
+    )
+    webapp.add_route(
+        "/u/{username}/w/{slug}",
+        controller="workflow",
+        action="display_by_username_and_slug",
+        requirements=USERNAME_REQS,
+    )
+    webapp.add_route(
+        "/u/{username}/w/{slug}/{format}",
+        controller="workflow",
+        action="display_by_username_and_slug",
+        requirements=USERNAME_REQS,
+    )
+    webapp.add_route(
+        "/u/{username}/v/{slug}",
+        controller="visualization",
+        action="display_by_username_and_slug",
+        requirements=USERNAME_REQS,
+    )
 
     # TODO: Refactor above routes into external method to allow testing in
     # isolation as well.
@@ -118,11 +173,11 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     if wsgi_preflight:
         # API OPTIONS RESPONSE
         webapp.mapper.connect(
-            'options',
-            '/api/{path_info:.*?}',
-            controller='authenticate',
-            action='options',
-            conditions={'method': ['OPTIONS']},
+            "options",
+            "/api/{path_info:.*?}",
+            controller="authenticate",
+            action="options",
+            conditions={"method": ["OPTIONS"]},
         )
 
     # CLIENTSIDE ROUTES
@@ -130,88 +185,92 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     # The following routes don't bootstrap any information, simply provide the
     # base analysis interface at which point the application takes over.
 
-    webapp.add_client_route('/admin/data_tables', 'admin')
-    webapp.add_client_route('/admin/data_types', 'admin')
-    webapp.add_client_route('/admin/jobs', 'admin')
-    webapp.add_client_route('/admin/invocations', 'admin')
-    webapp.add_client_route('/admin/toolbox_dependencies', 'admin')
-    webapp.add_client_route('/admin/data_manager{path_info:.*}', 'admin')
-    webapp.add_client_route('/admin/error_stack', 'admin')
-    webapp.add_client_route('/admin/users', 'admin')
-    webapp.add_client_route('/admin/users/create', 'admin')
-    webapp.add_client_route('/admin/display_applications', 'admin')
-    webapp.add_client_route('/admin/reset_metadata', 'admin')
-    webapp.add_client_route('/admin/roles', 'admin')
-    webapp.add_client_route('/admin/forms', 'admin')
-    webapp.add_client_route('/admin/groups', 'admin')
-    webapp.add_client_route('/admin/repositories', 'admin')
-    webapp.add_client_route('/admin/sanitize_allow', 'admin')
-    webapp.add_client_route('/admin/tool_versions', 'admin')
-    webapp.add_client_route('/admin/toolshed', 'admin')
-    webapp.add_client_route('/admin/quotas', 'admin')
-    webapp.add_client_route('/admin/form/{form_id}', 'admin')
-    webapp.add_client_route('/admin/api_keys', 'admin')
-    webapp.add_client_route('/login/confirm')
-    webapp.add_client_route('/tools/view')
-    webapp.add_client_route('/tools/json')
-    webapp.add_client_route('/tours')
-    webapp.add_client_route('/tours/{tour_id}')
-    webapp.add_client_route('/user')
-    webapp.add_client_route('/user/{form_id}')
-    webapp.add_client_route('/welcome/new')
-    webapp.add_client_route('/visualizations')
-    webapp.add_client_route('/visualizations/edit')
-    webapp.add_client_route('/visualizations/sharing')
-    webapp.add_client_route('/visualizations/list_published')
-    webapp.add_client_route('/visualizations/list')
-    webapp.add_client_route('/pages/list')
-    webapp.add_client_route('/pages/list_published')
-    webapp.add_client_route('/pages/create')
-    webapp.add_client_route('/pages/edit')
-    webapp.add_client_route('/pages/sharing')
-    webapp.add_client_route('/histories/citations')
-    webapp.add_client_route('/histories/list')
-    webapp.add_client_route('/histories/import')
-    webapp.add_client_route('/histories/{history_id}/export')
-    webapp.add_client_route('/histories/list_published')
-    webapp.add_client_route('/histories/list_shared')
-    webapp.add_client_route('/histories/rename')
-    webapp.add_client_route('/histories/sharing')
-    webapp.add_client_route('/histories/permissions')
-    webapp.add_client_route('/histories/view')
-    webapp.add_client_route('/histories/show_structure')
-    webapp.add_client_route('/datasets/list')
-    webapp.add_client_route('/datasets/edit')
-    webapp.add_client_route('/collection/edit/{collection_id}')
-    webapp.add_client_route('/datasets/error')
-    webapp.add_client_route('/jobs/{job_id}/view')
-    webapp.add_client_route('/datasets/{dataset_id}/details')
-    webapp.add_client_route('/datasets/{dataset_id}/show_params')
-    webapp.add_client_route('/workflows/list')
-    webapp.add_client_route('/workflows/list_published')
-    webapp.add_client_route('/workflows/create')
-    webapp.add_client_route('/workflows/run')
-    webapp.add_client_route('/workflows/import')
-    webapp.add_client_route('/workflows/trs_import')
-    webapp.add_client_route('/workflows/trs_search')
-    webapp.add_client_route('/workflows/invocations')
-    webapp.add_client_route('/workflows/invocations/report')
+    webapp.add_client_route("/admin/data_tables", "admin")
+    webapp.add_client_route("/admin/data_types", "admin")
+    webapp.add_client_route("/admin/jobs", "admin")
+    webapp.add_client_route("/admin/invocations", "admin")
+    webapp.add_client_route("/admin/toolbox_dependencies", "admin")
+    webapp.add_client_route("/admin/data_manager{path_info:.*}", "admin")
+    webapp.add_client_route("/admin/error_stack", "admin")
+    webapp.add_client_route("/admin/users", "admin")
+    webapp.add_client_route("/admin/users/create", "admin")
+    webapp.add_client_route("/admin/display_applications", "admin")
+    webapp.add_client_route("/admin/reset_metadata", "admin")
+    webapp.add_client_route("/admin/roles", "admin")
+    webapp.add_client_route("/admin/forms", "admin")
+    webapp.add_client_route("/admin/groups", "admin")
+    webapp.add_client_route("/admin/repositories", "admin")
+    webapp.add_client_route("/admin/sanitize_allow", "admin")
+    webapp.add_client_route("/admin/tool_versions", "admin")
+    webapp.add_client_route("/admin/toolshed", "admin")
+    webapp.add_client_route("/admin/quotas", "admin")
+    webapp.add_client_route("/admin/form/{form_id}", "admin")
+    webapp.add_client_route("/admin/api_keys", "admin")
+    webapp.add_client_route("/login/confirm")
+    webapp.add_client_route("/tools/view")
+    webapp.add_client_route("/tools/json")
+    webapp.add_client_route("/tours")
+    webapp.add_client_route("/tours/{tour_id}")
+    webapp.add_client_route("/user")
+    webapp.add_client_route("/user/{form_id}")
+    webapp.add_client_route("/welcome/new")
+    webapp.add_client_route("/visualizations")
+    webapp.add_client_route("/visualizations/edit")
+    webapp.add_client_route("/visualizations/sharing")
+    webapp.add_client_route("/visualizations/list_published")
+    webapp.add_client_route("/visualizations/list")
+    webapp.add_client_route("/pages/list")
+    webapp.add_client_route("/pages/list_published")
+    webapp.add_client_route("/pages/create")
+    webapp.add_client_route("/pages/edit")
+    webapp.add_client_route("/pages/sharing")
+    webapp.add_client_route("/histories/citations")
+    webapp.add_client_route("/histories/list")
+    webapp.add_client_route("/histories/import")
+    webapp.add_client_route("/histories/{history_id}/export")
+    webapp.add_client_route("/histories/list_published")
+    webapp.add_client_route("/histories/list_shared")
+    webapp.add_client_route("/histories/rename")
+    webapp.add_client_route("/histories/sharing")
+    webapp.add_client_route("/histories/permissions")
+    webapp.add_client_route("/histories/view")
+    webapp.add_client_route("/histories/show_structure")
+    webapp.add_client_route("/datasets/list")
+    webapp.add_client_route("/datasets/edit")
+    webapp.add_client_route("/collection/edit/{collection_id}")
+    webapp.add_client_route("/datasets/error")
+    webapp.add_client_route("/jobs/{job_id}/view")
+    webapp.add_client_route("/datasets/{dataset_id}/details")
+    webapp.add_client_route("/datasets/{dataset_id}/show_params")
+    webapp.add_client_route("/workflows/list")
+    webapp.add_client_route("/workflows/list_published")
+    webapp.add_client_route("/workflows/create")
+    webapp.add_client_route("/workflows/run")
+    webapp.add_client_route("/workflows/import")
+    webapp.add_client_route("/workflows/trs_import")
+    webapp.add_client_route("/workflows/trs_search")
+    webapp.add_client_route("/workflows/invocations")
+    webapp.add_client_route("/workflows/invocations/report")
     # webapp.add_client_route('/workflows/invocations/view_bco')
-    webapp.add_client_route('/custom_builds')
-    webapp.add_client_route('/interactivetool_entry_points/list')
-    webapp.add_client_route('/libraries{path:.*?}')
+    webapp.add_client_route("/custom_builds")
+    webapp.add_client_route("/interactivetool_entry_points/list")
+    webapp.add_client_route("/libraries{path:.*?}")
 
     # ==== Done
     # Indicate that all configuration settings have been provided
     webapp.finalize_config()
 
     # Wrap the webapp in some useful middleware
-    if kwargs.get('middleware', True):
+    if kwargs.get("middleware", True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
-    if asbool(kwargs.get('static_enabled', True)):
-        webapp = wrap_if_allowed(webapp, app.application_stack, wrap_in_static,
-                                 args=(global_conf,),
-                                 kwargs=dict(plugin_frameworks=[app.visualizations_registry], **kwargs))
+    if asbool(kwargs.get("static_enabled", True)):
+        webapp = wrap_if_allowed(
+            webapp,
+            app.application_stack,
+            wrap_in_static,
+            args=(global_conf,),
+            kwargs=dict(plugin_frameworks=[app.visualizations_registry], **kwargs),
+        )
     app.application_stack.register_postfork_function(postfork_setup)
 
     for th in threading.enumerate():
@@ -231,470 +290,821 @@ uwsgi_app_factory = uwsgi_app
 
 def postfork_setup():
     from galaxy.app import app
+
     app.application_stack.log_startup()
 
 
 def populate_api_routes(webapp, app):
-    webapp.add_api_controllers('galaxy.webapps.galaxy.api', app)
+    webapp.add_api_controllers("galaxy.webapps.galaxy.api", app)
 
     valid_history_contents_types = [
-        'dataset',
-        'dataset_collection',
+        "dataset",
+        "dataset_collection",
     ]
 
     # Accesss HDA details via histories/{history_id}/contents/datasets/{hda_id}
     # and HDCA details via histories/{history_id}/contents/dataset_collections/{hdca_id}
-    webapp.mapper.resource("content_typed",
-                           "{type:%s}s" % "|".join(valid_history_contents_types),
-                           name_prefix="history_",
-                           controller='history_contents',
-                           path_prefix='/api/histories/{history_id}/contents',
-                           parent_resources=dict(member_name='history', collection_name='histories'))
+    webapp.mapper.resource(
+        "content_typed",
+        "{type:%s}s" % "|".join(valid_history_contents_types),
+        name_prefix="history_",
+        controller="history_contents",
+        path_prefix="/api/histories/{history_id}/contents",
+        parent_resources=dict(member_name="history", collection_name="histories"),
+    )
     # Legacy access to HDA details via histories/{history_id}/contents/{hda_id}
-    webapp.mapper.resource('content',
-                           'contents',
-                           controller='history_contents',
-                           name_prefix='history_',
-                           path_prefix='/api/histories/{history_id}',
-                           parent_resources=dict(member_name='history', collection_name='histories'))
-    webapp.mapper.connect("history_contents_batch_update",
-                          "/api/histories/{history_id}/contents",
-                          controller="history_contents",
-                          action="update_batch",
-                          conditions=dict(method=["PUT"]))
-    webapp.mapper.connect("history_contents_display",
-                          "/api/histories/{history_id}/contents/{history_content_id}/display",
-                          controller="datasets",
-                          action="display",
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("history_contents_update_permissions",
-                          "/api/histories/{history_id}/contents/{history_content_id}/permissions",
-                          controller="history_contents",
-                          action="update_permissions",
-                          conditions=dict(method=["PUT"]))
-    webapp.mapper.connect("history_contents_validate",
-                          "/api/histories/{history_id}/contents/{history_content_id}/validate",
-                          controller="history_contents",
-                          action="validate",
-                          conditions=dict(method=["PUT"]))
-    webapp.mapper.connect("history_contents_extra_files",
-                          "/api/histories/{history_id}/contents/{history_content_id}/extra_files",
-                          controller="datasets",
-                          action="extra_files",
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("history_content_as_text",
-                          "/api/datasets/{dataset_id}/get_content_as_text",
-                          controller="datasets",
-                          action="get_content_as_text",
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('dataset_storage',
-                          '/api/datasets/{dataset_id}/storage',
-                          controller='datasets',
-                          action='show_storage',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('dataset_inheritance_chain',
-                          '/api/datasets/{dataset_id}/inheritance_chain',
-                          controller='datasets',
-                          action='show_inheritance_chain',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("history_contents_metadata_file",
-                          "/api/histories/{history_id}/contents/{history_content_id}/metadata_file",
-                          controller="datasets",
-                          action="get_metadata_file",
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("/api/histories/{history_id}/contents/{direction:near|before|after}/{hid}/{limit}",
-                          action="contents_near",
-                          controller='history_contents',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.resource('user',
-                           'users',
-                           controller='group_users',
-                           name_prefix='group_',
-                           path_prefix='/api/groups/{group_id}',
-                           parent_resources=dict(member_name='group', collection_name='groups'))
-    webapp.mapper.resource('role',
-                           'roles',
-                           controller='group_roles',
-                           name_prefix='group_',
-                           path_prefix='/api/groups/{group_id}',
-                           parent_resources=dict(member_name='group', collection_name='groups'))
-    _add_item_tags_controller(webapp,
-                              name_prefix="history_content_",
-                              path_prefix='/api/histories/{history_id}/contents/{history_content_id}')
-    webapp.mapper.connect('/api/histories/published', action='published', controller="histories", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/histories/shared_with_me', action='shared_with_me', controller="histories")
+    webapp.mapper.resource(
+        "content",
+        "contents",
+        controller="history_contents",
+        name_prefix="history_",
+        path_prefix="/api/histories/{history_id}",
+        parent_resources=dict(member_name="history", collection_name="histories"),
+    )
+    webapp.mapper.connect(
+        "history_contents_batch_update",
+        "/api/histories/{history_id}/contents",
+        controller="history_contents",
+        action="update_batch",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "history_contents_display",
+        "/api/histories/{history_id}/contents/{history_content_id}/display",
+        controller="datasets",
+        action="display",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "history_contents_update_permissions",
+        "/api/histories/{history_id}/contents/{history_content_id}/permissions",
+        controller="history_contents",
+        action="update_permissions",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "history_contents_validate",
+        "/api/histories/{history_id}/contents/{history_content_id}/validate",
+        controller="history_contents",
+        action="validate",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "history_contents_extra_files",
+        "/api/histories/{history_id}/contents/{history_content_id}/extra_files",
+        controller="datasets",
+        action="extra_files",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "history_content_as_text",
+        "/api/datasets/{dataset_id}/get_content_as_text",
+        controller="datasets",
+        action="get_content_as_text",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "dataset_storage",
+        "/api/datasets/{dataset_id}/storage",
+        controller="datasets",
+        action="show_storage",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "dataset_inheritance_chain",
+        "/api/datasets/{dataset_id}/inheritance_chain",
+        controller="datasets",
+        action="show_inheritance_chain",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "history_contents_metadata_file",
+        "/api/histories/{history_id}/contents/{history_content_id}/metadata_file",
+        controller="datasets",
+        action="get_metadata_file",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/histories/{history_id}/contents/{direction:near|before|after}/{hid}/{limit}",
+        action="contents_near",
+        controller="history_contents",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.resource(
+        "user",
+        "users",
+        controller="group_users",
+        name_prefix="group_",
+        path_prefix="/api/groups/{group_id}",
+        parent_resources=dict(member_name="group", collection_name="groups"),
+    )
+    webapp.mapper.resource(
+        "role",
+        "roles",
+        controller="group_roles",
+        name_prefix="group_",
+        path_prefix="/api/groups/{group_id}",
+        parent_resources=dict(member_name="group", collection_name="groups"),
+    )
+    _add_item_tags_controller(
+        webapp, name_prefix="history_content_", path_prefix="/api/histories/{history_id}/contents/{history_content_id}"
+    )
+    webapp.mapper.connect(
+        "/api/histories/published", action="published", controller="histories", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect("/api/histories/shared_with_me", action="shared_with_me", controller="histories")
 
-    webapp.mapper.connect('cloud_storage',
-                          '/api/cloud/storage/',
-                          controller='cloud',
-                          action='index',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('cloud_storage_get',
-                          '/api/cloud/storage/get',
-                          controller='cloud',
-                          action='get',
-                          conditions=dict(method=["POST"]))
-    webapp.mapper.connect('cloud_storage_send',
-                          '/api/cloud/storage/send',
-                          controller='cloud',
-                          action='send',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "cloud_storage", "/api/cloud/storage/", controller="cloud", action="index", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "cloud_storage_get",
+        "/api/cloud/storage/get",
+        controller="cloud",
+        action="get",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "cloud_storage_send",
+        "/api/cloud/storage/send",
+        controller="cloud",
+        action="send",
+        conditions=dict(method=["POST"]),
+    )
 
-    _add_item_tags_controller(webapp,
-                              name_prefix="history_",
-                              path_prefix='/api/histories/{history_id}')
-    _add_item_tags_controller(webapp,
-                              name_prefix="workflow_",
-                              path_prefix='/api/workflows/{workflow_id}')
-    _add_item_annotation_controller(webapp,
-                                    name_prefix="history_content_",
-                                    path_prefix='/api/histories/{history_id}/contents/{history_content_id}')
-    _add_item_annotation_controller(webapp,
-                                    name_prefix="history_",
-                                    path_prefix='/api/histories/{history_id}')
-    _add_item_annotation_controller(webapp,
-                                    name_prefix="workflow_",
-                                    path_prefix='/api/workflows/{workflow_id}')
-    _add_item_provenance_controller(webapp,
-                                    name_prefix="history_content_",
-                                    path_prefix='/api/histories/{history_id}/contents/{history_content_id}')
+    _add_item_tags_controller(webapp, name_prefix="history_", path_prefix="/api/histories/{history_id}")
+    _add_item_tags_controller(webapp, name_prefix="workflow_", path_prefix="/api/workflows/{workflow_id}")
+    _add_item_annotation_controller(
+        webapp, name_prefix="history_content_", path_prefix="/api/histories/{history_id}/contents/{history_content_id}"
+    )
+    _add_item_annotation_controller(webapp, name_prefix="history_", path_prefix="/api/histories/{history_id}")
+    _add_item_annotation_controller(webapp, name_prefix="workflow_", path_prefix="/api/workflows/{workflow_id}")
+    _add_item_provenance_controller(
+        webapp, name_prefix="history_content_", path_prefix="/api/histories/{history_id}/contents/{history_content_id}"
+    )
 
-    webapp.mapper.resource('dataset', 'datasets', path_prefix='/api')
-    webapp.mapper.resource('tool_data', 'tool_data', path_prefix='/api')
-    webapp.mapper.connect('/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data")
-    webapp.mapper.connect('/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data")
-    webapp.mapper.connect('/api/tool_data/{id:.+?}/reload', action='reload', controller="tool_data")
+    webapp.mapper.resource("dataset", "datasets", path_prefix="/api")
+    webapp.mapper.resource("tool_data", "tool_data", path_prefix="/api")
+    webapp.mapper.connect(
+        "/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}",
+        action="download_field_file",
+        controller="tool_data",
+    )
+    webapp.mapper.connect("/api/tool_data/{id:.+?}/fields/{value:.+?}", action="show_field", controller="tool_data")
+    webapp.mapper.connect("/api/tool_data/{id:.+?}/reload", action="reload", controller="tool_data")
 
-    webapp.mapper.resource('dataset_collection', 'dataset_collections', path_prefix='/api')
-    webapp.mapper.connect('contents_dataset_collection',
-        '/api/dataset_collections/{hdca_id}/contents/{parent_id}',
+    webapp.mapper.resource("dataset_collection", "dataset_collections", path_prefix="/api")
+    webapp.mapper.connect(
+        "contents_dataset_collection",
+        "/api/dataset_collections/{hdca_id}/contents/{parent_id}",
         controller="dataset_collections",
-        action="contents")
+        action="contents",
+    )
 
-    webapp.mapper.resource('form', 'forms', path_prefix='/api')
-    webapp.mapper.resource('role', 'roles', path_prefix='/api')
-    webapp.mapper.resource('upload', 'uploads', path_prefix='/api')
-    webapp.mapper.connect('/api/upload/resumable_upload/{session_id}', controller="uploads", action="hooks", conditions=dict(method=['PATCH']))
-    webapp.mapper.connect('/api/upload/resumable_upload', controller="uploads", action="hooks")
-    webapp.mapper.connect('/api/upload/hooks', controller="uploads", action="hooks", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/ftp_files', controller='remote_files')
-    webapp.mapper.connect('/api/remote_files', action='index', controller='remote_files', conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/remote_files/plugins', action='plugins', controller='remote_files', conditions=dict(method=["GET"]))
-    webapp.mapper.resource('group', 'groups', path_prefix='/api')
-    webapp.mapper.resource_with_deleted('quota', 'quotas', path_prefix='/api')
+    webapp.mapper.resource("form", "forms", path_prefix="/api")
+    webapp.mapper.resource("role", "roles", path_prefix="/api")
+    webapp.mapper.resource("upload", "uploads", path_prefix="/api")
+    webapp.mapper.connect(
+        "/api/upload/resumable_upload/{session_id}",
+        controller="uploads",
+        action="hooks",
+        conditions=dict(method=["PATCH"]),
+    )
+    webapp.mapper.connect("/api/upload/resumable_upload", controller="uploads", action="hooks")
+    webapp.mapper.connect("/api/upload/hooks", controller="uploads", action="hooks", conditions=dict(method=["POST"]))
+    webapp.mapper.connect("/api/ftp_files", controller="remote_files")
+    webapp.mapper.connect(
+        "/api/remote_files", action="index", controller="remote_files", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "/api/remote_files/plugins", action="plugins", controller="remote_files", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.resource("group", "groups", path_prefix="/api")
+    webapp.mapper.resource_with_deleted("quota", "quotas", path_prefix="/api")
 
-    webapp.mapper.connect('/api/cloud/authz/', action='index', controller='cloudauthz', conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/cloud/authz/',
-                          action='create',
-                          controller='cloudauthz',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect("/api/cloud/authz/", action="index", controller="cloudauthz", conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "/api/cloud/authz/", action="create", controller="cloudauthz", conditions=dict(method=["POST"])
+    )
 
-    webapp.mapper.connect('delete_cloudauthz_item',
-                          '/api/cloud/authz/{encoded_authz_id}',
-                          action='delete',
-                          controller='cloudauthz',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "delete_cloudauthz_item",
+        "/api/cloud/authz/{encoded_authz_id}",
+        action="delete",
+        controller="cloudauthz",
+        conditions=dict(method=["DELETE"]),
+    )
 
-    webapp.mapper.connect('upload_cloudauthz_item',
-                          '/api/cloud/authz/{encoded_authz_id}',
-                          action='update',
-                          controller="cloudauthz",
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "upload_cloudauthz_item",
+        "/api/cloud/authz/{encoded_authz_id}",
+        action="update",
+        controller="cloudauthz",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_custom_builds_metadata',
-                          '/api/histories/{id}/custom_builds_metadata',
-                          controller='histories',
-                          action='get_custom_builds_metadata',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_custom_builds_metadata",
+        "/api/histories/{id}/custom_builds_metadata",
+        controller="histories",
+        action="get_custom_builds_metadata",
+        conditions=dict(method=["GET"]),
+    )
 
     # =======================
     # ====== TOOLS API ======
     # =======================
 
-    webapp.mapper.connect('/api/tools/fetch', action='fetch', controller='tools', conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/tools/all_requirements', action='all_requirements', controller="tools")
-    webapp.mapper.connect('/api/tools/error_stack', action='error_stack', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/build', action='build', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/reload', action='reload', controller="tools")
-    webapp.mapper.connect('/api/tools/tests_summary', action='tests_summary', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/test_data_path', action='test_data_path', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/test_data_download', action='test_data_download', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/test_data', action='test_data', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/citations', action='citations', controller="tools")
-    webapp.mapper.connect('/api/tools/{tool_id:.+?}/convert', action='conversion', controller="tools", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/tools/{id:.+?}/xrefs', action='xrefs', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/download', action='download', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/raw_tool_source', action='raw_tool_source', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/requirements', action='requirements', controller="tools")
-    webapp.mapper.connect('/api/tools/{id:.+?}/install_dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/tools/{id:.+?}/dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/tools/{id:.+?}/dependencies', action='uninstall_dependencies', controller="tools", conditions=dict(method=["DELETE"]))
-    webapp.mapper.connect('/api/tools/{id:.+?}/build_dependency_cache', action='build_dependency_cache', controller="tools", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/tools/{id:.+?}', action='show', controller="tools")
-    webapp.mapper.resource('tool', 'tools', path_prefix='/api')
-    webapp.mapper.resource('dynamic_tools', 'dynamic_tools', path_prefix='/api')
-
-    webapp.mapper.connect('/api/sanitize_allow', action='index', controller='sanitize_allow', conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/sanitize_allow', action='create', controller='sanitize_allow', conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/sanitize_allow', action='delete', controller='sanitize_allow', conditions=dict(method=["DELETE"]))
-
-    webapp.mapper.connect('/api/entry_points', action='index', controller="tool_entry_points")
-    webapp.mapper.connect('/api/entry_points/{id:.+?}/access', action='access_entry_point', controller="tool_entry_points")
-    webapp.mapper.connect('/api/entry_points/{id:.+?}', action='stop_entry_point', controller="tool_entry_points", conditions={'method': ['DELETE']})
-
-    webapp.mapper.connect('/api/dependency_resolvers/clean', action="clean", controller="tool_dependencies", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/dependency_resolvers/dependency', action="manager_dependency", controller="tool_dependencies", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/dependency_resolvers/dependency', action="install_dependency", controller="tool_dependencies", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/dependency_resolvers/requirements', action="manager_requirements", controller="tool_dependencies")
-    webapp.mapper.connect('/api/dependency_resolvers/unused_paths', action="unused_dependency_paths", controller="tool_dependencies", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/dependency_resolvers/unused_paths', action="delete_unused_dependency_paths", controller="tool_dependencies", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/dependency_resolvers/toolbox', controller="tool_dependencies", action="summarize_toolbox", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/dependency_resolvers/toolbox/install', controller="tool_dependencies", action="toolbox_install", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/dependency_resolvers/toolbox/uninstall', controller="tool_dependencies", action="toolbox_uninstall", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/dependency_resolvers/{index}/clean', action="clean", controller="tool_dependencies", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/dependency_resolvers/{index}/dependency', action="resolver_dependency", controller="tool_dependencies", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/dependency_resolvers/{index}/dependency', action="install_dependency", controller="tool_dependencies", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/dependency_resolvers/{index}/requirements', action="resolver_requirements", controller="tool_dependencies")
-    webapp.mapper.resource('dependency_resolver', 'dependency_resolvers', controller="tool_dependencies", path_prefix='api')
-    webapp.mapper.connect('/api/container_resolvers', action="index", controller="container_resolution", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/container_resolvers/resolve', action="resolve", controller="container_resolution", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/container_resolvers/toolbox', action="resolve_toolbox", controller="container_resolution", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/container_resolvers/resolve/install', action="resolve_with_install", controller="container_resolution", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/container_resolvers/toolbox/install', action="resolve_toolbox_with_install", controller="container_resolution", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/container_resolvers/{index}', action="show", controller="container_resolution", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/container_resolvers/{index}/resolve', action="resolve", controller="container_resolution", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/container_resolvers/{index}/toolbox', action="resolve_toolbox", controller="container_resolution", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/container_resolvers/{index}/resolve/install', action="resolve_with_install", controller="container_resolution", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/container_resolvers/{index}/toolbox/install', action="resolve_toolbox_with_install", controller="container_resolution", conditions=dict(method=["POST"]))
-    webapp.mapper.connect('/api/workflows/get_tool_predictions', action='get_tool_predictions', controller="workflows", conditions=dict(method=["POST"]))
-
-    webapp.mapper.resource_with_deleted('user', 'users', path_prefix='/api')
-    webapp.mapper.resource('genome', 'genomes', path_prefix='/api')
-    webapp.mapper.connect('/api/genomes/{id}/indexes', controller='genomes', action='indexes')
-    webapp.mapper.connect('/api/genomes/{id}/sequences', controller='genomes', action='sequences')
-    webapp.mapper.resource('visualization', 'visualizations', path_prefix='/api')
-    webapp.mapper.connect('/api/visualizations/{id}/sharing', action='sharing', controller="visualizations", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/visualizations/{id}/enable_link_access', action='enable_link_access', controller="visualizations", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/visualizations/{id}/disable_link_access', action='disable_link_access', controller="visualizations", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/visualizations/{id}/publish', action='publish', controller="visualizations", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/visualizations/{id}/unpublish', action='unpublish', controller="visualizations", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/visualizations/{id}/share_with_users', action='share_with_users', controller="visualizations", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/visualizations/{id}/slug', action='set_slug', controller="visualizations", conditions=dict(method=["PUT"]))
-    webapp.mapper.resource('plugins', 'plugins', path_prefix='/api')
-    webapp.mapper.connect('/api/workflows/build_module', action='build_module', controller="workflows")
-    webapp.mapper.connect('/api/workflows/menu', action='get_workflow_menu', controller="workflows", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/workflows/menu', action='set_workflow_menu', controller="workflows", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/workflows/{id}/refactor', action='refactor', controller="workflows", conditions=dict(method=["PUT"]))
-    webapp.mapper.resource('workflow', 'workflows', path_prefix='/api')
-    webapp.mapper.connect('/api/licenses', controller='licenses', action='index', conditions=dict(method="GET"))
-    webapp.mapper.connect('/api/licenses/{id}', controller='licenses', action='get', conditions=dict(method="GET"))
-    webapp.mapper.resource_with_deleted('history', 'histories', path_prefix='/api')
-    webapp.mapper.connect('/api/histories/{history_id}/citations', action='citations', controller="histories")
-    webapp.mapper.connect('/api/histories/{id}/sharing', action='sharing', controller="histories", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/histories/{id}/enable_link_access', action='enable_link_access', controller="histories", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/histories/{id}/disable_link_access', action='disable_link_access', controller="histories", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/histories/{id}/publish', action='publish', controller="histories", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/histories/{id}/unpublish', action='unpublish', controller="histories", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/histories/{id}/share_with_users', action='share_with_users', controller="histories", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/histories/{id}/slug', action='set_slug', controller="histories", conditions=dict(method=["PUT"]))
+    webapp.mapper.connect("/api/tools/fetch", action="fetch", controller="tools", conditions=dict(method=["POST"]))
+    webapp.mapper.connect("/api/tools/all_requirements", action="all_requirements", controller="tools")
+    webapp.mapper.connect("/api/tools/error_stack", action="error_stack", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/build", action="build", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/reload", action="reload", controller="tools")
+    webapp.mapper.connect("/api/tools/tests_summary", action="tests_summary", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/test_data_path", action="test_data_path", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/test_data_download", action="test_data_download", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/test_data", action="test_data", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/diagnostics", action="diagnostics", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/citations", action="citations", controller="tools")
     webapp.mapper.connect(
-        'dynamic_tool_confs',
-        '/api/configuration/dynamic_tool_confs',
-        controller="configuration",
-        action="dynamic_tool_confs"
+        "/api/tools/{tool_id:.+?}/convert", action="conversion", controller="tools", conditions=dict(method=["POST"])
+    )
+    webapp.mapper.connect("/api/tools/{id:.+?}/xrefs", action="xrefs", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/download", action="download", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/raw_tool_source", action="raw_tool_source", controller="tools")
+    webapp.mapper.connect("/api/tools/{id:.+?}/requirements", action="requirements", controller="tools")
+    webapp.mapper.connect(
+        "/api/tools/{id:.+?}/install_dependencies",
+        action="install_dependencies",
+        controller="tools",
+        conditions=dict(method=["POST"]),
     )
     webapp.mapper.connect(
-        'tool_lineages',
-        '/api/configuration/tool_lineages',
-        controller="configuration",
-        action="tool_lineages"
+        "/api/tools/{id:.+?}/dependencies",
+        action="install_dependencies",
+        controller="tools",
+        conditions=dict(method=["POST"]),
     )
     webapp.mapper.connect(
-        '/api/configuration/toolbox',
+        "/api/tools/{id:.+?}/dependencies",
+        action="uninstall_dependencies",
+        controller="tools",
+        conditions=dict(method=["DELETE"]),
+    )
+    webapp.mapper.connect(
+        "/api/tools/{id:.+?}/build_dependency_cache",
+        action="build_dependency_cache",
+        controller="tools",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect("/api/tools/{id:.+?}", action="show", controller="tools")
+    webapp.mapper.resource("tool", "tools", path_prefix="/api")
+    webapp.mapper.resource("dynamic_tools", "dynamic_tools", path_prefix="/api")
+
+    webapp.mapper.connect(
+        "/api/sanitize_allow", action="index", controller="sanitize_allow", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "/api/sanitize_allow", action="create", controller="sanitize_allow", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "/api/sanitize_allow", action="delete", controller="sanitize_allow", conditions=dict(method=["DELETE"])
+    )
+
+    webapp.mapper.connect("/api/entry_points", action="index", controller="tool_entry_points")
+    webapp.mapper.connect(
+        "/api/entry_points/{id:.+?}/access", action="access_entry_point", controller="tool_entry_points"
+    )
+    webapp.mapper.connect(
+        "/api/entry_points/{id:.+?}",
+        action="stop_entry_point",
+        controller="tool_entry_points",
+        conditions={"method": ["DELETE"]},
+    )
+
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/clean",
+        action="clean",
+        controller="tool_dependencies",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/dependency",
+        action="manager_dependency",
+        controller="tool_dependencies",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/dependency",
+        action="install_dependency",
+        controller="tool_dependencies",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/requirements", action="manager_requirements", controller="tool_dependencies"
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/unused_paths",
+        action="unused_dependency_paths",
+        controller="tool_dependencies",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/unused_paths",
+        action="delete_unused_dependency_paths",
+        controller="tool_dependencies",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/toolbox",
+        controller="tool_dependencies",
+        action="summarize_toolbox",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/toolbox/install",
+        controller="tool_dependencies",
+        action="toolbox_install",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/toolbox/uninstall",
+        controller="tool_dependencies",
+        action="toolbox_uninstall",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/{index}/clean",
+        action="clean",
+        controller="tool_dependencies",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/{index}/dependency",
+        action="resolver_dependency",
+        controller="tool_dependencies",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/{index}/dependency",
+        action="install_dependency",
+        controller="tool_dependencies",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/dependency_resolvers/{index}/requirements", action="resolver_requirements", controller="tool_dependencies"
+    )
+    webapp.mapper.resource(
+        "dependency_resolver", "dependency_resolvers", controller="tool_dependencies", path_prefix="api"
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers", action="index", controller="container_resolution", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/resolve",
+        action="resolve",
+        controller="container_resolution",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/toolbox",
+        action="resolve_toolbox",
+        controller="container_resolution",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/resolve/install",
+        action="resolve_with_install",
+        controller="container_resolution",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/toolbox/install",
+        action="resolve_toolbox_with_install",
+        controller="container_resolution",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/{index}",
+        action="show",
+        controller="container_resolution",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/{index}/resolve",
+        action="resolve",
+        controller="container_resolution",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/{index}/toolbox",
+        action="resolve_toolbox",
+        controller="container_resolution",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/{index}/resolve/install",
+        action="resolve_with_install",
+        controller="container_resolution",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/container_resolvers/{index}/toolbox/install",
+        action="resolve_toolbox_with_install",
+        controller="container_resolution",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "/api/workflows/get_tool_predictions",
+        action="get_tool_predictions",
+        controller="workflows",
+        conditions=dict(method=["POST"]),
+    )
+
+    webapp.mapper.resource_with_deleted("user", "users", path_prefix="/api")
+    webapp.mapper.resource("genome", "genomes", path_prefix="/api")
+    webapp.mapper.connect("/api/genomes/{id}/indexes", controller="genomes", action="indexes")
+    webapp.mapper.connect("/api/genomes/{id}/sequences", controller="genomes", action="sequences")
+    webapp.mapper.resource("visualization", "visualizations", path_prefix="/api")
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/sharing",
+        action="sharing",
+        controller="visualizations",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/enable_link_access",
+        action="enable_link_access",
+        controller="visualizations",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/disable_link_access",
+        action="disable_link_access",
+        controller="visualizations",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/publish",
+        action="publish",
+        controller="visualizations",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/unpublish",
+        action="unpublish",
+        controller="visualizations",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/share_with_users",
+        action="share_with_users",
+        controller="visualizations",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/visualizations/{id}/slug", action="set_slug", controller="visualizations", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.resource("plugins", "plugins", path_prefix="/api")
+    webapp.mapper.connect("/api/workflows/build_module", action="build_module", controller="workflows")
+    webapp.mapper.connect(
+        "/api/workflows/menu", action="get_workflow_menu", controller="workflows", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "/api/workflows/menu", action="set_workflow_menu", controller="workflows", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "/api/workflows/{id}/refactor", action="refactor", controller="workflows", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.resource("workflow", "workflows", path_prefix="/api")
+    webapp.mapper.connect("/api/licenses", controller="licenses", action="index", conditions=dict(method="GET"))
+    webapp.mapper.connect("/api/licenses/{id}", controller="licenses", action="get", conditions=dict(method="GET"))
+    webapp.mapper.resource_with_deleted("history", "histories", path_prefix="/api")
+    webapp.mapper.connect("/api/histories/{history_id}/citations", action="citations", controller="histories")
+    webapp.mapper.connect(
+        "/api/histories/{id}/sharing", action="sharing", controller="histories", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "/api/histories/{id}/enable_link_access",
+        action="enable_link_access",
+        controller="histories",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/histories/{id}/disable_link_access",
+        action="disable_link_access",
+        controller="histories",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/histories/{id}/publish", action="publish", controller="histories", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "/api/histories/{id}/unpublish", action="unpublish", controller="histories", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "/api/histories/{id}/share_with_users",
+        action="share_with_users",
+        controller="histories",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/histories/{id}/slug", action="set_slug", controller="histories", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "dynamic_tool_confs",
+        "/api/configuration/dynamic_tool_confs",
+        controller="configuration",
+        action="dynamic_tool_confs",
+    )
+    webapp.mapper.connect(
+        "tool_lineages", "/api/configuration/tool_lineages", controller="configuration", action="tool_lineages"
+    )
+    webapp.mapper.connect(
+        "/api/configuration/toolbox",
         controller="configuration",
         action="reload_toolbox",
-        conditions=dict(method=["PUT"])
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.resource("configuration", "configuration", path_prefix="/api")
+    webapp.mapper.connect(
+        "configuration_version",
+        "/api/version",
+        controller="configuration",
+        action="version",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "api_whoami", "/api/whoami", controller="configuration", action="whoami", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "api_decode",
+        "/api/configuration/decode/{encoded_id}",
+        controller="configuration",
+        action="decode_id",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.resource(
+        "datatype",
+        "datatypes",
+        path_prefix="/api",
+        collection={
+            "sniffers": "GET",
+            "mapping": "GET",
+            "converters": "GET",
+            "edam_data": "GET",
+            "edam_formats": "GET",
+            "types_and_mapping": "GET",
+        },
+        parent_resources=dict(member_name="datatype", collection_name="datatypes"),
+    )
+    webapp.mapper.resource("search", "search", path_prefix="/api")
+    webapp.mapper.connect("/api/pages/{id}.pdf", action="show_pdf", controller="pages", conditions=dict(method=["GET"]))
+    webapp.mapper.resource("page", "pages", path_prefix="/api")
+    webapp.mapper.connect(
+        "/api/pages/{id}/sharing", action="sharing", controller="pages", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "/api/pages/{id}/enable_link_access",
+        action="enable_link_access",
+        controller="pages",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/pages/{id}/disable_link_access",
+        action="disable_link_access",
+        controller="pages",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/pages/{id}/publish", action="publish", controller="pages", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "/api/pages/{id}/unpublish", action="unpublish", controller="pages", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "/api/pages/{id}/share_with_users",
+        action="share_with_users",
+        controller="pages",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "/api/pages/{id}/slug", action="set_slug", controller="pages", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.resource(
+        "revision",
+        "revisions",
+        path_prefix="/api/pages/{page_id}",
+        controller="page_revisions",
+        parent_resources=dict(member_name="page", collection_name="pages"),
     )
-    webapp.mapper.resource('configuration', 'configuration', path_prefix='/api')
-    webapp.mapper.connect("configuration_version",
-                          "/api/version", controller="configuration",
-                          action="version", conditions=dict(method=["GET"]))
-    webapp.mapper.connect("api_whoami",
-                          "/api/whoami", controller='configuration',
-                          action='whoami',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("api_decode",
-                          "/api/configuration/decode/{encoded_id}", controller='configuration',
-                          action='decode_id',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.resource('datatype',
-                           'datatypes',
-                           path_prefix='/api',
-                           collection={'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET', 'edam_data': 'GET', 'edam_formats': 'GET', 'types_and_mapping': 'GET'},
-                           parent_resources=dict(member_name='datatype', collection_name='datatypes'))
-    webapp.mapper.resource('search', 'search', path_prefix='/api')
-    webapp.mapper.connect('/api/pages/{id}.pdf', action='show_pdf', controller="pages", conditions=dict(method=["GET"]))
-    webapp.mapper.resource('page', 'pages', path_prefix="/api")
-    webapp.mapper.connect('/api/pages/{id}/sharing', action='sharing', controller="pages", conditions=dict(method=["GET"]))
-    webapp.mapper.connect('/api/pages/{id}/enable_link_access', action='enable_link_access', controller="pages", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/pages/{id}/disable_link_access', action='disable_link_access', controller="pages", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/pages/{id}/publish', action='publish', controller="pages", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/pages/{id}/unpublish', action='unpublish', controller="pages", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/pages/{id}/share_with_users', action='share_with_users', controller="pages", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect('/api/pages/{id}/slug', action='set_slug', controller="pages", conditions=dict(method=["PUT"]))
-    webapp.mapper.resource('revision', 'revisions',
-                           path_prefix='/api/pages/{page_id}',
-                           controller='page_revisions',
-                           parent_resources=dict(member_name='page', collection_name='pages'))
 
-    webapp.mapper.connect("history_exports",
-                          "/api/histories/{id}/exports", controller="histories",
-                          action="index_exports", conditions=dict(method=["GET"]))
-    webapp.mapper.connect("history_archive_export",
-                          "/api/histories/{id}/exports", controller="histories",
-                          action="archive_export", conditions=dict(method=["PUT"]))
-    webapp.mapper.connect("history_archive_download",
-                          "/api/histories/{id}/exports/{jeha_id}", controller="histories",
-                          action="archive_download", conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "history_exports",
+        "/api/histories/{id}/exports",
+        controller="histories",
+        action="index_exports",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "history_archive_export",
+        "/api/histories/{id}/exports",
+        controller="histories",
+        action="archive_export",
+        conditions=dict(method=["PUT"]),
+    )
+    webapp.mapper.connect(
+        "history_archive_download",
+        "/api/histories/{id}/exports/{jeha_id}",
+        controller="histories",
+        action="archive_download",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('/api/histories/{history_id}/contents/archive',
-                          controller='history_contents', action='archive')
-    webapp.mapper.connect('/api/histories/{history_id}/contents/archive/{filename}{.format}',
-                          controller='history_contents', action='archive')
-    webapp.mapper.connect("/api/histories/{history_id}/contents/dataset_collections/{id}/download",
-                          controller='history_contents',
-                          action='download_dataset_collection',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("/api/dataset_collections/{id}/download",
-                          controller='history_contents',
-                          action='download_dataset_collection',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "/api/histories/{history_id}/contents/archive", controller="history_contents", action="archive"
+    )
+    webapp.mapper.connect(
+        "/api/histories/{history_id}/contents/archive/{filename}{.format}",
+        controller="history_contents",
+        action="archive",
+    )
+    webapp.mapper.connect(
+        "/api/histories/{history_id}/contents/dataset_collections/{id}/download",
+        controller="history_contents",
+        action="download_dataset_collection",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "/api/dataset_collections/{id}/download",
+        controller="history_contents",
+        action="download_dataset_collection",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect("/api/dataset_collections/{id}/copy",
-                          controller='dataset_collections',
-                          action='update',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "/api/dataset_collections/{id}/copy",
+        controller="dataset_collections",
+        action="update",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect("/api/dataset_collections/{id}/attributes",
-                          controller='dataset_collections',
-                          action='attributes',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "/api/dataset_collections/{id}/attributes",
+        controller="dataset_collections",
+        action="attributes",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect("api_suitable_converters",
-                          "/api/dataset_collections/{id}/suitable_converters",
-                          controller='dataset_collections',
-                          action='suitable_converters',
-                          conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "api_suitable_converters",
+        "/api/dataset_collections/{id}/suitable_converters",
+        controller="dataset_collections",
+        action="suitable_converters",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect("/api/histories/{history_id}/jobs_summary",
-                          action="index_jobs_summary",
-                          controller='history_contents',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "/api/histories/{history_id}/jobs_summary",
+        action="index_jobs_summary",
+        controller="history_contents",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect("/api/histories/{history_id}/contents/{type:%s}s/{id}/jobs_summary" % "|".join(valid_history_contents_types),
-                          action="show_jobs_summary",
-                          controller='history_contents',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "/api/histories/{history_id}/contents/{type:%s}s/{id}/jobs_summary" % "|".join(valid_history_contents_types),
+        action="show_jobs_summary",
+        controller="history_contents",
+        conditions=dict(method=["GET"]),
+    )
     # ---- visualizations registry ---- generic template renderer
     # @deprecated: this route should be considered deprecated
-    webapp.add_route('/visualization/show/{visualization_name}', controller='visualization', action='render', visualization_name=None)
+    webapp.add_route(
+        "/visualization/show/{visualization_name}", controller="visualization", action="render", visualization_name=None
+    )
 
     # provide an alternate route to visualization plugins that's closer to their static assets
     # (/plugins/visualizations/{visualization_name}/static) and allow them to use relative urls to those
-    webapp.mapper.connect('visualization_plugin', '/plugins/visualizations/{visualization_name}/show',
-        controller='visualization', action='render')
-    webapp.mapper.connect('saved_visualization', '/plugins/visualizations/{visualization_name}/saved',
-        controller='visualization', action='saved')
+    webapp.mapper.connect(
+        "visualization_plugin",
+        "/plugins/visualizations/{visualization_name}/show",
+        controller="visualization",
+        action="render",
+    )
+    webapp.mapper.connect(
+        "saved_visualization",
+        "/plugins/visualizations/{visualization_name}/saved",
+        controller="visualization",
+        action="saved",
+    )
     # same with IE's
-    webapp.mapper.connect('interactive_environment_plugin', '/plugins/interactive_environments/{visualization_name}/show',
-        controller='visualization', action='render')
-    webapp.mapper.connect('saved_interactive_environment', '/plugins/interactive_environments/{visualization_name}/saved',
-        controller='visualization', action='saved')
+    webapp.mapper.connect(
+        "interactive_environment_plugin",
+        "/plugins/interactive_environments/{visualization_name}/show",
+        controller="visualization",
+        action="render",
+    )
+    webapp.mapper.connect(
+        "saved_interactive_environment",
+        "/plugins/interactive_environments/{visualization_name}/saved",
+        controller="visualization",
+        action="saved",
+    )
 
     # Deprecated in favor of POST /api/workflows with 'workflow' in payload.
-    webapp.mapper.connect('import_workflow_deprecated',
-                          '/api/workflows/upload',
-                          controller='workflows',
-                          action='import_new_workflow_deprecated',
-                          conditions=dict(method=['POST']))
-    webapp.mapper.connect('workflow_dict',
-                          '/api/workflows/{workflow_id}/download',
-                          controller='workflows',
-                          action='workflow_dict',
-                          conditions=dict(method=['GET']))
-    webapp.mapper.connect('show_versions',
-                          '/api/workflows/{workflow_id}/versions',
-                          controller='workflows',
-                          action='show_versions',
-                          conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "import_workflow_deprecated",
+        "/api/workflows/upload",
+        controller="workflows",
+        action="import_new_workflow_deprecated",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "workflow_dict",
+        "/api/workflows/{workflow_id}/download",
+        controller="workflows",
+        action="workflow_dict",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "show_versions",
+        "/api/workflows/{workflow_id}/versions",
+        controller="workflows",
+        action="show_versions",
+        conditions=dict(method=["GET"]),
+    )
     # Preserve the following download route for now for dependent applications  -- deprecate at some point
-    webapp.mapper.connect('workflow_dict',
-                          '/api/workflows/download/{workflow_id}',
-                          controller='workflows',
-                          action='workflow_dict',
-                          conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "workflow_dict",
+        "/api/workflows/download/{workflow_id}",
+        controller="workflows",
+        action="workflow_dict",
+        conditions=dict(method=["GET"]),
+    )
     # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload.
-    webapp.mapper.connect('import_shared_workflow_deprecated',
-                          '/api/workflows/import',
-                          controller='workflows',
-                          action='import_shared_workflow_deprecated',
-                          conditions=dict(method=['POST']))
+    webapp.mapper.connect(
+        "import_shared_workflow_deprecated",
+        "/api/workflows/import",
+        controller="workflows",
+        action="import_shared_workflow_deprecated",
+        conditions=dict(method=["POST"]),
+    )
 
     webapp.mapper.connect(
-        'trs_search',
-        '/api/trs_search',
-        controller='trs_search',
-        action="index",
-        conditions=dict(method=['GET'])
+        "trs_search", "/api/trs_search", controller="trs_search", action="index", conditions=dict(method=["GET"])
     )
     webapp.mapper.connect(
-        'trs_consume_get_servers',
-        '/api/trs_consume/servers',
-        controller='trs_consumer',
+        "trs_consume_get_servers",
+        "/api/trs_consume/servers",
+        controller="trs_consumer",
         action="get_servers",
-        conditions=dict(method=['GET'])
+        conditions=dict(method=["GET"]),
     )
     webapp.mapper.connect(
-        'trs_consume_get_tool',
-        '/api/trs_consume/{trs_server}/tools/{tool_id}',
-        controller='trs_consumer',
+        "trs_consume_get_tool",
+        "/api/trs_consume/{trs_server}/tools/{tool_id}",
+        controller="trs_consumer",
         action="get_tool",
-        conditions=dict(method=['GET'])
+        conditions=dict(method=["GET"]),
     )
     webapp.mapper.connect(
-        'trs_consume_get_tool_versions',
-        '/api/trs_consume/{trs_server}/tools/{tool_id}/versions',
-        controller='trs_consumer',
+        "trs_consume_get_tool_versions",
+        "/api/trs_consume/{trs_server}/tools/{tool_id}/versions",
+        controller="trs_consumer",
         action="get_tool_versions",
-        conditions=dict(method=['GET'])
+        conditions=dict(method=["GET"]),
     )
     webapp.mapper.connect(
-        'trs_consume_get_tool_version',
-        '/api/trs_consume/{trs_server}/tools/{tool_id}/versions/{version_id}',
-        controller='trs_consumer',
+        "trs_consume_get_tool_version",
+        "/api/trs_consume/{trs_server}/tools/{tool_id}/versions/{version_id}",
+        controller="trs_consumer",
         action="get_tool_version",
-        conditions=dict(method=['GET'])
+        conditions=dict(method=["GET"]),
     )
     webapp.mapper.connect(
-        'trs_consume_import_tool_version',
-        '/api/trs_consume/{trs_server}/tools/{tool_id}/versions/{version_id}/import',
-        controller='trs_consumer',
+        "trs_consume_import_tool_version",
+        "/api/trs_consume/{trs_server}/tools/{tool_id}/versions/{version_id}/import",
+        controller="trs_consumer",
         action="import_tool_version",
-        conditions=dict(method=['POST'])
+        conditions=dict(method=["POST"]),
     )
 
     # route for creating/getting converted datasets
-    webapp.mapper.connect('/api/datasets/{dataset_id}/converted', controller='datasets', action='converted', ext=None)
-    webapp.mapper.connect('/api/datasets/{dataset_id}/converted/{ext}', controller='datasets', action='converted')
-    webapp.mapper.connect('/api/datasets/{dataset_id}/permissions', controller='datasets', action='update_permissions', conditions=dict(method=["PUT"]))
+    webapp.mapper.connect("/api/datasets/{dataset_id}/converted", controller="datasets", action="converted", ext=None)
+    webapp.mapper.connect("/api/datasets/{dataset_id}/converted/{ext}", controller="datasets", action="converted")
+    webapp.mapper.connect(
+        "/api/datasets/{dataset_id}/permissions",
+        controller="datasets",
+        action="update_permissions",
+        conditions=dict(method=["PUT"]),
+    )
 
     webapp.mapper.connect(
-        'list_invocations',
-        '/api/invocations',
-        controller='workflows',
-        action='index_invocations',
-        conditions=dict(method=['GET'])
+        "list_invocations",
+        "/api/invocations",
+        controller="workflows",
+        action="index_invocations",
+        conditions=dict(method=["GET"]),
     )
 
     # API refers to usages and invocations - these mean the same thing but the
@@ -706,551 +1116,712 @@ def populate_api_routes(webapp, app):
     for noun, suffix in invoke_names.items():
         name = f"{noun}{suffix}"
         webapp.mapper.connect(
-            f'list_workflow_{name}',
-            '/api/workflows/{workflow_id}/%s' % noun,
-            controller='workflows',
-            action='index_invocations',
-            conditions=dict(method=['GET'])
+            f"list_workflow_{name}",
+            "/api/workflows/{workflow_id}/%s" % noun,
+            controller="workflows",
+            action="index_invocations",
+            conditions=dict(method=["GET"]),
         )
         webapp.mapper.connect(
-            f'workflow_{name}',
-            '/api/workflows/{workflow_id}/%s' % noun,
-            controller='workflows',
-            action='invoke',
-            conditions=dict(method=['POST'])
+            f"workflow_{name}",
+            "/api/workflows/{workflow_id}/%s" % noun,
+            controller="workflows",
+            action="invoke",
+            conditions=dict(method=["POST"]),
         )
 
     def connect_invocation_endpoint(endpoint_name, endpoint_suffix, action, conditions=None):
         # /api/invocations/<invocation_id>
         # /api/workflows/<workflow_id>/invocations/<invocation_id>
         # /api/workflows/<workflow_id>/usage/<invocation_id> (deprecated)
-        conditions = conditions or dict(method=['GET'])
+        conditions = conditions or dict(method=["GET"])
         webapp.mapper.connect(
-            f'workflow_invocation_{endpoint_name}',
+            f"workflow_invocation_{endpoint_name}",
             f"/api/workflows/{{workflow_id}}/invocations/{{invocation_id}}{endpoint_suffix}",
-            controller='workflows',
+            controller="workflows",
             action=action,
             conditions=conditions,
         )
         webapp.mapper.connect(
-            f'workflow_usage_{endpoint_name}',
+            f"workflow_usage_{endpoint_name}",
             f"/api/workflows/{{workflow_id}}/usage/{{invocation_id}}{endpoint_suffix}",
-            controller='workflows',
+            controller="workflows",
             action=action,
             conditions=conditions,
         )
         webapp.mapper.connect(
-            f'invocation_{endpoint_name}',
+            f"invocation_{endpoint_name}",
             f"/api/invocations/{{invocation_id}}{endpoint_suffix}",
-            controller='workflows',
+            controller="workflows",
             action=action,
             conditions=conditions,
         )
 
-    connect_invocation_endpoint('show', '', action='show_invocation')
-    connect_invocation_endpoint('show_report', '/report', action='show_invocation_report')
-    connect_invocation_endpoint('show_report_pdf', '/report.pdf', action='show_invocation_report_pdf')
-    connect_invocation_endpoint('biocompute/download', '/biocompute/download', action='download_invocation_bco')
-    connect_invocation_endpoint('biocompute', '/biocompute', action='export_invocation_bco')
-    connect_invocation_endpoint('jobs_summary', '/jobs_summary', action='invocation_jobs_summary')
-    connect_invocation_endpoint('step_jobs_summary', '/step_jobs_summary', action='invocation_step_jobs_summary')
-    connect_invocation_endpoint('cancel', '', action='cancel_invocation', conditions=dict(method=['DELETE']))
-    connect_invocation_endpoint('show_step', '/steps/{step_id}', action='invocation_step')
-    connect_invocation_endpoint('update_step', '/steps/{step_id}', action='update_invocation_step', conditions=dict(method=['PUT']))
+    connect_invocation_endpoint("show", "", action="show_invocation")
+    connect_invocation_endpoint("show_report", "/report", action="show_invocation_report")
+    connect_invocation_endpoint("show_report_pdf", "/report.pdf", action="show_invocation_report_pdf")
+    connect_invocation_endpoint("biocompute/download", "/biocompute/download", action="download_invocation_bco")
+    connect_invocation_endpoint("biocompute", "/biocompute", action="export_invocation_bco")
+    connect_invocation_endpoint("jobs_summary", "/jobs_summary", action="invocation_jobs_summary")
+    connect_invocation_endpoint("step_jobs_summary", "/step_jobs_summary", action="invocation_step_jobs_summary")
+    connect_invocation_endpoint("cancel", "", action="cancel_invocation", conditions=dict(method=["DELETE"]))
+    connect_invocation_endpoint("show_step", "/steps/{step_id}", action="invocation_step")
+    connect_invocation_endpoint(
+        "update_step", "/steps/{step_id}", action="update_invocation_step", conditions=dict(method=["PUT"])
+    )
 
     # ============================
     # ===== AUTHENTICATE API =====
     # ============================
 
-    webapp.mapper.connect('api_key_retrieval',
-                          '/api/authenticate/baseauth/',
-                          controller='authenticate',
-                          action='get_api_key',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "api_key_retrieval",
+        "/api/authenticate/baseauth/",
+        controller="authenticate",
+        action="get_api_key",
+        conditions=dict(method=["GET"]),
+    )
 
     # ======================================
     # ====== DISPLAY APPLICATIONS API ======
     # ======================================
 
-    webapp.mapper.connect('index',
-                          '/api/display_applications',
-                          controller='display_applications',
-                          action='index',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "index",
+        "/api/display_applications",
+        controller="display_applications",
+        action="index",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('reload',
-                          '/api/display_applications/reload',
-                          controller='display_applications',
-                          action='reload',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "reload",
+        "/api/display_applications/reload",
+        controller="display_applications",
+        action="reload",
+        conditions=dict(method=["POST"]),
+    )
 
     # =====================
     # ===== TOURS API =====
     # =====================
 
-    webapp.mapper.connect('index',
-                          '/api/tours',
-                          controller='tours',
-                          action='index',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect("index", "/api/tours", controller="tours", action="index", conditions=dict(method=["GET"]))
 
-    webapp.mapper.connect('show',
-                          '/api/tours/{tour_id}',
-                          controller='tours',
-                          action='show',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "show", "/api/tours/{tour_id}", controller="tours", action="show", conditions=dict(method=["GET"])
+    )
 
-    webapp.mapper.connect('update_tour',
-                          '/api/tours/{tour_id}',
-                          controller='tours',
-                          action='update_tour',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "update_tour",
+        "/api/tours/{tour_id}",
+        controller="tours",
+        action="update_tour",
+        conditions=dict(method=["POST"]),
+    )
 
     # ================================
     # ===== USERS API =====
     # ================================
 
-    webapp.mapper.connect('api_key',
-                          '/api/users/{id}/api_key',
-                          controller='users',
-                          action='api_key',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "api_key", "/api/users/{id}/api_key", controller="users", action="api_key", conditions=dict(method=["POST"])
+    )
 
-    webapp.mapper.connect('api_key',
-                          '/api/users/{id}/api_key',
-                          controller='users',
-                          action='get_or_create_api_key',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "api_key",
+        "/api/users/{id}/api_key",
+        controller="users",
+        action="get_or_create_api_key",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('get_api_key',
-                          '/api/users/{id}/api_key/inputs',
-                          controller='users',
-                          action='get_api_key',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_api_key",
+        "/api/users/{id}/api_key/inputs",
+        controller="users",
+        action="get_api_key",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_api_key',
-                          '/api/users/{id}/api_key/inputs',
-                          controller='users',
-                          action='set_api_key',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_api_key",
+        "/api/users/{id}/api_key/inputs",
+        controller="users",
+        action="set_api_key",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_information',
-                          '/api/users/{id}/information/inputs',
-                          controller='users',
-                          action='get_information',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_information",
+        "/api/users/{id}/information/inputs",
+        controller="users",
+        action="get_information",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_information',
-                          '/api/users/{id}/information/inputs',
-                          controller='users',
-                          action='set_information',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_information",
+        "/api/users/{id}/information/inputs",
+        controller="users",
+        action="set_information",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_password',
-                          '/api/users/{id}/password/inputs',
-                          controller='users',
-                          action='get_password',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_password",
+        "/api/users/{id}/password/inputs",
+        controller="users",
+        action="get_password",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_password',
-                          '/api/users/{id}/password/inputs',
-                          controller='users',
-                          action='set_password',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_password",
+        "/api/users/{id}/password/inputs",
+        controller="users",
+        action="set_password",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_permissions',
-                          '/api/users/{id}/permissions/inputs',
-                          controller='users',
-                          action='get_permissions',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_permissions",
+        "/api/users/{id}/permissions/inputs",
+        controller="users",
+        action="get_permissions",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_permissions',
-                          '/api/users/{id}/permissions/inputs',
-                          controller='users',
-                          action='set_permissions',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_permissions",
+        "/api/users/{id}/permissions/inputs",
+        controller="users",
+        action="set_permissions",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_toolbox_filters',
-                          '/api/users/{id}/toolbox_filters/inputs',
-                          controller='users',
-                          action='get_toolbox_filters',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_toolbox_filters",
+        "/api/users/{id}/toolbox_filters/inputs",
+        controller="users",
+        action="get_toolbox_filters",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_toolbox_filters',
-                          '/api/users/{id}/toolbox_filters/inputs',
-                          controller='users',
-                          action='set_toolbox_filters',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_toolbox_filters",
+        "/api/users/{id}/toolbox_filters/inputs",
+        controller="users",
+        action="set_toolbox_filters",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_communication',
-                          '/api/users/{id}/communication/inputs',
-                          controller='users',
-                          action='get_communication',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_communication",
+        "/api/users/{id}/communication/inputs",
+        controller="users",
+        action="get_communication",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_communication',
-                          '/api/users/{id}/communication/inputs',
-                          controller='users',
-                          action='set_communication',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_communication",
+        "/api/users/{id}/communication/inputs",
+        controller="users",
+        action="set_communication",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('get_custom_builds',
-                          '/api/users/{id}/custom_builds',
-                          controller='users',
-                          action='get_custom_builds',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "get_custom_builds",
+        "/api/users/{id}/custom_builds",
+        controller="users",
+        action="get_custom_builds",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('add_custom_builds',
-                          '/api/users/{id}/custom_builds/{key}',
-                          controller='users',
-                          action='add_custom_builds',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "add_custom_builds",
+        "/api/users/{id}/custom_builds/{key}",
+        controller="users",
+        action="add_custom_builds",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('delete_custom_builds',
-                          '/api/users/{id}/custom_builds/{key}',
-                          controller='users',
-                          action='delete_custom_builds',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "delete_custom_builds",
+        "/api/users/{id}/custom_builds/{key}",
+        controller="users",
+        action="delete_custom_builds",
+        conditions=dict(method=["DELETE"]),
+    )
 
-    webapp.mapper.connect('set_favorite_tool',
-                          '/api/users/{id}/favorites/{object_type}',
-                          controller='users',
-                          action='set_favorite',
-                          conditions=dict(method=["PUT"]))
+    webapp.mapper.connect(
+        "set_favorite_tool",
+        "/api/users/{id}/favorites/{object_type}",
+        controller="users",
+        action="set_favorite",
+        conditions=dict(method=["PUT"]),
+    )
 
-    webapp.mapper.connect('remove_favorite_tool',
-                          '/api/users/{id}/favorites/{object_type}/{object_id:.*?}',
-                          controller='users',
-                          action='remove_favorite',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "remove_favorite_tool",
+        "/api/users/{id}/favorites/{object_type}/{object_id:.*?}",
+        controller="users",
+        action="remove_favorite",
+        conditions=dict(method=["DELETE"]),
+    )
 
     # ========================
     # ===== WEBHOOKS API =====
     # ========================
 
-    webapp.mapper.connect('get_all_webhooks',
-                          '/api/webhooks',
-                          controller='webhooks',
-                          action='all_webhooks',
-                          conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "get_all_webhooks",
+        "/api/webhooks",
+        controller="webhooks",
+        action="all_webhooks",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('get_webhook_data',
-                          '/api/webhooks/{webhook_id}/data',
-                          controller='webhooks',
-                          action='webhook_data',
-                          conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "get_webhook_data",
+        "/api/webhooks/{webhook_id}/data",
+        controller="webhooks",
+        action="webhook_data",
+        conditions=dict(method=["GET"]),
+    )
 
     # ====================
     # ===== TAGS API =====
     # ====================
 
-    webapp.mapper.connect('update_tags',
-                          '/api/tags',
-                          controller='tags',
-                          action='update',
-                          conditions=dict(method=['PUT']))
+    webapp.mapper.connect(
+        "update_tags", "/api/tags", controller="tags", action="update", conditions=dict(method=["PUT"])
+    )
 
     # =======================
     # ===== LIBRARY API =====
     # =======================
 
-    webapp.mapper.connect('update_library',
-                          '/api/libraries/{id}',
-                          controller='libraries',
-                          action='update',
-                          conditions=dict(method=["PATCH", "PUT"]))
+    webapp.mapper.connect(
+        "update_library",
+        "/api/libraries/{id}",
+        controller="libraries",
+        action="update",
+        conditions=dict(method=["PATCH", "PUT"]),
+    )
 
-    webapp.mapper.connect('show_library_permissions',
-                          '/api/libraries/{encoded_library_id}/permissions',
-                          controller='libraries',
-                          action='get_permissions',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "show_library_permissions",
+        "/api/libraries/{encoded_library_id}/permissions",
+        controller="libraries",
+        action="get_permissions",
+        conditions=dict(method=["GET"]),
+    )
 
     # POST for legacy reasons, but this should be a PUT.
-    webapp.mapper.connect('set_library_permissions',
-                          '/api/libraries/{encoded_library_id}/permissions',
-                          controller='libraries',
-                          action='set_permissions',
-                          conditions=dict(method=["POST", "PUT"]))
+    webapp.mapper.connect(
+        "set_library_permissions",
+        "/api/libraries/{encoded_library_id}/permissions",
+        controller="libraries",
+        action="set_permissions",
+        conditions=dict(method=["POST", "PUT"]),
+    )
 
-    webapp.mapper.connect('show_ld_item',
-                          '/api/libraries/datasets/{id}',
-                          controller='library_datasets',
-                          action='show',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "show_ld_item",
+        "/api/libraries/datasets/{id}",
+        controller="library_datasets",
+        action="show",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('load_ld',
-                          '/api/libraries/datasets/',
-                          controller='library_datasets',
-                          action='load',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "load_ld",
+        "/api/libraries/datasets/",
+        controller="library_datasets",
+        action="load",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect('show_version_of_ld_item',
-                          '/api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}',
-                          controller='library_datasets',
-                          action='show_version',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "show_version_of_ld_item",
+        "/api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}",
+        controller="library_datasets",
+        action="show_version",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('update_ld',
-                          '/api/libraries/datasets/{encoded_dataset_id}',
-                          controller='library_datasets',
-                          action='update',
-                          conditions=dict(method=["PATCH"]))
+    webapp.mapper.connect(
+        "update_ld",
+        "/api/libraries/datasets/{encoded_dataset_id}",
+        controller="library_datasets",
+        action="update",
+        conditions=dict(method=["PATCH"]),
+    )
 
-    webapp.mapper.connect('show_legitimate_ld_roles',
-                          '/api/libraries/datasets/{encoded_dataset_id}/permissions',
-                          controller='library_datasets',
-                          action='show_roles',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "show_legitimate_ld_roles",
+        "/api/libraries/datasets/{encoded_dataset_id}/permissions",
+        controller="library_datasets",
+        action="show_roles",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('update_ld_permissions',
-                          '/api/libraries/datasets/{encoded_dataset_id}/permissions',
-                          controller='library_datasets',
-                          action='update_permissions',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "update_ld_permissions",
+        "/api/libraries/datasets/{encoded_dataset_id}/permissions",
+        controller="library_datasets",
+        action="update_permissions",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect('delete_ld_item',
-                          '/api/libraries/datasets/{encoded_dataset_id}',
-                          controller='library_datasets',
-                          action='delete',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "delete_ld_item",
+        "/api/libraries/datasets/{encoded_dataset_id}",
+        controller="library_datasets",
+        action="delete",
+        conditions=dict(method=["DELETE"]),
+    )
 
-    webapp.mapper.connect('download_ld_items',
-                          '/api/libraries/datasets/download/{archive_format}',
-                          controller='library_datasets',
-                          action='download',
-                          conditions=dict(method=["POST", "GET"]))
+    webapp.mapper.connect(
+        "download_ld_items",
+        "/api/libraries/datasets/download/{archive_format}",
+        controller="library_datasets",
+        action="download",
+        conditions=dict(method=["POST", "GET"]),
+    )
 
-    webapp.mapper.resource_with_deleted('library',
-                                        'libraries',
-                                        path_prefix='/api')
+    webapp.mapper.resource_with_deleted("library", "libraries", path_prefix="/api")
 
-    webapp.mapper.resource('content',
-                           'contents',
-                           controller='library_contents',
-                           name_prefix='library_',
-                           path_prefix='/api/libraries/{library_id}',
-                           parent_resources=dict(member_name='library', collection_name='libraries'))
+    webapp.mapper.resource(
+        "content",
+        "contents",
+        controller="library_contents",
+        name_prefix="library_",
+        path_prefix="/api/libraries/{library_id}",
+        parent_resources=dict(member_name="library", collection_name="libraries"),
+    )
 
-    _add_item_extended_metadata_controller(webapp,
-                                           name_prefix="library_dataset_",
-                                           path_prefix='/api/libraries/{library_id}/contents/{library_content_id}')
+    _add_item_extended_metadata_controller(
+        webapp, name_prefix="library_dataset_", path_prefix="/api/libraries/{library_id}/contents/{library_content_id}"
+    )
 
     # =======================
     # ===== FOLDERS API =====
     # =======================
 
-    webapp.mapper.connect('add_history_datasets_to_library',
-                          '/api/folders/{encoded_folder_id}/contents',
-                          controller='folder_contents',
-                          action='create',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "add_history_datasets_to_library",
+        "/api/folders/{encoded_folder_id}/contents",
+        controller="folder_contents",
+        action="create",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect('create_folder',
-                          '/api/folders/{encoded_parent_folder_id}',
-                          controller='folders',
-                          action='create',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "create_folder",
+        "/api/folders/{encoded_parent_folder_id}",
+        controller="folders",
+        action="create",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect('delete_folder',
-                          '/api/folders/{encoded_folder_id}',
-                          controller='folders',
-                          action='delete',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "delete_folder",
+        "/api/folders/{encoded_folder_id}",
+        controller="folders",
+        action="delete",
+        conditions=dict(method=["DELETE"]),
+    )
 
-    webapp.mapper.connect('update_folder',
-                          '/api/folders/{encoded_folder_id}',
-                          controller='folders',
-                          action='update',
-                          conditions=dict(method=["PATCH", "PUT"]))
+    webapp.mapper.connect(
+        "update_folder",
+        "/api/folders/{encoded_folder_id}",
+        controller="folders",
+        action="update",
+        conditions=dict(method=["PATCH", "PUT"]),
+    )
 
-    webapp.mapper.resource('folder',
-                           'folders',
-                           path_prefix='/api')
+    webapp.mapper.resource("folder", "folders", path_prefix="/api")
 
-    webapp.mapper.connect('show_folder_permissions',
-                          '/api/folders/{encoded_folder_id}/permissions',
-                          controller='folders',
-                          action='get_permissions',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "show_folder_permissions",
+        "/api/folders/{encoded_folder_id}/permissions",
+        controller="folders",
+        action="get_permissions",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('set_folder_permissions',
-                          '/api/folders/{encoded_folder_id}/permissions',
-                          controller='folders',
-                          action='set_permissions',
-                          conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "set_folder_permissions",
+        "/api/folders/{encoded_folder_id}/permissions",
+        controller="folders",
+        action="set_permissions",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.resource('content',
-                           'contents',
-                           controller='folder_contents',
-                           name_prefix='folder_',
-                           path_prefix='/api/folders/{folder_id}',
-                           parent_resources=dict(member_name='folder', collection_name='folders'),
-                           conditions=dict(method=["GET"]))
+    webapp.mapper.resource(
+        "content",
+        "contents",
+        controller="folder_contents",
+        name_prefix="folder_",
+        path_prefix="/api/folders/{folder_id}",
+        parent_resources=dict(member_name="folder", collection_name="folders"),
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.resource('job',
-                           'jobs',
-                           path_prefix='/api')
-    webapp.mapper.connect('job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict(method=['POST']))
-    webapp.mapper.connect('job_inputs', '/api/jobs/{id}/inputs', controller='jobs', action='inputs', conditions=dict(method=['GET']))
-    webapp.mapper.connect('job_outputs', '/api/jobs/{id}/outputs', controller='jobs', action='outputs', conditions=dict(method=['GET']))
-    webapp.mapper.connect('build_for_rerun', '/api/jobs/{id}/build_for_rerun', controller='jobs', action='build_for_rerun', conditions=dict(method=['GET']))
-    webapp.mapper.connect('resume', '/api/jobs/{id}/resume', controller='jobs', action='resume', conditions=dict(method=['PUT']))
-    webapp.mapper.connect('job_error', '/api/jobs/{id}/error', controller='jobs', action='error', conditions=dict(method=['POST']))
-    webapp.mapper.connect('common_problems', '/api/jobs/{id}/common_problems', controller='jobs', action='common_problems', conditions=dict(method=['GET']))
+    webapp.mapper.resource("job", "jobs", path_prefix="/api")
+    webapp.mapper.connect(
+        "job_search", "/api/jobs/search", controller="jobs", action="search", conditions=dict(method=["POST"])
+    )
+    webapp.mapper.connect(
+        "job_inputs", "/api/jobs/{id}/inputs", controller="jobs", action="inputs", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "job_outputs", "/api/jobs/{id}/outputs", controller="jobs", action="outputs", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "build_for_rerun",
+        "/api/jobs/{id}/build_for_rerun",
+        controller="jobs",
+        action="build_for_rerun",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "resume", "/api/jobs/{id}/resume", controller="jobs", action="resume", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "job_error", "/api/jobs/{id}/error", controller="jobs", action="error", conditions=dict(method=["POST"])
+    )
+    webapp.mapper.connect(
+        "common_problems",
+        "/api/jobs/{id}/common_problems",
+        controller="jobs",
+        action="common_problems",
+        conditions=dict(method=["GET"]),
+    )
     # Job metrics and parameters by job id or dataset id (for slightly different accessibility checking)
-    webapp.mapper.connect('metrics', '/api/jobs/{job_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
-    webapp.mapper.connect('destination_params', '/api/jobs/{job_id}/destination_params', controller='jobs', action='destination_params', conditions=dict(method=['GET']))
-    webapp.mapper.connect('show_job_lock', '/api/job_lock', controller='jobs', action='show_job_lock', conditions=dict(method=['GET']))
-    webapp.mapper.connect('update_job_lock', '/api/job_lock', controller='jobs', action='update_job_lock', conditions=dict(method=['PUT']))
-    webapp.mapper.connect('dataset_metrics', '/api/datasets/{dataset_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
-    webapp.mapper.connect('parameters_display', '/api/jobs/{job_id}/parameters_display', controller='jobs', action='parameters_display', conditions=dict(method=['GET']))
-    webapp.mapper.connect('dataset_parameters_display', '/api/datasets/{dataset_id}/parameters_display', controller='jobs', action='parameters_display', conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "metrics", "/api/jobs/{job_id}/metrics", controller="jobs", action="metrics", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "destination_params",
+        "/api/jobs/{job_id}/destination_params",
+        controller="jobs",
+        action="destination_params",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "show_job_lock", "/api/job_lock", controller="jobs", action="show_job_lock", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.connect(
+        "update_job_lock", "/api/job_lock", controller="jobs", action="update_job_lock", conditions=dict(method=["PUT"])
+    )
+    webapp.mapper.connect(
+        "dataset_metrics",
+        "/api/datasets/{dataset_id}/metrics",
+        controller="jobs",
+        action="metrics",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "parameters_display",
+        "/api/jobs/{job_id}/parameters_display",
+        controller="jobs",
+        action="parameters_display",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "dataset_parameters_display",
+        "/api/datasets/{dataset_id}/parameters_display",
+        controller="jobs",
+        action="parameters_display",
+        conditions=dict(method=["GET"]),
+    )
 
     # Job files controllers. Only for consumption by remote job runners.
-    webapp.mapper.resource('file',
-                           'files',
-                           controller="job_files",
-                           name_prefix="job_",
-                           path_prefix='/api/jobs/{job_id}',
-                           parent_resources=dict(member_name="job", collection_name="jobs"))
-    webapp.mapper.resource('port',
-                           'ports',
-                           controller="job_ports",
-                           name_prefix="job_",
-                           path_prefix='/api/jobs/{job_id}',
-                           parent_resources=dict(member_name="job", collection_name="jobs"))
+    webapp.mapper.resource(
+        "file",
+        "files",
+        controller="job_files",
+        name_prefix="job_",
+        path_prefix="/api/jobs/{job_id}",
+        parent_resources=dict(member_name="job", collection_name="jobs"),
+    )
+    webapp.mapper.resource(
+        "port",
+        "ports",
+        controller="job_ports",
+        name_prefix="job_",
+        path_prefix="/api/jobs/{job_id}",
+        parent_resources=dict(member_name="job", collection_name="jobs"),
+    )
 
-    _add_item_extended_metadata_controller(webapp,
-                                           name_prefix="history_dataset_",
-                                           path_prefix='/api/histories/{history_id}/contents/{history_content_id}')
+    _add_item_extended_metadata_controller(
+        webapp, name_prefix="history_dataset_", path_prefix="/api/histories/{history_id}/contents/{history_content_id}"
+    )
 
     # ====================
     # ===== TOOLSHED =====
     # ====================
 
     # Handle displaying tool help images and README file images contained in repositories installed from the tool shed.
-    webapp.add_route('/admin_toolshed/static/images/{repository_id}/{image_file:.+?}',
-                     controller='admin_toolshed',
-                     action='display_image_in_repository',
-                     repository_id=None,
-                     image_file=None)
+    webapp.add_route(
+        "/admin_toolshed/static/images/{repository_id}/{image_file:.+?}",
+        controller="admin_toolshed",
+        action="display_image_in_repository",
+        repository_id=None,
+        image_file=None,
+    )
 
     # Do the same but without a repository id
-    webapp.add_route('/shed_tool_static/{shed}/{owner}/{repo}/{tool}/{version}/{image_file:.+?}',
-                     controller='shed_tool_static',
-                     action='index',
-                     shed=None,
-                     owner=None,
-                     repo=None,
-                     tool=None,
-                     version=None,
-                     image_file=None)
+    webapp.add_route(
+        "/shed_tool_static/{shed}/{owner}/{repo}/{tool}/{version}/{image_file:.+?}",
+        controller="shed_tool_static",
+        action="index",
+        shed=None,
+        owner=None,
+        repo=None,
+        tool=None,
+        version=None,
+        image_file=None,
+    )
 
-    webapp.mapper.connect('tool_shed_contents',
-                          '/api/tool_shed/contents',
-                          controller='toolshed',
-                          action='show',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "tool_shed_contents",
+        "/api/tool_shed/contents",
+        controller="toolshed",
+        action="show",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('tool_shed_category_contents',
-                          '/api/tool_shed/category',
-                          controller='toolshed',
-                          action='category',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "tool_shed_category_contents",
+        "/api/tool_shed/category",
+        controller="toolshed",
+        action="category",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('tool_shed_repository_details',
-                          '/api/tool_shed/repository',
-                          controller='toolshed',
-                          action='repository',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "tool_shed_repository_details",
+        "/api/tool_shed/repository",
+        controller="toolshed",
+        action="repository",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('tool_sheds',
-                          '/api/tool_shed',
-                          controller='toolshed',
-                          action='index',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "tool_sheds", "/api/tool_shed", controller="toolshed", action="index", conditions=dict(method=["GET"])
+    )
 
-    webapp.mapper.connect('tool_shed_search',
-                          '/api/tool_shed/search',
-                          controller='toolshed',
-                          action='search',
-                          conditions=dict(method=["GET", "POST"]))
+    webapp.mapper.connect(
+        "tool_shed_search",
+        "/api/tool_shed/search",
+        controller="toolshed",
+        action="search",
+        conditions=dict(method=["GET", "POST"]),
+    )
 
-    webapp.mapper.connect('tool_shed_request',
-                          '/api/tool_shed/request',
-                          controller='toolshed',
-                          action='request',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "tool_shed_request",
+        "/api/tool_shed/request",
+        controller="toolshed",
+        action="request",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('tool_shed_status',
-                          '/api/tool_shed/status',
-                          controller='toolshed',
-                          action='status',
-                          conditions=dict(method=["GET", "POST"]))
+    webapp.mapper.connect(
+        "tool_shed_status",
+        "/api/tool_shed/status",
+        controller="toolshed",
+        action="status",
+        conditions=dict(method=["GET", "POST"]),
+    )
 
-    webapp.mapper.connect('shed_tool_json',
-                          '/api/tool_shed/tool_json',
-                          controller='toolshed',
-                          action='tool_json',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "shed_tool_json",
+        "/api/tool_shed/tool_json",
+        controller="toolshed",
+        action="tool_json",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('tool_shed_repository',
-                          '/api/tool_shed_repositories/:id/status',
-                          controller='tool_shed_repositories',
-                          action='status',
-                          conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "tool_shed_repository",
+        "/api/tool_shed_repositories/:id/status",
+        controller="tool_shed_repositories",
+        action="status",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('install_repository',
-                          '/api/tool_shed_repositories',
-                          controller='tool_shed_repositories',
-                          action='install_repository_revision',
-                          conditions=dict(method=['POST']))
+    webapp.mapper.connect(
+        "install_repository",
+        "/api/tool_shed_repositories",
+        controller="tool_shed_repositories",
+        action="install_repository_revision",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect('install_repository',
-                          '/api/tool_shed_repositories/install',
-                          controller='tool_shed_repositories',
-                          action='install',
-                          conditions=dict(method=['POST']))
+    webapp.mapper.connect(
+        "install_repository",
+        "/api/tool_shed_repositories/install",
+        controller="tool_shed_repositories",
+        action="install",
+        conditions=dict(method=["POST"]),
+    )
 
-    webapp.mapper.connect('check_for_updates',
-                          '/api/tool_shed_repositories/check_for_updates',
-                          controller='tool_shed_repositories',
-                          action='check_for_updates',
-                          conditions=dict(method=['GET']))
+    webapp.mapper.connect(
+        "check_for_updates",
+        "/api/tool_shed_repositories/check_for_updates",
+        controller="tool_shed_repositories",
+        action="check_for_updates",
+        conditions=dict(method=["GET"]),
+    )
 
-    webapp.mapper.connect('tool_shed_repository',
-                          '/api/tool_shed_repositories',
-                          controller='tool_shed_repositories',
-                          action='uninstall_repository',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "tool_shed_repository",
+        "/api/tool_shed_repositories",
+        controller="tool_shed_repositories",
+        action="uninstall_repository",
+        conditions=dict(method=["DELETE"]),
+    )
 
-    webapp.mapper.connect('tool_shed_repository',
-                          '/api/tool_shed_repositories/{id}',
-                          controller='tool_shed_repositories',
-                          action='uninstall_repository',
-                          conditions=dict(method=["DELETE"]))
+    webapp.mapper.connect(
+        "tool_shed_repository",
+        "/api/tool_shed_repositories/{id}",
+        controller="tool_shed_repositories",
+        action="uninstall_repository",
+        conditions=dict(method=["DELETE"]),
+    )
 
-    webapp.mapper.connect('reset_metadata_on_selected_installed_repositories',
-                          '/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories',
-                          controller='tool_shed_repositories',
-                          action='reset_metadata_on_selected_installed_repositories',
-                          conditions=dict(method=['POST']))
+    webapp.mapper.connect(
+        "reset_metadata_on_selected_installed_repositories",
+        "/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories",
+        controller="tool_shed_repositories",
+        action="reset_metadata_on_selected_installed_repositories",
+        conditions=dict(method=["POST"]),
+    )
 
     # Galaxy API for tool shed features.
-    webapp.mapper.resource('tool_shed_repository',
-                           'tool_shed_repositories',
-                           member={'repair_repository_revision': 'POST',
-                                   'exported_workflows': 'GET',
-                                   'import_workflow': 'POST',
-                                   'import_workflows': 'POST'},
-                           collection={'get_latest_installable_revision': 'POST',
-                                       'reset_metadata_on_installed_repositories': 'POST'},
-                           controller='tool_shed_repositories',
-                           name_prefix='tool_shed_repository_',
-                           path_prefix='/api',
-                           new={'install_repository_revision': 'POST'},
-                           parent_resources=dict(member_name='tool_shed_repository', collection_name='tool_shed_repositories'))
+    webapp.mapper.resource(
+        "tool_shed_repository",
+        "tool_shed_repositories",
+        member={
+            "repair_repository_revision": "POST",
+            "exported_workflows": "GET",
+            "import_workflow": "POST",
+            "import_workflows": "POST",
+        },
+        collection={"get_latest_installable_revision": "POST", "reset_metadata_on_installed_repositories": "POST"},
+        controller="tool_shed_repositories",
+        name_prefix="tool_shed_repository_",
+        path_prefix="/api",
+        new={"install_repository_revision": "POST"},
+        parent_resources=dict(member_name="tool_shed_repository", collection_name="tool_shed_repositories"),
+    )
 
     # ==== Trace/Metrics Logger
     # Connect logger from app
@@ -1262,8 +1833,9 @@ def populate_api_routes(webapp, app):
     #    controller="metrics", action="index", conditions=dict( method=["GET"] ) )
     # webapp.mapper.connect( "show", "/api/metrics/{id}",
     #    controller="metrics", action="show", conditions=dict( method=["GET"] ) )
-    webapp.mapper.connect("create", "/api/metrics", controller="metrics",
-                          action="create", conditions=dict(method=["POST"]))
+    webapp.mapper.connect(
+        "create", "/api/metrics", controller="metrics", action="create", conditions=dict(method=["POST"])
+    )
 
 
 def _add_item_tags_controller(webapp, name_prefix, path_prefix, **kwd):
@@ -1273,25 +1845,39 @@ def _add_item_tags_controller(webapp, name_prefix, path_prefix, **kwd):
     path = f"{path_prefix}/tags"
     map = webapp.mapper
     # Allow view items' tags.
-    map.connect(name, path,
-                controller=controller, action="index",
-                conditions=dict(method=["GET"]))
+    map.connect(name, path, controller=controller, action="index", conditions=dict(method=["GET"]))
     # Allow remove tag from item
-    map.connect(f"{name}_delete", "%s/tags/{tag_name}" % path_prefix,
-                controller=controller, action="delete",
-                conditions=dict(method=["DELETE"]))
+    map.connect(
+        f"{name}_delete",
+        "%s/tags/{tag_name}" % path_prefix,
+        controller=controller,
+        action="delete",
+        conditions=dict(method=["DELETE"]),
+    )
     # Allow create a new tag with from name
-    map.connect(f"{name}_create", "%s/tags/{tag_name}" % path_prefix,
-                controller=controller, action="create",
-                conditions=dict(method=["POST"]))
+    map.connect(
+        f"{name}_create",
+        "%s/tags/{tag_name}" % path_prefix,
+        controller=controller,
+        action="create",
+        conditions=dict(method=["POST"]),
+    )
     # Allow update tag value
-    map.connect(f"{name}_update", "%s/tags/{tag_name}" % path_prefix,
-                controller=controller, action="update",
-                conditions=dict(method=["PUT"]))
+    map.connect(
+        f"{name}_update",
+        "%s/tags/{tag_name}" % path_prefix,
+        controller=controller,
+        action="update",
+        conditions=dict(method=["PUT"]),
+    )
     # Allow show tag by name
-    map.connect(f"{name}_show", "%s/tags/{tag_name}" % path_prefix,
-                controller=controller, action="show",
-                conditions=dict(method=["GET"]))
+    map.connect(
+        f"{name}_show",
+        "%s/tags/{tag_name}" % path_prefix,
+        controller=controller,
+        action="show",
+        conditions=dict(method=["GET"]),
+    )
 
 
 def _add_item_extended_metadata_controller(webapp, name_prefix, path_prefix, **kwd):
@@ -1323,81 +1909,105 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     # Merge the global and local configurations
     conf = global_conf.copy()
     conf.update(local_conf)
-    debug = asbool(conf.get('debug', False))
+    debug = asbool(conf.get("debug", False))
     # First put into place httpexceptions, which must be most closely
     # wrapped around the application (it can interact poorly with
     # other middleware):
-    app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,))
+    app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name="paste.httpexceptions", args=(conf,))
     # Statsd request timing and profiling
-    statsd_host = conf.get('statsd_host', None)
+    statsd_host = conf.get("statsd_host", None)
     if statsd_host:
         from galaxy.web.framework.middleware.statsd import StatsdMiddleware
-        app = wrap_if_allowed(app, stack, StatsdMiddleware,
-                              args=(statsd_host,
-                                    conf.get('statsd_port', 8125),
-                                    conf.get('statsd_prefix', 'galaxy'),
-                                    conf.get('statsd_influxdb', False),
-                                    conf.get('statsd_mock_calls', False)))
+
+        app = wrap_if_allowed(
+            app,
+            stack,
+            StatsdMiddleware,
+            args=(
+                statsd_host,
+                conf.get("statsd_port", 8125),
+                conf.get("statsd_prefix", "galaxy"),
+                conf.get("statsd_influxdb", False),
+                conf.get("statsd_mock_calls", False),
+            ),
+        )
         log.info("Enabling 'statsd' middleware")
     # If we're using remote_user authentication, add middleware that
     # protects Galaxy from improperly configured authentication in the
     # upstream server
-    single_user = conf.get('single_user', None)
-    use_remote_user = asbool(conf.get('use_remote_user', False)) or single_user
+    single_user = conf.get("single_user", None)
+    use_remote_user = asbool(conf.get("use_remote_user", False)) or single_user
     if use_remote_user:
         from galaxy.web.framework.middleware.remoteuser import RemoteUser
-        app = wrap_if_allowed(app, stack, RemoteUser,
-                              kwargs=dict(
-                                  maildomain=conf.get('remote_user_maildomain', None),
-                                  display_servers=util.listify(conf.get('display_servers', '')),
-                                  single_user=single_user,
-                                  admin_users=conf.get('admin_users', '').split(','),
-                                  remote_user_header=conf.get('remote_user_header', 'HTTP_REMOTE_USER'),
-                                  remote_user_secret_header=conf.get('remote_user_secret', None),
-                                  normalize_remote_user_email=conf.get('normalize_remote_user_email', False)))
+
+        app = wrap_if_allowed(
+            app,
+            stack,
+            RemoteUser,
+            kwargs=dict(
+                maildomain=conf.get("remote_user_maildomain", None),
+                display_servers=util.listify(conf.get("display_servers", "")),
+                single_user=single_user,
+                admin_users=conf.get("admin_users", "").split(","),
+                remote_user_header=conf.get("remote_user_header", "HTTP_REMOTE_USER"),
+                remote_user_secret_header=conf.get("remote_user_secret", None),
+                normalize_remote_user_email=conf.get("normalize_remote_user_email", False),
+            ),
+        )
     # The recursive middleware allows for including requests in other
     # requests or forwarding of requests, all on the server side.
-    if asbool(conf.get('use_recursive', True)):
+    if asbool(conf.get("use_recursive", True)):
         from paste import recursive
+
         app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
     # If sentry logging is enabled, log here before propogating up to
     # the error middleware
-    sentry_dsn = conf.get('sentry_dsn', None)
+    sentry_dsn = conf.get("sentry_dsn", None)
     if sentry_dsn:
         from sentry_sdk.integrations.wsgi import SentryWsgiMiddleware
+
         app = wrap_if_allowed(app, stack, SentryWsgiMiddleware)
     # Various debug middleware that can only be turned on if the debug
     # flag is set, either because they are insecure or greatly hurt
     # performance
     if debug:
         # Middleware to check for WSGI compliance
-        if asbool(conf.get('use_lint', False)):
+        if asbool(conf.get("use_lint", False)):
             from paste import lint
-            app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
+
+            app = wrap_if_allowed(app, stack, lint.make_middleware, name="paste.lint", args=(conf,))
         # Middleware to run the python profiler on each request
-        if asbool(conf.get('use_profile', False)):
+        if asbool(conf.get("use_profile", False)):
             from paste.debug import profile
+
             app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
     # Error middleware
     app = wrap_if_allowed(app, stack, ErrorMiddleware, args=(conf,))
     # Transaction logging (apache access.log style)
-    if asbool(conf.get('use_translogger', True)):
+    if asbool(conf.get("use_translogger", True)):
         from galaxy.web.framework.middleware.translogger import TransLogger
+
         app = wrap_if_allowed(app, stack, TransLogger)
     # X-Forwarded-Host handling
     app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
     # Request ID middleware
     app = wrap_if_allowed(app, stack, RequestIDMiddleware)
     # TUS upload middleware
-    app = wrap_if_allowed(app, stack, TusMiddleware, kwargs={
-        'upload_path': urljoin(f"{application_stack.config.galaxy_url_prefix}/", 'api/upload/resumable_upload'),
-        'tmp_dir': application_stack.config.new_file_path,
-        'max_size': application_stack.config.maximum_upload_file_size
-    })
+    app = wrap_if_allowed(
+        app,
+        stack,
+        TusMiddleware,
+        kwargs={
+            "upload_path": urljoin(f"{application_stack.config.galaxy_url_prefix}/", "api/upload/resumable_upload"),
+            "tmp_dir": application_stack.config.new_file_path,
+            "max_size": application_stack.config.maximum_upload_file_size,
+        },
+    )
     # api batch call processing middleware
     app = wrap_if_allowed(app, stack, BatchMiddleware, args=(webapp, {}))
-    if asbool(conf.get('enable_per_request_sql_debugging', False)):
+    if asbool(conf.get("enable_per_request_sql_debugging", False)):
         from galaxy.web.framework.middleware.sqldebug import SQLDebugMiddleware
+
         app = wrap_if_allowed(app, stack, SQLDebugMiddleware, args=(webapp, {}))
     return app
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py b/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py
index 0c405f1b646..1552c62b2f7 100644
--- a/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py
+++ b/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py
@@ -11,7 +11,7 @@ def render_item(trans, entity, children):
     """
     Form HTML template for each item in the history
     """
-    template = ''
+    template = ""
     entity_name = entity.__class__.__name__
     if entity_name == "HistoryDatasetAssociation":
         template = render_item_hda(trans, entity, children)
@@ -26,13 +26,13 @@ def render_item_hda(trans, hda, children):
     """
     Render hdas as a id'd stub for js to fill later
     """
-    template = ''
+    template = ""
     if hda.copied_from_history_dataset_association:
         template = render_hda_copied_from_history(trans, hda, children)
     elif hda.copied_from_library_dataset_dataset_association:
         template = render_hda_copied_from_library(trans, hda, children)
     else:
-        template = f"<div id=\"hda-{trans.security.encode_id(hda.id)}\" class=\"dataset hda state-{hda.state}\"></div>"
+        template = f'<div id="hda-{trans.security.encode_id(hda.id)}" class="dataset hda state-{hda.state}"></div>'
     return template
 
 
@@ -40,19 +40,19 @@ def render_hda_copied_from_history(trans, hda, children):
     """
     Wrap an hda in info about the history from where it was copied
     """
-    template = ''
+    template = ""
     id = trans.security.encode_id(hda.id)
     history_id = trans.security.encode_id(hda.copied_from_history_dataset_association.history_id)
     url = url_for(f"/histories/view?id={history_id}")
     template = '<div class="copied-from"><div class="header"><div>'
     template += '<span class="light"> Copied from history dataset: </span>'
-    template += f"<span class=\"bold\">{hda.copied_from_history_dataset_association.name}</span>"
+    template += f'<span class="bold">{hda.copied_from_history_dataset_association.name}</span>'
     template += '</div><div class="copied-from-source">'
     template += '<span class="light">History: </span>'
     template += '<span class="bold">'
-    template += f"<a href=\"{url}\">{hda.copied_from_history_dataset_association.history.name}</a>"
-    template += '</span></div></div>'
-    template += f"<div id=\"hda-{id}\" class=\"dataset hda state-{hda.state}\"></div></div>"
+    template += f'<a href="{url}">{hda.copied_from_history_dataset_association.history.name}</a>'
+    template += "</span></div></div>"
+    template += f'<div id="hda-{id}" class="dataset hda state-{hda.state}"></div></div>'
     return template
 
 
@@ -60,22 +60,22 @@ def render_hda_copied_from_library(trans, hda, children):
     """
     Wrap an hda in info about the library from where it was copied
     """
-    template = ''
+    template = ""
     id = trans.security.encode_id(hda.id)
     folder = hda.copied_from_library_dataset_dataset_association.library_dataset.folder
     folder_id = f"F{trans.security.encode_id(folder.id)}"
     url = url_for(f"/libraries/folders/{folder_id}")
     template = '<div class="copied-from">'
     template += '<div class="header">'
-    template += '<div>'
+    template += "<div>"
     template += '<span class="light">Copied from library dataset:</span>'
-    template += f"<span class=\"bold\">{hda.copied_from_library_dataset_dataset_association.name}</span>"
-    template += '</div>'
+    template += f'<span class="bold">{hda.copied_from_library_dataset_dataset_association.name}</span>'
+    template += "</div>"
     template += '<div class="copied-from-source">'
     template += '<span class="light">Library: </span>'
     template += '<span class="bold">'
-    template += f"<a href=\"{url}\">{folder.name}</a></span></div></div>"
-    template += f"<div id=\"hda-{id}\" class=\"dataset hda state-{hda.state}\"></div></div>"
+    template += f'<a href="{url}">{folder.name}</a></span></div></div>'
+    template += f'<div id="hda-{id}" class="dataset hda state-{hda.state}"></div></div>'
     return template
 
 
@@ -83,7 +83,7 @@ def render_item_job(trans, job, children):
     """
     Render a job and its children (hdas)
     """
-    template = ''
+    template = ""
     template = '<div class="tool">'
     tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version)
     if tool:
@@ -91,27 +91,27 @@ def render_item_job(trans, job, children):
         tool_desc = tool.description
     else:
         tool_name = f"Unknown tool with id: {job.tool_id}"
-        tool_desc = ''
+        tool_desc = ""
     params_object = None
     try:
         params_object = job.get_param_values(trans.app, ignore_errors=True)
     except Exception:
         pass
-    template += f"<div class=\"header\"><div><span class=\"bold\">{tool_name}</span>"
-    template += f"<span class=\"light\"> - {tool_desc}</span></div>"
+    template += f'<div class="header"><div><span class="bold">{tool_name}</span>'
+    template += f'<span class="light"> - {tool_desc}</span></div>'
     if tool and params_object:
         template += '<table class="job-inputs">'
         template += inputs_recursive(trans, tool.inputs, params_object, depth=1)
-        template += '</table>'
+        template += "</table>"
     else:
-        template += '<em>No parameter data available</em>'
-    template += '</div>'
+        template += "<em>No parameter data available</em>"
+    template += "</div>"
     template += '<div class="body">'
-    child_template = ''
+    child_template = ""
     for e, c in reversed(children):
         child_template += render_item(trans, e, c)
     template += child_template
-    template += '</div></div>'
+    template += "</div></div>"
     return template
 
 
@@ -119,11 +119,11 @@ def render_item_wf(trans, wf, children):
     """
     Render a workflow and its children (jobs)
     """
-    template = f"<div class=\"workflow\"><div class=\"header\"><span class=\"bold\">{wf.workflow.name}</span>"
+    template = f'<div class="workflow"><div class="header"><span class="bold">{wf.workflow.name}</span>'
     template += '<span class="light">- Workflow</span></div><div class="body">'
     for e, c in reversed(children):
         template += render_item(trans, e, c)
-    template += '</div></div>'
+    template += "</div></div>"
     return template
 
 
@@ -131,14 +131,14 @@ def inputs_recursive_indent(text, depth):
     """
     Add an indentation depending on the depth in a <tr>
     """
-    return f"<td style=\"padding-left:{str((depth - 1) * 10)}px\">{text}</td>"
+    return f'<td style="padding-left:{str((depth - 1) * 10)}px">{text}</td>'
 
 
 def inputs_recursive(trans, input_params, param_values, depth=1, upgrade_messages=None):
     """
     Recursive method for tool parameter section
     """
-    tool_parameter_template = ''
+    tool_parameter_template = ""
     if upgrade_messages is None:
         upgrade_messages = {}
 
@@ -148,54 +148,70 @@ def inputs_recursive(trans, input_params, param_values, depth=1, upgrade_message
                 for i in range(len(param_values[input.name])):
                     inputs_recursive(trans, input.inputs, param_values[input.name][i], depth=depth + 1)
             elif input.type == "section":
-                tool_parameter_template += '<tr>'
+                tool_parameter_template += "<tr>"
                 tool_parameter_template += inputs_recursive_indent(text=input.name, depth=depth)
-                tool_parameter_template += '<td></td></tr>'
-                inputs_recursive(trans, input.inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name))
+                tool_parameter_template += "<td></td></tr>"
+                inputs_recursive(
+                    trans,
+                    input.inputs,
+                    param_values[input.name],
+                    depth=depth + 1,
+                    upgrade_messages=upgrade_messages.get(input.name),
+                )
             elif input.type == "conditional":
                 try:
-                    current_case = param_values[input.name]['__current_case__']
+                    current_case = param_values[input.name]["__current_case__"]
                     is_valid = True
                 except Exception:
                     current_case = None
                     is_valid = False
                 if is_valid:
-                    tool_parameter_template += '<tr>'
+                    tool_parameter_template += "<tr>"
                     tool_parameter_template += inputs_recursive_indent(text=input.test_param.label, depth=depth)
                     tool_parameter_template += f"<td>{input.cases[current_case].value}</td><td></td></tr>"
-                    inputs_recursive(trans, input.cases[current_case].inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name))
+                    inputs_recursive(
+                        trans,
+                        input.cases[current_case].inputs,
+                        param_values[input.name],
+                        depth=depth + 1,
+                        upgrade_messages=upgrade_messages.get(input.name),
+                    )
                 else:
-                    tool_parameter_template += '<tr>'
+                    tool_parameter_template += "<tr>"
                     tool_parameter_template += inputs_recursive_indent(text=input.name, depth=depth)
-                    tool_parameter_template += '<td><em> The previously used value is no longer valid </em></td><td></td></tr>'
+                    tool_parameter_template += (
+                        "<td><em> The previously used value is no longer valid </em></td><td></td></tr>"
+                    )
             elif input.type == "upload_dataset":
-                tool_parameter_template += '<tr>'
+                tool_parameter_template += "<tr>"
                 tool_parameter_template += inputs_recursive_indent(text=input.group_title(param_values), depth=depth)
-                tool_parameter_template += f"<td>{str(len(param_values[input.name]))} uploaded datasets</td><td></td></tr>"
+                tool_parameter_template += (
+                    f"<td>{str(len(param_values[input.name]))} uploaded datasets</td><td></td></tr>"
+                )
             elif input.type == "data":
-                tool_parameter_template += '<tr>'
+                tool_parameter_template += "<tr>"
                 tool_parameter_template += inputs_recursive_indent(text=input.label, depth=depth)
-                tool_parameter_template += '<td>'
+                tool_parameter_template += "<td>"
                 for i, element in enumerate(listify(param_values[input.name])):
                     if i > 0:
-                        tool_parameter_template += ','
+                        tool_parameter_template += ","
                     if element.history_content_type == "dataset":
                         hda = element
                         encoded_id = trans.security.encode_id(hda.id)
                         dataset_info_url = url_for(controller="dataset", action="details", dataset_id=encoded_id)
-                        tool_parameter_template += f"<a target=\"galaxy_main\" data-hda-id=\"{encoded_id}\""
-                        tool_parameter_template += f"href=\"{dataset_info_url}\">{str(hda.hid)}:{hda.name}</a>"
+                        tool_parameter_template += f'<a target="galaxy_main" data-hda-id="{encoded_id}"'
+                        tool_parameter_template += f'href="{dataset_info_url}">{str(hda.hid)}:{hda.name}</a>'
                     else:
                         tool_parameter_template += f"{str(element.hid)}:{element.name}"
-                    tool_parameter_template += '</td><td></td></tr>'
+                    tool_parameter_template += "</td><td></td></tr>"
             elif input.visible:
                 label = input.label if (hasattr(input, "label") and input.label) else input.name
-                tool_parameter_template += '<tr>'
+                tool_parameter_template += "<tr>"
                 tool_parameter_template += inputs_recursive_indent(text=label, depth=depth)
                 tool_parameter_template += f"<td>{input.value_to_display_text(param_values[input.name])}</td>"
                 tool_parameter_template += f"<td>{upgrade_messages.get(input.name, '')}</td></tr>"
         else:
-            tool_parameter_template += '<tr>'
+            tool_parameter_template += "<tr>"
             if input.type == "conditional":
                 label = input.test_param.label
             elif input.type == "repeat":
@@ -203,5 +219,7 @@ def inputs_recursive(trans, input_params, param_values, depth=1, upgrade_message
             else:
                 label = input.label or input.name
                 tool_parameter_template += inputs_recursive_indent(text=label, depth=depth)
-                tool_parameter_template += '<td><em> not used (parameter was added after this job was run)</em></td><td></td></tr>'
+                tool_parameter_template += (
+                    "<td><em> not used (parameter was added after this job was run)</em></td><td></td></tr>"
+                )
     return tool_parameter_template
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index b7570ea24a0..6c9debda1fa 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -1,13 +1,19 @@
 import logging
 
-from sqlalchemy import false, func
+from sqlalchemy import (
+    false,
+    func,
+)
 
 from galaxy import (
     model,
     util,
-    web
+    web,
+)
+from galaxy.exceptions import (
+    ActionInputError,
+    MessageException,
 )
-from galaxy.exceptions import ActionInputError, MessageException
 from galaxy.managers.quotas import QuotaManager
 from galaxy.model import tool_shed_install as install_model
 from galaxy.security.validate_user_input import validate_password
@@ -18,16 +24,17 @@ from galaxy.util import (
     sanitize_text,
 )
 from galaxy.web import url_for
-from galaxy.web.framework.helpers import grids, time_ago
+from galaxy.web.framework.helpers import (
+    grids,
+    time_ago,
+)
 from galaxy.webapps.base import controller
 from tool_shed.util.web_util import escape
 
-
 log = logging.getLogger(__name__)
 
 
 class UserListGrid(grids.Grid):
-
     class EmailColumn(grids.TextColumn):
         def get_value(self, trans, grid, user):
             return escape(user.email)
@@ -36,7 +43,7 @@ class UserListGrid(grids.Grid):
         def get_value(self, trans, grid, user):
             if user.username:
                 return escape(user.username)
-            return 'not set'
+            return "not set"
 
     class StatusColumn(grids.GridColumn):
         def get_value(self, trans, grid, user):
@@ -61,20 +68,24 @@ class UserListGrid(grids.Grid):
     class ExternalColumn(grids.GridColumn):
         def get_value(self, trans, grid, user):
             if user.external:
-                return 'yes'
-            return 'no'
+                return "yes"
+            return "no"
 
     class LastLoginColumn(grids.GridColumn):
         def get_value(self, trans, grid, user):
             if user.galaxy_sessions:
                 return self.format(user.galaxy_sessions[0].update_time)
-            return 'never'
+            return "never"
 
         def sort(self, trans, query, ascending, column_name=None):
-            last_login_subquery = trans.sa_session.query(
-                model.GalaxySession.table.c.user_id,
-                func.max(model.GalaxySession.table.c.update_time).label("last_login")
-            ).group_by(model.GalaxySession.table.c.user_id).subquery()
+            last_login_subquery = (
+                trans.sa_session.query(
+                    model.GalaxySession.table.c.user_id,
+                    func.max(model.GalaxySession.table.c.update_time).label("last_login"),
+                )
+                .group_by(model.GalaxySession.table.c.user_id)
+                .subquery()
+            )
             query = query.outerjoin((last_login_subquery, model.User.table.c.id == last_login_subquery.c.user_id))
 
             if not ascending:
@@ -85,14 +96,14 @@ class UserListGrid(grids.Grid):
 
     class TimeCreatedColumn(grids.GridColumn):
         def get_value(self, trans, grid, user):
-            return user.create_time.strftime('%x')
+            return user.create_time.strftime("%x")
 
     class ActivatedColumn(grids.GridColumn):
         def get_value(self, trans, grid, user):
             if user.active:
-                return 'Y'
+                return "Y"
             else:
-                return 'N'
+                return "N"
 
     class DiskUsageColumn(grids.GridColumn):
         def get_value(self, trans, grid, user):
@@ -116,16 +127,15 @@ class UserListGrid(grids.Grid):
     model_class = model.User
     default_sort_key = "email"
     columns = [
-        EmailColumn("Email",
-                    key="email",
-                    link=(lambda item: dict(controller="user", action="information", id=item.id, webapp="galaxy")),
-                    attach_popup=True,
-                    filterable="advanced",
-                    target="top"),
-        UserNameColumn("User Name",
-                       key="username",
-                       attach_popup=False,
-                       filterable="advanced"),
+        EmailColumn(
+            "Email",
+            key="email",
+            link=(lambda item: dict(controller="user", action="information", id=item.id, webapp="galaxy")),
+            attach_popup=True,
+            filterable="advanced",
+            target="top",
+        ),
+        UserNameColumn("User Name", key="username", attach_popup=False, filterable="advanced"),
         LastLoginColumn("Last Login", format=time_ago, key="last_login", sortable=True),
         DiskUsageColumn("Disk Usage", key="disk_usage", attach_popup=False),
         StatusColumn("Status", attach_popup=False, key="deleted"),
@@ -136,43 +146,47 @@ class UserListGrid(grids.Grid):
         ExternalColumn("External", attach_popup=False, key="external"),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
-        grids.PurgedColumn("Purged", key="purged", visible=False, filterable="advanced")
-    ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Create new user", url_args=dict(action="users/create"))
+        grids.PurgedColumn("Purged", key="purged", visible=False, filterable="advanced"),
     ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    global_actions = [grids.GridAction("Create new user", url_args=dict(action="users/create"))]
     operations = [
-        grids.GridOperation("Manage Information",
-                            condition=(lambda item: not item.deleted),
-                            allow_multiple=False,
-                            url_args=dict(controller="user", action="information", webapp="galaxy")),
-        grids.GridOperation("Manage Roles and Groups",
-                            condition=(lambda item: not item.deleted),
-                            allow_multiple=False,
-                            url_args=dict(action="form/manage_roles_and_groups_for_user")),
-        grids.GridOperation("Reset Password",
-                            condition=(lambda item: not item.deleted),
-                            allow_multiple=True,
-                            url_args=dict(action="form/reset_user_password"),
-                            target="top"),
-        grids.GridOperation("Recalculate Disk Usage",
-                            condition=(lambda item: not item.deleted),
-                            allow_multiple=False),
-        grids.GridOperation("Generate New API Key",
-                            allow_multiple=False,
-                            async_compatible=True)
+        grids.GridOperation(
+            "Manage Information",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(controller="user", action="information", webapp="galaxy"),
+        ),
+        grids.GridOperation(
+            "Manage Roles and Groups",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/manage_roles_and_groups_for_user"),
+        ),
+        grids.GridOperation(
+            "Reset Password",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=True,
+            url_args=dict(action="form/reset_user_password"),
+            target="top",
+        ),
+        grids.GridOperation("Recalculate Disk Usage", condition=(lambda item: not item.deleted), allow_multiple=False),
+        grids.GridOperation("Generate New API Key", allow_multiple=False, async_compatible=True),
     ]
 
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True, purged=False)),
         grids.GridColumnFilter("Purged", args=dict(purged=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
     num_rows_per_page = 50
     use_paging = True
@@ -184,7 +198,6 @@ class UserListGrid(grids.Grid):
 
 
 class RoleListGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
         def get_value(self, trans, grid, role):
             return escape(role.name)
@@ -193,7 +206,7 @@ class RoleListGrid(grids.Grid):
         def get_value(self, trans, grid, role):
             if role.description:
                 return escape(role.description)
-            return ''
+            return ""
 
     class TypeColumn(grids.TextColumn):
         def get_value(self, trans, grid, role):
@@ -223,59 +236,57 @@ class RoleListGrid(grids.Grid):
     model_class = model.Role
     default_sort_key = "name"
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   link=(lambda item: dict(action="form/manage_users_and_groups_for_role", id=item.id, webapp="galaxy")),
-                   model_class=model.Role,
-                   attach_popup=True,
-                   filterable="advanced",
-                   target="top"),
-        DescriptionColumn("Description",
-                          key='description',
-                          model_class=model.Role,
-                          attach_popup=False,
-                          filterable="advanced"),
-        TypeColumn("Type",
-                   key='type',
-                   model_class=model.Role,
-                   attach_popup=False,
-                   filterable="advanced"),
+        NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(action="form/manage_users_and_groups_for_role", id=item.id, webapp="galaxy")),
+            model_class=model.Role,
+            attach_popup=True,
+            filterable="advanced",
+            target="top",
+        ),
+        DescriptionColumn(
+            "Description", key="description", model_class=model.Role, attach_popup=False, filterable="advanced"
+        ),
+        TypeColumn("Type", key="type", model_class=model.Role, attach_popup=False, filterable="advanced"),
         GroupsColumn("Groups", attach_popup=False),
         UsersColumn("Users", attach_popup=False),
         StatusColumn("Status", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
-        grids.GridColumn("Last Updated", key="update_time")
+        grids.GridColumn("Last Updated", key="update_time"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0], columns[1], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Add new role", url_args=dict(action="form/create_role"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    global_actions = [grids.GridAction("Add new role", url_args=dict(action="form/create_role"))]
+    operations = [
+        grids.GridOperation(
+            "Edit Name/Description",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/rename_role"),
+        ),
+        grids.GridOperation(
+            "Edit Permissions",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/manage_users_and_groups_for_role", webapp="galaxy"),
+        ),
+        grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True),
+        grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True),
+        grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True),
     ]
-    operations = [grids.GridOperation("Edit Name/Description",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/rename_role")),
-                  grids.GridOperation("Edit Permissions",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/manage_users_and_groups_for_role", webapp="galaxy")),
-                  grids.GridOperation("Delete",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=True),
-                  grids.GridOperation("Undelete",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True),
-                  grids.GridOperation("Purge",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True)]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
     num_rows_per_page = 50
     use_paging = True
@@ -285,7 +296,6 @@ class RoleListGrid(grids.Grid):
 
 
 class GroupListGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
         def get_value(self, trans, grid, group):
             return escape(group.name)
@@ -314,55 +324,54 @@ class GroupListGrid(grids.Grid):
     model_class = model.Group
     default_sort_key = "name"
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   link=(lambda item: dict(action="form/manage_users_and_roles_for_group", id=item.id, webapp="galaxy")),
-                   model_class=model.Group,
-                   attach_popup=True,
-                   filterable="advanced"),
+        NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(action="form/manage_users_and_roles_for_group", id=item.id, webapp="galaxy")),
+            model_class=model.Group,
+            attach_popup=True,
+            filterable="advanced",
+        ),
         UsersColumn("Users", attach_popup=False),
         RolesColumn("Roles", attach_popup=False),
         StatusColumn("Status", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
-        grids.GridColumn("Last Updated", key="update_time", format=pretty_print_time_interval)
+        grids.GridColumn("Last Updated", key="update_time", format=pretty_print_time_interval),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Add new group", url_args=dict(action="form/create_group"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard"
+        )
+    )
+    global_actions = [grids.GridAction("Add new group", url_args=dict(action="form/create_group"))]
+    operations = [
+        grids.GridOperation(
+            "Edit Name",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/rename_group"),
+        ),
+        grids.GridOperation(
+            "Edit Permissions",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/manage_users_and_roles_for_group", webapp="galaxy"),
+        ),
+        grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True),
+        grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True),
+        grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True),
     ]
-    operations = [grids.GridOperation("Edit Name",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/rename_group")),
-                  grids.GridOperation("Edit Permissions",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/manage_users_and_roles_for_group", webapp="galaxy")),
-                  grids.GridOperation("Delete",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=True),
-                  grids.GridOperation("Undelete",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True),
-                  grids.GridOperation("Purge",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True)]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
     num_rows_per_page = 50
     use_paging = True
 
 
 class QuotaListGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
         def get_value(self, trans, grid, quota):
             return escape(quota.name)
@@ -371,7 +380,7 @@ class QuotaListGrid(grids.Grid):
         def get_value(self, trans, grid, quota):
             if quota.description:
                 return escape(quota.description)
-            return ''
+            return ""
 
     class AmountColumn(grids.TextColumn):
         def get_value(self, trans, grid, quota):
@@ -402,103 +411,109 @@ class QuotaListGrid(grids.Grid):
     model_class = model.Quota
     default_sort_key = "name"
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   link=(lambda item: dict(action="form/edit_quota", id=item.id)),
-                   model_class=model.Quota,
-                   attach_popup=True,
-                   filterable="advanced"),
-        DescriptionColumn("Description",
-                          key='description',
-                          model_class=model.Quota,
-                          attach_popup=False,
-                          filterable="advanced"),
-        AmountColumn("Amount",
-                     key='amount',
-                     model_class=model.Quota,
-                     attach_popup=False),
+        NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(action="form/edit_quota", id=item.id)),
+            model_class=model.Quota,
+            attach_popup=True,
+            filterable="advanced",
+        ),
+        DescriptionColumn(
+            "Description", key="description", model_class=model.Quota, attach_popup=False, filterable="advanced"
+        ),
+        AmountColumn("Amount", key="amount", model_class=model.Quota, attach_popup=False),
         UsersColumn("Users", attach_popup=False),
         GroupsColumn("Groups", attach_popup=False),
         StatusColumn("Status", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced")
+        grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Add new quota", dict(action="form/create_quota"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    global_actions = [grids.GridAction("Add new quota", dict(action="form/create_quota"))]
+    operations = [
+        grids.GridOperation(
+            "Rename",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/rename_quota"),
+        ),
+        grids.GridOperation(
+            "Change amount",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/edit_quota"),
+        ),
+        grids.GridOperation(
+            "Manage users and groups",
+            condition=(lambda item: not item.default and not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/manage_users_and_groups_for_quota"),
+        ),
+        grids.GridOperation(
+            "Set as different type of default",
+            condition=(lambda item: item.default),
+            allow_multiple=False,
+            url_args=dict(action="form/set_quota_default"),
+        ),
+        grids.GridOperation(
+            "Set as default",
+            condition=(lambda item: not item.default and not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="form/set_quota_default"),
+        ),
+        grids.GridOperation(
+            "Unset as default", condition=(lambda item: item.default and not item.deleted), allow_multiple=False
+        ),
+        grids.GridOperation(
+            "Delete", condition=(lambda item: not item.deleted and not item.default), allow_multiple=True
+        ),
+        grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True),
+        grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True),
     ]
-    operations = [grids.GridOperation("Rename",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/rename_quota")),
-                  grids.GridOperation("Change amount",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/edit_quota")),
-                  grids.GridOperation("Manage users and groups",
-                                      condition=(lambda item: not item.default and not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/manage_users_and_groups_for_quota")),
-                  grids.GridOperation("Set as different type of default",
-                                      condition=(lambda item: item.default),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/set_quota_default")),
-                  grids.GridOperation("Set as default",
-                                      condition=(lambda item: not item.default and not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="form/set_quota_default")),
-                  grids.GridOperation("Unset as default",
-                                      condition=(lambda item: item.default and not item.deleted),
-                                      allow_multiple=False),
-                  grids.GridOperation("Delete",
-                                      condition=(lambda item: not item.deleted and not item.default),
-                                      allow_multiple=True),
-                  grids.GridOperation("Undelete",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True),
-                  grids.GridOperation("Purge",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True)]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
         grids.GridColumnFilter("Purged", args=dict(purged=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
     num_rows_per_page = 50
     use_paging = True
 
 
 class ToolVersionListGrid(grids.Grid):
-
     class ToolIdColumn(grids.TextColumn):
         def get_value(self, trans, grid, tool_version):
             toolbox = trans.app.toolbox
             if toolbox.has_tool(tool_version.tool_id, exact=True):
-                link = url_for(controller='tool_runner', tool_id=tool_version.tool_id)
+                link = url_for(controller="tool_runner", tool_id=tool_version.tool_id)
                 link_str = f'<a target="_blank" href="{link}">'
                 return f'<div class="count-box state-color-ok">{link_str}{tool_version.tool_id}</a></div>'
             return tool_version.tool_id
 
     class ToolVersionsColumn(grids.TextColumn):
         def get_value(self, trans, grid, tool_version):
-            tool_ids_str = ''
+            tool_ids_str = ""
             toolbox = trans.app.toolbox
             tool = toolbox._tools_by_id.get(tool_version.tool_id)
             if tool:
                 for tool_id in tool.lineage.tool_ids:
                     if toolbox.has_tool(tool_id, exact=True):
-                        link = url_for(controller='tool_runner', tool_id=tool_id)
+                        link = url_for(controller="tool_runner", tool_id=tool_id)
                         link_str = f'<a target="_blank" href="{link}">'
                         tool_ids_str += f'<div class="count-box state-color-ok">{link_str}{tool_id}</a></div><br/>'
                     else:
-                        tool_ids_str += f'{tool_version.tool_id}<br/>'
+                        tool_ids_str += f"{tool_version.tool_id}<br/>"
             else:
-                tool_ids_str += f'{tool_version.tool_id}<br/>'
+                tool_ids_str += f"{tool_version.tool_id}<br/>"
             return tool_ids_str
 
     # Grid definition
@@ -506,16 +521,14 @@ class ToolVersionListGrid(grids.Grid):
     model_class = install_model.ToolVersion
     default_sort_key = "tool_id"
     columns = [
-        ToolIdColumn("Tool id",
-                     key='tool_id',
-                     attach_popup=False),
-        ToolVersionsColumn("Version lineage by tool id (parent/child ordered)")
+        ToolIdColumn("Tool id", key="tool_id", attach_popup=False),
+        ToolVersionsColumn("Version lineage by tool id (parent/child ordered)"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search tool id",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search tool id", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard"
+        )
+    )
     num_rows_per_page = 50
     use_paging = True
 
@@ -530,17 +543,27 @@ class AdminGalaxy(controller.JSAppLauncher):
     group_list_grid = GroupListGrid()
     quota_list_grid = QuotaListGrid()
     tool_version_list_grid = ToolVersionListGrid()
-    delete_operation = grids.GridOperation("Delete", condition=(lambda item: not item.deleted and not item.purged), allow_multiple=True)
-    undelete_operation = grids.GridOperation("Undelete", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True)
-    purge_operation = grids.GridOperation("Purge", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True)
+    delete_operation = grids.GridOperation(
+        "Delete", condition=(lambda item: not item.deleted and not item.purged), allow_multiple=True
+    )
+    undelete_operation = grids.GridOperation(
+        "Undelete", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True
+    )
+    purge_operation = grids.GridOperation(
+        "Purge", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True
+    )
     impersonate_operation = grids.GridOperation(
         "Impersonate",
         url_args=dict(controller="admin", action="impersonate"),
         condition=(lambda item: not item.deleted and not item.purged),
-        allow_multiple=False
+        allow_multiple=False,
+    )
+    activate_operation = grids.GridOperation(
+        "Activate User", condition=(lambda item: not item.active), allow_multiple=False
+    )
+    resend_activation_email = grids.GridOperation(
+        "Resend Activation Email", condition=(lambda item: not item.active), allow_multiple=False
     )
-    activate_operation = grids.GridOperation("Activate User", condition=(lambda item: not item.active), allow_multiple=False)
-    resend_activation_email = grids.GridOperation("Resend Activation Email", condition=(lambda item: not item.active), allow_multiple=False)
 
     def __init__(self, app):
         super().__init__(app)
@@ -557,40 +580,38 @@ class AdminGalaxy(controller.JSAppLauncher):
         """
         Endpoint for admin clientside routes.
         """
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         settings = {
-            'is_repo_installed': trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None,
-            'installing_repository_ids': get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True),
-            'is_tool_shed_installed': bool(trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds)
+            "is_repo_installed": trans.install_model.context.query(trans.install_model.ToolShedRepository).first()
+            is not None,
+            "installing_repository_ids": get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True),
+            "is_tool_shed_installed": bool(trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds),
         }
-        return self._bootstrapped_client(trans, app_name='admin', settings=settings, message=message, status=status)
+        return self._bootstrapped_client(trans, app_name="admin", settings=settings, message=message, status=status)
 
     @web.expose
     @web.json
     @web.require_admin
     def data_tables_list(self, trans, **kwd):
         data = []
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'done')
-        sorted_data_tables = sorted(
-            trans.app.tool_data_tables.get_tables().items()
-        )
+        message = kwd.get("message", "")
+        status = kwd.get("status", "done")
+        sorted_data_tables = sorted(trans.app.tool_data_tables.get_tables().items())
 
         for _data_table_elem_name, data_table in sorted_data_tables:
             for filename, file_dict in data_table.filenames.items():
-                file_missing = ['file missing'] \
-                    if not file_dict.get('found') else []
-                data.append({
-                    'name': data_table.name,
-                    'filename': filename,
-                    'tool_data_path': file_dict.get('tool_data_path'),
-                    'errors': ', '.join(file_missing + [
-                        error for error in file_dict.get('errors', [])
-                    ]),
-                })
+                file_missing = ["file missing"] if not file_dict.get("found") else []
+                data.append(
+                    {
+                        "name": data_table.name,
+                        "filename": filename,
+                        "tool_data_path": file_dict.get("tool_data_path"),
+                        "errors": ", ".join(file_missing + [error for error in file_dict.get("errors", [])]),
+                    }
+                )
 
-        return {'data': data, 'message': message, 'status': status}
+        return {"data": data, "message": message, "status": status}
 
     @web.expose
     @web.json
@@ -598,44 +619,43 @@ class AdminGalaxy(controller.JSAppLauncher):
     def data_types_list(self, trans, **kwd):
         datatypes = []
         keys = set()
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'done')
-        for dtype in sorted(trans.app.datatypes_registry.datatype_elems,
-                           key=lambda dtype: dtype.get('extension')):
+        message = kwd.get("message", "")
+        status = kwd.get("status", "done")
+        for dtype in sorted(trans.app.datatypes_registry.datatype_elems, key=lambda dtype: dtype.get("extension")):
             attrib = dict(dtype.attrib)
             datatypes.append(attrib)
             keys |= set(attrib.keys())
-        return {'keys': list(keys), 'data': datatypes, 'message': message, 'status': status}
+        return {"keys": list(keys), "data": datatypes, "message": message, "status": status}
 
     @web.expose
     @web.json
     @web.require_admin
     def users_list(self, trans, **kwd):
-        message = kwd.get('message', '')
-        status = kwd.get('status', '')
-        if 'operation' in kwd:
-            id = kwd.get('id')
+        message = kwd.get("message", "")
+        status = kwd.get("status", "")
+        if "operation" in kwd:
+            id = kwd.get("id")
             if not id:
-                message, status = (f'Invalid user id ({str(id)}) received.', 'error')
+                message, status = (f"Invalid user id ({str(id)}) received.", "error")
             ids = util.listify(id)
-            operation = kwd['operation'].lower()
-            if operation == 'delete':
+            operation = kwd["operation"].lower()
+            if operation == "delete":
                 message, status = self._delete_user(trans, ids)
-            elif operation == 'undelete':
+            elif operation == "undelete":
                 message, status = self._undelete_user(trans, ids)
-            elif operation == 'purge':
+            elif operation == "purge":
                 message, status = self._purge_user(trans, ids)
-            elif operation == 'recalculate disk usage':
+            elif operation == "recalculate disk usage":
                 message, status = self._recalculate_user(trans, id)
-            elif operation == 'generate new api key':
+            elif operation == "generate new api key":
                 message, status = self._new_user_apikey(trans, id)
-            elif operation == 'activate user':
+            elif operation == "activate user":
                 message, status = self._activate_user(trans, id)
-            elif operation == 'resend activation email':
+            elif operation == "resend activation email":
                 message, status = self._resend_activation_email(trans, id)
         if message and status:
-            kwd['message'] = util.sanitize_text(message)
-            kwd['status'] = status
+            kwd["message"] = util.sanitize_text(message)
+            kwd["status"] = status
         if trans.app.config.allow_user_deletion:
             if self.delete_operation not in self.user_list_grid.operations:
                 self.user_list_grid.operations.append(self.delete_operation)
@@ -655,198 +675,211 @@ class AdminGalaxy(controller.JSAppLauncher):
     @web.legacy_expose_api
     @web.require_admin
     def quotas_list(self, trans, payload=None, **kwargs):
-        message = kwargs.get('message', '')
-        status = kwargs.get('status', '')
-        if 'operation' in kwargs:
-            id = kwargs.get('id')
+        message = kwargs.get("message", "")
+        status = kwargs.get("status", "")
+        if "operation" in kwargs:
+            id = kwargs.get("id")
             if not id:
-                return self.message_exception(trans, f'Invalid quota id ({str(id)}) received.')
+                return self.message_exception(trans, f"Invalid quota id ({str(id)}) received.")
             quotas = []
             for quota_id in util.listify(id):
                 try:
                     quotas.append(get_quota(trans, quota_id))
                 except MessageException as e:
                     return self.message_exception(trans, util.unicodify(e))
-            operation = kwargs.pop('operation').lower()
+            operation = kwargs.pop("operation").lower()
             try:
-                if operation == 'delete':
+                if operation == "delete":
                     message = self.quota_manager.delete_quota(quotas)
-                elif operation == 'undelete':
+                elif operation == "undelete":
                     message = self.quota_manager.undelete_quota(quotas)
-                elif operation == 'purge':
+                elif operation == "purge":
                     message = self.quota_manager.purge_quota(quotas)
-                elif operation == 'unset as default':
+                elif operation == "unset as default":
                     message = self.quota_manager.unset_quota_default(quotas[0])
             except ActionInputError as e:
-                message, status = (e.err_msg, 'error')
+                message, status = (e.err_msg, "error")
         if message:
-            kwargs['message'] = util.sanitize_text(message)
-            kwargs['status'] = status or 'done'
+            kwargs["message"] = util.sanitize_text(message)
+            kwargs["status"] = status or "done"
         return self.quota_list_grid(trans, **kwargs)
 
     @web.legacy_expose_api
     @web.require_admin
     def create_quota(self, trans, payload=None, **kwd):
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             all_users = []
             all_groups = []
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 all_users.append((user.email, trans.security.encode_id(user.id)))
-            for group in trans.sa_session.query(trans.app.model.Group) \
-                                         .filter(trans.app.model.Group.deleted == false()) \
-                                         .order_by(trans.app.model.Group.name):
+            for group in (
+                trans.sa_session.query(trans.app.model.Group)
+                .filter(trans.app.model.Group.deleted == false())
+                .order_by(trans.app.model.Group.name)
+            ):
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
-            default_options = [('No', 'no')]
+            default_options = [("No", "no")]
             for type_ in trans.app.model.DefaultQuotaAssociation.types:
                 default_options.append((f"Yes, {type_}", type_))
-            return {'title': 'Create Quota',
-                    'inputs': [
-                        {
-                            'name': 'name',
-                            'label': 'Name'
-                        }, {
-                            'name': 'description',
-                            'label': 'Description'
-                        }, {
-                            'name': 'amount',
-                            'label': 'Amount',
-                            'help': 'Examples: "10000MB", "99 gb", "0.2T", "unlimited"'
-                        }, {
-                            'name': 'operation',
-                            'label': 'Assign, increase by amount, or decrease by amount?',
-                            'options': [('=', '='), ('+', '+'), ('-', '-')]
-                        }, {
-                            'name': 'default',
-                            'label': 'Is this quota a default for a class of users (if yes, what type)?',
-                            'options': default_options,
-                            'help': 'Warning: Any users or groups associated with this quota will be disassociated.'
-                        },
-                        build_select_input('in_groups', 'Groups', all_groups, []),
-                        build_select_input('in_users', 'Users', all_users, [])]}
+            return {
+                "title": "Create Quota",
+                "inputs": [
+                    {"name": "name", "label": "Name"},
+                    {"name": "description", "label": "Description"},
+                    {"name": "amount", "label": "Amount", "help": 'Examples: "10000MB", "99 gb", "0.2T", "unlimited"'},
+                    {
+                        "name": "operation",
+                        "label": "Assign, increase by amount, or decrease by amount?",
+                        "options": [("=", "="), ("+", "+"), ("-", "-")],
+                    },
+                    {
+                        "name": "default",
+                        "label": "Is this quota a default for a class of users (if yes, what type)?",
+                        "options": default_options,
+                        "help": "Warning: Any users or groups associated with this quota will be disassociated.",
+                    },
+                    build_select_input("in_groups", "Groups", all_groups, []),
+                    build_select_input("in_users", "Users", all_users, []),
+                ],
+            }
         else:
             try:
                 quota, message = self.quota_manager.create_quota(payload, decode_id=trans.security.decode_id)
-                return {'message': message}
+                return {"message": message}
             except ActionInputError as e:
                 return self.message_exception(trans, e.err_msg)
 
     @web.legacy_expose_api
     @web.require_admin
     def rename_quota(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No quota id received for renaming.')
+            return self.message_exception(trans, "No quota id received for renaming.")
         quota = get_quota(trans, id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             return {
-                'title': 'Change quota name and description for \'%s\'' % util.sanitize_text(quota.name),
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name',
-                    'value': quota.name
-                }, {
-                    'name': 'description',
-                    'label': 'Description',
-                    'value': quota.description
-                }]
+                "title": "Change quota name and description for '%s'" % util.sanitize_text(quota.name),
+                "inputs": [
+                    {"name": "name", "label": "Name", "value": quota.name},
+                    {"name": "description", "label": "Description", "value": quota.description},
+                ],
             }
         else:
             try:
-                return {'message': self.quota_manager.rename_quota(quota, util.Params(payload))}
+                return {"message": self.quota_manager.rename_quota(quota, util.Params(payload))}
             except ActionInputError as e:
                 return self.message_exception(trans, e.err_msg)
 
     @web.legacy_expose_api
     @web.require_admin
     def manage_users_and_groups_for_quota(self, trans, payload=None, **kwd):
-        quota_id = kwd.get('id')
+        quota_id = kwd.get("id")
         if not quota_id:
-            return self.message_exception(trans, f'Invalid quota id ({str(quota_id)}) received')
+            return self.message_exception(trans, f"Invalid quota id ({str(quota_id)}) received")
         quota = get_quota(trans, quota_id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             in_users = []
             all_users = []
             in_groups = []
             all_groups = []
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 if user in [x.user for x in quota.users]:
                     in_users.append(trans.security.encode_id(user.id))
                 all_users.append((user.email, trans.security.encode_id(user.id)))
-            for group in trans.sa_session.query(trans.app.model.Group) \
-                                         .filter(trans.app.model.Group.deleted == false()) \
-                                         .order_by(trans.app.model.Group.name):
+            for group in (
+                trans.sa_session.query(trans.app.model.Group)
+                .filter(trans.app.model.Group.deleted == false())
+                .order_by(trans.app.model.Group.name)
+            ):
                 if group in [x.group for x in quota.groups]:
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
-            return {'title': 'Quota \'%s\'' % quota.name,
-                    'message': 'Quota \'%s\' is currently associated with %d user(s) and %d group(s).' %
-                    (quota.name, len(in_users), len(in_groups)),
-                    'status': 'info',
-                    'inputs': [build_select_input('in_groups', 'Groups', all_groups, in_groups),
-                              build_select_input('in_users', 'Users', all_users, in_users)]}
+            return {
+                "title": "Quota '%s'" % quota.name,
+                "message": "Quota '%s' is currently associated with %d user(s) and %d group(s)."
+                % (quota.name, len(in_users), len(in_groups)),
+                "status": "info",
+                "inputs": [
+                    build_select_input("in_groups", "Groups", all_groups, in_groups),
+                    build_select_input("in_users", "Users", all_users, in_users),
+                ],
+            }
         else:
             try:
-                return {'message': self.quota_manager.manage_users_and_groups_for_quota(quota, util.Params(payload), decode_id=trans.security.decode_id)}
+                return {
+                    "message": self.quota_manager.manage_users_and_groups_for_quota(
+                        quota, util.Params(payload), decode_id=trans.security.decode_id
+                    )
+                }
             except ActionInputError as e:
                 return self.message_exception(trans, e.err_msg)
 
     @web.legacy_expose_api
     @web.require_admin
     def edit_quota(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No quota id received for renaming.')
+            return self.message_exception(trans, "No quota id received for renaming.")
         quota = get_quota(trans, id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             return {
-                'title': 'Edit quota size for \'%s\'' % util.sanitize_text(quota.name),
-                'inputs': [{
-                    'name': 'amount',
-                    'label': 'Amount',
-                    'value': quota.display_amount,
-                    'help': 'Examples: "10000MB", "99 gb", "0.2T", "unlimited"'
-                }, {
-                    'name': 'operation',
-                    'label': 'Assign, increase by amount, or decrease by amount?',
-                    'options': [('=', '='), ('+', '+'), ('-', '-')],
-                    'value': quota.operation
-                }]
+                "title": "Edit quota size for '%s'" % util.sanitize_text(quota.name),
+                "inputs": [
+                    {
+                        "name": "amount",
+                        "label": "Amount",
+                        "value": quota.display_amount,
+                        "help": 'Examples: "10000MB", "99 gb", "0.2T", "unlimited"',
+                    },
+                    {
+                        "name": "operation",
+                        "label": "Assign, increase by amount, or decrease by amount?",
+                        "options": [("=", "="), ("+", "+"), ("-", "-")],
+                        "value": quota.operation,
+                    },
+                ],
             }
         else:
             try:
-                return {'message': self.quota_manager.edit_quota(quota, util.Params(payload))}
+                return {"message": self.quota_manager.edit_quota(quota, util.Params(payload))}
             except ActionInputError as e:
                 return self.message_exception(trans, e.err_msg)
 
     @web.legacy_expose_api
     @web.require_admin
     def set_quota_default(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No quota id received for renaming.')
+            return self.message_exception(trans, "No quota id received for renaming.")
         quota = get_quota(trans, id)
-        if trans.request.method == 'GET':
-            default_value = quota.default[0].type if quota.default else 'no'
-            default_options = [('No', 'no')]
+        if trans.request.method == "GET":
+            default_value = quota.default[0].type if quota.default else "no"
+            default_options = [("No", "no")]
             for typ in trans.app.model.DefaultQuotaAssociation.types.__members__.values():
                 default_options.append((f"Yes, {typ}", typ))
             return {
-                'title': 'Set quota default for \'%s\'' % util.sanitize_text(quota.name),
-                'inputs': [{
-                    'name': 'default',
-                    'label': 'Assign, increase by amount, or decrease by amount?',
-                    'options': default_options,
-                    'value': default_value,
-                    'help': 'Warning: Any users or groups associated with this quota will be disassociated.'
-                }]
+                "title": "Set quota default for '%s'" % util.sanitize_text(quota.name),
+                "inputs": [
+                    {
+                        "name": "default",
+                        "label": "Assign, increase by amount, or decrease by amount?",
+                        "options": default_options,
+                        "value": default_value,
+                        "help": "Warning: Any users or groups associated with this quota will be disassociated.",
+                    }
+                ],
             }
         else:
             try:
-                return {'message': self.quota_manager.set_quota_default(quota, util.Params(payload))}
+                return {"message": self.quota_manager.set_quota_default(quota, util.Params(payload))}
             except ActionInputError as e:
                 return self.message_exception(trans, e.err_msg)
 
@@ -856,19 +889,22 @@ class AdminGalaxy(controller.JSAppLauncher):
         if not trans.app.config.allow_user_impersonation:
             return trans.show_error_message("User impersonation is not enabled in this instance of Galaxy.")
         user = None
-        user_id = kwd.get('id', None)
+        user_id = kwd.get("id", None)
         if user_id is not None:
             try:
                 user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
                 if user:
                     trans.handle_user_logout()
                     trans.handle_user_login(user)
-                    return trans.show_message(f"You are now logged in as {user.email}, <a target=\"_top\" href=\"{url_for(controller='root')}\">return to the home page</a>", use_panels=True)
+                    return trans.show_message(
+                        f"You are now logged in as {user.email}, <a target=\"_top\" href=\"{url_for(controller='root')}\">return to the home page</a>",
+                        use_panels=True,
+                    )
             except Exception:
                 log.exception("Error fetching user for impersonation")
-        return trans.response.send_redirect(web.url_for(controller='admin',
-                                                        action='users',
-                                                        message="Invalid user selected", status="error"))
+        return trans.response.send_redirect(
+            web.url_for(controller="admin", action="users", message="Invalid user selected", status="error")
+        )
 
     @web.legacy_expose_api
     @web.require_admin
@@ -879,67 +915,78 @@ class AdminGalaxy(controller.JSAppLauncher):
     @web.json
     @web.require_admin
     def roles_list(self, trans, **kwargs):
-        message = kwargs.get('message')
-        status = kwargs.get('status')
-        if 'operation' in kwargs:
-            id = kwargs.get('id', None)
+        message = kwargs.get("message")
+        status = kwargs.get("status")
+        if "operation" in kwargs:
+            id = kwargs.get("id", None)
             if not id:
-                message, status = (f'Invalid role id ({str(id)}) received.', 'error')
+                message, status = (f"Invalid role id ({str(id)}) received.", "error")
             ids = util.listify(id)
-            operation = kwargs['operation'].lower().replace('+', ' ')
-            if operation == 'delete':
+            operation = kwargs["operation"].lower().replace("+", " ")
+            if operation == "delete":
                 message, status = self._delete_role(trans, ids)
-            elif operation == 'undelete':
+            elif operation == "undelete":
                 message, status = self._undelete_role(trans, ids)
-            elif operation == 'purge':
+            elif operation == "purge":
                 message, status = self._purge_role(trans, ids)
         if message and status:
-            kwargs['message'] = util.sanitize_text(message)
-            kwargs['status'] = status
+            kwargs["message"] = util.sanitize_text(message)
+            kwargs["status"] = status
         return self.role_list_grid(trans, **kwargs)
 
     @web.legacy_expose_api
     @web.require_admin
     def create_role(self, trans, payload=None, **kwd):
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             all_users = []
             all_groups = []
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 all_users.append((user.email, trans.security.encode_id(user.id)))
-            for group in trans.sa_session.query(trans.app.model.Group) \
-                                         .filter(trans.app.model.Group.deleted == false()) \
-                                         .order_by(trans.app.model.Group.name):
+            for group in (
+                trans.sa_session.query(trans.app.model.Group)
+                .filter(trans.app.model.Group.deleted == false())
+                .order_by(trans.app.model.Group.name)
+            ):
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                'title': 'Create Role',
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name'
-                }, {
-                    'name': 'description',
-                    'label': 'Description'
-                },
-                    build_select_input('in_groups', 'Groups', all_groups, []),
-                    build_select_input('in_users', 'Users', all_users, []), {
-                    'name': 'auto_create',
-                    'label': 'Create a new group of the same name for this role:',
-                    'type': 'boolean',
-                    'optional': True,
-                }]}
+                "title": "Create Role",
+                "inputs": [
+                    {"name": "name", "label": "Name"},
+                    {"name": "description", "label": "Description"},
+                    build_select_input("in_groups", "Groups", all_groups, []),
+                    build_select_input("in_users", "Users", all_users, []),
+                    {
+                        "name": "auto_create",
+                        "label": "Create a new group of the same name for this role:",
+                        "type": "boolean",
+                        "optional": True,
+                    },
+                ],
+            }
         else:
-            name = util.restore_text(payload.get('name', ''))
-            description = util.restore_text(payload.get('description', ''))
-            auto_create_checked = payload.get('auto_create')
-            in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
-            in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))]
+            name = util.restore_text(payload.get("name", ""))
+            description = util.restore_text(payload.get("description", ""))
+            auto_create_checked = payload.get("auto_create")
+            in_users = [
+                trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_users"))
+            ]
+            in_groups = [
+                trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_groups"))
+            ]
             if not name or not description:
-                return self.message_exception(trans, 'Enter a valid name and a description.')
+                return self.message_exception(trans, "Enter a valid name and a description.")
             elif trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.name == name).first():
-                return self.message_exception(trans, 'Role names must be unique and a role with that name already exists, so choose another name.')
+                return self.message_exception(
+                    trans, "Role names must be unique and a role with that name already exists, so choose another name."
+                )
             elif None in in_users or None in in_groups:
-                return self.message_exception(trans, 'One or more invalid user/group id has been provided.')
+                return self.message_exception(trans, "One or more invalid user/group id has been provided.")
             else:
                 # Create the role
                 role = trans.app.model.Role(name=name, description=description, type=trans.app.model.Role.types.ADMIN)
@@ -955,7 +1002,10 @@ class AdminGalaxy(controller.JSAppLauncher):
                 if auto_create_checked:
                     # Check if role with same name already exists
                     if trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.name == name).first():
-                        return self.message_exception(trans, 'A group with that name already exists, so choose another name or disable group creation.')
+                        return self.message_exception(
+                            trans,
+                            "A group with that name already exists, so choose another name or disable group creation.",
+                        )
                     # Create the group
                     group = trans.app.model.Group(name=name)
                     trans.sa_session.add(group)
@@ -968,82 +1018,95 @@ class AdminGalaxy(controller.JSAppLauncher):
                 trans.sa_session.flush()
                 message = f"Role '{role.name}' has been created with {len(in_users)} associated users and {num_in_groups} associated groups."
                 if auto_create_checked:
-                    message += 'One of the groups associated with this role is the newly created group with the same name.'
-                return {'message': message}
+                    message += (
+                        "One of the groups associated with this role is the newly created group with the same name."
+                    )
+                return {"message": message}
 
     @web.legacy_expose_api
     @web.require_admin
     def rename_role(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No role id received for renaming.')
+            return self.message_exception(trans, "No role id received for renaming.")
         role = get_role(trans, id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             return {
-                'title': 'Change role name and description for \'%s\'' % util.sanitize_text(role.name),
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name',
-                    'value': role.name
-                }, {
-                    'name': 'description',
-                    'label': 'Description',
-                    'value': role.description
-                }]
+                "title": "Change role name and description for '%s'" % util.sanitize_text(role.name),
+                "inputs": [
+                    {"name": "name", "label": "Name", "value": role.name},
+                    {"name": "description", "label": "Description", "value": role.description},
+                ],
             }
         else:
             old_name = role.name
-            new_name = util.restore_text(payload.get('name'))
-            new_description = util.restore_text(payload.get('description'))
+            new_name = util.restore_text(payload.get("name"))
+            new_description = util.restore_text(payload.get("description"))
             if not new_name:
-                return self.message_exception(trans, 'Enter a valid role name.')
+                return self.message_exception(trans, "Enter a valid role name.")
             else:
-                existing_role = trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.name == new_name).first()
+                existing_role = (
+                    trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.name == new_name).first()
+                )
                 if existing_role and existing_role.id != role.id:
-                    return self.message_exception(trans, 'A role with that name already exists.')
+                    return self.message_exception(trans, "A role with that name already exists.")
                 else:
                     if not (role.name == new_name and role.description == new_description):
                         role.name = new_name
                         role.description = new_description
                         trans.sa_session.add(role)
                         trans.sa_session.flush()
-            return {'message': f'Role \'{old_name}\' has been renamed to \'{new_name}\'.'}
+            return {"message": f"Role '{old_name}' has been renamed to '{new_name}'."}
 
     @web.legacy_expose_api
     @web.require_admin
     def manage_users_and_groups_for_role(self, trans, payload=None, **kwd):
-        role_id = kwd.get('id')
+        role_id = kwd.get("id")
         if not role_id:
-            return self.message_exception(trans, f'Invalid role id ({str(role_id)}) received')
+            return self.message_exception(trans, f"Invalid role id ({str(role_id)}) received")
         role = get_role(trans, role_id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             in_users = []
             all_users = []
             in_groups = []
             all_groups = []
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 if user in [x.user for x in role.users]:
                     in_users.append(trans.security.encode_id(user.id))
                 all_users.append((user.email, trans.security.encode_id(user.id)))
-            for group in trans.sa_session.query(trans.app.model.Group) \
-                                         .filter(trans.app.model.Group.deleted == false()) \
-                                         .order_by(trans.app.model.Group.name):
+            for group in (
+                trans.sa_session.query(trans.app.model.Group)
+                .filter(trans.app.model.Group.deleted == false())
+                .order_by(trans.app.model.Group.name)
+            ):
                 if group in [x.group for x in role.groups]:
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
-            return {'title': 'Role \'%s\'' % role.name,
-                    'message': 'Role \'%s\' is currently associated with %d user(s) and %d group(s).' %
-                    (role.name, len(in_users), len(in_groups)),
-                    'status': 'info',
-                    'inputs': [build_select_input('in_groups', 'Groups', all_groups, in_groups),
-                              build_select_input('in_users', 'Users', all_users, in_users)]}
+            return {
+                "title": "Role '%s'" % role.name,
+                "message": "Role '%s' is currently associated with %d user(s) and %d group(s)."
+                % (role.name, len(in_users), len(in_groups)),
+                "status": "info",
+                "inputs": [
+                    build_select_input("in_groups", "Groups", all_groups, in_groups),
+                    build_select_input("in_users", "Users", all_users, in_users),
+                ],
+            }
         else:
-            in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
-            in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))]
+            in_users = [
+                trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_users"))
+            ]
+            in_groups = [
+                trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_groups"))
+            ]
             if None in in_users or None in in_groups:
-                return self.message_exception(trans, 'One or more invalid user/group id has been provided.')
+                return self.message_exception(trans, "One or more invalid user/group id has been provided.")
             for ura in role.users:
                 user = trans.sa_session.query(trans.app.model.User).get(ura.user_id)
                 if user not in in_users:
@@ -1059,17 +1122,19 @@ class AdminGalaxy(controller.JSAppLauncher):
                     trans.sa_session.flush()
             trans.app.security_agent.set_entity_role_associations(roles=[role], users=in_users, groups=in_groups)
             trans.sa_session.refresh(role)
-            return {'message': f"Role '{role.name}' has been updated with {len(in_users)} associated users and {len(in_groups)} associated groups."}
+            return {
+                "message": f"Role '{role.name}' has been updated with {len(in_users)} associated users and {len(in_groups)} associated groups."
+            }
 
     def _delete_role(self, trans, ids):
-        message = 'Deleted %d roles: ' % len(ids)
+        message = "Deleted %d roles: " % len(ids)
         for role_id in ids:
             role = get_role(trans, role_id)
             role.deleted = True
             trans.sa_session.add(role)
             trans.sa_session.flush()
-            message += f' {role.name} '
-        return (message, 'done')
+            message += f" {role.name} "
+        return (message, "done")
 
     def _undelete_role(self, trans, ids):
         count = 0
@@ -1124,136 +1189,163 @@ class AdminGalaxy(controller.JSAppLauncher):
     @web.legacy_expose_api
     @web.require_admin
     def groups_list(self, trans, **kwargs):
-        message = kwargs.get('message')
-        status = kwargs.get('status')
-        if 'operation' in kwargs:
-            id = kwargs.get('id')
+        message = kwargs.get("message")
+        status = kwargs.get("status")
+        if "operation" in kwargs:
+            id = kwargs.get("id")
             if not id:
-                return self.message_exception(trans, f'Invalid group id ({str(id)}) received.')
+                return self.message_exception(trans, f"Invalid group id ({str(id)}) received.")
             ids = util.listify(id)
-            operation = kwargs['operation'].lower().replace('+', ' ')
-            if operation == 'delete':
+            operation = kwargs["operation"].lower().replace("+", " ")
+            if operation == "delete":
                 message, status = self._delete_group(trans, ids)
-            elif operation == 'undelete':
+            elif operation == "undelete":
                 message, status = self._undelete_group(trans, ids)
-            elif operation == 'purge':
+            elif operation == "purge":
                 message, status = self._purge_group(trans, ids)
         if message and status:
-            kwargs['message'] = util.sanitize_text(message)
-            kwargs['status'] = status
+            kwargs["message"] = util.sanitize_text(message)
+            kwargs["status"] = status
         return self.group_list_grid(trans, **kwargs)
 
     @web.legacy_expose_api
     @web.require_admin
     def rename_group(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No group id received for renaming.')
+            return self.message_exception(trans, "No group id received for renaming.")
         group = get_group(trans, id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             return {
-                'title': 'Change group name for \'%s\'' % util.sanitize_text(group.name),
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name',
-                    'value': group.name
-                }]
+                "title": "Change group name for '%s'" % util.sanitize_text(group.name),
+                "inputs": [{"name": "name", "label": "Name", "value": group.name}],
             }
         else:
             old_name = group.name
-            new_name = util.restore_text(payload.get('name'))
+            new_name = util.restore_text(payload.get("name"))
             if not new_name:
-                return self.message_exception(trans, 'Enter a valid group name.')
+                return self.message_exception(trans, "Enter a valid group name.")
             else:
-                existing_group = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.name == new_name).first()
+                existing_group = (
+                    trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.name == new_name).first()
+                )
                 if existing_group and existing_group.id != group.id:
-                    return self.message_exception(trans, 'A group with that name already exists.')
+                    return self.message_exception(trans, "A group with that name already exists.")
                 else:
                     if not (group.name == new_name):
                         group.name = new_name
                         trans.sa_session.add(group)
                         trans.sa_session.flush()
-            return {'message': f'Group \'{old_name}\' has been renamed to \'{new_name}\'.'}
+            return {"message": f"Group '{old_name}' has been renamed to '{new_name}'."}
 
     @web.legacy_expose_api
     @web.require_admin
     def manage_users_and_roles_for_group(self, trans, payload=None, **kwd):
-        group_id = kwd.get('id')
+        group_id = kwd.get("id")
         if not group_id:
-            return self.message_exception(trans, f'Invalid group id ({str(group_id)}) received')
+            return self.message_exception(trans, f"Invalid group id ({str(group_id)}) received")
         group = get_group(trans, group_id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             in_users = []
             all_users = []
             in_roles = []
             all_roles = []
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 if user in [x.user for x in group.users]:
                     in_users.append(trans.security.encode_id(user.id))
                 all_users.append((user.email, trans.security.encode_id(user.id)))
-            for role in trans.sa_session.query(trans.app.model.Role) \
-                                        .filter(trans.app.model.Role.deleted == false()) \
-                                        .order_by(trans.app.model.Role.name):
+            for role in (
+                trans.sa_session.query(trans.app.model.Role)
+                .filter(trans.app.model.Role.deleted == false())
+                .order_by(trans.app.model.Role.name)
+            ):
                 if role in [x.role for x in group.roles]:
                     in_roles.append(trans.security.encode_id(role.id))
                 all_roles.append((role.name, trans.security.encode_id(role.id)))
-            return {'title': 'Group \'%s\'' % group.name,
-                    'message': 'Group \'%s\' is currently associated with %d user(s) and %d role(s).' %
-                    (group.name, len(in_users), len(in_roles)),
-                    'status': 'info',
-                    'inputs': [build_select_input('in_roles', 'Roles', all_roles, in_roles),
-                              build_select_input('in_users', 'Users', all_users, in_users)]}
+            return {
+                "title": "Group '%s'" % group.name,
+                "message": "Group '%s' is currently associated with %d user(s) and %d role(s)."
+                % (group.name, len(in_users), len(in_roles)),
+                "status": "info",
+                "inputs": [
+                    build_select_input("in_roles", "Roles", all_roles, in_roles),
+                    build_select_input("in_users", "Users", all_users, in_users),
+                ],
+            }
         else:
-            in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
-            in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]
+            in_users = [
+                trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_users"))
+            ]
+            in_roles = [
+                trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_roles"))
+            ]
             if None in in_users or None in in_roles:
-                return self.message_exception(trans, 'One or more invalid user/role id has been provided.')
+                return self.message_exception(trans, "One or more invalid user/role id has been provided.")
             trans.app.security_agent.set_entity_group_associations(groups=[group], users=in_users, roles=in_roles)
             trans.sa_session.refresh(group)
-            return {'message': f"Group '{group.name}' has been updated with {len(in_users)} associated users and {len(in_roles)} associated roles."}
+            return {
+                "message": f"Group '{group.name}' has been updated with {len(in_users)} associated users and {len(in_roles)} associated roles."
+            }
 
     @web.legacy_expose_api
     @web.require_admin
     def create_group(self, trans, payload=None, **kwd):
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             all_users = []
             all_roles = []
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 all_users.append((user.email, trans.security.encode_id(user.id)))
-            for role in trans.sa_session.query(trans.app.model.Role) \
-                                        .filter(trans.app.model.Role.deleted == false()) \
-                                        .order_by(trans.app.model.Role.name):
+            for role in (
+                trans.sa_session.query(trans.app.model.Role)
+                .filter(trans.app.model.Role.deleted == false())
+                .order_by(trans.app.model.Role.name)
+            ):
                 all_roles.append((role.name, trans.security.encode_id(role.id)))
             return {
-                'title': 'Create Group',
-                'title_id': 'create-group',
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name'
-                },
-                    build_select_input('in_roles', 'Roles', all_roles, []),
-                    build_select_input('in_users', 'Users', all_users, []), {
-                    'name': 'auto_create',
-                    'label': 'Create a new role of the same name for this group:',
-                    'type': 'boolean',
-                    'optional': True,
-                }]
+                "title": "Create Group",
+                "title_id": "create-group",
+                "inputs": [
+                    {"name": "name", "label": "Name"},
+                    build_select_input("in_roles", "Roles", all_roles, []),
+                    build_select_input("in_users", "Users", all_users, []),
+                    {
+                        "name": "auto_create",
+                        "label": "Create a new role of the same name for this group:",
+                        "type": "boolean",
+                        "optional": True,
+                    },
+                ],
             }
         else:
-            name = util.restore_text(payload.get('name', ''))
-            auto_create_checked = payload.get('auto_create')
-            in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
-            in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]
+            name = util.restore_text(payload.get("name", ""))
+            auto_create_checked = payload.get("auto_create")
+            in_users = [
+                trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_users"))
+            ]
+            in_roles = [
+                trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_roles"))
+            ]
             if not name:
-                return self.message_exception(trans, 'Enter a valid name.')
+                return self.message_exception(trans, "Enter a valid name.")
             elif trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.name == name).first():
-                return self.message_exception(trans, 'Group names must be unique and a group with that name already exists, so choose another name.')
+                return self.message_exception(
+                    trans,
+                    "Group names must be unique and a group with that name already exists, so choose another name.",
+                )
             elif None in in_users or None in in_roles:
-                return self.message_exception(trans, 'One or more invalid user/role id has been provided.')
+                return self.message_exception(trans, "One or more invalid user/role id has been provided.")
             else:
                 # Create the role
                 group = trans.app.model.Group(name=name)
@@ -1269,9 +1361,12 @@ class AdminGalaxy(controller.JSAppLauncher):
                 if auto_create_checked:
                     # Check if role with same name already exists
                     if trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.name == name).first():
-                        return self.message_exception(trans, 'A role with that name already exists, so choose another name or disable role creation.')
+                        return self.message_exception(
+                            trans,
+                            "A role with that name already exists, so choose another name or disable role creation.",
+                        )
                     # Create the role
-                    role = trans.app.model.Role(name=name, description=f'Role for group {name}')
+                    role = trans.app.model.Role(name=name, description=f"Role for group {name}")
                     trans.sa_session.add(role)
                     # Associate the group with the role
                     gra = trans.model.GroupRoleAssociation(group, role)
@@ -1280,20 +1375,26 @@ class AdminGalaxy(controller.JSAppLauncher):
                 else:
                     num_in_roles = len(in_roles)
                 trans.sa_session.flush()
-                message = 'Group \'%s\' has been created with %d associated users and %d associated roles.' % (group.name, len(in_users), num_in_roles)
+                message = "Group '%s' has been created with %d associated users and %d associated roles." % (
+                    group.name,
+                    len(in_users),
+                    num_in_roles,
+                )
                 if auto_create_checked:
-                    message += 'One of the roles associated with this group is the newly created role with the same name.'
-                return {'message': message}
+                    message += (
+                        "One of the roles associated with this group is the newly created role with the same name."
+                    )
+                return {"message": message}
 
     def _delete_group(self, trans, ids):
-        message = 'Deleted %d groups: ' % len(ids)
+        message = "Deleted %d groups: " % len(ids)
         for group_id in ids:
             group = get_group(trans, group_id)
             group.deleted = True
             trans.sa_session.add(group)
             trans.sa_session.flush()
-            message += f' {group.name} '
-        return (message, 'done')
+            message += f" {group.name} "
+        return (message, "done")
 
     def _undelete_group(self, trans, ids):
         count = 0
@@ -1328,25 +1429,25 @@ class AdminGalaxy(controller.JSAppLauncher):
     @web.expose
     @web.require_admin
     def create_new_user(self, trans, **kwd):
-        return trans.response.send_redirect(web.url_for(controller='user',
-                                                        action='create',
-                                                        cntrller='admin'))
+        return trans.response.send_redirect(web.url_for(controller="user", action="create", cntrller="admin"))
 
     @web.legacy_expose_api
     @web.require_admin
     def reset_user_password(self, trans, payload=None, **kwd):
-        users = {user_id: get_user(trans, user_id) for user_id in util.listify(kwd.get('id'))}
+        users = {user_id: get_user(trans, user_id) for user_id in util.listify(kwd.get("id"))}
         if users:
-            if trans.request.method == 'GET':
+            if trans.request.method == "GET":
                 return {
-                    'message': f"Changes password(s) for: {', '.join(user.email for user in users.values())}.",
-                    'status': 'info',
-                    'inputs': [{'name': 'password', 'label': 'New password', 'type': 'password'},
-                              {'name': 'confirm', 'label': 'Confirm password', 'type': 'password'}]
+                    "message": f"Changes password(s) for: {', '.join(user.email for user in users.values())}.",
+                    "status": "info",
+                    "inputs": [
+                        {"name": "password", "label": "New password", "type": "password"},
+                        {"name": "confirm", "label": "Confirm password", "type": "password"},
+                    ],
                 }
             else:
-                password = payload.get('password')
-                confirm = payload.get('confirm')
+                password = payload.get("password")
+                confirm = payload.get("confirm")
                 message = validate_password(trans, password, confirm)
                 if message:
                     return self.message_exception(trans, message)
@@ -1354,19 +1455,19 @@ class AdminGalaxy(controller.JSAppLauncher):
                     user.set_password_cleartext(password)
                     trans.sa_session.add(user)
                     trans.sa_session.flush()
-                return {'message': 'Passwords reset for %d user(s).' % len(users)}
+                return {"message": "Passwords reset for %d user(s)." % len(users)}
         else:
-            return self.message_exception(trans, 'Please specify user ids.')
+            return self.message_exception(trans, "Please specify user ids.")
 
     def _delete_user(self, trans, ids):
-        message = 'Deleted %d users: ' % len(ids)
+        message = "Deleted %d users: " % len(ids)
         for user_id in ids:
             user = get_user(trans, user_id)
             # Actually do the delete
             self.user_manager.delete(user)
             # Accumulate messages for the return message
-            message += f' {user.email} '
-        return (message, 'done')
+            message += f" {user.email} "
+        return (message, "done")
 
     def _undelete_user(self, trans, ids):
         count = 0
@@ -1377,9 +1478,9 @@ class AdminGalaxy(controller.JSAppLauncher):
             self.user_manager.undelete(user)
             # Count and accumulate messages to return to the admin panel
             count += 1
-            undeleted_users += f' {user.email}'
-        message = 'Undeleted %d users: %s' % (count, undeleted_users)
-        return (message, 'done')
+            undeleted_users += f" {user.email}"
+        message = "Undeleted %d users: %s" % (count, undeleted_users)
+        return (message, "done")
 
     def _purge_user(self, trans, ids):
         # This method should only be called for a User that has previously been deleted.
@@ -1393,33 +1494,32 @@ class AdminGalaxy(controller.JSAppLauncher):
         # - UserRoleAssociation where user_id == User.id EXCEPT FOR THE PRIVATE ROLE
         # - UserAddress where user_id == User.id
         # Purging Histories and Datasets must be handled via the cleanup_datasets.py script
-        message = 'Purged %d users: ' % len(ids)
+        message = "Purged %d users: " % len(ids)
         for user_id in ids:
             user = get_user(trans, user_id)
             self.user_manager.purge(user)
-            message += f'\t{user.email}\n '
-        return (message, 'done')
+            message += f"\t{user.email}\n "
+        return (message, "done")
 
     def _recalculate_user(self, trans, user_id):
         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
         if not user:
-            return (f'User not found for id ({sanitize_text(str(user_id))})', 'error')
+            return (f"User not found for id ({sanitize_text(str(user_id))})", "error")
         current = user.get_disk_usage()
         user.calculate_and_set_disk_usage()
         new = user.get_disk_usage()
         if new in (current, None):
-            message = f'Usage is unchanged at {nice_size(current)}.'
+            message = f"Usage is unchanged at {nice_size(current)}."
         else:
-            message = f'Usage has changed by {nice_size(new - current)} to {nice_size(new)}.'
-        return (message, 'done')
+            message = f"Usage has changed by {nice_size(new - current)} to {nice_size(new)}."
+        return (message, "done")
 
     def _new_user_apikey(self, trans, user_id):
         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
         if not user:
-            return (f'User not found for id ({sanitize_text(str(user_id))})', 'error')
+            return (f"User not found for id ({sanitize_text(str(user_id))})", "error")
         new_key = trans.app.model.APIKeys(
-            user_id=trans.security.decode_id(user_id),
-            key=trans.app.security.get_new_guid()
+            user_id=trans.security.decode_id(user_id), key=trans.app.security.get_new_guid()
         )
         trans.sa_session.add(new_key)
         trans.sa_session.flush()
@@ -1428,33 +1528,36 @@ class AdminGalaxy(controller.JSAppLauncher):
     def _activate_user(self, trans, user_id):
         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
         if not user:
-            return (f'User not found for id ({sanitize_text(str(user_id))})', 'error')
+            return (f"User not found for id ({sanitize_text(str(user_id))})", "error")
         self.user_manager.activate(user)
-        return (f'Activated user: {user.email}.', 'done')
+        return (f"Activated user: {user.email}.", "done")
 
     def _resend_activation_email(self, trans, user_id):
         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
         if not user:
-            return (f'User not found for id ({sanitize_text(str(user_id))})', 'error')
+            return (f"User not found for id ({sanitize_text(str(user_id))})", "error")
         if self.user_manager.send_activation_email(trans, user.email, user.username):
-            return (f'Activation email has been sent to user: {user.email}.', 'done')
+            return (f"Activation email has been sent to user: {user.email}.", "done")
         else:
-            return (f'Unable to send activation email to user: {user.email}.', 'error')
+            return (f"Unable to send activation email to user: {user.email}.", "error")
 
     @web.legacy_expose_api
     @web.require_admin
     def manage_roles_and_groups_for_user(self, trans, payload=None, **kwd):
-        user_id = kwd.get('id')
+        user_id = kwd.get("id")
         if not user_id:
-            return self.message_exception(trans, f'Invalid user id ({str(user_id)}) received')
+            return self.message_exception(trans, f"Invalid user id ({str(user_id)}) received")
         user = get_user(trans, user_id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             in_roles = []
             all_roles = []
             in_groups = []
             all_groups = []
-            for role in trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.deleted == false()) \
-                    .order_by(trans.app.model.Role.name):
+            for role in (
+                trans.sa_session.query(trans.app.model.Role)
+                .filter(trans.app.model.Role.deleted == false())
+                .order_by(trans.app.model.Role.name)
+            ):
                 if role in [x.role for x in user.roles]:
                     in_roles.append(trans.security.encode_id(role.id))
                 if role.type != trans.app.model.Role.types.PRIVATE:
@@ -1463,21 +1566,34 @@ class AdminGalaxy(controller.JSAppLauncher):
                     # role, which should always be in in_roles.  The check above is added as an additional
                     # precaution, since for a period of time we were including private roles in the form fields.
                     all_roles.append((role.name, trans.security.encode_id(role.id)))
-            for group in trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.deleted == false()) \
-                    .order_by(trans.app.model.Group.name):
+            for group in (
+                trans.sa_session.query(trans.app.model.Group)
+                .filter(trans.app.model.Group.deleted == false())
+                .order_by(trans.app.model.Group.name)
+            ):
                 if group in [x.group for x in user.groups]:
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
-            return {'title': f"Roles and groups for '{user.email}'",
-                    'message': f"User '{user.email}' is currently associated with {len(in_roles) - 1} role(s) and is a member of {len(in_groups)} group(s).",
-                    'status': 'info',
-                    'inputs': [build_select_input('in_roles', 'Roles', all_roles, in_roles),
-                              build_select_input('in_groups', 'Groups', all_groups, in_groups)]}
+            return {
+                "title": f"Roles and groups for '{user.email}'",
+                "message": f"User '{user.email}' is currently associated with {len(in_roles) - 1} role(s) and is a member of {len(in_groups)} group(s).",
+                "status": "info",
+                "inputs": [
+                    build_select_input("in_roles", "Roles", all_roles, in_roles),
+                    build_select_input("in_groups", "Groups", all_groups, in_groups),
+                ],
+            }
         else:
-            in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]
-            in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))]
+            in_roles = [
+                trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_roles"))
+            ]
+            in_groups = [
+                trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x))
+                for x in util.listify(payload.get("in_groups"))
+            ]
             if None in in_groups or None in in_roles:
-                return self.message_exception(trans, 'One or more invalid role/group id has been provided.')
+                return self.message_exception(trans, "One or more invalid role/group id has been provided.")
 
             # make sure the user is not dis-associating himself from his private role
             private_role = trans.app.security_agent.get_private_user_role(user)
@@ -1486,18 +1602,22 @@ class AdminGalaxy(controller.JSAppLauncher):
 
             trans.app.security_agent.set_entity_user_associations(users=[user], roles=in_roles, groups=in_groups)
             trans.sa_session.refresh(user)
-            return {'message': f"User '{user.email}' has been updated with {len(in_roles) - 1} associated roles and {len(in_groups)} associated groups (private roles are not displayed)."}
+            return {
+                "message": f"User '{user.email}' has been updated with {len(in_roles) - 1} associated roles and {len(in_groups)} associated groups (private roles are not displayed)."
+            }
 
     @web.expose
     @web.require_admin
-    def manage_tool_dependencies(self,
-                                 trans,
-                                 install_dependencies=False,
-                                 uninstall_dependencies=False,
-                                 remove_unused_dependencies=False,
-                                 selected_tool_ids=None,
-                                 selected_environments_to_uninstall=None,
-                                 viewkey='View tool-centric dependencies'):
+    def manage_tool_dependencies(
+        self,
+        trans,
+        install_dependencies=False,
+        uninstall_dependencies=False,
+        remove_unused_dependencies=False,
+        selected_tool_ids=None,
+        selected_environments_to_uninstall=None,
+        viewkey="View tool-centric dependencies",
+    ):
         if not selected_tool_ids:
             selected_tool_ids = []
         if not selected_environments_to_uninstall:
@@ -1517,25 +1637,30 @@ class AdminGalaxy(controller.JSAppLauncher):
             if not isinstance(selected_environments_to_uninstall, list):
                 selected_environments_to_uninstall = [selected_environments_to_uninstall]
             view.remove_unused_dependency_paths(selected_environments_to_uninstall)
-        return trans.fill_template('/webapps/galaxy/admin/manage_dependencies.mako',
-                                   tools=tools_by_id,
-                                   requirements_status=view.toolbox_requirements_status,
-                                   tool_ids_by_requirements=view.tool_ids_by_requirements,
-                                   unused_environments=view.unused_dependency_paths,
-                                   viewkey=viewkey)
+        return trans.fill_template(
+            "/webapps/galaxy/admin/manage_dependencies.mako",
+            tools=tools_by_id,
+            requirements_status=view.toolbox_requirements_status,
+            tool_ids_by_requirements=view.tool_ids_by_requirements,
+            unused_environments=view.unused_dependency_paths,
+            viewkey=viewkey,
+        )
+
 
 # ---- Utility methods -------------------------------------------------------
 
 
 def build_select_input(name, label, options, value):
-    return {'type': 'select',
-            'multiple': True,
-            'optional': True,
-            'individual': True,
-            'name': name,
-            'label': label,
-            'options': options,
-            'value': value}
+    return {
+        "type": "select",
+        "multiple": True,
+        "optional": True,
+        "individual": True,
+        "name": name,
+        "label": label,
+        "options": options,
+        "value": value,
+    }
 
 
 def get_user(trans, user_id):
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 416f8cc0b54..213a1304290 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -6,7 +6,10 @@ from functools import wraps
 from sqlalchemy import or_
 
 import tool_shed.repository_types.util as rt_util
-from galaxy import util, web
+from galaxy import (
+    util,
+    web,
+)
 from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.tool_shed.galaxy_install import install_manager
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
@@ -22,7 +25,9 @@ from tool_shed.util import (
     hg_util,
     readme_util,
     repository_util,
-    shed_util_common as suc,
+)
+from tool_shed.util import shed_util_common as suc
+from tool_shed.util import (
     tool_dependency_util,
     tool_util,
 )
@@ -52,44 +57,57 @@ class AdminToolshed(AdminGalaxy):
     @legacy_tool_shed_endpoint
     def activate_repository(self, trans, **kwd):
         """Activate a repository that was deactivated but not uninstalled."""
-        repository_id = kwd['id']
+        repository_id = kwd["id"]
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         try:
             trans.app.installed_repository_manager.activate_repository(repository)
-            message = f'The <b>{escape(repository.name)}</b> repository has been activated.'
-            status = 'done'
+            message = f"The <b>{escape(repository.name)}</b> repository has been activated."
+            status = "done"
         except Exception as e:
             error_message = f"Error activating repository {escape(repository.name)}: {unicodify(e)}"
             log.exception(error_message)
-            message = '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository.  Click <a href="%s">here</a> to uninstall the repository.' \
-                % (error_message, web.url_for(controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id(repository.id)))
-            status = 'error'
-        return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                        action='manage_repository',
-                                                        id=repository_id,
-                                                        message=message,
-                                                        status=status))
+            message = (
+                '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository.  Click <a href="%s">here</a> to uninstall the repository.'
+                % (
+                    error_message,
+                    web.url_for(
+                        controller="admin_toolshed",
+                        action="deactivate_or_uninstall_repository",
+                        id=trans.security.encode_id(repository.id),
+                    ),
+                )
+            )
+            status = "error"
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="admin_toolshed",
+                action="manage_repository",
+                id=repository_id,
+                message=message,
+                status=status,
+            )
+        )
 
     @web.legacy_expose_api
     @web.require_admin
     @legacy_tool_shed_endpoint
     def browse_repositories(self, trans, **kwd):
-        message = kwd.get('message', '')
-        status = kwd.get('status', '')
-        if 'operation' in kwd:
-            operation = kwd.pop('operation').lower()
+        message = kwd.get("message", "")
+        status = kwd.get("status", "")
+        if "operation" in kwd:
+            operation = kwd.pop("operation").lower()
             if operation == "update tool shed status":
-                message, status = repository_util.check_for_updates(trans.app, trans.install_model, kwd.get('id'))
+                message, status = repository_util.check_for_updates(trans.app, trans.install_model, kwd.get("id"))
         if message and status:
-            kwd['message'] = util.sanitize_text(message)
-            kwd['status'] = 'success' if status in ['ok', 'done', 'success'] else 'error'
+            kwd["message"] = util.sanitize_text(message)
+            kwd["status"] = "success" if status in ["ok", "done", "success"] else "error"
         return self.installed_repository_grid(trans, **kwd)
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def restore_repository(self, trans, **kwd):
-        repository_id = kwd['id']
+        repository_id = kwd["id"]
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         if repository.uninstalled:
             # Since we're reinstalling the repository we need to find the latest changeset revision to which it can
@@ -97,44 +115,51 @@ class AdminToolshed(AdminGalaxy):
             # repository dependencies and tool dependencies will be current.  Only allow selecting a different section
             # in the tool panel if the repository was uninstalled and it contained tools that should be displayed in
             # the tool panel.
-            changeset_revision_dict = trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(repository)
-            current_changeset_revision = changeset_revision_dict.get('changeset_revision', None)
-            current_ctx_rev = changeset_revision_dict.get('ctx_rev', None)
+            changeset_revision_dict = trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(
+                repository
+            )
+            current_changeset_revision = changeset_revision_dict.get("changeset_revision", None)
+            current_ctx_rev = changeset_revision_dict.get("ctx_rev", None)
             if current_changeset_revision and current_ctx_rev:
                 if current_ctx_rev == repository.ctx_rev:
                     # The uninstalled repository is current.
-                    return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                    action='reselect_tool_panel_section',
-                                                                    **kwd))
+                    return trans.response.send_redirect(
+                        web.url_for(controller="admin_toolshed", action="reselect_tool_panel_section", **kwd)
+                    )
                 else:
                     # The uninstalled repository has updates available in the tool shed.
-                    updated_repo_info_dict = \
-                        self.get_updated_repository_information(trans=trans,
-                                                                repository_id=trans.security.encode_id(repository.id),
-                                                                repository_name=repository.name,
-                                                                repository_owner=repository.owner,
-                                                                changeset_revision=current_changeset_revision)
+                    updated_repo_info_dict = self.get_updated_repository_information(
+                        trans=trans,
+                        repository_id=trans.security.encode_id(repository.id),
+                        repository_name=repository.name,
+                        repository_owner=repository.owner,
+                        changeset_revision=current_changeset_revision,
+                    )
                     json_repo_info_dict = json.dumps(updated_repo_info_dict)
                     encoded_repo_info_dict = encoding_util.tool_shed_encode(json_repo_info_dict)
-                    kwd['latest_changeset_revision'] = current_changeset_revision
-                    kwd['latest_ctx_rev'] = current_ctx_rev
-                    kwd['updated_repo_info_dict'] = encoded_repo_info_dict
-                    return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                    action='reselect_tool_panel_section',
-                                                                    **kwd))
+                    kwd["latest_changeset_revision"] = current_changeset_revision
+                    kwd["latest_ctx_rev"] = current_ctx_rev
+                    kwd["updated_repo_info_dict"] = encoded_repo_info_dict
+                    return trans.response.send_redirect(
+                        web.url_for(controller="admin_toolshed", action="reselect_tool_panel_section", **kwd)
+                    )
             else:
                 message = f"Unable to get latest revision for repository <b>{escape(str(repository.name))}</b> from "
                 message += "the Tool Shed, so repository re-installation is not possible at this time."
                 status = "error"
-                return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                action='manage_repository',
-                                                                id=repository_id,
-                                                                message=message,
-                                                                status=status))
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="admin_toolshed",
+                        action="manage_repository",
+                        id=repository_id,
+                        message=message,
+                        status=status,
+                    )
+                )
         else:
-            return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                            action='activate_repository',
-                                                            **kwd))
+            return trans.response.send_redirect(
+                web.url_for(controller="admin_toolshed", action="activate_repository", **kwd)
+            )
 
     @web.expose
     def display_image_in_repository(self, trans, **kwd):
@@ -149,62 +174,66 @@ class AdminToolshed(AdminGalaxy):
         .. image:: some_image.jpg
         .. image:: /deep/some_image.png
         """
-        repository_id = kwd.get('repository_id', None)
-        relative_path_to_image_file = kwd.get('image_file', None)
+        repository_id = kwd.get("repository_id", None)
+        relative_path_to_image_file = kwd.get("image_file", None)
         if repository_id and relative_path_to_image_file:
             repository = repository_util.get_tool_shed_repository_by_id(trans.app, repository_id)
             if repository:
                 repo_files_dir = repository.repo_files_directory(trans.app)
                 # The following line sometimes returns None.  TODO: Figure out why.
-                path_to_file = repository_util.get_absolute_path_to_file_in_repository(repo_files_dir, relative_path_to_image_file)
+                path_to_file = repository_util.get_absolute_path_to_file_in_repository(
+                    repo_files_dir, relative_path_to_image_file
+                )
                 if path_to_file and os.path.exists(path_to_file):
                     file_name = os.path.basename(relative_path_to_image_file)
                     try:
-                        extension = file_name.split('.')[-1]
+                        extension = file_name.split(".")[-1]
                     except Exception:
                         extension = None
                     if extension:
                         mimetype = trans.app.datatypes_registry.get_mimetype_by_extension(extension)
                         if mimetype:
                             trans.response.set_content_type(mimetype)
-                    return open(path_to_file, 'rb')
+                    return open(path_to_file, "rb")
         return None
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def view_tool_metadata(self, trans, repository_id, tool_id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         repository_metadata = repository.metadata_
         shed_config_dict = repository.get_shed_config_dict(trans.app)
         tool_metadata = {}
         tool_lineage = []
         tool = None
-        if 'tools' in repository_metadata:
-            for tool_metadata_dict in repository_metadata['tools']:
-                if tool_metadata_dict['id'] == tool_id:
+        if "tools" in repository_metadata:
+            for tool_metadata_dict in repository_metadata["tools"]:
+                if tool_metadata_dict["id"] == tool_id:
                     tool_metadata = tool_metadata_dict
-                    tool_config = tool_metadata['tool_config']
-                    if shed_config_dict and shed_config_dict.get('tool_path'):
-                        tool_config = os.path.join(shed_config_dict.get('tool_path'), tool_config)
-                    tool = trans.app.toolbox.get_tool(tool_id=tool_metadata['guid'], exact=True)
+                    tool_config = tool_metadata["tool_config"]
+                    if shed_config_dict and shed_config_dict.get("tool_path"):
+                        tool_config = os.path.join(shed_config_dict.get("tool_path"), tool_config)
+                    tool = trans.app.toolbox.get_tool(tool_id=tool_metadata["guid"], exact=True)
                     if not tool:
-                        tool = trans.app.toolbox.load_tool(os.path.abspath(tool_config), guid=tool_metadata['guid'])
+                        tool = trans.app.toolbox.load_tool(os.path.abspath(tool_config), guid=tool_metadata["guid"])
                         if tool:
                             tool._lineage = trans.app.toolbox._lineage_map.register(tool)
                     if tool:
                         tool_lineage = tool.lineage.get_version_ids(reverse=True)
                     break
-        return trans.fill_template("/admin/tool_shed_repository/view_tool_metadata.mako",
-                                   repository=repository,
-                                   repository_metadata=repository_metadata,
-                                   tool=tool,
-                                   tool_metadata=tool_metadata,
-                                   tool_lineage=tool_lineage,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/admin/tool_shed_repository/view_tool_metadata.mako",
+            repository=repository,
+            repository_metadata=repository_metadata,
+            tool=tool,
+            tool_metadata=tool_metadata,
+            tool_lineage=tool_lineage,
+            message=message,
+            status=status,
+        )
 
     @web.json
     @web.require_admin
@@ -226,24 +255,32 @@ class AdminToolshed(AdminGalaxy):
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
         if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
-            message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required "
-            message += "parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
-                (str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
+            message = (
+                "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required "
+            )
+            message += (
+                "parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s "
+                % (str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
+            )
             raise Exception(message)
         params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision)
-        pathspec = ['repository', 'get_tool_dependencies']
-        raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        pathspec = ["repository", "get_tool_dependencies"]
+        raw_text = util.url_get(
+            tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         if len(raw_text) > 2:
             encoded_text = json.loads(raw_text)
             text = encoding_util.tool_shed_decode(encoded_text)
         else:
-            text = ''
+            text = ""
         return text
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
-    def get_updated_repository_information(self, trans, repository_id, repository_name, repository_owner, changeset_revision):
+    def get_updated_repository_information(
+        self, trans, repository_id, repository_name, repository_owner, changeset_revision
+    ):
         """
         Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall
         an updated revision of an uninstalled tool shed repository.
@@ -252,14 +289,16 @@ class AdminToolshed(AdminGalaxy):
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
         if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
             message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following "
-            message += "required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
-                (str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
+            message += (
+                "required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s "
+                % (str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
+            )
             raise Exception(message)
-        params = dict(name=str(repository_name),
-                      owner=str(repository_owner),
-                      changeset_revision=changeset_revision)
-        pathspec = ['repository', 'get_updated_repository_information']
-        raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+        params = dict(name=str(repository_name), owner=str(repository_owner), changeset_revision=changeset_revision)
+        pathspec = ["repository", "get_updated_repository_information"]
+        raw_text = util.url_get(
+            tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         repo_information_dict = json.loads(raw_text)
         return repo_information_dict
 
@@ -275,84 +314,110 @@ class AdminToolshed(AdminGalaxy):
         tool shed repository.
         """
         # Get the tool_shed_repository from one of the tool_dependencies.
-        message = str(escape(kwd.get('message', '')))
-        status = kwd.get('status', 'done')
-        err_msg = ''
+        message = str(escape(kwd.get("message", "")))
+        status = kwd.get("status", "done")
+        err_msg = ""
         tool_shed_repository = tool_dependencies[0].tool_shed_repository
         # Get the tool_dependencies.xml file from the repository.
-        tool_dependencies_config = hg_util.get_config_from_disk(rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME,
-                                                                tool_shed_repository.repo_path(trans.app))
+        tool_dependencies_config = hg_util.get_config_from_disk(
+            rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path(trans.app)
+        )
         itdm = install_manager.InstallToolDependencyManager(trans.app)
-        installed_tool_dependencies = itdm.install_specified_tool_dependencies(tool_shed_repository=tool_shed_repository,
-                                                                               tool_dependencies_config=tool_dependencies_config,
-                                                                               tool_dependencies=tool_dependencies)
+        installed_tool_dependencies = itdm.install_specified_tool_dependencies(
+            tool_shed_repository=tool_shed_repository,
+            tool_dependencies_config=tool_dependencies_config,
+            tool_dependencies=tool_dependencies,
+        )
         for installed_tool_dependency in installed_tool_dependencies:
             if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR:
                 text = unicodify(installed_tool_dependency.error_message)
                 if text is not None:
-                    err_msg += f'  {text}'
+                    err_msg += f"  {text}"
         if err_msg:
             message += err_msg
-            status = 'error'
+            status = "error"
         message += f"Installed tool dependencies: {', '.join(td.name for td in installed_tool_dependencies)}"
         td_ids = [trans.security.encode_id(td.id) for td in tool_shed_repository.tool_dependencies]
-        return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                        action='manage_tool_dependencies',
-                                                        tool_dependency_ids=td_ids,
-                                                        message=message,
-                                                        status=status))
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="admin_toolshed",
+                action="manage_tool_dependencies",
+                tool_dependency_ids=td_ids,
+                message=message,
+                status=status,
+            )
+        )
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def install_latest_repository_revision(self, trans, **kwd):
         """Install the latest installable revision of a repository that has been previously installed."""
-        repository_id = kwd.get('id', None)
+        repository_id = kwd.get("id", None)
         if repository_id is not None:
             repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
             if repository is not None:
-                tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
+                tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
+                    trans.app, str(repository.tool_shed)
+                )
                 name = str(repository.name)
                 owner = str(repository.owner)
-                params = dict(galaxy_url=web.url_for('/', qualified=True),
-                              name=name,
-                              owner=owner)
-                pathspec = ['repository', 'get_latest_downloadable_changeset_revision']
-                raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+                params = dict(galaxy_url=web.url_for("/", qualified=True), name=name, owner=owner)
+                pathspec = ["repository", "get_latest_downloadable_changeset_revision"]
+                raw_text = util.url_get(
+                    tool_shed_url,
+                    auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                    pathspec=pathspec,
+                    params=params,
+                )
                 url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
                 latest_downloadable_revision = json.loads(raw_text)
                 if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
-                    return trans.show_error_message(f'Error retrieving the latest downloadable revision for this repository via the url <b>{url}</b>.')
+                    return trans.show_error_message(
+                        f"Error retrieving the latest downloadable revision for this repository via the url <b>{url}</b>."
+                    )
                 else:
                     # Make sure the latest changeset_revision of the repository has not already been installed.
                     # Updates to installed repository revisions may have occurred, so make sure to locate the
                     # appropriate repository revision if one exists.  We need to create a temporary repo_info_tuple
                     # with the following entries to handle this.
                     # ( description, clone_url, changeset_revision, ctx_rev, owner, repository_dependencies, tool_dependencies )
-                    tmp_clone_url = util.build_url(tool_shed_url, pathspec=['repos', owner, name])
+                    tmp_clone_url = util.build_url(tool_shed_url, pathspec=["repos", owner, name])
                     tmp_repo_info_tuple = (None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None)
-                    installed_repository, installed_changeset_revision = \
-                        repository_util.repository_was_previously_installed(trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False)
+                    (
+                        installed_repository,
+                        installed_changeset_revision,
+                    ) = repository_util.repository_was_previously_installed(
+                        trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False
+                    )
                     if installed_repository:
                         current_changeset_revision = str(installed_repository.changeset_revision)
-                        message = 'Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed.' % \
-                            (latest_downloadable_revision, name, owner)
+                        message = (
+                            "Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed."
+                            % (latest_downloadable_revision, name, owner)
+                        )
                         if current_changeset_revision != latest_downloadable_revision:
-                            message += f'  The current changeset revision is <b>{current_changeset_revision}</b>.'
+                            message += f"  The current changeset revision is <b>{current_changeset_revision}</b>."
                         return trans.show_error_message(message)
                     else:
                         # Install the latest downloadable revision of the repository.
-                        params = dict(name=name,
-                                      owner=owner,
-                                      changeset_revisions=str(latest_downloadable_revision),
-                                      galaxy_url=web.url_for('/', qualified=True))
-                        pathspec = ['repository', 'install_repositories_by_revision']
+                        params = dict(
+                            name=name,
+                            owner=owner,
+                            changeset_revisions=str(latest_downloadable_revision),
+                            galaxy_url=web.url_for("/", qualified=True),
+                        )
+                        pathspec = ["repository", "install_repositories_by_revision"]
                         url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
                         return trans.response.send_redirect(url)
             else:
-                return trans.show_error_message(f'Cannot locate installed tool shed repository with encoded id <b>{str(repository_id)}</b>.')
+                return trans.show_error_message(
+                    f"Cannot locate installed tool shed repository with encoded id <b>{str(repository_id)}</b>."
+                )
         else:
-            return trans.show_error_message('The request parameters did not include the required encoded <b>id</b> of installed repository.')
+            return trans.show_error_message(
+                "The request parameters did not include the required encoded <b>id</b> of installed repository."
+            )
 
     @web.expose
     @web.require_admin
@@ -362,88 +427,96 @@ class AdminToolshed(AdminGalaxy):
         Updating an installed tool shed repository where new tool dependencies but no new repository
         dependencies are included in the updated revision.
         """
-        updating_repository_id = kwd.get('updating_repository_id', None)
+        updating_repository_id = kwd.get("updating_repository_id", None)
         repository = repository_util.get_installed_tool_shed_repository(trans.app, updating_repository_id)
         # All received dependencies need to be installed - confirmed by the caller.
-        encoded_tool_dependencies_dict = kwd.get('encoded_tool_dependencies_dict', None)
+        encoded_tool_dependencies_dict = kwd.get("encoded_tool_dependencies_dict", None)
         if encoded_tool_dependencies_dict is not None:
             tool_dependencies_dict = encoding_util.tool_shed_decode(encoded_tool_dependencies_dict)
         else:
             tool_dependencies_dict = {}
-        encoded_relative_install_dir = kwd.get('encoded_relative_install_dir', None)
+        encoded_relative_install_dir = kwd.get("encoded_relative_install_dir", None)
         if encoded_relative_install_dir is not None:
             relative_install_dir = encoding_util.tool_shed_decode(encoded_relative_install_dir)
         else:
-            relative_install_dir = ''
-        updating_to_changeset_revision = kwd.get('updating_to_changeset_revision', None)
-        updating_to_ctx_rev = kwd.get('updating_to_ctx_rev', None)
-        encoded_updated_metadata = kwd.get('encoded_updated_metadata', None)
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        if 'install_tool_dependencies_with_update_button' in kwd:
+            relative_install_dir = ""
+        updating_to_changeset_revision = kwd.get("updating_to_changeset_revision", None)
+        updating_to_ctx_rev = kwd.get("updating_to_ctx_rev", None)
+        encoded_updated_metadata = kwd.get("encoded_updated_metadata", None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        if "install_tool_dependencies_with_update_button" in kwd:
             # Now that the user has chosen whether to install tool dependencies or not, we can
             # update the repository record with the changes in the updated revision.
             if encoded_updated_metadata:
                 updated_metadata = encoding_util.tool_shed_decode(encoded_updated_metadata)
             else:
                 updated_metadata = None
-            repository = trans.app.update_repository_manager.update_repository_record(repository=repository,
-                                                                                      updated_metadata_dict=updated_metadata,
-                                                                                      updated_changeset_revision=updating_to_changeset_revision,
-                                                                                      updated_ctx_rev=updating_to_ctx_rev)
+            repository = trans.app.update_repository_manager.update_repository_record(
+                repository=repository,
+                updated_metadata_dict=updated_metadata,
+                updated_changeset_revision=updating_to_changeset_revision,
+                updated_ctx_rev=updating_to_ctx_rev,
+            )
             if tool_dependencies_dict:
-                tool_dependencies = tool_dependency_util.create_tool_dependency_objects(trans.app,
-                                                                                        repository,
-                                                                                        relative_install_dir,
-                                                                                        set_status=False)
-                message = "The installed repository named '%s' has been updated to change set revision '%s'.  " % \
-                    (escape(str(repository.name)), updating_to_changeset_revision)
+                tool_dependencies = tool_dependency_util.create_tool_dependency_objects(
+                    trans.app, repository, relative_install_dir, set_status=False
+                )
+                message = "The installed repository named '%s' has been updated to change set revision '%s'.  " % (
+                    escape(str(repository.name)),
+                    updating_to_changeset_revision,
+                )
                 self.initiate_tool_dependency_installation(trans, tool_dependencies, message=message, status=status)
         # Handle tool dependencies check box.
         if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies:
             if tool_dependencies_dict:
-                message = ("Tool dependencies defined in this repository can be automatically installed if you set "
-                           "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
-                           "(galaxy.yml) and restart your Galaxy server.")
+                message = (
+                    "Tool dependencies defined in this repository can be automatically installed if you set "
+                    "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
+                    "(galaxy.yml) and restart your Galaxy server."
+                )
                 status = "warning"
             install_tool_dependencies_check_box_checked = False
         else:
             install_tool_dependencies_check_box_checked = True
-        install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies',
-                                                            value=install_tool_dependencies_check_box_checked)
+        install_tool_dependencies_check_box = CheckboxField(
+            "install_tool_dependencies", value=install_tool_dependencies_check_box_checked
+        )
         view = views.DependencyResolversView(self.app)
         if view.installable_resolvers:
-            install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', value=True)
+            install_resolver_dependencies_check_box = CheckboxField("install_resolver_dependencies", value=True)
         else:
             install_resolver_dependencies_check_box = None
-        return trans.fill_template('/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
-                                   repository=repository,
-                                   updating_repository_id=updating_repository_id,
-                                   updating_to_ctx_rev=updating_to_ctx_rev,
-                                   updating_to_changeset_revision=updating_to_changeset_revision,
-                                   encoded_updated_metadata=encoded_updated_metadata,
-                                   encoded_relative_install_dir=encoded_relative_install_dir,
-                                   encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
-                                   install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
-                                   install_tool_dependencies_check_box=install_tool_dependencies_check_box,
-                                   tool_dependencies_dict=tool_dependencies_dict,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/admin/tool_shed_repository/install_tool_dependencies_with_update.mako",
+            repository=repository,
+            updating_repository_id=updating_repository_id,
+            updating_to_ctx_rev=updating_to_ctx_rev,
+            updating_to_changeset_revision=updating_to_changeset_revision,
+            encoded_updated_metadata=encoded_updated_metadata,
+            encoded_relative_install_dir=encoded_relative_install_dir,
+            encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
+            install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
+            install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+            tool_dependencies_dict=tool_dependencies_dict,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def install_repositories(self, trans, **kwd):
-        reinstalling = util.string_as_bool(kwd.get('reinstalling', False))
-        encoded_kwd = kwd.get('encoded_kwd')
+        reinstalling = util.string_as_bool(kwd.get("reinstalling", False))
+        encoded_kwd = kwd.get("encoded_kwd")
         decoded_kwd = encoding_util.tool_shed_decode(encoded_kwd) if encoded_kwd else {}
-        install_resolver_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_resolver_dependencies', ''))
-        install_tool_dependencies = CheckboxField.is_checked(decoded_kwd.get('install_tool_dependencies', ''))
-        decoded_kwd['install_resolver_dependencies'] = install_resolver_dependencies
-        decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
-        tsr_ids = decoded_kwd.get('tool_shed_repository_ids')
+        install_resolver_dependencies = CheckboxField.is_checked(decoded_kwd.get("install_resolver_dependencies", ""))
+        install_tool_dependencies = CheckboxField.is_checked(decoded_kwd.get("install_tool_dependencies", ""))
+        decoded_kwd["install_resolver_dependencies"] = install_resolver_dependencies
+        decoded_kwd["install_tool_dependencies"] = install_tool_dependencies
+        tsr_ids = decoded_kwd.get("tool_shed_repository_ids")
         if not tsr_ids:
-            return self.message_exception(trans, 'Repository ids missing.')
+            return self.message_exception(trans, "Repository ids missing.")
         irm = install_manager.InstallRepositoryManager(trans.app)
         try:
             tool_shed_repositories = irm.install_repositories(
@@ -460,40 +533,48 @@ class AdminToolshed(AdminGalaxy):
     @web.require_admin
     @legacy_tool_shed_endpoint
     def manage_repository(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_id = kwd.get("id", None)
         if repository_id is None:
-            return trans.show_error_message('Missing required encoded repository id.')
+            return trans.show_error_message("Missing required encoded repository id.")
         if repository_id and isinstance(repository_id, list):
             # FIXME: This is a hack that avoids unhandled and duplicate url parameters leaking in.
             # This should be handled somewhere in the grids system, but given the legacy status
             # this should be OK.
-            repository_id = [r for r in repository_id if '=' not in r][0]  # This method only work for a single repo id
-        operation = kwd.get('operation', None)
+            repository_id = [r for r in repository_id if "=" not in r][0]  # This method only work for a single repo id
+        operation = kwd.get("operation", None)
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         if repository is None:
-            return trans.show_error_message('Invalid repository specified.')
+            return trans.show_error_message("Invalid repository specified.")
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
         name = str(repository.name)
         owner = str(repository.owner)
         installed_changeset_revision = str(repository.installed_changeset_revision)
         if repository.status in [trans.install_model.ToolShedRepository.installation_status.CLONING]:
             tool_shed_repository_ids = [repository_id]
-            return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                            action='monitor_repository_installation',
-                                                            tool_shed_repository_ids=tool_shed_repository_ids))
-        if repository.can_install and operation == 'install':
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="admin_toolshed",
+                    action="monitor_repository_installation",
+                    tool_shed_repository_ids=tool_shed_repository_ids,
+                )
+            )
+        if repository.can_install and operation == "install":
             # Send a request to the tool shed to install the repository.
-            params = dict(name=name,
-                          owner=owner,
-                          changeset_revisions=installed_changeset_revision,
-                          galaxy_url=web.url_for('/', qualified=True))
-            pathspec = ['repository', 'install_repositories_by_revision']
+            params = dict(
+                name=name,
+                owner=owner,
+                changeset_revisions=installed_changeset_revision,
+                galaxy_url=web.url_for("/", qualified=True),
+            )
+            pathspec = ["repository", "install_repositories_by_revision"]
             url = util.build_url(tool_shed_url, pathspec=pathspec, params=params)
             return trans.response.send_redirect(url)
-        description = kwd.get('description', repository.description)
-        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(trans.app, repository)
+        description = kwd.get("description", repository.description)
+        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
+            trans.app, repository
+        )
         if relative_install_dir:
             repo_files_dir = os.path.abspath(os.path.join(tool_path, relative_install_dir, name))
         else:
@@ -506,29 +587,33 @@ class AdminToolshed(AdminGalaxy):
         elif repository.can_install:
             message = "This repository is not installed.  You can install it by choosing  <b>Install</b> from the <b>Repository Actions</b> menu."
             status = "error"
-        elif kwd.get('edit_repository_button', False):
+        elif kwd.get("edit_repository_button", False):
             if description != repository.description:
                 repository.description = description
                 trans.install_model.context.add(repository)
                 trans.install_model.context.flush()
             message = "The repository information has been updated."
         dd = dependency_display.DependencyDisplayer(trans.app)
-        containers_dict = dd.populate_containers_dict_from_repository_metadata(tool_shed_url=tool_shed_url,
-                                                                               tool_path=tool_path,
-                                                                               repository=repository,
-                                                                               reinstalling=False,
-                                                                               required_repo_info_dicts=None)
+        containers_dict = dd.populate_containers_dict_from_repository_metadata(
+            tool_shed_url=tool_shed_url,
+            tool_path=tool_path,
+            repository=repository,
+            reinstalling=False,
+            required_repo_info_dicts=None,
+        )
         view = views.DependencyResolversView(self.app)
         tool_requirements_d = suc.get_requirements_from_repository(repository)
         requirements_status = view.get_requirements_status(tool_requirements_d, repository.installed_tool_dependencies)
-        return trans.fill_template('/admin/tool_shed_repository/manage_repository.mako',
-                                   repository=repository,
-                                   description=description,
-                                   repo_files_dir=repo_files_dir,
-                                   containers_dict=containers_dict,
-                                   requirements_status=requirements_status,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/admin/tool_shed_repository/manage_repository.mako",
+            repository=repository,
+            description=description,
+            repo_files_dir=repo_files_dir,
+            containers_dict=containers_dict,
+            requirements_status=requirements_status,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
@@ -546,60 +631,72 @@ class AdminToolshed(AdminGalaxy):
         for tsr_id in tsr_ids:
             clause_list.append(trans.install_model.ToolShedRepository.table.c.id == tsr_id)
         query = trans.install_model.session.query(trans.install_model.ToolShedRepository).filter(or_(*clause_list))
-        return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
-                                   tool_shed_repositories=tool_shed_repositories,
-                                   query=query,
-                                   message=escape(kwd.get('message', '')),
-                                   status=kwd.get('status'))
+        return trans.fill_template(
+            "admin/tool_shed_repository/monitor_repository_installation.mako",
+            tool_shed_repositories=tool_shed_repositories,
+            query=query,
+            message=escape(kwd.get("message", "")),
+            status=kwd.get("status"),
+        )
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def prepare_for_install(self, trans, **kwd):
         if not suc.have_shed_tool_conf_for_install(trans.app):
-            message = 'The <b>tool_config_file</b> setting in <b>galaxy.ini</b> must include at least one '
-            message += 'shed tool configuration file name with a <b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> '
-            message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
-            message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
+            message = "The <b>tool_config_file</b> setting in <b>galaxy.ini</b> must include at least one "
+            message += (
+                "shed tool configuration file name with a <b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> "
+            )
+            message += "attribute value which is a directory relative to the Galaxy installation directory in order "
+            message += (
+                "to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> "
+            )
             message += 'whose <b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="database/shed_tools"&gt;</b>).<p/>See the '
-            message += '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation '
-            message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
-            message += 'Shed wiki for all of the details.'
+            message += (
+                '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation '
+            )
+            message += (
+                "of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool "
+            )
+            message += "Shed wiki for all of the details."
             return trans.show_error_message(message)
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        shed_tool_conf = kwd.get('shed_tool_conf', None)
-        tool_shed_url = kwd.get('tool_shed_url', '')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        shed_tool_conf = kwd.get("shed_tool_conf", None)
+        tool_shed_url = kwd.get("tool_shed_url", "")
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
         # Handle repository dependencies, which do not include those that are required only for compiling a dependent
         # repository's tool dependencies.
-        has_repository_dependencies = util.string_as_bool(kwd.get('has_repository_dependencies', False))
-        install_repository_dependencies = kwd.get('install_repository_dependencies', '')
+        has_repository_dependencies = util.string_as_bool(kwd.get("has_repository_dependencies", False))
+        install_repository_dependencies = kwd.get("install_repository_dependencies", "")
         # Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
-        new_tool_panel_section_label = kwd.get('new_tool_panel_section_label', '')
-        tool_panel_section_id = kwd.get('tool_panel_section_id', '')
+        new_tool_panel_section_label = kwd.get("new_tool_panel_section_label", "")
+        tool_panel_section_id = kwd.get("tool_panel_section_id", "")
         tool_panel_section_keys = []
         # One or more repositories may include tools, but not necessarily all of them.
-        includes_tools = util.string_as_bool(kwd.get('includes_tools', False))
+        includes_tools = util.string_as_bool(kwd.get("includes_tools", False))
         # Some tools should not be displayed in the tool panel (e.g., DataManager tools and datatype converters).
-        includes_tools_for_display_in_tool_panel = util.string_as_bool(kwd.get('includes_tools_for_display_in_tool_panel', False))
-        includes_tool_dependencies = util.string_as_bool(kwd.get('includes_tool_dependencies', False))
-        install_resolver_dependencies = kwd.get('install_resolver_dependencies', '')
-        install_tool_dependencies = kwd.get('install_tool_dependencies', '')
+        includes_tools_for_display_in_tool_panel = util.string_as_bool(
+            kwd.get("includes_tools_for_display_in_tool_panel", False)
+        )
+        includes_tool_dependencies = util.string_as_bool(kwd.get("includes_tool_dependencies", False))
+        install_resolver_dependencies = kwd.get("install_resolver_dependencies", "")
+        install_tool_dependencies = kwd.get("install_tool_dependencies", "")
         # In addition to installing new repositories, this method is called when updating an installed repository
         # to a new changeset_revision where the update includes newly defined repository dependencies.
-        updating = util.asbool(kwd.get('updating', False))
-        updating_repository_id = kwd.get('updating_repository_id', None)
-        updating_to_changeset_revision = kwd.get('updating_to_changeset_revision', None)
-        updating_to_ctx_rev = kwd.get('updating_to_ctx_rev', None)
-        encoded_updated_metadata = kwd.get('encoded_updated_metadata', None)
-        encoded_repo_info_dicts = kwd.get('encoded_repo_info_dicts', '')
+        updating = util.asbool(kwd.get("updating", False))
+        updating_repository_id = kwd.get("updating_repository_id", None)
+        updating_to_changeset_revision = kwd.get("updating_to_changeset_revision", None)
+        updating_to_ctx_rev = kwd.get("updating_to_ctx_rev", None)
+        encoded_updated_metadata = kwd.get("encoded_updated_metadata", None)
+        encoded_repo_info_dicts = kwd.get("encoded_repo_info_dicts", "")
         if encoded_repo_info_dicts:
             encoded_repo_info_dicts = encoded_repo_info_dicts.split(encoding_util.encoding_sep)
         if not encoded_repo_info_dicts:
             # The request originated in the tool shed via a tool search or from this controller's
             # update_to_changeset_revision() method.
-            repository_ids = kwd.get('repository_ids', None)
+            repository_ids = kwd.get("repository_ids", None)
             if updating:
                 # We have updated an installed repository where the updates included newly defined repository
                 # and possibly tool dependencies.  We will have arrived here only if the updates include newly
@@ -612,50 +709,69 @@ class AdminToolshed(AdminGalaxy):
                 # For backward compatibility to the 12/20/12 Galaxy release.
                 try:
                     params = dict(name=str(repository.name), owner=str(repository.owner))
-                    pathspec = ['repository', 'get_repository_id']
-                    repository_ids = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+                    pathspec = ["repository", "get_repository_id"]
+                    repository_ids = util.url_get(
+                        tool_shed_url,
+                        auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                        pathspec=pathspec,
+                        params=params,
+                    )
                 except Exception as e:
                     # The Tool Shed cannot handle the get_repository_id request, so the code must be older than the
                     # 04/2014 Galaxy release when it was introduced.  It will be safest to error out and let the
                     # Tool Shed admin update the Tool Shed to a later release.
-                    message = f'The updates available for the repository <b>{escape(str(repository.name))}</b> '
-                    message += 'include newly defined repository or tool dependency definitions, and attempting '
-                    message += 'to update the repository resulted in the following error.  Contact the Tool Shed '
-                    message += f'administrator if necessary.<br/>{unicodify(e)}'
+                    message = f"The updates available for the repository <b>{escape(str(repository.name))}</b> "
+                    message += "include newly defined repository or tool dependency definitions, and attempting "
+                    message += "to update the repository resulted in the following error.  Contact the Tool Shed "
+                    message += f"administrator if necessary.<br/>{unicodify(e)}"
                     return trans.show_error_message(message)
                 changeset_revisions = updating_to_changeset_revision
             else:
-                changeset_revisions = kwd.get('changeset_revisions', None)
+                changeset_revisions = kwd.get("changeset_revisions", None)
             # Get the information necessary to install each repository.
             params = dict(repository_ids=str(repository_ids), changeset_revisions=str(changeset_revisions))
-            pathspec = ['repository', 'get_repository_information']
-            raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+            pathspec = ["repository", "get_repository_information"]
+            raw_text = util.url_get(
+                tool_shed_url,
+                auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                pathspec=pathspec,
+                params=params,
+            )
             repo_information_dict = json.loads(raw_text)
-            for encoded_repo_info_dict in repo_information_dict.get('repo_info_dicts', []):
+            for encoded_repo_info_dict in repo_information_dict.get("repo_info_dicts", []):
                 decoded_repo_info_dict = encoding_util.tool_shed_decode(encoded_repo_info_dict)
                 if not includes_tools:
-                    includes_tools = util.string_as_bool(decoded_repo_info_dict.get('includes_tools', False))
+                    includes_tools = util.string_as_bool(decoded_repo_info_dict.get("includes_tools", False))
                 if not includes_tools_for_display_in_tool_panel:
-                    includes_tools_for_display_in_tool_panel = \
-                        util.string_as_bool(decoded_repo_info_dict.get('includes_tools_for_display_in_tool_panel', False))
+                    includes_tools_for_display_in_tool_panel = util.string_as_bool(
+                        decoded_repo_info_dict.get("includes_tools_for_display_in_tool_panel", False)
+                    )
                 if not has_repository_dependencies:
-                    has_repository_dependencies = util.string_as_bool(repo_information_dict.get('has_repository_dependencies', False))
+                    has_repository_dependencies = util.string_as_bool(
+                        repo_information_dict.get("has_repository_dependencies", False)
+                    )
                 if not includes_tool_dependencies:
-                    includes_tool_dependencies = util.string_as_bool(repo_information_dict.get('includes_tool_dependencies', False))
-            encoded_repo_info_dicts = util.listify(repo_information_dict.get('repo_info_dicts', []))
-        repo_info_dicts = [encoding_util.tool_shed_decode(encoded_repo_info_dict) for encoded_repo_info_dict in encoded_repo_info_dicts]
+                    includes_tool_dependencies = util.string_as_bool(
+                        repo_information_dict.get("includes_tool_dependencies", False)
+                    )
+            encoded_repo_info_dicts = util.listify(repo_information_dict.get("repo_info_dicts", []))
+        repo_info_dicts = [
+            encoding_util.tool_shed_decode(encoded_repo_info_dict) for encoded_repo_info_dict in encoded_repo_info_dicts
+        ]
         dd = dependency_display.DependencyDisplayer(trans.app)
         install_repository_manager = install_manager.InstallRepositoryManager(trans.app)
-        if kwd.get('select_tool_panel_section_button', False):
+        if kwd.get("select_tool_panel_section_button", False):
             if updating:
                 repository = repository_util.get_tool_shed_repository_by_id(trans.app, updating_repository_id)
                 decoded_updated_metadata = encoding_util.tool_shed_decode(encoded_updated_metadata)
                 # Now that the user has decided whether they will handle dependencies, we can update
                 # the repository to the latest revision.
-                repository = trans.app.update_repository_manager.update_repository_record(repository=repository,
-                                                                                          updated_metadata_dict=decoded_updated_metadata,
-                                                                                          updated_changeset_revision=updating_to_changeset_revision,
-                                                                                          updated_ctx_rev=updating_to_ctx_rev)
+                repository = trans.app.update_repository_manager.update_repository_record(
+                    repository=repository,
+                    updated_metadata_dict=decoded_updated_metadata,
+                    updated_changeset_revision=updating_to_changeset_revision,
+                    updated_ctx_rev=updating_to_ctx_rev,
+                )
             install_repository_dependencies = CheckboxField.is_checked(install_repository_dependencies)
             if includes_tool_dependencies:
                 install_tool_dependencies = CheckboxField.is_checked(install_tool_dependencies)
@@ -663,77 +779,94 @@ class AdminToolshed(AdminGalaxy):
                 install_tool_dependencies = False
             install_resolver_dependencies = CheckboxField.is_checked(install_resolver_dependencies)
             tool_path = suc.get_tool_path_by_shed_tool_conf_filename(trans.app, shed_tool_conf)
-            installation_dict = dict(install_repository_dependencies=install_repository_dependencies,
-                                     new_tool_panel_section_label=new_tool_panel_section_label,
-                                     no_changes_checked=False,
-                                     repo_info_dicts=repo_info_dicts,
-                                     tool_panel_section_id=tool_panel_section_id,
-                                     tool_path=tool_path,
-                                     tool_shed_url=tool_shed_url)
-            created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
-                install_repository_manager.handle_tool_shed_repositories(installation_dict)
+            installation_dict = dict(
+                install_repository_dependencies=install_repository_dependencies,
+                new_tool_panel_section_label=new_tool_panel_section_label,
+                no_changes_checked=False,
+                repo_info_dicts=repo_info_dicts,
+                tool_panel_section_id=tool_panel_section_id,
+                tool_path=tool_path,
+                tool_shed_url=tool_shed_url,
+            )
+            (
+                created_or_updated_tool_shed_repositories,
+                tool_panel_section_keys,
+                repo_info_dicts,
+                filtered_repo_info_dicts,
+            ) = install_repository_manager.handle_tool_shed_repositories(installation_dict)
             if created_or_updated_tool_shed_repositories:
-                installation_dict = dict(created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
-                                         filtered_repo_info_dicts=filtered_repo_info_dicts,
-                                         has_repository_dependencies=has_repository_dependencies,
-                                         includes_tool_dependencies=includes_tool_dependencies,
-                                         includes_tools=includes_tools,
-                                         includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                                         install_repository_dependencies=install_repository_dependencies,
-                                         install_resolver_dependencies=install_resolver_dependencies,
-                                         install_tool_dependencies=install_tool_dependencies,
-                                         message=message,
-                                         new_tool_panel_section_label=new_tool_panel_section_label,
-                                         shed_tool_conf=shed_tool_conf,
-                                         status=status,
-                                         tool_panel_section_id=tool_panel_section_id,
-                                         tool_panel_section_keys=tool_panel_section_keys,
-                                         tool_path=tool_path,
-                                         tool_shed_url=tool_shed_url)
-                encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
-                    install_repository_manager.initiate_repository_installation(installation_dict)
-                return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
-                                           encoded_kwd=encoded_kwd,
-                                           query=query,
-                                           tool_shed_repositories=tool_shed_repositories,
-                                           initiate_repository_installation_ids=encoded_repository_ids,
-                                           reinstalling=False)
+                installation_dict = dict(
+                    created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
+                    filtered_repo_info_dicts=filtered_repo_info_dicts,
+                    has_repository_dependencies=has_repository_dependencies,
+                    includes_tool_dependencies=includes_tool_dependencies,
+                    includes_tools=includes_tools,
+                    includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+                    install_repository_dependencies=install_repository_dependencies,
+                    install_resolver_dependencies=install_resolver_dependencies,
+                    install_tool_dependencies=install_tool_dependencies,
+                    message=message,
+                    new_tool_panel_section_label=new_tool_panel_section_label,
+                    shed_tool_conf=shed_tool_conf,
+                    status=status,
+                    tool_panel_section_id=tool_panel_section_id,
+                    tool_panel_section_keys=tool_panel_section_keys,
+                    tool_path=tool_path,
+                    tool_shed_url=tool_shed_url,
+                )
+                (
+                    encoded_kwd,
+                    query,
+                    tool_shed_repositories,
+                    encoded_repository_ids,
+                ) = install_repository_manager.initiate_repository_installation(installation_dict)
+                return trans.fill_template(
+                    "admin/tool_shed_repository/monitor_repository_installation.mako",
+                    encoded_kwd=encoded_kwd,
+                    query=query,
+                    tool_shed_repositories=tool_shed_repositories,
+                    initiate_repository_installation_ids=encoded_repository_ids,
+                    reinstalling=False,
+                )
             else:
-                kwd['message'] = message if message else 'Repository has already been installed.'
-                kwd['status'] = status
-                return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                                action='monitor_repository_installation',
-                                                                **kwd))
+                kwd["message"] = message if message else "Repository has already been installed."
+                kwd["status"] = status
+                return trans.response.send_redirect(
+                    web.url_for(controller="admin_toolshed", action="monitor_repository_installation", **kwd)
+                )
         shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field(trans.app)
         tool_path = suc.get_tool_path_by_shed_tool_conf_filename(trans.app, shed_tool_conf)
         tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
-        tool_requirements = suc.get_tool_shed_repo_requirements(app=trans.app,
-                                                                tool_shed_url=tool_shed_url,
-                                                                repo_info_dicts=repo_info_dicts)
+        tool_requirements = suc.get_tool_shed_repo_requirements(
+            app=trans.app, tool_shed_url=tool_shed_url, repo_info_dicts=repo_info_dicts
+        )
         view = views.DependencyResolversView(self.app)
         requirements_status = view.get_requirements_status(tool_requirements)
         if len(repo_info_dicts) == 1:
             # If we're installing or updating a single repository, see if it contains a readme or
             # dependencies that we can display.
             repo_info_dict = repo_info_dicts[0]
-            dependencies_for_repository_dict = \
-                trans.app.installed_repository_manager.get_dependencies_for_repository(tool_shed_url,
-                                                                                       repo_info_dict,
-                                                                                       includes_tool_dependencies,
-                                                                                       updating=updating)
+            dependencies_for_repository_dict = trans.app.installed_repository_manager.get_dependencies_for_repository(
+                tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=updating
+            )
             if not has_repository_dependencies:
-                has_repository_dependencies = dependencies_for_repository_dict.get('has_repository_dependencies', False)
+                has_repository_dependencies = dependencies_for_repository_dict.get("has_repository_dependencies", False)
             if not includes_tool_dependencies:
-                includes_tool_dependencies = dependencies_for_repository_dict.get('includes_tool_dependencies', False)
+                includes_tool_dependencies = dependencies_for_repository_dict.get("includes_tool_dependencies", False)
             if not includes_tools:
-                includes_tools = dependencies_for_repository_dict.get('includes_tools', False)
+                includes_tools = dependencies_for_repository_dict.get("includes_tools", False)
             if not includes_tools_for_display_in_tool_panel:
-                includes_tools_for_display_in_tool_panel = \
-                    dependencies_for_repository_dict.get('includes_tools_for_display_in_tool_panel', False)
-            installed_repository_dependencies = dependencies_for_repository_dict.get('installed_repository_dependencies', None)
-            installed_tool_dependencies = dependencies_for_repository_dict.get('installed_tool_dependencies', None)
-            missing_repository_dependencies = dependencies_for_repository_dict.get('missing_repository_dependencies', None)
-            missing_tool_dependencies = dependencies_for_repository_dict.get('missing_tool_dependencies', None)
+                includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get(
+                    "includes_tools_for_display_in_tool_panel", False
+                )
+            installed_repository_dependencies = dependencies_for_repository_dict.get(
+                "installed_repository_dependencies", None
+            )
+            installed_tool_dependencies = dependencies_for_repository_dict.get("installed_tool_dependencies", None)
+            missing_repository_dependencies = dependencies_for_repository_dict.get(
+                "missing_repository_dependencies", None
+            )
+            missing_tool_dependencies = dependencies_for_repository_dict.get("missing_tool_dependencies", None)
             readme_files_dict = readme_util.get_readme_files_dict_for_display(trans.app, tool_shed_url, repo_info_dict)
             # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've
             # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the
@@ -744,37 +877,47 @@ class AdminToolshed(AdminGalaxy):
             # missing.  The 3rd scenario is where we're updating an installed repository and the updates include newly
             # defined repository (and possibly tool) dependencies.  In this case, merging will result in newly defined
             # dependencies to be lost.  We pass the updating parameter to make sure merging occurs only when appropriate.
-            containers_dict = \
-                dd.populate_containers_dict_for_new_install(tool_shed_url=tool_shed_url,
-                                                            tool_path=tool_path,
-                                                            readme_files_dict=readme_files_dict,
-                                                            installed_repository_dependencies=installed_repository_dependencies,
-                                                            missing_repository_dependencies=missing_repository_dependencies,
-                                                            installed_tool_dependencies=installed_tool_dependencies,
-                                                            missing_tool_dependencies=missing_tool_dependencies,
-                                                            updating=updating)
+            containers_dict = dd.populate_containers_dict_for_new_install(
+                tool_shed_url=tool_shed_url,
+                tool_path=tool_path,
+                readme_files_dict=readme_files_dict,
+                installed_repository_dependencies=installed_repository_dependencies,
+                missing_repository_dependencies=missing_repository_dependencies,
+                installed_tool_dependencies=installed_tool_dependencies,
+                missing_tool_dependencies=missing_tool_dependencies,
+                updating=updating,
+            )
         else:
             # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies.
             containers_dicts = []
             for repo_info_dict in repo_info_dicts:
-                dependencies_for_repository_dict = \
-                    trans.app.installed_repository_manager.get_dependencies_for_repository(tool_shed_url,
-                                                                                           repo_info_dict,
-                                                                                           includes_tool_dependencies,
-                                                                                           updating=updating)
+                dependencies_for_repository_dict = (
+                    trans.app.installed_repository_manager.get_dependencies_for_repository(
+                        tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=updating
+                    )
+                )
                 if not has_repository_dependencies:
-                    has_repository_dependencies = dependencies_for_repository_dict.get('has_repository_dependencies', False)
+                    has_repository_dependencies = dependencies_for_repository_dict.get(
+                        "has_repository_dependencies", False
+                    )
                 if not includes_tool_dependencies:
-                    includes_tool_dependencies = dependencies_for_repository_dict.get('includes_tool_dependencies', False)
+                    includes_tool_dependencies = dependencies_for_repository_dict.get(
+                        "includes_tool_dependencies", False
+                    )
                 if not includes_tools:
-                    includes_tools = dependencies_for_repository_dict.get('includes_tools', False)
+                    includes_tools = dependencies_for_repository_dict.get("includes_tools", False)
                 if not includes_tools_for_display_in_tool_panel:
-                    includes_tools_for_display_in_tool_panel = \
-                        dependencies_for_repository_dict.get('includes_tools_for_display_in_tool_panel', False)
-                installed_repository_dependencies = dependencies_for_repository_dict.get('installed_repository_dependencies', None)
-                installed_tool_dependencies = dependencies_for_repository_dict.get('installed_tool_dependencies', None)
-                missing_repository_dependencies = dependencies_for_repository_dict.get('missing_repository_dependencies', None)
-                missing_tool_dependencies = dependencies_for_repository_dict.get('missing_tool_dependencies', None)
+                    includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get(
+                        "includes_tools_for_display_in_tool_panel", False
+                    )
+                installed_repository_dependencies = dependencies_for_repository_dict.get(
+                    "installed_repository_dependencies", None
+                )
+                installed_tool_dependencies = dependencies_for_repository_dict.get("installed_tool_dependencies", None)
+                missing_repository_dependencies = dependencies_for_repository_dict.get(
+                    "missing_repository_dependencies", None
+                )
+                missing_tool_dependencies = dependencies_for_repository_dict.get("missing_tool_dependencies", None)
                 containers_dict = dd.populate_containers_dict_for_new_install(
                     tool_shed_url=tool_shed_url,
                     tool_path=tool_path,
@@ -783,7 +926,7 @@ class AdminToolshed(AdminGalaxy):
                     missing_repository_dependencies=missing_repository_dependencies,
                     installed_tool_dependencies=installed_tool_dependencies,
                     missing_tool_dependencies=missing_tool_dependencies,
-                    updating=updating
+                    updating=updating,
                 )
                 containers_dicts.append(containers_dict)
             # Merge all containers into a single container.
@@ -798,40 +941,43 @@ class AdminToolshed(AdminGalaxy):
             install_tool_dependencies_check_box_checked = False
         else:
             install_tool_dependencies_check_box_checked = True
-        install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies',
-                                                            value=install_tool_dependencies_check_box_checked)
+        install_tool_dependencies_check_box = CheckboxField(
+            "install_tool_dependencies", value=install_tool_dependencies_check_box_checked
+        )
         # Handle repository dependencies check box.
-        install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', value=True)
+        install_repository_dependencies_check_box = CheckboxField("install_repository_dependencies", value=True)
         view = views.DependencyResolversView(self.app)
         if view.installable_resolvers:
-            install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', value=True)
+            install_resolver_dependencies_check_box = CheckboxField("install_resolver_dependencies", value=True)
         else:
             install_resolver_dependencies_check_box = None
         encoded_repo_info_dicts = encoding_util.encoding_sep.join(encoded_repo_info_dicts)
-        tool_shed_url = kwd['tool_shed_url']
-        return trans.fill_template('/admin/tool_shed_repository/select_tool_panel_section.mako',
-                                   encoded_repo_info_dicts=encoded_repo_info_dicts,
-                                   updating=updating,
-                                   updating_repository_id=updating_repository_id,
-                                   updating_to_ctx_rev=updating_to_ctx_rev,
-                                   updating_to_changeset_revision=updating_to_changeset_revision,
-                                   encoded_updated_metadata=encoded_updated_metadata,
-                                   includes_tools=includes_tools,
-                                   includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                                   includes_tool_dependencies=includes_tool_dependencies,
-                                   install_tool_dependencies_check_box=install_tool_dependencies_check_box,
-                                   install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
-                                   has_repository_dependencies=has_repository_dependencies,
-                                   install_repository_dependencies_check_box=install_repository_dependencies_check_box,
-                                   new_tool_panel_section_label=new_tool_panel_section_label,
-                                   containers_dict=containers_dict,
-                                   shed_tool_conf=shed_tool_conf,
-                                   shed_tool_conf_select_field=shed_tool_conf_select_field,
-                                   tool_panel_section_select_field=tool_panel_section_select_field,
-                                   tool_shed_url=tool_shed_url,
-                                   requirements_status=requirements_status,
-                                   message=message,
-                                   status=status)
+        tool_shed_url = kwd["tool_shed_url"]
+        return trans.fill_template(
+            "/admin/tool_shed_repository/select_tool_panel_section.mako",
+            encoded_repo_info_dicts=encoded_repo_info_dicts,
+            updating=updating,
+            updating_repository_id=updating_repository_id,
+            updating_to_ctx_rev=updating_to_ctx_rev,
+            updating_to_changeset_revision=updating_to_changeset_revision,
+            encoded_updated_metadata=encoded_updated_metadata,
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            includes_tool_dependencies=includes_tool_dependencies,
+            install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+            install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
+            has_repository_dependencies=has_repository_dependencies,
+            install_repository_dependencies_check_box=install_repository_dependencies_check_box,
+            new_tool_panel_section_label=new_tool_panel_section_label,
+            containers_dict=containers_dict,
+            shed_tool_conf=shed_tool_conf,
+            shed_tool_conf_select_field=shed_tool_conf_select_field,
+            tool_panel_section_select_field=tool_panel_section_select_field,
+            tool_shed_url=tool_shed_url,
+            requirements_status=requirements_status,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
@@ -842,24 +988,25 @@ class AdminToolshed(AdminGalaxy):
         and tool dependencies of the repository.
         """
         rdim = repository_dependency_manager.RepositoryDependencyInstallManager(trans.app)
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_id = kwd['id']
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_id = kwd["id"]
         tool_shed_repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
-        no_changes = kwd.get('no_changes', '')
+        no_changes = kwd.get("no_changes", "")
         no_changes_checked = CheckboxField.is_checked(no_changes)
-        install_repository_dependencies = CheckboxField.is_checked(kwd.get('install_repository_dependencies', ''))
-        install_tool_dependencies = CheckboxField.is_checked(kwd.get('install_tool_dependencies', ''))
-        install_resolver_dependencies = CheckboxField.is_checked(kwd.get('install_resolver_dependencies', ''))
+        install_repository_dependencies = CheckboxField.is_checked(kwd.get("install_repository_dependencies", ""))
+        install_tool_dependencies = CheckboxField.is_checked(kwd.get("install_tool_dependencies", ""))
+        install_resolver_dependencies = CheckboxField.is_checked(kwd.get("install_resolver_dependencies", ""))
         if not suc.have_shed_tool_conf_for_install(trans.app):
             raise Exception("No valid shed tool configuration file available, please configure one")
-        shed_tool_conf, tool_path, relative_install_dir = \
-            suc.get_tool_panel_config_tool_path_install_dir(trans.app, tool_shed_repository)
+        shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
+            trans.app, tool_shed_repository
+        )
         repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository)
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_repository.tool_shed)
         tool_section = None
-        tool_panel_section_id = kwd.get('tool_panel_section_id', '')
-        new_tool_panel_section_label = kwd.get('new_tool_panel_section_label', '')
+        tool_panel_section_id = kwd.get("tool_panel_section_id", "")
+        new_tool_panel_section_label = kwd.get("new_tool_panel_section_label", "")
         tool_panel_section_key = None
         tool_panel_section_keys = []
         metadata = tool_shed_repository.metadata_
@@ -869,105 +1016,118 @@ class AdminToolshed(AdminGalaxy):
         if tool_shed_repository.includes_tools_for_display_in_tool_panel:
             tpm = tool_panel_manager.ToolPanelManager(trans.app)
             # Handle the selected tool panel location for loading tools included in the tool shed repository.
-            tool_section, tool_panel_section_key = \
-                tpm.handle_tool_panel_selection(toolbox=trans.app.toolbox,
-                                                metadata=metadata,
-                                                no_changes_checked=no_changes_checked,
-                                                tool_panel_section_id=tool_panel_section_id,
-                                                new_tool_panel_section_label=new_tool_panel_section_label)
+            tool_section, tool_panel_section_key = tpm.handle_tool_panel_selection(
+                toolbox=trans.app.toolbox,
+                metadata=metadata,
+                no_changes_checked=no_changes_checked,
+                tool_panel_section_id=tool_panel_section_id,
+                new_tool_panel_section_label=new_tool_panel_section_label,
+            )
             if tool_section is not None:
                 # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't...
                 tool_panel_section_id = str(tool_section.id)
         if tool_shed_repository.status == trans.install_model.ToolShedRepository.installation_status.UNINSTALLED:
-            repository_type = suc.get_repository_type_from_tool_shed(trans.app,
-                                                                     tool_shed_url,
-                                                                     tool_shed_repository.name,
-                                                                     tool_shed_repository.owner)
+            repository_type = suc.get_repository_type_from_tool_shed(
+                trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner
+            )
             if repository_type == rt_util.TOOL_DEPENDENCY_DEFINITION:
                 # Repositories of type tool_dependency_definition must get the latest
                 # metadata from the Tool Shed since they have only a single installable
                 # revision.
-                raw_text = suc.get_tool_dependency_definition_metadata_from_tool_shed(trans.app,
-                                                                                      tool_shed_url,
-                                                                                      tool_shed_repository.name,
-                                                                                      tool_shed_repository.owner)
+                raw_text = suc.get_tool_dependency_definition_metadata_from_tool_shed(
+                    trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner
+                )
                 new_meta = json.loads(raw_text)
                 # Clean up old repository dependency and tool dependency relationships.
                 suc.clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url)
             # The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall
             # so the repository_installation_updater will function.
-            tool_shed_repository = repository_util.create_or_update_tool_shed_repository(app=trans.app,
-                                                                                         name=tool_shed_repository.name,
-                                                                                         description=tool_shed_repository.description,
-                                                                                         installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                                         ctx_rev=tool_shed_repository.ctx_rev,
-                                                                                         repository_clone_url=repository_clone_url,
-                                                                                         status=trans.install_model.ToolShedRepository.installation_status.NEW,
-                                                                                         metadata_dict=metadata,
-                                                                                         current_changeset_revision=tool_shed_repository.changeset_revision,
-                                                                                         owner=tool_shed_repository.owner,
-                                                                                         dist_to_shed=tool_shed_repository.dist_to_shed)
-        ctx_rev = suc.get_ctx_rev(trans.app,
-                                  tool_shed_url,
-                                  tool_shed_repository.name,
-                                  tool_shed_repository.owner,
-                                  tool_shed_repository.installed_changeset_revision)
+            tool_shed_repository = repository_util.create_or_update_tool_shed_repository(
+                app=trans.app,
+                name=tool_shed_repository.name,
+                description=tool_shed_repository.description,
+                installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
+                ctx_rev=tool_shed_repository.ctx_rev,
+                repository_clone_url=repository_clone_url,
+                status=trans.install_model.ToolShedRepository.installation_status.NEW,
+                metadata_dict=metadata,
+                current_changeset_revision=tool_shed_repository.changeset_revision,
+                owner=tool_shed_repository.owner,
+                dist_to_shed=tool_shed_repository.dist_to_shed,
+            )
+        ctx_rev = suc.get_ctx_rev(
+            trans.app,
+            tool_shed_url,
+            tool_shed_repository.name,
+            tool_shed_repository.owner,
+            tool_shed_repository.installed_changeset_revision,
+        )
         repo_info_dicts = []
-        repo_info_dict = kwd.get('repo_info_dict', None)
+        repo_info_dict = kwd.get("repo_info_dict", None)
         if repo_info_dict:
             if isinstance(repo_info_dict, str):
                 repo_info_dict = encoding_util.tool_shed_decode(repo_info_dict)
         else:
             # Entering this else block occurs only if the tool_shed_repository does not include any valid tools.
             if install_repository_dependencies:
-                repository_dependencies = \
-                    rdim.get_repository_dependencies_for_installed_tool_shed_repository(trans.app,
-                                                                                        tool_shed_repository)
+                repository_dependencies = rdim.get_repository_dependencies_for_installed_tool_shed_repository(
+                    trans.app, tool_shed_repository
+                )
             else:
                 repository_dependencies = None
             if metadata:
-                tool_dependencies = metadata.get('tool_dependencies', None)
+                tool_dependencies = metadata.get("tool_dependencies", None)
             else:
                 tool_dependencies = None
-            repo_info_dict = repository_util.create_repo_info_dict(trans.app,
-                                                                   repository_clone_url=repository_clone_url,
-                                                                   changeset_revision=tool_shed_repository.changeset_revision,
-                                                                   ctx_rev=ctx_rev,
-                                                                   repository_owner=tool_shed_repository.owner,
-                                                                   repository_name=tool_shed_repository.name,
-                                                                   tool_dependencies=tool_dependencies,
-                                                                   repository_dependencies=repository_dependencies)
+            repo_info_dict = repository_util.create_repo_info_dict(
+                trans.app,
+                repository_clone_url=repository_clone_url,
+                changeset_revision=tool_shed_repository.changeset_revision,
+                ctx_rev=ctx_rev,
+                repository_owner=tool_shed_repository.owner,
+                repository_name=tool_shed_repository.name,
+                tool_dependencies=tool_dependencies,
+                repository_dependencies=repository_dependencies,
+            )
         if repo_info_dict not in repo_info_dicts:
             repo_info_dicts.append(repo_info_dict)
         # Make sure all tool_shed_repository records exist.
-        created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
-            rdim.create_repository_dependency_objects(tool_path=tool_path,
-                                                      tool_shed_url=tool_shed_url,
-                                                      repo_info_dicts=repo_info_dicts,
-                                                      install_repository_dependencies=install_repository_dependencies,
-                                                      no_changes_checked=no_changes_checked,
-                                                      tool_panel_section_id=tool_panel_section_id)
+        (
+            created_or_updated_tool_shed_repositories,
+            tool_panel_section_keys,
+            repo_info_dicts,
+            filtered_repo_info_dicts,
+        ) = rdim.create_repository_dependency_objects(
+            tool_path=tool_path,
+            tool_shed_url=tool_shed_url,
+            repo_info_dicts=repo_info_dicts,
+            install_repository_dependencies=install_repository_dependencies,
+            no_changes_checked=no_changes_checked,
+            tool_panel_section_id=tool_panel_section_id,
+        )
         # Default the selected tool panel location for loading tools included in each newly installed required
         # tool shed repository to the location selected for the repository selected for re-installation.
         for index, tps_key in enumerate(tool_panel_section_keys):
             if tps_key is None:
                 tool_panel_section_keys[index] = tool_panel_section_key
         encoded_repository_ids = [trans.security.encode_id(r.id) for r in created_or_updated_tool_shed_repositories]
-        new_kwd = dict(includes_tool_dependencies=includes_tool_dependencies,
-                       includes_tools=tool_shed_repository.includes_tools,
-                       includes_tools_for_display_in_tool_panel=tool_shed_repository.includes_tools_for_display_in_tool_panel,
-                       install_tool_dependencies=install_tool_dependencies,
-                       install_resolver_dependencies=install_resolver_dependencies,
-                       repo_info_dicts=filtered_repo_info_dicts,
-                       message=message,
-                       new_tool_panel_section_label=new_tool_panel_section_label,
-                       shed_tool_conf=shed_tool_conf,
-                       status=status,
-                       tool_panel_section_id=tool_panel_section_id,
-                       tool_path=tool_path,
-                       tool_panel_section_keys=tool_panel_section_keys,
-                       tool_shed_repository_ids=encoded_repository_ids,
-                       tool_shed_url=tool_shed_url)
+        new_kwd = dict(
+            includes_tool_dependencies=includes_tool_dependencies,
+            includes_tools=tool_shed_repository.includes_tools,
+            includes_tools_for_display_in_tool_panel=tool_shed_repository.includes_tools_for_display_in_tool_panel,
+            install_tool_dependencies=install_tool_dependencies,
+            install_resolver_dependencies=install_resolver_dependencies,
+            repo_info_dicts=filtered_repo_info_dicts,
+            message=message,
+            new_tool_panel_section_label=new_tool_panel_section_label,
+            shed_tool_conf=shed_tool_conf,
+            status=status,
+            tool_panel_section_id=tool_panel_section_id,
+            tool_path=tool_path,
+            tool_panel_section_keys=tool_panel_section_keys,
+            tool_shed_repository_ids=encoded_repository_ids,
+            tool_shed_url=tool_shed_url,
+        )
         encoded_kwd = encoding_util.tool_shed_encode(new_kwd)
         tsr_ids = [r.id for r in created_or_updated_tool_shed_repositories]
         tool_shed_repositories = []
@@ -977,14 +1137,15 @@ class AdminToolshed(AdminGalaxy):
         clause_list = []
         for tsr_id in tsr_ids:
             clause_list.append(trans.install_model.ToolShedRepository.table.c.id == tsr_id)
-        query = trans.install_model.session.query(trans.install_model.ToolShedRepository) \
-                                           .filter(or_(*clause_list))
-        return trans.fill_template('admin/tool_shed_repository/monitor_repository_installation.mako',
-                                   encoded_kwd=encoded_kwd,
-                                   query=query,
-                                   tool_shed_repositories=tool_shed_repositories,
-                                   initiate_repository_installation_ids=encoded_repository_ids,
-                                   reinstalling=True)
+        query = trans.install_model.session.query(trans.install_model.ToolShedRepository).filter(or_(*clause_list))
+        return trans.fill_template(
+            "admin/tool_shed_repository/monitor_repository_installation.mako",
+            encoded_kwd=encoded_kwd,
+            query=query,
+            tool_shed_repositories=tool_shed_repositories,
+            initiate_repository_installation_ids=encoded_repository_ids,
+            reinstalling=True,
+        )
 
     @web.json
     @web.do_not_cache
@@ -996,13 +1157,23 @@ class AdminToolshed(AdminGalaxy):
             status_list = util.listify(status_list)
             for tup in zip(ids, status_list):
                 id, status = tup
-                repository = trans.install_model.context.query(trans.install_model.ToolShedRepository).get(trans.security.decode_id(id))
+                repository = trans.install_model.context.query(trans.install_model.ToolShedRepository).get(
+                    trans.security.decode_id(id)
+                )
                 if repository.status != status:
-                    rval.append(dict(id=id,
-                                     status=repository.status,
-                                     html_status=unicodify(trans.fill_template("admin/tool_shed_repository/repository_installation_status.mako",
-                                                                               repository=repository),
-                                                           'utf-8')))
+                    rval.append(
+                        dict(
+                            id=id,
+                            status=repository.status,
+                            html_status=unicodify(
+                                trans.fill_template(
+                                    "admin/tool_shed_repository/repository_installation_status.mako",
+                                    repository=repository,
+                                ),
+                                "utf-8",
+                            ),
+                        )
+                    )
         return rval
 
     @web.expose
@@ -1016,27 +1187,29 @@ class AdminToolshed(AdminGalaxy):
         have been retrieved from the tool shed and passed in the received kwd.  In this case, the stored
         tool shed repository metadata from the Galaxy database will not be used since it is outdated.
         """
-        message = ''
-        status = 'done'
-        repository_id = kwd.get('id', None)
-        latest_changeset_revision = kwd.get('latest_changeset_revision', None)
-        latest_ctx_rev = kwd.get('latest_ctx_rev', None)
+        message = ""
+        status = "done"
+        repository_id = kwd.get("id", None)
+        latest_changeset_revision = kwd.get("latest_changeset_revision", None)
+        latest_ctx_rev = kwd.get("latest_ctx_rev", None)
         tool_shed_repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository)
         metadata = tool_shed_repository.metadata_
-        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(tool_shed_repository.tool_shed))
+        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
+            trans.app, str(tool_shed_repository.tool_shed)
+        )
         tool_path = tool_shed_repository.get_tool_relative_path(trans.app)[0]
         if latest_changeset_revision and latest_ctx_rev:
             # There are updates available in the tool shed for the repository, so use the received
             # dependency information which was retrieved from the tool shed.
-            encoded_updated_repo_info_dict = kwd.get('updated_repo_info_dict', None)
+            encoded_updated_repo_info_dict = kwd.get("updated_repo_info_dict", None)
             updated_repo_info_dict = encoding_util.tool_shed_decode(encoded_updated_repo_info_dict)
-            readme_files_dict = updated_repo_info_dict.get('readme_files_dict', None)
-            includes_data_managers = updated_repo_info_dict.get('includes_data_managers', False)
-            includes_datatypes = updated_repo_info_dict.get('includes_datatypes', False)
-            includes_workflows = updated_repo_info_dict.get('includes_workflows', False)
-            includes_tool_dependencies = updated_repo_info_dict.get('includes_tool_dependencies', False)
-            repo_info_dict = updated_repo_info_dict['repo_info_dict']
+            readme_files_dict = updated_repo_info_dict.get("readme_files_dict", None)
+            includes_data_managers = updated_repo_info_dict.get("includes_data_managers", False)
+            includes_datatypes = updated_repo_info_dict.get("includes_datatypes", False)
+            includes_workflows = updated_repo_info_dict.get("includes_workflows", False)
+            includes_tool_dependencies = updated_repo_info_dict.get("includes_tool_dependencies", False)
+            repo_info_dict = updated_repo_info_dict["repo_info_dict"]
         else:
             # There are no updates available from the tool shed for the repository, so use its locally stored metadata.
             includes_data_managers = False
@@ -1046,99 +1219,114 @@ class AdminToolshed(AdminGalaxy):
             readme_files_dict = None
             tool_dependencies = None
             if metadata:
-                if 'data_manager' in metadata:
+                if "data_manager" in metadata:
                     includes_data_managers = True
-                if 'datatypes' in metadata:
+                if "datatypes" in metadata:
                     includes_datatypes = True
-                if 'tool_dependencies' in metadata:
+                if "tool_dependencies" in metadata:
                     includes_tool_dependencies = True
-                if 'workflows' in metadata:
+                if "workflows" in metadata:
                     includes_workflows = True
                 # Since we're reinstalling, we need to send a request to the tool shed to get the README files.
-                params = dict(name=tool_shed_repository.name,
-                              owner=tool_shed_repository.owner,
-                              changeset_revision=tool_shed_repository.installed_changeset_revision)
-                pathspec = ['repository', 'get_readme_files']
-                raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+                params = dict(
+                    name=tool_shed_repository.name,
+                    owner=tool_shed_repository.owner,
+                    changeset_revision=tool_shed_repository.installed_changeset_revision,
+                )
+                pathspec = ["repository", "get_readme_files"]
+                raw_text = util.url_get(
+                    tool_shed_url,
+                    auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                    pathspec=pathspec,
+                    params=params,
+                )
                 readme_files_dict = json.loads(raw_text)
-                tool_dependencies = metadata.get('tool_dependencies', None)
+                tool_dependencies = metadata.get("tool_dependencies", None)
             rdim = repository_dependency_manager.RepositoryDependencyInstallManager(trans.app)
-            repository_dependencies = \
-                rdim.get_repository_dependencies_for_installed_tool_shed_repository(trans.app,
-                                                                                    tool_shed_repository)
-            repo_info_dict = repository_util.create_repo_info_dict(trans.app,
-                                                                   repository_clone_url=repository_clone_url,
-                                                                   changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                   ctx_rev=tool_shed_repository.ctx_rev,
-                                                                   repository_owner=tool_shed_repository.owner,
-                                                                   repository_name=tool_shed_repository.name,
-                                                                   tool_dependencies=tool_dependencies,
-                                                                   repository_dependencies=repository_dependencies)
+            repository_dependencies = rdim.get_repository_dependencies_for_installed_tool_shed_repository(
+                trans.app, tool_shed_repository
+            )
+            repo_info_dict = repository_util.create_repo_info_dict(
+                trans.app,
+                repository_clone_url=repository_clone_url,
+                changeset_revision=tool_shed_repository.installed_changeset_revision,
+                ctx_rev=tool_shed_repository.ctx_rev,
+                repository_owner=tool_shed_repository.owner,
+                repository_name=tool_shed_repository.name,
+                tool_dependencies=tool_dependencies,
+                repository_dependencies=repository_dependencies,
+            )
         irm = trans.app.installed_repository_manager
-        dependencies_for_repository_dict = irm.get_dependencies_for_repository(tool_shed_url,
-                                                                               repo_info_dict,
-                                                                               includes_tool_dependencies,
-                                                                               updating=True)
-        includes_tool_dependencies = dependencies_for_repository_dict.get('includes_tool_dependencies', False)
-        includes_tools = dependencies_for_repository_dict.get('includes_tools', False)
-        includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get('includes_tools_for_display_in_tool_panel', False)
-        installed_repository_dependencies = dependencies_for_repository_dict.get('installed_repository_dependencies', None)
-        installed_tool_dependencies = dependencies_for_repository_dict.get('installed_tool_dependencies', None)
-        missing_repository_dependencies = dependencies_for_repository_dict.get('missing_repository_dependencies', None)
-        missing_tool_dependencies = dependencies_for_repository_dict.get('missing_tool_dependencies', None)
+        dependencies_for_repository_dict = irm.get_dependencies_for_repository(
+            tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=True
+        )
+        includes_tool_dependencies = dependencies_for_repository_dict.get("includes_tool_dependencies", False)
+        includes_tools = dependencies_for_repository_dict.get("includes_tools", False)
+        includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get(
+            "includes_tools_for_display_in_tool_panel", False
+        )
+        installed_repository_dependencies = dependencies_for_repository_dict.get(
+            "installed_repository_dependencies", None
+        )
+        installed_tool_dependencies = dependencies_for_repository_dict.get("installed_tool_dependencies", None)
+        missing_repository_dependencies = dependencies_for_repository_dict.get("missing_repository_dependencies", None)
+        missing_tool_dependencies = dependencies_for_repository_dict.get("missing_tool_dependencies", None)
         if installed_repository_dependencies or missing_repository_dependencies:
             has_repository_dependencies = True
         else:
             has_repository_dependencies = False
         if includes_tools_for_display_in_tool_panel:
             # Get the location in the tool panel in which the tools were originally loaded.
-            if 'tool_panel_section' in metadata:
-                tool_panel_dict = metadata['tool_panel_section']
+            if "tool_panel_section" in metadata:
+                tool_panel_dict = metadata["tool_panel_section"]
                 if tool_panel_dict:
                     if tool_util.panel_entry_per_tool(tool_panel_dict):
                         # The following forces everything to be loaded into 1 section (or no section) in the tool panel.
                         tool_section_dicts = tool_panel_dict[next(iter(tool_panel_dict.keys()))]
                         tool_section_dict = tool_section_dicts[0]
-                        original_section_name = tool_section_dict['name']
+                        original_section_name = tool_section_dict["name"]
                     else:
-                        original_section_name = tool_panel_dict['name']
+                        original_section_name = tool_panel_dict["name"]
                 else:
-                    original_section_name = ''
+                    original_section_name = ""
             else:
-                original_section_name = ''
+                original_section_name = ""
             tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
-            no_changes_check_box = CheckboxField('no_changes', value=True)
+            no_changes_check_box = CheckboxField("no_changes", value=True)
             if original_section_name:
-                message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>.  " \
+                message += (
+                    "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>.  "
                     % (escape(tool_shed_repository.name), original_section_name)
+                )
                 message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a "
                 message += "different section in the tool panel.  "
-                status = 'warning'
+                status = "warning"
             else:
                 message += f"The tools contained in your <b>{escape(tool_shed_repository.name)}</b> repository were last loaded into the tool panel outside of any sections.  "
                 message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section.  "
-                status = 'warning'
+                status = "warning"
         else:
             no_changes_check_box = None
-            original_section_name = ''
+            original_section_name = ""
             tool_panel_section_select_field = None
         shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field(trans.app)
         dd = dependency_display.DependencyDisplayer(trans.app)
-        containers_dict = \
-            dd.populate_containers_dict_for_new_install(tool_shed_url=tool_shed_url,
-                                                        tool_path=tool_path,
-                                                        readme_files_dict=readme_files_dict,
-                                                        installed_repository_dependencies=installed_repository_dependencies,
-                                                        missing_repository_dependencies=missing_repository_dependencies,
-                                                        installed_tool_dependencies=installed_tool_dependencies,
-                                                        missing_tool_dependencies=missing_tool_dependencies,
-                                                        updating=False)
+        containers_dict = dd.populate_containers_dict_for_new_install(
+            tool_shed_url=tool_shed_url,
+            tool_path=tool_path,
+            readme_files_dict=readme_files_dict,
+            installed_repository_dependencies=installed_repository_dependencies,
+            missing_repository_dependencies=missing_repository_dependencies,
+            installed_tool_dependencies=installed_tool_dependencies,
+            missing_tool_dependencies=missing_tool_dependencies,
+            updating=False,
+        )
         # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of
         # installed repository dependencies since each displayed repository dependency will display a status,
         # whether installed or missing.
         containers_dict = dd.merge_missing_repository_dependencies_to_installed_container(containers_dict)
         # Handle repository dependencies check box.
-        install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', value=True)
+        install_repository_dependencies_check_box = CheckboxField("install_repository_dependencies", value=True)
         # Handle tool dependencies check box.
         if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies:
             if includes_tool_dependencies:
@@ -1148,49 +1336,53 @@ class AdminToolshed(AdminGalaxy):
             install_tool_dependencies_check_box_checked = False
         else:
             install_tool_dependencies_check_box_checked = True
-        install_tool_dependencies_check_box = CheckboxField('install_tool_dependencies', value=install_tool_dependencies_check_box_checked)
+        install_tool_dependencies_check_box = CheckboxField(
+            "install_tool_dependencies", value=install_tool_dependencies_check_box_checked
+        )
         view = views.DependencyResolversView(self.app)
         if view.installable_resolvers:
-            install_resolver_dependencies_check_box = CheckboxField('install_resolver_dependencies', value=True)
+            install_resolver_dependencies_check_box = CheckboxField("install_resolver_dependencies", value=True)
         else:
             install_resolver_dependencies_check_box = None
-        return trans.fill_template('/admin/tool_shed_repository/reselect_tool_panel_section.mako',
-                                   repository=tool_shed_repository,
-                                   no_changes_check_box=no_changes_check_box,
-                                   original_section_name=original_section_name,
-                                   includes_data_managers=includes_data_managers,
-                                   includes_datatypes=includes_datatypes,
-                                   includes_tools=includes_tools,
-                                   includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                                   includes_tool_dependencies=includes_tool_dependencies,
-                                   includes_workflows=includes_workflows,
-                                   has_repository_dependencies=has_repository_dependencies,
-                                   install_repository_dependencies_check_box=install_repository_dependencies_check_box,
-                                   install_tool_dependencies_check_box=install_tool_dependencies_check_box,
-                                   install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
-                                   containers_dict=containers_dict,
-                                   tool_panel_section_select_field=tool_panel_section_select_field,
-                                   shed_tool_conf_select_field=shed_tool_conf_select_field,
-                                   encoded_repo_info_dict=encoding_util.tool_shed_encode(repo_info_dict),
-                                   repo_info_dict=repo_info_dict,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/admin/tool_shed_repository/reselect_tool_panel_section.mako",
+            repository=tool_shed_repository,
+            no_changes_check_box=no_changes_check_box,
+            original_section_name=original_section_name,
+            includes_data_managers=includes_data_managers,
+            includes_datatypes=includes_datatypes,
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            includes_tool_dependencies=includes_tool_dependencies,
+            includes_workflows=includes_workflows,
+            has_repository_dependencies=has_repository_dependencies,
+            install_repository_dependencies_check_box=install_repository_dependencies_check_box,
+            install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+            install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
+            containers_dict=containers_dict,
+            tool_panel_section_select_field=tool_panel_section_select_field,
+            shed_tool_conf_select_field=shed_tool_conf_select_field,
+            encoded_repo_info_dict=encoding_util.tool_shed_encode(repo_info_dict),
+            repo_info_dict=repo_info_dict,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def uninstall_tool_dependencies(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(as_string=False, **kwd)
         if not tool_dependency_ids:
-            tool_dependency_ids = util.listify(kwd.get('id', None))
+            tool_dependency_ids = util.listify(kwd.get("id", None))
         tool_dependencies = []
         for tool_dependency_id in tool_dependency_ids:
             tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_id)
             tool_dependencies.append(tool_dependency)
         tool_shed_repository = tool_dependencies[0].tool_shed_repository
-        if kwd.get('uninstall_tool_dependencies_button', False):
+        if kwd.get("uninstall_tool_dependencies_button", False):
             errors = False
             # Filter tool dependencies to only those that are installed but in an error state.
             tool_dependencies_for_uninstallation = []
@@ -1201,46 +1393,51 @@ class AdminToolshed(AdminGalaxy):
                 uninstalled, error_message = tool_dependency_util.remove_tool_dependency(trans.app, tool_dependency)
                 if error_message:
                     errors = True
-                    message = f'{message}  {error_message}'
+                    message = f"{message}  {error_message}"
             if errors:
                 message = f"Error attempting to uninstall tool dependencies: {message}"
-                status = 'error'
+                status = "error"
             else:
-                message = "These tool dependencies have been uninstalled: %s" % \
-                    ','.join(td.name for td in tool_dependencies_for_uninstallation)
+                message = "These tool dependencies have been uninstalled: %s" % ",".join(
+                    td.name for td in tool_dependencies_for_uninstallation
+                )
             td_ids = [trans.security.encode_id(td.id) for td in tool_shed_repository.tool_dependencies]
-            return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                            action='manage_repository_tool_dependencies',
-                                                            tool_dependency_ids=td_ids,
-                                                            status=status,
-                                                            message=message))
-        return trans.fill_template('/admin/tool_shed_repository/uninstall_tool_dependencies.mako',
-                                   repository=tool_shed_repository,
-                                   tool_dependency_ids=tool_dependency_ids,
-                                   tool_dependencies=tool_dependencies,
-                                   message=message,
-                                   status=status)
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="admin_toolshed",
+                    action="manage_repository_tool_dependencies",
+                    tool_dependency_ids=td_ids,
+                    status=status,
+                    message=message,
+                )
+            )
+        return trans.fill_template(
+            "/admin/tool_shed_repository/uninstall_tool_dependencies.mako",
+            repository=tool_shed_repository,
+            tool_dependency_ids=tool_dependency_ids,
+            tool_dependencies=tool_dependencies,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     @legacy_tool_shed_endpoint
     def update_to_changeset_revision(self, trans, **kwd):
         """Update a cloned repository to the latest revision possible."""
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        tool_shed_url = kwd.get('tool_shed_url', '')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        tool_shed_url = kwd.get("tool_shed_url", "")
         # Handle protocol changes over time.
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
-        latest_changeset_revision = kwd.get('latest_changeset_revision', None)
-        latest_ctx_rev = kwd.get('latest_ctx_rev', None)
-        repository = repository_util.get_installed_repository(trans.app,
-                                                              tool_shed=tool_shed_url,
-                                                              name=name,
-                                                              owner=owner,
-                                                              changeset_revision=changeset_revision)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
+        latest_changeset_revision = kwd.get("latest_changeset_revision", None)
+        latest_ctx_rev = kwd.get("latest_ctx_rev", None)
+        repository = repository_util.get_installed_repository(
+            trans.app, tool_shed=tool_shed_url, name=name, owner=owner, changeset_revision=changeset_revision
+        )
         if changeset_revision and latest_changeset_revision and latest_ctx_rev:
             if changeset_revision == latest_changeset_revision:
                 message = f"The installed repository named '{name}' is current, there are no updates available.  "
@@ -1251,42 +1448,56 @@ class AdminToolshed(AdminGalaxy):
                     tool_shed_url=tool_shed_url,
                     latest_ctx_rev=latest_ctx_rev,
                     latest_changeset_revision=latest_changeset_revision,
-                    install_new_dependencies=False
+                    install_new_dependencies=False,
                 )
-                if install_dependencies == 'repository':
+                if install_dependencies == "repository":
                     # Updates received include newly defined repository dependencies, so allow the user
                     # the option of installting them.  We cannot update the repository with the changes
                     # until that happens, so we have to send them along.
-                    new_kwd = dict(tool_shed_url=tool_shed_url,
-                                   updating_repository_id=trans.security.encode_id(repository.id),
-                                   updating_to_ctx_rev=latest_ctx_rev,
-                                   updating_to_changeset_revision=latest_changeset_revision,
-                                   encoded_updated_metadata=encoding_util.tool_shed_encode(irmm_metadata_dict),
-                                   updating=True)
+                    new_kwd = dict(
+                        tool_shed_url=tool_shed_url,
+                        updating_repository_id=trans.security.encode_id(repository.id),
+                        updating_to_ctx_rev=latest_ctx_rev,
+                        updating_to_changeset_revision=latest_changeset_revision,
+                        encoded_updated_metadata=encoding_util.tool_shed_encode(irmm_metadata_dict),
+                        updating=True,
+                    )
                     return self.prepare_for_install(trans, **new_kwd)
-                elif install_dependencies == 'tool':
+                elif install_dependencies == "tool":
                     # Updates received did not include any newly defined repository dependencies but did include
                     # newly defined tool dependencies.  If the newly defined tool dependencies are not the same
                     # as the originally defined tool dependencies, we need to install them.
                     relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(trans.app, repository)[2]
-                    encoded_tool_dependencies_dict = encoding_util.tool_shed_encode(irmm_metadata_dict.get('tool_dependencies', {}))
+                    encoded_tool_dependencies_dict = encoding_util.tool_shed_encode(
+                        irmm_metadata_dict.get("tool_dependencies", {})
+                    )
                     encoded_relative_install_dir = encoding_util.tool_shed_encode(relative_install_dir)
-                    new_kwd = dict(updating_repository_id=trans.security.encode_id(repository.id),
-                                   updating_to_ctx_rev=latest_ctx_rev,
-                                   updating_to_changeset_revision=latest_changeset_revision,
-                                   encoded_updated_metadata=encoding_util.tool_shed_encode(irmm_metadata_dict),
-                                   encoded_relative_install_dir=encoded_relative_install_dir,
-                                   encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
-                                   message=message,
-                                   status=status)
+                    new_kwd = dict(
+                        updating_repository_id=trans.security.encode_id(repository.id),
+                        updating_to_ctx_rev=latest_ctx_rev,
+                        updating_to_changeset_revision=latest_changeset_revision,
+                        encoded_updated_metadata=encoding_util.tool_shed_encode(irmm_metadata_dict),
+                        encoded_relative_install_dir=encoded_relative_install_dir,
+                        encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
+                        message=message,
+                        status=status,
+                    )
                     return self.install_tool_dependencies_with_update(trans, **new_kwd)
-                message = "The installed repository named '%s' has been updated to change set revision '%s'.  " % \
-                    (name, latest_changeset_revision)
+                message = "The installed repository named '%s' has been updated to change set revision '%s'.  " % (
+                    name,
+                    latest_changeset_revision,
+                )
         else:
-            message = f"The latest changeset revision could not be retrieved for the installed repository named '{name}'.  "
-            status = 'error'
-        return trans.response.send_redirect(web.url_for(controller='admin_toolshed',
-                                                        action='manage_repository',
-                                                        id=trans.security.encode_id(repository.id),
-                                                        message=message,
-                                                        status=status))
+            message = (
+                f"The latest changeset revision could not be retrieved for the installed repository named '{name}'.  "
+            )
+            status = "error"
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="admin_toolshed",
+                action="manage_repository",
+                id=trans.security.encode_id(repository.id),
+                message=message,
+                status=status,
+            )
+        )
diff --git a/lib/galaxy/webapps/galaxy/controllers/async.py b/lib/galaxy/webapps/galaxy/controllers/async.py
index 3b9d23da0f1..8a51d246a00 100644
--- a/lib/galaxy/webapps/galaxy/controllers/async.py
+++ b/lib/galaxy/webapps/galaxy/controllers/async.py
@@ -20,7 +20,6 @@ log = logging.getLogger(__name__)
 
 
 class ASync(BaseUIController):
-
     @web.expose
     def default(self, trans, tool_id=None, data_id=None, data_secret=None, **kwd):
         """Catches the tool id and redirects as needed"""
@@ -43,8 +42,8 @@ class ASync(BaseUIController):
         URL = params.URL
         data_id = params.data_id
 
-        log.debug(f'async dataid -> {data_id}')
-        trans.log_event(f'Async dataid -> {str(data_id)}')
+        log.debug(f"async dataid -> {data_id}")
+        trans.log_event(f"Async dataid -> {str(data_id)}")
 
         # initialize the tool
         toolbox = self.get_toolbox()
@@ -63,17 +62,19 @@ class ASync(BaseUIController):
             if not data:
                 return f"Data {data_id} does not exist or has already been deleted"
 
-            if STATUS == 'OK':
+            if STATUS == "OK":
                 key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id))
                 if key != data_secret:
                     return f"You do not have permission to alter data {data_id}."
                 # push the job into the queue
                 data.state = data.blurb = data.states.RUNNING
-                log.debug(f'executing tool {tool.id}')
-                trans.log_event(f'Async executing tool {tool.id}', tool_id=tool.id)
+                log.debug(f"executing tool {tool.id}")
+                trans.log_event(f"Async executing tool {tool.id}", tool_id=tool.id)
                 galaxy_url = f"{trans.request.base}/async/{tool_id}/{data.id}/{key}"
                 galaxy_url = params.get("GALAXY_URL", galaxy_url)
-                params = dict(URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext)
+                params = dict(
+                    URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext
+                )
 
                 # Assume there is exactly one output file possible
                 TOOL_OUTPUT_TYPE = None
@@ -92,8 +93,8 @@ class ASync(BaseUIController):
                 job, *_ = tool.execute(trans, incoming=params, history=original_history)
                 trans.app.job_manager.enqueue(job, tool=tool)
             else:
-                log.debug(f'async error -> {STATUS}')
-                trans.log_event(f'Async error -> {STATUS}')
+                log.debug(f"async error -> {STATUS}")
+                trans.log_event(f"Async error -> {STATUS}")
                 data.state = data.blurb = "error"
                 data.info = f"Error -> {STATUS}"
 
@@ -107,8 +108,8 @@ class ASync(BaseUIController):
             GALAXY_TYPE = None
             if params.data_type:
                 GALAXY_TYPE = params.data_type
-            elif params.galaxyFileFormat == 'wig':  # this is an undocumented legacy special case
-                GALAXY_TYPE = 'wig'
+            elif params.galaxyFileFormat == "wig":  # this is an undocumented legacy special case
+                GALAXY_TYPE = "wig"
             elif params.GALAXY_TYPE:
                 GALAXY_TYPE = params.GALAXY_TYPE
             else:
@@ -128,9 +129,9 @@ class ASync(BaseUIController):
             if GALAXY_TYPE is None:
                 raise Exception("Error: ToolOutput object not found")
 
-            GALAXY_NAME = params.name or params.GALAXY_NAME or f'{tool.name} query'
-            GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or ''
-            GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?'
+            GALAXY_NAME = params.name or params.GALAXY_NAME or f"{tool.name} query"
+            GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or ""
+            GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or "?"
 
             # data = datatypes.factory(ext=GALAXY_TYPE)()
             # data.ext   = GALAXY_TYPE
@@ -140,12 +141,18 @@ class ASync(BaseUIController):
             # data.state = jobs.JOB_OK
             # history.datasets.add_dataset( data )
 
-            data = trans.app.model.HistoryDatasetAssociation(create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE)
-            trans.app.security_agent.set_all_dataset_permissions(data.dataset, trans.app.security_agent.history_get_default_permissions(trans.history))
+            data = trans.app.model.HistoryDatasetAssociation(
+                create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE
+            )
+            trans.app.security_agent.set_all_dataset_permissions(
+                data.dataset, trans.app.security_agent.history_get_default_permissions(trans.history)
+            )
             data.name = GALAXY_NAME
             data.dbkey = GALAXY_BUILD
             data.info = GALAXY_INFO
-            trans.sa_session.add(data)  # Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change)
+            trans.sa_session.add(
+                data
+            )  # Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change)
             data.state = data.states.NEW
             trans.history.add_dataset(data, genome_build=GALAXY_BUILD)
             trans.sa_session.add(trans.history)
@@ -157,21 +164,21 @@ class ASync(BaseUIController):
             try:
                 key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id))
                 galaxy_url = f"{trans.request.base}/async/{tool_id}/{data.id}/{key}"
-                params.update({'GALAXY_URL': galaxy_url})
-                params.update({'data_id': data.id})
+                params.update({"GALAXY_URL": galaxy_url})
+                params.update({"data_id": data.id})
 
                 # Use provided URL or fallback to tool action
                 url = URL or tool.action
                 # Does url already have query params?
-                if '?' in url:
-                    url_join_char = '&'
+                if "?" in url:
+                    url_join_char = "&"
                 else:
-                    url_join_char = '?'
+                    url_join_char = "?"
                 url = f"{url}{url_join_char}{urlencode(params.flatten())}"
                 log.debug(f"connecting to -> {url}")
                 trans.log_event(f"Async connecting to -> {url}")
                 text = requests.get(url, timeout=DEFAULT_SOCKET_TIMEOUT).text.strip()
-                if not text.endswith('OK'):
+                if not text.endswith("OK"):
                     raise Exception(text)
                 data.state = data.blurb = data.states.RUNNING
             except Exception as e:
@@ -180,4 +187,4 @@ class ASync(BaseUIController):
 
             trans.sa_session.flush()
 
-        return trans.fill_template('root/tool_runner.mako', out_data={}, num_jobs=1, job_errors=[])
+        return trans.fill_template("root/tool_runner.mako", out_data={}, num_jobs=1, job_errors=[])
diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py
index c7a8abe007f..e8cf5957f94 100644
--- a/lib/galaxy/webapps/galaxy/controllers/authnz.py
+++ b/lib/galaxy/webapps/galaxy/controllers/authnz.py
@@ -9,19 +9,20 @@ import logging
 
 import jwt
 
-from galaxy import exceptions
-from galaxy import web
+from galaxy import (
+    exceptions,
+    web,
+)
 from galaxy.util import url_get
 from galaxy.web import url_for
 from galaxy.webapps.base.controller import JSAppLauncher
 
 log = logging.getLogger(__name__)
 
-PROVIDER_COOKIE_NAME = 'galaxy-oidc-provider'
+PROVIDER_COOKIE_NAME = "galaxy-oidc-provider"
 
 
 class OIDC(JSAppLauncher):
-
     @web.json
     @web.expose
     @web.require_login("list third-party identities")
@@ -40,26 +41,34 @@ class OIDC(JSAppLauncher):
         """
         rtv = []
         for authnz in trans.user.social_auth:
-            rtv.append({'id': trans.app.security.encode_id(authnz.id), 'provider': authnz.provider, 'email': authnz.uid})
+            rtv.append(
+                {"id": trans.app.security.encode_id(authnz.id), "provider": authnz.provider, "email": authnz.uid}
+            )
         # Add cilogon and custos identities
         for token in trans.user.custos_auth:
             # for purely displaying the info to user, we bypass verification of
             # signature, audience, and expiration as that's potentially useful
             # information to share with the end user
             try:
-                userinfo = jwt.decode(token.id_token, options={'verify_signature': False, 'verify_aud': False, 'verify_exp': False})
-                rtv.append({
-                    'id': trans.app.security.encode_id(token.id),
-                    'provider': token.provider,
-                    'email': userinfo['email'],
-                    'expiration': str(datetime.datetime.utcfromtimestamp(userinfo['exp']))
-                })
+                userinfo = jwt.decode(
+                    token.id_token, options={"verify_signature": False, "verify_aud": False, "verify_exp": False}
+                )
+                rtv.append(
+                    {
+                        "id": trans.app.security.encode_id(token.id),
+                        "provider": token.provider,
+                        "email": userinfo["email"],
+                        "expiration": str(datetime.datetime.utcfromtimestamp(userinfo["exp"])),
+                    }
+                )
             except Exception:
-                rtv.append({
-                    'id': trans.app.security.encode_id(token.id),
-                    'provider': token.provider,
-                    'error': "Unable to decode token"
-                })
+                rtv.append(
+                    {
+                        "id": trans.app.security.encode_id(token.id),
+                        "provider": token.provider,
+                        "error": "Unable to decode token",
+                    }
+                )
         return rtv
 
     @web.json
@@ -77,27 +86,34 @@ class OIDC(JSAppLauncher):
 
     @web.expose
     def callback(self, trans, provider, idphint=None, **kwargs):
-        user = trans.user.username if trans.user is not None else 'anonymous'
+        user = trans.user.username if trans.user is not None else "anonymous"
         if not bool(kwargs):
             log.error(f"OIDC callback received no data for provider `{provider}` and user `{user}`")
             return trans.show_error_message(
-                'Did not receive any information from the `{}` identity provider to complete user `{}` authentication '
-                'flow. Please try again, and if the problem persists, contact the Galaxy instance admin. Also note '
-                'that this endpoint is to receive authentication callbacks only, and should not be called/reached by '
-                'a user.'.format(provider, user))
-        if 'error' in kwargs:
-            log.error("Error handling authentication callback from `{}` identity provider for user `{}` login request."
-                      " Error message: {}".format(provider, user, kwargs.get('error', 'None')))
-            return trans.show_error_message('Failed to handle authentication callback from {}. '
-                                            'Please try again, and if the problem persists, contact '
-                                            'the Galaxy instance admin'.format(provider))
+                "Did not receive any information from the `{}` identity provider to complete user `{}` authentication "
+                "flow. Please try again, and if the problem persists, contact the Galaxy instance admin. Also note "
+                "that this endpoint is to receive authentication callbacks only, and should not be called/reached by "
+                "a user.".format(provider, user)
+            )
+        if "error" in kwargs:
+            log.error(
+                "Error handling authentication callback from `{}` identity provider for user `{}` login request."
+                " Error message: {}".format(provider, user, kwargs.get("error", "None"))
+            )
+            return trans.show_error_message(
+                "Failed to handle authentication callback from {}. "
+                "Please try again, and if the problem persists, contact "
+                "the Galaxy instance admin".format(provider)
+            )
         try:
-            success, message, (redirect_url, user) = trans.app.authnz_manager.callback(provider,
-                                                                                kwargs.get('state', ' '),
-                                                                                kwargs['code'],
-                                                                                trans,
-                                                                                login_redirect_url=url_for('/'),
-                                                                                idphint=idphint)
+            success, message, (redirect_url, user) = trans.app.authnz_manager.callback(
+                provider,
+                kwargs.get("state", " "),
+                kwargs["code"],
+                trans,
+                login_redirect_url=url_for("/"),
+                idphint=idphint,
+            )
         except exceptions.AuthenticationFailed:
             raise
         if success is False:
@@ -105,13 +121,15 @@ class OIDC(JSAppLauncher):
         if "?confirm" in redirect_url:
             return trans.response.send_redirect(url_for(redirect_url))
         elif redirect_url is None:
-            redirect_url = url_for('/')
+            redirect_url = url_for("/")
 
         user = user if user is not None else trans.user
         if user is None:
-            return trans.show_error_message("An unknown error occurred when handling the callback from `{}` "
-                                            "identity provider. Please try again, and if the problem persists, "
-                                            "contact the Galaxy instance admin.".format(provider))
+            return trans.show_error_message(
+                "An unknown error occurred when handling the callback from `{}` "
+                "identity provider. Please try again, and if the problem persists, "
+                "contact the Galaxy instance admin.".format(provider)
+            )
         trans.handle_user_login(user)
         # Record which idp provider was logged into, so we can logout of it later
         trans.set_cookie(value=provider, name=PROVIDER_COOKIE_NAME)
@@ -120,25 +138,28 @@ class OIDC(JSAppLauncher):
     @web.expose
     def create_user(self, trans, provider, **kwargs):
         try:
-            success, message, (redirect_url, user) = trans.app.authnz_manager.create_user(provider,
-                                                                                          token=kwargs.get('token', ' '),
-                                                                                          trans=trans,
-                                                                                          login_redirect_url=url_for('/'))
+            success, message, (redirect_url, user) = trans.app.authnz_manager.create_user(
+                provider, token=kwargs.get("token", " "), trans=trans, login_redirect_url=url_for("/")
+            )
         except exceptions.AuthenticationFailed as e:
-            return trans.response.send_redirect(f"{trans.request.base + url_for('/')}root/login?message={str(e) or 'Duplicate Email'}")
+            return trans.response.send_redirect(
+                f"{trans.request.base + url_for('/')}root/login?message={str(e) or 'Duplicate Email'}"
+            )
 
         if success is False:
             return trans.show_error_message(message)
         user = user if user is not None else trans.user
         if user is None:
-            return trans.show_error_message("An unknown error occurred when handling the callback from `{}` "
-                                            "identity provider. Please try again, and if the problem persists, "
-                                            "contact the Galaxy instance admin.".format(provider))
+            return trans.show_error_message(
+                "An unknown error occurred when handling the callback from `{}` "
+                "identity provider. Please try again, and if the problem persists, "
+                "contact the Galaxy instance admin.".format(provider)
+            )
         trans.handle_user_login(user)
         # Record which idp provider was logged into, so we can logout of it later
         trans.set_cookie(value=provider, name=PROVIDER_COOKIE_NAME)
         if redirect_url is None:
-            redirect_url = url_for('/')
+            redirect_url = url_for("/")
         return trans.response.send_redirect(url_for(redirect_url))
 
     @web.expose
@@ -147,52 +168,54 @@ class OIDC(JSAppLauncher):
         if trans.user is None:
             # Only logged in users are allowed here.
             return
-        success, message, redirect_url = trans.app.authnz_manager.disconnect(provider,
-                                                                             trans,
-                                                                             email,
-                                                                             disconnect_redirect_url=url_for('/'))
+        success, message, redirect_url = trans.app.authnz_manager.disconnect(
+            provider, trans, email, disconnect_redirect_url=url_for("/")
+        )
         if success is False:
             return trans.show_error_message(message)
         if redirect_url is None:
-            redirect_url = url_for('/')
+            redirect_url = url_for("/")
         return trans.response.send_redirect(redirect_url)
 
     @web.json
     @web.expose
     def logout(self, trans, provider, **kwargs):
         post_logout_redirect_url = f"{trans.request.base + url_for('/')}root/login?is_logout_redirect=true"
-        success, message, redirect_uri = trans.app.authnz_manager.logout(provider,
-                                                                         trans,
-                                                                         post_logout_redirect_url=post_logout_redirect_url)
+        success, message, redirect_uri = trans.app.authnz_manager.logout(
+            provider, trans, post_logout_redirect_url=post_logout_redirect_url
+        )
         if success:
-            return {'redirect_uri': redirect_uri}
+            return {"redirect_uri": redirect_uri}
         else:
-            return {'message': message}
+            return {"message": message}
 
     @web.expose
     def get_logout_url(self, trans, provider=None, **kwargs):
         idp_provider = provider if provider else trans.get_cookie(name=PROVIDER_COOKIE_NAME)
         if idp_provider:
-            return trans.response.send_redirect(url_for(controller='authnz', action='logout', provider=idp_provider))
+            return trans.response.send_redirect(url_for(controller="authnz", action="logout", provider=idp_provider))
 
     @web.expose
     @web.json
     def get_cilogon_idps(self, trans, **kwargs):
         allowed_idps = trans.app.authnz_manager.get_allowed_idps()
         try:
-            cilogon_idps = json.loads(url_get('https://cilogon.org/idplist/', params=dict(kwargs)))
+            cilogon_idps = json.loads(url_get("https://cilogon.org/idplist/", params=dict(kwargs)))
         except Exception as e:
             raise Exception(f"Invalid server response. {str(e)}.")
 
-        if (allowed_idps):
-            validated_idps = list(filter(lambda idp: idp['EntityID'] in allowed_idps, cilogon_idps))
+        if allowed_idps:
+            validated_idps = list(filter(lambda idp: idp["EntityID"] in allowed_idps, cilogon_idps))
 
             if not (len(validated_idps) == len(allowed_idps)):
-                validated_entity_ids = [entity['EntityID'] for entity in validated_idps]
+                validated_entity_ids = [entity["EntityID"] for entity in validated_idps]
 
                 for idp in allowed_idps:
-                    if (idp not in validated_entity_ids):
-                        log.debug("Invalid EntityID entered: %s. Use https://cilogon.org/idplist/ to find desired institution's EntityID.", idp)
+                    if idp not in validated_entity_ids:
+                        log.debug(
+                            "Invalid EntityID entered: %s. Use https://cilogon.org/idplist/ to find desired institution's EntityID.",
+                            idp,
+                        )
 
             return validated_idps
         else:
diff --git a/lib/galaxy/webapps/galaxy/controllers/data_manager.py b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
index 2a79e154056..17a1f135f1f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py
+++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
@@ -4,88 +4,109 @@ from json import loads
 import paste.httpexceptions
 
 from galaxy import web
-from galaxy.util import nice_size, unicodify
+from galaxy.util import (
+    nice_size,
+    unicodify,
+)
 from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
 
 
 class DataManager(BaseUIController):
-
     @web.expose
     @web.json
     def data_managers_list(self, trans, **kwd):
         not_is_admin = not trans.user_is_admin
         if not_is_admin and not trans.app.config.enable_data_manager_user_view:
-            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'info')
+            raise paste.httpexceptions.HTTPUnauthorized(
+                "This Galaxy instance is not configured to allow non-admins to view the data manager."
+            )
+        message = kwd.get("message", "")
+        status = kwd.get("status", "info")
         data_managers = []
-        for data_manager_id, data_manager in sorted(trans.app.data_managers.data_managers.items(),
-                                                    key=lambda data_manager: data_manager[1].name):
-            data_managers.append({'toolUrl': web.url_for(controller='root',
-                                                         tool_id=data_manager.tool.id),
-                                  'id': data_manager_id,
-                                  'name': data_manager.name,
-                                  'description': data_manager.description.lower()})
+        for data_manager_id, data_manager in sorted(
+            trans.app.data_managers.data_managers.items(), key=lambda data_manager: data_manager[1].name
+        ):
+            data_managers.append(
+                {
+                    "toolUrl": web.url_for(controller="root", tool_id=data_manager.tool.id),
+                    "id": data_manager_id,
+                    "name": data_manager.name,
+                    "description": data_manager.description.lower(),
+                }
+            )
         data_tables = []
         managed_table_names = trans.app.data_managers.managed_data_tables.keys()
         for table_name in sorted(trans.app.tool_data_tables.get_tables().keys()):
-            data_tables.append({'name': table_name,
-                                'managed': True if table_name in managed_table_names else False})
+            data_tables.append({"name": table_name, "managed": True if table_name in managed_table_names else False})
 
-        return {'dataManagers': data_managers,
-                'dataTables': data_tables,
-                'viewOnly': not_is_admin,
-                'message': message,
-                'status': status}
+        return {
+            "dataManagers": data_managers,
+            "dataTables": data_tables,
+            "viewOnly": not_is_admin,
+            "message": message,
+            "status": status,
+        }
 
     @web.expose
     @web.json
     def jobs_list(self, trans, **kwd):
         not_is_admin = not trans.user_is_admin
         if not_is_admin and not trans.app.config.enable_data_manager_user_view:
-            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'info')
-        data_manager_id = kwd.get('id', None)
+            raise paste.httpexceptions.HTTPUnauthorized(
+                "This Galaxy instance is not configured to allow non-admins to view the data manager."
+            )
+        message = kwd.get("message", "")
+        status = kwd.get("status", "info")
+        data_manager_id = kwd.get("id", None)
         data_manager = trans.app.data_managers.get_manager(data_manager_id)
         if data_manager is None:
-            return {'message': f"Invalid Data Manager ({data_manager_id}) was requested",
-                    'status': "error"}
+            return {"message": f"Invalid Data Manager ({data_manager_id}) was requested", "status": "error"}
         jobs = []
-        for assoc in trans.sa_session.query(trans.app.model.DataManagerJobAssociation).filter_by(data_manager_id=data_manager_id):
+        for assoc in trans.sa_session.query(trans.app.model.DataManagerJobAssociation).filter_by(
+            data_manager_id=data_manager_id
+        ):
             j = assoc.job
-            jobs.append({
-                'id': j.id,
-                'encId': trans.security.encode_id(j.id),
-                'runUrl': web.url_for(controller="tool_runner", action="rerun", job_id=trans.security.encode_id(j.id)),
-                'user': j.history.user.email if j.history and j.history.user else "anonymous",
-                'updateTime': j.update_time.isoformat(),
-                'state': j.state,
-                'commandLine': j.command_line,
-                'jobRunnerName': j.job_runner_name,
-                'jobRunnerExternalId': j.job_runner_external_id
-            })
+            jobs.append(
+                {
+                    "id": j.id,
+                    "encId": trans.security.encode_id(j.id),
+                    "runUrl": web.url_for(
+                        controller="tool_runner", action="rerun", job_id=trans.security.encode_id(j.id)
+                    ),
+                    "user": j.history.user.email if j.history and j.history.user else "anonymous",
+                    "updateTime": j.update_time.isoformat(),
+                    "state": j.state,
+                    "commandLine": j.command_line,
+                    "jobRunnerName": j.job_runner_name,
+                    "jobRunnerExternalId": j.job_runner_external_id,
+                }
+            )
         jobs.reverse()
-        return {'dataManager': {'name': data_manager.name,
-                                'description': data_manager.description.lower(),
-                                'toolUrl': web.url_for(controller='root',
-                                                       tool_id=data_manager.tool.id)},
-                'jobs': jobs,
-                'viewOnly': not_is_admin,
-                'message': message,
-                'status': status}
+        return {
+            "dataManager": {
+                "name": data_manager.name,
+                "description": data_manager.description.lower(),
+                "toolUrl": web.url_for(controller="root", tool_id=data_manager.tool.id),
+            },
+            "jobs": jobs,
+            "viewOnly": not_is_admin,
+            "message": message,
+            "status": status,
+        }
 
     @web.expose
     @web.json
     def job_info(self, trans, **kwd):
         not_is_admin = not trans.user_is_admin
         if not_is_admin and not trans.app.config.enable_data_manager_user_view:
-            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'info')
-        job_id = kwd.get('id', None)
+            raise paste.httpexceptions.HTTPUnauthorized(
+                "This Galaxy instance is not configured to allow non-admins to view the data manager."
+            )
+        message = kwd.get("message", "")
+        status = kwd.get("status", "info")
+        job_id = kwd.get("id", None)
         try:
             job_id = trans.security.decode_id(job_id)
             job = trans.sa_session.query(trans.app.model.Job).get(job_id)
@@ -93,8 +114,7 @@ class DataManager(BaseUIController):
             job = None
             log.error(f"Bad job id ({job_id}) passed to job_info: {e}")
         if not job:
-            return {'message': f"Invalid job ({job_id}) was requested",
-                    'status': "error"}
+            return {"message": f"Invalid job ({job_id}) was requested", "status": "error"}
         data_manager_id = job.data_manager_association.data_manager_id
         data_manager = trans.app.data_managers.get_manager(data_manager_id)
         hdas = [assoc.dataset for assoc in job.get_output_datasets()]
@@ -102,41 +122,46 @@ class DataManager(BaseUIController):
         data_manager_output = []
         error_messages = []
         for hda in hdas:
-            hda_info.append({'id': hda.id,
-                             'encId': trans.security.encode_id(hda.id),
-                             'name': hda.name,
-                             'created': unicodify(hda.create_time.strftime(trans.app.config.pretty_datetime_format)),
-                             'fileSize': nice_size(hda.dataset.file_size),
-                             'fileName': hda.file_name,
-                             'infoUrl': web.url_for(controller='dataset',
-                                                    action='show_params',
-                                                    dataset_id=trans.security.encode_id(hda.id))})
+            hda_info.append(
+                {
+                    "id": hda.id,
+                    "encId": trans.security.encode_id(hda.id),
+                    "name": hda.name,
+                    "created": unicodify(hda.create_time.strftime(trans.app.config.pretty_datetime_format)),
+                    "fileSize": nice_size(hda.dataset.file_size),
+                    "fileName": hda.file_name,
+                    "infoUrl": web.url_for(
+                        controller="dataset", action="show_params", dataset_id=trans.security.encode_id(hda.id)
+                    ),
+                }
+            )
             try:
                 data_manager_json = loads(open(hda.get_file_name()).read())
             except Exception as e:
                 data_manager_json = {}
                 error_messages.append(f"Unable to obtain data_table info for hda ({hda.id}): {e}")
             values = []
-            for key, value in data_manager_json.get('data_tables', {}).items():
+            for key, value in data_manager_json.get("data_tables", {}).items():
                 values.append((key, value))
             data_manager_output.append(values)
-        return {'jobId': job_id,
-                'exitCode': job.exit_code,
-                'runUrl': web.url_for(controller="tool_runner",
-                                      action="rerun",
-                                      job_id=trans.security.encode_id(job.id)),
-                'commandLine': job.command_line,
-                'dataManager': {'id': data_manager_id,
-                                'name': data_manager.name,
-                                'description': data_manager.description.lower(),
-                                'toolUrl': web.url_for(controller='root',
-                                                       tool_id=data_manager.tool.id)},
-                'hdaInfo': hda_info,
-                'dataManagerOutput': data_manager_output,
-                'errorMessages': error_messages,
-                'viewOnly': not_is_admin,
-                'message': message,
-                'status': status}
+        return {
+            "jobId": job_id,
+            "exitCode": job.exit_code,
+            "runUrl": web.url_for(controller="tool_runner", action="rerun", job_id=trans.security.encode_id(job.id)),
+            "commandLine": job.command_line,
+            "dataManager": {
+                "id": data_manager_id,
+                "name": data_manager.name,
+                "description": data_manager.description.lower(),
+                "toolUrl": web.url_for(controller="root", tool_id=data_manager.tool.id),
+            },
+            "hdaInfo": hda_info,
+            "dataManagerOutput": data_manager_output,
+            "errorMessages": error_messages,
+            "viewOnly": not_is_admin,
+            "message": message,
+            "status": status,
+        }
 
     @web.expose
     @web.json
@@ -146,23 +171,27 @@ class DataManager(BaseUIController):
     def tool_data_table_info_1(self, trans, **kwd):
         not_is_admin = not trans.user_is_admin
         if not_is_admin and not trans.app.config.enable_data_manager_user_view:
-            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'info')
-        data_table_name = kwd.get('table_name', None)
+            raise paste.httpexceptions.HTTPUnauthorized(
+                "This Galaxy instance is not configured to allow non-admins to view the data manager."
+            )
+        message = kwd.get("message", "")
+        status = kwd.get("status", "info")
+        data_table_name = kwd.get("table_name", None)
         if not data_table_name:
-            return {'message': "No data table was requested.",
-                    'status': "error"}
+            return {"message": "No data table was requested.", "status": "error"}
         data_table = trans.app.tool_data_tables.get(data_table_name, None)
         if data_table is None:
-            return {'message': f"Invalid data table '{data_table_name}' was requested.",
-                    'status': "error"}
-        return {'dataTable': {'name': data_table.name,
-                              'columns': data_table.get_column_name_list(),
-                              'data': data_table.data},
-                'viewOnly': not_is_admin,
-                'message': message,
-                'status': status}
+            return {"message": f"Invalid data table '{data_table_name}' was requested.", "status": "error"}
+        return {
+            "dataTable": {
+                "name": data_table.name,
+                "columns": data_table.get_column_name_list(),
+                "data": data_table.data,
+            },
+            "viewOnly": not_is_admin,
+            "message": message,
+            "status": status,
+        }
 
     @web.expose
     @web.json
@@ -173,73 +202,62 @@ class DataManager(BaseUIController):
         # Reload the tool data tables
         table_names = self.app.tool_data_tables.reload_tables(table_names=table_name)
         trans.app.queue_worker.send_control_task(
-            'reload_tool_data_tables',
-            noop_self=True,
-            kwargs={'table_name': table_name}
+            "reload_tool_data_tables", noop_self=True, kwargs={"table_name": table_name}
         )
         data = None
         if table_names:
-            message = "Reloaded data table{} '{}'.".format('s'[len(table_names) == 1:],
-                                                       ', '.join(table_names))
-            data = self.tool_data_table_info_1(trans,
-                                               table_name=table_names[0],
-                                               message=message,
-                                               status="done")
+            message = "Reloaded data table{} '{}'.".format("s"[len(table_names) == 1 :], ", ".join(table_names))
+            data = self.tool_data_table_info_1(trans, table_name=table_names[0], message=message, status="done")
         else:
-            data = {'message': "No data tables have been reloaded.",
-                    'status': "error"}
+            data = {"message": "No data tables have been reloaded.", "status": "error"}
         return data
 
     @web.expose
     @web.json
     @web.require_admin
     def tool_data_table_items(self, trans, **kwd):
-        data = {'columns': [], 'items': []}
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'info')
-        table_name = kwd.get('table_name', None)
+        data = {"columns": [], "items": []}
+        message = kwd.get("message", "")
+        status = kwd.get("status", "info")
+        table_name = kwd.get("table_name", None)
 
         if not table_name:
             return {
-                'data': data,
-                'message': 'No Data table name provided.',
-                'status': 'warning',
+                "data": data,
+                "message": "No Data table name provided.",
+                "status": "warning",
             }
 
         data_table = trans.app.tool_data_tables.get(table_name, None)
 
         if data_table is None:
-            return {
-                'data': data,
-                'message': f'Invalid Data table ({table_name}) was requested',
-                'status': 'error'
-            }
+            return {"data": data, "message": f"Invalid Data table ({table_name}) was requested", "status": "error"}
 
         columns = data_table.get_column_name_list()
         rows = [dict(zip(columns, table_row)) for table_row in data_table.data]
-        data['columns'] = columns
-        data['items'] = rows
+        data["columns"] = columns
+        data["items"] = rows
 
-        return {'data': data, 'message': message, 'status': status}
+        return {"data": data, "message": message, "status": status}
 
     @web.expose
     @web.json
     @web.require_admin
     def reload_tool_data_table(self, trans, **kwd):
-        table_name = kwd.get('table_name', None)
+        table_name = kwd.get("table_name", None)
 
         if not table_name:
             return {
-                'message': 'No data table has been reloaded.',
-                'status': 'error',
+                "message": "No data table has been reloaded.",
+                "status": "error",
             }
 
         redirect_url = web.url_for(
-            controller='data_manager',
-            action='tool_data_table_items',
+            controller="data_manager",
+            action="tool_data_table_items",
             table_name=table_name,
             message=f'The data table "{table_name}" has been reloaded.',
-            status='done',
+            status="done",
         )
 
         return trans.response.send_redirect(redirect_url)
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index eac8a869620..ff34047a6d1 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -12,26 +12,41 @@ from galaxy import (
     datatypes,
     model,
     util,
-    web
+    web,
 )
 from galaxy.datatypes import sniff
 from galaxy.datatypes.data import DatatypeConverterNotFoundException
-from galaxy.datatypes.display_applications.util import decode_dataset_user, encode_dataset_user
+from galaxy.datatypes.display_applications.util import (
+    decode_dataset_user,
+    encode_dataset_user,
+)
 from galaxy.exceptions import RequestParameterInvalidException
-from galaxy.managers.hdas import HDADeserializer, HDAManager
+from galaxy.managers.hdas import (
+    HDADeserializer,
+    HDAManager,
+)
 from galaxy.managers.histories import HistoryManager
-from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
+from galaxy.model.item_attrs import (
+    UsesAnnotations,
+    UsesItemRatings,
+)
 from galaxy.structured_app import StructuredApp
 from galaxy.util import (
     inflector,
     sanitize_text,
-    smart_str
+    smart_str,
 )
 from galaxy.util.checkers import check_binary
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import form_builder
 from galaxy.web.framework.helpers import iff
-from galaxy.webapps.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesExtendedMetadataMixin
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    ERROR,
+    SUCCESS,
+    url_for,
+    UsesExtendedMetadataMixin,
+)
 from ..api import depends
 
 log = logging.getLogger(__name__)
@@ -40,7 +55,8 @@ comptypes = []
 
 try:
     import zlib  # noqa: F401
-    comptypes.append('zip')
+
+    comptypes.append("zip")
 except ImportError:
     pass
 
@@ -54,10 +70,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         super().__init__(app)
 
     def _get_job_for_dataset(self, trans, dataset_id):
-        '''
+        """
         Return the job for the given dataset. This will throw an error if the
         dataset is either nonexistent or inaccessible to the user.
-        '''
+        """
         hda = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(self.decode_id(dataset_id))
         assert hda and self._can_access_dataset(trans, hda)
         return hda.creating_job
@@ -66,19 +82,23 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         roles = trans.get_current_user_roles()
         if additional_roles:
             roles = roles + additional_roles
-        return (allow_admin and trans.user_is_admin) or trans.app.security_agent.can_access_dataset(roles, dataset_association.dataset)
+        return (allow_admin and trans.user_is_admin) or trans.app.security_agent.can_access_dataset(
+            roles, dataset_association.dataset
+        )
 
     @web.expose
     def errors(self, trans, id):
         hda = trans.sa_session.query(model.HistoryDatasetAssociation).get(self.decode_id(id))
 
         if not hda or not self._can_access_dataset(trans, hda):
-            return trans.show_error_message("Either this dataset does not exist or you do not have permission to access it.")
+            return trans.show_error_message(
+                "Either this dataset does not exist or you do not have permission to access it."
+            )
         return trans.fill_template("dataset/errors.mako", hda=hda)
 
     @web.expose
     def stdout(self, trans, dataset_id=None, **kwargs):
-        trans.response.set_content_type('text/plain')
+        trans.response.set_content_type("text/plain")
         stdout = ""
         try:
             job = self._get_job_for_dataset(trans, dataset_id)
@@ -90,7 +110,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     @web.expose
     # TODO: Migrate stderr and stdout to use _get_job_for_dataset; it wasn't tested.
     def stderr(self, trans, dataset_id=None, **kwargs):
-        trans.response.set_content_type('text/plain')
+        trans.response.set_content_type("text/plain")
         stderr = ""
         try:
             job = self._get_job_for_dataset(trans, dataset_id)
@@ -101,7 +121,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
     @web.expose
     def exit_code(self, trans, dataset_id=None, **kwargs):
-        trans.response.set_content_type('text/plain')
+        trans.response.set_content_type("text/plain")
         exit_code = ""
         try:
             job = self._get_job_for_dataset(trans, dataset_id)
@@ -112,28 +132,28 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
     @web.expose
     def default(self, trans, dataset_id=None, **kwd):
-        return 'This link may not be followed from within Galaxy.'
+        return "This link may not be followed from within Galaxy."
 
     @web.expose
     def get_metadata_file(self, trans, hda_id, metadata_name):
-        """ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files) """
+        """Allows the downloading of metadata files associated with datasets (eg. bai index for bam files)"""
         data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(self.decode_id(hda_id))
         if not data or not self._can_access_dataset(trans, data):
             return trans.show_error_message("You are not allowed to access this dataset")
 
-        fname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in data.name)[0:150]
+        fname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in data.name)[0:150]
 
         file_ext = data.metadata.spec.get(metadata_name).get("file_ext", metadata_name)
         trans.response.headers["Content-Type"] = "application/octet-stream"
         trans.response.headers["Content-Disposition"] = f'attachment; filename="Galaxy{data.hid}-[{fname}].{file_ext}"'
-        return open(data.metadata.get(metadata_name).file_name, 'rb')
+        return open(data.metadata.get(metadata_name).file_name, "rb")
 
     def _check_dataset(self, trans, hda_id):
         # DEPRECATION: We still support unencoded ids for backward compatibility
         try:
             data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(self.decode_id(hda_id))
             if data is None:
-                raise ValueError(f'Invalid reference dataset id: {hda_id}.')
+                raise ValueError(f"Invalid reference dataset id: {hda_id}.")
         except Exception:
             try:
                 data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(int(hda_id))
@@ -148,14 +168,16 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         if data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.history.user)):
             return trans.show_error_message("The dataset you are attempting to view has been deleted.")
         if data.state == trans.model.Dataset.states.UPLOAD:
-            return trans.show_error_message("Please wait until this dataset finishes uploading before attempting to view it.")
+            return trans.show_error_message(
+                "Please wait until this dataset finishes uploading before attempting to view it."
+            )
         return data
 
     @web.expose
     @web.json
     def transfer_status(self, trans, dataset_id, filename=None):
-        """ Primarily used for the S3ObjectStore - get the status of data transfer
-        if the file is not in cache """
+        """Primarily used for the S3ObjectStore - get the status of data transfer
+        if the file is not in cache"""
         data = self._check_dataset(trans, dataset_id)
         if isinstance(data, str):
             return data
@@ -171,7 +193,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             return trans.app.object_store.file_ready(data.dataset)
 
     @web.expose
-    def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd):
+    def display(
+        self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd
+    ):
         data = self._check_dataset(trans, dataset_id)
         if not isinstance(data, trans.app.model.DatasetInstance):
             return data
@@ -188,7 +212,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         # Ensure ck_size is an integer before passing through to datatypes.
         if ck_size:
             ck_size = int(ck_size)
-        display_data, headers = data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)
+        display_data, headers = data.datatype.display_data(
+            trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd
+        )
         trans.response.headers.update(headers)
         return display_data
 
@@ -202,80 +228,95 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
         if self._can_access_dataset(trans, data):
             if data.state == trans.model.Dataset.states.UPLOAD:
-                return self.message_exception(trans, 'Please wait until this dataset finishes uploading before attempting to edit its metadata.')
+                return self.message_exception(
+                    trans, "Please wait until this dataset finishes uploading before attempting to edit its metadata."
+                )
             # let's not overwrite the imported datatypes module with the variable datatypes?
             # the built-in 'id' is overwritten in lots of places as well
-            ldatatypes = [(dtype_name, dtype_name) for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.items() if dtype_value.is_datatype_change_allowed()]
+            ldatatypes = [
+                (dtype_name, dtype_name)
+                for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.items()
+                if dtype_value.is_datatype_change_allowed()
+            ]
             ldatatypes.sort()
-            all_roles = [(r.name, trans.security.encode_id(r.id)) for r in trans.app.security_agent.get_legitimate_roles(trans, data.dataset, 'root')]
+            all_roles = [
+                (r.name, trans.security.encode_id(r.id))
+                for r in trans.app.security_agent.get_legitimate_roles(trans, data.dataset, "root")
+            ]
             data_metadata = [(name, spec) for name, spec in data.metadata.spec.items()]
             converters_collection = [(key, value.name) for key, value in data.get_converter_types().items()]
-            can_manage_dataset = trans.app.security_agent.can_manage_dataset(trans.get_current_user_roles(), data.dataset)
+            can_manage_dataset = trans.app.security_agent.can_manage_dataset(
+                trans.get_current_user_roles(), data.dataset
+            )
             # attribute editing
-            attribute_inputs = [{
-                'name': 'name',
-                'type': 'text',
-                'label': 'Name',
-                'value': data.get_display_name()
-            }, {
-                'name': 'info',
-                'type': 'text',
-                'area': True,
-                'label': 'Info',
-                'value': data.info
-            }, {
-                'name': 'annotation',
-                'type': 'text',
-                'area': True,
-                'label': 'Annotation',
-                'value': self.get_item_annotation_str(trans.sa_session, trans.user, data),
-                'help': 'Add an annotation or notes to a dataset; annotations are available when a history is viewed.'
-            }]
+            attribute_inputs = [
+                {"name": "name", "type": "text", "label": "Name", "value": data.get_display_name()},
+                {"name": "info", "type": "text", "area": True, "label": "Info", "value": data.info},
+                {
+                    "name": "annotation",
+                    "type": "text",
+                    "area": True,
+                    "label": "Annotation",
+                    "value": self.get_item_annotation_str(trans.sa_session, trans.user, data),
+                    "help": "Add an annotation or notes to a dataset; annotations are available when a history is viewed.",
+                },
+            ]
             for name, spec in data_metadata:
                 if spec.visible:
                     attributes = data.metadata.get_metadata_parameter(name, trans=trans)
                     if type(attributes) is form_builder.SelectField:
-                        attribute_inputs.append({
-                            'type': 'select',
-                            'multiple': attributes.multiple,
-                            'optional': spec.get('optional'),
-                            'name': name,
-                            'label': spec.desc,
-                            'options': attributes.options,
-                            'value': attributes.value if attributes.multiple else [attributes.value]
-                        })
+                        attribute_inputs.append(
+                            {
+                                "type": "select",
+                                "multiple": attributes.multiple,
+                                "optional": spec.get("optional"),
+                                "name": name,
+                                "label": spec.desc,
+                                "options": attributes.options,
+                                "value": attributes.value if attributes.multiple else [attributes.value],
+                            }
+                        )
                     elif type(attributes) is form_builder.TextField:
-                        attribute_inputs.append({
-                            'type': 'text',
-                            'name': name,
-                            'label': spec.desc,
-                            'value': attributes.value,
-                            'readonly': spec.get('readonly')
-                        })
+                        attribute_inputs.append(
+                            {
+                                "type": "text",
+                                "name": name,
+                                "label": spec.desc,
+                                "value": attributes.value,
+                                "readonly": spec.get("readonly"),
+                            }
+                        )
             if data.missing_meta():
                 message = 'Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.'
-                status = 'warning'
+                status = "warning"
             # datatype conversion
-            conversion_options = [(f"{convert_id} (using '{convert_name}')", convert_id) for convert_id, convert_name in converters_collection]
+            conversion_options = [
+                (f"{convert_id} (using '{convert_name}')", convert_id)
+                for convert_id, convert_name in converters_collection
+            ]
             conversion_disable = len(conversion_options) == 0
-            conversion_inputs = [{
-                'type': 'select',
-                'name': 'target_type',
-                'label': 'Target datatype',
-                'help': 'This will create a new dataset with the contents of this dataset converted to a new format.',
-                'options': conversion_options
-            }]
+            conversion_inputs = [
+                {
+                    "type": "select",
+                    "name": "target_type",
+                    "label": "Target datatype",
+                    "help": "This will create a new dataset with the contents of this dataset converted to a new format.",
+                    "options": conversion_options,
+                }
+            ]
             # datatype changing
             datatype_options = [(ext_name, ext_id) for ext_id, ext_name in ldatatypes]
             datatype_disable = len(datatype_options) == 0
-            datatype_inputs = [{
-                'type': 'select',
-                'name': 'datatype',
-                'label': 'New Type',
-                'options': datatype_options,
-                'value': [ext_id for ext_id, ext_name in ldatatypes if ext_id == data.ext],
-                'help': 'This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.',
-            }]
+            datatype_inputs = [
+                {
+                    "type": "select",
+                    "name": "datatype",
+                    "label": "New Type",
+                    "options": datatype_options,
+                    "value": [ext_id for ext_id, ext_name in ldatatypes if ext_id == data.ext],
+                    "help": "This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.",
+                }
+            ]
             # permissions
             permission_disable = True
             permission_inputs = list()
@@ -289,91 +330,102 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                             help_text = f"{action.description}<br/>NOTE: Users must have every role associated with this dataset in order to access it."
                         else:
                             help_text = action.description
-                        permission_inputs.append({
-                            'type': 'select',
-                            'multiple': True,
-                            'optional': True,
-                            'name': index,
-                            'label': action.action,
-                            'help': help_text,
-                            'options': all_roles,
-                            'value': in_roles.get(action.action),
-                            'readonly': not can_manage_dataset
-                        })
+                        permission_inputs.append(
+                            {
+                                "type": "select",
+                                "multiple": True,
+                                "optional": True,
+                                "name": index,
+                                "label": action.action,
+                                "help": help_text,
+                                "options": all_roles,
+                                "value": in_roles.get(action.action),
+                                "readonly": not can_manage_dataset,
+                            }
+                        )
                     permission_disable = not can_manage_dataset
                 else:
-                    permission_inputs.append({
-                        'name': 'access_public',
-                        'type': 'hidden',
-                        'label': 'This dataset is accessible by everyone (it is public).',
-                        'readonly': True
-                    })
+                    permission_inputs.append(
+                        {
+                            "name": "access_public",
+                            "type": "hidden",
+                            "label": "This dataset is accessible by everyone (it is public).",
+                            "readonly": True,
+                        }
+                    )
             else:
-                permission_inputs.append({
-                    'name': 'no_access',
-                    'type': 'hidden',
-                    'label': 'Permissions not available (not logged in).',
-                    'readonly': True
-                })
+                permission_inputs.append(
+                    {
+                        "name": "no_access",
+                        "type": "hidden",
+                        "label": "Permissions not available (not logged in).",
+                        "readonly": True,
+                    }
+                )
             return {
-                'display_name': data.get_display_name(),
-                'message': message,
-                'status': status,
-                'dataset_id': dataset_id,
-                'attribute_inputs': attribute_inputs,
-                'conversion_inputs': conversion_inputs,
-                'conversion_disable': conversion_disable,
-                'datatype_inputs': datatype_inputs,
-                'datatype_disable': datatype_disable,
-                'permission_inputs': permission_inputs,
-                'permission_disable': permission_disable
+                "display_name": data.get_display_name(),
+                "message": message,
+                "status": status,
+                "dataset_id": dataset_id,
+                "attribute_inputs": attribute_inputs,
+                "conversion_inputs": conversion_inputs,
+                "conversion_disable": conversion_disable,
+                "datatype_inputs": datatype_inputs,
+                "datatype_disable": datatype_disable,
+                "permission_inputs": permission_inputs,
+                "permission_disable": permission_disable,
             }
         else:
-            return self.message_exception(trans, 'You do not have permission to edit this dataset\'s ( id: %s ) information.' % str(dataset_id))
+            return self.message_exception(
+                trans, "You do not have permission to edit this dataset's ( id: %s ) information." % str(dataset_id)
+            )
 
     @web.expose_api_anonymous
     def set_edit(self, trans, payload=None, **kwd):
         """Allows user to modify parameters of an HDA."""
-        status = 'success'
-        operation = payload.get('operation')
-        dataset_id = payload.get('dataset_id')
+        status = "success"
+        operation = payload.get("operation")
+        dataset_id = payload.get("dataset_id")
         data, message = self._get_dataset_for_edit(trans, dataset_id)
         if message:
             return message
 
-        if operation == 'attributes':
+        if operation == "attributes":
             # The user clicked the Save button on the 'Edit Attributes' form
-            data.name = payload.get('name')
-            data.info = payload.get('info')
+            data.name = payload.get("name")
+            data.info = payload.get("info")
             if data.ok_to_edit_metadata():
                 # The following for loop will save all metadata_spec items
                 for name, spec in data.datatype.metadata_spec.items():
-                    if not spec.get('readonly'):
+                    if not spec.get("readonly"):
                         setattr(data.metadata, name, spec.unwrap(payload.get(name) or None))
                 data.datatype.after_setting_metadata(data)
                 # Sanitize annotation before adding it.
-                if payload.get('annotation'):
-                    annotation = sanitize_html(payload.get('annotation'))
+                if payload.get("annotation"):
+                    annotation = sanitize_html(payload.get("annotation"))
                     self.add_item_annotation(trans.sa_session, trans.get_user(), data, annotation)
                 # if setting metadata previously failed and all required elements have now been set, clear the failed state.
                 if data._state == trans.model.Dataset.states.FAILED_METADATA and not data.missing_meta():
                     data._state = None
-                message = f'Attributes updated. {message}' if message else 'Attributes updated.'
+                message = f"Attributes updated. {message}" if message else "Attributes updated."
             else:
-                message = 'Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.'
-                status = 'warning'
+                message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata."
+                status = "warning"
             trans.sa_session.flush()
-        elif operation == 'datatype':
+        elif operation == "datatype":
             # The user clicked the Save button on the 'Change data type' form
-            datatype = payload.get('datatype')
-            self.hda_deserializer.deserialize(data, {'datatype': datatype}, trans=trans)
-            message = f'Changed the type to {datatype}.'
-        elif operation == 'datatype_detect':
+            datatype = payload.get("datatype")
+            self.hda_deserializer.deserialize(data, {"datatype": datatype}, trans=trans)
+            message = f"Changed the type to {datatype}."
+        elif operation == "datatype_detect":
             # The user clicked the 'Detect datatype' button on the 'Change data type' form
             if data.datatype.is_datatype_change_allowed():
                 # prevent modifying datatype when dataset is queued or running as input/output
                 if not data.ok_to_edit_metadata():
-                    return self.message_exception(trans, 'This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them.')
+                    return self.message_exception(
+                        trans,
+                        "This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them.",
+                    )
                 else:
                     path = data.dataset.file_name
                     is_binary = check_binary(path)
@@ -381,24 +433,27 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                     trans.app.datatypes_registry.change_datatype(data, datatype)
                     trans.sa_session.flush()
                     job, *_ = trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
-                        trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': data},
-                        overwrite=False)  # overwrite is False as per existing behavior
+                        trans.app.datatypes_registry.set_external_metadata_tool,
+                        trans,
+                        incoming={"input1": data},
+                        overwrite=False,
+                    )  # overwrite is False as per existing behavior
                     trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)
-                    message = f'Detection was finished and changed the datatype to {datatype}.'
+                    message = f"Detection was finished and changed the datatype to {datatype}."
             else:
                 return self.message_exception(trans, f'Changing datatype "{data.extension}" is not allowed.')
-        elif operation == 'autodetect':
+        elif operation == "autodetect":
             # The user clicked the Auto-detect button on the 'Edit Attributes' form
             self.hda_manager.set_metadata(trans, data, overwrite=True)
             message = "Auto-detect operation successfully submitted."
-        elif operation == 'conversion':
-            target_type = payload.get('target_type')
+        elif operation == "conversion":
+            target_type = payload.get("target_type")
             if target_type:
                 try:
                     message = data.datatype.convert_dataset(trans, data, target_type)
                 except DatatypeConverterNotFoundException as e:
                     return self.message_exception(trans, str(e))
-        elif operation == 'permission':
+        elif operation == "permission":
             # Adapt form request to API - style.
             payload_permissions = {}
             for key, value in {"DATASET_MANAGE_PERMISSIONS": "manage_ids", "DATASET_ACCESS": "access_ids"}.items():
@@ -408,13 +463,13 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             self.hda_manager.update_permissions(
                 trans,
                 data,
-                action='set_permissions',
+                action="set_permissions",
                 **payload_permissions,
             )
-            message = 'Your changes completed successfully.'
+            message = "Your changes completed successfully."
         else:
-            return self.message_exception(trans, f'Invalid operation identifier ({operation}).')
-        return {'status': status, 'message': sanitize_text(message)}
+            return self.message_exception(trans, f"Invalid operation identifier ({operation}).")
+        return {"status": status, "message": sanitize_text(message)}
 
     def _get_dataset_for_edit(self, trans, dataset_id):
         if dataset_id is not None:
@@ -422,25 +477,29 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
         else:
             trans.log_event("dataset_id is None, cannot load a dataset to edit.")
-            return None, self.message_exception(trans, 'You must provide a dataset id to edit attributes.')
+            return None, self.message_exception(trans, "You must provide a dataset id to edit attributes.")
         if data is None:
             trans.log_event(f"Problem retrieving dataset id ({dataset_id}).")
-            return None, self.message_exception(trans, 'The dataset id is invalid.')
+            return None, self.message_exception(trans, "The dataset id is invalid.")
         if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:
             trans.log_event(f"User attempted to edit a dataset they do not own (encoded: {dataset_id}, decoded: {id}).")
-            return None, self.message_exception(trans, 'The dataset id is invalid.')
+            return None, self.message_exception(trans, "The dataset id is invalid.")
         if data.history.user and not data.dataset.has_manage_permissions_roles(trans.app.security_agent):
             # Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
             # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
             # permission.  In this case, we'll reset this permission to the hda user's private role.
-            manage_permissions_action = trans.app.security_agent.get_action(trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action)
-            permissions = {manage_permissions_action: [trans.app.security_agent.get_private_user_role(data.history.user)]}
+            manage_permissions_action = trans.app.security_agent.get_action(
+                trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action
+            )
+            permissions = {
+                manage_permissions_action: [trans.app.security_agent.get_private_user_role(data.history.user)]
+            }
             trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
         return data, None
 
     @web.expose
     def imp(self, trans, dataset_id=None, **kwd):
-        """ Import another user's dataset via a shared URL; dataset is added to user's current history. """
+        """Import another user's dataset via a shared URL; dataset is added to user's current history."""
         # Set referer message.
         referer = trans.request.referer
         if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"):
@@ -449,27 +508,39 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             referer_message = f"<a href='{url_for('/')}'>go to Galaxy's start page</a>"
         # Error checking.
         if not dataset_id:
-            return trans.show_error_message(f"You must specify a dataset to import. You can {referer_message}.", use_panels=True)
+            return trans.show_error_message(
+                f"You must specify a dataset to import. You can {referer_message}.", use_panels=True
+            )
         # Do import.
         cur_history = trans.get_history(create=True)
         status, message = self._copy_datasets(trans, [dataset_id], [cur_history], imported=True)
-        message = f"Dataset imported. <br>You can <a href='{url_for('/')}'>start using the dataset</a> or {referer_message}."
+        message = (
+            f"Dataset imported. <br>You can <a href='{url_for('/')}'>start using the dataset</a> or {referer_message}."
+        )
         return trans.show_message(message, type=status, use_panels=True)
 
     @web.expose
     @web.json
     @web.require_login("use Galaxy datasets")
     def get_name_and_link_async(self, trans, id=None):
-        """ Returns dataset's name and link. """
+        """Returns dataset's name and link."""
         decoded_id = self.decode_id(id)
         dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
         dataset = self.hda_manager.error_if_uploading(dataset)
-        return_dict = {"name": dataset.name, "link": url_for(controller='dataset', action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id(dataset.id))}
+        return_dict = {
+            "name": dataset.name,
+            "link": url_for(
+                controller="dataset",
+                action="display_by_username_and_slug",
+                username=dataset.history.user.username,
+                slug=trans.security.encode_id(dataset.id),
+            ),
+        }
         return return_dict
 
     @web.expose
     def get_embed_html_async(self, trans, id):
-        """ Returns HTML for embedding a dataset in a page. """
+        """Returns HTML for embedding a dataset in a page."""
         decoded_id = self.decode_id(id)
         dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
         dataset = self.hda_manager.error_if_uploading(dataset)
@@ -479,14 +550,14 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     @web.expose
     @web.require_login("use Galaxy datasets")
     def set_accessible_async(self, trans, id=None, accessible=False):
-        """ Does nothing because datasets do not have an importable/accessible attribute. This method could potentially set another attribute. """
+        """Does nothing because datasets do not have an importable/accessible attribute. This method could potentially set another attribute."""
         return
 
     @web.expose
     @web.require_login("rate items")
     @web.json
     def rate_async(self, trans, id, rating):
-        """ Rate a dataset asynchronously and return updated community data. """
+        """Rate a dataset asynchronously and return updated community data."""
 
         decoded_id = self.decode_id(id)
         dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
@@ -501,7 +572,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True):
-        """ Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id. """
+        """Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id."""
         id = slug
         decoded_id = self.decode_id(id)
         dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
@@ -521,9 +592,13 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
             # If data is binary or an image, stream without template; otherwise, use display template.
             # TODO: figure out a way to display images in display template.
-            if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.text.Html):
+            if (
+                isinstance(dataset.datatype, datatypes.binary.Binary)
+                or isinstance(dataset.datatype, datatypes.images.Image)
+                or isinstance(dataset.datatype, datatypes.text.Html)
+            ):
                 trans.response.set_content_type(dataset.get_mime())
-                return open(dataset.file_name, 'rb')
+                return open(dataset.file_name, "rb")
             else:
                 # Get rating data.
                 user_item_rating = 0
@@ -535,16 +610,22 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                         user_item_rating = 0
                 ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, dataset)
 
-                return trans.fill_template_mako("/dataset/display.mako", item=dataset, item_data=dataset_data,
-                                                truncated=truncated, user_item_rating=user_item_rating,
-                                                ave_item_rating=ave_item_rating, num_ratings=num_ratings,
-                                                first_chunk=first_chunk)
+                return trans.fill_template_mako(
+                    "/dataset/display.mako",
+                    item=dataset,
+                    item_data=dataset_data,
+                    truncated=truncated,
+                    user_item_rating=user_item_rating,
+                    ave_item_rating=ave_item_rating,
+                    num_ratings=num_ratings,
+                    first_chunk=first_chunk,
+                )
         else:
             raise web.httpexceptions.HTTPNotFound()
 
     @web.expose
     def get_item_content_async(self, trans, id):
-        """ Returns item content in HTML format. """
+        """Returns item content in HTML format."""
 
         decoded_id = self.decode_id(id)
         dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
@@ -554,7 +635,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         truncated, dataset_data = self.hda_manager.text_data(dataset, preview=True)
         # Get annotation.
         dataset.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, dataset)
-        return trans.fill_template_mako("/dataset/item_content.mako", item=dataset, item_data=dataset_data, truncated=truncated)
+        return trans.fill_template_mako(
+            "/dataset/item_content.mako", item=dataset, item_data=dataset_data, truncated=truncated
+        )
 
     @web.expose
     def annotate_async(self, trans, id, new_annotation=None, **kwargs):
@@ -580,48 +663,69 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             web.httpexceptions.HTTPNotFound()
         annotation = self.get_item_annotation_str(trans.sa_session, trans.user, dataset)
         if annotation and isinstance(annotation, str):
-            annotation = annotation.encode('ascii', 'replace')  # paste needs ascii here
+            annotation = annotation.encode("ascii", "replace")  # paste needs ascii here
         return annotation
 
     @web.expose
     def display_at(self, trans, dataset_id, filename=None, **kwd):
         """Sets up a dataset permissions so it is viewable at an external site"""
         if not trans.app.config.enable_old_display_applications:
-            return trans.show_error_message("This method of accessing external display applications has been disabled by a Galaxy administrator.")
+            return trans.show_error_message(
+                "This method of accessing external display applications has been disabled by a Galaxy administrator."
+            )
         site = filename
         data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dataset_id)
         if not data:
-            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(f"Invalid reference dataset id: {str(dataset_id)}.")
-        if 'display_url' not in kwd or 'redirect_url' not in kwd:
-            return trans.show_error_message('Invalid parameters specified for "display at" link, please contact a Galaxy administrator')
+            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(
+                f"Invalid reference dataset id: {str(dataset_id)}."
+            )
+        if "display_url" not in kwd or "redirect_url" not in kwd:
+            return trans.show_error_message(
+                'Invalid parameters specified for "display at" link, please contact a Galaxy administrator'
+            )
         try:
-            redirect_url = kwd['redirect_url'] % quote_plus(kwd['display_url'])
+            redirect_url = kwd["redirect_url"] % quote_plus(kwd["display_url"])
         except Exception:
-            redirect_url = kwd['redirect_url']  # not all will need custom text
+            redirect_url = kwd["redirect_url"]  # not all will need custom text
         if trans.app.security_agent.dataset_is_public(data.dataset):
             return trans.response.send_redirect(redirect_url)  # anon access already permitted by rbac
         if self._can_access_dataset(trans, data):
             trans.app.host_security_agent.set_dataset_permissions(data, trans.user, site)
             return trans.response.send_redirect(redirect_url)
         else:
-            return trans.show_error_message("You are not allowed to view this dataset at external sites.  Please contact your Galaxy administrator to acquire management permissions for this dataset.")
+            return trans.show_error_message(
+                "You are not allowed to view this dataset at external sites.  Please contact your Galaxy administrator to acquire management permissions for this dataset."
+            )
 
     @web.expose
     @web.do_not_cache
-    def display_application(self, trans, dataset_id=None, user_id=None, app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None, **kwds):
+    def display_application(
+        self,
+        trans,
+        dataset_id=None,
+        user_id=None,
+        app_name=None,
+        link_name=None,
+        app_action=None,
+        action_param=None,
+        action_param_extra=None,
+        **kwds,
+    ):
         """Access to external display applications"""
         # Build list of parameters to pass in to display application logic (app_kwds)
         app_kwds = {}
         for name, value in dict(kwds).items():  # clone kwds because we remove stuff as we go.
             if name.startswith("app_"):
-                app_kwds[name[len("app_"):]] = value
+                app_kwds[name[len("app_") :]] = value
                 del kwds[name]
         if kwds:
             log.debug(f"Unexpected Keywords passed to display_application: {kwds}")  # route memory?
         # decode ids
         data, user = decode_dataset_user(trans, dataset_id, user_id)
         if not data:
-            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(f"Invalid reference dataset id: {str(dataset_id)}.")
+            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(
+                f"Invalid reference dataset id: {str(dataset_id)}."
+            )
         if user is None:
             user = trans.user
         if user:
@@ -640,7 +744,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             display_app = trans.app.datatypes_registry.display_applications.get(app_name)
             if not display_app:
                 log.debug("Unknown display application has been requested: %s", app_name)
-                return paste.httpexceptions.HTTPNotFound(f"The requested display application ({app_name}) is not available.")
+                return paste.httpexceptions.HTTPNotFound(
+                    f"The requested display application ({app_name}) is not available."
+                )
             dataset_hash, user_hash = encode_dataset_user(trans, data, user)
             try:
                 display_link = display_app.get_link(link_name, data, dataset_hash, user_hash, trans, app_kwds)
@@ -652,16 +758,28 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 log.debug("Unknown display link has been requested: %s", link_name)
                 return paste.httpexceptions.HTTPNotFound(f"Unknown display link has been requested: {link_name}")
             if data.state == data.states.ERROR:
-                msg.append(('This dataset is in an error state, you cannot view it at an external display application.', 'error'))
+                msg.append(
+                    (
+                        "This dataset is in an error state, you cannot view it at an external display application.",
+                        "error",
+                    )
+                )
             elif data.deleted:
-                msg.append(('This dataset has been deleted, you cannot view it at an external display application.', 'error'))
+                msg.append(
+                    ("This dataset has been deleted, you cannot view it at an external display application.", "error")
+                )
             elif data.state != data.states.OK:
-                msg.append(('You must wait for this dataset to be created before you can view it at an external display application.', 'info'))
+                msg.append(
+                    (
+                        "You must wait for this dataset to be created before you can view it at an external display application.",
+                        "info",
+                    )
+                )
                 refresh = True
             else:
                 # We have permissions, dataset is not deleted and is in OK state, allow access
                 if display_link.display_ready():
-                    if app_action in ['data', 'param']:
+                    if app_action in ["data", "param"]:
                         assert action_param, "An action param must be provided for a data or param action"
                         # data is used for things with filenames that could be passed off to a proxy
                         # in case some display app wants all files to be in the same 'directory',
@@ -675,15 +793,17 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                         value = display_link.get_param_value(action_param)
                         assert value, f"An invalid parameter name was provided: {action_param}"
                         assert value.parameter.viewable, "This parameter is not viewable."
-                        if value.parameter.type == 'data':
+                        if value.parameter.type == "data":
                             try:
                                 if action_param_extra:
-                                    assert value.parameter.allow_extra_files_access, f"Extra file content requested ({action_param_extra}), but allow_extra_files_access is False."
+                                    assert (
+                                        value.parameter.allow_extra_files_access
+                                    ), f"Extra file content requested ({action_param_extra}), but allow_extra_files_access is False."
                                     file_name = os.path.join(value.extra_files_path, action_param_extra)
                                 else:
                                     file_name = value.file_name
                                 content_length = os.path.getsize(file_name)
-                                rval = open(file_name, 'rb')
+                                rval = open(file_name, "rb")
                             except OSError as e:
                                 log.debug("Unable to access requested file in display application: %s", e)
                                 return paste.httpexceptions.HTTPNotFound("This file is no longer available.")
@@ -695,41 +815,55 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                             trans.set_cors_origin()
                             trans.set_cors_allow()
                         trans.response.set_content_type(value.mime_type(action_param_extra=action_param_extra))
-                        trans.response.headers['Content-Length'] = str(content_length)
+                        trans.response.headers["Content-Length"] = str(content_length)
                         return rval
                     elif app_action is None:
                         # redirect user to url generated by display link
                         return trans.response.send_redirect(display_link.display_url())
                     else:
-                        msg.append((f'Invalid action provided: {app_action}', 'error'))
+                        msg.append((f"Invalid action provided: {app_action}", "error"))
                 else:
                     if app_action is None:
                         if trans.history != data.history:
-                            msg.append(('You must import this dataset into your current history before you can view it at the desired display application.', 'error'))
+                            msg.append(
+                                (
+                                    "You must import this dataset into your current history before you can view it at the desired display application.",
+                                    "error",
+                                )
+                            )
                         else:
                             refresh = True
-                            msg.append(('Launching this display application required additional datasets to be generated, you can view the status of these jobs below. ', 'info'))
+                            msg.append(
+                                (
+                                    "Launching this display application required additional datasets to be generated, you can view the status of these jobs below. ",
+                                    "info",
+                                )
+                            )
                             if not display_link.preparing_display():
                                 display_link.prepare_display()
                             preparable_steps = display_link.get_prepare_steps()
                     else:
-                        raise Exception(f'Attempted a view action ({app_action}) on a non-ready display application')
-            return trans.fill_template_mako("dataset/display_application/display.mako",
-                                            msg=msg,
-                                            display_app=display_app,
-                                            display_link=display_link,
-                                            refresh=refresh,
-                                            preparable_steps=preparable_steps)
-        return trans.show_error_message('You do not have permission to view this dataset at an external display application.')
+                        raise Exception(f"Attempted a view action ({app_action}) on a non-ready display application")
+            return trans.fill_template_mako(
+                "dataset/display_application/display.mako",
+                msg=msg,
+                display_app=display_app,
+                display_link=display_link,
+                refresh=refresh,
+                preparable_steps=preparable_steps,
+            )
+        return trans.show_error_message(
+            "You do not have permission to view this dataset at an external display application."
+        )
 
     def _delete(self, trans, dataset_id):
         message = None
-        status = 'done'
+        status = "done"
         id = None
         try:
             id = self.decode_id(dataset_id)
             hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
-            assert hda, f'Invalid HDA: {id}'
+            assert hda, f"Invalid HDA: {id}"
             # Walk up parent datasets to find the containing history
             topmost_parent = hda
             while topmost_parent.parent:
@@ -742,22 +876,22 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             self.hda_manager.stop_creating_job(hda)
             trans.sa_session.flush()
         except Exception:
-            msg = f'HDA deletion failed (encoded: {dataset_id}, decoded: {id})'
+            msg = f"HDA deletion failed (encoded: {dataset_id}, decoded: {id})"
             log.exception(msg)
             trans.log_event(msg)
-            message = 'Dataset deletion failed'
-            status = 'error'
+            message = "Dataset deletion failed"
+            status = "error"
         return (message, status)
 
     def _undelete(self, trans, dataset_id):
         message = None
-        status = 'done'
+        status = "done"
         id = None
         try:
             id = self.decode_id(dataset_id)
             history = trans.get_history()
             hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
-            assert hda and hda.undeletable, f'Invalid HDA: {id}'
+            assert hda and hda.undeletable, f"Invalid HDA: {id}"
             # Walk up parent datasets to find the containing history
             topmost_parent = hda
             while topmost_parent.parent:
@@ -768,11 +902,11 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             trans.sa_session.flush()
             trans.log_event(f"Dataset id {str(id)} has been undeleted")
         except Exception:
-            msg = f'HDA undeletion failed (encoded: {dataset_id}, decoded: {id})'
+            msg = f"HDA undeletion failed (encoded: {dataset_id}, decoded: {id})"
             log.exception(msg)
             trans.log_event(msg)
-            message = 'Dataset undeletion failed'
-            status = 'error'
+            message = "Dataset undeletion failed"
+            status = "error"
         return (message, status)
 
     def _unhide(self, trans, dataset_id):
@@ -797,21 +931,21 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
     def _purge(self, trans, dataset_id):
         message = None
-        status = 'done'
+        status = "done"
         try:
             id = self.decode_id(dataset_id)
             user = trans.get_user()
             hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
             # Invalid HDA
-            assert hda, 'Invalid history dataset ID'
+            assert hda, "Invalid history dataset ID"
 
             # If the user is anonymous, make sure the HDA is owned by the current session.
             if not user:
                 current_history_id = trans.galaxy_session.current_history_id
-                assert hda.history.id == current_history_id, 'Data does not belong to current user'
+                assert hda.history.id == current_history_id, "Data does not belong to current user"
             # If the user is known, make sure the HDA is owned by the current user.
             else:
-                assert hda.history.user == user, 'Data does not belong to current user'
+                assert hda.history.user == user, "Data does not belong to current user"
 
             # Ensure HDA is deleted
             hda.deleted = True
@@ -829,28 +963,38 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             if hda.dataset.user_can_purge:
                 try:
                     hda.dataset.full_delete()
-                    trans.log_event(f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}")
+                    trans.log_event(
+                        f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}"
+                    )
                     trans.sa_session.add(hda.dataset)
                 except Exception:
-                    log.exception(f'Unable to purge dataset ({hda.dataset.id}) on purge of HDA ({hda.id}):')
+                    log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of HDA ({hda.id}):")
             trans.sa_session.flush()
         except Exception:
-            msg = f'HDA purge failed (encoded: {dataset_id}, decoded: {id})'
+            msg = f"HDA purge failed (encoded: {dataset_id}, decoded: {id})"
             log.exception(msg)
             trans.log_event(msg)
-            message = 'Dataset removal from disk failed'
-            status = 'error'
+            message = "Dataset removal from disk failed"
+            status = "error"
         return (message, status)
 
     @web.expose
     def delete(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
         message, status = self._delete(trans, dataset_id)
-        return trans.response.send_redirect(web.url_for(controller='root', action='history', show_deleted=show_deleted_on_refresh, message=message, status=status))
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="root",
+                action="history",
+                show_deleted=show_deleted_on_refresh,
+                message=message,
+                status=status,
+            )
+        )
 
     @web.expose
     def delete_async(self, trans, dataset_id, filename):
         message, status = self._delete(trans, dataset_id)
-        if status == 'done':
+        if status == "done":
             return "OK"
         else:
             raise Exception(message)
@@ -858,12 +1002,14 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     @web.expose
     def undelete(self, trans, dataset_id, filename):
         message, status = self._undelete(trans, dataset_id)
-        return trans.response.send_redirect(web.url_for(controller='root', action='history', show_deleted=True, message=message, status=status))
+        return trans.response.send_redirect(
+            web.url_for(controller="root", action="history", show_deleted=True, message=message, status=status)
+        )
 
     @web.expose
     def undelete_async(self, trans, dataset_id, filename):
         message, status = self._undelete(trans, dataset_id)
-        if status == 'done':
+        if status == "done":
             return "OK"
         else:
             raise Exception(message)
@@ -871,7 +1017,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     @web.expose
     def unhide(self, trans, dataset_id, filename):
         if self._unhide(trans, dataset_id):
-            return trans.response.send_redirect(web.url_for(controller='root', action='history', show_hidden=True))
+            return trans.response.send_redirect(web.url_for(controller="root", action="history", show_hidden=True))
         raise Exception("Error unhiding")
 
     @web.expose
@@ -880,8 +1026,16 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             message, status = self._purge(trans, dataset_id)
         else:
             message = "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator."
-            status = 'error'
-        return trans.response.send_redirect(web.url_for(controller='root', action='history', show_deleted=show_deleted_on_refresh, message=message, status=status))
+            status = "error"
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="root",
+                action="history",
+                show_deleted=show_deleted_on_refresh,
+                message=message,
+                status=status,
+            )
+        )
 
     @web.expose
     def purge_async(self, trans, dataset_id, filename):
@@ -889,18 +1043,30 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             message, status = self._purge(trans, dataset_id)
         else:
             message = "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator."
-            status = 'error'
-        if status == 'done':
+            status = "error"
+        if status == "done":
             return "OK"
         else:
             raise Exception(message)
 
     @web.expose
-    def copy_datasets(self, trans, source_history=None, source_content_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd):
+    def copy_datasets(
+        self,
+        trans,
+        source_history=None,
+        source_content_ids="",
+        target_history_id=None,
+        target_history_ids="",
+        new_history_name="",
+        do_copy=False,
+        **kwd,
+    ):
         user = trans.get_user()
         if source_history is not None:
             decoded_source_history_id = self.decode_id(source_history)
-            history = self.history_manager.get_owned(decoded_source_history_id, trans.user, current_history=trans.history)
+            history = self.history_manager.get_owned(
+                decoded_source_history_id, trans.user, current_history=trans.history
+            )
             current_history = trans.get_history()
         else:
             history = current_history = trans.get_history()
@@ -908,8 +1074,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         if source_content_ids:
             if not isinstance(source_content_ids, list):
                 source_content_ids = source_content_ids.split(",")
-            encoded_dataset_collection_ids = [s[len("dataset_collection|"):] for s in source_content_ids if s.startswith("dataset_collection|")]
-            encoded_dataset_ids = [s[len("dataset|"):] for s in source_content_ids if s.startswith("dataset|")]
+            encoded_dataset_collection_ids = [
+                s[len("dataset_collection|") :] for s in source_content_ids if s.startswith("dataset_collection|")
+            ]
+            encoded_dataset_ids = [s[len("dataset|") :] for s in source_content_ids if s.startswith("dataset|")]
             decoded_dataset_collection_ids = set(map(self.decode_id, encoded_dataset_collection_ids))
             decoded_dataset_ids = set(map(self.decode_id, encoded_dataset_ids))
         else:
@@ -930,7 +1098,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         new_history = None
         if do_copy:
             invalid_contents = 0
-            if not (decoded_dataset_ids or decoded_dataset_collection_ids) or not (target_history_ids or new_history_name):
+            if not (decoded_dataset_ids or decoded_dataset_collection_ids) or not (
+                target_history_ids or new_history_name
+            ):
                 error_msg = "You must provide both source datasets and target histories. "
             else:
                 if new_history_name:
@@ -941,13 +1111,28 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                     trans.sa_session.flush()
                     target_history_ids.append(new_history.id)
                 if user:
-                    target_histories = [hist for hist in map(trans.sa_session.query(trans.app.model.History).get, target_history_ids) if hist is not None and hist.user == user]
+                    target_histories = [
+                        hist
+                        for hist in map(trans.sa_session.query(trans.app.model.History).get, target_history_ids)
+                        if hist is not None and hist.user == user
+                    ]
                 else:
                     target_histories = [history]
                 if len(target_histories) != len(target_history_ids):
-                    error_msg = error_msg + "You do not have permission to add datasets to %i requested histories.  " % (len(target_history_ids) - len(target_histories))
-                source_contents = list(map(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get, decoded_dataset_ids))
-                source_contents.extend(map(trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get, decoded_dataset_collection_ids))
+                    error_msg = (
+                        error_msg
+                        + "You do not have permission to add datasets to %i requested histories.  "
+                        % (len(target_history_ids) - len(target_histories))
+                    )
+                source_contents = list(
+                    map(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get, decoded_dataset_ids)
+                )
+                source_contents.extend(
+                    map(
+                        trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get,
+                        decoded_dataset_collection_ids,
+                    )
+                )
                 source_contents.sort(key=lambda content: content.hid)
                 for content in source_contents:
                     if content is None:
@@ -969,34 +1154,48 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                             hist.add_pending_items()
                 trans.sa_session.flush()
                 if current_history in target_histories:
-                    refresh_frames = ['history']
-                hist_names_str = ", ".join('<a href="%s" target="_top">%s</a>' %
-                                           (url_for(controller="history", action="switch_to_history",
-                                                    hist_id=trans.security.encode_id(hist.id)), escape(hist.name))
-                                           for hist in target_histories)
+                    refresh_frames = ["history"]
+                hist_names_str = ", ".join(
+                    '<a href="%s" target="_top">%s</a>'
+                    % (
+                        url_for(
+                            controller="history", action="switch_to_history", hist_id=trans.security.encode_id(hist.id)
+                        ),
+                        escape(hist.name),
+                    )
+                    for hist in target_histories
+                )
                 num_source = len(source_content_ids) - invalid_contents
                 num_target = len(target_histories)
-                done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str)
+                done_msg = "%i %s copied to %i %s: %s." % (
+                    num_source,
+                    inflector.cond_plural(num_source, "dataset"),
+                    num_target,
+                    inflector.cond_plural(num_target, "history"),
+                    hist_names_str,
+                )
                 trans.sa_session.refresh(history)
         source_contents = history.active_contents
         target_histories = [history]
         if user:
             target_histories = user.active_histories
-        return trans.fill_template("/dataset/copy_view.mako",
-                                   source_history=history,
-                                   current_history=current_history,
-                                   source_content_ids=source_content_ids,
-                                   target_history_id=target_history_id,
-                                   target_history_ids=target_history_ids,
-                                   source_contents=source_contents,
-                                   target_histories=target_histories,
-                                   new_history_name=new_history_name,
-                                   done_msg=done_msg,
-                                   error_msg=error_msg,
-                                   refresh_frames=refresh_frames)
+        return trans.fill_template(
+            "/dataset/copy_view.mako",
+            source_history=history,
+            current_history=current_history,
+            source_content_ids=source_content_ids,
+            target_history_id=target_history_id,
+            target_history_ids=target_history_ids,
+            source_contents=source_contents,
+            target_histories=target_histories,
+            new_history_name=new_history_name,
+            done_msg=done_msg,
+            error_msg=error_msg,
+            refresh_frames=refresh_frames,
+        )
 
     def _copy_datasets(self, trans, dataset_ids, target_histories, imported=False):
-        """ Helper method for copying datasets. """
+        """Helper method for copying datasets."""
         user = trans.get_user()
         done_msg = error_msg = ""
 
@@ -1007,7 +1206,11 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             # User must own target histories to copy datasets to them.
             for history in target_histories:
                 if user != history.user:
-                    error_msg = error_msg + "You do not have permission to add datasets to %i requested histories.  " % (len(target_histories))
+                    error_msg = (
+                        error_msg
+                        + "You do not have permission to add datasets to %i requested histories.  "
+                        % (len(target_histories))
+                    )
             for dataset_id in dataset_ids:
                 decoded_id = self.decode_id(dataset_id)
                 data = self.hda_manager.get_accessible(decoded_id, trans.user)
@@ -1024,8 +1227,12 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                         hist.add_dataset(dataset_copy)
             trans.sa_session.flush()
             num_datasets_copied = len(dataset_ids) - invalid_datasets
-            done_msg = "%i dataset%s copied to %i histor%s." % \
-                (num_datasets_copied, iff(num_datasets_copied == 1, "", "s"), len(target_histories), iff(len(target_histories) == 1, "y", "ies"))
+            done_msg = "%i dataset%s copied to %i histor%s." % (
+                num_datasets_copied,
+                iff(num_datasets_copied == 1, "", "s"),
+                len(target_histories),
+                iff(len(target_histories) == 1, "y", "ies"),
+            )
             trans.sa_session.refresh(history)
 
         if error_msg != "":
diff --git a/lib/galaxy/webapps/galaxy/controllers/error.py b/lib/galaxy/webapps/galaxy/controllers/error.py
index ea8190898bb..a322c6bfd44 100644
--- a/lib/galaxy/webapps/galaxy/controllers/error.py
+++ b/lib/galaxy/webapps/galaxy/controllers/error.py
@@ -1,4 +1,7 @@
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 
 
 class Error(BaseUIController):
diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py
index fe9bda6d77c..0d7877bea72 100644
--- a/lib/galaxy/webapps/galaxy/controllers/forms.py
+++ b/lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -4,9 +4,19 @@ import re
 
 from markupsafe import escape
 
-from galaxy import model, util
-from galaxy.web.framework.helpers import grids, iff, time_ago
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy import (
+    model,
+    util,
+)
+from galaxy.web.framework.helpers import (
+    grids,
+    iff,
+    time_ago,
+)
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 
 log = logging.getLogger(__name__)
 
@@ -41,39 +51,39 @@ class FormsGrid(grids.Grid):
     use_paging = True
     default_filter = dict(deleted="False")
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   model_class=model.FormDefinition,
-                   link=(lambda item: iff(item.deleted, None, dict(controller="admin", action="form/edit_form", id=item.id))),
-                   attach_popup=True,
-                   filterable="advanced"),
-        DescriptionColumn("Description",
-                          key="desc",
-                          model_class=model.FormDefinition,
-                          filterable="advanced"),
+        NameColumn(
+            "Name",
+            key="name",
+            model_class=model.FormDefinition,
+            link=(lambda item: iff(item.deleted, None, dict(controller="admin", action="form/edit_form", id=item.id))),
+            attach_popup=True,
+            filterable="advanced",
+        ),
+        DescriptionColumn("Description", key="desc", model_class=model.FormDefinition, filterable="advanced"),
         TypeColumn("Type"),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
         StatusColumn("Status"),
-        grids.DeletedColumn("Deleted",
-                            key="deleted",
-                            visible=False,
-                            filterable="advanced")
+        grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
     operations = [
         grids.GridOperation("Delete", allow_multiple=True, condition=(lambda item: not item.deleted)),
         grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
     ]
-    global_actions = [
-        grids.GridAction("Create new form", dict(controller="admin", action="form/create_form"))
-    ]
+    global_actions = [grids.GridAction("Create new form", dict(controller="admin", action="form/create_form"))]
 
     def build_initial_query(self, trans, **kwargs):
-        return trans.sa_session.query(self.model_class).join(model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id)
+        return trans.sa_session.query(self.model_class).join(
+            model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id
+        )
 
 
 class Forms(BaseUIController):
@@ -82,147 +92,133 @@ class Forms(BaseUIController):
     @web.legacy_expose_api
     @web.require_admin
     def forms_list(self, trans, payload=None, **kwd):
-        message = kwd.get('message', '')
-        status = kwd.get('status', '')
-        if 'operation' in kwd:
-            id = kwd.get('id')
+        message = kwd.get("message", "")
+        status = kwd.get("status", "")
+        if "operation" in kwd:
+            id = kwd.get("id")
             if not id:
-                return self.message_exception(trans, f'Invalid form id ({str(id)}) received.')
+                return self.message_exception(trans, f"Invalid form id ({str(id)}) received.")
             ids = util.listify(id)
-            operation = kwd['operation'].lower()
-            if operation == 'delete':
+            operation = kwd["operation"].lower()
+            if operation == "delete":
                 message, status = self._delete_form(trans, ids)
-            elif operation == 'undelete':
+            elif operation == "undelete":
                 message, status = self._undelete_form(trans, ids)
         if message and status:
-            kwd['message'] = util.sanitize_text(message)
-            kwd['status'] = status
+            kwd["message"] = util.sanitize_text(message)
+            kwd["status"] = status
         return self.forms_grid(trans, **kwd)
 
     @web.legacy_expose_api
     @web.require_admin
     def create_form(self, trans, payload=None, **kwd):
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             fd_types = sorted(trans.app.model.FormDefinition.types.__members__.items())
             return {
-                'title': 'Create new form',
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name'
-                }, {
-                    'name': 'desc',
-                    'label': 'Description'
-                }, {
-                    'name': 'type',
-                    'type': 'select',
-                    'options': [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
-                    'label': 'Type'
-                }, {
-                    'name': 'csv_file',
-                    'label': 'Import from CSV',
-                    'type': 'upload',
-                    'help': 'Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.'
-                }]
+                "title": "Create new form",
+                "inputs": [
+                    {"name": "name", "label": "Name"},
+                    {"name": "desc", "label": "Description"},
+                    {
+                        "name": "type",
+                        "type": "select",
+                        "options": [("None", "none")] + [(ft[1], ft[1]) for ft in fd_types],
+                        "label": "Type",
+                    },
+                    {
+                        "name": "csv_file",
+                        "label": "Import from CSV",
+                        "type": "upload",
+                        "help": "Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.",
+                    },
+                ],
             }
         else:
             # csv-file format: label, helptext, type, default, selectlist, required '''
-            csv_file = payload.get('csv_file')
+            csv_file = payload.get("csv_file")
             index = 0
             if csv_file:
                 lines = csv_file.splitlines()
                 for line in lines:
-                    row = line.split(',')
+                    row = line.split(",")
                     if len(row) >= 6:
-                        prefix = 'fields_%i|' % index
-                        payload[f"{prefix}name"] = '%i_imported_field' % (index + 1)
+                        prefix = "fields_%i|" % index
+                        payload[f"{prefix}name"] = "%i_imported_field" % (index + 1)
                         payload[f"{prefix}label"] = row[0]
                         payload[f"{prefix}helptext"] = row[1]
                         payload[f"{prefix}type"] = row[2]
                         payload[f"{prefix}default"] = row[3]
-                        payload[f"{prefix}selectlist"] = row[4].split(',')
-                        payload[f"{prefix}required"] = row[5].lower() == 'true'
+                        payload[f"{prefix}selectlist"] = row[4].split(",")
+                        payload[f"{prefix}required"] = row[5].lower() == "true"
                     index = index + 1
             new_form, message = self.save_form_definition(trans, None, payload)
             if new_form is None:
                 return self.message_exception(trans, message)
-            imported = (' with %i imported fields' % index) if index > 0 else ''
+            imported = (" with %i imported fields" % index) if index > 0 else ""
             message = f"The form '{payload.get('name')}' has been created{imported}."
-            return {'message': util.sanitize_text(message)}
+            return {"message": util.sanitize_text(message)}
 
     @web.legacy_expose_api
     @web.require_admin
     def edit_form(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No form id received for editing.')
+            return self.message_exception(trans, "No form id received for editing.")
         form = get_form(trans, id)
         latest_form = form.latest_form
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             fd_types = sorted(trans.app.model.FormDefinition.types.__members__.items())
-            ff_types = [(t.__name__.replace('Field', ''), t.__name__) for t in trans.model.FormDefinition.supported_field_types]
+            ff_types = [
+                (t.__name__.replace("Field", ""), t.__name__) for t in trans.model.FormDefinition.supported_field_types
+            ]
             field_cache = []
-            field_inputs = [{
-                'name': 'name',
-                'label': 'Name',
-                'value': 'field_name',
-                'help': 'The field name must be unique for each field and must contain only alphanumeric characters and underscore.'
-            }, {
-                'name': 'label',
-                'label': 'Label',
-                'value': 'Field label'
-            }, {
-                'name': 'helptext',
-                'label': 'Help text'
-            }, {
-                'name': 'type',
-                'label': 'Type',
-                'type': 'select',
-                'options': ff_types
-            }, {
-                'name': 'default',
-                'label': 'Default value'
-            }, {
-                'name': 'selectlist',
-                'label': 'Options',
-                'help': '*Only for fields which allow multiple selections, provide comma-separated values.'
-            }, {
-                'name': 'required',
-                'label': 'Required',
-                'type': 'boolean',
-                'value': 'false'
-            }]
+            field_inputs = [
+                {
+                    "name": "name",
+                    "label": "Name",
+                    "value": "field_name",
+                    "help": "The field name must be unique for each field and must contain only alphanumeric characters and underscore.",
+                },
+                {"name": "label", "label": "Label", "value": "Field label"},
+                {"name": "helptext", "label": "Help text"},
+                {"name": "type", "label": "Type", "type": "select", "options": ff_types},
+                {"name": "default", "label": "Default value"},
+                {
+                    "name": "selectlist",
+                    "label": "Options",
+                    "help": "*Only for fields which allow multiple selections, provide comma-separated values.",
+                },
+                {"name": "required", "label": "Required", "type": "boolean", "value": "false"},
+            ]
             form_dict = {
-                'title': 'Edit form for \'%s\'' % (util.sanitize_text(latest_form.name)),
-                'inputs': [{
-                    'name': 'name',
-                    'label': 'Name',
-                    'value': latest_form.name
-                }, {
-                    'name': 'desc',
-                    'label': 'Description',
-                    'value': latest_form.desc
-                }, {
-                    'name': 'type',
-                    'type': 'select',
-                    'options': [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
-                    'label': 'Type',
-                    'value': latest_form.type
-                }, {
-                    'name': 'fields',
-                    'title': 'Field',
-                    'type': 'repeat',
-                    'cache': field_cache,
-                    'inputs': field_inputs
-                }]
+                "title": "Edit form for '%s'" % (util.sanitize_text(latest_form.name)),
+                "inputs": [
+                    {"name": "name", "label": "Name", "value": latest_form.name},
+                    {"name": "desc", "label": "Description", "value": latest_form.desc},
+                    {
+                        "name": "type",
+                        "type": "select",
+                        "options": [("None", "none")] + [(ft[1], ft[1]) for ft in fd_types],
+                        "label": "Type",
+                        "value": latest_form.type,
+                    },
+                    {
+                        "name": "fields",
+                        "title": "Field",
+                        "type": "repeat",
+                        "cache": field_cache,
+                        "inputs": field_inputs,
+                    },
+                ],
             }
             for field in latest_form.fields:
                 new_field = copy.deepcopy(field_inputs)
                 for field_input in new_field:
-                    field_value = field.get(field_input['name'])
+                    field_value = field.get(field_input["name"])
                     if field_value:
                         if isinstance(field_value, list):
-                            field_value = ','.join(field_value)
-                        field_input['value'] = str(field_value)
+                            field_value = ",".join(field_value)
+                        field_input["value"] = str(field_value)
                 field_cache.append(new_field)
             return form_dict
         else:
@@ -230,71 +226,71 @@ class Forms(BaseUIController):
             if new_form is None:
                 return self.message_exception(trans, message)
             message = f"The form '{payload.get('name')}' has been updated."
-            return {'message': util.sanitize_text(message)}
+            return {"message": util.sanitize_text(message)}
 
     def get_current_form(self, trans, payload=None, **kwd):
-        '''
+        """
         This method gets all the unsaved user-entered form details and returns a
         dictionary containing the name, desc, type, layout & fields of the form
-        '''
-        name = payload.get('name')
-        desc = payload.get('desc') or ''
-        type = payload.get('type')
+        """
+        name = payload.get("name")
+        desc = payload.get("desc") or ""
+        type = payload.get("type")
         fields = []
         index = 0
         while True:
-            prefix = 'fields_%i|' % index
+            prefix = "fields_%i|" % index
             if f"{prefix}label" in payload:
-                field_attributes = ['name', 'label', 'helptext', 'required', 'type', 'selectlist', 'default']
-                field_dict = {attr: payload.get(f'{prefix}{attr}') for attr in field_attributes}
-                field_dict['visible'] = True
-                field_dict['required'] = field_dict['required'] == 'true'
-                if isinstance(field_dict['selectlist'], str):
-                    field_dict['selectlist'] = field_dict['selectlist'].split(',')
+                field_attributes = ["name", "label", "helptext", "required", "type", "selectlist", "default"]
+                field_dict = {attr: payload.get(f"{prefix}{attr}") for attr in field_attributes}
+                field_dict["visible"] = True
+                field_dict["required"] = field_dict["required"] == "true"
+                if isinstance(field_dict["selectlist"], str):
+                    field_dict["selectlist"] = field_dict["selectlist"].split(",")
                 else:
-                    field_dict['selectlist'] = []
+                    field_dict["selectlist"] = []
                 fields.append(field_dict)
                 index = index + 1
             else:
                 break
-        return dict(name=name,
-                    desc=desc,
-                    type=type,
-                    layout=[],
-                    fields=fields)
+        return dict(name=name, desc=desc, type=type, layout=[], fields=fields)
 
     def save_form_definition(self, trans, form_id=None, payload=None, **kwd):
-        '''
+        """
         This method saves a form given an id
-        '''
-        if not payload.get('name'):
-            return None, 'Please provide a form name.'
-        if payload.get('type') == 'none':
-            return None, 'Please select a form type.'
+        """
+        if not payload.get("name"):
+            return None, "Please provide a form name."
+        if payload.get("type") == "none":
+            return None, "Please select a form type."
         current_form = self.get_current_form(trans, payload)
         # validate fields
         field_names_dict = {}
-        for field in current_form['fields']:
-            if not field['label']:
-                return None, 'All the field labels must be completed.'
-            if not VALID_FIELDNAME_RE.match(field['name']):
+        for field in current_form["fields"]:
+            if not field["label"]:
+                return None, "All the field labels must be completed."
+            if not VALID_FIELDNAME_RE.match(field["name"]):
                 return None, f"{field['name']} is not a valid field name."
-            if field['name'] in field_names_dict:
+            if field["name"] in field_names_dict:
                 return None, f"Each field name must be unique in the form definition. {field['name']} is not unique."
             else:
-                field_names_dict[field['name']] = 1
+                field_names_dict[field["name"]] = 1
         # create a new form definition
-        form_definition = trans.app.model.FormDefinition(name=current_form['name'],
-                                                         desc=current_form['desc'],
-                                                         fields=current_form['fields'],
-                                                         form_definition_current=None,
-                                                         form_type=current_form['type'],
-                                                         layout=current_form['layout'])
+        form_definition = trans.app.model.FormDefinition(
+            name=current_form["name"],
+            desc=current_form["desc"],
+            fields=current_form["fields"],
+            form_definition_current=None,
+            form_type=current_form["type"],
+            layout=current_form["layout"],
+        )
         # save changes to the existing form
         if form_id:
-            form_definition_current = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).get(trans.security.decode_id(form_id))
+            form_definition_current = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).get(
+                trans.security.decode_id(form_id)
+            )
             if form_definition_current is None:
-                return None, f'Invalid form id ({form_id}) provided. Cannot save form.'
+                return None, f"Invalid form id ({form_id}) provided. Cannot save form."
         else:
             form_definition_current = trans.app.model.FormDefinitionCurrent()
         # create corresponding row in the form_definition_current table
@@ -312,7 +308,7 @@ class Forms(BaseUIController):
             form.deleted = True
             trans.sa_session.add(form)
             trans.sa_session.flush()
-        return ('Deleted %i form(s).' % len(ids), 'done')
+        return ("Deleted %i form(s)." % len(ids), "done")
 
     @web.expose
     @web.require_admin
@@ -322,7 +318,8 @@ class Forms(BaseUIController):
             form.deleted = False
             trans.sa_session.add(form)
             trans.sa_session.flush()
-        return ('Undeleted %i form(s).' % len(ids), 'done')
+        return ("Undeleted %i form(s)." % len(ids), "done")
+
 
 # ---- Utility methods -------------------------------------------------------
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 0b964c3e33a..b6d1e77f768 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -4,22 +4,24 @@ from markupsafe import escape
 from sqlalchemy import (
     false,
     null,
-    true
+    true,
 )
 from sqlalchemy.orm import (
     eagerload,
     joinedload,
-    undefer
+    undefer,
 )
 
-from galaxy import exceptions
-from galaxy import model
-from galaxy import web
+from galaxy import (
+    exceptions,
+    model,
+    web,
+)
 from galaxy.managers import histories
 from galaxy.managers.sharable import SlugBuilder
 from galaxy.model.item_attrs import (
     UsesAnnotations,
-    UsesItemRatings
+    UsesItemRatings,
 )
 from galaxy.structured_app import StructuredApp
 from galaxy.util import (
@@ -27,16 +29,16 @@ from galaxy.util import (
     parse_int,
     sanitize_text,
     string_as_bool,
-    unicodify
+    unicodify,
 )
 from galaxy.web import (
     expose_api_anonymous,
-    url_for
+    url_for,
 )
 from galaxy.web.framework.helpers import (
     grids,
     iff,
-    time_ago
+    time_ago,
 )
 from galaxy.webapps.base.controller import (
     BaseUIController,
@@ -49,7 +51,6 @@ from galaxy.webapps.base.controller import (
 from ._create_history_template import render_item
 from ..api import depends
 
-
 log = logging.getLogger(__name__)
 
 
@@ -103,38 +104,72 @@ class HistoryListGrid(grids.Grid):
         HistoryListNameColumn("Name", key="name", attach_popup=True, filterable="advanced"),
         ItemCountColumn("Items", key="item_count", sortable=False),
         grids.GridColumn("Datasets", key="datasets_by_state", sortable=False, nowrap=True, delayed=True),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation,
-                                   filterable="advanced", grid_name="HistoryListGrid"),
-        grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False, use_shared_with_count=True),
+        grids.IndividualTagsColumn(
+            "Tags",
+            key="tags",
+            model_tag_association_class=model.HistoryTagAssociation,
+            filterable="advanced",
+            grid_name="HistoryListGrid",
+        ),
+        grids.SharingStatusColumn(
+            "Sharing", key="sharing", filterable="advanced", sortable=False, use_shared_with_count=True
+        ),
         grids.GridColumn("Size on Disk", key="disk_size", sortable=False, delayed=True),
         grids.GridColumn("Created", key="create_time", format=time_ago),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
-        DeletedColumn("Status", key="deleted", filterable="advanced")
+        DeletedColumn("Status", key="deleted", filterable="advanced"),
     ]
     columns.append(
         grids.MulticolFilterColumn(
             "search history names and tags",
             cols_to_filter=[columns[0], columns[3]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
-    global_actions = [
-        grids.GridAction("Import history", dict(controller="", action="histories/import"))
-    ]
+    global_actions = [grids.GridAction("Import history", dict(controller="", action="histories/import"))]
     operations = [
-        grids.GridOperation("Switch", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=True),
+        grids.GridOperation(
+            "Switch", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=True
+        ),
         grids.GridOperation("View", allow_multiple=False, url_args=dict(controller="", action="histories/view")),
-        grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="histories/sharing")),
-        grids.GridOperation("Change Permissions", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="histories/permissions")),
-        grids.GridOperation("Copy", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False),
-        grids.GridOperation("Rename", condition=(lambda item: not item.deleted), url_args=dict(controller="", action="histories/rename"), target="top"),
+        grids.GridOperation(
+            "Share or Publish",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            url_args=dict(controller="", action="histories/sharing"),
+        ),
+        grids.GridOperation(
+            "Change Permissions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            url_args=dict(controller="", action="histories/permissions"),
+        ),
+        grids.GridOperation(
+            "Copy", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False
+        ),
+        grids.GridOperation(
+            "Rename",
+            condition=(lambda item: not item.deleted),
+            url_args=dict(controller="", action="histories/rename"),
+            target="top",
+        ),
         grids.GridOperation("Delete", condition=(lambda item: not item.deleted), async_compatible=True),
-        grids.GridOperation("Delete Permanently", condition=(lambda item: not item.purged), confirm="History contents will be removed from disk, this cannot be undone.  Continue?", async_compatible=True),
-        grids.GridOperation("Undelete", condition=(lambda item: item.deleted and not item.purged), async_compatible=True),
+        grids.GridOperation(
+            "Delete Permanently",
+            condition=(lambda item: not item.purged),
+            confirm="History contents will be removed from disk, this cannot be undone.  Continue?",
+            async_compatible=True,
+        ),
+        grids.GridOperation(
+            "Undelete", condition=(lambda item: item.deleted and not item.purged), async_compatible=True
+        ),
     ]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All')),
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
     default_filter = dict(name="All", deleted="False", tags="All", sharing="All")
     num_rows_per_page = 15
@@ -153,8 +188,8 @@ class SharedHistoryListGrid(grids.Grid):
     # Custom column types
     class DatasetsByStateColumn(grids.GridColumn):
         def get_value(self, trans, grid, history):
-            rval = ''
-            for state in ('ok', 'running', 'queued', 'error'):
+            rval = ""
+            for state in ("ok", "running", "queued", "error"):
                 total = sum(1 for d in history.active_datasets if d.state == state)
                 if total:
                     rval += f'<div class="count-box state-color-{state}">{total}</div>'
@@ -173,16 +208,16 @@ class SharedHistoryListGrid(grids.Grid):
         DatasetsByStateColumn("Datasets", sortable=False),
         grids.GridColumn("Created", key="create_time", format=time_ago),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
-        SharedByColumn("Shared by", key="user_id")
+        SharedByColumn("Shared by", key="user_id"),
     ]
     operations = [
         grids.GridOperation("View", allow_multiple=False, url_args=dict(controller="", action="histories/view")),
         grids.GridOperation("Copy", allow_multiple=False),
-        grids.GridOperation("Unshare", allow_multiple=False)
+        grids.GridOperation("Unshare", allow_multiple=False),
     ]
 
     def build_initial_query(self, trans, **kwargs):
-        return trans.sa_session.query(self.model_class).join('users_shared_with')
+        return trans.sa_session.query(self.model_class).join("users_shared_with")
 
     def apply_query_filter(self, trans, query, **kwargs):
         return query.filter(model.HistoryUserShareAssociation.user == trans.user)
@@ -200,17 +235,31 @@ class HistoryAllPublishedGrid(grids.Grid):
     num_rows_per_page = 50
     columns = [
         NameURLColumn("Name", key="name", filterable="advanced"),
-        grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced"),
+        grids.OwnerAnnotationColumn(
+            "Annotation",
+            key="annotation",
+            model_annotation_association_class=model.HistoryAnnotationAssociation,
+            filterable="advanced",
+        ),
         grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"),
         grids.CommunityRatingColumn("Community Rating", key="rating"),
-        grids.CommunityTagsColumn("Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid"),
-        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
+        grids.CommunityTagsColumn(
+            "Community Tags",
+            key="tags",
+            model_tag_association_class=model.HistoryTagAssociation,
+            filterable="advanced",
+            grid_name="PublicHistoryListGrid",
+        ),
+        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago),
     ]
     columns.append(
         grids.MulticolFilterColumn(
             "Search name, annotation, owner, and tags",
             cols_to_filter=[columns[0], columns[1], columns[2], columns[4]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def build_initial_query(self, trans, **kwargs):
@@ -227,11 +276,19 @@ class HistoryAllPublishedGrid(grids.Grid):
         # - Eager load annotations - this causes a left join which might be inefficient if there were
         #   potentially many items per history (like if joining HDAs for instance) but there should only
         #   be at most one so this is fine.
-        return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
+        return (
+            trans.sa_session.query(self.model_class)
+            .join("user")
+            .options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
+        )
 
     def apply_query_filter(self, trans, query, **kwargs):
         # A public history is published, has a slug, and is not deleted.
-        return query.filter(self.model_class.published == true()).filter(self.model_class.slug != null()).filter(self.model_class.deleted == false())
+        return (
+            query.filter(self.model_class.published == true())
+            .filter(self.model_class.slug != null())
+            .filter(self.model_class.deleted == false())
+        )
 
 
 class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings):
@@ -250,7 +307,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     @web.expose
     def list_as_xml(self, trans):
         """XML history list for functional tests"""
-        trans.response.set_content_type('text/xml')
+        trans.response.set_content_type("text/xml")
         return trans.fill_template("/history/list_as_xml.mako")
 
     # ......................................................................... lists
@@ -268,17 +325,19 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     def list(self, trans, **kwargs):
         """List all available histories"""
         current_history = trans.get_history()
-        message = kwargs.get('message')
-        status = kwargs.get('status')
-        if 'operation' in kwargs:
-            operation = kwargs['operation'].lower()
-            history_ids = listify(kwargs.get('id', []))
+        message = kwargs.get("message")
+        status = kwargs.get("status")
+        if "operation" in kwargs:
+            operation = kwargs["operation"].lower()
+            history_ids = listify(kwargs.get("id", []))
             # Display no message by default
             status, message = None, None
             # Load the histories and ensure they all belong to the current user
             histories = []
             for history_id in history_ids:
-                history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
+                history = self.history_manager.get_owned(
+                    self.decode_id(history_id), trans.user, current_history=trans.history
+                )
                 if history:
                     # Ensure history is owned by current user
                     if history.user_id is not None and trans.user:
@@ -294,25 +353,25 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                     # to root is needed; if grid is not using panels, it is nested
                     # in the main Galaxy UI and refreshing the history frame
                     # is sufficient.
-                    use_panels = kwargs.get('use_panels', False) == 'True'
+                    use_panels = kwargs.get("use_panels", False) == "True"
                     if use_panels:
                         return trans.response.send_redirect(url_for("/"))
                     else:
-                        kwargs['refresh_frames'] = ['history']
+                        kwargs["refresh_frames"] = ["history"]
                 elif operation in ("delete", "delete permanently"):
                     status, message = self._list_delete(trans, histories, purge=(operation == "delete permanently"))
                     if current_history in histories:
                         # Deleted the current history, so a new, empty history was
                         # created automatically, and we need to refresh the history frame
-                        kwargs['refresh_frames'] = ['history']
+                        kwargs["refresh_frames"] = ["history"]
                 elif operation == "undelete":
                     status, message = self._list_undelete(trans, histories)
 
                 trans.sa_session.flush()
         # Render the list view
         if message and status:
-            kwargs['message'] = sanitize_text(message)
-            kwargs['status'] = status
+            kwargs["message"] = sanitize_text(message)
+            kwargs["status"] = status
         return self.stored_list_grid(trans, **kwargs)
 
     def _list_delete(self, trans, histories, purge=False):
@@ -397,9 +456,11 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         new_history = histories[0]
         galaxy_session = trans.get_galaxy_session()
         try:
-            association = trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation) \
-                                          .filter_by(session_id=galaxy_session.id, history_id=new_history.id) \
-                                          .first()
+            association = (
+                trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation)
+                .filter_by(session_id=galaxy_session.id, history_id=new_history.id)
+                .first()
+            )
         except Exception:
             association = None
         new_history.add_galaxy_session(galaxy_session, association=association)
@@ -415,24 +476,27 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     def list_shared(self, trans, **kwargs):
         """List histories shared with current user by others"""
         status = message = None
-        if 'operation' in kwargs:
-            ids = listify(kwargs.get('id', []))
-            operation = kwargs['operation'].lower()
-            if operation == 'unshare':
+        if "operation" in kwargs:
+            ids = listify(kwargs.get("id", []))
+            operation = kwargs["operation"].lower()
+            if operation == "unshare":
                 if not ids:
                     message = "Select a history to unshare"
-                    status = 'error'
+                    status = "error"
                 for id in ids:
                     # No need to check security, association below won't yield a
                     # hit if this user isn't having the history shared with her.
                     history = self.history_manager.by_id(self.decode_id(id))
                     # Current user is the user with which the histories were shared
-                    association = (trans.sa_session.query(trans.app.model.HistoryUserShareAssociation)
-                                   .filter_by(user=trans.user, history=history).one())
+                    association = (
+                        trans.sa_session.query(trans.app.model.HistoryUserShareAssociation)
+                        .filter_by(user=trans.user, history=history)
+                        .one()
+                    )
                     trans.sa_session.delete(association)
                     trans.sa_session.flush()
                 message = "Unshared %d shared histories" % len(ids)
-                status = 'done'
+                status = "done"
         # Render the list view
         return self.shared_list_grid(trans, status=status, message=message, **kwargs)
 
@@ -442,20 +506,20 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         Return a history in xml format.
         """
         if trans.app.config.require_login and not trans.user:
-            return trans.fill_template('/no_access.mako', message='Please log in to access Galaxy histories.')
+            return trans.fill_template("/no_access.mako", message="Please log in to access Galaxy histories.")
 
         if id:
-            history = self.history_manager.get_accessible(self.decode_id(id), trans.user,
-                current_history=trans.history)
+            history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history)
         else:
             history = trans.get_history(most_recent=True, create=True)
 
-        trans.response.set_content_type('text/xml')
+        trans.response.set_content_type("text/xml")
         return trans.fill_template_mako(
             "history/as_xml.mako",
             history=history,
             show_deleted=string_as_bool(show_deleted),
-            show_hidden=string_as_bool(show_hidden))
+            show_hidden=string_as_bool(show_hidden),
+        )
 
     @web.expose
     @web.json
@@ -472,12 +536,26 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         # Expunge history from the session to allow us to force a reload
         # with a bunch of eager loaded joins
         trans.sa_session.expunge(trans.history)
-        history = trans.sa_session.query(model.History).options(
-            joinedload('active_datasets').joinedload('creating_job_associations').joinedload('job').joinedload('workflow_invocation_step').joinedload('workflow_invocation').joinedload('workflow'),
-        ).get(id)
-        if not (history and ((history.user and trans.user and history.user.id == trans.user.id)
-                             or (trans.history and history.id == trans.history.id)
-                             or trans.user_is_admin)):
+        history = (
+            trans.sa_session.query(model.History)
+            .options(
+                joinedload("active_datasets")
+                .joinedload("creating_job_associations")
+                .joinedload("job")
+                .joinedload("workflow_invocation_step")
+                .joinedload("workflow_invocation")
+                .joinedload("workflow"),
+            )
+            .get(id)
+        )
+        if not (
+            history
+            and (
+                (history.user and trans.user and history.user.id == trans.user.id)
+                or (trans.history and history.id == trans.history.id)
+                or trans.user_is_admin
+            )
+        ):
             return trans.show_error_message("Cannot display history structure.")
         # Resolve jobs and workflow invocations for the datasets in the history
         # items is filled with items (hdas, jobs, or workflows) that go at the
@@ -529,22 +607,19 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         items.sort(key=(lambda x: x[0].create_time), reverse=True)
         # logic taken from mako files
         from galaxy.managers import hdas
+
         hda_serializer = hdas.HDASerializer(trans.app)
         hda_dicts = []
         id_hda_dict_map = {}
         for hda in history.active_datasets:
-            hda_dict = hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, view='detailed')
-            id_hda_dict_map[hda_dict['id']] = hda_dict
+            hda_dict = hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, view="detailed")
+            id_hda_dict_map[hda_dict["id"]] = hda_dict
             hda_dicts.append(hda_dict)
 
-        html_template = ''
+        html_template = ""
         for entity, children in items:
             html_template += render_item(trans, entity, children)
-        return {
-            'name': history.name,
-            'history_json': hda_dicts,
-            'template': html_template
-        }
+        return {"name": history.name, "history_json": hda_dicts, "template": html_template}
 
     @expose_api_anonymous
     def view(self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True):
@@ -558,8 +633,9 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         history_dictionary = {}
         user_is_owner = False
         if id:
-            history_to_view = self.history_manager.get_accessible(self.decode_id(id), trans.user,
-                current_history=trans.history)
+            history_to_view = self.history_manager.get_accessible(
+                self.decode_id(id), trans.user, current_history=trans.history
+            )
             user_is_owner = history_to_view.user == trans.user
             history_is_current = history_to_view == trans.history
         else:
@@ -568,8 +644,9 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             history_is_current = True
 
         # include all datasets: hidden, deleted, and purged
-        history_dictionary = self.history_serializer.serialize_to_view(history_to_view,
-            view='dev-detailed', user=trans.user, trans=trans)
+        history_dictionary = self.history_serializer.serialize_to_view(
+            history_to_view, view="dev-detailed", user=trans.user, trans=trans
+        )
 
         return {
             "history": history_dictionary,
@@ -578,21 +655,25 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             "show_deleted": show_deleted,
             "show_hidden": show_hidden,
             "use_panels": use_panels,
-            "allow_user_dataset_purge": trans.app.config.allow_user_dataset_purge
+            "allow_user_dataset_purge": trans.app.config.allow_user_dataset_purge,
         }
 
     @web.require_login("use more than one Galaxy history")
     @web.expose
-    def view_multiple(self, trans, include_deleted_histories=False, order='update_time', limit=10):
-        """
-        """
+    def view_multiple(self, trans, include_deleted_histories=False, order="update_time", limit=10):
+        """ """
         current_history_id = trans.security.encode_id(trans.history.id)
         # TODO: allow specifying user_id for admin?
         include_deleted_histories = string_as_bool(include_deleted_histories)
         limit = parse_int(limit, min_val=1, default=10, allow_none=True)
 
-        return trans.fill_template_mako("history/view_multiple.mako", current_history_id=current_history_id,
-            include_deleted_histories=include_deleted_histories, order=order, limit=limit)
+        return trans.fill_template_mako(
+            "history/view_multiple.mako",
+            current_history_id=current_history_id,
+            include_deleted_histories=include_deleted_histories,
+            order=order,
+            limit=limit,
+        )
 
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug):
@@ -602,9 +683,13 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         # Get history.
         session = trans.sa_session
         user = session.query(model.User).filter_by(username=username).first()
-        history = trans.sa_session.query(model.History) \
-            .options(eagerload('tags')).options(eagerload('annotations')) \
-            .filter_by(user=user, slug=slug, deleted=False).first()
+        history = (
+            trans.sa_session.query(model.History)
+            .options(eagerload("tags"))
+            .options(eagerload("annotations"))
+            .filter_by(user=user, slug=slug, deleted=False)
+            .first()
+        )
         if history is None:
             raise web.httpexceptions.HTTPNotFound()
         # Security check raises error if user cannot access history.
@@ -622,13 +707,21 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
 
         # create ownership flag for template, dictify models
         user_is_owner = trans.user == history.user
-        history_dictionary = self.history_serializer.serialize_to_view(history,
-            view='dev-detailed', user=trans.user, trans=trans)
-        history_dictionary['annotation'] = self.get_item_annotation_str(trans.sa_session, history.user, history)
+        history_dictionary = self.history_serializer.serialize_to_view(
+            history, view="dev-detailed", user=trans.user, trans=trans
+        )
+        history_dictionary["annotation"] = self.get_item_annotation_str(trans.sa_session, history.user, history)
 
-        return trans.fill_template_mako("history/display.mako", item=history, item_data=[],
-            user_is_owner=user_is_owner, history_dict=history_dictionary,
-            user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings)
+        return trans.fill_template_mako(
+            "history/display.mako",
+            item=history,
+            item_data=[],
+            user_is_owner=user_is_owner,
+            history_dict=history_dictionary,
+            user_item_rating=user_item_rating,
+            ave_item_rating=ave_item_rating,
+            num_ratings=num_ratings,
+        )
 
     @web.legacy_expose_api
     @web.require_login("changing default permissions")
@@ -636,11 +729,11 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         """
         Sets the permissions on a history.
         """
-        history_id = kwd.get('id')
+        history_id = kwd.get("id")
         if not history_id:
-            return self.message_exception(trans, f'Invalid history id ({str(history_id)}) received')
+            return self.message_exception(trans, f"Invalid history id ({str(history_id)}) received")
         history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             inputs = []
             all_roles = trans.user.all_roles()
             current_actions = history.default_permissions
@@ -649,24 +742,30 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                 for a in current_actions:
                     if a.action == action.action:
                         in_roles.add(a.role)
-                inputs.append({'type': 'select',
-                               'multiple': True,
-                               'optional': True,
-                               'individual': True,
-                               'name': action_key,
-                               'label': action.action,
-                               'help': action.description,
-                               'options': [(role.name, trans.security.encode_id(role.id)) for role in set(all_roles)],
-                               'value': [trans.security.encode_id(role.id) for role in in_roles]})
-            return {'title': 'Change default dataset permissions for history \'%s\'' % history.name, 'inputs': inputs}
+                inputs.append(
+                    {
+                        "type": "select",
+                        "multiple": True,
+                        "optional": True,
+                        "individual": True,
+                        "name": action_key,
+                        "label": action.action,
+                        "help": action.description,
+                        "options": [(role.name, trans.security.encode_id(role.id)) for role in set(all_roles)],
+                        "value": [trans.security.encode_id(role.id) for role in in_roles],
+                    }
+                )
+            return {"title": "Change default dataset permissions for history '%s'" % history.name, "inputs": inputs}
         else:
             permissions = {}
             for action_key, action in trans.app.model.Dataset.permitted_actions.items():
                 in_roles = payload.get(action_key) or []
-                in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in in_roles]
+                in_roles = [
+                    trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in in_roles
+                ]
                 permissions[trans.app.security_agent.get_action(action.action)] = in_roles
             trans.app.security_agent.history_set_default_permissions(history, permissions)
-            return {'message': 'Default history \'%s\' dataset permissions have been changed.' % history.name}
+            return {"message": "Default history '%s' dataset permissions have been changed." % history.name}
 
     @web.legacy_expose_api
     @web.require_login("make datasets private")
@@ -680,11 +779,13 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         if all_histories:
             histories = trans.user.histories
         elif history_id:
-            history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
+            history = self.history_manager.get_owned(
+                self.decode_id(history_id), trans.user, current_history=trans.history
+            )
             if history:
                 histories.append(history)
         if not histories:
-            return self.message_exception(trans, 'Invalid history or histories specified.')
+            return self.message_exception(trans, "Invalid history or histories specified.")
         private_role = trans.app.security_agent.get_private_user_role(trans.user)
         user_roles = trans.user.all_roles()
         private_permissions = {
@@ -696,26 +797,30 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             trans.app.security_agent.history_set_default_permissions(history, private_permissions)
             # Set private role for all datasets
             for hda in history.datasets:
-                if (not hda.dataset.library_associations
-                        and not trans.app.security_agent.dataset_is_private_to_user(trans, hda.dataset)
-                        and trans.app.security_agent.can_manage_dataset(user_roles, hda.dataset)):
+                if (
+                    not hda.dataset.library_associations
+                    and not trans.app.security_agent.dataset_is_private_to_user(trans, hda.dataset)
+                    and trans.app.security_agent.can_manage_dataset(user_roles, hda.dataset)
+                ):
                     # If it's not private to me, and I can manage it, set fixed private permissions.
                     trans.app.security_agent.set_all_dataset_permissions(hda.dataset, private_permissions)
                     if not trans.app.security_agent.dataset_is_private_to_user(trans, hda.dataset):
-                        raise exceptions.InternalServerError('An error occurred and the dataset is NOT private.')
-        return {'message': f"Success, requested permissions have been changed in {'all histories' if all_histories else history.name}."}
+                        raise exceptions.InternalServerError("An error occurred and the dataset is NOT private.")
+        return {
+            "message": f"Success, requested permissions have been changed in {'all histories' if all_histories else history.name}."
+        }
 
     @web.expose
     def adjust_hidden(self, trans, id=None, **kwd):
-        """ THIS METHOD IS A TEMPORARY ADDITION. It'll allow us to fix the
+        """THIS METHOD IS A TEMPORARY ADDITION. It'll allow us to fix the
         regression in history-wide actions, and will be removed in the first
-        release after 17.01 """
-        action = kwd.get('user_action', None)
-        if action == 'delete':
+        release after 17.01"""
+        action = kwd.get("user_action", None)
+        if action == "delete":
             for hda in trans.history.datasets:
                 if not hda.visible:
                     hda.mark_deleted()
-        elif action == 'unhide':
+        elif action == "unhide":
             trans.history.unhide_datasets()
         trans.sa_session.flush()
 
@@ -736,12 +841,16 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                 if hda.dataset.user_can_purge:
                     try:
                         hda.dataset.full_delete()
-                        trans.log_event(f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}")
+                        trans.log_event(
+                            f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}"
+                        )
                         trans.sa_session.add(hda.dataset)
                     except Exception:
-                        log.exception(f'Unable to purge dataset ({hda.dataset.id}) on purge of hda ({hda.id}):')
+                        log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of hda ({hda.id}):")
                 count += 1
-            return trans.show_ok_message("%d datasets have been deleted permanently" % count, refresh_frames=['history'])
+            return trans.show_ok_message(
+                "%d datasets have been deleted permanently" % count, refresh_frames=["history"]
+            )
         return trans.show_error_message("Cannot purge deleted datasets from this session.")
 
     @web.expose
@@ -749,7 +858,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         """Resume paused jobs the active history -- this does not require a logged in user."""
         if not ids and string_as_bool(current):
             histories = [trans.get_history()]
-            refresh_frames = ['history']
+            refresh_frames = ["history"]
         else:
             raise NotImplementedError("You can currently only resume all the datasets of the current history.")
         for history in histories:
@@ -763,7 +872,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     @web.require_login("rate items")
     @web.json
     def rate_async(self, trans, id, rating):
-        """ Rate a history asynchronously and return updated community data. """
+        """Rate a history asynchronously and return updated community data."""
         history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history)
         if not history:
             return trans.show_error_message("The specified history does not exist.")
@@ -776,24 +885,29 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     @web.json
     @web.require_login("get history name and link")
     def get_name_and_link_async(self, trans, id=None):
-        """ Returns history's name and link. """
+        """Returns history's name and link."""
         history = self.history_manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history)
         if self.slug_builder.create_item_slug(trans.sa_session, history):
             trans.sa_session.flush()
         return_dict = {
             "name": history.name,
-            "link": url_for(controller='history', action="display_by_username_and_slug",
-                            username=history.user.username, slug=history.slug)}
+            "link": url_for(
+                controller="history",
+                action="display_by_username_and_slug",
+                username=history.user.username,
+                slug=history.slug,
+            ),
+        }
         return return_dict
         # TODO: used in page/editor.mako
 
     @web.expose
     @web.require_login("set history's accessible flag")
     def set_accessible_async(self, trans, id=None, accessible=False):
-        """ Set history's importable attribute and slug. """
+        """Set history's importable attribute and slug."""
         history = self.history_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history)
         # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
-        importable = accessible in ['True', 'true', 't', 'T']
+        importable = accessible in ["True", "true", "t", "T"]
         if history and history.importable != importable:
             if importable:
                 self._make_item_accessible(trans.sa_session, history)
@@ -806,45 +920,46 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     @web.legacy_expose_api
     @web.require_login("rename histories")
     def rename(self, trans, payload=None, **kwd):
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No history id received for renaming.')
+            return self.message_exception(trans, "No history id received for renaming.")
         user = trans.get_user()
         id = listify(id)
         histories = []
         for history_id in id:
-            history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
+            history = self.history_manager.get_owned(
+                self.decode_id(history_id), trans.user, current_history=trans.history
+            )
             if history and history.user_id == user.id:
                 histories.append(history)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             return {
-                'title': 'Change history name(s)',
-                'inputs': [{
-                    'name': 'name_%i' % i,
-                    'label': f'Current: {h.name}',
-                    'value': h.name
-                } for i, h in enumerate(histories)]
+                "title": "Change history name(s)",
+                "inputs": [
+                    {"name": "name_%i" % i, "label": f"Current: {h.name}", "value": h.name}
+                    for i, h in enumerate(histories)
+                ],
             }
         else:
             messages = []
             for i, h in enumerate(histories):
                 cur_name = h.get_display_name()
-                new_name = payload.get('name_%i' % i)
+                new_name = payload.get("name_%i" % i)
                 # validate name is empty
                 if not isinstance(new_name, str) or not new_name.strip():
-                    messages.append('You must specify a valid name for History \'%s\'.' % cur_name)
+                    messages.append("You must specify a valid name for History '%s'." % cur_name)
                 # skip if not the owner
                 elif h.user_id != user.id:
-                    messages.append('History \'%s\' does not appear to belong to you.' % cur_name)
+                    messages.append("History '%s' does not appear to belong to you." % cur_name)
                 # skip if it wouldn't be a change
                 elif new_name != cur_name:
                     h.name = new_name
                     trans.sa_session.add(h)
                     trans.sa_session.flush()
-                    trans.log_event(f'History renamed: id: {str(h.id)}, renamed to: {new_name}')
+                    trans.log_event(f"History renamed: id: {str(h.id)}, renamed to: {new_name}")
                     messages.append(f"History '{cur_name}' renamed to '{new_name}'.")
-            message = sanitize_text(' '.join(messages)) if messages else 'History names remain unchanged.'
-            return {'message': message, 'status': 'success'}
+            message = sanitize_text(" ".join(messages)) if messages else "History names remain unchanged."
+            return {"message": message, "status": "success"}
 
     # ------------------------------------------------------------------------- current history
     @web.expose
@@ -861,7 +976,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
 
     def history_data(self, trans, history):
         """Return the given history in a serialized, dictionary form."""
-        return self.history_serializer.serialize_to_view(history, view='dev-detailed', user=trans.user, trans=trans)
+        return self.history_serializer.serialize_to_view(history, view="dev-detailed", user=trans.user, trans=trans)
 
     # TODO: combine these next two - poss. with a redirect flag
     # @web.require_login( "switch to a history" )
@@ -875,7 +990,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             return self.history_data(trans, history)
         except exceptions.MessageException as msg_exc:
             trans.response.status = msg_exc.status_code
-            return {'err_msg': msg_exc.err_msg, 'err_code': msg_exc.err_code.code}
+            return {"err_msg": msg_exc.err_msg, "err_code": msg_exc.err_code.code}
 
     @web.json
     @web.do_not_cache
@@ -889,4 +1004,5 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         """Create a new, current history for the current user"""
         new_history = trans.new_history(name)
         return self.history_data(trans, new_history)
+
     # TODO: /history/current to do all of the above: if ajax, return json; if post, read id and set to current
diff --git a/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py b/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
index b0d29c9d50d..2a13cf0d546 100644
--- a/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
+++ b/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
@@ -3,15 +3,16 @@ API check for whether the current session's interactive environment launch is re
 """
 import logging
 
-from galaxy.web import expose, json
+from galaxy.web import (
+    expose,
+    json,
+)
 from galaxy.webapps.base.controller import BaseUIController
 
-
 log = logging.getLogger(__name__)
 
 
 class InteractiveEnvironmentsController(BaseUIController):
-
     @expose
     @json
     def ready(self, trans, **kwd):
@@ -31,21 +32,35 @@ class InteractiveEnvironmentsController(BaseUIController):
         try:
             interface = self.app.containers[proxy_map.container_interface]
         except KeyError:
-            log.error('Invalid container interface key: %s', proxy_map.container_interface)
+            log.error("Invalid container interface key: %s", proxy_map.container_interface)
             return None
         container = interface.get_container(proxy_map.container_ids[0])
         if not proxy_map.port > 0:
             # a negative port means it failed to be determined at launch time; the negated negative port is the
             # container port
-            log.debug("Container %s (%s) mapping for port %s is not set in the proxy, attempting to get port mapping "
-                      "now", container.name, container.id, -proxy_map.port)
+            log.debug(
+                "Container %s (%s) mapping for port %s is not set in the proxy, attempting to get port mapping " "now",
+                container.name,
+                container.id,
+                -proxy_map.port,
+            )
             mapping = container.map_port(-proxy_map.port)
             if mapping:
-                log.info("Container %s (%s) port %s accessible at: %s:%s", container.name, container.id,
-                         -proxy_map.port, mapping.hostaddr, mapping.hostport)
+                log.info(
+                    "Container %s (%s) port %s accessible at: %s:%s",
+                    container.name,
+                    container.id,
+                    -proxy_map.port,
+                    mapping.hostaddr,
+                    mapping.hostport,
+                )
                 self.app.proxy_manager.update_proxy(trans, host=mapping.hostaddr, port=mapping.hostport)
             else:
-                log.warning("Container %s (%s) mapping for port %s cannot be determined!", container.name, container.id,
-                            -proxy_map.port)
+                log.warning(
+                    "Container %s (%s) mapping for port %s cannot be determined!",
+                    container.name,
+                    container.id,
+                    -proxy_map.port,
+                )
                 return False
         return container.is_ready()
diff --git a/lib/galaxy/webapps/galaxy/controllers/library.py b/lib/galaxy/webapps/galaxy/controllers/library.py
index 2d2630f19af..6b4d1fe229f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library.py
@@ -3,20 +3,14 @@ import logging
 from galaxy import web
 from galaxy.webapps.base.controller import BaseUIController
 
-
 log = logging.getLogger(__name__)
 
 
 class Library(BaseUIController):
-
     @web.expose
     def list(self, trans, **kwd):
         # define app configuration for generic mako template
-        app = {
-            'jscript': "library"
-        }
-        return trans.fill_template('galaxy.panels.mako',
-                                   config={
-                                       'title': 'Data Libraries',
-                                       'app': app,
-                                       'bundle': 'extended'})
+        app = {"jscript": "library"}
+        return trans.fill_template(
+            "galaxy.panels.mako", config={"title": "Data Libraries", "app": app, "bundle": "extended"}
+        )
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 45c1f7bab44..4ba9fc15f71 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -2,21 +2,24 @@ from markupsafe import escape
 from sqlalchemy import (
     desc,
     false,
-    true
+    true,
 )
 from sqlalchemy.orm import (
     eagerload,
-    undefer
+    undefer,
 )
 
 from galaxy import (
     exceptions,
     model,
     util,
-    web
+    web,
 )
 from galaxy.managers.hdas import HDAManager
-from galaxy.managers.histories import HistoryManager, HistorySerializer
+from galaxy.managers.histories import (
+    HistoryManager,
+    HistorySerializer,
+)
 from galaxy.managers.pages import (
     get_page_identifiers,
     PageContentProcessor,
@@ -30,17 +33,17 @@ from galaxy.util import unicodify
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import (
     error,
-    url_for
+    url_for,
 )
 from galaxy.web.framework.helpers import (
     grids,
-    time_ago
+    time_ago,
 )
 from galaxy.webapps.base.controller import (
     BaseUIController,
     SharableMixin,
     UsesStoredWorkflowMixin,
-    UsesVisualizationMixin
+    UsesVisualizationMixin,
 )
 from ..api import depends
 
@@ -56,7 +59,9 @@ class PageListGrid(grids.Grid):
     # Custom column.
     class URLColumn(grids.PublicURLColumn):
         def get_value(self, trans, grid, item):
-            return url_for(controller='page', action='display_by_username_and_slug', username=item.user.username, slug=item.slug)
+            return url_for(
+                controller="page", action="display_by_username_and_slug", username=item.user.username, slug=item.slug
+            )
 
     # Grid definition
     use_panels = True
@@ -65,26 +70,53 @@ class PageListGrid(grids.Grid):
     default_filter = {"published": "All", "tags": "All", "title": "All", "sharing": "All"}
     default_sort_key = "-update_time"
     columns = [
-        grids.TextColumn("Title", key="title", attach_popup=True, filterable="advanced", link=(lambda item: dict(action="display_by_username_and_slug", username=item.user.username, slug=item.slug))),
+        grids.TextColumn(
+            "Title",
+            key="title",
+            attach_popup=True,
+            filterable="advanced",
+            link=(
+                lambda item: dict(action="display_by_username_and_slug", username=item.user.username, slug=item.slug)
+            ),
+        ),
         URLColumn("Public URL"),
-        grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid"),
+        grids.OwnerAnnotationColumn(
+            "Annotation",
+            key="annotation",
+            model_annotation_association_class=model.PageAnnotationAssociation,
+            filterable="advanced",
+        ),
+        grids.IndividualTagsColumn(
+            "Tags",
+            key="tags",
+            model_tag_association_class=model.PageTagAssociation,
+            filterable="advanced",
+            grid_name="PageListGrid",
+        ),
         grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False),
         grids.GridColumn("Created", key="create_time", format=time_ago),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
     ]
-    columns.append(grids.MulticolFilterColumn(
-        "Search",
-        cols_to_filter=[columns[0], columns[2]],
-        key="free-text-search", visible=False, filterable="standard"))
-    global_actions = [
-        grids.GridAction("Add new page", dict(controller="", action="pages/create"))
-    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    global_actions = [grids.GridAction("Add new page", dict(controller="", action="pages/create"))]
     operations = [
         grids.DisplayByUsernameAndSlugGridOperation("View", allow_multiple=False),
         grids.GridOperation("Edit content", allow_multiple=False, url_args=dict(action="edit_content")),
         grids.GridOperation("Edit attributes", allow_multiple=False, url_args=dict(controller="", action="pages/edit")),
-        grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="pages/sharing")),
+        grids.GridOperation(
+            "Share or Publish",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            url_args=dict(controller="", action="pages/sharing"),
+        ),
         grids.GridOperation("Delete", confirm="Are you sure you want to delete this page?"),
     ]
 
@@ -101,26 +133,40 @@ class PageAllPublishedGrid(grids.Grid):
     default_filter = dict(title="All", username="All")
     columns = [
         grids.PublicURLColumn("Title", key="title", filterable="advanced"),
-        grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced"),
+        grids.OwnerAnnotationColumn(
+            "Annotation",
+            key="annotation",
+            model_annotation_association_class=model.PageAnnotationAssociation,
+            filterable="advanced",
+        ),
         grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"),
         grids.CommunityRatingColumn("Community Rating", key="rating"),
-        grids.CommunityTagsColumn("Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid"),
-        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
+        grids.CommunityTagsColumn(
+            "Community Tags",
+            key="tags",
+            model_tag_association_class=model.PageTagAssociation,
+            filterable="advanced",
+            grid_name="PageAllPublishedGrid",
+        ),
+        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago),
     ]
     columns.append(
         grids.MulticolFilterColumn(
             "Search title, annotation, owner, and tags",
             cols_to_filter=[columns[0], columns[1], columns[2], columns[4]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def build_initial_query(self, trans, **kwargs):
         # See optimization description comments and TODO for tags in matching public histories query.
-        return trans.sa_session.query(self.model_class).join("user").filter(
-            model.User.deleted == false()).options(
-                eagerload("user").load_only("username"),
-                eagerload("annotations"),
-                undefer("average_rating")
+        return (
+            trans.sa_session.query(self.model_class)
+            .join("user")
+            .filter(model.User.deleted == false())
+            .options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
         )
 
     def apply_query_filter(self, trans, query, **kwargs):
@@ -128,7 +174,8 @@ class PageAllPublishedGrid(grids.Grid):
 
 
 class ItemSelectionGrid(grids.Grid):
-    """ Base class for pages' item selection grids. """
+    """Base class for pages' item selection grids."""
+
     # Custom columns.
     class NameColumn(grids.TextColumn):
         def get_value(self, trans, grid, item):
@@ -149,13 +196,16 @@ class ItemSelectionGrid(grids.Grid):
 
 
 class HistorySelectionGrid(ItemSelectionGrid):
-    """ Grid for selecting histories. """
+    """Grid for selecting histories."""
+
     # Grid definition.
     title = "Saved Histories"
     model_class = model.History
     columns = [
         ItemSelectionGrid.NameColumn("Name", key="name", filterable="advanced"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"),
+        grids.IndividualTagsColumn(
+            "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"
+        ),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
@@ -165,7 +215,10 @@ class HistorySelectionGrid(ItemSelectionGrid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[1]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def apply_query_filter(self, trans, query, **kwargs):
@@ -173,13 +226,19 @@ class HistorySelectionGrid(ItemSelectionGrid):
 
 
 class HistoryDatasetAssociationSelectionGrid(ItemSelectionGrid):
-    """ Grid for selecting HDAs. """
+    """Grid for selecting HDAs."""
+
     # Grid definition.
     title = "Saved Datasets"
     model_class = model.HistoryDatasetAssociation
     columns = [
         ItemSelectionGrid.NameColumn("Name", key="name", filterable="advanced"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"),
+        grids.IndividualTagsColumn(
+            "Tags",
+            key="tags",
+            model_tag_association_class=model.HistoryDatasetAssociationTagAssociation,
+            filterable="advanced",
+        ),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
@@ -189,23 +248,31 @@ class HistoryDatasetAssociationSelectionGrid(ItemSelectionGrid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[1]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def apply_query_filter(self, trans, query, **kwargs):
         # To filter HDAs by user, need to join HDA and History table and then filter histories by user. This is necessary because HDAs do not have
         # a user relation.
-        return query.select_from(model.HistoryDatasetAssociation.table.join(model.History.table)).filter(model.History.user == trans.user)
+        return query.select_from(model.HistoryDatasetAssociation.table.join(model.History.table)).filter(
+            model.History.user == trans.user
+        )
 
 
 class WorkflowSelectionGrid(ItemSelectionGrid):
-    """ Grid for selecting workflows. """
+    """Grid for selecting workflows."""
+
     # Grid definition.
     title = "Saved Workflows"
     model_class = model.StoredWorkflow
     columns = [
         ItemSelectionGrid.NameColumn("Name", key="name", filterable="advanced"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"),
+        grids.IndividualTagsColumn(
+            "Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"
+        ),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
@@ -215,18 +282,24 @@ class WorkflowSelectionGrid(ItemSelectionGrid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[1]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
 
 class PageSelectionGrid(ItemSelectionGrid):
-    """ Grid for selecting pages. """
+    """Grid for selecting pages."""
+
     # Grid definition.
     title = "Saved Pages"
     model_class = model.Page
     columns = [
         grids.TextColumn("Title", key="title", filterable="advanced"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"),
+        grids.IndividualTagsColumn(
+            "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"
+        ),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
         # Columns that are valid for filtering but are not visible.
         grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
@@ -236,19 +309,29 @@ class PageSelectionGrid(ItemSelectionGrid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[1]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
 
 class VisualizationSelectionGrid(ItemSelectionGrid):
-    """ Grid for selecting visualizations. """
+    """Grid for selecting visualizations."""
+
     # Grid definition.
     title = "Saved Visualizations"
     model_class = model.Visualization
     columns = [
         grids.TextColumn("Title", key="title", filterable="advanced"),
         grids.TextColumn("Type", key="type"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid"),
+        grids.IndividualTagsColumn(
+            "Tags",
+            key="tags",
+            model_tag_association_class=model.VisualizationTagAssociation,
+            filterable="advanced",
+            grid_name="VisualizationListGrid",
+        ),
         grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
     ]
@@ -256,13 +339,15 @@ class VisualizationSelectionGrid(ItemSelectionGrid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[2]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
 
 # Adapted from the _BaseHTMLProcessor class of https://github.com/kurtmckee/feedparser
-class PageController(BaseUIController, SharableMixin,
-                     UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings):
+class PageController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings):
 
     _page_list = PageListGrid()
     _all_published_list = PageAllPublishedGrid()
@@ -285,12 +370,12 @@ class PageController(BaseUIController, SharableMixin,
     @web.json
     @web.require_login()
     def list(self, trans, *args, **kwargs):
-        """ List user's pages. """
+        """List user's pages."""
         # Handle operation
-        if 'operation' in kwargs and 'id' in kwargs:
+        if "operation" in kwargs and "id" in kwargs:
             session = trans.sa_session
-            operation = kwargs['operation'].lower()
-            ids = util.listify(kwargs['id'])
+            operation = kwargs["operation"].lower()
+            ids = util.listify(kwargs["id"])
             for id in ids:
                 item = session.query(model.Page).get(self.decode_id(id))
                 if operation == "delete":
@@ -299,28 +384,29 @@ class PageController(BaseUIController, SharableMixin,
 
         # Build grid dictionary.
         grid = self._page_list(trans, *args, **kwargs)
-        grid['shared_by_others'] = self._get_shared(trans)
+        grid["shared_by_others"] = self._get_shared(trans)
         return grid
 
     @web.expose
     @web.json
     def list_published(self, trans, *args, **kwargs):
         grid = self._all_published_list(trans, *args, **kwargs)
-        grid['shared_by_others'] = self._get_shared(trans)
+        grid["shared_by_others"] = self._get_shared(trans)
         return grid
 
     def _get_shared(self, trans):
         """Identify shared pages"""
-        shared_by_others = trans.sa_session \
-            .query(model.PageUserShareAssociation) \
-            .filter_by(user=trans.get_user()) \
-            .join(model.Page.table) \
-            .filter(model.Page.deleted == false()) \
-            .order_by(desc(model.Page.update_time)) \
+        shared_by_others = (
+            trans.sa_session.query(model.PageUserShareAssociation)
+            .filter_by(user=trans.get_user())
+            .join(model.Page.table)
+            .filter(model.Page.deleted == false())
+            .order_by(desc(model.Page.update_time))
             .all()
-        return [{'username': p.page.user.username,
-                 'slug': p.page.slug,
-                 'title': p.page.title} for p in shared_by_others]
+        )
+        return [
+            {"username": p.page.user.username, "slug": p.page.slug, "title": p.page.title} for p in shared_by_others
+        ]
 
     @web.legacy_expose_api
     @web.require_login("create pages")
@@ -328,7 +414,7 @@ class PageController(BaseUIController, SharableMixin,
         """
         Create a new page.
         """
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             form_title = "Create new Page"
             title = ""
             slug = ""
@@ -345,41 +431,47 @@ class PageController(BaseUIController, SharableMixin,
                 content_format_hide = True
                 content_hide = False
             return {
-                'title': form_title,
-                'inputs': [{
-                    'name': 'title',
-                    'label': 'Name',
-                    'value': title,
-                }, {
-                    'name': 'slug',
-                    'label': 'Identifier',
-                    'help': 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).',
-                    'value': slug,
-                }, {
-                    'name': 'annotation',
-                    'label': 'Annotation',
-                    'help': 'A description of the page. The annotation is shown alongside published pages.'
-                }, {
-                    'name': 'content_format',
-                    'label': 'Content Format',
-                    'type': 'select',
-                    'hidden': content_format_hide,
-                    'options': [('Markdown', 'markdown'), ('HTML', 'html')],
-                    'help': 'Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.'
-                }, {
-                    'name': 'content',
-                    'label': 'Content',
-                    'area': True,
-                    'value': content,
-                    'hidden': content_hide,
-                }]
+                "title": form_title,
+                "inputs": [
+                    {
+                        "name": "title",
+                        "label": "Name",
+                        "value": title,
+                    },
+                    {
+                        "name": "slug",
+                        "label": "Identifier",
+                        "help": "A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).",
+                        "value": slug,
+                    },
+                    {
+                        "name": "annotation",
+                        "label": "Annotation",
+                        "help": "A description of the page. The annotation is shown alongside published pages.",
+                    },
+                    {
+                        "name": "content_format",
+                        "label": "Content Format",
+                        "type": "select",
+                        "hidden": content_format_hide,
+                        "options": [("Markdown", "markdown"), ("HTML", "html")],
+                        "help": "Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.",
+                    },
+                    {
+                        "name": "content",
+                        "label": "Content",
+                        "area": True,
+                        "value": content,
+                        "hidden": content_hide,
+                    },
+                ],
             }
         else:
             try:
                 page = self.page_manager.create(trans, payload)
             except exceptions.MessageException as e:
                 return self.message_exception(trans, unicodify(e))
-            return {'message': 'Page \'%s\' successfully created.' % page.title, 'status': 'success'}
+            return {"message": "Page '%s' successfully created." % page.title, "status": "success"}
 
     @web.legacy_expose_api
     @web.require_login("edit pages")
@@ -387,45 +479,50 @@ class PageController(BaseUIController, SharableMixin,
         """
         Edit a page's attributes.
         """
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No page id received for editing.')
+            return self.message_exception(trans, "No page id received for editing.")
         decoded_id = self.decode_id(id)
         user = trans.get_user()
         p = trans.sa_session.query(model.Page).get(decoded_id)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             if p.slug is None:
                 self.slug_builder.create_item_slug(trans.sa_session, p)
             return {
-                'title': 'Edit page attributes',
-                'inputs': [{
-                    'name': 'title',
-                    'label': 'Name',
-                    'value': p.title
-                }, {
-                    'name': 'slug',
-                    'label': 'Identifier',
-                    'value': p.slug,
-                    'help': 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).'
-                }, {
-                    'name': 'annotation',
-                    'label': 'Annotation',
-                    'value': self.get_item_annotation_str(trans.sa_session, user, p),
-                    'help': 'A description of the page. The annotation is shown alongside published pages.'
-                }]
+                "title": "Edit page attributes",
+                "inputs": [
+                    {"name": "title", "label": "Name", "value": p.title},
+                    {
+                        "name": "slug",
+                        "label": "Identifier",
+                        "value": p.slug,
+                        "help": "A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).",
+                    },
+                    {
+                        "name": "annotation",
+                        "label": "Annotation",
+                        "value": self.get_item_annotation_str(trans.sa_session, user, p),
+                        "help": "A description of the page. The annotation is shown alongside published pages.",
+                    },
+                ],
             }
         else:
-            p_title = payload.get('title')
-            p_slug = payload.get('slug')
-            p_annotation = payload.get('annotation')
+            p_title = payload.get("title")
+            p_slug = payload.get("slug")
+            p_annotation = payload.get("annotation")
             if not p_title:
-                return self.message_exception(trans, 'Please provide a page name is required.')
+                return self.message_exception(trans, "Please provide a page name is required.")
             elif not p_slug:
-                return self.message_exception(trans, 'Please provide a unique identifier.')
+                return self.message_exception(trans, "Please provide a unique identifier.")
             elif not self._is_valid_slug(p_slug):
-                return self.message_exception(trans, 'Page identifier can only contain lowercase letters, numbers, and dashes (-).')
-            elif p_slug != p.slug and trans.sa_session.query(model.Page).filter_by(user=p.user, slug=p_slug, deleted=False).first():
-                return self.message_exception(trans, 'Page id must be unique.')
+                return self.message_exception(
+                    trans, "Page identifier can only contain lowercase letters, numbers, and dashes (-)."
+                )
+            elif (
+                p_slug != p.slug
+                and trans.sa_session.query(model.Page).filter_by(user=p.user, slug=p_slug, deleted=False).first()
+            ):
+                return self.message_exception(trans, "Page id must be unique.")
             else:
                 p.title = p_title
                 p.slug = p_slug
@@ -434,7 +531,7 @@ class PageController(BaseUIController, SharableMixin,
                     self.add_item_annotation(trans.sa_session, user, p, p_annotation)
                 trans.sa_session.add(p)
                 trans.sa_session.flush()
-            return {'message': 'Attributes of \'%s\' successfully saved.' % p.title, 'status': 'success'}
+            return {"message": "Attributes of '%s' successfully saved." % p.title, "status": "success"}
 
     @web.expose
     @web.require_login("edit pages")
@@ -455,7 +552,7 @@ class PageController(BaseUIController, SharableMixin,
 
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug):
-        """ Display page based on a username and slug. """
+        """Display page based on a username and slug."""
 
         # Get page.
         session = trans.sa_session
@@ -472,7 +569,7 @@ class PageController(BaseUIController, SharableMixin,
             processor = PageContentProcessor(trans, self._get_embed_html)
             processor.feed(page.latest_revision.content)
             # Output is string, so convert to unicode for display.
-            page_content = unicodify(processor.output(), 'utf-8')
+            page_content = unicodify(processor.output(), "utf-8")
             template = "page/display.mako"
         else:
             page_content = trans.security.encode_id(page.id)
@@ -488,21 +585,24 @@ class PageController(BaseUIController, SharableMixin,
                 user_item_rating = 0
         ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, page)
 
-        return trans.fill_template_mako(template, item=page,
-                                        item_data=page_content,
-                                        user_item_rating=user_item_rating,
-                                        ave_item_rating=ave_item_rating,
-                                        num_ratings=num_ratings,
-                                        content_only=True)
+        return trans.fill_template_mako(
+            template,
+            item=page,
+            item_data=page_content,
+            user_item_rating=user_item_rating,
+            ave_item_rating=ave_item_rating,
+            num_ratings=num_ratings,
+            content_only=True,
+        )
 
     @web.expose
     @web.require_login("use Galaxy pages")
     def set_accessible_async(self, trans, id=None, accessible=False):
-        """ Set page's importable attribute and slug. """
+        """Set page's importable attribute and slug."""
         page = self.get_page(trans, id)
 
         # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
-        importable = accessible in ['True', 'true', 't', 'T']
+        importable = accessible in ["True", "true", "t", "T"]
         if page.importable != importable:
             if importable:
                 self._make_item_accessible(trans.sa_session, page)
@@ -515,7 +615,7 @@ class PageController(BaseUIController, SharableMixin,
     @web.require_login("rate items")
     @web.json
     def rate_async(self, trans, id, rating):
-        """ Rate a page asynchronously and return updated community data. """
+        """Rate a page asynchronously and return updated community data."""
 
         page = self.get_page(trans, id, check_ownership=False, check_accessible=True)
         if not page:
@@ -528,7 +628,7 @@ class PageController(BaseUIController, SharableMixin,
 
     @web.expose
     def get_embed_html_async(self, trans, id):
-        """ Returns HTML for embedding a workflow in a page. """
+        """Returns HTML for embedding a workflow in a page."""
 
         # TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code.
         page = self.get_page(trans, id)
@@ -539,55 +639,57 @@ class PageController(BaseUIController, SharableMixin,
     @web.json
     @web.require_login("use Galaxy pages")
     def get_name_and_link_async(self, trans, id=None):
-        """ Returns page's name and link. """
+        """Returns page's name and link."""
         page = self.get_page(trans, id)
 
         if self.slug_builder.create_item_slug(trans.sa_session, page):
             trans.sa_session.flush()
-        return_dict = {"name": page.title, "link": url_for(controller='page',
-                                                           action="display_by_username_and_slug",
-                                                           username=page.user.username,
-                                                           slug=page.slug)}
+        return_dict = {
+            "name": page.title,
+            "link": url_for(
+                controller="page", action="display_by_username_and_slug", username=page.user.username, slug=page.slug
+            ),
+        }
         return return_dict
 
     @web.expose
     @web.json
     @web.require_login("select a history from saved histories")
     def list_histories_for_selection(self, trans, **kwargs):
-        """ Returns HTML that enables a user to select one or more histories. """
+        """Returns HTML that enables a user to select one or more histories."""
         return self._history_selection_grid(trans, **kwargs)
 
     @web.expose
     @web.json
     @web.require_login("select a workflow from saved workflows")
     def list_workflows_for_selection(self, trans, **kwargs):
-        """ Returns HTML that enables a user to select one or more workflows. """
+        """Returns HTML that enables a user to select one or more workflows."""
         return self._workflow_selection_grid(trans, **kwargs)
 
     @web.expose
     @web.json
     @web.require_login("select a visualization from saved visualizations")
     def list_visualizations_for_selection(self, trans, **kwargs):
-        """ Returns HTML that enables a user to select one or more visualizations. """
+        """Returns HTML that enables a user to select one or more visualizations."""
         return self._visualization_selection_grid(trans, **kwargs)
 
     @web.expose
     @web.json
     @web.require_login("select a page from saved pages")
     def list_pages_for_selection(self, trans, **kwargs):
-        """ Returns HTML that enables a user to select one or more pages. """
+        """Returns HTML that enables a user to select one or more pages."""
         return self._page_selection_grid(trans, **kwargs)
 
     @web.expose
     @web.json
     @web.require_login("select a dataset from saved datasets")
     def list_datasets_for_selection(self, trans, **kwargs):
-        """ Returns HTML that enables a user to select one or more datasets. """
+        """Returns HTML that enables a user to select one or more datasets."""
         return self._datasets_selection_grid(trans, **kwargs)
 
     @web.expose
     def get_editor_iframe(self, trans):
-        """ Returns the document for the page editor's iframe. """
+        """Returns the document for the page editor's iframe."""
         return trans.fill_template("page/wymiframe.mako")
 
     def get_page(self, trans, id, check_ownership=True, check_accessible=False):
@@ -617,16 +719,18 @@ class PageController(BaseUIController, SharableMixin,
 
         # include all datasets: hidden, deleted, and purged
         history_dictionary = self.history_serializer.serialize_to_view(
-            history, view='detailed', user=trans.user, trans=trans
+            history, view="detailed", user=trans.user, trans=trans
         )
-        contents = self.history_serializer.serialize_contents(history, 'contents', trans=trans, user=trans.user)
-        history_dictionary['annotation'] = history.annotation
+        contents = self.history_serializer.serialize_contents(history, "contents", trans=trans, user=trans.user)
+        history_dictionary["annotation"] = history.annotation
 
-        filled = trans.fill_template("history/embed.mako",
-                                     item=history,
-                                     user_is_owner=user_is_owner,
-                                     history_dict=history_dictionary,
-                                     content_dicts=contents)
+        filled = trans.fill_template(
+            "history/embed.mako",
+            item=history,
+            user_is_owner=user_is_owner,
+            history_dict=history_dictionary,
+            content_dicts=contents,
+        )
         return filled
 
     def _get_embedded_visualization_html(self, trans, encoded_id):
@@ -639,21 +743,24 @@ class PageController(BaseUIController, SharableMixin,
             return None
 
         # Fork to template based on visualization.type (registry or builtin).
-        if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins)
-                and (visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
+        if (trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins) and (
+            visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS
+        ):
             # if a registry visualization, load a version into an iframe :(
             # TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way
             # TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved')
             encoded_visualization_id = trans.security.encode_id(visualization.id)
-            return trans.fill_template('visualization/embed_in_frame.mako',
-                                       item=visualization,
-                                       encoded_visualization_id=encoded_visualization_id,
-                                       content_only=True)
+            return trans.fill_template(
+                "visualization/embed_in_frame.mako",
+                item=visualization,
+                encoded_visualization_id=encoded_visualization_id,
+                content_only=True,
+            )
 
         return trans.fill_template("visualization/embed.mako", item=visualization, item_data=None)
 
     def _get_embed_html(self, trans, item_class, item_id):
-        """ Returns HTML for embedding an item in a page. """
+        """Returns HTML for embedding an item in a page."""
         item_class = self.get_class(item_class)
         encoded_id, decoded_id = get_page_identifiers(item_id, trans.app)
         if item_class == model.History:
@@ -673,7 +780,9 @@ class PageController(BaseUIController, SharableMixin,
             workflow.annotation = self.get_item_annotation_str(trans.sa_session, workflow.user, workflow)
             if workflow:
                 self.get_stored_workflow_steps(trans, workflow)
-                return trans.fill_template("workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps)
+                return trans.fill_template(
+                    "workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps
+                )
 
         elif item_class == model.Visualization:
             return self._get_embedded_visualization_html(trans, encoded_id)
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index fe87ce1278f..eda5a45ae26 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -4,19 +4,16 @@ Contains the main interface in the Universe class
 
 import logging
 
-from webob.exc import (
-    HTTPNotFound
-)
+from webob.exc import HTTPNotFound
 
-from galaxy import (
-    web
+from galaxy import web
+from galaxy.managers.histories import (
+    HistoryManager,
+    HistorySerializer,
 )
-from galaxy.managers.histories import HistoryManager, HistorySerializer
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.structured_app import StructuredApp
-from galaxy.util import (
-    unicodify,
-)
+from galaxy.util import unicodify
 from galaxy.webapps.base import controller
 from ..api import depends
 
@@ -28,6 +25,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
     """
     Controller class that maps to the url root of Galaxy (i.e. '/').
     """
+
     history_manager: HistoryManager = depends(HistoryManager)
     history_serializer: HistorySerializer = depends(HistorySerializer)
 
@@ -39,7 +37,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         """
         Called on any url that does not match a controller method.
         """
-        raise HTTPNotFound('This link may not be followed from within Galaxy.')
+        raise HTTPNotFound("This link may not be followed from within Galaxy.")
 
     @web.expose
     def index(self, trans, tool_id=None, workflow_id=None, history_id=None, m_c=None, m_a=None, **kwd):
@@ -79,40 +77,44 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         """
         # directly redirect to oidc provider if 1) enable_oidc is True, 2)
         # there is only one oidc provider, 3) auth_conf.xml has no authenticators
-        if (trans.app.config.enable_oidc
-                and len(trans.app.config.oidc) == 1
-                and len(trans.app.auth_manager.authenticators) == 0
-                and is_logout_redirect is False):
+        if (
+            trans.app.config.enable_oidc
+            and len(trans.app.config.oidc) == 1
+            and len(trans.app.auth_manager.authenticators) == 0
+            and is_logout_redirect is False
+        ):
             provider = next(iter(trans.app.config.oidc.keys()))
             success, message, redirect_uri = trans.app.authnz_manager.authenticate(provider, trans)
             if success:
                 return trans.response.send_redirect(redirect_uri)
-        return self.template(trans, 'login',
-                             redirect=redirect,
-                             # an installation may have it's own welcome_url - show it here if they've set that
-                             welcome_url=web.url_for(controller='root', action='welcome'),
-                             show_welcome_with_login=trans.app.config.show_welcome_with_login)
+        return self.template(
+            trans,
+            "login",
+            redirect=redirect,
+            # an installation may have it's own welcome_url - show it here if they've set that
+            welcome_url=web.url_for(controller="root", action="welcome"),
+            show_welcome_with_login=trans.app.config.show_welcome_with_login,
+        )
 
     # ---- Tool related -----------------------------------------------------
 
     @web.expose
     def display_as(self, trans, id=None, display_app=None, **kwd):
-        """Returns a file in a format that can successfully be displayed in display_app.
-        """
+        """Returns a file in a format that can successfully be displayed in display_app."""
         # TODO: unencoded id
         data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
-        authz_method = 'rbac'
-        if 'authz_method' in kwd:
-            authz_method = kwd['authz_method']
+        authz_method = "rbac"
+        if "authz_method" in kwd:
+            authz_method = kwd["authz_method"]
         if data:
             current_user_roles = trans.get_current_user_roles()
-            if authz_method == 'rbac' and trans.app.security_agent.can_access_dataset(current_user_roles, data):
+            if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(current_user_roles, data):
                 trans.response.set_content_type(data.get_mime())
                 trans.log_event(f"Formatted dataset id {str(id)} for display at {display_app}")
                 return data.as_display_type(display_app, **kwd)
-            elif authz_method == 'display_at' and trans.app.host_security_agent.allow_action(trans.request.remote_addr,
-                                                                                             data.permitted_actions.DATASET_ACCESS,
-                                                                                             dataset=data):
+            elif authz_method == "display_at" and trans.app.host_security_agent.allow_action(
+                trans.request.remote_addr, data.permitted_actions.DATASET_ACCESS, dataset=data
+            ):
                 trans.response.set_content_type(data.get_mime())
                 return data.as_display_type(display_app, **kwd)
             else:
@@ -123,8 +125,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
     # ---- History management -----------------------------------------------
     @web.expose
     def clear_history(self, trans):
-        """Clears the history for a user.
-        """
+        """Clears the history for a user."""
         # TODO: unused? (seems to only be used in TwillTestCase)
         history = trans.get_history()
         for dataset in history.datasets:
@@ -153,9 +154,11 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
             new_history.user_id = user.id
             galaxy_session = trans.get_galaxy_session()
             try:
-                association = trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation) \
-                                              .filter_by(session_id=galaxy_session.id, history_id=new_history.id) \
-                                              .first()
+                association = (
+                    trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation)
+                    .filter_by(session_id=galaxy_session.id, history_id=new_history.id)
+                    .first()
+                )
             except Exception:
                 association = None
             new_history.add_galaxy_session(galaxy_session, association=association)
@@ -164,18 +167,24 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
             if not user_history.datasets:
                 trans.set_history(new_history)
             trans.log_event(f"History imported, id: {str(new_history.id)}, name: '{new_history.name}': ")
-            return trans.show_ok_message("""
+            return trans.show_ok_message(
+                """
                 History "{}" has been imported. Click <a href="{}">here</a>
-                to begin.""".format(new_history.name, web.url_for('/')))
+                to begin.""".format(
+                    new_history.name, web.url_for("/")
+                )
+            )
         elif not user_history.datasets or confirm:
             new_history = import_history.copy()
             new_history.name = f"imported: {new_history.name}"
             new_history.user_id = None
             galaxy_session = trans.get_galaxy_session()
             try:
-                association = trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation) \
-                                              .filter_by(session_id=galaxy_session.id, history_id=new_history.id) \
-                                              .first()
+                association = (
+                    trans.sa_session.query(trans.app.model.GalaxySessionToHistoryAssociation)
+                    .filter_by(session_id=galaxy_session.id, history_id=new_history.id)
+                    .first()
+                )
             except Exception:
                 association = None
             new_history.add_galaxy_session(galaxy_session, association=association)
@@ -183,13 +192,20 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
             trans.sa_session.flush()
             trans.set_history(new_history)
             trans.log_event(f"History imported, id: {str(new_history.id)}, name: '{new_history.name}': ")
-            return trans.show_ok_message("""
+            return trans.show_ok_message(
+                """
                 History "{}" has been imported. Click <a href="{}">here</a>
-                to begin.""".format(new_history.name, web.url_for('/')))
-        return trans.show_warn_message("""
+                to begin.""".format(
+                    new_history.name, web.url_for("/")
+                )
+            )
+        return trans.show_warn_message(
+            """
             Warning! If you import this history, you will lose your current
             history. Click <a href="%s">here</a> to confirm.
-            """ % web.url_for(controller='root', action='history_import', id=id, confirm=True))
+            """
+            % web.url_for(controller="root", action="history_import", id=id, confirm=True)
+        )
 
     @web.expose
     def history_new(self, trans, name=None):
@@ -198,24 +214,32 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         """
         trans.new_history(name=name)
         trans.log_event(f"Created new History, id: {str(trans.history.id)}.")
-        return trans.show_message("New history created", refresh_frames=['history'])
+        return trans.show_message("New history created", refresh_frames=["history"])
 
     @web.expose
-    def history_add_to(self, trans, history_id=None, file_data=None,
-                       name="Data Added to History", info=None, ext="txt", dbkey="?", copy_access_from=None, **kwd):
-        """Adds a POSTed file to a History.
-        """
+    def history_add_to(
+        self,
+        trans,
+        history_id=None,
+        file_data=None,
+        name="Data Added to History",
+        info=None,
+        ext="txt",
+        dbkey="?",
+        copy_access_from=None,
+        **kwd,
+    ):
+        """Adds a POSTed file to a History."""
         # TODO: unencoded id
         try:
             history = trans.sa_session.query(trans.app.model.History).get(history_id)
-            data = trans.app.model.HistoryDatasetAssociation(name=name,
-                                                             info=info,
-                                                             extension=ext,
-                                                             dbkey=dbkey,
-                                                             create_dataset=True,
-                                                             sa_session=trans.sa_session)
+            data = trans.app.model.HistoryDatasetAssociation(
+                name=name, info=info, extension=ext, dbkey=dbkey, create_dataset=True, sa_session=trans.sa_session
+            )
             if copy_access_from:
-                copy_access_from = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(copy_access_from)
+                copy_access_from = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(
+                    copy_access_from
+                )
                 trans.app.security_agent.copy_dataset_permissions(copy_access_from.dataset, data.dataset)
             else:
                 permissions = trans.app.security_agent.history_get_default_permissions(history)
diff --git a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
index 5560b1cc251..df8c74e2c1d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
+++ b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py
@@ -3,7 +3,10 @@ import os
 
 from galaxy import web
 from galaxy.exceptions import RequestParameterInvalidException
-from galaxy.util.path import join, safe_contains
+from galaxy.util.path import (
+    join,
+    safe_contains,
+)
 from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
@@ -16,7 +19,6 @@ def _asset_exists_and_is_safe(repo_path, asset_path):
 
 
 class ShedToolStatic(BaseUIController):
-
     @web.expose
     def index(self, trans, shed, owner, repo, tool, version, image_file):
         """
@@ -30,13 +32,13 @@ class ShedToolStatic(BaseUIController):
         .. image:: some_image.jpg
         .. image:: /deep/some_image.png
         """
-        guid = '/'.join((shed, 'repos', owner, repo, tool, version))
+        guid = "/".join((shed, "repos", owner, repo, tool, version))
         tool = trans.app.toolbox.get_tool(guid)
         repo_path = os.path.abspath(tool._repository_dir)
         found_path = None
 
-        if 'static/images' not in image_file:
-            asset_path = os.path.abspath(join(repo_path, 'static', 'images', image_file))
+        if "static/images" not in image_file:
+            asset_path = os.path.abspath(join(repo_path, "static", "images", image_file))
             if _asset_exists_and_is_safe(repo_path, asset_path):
                 found_path = asset_path
 
@@ -46,11 +48,11 @@ class ShedToolStatic(BaseUIController):
                 found_path = asset_path
 
         if found_path:
-            ext = os.path.splitext(image_file)[-1].lstrip('.')
+            ext = os.path.splitext(image_file)[-1].lstrip(".")
             if ext:
                 mime = trans.app.datatypes_registry.get_mimetype_by_extension(ext)
                 if mime:
                     trans.response.set_content_type(mime)
-            return open(found_path, 'rb')
+            return open(found_path, "rb")
         else:
             raise RequestParameterInvalidException()
diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py
index 5db26c4c4a0..68cb5299814 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tag.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tag.py
@@ -5,16 +5,21 @@ and provides autocomplete support.
 import logging
 
 from sqlalchemy.sql import select
-from sqlalchemy.sql.expression import and_, func
+from sqlalchemy.sql.expression import (
+    and_,
+    func,
+)
 
 from galaxy import web
-from galaxy.webapps.base.controller import BaseUIController, UsesTagsMixin
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    UsesTagsMixin,
+)
 
 log = logging.getLogger(__name__)
 
 
 class TagsController(BaseUIController, UsesTagsMixin):
-
     @web.expose
     @web.require_login("edit item tags")
     def get_tagging_elt_async(self, trans, item_id, item_class, elt_context=""):
@@ -24,13 +29,15 @@ class TagsController(BaseUIController, UsesTagsMixin):
         item = self._get_item(trans, item_class, trans.security.decode_id(item_id))
         if not item:
             return trans.show_error_message(f"No item of class {item_class} with id {item_id} ")
-        return trans.fill_template("/tagging_common.mako",
-                                   tag_type="individual",
-                                   user=trans.user,
-                                   tagged_item=item,
-                                   elt_context=elt_context,
-                                   tag_click_fn="default_tag_click_fn",
-                                   use_toggle_link=False)
+        return trans.fill_template(
+            "/tagging_common.mako",
+            tag_type="individual",
+            user=trans.user,
+            tagged_item=item,
+            elt_context=elt_context,
+            tag_click_fn="default_tag_click_fn",
+            use_toggle_link=False,
+        )
 
     @web.expose
     @web.require_login("add tag to an item")
@@ -88,7 +95,7 @@ class TagsController(BaseUIController, UsesTagsMixin):
             item = self._get_item(trans, item_class, trans.security.decode_id(item_id))
         user = trans.user
         item_class = self.get_class(item_class)
-        q = '' if q is None else q
+        q = "" if q is None else q
         if q.find(":") == -1:
             return self._get_tag_autocomplete_names(trans, q, limit, timestamp, user, item, item_class)
         else:
@@ -107,19 +114,22 @@ class TagsController(BaseUIController, UsesTagsMixin):
             item_class = item.__class__
         item_tag_assoc_class = self.get_tag_handler(trans).get_tag_assoc_class(item_class)
         # Build select statement.
-        cols_to_select = [item_tag_assoc_class.table.c.tag_id, func.count('*')]
+        cols_to_select = [item_tag_assoc_class.table.c.tag_id, func.count("*")]
         from_obj = item_tag_assoc_class.table.join(item_class.table).join(trans.app.model.Tag.table)
-        where_clause = and_(trans.app.model.Tag.table.c.name.like(f"{q}%"),
-                            item_tag_assoc_class.table.c.user_id == user.id)
+        where_clause = and_(
+            trans.app.model.Tag.table.c.name.like(f"{q}%"), item_tag_assoc_class.table.c.user_id == user.id
+        )
         order_by = [func.count("*").desc()]
         group_by = item_tag_assoc_class.table.c.tag_id
         # Do query and get result set.
-        query = select(columns=cols_to_select,
-                       from_obj=from_obj,
-                       whereclause=where_clause,
-                       group_by=group_by,
-                       order_by=order_by,
-                       limit=limit)
+        query = select(
+            columns=cols_to_select,
+            from_obj=from_obj,
+            whereclause=where_clause,
+            group_by=group_by,
+            order_by=order_by,
+            limit=limit,
+        )
         result_set = trans.sa_session.execute(query)
         # Create and return autocomplete data.
         ac_data = "#Header|Your Tags\n"
@@ -153,20 +163,24 @@ class TagsController(BaseUIController, UsesTagsMixin):
             item_class = item.__class__
         item_tag_assoc_class = self.get_tag_handler(trans).get_tag_assoc_class(item_class)
         # Build select statement.
-        cols_to_select = [item_tag_assoc_class.table.c.value, func.count('*')]
+        cols_to_select = [item_tag_assoc_class.table.c.value, func.count("*")]
         from_obj = item_tag_assoc_class.table.join(item_class.table).join(trans.app.model.Tag.table)
-        where_clause = and_(item_tag_assoc_class.table.c.user_id == user.id,
-                            trans.app.model.Tag.table.c.id == tag.id,
-                            item_tag_assoc_class.table.c.value.like(f"{tag_value}%"))
+        where_clause = and_(
+            item_tag_assoc_class.table.c.user_id == user.id,
+            trans.app.model.Tag.table.c.id == tag.id,
+            item_tag_assoc_class.table.c.value.like(f"{tag_value}%"),
+        )
         order_by = [func.count("*").desc(), item_tag_assoc_class.table.c.value]
         group_by = item_tag_assoc_class.table.c.value
         # Do query and get result set.
-        query = select(columns=cols_to_select,
-                       from_obj=from_obj,
-                       whereclause=where_clause,
-                       group_by=group_by,
-                       order_by=order_by,
-                       limit=limit)
+        query = select(
+            columns=cols_to_select,
+            from_obj=from_obj,
+            whereclause=where_clause,
+            group_by=group_by,
+            order_by=order_by,
+            limit=limit,
+        )
         result_set = trans.sa_session.execute(query)
         # Create and return autocomplete data.
         ac_data = f"#Header|Your Values for '{tag_name}'\n"
@@ -181,16 +195,14 @@ class TagsController(BaseUIController, UsesTagsMixin):
         most popular to least popular name.
         """
         # Build select stmt.
-        cols_to_select = [item_tag_assoc_class.table.c.user_tname, func.count('*')]
-        where_clause = and_(item_tag_assoc_class.table.c.user_id == user.id,
-                            item_tag_assoc_class.table.c.tag_id == tag.id)
+        cols_to_select = [item_tag_assoc_class.table.c.user_tname, func.count("*")]
+        where_clause = and_(
+            item_tag_assoc_class.table.c.user_id == user.id, item_tag_assoc_class.table.c.tag_id == tag.id
+        )
         group_by = item_tag_assoc_class.table.c.user_tname
         order_by = [func.count("*").desc()]
         # Do query and get result set.
-        query = select(columns=cols_to_select,
-                       whereclause=where_clause,
-                       group_by=group_by,
-                       order_by=order_by)
+        query = select(columns=cols_to_select, whereclause=where_clause, group_by=group_by, order_by=order_by)
         result_set = trans.sa_session.execute(query)
         user_tag_names = list()
         for row in result_set:
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index 1085c558825..209bee4bff4 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -8,7 +8,10 @@ from markupsafe import escape
 import galaxy.util
 from galaxy import web
 from galaxy.tools import DataSourceTool
-from galaxy.web import error, url_for
+from galaxy.web import (
+    error,
+    url_for,
+)
 from galaxy.webapps.base.controller import BaseUIController
 
 log = logging.getLogger(__name__)
@@ -18,13 +21,13 @@ class ToolRunner(BaseUIController):
 
     # Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back
     @web.expose
-    def biomart(self, trans, tool_id='biomart', **kwd):
+    def biomart(self, trans, tool_id="biomart", **kwd):
         """Catches the tool id and redirects as needed"""
         return self.index(trans, tool_id=tool_id, **kwd)
 
     # test to get hapmap to work, ideally, we could pass tool_id to hapmap biomart and receive it back
     @web.expose
-    def hapmapmart(self, trans, tool_id='hapmapmart', **kwd):
+    def hapmapmart(self, trans, tool_id="hapmapmart", **kwd):
         """Catches the tool id and redirects as needed"""
         return self.index(trans, tool_id=tool_id, **kwd)
 
@@ -34,44 +37,51 @@ class ToolRunner(BaseUIController):
         return self.index(trans, tool_id=tool_id, **kwd)
 
     def __get_tool(self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False):
-        tool_version_select_field, tools, tool = self.get_toolbox().get_tool_components(tool_id, tool_version, get_loaded_tools_by_lineage, set_selected)
+        tool_version_select_field, tools, tool = self.get_toolbox().get_tool_components(
+            tool_id, tool_version, get_loaded_tools_by_lineage, set_selected
+        )
         return tool
 
     @web.expose
     def index(self, trans, tool_id=None, from_noframe=None, **kwd):
         def __tool_404__():
-            log.error('index called with tool id \'%s\' but no such tool exists', tool_id)
-            trans.log_event('Tool id \'%s\' does not exist' % tool_id)
+            log.error("index called with tool id '%s' but no such tool exists", tool_id)
+            trans.log_event("Tool id '%s' does not exist" % tool_id)
             trans.response.status = 404
-            return trans.show_error_message('Tool \'%s\' does not exist.' % (escape(tool_id)))
+            return trans.show_error_message("Tool '%s' does not exist." % (escape(tool_id)))
+
         # tool id not available, redirect to main page
         if tool_id is None:
-            return trans.response.send_redirect(url_for(controller='root', action='welcome'))
+            return trans.response.send_redirect(url_for(controller="root", action="welcome"))
         tool = self.__get_tool(tool_id)
         # tool id is not matching, display an error
         if not tool:
             return __tool_404__()
         if tool.require_login and not trans.user:
-            redirect = url_for(controller='tool_runner', action='index', tool_id=tool_id, **kwd)
-            return trans.response.send_redirect(url_for(controller='user',
-                                                        action='login',
-                                                        cntrller='user',
-                                                        status='info',
-                                                        message='You must be logged in to use this tool.',
-                                                        redirect=redirect))
+            redirect = url_for(controller="tool_runner", action="index", tool_id=tool_id, **kwd)
+            return trans.response.send_redirect(
+                url_for(
+                    controller="user",
+                    action="login",
+                    cntrller="user",
+                    status="info",
+                    message="You must be logged in to use this tool.",
+                    redirect=redirect,
+                )
+            )
         if not tool.allow_user_access(trans.user):
             return __tool_404__()
         # FIXME: Tool class should define behavior
-        if tool.tool_type in ['default', 'interactivetool']:
-            return trans.response.send_redirect(url_for(controller='root', tool_id=tool_id))
+        if tool.tool_type in ["default", "interactivetool"]:
+            return trans.response.send_redirect(url_for(controller="root", tool_id=tool_id))
 
         # execute tool without displaying form (used for datasource tools)
         params = galaxy.util.Params(kwd, sanitize=False)
         # do param translation here, used by datasource tools
         if tool.input_translator:
             tool.input_translator.translate(params)
-        if 'runtool_btn' not in params.__dict__ and 'URL' not in params.__dict__:
-            error('Tool execution through the `tool_runner` requires a `runtool_btn` flag or `URL` parameter.')
+        if "runtool_btn" not in params.__dict__ and "URL" not in params.__dict__:
+            error("Tool execution through the `tool_runner` requires a `runtool_btn` flag or `URL` parameter.")
         # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
         # so make sure to create a new history if we've never had one before.
         history = tool.get_default_history_by_trans(trans, create=True)
@@ -80,8 +90,8 @@ class ToolRunner(BaseUIController):
         except Exception as e:
             error(galaxy.util.unicodify(e))
         if len(params) > 0:
-            trans.log_event(f'Tool params: {str(params)}', tool_id=tool_id)
-        return trans.fill_template('root/tool_runner.mako', **vars)
+            trans.log_event(f"Tool params: {str(params)}", tool_id=tool_id)
+        return trans.fill_template("root/tool_runner.mako", **vars)
 
     @web.expose
     def rerun(self, trans, id=None, job_id=None, **kwd):
@@ -104,7 +114,10 @@ class ToolRunner(BaseUIController):
             # Get the dataset object
             data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(id)
             # only allow rerunning if user is allowed access to the dataset.
-            if not (trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), data.dataset)):
+            if not (
+                trans.user_is_admin
+                or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), data.dataset)
+            ):
                 error("You are not allowed to access this dataset")
             # Get the associated job, if any.
             job = data.creating_job
@@ -137,7 +150,7 @@ class ToolRunner(BaseUIController):
         if isinstance(tool, DataSourceTool):
             link = url_for(tool.action, **tool.get_static_param_values(trans))
         else:
-            link = url_for(controller='tool_runner', tool_id=tool.id)
+            link = url_for(controller="tool_runner", tool_id=tool.id)
         return trans.response.send_redirect(link)
 
     @web.expose
@@ -145,4 +158,4 @@ class ToolRunner(BaseUIController):
         if not redirect_url:
             return trans.show_error_message("Required URL for redirection missing")
         trans.log_event(f"Redirecting to: {redirect_url}")
-        return trans.fill_template('root/redirect.mako', redirect_url=redirect_url)
+        return trans.fill_template("root/redirect.mako", redirect_url=redirect_url)
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 8e6b05b62ff..69fe0b55d6d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -3,7 +3,10 @@ Contains the user interface in the Universe class
 """
 
 import logging
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from urllib.parse import unquote
 
 from markupsafe import escape
@@ -11,22 +14,24 @@ from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.exceptions import Conflict
 from galaxy.managers import users
 from galaxy.queue_worker import send_local_control_task
 from galaxy.security.validate_user_input import (
     validate_email,
-    validate_publicname
+    validate_publicname,
 )
 from galaxy.structured_app import StructuredApp
-from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.web import url_for
+from galaxy.web import (
+    expose_api_anonymous_and_sessionless,
+    url_for,
+)
 from galaxy.webapps.base.controller import (
     BaseUIController,
     CreatesApiKeysMixin,
-    UsesFormDefinitionsMixin
+    UsesFormDefinitionsMixin,
 )
 from ..api import depends
 
@@ -34,7 +39,7 @@ log = logging.getLogger(__name__)
 
 
 def _filtered_registration_params_dict(payload):
-    return {k: v for (k, v) in payload.items() if k in ['email', 'username', 'password', 'confirm', 'subscribe']}
+    return {k: v for (k, v) in payload.items() if k in ["email", "username", "password", "confirm", "subscribe"]}
 
 
 class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
@@ -44,8 +49,15 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
     def __init__(self, app: StructuredApp):
         super().__init__(app)
 
-    def __handle_role_and_group_auto_creation(self, trans, user, roles, auto_create_roles=False,
-                                              auto_create_groups=False, auto_assign_roles_to_groups_only=False):
+    def __handle_role_and_group_auto_creation(
+        self,
+        trans,
+        user,
+        roles,
+        auto_create_roles=False,
+        auto_create_groups=False,
+        auto_assign_roles_to_groups_only=False,
+    ):
         for role_name in roles:
             role = None
             group = None
@@ -56,8 +68,12 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
                 except NoResultFound:
                     # or create it
                     role, num_in_groups = trans.app.security_agent.create_role(
-                        role_name, "Auto created upon user registration", [], [],
-                        create_group_for_role=auto_create_groups)
+                        role_name,
+                        "Auto created upon user registration",
+                        [],
+                        [],
+                        create_group_for_role=auto_create_groups,
+                    )
                     if auto_create_groups:
                         trans.log_event("Created role and group for auto-registered user.")
                     else:
@@ -65,8 +81,11 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
             if auto_create_groups:
                 # only create a group if not existing yet
                 try:
-                    group = self.sa_session.query(trans.app.model.Group).filter(
-                        trans.app.model.Group.name == role_name).first()
+                    group = (
+                        self.sa_session.query(trans.app.model.Group)
+                        .filter(trans.app.model.Group.name == role_name)
+                        .first()
+                    )
                 except NoResultFound:
                     group = self.model.Group(name=role_name)
                     self.sa_session.add(group)
@@ -91,8 +110,9 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         if autoreg["auto_reg"]:
             email = autoreg["email"]
             username = autoreg["username"]
-            message = " ".join((validate_email(trans, email, allow_empty=True),
-                                validate_publicname(trans, username))).rstrip()
+            message = " ".join(
+                (validate_email(trans, email, allow_empty=True), validate_publicname(trans, username))
+            ).rstrip()
             if not message:
                 user = self.user_manager.create(email=email, username=username, password="")
                 if trans.app.config.user_activation_on:
@@ -105,10 +125,13 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
                     trans.log_event("User logged in")
                 if "attributes" in autoreg and "roles" in autoreg["attributes"]:
                     self.__handle_role_and_group_auto_creation(
-                        trans, user, autoreg["attributes"]["roles"],
+                        trans,
+                        user,
+                        autoreg["attributes"]["roles"],
                         auto_create_groups=autoreg["auto_create_groups"],
                         auto_create_roles=autoreg["auto_create_roles"],
-                        auto_assign_roles_to_groups_only=autoreg["auto_assign_roles_to_groups_only"])
+                        auto_assign_roles_to_groups_only=autoreg["auto_assign_roles_to_groups_only"],
+                    )
             else:
                 message = f"Auto-registration failed, contact your local Galaxy administrator. {message}"
         else:
@@ -121,7 +144,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         return self.__validate_login(trans, payload, **kwd)
 
     def __validate_login(self, trans, payload=None, **kwd):
-        '''Handle Galaxy Log in'''
+        """Handle Galaxy Log in"""
         if not payload:
             payload = kwd
         message = trans.check_csrf_token(payload)
@@ -140,7 +163,9 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
             if message:
                 return self.message_exception(trans, message)
         elif user.deleted:
-            message = "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
+            message = (
+                "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
+            )
             if trans.app.config.error_email_to is not None:
                 message += f" Contact: {trans.app.config.error_email_to}."
             return self.message_exception(trans, message, sanitize=False)
@@ -152,8 +177,10 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         elif not trans.app.auth_manager.check_password(user, password):
             return self.message_exception(trans, "Invalid password.")
         elif trans.app.config.user_activation_on and not user.active:  # activation is ON and the user is INACTIVE
-            if (trans.app.config.activation_grace_period != 0):  # grace period is ON
-                if self.is_outside_grace_period(trans, user.create_time):  # User is outside the grace period. Login is disabled and he will have the activation email resent.
+            if trans.app.config.activation_grace_period != 0:  # grace period is ON
+                if self.is_outside_grace_period(
+                    trans, user.create_time
+                ):  # User is outside the grace period. Login is disabled and he will have the activation email resent.
                     message, status = self.resend_activation_email(trans, user.email, user.username)
                     return self.message_exception(trans, message, sanitize=False)
                 else:  # User is within the grace period, let him log in.
@@ -166,7 +193,11 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
             pw_expires = trans.app.config.password_expiration_period
             if pw_expires and user.last_password_change < datetime.today() - pw_expires:
                 # Password is expired, we don't log them in.
-                return {"message": "Your password has expired. Please reset or change it to access Galaxy.", "status": "warning", "expired_user": trans.security.encode_id(user.id)}
+                return {
+                    "message": "Your password has expired. Please reset or change it to access Galaxy.",
+                    "status": "warning",
+                    "expired_user": trans.security.encode_id(user.id),
+                }
             trans.handle_user_login(user)
             trans.log_event("User logged in")
             if pw_expires and user.last_password_change < datetime.today() - timedelta(days=pw_expires.days / 10):
@@ -202,7 +233,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         else:
             message = f"This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator. <a target=\"_top\" href=\"{url_for('/')}\">Return to the home page</a>."
             if trans.app.config.error_email_to is not None:
-                message += f' Error contact: {trans.app.config.error_email_to}.'
+                message += f" Error contact: {trans.app.config.error_email_to}."
         return message, is_activation_sent
 
     def is_outside_grace_period(self, trans, create_time):
@@ -213,7 +244,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         activation_grace_period = trans.app.config.activation_grace_period
         delta = timedelta(hours=int(activation_grace_period))
         time_difference = datetime.utcnow() - create_time
-        return (time_difference > delta or activation_grace_period == 0)
+        return time_difference > delta or activation_grace_period == 0
 
     @web.expose
     @web.json
@@ -226,11 +257,14 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
                 # Queue a quota recalculation (async) task -- this takes a
                 # while sometimes, so we don't want to block on logout.
                 from galaxy.celery.tasks import recalculate_user_disk_usage
+
                 recalculate_user_disk_usage.delay(user_id=trans.user.id)
             else:
-                send_local_control_task(trans.app,
-                                        "recalculate_user_disk_usage",
-                                        kwargs={"user_id": trans.security.encode_id(trans.user.id)})
+                send_local_control_task(
+                    trans.app,
+                    "recalculate_user_disk_usage",
+                    kwargs={"user_id": trans.security.encode_id(trans.user.id)},
+                )
         # Since logging an event requires a session, we'll log prior to ending the session
         trans.log_event("User logged out")
         trans.handle_user_logout(logout_all=logout_all)
@@ -261,30 +295,42 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         Check whether token fits the user and then activate the user's account.
         """
         params = util.Params(kwd, sanitize=False)
-        email = params.get('email', None)
+        email = params.get("email", None)
         if email is not None:
             email = unquote(email)
-        activation_token = params.get('activation_token', None)
+        activation_token = params.get("activation_token", None)
 
         if email is None or activation_token is None:
             #  We don't have the email or activation_token, show error.
-            return trans.show_error_message("You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller="root", action="index")
+            return trans.show_error_message(
+                "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>"
+            ) % web.url_for(controller="root", action="index")
         else:
             # Find the user
-            user = trans.sa_session.query(trans.app.model.User).filter(trans.app.model.User.table.c.email == email).first()
+            user = (
+                trans.sa_session.query(trans.app.model.User).filter(trans.app.model.User.table.c.email == email).first()
+            )
             if not user:
                 # Probably wrong email address
-                return trans.show_error_message("You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller="root", action="index")
+                return trans.show_error_message(
+                    "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>"
+                ) % web.url_for(controller="root", action="index")
             # If the user is active already don't try to activate
             if user.active is True:
-                return trans.show_ok_message("Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
+                return trans.show_ok_message(
+                    "Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>"
+                ) % web.url_for(controller="root", action="index")
             if user.activation_token == activation_token:
                 user.activation_token = None
                 self.user_manager.activate(user)
-                return trans.show_ok_message("Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
+                return trans.show_ok_message(
+                    "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>"
+                ) % web.url_for(controller="root", action="index")
             else:
                 #  Tokens don't match. Activation is denied.
-                return trans.show_error_message("You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
+                return trans.show_error_message(
+                    "You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>"
+                ) % web.url_for(controller="root", action="index")
         return
 
     @expose_api_anonymous_and_sessionless
@@ -319,12 +365,14 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
     def __get_redirect_url(self, redirect):
         if not redirect or redirect == "None":
             return None
-        root_url = url_for('/', qualified=True)
+        root_url = url_for("/", qualified=True)
         # compare urls, to prevent a redirect from pointing (directly) outside of galaxy
         # or to enter a logout/login loop
-        if not util.compare_urls(root_url, redirect, compare_path=False) or util.compare_urls(url_for(controller='user', action='logout', qualified=True), redirect):
-            log.warning('Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: %s', redirect)
+        if not util.compare_urls(root_url, redirect, compare_path=False) or util.compare_urls(
+            url_for(controller="user", action="logout", qualified=True), redirect
+        ):
+            log.warning("Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: %s", redirect)
             redirect = root_url
-        elif util.compare_urls(url_for(controller='user', action='logout', qualified=True), redirect):
+        elif util.compare_urls(url_for(controller="user", action="logout", qualified=True), redirect):
             redirect = root_url
         return redirect
diff --git a/lib/galaxy/webapps/galaxy/controllers/userskeys.py b/lib/galaxy/webapps/galaxy/controllers/userskeys.py
index 422c6f70734..91e6f0d3a6f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py
+++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py
@@ -6,9 +6,12 @@ from sqlalchemy import false
 
 from galaxy import (
     util,
-    web
+    web,
+)
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    UsesFormDefinitionsMixin,
 )
-from galaxy.webapps.base.controller import BaseUIController, UsesFormDefinitionsMixin
 
 
 class User(BaseUIController, UsesFormDefinitionsMixin):
@@ -23,7 +26,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
     @web.require_admin
     def admin_api_keys(self, trans, uid, **kwd):
         params = util.Params(kwd)
-        uid = params.get('uid', uid)
+        uid = params.get("uid", uid)
         new_key = trans.app.model.APIKeys()
         new_key.user_id = trans.security.decode_id(uid)
         new_key.key = trans.app.security.get_new_guid()
@@ -40,13 +43,16 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
     @web.json
     def get_all_users(self, trans):
         users = []
-        for user in trans.sa_session.query(trans.app.model.User) \
-                                    .filter(trans.app.model.User.table.c.deleted == false()) \
-                                    .order_by(trans.app.model.User.table.c.email):
+        for user in (
+            trans.sa_session.query(trans.app.model.User)
+            .filter(trans.app.model.User.table.c.deleted == false())
+            .order_by(trans.app.model.User.table.c.email)
+        ):
             uid = int(user.id)
             userkey = ""
-            for api_user in trans.sa_session.query(trans.app.model.APIKeys) \
-                    .filter(trans.app.model.APIKeys.user_id == uid):
+            for api_user in trans.sa_session.query(trans.app.model.APIKeys).filter(
+                trans.app.model.APIKeys.user_id == uid
+            ):
                 userkey = api_user.key
-            users.append({'uid': trans.security.encode_id(uid), 'email': user.email, 'key': userkey})
+            users.append({"uid": trans.security.encode_id(uid), "email": user.email, "key": userkey})
         return users
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index f7872bd544c..97865af03d6 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -6,7 +6,7 @@ import yaml
 from markupsafe import escape
 from paste.httpexceptions import (
     HTTPBadRequest,
-    HTTPNotFound
+    HTTPNotFound,
 )
 from sqlalchemy import (
     desc,
@@ -15,24 +15,42 @@ from sqlalchemy import (
     text,
     true,
 )
-from sqlalchemy.orm import eagerload, undefer
+from sqlalchemy.orm import (
+    eagerload,
+    undefer,
+)
 
-from galaxy import model, util, web
+from galaxy import (
+    model,
+    util,
+    web,
+)
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.sharable import SlugBuilder
-from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
+from galaxy.model.item_attrs import (
+    UsesAnnotations,
+    UsesItemRatings,
+)
 from galaxy.structured_app import StructuredApp
-from galaxy.util import sanitize_text, unicodify
+from galaxy.util import (
+    sanitize_text,
+    unicodify,
+)
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider
-from galaxy.visualization.genomes import decode_dbkey
-from galaxy.visualization.genomes import GenomeRegion
+from galaxy.visualization.genomes import (
+    decode_dbkey,
+    GenomeRegion,
+)
 from galaxy.visualization.plugins import registry
-from galaxy.web.framework.helpers import grids, time_ago
+from galaxy.web.framework.helpers import (
+    grids,
+    time_ago,
+)
 from galaxy.webapps.base.controller import (
     BaseUIController,
     SharableMixin,
-    UsesVisualizationMixin
+    UsesVisualizationMixin,
 )
 from ..api import depends
 
@@ -43,14 +61,14 @@ log = logging.getLogger(__name__)
 # -- Grids --
 #
 class HistoryDatasetsSelectionGrid(grids.Grid):
-
     class DbKeyColumn(grids.GridColumn):
         def filter(self, trans, user, query, dbkey):
-            """ Filter by dbkey through a raw SQL b/c metadata is a BLOB. """
+            """Filter by dbkey through a raw SQL b/c metadata is a BLOB."""
             dbkey_user, dbkey = decode_dbkey(dbkey)
             dbkey = dbkey.replace("'", "\\'")
-            return query.filter(or_(text(f"metadata like '%\"dbkey\": [\"{dbkey}\"]%'",
-                                         f"metadata like '%\"dbkey\": \"{dbkey}\"%'")))
+            return query.filter(
+                or_(text(f'metadata like \'%"dbkey": ["{dbkey}"]%\'', f'metadata like \'%"dbkey": "{dbkey}"%\''))
+            )
 
     class HistoryColumn(grids.GridColumn):
         def get_value(self, trans, grid, hda):
@@ -71,11 +89,16 @@ class HistoryDatasetsSelectionGrid(grids.Grid):
         grids.TextColumn("Type", key="extension", model_class=model.HistoryDatasetAssociation),
         grids.TextColumn("history_id", key="history_id", model_class=model.HistoryDatasetAssociation, visible=False),
         HistoryColumn("History", key="history", visible=True),
-        DbKeyColumn("Build", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False)
+        DbKeyColumn("Build", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False),
     ]
     columns.append(
-        grids.MulticolFilterColumn("Search name and filetype", cols_to_filter=[columns[1], columns[2]],
-                                   key="free-text-search", visible=False, filterable="standard")
+        grids.MulticolFilterColumn(
+            "Search name and filetype",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def build_initial_query(self, trans, **kwargs):
@@ -84,11 +107,13 @@ class HistoryDatasetsSelectionGrid(grids.Grid):
     def apply_query_filter(self, trans, query, **kwargs):
         if self.available_tracks is None:
             self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
-        return query.filter(model.History.user == trans.user) \
-                    .filter(model.HistoryDatasetAssociation.extension.in_(self.available_tracks)) \
-                    .filter(model.Dataset.state == model.Dataset.states.OK) \
-                    .filter(model.HistoryDatasetAssociation.deleted == false()) \
-                    .filter(model.HistoryDatasetAssociation.visible == true())
+        return (
+            query.filter(model.History.user == trans.user)
+            .filter(model.HistoryDatasetAssociation.extension.in_(self.available_tracks))
+            .filter(model.Dataset.state == model.Dataset.states.OK)
+            .filter(model.HistoryDatasetAssociation.deleted == false())
+            .filter(model.HistoryDatasetAssociation.visible == true())
+        )
 
 
 class LibraryDatasetsSelectionGrid(grids.Grid):
@@ -103,8 +128,13 @@ class LibraryDatasetsSelectionGrid(grids.Grid):
         grids.TextColumn("Type", key="extension", model_class=model.LibraryDatasetDatasetAssociation),
     ]
     columns.append(
-        grids.MulticolFilterColumn("Search name and filetype", cols_to_filter=[columns[1], columns[2]],
-                                   key="free-text-search", visible=False, filterable="standard")
+        grids.MulticolFilterColumn(
+            "Search name and filetype",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def build_initial_query(self, trans, **kwargs):
@@ -113,11 +143,13 @@ class LibraryDatasetsSelectionGrid(grids.Grid):
     def apply_query_filter(self, trans, query, **kwargs):
         if self.available_tracks is None:
             self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
-        return query.filter(model.LibraryDatasetDatasetAssociation.user == trans.user) \
-                    .filter(model.LibraryDatasetDatasetAssociation.extension.in_(self.available_tracks)) \
-                    .filter(model.Dataset.state == model.Dataset.states.OK) \
-                    .filter(model.LibraryDatasetDatasetAssociation.deleted == false()) \
-                    .filter(model.LibraryDatasetDatasetAssociation.visible == true())
+        return (
+            query.filter(model.LibraryDatasetDatasetAssociation.user == trans.user)
+            .filter(model.LibraryDatasetDatasetAssociation.extension.in_(self.available_tracks))
+            .filter(model.Dataset.state == model.Dataset.states.OK)
+            .filter(model.LibraryDatasetDatasetAssociation.deleted == false())
+            .filter(model.LibraryDatasetDatasetAssociation.visible == true())
+        )
 
 
 class TracksterSelectionGrid(grids.Grid):
@@ -129,16 +161,18 @@ class TracksterSelectionGrid(grids.Grid):
     columns = [
         grids.TextColumn("Title", key="title", model_class=model.Visualization, filterable="standard"),
         grids.TextColumn("Build", key="dbkey", model_class=model.Visualization),
-        grids.GridColumn("Last Updated", key="update_time", format=time_ago)
+        grids.GridColumn("Last Updated", key="update_time", format=time_ago),
     ]
 
     def build_initial_query(self, trans, **kwargs):
         return trans.sa_session.query(self.model_class)
 
     def apply_query_filter(self, trans, query, **kwargs):
-        return query.filter(self.model_class.user_id == trans.user.id) \
-                    .filter(self.model_class.deleted == false()) \
-                    .filter(self.model_class.type == "trackster")
+        return (
+            query.filter(self.model_class.user_id == trans.user.id)
+            .filter(self.model_class.deleted == false())
+            .filter(self.model_class.type == "trackster")
+        )
 
 
 class VisualizationListGrid(grids.Grid):
@@ -146,21 +180,21 @@ class VisualizationListGrid(grids.Grid):
         """
         Returns dictionary used to create item link.
         """
-        url_kwargs = dict(controller='visualization', id=item.id)
+        url_kwargs = dict(controller="visualization", id=item.id)
         # TODO: hack to build link to saved visualization - need trans in this function instead in order to do
         # link_data = trans.app.visualizations_registry.get_visualizations( trans, item )
         if item.type in registry.VisualizationsRegistry.BUILT_IN_VISUALIZATIONS:
-            url_kwargs['action'] = item.type
+            url_kwargs["action"] = item.type
         else:
-            url_kwargs['__route_name__'] = 'saved_visualization'
-            url_kwargs['visualization_name'] = item.type
-            url_kwargs['action'] = 'saved'
+            url_kwargs["__route_name__"] = "saved_visualization"
+            url_kwargs["visualization_name"] = item.type
+            url_kwargs["action"] = "saved"
         return url_kwargs
 
     def get_display_name(self, trans, item):
         if trans.app.visualizations_registry and item.type in trans.app.visualizations_registry.plugins:
             plugin = trans.app.visualizations_registry.plugins[item.type]
-            return plugin.config.get('name', item.type)
+            return plugin.config.get("name", item.type)
         return item.type
 
     # Grid definition
@@ -170,9 +204,15 @@ class VisualizationListGrid(grids.Grid):
     default_filter = dict(title="All", deleted="False", tags="All", sharing="All")
     columns = [
         grids.TextColumn("Title", key="title", attach_popup=True, link=get_url_args),
-        grids.TextColumn("Type", method='get_display_name'),
+        grids.TextColumn("Type", method="get_display_name"),
         grids.TextColumn("Build", key="dbkey"),
-        grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid"),
+        grids.IndividualTagsColumn(
+            "Tags",
+            key="tags",
+            model_tag_association_class=model.VisualizationTagAssociation,
+            filterable="advanced",
+            grid_name="VisualizationListGrid",
+        ),
         grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False),
         grids.GridColumn("Created", key="create_time", format=time_ago),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
@@ -181,14 +221,28 @@ class VisualizationListGrid(grids.Grid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[2]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
     operations = [
         grids.GridOperation("Open", allow_multiple=False, url_args=get_url_args),
-        grids.GridOperation("Edit Attributes", allow_multiple=False, url_args=dict(controller="", action='visualizations/edit')),
+        grids.GridOperation(
+            "Edit Attributes", allow_multiple=False, url_args=dict(controller="", action="visualizations/edit")
+        ),
         grids.GridOperation("Copy", allow_multiple=False, condition=(lambda item: not item.deleted)),
-        grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="visualizations/sharing")),
-        grids.GridOperation("Delete", condition=(lambda item: not item.deleted), confirm="Are you sure you want to delete this visualization?"),
+        grids.GridOperation(
+            "Share or Publish",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            url_args=dict(controller="", action="visualizations/sharing"),
+        ),
+        grids.GridOperation(
+            "Delete",
+            condition=(lambda item: not item.deleted),
+            confirm="Are you sure you want to delete this visualization?",
+        ),
     ]
 
     def apply_query_filter(self, trans, query, **kwargs):
@@ -204,29 +258,48 @@ class VisualizationAllPublishedGrid(grids.Grid):
     default_filter = dict(title="All", username="All")
     columns = [
         grids.PublicURLColumn("Title", key="title", filterable="advanced"),
-        grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced"),
+        grids.OwnerAnnotationColumn(
+            "Annotation",
+            key="annotation",
+            model_annotation_association_class=model.VisualizationAnnotationAssociation,
+            filterable="advanced",
+        ),
         grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"),
         grids.CommunityRatingColumn("Community Rating", key="rating"),
-        grids.CommunityTagsColumn("Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid"),
-        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
+        grids.CommunityTagsColumn(
+            "Community Tags",
+            key="tags",
+            model_tag_association_class=model.VisualizationTagAssociation,
+            filterable="advanced",
+            grid_name="VisualizationAllPublishedGrid",
+        ),
+        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago),
     ]
     columns.append(
         grids.MulticolFilterColumn(
             "Search title, annotation, owner, and tags",
             cols_to_filter=[columns[0], columns[1], columns[2], columns[4]],
-            key="free-text-search", visible=False, filterable="standard")
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
     )
 
     def build_initial_query(self, trans, **kwargs):
         # See optimization description comments and TODO for tags in matching public histories query.
-        return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
+        return (
+            trans.sa_session.query(self.model_class)
+            .join("user")
+            .options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
+        )
 
     def apply_query_filter(self, trans, query, **kwargs):
         return query.filter(self.model_class.deleted == false()).filter(self.model_class.published == true())
 
 
-class VisualizationController(BaseUIController, SharableMixin, UsesVisualizationMixin,
-                              UsesAnnotations, UsesItemRatings):
+class VisualizationController(
+    BaseUIController, SharableMixin, UsesVisualizationMixin, UsesAnnotations, UsesItemRatings
+):
     _visualization_list_grid = VisualizationListGrid()
     _published_list_grid = VisualizationAllPublishedGrid()
     _history_datasets_grid = HistoryDatasetsSelectionGrid()
@@ -254,7 +327,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.require_login("see a history's datasets that can added to this visualization")
     def list_history_datasets(self, trans, **kwargs):
         """List a history's datasets that can be added to a visualization."""
-        kwargs['show_item_checkboxes'] = 'True'
+        kwargs["show_item_checkboxes"] = "True"
         return self._history_datasets_grid(trans, **kwargs)
 
     @web.expose
@@ -262,7 +335,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.require_login("see a history's datasets that can added to this visualization")
     def list_library_datasets(self, trans, **kwargs):
         """List a library's datasets that can be added to a visualization."""
-        kwargs['show_item_checkboxes'] = 'True'
+        kwargs["show_item_checkboxes"] = "True"
         return self._library_datasets_grid(trans, **kwargs)
 
     @web.expose
@@ -274,18 +347,18 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.json
     def list_published(self, trans, *args, **kwargs):
         grid = self._published_list_grid(trans, **kwargs)
-        grid['shared_by_others'] = self._get_shared(trans)
+        grid["shared_by_others"] = self._get_shared(trans)
         return grid
 
     @web.legacy_expose_api
     @web.require_login("use Galaxy visualizations", use_panels=True)
     def list(self, trans, **kwargs):
-        message = kwargs.get('message')
-        status = kwargs.get('status')
-        if 'operation' in kwargs and 'id' in kwargs:
+        message = kwargs.get("message")
+        status = kwargs.get("status")
+        if "operation" in kwargs and "id" in kwargs:
             session = trans.sa_session
-            operation = kwargs['operation'].lower()
-            ids = util.listify(kwargs['id'])
+            operation = kwargs["operation"].lower()
+            ids = util.listify(kwargs["id"])
             for id in ids:
                 item = session.query(model.Visualization).get(self.decode_id(id))
                 if operation == "delete":
@@ -293,26 +366,28 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
                 if operation == "copy":
                     self.copy(trans, **kwargs)
             session.flush()
-        kwargs['embedded'] = True
+        kwargs["embedded"] = True
         if message and status:
-            kwargs['message'] = sanitize_text(message)
-            kwargs['status'] = status
+            kwargs["message"] = sanitize_text(message)
+            kwargs["status"] = status
         grid = self._visualization_list_grid(trans, **kwargs)
-        grid['shared_by_others'] = self._get_shared(trans)
+        grid["shared_by_others"] = self._get_shared(trans)
         return grid
 
     def _get_shared(self, trans):
         """Identify shared visualizations"""
-        shared_by_others = trans.sa_session \
-            .query(model.VisualizationUserShareAssociation) \
-            .filter_by(user=trans.get_user()) \
-            .join(model.Visualization.table) \
-            .filter(model.Visualization.deleted == false()) \
-            .order_by(desc(model.Visualization.update_time)) \
+        shared_by_others = (
+            trans.sa_session.query(model.VisualizationUserShareAssociation)
+            .filter_by(user=trans.get_user())
+            .join(model.Visualization.table)
+            .filter(model.Visualization.deleted == false())
+            .order_by(desc(model.Visualization.update_time))
             .all()
-        return [{'username': v.visualization.user.username,
-                 'slug': v.visualization.slug,
-                 'title': v.visualization.title} for v in shared_by_others]
+        )
+        return [
+            {"username": v.visualization.user.username, "slug": v.visualization.slug, "title": v.visualization.title}
+            for v in shared_by_others
+        ]
 
     #
     # -- Functions for operating on visualizations. --
@@ -321,7 +396,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.expose
     @web.require_login("use Galaxy visualizations", use_panels=True)
     def index(self, trans, *args, **kwargs):
-        """ Lists user's saved visualizations. """
+        """Lists user's saved visualizations."""
         return self.list(trans, *args, **kwargs)
 
     @web.expose
@@ -329,7 +404,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     def copy(self, trans, id, **kwargs):
         visualization = self.get_visualization(trans, id, check_ownership=False)
         user = trans.get_user()
-        owner = (visualization.user == user)
+        owner = visualization.user == user
         new_title = f"Copy of '{visualization.title}'"
         if not owner:
             new_title += f" shared by {visualization.user.email}"
@@ -348,11 +423,11 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.expose
     @web.require_login("use Galaxy visualizations")
     def set_accessible_async(self, trans, id=None, accessible=False):
-        """ Set visualization's importable attribute and slug. """
+        """Set visualization's importable attribute and slug."""
         visualization = self.get_visualization(trans, id)
 
         # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
-        importable = accessible in ['True', 'true', 't', 'T']
+        importable = accessible in ["True", "true", "t", "T"]
         if visualization and visualization.importable != importable:
             if importable:
                 self._make_item_accessible(trans.sa_session, visualization)
@@ -366,7 +441,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.require_login("rate items")
     @web.json
     def rate_async(self, trans, id, rating):
-        """ Rate a visualization asynchronously and return updated community data. """
+        """Rate a visualization asynchronously and return updated community data."""
 
         visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
         if not visualization:
@@ -380,7 +455,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
     @web.expose
     @web.require_login("share Galaxy visualizations")
     def imp(self, trans, id):
-        """ Import a visualization into user's workspace. """
+        """Import a visualization into user's workspace."""
         # Set referer message.
         referer = trans.request.referer
         if referer and not referer.startswith(f"{trans.request.application_url}{web.url_for('/login')}"):
@@ -392,9 +467,15 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         session = trans.sa_session
         visualization = self.get_visualization(trans, id, check_ownership=False)
         if visualization.importable is False:
-            return trans.show_error_message(f"The owner of this visualization has disabled imports via this link.<br>You can {referer_message}", use_panels=True)
+            return trans.show_error_message(
+                f"The owner of this visualization has disabled imports via this link.<br>You can {referer_message}",
+                use_panels=True,
+            )
         elif visualization.deleted:
-            return trans.show_error_message(f"You can't import this visualization because it has been deleted.<br>You can {referer_message}", use_panels=True)
+            return trans.show_error_message(
+                f"You can't import this visualization because it has been deleted.<br>You can {referer_message}",
+                use_panels=True,
+            )
         else:
             # Create imported visualization via copy.
             #   TODO: need to handle custom db keys.
@@ -409,16 +490,20 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
             # Redirect to load galaxy frames.
             return trans.show_ok_message(
                 message="""Visualization "%s" has been imported. <br>You can <a href="%s">start using this visualization</a> or %s."""
-                % (visualization.title, web.url_for('/visualizations/list'), referer_message), use_panels=True)
+                % (visualization.title, web.url_for("/visualizations/list"), referer_message),
+                use_panels=True,
+            )
 
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug):
-        """ Display visualization based on a username and slug. """
+        """Display visualization based on a username and slug."""
 
         # Get visualization.
         session = trans.sa_session
         user = session.query(model.User).filter_by(username=username).first()
-        visualization = trans.sa_session.query(model.Visualization).filter_by(user=user, slug=slug, deleted=False).first()
+        visualization = (
+            trans.sa_session.query(model.Visualization).filter_by(user=user, slug=slug, deleted=False).first()
+        )
         if visualization is None:
             raise web.httpexceptions.HTTPNotFound()
 
@@ -436,38 +521,57 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, visualization)
 
         # Fork to template based on visualization.type (registry or builtin).
-        if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins)
-                and (visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
+        if (trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins) and (
+            visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS
+        ):
             # if a registry visualization, load a version of display.mako that will load the vis into an iframe :(
             # TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way
             # TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved')
             encoded_visualization_id = trans.security.encode_id(visualization.id)
-            return trans.fill_template_mako('visualization/display_in_frame.mako',
-                                            item=visualization, encoded_visualization_id=encoded_visualization_id,
-                                            user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings,
-                                            content_only=True)
+            return trans.fill_template_mako(
+                "visualization/display_in_frame.mako",
+                item=visualization,
+                encoded_visualization_id=encoded_visualization_id,
+                user_item_rating=user_item_rating,
+                ave_item_rating=ave_item_rating,
+                num_ratings=num_ratings,
+                content_only=True,
+            )
 
         visualization_config = self.get_visualization_config(trans, visualization)
-        return trans.fill_template_mako("visualization/display.mako", item=visualization, item_data=visualization_config,
-                                        user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings,
-                                        content_only=True)
+        return trans.fill_template_mako(
+            "visualization/display.mako",
+            item=visualization,
+            item_data=visualization_config,
+            user_item_rating=user_item_rating,
+            ave_item_rating=ave_item_rating,
+            num_ratings=num_ratings,
+            content_only=True,
+        )
 
     @web.expose
     @web.json
     @web.require_login("get item name and link")
     def get_name_and_link_async(self, trans, id=None):
-        """ Returns visualization's name and link. """
+        """Returns visualization's name and link."""
         visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
 
         if self.slug_builder.create_item_slug(trans.sa_session, visualization):
             trans.sa_session.flush()
-        return_dict = {"name": visualization.title,
-                       "link": web.url_for(controller='visualization', action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug)}
+        return_dict = {
+            "name": visualization.title,
+            "link": web.url_for(
+                controller="visualization",
+                action="display_by_username_and_slug",
+                username=visualization.user.username,
+                slug=visualization.slug,
+            ),
+        }
         return return_dict
 
     @web.expose
     def get_item_content_async(self, trans, id):
-        """ Returns item content in HTML format. """
+        """Returns item content in HTML format."""
 
         # Get visualization, making sure it's accessible.
         visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
@@ -476,8 +580,13 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
 
         # Return content.
         visualization_config = self.get_visualization_config(trans, visualization)
-        return trans.fill_template_mako("visualization/item_content.mako", encoded_id=trans.security.encode_id(visualization.id),
-                                        item=visualization, item_data=visualization_config, content_only=True)
+        return trans.fill_template_mako(
+            "visualization/item_content.mako",
+            encoded_id=trans.security.encode_id(visualization.id),
+            item=visualization,
+            item_data=visualization_config,
+            content_only=True,
+        )
 
     @web.json
     def save(self, trans, vis_json=None, type=None, id=None, title=None, dbkey=None, annotation=None):
@@ -487,11 +596,11 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         """
         # Get visualization attributes from kwargs or from config.
         vis_config = loads(vis_json)
-        vis_type = type or vis_config['type']
-        vis_id = id or vis_config.get('id', None)
-        vis_title = title or vis_config.get('title', None)
-        vis_dbkey = dbkey or vis_config.get('dbkey', None)
-        vis_annotation = annotation or vis_config.get('annotation', None)
+        vis_type = type or vis_config["type"]
+        vis_id = id or vis_config.get("id", None)
+        vis_title = title or vis_config.get("title", None)
+        vis_dbkey = dbkey or vis_config.get("dbkey", None)
+        vis_annotation = annotation or vis_config.get("annotation", None)
         return self.save_visualization(trans, vis_config, vis_type, vis_id, vis_title, vis_dbkey, vis_annotation)
 
     @web.legacy_expose_api
@@ -500,53 +609,61 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         """
         Edit a visualization's attributes.
         """
-        id = kwd.get('id')
+        id = kwd.get("id")
         if not id:
-            return self.message_exception(trans, 'No visualization id received for editing.')
+            return self.message_exception(trans, "No visualization id received for editing.")
         trans_user = trans.get_user()
         v = self.get_visualization(trans, id, check_ownership=True)
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             if v.slug is None:
                 self.slug_builder.create_item_slug(trans.sa_session, v)
             return {
-                'title': 'Edit visualization attributes',
-                'inputs': [{
-                    'name': 'title',
-                    'label': 'Name',
-                    'value': v.title
-                }, {
-                    'name': 'slug',
-                    'label': 'Identifier',
-                    'value': v.slug,
-                    'help': 'A unique identifier that will be used for public links to this visualization. This field can only contain lowercase letters, numbers, and dashes (-).'
-                }, {
-                    'name': 'dbkey',
-                    'label': 'Build',
-                    'type': 'select',
-                    'optional': True,
-                    'value': v.dbkey,
-                    'options': trans.app.genomes.get_dbkeys(trans_user, chrom_info=True),
-                    'help': 'Parameter to associate your visualization with a database key.'
-                }, {
-                    'name': 'annotation',
-                    'label': 'Annotation',
-                    'value': self.get_item_annotation_str(trans.sa_session, trans.user, v),
-                    'help': 'A description of the visualization. The annotation is shown alongside published visualizations.'
-                }]
+                "title": "Edit visualization attributes",
+                "inputs": [
+                    {"name": "title", "label": "Name", "value": v.title},
+                    {
+                        "name": "slug",
+                        "label": "Identifier",
+                        "value": v.slug,
+                        "help": "A unique identifier that will be used for public links to this visualization. This field can only contain lowercase letters, numbers, and dashes (-).",
+                    },
+                    {
+                        "name": "dbkey",
+                        "label": "Build",
+                        "type": "select",
+                        "optional": True,
+                        "value": v.dbkey,
+                        "options": trans.app.genomes.get_dbkeys(trans_user, chrom_info=True),
+                        "help": "Parameter to associate your visualization with a database key.",
+                    },
+                    {
+                        "name": "annotation",
+                        "label": "Annotation",
+                        "value": self.get_item_annotation_str(trans.sa_session, trans.user, v),
+                        "help": "A description of the visualization. The annotation is shown alongside published visualizations.",
+                    },
+                ],
             }
         else:
-            v_title = payload.get('title')
-            v_slug = payload.get('slug')
-            v_dbkey = payload.get('dbkey')
-            v_annotation = payload.get('annotation')
+            v_title = payload.get("title")
+            v_slug = payload.get("slug")
+            v_dbkey = payload.get("dbkey")
+            v_annotation = payload.get("annotation")
             if not v_title:
-                return self.message_exception(trans, 'Please provide a visualization name is required.')
+                return self.message_exception(trans, "Please provide a visualization name is required.")
             elif not v_slug:
-                return self.message_exception(trans, 'Please provide a unique identifier.')
+                return self.message_exception(trans, "Please provide a unique identifier.")
             elif not self._is_valid_slug(v_slug):
-                return self.message_exception(trans, 'Visualization identifier can only contain lowercase letters, numbers, and dashes (-).')
-            elif v_slug != v.slug and trans.sa_session.query(model.Visualization).filter_by(user=v.user, slug=v_slug, deleted=False).first():
-                return self.message_exception(trans, 'Visualization id must be unique.')
+                return self.message_exception(
+                    trans, "Visualization identifier can only contain lowercase letters, numbers, and dashes (-)."
+                )
+            elif (
+                v_slug != v.slug
+                and trans.sa_session.query(model.Visualization)
+                .filter_by(user=v.user, slug=v_slug, deleted=False)
+                .first()
+            ):
+                return self.message_exception(trans, "Visualization id must be unique.")
             else:
                 v.title = v_title
                 v.slug = v_slug
@@ -556,7 +673,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
                     self.add_item_annotation(trans.sa_session, trans_user, v, v_annotation)
                 trans.sa_session.add(v)
                 trans.sa_session.flush()
-            return {'message': 'Attributes of \'%s\' successfully saved.' % v.title, 'status': 'success'}
+            return {"message": "Attributes of '%s' successfully saved." % v.title, "status": "success"}
 
     # ------------------------- registry.
     @web.expose
@@ -582,20 +699,23 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         :raises HTTPNotFound: if visualization_name isn't a registered plugin.
         """
         if not trans.app.visualizations_registry:
-            raise HTTPNotFound('No visualization registry (possibly disabled in galaxy.ini)')
+            raise HTTPNotFound("No visualization registry (possibly disabled in galaxy.ini)")
         return trans.app.visualizations_registry.get_plugin(visualization_name)
 
     def _handle_plugin_error(self, trans, visualization_name, exception):
         """
         Log, raise if debugging; log and show html message if not.
         """
-        log.exception('error rendering visualization (%s)', visualization_name)
+        log.exception("error rendering visualization (%s)", visualization_name)
         if trans.debug:
             raise exception
         return trans.show_error_message(
             "There was an error rendering the visualization. "
             + "Contact your Galaxy administrator if the problem persists."
-            + "<br/>Details: " + unicodify(exception), use_panels=False)
+            + "<br/>Details: "
+            + unicodify(exception),
+            use_panels=False,
+        )
 
     @web.expose
     @web.require_login("use Galaxy visualizations", use_panels=True)
@@ -604,17 +724,17 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         Save (on POST) or load (on GET) a visualization then render.
         """
         # TODO: consider merging saved and render at this point (could break saved URLs, tho)
-        if trans.request.method == 'POST':
+        if trans.request.method == "POST":
             self._POST_to_saved(trans, id=id, revision=revision, type=type, config=config, title=title, **kwargs)
 
         # check the id and load the saved visualization
         if id is None:
-            return HTTPBadRequest('A valid visualization id is required to load a visualization')
+            return HTTPBadRequest("A valid visualization id is required to load a visualization")
         visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
 
         # re-add title to kwargs for passing to render
         if title:
-            kwargs['title'] = title
+            kwargs["title"] = title
         plugin = self._get_plugin_from_registry(trans, visualization.type)
         try:
             return plugin.render_saved(visualization, trans=trans, **kwargs)
@@ -628,11 +748,11 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
 
         Uses POST/redirect/GET after a successful save, redirecting to GET.
         """
-        DEFAULT_VISUALIZATION_NAME = 'Unnamed Visualization'
+        DEFAULT_VISUALIZATION_NAME = "Unnamed Visualization"
 
         # post to saved in order to save a visualization
         if type is None or config is None:
-            return HTTPBadRequest('A visualization type and config are required to save a visualization')
+            return HTTPBadRequest("A visualization type and config are required to save a visualization")
         if isinstance(config, str):
             config = loads(config)
         title = title or DEFAULT_VISUALIZATION_NAME
@@ -647,7 +767,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         returned = self.save_visualization(trans, config, type, id, title)
 
         # redirect to GET to prevent annoying 'Do you want to post again?' dialog on page reload
-        render_url = web.url_for(controller='visualization', action='saved', id=returned.get('vis_id'))
+        render_url = web.url_for(controller="visualization", action="saved", id=returned.get("vis_id"))
         return trans.response.send_redirect(render_url)
 
     #
@@ -677,35 +797,31 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
                 decoded_id = self.decode_id(new_dataset_id)
                 hda = self.hda_manager.get_owned(decoded_id, trans.user, current_history=trans.user)
                 dbkey = hda.dbkey
-                if dbkey == '?':
+                if dbkey == "?":
                     dbkey = kwargs.get("dbkey", None)
 
             # save database key
-            app['default_dbkey'] = dbkey
+            app["default_dbkey"] = dbkey
         else:
             # load saved visualization
             vis = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
-            app['viz_config'] = self.get_visualization_config(trans, vis)
+            app["viz_config"] = self.get_visualization_config(trans, vis)
 
         # backup id
-        app['id'] = id
+        app["id"] = id
 
         # add dataset id
-        app['add_dataset'] = new_dataset_id
+        app["add_dataset"] = new_dataset_id
 
         # check for gene region
         gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
 
         # update gene region of saved visualization if user parses a new gene region in the url
         if gene_region.chrom is not None:
-            app['gene_region'] = {
-                'chrom': gene_region.chrom,
-                'start': gene_region.start,
-                'end': gene_region.end
-            }
+            app["gene_region"] = {"chrom": gene_region.chrom, "start": gene_region.start, "end": gene_region.end}
 
         # fill template
-        return trans.fill_template('galaxy.panels.mako', config={'right_panel': True, 'app': app, 'bundle': 'extended'})
+        return trans.fill_template("galaxy.panels.mako", config={"right_panel": True, "app": app, "bundle": "extended"})
 
     @web.expose
     def circster(self, trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None):
@@ -728,11 +844,14 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
             if not dbkey:
                 # If dbkey not specified, use dataset's dbkey.
                 dbkey = dataset.dbkey
-                if not dbkey or dbkey == '?':
+                if not dbkey or dbkey == "?":
                     # Circster requires a valid dbkey.
-                    return trans.show_error_message("You must set the dataset's dbkey to view it. You can set "
-                                                    "a dataset's dbkey by clicking on the pencil icon and editing "
-                                                    "its attributes.", use_panels=True)
+                    return trans.show_error_message(
+                        "You must set the dataset's dbkey to view it. You can set "
+                        "a dataset's dbkey by clicking on the pencil icon and editing "
+                        "its attributes.",
+                        use_panels=True,
+                    )
 
             vis = self.create_visualization(trans, type="genome", dbkey=dbkey, save=False)
 
@@ -743,31 +862,27 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
 
         # Add dataset if specified.
         if dataset:
-            viz_config['tracks'].append(self.get_new_track_config(trans, dataset))
+            viz_config["tracks"].append(self.get_new_track_config(trans, dataset))
 
         # Get genome info.
         chroms_info = self.app.genomes.chroms(trans, dbkey=dbkey)
-        genome = {'dbkey': dbkey, 'chroms_info': chroms_info}
+        genome = {"dbkey": dbkey, "chroms_info": chroms_info}
 
         # Add genome-wide data to each track in viz.
-        tracks = viz_config.get('tracks', [])
+        tracks = viz_config.get("tracks", [])
         for track in tracks:
-            dataset_dict = track['dataset']
-            dataset = self.get_hda_or_ldda(trans, dataset_dict['hda_ldda'], dataset_dict['id'])
+            dataset_dict = track["dataset"]
+            dataset = self.get_hda_or_ldda(trans, dataset_dict["hda_ldda"], dataset_dict["id"])
 
             genome_data = self._get_genome_data(trans, dataset, dbkey)
             if not isinstance(genome_data, str):
-                track['preloaded_data'] = genome_data
+                track["preloaded_data"] = genome_data
 
         # define app configuration for generic mako template
-        app = {
-            'jscript': "circster",
-            'viz_config': viz_config,
-            'genome': genome
-        }
+        app = {"jscript": "circster", "viz_config": viz_config, "genome": genome}
 
         # fill template
-        return trans.fill_template('galaxy.panels.mako', config={'app': app, 'bundle': 'extended'})
+        return trans.fill_template("galaxy.panels.mako", config={"app": app, "bundle": "extended"})
 
     @web.expose
     def sweepster(self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None):
@@ -776,7 +891,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         get the visualization with the given id; otherwise, create a new visualization using
         a given dataset and regions.
         """
-        regions = regions or '{}'
+        regions = regions or "{}"
         # Need to create history if necessary in order to create tool form.
         trans.get_history(most_recent=True, create=True)
 
@@ -784,22 +899,18 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
             # Loading a shared visualization.
             viz = self.get_visualization(trans, id)
             viz_config = self.get_visualization_config(trans, viz)
-            decoded_id = self.decode_id(viz_config['dataset_id'])
+            decoded_id = self.decode_id(viz_config["dataset_id"])
             dataset = self.hda_manager.get_owned(decoded_id, trans.user, current_history=trans.history)
         else:
             # Loading new visualization.
             dataset = self.get_hda_or_ldda(trans, hda_ldda, dataset_id)
             job = self.hda_manager.creating_job(dataset)
-            viz_config = {
-                'dataset_id': dataset_id,
-                'tool_id': job.tool_id,
-                'regions': loads(regions)
-            }
+            viz_config = {"dataset_id": dataset_id, "tool_id": job.tool_id, "regions": loads(regions)}
 
         # Add tool, dataset attributes to config based on id.
-        tool = trans.app.toolbox.get_tool(viz_config['tool_id'])
-        viz_config['tool'] = tool.to_dict(trans, io_details=True)
-        viz_config['dataset'] = trans.security.encode_dict_ids(dataset.to_dict())
+        tool = trans.app.toolbox.get_tool(viz_config["tool_id"])
+        viz_config["tool"] = tool.to_dict(trans, io_details=True)
+        viz_config["dataset"] = trans.security.encode_dict_ids(dataset.to_dict())
 
         return trans.fill_template_mako("visualization/sweepster.mako", config=viz_config)
 
@@ -815,7 +926,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         if id:
             visualization = self.get_visualization(trans, id)
             config = self.get_visualization_config(trans, visualization)
-            dataset_id = config.get('dataset_id', None)
+            dataset_id = config.get("dataset_id", None)
 
         # get the hda if we can, then its data using the phyloviz parsers
         if dataset_id:
@@ -831,18 +942,18 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         # ensure at least a default configuration (gen. an new/unsaved visualization)
         if not config:
             config = {
-                'dataset_id': dataset_id,
-                'title': hda.display_name(),
-                'ext': hda.datatype.file_ext,
-                'treeIndex': tree_index,
-                'saved_visualization': False
+                "dataset_id": dataset_id,
+                "title": hda.display_name(),
+                "ext": hda.datatype.file_ext,
+                "treeIndex": tree_index,
+                "saved_visualization": False,
             }
         return trans.fill_template_mako("visualization/phyloviz.mako", data=data, config=config)
 
     @web.expose
     @web.require_login("run Galaxy Interactive Environments")
     def gie_list(self, trans, **kwargs):
-        if not hasattr(self, 'gie_image_map'):
+        if not hasattr(self, "gie_image_map"):
             self.gie_image_map = {}
 
             for gie_dir in self.app.config.gie_dirs:
@@ -856,10 +967,10 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
                     if not os.path.exists(self._gie_config_dir(gie_path)):
                         continue
 
-                    if os.path.exists(self._gie_config_dir(gie_path, 'allowed_images.yml')):
-                        image_file = self._gie_config_dir(gie_path, 'allowed_images.yml')
-                    elif os.path.exists(self._gie_config_dir(gie_path, 'allowed_images.yml.sample')):
-                        image_file = self._gie_config_dir(gie_path, 'allowed_images.yml.sample')
+                    if os.path.exists(self._gie_config_dir(gie_path, "allowed_images.yml")):
+                        image_file = self._gie_config_dir(gie_path, "allowed_images.yml")
+                    elif os.path.exists(self._gie_config_dir(gie_path, "allowed_images.yml.sample")):
+                        image_file = self._gie_config_dir(gie_path, "allowed_images.yml.sample")
                     else:
                         continue
 
@@ -873,7 +984,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         )
 
     def _gie_config_dir(self, gie_path, *args):
-        nargs = [gie_path, 'config']
+        nargs = [gie_path, "config"]
         if len(args) > 0:
             nargs += args
         return os.path.join(*nargs)
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index f82f8da245e..43160e314fe 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -5,14 +5,22 @@ from html.parser import HTMLParser
 from http.client import HTTPConnection
 
 from markupsafe import escape
-from sqlalchemy import and_, desc
-from sqlalchemy.orm import eagerload, joinedload, lazyload, undefer
+from sqlalchemy import (
+    and_,
+    desc,
+)
+from sqlalchemy.orm import (
+    eagerload,
+    joinedload,
+    lazyload,
+    undefer,
+)
 from sqlalchemy.sql import expression
 
 from galaxy import (
     model,
     util,
-    web
+    web,
 )
 from galaxy.managers.sharable import SlugBuilder
 from galaxy.managers.workflows import (
@@ -24,10 +32,13 @@ from galaxy.security.validate_user_input import validate_publicname
 from galaxy.tools.parameters.basic import workflow_building_modes
 from galaxy.util import (
     FILENAME_VALID_CHARS,
-    unicodify
+    unicodify,
 )
 from galaxy.util.sanitize_html import sanitize_html
-from galaxy.web import error, url_for
+from galaxy.web import (
+    error,
+    url_for,
+)
 from galaxy.web.framework.helpers import (
     grids,
     time_ago,
@@ -35,26 +46,25 @@ from galaxy.web.framework.helpers import (
 from galaxy.webapps.base.controller import (
     BaseUIController,
     SharableMixin,
-    UsesStoredWorkflowMixin
+    UsesStoredWorkflowMixin,
 )
 from galaxy.workflow.extract import (
     extract_workflow,
-    summarize
+    summarize,
 )
 from galaxy.workflow.modules import (
     load_module_sections,
-    module_factory
+    module_factory,
 )
 from galaxy.workflow.render import (
     STANDALONE_SVG_TEMPLATE,
-    WorkflowCanvas
+    WorkflowCanvas,
 )
 
 log = logging.getLogger(__name__)
 
 
 class StoredWorkflowListGrid(grids.Grid):
-
     class StepsColumn(grids.GridColumn):
         def get_value(self, trans, grid, workflow):
             return len(workflow.latest_workflow.steps)
@@ -67,11 +77,13 @@ class StoredWorkflowListGrid(grids.Grid):
     default_sort_key = "-update_time"
     columns = [
         grids.TextColumn("Name", key="name", attach_popup=True, filterable="advanced"),
-        grids.IndividualTagsColumn("Tags",
-                                   "tags",
-                                   model_tag_association_class=model.StoredWorkflowTagAssociation,
-                                   filterable="advanced",
-                                   grid_name="StoredWorkflowListGrid"),
+        grids.IndividualTagsColumn(
+            "Tags",
+            "tags",
+            model_tag_association_class=model.StoredWorkflowTagAssociation,
+            filterable="advanced",
+            grid_name="StoredWorkflowListGrid",
+        ),
         StepsColumn("Steps"),
         grids.GridColumn("Created", key="create_time", format=time_ago),
         grids.GridColumn("Last Updated", key="update_time", format=time_ago),
@@ -80,11 +92,15 @@ class StoredWorkflowListGrid(grids.Grid):
         grids.MulticolFilterColumn(
             "Search",
             cols_to_filter=[columns[0], columns[1]],
-            key="free-text-search", visible=False, filterable="standard"
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
         )
     )
     operations = [
-        grids.GridOperation("Edit", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False),
+        grids.GridOperation(
+            "Edit", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False
+        ),
         grids.GridOperation("Run", condition=(lambda item: not item.deleted), async_compatible=False),
         grids.GridOperation("Copy", condition=(lambda item: not item.deleted), async_compatible=False),
         grids.GridOperation("Rename", condition=(lambda item: not item.deleted), async_compatible=False),
@@ -103,42 +119,47 @@ class StoredWorkflowAllPublishedGrid(grids.Grid):
     default_filter = dict(public_url="All", username="All", tags="All")
     columns = [
         grids.PublicURLColumn("Name", key="name", filterable="advanced", attach_popup=True),
-        grids.OwnerAnnotationColumn("Annotation",
-                                    key="annotation",
-                                    model_annotation_association_class=model.StoredWorkflowAnnotationAssociation,
-                                    filterable="advanced"),
+        grids.OwnerAnnotationColumn(
+            "Annotation",
+            key="annotation",
+            model_annotation_association_class=model.StoredWorkflowAnnotationAssociation,
+            filterable="advanced",
+        ),
         grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"),
         grids.CommunityRatingColumn("Community Rating", key="rating"),
-        grids.CommunityTagsColumn("Community Tags", key="tags",
-                                  model_tag_association_class=model.StoredWorkflowTagAssociation,
-                                  filterable="advanced", grid_name="PublicWorkflowListGrid"),
-        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
+        grids.CommunityTagsColumn(
+            "Community Tags",
+            key="tags",
+            model_tag_association_class=model.StoredWorkflowTagAssociation,
+            filterable="advanced",
+            grid_name="PublicWorkflowListGrid",
+        ),
+        grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago),
     ]
     columns.append(
         grids.MulticolFilterColumn(
             "Search name, annotation, owner, and tags",
             cols_to_filter=[columns[0], columns[1], columns[2], columns[4]],
-            key="free-text-search", visible=False, filterable="standard"
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
         )
     )
     operations = [
         grids.GridOperation(
-            'Run',
+            "Run",
             condition=(lambda item: not item.deleted),
             allow_multiple=False,
-            url_args=dict(controller='workflows', action="run")
+            url_args=dict(controller="workflows", action="run"),
         ),
         grids.GridOperation(
-            "Import",
-            condition=(lambda item: not item.deleted),
-            allow_multiple=False,
-            url_args=dict(action="imp")
+            "Import", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="imp")
         ),
         grids.GridOperation(
             "Save as File",
             condition=(lambda item: not item.deleted),
             allow_multiple=False,
-            url_args=dict(action="export_to_file")
+            url_args=dict(action="export_to_file"),
         ),
     ]
     num_rows_per_page = 50
@@ -148,19 +169,28 @@ class StoredWorkflowAllPublishedGrid(grids.Grid):
         # See optimization description comments and TODO for tags in matching public histories query.
         # In addition to that - be sure to lazyload the latest_workflow - it isn't needed and it causes all
         # of its steps to be eagerly loaded.
-        return trans.sa_session.query(self.model_class).join("user").options(lazyload("latest_workflow"), eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
+        return (
+            trans.sa_session.query(self.model_class)
+            .join("user")
+            .options(
+                lazyload("latest_workflow"),
+                eagerload("user").load_only("username"),
+                eagerload("annotations"),
+                undefer("average_rating"),
+            )
+        )
 
     def apply_query_filter(self, trans, query, **kwargs):
         # A public workflow is published, has a slug, and is not deleted.
-        return query.filter(
-            self.model_class.published == expression.true()).filter(
-            self.model_class.slug.isnot(None)).filter(
-            self.model_class.deleted == expression.false())
+        return (
+            query.filter(self.model_class.published == expression.true())
+            .filter(self.model_class.slug.isnot(None))
+            .filter(self.model_class.deleted == expression.false())
+        )
 
 
 # Simple HTML parser to get all content in a single tag.
 class SingleTagContentsParser(HTMLParser):
-
     def __init__(self, target_tag):
         # Cannot use super() because HTMLParser is an old-style class in Python2
         HTMLParser.__init__(self)
@@ -169,11 +199,11 @@ class SingleTagContentsParser(HTMLParser):
         self.tag_content = ""
 
     def handle_starttag(self, tag, attrs):
-        """ Called for each start tag. """
+        """Called for each start tag."""
         self.cur_tag = tag
 
     def handle_data(self, text):
-        """ Called for each block of plain text. """
+        """Called for each block of plain text."""
         if self.cur_tag == self.target_tag:
             self.tag_content += text
 
@@ -186,13 +216,13 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     @web.expose
     @web.require_login("use Galaxy workflows")
     def list_grid(self, trans, **kwargs):
-        """ List user's stored workflows. """
+        """List user's stored workflows."""
         # status = message = None
-        if 'operation' in kwargs:
-            operation = kwargs['operation'].lower()
+        if "operation" in kwargs:
+            operation = kwargs["operation"].lower()
             if operation == "rename":
                 return self.rename(trans, **kwargs)
-            history_ids = util.listify(kwargs.get('id', []))
+            history_ids = util.listify(kwargs.get("id", []))
             if operation == "sharing":
                 return self.sharing(trans, id=history_ids)
         return self.stored_list_grid(trans, **kwargs)
@@ -213,7 +243,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         return self.published_list_grid(trans, **kwargs)
 
     @web.expose
-    def display_by_username_and_slug(self, trans, username, slug, format='html'):
+    def display_by_username_and_slug(self, trans, username, slug, format="html"):
         """
         Display workflow based on a username and slug. Format can be html, json, or json-download.
         """
@@ -223,28 +253,30 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         user = session.query(model.User).filter_by(username=username).first()
         if not user:
             raise web.httpexceptions.HTTPNotFound()
-        stored_workflow = trans.sa_session.query(model.StoredWorkflow).filter_by(user=user, slug=slug, deleted=False).first()
+        stored_workflow = (
+            trans.sa_session.query(model.StoredWorkflow).filter_by(user=user, slug=slug, deleted=False).first()
+        )
         if not stored_workflow:
             raise web.httpexceptions.HTTPNotFound()
         encoded_id = trans.security.encode_id(stored_workflow.id)
 
         # Display workflow in requested format.
-        if format == 'html':
+        if format == "html":
             return self._display(trans, stored_workflow)
-        elif format == 'json':
+        elif format == "json":
             return self.for_direct_import(trans, encoded_id)
-        elif format == 'json-download':
+        elif format == "json-download":
             return self.export_to_file(trans, encoded_id)
 
     @web.expose
     def display_by_id(self, trans, id):
-        """ Display workflow based on id. """
+        """Display workflow based on id."""
         # Get workflow.
         stored_workflow = self.get_stored_workflow(trans, id)
         return self._display(trans, stored_workflow)
 
     def _display(self, trans, stored_workflow):
-        """ Diplay workflow as HTML page. """
+        """Diplay workflow as HTML page."""
 
         if stored_workflow is None:
             raise web.httpexceptions.HTTPNotFound()
@@ -253,7 +285,9 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         # Get data for workflow's steps.
         self.get_stored_workflow_steps(trans, stored_workflow)
         # Get annotations.
-        stored_workflow.annotation = self.get_item_annotation_str(trans.sa_session, stored_workflow.user, stored_workflow)
+        stored_workflow.annotation = self.get_item_annotation_str(
+            trans.sa_session, stored_workflow.user, stored_workflow
+        )
         for step in stored_workflow.latest_workflow.steps:
             step.annotation = self.get_item_annotation_str(trans.sa_session, stored_workflow.user, step)
         user_is_owner = True if trans.user == stored_workflow.user else False
@@ -266,17 +300,19 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             else:
                 user_item_rating = 0
         ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, stored_workflow)
-        return trans.fill_template_mako("workflow/display.mako",
-                                        item=stored_workflow,
-                                        item_data=stored_workflow.latest_workflow.steps,
-                                        user_item_rating=user_item_rating,
-                                        ave_item_rating=ave_item_rating,
-                                        num_ratings=num_ratings,
-                                        user_is_owner=user_is_owner)
+        return trans.fill_template_mako(
+            "workflow/display.mako",
+            item=stored_workflow,
+            item_data=stored_workflow.latest_workflow.steps,
+            user_item_rating=user_item_rating,
+            ave_item_rating=ave_item_rating,
+            num_ratings=num_ratings,
+            user_is_owner=user_is_owner,
+        )
 
     @web.expose
     def get_item_content_async(self, trans, id):
-        """ Returns item content in HTML format. """
+        """Returns item content in HTML format."""
 
         stored = self.get_stored_workflow(trans, id, False, True)
         if stored is None:
@@ -288,7 +324,9 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         stored.annotation = self.get_item_annotation_str(trans.sa_session, stored.user, stored)
         for step in stored.latest_workflow.steps:
             step.annotation = self.get_item_annotation_str(trans.sa_session, stored.user, step)
-        return trans.fill_template_mako("/workflow/item_content.mako", item=stored, item_data=stored.latest_workflow.steps)
+        return trans.fill_template_mako(
+            "/workflow/item_content.mako", item=stored, item_data=stored.latest_workflow.steps
+        )
 
     @web.expose
     @web.require_login("use Galaxy workflows")
@@ -297,18 +335,23 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         # Load workflow from database
         stored = self.get_stored_workflow(trans, id)
         if email:
-            other = trans.sa_session.query(model.User) \
-                                    .filter(and_(model.User.table.c.email == email,
-                                                 model.User.table.c.deleted == expression.false())) \
-                                    .first()
+            other = (
+                trans.sa_session.query(model.User)
+                .filter(and_(model.User.table.c.email == email, model.User.table.c.deleted == expression.false()))
+                .first()
+            )
             if not other:
                 mtype = "error"
                 msg = f"User '{escape(email)}' does not exist"
             elif other == trans.get_user():
                 mtype = "error"
-                msg = ("You cannot share a workflow with yourself")
-            elif trans.sa_session.query(model.StoredWorkflowUserShareAssociation) \
-                    .filter_by(user=other, stored_workflow=stored).count() > 0:
+                msg = "You cannot share a workflow with yourself"
+            elif (
+                trans.sa_session.query(model.StoredWorkflowUserShareAssociation)
+                .filter_by(user=other, stored_workflow=stored)
+                .count()
+                > 0
+            ):
                 mtype = "error"
                 msg = f"Workflow already shared with '{escape(email)}'"
             else:
@@ -319,24 +362,24 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
                 session.add(share)
                 session.flush()
                 trans.set_message(f"Workflow '{escape(stored.name)}' shared with user '{escape(other.email)}'")
-                return trans.response.send_redirect(url_for(controller='workflow', action='sharing', id=id))
-        return trans.fill_template("/ind_share_base.mako",
-                                   message=msg,
-                                   messagetype=mtype,
-                                   item=stored,
-                                   email=email,
-                                   use_panels=use_panels)
+                return trans.response.send_redirect(url_for(controller="workflow", action="sharing", id=id))
+        return trans.fill_template(
+            "/ind_share_base.mako", message=msg, messagetype=mtype, item=stored, email=email, use_panels=use_panels
+        )
 
     @web.expose
     @web.require_login("Share or export Galaxy workflows")
     def sharing(self, trans, id, **kwargs):
-        """ Handle workflow sharing. """
+        """Handle workflow sharing."""
         session = trans.sa_session
-        if 'unshare_me' in kwargs:
+        if "unshare_me" in kwargs:
             # Remove self from shared associations with workflow.
             stored = self.get_stored_workflow(trans, id, False, True)
-            association = session.query(model.StoredWorkflowUserShareAssociation) \
-                                 .filter_by(user=trans.user, stored_workflow=stored).one()
+            association = (
+                session.query(model.StoredWorkflowUserShareAssociation)
+                .filter_by(user=trans.user, stored_workflow=stored)
+                .one()
+            )
             session.delete(association)
             session.flush()
             return self.list(trans)
@@ -346,25 +389,28 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             session.add(stored)
 
             # Do operation on workflow.
-            if 'make_accessible_via_link' in kwargs:
+            if "make_accessible_via_link" in kwargs:
                 self._make_item_accessible(trans.sa_session, stored)
-            elif 'make_accessible_and_publish' in kwargs:
+            elif "make_accessible_and_publish" in kwargs:
                 self._make_item_accessible(trans.sa_session, stored)
                 stored.published = True
-            elif 'publish' in kwargs:
+            elif "publish" in kwargs:
                 stored.published = True
-            elif 'disable_link_access' in kwargs:
+            elif "disable_link_access" in kwargs:
                 stored.importable = False
-            elif 'unpublish' in kwargs:
+            elif "unpublish" in kwargs:
                 stored.published = False
-            elif 'disable_link_access_and_unpublish' in kwargs:
+            elif "disable_link_access_and_unpublish" in kwargs:
                 stored.importable = stored.published = False
-            elif 'unshare_user' in kwargs:
-                user = session.query(model.User).get(trans.security.decode_id(kwargs['unshare_user']))
+            elif "unshare_user" in kwargs:
+                user = session.query(model.User).get(trans.security.decode_id(kwargs["unshare_user"]))
                 if not user:
                     error("User not found for provided id")
-                association = session.query(model.StoredWorkflowUserShareAssociation) \
-                                     .filter_by(user=user, stored_workflow=stored).one()
+                association = (
+                    session.query(model.StoredWorkflowUserShareAssociation)
+                    .filter_by(user=user, stored_workflow=stored)
+                    .one()
+                )
                 session.delete(association)
 
             # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them.
@@ -377,13 +423,15 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     @web.expose
     @web.require_login("share Galaxy items")
     def set_public_username(self, trans, id, username, **kwargs):
-        """ Set user's public username and delegate to sharing() """
+        """Set user's public username and delegate to sharing()"""
         user = trans.get_user()
         # message from validate_publicname does not contain input, no need
         # to escape.
         message = validate_publicname(trans, username, user)
         if message:
-            return trans.fill_template("/workflow/sharing.mako", item=self.get_item(trans, id), message=message, status="error")
+            return trans.fill_template(
+                "/workflow/sharing.mako", item=self.get_item(trans, id), message=message, status="error"
+            )
         user.username = username
         trans.sa_session.flush()
         return self.sharing(trans, id, **kwargs)
@@ -402,15 +450,22 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         # Do import.
         stored = self.get_stored_workflow(trans, id, check_ownership=False)
         if stored.importable is False:
-            return trans.show_error_message(f"The owner of this workflow has disabled imports via this link.<br>You can {referer_message}", use_panels=True)
+            return trans.show_error_message(
+                f"The owner of this workflow has disabled imports via this link.<br>You can {referer_message}",
+                use_panels=True,
+            )
         elif stored.deleted:
-            return trans.show_error_message(f"You can't import this workflow because it has been deleted.<br>You can {referer_message}", use_panels=True)
+            return trans.show_error_message(
+                f"You can't import this workflow because it has been deleted.<br>You can {referer_message}",
+                use_panels=True,
+            )
         self._import_shared_workflow(trans, stored)
 
         # Redirect to load galaxy frames.
         return trans.show_ok_message(
             message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s."""
-            % (stored.name, web.url_for('/workflows/list'), referer_message))
+            % (stored.name, web.url_for("/workflows/list"), referer_message)
+        )
 
     @web.expose
     @web.require_login("use Galaxy workflows")
@@ -438,7 +493,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     @web.require_login("rate items")
     @web.json
     def rate_async(self, trans, id, rating):
-        """ Rate a workflow asynchronously and return updated community data. """
+        """Rate a workflow asynchronously and return updated community data."""
 
         stored = self.get_stored_workflow(trans, id, check_ownership=False, check_accessible=True)
         if not stored:
@@ -452,11 +507,11 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     @web.expose
     @web.require_login("use Galaxy workflows")
     def set_accessible_async(self, trans, id=None, accessible=False):
-        """ Set workflow's importable attribute and slug. """
+        """Set workflow's importable attribute and slug."""
         stored = self.get_stored_workflow(trans, id)
 
         # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
-        importable = accessible in ['True', 'true', 't', 'T']
+        importable = accessible in ["True", "true", "t", "T"]
         if stored and stored.importable != importable:
             if importable:
                 self._make_item_accessible(trans.sa_session, stored)
@@ -467,7 +522,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
 
     @web.expose
     def get_embed_html_async(self, trans, id):
-        """ Returns HTML for embedding a workflow in a page. """
+        """Returns HTML for embedding a workflow in a page."""
 
         # TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code.
         stored = self.get_stored_workflow(trans, id)
@@ -478,14 +533,18 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     @web.json
     @web.require_login("use Galaxy workflows")
     def get_name_and_link_async(self, trans, id=None):
-        """ Returns workflow's name and link. """
+        """Returns workflow's name and link."""
         stored = self.get_stored_workflow(trans, id)
 
-        return_dict = {"name": stored.name,
-                       "link": url_for(controller='workflow',
-                                       action="display_by_username_and_slug",
-                                       username=stored.user.username,
-                                       slug=stored.slug)}
+        return_dict = {
+            "name": stored.name,
+            "link": url_for(
+                controller="workflow",
+                action="display_by_username_and_slug",
+                username=stored.user.username,
+                slug=stored.slug,
+            ),
+        }
         return return_dict
 
     @web.expose
@@ -495,12 +554,16 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         try:
             svg = self._workflow_to_svg_canvas(trans, stored)
         except Exception:
-            status = 'error'
-            message = 'Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools.'
-            return trans.fill_template("/workflow/sharing.mako", use_panels=True, item=stored, status=status, message=message)
+            status = "error"
+            message = (
+                "Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools."
+            )
+            return trans.fill_template(
+                "/workflow/sharing.mako", use_panels=True, item=stored, status=status, message=message
+            )
         trans.response.set_content_type("image/svg+xml")
         s = STANDALONE_SVG_TEMPLATE % svg.tostring()
-        return s.encode('utf-8')
+        return s.encode("utf-8")
 
     @web.expose
     @web.require_login("use Galaxy workflows")
@@ -511,15 +574,19 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         if stored.user == user:
             owner = True
         else:
-            if trans.sa_session.query(model.StoredWorkflowUserShareAssociation) \
-                    .filter_by(user=user, stored_workflow=stored).count() == 0:
+            if (
+                trans.sa_session.query(model.StoredWorkflowUserShareAssociation)
+                .filter_by(user=user, stored_workflow=stored)
+                .count()
+                == 0
+            ):
                 error("Workflow is not owned by or shared with current user")
             owner = False
 
         # Copy.
         new_stored = model.StoredWorkflow()
-        if (save_as_name):
-            new_stored.name = f'{save_as_name}'
+        if save_as_name:
+            new_stored.name = f"{save_as_name}"
         else:
             new_stored.name = f"Copy of {stored.name}"
         new_stored.latest_workflow = stored.latest_workflow
@@ -536,31 +603,31 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         session.add(new_stored)
         session.flush()
         # Display the management page
-        message = f'Created new workflow with name: {escape(new_stored.name)}'
+        message = f"Created new workflow with name: {escape(new_stored.name)}"
         trans.set_message(message)
         return_url = f"{url_for('/')}workflow?status=done&message={escape(message)}"
         trans.response.send_redirect(return_url)
 
     @web.legacy_expose_api
     def create(self, trans, payload=None, **kwd):
-        if trans.request.method == 'GET':
+        if trans.request.method == "GET":
             return {
-                'title': 'Create Workflow',
-                'inputs': [{
-                    'name': 'workflow_name',
-                    'label': 'Name',
-                    'value': 'Unnamed workflow'
-                }, {
-                    'name': 'workflow_annotation',
-                    'label': 'Annotation',
-                    'help': 'A description of the workflow; annotation is shown alongside shared or published workflows.'
-                }]}
+                "title": "Create Workflow",
+                "inputs": [
+                    {"name": "workflow_name", "label": "Name", "value": "Unnamed workflow"},
+                    {
+                        "name": "workflow_annotation",
+                        "label": "Annotation",
+                        "help": "A description of the workflow; annotation is shown alongside shared or published workflows.",
+                    },
+                ],
+            }
         else:
             user = trans.get_user()
-            workflow_name = payload.get('workflow_name')
-            workflow_annotation = payload.get('workflow_annotation')
+            workflow_name = payload.get("workflow_name")
+            workflow_annotation = payload.get("workflow_annotation")
             if not workflow_name:
-                return self.message_exception(trans, 'Please provide a workflow name.')
+                return self.message_exception(trans, "Please provide a workflow name.")
             # Create the new stored workflow
             stored_workflow = model.StoredWorkflow()
             stored_workflow.name = workflow_name
@@ -578,13 +645,16 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             session = trans.sa_session
             session.add(stored_workflow)
             session.flush()
-            return {'id': trans.security.encode_id(stored_workflow.id), 'message': f'Workflow {workflow_name} has been created.'}
+            return {
+                "id": trans.security.encode_id(stored_workflow.id),
+                "message": f"Workflow {workflow_name} has been created.",
+            }
 
     @web.json
     def save_workflow_as(self, trans, workflow_name, workflow_data, workflow_annotation="", from_tool_form=False):
         """
-            Creates a new workflow based on Save As command. It is a new workflow, but
-            is created with workflow_data already present.
+        Creates a new workflow based on Save As command. It is a new workflow, but
+        is created with workflow_data already present.
         """
         user = trans.get_user()
         if workflow_name is not None:
@@ -619,11 +689,13 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             except MissingToolsException as e:
                 return dict(
                     name=e.workflow.name,
-                    message=("This workflow includes missing or invalid tools. "
-                             "It cannot be saved until the following steps are removed or the missing tools are enabled."),
+                    message=(
+                        "This workflow includes missing or invalid tools. "
+                        "It cannot be saved until the following steps are removed or the missing tools are enabled."
+                    ),
                     errors=e.errors,
                 )
-            return (trans.security.encode_id(stored_workflow.id))
+            return trans.security.encode_id(stored_workflow.id)
         else:
             # This is an error state, 'save as' must have a workflow_name
             log.exception("Error in Save As workflow: no name.")
@@ -637,7 +709,9 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         stored = self.get_stored_workflow(trans, id)
         # Mark as deleted and save
         stored.deleted = True
-        trans.user.stored_workflow_menu_entries = [entry for entry in trans.user.stored_workflow_menu_entries if entry.stored_workflow != stored]
+        trans.user.stored_workflow_menu_entries = [
+            entry for entry in trans.user.stored_workflow_menu_entries if entry.stored_workflow != stored
+        ]
         trans.sa_session.add(stored)
         trans.sa_session.flush()
         # Display the management page
@@ -664,11 +738,13 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         stored = self.get_stored_workflow(trans, id)
         # The following query loads all user-owned workflows,
         # So that they can be copied or inserted in the workflow editor.
-        workflows = trans.sa_session.query(model.StoredWorkflow) \
-            .filter_by(user=trans.user, deleted=False, hidden=False) \
-            .order_by(desc(model.StoredWorkflow.table.c.update_time)) \
-            .options(joinedload('latest_workflow').joinedload('steps')) \
+        workflows = (
+            trans.sa_session.query(model.StoredWorkflow)
+            .filter_by(user=trans.user, deleted=False, hidden=False)
+            .order_by(desc(model.StoredWorkflow.table.c.update_time))
+            .options(joinedload("latest_workflow").joinedload("steps"))
             .all()
+        )
         if version is None:
             version = len(stored.workflows) - 1
         else:
@@ -677,15 +753,16 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         # create workflow module models
         module_sections = []
         for module_section in load_module_sections(trans).values():
-            module_sections.append({
-                "title": module_section.get("title"),
-                "name": module_section.get("name"),
-                "elems": [{
-                    "name": elem.get("name"),
-                    "title": elem.get("title"),
-                    "description": elem.get("description")
-                } for elem in module_section.get("modules")]
-            })
+            module_sections.append(
+                {
+                    "title": module_section.get("title"),
+                    "name": module_section.get("name"),
+                    "elems": [
+                        {"name": elem.get("name"), "title": elem.get("title"), "description": elem.get("description")}
+                        for elem in module_section.get("modules")
+                    ],
+                }
+            )
 
         # create data manager tool models
         data_managers = []
@@ -693,21 +770,27 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             for data_manager_val in trans.app.data_managers.data_managers.values():
                 tool = data_manager_val.tool
                 if not tool.hidden:
-                    data_managers.append({
-                        "id": tool.id,
-                        "name": tool.name,
-                        "hidden": tool.hidden,
-                        "description": tool.description,
-                        "is_workflow_compatible": tool.is_workflow_compatible
-                    })
+                    data_managers.append(
+                        {
+                            "id": tool.id,
+                            "name": tool.name,
+                            "hidden": tool.hidden,
+                            "description": tool.description,
+                            "is_workflow_compatible": tool.is_workflow_compatible,
+                        }
+                    )
 
         # create workflow models
-        workflows = [{
-            'id': trans.security.encode_id(workflow.id),
-            'latest_id': trans.security.encode_id(workflow.latest_workflow.id),
-            'step_count': len(workflow.latest_workflow.steps),
-            'name': workflow.name
-        } for workflow in workflows if workflow.id != stored.id]
+        workflows = [
+            {
+                "id": trans.security.encode_id(workflow.id),
+                "latest_id": trans.security.encode_id(workflow.latest_workflow.id),
+                "step_count": len(workflow.latest_workflow.steps),
+                "name": workflow.name,
+            }
+            for workflow in workflows
+            if workflow.id != stored.id
+        ]
 
         # identify item tags
         item_tags = [tag for tag in stored.tags if tag.user == trans.user]
@@ -717,14 +800,14 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
 
         # build workflow editor model
         editor_config = {
-            'id': trans.security.encode_id(stored.id),
-            'name': stored.name,
-            'tags': item_tag_names,
-            'initialVersion': version,
-            'annotation': self.get_item_annotation_str(trans.sa_session, trans.user, stored),
-            'moduleSections': module_sections,
-            'dataManagers': data_managers,
-            'workflows': workflows
+            "id": trans.security.encode_id(stored.id),
+            "name": stored.name,
+            "tags": item_tag_names,
+            "initialVersion": version,
+            "annotation": self.get_item_annotation_str(trans.sa_session, trans.user, stored),
+            "moduleSections": module_sections,
+            "dataManagers": data_managers,
+            "workflows": workflows,
         }
 
         # parse to mako
@@ -764,16 +847,16 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         # Create myExperiment request.
         request_raw = trans.fill_template(
             "workflow/myexp_export.mako",
-            workflow_name=workflow_dict['name'],
-            workflow_description=workflow_dict['annotation'],
+            workflow_name=workflow_dict["name"],
+            workflow_description=workflow_dict["annotation"],
             workflow_content=workflow_content,
-            workflow_svg=self._workflow_to_svg_canvas(trans, stored).tostring()
+            workflow_svg=self._workflow_to_svg_canvas(trans, stored).tostring(),
         )
         # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters.
-        request = unicodify(request_raw.strip(), 'utf-8')
+        request = unicodify(request_raw.strip(), "utf-8")
 
         # Do request and get result.
-        auth_header = base64.b64encode(f'{myexp_username}:{myexp_password}')
+        auth_header = base64.b64encode(f"{myexp_username}:{myexp_password}")
         headers = {"Content-type": "text/xml", "Accept": "text/xml", "Authorization": f"Basic {auth_header}"}
         myexp_url = trans.app.config.myexperiment_target_url
         conn = HTTPConnection(myexp_url)
@@ -784,7 +867,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         conn.close()
 
         # Do simple parse of response to see if export successful and provide user feedback.
-        parser = SingleTagContentsParser('id')
+        parser = SingleTagContentsParser("id")
         parser.feed(response_data)
         myexp_workflow_id = parser.tag_content
         workflow_list_str = f" <br>Return to <a href='{url_for(controller='workflows', action='list')}'>workflow list."
@@ -792,12 +875,17 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             return trans.show_message(
                 """Workflow '{}' successfully exported to myExperiment. <br/>
                 <a href="http://{}/workflows/{}">Click here to view the workflow on myExperiment</a> {}
-                """.format(stored.name, myexp_url, myexp_workflow_id, workflow_list_str),
-                use_panels=True)
+                """.format(
+                    stored.name, myexp_url, myexp_workflow_id, workflow_list_str
+                ),
+                use_panels=True,
+            )
         else:
             return trans.show_error_message(
-                "Workflow '%s' could not be exported to myExperiment. Error: %s %s" %
-                (stored.name, response_data, workflow_list_str), use_panels=True)
+                "Workflow '%s' could not be exported to myExperiment. Error: %s %s"
+                % (stored.name, response_data, workflow_list_str),
+                use_panels=True,
+            )
 
     @web.json_pretty
     def for_direct_import(self, trans, id):
@@ -833,13 +921,22 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             trans.response.status = 400
             return "Workflow cannot be exported due to missing tools."
         sname = stored.name
-        sname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in sname)[0:150]
+        sname = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in sname)[0:150]
         trans.response.headers["Content-Disposition"] = f'attachment; filename="Galaxy-Workflow-{sname}.ga"'
-        trans.response.set_content_type('application/galaxy-archive')
+        trans.response.set_content_type("application/galaxy-archive")
         return stored_dict
 
     @web.expose
-    def build_from_current_history(self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None):
+    def build_from_current_history(
+        self,
+        trans,
+        job_ids=None,
+        dataset_ids=None,
+        dataset_collection_ids=None,
+        workflow_name=None,
+        dataset_names=None,
+        dataset_collection_names=None,
+    ):
         user = trans.get_user()
         history = trans.get_history()
         if not user:
@@ -848,10 +945,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             jobs, warnings = summarize(trans)
             # Render
             return trans.fill_template(
-                "workflow/build_from_current_history.mako",
-                jobs=jobs,
-                warnings=warnings,
-                history=history
+                "workflow/build_from_current_history.mako", jobs=jobs, warnings=warnings, history=history
             )
         else:
             # If there is just one dataset name selected or one dataset collection, these
@@ -866,14 +960,19 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
                 dataset_collection_ids=dataset_collection_ids,
                 workflow_name=workflow_name,
                 dataset_names=dataset_names,
-                dataset_collection_names=dataset_collection_names
+                dataset_collection_names=dataset_collection_names,
             )
             # Index page with message
             workflow_id = trans.security.encode_id(stored_workflow.id)
-            return trans.show_message('Workflow "%s" created from current history. '
-                                      'You can <a href="%s" target="_parent">edit</a> or <a href="%s" target="_parent">run</a> the workflow.'
-                                      % (escape(workflow_name), url_for(controller='workflow', action='editor', id=workflow_id),
-                                         url_for(controller='workflows', action='run', id=workflow_id)))
+            return trans.show_message(
+                'Workflow "%s" created from current history. '
+                'You can <a href="%s" target="_parent">edit</a> or <a href="%s" target="_parent">run</a> the workflow.'
+                % (
+                    escape(workflow_name),
+                    url_for(controller="workflow", action="editor", id=workflow_id),
+                    url_for(controller="workflows", action="run", id=workflow_id),
+                )
+            )
 
     def get_item(self, trans, id):
         return self.get_stored_workflow(trans, id)
@@ -941,7 +1040,9 @@ def _extend_with_matched_combos(single_inputs, multi_inputs):
         if multi_input_key == first_multi_input_key:
             continue
         if len(multi_input_values) != len(first_multi_value):
-            raise Exception("Failed to match up multi-select inputs, must select equal number of data files in each multiselect")
+            raise Exception(
+                "Failed to match up multi-select inputs, must select equal number of data files in each multiselect"
+            )
         for index, value in enumerate(multi_input_values):
             matched_multi_inputs[index][multi_input_key] = value
     return matched_multi_inputs
@@ -968,16 +1069,15 @@ def _copy_and_extend_inputs(inputs, key, value):
 
 
 def _split_inputs(kwargs):
-    """
-    """
-    input_keys = [a for a in kwargs if a.endswith('|input')]
+    """ """
+    input_keys = [a for a in kwargs if a.endswith("|input")]
     single_inputs = {}
     matched_multi_inputs = {}
     multiplied_multi_inputs = {}
     for input_key in input_keys:
         input_val = kwargs[input_key]
         if isinstance(input_val, list):
-            input_base = input_key[:-len("|input")]
+            input_base = input_key[: -len("|input")]
             mode_key = f"{input_base}|multi_mode"
             mode = kwargs.get(mode_key, "matched")
             if mode == "matched":
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index ebb28541572..df9a26baeba 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -1,7 +1,10 @@
 from pathlib import Path
 from typing import cast
 
-from fastapi import FastAPI, Request
+from fastapi import (
+    FastAPI,
+    Request,
+)
 from fastapi.middleware.wsgi import WSGIMiddleware
 from starlette.middleware.cors import CORSMiddleware
 from starlette.responses import (
@@ -16,7 +19,6 @@ from galaxy.webapps.base.api import (
 )
 from galaxy.webapps.base.webapp import config_allows_origin
 
-
 # https://fastapi.tiangolo.com/tutorial/metadata/#metadata-for-tags
 api_tags_metadata = [
     {
@@ -59,7 +61,6 @@ api_tags_metadata = [
 
 
 class GalaxyCORSMiddleware(CORSMiddleware):
-
     def __init__(self, *args, **kwds):
         self.config = kwds.pop("config")
         super().__init__(*args, **kwds)
@@ -75,7 +76,7 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
         @app.middleware("http")
         async def add_x_frame_options(request: Request, call_next):
             response = await call_next(request)
-            response.headers['X-Frame-Options'] = x_frame_options
+            response.headers["X-Frame-Options"] = x_frame_options
             return response
 
     nginx_x_accel_redirect_base = gx_app.config.nginx_x_accel_redirect_base
@@ -83,6 +84,7 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
 
     if gx_app.config.sentry_dsn:
         from sentry_sdk.integrations.asgi import SentryAsgiMiddleware
+
         app.add_middleware(SentryAsgiMiddleware)
 
     if nginx_x_accel_redirect_base or apache_xsendfile:
@@ -95,12 +97,12 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
             response = cast(FileResponse, response)
             if nginx_x_accel_redirect_base:
                 full_path = Path(nginx_x_accel_redirect_base) / response.path
-                response.headers['X-Accel-Redirect'] = str(full_path)
+                response.headers["X-Accel-Redirect"] = str(full_path)
             if apache_xsendfile:
-                response.headers['X-Sendfile'] = str(response.path)
+                response.headers["X-Sendfile"] = str(response.path)
             return response
 
-    if gx_app.config.get('allowed_origin_hostnames', None):
+    if gx_app.config.get("allowed_origin_hostnames", None):
         app.add_middleware(
             GalaxyCORSMiddleware,
             config=gx_app.config,
@@ -111,11 +113,11 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
     else:
 
         # handle CORS preflight requests - synchronize with wsgi behavior.
-        @app.options('/api/{rest_of_path:path}')
+        @app.options("/api/{rest_of_path:path}")
         async def preflight_handler(request: Request, rest_of_path: str) -> Response:
             response = Response()
-            response.headers['Access-Control-Allow-Headers'] = '*'
-            response.headers['Access-Control-Max-Age'] = '600'
+            response.headers["Access-Control-Allow-Headers"] = "*"
+            response.headers["Access-Control-Max-Age"] = "600"
             return response
 
 
@@ -128,10 +130,10 @@ def initialize_fast_app(gx_wsgi_webapp, gx_app):
     add_exception_handler(app)
     add_galaxy_middleware(app, gx_app)
     add_request_id_middleware(app)
-    include_all_package_routers(app, 'galaxy.webapps.galaxy.api')
+    include_all_package_routers(app, "galaxy.webapps.galaxy.api")
     wsgi_handler = WSGIMiddleware(gx_wsgi_webapp)
-    app.mount('/', wsgi_handler)
-    if gx_app.config.galaxy_url_prefix != '/':
+    app.mount("/", wsgi_handler)
+    if gx_app.config.galaxy_url_prefix != "/":
         parent_app = FastAPI()
         parent_app.mount(gx_app.config.galaxy_url_prefix, app=app)
         return parent_app
diff --git a/lib/galaxy/webapps/galaxy/fast_factory.py b/lib/galaxy/webapps/galaxy/fast_factory.py
index 576957e0af9..d2210e6f3fd 100644
--- a/lib/galaxy/webapps/galaxy/fast_factory.py
+++ b/lib/galaxy/webapps/galaxy/fast_factory.py
@@ -52,13 +52,15 @@ from .fast_app import initialize_fast_app
 
 def factory():
     props = WebappSetupProps(
-        app_name='galaxy',
+        app_name="galaxy",
         default_section_name=DEFAULT_CONFIG_SECTION,
-        env_config_file='GALAXY_CONFIG_FILE',
-        env_config_section='GALAXY_CONFIG_SECTION',
-        check_galaxy_root=True
+        env_config_file="GALAXY_CONFIG_FILE",
+        env_config_section="GALAXY_CONFIG_SECTION",
+        check_galaxy_root=True,
     )
     config_provider = WebappConfigResolver(props)
     config = config_provider.resolve_config()
-    gx_wsgi_webapp, gx_app = app_pair(global_conf=config.global_conf, load_app_kwds=config.load_app_kwds, wsgi_preflight=config.wsgi_preflight)
+    gx_wsgi_webapp, gx_app = app_pair(
+        global_conf=config.global_conf, load_app_kwds=config.load_app_kwds, wsgi_preflight=config.wsgi_preflight
+    )
     return initialize_fast_app(gx_wsgi_webapp, gx_app)
diff --git a/lib/galaxy/webapps/galaxy/services/base.py b/lib/galaxy/webapps/galaxy/services/base.py
index 40bb4733087..9df886960ed 100644
--- a/lib/galaxy/webapps/galaxy/services/base.py
+++ b/lib/galaxy/webapps/galaxy/services/base.py
@@ -59,7 +59,7 @@ class ServiceBase:
         """Returns an ORM compatible order_by clause using the order attribute and the given manager.
 
         The manager has to implement the `parse_order_by` function to support all the sortable model attributes."""
-        ORDER_BY_SEP_CHAR = ','
+        ORDER_BY_SEP_CHAR = ","
         if order_by_query and ORDER_BY_SEP_CHAR in order_by_query:
             return [manager.parse_order_by(o) for o in order_by_query.split(ORDER_BY_SEP_CHAR)]
         return manager.parse_order_by(order_by_query)
@@ -74,7 +74,9 @@ class ServiceBase:
         """
         Convenience method to get a model object with the specified checks.
         """
-        return get_object(trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
+        return get_object(
+            trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted
+        )
 
     def check_user_is_authenticated(self, trans: ProvidesUserContext):
         """Raises an exception if the request is anonymous."""
diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 2e38a52d0f2..f7061066591 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -1,7 +1,15 @@
 from logging import getLogger
-from typing import List, Optional, Set
+from typing import (
+    List,
+    Optional,
+    Set,
+)
 
-from pydantic import BaseModel, Extra, Field
+from pydantic import (
+    BaseModel,
+    Extra,
+    Field,
+)
 
 from galaxy import exceptions
 from galaxy.datatypes.registry import Registry
@@ -14,7 +22,10 @@ from galaxy.managers.collections_util import (
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.managers.hdcas import HDCAManager
 from galaxy.managers.histories import HistoryManager
-from galaxy.schema.fields import EncodedDatabaseIdField, ModelClassField
+from galaxy.schema.fields import (
+    EncodedDatabaseIdField,
+    ModelClassField,
+)
 from galaxy.schema.schema import (
     AnyHDCA,
     CreateNewCollectionPayload,
@@ -28,32 +39,22 @@ from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.webapps.base.controller import UsesLibraryMixinItems
 from galaxy.webapps.galaxy.services.base import ServiceBase
 
-
 log = getLogger(__name__)
 
 
 class UpdateCollectionAttributePayload(BaseModel):
     """Contains attributes that can be updated for all elements in a dataset collection."""
-    dbkey: str = Field(
-        ...,
-        description="TODO"
-    )
+
+    dbkey: str = Field(..., description="TODO")
 
     class Config:
         extra = Extra.forbid  # will cause validation to fail if extra attributes are included,
 
 
 class DatasetCollectionAttributesResult(BaseModel):
-    dbkey: str = Field(
-        ...,
-        description="TODO"
-    )
+    dbkey: str = Field(..., description="TODO")
     # Are the following fields really used/needed?
-    extension: str = Field(
-        ...,
-        description="The dataset file extension.",
-        example="txt"
-    )
+    extension: str = Field(..., description="The dataset file extension.", example="txt")
     model_class: str = ModelClassField("HistoryDatasetCollectionAssociation")
     dbkeys: Optional[Set[str]]
     extensions: Optional[Set[str]]
@@ -61,36 +62,25 @@ class DatasetCollectionAttributesResult(BaseModel):
 
 
 class SuitableConverter(BaseModel):
-    tool_id: str = Field(
-        ...,
-        description="The ID of the tool that can perform the type conversion."
-    )
-    name: str = Field(
-        ...,
-        description="The name of the converter."
-    )
-    target_type: str = Field(
-        ...,
-        description="The type to convert to."
-    )
-    original_type: str = Field(
-        ...,
-        description="The type to convert from."
-    )
+    tool_id: str = Field(..., description="The ID of the tool that can perform the type conversion.")
+    name: str = Field(..., description="The name of the converter.")
+    target_type: str = Field(..., description="The type to convert to.")
+    original_type: str = Field(..., description="The type to convert from.")
 
 
 class SuitableConverters(BaseModel):
     """Collection of converters that can be used on a particular dataset collection."""
+
     __root__: List[SuitableConverter]
 
 
 class DatasetCollectionContentElements(BaseModel):
     """Represents a collection of elements contained in the dataset collection."""
+
     __root__: List[DCESummary]
 
 
 class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
-
     def __init__(
         self,
         security: IdEncodingHelper,
@@ -136,11 +126,16 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
 
         dataset_collection_instance = self.collection_manager.create(trans=trans, **create_params)
         rval = dictify_dataset_collection_instance(
-            dataset_collection_instance, security=trans.security, url_builder=trans.url_builder, parent=create_params["parent"]
+            dataset_collection_instance,
+            security=trans.security,
+            url_builder=trans.url_builder,
+            parent=create_params["parent"],
         )
         return rval
 
-    def copy(self, trans: ProvidesHistoryContext, id: EncodedDatabaseIdField, payload: UpdateCollectionAttributePayload):
+    def copy(
+        self, trans: ProvidesHistoryContext, id: EncodedDatabaseIdField, payload: UpdateCollectionAttributePayload
+    ):
         """
         Iterate over all datasets of a collection and copy datasets with new attributes to a new collection.
         e.g attributes = {'dbkey': 'dm3'}
@@ -159,10 +154,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         Returns dbkey/extension for collection elements
         """
         dataset_collection_instance = self.collection_manager.get_dataset_collection_instance(
-            trans,
-            id=id,
-            instance_type=instance_type,
-            check_ownership=True
+            trans, id=id, instance_type=instance_type, check_ownership=True
         )
         rval = dataset_collection_instance.to_dict(view="dbkeysandextensions")
         return rval
@@ -205,7 +197,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
             security=trans.security,
             url_builder=trans.url_builder,
             parent=parent,
-            view='element'
+            view="element",
         )
         return rval
 
@@ -241,7 +233,9 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         # check to make sure the dsc is part of the validated hdca
         decoded_parent_id = self.decode_id(parent_id)
         if parent_id != hdca_id and not hdca.contains_collection(decoded_parent_id):
-            raise exceptions.ObjectNotFound('Requested dataset collection is not contained within indicated history content')
+            raise exceptions.ObjectNotFound(
+                "Requested dataset collection is not contained within indicated history content"
+            )
 
         # retrieve contents
         contents = self.collection_manager.get_collection_contents(trans, decoded_parent_id, limit=limit, offset=offset)
@@ -251,9 +245,11 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
             result = dictify_element_reference(dsc_element, recursive=False, security=trans.security)
             if result["element_type"] == DCEType.dataset_collection:
                 assert trans.url_builder
-                result["object"]["contents_url"] = trans.url_builder('contents_dataset_collection',
+                result["object"]["contents_url"] = trans.url_builder(
+                    "contents_dataset_collection",
                     hdca_id=self.encode_id(hdca.id),
-                    parent_id=self.encode_id(result["object"]["id"]))
+                    parent_id=self.encode_id(result["object"]["id"]),
+                )
             trans.security.encode_all_ids(result, recursive=True)
             return result
 
diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py
index 7295078771f..13346681041 100644
--- a/lib/galaxy/webapps/galaxy/services/datasets.py
+++ b/lib/galaxy/webapps/galaxy/services/datasets.py
@@ -70,6 +70,7 @@ DEFAULT_LIMIT = 500
 
 class RequestDataType(str, Enum):
     """Particular pieces of information that can be requested for a dataset."""
+
     state = "state"
     converted_datasets_state = "converted_datasets_state"
     data = "data"
@@ -133,6 +134,7 @@ class DatasetTextContentDetails(Model):
 
 class ConvertedDatasetsMap(BaseModel):
     """Map of `file extension` -> `converted dataset encoded id`"""
+
     __root__: Dict[str, EncodedDatabaseIdField]  # extension -> dataset ID
 
     class Config:
@@ -161,7 +163,6 @@ class BamDataResult(DataResult):
 
 
 class DatasetsService(ServiceBase, UsesVisualizationMixin):
-
     def __init__(
         self,
         security: IdEncodingHelper,
@@ -172,7 +173,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         ldda_manager: LDDAManager,
         history_contents_manager: HistoryContentsManager,
         history_contents_filters: HistoryContentsFilters,
-        data_provider_registry: DataProviderRegistry
+        data_provider_registry: DataProviderRegistry,
     ):
         super().__init__(security)
         self.history_manager = history_manager
@@ -186,11 +187,11 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
     @property
     def serializer_by_type(self) -> Dict[str, ModelSerializer]:
-        return {'dataset': self.hda_serializer, 'dataset_collection': self.hdca_serializer}
+        return {"dataset": self.hda_serializer, "dataset_collection": self.hdca_serializer}
 
     @property
     def dataset_manager_by_type(self) -> Dict[str, DatasetAssociationManager]:
-        return {'hda': self.hda_manager, 'ldda': self.ldda_manager}
+        return {"hda": self.hda_manager, "ldda": self.ldda_manager}
 
     def index(
         self,
@@ -205,7 +206,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         """
         user = self.get_authenticated_user(trans)
         filters = self.history_contents_filters.parse_query_filters(filter_query_params)
-        view = serialization_params.view or 'summary'
+        view = serialization_params.view or "summary"
         order_by = self.build_order_by(self.history_contents_manager, filter_query_params.order or "create_time-dsc")
         container = None
         if history_id:
@@ -219,7 +220,9 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             user_id=user.id,
         )
         return [
-            self.serializer_by_type[content.history_content_type].serialize_to_view(content, user=user, trans=trans, view=view)
+            self.serializer_by_type[content.history_content_type].serialize_to_view(
+                content, user=user, trans=trans, view=view
+            )
             for content in contents
         ]
 
@@ -244,7 +247,8 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             rval = self._dataset_state(dataset)
         elif data_type == RequestDataType.converted_datasets_state:
             rval = self._converted_datasets_state(
-                trans, dataset,
+                trans,
+                dataset,
                 chrom=extra_params.get("chrom", None),
                 retry=extra_params.get("retry", False),
             )
@@ -264,10 +268,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             # Default: return dataset as dict.
             if hda_ldda == DatasetSourceType.hda:
                 return self.hda_serializer.serialize_to_view(
-                    dataset,
-                    view=serialization_params.view or 'detailed',
-                    user=trans.user,
-                    trans=trans
+                    dataset, view=serialization_params.view or "detailed", user=trans.user, trans=trans
                 )
             else:
                 dataset_dict = dataset.to_dict()
@@ -355,7 +356,9 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         rval = []
         for root, directories, files in safe_walk(extra_files_path):
             for directory in directories:
-                rval.append({"class": "Directory", "path": os.path.relpath(os.path.join(root, directory), extra_files_path)})
+                rval.append(
+                    {"class": "Directory", "path": os.path.relpath(os.path.join(root, directory), extra_files_path)}
+                )
             for file in files:
                 rval.append({"class": "File", "path": os.path.relpath(os.path.join(root, file), extra_files_path)})
 
@@ -381,26 +384,25 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         """
         decoded_content_id = self.decode_id(history_content_id)
         headers = {}
-        rval: Any = ''
+        rval: Any = ""
         try:
             hda = self.hda_manager.get_accessible(decoded_content_id, trans.user)
             if raw:
-                if filename and filename != 'index':
+                if filename and filename != "index":
                     object_store = trans.app.object_store
                     dir_name = hda.dataset.extra_files_path_name
-                    file_path = object_store.get_filename(hda.dataset,
-                                                          extra_dir=dir_name,
-                                                          alt_name=filename)
+                    file_path = object_store.get_filename(hda.dataset, extra_dir=dir_name, alt_name=filename)
                 else:
                     file_path = hda.file_name
-                rval = open(file_path, 'rb')
+                rval = open(file_path, "rb")
             else:
                 rval, headers = hda.datatype.display_data(trans, hda, preview, filename, to_ext, **kwd)
         except galaxy_exceptions.MessageException:
             raise
         except Exception as e:
-            log.exception("Server error getting display data for dataset (%s) from history (%s)",
-                          history_content_id, history_id)
+            log.exception(
+                "Server error getting display data for dataset (%s) from history (%s)", history_content_id, history_id
+            )
             raise galaxy_exceptions.InternalServerError(f"Could not get display data for dataset: {util.unicodify(e)}")
         return rval, headers
 
@@ -409,14 +411,18 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         trans: ProvidesHistoryContext,
         dataset_id: EncodedDatabaseIdField,
     ) -> DatasetTextContentDetails:
-        """ Returns dataset content as Text. """
+        """Returns dataset content as Text."""
         user = self.get_authenticated_user(trans)
         decoded_id = self.decode_id(dataset_id)
         hda = self.hda_manager.get_accessible(decoded_id, user)
         hda = self.hda_manager.error_if_uploading(hda)
         truncated, dataset_data = self.hda_manager.text_data(hda, preview=True)
         item_url = web.url_for(
-            controller='dataset', action='display_by_username_and_slug', username=hda.history.user.username, slug=self.encode_id(hda.id), preview=False
+            controller="dataset",
+            action="display_by_username_and_slug",
+            username=hda.history.user.username,
+            slug=self.encode_id(hda.id),
+            preview=False,
         )
         return DatasetTextContentDetails(
             item_data=dataset_data,
@@ -440,13 +446,13 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         decoded_content_id = self.decode_id(history_content_id)
         hda = self.hda_manager.get_accessible(decoded_content_id, trans.user)
         file_ext = hda.metadata.spec.get(metadata_file).get("file_ext", metadata_file)
-        fname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in hda.name)[0:150]
+        fname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in hda.name)[0:150]
         headers = {}
         headers["Content-Type"] = "application/octet-stream"
         headers["Content-Disposition"] = f'attachment; filename="Galaxy{hda.hid}-[{fname}].{file_ext}"'
         file_path = hda.metadata.get(metadata_file).file_name
         if open_file:
-            return open(file_path, 'rb'), headers
+            return open(file_path, "rb"), headers
         return file_path, headers
 
     def converted_ext(
@@ -464,10 +470,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         serialization_params.default_view = "detailed"
         converted = self._get_or_create_converted(trans, hda, ext)
         return self.hda_serializer.serialize_to_view(
-            converted,
-            user=trans.user,
-            trans=trans,
-            **serialization_params.dict()
+            converted, user=trans.user, trans=trans, **serialization_params.dict()
         )
 
     def converted(
@@ -481,7 +484,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         """
         decoded_id = self.decode_id(dataset_id)
         hda = self.hda_manager.get_accessible(decoded_id, trans.user)
-        return self.hda_serializer.serialize_converted_datasets(hda, 'converted')
+        return self.hda_serializer.serialize_converted_datasets(hda, "converted")
 
     def _get_or_create_converted(self, trans, original: model.DatasetInstance, target_ext: str):
         try:
@@ -491,11 +494,9 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
         except model.NoConverterException:
             exc_data = dict(
-                source=original.ext,
-                target=target_ext,
-                available=list(original.get_converter_types().keys())
+                source=original.ext, target=target_ext, available=list(original.get_converter_types().keys())
             )
-            raise galaxy_exceptions.RequestParameterInvalidException('Conversion not possible', **exc_data)
+            raise galaxy_exceptions.RequestParameterInvalidException("Conversion not possible", **exc_data)
 
     def _dataset_in_use_state(self, dataset: model.DatasetInstance) -> bool:
         """
@@ -530,7 +531,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
         # Get datasources and check for messages (which indicate errors). Retry if flag is set.
         data_sources = dataset.get_datasources(trans)
-        messages_list = [data_source_dict['message'] for data_source_dict in data_sources.values()]
+        messages_list = [data_source_dict["message"] for data_source_dict in data_sources.values()]
         msg = self._get_highest_priority_msg(messages_list)
         if msg:
             if retry:
@@ -542,8 +543,9 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
         # If there is a chrom, check for data on the chrom.
         if chrom:
-            data_provider = self.data_provider_registry.get_data_provider(trans,
-                                                                          original_dataset=dataset, source='index')
+            data_provider = self.data_provider_registry.get_data_provider(
+                trans, original_dataset=dataset, source="index"
+            )
             if not data_provider.has_data(chrom):
                 return dataset.conversion_messages.NO_DATA
 
@@ -551,7 +553,10 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         return {"status": dataset.conversion_messages.DATA, "valid_chroms": None}
 
     def _search_features(
-        self, trans, dataset: model.DatasetInstance, query: Optional[str],
+        self,
+        trans,
+        dataset: model.DatasetInstance,
+        query: Optional[str],
     ) -> List[List[str]]:
         """
         Returns features, locations in dataset that match query. Format is a
@@ -595,7 +600,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
 
         # Get datasources and check for messages.
         data_sources = dataset.get_datasources(trans)
-        messages_list = [data_source_dict['message'] for data_source_dict in data_sources.values()]
+        messages_list = [data_source_dict["message"] for data_source_dict in data_sources.values()]
         return_message = self._get_highest_priority_msg(messages_list)
         if return_message:
             return return_message
@@ -607,7 +612,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         # Coverage mode uses index data.
         if mode == "Coverage":
             # Get summary using minimal cutoffs.
-            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source='index')
+            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
             return indexer.get_data(chrom, low, high, **kwargs)
 
         # TODO:
@@ -617,19 +622,19 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         # If mode is Auto, need to determine what type of data to return.
         if mode == "Auto":
             # Get stats from indexer.
-            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source='index')
+            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
             stats = indexer.get_data(chrom, low, high, stats=True)
 
             # If stats were requested, return them.
-            if 'stats' in kwargs:
-                if stats['data']['max'] == 0:
+            if "stats" in kwargs:
+                if stats["data"]["max"] == 0:
                     return DataResult(dataset_type=indexer.dataset_type, data=None)
                 else:
                     return stats
 
             # Stats provides features/base and resolution is bases/pixel, so
             # multiplying them yields features/pixel.
-            features_per_pixel = stats['data']['max'] * float(kwargs['resolution'])
+            features_per_pixel = stats["data"]["max"] * float(kwargs["resolution"])
 
             # Use heuristic based on features/pixel and region size to determine whether to
             # return coverage data. When zoomed out and region is large, features/pixel
@@ -643,7 +648,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         #
 
         # Get data provider.
-        data_provider = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source='data')
+        data_provider = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="data")
 
         # Allow max_vals top be data provider set if not passed
         if max_vals is None:
@@ -658,24 +663,33 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
                 # FIXME: increase region 1M each way to provide sequence for
                 # spliced/gapped reads. Probably should provide refseq object
                 # directly to data provider.
-                region = trans.app.genomes.reference(trans, dbkey=dataset.dbkey, chrom=chrom,
-                                                    low=(max(0, int(low) - 1000000)),
-                                                    high=(int(high) + 1000000))
+                region = trans.app.genomes.reference(
+                    trans,
+                    dbkey=dataset.dbkey,
+                    chrom=chrom,
+                    low=(max(0, int(low) - 1000000)),
+                    high=(int(high) + 1000000),
+                )
 
             # Get mean depth.
             if not indexer:
-                indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source='index')
+                indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
             stats = indexer.get_data(chrom, low, high, stats=True)
-            mean_depth = stats['data']['mean']
+            mean_depth = stats["data"]["mean"]
 
         # Get and return data from data_provider.
-        result = data_provider.get_data(chrom, int(low), int(high), int(start_val), int(max_vals),
-                                        ref_seq=region, mean_depth=mean_depth, **kwargs)
-        result.update({'dataset_type': data_provider.dataset_type, 'extra_info': extra_info})
+        result = data_provider.get_data(
+            chrom, int(low), int(high), int(start_val), int(max_vals), ref_seq=region, mean_depth=mean_depth, **kwargs
+        )
+        result.update({"dataset_type": data_provider.dataset_type, "extra_info": extra_info})
         return result
 
     def _raw_data(
-        self, trans, dataset, provider=None, **kwargs,
+        self,
+        trans,
+        dataset,
+        provider=None,
+        **kwargs,
     ) -> Union[model.Dataset.conversion_messages, BamDataResult, DataResult]:
         """
         Uses original (raw) dataset to return data. This method is useful
@@ -698,9 +712,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             elif dataset.datatype.has_dataprovider(provider):
                 kwargs = dataset.datatype.dataproviders[provider].parse_query_string_settings(kwargs)
                 # use dictionary to allow more than the data itself to be returned (data totals, other meta, etc.)
-                return DataResult(
-                    data=list(dataset.datatype.dataprovider(dataset, provider, **kwargs))
-                )
+                return DataResult(data=list(dataset.datatype.dataprovider(dataset, provider, **kwargs)))
 
             else:
                 raise dataproviders.exceptions.NoProviderAvailable(dataset.datatype, provider)
diff --git a/lib/galaxy/webapps/galaxy/services/histories.py b/lib/galaxy/webapps/galaxy/services/histories.py
index ba31c833a6e..1022ccffb5d 100644
--- a/lib/galaxy/webapps/galaxy/services/histories.py
+++ b/lib/galaxy/webapps/galaxy/services/histories.py
@@ -19,10 +19,8 @@ from sqlalchemy import (
     true,
 )
 
-from galaxy import (
-    exceptions as glx_exceptions,
-    model
-)
+from galaxy import exceptions as glx_exceptions
+from galaxy import model
 from galaxy.managers.citations import CitationsManager
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.managers.histories import (
@@ -130,10 +128,13 @@ class HistoriesService(ServiceBase):
         order_by = self.build_order_by(self.manager, filter_query_params.order)
 
         histories = self.manager.list(
-            filters=filters, order_by=order_by,
-            limit=filter_query_params.limit, offset=filter_query_params.offset)
+            filters=filters, order_by=order_by, limit=filter_query_params.limit, offset=filter_query_params.offset
+        )
 
-        rval = [self._serialize_history(trans, history, serialization_params, default_view="summary") for history in histories]
+        rval = [
+            self._serialize_history(trans, history, serialization_params, default_view="summary")
+            for history in histories
+        ]
         return rval
 
     def _get_deleted_filter(self, deleted: Optional[bool], filter_params: List[Tuple[str, str, str]]):
@@ -142,7 +143,7 @@ class HistoriesService(ServiceBase):
         try:
             # the consumer must explicitly ask for both deleted and non-deleted
             #   but pull it from the parsed params (as the filter system will error on None)
-            deleted_filter_index = filter_params.index(('deleted', 'eq', 'None'))
+            deleted_filter_index = filter_params.index(("deleted", "eq", "None"))
             filter_params.pop(deleted_filter_index)
             return []
         except ValueError:
@@ -154,7 +155,7 @@ class HistoriesService(ServiceBase):
 
         # the third option not handled here is 'return only deleted'
         #   if this is passed in (in the form below), simply return and let the filter system handle it
-        if ('deleted', 'eq', 'True') in filter_params:
+        if ("deleted", "eq", "True") in filter_params:
             return []
 
         # otherwise, do the default filter of removing the deleted histories
@@ -193,7 +194,9 @@ class HistoriesService(ServiceBase):
                 raise glx_exceptions.MessageException("Please provide a url or file.")
             job = self.manager.queue_history_import(trans, archive_type=archive_type, archive_source=archive_source)
             job_dict = job.to_dict()
-            job_dict["message"] = f"Importing history from source '{archive_source}'. This history will be visible when the import is complete."
+            job_dict[
+                "message"
+            ] = f"Importing history from source '{archive_source}'. This history will be visible when the import is complete."
             job_dict = trans.security.encode_all_ids(job_dict)
             return JobImportHistoryResponse.parse_obj(job_dict)
 
@@ -250,16 +253,10 @@ class HistoriesService(ServiceBase):
         """
         if history_id is None:  # By default display the most recent history
             history = self.manager.most_recent(
-                trans.user,
-                filters=(model.History.deleted == false()),
-                current_history=trans.history
+                trans.user, filters=(model.History.deleted == false()), current_history=trans.history
             )
         else:
-            history = self.manager.get_accessible(
-                self.decode_id(history_id),
-                trans.user,
-                current_history=trans.history
-            )
+            history = self.manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history)
         return self._serialize_history(trans, history, serialization_params)
 
     def update(
@@ -351,10 +348,17 @@ class HistoriesService(ServiceBase):
         current_user = trans.user
         filters = self.filters.parse_query_filters(filter_query_params)
         order_by = self.build_order_by(self.manager, filter_query_params.order)
-        histories = self.manager.list_shared_with(current_user,
-            filters=filters, order_by=order_by,
-            limit=filter_query_params.limit, offset=filter_query_params.offset)
-        rval = [self._serialize_history(trans, history, serialization_params, default_view="summary") for history in histories]
+        histories = self.manager.list_shared_with(
+            current_user,
+            filters=filters,
+            order_by=order_by,
+            limit=filter_query_params.limit,
+            offset=filter_query_params.offset,
+        )
+        rval = [
+            self._serialize_history(trans, history, serialization_params, default_view="summary")
+            for history in histories
+        ]
         return rval
 
     def published(
@@ -369,10 +373,15 @@ class HistoriesService(ServiceBase):
         filters = self.filters.parse_query_filters(filter_query_params)
         order_by = self.build_order_by(self.manager, filter_query_params.order)
         histories = self.manager.list_published(
-            filters=filters, order_by=order_by,
-            limit=filter_query_params.limit, offset=filter_query_params.offset,
+            filters=filters,
+            order_by=order_by,
+            limit=filter_query_params.limit,
+            offset=filter_query_params.offset,
         )
-        rval = [self._serialize_history(trans, history, serialization_params, default_view="summary") for history in histories]
+        rval = [
+            self._serialize_history(trans, history, serialization_params, default_view="summary")
+            for history in histories
+        ]
         return rval
 
     def citations(self, trans: ProvidesHistoryContext, history_id: EncodedDatabaseIdField):
@@ -481,9 +490,9 @@ class HistoriesService(ServiceBase):
         return self.manager.get_ready_history_export_file_path(trans, jeha)
 
     def get_archive_media_type(self, jeha: model.JobExportHistoryArchive):
-        media_type = 'application/x-tar'
+        media_type = "application/x-tar"
         if jeha.compressed:
-            media_type = 'application/x-gzip'
+            media_type = "application/x-gzip"
         return media_type
 
     # TODO: remove this function and HistoryManager.legacy_serve_ready_history_export when
@@ -512,20 +521,25 @@ class HistoriesService(ServiceBase):
         installed_builds = []
         for build in glob.glob(os.path.join(trans.app.config.len_file_path, "*.len")):
             installed_builds.append(os.path.basename(build).split(".len")[0])
-        fasta_hdas = trans.sa_session.query(model.HistoryDatasetAssociation) \
-            .filter_by(history=history, extension="fasta", deleted=False) \
+        fasta_hdas = (
+            trans.sa_session.query(model.HistoryDatasetAssociation)
+            .filter_by(history=history, extension="fasta", deleted=False)
             .order_by(model.HistoryDatasetAssociation.hid.desc())
+        )
         return CustomBuildsMetadataResponse(
             installed_builds=[LabelValuePair(label=ins, value=ins) for ins in installed_builds],
-            fasta_hdas=[LabelValuePair(label=f'{hda.hid}: {hda.name}', value=trans.security.encode_id(hda.id)) for hda in fasta_hdas],
+            fasta_hdas=[
+                LabelValuePair(label=f"{hda.hid}: {hda.name}", value=trans.security.encode_id(hda.id))
+                for hda in fasta_hdas
+            ],
         )
 
     def _serialize_history(
-            self,
-            trans: ProvidesHistoryContext,
-            history: model.History,
-            serialization_params: SerializationParams,
-            default_view: str = "detailed",
+        self,
+        trans: ProvidesHistoryContext,
+        history: model.History,
+        serialization_params: SerializationParams,
+        default_view: str = "detailed",
     ) -> AnyHistoryView:
         """
         Returns a dictionary with the corresponding values depending on the
@@ -533,9 +547,6 @@ class HistoriesService(ServiceBase):
         """
         serialization_params.default_view = default_view
         serialized_history = self.serializer.serialize_to_view(
-            history,
-            user=trans.user,
-            trans=trans,
-            **serialization_params.dict()
+            history, user=trans.user, trans=trans, **serialization_params.dict()
         )
         return serialized_history
diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
index a1a51b7364d..a4defb8869a 100644
--- a/lib/galaxy/webapps/galaxy/services/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -18,19 +18,15 @@ from pydantic import (
 )
 from typing_extensions import Literal
 
-from galaxy import (
-    exceptions,
-)
+from galaxy import exceptions
 from galaxy.managers import (
     folders,
     hdas,
     hdcas,
     histories,
-    history_contents
-)
-from galaxy.managers.base import (
-    ModelSerializer,
+    history_contents,
 )
+from galaxy.managers.base import ModelSerializer
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.collections_util import (
     api_payload_to_create_params,
@@ -52,9 +48,7 @@ from galaxy.schema import (
     FilterQueryParams,
     SerializationParams,
 )
-from galaxy.schema.fields import (
-    EncodedDatabaseIdField,
-)
+from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.schema.schema import (
     AnyHistoryContentItem,
     AnyJobStateSummary,
@@ -77,10 +71,9 @@ from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.webapps.galaxy.api.common import parse_serialization_params
 from galaxy.webapps.galaxy.services.base import ServiceBase
 
-
 log = logging.getLogger(__name__)
 
-DatasetDetailsType = Union[Set[EncodedDatabaseIdField], Literal['all']]
+DatasetDetailsType = Union[Set[EncodedDatabaseIdField], Literal["all"]]
 
 
 class DirectionOptions(str, Enum):
@@ -95,12 +88,14 @@ HistoryContentsFilterList = List[HistoryContentFilter]
 
 class HistoryContentsIndexParams(Model):
     """Query parameters exclusively used by the *new version* of `index` operation."""
-    v: Optional[Literal['dev']]
+
+    v: Optional[Literal["dev"]]
     dataset_details: Optional[DatasetDetailsType]
 
 
 class LegacyHistoryContentsIndexParams(Model):
     """Query parameters exclusively used by the *legacy version* of `index` operation."""
+
     ids: Optional[List[EncodedDatabaseIdField]]
     types: List[HistoryContentType]
     dataset_details: Optional[DatasetDetailsType]
@@ -110,6 +105,7 @@ class LegacyHistoryContentsIndexParams(Model):
 
 class HistoryContentsIndexJobsSummaryParams(Model):
     """Query parameters exclusively used by the `index_jobs_summary` operation."""
+
     ids: List[EncodedDatabaseIdField] = []
     types: List[JobSourceType] = []
 
@@ -210,10 +206,8 @@ class HistoriesContentsService(ServiceBase):
 
         .. note:: Anonymous users are allowed to get their current history contents.
         """
-        if params.v == 'dev':
-            return self.__index_v2(
-                trans, history_id, params, serialization_params, filter_query_params
-            )
+        if params.v == "dev":
+            return self.__index_v2(trans, history_id, params, serialization_params, filter_query_params)
         return self.__index_legacy(trans, history_id, legacy_params)
 
     def show(
@@ -258,10 +252,11 @@ class HistoriesContentsService(ServiceBase):
             return self.__show_dataset(trans, id, serialization_params)
         elif contents_type == HistoryContentType.dataset_collection:
             return self.__show_dataset_collection(trans, id, serialization_params, fuzzy_count)
-        raise exceptions.UnknownContentsType(f'Unknown contents type: {contents_type}')
+        raise exceptions.UnknownContentsType(f"Unknown contents type: {contents_type}")
 
     def index_jobs_summary(
-        self, trans,
+        self,
+        trans,
         params: HistoryContentsIndexJobsSummaryParams,
     ) -> List[AnyJobStateSummary]:
         """
@@ -279,13 +274,11 @@ class HistoriesContentsService(ServiceBase):
                 f"The number of ids ({len(ids)}) and types ({len(types)}) must match."
             )
         decoded_ids = self.decode_ids(ids)
-        return [
-            self.encode_all_ids(job_state)
-            for job_state in fetch_job_states(trans.sa_session, decoded_ids, types)
-        ]
+        return [self.encode_all_ids(job_state) for job_state in fetch_job_states(trans.sa_session, decoded_ids, types)]
 
     def show_jobs_summary(
-        self, trans,
+        self,
+        trans,
         id: EncodedDatabaseIdField,
         contents_type: HistoryContentType,
     ) -> AnyJobStateSummary:
@@ -335,11 +328,14 @@ class HistoriesContentsService(ServiceBase):
             raise exceptions.InternalServerError(error_message)
 
     def __stream_dataset_collection(self, trans, dataset_collection_instance):
-        archive = hdcas.stream_dataset_collection(dataset_collection_instance=dataset_collection_instance, upstream_mod_zip=trans.app.config.upstream_mod_zip)
+        archive = hdcas.stream_dataset_collection(
+            dataset_collection_instance=dataset_collection_instance, upstream_mod_zip=trans.app.config.upstream_mod_zip
+        )
         return archive
 
     def create(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         payload: CreateHistoryContentPayload,
         serialization_params: SerializationParams,
@@ -350,9 +346,7 @@ class HistoriesContentsService(ServiceBase):
         ..note:
             Currently, a user can only copy an HDA from a history that the user owns.
         """
-        history = self.history_manager.get_owned(
-            self.decode_id(history_id), trans.user, current_history=trans.history
-        )
+        history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
 
         history_content_type = payload.type
         if history_content_type == HistoryContentType.dataset:
@@ -363,10 +357,11 @@ class HistoriesContentsService(ServiceBase):
                 return self.__create_dataset(trans, history, payload, serialization_params)
         elif history_content_type == HistoryContentType.dataset_collection:
             return self.__create_dataset_collection(trans, history, payload, serialization_params)
-        raise exceptions.UnknownContentsType(f'Unknown contents type: {payload.type}')
+        raise exceptions.UnknownContentsType(f"Unknown contents type: {payload.type}")
 
     def update_permissions(
-        self, trans,
+        self,
+        trans,
         history_content_id: EncodedDatabaseIdField,
         payload: UpdateDatasetPermissionsPayload,
     ) -> DatasetAssociationRoles:
@@ -388,14 +383,17 @@ class HistoriesContentsService(ServiceBase):
                     RequestParameterMissingException
         """
         payload_dict = payload.dict(by_alias=True)
-        hda = self.hda_manager.get_owned(self.decode_id(history_content_id), trans.user, current_history=trans.history, trans=trans)
+        hda = self.hda_manager.get_owned(
+            self.decode_id(history_content_id), trans.user, current_history=trans.history, trans=trans
+        )
         assert hda is not None
         self.hda_manager.update_permissions(trans, hda, **payload_dict)
         roles = self.hda_manager.serialize_dataset_association_roles(trans, hda)
         return DatasetAssociationRoles.parse_obj(roles)
 
     def update(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         id: EncodedDatabaseIdField,
         payload: Dict[str, Any],
@@ -418,10 +416,11 @@ class HistoriesContentsService(ServiceBase):
         elif contents_type == HistoryContentType.dataset_collection:
             return self.__update_dataset_collection(trans, id, payload)
         else:
-            raise exceptions.UnknownContentsType(f'Unknown contents type: {contents_type}')
+            raise exceptions.UnknownContentsType(f"Unknown contents type: {contents_type}")
 
     def update_batch(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         payload: UpdateHistoryContentsBatchPayload,
         serialization_params: SerializationParams,
@@ -440,9 +439,7 @@ class HistoriesContentsService(ServiceBase):
         :returns:   an error object if an error occurred or a dictionary containing
                     any values that were different from the original and, therefore, updated
         """
-        history = self.history_manager.get_owned(
-            self.decode_id(history_id), trans.user, current_history=trans.history
-        )
+        history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
         items = payload.items
         hda_ids = []
         hdca_ids = []
@@ -459,20 +456,16 @@ class HistoriesContentsService(ServiceBase):
         for hda in hdas:
             self.__deserialize_dataset(trans, hda, payload_dict)
             serialization_params.default_view = "summary"
-            rval.append(self.hda_serializer.serialize_to_view(
-                hda, user=trans.user, trans=trans, **serialization_params.dict()
-            ))
+            rval.append(
+                self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **serialization_params.dict())
+            )
         for hdca_id in hdca_ids:
             self.__update_dataset_collection(trans, hdca_id, payload.dict(exclude_defaults=True))
             dataset_collection_instance = self.__get_accessible_collection(trans, hdca_id)
             rval.append(self.__collection_dict(trans, dataset_collection_instance, view="summary"))
         return rval
 
-    def validate(
-        self, trans,
-        history_id: EncodedDatabaseIdField,
-        history_content_id: EncodedDatabaseIdField
-    ):
+    def validate(self, trans, history_id: EncodedDatabaseIdField, history_content_id: EncodedDatabaseIdField):
         """
         Validates the metadata associated with a dataset within a History.
 
@@ -485,16 +478,15 @@ class HistoriesContentsService(ServiceBase):
         :returns:   TODO
         """
         decoded_id = self.decode_id(history_content_id)
-        history = self.history_manager.get_owned(
-            self.decode_id(history_id), trans.user, current_history=trans.history
-        )
+        history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
         hda = self.hda_manager.get_owned_ids([decoded_id], history=history)[0]
         if hda:
             self.hda_manager.set_metadata(trans, hda, overwrite=True, validate=True)
         return {}
 
     def delete(
-        self, trans,
+        self,
+        trans,
         id,
         serialization_params: SerializationParams,
         contents_type: HistoryContentType,
@@ -513,13 +505,14 @@ class HistoriesContentsService(ServiceBase):
             )
             return DeleteHistoryContentResult(id=id, deleted=True)
         else:
-            raise exceptions.UnknownContentsType(f'Unknown contents type: {contents_type}')
+            raise exceptions.UnknownContentsType(f"Unknown contents type: {contents_type}")
 
     def archive(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         filter_query_params: FilterQueryParams,
-        filename: Optional[str] = '',
+        filename: Optional[str] = "",
         dry_run: Optional[bool] = True,
     ) -> Union[HistoryContentsArchiveDryRunResult, ZipstreamWrapper]:
         """
@@ -536,9 +529,9 @@ class HistoriesContentsService(ServiceBase):
         # roughly from: http://stackoverflow.com/a/31976060 (windows, linux)
         invalid_filename_char_regex = re.compile(r'[:<>|\\\/\?\* "]')
         # path format string - dot separator between id and name
-        id_name_format = '{}.{}'
+        id_name_format = "{}.{}"
 
-        def name_to_filename(name, max_length=150, replace_with='_'):
+        def name_to_filename(name, max_length=150, replace_with="_"):
             # TODO: seems like shortening unicode with [:] would cause unpredictable display strings
             return invalid_filename_char_regex.sub(replace_with, name)[0:max_length]
 
@@ -548,11 +541,11 @@ class HistoriesContentsService(ServiceBase):
             parent_names = []
             for parent in parents:
                 # an HDCA
-                if hasattr(parent, 'hid'):
+                if hasattr(parent, "hid"):
                     name = name_to_filename(parent.name)
                     parent_names.append(id_name_format.format(parent.hid, name))
                 # a DCE
-                elif hasattr(parent, 'element_index'):
+                elif hasattr(parent, "element_index"):
                     name = name_to_filename(parent.element_identifier)
                     parent_names.append(id_name_format.format(parent.element_index, name))
             # NOTE: DCs are skipped and use the wrapping DCE info instead
@@ -574,7 +567,7 @@ class HistoriesContentsService(ServiceBase):
             content_container_id = content.hid
             content_name = name_to_filename(content.name)
             if parents:
-                if hasattr(parents[0], 'element_index'):
+                if hasattr(parents[0], "element_index"):
                     # if content is directly wrapped in a DCE, strip it from parents (and the resulting path)
                     # and instead replace the content id and name with the DCE index and identifier
                     parent_dce, parents = parents[0], parents[1:]
@@ -625,7 +618,8 @@ class HistoriesContentsService(ServiceBase):
         return archive
 
     def contents_near(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         serialization_params: SerializationParams,
         filter_params: HistoryContentsFilterList,
@@ -657,8 +651,8 @@ class HistoriesContentsService(ServiceBase):
             if history.update_time <= since:
                 return None
 
-        order_by_dsc = self.build_order_by(self.history_contents_manager, 'hid-dsc')
-        order_by_asc = self.build_order_by(self.history_contents_manager, 'hid-asc')
+        order_by_dsc = self.build_order_by(self.history_contents_manager, "hid-dsc")
+        order_by_asc = self.build_order_by(self.history_contents_manager, "hid-asc")
         min_hid, max_hid = self._get_filtered_extrema(history, filter_params, order_by_dsc, order_by_asc)
         up_total_count, down_total_count = self._get_total_counts(history, filter_params, hid)
 
@@ -668,31 +662,40 @@ class HistoriesContentsService(ServiceBase):
             expanded = self._expand_contents(trans, matches, serialization_params)
             expanded.reverse()
             item_counts = self._set_item_counts(
-                matches_up=len(matches), total_matches_up=up_total_count, total_matches_down=down_total_count)
+                matches_up=len(matches), total_matches_up=up_total_count, total_matches_down=down_total_count
+            )
 
         elif direction == DirectionOptions.before:  # seek down: contents <= hid (older)
             _hid_params = self._hid_less_than(hid)
             matches = self._get_matches(history, filter_params, _hid_params, order_by_dsc, limit, serialization_params)
             expanded = self._expand_contents(trans, matches, serialization_params)
             item_counts = self._set_item_counts(
-                matches_down=len(matches), total_matches_up=up_total_count, total_matches_down=down_total_count)
+                matches_down=len(matches), total_matches_up=up_total_count, total_matches_down=down_total_count
+            )
 
         elif direction == DirectionOptions.near:  # seek up, down; then reverse up, and combine
             up_limit, down_limit = self._get_limits(limit)
 
             _hid_params = self._hid_greater_than(hid)
-            up_matches = self._get_matches(history, filter_params, _hid_params, order_by_asc, up_limit, serialization_params)
+            up_matches = self._get_matches(
+                history, filter_params, _hid_params, order_by_asc, up_limit, serialization_params
+            )
             up_expanded = self._expand_contents(trans, up_matches, serialization_params)
             up_expanded.reverse()
 
             _hid_params = self._hid_less_or_equal_than(hid)  # note <=: we are including the item with hid == {hid}
-            down_matches = self._get_matches(history, filter_params, _hid_params, order_by_dsc, down_limit, serialization_params)
+            down_matches = self._get_matches(
+                history, filter_params, _hid_params, order_by_dsc, down_limit, serialization_params
+            )
             down_expanded = self._expand_contents(trans, down_matches, serialization_params)
 
             expanded = up_expanded + down_expanded
             item_counts = self._set_item_counts(
-                matches_up=len(up_matches), matches_down=len(down_matches), total_matches_up=up_total_count,
-                total_matches_down=down_total_count)
+                matches_up=len(up_matches),
+                matches_down=len(down_matches),
+                total_matches_up=up_total_count,
+                total_matches_down=down_total_count,
+            )
 
         stats = ContentsNearStats(
             max_hid=max_hid,
@@ -709,12 +712,12 @@ class HistoriesContentsService(ServiceBase):
 
     def _set_item_counts(self, *, matches_up=0, total_matches_up=0, matches_down=0, total_matches_down=0):
         counts = {}
-        counts['matches'] = matches_up + matches_down
-        counts['matches_up'] = matches_up
-        counts['matches_down'] = matches_down
-        counts['total_matches'] = total_matches_up + total_matches_down + 1  # + 1 for hid == {hid}
-        counts['total_matches_up'] = total_matches_up
-        counts['total_matches_down'] = total_matches_down
+        counts["matches"] = matches_up + matches_down
+        counts["matches_up"] = matches_up
+        counts["matches_down"] = matches_down
+        counts["total_matches"] = total_matches_up + total_matches_down + 1  # + 1 for hid == {hid}
+        counts["total_matches_up"] = total_matches_up
+        counts["total_matches_down"] = total_matches_down
         return counts
 
     def _hid_greater_than(self, hid: int) -> HistoryContentsFilterList:
@@ -727,7 +730,6 @@ class HistoriesContentsService(ServiceBase):
         return [["hid", "le", hid]]
 
     def _get_total_counts(self, history, filter_params, hid):
-
         def get_count(params, hid_params):
             params = params + hid_params
             count_filters = self.history_contents_filters.parse_filters(params)
@@ -741,16 +743,18 @@ class HistoriesContentsService(ServiceBase):
     def _get_matches(self, history, filter_params, hid_params, order_by, limit, serialization_params):
         params = filter_params + hid_params
         filters = self.history_contents_filters.parse_filters(params)
-        contents = self.history_contents_manager.contents(history,
+        contents = self.history_contents_manager.contents(
+            history,
             filters=filters,
             limit=limit,
             offset=0,
             order_by=order_by,
-            serialization_params=serialization_params)
+            serialization_params=serialization_params,
+        )
         return contents
 
     def _copy_excluding_update_time(self, filter_params):
-        return [f for f in filter_params if f[0] != 'update_time']
+        return [f for f in filter_params if f[0] != "update_time"]
 
     # Adds subquery details to initial contents results, perhaps better realized
     # as a proc or view.
@@ -758,32 +762,30 @@ class HistoriesContentsService(ServiceBase):
         rval = []
         for content in contents:
             if isinstance(content, HistoryDatasetAssociation):
-                dataset = self.hda_serializer.serialize_to_view(content,
-                    user=trans.user, trans=trans, **serialization_params.dict())
+                dataset = self.hda_serializer.serialize_to_view(
+                    content, user=trans.user, trans=trans, **serialization_params.dict()
+                )
                 rval.append(dataset)
             elif isinstance(content, HistoryDatasetCollectionAssociation):
-                collection = self.hdca_serializer.serialize_to_view(content,
-                    user=trans.user, trans=trans, **serialization_params.dict())
+                collection = self.hdca_serializer.serialize_to_view(
+                    content, user=trans.user, trans=trans, **serialization_params.dict()
+                )
                 rval.append(collection)
         return rval
 
     def _get_filtered_extrema(self, history, filter_params, order_by_dsc, order_by_asc):
-        extrema_params = parse_serialization_params(keys='hid', default_view='summary')
+        extrema_params = parse_serialization_params(keys="hid", default_view="summary")
         extrema_filter_params = self._copy_excluding_update_time(filter_params)
         extrema_filters = self.history_contents_filters.parse_filters(extrema_filter_params)
 
-        max_row_result = self.history_contents_manager.contents(history,
-            limit=1,
-            filters=extrema_filters,
-            order_by=order_by_dsc,
-            serialization_params=extrema_params)
+        max_row_result = self.history_contents_manager.contents(
+            history, limit=1, filters=extrema_filters, order_by=order_by_dsc, serialization_params=extrema_params
+        )
         max_row = max_row_result.pop() if len(max_row_result) else None
 
-        min_row_result = self.history_contents_manager.contents(history,
-            limit=1,
-            filters=extrema_filters,
-            order_by=order_by_asc,
-            serialization_params=extrema_params)
+        min_row_result = self.history_contents_manager.contents(
+            history, limit=1, filters=extrema_filters, order_by=order_by_asc, serialization_params=extrema_params
+        )
         min_row = min_row_result.pop() if len(min_row_result) else None
 
         max_hid = max_row.hid if max_row else None
@@ -792,10 +794,7 @@ class HistoriesContentsService(ServiceBase):
         return min_hid, max_hid
 
     def __delete_dataset(
-        self, trans,
-        id: EncodedDatabaseIdField,
-        purge: bool,
-        serialization_params: SerializationParams
+        self, trans, id: EncodedDatabaseIdField, purge: bool, serialization_params: SerializationParams
     ):
         hda = self.hda_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history)
         self.hda_manager.error_if_uploading(hda)
@@ -804,55 +803,47 @@ class HistoriesContentsService(ServiceBase):
             self.hda_manager.purge(hda)
         else:
             self.hda_manager.delete(hda)
-        serialization_params.default_view = 'detailed'
-        return self.hda_serializer.serialize_to_view(
-            hda, user=trans.user, trans=trans, **serialization_params.dict()
-        )
+        serialization_params.default_view = "detailed"
+        return self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **serialization_params.dict())
 
     def __update_dataset_collection(self, trans, id: EncodedDatabaseIdField, payload: Dict[str, Any]):
         return self.dataset_collection_manager.update(trans, "history", id, payload)
 
     def __update_dataset(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         id: EncodedDatabaseIdField,
         payload: Dict[str, Any],
-        serialization_params: SerializationParams
+        serialization_params: SerializationParams,
     ):
         # anon user: ensure that history ids match up and the history is the current,
         #   check for uploading, and use only the subset of attribute keys manipulatable by anon users
         decoded_id = self.decode_id(id)
-        history = self.history_manager.get_owned(
-            self.decode_id(history_id), trans.user, current_history=trans.history
-        )
+        history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
         hda = self.__datasets_for_update(trans, history, [decoded_id], payload)[0]
         if hda:
             self.__deserialize_dataset(trans, hda, payload)
-            serialization_params.default_view = 'detailed'
+            serialization_params.default_view = "detailed"
             return self.hda_serializer.serialize_to_view(
                 hda, user=trans.user, trans=trans, **serialization_params.dict()
             )
         return {}
 
-    def __datasets_for_update(
-        self, trans,
-        history: History,
-        hda_ids: List[int],
-        payload: Dict[str, Any]
-    ):
+    def __datasets_for_update(self, trans, history: History, hda_ids: List[int], payload: Dict[str, Any]):
         anonymous_user = not trans.user_is_admin and trans.user is None
         if anonymous_user:
             anon_allowed_payload = {}
-            if 'deleted' in payload:
-                anon_allowed_payload['deleted'] = payload['deleted']
-            if 'visible' in payload:
-                anon_allowed_payload['visible'] = payload['visible']
+            if "deleted" in payload:
+                anon_allowed_payload["deleted"] = payload["deleted"]
+            if "visible" in payload:
+                anon_allowed_payload["visible"] = payload["visible"]
             payload = anon_allowed_payload
 
         hdas = self.hda_manager.get_owned_ids(hda_ids, history=history)
 
         # only check_state if not deleting, otherwise cannot delete uploading files
-        check_state = not payload.get('deleted', False)
+        check_state = not payload.get("deleted", False)
         if check_state:
             for hda in hdas:
                 hda = self.hda_manager.error_if_uploading(hda)
@@ -862,11 +853,12 @@ class HistoriesContentsService(ServiceBase):
     def __deserialize_dataset(self, trans, hda, payload: Dict[str, Any]):
         self.hda_deserializer.deserialize(hda, payload, user=trans.user, trans=trans)
         # TODO: this should be an effect of deleting the hda
-        if payload.get('deleted', False):
+        if payload.get("deleted", False):
             self.hda_manager.stop_creating_job(hda)
 
     def __index_legacy(
-        self, trans,
+        self,
+        trans,
         history_id: EncodedDatabaseIdField,
         legacy_params: LegacyHistoryContentsIndexParams,
     ) -> List[AnyHistoryContentItem]:
@@ -905,11 +897,12 @@ class HistoriesContentsService(ServiceBase):
             limit=filter_query_params.limit,
             offset=filter_query_params.offset,
             order_by=order_by,
-            serialization_params=serialization_params
+            serialization_params=serialization_params,
         )
         return [
             self._serialize_content_item(
-                trans, content,
+                trans,
+                content,
                 dataset_details=params.dataset_details,
                 serialization_params=serialization_params,
             )
@@ -923,21 +916,21 @@ class HistoriesContentsService(ServiceBase):
         dataset_details: Optional[DatasetDetailsType] = None,
     ):
         encoded_content_id = self.encode_id(content.id)
-        detailed = dataset_details and (dataset_details == 'all' or (encoded_content_id in dataset_details))
+        detailed = dataset_details and (dataset_details == "all" or (encoded_content_id in dataset_details))
         if isinstance(content, HistoryDatasetAssociation):
-            view = 'detailed' if detailed else 'summary'
+            view = "detailed" if detailed else "summary"
             return self.hda_serializer.serialize_to_view(content, view=view, user=trans.user, trans=trans)
         elif isinstance(content, HistoryDatasetCollectionAssociation):
-            view = 'element' if detailed else 'collection'
+            view = "element" if detailed else "collection"
             return self.__collection_dict(trans, content, view=view)
 
     def _serialize_content_item(
-            self,
-            trans,
-            content,
-            dataset_details: Optional[DatasetDetailsType],
-            serialization_params: SerializationParams,
-            default_view: str = "summary",
+        self,
+        trans,
+        content,
+        dataset_details: Optional[DatasetDetailsType],
+        serialization_params: SerializationParams,
+        default_view: str = "summary",
     ):
         """
         Returns a dictionary with the appropriate values depending on the
@@ -949,13 +942,13 @@ class HistoriesContentsService(ServiceBase):
         serializer: Optional[ModelSerializer] = None
         if isinstance(content, HistoryDatasetAssociation):
             serializer = self.hda_serializer
-            if dataset_details and (dataset_details == 'all' or self.encode_id(content.id) in dataset_details):
+            if dataset_details and (dataset_details == "all" or self.encode_id(content.id) in dataset_details):
                 view = "detailed"
         elif isinstance(content, HistoryDatasetCollectionAssociation):
             serializer = self.hdca_serializer
 
         if serializer is None:
-            raise exceptions.UnknownContentsType(f'Unknown contents type: {content.content_type}')
+            raise exceptions.UnknownContentsType(f"Unknown contents type: {content.content_type}")
 
         rval = serializer.serialize_to_view(
             content, user=trans.user, trans=trans, view=view, **serialization_params_dict
@@ -963,13 +956,15 @@ class HistoriesContentsService(ServiceBase):
         # Override URL generation to use UrlBuilder
         if trans.url_builder:
             if rval.get("url"):
-                rval["url"] = trans.url_builder('history_content_typed',
-                    history_id=rval["history_id"], id=rval["id"], type=rval["history_content_type"]
+                rval["url"] = trans.url_builder(
+                    "history_content_typed",
+                    history_id=rval["history_id"],
+                    id=rval["id"],
+                    type=rval["history_content_type"],
                 )
             if rval.get("contents_url"):
-                rval["contents_url"] = trans.url_builder('contents_dataset_collection',
-                    hdca_id=rval["id"],
-                    parent_id=self.encode_id(content.collection_id)
+                rval["contents_url"] = trans.url_builder(
+                    "contents_dataset_collection", hdca_id=rval["id"], parent_id=self.encode_id(content.collection_id)
                 )
         return rval
 
@@ -979,27 +974,29 @@ class HistoriesContentsService(ServiceBase):
             security=trans.security,
             url_builder=trans.url_builder,
             parent=dataset_collection_instance.history,
-            **kwds
+            **kwds,
         )
 
     def _get_history(self, trans, history_id: EncodedDatabaseIdField) -> History:
         """Retrieves the History with the given ID or raises an error if the current user cannot access it."""
-        history = self.history_manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history)
+        history = self.history_manager.get_accessible(
+            self.decode_id(history_id), trans.user, current_history=trans.history
+        )
         return history
 
     def __show_dataset(
-        self, trans,
+        self,
+        trans,
         id: EncodedDatabaseIdField,
         serialization_params: SerializationParams,
     ):
         serialization_params.default_view = "detailed"
         hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
-        return self.hda_serializer.serialize_to_view(
-            hda, user=trans.user, trans=trans, **serialization_params.dict()
-        )
+        return self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **serialization_params.dict())
 
     def __show_dataset_collection(
-        self, trans,
+        self,
+        trans,
         id: EncodedDatabaseIdField,
         serialization_params: SerializationParams,
         fuzzy_count: Optional[int] = None,
@@ -1010,11 +1007,14 @@ class HistoriesContentsService(ServiceBase):
 
     def __get_accessible_collection(self, trans, id: EncodedDatabaseIdField):
         return self.dataset_collection_manager.get_dataset_collection_instance(
-            trans=trans, instance_type="history", id=id,
+            trans=trans,
+            instance_type="history",
+            id=id,
         )
 
     def __create_datasets_from_library_folder(
-        self, trans,
+        self,
+        trans,
         history: History,
         payload: CreateHistoryContentPayloadFromCopy,
         serialization_params: SerializationParams,
@@ -1037,23 +1037,26 @@ class HistoriesContentsService(ServiceBase):
                 rval = []
                 for subfolder in folder.active_folders:
                     if not admin:
-                        can_access, folder_ids = security_agent.check_folder_contents(trans.user, current_user_roles, subfolder)
+                        can_access, folder_ids = security_agent.check_folder_contents(
+                            trans.user, current_user_roles, subfolder
+                        )
                     if (admin or can_access) and not subfolder.deleted:
                         rval.extend(traverse(subfolder))
                 for ld in folder.datasets:
                     if not admin:
                         can_access = security_agent.can_access_dataset(
-                            current_user_roles,
-                            ld.library_dataset_dataset_association.dataset
+                            current_user_roles, ld.library_dataset_dataset_association.dataset
                         )
                     if (admin or can_access) and not ld.deleted:
                         rval.append(ld)
                 return rval
 
             for ld in traverse(folder):
-                hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
+                hda = ld.library_dataset_dataset_association.to_history_dataset_association(
+                    history, add_to_history=True
+                )
                 hda_dict = self.hda_serializer.serialize_to_view(
-                    hda, user=trans.user, trans=trans, default_view='detailed', **serialization_params.dict()
+                    hda, user=trans.user, trans=trans, default_view="detailed", **serialization_params.dict()
                 )
                 rval.append(hda_dict)
         else:
@@ -1064,15 +1067,15 @@ class HistoriesContentsService(ServiceBase):
         return rval
 
     def __create_dataset(
-        self, trans,
+        self,
+        trans,
         history: History,
         payload: CreateHistoryContentPayloadFromCopy,
         serialization_params: SerializationParams,
     ):
         source = payload.source
         if source not in (HistoryContentSource.library, HistoryContentSource.hda):
-            raise exceptions.RequestParameterInvalidException(
-                f"'source' must be either 'library' or 'hda': {source}")
+            raise exceptions.RequestParameterInvalidException(f"'source' must be either 'library' or 'hda': {source}")
         content = payload.content
         if content is None:
             raise exceptions.RequestParameterMissingException("'content' id of lda or hda is missing")
@@ -1087,17 +1090,14 @@ class HistoriesContentsService(ServiceBase):
             return None
 
         trans.sa_session.flush()
-        serialization_params.default_view = 'detailed'
-        return self.hda_serializer.serialize_to_view(
-            hda, user=trans.user, trans=trans, **serialization_params.dict()
-        )
+        serialization_params.default_view = "detailed"
+        return self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **serialization_params.dict())
 
     def __create_hda_from_ldda(self, trans, history: History, ldda_id: EncodedDatabaseIdField):
         decoded_ldda_id = self.decode_id(ldda_id)
         ld = self.ldda_manager.get(trans, decoded_ldda_id)
         if type(ld) is not LibraryDataset:
-            raise exceptions.RequestParameterInvalidException(
-                f"Library content id ( {ldda_id} ) is not a dataset")
+            raise exceptions.RequestParameterInvalidException(f"Library content id ( {ldda_id} ) is not a dataset")
         hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
         return hda
 
@@ -1110,45 +1110,46 @@ class HistoriesContentsService(ServiceBase):
         return hda
 
     def __create_dataset_collection(
-        self, trans,
+        self,
+        trans,
         history: History,
         payload: CreateHistoryContentPayloadFromCollection,
         serialization_params: SerializationParams,
     ):
         """Create hdca in a history from the list of element identifiers
 
-        :param history: history the new hdca should be added to
-        :param source: whether to create a new collection or copy existing one
-        :type  source: str
-        :param payload: dictionary structure containing:
-            :param collection_type: type (and depth) of the new collection
-            :type name: str
-            :param element_identifiers: list of elements that should be in the new collection
-                :param element: one member of the collection
-                    :param name: name of the element
-                    :type name: str
-                    :param src: source of the element (hda/ldda)
-                    :type src: str
-                    :param id: identifier
-                    :type id: str
-                    :param id: tags
-                    :type id: list
-                :type element: dict
-            :type name: list
-            :param name: name of the collection
-            :type name: str
-            :param hide_source_items: whether to mark the original hdas as hidden
-            :type name: bool
-            :param copy_elements: whether to copy HDAs when creating collection
-            :type name: bool
-        :type  payload: dict
+         :param history: history the new hdca should be added to
+         :param source: whether to create a new collection or copy existing one
+         :type  source: str
+         :param payload: dictionary structure containing:
+             :param collection_type: type (and depth) of the new collection
+             :type name: str
+             :param element_identifiers: list of elements that should be in the new collection
+                 :param element: one member of the collection
+                     :param name: name of the element
+                     :type name: str
+                     :param src: source of the element (hda/ldda)
+                     :type src: str
+                     :param id: identifier
+                     :type id: str
+                     :param id: tags
+                     :type id: list
+                 :type element: dict
+             :type name: list
+             :param name: name of the collection
+             :type name: str
+             :param hide_source_items: whether to mark the original hdas as hidden
+             :type name: bool
+             :param copy_elements: whether to copy HDAs when creating collection
+             :type name: bool
+         :type  payload: dict
 
-       .. note:: Elements may be nested depending on the collection_type
+        .. note:: Elements may be nested depending on the collection_type
 
-        :returns:   dataset collection information
-        :rtype:     dict
+         :returns:   dataset collection information
+         :rtype:     dict
 
-        :raises: RequestParameterInvalidException, RequestParameterMissingException
+         :raises: RequestParameterInvalidException, RequestParameterMissingException
         """
         source = payload.source or HistoryContentSource.new_collection
 
@@ -1156,10 +1157,7 @@ class HistoriesContentsService(ServiceBase):
         if source == HistoryContentSource.new_collection:
             create_params = api_payload_to_create_params(payload.dict())
             dataset_collection_instance = dataset_collection_manager.create(
-                trans,
-                parent=history,
-                history=history,
-                **create_params
+                trans, parent=history, history=history, **create_params
             )
         elif source == HistoryContentSource.hdca:
             content = payload.content
@@ -1169,7 +1167,9 @@ class HistoriesContentsService(ServiceBase):
             copy_required = dbkey is not None
             copy_elements = payload.copy_elements or copy_required
             if copy_required and not copy_elements:
-                raise exceptions.RequestParameterMissingException("copy_elements passed as 'false' but it is required to change specified attributes")
+                raise exceptions.RequestParameterMissingException(
+                    "copy_elements passed as 'false' but it is required to change specified attributes"
+                )
             dataset_instance_attributes = {}
             if dbkey is not None:
                 dataset_instance_attributes["dbkey"] = dbkey
@@ -1187,7 +1187,7 @@ class HistoriesContentsService(ServiceBase):
 
         # if the consumer specified keys or view, use the secondary serializer
         if serialization_params.view or serialization_params.keys:
-            serialization_params.default_view = 'detailed'
+            serialization_params.default_view = "detailed"
             return self.hdca_serializer.serialize_to_view(
                 dataset_collection_instance, user=trans.user, trans=trans, **serialization_params.dict()
             )
diff --git a/lib/galaxy/webapps/galaxy/services/libraries.py b/lib/galaxy/webapps/galaxy/services/libraries.py
index f54bea6605c..934143f70d0 100644
--- a/lib/galaxy/webapps/galaxy/services/libraries.py
+++ b/lib/galaxy/webapps/galaxy/services/libraries.py
@@ -70,7 +70,7 @@ class LibrariesService(ServiceBase):
         return LibrarySummaryList.parse_obj(libraries)
 
     def show(self, trans, id: EncodedDatabaseIdField) -> LibrarySummary:
-        """ Returns detailed information about a library.
+        """Returns detailed information about a library.
 
         :param  id:      the encoded id of the library
         :type   id:      an encoded id string
@@ -84,7 +84,7 @@ class LibrariesService(ServiceBase):
 
         :raises: MalformedId, ObjectNotFound
         """
-        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name='library'))
+        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name="library"))
         library_dict = self.library_manager.get_library_dict(trans, library)
         return LibrarySummary.parse_obj(library_dict)
 
@@ -112,26 +112,28 @@ class LibrariesService(ServiceBase):
     def update(self, trans, id: EncodedDatabaseIdField, payload: UpdateLibraryPayload) -> LibrarySummary:
         """Updates the library defined by an ``encoded_id`` with the data in the payload.
 
-       .. note:: Currently, only admin users can update libraries. Also the library must not be `deleted`.
+        .. note:: Currently, only admin users can update libraries. Also the library must not be `deleted`.
 
-        :param  id:      the encoded id of the library
-        :type   id:      an encoded id string
-        :param  payload: dictionary structure containing::
-            :param name:         new library's name, cannot be empty
-            :type  name:         str
-            :param description:  new library's description
-            :type  description:  str
-            :param synopsis:     new library's synopsis
-            :type  synopsis:     str
-        :type   payload: dict
-        :returns:   detailed library information
-        :rtype:     dict
-        :raises: RequestParameterMissingException
+         :param  id:      the encoded id of the library
+         :type   id:      an encoded id string
+         :param  payload: dictionary structure containing::
+             :param name:         new library's name, cannot be empty
+             :type  name:         str
+             :param description:  new library's description
+             :type  description:  str
+             :param synopsis:     new library's synopsis
+             :type  synopsis:     str
+         :type   payload: dict
+         :returns:   detailed library information
+         :rtype:     dict
+         :raises: RequestParameterMissingException
         """
-        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name='library'))
+        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name="library"))
         name = payload.name
-        if name == '':
-            raise exceptions.RequestParameterMissingException("Parameter 'name' of library is required. You cannot remove it.")
+        if name == "":
+            raise exceptions.RequestParameterMissingException(
+                "Parameter 'name' of library is required. You cannot remove it."
+            )
         updated_library = self.library_manager.update(trans, library, name, payload.description, payload.synopsis)
         library_dict = self.library_manager.get_library_dict(trans, updated_library)
         return LibrarySummary.parse_obj(library_dict)
@@ -152,7 +154,7 @@ class LibrariesService(ServiceBase):
 
         .. seealso:: :attr:`galaxy.model.Library.dict_element_visible_keys`
         """
-        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name='library'))
+        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name="library"))
         library = self.library_manager.delete(trans, library, undelete)
         library_dict = self.library_manager.get_library_dict(trans, library)
         return LibrarySummary.parse_obj(library_dict)
@@ -185,9 +187,11 @@ class LibrariesService(ServiceBase):
         """
         current_user_roles = trans.get_current_user_roles()
         is_admin = trans.user_is_admin
-        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name='library'))
+        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name="library"))
         if not (is_admin or trans.app.security_agent.can_manage_library_item(current_user_roles, library)):
-            raise exceptions.InsufficientPermissionsException('You do not have proper permission to access permissions of this library.')
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permission to access permissions of this library."
+            )
 
         if scope == LibraryPermissionScope.current or scope is None:
             roles = self.library_manager.get_current_roles(trans, library)
@@ -195,7 +199,9 @@ class LibrariesService(ServiceBase):
 
         #  Return roles that are available to select.
         elif scope == LibraryPermissionScope.available:
-            roles, total_roles = trans.app.security_agent.get_valid_roles(trans, library, query, page, page_limit, is_library_access)
+            roles, total_roles = trans.app.security_agent.get_valid_roles(
+                trans, library, query, page, page_limit, is_library_access
+            )
 
             return_roles = []
             for role in roles:
@@ -203,14 +209,13 @@ class LibrariesService(ServiceBase):
                 return_roles.append(dict(id=role_id, name=role.name, type=role.type))
             return LibraryAvailablePermissions(roles=return_roles, page=page, page_limit=page_limit, total=total_roles)
         else:
-            raise exceptions.RequestParameterInvalidException("The value of 'scope' parameter is invalid. Alllowed values: current, available")
+            raise exceptions.RequestParameterInvalidException(
+                "The value of 'scope' parameter is invalid. Alllowed values: current, available"
+            )
 
     def set_permissions(
         self, trans, id: EncodedDatabaseIdField, payload: Dict[str, Any]
-    ) -> Union[
-        LibraryLegacySummary,  # Old legacy response
-        LibraryCurrentPermissions,
-    ]:
+    ) -> Union[LibraryLegacySummary, LibraryCurrentPermissions,]:  # Old legacy response
         """Set permissions of the given library to the given role ids.
 
         :param  id:      the encoded id of the library to set the permissions of
@@ -237,79 +242,91 @@ class LibrariesService(ServiceBase):
         """
         is_admin = trans.user_is_admin
         current_user_roles = trans.get_current_user_roles()
-        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name='library'))
+        library = self.library_manager.get(trans, trans.security.decode_id(id, object_name="library"))
 
         if not (is_admin or trans.app.security_agent.can_manage_library_item(current_user_roles, library)):
-            raise exceptions.InsufficientPermissionsException('You do not have proper permission to modify permissions of this library.')
+            raise exceptions.InsufficientPermissionsException(
+                "You do not have proper permission to modify permissions of this library."
+            )
 
-        new_access_roles_ids = util.listify(payload.get('access_ids[]', None))
-        new_add_roles_ids = util.listify(payload.get('add_ids[]', None))
-        new_manage_roles_ids = util.listify(payload.get('manage_ids[]', None))
-        new_modify_roles_ids = util.listify(payload.get('modify_ids[]', None))
+        new_access_roles_ids = util.listify(payload.get("access_ids[]", None))
+        new_add_roles_ids = util.listify(payload.get("add_ids[]", None))
+        new_manage_roles_ids = util.listify(payload.get("manage_ids[]", None))
+        new_modify_roles_ids = util.listify(payload.get("modify_ids[]", None))
 
-        action = payload.get('action', None)
+        action = payload.get("action", None)
         if action is None:
             if payload is not None:
                 return self.set_permissions_old(trans, library, payload)
             else:
                 raise exceptions.RequestParameterMissingException('The mandatory parameter "action" is missing.')
-        elif action == 'remove_restrictions':
+        elif action == "remove_restrictions":
             is_public = self.library_manager.make_public(trans, library)
             if not is_public:
-                raise exceptions.InternalServerError('An error occurred while making library public.')
-        elif action == 'set_permissions':
+                raise exceptions.InternalServerError("An error occurred while making library public.")
+        elif action == "set_permissions":
 
             # ACCESS LIBRARY ROLES
             valid_access_roles = []
             invalid_access_roles_names = []
             for role_id in new_access_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
-                valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, library, is_library_access=True)
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
+                valid_roles, total_roles = trans.app.security_agent.get_valid_roles(
+                    trans, library, is_library_access=True
+                )
                 if role in valid_roles:
                     valid_access_roles.append(role)
                 else:
                     invalid_access_roles_names.append(role_id)
             if len(invalid_access_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the library access permission: {str(invalid_access_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the library access permission: {str(invalid_access_roles_names)}"
+                )
 
             # ADD TO LIBRARY ROLES
             valid_add_roles = []
             invalid_add_roles_names = []
             for role_id in new_add_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
                 valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, library)
                 if role in valid_roles:
                     valid_add_roles.append(role)
                 else:
                     invalid_add_roles_names.append(role_id)
             if len(invalid_add_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the add library item permission: {str(invalid_add_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the add library item permission: {str(invalid_add_roles_names)}"
+                )
 
             # MANAGE LIBRARY ROLES
             valid_manage_roles = []
             invalid_manage_roles_names = []
             for role_id in new_manage_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
                 valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, library)
                 if role in valid_roles:
                     valid_manage_roles.append(role)
                 else:
                     invalid_manage_roles_names.append(role_id)
             if len(invalid_manage_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the manage library permission: {str(invalid_manage_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the manage library permission: {str(invalid_manage_roles_names)}"
+                )
 
             # MODIFY LIBRARY ROLES
             valid_modify_roles = []
             invalid_modify_roles_names = []
             for role_id in new_modify_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
                 valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, library)
                 if role in valid_roles:
                     valid_modify_roles.append(role)
                 else:
                     invalid_modify_roles_names.append(role_id)
             if len(invalid_modify_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the modify library permission: {str(invalid_modify_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the modify library permission: {str(invalid_modify_roles_names)}"
+                )
 
             permissions = {trans.app.security_agent.permitted_actions.LIBRARY_ACCESS: valid_access_roles}
             permissions.update({trans.app.security_agent.permitted_actions.LIBRARY_ADD: valid_add_roles})
@@ -321,8 +338,10 @@ class LibrariesService(ServiceBase):
             # Copy the permissions to the root folder
             trans.app.security_agent.copy_library_permissions(trans, library, library.root_folder)
         else:
-            raise exceptions.RequestParameterInvalidException('The mandatory parameter "action" has an invalid value.'
-                                                              'Allowed values are: "remove_restrictions", set_permissions"')
+            raise exceptions.RequestParameterInvalidException(
+                'The mandatory parameter "action" has an invalid value.'
+                'Allowed values are: "remove_restrictions", set_permissions"'
+            )
         roles = self.library_manager.get_current_roles(trans, library)
         return LibraryCurrentPermissions.parse_obj(roles)
 
@@ -336,11 +355,16 @@ class LibrariesService(ServiceBase):
         permissions = {}
         for k, v in trans.app.model.Library.permitted_actions.items():
             role_params = params.get(f"{k}_in", [])
-            in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(role_params)]
+            in_roles = [
+                trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x))
+                for x in util.listify(role_params)
+            ]
             permissions[trans.app.security_agent.get_action(v.action)] = in_roles
         trans.app.security_agent.set_all_library_permissions(trans, library, permissions)
         trans.sa_session.refresh(library)
         # Copy the permissions to the root folder
         trans.app.security_agent.copy_library_permissions(trans, library, library.root_folder)
-        item = library.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id})
+        item = library.to_dict(
+            view="element", value_mapper={"id": trans.security.encode_id, "root_folder_id": trans.security.encode_id}
+        )
         return LibraryLegacySummary.parse_obj(item)
diff --git a/lib/galaxy/webapps/galaxy/services/library_folder_contents.py b/lib/galaxy/webapps/galaxy/services/library_folder_contents.py
index 025d1e60f9d..a7ebe6afaff 100644
--- a/lib/galaxy/webapps/galaxy/services/library_folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/library_folder_contents.py
@@ -2,7 +2,7 @@ import logging
 
 from galaxy import (
     exceptions,
-    util
+    util,
 )
 from galaxy.managers import base as managers_base
 from galaxy.managers.folders import FolderManager
@@ -33,7 +33,9 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
         """
         Convenience method to get a model object with the specified checks.
         """
-        return managers_base.get_object(trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
+        return managers_base.get_object(
+            trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted
+        )
 
     def index(self, trans, folder_id, limit=None, offset=None, search_text=None, include_deleted=False):
         """
@@ -74,14 +76,18 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
             pass
         else:
             if trans.user:
-                log.warning(f"SECURITY: User (id: {trans.user.id}) without proper access rights is trying to load folder with ID of {decoded_folder_id}")
+                log.warning(
+                    f"SECURITY: User (id: {trans.user.id}) without proper access rights is trying to load folder with ID of {decoded_folder_id}"
+                )
             else:
-                log.warning(f"SECURITY: Anonymous user is trying to load restricted folder with ID of {decoded_folder_id}")
-            raise exceptions.ObjectNotFound(f'Folder with the id provided ( {folder_id} ) was not found')
+                log.warning(
+                    f"SECURITY: Anonymous user is trying to load restricted folder with ID of {decoded_folder_id}"
+                )
+            raise exceptions.ObjectNotFound(f"Folder with the id provided ( {folder_id} ) was not found")
 
         folder_contents = []
-        update_time = ''
-        create_time = ''
+        update_time = ""
+        create_time = ""
 
         folders, datasets = self._apply_preferences(folder, include_deleted, search_text)
 
@@ -92,9 +98,13 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
             create_time = content_item.create_time.strftime(TIME_FORMAT)
 
             if content_item.api_type == FOLDER_TYPE_NAME:
-                encoded_id = f'F{encoded_id}'
-                can_modify = is_admin or (trans.user and trans.app.security_agent.can_modify_library_item(current_user_roles, folder))
-                can_manage = is_admin or (trans.user and trans.app.security_agent.can_manage_library_item(current_user_roles, folder))
+                encoded_id = f"F{encoded_id}"
+                can_modify = is_admin or (
+                    trans.user and trans.app.security_agent.can_modify_library_item(current_user_roles, folder)
+                )
+                can_manage = is_admin or (
+                    trans.user and trans.app.security_agent.can_manage_library_item(current_user_roles, folder)
+                )
                 update_time = content_item.update_time.strftime(TIME_FORMAT)
                 return_item.update(dict(can_modify=can_modify, can_manage=can_manage))
                 if content_item.description:
@@ -106,10 +116,19 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
                 #  Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency
                 dataset = content_item.library_dataset_dataset_association.dataset
                 is_unrestricted = trans.app.security_agent.dataset_is_public(dataset)
-                is_private = not is_unrestricted and trans.user and trans.app.security_agent.dataset_is_private_to_user(trans, dataset)
+                is_private = (
+                    not is_unrestricted
+                    and trans.user
+                    and trans.app.security_agent.dataset_is_private_to_user(trans, dataset)
+                )
 
                 # Can user manage the permissions on the dataset?
-                can_manage = is_admin or (trans.user and trans.app.security_agent.can_manage_dataset(current_user_roles, content_item.library_dataset_dataset_association.dataset))
+                can_manage = is_admin or (
+                    trans.user
+                    and trans.app.security_agent.can_manage_dataset(
+                        current_user_roles, content_item.library_dataset_dataset_association.dataset
+                    )
+                )
                 raw_size = int(content_item.library_dataset_dataset_association.get_size())
                 nice_size = util.nice_size(raw_size)
                 update_time = content_item.library_dataset_dataset_association.update_time.strftime(TIME_FORMAT)
@@ -120,17 +139,21 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
                 tag_manager = tags.GalaxyTagHandler(trans.sa_session)
                 ldda_tags = tag_manager.get_tags_str(content_item.library_dataset_dataset_association.tags)
 
-                return_item.update(dict(file_ext=library_dataset_dict['file_ext'],
-                                        date_uploaded=library_dataset_dict['date_uploaded'],
-                                        update_time=update_time,
-                                        is_unrestricted=is_unrestricted,
-                                        is_private=is_private,
-                                        can_manage=can_manage,
-                                        state=library_dataset_dict['state'],
-                                        file_size=nice_size,
-                                        raw_size=raw_size,
-                                        ldda_id=encoded_ldda_id,
-                                        tags=ldda_tags))
+                return_item.update(
+                    dict(
+                        file_ext=library_dataset_dict["file_ext"],
+                        date_uploaded=library_dataset_dict["date_uploaded"],
+                        update_time=update_time,
+                        is_unrestricted=is_unrestricted,
+                        is_private=is_private,
+                        can_manage=can_manage,
+                        state=library_dataset_dict["state"],
+                        file_size=nice_size,
+                        raw_size=raw_size,
+                        ldda_id=encoded_ldda_id,
+                        tags=ldda_tags,
+                    )
+                )
                 if content_item.library_dataset_dataset_association.message:
                     return_item.update(dict(message=content_item.library_dataset_dataset_association.message))
                 elif content_item.library_dataset_dataset_association.info:
@@ -138,20 +161,28 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
                     return_item.update(dict(message=content_item.library_dataset_dataset_association.info))
 
             # For every item include the default metadata
-            return_item.update(dict(id=encoded_id,
-                                    type=content_item.api_type,
-                                    name=content_item.name,
-                                    update_time=update_time,
-                                    create_time=create_time,
-                                    deleted=content_item.deleted))
+            return_item.update(
+                dict(
+                    id=encoded_id,
+                    type=content_item.api_type,
+                    name=content_item.name,
+                    update_time=update_time,
+                    create_time=create_time,
+                    deleted=content_item.deleted,
+                )
+            )
             folder_contents.append(return_item)
 
         # Return the reversed path so it starts with the library node.
         full_path = self._build_path(trans, folder)[::-1]
 
-        user_can_add_library_item = is_admin or trans.app.security_agent.can_add_library_item(current_user_roles, folder)
+        user_can_add_library_item = is_admin or trans.app.security_agent.can_add_library_item(
+            current_user_roles, folder
+        )
 
-        user_can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item(current_user_roles, folder)
+        user_can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item(
+            current_user_roles, folder
+        )
 
         parent_library_id = None
         if folder.parent_library is not None:
@@ -159,13 +190,15 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
 
         total_rows = len(folders) + len(datasets)
 
-        metadata = dict(full_path=full_path,
-                        total_rows=total_rows,
-                        can_add_library_item=user_can_add_library_item,
-                        can_modify_folder=user_can_modify_folder,
-                        folder_name=folder.name,
-                        folder_description=folder.description,
-                        parent_library_id=parent_library_id)
+        metadata = dict(
+            full_path=full_path,
+            total_rows=total_rows,
+            can_add_library_item=user_can_add_library_item,
+            can_modify_folder=user_can_modify_folder,
+            folder_name=folder.name,
+            folder_description=folder.description,
+            parent_library_id=parent_library_id,
+        )
         folder_container = dict(metadata=metadata, folder_contents=folder_contents)
         return folder_container
 
@@ -197,21 +230,28 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
         if trans.user_is_bootstrap_admin:
             raise exceptions.RealUserRequiredException("Only real users can create a new library file.")
         encoded_folder_id_16 = self.__decode_library_content_id(trans, encoded_folder_id)
-        from_hda_id = payload.pop('from_hda_id', None)
-        from_hdca_id = payload.pop('from_hdca_id', None)
-        ldda_message = payload.pop('ldda_message', '')
+        from_hda_id = payload.pop("from_hda_id", None)
+        from_hdca_id = payload.pop("from_hdca_id", None)
+        ldda_message = payload.pop("ldda_message", "")
         try:
             if from_hda_id:
                 decoded_hda_id = self.decode_id(from_hda_id)
-                return self._copy_hda_to_library_folder(trans, self.hda_manager, decoded_hda_id, encoded_folder_id_16, ldda_message)
+                return self._copy_hda_to_library_folder(
+                    trans, self.hda_manager, decoded_hda_id, encoded_folder_id_16, ldda_message
+                )
             if from_hdca_id:
                 decoded_hdca_id = self.decode_id(from_hdca_id)
-                return self._copy_hdca_to_library_folder(trans, self.hda_manager, decoded_hdca_id, encoded_folder_id_16, ldda_message)
+                return self._copy_hdca_to_library_folder(
+                    trans, self.hda_manager, decoded_hdca_id, encoded_folder_id_16, ldda_message
+                )
         except Exception as exc:
             # TODO handle exceptions better within the mixins
             exc_message = util.unicodify(exc)
-            if 'not accessible to the current user' in exc_message or 'You are not allowed to access this dataset' in exc_message:
-                raise exceptions.ItemAccessibilityException('You do not have access to the requested item')
+            if (
+                "not accessible to the current user" in exc_message
+                or "You are not allowed to access this dataset" in exc_message
+            ):
+                raise exceptions.ItemAccessibilityException("You do not have access to the requested item")
             else:
                 log.exception(exc)
                 raise exc
@@ -228,10 +268,12 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
 
         :raises:    MalformedId
         """
-        if ((len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith('F')):
+        if (len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith("F"):
             return encoded_folder_id[1:]
         else:
-            raise exceptions.MalformedId(f'Malformed folder id ( {str(encoded_folder_id)} ) specified, unable to decode.')
+            raise exceptions.MalformedId(
+                f"Malformed folder id ( {str(encoded_folder_id)} ) specified, unable to decode."
+            )
 
     def _build_path(self, trans, folder):
         """
@@ -247,7 +289,7 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
         path_to_root = []
         # We are almost in root
         encoded_id = trans.security.encode_id(folder.id)
-        path_to_root.append((f'F{encoded_id}', folder.name))
+        path_to_root.append((f"F{encoded_id}", folder.name))
         if folder.parent_id is not None:
             # We add the current folder and traverse up one folder.
             upper_folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(folder.parent_id)
@@ -280,7 +322,11 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
         current_folders = self._calculate_pagination(folders, offset, limit)
 
         for subfolder in current_folders:
-            if not subfolder.deleted or is_admin or trans.app.security_agent.can_modify_library_item(current_user_roles, subfolder):
+            if (
+                not subfolder.deleted
+                or is_admin
+                or trans.app.security_agent.can_modify_library_item(current_user_roles, subfolder)
+            ):
                 # Undeleted folders are non-restricted for now.
                 # Admins or users with MODIFY permissions can see deleted folders.
                 subfolder.api_type = FOLDER_TYPE_NAME
@@ -299,7 +345,9 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
                     dataset.api_type = FILE_TYPE_NAME
                     content_items.append(dataset)
             else:
-                if is_admin or trans.app.security_agent.can_access_dataset(current_user_roles, dataset.library_dataset_dataset_association.dataset):
+                if is_admin or trans.app.security_agent.can_access_dataset(
+                    current_user_roles, dataset.library_dataset_dataset_association.dataset
+                ):
                     # Admins or users with ACCESS permissions can see datasets.
                     dataset.api_type = FILE_TYPE_NAME
                     content_items.append(dataset)
@@ -308,13 +356,12 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
 
     def _calculate_pagination(self, items, offset: int, limit: int):
         if limit > 0:
-            paginated_items = items[offset:offset + limit]
+            paginated_items = items[offset : offset + limit]
         else:
             paginated_items = items[offset:]
         return paginated_items
 
     def _apply_preferences(self, folder, include_deleted: bool, search_text: str):
-
         def check_deleted(array, include_deleted):
             if include_deleted:
                 result_array = array
@@ -328,7 +375,7 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems):
             elif dataset.library_dataset_dataset_association.info:
                 description = dataset.library_dataset_dataset_association.info
             else:
-                description = ''
+                description = ""
 
             return search_text in dataset.name or search_text in description
 
diff --git a/lib/galaxy/webapps/galaxy/services/library_folders.py b/lib/galaxy/webapps/galaxy/services/library_folders.py
index a68c4e5ae86..a6562292042 100644
--- a/lib/galaxy/webapps/galaxy/services/library_folders.py
+++ b/lib/galaxy/webapps/galaxy/services/library_folders.py
@@ -33,12 +33,7 @@ class LibraryFoldersService(ServiceBase):
     and pydantic models to declare its parameters and return types.
     """
 
-    def __init__(
-        self,
-        security: IdEncodingHelper,
-        folder_manager: FolderManager,
-        role_manager: RoleManager
-    ):
+    def __init__(self, security: IdEncodingHelper, folder_manager: FolderManager, role_manager: RoleManager):
         super().__init__(security)
         self.folder_manager = folder_manager
         self.role_manager = role_manager
@@ -59,10 +54,7 @@ class LibraryFoldersService(ServiceBase):
         return LibraryFolderDetails.parse_obj(return_dict)
 
     def create(
-        self,
-        trans,
-        encoded_parent_folder_id: EncodedDatabaseIdField,
-        payload: CreateLibraryFolderPayload
+        self, trans, encoded_parent_folder_id: EncodedDatabaseIdField, payload: CreateLibraryFolderPayload
     ) -> LibraryFolderDetails:
         """
         Create a new folder object underneath the one specified in the parameters.
@@ -116,7 +108,9 @@ class LibraryFoldersService(ServiceBase):
         folder = self.folder_manager.get(trans, decoded_folder_id)
 
         if not (is_admin or trans.app.security_agent.can_manage_library_item(current_user_roles, folder)):
-            raise InsufficientPermissionsException('You do not have proper permission to access permissions of this folder.')
+            raise InsufficientPermissionsException(
+                "You do not have proper permission to access permissions of this folder."
+            )
 
         if scope is None or scope == LibraryPermissionScope.current:
             current_permissions = self.folder_manager.get_current_roles(trans, folder)
@@ -130,13 +124,12 @@ class LibraryFoldersService(ServiceBase):
                 return_roles.append(dict(id=role_id, name=role.name, type=role.type))
             return LibraryAvailablePermissions(roles=return_roles, page=page, page_limit=page_limit, total=total_roles)
         else:
-            raise RequestParameterInvalidException("The value of 'scope' parameter is invalid. Allowed values: current, available")
+            raise RequestParameterInvalidException(
+                "The value of 'scope' parameter is invalid. Allowed values: current, available"
+            )
 
     def set_permissions(
-        self,
-        trans,
-        encoded_folder_id: EncodedDatabaseIdField,
-        payload: dict
+        self, trans, encoded_folder_id: EncodedDatabaseIdField, payload: dict
     ) -> LibraryFolderCurrentPermissions:
         """
         Set permissions of the given folder to the given role ids.
@@ -165,22 +158,24 @@ class LibraryFoldersService(ServiceBase):
         decoded_folder_id = self.folder_manager.cut_and_decode(trans, encoded_folder_id)
         folder = self.folder_manager.get(trans, decoded_folder_id)
         if not (is_admin or trans.app.security_agent.can_manage_library_item(current_user_roles, folder)):
-            raise InsufficientPermissionsException('You do not have proper permission to modify permissions of this folder.')
+            raise InsufficientPermissionsException(
+                "You do not have proper permission to modify permissions of this folder."
+            )
 
-        new_add_roles_ids = util.listify(payload.get('add_ids[]', None))
-        new_manage_roles_ids = util.listify(payload.get('manage_ids[]', None))
-        new_modify_roles_ids = util.listify(payload.get('modify_ids[]', None))
+        new_add_roles_ids = util.listify(payload.get("add_ids[]", None))
+        new_manage_roles_ids = util.listify(payload.get("manage_ids[]", None))
+        new_modify_roles_ids = util.listify(payload.get("modify_ids[]", None))
 
-        action = payload.get('action', None)
+        action = payload.get("action", None)
         if action is None:
             raise RequestParameterMissingException('The mandatory parameter "action" is missing.')
-        elif action == 'set_permissions':
+        elif action == "set_permissions":
 
             # ADD TO LIBRARY ROLES
             valid_add_roles = []
             invalid_add_roles_names = []
             for role_id in new_add_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
                 #  Check whether role is in the set of allowed roles
                 valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, folder)
                 if role in valid_roles:
@@ -188,13 +183,15 @@ class LibraryFoldersService(ServiceBase):
                 else:
                     invalid_add_roles_names.append(role_id)
             if len(invalid_add_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the add library item permission: {str(invalid_add_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the add library item permission: {str(invalid_add_roles_names)}"
+                )
 
             # MANAGE FOLDER ROLES
             valid_manage_roles = []
             invalid_manage_roles_names = []
             for role_id in new_manage_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
                 #  Check whether role is in the set of allowed roles
                 valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, folder)
                 if role in valid_roles:
@@ -202,13 +199,15 @@ class LibraryFoldersService(ServiceBase):
                 else:
                     invalid_manage_roles_names.append(role_id)
             if len(invalid_manage_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the manage folder permission: {str(invalid_manage_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the manage folder permission: {str(invalid_manage_roles_names)}"
+                )
 
             # MODIFY FOLDER ROLES
             valid_modify_roles = []
             invalid_modify_roles_names = []
             for role_id in new_modify_roles_ids:
-                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name='role'))
+                role = self.role_manager.get(trans, trans.security.decode_id(role_id, object_name="role"))
                 #  Check whether role is in the set of allowed roles
                 valid_roles, total_roles = trans.app.security_agent.get_valid_roles(trans, folder)
                 if role in valid_roles:
@@ -216,7 +215,9 @@ class LibraryFoldersService(ServiceBase):
                 else:
                     invalid_modify_roles_names.append(role_id)
             if len(invalid_modify_roles_names) > 0:
-                log.warning(f"The following roles could not be added to the modify folder permission: {str(invalid_modify_roles_names)}")
+                log.warning(
+                    f"The following roles could not be added to the modify folder permission: {str(invalid_modify_roles_names)}"
+                )
 
             permissions = {trans.app.security_agent.permitted_actions.LIBRARY_ADD: valid_add_roles}
             permissions.update({trans.app.security_agent.permitted_actions.LIBRARY_MANAGE: valid_manage_roles})
@@ -224,12 +225,15 @@ class LibraryFoldersService(ServiceBase):
 
             trans.app.security_agent.set_all_library_permissions(trans, folder, permissions)
         else:
-            raise RequestParameterInvalidException('The mandatory parameter "action" has an invalid value.'
-                                                   'Allowed values are: "set_permissions"')
+            raise RequestParameterInvalidException(
+                'The mandatory parameter "action" has an invalid value.' 'Allowed values are: "set_permissions"'
+            )
         current_permissions = self.folder_manager.get_current_roles(trans, folder)
         return LibraryFolderCurrentPermissions.parse_obj(current_permissions)
 
-    def delete(self, trans, encoded_folder_id: EncodedDatabaseIdField, undelete: Optional[bool] = False) -> LibraryFolderDetails:
+    def delete(
+        self, trans, encoded_folder_id: EncodedDatabaseIdField, undelete: Optional[bool] = False
+    ) -> LibraryFolderDetails:
         """
         DELETE /api/folders/{encoded_folder_id}
 
@@ -253,25 +257,27 @@ class LibraryFoldersService(ServiceBase):
         folder_dict = self.folder_manager.get_folder_dict(trans, folder)
         return LibraryFolderDetails.parse_obj(folder_dict)
 
-    def update(self, trans, encoded_folder_id: EncodedDatabaseIdField, payload: UpdateLibraryFolderPayload) -> LibraryFolderDetails:
+    def update(
+        self, trans, encoded_folder_id: EncodedDatabaseIdField, payload: UpdateLibraryFolderPayload
+    ) -> LibraryFolderDetails:
         """
-        Update the folder defined by an ``encoded_folder_id``
-        with the data in the payload.
+         Update the folder defined by an ``encoded_folder_id``
+         with the data in the payload.
 
-       .. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
+        .. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
 
-        :param  id:      the encoded id of the folder
-        :type   id:      an encoded id string
+         :param  id:      the encoded id of the folder
+         :type   id:      an encoded id string
 
-        :param  payload: (required) dictionary structure containing::
-            'name':         new folder's name, cannot be empty
-            'description':  new folder's description
-        :type   payload: dict
+         :param  payload: (required) dictionary structure containing::
+             'name':         new folder's name, cannot be empty
+             'description':  new folder's description
+         :type   payload: dict
 
-        :returns:   detailed folder information
-        :rtype:     dict
+         :returns:   detailed folder information
+         :rtype:     dict
 
-        :raises: RequestParameterMissingException
+         :raises: RequestParameterMissingException
         """
         decoded_folder_id = self.folder_manager.cut_and_decode(trans, encoded_folder_id)
         folder = self.folder_manager.get(trans, decoded_folder_id)
diff --git a/lib/galaxy/webapps/galaxy/services/pages.py b/lib/galaxy/webapps/galaxy/services/pages.py
index f08fd0f8671..db50775fba4 100644
--- a/lib/galaxy/webapps/galaxy/services/pages.py
+++ b/lib/galaxy/webapps/galaxy/services/pages.py
@@ -4,12 +4,8 @@ from galaxy import (
     exceptions,
     model,
 )
-from galaxy.managers import (
-    base,
-)
-from galaxy.managers.markdown_util import (
-    internal_galaxy_markdown_to_pdf,
-)
+from galaxy.managers import base
+from galaxy.managers.markdown_util import internal_galaxy_markdown_to_pdf
 from galaxy.managers.pages import (
     PageManager,
     PageSerializer,
@@ -87,7 +83,7 @@ class PagesService(ServiceBase):
         """
         page = self.manager.create(trans, payload.dict())
         rval = trans.security.encode_all_ids(page.to_dict(), recursive=True)
-        rval['content'] = page.latest_revision.content
+        rval["content"] = page.latest_revision.content
         self.manager.rewrite_content_for_export(trans, rval)
         return PageSummary.parse_obj(rval)
 
@@ -95,7 +91,7 @@ class PagesService(ServiceBase):
         """
         Deletes a page (or marks it as deleted)
         """
-        page = base.get_object(trans, id, 'Page', check_ownership=True)
+        page = base.get_object(trans, id, "Page", check_ownership=True)
 
         # Mark a page as deleted
         page.deleted = True
@@ -109,10 +105,10 @@ class PagesService(ServiceBase):
         :rtype:     dict
         :returns:   Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision
         """
-        page = base.get_object(trans, id, 'Page', check_ownership=False, check_accessible=True)
+        page = base.get_object(trans, id, "Page", check_ownership=False, check_accessible=True)
         rval = trans.security.encode_all_ids(page.to_dict(), recursive=True)
-        rval['content'] = page.latest_revision.content
-        rval['content_format'] = page.latest_revision.content_format
+        rval["content"] = page.latest_revision.content
+        rval["content_format"] = page.latest_revision.content_format
         self.manager.rewrite_content_for_export(trans, rval)
         return PageDetails.parse_obj(rval)
 
@@ -125,7 +121,7 @@ class PagesService(ServiceBase):
         :rtype: dict
         :returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision
         """
-        page = base.get_object(trans, id, 'Page', check_ownership=False, check_accessible=True)
+        page = base.get_object(trans, id, "Page", check_ownership=False, check_accessible=True)
         if page.latest_revision.content_format != PageContentFormat.markdown.value:
             raise exceptions.RequestParameterInvalidException("PDF export only allowed for Markdown based pages")
         internal_galaxy_markdown = page.latest_revision.content
diff --git a/lib/galaxy/webapps/galaxy/services/quotas.py b/lib/galaxy/webapps/galaxy/services/quotas.py
index 11530167e0e..0c4c2018c7e 100644
--- a/lib/galaxy/webapps/galaxy/services/quotas.py
+++ b/lib/galaxy/webapps/galaxy/services/quotas.py
@@ -1,14 +1,15 @@
 import logging
-from typing import (
-    Optional,
-)
+from typing import Optional
 
 from sqlalchemy import (
     false,
-    true
+    true,
 )
 
-from galaxy import model, util
+from galaxy import (
+    model,
+    util,
+)
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.quotas import QuotaManager
 from galaxy.quota._schema import (
@@ -40,22 +41,22 @@ class QuotasService(ServiceBase):
         rval = []
         query = trans.sa_session.query(model.Quota)
         if deleted:
-            route = 'deleted_quota'
+            route = "deleted_quota"
             query = query.filter(model.Quota.deleted == true())
         else:
-            route = 'quota'
+            route = "quota"
             query = query.filter(model.Quota.deleted == false())
         for quota in query:
-            item = quota.to_dict(value_mapper={'id': trans.security.encode_id})
+            item = quota.to_dict(value_mapper={"id": trans.security.encode_id})
             encoded_id = trans.security.encode_id(quota.id)
-            item['url'] = self._url_for(route, id=encoded_id)
+            item["url"] = self._url_for(route, id=encoded_id)
             rval.append(item)
         return QuotaSummaryList.parse_obj(rval)
 
     def show(self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, deleted: bool = False) -> QuotaDetails:
         """Displays information about a quota."""
         quota = self.quota_manager.get_quota(trans, id, deleted=deleted)
-        rval = quota.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'total_disk_usage': float})
+        rval = quota.to_dict(view="element", value_mapper={"id": trans.security.encode_id, "total_disk_usage": float})
         return QuotaDetails.parse_obj(rval)
 
     def create(self, trans: ProvidesUserContext, params: CreateQuotaParams) -> CreateQuotaResult:
@@ -63,9 +64,9 @@ class QuotasService(ServiceBase):
         payload = params.dict()
         self.validate_in_users_and_groups(trans, payload)
         quota, message = self.quota_manager.create_quota(payload)
-        item = quota.to_dict(value_mapper={'id': trans.security.encode_id})
-        item['url'] = self._url_for('quota', id=trans.security.encode_id(quota.id))
-        item['message'] = message
+        item = quota.to_dict(value_mapper={"id": trans.security.encode_id})
+        item["url"] = self._url_for("quota", id=trans.security.encode_id(quota.id))
+        item["message"] = message
         return CreateQuotaResult.parse_obj(item)
 
     def update(self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, params: UpdateQuotaParams) -> str:
@@ -92,11 +93,15 @@ class QuotasService(ServiceBase):
         for method in methods:
             message = method(quota, params)
             messages.append(message)
-        return '; '.join(messages)
+        return "; ".join(messages)
 
-    def delete(self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, payload: Optional[DeleteQuotaPayload] = None) -> str:
+    def delete(
+        self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, payload: Optional[DeleteQuotaPayload] = None
+    ) -> str:
         """Marks a quota as deleted."""
-        quota = self.quota_manager.get_quota(trans, id, deleted=False)  # deleted quotas are not technically members of this collection
+        quota = self.quota_manager.get_quota(
+            trans, id, deleted=False
+        )  # deleted quotas are not technically members of this collection
         message = self.quota_manager.delete_quota(quota)
         if payload and payload.purge:
             message += self.quota_manager.purge_quota(quota)
@@ -111,6 +116,7 @@ class QuotasService(ServiceBase):
         """
         For convenience, in_users and in_groups can be encoded IDs or emails/group names in the API.
         """
+
         def get_id(item, model_class, column):
             try:
                 return trans.security.decode_id(item)
@@ -118,25 +124,28 @@ class QuotasService(ServiceBase):
                 pass  # maybe an email/group name
             # this will raise if the item is invalid
             return trans.sa_session.query(model_class).filter(column == item).first().id
+
         new_in_users = []
         new_in_groups = []
         invalid = []
-        for item in util.listify(payload.get('in_users', [])):
+        for item in util.listify(payload.get("in_users", [])):
             try:
                 new_in_users.append(get_id(item, model.User, model.User.email))
             except Exception:
                 invalid.append(item)
-        for item in util.listify(payload.get('in_groups', [])):
+        for item in util.listify(payload.get("in_groups", [])):
             try:
                 new_in_groups.append(get_id(item, model.Group, model.Group.name))
             except Exception:
                 invalid.append(item)
         if invalid:
-            msg = f"The following value(s) for associated users and/or groups could not be parsed: {', '.join(invalid)}."
+            msg = (
+                f"The following value(s) for associated users and/or groups could not be parsed: {', '.join(invalid)}."
+            )
             msg += "  Valid values are email addresses of users, names of groups, or IDs of both."
             raise Exception(msg)
-        payload['in_users'] = list(map(str, new_in_users))
-        payload['in_groups'] = list(map(str, new_in_groups))
+        payload["in_users"] = list(map(str, new_in_users))
+        payload["in_groups"] = list(map(str, new_in_groups))
 
     def _url_for(self, *args, **kargs):
         try:
diff --git a/lib/galaxy/webapps/galaxy/services/sharable.py b/lib/galaxy/webapps/galaxy/services/sharable.py
index ae776106c02..4a193a93a45 100644
--- a/lib/galaxy/webapps/galaxy/services/sharable.py
+++ b/lib/galaxy/webapps/galaxy/services/sharable.py
@@ -6,21 +6,15 @@ from typing import (
     Tuple,
 )
 
-from sqlalchemy import (
-    false,
-)
+from sqlalchemy import false
 
 from galaxy import exceptions
-from galaxy.managers import (
-    base,
-)
+from galaxy.managers import base
 from galaxy.managers.sharable import (
     SharableModelManager,
     SharableModelSerializer,
 )
-from galaxy.model import (
-    User,
-)
+from galaxy.model import User
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.schema.schema import (
     SetSlugPayload,
@@ -113,9 +107,11 @@ class ShareableService:
         return item
 
     def _get_sharing_status(self, trans, item):
-        status = self.serializer.serialize_to_view(item,
-            user=trans.user, trans=trans, default_view="sharing")
-        status["users_shared_with"] = [{"id": self.manager.app.security.encode_id(a.user.id), "email": a.user.email} for a in item.users_shared_with]
+        status = self.serializer.serialize_to_view(item, user=trans.user, trans=trans, default_view="sharing")
+        status["users_shared_with"] = [
+            {"id": self.manager.app.security.encode_id(a.user.id), "email": a.user.email}
+            for a in item.users_shared_with
+        ]
         return SharingStatus.parse_obj(status)
 
     def _get_users(self, trans, emails_or_ids: Optional[List] = None) -> Tuple[Set[User], Set[str]]:
@@ -129,10 +125,11 @@ class ShareableService:
                 continue
 
             send_to_user = None
-            if '@' in email_or_id:
+            if "@" in email_or_id:
                 email_address = email_or_id
-                send_to_user = self.manager.user_manager.by_email(email_address,
-                    filters=[User.table.c.deleted == false()])
+                send_to_user = self.manager.user_manager.by_email(
+                    email_address, filters=[User.table.c.deleted == false()]
+                )
             else:
                 try:
                     decoded_user_id = trans.security.decode_id(email_or_id)
diff --git a/lib/galaxy/webapps/galaxy/services/visualizations.py b/lib/galaxy/webapps/galaxy/services/visualizations.py
index cbebd307b98..c1701b23de4 100644
--- a/lib/galaxy/webapps/galaxy/services/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/services/visualizations.py
@@ -18,12 +18,7 @@ class VisualizationsService(ServiceBase):
     and pydantic models to declare its parameters and return types.
     """
 
-    def __init__(
-        self,
-        security: IdEncodingHelper,
-        manager: VisualizationManager,
-        serializer: VisualizationSerializer
-    ):
+    def __init__(self, security: IdEncodingHelper, manager: VisualizationManager, serializer: VisualizationSerializer):
         super().__init__(security)
         self.manager = manager
         self.serializer = serializer
diff --git a/lib/galaxy/webapps/galaxy/workers.py b/lib/galaxy/webapps/galaxy/workers.py
index 2f1300fe923..a1180886a6a 100644
--- a/lib/galaxy/webapps/galaxy/workers.py
+++ b/lib/galaxy/webapps/galaxy/workers.py
@@ -1,4 +1,5 @@
 import logging
+
 log = logging.getLogger(__name__)
 
 try:
diff --git a/lib/galaxy/webapps/reports/__init__.py b/lib/galaxy/webapps/reports/__init__.py
index 44642ab4c7a..1750c712869 100644
--- a/lib/galaxy/webapps/reports/__init__.py
+++ b/lib/galaxy/webapps/reports/__init__.py
@@ -3,4 +3,4 @@
 from galaxy.web.framework import url_for
 from galaxy.web.framework.decorators import expose
 
-__all__ = ('url_for', 'expose')
+__all__ = ("url_for", "expose")
diff --git a/lib/galaxy/webapps/reports/app.py b/lib/galaxy/webapps/reports/app.py
index 6e629034b78..7e31c52725b 100644
--- a/lib/galaxy/webapps/reports/app.py
+++ b/lib/galaxy/webapps/reports/app.py
@@ -32,13 +32,11 @@ class UniverseApplication(BasicSharedApp):
         else:
             db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE"
         # Setup the database engine and ORM
-        self.model = galaxy.model.mapping.init(self.config.file_path,
-                                               db_url,
-                                               self.config.database_engine_options)
+        self.model = galaxy.model.mapping.init(self.config.file_path, db_url, self.config.database_engine_options)
         if not self.config.database_connection:
             self.targets_mysql = False
         else:
-            self.targets_mysql = 'mysql' in self.config.database_connection
+            self.targets_mysql = "mysql" in self.config.database_connection
         # Security helper
         self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
 
diff --git a/lib/galaxy/webapps/reports/buildapp.py b/lib/galaxy/webapps/reports/buildapp.py
index 86508116077..fdd7a7c7df4 100644
--- a/lib/galaxy/webapps/reports/buildapp.py
+++ b/lib/galaxy/webapps/reports/buildapp.py
@@ -27,8 +27,9 @@ def add_ui_controllers(webapp, app):
     Search for controllers in the 'galaxy.webapps.controllers' module and add
     them to the webapp.
     """
-    from galaxy.webapps.base.controller import BaseUIController
     import galaxy.webapps.reports.controllers
+    from galaxy.webapps.base.controller import BaseUIController
+
     controller_dir = galaxy.webapps.reports.controllers.__path__[0]
     for fname in os.listdir(controller_dir):
         if not fname.startswith("_") and fname.endswith(".py"):
@@ -48,25 +49,23 @@ def app_factory(global_conf, load_app_kwds=None, **kwargs):
     """Return a wsgi application serving the root object"""
     # Create the Galaxy application unless passed in
     load_app_kwds = load_app_kwds or {}
-    kwargs = load_app_properties(
-        kwds=kwargs,
-        **load_app_kwds
-    )
-    if 'app' in kwargs:
-        app = kwargs.pop('app')
+    kwargs = load_app_properties(kwds=kwargs, **load_app_kwds)
+    if "app" in kwargs:
+        app = kwargs.pop("app")
     else:
         from galaxy.webapps.reports.app import UniverseApplication
+
         app = UniverseApplication(global_conf=global_conf, **kwargs)
     atexit.register(app.shutdown)
     # Create the universe WSGI application
-    webapp = ReportsWebApplication(app, session_cookie='galaxyreportssession', name="reports")
+    webapp = ReportsWebApplication(app, session_cookie="galaxyreportssession", name="reports")
     add_ui_controllers(webapp, app)
     # These two routes handle our simple needs at the moment
-    webapp.add_route('/{controller}/{action}', controller="root", action='index')
-    webapp.add_route('/{action}', controller='root', action='index')
+    webapp.add_route("/{controller}/{action}", controller="root", action="index")
+    webapp.add_route("/{action}", controller="root", action="index")
     webapp.finalize_config()
     # Wrap the webapp in some useful middleware
-    if kwargs.get('middleware', True):
+    if kwargs.get("middleware", True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
     return webapp
 
@@ -77,42 +76,49 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     # Merge the global and local configurations
     conf = global_conf.copy()
     conf.update(local_conf)
-    debug = asbool(conf.get('debug', False))
+    debug = asbool(conf.get("debug", False))
     # First put into place httpexceptions, which must be most closely
     # wrapped around the application (it can interact poorly with
     # other middleware):
-    app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,))
+    app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name="paste.httpexceptions", args=(conf,))
     # The recursive middleware allows for including requests in other
     # requests or forwarding of requests, all on the server side.
-    if asbool(conf.get('use_recursive', True)):
+    if asbool(conf.get("use_recursive", True)):
         from paste import recursive
+
         app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
     # Various debug middleware that can only be turned on if the debug
     # flag is set, either because they are insecure or greatly hurt
     # performance
     if debug:
         # Middleware to check for WSGI compliance
-        if asbool(conf.get('use_lint', True)):
+        if asbool(conf.get("use_lint", True)):
             from paste import lint
-            app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
+
+            app = wrap_if_allowed(app, stack, lint.make_middleware, name="paste.lint", args=(conf,))
         # Middleware to run the python profiler on each request
-        if asbool(conf.get('use_profile', False)):
+        if asbool(conf.get("use_profile", False)):
             import profile
+
             app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
         # Middleware that intercepts print statements and shows them on the
         # returned page
-        if asbool(conf.get('use_printdebug', True)):
+        if asbool(conf.get("use_printdebug", True)):
             from paste.debug import prints
+
             app = wrap_if_allowed(app, stack, prints.PrintDebugMiddleware, args=(conf,))
     # Error middleware
     import galaxy.web.framework.middleware.error
+
     app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
     # Transaction logging (apache access.log style)
-    if asbool(conf.get('use_translogger', True)):
+    if asbool(conf.get("use_translogger", True)):
         from paste.translogger import TransLogger
+
         app = wrap_if_allowed(app, stack, TransLogger)
     # X-Forwarded-Host handling
     from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
+
     app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
     return app
 
diff --git a/lib/galaxy/webapps/reports/config.py b/lib/galaxy/webapps/reports/config.py
index 1f65b90833b..f64e70c3082 100644
--- a/lib/galaxy/webapps/reports/config.py
+++ b/lib/galaxy/webapps/reports/config.py
@@ -10,7 +10,7 @@ log = logging.getLogger(__name__)
 
 def resolve_path(path, root):
     """If 'path' is relative make absolute by prepending 'root'"""
-    if not(os.path.isabs(path)):
+    if not (os.path.isabs(path)):
         path = os.path.join(root, path)
     return path
 
@@ -22,7 +22,7 @@ class ConfigurationError(Exception):
 class Configuration:
     def __init__(self, **kwargs):
         self.config_dict = kwargs
-        self.root = kwargs.get('root_dir', '.')
+        self.root = kwargs.get("root_dir", ".")
         # Database related configuration
         self.database = resolve_path(kwargs.get("database_file", "database/universe.sqlite"), self.root)
         self.database_connection = kwargs.get("database_connection", False)
@@ -33,23 +33,25 @@ class Configuration:
         self.id_secret = kwargs.get("id_secret", "USING THE DEFAULT IS NOT SECURE!")
         self.use_remote_user = string_as_bool(kwargs.get("use_remote_user", "False"))
         self.require_login = string_as_bool(kwargs.get("require_login", "False"))
-        self.template_cache_path = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates/reports"), self.root)
+        self.template_cache_path = resolve_path(
+            kwargs.get("template_cache_path", "database/compiled_templates/reports"), self.root
+        )
         self.allow_user_creation = string_as_bool(kwargs.get("allow_user_creation", "True"))
         self.allow_user_deletion = string_as_bool(kwargs.get("allow_user_deletion", "False"))
-        self.log_actions = string_as_bool(kwargs.get('log_actions', 'False'))
-        self.brand = kwargs.get('brand', None)
+        self.log_actions = string_as_bool(kwargs.get("log_actions", "False"))
+        self.brand = kwargs.get("brand", None)
         # Configuration for the message box directly below the masthead.
-        self.message_box_visible = string_as_bool(kwargs.get('message_box_visible', False))
-        self.message_box_content = kwargs.get('message_box_content', None)
-        self.message_box_class = kwargs.get('message_box_class', 'info')
-        self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
-        self.blog_url = kwargs.get('blog_url', None)
-        self.screencasts_url = kwargs.get('screencasts_url', None)
+        self.message_box_visible = string_as_bool(kwargs.get("message_box_visible", False))
+        self.message_box_content = kwargs.get("message_box_content", None)
+        self.message_box_class = kwargs.get("message_box_class", "info")
+        self.wiki_url = kwargs.get("wiki_url", "https://galaxyproject.org/")
+        self.blog_url = kwargs.get("blog_url", None)
+        self.screencasts_url = kwargs.get("screencasts_url", None)
         self.log_events = False
         self.cookie_path = kwargs.get("cookie_path", None)
         self.cookie_domain = kwargs.get("cookie_domain", None)
         # Error logging with sentry
-        self.sentry_dsn = kwargs.get('sentry_dsn', None)
+        self.sentry_dsn = kwargs.get("sentry_dsn", None)
 
         # Security/Policy Compliance
         self.redact_username_in_logs = False
@@ -65,7 +67,7 @@ class Configuration:
 
     def check(self):
         # Check that required directories exist
-        for path in (self.root, ):
+        for path in (self.root,):
             if not os.path.isdir(path):
                 raise ConfigurationError(f"Directory does not exist: {path}")
 
@@ -87,14 +89,14 @@ def get_database_engine_options(kwargs):
     the prefix "database_engine_option".
     """
     conversions = {
-        'convert_unicode': string_as_bool,
-        'pool_timeout': int,
-        'echo': string_as_bool,
-        'echo_pool': string_as_bool,
-        'pool_recycle': int,
-        'pool_size': int,
-        'max_overflow': int,
-        'pool_threadlocal': string_as_bool
+        "convert_unicode": string_as_bool,
+        "pool_timeout": int,
+        "echo": string_as_bool,
+        "echo_pool": string_as_bool,
+        "pool_recycle": int,
+        "pool_size": int,
+        "max_overflow": int,
+        "pool_threadlocal": string_as_bool,
     }
     prefix = "database_engine_option_"
     prefix_len = len(prefix)
diff --git a/lib/galaxy/webapps/reports/controllers/history.py b/lib/galaxy/webapps/reports/controllers/history.py
index 45510b80d7e..c183a82dcd1 100644
--- a/lib/galaxy/webapps/reports/controllers/history.py
+++ b/lib/galaxy/webapps/reports/controllers/history.py
@@ -6,7 +6,10 @@ from sqlalchemy import and_
 
 import galaxy.model
 from galaxy import util
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 
 log = logging.getLogger(__name__)
 
@@ -22,8 +25,8 @@ def int_to_octet(size):
         return "???"
     units = ("o", "Ko", "Mo", "Go", "To")
     no_unit = 0
-    while (size >= 1000):
-        size /= 1000.
+    while size >= 1000:
+        size /= 1000.0
         no_unit += 1
     try:
         return f"{size:.2f} {units[no_unit]}"
@@ -38,6 +41,7 @@ class History(BaseUIController):
     The name of function must be the same as as the field "action" of
     the "href" dict, in .mako templates (templates/webapps/reports).
     """
+
     @web.expose
     def history_and_dataset_per_user(self, trans, **kwd):
         """
@@ -46,13 +50,13 @@ class History(BaseUIController):
             - the number of history and their size
             - the number of dataset
         """
-        message = escape(util.restore_text(kwd.get('message', '')))
-        user_cutoff = int(kwd.get('user_cutoff', 60))
+        message = escape(util.restore_text(kwd.get("message", "")))
+        user_cutoff = int(kwd.get("user_cutoff", 60))
 
         # sort by history space, or by user mail or by number of history/dataset
-        sort_by = kwd.get('sorting', 'User')
-        sorting = 0 if sort_by == 'User' else 1 if sort_by == "HSort" else 2 if sort_by == "DSort" else 3
-        descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
+        sort_by = kwd.get("sorting", "User")
+        sorting = 0 if sort_by == "User" else 1 if sort_by == "HSort" else 2 if sort_by == "DSort" else 3
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
 
         # select count (h.id) as history, u.email as email
@@ -60,45 +64,60 @@ class History(BaseUIController):
         # where h.user_id = u.id and h.deleted='f'
         # group by email order by email desc
         histories = sa.select(
-            (sa.func.count(galaxy.model.History.table.c.id).label('history'),
-             galaxy.model.User.table.c.email.label('email')),
+            (
+                sa.func.count(galaxy.model.History.table.c.id).label("history"),
+                galaxy.model.User.table.c.email.label("email"),
+            ),
             from_obj=[sa.outerjoin(galaxy.model.History.table, galaxy.model.User.table)],
-            whereclause=and_(galaxy.model.History.table.c.user_id == galaxy.model.User.table.c.id,
-                             galaxy.model.History.table.c.deleted == 'f'),
-            group_by=['email'],
-            order_by=[sa.desc('email'), 'history'])
+            whereclause=and_(
+                galaxy.model.History.table.c.user_id == galaxy.model.User.table.c.id,
+                galaxy.model.History.table.c.deleted == "f",
+            ),
+            group_by=["email"],
+            order_by=[sa.desc("email"), "history"],
+        )
 
         # select u.email, count(d.id)
         # from galaxy_user u, dataset d, history_dataset_association hd,history h
         # where d.id=hd.dataset_id and h.id=hd.history_id and u.id = h.user_id and h.deleted='f'
         # group by u.email;
         datasets = sa.select(
-            (sa.func.count(galaxy.model.Dataset.table.c.id).label('dataset'),
-             sa.func.sum(galaxy.model.Dataset.table.c.total_size).label('size'),
-             galaxy.model.User.table.c.email.label('email')),
-            from_obj=[galaxy.model.User.table,
-                      galaxy.model.Dataset.table,
-                      galaxy.model.HistoryDatasetAssociation.table,
-                      galaxy.model.History.table],
-            whereclause=and_(galaxy.model.Dataset.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.dataset_id,
-                             galaxy.model.History.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.history_id,
-                             galaxy.model.History.table.c.user_id == galaxy.model.User.table.c.id,
-                             galaxy.model.History.table.c.deleted == 'f'),
-            group_by=['email'])
+            (
+                sa.func.count(galaxy.model.Dataset.table.c.id).label("dataset"),
+                sa.func.sum(galaxy.model.Dataset.table.c.total_size).label("size"),
+                galaxy.model.User.table.c.email.label("email"),
+            ),
+            from_obj=[
+                galaxy.model.User.table,
+                galaxy.model.Dataset.table,
+                galaxy.model.HistoryDatasetAssociation.table,
+                galaxy.model.History.table,
+            ],
+            whereclause=and_(
+                galaxy.model.Dataset.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.dataset_id,
+                galaxy.model.History.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.history_id,
+                galaxy.model.History.table.c.user_id == galaxy.model.User.table.c.id,
+                galaxy.model.History.table.c.deleted == "f",
+            ),
+            group_by=["email"],
+        )
 
         # execute requests, replace None fields by "Unknown"
         # transform lists to dict with email as key and
         # number of (history/dataset)/size of history as value
-        histories = {_.email if _.email is not None else "Unknown": int(_.history)
-                     for _ in trans.sa_session.execute(histories)}
-        datasets = {_.email if _.email is not None else "Unknown": (int(_.dataset), int(_.size))
-                    for _ in trans.sa_session.execute(datasets)}
+        histories = {
+            _.email if _.email is not None else "Unknown": int(_.history) for _ in trans.sa_session.execute(histories)
+        }
+        datasets = {
+            _.email if _.email is not None else "Unknown": (int(_.dataset), int(_.size))
+            for _ in trans.sa_session.execute(datasets)
+        }
 
         sort_keys = (
             lambda v: v[0].lower(),
             lambda v: histories.get(v, 0),
             lambda v: datasets.get(v, [0])[0],
-            lambda v: datasets.get(v, [0][0])[1]
+            lambda v: datasets.get(v, [0][0])[1],
         )
 
         # fetch all users
@@ -116,12 +135,14 @@ class History(BaseUIController):
             history = histories.get(user, 0)
             data[user] = ("%d (%s)" % (history, int_to_octet(dataset[1])), dataset[0])
 
-        return trans.fill_template('/webapps/reports/history_and_dataset_per_user.mako',
-                                   data=data,
-                                   user_cutoff=user_cutoff,
-                                   sorting=sorting,
-                                   descending=descending,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/history_and_dataset_per_user.mako",
+            data=data,
+            user_cutoff=user_cutoff,
+            sorting=sorting,
+            descending=descending,
+            message=message,
+        )
 
     @web.expose
     def history_and_dataset_type(self, trans, **kwd):
@@ -130,34 +151,44 @@ class History(BaseUIController):
             - the name of history
             - the number of dataset foreach type
         """
-        message = escape(util.restore_text(kwd.get('message', '')))
-        user_cutoff = int(kwd.get('user_cutoff', 60))
-        descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
+        message = escape(util.restore_text(kwd.get("message", "")))
+        user_cutoff = int(kwd.get("user_cutoff", 60))
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
-        user_selection = kwd.get('user_selection', None)
+        user_selection = kwd.get("user_selection", None)
 
         # select d.state, h.name
         # from dataset d, history h , history_dataset_association hda
         # where hda.history_id=h.id and hda.dataset_id=d.id order by h.state;
-        from_obj = [galaxy.model.Dataset.table, galaxy.model.History.table, galaxy.model.HistoryDatasetAssociation.table]
+        from_obj = [
+            galaxy.model.Dataset.table,
+            galaxy.model.History.table,
+            galaxy.model.HistoryDatasetAssociation.table,
+        ]
         if user_selection is not None:
             from_obj.append(galaxy.model.User.table)
-            whereclause = and_(galaxy.model.Dataset.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.dataset_id,
-                               galaxy.model.History.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.history_id,
-                               galaxy.model.User.table.c.id == galaxy.model.History.table.c.user_id,
-                               galaxy.model.User.table.c.email == user_selection)
+            whereclause = and_(
+                galaxy.model.Dataset.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.dataset_id,
+                galaxy.model.History.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.history_id,
+                galaxy.model.User.table.c.id == galaxy.model.History.table.c.user_id,
+                galaxy.model.User.table.c.email == user_selection,
+            )
         else:
-            whereclause = and_(galaxy.model.Dataset.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.dataset_id,
-                               galaxy.model.History.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.history_id)
-        histories = sa.select((galaxy.model.Dataset.table.c.state.label('state'),
-                               galaxy.model.History.table.c.name.label('name')),
-                              from_obj=from_obj,
-                              whereclause=whereclause,
-                              order_by=['name'])
+            whereclause = and_(
+                galaxy.model.Dataset.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.dataset_id,
+                galaxy.model.History.table.c.id == galaxy.model.HistoryDatasetAssociation.table.c.history_id,
+            )
+        histories = sa.select(
+            (galaxy.model.Dataset.table.c.state.label("state"), galaxy.model.History.table.c.name.label("name")),
+            from_obj=from_obj,
+            whereclause=whereclause,
+            order_by=["name"],
+        )
 
         # execute requests, replace None fields by "Unknown"
-        data = [(_.name if _.name is not None else "NoNamedHistory", _.state)
-                for _ in trans.sa_session.execute(histories)]
+        data = [
+            (_.name if _.name is not None else "NoNamedHistory", _.state) for _ in trans.sa_session.execute(histories)
+        ]
 
         # sort by names descending or ascending
         data.sort(key=lambda v: v[0].lower(), reverse=reverse)
@@ -178,15 +209,17 @@ class History(BaseUIController):
                     if len(datas) == user_cutoff:
                         break
                 # creation of a list containing the number of each status
-                datas[name] = ['-'] * number_of_possible_status
+                datas[name] = ["-"] * number_of_possible_status
             # to not execute it several times, we put it in a variable...
             no_status = possible_status.get(status[no], 6)
-            if datas[name][no_status] == '-':
+            if datas[name][no_status] == "-":
                 datas[name][no_status] = 0
             datas[name][no_status] += 1
 
-        return trans.fill_template('/webapps/reports/history_and_dataset_type.mako',
-                                   data=datas,
-                                   user_cutoff=user_cutoff,
-                                   descending=descending,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/history_and_dataset_type.mako",
+            data=datas,
+            user_cutoff=user_cutoff,
+            descending=descending,
+            message=message,
+        )
diff --git a/lib/galaxy/webapps/reports/controllers/home.py b/lib/galaxy/webapps/reports/controllers/home.py
index 745548c2673..b8ca77697ff 100644
--- a/lib/galaxy/webapps/reports/controllers/home.py
+++ b/lib/galaxy/webapps/reports/controllers/home.py
@@ -1,11 +1,17 @@
 import calendar
 import logging
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 
 import sqlalchemy as sa
 
 from galaxy import model
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 
 log = logging.getLogger(__name__)
@@ -14,7 +20,7 @@ log = logging.getLogger(__name__)
 class HomePage(BaseUIController, ReportQueryBuilder):
     @web.expose
     def run_stats(self, trans, **kwd):
-        message = ''
+        message = ""
         end_date = datetime.utcnow()
         end_date = datetime(end_date.year, end_date.month, end_date.day, end_date.hour)
         end_date_buffer = datetime(end_date.year, end_date.month, end_date.day, end_date.hour + 1)
@@ -29,30 +35,24 @@ class HomePage(BaseUIController, ReportQueryBuilder):
         et_dy_data = []
 
         recent_jobs = sa.select(
-            (
-                (model.Job.id),
-                (model.Job.create_time).label('create_time'),
-                (model.Job.update_time).label('update_time')
-            )
+            ((model.Job.id), (model.Job.create_time).label("create_time"), (model.Job.update_time).label("update_time"))
         )
 
         for job in trans.sa_session.execute(recent_jobs):
-            if(job.create_time >= start_days
-               and job.create_time < end_date_buffer):
-                if(job.create_time >= start_hours
-                   and job.create_time < end_date_buffer):
+            if job.create_time >= start_days and job.create_time < end_date_buffer:
+                if job.create_time >= start_hours and job.create_time < end_date_buffer:
                     # Get the creation time for the jobs in the past day
                     end_day = end_date.day
                     start_day = job.create_time.day
                     end_hour = end_date.hour
                     start_hour = job.create_time.hour
 
-                    if(end_day != start_day):
+                    if end_day != start_day:
                         hours = (end_hour + 24) - start_hour
                     else:
                         hours = end_hour - start_hour
 
-                    if(hours < 24):
+                    if hours < 24:
                         jc_hr_data[int(hours)] += 1
                     else:
                         jc_dy_data[23] += 1
@@ -62,35 +62,33 @@ class HomePage(BaseUIController, ReportQueryBuilder):
                 end_day = end_date.day
                 start_day = job.create_time.day
 
-                if(end_month != start_month):
+                if end_month != start_month:
                     month_weekday, month_range = calendar.monthrange(job.create_time.year, job.create_time.month)
                     day = (end_day + month_range) - start_day
                 else:
                     day = end_day - start_day
 
-                if(day < 30):
+                if day < 30:
                     jc_dy_data[int(day)] += 1
 
-            if(job.update_time >= start_days
-               and job.update_time < end_date_buffer):
-                if(job.update_time >= start_hours
-                   and job.update_time < end_date_buffer):
+            if job.update_time >= start_days and job.update_time < end_date_buffer:
+                if job.update_time >= start_hours and job.update_time < end_date_buffer:
                     # Get the time finishedfor the jobs in the past day
                     end_day = end_date.day
                     start_day = job.update_time.day
                     end_hour = end_date.hour
                     start_hour = job.update_time.hour
 
-                    if(end_day != start_day):
+                    if end_day != start_day:
                         hours = (end_hour + 23) - start_hour
                     else:
                         hours = end_hour - start_hour
 
-                    if(hours < 24):
+                    if hours < 24:
                         jf_hr_data[int(hours)] += 1
 
                         # Get the Elapsed Time for said job
-                        time = (job.update_time - job.create_time)
+                        time = job.update_time - job.create_time
                         seconds = time.seconds
                         minutes = seconds // 60
                         et_hr_data.append(minutes)
@@ -100,26 +98,28 @@ class HomePage(BaseUIController, ReportQueryBuilder):
                 end_day = end_date.day
                 start_day = job.update_time.day
 
-                if(end_month != start_month):
+                if end_month != start_month:
                     month_weekday, month_range = calendar.monthrange(job.update_time.year, job.update_time.month)
                     day = (end_day + (month_range - 1)) - start_day
                 else:
                     day = end_day - start_day
 
-                if(day < 30):
+                if day < 30:
                     jf_dy_data[int(day)] += 1
 
                     # Get the Elapsed Time for said job
-                    time = (job.update_time - job.create_time)
+                    time = job.update_time - job.create_time
                     seconds = time.seconds
                     minutes = seconds // 60
                     et_dy_data.append(minutes)
 
-        return trans.fill_template('/webapps/reports/run_stats.mako',
+        return trans.fill_template(
+            "/webapps/reports/run_stats.mako",
             jf_hr_data=jf_hr_data,
             jf_dy_data=jf_dy_data,
             jc_hr_data=jc_hr_data,
             jc_dy_data=jc_dy_data,
             et_hr_data=et_hr_data,
             et_dy_data=et_dy_data,
-            message=message)
+            message=message,
+        )
diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py
index e85cb5d1b1e..b0cdf720ea6 100644
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -5,17 +5,30 @@ from collections import namedtuple
 from datetime import (
     date,
     datetime,
-    timedelta
+    timedelta,
+)
+from math import (
+    ceil,
+    floor,
 )
-from math import ceil, floor
 
 import sqlalchemy as sa
 from markupsafe import escape
-from sqlalchemy import and_, not_, or_
+from sqlalchemy import (
+    and_,
+    not_,
+    or_,
+)
 
-from galaxy import model, util
+from galaxy import (
+    model,
+    util,
+)
 from galaxy.web.legacy_framework import grids
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 
 log = logging.getLogger(__name__)
@@ -34,8 +47,8 @@ class Timer:
         try:
             self.stop_time = datetime.now()
             self.time_delta = self.stop_time - self.start_time
-            del(self.stop_time)
-            del(self.start_time)
+            del self.stop_time
+            del self.start_time
         except NameError:
             print("You need to start before you can stop!")
 
@@ -54,10 +67,10 @@ def sorter(default_sort_id, kwd):
     """
     Initialize sorting variables
     """
-    SortSpec = namedtuple('SortSpec', ['sort_id', 'order', 'arrow', 'exc_order'])
+    SortSpec = namedtuple("SortSpec", ["sort_id", "order", "arrow", "exc_order"])
 
-    sort_id = kwd.get('sort_id')
-    order = kwd.get('order')
+    sort_id = kwd.get("sort_id")
+    order = kwd.get("order")
 
     # Parse the default value
     if sort_id == "default":
@@ -110,32 +123,34 @@ def get_curr_item(check_item, unique_items):
     render the item uniquely.
     """
     if check_item in unique_items:
-        return ('', unique_items)
+        return ("", unique_items)
     unique_items.add(check_item)
     return (check_item, unique_items)
 
 
 class SpecifiedDateListGrid(grids.Grid):
-
     class JobIdColumn(grids.IntegerColumn):
-
         def get_value(self, trans, grid, job):
             return job.id
 
     class StateColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, job):
             return f'<div class="count-box state-color-{job.state}">{job.state}</div>'
 
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'Unfinished':
-                return query.filter(not_(or_(model.Job.table.c.state == model.Job.states.OK,
-                                             model.Job.table.c.state == model.Job.states.ERROR,
-                                             model.Job.table.c.state == model.Job.states.DELETED)))
+            if column_filter == "Unfinished":
+                return query.filter(
+                    not_(
+                        or_(
+                            model.Job.table.c.state == model.Job.states.OK,
+                            model.Job.table.c.state == model.Job.states.ERROR,
+                            model.Job.table.c.state == model.Job.states.DELETED,
+                        )
+                    )
+                )
             return query
 
     class ToolColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, job):
             return job.tool_id
 
@@ -146,50 +161,49 @@ class SpecifiedDateListGrid(grids.Grid):
             return query
 
     class CreateTimeColumn(grids.DateTimeColumn):
-
         def get_value(self, trans, grid, job):
             return job.create_time.strftime("%b %d, %Y, %H:%M:%S")
 
     class UserColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, job):
             if job.user:
                 return escape(job.get_user_email())
-            return 'anonymous'
+            return "anonymous"
 
     class EmailColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
-            return query.filter(and_(model.Job.table.c.user_id == model.User.table.c.id,
-                                     model.User.table.c.email == column_filter))
+            return query.filter(
+                and_(model.Job.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter)
+            )
 
     class DestinationIdColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
             return query.filter(model.Job.table.c.destination_id == column_filter)
 
     class SpecifiedDateColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
             # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
             # so we need to figure out which type of date we have
-            if column_filter.count('-') == 2:  # We are filtering on a date like YYYY-MM-DD
+            if column_filter.count("-") == 2:  # We are filtering on a date like YYYY-MM-DD
                 year, month, day = map(int, column_filter.split("-"))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
-            if column_filter.count('-') == 1:  # We are filtering on a month like YYYY-MM
+            if column_filter.count("-") == 1:  # We are filtering on a month like YYYY-MM
                 year, month = map(int, column_filter.split("-"))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
 
-            return query.filter(and_(self.model_class.table.c.create_time >= start_date,
-                                     self.model_class.table.c.create_time < end_date))
+            return query.filter(
+                and_(
+                    self.model_class.table.c.create_time >= start_date, self.model_class.table.c.create_time < end_date
+                )
+            )
 
     # Grid definition
     use_async = False
@@ -197,59 +211,57 @@ class SpecifiedDateListGrid(grids.Grid):
     title = "Jobs"
     default_sort_key = "id"
     columns = [
-        JobIdColumn("Id",
-                    key="id",
-                    link=(lambda item: dict(operation="job_info", id=item.id, webapp="reports")),
-                    attach_popup=False,
-                    filterable="advanced"),
-        StateColumn("State",
-                    key="state",
-                    attach_popup=False),
-        DestinationIdColumn("Destination Id",
-                    key="destination_id",
-                    attach_popup=False),
-        ToolColumn("Tool Id",
-                   key="tool_id",
-                   link=(lambda item: dict(operation="tool_per_month", id=item.id, webapp="reports")),
-                   attach_popup=False),
-        CreateTimeColumn("Creation Time",
-                         key="create_time",
-                         attach_popup=False),
-        UserColumn("User",
-                   key="email",
-                   model_class=model.User,
-                   link=(lambda item: dict(operation="user_per_month", id=item.id, webapp="reports")),
-                   attach_popup=False),
+        JobIdColumn(
+            "Id",
+            key="id",
+            link=(lambda item: dict(operation="job_info", id=item.id, webapp="reports")),
+            attach_popup=False,
+            filterable="advanced",
+        ),
+        StateColumn("State", key="state", attach_popup=False),
+        DestinationIdColumn("Destination Id", key="destination_id", attach_popup=False),
+        ToolColumn(
+            "Tool Id",
+            key="tool_id",
+            link=(lambda item: dict(operation="tool_per_month", id=item.id, webapp="reports")),
+            attach_popup=False,
+        ),
+        CreateTimeColumn("Creation Time", key="create_time", attach_popup=False),
+        UserColumn(
+            "User",
+            key="email",
+            model_class=model.User,
+            link=(lambda item: dict(operation="user_per_month", id=item.id, webapp="reports")),
+            attach_popup=False,
+        ),
         # Columns that are valid for filtering but are not visible.
-        SpecifiedDateColumn("Specified Date",
-                            key="specified_date",
-                            visible=False),
-        EmailColumn("Email",
-                    key="email",
-                    model_class=model.User,
-                    visible=False),
-        grids.StateColumn("State",
-                          key="state",
-                          visible=False,
-                          filterable="advanced")
+        SpecifiedDateColumn("Specified Date", key="specified_date", visible=False),
+        EmailColumn("Email", key="email", model_class=model.User, visible=False),
+        grids.StateColumn("State", key="state", visible=False, filterable="advanced"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[1], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    default_filter = {'specified_date': 'All'}
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    default_filter = {"specified_date": "All"}
     num_rows_per_page = 50
     use_paging = True
 
     def build_initial_query(self, trans, **kwd):
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
         monitor_user_id = get_monitor_id(trans, monitor_email)
-        return trans.sa_session.query(self.model_class) \
-                               .join(model.User) \
-                               .filter(model.Job.table.c.user_id != monitor_user_id)\
-                               .enable_eagerloads(False)
+        return (
+            trans.sa_session.query(self.model_class)
+            .join(model.User)
+            .filter(model.Job.table.c.user_id != monitor_user_id)
+            .enable_eagerloads(False)
+        )
 
 
 class Jobs(BaseUIController, ReportQueryBuilder):
@@ -266,54 +278,48 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         # We add params to the keyword dict in this method in order to rename the param
         # with an "f-" prefix, simulating filtering by clicking a search link.  We have
         # to take this approach because the "-" character is illegal in HTTP requests.
-        kwd['sort_id'] = 'default'
-        kwd['order'] = 'default'
+        kwd["sort_id"] = "default"
+        kwd["order"] = "default"
 
-        if 'f-specified_date' in kwd and 'specified_date' not in kwd:
+        if "f-specified_date" in kwd and "specified_date" not in kwd:
             # The user clicked a State link in the Advanced Search box, so 'specified_date'
             # will have been eliminated.
             pass
-        elif 'specified_date' not in kwd:
-            kwd['f-specified_date'] = 'All'
+        elif "specified_date" not in kwd:
+            kwd["f-specified_date"] = "All"
         else:
-            kwd['f-specified_date'] = kwd['specified_date']
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+            kwd["f-specified_date"] = kwd["specified_date"]
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "job_info":
-                return trans.response.send_redirect(web.url_for(controller='jobs',
-                                                                action='job_info',
-                                                                **kwd))
+                return trans.response.send_redirect(web.url_for(controller="jobs", action="job_info", **kwd))
             elif operation == "tool_for_month":
-                kwd['f-tool_id'] = kwd['tool_id']
+                kwd["f-tool_id"] = kwd["tool_id"]
             elif operation == "tool_per_month":
                 # The received id is the job id, so we need to get the job's tool_id.
-                job_id = kwd.get('id', None)
+                job_id = kwd.get("id", None)
                 job = get_job(trans, job_id)
-                kwd['tool_id'] = job.tool_id
-                return trans.response.send_redirect(web.url_for(controller='jobs',
-                                                                action='tool_per_month',
-                                                                **kwd))
+                kwd["tool_id"] = job.tool_id
+                return trans.response.send_redirect(web.url_for(controller="jobs", action="tool_per_month", **kwd))
             elif operation == "user_for_month":
-                kwd['f-email'] = util.restore_text(kwd['email'])
+                kwd["f-email"] = util.restore_text(kwd["email"])
             elif operation == "user_for_month_by_destination":
-                kwd['f-email'] = util.restore_text(kwd['email'])
-                kwd['f-destination_id'] = kwd['destination_id']
+                kwd["f-email"] = util.restore_text(kwd["email"])
+                kwd["f-destination_id"] = kwd["destination_id"]
             elif operation == "user_per_month":
                 # The received id is the job id, so we need to get the id of the user
                 # that submitted the job.
-                job_id = kwd.get('id', None)
+                job_id = kwd.get("id", None)
                 job = get_job(trans, job_id)
-                kwd['email'] = job.get_user_email()
-                return trans.response.send_redirect(web.url_for(controller='jobs',
-                                                                action='user_per_month',
-                                                                **kwd))
+                kwd["email"] = job.get_user_email()
+                return trans.response.send_redirect(web.url_for(controller="jobs", action="user_per_month", **kwd))
             elif operation == "specified_date_in_error":
-                kwd['f-state'] = 'error'
+                kwd["f-state"] = "error"
             elif operation == "unfinished":
-                kwd['f-state'] = 'Unfinished'
+                kwd["f-state"] = "Unfinished"
             elif operation == "specified_tool_in_error":
-                kwd['f-state'] = 'error'
-                kwd['f-tool_id'] = kwd['tool_id']
+                kwd["f-state"] = "error"
+                kwd["f-tool_id"] = kwd["tool_id"]
         return self.specified_date_list_grid(trans, **kwd)
 
     def _calculate_trends_for_jobs(self, sa_session, jobs_query):
@@ -341,31 +347,28 @@ class Jobs(BaseUIController, ReportQueryBuilder):
             month_name = row.date.strftime("%B")
             year = int(row.date.strftime("%Y"))
 
-            if str(by_destination).lower() == 'true':
+            if str(by_destination).lower() == "true":
                 month_year_str = "%s %s" % (month_name, year)
                 curr_month_year_str, unique_month_year_strs = get_curr_item(month_year_str, unique_month_year_strs)
-                if curr_month_year_str == '':
-                    curr_month = ''
-                    curr_year = ''
+                if curr_month_year_str == "":
+                    curr_month = ""
+                    curr_year = ""
                 else:
                     curr_month = row.date.strftime("%B")
                     curr_year = row.date.strftime("%Y")
-                jobs.append((
-                    row.date.strftime("%Y-%m"),
-                    row.total_jobs,
-                    curr_month,
-                    curr_year,
-                    row.user_email,
-                    row.destination_id,
-                    row.execute_time
-                ))
+                jobs.append(
+                    (
+                        row.date.strftime("%Y-%m"),
+                        row.total_jobs,
+                        curr_month,
+                        curr_year,
+                        row.user_email,
+                        row.destination_id,
+                        row.execute_time,
+                    )
+                )
             else:
-                jobs.append((
-                    row.date.strftime("%Y-%m"),
-                    row.total_jobs,
-                    month_name,
-                    year
-                ))
+                jobs.append((row.date.strftime("%Y-%m"), row.total_jobs, month_name, year))
         return jobs
 
     @web.expose
@@ -373,12 +376,12 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         """
         Queries the DB for all jobs in given month, defaults to current month.
         """
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('date', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("date", kwd)
         offset = 0
         limit = 10
         sort_id = specs.sort_id
@@ -387,18 +390,18 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         _order = specs.exc_order
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
@@ -406,7 +409,7 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
         # If specified_date is not received, we'll default to the current month
-        specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
+        specified_date = kwd.get("specified_date", datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
 
         year, month = map(int, specified_month.split("-"))
@@ -416,22 +419,32 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         year_label = start_date.strftime("%Y")
 
         # Use to make the page table
-        month_jobs = sa.select((sa.func.date(model.Job.table.c.create_time).label('date'),
-                                sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                               whereclause=sa.and_(model.Job.table.c.user_id != monitor_user_id,
-                                                   model.Job.table.c.create_time >= start_date,
-                                                   model.Job.table.c.create_time < end_date),
-                               from_obj=[model.Job.table],
-                               group_by=['date'],
-                               order_by=[_order],
-                               offset=offset,
-                               limit=limit)
+        month_jobs = sa.select(
+            (
+                sa.func.date(model.Job.table.c.create_time).label("date"),
+                sa.func.count(model.Job.table.c.id).label("total_jobs"),
+            ),
+            whereclause=sa.and_(
+                model.Job.table.c.user_id != monitor_user_id,
+                model.Job.table.c.create_time >= start_date,
+                model.Job.table.c.create_time < end_date,
+            ),
+            from_obj=[model.Job.table],
+            group_by=["date"],
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
         # Use to make trendline
-        all_jobs = sa.select((model.Job.table.c.create_time.label('date'), model.Job.table.c.id.label('id')),
-                             whereclause=sa.and_(model.Job.table.c.user_id != monitor_user_id,
-                                                 model.Job.table.c.create_time >= start_date,
-                                                 model.Job.table.c.create_time < end_date))
+        all_jobs = sa.select(
+            (model.Job.table.c.create_time.label("date"), model.Job.table.c.id.label("id")),
+            whereclause=sa.and_(
+                model.Job.table.c.user_id != monitor_user_id,
+                model.Job.table.c.create_time >= start_date,
+                model.Job.table.c.create_time < end_date,
+            ),
+        )
 
         trends = dict()
         for job in trans.sa_session.execute(all_jobs):
@@ -449,38 +462,37 @@ class Jobs(BaseUIController, ReportQueryBuilder):
             row_dayname = row.date.strftime("%A")
             row_day = row.date.strftime("%d")
 
-            jobs.append((row_dayname,
-                         row_day,
-                         row.total_jobs,
-                         row.date))
+            jobs.append((row_dayname, row_day, row.total_jobs, row.date))
 
         pages_found = ceil(len(jobs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/jobs_specified_month_all.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   month_label=month_label,
-                                   year_label=year_label,
-                                   month=month,
-                                   page_specs=page_specs,
-                                   jobs=jobs,
-                                   trends=trends,
-                                   is_user_jobs_only=monitor_user_id,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/jobs_specified_month_all.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            month_label=month_label,
+            year_label=year_label,
+            month=month,
+            page_specs=page_specs,
+            jobs=jobs,
+            trends=trends,
+            is_user_jobs_only=monitor_user_id,
+            message=message,
+        )
 
     @web.expose
     def specified_month_in_error(self, trans, **kwd):
         """
         Queries the DB for the user jobs in error.
         """
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('date', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -489,18 +501,18 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
@@ -508,7 +520,7 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
         # If specified_date is not received, we'll default to the current month
-        specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
+        specified_date = kwd.get("specified_date", datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
         year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
@@ -516,24 +528,34 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         month_label = start_date.strftime("%B")
         year_label = start_date.strftime("%Y")
 
-        month_jobs_in_error = sa.select((sa.func.date(model.Job.table.c.create_time).label('date'),
-                                         sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                                        whereclause=sa.and_(model.Job.table.c.user_id != monitor_user_id,
-                                                            model.Job.table.c.state == 'error',
-                                                            model.Job.table.c.create_time >= start_date,
-                                                            model.Job.table.c.create_time < end_date),
-                                        from_obj=[model.Job.table],
-                                        group_by=['date'],
-                                        order_by=[_order],
-                                        offset=offset,
-                                        limit=limit)
+        month_jobs_in_error = sa.select(
+            (
+                sa.func.date(model.Job.table.c.create_time).label("date"),
+                sa.func.count(model.Job.table.c.id).label("total_jobs"),
+            ),
+            whereclause=sa.and_(
+                model.Job.table.c.user_id != monitor_user_id,
+                model.Job.table.c.state == "error",
+                model.Job.table.c.create_time >= start_date,
+                model.Job.table.c.create_time < end_date,
+            ),
+            from_obj=[model.Job.table],
+            group_by=["date"],
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
         # Use to make trendline
-        all_jobs_in_error = sa.select((model.Job.table.c.create_time.label('date'), model.Job.table.c.id.label('id')),
-                                      whereclause=sa.and_(model.Job.table.c.user_id != monitor_user_id,
-                                                          model.Job.table.c.state == 'error',
-                                                          model.Job.table.c.create_time >= start_date,
-                                                          model.Job.table.c.create_time < end_date))
+        all_jobs_in_error = sa.select(
+            (model.Job.table.c.create_time.label("date"), model.Job.table.c.id.label("id")),
+            whereclause=sa.and_(
+                model.Job.table.c.user_id != monitor_user_id,
+                model.Job.table.c.state == "error",
+                model.Job.table.c.create_time >= start_date,
+                model.Job.table.c.create_time < end_date,
+            ),
+        )
 
         trends = dict()
         for job in trans.sa_session.execute(all_jobs_in_error):
@@ -551,26 +573,25 @@ class Jobs(BaseUIController, ReportQueryBuilder):
             row_dayname = row.date.strftime("%A")
             row_day = row.date.strftime("%d")
 
-            jobs.append((row_dayname,
-                         row_day,
-                         row.total_jobs,
-                         row.date))
+            jobs.append((row_dayname, row_day, row.total_jobs, row.date))
 
         pages_found = ceil(len(jobs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/jobs_specified_month_in_error.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   month_label=month_label,
-                                   year_label=year_label,
-                                   month=month,
-                                   jobs=jobs,
-                                   trends=trends,
-                                   message=message,
-                                   is_user_jobs_only=monitor_user_id,
-                                   page_specs=page_specs)
+        return trans.fill_template(
+            "/webapps/reports/jobs_specified_month_in_error.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            month_label=month_label,
+            year_label=year_label,
+            month=month,
+            jobs=jobs,
+            trends=trends,
+            message=message,
+            is_user_jobs_only=monitor_user_id,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def per_month_all(self, trans, **kwd):
@@ -579,13 +600,13 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         by_destination param will group by User.email and
         Job.destination_id.
         """
-        by_destination = str(kwd.get('by_destination', False)).lower()
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        by_destination = str(kwd.get("by_destination", False)).lower()
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('date', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -594,18 +615,18 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
@@ -613,31 +634,40 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
         # Use to make the page table
-        if by_destination == 'true':
-            jobs_by_month = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
-                                       model.Job.table.c.destination_id.label('destination_id'),
-                                       sa.func.sum(model.Job.table.c.update_time - model.Job.table.c.create_time).label('execute_time'),
-                                       sa.func.count(model.Job.table.c.id).label('total_jobs'),
-                                       model.User.table.c.email.label('user_email')),
-                                      whereclause=model.Job.table.c.user_id != monitor_user_id,
-                                      from_obj=[sa.join(model.Job.table, model.User.table)],
-                                      group_by=['user_email', 'date', 'destination_id'],
-                                      order_by=[_order],
-                                      offset=offset,
-                                      limit=limit)
+        if by_destination == "true":
+            jobs_by_month = sa.select(
+                (
+                    self.select_month(model.Job.table.c.create_time).label("date"),
+                    model.Job.table.c.destination_id.label("destination_id"),
+                    sa.func.sum(model.Job.table.c.update_time - model.Job.table.c.create_time).label("execute_time"),
+                    sa.func.count(model.Job.table.c.id).label("total_jobs"),
+                    model.User.table.c.email.label("user_email"),
+                ),
+                whereclause=model.Job.table.c.user_id != monitor_user_id,
+                from_obj=[sa.join(model.Job.table, model.User.table)],
+                group_by=["user_email", "date", "destination_id"],
+                order_by=[_order],
+                offset=offset,
+                limit=limit,
+            )
         else:
-            jobs_by_month = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
-                                       sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                                      whereclause=model.Job.table.c.user_id != monitor_user_id,
-                                      from_obj=[model.Job.table],
-                                      group_by=self.group_by_month(model.Job.table.c.create_time),
-                                      order_by=[_order],
-                                      offset=offset,
-                                      limit=limit)
+            jobs_by_month = sa.select(
+                (
+                    self.select_month(model.Job.table.c.create_time).label("date"),
+                    sa.func.count(model.Job.table.c.id).label("total_jobs"),
+                ),
+                whereclause=model.Job.table.c.user_id != monitor_user_id,
+                from_obj=[model.Job.table],
+                group_by=self.group_by_month(model.Job.table.c.create_time),
+                order_by=[_order],
+                offset=offset,
+                limit=limit,
+            )
 
         # Use to make sparkline
-        all_jobs = sa.select((self.select_day(model.Job.table.c.create_time).label('date'),
-                              model.Job.table.c.id.label('id')))
+        all_jobs = sa.select(
+            (self.select_day(model.Job.table.c.create_time).label("date"), model.Job.table.c.id.label("id"))
+        )
 
         trends = self._calculate_trends_for_jobs(trans.sa_session, all_jobs)
         jobs = self._calculate_job_table(trans.sa_session, jobs_by_month, by_destination=by_destination)
@@ -645,19 +675,21 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         pages_found = ceil(len(jobs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        if by_destination == 'true':
-            page = '/webapps/reports/jobs_per_month_by_user_and_destination.mako'
+        if by_destination == "true":
+            page = "/webapps/reports/jobs_per_month_by_user_and_destination.mako"
         else:
-            page = '/webapps/reports/jobs_per_month_all.mako'
-        return trans.fill_template(page,
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   trends=trends,
-                                   jobs=jobs,
-                                   is_user_jobs_only=monitor_user_id,
-                                   message=message,
-                                   page_specs=page_specs)
+            page = "/webapps/reports/jobs_per_month_all.mako"
+        return trans.fill_template(
+            page,
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            trends=trends,
+            jobs=jobs,
+            is_user_jobs_only=monitor_user_id,
+            message=message,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def per_month_in_error(self, trans, **kwd):
@@ -665,12 +697,12 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         Queries the DB for user jobs in error. Filters out monitor jobs.
         """
 
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('date', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -679,18 +711,18 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
@@ -698,21 +730,24 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
         # Use to make the page table
-        jobs_in_error_by_month = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
-                                            sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                                           whereclause=sa.and_(model.Job.table.c.state == 'error',
-                                                               model.Job.table.c.user_id != monitor_user_id),
-                                           from_obj=[model.Job.table],
-                                           group_by=self.group_by_month(model.Job.table.c.create_time),
-                                           order_by=[_order],
-                                           offset=offset,
-                                           limit=limit)
+        jobs_in_error_by_month = sa.select(
+            (
+                self.select_month(model.Job.table.c.create_time).label("date"),
+                sa.func.count(model.Job.table.c.id).label("total_jobs"),
+            ),
+            whereclause=sa.and_(model.Job.table.c.state == "error", model.Job.table.c.user_id != monitor_user_id),
+            from_obj=[model.Job.table],
+            group_by=self.group_by_month(model.Job.table.c.create_time),
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
         # Use to make trendline
-        all_jobs = sa.select((self.select_day(model.Job.table.c.create_time).label('date'),
-                              model.Job.table.c.id.label('id')),
-                             whereclause=sa.and_(model.Job.table.c.state == 'error',
-                                                 model.Job.table.c.user_id != monitor_user_id))
+        all_jobs = sa.select(
+            (self.select_day(model.Job.table.c.create_time).label("date"), model.Job.table.c.id.label("id")),
+            whereclause=sa.and_(model.Job.table.c.state == "error", model.Job.table.c.user_id != monitor_user_id),
+        )
 
         trends = self._calculate_trends_for_jobs(trans.sa_session, all_jobs)
         jobs = self._calculate_job_table(trans.sa_session, jobs_in_error_by_month)
@@ -720,17 +755,19 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         pages_found = ceil(len(jobs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/jobs_per_month_in_error.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   trends=trends,
-                                   jobs=jobs,
-                                   message=message,
-                                   is_user_jobs_only=monitor_user_id,
-                                   page_specs=page_specs,
-                                   offset=offset,
-                                   limit=limit)
+        return trans.fill_template(
+            "/webapps/reports/jobs_per_month_in_error.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            trends=trends,
+            jobs=jobs,
+            message=message,
+            is_user_jobs_only=monitor_user_id,
+            page_specs=page_specs,
+            offset=offset,
+            limit=limit,
+        )
 
     @web.expose
     def per_user(self, trans, **kwd):
@@ -738,100 +775,108 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         Queries the DB for jobs per user.  The by_destination
         param will group by Job.destination_id.
         """
-        by_destination = str(kwd.get('by_destination', False)).lower()
+        by_destination = str(kwd.get("by_destination", False)).lower()
         total_time = Timer()
         q_time = Timer()
 
         total_time.start()
         params = util.Params(kwd)
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('user_email', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("user_email", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        time_period = kwd.get('spark_time')
+        time_period = kwd.get("spark_time")
         time_period, _time_period = get_spark_time(time_period)
         spark_limit = 30
         offset = 0
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
         jobs = []
-        if by_destination == 'true':
-            jobs_per_user = sa.select((model.User.table.c.email.label('user_email'),
-                                       sa.func.count(model.Job.table.c.id).label('total_jobs'),
-                                       model.Job.table.c.destination_id.label('destination_id')),
-                                      from_obj=[sa.outerjoin(model.Job.table, model.User.table)],
-                                      group_by=['user_email', 'destination_id'],
-                                      order_by=[_order],
-                                      offset=offset,
-                                      limit=limit)
+        if by_destination == "true":
+            jobs_per_user = sa.select(
+                (
+                    model.User.table.c.email.label("user_email"),
+                    sa.func.count(model.Job.table.c.id).label("total_jobs"),
+                    model.Job.table.c.destination_id.label("destination_id"),
+                ),
+                from_obj=[sa.outerjoin(model.Job.table, model.User.table)],
+                group_by=["user_email", "destination_id"],
+                order_by=[_order],
+                offset=offset,
+                limit=limit,
+            )
 
         else:
-            jobs_per_user = sa.select((model.User.table.c.email.label('user_email'),
-                                       sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                                      from_obj=[sa.outerjoin(model.Job.table, model.User.table)],
-                                      group_by=['user_email'],
-                                      order_by=[_order],
-                                      offset=offset,
-                                      limit=limit)
+            jobs_per_user = sa.select(
+                (model.User.table.c.email.label("user_email"), sa.func.count(model.Job.table.c.id).label("total_jobs")),
+                from_obj=[sa.outerjoin(model.Job.table, model.User.table)],
+                group_by=["user_email"],
+                order_by=[_order],
+                offset=offset,
+                limit=limit,
+            )
 
         q_time.start()
         unique_users = set()
         for row in trans.sa_session.execute(jobs_per_user):
-            if (row.user_email is None):
-                curr_user, unique_users = get_curr_item('Anonymous', unique_users)
-                if by_destination == 'true':
+            if row.user_email is None:
+                curr_user, unique_users = get_curr_item("Anonymous", unique_users)
+                if by_destination == "true":
                     jobs.append((curr_user, row.destination_id, row.total_jobs))
                 else:
                     jobs.append((curr_user, row.total_jobs))
-            elif (row.user_email == monitor_email):
+            elif row.user_email == monitor_email:
                 continue
             else:
                 curr_user, unique_users = get_curr_item(row.user_email, unique_users)
-                if by_destination == 'true':
+                if by_destination == "true":
                     jobs.append((curr_user, row.destination_id, row.total_jobs))
                 else:
                     jobs.append((curr_user, row.total_jobs))
         q_time.stop()
         query1time = q_time.time_elapsed()
 
-        users = sa.select([model.User.table.c.email],
-                          from_obj=[model.User.table])
+        users = sa.select([model.User.table.c.email], from_obj=[model.User.table])
 
-        all_jobs_per_user = sa.select((model.Job.table.c.id.label('id'),
-                                       model.Job.table.c.create_time.label('date'),
-                                       model.User.table.c.email.label('user_email')),
-                                      from_obj=[sa.outerjoin(model.Job.table, model.User.table)],
-                                      whereclause=model.User.table.c.email.in_(users))
+        all_jobs_per_user = sa.select(
+            (
+                model.Job.table.c.id.label("id"),
+                model.Job.table.c.create_time.label("date"),
+                model.User.table.c.email.label("user_email"),
+            ),
+            from_obj=[sa.outerjoin(model.Job.table, model.User.table)],
+            whereclause=model.User.table.c.email.in_(users),
+        )
 
         currday = datetime.today()
         trends = dict()
         q_time.start()
         for job in trans.sa_session.execute(all_jobs_per_user):
             if job.user_email is None:
-                curr_user = 'Anonymous'
+                curr_user = "Anonymous"
             else:
-                curr_user = re.sub(r'\W+', '', job.user_email)
+                curr_user = re.sub(r"\W+", "", job.user_email)
 
             try:
                 day = currday - job.date
@@ -856,23 +901,25 @@ class Jobs(BaseUIController, ReportQueryBuilder):
 
         total_time.stop()
         ttime = total_time.time_elapsed()
-        if by_destination == 'true':
-            page = '/webapps/reports/jobs_per_user_by_destination.mako'
+        if by_destination == "true":
+            page = "/webapps/reports/jobs_per_user_by_destination.mako"
         else:
-            page = '/webapps/reports/jobs_per_user.mako'
-        return trans.fill_template(page,
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   spark_limit=spark_limit,
-                                   time_period=time_period,
-                                   q1time=query1time,
-                                   q2time=query2time,
-                                   ttime=ttime,
-                                   trends=trends,
-                                   jobs=jobs,
-                                   message=message,
-                                   page_specs=page_specs)
+            page = "/webapps/reports/jobs_per_user.mako"
+        return trans.fill_template(
+            page,
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            spark_limit=spark_limit,
+            time_period=time_period,
+            q1time=query1time,
+            q2time=query2time,
+            ttime=ttime,
+            trends=trends,
+            jobs=jobs,
+            message=message,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def user_per_month(self, trans, **kwd):
@@ -880,38 +927,47 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         Queries the DB for jobs per user per month.  The
         by_destination param will group by Job.destination_id.
         """
-        by_destination = str(kwd.get('by_destination', False)).lower()
+        by_destination = str(kwd.get("by_destination", False)).lower()
         params = util.Params(kwd)
-        message = ''
+        message = ""
 
-        email = util.restore_text(params.get('email', ''))
-        specs = sorter('date', kwd)
+        email = util.restore_text(params.get("email", ""))
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
 
-        if by_destination == 'true':
-            q = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
-                           model.Job.table.c.destination_id.label('destination_id'),
-                           sa.func.sum(model.Job.table.c.update_time - model.Job.table.c.create_time).label('execute_time'),
-                           sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                          whereclause=model.User.table.c.email == email,
-                          from_obj=[sa.join(model.Job.table, model.User.table)],
-                          group_by=['date', 'destination_id'],
-                          order_by=[_order])
+        if by_destination == "true":
+            q = sa.select(
+                (
+                    self.select_month(model.Job.table.c.create_time).label("date"),
+                    model.Job.table.c.destination_id.label("destination_id"),
+                    sa.func.sum(model.Job.table.c.update_time - model.Job.table.c.create_time).label("execute_time"),
+                    sa.func.count(model.Job.table.c.id).label("total_jobs"),
+                ),
+                whereclause=model.User.table.c.email == email,
+                from_obj=[sa.join(model.Job.table, model.User.table)],
+                group_by=["date", "destination_id"],
+                order_by=[_order],
+            )
         else:
-            q = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
-                           sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                          whereclause=model.User.table.c.email == email,
-                          from_obj=[sa.join(model.Job.table, model.User.table)],
-                          group_by=self.group_by_month(model.Job.table.c.create_time),
-                          order_by=[_order])
+            q = sa.select(
+                (
+                    self.select_month(model.Job.table.c.create_time).label("date"),
+                    sa.func.count(model.Job.table.c.id).label("total_jobs"),
+                ),
+                whereclause=model.User.table.c.email == email,
+                from_obj=[sa.join(model.Job.table, model.User.table)],
+                group_by=self.group_by_month(model.Job.table.c.create_time),
+                order_by=[_order],
+            )
 
-        all_jobs_per_user = sa.select((model.Job.table.c.create_time.label('date'),
-                                       model.Job.table.c.id.label('job_id')),
-                                      whereclause=sa.and_(model.User.table.c.email == email),
-                                      from_obj=[sa.join(model.Job.table, model.User.table)])
+        all_jobs_per_user = sa.select(
+            (model.Job.table.c.create_time.label("date"), model.Job.table.c.id.label("job_id")),
+            whereclause=sa.and_(model.User.table.c.email == email),
+            from_obj=[sa.join(model.Job.table, model.User.table)],
+        )
 
         trends = dict()
         for job in trans.sa_session.execute(all_jobs_per_user):
@@ -932,71 +988,76 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         jobs = []
         unique_month_year_strs = set()
         for row in trans.sa_session.execute(q):
-            if by_destination == 'true':
+            if by_destination == "true":
                 month_year_str = "%s %s" % (row.date.strftime("%B"), row.date.strftime("%Y"))
                 curr_month_year_str, unique_month_year_strs = get_curr_item(month_year_str, unique_month_year_strs)
-                if curr_month_year_str == '':
-                    curr_month = ''
-                    curr_year = ''
+                if curr_month_year_str == "":
+                    curr_month = ""
+                    curr_year = ""
                 else:
                     curr_month = row.date.strftime("%B")
                     curr_year = row.date.strftime("%Y")
-                jobs.append((row.date.strftime("%Y-%m"),
-                             row.execute_time,
-                             row.total_jobs,
-                             curr_month,
-                             curr_year,
-                             row.destination_id))
+                jobs.append(
+                    (
+                        row.date.strftime("%Y-%m"),
+                        row.execute_time,
+                        row.total_jobs,
+                        curr_month,
+                        curr_year,
+                        row.destination_id,
+                    )
+                )
             else:
-                jobs.append((row.date.strftime("%Y-%m"),
-                             row.total_jobs,
-                             row.date.strftime("%B"),
-                             row.date.strftime("%Y")))
-        if by_destination == 'true':
-            page = '/webapps/reports/jobs_user_per_month_by_destination.mako'
+                jobs.append(
+                    (row.date.strftime("%Y-%m"), row.total_jobs, row.date.strftime("%B"), row.date.strftime("%Y"))
+                )
+        if by_destination == "true":
+            page = "/webapps/reports/jobs_user_per_month_by_destination.mako"
         else:
-            page = '/webapps/reports/jobs_user_per_month.mako'
-        return trans.fill_template(page,
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   id=kwd.get('id'),
-                                   trends=trends,
-                                   email=util.sanitize_text(email),
-                                   jobs=jobs,
-                                   message=message)
+            page = "/webapps/reports/jobs_user_per_month.mako"
+        return trans.fill_template(
+            page,
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            id=kwd.get("id"),
+            trends=trends,
+            email=util.sanitize_text(email),
+            jobs=jobs,
+            message=message,
+        )
 
     @web.expose
     def per_tool(self, trans, **kwd):
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('tool_id', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("tool_id", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        time_period = kwd.get('spark_time')
+        time_period = kwd.get("spark_time")
         time_period, _time_period = get_spark_time(time_period)
         spark_limit = 30
         offset = 0
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
@@ -1004,25 +1065,30 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
         jobs = []
-        q = sa.select((model.Job.table.c.tool_id.label('tool_id'),
-                       sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                      whereclause=model.Job.table.c.user_id != monitor_user_id,
-                      from_obj=[model.Job.table],
-                      group_by=['tool_id'],
-                      order_by=[_order],
-                      offset=offset,
-                      limit=limit)
+        q = sa.select(
+            (model.Job.table.c.tool_id.label("tool_id"), sa.func.count(model.Job.table.c.id).label("total_jobs")),
+            whereclause=model.Job.table.c.user_id != monitor_user_id,
+            from_obj=[model.Job.table],
+            group_by=["tool_id"],
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
-        all_jobs_per_tool = sa.select((model.Job.table.c.tool_id.label('tool_id'),
-                                       model.Job.table.c.id.label('id'),
-                                       self.select_day(model.Job.table.c.create_time).label('date')),
-                                      whereclause=model.Job.table.c.user_id != monitor_user_id,
-                                      from_obj=[model.Job.table])
+        all_jobs_per_tool = sa.select(
+            (
+                model.Job.table.c.tool_id.label("tool_id"),
+                model.Job.table.c.id.label("id"),
+                self.select_day(model.Job.table.c.create_time).label("date"),
+            ),
+            whereclause=model.Job.table.c.user_id != monitor_user_id,
+            from_obj=[model.Job.table],
+        )
 
         currday = date.today()
         trends = dict()
         for job in trans.sa_session.execute(all_jobs_per_tool):
-            curr_tool = re.sub(r'\W+', '', str(job.tool_id))
+            curr_tool = re.sub(r"\W+", "", str(job.tool_id))
             try:
                 day = currday - job.date
             except TypeError:
@@ -1040,23 +1106,24 @@ class Jobs(BaseUIController, ReportQueryBuilder):
                     trends[curr_tool][container] += 1
 
         for row in trans.sa_session.execute(q):
-            jobs.append((row.tool_id,
-                         row.total_jobs))
+            jobs.append((row.tool_id, row.total_jobs))
 
         pages_found = ceil(len(jobs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/jobs_per_tool.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   spark_limit=spark_limit,
-                                   time_period=time_period,
-                                   trends=trends,
-                                   jobs=jobs,
-                                   message=message,
-                                   is_user_jobs_only=monitor_user_id,
-                                   page_specs=page_specs)
+        return trans.fill_template(
+            "/webapps/reports/jobs_per_tool.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            spark_limit=spark_limit,
+            time_period=time_period,
+            trends=trends,
+            jobs=jobs,
+            message=message,
+            is_user_jobs_only=monitor_user_id,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def errors_per_tool(self, trans, **kwd):
@@ -1064,62 +1131,65 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         Queries the DB for user jobs in error. Filters out monitor jobs.
         """
 
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('tool_id', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("tool_id", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        time_period = kwd.get('spark_time')
+        time_period = kwd.get("spark_time")
         time_period, _time_period = get_spark_time(time_period)
         spark_limit = 30
         offset = 0
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
         # In case we don't know which is the monitor user we will query for all jobs
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
-        jobs_in_error_per_tool = sa.select((model.Job.table.c.tool_id.label('tool_id'),
-                                            sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                                           whereclause=sa.and_(model.Job.table.c.state == 'error',
-                                                               model.Job.table.c.user_id != monitor_user_id),
-                                           from_obj=[model.Job.table],
-                                           group_by=['tool_id'],
-                                           order_by=[_order],
-                                           offset=offset,
-                                           limit=limit)
+        jobs_in_error_per_tool = sa.select(
+            (model.Job.table.c.tool_id.label("tool_id"), sa.func.count(model.Job.table.c.id).label("total_jobs")),
+            whereclause=sa.and_(model.Job.table.c.state == "error", model.Job.table.c.user_id != monitor_user_id),
+            from_obj=[model.Job.table],
+            group_by=["tool_id"],
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
-        all_jobs_per_tool_errors = sa.select((self.select_day(model.Job.table.c.create_time).label('date'),
-                                              model.Job.table.c.id.label('id'),
-                                              model.Job.table.c.tool_id.label('tool_id')),
-                                             whereclause=sa.and_(model.Job.table.c.state == 'error',
-                                                                 model.Job.table.c.user_id != monitor_user_id),
-                                             from_obj=[model.Job.table])
+        all_jobs_per_tool_errors = sa.select(
+            (
+                self.select_day(model.Job.table.c.create_time).label("date"),
+                model.Job.table.c.id.label("id"),
+                model.Job.table.c.tool_id.label("tool_id"),
+            ),
+            whereclause=sa.and_(model.Job.table.c.state == "error", model.Job.table.c.user_id != monitor_user_id),
+            from_obj=[model.Job.table],
+        )
 
         currday = date.today()
         trends = dict()
         for job in trans.sa_session.execute(all_jobs_per_tool_errors):
-            curr_tool = re.sub(r'\W+', '', str(job.tool_id))
+            curr_tool = re.sub(r"\W+", "", str(job.tool_id))
             try:
                 day = currday - job.date
             except TypeError:
@@ -1143,25 +1213,27 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         pages_found = ceil(len(jobs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/jobs_errors_per_tool.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   spark_limit=spark_limit,
-                                   time_period=time_period,
-                                   trends=trends,
-                                   jobs=jobs,
-                                   message=message,
-                                   is_user_jobs_only=monitor_user_id,
-                                   page_specs=page_specs)
+        return trans.fill_template(
+            "/webapps/reports/jobs_errors_per_tool.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            spark_limit=spark_limit,
+            time_period=time_period,
+            trends=trends,
+            jobs=jobs,
+            message=message,
+            is_user_jobs_only=monitor_user_id,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def tool_per_month(self, trans, **kwd):
-        message = ''
+        message = ""
 
         params = util.Params(kwd)
-        monitor_email = params.get('monitor_email', 'monitor@bx.psu.edu')
-        specs = sorter('date', kwd)
+        monitor_email = params.get("monitor_email", "monitor@bx.psu.edu")
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -1169,23 +1241,29 @@ class Jobs(BaseUIController, ReportQueryBuilder):
         # In case we don't know which is the monitor user we will query for all jobs
         monitor_user_id = get_monitor_id(trans, monitor_email)
 
-        tool_id = params.get('tool_id', 'Add a column1')
-        specified_date = params.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
-        q = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
-                       sa.func.count(model.Job.table.c.id).label('total_jobs')),
-                      whereclause=sa.and_(model.Job.table.c.tool_id == tool_id,
-                                          model.Job.table.c.user_id != monitor_user_id),
-                      from_obj=[model.Job.table],
-                      group_by=self.group_by_month(model.Job.table.c.create_time),
-                      order_by=[_order])
+        tool_id = params.get("tool_id", "Add a column1")
+        specified_date = params.get("specified_date", datetime.utcnow().strftime("%Y-%m-%d"))
+        q = sa.select(
+            (
+                self.select_month(model.Job.table.c.create_time).label("date"),
+                sa.func.count(model.Job.table.c.id).label("total_jobs"),
+            ),
+            whereclause=sa.and_(model.Job.table.c.tool_id == tool_id, model.Job.table.c.user_id != monitor_user_id),
+            from_obj=[model.Job.table],
+            group_by=self.group_by_month(model.Job.table.c.create_time),
+            order_by=[_order],
+        )
 
         # Use to make sparkline
-        all_jobs_for_tool = sa.select((self.select_month(model.Job.table.c.create_time).label('month'),
-                                       self.select_day(model.Job.table.c.create_time).label('day'),
-                                       model.Job.table.c.id.label('id')),
-                                      whereclause=sa.and_(model.Job.table.c.tool_id == tool_id,
-                                                          model.Job.table.c.user_id != monitor_user_id),
-                             from_obj=[model.Job.table])
+        all_jobs_for_tool = sa.select(
+            (
+                self.select_month(model.Job.table.c.create_time).label("month"),
+                self.select_day(model.Job.table.c.create_time).label("day"),
+                model.Job.table.c.id.label("id"),
+            ),
+            whereclause=sa.and_(model.Job.table.c.tool_id == tool_id, model.Job.table.c.user_id != monitor_user_id),
+            from_obj=[model.Job.table],
+        )
         trends = dict()
         for job in trans.sa_session.execute(all_jobs_for_tool):
             job_day = int(job.day.strftime("%-d")) - 1
@@ -1204,29 +1282,26 @@ class Jobs(BaseUIController, ReportQueryBuilder):
 
         jobs = []
         for row in trans.sa_session.execute(q):
-            jobs.append((row.date.strftime("%Y-%m"),
-                         row.total_jobs,
-                         row.date.strftime("%B"),
-                         row.date.strftime("%Y")))
-        return trans.fill_template('/webapps/reports/jobs_tool_per_month.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   specified_date=specified_date,
-                                   tool_id=tool_id,
-                                   trends=trends,
-                                   jobs=jobs,
-                                   message=message,
-                                   is_user_jobs_only=monitor_user_id)
+            jobs.append((row.date.strftime("%Y-%m"), row.total_jobs, row.date.strftime("%B"), row.date.strftime("%Y")))
+        return trans.fill_template(
+            "/webapps/reports/jobs_tool_per_month.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            specified_date=specified_date,
+            tool_id=tool_id,
+            trends=trends,
+            jobs=jobs,
+            message=message,
+            is_user_jobs_only=monitor_user_id,
+        )
 
     @web.expose
     def job_info(self, trans, **kwd):
-        message = ''
-        job = trans.sa_session.query(model.Job) \
-                              .get(trans.security.decode_id(kwd.get('id', '')))
-        return trans.fill_template('/webapps/reports/job_info.mako',
-                                   job=job,
-                                   message=message)
+        message = ""
+        job = trans.sa_session.query(model.Job).get(trans.security.decode_id(kwd.get("id", "")))
+        return trans.fill_template("/webapps/reports/job_info.mako", job=job, message=message)
+
 
 # ---- Utility methods -------------------------------------------------------
 
@@ -1240,9 +1315,9 @@ def get_monitor_id(trans, monitor_email):
     A convenience method to obtain the monitor job id.
     """
     monitor_user_id = None
-    monitor_row = trans.sa_session.query(trans.model.User.id) \
-        .filter(trans.model.User.table.c.email == monitor_email) \
-        .first()
+    monitor_row = (
+        trans.sa_session.query(trans.model.User.id).filter(trans.model.User.table.c.email == monitor_email).first()
+    )
     if monitor_row is not None:
         monitor_user_id = monitor_row[0]
     return monitor_user_id
diff --git a/lib/galaxy/webapps/reports/controllers/query.py b/lib/galaxy/webapps/reports/controllers/query.py
index 3381557e860..5d8b62b44f2 100644
--- a/lib/galaxy/webapps/reports/controllers/query.py
+++ b/lib/galaxy/webapps/reports/controllers/query.py
@@ -4,27 +4,26 @@ import sqlalchemy as sa
 
 
 class ReportQueryBuilder:
-
     def group_by_month(self, column):
         if self.app.targets_mysql:
             return [sa.func.year(column), sa.func.month(sa.func.date(column))]
         else:
-            return [sa.func.date_trunc('month', sa.func.date(column))]
+            return [sa.func.date_trunc("month", sa.func.date(column))]
 
     def select_month(self, column):
         if self.app.targets_mysql:
             return sa.func.date(column)
         else:
-            return sa.func.date_trunc('month', sa.func.date(column))
+            return sa.func.date_trunc("month", sa.func.date(column))
 
     def group_by_day(self, column):
         if self.app.targets_mysql:
             return [sa.func.day(sa.func.date(column))]
         else:
-            return [sa.func.date_trunc('day', sa.func.date(column))]
+            return [sa.func.date_trunc("day", sa.func.date(column))]
 
     def select_day(self, column):
         if self.app.targets_mysql:
             return sa.func.date(column)
         else:
-            return sa.func.date_trunc('day', sa.func.date(column))
+            return sa.func.date_trunc("day", sa.func.date(column))
diff --git a/lib/galaxy/webapps/reports/controllers/root.py b/lib/galaxy/webapps/reports/controllers/root.py
index 896c61b0a2c..4fc0939bc2a 100644
--- a/lib/galaxy/webapps/reports/controllers/root.py
+++ b/lib/galaxy/webapps/reports/controllers/root.py
@@ -2,7 +2,7 @@ import logging
 
 from galaxy.webapps.base.controller import (
     BaseUIController,
-    web
+    web,
 )
 
 log = logging.getLogger(__name__)
@@ -11,4 +11,4 @@ log = logging.getLogger(__name__)
 class Report(BaseUIController):
     @web.expose
     def index(self, trans, **kwd):
-        return trans.fill_template('/webapps/reports/index.mako')
+        return trans.fill_template("/webapps/reports/index.mako")
diff --git a/lib/galaxy/webapps/reports/controllers/system.py b/lib/galaxy/webapps/reports/controllers/system.py
index d997f377dc3..6fad63d995d 100644
--- a/lib/galaxy/webapps/reports/controllers/system.py
+++ b/lib/galaxy/webapps/reports/controllers/system.py
@@ -1,13 +1,28 @@
 import logging
 import shutil
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from decimal import Decimal
 
-from sqlalchemy import and_, desc, false, null, true
+from sqlalchemy import (
+    and_,
+    desc,
+    false,
+    null,
+    true,
+)
 from sqlalchemy.orm import eagerload
 
-from galaxy import model, util
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy import (
+    model,
+    util,
+)
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 
 log = logging.getLogger(__name__)
 
@@ -16,56 +31,64 @@ class System(BaseUIController):
     @web.expose
     def index(self, trans, **kwd):
         params = util.Params(kwd)
-        message = ''
+        message = ""
         if params.userless_histories_days:
             userless_histories_days = params.userless_histories_days
         else:
-            userless_histories_days = '60'
+            userless_histories_days = "60"
         if params.deleted_histories_days:
             deleted_histories_days = params.deleted_histories_days
         else:
-            deleted_histories_days = '60'
+            deleted_histories_days = "60"
         if params.deleted_datasets_days:
             deleted_datasets_days = params.deleted_datasets_days
         else:
-            deleted_datasets_days = '60'
+            deleted_datasets_days = "60"
         file_path, disk_usage, datasets, file_size_str = self.disk_usage(trans, **kwd)
-        if 'action' in kwd:
-            if kwd['action'] == "userless_histories":
+        if "action" in kwd:
+            if kwd["action"] == "userless_histories":
                 userless_histories_days, message = self.userless_histories(trans, **kwd)
-            elif kwd['action'] == "deleted_histories":
+            elif kwd["action"] == "deleted_histories":
                 deleted_histories_days, message = self.deleted_histories(trans, **kwd)
-            elif kwd['action'] == "deleted_datasets":
+            elif kwd["action"] == "deleted_datasets":
                 deleted_datasets_days, message = self.deleted_datasets(trans, **kwd)
-        return trans.fill_template('/webapps/reports/system.mako',
-                                   file_path=file_path,
-                                   disk_usage=disk_usage,
-                                   datasets=datasets,
-                                   file_size_str=file_size_str,
-                                   userless_histories_days=userless_histories_days,
-                                   deleted_histories_days=deleted_histories_days,
-                                   deleted_datasets_days=deleted_datasets_days,
-                                   message=message,
-                                   nice_size=nice_size)
+        return trans.fill_template(
+            "/webapps/reports/system.mako",
+            file_path=file_path,
+            disk_usage=disk_usage,
+            datasets=datasets,
+            file_size_str=file_size_str,
+            userless_histories_days=userless_histories_days,
+            deleted_histories_days=deleted_histories_days,
+            deleted_datasets_days=deleted_datasets_days,
+            message=message,
+            nice_size=nice_size,
+        )
 
     def userless_histories(self, trans, **kwd):
         """The number of userless histories and associated datasets that have not been updated for the specified number of days."""
         params = util.Params(kwd)
-        message = ''
+        message = ""
         if params.userless_histories_days:
             userless_histories_days = int(params.userless_histories_days)
             cutoff_time = datetime.utcnow() - timedelta(days=userless_histories_days)
             history_count = 0
             dataset_count = 0
-            for history in trans.sa_session.query(model.History) \
-                    .filter(and_(model.History.table.c.user_id == null(),
+            for history in trans.sa_session.query(model.History).filter(
+                and_(
+                    model.History.table.c.user_id == null(),
                     model.History.table.c.deleted == true(),
-                    model.History.update_time < cutoff_time)):
+                    model.History.update_time < cutoff_time,
+                )
+            ):
                 for dataset in history.datasets:
                     if not dataset.deleted:
                         dataset_count += 1
                 history_count += 1
-            message = "%d userless histories ( including a total of %d datasets ) have not been updated for at least %d days." % (history_count, dataset_count, userless_histories_days)
+            message = (
+                "%d userless histories ( including a total of %d datasets ) have not been updated for at least %d days."
+                % (history_count, dataset_count, userless_histories_days)
+            )
         else:
             message = "Enter the number of days."
         return str(userless_histories_days), message
@@ -76,18 +99,24 @@ class System(BaseUIController):
         Also included is the number of datasets associated with the histories.
         """
         params = util.Params(kwd)
-        message = ''
+        message = ""
         if params.deleted_histories_days:
             deleted_histories_days = int(params.deleted_histories_days)
             cutoff_time = datetime.utcnow() - timedelta(days=deleted_histories_days)
             history_count = 0
             dataset_count = 0
             disk_space = 0
-            histories = trans.sa_session.query(model.History) \
-                .filter(and_(model.History.table.c.deleted == true(),
-                    model.History.table.c.purged == false(),
-                    model.History.update_time < cutoff_time)) \
-                .options(eagerload('datasets'))
+            histories = (
+                trans.sa_session.query(model.History)
+                .filter(
+                    and_(
+                        model.History.table.c.deleted == true(),
+                        model.History.table.c.purged == false(),
+                        model.History.update_time < cutoff_time,
+                    )
+                )
+                .options(eagerload("datasets"))
+            )
 
             for history in histories:
                 for hda in history.datasets:
@@ -98,8 +127,10 @@ class System(BaseUIController):
                         except Exception:
                             pass
                 history_count += 1
-            message = "%d histories ( including a total of %d datasets ) were deleted more than %d days ago, but have not yet been purged, " \
+            message = (
+                "%d histories ( including a total of %d datasets ) were deleted more than %d days ago, but have not yet been purged, "
                 "disk space: %s." % (history_count, dataset_count, deleted_histories_days, nice_size(disk_space, True))
+            )
         else:
             message = "Enter the number of days."
         return str(deleted_histories_days), message
@@ -107,45 +138,64 @@ class System(BaseUIController):
     def deleted_datasets(self, trans, **kwd):
         """The number of datasets that were deleted more than the specified number of days ago, but have not yet been purged."""
         params = util.Params(kwd)
-        message = ''
+        message = ""
         if params.deleted_datasets_days:
             deleted_datasets_days = int(params.deleted_datasets_days)
             cutoff_time = datetime.utcnow() - timedelta(days=deleted_datasets_days)
             dataset_count = 0
             disk_space = 0
-            for dataset in trans.sa_session.query(model.Dataset) \
-                .filter(and_(model.Dataset.table.c.deleted == true(),
+            for dataset in trans.sa_session.query(model.Dataset).filter(
+                and_(
+                    model.Dataset.table.c.deleted == true(),
                     model.Dataset.table.c.purged == false(),
-                    model.Dataset.table.c.update_time < cutoff_time)):
+                    model.Dataset.table.c.update_time < cutoff_time,
+                )
+            ):
                 dataset_count += 1
                 try:
                     disk_space += dataset.file_size
                 except Exception:
                     pass
-            message = "%d datasets were deleted more than %d days ago, but have not yet been purged," \
+            message = (
+                "%d datasets were deleted more than %d days ago, but have not yet been purged,"
                 " disk space: %s." % (dataset_count, deleted_datasets_days, nice_size(disk_space, True))
+            )
         else:
             message = "Enter the number of days."
         return str(deleted_datasets_days), message
 
     @web.expose
     def dataset_info(self, trans, **kwd):
-        message = ''
-        dataset = trans.sa_session.query(model.Dataset).get(trans.security.decode_id(kwd.get('id', '')))
+        message = ""
+        dataset = trans.sa_session.query(model.Dataset).get(trans.security.decode_id(kwd.get("id", "")))
         # Get all associated hdas and lddas that use the same disk file.
-        associated_hdas = trans.sa_session.query(trans.model.HistoryDatasetAssociation) \
-            .filter(and_(trans.model.HistoryDatasetAssociation.deleted == false(),
-            trans.model.HistoryDatasetAssociation.dataset_id == dataset.id)) \
+        associated_hdas = (
+            trans.sa_session.query(trans.model.HistoryDatasetAssociation)
+            .filter(
+                and_(
+                    trans.model.HistoryDatasetAssociation.deleted == false(),
+                    trans.model.HistoryDatasetAssociation.dataset_id == dataset.id,
+                )
+            )
             .all()
-        associated_lddas = trans.sa_session.query(trans.model.LibraryDatasetDatasetAssociation) \
-            .filter(and_(trans.model.LibraryDatasetDatasetAssociation.deleted == false(),
-            trans.model.LibraryDatasetDatasetAssociation.dataset_id == dataset.id)) \
+        )
+        associated_lddas = (
+            trans.sa_session.query(trans.model.LibraryDatasetDatasetAssociation)
+            .filter(
+                and_(
+                    trans.model.LibraryDatasetDatasetAssociation.deleted == false(),
+                    trans.model.LibraryDatasetDatasetAssociation.dataset_id == dataset.id,
+                )
+            )
             .all()
-        return trans.fill_template('/webapps/reports/dataset_info.mako',
-                                   dataset=dataset,
-                                   associated_hdas=associated_hdas,
-                                   associated_lddas=associated_lddas,
-                                   message=message)
+        )
+        return trans.fill_template(
+            "/webapps/reports/dataset_info.mako",
+            dataset=dataset,
+            associated_hdas=associated_hdas,
+            associated_lddas=associated_lddas,
+            message=message,
+        )
 
     def get_disk_usage(self, file_path):
         disk_usage = shutil.disk_usage(file_path)
@@ -156,12 +206,13 @@ class System(BaseUIController):
     def disk_usage(self, trans, **kwd):
         file_path = trans.app.config.file_path
         disk_usage = self.get_disk_usage(file_path)
-        min_file_size = 2 ** 32  # 4 Gb
+        min_file_size = 2**32  # 4 Gb
         file_size_str = nice_size(min_file_size)
-        datasets = trans.sa_session.query(model.Dataset) \
-                                   .filter(and_(model.Dataset.table.c.purged == false(),
-                                                model.Dataset.table.c.file_size > min_file_size)) \
-                                   .order_by(desc(model.Dataset.table.c.file_size))
+        datasets = (
+            trans.sa_session.query(model.Dataset)
+            .filter(and_(model.Dataset.table.c.purged == false(), model.Dataset.table.c.file_size > min_file_size))
+            .order_by(desc(model.Dataset.table.c.file_size))
+        )
         return file_path, disk_usage, datasets, file_size_str
 
 
@@ -171,7 +222,7 @@ def nice_size(size, include_bytes=False):
     nice_string = f"{size} bytes"
     try:
         nsize = Decimal(size)
-        for x in ['bytes', 'KB', 'MB', 'GB']:
+        for x in ["bytes", "KB", "MB", "GB"]:
             if nsize.compare(Decimal("1024.0")) == Decimal("-1"):
                 nice_string = f"{nsize:3.1f} {x}"
                 niced = True
@@ -180,7 +231,7 @@ def nice_size(size, include_bytes=False):
         if not niced:
             nice_string = f"{nsize:3.1f} TB"
             niced = True
-        if include_bytes and x != 'bytes':
+        if include_bytes and x != "bytes":
             nice_string = f"{nice_string} ({size} bytes)"
     except Exception:
         pass
diff --git a/lib/galaxy/webapps/reports/controllers/tools.py b/lib/galaxy/webapps/reports/controllers/tools.py
index 942d9478a68..38f7738a78f 100644
--- a/lib/galaxy/webapps/reports/controllers/tools.py
+++ b/lib/galaxy/webapps/reports/controllers/tools.py
@@ -8,10 +8,12 @@ from sqlalchemy import and_
 import galaxy.model
 from galaxy.util import (
     restore_text,
-    unicodify
+    unicodify,
+)
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
 )
-from galaxy.webapps.base.controller import BaseUIController, web
-
 
 log = logging.getLogger(__name__)
 
@@ -27,8 +29,8 @@ def int_to_octet(size):
         return "???"
     units = ("o", "Ko", "Mo", "Go", "To")
     no_unit = 0
-    while (size >= 1000):
-        size /= 1000.
+    while size >= 1000:
+        size /= 1000.0
         no_unit += 1
     try:
         return f"{size:.2f} {units[no_unit]}"
@@ -45,18 +47,18 @@ class Tools(BaseUIController):
     """
 
     def formatted(self, date, colored=False):
-        splited = str(date).split(',')
+        splited = str(date).split(",")
         if len(splited) == 2:
-            returned = "%s %dH" % (splited[0], int(splited[1].split(':')[0]))
+            returned = "%s %dH" % (splited[0], int(splited[1].split(":")[0]))
             if colored:
-                return f"<font color=\"red\">{returned}</font>"
+                return f'<font color="red">{returned}</font>'
             return returned
         else:
-            splited = tuple(float(_) for _ in str(date).split(':'))
+            splited = tuple(float(_) for _ in str(date).split(":"))
             if splited[0]:
-                returned = '%d h. %d min.' % splited[:2]
+                returned = "%d h. %d min." % splited[:2]
                 if colored:
-                    return f"<font color=\"orange\">{returned}</font>"
+                    return f'<font color="orange">{returned}</font>'
                 return returned
             if splited[1]:
                 return "%d min. %d sec." % splited[1:3]
@@ -71,34 +73,37 @@ class Tools(BaseUIController):
             - the number of jobs using this tool in error
         """
 
-        message = escape(restore_text(kwd.get('message', '')))
-        user_cutoff = int(kwd.get('user_cutoff', 60))
+        message = escape(restore_text(kwd.get("message", "")))
+        user_cutoff = int(kwd.get("user_cutoff", 60))
 
         # sort by history space, or by user mail or by number of history/dataset
-        sort_by = kwd.get('sorting', 'Tool')
-        sorting = 0 if sort_by == 'Tool' else 1 if sort_by == 'ok' else 2
-        descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
+        sort_by = kwd.get("sorting", "Tool")
+        sorting = 0 if sort_by == "Tool" else 1 if sort_by == "ok" else 2
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
         sort_keys = (
             lambda v: v.lower(),
             lambda v: tools_and_jobs_ok.get(v, 0),
-            lambda v: tools_and_jobs_error.get(v, 0))
+            lambda v: tools_and_jobs_error.get(v, 0),
+        )
 
         data = {}
 
         # select count(id), tool_id from job where state='ok' group by tool_id;
-        tools_and_jobs_ok = sa.select((galaxy.model.Job.table.c.tool_id .label('tool'),
-                                       sa.func.count(galaxy.model.Job.table.c.id).label('job')),
-                                      from_obj=[galaxy.model.Job.table],
-                                      whereclause=(galaxy.model.Job.table.c.state == 'ok'),
-                                      group_by=['tool'])
+        tools_and_jobs_ok = sa.select(
+            (galaxy.model.Job.table.c.tool_id.label("tool"), sa.func.count(galaxy.model.Job.table.c.id).label("job")),
+            from_obj=[galaxy.model.Job.table],
+            whereclause=(galaxy.model.Job.table.c.state == "ok"),
+            group_by=["tool"],
+        )
 
         # select count(id), tool_id from job where state='error' group by tool_id;
-        tools_and_jobs_error = sa.select((galaxy.model.Job.table.c.tool_id .label('tool'),
-                                          sa.func.count(galaxy.model.Job.table.c.id).label('job')),
-                                         from_obj=[galaxy.model.Job.table],
-                                         whereclause=(galaxy.model.Job.table.c.state == 'error'),
-                                         group_by=['tool'])
+        tools_and_jobs_error = sa.select(
+            (galaxy.model.Job.table.c.tool_id.label("tool"), sa.func.count(galaxy.model.Job.table.c.id).label("job")),
+            from_obj=[galaxy.model.Job.table],
+            whereclause=(galaxy.model.Job.table.c.state == "error"),
+            group_by=["tool"],
+        )
 
         tools_and_jobs_ok = dict(list(trans.sa_session.execute(tools_and_jobs_ok)))
         tools_and_jobs_error = dict(list(trans.sa_session.execute(tools_and_jobs_error)))
@@ -108,14 +113,16 @@ class Tools(BaseUIController):
         tools.sort(key=sort_keys[sorting], reverse=reverse)
 
         for tool in tools:
-            data[tool] = (str(tools_and_jobs_ok.get(tool, '-')), str(tools_and_jobs_error.get(tool, '-')))
+            data[tool] = (str(tools_and_jobs_ok.get(tool, "-")), str(tools_and_jobs_error.get(tool, "-")))
 
-        return trans.fill_template('/webapps/reports/tools_and_job_state.mako',
-                                   data=data,
-                                   user_cutoff=user_cutoff,
-                                   sorting=sorting,
-                                   descending=descending,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/tools_and_job_state.mako",
+            data=data,
+            user_cutoff=user_cutoff,
+            sorting=sorting,
+            descending=descending,
+            message=message,
+        )
 
     @web.expose
     def tools_and_job_state_per_month(self, trans, **kwd):
@@ -126,14 +133,14 @@ class Tools(BaseUIController):
             - the number of jobs using this tool in error
         """
 
-        message = escape(restore_text(kwd.get('message', '')))
-        user_cutoff = int(kwd.get('user_cutoff', 60))
+        message = escape(restore_text(kwd.get("message", "")))
+        user_cutoff = int(kwd.get("user_cutoff", 60))
 
         # sort by history space, or by user mail or by number of history/dataset
         # sort_by = kwd.get( 'sorting', 'Tool' )
         # sorting = 0 if sort_by == 'Tool' else 1 if sort_by == 'ok' else 2
         # descending = 1 if kwd.get( 'descending', 'desc' ) == 'desc' else -1
-        tool = kwd.get('tool', None)
+        tool = kwd.get("tool", None)
 
         if tool is None:
             raise TypeError("Tool can't be None")
@@ -141,18 +148,26 @@ class Tools(BaseUIController):
         data = {}
 
         # select count(id), create_time from job where state='ok' and tool_id=$tool group by date;
-        date_and_jobs_ok = sa.select((sa.func.date(galaxy.model.Job.table.c.create_time).label('date'),
-                                      sa.func.count(galaxy.model.Job.table.c.id).label('job')),
-                                     from_obj=[galaxy.model.Job.table],
-                                     whereclause=and_(galaxy.model.Job.table.c.state == 'ok', galaxy.model.Job.table.c.tool_id == tool),
-                                     group_by=['date'])
+        date_and_jobs_ok = sa.select(
+            (
+                sa.func.date(galaxy.model.Job.table.c.create_time).label("date"),
+                sa.func.count(galaxy.model.Job.table.c.id).label("job"),
+            ),
+            from_obj=[galaxy.model.Job.table],
+            whereclause=and_(galaxy.model.Job.table.c.state == "ok", galaxy.model.Job.table.c.tool_id == tool),
+            group_by=["date"],
+        )
 
         # select count(id), create_time from job where state='error' and tool_id=$tool group by date;
-        date_and_jobs_error = sa.select((sa.func.date(galaxy.model.Job.table.c.create_time).label('date'),
-                                         sa.func.count(galaxy.model.Job.table.c.id).label('job')),
-                                        from_obj=[galaxy.model.Job.table],
-                                        whereclause=and_(galaxy.model.Job.table.c.state == 'error', galaxy.model.Job.table.c.tool_id == tool),
-                                        group_by=['date'])
+        date_and_jobs_error = sa.select(
+            (
+                sa.func.date(galaxy.model.Job.table.c.create_time).label("date"),
+                sa.func.count(galaxy.model.Job.table.c.id).label("job"),
+            ),
+            from_obj=[galaxy.model.Job.table],
+            whereclause=and_(galaxy.model.Job.table.c.state == "error", galaxy.model.Job.table.c.tool_id == tool),
+            group_by=["date"],
+        )
 
         date_and_jobs_ok = dict(list(trans.sa_session.execute(date_and_jobs_ok)))
         date_and_jobs_error = dict(list(trans.sa_session.execute(date_and_jobs_error)))
@@ -168,11 +183,13 @@ class Tools(BaseUIController):
                 data[date_key][0] += int(date_and_jobs_ok.get(date, 0))
                 data[date_key][1] += int(date_and_jobs_error.get(date, 0))
 
-        return trans.fill_template('/webapps/reports/tools_and_job_state_per_month.mako',
-                                   data=data,
-                                   tool=tool,
-                                   user_cutoff=user_cutoff,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/tools_and_job_state_per_month.mako",
+            data=data,
+            tool=tool,
+            user_cutoff=user_cutoff,
+            message=message,
+        )
 
     @web.expose
     def tool_execution_time(self, trans, **kwd):
@@ -187,27 +204,29 @@ class Tools(BaseUIController):
         # liste des tools + temps moyen d'exec du job + temps d'execution du dernier job + tps min et max / mois (?)
         user_cutoff = int(kwd.get("user_cutoff", 60))
         sort_by = kwd.get("sort_by", "tool")
-        descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
         sort_by = 0 if sort_by == "tool" else 1 if sort_by == "avg" else 2 if sort_by == "min" else 3
-        color = True if kwd.get("color", '') == "True" else False
+        color = True if kwd.get("color", "") == "True" else False
 
         data = {}
         ordered_data = {}
 
-        sort_keys = (
-            lambda v: v.lower(),
-            lambda v: data[v]['avg'],
-            lambda v: data[v]['min'],
-            lambda v: data[v]['max'])
+        sort_keys = (lambda v: v.lower(), lambda v: data[v]["avg"], lambda v: data[v]["min"], lambda v: data[v]["max"])
 
-        jobs_times = sa.select((galaxy.model.Job.table.c.tool_id.label("name"),
-                                galaxy.model.Job.table.c.create_time.label("create_time"),
-                                galaxy.model.Job.table.c.update_time.label("update_time"),
-                                galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
-                               from_obj=[galaxy.model.Job.table])
+        jobs_times = sa.select(
+            (
+                galaxy.model.Job.table.c.tool_id.label("name"),
+                galaxy.model.Job.table.c.create_time.label("create_time"),
+                galaxy.model.Job.table.c.update_time.label("update_time"),
+                galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time,
+            ),
+            from_obj=[galaxy.model.Job.table],
+        )
 
-        jobs_times = [(name, (create, update, time)) for name, create, update, time in trans.sa_session.execute(jobs_times)]
+        jobs_times = [
+            (name, (create, update, time)) for name, create, update, time in trans.sa_session.execute(jobs_times)
+        ]
         for tool, attr in jobs_times:
             if tool not in data:
                 data[tool] = {"last": [(attr[1], attr[0])], "avg": [attr[2]]}
@@ -227,16 +246,20 @@ class Tools(BaseUIController):
             tools = tools[:user_cutoff]
         tools.sort(key=sort_keys[sort_by], reverse=reverse)
         for tool in tools:
-            ordered_data[tool] = {"min": self.formatted(data[tool]["min"], color),
-                                  "max": self.formatted(data[tool]["max"], color),
-                                  "avg": self.formatted(data[tool]["avg"], color),
-                                  "last": self.formatted(data[tool]["last"], color)}
+            ordered_data[tool] = {
+                "min": self.formatted(data[tool]["min"], color),
+                "max": self.formatted(data[tool]["max"], color),
+                "avg": self.formatted(data[tool]["avg"], color),
+                "last": self.formatted(data[tool]["last"], color),
+            }
 
-        return trans.fill_template('/webapps/reports/tool_execution_time.mako',
-                                   data=ordered_data,
-                                   descending=descending,
-                                   user_cutoff=user_cutoff,
-                                   sort_by=sort_by)
+        return trans.fill_template(
+            "/webapps/reports/tool_execution_time.mako",
+            data=ordered_data,
+            descending=descending,
+            user_cutoff=user_cutoff,
+            sort_by=sort_by,
+        )
 
     @web.expose
     def tool_execution_time_per_month(self, trans, **kwd):
@@ -250,11 +273,11 @@ class Tools(BaseUIController):
         # liste des tools + temps moyen d'exec du job + temps d'execution du dernier job + tps min et max / mois(?)
         user_cutoff = int(kwd.get("user_cutoff", 60))
         sort_by = kwd.get("sort_by", "month")
-        descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
         sort_by = 0 if sort_by == "month" else 1 if sort_by == "min" else 2 if sort_by == "max" else 3
         tool = kwd.get("tool", None)
-        color = True if kwd.get("color", '') == "True" else False
+        color = True if kwd.get("color", "") == "True" else False
 
         if tool is None:
             raise ValueError("Tool can't be None")
@@ -262,13 +285,17 @@ class Tools(BaseUIController):
         ordered_data = {}
         sort_keys = [(lambda v, i=i: v[i]) for i in range(4)]
 
-        jobs_times = sa.select((sa.func.date_trunc('month', galaxy.model.Job.table.c.create_time).label('date'),
-                                sa.func.max(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
-                                sa.func.avg(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
-                                sa.func.min(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time)),
-                               from_obj=[galaxy.model.Job.table],
-                               whereclause=galaxy.model.Job.table.c.tool_id == tool,
-                               group_by=['date'])
+        jobs_times = sa.select(
+            (
+                sa.func.date_trunc("month", galaxy.model.Job.table.c.create_time).label("date"),
+                sa.func.max(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
+                sa.func.avg(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
+                sa.func.min(galaxy.model.Job.table.c.update_time - galaxy.model.Job.table.c.create_time),
+            ),
+            from_obj=[galaxy.model.Job.table],
+            whereclause=galaxy.model.Job.table.c.tool_id == tool,
+            group_by=["date"],
+        )
 
         months = list(trans.sa_session.execute(jobs_times.execute))
         months.sort(key=sort_keys[sort_by], reverse=reverse)
@@ -276,27 +303,29 @@ class Tools(BaseUIController):
             months = months[:user_cutoff]
 
         for month in months:
-            ordered_data[str(month[0]).split(' ')[0][:-3]] = (self.formatted(month[1], color),
-                                                              self.formatted(month[2], color),
-                                                              self.formatted(month[3], color))
+            ordered_data[str(month[0]).split(" ")[0][:-3]] = (
+                self.formatted(month[1], color),
+                self.formatted(month[2], color),
+                self.formatted(month[3], color),
+            )
 
-        return trans.fill_template('/webapps/reports/tool_execution_time_per_month.mako',
-                                   data=ordered_data,
-                                   tool=tool,
-                                   descending=descending,
-                                   user_cutoff=user_cutoff,
-                                   sort_by=sort_by)
+        return trans.fill_template(
+            "/webapps/reports/tool_execution_time_per_month.mako",
+            data=ordered_data,
+            tool=tool,
+            descending=descending,
+            user_cutoff=user_cutoff,
+            sort_by=sort_by,
+        )
 
     @web.expose
     def tool_error_messages(self, trans, **kwd):
         tool_name = kwd.get("tool", None)
-        descending = 1 if kwd.get("descending", 'desc') == "desc" else -1
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
         sort_by = 0 if kwd.get("sort_by", "time") == "time" else 1
         cutoff = int(kwd.get("user_cutoff", 60))
-        sort_keys = (
-            lambda v: counter[v][1],
-            lambda v: counter[v][0])
+        sort_keys = (lambda v: counter[v][1], lambda v: counter[v][0])
 
         if tool_name is None:
             raise ValueError("Tool can't be none")
@@ -330,12 +359,12 @@ class Tools(BaseUIController):
             keys = keys[:cutoff]
         keys.sort(key=sort_keys[sort_by], reverse=reverse)
 
-        spaces = [' ', '\t', '    ']
+        spaces = [" ", "\t", "    "]
         for key in keys:
-            new_key = '</br>'.join(_ for _ in key.split('\n') if _ and _ not in spaces)
+            new_key = "</br>".join(_ for _ in key.split("\n") if _ and _ not in spaces)
             if len(new_key) >= 100:
                 to_replace = []
-                words = key.split('\n')
+                words = key.split("\n")
                 for word in words:
                     if word in to_replace:
                         continue
@@ -351,9 +380,11 @@ class Tools(BaseUIController):
                         new_key = new_key.replace(sentence, f"</br>{word}{' [this line in %d times]' % count}")
             data[new_key] = counter[key]
 
-        return trans.fill_template("/webapps/reports/tool_error_messages.mako",
-                                   data=data,
-                                   descending=descending,
-                                   tool_name=tool_name,
-                                   sort_by=sort_by,
-                                   user_cutoff=cutoff)
+        return trans.fill_template(
+            "/webapps/reports/tool_error_messages.mako",
+            data=data,
+            descending=descending,
+            tool_name=tool_name,
+            sort_by=sort_by,
+            user_cutoff=cutoff,
+        )
diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py
index 3b023b037de..773f2dcd691 100644
--- a/lib/galaxy/webapps/reports/controllers/users.py
+++ b/lib/galaxy/webapps/reports/controllers/users.py
@@ -4,7 +4,7 @@ import operator
 from datetime import (
     date,
     datetime,
-    timedelta
+    timedelta,
 )
 
 import sqlalchemy as sa
@@ -13,7 +13,10 @@ from sqlalchemy import false
 
 import galaxy.model
 from galaxy import util
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 from galaxy.webapps.reports.controllers.jobs import sorter
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 
@@ -21,76 +24,84 @@ log = logging.getLogger(__name__)
 
 
 class Users(BaseUIController, ReportQueryBuilder):
-
     @web.expose
     def registered_users(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
+        message = escape(util.restore_text(kwd.get("message", "")))
         num_users = trans.sa_session.query(galaxy.model.User).count()
-        return trans.fill_template('/webapps/reports/registered_users.mako', num_users=num_users, message=message)
+        return trans.fill_template("/webapps/reports/registered_users.mako", num_users=num_users, message=message)
 
     @web.expose
     def registered_users_per_month(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
-        specs = sorter('date', kwd)
+        message = escape(util.restore_text(kwd.get("message", "")))
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
 
-        q = sa.select((self.select_month(galaxy.model.User.table.c.create_time).label('date'),
-                       sa.func.count(galaxy.model.User.table.c.id).label('num_users')),
-                      from_obj=[galaxy.model.User.table],
-                      group_by=self.group_by_month(galaxy.model.User.table.c.create_time),
-                      order_by=[_order])
+        q = sa.select(
+            (
+                self.select_month(galaxy.model.User.table.c.create_time).label("date"),
+                sa.func.count(galaxy.model.User.table.c.id).label("num_users"),
+            ),
+            from_obj=[galaxy.model.User.table],
+            group_by=self.group_by_month(galaxy.model.User.table.c.create_time),
+            order_by=[_order],
+        )
         users = []
         for row in trans.sa_session.execute(q):
-            users.append((row.date.strftime("%Y-%m"),
-                          row.num_users,
-                          row.date.strftime("%B"),
-                          row.date.strftime("%Y")))
-        return trans.fill_template('/webapps/reports/registered_users_per_month.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   users=users,
-                                   message=message)
+            users.append((row.date.strftime("%Y-%m"), row.num_users, row.date.strftime("%B"), row.date.strftime("%Y")))
+        return trans.fill_template(
+            "/webapps/reports/registered_users_per_month.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            users=users,
+            message=message,
+        )
 
     @web.expose
     def specified_month(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
+        message = escape(util.restore_text(kwd.get("message", "")))
         # If specified_date is not received, we'll default to the current month
-        specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
+        specified_date = kwd.get("specified_date", datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
         year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
         year_label = start_date.strftime("%Y")
-        q = sa.select((self.select_day(galaxy.model.User.table.c.create_time).label('date'),
-                       sa.func.count(galaxy.model.User.table.c.id).label('num_users')),
-                      whereclause=sa.and_(galaxy.model.User.table.c.create_time >= start_date,
-                                          galaxy.model.User.table.c.create_time < end_date),
-                      from_obj=[galaxy.model.User.table],
-                      group_by=self.group_by_day(galaxy.model.User.table.c.create_time),
-                      order_by=[sa.desc('date')])
+        q = sa.select(
+            (
+                self.select_day(galaxy.model.User.table.c.create_time).label("date"),
+                sa.func.count(galaxy.model.User.table.c.id).label("num_users"),
+            ),
+            whereclause=sa.and_(
+                galaxy.model.User.table.c.create_time >= start_date, galaxy.model.User.table.c.create_time < end_date
+            ),
+            from_obj=[galaxy.model.User.table],
+            group_by=self.group_by_day(galaxy.model.User.table.c.create_time),
+            order_by=[sa.desc("date")],
+        )
         users = []
         for row in trans.sa_session.execute(q):
-            users.append((row.date.strftime("%Y-%m-%d"),
-                          row.date.strftime("%d"),
-                          row.num_users,
-                          row.date.strftime("%A")))
-        return trans.fill_template('/webapps/reports/registered_users_specified_month.mako',
-                                   month_label=month_label,
-                                   year_label=year_label,
-                                   month=month,
-                                   users=users,
-                                   message=message)
+            users.append(
+                (row.date.strftime("%Y-%m-%d"), row.date.strftime("%d"), row.num_users, row.date.strftime("%A"))
+            )
+        return trans.fill_template(
+            "/webapps/reports/registered_users_specified_month.mako",
+            month_label=month_label,
+            year_label=year_label,
+            month=month,
+            users=users,
+            message=message,
+        )
 
     @web.expose
     def specified_date(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
+        message = escape(util.restore_text(kwd.get("message", "")))
         # If specified_date is not received, we'll default to the current month
-        specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
+        specified_date = kwd.get("specified_date", datetime.utcnow().strftime("%Y-%m-%d"))
         year, month, day = map(int, specified_date.split("-"))
         start_date = date(year, month, day)
         end_date = start_date + timedelta(days=1)
@@ -98,28 +109,32 @@ class Users(BaseUIController, ReportQueryBuilder):
         day_label = start_date.strftime("%A")
         month_label = start_date.strftime("%B")
         year_label = start_date.strftime("%Y")
-        q = sa.select((self.select_day(galaxy.model.User.table.c.create_time).label('date'),
-                       galaxy.model.User.table.c.email),
-                      whereclause=sa.and_(galaxy.model.User.table.c.create_time >= start_date,
-                                          galaxy.model.User.table.c.create_time < end_date),
-                      from_obj=[galaxy.model.User.table],
-                      order_by=[galaxy.model.User.table.c.email])
+        q = sa.select(
+            (self.select_day(galaxy.model.User.table.c.create_time).label("date"), galaxy.model.User.table.c.email),
+            whereclause=sa.and_(
+                galaxy.model.User.table.c.create_time >= start_date, galaxy.model.User.table.c.create_time < end_date
+            ),
+            from_obj=[galaxy.model.User.table],
+            order_by=[galaxy.model.User.table.c.email],
+        )
         users = []
         for row in trans.sa_session.execute(q):
             users.append(row.email)
-        return trans.fill_template('/webapps/reports/registered_users_specified_date.mako',
-                                   specified_date=start_date,
-                                   day_label=day_label,
-                                   month_label=month_label,
-                                   year_label=year_label,
-                                   day_of_month=day_of_month,
-                                   users=users,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/registered_users_specified_date.mako",
+            specified_date=start_date,
+            day_label=day_label,
+            month_label=month_label,
+            year_label=year_label,
+            day_of_month=day_of_month,
+            users=users,
+            message=message,
+        )
 
     @web.expose
     def last_access_date(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
-        specs = sorter('one', kwd)
+        message = escape(util.restore_text(kwd.get("message", "")))
+        specs = sorter("one", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -127,7 +142,7 @@ class Users(BaseUIController, ReportQueryBuilder):
         def name_to_num(name):
             num = None
 
-            if name is not None and name.lower() == 'zero':
+            if name is not None and name.lower() == "zero":
                 num = 0
             else:
                 num = 1
@@ -139,14 +154,16 @@ class Users(BaseUIController, ReportQueryBuilder):
         else:
             _order = False
 
-        days_not_logged_in = kwd.get('days_not_logged_in', 90)
+        days_not_logged_in = kwd.get("days_not_logged_in", 90)
         if not days_not_logged_in:
             days_not_logged_in = 0
         cutoff_time = datetime.utcnow() - timedelta(days=int(days_not_logged_in))
         users = []
-        for user in trans.sa_session.query(galaxy.model.User) \
-                                    .filter(galaxy.model.User.table.c.deleted == false()) \
-                                    .order_by(galaxy.model.User.table.c.email):
+        for user in (
+            trans.sa_session.query(galaxy.model.User)
+            .filter(galaxy.model.User.table.c.deleted == false())
+            .order_by(galaxy.model.User.table.c.email)
+        ):
             if user.galaxy_sessions:
                 last_galaxy_session = user.galaxy_sessions[0]
                 if last_galaxy_session.update_time < cutoff_time:
@@ -155,18 +172,20 @@ class Users(BaseUIController, ReportQueryBuilder):
                 # The user has never logged in
                 users.append((user.email, "never logged in"))
         users = sorted(users, key=operator.itemgetter(name_to_num(sort_id)), reverse=_order)
-        return trans.fill_template('/webapps/reports/users_last_access_date.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   days_not_logged_in=days_not_logged_in,
-                                   users=users,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/users_last_access_date.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            days_not_logged_in=days_not_logged_in,
+            users=users,
+            message=message,
+        )
 
     @web.expose
     def user_disk_usage(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
-        specs = sorter('disk_usage', kwd)
+        message = escape(util.restore_text(kwd.get("message", "")))
+        specs = sorter("disk_usage", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -176,49 +195,55 @@ class Users(BaseUIController, ReportQueryBuilder):
         else:
             _order = False
 
-        user_cutoff = int(kwd.get('user_cutoff', 60))
+        user_cutoff = int(kwd.get("user_cutoff", 60))
         # disk_usage isn't indexed
         all_users = trans.sa_session.query(galaxy.model.User).all()
         sort_attrgetter = operator.attrgetter(str(sort_id))
         users = sorted(all_users, key=lambda x: sort_attrgetter(x) or 0, reverse=_order)
         if user_cutoff:
             users = users[:user_cutoff]
-        return trans.fill_template('/webapps/reports/users_user_disk_usage.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   users=users,
-                                   user_cutoff=user_cutoff,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/users_user_disk_usage.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            users=users,
+            user_cutoff=user_cutoff,
+            message=message,
+        )
 
     @web.expose
     def history_per_user(self, trans, **kwd):
-        message = escape(util.restore_text(kwd.get('message', '')))
-        user_cutoff = int(kwd.get('user_cutoff', 60))
-        sorting = 0 if kwd.get('sorting', 'User') == 'User' else 1
-        descending = 1 if kwd.get('descending', 'desc') == 'desc' else -1
+        message = escape(util.restore_text(kwd.get("message", "")))
+        user_cutoff = int(kwd.get("user_cutoff", 60))
+        sorting = 0 if kwd.get("sorting", "User") == "User" else 1
+        descending = 1 if kwd.get("descending", "desc") == "desc" else -1
         reverse = descending == 1
-        sort_keys = (
-            lambda v: v[0].lower(),
-            lambda v: v[1]
-        )
+        sort_keys = (lambda v: v[0].lower(), lambda v: v[1])
 
         req = sa.select(
-            (sa.func.count(galaxy.model.History.table.c.id).label('history'),
-             galaxy.model.User.table.c.username.label('username')),
+            (
+                sa.func.count(galaxy.model.History.table.c.id).label("history"),
+                galaxy.model.User.table.c.username.label("username"),
+            ),
             from_obj=[sa.outerjoin(galaxy.model.History.table, galaxy.model.User.table)],
             whereclause=galaxy.model.History.table.c.user_id == galaxy.model.User.table.c.id,
-            group_by=['username'],
-            order_by=[sa.desc('username'), 'history'])
+            group_by=["username"],
+            order_by=[sa.desc("username"), "history"],
+        )
 
-        histories = [(_.username if _.username is not None else "Unknown", _.history) for _ in trans.sa_session.execute(req)]
+        histories = [
+            (_.username if _.username is not None else "Unknown", _.history) for _ in trans.sa_session.execute(req)
+        ]
         histories.sort(key=sort_keys[sorting], reverse=reverse)
         if user_cutoff != 0:
             histories = histories[:user_cutoff]
 
-        return trans.fill_template('/webapps/reports/history_per_user.mako',
-                                   histories=histories,
-                                   user_cutoff=user_cutoff,
-                                   sorting=sorting,
-                                   descending=descending,
-                                   message=message)
+        return trans.fill_template(
+            "/webapps/reports/history_per_user.mako",
+            histories=histories,
+            user_cutoff=user_cutoff,
+            sorting=sorting,
+            descending=descending,
+            message=message,
+        )
diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py
index 5939224bd3b..6422ab8a309 100644
--- a/lib/galaxy/webapps/reports/controllers/workflows.py
+++ b/lib/galaxy/webapps/reports/controllers/workflows.py
@@ -5,23 +5,29 @@ from collections import namedtuple
 from datetime import (
     date,
     datetime,
-    timedelta
+    timedelta,
 )
 from math import (
     ceil,
-    floor
+    floor,
 )
 
 import sqlalchemy as sa
 from markupsafe import escape
 from sqlalchemy import and_
 
-from galaxy import model, util
+from galaxy import (
+    model,
+    util,
+)
 from galaxy.web.legacy_framework import grids
-from galaxy.webapps.base.controller import BaseUIController, web
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
 from galaxy.webapps.reports.controllers.jobs import (
     get_spark_time,
-    sorter
+    sorter,
 )
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
 
@@ -29,53 +35,59 @@ log = logging.getLogger(__name__)
 
 
 class SpecifiedDateListGrid(grids.Grid):
-
     class WorkflowNameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, stored_workflow):
             return escape(stored_workflow.name)
 
     class CreateTimeColumn(grids.DateTimeColumn):
-
         def get_value(self, trans, grid, stored_workflow):
             return stored_workflow.create_time
 
     class UserColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, stored_workflow):
             if stored_workflow.user:
                 return escape(stored_workflow.user.email)
-            return 'unknown'
+            return "unknown"
 
     class EmailColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
-            return query.filter(and_(model.StoredWorkflow.table.c.user_id == model.User.table.c.id,
-                                     model.User.table.c.email == column_filter))
+            return query.filter(
+                and_(
+                    model.StoredWorkflow.table.c.user_id == model.User.table.c.id,
+                    model.User.table.c.email == column_filter,
+                )
+            )
 
     class SpecifiedDateColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
             # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
             # so we need to figure out which type of date we have
-            if column_filter.count('-') == 2:
+            if column_filter.count("-") == 2:
                 # We are filtering on a date like YYYY-MM-DD
                 year, month, day = map(int, column_filter.split("-"))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
-                return query.filter(and_(self.model_class.table.c.create_time >= start_date,
-                                         self.model_class.table.c.create_time < end_date))
-            if column_filter.count('-') == 1:
+                return query.filter(
+                    and_(
+                        self.model_class.table.c.create_time >= start_date,
+                        self.model_class.table.c.create_time < end_date,
+                    )
+                )
+            if column_filter.count("-") == 1:
                 # We are filtering on a month like YYYY-MM
                 year, month = map(int, column_filter.split("-"))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
-                return query.filter(and_(self.model_class.table.c.create_time >= start_date,
-                                         self.model_class.table.c.create_time < end_date))
+                return query.filter(
+                    and_(
+                        self.model_class.table.c.create_time >= start_date,
+                        self.model_class.table.c.create_time < end_date,
+                    )
+                )
 
     # Grid definition
     use_async = False
@@ -83,40 +95,34 @@ class SpecifiedDateListGrid(grids.Grid):
     title = "Workflows"
     default_sort_key = "name"
     columns = [
-        WorkflowNameColumn("Name",
-                           key="name",
-                           attach_popup=False,
-                           filterable="advanced"),
-        CreateTimeColumn("Creation Time",
-                         key="create_time",
-                         attach_popup=False),
-        UserColumn("User",
-                   key="email",
-                   model_class=model.User,
-                   link=(lambda item: dict(operation="user_per_month", id=item.id, webapp="reports")),
-                   attach_popup=False),
+        WorkflowNameColumn("Name", key="name", attach_popup=False, filterable="advanced"),
+        CreateTimeColumn("Creation Time", key="create_time", attach_popup=False),
+        UserColumn(
+            "User",
+            key="email",
+            model_class=model.User,
+            link=(lambda item: dict(operation="user_per_month", id=item.id, webapp="reports")),
+            attach_popup=False,
+        ),
         # Columns that are valid for filtering but are not visible.
-        SpecifiedDateColumn("Specified Date",
-                            key="specified_date",
-                            visible=False),
-        EmailColumn("Email",
-                    key="email",
-                    model_class=model.User,
-                    visible=False),
+        SpecifiedDateColumn("Specified Date", key="specified_date", visible=False),
+        EmailColumn("Email", key="email", model_class=model.User, visible=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    default_filter = {'specified_date': 'All'}
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    default_filter = {"specified_date": "All"}
     num_rows_per_page = 50
     use_paging = True
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(self.model_class) \
-                               .join(model.User) \
-                               .enable_eagerloads(False)
+        return trans.sa_session.query(self.model_class).join(model.User).enable_eagerloads(False)
 
 
 class Workflows(BaseUIController, ReportQueryBuilder):
@@ -128,39 +134,37 @@ class Workflows(BaseUIController, ReportQueryBuilder):
         # We add params to the keyword dict in this method in order to rename the param
         # with an "f-" prefix, simulating filtering by clicking a search link.  We have
         # to take this approach because the "-" character is illegal in HTTP requests.
-        if 'f-specified_date' in kwd and 'specified_date' not in kwd:
+        if "f-specified_date" in kwd and "specified_date" not in kwd:
             # The user clicked a State link in the Advanced Search box, so 'specified_date'
             # will have been eliminated.
             pass
-        elif 'specified_date' not in kwd:
-            kwd['f-specified_date'] = 'All'
+        elif "specified_date" not in kwd:
+            kwd["f-specified_date"] = "All"
         else:
-            kwd['f-specified_date'] = kwd['specified_date']
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+            kwd["f-specified_date"] = kwd["specified_date"]
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "workflow_per_month":
                 # The received id is the stored_workflow id.
-                return trans.response.send_redirect(web.url_for(controller='workflows',
-                                                                action='workflow_per_month',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="workflows", action="workflow_per_month", **kwd)
+                )
             elif operation == "user_per_month":
-                stored_workflow_id = kwd.get('id', None)
+                stored_workflow_id = kwd.get("id", None)
                 workflow = get_workflow(trans, stored_workflow_id)
                 if workflow.user:
-                    kwd['email'] = workflow.user.email
+                    kwd["email"] = workflow.user.email
                 else:
-                    kwd['email'] = None  # For anonymous users ( shouldn't happen with workflows )
-                return trans.response.send_redirect(web.url_for(controller='workflows',
-                                                                action='user_per_month',
-                                                                **kwd))
+                    kwd["email"] = None  # For anonymous users ( shouldn't happen with workflows )
+                return trans.response.send_redirect(web.url_for(controller="workflows", action="user_per_month", **kwd))
         return self.specified_date_list_grid(trans, **kwd)
 
     @web.expose
     def per_month_all(self, trans, **kwd):
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
-        specs = sorter('date', kwd)
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
@@ -169,31 +173,36 @@ class Workflows(BaseUIController, ReportQueryBuilder):
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
-        q = sa.select((self.select_month(model.StoredWorkflow.table.c.create_time).label('date'),
-                       sa.func.count(model.StoredWorkflow.table.c.id).label('total_workflows')),
-                      from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)],
-                      group_by=self.group_by_month(model.StoredWorkflow.table.c.create_time),
-                      order_by=[_order],
-                      offset=offset,
-                      limit=limit)
+        q = sa.select(
+            (
+                self.select_month(model.StoredWorkflow.table.c.create_time).label("date"),
+                sa.func.count(model.StoredWorkflow.table.c.id).label("total_workflows"),
+            ),
+            from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)],
+            group_by=self.group_by_month(model.StoredWorkflow.table.c.create_time),
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
-        all_workflows = sa.select((self.select_day(model.StoredWorkflow.table.c.create_time).label('date'),
-                     model.StoredWorkflow.table.c.id))
+        all_workflows = sa.select(
+            (self.select_day(model.StoredWorkflow.table.c.create_time).label("date"), model.StoredWorkflow.table.c.id)
+        )
 
         trends = dict()
         for workflow in trans.sa_session.execute(all_workflows):
@@ -216,73 +225,79 @@ class Workflows(BaseUIController, ReportQueryBuilder):
             month_name = row.date.strftime("%B")
             year = int(row.date.strftime("%Y"))
 
-            workflows.append((row.date.strftime("%Y-%m"),
-                              row.total_workflows,
-                              month_name,
-                              year))
+            workflows.append((row.date.strftime("%Y-%m"), row.total_workflows, month_name, year))
 
         pages_found = ceil(len(workflows) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/workflows_per_month_all.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   trends=trends,
-                                   workflows=workflows,
-                                   message=message,
-                                   page_specs=page_specs)
+        return trans.fill_template(
+            "/webapps/reports/workflows_per_month_all.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            trends=trends,
+            workflows=workflows,
+            message=message,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def per_user(self, trans, **kwd):
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
-        specs = sorter('user_email', kwd)
+        specs = sorter("user_email", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        time_period = kwd.get('spark_time')
+        time_period = kwd.get("spark_time")
         time_period, _time_period = get_spark_time(time_period)
         spark_limit = 30
         offset = 0
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
         workflows = []
-        q = sa.select((model.User.table.c.email.label('user_email'),
-                       sa.func.count(model.StoredWorkflow.table.c.id).label('total_workflows')),
-                      from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)],
-                      group_by=['user_email'],
-                      order_by=[_order],
-                      offset=offset,
-                      limit=limit)
+        q = sa.select(
+            (
+                model.User.table.c.email.label("user_email"),
+                sa.func.count(model.StoredWorkflow.table.c.id).label("total_workflows"),
+            ),
+            from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)],
+            group_by=["user_email"],
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
-        all_workflows_per_user = sa.select((model.User.table.c.email.label('user_email'),
-                                            self.select_day(model.StoredWorkflow.table.c.create_time).label('date'),
-                                            model.StoredWorkflow.table.c.id),
-                                           from_obj=[sa.outerjoin(model.StoredWorkflow.table,
-                                                                  model.User.table)])
+        all_workflows_per_user = sa.select(
+            (
+                model.User.table.c.email.label("user_email"),
+                self.select_day(model.StoredWorkflow.table.c.create_time).label("date"),
+                model.StoredWorkflow.table.c.id,
+            ),
+            from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)],
+        )
         currday = datetime.today()
         trends = dict()
         for workflow in trans.sa_session.execute(all_workflows_per_user):
-            curr_user = re.sub(r'\W+', '', workflow.user_email)
+            curr_user = re.sub(r"\W+", "", workflow.user_email)
             try:
                 day = currday - workflow.date
             except TypeError:
@@ -300,46 +315,52 @@ class Workflows(BaseUIController, ReportQueryBuilder):
                     trends[curr_user][container] += 1
 
         for row in trans.sa_session.execute(q):
-            workflows.append((row.user_email,
-                              row.total_workflows))
+            workflows.append((row.user_email, row.total_workflows))
 
         pages_found = ceil(len(workflows) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/workflows_per_user.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   spark_limit=spark_limit,
-                                   trends=trends,
-                                   time_period=time_period,
-                                   workflows=workflows,
-                                   message=message,
-                                   page_specs=page_specs)
+        return trans.fill_template(
+            "/webapps/reports/workflows_per_user.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            spark_limit=spark_limit,
+            trends=trends,
+            time_period=time_period,
+            workflows=workflows,
+            message=message,
+            page_specs=page_specs,
+        )
 
     @web.expose
     def user_per_month(self, trans, **kwd):
         params = util.Params(kwd)
-        message = ''
-        specs = sorter('date', kwd)
+        message = ""
+        specs = sorter("date", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        email = util.restore_text(params.get('email', ''))
-        user_id = trans.security.decode_id(params.get('id', ''))
+        email = util.restore_text(params.get("email", ""))
+        user_id = trans.security.decode_id(params.get("id", ""))
 
-        q = sa.select((self.select_month(model.StoredWorkflow.table.c.create_time).label('date'),
-                       sa.func.count(model.StoredWorkflow.table.c.id).label('total_workflows')),
-                      whereclause=model.StoredWorkflow.table.c.user_id == user_id,
-                      from_obj=[model.StoredWorkflow.table],
-                      group_by=self.group_by_month(model.StoredWorkflow.table.c.create_time),
-                      order_by=[_order])
+        q = sa.select(
+            (
+                self.select_month(model.StoredWorkflow.table.c.create_time).label("date"),
+                sa.func.count(model.StoredWorkflow.table.c.id).label("total_workflows"),
+            ),
+            whereclause=model.StoredWorkflow.table.c.user_id == user_id,
+            from_obj=[model.StoredWorkflow.table],
+            group_by=self.group_by_month(model.StoredWorkflow.table.c.create_time),
+            order_by=[_order],
+        )
 
-        all_workflows_user_month = sa.select((self.select_day(model.StoredWorkflow.table.c.create_time).label('date'),
-                                              model.StoredWorkflow.table.c.id),
-                                             whereclause=model.StoredWorkflow.table.c.user_id == user_id,
-                                             from_obj=[model.StoredWorkflow.table])
+        all_workflows_user_month = sa.select(
+            (self.select_day(model.StoredWorkflow.table.c.create_time).label("date"), model.StoredWorkflow.table.c.id),
+            whereclause=model.StoredWorkflow.table.c.user_id == user_id,
+            from_obj=[model.StoredWorkflow.table],
+        )
 
         trends = dict()
         for workflow in trans.sa_session.execute(all_workflows_user_month):
@@ -359,75 +380,82 @@ class Workflows(BaseUIController, ReportQueryBuilder):
 
         workflows = []
         for row in trans.sa_session.execute(q):
-            workflows.append((row.date.strftime("%Y-%m"),
-                              row.total_workflows,
-                              row.date.strftime("%B"),
-                              row.date.strftime("%Y")))
-        return trans.fill_template('/webapps/reports/workflows_user_per_month.mako',
-                                   email=util.sanitize_text(email),
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   trends=trends,
-                                   workflows=workflows,
-                                   message=message)
+            workflows.append(
+                (row.date.strftime("%Y-%m"), row.total_workflows, row.date.strftime("%B"), row.date.strftime("%Y"))
+            )
+        return trans.fill_template(
+            "/webapps/reports/workflows_user_per_month.mako",
+            email=util.sanitize_text(email),
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            trends=trends,
+            workflows=workflows,
+            message=message,
+        )
 
     @web.expose
     def per_workflow(self, trans, **kwd):
-        message = ''
-        PageSpec = namedtuple('PageSpec', ['entries', 'offset', 'page', 'pages_found'])
+        message = ""
+        PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"])
 
-        specs = sorter('workflow_name', kwd)
+        specs = sorter("workflow_name", kwd)
         sort_id = specs.sort_id
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        time_period = kwd.get('spark_time')
+        time_period = kwd.get("spark_time")
         time_period, _time_period = get_spark_time(time_period)
         spark_limit = 30
         offset = 0
         limit = 10
 
         if "entries" in kwd:
-            entries = int(kwd.get('entries'))
+            entries = int(kwd.get("entries"))
         else:
             entries = 10
         limit = entries * 4
 
         if "offset" in kwd:
-            offset = int(kwd.get('offset'))
+            offset = int(kwd.get("offset"))
         else:
             offset = 0
 
         if "page" in kwd:
-            page = int(kwd.get('page'))
+            page = int(kwd.get("page"))
         else:
             page = 1
 
         # In case we don't know which is the monitor user we will query for all jobs
 
-        q = sa.select((model.Workflow.table.c.id.label('workflow_id'),
-                       sa.func.min(model.Workflow.table.c.name).label('workflow_name'),
-                       sa.func.count(model.WorkflowInvocation.table.c.id).label('total_runs')),
-                      from_obj=[model.Workflow.table,
-                                model.WorkflowInvocation.table],
-                      whereclause=sa.and_(model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id),
-                      group_by=[model.Workflow.table.c.id],
-                      order_by=[_order],
-                      offset=offset,
-                      limit=limit)
+        q = sa.select(
+            (
+                model.Workflow.table.c.id.label("workflow_id"),
+                sa.func.min(model.Workflow.table.c.name).label("workflow_name"),
+                sa.func.count(model.WorkflowInvocation.table.c.id).label("total_runs"),
+            ),
+            from_obj=[model.Workflow.table, model.WorkflowInvocation.table],
+            whereclause=sa.and_(model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id),
+            group_by=[model.Workflow.table.c.id],
+            order_by=[_order],
+            offset=offset,
+            limit=limit,
+        )
 
-        all_runs_per_workflow = sa.select((model.Workflow.table.c.id.label('workflow_id'),
-                                           model.Workflow.table.c.name.label('workflow_name'),
-                                           self.select_day(model.WorkflowInvocation.table.c.create_time).label('date')),
-                                          from_obj=[model.Workflow.table,
-                                                    model.WorkflowInvocation.table],
-                                          whereclause=sa.and_(model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id))
+        all_runs_per_workflow = sa.select(
+            (
+                model.Workflow.table.c.id.label("workflow_id"),
+                model.Workflow.table.c.name.label("workflow_name"),
+                self.select_day(model.WorkflowInvocation.table.c.create_time).label("date"),
+            ),
+            from_obj=[model.Workflow.table, model.WorkflowInvocation.table],
+            whereclause=sa.and_(model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id),
+        )
 
         currday = date.today()
         trends = dict()
         for run in trans.sa_session.execute(all_runs_per_workflow):
-            curr_tool = re.sub(r'\W+', '', str(run.workflow_id))
+            curr_tool = re.sub(r"\W+", "", str(run.workflow_id))
             try:
                 day = currday - run.date
             except TypeError:
@@ -446,23 +474,24 @@ class Workflows(BaseUIController, ReportQueryBuilder):
 
         runs = []
         for row in trans.sa_session.execute(q):
-            runs.append((row.workflow_name,
-                         row.total_runs,
-                         row.workflow_id))
+            runs.append((row.workflow_name, row.total_runs, row.workflow_id))
 
         pages_found = ceil(len(runs) / float(entries))
         page_specs = PageSpec(entries, offset, page, pages_found)
 
-        return trans.fill_template('/webapps/reports/workflows_per_workflow.mako',
-                                   order=order,
-                                   arrow=arrow,
-                                   sort_id=sort_id,
-                                   spark_limit=spark_limit,
-                                   time_period=time_period,
-                                   trends=trends,
-                                   runs=runs,
-                                   message=message,
-                                   page_specs=page_specs)
+        return trans.fill_template(
+            "/webapps/reports/workflows_per_workflow.mako",
+            order=order,
+            arrow=arrow,
+            sort_id=sort_id,
+            spark_limit=spark_limit,
+            time_period=time_period,
+            trends=trends,
+            runs=runs,
+            message=message,
+            page_specs=page_specs,
+        )
+
 
 # ---- Utility methods -------------------------------------------------------
 
diff --git a/lib/galaxy/webapps/reports/fast_app.py b/lib/galaxy/webapps/reports/fast_app.py
index f5affed37a9..46a72913a09 100644
--- a/lib/galaxy/webapps/reports/fast_app.py
+++ b/lib/galaxy/webapps/reports/fast_app.py
@@ -19,7 +19,7 @@ def initialize_fast_app(gx_webapp):
     )
     add_exception_handler(app)
     add_request_id_middleware(app)
-    include_all_package_routers(app, 'galaxy.webapps.reports.api')
+    include_all_package_routers(app, "galaxy.webapps.reports.api")
     wsgi_handler = WSGIMiddleware(gx_webapp)
-    app.mount('/', wsgi_handler)
+    app.mount("/", wsgi_handler)
     return app
diff --git a/lib/galaxy/webapps/reports/fast_factory.py b/lib/galaxy/webapps/reports/fast_factory.py
index 9158be2604e..380ec840c29 100644
--- a/lib/galaxy/webapps/reports/fast_factory.py
+++ b/lib/galaxy/webapps/reports/fast_factory.py
@@ -36,7 +36,7 @@ with the following command-line.
 
 from galaxy.main_config import (
     WebappConfigResolver,
-    WebappSetupProps
+    WebappSetupProps,
 )
 from galaxy.webapps.reports.buildapp import app_factory
 from .fast_app import initialize_fast_app
@@ -44,11 +44,13 @@ from .fast_app import initialize_fast_app
 
 def factory():
     props = WebappSetupProps(
-        app_name='reports',
-        default_section_name='reports',
-        env_config_file='GALAXY_REPORTS_CONFIG',
+        app_name="reports",
+        default_section_name="reports",
+        env_config_file="GALAXY_REPORTS_CONFIG",
     )
     config_provider = WebappConfigResolver(props)
     config = config_provider.resolve_config()
-    gx_webapp = app_factory(global_conf=config.global_conf, load_app_kwds=config.load_app_kwds, wsgi_preflight=config.wsgi_preflight)
+    gx_webapp = app_factory(
+        global_conf=config.global_conf, load_app_kwds=config.load_app_kwds, wsgi_preflight=config.wsgi_preflight
+    )
     return initialize_fast_app(gx_webapp)
diff --git a/lib/galaxy/webapps/util.py b/lib/galaxy/webapps/util.py
index 94ca01e864e..7295b52997c 100644
--- a/lib/galaxy/webapps/util.py
+++ b/lib/galaxy/webapps/util.py
@@ -4,7 +4,6 @@ import mako.exceptions
 
 from galaxy.util import unicodify
 
-
 log = logging.getLogger(__name__)
 
 
@@ -24,8 +23,11 @@ def build_template_error_formatters():
     def mako_html_data(exc_value):
         if isinstance(exc_value, (mako.exceptions.CompileException, mako.exceptions.SyntaxException)):
             return mako.exceptions.html_error_template().render(full=False, css=False)
-        if isinstance(exc_value, AttributeError) and exc_value.args[0].startswith("'Undefined' object has no attribute"):
+        if isinstance(exc_value, AttributeError) and exc_value.args[0].startswith(
+            "'Undefined' object has no attribute"
+        ):
             return mako.exceptions.html_error_template().render(full=False, css=False)
+
     formatters.append(mako_html_data)
     return formatters
 
@@ -42,7 +44,8 @@ def wrap_if_allowed_or_fail(app, stack, wrap, name=None, args=None, kwargs=None)
     if not stack.allowed_middleware(wrap):
         raise MiddlewareWrapUnsupported(
             "'%s' is enabled in your configuration but the %s application stack does not support it, this "
-            "middleware has been disabled" % (name, stack.name))
+            "middleware has been disabled" % (name, stack.name)
+        )
     args = args or []
     kwargs = kwargs or {}
     log.debug("Enabling '%s' middleware", name)
diff --git a/lib/galaxy/webhooks/__init__.py b/lib/galaxy/webhooks/__init__.py
index b5bdce45963..d22c96309d3 100644
--- a/lib/galaxy/webhooks/__init__.py
+++ b/lib/galaxy/webhooks/__init__.py
@@ -18,20 +18,20 @@ class Webhook:
         self.activate = activate
         self.weight = weight
         self.path = path
-        self.styles = ''
-        self.script = ''
-        self.helper = ''
+        self.styles = ""
+        self.script = ""
+        self.helper = ""
         self.config = {}
 
     def to_dict(self):
         return {
-            'id': self.id,
-            'type': self.type,
-            'activate': self.activate,
-            'weight': self.weight,
-            'styles': self.styles,
-            'script': self.script,
-            'config': self.config,
+            "id": self.id,
+            "type": self.type,
+            "activate": self.activate,
+            "weight": self.weight,
+            "styles": self.styles,
+            "script": self.script,
+            "config": self.config,
         }
 
 
@@ -51,7 +51,7 @@ class WebhooksRegistry:
     def load_webhooks(self):
         for directory in self.webhooks_directories:
             config_file_path = None
-            for config_file in ['config.yml', 'config.yaml']:
+            for config_file in ["config.yml", "config.yaml"]:
                 path = os.path.join(directory, config_file)
                 if os.path.isfile(path):
                     config_file_path = path
@@ -67,14 +67,14 @@ class WebhooksRegistry:
         with open(config_file_path) as fh:
             config = yaml.safe_load(fh)
 
-        weight = config.get('weight', 1)
+        weight = config.get("weight", 1)
         if weight < 1:
-            raise ValueError('Webhook weight must be greater or equal 1.')
+            raise ValueError("Webhook weight must be greater or equal 1.")
 
         webhook = Webhook(
-            config.get('id'),
-            config.get('type'),
-            config.get('activate', False),
+            config.get("id"),
+            config.get("type"),
+            config.get("activate", False),
             weight,
             webhook_dir,
         )
@@ -82,23 +82,23 @@ class WebhooksRegistry:
         # Read styles into a string, assuming all styles are in a
         # single file
         try:
-            styles_file = os.path.join(webhook_dir, 'styles.css')
+            styles_file = os.path.join(webhook_dir, "styles.css")
             with open(styles_file) as fh:
-                webhook.styles = fh.read().replace('\n', '')
+                webhook.styles = fh.read().replace("\n", "")
         except OSError:
             pass
 
         # Read script into a string, assuming everything is in a
         # single file
         try:
-            script_file = os.path.join(webhook_dir, 'script.js')
-            with open(script_file, encoding='utf-8') as fh:
+            script_file = os.path.join(webhook_dir, "script.js")
+            with open(script_file, encoding="utf-8") as fh:
                 webhook.script = fh.read()
         except OSError:
             pass
 
         # Save helper function path if it exists
-        helper_path = os.path.join(webhook_dir, '__init__.py')
+        helper_path = os.path.join(webhook_dir, "__init__.py")
         if os.path.isfile(helper_path):
             webhook.helper = helper_path
 
diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py
index ae9d9c0a115..0eb375169e8 100644
--- a/lib/galaxy/work/context.py
+++ b/lib/galaxy/work/context.py
@@ -1,14 +1,12 @@
 import abc
 from typing import Optional
 
-from galaxy.managers.context import (
-    ProvidesHistoryContext,
-)
+from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model import History
 
 
 class WorkRequestContext(ProvidesHistoryContext):
-    """ Stripped down implementation of Galaxy web transaction god object for
+    """Stripped down implementation of Galaxy web transaction god object for
     work request handling outside of web threads - uses mix-ins shared with
     GalaxyWebTransaction to provide app, user, and history context convenience
     methods - but nothing related to HTTP handling, mako views, etc....
@@ -92,7 +90,7 @@ class SessionRequestContext(WorkRequestContext):
     """Like WorkRequestContext, but provides access to galaxy session and request."""
 
     def __init__(self, **kwargs):
-        self.galaxy_session = kwargs.pop('galaxy_session', None)
+        self.galaxy_session = kwargs.pop("galaxy_session", None)
         self.__request: GalaxyAbstractRequest = kwargs.pop("request")
         self.__response: GalaxyAbstractResponse = kwargs.pop("response")
         super().__init__(**kwargs)
@@ -113,11 +111,19 @@ class SessionRequestContext(WorkRequestContext):
         return self.galaxy_session
 
 
-def proxy_work_context_for_history(trans: ProvidesHistoryContext, history: Optional[History] = None, workflow_building_mode=False):
+def proxy_work_context_for_history(
+    trans: ProvidesHistoryContext, history: Optional[History] = None, workflow_building_mode=False
+):
     """Create a WorkContext for supplied context with potentially different history.
 
     This provides semi-structured access to a transaction/work context with a supplied target
     history that is different from the user's current history (which also might change during
     the request).
     """
-    return WorkRequestContext(app=trans.app, user=trans.user, history=history or trans.history, url_builder=trans.url_builder, workflow_building_mode=workflow_building_mode)
+    return WorkRequestContext(
+        app=trans.app,
+        user=trans.user,
+        history=history or trans.history,
+        url_builder=trans.url_builder,
+        workflow_building_mode=workflow_building_mode,
+    )
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 1aacc814cf4..b5f8a6e56f4 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -4,21 +4,24 @@ histories.
 import logging
 from typing import Optional
 
-from galaxy import exceptions, model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
-    DataToolParameter
+    DataToolParameter,
 )
 from galaxy.tools.parameters.grouping import (
     Conditional,
     Repeat,
-    Section
+    Section,
 )
 from galaxy.util import listify
 from .steps import (
     attach_ordered_steps,
-    order_workflow_steps_with_levels
+    order_workflow_steps_with_levels,
 )
 
 log = logging.getLogger(__name__)
@@ -26,8 +29,26 @@ log = logging.getLogger(__name__)
 WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored"
 
 
-def extract_workflow(trans, user, history=None, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None):
-    steps = extract_steps(trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids, dataset_names=dataset_names, dataset_collection_names=None)
+def extract_workflow(
+    trans,
+    user,
+    history=None,
+    job_ids=None,
+    dataset_ids=None,
+    dataset_collection_ids=None,
+    workflow_name=None,
+    dataset_names=None,
+    dataset_collection_names=None,
+):
+    steps = extract_steps(
+        trans,
+        history=history,
+        job_ids=job_ids,
+        dataset_ids=dataset_ids,
+        dataset_collection_ids=dataset_collection_ids,
+        dataset_names=dataset_names,
+        dataset_collection_names=None,
+    )
     # Workflow to populate
     workflow = model.Workflow()
     workflow.name = workflow_name
@@ -40,8 +61,7 @@ def extract_workflow(trans, user, history=None, job_ids=None, dataset_ids=None,
     for i, steps_at_level in enumerate(levorder):
         for j, index in enumerate(steps_at_level):
             step = steps[index]
-            step.position = dict(top=(base_pos + 120 * j),
-                                 left=(base_pos + 220 * i))
+            step.position = dict(top=(base_pos + 120 * j), left=(base_pos + 220 * i))
     # Store it
     stored = model.StoredWorkflow()
     stored.user = user
@@ -53,7 +73,15 @@ def extract_workflow(trans, user, history=None, job_ids=None, dataset_ids=None,
     return stored
 
 
-def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_collection_ids=None, dataset_names=None, dataset_collection_names=None):
+def extract_steps(
+    trans,
+    history=None,
+    job_ids=None,
+    dataset_ids=None,
+    dataset_collection_ids=None,
+    dataset_names=None,
+    dataset_collection_names=None,
+):
     # Ensure job_ids and dataset_ids are lists (possibly empty)
     job_ids = listify(job_ids)
     dataset_ids = listify(dataset_ids)
@@ -72,7 +100,7 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
     # Input dataset steps
     for i, hid in enumerate(dataset_ids):
         step = model.WorkflowStep()
-        step.type = 'data_input'
+        step.type = "data_input"
         if dataset_names:
             name = dataset_names[i]
         else:
@@ -81,11 +109,11 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
             step.label = name
             step_labels.add(name)
         step.tool_inputs = dict(name=name)
-        hid_to_output_pair[hid] = (step, 'output')
+        hid_to_output_pair[hid] = (step, "output")
         steps.append(step)
     for i, hid in enumerate(dataset_collection_ids):
         step = model.WorkflowStep()
-        step.type = 'data_collection_input'
+        step.type = "data_collection_input"
         if hid not in summary.collection_types:
             raise exceptions.RequestParameterInvalidException(f"hid {hid} does not appear to be a collection")
         collection_type = summary.collection_types[hid]
@@ -97,7 +125,7 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
             step.label = name
             step_labels.add(name)
         step.tool_inputs = dict(name=name, collection_type=collection_type)
-        hid_to_output_pair[hid] = (step, 'output')
+        hid_to_output_pair[hid] = (step, "output")
         steps.append(step)
     # Tool steps
     for job_id in job_ids:
@@ -107,7 +135,7 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
         job = summary.job_id2representative_job[job_id]
         tool_inputs, associations = step_inputs(trans, job)
         step = model.WorkflowStep()
-        step.type = 'tool'
+        step.type = "tool"
         step.tool_id = job.tool_id
         step.tool_version = job.tool_version
         step.tool_inputs = tool_inputs
@@ -132,7 +160,7 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
                 conn.output_name = other_name
         steps.append(step)
         # Store created dataset hids
-        for assoc in (job.output_datasets + job.output_dataset_collection_instances):
+        for assoc in job.output_datasets + job.output_dataset_collection_instances:
             assoc_name = assoc.name
             if ToolOutputCollectionPart.is_named_collection_part_name(assoc_name):
                 continue
@@ -142,10 +170,14 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
                 hid = None
                 for implicit_pair in jobs[job]:
                     query_assoc_name, dataset_collection = implicit_pair
-                    if query_assoc_name == assoc_name or assoc_name.startswith(f"__new_primary_file_{query_assoc_name}|"):
+                    if query_assoc_name == assoc_name or assoc_name.startswith(
+                        f"__new_primary_file_{query_assoc_name}|"
+                    ):
                         hid = summary.hid(dataset_collection)
                 if hid is None:
-                    template = "Failed to find matching implicit job - job id is %s, implicit pairs are %s, assoc_name is %s."
+                    template = (
+                        "Failed to find matching implicit job - job id is %s, implicit pairs are %s, assoc_name is %s."
+                    )
                     message = template % (job.id, jobs[job], assoc_name)
                     log.warning(message)
                     raise Exception("Failed to extract job.")
@@ -182,7 +214,6 @@ class FakeJob:
 
 
 class DatasetCollectionCreationJob:
-
     def __init__(self, dataset_collection):
         self.is_fake = True
         self.id = f"fake_{dataset_collection.id}"
@@ -196,7 +227,7 @@ class DatasetCollectionCreationJob:
 
 
 def summarize(trans, history=None):
-    """ Return mapping of job description to datasets for active items in
+    """Return mapping of job description to datasets for active items in
     supplied history - needed for building workflow from a history.
 
     Formerly call get_job_dict in workflow web controller.
@@ -206,7 +237,6 @@ def summarize(trans, history=None):
 
 
 class WorkflowSummary:
-
     def __init__(self, trans, history):
         if not history:
             history = trans.get_history()
@@ -268,7 +298,10 @@ class WorkflowSummary:
             # Use the "first" job to represent all mapped jobs.
             representative_assoc = cja[0]
             representative_job = representative_assoc.job
-            if representative_job not in self.jobs or self.jobs[representative_job][0][1].history_content_type == "dataset":
+            if (
+                representative_job not in self.jobs
+                or self.jobs[representative_job][0][1].history_content_type == "dataset"
+            ):
                 self.jobs[representative_job] = [(representative_assoc.name, dataset_collection)]
                 if dataset_collection.implicit_output_name:
                     self.implicit_map_jobs.append(representative_job)
@@ -289,7 +322,9 @@ class WorkflowSummary:
 
             original_hda = self.__original_hda(dataset_instance)
             if not original_hda.creating_job_associations:
-                log.warning("An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!")
+                log.warning(
+                    "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!"
+                )
                 job = DatasetCollectionCreationJob(dataset_collection)
                 self.jobs[job] = [(None, dataset_collection)]
 
@@ -337,7 +372,7 @@ class WorkflowSummary:
 
     def __check_state(self, hda):
         # FIXME: Create "Dataset.is_finished"
-        if hda.state in ('new', 'running', 'queued'):
+        if hda.state in ("new", "running", "queued"):
             self.warnings.add(WARNING_SOME_DATASETS_NOT_READY)
             return
         return hda
@@ -345,7 +380,9 @@ class WorkflowSummary:
 
 def step_inputs(trans, job):
     tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version)
-    param_values = job.get_param_values(trans.app, ignore_errors=True)  # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
+    param_values = job.get_param_values(
+        trans.app, ignore_errors=True
+    )  # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
     associations = __cleanup_param_values(tool.inputs, param_values)
     tool_inputs = tool.params_to_strings(param_values, trans.app)
     return tool_inputs, associations
@@ -358,8 +395,8 @@ def __cleanup_param_values(inputs, values):
     """
     associations = []
     # dbkey is pushed in by the framework
-    if 'dbkey' in values:
-        del values['dbkey']
+    if "dbkey" in values:
+        del values["dbkey"]
     root_values = values
     root_input_keys = inputs.keys()
 
@@ -389,25 +426,26 @@ def __cleanup_param_values(inputs, values):
                 if key in values:
                     group_values = values[key]
                     for i, rep_values in enumerate(group_values):
-                        rep_index = rep_values['__index__']
+                        rep_index = rep_values["__index__"]
                         cleanup("%s%s_%d|" % (prefix, key, rep_index), input.inputs, group_values[i])
             elif isinstance(input, Conditional):
                 # Scrub dynamic resource related parameters from workflows,
                 # they cause problems and the workflow probably should include
                 # their state in workflow encoding.
-                if input.name == '__job_resource':
+                if input.name == "__job_resource":
                     if input.name in values:
                         del values[input.name]
                     return
                 if input.name in values:
                     group_values = values[input.name]
-                    current_case = group_values['__current_case__']
+                    current_case = group_values["__current_case__"]
                     cleanup(f"{prefix}{key}|", input.cases[current_case].inputs, group_values)
             elif isinstance(input, Section):
                 if input.name in values:
                     cleanup(f"{prefix}{key}|", input.inputs, values[input.name])
+
     cleanup("", inputs, values)
     return associations
 
 
-__all__ = ('summarize', 'extract_workflow')
+__all__ = ("summarize", "extract_workflow")
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index f3843e3c916..216c5f34c14 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -5,7 +5,14 @@ import json
 import logging
 import re
 from collections import defaultdict
-from typing import Any, cast, Dict, List, Optional, Union
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
 
 import packaging.version
 from typing_extensions import TypedDict
@@ -13,11 +20,14 @@ from typing_extensions import TypedDict
 from galaxy import (
     exceptions,
     model,
-    web
+    web,
 )
 from galaxy.exceptions import ToolMissingException
 from galaxy.job_execution.actions.post import ActionBox
-from galaxy.model import PostJobAction, Workflow
+from galaxy.model import (
+    PostJobAction,
+    Workflow,
+)
 from galaxy.model.dataset_collections import matching
 from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
 from galaxy.tools import (
@@ -27,11 +37,15 @@ from galaxy.tools import (
     WORKFLOW_SAFE_TOOL_VERSION_UPDATES,
 )
 from galaxy.tools.actions import filter_output
-from galaxy.tools.execute import execute, MappingParameters, PartialJobExecution
+from galaxy.tools.execute import (
+    execute,
+    MappingParameters,
+    PartialJobExecution,
+)
 from galaxy.tools.parameters import (
     check_param,
     params_to_incoming,
-    visit_input_values
+    visit_input_values,
 )
 from galaxy.tools.parameters.basic import (
     BaseDataToolParameter,
@@ -48,7 +62,7 @@ from galaxy.tools.parameters.basic import (
     runtime_to_json,
     SelectToolParameter,
     TextToolParameter,
-    workflow_building_modes
+    workflow_building_modes,
 )
 from galaxy.tools.parameters.grouping import (
     Conditional,
@@ -56,7 +70,10 @@ from galaxy.tools.parameters.grouping import (
 )
 from galaxy.tools.parameters.history_query import HistoryQuery
 from galaxy.tools.parameters.wrapped import make_dict_copy
-from galaxy.util import listify, unicodify
+from galaxy.util import (
+    listify,
+    unicodify,
+)
 from galaxy.util.bunch import Bunch
 from galaxy.util.json import safe_loads
 from galaxy.util.rules_dsl import RuleSet
@@ -74,7 +91,6 @@ RUNTIME_POST_JOB_ACTIONS_KEY = "__POST_JOB_ACTIONS__"
 
 
 class NoReplacement:
-
     def __str__(self):
         return "NO_REPLACEMENT singleton"
 
@@ -128,18 +144,18 @@ class WorkflowModule:
         return None
 
     def get_content_id(self):
-        """ If this component has an identifier external to the step (such
+        """If this component has an identifier external to the step (such
         as a tool or another workflow) return the identifier for that content.
         """
         return None
 
-    def get_tooltip(self, static_path=''):
+    def get_tooltip(self, static_path=""):
         return None
 
     # ---- Configuration time -----------------------------------------------
 
     def get_state(self, nested=True):
-        """ Return a serializable representation of the persistable state of
+        """Return a serializable representation of the persistable state of
         the step.
         """
         inputs = self.get_inputs()
@@ -186,18 +202,18 @@ class WorkflowModule:
         return state
 
     def get_errors(self, **kwargs):
-        """ This returns a step related error message as string or None """
+        """This returns a step related error message as string or None"""
         return None
 
     def get_inputs(self):
-        """ This returns inputs displayed in the workflow editor """
+        """This returns inputs displayed in the workflow editor"""
         return {}
 
     def get_all_inputs(self, data_only=False, connectable_only=False):
         return []
 
     def get_data_inputs(self):
-        """ Get configure time data input descriptions. """
+        """Get configure time data input descriptions."""
         return self.get_all_inputs(data_only=True)
 
     def get_all_outputs(self, data_only=False):
@@ -216,14 +232,11 @@ class WorkflowModule:
         """
 
     def add_dummy_datasets(self, connections=None, steps=None):
-        """ Replace connected inputs with placeholder/dummy values. """
+        """Replace connected inputs with placeholder/dummy values."""
 
     def get_config_form(self, step=None):
-        """ Serializes input parameters of a module into input dictionaries. """
-        return {
-            'title': self.name,
-            'inputs': [param.to_dict(self.trans) for param in self.get_inputs().values()]
-        }
+        """Serializes input parameters of a module into input dictionaries."""
+        return {"title": self.name, "inputs": [param.to_dict(self.trans) for param in self.get_inputs().values()]}
 
     # ---- Run time ---------------------------------------------------------
 
@@ -231,13 +244,13 @@ class WorkflowModule:
         raise TypeError("Abstract method")
 
     def get_runtime_inputs(self, **kwds):
-        """ Used internally by modules and when displaying inputs in workflow
+        """Used internally by modules and when displaying inputs in workflow
         editor and run workflow templates.
         """
         return {}
 
     def compute_runtime_state(self, trans, step=None, step_updates=None):
-        """ Determine the runtime state (potentially different from self.state
+        """Determine the runtime state (potentially different from self.state
         which describes configuration state). This (again unlike self.state) is
         currently always a `DefaultToolState` object.
 
@@ -266,7 +279,9 @@ class WorkflowModule:
 
                 return NO_REPLACEMENT
 
-            visit_input_values(self.get_runtime_inputs(), state.inputs, update_value, no_replacement_value=NO_REPLACEMENT)
+            visit_input_values(
+                self.get_runtime_inputs(), state.inputs, update_value, no_replacement_value=NO_REPLACEMENT
+            )
 
         if step_updates:
 
@@ -278,22 +293,24 @@ class WorkflowModule:
                     return value
                 return NO_REPLACEMENT
 
-            visit_input_values(self.get_runtime_inputs(), state.inputs, update_value, no_replacement_value=NO_REPLACEMENT)
+            visit_input_values(
+                self.get_runtime_inputs(), state.inputs, update_value, no_replacement_value=NO_REPLACEMENT
+            )
 
         return state, step_errors
 
     def encode_runtime_state(self, runtime_state):
-        """ Takes the computed runtime state and serializes it during run request creation. """
+        """Takes the computed runtime state and serializes it during run request creation."""
         return runtime_state.encode(Bunch(inputs=self.get_runtime_inputs()), self.trans.app)
 
     def decode_runtime_state(self, runtime_state):
-        """ Takes the serialized runtime state and decodes it when running the workflow. """
+        """Takes the serialized runtime state and decodes it when running the workflow."""
         state = DefaultToolState()
         state.decode(runtime_state, Bunch(inputs=self.get_runtime_inputs()), self.trans.app)
         return state
 
     def execute(self, trans, progress, invocation_step, use_cached_job=False):
-        """ Execute the given workflow invocation step.
+        """Execute the given workflow invocation step.
 
         Use the supplied workflow progress object to track outputs, find
         inputs, etc....
@@ -305,16 +322,18 @@ class WorkflowModule:
         raise TypeError("Abstract method")
 
     def do_invocation_step_action(self, step, action):
-        """ Update or set the workflow invocation state action - generic
+        """Update or set the workflow invocation state action - generic
         extension point meant to allows users to interact with interactive
         workflow modules. The action object returned from this method will
         be attached to the WorkflowInvocationStep and be available the next
         time the workflow scheduler visits the workflow.
         """
-        raise exceptions.RequestParameterInvalidException("Attempting to perform invocation step action on module that does not support actions.")
+        raise exceptions.RequestParameterInvalidException(
+            "Attempting to perform invocation step action on module that does not support actions."
+        )
 
     def recover_mapping(self, invocation_step, progress):
-        """ Re-populate progress object with information about connections
+        """Re-populate progress object with information about connections
         from previously executed steps recorded via invocation_steps.
         """
         outputs = {}
@@ -338,14 +357,10 @@ class WorkflowModule:
         Hopefully this can be reused for Tool and Subworkflow modules.
         """
 
-        collections_to_match = self._find_collections_to_match(
-            progress, step, all_inputs
-        )
+        collections_to_match = self._find_collections_to_match(progress, step, all_inputs)
         # Have implicit collections...
         if collections_to_match.has_collections():
-            collection_info = self.trans.app.dataset_collection_manager.match_collections(
-                collections_to_match
-            )
+            collection_info = self.trans.app.dataset_collection_manager.match_collections(collections_to_match)
         else:
             collection_info = None
 
@@ -370,7 +385,7 @@ class WorkflowModule:
                     # multiple="true" data input, acts like "list" collection_type.
                     # just need to figure out subcollection_type_description
                     history_query = HistoryQuery.from_collection_types(
-                        ['list'],
+                        ["list"],
                         dataset_collection_type_descriptions,
                     )
                     subcollection_type_description = history_query.can_map_over(data)
@@ -388,7 +403,9 @@ class WorkflowModule:
                 )
                 subcollection_type_description = history_query.can_map_over(data)
                 if subcollection_type_description:
-                    collections_to_match.add(name, data, subcollection_type=subcollection_type_description.collection_type)
+                    collections_to_match.add(
+                        name, data, subcollection_type=subcollection_type_description.collection_type
+                    )
                 continue
 
             if data is not NO_REPLACEMENT:
@@ -431,15 +448,15 @@ class SubWorkflowModule(WorkflowModule):
         step.subworkflow = self.subworkflow
 
     def get_name(self):
-        if hasattr(self.subworkflow, 'name'):
+        if hasattr(self.subworkflow, "name"):
             return self.subworkflow.name
         return self.name
 
     def get_all_inputs(self, data_only=False, connectable_only=False):
-        """ Get configure time data input descriptions. """
+        """Get configure time data input descriptions."""
         # Filter subworkflow steps and get inputs
         inputs = []
-        if hasattr(self.subworkflow, 'input_steps'):
+        if hasattr(self.subworkflow, "input_steps"):
             for step in self.subworkflow.input_steps:
                 name = step.label
                 if not name:
@@ -454,11 +471,11 @@ class SubWorkflowModule(WorkflowModule):
                     input_type=step.input_type,
                 )
                 step_type = step.type
-                if step_type == 'data_collection_input':
-                    input['collection_type'] = step.tool_inputs.get('collection_type') if step.tool_inputs else None
-                if step_type == 'parameter_input':
-                    input['type'] = step.tool_inputs['parameter_type']
-                input['optional'] = step.tool_inputs.get('optional', False)
+                if step_type == "data_collection_input":
+                    input["collection_type"] = step.tool_inputs.get("collection_type") if step.tool_inputs else None
+                if step_type == "parameter_input":
+                    input["type"] = step.tool_inputs["parameter_type"]
+                input["optional"] = step.tool_inputs.get("optional", False)
                 inputs.append(input)
         return inputs
 
@@ -471,7 +488,7 @@ class SubWorkflowModule(WorkflowModule):
     def version_changes(self):
         version_changes = []
         for m in self.get_modules():
-            if hasattr(m, 'version_changes'):
+            if hasattr(m, "version_changes"):
                 version_changes.extend(m.version_changes)
         return version_changes
 
@@ -481,9 +498,7 @@ class SubWorkflowModule(WorkflowModule):
         return {f"Step {i + 1}": upgrade_message for i, upgrade_message in enumerate(states) if upgrade_message} or None
 
     def get_errors(self, **kwargs):
-        errors1 = (
-            module.get_errors(include_tool_id=True) for module in self.get_modules()
-        )
+        errors1 = (module.get_errors(include_tool_id=True) for module in self.get_modules())
         errors2 = [e for e in errors1 if e]
         if any(errors2):
             return errors2
@@ -491,33 +506,41 @@ class SubWorkflowModule(WorkflowModule):
 
     def get_all_outputs(self, data_only=False):
         outputs = []
-        if hasattr(self.subworkflow, 'workflow_outputs'):
+        if hasattr(self.subworkflow, "workflow_outputs"):
             from galaxy.managers.workflows import WorkflowContentsManager
+
             workflow_contents_manager = WorkflowContentsManager(self.trans.app)
-            subworkflow_dict = workflow_contents_manager._workflow_to_dict_editor(trans=self.trans,
-                                                                                  stored=self.subworkflow.stored_workflow,
-                                                                                  workflow=self.subworkflow,
-                                                                                  tooltip=False,
-                                                                                  is_subworkflow=True)
-            for order_index in sorted(subworkflow_dict['steps']):
-                step = subworkflow_dict['steps'][order_index]
-                data_outputs = step['outputs']
-                for workflow_output in step['workflow_outputs']:
-                    label = workflow_output['label']
+            subworkflow_dict = workflow_contents_manager._workflow_to_dict_editor(
+                trans=self.trans,
+                stored=self.subworkflow.stored_workflow,
+                workflow=self.subworkflow,
+                tooltip=False,
+                is_subworkflow=True,
+            )
+            for order_index in sorted(subworkflow_dict["steps"]):
+                step = subworkflow_dict["steps"][order_index]
+                data_outputs = step["outputs"]
+                for workflow_output in step["workflow_outputs"]:
+                    label = workflow_output["label"]
                     if not label:
                         label = f"{order_index}:{workflow_output['output_name']}"
-                    workflow_output_uuid = workflow_output.get('uuid') or object()
+                    workflow_output_uuid = workflow_output.get("uuid") or object()
                     for data_output in data_outputs:
-                        data_output_uuid = data_output.get('uuid') or object()
-                        if data_output['name'] == workflow_output['output_name'] or data_output_uuid == workflow_output_uuid:
-                            data_output['name'] = label
+                        data_output_uuid = data_output.get("uuid") or object()
+                        if (
+                            data_output["name"] == workflow_output["output_name"]
+                            or data_output_uuid == workflow_output_uuid
+                        ):
+                            data_output["name"] = label
                             # That's the right data_output
                             break
                     else:
                         # This can happen when importing workflows with missing tools.
                         # We can't raise an exception here, as that would prevent loading
                         # the workflow.
-                        log.error(f"Workflow output '{workflow_output['output_name']}' defined, but not listed among data outputs")
+                        log.error(
+                            f"Workflow output '{workflow_output['output_name']}' defined, but not listed among data outputs"
+                        )
                         continue
                     outputs.append(data_output)
         return outputs
@@ -526,7 +549,7 @@ class SubWorkflowModule(WorkflowModule):
         return self.trans.security.encode_id(self.subworkflow.id)
 
     def execute(self, trans, progress, invocation_step, use_cached_job=False):
-        """ Execute the given workflow step in the given workflow invocation.
+        """Execute the given workflow step in the given workflow invocation.
         Use the supplied workflow progress object to track outputs, find
         inputs, etc...
         """
@@ -537,7 +560,9 @@ class SubWorkflowModule(WorkflowModule):
         subworkflow_progress = subworkflow_invoker.progress
         outputs = {}
         for workflow_output in subworkflow.workflow_outputs:
-            workflow_output_label = workflow_output.label or f"{workflow_output.workflow_step.order_index}:{workflow_output.output_name}"
+            workflow_output_label = (
+                workflow_output.label or f"{workflow_output.workflow_step.order_index}:{workflow_output.output_name}"
+            )
             replacement = subworkflow_progress.get_replacement_workflow_output(workflow_output)
             outputs[workflow_output_label] = replacement
         progress.set_step_outputs(invocation_step, outputs)
@@ -558,7 +583,7 @@ class SubWorkflowModule(WorkflowModule):
                 def callback(input, prefixed_name, prefixed_label, value=None, **kwds):
                     # All data parameters are represented as runtime values, skip them
                     # here.
-                    if input.type in ['data', 'data_collection']:
+                    if input.type in ["data", "data_collection"]:
                         return
 
                     if is_runtime_value(value) and runtime_to_json(value)["__class__"] != "ConnectedValue":
@@ -609,7 +634,15 @@ def optional_param(optional):
 
 def format_param(trans, formats):
     formats_val = "" if not formats else ",".join(formats)
-    source = dict(type="text", label="Format(s)", name="format", value=formats_val, optional=True, options=formats, help="Leave empty to auto-generate filtered list at runtime based on connections.")
+    source = dict(
+        type="text",
+        label="Format(s)",
+        name="format",
+        value=formats_val,
+        optional=True,
+        options=formats,
+        help="Leave empty to auto-generate filtered list at runtime based on connections.",
+    )
     source["options"] = [{"value": v, "label": v} for v in trans.app.datatypes_registry.datatypes_by_extension.keys()]
     format_value = TextToolParameter(None, source)
     return format_value
@@ -635,7 +668,7 @@ class InputModule(WorkflowModule):
     def execute(self, trans, progress, invocation_step, use_cached_job=False):
         invocation = invocation_step.workflow_invocation
         step = invocation_step.workflow_step
-        step_outputs = dict(output=step.state.inputs['input'])
+        step_outputs = dict(output=step.state.inputs["input"])
 
         # Web controller may set copy_inputs_to_history, API controller always sets
         # inputs.
@@ -645,11 +678,11 @@ class InputModule(WorkflowModule):
                 if content_type == "dataset":
                     new_hda = input_dataset_hda.copy()
                     invocation.history.add_dataset(new_hda)
-                    step_outputs['input_ds_copy'] = new_hda
+                    step_outputs["input_ds_copy"] = new_hda
                 elif content_type == "dataset_collection":
                     new_hdca = input_dataset_hda.copy()
                     invocation.history.add_dataset_collection(new_hdca)
-                    step_outputs['input_ds_copy'] = new_hdca
+                    step_outputs["input_ds_copy"] = new_hdca
                 else:
                     raise Exception("Unknown history content encountered")
         # If coming from UI - we haven't registered invocation inputs yet,
@@ -712,21 +745,21 @@ class InputDataModule(InputModule):
         format_def = parameter_def.get("format")
         optional = parameter_def["optional"]
         if format_def is None:
-            extensions = ['input']
+            extensions = ["input"]
         else:
             extensions = listify(format_def)
-        return [dict(name='output', extensions=extensions, optional=optional)]
+        return [dict(name="output", extensions=extensions, optional=optional)]
 
     def get_filter_set(self, connections=None):
         filter_set = []
         if connections:
             for oc in connections:
                 for ic in oc.input_step.module.get_data_inputs():
-                    if 'extensions' in ic and ic['extensions'] != 'input' and ic['name'] == oc.input_name:
-                        filter_set += ic['extensions']
+                    if "extensions" in ic and ic["extensions"] != "input" and ic["name"] == oc.input_name:
+                        filter_set += ic["extensions"]
         if not filter_set:
-            filter_set = ['data']
-        return ', '.join(filter_set)
+            filter_set = ["data"]
+        return ", ".join(filter_set)
 
     def get_runtime_inputs(self, connections=None):
         parameter_def = self._parse_state_into_dict()
@@ -737,14 +770,18 @@ class InputDataModule(InputModule):
             formats = self.get_filter_set(connections)
         else:
             formats = ",".join(listify(formats))
-        data_src = dict(name="input", label=self.label, multiple=False, type="data", format=formats, tag=tag, optional=optional)
+        data_src = dict(
+            name="input", label=self.label, multiple=False, type="data", format=formats, tag=tag, optional=optional
+        )
         input_param = DataToolParameter(None, data_src, self.trans)
         return dict(input=input_param)
 
     def get_inputs(self):
         parameter_def = self._parse_state_into_dict()
         tag = parameter_def["tag"]
-        tag_source = dict(name="tag", label="Tag filter", type="text", value=tag, help="Tags to automatically filter inputs")
+        tag_source = dict(
+            name="tag", label="Tag filter", type="text", value=tag, help="Tags to automatically filter inputs"
+        )
         input_tag = TextToolParameter(None, tag_source)
         optional = parameter_def["optional"]
         inputs = {}
@@ -765,14 +802,18 @@ class InputDataCollectionModule(InputModule):
         collection_type = parameter_def["collection_type"]
         tag = parameter_def["tag"]
         optional = parameter_def["optional"]
-        collection_type_source = dict(name="collection_type", label="Collection type", type="text", value=collection_type)
+        collection_type_source = dict(
+            name="collection_type", label="Collection type", type="text", value=collection_type
+        )
         collection_type_source["options"] = [
             {"value": "list", "label": "List of Datasets"},
             {"value": "paired", "label": "Dataset Pair"},
             {"value": "list:paired", "label": "List of Dataset Pairs"},
         ]
         input_collection_type = TextToolParameter(None, collection_type_source)
-        tag_source = dict(name="tag", label="Tag filter", type="text", value=tag, help="Tags to automatically filter inputs")
+        tag_source = dict(
+            name="tag", label="Tag filter", type="text", value=tag, help="Tags to automatically filter inputs"
+        )
         input_tag = TextToolParameter(None, tag_source)
         inputs = {}
         inputs["collection_type"] = input_collection_type
@@ -787,7 +828,14 @@ class InputDataCollectionModule(InputModule):
         optional = parameter_def["optional"]
         tag = parameter_def["tag"]
         formats = parameter_def.get("format")
-        collection_param_source = dict(name="input", label=self.label, type="data_collection", collection_type=collection_type, tag=tag, optional=optional)
+        collection_param_source = dict(
+            name="input",
+            label=self.label,
+            type="data_collection",
+            collection_type=collection_type,
+            tag=tag,
+            optional=optional,
+        )
         if formats:
             collection_param_source["format"] = ",".join(listify(formats))
         input_param = DataCollectionToolParameter(None, collection_param_source, self.trans)
@@ -798,15 +846,15 @@ class InputDataCollectionModule(InputModule):
         format_def = parameter_def.get("format")
         optional = parameter_def["optional"]
         if format_def is None:
-            extensions = ['input']
+            extensions = ["input"]
         else:
             extensions = listify(format_def)
         return [
             dict(
-                name='output',
+                name="output",
                 extensions=extensions,
                 collection=True,
-                collection_type=parameter_def.get('collection_type', self.default_collection_type),
+                collection_type=parameter_def.get("collection_type", self.default_collection_type),
                 optional=optional,
             )
         ]
@@ -828,7 +876,7 @@ class InputParameterModule(WorkflowModule):
     name = "Input parameter"
     default_parameter_type = "text"
     default_optional = False
-    default_default_value = ''
+    default_default_value = ""
     parameter_type = default_parameter_type
     optional = default_optional
     default_value = default_default_value
@@ -917,7 +965,9 @@ class InputParameterModule(WorkflowModule):
             when_this_type.inputs["optional"] = optional_cond
 
             specify_default_checked = "default" in parameter_def
-            specify_default_source = dict(name="specify_default", label="Specify a default value", type="boolean", checked=specify_default_checked)
+            specify_default_source = dict(
+                name="specify_default", label="Specify a default value", type="boolean", checked=specify_default_checked
+            )
             specify_default = BooleanToolParameter(None, specify_default_source)
             specify_default_cond = Conditional()
             specify_default_cond.name = "specify_default"
@@ -948,9 +998,9 @@ class InputParameterModule(WorkflowModule):
             optional_cond.cases = optional_cases
 
             if param_type == "text":
-                restrict_how_source: Dict[
-                    str, Union[str, List[Dict[str, Union[str, bool]]]]
-                ] = dict(name="how", label="Restrict Text Values?", type="select")
+                restrict_how_source: Dict[str, Union[str, List[Dict[str, Union[str, bool]]]]] = dict(
+                    name="how", label="Restrict Text Values?", type="select"
+                )
                 if parameter_def.get("restrictions") is not None:
                     restrict_how_value = "staticRestrictions"
                 elif parameter_def.get("restrictOnConnections") is True:
@@ -960,10 +1010,26 @@ class InputParameterModule(WorkflowModule):
                 else:
                     restrict_how_value = "none"
                 restrict_how_source["options"] = [
-                    {"value": "none", "label": "Do not specify restrictions (default).", "selected": restrict_how_value == "none"},
-                    {"value": "onConnections", "label": "Attempt restriction based on connections.", "selected": restrict_how_value == "onConnections"},
-                    {"value": "staticRestrictions", "label": "Provide list of all possible values.", "selected": restrict_how_value == "staticRestrictions"},
-                    {"value": "staticSuggestions", "label": "Provide list of suggested values.", "selected": restrict_how_value == "staticSuggestions"},
+                    {
+                        "value": "none",
+                        "label": "Do not specify restrictions (default).",
+                        "selected": restrict_how_value == "none",
+                    },
+                    {
+                        "value": "onConnections",
+                        "label": "Attempt restriction based on connections.",
+                        "selected": restrict_how_value == "onConnections",
+                    },
+                    {
+                        "value": "staticRestrictions",
+                        "label": "Provide list of all possible values.",
+                        "selected": restrict_how_value == "staticRestrictions",
+                    },
+                    {
+                        "value": "staticSuggestions",
+                        "label": "Provide list of suggested values.",
+                        "selected": restrict_how_value == "staticSuggestions",
+                    },
                 ]
                 restrictions_cond = Conditional()
                 restrictions_how = SelectToolParameter(None, restrict_how_source)
@@ -993,16 +1059,31 @@ class InputParameterModule(WorkflowModule):
                 if restrictions_list is None:
                     restrictions_list = []
                 restriction_values = self._parameter_option_def_to_tool_form_str(restrictions_list)
-                restrictions_source = dict(name="restrictions", label="Restricted Values", value=restriction_values, help="Comma-separated list of all permitted values")
+                restrictions_source = dict(
+                    name="restrictions",
+                    label="Restricted Values",
+                    value=restriction_values,
+                    help="Comma-separated list of all permitted values",
+                )
                 restrictions = TextToolParameter(None, restrictions_source)
 
-                suggestions_source = dict(name="suggestions", label="Suggested Values", value=restriction_values, help="Comma-separated list of some potential values")
+                suggestions_source = dict(
+                    name="suggestions",
+                    label="Suggested Values",
+                    value=restriction_values,
+                    help="Comma-separated list of some potential values",
+                )
                 suggestions = TextToolParameter(None, suggestions_source)
 
                 when_restrict_static_restrictions.inputs["restrictions"] = restrictions
                 when_restrict_static_suggestions.inputs["suggestions"] = suggestions
 
-                restrictions_cond_cases = [when_restrict_none, when_restrict_connections, when_restrict_static_restrictions, when_restrict_static_suggestions]
+                restrictions_cond_cases = [
+                    when_restrict_none,
+                    when_restrict_connections,
+                    when_restrict_static_restrictions,
+                    when_restrict_static_suggestions,
+                ]
                 restrictions_cond.cases = restrictions_cond_cases
                 when_this_type.inputs["restrictions"] = restrictions_cond
 
@@ -1037,8 +1118,9 @@ class InputParameterModule(WorkflowModule):
                     tool_inputs = module.tool.inputs  # may not be set, but we're catching the Exception below.
 
                     def callback(input, prefixed_name, context, **kwargs):
-                        if prefixed_name == connection.input_name and hasattr(input, 'get_options'):
+                        if prefixed_name == connection.input_name and hasattr(input, "get_options"):
                             static_options.append(input.get_options(self.trans, {}))
+
                     visit_input_values(tool_inputs, module.state.inputs, callback)
 
                 options = None
@@ -1052,7 +1134,9 @@ class InputParameterModule(WorkflowModule):
                     d = defaultdict(set)  # Collapse labels with same values
                     for label, value, _ in intxn_opts:
                         d[value].add(label)
-                    options = [{"label": ', '.join(label), "value": value, "selected": False} for value, label in d.items()]
+                    options = [
+                        {"label": ", ".join(label), "value": value, "selected": False} for value, label in d.items()
+                    ]
 
                 if options is not None:
                     parameter_kwds["options"] = options
@@ -1091,8 +1175,8 @@ class InputParameterModule(WorkflowModule):
         if optional:
             default_value = parameter_def.get("default", self.default_default_value)
             parameter_kwds["value"] = default_value
-            if parameter_type == 'boolean':
-                parameter_kwds['checked'] = default_value
+            if parameter_type == "boolean":
+                parameter_kwds["checked"] = default_value
 
         if "value" not in parameter_kwds and parameter_type in ["integer", "float"]:
             parameter_kwds["value"] = str(0)
@@ -1101,7 +1185,9 @@ class InputParameterModule(WorkflowModule):
             suggestion_values = parameter_def.get("suggestions")
             parameter_kwds["options"] = _parameter_def_list_to_options(suggestion_values)
 
-        input_source = dict(name="input", label=self.label, type=client_parameter_type, optional=optional, **parameter_kwds)
+        input_source = dict(
+            name="input", label=self.label, type=client_parameter_type, optional=optional, **parameter_kwds
+        )
         input = parameter_class(None, input_source)
         return dict(input=input)
 
@@ -1115,17 +1201,19 @@ class InputParameterModule(WorkflowModule):
             return []
 
         parameter_def = self._parse_state_into_dict()
-        return [dict(
-            name='output',
-            label=self.label,
-            type=parameter_def.get('parameter_type'),
-            optional=parameter_def['optional'],
-            parameter=True,
-        )]
+        return [
+            dict(
+                name="output",
+                label=self.label,
+                type=parameter_def.get("parameter_type"),
+                optional=parameter_def["optional"],
+                parameter=True,
+            )
+        ]
 
     def execute(self, trans, progress, invocation_step, use_cached_job=False):
         step = invocation_step.workflow_step
-        input_value = step.state.inputs['input']
+        input_value = step.state.inputs["input"]
         if input_value is None:
             default_value = safe_loads(step.tool_inputs.get("default", "{}"))
             # TODO: look at parameter type and infer if value should be a dictionary
@@ -1158,18 +1246,20 @@ class InputParameterModule(WorkflowModule):
         state = {
             "parameter_definition": {
                 "parameter_type": state["parameter_type"],
-                "optional": {
-                    "optional": str(state.get("optional", False))
-                }
+                "optional": {"optional": str(state.get("optional", False))},
             }
         }
         state["parameter_definition"]["restrictions"] = {}
         state["parameter_definition"]["restrictions"]["how"] = restrictions_how
 
         if restrictions_how == "staticRestrictions":
-            state["parameter_definition"]["restrictions"]["restrictions"] = self._parameter_option_def_to_tool_form_str(restrictions)
+            state["parameter_definition"]["restrictions"]["restrictions"] = self._parameter_option_def_to_tool_form_str(
+                restrictions
+            )
         if restrictions_how == "staticSuggestions":
-            state["parameter_definition"]["restrictions"]["suggestions"] = self._parameter_option_def_to_tool_form_str(suggestions)
+            state["parameter_definition"]["restrictions"]["suggestions"] = self._parameter_option_def_to_tool_form_str(
+                suggestions
+            )
         if default_set:
             state["parameter_definition"]["optional"]["specify_default"] = {}
             state["parameter_definition"]["optional"]["specify_default"]["specify_default"] = True
@@ -1240,9 +1330,10 @@ class InputParameterModule(WorkflowModule):
 
 
 class PauseModule(WorkflowModule):
-    """ Initially this module will unconditionally pause a workflow - will aim
+    """Initially this module will unconditionally pause a workflow - will aim
     to allow conditional pausing later on.
     """
+
     type = "pause"
     name = "Pause for dataset review"
 
@@ -1251,13 +1342,13 @@ class PauseModule(WorkflowModule):
             name="input",
             label="Dataset for Review",
             multiple=False,
-            extensions='input',
+            extensions="input",
             input_type="dataset",
         )
         return [input] if not data_only else []
 
     def get_all_outputs(self, data_only=False):
-        return [dict(name="output", label="Reviewed Dataset", extensions=['input'])]
+        return [dict(name="output", label="Reviewed Dataset", extensions=["input"])]
 
     def get_runtime_state(self):
         state = DefaultToolState()
@@ -1275,7 +1366,7 @@ class PauseModule(WorkflowModule):
             if action:
                 connection = step.input_connections_by_name["input"][0]
                 replacement = progress.replacement_for_connection(connection)
-                progress.set_step_outputs(invocation_step, {'output': replacement})
+                progress.set_step_outputs(invocation_step, {"output": replacement})
                 return
             elif action is False:
                 raise CancelWorkflowEvaluation()
@@ -1283,7 +1374,7 @@ class PauseModule(WorkflowModule):
         raise DelayedWorkflowEvaluation(why=delayed_why)
 
     def do_invocation_step_action(self, step, action):
-        """ Update or set the workflow invocation state action - generic
+        """Update or set the workflow invocation state action - generic
         extension point meant to allows users to interact with interactive
         workflow modules. The action object returned from this method will
         be attached to the WorkflowInvocationStep and be available the next
@@ -1302,7 +1393,9 @@ class ToolModule(WorkflowModule):
         self.tool_id = tool_id
         self.tool_version = str(tool_version) if tool_version else None
         self.tool_uuid = tool_uuid
-        self.tool = trans.app.toolbox.get_tool(tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid)
+        self.tool = trans.app.toolbox.get_tool(
+            tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid
+        )
         if self.tool:
             current_tool_id = self.tool.id
             current_tool_version = str(self.tool.version)
@@ -1312,12 +1405,20 @@ class ToolModule(WorkflowModule):
                 if safe_version and self.tool.lineage:
                     # tool versions are sorted from old to new, so check newest version first
                     for lineage_version in reversed(self.tool.lineage.tool_versions):
-                        if safe_version.current_version >= packaging.version.parse(lineage_version) >= safe_version.min_version:
-                            self.tool = trans.app.toolbox.get_tool(tool_id, tool_version=lineage_version, exact=True, tool_uuid=tool_uuid)
+                        if (
+                            safe_version.current_version
+                            >= packaging.version.parse(lineage_version)
+                            >= safe_version.min_version
+                        ):
+                            self.tool = trans.app.toolbox.get_tool(
+                                tool_id, tool_version=lineage_version, exact=True, tool_uuid=tool_uuid
+                            )
                             safe_version_found = True
                             break
                 if not safe_version_found:
-                    log.info(f"Exact tool specified during workflow module creation for [{tool_id}] but couldn't find correct version [{tool_version}].")
+                    log.info(
+                        f"Exact tool specified during workflow module creation for [{tool_id}] but couldn't find correct version [{tool_version}]."
+                    )
                     self.tool = None
         self.post_job_actions = {}
         self.runtime_post_job_actions = {}
@@ -1328,11 +1429,11 @@ class ToolModule(WorkflowModule):
 
     @classmethod
     def from_dict(Class, trans, d, **kwds):
-        tool_id = d.get('content_id') or d.get('tool_id')
-        tool_version = d.get('tool_version')
+        tool_id = d.get("content_id") or d.get("tool_id")
+        tool_version = d.get("tool_version")
         if tool_version:
             tool_version = str(tool_version)
-        tool_uuid = d.get('tool_uuid', None)
+        tool_uuid = d.get("tool_uuid", None)
         if tool_id is None and tool_uuid is None:
             tool_representation = d.get("tool_representation")
             if tool_representation:
@@ -1341,20 +1442,18 @@ class ToolModule(WorkflowModule):
                 }
                 if not trans.user_is_admin:
                     raise exceptions.AdminRequiredException("Only admin users can create tools dynamically.")
-                dynamic_tool = trans.app.dynamic_tool_manager.create_tool(
-                    trans, create_request, allow_load=False
-                )
+                dynamic_tool = trans.app.dynamic_tool_manager.create_tool(trans, create_request, allow_load=False)
                 tool_uuid = dynamic_tool.uuid
         if tool_id is None and tool_uuid is None:
             raise exceptions.RequestParameterInvalidException(f"No content id could be located for for step [{d}]")
         module = super().from_dict(trans, d, tool_id=tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds)
-        module.post_job_actions = d.get('post_job_actions', {})
-        module.workflow_outputs = d.get('workflow_outputs', [])
+        module.post_job_actions = d.get("post_job_actions", {})
+        module.workflow_outputs = d.get("workflow_outputs", [])
         if module.tool:
             message = ""
             if tool_id != module.tool_id:
                 message += f"The tool (id '{tool_id}') specified in this step is not available. Using the tool with id {module.tool_id} instead."
-            if d.get('tool_version', 'Unspecified') != module.get_version():
+            if d.get("tool_version", "Unspecified") != module.get_version():
                 message += f"{tool_id}: using version '{module.get_version()}' instead of version '{d.get('tool_version', 'Unspecified')}' specified in this workflow."
             if message:
                 log.debug(message)
@@ -1365,25 +1464,36 @@ class ToolModule(WorkflowModule):
     def from_workflow_step(Class, trans, step, **kwds):
         tool_version = step.tool_version
         tool_uuid = step.tool_uuid
-        kwds['exact_tools'] = False
-        module = super().from_workflow_step(trans, step, tool_id=step.tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds)
+        kwds["exact_tools"] = False
+        module = super().from_workflow_step(
+            trans, step, tool_id=step.tool_id, tool_version=tool_version, tool_uuid=tool_uuid, **kwds
+        )
         module.workflow_outputs = step.workflow_outputs
         module.post_job_actions = {}
         for pja in step.post_job_actions:
             module.post_job_actions[pja.action_type] = pja
         if module.tool:
             message = ""
-            if step.tool_id and step.tool_id != module.tool.id or step.tool_version and step.tool_version != module.tool.version:  # This means the exact version of the tool is not installed. We inform the user.
+            if (
+                step.tool_id
+                and step.tool_id != module.tool.id
+                or step.tool_version
+                and step.tool_version != module.tool.version
+            ):  # This means the exact version of the tool is not installed. We inform the user.
                 old_tool_shed = step.tool_id.split("/repos/")[0]
-                if old_tool_shed not in module.tool.id:  # Only display the following warning if the tool comes from a different tool shed
+                if (
+                    old_tool_shed not in module.tool.id
+                ):  # Only display the following warning if the tool comes from a different tool shed
                     old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed)
-                    if not old_tool_shed_url:  # a tool from a different tool_shed has been found, but the original tool shed has been deactivated
+                    if (
+                        not old_tool_shed_url
+                    ):  # a tool from a different tool_shed has been found, but the original tool shed has been deactivated
                         old_tool_shed_url = f"http://{old_tool_shed}"  # let's just assume it's either http, or a http is forwarded to https.
                     old_url = f"{old_tool_shed_url}/view/{module.tool.repository_owner}/{module.tool.repository_name}/"
                     new_url = f"{module.tool.sharable_url}/{module.tool.changeset_revision}/"
                     new_tool_shed_url = new_url.split("/view")[0]
-                    message += f"The tool \'{module.tool.name}\', version {tool_version} by the owner {module.tool.repository_owner} installed from <a href=\"{old_url}\" target=\"_blank\">{old_tool_shed_url}</a> is not available. "
-                    message += f"A derivation of this tool installed from <a href=\"{new_url}\" target=\"_blank\">{new_tool_shed_url}</a> will be used instead. "
+                    message += f'The tool \'{module.tool.name}\', version {tool_version} by the owner {module.tool.repository_owner} installed from <a href="{old_url}" target="_blank">{old_tool_shed_url}</a> is not available. '
+                    message += f'A derivation of this tool installed from <a href="{new_url}" target="_blank">{new_tool_shed_url}</a> will be used instead. '
             if step.tool_version and (step.tool_version != module.tool.version):
                 message += f"<span title=\"tool id '{step.tool_id}'\">Using version '{module.tool.version}' instead of version '{step.tool_version}' specified in this workflow. "
             if message:
@@ -1421,9 +1531,9 @@ class ToolModule(WorkflowModule):
     def get_version(self):
         return self.tool.version if self.tool else self.tool_version
 
-    def get_tooltip(self, static_path=''):
+    def get_tooltip(self, static_path=""):
         if self.tool and self.tool.help:
-            return self.tool.help.render(host_url=web.url_for('/'), static_path=static_path)
+            return self.tool.help.render(host_url=web.url_for("/"), static_path=static_path)
 
     # ---- Configuration time -----------------------------------------------
 
@@ -1445,7 +1555,7 @@ class ToolModule(WorkflowModule):
         if self.tool:
 
             def callback(input, prefixed_name, prefixed_label, value=None, **kwargs):
-                visible = not hasattr(input, 'hidden') or not input.hidden
+                visible = not hasattr(input, "hidden") or not input.hidden
                 input_type = input.type
                 is_data = isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter)
                 is_connectable = is_runtime_value(value) and runtime_to_json(value)["__class__"] == "ConnectedValue"
@@ -1459,23 +1569,28 @@ class ToolModule(WorkflowModule):
                     skip = not visible
                 if not skip:
                     if isinstance(input, DataToolParameter):
-                        inputs.append(dict(
-                            name=prefixed_name,
-                            label=prefixed_label,
-                            multiple=input.multiple,
-                            extensions=input.extensions,
-                            optional=input.optional,
-                            input_type="dataset", ))
+                        inputs.append(
+                            dict(
+                                name=prefixed_name,
+                                label=prefixed_label,
+                                multiple=input.multiple,
+                                extensions=input.extensions,
+                                optional=input.optional,
+                                input_type="dataset",
+                            )
+                        )
                     elif isinstance(input, DataCollectionToolParameter):
-                        inputs.append(dict(
-                            name=prefixed_name,
-                            label=prefixed_label,
-                            multiple=input.multiple,
-                            input_type="dataset_collection",
-                            collection_types=input.collection_types,
-                            optional=input.optional,
-                            extensions=input.extensions,
-                        ))
+                        inputs.append(
+                            dict(
+                                name=prefixed_name,
+                                label=prefixed_label,
+                                multiple=input.multiple,
+                                input_type="dataset_collection",
+                                collection_types=input.collection_types,
+                                optional=input.optional,
+                                extensions=input.extensions,
+                            )
+                        )
                     else:
                         inputs.append(
                             dict(
@@ -1499,7 +1614,7 @@ class ToolModule(WorkflowModule):
                     continue
                 extra_kwds = {}
                 if isinstance(tool_output, ToolExpressionOutput):
-                    extra_kwds['parameter'] = True
+                    extra_kwds["parameter"] = True
                 if tool_output.collection:
                     extra_kwds["collection"] = True
                     collection_type = tool_output.structure.collection_type
@@ -1512,34 +1627,28 @@ class ToolModule(WorkflowModule):
                                 collection_type = rule_set.collection_type
                     extra_kwds["collection_type"] = collection_type
                     extra_kwds["collection_type_source"] = tool_output.structure.collection_type_source
-                    formats = ['input']  # TODO: fix
+                    formats = ["input"]  # TODO: fix
                 elif tool_output.format_source is not None:
-                    formats = ['input']  # default to special name "input" which remove restrictions on connections
+                    formats = ["input"]  # default to special name "input" which remove restrictions on connections
                 else:
                     formats = [tool_output.format]
                 for change_elem in tool_output.change_format:
-                    for when_elem in change_elem.findall('when'):
-                        format = when_elem.get('format', None)
+                    for when_elem in change_elem.findall("when"):
+                        format = when_elem.get("format", None)
                         if format and format not in formats:
                             formats.append(format)
                 if tool_output.label:
                     try:
                         params = make_dict_copy(self.state.inputs)
-                        params['on_string'] = 'input dataset(s)'
-                        params['tool'] = self.tool
-                        extra_kwds['label'] = fill_template(tool_output.label,
-                                                            context=params,
-                                                            python_template_version=self.tool.python_template_version)
+                        params["on_string"] = "input dataset(s)"
+                        params["tool"] = self.tool
+                        extra_kwds["label"] = fill_template(
+                            tool_output.label, context=params, python_template_version=self.tool.python_template_version
+                        )
                     except Exception:
                         pass
                 data_outputs.append(
-                    dict(
-                        name=name,
-                        extensions=formats,
-                        type=tool_output.output_type,
-                        optional=False,
-                        **extra_kwds
-                    )
+                    dict(name=name, extensions=formats, type=tool_output.output_type, optional=False, **extra_kwds)
                 )
         return data_outputs
 
@@ -1565,15 +1674,24 @@ class ToolModule(WorkflowModule):
             # Any input needs to have value RuntimeValue or obtain the value from connected steps
             def callback(input, prefixed_name, context, **kwargs):
                 input_type = input.type
-                is_data = input_type in ['data', 'data_collection']
-                if is_data and connections is not None and steps is not None and self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY:
+                is_data = input_type in ["data", "data_collection"]
+                if (
+                    is_data
+                    and connections is not None
+                    and steps is not None
+                    and self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY
+                ):
                     if prefixed_name in input_connections_by_name:
                         connection = input_connections_by_name[prefixed_name]
-                        output_step = next(output_step for output_step in steps if connection.output_step_id == output_step.id)
-                        if output_step.type.startswith('data'):
+                        output_step = next(
+                            output_step for output_step in steps if connection.output_step_id == output_step.id
+                        )
+                        if output_step.type.startswith("data"):
                             output_inputs = output_step.module.get_runtime_inputs(connections=connections)
-                            output_value = output_inputs['input'].get_initial_value(self.trans, context)
-                            if input_type == "data" and isinstance(output_value, self.trans.app.model.HistoryDatasetCollectionAssociation):
+                            output_value = output_inputs["input"].get_initial_value(self.trans, context)
+                            if input_type == "data" and isinstance(
+                                output_value, self.trans.app.model.HistoryDatasetCollectionAssociation
+                            ):
                                 return output_value.to_hda_representative()
                             return output_value
                         return ConnectedValue()
@@ -1581,10 +1699,10 @@ class ToolModule(WorkflowModule):
                         return input.get_initial_value(self.trans, context)
                 elif (is_data and connections is None) or prefixed_name in input_connections_by_name:
                     return ConnectedValue()
+
             visit_input_values(self.tool.inputs, self.state.inputs, callback)
         else:
-            raise ToolMissingException(f"Tool {self.tool_id} missing. Cannot add dummy datasets.",
-                                       tool_id=self.tool_id)
+            raise ToolMissingException(f"Tool {self.tool_id} missing. Cannot add dummy datasets.", tool_id=self.tool_id)
 
     def get_post_job_actions(self, incoming):
         return ActionBox.handle_incoming(incoming)
@@ -1592,7 +1710,7 @@ class ToolModule(WorkflowModule):
     # ---- Run time ---------------------------------------------------------
 
     def recover_state(self, state, **kwds):
-        """ Recover state `dict` from simple dictionary describing configuration
+        """Recover state `dict` from simple dictionary describing configuration
         state (potentially from persisted step state).
 
         Sub-classes should supply a `default_state` method which contains the
@@ -1684,11 +1802,12 @@ class ToolModule(WorkflowModule):
                     state.inputs[RUNTIME_STEP_META_STATE_KEY] = step_metadata_runtime_state
             return state, step_errors
         else:
-            raise ToolMissingException(f"Tool {self.tool_id} missing. Cannot compute runtime state.",
-                                       tool_id=self.tool_id)
+            raise ToolMissingException(
+                f"Tool {self.tool_id} missing. Cannot compute runtime state.", tool_id=self.tool_id
+            )
 
     def decode_runtime_state(self, runtime_state):
-        """ Take runtime state from persisted invocation and convert it
+        """Take runtime state from persisted invocation and convert it
         into a DefaultToolState object for use during workflow invocation.
         """
         if self.tool:
@@ -1697,8 +1816,9 @@ class ToolModule(WorkflowModule):
                 self.__restore_step_meta_runtime_state(json.loads(runtime_state[RUNTIME_STEP_META_STATE_KEY]))
             return state
         else:
-            raise ToolMissingException(f"Tool {self.tool_id} missing. Cannot recover runtime state.",
-                                       tool_id=self.tool_id)
+            raise ToolMissingException(
+                f"Tool {self.tool_id} missing. Cannot recover runtime state.", tool_id=self.tool_id
+            )
 
     def execute(self, trans, progress, invocation_step, use_cached_job=False):
         invocation = invocation_step.workflow_invocation
@@ -1741,13 +1861,13 @@ class ToolModule(WorkflowModule):
                 replacement: Union[model.Dataset, NoReplacement] = NO_REPLACEMENT
                 dataset_instance: Optional[model.Dataset] = None
                 if iteration_elements and prefixed_name in iteration_elements:
-                    dataset_instance = getattr(iteration_elements[prefixed_name], 'dataset_instance', None)
+                    dataset_instance = getattr(iteration_elements[prefixed_name], "dataset_instance", None)
                     if isinstance(input, DataToolParameter) and dataset_instance:
                         # Pull out dataset instance (=HDA) from element and set a temporary element_identifier attribute
                         # See https://github.com/galaxyproject/galaxy/pull/1693 for context.
                         replacement = dataset_instance
                         temp = iteration_elements[prefixed_name]
-                        if hasattr(temp, 'element_identifier') and temp.element_identifier:
+                        if hasattr(temp, "element_identifier") and temp.element_identifier:
                             replacement.element_identifier = temp.element_identifier  # type: ignore[attr-defined]
                     else:
                         # If collection - just use element model object.
@@ -1758,9 +1878,7 @@ class ToolModule(WorkflowModule):
                 if replacement is not NO_REPLACEMENT:
                     if not isinstance(input, BaseDataToolParameter):
                         # Probably a parameter that can be replaced
-                        dataset2: model.Dataset = cast(
-                            model.Dataset, dataset_instance or replacement
-                        )
+                        dataset2: model.Dataset = cast(model.Dataset, dataset_instance or replacement)
                         if getattr(dataset2, "extension", None) == "expression.json":
                             with open(dataset2.file_name) as f:
                                 replacement = json.load(f)
@@ -1770,7 +1888,13 @@ class ToolModule(WorkflowModule):
 
             try:
                 # Replace DummyDatasets with historydatasetassociations
-                visit_input_values(tool.inputs, execution_state.inputs, callback, no_replacement_value=NO_REPLACEMENT, replace_optional_connections=True)
+                visit_input_values(
+                    tool.inputs,
+                    execution_state.inputs,
+                    callback,
+                    no_replacement_value=NO_REPLACEMENT,
+                    replace_optional_connections=True,
+                )
             except KeyError as k:
                 message_template = "Error due to input mapping of '%s' in '%s'.  A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow."
                 message = message_template % (tool.name, unicodify(k))
@@ -1817,7 +1941,7 @@ class ToolModule(WorkflowModule):
                 validate_outputs=validate_outputs,
                 job_callback=lambda job: self._handle_post_job_actions(step, job, invocation.replacement_dict),
                 completed_jobs=completed_jobs,
-                workflow_resource_parameters=resource_parameters
+                workflow_resource_parameters=resource_parameters,
             )
             complete = True
         except PartialJobExecution as pje:
@@ -1856,7 +1980,9 @@ class ToolModule(WorkflowModule):
         effective_post_job_actions = self._effective_post_job_actions(step)
         for pja in effective_post_job_actions:
             if pja.action_type in ActionBox.mapped_over_output_actions:
-                ActionBox.execute_on_mapped_over(self.trans, self.trans.sa_session, pja, step_inputs, step_outputs, replacement_dict)
+                ActionBox.execute_on_mapped_over(
+                    self.trans, self.trans.sa_session, pja, step_inputs, step_outputs, replacement_dict
+                )
 
     def _handle_post_job_actions(self, step, job, replacement_dict):
         # Create new PJA associations with the created job, to be run on completion.
@@ -1881,36 +2007,35 @@ class ToolModule(WorkflowModule):
             self.runtime_post_job_actions = step_runtime_state[RUNTIME_POST_JOB_ACTIONS_KEY]
 
     def __step_meta_runtime_state(self):
-        """ Build a dictionary a of meta-step runtime state (state about how
+        """Build a dictionary a of meta-step runtime state (state about how
         the workflow step - not the tool state) to be serialized with the Tool
         state.
         """
         return {RUNTIME_POST_JOB_ACTIONS_KEY: self.runtime_post_job_actions}
 
     def __to_pja(self, key, value, step):
-        if 'output_name' in value:
-            output_name = value['output_name']
+        if "output_name" in value:
+            output_name = value["output_name"]
         else:
             output_name = None
-        if 'action_arguments' in value:
-            action_arguments = value['action_arguments']
+        if "action_arguments" in value:
+            action_arguments = value["action_arguments"]
         else:
             action_arguments = None
-        return PostJobAction(value['action_type'], step, output_name, action_arguments)
+        return PostJobAction(value["action_type"], step, output_name, action_arguments)
 
     def get_replacement_parameters(self, step):
         """Return a list of replacement parameters."""
         replacement_parameters = set()
         for pja in step.post_job_actions:
             for argument in pja.action_arguments.values():
-                for match in re.findall(r'\$\{(.+?)\}', unicodify(argument)):
+                for match in re.findall(r"\$\{(.+?)\}", unicodify(argument)):
                     replacement_parameters.add(match)
 
         return list(replacement_parameters)
 
 
 class WorkflowModuleFactory:
-
     def __init__(self, module_types):
         self.module_types = module_types
 
@@ -1918,8 +2043,10 @@ class WorkflowModuleFactory:
         """
         Return module initialized from the data in dictionary `d`.
         """
-        type = d['type']
-        assert type in self.module_types, f"Unexpected workflow step type [{type}] not found in [{self.module_types.keys()}]"
+        type = d["type"]
+        assert (
+            type in self.module_types
+        ), f"Unexpected workflow step type [{type}] not found in [{self.module_types.keys()}]"
         return self.module_types[type].from_dict(trans, d, **kwargs)
 
     def from_workflow_step(self, trans, step, **kwargs):
@@ -1946,42 +2073,34 @@ module_factory = WorkflowModuleFactory(module_types)
 
 
 def load_module_sections(trans):
-    """ Get abstract description of the workflow modules this Galaxy instance
+    """Get abstract description of the workflow modules this Galaxy instance
     is configured with.
     """
     module_sections = {}
-    module_sections['inputs'] = {
+    module_sections["inputs"] = {
         "name": "inputs",
         "title": "Inputs",
         "modules": [
-            {
-                "name": "data_input",
-                "title": "Input Dataset",
-                "description": "Input dataset"
-            },
+            {"name": "data_input", "title": "Input Dataset", "description": "Input dataset"},
             {
                 "name": "data_collection_input",
                 "title": "Input Dataset Collection",
-                "description": "Input dataset collection"
+                "description": "Input dataset collection",
             },
             {
                 "name": "parameter_input",
                 "title": "Parameter Input",
-                "description": "Simple inputs used for workflow logic"
+                "description": "Simple inputs used for workflow logic",
             },
         ],
     }
 
     if trans.app.config.enable_beta_workflow_modules:
-        module_sections['experimental'] = {
+        module_sections["experimental"] = {
             "name": "experimental",
             "title": "Experimental",
             "modules": [
-                {
-                    "name": "pause",
-                    "title": "Pause Workflow for Dataset Review",
-                    "description": "Pause for Review"
-                }
+                {"name": "pause", "title": "Pause Workflow for Dataset Review", "description": "Pause for Review"}
             ],
         }
 
@@ -1989,7 +2108,6 @@ def load_module_sections(trans):
 
 
 class DelayedWorkflowEvaluation(Exception):
-
     def __init__(self, why=None):
         self.why = why
 
@@ -1999,15 +2117,15 @@ class CancelWorkflowEvaluation(Exception):
 
 
 class WorkflowModuleInjector:
-    """ Injects workflow step objects from the ORM with appropriate module and
-    module generated/influenced state. """
+    """Injects workflow step objects from the ORM with appropriate module and
+    module generated/influenced state."""
 
     def __init__(self, trans, allow_tool_state_corrections=False):
         self.trans = trans
         self.allow_tool_state_corrections = allow_tool_state_corrections
 
     def inject(self, step, step_args=None, steps=None, **kwargs):
-        """ Pre-condition: `step` is an ORM object coming from the database, if
+        """Pre-condition: `step` is an ORM object coming from the database, if
         supplied `step_args` is the representation of the inputs for that step
         supplied via web form.
 
@@ -2051,7 +2169,7 @@ class WorkflowModuleInjector:
 
 
 def populate_module_and_state(trans, workflow, param_map, allow_tool_state_corrections=False, module_injector=None):
-    """ Used by API but not web controller, walks through a workflow's steps
+    """Used by API but not web controller, walks through a workflow's steps
     and populates transient module and state attributes on each.
     """
     if module_injector is None:
@@ -2065,4 +2183,6 @@ def populate_module_and_state(trans, workflow, param_map, allow_tool_state_corre
             if allow_tool_state_corrections:
                 log.debug('Workflow step "%i" had upgrade messages: %s', step.id, step.upgrade_messages)
             else:
-                raise exceptions.MessageException(step.upgrade_messages, err_data={step.order_index: step.upgrade_messages})
+                raise exceptions.MessageException(
+                    step.upgrade_messages, err_data={step.order_index: step.upgrade_messages}
+                )
diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index c823e428f34..2ae36797568 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -1,12 +1,11 @@
 import logging
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
-from galaxy.exceptions import (
-    RequestParameterInvalidException,
-)
-from galaxy.tools.parameters import (
-    visit_input_values,
-)
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.tools.parameters import visit_input_values
 from galaxy.tools.parameters.basic import (
     ConnectedValue,
     contains_workflow_parameter,
@@ -51,7 +50,6 @@ log = logging.getLogger(__name__)
 
 
 class WorkflowRefactorExecutor:
-
     def __init__(self, raw_workflow_description, workflow, module_injector):
         # we mostly use the ga representation, but there may be cases where the
         # models/modules of existing workflow are more usable.
@@ -70,9 +68,7 @@ class WorkflowRefactorExecutor:
             refactor_method_name = f"_apply_{action_type}"
             refactor_method = getattr(self, refactor_method_name, None)
             if refactor_method is None:
-                raise RequestParameterInvalidException(
-                    f"Unknown workflow editing action encountered [{action_type}]"
-                )
+                raise RequestParameterInvalidException(f"Unknown workflow editing action encountered [{action_type}]")
             execution = RefactorActionExecution(
                 action=action.dict(),
                 messages=[],
@@ -157,11 +153,7 @@ class WorkflowRefactorExecutor:
             add_step_kwds["label"] = action.label
 
         add_step_action = AddStepAction(
-            action_type="add_step",
-            type=module_type,
-            tool_state=tool_state,
-            position=action.position,
-            **add_step_kwds
+            action_type="add_step", type=module_type, tool_state=tool_state, position=action.position, **add_step_kwds
         )
         self._apply_add_step(add_step_action, execution)
 
@@ -192,10 +184,12 @@ class WorkflowRefactorExecutor:
         all_input_connections = input_step_dict.get("input_connections")
         self.normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=True)
         input_connections = all_input_connections[input_name]
-        input_connections.append({
-            'id': output_order_index,
-            'output_name': output_name,
-        })
+        input_connections.append(
+            {
+                "id": output_order_index,
+                "output_name": output_name,
+            }
+        )
 
     def _apply_fill_defaults(self, action: FileDefaultsAction, execution: RefactorActionExecution):
         for _, step in self._iterate_over_step_pairs(execution):
@@ -223,7 +217,9 @@ class WorkflowRefactorExecutor:
                 input_def = input
                 break
         if input_def is None:
-            raise RequestParameterInvalidException(f"Failed to find input with name {input_name} on step {input_step_dict['id']} - input names found {found_input_names}")
+            raise RequestParameterInvalidException(
+                f"Failed to find input with name {input_name} on step {input_step_dict['id']} - input names found {found_input_names}"
+            )
         if input_def.get("multiple", False):
             raise RequestParameterInvalidException("Cannot extract input for multi-input inputs")
 
@@ -271,7 +267,7 @@ class WorkflowRefactorExecutor:
             def callback(input, prefixed_name, context, value=None, **kwargs):
                 nonlocal replace_tool_state
                 # data parameters cannot have untyped parameter values
-                if input.type in ['data', 'data_collection']:
+                if input.type in ["data", "data_collection"]:
                     return NO_REPLACEMENT
 
                 if not contains_workflow_parameter(value):
@@ -283,6 +279,7 @@ class WorkflowRefactorExecutor:
                     return runtime_to_json(ConnectedValue())
                 else:
                     return NO_REPLACEMENT
+
             visit_input_values(tool.inputs, tool_inputs.inputs, callback, no_replacement_value=NO_REPLACEMENT)
             if replace_tool_state:
                 step_def["tool_state"] = step.module.get_tool_state()
@@ -293,7 +290,9 @@ class WorkflowRefactorExecutor:
                 rename_pjas.append(post_job_action)
 
         if len(target_tool_inputs) == 0 and len(rename_pjas) == 0:
-            raise RequestParameterInvalidException(f"Failed to find {target_value} in the tool state or any workflow steps.")
+            raise RequestParameterInvalidException(
+                f"Failed to find {target_value} in the tool state or any workflow steps."
+            )
 
         as_parameter_type = {
             "text": "text",
@@ -306,12 +305,16 @@ class WorkflowRefactorExecutor:
         for _, tool_input, _ in target_tool_inputs:
             tool_input_type = tool_input.type
             if tool_input_type not in as_parameter_type:
-                raise RequestParameterInvalidException("Extracting inputs for parameters on tool inputs of type {tool_input_type} is unsupported")
+                raise RequestParameterInvalidException(
+                    "Extracting inputs for parameters on tool inputs of type {tool_input_type} is unsupported"
+                )
             target_parameter_type = as_parameter_type[tool_input_type]
             target_parameter_types.add(target_parameter_type)
 
         if len(target_parameter_types) > 1:
-            raise RequestParameterInvalidException("Extracting inputs for parameters on conflicting tool input types (e.g. numeric and non-numeric) input types is unsupported")
+            raise RequestParameterInvalidException(
+                "Extracting inputs for parameters on conflicting tool input types (e.g. numeric and non-numeric) input types is unsupported"
+            )
 
         if len(target_parameter_types) == 1:
             (target_parameter_type,) = target_parameter_types
@@ -346,7 +349,9 @@ class WorkflowRefactorExecutor:
             )
             self._apply_connect(connect_action, execution)
 
-    def _apply_remove_unlabeled_workflow_outputs(self, action: RemoveUnlabeledWorkflowOutputs, execution: RefactorActionExecution):
+    def _apply_remove_unlabeled_workflow_outputs(
+        self, action: RemoveUnlabeledWorkflowOutputs, execution: RefactorActionExecution
+    ):
         for step in self._as_dict["steps"].values():
             new_outputs = []
             for workflow_output in step.get("workflow_outputs", []):
@@ -361,16 +366,12 @@ class WorkflowRefactorExecutor:
         trans = self.module_injector.trans
         content_id = action.content_id
         if content_id is None:
-            old_workflow = trans.app.workflow_manager.get_owned_workflow(
-                trans, step_def["content_id"]
-            )
+            old_workflow = trans.app.workflow_manager.get_owned_workflow(trans, step_def["content_id"])
             stored_workflow = old_workflow.stored_workflow
             content_id = trans.security.encode_id(stored_workflow.latest_workflow.id)
         step_def["content_id"] = content_id
         step = self.workflow.steps[step_def["id"]]
-        new_workflow = trans.app.workflow_manager.get_owned_workflow(
-            trans, content_id
-        )
+        new_workflow = trans.app.workflow_manager.get_owned_workflow(trans, content_id)
         step.subworkflow = new_workflow
         self._inject_for_updated_step(step, execution)
 
@@ -399,11 +400,13 @@ class WorkflowRefactorExecutor:
 
     def _apply_upgrade_all_steps(self, action: UpgradeAllStepsAction, execution: RefactorActionExecution):
         for step_order_index, step in self._as_dict["steps"].items():
-            if step.get('type') == 'subworkflow':
-                step_action_s = UpgradeSubworkflowAction(action_type='upgrade_subworkflow', step={'order_index': step_order_index})
+            if step.get("type") == "subworkflow":
+                step_action_s = UpgradeSubworkflowAction(
+                    action_type="upgrade_subworkflow", step={"order_index": step_order_index}
+                )
                 self._apply_upgrade_subworkflow(step_action_s, execution)
-            elif step.get('type') == 'tool':
-                step_action_t = UpgradeToolAction(action_type='upgrade_tool', step={'order_index': step_order_index})
+            elif step.get("type") == "tool":
+                step_action_t = UpgradeToolAction(action_type="upgrade_tool", step={"order_index": step_order_index})
                 self._apply_upgrade_tool(step_action_t, execution)
 
     def _find_step(self, step_reference: step_reference_union):
@@ -466,9 +469,7 @@ class WorkflowRefactorExecutor:
                         step_label=step.label,
                         order_index=step.order_index,
                     )
-                    execution.messages.append(
-                        message
-                    )
+                    execution.messages.append(message)
             if getattr(step.module, "version_changes", None):
                 for version_change in step.module.version_changes:
                     message = RefactorActionExecutionMessage(
@@ -477,9 +478,7 @@ class WorkflowRefactorExecutor:
                         step_label=step.label,
                         order_index=step.order_index,
                     )
-                    execution.messages.append(
-                        message
-                    )
+                    execution.messages.append(message)
 
         return step
 
@@ -533,7 +532,9 @@ class WorkflowRefactorExecutor:
             if matching_input is None:
                 inputs_to_delete.append(input_name)
                 for input_connection in _listify_connections(input_connections):
-                    message_text = f"Tool or subworkflow input '{input_name}' no longer available, dropping connection to it."
+                    message_text = (
+                        f"Tool or subworkflow input '{input_name}' no longer available, dropping connection to it."
+                    )
                     from_order_index = input_connection["id"]
                     from_step_label = self._as_dict["steps"].get(from_order_index, {}).get("label")
                     message = RefactorActionExecutionMessage(
@@ -546,9 +547,7 @@ class WorkflowRefactorExecutor:
                         from_order_index=from_order_index,
                         from_step_label=from_step_label,
                     )
-                    execution.messages.append(
-                        message
-                    )
+                    execution.messages.append(message)
 
         for input_name in inputs_to_delete:
             del all_input_connections[input_name]
@@ -578,9 +577,7 @@ class WorkflowRefactorExecutor:
                                 from_step_label=upgrade_label,
                                 from_order_index=upgrade_order_index,
                             )
-                            execution.messages.append(
-                                message
-                            )
+                            execution.messages.append(message)
                     if include:
                         rebuilt_valid_connections.append(input_connection)
                 all_input_connections[input_name] = rebuilt_valid_connections
@@ -603,9 +600,7 @@ class WorkflowRefactorExecutor:
                     output_name=workflow_output.get("output_name"),
                     output_label=output_label,
                 )
-                execution.messages.append(
-                    message
-                )
+                execution.messages.append(message)
 
     @staticmethod
     def normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=False):
diff --git a/lib/galaxy/workflow/refactor/schema.py b/lib/galaxy/workflow/refactor/schema.py
index 544eccc828b..02f03798676 100644
--- a/lib/galaxy/workflow/refactor/schema.py
+++ b/lib/galaxy/workflow/refactor/schema.py
@@ -1,5 +1,11 @@
 from enum import Enum
-from typing import Any, Dict, List, Optional, Union
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
 
 from pydantic import (
     BaseModel,
@@ -10,12 +16,17 @@ from typing_extensions import Literal
 LABEL_DESCRIPTION = "The unique label of the step being referenced."
 INPUT_NAME_DESCRIPTION = "The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input')."
 input_name_field = Field(description=INPUT_NAME_DESCRIPTION)
-output_name_field = Field(description="The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.", default="output")
+output_name_field = Field(
+    description="The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.",
+    default="output",
+)
 step_target_field = Field(description="The target step for this action.")
 
 
 class StepReferenceByOrderIndex(BaseModel):
-    order_index: int = Field(description="The order_index of the step being referenced. The order indices of a workflow start at 0.")
+    order_index: int = Field(
+        description="The order_index of the step being referenced. The order indices of a workflow start at 0."
+    )
 
 
 class StepReferenceByLabel(BaseModel):
@@ -75,9 +86,7 @@ class Action(BaseAction):
         try:
             action_type = values["action_type"]
         except KeyError:
-            raise ValueError(
-                f"Missing required 'action_type' field for refactoring action: {values}"
-            )
+            raise ValueError(f"Missing required 'action_type' field for refactoring action: {values}")
         try:
             return ACTION_CLASSES_BY_TYPE[action_type](**values)
         except KeyError:
@@ -85,13 +94,13 @@ class Action(BaseAction):
 
 
 class UpdateStepLabelAction(BaseAction):
-    action_type: Literal['update_step_label']
+    action_type: Literal["update_step_label"]
     label: str = Field(description=LABEL_DESCRIPTION)
     step: step_reference_union = step_target_field
 
 
 class UpdateStepPositionAction(BaseAction):
-    action_type: Literal['update_step_position']
+    action_type: Literal["update_step_position"]
     step: step_reference_union = step_target_field
     position: Position
 
@@ -103,27 +112,30 @@ class AddStepAction(BaseAction):
     and this step may cause other steps to have their output_index
     adjusted.
     """
-    action_type: Literal['add_step']
+
+    action_type: Literal["add_step"]
     type: str = Field(description="Module type of the step to add, see galaxy.workflow.modules for available types.")
     tool_state: Optional[Dict[str, Any]]
-    label: Optional[str] = Field(description="A unique label for the step being added, must be distinct from the labels already present in the workflow.")
+    label: Optional[str] = Field(
+        description="A unique label for the step being added, must be distinct from the labels already present in the workflow."
+    )
     position: Optional[Position] = Field(description="The location of the step in the Galaxy workflow editor.")
 
 
 class ConnectAction(BaseAction):
-    action_type: Literal['connect']
+    action_type: Literal["connect"]
     input: input_reference_union
     output: output_reference_union
 
 
 class DisconnectAction(BaseAction):
-    action_type: Literal['disconnect']
+    action_type: Literal["disconnect"]
     input: input_reference_union
     output: output_reference_union
 
 
 class AddInputAction(BaseAction):
-    action_type: Literal['add_input']
+    action_type: Literal["add_input"]
     type: str
     label: Optional[str]
     position: Optional[Position]
@@ -136,40 +148,40 @@ class AddInputAction(BaseAction):
 
 
 class ExtractInputAction(BaseAction):
-    action_type: Literal['extract_input']
+    action_type: Literal["extract_input"]
     input: input_reference_union
     label: Optional[str]
     position: Optional[Position]
 
 
 class ExtractUntypedParameter(BaseAction):
-    action_type: Literal['extract_untyped_parameter']
+    action_type: Literal["extract_untyped_parameter"]
     name: str
     label: Optional[str]  # defaults to name if unset
     position: Optional[Position]
 
 
 class RemoveUnlabeledWorkflowOutputs(BaseAction):
-    action_type: Literal['remove_unlabeled_workflow_outputs']
+    action_type: Literal["remove_unlabeled_workflow_outputs"]
 
 
 class UpdateNameAction(BaseAction):
-    action_type: Literal['update_name']
+    action_type: Literal["update_name"]
     name: str
 
 
 class UpdateAnnotationAction(BaseAction):
-    action_type: Literal['update_annotation']
+    action_type: Literal["update_annotation"]
     annotation: str
 
 
 class UpdateLicenseAction(BaseAction):
-    action_type: Literal['update_license']
+    action_type: Literal["update_license"]
     license: str
 
 
 class UpdateCreatorAction(BaseAction):
-    action_type: Literal['update_creator']
+    action_type: Literal["update_creator"]
     creator: Any
 
 
@@ -178,27 +190,27 @@ class Report(BaseModel):
 
 
 class UpdateReportAction(BaseAction):
-    action_type: Literal['update_report']
+    action_type: Literal["update_report"]
     report: Report
 
 
 class UpdateOutputLabelAction(BaseAction):
-    action_type: Literal['update_output_label']
+    action_type: Literal["update_output_label"]
     output: output_reference_union  # TODO: allow reference by output_label
     output_label: str
 
 
 class FillStepDefaultsAction(BaseAction):
-    action_type: Literal['fill_step_defaults']
+    action_type: Literal["fill_step_defaults"]
     step: step_reference_union
 
 
 class FileDefaultsAction(BaseAction):
-    action_type: Literal['fill_defaults']
+    action_type: Literal["fill_defaults"]
 
 
 class UpgradeSubworkflowAction(BaseAction):
-    action_type: Literal['upgrade_subworkflow']
+    action_type: Literal["upgrade_subworkflow"]
     step: step_reference_union = step_target_field
     # Once we start storing these actions in the database, this needs to be decoded
     # before adding it into the database.
@@ -206,13 +218,13 @@ class UpgradeSubworkflowAction(BaseAction):
 
 
 class UpgradeToolAction(BaseAction):
-    action_type: Literal['upgrade_tool']
+    action_type: Literal["upgrade_tool"]
     step: step_reference_union = step_target_field
     tool_version: Optional[str]
 
 
 class UpgradeAllStepsAction(BaseAction):
-    action_type: Literal['upgrade_all_steps']
+    action_type: Literal["upgrade_all_steps"]
 
 
 union_action_classes = Union[
@@ -258,10 +270,10 @@ class RefactorActions(BaseModel):
 
 
 class RefactorActionExecutionMessageTypeEnum(str, Enum):
-    tool_version_change = 'tool_version_change'
-    tool_state_adjustment = 'tool_state_adjustment'
-    connection_drop_forced = 'connection_drop_forced'
-    workflow_output_drop_forced = 'workflow_output_drop_forced'
+    tool_version_change = "tool_version_change"
+    tool_state_adjustment = "tool_state_adjustment"
+    connection_drop_forced = "connection_drop_forced"
+    workflow_output_drop_forced = "workflow_output_drop_forced"
 
 
 INPUT_REFERENCE = """
@@ -280,16 +292,26 @@ class RefactorActionExecutionMessage(BaseModel):
     message_type: RefactorActionExecutionMessageTypeEnum
     step_label: Optional[str] = Field(description=f"Reference to the step the message refers to. ${INPUT_REFERENCE}")
     order_index: Optional[int] = Field(description=f"Reference to the step the message refers to. ${INPUT_REFERENCE}")
-    input_name: Optional[str] = Field(description=f"""If this message is about an input to a step,
-this field describes the target input name. ${INPUT_NAME_DESCRIPTION}""")
-    output_name: Optional[str] = Field(description="""If this message is about an output to a step,
+    input_name: Optional[str] = Field(
+        description=f"""If this message is about an input to a step,
+this field describes the target input name. ${INPUT_NAME_DESCRIPTION}"""
+    )
+    output_name: Optional[str] = Field(
+        description="""If this message is about an output to a step,
 this field describes the target output name. The output name as defined by the workflow module corresponding to the step being referenced.
-""")
-    from_step_label: Optional[str] = Field(description="""For dropped connections these optional attributes refer to the output
-side of the connection that was dropped.""")
-    from_order_index: Optional[int] = Field(description="""For dropped connections these optional attributes refer to the output
-side of the connection that was dropped.""")
-    output_label: Optional[str] = Field(description="If the message_type is workflow_output_drop_forced, this is the output label dropped.")
+"""
+    )
+    from_step_label: Optional[str] = Field(
+        description="""For dropped connections these optional attributes refer to the output
+side of the connection that was dropped."""
+    )
+    from_order_index: Optional[int] = Field(
+        description="""For dropped connections these optional attributes refer to the output
+side of the connection that was dropped."""
+    )
+    output_label: Optional[str] = Field(
+        description="If the message_type is workflow_output_drop_forced, this is the output label dropped."
+    )
 
 
 class RefactorActionExecution(BaseModel):
diff --git a/lib/galaxy/workflow/render.py b/lib/galaxy/workflow/render.py
index 393a3429027..cc9f6bd7ab8 100644
--- a/lib/galaxy/workflow/render.py
+++ b/lib/galaxy/workflow/render.py
@@ -9,9 +9,8 @@ STANDALONE_SVG_TEMPLATE = """<?xml version="1.0" standalone="no"?>
 
 
 class WorkflowCanvas:
-
     def __init__(self):
-        self.canvas = svgwrite.Drawing(profile='full')
+        self.canvas = svgwrite.Drawing(profile="full")
 
         self.connectors = []
         self.boxes = []
@@ -37,23 +36,29 @@ class WorkflowCanvas:
         return self.canvas
 
     def add_boxes(self, step_dict, width, name_fill):
-        x, y = step_dict['position']['left'], step_dict['position']['top']
-        self.boxes.append(svgwrite.shapes.Rect((x - MARGIN, y), (width, 30), fill=name_fill, stroke='#000000'))
-        box_height = (len(step_dict['data_inputs']) + len(step_dict['data_outputs'])) * LINE_SPACING + MARGIN
+        x, y = step_dict["position"]["left"], step_dict["position"]["top"]
+        self.boxes.append(svgwrite.shapes.Rect((x - MARGIN, y), (width, 30), fill=name_fill, stroke="#000000"))
+        box_height = (len(step_dict["data_inputs"]) + len(step_dict["data_outputs"])) * LINE_SPACING + MARGIN
         # Draw separator line.
-        if len(step_dict['data_inputs']) > 0:
+        if len(step_dict["data_inputs"]) > 0:
             box_height += LINE_SPACING
-            sep_y = y + len(step_dict['data_inputs']) * LINE_SPACING + 40
-            self.text.append(svgwrite.shapes.Line((x - MARGIN, sep_y), (x + width - MARGIN, sep_y), stroke=svgwrite.rgb(0, 0, 0)))
+            sep_y = y + len(step_dict["data_inputs"]) * LINE_SPACING + 40
+            self.text.append(
+                svgwrite.shapes.Line((x - MARGIN, sep_y), (x + width - MARGIN, sep_y), stroke=svgwrite.rgb(0, 0, 0))
+            )
         # Define an input/output box.
-        self.boxes.append(svgwrite.shapes.Rect((x - MARGIN, y + 30), (width, box_height), fill="#ffffff", stroke=svgwrite.rgb(0, 0, 0)))
+        self.boxes.append(
+            svgwrite.shapes.Rect(
+                (x - MARGIN, y + 30), (width, box_height), fill="#ffffff", stroke=svgwrite.rgb(0, 0, 0)
+            )
+        )
 
     def add_text(self, module_data_inputs, module_data_outputs, step, module_name):
-        left, top = step.position['left'], step.position['top']
+        left, top = step.position["left"], step.position["top"]
         x, y = left, top
         order_index = step.order_index
         max_len = len(module_name) * 1.5
-        self.text.append(svgwrite.text.Text(module_name, (x, y + 20), style='font-size:14px'))
+        self.text.append(svgwrite.text.Text(module_name, (x, y + 20), style="font-size:14px"))
         y += 45
         count = 0
         in_pos = self.in_pos
@@ -62,31 +67,31 @@ class WorkflowCanvas:
             cur_y = y + count * LINE_SPACING
             if order_index not in in_pos:
                 in_pos[order_index] = {}
-            in_pos[order_index][di['name']] = (x, cur_y)
-            self.text.append(svgwrite.text.Text(di['label'], (x, cur_y), style='font-size:10px'))
+            in_pos[order_index][di["name"]] = (x, cur_y)
+            self.text.append(svgwrite.text.Text(di["label"], (x, cur_y), style="font-size:10px"))
             count += 1
-            max_len = max(max_len, len(di['label']))
+            max_len = max(max_len, len(di["label"]))
         if len(module_data_inputs) > 0:
             y += LINE_SPACING
         for do in module_data_outputs:
             cur_y = y + count * LINE_SPACING
             if order_index not in out_pos:
                 out_pos[order_index] = {}
-            out_pos[order_index][do['name']] = (x, cur_y)
-            self.text.append(svgwrite.text.Text(do['name'], (x, cur_y), style='font-size:10px'))
+            out_pos[order_index][do["name"]] = (x, cur_y)
+            self.text.append(svgwrite.text.Text(do["name"], (x, cur_y), style="font-size:10px"))
             count += 1
-            max_len = max(max_len, len(do['name']))
+            max_len = max(max_len, len(do["name"]))
         self.widths[order_index] = max_len * 5.5
         self.max_x = max(self.max_x, left)
         self.max_y = max(self.max_y, top)
         self.max_width = max(self.max_width, self.widths[order_index])
 
     def add_connection(self, step_dict, conn, output_dict):
-        in_coords = self.in_pos[step_dict['id']][conn]
+        in_coords = self.in_pos[step_dict["id"]][conn]
         # out_pos_index will be a step number like 1, 2, 3...
-        out_pos_index = output_dict['id']
+        out_pos_index = output_dict["id"]
         # out_pos_name will be a string like 'o', 'o2', etc.
-        out_pos_name = output_dict['output_name']
+        out_pos_name = output_dict["output_name"]
         if out_pos_index in self.out_pos:
             # out_conn_index_dict will be something like:
             # 7: {'o': (824.5, 618)}
@@ -99,53 +104,60 @@ class WorkflowCanvas:
                 if out_conn_index_dict:
                     key = next(iter(out_conn_index_dict.keys()))
                     out_conn_pos = self.out_pos[out_pos_index][key]
-        adjusted = (out_conn_pos[0] + self.widths[output_dict['id']], out_conn_pos[1])
-        self.text.append(svgwrite.shapes.Circle(center=(out_conn_pos[0] + self.widths[output_dict['id']] - MARGIN,
-                                                        out_conn_pos[1] - MARGIN),
-                                                r=5,
-                                                fill="#ffffff",
-                                                stroke="#000000"))
-        marker = self.canvas.marker(overflow='visible',
-                                    refX="0", refY="5",
-                                    viewBox="0 0 10 5",
-                                    markerWidth="8",
-                                    markerHeight="10",
-                                    markerUnits="strokeWidth",
-                                    orient="auto", stroke="none", fill="black")
+        adjusted = (out_conn_pos[0] + self.widths[output_dict["id"]], out_conn_pos[1])
+        self.text.append(
+            svgwrite.shapes.Circle(
+                center=(out_conn_pos[0] + self.widths[output_dict["id"]] - MARGIN, out_conn_pos[1] - MARGIN),
+                r=5,
+                fill="#ffffff",
+                stroke="#000000",
+            )
+        )
+        marker = self.canvas.marker(
+            overflow="visible",
+            refX="0",
+            refY="5",
+            viewBox="0 0 10 5",
+            markerWidth="8",
+            markerHeight="10",
+            markerUnits="strokeWidth",
+            orient="auto",
+            stroke="none",
+            fill="black",
+        )
         marker.add(self.canvas.path(d="M 0 0 L 10 5 L 0 10 z"))
         self.canvas.defs.add(marker)
-        conn = svgwrite.shapes.Line((adjusted[0], adjusted[1] - MARGIN),
-                                    (in_coords[0] - 10, in_coords[1]),
-                                    stroke="#000000")
-        conn['marker-end'] = marker.get_funciri()
+        conn = svgwrite.shapes.Line(
+            (adjusted[0], adjusted[1] - MARGIN), (in_coords[0] - 10, in_coords[1]), stroke="#000000"
+        )
+        conn["marker-end"] = marker.get_funciri()
         self.connectors.append(conn)
 
     def add_steps(self, highlight_errors=False):
         # Only highlight missing tools if displaying in the tool shed.
         for step_dict in self.data:
-            tool_unavailable = step_dict.get('tool_errors', False)
+            tool_unavailable = step_dict.get("tool_errors", False)
             if highlight_errors and tool_unavailable:
                 fill = "#EBBCB2"
             else:
                 fill = "#EBD9B2"
-            width = self.widths[step_dict['id']]
+            width = self.widths[step_dict["id"]]
             self.add_boxes(step_dict, width, fill)
-            for conn, output_dict in step_dict['input_connections'].items():
+            for conn, output_dict in step_dict["input_connections"].items():
                 self.add_connection(step_dict, conn, output_dict)
 
     def populate_data_for_step(self, step, module_name, module_data_inputs, module_data_outputs, tool_errors=None):
         step_dict = {
-            'id': step.order_index,
-            'data_inputs': module_data_inputs,
-            'data_outputs': module_data_outputs,
-            'position': step.position
+            "id": step.order_index,
+            "data_inputs": module_data_inputs,
+            "data_outputs": module_data_outputs,
+            "position": step.position,
         }
         if tool_errors:
-            step_dict['tool_errors'] = tool_errors
+            step_dict["tool_errors"] = tool_errors
         input_conn_dict = {}
         for conn in step.input_connections:
-            input_conn_dict[conn.input_name] = \
-                dict(id=conn.output_step.order_index, output_name=conn.output_name)
-        step_dict['input_connections'] = input_conn_dict
+            input_conn_dict[conn.input_name] = dict(id=conn.output_step.order_index, output_name=conn.output_name)
+        step_dict["input_connections"] = input_conn_dict
         self.data.append(step_dict)
         self.add_text(module_data_inputs, module_data_outputs, step, module_name)
diff --git a/lib/galaxy/workflow/reports/__init__.py b/lib/galaxy/workflow/reports/__init__.py
index a1340e31bc8..866f17c28b4 100644
--- a/lib/galaxy/workflow/reports/__init__.py
+++ b/lib/galaxy/workflow/reports/__init__.py
@@ -6,7 +6,8 @@ DEFAULT_REPORT_GENERATOR_TYPE = "markdown"
 
 def generate_report(trans, invocation, runtime_report_config_json=None, plugin_type=None, target_format="json"):
     import galaxy.workflow.reports.generators
-    plugin_classes = plugin_config.plugins_dict(galaxy.workflow.reports.generators, 'plugin_type')
+
+    plugin_classes = plugin_config.plugins_dict(galaxy.workflow.reports.generators, "plugin_type")
     plugin_type = plugin_type or DEFAULT_REPORT_GENERATOR_TYPE
     plugin = plugin_classes[plugin_type]()
     if target_format == "json":
diff --git a/lib/galaxy/workflow/reports/generators/__init__.py b/lib/galaxy/workflow/reports/generators/__init__.py
index 65adc127c19..933484c72b6 100644
--- a/lib/galaxy/workflow/reports/generators/__init__.py
+++ b/lib/galaxy/workflow/reports/generators/__init__.py
@@ -2,7 +2,7 @@
 """
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
 from galaxy.managers import workflows
@@ -15,8 +15,7 @@ from galaxy.schema import PdfDocumentType
 
 
 class WorkflowReportGeneratorPlugin(metaclass=ABCMeta):
-    """
-    """
+    """ """
 
     @property
     @abstractmethod
@@ -25,25 +24,24 @@ class WorkflowReportGeneratorPlugin(metaclass=ABCMeta):
 
     @abstractmethod
     def generate_report_json(self, trans, invocation, runtime_report_config_json=None):
-        """
-        """
+        """ """
 
     @abstractmethod
     def generate_report_pdf(self, trans, invocation, runtime_report_config_json=None):
-        """
-        """
+        """ """
 
 
 class WorkflowMarkdownGeneratorPlugin(WorkflowReportGeneratorPlugin, metaclass=ABCMeta):
     """WorkflowReportGeneratorPlugin that generates markdown as base report."""
 
     def generate_report_json(self, trans, invocation, runtime_report_config_json=None):
-        """
-        """
+        """ """
         workflow_manager = workflows.WorkflowsManager(trans.app)
         workflow_encoded_id = trans.app.security.encode_id(invocation.workflow_id)
         workflow = workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id, by_stored_id=False)
-        internal_markdown = self._generate_internal_markdown(trans, invocation, runtime_report_config_json=runtime_report_config_json)
+        internal_markdown = self._generate_internal_markdown(
+            trans, invocation, runtime_report_config_json=runtime_report_config_json
+        )
         export_markdown, extra_rendering_data = ready_galaxy_markdown_for_export(trans, internal_markdown)
         rval = {
             "render_format": "markdown",  # Presumably the frontend could render things other ways.
@@ -58,7 +56,9 @@ class WorkflowMarkdownGeneratorPlugin(WorkflowReportGeneratorPlugin, metaclass=A
         return rval
 
     def generate_report_pdf(self, trans, invocation, runtime_report_config_json=None):
-        internal_markdown = self._generate_internal_markdown(trans, invocation, runtime_report_config_json=runtime_report_config_json)
+        internal_markdown = self._generate_internal_markdown(
+            trans, invocation, runtime_report_config_json=runtime_report_config_json
+        )
         return internal_galaxy_markdown_to_pdf(trans, internal_markdown, PdfDocumentType.invocation_report)
 
     @abstractmethod
@@ -66,6 +66,8 @@ class WorkflowMarkdownGeneratorPlugin(WorkflowReportGeneratorPlugin, metaclass=A
         """ """
 
     def _generate_internal_markdown(self, trans, invocation, runtime_report_config_json=None):
-        workflow_markdown = self._generate_report_markdown(trans, invocation, runtime_report_config_json=runtime_report_config_json)
+        workflow_markdown = self._generate_report_markdown(
+            trans, invocation, runtime_report_config_json=runtime_report_config_json
+        )
         internal_markdown = resolve_invocation_markdown(trans, invocation, workflow_markdown)
         return internal_markdown
diff --git a/lib/galaxy/workflow/reports/generators/markdown.py b/lib/galaxy/workflow/reports/generators/markdown.py
index 95f8b8a7483..44ccbb759ec 100644
--- a/lib/galaxy/workflow/reports/generators/markdown.py
+++ b/lib/galaxy/workflow/reports/generators/markdown.py
@@ -43,4 +43,4 @@ class MarkdownWorkflowMarkdownReportGeneratorPlugin(WorkflowMarkdownGeneratorPlu
         return markdown
 
 
-__all__ = ('MarkdownWorkflowMarkdownReportGeneratorPlugin', )
+__all__ = ("MarkdownWorkflowMarkdownReportGeneratorPlugin",)
diff --git a/lib/galaxy/workflow/resources/__init__.py b/lib/galaxy/workflow/resources/__init__.py
index 01445a4a45d..29df790a05b 100644
--- a/lib/galaxy/workflow/resources/__init__.py
+++ b/lib/galaxy/workflow/resources/__init__.py
@@ -34,7 +34,9 @@ def get_resource_mapper_function(app):
 
         if "by_group" in mapper_definition:
             by_group = mapper_definition["by_group"]
-            return functools.partial(_resource_parameters_by_group, by_group=by_group, workflow_resource_params=workflow_resource_params)
+            return functools.partial(
+                _resource_parameters_by_group, by_group=by_group, workflow_resource_params=workflow_resource_params
+            )
         else:
             raise Exception("Currently workflow parameter mapper definitions require a by_group definition.")
 
@@ -64,15 +66,15 @@ def _resource_parameters_by_group(trans, **kwds):
         user_groups = []
         for g in user.groups:
             user_groups.append(g.group.name)
-        default_group = by_group.get('default', None)
+        default_group = by_group.get("default", None)
         for group_name, group_def in by_group.get("groups", {}).items():
             if group_name == default_group or group_name in user_groups:
                 for tag in group_def:
                     if type(tag) is dict:
-                        if tag.get('name') not in user_permissions:
-                            user_permissions[tag.get('name')] = {}
-                        for option in tag.get('options'):
-                            user_permissions[tag.get('name')][option] = {}
+                        if tag.get("name") not in user_permissions:
+                            user_permissions[tag.get("name")] = {}
+                        for option in tag.get("options"):
+                            user_permissions[tag.get("name")][option] = {}
                     else:
                         if tag not in user_permissions:
                             user_permissions[tag] = {}
@@ -87,28 +89,27 @@ def get_workflow_parameter_list(params, user_permissions):
     param_list = []
     for param_elem in params.values():
         attr = deepcopy(param_elem.attrib)
-        if attr['name'] in user_permissions:
+        if attr["name"] in user_permissions:
             # Allow 'select' type parameters to be used
-            if attr['type'] == 'select':
+            if attr["type"] == "select":
                 option_data = []
                 reject_list = []
                 for option_elem in param_elem.findall("option"):
-                    if option_elem.attrib['value'] in user_permissions[attr['name']]:
-                        option_data.append({
-                            'label': option_elem.attrib['label'],
-                            'value': option_elem.attrib['value']
-                        })
+                    if option_elem.attrib["value"] in user_permissions[attr["name"]]:
+                        option_data.append({"label": option_elem.attrib["label"], "value": option_elem.attrib["value"]})
                     else:
-                        reject_list.append(option_elem.attrib['label'])
-                attr['data'] = option_data
+                        reject_list.append(option_elem.attrib["label"])
+                attr["data"] = option_data
                 attr_help = ""
-                if 'help' in attr:
-                    attr_help = attr['help']
+                if "help" in attr:
+                    attr_help = attr["help"]
                 if reject_list:
-                    attr_help += "<br/><br/>The following options are available but disabled.<br/>" + \
-                                 str(reject_list) + \
-                                 "<br/>If you believe this is a mistake, please contact your Galaxy admin."
-                attr['help'] = attr_help
+                    attr_help += (
+                        "<br/><br/>The following options are available but disabled.<br/>"
+                        + str(reject_list)
+                        + "<br/>If you believe this is a mistake, please contact your Galaxy admin."
+                    )
+                attr["help"] = attr_help
 
             param_list.append(attr)
     return param_list
@@ -117,38 +118,57 @@ def get_workflow_parameter_list(params, user_permissions):
 def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_params):
     valid = True
     try:
-        if 'default' not in by_group:
+        if "default" not in by_group:
             raise Exception("'workflow_resource_params_mapper' YAML file is malformed, 'default' attribute not found!")
-        default_group = by_group['default']
-        if 'groups' not in by_group:
+        default_group = by_group["default"]
+        if "groups" not in by_group:
             raise Exception("'workflow_resource_params_mapper' YAML file is malformed, 'groups' attribute not found!")
-        if default_group not in by_group['groups']:
-            raise Exception("'workflow_resource_params_mapper' YAML file is malformed, default group with title '"
-                            + default_group + "' not found in 'groups'!")
-        for group in by_group['groups']:
-            for attrib in by_group['groups'][group]:
+        if default_group not in by_group["groups"]:
+            raise Exception(
+                "'workflow_resource_params_mapper' YAML file is malformed, default group with title '"
+                + default_group
+                + "' not found in 'groups'!"
+            )
+        for group in by_group["groups"]:
+            for attrib in by_group["groups"][group]:
                 if type(attrib) is dict:
-                    if 'name' not in attrib:
-                        raise Exception("'workflow_resource_params_mapper' YAML file is malformed, "
-                                        "'name' attribute not found in attribute of group '" + group + "'!")
-                    if attrib['name'] not in workflow_resource_params:
-                        raise Exception("'workflow_resource_params_mapper' YAML file is malformed, group with name '"
-                                        + attrib['name'] + "' not found in 'workflow_resource_params'!")
-                    if 'options' not in attrib:
-                        raise Exception("'workflow_resource_params_mapper' YAML file is malformed, "
-                                        "'options' attribute not found in attribute of group '" + group + "'!")
+                    if "name" not in attrib:
+                        raise Exception(
+                            "'workflow_resource_params_mapper' YAML file is malformed, "
+                            "'name' attribute not found in attribute of group '" + group + "'!"
+                        )
+                    if attrib["name"] not in workflow_resource_params:
+                        raise Exception(
+                            "'workflow_resource_params_mapper' YAML file is malformed, group with name '"
+                            + attrib["name"]
+                            + "' not found in 'workflow_resource_params'!"
+                        )
+                    if "options" not in attrib:
+                        raise Exception(
+                            "'workflow_resource_params_mapper' YAML file is malformed, "
+                            "'options' attribute not found in attribute of group '" + group + "'!"
+                        )
 
                     valid_options = []
-                    for param_option in workflow_resource_params[attrib['name']]:
-                        valid_options.append(param_option.attrib['value'])
-                    for option in attrib['options']:
+                    for param_option in workflow_resource_params[attrib["name"]]:
+                        valid_options.append(param_option.attrib["value"])
+                    for option in attrib["options"]:
                         if option not in valid_options:
-                            raise Exception("'workflow_resource_params_mapper' YAML file is malformed, '" + option
-                                            + "' in 'options' of '" + attrib['name'] + "' not found in attribute of group '" + group + "'!")
+                            raise Exception(
+                                "'workflow_resource_params_mapper' YAML file is malformed, '"
+                                + option
+                                + "' in 'options' of '"
+                                + attrib["name"]
+                                + "' not found in attribute of group '"
+                                + group
+                                + "'!"
+                            )
                 else:
                     if attrib not in workflow_resource_params:
-                        raise Exception("'workflow_resource_params_mapper' YAML file is malformed, attribute with name "
-                                        "'" + attrib + "' not found in 'workflow_resource_params'!")
+                        raise Exception(
+                            "'workflow_resource_params_mapper' YAML file is malformed, attribute with name "
+                            "'" + attrib + "' not found in 'workflow_resource_params'!"
+                        )
 
     except Exception as e:
         log.exception(e)
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index bcb1d1b7d87..ac5af627826 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -1,6 +1,9 @@
 import logging
 import uuid
-from typing import List, Union
+from typing import (
+    List,
+    Union,
+)
 
 from galaxy import model
 from galaxy.util import ExecutionTimer
@@ -8,7 +11,7 @@ from galaxy.workflow import modules
 from galaxy.workflow.run_request import (
     workflow_request_to_run_config,
     workflow_run_config_to_request,
-    WorkflowRunConfig
+    WorkflowRunConfig,
 )
 
 log = logging.getLogger(__name__)
@@ -20,10 +23,14 @@ def schedule(trans, workflow, workflow_run_config, workflow_invocation):
 
 
 def __invoke(trans, workflow, workflow_run_config, workflow_invocation=None, populate_state=False):
-    """ Run the supplied workflow in the supplied target_history.
-    """
+    """Run the supplied workflow in the supplied target_history."""
     if populate_state:
-        modules.populate_module_and_state(trans, workflow, workflow_run_config.param_map, allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections)
+        modules.populate_module_and_state(
+            trans,
+            workflow,
+            workflow_run_config.param_map,
+            allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections,
+        )
 
     invoker = WorkflowInvoker(
         trans,
@@ -61,14 +68,18 @@ def __invoke(trans, workflow, workflow_run_config, workflow_invocation=None, pop
 def queue_invoke(trans, workflow, workflow_run_config, request_params=None, populate_state=True, flush=True):
     request_params = request_params or {}
     if populate_state:
-        modules.populate_module_and_state(trans, workflow, workflow_run_config.param_map, allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections)
+        modules.populate_module_and_state(
+            trans,
+            workflow,
+            workflow_run_config.param_map,
+            allow_tool_state_corrections=workflow_run_config.allow_tool_state_corrections,
+        )
     workflow_invocation = workflow_run_config_to_request(trans, workflow_run_config, workflow)
     workflow_invocation.workflow = workflow
     return trans.app.workflow_scheduling_manager.queue(workflow_invocation, request_params, flush=flush)
 
 
 class WorkflowInvoker:
-
     def __init__(self, trans, workflow, workflow_run_config, workflow_invocation=None, progress=None):
         self.trans = trans
         self.workflow = workflow
@@ -102,7 +113,9 @@ class WorkflowInvoker:
                 workflow_run_config.inputs,
                 module_injector,
                 param_map=workflow_run_config.param_map,
-                jobs_per_scheduling_iteration=getattr(trans.app.config, "maximum_workflow_jobs_per_scheduling_iteration", -1),
+                jobs_per_scheduling_iteration=getattr(
+                    trans.app.config, "maximum_workflow_jobs_per_scheduling_iteration", -1
+                ),
             )
         self.progress = progress
 
@@ -111,7 +124,9 @@ class WorkflowInvoker:
         config = self.trans.app.config
         maximum_duration = getattr(config, "maximum_workflow_invocation_duration", -1)
         if maximum_duration > 0 and workflow_invocation.seconds_since_created > maximum_duration:
-            log.debug(f"Workflow invocation [{workflow_invocation.id}] exceeded maximum number of seconds allowed for scheduling [{maximum_duration}], failing.")
+            log.debug(
+                f"Workflow invocation [{workflow_invocation.id}] exceeded maximum number of seconds allowed for scheduling [{maximum_duration}], failing."
+            )
             workflow_invocation.state = model.WorkflowInvocation.states.FAILED
             # All jobs ran successfully, so we can save now
             self.trans.sa_session.add(workflow_invocation)
@@ -141,17 +156,17 @@ class WorkflowInvoker:
                     workflow_invocation_step = model.WorkflowInvocationStep()
                     workflow_invocation_step.workflow_invocation = workflow_invocation
                     workflow_invocation_step.workflow_step = step
-                    workflow_invocation_step.state = 'new'
+                    workflow_invocation_step.state = "new"
 
                     workflow_invocation.steps.append(workflow_invocation_step)
 
                 incomplete_or_none = self._invoke_step(workflow_invocation_step)
                 if incomplete_or_none is False:
                     step_delayed = delayed_steps = True
-                    workflow_invocation_step.state = 'ready'
+                    workflow_invocation_step.state = "ready"
                     self.progress.mark_step_outputs_delayed(step, why="Not all jobs scheduled for state.")
                 else:
-                    workflow_invocation_step.state = 'scheduled'
+                    workflow_invocation_step.state = "scheduled"
             except modules.DelayedWorkflowEvaluation as de:
                 step_delayed = delayed_steps = True
                 self.progress.mark_step_outputs_delayed(step, why=de.why)
@@ -180,7 +195,7 @@ class WorkflowInvoker:
         return self.progress.outputs
 
     def __check_implicitly_dependent_steps(self, step):
-        """ Method will delay the workflow evaluation if implicitly dependent
+        """Method will delay the workflow evaluation if implicitly dependent
         steps (steps dependent but not through an input->output way) are not
         yet complete.
         """
@@ -197,7 +212,7 @@ class WorkflowInvoker:
             delayed_why = f"depends on step [{output_id}] but that step has not been invoked yet"
             raise modules.DelayedWorkflowEvaluation(why=delayed_why)
 
-        if step_invocation.state != 'scheduled':
+        if step_invocation.state != "scheduled":
             delayed_why = f"depends on step [{output_id}] job has not finished scheduling yet"
             raise modules.DelayedWorkflowEvaluation(delayed_why)
 
@@ -205,17 +220,18 @@ class WorkflowInvoker:
         for job in step_invocation.jobs:
             # At least one job in incomplete.
             if not job.finished:
-                delayed_why = f"depends on step [{output_id}] but one or more jobs created from that step have not finished yet"
+                delayed_why = (
+                    f"depends on step [{output_id}] but one or more jobs created from that step have not finished yet"
+                )
                 raise modules.DelayedWorkflowEvaluation(why=delayed_why)
 
             if job.state != job.states.OK:
                 raise modules.CancelWorkflowEvaluation()
 
     def _invoke_step(self, invocation_step):
-        incomplete_or_none = invocation_step.workflow_step.module.execute(self.trans,
-                                                                          self.progress,
-                                                                          invocation_step,
-                                                                          use_cached_job=self.workflow_invocation.use_cached_job)
+        incomplete_or_none = invocation_step.workflow_step.module.execute(
+            self.trans, self.progress, invocation_step, use_cached_job=self.workflow_invocation.use_cached_job
+        )
         return incomplete_or_none
 
 
@@ -223,8 +239,9 @@ STEP_OUTPUT_DELAYED = object()
 
 
 class WorkflowProgress:
-
-    def __init__(self, workflow_invocation, inputs_by_step_id, module_injector, param_map, jobs_per_scheduling_iteration=-1):
+    def __init__(
+        self, workflow_invocation, inputs_by_step_id, module_injector, param_map, jobs_per_scheduling_iteration=-1
+    ):
         self.outputs = {}
         self.module_injector = module_injector
         self.workflow_invocation = workflow_invocation
@@ -254,7 +271,7 @@ class WorkflowProgress:
         step_invocations_by_id = self.workflow_invocation.step_invocations_by_step_id()
         for step in steps:
             step_id = step.id
-            if not hasattr(step, 'module'):
+            if not hasattr(step, "module"):
                 self.module_injector.inject(step, step_args=self.param_map.get(step.id, {}))
                 if step_id not in step_states:
                     template = "Workflow invocation [%s] has no step state for step id [%s]. States ids are %s."
@@ -264,7 +281,7 @@ class WorkflowProgress:
                 step.state = step.module.decode_runtime_state(runtime_state)
 
             invocation_step = step_invocations_by_id.get(step_id, None)
-            if invocation_step and invocation_step.state == 'scheduled':
+            if invocation_step and invocation_step.state == "scheduled":
                 self._recover_mapping(invocation_step)
             else:
                 remaining_steps.append((step, invocation_step))
@@ -329,7 +346,9 @@ class WorkflowProgress:
 
         if isinstance(replacement, model.DatasetCollection):
             raise NotImplementedError
-        if not is_data and isinstance(replacement, (model.HistoryDatasetAssociation, model.HistoryDatasetCollectionAssociation)):
+        if not is_data and isinstance(
+            replacement, (model.HistoryDatasetAssociation, model.HistoryDatasetCollectionAssociation)
+        ):
             if isinstance(replacement, model.HistoryDatasetAssociation):
                 if replacement.is_pending:
                     raise modules.DelayedWorkflowEvaluation()
@@ -367,16 +386,16 @@ class WorkflowProgress:
 
         if self.inputs_by_step_id:
             step_id = step.id
-            if step_id not in self.inputs_by_step_id and 'output' not in outputs:
+            if step_id not in self.inputs_by_step_id and "output" not in outputs:
                 default_value = step.input_default_value
                 if default_value:
-                    outputs['output'] = default_value
+                    outputs["output"] = default_value
                 else:
                     template = "Step with id %s not found in inputs_step_id (%s)"
                     message = template % (step.log_str(), self.inputs_by_step_id)
                     raise ValueError(message)
             elif step_id in self.inputs_by_step_id:
-                outputs['output'] = self.inputs_by_step_id[step_id]
+                outputs["output"] = self.inputs_by_step_id[step_id]
 
         self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
 
@@ -464,12 +483,7 @@ class WorkflowProgress:
             if not connection_found:
                 raise Exception("Could not find connections for all subworkflow inputs.")
 
-        return WorkflowProgress(
-            subworkflow_invocation,
-            subworkflow_inputs,
-            self.module_injector,
-            param_map=param_map
-        )
+        return WorkflowProgress(subworkflow_invocation, subworkflow_inputs, self.module_injector, param_map=param_map)
 
     def _recover_mapping(self, step_invocation):
         try:
@@ -478,4 +492,4 @@ class WorkflowProgress:
             self.mark_step_outputs_delayed(step_invocation.workflow_step, de.why)
 
 
-__all__ = ('queue_invoke', 'WorkflowRunConfig')
+__all__ = ("queue_invoke", "WorkflowRunConfig")
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index bf830e41064..6cb858ac948 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -5,18 +5,18 @@ from typing import Dict
 
 from galaxy import (
     exceptions,
-    model
+    model,
 )
 from galaxy.tools.parameters.meta import expand_workflow_inputs
 from galaxy.workflow.resources import get_resource_mapper_function
 
-INPUT_STEP_TYPES = ['data_input', 'data_collection_input', 'parameter_input']
+INPUT_STEP_TYPES = ["data_input", "data_collection_input", "parameter_input"]
 
 log = logging.getLogger(__name__)
 
 
 class WorkflowRunConfig:
-    """ Wrapper around all the ways a workflow execution can be parameterized.
+    """Wrapper around all the ways a workflow execution can be parameterized.
 
     :param target_history: History to execute workflow in.
     :type target_history: galaxy.model.History.
@@ -43,14 +43,17 @@ class WorkflowRunConfig:
     :type param_map: dict
     """
 
-    def __init__(self, target_history,
-                 replacement_dict,
-                 copy_inputs_to_history=False,
-                 inputs=None,
-                 param_map=None,
-                 allow_tool_state_corrections=False,
-                 use_cached_job=False,
-                 resource_params=None):
+    def __init__(
+        self,
+        target_history,
+        replacement_dict,
+        copy_inputs_to_history=False,
+        inputs=None,
+        param_map=None,
+        allow_tool_state_corrections=False,
+        use_cached_job=False,
+        resource_params=None,
+    ):
         self.target_history = target_history
         self.replacement_dict = replacement_dict
         self.copy_inputs_to_history = copy_inputs_to_history
@@ -75,9 +78,11 @@ def _normalize_inputs(steps, inputs, inputs_by):
             elif inputs_by_el == "step_uuid":
                 possible_input_keys.append(str(step.uuid))
             elif inputs_by_el == "name":
-                possible_input_keys.append(step.label or step.tool_inputs.get('name'))
+                possible_input_keys.append(step.label or step.tool_inputs.get("name"))
             else:
-                raise exceptions.MessageException("Workflow cannot be run because unexpected inputs_by value specified.")
+                raise exceptions.MessageException(
+                    "Workflow cannot be run because unexpected inputs_by value specified."
+                )
         inputs_key = None
         for possible_input_key in possible_input_keys:
             if possible_input_key in inputs:
@@ -97,7 +102,7 @@ def _normalize_inputs(steps, inputs, inputs_by):
 
 
 def _normalize_step_parameters(steps, param_map, legacy=False, already_normalized=False):
-    """ Take a complex param_map that can reference parameters by
+    """Take a complex param_map that can reference parameters by
     step_id in the new flexible way or in the old one-parameter
     per step fashion or by tool id and normalize the parameters so
     everything is referenced by a numeric step id.
@@ -110,14 +115,18 @@ def _normalize_step_parameters(steps, param_map, legacy=False, already_normalize
             param_dict = _step_parameters(step, param_map, legacy=legacy)
         if step.type == "subworkflow" and param_dict:
             if not already_normalized:
-                raise exceptions.RequestParameterInvalidException("Specifying subworkflow step parameters requires already_normalized to be specified as true.")
+                raise exceptions.RequestParameterInvalidException(
+                    "Specifying subworkflow step parameters requires already_normalized to be specified as true."
+                )
             subworkflow_param_dict: Dict[str, Dict[str, str]] = {}
             for key, value in param_dict.items():
                 step_index, param_name = key.split("|", 1)
                 if step_index not in subworkflow_param_dict:
                     subworkflow_param_dict[step_index] = {}
                 subworkflow_param_dict[step_index][param_name] = value
-            param_dict = _normalize_step_parameters(step.subworkflow.steps, subworkflow_param_dict, legacy=legacy, already_normalized=already_normalized)
+            param_dict = _normalize_step_parameters(
+                step.subworkflow.steps, subworkflow_param_dict, legacy=legacy, already_normalized=already_normalized
+            )
         if param_dict:
             normalized_param_map[step.id] = param_dict
     return normalized_param_map
@@ -158,10 +167,10 @@ def _step_parameters(step, param_map, legacy=False):
         uuid_params = param_map.get(str(step_uuid), {})
         param_dict.update(uuid_params)
     if param_dict:
-        if 'param' in param_dict and 'value' in param_dict:
-            param_dict[param_dict['param']] = param_dict['value']
-            del param_dict['param']
-            del param_dict['value']
+        if "param" in param_dict and "value" in param_dict:
+            param_dict[param_dict["param"]] = param_dict["value"]
+            del param_dict["param"]
+            del param_dict["value"]
     # Inputs can be nested dict, but Galaxy tool code wants nesting of keys (e.g.
     # cond1|moo=4 instead of cond1: {moo: 4} ).
     new_params = _flatten_step_params(param_dict)
@@ -182,7 +191,7 @@ def _flatten_step_params(param_dict, prefix=""):
         else:
             effective_key = key
         value = param_dict[key]
-        if isinstance(value, dict) and (not ('src' in value and 'id' in value) and key != "__POST_JOB_ACTIONS__"):
+        if isinstance(value, dict) and (not ("src" in value and "id" in value) and key != "__POST_JOB_ACTIONS__"):
             new_params.update(_flatten_step_params(value, effective_key))
         else:
             new_params[effective_key] = value
@@ -191,30 +200,34 @@ def _flatten_step_params(param_dict, prefix=""):
 
 def _get_target_history(trans, workflow, payload, param_keys=None, index=0):
     param_keys = param_keys or []
-    history_name = payload.get('new_history_name', None)
-    history_id = payload.get('history_id', None)
-    history_param = payload.get('history', None)
+    history_name = payload.get("new_history_name", None)
+    history_id = payload.get("history_id", None)
+    history_param = payload.get("history", None)
     if [history_name, history_id, history_param].count(None) < 2:
-        raise exceptions.RequestParameterInvalidException("Specified workflow target history multiple ways - at most one of 'history', 'history_id', and 'new_history_name' may be specified.")
+        raise exceptions.RequestParameterInvalidException(
+            "Specified workflow target history multiple ways - at most one of 'history', 'history_id', and 'new_history_name' may be specified."
+        )
     if history_param:
-        if history_param.startswith('hist_id='):
+        if history_param.startswith("hist_id="):
             history_id = history_param[8:]
         else:
             history_name = history_param
     if history_id:
         history_manager = trans.app.history_manager
-        target_history = history_manager.get_owned(trans.security.decode_id(history_id), trans.user, current_history=trans.history)
+        target_history = history_manager.get_owned(
+            trans.security.decode_id(history_id), trans.user, current_history=trans.history
+        )
     else:
         if history_name:
             nh_name = history_name
         else:
-            nh_name = f'History from {workflow.name} workflow'
+            nh_name = f"History from {workflow.name} workflow"
         if len(param_keys) <= index:
             raise exceptions.MessageException("Incorrect expansion of workflow batch parameters.")
         ids = param_keys[index]
         nids = len(ids)
         if nids == 1:
-            nh_name = f'{nh_name} on {ids[0]}'
+            nh_name = f"{nh_name} on {ids[0]}"
         elif nids > 1:
             nh_name = f"{nh_name} on {', '.join(ids[0:-1])} and {ids[-1]}"
         new_history = trans.app.model.History(user=trans.user, name=nh_name)
@@ -226,8 +239,8 @@ def _get_target_history(trans, workflow, payload, param_keys=None, index=0):
 
 def build_workflow_run_configs(trans, workflow, payload):
     app = trans.app
-    allow_tool_state_corrections = payload.get('allow_tool_state_corrections', False)
-    use_cached_job = payload.get('use_cached_job', False)
+    allow_tool_state_corrections = payload.get("allow_tool_state_corrections", False)
+    use_cached_job = payload.get("use_cached_job", False)
 
     # Sanity checks.
     if len(workflow.steps) == 0:
@@ -235,37 +248,43 @@ def build_workflow_run_configs(trans, workflow, payload):
     if workflow.has_cycles:
         raise exceptions.MessageException("Workflow cannot be run because it contains cycles")
 
-    if 'step_parameters' in payload and 'parameters' in payload:
-        raise exceptions.RequestParameterInvalidException("Cannot specify both legacy parameters and step_parameters attributes.")
-    if 'inputs' in payload and 'ds_map' in payload:
+    if "step_parameters" in payload and "parameters" in payload:
+        raise exceptions.RequestParameterInvalidException(
+            "Cannot specify both legacy parameters and step_parameters attributes."
+        )
+    if "inputs" in payload and "ds_map" in payload:
         raise exceptions.RequestParameterInvalidException("Cannot specify both legacy ds_map and input attributes.")
 
-    add_to_history = 'no_add_to_history' not in payload
-    legacy = payload.get('legacy', False)
-    already_normalized = payload.get('parameters_normalized', False)
-    raw_parameters = payload.get('parameters', {})
+    add_to_history = "no_add_to_history" not in payload
+    legacy = payload.get("legacy", False)
+    already_normalized = payload.get("parameters_normalized", False)
+    raw_parameters = payload.get("parameters", {})
 
     run_configs = []
-    unexpanded_param_map = _normalize_step_parameters(workflow.steps, raw_parameters, legacy=legacy, already_normalized=already_normalized)
-    unexpanded_inputs = payload.get('inputs', None)
-    inputs_by = payload.get('inputs_by', None)
+    unexpanded_param_map = _normalize_step_parameters(
+        workflow.steps, raw_parameters, legacy=legacy, already_normalized=already_normalized
+    )
+    unexpanded_inputs = payload.get("inputs", None)
+    inputs_by = payload.get("inputs_by", None)
     # New default is to reference steps by index of workflow step
     # which is intrinsic to the workflow and independent of the state
     # of Galaxy at the time of workflow import.
-    default_inputs_by = 'step_index|step_uuid'
+    default_inputs_by = "step_index|step_uuid"
     inputs_by = inputs_by or default_inputs_by
 
     if unexpanded_inputs is None:
         # Default to legacy behavior - read ds_map and reference steps
         # by unencoded step id (a raw database id).
-        unexpanded_inputs = payload.get('ds_map', {})
+        unexpanded_inputs = payload.get("ds_map", {})
         if legacy:
-            default_inputs_by = 'step_id|step_uuid'
+            default_inputs_by = "step_id|step_uuid"
         inputs_by = inputs_by or default_inputs_by
     else:
         unexpanded_inputs = unexpanded_inputs or {}
 
-    expanded_params, expanded_param_keys, expanded_inputs = expand_workflow_inputs(unexpanded_param_map, unexpanded_inputs)
+    expanded_params, expanded_param_keys, expanded_inputs = expand_workflow_inputs(
+        unexpanded_param_map, unexpanded_inputs
+    )
     for index, (param_map, inputs) in enumerate(zip(expanded_params, expanded_inputs)):
         history = _get_target_history(trans, workflow, payload, expanded_param_keys, index)
         if inputs or not already_normalized:
@@ -292,54 +311,78 @@ def build_workflow_run_configs(trans, workflow, payload):
             if input_dict is None:
                 continue
             step = steps_by_id[key]
-            if step.type == 'parameter_input':
+            if step.type == "parameter_input":
                 continue
-            if 'src' not in input_dict:
-                raise exceptions.RequestParameterInvalidException(f"Not input source type defined for input '{input_dict}'.")
-            if 'id' not in input_dict:
+            if "src" not in input_dict:
+                raise exceptions.RequestParameterInvalidException(
+                    f"Not input source type defined for input '{input_dict}'."
+                )
+            if "id" not in input_dict:
                 raise exceptions.RequestParameterInvalidException(f"Not input id defined for input '{input_dict}'.")
-            if 'content' in input_dict:
-                raise exceptions.RequestParameterInvalidException(f"Input cannot specify explicit 'content' attribute {input_dict}'.")
-            input_source = input_dict['src']
-            input_id = input_dict['id']
+            if "content" in input_dict:
+                raise exceptions.RequestParameterInvalidException(
+                    f"Input cannot specify explicit 'content' attribute {input_dict}'."
+                )
+            input_source = input_dict["src"]
+            input_id = input_dict["id"]
             try:
-                if input_source == 'ldda':
-                    ldda = trans.sa_session.query(app.model.LibraryDatasetDatasetAssociation).get(trans.security.decode_id(input_id))
-                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset)
+                if input_source == "ldda":
+                    ldda = trans.sa_session.query(app.model.LibraryDatasetDatasetAssociation).get(
+                        trans.security.decode_id(input_id)
+                    )
+                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
+                        trans.get_current_user_roles(), ldda.dataset
+                    )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
-                elif input_source == 'ld':
-                    ldda = trans.sa_session.query(app.model.LibraryDataset).get(trans.security.decode_id(input_id)).library_dataset_dataset_association
-                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset)
+                elif input_source == "ld":
+                    ldda = (
+                        trans.sa_session.query(app.model.LibraryDataset)
+                        .get(trans.security.decode_id(input_id))
+                        .library_dataset_dataset_association
+                    )
+                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
+                        trans.get_current_user_roles(), ldda.dataset
+                    )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
-                elif input_source == 'hda':
+                elif input_source == "hda":
                     # Get dataset handle, add to dict and history if necessary
-                    content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get(trans.security.decode_id(input_id))
-                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), content.dataset)
-                elif input_source == 'uuid':
-                    dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid == input_id).first()
+                    content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get(
+                        trans.security.decode_id(input_id)
+                    )
+                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
+                        trans.get_current_user_roles(), content.dataset
+                    )
+                elif input_source == "uuid":
+                    dataset = (
+                        trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid == input_id).first()
+                    )
                     if dataset is None:
                         # this will need to be changed later. If federation code is avalible, then a missing UUID
                         # could be found amoung fereration partners
                         raise exceptions.RequestParameterInvalidException(f"Input cannot find UUID: {input_id}.")
-                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), dataset)
+                    assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
+                        trans.get_current_user_roles(), dataset
+                    )
                     content = history.add_dataset(dataset)
-                elif input_source == 'hdca':
-                    content = app.dataset_collection_manager.get_dataset_collection_instance(trans, 'history', input_id)
+                elif input_source == "hdca":
+                    content = app.dataset_collection_manager.get_dataset_collection_instance(trans, "history", input_id)
                 else:
-                    raise exceptions.RequestParameterInvalidException(f"Unknown workflow input source '{input_source}' specified.")
+                    raise exceptions.RequestParameterInvalidException(
+                        f"Unknown workflow input source '{input_source}' specified."
+                    )
                 if add_to_history and content.history != history:
                     content = content.copy(flush=False)
                     history.stage_addition(content)
-                input_dict['content'] = content
+                input_dict["content"] = content
             except AssertionError:
                 raise exceptions.ItemAccessibilityException(f"Invalid workflow input '{input_id}' specified")
         for key in set(normalized_inputs.keys()):
             value = normalized_inputs[key]
-            if isinstance(value, dict) and 'content' in value:
-                normalized_inputs[key] = value['content']
+            if isinstance(value, dict) and "content" in value:
+                normalized_inputs[key] = value["content"]
             else:
                 normalized_inputs[key] = value
-        resource_params = payload.get('resource_params', {})
+        resource_params = payload.get("resource_params", {})
         if resource_params:
             # quick attempt to validate parameters, just handle select options now since is what
             # is needed for DTD - arbitrary plugins can define arbitrary logic at runtime in the
@@ -361,22 +404,26 @@ def build_workflow_run_configs(trans, workflow, payload):
                         if value is None:
                             valid_option = True
                         else:
-                            for option_elem in resource_parameter.get('data'):
+                            for option_elem in resource_parameter.get("data"):
                                 option_value = option_elem.get("value")
                                 if value == option_value:
                                     valid_option = True
                         if not valid_option:
-                            raise exceptions.RequestParameterInvalidException(f"Invalid value for parameter '{name}' found.")
+                            raise exceptions.RequestParameterInvalidException(
+                                f"Invalid value for parameter '{name}' found."
+                            )
         history.add_pending_items()
-        run_configs.append(WorkflowRunConfig(
-            target_history=history,
-            replacement_dict=payload.get('replacement_params', {}),
-            inputs=normalized_inputs,
-            param_map=param_map,
-            allow_tool_state_corrections=allow_tool_state_corrections,
-            use_cached_job=use_cached_job,
-            resource_params=resource_params,
-        ))
+        run_configs.append(
+            WorkflowRunConfig(
+                target_history=history,
+                replacement_dict=payload.get("replacement_params", {}),
+                inputs=normalized_inputs,
+                param_map=param_map,
+                allow_tool_state_corrections=allow_tool_state_corrections,
+                use_cached_job=use_cached_job,
+                resource_params=resource_params,
+            )
+        )
 
     return run_configs
 
@@ -416,7 +463,7 @@ def workflow_run_config_to_request(trans, run_config, workflow):
                 inputs={},
                 param_map=run_config.param_map.get(step.order_index, {}),
                 allow_tool_state_corrections=run_config.allow_tool_state_corrections,
-                resource_params=run_config.resource_params
+                resource_params=run_config.resource_params,
             )
             subworkflow_invocation = workflow_run_config_to_request(
                 trans,
@@ -447,7 +494,9 @@ def workflow_run_config_to_request(trans, run_config, workflow):
     resource_parameters = run_config.resource_params
     for key, value in resource_parameters.items():
         add_parameter(key, value, param_types.RESOURCE_PARAMETERS)
-    add_parameter("copy_inputs_to_history", "true" if run_config.copy_inputs_to_history else "false", param_types.META_PARAMETERS)
+    add_parameter(
+        "copy_inputs_to_history", "true" if run_config.copy_inputs_to_history else "false", param_types.META_PARAMETERS
+    )
     add_parameter("use_cached_job", "true" if run_config.use_cached_job else "false", param_types.META_PARAMETERS)
     return workflow_invocation
 
@@ -468,9 +517,9 @@ def workflow_request_to_run_config(work_request_context, workflow_invocation):
             replacement_dict[parameter.name] = parameter.value
         elif parameter_type == param_types.META_PARAMETERS:
             if parameter.name == "copy_inputs_to_history":
-                copy_inputs_to_history = (parameter.value == "true")
-            if parameter.name == 'use_cached_job':
-                use_cached_job = (parameter.value == 'true')
+                copy_inputs_to_history = parameter.value == "true"
+            if parameter.name == "use_cached_job":
+                use_cached_job = parameter.value == "true"
         elif parameter_type == param_types.RESOURCE_PARAMETERS:
             resource_params[parameter.name] = parameter.value
         elif parameter_type == param_types.STEP_PARAMETERS:
@@ -486,7 +535,9 @@ def workflow_request_to_run_config(work_request_context, workflow_invocation):
         if step_label and step_label not in replacement_dict:
             replacement_dict[step_label] = str(parameter_value)
     if copy_inputs_to_history is None:
-        raise exceptions.InconsistentDatabase("Failed to find copy_inputs_to_history parameter loading workflow_invocation from database.")
+        raise exceptions.InconsistentDatabase(
+            "Failed to find copy_inputs_to_history parameter loading workflow_invocation from database."
+        )
     workflow_run_config = WorkflowRunConfig(
         target_history=history,
         replacement_dict=replacement_dict,
diff --git a/lib/galaxy/workflow/schedulers/__init__.py b/lib/galaxy/workflow/schedulers/__init__.py
index 502b0d950ae..333e4f678ca 100644
--- a/lib/galaxy/workflow/schedulers/__init__.py
+++ b/lib/galaxy/workflow/schedulers/__init__.py
@@ -4,12 +4,12 @@ scheduling plugins will almost certainly change.
 """
 from abc import (
     ABCMeta,
-    abstractmethod
+    abstractmethod,
 )
 
 
 class WorkflowSchedulingPlugin(metaclass=ABCMeta):
-    """ A plugin defining how Galaxy should schedule plugins. By default
+    """A plugin defining how Galaxy should schedule plugins. By default
     plugins are passive and should monitor Galaxy's work queue for
     WorkflowRequests. Inherit from ActiveWorkflowSchedulingPlugin instead if
     the scheduling plugin should be forced (i.e. if scheduling happen all at
@@ -19,23 +19,21 @@ class WorkflowSchedulingPlugin(metaclass=ABCMeta):
     @property
     @abstractmethod
     def plugin_type(self):
-        """ Short string providing labelling this plugin """
+        """Short string providing labelling this plugin"""
 
     def startup(self, app):
-        """ Called when Galaxy starts up if the plugin is enabled.
-        """
+        """Called when Galaxy starts up if the plugin is enabled."""
 
     def shutdown(self):
-        """ Called when Galaxy is shutting down, workflow scheduling should
+        """Called when Galaxy is shutting down, workflow scheduling should
         end.
         """
 
 
 class ActiveWorkflowSchedulingPlugin(WorkflowSchedulingPlugin, metaclass=ABCMeta):
-
     @abstractmethod
     def schedule(self, workflow_invocation):
-        """ Optionally return one or more commands to instrument job. These
+        """Optionally return one or more commands to instrument job. These
         commands will be executed on the compute server prior to the job
         running.
         """
diff --git a/lib/galaxy/workflow/schedulers/core.py b/lib/galaxy/workflow/schedulers/core.py
index 8eacd3abf8b..a4a51d4f17b 100644
--- a/lib/galaxy/workflow/schedulers/core.py
+++ b/lib/galaxy/workflow/schedulers/core.py
@@ -4,7 +4,10 @@ it simply schedules the whole workflow up front when offered.
 import logging
 
 from galaxy.work import context
-from galaxy.workflow import run, run_request
+from galaxy.workflow import (
+    run,
+    run_request,
+)
 from ..schedulers import ActiveWorkflowSchedulingPlugin
 
 log = logging.getLogger(__name__)
@@ -26,14 +29,9 @@ class CoreWorkflowSchedulingPlugin(ActiveWorkflowSchedulingPlugin):
         workflow = workflow_invocation.workflow
         history = workflow_invocation.history
         request_context = context.WorkRequestContext(
-            app=self.app,
-            history=history,
-            user=history.user
+            app=self.app, history=history, user=history.user
         )  # trans-like object not tied to a web-thread.
-        workflow_run_config = run_request.workflow_request_to_run_config(
-            request_context,
-            workflow_invocation
-        )
+        workflow_run_config = run_request.workflow_request_to_run_config(request_context, workflow_invocation)
         run.schedule(
             trans=request_context,
             workflow=workflow,
@@ -42,4 +40,4 @@ class CoreWorkflowSchedulingPlugin(ActiveWorkflowSchedulingPlugin):
         )
 
 
-__all__ = ('CoreWorkflowSchedulingPlugin', )
+__all__ = ("CoreWorkflowSchedulingPlugin",)
diff --git a/lib/galaxy/workflow/scheduling_manager.py b/lib/galaxy/workflow/scheduling_manager.py
index 7e5ff9af1fc..31e5f8138dc 100644
--- a/lib/galaxy/workflow/scheduling_manager.py
+++ b/lib/galaxy/workflow/scheduling_manager.py
@@ -9,7 +9,10 @@ from galaxy.util import plugin_config
 from galaxy.util.custom_logging import get_logger
 from galaxy.util.monitors import Monitors
 from galaxy.util.xml_macros import load
-from galaxy.web_stack.handlers import ConfiguresHandlers, HANDLER_ASSIGNMENT_METHODS
+from galaxy.web_stack.handlers import (
+    ConfiguresHandlers,
+    HANDLER_ASSIGNMENT_METHODS,
+)
 from galaxy.web_stack.message import WorkflowSchedulingMessage
 
 log = get_logger(__name__)
@@ -19,17 +22,22 @@ DEFAULT_SCHEDULER_PLUGIN_TYPE = "core"
 
 EXCEPTION_MESSAGE_SHUTDOWN = "Exception raised while attempting to shutdown workflow scheduler."
 EXCEPTION_MESSAGE_NO_SCHEDULERS = "Failed to defined workflow schedulers - no workflow schedulers defined."
-EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER = "Failed to defined workflow schedulers - no workflow scheduler found for default id '%s'."
-EXCEPTION_MESSAGE_DUPLICATE_SCHEDULERS = "Failed to defined workflow schedulers - workflow scheduling plugin id '%s' duplicated."
+EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER = (
+    "Failed to defined workflow schedulers - no workflow scheduler found for default id '%s'."
+)
+EXCEPTION_MESSAGE_DUPLICATE_SCHEDULERS = (
+    "Failed to defined workflow schedulers - workflow scheduling plugin id '%s' duplicated."
+)
 EXCEPTION_MESSAGE_SERIALIZE = "Parallelization is not desired but handler assignment methods are non-deterministic. Set DB_PREASSIGN in workflow_schedulers_conf.xml."
 
 
 class WorkflowSchedulingManager(ConfiguresHandlers):
-    """ A workflow scheduling manager based loosely on pattern established by
+    """A workflow scheduling manager based loosely on pattern established by
     ``galaxy.manager.JobManager``. Only schedules workflows on handler
     processes.
     """
-    DEFAULT_BASE_HANDLER_POOLS = ('workflow-schedulers', 'job-handlers')
+
+    DEFAULT_BASE_HANDLER_POOLS = ("workflow-schedulers", "job-handlers")
     UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS = {
         HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE,
     }
@@ -68,10 +76,10 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
 
         if self._is_workflow_handler():
             if self.__handlers_config.use_messaging:
-                WorkflowSchedulingMessage().bind_default_handler(self, '_handle_message')
+                WorkflowSchedulingMessage().bind_default_handler(self, "_handle_message")
                 self.app.application_stack.register_message_handler(
-                    self._handle_message,
-                    name=WorkflowSchedulingMessage.target)
+                    self._handle_message, name=WorkflowSchedulingMessage.target
+                )
         else:
             # Process should not schedule workflows but should check for any unassigned to handlers
             self.__startup_recovery()
@@ -79,8 +87,9 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
     def __startup_recovery(self):
         sa_session = self.app.model.context
         for invocation_id in model.WorkflowInvocation.poll_unhandled_workflow_ids(sa_session):
-            log.info("(%s) Handler unassigned at startup, resubmitting workflow invocation for assignment",
-                     invocation_id)
+            log.info(
+                "(%s) Handler unassigned at startup, resubmitting workflow invocation for assignment", invocation_id
+            )
             workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id)
             self._assign_handler(workflow_invocation)
 
@@ -92,9 +101,13 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
             sa_session.add(workflow_invocation)
             sa_session.flush()
         else:
-            log.warning("(%s) Handler '%s' received setup message for workflow invocation but handler '%s' is"
-                        " already assigned, ignoring", workflow_invocation.id, self.app.config.server_name,
-                        workflow_invocation.handler)
+            log.warning(
+                "(%s) Handler '%s' received setup message for workflow invocation but handler '%s' is"
+                " already assigned, ignoring",
+                workflow_invocation.id,
+                self.app.config.server_name,
+                workflow_invocation.handler,
+            )
 
     def _is_workflow_handler(self):
         # If we have explicitly configured handlers, check them.
@@ -113,7 +126,7 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
         sa_session.flush()
 
     def _message_callback(self, workflow_invocation):
-        return WorkflowSchedulingMessage(task='setup', workflow_invocation_id=workflow_invocation.id)
+        return WorkflowSchedulingMessage(task="setup", workflow_invocation_id=workflow_invocation.id)
 
     def _assign_handler(self, workflow_invocation, flush=True):
         # Use random-ish integer history_id to produce a consistent index to pick
@@ -124,8 +137,13 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
         if self.app.config.parallelize_workflow_scheduling_within_histories:
             random_index = None
         return self.__handlers_config.assign_handler(
-            workflow_invocation, configured=None, index=random_index, queue_callback=queue_callback,
-            message_callback=message_callback, flush=flush)
+            workflow_invocation,
+            configured=None,
+            index=random_index,
+            queue_callback=queue_callback,
+            message_callback=message_callback,
+            flush=flush,
+        )
 
     def shutdown(self):
         exception = None
@@ -164,7 +182,7 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
             workflow_scheduler.startup(self.app)
 
     def __plugins_dict(self):
-        return plugin_config.plugins_dict(galaxy.workflow.schedulers, 'plugin_type')
+        return plugin_config.plugins_dict(galaxy.workflow.schedulers, "plugin_type")
 
     @property
     def __stack_has_pool(self):
@@ -175,7 +193,9 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
     def __init_schedulers(self):
         config_file = self.app.config.workflow_schedulers_config_file
         use_default_scheduler = False
-        if not config_file or (not os.path.exists(config_file) and not self.app.config.is_set('workflow_schedulers_config_file')):
+        if not config_file or (
+            not os.path.exists(config_file) and not self.app.config.is_set("workflow_schedulers_config_file")
+        ):
             log.info("No workflow schedulers plugin config file defined, using default scheduler.")
             use_default_scheduler = True
         elif not os.path.exists(config_file):
@@ -185,7 +205,7 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
         if use_default_scheduler:
             self.__init_default_scheduler()
         else:
-            self.DEFAULT_BASE_HANDLER_POOLS = ('workflow-schedulers',)
+            self.DEFAULT_BASE_HANDLER_POOLS = ("workflow-schedulers",)
             plugins_element = load(config_file).getroot()
             self.__init_schedulers_for_element(plugins_element)
 
@@ -202,7 +222,7 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
 
     def __init_schedulers_for_element(self, plugins_element):
         plugins_kwds = dict(plugins_element.items())
-        self.default_scheduler_id = plugins_kwds.get('default', DEFAULT_SCHEDULER_ID)
+        self.default_scheduler_id = plugins_kwds.get("default", DEFAULT_SCHEDULER_ID)
         for config_element in plugins_element:
             config_element_tag = config_element.tag
             if config_element_tag == "handlers":
@@ -210,21 +230,24 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
 
                 # Determine the default handler(s)
                 self.default_handler_id = self._get_default(
-                    self.app.config, config_element, list(self.handlers.keys()), required=False)
+                    self.app.config, config_element, list(self.handlers.keys()), required=False
+                )
             else:
                 plugin_type = config_element_tag
                 plugin_element = config_element
                 # Configuring a scheduling plugin...
                 plugin_kwds = dict(plugin_element.items())
-                workflow_scheduler_id = plugin_kwds.get('id', None)
+                workflow_scheduler_id = plugin_kwds.get("id", None)
                 self.__init_plugin(plugin_type, workflow_scheduler_id, **plugin_kwds)
 
         if not self.workflow_schedulers:
             raise Exception(EXCEPTION_MESSAGE_NO_SCHEDULERS)
         if self.default_scheduler_id not in self.workflow_schedulers:
             raise Exception(EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER % self.default_scheduler_id)
-        if self.app.config.parallelize_workflow_scheduling_within_histories \
-                and not self.deterministic_handler_assignment:
+        if (
+            self.app.config.parallelize_workflow_scheduling_within_histories
+            and not self.deterministic_handler_assignment
+        ):
             if self.__handlers_configured:
                 # There's an explicit configuration, the admin should fix it.
                 raise Exception(EXCEPTION_MESSAGE_SERIALIZE)
@@ -240,9 +263,9 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
             self._set_default_handler_assignment_methods()
         else:
             self.app.application_stack.init_job_handling(self)
-        log.info("Workflow scheduling handler assignment method(s): %s", ', '.join(self.handler_assignment_methods))
+        log.info("Workflow scheduling handler assignment method(s): %s", ", ".join(self.handler_assignment_methods))
         for tag, handlers in [(t, h) for t, h in self.handlers.items() if isinstance(h, list)]:
-            log.info("Tag [%s] handlers: %s", tag, ', '.join(handlers))
+            log.info("Tag [%s] handlers: %s", tag, ", ".join(handlers))
         self.__handlers_configured = True
 
     def __init_plugin(self, plugin_type, workflow_scheduler_id=None, **kwds):
@@ -262,19 +285,22 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
 
 
 class WorkflowRequestMonitor(Monitors):
-
     def __init__(self, app, workflow_scheduling_manager):
         self.app = app
         self.workflow_scheduling_manager = workflow_scheduling_manager
-        self._init_monitor_thread(name="WorkflowRequestMonitor.monitor_thread", target=self.__monitor, config=app.config)
+        self._init_monitor_thread(
+            name="WorkflowRequestMonitor.monitor_thread", target=self.__monitor, config=app.config
+        )
         self.invocation_grabber = None
         self_handler_tags = set(self.app.job_config.self_handler_tags)
         self_handler_tags.add(self.workflow_scheduling_manager.default_handler_id)
-        handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.workflow_scheduling_manager.handler_assignment_methods)
+        handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(
+            self.workflow_scheduling_manager.handler_assignment_methods
+        )
         if handler_assignment_method:
             self.invocation_grabber = ItemGrabber(
                 app=app,
-                grab_type='WorkflowInvocation',
+                grab_type="WorkflowInvocation",
                 handler_assignment_method=handler_assignment_method,
                 max_grab=self.workflow_scheduling_manager.handler_max_grab,
                 self_handler_tags=self_handler_tags,
@@ -289,8 +315,8 @@ class WorkflowRequestMonitor(Monitors):
                     self.invocation_grabber.grab_unhandled_items()
 
                 monitor_step_timer = self.app.execution_timer_factory.get_timer(
-                    'internal.galaxy.workflows.scheduling_manager.monitor_step',
-                    'Workflow scheduling manager monitor step complete.'
+                    "internal.galaxy.workflows.scheduling_manager.monitor_step",
+                    "Workflow scheduling manager monitor step complete.",
                 )
                 for workflow_scheduler_id, workflow_scheduler in to_monitor.items():
                     if not self.monitor_running:
@@ -299,7 +325,7 @@ class WorkflowRequestMonitor(Monitors):
                     self.__schedule(workflow_scheduler_id, workflow_scheduler)
                 log.trace(monitor_step_timer.to_str())
             except Exception:
-                log.exception('An exception occured scheduling while scheduling workflows')
+                log.exception("An exception occured scheduling while scheduling workflows")
             self._monitor_sleep(1)
 
     def __schedule(self, workflow_scheduler_id, workflow_scheduler):
diff --git a/lib/galaxy/workflow/steps.py b/lib/galaxy/workflow/steps.py
index 1ff7e7e2bd8..be23fc37cee 100644
--- a/lib/galaxy/workflow/steps.py
+++ b/lib/galaxy/workflow/steps.py
@@ -6,12 +6,12 @@ import math
 from galaxy.util.topsort import (
     CycleError,
     topsort,
-    topsort_levels
+    topsort_levels,
 )
 
 
 def attach_ordered_steps(workflow, steps):
-    """ Attempt to topologically order steps and attach to workflow. If this
+    """Attempt to topologically order steps and attach to workflow. If this
     fails - the workflow contains cycles so it mark it as such.
     """
     ordered_steps = order_workflow_steps(steps)
@@ -30,10 +30,10 @@ def order_workflow_steps(steps):
     """
     position_data_available = True
     for step in steps:
-        if not step.position or 'left' not in step.position or 'top' not in step.position:
+        if not step.position or "left" not in step.position or "top" not in step.position:
             position_data_available = False
     if position_data_available:
-        steps.sort(key=lambda _: math.sqrt(_.position['left'] ** 2 + _.position['top'] ** 2))
+        steps.sort(key=lambda _: math.sqrt(_.position["left"] ** 2 + _.position["top"] ** 2))
     try:
         edges = sorted(edgelist_for_workflow_steps(steps))
         node_order = topsort(edges)
diff --git a/lib/galaxy/workflow/trs_proxy.py b/lib/galaxy/workflow/trs_proxy.py
index a95e1831aa3..adcdc391d6d 100644
--- a/lib/galaxy/workflow/trs_proxy.py
+++ b/lib/galaxy/workflow/trs_proxy.py
@@ -40,7 +40,7 @@ def parse_search_kwds(search_query):
         "descriptorType": "GALAXY",
     }
     if description_term and description_term.strip():
-        query_kwd["description"] = description_term,
+        query_kwd["description"] = (description_term,)
 
     if keyed_terms is not None:
         for (key, value) in keyed_terms:
@@ -49,7 +49,6 @@ def parse_search_kwds(search_query):
 
 
 class TrsProxy:
-
     def __init__(self, config=None):
         config_file = getattr(config, "trs_servers_config_file", None)
         if config_file and os.path.exists(config_file):
@@ -92,6 +91,7 @@ class TrsProxy:
     def _quote(self, tool_id, **kwd):
         if asbool(kwd.get("tool_id_b64_encoded", False)):
             import base64
+
             tool_id = base64.b64decode(tool_id)
         tool_id = urllib.parse.quote_plus(tool_id)
         return tool_id
diff --git a/lib/galaxy_ext/container_monitor/monitor.py b/lib/galaxy_ext/container_monitor/monitor.py
index 9a11257a873..2e4462b2395 100644
--- a/lib/galaxy_ext/container_monitor/monitor.py
+++ b/lib/galaxy_ext/container_monitor/monitor.py
@@ -18,15 +18,14 @@ from galaxy.util.sockets import get_ip
 
 def parse_ports(container_name, connection_configuration):
     while True:
-        ports_command = docker_util.build_docker_simple_command("port", container_name=container_name, **connection_configuration)
+        ports_command = docker_util.build_docker_simple_command(
+            "port", container_name=container_name, **connection_configuration
+        )
         with tempfile.TemporaryFile(prefix="docker_port_") as stdout_file:
-            exit_code = subprocess.call(ports_command,
-                                        shell=True,
-                                        stdout=stdout_file,
-                                        preexec_fn=os.setpgrp)
+            exit_code = subprocess.call(ports_command, shell=True, stdout=stdout_file, preexec_fn=os.setpgrp)
             if exit_code == 0:
                 stdout_file.seek(0)
-                ports_raw = stdout_file.read().decode('utf-8')
+                ports_raw = stdout_file.read().decode("utf-8")
                 return ports_raw
 
 
@@ -55,8 +54,8 @@ def main():
                 ports = docker_util.parse_port_text(ports_raw)
                 if host_ip is not None:
                     for key in ports:
-                        if ports[key]['host'] == '0.0.0.0':
-                            ports[key]['host'] = host_ip
+                        if ports[key]["host"] == "0.0.0.0":
+                            ports[key]["host"] = host_ip
                 if callback_url:
                     requests.post(callback_url, json={"container_runtime": ports}, timeout=DEFAULT_SOCKET_TIMEOUT)
                 else:
diff --git a/lib/galaxy_ext/expressions/handle_job.py b/lib/galaxy_ext/expressions/handle_job.py
index 0001520bb01..0d21f75cd29 100644
--- a/lib/galaxy_ext/expressions/handle_job.py
+++ b/lib/galaxy_ext/expressions/handle_job.py
@@ -38,8 +38,8 @@ def run(environment_path=None):
     del inputs["outputs"]
     result = evaluate(None, inputs)
 
-    if '__error_message' in result:
-        raise Exception(result['__error_message'])
+    if "__error_message" in result:
+        raise Exception(result["__error_message"])
     for output in outputs:
         path = output["path"]
         from_expression = output["from_expression"]
diff --git a/lib/galaxy_ext/metadata/set_metadata.py b/lib/galaxy_ext/metadata/set_metadata.py
index 380e3de3336..d28c3b2c569 100644
--- a/lib/galaxy_ext/metadata/set_metadata.py
+++ b/lib/galaxy_ext/metadata/set_metadata.py
@@ -19,4 +19,4 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 
 from galaxy.metadata.set_metadata import set_metadata
 
-__all__ = ('set_metadata', )
+__all__ = ("set_metadata",)
diff --git a/lib/galaxy_test/api/_framework.py b/lib/galaxy_test/api/_framework.py
index cb4db22ecc2..e5d9f8b7f9f 100644
--- a/lib/galaxy_test/api/_framework.py
+++ b/lib/galaxy_test/api/_framework.py
@@ -1,8 +1,12 @@
 from typing import Optional
-from unittest import SkipTest, TestCase
+from unittest import (
+    SkipTest,
+    TestCase,
+)
 
 from galaxy_test.base.api import UsesApiTestCaseMixin
 from galaxy_test.base.testcase import FunctionalTestCase
+
 try:
     from galaxy_test.driver.driver_util import GalaxyTestDriver
 except ImportError:
@@ -25,4 +29,4 @@ class ApiTestCase(FunctionalTestCase, UsesApiTestCaseMixin, TestCase):
         return self._test_driver
 
 
-__all__ = ('ApiTestCase', )
+__all__ = ("ApiTestCase",)
diff --git a/lib/galaxy_test/api/conftest.py b/lib/galaxy_test/api/conftest.py
index 4e896e0a2b7..78077b097b6 100644
--- a/lib/galaxy_test/api/conftest.py
+++ b/lib/galaxy_test/api/conftest.py
@@ -34,28 +34,27 @@ def pytest_configure(config):
 
 
 class JsonReportHooks:
-
     def pytest_json_runtest_metadata(self, item, call):
-        if call.when == 'setup':
+        if call.when == "setup":
             statsd.CURRENT_TEST = str(uuid.uuid4())
             statsd.CURRENT_TEST_METRICS = {"timing": {}, "counter": {}}
             return {}
-        if call.when == 'teardown':
+        if call.when == "teardown":
             statsd.CURRENT_TEST = None
             statsd.CURRENT_TEST_METRICS = None
             return {}
-        if call.when != 'call':
+        if call.when != "call":
             return {}
         return {
-            'start': call.start,
-            'stop': call.stop,
-            'uuid': statsd.CURRENT_TEST,
-            'local_metrics': statsd.CURRENT_TEST_METRICS,
+            "start": call.start,
+            "stop": call.stop,
+            "uuid": statsd.CURRENT_TEST,
+            "local_metrics": statsd.CURRENT_TEST_METRICS,
         }
 
     def pytest_json_modifyreport(self, json_report):
         if os.environ.get("GALAXY_TEST_COLLECT_STATSD", "0") != "0":
-            for test in json_report['tests']:
-                metadata = test['metadata']
-                test_uuid = metadata['uuid']
-                metadata['statsd_metrics'] = get_timings(test_uuid)
+            for test in json_report["tests"]:
+                metadata = test["metadata"]
+                test_uuid = metadata["uuid"]
+                metadata["statsd_metrics"] = get_timings(test_uuid)
diff --git a/lib/galaxy_test/api/sharable.py b/lib/galaxy_test/api/sharable.py
index 47144b61566..3822cbc5abd 100644
--- a/lib/galaxy_test/api/sharable.py
+++ b/lib/galaxy_test/api/sharable.py
@@ -1,11 +1,15 @@
-from typing import Any, Dict, List
+from typing import (
+    Any,
+    Dict,
+    List,
+)
 from unittest import SkipTest
 
 from galaxy_test.base.api import UsesApiTestCaseMixin
 
 
 class SharingApiTests(UsesApiTestCaseMixin):
-    """ Includes some tests for the sharing functionality of a particular resource type."""
+    """Includes some tests for the sharing functionality of a particular resource type."""
 
     # The api_name has to be set to the appropriate value in the class using these tests.
     api_name: str
@@ -21,7 +25,9 @@ class SharingApiTests(UsesApiTestCaseMixin):
     def test_sharing_get_status(self):
         resource_id = self.create("resource-to-share")
         sharing_response = self._get_resource_sharing_status(resource_id)
-        self._assert_has_keys(sharing_response, "title", "importable", "id", "username_and_slug", "published", "users_shared_with")
+        self._assert_has_keys(
+            sharing_response, "title", "importable", "id", "username_and_slug", "published", "users_shared_with"
+        )
 
     def test_sharing_access(self):
         resource_id = self.create("resource-to-enable-link-access")
@@ -151,7 +157,9 @@ class SharingApiTests(UsesApiTestCaseMixin):
         self._assert_status_code_is(sharing_response, 200)
         return sharing_response.json()
 
-    def _set_resource_sharing(self, resource_id: str, action: str, payload: Any = None, expect_response_status: int = 200):
+    def _set_resource_sharing(
+        self, resource_id: str, action: str, payload: Any = None, expect_response_status: int = 200
+    ):
         sharing_response = self._put(f"{self.api_name}/{resource_id}/{action}", data=payload, json=True)
         self._assert_status_code_is(sharing_response, expect_response_status)
         return sharing_response.json()
diff --git a/lib/galaxy_test/api/test_api_batch.py b/lib/galaxy_test/api/test_api_batch.py
index cbdbd11139f..788417b7109 100644
--- a/lib/galaxy_test/api/test_api_batch.py
+++ b/lib/galaxy_test/api/test_api_batch.py
@@ -6,12 +6,11 @@ from ._framework import ApiTestCase
 
 
 class ApiBatchTestCase(ApiTestCase):
-
     def _get_api_key(self, admin=False):
         return self.galaxy_interactor.api_key if not admin else self.galaxy_interactor.master_api_key
 
     def _with_key(self, url, admin=False):
-        sep = '&' if '?' in url else '?'
+        sep = "&" if "?" in url else "?"
         return f"{url + sep}key={self._get_api_key(admin=admin)}"
 
     def _post_batch(self, batch):
@@ -21,10 +20,9 @@ class ApiBatchTestCase(ApiTestCase):
     # ---- tests
     def test_simple_array(self):
         batch = [
-            dict(url=self._with_key('/api/histories')),
-            dict(url=self._with_key('/api/histories'),
-                 method='POST', body=json.dumps(dict(name='Wat'))),
-            dict(url=self._with_key('/api/histories')),
+            dict(url=self._with_key("/api/histories")),
+            dict(url=self._with_key("/api/histories"), method="POST", body=json.dumps(dict(name="Wat"))),
+            dict(url=self._with_key("/api/histories")),
         ]
         response = self._post_batch(batch)
         response = response.json()
@@ -32,38 +30,34 @@ class ApiBatchTestCase(ApiTestCase):
         self.assertEqual(len(response), 3)
 
     def test_unallowed_route(self):
-        batch = [
-            dict(url=self._with_key('/api/workflow'))
-        ]
+        batch = [dict(url=self._with_key("/api/workflow"))]
         response = self._post_batch(batch)
         response = response.json()
         self.assertIsInstance(response, list)
-        self.assertEqual(response[0]['status'], 403)
+        self.assertEqual(response[0]["status"], 403)
 
     def test_404_route(self):
         # needs to be within the allowed routes
-        batch = [
-            dict(url=self._with_key('/api/histories_bler'))
-        ]
+        batch = [dict(url=self._with_key("/api/histories_bler"))]
         response = self._post_batch(batch)
         response = response.json()
         self.assertIsInstance(response, list)
-        self.assertEqual(response[0]['status'], 404)
+        self.assertEqual(response[0]["status"], 404)
 
     def test_errors(self):
         batch = [
-            dict(url=self._with_key('/api/histories/abc123')),
-            dict(url=self._with_key('/api/jobs'), method='POST', body=json.dumps(dict(name='Wat'))),
+            dict(url=self._with_key("/api/histories/abc123")),
+            dict(url=self._with_key("/api/jobs"), method="POST", body=json.dumps(dict(name="Wat"))),
         ]
         response = self._post_batch(batch)
         response = response.json()
         self.assertIsInstance(response, list)
-        self.assertEqual(response[0]['status'], 400)
-        self.assertEqual(response[1]['status'], 501)
+        self.assertEqual(response[0]["status"], 400)
+        self.assertEqual(response[1]["status"], 501)
 
     def test_querystring_params(self):
-        post_data = dict(name='test')
-        create_response = self._post('histories', data=post_data).json()
+        post_data = dict(name="test")
+        create_response = self._post("histories", data=post_data).json()
 
         history_url = f"/api/histories/{create_response['id']}"
         history_url_with_keys = f"{history_url}?v=dev&keys=size,non_ready_jobs"
@@ -75,5 +69,5 @@ class ApiBatchTestCase(ApiTestCase):
         response = self._post_batch(batch)
         response = response.json()
         self.assertEqual(len(response), 2)
-        self.assertEqual(len(response[0]['body'].keys()), 2)
-        self.assertEqual(response[1]['body'], [])
+        self.assertEqual(len(response[0]["body"].keys()), 2)
+        self.assertEqual(response[1]["body"], [])
diff --git a/lib/galaxy_test/api/test_authenticate.py b/lib/galaxy_test/api/test_authenticate.py
index 613fd80640d..fc63dc1a0a6 100644
--- a/lib/galaxy_test/api/test_authenticate.py
+++ b/lib/galaxy_test/api/test_authenticate.py
@@ -9,7 +9,6 @@ TEST_USER_PASSWORD = "testpassword1"
 
 
 class AuthenticationApiTestCase(ApiTestCase):
-
     def test_auth(self):
         self._setup_user(TEST_USER_EMAIL, TEST_USER_PASSWORD)
         baseauth_url = self._api_url("authenticate/baseauth", use_key=False)
diff --git a/lib/galaxy_test/api/test_configuration.py b/lib/galaxy_test/api/test_configuration.py
index f0e73b98cb7..b3c8f296d08 100644
--- a/lib/galaxy_test/api/test_configuration.py
+++ b/lib/galaxy_test/api/test_configuration.py
@@ -6,28 +6,27 @@ from galaxy_test.base.api_util import TEST_USER
 from ._framework import ApiTestCase
 
 TEST_KEYS_FOR_ALL_USERS = [
-    'enable_unique_workflow_defaults',
-    'ftp_upload_site',
-    'wiki_url',
-    'support_url',
-    'logo_url',
-    'terms_url',
-    'allow_user_dataset_purge',
+    "enable_unique_workflow_defaults",
+    "ftp_upload_site",
+    "wiki_url",
+    "support_url",
+    "logo_url",
+    "terms_url",
+    "allow_user_dataset_purge",
 ]
 TEST_KEYS_FOR_ADMIN_ONLY = [
-    'library_import_dir',
-    'user_library_import_dir',
-    'allow_library_path_paste',
-    'allow_user_deletion',
+    "library_import_dir",
+    "user_library_import_dir",
+    "allow_library_path_paste",
+    "allow_user_deletion",
 ]
 
 
 class ConfigurationApiTestCase(ApiTestCase):
-
     def test_whoami(self):
         response = self._get("whoami")
         self._assert_status_code_is(response, 200)
-        assert response.json()['email'] == TEST_USER
+        assert response.json()["email"] == TEST_USER
 
     def test_normal_user_configuration(self):
         config = self._get_configuration()
@@ -54,5 +53,5 @@ class ConfigurationApiTestCase(ApiTestCase):
         response = self._get("version")
         self._assert_status_code_is(response, 200)
         data = response.json()
-        assert 'version_major' in data
-        assert 'version_minor' in data
+        assert "version_major" in data
+        assert "version_minor" in data
diff --git a/lib/galaxy_test/api/test_dataset_collections.py b/lib/galaxy_test/api/test_dataset_collections.py
index e81d65cc0a9..cf7982a097b 100644
--- a/lib/galaxy_test/api/test_dataset_collections.py
+++ b/lib/galaxy_test/api/test_dataset_collections.py
@@ -4,7 +4,11 @@ from io import BytesIO
 from typing import List
 
 from galaxy_test.base.api_asserts import assert_object_id_error
-from galaxy_test.base.populators import DatasetCollectionPopulator, DatasetPopulator, skip_if_github_down
+from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    skip_if_github_down,
+)
 from ._framework import ApiTestCase
 
 
@@ -51,9 +55,7 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         dataset_collection = self._check_create_response(pair_create_response)
         hdca_id = dataset_collection["id"]
 
-        element_identifiers = [
-            dict(name="test1", src="hdca", id=hdca_id)
-        ]
+        element_identifiers = [dict(name="test1", src="hdca", id=hdca_id)]
 
         payload = dict(
             instance_type="history",
@@ -95,31 +97,37 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         assert pair_1_element_1["element_index"] == 0
 
     def test_list_download(self):
-        fetch_response = self.dataset_collection_populator.create_list_in_history(self.history_id, direct_upload=True).json()
+        fetch_response = self.dataset_collection_populator.create_list_in_history(
+            self.history_id, direct_upload=True
+        ).json()
         dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
         returned_dce = dataset_collection["elements"]
         assert len(returned_dce) == 3, dataset_collection
-        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
+        create_response = self._download_dataset_collection(
+            history_id=self.history_id, hdca_id=dataset_collection["id"]
+        )
         self._assert_status_code_is(create_response, 200)
         archive = zipfile.ZipFile(BytesIO(create_response.content))
         namelist = archive.namelist()
         assert len(namelist) == 3, f"Expected 3 elements in [{namelist}]"
-        collection_name = dataset_collection['name']
+        collection_name = dataset_collection["name"]
         for element, zip_path in zip(returned_dce, namelist):
             assert f"{collection_name}/{element['element_identifier']}.{element['object']['file_ext']}" == zip_path
 
     def test_pair_download(self):
-        fetch_response = self.dataset_collection_populator.create_pair_in_history(self.history_id, direct_upload=True).json()
+        fetch_response = self.dataset_collection_populator.create_pair_in_history(
+            self.history_id, direct_upload=True
+        ).json()
         dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
         returned_dce = dataset_collection["elements"]
         assert len(returned_dce) == 2, dataset_collection
-        hdca_id = dataset_collection['id']
+        hdca_id = dataset_collection["id"]
         create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=hdca_id)
         self._assert_status_code_is(create_response, 200)
         archive = zipfile.ZipFile(BytesIO(create_response.content))
         namelist = archive.namelist()
         assert len(namelist) == 2, f"Expected 2 elements in [{namelist}]"
-        collection_name = dataset_collection['name']
+        collection_name = dataset_collection["name"]
         for element, zip_path in zip(returned_dce, namelist):
             assert f"{collection_name}/{element['element_identifier']}.{element['object']['file_ext']}" == zip_path
 
@@ -128,34 +136,45 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
         returned_dce = dataset_collection["elements"]
         assert len(returned_dce) == 1, dataset_collection
-        list_collection_name = dataset_collection['name']
+        list_collection_name = dataset_collection["name"]
         pair = returned_dce[0]
-        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
+        create_response = self._download_dataset_collection(
+            history_id=self.history_id, hdca_id=dataset_collection["id"]
+        )
         self._assert_status_code_is(create_response, 200)
         archive = zipfile.ZipFile(BytesIO(create_response.content))
         namelist = archive.namelist()
         assert len(namelist) == 2, f"Expected 2 elements in [{namelist}]"
-        pair_collection_name = pair['element_identifier']
-        for element, zip_path in zip(pair['object']['elements'], namelist):
-            assert f"{list_collection_name}/{pair_collection_name}/{element['element_identifier']}.{element['object']['file_ext']}" == zip_path
+        pair_collection_name = pair["element_identifier"]
+        for element, zip_path in zip(pair["object"]["elements"], namelist):
+            assert (
+                f"{list_collection_name}/{pair_collection_name}/{element['element_identifier']}.{element['object']['file_ext']}"
+                == zip_path
+            )
 
     def test_list_list_download(self):
         dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(self.history_id).json()
         self.dataset_collection_populator.wait_for_dataset_collection(dataset_collection, assert_ok=True)
         returned_dce = dataset_collection["elements"]
         assert len(returned_dce) == 1, dataset_collection
-        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
+        create_response = self._download_dataset_collection(
+            history_id=self.history_id, hdca_id=dataset_collection["id"]
+        )
         self._assert_status_code_is(create_response, 200)
         archive = zipfile.ZipFile(BytesIO(create_response.content))
         namelist = archive.namelist()
         assert len(namelist) == 3, f"Expected 3 elements in [{namelist}]"
 
     def test_list_list_list_download(self):
-        dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(self.history_id, collection_type='list:list:list').json()
+        dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(
+            self.history_id, collection_type="list:list:list"
+        ).json()
         self.dataset_collection_populator.wait_for_dataset_collection(dataset_collection, assert_ok=True)
         returned_dce = dataset_collection["elements"]
         assert len(returned_dce) == 1, dataset_collection
-        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
+        create_response = self._download_dataset_collection(
+            history_id=self.history_id, hdca_id=dataset_collection["id"]
+        )
         self._assert_status_code_is(create_response, 200)
         archive = zipfile.ZipFile(BytesIO(create_response.content))
         namelist = archive.namelist()
@@ -189,14 +208,23 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         self._assert_status_code_is(create_response, 400)
 
     def test_upload_collection(self):
-        elements = [{"src": "files", "dbkey": "hg19", "info": "my cool bed", "tags": ["name:data1", "group:condition:treated", "machine:illumina"]}]
-        targets = [{
-            "destination": {"type": "hdca"},
-            "elements": elements,
-            "collection_type": "list",
-            "name": "Test upload",
-            "tags": ["name:collection1"]
-        }]
+        elements = [
+            {
+                "src": "files",
+                "dbkey": "hg19",
+                "info": "my cool bed",
+                "tags": ["name:data1", "group:condition:treated", "machine:illumina"],
+            }
+        ]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": "list",
+                "name": "Test upload",
+                "tags": ["name:collection1"],
+            }
+        ]
         payload = {
             "history_id": self.history_id,
             "targets": json.dumps(targets),
@@ -218,12 +246,14 @@ class DatasetCollectionApiTestCase(ApiTestCase):
 
     def test_upload_nested(self):
         elements = [{"name": "samp1", "elements": [{"src": "files", "dbkey": "hg19", "info": "my cool bed"}]}]
-        targets = [{
-            "destination": {"type": "hdca"},
-            "elements": elements,
-            "collection_type": "list:list",
-            "name": "Test upload",
-        }]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": "list:list",
+                "name": "Test upload",
+            }
+        ]
         payload = {
             "history_id": self.history_id,
             "targets": json.dumps(targets),
@@ -238,12 +268,20 @@ class DatasetCollectionApiTestCase(ApiTestCase):
 
     @skip_if_github_down
     def test_upload_collection_from_url(self):
-        elements = [{"src": "url", "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed", "info": "my cool bed"}]
-        targets = [{
-            "destination": {"type": "hdca"},
-            "elements": elements,
-            "collection_type": "list",
-        }]
+        elements = [
+            {
+                "src": "url",
+                "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed",
+                "info": "my cool bed",
+            }
+        ]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": "list",
+            }
+        ]
         payload = {
             "history_id": self.history_id,
             "targets": json.dumps(targets),
@@ -258,13 +296,15 @@ class DatasetCollectionApiTestCase(ApiTestCase):
 
     @skip_if_github_down
     def test_upload_collection_failed_expansion_url(self):
-        targets = [{
-            "destination": {"type": "hdca"},
-            "elements_from": "bagit",
-            "collection_type": "list",
-            "src": "url",
-            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed",
-        }]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements_from": "bagit",
+                "collection_type": "list",
+                "src": "url",
+                "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed",
+            }
+        ]
         payload = {
             "history_id": self.history_id,
             "targets": json.dumps(targets),
@@ -308,21 +348,23 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         hdca, contents_url = self._create_collection_contents_pair()
         response = self._get(contents_url)
         self._assert_status_code_is(response, 200)
-        fake_collection_id = '5d7db0757a2eb7ef'
+        fake_collection_id = "5d7db0757a2eb7ef"
         fake_contents_url = f"/api/dataset_collections/{hdca['id']}/contents/{fake_collection_id}"
         error_response = self._get(fake_contents_url)
         assert_object_id_error(error_response)
 
     def test_show_dataset_collection(self):
-        fetch_response = self.dataset_collection_populator.create_list_in_history(self.history_id, direct_upload=True).json()
+        fetch_response = self.dataset_collection_populator.create_list_in_history(
+            self.history_id, direct_upload=True
+        ).json()
         dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
         returned_dce = dataset_collection["elements"]
         assert len(returned_dce) == 3, dataset_collection
-        hdca_id = dataset_collection['id']
+        hdca_id = dataset_collection["id"]
         dataset_collection_url = f"/api/dataset_collections/{hdca_id}"
         dataset_collection = self._get(dataset_collection_url).json()
-        assert dataset_collection['id'] == hdca_id
-        assert dataset_collection['collection_type'] == 'list'
+        assert dataset_collection["id"] == hdca_id
+        assert dataset_collection["collection_type"] == "list"
 
     def test_show_dataset_collection_contents(self):
         # Get contents_url from history contents, use it to show the first level
@@ -333,16 +375,16 @@ class DatasetCollectionApiTestCase(ApiTestCase):
 
         # check root contents for this collection
         root_contents = self._get(root_contents_url).json()
-        assert len(root_contents) == len(hdca['elements'])
-        self._compare_collection_contents_elements(root_contents, hdca['elements'])
+        assert len(root_contents) == len(hdca["elements"])
+        self._compare_collection_contents_elements(root_contents, hdca["elements"])
 
         # drill down, retrieve nested collection contents
-        assert 'object' in root_contents[0]
-        assert 'contents_url' in root_contents[0]['object']
-        drill_contents_url = root_contents[0]['object']['contents_url']
+        assert "object" in root_contents[0]
+        assert "contents_url" in root_contents[0]["object"]
+        drill_contents_url = root_contents[0]["object"]["contents_url"]
         drill_contents = self._get(drill_contents_url).json()
-        assert len(drill_contents) == len(hdca['elements'][0]['object']['elements'])
-        self._compare_collection_contents_elements(drill_contents, hdca['elements'][0]['object']['elements'])
+        assert len(drill_contents) == len(hdca["elements"][0]["object"]["elements"])
+        self._compare_collection_contents_elements(drill_contents, hdca["elements"][0]["object"]["elements"])
 
     def test_collection_contents_limit_offset(self):
         # check limit/offset params for collection contents endpoint
@@ -351,92 +393,107 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         # check limit
         limited_contents = self._get(f"{root_contents_url}?limit=1").json()
         assert len(limited_contents) == 1
-        assert limited_contents[0]['element_index'] == 0
+        assert limited_contents[0]["element_index"] == 0
 
         # check offset
         offset_contents = self._get(f"{root_contents_url}?offset=1").json()
         assert len(offset_contents) == 1
-        assert offset_contents[0]['element_index'] == 1
+        assert offset_contents[0]["element_index"] == 1
 
     def test_get_suitable_converters_single_datatype(self):
-        response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[
-            {
-                "name": "test0",
-                "elements": [
-                    {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
-                    {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
-                ]
-            },
-            {
-                "name": "test1",
-                "elements": [
-                    {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "bed"},
-                    {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "bed"},
-                ]
-            }
-        ])
+        response = self.dataset_collection_populator.upload_collection(
+            self.history_id,
+            "list:paired",
+            elements=[
+                {
+                    "name": "test0",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
+                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
+                    ],
+                },
+                {
+                    "name": "test1",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "bed"},
+                        {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "bed"},
+                    ],
+                },
+            ],
+        )
         self._assert_status_code_is(response, 200)
         hdca_list_id = response.json()["outputs"][0]["id"]
         converters = self._get("dataset_collections/" + hdca_list_id + "/suitable_converters")
         expected = [  # This list is subject to change, but it's unlikely we'll be removing converters
-            'CONVERTER_bed_to_fli_0',
-            'CONVERTER_bed_gff_or_vcf_to_bigwig_0',
-            'CONVERTER_bed_to_gff_0',
-            'CONVERTER_interval_to_bgzip_0',
-            'tabular_to_csv',
-            'CONVERTER_interval_to_bed6_0',
-            'CONVERTER_interval_to_bedstrict_0',
-            'CONVERTER_interval_to_tabix_0',
-            'CONVERTER_interval_to_bed12_0']
+            "CONVERTER_bed_to_fli_0",
+            "CONVERTER_bed_gff_or_vcf_to_bigwig_0",
+            "CONVERTER_bed_to_gff_0",
+            "CONVERTER_interval_to_bgzip_0",
+            "tabular_to_csv",
+            "CONVERTER_interval_to_bed6_0",
+            "CONVERTER_interval_to_bedstrict_0",
+            "CONVERTER_interval_to_tabix_0",
+            "CONVERTER_interval_to_bed12_0",
+        ]
         actual = []
         for converter in converters.json():
             actual.append(converter["tool_id"])
         missing_expected_converters = set(expected) - set(actual)
-        assert not missing_expected_converters, f"Expected converter(s) {', '.join(missing_expected_converters)} missing from response"
+        assert (
+            not missing_expected_converters
+        ), f"Expected converter(s) {', '.join(missing_expected_converters)} missing from response"
 
     def test_get_suitable_converters_different_datatypes_matches(self):
-        response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[
-            {
-                "name": "test0",
-                "elements": [
-                    {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
-                    {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
-                ]
-            },
-            {
-                "name": "test1",
-                "elements": [
-                    {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "tabular"},
-                    {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "tabular"},
-                ]
-            }
-        ])
+        response = self.dataset_collection_populator.upload_collection(
+            self.history_id,
+            "list:paired",
+            elements=[
+                {
+                    "name": "test0",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
+                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
+                    ],
+                },
+                {
+                    "name": "test1",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "tabular"},
+                        {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "tabular"},
+                    ],
+                },
+            ],
+        )
         self._assert_status_code_is(response, 200)
         hdca_list_id = response.json()["outputs"][0]["id"]
         converters = self._get("dataset_collections/" + hdca_list_id + "/suitable_converters")
-        expected = 'tabular_to_csv'
+        expected = "tabular_to_csv"
         actual = []
         for converter in converters.json():
             actual.append(converter["tool_id"])
         assert expected in actual
 
     def test_get_suitable_converters_different_datatypes_no_matches(self):
-        response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[
-            {
-                "name": "test0",
-                "elements": [
-                    {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
-                    {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
-                ]
-            },
-            {
-                "name": "test1",
-                "elements": [
-                    {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "fasta"},
-                    {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "fasta"},
-                ]
-            }
-        ])
+        response = self.dataset_collection_populator.upload_collection(
+            self.history_id,
+            "list:paired",
+            elements=[
+                {
+                    "name": "test0",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "bed"},
+                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "bed"},
+                    ],
+                },
+                {
+                    "name": "test1",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "fasta"},
+                        {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "fasta"},
+                    ],
+                },
+            ],
+        )
         self._assert_status_code_is(response, 200)
         hdca_list_id = response.json()["outputs"][0]["id"]
         converters = self._get("dataset_collections/" + hdca_list_id + "/suitable_converters")
@@ -447,40 +504,42 @@ class DatasetCollectionApiTestCase(ApiTestCase):
 
     def test_collection_tools_tag_propagation(self):
         elements = [{"src": "files", "tags": ["name:element_tag"]}]
-        targets = [{
-            "destination": {"type": "hdca"},
-            "elements": elements,
-            "collection_type": "list",
-            "name": "Test collection",
-            "tags": ["name:collection_tag"]
-        }]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": "list",
+                "name": "Test collection",
+                "tags": ["name:collection_tag"],
+            }
+        ]
         payload = {
             "history_id": self.history_id,
             "targets": json.dumps(targets),
             "__files": {"files_0|file_data": open(self.test_data_resolver.get_filename("4.bed"))},
         }
-        hdca_id = self.dataset_populator.fetch(payload).json()['output_collections'][0]['id']
+        hdca_id = self.dataset_populator.fetch(payload).json()["output_collections"][0]["id"]
         inputs = {
             "input": {"batch": False, "src": "hdca", "id": hdca_id},
         }
         payload = self.dataset_populator.run_tool_payload(
-            tool_id='__FILTER_FAILED_DATASETS__',
+            tool_id="__FILTER_FAILED_DATASETS__",
             inputs=inputs,
             history_id=self.history_id,
-            input_format='legacy',
+            input_format="legacy",
         )
         response = self._post("tools", payload).json()
         self.dataset_populator.wait_for_history(self.history_id, assert_ok=False)
         output_collection = response["output_collections"][0]
         # collection should not inherit tags from input collection elements, only parent collection
-        assert output_collection['tags'] == ["name:collection_tag"]
-        element = output_collection['elements'][0]
+        assert output_collection["tags"] == ["name:collection_tag"]
+        element = output_collection["elements"][0]
         # new element hda should have tags copied from old hda
-        assert element['object']['tags'] == ['name:element_tag']
+        assert element["object"]["tags"] == ["name:element_tag"]
 
     def _compare_collection_contents_elements(self, contents_elements, hdca_elements):
         # compare collection api results to existing hdca element contents
-        fields = ['element_identifier', 'element_index', 'element_type', 'id', 'model_class']
+        fields = ["element_identifier", "element_index", "element_type", "id", "model_class"]
         for (content_element, hdca_element) in zip(contents_elements, hdca_elements):
             for f in fields:
                 assert content_element[f] == hdca_element[f]
@@ -501,10 +560,10 @@ class DatasetCollectionApiTestCase(ApiTestCase):
         # filter out the collection we just made id = hdca.id
         # make sure the contents_url appears
         def find_hdca(c):
-            return c['history_content_type'] == 'dataset_collection' and c['id'] == hdca['id']
+            return c["history_content_type"] == "dataset_collection" and c["id"] == hdca["id"]
 
         matches = list(filter(find_hdca, json))
         assert len(matches) == 1
-        assert 'contents_url' in matches[0]
+        assert "contents_url" in matches[0]
 
-        return matches[0]['contents_url']
+        return matches[0]["contents_url"]
diff --git a/lib/galaxy_test/api/test_datasets.py b/lib/galaxy_test/api/test_datasets.py
index 88488736c01..a9b0e79698a 100644
--- a/lib/galaxy_test/api/test_datasets.py
+++ b/lib/galaxy_test/api/test_datasets.py
@@ -22,79 +22,101 @@ class DatasetsApiTestCase(ApiTestCase):
         self._assert_status_code_is(index_response, 200)
 
     def test_search_datasets(self):
-        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
-        payload = {'limit': 1, 'offset': 0}
+        hda_id = self.dataset_populator.new_dataset(self.history_id)["id"]
+        payload = {"limit": 1, "offset": 0}
         index_response = self._get("datasets", payload).json()
         assert len(index_response) == 1
-        assert index_response[0]['id'] == hda_id
-        hdca_id = self.dataset_collection_populator.create_list_in_history(self.history_id,
-                                                                           contents=["1\n2\n3"]).json()['id']
-        index_payload_1 = {'limit': 3, 'offset': 0}
+        assert index_response[0]["id"] == hda_id
+        hdca_id = self.dataset_collection_populator.create_list_in_history(
+            self.history_id, contents=["1\n2\n3"]
+        ).json()["id"]
+        index_payload_1 = {"limit": 3, "offset": 0}
         index_response = self._get("datasets", index_payload_1).json()
         assert len(index_response) == 3
-        assert index_response[0]['id'] == hdca_id
-        assert index_response[0]['history_content_type'] == 'dataset_collection'
-        assert index_response[2]['id'] == hda_id
-        assert index_response[2]['history_content_type'] == 'dataset'
-        index_payload_2 = {'limit': 2, 'offset': 0, 'q': ['history_content_type'], 'qv': ['dataset']}
+        assert index_response[0]["id"] == hdca_id
+        assert index_response[0]["history_content_type"] == "dataset_collection"
+        assert index_response[2]["id"] == hda_id
+        assert index_response[2]["history_content_type"] == "dataset"
+        index_payload_2 = {"limit": 2, "offset": 0, "q": ["history_content_type"], "qv": ["dataset"]}
         index_response = self._get("datasets", index_payload_2).json()
-        assert index_response[1]['id'] == hda_id
+        assert index_response[1]["id"] == hda_id
 
     def test_search_by_tag(self):
-        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
+        hda_id = self.dataset_populator.new_dataset(self.history_id)["id"]
         update_payload = {
-            'tags': ['cool:new_tag', 'cool:another_tag'],
+            "tags": ["cool:new_tag", "cool:another_tag"],
         }
-        updated_hda = self._put(
-            f"histories/{self.history_id}/contents/{hda_id}",
-            update_payload, json=True).json()
-        assert 'cool:new_tag' in updated_hda['tags']
-        assert 'cool:another_tag' in updated_hda['tags']
-        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag'], 'qv': ['dataset', 'cool:new_tag']}
+        updated_hda = self._put(f"histories/{self.history_id}/contents/{hda_id}", update_payload, json=True).json()
+        assert "cool:new_tag" in updated_hda["tags"]
+        assert "cool:another_tag" in updated_hda["tags"]
+        payload = {"limit": 10, "offset": 0, "q": ["history_content_type", "tag"], "qv": ["dataset", "cool:new_tag"]}
         index_response = self._get("datasets", payload).json()
         assert len(index_response) == 1
-        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-contains'],
-                   'qv': ['dataset', 'new_tag']}
+        payload = {
+            "limit": 10,
+            "offset": 0,
+            "q": ["history_content_type", "tag-contains"],
+            "qv": ["dataset", "new_tag"],
+        }
         index_response = self._get("datasets", payload).json()
         assert len(index_response) == 1
-        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-contains'], 'qv': ['dataset', 'notag']}
+        payload = {"limit": 10, "offset": 0, "q": ["history_content_type", "tag-contains"], "qv": ["dataset", "notag"]}
         index_response = self._get("datasets", payload).json()
         assert len(index_response) == 0
 
     def test_search_by_tool_id(self):
         self.dataset_populator.new_dataset(self.history_id)
-        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id'], 'qv': ['dataset', 'upload1']}
+        payload = {"limit": 1, "offset": 0, "q": ["history_content_type", "tool_id"], "qv": ["dataset", "upload1"]}
         assert len(self._get("datasets", payload).json()) == 1
-        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id'], 'qv': ['dataset', 'uploadX']}
+        payload = {"limit": 1, "offset": 0, "q": ["history_content_type", "tool_id"], "qv": ["dataset", "uploadX"]}
         assert len(self._get("datasets", payload).json()) == 0
-        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id-contains'], 'qv': ['dataset', 'pload1']}
+        payload = {
+            "limit": 1,
+            "offset": 0,
+            "q": ["history_content_type", "tool_id-contains"],
+            "qv": ["dataset", "pload1"],
+        }
         assert len(self._get("datasets", payload).json()) == 1
-        self.dataset_collection_populator.create_list_in_history(self.history_id,
-                                                                 name="search by tool id",
-                                                                 contents=["1\n2\n3"]).json()
+        self.dataset_collection_populator.create_list_in_history(
+            self.history_id, name="search by tool id", contents=["1\n2\n3"]
+        ).json()
         self.dataset_populator.wait_for_history(self.history_id)
-        payload = {'limit': 10, 'offset': 0, 'history_id': self.history_id, 'q': ['name', 'tool_id'],
-                   'qv': ['search by tool id', 'upload1']}
+        payload = {
+            "limit": 10,
+            "offset": 0,
+            "history_id": self.history_id,
+            "q": ["name", "tool_id"],
+            "qv": ["search by tool id", "upload1"],
+        }
         result = self._get("datasets", payload).json()
-        assert result[0]['name'] == 'search by tool id', result
-        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id'],
-                   'qv': ['dataset_collection', 'uploadX']}
+        assert result[0]["name"] == "search by tool id", result
+        payload = {
+            "limit": 1,
+            "offset": 0,
+            "q": ["history_content_type", "tool_id"],
+            "qv": ["dataset_collection", "uploadX"],
+        }
         result = self._get("datasets", payload).json()
         assert len(result) == 0
 
     def test_invalid_search(self):
-        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-invalid_op'], 'qv': ['dataset', 'notag']}
+        payload = {
+            "limit": 10,
+            "offset": 0,
+            "q": ["history_content_type", "tag-invalid_op"],
+            "qv": ["dataset", "notag"],
+        }
         index_response = self._get("datasets", payload)
         self._assert_status_code_is(index_response, 400)
-        assert index_response.json()['err_msg'] == 'bad op in filter'
+        assert index_response.json()["err_msg"] == "bad op in filter"
 
     def test_search_returns_only_accessible(self):
-        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
+        hda_id = self.dataset_populator.new_dataset(self.history_id)["id"]
         with self._different_user():
-            payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type'], 'qv': ['dataset']}
+            payload = {"limit": 10, "offset": 0, "q": ["history_content_type"], "qv": ["dataset"]}
             index_response = self._get("datasets", payload).json()
             for item in index_response:
-                assert hda_id != item['id']
+                assert hda_id != item["id"]
 
     def test_show(self):
         hda1 = self.dataset_populator.new_dataset(self.history_id)
@@ -104,7 +126,7 @@ class DatasetsApiTestCase(ApiTestCase):
 
     def test_show_permission_denied(self):
         hda = self.dataset_populator.new_dataset(self.history_id)
-        self.dataset_populator.make_private(history_id=self.history_id, dataset_id=hda['id'])
+        self.dataset_populator.make_private(history_id=self.history_id, dataset_id=hda["id"])
         with self._different_user():
             show_response = self._get(f"datasets/{hda['id']}")
             self._assert_status_code_is(show_response, 403)
@@ -112,7 +134,7 @@ class DatasetsApiTestCase(ApiTestCase):
     def test_admin_can_update_permissions(self):
         # Create private dataset
         hda = self.dataset_populator.new_dataset(self.history_id)
-        dataset_id = hda['id']
+        dataset_id = hda["id"]
         self.dataset_populator.make_private(history_id=self.history_id, dataset_id=dataset_id)
 
         # Admin removes restrictions
@@ -131,49 +153,47 @@ class DatasetsApiTestCase(ApiTestCase):
         assert input_hda["id"] == query_hda["id"]
 
     def test_display(self):
-        contents = textwrap.dedent("""\
+        contents = textwrap.dedent(
+            """\
         1   2   3   4
         A   B   C   D
         10  20  30  40
-        """)
+        """
+        )
         hda1 = self.dataset_populator.new_dataset(self.history_id, content=contents)
         self.dataset_populator.wait_for_history(self.history_id)
-        display_response = self._get(f"histories/{self.history_id}/contents/{hda1['id']}/display", {
-            'raw': 'True'
-        })
+        display_response = self._get(f"histories/{self.history_id}/contents/{hda1['id']}/display", {"raw": "True"})
         self._assert_status_code_is(display_response, 200)
         assert display_response.text == contents
 
     def test_tag_change(self):
-        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
+        hda_id = self.dataset_populator.new_dataset(self.history_id)["id"]
         payload = {
-            'item_id': hda_id,
-            'item_class': 'HistoryDatasetAssociation',
-            'item_tags': ['cool:tag_a', 'cool:tag_b', 'tag_c', 'name:tag_d', '#tag_e'],
+            "item_id": hda_id,
+            "item_class": "HistoryDatasetAssociation",
+            "item_tags": ["cool:tag_a", "cool:tag_b", "tag_c", "name:tag_d", "#tag_e"],
         }
 
         put_response = self._put("tags", data=payload, json=True)
         self._assert_status_code_is_ok(put_response)
-        updated_hda = self._get(
-            f"histories/{self.history_id}/contents/{hda_id}").json()
-        assert 'cool:tag_a' in updated_hda['tags']
-        assert 'cool:tag_b' in updated_hda['tags']
-        assert 'tag_c' in updated_hda['tags']
-        assert 'name:tag_d' in updated_hda['tags']
-        assert 'name:tag_e' in updated_hda['tags']
+        updated_hda = self._get(f"histories/{self.history_id}/contents/{hda_id}").json()
+        assert "cool:tag_a" in updated_hda["tags"]
+        assert "cool:tag_b" in updated_hda["tags"]
+        assert "tag_c" in updated_hda["tags"]
+        assert "name:tag_d" in updated_hda["tags"]
+        assert "name:tag_e" in updated_hda["tags"]
 
     @skip_without_tool("cat_data_and_sleep")
     def test_update_datatype(self):
-        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
-        original_hda = self._get(
-            f"histories/{self.history_id}/contents/{hda_id}").json()
-        assert original_hda['extension'] == 'txt'
-        assert original_hda['data_type'] == 'galaxy.datatypes.data.Text'
-        assert 'scatterplot' not in [viz['name'] for viz in original_hda['visualizations']]
+        hda_id = self.dataset_populator.new_dataset(self.history_id)["id"]
+        original_hda = self._get(f"histories/{self.history_id}/contents/{hda_id}").json()
+        assert original_hda["extension"] == "txt"
+        assert original_hda["data_type"] == "galaxy.datatypes.data.Text"
+        assert "scatterplot" not in [viz["name"] for viz in original_hda["visualizations"]]
 
         inputs = {
-            'input1': {'src': 'hda', 'id': hda_id},
-            'sleep_time': 10,
+            "input1": {"src": "hda", "id": hda_id},
+            "sleep_time": 10,
         }
         run_response = self.dataset_populator.run_tool_raw(
             "cat_data_and_sleep",
@@ -183,20 +203,20 @@ class DatasetsApiTestCase(ApiTestCase):
         queued_id = run_response.json()["outputs"][0]["id"]
 
         update_while_incomplete_response = self._put(  # try updating datatype while used as output of a running job
-            f"histories/{self.history_id}/contents/{queued_id}",
-            data={'datatype': 'tabular'}, json=True)
+            f"histories/{self.history_id}/contents/{queued_id}", data={"datatype": "tabular"}, json=True
+        )
         self._assert_status_code_is(update_while_incomplete_response, 400)
 
         self.dataset_populator.wait_for_history_jobs(self.history_id)  # now wait for upload to complete
 
         successful_updated_hda_response = self._put(
-            f"histories/{self.history_id}/contents/{hda_id}",
-            data={'datatype': 'tabular'}, json=True).json()
-        assert successful_updated_hda_response['extension'] == 'tabular'
-        assert successful_updated_hda_response['data_type'] == 'galaxy.datatypes.tabular.Tabular'
-        assert 'scatterplot' in [viz['name'] for viz in successful_updated_hda_response['visualizations']]
+            f"histories/{self.history_id}/contents/{hda_id}", data={"datatype": "tabular"}, json=True
+        ).json()
+        assert successful_updated_hda_response["extension"] == "tabular"
+        assert successful_updated_hda_response["data_type"] == "galaxy.datatypes.tabular.Tabular"
+        assert "scatterplot" in [viz["name"] for viz in successful_updated_hda_response["visualizations"]]
 
         invalidly_updated_hda_response = self._put(  # try updating with invalid datatype
-            f"histories/{self.history_id}/contents/{hda_id}",
-            data={'datatype': 'invalid'}, json=True)
+            f"histories/{self.history_id}/contents/{hda_id}", data={"datatype": "invalid"}, json=True
+        )
         self._assert_status_code_is(invalidly_updated_hda_response, 400)
diff --git a/lib/galaxy_test/api/test_datatypes.py b/lib/galaxy_test/api/test_datatypes.py
index 3cc25f8eadf..e3e4a21b250 100644
--- a/lib/galaxy_test/api/test_datatypes.py
+++ b/lib/galaxy_test/api/test_datatypes.py
@@ -8,7 +8,6 @@ HIDDEN_DURING_UPLOAD_DATATYPE = "fli"
 
 
 class DatatypesApiTestCase(ApiTestCase):
-
     def test_index(self):
         datatypes = self._index_datatypes()
         for common_type in ["tabular", "fasta"]:
@@ -72,15 +71,15 @@ class DatatypesApiTestCase(ApiTestCase):
         assert found_fasta_to_tabular
 
     def test_converter_present_after_toolbox_reload(self):
-        response = self._get("tools", data={'tool_id': 'CONVERTER_fasta_to_tabular'})
+        response = self._get("tools", data={"tool_id": "CONVERTER_fasta_to_tabular"})
         self._assert_status_code_is(response, 200)
         converters = len(response.json())
         assert converters == 1
-        url = self._api_url('configuration/toolbox')
+        url = self._api_url("configuration/toolbox")
         put_response = put(url, params=dict(key=self.master_api_key))
         self._assert_status_code_is(put_response, 200)
         time.sleep(2)
-        response = self._get("tools", data={'tool_id': 'CONVERTER_fasta_to_tabular'})
+        response = self._get("tools", data={"tool_id": "CONVERTER_fasta_to_tabular"})
         self._assert_status_code_is(response, 200)
         assert converters == len(response.json())
 
diff --git a/lib/galaxy_test/api/test_display_applications.py b/lib/galaxy_test/api/test_display_applications.py
index f71f0bf286c..419629470dd 100644
--- a/lib/galaxy_test/api/test_display_applications.py
+++ b/lib/galaxy_test/api/test_display_applications.py
@@ -5,7 +5,6 @@ from ._framework import ApiTestCase
 
 
 class DisplayApplicationsApiTestCase(ApiTestCase):
-
     def test_index(self):
         response = self._get("display_applications")
         self._assert_status_code_is(response, 200)
@@ -25,7 +24,7 @@ class DisplayApplicationsApiTestCase(ApiTestCase):
         display_apps = response.json()
         all_ids = [display_app["id"] for display_app in display_apps]
         input_ids = self._get_half_random_items(all_ids)
-        payload = {'ids': input_ids}
+        payload = {"ids": input_ids}
         response = self._post("display_applications/reload", payload, admin=True)
         self._assert_status_code_is(response, 200)
         reloaded = response.json()["reloaded"]
@@ -34,7 +33,7 @@ class DisplayApplicationsApiTestCase(ApiTestCase):
 
     def test_reload_unknow_returns_as_failed(self):
         unknown_id = "unknown"
-        payload = {'ids': [unknown_id]}
+        payload = {"ids": [unknown_id]}
         response = self._post("display_applications/reload", payload, admin=True)
         self._assert_status_code_is(response, 200)
         reloaded = response.json()["reloaded"]
diff --git a/lib/galaxy_test/api/test_folder_contents.py b/lib/galaxy_test/api/test_folder_contents.py
index cd7d04108b8..272280d8ed0 100644
--- a/lib/galaxy_test/api/test_folder_contents.py
+++ b/lib/galaxy_test/api/test_folder_contents.py
@@ -13,7 +13,6 @@ from ._framework import ApiTestCase
 
 
 class FolderContentsApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -111,7 +110,7 @@ class FolderContentsApiTestCase(ApiTestCase):
         self._assert_status_code_is(response, 200)
         contents = response.json()["folder_contents"]
         assert len(contents) == limit
-        expected_query_result = original_contents[offset:offset + limit]
+        expected_query_result = original_contents[offset : offset + limit]
         for index in range(limit):
             assert contents[index]["id"] == expected_query_result[index]["id"]
 
@@ -234,7 +233,9 @@ class FolderContentsApiTestCase(ApiTestCase):
         return hda_id
 
     def _create_hdca_with_contents(self, contents: List[str]) -> str:
-        hdca = self.dataset_collection_populator.create_list_in_history(self.history_id, contents=contents, direct_upload=True).json()["outputs"][0]
+        hdca = self.dataset_collection_populator.create_list_in_history(
+            self.history_id, contents=contents, direct_upload=True
+        ).json()["outputs"][0]
         hdca_id = hdca["id"]
         return hdca_id
 
diff --git a/lib/galaxy_test/api/test_folders.py b/lib/galaxy_test/api/test_folders.py
index 9fae67aa8e9..77a8a9836e5 100644
--- a/lib/galaxy_test/api/test_folders.py
+++ b/lib/galaxy_test/api/test_folders.py
@@ -3,7 +3,6 @@ from ._framework import ApiTestCase
 
 
 class FoldersApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.library_populator = LibraryPopulator(self.galaxy_interactor)
@@ -33,7 +32,7 @@ class FoldersApiTestCase(ApiTestCase):
         data = {
             "add_ids[]": [role_id],
             "manage_ids[]": role_id,  # string-lists also supported
-            "modify_ids[]": [role_id]
+            "modify_ids[]": [role_id],
         }
         response = self._post(f"folders/{folder_id}/permissions?action={action}", data=data, admin=True, json=True)
         self._assert_status_code_is(response, 200)
@@ -128,7 +127,7 @@ class FoldersApiTestCase(ApiTestCase):
             "update_time",
             "deleted",
             "library_path",
-            "parent_library_id"
+            "parent_library_id",
         )
 
     def _assert_valid_permissions(self, permissions):
diff --git a/lib/galaxy_test/api/test_framework.py b/lib/galaxy_test/api/test_framework.py
index 3bc3f51ec0b..4a750411da0 100644
--- a/lib/galaxy_test/api/test_framework.py
+++ b/lib/galaxy_test/api/test_framework.py
@@ -4,10 +4,9 @@ from ._framework import ApiTestCase
 
 
 class ApiFrameworkTestCase(ApiTestCase):
-
     def test_default_xframe_options(self):
         get_response = self._get("licenses")
-        assert get_response.headers['x-frame-options'] == "SAMEORIGIN"
+        assert get_response.headers["x-frame-options"] == "SAMEORIGIN"
 
     # Next several tests test the API's run_as functionality.
     def test_user_cannont_run_as(self):
@@ -15,8 +14,9 @@ class ApiFrameworkTestCase(ApiTestCase):
         post_data = dict(name="TestHistory1")
         # Normal user cannot run_as...
         create_response = self._post(
-            "histories", data=post_data,
-            headers={'run-as': run_as_user["id"]},
+            "histories",
+            data=post_data,
+            headers={"run-as": run_as_user["id"]},
         )
         self._assert_status_code_is(create_response, 403)
 
@@ -24,8 +24,10 @@ class ApiFrameworkTestCase(ApiTestCase):
         post_data = dict(name="TestHistory1")
         # admin user can run_as, but this user doesn't exist, expect 400.
         create_response = self._post(
-            "histories", data=post_data,
-            headers={'run-as': "another_user"}, admin=True,
+            "histories",
+            data=post_data,
+            headers={"run-as": "another_user"},
+            admin=True,
         )
         self._assert_status_code_is(create_response, 400)
 
@@ -35,7 +37,9 @@ class ApiFrameworkTestCase(ApiTestCase):
         # Use run_as with admin user and for another user just created, this
         # should work.
         create_response = self._post(
-            "histories", data=post_data,
-            headers={'run-as': run_as_user["id"]}, admin=True,
+            "histories",
+            data=post_data,
+            headers={"run-as": run_as_user["id"]},
+            admin=True,
         )
         self._assert_status_code_is(create_response, 200)
diff --git a/lib/galaxy_test/api/test_group_roles.py b/lib/galaxy_test/api/test_group_roles.py
index 67b00527ec3..e631a5b80d5 100644
--- a/lib/galaxy_test/api/test_group_roles.py
+++ b/lib/galaxy_test/api/test_group_roles.py
@@ -5,7 +5,6 @@ from ._framework import ApiTestCase
 
 
 class GroupRolesApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
diff --git a/lib/galaxy_test/api/test_group_users.py b/lib/galaxy_test/api/test_group_users.py
index 7f1045e6851..77df40867fa 100644
--- a/lib/galaxy_test/api/test_group_users.py
+++ b/lib/galaxy_test/api/test_group_users.py
@@ -5,7 +5,6 @@ from ._framework import ApiTestCase
 
 
 class GroupUsersApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
diff --git a/lib/galaxy_test/api/test_groups.py b/lib/galaxy_test/api/test_groups.py
index 23a7450efff..3771bf6a81d 100644
--- a/lib/galaxy_test/api/test_groups.py
+++ b/lib/galaxy_test/api/test_groups.py
@@ -3,7 +3,6 @@ from ._framework import ApiTestCase
 
 
 class GroupsApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index fc7983d10a9..059bedfd0e3 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -1,8 +1,6 @@
 import time
 
-from requests import (
-    put
-)
+from requests import put
 
 from galaxy_test.api.sharable import SharingApiTests
 from galaxy_test.base.populators import (
@@ -14,7 +12,6 @@ from ._framework import ApiTestCase
 
 
 class BaseHistories:
-
     def _show(self, history_id):
         return self._get(f"histories/{history_id}").json()
 
@@ -32,7 +29,6 @@ class BaseHistories:
 
 
 class HistoriesApiTestCase(ApiTestCase, BaseHistories):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -60,16 +56,23 @@ class HistoriesApiTestCase(ApiTestCase, BaseHistories):
         history_id = self._create_history("TestHistoryForShow")["id"]
         show_response = self._show(history_id)
         self._assert_has_key(
-            show_response,
-            'id', 'name', 'annotation', 'size', 'contents_url',
-            'state', 'state_details', 'state_ids'
+            show_response, "id", "name", "annotation", "size", "contents_url", "state", "state_details", "state_ids"
         )
 
         state_details = show_response["state_details"]
         state_ids = show_response["state_ids"]
         states = [
-            'discarded', 'empty', 'error', 'failed_metadata', 'new',
-            'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload'
+            "discarded",
+            "empty",
+            "error",
+            "failed_metadata",
+            "new",
+            "ok",
+            "paused",
+            "queued",
+            "running",
+            "setting_metadata",
+            "upload",
         ]
         assert isinstance(state_details, dict)
         assert isinstance(state_ids, dict)
@@ -114,7 +117,7 @@ class HistoriesApiTestCase(ApiTestCase, BaseHistories):
 
     def test_purge(self):
         history_id = self._create_history("TestHistoryForPurge")["id"]
-        data = {'purge': True}
+        data = {"purge": True}
         self._delete(f"histories/{history_id}", data=data, json=True)
         show_response = self._show(history_id)
         assert show_response["deleted"]
@@ -134,7 +137,7 @@ class HistoriesApiTestCase(ApiTestCase, BaseHistories):
         show_response = self._show(history_id)
         assert show_response["name"] == "New Name"
 
-        unicode_name = '桜ゲノム'
+        unicode_name = "桜ゲノム"
         self._update(history_id, {"name": unicode_name})
         show_response = self._show(history_id)
         assert show_response["name"] == unicode_name, show_response
@@ -182,7 +185,7 @@ class HistoriesApiTestCase(ApiTestCase, BaseHistories):
         for str_key in ["name", "annotation"]:
             assert self._update(history_id, {str_key: False}).status_code == 400
 
-        for bool_key in ['deleted', 'importable', 'published']:
+        for bool_key in ["deleted", "importable", "published"]:
             assert self._update(history_id, {bool_key: "a string"}).status_code == 400
 
         assert self._update(history_id, {"tags": "a simple string"}).status_code == 400
@@ -217,29 +220,32 @@ class HistoriesApiTestCase(ApiTestCase, BaseHistories):
 
     def test_copy_history(self):
         history_id = self.dataset_populator.new_history()
-        fetch_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"], direct_upload=True)
+        fetch_response = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["Hello", "World"], direct_upload=True
+        )
         dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response.json())
         copied_history_response = self.dataset_populator.copy_history(history_id)
         copied_history_response.raise_for_status()
         copied_history = copied_history_response.json()
-        copied_collection = self.dataset_populator.get_history_collection_details(history_id=copied_history['id'], history_content_type="dataset_collection")
-        assert dataset_collection['name'] == copied_collection['name']
-        assert dataset_collection['id'] != copied_collection['id']
-        assert len(dataset_collection['elements']) == len(copied_collection['elements']) == 2
-        source_element = dataset_collection['elements'][0]
-        copied_element = copied_collection['elements'][0]
-        assert source_element['element_identifier'] == copied_element['element_identifier'] == 'data0'
-        assert source_element['id'] != copied_element['id']
-        source_hda = source_element['object']
-        copied_hda = copied_element['object']
-        assert source_hda['name'] == copied_hda['name'] == 'data0'
-        assert source_hda['id'] != copied_hda['id']
-        assert source_hda['history_id'] != copied_hda['history_id']
-        assert source_hda['hid'] == copied_hda['hid'] == 2
+        copied_collection = self.dataset_populator.get_history_collection_details(
+            history_id=copied_history["id"], history_content_type="dataset_collection"
+        )
+        assert dataset_collection["name"] == copied_collection["name"]
+        assert dataset_collection["id"] != copied_collection["id"]
+        assert len(dataset_collection["elements"]) == len(copied_collection["elements"]) == 2
+        source_element = dataset_collection["elements"][0]
+        copied_element = copied_collection["elements"][0]
+        assert source_element["element_identifier"] == copied_element["element_identifier"] == "data0"
+        assert source_element["id"] != copied_element["id"]
+        source_hda = source_element["object"]
+        copied_hda = copied_element["object"]
+        assert source_hda["name"] == copied_hda["name"] == "data0"
+        assert source_hda["id"] != copied_hda["id"]
+        assert source_hda["history_id"] != copied_hda["history_id"]
+        assert source_hda["hid"] == copied_hda["hid"] == 2
 
 
 class ImportExportTests(BaseHistories):
-
     def _set_up_populators(self):
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
         self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
@@ -258,7 +264,13 @@ class ImportExportTests(BaseHistories):
             assert hda["purged"] is True
 
         self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check)
-        self._check_imported_dataset(history_id=imported_history_id, hid=2, has_job=False, hda_checker=check_discarded, job_checker=upload_job_check)
+        self._check_imported_dataset(
+            history_id=imported_history_id,
+            hid=2,
+            has_job=False,
+            hda_checker=check_discarded,
+            job_checker=upload_job_check,
+        )
 
         imported_content = self.dataset_populator.get_history_dataset_content(
             history_id=imported_history_id,
@@ -267,8 +279,8 @@ class ImportExportTests(BaseHistories):
         assert imported_content == "1 2 3\n"
 
     def test_import_1901_histories(self):
-        f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), 'rb')
-        import_data = dict(archive_source='', archive_file=f)
+        f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), "rb")
+        import_data = dict(archive_source="", archive_file=f)
         self._import_history_and_wait(import_data, "API Test History", wait_on_history_length=2)
 
     def test_import_export_include_deleted(self):
@@ -278,7 +290,9 @@ class ImportExportTests(BaseHistories):
         deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=True)
         self.dataset_populator.delete_dataset(history_id, deleted_hda["id"])
 
-        imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=2, export_kwds={"include_deleted": "True"})
+        imported_history_id = self._reimport_history(
+            history_id, history_name, wait_on_history_length=2, export_kwds={"include_deleted": "True"}
+        )
         self._assert_history_length(imported_history_id, 2)
 
         def upload_job_check(job):
@@ -290,7 +304,9 @@ class ImportExportTests(BaseHistories):
             assert hda["purged"] is False, hda
 
         self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check)
-        self._check_imported_dataset(history_id=imported_history_id, hid=2, hda_checker=check_deleted_not_purged, job_checker=upload_job_check)
+        self._check_imported_dataset(
+            history_id=imported_history_id, hid=2, hda_checker=check_deleted_not_purged, job_checker=upload_job_check
+        )
 
         imported_content = self.dataset_populator.get_history_dataset_content(
             history_id=imported_history_id,
@@ -302,10 +318,12 @@ class ImportExportTests(BaseHistories):
     def test_import_export_failed_job(self):
         history_name = "for_export_include_failed_job"
         history_id = self.dataset_populator.new_history(name=history_name)
-        self.dataset_populator.run_tool_raw('job_properties', inputs={'failbool': True}, history_id=history_id)
+        self.dataset_populator.run_tool_raw("job_properties", inputs={"failbool": True}, history_id=history_id)
         self.dataset_populator.wait_for_history(history_id, assert_ok=False)
 
-        imported_history_id = self._reimport_history(history_id, history_name, assert_ok=False, wait_on_history_length=4, export_kwds={"include_deleted": "True"})
+        imported_history_id = self._reimport_history(
+            history_id, history_name, assert_ok=False, wait_on_history_length=4, export_kwds={"include_deleted": "True"}
+        )
         self._assert_history_length(imported_history_id, 4)
 
         def check_failed(hda_or_job):
@@ -314,12 +332,16 @@ class ImportExportTests(BaseHistories):
 
         self.dataset_populator._summarize_history(imported_history_id)
 
-        self._check_imported_dataset(history_id=imported_history_id, hid=1, assert_ok=False, hda_checker=check_failed, job_checker=check_failed)
+        self._check_imported_dataset(
+            history_id=imported_history_id, hid=1, assert_ok=False, hda_checker=check_failed, job_checker=check_failed
+        )
 
     def test_import_metadata_regeneration(self):
         history_name = "for_import_metadata_regeneration"
         history_id = self.dataset_populator.new_history(name=history_name)
-        self.dataset_populator.new_dataset(history_id, content=open(self.test_data_resolver.get_filename("1.bam"), 'rb'), file_type='bam', wait=True)
+        self.dataset_populator.new_dataset(
+            history_id, content=open(self.test_data_resolver.get_filename("1.bam"), "rb"), file_type="bam", wait=True
+        )
         imported_history_id = self._reimport_history(history_id, history_name)
         self._assert_history_length(imported_history_id, 1)
         self._check_imported_dataset(history_id=imported_history_id, hid=1)
@@ -345,7 +367,9 @@ class ImportExportTests(BaseHistories):
     def test_import_export_collection(self):
         history_name = "for_export_with_collections"
         history_id = self.dataset_populator.new_history(name=history_name)
-        self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"], direct_upload=True)
+        self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["Hello", "World"], direct_upload=True
+        )
 
         imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=3)
         self._assert_history_length(imported_history_id, 3)
@@ -362,7 +386,9 @@ class ImportExportTests(BaseHistories):
             assert element0["hid"] == 2
             assert element1["hid"] == 3
 
-        self._check_imported_collection(imported_history_id, hid=1, collection_type="list", elements_checker=check_elements)
+        self._check_imported_collection(
+            imported_history_id, hid=1, collection_type="list", elements_checker=check_elements
+        )
 
     def test_import_export_nested_collection(self):
         history_name = "for_export_with_nested_collections"
@@ -382,15 +408,23 @@ class ImportExportTests(BaseHistories):
             assert len(child_elements) == 2
             assert element0["collection_type"] == "paired"
 
-        self._check_imported_collection(imported_history_id, hid=1, collection_type="list:paired", elements_checker=check_elements)
+        self._check_imported_collection(
+            imported_history_id, hid=1, collection_type="list:paired", elements_checker=check_elements
+        )
 
-    def _reimport_history(self, history_id, history_name, wait_on_history_length=None, assert_ok=True, export_kwds=None):
+    def _reimport_history(
+        self, history_id, history_name, wait_on_history_length=None, assert_ok=True, export_kwds=None
+    ):
         # Ensure the history is ready to go...
         export_kwds = export_kwds or {}
         self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok)
 
         return self.dataset_populator.reimport_history(
-            history_id, history_name, wait_on_history_length=wait_on_history_length, export_kwds=export_kwds, api_key=self.galaxy_interactor.api_key
+            history_id,
+            history_name,
+            wait_on_history_length=wait_on_history_length,
+            export_kwds=export_kwds,
+            api_key=self.galaxy_interactor.api_key,
         )
 
     def _import_history_and_wait(self, import_data, history_name, wait_on_history_length=None):
@@ -408,7 +442,9 @@ class ImportExportTests(BaseHistories):
         contents = contents_response.json()
         assert len(contents) == n, contents
 
-    def _check_imported_dataset(self, history_id, hid, assert_ok=True, has_job=True, hda_checker=None, job_checker=None):
+    def _check_imported_dataset(
+        self, history_id, hid, assert_ok=True, has_job=True, hda_checker=None, job_checker=None
+    ):
         imported_dataset_metadata = self.dataset_populator.get_history_dataset_details(
             history_id=history_id,
             hid=hid,
@@ -428,8 +464,8 @@ class ImportExportTests(BaseHistories):
             job_details = self.dataset_populator.get_job_details(job_id, full=True)
             assert job_details.status_code == 200, job_details.content
             job = job_details.json()
-            assert 'history_id' in job, job
-            assert job['history_id'] == history_id, job
+            assert "history_id" in job, job
+            assert job["history_id"] == history_id, job
 
             if job_checker is not None:
                 job_checker(job)
@@ -451,7 +487,6 @@ class ImportExportTests(BaseHistories):
 
 
 class ImportExportHistoryTestCase(ApiTestCase, ImportExportTests):
-
     def setUp(self):
         super().setUp()
         self._set_up_populators()
@@ -495,10 +530,7 @@ class SharingHistoryTestCase(ApiTestCase, BaseHistories, SharingApiTests):
         assert not sharing_response["users_shared_with"]
 
         # Now we provide the share_option
-        payload = {
-            "user_ids": [target_user_id],
-            "share_option": "make_accessible_to_shared"
-        }
+        payload = {"user_ids": [target_user_id], "share_option": "make_accessible_to_shared"}
         sharing_response = self._share_history_with_payload(history_id, payload)
         assert sharing_response["users_shared_with"]
         assert sharing_response["users_shared_with"][0]["id"] == target_user_id
@@ -531,10 +563,7 @@ class SharingHistoryTestCase(ApiTestCase, BaseHistories, SharingApiTests):
 
         # Trying to change the permissions when sharing should fail
         # because we don't have manage permissions
-        payload = {
-            "user_ids": [target_user_id],
-            "share_option": "make_public"
-        }
+        payload = {"user_ids": [target_user_id], "share_option": "make_public"}
         sharing_response = self._share_history_with_payload(history_id, payload)
         assert sharing_response["extra"]
         assert sharing_response["extra"]["can_share"] is False
@@ -542,10 +571,7 @@ class SharingHistoryTestCase(ApiTestCase, BaseHistories, SharingApiTests):
         assert not sharing_response["users_shared_with"]
 
         # we can share if we don't try to make any permission changes
-        payload = {
-            "user_ids": [target_user_id],
-            "share_option": "no_changes"
-        }
+        payload = {"user_ids": [target_user_id], "share_option": "no_changes"}
         sharing_response = self._share_history_with_payload(history_id, payload)
         assert not sharing_response["errors"]
         assert sharing_response["users_shared_with"]
diff --git a/lib/galaxy_test/api/test_history_contents.py b/lib/galaxy_test/api/test_history_contents.py
index d1d83b7ab04..1679fefa3f1 100644
--- a/lib/galaxy_test/api/test_history_contents.py
+++ b/lib/galaxy_test/api/test_history_contents.py
@@ -18,7 +18,6 @@ from ._framework import ApiTestCase
 
 # TODO: Test anonymous access.
 class HistoryContentsApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -115,7 +114,9 @@ class HistoryContentsApiTestCase(ApiTestCase):
         user_id = self.dataset_populator.user_id()
         with self._different_user():
             different_user_id = self.dataset_populator.user_id()
-        combined_user_role = self.dataset_populator.create_role([user_id, different_user_id], description="role for testing permissions")
+        combined_user_role = self.dataset_populator.create_role(
+            [user_id, different_user_id], description="role for testing permissions"
+        )
 
         payload = {
             "access": [combined_user_role["id"]],
@@ -166,7 +167,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
     def test_hda_copy(self):
         hda1 = self.dataset_populator.new_dataset(self.history_id)
         create_data = dict(
-            source='hda',
+            source="hda",
             content=hda1["id"],
         )
         second_history_id = self.dataset_populator.new_history()
@@ -178,7 +179,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
     def test_library_copy(self):
         ld = self.library_populator.new_library_dataset("lda_test_library")
         create_data = dict(
-            source='library',
+            source="library",
             content=ld["id"],
         )
         assert self.__count_contents(self.history_id) == 0
@@ -200,7 +201,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
         update_response = self._update(hda1["id"], dict(name="Updated Name"))
         assert self.__show(hda1).json()["name"] == "Updated Name"
 
-        unicode_name = 'ржевский сапоги'
+        unicode_name = "ржевский сапоги"
         update_response = self._update(hda1["id"], dict(name=unicode_name))
         updated_hda = self.__show(hda1).json()
         assert updated_hda["name"] == unicode_name, updated_hda
@@ -216,7 +217,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
             "dbkey": "?",
             "annotation": None,
             "info": "my info is",
-            "operation": "attributes"
+            "operation": "attributes",
         }
         update_response = self._set_edit_update(data)
         # No key or anything supplied, expect a permission problem.
@@ -271,7 +272,9 @@ class HistoryContentsApiTestCase(ApiTestCase):
         assert objects[0]["visible"] is False
 
         # update both flags
-        payload = dict(items=[{"history_content_type": "dataset_collection", "id": hdca["id"]}], deleted=False, visible=True)
+        payload = dict(
+            items=[{"history_content_type": "dataset_collection", "id": hdca["id"]}], deleted=False, visible=True
+        )
         update_response = self._update_batch(payload)
         objects = update_response.json()
         assert objects[0]["deleted"] is False
@@ -279,7 +282,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
     def test_update_type_failures(self):
         hda1 = self._wait_for_new_hda()
-        update_response = self._update(hda1["id"], dict(deleted='not valid'))
+        update_response = self._update(hda1["id"], dict(deleted="not valid"))
         self._assert_status_code_is(update_response, 400)
 
     def _wait_for_new_hda(self):
@@ -314,7 +317,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
     def test_delete_anon(self):
         with self._different_user(anon=True):
-            history_id = self._get(urllib.parse.urljoin(self.url, "history/current_history_json")).json()['id']
+            history_id = self._get(urllib.parse.urljoin(self.url, "history/current_history_json")).json()["id"]
             hda1 = self.dataset_populator.new_dataset(history_id)
             self.dataset_populator.wait_for_history(history_id)
             assert str(self.__show(hda1).json()["deleted"]).lower() == "false"
@@ -327,24 +330,21 @@ class HistoryContentsApiTestCase(ApiTestCase):
         with self._different_user(anon=True):
             delete_response = self._delete(f"histories/{self.history_id}/contents/{hda1['id']}")
             assert delete_response.status_code == 403
-            assert delete_response.json()['err_msg'] == 'HistoryDatasetAssociation is not owned by user'
+            assert delete_response.json()["err_msg"] == "HistoryDatasetAssociation is not owned by user"
 
     def test_purge(self):
         hda1 = self.dataset_populator.new_dataset(self.history_id)
         self.dataset_populator.wait_for_history(self.history_id)
         assert str(self.__show(hda1).json()["deleted"]).lower() == "false"
         assert str(self.__show(hda1).json()["purged"]).lower() == "false"
-        data = {'purge': True}
+        data = {"purge": True}
         delete_response = self._delete(f"histories/{self.history_id}/contents/{hda1['id']}", data=data, json=True)
         assert delete_response.status_code < 300  # Something in the 200s :).
         assert str(self.__show(hda1).json()["deleted"]).lower() == "true"
         assert str(self.__show(hda1).json()["purged"]).lower() == "true"
 
     def test_dataset_collection_creation_on_contents(self):
-        payload = self.dataset_collection_populator.create_pair_payload(
-            self.history_id,
-            type="dataset_collection"
-        )
+        payload = self.dataset_collection_populator.create_pair_payload(self.history_id, type="dataset_collection")
         endpoint = f"histories/{self.history_id}/contents"
         self._check_pair_creation(endpoint, payload)
 
@@ -357,30 +357,27 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
     def test_dataset_collection_create_from_exisiting_datasets_with_new_tags(self):
         with self.dataset_populator.test_history() as history_id:
-            hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id']
-            hda2_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id']
-            update_response = self._update(hda2_id, dict(tags=['existing:tag']), history_id=history_id).json()
-            assert update_response['tags'] == ['existing:tag']
-            creation_payload = {'collection_type': 'list',
-                                'history_id': history_id,
-                                'element_identifiers': [{'id': hda_id,
-                                                         'src': 'hda',
-                                                         'name': 'element_id1',
-                                                         'tags': ['my_new_tag']},
-                                                        {'id': hda2_id,
-                                                         'src': 'hda',
-                                                         'name': 'element_id2',
-                                                         'tags': ['another_new_tag']}
-                                                        ],
-                                'type': 'dataset_collection',
-                                'copy_elements': True}
+            hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")["id"]
+            hda2_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")["id"]
+            update_response = self._update(hda2_id, dict(tags=["existing:tag"]), history_id=history_id).json()
+            assert update_response["tags"] == ["existing:tag"]
+            creation_payload = {
+                "collection_type": "list",
+                "history_id": history_id,
+                "element_identifiers": [
+                    {"id": hda_id, "src": "hda", "name": "element_id1", "tags": ["my_new_tag"]},
+                    {"id": hda2_id, "src": "hda", "name": "element_id2", "tags": ["another_new_tag"]},
+                ],
+                "type": "dataset_collection",
+                "copy_elements": True,
+            }
             r = self._post(f"histories/{self.history_id}/contents", creation_payload, json=True).json()
-            assert r['elements'][0]['object']['id'] != hda_id, "HDA has not been copied"
-            assert len(r['elements'][0]['object']['tags']) == 1
-            assert r['elements'][0]['object']['tags'][0] == 'my_new_tag'
-            assert len(r['elements'][1]['object']['tags']) == 2, r['elements'][1]['object']['tags']
+            assert r["elements"][0]["object"]["id"] != hda_id, "HDA has not been copied"
+            assert len(r["elements"][0]["object"]["tags"]) == 1
+            assert r["elements"][0]["object"]["tags"][0] == "my_new_tag"
+            assert len(r["elements"][1]["object"]["tags"]) == 2, r["elements"][1]["object"]["tags"]
             original_hda = self.dataset_populator.get_history_dataset_details(history_id=history_id, dataset_id=hda_id)
-            assert len(original_hda['tags']) == 0, original_hda['tags']
+            assert len(original_hda["tags"]) == 0, original_hda["tags"]
 
     def _check_pair_creation(self, endpoint, payload):
         pre_collection_count = self.__count_contents(type="dataset_collection")
@@ -420,10 +417,12 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
     @skip_without_tool("collection_creates_list")
     def test_jobs_summary_simple_hdca(self):
-        create_response = self.dataset_collection_populator.create_list_in_history(self.history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
+        create_response = self.dataset_collection_populator.create_list_in_history(
+            self.history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]
+        )
         hdca_id = create_response.json()["id"]
         run = self.dataset_populator.run_collection_creates_list(self.history_id, hdca_id)
-        collections = run['output_collections']
+        collections = run["output_collections"]
         collection = collections[0]
         jobs_summary_url = f"histories/{self.history_id}/contents/dataset_collections/{collection['id']}/jobs_summary"
         jobs_summary_response = self._get(jobs_summary_url)
@@ -433,14 +432,16 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
     @skip_without_tool("cat1")
     def test_jobs_summary_implicit_hdca(self):
-        create_response = self.dataset_collection_populator.create_pair_in_history(self.history_id, contents=["123", "456"])
+        create_response = self.dataset_collection_populator.create_pair_in_history(
+            self.history_id, contents=["123", "456"]
+        )
         hdca_id = create_response.json()["id"]
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=self.history_id)
         self.dataset_populator.wait_for_history_jobs(self.history_id)
-        collections = run['implicit_collections']
+        collections = run["implicit_collections"]
         collection = collections[0]
         jobs_summary_url = f"histories/{self.history_id}/contents/dataset_collections/{collection['id']}/jobs_summary"
         jobs_summary_response = self._get(jobs_summary_url)
@@ -451,17 +452,16 @@ class HistoryContentsApiTestCase(ApiTestCase):
         assert states.get("ok") == 2, states
 
     def test_dataset_collection_hide_originals(self):
-        payload = self.dataset_collection_populator.create_pair_payload(
-            self.history_id,
-            type="dataset_collection"
-        )
+        payload = self.dataset_collection_populator.create_pair_payload(self.history_id, type="dataset_collection")
 
         payload["hide_source_items"] = True
         dataset_collection_response = self._post(f"histories/{self.history_id}/contents", payload, json=True)
         self.__check_create_collection_response(dataset_collection_response)
 
         contents_response = self._get(f"histories/{self.history_id}/contents")
-        datasets = [d for d in contents_response.json() if d["history_content_type"] == "dataset" and d["hid"] in [1, 2]]
+        datasets = [
+            d for d in contents_response.json() if d["history_content_type"] == "dataset" and d["hid"] in [1, 2]
+        ]
         # Assert two datasets in source were hidden.
         assert len(datasets) == 2
         assert not datasets[0]["visible"]
@@ -479,23 +479,14 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
     def test_update_batch_dataset_collection(self):
         hdca = self._create_pair_collection()
-        body = {
-            "items": [{
-                "history_content_type": "dataset_collection",
-                "id": hdca["id"]
-            }],
-            "name": "newnameforpair"
-        }
+        body = {"items": [{"history_content_type": "dataset_collection", "id": hdca["id"]}], "name": "newnameforpair"}
         update_response = self._put(f"histories/{self.history_id}/contents", data=body, json=True)
         self._assert_status_code_is(update_response, 200)
         show_response = self.__show(hdca)
         assert str(show_response.json()["name"]) == "newnameforpair"
 
     def _create_pair_collection(self):
-        payload = self.dataset_collection_populator.create_pair_payload(
-            self.history_id,
-            type="dataset_collection"
-        )
+        payload = self.dataset_collection_populator.create_pair_payload(self.history_id, type="dataset_collection")
         dataset_collection_response = self._post(f"histories/{self.history_id}/contents", payload, json=True)
         self._assert_status_code_is(dataset_collection_response, 200)
         hdca = dataset_collection_response.json()
@@ -506,11 +497,13 @@ class HistoryContentsApiTestCase(ApiTestCase):
         hdca_id = hdca["id"]
         second_history_id = self.dataset_populator.new_history()
         create_data = dict(
-            source='hdca',
+            source="hdca",
             content=hdca_id,
         )
         assert len(self._get(f"histories/{second_history_id}/contents/dataset_collections").json()) == 0
-        create_response = self._post(f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True)
+        create_response = self._post(
+            f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True
+        )
         self.__check_create_collection_response(create_response)
         contents = self._get(f"histories/{second_history_id}/contents/dataset_collections").json()
         assert len(contents) == 1
@@ -523,10 +516,12 @@ class HistoryContentsApiTestCase(ApiTestCase):
         hdca_id = hdca["id"]
         assert hdca["elements"][0]["object"]["metadata_dbkey"] == "?"
         assert hdca["elements"][0]["object"]["genome_build"] == "?"
-        create_data = {'source': 'hdca', 'content': hdca_id, 'dbkey': 'hg19'}
-        create_response = self._post(f"histories/{self.history_id}/contents/dataset_collections", create_data, json=True)
+        create_data = {"source": "hdca", "content": hdca_id, "dbkey": "hg19"}
+        create_response = self._post(
+            f"histories/{self.history_id}/contents/dataset_collections", create_data, json=True
+        )
         collection = self.__check_create_collection_response(create_response)
-        new_forward = collection['elements'][0]['object']
+        new_forward = collection["elements"][0]["object"]
         assert new_forward["metadata_dbkey"] == "hg19"
         assert new_forward["genome_build"] == "hg19"
 
@@ -535,12 +530,14 @@ class HistoryContentsApiTestCase(ApiTestCase):
         hdca_id = hdca["id"]
         second_history_id = self.dataset_populator.new_history()
         create_data = dict(
-            source='hdca',
+            source="hdca",
             content=hdca_id,
             copy_elements=True,
         )
         assert len(self._get(f"histories/{second_history_id}/contents/dataset_collections").json()) == 0
-        create_response = self._post(f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True)
+        create_response = self._post(
+            f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True
+        )
         self.__check_create_collection_response(create_response)
 
         contents = self._get(f"histories/{second_history_id}/contents/dataset_collections").json()
@@ -581,10 +578,12 @@ class HistoryContentsApiTestCase(ApiTestCase):
         assert hda["hda_ldda"] == "hda"
         assert hda["history_content_type"] == "dataset"
         assert hda["copied_from_ldda_id"] == ldda_id
-        assert hda['history_id'] == history_id
+        assert hda["history_id"] == history_id
 
     def test_hdca_from_inaccessible_library_datasets(self):
-        library, library_dataset = self.library_populator.new_library_dataset_in_private_library("HDCACreateInaccesibleLibrary")
+        library, library_dataset = self.library_populator.new_library_dataset_in_private_library(
+            "HDCACreateInaccesibleLibrary"
+        )
         ldda_id = library_dataset["id"]
         element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}]
         create_data = dict(
@@ -596,7 +595,9 @@ class HistoryContentsApiTestCase(ApiTestCase):
         )
         with self._different_user():
             second_history_id = self.dataset_populator.new_history()
-            create_response = self._post(f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True)
+            create_response = self._post(
+                f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True
+            )
             self._assert_status_code_is(create_response, 403)
 
     def __check_create_collection_response(self, response):
@@ -606,7 +607,9 @@ class HistoryContentsApiTestCase(ApiTestCase):
         return dataset_collection
 
     def __show(self, contents):
-        show_response = self._get(f"histories/{self.history_id}/contents/{contents['history_content_type']}s/{contents['id']}")
+        show_response = self._get(
+            f"histories/{self.history_id}/contents/{contents['history_content_type']}s/{contents['id']}"
+        )
         return show_response
 
     def __count_contents(self, history_id=None, **kwds):
@@ -632,15 +635,17 @@ class HistoryContentsApiTestCase(ApiTestCase):
         assert input_hda["id"] == query_hda["id"]
 
     def test_job_state_summary_field(self):
-        create_response = self.dataset_collection_populator.create_pair_in_history(self.history_id, contents=["123", "456"])
+        create_response = self.dataset_collection_populator.create_pair_in_history(
+            self.history_id, contents=["123", "456"]
+        )
         self._assert_status_code_is(create_response, 200)
         contents_response = self._get(f"histories/{self.history_id}/contents?v=dev&keys=job_state_summary&view=summary")
         self._assert_status_code_is(contents_response, 200)
         contents = contents_response.json()
-        for c in filter(lambda c: c['history_content_type'] == 'dataset_collection', contents):
+        for c in filter(lambda c: c["history_content_type"] == "dataset_collection", contents):
             assert isinstance(c, dict)
-            assert 'job_state_summary' in c
-            assert isinstance(c['job_state_summary'], dict)
+            assert "job_state_summary" in c
+            assert isinstance(c["job_state_summary"], dict)
 
     def _get_content(self, history_id, update_time):
         return self._get(f"/api/histories/{history_id}/contents/near/100/100?update_time-gt={update_time}").json()
@@ -658,7 +663,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
     def test_history_contents_near_with_since(self):
         with self.dataset_populator.test_history() as history_id:
             original_history = self._get(f"/api/histories/{history_id}").json()
-            original_history_stamp = original_history['update_time']
+            original_history_stamp = original_history["update_time"]
 
             # check empty contents, with no since flag, should return an empty 200 result
             history_contents = self._get(f"/api/histories/{history_id}/contents/near/100/100")
@@ -666,7 +671,9 @@ class HistoryContentsApiTestCase(ApiTestCase):
             assert len(history_contents.json()) == 0
 
             # adding a since parameter, should return a 204 if history has not changed at all
-            history_contents = self._get(f"/api/histories/{history_id}/contents/near/100/100?since={original_history_stamp}")
+            history_contents = self._get(
+                f"/api/histories/{history_id}/contents/near/100/100?since={original_history_stamp}"
+            )
             assert history_contents.status_code == 204
 
             # add some stuff
@@ -680,19 +687,21 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
             # check to make sure the history date has actually changed due to changing the contents
             changed_history = self._get(f"/api/histories/{history_id}").json()
-            changed_history_stamp = changed_history['update_time']
+            changed_history_stamp = changed_history["update_time"]
             assert original_history_stamp != changed_history_stamp
 
             # a repeated contents request with since=original_history_stamp should now return data
             # because we have added datasets and the update_time should have been changed
-            changed_content = self._get(f"/api/histories/{history_id}/contents/near/100/100?since={original_history_stamp}")
+            changed_content = self._get(
+                f"/api/histories/{history_id}/contents/near/100/100?since={original_history_stamp}"
+            )
             assert changed_content.status_code == 200
             assert len(changed_content.json()) == 4
 
     def test_history_contents_near_since_with_standard_iso8601_date(self):
         with self.dataset_populator.test_history() as history_id:
             original_history = self._get(f"/api/histories/{history_id}").json()
-            original_history_stamp = original_history['update_time']
+            original_history_stamp = original_history["update_time"]
 
             # this is the standard date format that javascript will emit using .toISOString(), it
             # should be the expected date format for any modern api
@@ -700,25 +709,27 @@ class HistoryContentsApiTestCase(ApiTestCase):
 
             # checking to make sure that the same exact history.update_time returns a "not changed"
             # result after date parsing
-            valid_iso8601_date = original_history_stamp + 'Z'
+            valid_iso8601_date = original_history_stamp + "Z"
             encoded_valid_date = urllib.parse.quote_plus(valid_iso8601_date)
-            history_contents = self._get(f"/api/histories/{history_id}/contents/near/100/100?since={encoded_valid_date}")
+            history_contents = self._get(
+                f"/api/histories/{history_id}/contents/near/100/100?since={encoded_valid_date}"
+            )
             assert history_contents.status_code == 204
 
             # test parsing for other standard is08601 formats
-            sample_formats = ['2021-08-26T15:53:02+00:00', '2021-08-26T15:53:02Z', '2002-10-10T12:00:00-05:00']
+            sample_formats = ["2021-08-26T15:53:02+00:00", "2021-08-26T15:53:02Z", "2002-10-10T12:00:00-05:00"]
             for date_str in sample_formats:
                 encoded_date = urllib.parse.quote_plus(date_str)  # handles pluses, minuses
                 history_contents = self._get(f"/api/histories/{history_id}/contents/near/100/100?since={encoded_date}")
                 self._assert_status_code_is_ok(history_contents)
 
-    @skip_without_tool('cat_data_and_sleep')
+    @skip_without_tool("cat_data_and_sleep")
     def test_history_contents_near_with_update_time_implicit_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id=history_id).json()['id']
+            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id=history_id).json()["id"]
             self.dataset_populator.wait_for_history(history_id)
             inputs = {
-                "input1": {'batch': True, 'values': [{"src": "hdca", "id": hdca_id}]},
+                "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
                 "sleep_time": 2,
             }
             response = self.dataset_populator.run_tool(
@@ -727,31 +738,43 @@ class HistoryContentsApiTestCase(ApiTestCase):
                 history_id,
             )
             update_time = datetime.utcnow().isoformat()
-            collection_id = response['implicit_collections'][0]['id']
+            collection_id = response["implicit_collections"][0]["id"]
             for _ in range(20):
                 time.sleep(1)
                 update = self._get_content(history_id, update_time=update_time)
-                if any(c for c in update if c['history_content_type'] == 'dataset_collection' and c['job_state_summary']['ok'] == 3):
+                if any(
+                    c
+                    for c in update
+                    if c["history_content_type"] == "dataset_collection" and c["job_state_summary"]["ok"] == 3
+                ):
                     return
-            raise Exception(f"History content update time query did not include final update for implicit collection {collection_id}")
+            raise Exception(
+                f"History content update time query did not include final update for implicit collection {collection_id}"
+            )
 
-    @skip_without_tool('collection_creates_dynamic_nested')
+    @skip_without_tool("collection_creates_dynamic_nested")
     def test_history_contents_near_with_update_time_explicit_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            inputs = {'foo': 'bar', 'sleep_time': 2}
+            inputs = {"foo": "bar", "sleep_time": 2}
             response = self.dataset_populator.run_tool(
                 "collection_creates_dynamic_nested",
                 inputs,
                 history_id,
             )
             update_time = datetime.utcnow().isoformat()
-            collection_id = response['output_collections'][0]['id']
+            collection_id = response["output_collections"][0]["id"]
             for _ in range(20):
                 time.sleep(1)
                 update = self._get_content(history_id, update_time=update_time)
-                if any(c for c in update if c['history_content_type'] == 'dataset_collection' and c['populated_state'] == 'ok'):
+                if any(
+                    c
+                    for c in update
+                    if c["history_content_type"] == "dataset_collection" and c["populated_state"] == "ok"
+                ):
                     return
-            raise Exception(f"History content update time query did not include populated_state update for dynamic nested collection {collection_id}")
+            raise Exception(
+                f"History content update time query did not include populated_state update for dynamic nested collection {collection_id}"
+            )
 
     def test_index_filter_by_type(self):
         history_id = self.dataset_populator.new_history()
@@ -795,7 +818,9 @@ class HistoryContentsApiTestCase(ApiTestCase):
         self._assert_status_code_is_ok(create_homogeneous_response)
 
     def _assert_collection_has_expected_elements_datatypes(self, history_id, collection_name, expected_datatypes):
-        contents_response = self._get(f"histories/{history_id}/contents?v=dev&view=betawebclient&q=name-eq&qv={collection_name}")
+        contents_response = self._get(
+            f"histories/{history_id}/contents?v=dev&view=betawebclient&q=name-eq&qv={collection_name}"
+        )
         self._assert_status_code_is(contents_response, 200)
         collection = contents_response.json()[0]
         self.assertCountEqual(collection["elements_datatypes"], expected_datatypes)
@@ -805,6 +830,7 @@ class HistoryContentsApiNearTestCase(ApiTestCase):
     """
     Test the /api/histories/{history_id}/contents/{direction}/{hid}/{limit} endpoint.
     """
+
     NEAR = DirectionOptions.near
     BEFORE = DirectionOptions.before
     AFTER = DirectionOptions.after
@@ -827,87 +853,87 @@ class HistoryContentsApiNearTestCase(ApiTestCase):
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.NEAR, hid=1)
             assert len(result) == 8
-            assert result[0]['hid'] == 8
-            assert result[1]['hid'] == 7
-            assert result[2]['hid'] == 6
-            assert result[3]['hid'] == 5
-            assert result[4]['hid'] == 4
-            assert result[5]['hid'] == 3
-            assert result[6]['hid'] == 2
-            assert result[7]['hid'] == 1
+            assert result[0]["hid"] == 8
+            assert result[1]["hid"] == 7
+            assert result[2]["hid"] == 6
+            assert result[3]["hid"] == 5
+            assert result[4]["hid"] == 4
+            assert result[5]["hid"] == 3
+            assert result[6]["hid"] == 2
+            assert result[7]["hid"] == 1
 
     def test_near_even_limit(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.NEAR, hid=5, limit=3)
             assert len(result) == 3
-            assert result[0]['hid'] == 6  # hid + 1
-            assert result[1]['hid'] == 5  # hid
-            assert result[2]['hid'] == 4  # hid - 1
+            assert result[0]["hid"] == 6  # hid + 1
+            assert result[1]["hid"] == 5  # hid
+            assert result[2]["hid"] == 4  # hid - 1
 
     def test_near_odd_limit(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.NEAR, hid=5, limit=4)
             assert len(result) == 4
-            assert result[0]['hid'] == 7  # hid + 2
-            assert result[1]['hid'] == 6  # hid + 1
-            assert result[2]['hid'] == 5  # hid
-            assert result[3]['hid'] == 4  # hid - 1
+            assert result[0]["hid"] == 7  # hid + 2
+            assert result[1]["hid"] == 6  # hid + 1
+            assert result[2]["hid"] == 5  # hid
+            assert result[3]["hid"] == 4  # hid - 1
 
     def test_near_less_than_before_limit(self):  # n before < limit // 2
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.NEAR, hid=1, limit=3)
             assert len(result) == 2
-            assert result[0]['hid'] == 2  # hid + 1
-            assert result[1]['hid'] == 1  # hid (there's nothing before hid=1)
+            assert result[0]["hid"] == 2  # hid + 1
+            assert result[1]["hid"] == 1  # hid (there's nothing before hid=1)
 
     def test_near_less_than_after_limit(self):  # n after < limit // 2 + 1
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.NEAR, hid=8, limit=3)
             assert len(result) == 2
-            assert result[0]['hid'] == 8  # hid (there's nothing after hid=8)
-            assert result[1]['hid'] == 7  # hid - 1
+            assert result[0]["hid"] == 8  # hid (there's nothing after hid=8)
+            assert result[1]["hid"] == 7  # hid - 1
 
     def test_near_less_than_before_and_after_limit(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id, n=1)
             result = self._get_content(history_id, self.NEAR, hid=2, limit=10)
             assert len(result) == 4
-            assert result[0]['hid'] == 4  # hid + 2  (can't go after hid=4)
-            assert result[1]['hid'] == 3  # hid + 1
-            assert result[2]['hid'] == 2  # hid
-            assert result[3]['hid'] == 1  # hid - 1  (can't go before hid=1)
+            assert result[0]["hid"] == 4  # hid + 2  (can't go after hid=4)
+            assert result[1]["hid"] == 3  # hid + 1
+            assert result[2]["hid"] == 2  # hid
+            assert result[3]["hid"] == 1  # hid - 1  (can't go before hid=1)
 
     def test_before(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.BEFORE, hid=5, limit=3)
             assert len(result) == 3
-            assert result[0]['hid'] == 4  # hid - 1
-            assert result[1]['hid'] == 3  # hid - 2
-            assert result[2]['hid'] == 2  # hid - 3
+            assert result[0]["hid"] == 4  # hid - 1
+            assert result[1]["hid"] == 3  # hid - 2
+            assert result[2]["hid"] == 2  # hid - 3
 
     def test_before_less_than_limit(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.BEFORE, hid=2, limit=3)
             assert len(result) == 1
-            assert result[0]['hid'] == 1  # hid - 1
+            assert result[0]["hid"] == 1  # hid - 1
 
     def test_after(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.AFTER, hid=5, limit=2)
             assert len(result) == 2
-            assert result[0]['hid'] == 7  # hid + 2 (hid + 3 not included: tests reversed order)
-            assert result[1]['hid'] == 6  # hid + 1
+            assert result[0]["hid"] == 7  # hid + 2 (hid + 3 not included: tests reversed order)
+            assert result[1]["hid"] == 6  # hid + 1
 
     def test_after_less_than_limit(self):
         with self.dataset_populator.test_history() as history_id:
             self._create_list_in_history(history_id)
             result = self._get_content(history_id, self.AFTER, hid=7, limit=3)
             assert len(result) == 1
-            assert result[0]['hid'] == 8  # hid + 1
+            assert result[0]["hid"] == 8  # hid + 1
diff --git a/lib/galaxy_test/api/test_history_contents_provenance.py b/lib/galaxy_test/api/test_history_contents_provenance.py
index 2951116b040..f207492fabb 100644
--- a/lib/galaxy_test/api/test_history_contents_provenance.py
+++ b/lib/galaxy_test/api/test_history_contents_provenance.py
@@ -3,14 +3,13 @@ from ._framework import ApiTestCase
 
 
 class TestProvenance(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
     def test_show_prov(self):
         history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='for prov')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="for prov")
         prov_response = self._get(f"histories/{history_id}/contents/{new_dataset1['id']}/provenance")
         self._assert_status_code_is(prov_response, 200)
         self._assert_has_keys(prov_response.json(), "job_id", "id", "stdout", "stderr", "parameters", "tool_id")
diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index 9af31548f73..11b35a697f9 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -17,13 +17,12 @@ from galaxy_test.base.populators import (
     uses_test_history,
     wait_on,
     wait_on_state,
-    WorkflowPopulator
+    WorkflowPopulator,
 )
 from ._framework import ApiTestCase
 
 
 class JobsApiTestCase(ApiTestCase, TestsTools):
-
     def setUp(self):
         super().setUp()
         self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
@@ -53,11 +52,11 @@ class JobsApiTestCase(ApiTestCase, TestsTools):
         self.__history_with_new_dataset(history_id)
         jobs_response = self._get("jobs?view=admin_job_list", admin=False)
         assert jobs_response.status_code == 403
-        assert jobs_response.json()['err_msg'] == 'Only admins can use the admin_job_list view'
+        assert jobs_response.json()["err_msg"] == "Only admins can use the admin_job_list view"
 
         jobs = self._get("jobs?view=admin_job_list", admin=True).json()
         job = jobs[0]
-        self._assert_has_keys(job, "command_line", "external_id", 'handler')
+        self._assert_has_keys(job, "command_line", "external_id", "handler")
 
     @uses_test_history(require_new=True)
     def test_index_state_filter(self, history_id):
@@ -74,7 +73,7 @@ class JobsApiTestCase(ApiTestCase, TestsTools):
             if original_count < new_count:
                 count_increased = True
                 break
-            time.sleep(.1)
+            time.sleep(0.1)
 
         if not count_increased:
             template = "Jobs in ok state did not increase (was %d, now %d)"
@@ -126,9 +125,11 @@ steps:
     in:
       input1: input1
 """
-        summary = self.workflow_populator.run_workflow(workflow_simple, history_id=history_id, test_data={"input1": "hello world"})
+        summary = self.workflow_populator.run_workflow(
+            workflow_simple, history_id=history_id, test_data={"input1": "hello world"}
+        )
         invocation_id = summary.invocation_id
-        workflow_id = self._get(f"invocations/{invocation_id}").json()['workflow_id']
+        workflow_id = self._get(f"invocations/{invocation_id}").json()["workflow_id"]
         self.workflow_populator.wait_for_invocation(workflow_id, invocation_id)
         jobs1 = self.__jobs_index(data={"workflow_id": workflow_id})
         assert len(jobs1) == 1
@@ -138,7 +139,8 @@ steps:
 
     @uses_test_history(require_new=True)
     def test_index_workflow_filter_implicit_jobs(self, history_id):
-        workflow_id = self.workflow_populator.upload_yaml_workflow("""
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   input_datasets: collection
@@ -147,17 +149,22 @@ steps:
     tool_id: multi_data_optional
     in:
       input1: input_datasets
-""")
+"""
+        )
         hdca_id = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         inputs = {
-            '0': self.dataset_populator.ds_entry(hdca_id),
+            "0": self.dataset_populator.ds_entry(hdca_id),
         }
-        invocation_id = self.workflow_populator.invoke_workflow_and_wait(workflow_id, history_id=history_id, inputs=inputs, assert_ok=True)
+        invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+            workflow_id, history_id=history_id, inputs=inputs, assert_ok=True
+        )
         jobs1 = self.__jobs_index(data={"workflow_id": workflow_id})
         jobs2 = self.__jobs_index(data={"invocation_id": invocation_id})
         assert len(jobs1) == len(jobs2) == 1
-        second_invocation_id = self.workflow_populator.invoke_workflow_and_wait(workflow_id, history_id=history_id, inputs=inputs, assert_ok=True)
+        second_invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+            workflow_id, history_id=history_id, inputs=inputs, assert_ok=True
+        )
         workflow_jobs = self.__jobs_index(data={"workflow_id": workflow_id})
         second_invocation_jobs = self.__jobs_index(data={"invocation_id": second_invocation_id})
         assert len(workflow_jobs) == 2
@@ -210,20 +217,22 @@ steps:
 
         jobs_response = self._get("jobs")
         first_job = jobs_response.json()[0]
-        self._assert_has_key(first_job, 'id', 'state', 'exit_code', 'update_time', 'create_time')
+        self._assert_has_key(first_job, "id", "state", "exit_code", "update_time", "create_time")
 
         job_id = first_job["id"]
         show_jobs_response = self._get(f"jobs/{job_id}")
         self._assert_status_code_is(show_jobs_response, 200)
 
         job_details = show_jobs_response.json()
-        self._assert_has_key(job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time')
+        self._assert_has_key(job_details, "id", "state", "exit_code", "update_time", "create_time")
 
         show_jobs_response = self._get(f"jobs/{job_id}", {"full": True})
         self._assert_status_code_is(show_jobs_response, 200)
 
         job_details = show_jobs_response.json()
-        self._assert_has_key(job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time', 'stdout', 'stderr', 'job_messages')
+        self._assert_has_key(
+            job_details, "id", "state", "exit_code", "update_time", "create_time", "stdout", "stderr", "job_messages"
+        )
 
     @uses_test_history(require_new=True)
     def test_show_security(self, history_id):
@@ -249,7 +258,7 @@ steps:
 
     def _run_detect_errors(self, history_id, inputs):
         payload = self.dataset_populator.run_tool_payload(
-            tool_id='detect_errors_aggressive',
+            tool_id="detect_errors_aggressive",
             inputs=inputs,
             history_id=history_id,
         )
@@ -258,25 +267,27 @@ steps:
     @skip_without_tool("detect_errors_aggressive")
     def test_unhide_on_error(self):
         with self.dataset_populator.test_history() as history_id:
-            inputs = {'error_bool': 'true'}
+            inputs = {"error_bool": "true"}
             run_response = self._run_detect_errors(history_id=history_id, inputs=inputs)
-            job_id = run_response['jobs'][0]["id"]
+            job_id = run_response["jobs"][0]["id"]
             self.dataset_populator.wait_for_job(job_id)
             job = self.dataset_populator.get_job_details(job_id).json()
-            assert job['state'] == 'error'
-            dataset = self.dataset_populator.get_history_dataset_details(history_id=history_id,
-                                                                         dataset_id=run_response['outputs'][0]['id'],
-                                                                         assert_ok=False)
-            assert dataset['visible']
+            assert job["state"] == "error"
+            dataset = self.dataset_populator.get_history_dataset_details(
+                history_id=history_id, dataset_id=run_response["outputs"][0]["id"], assert_ok=False
+            )
+            assert dataset["visible"]
 
     def _run_map_over_error(self, history_id):
-        hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("sample1-1", "1 2 3")]).json()
+        hdca1 = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=[("sample1-1", "1 2 3")]
+        ).json()
         inputs = {
-            'error_bool': 'true',
-            'dataset': {
-                'batch': True,
-                'values': [{'src': 'hdca', 'id': hdca1['id']}],
-            }
+            "error_bool": "true",
+            "dataset": {
+                "batch": True,
+                "values": [{"src": "hdca", "id": hdca1["id"]}],
+            },
         }
         return self._run_detect_errors(history_id=history_id, inputs=inputs)
 
@@ -284,56 +295,56 @@ steps:
     def test_no_unhide_on_error_if_mapped_over(self):
         with self.dataset_populator.test_history() as history_id:
             run_response = self._run_map_over_error(history_id)
-            job_id = run_response['jobs'][0]["id"]
+            job_id = run_response["jobs"][0]["id"]
             self.dataset_populator.wait_for_job(job_id)
             job = self.dataset_populator.get_job_details(job_id).json()
-            assert job['state'] == 'error'
-            dataset = self.dataset_populator.get_history_dataset_details(history_id=history_id,
-                                                                         dataset_id=run_response['outputs'][0]['id'],
-                                                                         assert_ok=False)
-            assert not dataset['visible']
+            assert job["state"] == "error"
+            dataset = self.dataset_populator.get_history_dataset_details(
+                history_id=history_id, dataset_id=run_response["outputs"][0]["id"], assert_ok=False
+            )
+            assert not dataset["visible"]
 
     def test_no_hide_on_rerun(self):
         with self.dataset_populator.test_history() as history_id:
             run_response = self._run_map_over_error(history_id)
-            job_id = run_response['jobs'][0]["id"]
+            job_id = run_response["jobs"][0]["id"]
             self.dataset_populator.wait_for_job(job_id)
             failed_hdca = self.dataset_populator.get_history_collection_details(
                 history_id=history_id,
-                content_id=run_response['implicit_collections'][0]['id'],
+                content_id=run_response["implicit_collections"][0]["id"],
                 assert_ok=False,
             )
-            first_update_time = failed_hdca['update_time']
-            assert failed_hdca['visible']
+            first_update_time = failed_hdca["update_time"]
+            assert failed_hdca["visible"]
             rerun_params = self._get(f"jobs/{job_id}/build_for_rerun").json()
-            inputs = rerun_params['state_inputs']
-            inputs['rerun_remap_job_id'] = job_id
+            inputs = rerun_params["state_inputs"]
+            inputs["rerun_remap_job_id"] = job_id
             rerun_response = self._run_detect_errors(history_id=history_id, inputs=inputs)
-            rerun_job_id = rerun_response['jobs'][0]["id"]
+            rerun_job_id = rerun_response["jobs"][0]["id"]
             self.dataset_populator.wait_for_job(rerun_job_id)
             # Verify source hdca is still visible
             hdca = self.dataset_populator.get_history_collection_details(
                 history_id=history_id,
-                content_id=run_response['implicit_collections'][0]['id'],
+                content_id=run_response["implicit_collections"][0]["id"],
                 assert_ok=False,
             )
-            assert hdca['visible']
-            assert isoparse(hdca['update_time']) > (isoparse(first_update_time))
+            assert hdca["visible"]
+            assert isoparse(hdca["update_time"]) > (isoparse(first_update_time))
 
-    @skip_without_tool('empty_output')
+    @skip_without_tool("empty_output")
     def test_common_problems(self):
         with self.dataset_populator.test_history() as history_id:
             empty_run_response = self.dataset_populator.run_tool(
-                tool_id='empty_output',
+                tool_id="empty_output",
                 inputs={},
                 history_id=history_id,
             )
             empty_hda = empty_run_response["outputs"][0]
             cat_empty_twice_run_response = self.dataset_populator.run_tool(
-                tool_id='cat1',
+                tool_id="cat1",
                 inputs={
-                    'input1': {'src': 'hda', 'id': empty_hda['id']},
-                    'queries_0|input2': {'src': 'hda', 'id': empty_hda['id']}
+                    "input1": {"src": "hda", "id": empty_hda["id"]},
+                    "queries_0|input2": {"src": "hda", "id": empty_hda["id"]},
                 },
                 history_id=history_id,
             )
@@ -348,37 +359,36 @@ steps:
             assert not empty_output_common_problems_response["has_duplicate_inputs"]
             assert cat_empty_common_problems_response["has_duplicate_inputs"]
 
-    @skip_without_tool('detect_errors_aggressive')
+    @skip_without_tool("detect_errors_aggressive")
     def test_report_error(self):
         with self.dataset_populator.test_history() as history_id:
             self._run_error_report(history_id)
 
-    @skip_without_tool('detect_errors_aggressive')
+    @skip_without_tool("detect_errors_aggressive")
     def test_report_error_anon(self):
         with self._different_user(anon=True):
-            history_id = self._get(urllib.parse.urljoin(self.url, "history/current_history_json")).json()['id']
+            history_id = self._get(urllib.parse.urljoin(self.url, "history/current_history_json")).json()["id"]
             self._run_error_report(history_id)
 
     def _run_error_report(self, history_id):
         payload = self.dataset_populator.run_tool_payload(
-            tool_id='detect_errors_aggressive',
-            inputs={'error_bool': 'true'},
+            tool_id="detect_errors_aggressive",
+            inputs={"error_bool": "true"},
             history_id=history_id,
         )
         run_response = self._post("tools", data=payload).json()
-        job_id = run_response['jobs'][0]["id"]
+        job_id = run_response["jobs"][0]["id"]
         self.dataset_populator.wait_for_job(job_id)
-        dataset_id = run_response['outputs'][0]['id']
-        response = self._post(f'jobs/{job_id}/error',
-                              data={'dataset_id': dataset_id})
+        dataset_id = run_response["outputs"][0]["id"]
+        response = self._post(f"jobs/{job_id}/error", data={"dataset_id": dataset_id})
         assert response.status_code == 200, response.text
 
-    @skip_without_tool('detect_errors_aggressive')
+    @skip_without_tool("detect_errors_aggressive")
     def test_report_error_bootstrap_admin(self):
         with self.dataset_populator.test_history() as history_id:
             payload = self.dataset_populator.run_tool_payload(
-                tool_id='detect_errors_aggressive',
-                inputs={'error_bool': 'true'},
+                tool_id="detect_errors_aggressive",
+                inputs={"error_bool": "true"},
                 history_id=history_id,
             )
             run_response = self._post("tools", data=payload, key=self.master_api_key)
@@ -478,20 +488,21 @@ steps:
         wait_on_state(job_state, assert_ok=True)
 
         if output_dataset_paths_exist:
-            time.sleep(.5)
+            time.sleep(0.5)
             # Make sure the non-purged dataset is on disk and the purged one is not.
             assert os.path.exists(output_dataset_paths[1])
             assert not os.path.exists(output_dataset_paths[0])
 
     def _hack_to_skip_test_if_state_ok(self, job_state):
         from nose.plugins.skip import SkipTest
+
         if job_state().json()["state"] == "ok":
             message = "Job state switch from running to ok too quickly - the rest of the test requires the job to be in a running state. Skipping test."
             raise SkipTest(message)
 
     def _setup_running_two_output_job(self, history_id, sleep_time):
         payload = self.dataset_populator.run_tool_payload(
-            tool_id='create_2',
+            tool_id="create_2",
             inputs=dict(
                 sleep_time=sleep_time,
             ),
@@ -530,11 +541,11 @@ steps:
         hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t40.0\n")
         # Submit first job
         payload = self.dataset_populator.run_tool_payload(
-            tool_id='cat_data_and_sleep',
+            tool_id="cat_data_and_sleep",
             inputs={
-                'sleep_time': 15,
-                'input1': {'src': 'hda', 'id': hda2['id']},
-                'queries_0|input2': {'src': 'hda', 'id': hda2['id']}
+                "sleep_time": 15,
+                "input1": {"src": "hda", "id": hda2["id"]},
+                "queries_0|input2": {"src": "hda", "id": hda2["id"]},
             },
             history_id=history_id,
         )
@@ -542,31 +553,29 @@ steps:
         output = run_response["outputs"][0]
         # Submit second job that waits on job1
         payload = self.dataset_populator.run_tool_payload(
-            tool_id='cat1',
-            inputs={
-                'input1': {'src': 'hda', 'id': hda1['id']},
-                'queries_0|input2': {'src': 'hda', 'id': output['id']}
-            },
+            tool_id="cat1",
+            inputs={"input1": {"src": "hda", "id": hda1["id"]}, "queries_0|input2": {"src": "hda", "id": output["id"]}},
             history_id=history_id,
         )
         run_response = self._post("tools", data=payload).json()
-        job_id = run_response['jobs'][0]['id']
+        job_id = run_response["jobs"][0]["id"]
         output = run_response["outputs"][0]
         # Delete second jobs input while second job is waiting for first job
         delete_response = self._delete(f"histories/{history_id}/contents/{hda1['id']}")
         self._assert_status_code_is(delete_response, 200)
         self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=False)
         dataset_details = self._get(f"histories/{history_id}/contents/{output['id']}").json()
-        assert dataset_details['state'] == 'paused'
+        assert dataset_details["state"] == "paused"
         # Undelete input dataset
-        undelete_response = self._put(f"histories/{history_id}/contents/{hda1['id']}",
-                                      data={'deleted': False}, json=True)
+        undelete_response = self._put(
+            f"histories/{history_id}/contents/{hda1['id']}", data={"deleted": False}, json=True
+        )
         self._assert_status_code_is(undelete_response, 200)
         resume_response = self._put(f"jobs/{job_id}/resume")
         self._assert_status_code_is(resume_response, 200)
         self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=True)
         dataset_details = self._get(f"histories/{history_id}/contents/{output['id']}").json()
-        assert dataset_details['state'] == 'ok'
+        assert dataset_details["state"] == "ok"
 
     def _get_history_item_as_admin(self, history_id, item_id):
         response = self._get(f"histories/{history_id}/contents/{item_id}?view=detailed", admin=True)
@@ -581,16 +590,12 @@ steps:
         copy_payload = {"content": dataset_id, "source": "hda", "type": "dataset"}
         copy_response = self._post(f"histories/{new_history_id}/contents", data=copy_payload, json=True)
         self._assert_status_code_is(copy_response, 200)
-        inputs = json.dumps({
-            'input1': {'src': 'hda', 'id': dataset_id}
-        })
-        self._job_search(tool_id='cat1', history_id=history_id, inputs=inputs)
+        inputs = json.dumps({"input1": {"src": "hda", "id": dataset_id}})
+        self._job_search(tool_id="cat1", history_id=history_id, inputs=inputs)
         # We test that a job can be found even if the dataset has been copied to another history
-        new_dataset_id = copy_response.json()['id']
-        copied_inputs = json.dumps({
-            'input1': {'src': 'hda', 'id': new_dataset_id}
-        })
-        search_payload = self._search_payload(history_id=history_id, tool_id='cat1', inputs=copied_inputs)
+        new_dataset_id = copy_response.json()["id"]
+        copied_inputs = json.dumps({"input1": {"src": "hda", "id": new_dataset_id}})
+        search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=copied_inputs)
         self._search(search_payload, expected_search_count=1)
         # Now we delete the original input HDA that was used -- we should still be able to find the job
         delete_respone = self._delete(f"histories/{history_id}/contents/{dataset_id}")
@@ -605,95 +610,105 @@ steps:
     def test_search_handle_identifiers(self, history_id):
         # Test that input name and element identifier of a jobs' output must match for a job to be returned.
         dataset_id = self.__history_with_ok_dataset(history_id)
-        inputs = json.dumps({
-            'input1': {'src': 'hda', 'id': dataset_id}
-        })
-        self._job_search(tool_id='identifier_single', history_id=history_id, inputs=inputs)
+        inputs = json.dumps({"input1": {"src": "hda", "id": dataset_id}})
+        self._job_search(tool_id="identifier_single", history_id=history_id, inputs=inputs)
         dataset_details = self._get(f"histories/{history_id}/contents/{dataset_id}").json()
-        dataset_details['name'] = 'Renamed Test Dataset'
-        dataset_update_response = self._put(f"histories/{history_id}/contents/{dataset_id}", data=dict(name='Renamed Test Dataset'), json=True)
+        dataset_details["name"] = "Renamed Test Dataset"
+        dataset_update_response = self._put(
+            f"histories/{history_id}/contents/{dataset_id}", data=dict(name="Renamed Test Dataset"), json=True
+        )
         self._assert_status_code_is(dataset_update_response, 200)
-        assert dataset_update_response.json()['name'] == 'Renamed Test Dataset'
-        search_payload = self._search_payload(history_id=history_id, tool_id='identifier_single', inputs=inputs)
+        assert dataset_update_response.json()["name"] == "Renamed Test Dataset"
+        search_payload = self._search_payload(history_id=history_id, tool_id="identifier_single", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
     @uses_test_history(require_new=True)
     def test_search_delete_outputs(self, history_id):
         dataset_id = self.__history_with_ok_dataset(history_id)
-        inputs = json.dumps({
-            'input1': {'src': 'hda', 'id': dataset_id}
-        })
-        tool_response = self._job_search(tool_id='cat1', history_id=history_id, inputs=inputs)
-        output_id = tool_response.json()['outputs'][0]['id']
+        inputs = json.dumps({"input1": {"src": "hda", "id": dataset_id}})
+        tool_response = self._job_search(tool_id="cat1", history_id=history_id, inputs=inputs)
+        output_id = tool_response.json()["outputs"][0]["id"]
         delete_respone = self._delete(f"histories/{history_id}/contents/{output_id}")
         self._assert_status_code_is(delete_respone, 200)
-        search_payload = self._search_payload(history_id=history_id, tool_id='cat1', inputs=inputs)
+        search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
     @uses_test_history(require_new=True)
     def test_search_with_hdca_list_input(self, history_id):
-        list_id_a = self.__history_with_ok_collection(collection_type='list', history_id=history_id)
-        list_id_b = self.__history_with_ok_collection(collection_type='list', history_id=history_id)
-        inputs = json.dumps({
-            'f1': {'src': 'hdca', 'id': list_id_a},
-            'f2': {'src': 'hdca', 'id': list_id_b},
-        })
-        tool_response = self._job_search(tool_id='multi_data_param', history_id=history_id, inputs=inputs)
+        list_id_a = self.__history_with_ok_collection(collection_type="list", history_id=history_id)
+        list_id_b = self.__history_with_ok_collection(collection_type="list", history_id=history_id)
+        inputs = json.dumps(
+            {
+                "f1": {"src": "hdca", "id": list_id_a},
+                "f2": {"src": "hdca", "id": list_id_b},
+            }
+        )
+        tool_response = self._job_search(tool_id="multi_data_param", history_id=history_id, inputs=inputs)
         # We switch the inputs, this should not return a match
-        inputs_switched = json.dumps({
-            'f2': {'src': 'hdca', 'id': list_id_a},
-            'f1': {'src': 'hdca', 'id': list_id_b},
-        })
-        search_payload = self._search_payload(history_id=history_id, tool_id='multi_data_param', inputs=inputs_switched)
+        inputs_switched = json.dumps(
+            {
+                "f2": {"src": "hdca", "id": list_id_a},
+                "f1": {"src": "hdca", "id": list_id_b},
+            }
+        )
+        search_payload = self._search_payload(history_id=history_id, tool_id="multi_data_param", inputs=inputs_switched)
         self._search(search_payload, expected_search_count=0)
         # We delete the ouput (this is a HDA, as multi_data_param reduces collections)
         # and use the correct input job definition, the job should not be found
-        output_id = tool_response.json()['outputs'][0]['id']
+        output_id = tool_response.json()["outputs"][0]["id"]
         delete_respone = self._delete(f"histories/{history_id}/contents/{output_id}")
         self._assert_status_code_is(delete_respone, 200)
-        search_payload = self._search_payload(history_id=history_id, tool_id='multi_data_param', inputs=inputs)
+        search_payload = self._search_payload(history_id=history_id, tool_id="multi_data_param", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
     @uses_test_history(require_new=True)
     def test_search_delete_hdca_output(self, history_id):
-        list_id_a = self.__history_with_ok_collection(collection_type='list', history_id=history_id)
-        inputs = json.dumps({
-            'input1': {'src': 'hdca', 'id': list_id_a},
-        })
-        tool_response = self._job_search(tool_id='collection_creates_list', history_id=history_id, inputs=inputs)
-        output_id = tool_response.json()['outputs'][0]['id']
+        list_id_a = self.__history_with_ok_collection(collection_type="list", history_id=history_id)
+        inputs = json.dumps(
+            {
+                "input1": {"src": "hdca", "id": list_id_a},
+            }
+        )
+        tool_response = self._job_search(tool_id="collection_creates_list", history_id=history_id, inputs=inputs)
+        output_id = tool_response.json()["outputs"][0]["id"]
         # We delete a single tool output, no job should be returned
         delete_respone = self._delete(f"histories/{history_id}/contents/{output_id}")
         self._assert_status_code_is(delete_respone, 200)
-        search_payload = self._search_payload(history_id=history_id, tool_id='collection_creates_list', inputs=inputs)
+        search_payload = self._search_payload(history_id=history_id, tool_id="collection_creates_list", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
-        tool_response = self._job_search(tool_id='collection_creates_list', history_id=history_id, inputs=inputs)
-        output_collection_id = tool_response.json()['output_collections'][0]['id']
+        tool_response = self._job_search(tool_id="collection_creates_list", history_id=history_id, inputs=inputs)
+        output_collection_id = tool_response.json()["output_collections"][0]["id"]
         # We delete a collection output, no job should be returned
         delete_respone = self._delete(f"histories/{history_id}/contents/dataset_collections/{output_collection_id}")
         self._assert_status_code_is(delete_respone, 200)
-        search_payload = self._search_payload(history_id=history_id, tool_id='collection_creates_list', inputs=inputs)
+        search_payload = self._search_payload(history_id=history_id, tool_id="collection_creates_list", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
     @uses_test_history(require_new=True)
     def test_search_with_hdca_pair_input(self, history_id):
-        list_id_a = self.__history_with_ok_collection(collection_type='pair', history_id=history_id)
-        inputs = json.dumps({
-            'f1': {'src': 'hdca', 'id': list_id_a},
-            'f2': {'src': 'hdca', 'id': list_id_a},
-        })
-        self._job_search(tool_id='multi_data_param', history_id=history_id, inputs=inputs)
+        list_id_a = self.__history_with_ok_collection(collection_type="pair", history_id=history_id)
+        inputs = json.dumps(
+            {
+                "f1": {"src": "hdca", "id": list_id_a},
+                "f2": {"src": "hdca", "id": list_id_a},
+            }
+        )
+        self._job_search(tool_id="multi_data_param", history_id=history_id, inputs=inputs)
         # We test that a job can be found even if the collection has been copied to another history
         new_history_id = self.dataset_populator.new_history()
         copy_payload = {"content": list_id_a, "source": "hdca", "type": "dataset_collection"}
         copy_response = self._post(f"histories/{new_history_id}/contents", data=copy_payload, json=True)
         self._assert_status_code_is(copy_response, 200)
-        new_list_a = copy_response.json()['id']
-        copied_inputs = json.dumps({
-            'f1': {'src': 'hdca', 'id': new_list_a},
-            'f2': {'src': 'hdca', 'id': new_list_a},
-        })
-        search_payload = self._search_payload(history_id=new_history_id, tool_id='multi_data_param', inputs=copied_inputs)
+        new_list_a = copy_response.json()["id"]
+        copied_inputs = json.dumps(
+            {
+                "f1": {"src": "hdca", "id": new_list_a},
+                "f2": {"src": "hdca", "id": new_list_a},
+            }
+        )
+        search_payload = self._search_payload(
+            history_id=new_history_id, tool_id="multi_data_param", inputs=copied_inputs
+        )
         self._search(search_payload, expected_search_count=1)
         # Now we delete the original input HDCA that was used -- we should still be able to find the job
         delete_respone = self._delete(f"histories/{history_id}/contents/dataset_collections/{list_id_a}")
@@ -706,24 +721,28 @@ steps:
 
     @uses_test_history(require_new=True)
     def test_search_with_hdca_list_pair_input(self, history_id):
-        list_id_a = self.__history_with_ok_collection(collection_type='list:pair', history_id=history_id)
-        inputs = json.dumps({
-            'f1': {'src': 'hdca', 'id': list_id_a},
-            'f2': {'src': 'hdca', 'id': list_id_a},
-        })
-        self._job_search(tool_id='multi_data_param', history_id=history_id, inputs=inputs)
+        list_id_a = self.__history_with_ok_collection(collection_type="list:pair", history_id=history_id)
+        inputs = json.dumps(
+            {
+                "f1": {"src": "hdca", "id": list_id_a},
+                "f2": {"src": "hdca", "id": list_id_a},
+            }
+        )
+        self._job_search(tool_id="multi_data_param", history_id=history_id, inputs=inputs)
 
     @uses_test_history(require_new=True)
     def test_search_with_hdca_list_pair_collection_mapped_over_pair_input(self, history_id):
-        list_id_a = self.__history_with_ok_collection(collection_type='list:pair', history_id=history_id)
-        inputs = json.dumps({
-            'f1': {'batch': True, 'values': [{'src': 'hdca', 'id': list_id_a, 'map_over_type': 'paired'}]},
-        })
-        self._job_search(tool_id='collection_paired_test', history_id=history_id, inputs=inputs)
+        list_id_a = self.__history_with_ok_collection(collection_type="list:pair", history_id=history_id)
+        inputs = json.dumps(
+            {
+                "f1": {"batch": True, "values": [{"src": "hdca", "id": list_id_a, "map_over_type": "paired"}]},
+            }
+        )
+        self._job_search(tool_id="collection_paired_test", history_id=history_id, inputs=inputs)
 
     def _get_simple_rerun_params(self, history_id, private=False):
-        list_id_a = self.__history_with_ok_collection(collection_type='list:pair', history_id=history_id)
-        inputs = {'f1': {'batch': True, 'values': [{'src': 'hdca', 'id': list_id_a, 'map_over_type': 'paired'}]}}
+        list_id_a = self.__history_with_ok_collection(collection_type="list:pair", history_id=history_id)
+        inputs = {"f1": {"batch": True, "values": [{"src": "hdca", "id": list_id_a, "map_over_type": "paired"}]}}
         run_response = self._run(
             history_id=history_id,
             tool_id="collection_paired_test",
@@ -735,11 +754,11 @@ steps:
         # Since we call rerun on the first (and only) job we should get the expanded input
         # which is a dataset collection element (and not the list:pair hdca that was used as input to the original
         # job).
-        assert rerun_params['state_inputs']['f1']['values'][0]['src'] == 'dce'
+        assert rerun_params["state_inputs"]["f1"]["values"][0]["src"] == "dce"
         if private:
             hdca = self.dataset_populator.get_history_collection_details(history_id=history_id, content_id=list_id_a)
-            for element in hdca['elements'][0]['object']['elements']:
-                self.dataset_populator.make_private(history_id, element['object']['id'])
+            for element in hdca["elements"][0]["object"]["elements"]:
+                self.dataset_populator.make_private(history_id, element["object"]["id"])
         return rerun_params
 
     @skip_without_tool("collection_paired_test")
@@ -749,7 +768,7 @@ steps:
         self._run(
             history_id=history_id,
             tool_id="collection_paired_test",
-            inputs=rerun_params['state_inputs'],
+            inputs=rerun_params["state_inputs"],
             wait_for_job=True,
             assert_ok=True,
         )
@@ -763,7 +782,7 @@ steps:
             response = self._run(
                 history_id=other_history_id,
                 tool_id="collection_paired_test",
-                inputs=rerun_params['state_inputs'],
+                inputs=rerun_params["state_inputs"],
                 wait_for_job=False,
                 assert_ok=False,
             )
@@ -772,19 +791,20 @@ steps:
     @skip_without_tool("identifier_collection")
     @uses_test_history(require_new=False)
     def test_job_build_for_rerun_list_list(self, history_id):
-        list_id_a = self.__history_with_ok_collection(collection_type='list', history_id=history_id)
-        list_id_b = self.__history_with_ok_collection(collection_type='list', history_id=history_id)
+        list_id_a = self.__history_with_ok_collection(collection_type="list", history_id=history_id)
+        list_id_b = self.__history_with_ok_collection(collection_type="list", history_id=history_id)
         list_list = self.dataset_collection_populator.create_nested_collection(
             history_id=history_id,
-            collection_type='list:list',
-            name='list list collection',
-            collection=[list_id_a, list_id_b]).json()
-        list_list_id = list_list['id']
-        first_element = list_list['elements'][0]
-        assert first_element['element_type'] == 'dataset_collection'
-        assert first_element['element_identifier'] == 'test0'
-        assert first_element['model_class'] == 'DatasetCollectionElement'
-        inputs = {'input1': {'batch': True, 'values': [{'src': 'hdca', 'id': list_list_id, 'map_over_type': 'list'}]}}
+            collection_type="list:list",
+            name="list list collection",
+            collection=[list_id_a, list_id_b],
+        ).json()
+        list_list_id = list_list["id"]
+        first_element = list_list["elements"][0]
+        assert first_element["element_type"] == "dataset_collection"
+        assert first_element["element_identifier"] == "test0"
+        assert first_element["model_class"] == "DatasetCollectionElement"
+        inputs = {"input1": {"batch": True, "values": [{"src": "hdca", "id": list_list_id, "map_over_type": "list"}]}}
         run_response = self._run(
             history_id=history_id,
             tool_id="identifier_collection",
@@ -792,22 +812,26 @@ steps:
             wait_for_job=True,
             assert_ok=True,
         )
-        assert len(run_response['jobs']) == 2
+        assert len(run_response["jobs"]) == 2
         rerun_params = self._get(f"jobs/{run_response['jobs'][0]['id']}/build_for_rerun").json()
         # Since we call rerun on the first (and only) job we should get the expanded input
         # which is a dataset collection element (and not the list:list hdca that was used as input to the original
         # job).
-        assert rerun_params['state_inputs']['input1']['values'][0]['src'] == 'dce'
+        assert rerun_params["state_inputs"]["input1"]["values"][0]["src"] == "dce"
         rerun_response = self._run(
             history_id=history_id,
             tool_id="identifier_collection",
-            inputs=rerun_params['state_inputs'],
+            inputs=rerun_params["state_inputs"],
             wait_for_job=True,
             assert_ok=True,
         )
-        assert len(rerun_response['jobs']) == 1
-        rerun_content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=rerun_response['outputs'][0])
-        run_content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=run_response['outputs'][0])
+        assert len(rerun_response["jobs"]) == 1
+        rerun_content = self.dataset_populator.get_history_dataset_content(
+            history_id=history_id, dataset=rerun_response["outputs"][0]
+        )
+        run_content = self.dataset_populator.get_history_dataset_content(
+            history_id=history_id, dataset=run_response["outputs"][0]
+        )
         assert rerun_content == run_content
 
     def _job_search(self, tool_id, history_id, inputs):
@@ -820,13 +844,8 @@ steps:
         self._search(search_payload, expected_search_count=1)
         return tool_response
 
-    def _search_payload(self, history_id, tool_id, inputs, state='ok'):
-        search_payload = dict(
-            tool_id=tool_id,
-            inputs=inputs,
-            history_id=history_id,
-            state=state
-        )
+    def _search_payload(self, history_id, tool_id, inputs, state="ok"):
+        search_payload = dict(tool_id=tool_id, inputs=inputs, history_id=history_id, state=state)
         return search_payload
 
     def _search(self, payload, expected_search_count=1):
@@ -837,7 +856,10 @@ steps:
             if search_count == expected_search_count:
                 break
             time.sleep(1)
-        assert search_count == expected_search_count, "expected to find %d jobs, got %d jobs" % (expected_search_count, search_count)
+        assert search_count == expected_search_count, "expected to find %d jobs, got %d jobs" % (
+            expected_search_count,
+            search_count,
+        )
         return search_count
 
     def _search_count(self, search_payload):
@@ -850,8 +872,8 @@ steps:
         jobs_response = self._get("jobs", data=dict(state=states))
         self._assert_status_code_is(jobs_response, 200)
         jobs = jobs_response.json()
-        assert not [j for j in jobs if not j['state'] in states]
-        return [j for j in jobs if j['tool_id'] == 'upload1']
+        assert not [j for j in jobs if not j["state"] in states]
+        return [j for j in jobs if j["tool_id"] == "upload1"]
 
     def __history_with_new_dataset(self, history_id):
         dataset_id = self.dataset_populator.new_dataset(history_id)["id"]
@@ -861,17 +883,21 @@ steps:
         dataset_id = self.dataset_populator.new_dataset(history_id, wait=True)["id"]
         return dataset_id
 
-    def __history_with_ok_collection(self, collection_type='list', history_id=None):
+    def __history_with_ok_collection(self, collection_type="list", history_id=None):
         if not history_id:
             history_id = self.dataset_populator.new_history()
-        if collection_type == 'list':
-            fetch_response = self.dataset_collection_populator.create_list_in_history(history_id, direct_upload=True).json()
-        elif collection_type == 'pair':
-            fetch_response = self.dataset_collection_populator.create_pair_in_history(history_id, direct_upload=True).json()
-        elif collection_type == 'list:pair':
+        if collection_type == "list":
+            fetch_response = self.dataset_collection_populator.create_list_in_history(
+                history_id, direct_upload=True
+            ).json()
+        elif collection_type == "pair":
+            fetch_response = self.dataset_collection_populator.create_pair_in_history(
+                history_id, direct_upload=True
+            ).json()
+        elif collection_type == "list:pair":
             fetch_response = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()
         self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
-        return fetch_response["outputs"][0]['id']
+        return fetch_response["outputs"][0]["id"]
 
     def __jobs_index(self, **kwds):
         jobs_response = self._get("jobs", **kwds)
diff --git a/lib/galaxy_test/api/test_libraries.py b/lib/galaxy_test/api/test_libraries.py
index 0b55bfac9d9..e151056ea0f 100644
--- a/lib/galaxy_test/api/test_libraries.py
+++ b/lib/galaxy_test/api/test_libraries.py
@@ -12,12 +12,11 @@ from galaxy_test.base.populators import (
 )
 from ._framework import ApiTestCase
 
-FILE_URL = 'https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed'
+FILE_URL = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed"
 FILE_MD5 = "37b59762b59fff860460522d271bc111"
 
 
 class LibrariesApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -56,26 +55,26 @@ class LibrariesApiTestCase(ApiTestCase):
         create_response = self._delete(f"libraries/{library['id']}", admin=False, anon=True)
         self._assert_status_code_is(create_response, 403)
         # Anons can't update libs
-        data = dict(name="ChangedName", description="ChangedDescription", synopsis='ChangedSynopsis')
+        data = dict(name="ChangedName", description="ChangedDescription", synopsis="ChangedSynopsis")
         create_response = self._patch(f"libraries/{library['id']}", data=data, admin=False, anon=True)
         self._assert_status_code_is(create_response, 403)
 
     def test_update(self):
         library = self.library_populator.new_library("UpdateTestLibrary")
-        data = dict(name='ChangedName', description='ChangedDescription', synopsis='ChangedSynopsis')
+        data = dict(name="ChangedName", description="ChangedDescription", synopsis="ChangedSynopsis")
         create_response = self._patch(f"libraries/{library['id']}", data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         library = create_response.json()
-        self._assert_has_keys(library, 'name', 'description', 'synopsis')
-        assert library['name'] == 'ChangedName'
-        assert library['description'] == 'ChangedDescription'
-        assert library['synopsis'] == 'ChangedSynopsis'
+        self._assert_has_keys(library, "name", "description", "synopsis")
+        assert library["name"] == "ChangedName"
+        assert library["description"] == "ChangedDescription"
+        assert library["synopsis"] == "ChangedSynopsis"
 
     def test_update_non_admins_with_permission(self):
         library = self.library_populator.new_library("UpdateTestLibraryNonAdmin")
         library_id = library["id"]
         role_id = self.library_populator.user_private_role_id()
-        data = dict(name='ChangedName', description='ChangedDescription', synopsis='ChangedSynopsis')
+        data = dict(name="ChangedName", description="ChangedDescription", synopsis="ChangedSynopsis")
         # User has no permission by default
         create_response = self._patch(f"libraries/{library['id']}", data=data)
         self._assert_status_code_is(create_response, 403)
@@ -84,10 +83,10 @@ class LibrariesApiTestCase(ApiTestCase):
         create_response = self._patch(f"libraries/{library['id']}", data=data)
         self._assert_status_code_is(create_response, 200)
         library = create_response.json()
-        self._assert_has_keys(library, 'name', 'description', 'synopsis')
-        assert library['name'] == 'ChangedName'
-        assert library['description'] == 'ChangedDescription'
-        assert library['synopsis'] == 'ChangedSynopsis'
+        self._assert_has_keys(library, "name", "description", "synopsis")
+        assert library["name"] == "ChangedName"
+        assert library["description"] == "ChangedDescription"
+        assert library["synopsis"] == "ChangedSynopsis"
 
     def test_create_private_library_legacy_permissions(self):
         library = self.library_populator.new_library("LegacyPermissionTestLibrary")
@@ -117,7 +116,13 @@ class LibrariesApiTestCase(ApiTestCase):
         library = self.library_populator.new_library("GetCurrentPermissionTestLibrary")
         library_id = library["id"]
         current = self.library_populator.get_permissions(library_id, scope="current")
-        self._assert_has_keys(current, "access_library_role_list", "modify_library_role_list", "manage_library_role_list", "add_library_item_role_list")
+        self._assert_has_keys(
+            current,
+            "access_library_role_list",
+            "modify_library_role_list",
+            "manage_library_role_list",
+            "add_library_item_role_list",
+        )
 
         role_id = self.library_populator.user_private_role_id()
         self.library_populator.set_permissions_with_action(library_id, role_id, action="set_permissions")
@@ -157,7 +162,9 @@ class LibrariesApiTestCase(ApiTestCase):
     def test_create_library_dataset_bootstrap_user(self, library_name="private_dataset", wait=True):
         library = self.library_populator.new_private_library(library_name)
         payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test")
-        create_response = self.galaxy_interactor.post("libraries/%s/contents" % library["id"], payload, files=files, key=self.master_api_key)
+        create_response = self.galaxy_interactor.post(
+            "libraries/%s/contents" % library["id"], payload, files=files, key=self.master_api_key
+        )
         self._assert_status_code_is(create_response, 400)
 
     def test_create_dataset_denied(self):
@@ -176,13 +183,15 @@ class LibrariesApiTestCase(ApiTestCase):
         library = self.library_populator.new_private_library("ForCreateDatasets")
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
+        folder_id = folder_response.json()[0]["id"]
         history_id = self.dataset_populator.new_history()
-        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id']
+        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")["id"]
         return f"folders/{folder_id}/contents", {"from_hda_id": hda_id}
 
     def test_show_private_dataset_permissions(self):
-        library, library_dataset = self.library_populator.new_library_dataset_in_private_library("ForCreateDatasets", wait=True)
+        library, library_dataset = self.library_populator.new_library_dataset_in_private_library(
+            "ForCreateDatasets", wait=True
+        )
         with self._different_user():
             with pytest.raises(requests.exceptions.HTTPError) as exc_info:
                 self.library_populator.show_ld(library["id"], library_dataset["id"])
@@ -190,7 +199,9 @@ class LibrariesApiTestCase(ApiTestCase):
             self._assert_status_code_is(exc_info.value.response, 400)
 
     def test_create_dataset(self):
-        library, library_dataset = self.library_populator.new_library_dataset_in_private_library("ForCreateDatasets", wait=True)
+        library, library_dataset = self.library_populator.new_library_dataset_in_private_library(
+            "ForCreateDatasets", wait=True
+        )
         self._assert_has_keys(library_dataset, "peek", "data_type")
         assert library_dataset["peek"].find("create_test") >= 0
         assert library_dataset["file_ext"] == "txt", library_dataset["file_ext"]
@@ -208,10 +219,7 @@ class LibrariesApiTestCase(ApiTestCase):
     def test_fetch_upload_to_folder(self):
         history_id, library, destination = self._setup_fetch_to_folder("flat_zip")
         items = [{"src": "files", "dbkey": "hg19", "info": "my cool bed", "created_from_basename": "4.bed"}]
-        targets = [{
-            "destination": destination,
-            "items": items
-        }]
+        targets = [{"destination": destination, "items": items}]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -228,14 +236,17 @@ class LibrariesApiTestCase(ApiTestCase):
     def test_fetch_zip_to_folder(self):
         history_id, library, destination = self._setup_fetch_to_folder("flat_zip")
         bed_test_data_path = self.test_data_resolver.get_filename("4.bed.zip")
-        targets = [{
-            "destination": destination,
-            "items_from": "archive", "src": "files",
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items_from": "archive",
+                "src": "files",
+            }
+        ]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
-            "__files": {"files_0|file_data": open(bed_test_data_path, 'rb')}
+            "__files": {"files_0|file_data": open(bed_test_data_path, "rb")},
         }
         self.dataset_populator.fetch(payload)
         dataset = self.library_populator.get_library_contents_with_path(library["id"], "/4.bed")
@@ -247,26 +258,30 @@ class LibrariesApiTestCase(ApiTestCase):
         assert dataset["file_size"] == 61, dataset
 
     def test_fetch_single_url_with_invalid_datatype(self):
-        _, response = self._fetch_single_url_to_folder('xxx', assert_ok=False)
+        _, response = self._fetch_single_url_to_folder("xxx", assert_ok=False)
         self._assert_status_code_is(response, 400)
-        assert response.json()['err_msg'] == "Requested extension 'xxx' unknown, cannot upload dataset."
+        assert response.json()["err_msg"] == "Requested extension 'xxx' unknown, cannot upload dataset."
 
-    def _fetch_single_url_to_folder(self, file_type='auto', assert_ok=True):
+    def _fetch_single_url_to_folder(self, file_type="auto", assert_ok=True):
         history_id, library, destination = self._setup_fetch_to_folder("single_url")
-        items = [{
-            "src": "url",
-            "url": FILE_URL,
-            "MD5": FILE_MD5,
-            "ext": file_type,
-        }]
-        targets = [{
-            "destination": destination,
-            "items": items,
-        }]
+        items = [
+            {
+                "src": "url",
+                "url": FILE_URL,
+                "MD5": FILE_MD5,
+                "ext": file_type,
+            }
+        ]
+        targets = [
+            {
+                "destination": destination,
+                "items": items,
+            }
+        ]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
-            "validate_hashes": True
+            "validate_hashes": True,
         }
         return library, self.dataset_populator.fetch(payload, assert_ok=assert_ok)
 
@@ -274,13 +289,13 @@ class LibrariesApiTestCase(ApiTestCase):
         library = self.library_populator.new_private_library("ForLegacyUpload")
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
+        folder_id = folder_response.json()[0]["id"]
         payload = {
-            'folder_id': folder_id,
-            'create_type': 'file',
-            'file_type': 'xxx',
-            'upload_option': 'upload_file',
-            'files_0|url_paste': FILE_URL,
+            "folder_id": folder_id,
+            "create_type": "file",
+            "file_type": "xxx",
+            "upload_option": "upload_file",
+            "files_0|url_paste": FILE_URL,
         }
         create_response = self._post(f"libraries/{library['id']}/contents", payload)
         self._assert_status_code_is(create_response, 400)
@@ -291,20 +306,24 @@ class LibrariesApiTestCase(ApiTestCase):
         # Exception handling is really rough here - we should be creating a dataset in error instead
         # of just failing the job like this.
         history_id, library, destination = self._setup_fetch_to_folder("single_url")
-        items = [{
-            "src": "url",
-            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed",
-            "MD5": "37b59762b59fff860460522d271bc112",
-            "name": "4.bed",
-        }]
-        targets = [{
-            "destination": destination,
-            "items": items,
-        }]
+        items = [
+            {
+                "src": "url",
+                "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed",
+                "MD5": "37b59762b59fff860460522d271bc112",
+                "name": "4.bed",
+            }
+        ]
+        targets = [
+            {
+                "destination": destination,
+                "items": items,
+            }
+        ]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
-            "validate_hashes": True
+            "validate_hashes": True,
         }
         tool_response = self.dataset_populator.fetch(payload, assert_ok=False)
         job = self.dataset_populator.check_run(tool_response)
@@ -320,12 +339,14 @@ class LibrariesApiTestCase(ApiTestCase):
     @skip_if_github_down
     def test_fetch_url_archive_to_folder(self):
         history_id, library, destination = self._setup_fetch_to_folder("single_url")
-        targets = [{
-            "destination": destination,
-            "items_from": "archive",
-            "src": "url",
-            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed.zip",
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items_from": "archive",
+                "src": "url",
+                "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed.zip",
+            }
+        ]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -338,10 +359,13 @@ class LibrariesApiTestCase(ApiTestCase):
     def test_fetch_bagit_archive_to_folder(self):
         history_id, library, destination = self._setup_fetch_to_folder("bagit_archive")
         example_bag_path = self.test_data_resolver.get_filename("example-bag.zip")
-        targets = [{
-            "destination": destination,
-            "items_from": "bagit_archive", "src": "files",
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items_from": "bagit_archive",
+                "src": "files",
+            }
+        ]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -361,10 +385,10 @@ class LibrariesApiTestCase(ApiTestCase):
         library = self.library_populator.new_private_library("ForCreateDatasets")
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
+        folder_id = folder_response.json()[0]["id"]
         history_id = self.dataset_populator.new_history()
-        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id']
-        payload = {'from_hda_id': hda_id}
+        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")["id"]
+        payload = {"from_hda_id": hda_id}
         create_response = self._post(f"folders/{folder_id}/contents", payload)
         self._assert_status_code_is(create_response, 200)
         self._assert_has_keys(create_response.json(), "name", "id")
@@ -373,57 +397,62 @@ class LibrariesApiTestCase(ApiTestCase):
         library = self.library_populator.new_private_library("ForCreateDatasets")
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
+        folder_id = folder_response.json()[0]["id"]
         subfolder_response = self._create_subfolder(folder_id)
         self._assert_status_code_is(folder_response, 200)
         print(subfolder_response.json())
-        subfolder_id = subfolder_response.json()['id']
+        subfolder_id = subfolder_response.json()["id"]
         history_id = self.dataset_populator.new_history()
-        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3 sub")['id']
-        payload = {'from_hda_id': hda_id}
+        hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3 sub")["id"]
+        payload = {"from_hda_id": hda_id}
         create_response = self._post(f"folders/{subfolder_id}/contents", payload)
         self._assert_status_code_is(create_response, 200)
         self._assert_has_keys(create_response.json(), "name", "id")
-        dataset_update_time = create_response.json()['update_time']
+        dataset_update_time = create_response.json()["update_time"]
         container_fetch_response = self.galaxy_interactor.get(f"folders/{folder_id}/contents")
-        container_update_time = container_fetch_response.json()['folder_contents'][0]['update_time']
+        container_update_time = container_fetch_response.json()["folder_contents"][0]["update_time"]
         assert dataset_update_time == container_update_time, container_fetch_response
 
     def _patch_library_dataset(self, library_dataset_id, data):
         create_response = self._patch(f"libraries/datasets/{library_dataset_id}", data=data)
         self._assert_status_code_is(create_response, 200)
         ld = create_response.json()
-        library_id = ld['parent_library_id']
+        library_id = ld["parent_library_id"]
         return self.library_populator.wait_on_library_dataset(library_id, ld["id"])
 
     def test_update_dataset_in_folder(self):
         ld = self._create_dataset_in_folder_in_library("ForUpdateDataset", content=">seq\nATGC", wait=True).json()
-        data = {'name': 'updated_name', 'file_ext': 'fasta', 'misc_info': 'updated_info', 'genome_build': 'updated_genome_build'}
-        ld_updated = self._patch_library_dataset(ld['id'], data)
+        data = {
+            "name": "updated_name",
+            "file_ext": "fasta",
+            "misc_info": "updated_info",
+            "genome_build": "updated_genome_build",
+        }
+        ld_updated = self._patch_library_dataset(ld["id"], data)
         self._assert_has_keys(ld_updated, "name", "file_ext", "misc_info", "genome_build")
 
     def test_update_dataset_tags(self):
         ld = self._create_dataset_in_folder_in_library("ForTagtestDataset", wait=True).json()
         data = {"tags": ["#Lancelot", "name:Holy Grail", "blue"]}
-        ld_updated = self._patch_library_dataset(ld['id'], data)
+        ld_updated = self._patch_library_dataset(ld["id"], data)
         self._assert_has_keys(ld_updated, "tags")
         assert ld_updated["tags"] == "name:Lancelot, name:HolyGrail, blue"
 
     def test_invalid_update_dataset_in_folder(self):
         ld = self._create_dataset_in_folder_in_library("ForInvalidUpdateDataset", wait=True).json()
-        data = {'file_ext': 'nonexisting_type'}
+        data = {"file_ext": "nonexisting_type"}
         create_response = self._patch(f"libraries/datasets/{ld['id']}", data=data)
         self._assert_status_code_is(create_response, 400)
-        assert 'This Galaxy does not recognize the datatype of:' in create_response.json()['err_msg']
+        assert "This Galaxy does not recognize the datatype of:" in create_response.json()["err_msg"]
 
     def test_detect_datatype_of_dataset_in_folder(self):
         ld = self._create_dataset_in_folder_in_library("ForDetectDataset", wait=True).json()
-        data = {'file_ext': 'data'}
-        ld_updated = self._patch_library_dataset(ld['id'], data)
+        data = {"file_ext": "data"}
+        ld_updated = self._patch_library_dataset(ld["id"], data)
         self._assert_has_keys(ld_updated, "file_ext")
         assert ld_updated["file_ext"] == "data"
-        data = {'file_ext': 'auto'}
-        ld_updated = self._patch_library_dataset(ld['id'], data)
+        data = {"file_ext": "auto"}
+        ld_updated = self._patch_library_dataset(ld["id"], data)
         self._assert_has_keys(ld_updated, "file_ext")
         assert ld_updated["file_ext"] == "txt"
 
@@ -437,33 +466,35 @@ class LibrariesApiTestCase(ApiTestCase):
         ld = self._create_dataset_in_folder_in_library("ForHistoryImport").json()
         history_id = self.dataset_populator.new_history()
         url = f"histories/{history_id}/contents"
-        collection_name = 'Paired-end data (from library)'
+        collection_name = "Paired-end data (from library)"
         payload = {
-            'name': collection_name,
-            'collection_type': 'list:paired',
+            "name": collection_name,
+            "collection_type": "list:paired",
             "type": "dataset_collection",
-            'element_identifiers': [
+            "element_identifiers": [
                 {
-                    'src': 'new_collection',
-                    'name': 'pair1',
-                    'collection_type': 'paired',
-                    'element_identifiers': [{'name': 'forward', 'src': 'ldda', 'id': ld['id']},
-                                            {'name': 'reverse', 'src': 'ldda', 'id': ld['id']}]
+                    "src": "new_collection",
+                    "name": "pair1",
+                    "collection_type": "paired",
+                    "element_identifiers": [
+                        {"name": "forward", "src": "ldda", "id": ld["id"]},
+                        {"name": "reverse", "src": "ldda", "id": ld["id"]},
+                    ],
                 }
-            ]
+            ],
         }
         new_collection = self._post(url, payload, json=True).json()
-        assert new_collection['name'] == collection_name
-        pair = new_collection['elements'][0]
-        assert pair['element_identifier'] == 'pair1'
-        assert pair['object']['elements'][0]['object']['history_id'] == history_id
+        assert new_collection["name"] == collection_name
+        pair = new_collection["elements"][0]
+        assert pair["element_identifier"] == "pair1"
+        assert pair["object"]["elements"][0]["object"]["history_id"] == history_id
 
     def _import_to_history(self, visible=True):
         ld = self._create_dataset_in_folder_in_library("ForHistoryImport").json()
         history_id = self.dataset_populator.new_history()
         url = f"histories/{history_id}/contents"
-        collection_name = 'new_collection_name'
-        element_identifer = 'new_element_identifier'
+        collection_name = "new_collection_name"
+        element_identifer = "new_element_identifier"
         payload = {
             "collection_type": "list",
             "history_content_type": "dataset_collection",
@@ -471,49 +502,55 @@ class LibrariesApiTestCase(ApiTestCase):
             "history_id": history_id,
             "name": collection_name,
             "hide_source_items": not visible,
-            "element_identifiers": [{
-                "id": ld['id'],
-                "name": element_identifer,
-                "src": "ldda"}],
+            "element_identifiers": [{"id": ld["id"], "name": element_identifer, "src": "ldda"}],
             "type": "dataset_collection",
-            "elements": []
+            "elements": [],
         }
         new_collection = self._post(url, payload, json=True).json()
-        assert new_collection['name'] == collection_name
-        assert new_collection['element_count'] == 1
-        element = new_collection['elements'][0]
-        assert element['element_identifier'] == element_identifer
-        assert element['object']['visible'] == visible
+        assert new_collection["name"] == collection_name
+        assert new_collection["element_count"] == 1
+        element = new_collection["elements"][0]
+        assert element["element_identifier"] == element_identifer
+        assert element["object"]["visible"] == visible
 
     def test_create_datasets_in_library_from_collection(self):
         library = self.library_populator.new_private_library("ForCreateDatasetsFromCollection")
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
+        folder_id = folder_response.json()[0]["id"]
         history_id = self.dataset_populator.new_history()
-        hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["xxx", "yyy"], direct_upload=True).json()["outputs"][0]["id"]
-        payload = {'from_hdca_id': hdca_id, 'create_type': 'file', 'folder_id': folder_id}
+        hdca_id = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["xxx", "yyy"], direct_upload=True
+        ).json()["outputs"][0]["id"]
+        payload = {"from_hdca_id": hdca_id, "create_type": "file", "folder_id": folder_id}
         create_response = self._post(f"libraries/{library['id']}/contents", payload)
         self._assert_status_code_is(create_response, 200)
 
     def test_create_datasets_in_folder_from_collection(self):
         library = self.library_populator.new_private_library("ForCreateDatasetsFromCollection")
         history_id = self.dataset_populator.new_history()
-        hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["xxx", "yyy"], direct_upload=True).json()["outputs"][0]["id"]
+        hdca_id = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["xxx", "yyy"], direct_upload=True
+        ).json()["outputs"][0]["id"]
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
-        payload = {'from_hdca_id': hdca_id}
+        folder_id = folder_response.json()[0]["id"]
+        payload = {"from_hdca_id": hdca_id}
         create_response = self._post(f"folders/{folder_id}/contents", payload)
         self._assert_status_code_is(create_response, 200)
         assert len(create_response.json()) == 2
         # Also test that anything different from a flat dataset collection list
         # is refused
-        hdca_pair_id = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()["outputs"][0]['id']
-        payload = {'from_hdca_id': hdca_pair_id}
+        hdca_pair_id = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()["outputs"][
+            0
+        ]["id"]
+        payload = {"from_hdca_id": hdca_pair_id}
         create_response = self._post(f"folders/{folder_id}/contents", payload)
         self._assert_status_code_is(create_response, 501)
-        assert create_response.json()['err_msg'] == 'Cannot add nested collections to library. Please flatten your collection first.'
+        assert (
+            create_response.json()["err_msg"]
+            == "Cannot add nested collections to library. Please flatten your collection first."
+        )
 
     def _create_folder(self, library):
         create_data = dict(
@@ -534,9 +571,9 @@ class LibrariesApiTestCase(ApiTestCase):
         library = self.library_populator.new_private_library(library_name)
         folder_response = self._create_folder(library)
         self._assert_status_code_is(folder_response, 200)
-        folder_id = folder_response.json()[0]['id']
+        folder_id = folder_response.json()[0]["id"]
         history_id = self.dataset_populator.new_history()
-        hda_id = self.dataset_populator.new_dataset(history_id, content=content, wait=wait)['id']
-        payload = {'from_hda_id': hda_id, 'create_type': 'file', 'folder_id': folder_id}
+        hda_id = self.dataset_populator.new_dataset(history_id, content=content, wait=wait)["id"]
+        payload = {"from_hda_id": hda_id, "create_type": "file", "folder_id": folder_id}
         ld = self._post(f"libraries/{folder_id}/contents", payload)
         return ld
diff --git a/lib/galaxy_test/api/test_licenses.py b/lib/galaxy_test/api/test_licenses.py
index 6b7a0ef3b0a..87fb30b9ed9 100644
--- a/lib/galaxy_test/api/test_licenses.py
+++ b/lib/galaxy_test/api/test_licenses.py
@@ -2,7 +2,6 @@ from ._framework import ApiTestCase
 
 
 class LicensesApiTestCase(ApiTestCase):
-
     def test_index(self):
         response = self._get("licenses")
         self._assert_status_code_is(response, 200)
diff --git a/lib/galaxy_test/api/test_page_revisions.py b/lib/galaxy_test/api/test_page_revisions.py
index b52b676ceb9..4548c1263f6 100644
--- a/lib/galaxy_test/api/test_page_revisions.py
+++ b/lib/galaxy_test/api/test_page_revisions.py
@@ -3,14 +3,13 @@ from .test_pages import BasePageApiTestCase
 
 
 class PageRevisionsApiTestCase(BasePageApiTestCase):
-
     def test_create(self):
         page_json = self._create_valid_page_with_slug("pr1")
         revision_data = dict(content="<p>NewContent!</p>")
         page_revision_response = self._post(f"pages/{page_json['id']}/revisions", data=revision_data)
         self._assert_status_code_is(page_revision_response, 200)
         page_revision_json = page_revision_response.json()
-        self._assert_has_keys(page_revision_json, 'id', 'content')
+        self._assert_has_keys(page_revision_json, "id", "content")
 
     def test_403_if_create_revision_on_unowned_page(self):
         page_json = self._create_valid_page_as("pr2@bx.psu.edu", "pr2")
@@ -32,4 +31,4 @@ class PageRevisionsApiTestCase(BasePageApiTestCase):
         revisions_url = f"pages/{self._random_key()}/revisions"
         revisions_response = self._get(revisions_url)
         self._assert_status_code_is(revisions_response, 400)
-        self._assert_error_code_is(revisions_response, error_codes.error_codes_by_name['MALFORMED_ID'])
+        self._assert_error_code_is(revisions_response, error_codes.error_codes_by_name["MALFORMED_ID"])
diff --git a/lib/galaxy_test/api/test_pages.py b/lib/galaxy_test/api/test_pages.py
index b8783e34e0d..fd7231d243d 100644
--- a/lib/galaxy_test/api/test_pages.py
+++ b/lib/galaxy_test/api/test_pages.py
@@ -5,12 +5,15 @@ from requests import delete
 from galaxy.exceptions import error_codes
 from galaxy_test.api.sharable import SharingApiTests
 from galaxy_test.base import api_asserts
-from galaxy_test.base.populators import DatasetPopulator, skip_without_tool, WorkflowPopulator
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    skip_without_tool,
+    WorkflowPopulator,
+)
 from ._framework import ApiTestCase
 
 
 class BasePageApiTestCase(ApiTestCase):
-
     def _create_valid_page_with_slug(self, slug):
         page_request = self._test_page_payload(slug=slug)
         page_response = self._post("pages", page_request, json=True)
@@ -20,7 +23,7 @@ class BasePageApiTestCase(ApiTestCase):
     def _create_valid_page_as(self, other_email, slug):
         run_as_user = self._setup_user(other_email)
         page_request = self._test_page_payload(slug=slug)
-        page_response = self._post("pages", page_request, headers={'run-as': run_as_user["id"]}, admin=True, json=True)
+        page_response = self._post("pages", page_request, headers={"run-as": run_as_user["id"]}, admin=True, json=True)
         self._assert_status_code_is(page_response, 200)
         return page_response.json()
 
@@ -65,7 +68,8 @@ input_1:
   type: File
 """
         with self.dataset_populator.test_history() as history_id:
-            summary = self.workflow_populator.run_workflow("""
+            summary = self.workflow_populator.run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input_1: data
@@ -77,7 +81,10 @@ steps:
     tool_id: cat
     in:
       input1: input_1
-""", test_data=test_data, history_id=history_id)
+""",
+                test_data=test_data,
+                history_id=history_id,
+            )
 
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
@@ -136,14 +143,14 @@ steps:
 
     def test_page_requires_name(self):
         page_request = self._test_page_payload(slug="requires-name")
-        del page_request['title']
+        del page_request["title"]
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 400)
         self._assert_error_code_is(page_response, error_codes.error_codes_by_name["USER_REQUEST_MISSING_PARAMETER"])
 
     def test_page_requires_slug(self):
         page_request = self._test_page_payload()
-        del page_request['slug']
+        del page_request["slug"]
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 400)
 
@@ -165,14 +172,14 @@ steps:
 
     def test_400_on_invalid_id_encoding(self):
         page_request = self._test_page_payload(slug="invalid-id-encding")
-        page_request["content"] = '''<p>Page!<div class="embedded-item" id="History-invaidencodedid"></div></p>'''
+        page_request["content"] = """<p>Page!<div class="embedded-item" id="History-invaidencodedid"></div></p>"""
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 400)
         self._assert_error_code_is(page_response, error_codes.error_codes_by_name["MALFORMED_ID"])
 
     def test_400_on_invalid_id_encoding_markdown(self):
         page_request = self._test_page_payload(slug="invalid-id-encding-markdown", content_format="markdown")
-        page_request["content"] = '''```galaxy\nhistory_dataset_display(history_dataset_id=badencoding)\n```\n'''
+        page_request["content"] = """```galaxy\nhistory_dataset_display(history_dataset_id=badencoding)\n```\n"""
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 400)
         self._assert_error_code_is(page_response, error_codes.error_codes_by_name["MALFORMED_ID"])
@@ -180,7 +187,7 @@ steps:
     def test_400_on_invalid_embedded_content(self):
         valid_id = self.dataset_populator.new_history()
         page_request = self._test_page_payload(slug="invalid-embed-content")
-        page_request["content"] = f'''<p>Page!<div class="embedded-item" id="CoolObject-{valid_id}"></div></p>'''
+        page_request["content"] = f"""<p>Page!<div class="embedded-item" id="CoolObject-{valid_id}"></div></p>"""
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 400)
         self._assert_error_code_is(page_response, error_codes.error_codes_by_name["USER_REQUEST_INVALID_PARAMETER"])
@@ -188,7 +195,7 @@ steps:
 
     def test_400_on_invalid_markdown_call(self):
         page_request = self._test_page_payload(slug="invalid-markdown-call", content_format="markdown")
-        page_request["content"] = '''```galaxy\njob_metrics(job_id)\n```\n'''
+        page_request["content"] = """```galaxy\njob_metrics(job_id)\n```\n"""
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 400)
         self._assert_error_code_is(page_response, error_codes.error_codes_by_name["MALFORMED_CONTENTS"])
@@ -218,10 +225,12 @@ steps:
         page_request = self._test_page_payload(slug="md-page-to-pdf-not-implemented", content_format="markdown")
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 200)
-        page_id = page_response.json()['id']
+        page_id = page_response.json()["id"]
         pdf_response = self._get(f"pages/{page_id}.pdf")
         api_asserts.assert_status_code_is(pdf_response, 501)
-        api_asserts.assert_error_code_is(pdf_response, error_codes.error_codes_by_name["SERVER_NOT_CONFIGURED_FOR_REQUEST"])
+        api_asserts.assert_error_code_is(
+            pdf_response, error_codes.error_codes_by_name["SERVER_NOT_CONFIGURED_FOR_REQUEST"]
+        )
 
     def test_pdf_when_service_available(self):
         configuration = self.dataset_populator.get_configuration()
@@ -231,17 +240,17 @@ steps:
         page_request = self._test_page_payload(slug="md-page-to-pdf", content_format="markdown")
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 200)
-        page_id = page_response.json()['id']
+        page_id = page_response.json()["id"]
         pdf_response = self._get(f"pages/{page_id}.pdf")
         api_asserts.assert_status_code_is(pdf_response, 200)
-        assert "application/pdf" in pdf_response.headers['content-type']
+        assert "application/pdf" in pdf_response.headers["content-type"]
         assert pdf_response.content[0:4] == b"%PDF"
 
     def test_400_on_download_pdf_when_unsupported_content_format(self):
         page_request = self._test_page_payload(slug="html-page-to-pdf", content_format="html")
         page_response = self._post("pages", page_request, json=True)
         self._assert_status_code_is(page_response, 200)
-        page_id = page_response.json()['id']
+        page_id = page_response.json()["id"]
         pdf_response = self._get(f"pages/{page_id}.pdf")
         self._assert_status_code_is(pdf_response, 400)
 
diff --git a/lib/galaxy_test/api/test_roles.py b/lib/galaxy_test/api/test_roles.py
index 604b4216589..7dbcea5dc70 100644
--- a/lib/galaxy_test/api/test_roles.py
+++ b/lib/galaxy_test/api/test_roles.py
@@ -4,20 +4,16 @@ from galaxy_test.base.api_asserts import (
     assert_has_keys,
     assert_status_code_is,
 )
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
 
 
 class RolesApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
     def test_list_and_show(self):
-
         def check_roles_response(response):
             assert_status_code_is(response, 200)
             as_list = response.json()
@@ -67,7 +63,7 @@ class RolesApiTestCase(ApiTestCase):
         }
         response = self._post("roles", payload, admin=True, json=True)
         assert_status_code_is(response, 400)
-        assert_error_code_is(response, error_codes.error_codes_by_name['USER_REQUEST_MISSING_PARAMETER'].code)
+        assert_error_code_is(response, error_codes.error_codes_by_name["USER_REQUEST_MISSING_PARAMETER"].code)
         assert "description" in response.json()["err_msg"]
 
         # Test missing name
@@ -78,7 +74,7 @@ class RolesApiTestCase(ApiTestCase):
         }
         response = self._post("roles", payload, admin=True, json=True)
         assert_status_code_is(response, 400)
-        assert_error_code_is(response, error_codes.error_codes_by_name['USER_REQUEST_MISSING_PARAMETER'].code)
+        assert_error_code_is(response, error_codes.error_codes_by_name["USER_REQUEST_MISSING_PARAMETER"].code)
         assert "name" in response.json()["err_msg"]
 
         # Test invalid type for name
@@ -89,7 +85,7 @@ class RolesApiTestCase(ApiTestCase):
         }
         response = self._post("roles", payload, admin=True, json=True)
         assert_status_code_is(response, 400)
-        assert_error_code_is(response, error_codes.error_codes_by_name['USER_REQUEST_INVALID_PARAMETER'].code)
+        assert_error_code_is(response, error_codes.error_codes_by_name["USER_REQUEST_INVALID_PARAMETER"].code)
         assert "name" in response.json()["err_msg"]
         assert "validation_errors" in response.json()
 
diff --git a/lib/galaxy_test/api/test_search.py b/lib/galaxy_test/api/test_search.py
index a44d866e8e4..a3369684a70 100644
--- a/lib/galaxy_test/api/test_search.py
+++ b/lib/galaxy_test/api/test_search.py
@@ -5,7 +5,6 @@ from ._framework import ApiTestCase
 
 
 class SearchApiTestCase(ApiTestCase):
-
     def test_search_workflows(self):
         workflow_populator = WorkflowPopulator(self.galaxy_interactor)
         workflow_id = workflow_populator.simple_workflow("test_for_search")
diff --git a/lib/galaxy_test/api/test_tool_data.py b/lib/galaxy_test/api/test_tool_data.py
index 0c9b4843c51..db18ccf4e47 100644
--- a/lib/galaxy_test/api/test_tool_data.py
+++ b/lib/galaxy_test/api/test_tool_data.py
@@ -11,7 +11,6 @@ from ._framework import ApiTestCase
 
 
 class ToolDataApiTestCase(ApiTestCase):
-
     def test_admin_only(self):
         index_response = self._get("tool_data", admin=False)
         self._assert_status_code_is(index_response, 403)
@@ -53,7 +52,7 @@ class ToolDataApiTestCase(ApiTestCase):
         self._assert_status_code_is(show_response, 200)
         print(show_response.content)
         data_table = show_response.json()
-        assert data_table["columns"] == ['value', 'dbkey', 'name', 'path']
+        assert data_table["columns"] == ["value", "dbkey", "name", "path"]
 
     def test_show_unknown_raises_404(self):
         show_response = self._get("tool_data/unknown", admin=True)
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index 7454db58f54..14c5f1e2899 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -6,11 +6,17 @@ import zipfile
 from io import BytesIO
 
 import pytest
-from requests import get, put
+from requests import (
+    get,
+    put,
+)
 
 from galaxy.util import galaxy_root_path
 from galaxy_test.base import rules_test_data
-from galaxy_test.base.api_asserts import assert_has_keys, assert_status_code_is
+from galaxy_test.base.api_asserts import (
+    assert_has_keys,
+    assert_status_code_is,
+)
 from galaxy_test.base.populators import (
     BaseDatasetCollectionPopulator,
     BaseDatasetPopulator,
@@ -24,27 +30,26 @@ from galaxy_test.base.populators import (
 )
 from ._framework import ApiTestCase
 
-
 MINIMAL_TOOL = {
-    'id': "minimal_tool",
-    'name': "Minimal Tool",
-    'class': "GalaxyTool",
-    'version': "1.0.0",
-    'command': "echo 'Hello World' > $output1",
-    'inputs': [],
-    'outputs': dict(
-        output1=dict(format='txt'),
-    )
+    "id": "minimal_tool",
+    "name": "Minimal Tool",
+    "class": "GalaxyTool",
+    "version": "1.0.0",
+    "command": "echo 'Hello World' > $output1",
+    "inputs": [],
+    "outputs": dict(
+        output1=dict(format="txt"),
+    ),
 }
 MINIMAL_TOOL_NO_ID = {
-    'name': "Minimal Tool",
-    'class': "GalaxyTool",
-    'version': "1.0.0",
-    'command': "echo 'Hello World 2' > $output1",
-    'inputs': [],
-    'outputs': dict(
-        output1=dict(format='txt'),
-    )
+    "name": "Minimal Tool",
+    "class": "GalaxyTool",
+    "version": "1.0.0",
+    "command": "echo 'Hello World 2' > $output1",
+    "inputs": [],
+    "outputs": dict(
+        output1=dict(format="txt"),
+    ),
 }
 
 
@@ -53,15 +58,17 @@ class TestsTools:
     dataset_collection_populator: BaseDatasetCollectionPopulator
 
     def _build_pair(self, history_id, contents):
-        create_response = self.dataset_collection_populator.create_pair_in_history(history_id, contents=contents, direct_upload=True)
+        create_response = self.dataset_collection_populator.create_pair_in_history(
+            history_id, contents=contents, direct_upload=True
+        )
         hdca_id = create_response.json()["outputs"][0]["id"]
         return hdca_id
 
     def _run_and_check_simple_collection_mapping(self, history_id, inputs):
         create = self._run_cat(history_id, inputs=inputs, assert_ok=True)
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         assert len(jobs) == 2
         assert len(outputs) == 2
         assert len(implicit_collections) == 1
@@ -73,9 +80,20 @@ class TestsTools:
         assert output2_content.strip() == "456"
 
     def _run_cat(self, history_id, inputs, assert_ok=False, **kwargs):
-        return self._run('cat', history_id, inputs, assert_ok=assert_ok, **kwargs)
+        return self._run("cat", history_id, inputs, assert_ok=assert_ok, **kwargs)
 
-    def _run(self, tool_id=None, history_id=None, inputs=None, tool_uuid=None, assert_ok=False, tool_version=None, use_cached_job=False, wait_for_job=False, input_format='legacy'):
+    def _run(
+        self,
+        tool_id=None,
+        history_id=None,
+        inputs=None,
+        tool_uuid=None,
+        assert_ok=False,
+        tool_version=None,
+        use_cached_job=False,
+        wait_for_job=False,
+        input_format="legacy",
+    ):
         if inputs is None:
             inputs = {}
         if tool_id is None:
@@ -87,25 +105,24 @@ class TestsTools:
             input_format=input_format,
         )
         if tool_uuid:
-            payload['tool_uuid'] = tool_uuid
+            payload["tool_uuid"] = tool_uuid
         if tool_version is not None:
             payload["tool_version"] = tool_version
         if use_cached_job:
-            payload['use_cached_job'] = True
+            payload["use_cached_job"] = True
         create_response = self.dataset_populator._post("tools", data=payload)
         if wait_for_job:
-            self.dataset_populator.wait_for_job(job_id=create_response.json()['jobs'][0]['id'])
+            self.dataset_populator.wait_for_job(job_id=create_response.json()["jobs"][0]["id"])
         if assert_ok:
             assert_status_code_is(create_response, 200)
             create = create_response.json()
-            assert_has_keys(create, 'outputs')
+            assert_has_keys(create, "outputs")
             return create
         else:
             return create_response
 
 
 class ToolsTestCase(ApiTestCase, TestsTools):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -151,7 +168,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         requirements = requirements_response.json()
         assert len(requirements) == 1, requirements
         requirement = requirements[0]
-        assert requirement['name'] == 'samtools', requirement
+        assert requirement["name"] == "samtools", requirement
 
     @skip_without_tool("cat1")
     def test_show_repeat(self):
@@ -173,7 +190,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
         cond_info = tool_info["inputs"][2]
         self._assert_has_keys(cond_info, "cases", "test_param")
-        self._assert_has_keys(cond_info["test_param"], 'name', 'type', 'label', 'help')
+        self._assert_has_keys(cond_info["test_param"], "name", "type", "label", "help")
 
         cases = cond_info["cases"]
         assert len(cases) == 2
@@ -186,7 +203,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         self._assert_has_keys(case2, "value", "inputs")
         case2_inputs = case2["inputs"]
         assert len(case2_inputs) == 1
-        self._assert_has_keys(case2_inputs[0], 'name', 'type', 'label', 'help', 'argument')
+        self._assert_has_keys(case2_inputs[0], "name", "type", "label", "help", "argument")
         assert case2_inputs[0]["name"] == "seed"
 
     @skip_without_tool("multi_data_param")
@@ -308,7 +325,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def _show_valid_tool(self, tool_id, tool_version=None):
         data = dict(io_details=True)
         if tool_version:
-            data['tool_version'] = tool_version
+            data["tool_version"] = tool_version
         tool_show_response = self._get(f"tools/{tool_id}", data=data)
         self._assert_status_code_is(tool_show_response, 200)
         tool_info = tool_show_response.json()
@@ -318,7 +335,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("model_attributes")
     @uses_test_history(require_new=False)
     def test_model_attributes_sanitization(self, history_id):
-        cool_name_with_quote = "cool name with a quo\"te"
+        cool_name_with_quote = 'cool name with a quo"te'
         cool_name_without_quote = "cool name with a quo__dq__te"
 
         current_user = self._get("users/current").json()
@@ -330,7 +347,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         self.assertEqual(len(response["addresses"]), 1)
         self.assertEqual(response["addresses"][0]["desc"], cool_name_with_quote)
 
-        hda1 = self.dataset_populator.new_dataset(history_id, content='1\t2\t3', name=cool_name_with_quote)
+        hda1 = self.dataset_populator.new_dataset(history_id, content="1\t2\t3", name=cool_name_with_quote)
         assert hda1["name"] == cool_name_with_quote
 
         rval = self._run(
@@ -340,7 +357,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             assert_ok=True,
             wait_for_job=True,
         )
-        sanitized_dataset_name = self.dataset_populator.get_history_dataset_content(history_id, dataset=rval["outputs"][0])
+        sanitized_dataset_name = self.dataset_populator.get_history_dataset_content(
+            history_id, dataset=rval["outputs"][0]
+        )
         assert sanitized_dataset_name.strip() == cool_name_without_quote
 
         sanitized_email = self.dataset_populator.get_history_dataset_content(history_id, dataset=rval["outputs"][1])
@@ -351,7 +370,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     @skip_without_tool("composite_output")
     def test_test_data_filepath_security(self):
-        test_data_response = self._get(f"tools/{'composite_output'}/test_data_path?filename=../CONTRIBUTORS.md", admin=True)
+        test_data_response = self._get(
+            f"tools/{'composite_output'}/test_data_path?filename=../CONTRIBUTORS.md", admin=True
+        )
         assert test_data_response.status_code == 404, test_data_response.text
 
     @skip_without_tool("composite_output")
@@ -364,8 +385,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         test_data_response = self._get(f"tools/{'dbkey_filter_multi_input'}/test_data")
         assert test_data_response.status_code == 200
         test_case = test_data_response.json()[0]
-        assert test_case['required_data_tables'][0] == 'test_fasta_indexes'
-        assert len(test_case['required_loc_files']) == 0
+        assert test_case["required_data_tables"][0] == "test_fasta_indexes"
+        assert len(test_case["required_loc_files"]) == 0
 
     @skip_without_tool("composite_output")
     def test_test_data_composite_output(self):
@@ -385,8 +406,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         test_data = test_data_response.json()
         assert len(test_data) == 2
         test_case = test_data[0]
-        assert len(test_case['required_data_tables']) == 0
-        assert len(test_case['required_loc_files']) == 0
+        assert len(test_case["required_data_tables"]) == 0
+        assert len(test_case["required_loc_files"]) == 0
         self._assert_has_keys(test_case, "inputs", "outputs", "output_collections", "required_files")
         assert len(test_case["inputs"]) == 3, test_case
 
@@ -423,7 +444,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("cat1")
     def test_test_data_download(self):
         test_data_response = self._get(f"tools/{'cat1'}/test_data_download?filename=1.bed")
-        assert test_data_response.status_code == 200, test_data_response.text.startswith('chr')
+        assert test_data_response.status_code == 200, test_data_response.text.startswith("chr")
 
     @skip_without_tool("composite_output")
     def test_test_data_downloads_security(self):
@@ -437,7 +458,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         with zipfile.ZipFile(BytesIO(test_data_response.content)) as contents:
             namelist = contents.namelist()
         assert len(namelist) == 6
-        expected_names = {'velveth_test1/Roadmaps', 'velveth_test1/output.html', 'velveth_test1/Sequences', 'velveth_test1/Log', 'velveth_test1/output/', 'velveth_test1/output/1'}
+        expected_names = {
+            "velveth_test1/Roadmaps",
+            "velveth_test1/output.html",
+            "velveth_test1/Sequences",
+            "velveth_test1/Log",
+            "velveth_test1/output/",
+            "velveth_test1/output/1",
+        }
         assert set(namelist) == expected_names
 
     @uses_test_history(require_new=False)
@@ -450,7 +478,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             "id": hda1["id"],
             "source_type": "fasta",
             "target_type": "tabular",
-            "history_id": history_id
+            "history_id": history_id,
         }
         create_response = self._post("tools/CONVERTER_fasta_to_tabular/convert", data=payload)
         self.dataset_populator.wait_for_job(create_response.json()["jobs"][0]["id"], assert_ok=True)
@@ -464,12 +492,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         fasta1_contents = open(self.get_filename("1.fasta")).read()
         hda1 = self.dataset_populator.new_dataset(history_id, content=fasta1_contents)
 
-        payload = {
-            "src": "hda",
-            "id": hda1["id"],
-            "source_type": "fasta",
-            "target_type": "tabular"
-        }
+        payload = {"src": "hda", "id": hda1["id"], "source_type": "fasta", "target_type": "tabular"}
         create_response = self._post("tools/CONVERTER_fasta_to_tabular/convert", data=payload)
         self.dataset_populator.wait_for_job(create_response.json()["jobs"][0]["id"], assert_ok=True)
         create_response.raise_for_status()
@@ -485,15 +508,15 @@ class ToolsTestCase(ApiTestCase, TestsTools):
                 "elements": [
                     {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "fasta"},
                     {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "fasta"},
-                ]
+                ],
             },
             {
                 "name": "test1",
                 "elements": [
                     {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "fasta"},
                     {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "fasta"},
-                ]
-            }
+                ],
+            },
         ]
         hdca1 = self.dataset_collection_populator.upload_collection(history_id, "list:paired", elements=data)
         self._assert_status_code_is(hdca1, 200)
@@ -503,7 +526,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             "id": hdca1.json()["outputs"][0]["id"],
             "source_type": "fasta",
             "target_type": "tabular",
-            "history_id": history_id
+            "history_id": history_id,
         }
         create_response = self._post("tools/CONVERTER_fasta_to_tabular/convert", payload)
 
@@ -528,8 +551,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             self.assertEqual(len(outputs), 2)
             output_forward = outputs[0]
             output_reverse = outputs[1]
-            output_forward_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output_forward)
-            output_reverse_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output_reverse)
+            output_forward_content = self.dataset_populator.get_history_dataset_content(
+                history_id, dataset=output_forward
+            )
+            output_reverse_content = self.dataset_populator.get_history_dataset_content(
+                history_id, dataset=output_reverse
+            )
             assert output_forward_content.strip() == "123"
             assert output_reverse_content.strip() == "456"
 
@@ -541,34 +568,52 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def test_unzip_nested(self):
         with self.dataset_populator.test_history() as history_id:
-            response = self.dataset_collection_populator.upload_collection(history_id, "list:paired", elements=[
-                {
-                    "name": "test0",
-                    "elements": [
-                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "txt", "tags": ["#foo"]},
-                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "txt", "tags": ["#bar"]},
-                    ]
-                }
-            ])
+            response = self.dataset_collection_populator.upload_collection(
+                history_id,
+                "list:paired",
+                elements=[
+                    {
+                        "name": "test0",
+                        "elements": [
+                            {
+                                "src": "pasted",
+                                "paste_content": "123\n",
+                                "name": "forward",
+                                "ext": "txt",
+                                "tags": ["#foo"],
+                            },
+                            {
+                                "src": "pasted",
+                                "paste_content": "456\n",
+                                "name": "reverse",
+                                "ext": "txt",
+                                "tags": ["#bar"],
+                            },
+                        ],
+                    }
+                ],
+            )
             self._assert_status_code_is(response, 200)
             hdca_id = response.json()["outputs"][0]["id"]
             inputs = {
                 "input": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'map_over_type': 'paired', 'id': hdca_id}],
+                    "batch": True,
+                    "values": [{"src": "hdca", "map_over_type": "paired", "id": hdca_id}],
                 }
             }
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             response = self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True)
             implicit_collections = response["implicit_collections"]
             self.assertEqual(len(implicit_collections), 2)
-            unzipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=implicit_collections[0]["hid"])
+            unzipped_hdca = self.dataset_populator.get_history_collection_details(
+                history_id, hid=implicit_collections[0]["hid"]
+            )
             assert unzipped_hdca["elements"][0]["element_type"] == "hda", unzipped_hdca
 
     def test_zip_inputs(self):
         with self.dataset_populator.test_history() as history_id:
-            hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='1\t2\t3'))
-            hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='4\t5\t6'))
+            hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="1\t2\t3"))
+            hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="4\t5\t6"))
             inputs = {
                 "input_forward": hda1,
                 "input_reverse": hda2,
@@ -578,13 +623,15 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             output_collections = response["output_collections"]
             self.assertEqual(len(output_collections), 1)
             self.dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
-            zipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_collections[0]["hid"])
+            zipped_hdca = self.dataset_populator.get_history_collection_details(
+                history_id, hid=output_collections[0]["hid"]
+            )
             assert zipped_hdca["collection_type"] == "paired"
 
     @skip_without_tool("__ZIP_COLLECTION__")
     @uses_test_history(require_new=False)
     def test_collection_operation_dataset_input_permissions(self, history_id):
-        hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='1\t2\t3'))
+        hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="1\t2\t3"))
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         self.dataset_populator.make_private(history_id, hda1["id"])
         inputs = {
@@ -614,30 +661,40 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def test_zip_list_inputs(self):
         with self.dataset_populator.test_history() as history_id:
-            hdca1_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]).json()["id"]
-            hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["1\n2\n3\n4", "5\n6\n7\n8"]).json()["id"]
+            hdca1_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]
+            ).json()["id"]
+            hdca2_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["1\n2\n3\n4", "5\n6\n7\n8"]
+            ).json()["id"]
             inputs = {
-                "input_forward": {'batch': True, 'values': [{"src": "hdca", "id": hdca1_id}]},
-                "input_reverse": {'batch': True, 'values': [{"src": "hdca", "id": hdca2_id}]},
+                "input_forward": {"batch": True, "values": [{"src": "hdca", "id": hdca1_id}]},
+                "input_reverse": {"batch": True, "values": [{"src": "hdca", "id": hdca2_id}]},
             }
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             response = self._run("__ZIP_COLLECTION__", history_id, inputs, assert_ok=True)
             implicit_collections = response["implicit_collections"]
             self.assertEqual(len(implicit_collections), 1)
             self.dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
-            zipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=implicit_collections[0]["hid"])
+            zipped_hdca = self.dataset_populator.get_history_collection_details(
+                history_id, hid=implicit_collections[0]["hid"]
+            )
             assert zipped_hdca["collection_type"] == "list:paired"
 
-    @skip_without_tool('__FILTER_FAILED_DATASETS__')
+    @skip_without_tool("__FILTER_FAILED_DATASETS__")
     def test_filter_failed_list(self):
         with self.dataset_populator.test_history() as history_id:
-            ok_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()["id"]
+            ok_hdca_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["0", "1", "0", "1"]
+            ).json()["id"]
             response = self.dataset_populator.run_exit_code_from_file(history_id, ok_hdca_id)
 
             mixed_implicit_collections = response["implicit_collections"]
             self.assertEqual(len(mixed_implicit_collections), 1)
             mixed_hdca_hid = mixed_implicit_collections[0]["hid"]
-            mixed_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=mixed_hdca_hid, wait=False)
+            mixed_hdca = self.dataset_populator.get_history_collection_details(
+                history_id, hid=mixed_hdca_hid, wait=False
+            )
 
             def get_state(dce):
                 return dce["object"]["state"]
@@ -645,46 +702,64 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             mixed_states = [get_state(_) for _ in mixed_hdca["elements"]]
             assert mixed_states == ["ok", "error", "ok", "error"], mixed_states
 
-            filtered_hdca = self._run_filter(history_id=history_id, failed_hdca_id=mixed_hdca['id'])
+            filtered_hdca = self._run_filter(history_id=history_id, failed_hdca_id=mixed_hdca["id"])
             filtered_states = [get_state(_) for _ in filtered_hdca["elements"]]
             assert filtered_states == ["ok", "ok"], filtered_states
 
-    @skip_without_tool('__FILTER_FAILED_DATASETS__')
+    @skip_without_tool("__FILTER_FAILED_DATASETS__")
     def test_filter_failed_list_paired(self):
         with self.dataset_populator.test_history() as history_id:
-            pair1 = self.dataset_collection_populator.create_pair_in_history(history_id, contents=["0", "0"]).json()["id"]
-            pair2 = self.dataset_collection_populator.create_pair_in_history(history_id, contents=["0", "1"]).json()["id"]
-            ok_hdca_id = self.dataset_collection_populator.create_list_from_pairs(history_id, [pair1, pair2]).json()['id']
+            pair1 = self.dataset_collection_populator.create_pair_in_history(history_id, contents=["0", "0"]).json()[
+                "id"
+            ]
+            pair2 = self.dataset_collection_populator.create_pair_in_history(history_id, contents=["0", "1"]).json()[
+                "id"
+            ]
+            ok_hdca_id = self.dataset_collection_populator.create_list_from_pairs(history_id, [pair1, pair2]).json()[
+                "id"
+            ]
             response = self.dataset_populator.run_exit_code_from_file(history_id, ok_hdca_id)
 
             mixed_implicit_collections = response["implicit_collections"]
             self.assertEqual(len(mixed_implicit_collections), 1)
             mixed_hdca_hid = mixed_implicit_collections[0]["hid"]
-            mixed_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=mixed_hdca_hid, wait=False)
+            mixed_hdca = self.dataset_populator.get_history_collection_details(
+                history_id, hid=mixed_hdca_hid, wait=False
+            )
 
             def get_state(dce):
                 return dce["object"]["state"]
 
-            mixed_states = [get_state(element) for _ in mixed_hdca["elements"] for element in _['object']['elements']]
+            mixed_states = [get_state(element) for _ in mixed_hdca["elements"] for element in _["object"]["elements"]]
             assert mixed_states == ["ok", "ok", "ok", "error"], mixed_states
 
-            filtered_hdca = self._run_filter(history_id=history_id, failed_hdca_id=mixed_hdca['id'])
-            filtered_states = [get_state(element) for _ in filtered_hdca["elements"] for element in _['object']['elements']]
+            filtered_hdca = self._run_filter(history_id=history_id, failed_hdca_id=mixed_hdca["id"])
+            filtered_states = [
+                get_state(element) for _ in filtered_hdca["elements"] for element in _["object"]["elements"]
+            ]
             assert filtered_states == ["ok", "ok"], filtered_states
 
             # Also try list:list:paired
-            llp = self.dataset_collection_populator.create_nested_collection(history_id=history_id,
-                                                                  collection_type="list:list:paired",
-                                                                  collection=[mixed_hdca['id']]).json()
+            llp = self.dataset_collection_populator.create_nested_collection(
+                history_id=history_id, collection_type="list:list:paired", collection=[mixed_hdca["id"]]
+            ).json()
 
-            filtered_nested_hdca = self._run_filter(history_id=history_id, failed_hdca_id=llp['id'], batch=True)
-            filtered_states = [get_state(element) for _ in filtered_nested_hdca["elements"] for parent_element in _['object']['elements'] for element in parent_element['object']['elements']]
+            filtered_nested_hdca = self._run_filter(history_id=history_id, failed_hdca_id=llp["id"], batch=True)
+            filtered_states = [
+                get_state(element)
+                for _ in filtered_nested_hdca["elements"]
+                for parent_element in _["object"]["elements"]
+                for element in parent_element["object"]["elements"]
+            ]
             assert filtered_states == ["ok", "ok"], filtered_states
 
     def _run_filter(self, history_id, failed_hdca_id, batch=False):
         if batch:
             inputs = {
-                "input": {"batch": batch, "values": [{"map_over_type": "list:paired", "src": "hdca", "id": failed_hdca_id}]},
+                "input": {
+                    "batch": batch,
+                    "values": [{"map_over_type": "list:paired", "src": "hdca", "id": failed_hdca_id}],
+                },
             }
         else:
             inputs = {
@@ -694,7 +769,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         self.dataset_populator.wait_for_history(history_id, assert_ok=False)
         filter_output_collections = response["output_collections"]
         if batch:
-            return response['implicit_collections'][0]
+            return response["implicit_collections"][0]
         self.assertEqual(len(filter_output_collections), 1)
         filtered_hid = filter_output_collections[0]["hid"]
         filtered_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=filtered_hid, wait=False)
@@ -704,10 +779,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         with self.dataset_populator.test_history() as history_id:
             inputs = stage_rules_example(self.galaxy_interactor, history_id, example)
             hdca = inputs["input"]
-            inputs = {
-                "input": {"src": "hdca", "id": hdca["id"]},
-                "rules": example["rules"]
-            }
+            inputs = {"input": {"src": "hdca", "id": hdca["id"]}, "rules": example["rules"]}
             self.dataset_populator.wait_for_history(history_id)
             response = self._run("__APPLY_RULES__", history_id, inputs, assert_ok=True)
             output_collections = response["output_collections"]
@@ -764,10 +836,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_library_data_param(self):
         with self.dataset_populator.test_history() as history_id:
             ld = LibraryPopulator(self.galaxy_interactor).new_library_dataset("lda_test_library")
-            inputs = {
-                "library_dataset": ld["ldda_id"],
-                "library_dataset_multiple": [ld["ldda_id"], ld["ldda_id"]]
-            }
+            inputs = {"library_dataset": ld["ldda_id"], "library_dataset_multiple": [ld["ldda_id"], ld["ldda_id"]]}
             response = self._run("library_data", history_id, inputs, assert_ok=True)
             output = response["outputs"]
             output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
@@ -778,11 +847,11 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("multi_data_param")
     def test_multidata_param(self):
         with self.dataset_populator.test_history() as history_id:
-            hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='1\t2\t3'))
-            hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='4\t5\t6'))
+            hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="1\t2\t3"))
+            hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="4\t5\t6"))
             inputs = {
-                "f1": {'batch': False, 'values': [hda1, hda2]},
-                "f2": {'batch': False, 'values': [hda2, hda1]},
+                "f1": {"batch": False, "values": [hda1, hda2]},
+                "f2": {"batch": False, "values": [hda2, hda1]},
             }
             response = self._run("multi_data_param", history_id, inputs, assert_ok=True)
             output1 = response["outputs"][0]
@@ -796,7 +865,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_run_cat1(self, history_id):
         # Run simple non-upload tool with an input data parameter.
-        new_dataset = self.dataset_populator.new_dataset(history_id, content='Cat1Test')
+        new_dataset = self.dataset_populator.new_dataset(history_id, content="Cat1Test")
         inputs = dict(
             input1=dataset_to_param(new_dataset),
         )
@@ -810,18 +879,20 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=True)
     def test_run_cat1_use_cached_job(self, history_id):
         # Run simple non-upload tool with an input data parameter.
-        new_dataset = self.dataset_populator.new_dataset(history_id, content='Cat1Test')
+        new_dataset = self.dataset_populator.new_dataset(history_id, content="Cat1Test")
         inputs = dict(
             input1=dataset_to_param(new_dataset),
         )
         outputs_one = self._run_cat1(history_id, inputs=inputs, assert_ok=True, wait_for_job=True)
         outputs_two = self._run_cat1(history_id, inputs=inputs, use_cached_job=False, assert_ok=True, wait_for_job=True)
-        outputs_three = self._run_cat1(history_id, inputs=inputs, use_cached_job=True, assert_ok=True, wait_for_job=True)
+        outputs_three = self._run_cat1(
+            history_id, inputs=inputs, use_cached_job=True, assert_ok=True, wait_for_job=True
+        )
         dataset_details = []
         for output in [outputs_one, outputs_two, outputs_three]:
-            output_id = output['outputs'][0]['id']
+            output_id = output["outputs"][0]["id"]
             dataset_details.append(self._get(f"datasets/{output_id}").json())
-        filenames = [dd['file_name'] for dd in dataset_details]
+        filenames = [dd["file_name"] for dd in dataset_details]
         assert len(filenames) == 3, filenames
         assert len(set(filenames)) <= 2, filenames
 
@@ -829,7 +900,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_run_cat1_listified_param(self, history_id):
         # Run simple non-upload tool with an input data parameter.
-        new_dataset = self.dataset_populator.new_dataset(history_id, content='Cat1Testlistified')
+        new_dataset = self.dataset_populator.new_dataset(history_id, content="Cat1Testlistified")
         inputs = dict(
             input1=[dataset_to_param(new_dataset)],
         )
@@ -844,7 +915,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_run_by_versions(self, history_id):
         for version in ["0.1", "0.2"]:
             # Run simple non-upload tool with an input data parameter.
-            outputs = self._run_and_get_outputs(tool_id="multiple_versions", history_id=history_id, tool_version=version)
+            outputs = self._run_and_get_outputs(
+                tool_id="multiple_versions", history_id=history_id, tool_version=version
+            )
             self.assertEqual(len(outputs), 1)
             output1 = outputs[0]
             output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
@@ -869,16 +942,16 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_show_with_wrong_tool_version_in_tool_id(self, history_id):
         tool_info = self._show_valid_tool("multiple_versions", tool_version="0.01")
         # Return last version
-        assert tool_info['version'] == "0.2"
+        assert tool_info["version"] == "0.2"
 
     @skip_without_tool("cat1")
     @uses_test_history(require_new=False)
     def test_run_cat1_single_meta_wrapper(self, history_id):
         # Wrap input in a no-op meta parameter wrapper like Sam is planning to
         # use for all UI API submissions.
-        new_dataset = self.dataset_populator.new_dataset(history_id, content='123')
+        new_dataset = self.dataset_populator.new_dataset(history_id, content="123")
         inputs = dict(
-            input1={'batch': False, 'values': [dataset_to_param(new_dataset)]},
+            input1={"batch": False, "values": [dataset_to_param(new_dataset)]},
         )
         outputs = self._cat1_outputs(history_id, inputs=inputs)
         self.assertEqual(len(outputs), 1)
@@ -889,7 +962,6 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("cat1")
     @uses_test_history(require_new=False)
     def test_guess_derived_permissions(self, history_id):
-
         def assert_inputs(inputs, can_be_used=True):
             # Until we make the dataset private, _different_user() can use it:
             with self._different_user_and_history() as other_history_id:
@@ -899,7 +971,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
                 else:
                     self._assert_dataset_permission_denied_response(response)
 
-        new_dataset = self.dataset_populator.new_dataset(history_id, content='Cat1Test')
+        new_dataset = self.dataset_populator.new_dataset(history_id, content="Cat1Test")
         inputs = dict(
             input1=dataset_to_param(new_dataset),
         )
@@ -930,7 +1002,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             element0 = elements[0]["object"]
             return element0["id"]
 
-        response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"], direct_upload=True)
+        response = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"], direct_upload=True
+        )
         self._assert_status_code_is(response, 200)
         hdca = response.json()["output_collections"][0]
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
@@ -963,7 +1037,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_validation(self, history_id):
         inputs = {
-            'select_param': "\" ; echo \"moo",
+            "select_param": '" ; echo "moo',
         }
         response = self._run("validation_default", history_id, inputs)
         self._assert_status_code_is(response, 400)
@@ -971,10 +1045,10 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("validation_empty_dataset")
     @uses_test_history(require_new=False)
     def test_validation_empty_dataset(self, history_id):
-        outputs = self._run_and_get_outputs('empty_output', history_id)
+        outputs = self._run_and_get_outputs("empty_output", history_id)
         empty_dataset = outputs[0]
         inputs = {
-            'input1': dataset_to_param(empty_dataset),
+            "input1": dataset_to_param(empty_dataset),
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         response = self._run("validation_empty_dataset", history_id, inputs)
@@ -984,8 +1058,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_validation_in_repeat(self, history_id):
         inputs = {
-            'r1_0|text': "123",
-            'r2_0|text': "",
+            "r1_0|text": "123",
+            "r2_0|text": "",
         }
         response = self._run("validation_repeat", history_id, inputs)
         self._assert_status_code_is(response, 400)
@@ -994,7 +1068,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_select_legal_values(self, history_id):
         inputs = {
-            'select_ex': 'not_option',
+            "select_ex": "not_option",
         }
         response = self._run("multi_select", history_id, inputs)
         self._assert_status_code_is(response, 400)
@@ -1002,10 +1076,10 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("column_param")
     @uses_test_history(require_new=False)
     def test_column_legal_values(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='#col1\tcol2')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="#col1\tcol2")
         inputs = {
-            'input1': {"src": "hda", "id": new_dataset1["id"]},
-            'col': "' ; echo 'moo",
+            "input1": {"src": "hda", "id": new_dataset1["id"]},
+            "col": "' ; echo 'moo",
         }
         response = self._run("column_param", history_id, inputs)
         # This needs to either fail at submit time or at job prepare time, but we have
@@ -1023,16 +1097,16 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             "f1": {"src": "hdca", "id": hdca_id},
         }
         output = self._run("collection_paired_test", history_id, inputs, assert_ok=True)
-        assert len(output['jobs']) == 1
-        assert len(output['implicit_collections']) == 0
-        assert len(output['outputs']) == 1
+        assert len(output["jobs"]) == 1
+        assert len(output["implicit_collections"]) == 0
+        assert len(output["outputs"]) == 1
         contents = self.dataset_populator.get_history_dataset_content(history_id, hid=4)
         assert contents.strip() == "123\n456", contents
 
     @skip_without_tool("collection_creates_pair")
     @uses_test_history(require_new=False)
     def test_paired_collection_output(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123\n456\n789\n0ab')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123\n456\n789\n0ab")
         inputs = {
             "input1": {"src": "hda", "id": new_dataset1["id"]},
         }
@@ -1048,7 +1122,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("collection_creates_list")
     @uses_test_history(require_new=False)
     def test_list_collection_output(self, history_id):
-        create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
+        create_response = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]
+        )
         hdca_id = create_response.json()["id"]
         create = self.dataset_populator.run_collection_creates_list(history_id, hdca_id)
         output_collection = self._assert_one_job_one_collection_run(create)
@@ -1061,8 +1137,10 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_list_collection_output_format_source(self, history_id):
         # test using format_source with a tool
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='#col1\tcol2')
-        create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\tb\nc\td", "e\tf\ng\th"])
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="#col1\tcol2")
+        create_response = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["a\tb\nc\td", "e\tf\ng\th"]
+        )
         hdca_id = create_response.json()["id"]
         inputs = {
             "header": {"src": "hda", "id": new_dataset1["id"]},
@@ -1080,9 +1158,11 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("collection_split_on_column")
     @uses_test_history(require_new=False)
     def test_dynamic_list_output(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='samp1\t1\nsamp1\t3\nsamp2\t2\nsamp2\t4\n')
+        new_dataset1 = self.dataset_populator.new_dataset(
+            history_id, content="samp1\t1\nsamp1\t3\nsamp2\t2\nsamp2\t4\n"
+        )
         inputs = {
-            'input1': dataset_to_param(new_dataset1),
+            "input1": dataset_to_param(new_dataset1),
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create = self._run("collection_split_on_column", history_id, inputs, assert_ok=True)
@@ -1094,7 +1174,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         self.assertEqual(output_collection["name"], "Table split on first column")
         self.dataset_populator.wait_for_job(create["jobs"][0]["id"], assert_ok=True)
 
-        get_collection_response = self._get(f"dataset_collections/{output_collection['id']}", data={"instance_type": "history"})
+        get_collection_response = self._get(
+            f"dataset_collections/{output_collection['id']}", data={"instance_type": "history"}
+        )
         self._assert_status_code_is(get_collection_response, 200)
 
         output_collection = get_collection_response.json()
@@ -1112,18 +1194,18 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("collection_creates_dynamic_nested")
     @uses_test_history(require_new=False)
     def test_dynamic_list_output_datasets_in_failed_state(self, history_id):
-        inputs = {
-            'fail_bool': True
-        }
+        inputs = {"fail_bool": True}
         create = self._run("collection_creates_dynamic_nested", history_id, inputs, assert_ok=False, wait_for_job=True)
         self._assert_status_code_is(create, 200)
-        collection = self._get(f"dataset_collections/{create.json()['output_collections'][0]['id']}", data={"instance_type": "history"}).json()
-        assert collection['element_count'] == 3
-        for nested_collection in collection['elements']:
-            nested_collection = nested_collection['object']
-            assert nested_collection['element_count'] == 2
-            for element in nested_collection['elements']:
-                assert element['object']['state'] == 'error'
+        collection = self._get(
+            f"dataset_collections/{create.json()['output_collections'][0]['id']}", data={"instance_type": "history"}
+        ).json()
+        assert collection["element_count"] == 3
+        for nested_collection in collection["elements"]:
+            nested_collection = nested_collection["object"]
+            assert nested_collection["element_count"] == 2
+            for element in nested_collection["elements"]:
+                assert element["object"]["state"] == "error"
 
     def test_nonadmin_users_cannot_create_tools(self):
         payload = dict(
@@ -1146,7 +1228,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def test_dynamic_tool_from_path(self):
         # Create tool.
-        dynamic_tool_path = os.path.join(galaxy_root_path, "lib", "galaxy_test", "base", "data", "minimal_tool_no_id.json")
+        dynamic_tool_path = os.path.join(
+            galaxy_root_path, "lib", "galaxy_test", "base", "data", "minimal_tool_no_id.json"
+        )
         tool_response = self.dataset_populator.create_tool_from_path(dynamic_tool_path)
         self._assert_has_keys(tool_response, "uuid")
 
@@ -1199,7 +1283,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         response = self._get("tools/cat1/raw_tool_source", admin=True)
         response.raise_for_status()
         assert "Concatenate datasets" in response.text
-        assert response.headers["language"] == 'xml'
+        assert response.headers["language"] == "xml"
 
     def test_show_tool_source_denied(self):
         with self._different_user(anon=True):
@@ -1224,12 +1308,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_run_cat1_with_two_inputs(self, history_id):
         # Run tool with an multiple data parameter and grouping (repeat)
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='Cat1Test')
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content='Cat2Test')
-        inputs = {
-            'input1': dataset_to_param(new_dataset1),
-            'queries_0|input2': dataset_to_param(new_dataset2)
-        }
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="Cat1Test")
+        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="Cat2Test")
+        inputs = {"input1": dataset_to_param(new_dataset1), "queries_0|input2": dataset_to_param(new_dataset2)}
         outputs = self._cat1_outputs(history_id, inputs=inputs)
         self.assertEqual(len(outputs), 1)
         output1 = outputs[0]
@@ -1244,12 +1325,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         # we observed very subtle problems with HDA state changes on other files being flushed at
         # the same time. This tests txt datasets finalized before and after the bam outputs as
         # well as other bam files all flush properly during job completion.
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123\n456\n789')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123\n456\n789")
         inputs = {
-            'input1': dataset_to_param(new_dataset1),
-            'reference': dataset_to_param(new_dataset1),
+            "input1": dataset_to_param(new_dataset1),
+            "reference": dataset_to_param(new_dataset1),
         }
-        outputs = self._run_and_get_outputs('mapper_two', history_id, inputs)
+        outputs = self._run_and_get_outputs("mapper_two", history_id, inputs)
         assert len(outputs) == 4
         for output in outputs:
             details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output)
@@ -1258,10 +1339,10 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("qc_stdout")
     @uses_test_history(require_new=False)
     def test_qc_messages(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123\n456\n789')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123\n456\n789")
         inputs = {
-            'input1': dataset_to_param(new_dataset1),
-            'quality': 3,
+            "input1": dataset_to_param(new_dataset1),
+            "quality": 3,
         }
         create = self._run("qc_stdout", history_id, inputs, wait_for_job=True, assert_ok=True)
         assert "jobs" in create, create
@@ -1277,13 +1358,13 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("cat1")
     @uses_test_history(require_new=False)
     def test_multirun_cat1(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123')
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123")
+        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456")
         datasets = [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)]
         inputs = {
             "input1": {
-                'batch': True,
-                'values': datasets,
+                "batch": True,
+                "values": datasets,
             },
         }
         self._check_cat1_multirun(history_id, inputs)
@@ -1301,15 +1382,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("random_lines1")
     @uses_test_history(require_new=False)
     def test_multirun_non_data_parameter(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123\n456\n789')
-        inputs = {
-            'input': dataset_to_param(new_dataset1),
-            'num_lines': {'batch': True, 'values': [1, 2, 3]}
-        }
-        outputs = self._run_and_get_outputs('random_lines1', history_id, inputs)
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123\n456\n789")
+        inputs = {"input": dataset_to_param(new_dataset1), "num_lines": {"batch": True, "values": [1, 2, 3]}}
+        outputs = self._run_and_get_outputs("random_lines1", history_id, inputs)
         # Assert we have three outputs with 1, 2, and 3 lines respectively.
         assert len(outputs) == 3
-        outputs_contents = [self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs]
+        outputs_contents = [
+            self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs
+        ]
         assert sorted(len(c.split("\n")) for c in outputs_contents) == [1, 2, 3]
 
     @skip_without_tool("cat1")
@@ -1317,7 +1397,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun()
         inputs = {
             "input1": common_dataset,
-            'queries_0|input2': {'batch': True, 'values': repeat_datasets},
+            "queries_0|input2": {"batch": True, "values": repeat_datasets},
         }
         self._check_repeat_multirun(history_id, inputs)
 
@@ -1325,8 +1405,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_multirun_in_repeat_mismatch(self):
         history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun()
         inputs = {
-            "input1": {'batch': False, 'values': [common_dataset]},
-            'queries_0|input2': {'batch': True, 'values': repeat_datasets},
+            "input1": {"batch": False, "values": [common_dataset]},
+            "queries_0|input2": {"batch": True, "values": repeat_datasets},
         }
         self._check_repeat_multirun(history_id, inputs)
 
@@ -1334,12 +1414,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_multirun_on_multiple_inputs(self):
         history_id, first_two, second_two = self._setup_two_multiruns()
         inputs = {
-            "input1": {'batch': True, 'values': first_two},
-            'queries_0|input2': {'batch': True, 'values': second_two},
+            "input1": {"batch": True, "values": first_two},
+            "queries_0|input2": {"batch": True, "values": second_two},
         }
         outputs = self._cat1_outputs(history_id, inputs=inputs)
         self.assertEqual(len(outputs), 2)
-        outputs_contents = [self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs]
+        outputs_contents = [
+            self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs
+        ]
         assert "123\n789" in outputs_contents
         assert "456\n0ab" in outputs_contents
 
@@ -1347,11 +1429,13 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_multirun_on_multiple_inputs_unlinked(self):
         history_id, first_two, second_two = self._setup_two_multiruns()
         inputs = {
-            "input1": {'batch': True, 'linked': False, 'values': first_two},
-            'queries_0|input2': {'batch': True, 'linked': False, 'values': second_two},
+            "input1": {"batch": True, "linked": False, "values": first_two},
+            "queries_0|input2": {"batch": True, "linked": False, "values": second_two},
         }
         outputs = self._cat1_outputs(history_id, inputs=inputs)
-        outputs_contents = [self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs]
+        outputs_contents = [
+            self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs
+        ]
         self.assertEqual(len(outputs), 4)
         assert "123\n789" in outputs_contents
         assert "456\n0ab" in outputs_contents
@@ -1367,57 +1451,55 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         def register_job_data(job_data):
             job_data_list.append(job_data)
 
-        tool_test_dicts = [{
-            "inputs": {
-                "input": ["simple_line.txt"],
-                "index": ["hg18_value"],
-            },
-            "outputs": {},
-            "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hg18'}]],
-        }]
+        tool_test_dicts = [
+            {
+                "inputs": {
+                    "input": ["simple_line.txt"],
+                    "index": ["hg18_value"],
+                },
+                "outputs": {},
+                "required_files": [["simple_line.txt", {"value": "simple_line.txt", "dbkey": "hg18"}]],
+            }
+        ]
         dynamic_param_error = None
         test_driver = self.driver_or_skip_test_if_remote()
         try:
-            test_driver.run_tool_test(
-                "dbkey_output_action",
-                tool_test_dicts=tool_test_dicts
-            )
+            test_driver.run_tool_test("dbkey_output_action", tool_test_dicts=tool_test_dicts)
         except Exception as e:
             dynamic_param_error = getattr(e, "dynamic_param_error", False)
         assert dynamic_param_error is None
 
-        tool_test_dicts = [{
-            "inputs": {
-                "input": ["simple_line.txt"],
-                "index": ["hg18_value"],
-            },
-            "outputs": {},
-            "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hgnot18'}]],
-        }]
+        tool_test_dicts = [
+            {
+                "inputs": {
+                    "input": ["simple_line.txt"],
+                    "index": ["hg18_value"],
+                },
+                "outputs": {},
+                "required_files": [["simple_line.txt", {"value": "simple_line.txt", "dbkey": "hgnot18"}]],
+            }
+        ]
         dynamic_param_error = None
         try:
-            test_driver.run_tool_test(
-                "dbkey_output_action",
-                tool_test_dicts=tool_test_dicts
-            )
+            test_driver.run_tool_test("dbkey_output_action", tool_test_dicts=tool_test_dicts)
         except Exception as e:
             dynamic_param_error = getattr(e, "dynamic_param_error", False)
         assert dynamic_param_error
 
-        tool_test_dicts = [{
-            "inputs": {
-                "input": ["simple_line.txt"],
-                "index": ["hgnot18"],
-            },
-            "outputs": {},
-            "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hg18'}]],
-        }]
+        tool_test_dicts = [
+            {
+                "inputs": {
+                    "input": ["simple_line.txt"],
+                    "index": ["hgnot18"],
+                },
+                "outputs": {},
+                "required_files": [["simple_line.txt", {"value": "simple_line.txt", "dbkey": "hg18"}]],
+            }
+        ]
         dynamic_param_error = None
         try:
             test_driver.run_tool_test(
-                "dbkey_output_action",
-                tool_test_dicts=tool_test_dicts,
-                register_job_data=register_job_data
+                "dbkey_output_action", tool_test_dicts=tool_test_dicts, register_job_data=register_job_data
             )
         except Exception as e:
             dynamic_param_error = getattr(e, "dynamic_param_error", False)
@@ -1443,9 +1525,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         assert job_data["status"] == "skip"
 
     def _assert_one_job_one_collection_run(self, create):
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
-        collections = create['output_collections']
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
+        collections = create["output_collections"]
 
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1480,13 +1562,13 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def _setup_repeat_multirun(self):
         history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123')
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456')
-        common_dataset = self.dataset_populator.new_dataset(history_id, content='Common')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123")
+        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456")
+        common_dataset = self.dataset_populator.new_dataset(history_id, content="Common")
         return (
             history_id,
             dataset_to_param(common_dataset),
-            [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)]
+            [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)],
         )
 
     def _check_repeat_multirun(self, history_id, inputs):
@@ -1501,14 +1583,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def _setup_two_multiruns(self):
         history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123')
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456')
-        new_dataset3 = self.dataset_populator.new_dataset(history_id, content='789')
-        new_dataset4 = self.dataset_populator.new_dataset(history_id, content='0ab')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123")
+        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456")
+        new_dataset3 = self.dataset_populator.new_dataset(history_id, content="789")
+        new_dataset4 = self.dataset_populator.new_dataset(history_id, content="0ab")
         return (
             history_id,
             [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)],
-            [dataset_to_param(new_dataset3), dataset_to_param(new_dataset4)]
+            [dataset_to_param(new_dataset3), dataset_to_param(new_dataset4)],
         )
 
     @skip_without_tool("cat")
@@ -1516,21 +1598,21 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_map_over_collection(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         self._run_and_check_simple_collection_mapping(history_id, inputs)
 
     @skip_without_tool("cat1")
     @uses_test_history(require_new=False)
     def test_map_over_empty_collection(self, history_id):
-        hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[]).json()['id']
+        hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[]).json()["id"]
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         create = self._run_cat1(history_id, inputs=inputs, assert_ok=True)
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 0)
         self.assertEqual(len(outputs), 0)
         self.assertEqual(len(implicit_collections), 1)
@@ -1545,12 +1627,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             hdca_id = self._build_pair(history_id, ["123", "456"])
             inputs = {
                 "input_cond|dispatch": use_action,
-                "input_cond|input": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+                "input_cond|input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
             }
-            create = self._run('output_action_change_format', history_id, inputs).json()
-            outputs = create['outputs']
-            jobs = create['jobs']
-            implicit_collections = create['implicit_collections']
+            create = self._run("output_action_change_format", history_id, inputs).json()
+            outputs = create["outputs"]
+            jobs = create["jobs"]
+            implicit_collections = create["implicit_collections"]
             self.assertEqual(len(jobs), 2)
             self.assertEqual(len(outputs), 2)
             self.assertEqual(len(implicit_collections), 1)
@@ -1565,13 +1647,11 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_map_over_with_nested_paired_output_format_actions(self, history_id):
         hdca_id = self.__build_nested_list(history_id)
-        inputs = {
-            "input": {'batch': True, 'values': [dict(map_over_type='paired', src="hdca", id=hdca_id)]}
-        }
-        create = self._run('output_action_change_format_paired', history_id, inputs).json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        inputs = {"input": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]}}
+        create = self._run("output_action_change_format_paired", history_id, inputs).json()
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(outputs), 2)
         self.assertEqual(len(implicit_collections), 1)
@@ -1583,13 +1663,13 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_map_over_with_output_filter_no_filtering(self, history_id):
         hdca_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
         inputs = {
-            "input_1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input_1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
             "produce_out_1": "true",
             "filter_text_1": "foo",
         }
-        create = self._run('output_filter_with_input', history_id, inputs).json()
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        create = self._run("output_filter_with_input", history_id, inputs).json()
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 3)
         self.assertEqual(len(implicit_collections), 3)
         self._check_implicit_collection_populated(create)
@@ -1597,13 +1677,15 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("output_filter_with_input_optional")
     @uses_test_history(require_new=False)
     def test_map_over_with_output_filter_on_optional_input(self, history_id):
-        hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["myinputs"]).json()["id"]
+        hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["myinputs"]).json()[
+            "id"
+        ]
         inputs = {
-            "input_1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input_1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
-        create = self._run('output_filter_with_input_optional', history_id, inputs).json()
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        create = self._run("output_filter_with_input_optional", history_id, inputs).json()
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.dataset_populator.wait_for_job(jobs[0]["id"], assert_ok=True)
         self.assertEqual(len(implicit_collections), 1)
@@ -1614,13 +1696,13 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_map_over_with_output_filter_one_filtered(self, history_id):
         hdca_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
         inputs = {
-            "input_1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input_1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
             "produce_out_1": "true",
             "filter_text_1": "bar",
         }
-        create = self._run('output_filter_with_input', history_id, inputs).json()
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        create = self._run("output_filter_with_input", history_id, inputs).json()
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 3)
         self.assertEqual(len(implicit_collections), 2)
         self._check_implicit_collection_populated(create)
@@ -1632,12 +1714,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         inputs = {
             "columnList": "c1,c2,c3,c4,c5",
             "delimiter": "T",
-            "input": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
-        create = self._run('Cut1', history_id, inputs).json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        create = self._run("Cut1", history_id, inputs).json()
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(outputs), 2)
         self.assertEqual(len(implicit_collections), 1)
@@ -1652,17 +1734,17 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_map_over_with_discovered_output_collection_elements(self, history_id):
         hdca_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
-        inputs = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}
-        }
-        create = self._run('collection_creates_dynamic_list_of_pairs', history_id, inputs).json()
-        implicit_collections = create['implicit_collections']
+        inputs = {"input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}}
+        create = self._run("collection_creates_dynamic_list_of_pairs", history_id, inputs).json()
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(implicit_collections), 1)
-        self.assertEqual(implicit_collections[0]['collection_type'], 'list:list:paired')
-        self.assertEqual(implicit_collections[0]['elements'][0]['object']['element_count'], None)
+        self.assertEqual(implicit_collections[0]["collection_type"], "list:list:paired")
+        self.assertEqual(implicit_collections[0]["elements"][0]["object"]["element_count"], None)
         self.dataset_populator.wait_for_job(create["jobs"][0]["id"], assert_ok=True)
         hdca = self._get(f"histories/{history_id}/contents/dataset_collections/{implicit_collections[0]['id']}").json()
-        self.assertEqual(hdca['elements'][0]['object']['elements'][0]['object']['elements'][0]['element_identifier'], 'forward')
+        self.assertEqual(
+            hdca["elements"][0]["object"]["elements"][0]["object"]["elements"][0]["element_identifier"], "forward"
+        )
 
     def _bed_list(self, history_id):
         bed1_contents = open(self.get_filename("1.bed")).read()
@@ -1676,14 +1758,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_identifier_in_map(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         create_response = self._run("identifier_single", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(outputs), 2)
         self.assertEqual(len(implicit_collections), 1)
@@ -1697,16 +1779,16 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("identifier_single")
     @uses_test_history(require_new=False)
     def test_identifier_outside_map(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123', name="Plain HDA")
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123", name="Plain HDA")
         inputs = {
-            "input1": {'src': 'hda', 'id': new_dataset1["id"]},
+            "input1": {"src": "hda", "id": new_dataset1["id"]},
         }
         create_response = self._run("identifier_single", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1719,21 +1801,21 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_list_selectable_in_multidata_input(self, history_id):
         self.dataset_collection_populator.create_list_in_history(history_id, contents=["123", "456"])
         build = self.dataset_populator.build_tool_state("identifier_multiple", history_id)
-        assert len(build['inputs'][0]['options']['hdca']) == 1
+        assert len(build["inputs"][0]["options"]["hdca"]) == 1
 
     @skip_without_tool("identifier_multiple")
     @uses_test_history(require_new=False)
     def test_identifier_in_multiple_reduce(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "input1": {'src': 'hdca', 'id': hdca_id},
+            "input1": {"src": "hdca", "id": hdca_id},
         }
         create_response = self._run("identifier_multiple", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1746,14 +1828,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_identifier_map_over_multiple_input_in_conditional(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "outer_cond|input1": {'src': 'hdca', 'id': hdca_id},
+            "outer_cond|input1": {"src": "hdca", "id": hdca_id},
         }
         create_response = self._run("identifier_in_conditional", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1767,18 +1849,16 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
             "outer_cond": {
-                'multi_input': True,
-                "input1": {
-                    'id': hdca_id, 'src': 'hdca'
-                },
+                "multi_input": True,
+                "input1": {"id": hdca_id, "src": "hdca"},
             },
         }
-        create_response = self._run("identifier_in_conditional", history_id, inputs, input_format='21.01')
+        create_response = self._run("identifier_in_conditional", history_id, inputs, input_format="21.01")
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1791,22 +1871,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_identifier_multiple_reduce_in_repeat_new_payload_form(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "the_repeat": [
-                {
-                    "the_data": {
-                        "input1": {
-                            'src': 'hdca', 'id': hdca_id
-                        }
-                    }
-                }
-            ],
+            "the_repeat": [{"the_data": {"input1": {"src": "hdca", "id": hdca_id}}}],
         }
-        create_response = self._run("identifier_multiple_in_repeat", history_id, inputs, input_format='21.01')
+        create_response = self._run("identifier_multiple_in_repeat", history_id, inputs, input_format="21.01")
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1820,15 +1892,15 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         # Run cat tool, so HDA names are different from element identifiers
         hdca_id = self._build_pair(history_id, ["123", "456"], run_cat=True)
         inputs = {
-            "outer_cond|input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "outer_cond|input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
             "outer_cond|multi_input": False,
         }
         create_response = self._run("identifier_in_conditional", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(outputs), 2)
         self.assertEqual(len(implicit_collections), 1)
@@ -1844,14 +1916,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_identifier_multiple_reduce_in_conditional(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "outer_cond|inner_cond|input1": {'src': 'hdca', 'id': hdca_id},
+            "outer_cond|inner_cond|input1": {"src": "hdca", "id": hdca_id},
         }
         create_response = self._run("identifier_multiple_in_conditional", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1864,14 +1936,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_identifier_multiple_reduce_in_repeat(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "the_repeat_0|the_data|input1": {'src': 'hdca', 'id': hdca_id},
+            "the_repeat_0|the_data|input1": {"src": "hdca", "id": hdca_id},
         }
         create_response = self._run("identifier_multiple_in_repeat", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1883,14 +1955,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_identifier_single_in_repeat(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "the_repeat_0|the_data|input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]}
-        }
+        inputs = {"the_repeat_0|the_data|input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}}
         create_response = self._run("identifier_single_in_repeat", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(implicit_collections), 1)
         output_collection = implicit_collections[0]
@@ -1903,16 +1973,16 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("identifier_multiple_in_conditional")
     @uses_test_history(require_new=False)
     def test_identifier_multiple_in_conditional(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123', name="Normal HDA1")
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123", name="Normal HDA1")
         inputs = {
-            "outer_cond|inner_cond|input1": {'src': 'hda', 'id': new_dataset1["id"]},
+            "outer_cond|inner_cond|input1": {"src": "hda", "id": new_dataset1["id"]},
         }
         create_response = self._run("identifier_multiple_in_conditional", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1923,20 +1993,15 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("identifier_multiple")
     @uses_test_history(require_new=False)
     def test_identifier_with_multiple_normal_datasets(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123', name="Normal HDA1")
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456', name="Normal HDA2")
-        inputs = {
-            "input1": [
-                {'src': 'hda', 'id': new_dataset1["id"]},
-                {'src': 'hda', 'id': new_dataset2["id"]}
-            ]
-        }
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123", name="Normal HDA1")
+        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456", name="Normal HDA2")
+        inputs = {"input1": [{"src": "hda", "id": new_dataset1["id"]}, {"src": "hda", "id": new_dataset2["id"]}]}
         create_response = self._run("identifier_multiple", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         self.assertEqual(len(implicit_collections), 0)
@@ -1960,20 +2025,20 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         dataset_collection = create_response.json()
 
         inputs = {
-            "input1": {'src': 'hdca', 'id': dataset_collection['id']},
+            "input1": {"src": "hdca", "id": dataset_collection["id"]},
         }
 
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create_response = self._run("identifier_collection", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
-        jobs = create['jobs']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 1)
         output1 = outputs[0]
         output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        self.assertEqual(output1_content.strip(), '\n'.join(d['name'] for d in element_identifiers))
+        self.assertEqual(output1_content.strip(), "\n".join(d["name"] for d in element_identifiers))
 
     @skip_without_tool("identifier_in_actions")
     @uses_test_history(require_new=False)
@@ -1991,14 +2056,14 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         dataset_collection = create_response.json()
 
         inputs = {
-            "input": {'batch': True, 'values': [{'src': 'hdca', 'id': dataset_collection['id']}]},
+            "input": {"batch": True, "values": [{"src": "hdca", "id": dataset_collection["id"]}]},
         }
 
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create_response = self._run("identifier_in_actions", history_id, inputs)
         self._assert_status_code_is(create_response, 200)
         create = create_response.json()
-        outputs = create['outputs']
+        outputs = create["outputs"]
         output1 = outputs[0]
 
         output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output1)
@@ -2009,7 +2074,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_map_over_nested_collections(self, history_id):
         hdca_id = self.__build_nested_list(history_id)
         inputs = {
-            "input1": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]},
+            "input1": {"batch": True, "values": [dict(src="hdca", id=hdca_id)]},
         }
         self._check_simple_cat1_over_nested_collections(history_id, inputs)
 
@@ -2018,12 +2083,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_paired_input_map_over_nested_collections(self, history_id):
         hdca_id = self.__build_nested_list(history_id)
         inputs = {
-            "input1": {'batch': True, 'values': [dict(map_over_type='paired', src="hdca", id=hdca_id)]},
+            "input1": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]},
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create = self._run("collection_paired_structured_like", history_id, inputs, assert_ok=True)
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(implicit_collections), 1)
         implicit_collection = implicit_collections[0]
@@ -2037,12 +2102,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         hdca_id = self.__build_nested_list(history_id)
         inputs = {
             "cond|cond_param": "paired",
-            "cond|input1": {'batch': True, 'values': [dict(map_over_type='paired', src="hdca", id=hdca_id)]},
+            "cond|input1": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]},
         }
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         create = self._run("collection_paired_conditional_structured_like", history_id, inputs, assert_ok=True)
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 2)
         self.assertEqual(len(implicit_collections), 1)
         implicit_collection = implicit_collections[0]
@@ -2052,9 +2117,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def _check_simple_cat1_over_nested_collections(self, history_id, inputs):
         create = self._run_cat1(history_id, inputs=inputs, assert_ok=True)
-        outputs = create['outputs']
-        jobs = create['jobs']
-        implicit_collections = create['implicit_collections']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
         self.assertEqual(len(jobs), 4)
         self.assertEqual(len(outputs), 4)
         self.assertEqual(len(implicit_collections), 1)
@@ -2078,8 +2143,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
         hdca2_id = self._build_pair(history_id, ["789\n", "0ab\n"])
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca1_id}]},
-            "queries_0|input2": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca2_id}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca1_id}]},
+            "queries_0|input2": {"batch": True, "values": [{"src": "hdca", "id": hdca2_id}]},
         }
         self._check_map_cat1_over_two_collections(history_id, inputs)
 
@@ -2087,7 +2152,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         response = self._run_cat1(history_id, inputs)
         self._assert_status_code_is(response, 200)
         response_object = response.json()
-        outputs = response_object['outputs']
+        outputs = response_object["outputs"]
         self.assertEqual(len(outputs), 2)
         output1 = outputs[0]
         output2 = outputs[1]
@@ -2097,8 +2162,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         self.assertEqual(output1_content.strip(), "123\n789")
         self.assertEqual(output2_content.strip(), "456\n0ab")
 
-        self.assertEqual(len(response_object['jobs']), 2)
-        self.assertEqual(len(response_object['implicit_collections']), 1)
+        self.assertEqual(len(response_object["jobs"]), 2)
+        self.assertEqual(len(response_object["implicit_collections"]), 1)
 
     @skip_without_tool("cat1")
     @uses_test_history(require_new=False)
@@ -2106,17 +2171,17 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
         hdca2_id = self._build_pair(history_id, ["789\n", "0ab\n"])
         inputs = {
-            "input1": {'batch': True, 'linked': False, 'values': [{'src': 'hdca', 'id': hdca1_id}]},
-            "queries_0|input2": {'batch': True, 'linked': False, 'values': [{'src': 'hdca', 'id': hdca2_id}]},
+            "input1": {"batch": True, "linked": False, "values": [{"src": "hdca", "id": hdca1_id}]},
+            "queries_0|input2": {"batch": True, "linked": False, "values": [{"src": "hdca", "id": hdca2_id}]},
         }
         response = self._run_cat1(history_id, inputs)
         self._assert_status_code_is(response, 200)
         response_object = response.json()
-        outputs = response_object['outputs']
+        outputs = response_object["outputs"]
         self.assertEqual(len(outputs), 4)
 
-        self.assertEqual(len(response_object['jobs']), 4)
-        implicit_collections = response_object['implicit_collections']
+        self.assertEqual(len(response_object["jobs"]), 4)
+        implicit_collections = response_object["implicit_collections"]
         self.assertEqual(len(implicit_collections), 1)
         implicit_collection = implicit_collections[0]
         self.assertEqual(implicit_collection["collection_type"], "paired:paired")
@@ -2156,51 +2221,60 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @uses_test_history(require_new=False)
     def test_map_over_collected_and_individual_datasets(self, history_id):
         hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='789')
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content='0ab')
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="789")
+        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="0ab")
 
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca1_id}]},
-            "queries_0|input2": {'batch': True, 'values': [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca1_id}]},
+            "queries_0|input2": {
+                "batch": True,
+                "values": [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)],
+            },
         }
         response = self._run_cat1(history_id, inputs)
         self._assert_status_code_is(response, 200)
         response_object = response.json()
-        outputs = response_object['outputs']
+        outputs = response_object["outputs"]
         self.assertEqual(len(outputs), 2)
 
-        self.assertEqual(len(response_object['jobs']), 2)
-        self.assertEqual(len(response_object['implicit_collections']), 1)
+        self.assertEqual(len(response_object["jobs"]), 2)
+        self.assertEqual(len(response_object["implicit_collections"]), 1)
 
     @skip_without_tool("identifier_source")
     def test_default_identifier_source_map_over(self):
         with self.dataset_populator.test_history() as history_id:
-            input_a_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("A", "A content")]).json()['id']
-            input_b_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("B", "B content")]).json()['id']
+            input_a_hdca_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("A", "A content")]
+            ).json()["id"]
+            input_b_hdca_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("B", "B content")]
+            ).json()["id"]
             inputs = {
-                "inputA": {'batch': True, 'values': [dict(src="hdca", id=input_a_hdca_id)]},
-                "inputB": {'batch': True, 'values': [dict(src="hdca", id=input_b_hdca_id)]},
+                "inputA": {"batch": True, "values": [dict(src="hdca", id=input_a_hdca_id)]},
+                "inputB": {"batch": True, "values": [dict(src="hdca", id=input_b_hdca_id)]},
             }
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             create = self._run("identifier_source", history_id, inputs, assert_ok=True)
-            for implicit_collection in create['implicit_collections']:
-                if implicit_collection['output_name'] == 'outputA':
-                    assert implicit_collection['elements'][0]['element_identifier'] == 'A'
+            for implicit_collection in create["implicit_collections"]:
+                if implicit_collection["output_name"] == "outputA":
+                    assert implicit_collection["elements"][0]["element_identifier"] == "A"
                 else:
-                    assert implicit_collection['elements'][0]['element_identifier'] == 'B'
+                    assert implicit_collection["elements"][0]["element_identifier"] == "B"
 
     @skip_without_tool("collection_creates_pair")
     def test_map_over_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
+            create_response = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]
+            )
             hdca_id = create_response.json()["id"]
             inputs = {
-                "input1": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]},
+                "input1": {"batch": True, "values": [dict(src="hdca", id=hdca_id)]},
             }
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             create = self._run("collection_creates_pair", history_id, inputs, assert_ok=True)
-            jobs = create['jobs']
-            implicit_collections = create['implicit_collections']
+            jobs = create["jobs"]
+            implicit_collections = create["implicit_collections"]
             self.assertEqual(len(jobs), 2)
             self.assertEqual(len(implicit_collections), 1)
             implicit_collection = implicit_collections[0]
@@ -2242,12 +2316,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
             inputs = {
                 "input1": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'id': hdca1_id}],
+                    "batch": True,
+                    "values": [{"src": "hdca", "id": hdca1_id}],
                 },
                 "queries_0|input2": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'id': hdca2_id}],
+                    "batch": True,
+                    "values": [{"src": "hdca", "id": hdca2_id}],
                 },
             }
             run_response = self._run_cat1(history_id, inputs)
@@ -2258,40 +2332,54 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("__FILTER_FROM_FILE__")
     def test_map_over_collection_structured_like(self):
         with self.dataset_populator.test_history() as history_id:
-            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("A", "A"), ("B", "B")]).json()['id']
+            hdca_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("A", "A"), ("B", "B")]
+            ).json()["id"]
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                "input": {'values': [dict(src="hdca", id=hdca_id)]},
-                "how|filter_source": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]}
+                "input": {"values": [dict(src="hdca", id=hdca_id)]},
+                "how|filter_source": {"batch": True, "values": [dict(src="hdca", id=hdca_id)]},
             }
-            implicit_collections = self._run("__FILTER_FROM_FILE__", history_id, inputs, assert_ok=True)['implicit_collections']
+            implicit_collections = self._run("__FILTER_FROM_FILE__", history_id, inputs, assert_ok=True)[
+                "implicit_collections"
+            ]
             discarded_collection, filtered_collection = implicit_collections
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             history_contents = self.dataset_populator._get_contents_request(history_id).json()
             # We should have a final collection count of 3 (2 nested collections, plus the input collection)
-            new_collections = len([c for c in history_contents if c['history_content_type'] == 'dataset_collection']) - 1
-            assert new_collections == 2, "Expected to generate 4 new, filtered collections, but got %d collections" % new_collections
-            assert filtered_collection['collection_type'] == discarded_collection['collection_type'] == 'list:list', filtered_collection
-            collection_details = self.dataset_populator.get_history_collection_details(history_id, hid=filtered_collection['hid'])
-            assert collection_details['element_count'] == 2
-            first_collection_level = collection_details['elements'][0]
-            assert first_collection_level['element_type'] == 'dataset_collection'
-            second_collection_level = first_collection_level['object']
-            assert second_collection_level['collection_type'] == 'list'
-            assert second_collection_level['elements'][0]['element_type'] == 'hda'
+            new_collections = (
+                len([c for c in history_contents if c["history_content_type"] == "dataset_collection"]) - 1
+            )
+            assert new_collections == 2, (
+                "Expected to generate 4 new, filtered collections, but got %d collections" % new_collections
+            )
+            assert (
+                filtered_collection["collection_type"] == discarded_collection["collection_type"] == "list:list"
+            ), filtered_collection
+            collection_details = self.dataset_populator.get_history_collection_details(
+                history_id, hid=filtered_collection["hid"]
+            )
+            assert collection_details["element_count"] == 2
+            first_collection_level = collection_details["elements"][0]
+            assert first_collection_level["element_type"] == "dataset_collection"
+            second_collection_level = first_collection_level["object"]
+            assert second_collection_level["collection_type"] == "list"
+            assert second_collection_level["elements"][0]["element_type"] == "hda"
 
     @skip_without_tool("collection_type_source")
     def test_map_over_collection_type_source(self):
         with self.dataset_populator.test_history() as history_id:
-            hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("A", "A"), ("B", "B")]).json()['id']
+            hdca_id = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("A", "A"), ("B", "B")]
+            ).json()["id"]
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                "input_collect": {'values': [dict(src="hdca", id=hdca_id)]},
-                "header": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]}
+                "input_collect": {"values": [dict(src="hdca", id=hdca_id)]},
+                "header": {"batch": True, "values": [dict(src="hdca", id=hdca_id)]},
             }
             self._run("collection_type_source", history_id, inputs, assert_ok=True, wait_for_job=True)
             collection_details = self.dataset_populator.get_history_collection_details(history_id, hid=4)
-            assert collection_details['elements'][0]['object']['elements'][0]['element_type'] == 'hda'
+            assert collection_details["elements"][0]["object"]["elements"][0]["element_type"] == "hda"
 
     @skip_without_tool("multi_data_param")
     def test_reduce_collections_legacy(self):
@@ -2310,8 +2398,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
             hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
             inputs = {
-                "f1": {'src': 'hdca', 'id': hdca1_id},
-                "f2": {'src': 'hdca', 'id': hdca2_id},
+                "f1": {"src": "hdca", "id": hdca1_id},
+                "f2": {"src": "hdca", "id": hdca2_id},
             }
             self._check_simple_reduce_job(history_id, inputs)
 
@@ -2321,18 +2409,20 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
             hdca2_id = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()["id"]
             inputs = {
-                "f1": {'src': 'hdca', 'id': hdca1_id},
+                "f1": {"src": "hdca", "id": hdca1_id},
                 "f2": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'map_over_type': 'list', 'id': hdca2_id}],
-                }
+                    "batch": True,
+                    "values": [{"src": "hdca", "map_over_type": "list", "id": hdca2_id}],
+                },
             }
             create = self._run("multi_data_param", history_id, inputs, assert_ok=True)
-            jobs = create['jobs']
-            implicit_collections = create['implicit_collections']
+            jobs = create["jobs"]
+            implicit_collections = create["implicit_collections"]
             self.assertEqual(len(jobs), 1)
             self.assertEqual(len(implicit_collections), 2)
-            output_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=implicit_collections[0]["hid"])
+            output_hdca = self.dataset_populator.get_history_collection_details(
+                history_id, hid=implicit_collections[0]["hid"]
+            )
             assert output_hdca["collection_type"] == "list"
 
     @skip_without_tool("column_multi_param")
@@ -2346,43 +2436,47 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             with pytest.raises(AssertionError):
                 self._run_implicit_collection_and_reduce(history_id=history_id, param="X")
         details = self.dataset_populator.get_history_dataset_details(history_id=history_id, hid=3, assert_ok=False)
-        assert details['state'] == "error"
-        assert "parameter 'col': an invalid option" in details['misc_info']
+        assert details["state"] == "error"
+        assert "parameter 'col': an invalid option" in details["misc_info"]
 
     def _run_implicit_collection_and_reduce(self, history_id, param):
         fasta_path = self.test_data_resolver.get_filename("1.fasta")
         with open(fasta_path) as fasta_fh:
             fasta_content = fasta_fh.read()
-            response = self.dataset_collection_populator.upload_collection(history_id, "list", elements=[
-                {
-                    "name": "test0",
-                    "src": "pasted",
-                    "paste_content": fasta_content,
-                    "ext": "fasta",
-                }
-            ])
+            response = self.dataset_collection_populator.upload_collection(
+                history_id,
+                "list",
+                elements=[
+                    {
+                        "name": "test0",
+                        "src": "pasted",
+                        "paste_content": fasta_content,
+                        "ext": "fasta",
+                    }
+                ],
+            )
             self._assert_status_code_is(response, 200)
             hdca_id = response.json()["outputs"][0]["id"]
             inputs = {
-                "input1": {'src': 'hdca', 'id': hdca_id},
+                "input1": {"src": "hdca", "id": hdca_id},
                 "col": param,
             }
             create = self._run("column_multi_param", history_id, inputs, assert_ok=True)
-            jobs = create['jobs']
+            jobs = create["jobs"]
             self.assertEqual(len(jobs), 1)
             content = self.dataset_populator.get_history_dataset_content(history_id, hid=3)
-            assert content.strip() == 'hg17', content
+            assert content.strip() == "hg17", content
 
     @skip_without_tool("multi_data_repeat")
     def test_reduce_collections_in_repeat(self):
         with self.dataset_populator.test_history() as history_id:
             hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
             inputs = {
-                "outer_repeat_0|f1": {'src': 'hdca', 'id': hdca1_id},
+                "outer_repeat_0|f1": {"src": "hdca", "id": hdca1_id},
             }
             create = self._run("multi_data_repeat", history_id, inputs, assert_ok=True)
-            outputs = create['outputs']
-            jobs = create['jobs']
+            outputs = create["outputs"]
+            jobs = create["jobs"]
             self.assertEqual(len(jobs), 1)
             self.assertEqual(len(outputs), 1)
             output1 = outputs[0]
@@ -2397,8 +2491,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
                 "outer_repeat_0|f1": f"__collection_reduce__|{hdca1_id}",
             }
             create = self._run("multi_data_repeat", history_id, inputs, assert_ok=True)
-            outputs = create['outputs']
-            jobs = create['jobs']
+            outputs = create["outputs"]
+            jobs = create["jobs"]
             self.assertEqual(len(jobs), 1)
             self.assertEqual(len(outputs), 1)
             output1 = outputs[0]
@@ -2411,12 +2505,12 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             hdca1_id = self._build_pair(history_id, ["123\n", "456\n"])
             hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
             inputs = {
-                "f1": [{'src': 'hdca', 'id': hdca1_id}, {'src': 'hdca', 'id': hdca2_id}],
-                "f2": [{'src': 'hdca', 'id': hdca1_id}],
+                "f1": [{"src": "hdca", "id": hdca1_id}, {"src": "hdca", "id": hdca2_id}],
+                "f2": [{"src": "hdca", "id": hdca1_id}],
             }
             create = self._run("multi_data_param", history_id, inputs, assert_ok=True)
-            outputs = create['outputs']
-            jobs = create['jobs']
+            outputs = create["outputs"]
+            jobs = create["jobs"]
             self.assertEqual(len(jobs), 1)
             self.assertEqual(len(outputs), 2)
             output1, output2 = outputs
@@ -2427,8 +2521,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def _check_simple_reduce_job(self, history_id, inputs):
         create = self._run("multi_data_param", history_id, inputs, assert_ok=True)
-        outputs = create['outputs']
-        jobs = create['jobs']
+        outputs = create["outputs"]
+        jobs = create["jobs"]
         self.assertEqual(len(jobs), 1)
         self.assertEqual(len(outputs), 2)
         output1, output2 = outputs
@@ -2443,8 +2537,8 @@ class ToolsTestCase(ApiTestCase, TestsTools):
             hdca_list_id = self.__build_nested_list(history_id)
             inputs = {
                 "f1": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'map_over_type': 'paired', 'id': hdca_list_id}],
+                    "batch": True,
+                    "values": [{"src": "hdca", "map_over_type": "paired", "id": hdca_list_id}],
                 }
             }
             self._check_simple_subcollection_mapping(history_id, inputs)
@@ -2466,16 +2560,18 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_combined_mapping_and_subcollection_mapping(self):
         with self.dataset_populator.test_history() as history_id:
             nested_list_id = self.__build_nested_list(history_id)
-            create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["xxx\n", "yyy\n"])
+            create_response = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["xxx\n", "yyy\n"]
+            )
             list_id = create_response.json()["id"]
             inputs = {
                 "f1": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'map_over_type': 'paired', 'id': nested_list_id}],
+                    "batch": True,
+                    "values": [{"src": "hdca", "map_over_type": "paired", "id": nested_list_id}],
                 },
                 "f2": {
-                    'batch': True,
-                    'values': [{'src': 'hdca', 'id': list_id}],
+                    "batch": True,
+                    "values": [{"src": "hdca", "id": list_id}],
                 },
             }
             self._check_combined_mapping_and_subcollection_mapping(history_id, inputs)
@@ -2507,10 +2603,10 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
     def _run_outputs(self, create_response):
         self._assert_status_code_is(create_response, 200)
-        return create_response.json()['outputs']
+        return create_response.json()["outputs"]
 
     def _run_cat1(self, history_id, inputs, assert_ok=False, **kwargs):
-        return self._run('cat1', history_id, inputs, assert_ok=assert_ok, **kwargs)
+        return self._run("cat1", history_id, inputs, assert_ok=assert_ok, **kwargs)
 
     def __tool_ids(self):
         index = self._get("tools")
@@ -2561,9 +2657,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("expression_forty_two")
     def test_galaxy_expression_tool_simplest(self):
         history_id = self.dataset_populator.new_history()
-        run_response = self._run(
-            "expression_forty_two", history_id
-        )
+        run_response = self._run("expression_forty_two", history_id)
         self._assert_status_code_is(run_response, 200)
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         output_content = self.dataset_populator.get_history_dataset_content(history_id)
@@ -2573,11 +2667,9 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     def test_galaxy_expression_tool_simple(self):
         history_id = self.dataset_populator.new_history()
         inputs = {
-            'input1': '7',
+            "input1": "7",
         }
-        run_response = self._run(
-            "expression_parse_int", history_id, inputs
-        )
+        run_response = self._run("expression_parse_int", history_id, inputs)
         self._assert_status_code_is(run_response, 200)
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         output_content = self.dataset_populator.get_history_dataset_content(history_id)
@@ -2586,83 +2678,93 @@ class ToolsTestCase(ApiTestCase, TestsTools):
     @skip_without_tool("expression_log_line_count")
     def test_galaxy_expression_metadata(self):
         history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n11\n12\n13\n14')
-        inputs = {
-            'input1': dataset_to_param(new_dataset1),
-        }
-        run_response = self._run(
-            "expression_log_line_count", history_id, inputs
+        new_dataset1 = self.dataset_populator.new_dataset(
+            history_id, content="1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n11\n12\n13\n14"
         )
+        inputs = {
+            "input1": dataset_to_param(new_dataset1),
+        }
+        run_response = self._run("expression_log_line_count", history_id, inputs)
         self._assert_status_code_is(run_response, 200)
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         output_content = self.dataset_populator.get_history_dataset_content(history_id)
         self.assertEqual(output_content, "3")
 
     def __build_group_list(self, history_id):
-        response = self.dataset_collection_populator.upload_collection(history_id, "list", elements=[
-            {
-                "name": "test0",
-                "src": "pasted",
-                "paste_content": "123\n",
-                "ext": "txt",
-                "tags": ["group:type:paired-end", "group:condition:treated"],
-            },
-            {
-                "name": "test1",
-                "src": "pasted",
-                "paste_content": "456\n",
-                "ext": "txt",
-                "tags": ["group:type:single", "group:condition:treated"],
-            },
-            {
-                "name": "test2",
-                "src": "pasted",
-                "paste_content": "789\n",
-                "ext": "txt",
-                "tags": ["group:type:paired-end", "group:condition:untreated"],
-            },
-            {
-                "name": "test3",
-                "src": "pasted",
-                "paste_content": "0ab\n",
-                "ext": "txt",
-                "tags": ["group:type:single", "group:condition:untreated"],
-            }
-        ])
+        response = self.dataset_collection_populator.upload_collection(
+            history_id,
+            "list",
+            elements=[
+                {
+                    "name": "test0",
+                    "src": "pasted",
+                    "paste_content": "123\n",
+                    "ext": "txt",
+                    "tags": ["group:type:paired-end", "group:condition:treated"],
+                },
+                {
+                    "name": "test1",
+                    "src": "pasted",
+                    "paste_content": "456\n",
+                    "ext": "txt",
+                    "tags": ["group:type:single", "group:condition:treated"],
+                },
+                {
+                    "name": "test2",
+                    "src": "pasted",
+                    "paste_content": "789\n",
+                    "ext": "txt",
+                    "tags": ["group:type:paired-end", "group:condition:untreated"],
+                },
+                {
+                    "name": "test3",
+                    "src": "pasted",
+                    "paste_content": "0ab\n",
+                    "ext": "txt",
+                    "tags": ["group:type:single", "group:condition:untreated"],
+                },
+            ],
+        )
         self._assert_status_code_is(response, 200)
         hdca_list_id = response.json()["outputs"][0]["id"]
         return hdca_list_id
 
     def __build_nested_list(self, history_id):
-        response = self.dataset_collection_populator.upload_collection(history_id, "list:paired", elements=[
-            {
-                "name": "test0",
-                "elements": [
-                    {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "txt"},
-                    {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "txt"},
-                ]
-            },
-            {
-                "name": "test1",
-                "elements": [
-                    {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "txt"},
-                    {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "txt"},
-                ]
-            }
-        ])
+        response = self.dataset_collection_populator.upload_collection(
+            history_id,
+            "list:paired",
+            elements=[
+                {
+                    "name": "test0",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "txt"},
+                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "txt"},
+                    ],
+                },
+                {
+                    "name": "test1",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "txt"},
+                        {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "txt"},
+                    ],
+                },
+            ],
+        )
         self._assert_status_code_is(response, 200)
         hdca_list_id = response.json()["outputs"][0]["id"]
         return hdca_list_id
 
     def _build_pair(self, history_id, contents, run_cat=False):
-        create_response = self.dataset_collection_populator.create_pair_in_history(history_id, contents=contents, direct_upload=True)
+        create_response = self.dataset_collection_populator.create_pair_in_history(
+            history_id, contents=contents, direct_upload=True
+        )
         hdca_id = create_response.json()["output_collections"][0]["id"]
         inputs = {
-            "input1": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]},
+            "input1": {"batch": True, "values": [dict(src="hdca", id=hdca_id)]},
         }
         if run_cat:
             outputs = self._run_cat(history_id, inputs=inputs, assert_ok=True)
-            hdca_id = outputs['implicit_collections'][0]['id']
+            hdca_id = outputs["implicit_collections"][0]["id"]
         return hdca_id
 
     def _assert_dataset_permission_denied_response(self, response):
@@ -2680,7 +2782,4 @@ class ToolsTestCase(ApiTestCase, TestsTools):
 
 
 def dataset_to_param(dataset):
-    return dict(
-        src='hda',
-        id=dataset['id']
-    )
+    return dict(src="hda", id=dataset["id"])
diff --git a/lib/galaxy_test/api/test_tools_upload.py b/lib/galaxy_test/api/test_tools_upload.py
index 3958322fa4d..28c5a921c77 100644
--- a/lib/galaxy_test/api/test_tools_upload.py
+++ b/lib/galaxy_test/api/test_tools_upload.py
@@ -25,25 +25,24 @@ from ._framework import ApiTestCase
 
 
 class ToolsUploadTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
     def test_upload1_paste(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id, 'Hello World')
+            payload = self.dataset_populator.upload_payload(history_id, "Hello World")
             create_response = self._post("tools", data=payload)
-            self._assert_has_keys(create_response.json(), 'outputs')
+            self._assert_has_keys(create_response.json(), "outputs")
 
     def test_upload1_paste_bad_datatype(self):
         # Check that you get a nice message if you upload an incorrect datatype
         with self.dataset_populator.test_history() as history_id:
             file_type = "johnsawesomebutfakedatatype"
-            payload = self.dataset_populator.upload_payload(history_id, 'Hello World', file_type=file_type)
+            payload = self.dataset_populator.upload_payload(history_id, "Hello World", file_type=file_type)
             create = self._post("tools", data=payload).json()
-            self._assert_has_keys(create, 'err_msg')
-            assert file_type in create['err_msg']
+            self._assert_has_keys(create, "err_msg")
+            assert file_type in create["err_msg"]
 
     # upload1 rewrites content with posix lines by default but this can be disabled by setting
     # to_posix_lines=None in the request. Newer fetch API does not do this by default prefering
@@ -100,7 +99,7 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_fetch_tab_to_space_off_by_default(self):
         table = ONE_TO_SIX_WITH_SPACES
-        result_content = self._upload_and_get_content(table, api='fetch')
+        result_content = self._upload_and_get_content(table, api="fetch")
         self.assertEqual(result_content, table)
 
     def test_upload_tab_to_space(self):
@@ -137,11 +136,9 @@ class ToolsUploadTestCase(ApiTestCase):
         # TODO: this should definitely be fixed to allow auto decompression via that API.
         fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz")
         with open(fastqgz_path, "rb") as fh:
-            details = self._upload_and_get_details(fh,
-                                                   api="fetch",
-                                                   history_id=history_id,
-                                                   assert_ok=False,
-                                                   auto_decompress=True)
+            details = self._upload_and_get_details(
+                fh, api="fetch", history_id=history_id, assert_ok=False, auto_decompress=True
+            )
         assert details["state"] == "ok"
         assert details["file_ext"] == "fastqsanger.gz", details
 
@@ -182,11 +179,9 @@ class ToolsUploadTestCase(ApiTestCase):
         # TODO: this should definitely be fixed to allow auto decompression via that API.
         bedgz_path = TestDataResolver().get_filename("4.bed.gz")
         with open(bedgz_path, "rb") as fh:
-            details = self._upload_and_get_details(fh,
-                                                   api="fetch",
-                                                   history_id=history_id,
-                                                   auto_decompress=True,
-                                                   assert_ok=False)
+            details = self._upload_and_get_details(
+                fh, api="fetch", history_id=history_id, auto_decompress=True, assert_ok=False
+            )
         assert details["state"] == "ok"
         assert details["file_ext"] == "bed"
 
@@ -244,37 +239,26 @@ class ToolsUploadTestCase(ApiTestCase):
         }
         inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False)
         dataset = datasets[0][0]
-        content = self.dataset_populator.get_history_dataset_content(
-            history_id=history_id,
-            dataset=dataset
-        )
+        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
         # By default this appends the newline.
         self.assertEqual(content, "This is a line of text.\n")
 
     @uses_test_history(require_new=False)
     def test_stage_object(self, history_id):
-        job = {
-            "input1": "randomstr"
-        }
-        inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)
-        dataset = datasets[0][0]
-        content = self.dataset_populator.get_history_dataset_content(
-            history_id=history_id,
-            dataset=dataset
+        job = {"input1": "randomstr"}
+        inputs, datasets = stage_inputs(
+            self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False
         )
+        dataset = datasets[0][0]
+        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
         self.assertEqual(content.strip(), '"randomstr"')
 
     @uses_test_history(require_new=False)
     def test_stage_object_fetch(self, history_id):
-        job = {
-            "input1": "randomstr"
-        }
+        job = {"input1": "randomstr"}
         inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False)
         dataset = datasets[0][0]
-        content = self.dataset_populator.get_history_dataset_content(
-            history_id=history_id,
-            dataset=dataset
-        )
+        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
         self.assertEqual(content, '"randomstr"')
 
     @uses_test_history(require_new=False)
@@ -287,37 +271,32 @@ class ToolsUploadTestCase(ApiTestCase):
                 "dbkey": "hg19",
             }
         }
-        inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, to_posix_lines=False)
-        dataset = datasets[0][0]
-        content = self.dataset_populator.get_history_dataset_content(
-            history_id=history_id,
-            dataset=dataset
+        inputs, datasets = stage_inputs(
+            self.galaxy_interactor, history_id, job, use_path_paste=False, to_posix_lines=False
         )
+        dataset = datasets[0][0]
+        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
         # By default this appends the newline, but we disabled with 'to_posix_lines=False' above.
         self.assertEqual(content, "This is a line of text.")
-        details = self.dataset_populator.get_history_dataset_details(
-            history_id=history_id,
-            dataset=dataset
-        )
+        details = self.dataset_populator.get_history_dataset_details(history_id=history_id, dataset=dataset)
         assert details["genome_build"] == "hg19"
 
     @uses_test_history(require_new=False)
     @skip_if_github_down
     def test_upload_multiple_mixed_success(self, history_id):
         destination = {"type": "hdas"}
-        targets = [{
-            "destination": destination,
-            "items": [
-                {
-                    "src": "url",
-                    "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed"
-                },
-                {
-                    "src": "url",
-                    "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed"
-                }
-            ]
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items": [
+                    {"src": "url", "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed"},
+                    {
+                        "src": "url",
+                        "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed",
+                    },
+                ],
+            }
+        ]
         payload = {
             "history_id": history_id,
             "targets": json.dumps(targets),
@@ -339,26 +318,26 @@ class ToolsUploadTestCase(ApiTestCase):
         item = {
             "src": "url",
             "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bam",
-            "ext": "bam"
+            "ext": "bam",
         }
-        output = self.dataset_populator.fetch_hda(
-            history_id, item
-        )
+        output = self.dataset_populator.fetch_hda(history_id, item)
         self.dataset_populator.get_history_dataset_details(history_id, dataset=output, assert_ok=True)
 
     @uses_test_history(require_new=False)
     @skip_if_github_down
     def test_fetch_html_from_url(self, history_id):
         destination = {"type": "hdas"}
-        targets = [{
-            "destination": destination,
-            "items": [
-                {
-                    "src": "url",
-                    "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/html_file.txt",
-                },
-            ]
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items": [
+                    {
+                        "src": "url",
+                        "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/html_file.txt",
+                    },
+                ],
+            }
+        ]
         payload = {
             "history_id": history_id,
             "targets": json.dumps(targets),
@@ -366,22 +345,25 @@ class ToolsUploadTestCase(ApiTestCase):
         fetch_response = self.dataset_populator.fetch(payload)
         self._assert_status_code_is(fetch_response, 200)
         response = fetch_response.json()
-        output = response['outputs'][0]
-        job = response['jobs'][0]
-        self.dataset_populator.wait_for_job(job['id'])
+        output = response["outputs"][0]
+        job = response["jobs"][0]
+        self.dataset_populator.wait_for_job(job["id"])
         dataset = self.dataset_populator.get_history_dataset_details(history_id, dataset=output, assert_ok=False)
-        assert dataset['state'] == 'error'
-        assert dataset['name'] == 'html_file.txt'
+        assert dataset["state"] == "error"
+        assert dataset["name"] == "html_file.txt"
 
     @skip_without_datatype("velvet")
     def test_composite_datatype(self):
         with self.dataset_populator.test_history() as history_id:
-            dataset = self._velvet_upload(history_id, extra_inputs={
-                "files_1|url_paste": "roadmaps content",
-                "files_1|type": "upload_dataset",
-                "files_2|url_paste": "log content",
-                "files_2|type": "upload_dataset",
-            })
+            dataset = self._velvet_upload(
+                history_id,
+                extra_inputs={
+                    "files_1|url_paste": "roadmaps content",
+                    "files_1|type": "upload_dataset",
+                    "files_2|url_paste": "log content",
+                    "files_2|type": "upload_dataset",
+                },
+            )
 
             roadmaps_content = self._get_roadmaps_content(history_id, dataset)
             assert roadmaps_content.strip() == "roadmaps content", roadmaps_content
@@ -415,7 +397,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "test-data/simple_line.txt",
                     "test-data/simple_line_alternative.txt",
                     "test-data/simple_line_x2.txt",
-                ]
+                ],
             }
         }
         inputs, datsets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False)
@@ -431,23 +413,28 @@ class ToolsUploadTestCase(ApiTestCase):
                     "test-data/simple_line.txt",
                     "test-data/simple_line_alternative.txt",
                     "test-data/simple_line_x2.txt",
-                ]
+                ],
             }
         }
-        inputs, datsets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)
+        inputs, datsets = stage_inputs(
+            self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False
+        )
 
     @skip_without_datatype("velvet")
     @uses_test_history(require_new=False)
     def test_composite_datatype_space_to_tab(self, history_id):
         # Like previous test but set one upload with space_to_tab to True to
         # verify that works.
-        dataset = self._velvet_upload(history_id, extra_inputs={
-            "files_1|url_paste": "roadmaps content",
-            "files_1|type": "upload_dataset",
-            "files_1|space_to_tab": "Yes",
-            "files_2|url_paste": "log content",
-            "files_2|type": "upload_dataset",
-        })
+        dataset = self._velvet_upload(
+            history_id,
+            extra_inputs={
+                "files_1|url_paste": "roadmaps content",
+                "files_1|type": "upload_dataset",
+                "files_1|space_to_tab": "Yes",
+                "files_2|url_paste": "log content",
+                "files_2|type": "upload_dataset",
+            },
+        )
 
         roadmaps_content = self._get_roadmaps_content(history_id, dataset)
         assert roadmaps_content.strip() == "roadmaps\tcontent", roadmaps_content
@@ -457,13 +444,16 @@ class ToolsUploadTestCase(ApiTestCase):
         # Like previous test but set one upload with space_to_tab to True to
         # verify that works.
         with self.dataset_populator.test_history() as history_id:
-            dataset = self._velvet_upload(history_id, extra_inputs={
-                "files_1|url_paste": "roadmaps\rcontent",
-                "files_1|type": "upload_dataset",
-                "files_1|space_to_tab": "Yes",
-                "files_2|url_paste": "log\rcontent",
-                "files_2|type": "upload_dataset",
-            })
+            dataset = self._velvet_upload(
+                history_id,
+                extra_inputs={
+                    "files_1|url_paste": "roadmaps\rcontent",
+                    "files_1|type": "upload_dataset",
+                    "files_1|space_to_tab": "Yes",
+                    "files_2|url_paste": "log\rcontent",
+                    "files_2|type": "upload_dataset",
+                },
+            )
 
             roadmaps_content = self._get_roadmaps_content(history_id, dataset)
             assert roadmaps_content.strip() == "roadmaps\ncontent", roadmaps_content
@@ -480,13 +470,15 @@ class ToolsUploadTestCase(ApiTestCase):
     def test_upload_composite_as_tar(self, history_id):
         tar_path = self.test_data_resolver.get_filename("testdir.tar")
         with open(tar_path, "rb") as tar_f:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 extra_inputs={
                     "files_1|file_data": tar_f,
                     "files_1|NAME": "composite",
                     "file_count": "2",
                     "force_composite": "True",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -498,21 +490,25 @@ class ToolsUploadTestCase(ApiTestCase):
         tar_path = self.test_data_resolver.get_filename("testdir.tar")
         with open(tar_path, "rb") as tar_f:
             destination = {"type": "hdas"}
-            targets = [{
-                "destination": destination,
-                "items": [{
-                    "src": "pasted",
-                    "paste_content": "Test123\n",
-                    "ext": "txt",
-                    "extra_files": {
-                        "items_from": "archive",
-                        "src": "files",
-                        # Prevent Galaxy from checking for a single file in
-                        # a directory and re-interpreting the archive
-                        "fuzzy_root": False,
-                    }
-                }],
-            }]
+            targets = [
+                {
+                    "destination": destination,
+                    "items": [
+                        {
+                            "src": "pasted",
+                            "paste_content": "Test123\n",
+                            "ext": "txt",
+                            "extra_files": {
+                                "items_from": "archive",
+                                "src": "files",
+                                # Prevent Galaxy from checking for a single file in
+                                # a directory and re-interpreting the archive
+                                "fuzzy_root": False,
+                            },
+                        }
+                    ],
+                }
+            ]
             payload = {
                 "history_id": history_id,
                 "targets": json.dumps(targets),
@@ -550,13 +546,15 @@ class ToolsUploadTestCase(ApiTestCase):
     def test_upload_composite_from_bad_tar(self, history_id):
         tar_path = self.test_data_resolver.get_filename("unsafe.tar")
         with open(tar_path, "rb") as tar_f:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 extra_inputs={
                     "files_1|file_data": tar_f,
                     "files_1|NAME": "composite",
                     "file_count": "2",
                     "force_composite": "True",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response, assert_ok=False)
@@ -576,10 +574,7 @@ class ToolsUploadTestCase(ApiTestCase):
     def test_fetch_bam_file(self, history_id):
         bam_path = TestDataResolver().get_filename("1.bam")
         with open(bam_path, "rb") as fh:
-            details = self._upload_and_get_details(fh,
-                                                   api="fetch",
-                                                   history_id=history_id,
-                                                   assert_ok=False)
+            details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=False)
         assert details["state"] == "ok"
         assert details["file_ext"] == "bam", details
 
@@ -592,7 +587,9 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_fetch_metadata(self):
         table = ONE_TO_SIX_WITH_SPACES
-        details = self._upload_and_get_details(table, api='fetch', dbkey="hg19", info="cool upload", tags=["name:data", "group:type:paired-end"])
+        details = self._upload_and_get_details(
+            table, api="fetch", dbkey="hg19", info="cool upload", tags=["name:data", "group:type:paired-end"]
+        )
         assert details.get("genome_build") == "hg19"
         assert details.get("misc_info") == "cool upload", details
         tags = details.get("tags")
@@ -602,7 +599,9 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_multiple_files_1(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 dbkey="hg19",
                 extra_inputs={
                     "files_1|url_paste": "SecondOutputContent",
@@ -610,7 +609,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "files_1|file_type": "tabular",
                     "files_1|dbkey": "hg18",
                     "file_count": "2",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -629,7 +628,9 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_multiple_files_2(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 file_type="tabular",
                 dbkey="hg19",
                 extra_inputs={
@@ -638,7 +639,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "files_1|file_type": "txt",
                     "files_1|dbkey": "hg18",
                     "file_count": "2",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -657,7 +658,9 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_multiple_files_3(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 file_type="tabular",
                 dbkey="hg19",
                 extra_inputs={
@@ -668,7 +671,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "files_1|file_type": "txt",
                     "files_1|dbkey": "hg18",
                     "file_count": "2",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -687,7 +690,9 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_multiple_files_no_dbkey(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 file_type="tabular",
                 dbkey=None,
                 extra_inputs={
@@ -696,7 +701,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "files_1|NAME": "SecondOutputName",
                     "files_1|file_type": "txt",
                     "file_count": "2",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -715,7 +720,8 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_multiple_files_space_to_tab(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id,
+            payload = self.dataset_populator.upload_payload(
+                history_id,
                 content=ONE_TO_SIX_WITH_SPACES,
                 file_type="tabular",
                 dbkey="hg19",
@@ -730,7 +736,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "files_2|file_type": "txt",
                     "files_2|space_to_tab": "Yes",
                     "file_count": "3",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -748,7 +754,8 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_multiple_files_posix_lines(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id,
+            payload = self.dataset_populator.upload_payload(
+                history_id,
                 content=ONE_TO_SIX_ON_WINDOWS,
                 file_type="tabular",
                 dbkey="hg19",
@@ -763,7 +770,7 @@ class ToolsUploadTestCase(ApiTestCase):
                     "files_2|NAME": "ThirdOutputName",
                     "files_2|file_type": "txt",
                     "file_count": "3",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -781,13 +788,15 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_force_composite(self):
         with self.dataset_populator.test_history() as history_id:
-            payload = self.dataset_populator.upload_payload(history_id, "Test123",
+            payload = self.dataset_populator.upload_payload(
+                history_id,
+                "Test123",
                 extra_inputs={
                     "files_1|url_paste": "CompositeContent",
                     "files_1|NAME": "composite",
                     "file_count": "2",
                     "force_composite": "True",
-                }
+                },
             )
             run_response = self.dataset_populator.tools_post(payload)
             self.dataset_populator.wait_for_tool_run(history_id, run_response)
@@ -802,22 +811,26 @@ class ToolsUploadTestCase(ApiTestCase):
 
     def test_upload_from_invalid_url(self):
         with pytest.raises(AssertionError):
-            self._upload('https://foo.invalid', assert_ok=False)
+            self._upload("https://foo.invalid", assert_ok=False)
 
     @skip_if_site_down("https://usegalaxy.org")
     def test_upload_from_404_url(self):
-        history_id, new_dataset = self._upload('https://usegalaxy.org/bla123', assert_ok=False)
-        dataset_details = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=False)
-        assert dataset_details['state'] == 'error', f"expected dataset state to be 'error', but got '{dataset_details['state']}'"
+        history_id, new_dataset = self._upload("https://usegalaxy.org/bla123", assert_ok=False)
+        dataset_details = self.dataset_populator.get_history_dataset_details(
+            history_id, dataset_id=new_dataset["id"], assert_ok=False
+        )
+        assert (
+            dataset_details["state"] == "error"
+        ), f"expected dataset state to be 'error', but got '{dataset_details['state']}'"
 
     @skip_if_site_down("https://usegalaxy.org")
     def test_upload_from_valid_url(self):
-        history_id, new_dataset = self._upload('https://usegalaxy.org/api/version')
+        history_id, new_dataset = self._upload("https://usegalaxy.org/api/version")
         self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=True)
 
     @skip_if_site_down("https://usegalaxy.org")
     def test_upload_from_valid_url_spaces(self):
-        history_id, new_dataset = self._upload('  https://usegalaxy.org/api/version  ')
+        history_id, new_dataset = self._upload("  https://usegalaxy.org/api/version  ")
         self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=True)
 
     def test_upload_and_validate_invalid(self):
@@ -825,22 +838,22 @@ class ToolsUploadTestCase(ApiTestCase):
         with open(path, "rb") as fh:
             metadata = self._upload_and_get_details(fh, file_type="fastqcssanger")
         assert "validated_state" in metadata
-        assert metadata['validated_state'] == 'unknown'
+        assert metadata["validated_state"] == "unknown"
         history_id = metadata["history_id"]
         dataset_id = metadata["id"]
         terminal_validated_state = self.dataset_populator.validate_dataset_and_wait(history_id, dataset_id)
-        assert terminal_validated_state == 'invalid', terminal_validated_state
+        assert terminal_validated_state == "invalid", terminal_validated_state
 
     def test_upload_and_validate_valid(self):
         path = TestDataResolver().get_filename("1.fastqsanger")
         with open(path, "rb") as fh:
             metadata = self._upload_and_get_details(fh, file_type="fastqsanger")
         assert "validated_state" in metadata
-        assert metadata['validated_state'] == 'unknown'
+        assert metadata["validated_state"] == "unknown"
         history_id = metadata["history_id"]
         dataset_id = metadata["id"]
         terminal_validated_state = self.dataset_populator.validate_dataset_and_wait(history_id, dataset_id)
-        assert terminal_validated_state == 'ok', terminal_validated_state
+        assert terminal_validated_state == "ok", terminal_validated_state
 
     def _velvet_upload(self, history_id, extra_inputs):
         payload = self.dataset_populator.upload_payload(
@@ -859,7 +872,9 @@ class ToolsUploadTestCase(ApiTestCase):
         return dataset
 
     def _get_roadmaps_content(self, history_id, dataset):
-        roadmaps_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=dataset, filename="Roadmaps")
+        roadmaps_content = self.dataset_populator.get_history_dataset_content(
+            history_id, dataset=dataset, filename="Roadmaps"
+        )
         return roadmaps_content
 
     def _upload_and_get_content(self, content, **upload_kwds):
@@ -884,33 +899,38 @@ class ToolsUploadTestCase(ApiTestCase):
                 "elements": [element],
             }
             targets = json.dumps([target])
-            payload = {
-                "history_id": history_id,
-                "targets": targets,
-                "__files": {"files_0|file_data": content}
-            }
+            payload = {"history_id": history_id, "targets": targets, "__files": {"files_0|file_data": content}}
             new_dataset = self.dataset_populator.fetch(payload, assert_ok=assert_ok).json()["outputs"][0]
         self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok)
         return history_id, new_dataset
 
     def test_upload_dataset_resumable(self):
-
         def upload_file(url, path, api_key, history_id):
             filename = os.path.basename(path)
             metadata = {
-                'filename': filename,
-                'history_id': history_id,
+                "filename": filename,
+                "history_id": history_id,
             }
-            my_client = client.TusClient(url, headers={'x-api-key': api_key})
+            my_client = client.TusClient(url, headers={"x-api-key": api_key})
 
             # Upload a file to a tus server.
             uploader = my_client.uploader(path, metadata=metadata)
             uploader.upload()
-            return uploader.url.rsplit('/', 1)[1]
+            return uploader.url.rsplit("/", 1)[1]
 
         with self.dataset_populator.test_history() as history_id:
-            session_id = upload_file(url=urllib.parse.urljoin(self.url, "api/upload/resumable_upload"), path=TestDataResolver().get_filename("1.fastqsanger.gz"), api_key=self.galaxy_interactor.api_key, history_id=history_id)
-            hda = self._upload_and_get_details(content=json.dumps({'session_id': session_id}), api='fetch', ext='fastqsanger.gz', name='1.fastqsanger.gz')
-            assert hda['name'] == '1.fastqsanger.gz'
-            assert hda['file_ext'] == 'fastqsanger.gz'
-            assert hda['state'] == 'ok'
+            session_id = upload_file(
+                url=urllib.parse.urljoin(self.url, "api/upload/resumable_upload"),
+                path=TestDataResolver().get_filename("1.fastqsanger.gz"),
+                api_key=self.galaxy_interactor.api_key,
+                history_id=history_id,
+            )
+            hda = self._upload_and_get_details(
+                content=json.dumps({"session_id": session_id}),
+                api="fetch",
+                ext="fastqsanger.gz",
+                name="1.fastqsanger.gz",
+            )
+            assert hda["name"] == "1.fastqsanger.gz"
+            assert hda["file_ext"] == "fastqsanger.gz"
+            assert hda["state"] == "ok"
diff --git a/lib/galaxy_test/api/test_tours.py b/lib/galaxy_test/api/test_tours.py
index 6c2ecde6836..e63873fece5 100644
--- a/lib/galaxy_test/api/test_tours.py
+++ b/lib/galaxy_test/api/test_tours.py
@@ -2,7 +2,6 @@ from ._framework import ApiTestCase
 
 
 class TourApiTestCase(ApiTestCase):
-
     def test_index(self):
         response = self._get("tours")
         self._assert_status_code_is(response, 200)
diff --git a/lib/galaxy_test/api/test_users.py b/lib/galaxy_test/api/test_users.py
index e6fbfec6ee4..386dd543207 100644
--- a/lib/galaxy_test/api/test_users.py
+++ b/lib/galaxy_test/api/test_users.py
@@ -3,7 +3,7 @@ import json
 from requests import (
     delete,
     get,
-    put
+    put,
 )
 
 from galaxy_test.base.api_asserts import assert_object_id_error
@@ -17,7 +17,6 @@ TEST_USER_EMAIL_UNDELETE = "user_for_undelete_test@bx.psu.edu"
 
 
 class UsersApiTestCase(ApiTestCase):
-
     def test_index(self):
         self._setup_user(TEST_USER_EMAIL)
         all_users_response = self._get("users", admin=True)
@@ -44,19 +43,19 @@ class UsersApiTestCase(ApiTestCase):
             self.__assert_matches_user(user, show_response.json())
 
     def test_update(self):
-        new_name = 'linnaeus'
+        new_name = "linnaeus"
         user = self._setup_user(TEST_USER_EMAIL)
-        not_the_user = self._setup_user('email@example.com')
+        not_the_user = self._setup_user("email@example.com")
         with self._different_user(email=TEST_USER_EMAIL):
 
             # working
             update_response = self.__update(user, username=new_name)
             self._assert_status_code_is(update_response, 200)
             update_json = update_response.json()
-            self.assertEqual(update_json['username'], new_name)
+            self.assertEqual(update_json["username"], new_name)
 
             # too short
-            update_response = self.__update(user, username='mu')
+            update_response = self.__update(user, username="mu")
             self._assert_status_code_is(update_response, 400)
 
             # not them
@@ -64,25 +63,25 @@ class UsersApiTestCase(ApiTestCase):
             self._assert_status_code_is(update_response, 403)
 
             # non-existent
-            no_user_id = '5d7db0757a2eb7ef'
+            no_user_id = "5d7db0757a2eb7ef"
             update_url = self._api_url(f"users/{no_user_id}", use_key=True)
             update_response = put(update_url, data=json.dumps(dict(username=new_name)))
             assert_object_id_error(update_response)
 
     def test_admin_update(self):
-        new_name = 'flexo'
+        new_name = "flexo"
         user = self._setup_user(TEST_USER_EMAIL)
         update_url = self._api_url(f"users/{user['id']}", params=dict(key=self.master_api_key))
         update_response = put(update_url, data=json.dumps(dict(username=new_name)))
         self._assert_status_code_is(update_response, 200)
         update_json = update_response.json()
-        self.assertEqual(update_json['username'], new_name)
+        self.assertEqual(update_json["username"], new_name)
 
     def test_delete_user(self):
         user = self._setup_user(TEST_USER_EMAIL_DELETE)
         self._delete(f"users/{user['id']}", admin=True)
         updated_user = self._get(f"users/deleted/{user['id']}", admin=True).json()
-        assert updated_user['deleted'] is True, updated_user
+        assert updated_user["deleted"] is True, updated_user
 
     def test_purge_user(self):
         """Delete user and then purge them."""
@@ -92,21 +91,21 @@ class UsersApiTestCase(ApiTestCase):
         data = dict(purge="True")
         response = self._delete(f"users/{user['id']}", data=data, admin=True)
         self._assert_status_code_is_ok(response)
-        payload = {'deleted': "True"}
+        payload = {"deleted": "True"}
         purged_user = self._get(f"users/{user['id']}", payload, admin=True).json()
-        assert purged_user['deleted'] is True, purged_user
-        assert purged_user['purged'] is True, purged_user
+        assert purged_user["deleted"] is True, purged_user
+        assert purged_user["purged"] is True, purged_user
 
     def test_undelete_user(self):
         """Delete user and then undelete them."""
         user = self._setup_user(TEST_USER_EMAIL_UNDELETE)
         self._delete(f"users/{user['id']}", admin=True)
-        payload = {'deleted': "True"}
+        payload = {"deleted": "True"}
         deleted_user = self._get(f"users/{user['id']}", payload, admin=True).json()
-        assert deleted_user['deleted'] is True, deleted_user
+        assert deleted_user["deleted"] is True, deleted_user
         self._post(f"users/deleted/{user['id']}/undelete", admin=True)
         undeleted_user = self._get(f"users/{user['id']}", admin=True).json()
-        assert undeleted_user['deleted'] is False, undeleted_user
+        assert undeleted_user["deleted"] is False, undeleted_user
 
     def test_information(self):
         user = self._setup_user(TEST_USER_EMAIL)
@@ -152,11 +151,16 @@ class UsersApiTestCase(ApiTestCase):
         self._assert_status_code_is_ok(delete_response)
         self.assertEqual(delete_response.json()["tools"], [])
         # delete non-existing tool favorite
-        url = self._api_url(f"users/{user['id']}/favorites/tools/madeuptoolthatdoes/not/exist/in/favs", params=dict(key=self.master_api_key))
+        url = self._api_url(
+            f"users/{user['id']}/favorites/tools/madeuptoolthatdoes/not/exist/in/favs",
+            params=dict(key=self.master_api_key),
+        )
         delete_response = delete(url)
         self._assert_status_code_is(delete_response, 404)
         # delete non existing workflow favorite
-        url = self._api_url(f"users/{user['id']}/favorites/workflows/1as5das5das56d465", params=dict(key=self.master_api_key))
+        url = self._api_url(
+            f"users/{user['id']}/favorites/workflows/1as5das5das56d465", params=dict(key=self.master_api_key)
+        )
         delete_response = delete(url)
         self._assert_status_code_is(delete_response, 400)
 
diff --git a/lib/galaxy_test/api/test_visualizations.py b/lib/galaxy_test/api/test_visualizations.py
index 6fc8848346d..b081b0848be 100644
--- a/lib/galaxy_test/api/test_visualizations.py
+++ b/lib/galaxy_test/api/test_visualizations.py
@@ -1,23 +1,15 @@
 import json
 import uuid
 
-from requests import (
-    put
-)
+from requests import put
 
 from galaxy_test.api.sharable import SharingApiTests
 from galaxy_test.base.api_asserts import assert_has_keys
 from ._framework import ApiTestCase
 
-INDEX_KEYS = [
-    'id', 'title', 'type', 'dbkey', 'url'
-]
-SHOW_KEYS = INDEX_KEYS + [
-    'user_id', 'model_class', 'revisions', 'latest_revision', 'annotation'
-]
-REVISION_KEYS = [
-    'id', 'title', 'visualization_id', 'dbkey', 'model_class', 'config'
-]
+INDEX_KEYS = ["id", "title", "type", "dbkey", "url"]
+SHOW_KEYS = INDEX_KEYS + ["user_id", "model_class", "revisions", "latest_revision", "annotation"]
+REVISION_KEYS = ["id", "title", "visualization_id", "dbkey", "model_class", "config"]
 
 
 class VisualizationsApiTestCase(ApiTestCase, SharingApiTests):
@@ -42,11 +34,11 @@ class VisualizationsApiTestCase(ApiTestCase, SharingApiTests):
         self._show_viz(viz_id, assert_ok=True)
 
     def test_create_fails_without_title(self):
-        response = self._raw_create_viz(title='')
+        response = self._raw_create_viz(title="")
         self._assert_status_code_is(response, 400)
 
     def test_create_fails_with_bad_slug(self):
-        response = self._raw_create_viz(slug='123_()')
+        response = self._raw_create_viz(slug="123_()")
         self._assert_status_code_is(response, 400)
 
     def test_create_fails_with_invalid_config(self):
@@ -57,7 +49,9 @@ class VisualizationsApiTestCase(ApiTestCase, SharingApiTests):
         viz_id, _ = self._create_viz()
         sharing_response = self._get(f"visualizations/{viz_id}/sharing")
         self._assert_status_code_is(sharing_response, 200)
-        self._assert_has_keys(sharing_response.json(), "title", "importable", "id", "username_and_slug", "published", "users_shared_with")
+        self._assert_has_keys(
+            sharing_response.json(), "title", "importable", "id", "username_and_slug", "published", "users_shared_with"
+        )
 
     def test_update_title(self):
         viz_id, viz = self._create_viz()
@@ -82,18 +76,24 @@ class VisualizationsApiTestCase(ApiTestCase, SharingApiTests):
     def _raw_create_viz(self, title=None, slug=None, config=None):
         uuid_str = str(uuid.uuid4())
 
-        title = title if title is not None else 'Test Visualization'
-        slug = slug if slug is not None else f'test-visualization-{uuid_str}'
-        config = config if config is not None else json.dumps({
-            "x": 10,
-            "y": 12,
-        })
+        title = title if title is not None else "Test Visualization"
+        slug = slug if slug is not None else f"test-visualization-{uuid_str}"
+        config = (
+            config
+            if config is not None
+            else json.dumps(
+                {
+                    "x": 10,
+                    "y": 12,
+                }
+            )
+        )
         create_payload = {
             "title": title,
             "slug": slug,
-            "type": 'example',
-            "dbkey": 'hg17',
-            "annotation": 'this is a test of the emergency visualization system',
+            "type": "example",
+            "dbkey": "hg17",
+            "annotation": "this is a test of the emergency visualization system",
             "config": config,
         }
         response = self._post("visualizations", data=create_payload)
diff --git a/lib/galaxy_test/api/test_webhooks.py b/lib/galaxy_test/api/test_webhooks.py
index 42a287322a4..41c5ab13f75 100644
--- a/lib/galaxy_test/api/test_webhooks.py
+++ b/lib/galaxy_test/api/test_webhooks.py
@@ -2,24 +2,22 @@ from ._framework import ApiTestCase
 
 
 class WebhooksApiTestCase(ApiTestCase):
-
     def setUp(self):
         super().setUp()
 
     def test_get_all(self):
-        response = self._get('webhooks')
+        response = self._get("webhooks")
 
         self._assert_status_code_is(response, 200)
         webhook_objs = self._assert_are_webhooks(response)
         ids = self._get_webhook_ids(webhook_objs)
-        for expected_id in ['history_test1', 'history_test2', 'masthead_test',
-                            'phdcomics', 'trans_object', 'xkcd']:
+        for expected_id in ["history_test1", "history_test2", "masthead_test", "phdcomics", "trans_object", "xkcd"]:
             assert expected_id in ids
 
     def test_get_data(self):
-        response = self._get('webhooks/trans_object/data')
+        response = self._get("webhooks/trans_object/data")
         self._assert_status_code_is(response, 200)
-        self._assert_has_keys(response.json(), 'username')
+        self._assert_has_keys(response.json(), "username")
 
     def _assert_are_webhooks(self, response):
         response_list = response.json()
@@ -30,9 +28,8 @@ class WebhooksApiTestCase(ApiTestCase):
 
     def _assert_is_webhook(self, obj):
         assert isinstance(obj, dict)
-        self._assert_has_keys(obj,
-            'id', 'type', 'activate', 'weight', 'script', 'styles', 'config')
+        self._assert_has_keys(obj, "id", "type", "activate", "weight", "script", "styles", "config")
 
     def _get_webhook_ids(self, webhook_objs):
-        names = [w.get('id') for w in webhook_objs]
+        names = [w.get("id") for w in webhook_objs]
         return names
diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py
index 1a4a34ae504..ec7ca769502 100644
--- a/lib/galaxy_test/api/test_workflow_extraction.py
+++ b/lib/galaxy_test/api/test_workflow_extraction.py
@@ -1,9 +1,15 @@
 import functools
 import operator
 from collections import namedtuple
-from json import dumps, loads
+from json import (
+    dumps,
+    loads,
+)
 
-from galaxy_test.base.populators import skip_without_tool, summarize_instance_history_on_error
+from galaxy_test.base.populators import (
+    skip_without_tool,
+    summarize_instance_history_on_error,
+)
 from .test_workflows import BaseWorkflowsApiTestCase
 
 
@@ -46,7 +52,7 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
         for old_dataset in old_contents:
             self.__copy_content_to_history(self.history_id, old_dataset)
         new_contents = self._history_contents()
-        input_hids = [c["hid"] for c in new_contents[(offset + 0):(offset + 2)]]
+        input_hids = [c["hid"] for c in new_contents[(offset + 0) : (offset + 2)]]
         cat1_job_id = self.__job_id(self.history_id, new_contents[(offset + 2)]["id"])
 
         def reimport_jobs_ids(new_history_id):
@@ -69,7 +75,7 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
         for old_dataset in old_contents:
             self.__copy_content_to_history(self.history_id, old_dataset)
         new_contents = self._history_contents()
-        input_hids = [c["hid"] for c in new_contents[(offset + 0):(offset + 2)]]
+        input_hids = [c["hid"] for c in new_contents[(offset + 0) : (offset + 2)]]
 
         def reimport_jobs_ids(new_history_id):
             return [j["id"] for j in self.dataset_populator.history_jobs(new_history_id) if j["tool_id"] == "cat1"]
@@ -110,7 +116,10 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
 
     def test_extract_copied_mapping_from_history_reimported(self):
         import unittest
-        raise unittest.SkipTest("Mapping connection for copied collections not yet implemented in history import/export")
+
+        raise unittest.SkipTest(
+            "Mapping connection for copied collections not yet implemented in history import/export"
+        )
 
         old_history_id = self.dataset_populator.new_history()
         hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_singleton(old_history_id)
@@ -120,7 +129,9 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
             self.__copy_content_to_history(self.history_id, old_content)
 
         def reimport_jobs_ids(new_history_id):
-            rval = [j["id"] for j in self.dataset_populator.history_jobs(new_history_id) if j["tool_id"] == "random_lines1"]
+            rval = [
+                j["id"] for j in self.dataset_populator.history_jobs(new_history_id) if j["tool_id"] == "random_lines1"
+            ]
             assert len(rval) == 2
             print(rval)
             return rval
@@ -139,12 +150,11 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
     @skip_without_tool("random_lines1")
     @skip_without_tool("multi_data_param")
     def test_extract_reduction_from_history(self):
-        hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"]).json()
+        hdca = self.dataset_collection_populator.create_pair_in_history(
+            self.history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"]
+        ).json()
         hdca_id = hdca["id"]
-        inputs1 = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
-            "num_lines": 2
-        }
+        inputs1 = {"input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}, "num_lines": 2}
         implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id(self.history_id, "random_lines1", inputs1)
         inputs2 = {
             "f1": {"src": "hdca", "id": implicit_hdca1["id"]},
@@ -180,7 +190,8 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase):
 
     @skip_without_tool("collection_paired_test")
     def test_extract_workflows_with_dataset_collections(self):
-        jobs_summary = self._run_workflow("""
+        jobs_summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - label: text_input1
@@ -192,7 +203,8 @@ steps:
 test_data:
   text_input1:
     collection_type: paired
-""")
+"""
+        )
         job_id = self._job_id_for_tool(jobs_summary.jobs, "collection_paired_test")
         downloaded_workflow = self._extract_and_download_workflow(
             reimport_as="extract_from_history_with_basic_collections",
@@ -205,7 +217,7 @@ test_data:
             verify_connected=True,
             data_input_count=0,
             data_collection_input_count=1,
-            tool_ids=["collection_paired_test"]
+            tool_ids=["collection_paired_test"],
         )
 
         collection_step = self._get_steps_of_type(downloaded_workflow, "data_collection_input", expected_len=1)[0]
@@ -214,7 +226,8 @@ test_data:
 
     @skip_without_tool("cat_collection")
     def test_subcollection_mapping(self):
-        jobs_summary = self._run_workflow("""
+        jobs_summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - label: text_input1
@@ -231,7 +244,8 @@ steps:
 test_data:
   text_input1:
     collection_type: "list:paired"
-        """)
+        """
+        )
         job1_id = self._job_id_for_tool(jobs_summary.jobs, "cat1")
         job2_id = self._job_id_for_tool(jobs_summary.jobs, "cat_collection")
         downloaded_workflow = self._extract_and_download_workflow(
@@ -255,7 +269,8 @@ test_data:
     @skip_without_tool("cat_list")
     @skip_without_tool("collection_creates_dynamic_nested")
     def test_subcollection_reduction(self):
-        jobs_summary = self._run_workflow("""
+        jobs_summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   creates_nested_list:
@@ -264,7 +279,8 @@ steps:
     tool_id: cat_list
     in:
       input1: creates_nested_list/list_output
-""")
+"""
+        )
         job1_id = self._job_id_for_tool(jobs_summary.jobs, "cat_list")
         job2_id = self._job_id_for_tool(jobs_summary.jobs, "collection_creates_dynamic_nested")
         self._extract_and_download_workflow(
@@ -277,7 +293,8 @@ steps:
 
     @skip_without_tool("collection_split_on_column")
     def test_extract_workflow_with_output_collections(self):
-        jobs_summary = self._run_workflow("""
+        jobs_summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - label: text_input1
@@ -304,7 +321,8 @@ steps:
 test_data:
   text_input1: "samp1\t10.0\nsamp2\t20.0\n"
   text_input2: "samp1\t30.0\nsamp2\t40.0\n"
-""")
+"""
+        )
         tool_ids = ["cat1", "collection_split_on_column", "cat_list"]
         job_ids = [functools.partial(self._job_id_for_tool, jobs_summary.jobs)(_) for _ in tool_ids]
         downloaded_workflow = self._extract_and_download_workflow(
@@ -324,7 +342,8 @@ test_data:
     @skip_without_tool("collection_creates_pair")
     @summarize_instance_history_on_error
     def test_extract_with_mapped_output_collections(self):
-        jobs_summary = self._run_workflow("""
+        jobs_summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - label: text_input1
@@ -356,7 +375,8 @@ test_data:
         content: "samp1\t10.0\nsamp2\t20.0\n"
       - identifier: samp2
         content: "samp1\t30.0\nsamp2\t40.0\n"
-""")
+"""
+        )
         tool_ids = ["cat1", "collection_creates_pair", "cat_collection", "cat_list"]
         job_ids = [functools.partial(self._job_id_for_tool, jobs_summary.jobs)(_) for _ in tool_ids]
         downloaded_workflow = self._extract_and_download_workflow(
@@ -385,32 +405,22 @@ test_data:
         return tool_jobs[-1]
 
     def __run_random_lines_mapped_over_pair(self, history_id):
-        hdca = self.dataset_collection_populator.create_pair_in_history(history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"]).json()
+        hdca = self.dataset_collection_populator.create_pair_in_history(
+            history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"]
+        ).json()
         hdca_id = hdca["id"]
-        inputs1 = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
-            "num_lines": 2
-        }
+        inputs1 = {"input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}, "num_lines": 2}
         implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id(history_id, "random_lines1", inputs1)
-        inputs2 = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": implicit_hdca1["id"]}]},
-            "num_lines": 1
-        }
+        inputs2 = {"input": {"batch": True, "values": [{"src": "hdca", "id": implicit_hdca1["id"]}]}, "num_lines": 1}
         _, job_id2 = self._run_tool_get_collection_and_job_id(history_id, "random_lines1", inputs2)
         return hdca, job_id1, job_id2
 
     def __run_random_lines_mapped_over_singleton(self, history_id):
         hdca = self.dataset_collection_populator.create_list_in_history(history_id, contents=["1 2 3\n4 5 6"]).json()
         hdca_id = hdca["id"]
-        inputs1 = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
-            "num_lines": 2
-        }
+        inputs1 = {"input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}, "num_lines": 2}
         implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id(history_id, "random_lines1", inputs1)
-        inputs2 = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": implicit_hdca1["id"]}]},
-            "num_lines": 1
-        }
+        inputs2 = {"input": {"batch": True, "values": [{"src": "hdca", "id": implicit_hdca1["id"]}]}, "num_lines": 1}
         _, job_id2 = self._run_tool_get_collection_and_job_id(history_id, "random_lines1", inputs2)
         return hdca, job_id1, job_id2
 
@@ -450,17 +460,11 @@ test_data:
 
     def __copy_content_to_history(self, history_id, content):
         if content["history_content_type"] == "dataset":
-            payload = dict(
-                source="hda",
-                content=content["id"]
-            )
+            payload = dict(source="hda", content=content["id"])
             response = self._post(f"histories/{history_id}/contents/datasets", payload, json=True)
 
         else:
-            payload = dict(
-                source="hdca",
-                content=content["id"]
-            )
+            payload = dict(source="hdca", content=content["id"])
             response = self._post(f"histories/{history_id}/contents/dataset_collections", payload, json=True)
         self._assert_status_code_is(response, 200)
         return response.json()
@@ -499,11 +503,16 @@ test_data:
                 history_length = self.dataset_populator.history_length(history_id)
 
             new_history_id = self.dataset_populator.reimport_history(
-                history_id, history_name, wait_on_history_length=history_length, export_kwds={}, api_key=self.galaxy_interactor.api_key
+                history_id,
+                history_name,
+                wait_on_history_length=history_length,
+                export_kwds={},
+                api_key=self.galaxy_interactor.api_key,
             )
             # wait a little more for those jobs, todo fix to wait for history imported false or
             # for a specific number of jobs...
             import time
+
             time.sleep(1)
 
             if "reimport_jobs_ids" in extract_payload:
@@ -513,8 +522,14 @@ test_data:
                 # Assume no copying or anything so just straight map job ids by index.
 
                 # Jobs are created after datasets, need to also wait on those...
-                history_jobs = [j for j in self.dataset_populator.history_jobs(history_id) if j["tool_id"] != "__EXPORT_HISTORY__"]
-                new_history_jobs = [j for j in self.dataset_populator.history_jobs(new_history_id) if j["tool_id"] != "__EXPORT_HISTORY__"]
+                history_jobs = [
+                    j for j in self.dataset_populator.history_jobs(history_id) if j["tool_id"] != "__EXPORT_HISTORY__"
+                ]
+                new_history_jobs = [
+                    j
+                    for j in self.dataset_populator.history_jobs(new_history_id)
+                    if j["tool_id"] != "__EXPORT_HISTORY__"
+                ]
 
                 history_job_ids = [j["id"] for j in history_jobs]
                 new_history_job_ids = [j["id"] for j in new_history_jobs]
@@ -592,7 +607,7 @@ test_data:
         data_collection_input_count=None,
         tool_ids=None,
     ):
-        steps = workflow['steps']
+        steps = workflow["steps"]
 
         if step_count is not None:
             assert len(steps) == step_count
@@ -612,7 +627,7 @@ test_data:
         disconnected_inputs = []
 
         for value in steps.values():
-            if value['type'] == "tool":
+            if value["type"] == "tool":
                 input_connections = value["input_connections"]
                 if not input_connections:
                     disconnected_inputs.append(value)
@@ -623,4 +638,4 @@ test_data:
             raise AssertionError(message)
 
 
-RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs'])
+RunJobsSummary = namedtuple("RunJobsSummary", ["history_id", "workflow_id", "inputs", "jobs"])
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 5cddfb32b54..211d7c1fb5a 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -4,11 +4,22 @@ import shutil
 import time
 from json import dumps
 from tempfile import mkdtemp
-from typing import Any, cast, Dict, Optional, Tuple, Union
+from typing import (
+    Any,
+    cast,
+    Dict,
+    Optional,
+    Tuple,
+    Union,
+)
 from uuid import uuid4
 
 import pytest
-from requests import delete, get, put
+from requests import (
+    delete,
+    get,
+    put,
+)
 
 from galaxy.exceptions import error_codes
 from galaxy_test.base import rules_test_data
@@ -18,7 +29,7 @@ from galaxy_test.base.populators import (
     RunJobsSummary,
     skip_without_tool,
     wait_on,
-    WorkflowPopulator
+    WorkflowPopulator,
 )
 from galaxy_test.base.workflow_fixtures import (
     WORKFLOW_NESTED_REPLACEMENT_PARAMETER,
@@ -43,7 +54,6 @@ from galaxy_test.base.workflow_fixtures import (
 )
 from ._framework import ApiTestCase
 
-
 WORKFLOW_SIMPLE = """
 class: GalaxyWorkflow
 name: Simple Workflow
@@ -124,10 +134,14 @@ class BaseWorkflowsApiTestCase(ApiTestCase):
     def _upload_yaml_workflow(self, has_yaml, **kwds) -> str:
         return self.workflow_populator.upload_yaml_workflow(has_yaml, **kwds)
 
-    def _setup_workflow_run(self, workflow: Optional[Dict[str, Any]] = None, inputs_by: str = 'step_id', history_id: Optional[str] = None, workflow_id: Optional[str] = None) -> Tuple[Dict[str, Any], str, str]:
-        return self.workflow_populator.setup_workflow_run(
-            workflow, inputs_by, history_id, workflow_id
-        )
+    def _setup_workflow_run(
+        self,
+        workflow: Optional[Dict[str, Any]] = None,
+        inputs_by: str = "step_id",
+        history_id: Optional[str] = None,
+        workflow_id: Optional[str] = None,
+    ) -> Tuple[Dict[str, Any], str, str]:
+        return self.workflow_populator.setup_workflow_run(workflow, inputs_by, history_id, workflow_id)
 
     def _ds_entry(self, history_content):
         return self.dataset_populator.ds_entry(history_content)
@@ -176,7 +190,8 @@ class ChangeDatatypeTestCase:
 
     def test_assign_column_pja(self):
         with self.dataset_populator.test_history() as history_id:
-            self.workflow_populator.run_workflow("""
+            self.workflow_populator.run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -192,15 +207,20 @@ steps:
           chromCol: 1
           endCol: 2
           startCol: 3
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.bed
   type: File
-""", history_id=history_id)
-            details_dataset_new_col = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+            )
+            details_dataset_new_col = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=2, wait=True, assert_ok=True
+            )
             assert details_dataset_new_col["history_content_type"] == "dataset", details_dataset_new_col
-            assert details_dataset_new_col['metadata_endCol'] == 2
-            assert details_dataset_new_col['metadata_startCol'] == 3
+            assert details_dataset_new_col["metadata_endCol"] == 2
+            assert details_dataset_new_col["metadata_startCol"] == 3
 
 
 # Workflow API TODO:
@@ -209,7 +229,6 @@ input1:
 #    /workflows with id in payload.
 # - Much more testing obviously, always more testing.
 class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
-
     def test_show_valid(self):
         workflow_id = self.workflow_populator.simple_workflow("dummy")
         workflow_id = self.workflow_populator.simple_workflow("test_regular")
@@ -246,7 +265,7 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         with self._different_user():
             with pytest.raises(AssertionError) as excinfo:
                 self._download_workflow(workflow_id)
-            assert '403' in str(excinfo.value)
+            assert "403" in str(excinfo.value)
         workflows_url = self._api_url(f"workflows/{workflow_id}/download")
         assert get(workflows_url).status_code == 403
 
@@ -255,7 +274,7 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         workflows_url = self._api_url(f"workflows/{workflow_id}/download")
         response = get(workflows_url)
         response.raise_for_status()
-        assert response.json()['a_galaxy_workflow'] == 'true'
+        assert response.json()["a_galaxy_workflow"] == "true"
 
     def test_delete(self):
         workflow_id = self.workflow_populator.simple_workflow("test_delete")
@@ -282,27 +301,27 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
     def test_index_deleted(self):
         workflow_id = self.workflow_populator.simple_workflow("test_delete")
         workflow_index = self._get("workflows").json()
-        assert [w for w in workflow_index if w['id'] == workflow_id]
+        assert [w for w in workflow_index if w["id"] == workflow_id]
         workflow_url = self._api_url(f"workflows/{workflow_id}", use_key=True)
         delete_response = delete(workflow_url)
         self._assert_status_code_is(delete_response, 200)
         workflow_index = self._get("workflows").json()
-        assert not [w for w in workflow_index if w['id'] == workflow_id]
+        assert not [w for w in workflow_index if w["id"] == workflow_id]
         workflow_index = self._get("workflows?show_deleted=true").json()
-        assert [w for w in workflow_index if w['id'] == workflow_id]
+        assert [w for w in workflow_index if w["id"] == workflow_id]
 
     def test_index_hidden(self):
         workflow_id = self.workflow_populator.simple_workflow("test_delete")
         workflow_index = self._get("workflows").json()
-        workflow = [w for w in workflow_index if w['id'] == workflow_id][0]
-        workflow['hidden'] = True
+        workflow = [w for w in workflow_index if w["id"] == workflow_id][0]
+        workflow["hidden"] = True
         update_response = self.workflow_populator.update_workflow(workflow_id, workflow)
         self._assert_status_code_is(update_response, 200)
-        assert update_response.json()['hidden']
+        assert update_response.json()["hidden"]
         workflow_index = self._get("workflows").json()
-        assert not [w for w in workflow_index if w['id'] == workflow_id]
+        assert not [w for w in workflow_index if w["id"] == workflow_id]
         workflow_index = self._get("workflows?show_hidden=true").json()
-        assert [w for w in workflow_index if w['id'] == workflow_id]
+        assert [w for w in workflow_index if w["id"] == workflow_id]
 
     def test_upload(self):
         self.__test_upload(use_deprecated_route=False)
@@ -314,7 +333,9 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         response = self.__test_upload(import_tools=True, assert_ok=False)
         assert response.status_code == 403
 
-    def __test_upload(self, use_deprecated_route=False, name="test_import", workflow=None, assert_ok=True, import_tools=False):
+    def __test_upload(
+        self, use_deprecated_route=False, name="test_import", workflow=None, assert_ok=True, import_tools=False
+    ):
         if workflow is None:
             workflow = self.workflow_populator.load_workflow(name=name)
         data = dict(
@@ -333,8 +354,11 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         return upload_response
 
     def test_get_tool_predictions(self):
-        request = {"tool_sequence": "Cut1", "remote_model_url": "https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5"}
-        actual_recommendations = ['Filter1', 'cat1', 'addValue', 'comp1', 'Grep1']
+        request = {
+            "tool_sequence": "Cut1",
+            "remote_model_url": "https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5",
+        }
+        actual_recommendations = ["Filter1", "cat1", "addValue", "comp1", "Grep1"]
         route = "workflows/get_tool_predictions"
         response = self._post(route, data=request)
         recommendation_response = response.json()
@@ -389,9 +413,9 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         def tweak_step(step):
             order_index, step_dict = step
             check_label_and_uuid(order_index, step_dict)
-            assert step_dict['position']['top'] != 1
-            assert step_dict['position']['left'] != 1
-            step_dict['position'] = {'top': 1, 'left': 1}
+            assert step_dict["position"]["top"] != 1
+            assert step_dict["position"]["left"] != 1
+            step_dict["position"] = {"top": 1, "left": 1}
 
         map(tweak_step, steps.items())
 
@@ -400,11 +424,11 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         def check_step(step):
             order_index, step_dict = step
             check_label_and_uuid(order_index, step_dict)
-            assert step_dict['position']['top'] == 1
-            assert step_dict['position']['left'] == 1
+            assert step_dict["position"]["top"] == 1
+            assert step_dict["position"]["left"] == 1
 
         updated_workflow_content = self._download_workflow(workflow_id)
-        map(check_step, updated_workflow_content['steps'].items())
+        map(check_step, updated_workflow_content["steps"].items())
 
         # Re-update against original workflow...
         update(original_workflow)
@@ -412,21 +436,21 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         updated_workflow_content = self._download_workflow(workflow_id)
 
         # Make sure the positions have been updated.
-        map(tweak_step, updated_workflow_content['steps'].items())
+        map(tweak_step, updated_workflow_content["steps"].items())
 
     def test_update_tags(self):
         workflow_object = self.workflow_populator.load_workflow(name="test_import")
         upload_response = self.__test_upload(workflow=workflow_object)
         workflow = upload_response.json()
-        workflow['tags'] = ['a_tag', 'b_tag']
-        update_response = self._update_workflow(workflow['id'], workflow).json()
-        assert update_response['tags'] == ['a_tag', 'b_tag']
-        del workflow['tags']
-        update_response = self._update_workflow(workflow['id'], workflow).json()
-        assert update_response['tags'] == ['a_tag', 'b_tag']
-        workflow['tags'] = []
-        update_response = self._update_workflow(workflow['id'], workflow).json()
-        assert update_response['tags'] == []
+        workflow["tags"] = ["a_tag", "b_tag"]
+        update_response = self._update_workflow(workflow["id"], workflow).json()
+        assert update_response["tags"] == ["a_tag", "b_tag"]
+        del workflow["tags"]
+        update_response = self._update_workflow(workflow["id"], workflow).json()
+        assert update_response["tags"] == ["a_tag", "b_tag"]
+        workflow["tags"] = []
+        update_response = self._update_workflow(workflow["id"], workflow).json()
+        assert update_response["tags"] == []
 
     def test_update_name(self):
         original_name = "test update name"
@@ -434,19 +458,20 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         workflow_object["license"] = "AAL"
         upload_response = self.__test_upload(workflow=workflow_object, name=original_name)
         workflow = upload_response.json()
-        workflow_id = workflow['id']
-        assert workflow['name'] == original_name
+        workflow_id = workflow["id"]
+        assert workflow["name"] == original_name
         workflow_dict = self.workflow_populator.download_workflow(workflow_id)
         assert workflow_dict["license"] == "AAL"
 
         data = {"name": "my cool new name"}
-        update_response = self._update_workflow(workflow['id'], data).json()
-        assert update_response['name'] == "my cool new name"
+        update_response = self._update_workflow(workflow["id"], data).json()
+        assert update_response["name"] == "my cool new name"
         workflow_dict = self.workflow_populator.download_workflow(workflow_id)
         assert workflow_dict["license"] == "AAL"
 
     def test_refactor(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow("""
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -455,7 +480,8 @@ steps:
     tool_id: cat
     in:
       input1: test_input
-""")
+"""
+        )
         actions = [
             {"action_type": "update_step_label", "step": {"order_index": 0}, "label": "new_label"},
         ]
@@ -465,7 +491,9 @@ steps:
         assert refactor_response.json()["workflow"]["steps"]["0"]["label"] == "new_label"
 
         # perform refactoring as dry run but specify editor style response
-        refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=True, style="editor")
+        refactor_response = self.workflow_populator.refactor_workflow(
+            workflow_id, actions, dry_run=True, style="editor"
+        )
         refactor_response.raise_for_status()
         assert refactor_response.json()["workflow"]["steps"]["0"]["label"] == "new_label"
 
@@ -521,7 +549,8 @@ steps:
             self._assert_user_has_workflow_with_name("imported: test_import_published_deprecated")
 
     def test_import_export_dynamic(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - type: input
@@ -547,7 +576,8 @@ steps:
           $link: embed1/output1
 test_data:
   input1: "hello world"
-""")
+"""
+        )
         downloaded_workflow = self._download_workflow(workflow_id)
         # The _upload_yaml_workflow entry point uses an admin key, but if we try to
         # do the raw re-import as a regular user we expect a 403 error.
@@ -571,18 +601,18 @@ test_data:
     def test_import_subworkflows(self):
         def get_subworkflow_content_id(workflow_id):
             workflow_contents = self._download_workflow(workflow_id, style="editor")
-            steps = workflow_contents['steps']
+            steps = workflow_contents["steps"]
             subworkflow_step = next(s for s in steps.values() if s["type"] == "subworkflow")
-            return subworkflow_step['content_id']
+            return subworkflow_step["content_id"]
 
         workflow_id = self._upload_yaml_workflow(WORKFLOW_NESTED_SIMPLE, publish=True)
         subworkflow_content_id = get_subworkflow_content_id(workflow_id)
         instance_response = self._get(f"workflows/{subworkflow_content_id}?instance=true")
         self._assert_status_code_is(instance_response, 200)
         subworkflow = instance_response.json()
-        assert subworkflow['inputs']['0']['label'] == 'inner_input'
-        assert subworkflow['name'] == 'Workflow'
-        assert subworkflow['hidden']
+        assert subworkflow["inputs"]["0"]["label"] == "inner_input"
+        assert subworkflow["name"] == "Workflow"
+        assert subworkflow["hidden"]
         with self._different_user():
             other_import_response = self.__import_workflow(workflow_id)
             self._assert_status_code_is(other_import_response, 200)
@@ -591,7 +621,8 @@ test_data:
             assert subworkflow_content_id != imported_subworkflow_content_id
 
     def test_subworkflow_inputs_optional_editor(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   nested_workflow:
@@ -603,9 +634,10 @@ steps:
       outputs:
         - outputSource: inner_input/output
       steps: []
-""")
+"""
+        )
         workflow_contents = self._download_workflow(workflow_id, style="editor")
-        assert workflow_contents['steps']['0']['inputs'][0]['optional']
+        assert workflow_contents["steps"]["0"]["inputs"][0]["optional"]
 
     def test_not_importable_prevents_import(self):
         workflow_id = self.workflow_populator.simple_workflow("test_not_importportable")
@@ -652,18 +684,18 @@ steps:
         for step in downloaded_workflow["steps"].values():
             self._assert_has_keys(
                 step,
-                'id',
-                'type',
-                'tool_id',
-                'tool_version',
-                'name',
-                'tool_state',
-                'annotation',
-                'inputs',
-                'workflow_outputs',
-                'outputs'
+                "id",
+                "type",
+                "tool_id",
+                "tool_version",
+                "name",
+                "tool_state",
+                "annotation",
+                "inputs",
+                "workflow_outputs",
+                "outputs",
             )
-            if step['type'] == "tool":
+            if step["type"] == "tool":
                 self._assert_has_keys(step, "post_job_actions")
 
     def test_export_format2(self):
@@ -678,23 +710,23 @@ steps:
         for step in downloaded_workflow["steps"].values():
             self._assert_has_keys(
                 step,
-                'id',
-                'type',
-                'content_id',
-                'name',
-                'tool_state',
-                'tooltip',
-                'inputs',
-                'outputs',
-                'config_form',
-                'annotation',
-                'post_job_actions',
-                'workflow_outputs',
-                'uuid',
-                'label',
+                "id",
+                "type",
+                "content_id",
+                "name",
+                "tool_state",
+                "tooltip",
+                "inputs",
+                "outputs",
+                "config_form",
+                "annotation",
+                "post_job_actions",
+                "workflow_outputs",
+                "uuid",
+                "label",
             )
 
-    @skip_without_tool('output_filter_with_input')
+    @skip_without_tool("output_filter_with_input")
     def test_export_editor_filtered_outputs(self):
         template = """
 class: GalaxyWorkflow
@@ -706,41 +738,44 @@ steps:
       produce_collection: false
       produce_paired_collection: false
 """
-        workflow_id = self._upload_yaml_workflow(template.format(produce_out_1='false', filter_text_1='false'))
+        workflow_id = self._upload_yaml_workflow(template.format(produce_out_1="false", filter_text_1="false"))
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
-        outputs = downloaded_workflow['steps']['0']['outputs']
+        outputs = downloaded_workflow["steps"]["0"]["outputs"]
         assert len(outputs) == 1
-        assert outputs[0]['name'] == 'out_3'
-        workflow_id = self._upload_yaml_workflow(template.format(produce_out_1='true', filter_text_1='false'))
+        assert outputs[0]["name"] == "out_3"
+        workflow_id = self._upload_yaml_workflow(template.format(produce_out_1="true", filter_text_1="false"))
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
-        outputs = downloaded_workflow['steps']['0']['outputs']
+        outputs = downloaded_workflow["steps"]["0"]["outputs"]
         assert len(outputs) == 2
-        assert outputs[0]['name'] == 'out_1'
-        assert outputs[1]['name'] == 'out_3'
-        workflow_id = self._upload_yaml_workflow(template.format(produce_out_1='true', filter_text_1='foo'))
+        assert outputs[0]["name"] == "out_1"
+        assert outputs[1]["name"] == "out_3"
+        workflow_id = self._upload_yaml_workflow(template.format(produce_out_1="true", filter_text_1="foo"))
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
-        outputs = downloaded_workflow['steps']['0']['outputs']
+        outputs = downloaded_workflow["steps"]["0"]["outputs"]
         assert len(outputs) == 3
-        assert outputs[0]['name'] == 'out_1'
-        assert outputs[1]['name'] == 'out_2'
-        assert outputs[2]['name'] == 'out_3'
+        assert outputs[0]["name"] == "out_1"
+        assert outputs[1]["name"] == "out_2"
+        assert outputs[2]["name"] == "out_3"
 
-    @skip_without_tool('output_filter_exception_1')
+    @skip_without_tool("output_filter_exception_1")
     def test_export_editor_filtered_outputs_exception_handling(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - tool_id: output_filter_exception_1
-""")
+"""
+        )
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
-        outputs = downloaded_workflow['steps']['0']['outputs']
+        outputs = downloaded_workflow["steps"]["0"]["outputs"]
         assert len(outputs) == 2
-        assert outputs[0]['name'] == 'out_1'
-        assert outputs[1]['name'] == 'out_2'
+        assert outputs[0]["name"] == "out_1"
+        assert outputs[1]["name"] == "out_2"
 
-    @skip_without_tool('collection_type_source')
+    @skip_without_tool("collection_type_source")
     def test_export_editor_collection_type_source(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   - id: text_input1
@@ -750,17 +785,19 @@ steps:
   - tool_id: collection_type_source
     in:
       input_collect: text_input1
-""")
+"""
+        )
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
-        steps = downloaded_workflow['steps']
+        steps = downloaded_workflow["steps"]
         assert len(steps) == 2
         # Non-subworkflow collection_type_source tools will be handled by the client,
         # so collection_type should be None here.
-        assert steps['1']['outputs'][0]['collection_type'] is None
+        assert steps["1"]["outputs"][0]["collection_type"] is None
 
-    @skip_without_tool('collection_type_source')
+    @skip_without_tool("collection_type_source")
     def test_export_editor_subworkflow_collection_type_source(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -782,19 +819,20 @@ steps:
             input_collect: inner_input
     in:
       inner_input: outer_input
-""")
+"""
+        )
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
-        steps = downloaded_workflow['steps']
+        steps = downloaded_workflow["steps"]
         assert len(steps) == 2
-        assert steps['1']['type'] == 'subworkflow'
-        assert steps['1']['outputs'][0]['collection_type'] == 'list:paired'
+        assert steps["1"]["type"] == "subworkflow"
+        assert steps["1"]["outputs"][0]["collection_type"] == "list:paired"
 
     def test_import_missing_tool(self):
         workflow = self.workflow_populator.load_workflow_from_resource(name="test_workflow_missing_tool")
         workflow_id = self.workflow_populator.create_workflow(workflow)
         workflow_description = self._show_workflow(workflow_id)
         steps = workflow_description["steps"]
-        missing_tool_steps = [v for v in steps.values() if v['tool_id'] == 'cat_missing_tool']
+        missing_tool_steps = [v for v in steps.values() if v["tool_id"] == "cat_missing_tool"]
         assert len(missing_tool_steps) == 1
 
     def test_import_no_tool_id(self):
@@ -822,28 +860,29 @@ steps:
 
     @skip_without_tool("cat1")
     def test_run_workflow_by_index(self):
-        self.__run_cat_workflow(inputs_by='step_index')
+        self.__run_cat_workflow(inputs_by="step_index")
 
     @skip_without_tool("cat1")
     def test_run_workflow_by_uuid(self):
-        self.__run_cat_workflow(inputs_by='step_uuid')
+        self.__run_cat_workflow(inputs_by="step_uuid")
 
     @skip_without_tool("cat1")
     def test_run_workflow_by_uuid_implicitly(self):
-        self.__run_cat_workflow(inputs_by='uuid_implicitly')
+        self.__run_cat_workflow(inputs_by="uuid_implicitly")
 
     @skip_without_tool("cat1")
     def test_run_workflow_by_name(self):
-        self.__run_cat_workflow(inputs_by='name')
+        self.__run_cat_workflow(inputs_by="name")
 
     @skip_without_tool("cat1")
     def test_run_workflow(self):
-        self.__run_cat_workflow(inputs_by='step_id')
+        self.__run_cat_workflow(inputs_by="step_id")
 
     @skip_without_tool("multiple_versions")
     def test_run_versioned_tools(self):
         with self.dataset_populator.test_history() as history_01_id:
-            workflow_version_01 = self._upload_yaml_workflow("""
+            workflow_version_01 = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 steps:
   multiple:
@@ -851,11 +890,13 @@ steps:
     tool_version: "0.1"
     state:
       inttest: 0
-""")
+"""
+            )
             self.workflow_populator.invoke_workflow_and_wait(workflow_version_01, history_id=history_01_id)
 
         with self.dataset_populator.test_history() as history_02_id:
-            workflow_version_02 = self._upload_yaml_workflow("""
+            workflow_version_02 = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 steps:
   multiple:
@@ -863,7 +904,8 @@ steps:
     tool_version: "0.2"
     state:
       inttest: 1
-""")
+"""
+            )
             self.workflow_populator.invoke_workflow_and_wait(workflow_version_02, history_id=history_02_id)
 
     def __run_cat_workflow(self, inputs_by):
@@ -871,22 +913,29 @@ steps:
         workflow["steps"]["0"]["uuid"] = str(uuid4())
         workflow["steps"]["1"]["uuid"] = str(uuid4())
         workflow_request, _, workflow_id = self._setup_workflow_run(workflow, inputs_by=inputs_by)
-        invocation_id = self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
+        invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+            workflow_id, request=workflow_request, assert_ok=True
+        )
         invocation = self._invocation_details(workflow_id, invocation_id)
         assert invocation["state"] == "scheduled", invocation
 
     def test_run_workflow_with_missing_tool(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 steps:
   step1:
     tool_id: nonexistent_tool
     tool_version: "0.1"
-""")
+"""
+            )
             invocation_response = self.__invoke_workflow(workflow_id, history_id=history_id, assert_ok=False)
             self._assert_status_code_is(invocation_response, 400)
-            self.assertEqual(invocation_response.json().get('err_msg'), "Workflow was not invoked; the following required tools are not installed: nonexistent_tool")
+            self.assertEqual(
+                invocation_response.json().get("err_msg"),
+                "Workflow was not invoked; the following required tools are not installed: nonexistent_tool",
+            )
 
     @skip_without_tool("collection_creates_pair")
     def test_workflow_run_output_collections(self) -> None:
@@ -897,7 +946,8 @@ steps:
     @skip_without_tool("job_properties")
     @skip_without_tool("identifier_multiple_in_conditional")
     def test_workflow_resume_from_failed_step(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   job_props:
@@ -919,31 +969,39 @@ steps:
     in:
       input1: identifier/output1
       queries_0|input2: identifier/output1
-""")
+"""
+        )
         with self.dataset_populator.test_history() as history_id:
             self.workflow_populator.invoke_workflow_and_wait(workflow_id, history_id=history_id, assert_ok=False)
-            failed_dataset_one = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=False)
-            assert failed_dataset_one['state'] == 'error', failed_dataset_one
-            paused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, wait=True, assert_ok=False)
-            assert paused_dataset['state'] == 'paused', paused_dataset
-            inputs = {"thebool": "false",
-                      "failbool": "false",
-                      "rerun_remap_job_id": failed_dataset_one['creating_job']}
+            failed_dataset_one = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=1, wait=True, assert_ok=False
+            )
+            assert failed_dataset_one["state"] == "error", failed_dataset_one
+            paused_dataset = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=5, wait=True, assert_ok=False
+            )
+            assert paused_dataset["state"] == "paused", paused_dataset
+            inputs = {"thebool": "false", "failbool": "false", "rerun_remap_job_id": failed_dataset_one["creating_job"]}
             self.dataset_populator.run_tool(
-                tool_id='job_properties',
+                tool_id="job_properties",
                 inputs=inputs,
                 history_id=history_id,
             )
-            unpaused_dataset_1 = self.dataset_populator.get_history_dataset_details(history_id, hid=5, wait=True, assert_ok=False)
-            assert unpaused_dataset_1['state'] == 'ok'
+            unpaused_dataset_1 = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=5, wait=True, assert_ok=False
+            )
+            assert unpaused_dataset_1["state"] == "ok"
             self.dataset_populator.wait_for_history(history_id, assert_ok=False)
-            unpaused_dataset_2 = self.dataset_populator.get_history_dataset_details(history_id, hid=6, wait=True, assert_ok=False)
-            assert unpaused_dataset_2['state'] == 'ok'
+            unpaused_dataset_2 = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=6, wait=True, assert_ok=False
+            )
+            assert unpaused_dataset_2["state"] == "ok"
 
     @skip_without_tool("job_properties")
     @skip_without_tool("collection_creates_list")
     def test_workflow_resume_from_failed_step_with_hdca_input(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   job_props:
@@ -959,39 +1017,50 @@ steps:
     tool_id: identifier_collection
     in:
       input1: list_in_list_out/list_output
-""")
+"""
+        )
         with self.dataset_populator.test_history() as history_id:
             invocation_id = self.__invoke_workflow(workflow_id, history_id=history_id)
-            self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id, assert_ok=False)
-            failed_dataset_one = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=False)
-            assert failed_dataset_one['state'] == 'error', failed_dataset_one
-            paused_colletion = self.dataset_populator.get_history_collection_details(history_id, hid=7, wait=True, assert_ok=False)
-            first_paused_element = paused_colletion['elements'][0]['object']
-            assert first_paused_element['state'] == 'paused', first_paused_element
-            dependent_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=8, wait=True,
-                                                                                   assert_ok=False)
-            assert dependent_dataset['state'] == 'paused'
-            inputs = {"thebool": "false",
-                      "failbool": "false",
-                      "rerun_remap_job_id": failed_dataset_one['creating_job']}
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id, workflow_id, invocation_id, assert_ok=False
+            )
+            failed_dataset_one = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=1, wait=True, assert_ok=False
+            )
+            assert failed_dataset_one["state"] == "error", failed_dataset_one
+            paused_colletion = self.dataset_populator.get_history_collection_details(
+                history_id, hid=7, wait=True, assert_ok=False
+            )
+            first_paused_element = paused_colletion["elements"][0]["object"]
+            assert first_paused_element["state"] == "paused", first_paused_element
+            dependent_dataset = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=8, wait=True, assert_ok=False
+            )
+            assert dependent_dataset["state"] == "paused"
+            inputs = {"thebool": "false", "failbool": "false", "rerun_remap_job_id": failed_dataset_one["creating_job"]}
             self.dataset_populator.run_tool(
-                tool_id='job_properties',
+                tool_id="job_properties",
                 inputs=inputs,
                 history_id=history_id,
             )
-            paused_colletion = self.dataset_populator.get_history_collection_details(history_id, hid=7, wait=True, assert_ok=False)
-            first_paused_element = paused_colletion['elements'][0]['object']
-            assert first_paused_element['state'] == 'ok'
+            paused_colletion = self.dataset_populator.get_history_collection_details(
+                history_id, hid=7, wait=True, assert_ok=False
+            )
+            first_paused_element = paused_colletion["elements"][0]["object"]
+            assert first_paused_element["state"] == "ok"
             self.dataset_populator.wait_for_history(history_id, assert_ok=False)
-            dependent_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=8, wait=True, assert_ok=False)
-            assert dependent_dataset['name'].startswith('identifier_collection')
-            assert dependent_dataset['state'] == 'ok'
+            dependent_dataset = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=8, wait=True, assert_ok=False
+            )
+            assert dependent_dataset["name"].startswith("identifier_collection")
+            assert dependent_dataset["state"] == "ok"
 
     @skip_without_tool("fail_identifier")
     @skip_without_tool("identifier_collection")
     def test_workflow_resume_with_mapped_over_input(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow("""
+            self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input_datasets: collection
@@ -1016,36 +1085,45 @@ test_data:
       - identifier: success
         value: 1.fastq
         type: File
-""", history_id=history_id, assert_ok=False, wait=True)
+""",
+                history_id=history_id,
+                assert_ok=False,
+                wait=True,
+            )
             history_contents = self.dataset_populator._get_contents_request(history_id=history_id).json()
             first_input = history_contents[1]
-            assert first_input['history_content_type'] == 'dataset'
+            assert first_input["history_content_type"] == "dataset"
             paused_dataset = history_contents[-1]
             failed_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, assert_ok=False)
-            assert paused_dataset['state'] == 'paused', paused_dataset
-            assert failed_dataset['state'] == 'error', failed_dataset
-            inputs = {"input1": {'values': [{'src': 'hda',
-                                             'id': first_input['id']}]
-                                 },
-                      "failbool": "false",
-                      "rerun_remap_job_id": failed_dataset['creating_job']}
+            assert paused_dataset["state"] == "paused", paused_dataset
+            assert failed_dataset["state"] == "error", failed_dataset
+            inputs = {
+                "input1": {"values": [{"src": "hda", "id": first_input["id"]}]},
+                "failbool": "false",
+                "rerun_remap_job_id": failed_dataset["creating_job"],
+            }
             run_dict = self.dataset_populator.run_tool(
-                tool_id='fail_identifier',
+                tool_id="fail_identifier",
                 inputs=inputs,
                 history_id=history_id,
             )
-            unpaused_dataset = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=False)
-            assert unpaused_dataset['state'] == 'ok'
+            unpaused_dataset = self.dataset_populator.get_history_dataset_details(
+                history_id, wait=True, assert_ok=False
+            )
+            assert unpaused_dataset["state"] == "ok"
             contents = self.dataset_populator.get_history_dataset_content(history_id, hid=7, assert_ok=False)
-            assert contents == 'fail\nsuccess\n', contents
-            replaced_hda_id = run_dict['outputs'][0]['id']
-            replaced_hda = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=replaced_hda_id, wait=True, assert_ok=False)
-            assert not replaced_hda['visible'], replaced_hda
+            assert contents == "fail\nsuccess\n", contents
+            replaced_hda_id = run_dict["outputs"][0]["id"]
+            replaced_hda = self.dataset_populator.get_history_dataset_details(
+                history_id, dataset_id=replaced_hda_id, wait=True, assert_ok=False
+            )
+            assert not replaced_hda["visible"], replaced_hda
 
     def test_workflow_resume_with_mapped_over_collection_input(self):
         # Test that replacement and resume also works if the failed job re-run works on a input DCE
         with self.dataset_populator.test_history() as history_id:
-            job_summary = self._run_workflow("""
+            job_summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input_collection: collection
@@ -1065,43 +1143,60 @@ steps:
 test_data:
   input_collection:
     collection_type: "list:list:paired"
-""", history_id=history_id, assert_ok=False, wait=True)
+""",
+                history_id=history_id,
+                assert_ok=False,
+                wait=True,
+            )
             invocation = self.workflow_populator.get_invocation(job_summary.invocation_id, step_details=True)
             # TODO: return steps sorted by order_index ? Why don't we do that ??
-            invocation['steps'].sort(key=lambda step: step['order_index'])
-            failed_step = invocation['steps'][1]
-            assert failed_step['jobs'][0]['state'] == 'error'
-            failed_hdca_id = failed_step['output_collections']['list_output']['id']
-            failed_hdca = self.dataset_populator.get_history_collection_details(history_id=history_id, content_id=failed_hdca_id, assert_ok=False)
-            assert failed_hdca['elements'][0]['object']['elements'][0]['object']['elements'][0]['object']['state'] == 'error'
-            paused_step = invocation['steps'][2]
+            invocation["steps"].sort(key=lambda step: step["order_index"])
+            failed_step = invocation["steps"][1]
+            assert failed_step["jobs"][0]["state"] == "error"
+            failed_hdca_id = failed_step["output_collections"]["list_output"]["id"]
+            failed_hdca = self.dataset_populator.get_history_collection_details(
+                history_id=history_id, content_id=failed_hdca_id, assert_ok=False
+            )
+            assert (
+                failed_hdca["elements"][0]["object"]["elements"][0]["object"]["elements"][0]["object"]["state"]
+                == "error"
+            )
+            paused_step = invocation["steps"][2]
             # job not created, input in error state
-            assert paused_step['jobs'][0]['state'] == 'paused'
-            input_hdca = self.dataset_populator.get_history_collection_details(history_id=history_id, content_id=job_summary.inputs['input_collection']['id'], assert_ok=False)
+            assert paused_step["jobs"][0]["state"] == "paused"
+            input_hdca = self.dataset_populator.get_history_collection_details(
+                history_id=history_id, content_id=job_summary.inputs["input_collection"]["id"], assert_ok=False
+            )
             # now re-run errored job
-            inputs = {"input1": {'values': [{'src': 'dce',
-                                             'id': input_hdca['elements'][0]['id']}]
-                                 },
-                      "failbool": "false",
-                      "rerun_remap_job_id": failed_step['jobs'][0]['id']}
+            inputs = {
+                "input1": {"values": [{"src": "dce", "id": input_hdca["elements"][0]["id"]}]},
+                "failbool": "false",
+                "rerun_remap_job_id": failed_step["jobs"][0]["id"],
+            }
             run_response = self.dataset_populator.run_tool(
-                tool_id='collection_creates_list_of_pairs',
+                tool_id="collection_creates_list_of_pairs",
                 inputs=inputs,
                 history_id=history_id,
             )
             assert not run_response["output_collections"][0]["visible"]
-            self.dataset_populator.wait_for_job(paused_step['jobs'][0]['id'])
+            self.dataset_populator.wait_for_job(paused_step["jobs"][0]["id"])
             invocation = self.workflow_populator.get_invocation(job_summary.invocation_id, step_details=True)
-            rerun_step = invocation['steps'][1]
-            assert rerun_step['jobs'][0]['state'] == 'ok'
-            replaced_hdca = self.dataset_populator.get_history_collection_details(history_id=history_id, content_id=failed_hdca_id, assert_ok=False)
-            assert replaced_hdca['elements'][0]['object']['elements'][0]['object']['elements'][0]['object']['state'] == 'ok'
+            rerun_step = invocation["steps"][1]
+            assert rerun_step["jobs"][0]["state"] == "ok"
+            replaced_hdca = self.dataset_populator.get_history_collection_details(
+                history_id=history_id, content_id=failed_hdca_id, assert_ok=False
+            )
+            assert (
+                replaced_hdca["elements"][0]["object"]["elements"][0]["object"]["elements"][0]["object"]["state"]
+                == "ok"
+            )
 
-    @skip_without_tool('multi_data_optional')
+    @skip_without_tool("multi_data_optional")
     def test_workflow_list_list_multi_data_map_over(self):
         # Test that a list:list is reduced to list with a multiple="true" data input
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input_datasets: collection
@@ -1110,32 +1205,37 @@ steps:
     tool_id: multi_data_optional
     in:
       input1: input_datasets
-""")
+"""
+            )
             with self.dataset_populator.test_history() as history_id:
                 hdca_id = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
                 self.dataset_populator.wait_for_history(history_id, assert_ok=True)
                 inputs = {
-                    '0': self._ds_entry(hdca_id),
+                    "0": self._ds_entry(hdca_id),
                 }
                 invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
                 self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
                 output_collection = self.dataset_populator.get_history_collection_details(history_id, hid=6)
-                assert output_collection['collection_type'] == 'list'
-                assert output_collection['job_source_type'] == 'ImplicitCollectionJobs'
+                assert output_collection["collection_type"] == "list"
+                assert output_collection["job_source_type"] == "ImplicitCollectionJobs"
 
     @skip_without_tool("cat_list")
     @skip_without_tool("collection_creates_pair")
     def test_workflow_run_output_collection_mapping(self):
         workflow_id = self._upload_yaml_workflow(WORKFLOW_WITH_OUTPUT_COLLECTION_MAPPING)
         with self.dataset_populator.test_history() as history_id:
-            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]).json()
+            hdca1 = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]
+            ).json()
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                '0': self._ds_entry(hdca1),
+                "0": self._ds_entry(hdca1),
             }
             invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
             self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
-            self.assertEqual("a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0))
+            self.assertEqual(
+                "a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0)
+            )
 
     @skip_without_tool("cat_list")
     @skip_without_tool("collection_split_on_column")
@@ -1154,7 +1254,8 @@ steps:
         # A more advanced output collection workflow, testing regression of
         # https://github.com/galaxyproject/galaxy/issues/776
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   test_input_1: data
@@ -1170,15 +1271,16 @@ steps:
     in:
       queries_0|input: test_input_1
       queries2_0|input2: split_up/split_output
-""")
+"""
+            )
             hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
             hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
             hda3 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t60.0\n")
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                '0': self._ds_entry(hda1),
-                '1': self._ds_entry(hda2),
-                '2': self._ds_entry(hda3),
+                "0": self._ds_entry(hda1),
+                "1": self._ds_entry(hda2),
+                "2": self._ds_entry(hda3),
             }
             invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
             self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
@@ -1192,7 +1294,8 @@ steps:
     def test_workflow_run_dynamic_output_collections_3(self):
         # Test a workflow that create a list:list:list followed by a mapping step.
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input1: data
@@ -1215,13 +1318,14 @@ steps:
     tool_id: cat
     in:
       input1: split_up_2/split_output
-""")
+"""
+            )
             hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
             hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t40.0\n")
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                '0': self._ds_entry(hda1),
-                '1': self._ds_entry(hda2),
+                "0": self._ds_entry(hda1),
+                "1": self._ds_entry(hda2),
             }
             invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
             self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
@@ -1239,11 +1343,12 @@ steps:
             assert current["tag"] == tag_test[count]
             count += 1
 
-    @skip_without_tool('column_param')
+    @skip_without_tool("column_param")
     def test_empty_file_data_column_specified(self):
         # Regression test for https://github.com/galaxyproject/galaxy/pull/10981
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""class: GalaxyWorkflow
+            self._run_jobs(
+                """class: GalaxyWorkflow
 steps:
   empty_output:
     tool_id: empty_output
@@ -1257,13 +1362,16 @@ steps:
     state:
       col: 2
       col_names: 'B'
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
-    @skip_without_tool('column_param_list')
+    @skip_without_tool("column_param_list")
     def test_comma_separated_columns(self):
         # Regression test for https://github.com/galaxyproject/galaxy/pull/10981
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""class: GalaxyWorkflow
+            self._run_jobs(
+                """class: GalaxyWorkflow
 steps:
   empty_output:
     tool_id: empty_output
@@ -1277,12 +1385,15 @@ steps:
     state:
       col: '2,3'
       col_names: 'B'
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
-    @skip_without_tool('column_param')
+    @skip_without_tool("column_param")
     def test_runtime_data_column_parameter(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""class: GalaxyWorkflow
+            self._run_jobs(
+                """class: GalaxyWorkflow
 inputs:
     bed_input: data
 steps:
@@ -1306,7 +1417,9 @@ test_data:
     value: 1.bed
     file_type: bed
     type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
     @skip_without_tool("mapper")
     @skip_without_tool("pileup")
@@ -1314,7 +1427,8 @@ test_data:
         # Testing regression of
         # https://github.com/galaxyproject/galaxy/issues/1514
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input_fastqs: collection
@@ -1343,25 +1457,40 @@ test_data:
   reference:
     value: 1.fasta
     type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
     def test_run_subworkflow_simple(self) -> None:
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_workflow(WORKFLOW_NESTED_SIMPLE, test_data="""
+            summary = self._run_workflow(
+                WORKFLOW_NESTED_SIMPLE,
+                test_data="""
 outer_input:
   value: 1.bed
   type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             invocation_id = summary.invocation_id
 
             content = self.dataset_populator.get_history_dataset_content(history_id)
-            self.assertEqual("chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", content)
-            steps = self.workflow_populator.get_invocation(invocation_id)['steps']
-            assert sum(1 for step in steps if step['subworkflow_invocation_id'] is None) == 3
-            subworkflow_invocation_id = [step['subworkflow_invocation_id'] for step in steps if step['subworkflow_invocation_id']][0]
+            self.assertEqual(
+                "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
+                content,
+            )
+            steps = self.workflow_populator.get_invocation(invocation_id)["steps"]
+            assert sum(1 for step in steps if step["subworkflow_invocation_id"] is None) == 3
+            subworkflow_invocation_id = [
+                step["subworkflow_invocation_id"] for step in steps if step["subworkflow_invocation_id"]
+            ][0]
             subworkflow_invocation = self.workflow_populator.get_invocation(subworkflow_invocation_id)
-            assert [step for step in subworkflow_invocation['steps'] if step['order_index'] == 0][0]['workflow_step_label'] == 'inner_input'
-            assert [step for step in subworkflow_invocation['steps'] if step['order_index'] == 1][0]['workflow_step_label'] == 'random_lines'
+            assert [step for step in subworkflow_invocation["steps"] if step["order_index"] == 0][0][
+                "workflow_step_label"
+            ] == "inner_input"
+            assert [step for step in subworkflow_invocation["steps"] if step["order_index"] == 1][0][
+                "workflow_step_label"
+            ] == "random_lines"
 
             bco = self.workflow_populator.get_biocompute_object(invocation_id)
             self.workflow_populator.validate_biocompute_object(bco)
@@ -1369,14 +1498,18 @@ outer_input:
     @skip_without_tool("random_lines1")
     def test_run_subworkflow_runtime_parameters(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_NESTED_RUNTIME_PARAMETER, test_data="""
+            self._run_jobs(
+                WORKFLOW_NESTED_RUNTIME_PARAMETER,
+                test_data="""
 step_parameters:
   '1':
     '1|num_lines': 2
 outer_input:
   value: 1.bed
   type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert len([x for x in content.split("\n") if x]) == 2
@@ -1474,7 +1607,7 @@ test_data:
 
             # Wait for the workflow to finish scheduling and ensure both the invocation
             # and the history are in valid states.
-            invocation_scheduled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, 'scheduled')
+            invocation_scheduled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, "scheduled")
             assert invocation_scheduled, "Workflow state is not scheduled..."
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
 
@@ -1496,7 +1629,8 @@ test_data:
                 content = self.dataset_populator.get_history_dataset_content(history_id)
                 self.assertEqual(
                     "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
-                    content)
+                    content,
+                )
 
         run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX)
 
@@ -1504,7 +1638,8 @@ test_data:
     @skip_without_tool("collection_paired_test")
     def test_workflow_run_zip_collections(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   test_input_1: data
@@ -1523,13 +1658,14 @@ steps:
     tool_id: collection_paired_test
     in:
       f1: zip_it/output
-""")
+"""
+            )
             hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
             hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                '0': self._ds_entry(hda1),
-                '1': self._ds_entry(hda2),
+                "0": self._ds_entry(hda1),
+                "1": self._ds_entry(hda2),
             }
             invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
             self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
@@ -1539,7 +1675,8 @@ steps:
     @skip_without_tool("collection_paired_test")
     def test_workflow_flatten(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 steps:
   nested:
@@ -1553,18 +1690,22 @@ steps:
       input:
         $link: nested/list_output
       join_identifier: '-'
-""", test_data={}, history_id=history_id)
+""",
+                test_data={},
+                history_id=history_id,
+            )
             details = self.dataset_populator.get_history_collection_details(history_id, hid=14)
-            assert details['collection_type'] == "list"
+            assert details["collection_type"] == "list"
             elements = details["elements"]
-            identifiers = [e['element_identifier'] for e in elements]
+            identifiers = [e["element_identifier"] for e in elements]
             assert len(identifiers) == 6
             assert "oe1-ie1" in identifiers
 
     @skip_without_tool("collection_paired_test")
     def test_workflow_flatten_with_mapped_over_execution(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(r"""
+            self._run_jobs(
+                r"""
 class: GalaxyWorkflow
 inputs:
   input_fastqs: collection
@@ -1584,17 +1725,19 @@ test_data:
     elements:
       - identifier: samp1
         content: "0\n1"
-""", history_id=history_id)
-            history = self._get(f'histories/{history_id}/contents').json()
+""",
+                history_id=history_id,
+            )
+            history = self._get(f"histories/{history_id}/contents").json()
             flattened_collection = history[-1]
-            assert flattened_collection['history_content_type'] == 'dataset_collection'
-            assert flattened_collection['collection_type'] == 'list'
-            assert flattened_collection['element_count'] == 2
+            assert flattened_collection["history_content_type"] == "dataset_collection"
+            assert flattened_collection["collection_type"] == "list"
+            assert flattened_collection["element_count"] == 2
             nested_collection = self.dataset_populator.get_history_collection_details(history_id, hid=3)
-            assert nested_collection['collection_type'] == 'list:list'
-            assert nested_collection['element_count'] == 1
-            assert nested_collection['elements'][0]['object']['populated']
-            assert nested_collection['elements'][0]['object']['element_count'] == 2
+            assert nested_collection["collection_type"] == "list:list"
+            assert nested_collection["element_count"] == 1
+            assert nested_collection["elements"][0]["object"]["populated"]
+            assert nested_collection["elements"][0]["object"]["element_count"] == 2
 
     @skip_without_tool("cat")
     def test_workflow_invocation_report_1(self):
@@ -1604,7 +1747,8 @@ input_1:
   type: File
 """
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_workflow("""
+            summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input_1: data
@@ -1616,7 +1760,10 @@ steps:
     tool_id: cat
     in:
       input1: input_1
-""", test_data=test_data, history_id=history_id)
+""",
+                test_data=test_data,
+                history_id=history_id,
+            )
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
             report_json = self.workflow_populator.workflow_report_json(workflow_id, invocation_id)
@@ -1632,9 +1779,7 @@ steps:
     def test_workflow_invocation_report_custom(self):
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_workflow(
-                WORKFLOW_WITH_CUSTOM_REPORT_1,
-                test_data=WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA,
-                history_id=history_id
+                WORKFLOW_WITH_CUSTOM_REPORT_1, test_data=WORKFLOW_WITH_CUSTOM_REPORT_1_TEST_DATA, history_id=history_id
             )
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
@@ -1659,18 +1804,25 @@ steps:
             invocation_id = summary.invocation_id
             bco = self.workflow_populator.get_biocompute_object(invocation_id)
             self.workflow_populator.validate_biocompute_object(bco)
-            self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
+            self.assertEqual(bco["provenance_domain"]["name"], "Simple Workflow")
 
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow(WORKFLOW_WITH_RULES_1, history_id=history_id, wait=True, assert_ok=True, round_trip_format_conversion=True)
+            self._run_workflow(
+                WORKFLOW_WITH_RULES_1,
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+                round_trip_format_conversion=True,
+            )
             output_content = self.dataset_populator.get_history_collection_details(history_id, hid=6)
             rules_test_data.check_example_2(output_content, self.dataset_populator)
 
     def test_filter_failed_mapping(self):
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_workflow("""
+            summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input_c: collection
@@ -1693,7 +1845,8 @@ steps:
     state:
       input1:
         $link: filtered_collection
-""", test_data="""
+""",
+                test_data="""
 input_c:
   collection_type: list
   elements:
@@ -1701,7 +1854,11 @@ input_c:
       content: "0"
     - identifier: i2
       content: "1"
-""", history_id=history_id, wait=True, assert_ok=False)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=False,
+            )
             jobs = summary.jobs
 
             def filter_jobs_by_tool(tool_id):
@@ -1716,15 +1873,21 @@ input_c:
     def test_workflow_request(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_queue")
         workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow)
-        run_workflow_response = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request, assert_ok=True)
+        run_workflow_response = self.workflow_populator.invoke_workflow_raw(
+            workflow_id, workflow_request, assert_ok=True
+        )
         invocation_id = run_workflow_response.json()["id"]
         self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
 
     def test_workflow_new_autocreated_history(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_new_autocreated_history")
         workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow)
-        del workflow_request['history']  # Not passing a history param means asking for a new history to be automatically created
-        run_workflow_dict = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request, assert_ok=True).json()
+        del workflow_request[
+            "history"
+        ]  # Not passing a history param means asking for a new history to be automatically created
+        run_workflow_dict = self.workflow_populator.invoke_workflow_raw(
+            workflow_id, workflow_request, assert_ok=True
+        ).json()
         new_history_id = run_workflow_dict["history_id"]
         assert history_id != new_history_id
         invocation_id = run_workflow_dict["id"]
@@ -1741,7 +1904,9 @@ input_c:
             self._assert_has_keys(invocation, "id", "outputs", "output_collections")
             assert len(invocation["output_collections"]) == 0
             assert len(invocation["outputs"]) == 1
-            output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=invocation["outputs"]["wf_output_1"]["id"])
+            output_content = self.dataset_populator.get_history_dataset_content(
+                history_id, dataset_id=invocation["outputs"]["wf_output_1"]["id"]
+            )
             assert "hello world" == output_content.strip()
 
     @skip_without_tool("cat")
@@ -1756,7 +1921,9 @@ input_c:
             self._assert_has_keys(invocation, "id", "outputs", "output_collections")
             assert len(invocation["output_collections"]) == 1
             assert len(invocation["outputs"]) == 0
-            output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
+            output_content = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"]
+            )
             self._assert_has_keys(output_content, "id", "elements")
             assert output_content["collection_type"] == "list"
             elements = output_content["elements"]
@@ -1765,7 +1932,8 @@ input_c:
             assert elements0["element_identifier"] == "el1"
 
     def _run_workflow_with_output_collections(self, history_id) -> RunJobsSummary:
-        summary = self._run_workflow("""
+        summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -1779,7 +1947,8 @@ steps:
     tool_id: cat
     in:
       input1: input1
-""", test_data="""
+""",
+            test_data="""
 input1:
   collection_type: list
   name: the_dataset_list
@@ -1787,11 +1956,15 @@ input1:
     - identifier: el1
       value: 1.fastq
       type: File
-""", history_id=history_id, round_trip_format_conversion=True)
+""",
+            history_id=history_id,
+            round_trip_format_conversion=True,
+        )
         return summary
 
     def _run_workflow_with_inputs_as_outputs(self, history_id) -> RunJobsSummary:
-        summary = self._run_workflow("""
+        summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -1802,7 +1975,10 @@ outputs:
   wf_output_param:
     outputSource: text_input
 steps: []
-""", test_data={"input1": "hello world", "text_input": {"value": "A text variable", "type": "raw"}}, history_id=history_id)
+""",
+            test_data={"input1": "hello world", "text_input": {"value": "A text variable", "type": "raw"}},
+            history_id=history_id,
+        )
         return summary
 
     def test_workflow_input_as_output(self):
@@ -1819,12 +1995,15 @@ steps: []
             assert len(invocation["output_values"]) == 1
             assert "wf_output_param" in invocation["output_values"]
             assert invocation["output_values"]["wf_output_param"] == "A text variable", invocation["output_values"]
-            output_content = self.dataset_populator.get_history_dataset_content(history_id, content_id=invocation["outputs"]["wf_output_1"]["id"])
+            output_content = self.dataset_populator.get_history_dataset_content(
+                history_id, content_id=invocation["outputs"]["wf_output_1"]["id"]
+            )
             assert output_content == "hello world\n"
 
     def test_subworkflow_output_as_output(self):
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_workflow("""
+            summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -1843,7 +2022,10 @@ steps:
       steps: []
     in:
       inner_input: input1
-""", test_data={"input1": "hello world"}, history_id=history_id)
+""",
+                test_data={"input1": "hello world"},
+                history_id=history_id,
+            )
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
             invocation_response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}")
@@ -1852,13 +2034,16 @@ steps:
             self._assert_has_keys(invocation, "id", "outputs", "output_collections")
             assert len(invocation["output_collections"]) == 0
             assert len(invocation["outputs"]) == 1
-            output_content = self.dataset_populator.get_history_dataset_content(history_id, content_id=invocation["outputs"]["wf_output_1"]["id"])
+            output_content = self.dataset_populator.get_history_dataset_content(
+                history_id, content_id=invocation["outputs"]["wf_output_1"]["id"]
+            )
             assert output_content == "hello world\n"
 
     @skip_without_tool("cat")
     def test_workflow_input_mapping(self):
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_workflow("""
+            summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -1870,7 +2055,8 @@ steps:
     tool_id: cat
     in:
       input1: input1
-""", test_data="""
+""",
+                test_data="""
 input1:
   collection_type: list
   name: the_dataset_list
@@ -1881,7 +2067,9 @@ input1:
     - identifier: el2
       value: 1.fastq
       type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
             invocation_response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}")
@@ -1890,7 +2078,9 @@ input1:
             self._assert_has_keys(invocation, "id", "outputs", "output_collections")
             assert len(invocation["output_collections"]) == 1
             assert len(invocation["outputs"]) == 0
-            output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
+            output_content = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"]
+            )
             self._assert_has_keys(output_content, "id", "elements")
             elements = output_content["elements"]
             assert len(elements) == 2
@@ -1900,7 +2090,8 @@ input1:
     @skip_without_tool("collection_creates_pair")
     def test_workflow_run_input_mapping_with_output_collections(self):
         with self.dataset_populator.test_history() as history_id:
-            summary = self._run_workflow("""
+            summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input: data
@@ -1912,7 +2103,8 @@ steps:
     tool_id: collection_creates_pair
     in:
       input1: text_input
-""", test_data="""
+""",
+                test_data="""
 text_input:
   collection_type: list
   name: the_dataset_list
@@ -1923,7 +2115,9 @@ text_input:
     - identifier: el2
       value: 1.fastq
       type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             workflow_id = summary.workflow_id
             invocation_id = summary.invocation_id
             invocation_response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}")
@@ -1932,7 +2126,9 @@ text_input:
             self._assert_has_keys(invocation, "id", "outputs", "output_collections")
             assert len(invocation["output_collections"]) == 1
             assert len(invocation["outputs"]) == 0
-            output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"])
+            output_content = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=invocation["output_collections"]["wf_output_1"]["id"]
+            )
             self._assert_has_keys(output_content, "id", "elements")
             assert output_content["collection_type"] == "list:paired", output_content
             elements = output_content["elements"]
@@ -1945,24 +2141,24 @@ text_input:
             jobs_summary_response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary")
             self._assert_status_code_is(jobs_summary_response, 200)
             jobs_summary = jobs_summary_response.json()
-            assert 'states' in jobs_summary
+            assert "states" in jobs_summary
 
-            invocation_states = jobs_summary['states']
-            assert invocation_states and 'ok' in invocation_states, jobs_summary
-            assert invocation_states['ok'] == 2, jobs_summary
-            assert jobs_summary['model'] == 'WorkflowInvocation', jobs_summary
+            invocation_states = jobs_summary["states"]
+            assert invocation_states and "ok" in invocation_states, jobs_summary
+            assert invocation_states["ok"] == 2, jobs_summary
+            assert jobs_summary["model"] == "WorkflowInvocation", jobs_summary
 
             jobs_summary_response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary")
             self._assert_status_code_is(jobs_summary_response, 200)
             jobs_summary = jobs_summary_response.json()
             assert len(jobs_summary) == 1
             collection_summary = jobs_summary[0]
-            assert 'states' in collection_summary
+            assert "states" in collection_summary
 
-            collection_states = collection_summary['states']
-            assert collection_states and 'ok' in collection_states, collection_states
-            assert collection_states['ok'] == 2, collection_summary
-            assert collection_summary['model'] == 'ImplicitCollectionJobs', collection_summary
+            collection_states = collection_summary["states"]
+            assert collection_states and "ok" in collection_states, collection_states
+            assert collection_states["ok"] == 2, collection_summary
+            assert collection_summary["model"] == "ImplicitCollectionJobs", collection_summary
 
     def test_workflow_run_input_mapping_with_subworkflows(self):
         with self.dataset_populator.test_history() as history_id:
@@ -1989,7 +2185,9 @@ outer_input:
             self._assert_has_keys(invocation, "id", "outputs", "output_collections")
             assert len(invocation["output_collections"]) == 1, invocation
             assert len(invocation["outputs"]) == 0
-            output_content = self.dataset_populator.get_history_collection_details(history_id, content_id=invocation["output_collections"]["outer_output"]["id"])
+            output_content = self.dataset_populator.get_history_collection_details(
+                history_id, content_id=invocation["output_collections"]["outer_output"]["id"]
+            )
             self._assert_has_keys(output_content, "id", "elements")
             assert output_content["collection_type"] == "list", output_content
             elements = output_content["elements"]
@@ -2006,7 +2204,8 @@ outer_input:
         # evaluation. Testing rescheduling and propagating connections within a subworkflow
         # is handled by the next test case.
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow("""
+            self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -2051,8 +2250,15 @@ test_data:
   outer_input:
     value: 1.bed
     type: File
-""", history_id=history_id, wait=True, round_trip_format_conversion=True)
-            self.assertEqual("chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
+""",
+                history_id=history_id,
+                wait=True,
+                round_trip_format_conversion=True,
+            )
+            self.assertEqual(
+                "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
+                self.dataset_populator.get_history_dataset_content(history_id),
+            )
             # self.assertEqual("chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
 
     @skip_without_tool("cat_list")
@@ -2064,7 +2270,8 @@ test_data:
         # delayed, but this also tests recovering and handling scheduling within the subworkflow
         # since the delayed step (split) isn't the last step of the subworkflow.
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -2109,19 +2316,28 @@ steps:
     tool_id: cat_list
     in:
       input1: nested_workflow/workflow_output
-""", test_data="""
+""",
+                test_data="""
 outer_input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, round_trip_format_conversion=True)
-            self.assertEqual("chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
+""",
+                history_id=history_id,
+                wait=True,
+                round_trip_format_conversion=True,
+            )
+            self.assertEqual(
+                "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
+                self.dataset_populator.get_history_dataset_content(history_id),
+            )
 
     @skip_without_tool("cat_list")
     @skip_without_tool("random_lines1")
     @skip_without_tool("split")
     def test_recover_mapping_in_subworkflow(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -2161,19 +2377,28 @@ steps:
     tool_id: cat_list
     in:
       input1: nested_workflow/workflow_output
-""", test_data="""
+""",
+                test_data="""
 outer_input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, round_trip_format_conversion=True)
-            self.assertEqual("chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id))
+""",
+                history_id=history_id,
+                wait=True,
+                round_trip_format_conversion=True,
+            )
+            self.assertEqual(
+                "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
+                self.dataset_populator.get_history_dataset_content(history_id),
+            )
 
     @skip_without_tool("empty_list")
     @skip_without_tool("count_list")
     @skip_without_tool("random_lines1")
     def test_empty_list_mapping(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -2198,17 +2423,22 @@ steps:
     tool_id: count_list
     in:
       input1: random_lines/out_file1
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True)
+""",
+                history_id=history_id,
+                wait=True,
+            )
             self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id))
 
     @skip_without_tool("random_lines1")
     def test_change_datatype_collection_map_over(self):
         with self.dataset_populator.test_history() as history_id:
-            jobs_summary = self._run_workflow("""
+            jobs_summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input1: collection
@@ -2220,21 +2450,25 @@ steps:
     outputs:
         out_file1:
           change_datatype: csv
-""", test_data="""
+""",
+                test_data="""
 text_input1:
   collection_type: "list:paired"
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             hdca = self.dataset_populator.get_history_collection_details(history_id=jobs_summary.history_id, hid=4)
-            assert hdca['collection_type'] == 'list:paired'
-            assert len(hdca['elements'][0]['object']["elements"]) == 2
-            forward, reverse = hdca['elements'][0]['object']["elements"]
-            assert forward['object']['file_ext'] == 'csv'
-            assert reverse['object']['file_ext'] == 'csv'
+            assert hdca["collection_type"] == "list:paired"
+            assert len(hdca["elements"][0]["object"]["elements"]) == 2
+            forward, reverse = hdca["elements"][0]["object"]["elements"]
+            assert forward["object"]["file_ext"] == "csv"
+            assert reverse["object"]["file_ext"] == "csv"
 
     @skip_without_tool("collection_type_source_map_over")
     def test_mapping_and_subcollection_mapping(self):
         with self.dataset_populator.test_history() as history_id:
-            jobs_summary = self._run_workflow("""
+            jobs_summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input1: collection
@@ -2243,20 +2477,24 @@ steps:
     tool_id: collection_type_source_map_over
     in:
       input_collect: text_input1
-""", test_data="""
+""",
+                test_data="""
 text_input1:
   collection_type: "list:paired"
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             hdca = self.dataset_populator.get_history_collection_details(history_id=jobs_summary.history_id, hid=1)
-            assert hdca['collection_type'] == 'list:paired'
-            assert len(hdca['elements'][0]['object']["elements"]) == 2
+            assert hdca["collection_type"] == "list:paired"
+            assert len(hdca["elements"][0]["object"]["elements"]) == 2
 
     @skip_without_tool("empty_list")
     @skip_without_tool("count_multi_file")
     @skip_without_tool("random_lines1")
     def test_empty_list_reduction(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow("""
+            self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -2281,11 +2519,16 @@ steps:
     tool_id: count_multi_file
     in:
       input1: random_lines/out_file1
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, round_trip_format_conversion=True)
+""",
+                history_id=history_id,
+                wait=True,
+                round_trip_format_conversion=True,
+            )
             self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id))
 
     @skip_without_tool("cat")
@@ -2304,7 +2547,7 @@ input1:
 
             self._delete(f"histories/{history_id}")
 
-            invocation_cancelled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, 'cancelled')
+            invocation_cancelled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, "cancelled")
             assert invocation_cancelled, "Workflow state is not cancelled..."
 
     @skip_without_tool("cat")
@@ -2324,7 +2567,7 @@ input1:
 
             self._delete(f"histories/{history_id}")
 
-            invocation_cancelled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, 'cancelled')
+            invocation_cancelled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, "cancelled")
             assert invocation_cancelled, "Workflow state is not cancelled..."
 
     @skip_without_tool("cat")
@@ -2348,7 +2591,7 @@ input1:
 
             # Wait for the workflow to finish scheduling and ensure both the invocation
             # and the history are in valid states.
-            invocation_scheduled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, 'scheduled')
+            invocation_scheduled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, "scheduled")
             assert invocation_scheduled, "Workflow state is not scheduled..."
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
 
@@ -2372,7 +2615,7 @@ input1:
             self.__review_paused_steps(uploaded_workflow_id, invocation_id, order_index=2, action=False)
 
             # Ensure the workflow eventually becomes cancelled.
-            invocation_cancelled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, 'cancelled')
+            invocation_cancelled = self._wait_for_invocation_state(uploaded_workflow_id, invocation_id, "cancelled")
             assert invocation_cancelled, "Workflow state is not cancelled..."
 
     @skip_without_tool("head")
@@ -2381,10 +2624,12 @@ input1:
             workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_map_reduce_pause")
             uploaded_workflow_id = self.workflow_populator.create_workflow(workflow)
             hda1 = self.dataset_populator.new_dataset(history_id, content="reviewed\nunreviewed")
-            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=["1\n2\n3", "4\n5\n6"]).json()
+            hdca1 = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["1\n2\n3", "4\n5\n6"]
+            ).json()
             index_map = {
-                '0': self._ds_entry(hda1),
-                '1': self._ds_entry(hdca1),
+                "0": self._ds_entry(hda1),
+                "1": self._ds_entry(hdca1),
             }
             invocation_id = self.__invoke_workflow(uploaded_workflow_id, inputs=index_map, history_id=history_id)
 
@@ -2401,8 +2646,10 @@ input1:
             self.__review_paused_steps(uploaded_workflow_id, invocation_id, order_index=4, action=True)
             self.workflow_populator.wait_for_invocation_and_jobs(history_id, uploaded_workflow_id, invocation_id)
             invocation = self._invocation_details(uploaded_workflow_id, invocation_id)
-            assert invocation['state'] == 'scheduled'
-            self.assertEqual("reviewed\n1\nreviewed\n4\n", self.dataset_populator.get_history_dataset_content(history_id))
+            assert invocation["state"] == "scheduled"
+            self.assertEqual(
+                "reviewed\n1\nreviewed\n4\n", self.dataset_populator.get_history_dataset_content(history_id)
+            )
 
     @skip_without_tool("cat")
     def test_cancel_workflow_invocation(self):
@@ -2425,7 +2672,7 @@ input1:
             self._assert_status_code_is(delete_response, 200)
 
             invocation = self._invocation_details(uploaded_workflow_id, invocation_id)
-            assert invocation['state'] == 'cancelled'
+            assert invocation["state"] == "cancelled"
 
     @skip_without_tool("cat")
     def test_pause_outputs_with_deleted_inputs(self):
@@ -2438,7 +2685,8 @@ input1:
     def _deleted_inputs_workflow(self, purge):
         # We run a workflow on a collection with a deleted element.
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -2453,14 +2701,16 @@ steps:
     tool_id: cat
     in:
       input1: first_cat/out_file1
-""")
+"""
+            )
             DELETED = 0
             PAUSED_1 = 3
             PAUSED_2 = 5
-            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id,
-                                                                             contents=[("sample1-1", "1 2 3")]).json()
+            hdca1 = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("sample1-1", "1 2 3")]
+            ).json()
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-            deleted_id = hdca1['elements'][DELETED]['object']['id']
+            deleted_id = hdca1["elements"][DELETED]["object"]["id"]
             r = self._delete(f"histories/{history_id}/contents/{deleted_id}?purge={purge}")
             label_map = {"input1": self._ds_entry(hdca1)}
             workflow_request = dict(
@@ -2472,19 +2722,22 @@ steps:
             invocation_id = r.json()["id"]
             # If this starts failing we may have prevented running workflows on collections with deleted members,
             # in which case we can disable this test.
-            self.workflow_populator.wait_for_invocation_and_jobs(workflow_id, history_id, invocation_id, assert_ok=False)
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                workflow_id, history_id, invocation_id, assert_ok=False
+            )
             # Why is this sleep needed? -John
             if not purge:
                 time.sleep(5)
             contents = self.__history_contents(history_id)
-            assert contents[DELETED]['deleted']
-            state = 'error' if purge else 'paused'
-            assert contents[PAUSED_1]['state'] == state
-            assert contents[PAUSED_2]['state'] == 'paused'
+            assert contents[DELETED]["deleted"]
+            state = "error" if purge else "paused"
+            assert contents[PAUSED_1]["state"] == state
+            assert contents[PAUSED_2]["state"] == "paused"
 
     def test_run_with_implicit_connection(self):
         with self.dataset_populator.test_history() as history_id:
-            run_summary = self._run_workflow("""
+            run_summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -2512,7 +2765,12 @@ steps:
       seed_source:
         seed_source_selector: set_seed
         seed: asdf
-""", test_data={"test_input": "hello world"}, history_id=history_id, wait=False, round_trip_format_conversion=True)
+""",
+                test_data={"test_input": "hello world"},
+                history_id=history_id,
+                wait=False,
+                round_trip_format_conversion=True,
+            )
             history_id = run_summary.history_id
             workflow_id = run_summary.workflow_id
             invocation_id = run_summary.invocation_id
@@ -2520,7 +2778,7 @@ steps:
             wait_on(lambda: len(self._history_jobs(history_id)) >= 2 or None, "history jobs")
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             invocation = self._invocation_details(workflow_id, invocation_id)
-            assert invocation['state'] != 'scheduled', invocation
+            assert invocation["state"] != "scheduled", invocation
             # Expect two jobs - the upload and first cat. randomlines shouldn't run
             # it is implicitly dependent on second cat.
             self._assert_history_job_count(history_id, 2)
@@ -2531,28 +2789,45 @@ steps:
 
     def test_run_with_optional_data_specified_to_multi_data(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_DATA, test_data="""
+            self._run_workflow(
+                WORKFLOW_OPTIONAL_TRUE_INPUT_DATA,
+                test_data="""
 input1:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+            )
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert "CCDS989.1_cds_0_0_chr1_147962193_r" in content
 
     def test_run_with_optional_data_unspecified_to_multi_data(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_OPTIONAL_TRUE_INPUT_DATA, test_data={}, history_id=history_id, wait=True, assert_ok=True)
+            self._run_jobs(
+                WORKFLOW_OPTIONAL_TRUE_INPUT_DATA, test_data={}, history_id=history_id, wait=True, assert_ok=True
+            )
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert "No input selected" in content
 
     def test_run_with_non_optional_data_unspecified_fails_invocation(self):
         with self.dataset_populator.test_history() as history_id:
-            error = self._run_jobs(WORKFLOW_OPTIONAL_FALSE_INPUT_DATA, test_data={}, history_id=history_id, wait=False, assert_ok=False, expected_response=400)
+            error = self._run_jobs(
+                WORKFLOW_OPTIONAL_FALSE_INPUT_DATA,
+                test_data={},
+                history_id=history_id,
+                wait=False,
+                assert_ok=False,
+                expected_response=400,
+            )
             self._assert_failed_on_non_optional_input(error, "input1")
 
     def test_run_with_optional_collection_specified(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, test_data="""
+            self._run_jobs(
+                WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION,
+                test_data="""
 input1:
   collection_type: paired
   name: the_dataset_pair
@@ -2563,19 +2838,32 @@ input1:
     - identifier: reverse
       value: 1.fastq
       type: File
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+            )
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert "GAATTGATCAGGACATAGGACAACTGTAGGCACCAT" in content
 
     def test_run_with_optional_collection_unspecified(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, test_data={}, history_id=history_id, wait=True, assert_ok=True)
+            self._run_jobs(
+                WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, test_data={}, history_id=history_id, wait=True, assert_ok=True
+            )
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert "No input specified." in content
 
     def test_run_with_non_optional_collection_unspecified_fails_invocation(self):
         with self.dataset_populator.test_history() as history_id:
-            error = self._run_jobs(WORKFLOW_OPTIONAL_FALSE_INPUT_COLLECTION, test_data={}, history_id=history_id, wait=False, assert_ok=False, expected_response=400)
+            error = self._run_jobs(
+                WORKFLOW_OPTIONAL_FALSE_INPUT_COLLECTION,
+                test_data={},
+                history_id=history_id,
+                wait=False,
+                assert_ok=False,
+                expected_response=400,
+            )
             self._assert_failed_on_non_optional_input(error, "input1")
 
     def _assert_failed_on_non_optional_input(self, error, input_name):
@@ -2586,7 +2874,8 @@ input1:
 
     def test_run_with_validated_parameter_connection_optional(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow("""
+            self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input: text
@@ -2597,11 +2886,16 @@ steps:
       r2:
       - text:
           $link: text_input
-""", test_data="""
+""",
+                test_data="""
 text_input:
   value: "abd"
   type: raw
-""", history_id=history_id, wait=True, round_trip_format_conversion=True)
+""",
+                history_id=history_id,
+                wait=True,
+                round_trip_format_conversion=True,
+            )
             jobs = self._history_jobs(history_id)
             assert len(jobs) == 1
 
@@ -2609,37 +2903,55 @@ text_input:
         with self.dataset_populator.test_history() as history_id:
             failed = False
             try:
-                self._run_jobs(WORKFLOW_PARAMETER_INPUT_INTEGER_REQUIRED, test_data="""
+                self._run_jobs(
+                    WORKFLOW_PARAMETER_INPUT_INTEGER_REQUIRED,
+                    test_data="""
 data_input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+                    history_id=history_id,
+                    wait=True,
+                    assert_ok=True,
+                )
             except AssertionError as e:
-                assert '(int_input) is not optional' in str(e)
+                assert "(int_input) is not optional" in str(e)
                 failed = True
             assert failed
-            run_response = self._run_workflow(WORKFLOW_PARAMETER_INPUT_INTEGER_REQUIRED, test_data="""
+            run_response = self._run_workflow(
+                WORKFLOW_PARAMETER_INPUT_INTEGER_REQUIRED,
+                test_data="""
 data_input:
   value: 1.bed
   type: File
 int_input:
   value: 1
   type: raw
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+            )
             # self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert len(content.splitlines()) == 1, content
             invocation = self.workflow_populator.get_invocation(run_response.invocation_id)
-            assert invocation['input_step_parameters']['int_input']['parameter_value'] == 1
+            assert invocation["input_step_parameters"]["int_input"]["parameter_value"] == 1
 
-            run_response = self._run_workflow(WORKFLOW_PARAMETER_INPUT_INTEGER_OPTIONAL, test_data="""
+            run_response = self._run_workflow(
+                WORKFLOW_PARAMETER_INPUT_INTEGER_OPTIONAL,
+                test_data="""
 data_input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+            )
             invocation = self.workflow_populator.get_invocation(run_response.invocation_id)
             # Optional step parameter without default value will not be recorded.
-            assert 'int_input' not in invocation['input_step_parameters']
+            assert "int_input" not in invocation["input_step_parameters"]
 
     def test_run_with_int_parameter_nested(self):
         with self.dataset_populator.test_history() as history_id:
@@ -2647,29 +2959,38 @@ data_input:
             workflow_id = self.workflow_populator.create_workflow(workflow)
             hda: dict = self.dataset_populator.new_dataset(history_id, content="1 2 3")
             workflow_request = {
-                'history_id': history_id,
-                'inputs_by': 'name',
-                'inputs': json.dumps({
-                    'input_dataset': {'src': 'hda', 'id': hda['id']},
-                    'int_parameter': 1,
-                })
+                "history_id": history_id,
+                "inputs_by": "name",
+                "inputs": json.dumps(
+                    {
+                        "input_dataset": {"src": "hda", "id": hda["id"]},
+                        "int_parameter": 1,
+                    }
+                ),
             }
             self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
 
     def test_run_with_validated_parameter_connection_default_values(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_PARAMETER_INPUT_INTEGER_DEFAULT, test_data="""
+            self._run_jobs(
+                WORKFLOW_PARAMETER_INPUT_INTEGER_DEFAULT,
+                test_data="""
 data_input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+            )
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert len(content.splitlines()) == 3, content
 
     def test_run_with_validated_parameter_connection_invalid(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input: text
@@ -2680,15 +3001,21 @@ steps:
       r2:
       - text:
           $link: text_input
-""", test_data="""
+""",
+                test_data="""
 text_input:
   value: ""
   type: raw
-""", history_id=history_id, wait=True, assert_ok=False)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=False,
+            )
 
     def test_run_with_text_input_connection(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   data_input: data
@@ -2704,14 +3031,17 @@ steps:
         seed_source_selector: set_seed
         seed:
           $link: text_input
-""", test_data="""
+""",
+                test_data="""
 data_input:
   value: 1.bed
   type: File
 text_input:
   value: asdf
   type: raw
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             content = self.dataset_populator.get_history_dataset_content(history_id)
@@ -2719,7 +3049,8 @@ text_input:
 
     def test_run_with_numeric_input_connection(self):
         history_id = self.dataset_populator.new_history()
-        self._run_jobs("""
+        self._run_jobs(
+            """
 class: GalaxyWorkflow
 steps:
 - label: forty_two
@@ -2732,7 +3063,9 @@ steps:
     inttest:
       $link: forty_two/out1
 test_data: {}
-""", history_id=history_id)
+""",
+            history_id=history_id,
+        )
 
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         content = self.dataset_populator.get_history_dataset_content(history_id)
@@ -2742,12 +3075,13 @@ test_data: {}
         str_4point14 = lines[2]
         assert lines[3] == ""
         assert int(str_43) == 43
-        assert abs(float(str_4point14) - 4.14) < .0001
+        assert abs(float(str_4point14) - 4.14) < 0.0001
 
     @skip_without_tool("param_value_from_file")
     def test_expression_tool_map_over(self):
         history_id = self.dataset_populator.new_history()
-        self._run_jobs("""
+        self._run_jobs(
+            """
 class: GalaxyWorkflow
 inputs:
   text_input1: collection
@@ -2771,23 +3105,34 @@ test_data:
         content: A
       - identifier: B
         content: B
-""", history_id=history_id)
-        history_contents = self._get(f'histories/{history_id}/contents').json()
-        collection = [c for c in history_contents if c['history_content_type'] == 'dataset_collection' and c['name'] == 'replaced_param_collection'][0]
-        collection_details = self._get(collection['url']).json()
-        assert collection_details['element_count'] == 2
-        elements = collection_details['elements']
-        assert elements[0]['element_identifier'] == 'A'
-        assert elements[1]['element_identifier'] == 'B'
-        element_a_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=elements[0]['object'])
-        element_b_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=elements[1]['object'])
-        assert element_a_content.strip() == 'A'
-        assert element_b_content.strip() == 'B'
+""",
+            history_id=history_id,
+        )
+        history_contents = self._get(f"histories/{history_id}/contents").json()
+        collection = [
+            c
+            for c in history_contents
+            if c["history_content_type"] == "dataset_collection" and c["name"] == "replaced_param_collection"
+        ][0]
+        collection_details = self._get(collection["url"]).json()
+        assert collection_details["element_count"] == 2
+        elements = collection_details["elements"]
+        assert elements[0]["element_identifier"] == "A"
+        assert elements[1]["element_identifier"] == "B"
+        element_a_content = self.dataset_populator.get_history_dataset_content(
+            history_id, dataset=elements[0]["object"]
+        )
+        element_b_content = self.dataset_populator.get_history_dataset_content(
+            history_id, dataset=elements[1]["object"]
+        )
+        assert element_a_content.strip() == "A"
+        assert element_b_content.strip() == "B"
 
-    @skip_without_tool('create_input_collection')
+    @skip_without_tool("create_input_collection")
     def test_workflow_optional_input_text_parameter_reevaluation(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   text_input:
@@ -2830,28 +3175,34 @@ steps:
           outputs:
             out_file1:
               rename: "#{inner_text_input} suffix"
-        """, history_id=history_id)
+        """,
+                history_id=history_id,
+            )
 
-    @skip_without_tool('cat1')
+    @skip_without_tool("cat1")
     def test_workflow_rerun_with_use_cached_job(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_run")
         # We launch a workflow
         with self.dataset_populator.test_history() as history_id_one, self.dataset_populator.test_history() as history_id_two:
             workflow_request, _, workflow_id = self._setup_workflow_run(workflow, history_id=history_id_one)
-            invocation_id = self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
+            invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+                workflow_id, request=workflow_request, assert_ok=True
+            )
             invocation_1 = self.workflow_populator.get_invocation(invocation_id)
             # We copy the workflow inputs to a new history
             new_workflow_request = workflow_request.copy()
-            new_ds_map = json.loads(new_workflow_request['ds_map'])
-            for key, input_values in invocation_1['inputs'].items():
-                copy_payload = {"content": input_values['id'], "source": "hda", "type": "dataset"}
+            new_ds_map = json.loads(new_workflow_request["ds_map"])
+            for key, input_values in invocation_1["inputs"].items():
+                copy_payload = {"content": input_values["id"], "source": "hda", "type": "dataset"}
                 copy_response = self._post(f"histories/{history_id_two}/contents", data=copy_payload, json=True).json()
-                new_ds_map[key]['id'] = copy_response['id']
-            new_workflow_request['ds_map'] = json.dumps(new_ds_map, sort_keys=True)
-            new_workflow_request['history'] = f"hist_id={history_id_two}"
-            new_workflow_request['use_cached_job'] = True
+                new_ds_map[key]["id"] = copy_response["id"]
+            new_workflow_request["ds_map"] = json.dumps(new_ds_map, sort_keys=True)
+            new_workflow_request["history"] = f"hist_id={history_id_two}"
+            new_workflow_request["use_cached_job"] = True
             # We run the workflow again, it should not produce any new outputs
-            new_workflow_response = self.workflow_populator.invoke_workflow_raw(workflow_id, new_workflow_request, assert_ok=True).json()
+            new_workflow_response = self.workflow_populator.invoke_workflow_raw(
+                workflow_id, new_workflow_request, assert_ok=True
+            ).json()
             invocation_id = new_workflow_response["id"]
             self.workflow_populator.wait_for_invocation_and_jobs(history_id_two, workflow_id, invocation_id)
 
@@ -2863,10 +3214,11 @@ steps:
 
             first_wf_output = self._get(f"datasets/{first_wf_output_hda['id']}").json()
             second_wf_output = self._get(f"datasets/{second_wf_output_hda['id']}").json()
-            assert first_wf_output['file_name'] == second_wf_output['file_name'], \
-                f"first output:\n{first_wf_output}\nsecond output:\n{second_wf_output}"
+            assert (
+                first_wf_output["file_name"] == second_wf_output["file_name"]
+            ), f"first output:\n{first_wf_output}\nsecond output:\n{second_wf_output}"
 
-    @skip_without_tool('cat1')
+    @skip_without_tool("cat1")
     def test_nested_workflow_rerun_with_use_cached_job(self):
         with self.dataset_populator.test_history() as history_id_one, self.dataset_populator.test_history() as history_id_two:
             test_data = """
@@ -2874,31 +3226,38 @@ outer_input:
   value: 1.bed
   type: File
 """
-            run_jobs_summary = self._run_workflow(WORKFLOW_NESTED_SIMPLE, test_data=test_data, history_id=history_id_one)
+            run_jobs_summary = self._run_workflow(
+                WORKFLOW_NESTED_SIMPLE, test_data=test_data, history_id=history_id_one
+            )
             workflow_id = run_jobs_summary.workflow_id
             workflow_request = run_jobs_summary.workflow_request
             # We copy the inputs to a new history and re-run the workflow
-            inputs = json.loads(workflow_request['inputs'])
-            dataset_type = inputs['outer_input']['src']
-            dataset_id = inputs['outer_input']['id']
+            inputs = json.loads(workflow_request["inputs"])
+            dataset_type = inputs["outer_input"]["src"]
+            dataset_id = inputs["outer_input"]["id"]
             copy_payload = {"content": dataset_id, "source": dataset_type, "type": "dataset"}
             copy_response = self._post(f"histories/{history_id_two}/contents", data=copy_payload, json=True)
             self._assert_status_code_is(copy_response, 200)
-            new_dataset_id = copy_response.json()['id']
-            inputs['outer_input']['id'] = new_dataset_id
-            workflow_request['use_cached_job'] = True
-            workflow_request['history'] = f"hist_id={history_id_two}"
-            workflow_request['inputs'] = json.dumps(inputs)
-            self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=run_jobs_summary.workflow_request, assert_ok=True)
+            new_dataset_id = copy_response.json()["id"]
+            inputs["outer_input"]["id"] = new_dataset_id
+            workflow_request["use_cached_job"] = True
+            workflow_request["history"] = f"hist_id={history_id_two}"
+            workflow_request["inputs"] = json.dumps(inputs)
+            self.workflow_populator.invoke_workflow_and_wait(
+                workflow_id, request=run_jobs_summary.workflow_request, assert_ok=True
+            )
             # Now make sure that the HDAs in each history point to the same dataset instances
             history_one_contents = self.__history_contents(history_id_one)
             history_two_contents = self.__history_contents(history_id_two)
             assert len(history_one_contents) == len(history_two_contents)
             for i, (item_one, item_two) in enumerate(zip(history_one_contents, history_two_contents)):
-                assert item_one['dataset_id'] == item_two['dataset_id'], \
-                    'Dataset ids should match, but "%s" and "%s" are not the same for History item %i.' % (item_one['dataset_id'],
-                                                                                                           item_two['dataset_id'],
-                                                                                                           i + 1)
+                assert (
+                    item_one["dataset_id"] == item_two["dataset_id"]
+                ), 'Dataset ids should match, but "%s" and "%s" are not the same for History item %i.' % (
+                    item_one["dataset_id"],
+                    item_two["dataset_id"],
+                    i + 1,
+                )
 
     def test_cannot_run_inaccessible_workflow(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_run_cannot_access")
@@ -2934,15 +3293,23 @@ outer_input:
         workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_matching_lists")
         workflow_id = self.workflow_populator.create_workflow(workflow)
         with self.dataset_populator.test_history() as history_id:
-            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("sample1-1", "1 2 3"), ("sample2-1", "7 8 9")]).json()
-            hdca2 = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("sample1-2", "4 5 6"), ("sample2-2", "0 a b")]).json()
+            hdca1 = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("sample1-1", "1 2 3"), ("sample2-1", "7 8 9")]
+            ).json()
+            hdca2 = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=[("sample1-2", "4 5 6"), ("sample2-2", "0 a b")]
+            ).json()
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             label_map = {"list1": self._ds_entry(hdca1), "list2": self._ds_entry(hdca2)}
             workflow_request = dict(
                 ds_map=self.workflow_populator.build_ds_map(workflow_id, label_map),
             )
-            self.workflow_populator.invoke_workflow_and_wait(workflow_id, history_id=history_id, request=workflow_request, assert_ok=True)
-            self.assertEqual("1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content(history_id))
+            self.workflow_populator.invoke_workflow_and_wait(
+                workflow_id, history_id=history_id, request=workflow_request, assert_ok=True
+            )
+            self.assertEqual(
+                "1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content(history_id)
+            )
 
     def test_workflow_stability(self):
         # Run this index stability test with following command:
@@ -2972,10 +3339,7 @@ outer_input:
         self._assert_error_code_is(response, error_codes.error_codes_by_name["USER_REQUEST_MISSING_PARAMETER"])
 
     def test_invalid_create_multiple_types(self):
-        data = {
-            'shared_workflow_id': '1234567890abcdef',
-            'from_history_id': '1234567890abcdef'
-        }
+        data = {"shared_workflow_id": "1234567890abcdef", "from_history_id": "1234567890abcdef"}
         response = self._post("workflows", data)
         self._assert_status_code_is(response, 400)
         self._assert_error_code_is(response, error_codes.error_codes_by_name["USER_REQUEST_INVALID_PARAMETER"])
@@ -2983,9 +3347,11 @@ outer_input:
     @skip_without_tool("cat1")
     def test_run_with_pja(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_pja_run", add_pja=True)
-        workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow, inputs_by='step_index')
+        workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow, inputs_by="step_index")
         workflow_request["replacement_params"] = dumps(dict(replaceme="was replaced"))
-        run_workflow_response = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request, assert_ok=True)
+        run_workflow_response = self.workflow_populator.invoke_workflow_raw(
+            workflow_id, workflow_request, assert_ok=True
+        )
         invocation_id = run_workflow_response.json()["id"]
         self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id, assert_ok=True)
         content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
@@ -2994,24 +3360,32 @@ outer_input:
     @skip_without_tool("hidden_param")
     def test_hidden_param_in_workflow(self):
         with self.dataset_populator.test_history() as history_id:
-            run_object = self._run_workflow("""
+            run_object = self._run_workflow(
+                """
 class: GalaxyWorkflow
 steps:
   step1:
     tool_id: hidden_param
-""", test_data={}, history_id=history_id, wait=False)
-            self.workflow_populator.wait_for_invocation_and_jobs(history_id, run_object.workflow_id, run_object.invocation_id)
+""",
+                test_data={},
+                history_id=history_id,
+                wait=False,
+            )
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id, run_object.workflow_id, run_object.invocation_id
+            )
             contents = self.__history_contents(history_id)
             assert len(contents) == 1
             okay_dataset = contents[0]
             assert okay_dataset["state"] == "ok"
             content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
-            assert content == '1\n'
+            assert content == "1\n"
 
     @skip_without_tool("output_filter")
     def test_optional_workflow_output(self):
         with self.dataset_populator.test_history() as history_id:
-            run_object = self._run_workflow("""
+            run_object = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs: []
 outputs:
@@ -3024,8 +3398,14 @@ steps:
       produce_out_1: False
       filter_text_1: '1'
       produce_collection: False
-""", test_data={}, history_id=history_id, wait=False)
-            self.workflow_populator.wait_for_invocation_and_jobs(history_id, run_object.workflow_id, run_object.invocation_id)
+""",
+                test_data={},
+                history_id=history_id,
+                wait=False,
+            )
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id, run_object.workflow_id, run_object.invocation_id
+            )
             contents = self.__history_contents(history_id)
             assert len(contents) == 1
             okay_dataset = contents[0]
@@ -3041,7 +3421,8 @@ input1:
     - identifier: A
       content: A
 """
-            run_object = self._run_workflow("""
+            run_object = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -3055,8 +3436,14 @@ steps:
     tool_id: output_filter_with_input_optional
     in:
       input_1: input1
-""", test_data=test_data, history_id=history_id, wait=False)
-            self.workflow_populator.wait_for_invocation_and_jobs(history_id, run_object.workflow_id, run_object.invocation_id)
+""",
+                test_data=test_data,
+                history_id=history_id,
+                wait=False,
+            )
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id, run_object.workflow_id, run_object.invocation_id
+            )
             contents = self.__history_contents(history_id)
             assert len(contents) == 4
             for content in contents:
@@ -3069,7 +3456,8 @@ steps:
     @skip_without_tool("cat")
     def test_run_rename_on_mapped_over_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -3083,7 +3471,8 @@ steps:
     outputs:
       out_file1:
         rename: "my new name"
-""", test_data="""
+""",
+                test_data="""
 input1:
   collection_type: list
   name: the_dataset_list
@@ -3091,12 +3480,16 @@ input1:
     - identifier: el1
       value: 1.fastq
       type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             content = self.dataset_populator.get_history_dataset_details(history_id, hid=4, wait=True, assert_ok=True)
             name = content["name"]
             assert name == "my new name", name
             assert content["history_content_type"] == "dataset"
-            content = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+            content = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
             name = content["name"]
             assert content["history_content_type"] == "dataset_collection", content
             assert name == "my new name", name
@@ -3104,7 +3497,8 @@ input1:
     @skip_without_tool("cat")
     def test_run_rename_based_on_inputs_on_mapped_over_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -3118,7 +3512,8 @@ steps:
     outputs:
       out_file1:
         rename: "#{input1} suffix"
-""", test_data="""
+""",
+                test_data="""
 input1:
   collection_type: list
   name: the_dataset_list
@@ -3126,8 +3521,12 @@ input1:
     - identifier: el1
       value: 1.fastq
       type: File
-""", history_id=history_id)
-            content = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+            )
+            content = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
             name = content["name"]
             assert content["history_content_type"] == "dataset_collection", content
             assert name == "the_dataset_list suffix", name
@@ -3135,7 +3534,8 @@ input1:
     @skip_without_tool("collection_creates_pair")
     def test_run_rename_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3146,21 +3546,27 @@ steps:
     outputs:
       paired_output:
         rename: "my new name"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=4, wait=True, assert_ok=True)
-            assert details1['elements'][0]['object']['visible'] is False
+""",
+                history_id=history_id,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=4, wait=True, assert_ok=True
+            )
+            assert details1["elements"][0]["object"]["visible"] is False
             assert details1["name"] == "my new name", details1
             assert details1["history_content_type"] == "dataset_collection"
 
     @skip_without_tool("__BUILD_LIST__")
     def test_run_build_list_hide_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3175,21 +3581,27 @@ steps:
     outputs:
       output:
         hide: true
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
-            assert details1['elements'][0]['object']['visible'] is False
+""",
+                history_id=history_id,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
+            assert details1["elements"][0]["object"]["visible"] is False
             assert details1["name"] == "data 1 (as list)", details1
             assert details1["visible"] is False
 
     @skip_without_tool("__BUILD_LIST__")
     def test_run_build_list_delete_intermediate_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3204,15 +3616,19 @@ steps:
     outputs:
       output:
         delete_intermediate_datasets: true
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True,
-                                                                             assert_ok=True)
-            assert details1['elements'][0]['object']['visible'] is False
+""",
+                history_id=history_id,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
+            assert details1["elements"][0]["object"]["visible"] is False
             assert details1["name"] == "data 1 (as list)", details1
             # FIXME: this doesn't work because the workflow is still being scheduled
             # TODO: Implement a way to run PJAs that couldn't be run during/after the job
@@ -3222,7 +3638,8 @@ input1:
     @skip_without_tool("__BUILD_LIST__")
     def test_run_build_list_change_datatype_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3244,27 +3661,33 @@ steps:
       datasets:
       - id_cond:
           id_select: idx
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   file_type: fasta
   name: fasta1
-""", history_id=history_id)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True,
-                                                                             assert_ok=True)
+""",
+                history_id=history_id,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
             assert details1["name"] == "data 1 (as list)", details1
-            assert details1['elements'][0]['object']['visible'] is False
-            assert details1['elements'][0]['object']['file_ext'] == 'txt'
-            details2 = self.dataset_populator.get_history_collection_details(history_id, hid=5, wait=True,
-                                                                             assert_ok=True)
+            assert details1["elements"][0]["object"]["visible"] is False
+            assert details1["elements"][0]["object"]["file_ext"] == "txt"
+            details2 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=5, wait=True, assert_ok=True
+            )
             # Also check that we don't overwrite the original HDA's datatype
-            assert details2['elements'][0]['object']['file_ext'] == 'fasta'
+            assert details2["elements"][0]["object"]["file_ext"] == "fasta"
 
     @skip_without_tool("__BUILD_LIST__")
     def test_run_build_list_rename_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3279,22 +3702,27 @@ steps:
     outputs:
       output:
         rename: "my new name"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True,
-                                                                             assert_ok=True)
-            assert details1['elements'][0]['object']['visible'] is False
+""",
+                history_id=history_id,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
+            assert details1["elements"][0]["object"]["visible"] is False
             assert details1["name"] == "my new name", details1
             assert details1["history_content_type"] == "dataset_collection"
 
     @skip_without_tool("create_2")
     def test_run_rename_multiple_outputs(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs: []
 steps:
@@ -3307,7 +3735,10 @@ steps:
         rename: "my new name"
       out_file2:
         rename: "my other new name"
-""", test_data={}, history_id=history_id)
+""",
+                test_data={},
+                history_id=history_id,
+            )
         details1 = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=True)
         details2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
 
@@ -3326,7 +3757,8 @@ steps:
     @skip_without_tool("cat")
     def test_run_rename_when_resuming_jobs(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3347,35 +3779,43 @@ steps:
     outputs:
       out_file1:
         rename: "#{input1} suffix"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fail
-""", history_id=history_id, wait=True, assert_ok=False)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=False,
+            )
             content = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=False)
             name = content["name"]
-            assert content['state'] == 'error', content
+            assert content["state"] == "error", content
             input1 = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=False)
-            job_id = content['creating_job']
-            inputs = {"input1": {'values': [{'src': 'hda',
-                                             'id': input1['id']}]
-                                 },
-                      "failbool": "false",
-                      "rerun_remap_job_id": job_id}
+            job_id = content["creating_job"]
+            inputs = {
+                "input1": {"values": [{"src": "hda", "id": input1["id"]}]},
+                "failbool": "false",
+                "rerun_remap_job_id": job_id,
+            }
             self.dataset_populator.run_tool(
-                tool_id='fail_identifier',
+                tool_id="fail_identifier",
                 inputs=inputs,
                 history_id=history_id,
             )
-            unpaused_dataset = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=False)
-            assert unpaused_dataset['state'] == 'ok'
-            assert unpaused_dataset['name'] == f"{name} suffix"
+            unpaused_dataset = self.dataset_populator.get_history_dataset_details(
+                history_id, wait=True, assert_ok=False
+            )
+            assert unpaused_dataset["state"] == "ok"
+            assert unpaused_dataset["name"] == f"{name} suffix"
 
     @skip_without_tool("cat")
     def test_run_rename_based_on_input_recursive(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3387,12 +3827,15 @@ steps:
     outputs:
       out_file1:
         rename: "#{input1} #{input1 | upper} suffix"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: '#{input1}'
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
             name = content["name"]
             assert name == "#{input1} #{INPUT1} suffix", name
@@ -3400,7 +3843,8 @@ input1:
     @skip_without_tool("cat")
     def test_run_rename_based_on_input_repeat(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3417,7 +3861,8 @@ steps:
     outputs:
       out_file1:
         rename: "#{queries_0.input2| basename} suffix"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
@@ -3426,7 +3871,9 @@ input2:
   value: 1.fasta
   type: File
   name: fasta2
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
             name = content["name"]
             assert name == "fasta2 suffix", name
@@ -3434,7 +3881,8 @@ input2:
     @skip_without_tool("mapper2")
     def test_run_rename_based_on_input_conditional(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   fasta_input: data
@@ -3454,7 +3902,8 @@ steps:
         # Wish it was qualified for conditionals but it doesn't seem to be. -John
         # rename: "#{fastq_input.fastq_input1 | basename} suffix"
         rename: "#{fastq_input1 | basename} suffix"
-""", test_data="""
+""",
+                test_data="""
 fasta_input:
   value: 1.fasta
   type: File
@@ -3465,7 +3914,9 @@ fastq_input:
   type: File
   name: fastq1
   file_type: fastqsanger
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
             name = content["name"]
             assert name == "fastq1 suffix", name
@@ -3473,7 +3924,8 @@ fastq_input:
     @skip_without_tool("mapper2")
     def test_run_rename_based_on_input_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   fasta_input: data
@@ -3493,7 +3945,8 @@ steps:
         # Wish it was qualified for conditionals but it doesn't seem to be. -John
         # rename: "#{fastq_input.fastq_input1 | basename} suffix"
         rename: "#{fastq_input1} suffix"
-""", test_data="""
+""",
+                test_data="""
 fasta_input:
   value: 1.fasta
   type: File
@@ -3509,7 +3962,9 @@ fastq_inputs:
     - identifier: reverse
       value: 1.fastq
       type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
             name = content["name"]
             assert name == "the_dataset_pair suffix", name
@@ -3517,7 +3972,8 @@ fastq_inputs:
     @skip_without_tool("collection_creates_pair")
     def test_run_hide_on_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3530,13 +3986,18 @@ steps:
     outputs:
       paired_output:
         hide: true
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=4, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=4, wait=True, assert_ok=True
+            )
 
             assert details1["history_content_type"] == "dataset_collection"
             assert not details1["visible"], details1
@@ -3544,7 +4005,8 @@ input1:
     @skip_without_tool("cat")
     def test_run_hide_on_mapped_over_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   - id: input1
@@ -3558,7 +4020,8 @@ steps:
     outputs:
       out_file1:
         hide: true
-""", test_data="""
+""",
+                test_data="""
 input1:
   collection_type: list
   name: the_dataset_list
@@ -3566,20 +4029,25 @@ input1:
     - identifier: el1
       value: 1.fastq
       type: File
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
 
             content = self.dataset_populator.get_history_dataset_details(history_id, hid=4, wait=True, assert_ok=True)
             assert content["history_content_type"] == "dataset"
             assert not content["visible"]
 
-            content = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+            content = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
             assert content["history_content_type"] == "dataset_collection", content
             assert not content["visible"]
 
     @skip_without_tool("cat")
     def test_tag_auto_propagation(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3599,12 +4067,16 @@ steps:
     tool_id: cat
     in:
       input1: first_cat/out_file1
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id, round_trip_format_conversion=True)
+""",
+                history_id=history_id,
+                round_trip_format_conversion=True,
+            )
 
             details0 = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
             tags = details0["tags"]
@@ -3622,7 +4094,8 @@ input1:
     @skip_without_tool("collection_creates_pair")
     def test_run_add_tag_on_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3635,13 +4108,19 @@ steps:
       paired_output:
         add_tags:
             - "name:foo"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id, round_trip_format_conversion=True)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=4, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                round_trip_format_conversion=True,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=4, wait=True, assert_ok=True
+            )
 
             assert details1["history_content_type"] == "dataset_collection"
             assert details1["tags"][0] == "name:foo", details1
@@ -3649,7 +4128,8 @@ input1:
     @skip_without_tool("cat")
     def test_run_add_tag_on_mapped_over_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -3664,7 +4144,8 @@ steps:
       out_file1:
         add_tags:
             - "name:foo"
-""", test_data="""
+""",
+                test_data="""
 input1:
   collection_type: list
   name: the_dataset_list
@@ -3672,8 +4153,13 @@ input1:
     - identifier: el1
       value: 1.fastq
       type: File
-""", history_id=history_id, round_trip_format_conversion=True)
-            details1 = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                round_trip_format_conversion=True,
+            )
+            details1 = self.dataset_populator.get_history_collection_details(
+                history_id, hid=3, wait=True, assert_ok=True
+            )
 
             assert details1["history_content_type"] == "dataset_collection"
             assert details1["tags"][0] == "name:foo", details1
@@ -3682,7 +4168,8 @@ input1:
     @skip_without_tool("cat")
     def test_run_remove_tag_on_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3703,19 +4190,29 @@ steps:
       paired_output:
         remove_tags:
           - "name:foo"
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
-""", history_id=history_id, round_trip_format_conversion=True)
-            details_dataset_with_tag = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
+""",
+                history_id=history_id,
+                round_trip_format_conversion=True,
+            )
+            details_dataset_with_tag = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=2, wait=True, assert_ok=True
+            )
 
             assert details_dataset_with_tag["history_content_type"] == "dataset", details_dataset_with_tag
             assert details_dataset_with_tag["tags"][0] == "name:foo", details_dataset_with_tag
 
-            details_collection_without_tag = self.dataset_populator.get_history_collection_details(history_id, hid=5, wait=True, assert_ok=True)
-            assert details_collection_without_tag["history_content_type"] == "dataset_collection", details_collection_without_tag
+            details_collection_without_tag = self.dataset_populator.get_history_collection_details(
+                history_id, hid=5, wait=True, assert_ok=True
+            )
+            assert (
+                details_collection_without_tag["history_content_type"] == "dataset_collection"
+            ), details_collection_without_tag
             assert len(details_collection_without_tag["tags"]) == 0, details_collection_without_tag
 
     @skip_without_tool("cat1")
@@ -3725,7 +4222,7 @@ input1:
         workflow["steps"]["0"]["uuid"] = uuid0
         workflow["steps"]["1"]["uuid"] = uuid1
         workflow["steps"]["2"]["uuid"] = uuid2
-        workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow, inputs_by='step_index')
+        workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow, inputs_by="step_index")
         workflow_request["replacement_params"] = dumps(dict(replaceme="was replaced"))
         pja_map = {
             "RenameDatasetActionout_file1": dict(
@@ -3734,9 +4231,7 @@ input1:
                 action_arguments=dict(newname="foo ${replaceme}"),
             )
         }
-        workflow_request["parameters"] = dumps({
-            uuid2: {"__POST_JOB_ACTIONS__": pja_map}
-        })
+        workflow_request["parameters"] = dumps({uuid2: {"__POST_JOB_ACTIONS__": pja_map}})
 
         self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
         content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
@@ -3750,7 +4245,8 @@ input1:
 
     @skip_without_tool("cat1")
     def test_run_with_delayed_runtime_pja(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -3767,14 +4263,16 @@ steps:
     tool_id: cat1
     in:
       input1: the_pause
-""", round_trip_format_conversion=True)
+""",
+            round_trip_format_conversion=True,
+        )
         downloaded_workflow = self._download_workflow(workflow_id)
         uuid_dict = {int(index): step["uuid"] for index, step in downloaded_workflow["steps"].items()}
         with self.dataset_populator.test_history() as history_id:
             hda = self.dataset_populator.new_dataset(history_id, content="1 2 3")
             self.dataset_populator.wait_for_history(history_id)
             inputs = {
-                '0': self._ds_entry(hda),
+                "0": self._ds_entry(hda),
             }
             uuid2 = uuid_dict[3]
             workflow_request = {}
@@ -3786,10 +4284,10 @@ steps:
                     action_arguments=dict(newname="foo ${replaceme}"),
                 )
             }
-            workflow_request["parameters"] = dumps({
-                uuid2: {"__POST_JOB_ACTIONS__": pja_map}
-            })
-            invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, request=workflow_request, history_id=history_id)
+            workflow_request["parameters"] = dumps({uuid2: {"__POST_JOB_ACTIONS__": pja_map}})
+            invocation_id = self.__invoke_workflow(
+                workflow_id, inputs=inputs, request=workflow_request, history_id=history_id
+            )
 
             time.sleep(2)
             self.dataset_populator.wait_for_history(history_id)
@@ -3803,7 +4301,8 @@ steps:
     @skip_without_tool("cat1")
     def test_delete_intermediate_datasets_pja_1(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3826,7 +4325,10 @@ steps:
     outputs:
       out_file1:
         delete_intermediate_datasets: true
-""", test_data={"input1": "hello world"}, history_id=history_id)
+""",
+                test_data={"input1": "hello world"},
+                history_id=history_id,
+            )
             hda1 = self.dataset_populator.get_history_dataset_details(history_id, hid=1)
             hda2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
             hda3 = self.dataset_populator.get_history_dataset_details(history_id, hid=3)
@@ -3842,7 +4344,8 @@ steps:
     @skip_without_tool("cat1")
     def test_validated_post_job_action_validated(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3857,21 +4360,29 @@ steps:
     post_job_actions:
       ValidateOutputsAction:
         action_type: ValidateOutputsAction
-""", test_data={"input1": {"type": "File", "file_type": "fastqsanger", "value": "1.fastqsanger"}}, history_id=history_id)
+""",
+                test_data={"input1": {"type": "File", "file_type": "fastqsanger", "value": "1.fastqsanger"}},
+                history_id=history_id,
+            )
             hda2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
             assert hda2["validated_state"] == "ok"
 
     @skip_without_tool("cat1")
     def test_validated_post_job_action_unvalidated_default(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": {"type": "File", "file_type": "fastqsanger", "value": "1.fastqsanger"}}, history_id=history_id)
+            self._run_jobs(
+                WORKFLOW_SIMPLE,
+                test_data={"input1": {"type": "File", "file_type": "fastqsanger", "value": "1.fastqsanger"}},
+                history_id=history_id,
+            )
             hda2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
             assert hda2["validated_state"] == "unknown"
 
     @skip_without_tool("cat1")
     def test_validated_post_job_action_invalid(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -3886,12 +4397,16 @@ steps:
     post_job_actions:
       ValidateOutputsAction:
         action_type: ValidateOutputsAction
-""", test_data={"input1": {"type": "File", "file_type": "fastqcssanger", "value": "1.fastqsanger"}}, history_id=history_id)
+""",
+                test_data={"input1": {"type": "File", "file_type": "fastqcssanger", "value": "1.fastqsanger"}},
+                history_id=history_id,
+            )
             hda2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
             assert hda2["validated_state"] == "invalid"
 
     def test_value_restriction_with_select_and_text_param(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow("""
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   select_text:
@@ -3906,12 +4421,13 @@ steps:
     tool_id: param_text_option
     in:
       text_param: select_text
-""")
+"""
+        )
         with self.dataset_populator.test_history() as history_id:
-            run_workflow = self._download_workflow(workflow_id, style='run', history_id=history_id)
-        options = run_workflow['steps'][0]['inputs'][0]['options']
+            run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
+        options = run_workflow["steps"][0]["inputs"][0]["options"]
         assert len(options) == 5
-        assert options[0] == ['Ex1', '--ex1', False]
+        assert options[0] == ["Ex1", "--ex1", False]
 
     @skip_without_tool("random_lines1")
     def test_run_replace_params_by_tool(self):
@@ -3925,10 +4441,12 @@ steps:
     @skip_without_tool("random_lines1")
     def test_run_replace_params_by_uuid(self):
         workflow_request, history_id, workflow_id = self._setup_random_x2_workflow("test_for_replace_")
-        workflow_request["parameters"] = dumps({
-            "58dffcc9-bcb7-4117-a0e1-61513524b3b1": dict(num_lines=4),
-            "58dffcc9-bcb7-4117-a0e1-61513524b3b2": dict(num_lines=3),
-        })
+        workflow_request["parameters"] = dumps(
+            {
+                "58dffcc9-bcb7-4117-a0e1-61513524b3b1": dict(num_lines=4),
+                "58dffcc9-bcb7-4117-a0e1-61513524b3b2": dict(num_lines=3),
+            }
+        )
         self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
         # Would be 8 and 6 without modification
         self.__assert_lines_hid_line_count_is(history_id, 2, 4)
@@ -3945,11 +4463,22 @@ steps:
             hda3 = self.dataset_populator.new_dataset(history_id, content="7 8 9")
             hda4 = self.dataset_populator.new_dataset(history_id, content="10 11 12")
             parameters = {
-                "0": {"input": {"batch": True, "values": [{"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"},
-                                                          {"id": hda2.get("id"), "hid": hda2.get("hid"), "src": "hda"},
-                                                          {"id": hda3.get("id"), "hid": hda2.get("hid"), "src": "hda"},
-                                                          {"id": hda4.get("id"), "hid": hda2.get("hid"), "src": "hda"}]}},
-                "1": {"input": {"batch": False, "values": [{"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"}]}, "exp": "2"}}
+                "0": {
+                    "input": {
+                        "batch": True,
+                        "values": [
+                            {"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"},
+                            {"id": hda2.get("id"), "hid": hda2.get("hid"), "src": "hda"},
+                            {"id": hda3.get("id"), "hid": hda2.get("hid"), "src": "hda"},
+                            {"id": hda4.get("id"), "hid": hda2.get("hid"), "src": "hda"},
+                        ],
+                    }
+                },
+                "1": {
+                    "input": {"batch": False, "values": [{"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"}]},
+                    "exp": "2",
+                },
+            }
             workflow_request = {
                 "history_id": history_id,
                 "batch": True,
@@ -3984,13 +4513,21 @@ steps:
             hda3 = self.dataset_populator.new_dataset(history_id, content="7 8 9")
             hda4 = self.dataset_populator.new_dataset(history_id, content="10 11 12")
             inputs = {
-                "coolinput": {"batch": True, "values": [{"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"},
-                                                        {"id": hda2.get("id"), "hid": hda2.get("hid"), "src": "hda"},
-                                                        {"id": hda3.get("id"), "hid": hda2.get("hid"), "src": "hda"},
-                                                        {"id": hda4.get("id"), "hid": hda2.get("hid"), "src": "hda"}]}
+                "coolinput": {
+                    "batch": True,
+                    "values": [
+                        {"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"},
+                        {"id": hda2.get("id"), "hid": hda2.get("hid"), "src": "hda"},
+                        {"id": hda3.get("id"), "hid": hda2.get("hid"), "src": "hda"},
+                        {"id": hda4.get("id"), "hid": hda2.get("hid"), "src": "hda"},
+                    ],
+                }
             }
             parameters = {
-                "1": {"input": {"batch": False, "values": [{"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"}]}, "exp": "2"}
+                "1": {
+                    "input": {"batch": False, "values": [{"id": hda1.get("id"), "hid": hda1.get("hid"), "src": "hda"}]},
+                    "exp": "2",
+                }
             }
             workflow_request = {
                 "history_id": history_id,
@@ -4019,16 +4556,19 @@ steps:
 
     @skip_without_tool("validation_default")
     def test_parameter_substitution_sanitization(self):
-        substitions = dict(input1="\" ; echo \"moo")
+        substitions = dict(input1='" ; echo "moo')
         run_workflow_response, history_id = self._run_validation_workflow_with_substitions(substitions)
 
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        self.assertEqual("__dq__ X echo __dq__moo\n", self.dataset_populator.get_history_dataset_content(history_id, hid=1))
+        self.assertEqual(
+            "__dq__ X echo __dq__moo\n", self.dataset_populator.get_history_dataset_content(history_id, hid=1)
+        )
 
     @skip_without_tool("validation_repeat")
     def test_parameter_substitution_validation_value_errors_0(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow("""
+            workflow_id = self._upload_yaml_workflow(
+                """
 class: GalaxyWorkflow
 steps:
   validation:
@@ -4036,10 +4576,10 @@ steps:
     state:
       r2:
         - text: "abd"
-""")
+"""
+            )
             workflow_request = dict(
-                history=f"hist_id={history_id}",
-                parameters=dumps(dict(validation_repeat={"r2_0|text": ""}))
+                history=f"hist_id={history_id}", parameters=dumps(dict(validation_repeat={"r2_0|text": ""}))
             )
             url = f"workflows/{workflow_id}/invocations"
             invocation_response = self._post(url, data=workflow_request)
@@ -4048,7 +4588,7 @@ steps:
 
     @skip_without_tool("validation_default")
     def test_parameter_substitution_validation_value_errors_1(self):
-        substitions = dict(select_param="\" ; echo \"moo")
+        substitions = dict(select_param='" ; echo "moo')
         run_workflow_response, history_id = self._run_validation_workflow_with_substitions(substitions)
 
         self._assert_status_code_is(run_workflow_response, 400)
@@ -4056,7 +4596,8 @@ steps:
     @skip_without_tool("validation_repeat")
     def test_workflow_import_state_validation_1(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 steps:
   validation:
@@ -4064,7 +4605,12 @@ steps:
     state:
       r2:
       - text: ""
-""", history_id=history_id, wait=False, expected_response=400, assert_ok=False)
+""",
+                history_id=history_id,
+                wait=False,
+                expected_response=400,
+                assert_ok=False,
+            )
 
     def _run_validation_workflow_with_substitions(self, substitions):
         workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_validation_1")
@@ -4073,14 +4619,16 @@ steps:
         workflow_request = dict(
             history=f"hist_id={history_id}",
             workflow_id=uploaded_workflow_id,
-            parameters=dumps(dict(validation_default=substitions))
+            parameters=dumps(dict(validation_default=substitions)),
         )
         run_workflow_response = self.workflow_populator.invoke_workflow_raw(uploaded_workflow_id, workflow_request)
         return run_workflow_response, history_id
 
     @skip_without_tool("random_lines1")
     def test_run_replace_params_by_steps(self):
-        workflow_request, history_id, workflow_id, steps = self._setup_random_x2_workflow_steps("test_for_replace_step_params")
+        workflow_request, history_id, workflow_id, steps = self._setup_random_x2_workflow_steps(
+            "test_for_replace_step_params"
+        )
         params = dumps({str(steps[1]["id"]): dict(num_lines=5)})
         workflow_request["parameters"] = params
         self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
@@ -4090,27 +4638,34 @@ steps:
 
     @skip_without_tool("random_lines1")
     def test_run_replace_params_nested(self):
-        workflow_request, history_id, workflow_id, steps = self._setup_random_x2_workflow_steps("test_for_replace_step_params_nested")
+        workflow_request, history_id, workflow_id, steps = self._setup_random_x2_workflow_steps(
+            "test_for_replace_step_params_nested"
+        )
         seed_source = dict(
             seed_source_selector="set_seed",
             seed="moo",
         )
-        params = dumps({str(steps[0]["id"]): dict(num_lines=1, seed_source=seed_source),
-                        str(steps[1]["id"]): dict(num_lines=1, seed_source=seed_source)})
+        params = dumps(
+            {
+                str(steps[0]["id"]): dict(num_lines=1, seed_source=seed_source),
+                str(steps[1]["id"]): dict(num_lines=1, seed_source=seed_source),
+            }
+        )
         workflow_request["parameters"] = params
         self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
         self.assertEqual("2\n", self.dataset_populator.get_history_dataset_content(history_id))
 
     @skip_without_tool("random_lines1")
     def test_run_replace_params_nested_normalized(self):
-        workflow_request, history_id, workflow_id, steps = self._setup_random_x2_workflow_steps("test_for_replace_step_normalized_params_nested")
+        workflow_request, history_id, workflow_id, steps = self._setup_random_x2_workflow_steps(
+            "test_for_replace_step_normalized_params_nested"
+        )
         parameters = {
             "num_lines": 1,
             "seed_source|seed_source_selector": "set_seed",
             "seed_source|seed": "moo",
         }
-        params = dumps({str(steps[0]["id"]): parameters,
-                        str(steps[1]["id"]): parameters})
+        params = dumps({str(steps[0]["id"]): parameters, str(steps[1]["id"]): parameters})
         workflow_request["parameters"] = params
         workflow_request["parameters_normalized"] = False
         self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request, assert_ok=True)
@@ -4119,14 +4674,21 @@ steps:
     @skip_without_tool("random_lines1")
     def test_run_replace_params_over_default(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(WORKFLOW_ONE_STEP_DEFAULT, test_data="""
+            self._run_jobs(
+                WORKFLOW_ONE_STEP_DEFAULT,
+                test_data="""
 step_parameters:
   '1':
     num_lines: 4
 input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=True, assert_ok=True, round_trip_format_conversion=True)
+""",
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+                round_trip_format_conversion=True,
+            )
             result = self.dataset_populator.get_history_dataset_content(history_id)
             assert result.count("\n") == 4
 
@@ -4140,7 +4702,8 @@ input:
     @skip_without_tool("random_lines1")
     def test_run_replace_params_over_default_delayed(self):
         with self.dataset_populator.test_history() as history_id:
-            run_summary = self._run_workflow("""
+            run_summary = self._run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input: data
@@ -4159,14 +4722,18 @@ steps:
       input: the_pause
       num_lines:
         default: 6
-""", test_data="""
+""",
+                test_data="""
 step_parameters:
   '3':
     num_lines: 4
 input:
   value: 1.bed
   type: File
-""", history_id=history_id, wait=False)
+""",
+                history_id=history_id,
+                wait=False,
+            )
             wait_on(lambda: len(self._history_jobs(history_id)) >= 2 or None, "history jobs")
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
 
@@ -4192,39 +4759,54 @@ input:
     def test_invocation_filtering(self):
         with self._different_user(email=f"{uuid4()}@test.com"):
             # new user, start with no invocations
-            assert not self._assert_invocation_for_url_is('invocations')
-            self._run_jobs("""
+            assert not self._assert_invocation_for_url_is("invocations")
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input:
     type: data
     optional: true
 steps: []
-""", wait=False)
-            first_invocation = self._assert_invocation_for_url_is('invocations')
+""",
+                wait=False,
+            )
+            first_invocation = self._assert_invocation_for_url_is("invocations")
             new_history_id = self.dataset_populator.new_history()
             # new history has no invocations
             assert not self._assert_invocation_for_url_is(f"invocations?history_id={new_history_id}")
-            self._run_jobs("""
+            self._run_jobs(
+                """
 class: GalaxyWorkflow
 inputs:
   input:
     type: data
     optional: true
 steps: []
-""", history_id=new_history_id, wait=False)
+""",
+                history_id=new_history_id,
+                wait=False,
+            )
             # new history has one invocation now
             new_invocation = self._assert_invocation_for_url_is(f"invocations?history_id={new_history_id}")
             # filter invocation by workflow instance id
-            self._assert_invocation_for_url_is(f"invocations?workflow_id={first_invocation['workflow_id']}&instance=true", first_invocation)
+            self._assert_invocation_for_url_is(
+                f"invocations?workflow_id={first_invocation['workflow_id']}&instance=true", first_invocation
+            )
             # limit to 1, newest invocation first by default
             self._assert_invocation_for_url_is("invocations?limit=1", target_invocation=new_invocation)
             # limit to 1, descending sort on date
-            self._assert_invocation_for_url_is("invocations?limit=1&sort_by=create_time&sort_desc=true", target_invocation=new_invocation)
+            self._assert_invocation_for_url_is(
+                "invocations?limit=1&sort_by=create_time&sort_desc=true", target_invocation=new_invocation
+            )
             # limit to 1, ascending sort on date
-            self._assert_invocation_for_url_is("invocations?limit=1&sort_by=create_time&sort_desc=false", target_invocation=first_invocation)
+            self._assert_invocation_for_url_is(
+                "invocations?limit=1&sort_by=create_time&sort_desc=false", target_invocation=first_invocation
+            )
             # limit to 1, ascending sort on date, offset 1
-            self._assert_invocation_for_url_is("invocations?limit=1&sort_by=create_time&sort_desc=false&offset=1", target_invocation=new_invocation)
+            self._assert_invocation_for_url_is(
+                "invocations?limit=1&sort_by=create_time&sort_desc=false&offset=1", target_invocation=new_invocation
+            )
 
     def _assert_invocation_for_url_is(self, route, target_invocation=None):
         response = self._get(route)
@@ -4232,7 +4814,7 @@ steps: []
         invocations = response.json()
         if target_invocation:
             assert len(invocations) == 1
-            assert invocations[0]['id'] == target_invocation['id']
+            assert invocations[0]["id"] == target_invocation["id"]
         if invocations:
             assert len(invocations) == 1
             return invocations[0]
@@ -4273,7 +4855,7 @@ steps: []
         assert invocation_id in invocation_ids
 
         # Wait for the invocation to be fully scheduled, so we have details on all steps.
-        self._wait_for_invocation_state(workflow_id, invocation_id, 'scheduled')
+        self._wait_for_invocation_state(workflow_id, invocation_id, "scheduled")
         usage_details = self._invocation_details(workflow_id, invocation_id)
 
         invocation_steps = usage_details["steps"]
@@ -4293,7 +4875,9 @@ steps: []
         assert job_id is not None
 
         invocation_tool_step_id = invocation_tool_step["id"]
-        invocation_tool_step_response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}/steps/{invocation_tool_step_id}")
+        invocation_tool_step_response = self._get(
+            f"workflows/{workflow_id}/invocations/{invocation_id}/steps/{invocation_tool_step_id}"
+        )
         self._assert_status_code_is(invocation_tool_step_response, 200)
         self._assert_has_keys(invocation_tool_step_response.json(), "id", "order_index", "job_id")
 
@@ -4349,7 +4933,8 @@ steps: []
 
     def _run_mapping_workflow(self):
         history_id = self.dataset_populator.new_history()
-        summary = self._run_workflow("""
+        summary = self._run_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   input_c: collection
@@ -4358,7 +4943,8 @@ steps:
     tool_id: cat1
     in:
        input1: input_c
-""", test_data="""
+""",
+            test_data="""
 input_c:
   collection_type: list
   elements:
@@ -4366,7 +4952,11 @@ input_c:
       content: "0"
     - identifier: i2
       content: "1"
-""", history_id=history_id, wait=True, assert_ok=True)
+""",
+            history_id=history_id,
+            wait=True,
+            assert_ok=True,
+        )
         workflow_id = summary.workflow_id
         invocation_id = summary.invocation_id
         return workflow_id, invocation_id
@@ -4382,9 +4972,11 @@ input_c:
             response = self._get(f"workflows/{other_id}/usage")
             self._assert_status_code_is(response, 200)
             assert len(response.json()) == 0
-            run_workflow_response = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request, assert_ok=True)
+            run_workflow_response = self.workflow_populator.invoke_workflow_raw(
+                workflow_id, workflow_request, assert_ok=True
+            )
             run_workflow_dict = run_workflow_response.json()
-            invocation_id = run_workflow_dict['id']
+            invocation_id = run_workflow_dict["id"]
             usage_details_response = self._get(f"workflows/{other_id}/usage/{invocation_id}")
             self._assert_status_code_is(usage_details_response, 200)
 
@@ -4396,9 +4988,11 @@ input_c:
             response = self._get(f"workflows/{workflow_id}/usage")
             self._assert_status_code_is(response, 200)
             assert len(response.json()) == 0
-            run_workflow_response = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request, assert_ok=True)
+            run_workflow_response = self.workflow_populator.invoke_workflow_raw(
+                workflow_id, workflow_request, assert_ok=True
+            )
             run_workflow_dict = run_workflow_response.json()
-            invocation_id = run_workflow_dict['id']
+            invocation_id = run_workflow_dict["id"]
             usage_details_response = self._get(f"workflows/{workflow_id}/usage/{invocation_id}")
             self._assert_status_code_is(usage_details_response, 200)
 
@@ -4409,9 +5003,11 @@ input_c:
         response = self._get(f"workflows/{workflow_id}/usage")
         self._assert_status_code_is(response, 200)
         assert len(response.json()) == 0
-        run_workflow_response = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request, assert_ok=True)
+        run_workflow_response = self.workflow_populator.invoke_workflow_raw(
+            workflow_id, workflow_request, assert_ok=True
+        )
         run_workflow_dict = run_workflow_response.json()
-        invocation_id = run_workflow_dict['id']
+        invocation_id = run_workflow_dict["id"]
         with self._different_user():
             usage_details_response = self._get(f"workflows/{workflow_id}/usage/{invocation_id}")
             self._assert_status_code_is(usage_details_response, 403)
@@ -4419,11 +5015,11 @@ input_c:
     def test_workflow_publishing(self):
         workflow_id = self.workflow_populator.simple_workflow("dummy")
         response = self._show_workflow(workflow_id)
-        assert not response['published']
-        published_worklow = self._put(f'workflows/{workflow_id}', data={'published': True}, json=True).json()
-        assert published_worklow['published']
-        unpublished_worklow = self._put(f'workflows/{workflow_id}', data={'published': False}, json=True).json()
-        assert not unpublished_worklow['published']
+        assert not response["published"]
+        published_worklow = self._put(f"workflows/{workflow_id}", data={"published": True}, json=True).json()
+        assert published_worklow["published"]
+        unpublished_worklow = self._put(f"workflows/{workflow_id}", data={"published": False}, json=True).json()
+        assert not unpublished_worklow["published"]
 
     def test_workflow_from_path_requires_admin(self):
         # There are two ways to import workflows from paths, just verify both require an admin.
@@ -4449,7 +5045,7 @@ input_c:
         workflow_id = self.workflow_populator.create_workflow(workflow)
         hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
         index_map = {
-            '0': self._ds_entry(hda1),
+            "0": self._ds_entry(hda1),
         }
         invocation_id = self.__invoke_workflow(
             workflow_id,
@@ -4462,27 +5058,27 @@ input_c:
         target_state_reached = False
         for _ in range(50):
             invocation = self._invocation_details(workflow_id, invocation_id)
-            if invocation['state'] != 'new':
+            if invocation["state"] != "new":
                 target_state_reached = True
                 break
 
-            time.sleep(.25)
+            time.sleep(0.25)
 
         return target_state_reached
 
     def _assert_invocation_non_terminal(self, workflow_id, invocation_id):
         invocation = self._invocation_details(workflow_id, invocation_id)
-        assert invocation['state'] in ['ready', 'new'], invocation
+        assert invocation["state"] in ["ready", "new"], invocation
 
     def _wait_for_invocation_state(self, workflow_id, invocation_id, target_state):
         target_state_reached = False
         for _ in range(25):
             invocation = self._invocation_details(workflow_id, invocation_id)
-            if invocation['state'] == target_state:
+            if invocation["state"] == target_state:
                 target_state_reached = True
                 break
 
-            time.sleep(.5)
+            time.sleep(0.5)
 
         return target_state_reached
 
@@ -4528,7 +5124,9 @@ input_c:
         workflow_summary_response = self._get(f"workflows/{workflow_id}")
         self._assert_status_code_is(workflow_summary_response, 200)
         steps = workflow_summary_response.json()["steps"]
-        return sorted((step for step in steps.values() if step["tool_id"] == "random_lines1"), key=lambda step: step["id"])
+        return sorted(
+            (step for step in steps.values() if step["tool_id"] == "random_lines1"), key=lambda step: step["id"]
+        )
 
     def _setup_random_x2_workflow(self, name: str):
         workflow = self.workflow_populator.load_random_x2_workflow(name)
@@ -4540,18 +5138,20 @@ input_c:
         hda1 = self.dataset_populator.new_dataset(history_id, content=ten_lines)
         workflow_request = dict(
             history=f"hist_id={history_id}",
-            ds_map=dumps({
-                key: self._ds_entry(hda1),
-            }),
+            ds_map=dumps(
+                {
+                    key: self._ds_entry(hda1),
+                }
+            ),
         )
         return workflow_request, history_id, uploaded_workflow_id
 
     def __review_paused_steps(self, uploaded_workflow_id, invocation_id, order_index, action=True):
         invocation = self._invocation_details(uploaded_workflow_id, invocation_id)
         invocation_steps = invocation["steps"]
-        pause_steps = [s for s in invocation_steps if s['order_index'] == order_index]
+        pause_steps = [s for s in invocation_steps if s["order_index"] == order_index]
         for pause_step in pause_steps:
-            pause_step_id = pause_step['id']
+            pause_step_id = pause_step["id"]
 
             self._execute_invocation_step_action(uploaded_workflow_id, invocation_id, pause_step_id, action=action)
 
@@ -4591,24 +5191,17 @@ input_c:
         return show_response.json()
 
     def _assert_looks_like_instance_workflow_representation(self, workflow):
-        self._assert_has_keys(
-            workflow,
-            'url',
-            'owner',
-            'inputs',
-            'annotation',
-            'steps'
-        )
+        self._assert_has_keys(workflow, "url", "owner", "inputs", "annotation", "steps")
         for step in workflow["steps"].values():
             self._assert_has_keys(
                 step,
-                'id',
-                'type',
-                'tool_id',
-                'tool_version',
-                'annotation',
-                'tool_inputs',
-                'input_steps',
+                "id",
+                "type",
+                "tool_id",
+                "tool_version",
+                "annotation",
+                "tool_inputs",
+                "input_steps",
             )
 
     def _all_user_invocation_ids(self):
@@ -4623,7 +5216,8 @@ class AdminWorkflowsApiTestCase(BaseWorkflowsApiTestCase):
     require_admin_user = True
 
     def test_import_export_dynamic_tools(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - type: input
@@ -4649,7 +5243,8 @@ steps:
           $link: embed1/output1
 test_data:
   input1: "hello world"
-""")
+"""
+        )
         downloaded_workflow = self._download_workflow(workflow_id)
         response = self.workflow_populator.create_workflow_response(downloaded_workflow)
         workflow_id = response.json()["id"]
@@ -4657,8 +5252,13 @@ test_data:
         hda1 = self.dataset_populator.new_dataset(history_id, content="Hello World Second!")
         workflow_request = dict(
             inputs_by="name",
-            inputs=json.dumps({'input1': self._ds_entry(hda1)}),
+            inputs=json.dumps({"input1": self._ds_entry(hda1)}),
+        )
+        invocation_id = self.workflow_populator.invoke_workflow(
+            workflow_id, history_id=history_id, request=workflow_request, assert_ok=True
         )
-        invocation_id = self.workflow_populator.invoke_workflow(workflow_id, history_id=history_id, request=workflow_request, assert_ok=True)
         self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
-        self.assertEqual("Hello World Second!\nhello world 2\n", self.dataset_populator.get_history_dataset_content(history_id, hid=4))
+        self.assertEqual(
+            "Hello World Second!\nhello world 2\n",
+            self.dataset_populator.get_history_dataset_content(history_id, hid=4),
+        )
diff --git a/lib/galaxy_test/api/test_workflows_cwl.py b/lib/galaxy_test/api/test_workflows_cwl.py
index d5da915eb29..007e6bdfd3b 100644
--- a/lib/galaxy_test/api/test_workflows_cwl.py
+++ b/lib/galaxy_test/api/test_workflows_cwl.py
@@ -9,6 +9,4 @@ class BaseCwlWorkflowTestCase(BaseWorkflowsApiTestCase):
 
     def setUp(self):
         super().setUp()
-        self.cwl_populator = CwlPopulator(
-            self.dataset_populator, self.workflow_populator
-        )
+        self.cwl_populator = CwlPopulator(self.dataset_populator, self.workflow_populator)
diff --git a/lib/galaxy_test/api/test_workflows_from_yaml.py b/lib/galaxy_test/api/test_workflows_from_yaml.py
index c5c3a3ed404..5fb4df0e7d0 100644
--- a/lib/galaxy_test/api/test_workflows_from_yaml.py
+++ b/lib/galaxy_test/api/test_workflows_from_yaml.py
@@ -16,7 +16,6 @@ WORKFLOWS_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
 
 class WorkflowsFromYamlApiTestCase(BaseWorkflowsApiTestCase):
-
     def setUp(self):
         super().setUp()
 
@@ -32,31 +31,37 @@ class WorkflowsFromYamlApiTestCase(BaseWorkflowsApiTestCase):
 
         assert workflow["annotation"].startswith("Simple workflow that ")
 
-        tool_count = {'random_lines1': 0, 'cat1': 0}
+        tool_count = {"random_lines1": 0, "cat1": 0}
         input_found = False
-        for step in workflow['steps'].values():
-            step_type = step['type']
+        for step in workflow["steps"].values():
+            step_type = step["type"]
             if step_type == "data_input":
-                assert step['label'] == 'the_input'
+                assert step["label"] == "the_input"
                 input_found = True
             else:
-                tool_id = step['tool_id']
+                tool_id = step["tool_id"]
                 tool_count[tool_id] += 1
                 if tool_id == "random_lines1":
-                    assert step['label'] == "random_line_label"
+                    assert step["label"] == "random_line_label"
 
         assert input_found
-        assert tool_count['random_lines1'] == 1
-        assert tool_count['cat1'] == 2
+        assert tool_count["random_lines1"] == 1
+        assert tool_count["cat1"] == 2
 
-        workflow_as_format2 = self._upload_and_download(WORKFLOW_SIMPLE_CAT_AND_RANDOM_LINES, client_convert=False, style="format2")
+        workflow_as_format2 = self._upload_and_download(
+            WORKFLOW_SIMPLE_CAT_AND_RANDOM_LINES, client_convert=False, style="format2"
+        )
         assert workflow_as_format2["doc"].startswith("Simple workflow that")
 
     def test_simple_output_actions(self):
         history_id = self.dataset_populator.new_history()
-        self._run_jobs(WORKFLOW_WITH_OUTPUT_ACTIONS, test_data="""
+        self._run_jobs(
+            WORKFLOW_WITH_OUTPUT_ACTIONS,
+            test_data="""
 input1: "hello world"
-""", history_id=history_id)
+""",
+            history_id=history_id,
+        )
 
         details1 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
         assert not details1["visible"]
@@ -66,7 +71,12 @@ input1: "hello world"
 
     def test_inputs_to_steps(self):
         history_id = self.dataset_populator.new_history()
-        self._run_jobs(WORKFLOW_SIMPLE_CAT_TWICE, test_data={"input1": "hello world"}, history_id=history_id, round_trip_format_conversion=True)
+        self._run_jobs(
+            WORKFLOW_SIMPLE_CAT_TWICE,
+            test_data={"input1": "hello world"},
+            history_id=history_id,
+            round_trip_format_conversion=True,
+        )
         contents1 = self.dataset_populator.get_history_dataset_content(history_id)
         self.assertEqual(contents1.strip(), "hello world\nhello world")
 
@@ -92,7 +102,8 @@ input1: "hello world"
         self._assert_is_runtime_input(tool_state["num_lines"])
 
     def test_subworkflow_simple(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -117,7 +128,9 @@ steps:
               seed: asdf
     in:
       inner_input: first_cat/out_file1
-""", client_convert=False)
+""",
+            client_convert=False,
+        )
         workflow = self.workflow_populator.download_workflow(workflow_id)
         by_label = self._steps_by_label(workflow)
         if "nested_workflow" not in by_label:
@@ -186,12 +199,18 @@ $graph:
         inner_input: nested_workflow_1/inner_output
 """
         history_id = self.dataset_populator.new_history()
-        self._run_jobs(duplicate_subworkflow_invocate_wf, test_data={"outer_input": "hello world"}, history_id=history_id, client_convert=False)
+        self._run_jobs(
+            duplicate_subworkflow_invocate_wf,
+            test_data={"outer_input": "hello world"},
+            history_id=history_id,
+            client_convert=False,
+        )
         content = self.dataset_populator.get_history_dataset_content(history_id)
         assert content == "hello world\nhello world\nhello world\nhello world\n"
 
     def test_pause(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   test_input:
@@ -209,11 +228,13 @@ steps:
     tool_id: cat1
     in:
       input1: the_pause
-""")
+"""
+        )
         self.workflow_populator.dump_workflow(workflow_id)
 
     def test_implicit_connections(self):
-        workflow_id = self._upload_yaml_workflow("""
+        workflow_id = self._upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -237,12 +258,14 @@ steps:
     state:
       input1:
         $link: test_input
-""")
+"""
+        )
         self.workflow_populator.dump_workflow(workflow_id)
 
     @uses_test_history()
     def test_conditional_ints(self, history_id):
-        self._run_jobs("""
+        self._run_jobs(
+            """
 class: GalaxyWorkflow
 steps:
   test_input:
@@ -252,12 +275,17 @@ steps:
         use: true
       files:
         attach_files: false
-""", test_data={}, history_id=history_id, round_trip_format_conversion=True)
+""",
+            test_data={},
+            history_id=history_id,
+            round_trip_format_conversion=True,
+        )
         content = self.dataset_populator.get_history_dataset_content(history_id)
         assert "no file specified" in content
         assert "7 7 4" in content
 
-        self._run_jobs("""
+        self._run_jobs(
+            """
 class: GalaxyWorkflow
 steps:
   test_input:
@@ -268,14 +296,19 @@ steps:
         p3v: 5
       files:
         attach_files: false
-""", test_data={}, history_id=history_id, round_trip_format_conversion=True)
+""",
+            test_data={},
+            history_id=history_id,
+            round_trip_format_conversion=True,
+        )
         content = self.dataset_populator.get_history_dataset_content(history_id)
         assert "no file specified" in content
         assert "7 7 5" in content
 
     def test_workflow_embed_tool(self):
         history_id = self.dataset_populator.new_history()
-        self._run_jobs("""
+        self._run_jobs(
+            """
 class: GalaxyWorkflow
 steps:
   - type: input
@@ -301,7 +334,9 @@ steps:
             $link: embed1/output1
 test_data:
   input1: "hello world"
-""", history_id=history_id)
+""",
+            history_id=history_id,
+        )
 
         content = self.dataset_populator.get_history_dataset_content(history_id)
         self.assertEqual(content, "hello world\nhello world 2\n")
@@ -309,15 +344,8 @@ test_data:
     def test_workflow_import_tool(self):
         history_id = self.dataset_populator.new_history()
         workflow_path = os.path.join(WORKFLOWS_DIRECTORY, "embed_test_1.gxwf.yml")
-        jobs_descriptions = {
-            "test_data": {"input1": "hello world"}
-        }
-        self._run_jobs(
-            workflow_path,
-            source_type="path",
-            jobs_descriptions=jobs_descriptions,
-            history_id=history_id
-        )
+        jobs_descriptions = {"test_data": {"input1": "hello world"}}
+        self._run_jobs(workflow_path, source_type="path", jobs_descriptions=jobs_descriptions, history_id=history_id)
         content = self.dataset_populator.get_history_dataset_content(history_id)
         self.assertEqual(content, "hello world\nhello world 2\n")
 
@@ -333,5 +361,5 @@ test_data:
         by_label = {}
         assert "steps" in workflow_as_dict, workflow_as_dict
         for step in workflow_as_dict["steps"].values():
-            by_label[step['label']] = step
+            by_label[step["label"]] = step
         return by_label
diff --git a/lib/galaxy_test/base/api.py b/lib/galaxy_test/base/api.py
index dff3de1ffb5..76481e3443c 100644
--- a/lib/galaxy_test/base/api.py
+++ b/lib/galaxy_test/base/api.py
@@ -28,9 +28,9 @@ class UsesApiTestCaseMixin:
     url: str
 
     def tearDown(self):
-        if os.environ.get('GALAXY_TEST_EXTERNAL') is None:
+        if os.environ.get("GALAXY_TEST_EXTERNAL") is None:
             # Only kill running jobs after test for managed test instances
-            for job in self.galaxy_interactor.get('jobs?state=running&?user_details=true').json():
+            for job in self.galaxy_interactor.get("jobs?state=running&?user_details=true").json():
                 self._delete(f"jobs/{job['id']}")
 
     def _api_url(self, path, params=None, use_key=None, use_admin_key=None):
@@ -66,7 +66,7 @@ class UsesApiTestCaseMixin:
 
     @contextmanager
     def _different_user(self, email=OTHER_USER, anon=False):
-        """ Use in test cases to switch get/post operations to act as new user
+        """Use in test cases to switch get/post operations to act as new user
 
         ..code-block:: python
 
@@ -129,7 +129,7 @@ class UsesApiTestCaseMixin:
 
 
 class ApiTestInteractor(BaseInteractor):
-    """ Specialized variant of the API interactor (originally developed for
+    """Specialized variant of the API interactor (originally developed for
     tool functional tests) for testing the API generally.
     """
 
diff --git a/lib/galaxy_test/base/api_asserts.py b/lib/galaxy_test/base/api_asserts.py
index 23e31f39627..b3292154eb3 100644
--- a/lib/galaxy_test/base/api_asserts.py
+++ b/lib/galaxy_test/base/api_asserts.py
@@ -1,6 +1,11 @@
 """Utility methods for making assertions about Galaxy API responses, etc...
 """
-from typing import Any, cast, Dict, Union
+from typing import (
+    Any,
+    cast,
+    Dict,
+    Union,
+)
 
 from requests import Response
 
diff --git a/lib/galaxy_test/base/env.py b/lib/galaxy_test/base/env.py
index bd6014281a4..ad652ac8c62 100644
--- a/lib/galaxy_test/base/env.py
+++ b/lib/galaxy_test/base/env.py
@@ -4,14 +4,17 @@ import fcntl
 import os
 import socket
 import struct
-from typing import Optional, Tuple
+from typing import (
+    Optional,
+    Tuple,
+)
 
-DEFAULT_WEB_HOST = socket.gethostbyname('localhost')
+DEFAULT_WEB_HOST = socket.gethostbyname("localhost")
 
 
 def setup_keep_outdir() -> str:
-    keep_outdir = os.environ.get('GALAXY_TEST_SAVE', '')
-    if keep_outdir > '':
+    keep_outdir = os.environ.get("GALAXY_TEST_SAVE", "")
+    if keep_outdir > "":
         try:
             os.makedirs(keep_outdir)
         except Exception:
@@ -20,20 +23,18 @@ def setup_keep_outdir() -> str:
 
 
 def target_url_parts() -> Tuple[str, Optional[str], str]:
-    host = socket.gethostbyname(os.environ.get('GALAXY_TEST_HOST', DEFAULT_WEB_HOST))
-    port = os.environ.get('GALAXY_TEST_PORT')
+    host = socket.gethostbyname(os.environ.get("GALAXY_TEST_HOST", DEFAULT_WEB_HOST))
+    port = os.environ.get("GALAXY_TEST_PORT")
     if port:
         default_url = f"http://{host}:{port}"
     else:
         default_url = f"http://{host}"
-    url = os.environ.get('GALAXY_TEST_EXTERNAL', default_url)
+    url = os.environ.get("GALAXY_TEST_EXTERNAL", default_url)
     return host, port, url
 
 
 def get_ip_address(ifname: str) -> str:
     s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
-    return socket.inet_ntoa(fcntl.ioctl(
-        s.fileno(),
-        0x8915,  # SIOCGIFADDR
-        struct.pack('256s', ifname[:15].encode('utf-8'))
-    )[20:24])
+    return socket.inet_ntoa(
+        fcntl.ioctl(s.fileno(), 0x8915, struct.pack("256s", ifname[:15].encode("utf-8")))[20:24]  # SIOCGIFADDR
+    )
diff --git a/lib/galaxy_test/base/instrument.py b/lib/galaxy_test/base/instrument.py
index 9ba2be9043d..7f5b527bb01 100644
--- a/lib/galaxy_test/base/instrument.py
+++ b/lib/galaxy_test/base/instrument.py
@@ -35,17 +35,22 @@ def fetch_job_data():
 
 
 class StructuredTestDataPlugin(Plugin):
-    name = 'structureddata'
+    name = "structureddata"
 
     def options(self, parser, env):
         super().options(parser, env=env)
         parser.add_option(
-            '--structured-data-file', action='store',
-            dest='structured_data_file', metavar="FILE",
-            default=env.get('NOSE_STRUCTURED_DATA', 'structured_test_data.json'),
-            help=("Path to JSON file to store the Galaxy structured data report in."
-                  "Default is structured_test_data.json in the working directory "
-                  "[NOSE_STRUCTURED_DATA]"))
+            "--structured-data-file",
+            action="store",
+            dest="structured_data_file",
+            metavar="FILE",
+            default=env.get("NOSE_STRUCTURED_DATA", "structured_test_data.json"),
+            help=(
+                "Path to JSON file to store the Galaxy structured data report in."
+                "Default is structured_test_data.json in the working directory "
+                "[NOSE_STRUCTURED_DATA]"
+            ),
+        )
 
     def configure(self, options, conf):
         super().configure(options, conf)
@@ -53,7 +58,7 @@ class StructuredTestDataPlugin(Plugin):
         if not self.enabled:
             return
         self.tests = []
-        self.structured_data_report_file = open(options.structured_data_file, 'w')
+        self.structured_data_report_file = open(options.structured_data_file, "w")
 
     def finalize(self, result):
         pass
@@ -63,9 +68,9 @@ class StructuredTestDataPlugin(Plugin):
         id = test.id()
         has_data = job_data is not NO_JOB_DATA
         entry = {
-            'id': id,
-            'has_data': has_data,
-            'data': job_data if has_data else None,
+            "id": id,
+            "has_data": has_data,
+            "data": job_data if has_data else None,
         }
         self.tests.append(entry)
 
@@ -75,8 +80,8 @@ class StructuredTestDataPlugin(Plugin):
 
     def report(self, stream):
         report_obj = {
-            'version': '0.1',
-            'tests': self.tests,
+            "version": "0.1",
+            "tests": self.tests,
         }
         json.dump(report_obj, self.structured_data_report_file)
         self.structured_data_report_file.close()
diff --git a/lib/galaxy_test/base/interactor.py b/lib/galaxy_test/base/interactor.py
index 3e48e6c8e76..45c055ce817 100644
--- a/lib/galaxy_test/base/interactor.py
+++ b/lib/galaxy_test/base/interactor.py
@@ -2,7 +2,6 @@ from galaxy.tool_util.verify.interactor import GalaxyInteractorApi
 
 
 class TestCaseGalaxyInteractor(GalaxyInteractorApi):
-
     def __init__(self, functional_test_case, test_user=None, api_key=None):
         self.functional_test_case = functional_test_case
         super().__init__(
diff --git a/lib/galaxy_test/base/nose_util.py b/lib/galaxy_test/base/nose_util.py
index 16fb9138d9c..98652f530da 100644
--- a/lib/galaxy_test/base/nose_util.py
+++ b/lib/galaxy_test/base/nose_util.py
@@ -17,9 +17,7 @@ def run(test_config, plugins=None):
         loader = plug_loader
     tests = loader.loadTestsFromNames(test_config.testNames)
     test_runner = nose.core.TextTestRunner(
-        stream=test_config.stream,
-        verbosity=test_config.verbosity,
-        config=test_config
+        stream=test_config.stream, verbosity=test_config.verbosity, config=test_config
     )
     plug_runner = test_config.plugins.prepareTestRunner(test_runner)
     if plug_runner is not None:
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index 78d70832ee7..9407309fb00 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -45,7 +45,10 @@ import string
 import time
 import unittest
 import urllib.parse
-from abc import ABCMeta, abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod,
+)
 from functools import wraps
 from io import StringIO
 from operator import itemgetter
@@ -78,8 +81,8 @@ from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.tool_util.verify.wait import (
     timeout_type,
     TimeoutAssertionError,
-    wait_on as tool_util_wait_on,
 )
+from galaxy.tool_util.verify.wait import wait_on as tool_util_wait_on
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     galaxy_root_path,
@@ -88,7 +91,6 @@ from galaxy.util import (
 from . import api_asserts
 from .api import ApiTestInteractor
 
-
 CWL_TOOL_DIRECTORY = os.path.join(galaxy_root_path, "test", "functional", "tools", "cwl_tools")
 
 # Simple workflow that takes an input and call cat wrapper on it.
@@ -104,7 +106,6 @@ SKIP_FLAKEY_TESTS_ON_ERROR = os.environ.get("GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ER
 
 
 def flakey(method):
-
     @wraps(method)
     def wrapped_method(test_case, *args, **kwargs):
         try:
@@ -127,7 +128,6 @@ def skip_without_tool(tool_id):
     """
 
     def method_wrapper(method):
-
         def get_tool_ids(api_test_case):
             index = api_test_case.galaxy_interactor.get("tools", data=dict(in_panel=False))
             tools = index.json()
@@ -178,7 +178,6 @@ def is_site_up(url):
 
 
 def skip_if_site_down(url):
-
     def method_wrapper(method):
         @wraps(method)
         def wrapped_method(api_test_case, *args, **kwargs):
@@ -207,8 +206,7 @@ def summarize_instance_history_on_error(method):
 
 
 def uses_test_history(**test_history_kwd):
-    """Can override require_new and cancel_executions using kwds to decorator.
-    """
+    """Can override require_new and cancel_executions using kwds to decorator."""
 
     def method_wrapper(method):
         @wraps(method)
@@ -224,6 +222,7 @@ def uses_test_history(**test_history_kwd):
 def _raise_skip_if(check, *args):
     if check:
         from nose.plugins.skip import SkipTest
+
         raise SkipTest(*args)
 
 
@@ -242,14 +241,12 @@ def conformance_tests_gen(directory, filename="conformance_tests.yaml"):
 
 
 class CwlRun:
-
     def __init__(self, dataset_populator, history_id):
         self.dataset_populator = dataset_populator
         self.history_id = history_id
 
 
 class CwlToolRun(CwlRun):
-
     def __init__(self, dataset_populator, history_id, run_response):
         super().__init__(dataset_populator, history_id)
         self.run_response = run_response
@@ -263,7 +260,6 @@ class CwlToolRun(CwlRun):
 
 
 class CwlWorkflowRun(CwlRun):
-
     def __init__(self, dataset_populator, workflow_populator, history_id, workflow_id, invocation_id):
         super().__init__(dataset_populator, history_id)
         self.workflow_populator = workflow_populator
@@ -271,13 +267,10 @@ class CwlWorkflowRun(CwlRun):
         self.invocation_id = invocation_id
 
     def wait(self):
-        self.workflow_populator.wait_for_invocation_and_jobs(
-            self.history_id, self.workflow_id, self.invocation_id
-        )
+        self.workflow_populator.wait_for_invocation_and_jobs(self.history_id, self.workflow_id, self.invocation_id)
 
 
 class CwlPopulator:
-
     def __init__(self, dataset_populator, workflow_populator):
         self.dataset_populator = dataset_populator
         self.workflow_populator = workflow_populator
@@ -331,7 +324,9 @@ class CwlPopulator:
             # workflows as well, and then make it the default. Or decide they are safe.
             "allow_tool_state_corrections": True,
         }
-        invocation_id = self.workflow_populator.invoke_workflow(workflow_id, history_id=history_id, inputs=job, request=request, inputs_by="name")
+        invocation_id = self.workflow_populator.invoke_workflow(
+            workflow_id, history_id=history_id, inputs=job, request=request, inputs_by="name"
+        )
         return CwlWorkflowRun(self.dataset_populator, self.workflow_populator, history_id, workflow_id, invocation_id)
 
     def run_cwl_job(
@@ -452,7 +447,7 @@ class BasePopulator(metaclass=ABCMeta):
 
 
 class BaseDatasetPopulator(BasePopulator):
-    """ Abstract description of API operations optimized for testing
+    """Abstract description of API operations optimized for testing
     Galaxy - implementations must implement _get, _post and _delete.
     """
 
@@ -466,17 +461,22 @@ class BaseDatasetPopulator(BasePopulator):
         return run_response.json()["outputs"][0]
 
     def new_dataset_request(self, history_id: str, content=None, wait: bool = False, **kwds) -> requests.Response:
-        """Lower-level dataset creation that returns the upload tool response object.
-        """
+        """Lower-level dataset creation that returns the upload tool response object."""
         if content is None and "ftp_files" not in kwds:
             content = "TestData123"
         payload = self.upload_payload(history_id, content=content, **kwds)
         run_response = self.tools_post(payload)
         if wait:
-            self.wait_for_tool_run(history_id, run_response, assert_ok=kwds.get('assert_ok', True))
+            self.wait_for_tool_run(history_id, run_response, assert_ok=kwds.get("assert_ok", True))
         return run_response
 
-    def fetch(self, payload: dict, assert_ok: bool = True, timeout: timeout_type = DEFAULT_TIMEOUT, wait: Optional[bool] = None):
+    def fetch(
+        self,
+        payload: dict,
+        assert_ok: bool = True,
+        timeout: timeout_type = DEFAULT_TIMEOUT,
+        wait: Optional[bool] = None,
+    ):
         tool_response = self._post("tools/fetch", data=payload)
         if wait is None:
             wait = assert_ok
@@ -492,10 +492,12 @@ class BaseDatasetPopulator(BasePopulator):
 
     def fetch_hdas(self, history_id: str, items: List[Dict[str, Any]], wait: bool = True) -> List[Dict[str, Any]]:
         destination = {"type": "hdas"}
-        targets = [{
-            "destination": destination,
-            "items": items,
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items": items,
+            }
+        ]
         payload = {
             "history_id": history_id,
             "targets": json.dumps(targets),
@@ -512,11 +514,17 @@ class BaseDatasetPopulator(BasePopulator):
 
     def tag_dataset(self, history_id, hda_id, tags):
         url = f"histories/{history_id}/contents/{hda_id}"
-        response = self._put(url, {'tags': tags}, json=True)
+        response = self._put(url, {"tags": tags}, json=True)
         response.raise_for_status()
         return response.json()
 
-    def wait_for_tool_run(self, history_id: str, run_response: requests.Response, timeout: timeout_type = DEFAULT_TIMEOUT, assert_ok: bool = True):
+    def wait_for_tool_run(
+        self,
+        history_id: str,
+        run_response: requests.Response,
+        timeout: timeout_type = DEFAULT_TIMEOUT,
+        assert_ok: bool = True,
+    ):
         job = self.check_run(run_response)
         self.wait_for_job(job["id"], timeout=timeout)
         self.wait_for_history(history_id, assert_ok=assert_ok, timeout=timeout)
@@ -528,15 +536,18 @@ class BaseDatasetPopulator(BasePopulator):
         job = run["jobs"][0]
         return job
 
-    def wait_for_history(self, history_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT) -> str:
+    def wait_for_history(
+        self, history_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT
+    ) -> str:
         try:
-            return wait_on_state(lambda: self._get(f"histories/{history_id}"), desc="history state", assert_ok=assert_ok, timeout=timeout)
+            return wait_on_state(
+                lambda: self._get(f"histories/{history_id}"), desc="history state", assert_ok=assert_ok, timeout=timeout
+            )
         except AssertionError:
             self._summarize_history(history_id)
             raise
 
     def wait_for_history_jobs(self, history_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT):
-
         def has_active_jobs():
             active_jobs = self.active_history_jobs(history_id)
             if len(active_jobs) == 0:
@@ -555,7 +566,9 @@ class BaseDatasetPopulator(BasePopulator):
             self.wait_for_history(history_id, assert_ok=True, timeout=timeout)
 
     def wait_for_job(self, job_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT):
-        return wait_on_state(lambda: self.get_job_details(job_id), desc="job state", assert_ok=assert_ok, timeout=timeout)
+        return wait_on_state(
+            lambda: self.get_job_details(job_id), desc="job state", assert_ok=assert_ok, timeout=timeout
+        )
 
     def get_job_details(self, job_id: str, full: bool = False) -> Response:
         return self._get(f"jobs/{job_id}?full={full}")
@@ -584,7 +597,7 @@ class BaseDatasetPopulator(BasePopulator):
         delete_response.raise_for_status()
 
     def delete_dataset(self, history_id: str, content_id: str, purge: bool = False) -> Response:
-        delete_response = self._delete(f"histories/{history_id}/contents/{content_id}", {'purge': purge}, json=True)
+        delete_response = self._delete(f"histories/{history_id}/contents/{content_id}", {"purge": purge}, json=True)
         return delete_response
 
     def create_tool_from_path(self, tool_path: str) -> Dict[str, Any]:
@@ -664,20 +677,20 @@ class BaseDatasetPopulator(BasePopulator):
     def upload_payload(self, history_id: str, content: Optional[str] = None, **kwds) -> dict:
         name = kwds.get("name", "Test_Dataset")
         dbkey = kwds.get("dbkey", "?")
-        file_type = kwds.get("file_type", 'txt')
+        file_type = kwds.get("file_type", "txt")
         upload_params = {
-            'files_0|NAME': name,
-            'dbkey': dbkey,
-            'file_type': file_type,
+            "files_0|NAME": name,
+            "dbkey": dbkey,
+            "file_type": file_type,
         }
         if dbkey is None:
             del upload_params["dbkey"]
         if content is None:
             upload_params["files_0|ftp_files"] = kwds.get("ftp_files")
-        elif hasattr(content, 'read'):
+        elif hasattr(content, "read"):
             upload_params["files_0|file_data"] = content
         else:
-            upload_params['files_0|url_paste'] = content
+            upload_params["files_0|url_paste"] = content
 
         if "to_posix_lines" in kwds:
             upload_params["files_0|to_posix_lines"] = kwds["to_posix_lines"]
@@ -687,10 +700,7 @@ class BaseDatasetPopulator(BasePopulator):
             upload_params["files_0|auto_decompress"] = kwds["auto_decompress"]
         upload_params.update(kwds.get("extra_inputs", {}))
         return self.run_tool_payload(
-            tool_id='upload1',
-            inputs=upload_params,
-            history_id=history_id,
-            upload_type='upload_dataset'
+            tool_id="upload1", inputs=upload_params, history_id=history_id, upload_type="upload_dataset"
         )
 
     def get_remote_files(self, target: str = "ftp") -> dict:
@@ -708,12 +718,7 @@ class BaseDatasetPopulator(BasePopulator):
                 kwds["__files"][key] = value
                 del inputs[key]
 
-        return dict(
-            tool_id=tool_id,
-            inputs=json.dumps(inputs),
-            history_id=history_id,
-            **kwds
-        )
+        return dict(tool_id=tool_id, inputs=json.dumps(inputs), history_id=history_id, **kwds)
 
     def build_tool_state(self, tool_id: str, history_id: str):
         response = self._post(f"tools/{tool_id}/build?history_id={history_id}")
@@ -733,16 +738,16 @@ class BaseDatasetPopulator(BasePopulator):
         tool_response = self._post(url, data=payload)
         return tool_response
 
-    def get_history_dataset_content(self, history_id: str, wait=True, filename=None, type='text', raw=False, **kwds):
+    def get_history_dataset_content(self, history_id: str, wait=True, filename=None, type="text", raw=False, **kwds):
         dataset_id = self.__history_content_id(history_id, wait=wait, **kwds)
         data = {}
         if filename:
             data["filename"] = filename
         if raw:
-            data['raw'] = True
+            data["raw"] = True
         display_response = self._get_contents_request(history_id, f"/{dataset_id}/display", data=data)
         assert display_response.status_code == 200, display_response.text
-        if type == 'text':
+        if type == "text":
             return display_response.text
         else:
             return display_response.content
@@ -795,7 +800,7 @@ class BaseDatasetPopulator(BasePopulator):
 
     def run_exit_code_from_file(self, history_id: str, hdca_id: str) -> dict:
         exit_code_inputs = {
-            "input": {'batch': True, 'values': [{"src": "hdca", "id": hdca_id}]},
+            "input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         response = self.run_tool("exit_code_from_file", exit_code_inputs, history_id)
         self.wait_for_history(history_id, assert_ok=False)
@@ -825,8 +830,10 @@ class BaseDatasetPopulator(BasePopulator):
                     raise Exception(f"Could not find content with HID [{hid}] in [{history_contents}]")
             else:
                 # No hid specified - just grab most recent element of correct content type
-                if kwds.get('history_content_type'):
-                    history_contents = [c for c in history_contents if c['history_content_type'] == kwds['history_content_type']]
+                if kwds.get("history_content_type"):
+                    history_contents = [
+                        c for c in history_contents if c["history_content_type"] == kwds["history_content_type"]
+                    ]
                 history_content_id = history_contents[-1]["id"]
         return history_content_id
 
@@ -839,9 +846,12 @@ class BaseDatasetPopulator(BasePopulator):
         return self._get(url, data=data)
 
     def ds_entry(self, history_content: dict) -> dict:
-        src = 'hda'
-        if 'history_content_type' in history_content and history_content['history_content_type'] == "dataset_collection":
-            src = 'hdca'
+        src = "hda"
+        if (
+            "history_content_type" in history_content
+            and history_content["history_content_type"] == "dataset_collection"
+        ):
+            src = "hdca"
         return dict(src=src, id=history_content["id"])
 
     def dataset_storage_info(self, dataset_id: str) -> dict:
@@ -924,23 +934,20 @@ class BaseDatasetPopulator(BasePopulator):
 
         def validated():
             metadata = self.get_history_dataset_details(history_id, dataset_id=dataset_id)
-            validated_state = metadata['validated_state']
-            if validated_state == 'unknown':
+            validated_state = metadata["validated_state"]
+            if validated_state == "unknown":
                 return
             else:
                 return validated_state
 
-        return wait_on(
-            validated,
-            "dataset validation"
-        )
+        return wait_on(validated, "dataset validation")
 
     def setup_history_for_export_testing(self, history_name):
         history_id = self.new_history(name=history_name)
         hda = self.new_dataset(history_id, content="1 2 3")
-        tags = ['name:name']
-        response = self.tag_dataset(history_id, hda['id'], tags=tags)
-        assert response['tags'] == tags
+        tags = ["name:name"]
+        response = self.tag_dataset(history_id, hda["id"], tags=tags)
+        assert response["tags"] == tags
         deleted_hda = self.new_dataset(history_id, content="1 2 3", wait=True)
         self.delete_dataset(history_id, deleted_hda["id"])
         deleted_details = self.get_history_dataset_details(history_id, id=deleted_hda["id"])
@@ -953,6 +960,7 @@ class BaseDatasetPopulator(BasePopulator):
         put_response.raise_for_status()
 
         if put_response.status_code == 202:
+
             def export_ready_response():
                 put_response = self._put(url)
                 if put_response.status_code == 202:
@@ -971,7 +979,7 @@ class BaseDatasetPopulator(BasePopulator):
         put_response = self.prepare_export(history_id, data)
         response = put_response.json()
         api_asserts.assert_has_keys(response, "download_url")
-        download_url = urllib.parse.urljoin(self.galaxy_interactor.api_url, response["download_url"].strip('/'))
+        download_url = urllib.parse.urljoin(self.galaxy_interactor.api_url, response["download_url"].strip("/"))
 
         if check_download:
             self.get_export_url(download_url, api_key)
@@ -1021,7 +1029,6 @@ class BaseDatasetPopulator(BasePopulator):
         return history_index_response.json()
 
     def wait_on_history_length(self, history_id, wait_on_history_length):
-
         def history_has_length():
             history_length = self.history_length(history_id)
             return None if history_length != wait_on_history_length else True
@@ -1052,14 +1059,19 @@ class BaseDatasetPopulator(BasePopulator):
 
     def get_random_name(self, prefix=None, suffix=None, len=10):
         # stolen from navigates_galaxy.py
-        return '{}{}{}'.format(
-            prefix or '',
-            ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(len)),
-            suffix or '',
+        return "{}{}{}".format(
+            prefix or "",
+            "".join(random.choice(string.ascii_lowercase + string.digits) for _ in range(len)),
+            suffix or "",
         )
 
     def wait_for_dataset(self, history_id, dataset_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
-        return wait_on_state(lambda: self._get(f"histories/{history_id}/contents/{dataset_id}"), desc="dataset state", assert_ok=assert_ok, timeout=timeout)
+        return wait_on_state(
+            lambda: self._get(f"histories/{history_id}/contents/{dataset_id}"),
+            desc="dataset state",
+            assert_ok=assert_ok,
+            timeout=timeout,
+        )
 
 
 class GalaxyInteractorHttpMixin:
@@ -1089,7 +1101,6 @@ class GalaxyInteractorHttpMixin:
 
 
 class DatasetPopulator(GalaxyInteractorHttpMixin, BaseDatasetPopulator):
-
     def __init__(self, galaxy_interactor):
         self.galaxy_interactor = galaxy_interactor
 
@@ -1099,7 +1110,7 @@ class DatasetPopulator(GalaxyInteractorHttpMixin, BaseDatasetPopulator):
 
 class BaseWorkflowPopulator(BasePopulator):
     dataset_populator: BaseDatasetPopulator
-    dataset_collection_populator: 'BaseDatasetCollectionPopulator'
+    dataset_collection_populator: "BaseDatasetCollectionPopulator"
 
     def load_workflow(self, name: str, content: str = workflow_str, add_pja=False) -> dict:
         workflow = json.loads(content)
@@ -1145,10 +1156,7 @@ class BaseWorkflowPopulator(BasePopulator):
         return uploaded_workflow_id
 
     def create_workflow_response(self, workflow: Dict[str, Any], **create_kwds) -> Response:
-        data = dict(
-            workflow=json.dumps(workflow),
-            **create_kwds
-        )
+        data = dict(workflow=json.dumps(workflow), **create_kwds)
         upload_response = self._post("workflows/upload", data=data)
         return upload_response
 
@@ -1162,11 +1170,15 @@ class BaseWorkflowPopulator(BasePopulator):
             workflow_yaml_wrapped = self.download_workflow(workflow_id, style="format2_wrapped_yaml")
             assert "yaml_content" in workflow_yaml_wrapped, workflow_yaml_wrapped
             round_trip_converted_content = workflow_yaml_wrapped["yaml_content"]
-            workflow_id = self.upload_yaml_workflow(round_trip_converted_content, client_convert=False, round_trip_conversion=False)
+            workflow_id = self.upload_yaml_workflow(
+                round_trip_converted_content, client_convert=False, round_trip_conversion=False
+            )
 
         return workflow_id
 
-    def wait_for_invocation(self, workflow_id: str, invocation_id: str, timeout: timeout_type = DEFAULT_TIMEOUT, assert_ok: bool = True):
+    def wait_for_invocation(
+        self, workflow_id: str, invocation_id: str, timeout: timeout_type = DEFAULT_TIMEOUT, assert_ok: bool = True
+    ):
         url = f"workflows/{workflow_id}/usage/{invocation_id}"
 
         def workflow_state():
@@ -1179,8 +1191,11 @@ class BaseWorkflowPopulator(BasePopulator):
         api_asserts.assert_status_code_is(history_invocations_response, 200)
         return history_invocations_response.json()
 
-    def wait_for_history_workflows(self, history_id, assert_ok=True, timeout=DEFAULT_TIMEOUT, expected_invocation_count=None):
+    def wait_for_history_workflows(
+        self, history_id, assert_ok=True, timeout=DEFAULT_TIMEOUT, expected_invocation_count=None
+    ):
         if expected_invocation_count is not None:
+
             def invocation_count():
                 invocations = self.history_invocations(history_id)
                 if len(invocations) == expected_invocation_count:
@@ -1193,13 +1208,13 @@ class BaseWorkflowPopulator(BasePopulator):
             self.wait_for_workflow(workflow_id, invocation_id, history_id, timeout=timeout, assert_ok=assert_ok)
 
     def wait_for_workflow(self, workflow_id, invocation_id, history_id, assert_ok=True, timeout=DEFAULT_TIMEOUT):
-        """ Wait for a workflow invocation to completely schedule and then history
-        to be complete. """
+        """Wait for a workflow invocation to completely schedule and then history
+        to be complete."""
         self.wait_for_invocation(workflow_id, invocation_id, timeout=timeout, assert_ok=assert_ok)
         self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=assert_ok, timeout=timeout)
 
     def get_invocation(self, invocation_id, step_details=False):
-        r = self._get(f"invocations/{invocation_id}", data={'step_details': step_details})
+        r = self._get(f"invocations/{invocation_id}", data={"step_details": step_details})
         r.raise_for_status()
         return r.json()
 
@@ -1208,15 +1223,37 @@ class BaseWorkflowPopulator(BasePopulator):
         bco_response.raise_for_status()
         return bco_response.json()
 
-    def validate_biocompute_object(self, bco, expected_schema_version='https://w3id.org/ieee/ieee-2791-schema/2791object.json'):
+    def validate_biocompute_object(
+        self, bco, expected_schema_version="https://w3id.org/ieee/ieee-2791-schema/2791object.json"
+    ):
         # TODO: actually use jsonref and jsonschema to validate this someday
-        api_asserts.assert_has_keys(bco, "object_id", "spec_version", "etag", "provenance_domain", "usability_domain", "description_domain", "execution_domain", "parametric_domain", "io_domain", "error_domain")
-        assert bco['spec_version'] == expected_schema_version
-        api_asserts.assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
-        api_asserts.assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
-        for p in bco['parametric_domain']:
+        api_asserts.assert_has_keys(
+            bco,
+            "object_id",
+            "spec_version",
+            "etag",
+            "provenance_domain",
+            "usability_domain",
+            "description_domain",
+            "execution_domain",
+            "parametric_domain",
+            "io_domain",
+            "error_domain",
+        )
+        assert bco["spec_version"] == expected_schema_version
+        api_asserts.assert_has_keys(bco["description_domain"], "keywords", "xref", "platform", "pipeline_steps")
+        api_asserts.assert_has_keys(
+            bco["execution_domain"],
+            "script_access_type",
+            "script",
+            "script_driver",
+            "software_prerequisites",
+            "external_data_endpoints",
+            "environment_variables",
+        )
+        for p in bco["parametric_domain"]:
             api_asserts.assert_has_keys(p, "param", "value", "step")
-        api_asserts.assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
+        api_asserts.assert_has_keys(bco["io_domain"], "input_subdomain", "output_subdomain")
 
     def invoke_workflow_raw(self, workflow_id: str, request: dict, assert_ok: bool = False) -> Response:
         url = f"workflows/{workflow_id}/invocations"
@@ -1225,7 +1262,15 @@ class BaseWorkflowPopulator(BasePopulator):
             invocation_response.raise_for_status()
         return invocation_response
 
-    def invoke_workflow(self, workflow_id: str, history_id: Optional[str] = None, inputs: Optional[dict] = None, request: Optional[dict] = None, assert_ok: bool = True, inputs_by: str = 'step_index'):
+    def invoke_workflow(
+        self,
+        workflow_id: str,
+        history_id: Optional[str] = None,
+        inputs: Optional[dict] = None,
+        request: Optional[dict] = None,
+        assert_ok: bool = True,
+        inputs_by: str = "step_index",
+    ):
         if inputs is None:
             inputs = {}
 
@@ -1247,8 +1292,17 @@ class BaseWorkflowPopulator(BasePopulator):
         else:
             return invocation_response
 
-    def invoke_workflow_and_wait(self, workflow_id: str, history_id: Optional[str] = None, inputs: Optional[dict] = None, request: Optional[dict] = None, assert_ok: bool = True):
-        invoke_return = self.invoke_workflow(workflow_id, history_id=history_id, inputs=inputs, request=request, assert_ok=assert_ok)
+    def invoke_workflow_and_wait(
+        self,
+        workflow_id: str,
+        history_id: Optional[str] = None,
+        inputs: Optional[dict] = None,
+        request: Optional[dict] = None,
+        assert_ok: bool = True,
+    ):
+        invoke_return = self.invoke_workflow(
+            workflow_id, history_id=history_id, inputs=inputs, request=request, assert_ok=assert_ok
+        )
         if assert_ok:
             invocation_id = invoke_return
         else:
@@ -1259,7 +1313,7 @@ class BaseWorkflowPopulator(BasePopulator):
         if history_id is None and request:
             history_id = request["history"]
             if history_id.startswith("hist_id="):
-                history_id = history_id[len("hist_id="):]
+                history_id = history_id[len("hist_id=") :]
         self.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=assert_ok)
         return invoke_return
 
@@ -1268,12 +1322,14 @@ class BaseWorkflowPopulator(BasePopulator):
         api_asserts.assert_status_code_is(response, 200)
         return response.json()
 
-    def download_workflow(self, workflow_id: str, style: Optional[str] = None, history_id: Optional[str] = None) -> dict:
+    def download_workflow(
+        self, workflow_id: str, style: Optional[str] = None, history_id: Optional[str] = None
+    ) -> dict:
         params = {}
         if style is not None:
             params["style"] = style
         if history_id is not None:
-            params['history_id'] = history_id
+            params["history_id"] = history_id
         response = self._get(f"workflows/{workflow_id}/download", data=params)
         api_asserts.assert_status_code_is(response, 200)
         if style != "format2":
@@ -1282,14 +1338,14 @@ class BaseWorkflowPopulator(BasePopulator):
             return ordered_load(response.text)
 
     def update_workflow(self, workflow_id: str, workflow_object: dict) -> Response:
-        data = dict(
-            workflow=workflow_object
-        )
-        raw_url = f'workflows/{workflow_id}'
+        data = dict(workflow=workflow_object)
+        raw_url = f"workflows/{workflow_id}"
         put_response = self._put(raw_url, data, json=True)
         return put_response
 
-    def refactor_workflow(self, workflow_id: str, actions: list, dry_run: Optional[bool] = None, style: Optional[str] = None) -> Response:
+    def refactor_workflow(
+        self, workflow_id: str, actions: list, dry_run: Optional[bool] = None, style: Optional[str] = None
+    ) -> Response:
         data: Dict[str, Any] = dict(
             actions=actions,
         )
@@ -1297,7 +1353,7 @@ class BaseWorkflowPopulator(BasePopulator):
             data["style"] = style
         if dry_run is not None:
             data["dry_run"] = dry_run
-        raw_url = f'workflows/{workflow_id}/refactor'
+        raw_url = f"workflows/{workflow_id}/refactor"
         put_response = self._put(raw_url, data, json=True)
         return put_response
 
@@ -1308,7 +1364,20 @@ class BaseWorkflowPopulator(BasePopulator):
         put_respose = self.update_workflow(workflow_id, workflow_object)
         put_respose.raise_for_status()
 
-    def run_workflow(self, has_workflow, test_data=None, history_id=None, wait=True, source_type=None, jobs_descriptions=None, expected_response=200, assert_ok=True, client_convert=None, round_trip_format_conversion=False, raw_yaml=False):
+    def run_workflow(
+        self,
+        has_workflow,
+        test_data=None,
+        history_id=None,
+        wait=True,
+        source_type=None,
+        jobs_descriptions=None,
+        expected_response=200,
+        assert_ok=True,
+        client_convert=None,
+        round_trip_format_conversion=False,
+        raw_yaml=False,
+    ):
         """High-level wrapper around workflow API, etc. to invoke format 2 workflows."""
         workflow_populator = self
         if client_convert is None:
@@ -1319,7 +1388,7 @@ class BaseWorkflowPopulator(BasePopulator):
             source_type=source_type,
             client_convert=client_convert,
             round_trip_format_conversion=round_trip_format_conversion,
-            raw_yaml=raw_yaml
+            raw_yaml=raw_yaml,
         )
 
         if test_data is None:
@@ -1332,17 +1401,19 @@ class BaseWorkflowPopulator(BasePopulator):
         if not isinstance(test_data, dict):
             test_data = yaml.safe_load(test_data)
 
-        parameters = test_data.pop('step_parameters', {})
+        parameters = test_data.pop("step_parameters", {})
         replacement_parameters = test_data.pop("replacement_parameters", {})
         if history_id is None:
             history_id = self.dataset_populator.new_history()
-        inputs, label_map, has_uploads = load_data_dict(history_id, test_data, self.dataset_populator, self.dataset_collection_populator)
+        inputs, label_map, has_uploads = load_data_dict(
+            history_id, test_data, self.dataset_populator, self.dataset_collection_populator
+        )
         workflow_request: Dict[str, Any] = dict(
             history=f"hist_id={history_id}",
             workflow_id=workflow_id,
         )
         workflow_request["inputs"] = json.dumps(label_map)
-        workflow_request["inputs_by"] = 'name'
+        workflow_request["inputs_by"] = "name"
         if parameters:
             workflow_request["parameters"] = json.dumps(parameters)
             workflow_request["parameters_normalized"] = True
@@ -1356,7 +1427,7 @@ class BaseWorkflowPopulator(BasePopulator):
         if expected_response != 200:
             assert not assert_ok
             return invocation
-        invocation_id = invocation.get('id')
+        invocation_id = invocation.get("id")
         if invocation_id:
             # Wait for workflow to become fully scheduled and then for all jobs
             # complete.
@@ -1370,7 +1441,7 @@ class BaseWorkflowPopulator(BasePopulator):
                 inputs=inputs,
                 jobs=jobs,
                 invocation=invocation,
-                workflow_request=workflow_request
+                workflow_request=workflow_request,
             )
 
     def dump_workflow(self, workflow_id, style=None):
@@ -1395,7 +1466,13 @@ class BaseWorkflowPopulator(BasePopulator):
                 ds_map[key] = label_map[label]
         return json.dumps(ds_map)
 
-    def setup_workflow_run(self, workflow: Optional[Dict[str, Any]] = None, inputs_by: str = 'step_id', history_id: Optional[str] = None, workflow_id: Optional[str] = None) -> Tuple[Dict[str, Any], str, str]:
+    def setup_workflow_run(
+        self,
+        workflow: Optional[Dict[str, Any]] = None,
+        inputs_by: str = "step_id",
+        history_id: Optional[str] = None,
+        workflow_id: Optional[str] = None,
+    ) -> Tuple[Dict[str, Any], str, str]:
         ds_entry = self.dataset_populator.ds_entry
         if not workflow_id:
             assert workflow, "If workflow_id not specified, must specify a workflow dictionary to load"
@@ -1407,23 +1484,17 @@ class BaseWorkflowPopulator(BasePopulator):
         workflow_request = dict(
             history=f"hist_id={history_id}",
         )
-        label_map = {
-            'WorkflowInput1': ds_entry(hda1),
-            'WorkflowInput2': ds_entry(hda2)
-        }
-        if inputs_by == 'step_id':
+        label_map = {"WorkflowInput1": ds_entry(hda1), "WorkflowInput2": ds_entry(hda2)}
+        if inputs_by == "step_id":
             ds_map = self.build_ds_map(workflow_id, label_map)
             workflow_request["ds_map"] = ds_map
         elif inputs_by == "step_index":
-            index_map = {
-                '0': ds_entry(hda1),
-                '1': ds_entry(hda2)
-            }
+            index_map = {"0": ds_entry(hda1), "1": ds_entry(hda2)}
             workflow_request["inputs"] = json.dumps(index_map)
-            workflow_request["inputs_by"] = 'step_index'
+            workflow_request["inputs_by"] = "step_index"
         elif inputs_by == "name":
             workflow_request["inputs"] = json.dumps(label_map)
-            workflow_request["inputs_by"] = 'name'
+            workflow_request["inputs_by"] = "name"
         elif inputs_by in ["step_uuid", "uuid_implicitly"]:
             assert workflow, f"Must specify workflow for this inputs_by {inputs_by} parameter value"
             uuid_map = {
@@ -1440,9 +1511,9 @@ class BaseWorkflowPopulator(BasePopulator):
         state = self.wait_for_invocation(workflow_id, invocation_id)
         if assert_ok:
             assert state == "scheduled", state
-        time.sleep(.5)
+        time.sleep(0.5)
         self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=assert_ok)
-        time.sleep(.5)
+        time.sleep(0.5)
 
 
 class RunJobsSummary(NamedTuple):
@@ -1456,7 +1527,6 @@ class RunJobsSummary(NamedTuple):
 
 
 class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, ImporterGalaxyInterface):
-
     def __init__(self, galaxy_interactor):
         self.galaxy_interactor = galaxy_interactor
         self.dataset_populator = DatasetPopulator(galaxy_interactor)
@@ -1467,7 +1537,7 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
     def import_workflow(self, workflow, **kwds) -> Dict[str, Any]:
         workflow_str = json.dumps(workflow, indent=4)
         data = {
-            'workflow': workflow_str,
+            "workflow": workflow_str,
         }
         data.update(**kwds)
         upload_response = self._post("workflows", data=data)
@@ -1475,7 +1545,7 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
         return upload_response.json()
 
     def import_tool(self, tool) -> Dict[str, Any]:
-        """ Import a workflow via POST /api/workflows or
+        """Import a workflow via POST /api/workflows or
         comparable interface into Galaxy.
         """
         upload_response = self._import_tool_response(tool)
@@ -1484,9 +1554,7 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
 
     def _import_tool_response(self, tool) -> Response:
         tool_str = json.dumps(tool, indent=4)
-        data = {
-            'representation': tool_str
-        }
+        data = {"representation": tool_str}
         upload_response = self._post("dynamic_tools", data=data, admin=True)
         return upload_response
 
@@ -1509,7 +1577,7 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
 
         scale_workflow_steps = [
             {"tool_id": "create_input_collection", "state": {"collection_size": collection_size}, "label": "wf_input"},
-            {"tool_id": "cat", "state": {"input1": self._link("wf_input", "output")}, "label": "cat_0"}
+            {"tool_id": "cat", "state": {"input1": self._link("wf_input", "output")}, "label": "cat_0"},
         ]
 
         for i in range(workflow_depth):
@@ -1531,7 +1599,11 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
 
         scale_workflow_steps = [
             {"tool_id": "create_input_collection", "state": {"collection_size": collection_size}, "label": "wf_input"},
-            {"tool_id": "cat", "state": {"input1": self._link("wf_input"), "input2": self._link("wf_input")}, "label": "cat_0"}
+            {
+                "tool_id": "cat",
+                "state": {"input1": self._link("wf_input"), "input2": self._link("wf_input")},
+                "label": "cat_0",
+            },
         ]
 
         for i in range(workflow_depth):
@@ -1580,7 +1652,6 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
 
 
 class LibraryPopulator:
-
     def __init__(self, galaxy_interactor):
         self.galaxy_interactor = galaxy_interactor
         self.dataset_populator = DatasetPopulator(galaxy_interactor)
@@ -1610,7 +1681,7 @@ class LibraryPopulator:
         page: Optional[int] = 1,
         page_limit: Optional[int] = 1000,
         q: Optional[str] = None,
-        admin: Optional[bool] = True
+        admin: Optional[bool] = True,
     ):
         query = f"&q={q}" if q else ""
         response = self.galaxy_interactor.get(
@@ -1664,7 +1735,9 @@ class LibraryPopulator:
         self._set_permissions(library_id, permissions)
 
     def _set_permissions(self, library_id, permissions):
-        response = self.galaxy_interactor.post(f"libraries/{library_id}/permissions", data=permissions, admin=True, json=True)
+        response = self.galaxy_interactor.post(
+            f"libraries/{library_id}/permissions", data=permissions, admin=True, json=True
+        )
         api_asserts.assert_status_code_is(response, 200)
 
     def user_email(self):
@@ -1771,10 +1844,9 @@ class BaseDatasetCollectionPopulator:
     dataset_populator: BaseDatasetPopulator
 
     def create_list_from_pairs(self, history_id, pairs, name="Dataset Collection from pairs"):
-        return self.create_nested_collection(history_id=history_id,
-                                             collection=pairs,
-                                             collection_type='list:paired',
-                                             name=name)
+        return self.create_nested_collection(
+            history_id=history_id, collection=pairs, collection_type="list:paired", name=name
+        )
 
     def nested_collection_identifiers(self, history_id, collection_type):
         rank_types = list(reversed(collection_type.split(":")))
@@ -1788,16 +1860,20 @@ class BaseDatasetCollectionPopulator:
 
         for i, rank_type in enumerate(reversed(rank_types[1:])):
             name = f"test_level_{i + 1}" if rank_type == "list" else "paired"
-            identifiers = [dict(
-                src="new_collection",
-                name=name,
-                collection_type=nested_collection_type,
-                element_identifiers=identifiers,
-            )]
+            identifiers = [
+                dict(
+                    src="new_collection",
+                    name=name,
+                    collection_type=nested_collection_type,
+                    element_identifiers=identifiers,
+                )
+            ]
             nested_collection_type = f"{rank_type}:{nested_collection_type}"
         return identifiers
 
-    def create_nested_collection(self, history_id, collection_type, name=None, collection=None, element_identifiers=None):
+    def create_nested_collection(
+        self, history_id, collection_type, name=None, collection=None, element_identifiers=None
+    ):
         """Create a nested collection either from collection or using collection_type)."""
         assert collection_type is not None
         name = name or f"Test {collection_type}"
@@ -1805,11 +1881,7 @@ class BaseDatasetCollectionPopulator:
             assert element_identifiers is None
             element_identifiers = []
             for i, pair in enumerate(collection):
-                element_identifiers.append(dict(
-                    name=f"test{i}",
-                    src="hdca",
-                    id=pair
-                ))
+                element_identifiers.append(dict(name=f"test{i}", src="hdca", id=pair))
         if element_identifiers is None:
             element_identifiers = self.nested_collection_identifiers(history_id, collection_type)
 
@@ -1823,46 +1895,44 @@ class BaseDatasetCollectionPopulator:
         return self.__create(payload)
 
     def create_list_of_pairs_in_history(self, history_id, **kwds):
-        return self.upload_collection(history_id, "list:paired", elements=[
-            {
-                "name": "test0",
-                "elements": [
-                    {"src": "pasted", "paste_content": "TestData123", "name": "forward"},
-                    {"src": "pasted", "paste_content": "TestData123", "name": "reverse"},
-                ]
-            }
-        ])
+        return self.upload_collection(
+            history_id,
+            "list:paired",
+            elements=[
+                {
+                    "name": "test0",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "TestData123", "name": "forward"},
+                        {"src": "pasted", "paste_content": "TestData123", "name": "reverse"},
+                    ],
+                }
+            ],
+        )
 
     def create_list_of_list_in_history(self, history_id, **kwds):
         # create_nested_collection will generate nested collection from just datasets,
         # this function uses recursive generation of history hdcas.
-        collection_type = kwds.pop('collection_type', 'list:list')
-        collection_types = collection_type.split(':')
-        list = self.create_list_in_history(history_id, **kwds).json()['id']
-        current_collection_type = 'list'
+        collection_type = kwds.pop("collection_type", "list:list")
+        collection_types = collection_type.split(":")
+        list = self.create_list_in_history(history_id, **kwds).json()["id"]
+        current_collection_type = "list"
         for collection_type in collection_types[1:]:
             current_collection_type = f"{current_collection_type}:{collection_type}"
-            response = self.create_nested_collection(history_id=history_id,
-                                                     collection_type=current_collection_type,
-                                                     name=current_collection_type,
-                                                     collection=[list])
-            list = response.json()['id']
+            response = self.create_nested_collection(
+                history_id=history_id,
+                collection_type=current_collection_type,
+                name=current_collection_type,
+                collection=[list],
+            )
+            list = response.json()["id"]
         return response
 
     def create_pair_in_history(self, history_id, **kwds):
-        payload = self.create_pair_payload(
-            history_id,
-            instance_type="history",
-            **kwds
-        )
+        payload = self.create_pair_payload(history_id, instance_type="history", **kwds)
         return self.__create(payload)
 
     def create_list_in_history(self, history_id, **kwds):
-        payload = self.create_list_payload(
-            history_id,
-            instance_type="history",
-            **kwds
-        )
+        payload = self.create_list_payload(history_id, instance_type="history", **kwds)
         return self.__create(payload)
 
     def upload_collection(self, history_id, collection_type, elements, **kwds):
@@ -1873,7 +1943,9 @@ class BaseDatasetCollectionPopulator:
         return self.__create_payload(history_id, identifiers_func=self.list_identifiers, collection_type="list", **kwds)
 
     def create_pair_payload(self, history_id, **kwds):
-        return self.__create_payload(history_id, identifiers_func=self.pair_identifiers, collection_type="paired", **kwds)
+        return self.__create_payload(
+            history_id, identifiers_func=self.pair_identifiers, collection_type="paired", **kwds
+        )
 
     def __create_payload(self, *args, **kwds):
         direct_upload = kwds.pop("direct_upload", False)
@@ -1925,12 +1997,14 @@ class BaseDatasetCollectionPopulator:
 
         name = kwds.get("name", "Test Dataset Collection")
 
-        targets = [{
-            "destination": {"type": "hdca"},
-            "elements": elements,
-            "collection_type": collection_type,
-            "name": name,
-        }]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": collection_type,
+                "name": name,
+            }
+        ]
         payload = dict(
             history_id=history_id,
             targets=json.dumps(targets),
@@ -1940,7 +2014,9 @@ class BaseDatasetCollectionPopulator:
     def wait_for_fetched_collection(self, fetch_response):
         self.dataset_populator.wait_for_job(fetch_response["jobs"][0]["id"], assert_ok=True)
         initial_dataset_collection = fetch_response["outputs"][0]
-        dataset_collection = self.dataset_populator.get_history_collection_details(initial_dataset_collection["history_id"], hid=initial_dataset_collection["hid"])
+        dataset_collection = self.dataset_populator.get_history_collection_details(
+            initial_dataset_collection["history_id"], hid=initial_dataset_collection["hid"]
+        )
         return dataset_collection
 
     def __create_payload_collection(self, history_id, identifiers_func, collection_type, **kwds):
@@ -1955,11 +2031,7 @@ class BaseDatasetCollectionPopulator:
         if "name" not in kwds:
             kwds["name"] = "Test Dataset Collection"
 
-        payload = dict(
-            history_id=history_id,
-            collection_type=collection_type,
-            **kwds
-        )
+        payload = dict(history_id=history_id, collection_type=collection_type, **kwds)
         return payload
 
     def pair_identifiers(self, history_id, contents=None):
@@ -1980,11 +2052,13 @@ class BaseDatasetCollectionPopulator:
 
             def hda_to_identifier(i, hda):
                 return dict(name=contents[i][0], src="hda", id=hda["id"])
+
         else:
             hdas = self.__datasets(history_id, count=count, contents=contents)
 
             def hda_to_identifier(i, hda):
                 return dict(name=f"data{i + 1}", src="hda", id=hda["id"])
+
         element_identifiers = [hda_to_identifier(i, hda) for (i, hda) in enumerate(hdas)]
         return element_identifiers
 
@@ -2008,13 +2082,15 @@ class BaseDatasetCollectionPopulator:
 
     def wait_for_dataset_collection(self, create_payload, assert_ok=False, timeout=DEFAULT_TIMEOUT):
         for element in create_payload["elements"]:
-            if element['element_type'] == 'hda':
-                self.dataset_populator.wait_for_dataset(history_id=element['object']['history_id'],
-                                                        dataset_id=element['object']['id'],
-                                                        assert_ok=assert_ok,
-                                                        timeout=timeout)
-            elif element['element_type'] == 'dataset_collection':
-                self.wait_for_dataset_collection(element['object'], assert_ok=assert_ok, timeout=timeout)
+            if element["element_type"] == "hda":
+                self.dataset_populator.wait_for_dataset(
+                    history_id=element["object"]["history_id"],
+                    dataset_id=element["object"]["id"],
+                    assert_ok=assert_ok,
+                    timeout=timeout,
+                )
+            elif element["element_type"] == "dataset_collection":
+                self.wait_for_dataset_collection(element["object"], assert_ok=assert_ok, timeout=timeout)
 
     @abstractmethod
     def _create_collection(self, payload: dict) -> Response:
@@ -2022,7 +2098,6 @@ class BaseDatasetCollectionPopulator:
 
 
 class DatasetCollectionPopulator(BaseDatasetCollectionPopulator):
-
     def __init__(self, galaxy_interactor: ApiTestInteractor):
         self.galaxy_interactor = galaxy_interactor
         self.dataset_populator = DatasetPopulator(galaxy_interactor)
@@ -2049,7 +2124,7 @@ def load_data_dict(history_id, test_data, dataset_populator, dataset_collection_
 
     for key, value in test_data.items():
         is_dict = isinstance(value, dict)
-        if is_dict and ("elements" in value or value.get('collection_type')):
+        if is_dict and ("elements" in value or value.get("collection_type")):
             elements_data = value.get("elements", [])
             elements = []
             for element_data in elements_data:
@@ -2070,15 +2145,27 @@ def load_data_dict(history_id, test_data, dataset_populator, dataset_collection_
             new_collection_kwds = {}
             if "name" in value:
                 new_collection_kwds["name"] = value["name"]
-            collection_type = value.get('collection_type', '')
+            collection_type = value.get("collection_type", "")
             if collection_type == "list:paired":
-                fetch_response = dataset_collection_populator.create_list_of_pairs_in_history(history_id, contents=elements, **new_collection_kwds).json()
-            elif collection_type and ':' in collection_type:
-                fetch_response = {'outputs': [dataset_collection_populator.create_nested_collection(history_id, collection_type=collection_type, **new_collection_kwds).json()]}
+                fetch_response = dataset_collection_populator.create_list_of_pairs_in_history(
+                    history_id, contents=elements, **new_collection_kwds
+                ).json()
+            elif collection_type and ":" in collection_type:
+                fetch_response = {
+                    "outputs": [
+                        dataset_collection_populator.create_nested_collection(
+                            history_id, collection_type=collection_type, **new_collection_kwds
+                        ).json()
+                    ]
+                }
             elif collection_type == "list":
-                fetch_response = dataset_collection_populator.create_list_in_history(history_id, contents=elements, direct_upload=True, **new_collection_kwds).json()
+                fetch_response = dataset_collection_populator.create_list_in_history(
+                    history_id, contents=elements, direct_upload=True, **new_collection_kwds
+                ).json()
             else:
-                fetch_response = dataset_collection_populator.create_pair_in_history(history_id, contents=elements or None, direct_upload=True, **new_collection_kwds).json()
+                fetch_response = dataset_collection_populator.create_pair_in_history(
+                    history_id, contents=elements or None, direct_upload=True, **new_collection_kwds
+                ).json()
             hdca_output = fetch_response["outputs"][0]
             hdca = dataset_populator.ds_entry(hdca_output)
             hdca["hid"] = hdca_output["hid"]
@@ -2089,9 +2176,7 @@ def load_data_dict(history_id, test_data, dataset_populator, dataset_collection_
             input_type = value["type"]
             if input_type == "File":
                 content = open_test_data(value)
-                new_dataset_kwds = {
-                    "content": content
-                }
+                new_dataset_kwds = {"content": content}
                 if "name" in value:
                     new_dataset_kwds["name"] = value["name"]
                 if "file_type" in value:
@@ -2121,7 +2206,7 @@ def stage_inputs(
     use_fetch_api=True,
     to_posix_lines=True,
     tool_or_workflow="workflow",
-    job_dir=None
+    job_dir=None,
 ):
     """Alternative to load_data_dict that uses production-style workflow inputs."""
     kwds = dict(
@@ -2132,9 +2217,7 @@ def stage_inputs(
     )
     if job_dir is not None:
         kwds["job_dir"] = job_dir
-    inputs, datasets = InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(
-        tool_or_workflow, **kwds
-    )
+    inputs, datasets = InteractorStaging(galaxy_interactor, use_fetch_api=use_fetch_api).stage(tool_or_workflow, **kwds)
     return inputs, datasets
 
 
@@ -2147,7 +2230,9 @@ def stage_rules_example(galaxy_interactor, history_id, example):
     return inputs
 
 
-def wait_on_state(state_func: Callable, desc="state", skip_states=None, ok_states=None, assert_ok=False, timeout=DEFAULT_TIMEOUT) -> str:
+def wait_on_state(
+    state_func: Callable, desc="state", skip_states=None, ok_states=None, assert_ok=False, timeout=DEFAULT_TIMEOUT
+) -> str:
     def get_state():
         response = state_func()
         assert response.status_code == 200, f"Failed to fetch state update while waiting. [{response.content}]"
@@ -2172,6 +2257,7 @@ def wait_on_state(state_func: Callable, desc="state", skip_states=None, ok_state
 
 class GiHttpMixin:
     """Mixin for adapting Galaxy testing populators helpers to bioblend."""
+
     _gi: GalaxyClient
 
     @property
@@ -2190,26 +2276,26 @@ class GiHttpMixin:
         if data is None:
             data = {}
         data = data.copy()
-        data['key'] = self._gi.key
+        data["key"] = self._gi.key
         return requests.post(self._url(route), data=data, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
 
     def _put(self, route, data=None, headers=None, admin=False, json: bool = False):
         if data is None:
             data = {}
         data = data.copy()
-        data['key'] = self._gi.key
+        data["key"] = self._gi.key
         return requests.put(self._url(route), data=data, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
 
     def _delete(self, route, data=None, headers=None, admin=False, json: bool = False):
         if data is None:
             data = {}
         data = data.copy()
-        data['key'] = self._gi.key
+        data["key"] = self._gi.key
         return requests.delete(self._url(route), data=data, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
 
     def _url(self, route):
         if route.startswith("/api/"):
-            route = route[len("/api/"):]
+            route = route[len("/api/") :]
 
         return f"{self._api_url()}/{route}"
 
diff --git a/lib/galaxy_test/base/rules_test_data.py b/lib/galaxy_test/base/rules_test_data.py
index 57916ea749e..1530c0a0598 100644
--- a/lib/galaxy_test/base/rules_test_data.py
+++ b/lib/galaxy_test/base/rules_test_data.py
@@ -100,7 +100,7 @@ EXAMPLE_1 = {
                 "contents": "1",
                 "class": "File",
             },
-        ]
+        ],
     },
     "check": check_example_1,
     "output_hid": 6,
@@ -117,7 +117,7 @@ EXAMPLE_2 = {
             {
                 "type": "add_column_metadata",
                 "value": "identifier0",
-            }
+            },
         ],
         "mapping": [
             {
@@ -139,7 +139,7 @@ EXAMPLE_2 = {
                 "contents": "1",
                 "class": "File",
             },
-        ]
+        ],
     },
     "check": check_example_2,
     "output_hid": 6,
@@ -161,7 +161,7 @@ EXAMPLE_3 = {
                 "type": "add_column_concatenate",
                 "target_column_0": 0,
                 "target_column_1": 1,
-            }
+            },
         ],
         "mapping": [
             {
@@ -176,19 +176,11 @@ EXAMPLE_3 = {
             {
                 "identifier": "test0",
                 "elements": [
-                    {
-                        "identifier": "forward",
-                        "class": "File",
-                        "contents": "TestData123"
-                    },
-                    {
-                        "identifier": "reverse",
-                        "class": "File",
-                        "contents": "TestData123"
-                    },
-                ]
+                    {"identifier": "forward", "class": "File", "contents": "TestData123"},
+                    {"identifier": "reverse", "class": "File", "contents": "TestData123"},
+                ],
             }
-        ]
+        ],
     },
     "check": check_example_3,
     "output_hid": 6,
@@ -202,11 +194,7 @@ EXAMPLE_4 = {
                 "type": "add_column_metadata",
                 "value": "identifier0",
             },
-            {
-                "type": "add_column_group_tag_value",
-                "value": "type",
-                "default_value": "unused"
-            }
+            {"type": "add_column_group_tag_value", "value": "type", "default_value": "unused"},
         ],
         "mapping": [
             {
@@ -218,25 +206,10 @@ EXAMPLE_4 = {
     "test_data": {
         "type": "list",
         "elements": [
-            {
-                "identifier": "i1",
-                "contents": "0",
-                "class": "File",
-                "tags": ["random", "group:type:single"]
-            },
-            {
-                "identifier": "i2",
-                "contents": "1",
-                "class": "File",
-                "tags": ["random", "group:type:paired"]
-            },
-            {
-                "identifier": "i3",
-                "contents": "2",
-                "class": "File",
-                "tags": ["random", "group:type:paired"]
-            },
-        ]
+            {"identifier": "i1", "contents": "0", "class": "File", "tags": ["random", "group:type:single"]},
+            {"identifier": "i2", "contents": "1", "class": "File", "tags": ["random", "group:type:paired"]},
+            {"identifier": "i3", "contents": "2", "class": "File", "tags": ["random", "group:type:paired"]},
+        ],
     },
     "check": check_example_4,
     "output_hid": 8,
@@ -250,11 +223,7 @@ EXAMPLE_5 = {
                 "type": "add_column_metadata",
                 "value": "identifier0",
             },
-            {
-                "type": "add_column_group_tag_value",
-                "value": "type",
-                "default_value": "unused"
-            }
+            {"type": "add_column_group_tag_value", "value": "type", "default_value": "unused"},
         ],
         "mapping": [
             {
@@ -274,25 +243,10 @@ EXAMPLE_5 = {
     "test_data": {
         "type": "list",
         "elements": [
-            {
-                "identifier": "i1",
-                "contents": "0",
-                "class": "File",
-                "tags": ["random", "group:type:single"]
-            },
-            {
-                "identifier": "i2",
-                "contents": "1",
-                "class": "File",
-                "tags": ["random", "group:type:paired"]
-            },
-            {
-                "identifier": "i3",
-                "contents": "2",
-                "class": "File",
-                "tags": ["random", "group:type:paired"]
-            },
-        ]
+            {"identifier": "i1", "contents": "0", "class": "File", "tags": ["random", "group:type:single"]},
+            {"identifier": "i2", "contents": "1", "class": "File", "tags": ["random", "group:type:paired"]},
+            {"identifier": "i3", "contents": "2", "class": "File", "tags": ["random", "group:type:paired"]},
+        ],
     },
     "check": check_example_5,
     "output_hid": 8,
@@ -309,7 +263,7 @@ EXAMPLE_6 = {
             {
                 "type": "add_column_metadata",
                 "value": "tags",
-            }
+            },
         ],
         "mapping": [
             {
@@ -325,25 +279,10 @@ EXAMPLE_6 = {
     "test_data": {
         "type": "list",
         "elements": [
-            {
-                "identifier": "i1",
-                "contents": "0",
-                "class": "File",
-                "tags": ["random", "group:type:single"]
-            },
-            {
-                "identifier": "i2",
-                "contents": "1",
-                "class": "File",
-                "tags": ["random", "group:type:paired"]
-            },
-            {
-                "identifier": "i3",
-                "contents": "2",
-                "class": "File",
-                "tags": ["random", "group:type:paired"]
-            },
-        ]
+            {"identifier": "i1", "contents": "0", "class": "File", "tags": ["random", "group:type:single"]},
+            {"identifier": "i2", "contents": "1", "class": "File", "tags": ["random", "group:type:paired"]},
+            {"identifier": "i3", "contents": "2", "class": "File", "tags": ["random", "group:type:paired"]},
+        ],
     },
     "check": check_example_6,
     "output_hid": 8,
diff --git a/lib/galaxy_test/base/testcase.py b/lib/galaxy_test/base/testcase.py
index 2de8150d027..e627bccaad1 100644
--- a/lib/galaxy_test/base/testcase.py
+++ b/lib/galaxy_test/base/testcase.py
@@ -1,10 +1,16 @@
 import logging
 import os
 import unittest
-from typing import Any, Optional
+from typing import (
+    Any,
+    Optional,
+)
 
 from galaxy.tool_util.verify.test_data import TestDataResolver
-from galaxy_test.base.env import setup_keep_outdir, target_url_parts
+from galaxy_test.base.env import (
+    setup_keep_outdir,
+    target_url_parts,
+)
 
 log = logging.getLogger(__name__)
 
@@ -16,6 +22,7 @@ class FunctionalTestCase(unittest.TestCase):
     needs to be launched to run the test, this base class assumes a
     server is already running.
     """
+
     galaxy_driver_class: Optional[type] = None
     history_id: Optional[str]
     host: str
@@ -26,7 +33,7 @@ class FunctionalTestCase(unittest.TestCase):
     _test_driver: Optional[Any]
 
     def setUp(self) -> None:
-        self.history_id = os.environ.get('GALAXY_TEST_HISTORY_ID', None)
+        self.history_id = os.environ.get("GALAXY_TEST_HISTORY_ID", None)
         self.host, self.port, self.url = target_url_parts()
         server_wrapper = self._test_driver and self._test_driver.server_wrappers[0]
         if server_wrapper:
diff --git a/lib/galaxy_test/base/uses_shed.py b/lib/galaxy_test/base/uses_shed.py
index 9ee171dce88..753508cefd6 100644
--- a/lib/galaxy_test/base/uses_shed.py
+++ b/lib/galaxy_test/base/uses_shed.py
@@ -11,8 +11,10 @@ from galaxy.tool_util.verify.interactor import GalaxyInteractorApi
 from galaxy.util import unicodify
 from galaxy_test.base.api_asserts import assert_status_code_is
 from galaxy_test.base.populators import DEFAULT_TIMEOUT
-from galaxy_test.driver.driver_util import FRAMEWORK_UPLOAD_TOOL_CONF, GalaxyTestDriver
-
+from galaxy_test.driver.driver_util import (
+    FRAMEWORK_UPLOAD_TOOL_CONF,
+    GalaxyTestDriver,
+)
 
 # Needs a longer timeout because of the conda_auto_install.
 CONDA_AUTO_INSTALL_JOB_TIMEOUT = DEFAULT_TIMEOUT * 3
@@ -20,9 +22,11 @@ CONDA_AUTO_INSTALL_JOB_TIMEOUT = DEFAULT_TIMEOUT * 3
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 TOOL_SHEDS_CONF = os.path.join(SCRIPT_DIRECTORY, "tool_sheds_conf.xml")
 
-SHED_TOOL_CONF = string.Template("""<?xml version="1.0"?>
+SHED_TOOL_CONF = string.Template(
+    """<?xml version="1.0"?>
 <toolbox tool_path="$shed_tools_path">
-</toolbox>""")
+</toolbox>"""
+)
 
 SHED_DATA_MANAGER_CONF = """<?xml version="1.0"?>
 <data_managers>
@@ -37,6 +41,7 @@ class UsesShed:
     @property
     def _app(self) -> UniverseApplication:
         ...
+
     shed_tools_dir: ClassVar[str]
     shed_tool_data_dir: ClassVar[str]
     conda_tmp_prefix: ClassVar[str]
@@ -48,18 +53,18 @@ class UsesShed:
         cls.shed_tools_dir = tempfile.mkdtemp()
         cls.shed_tool_data_dir = tempfile.mkdtemp()
         cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir])
-        shed_tool_config = os.path.join(cls.shed_tools_dir, 'shed_tool_conf.xml')
+        shed_tool_config = os.path.join(cls.shed_tools_dir, "shed_tool_conf.xml")
         config["tool_sheds_config_file"] = TOOL_SHEDS_CONF
         config["tool_config_file"] = FRAMEWORK_UPLOAD_TOOL_CONF
         config["shed_tool_config_file"] = shed_tool_config
-        config["shed_data_manager_config_file"] = os.path.join(cls.shed_tool_data_dir, 'shed_data_manager_config_file')
-        config["shed_tool_data_table_config"] = os.path.join(cls.shed_tool_data_dir, 'shed_data_table_conf.xml')
+        config["shed_data_manager_config_file"] = os.path.join(cls.shed_tool_data_dir, "shed_data_manager_config_file")
+        config["shed_tool_data_table_config"] = os.path.join(cls.shed_tool_data_dir, "shed_data_table_conf.xml")
         config["shed_tool_data_path"] = cls.shed_tool_data_dir
-        with open(shed_tool_config, 'w') as tool_conf_file:
+        with open(shed_tool_config, "w") as tool_conf_file:
             tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=cls.shed_tools_dir))
-        with open(config["shed_data_manager_config_file"], 'w') as shed_data_config:
+        with open(config["shed_data_manager_config_file"], "w") as shed_data_config:
             shed_data_config.write(SHED_DATA_MANAGER_CONF)
-        with open(config["shed_tool_data_table_config"], 'w') as shed_data_table_config:
+        with open(config["shed_tool_data_table_config"], "w") as shed_data_table_config:
             shed_data_table_config.write(SHED_DATA_TABLES)
 
     @classmethod
@@ -69,7 +74,9 @@ class UsesShed:
         cls._test_driver.temp_directories.append(cls.conda_tmp_prefix)
         config["conda_auto_init"] = True
         config["conda_auto_install"] = True
-        config["conda_prefix"] = os.environ.get('GALAXY_TEST_CONDA_PREFIX') or os.path.join(cls.conda_tmp_prefix, 'conda')
+        config["conda_prefix"] = os.environ.get("GALAXY_TEST_CONDA_PREFIX") or os.path.join(
+            cls.conda_tmp_prefix, "conda"
+        )
 
     def setup_shed_config(self):
         shutil.rmtree(self._app.config.shed_tools_dir, ignore_errors=True)
@@ -78,7 +85,7 @@ class UsesShed:
         with open(self._app.config.shed_tool_config_file, "w") as tool_conf_file:
             tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=self._app.config.shed_tools_dir))
         # deleting the containing folder doesn't trigger a toolbox reload, so signal it now and wait until it's done
-        self._app.queue_worker.send_control_task('reload_toolbox', get_response=True)
+        self._app.queue_worker.send_control_task("reload_toolbox", get_response=True)
 
     def reset_shed_tools(self):
         self.setup_shed_config()
@@ -96,29 +103,34 @@ class UsesShed:
         model.context.flush()
 
     def delete_repo_request(self, payload):
-        return self.galaxy_interactor._delete('tool_shed_repositories', data=payload, admin=True)
+        return self.galaxy_interactor._delete("tool_shed_repositories", data=payload, admin=True)
 
     def install_repo_request(self, payload):
-        return self.galaxy_interactor._post('tool_shed_repositories/new/install_repository_revision', data=payload, admin=True)
+        return self.galaxy_interactor._post(
+            "tool_shed_repositories/new/install_repository_revision", data=payload, admin=True
+        )
 
-    def repository_operation(self, operation, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
-        payload = {
-            'tool_shed_url': tool_shed_url,
-            'name': name,
-            'owner': owner,
-            'changeset_revision': changeset
-        }
+    def repository_operation(self, operation, owner, name, changeset, tool_shed_url="https://toolshed.g2.bx.psu.edu"):
+        payload = {"tool_shed_url": tool_shed_url, "name": name, "owner": owner, "changeset_revision": changeset}
         create_response = operation(payload)
         assert_status_code_is(create_response, 200)
         return create_response.json()
 
-    def install_repository(self, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
+    def install_repository(self, owner, name, changeset, tool_shed_url="https://toolshed.g2.bx.psu.edu"):
         try:
-            return self.repository_operation(operation=self.install_repo_request, owner=owner, name=name, changeset=changeset, tool_shed_url=tool_shed_url)
+            return self.repository_operation(
+                operation=self.install_repo_request,
+                owner=owner,
+                name=name,
+                changeset=changeset,
+                tool_shed_url=tool_shed_url,
+            )
         except AssertionError as e:
             if "Error attempting to retrieve installation information from tool shed" in unicodify(e):
                 pytest.skip("Toolshed '%s' unavailable" % tool_shed_url)
             raise
 
-    def uninstall_repository(self, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
-        return self.repository_operation(operation=self.delete_repo_request, owner=owner, name=name, changeset=changeset, tool_shed_url=tool_shed_url)
+    def uninstall_repository(self, owner, name, changeset, tool_shed_url="https://toolshed.g2.bx.psu.edu"):
+        return self.repository_operation(
+            operation=self.delete_repo_request, owner=owner, name=name, changeset=changeset, tool_shed_url=tool_shed_url
+        )
diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index 07e8ad2a81b..a20a769c6ba 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -29,13 +29,26 @@ from galaxy.app import UniverseApplication as GalaxyUniverseApplication
 from galaxy.app_unittest_utils.celery_helper import rebind_container_to_task
 from galaxy.config import LOGGING_CONFIG_DEFAULT
 from galaxy.model import mapping
-from galaxy.model.database_utils import create_database, database_exists
+from galaxy.model.database_utils import (
+    create_database,
+    database_exists,
+)
 from galaxy.model.tool_shed_install import mapping as toolshed_mapping
-from galaxy.tool_util.verify.interactor import GalaxyInteractorApi, verify_tool
-from galaxy.util import asbool, download_to_file, galaxy_directory
+from galaxy.tool_util.verify.interactor import (
+    GalaxyInteractorApi,
+    verify_tool,
+)
+from galaxy.util import (
+    asbool,
+    download_to_file,
+    galaxy_directory,
+)
 from galaxy.util.properties import load_app_properties
 from galaxy.webapps.galaxy import buildapp
-from galaxy_test.base.api_util import get_admin_api_key, get_user_api_key
+from galaxy_test.base.api_util import (
+    get_admin_api_key,
+    get_user_api_key,
+)
 from galaxy_test.base.env import (
     DEFAULT_WEB_HOST,
     target_url_parts,
@@ -55,11 +68,10 @@ FRAMEWORK_TOOLS_DIR = os.path.join(GALAXY_TEST_DIRECTORY, "functional", "tools")
 FRAMEWORK_UPLOAD_TOOL_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "upload_tool_conf.xml")
 FRAMEWORK_SAMPLE_TOOLS_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "samples_tool_conf.xml")
 FRAMEWORK_DATATYPES_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "sample_datatypes_conf.xml")
-MIGRATED_TOOL_PANEL_CONFIG = 'config/migrated_tools_conf.xml'
-INSTALLED_TOOL_PANEL_CONFIGS = [
-    os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', 'config/shed_tool_conf.xml')
-]
-REALTIME_PROXY_TEMPLATE = string.Template(r"""
+MIGRATED_TOOL_PANEL_CONFIG = "config/migrated_tools_conf.xml"
+INSTALLED_TOOL_PANEL_CONFIGS = [os.environ.get("GALAXY_TEST_SHED_TOOL_CONF", "config/shed_tool_conf.xml")]
+REALTIME_PROXY_TEMPLATE = string.Template(
+    r"""
 uwsgi:
   http-raw-body: true
   interactivetools_map: $tempdir/interactivetools_map.sqlite
@@ -75,10 +87,11 @@ uwsgi:
   route: .* break:404 Not Found
 
   route-label: endendend
-""")
+"""
+)
 
 DEFAULT_LOCALES = "en"
-USE_UVICORN = asbool(os.environ.get('GALAXY_TEST_USE_UVICORN', True))
+USE_UVICORN = asbool(os.environ.get("GALAXY_TEST_USE_UVICORN", True))
 
 log = logging.getLogger("test_driver")
 
@@ -91,19 +104,19 @@ install_context = None
 
 
 def setup_tool_shed_tmp_dir():
-    tool_shed_test_tmp_dir = os.environ.get('TOOL_SHED_TEST_TMP_DIR', None)
+    tool_shed_test_tmp_dir = os.environ.get("TOOL_SHED_TEST_TMP_DIR", None)
     if tool_shed_test_tmp_dir is None:
         tool_shed_test_tmp_dir = os.path.realpath(tempfile.mkdtemp())
     # Here's the directory where everything happens.  Temporary directories are created within this directory to contain
     # the hgweb.config file, the database, new repositories, etc.  Since the tool shed browses repository contents via HTTP,
     # the full path to the temporary directroy wher eht repositories are located cannot contain invalid url characters.
-    os.environ['TOOL_SHED_TEST_TMP_DIR'] = tool_shed_test_tmp_dir
+    os.environ["TOOL_SHED_TEST_TMP_DIR"] = tool_shed_test_tmp_dir
     return tool_shed_test_tmp_dir
 
 
 def get_galaxy_test_tmp_dir():
     """Create test directory for use by Galaxy server being setup for testing."""
-    galaxy_test_tmp_dir = os.environ.get('GALAXY_TEST_TMP_DIR', None)
+    galaxy_test_tmp_dir = os.environ.get("GALAXY_TEST_TMP_DIR", None)
     if galaxy_test_tmp_dir is None:
         galaxy_test_tmp_dir = tempfile.mkdtemp()
     return galaxy_test_tmp_dir
@@ -112,8 +125,8 @@ def get_galaxy_test_tmp_dir():
 def configure_environment():
     """Hack up environment for test cases."""
     # no op remove if unused
-    if 'HTTP_ACCEPT_LANGUAGE' not in os.environ:
-        os.environ['HTTP_ACCEPT_LANGUAGE'] = DEFAULT_LOCALES
+    if "HTTP_ACCEPT_LANGUAGE" not in os.environ:
+        os.environ["HTTP_ACCEPT_LANGUAGE"] = DEFAULT_LOCALES
 
     # Used by get_filename in tool shed's twilltestcase.
     if "TOOL_SHED_TEST_FILE_DIR" not in os.environ:
@@ -132,8 +145,8 @@ def ensure_test_file_dir_set():
 
     Return first directory for backward compat.
     """
-    galaxy_test_file_dir = os.environ.get('GALAXY_TEST_FILE_DIR', GALAXY_TEST_FILE_DIR)
-    os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir
+    galaxy_test_file_dir = os.environ.get("GALAXY_TEST_FILE_DIR", GALAXY_TEST_FILE_DIR)
+    os.environ["GALAXY_TEST_FILE_DIR"] = galaxy_test_file_dir
     first_test_file_dir = galaxy_test_file_dir.split(",")[0]
     return first_test_file_dir
 
@@ -163,9 +176,9 @@ def setup_galaxy_config(
     tmpdir = os.path.realpath(tmpdir)
     if not os.path.exists(tmpdir):
         os.makedirs(tmpdir)
-    template_cache_path = tempfile.mkdtemp(prefix='compiled_templates_', dir=tmpdir)
-    new_file_path = tempfile.mkdtemp(prefix='new_files_path_', dir=tmpdir)
-    job_working_directory = tempfile.mkdtemp(prefix='job_working_directory_', dir=tmpdir)
+    template_cache_path = tempfile.mkdtemp(prefix="compiled_templates_", dir=tmpdir)
+    new_file_path = tempfile.mkdtemp(prefix="new_files_path_", dir=tmpdir)
+    job_working_directory = tempfile.mkdtemp(prefix="job_working_directory_", dir=tmpdir)
 
     user_library_import_dir: Optional[str]
     if use_test_file_dir:
@@ -173,7 +186,7 @@ def setup_galaxy_config(
         if not os.path.isabs(first_test_file_dir):
             first_test_file_dir = os.path.join(galaxy_root, first_test_file_dir)
         library_import_dir = first_test_file_dir
-        import_dir = os.path.join(first_test_file_dir, 'users')
+        import_dir = os.path.join(first_test_file_dir, "users")
         if os.path.exists(import_dir):
             user_library_import_dir = import_dir
         else:
@@ -181,31 +194,34 @@ def setup_galaxy_config(
     else:
         user_library_import_dir = None
         library_import_dir = None
-    job_config_file = os.environ.get('GALAXY_TEST_JOB_CONFIG_FILE', default_job_config_file)
-    tool_path = os.environ.get('GALAXY_TEST_TOOL_PATH', 'tools')
+    job_config_file = os.environ.get("GALAXY_TEST_JOB_CONFIG_FILE", default_job_config_file)
+    tool_path = os.environ.get("GALAXY_TEST_TOOL_PATH", "tools")
     tool_data_table_config_path = _tool_data_table_config_path(default_tool_data_table_config_path)
     default_data_manager_config = None
-    for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml']:
+    for data_manager_config in ["config/data_manager_conf.xml", "data_manager_conf.xml"]:
         if os.path.exists(data_manager_config):
             default_data_manager_config = data_manager_config
-    data_manager_config_file = 'test/functional/tools/sample_data_manager_conf.xml'
+    data_manager_config_file = "test/functional/tools/sample_data_manager_conf.xml"
     if default_data_manager_config is not None:
         data_manager_config_file = f"{default_data_manager_config},{data_manager_config_file}"
     master_api_key = get_admin_api_key()
-    cleanup_job = 'never' if ("GALAXY_TEST_NO_CLEANUP" in os.environ
-                              or "TOOL_SHED_TEST_NO_CLEANUP" in os.environ) else 'onsuccess'
+    cleanup_job = (
+        "never"
+        if ("GALAXY_TEST_NO_CLEANUP" in os.environ or "TOOL_SHED_TEST_NO_CLEANUP" in os.environ)
+        else "onsuccess"
+    )
 
     # Data Manager testing temp path
     # For storing Data Manager outputs and .loc files so that real ones don't get clobbered
-    galaxy_data_manager_data_path = tempfile.mkdtemp(prefix='data_manager_tool-data', dir=tmpdir)
+    galaxy_data_manager_data_path = tempfile.mkdtemp(prefix="data_manager_tool-data", dir=tmpdir)
 
     if allow_tool_conf_override:
-        tool_conf = os.environ.get('GALAXY_TEST_TOOL_CONF', default_tool_conf)
+        tool_conf = os.environ.get("GALAXY_TEST_TOOL_CONF", default_tool_conf)
     else:
         tool_conf = default_tool_conf
-    conda_auto_install = os.environ.get('GALAXY_TEST_CONDA_AUTO_INSTALL', conda_auto_install)
-    conda_auto_init = os.environ.get('GALAXY_TEST_CONDA_AUTO_INIT', conda_auto_init)
-    conda_prefix = os.environ.get('GALAXY_TEST_CONDA_PREFIX')
+    conda_auto_install = os.environ.get("GALAXY_TEST_CONDA_AUTO_INSTALL", conda_auto_install)
+    conda_auto_init = os.environ.get("GALAXY_TEST_CONDA_AUTO_INIT", conda_auto_init)
+    conda_prefix = os.environ.get("GALAXY_TEST_CONDA_PREFIX")
     if tool_conf is None:
         # As a fallback always at least allow upload.
         tool_conf = FRAMEWORK_UPLOAD_TOOL_CONF
@@ -220,12 +236,12 @@ def setup_galaxy_config(
     tool_data_table_config_path = _resolve_relative_config_paths(tool_data_table_config_path)
 
     config = dict(
-        admin_users='test@bx.psu.edu',
+        admin_users="test@bx.psu.edu",
         allow_library_path_paste=True,
         allow_path_paste=allow_path_paste,
         allow_user_creation=True,
         allow_user_deletion=True,
-        api_allow_run_as='test@bx.psu.edu',
+        api_allow_run_as="test@bx.psu.edu",
         auto_configure_logging=logging_config_file is None,
         chunk_upload_size=100,
         conda_prefix=conda_prefix,
@@ -239,7 +255,7 @@ def setup_galaxy_config(
         expose_dataset_path=True,
         ftp_upload_purge=False,
         galaxy_data_manager_data_path=galaxy_data_manager_data_path,
-        id_secret='changethisinproductiontoo',
+        id_secret="changethisinproductiontoo",
         job_config_file=job_config_file,
         job_working_directory=job_working_directory,
         library_import_dir=library_import_dir,
@@ -266,7 +282,9 @@ def setup_galaxy_config(
     if default_shed_tool_data_table_config:
         config["shed_tool_data_table_config"] = default_shed_tool_data_table_config
     if not use_shared_connection_for_amqp:
-        config["amqp_internal_connection"] = f"sqlalchemy+sqlite:///{os.path.join(tmpdir, 'control.sqlite')}?isolation_level=IMMEDIATE"
+        config[
+            "amqp_internal_connection"
+        ] = f"sqlalchemy+sqlite:///{os.path.join(tmpdir, 'control.sqlite')}?isolation_level=IMMEDIATE"
 
     config.update(database_conf(tmpdir, prefer_template_database=prefer_template_database))
     config.update(install_database_conf(tmpdir, default_merged=default_install_db_merged))
@@ -301,16 +319,16 @@ backends:
         config["object_store_config_file"] = object_store_config
 
     if datatypes_conf is not None:
-        config['datatypes_config_file'] = datatypes_conf
+        config["datatypes_config_file"] = datatypes_conf
     if enable_tool_shed_check:
         config["enable_tool_shed_check"] = enable_tool_shed_check
         config["hours_between_check"] = 0.001
-    tool_dependency_dir = os.environ.get('GALAXY_TOOL_DEPENDENCY_DIR')
+    tool_dependency_dir = os.environ.get("GALAXY_TOOL_DEPENDENCY_DIR")
     if tool_dependency_dir:
         config["tool_dependency_dir"] = tool_dependency_dir
     # Used by shed's twill dependency stuff
     # TODO: read from Galaxy's config API.
-    os.environ["GALAXY_TEST_TOOL_DEPENDENCY_DIR"] = tool_dependency_dir or os.path.join(tmpdir, 'dependencies')
+    os.environ["GALAXY_TEST_TOOL_DEPENDENCY_DIR"] = tool_dependency_dir or os.path.join(tmpdir, "dependencies")
     return config
 
 
@@ -318,22 +336,24 @@ def _resolve_relative_config_paths(config_option):
     # If option is not None, split into paths, resolve each w.r.t. root, then rebuild as csv string.
     if config_option is not None:
         resolved = []
-        for path in config_option.split(','):
+        for path in config_option.split(","):
             resolved.append(os.path.join(galaxy_root, path.strip()))
-        return ','.join(resolved)
+        return ",".join(resolved)
 
 
 def _tool_data_table_config_path(default_tool_data_table_config_path=None):
-    tool_data_table_config_path = os.environ.get('GALAXY_TEST_TOOL_DATA_TABLE_CONF', default_tool_data_table_config_path)
+    tool_data_table_config_path = os.environ.get(
+        "GALAXY_TEST_TOOL_DATA_TABLE_CONF", default_tool_data_table_config_path
+    )
     if tool_data_table_config_path is None:
         # ... otherwise find whatever Galaxy would use as the default and
         # the sample data for functional tests to that.
-        default_tool_data_config = 'lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
-        for tool_data_config in ['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml']:
+        default_tool_data_config = "lib/galaxy/config/sample/tool_data_table_conf.xml.sample"
+        for tool_data_config in ["config/tool_data_table_conf.xml", "tool_data_table_conf.xml"]:
             if os.path.exists(tool_data_config):
                 default_tool_data_config = tool_data_config
-        test_tool_data_config = 'test/functional/tool-data/sample_tool_data_tables.xml'
-        tool_data_table_config_path = f'{default_tool_data_config},{test_tool_data_config}'
+        test_tool_data_config = "test/functional/tool-data/sample_tool_data_tables.xml"
+        tool_data_table_config_path = f"{default_tool_data_config},{test_tool_data_config}"
     return tool_data_table_config_path
 
 
@@ -408,7 +428,7 @@ def database_conf(db_path, prefix="GALAXY", prefer_template_database=False):
             if not database_exists(database_connection):
                 # We pass by migrations and instantiate the current table
                 create_database(database_connection)
-                mapping.init('/tmp', database_connection, create_tables=True, map_install_models=True)
+                mapping.init("/tmp", database_connection, create_tables=True, map_install_models=True)
                 toolshed_mapping.init(database_connection, create_tables=True)
                 check_migrate_databases = False
     else:
@@ -423,11 +443,11 @@ def database_conf(db_path, prefix="GALAXY", prefer_template_database=False):
             # cases (namely tool shed tests expecting clean database).
             copy_database_template(os.environ[template_var], db_path)
             database_auto_migrate = True
-        database_connection = f'sqlite:///{db_path}'
+        database_connection = f"sqlite:///{db_path}"
     config = {
         "check_migrate_databases": check_migrate_databases,
         "database_connection": database_connection,
-        "database_auto_migrate": database_auto_migrate
+        "database_auto_migrate": database_auto_migrate,
     }
     if not database_connection.startswith("sqlite://"):
         config["database_engine_option_max_overflow"] = "20"
@@ -439,13 +459,13 @@ def database_conf(db_path, prefix="GALAXY", prefer_template_database=False):
 
 def install_database_conf(db_path, default_merged=False):
     install_galaxy_database_connection: Optional[str]
-    if 'GALAXY_TEST_INSTALL_DBURI' in os.environ:
-        install_galaxy_database_connection = os.environ['GALAXY_TEST_INSTALL_DBURI']
-    elif asbool(os.environ.get('GALAXY_TEST_INSTALL_DB_MERGED', default_merged)):
+    if "GALAXY_TEST_INSTALL_DBURI" in os.environ:
+        install_galaxy_database_connection = os.environ["GALAXY_TEST_INSTALL_DBURI"]
+    elif asbool(os.environ.get("GALAXY_TEST_INSTALL_DB_MERGED", default_merged)):
         install_galaxy_database_connection = None
     else:
-        install_galaxy_db_path = os.path.join(db_path, 'install.sqlite')
-        install_galaxy_database_connection = f'sqlite:///{install_galaxy_db_path}'
+        install_galaxy_db_path = os.path.join(db_path, "install.sqlite")
+        install_galaxy_database_connection = f"sqlite:///{install_galaxy_db_path}"
     conf = {}
     if install_galaxy_database_connection is not None:
         conf["install_database_connection"] = install_galaxy_database_connection
@@ -463,7 +483,7 @@ def database_files_path(test_tmpdir, prefix="GALAXY"):
         db_path = os.environ[environ_var]
     else:
         tempdir = tempfile.mkdtemp(dir=test_tmpdir)
-        db_path = os.path.join(tempdir, 'database')
+        db_path = os.path.join(tempdir, "database")
     return db_path
 
 
@@ -483,11 +503,11 @@ def _get_static_settings():
         static_enabled=True,
         static_cache_time=360,
         static_dir=static_dir,
-        static_images_dir=os.path.join(static_dir, 'images', ''),
-        static_favicon_dir=os.path.join(static_dir, 'favicon.ico'),
-        static_scripts_dir=os.path.join(static_dir, 'scripts', ''),
-        static_style_dir=os.path.join(static_dir, 'style'),
-        static_robots_txt=os.path.join(static_dir, 'robots.txt'),
+        static_images_dir=os.path.join(static_dir, "images", ""),
+        static_favicon_dir=os.path.join(static_dir, "favicon.ico"),
+        static_scripts_dir=os.path.join(static_dir, "scripts", ""),
+        static_style_dir=os.path.join(static_dir, "style"),
+        static_robots_txt=os.path.join(static_dir, "robots.txt"),
     )
 
 
@@ -502,8 +522,8 @@ def get_webapp_global_conf():
 def wait_for_http_server(host, port, prefix=None, sleep_amount=0.1, sleep_tries=150):
     """Wait for an HTTP server to boot up."""
     # Test if the server is up
-    prefix = prefix or '/'
-    if not prefix.endswith('/'):
+    prefix = prefix or "/"
+    if not prefix.endswith("/"):
         prefix = f"{prefix}/"
     for _ in range(sleep_tries):
         # directly test the app, not the proxy
@@ -526,7 +546,7 @@ def wait_for_http_server(host, port, prefix=None, sleep_amount=0.1, sleep_tries=
 def attempt_port(port):
     sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
     try:
-        sock.bind(('', port))
+        sock.bind(("", port))
         sock.close()
         return port
     except OSError:
@@ -544,7 +564,7 @@ def attempt_ports(port):
             port = attempt_port(random.randint(8000, 10000))
             if port:
                 port = str(port)
-                os.environ['GALAXY_WEB_PORT'] = port
+                os.environ["GALAXY_WEB_PORT"] = port
                 return port
 
         raise Exception(f"Unable to open a port between {8000} and {10000} to start Galaxy server")
@@ -570,10 +590,11 @@ def uvicorn_serve(app, port, host=None):
     Return the port the webapp is running on.
     """
     import asyncio
-    from uvicorn.server import Server
-    from uvicorn.config import Config
 
-    access_log = False if 'GALAXY_TEST_DISABLE_ACCESS_LOG' in os.environ else True
+    from uvicorn.config import Config
+    from uvicorn.server import Server
+
+    access_log = False if "GALAXY_TEST_DISABLE_ACCESS_LOG" in os.environ else True
     config = Config(app, host=host, port=int(port), access_log=access_log)
     server = Server(config=config)
 
@@ -625,6 +646,7 @@ def setup_shed_tools_for_test(app, tmpdir, testing_migrated_tools, testing_insta
         for installed_tool_panel_config in INSTALLED_TOOL_PANEL_CONFIGS:
             tool_configs.append(installed_tool_panel_config)
         from galaxy import tools  # delay import because this brings in so many modules for small tests # noqa: E402
+
         app.toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
 
 
@@ -636,11 +658,9 @@ def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication:
     to sqlalchemy database context for Galaxy and install databases.
     """
     log.info("Galaxy database connection: %s", simple_kwargs["database_connection"])
-    simple_kwargs['global_conf'] = get_webapp_global_conf()
-    simple_kwargs['global_conf']['__file__'] = "lib/galaxy/config/sample/galaxy.yml.sample"
-    simple_kwargs = load_app_properties(
-        kwds=simple_kwargs
-    )
+    simple_kwargs["global_conf"] = get_webapp_global_conf()
+    simple_kwargs["global_conf"]["__file__"] = "lib/galaxy/config/sample/galaxy.yml.sample"
+    simple_kwargs = load_app_properties(kwds=simple_kwargs)
     # Build the Universe Application
     app = GalaxyUniverseApplication(**simple_kwargs)
     if not simple_kwargs.get("enable_celery_tasks"):
@@ -671,8 +691,8 @@ def build_shed_app(simple_kwargs):
     """
     log.info("Tool shed database connection: %s", simple_kwargs["database_connection"])
     # TODO: Simplify global_conf to match Galaxy above...
-    simple_kwargs['__file__'] = 'tool_shed_wsgi.yml.sample'
-    simple_kwargs['global_conf'] = get_webapp_global_conf()
+    simple_kwargs["__file__"] = "tool_shed_wsgi.yml.sample"
+    simple_kwargs["global_conf"] = get_webapp_global_conf()
 
     app = ToolshedUniverseApplication(**simple_kwargs)
     log.info("Embedded Toolshed application started")
@@ -702,7 +722,7 @@ def explicitly_configured_host_and_port(prefix, config_object):
     if port is None:
         os.environ["GALAXY_TEST_PORT_RANDOM"] = "1"
     else:
-        os.environ['GALAXY_WEB_PORT'] = port
+        os.environ["GALAXY_WEB_PORT"] = port
 
     return host, port
 
@@ -716,7 +736,6 @@ def set_and_wait_for_http_target(prefix, host, port, url_prefix, sleep_amount=0.
 
 
 class ServerWrapper:
-
     def __init__(self, name, host, port, prefix=""):
         self.name = name
         self.host = host
@@ -732,7 +751,6 @@ class ServerWrapper:
 
 
 class EmbeddedServerWrapper(ServerWrapper):
-
     def __init__(self, app, server, name, host, port, prefix="", thread=None):
         super().__init__(name, host, port, prefix)
         self._app = app
@@ -770,7 +788,6 @@ class EmbeddedServerWrapper(ServerWrapper):
 
 
 class UwsgiServerWrapper(ServerWrapper):
-
     def __init__(self, p, name, host, port):
         super().__init__(name, host, port)
         self._p = p
@@ -789,7 +806,7 @@ class UwsgiServerWrapper(ServerWrapper):
             os.killpg(os.getpgid(self._p.pid), signal.SIGTERM)
         except Exception:
             pass
-        time.sleep(.1)
+        time.sleep(0.1)
         try:
             os.killpg(os.getpgid(self._p.pid), signal.SIGKILL)
         except Exception:
@@ -810,7 +827,7 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
         interactive_tool_defaults = {
             "interactivetools_prefix": "interactivetool",
             "interactivetools_map": os.path.join(tempdir, "interactivetools_map.sqlite"),
-            "interactivetools_enable": True
+            "interactivetools_enable": True,
         }
         for key, value in interactive_tool_defaults.items():
             if key not in config["galaxy"]:
@@ -828,7 +845,9 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
         with open(yaml_config_path, "w") as f:
             test_port = str(port) if port else r"[0-9]+"
             test_host = re.escape(host) if host else "localhost"
-            uwsgi_section = REALTIME_PROXY_TEMPLATE.safe_substitute(test_host=test_host, test_port=test_port, tempdir=tempdir)
+            uwsgi_section = REALTIME_PROXY_TEMPLATE.safe_substitute(
+                test_host=test_host, test_port=test_port, tempdir=tempdir
+            )
             f.write(uwsgi_section)
             f.write(old_contents)
 
@@ -845,25 +864,21 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
             "--die-on-term",
         ]
         for path in sys.path:
-            uwsgi_command.append('--pythonpath')
+            uwsgi_command.append("--pythonpath")
             uwsgi_command.append(path)
 
-        handle_uwsgi_cli_command = getattr(
-            config_object, "handle_uwsgi_cli_command", None
-        )
+        handle_uwsgi_cli_command = getattr(config_object, "handle_uwsgi_cli_command", None)
         if handle_uwsgi_cli_command is not None:
             handle_uwsgi_cli_command(uwsgi_command)
 
         # we don't want to quote every argument but we don't want to print unquoted ones either, so do this
-        log.info("Starting uwsgi with command line: %s", ' '.join(shlex.quote(x) for x in uwsgi_command))
+        log.info("Starting uwsgi with command line: %s", " ".join(shlex.quote(x) for x in uwsgi_command))
         p = subprocess.Popen(
             uwsgi_command,
             cwd=galaxy_root,
             preexec_fn=os.setsid,
         )
-        return UwsgiServerWrapper(
-            p, name, host, port
-        )
+        return UwsgiServerWrapper(p, name, host, port)
 
     port = attempt_ports(port)
     server_wrapper = attempt_port_bind(port)
@@ -883,13 +898,14 @@ def launch_uvicorn(webapp_factory, prefix=DEFAULT_CONFIG_PREFIX, galaxy_config=N
     gx_app = build_galaxy_app(galaxy_config)
 
     gx_wsgi_webapp = webapp_factory(
-        galaxy_config['global_conf'],
+        galaxy_config["global_conf"],
         app=gx_app,
         use_translogger=False,
         static_enabled=True,
-        register_shutdown_at_exit=False
+        register_shutdown_at_exit=False,
     )
     from galaxy.webapps.galaxy.fast_app import initialize_fast_app
+
     app = initialize_fast_app(gx_wsgi_webapp, gx_app)
     server, port, thread = uvicorn_serve(app, host=host, port=port)
     set_and_wait_for_http_target(prefix, host, port, url_prefix=gx_app.config.galaxy_url_prefix)
@@ -911,21 +927,12 @@ def launch_server(app, webapp_factory, kwargs, prefix=DEFAULT_CONFIG_PREFIX, con
     host, port = explicitly_configured_host_and_port(prefix, config_object)
 
     webapp = webapp_factory(
-        kwargs['global_conf'],
-        app=app,
-        use_translogger=False,
-        static_enabled=True,
-        register_shutdown_at_exit=False
-    )
-    server, port = serve_webapp(
-        webapp,
-        host=host, port=port
+        kwargs["global_conf"], app=app, use_translogger=False, static_enabled=True, register_shutdown_at_exit=False
     )
+    server, port = serve_webapp(webapp, host=host, port=port)
     set_and_wait_for_http_target(prefix, host, port, url_prefix="/")
     log.info(f"Embedded paste web server for {name} started at {host}:{port}")
-    return EmbeddedServerWrapper(
-        app, server, name, host, port
-    )
+    return EmbeddedServerWrapper(app, server, name, host, port)
 
 
 class TestDriver:
@@ -935,6 +942,7 @@ class TestDriver:
     down. This is somewhat like a Python TestCase - but different
     because it is meant to provide a main() endpoint.
     """
+
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
 
     def __init__(self):
@@ -993,11 +1001,11 @@ class GalaxyTestDriver(TestDriver):
     def _configure(self, config_object=None):
         """Setup various variables used to launch a Galaxy server."""
         config_object = self._ensure_config_object(config_object)
-        self.external_galaxy = os.environ.get('GALAXY_TEST_EXTERNAL', None)
+        self.external_galaxy = os.environ.get("GALAXY_TEST_EXTERNAL", None)
 
         # Allow a particular test to force uwsgi or any test to use uwsgi with
         # the GALAXY_TEST_UWSGI environment variable.
-        use_uwsgi = bool(os.environ.get('GALAXY_TEST_UWSGI', None))
+        use_uwsgi = bool(os.environ.get("GALAXY_TEST_UWSGI", None))
         if not use_uwsgi:
             if getattr(config_object, "require_uwsgi", None):
                 use_uwsgi = True
@@ -1009,11 +1017,13 @@ class GalaxyTestDriver(TestDriver):
             self.else_use_uvicorn = False
 
         # Allow controlling the log format
-        log_format = os.environ.get('GALAXY_TEST_LOG_FORMAT', None)
+        log_format = os.environ.get("GALAXY_TEST_LOG_FORMAT", None)
         if not log_format and use_uwsgi:
-            log_format = "%(name)s %(levelname)-5.5s %(asctime)s " \
-                         "[p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] " \
-                         "[%(threadName)s] %(message)s"
+            log_format = (
+                "%(name)s %(levelname)-5.5s %(asctime)s "
+                "[p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] "
+                "[%(threadName)s] %(message)s"
+            )
 
         self.log_format = log_format
 
@@ -1078,10 +1088,7 @@ class GalaxyTestDriver(TestDriver):
                         use_shared_connection_for_amqp=getattr(config_object, "use_shared_connection_for_amqp", False),
                         allow_tool_conf_override=self.allow_tool_conf_override,
                     )
-                    galaxy_config = setup_galaxy_config(
-                        galaxy_db_path,
-                        **setup_galaxy_config_kwds
-                    )
+                    galaxy_config = setup_galaxy_config(galaxy_db_path, **setup_galaxy_config_kwds)
 
                     isolate_galaxy_config = getattr(config_object, "isolate_galaxy_config", False)
                     if isolate_galaxy_config:
@@ -1090,9 +1097,7 @@ class GalaxyTestDriver(TestDriver):
                     self._saved_galaxy_config = galaxy_config
 
             if galaxy_config is not None:
-                handle_galaxy_config_kwds = handle_config or getattr(
-                    config_object, "handle_galaxy_config_kwds", None
-                )
+                handle_galaxy_config_kwds = handle_config or getattr(config_object, "handle_galaxy_config_kwds", None)
                 if handle_galaxy_config_kwds is not None:
                     handle_galaxy_config_kwds(galaxy_config)
 
@@ -1118,7 +1123,9 @@ class GalaxyTestDriver(TestDriver):
                     galaxy_config,
                     config_object=config_object,
                 )
-                log.info(f"Functional tests will be run against external Galaxy server {server_wrapper.host}:{server_wrapper.port}")
+                log.info(
+                    f"Functional tests will be run against external Galaxy server {server_wrapper.host}:{server_wrapper.port}"
+                )
             self.server_wrappers.append(server_wrapper)
         else:
             log.info(f"Functional tests will be run against test managed Galaxy server {self.external_galaxy}")
@@ -1131,12 +1138,7 @@ class GalaxyTestDriver(TestDriver):
         return config_object
 
     def setup_shed_tools(self, testing_migrated_tools=False, testing_installed_tools=True):
-        setup_shed_tools_for_test(
-            self.app,
-            self.galaxy_test_tmp_dir,
-            testing_migrated_tools,
-            testing_installed_tools
-        )
+        setup_shed_tools_for_test(self.app, self.galaxy_test_tmp_dir, testing_migrated_tools, testing_installed_tools)
 
     def build_tool_tests(self, testing_shed_tools=None, return_test_classes=False):
         if self.app is None:
@@ -1150,6 +1152,7 @@ class GalaxyTestDriver(TestDriver):
         # If functional.test_toolbox is imported before database_contexts.galaxy_content
         # is set, sa_session will be None in all methods that use it.
         import functional.test_toolbox
+
         functional.test_toolbox.toolbox = self.app.toolbox
         # When testing data managers, do not test toolbox.
         test_classes = functional.test_toolbox.build_tests(
@@ -1178,7 +1181,7 @@ class GalaxyTestDriver(TestDriver):
             test_index=index,
             galaxy_interactor=galaxy_interactor,
             resource_parameters=resource_parameters,
-            **kwd
+            **kwd,
         )
 
 
diff --git a/lib/galaxy_test/driver/integration_util.py b/lib/galaxy_test/driver/integration_util.py
index 0f1f3b957c8..ec1adf7aaed 100644
--- a/lib/galaxy_test/driver/integration_util.py
+++ b/lib/galaxy_test/driver/integration_util.py
@@ -6,7 +6,11 @@ testing configuration.
 """
 import os
 from typing import ClassVar
-from unittest import skip, SkipTest, TestCase
+from unittest import (
+    skip,
+    SkipTest,
+    TestCase,
+)
 
 import pytest
 
@@ -19,7 +23,7 @@ from .driver_util import GalaxyTestDriver
 NO_APP_MESSAGE = "test_case._app called though no Galaxy has been configured."
 # Following should be for Homebrew Rabbitmq and Docker on Mac "amqp://guest:guest@localhost:5672//"
 AMQP_URL = os.environ.get("GALAXY_TEST_AMQP_URL", None)
-POSTGRES_CONFIGURED = 'postgres' in os.environ.get("GALAXY_TEST_DBURI", '')
+POSTGRES_CONFIGURED = "postgres" in os.environ.get("GALAXY_TEST_DBURI", "")
 
 
 def _identity(func):
@@ -60,7 +64,7 @@ def skip_unless_kubernetes():
 
 
 def k8s_config_path():
-    return os.environ.get('GALAXY_TEST_KUBE_CONFIG_PATH', '~/.kube/config')
+    return os.environ.get("GALAXY_TEST_KUBE_CONFIG_PATH", "~/.kube/config")
 
 
 def skip_unless_fixed_port():
@@ -79,6 +83,7 @@ def skip_if_github_workflow():
 
 class IntegrationInstance(UsesApiTestCaseMixin):
     """Unit test case with utilities for spinning up Galaxy."""
+
     _test_driver: GalaxyTestDriver  # Optional in parent class, but required for integration tests.
 
     _app_available: ClassVar[bool]
@@ -116,7 +121,7 @@ class IntegrationInstance(UsesApiTestCaseMixin):
         server_wrapper = self._test_driver.server_wrappers[0]
         host = server_wrapper.host
         port = server_wrapper.port
-        prefix = server_wrapper.prefix or ''
+        prefix = server_wrapper.prefix or ""
         self.url = f"http://{host}:{port}{prefix.rstrip('/')}/"
         self._setup_interactor()
 
@@ -193,7 +198,6 @@ class IntegrationTestCase(IntegrationInstance, TestCase):
 
 
 def integration_module_instance(clazz):
-
     def _instance():
         instance = clazz()
         instance.setUpClass()
@@ -201,11 +205,10 @@ def integration_module_instance(clazz):
         yield instance
         instance.tearDownClass()
 
-    return pytest.fixture(scope='module')(_instance)
+    return pytest.fixture(scope="module")(_instance)
 
 
 def integration_tool_runner(tool_ids):
-
     def test_tools(instance, tool_id):
         instance._run_tool_test(tool_id)
 
diff --git a/lib/galaxy_test/driver/testcase.py b/lib/galaxy_test/driver/testcase.py
index 4de25244ac9..32eea4bf55a 100644
--- a/lib/galaxy_test/driver/testcase.py
+++ b/lib/galaxy_test/driver/testcase.py
@@ -3,6 +3,6 @@ from .driver_util import GalaxyTestDriver
 
 
 class DrivenFunctionalTestCase(FunctionalTestCase):
-    """Variant of FunctionalTestCase that can launch Galaxy instances.
-    """
+    """Variant of FunctionalTestCase that can launch Galaxy instances."""
+
     galaxy_driver_class = GalaxyTestDriver
diff --git a/lib/galaxy_test/performance/_framework.py b/lib/galaxy_test/performance/_framework.py
index f11dda0bc39..ec965d6594a 100644
--- a/lib/galaxy_test/performance/_framework.py
+++ b/lib/galaxy_test/performance/_framework.py
@@ -1,3 +1,3 @@
 from galaxy_test.api._framework import ApiTestCase as PerformanceTestCase
 
-__all__ = ('PerformanceTestCase',)
+__all__ = ("PerformanceTestCase",)
diff --git a/lib/galaxy_test/performance/test_workflow_framework_performance.py b/lib/galaxy_test/performance/test_workflow_framework_performance.py
index e1938101668..02ea0f21866 100644
--- a/lib/galaxy_test/performance/test_workflow_framework_performance.py
+++ b/lib/galaxy_test/performance/test_workflow_framework_performance.py
@@ -1,16 +1,20 @@
 import os
 
-from galaxy_test.base.populators import (
-    WorkflowPopulator,
-)
+from galaxy_test.base.populators import WorkflowPopulator
 from ._framework import PerformanceTestCase
 
 GALAXY_TEST_PERFORMANCE_TIMEOUT_DEFAULT = 5000
-GALAXY_TEST_PERFORMANCE_TIMEOUT = int(os.environ.get("GALAXY_TEST_PERFORMANCE_TIMEOUT", GALAXY_TEST_PERFORMANCE_TIMEOUT_DEFAULT))
+GALAXY_TEST_PERFORMANCE_TIMEOUT = int(
+    os.environ.get("GALAXY_TEST_PERFORMANCE_TIMEOUT", GALAXY_TEST_PERFORMANCE_TIMEOUT_DEFAULT)
+)
 GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE_DEFAULT = 4
-GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE = int(os.environ.get("GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE", GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE_DEFAULT))
+GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE = int(
+    os.environ.get("GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE", GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE_DEFAULT)
+)
 GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH_DEFAULT = 3
-GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH = int(os.environ.get("GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH", GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH_DEFAULT))
+GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH = int(
+    os.environ.get("GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH", GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH_DEFAULT)
+)
 
 
 class WorkflowFrameworkPerformanceTestCase(PerformanceTestCase):
diff --git a/lib/galaxy_test/selenium/framework.py b/lib/galaxy_test/selenium/framework.py
index 5d73169f01c..e5f787833a7 100644
--- a/lib/galaxy_test/selenium/framework.py
+++ b/lib/galaxy_test/selenium/framework.py
@@ -5,8 +5,15 @@ import json
 import os
 import traceback
 import unittest
-from functools import partial, wraps
-from typing import Any, Dict, TYPE_CHECKING
+from functools import (
+    partial,
+    wraps,
+)
+from typing import (
+    Any,
+    Dict,
+    TYPE_CHECKING,
+)
 
 import requests
 from gxformat2 import (
@@ -15,12 +22,8 @@ from gxformat2 import (
 )
 from requests.models import Response
 
-from galaxy.selenium import (
-    driver_factory,
-)
-from galaxy.selenium.context import (
-    GalaxySeleniumContext,
-)
+from galaxy.selenium import driver_factory
+from galaxy.selenium.context import GalaxySeleniumContext
 from galaxy.selenium.navigates_galaxy import (
     NavigatesGalaxy,
     retry_during_transitions,
@@ -33,8 +36,12 @@ from galaxy.util import (
 from galaxy_test.base import populators
 from galaxy_test.base.api import UsesApiTestCaseMixin
 from galaxy_test.base.api_util import get_admin_api_key
-from galaxy_test.base.env import DEFAULT_WEB_HOST, get_ip_address
+from galaxy_test.base.env import (
+    DEFAULT_WEB_HOST,
+    get_ip_address,
+)
 from galaxy_test.base.testcase import FunctionalTestCase
+
 try:
     from galaxy_test.driver.driver_util import GalaxyTestDriver
 except ImportError:
@@ -54,8 +61,12 @@ GALAXY_TEST_SCREENSHOTS_DIRECTORY = os.environ.get("GALAXY_TEST_SCREENSHOTS_DIRE
 # Test browser can be ["CHROME", "FIREFOX", "OPERA"]
 GALAXY_TEST_SELENIUM_BROWSER = os.environ.get("GALAXY_TEST_SELENIUM_BROWSER", driver_factory.DEFAULT_SELENIUM_BROWSER)
 GALAXY_TEST_SELENIUM_REMOTE = os.environ.get("GALAXY_TEST_SELENIUM_REMOTE", driver_factory.DEFAULT_SELENIUM_REMOTE)
-GALAXY_TEST_SELENIUM_REMOTE_PORT = os.environ.get("GALAXY_TEST_SELENIUM_REMOTE_PORT", driver_factory.DEFAULT_SELENIUM_REMOTE_PORT)
-GALAXY_TEST_SELENIUM_REMOTE_HOST = os.environ.get("GALAXY_TEST_SELENIUM_REMOTE_HOST", driver_factory.DEFAULT_SELENIUM_REMOTE_HOST)
+GALAXY_TEST_SELENIUM_REMOTE_PORT = os.environ.get(
+    "GALAXY_TEST_SELENIUM_REMOTE_PORT", driver_factory.DEFAULT_SELENIUM_REMOTE_PORT
+)
+GALAXY_TEST_SELENIUM_REMOTE_HOST = os.environ.get(
+    "GALAXY_TEST_SELENIUM_REMOTE_HOST", driver_factory.DEFAULT_SELENIUM_REMOTE_HOST
+)
 GALAXY_TEST_SELENIUM_HEADLESS = os.environ.get("GALAXY_TEST_SELENIUM_HEADLESS", DEFAULT_SELENIUM_HEADLESS)
 GALAXY_TEST_EXTERNAL_FROM_SELENIUM = os.environ.get("GALAXY_TEST_EXTERNAL_FROM_SELENIUM", None)
 # Auto-retry selenium tests this many times.
@@ -64,20 +75,23 @@ GALAXY_TEST_SELENIUM_RETRIES = int(os.environ.get("GALAXY_TEST_SELENIUM_RETRIES"
 GALAXY_TEST_SELENIUM_USER_EMAIL = os.environ.get("GALAXY_TEST_SELENIUM_USER_EMAIL", None)
 GALAXY_TEST_SELENIUM_USER_PASSWORD = os.environ.get("GALAXY_TEST_SELENIUM_USER_PASSWORD", None)
 GALAXY_TEST_SELENIUM_ADMIN_USER_EMAIL = os.environ.get("GALAXY_TEST_SELENIUM_ADMIN_USER_EMAIL", DEFAULT_ADMIN_USER)
-GALAXY_TEST_SELENIUM_ADMIN_USER_PASSWORD = os.environ.get("GALAXY_TEST_SELENIUM_ADMIN_USER_PASSWORD", DEFAULT_ADMIN_PASSWORD)
+GALAXY_TEST_SELENIUM_ADMIN_USER_PASSWORD = os.environ.get(
+    "GALAXY_TEST_SELENIUM_ADMIN_USER_PASSWORD", DEFAULT_ADMIN_PASSWORD
+)
 GALAXY_TEST_SELENIUM_BETA_HISTORY = os.environ.get("GALAXY_TEST_SELENIUM_BETA_HISTORY", "0") == "1"
 
 # JS code to execute in Galaxy JS console to setup localStorage of session for logging and
 # logging "flatten" messages because it seems Selenium (with Chrome at least) only grabs
 # the first argument to console.XXX when recovering the browser log.
-SETUP_LOGGING_JS = '''
+SETUP_LOGGING_JS = """
 window.localStorage && window.localStorage.setItem("galaxy:debug", true);
 window.localStorage && window.localStorage.setItem("galaxy:debug:flatten", true);
-'''
+"""
 
 try:
     from nose.tools import nottest
 except ImportError:
+
     def nottest(x):
         return x
 
@@ -104,6 +118,7 @@ def managed_history(f):
                     self.api_delete(f"histories/{current_history_id}")
                 except Exception:
                     print("Faild to cleanup managed history, selenium connection corrupted somehow?")
+
     return func_wrapper
 
 
@@ -164,14 +179,18 @@ def selenium_test(f):
                 dump_test_information(self, test_name)
                 if retry_attempts < GALAXY_TEST_SELENIUM_RETRIES:
                     retry_attempts += 1
-                    print(f"Test function [{test_name}] threw an exception, retrying. Failed attempts - {retry_attempts}.")
+                    print(
+                        f"Test function [{test_name}] threw an exception, retrying. Failed attempts - {retry_attempts}."
+                    )
                 else:
                     raise
 
     return func_wrapper
 
 
-retry_assertion_during_transitions = partial(retry_during_transitions, exception_check=lambda e: isinstance(e, AssertionError))
+retry_assertion_during_transitions = partial(
+    retry_during_transitions, exception_check=lambda e: isinstance(e, AssertionError)
+)
 
 
 class TestSnapshot:
@@ -277,8 +296,7 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
         self.snapshots.append(TestSnapshot(self.driver, len(self.snapshots), description))
 
     def get_download_path(self):
-        """Returns default download path
-        """
+        """Returns default download path"""
         return DEFAULT_DOWNLOAD_PATH
 
     def api_interactor_for_logged_in_user(self):
@@ -325,7 +343,9 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
 
     def login(self):
         if GALAXY_TEST_SELENIUM_USER_EMAIL:
-            assert GALAXY_TEST_SELENIUM_USER_PASSWORD, "If GALAXY_TEST_SELENIUM_USER_EMAIL is set, a password must be set also with GALAXY_TEST_SELENIUM_USER_PASSWORD"
+            assert (
+                GALAXY_TEST_SELENIUM_USER_PASSWORD
+            ), "If GALAXY_TEST_SELENIUM_USER_EMAIL is set, a password must be set also with GALAXY_TEST_SELENIUM_USER_PASSWORD"
             self.home()
             self.submit_login(
                 email=GALAXY_TEST_SELENIUM_USER_EMAIL,
@@ -379,10 +399,7 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
 
     def admin_login(self):
         self.home()
-        self.submit_login(
-            GALAXY_TEST_SELENIUM_ADMIN_USER_EMAIL,
-            GALAXY_TEST_SELENIUM_ADMIN_USER_PASSWORD
-        )
+        self.submit_login(GALAXY_TEST_SELENIUM_ADMIN_USER_EMAIL, GALAXY_TEST_SELENIUM_ADMIN_USER_PASSWORD)
         with self.main_panel():
             self.assert_no_error_message()
         return GALAXY_TEST_SELENIUM_ADMIN_USER_EMAIL
@@ -408,7 +425,9 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
         """
         visualization_names = self.history_panel_item_available_visualizations(hid)
         if visualization_name not in visualization_names:
-            raise unittest.SkipTest(f"Skipping test, visualization [{visualization_name}] doesn't appear to be configured.")
+            raise unittest.SkipTest(
+                f"Skipping test, visualization [{visualization_name}] doesn't appear to be configured."
+            )
 
 
 class SeleniumTestCase(FunctionalTestCase, TestWithSeleniumMixin):
@@ -473,7 +492,6 @@ else:
 
 
 class UsesLibraryAssertions(NavigatesGalaxyMixin):
-
     @retry_assertion_during_transitions
     def assert_num_displayed_items_is(self, n):
         num_displayed = self.num_displayed_items()
@@ -484,7 +502,6 @@ class UsesLibraryAssertions(NavigatesGalaxyMixin):
 
 
 class UsesHistoryItemAssertions(NavigatesGalaxyMixin):
-
     def assert_item_peek_includes(self, hid, expected):
         item_body = self.history_panel_item_component(hid=hid)
         peek_text = item_body.peek.wait_for_text()
@@ -520,7 +537,7 @@ class UsesHistoryItemAssertions(NavigatesGalaxyMixin):
 def default_web_host_for_selenium_tests():
     if asbool(GALAXY_TEST_SELENIUM_REMOTE):
         try:
-            dev_ip = get_ip_address('docker0')
+            dev_ip = get_ip_address("docker0")
             return dev_ip
         except OSError:
             return DEFAULT_WEB_HOST
@@ -543,7 +560,10 @@ def headless_selenium():
         return False
 
     if GALAXY_TEST_SELENIUM_HEADLESS == "auto":
-        if driver_factory.is_virtual_display_available() or driver_factory.get_local_browser(GALAXY_TEST_SELENIUM_BROWSER) == "CHROME":
+        if (
+            driver_factory.is_virtual_display_available()
+            or driver_factory.get_local_browser(GALAXY_TEST_SELENIUM_BROWSER) == "CHROME"
+        ):
             return True
         else:
             return False
@@ -556,7 +576,10 @@ def use_virtual_display():
         return False
 
     if GALAXY_TEST_SELENIUM_HEADLESS == "auto":
-        if driver_factory.is_virtual_display_available() and not driver_factory.get_local_browser(GALAXY_TEST_SELENIUM_BROWSER) == "CHROME":
+        if (
+            driver_factory.is_virtual_display_available()
+            and not driver_factory.get_local_browser(GALAXY_TEST_SELENIUM_BROWSER) == "CHROME"
+        ):
             return True
         else:
             return False
@@ -566,6 +589,7 @@ def use_virtual_display():
 
 class SeleniumSessionGetPostMixin:
     """Mixin for adapting Galaxy testing populators helpers to Selenium session backed bioblend."""
+
     selenium_context: GalaxySeleniumContext
 
     @property
@@ -598,7 +622,9 @@ class SeleniumSessionGetPostMixin:
             full_url = f"{full_url}?key={self._mixin_admin_api_key}"
         else:
             cookies = self.selenium_context.selenium_to_requests_cookies()
-        request_kwd = self._prepare_request_data(dict(cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT, files=files), data, as_json=json)
+        request_kwd = self._prepare_request_data(
+            dict(cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT, files=files), data, as_json=json
+        )
         response = requests.post(full_url, **request_kwd)
         return response
 
@@ -610,7 +636,9 @@ class SeleniumSessionGetPostMixin:
             full_url = f"{full_url}?key={self._mixin_admin_api_key}"
         else:
             cookies = self.selenium_context.selenium_to_requests_cookies()
-        request_kwd = self._prepare_request_data(dict(cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT), data, as_json=json)
+        request_kwd = self._prepare_request_data(
+            dict(cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT), data, as_json=json
+        )
         response = requests.delete(full_url, **request_kwd)
         return response
 
@@ -622,15 +650,17 @@ class SeleniumSessionGetPostMixin:
             full_url = f"{full_url}?key={self._mixin_admin_api_key}"
         else:
             cookies = self.selenium_context.selenium_to_requests_cookies()
-        request_kwd = self._prepare_request_data(dict(cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT), data, as_json=json)
+        request_kwd = self._prepare_request_data(
+            dict(cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT), data, as_json=json
+        )
         response = requests.put(full_url, **request_kwd)
         return response
 
     def _prepare_request_data(self, request_kwd: Dict[str, Any], data: Dict[str, Any], as_json: bool = False):
         if as_json:
-            request_kwd['json'] = data
+            request_kwd["json"] = data
         else:
-            request_kwd['data'] = data
+            request_kwd["data"] = data
         return request_kwd
 
 
@@ -657,7 +687,9 @@ class SeleniumSessionDatasetCollectionPopulator(SeleniumSessionGetPostMixin, pop
         return create_response
 
 
-class SeleniumSessionWorkflowPopulator(SeleniumSessionGetPostMixin, populators.BaseWorkflowPopulator, ImporterGalaxyInterface):
+class SeleniumSessionWorkflowPopulator(
+    SeleniumSessionGetPostMixin, populators.BaseWorkflowPopulator, ImporterGalaxyInterface
+):
 
     """Implementation of BaseWorkflowPopulator backed by bioblend."""
 
@@ -670,7 +702,7 @@ class SeleniumSessionWorkflowPopulator(SeleniumSessionGetPostMixin, populators.B
     def import_workflow(self, workflow: dict, **kwds) -> dict:
         workflow_str = json.dumps(workflow, indent=4)
         data = {
-            'workflow': workflow_str,
+            "workflow": workflow_str,
         }
         data.update(**kwds)
         upload_response = self._post("workflows", data=data)
diff --git a/lib/galaxy_test/selenium/test_admin_app.py b/lib/galaxy_test/selenium/test_admin_app.py
index 30375f4c37a..a5749dbb887 100644
--- a/lib/galaxy_test/selenium/test_admin_app.py
+++ b/lib/galaxy_test/selenium/test_admin_app.py
@@ -15,31 +15,31 @@ class AdminAppTestCase(SeleniumTestCase):
         self.admin_login()
         self.admin_open()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_landing')
+        self.screenshot("admin_landing")
         admin_component.index.allowlist.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_allowlist_landing')
+        self.screenshot("admin_allowlist_landing")
         admin_component.allowlist.local.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_allowlist_local_landing')
+        self.screenshot("admin_allowlist_local_landing")
         # This should be updated if the list of built-in converters is changed.
         render_button = self.driver.find_element_by_xpath("//td[.='CONVERTER_bam_to_bigwig_0']/following::td/button")
         render_button.click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_allowlist_converter_html_rendered')
+        self.screenshot("admin_allowlist_converter_html_rendered")
         admin_component.allowlist.rendered_active.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_allowlist_render_landing')
+        self.screenshot("admin_allowlist_render_landing")
         self.sleep_for(self.wait_types.UX_RENDER)
         sanitize_button = self.driver.find_element_by_xpath("//td[.='CONVERTER_bam_to_bigwig_0']/following::td/button")
         sanitize_button.click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_allowlist_converter_sanitized')
+        self.screenshot("admin_allowlist_converter_sanitized")
 
     @selenium_test
     @flakey
     def test_admin_toolshed(self):
-        '''
+        """
         This tests installing a repository, checking for upgrades, and uninstalling.
 
         A repository named a_selenium_test_repo has been created for this test,
@@ -48,35 +48,37 @@ class AdminAppTestCase(SeleniumTestCase):
         on the 'Installed Only' view. Unfortunately, since this test relies on the presence
         of the toolshed server, in some cases it will fail even if the galaxy code is correct,
         necessitating the use of the @flakey decorator.
-        '''
-        repository_name = 'a_selenium_test_repo'
+        """
+        repository_name = "a_selenium_test_repo"
         admin_component = self.components.admin
         self.admin_login()
         self.admin_open()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_landing')
+        self.screenshot("admin_landing")
         admin_component.index.toolshed.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_toolshed_landing')
-        repo_search_input = self.driver.find_element_by_id('toolshed-repo-search')
+        self.screenshot("admin_toolshed_landing")
+        repo_search_input = self.driver.find_element_by_id("toolshed-repo-search")
         repo_search_input.clear()
         repo_search_input.send_keys(repository_name)
         # If this hasn't succeeded after 30 seconds, the @flakey context should
         # allow the test to still pass, since there should definitely be results
         # after 30 seconds.
         self.sleep_for(self.wait_types.SHED_SEARCH)
-        self.screenshot('admin_toolshed_search')
+        self.screenshot("admin_toolshed_search")
         admin_component.toolshed.search_results.wait_for_visible()
         repository_row = self.driver.find_element_by_link_text(repository_name)
         repository_row.click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_toolshed_repo_details')
+        self.screenshot("admin_toolshed_repo_details")
         install_button = self.driver.find_element_by_xpath("(//button[contains(., 'Install')])[2]")
         install_button.click()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot('admin_toolshed_repo_install_settings')
+        self.screenshot("admin_toolshed_repo_install_settings")
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        ok_button = self.driver.find_element_by_xpath("//*[@id='repo-install-settings___BV_modal_footer_']/button[contains(., 'OK')]")
+        ok_button = self.driver.find_element_by_xpath(
+            "//*[@id='repo-install-settings___BV_modal_footer_']/button[contains(., 'OK')]"
+        )
         ok_button.click()
         self.sleep_for(self.wait_types.REPO_INSTALL)
         installed_only = self.driver.find_element_by_xpath("//span[contains(. ,'Installed Only')]/../../input")
@@ -84,17 +86,17 @@ class AdminAppTestCase(SeleniumTestCase):
         self.sleep_for(self.wait_types.UX_TRANSITION)
         # This serves as a check for the presence of the upgrade notification.
         admin_component.toolshed.upgrade_notification.wait_for_visible()
-        self.screenshot('admin_toolshed_repo_installed')
+        self.screenshot("admin_toolshed_repo_installed")
         repository_row = self.driver.find_element_by_xpath(f"//div[contains(text(), '{repository_name}')]/..")
         repository_row.click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        self.screenshot('admin_toolshed_installed_only')
+        self.screenshot("admin_toolshed_installed_only")
         # Unfortunately reusing the element isn't feasible, since the div
         # containing the button gets replaced with a new div and button.
         uninstall_button = self.driver.find_element_by_xpath("(//button[contains(., 'Uninstall')])[1]")
         uninstall_button.click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        self.screenshot('admin_toolshed_repo_uninstalled')
+        self.screenshot("admin_toolshed_repo_uninstalled")
 
     @selenium_test
     def test_admin_dependencies_display(self):
@@ -105,9 +107,9 @@ class AdminAppTestCase(SeleniumTestCase):
         admin_component.index.dependencies.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         # Ensure that tabs are visible
-        self.driver.find_element_by_link_text('Dependencies')
-        self.driver.find_element_by_link_text('Containers')
-        unused_link = self.driver.find_element_by_link_text('Unused')
+        self.driver.find_element_by_link_text("Dependencies")
+        self.driver.find_element_by_link_text("Containers")
+        unused_link = self.driver.find_element_by_link_text("Unused")
         # Ensure that #manage-resolver-type is visible.
         admin_component.manage_dependencies.resolver_type.wait_for_visible()
         self.screenshot("admin_dependencies_landing")
@@ -217,9 +219,7 @@ class AdminAppTestCase(SeleniumTestCase):
                 history_id=history_id,
             )
             job_id = run_response.json()["jobs"][0]["id"]
-            self.dataset_populator.wait_for_tool_run(history_id=history_id,
-                                                     run_response=run_response,
-                                                     assert_ok=False)
+            self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, assert_ok=False)
 
         admin_component.dm_jobs_button(data_manager="test-data-manager").wait_for_and_click()
         admin_component.dm_jobs_breadcrumb.wait_for_visible()
diff --git a/lib/galaxy_test/selenium/test_anon_history.py b/lib/galaxy_test/selenium/test_anon_history.py
index 5c29ecaa970..53cf6687fd6 100644
--- a/lib/galaxy_test/selenium/test_anon_history.py
+++ b/lib/galaxy_test/selenium/test_anon_history.py
@@ -1,11 +1,10 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
 class AnonymousHistoriesTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_anon_history_landing(self):
         self.home()
diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index 95f3fec7057..15afee91b11 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -22,7 +22,7 @@ class ChangePasswordTestCase(SeleniumTestCase):
     def test_new_password_password(self):
         self.register_and_change_password()
         self.fill_input_fields(self.default_password, "", self._get_random_password())
-        self.assert_error_message(contains='Please provide a new password.')
+        self.assert_error_message(contains="Please provide a new password.")
 
     @selenium_test
     def test_no_password_confirmation(self):
@@ -30,7 +30,7 @@ class ChangePasswordTestCase(SeleniumTestCase):
         password = self._get_random_password()
         confirmation = self._get_random_password()
         self.fill_input_fields(self.default_password, password, confirmation)
-        self.assert_error_message(contains='Passwords do not match.')
+        self.assert_error_message(contains="Passwords do not match.")
 
     @selenium_test
     def test_currect_password_incorrect(self):
@@ -38,14 +38,14 @@ class ChangePasswordTestCase(SeleniumTestCase):
         password = self._get_random_password()
         assert self.default_password != password
         self.fill_input_fields(password, password, password)
-        self.assert_error_message(contains='Invalid current password.')
+        self.assert_error_message(contains="Invalid current password.")
 
     @selenium_test
     def test_new_password_short(self):
         self.register_and_change_password()
         password = self._get_random_password(len=3)
         self.fill_input_fields(self.default_password, password, password)
-        self.assert_error_message(contains='Use a password of at least 6 characters.')
+        self.assert_error_message(contains="Use a password of at least 6 characters.")
 
     @selenium_test
     def test_new_password_same_password(self):
diff --git a/lib/galaxy_test/selenium/test_collection_builders.py b/lib/galaxy_test/selenium/test_collection_builders.py
index c34eeea4ee9..f72ee720b28 100644
--- a/lib/galaxy_test/selenium/test_collection_builders.py
+++ b/lib/galaxy_test/selenium/test_collection_builders.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -17,7 +17,9 @@ class CollectionBuildersTestCase(SeleniumTestCase):
         if self.is_beta_history():
             self._collection_dropdown("build list")
         else:
-            self.history_panel_multi_operation_action_click(self.navigation.history_panel.multi_operations.labels.build_list)
+            self.history_panel_multi_operation_action_click(
+                self.navigation.history_panel.multi_operations.labels.build_list
+            )
 
         self.collection_builder_set_name("my cool list")
         self.screenshot("collection_builder_list")
@@ -33,7 +35,9 @@ class CollectionBuildersTestCase(SeleniumTestCase):
         if self.is_beta_history():
             self._collection_dropdown("build list")
         else:
-            self.history_panel_multi_operation_action_click(self.navigation.history_panel.multi_operations.labels.build_list)
+            self.history_panel_multi_operation_action_click(
+                self.navigation.history_panel.multi_operations.labels.build_list
+            )
 
         # this toggles the checkbox to not hide originals
         self.collection_builder_hide_originals()
@@ -52,7 +56,9 @@ class CollectionBuildersTestCase(SeleniumTestCase):
         if self.is_beta_history():
             self._collection_dropdown("build pair")
         else:
-            self.history_panel_multi_operation_action_click(self.navigation.history_panel.multi_operations.labels.build_pair)
+            self.history_panel_multi_operation_action_click(
+                self.navigation.history_panel.multi_operations.labels.build_pair
+            )
 
         self.collection_builder_set_name("my awesome pair")
         self.screenshot("collection_builder_pair")
@@ -70,7 +76,9 @@ class CollectionBuildersTestCase(SeleniumTestCase):
         if self.is_beta_history():
             self._collection_dropdown("build list of pairs")
         else:
-            self.history_panel_multi_operation_action_click(self.navigation.history_panel.multi_operations.labels.build_list_pairs)
+            self.history_panel_multi_operation_action_click(
+                self.navigation.history_panel.multi_operations.labels.build_list_pairs
+            )
 
         self.collection_builder_clear_filters()
         self.collection_builder_click_paired_item("forward", 0)
@@ -101,7 +109,9 @@ class CollectionBuildersTestCase(SeleniumTestCase):
         if self.is_beta_history():
             self._collection_dropdown("build list of pairs")
         else:
-            self.history_panel_multi_operation_action_click(self.navigation.history_panel.multi_operations.labels.build_list_pairs)
+            self.history_panel_multi_operation_action_click(
+                self.navigation.history_panel.multi_operations.labels.build_list_pairs
+            )
 
         self.wait_for_and_click(self.navigation.collection_builders.selectors.clear_filters)
 
@@ -141,7 +151,9 @@ class CollectionBuildersTestCase(SeleniumTestCase):
         if self.is_beta_history():
             self._collection_dropdown("build collection from rules")
         else:
-            self.history_panel_multi_operation_action_click(self.navigation.history_panel.multi_operations.labels.build_from_rules)
+            self.history_panel_multi_operation_action_click(
+                self.navigation.history_panel.multi_operations.labels.build_from_rules
+            )
 
         self.collection_builder_set_name("my cool list")
         self.screenshot("collection_builder_rules_list")
@@ -188,7 +200,7 @@ class CollectionBuildersTestCase(SeleniumTestCase):
                 self.history_panel_muli_operation_select_hid(hid)
 
     def _show_hidden_content(self):
-        """Switches the beta hidden filter toggle on """
+        """Switches the beta hidden filter toggle on"""
         self.sleep_for(self.wait_types.UX_RENDER)
         self.beta_history_element("content filter toggle").wait_for_and_click()
         self.beta_history_element("show hidden filter toggle").wait_for_and_click()
diff --git a/lib/galaxy_test/selenium/test_collection_edit.py b/lib/galaxy_test/selenium/test_collection_edit.py
index f753f93ad73..08106a04848 100644
--- a/lib/galaxy_test/selenium/test_collection_edit.py
+++ b/lib/galaxy_test/selenium/test_collection_edit.py
@@ -2,7 +2,7 @@ from selenium.webdriver.common.keys import Keys
 
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
diff --git a/lib/galaxy_test/selenium/test_custom_builds.py b/lib/galaxy_test/selenium/test_custom_builds.py
index 1a28faa129a..27cfe8b2889 100644
--- a/lib/galaxy_test/selenium/test_custom_builds.py
+++ b/lib/galaxy_test/selenium/test_custom_builds.py
@@ -6,7 +6,6 @@ from .framework import (
 
 
 class CustomBuildsTestcase(SharedStateSeleniumTestCase):
-
     @selenium_test
     def test_build_add(self):
         self._login()
@@ -54,31 +53,31 @@ class CustomBuildsTestcase(SharedStateSeleniumTestCase):
         option = self.wait_for_sizzle_selector_clickable('option[value="text"]')
         option.click()
         content_area = self.wait_for_and_click_selector('textarea[id="len-file-text-area"]')
-        content_area.send_keys('content')
+        content_area.send_keys("content")
 
-        self.wait_for_and_click_selector('button#save')
+        self.wait_for_and_click_selector("button#save")
 
     def delete_custom_build(self, build_name):
         delete_button = None
-        grid = self.wait_for_selector('table.grid > tbody')
-        for row in grid.find_elements_by_tag_name('tr'):
-            td = row.find_elements_by_tag_name('td')
+        grid = self.wait_for_selector("table.grid > tbody")
+        for row in grid.find_elements_by_tag_name("tr"):
+            td = row.find_elements_by_tag_name("td")
             name = td[0].text
             if name == build_name:
-                delete_button = td[3].find_element_by_css_selector('.fa-trash-o')
+                delete_button = td[3].find_element_by_css_selector(".fa-trash-o")
                 break
 
         if delete_button is None:
-            raise AssertionError(f'Failed to find custom build with name [{build_name}]')
+            raise AssertionError(f"Failed to find custom build with name [{build_name}]")
 
         delete_button.click()
 
     def get_custom_builds(self):
         self.sleep_for(self.wait_types.UX_RENDER)
         builds = []
-        grid = self.wait_for_selector('table.grid > tbody')
-        for row in grid.find_elements_by_tag_name('tr'):
-            name = row.find_elements_by_tag_name('td')[0].text
+        grid = self.wait_for_selector("table.grid > tbody")
+        for row in grid.find_elements_by_tag_name("tr"):
+            name = row.find_elements_by_tag_name("td")[0].text
             builds.append(name)
         return builds
 
diff --git a/lib/galaxy_test/selenium/test_histories_list.py b/lib/galaxy_test/selenium/test_histories_list.py
index ee276a4fa89..1b241d26993 100644
--- a/lib/galaxy_test/selenium/test_histories_list.py
+++ b/lib/galaxy_test/selenium/test_histories_list.py
@@ -6,7 +6,6 @@ from .framework import (
 
 
 class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
-
     @selenium_test
     def test_histories_list(self):
         self._login()
@@ -18,7 +17,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self._login()
         self.navigate_to_histories_page()
         self.screenshot("histories_saved_grid")
-        self.click_grid_popup_option(self.history2_name, 'Switch')
+        self.click_grid_popup_option(self.history2_name, "Switch")
         self.sleep_for(self.wait_types.UX_RENDER)
 
         @retry_assertion_during_transitions
@@ -31,8 +30,8 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     def test_history_view(self):
         self._login()
         self.navigate_to_histories_page()
-        self.click_grid_popup_option(self.history2_name, 'View')
-        history_name = self.wait_for_selector('.name.editable-text')
+        self.click_grid_popup_option(self.history2_name, "View")
+        history_name = self.wait_for_selector(".name.editable-text")
         self.assertEqual(history_name.text, self.history2_name)
 
     @selenium_test
@@ -41,13 +40,13 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.navigate_to_histories_page()
 
         # Publish the history
-        self.click_grid_popup_option(self.history2_name, 'Share or Publish')
+        self.click_grid_popup_option(self.history2_name, "Share or Publish")
         self.make_accessible_and_publishable()
 
         self.navigate_to_histories_page()
 
         self.histories_click_advanced_search()
-        self.select_filter('sharing', 'published')
+        self.select_filter("sharing", "published")
         self.sleep_for(self.wait_types.UX_RENDER)
 
         self.assert_histories_in_grid([self.history2_name])
@@ -57,10 +56,10 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self._login()
         self.navigate_to_histories_page()
 
-        self.click_grid_popup_option('Unnamed history', 'Rename')
+        self.click_grid_popup_option("Unnamed history", "Rename")
 
         # Rename the history
-        history_name_input = self.wait_for_selector('.ui-form-element input.ui-input')
+        history_name_input = self.wait_for_selector(".ui-form-element input.ui-input")
         history_name_input.clear()
         history_name_input.send_keys(self.history1_name)
 
@@ -76,19 +75,19 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.navigate_to_histories_page()
 
         # Delete the history
-        self.click_grid_popup_option(self.history2_name, 'Delete')
+        self.click_grid_popup_option(self.history2_name, "Delete")
 
         self.assert_histories_in_grid([self.history2_name], False)
 
         self.histories_click_advanced_search()
-        self.select_filter('deleted', 'True')
+        self.select_filter("deleted", "True")
         self.sleep_for(self.wait_types.UX_RENDER)
 
         # Restore the history
-        self.click_grid_popup_option(self.history2_name, 'Undelete')
+        self.click_grid_popup_option(self.history2_name, "Undelete")
 
         self.assert_grid_histories_are([])
-        self.select_filter('deleted', 'False')
+        self.select_filter("deleted", "False")
 
         self.assert_histories_in_grid([self.history2_name])
 
@@ -100,14 +99,14 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.navigate_to_histories_page()
         self.assert_histories_in_grid([self.history4_name])
 
-        self.click_grid_popup_option(self.history4_name, 'Delete Permanently')
+        self.click_grid_popup_option(self.history4_name, "Delete Permanently")
         alert = self.driver.switch_to.alert
         alert.accept()
 
         self.assert_histories_in_grid([self.history4_name], False)
 
         self.histories_click_advanced_search()
-        self.select_filter('deleted', 'True')
+        self.select_filter("deleted", "True")
 
         self.assert_histories_in_grid([self.history4_name])
 
@@ -126,7 +125,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.assert_histories_in_grid([self.history2_name, self.history3_name], False)
 
         self.histories_click_advanced_search()
-        self.select_filter('deleted', 'True')
+        self.select_filter("deleted", "True")
         self.sleep_for(self.wait_types.UX_RENDER)
 
         # Restore multiple histories
@@ -136,7 +135,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.assert_grid_histories_are([])
         # Following msg popups but goes away and so can cause transient errors.
         # self.wait_for_selector_visible('.donemessage')
-        self.select_filter('deleted', 'False')
+        self.select_filter("deleted", "False")
 
         self.assert_histories_in_grid([self.history2_name, self.history3_name])
 
@@ -171,7 +170,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
         self.assert_grid_histories_are([self.history2_name])
 
-        self.unset_filter('free-text-search', self.history2_name)
+        self.unset_filter("free-text-search", self.history2_name)
         search_input = self.components.grids.free_text_search.wait_for_visible()
         search_input.send_keys(self.history4_name)
         self.send_enter(search_input)
@@ -187,26 +186,26 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
         self.histories_click_advanced_search()
 
-        name_filter_selector = '#input-name-filter'
-        tags_filter_selector = '#input-tags-filter'
+        name_filter_selector = "#input-name-filter"
+        tags_filter_selector = "#input-tags-filter"
 
         # Search by name
         self.set_filter(name_filter_selector, self.history2_name)
         self.assert_grid_histories_are([self.history2_name])
-        self.unset_filter('name', self.history2_name)
+        self.unset_filter("name", self.history2_name)
 
         self.set_filter(name_filter_selector, self.history4_name)
         self.assert_grid_histories_are([])
-        self.unset_filter('name', self.history4_name)
+        self.unset_filter("name", self.history4_name)
 
         # Search by tags
         self.set_filter(tags_filter_selector, self.history3_tags[0])
         self.assert_grid_histories_are([self.history3_name])
-        self.unset_filter('tags', self.history3_tags[0])
+        self.unset_filter("tags", self.history3_tags[0])
 
         self.set_filter(tags_filter_selector, self.history4_tags[0])
         self.assert_grid_histories_are([])
-        self.unset_filter('tags', self.history4_tags[0])
+        self.unset_filter("tags", self.history4_tags[0])
 
     @selenium_test
     def test_tags(self):
@@ -215,7 +214,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
         # Insert a tag
         tags_cell = self.get_history_tags_cell(self.history2_name)
-        tag_area = tags_cell.find_element_by_css_selector('.ti-new-tag-input-wrapper input')
+        tag_area = tags_cell.find_element_by_css_selector(".ti-new-tag-input-wrapper input")
         tag_area.click()
         tag_area.send_keys(self.history2_tags[0])
         self.send_enter(tag_area)
@@ -224,7 +223,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
         # Search by tag
         tags_cell = self.get_history_tags_cell(self.history2_name)
-        tag = tags_cell.find_element_by_css_selector('.ti-tag-center')
+        tag = tags_cell.find_element_by_css_selector(".ti-tag-center")
         tag.click()
 
         self.assert_grid_histories_are([self.history2_name], False)
@@ -260,8 +259,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.sleep_for(self.wait_types.UX_RENDER)
 
     def unset_filter(self, filter_key, filter_value):
-        close_button_selector = 'a[filter_key="%s"][filter_val="%s"]' % \
-            (filter_key, filter_value)
+        close_button_selector = 'a[filter_key="%s"][filter_val="%s"]' % (filter_key, filter_value)
         self.wait_for_and_click_selector(close_button_selector)
         self.sleep_for(self.wait_types.UX_RENDER)
 
@@ -291,23 +289,23 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
     def get_history_tags_cell(self, history_name):
         tags_cell = None
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            td = row.find_elements_by_tag_name('td')
+        grid = self.wait_for_selector("#grid-table-body")
+        for row in grid.find_elements_by_tag_name("tr"):
+            td = row.find_elements_by_tag_name("td")
             if td[1].text == history_name:
                 tags_cell = td[4]
                 break
 
         if tags_cell is None:
-            raise AssertionError(f'Failed to find history with name [{history_name}]')
+            raise AssertionError(f"Failed to find history with name [{history_name}]")
 
         return tags_cell
 
     def check_histories(self, histories):
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            td = row.find_elements_by_tag_name('td')
+        grid = self.wait_for_selector("#grid-table-body")
+        for row in grid.find_elements_by_tag_name("tr"):
+            td = row.find_elements_by_tag_name("td")
             history_name = td[1].text
             if history_name in histories:
-                checkbox = td[0].find_element_by_tag_name('input')
+                checkbox = td[0].find_element_by_tag_name("input")
                 checkbox.click()
diff --git a/lib/galaxy_test/selenium/test_history_copy_elements.py b/lib/galaxy_test/selenium/test_history_copy_elements.py
index 3ccc6864c6c..840a307473a 100644
--- a/lib/galaxy_test/selenium/test_history_copy_elements.py
+++ b/lib/galaxy_test/selenium/test_history_copy_elements.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -11,7 +11,9 @@ class HistoryCopyElementsTestCase(SeleniumTestCase):
     @selenium_test
     def test_copy_hdca(self):
         history_id = self.current_history_id()
-        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_collection = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json()
         input_hid = input_collection["hid"]
 
         failed_response = self.dataset_populator.run_exit_code_from_file(history_id, input_collection["id"])
diff --git a/lib/galaxy_test/selenium/test_history_dataset_state.py b/lib/galaxy_test/selenium/test_history_dataset_state.py
index 09f96783413..717079f4a1b 100644
--- a/lib/galaxy_test/selenium/test_history_dataset_state.py
+++ b/lib/galaxy_test/selenium/test_history_dataset_state.py
@@ -5,15 +5,15 @@ from .framework import (
 )
 
 BUTTON_TOOLTIPS = {
-    "display": 'View data',
-    "edit": 'Edit attributes',
-    "delete": 'Delete',
-    "download": 'Download',
-    "info": 'View details',
-    "rerun": 'Run this job again',
+    "display": "View data",
+    "edit": "Edit attributes",
+    "delete": "Delete",
+    "download": "Download",
+    "info": "View details",
+    "rerun": "Run this job again",
 }
-EXPECTED_TOOLHELP_TITLE_TEXT = 'Tool help for Data Fetch'
-TEST_DBKEY_TEXT = 'Honeybee (Apis mellifera): apiMel3 (apiMel3)'
+EXPECTED_TOOLHELP_TITLE_TEXT = "Tool help for Data Fetch"
+TEST_DBKEY_TEXT = "Honeybee (Apis mellifera): apiMel3 (apiMel3)"
 FIRST_HID = 1
 
 
@@ -27,7 +27,7 @@ class HistoryDatasetStateTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
 
         self.assert_item_summary_includes(FIRST_HID, "1 sequence")
         self.assert_item_dbkey_displayed_as(FIRST_HID, "?")
-        self.assert_item_info_includes(FIRST_HID, 'uploaded fasta file')
+        self.assert_item_info_includes(FIRST_HID, "uploaded fasta file")
         self.assert_item_peek_includes(FIRST_HID, ">hg17")
 
         self.screenshot("history_panel_dataset_before_click_dbkey")
@@ -42,8 +42,11 @@ class HistoryDatasetStateTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
             # need to redo tooltip stuff for beta history panel...
             toolhelp_title_text = item.toolhelp_title.wait_for_visible().text
             # assert tool helptext
-            assert EXPECTED_TOOLHELP_TITLE_TEXT == toolhelp_title_text, "Toolhelp title [{}] was not expected text [{}].".format(
-                EXPECTED_TOOLHELP_TITLE_TEXT, toolhelp_title_text)
+            assert (
+                EXPECTED_TOOLHELP_TITLE_TEXT == toolhelp_title_text
+            ), "Toolhelp title [{}] was not expected text [{}].".format(
+                EXPECTED_TOOLHELP_TITLE_TEXT, toolhelp_title_text
+            )
 
         self.screenshot("history_panel_dataset_expanded")
 
@@ -62,7 +65,8 @@ class HistoryDatasetStateTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         self.components.edit_dataset_attributes.database_build_dropdown.wait_for_and_click()
         # choose database option from 'Database/Build' dropdown, that equals to dbkey_text
         self.components.edit_dataset_attributes.dbkey_dropdown_results.dbkey_dropdown_option(
-            dbkey_text=TEST_DBKEY_TEXT).wait_for_and_click()
+            dbkey_text=TEST_DBKEY_TEXT
+        ).wait_for_and_click()
         self.components.edit_dataset_attributes.save_btn.wait_for_and_click()
         if self.is_beta_history():
             self.sleep_for(self.wait_types.JOB_COMPLETION)
@@ -82,7 +86,7 @@ class HistoryDatasetStateTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
 
     def _assert_title_buttons(self, hid, expected_buttons=None):
         if expected_buttons is None:
-            expected_buttons = ['display', 'edit', 'delete']
+            expected_buttons = ["display", "edit", "delete"]
         self._assert_buttons(hid, expected_buttons)
 
     def _assert_action_buttons(self, hid, expected_buttons=None):
diff --git a/lib/galaxy_test/selenium/test_history_export.py b/lib/galaxy_test/selenium/test_history_export.py
index 0a6b6caa678..3edf559adf5 100644
--- a/lib/galaxy_test/selenium/test_history_export.py
+++ b/lib/galaxy_test/selenium/test_history_export.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
diff --git a/lib/galaxy_test/selenium/test_history_multi_view.py b/lib/galaxy_test/selenium/test_history_multi_view.py
index 15fffe358e9..81b9ad9278f 100644
--- a/lib/galaxy_test/selenium/test_history_multi_view.py
+++ b/lib/galaxy_test/selenium/test_history_multi_view.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -11,7 +11,9 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
     @selenium_test
     def test_create_new_old_slides_next(self):
         history_id = self.current_history_id()
-        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_collection = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json()
         input_hid = input_collection["hid"]
 
         self.home()
@@ -39,7 +41,9 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
     @selenium_test
     def test_list_list_list_display(self):
         history_id = self.current_history_id()
-        method = self.dataset_collection_populator.create_nested_collection(history_id, collection_type="list:list:list").json
+        method = self.dataset_collection_populator.create_nested_collection(
+            history_id, collection_type="list:list:list"
+        ).json
         selector = self.prepare_multi_history_view(method)
 
         first_level_element_selector = selector.descendant(".dataset-collection-element")
@@ -55,7 +59,9 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
     @selenium_test
     def test_copy_history(self):
         history_id = self.current_history_id()
-        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+        method = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json
 
         self.prepare_multi_history_view(method)
         self.copy_history(history_id)
@@ -64,7 +70,9 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
     @selenium_test
     def test_delete_history(self):
         history_id = self.current_history_id()
-        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+        method = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json
 
         self.prepare_multi_history_view(method)
         self.copy_history(history_id)
@@ -78,7 +86,9 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
     @selenium_test
     def test_purge_history(self):
         history_id = self.current_history_id()
-        method = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json
+        method = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json
 
         self.prepare_multi_history_view(method)
         self.copy_history(history_id)
@@ -93,7 +103,7 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
 
     @selenium_test
     def test_switch_history(self):
-        '''
+        """
         1. Load the multi history view. There should be a selector for the button
            to create a new history.
         2. Create a new history. This *should* automatically switch to the newly
@@ -102,7 +112,7 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
            previously created history that allows switching back to that one, and
            the history ID should now match the ID of the history with which we
            started.
-        '''
+        """
         self.home()
         original_history_id = self.current_history_id()
         # Load the multi-view
@@ -128,7 +138,9 @@ class HistoryMultiViewTestCase(SeleniumTestCase):
         histories = self.components.multi_history_view.histories.all()
         assert len(histories) == histories_number
         # search for history with history_id
-        assert should_exist == any(history.get_attribute("id") == f"history-column-{history_id}" for history in histories)
+        assert should_exist == any(
+            history.get_attribute("id") == f"history-column-{history_id}" for history in histories
+        )
 
     def copy_history(self, history_id):
         self.components.multi_history_view.history_dropdown_btn(history_id=history_id).wait_for_and_click()
diff --git a/lib/galaxy_test/selenium/test_history_options.py b/lib/galaxy_test/selenium/test_history_options.py
index c517611f5fb..1b0c95a8851 100644
--- a/lib/galaxy_test/selenium/test_history_options.py
+++ b/lib/galaxy_test/selenium/test_history_options.py
@@ -1,11 +1,10 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
 class HistoryOptionsTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_options(self):
         self.register()
@@ -21,7 +20,7 @@ class HistoryOptionsTestCase(SeleniumTestCase):
         self.wait_for_absent_or_hidden(menu_selector)
 
         hid = 1
-        self.history_panel_wait_for_hid_state(hid, 'ok')
+        self.history_panel_wait_for_hid_state(hid, "ok")
         self.history_panel_click_item_title(hid=hid, wait=True)
         item_component = self.history_panel_item_body_component(hid=hid)
         item_component.wait_for_visible()
diff --git a/lib/galaxy_test/selenium/test_history_panel.py b/lib/galaxy_test/selenium/test_history_panel.py
index fbbb9a3b2ec..976cc70144c 100644
--- a/lib/galaxy_test/selenium/test_history_panel.py
+++ b/lib/galaxy_test/selenium/test_history_panel.py
@@ -1,15 +1,12 @@
 import pytest
 
-from galaxy.selenium.navigates_galaxy import (
-    edit_details
-)
+from galaxy.selenium.navigates_galaxy import edit_details
 from .framework import (
     retry_assertion_during_transitions,
     selenium_test,
     SeleniumTestCase,
 )
 
-
 NEW_HISTORY_NAME = "New History Name"
 
 
@@ -41,7 +38,9 @@ class HistoryPanelTestCase(SeleniumTestCase):
     @selenium_test
     def test_history_rename_confirm_with_click(self):
         if self.is_beta_history():
-            raise pytest.skip("Beta History Panel has explicit editing toggle mode, so can not click off to the side to save")
+            raise pytest.skip(
+                "Beta History Panel has explicit editing toggle mode, so can not click off to the side to save"
+            )
         editable_text_input_element = self.history_panel_name_input()
         editable_text_input_element.send_keys(NEW_HISTORY_NAME)
         self.click_center()
@@ -100,18 +99,15 @@ class HistoryPanelTestCase(SeleniumTestCase):
         history_panel = self.components.history_panel
 
         @retry_assertion_during_transitions
-        def assert_current_annotation(expected, error_message="History annotation",
-                                      is_equal=True):
+        def assert_current_annotation(expected, error_message="History annotation", is_equal=True):
 
             text_component = history_panel.annotation_editable_text
             current_annotation = text_component.wait_for_visible()
             error_message += " given: [%s] expected [%s] "
             if is_equal:
-                assert current_annotation.text == expected, error_message % (
-                    current_annotation.text, expected)
+                assert current_annotation.text == expected, error_message % (current_annotation.text, expected)
             else:
-                assert current_annotation.text != expected, error_message % (
-                    current_annotation.text, expected)
+                assert current_annotation.text != expected, error_message % (current_annotation.text, expected)
 
         def set_random_annotation(clear_text=True):
             random_annotation = self._get_random_name(prefix="arbitrary_annotation_")
@@ -128,15 +124,17 @@ class HistoryPanelTestCase(SeleniumTestCase):
         # change annotation text
         changed_annotation = set_random_annotation()
 
-        assert_current_annotation(initial_annotation, error_message="History annotation was not changed!",
-                                  is_equal=False)
-        assert_current_annotation(changed_annotation,
-                                  error_message="History annotation was changed, but annotation text is wrong!",
-                                  is_equal=True)
+        assert_current_annotation(
+            initial_annotation, error_message="History annotation was not changed!", is_equal=False
+        )
+        assert_current_annotation(
+            changed_annotation,
+            error_message="History annotation was changed, but annotation text is wrong!",
+            is_equal=True,
+        )
 
     @selenium_test
     def test_history_panel_tags_change(self):
-
         def create_tags(size):
             history_panel_tags = list()
             for i in range(size):
diff --git a/lib/galaxy_test/selenium/test_history_panel_collections.py b/lib/galaxy_test/selenium/test_history_panel_collections.py
index 8377496ba14..e7efa96b4ee 100644
--- a/lib/galaxy_test/selenium/test_history_panel_collections.py
+++ b/lib/galaxy_test/selenium/test_history_panel_collections.py
@@ -4,14 +4,14 @@ import pytest
 
 from galaxy.selenium.navigates_galaxy import (
     edit_details,
-    WAIT_TYPES
+    WAIT_TYPES,
 )
 from galaxy_test.base.api_asserts import assert_status_code_is
 from galaxy_test.base.populators import flakey
 from .framework import (
     retry_assertion_during_transitions,
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -26,7 +26,7 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
         input_hid = input_collection["hid"]
         failed_hid = failed_collection["hid"]
         ok_inputs = {
-            "input1": {'batch': True, 'values': [{"src": "hdca", "id": input_collection["id"]}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": input_collection["id"]}]},
             "sleep_time": 0,
         }
         ok_response = self.dataset_populator.run_tool(
@@ -51,9 +51,11 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
     @flakey  # Some times a Paste web thread will stall when jobs are running.
     def test_mapping_collection_states_running(self):
         history_id = self.current_history_id()
-        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1"]).json()
+        input_collection = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1"]
+        ).json()
         running_inputs = {
-            "input1": {'batch': True, 'values': [{"src": "hdca", "id": input_collection["id"]}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": input_collection["id"]}]},
             "sleep_time": 60,
         }
         running_response = self.dataset_populator.run_tool_raw(
@@ -79,16 +81,12 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
     @selenium_test
     def test_output_collection_states_terminal(self):
         history_id = self.current_history_id()
-        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_collection = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json()
 
-        ok_inputs = {
-            "input1": {"src": "hdca", "id": input_collection["id"]}
-        }
-        ok_response = self.dataset_populator.run_tool(
-            "collection_creates_list",
-            ok_inputs,
-            history_id
-        )
+        ok_inputs = {"input1": {"src": "hdca", "id": input_collection["id"]}}
+        ok_response = self.dataset_populator.run_tool("collection_creates_list", ok_inputs, history_id)
         ok_hid = ok_response["output_collections"][0]["hid"]
         assert ok_hid > 0
 
@@ -282,7 +280,9 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
         if self.is_beta_history():
             raise pytest.skip("Beta history can scroll through collections of any length")
         history_id = self.current_history_id()
-        collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        collection = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json()
         collection_hid = collection["hid"]
 
         with self.local_storage("collectionFuzzyCountDefault", 2):
@@ -296,7 +296,9 @@ class HistoryPanelCollectionsTestCase(SeleniumTestCase):
 
     def _generate_partially_failed_collection_with_input(self):
         history_id = self.current_history_id()
-        input_collection = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()
+        input_collection = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["0", "1", "0", "1"]
+        ).json()
         failed_response = self.dataset_populator.run_exit_code_from_file(history_id, input_collection["id"])
         failed_collection = failed_response["implicit_collections"][0]
         return input_collection, failed_collection
diff --git a/lib/galaxy_test/selenium/test_history_panel_pagination.py b/lib/galaxy_test/selenium/test_history_panel_pagination.py
index e5802e708db..3ee25b025a7 100644
--- a/lib/galaxy_test/selenium/test_history_panel_pagination.py
+++ b/lib/galaxy_test/selenium/test_history_panel_pagination.py
@@ -3,7 +3,7 @@ import pytest
 from galaxy_test.base.populators import flakey
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -19,11 +19,11 @@ class HistoryPanelPaginationTestCase(SeleniumTestCase):
 
         history_id = self.current_history_id()
 
-        self.dataset_populator.new_dataset(history_id, content='1\t2\t3', name="data1")
-        self.dataset_populator.new_dataset(history_id, content='2\t3\t4', name="data2")
-        self.dataset_populator.new_dataset(history_id, content='3\t4\t5', name="data3")
-        self.dataset_populator.new_dataset(history_id, content='4\t5\t6', name="data4")
-        self.dataset_populator.new_dataset(history_id, content='5\t6\t7', name="data5")
+        self.dataset_populator.new_dataset(history_id, content="1\t2\t3", name="data1")
+        self.dataset_populator.new_dataset(history_id, content="2\t3\t4", name="data2")
+        self.dataset_populator.new_dataset(history_id, content="3\t4\t5", name="data3")
+        self.dataset_populator.new_dataset(history_id, content="4\t5\t6", name="data4")
+        self.dataset_populator.new_dataset(history_id, content="5\t6\t7", name="data5")
 
         self.home()
         for hid in [1, 2, 3, 4, 5]:
diff --git a/lib/galaxy_test/selenium/test_history_sharing.py b/lib/galaxy_test/selenium/test_history_sharing.py
index ad707a8ac50..4cfe2427861 100644
--- a/lib/galaxy_test/selenium/test_history_sharing.py
+++ b/lib/galaxy_test/selenium/test_history_sharing.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 # Remove hack when submit_login works more consistently.
@@ -8,7 +8,6 @@ VALID_LOGIN_RETRIES = 3
 
 
 class HistorySharingTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_sharing_valid(self):
         user1_email, user2_email, history_id = self.setup_two_users_with_one_shared_history()
@@ -61,14 +60,14 @@ class HistorySharingTestCase(SeleniumTestCase):
         user1_email = self._get_random_email()
         self.register(user1_email)
         self.share_history_with_user(user_email="invalid_user@test.com")
-        self.assert_error_message(contains='is not a valid Galaxy user')
+        self.assert_error_message(contains="is not a valid Galaxy user")
 
     @selenium_test
     def test_sharing_with_self(self):
         user1_email = self._get_random_email()
         self.register(user1_email)
         self.share_history_with_user(user_email=user1_email)
-        self.assert_error_message(contains='You cannot share resources with yourself')
+        self.assert_error_message(contains="You cannot share resources with yourself")
 
     def setup_two_users_with_one_shared_history(self, share_by_id=False):
         user1_email = self._get_random_email()
diff --git a/lib/galaxy_test/selenium/test_history_structure.py b/lib/galaxy_test/selenium/test_history_structure.py
index 58b2714e6bc..ac513420935 100644
--- a/lib/galaxy_test/selenium/test_history_structure.py
+++ b/lib/galaxy_test/selenium/test_history_structure.py
@@ -1,7 +1,7 @@
 from .framework import (
     managed_history,
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
diff --git a/lib/galaxy_test/selenium/test_library_contents.py b/lib/galaxy_test/selenium/test_library_contents.py
index 44668788d00..f50ca850979 100644
--- a/lib/galaxy_test/selenium/test_library_contents.py
+++ b/lib/galaxy_test/selenium/test_library_contents.py
@@ -6,7 +6,7 @@ from .framework import (
     retry_during_transitions,
     selenium_test,
     SeleniumTestCase,
-    UsesLibraryAssertions
+    UsesLibraryAssertions,
 )
 
 
diff --git a/lib/galaxy_test/selenium/test_library_to_collections.py b/lib/galaxy_test/selenium/test_library_to_collections.py
index 4d0136c9ce5..8f8cf87aeb7 100644
--- a/lib/galaxy_test/selenium/test_library_to_collections.py
+++ b/lib/galaxy_test/selenium/test_library_to_collections.py
@@ -1,7 +1,7 @@
 from .framework import (
     selenium_test,
     SeleniumTestCase,
-    UsesLibraryAssertions
+    UsesLibraryAssertions,
 )
 
 
@@ -61,8 +61,9 @@ class LibraryToCollectionsTestCase(SeleniumTestCase, UsesLibraryAssertions):
 
         if collection_option is not None:
             self.components.libraries.folder.export_to_history_paired_option(
-                collection_option=collection_option).wait_for_and_click()
-        self.screenshot(f'libraries_to_collection_landing_is_new_history={is_new_history}')
+                collection_option=collection_option
+            ).wait_for_and_click()
+        self.screenshot(f"libraries_to_collection_landing_is_new_history={is_new_history}")
         self.components.libraries.folder.import_datasets_ok_button.wait_for_and_click()
         self.build_collection_and_assert()
         if is_new_history:
@@ -70,16 +71,21 @@ class LibraryToCollectionsTestCase(SeleniumTestCase, UsesLibraryAssertions):
 
     def list_of_pairs_export(self, is_new_history=False):
         history_name = self._get_random_name()
-        self.prepare_library_for_data_export(["bam_from_sam.bam", "asian_chars_1.txt", "1.bam", "1.bed"],
-                                             history_name if is_new_history else None)
+        self.prepare_library_for_data_export(
+            ["bam_from_sam.bam", "asian_chars_1.txt", "1.bam", "1.bed"], history_name if is_new_history else None
+        )
         self.components.libraries.folder.export_to_history_options.wait_for_and_click()
-        self.components.libraries.folder.export_to_history_paired_option(collection_option="list:paired").wait_for_and_click()
-        self.screenshot(f'test_export_pairs_list={is_new_history}')
+        self.components.libraries.folder.export_to_history_paired_option(
+            collection_option="list:paired"
+        ).wait_for_and_click()
+        self.screenshot(f"test_export_pairs_list={is_new_history}")
         self.components.libraries.folder.import_datasets_ok_button.wait_for_and_click()
         self.components.libraries.folder.clear_filters.wait_for_and_click()
         self.collection_builder_click_paired_item("forward", 0)
         self.collection_builder_click_paired_item("reverse", 1)
-        self.components.libraries.folder.export_to_history_collection_name.wait_for_and_send_keys(self._get_random_name())
+        self.components.libraries.folder.export_to_history_collection_name.wait_for_and_send_keys(
+            self._get_random_name()
+        )
         self.collection_builder_create()
         self.home()
         self.history_panel_wait_for_hid_ok(3)
diff --git a/lib/galaxy_test/selenium/test_login.py b/lib/galaxy_test/selenium/test_login.py
index 4a954450c7f..85418d85ff7 100644
--- a/lib/galaxy_test/selenium/test_login.py
+++ b/lib/galaxy_test/selenium/test_login.py
@@ -1,11 +1,10 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
 class LoginTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_logging_in(self):
         email = self._get_random_email()
@@ -18,7 +17,7 @@ class LoginTestCase(SeleniumTestCase):
 
     @selenium_test
     def test_invalid_logins(self):
-        bad_emails = ['test2@test.org', 'test', '', "'; SELECT * FROM galaxy_user WHERE 'u' = 'u';"]
+        bad_emails = ["test2@test.org", "test", "", "'; SELECT * FROM galaxy_user WHERE 'u' = 'u';"]
         for bad_email in bad_emails:
             self.home()
             self.submit_login(bad_email, assert_valid=False)
@@ -26,7 +25,7 @@ class LoginTestCase(SeleniumTestCase):
 
     @selenium_test
     def test_invalid_passwords(self):
-        bad_passwords = ['1234', '', '; SELECT * FROM galaxy_user']
+        bad_passwords = ["1234", "", "; SELECT * FROM galaxy_user"]
         for bad_password in bad_passwords:
             self.home()
             self.submit_login(self._get_random_email(), password=bad_password, assert_valid=False)
diff --git a/lib/galaxy_test/selenium/test_personal_information.py b/lib/galaxy_test/selenium/test_personal_information.py
index 89ed12c7f92..42a1abf0983 100644
--- a/lib/galaxy_test/selenium/test_personal_information.py
+++ b/lib/galaxy_test/selenium/test_personal_information.py
@@ -5,30 +5,29 @@ from .framework import (
 
 
 class ManageInformationTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_api_key(self):
-        '''
+        """
         This test views and resets the API key. In automated testing scenarios,
         this means the initial API key will be None, which renders as
         'Not available.'
-        '''
+        """
         self.login()
-        self.assertEqual(self.get_api_key(), 'Not available.')
+        self.assertEqual(self.get_api_key(), "Not available.")
         api_key = self.get_api_key()
         self.navigate_to_user_preferences()
         self.components.preferences.manage_api_key.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        new_key_button = self.driver.find_element_by_id('submit')
+        new_key_button = self.driver.find_element_by_id("submit")
         api_key_input = self.driver.find_element_by_css_selector("[data-label='Current API key:'] > input")
         # Assert that what's rendered on screen is what the API is returning
-        self.assertEqual(api_key_input.get_property('value'), api_key)
+        self.assertEqual(api_key_input.get_property("value"), api_key)
         self.action_chains().move_to_element(new_key_button).click().perform()
         self.sleep_for(self.wait_types.UX_TRANSITION)
         new_api_key = self.get_api_key()
         api_key_input = self.driver.find_element_by_css_selector("[data-label='Current API key:'] > input")
         # And assert that this has now changed, and still renders correctly
-        self.assertEqual(new_api_key, api_key_input.get_property('value'))
+        self.assertEqual(new_api_key, api_key_input.get_property("value"))
 
     @selenium_test
     def test_change_email(self):
@@ -66,7 +65,7 @@ class ManageInformationTestCase(SeleniumTestCase):
             return self.driver.find_element_by_css_selector("input[id='username']")
 
         def assert_public_name(expected_name):
-            self.assertTrue(expected_name == get_name_input_field().get_attribute('value'))
+            self.assertTrue(expected_name == get_name_input_field().get_attribute("value"))
 
         public_name = "user-public-name"
         self.register(username=public_name)
@@ -96,8 +95,17 @@ class ManageInformationTestCase(SeleniumTestCase):
         self.navigate_to_manage_information()
         self.components.change_user_address.address_button.wait_for_and_click()
 
-        address_field_labels = ["Short address description", "Name", "Institution", "Address", "City",
-                                "State/Province/Region", "Postal Code", "Country", "Phone"]
+        address_field_labels = [
+            "Short address description",
+            "Name",
+            "Institution",
+            "Address",
+            "City",
+            "State/Province/Region",
+            "Postal Code",
+            "Country",
+            "Phone",
+        ]
 
         address_fields = {}
         # fill address fields with random data
@@ -116,7 +124,7 @@ class ManageInformationTestCase(SeleniumTestCase):
         # check if address was saved correctly
         for input_field_label in address_fields.keys():
             input_field = self.get_address_input_field(get_address_form(), input_field_label)
-            self.assertTrue(input_field.get_attribute('value') == address_fields[input_field_label])
+            self.assertTrue(input_field.get_attribute("value") == address_fields[input_field_label])
 
     def navigate_to_manage_information(self):
         self.navigate_to_user_preferences()
@@ -131,7 +139,6 @@ class ManageInformationTestCase(SeleniumTestCase):
 
 
 class DeleteCurrentAccountTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_delete_account(self):
         email = self._get_random_email()
@@ -143,5 +150,7 @@ class DeleteCurrentAccountTestCase(SeleniumTestCase):
         delete_confirmation_field.send_keys(email)
         self.components.preferences.delete_account_ok_btn.wait_for_and_click()
         self.submit_login(email=email, assert_valid=False)
-        self.assert_error_message(contains='This account has been marked deleted, contact your local Galaxy'
-                                           ' administrator to restore the account.')
+        self.assert_error_message(
+            contains="This account has been marked deleted, contact your local Galaxy"
+            " administrator to restore the account."
+        )
diff --git a/lib/galaxy_test/selenium/test_published_histories_grid.py b/lib/galaxy_test/selenium/test_published_histories_grid.py
index fd1f91fb0ee..4496ad0024f 100644
--- a/lib/galaxy_test/selenium/test_published_histories_grid.py
+++ b/lib/galaxy_test/selenium/test_published_histories_grid.py
@@ -6,7 +6,6 @@ from .framework import (
 
 
 class HistoryGridTestCase(SharedStateSeleniumTestCase):
-
     @selenium_test
     def test_history_grid_histories(self):
         self.navigate_to_published_histories_page()
@@ -19,7 +18,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
         self.published_grid_search_for(self.history1_name)
         self.assert_grid_histories_are([self.history1_name])
 
-        self.unset_filter('free-text-search', self.history1_name)
+        self.unset_filter("free-text-search", self.history1_name)
         self.published_grid_search_for(self.history4_name)
 
         self.assert_grid_histories_are([])
@@ -28,38 +27,38 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
     def test_history_grid_search_advanced(self):
         self.navigate_to_published_histories_page()
 
-        self.wait_for_and_click_selector('#standard-search .advanced-search-toggle')
+        self.wait_for_and_click_selector("#standard-search .advanced-search-toggle")
 
-        name_filter_selector = '#input-name-filter'
-        annot_filter_selector = '#input-annotation-filter'
-        owner_filter_selector = '#input-username-filter'
-        tags_filter_selector = '#input-tags-filter'
+        name_filter_selector = "#input-name-filter"
+        annot_filter_selector = "#input-annotation-filter"
+        owner_filter_selector = "#input-username-filter"
+        tags_filter_selector = "#input-tags-filter"
 
         # Search by name
         self.set_filter(name_filter_selector, self.history1_name)
         self.screenshot("histories_published_grid_advanced")
         self.assert_grid_histories_are([self.history1_name])
-        self.unset_filter('name', self.history1_name)
+        self.unset_filter("name", self.history1_name)
 
         self.set_filter(name_filter_selector, self.history4_name)
         self.assert_grid_histories_are([])
-        self.unset_filter('name', self.history4_name)
+        self.unset_filter("name", self.history4_name)
 
         # Search by annotation
         self.set_filter(annot_filter_selector, self.history3_annot)
         self.assert_grid_histories_are([self.history3_name])
-        self.unset_filter('annotation', self.history3_annot)
+        self.unset_filter("annotation", self.history3_annot)
 
         # Search by owner
-        owner = self.user2_email.split('@')[0]
+        owner = self.user2_email.split("@")[0]
         self.set_filter(owner_filter_selector, owner)
         self.assert_grid_histories_are([self.history2_name])
-        self.unset_filter('username', owner)
+        self.unset_filter("username", owner)
 
         # Search by tags
         self.set_filter(tags_filter_selector, self.history1_tags[0])
         self.assert_grid_histories_are([self.history1_name, self.history3_name], False)
-        self.unset_filter('tags', self.history1_tags[0])
+        self.unset_filter("tags", self.history1_tags[0])
 
     # Trying to address an intermittent failure by injecting a small rendering
     # sleep. to be honest, I'm not sure that the timing is the issue, because
@@ -69,14 +68,14 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
     def test_history_grid_sort_by_name(self):
         self.navigate_to_published_histories_page()
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.wait_for_and_click_selector('th#name-header > a')
+        self.wait_for_and_click_selector("th#name-header > a")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_grid_histories_are(sorted(self.all_histories))
 
     @selenium_test
     def test_history_grid_sort_by_owner(self):
         self.navigate_to_published_histories_page()
-        self.wait_for_and_click_selector('th#username-header > a')
+        self.wait_for_and_click_selector("th#username-header > a")
         self.assert_grid_histories_sorted_by_owner()
 
     @selenium_test
@@ -84,18 +83,18 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
         self.navigate_to_published_histories_page()
 
         tags = None
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            td = row.find_elements_by_tag_name('td')
+        grid = self.wait_for_selector("#grid-table-body")
+        for row in grid.find_elements_by_tag_name("tr"):
+            td = row.find_elements_by_tag_name("td")
             name = td[0].text
             if name == self.history1_name:
                 tags = td[4]
                 break
 
         if tags is None:
-            raise AssertionError(f'Failed to find history with name [{self.history1_name}]')
+            raise AssertionError(f"Failed to find history with name [{self.history1_name}]")
 
-        tag_button_selector = 'div.tag-name'
+        tag_button_selector = "div.tag-name"
         tag_buttons = tags.find_elements_by_css_selector(tag_button_selector)
         tag_button_text = None
         target_tag_button_text = self.history1_tags[0]
@@ -112,9 +111,9 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
     def get_histories(self, sleep=False):
         self.sleep_for(self.wait_types.UX_RENDER)
         names = []
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            cell = row.find_elements_by_tag_name('td')[0]  # Name
+        grid = self.wait_for_selector("#grid-table-body")
+        for row in grid.find_elements_by_tag_name("tr"):
+            cell = row.find_elements_by_tag_name("td")[0]  # Name
             names.append(cell.text)
         return names
 
@@ -132,7 +131,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
         actual_histories = self.get_histories()
 
         # Filter out histories created by other tests
-        all_histories = self.all_histories + ['No items']
+        all_histories = self.all_histories + ["No items"]
         actual_histories = [x for x in actual_histories if x in all_histories]
 
         if not sort_matters:
@@ -155,8 +154,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
         self.send_enter(filter_input)
 
     def unset_filter(self, filter_key, filter_value):
-        close_link_selector = 'a[filter_key="%s"][filter_val="%s"]' % \
-            (filter_key, filter_value)
+        close_link_selector = 'a[filter_key="%s"][filter_val="%s"]' % (filter_key, filter_value)
         self.wait_for_and_click_selector(close_link_selector)
         self.sleep_for(self.wait_types.UX_RENDER)
 
@@ -165,8 +163,8 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
         tag2 = self._get_random_name(len=5)
         tag3 = self._get_random_name(len=5)
 
-        HistoryGridTestCase.user1_email = self._get_random_email('test1')
-        HistoryGridTestCase.user2_email = self._get_random_email('test2')
+        HistoryGridTestCase.user1_email = self._get_random_email("test1")
+        HistoryGridTestCase.user2_email = self._get_random_email("test2")
         HistoryGridTestCase.history1_name = self._get_random_name()
         HistoryGridTestCase.history2_name = self._get_random_name()
         HistoryGridTestCase.history3_name = self._get_random_name()
@@ -198,7 +196,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase):
         self.history_panel_create_new_with_name(name)
 
     def publish_current_history(self):
-        self.click_history_option('Share or Publish')
+        self.click_history_option("Share or Publish")
         self.make_accessible_and_publishable()
 
     def navigate_to_published_histories_page(self):
diff --git a/lib/galaxy_test/selenium/test_registration.py b/lib/galaxy_test/selenium/test_registration.py
index a73f83cfb6a..34aeffc53a6 100644
--- a/lib/galaxy_test/selenium/test_registration.py
+++ b/lib/galaxy_test/selenium/test_registration.py
@@ -1,11 +1,10 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
 class RegistrationTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_landing(self):
         # loading galaxy homepage
@@ -51,34 +50,34 @@ class RegistrationTestCase(SeleniumTestCase):
         self.register(email1, password, username, confirm)
         self.logout_if_needed()
         self.register(email2, password, username, confirm, assert_valid=False)
-        self.assert_error_message(contains='Public name is taken')
+        self.assert_error_message(contains="Public name is taken")
 
     @selenium_test
     def test_bad_emails(self):
-        bad_emails = ['bob', 'bob@', 'bob@idontwanttocleanup', 'bob.cantmakeme']
+        bad_emails = ["bob", "bob@", "bob@idontwanttocleanup", "bob.cantmakeme"]
         good_email = self._get_random_email()
         password = self.default_password
         confirm = password
         username = good_email.split("@")[0]
         for bad_email in bad_emails:
             self.register(bad_email, password, username, confirm, assert_valid=False)
-            self.assert_error_message(contains='The format of the email address is not correct.')
+            self.assert_error_message(contains="The format of the email address is not correct.")
 
     @selenium_test
     def test_short_password(self):
         self.register(password="1234", assert_valid=False)
-        self.assert_error_message(contains='Use a password of at least 6 characters')
+        self.assert_error_message(contains="Use a password of at least 6 characters")
 
     @selenium_test
     def test_password_confirmation(self):
-        bad_confirms = ['1234', '12345678', '123456 7']
+        bad_confirms = ["1234", "12345678", "123456 7"]
         for bad_confirm in bad_confirms:
             self.register(confirm=bad_confirm, assert_valid=False)
-            self.assert_error_message(contains='Passwords do not match')
+            self.assert_error_message(contains="Passwords do not match")
 
     @selenium_test
     def test_bad_usernames(self):
-        bad_usernames = ['BOBERT', 'Robert Paulson', 'bobert!']
+        bad_usernames = ["BOBERT", "Robert Paulson", "bobert!"]
         for bad_username in bad_usernames:
             self.register(username=bad_username, assert_valid=False)
-            self.assert_error_message(contains='Public name must contain only ')
+            self.assert_error_message(contains="Public name must contain only ")
diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py
index 8bbd5890aa1..d6cc6b02c30 100644
--- a/lib/galaxy_test/selenium/test_sign_out.py
+++ b/lib/galaxy_test/selenium/test_sign_out.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
diff --git a/lib/galaxy_test/selenium/test_sizzle_loading.py b/lib/galaxy_test/selenium/test_sizzle_loading.py
index 94fdd6bb588..cebf6b3f7c7 100644
--- a/lib/galaxy_test/selenium/test_sizzle_loading.py
+++ b/lib/galaxy_test/selenium/test_sizzle_loading.py
@@ -1,11 +1,10 @@
 from .framework import (
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
 class SizzleLoadingTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_sizzle_loads(self):
         self.home()
diff --git a/lib/galaxy_test/selenium/test_stock_tours.py b/lib/galaxy_test/selenium/test_stock_tours.py
index 047eec80c70..e3bd9032e96 100644
--- a/lib/galaxy_test/selenium/test_stock_tours.py
+++ b/lib/galaxy_test/selenium/test_stock_tours.py
@@ -11,7 +11,6 @@ STOCK_TOURS_DIRECTORY = os.path.join(galaxy_root_path, "config", "plugins", "tou
 
 
 class TestStockToursTestCase(SeleniumTestCase):
-
     @selenium_test
     def test_core_galaxy_ui(self):
         sleep_on_steps = {
@@ -19,10 +18,7 @@ class TestStockToursTestCase(SeleniumTestCase):
             "Select a tool": 2 * TIMEOUT_MULTIPLIER,
             "History": 20 * TIMEOUT_MULTIPLIER,
         }
-        self.run_tour(
-            os.path.join(STOCK_TOURS_DIRECTORY, "core.galaxy_ui.yaml"),
-            sleep_on_steps=sleep_on_steps
-        )
+        self.run_tour(os.path.join(STOCK_TOURS_DIRECTORY, "core.galaxy_ui.yaml"), sleep_on_steps=sleep_on_steps)
 
     @selenium_test
     def test_core_scratchbook(self):
diff --git a/lib/galaxy_test/selenium/test_tool_describing_tours.py b/lib/galaxy_test/selenium/test_tool_describing_tours.py
index 1a2fd4e0b8c..0247d69dcd8 100644
--- a/lib/galaxy_test/selenium/test_tool_describing_tours.py
+++ b/lib/galaxy_test/selenium/test_tool_describing_tours.py
@@ -1,10 +1,12 @@
 import unittest
 
-from .framework import selenium_test, SeleniumTestCase
+from .framework import (
+    selenium_test,
+    SeleniumTestCase,
+)
 
 
 class ToolDescribingToursTestCase(SeleniumTestCase):
-
     def setUp(self):
         super().setUp()
         self.home()
@@ -14,7 +16,7 @@ class ToolDescribingToursTestCase(SeleniumTestCase):
         """Ensure a tour without data is generated and pops up."""
         self._ensure_tdt_available()
 
-        self.tool_open('environment_variables')
+        self.tool_open("environment_variables")
 
         self.tool_form_generate_tour()
 
@@ -33,7 +35,7 @@ class ToolDescribingToursTestCase(SeleniumTestCase):
         """Ensure a tour with data populates history."""
         self._ensure_tdt_available()
 
-        self.tool_open('md5sum')
+        self.tool_open("md5sum")
 
         self.tool_form_generate_tour()
 
@@ -71,10 +73,10 @@ class ToolDescribingToursTestCase(SeleniumTestCase):
         self.screenshot("tool_describing_tour_3_after_execute")
 
     def _ensure_tdt_available(self):
-        """ Skip a test if the webhook TDT doesn't appear. """
-        response = self.api_get('webhooks', raw=True)
+        """Skip a test if the webhook TDT doesn't appear."""
+        response = self.api_get("webhooks", raw=True)
         self.assertEqual(response.status_code, 200)
         data = response.json()
-        webhooks = [x['id'] for x in data]
-        if 'tour_generator' not in webhooks:
+        webhooks = [x["id"] for x in data]
+        if "tour_generator" not in webhooks:
             raise unittest.SkipTest('Skipping test, webhook "Tool-Describing-Tours" doesn\'t appear to be configured.')
diff --git a/lib/galaxy_test/selenium/test_tool_form.py b/lib/galaxy_test/selenium/test_tool_form.py
index f2f5ab57b52..13176b6f1d6 100644
--- a/lib/galaxy_test/selenium/test_tool_form.py
+++ b/lib/galaxy_test/selenium/test_tool_form.py
@@ -19,7 +19,6 @@ from .framework import (
 
 
 class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
-
     @selenium_test
     def test_run_tool_verify_contents_by_peek(self):
         self._run_environment_test_tool()
@@ -60,19 +59,19 @@ class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         assert format_found
 
         job_outputs = self._table_to_key_value_elements("table#job-outputs")
-        assert job_outputs[0][0].text == 'environment_variables'
+        assert job_outputs[0][0].text == "environment_variables"
         assert "View data\nEdit attributes\nDelete" in job_outputs[0][1].text
         job_outputs[0][1].click()
-        assert job_outputs[0][1].find_element_by_css_selector('pre').text == '42\nmoo\nNOTTHREE'
+        assert job_outputs[0][1].find_element_by_css_selector("pre").text == "42\nmoo\nNOTTHREE"
         dataset_operations = self.wait_for_selector_visible("table#job-outputs div.dropdown")
         dataset_operations.click()
         menu = self.wait_for_selector_visible("table#job-outputs div.dropdown ul")
-        self.click_menu_item(menu, 'Run job again')
+        self.click_menu_item(menu, "Run job again")
         self.components.tool_form.execute.wait_for_visible()
 
     @staticmethod
     def click_menu_item(menu, text):
-        for element in menu.find_elements_by_css_selector('a'):
+        for element in menu.find_elements_by_css_selector("a"):
             if element.text == text:
                 return element.click()
 
@@ -204,14 +203,16 @@ class LoggedInToolFormTestCase(SeleniumTestCase):
         self.home()
         self.upload_rule_start()
         self.upload_rule_set_data_type("Collection")
-        self.components.upload.rule_source_content.wait_for_and_send_keys("""https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated1fb.txt treated_single_1
+        self.components.upload.rule_source_content.wait_for_and_send_keys(
+            """https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated1fb.txt treated_single_1
 https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated2fb.txt treated_paired_2
 https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/treated3fb.txt treated_paired_3
 https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated1fb.txt untreated_single_4
 https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated2fb.txt untreated_single_5
 https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated3fb.txt untreated_paired_6
 https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-data/rules/untreated4fb.txt untreated_paired_7
-""")
+"""
+        )
         self.screenshot("rules_apply_rules_example_4_1_input_paste")
         self.upload_rule_build()
         rule_builder = self.components.rule_builder
@@ -234,12 +235,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
                     "type": "add_column_metadata",
                     "value": "identifier0",
                 },
-                {
-                    "type": "add_column_regex",
-                    "target_column": 0,
-                    "expression": "(.*)_(.*)_.*",
-                    "group_count": 2
-                }
+                {"type": "add_column_regex", "target_column": 0, "expression": "(.*)_(.*)_.*", "group_count": 2},
             ],
             "mapping": [
                 {
@@ -253,7 +249,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
             hid=1,
             landing_screenshot="rules_apply_rules_example_4_5_apply_rules_landing",
             rule_init_screenshot="rules_apply_rules_example_4_6_apply_rules_init_flat",
-            rule_complete_screenshot="rules_apply_rules_example_4_7_apply_rules_add_depth"
+            rule_complete_screenshot="rules_apply_rules_example_4_7_apply_rules_add_depth",
         )
         self.history_panel_wait_for_hid_ok(16)
         self.history_multi_view_display_collection_contents(16, "list:list:list")
@@ -284,7 +280,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
         self._tool_apply_with_source(
             invert_rules,
             rule_init_screenshot="rules_apply_rules_example_4_9_apply_rules_init_nested",
-            rule_complete_screenshot="rules_apply_rules_example_4_10_apply_rules_inverted"
+            rule_complete_screenshot="rules_apply_rules_example_4_10_apply_rules_inverted",
         )
         self.history_panel_wait_for_hid_ok(24)
         self.history_multi_view_display_collection_contents(24, "list:list:list")
@@ -301,7 +297,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
                     "target_column": 0,
                     "expression": ".*_single_.*",
                     "invert": False,
-                }
+                },
             ],
             "mapping": [
                 {
@@ -311,9 +307,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
             ],
         }
         self._tool_apply_with_source(
-            filter_rules,
-            hid=1,
-            rule_complete_screenshot="rules_apply_rules_example_4_12_apply_rules_filter"
+            filter_rules, hid=1, rule_complete_screenshot="rules_apply_rules_example_4_12_apply_rules_filter"
         )
         self.history_panel_wait_for_hid_ok(28)
         self.history_multi_view_display_collection_contents(28, "list")
@@ -331,12 +325,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
                     "expression": ".*_single_.*",
                     "invert": False,
                 },
-                {
-                    "type": "add_column_regex",
-                    "target_column": 0,
-                    "expression": "(.*)_single_.*",
-                    "group_count": 1
-                }
+                {"type": "add_column_regex", "target_column": 0, "expression": "(.*)_single_.*", "group_count": 1},
             ],
             "mapping": [
                 {
@@ -348,7 +337,7 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
         self._tool_apply_with_source(
             filter_and_nest_rules,
             hid=1,
-            rule_complete_screenshot="rules_apply_rules_example_4_14_apply_rules_filtered_and_nested"
+            rule_complete_screenshot="rules_apply_rules_example_4_14_apply_rules_filtered_and_nested",
         )
         self.history_panel_wait_for_hid_ok(32)
         self.history_multi_view_display_collection_contents(32, "list:list")
@@ -377,7 +366,9 @@ https://raw.githubusercontent.com/jmchilton/galaxy/apply_rules_tutorials/test-da
         output_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_hid, wait=False)
         example["check"](output_hdca, self.dataset_populator)
 
-    def _tool_apply_with_source(self, rules_json, hid=None, landing_screenshot=None, rule_init_screenshot=None, rule_complete_screenshot=None):
+    def _tool_apply_with_source(
+        self, rules_json, hid=None, landing_screenshot=None, rule_init_screenshot=None, rule_complete_screenshot=None
+    ):
         self._tool_open_apply_rules()
         if hid:
             self.tool_set_value("input", f"{hid}:", expected_type="data_collection")
diff --git a/lib/galaxy_test/selenium/test_uploads.py b/lib/galaxy_test/selenium/test_uploads.py
index 2c89166063c..b94de653115 100644
--- a/lib/galaxy_test/selenium/test_uploads.py
+++ b/lib/galaxy_test/selenium/test_uploads.py
@@ -11,7 +11,6 @@ from .framework import (
 
 
 class UploadsTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
-
     @selenium_test
     def test_upload_simplest(self):
         self.perform_upload(self.get_filename("1.sam"))
@@ -22,7 +21,7 @@ class UploadsTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
 
         hda = history_contents[0]
-        assert hda["name"] == '1.sam', hda
+        assert hda["name"] == "1.sam", hda
         assert hda["extension"] == "sam", hda
 
         self.history_panel_click_item_title(hid=1, wait=True)
@@ -34,7 +33,7 @@ class UploadsTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         self.history_panel_wait_for_hid_ok(1)
         history_contents = self.history_contents()
         hda = history_contents[0]
-        assert hda["name"] == '1.sam'
+        assert hda["name"] == "1.sam"
         assert hda["extension"] == "txt", hda
 
     @selenium_test
@@ -51,7 +50,7 @@ class UploadsTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         self.history_panel_wait_for_hid_ok(1)
         history_contents = self.history_contents()
         hda = history_contents[0]
-        assert hda["name"] == '1.sam'
+        assert hda["name"] == "1.sam"
         assert hda["extension"] == "txt", hda
 
     @selenium_test
@@ -89,18 +88,25 @@ class UploadsTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
 
     @selenium_test
     def test_upload_pair_specify_extension(self):
-        self.upload_list([self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Pair", ext="txt", hide_source_items=False)
+        self.upload_list(
+            [self.get_filename("1.tabular"), self.get_filename("2.tabular")],
+            name="Test Pair",
+            ext="txt",
+            hide_source_items=False,
+        )
         self.history_panel_wait_for_hid_ok(5)
         self.history_panel_wait_for_hid_ok(1)
 
         history_contents = self.history_contents()
         hda = history_contents[0]
-        assert hda["name"] == '1.tabular'
+        assert hda["name"] == "1.tabular"
         assert hda["extension"] == "txt", hda
 
     @selenium_test
     def test_upload_paired_list(self):
-        self.upload_paired_list([self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Paired List")
+        self.upload_paired_list(
+            [self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Paired List"
+        )
         self.history_panel_wait_for_hid_ok(3)
         # Make sure modals disappeared - both collection creator (TODO: upload).
         self.wait_for_selector_absent_or_hidden(".collection-creator")
@@ -120,13 +126,15 @@ class UploadsTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         self.upload_rule_start()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("rules_example_1_1_rules_landing")
-        self.components.upload.rule_source_content.wait_for_and_send_keys("""study_accession sample_accession    experiment_accession    fastq_ftp
+        self.components.upload.rule_source_content.wait_for_and_send_keys(
+            """study_accession sample_accession    experiment_accession    fastq_ftp
 PRJDA60709  SAMD00016379    DRX000475   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000770/DRR000770.fastq.gz
 PRJDA60709  SAMD00016383    DRX000476   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000771/DRR000771.fastq.gz
 PRJDA60709  SAMD00016380    DRX000477   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000772/DRR000772.fastq.gz
 PRJDA60709  SAMD00016378    DRX000478   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000773/DRR000773.fastq.gz
 PRJDA60709  SAMD00016381    DRX000479   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000774/DRR000774.fastq.gz
-PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000775/DRR000775.fastq.gz""")
+PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000775/DRR000775.fastq.gz"""
+        )
         self._wait_for_upload_modal()
         self.screenshot("rules_example_1_2_paste")
         self.upload_rule_build()
@@ -207,7 +215,9 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         self.rule_builder_remove_columns(["D"], screenshot_name="rules_example_3_7_removed_column")
         self.rule_builder_split_columns(["D"], ["E"], screenshot_name="rules_example_3_8_split_columns")
         self.screenshot("rules_example_3_9_columns_are_split")
-        self.rule_builder_add_regex_groups("D", 1, r".*_(\d).fastq.gz", screenshot_name="rules_example_3_10_regex_paired")
+        self.rule_builder_add_regex_groups(
+            "D", 1, r".*_(\d).fastq.gz", screenshot_name="rules_example_3_10_regex_paired"
+        )
         self.screenshot("rules_example_3_11_has_paired_id")
         self.rule_builder_swap_columns("D", "E", screenshot_name="rules_example_3_12_swap_columns")
         self.screenshot("rules_example_3_13_swapped_columns")
@@ -234,7 +244,9 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         self.screenshot("rules_example_4_3_basic_rules")
         self.rule_builder_sort("A", screenshot_name="rules_example_4_4_sort")
 
-        self.rule_builder_add_regex_replacement("A", ".*", "http://www.uniprot.org/uniprot/\\0.fasta", screenshot_name="rules_example_4_5_url")
+        self.rule_builder_add_regex_replacement(
+            "A", ".*", "http://www.uniprot.org/uniprot/\\0.fasta", screenshot_name="rules_example_4_5_url"
+        )
         self.screenshot("rules_example_4_6_url_built")
         self.rule_builder_set_mapping("list-identifiers", "A")
         self.rule_builder_set_mapping("url", "C")
@@ -271,12 +283,16 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         self.screenshot("rules_example_5_3_initial_rules")
         self.rule_builder_add_value("fasta", screenshot_name="rules_example_5_4_fasta")
         self.rule_builder_add_value("UP000052092 FASTA")
-        self.rule_builder_add_regex_replacement("A", ".*", "http://www.uniprot.org/uniprot/\\0.gff", screenshot_name="rules_example_5_5_url")
+        self.rule_builder_add_regex_replacement(
+            "A", ".*", "http://www.uniprot.org/uniprot/\\0.gff", screenshot_name="rules_example_5_5_url"
+        )
         self.rule_builder_add_value("gff3")
         self.rule_builder_add_value("UP000052092 GFF3")
         self._scroll_to_end_of_table()
         self.screenshot("rules_example_5_6_presplit")
-        self.rule_builder_split_columns(["C", "D", "E"], ["F", "G", "H"], screenshot_name="rules_example_5_7_split_columns")
+        self.rule_builder_split_columns(
+            ["C", "D", "E"], ["F", "G", "H"], screenshot_name="rules_example_5_7_split_columns"
+        )
         self.screenshot("rules_example_5_8_split")
         self.rule_builder_set_mapping("file-type", "D")
         self.rule_builder_set_mapping("collection-name", "E")
@@ -310,7 +326,9 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         self._scroll_to_end_of_table()
         self.screenshot("rules_example_6_3_end_of_table")
         self.rule_builder_add_regex_groups("L", 1, r"([^\d]+)\d+", screenshot_name="rules_example_6_4_regex")
-        self.rule_builder_set_mapping("list-identifiers", ["M", "A"], screenshot_name="rules_example_6_5_multiple_identifiers_edit")
+        self.rule_builder_set_mapping(
+            "list-identifiers", ["M", "A"], screenshot_name="rules_example_6_5_multiple_identifiers_edit"
+        )
         self._scroll_to_end_of_table()
         self.screenshot("rules_example_6_6_multiple_identifiers")
         self.rule_builder_set_collection_name("PRJNA355367")
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 45bc3c79fae..f786ef6c5f3 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -19,7 +19,7 @@ from .framework import (
     retry_assertion_during_transitions,
     retry_during_transitions,
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -69,7 +69,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
 
         editor.canvas_body.wait_for_visible()
 
-        new_annotation = 'look new annotation'
+        new_annotation = "look new annotation"
         edit_annotation.wait_for_and_send_keys(new_annotation)
         self.assert_workflow_has_changes_and_save()
         self.workflow_index_open_with_name(name)
@@ -97,29 +97,29 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         editor = self.components.workflow_editor
         node = editor.node._(label="select_from_dataset_optional")
         node.title.wait_for_and_click()
-        self.components.tool_form.parameter_checkbox(parameter='select_single').wait_for_and_click()
+        self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
         # External (selenium-side) debounce hack for old backbone input
         # TODO: remove when form elements are all converted.
-        self.components.tool_form.parameter_input(parameter='select_single').wait_for_and_send_keys('parameter valu')
+        self.components.tool_form.parameter_input(parameter="select_single").wait_for_and_send_keys("parameter valu")
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.components.tool_form.parameter_input(parameter='select_single').wait_for_and_send_keys('e')
+        self.components.tool_form.parameter_input(parameter="select_single").wait_for_and_send_keys("e")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
-        tool_state = json.loads(workflow['steps']['0']['tool_state'])
-        assert tool_state['select_single'] == 'parameter value'
+        tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
+        assert tool_state["select_single"] == "parameter value"
         # Disable optional button, resets value to null
-        self.components.tool_form.parameter_checkbox(parameter='select_single').wait_for_and_click()
+        self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
-        tool_state = json.loads(workflow['steps']['0']['tool_state'])
-        assert tool_state['select_single'] is None
+        tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
+        assert tool_state["select_single"] is None
         # Enable button but don't provide a value
-        self.components.tool_form.parameter_checkbox(parameter='select_single').wait_for_and_click()
+        self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
-        tool_state = json.loads(workflow['steps']['0']['tool_state'])
-        assert tool_state['select_single'] == ""
+        tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
+        assert tool_state["select_single"] == ""
 
     @selenium_test
     def test_data_input(self):
@@ -172,7 +172,8 @@ class WorkflowEditorTestCase(SeleniumTestCase):
 
     @selenium_test
     def test_data_column_input_editing(self):
-        self.open_in_workflow_editor("""
+        self.open_in_workflow_editor(
+            """
 class: GalaxyWorkflow
 steps:
   column_param_list:
@@ -180,24 +181,25 @@ steps:
     state:
       col: ["1","2","3"]
       col_names: ["a", "b", "c"]
-      """)
+      """
+        )
         editor = self.components.workflow_editor
         node = editor.node._(label="column_param_list")
         node.title.wait_for_and_click()
-        columns = self.components.tool_form.parameter_textarea(parameter='col')
+        columns = self.components.tool_form.parameter_textarea(parameter="col")
         textarea_columns = columns.wait_for_visible()
-        assert textarea_columns.get_attribute('value') == '1\n2\n3\n'
-        column_names = self.components.tool_form.parameter_textarea(parameter='col_names')
+        assert textarea_columns.get_attribute("value") == "1\n2\n3\n"
+        column_names = self.components.tool_form.parameter_textarea(parameter="col_names")
         textarea_column_names = column_names.wait_for_visible()
-        assert textarea_column_names.get_attribute('value') == 'a\nb\nc\n'
+        assert textarea_column_names.get_attribute("value") == "a\nb\nc\n"
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.set_text_element(columns, '4\n5\n6\n')
+        self.set_text_element(columns, "4\n5\n6\n")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         self.driver.refresh()
         node.title.wait_for_and_click()
         textarea_columns = columns.wait_for_visible()
-        assert textarea_columns.get_attribute('value') == '4\n5\n6\n'
+        assert textarea_columns.get_attribute("value") == "4\n5\n6\n"
 
     @selenium_test
     def test_integer_input(self):
@@ -226,7 +228,8 @@ steps:
 
     @selenium_test
     def test_non_data_connections(self):
-        self.open_in_workflow_editor("""
+        self.open_in_workflow_editor(
+            """
 class: GalaxyWorkflow
 inputs:
   input_int: integer
@@ -236,7 +239,8 @@ steps:
     label: tool_exec
     in:
       inttest: input_int
-""")
+"""
+        )
         self.screenshot("workflow_editor_parameter_connection_simple")
         self.assert_connected("input_int#output", "tool_exec#inttest")
 
@@ -269,7 +273,9 @@ steps:
         tool_input.wait_for_visible()
         collapse_input.wait_for_absent_or_hidden()
 
-        self.workflow_editor_connect("input_int#output", "tool_exec#inttest", screenshot_partial="workflow_editor_parameter_connection_dragging")
+        self.workflow_editor_connect(
+            "input_int#output", "tool_exec#inttest", screenshot_partial="workflow_editor_parameter_connection_dragging"
+        )
         self.assert_connected("input_int#output", "tool_exec#inttest")
 
     @selenium_test
@@ -277,7 +283,8 @@ steps:
         # Use auto_layout=false, which prevents placing any
         # step outside of the scroll area
         # xref: https://github.com/galaxyproject/galaxy/issues/13211
-        self.open_in_workflow_editor("""
+        self.open_in_workflow_editor(
+            """
 class: GalaxyWorkflow
 inputs:
   input_collection:
@@ -294,19 +301,23 @@ steps:
       text_param: param_value_from_file/text_param
   collection_input:
     tool_id: identifier_collection
-""", auto_layout=False)
+""",
+            auto_layout=False,
+        )
         self.workflow_editor_connect("text_input_step#out_file1", "collection_input#input1")
         self.assert_connected("text_input_step#out_file1", "collection_input#input1")
 
     def test_connecting_display_in_upload_false_connections(self):
-        self.open_in_workflow_editor("""
+        self.open_in_workflow_editor(
+            """
 class: GalaxyWorkflow
 steps:
   step1:
     tool_id: test_sam_to_bam_conversions
   step2:
     tool_id: test_sam_to_bam_conversions
-        """)
+        """
+        )
 
         self.workflow_editor_connect("step1#qname_input_sorted_bam_output", "step2#input5")
         self.assert_connected("step1#qname_input_sorted_bam_output", "step2#input5")
@@ -328,7 +339,9 @@ steps:
         self.assert_not_connected("input1#output", "first_cat#input1")
         self.screenshot("workflow_editor_connection_destroyed")
 
-        self.workflow_editor_connect("input1#output", "first_cat#input1", screenshot_partial="workflow_editor_connection_dragging")
+        self.workflow_editor_connect(
+            "input1#output", "first_cat#input1", screenshot_partial="workflow_editor_connection_dragging"
+        )
         self.assert_connected("input1#output", "first_cat#input1")
 
     @selenium_test
@@ -445,7 +458,8 @@ steps:
     @selenium_test
     def test_editor_tool_upgrade(self):
         workflow_populator = self.workflow_populator
-        workflow_id = workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
+        workflow_id = workflow_populator.upload_yaml_workflow(
+            """class: GalaxyWorkflow
 inputs: []
 steps:
   - tool_id: multiple_versions
@@ -453,18 +467,20 @@ steps:
     label: multiple_versions
     state:
       foo: bar
-        """, exact_tools=True)
+        """,
+            exact_tools=True,
+        )
         self.workflow_index_open()
         self.workflow_index_click_option("Edit")
         editor = self.components.workflow_editor
         editor.node._(label="multiple_versions").wait_for_and_click()
         editor.tool_version_button.wait_for_and_click()
-        assert self.select_dropdown_item('Switch to 0.2'), 'Switch to tool version dropdown item not found'
+        assert self.select_dropdown_item("Switch to 0.2"), "Switch to tool version dropdown item not found"
         self.screenshot("workflow_editor_version_update")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
-        assert workflow['steps']['0']['tool_version'] == '0.2'
+        assert workflow["steps"]["0"]["tool_version"] == "0.2"
 
     @selenium_test
     def test_editor_tool_upgrade_message(self):
@@ -482,8 +498,9 @@ steps:
         workflow_populator = self.workflow_populator
         embedded_workflow = yaml.safe_load(WORKFLOW_WITH_OLD_TOOL_VERSION)
         # Create invalid tool state
-        embedded_workflow['steps']['mul_versions']['state']['inttest'] = 'Invalid'
-        outer_workflow = yaml.safe_load("""
+        embedded_workflow["steps"]["mul_versions"]["state"]["inttest"] = "Invalid"
+        outer_workflow = yaml.safe_load(
+            """
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -492,8 +509,9 @@ steps:
     run: {}
     in:
       input1: outer_input
-        """)
-        outer_workflow['steps']['nested_workflow']['run'] = embedded_workflow
+        """
+        )
+        outer_workflow["steps"]["nested_workflow"]["run"] = embedded_workflow
         workflow_populator.upload_yaml_workflow(json.dumps(outer_workflow), exact_tools=True)
         self.workflow_index_open()
         self.workflow_index_click_option("Edit")
@@ -507,8 +525,8 @@ steps:
     @staticmethod
     def set_text_element(element, value):
         # Try both, no harm here
-        element.wait_for_and_send_keys(Keys.CONTROL, 'a')
-        element.wait_for_and_send_keys(Keys.COMMAND, 'a')
+        element.wait_for_and_send_keys(Keys.CONTROL, "a")
+        element.wait_for_and_send_keys(Keys.COMMAND, "a")
         element.wait_for_and_send_keys(Keys.BACKSPACE)
         element.wait_for_and_send_keys(value)
 
@@ -520,43 +538,44 @@ steps:
         editor = self.components.workflow_editor
         cat_node = editor.node._(label="first_cat")
         cat_node.wait_for_and_click()
-        self.set_text_element(editor.label_input, 'source label')
+        self.set_text_element(editor.label_input, "source label")
         # Select node using new label, ensures labels are synced between side panel and node
         cat_node = editor.node._(label="source label")
         self.assert_workflow_has_changes_and_save()
         editor.annotation_input.wait_for_and_send_keys("source annotation")
         self.assert_workflow_has_changes_and_save()
-        editor.configure_output(output='out_file1').wait_for_and_click()
-        output_label = editor.label_output(output='out_file1')
-        self.set_text_element(output_label, 'workflow output label')
-        self.set_text_element(editor.rename_output, 'renamed_output')
+        editor.configure_output(output="out_file1").wait_for_and_click()
+        output_label = editor.label_output(output="out_file1")
+        self.set_text_element(output_label, "workflow output label")
+        self.set_text_element(editor.rename_output, "renamed_output")
         editor.change_datatype.wait_for_and_click()
-        editor.select_dataype_text_search.wait_for_and_send_keys('bam')
-        editor.select_datatype(datatype='bam').wait_for_and_click()
-        self.set_text_element(editor.add_tags, '#crazynewtag')
-        self.set_text_element(editor.remove_tags, '#oldboringtag')
+        editor.select_dataype_text_search.wait_for_and_send_keys("bam")
+        editor.select_datatype(datatype="bam").wait_for_and_click()
+        self.set_text_element(editor.add_tags, "#crazynewtag")
+        self.set_text_element(editor.remove_tags, "#oldboringtag")
         self.sleep_for(self.wait_types.UX_RENDER)
         cat_node.clone.wait_for_and_click()
-        editor.label_input.wait_for_and_send_keys('cloned label')
-        output_label = editor.label_output(output='out_file1')
-        self.set_text_element(output_label, 'cloned output label')
+        editor.label_input.wait_for_and_send_keys("cloned label")
+        output_label = editor.label_output(output="out_file1")
+        self.set_text_element(output_label, "cloned output label")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         edited_workflow = self.workflow_populator.download_workflow(workflow_id)
-        source_step = next(iter(step for step in edited_workflow['steps'].values() if step['label'] == 'source label'))
-        cloned_step = next(iter(step for step in edited_workflow['steps'].values() if step['label'] == 'cloned label'))
-        assert source_step['annotation'] == cloned_step['annotation'] == "source annotation"
-        assert source_step['workflow_outputs'][0]['label'] == 'workflow output label'
-        assert cloned_step['workflow_outputs'][0]['label'] == 'cloned output label'
-        assert len(source_step['post_job_actions']) == len(cloned_step['post_job_actions']) == 4
-        assert source_step['post_job_actions'] == cloned_step['post_job_actions']
+        source_step = next(iter(step for step in edited_workflow["steps"].values() if step["label"] == "source label"))
+        cloned_step = next(iter(step for step in edited_workflow["steps"].values() if step["label"] == "cloned label"))
+        assert source_step["annotation"] == cloned_step["annotation"] == "source annotation"
+        assert source_step["workflow_outputs"][0]["label"] == "workflow output label"
+        assert cloned_step["workflow_outputs"][0]["label"] == "cloned output label"
+        assert len(source_step["post_job_actions"]) == len(cloned_step["post_job_actions"]) == 4
+        assert source_step["post_job_actions"] == cloned_step["post_job_actions"]
 
     @selenium_test
     def test_editor_embed_workflow(self):
         workflow_populator = self.workflow_populator
         child_workflow_name = self._get_random_name()
         workflow_populator.upload_yaml_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, name=child_workflow_name)
-        parent_workflow_id = workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
+        parent_workflow_id = workflow_populator.upload_yaml_workflow(
+            """class: GalaxyWorkflow
 inputs: []
 steps:
   - tool_id: multiple_versions
@@ -564,7 +583,8 @@ steps:
     label: multiple_versions
     state:
       foo: bar
-        """)
+        """
+        )
         self.workflow_index_open()
         self.workflow_index_click_option("Edit")
         editor = self.components.workflow_editor
@@ -575,10 +595,10 @@ steps:
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(parent_workflow_id)
-        subworkflow_step = workflow['steps']['1']
-        assert subworkflow_step['name'] == child_workflow_name
-        assert subworkflow_step['type'] == 'subworkflow'
-        assert subworkflow_step['subworkflow']['a_galaxy_workflow'] == 'true'
+        subworkflow_step = workflow["steps"]["1"]
+        assert subworkflow_step["name"] == child_workflow_name
+        assert subworkflow_step["type"] == "subworkflow"
+        assert subworkflow_step["subworkflow"]["a_galaxy_workflow"] == "true"
 
     @selenium_test
     def test_editor_invalid_tool_state(self):
@@ -593,7 +613,8 @@ steps:
     @selenium_test
     def test_missing_tools(self):
         workflow_populator = self.workflow_populator
-        workflow_populator.upload_yaml_workflow("""
+        workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   - id: input1
@@ -602,7 +623,8 @@ steps:
     label: first_cat
     state:
       foo: bar
-""")
+"""
+        )
         self.workflow_index_open()
         self.workflow_index_click_option("Edit")
         self.assert_modal_has_text("Tool is not installed")
@@ -628,7 +650,7 @@ steps:
         # parse workflow table
         table_elements = self.workflow_index_table_elements()
         self.sleep_for(self.wait_types.UX_RENDER)
-        bookmark_td = table_elements[0].find_elements_by_tag_name('td')[4]
+        bookmark_td = table_elements[0].find_elements_by_tag_name("td")[4]
 
         # get bookmark pseudo element
         # https://stackoverflow.com/questions/45427223/click-on-pseudo-element-using-selenium
@@ -756,7 +778,9 @@ steps:
         edit_annotation = self.components.workflow_editor.edit_annotation
         edit_annotation_element = edit_annotation.wait_for_visible()
         actual_annotation = edit_annotation_element.get_attribute("value")
-        assert expected_annotation in actual_annotation, f"'{expected_annotation}' unequal annotation '{actual_annotation}'"
+        assert (
+            expected_annotation in actual_annotation
+        ), f"'{expected_annotation}' unequal annotation '{actual_annotation}'"
 
     @retry_assertion_during_transitions
     def assert_modal_has_text(self, expected_text):
diff --git a/lib/galaxy_test/selenium/test_workflow_invocation_details.py b/lib/galaxy_test/selenium/test_workflow_invocation_details.py
index d8204d07edd..42e8c95580d 100644
--- a/lib/galaxy_test/selenium/test_workflow_invocation_details.py
+++ b/lib/galaxy_test/selenium/test_workflow_invocation_details.py
@@ -1,10 +1,8 @@
-from galaxy_test.base.workflow_fixtures import (
-    WORKFLOW_WITH_OUTPUT_COLLECTION,
-)
+from galaxy_test.base.workflow_fixtures import WORKFLOW_WITH_OUTPUT_COLLECTION
 from .framework import (
     retry_assertion_during_transitions,
     selenium_test,
-    SeleniumTestCase
+    SeleniumTestCase,
 )
 
 
@@ -16,7 +14,9 @@ class WorkflowInvocationDetailsTestCase(SeleniumTestCase):
     def test_job_details(self):
         gx_selenium_context = self
         history_id = gx_selenium_context.dataset_populator.new_history()
-        gx_selenium_context.workflow_populator.run_workflow(WORKFLOW_WITH_OUTPUT_COLLECTION, history_id=history_id, assert_ok=True, wait=True)
+        gx_selenium_context.workflow_populator.run_workflow(
+            WORKFLOW_WITH_OUTPUT_COLLECTION, history_id=history_id, assert_ok=True, wait=True
+        )
         gx_selenium_context.navigate_to_invocations()
         invocations = gx_selenium_context.components.invocations
         invocations.invocations_table.wait_for_visible()
@@ -65,10 +65,13 @@ class WorkflowInvocationDetailsTestCase(SeleniumTestCase):
         self.screenshot("invocations_job_table")
 
         invocations.step_job_information(order_index="1").wait_for_visible()
-        assert "collection_creates_pair" in invocations.step_job_information_tool_id(order_index="1").wait_for_visible().text
+        assert (
+            "collection_creates_pair"
+            in invocations.step_job_information_tool_id(order_index="1").wait_for_visible().text
+        )
 
         invocations.step_output_collection(order_index="1").wait_for_and_click()
         invocations.step_output_collection_toggle(order_index="1").wait_for_and_click()
         invocations.step_output_collection_element_identifier(element_identifier="forward").wait_for_and_click()
         datatype = invocations.step_output_collection_element_datatype(order_index="1").wait_for_text()
-        assert datatype == 'txt'
+        assert datatype == "txt"
diff --git a/lib/galaxy_test/selenium/test_workflow_management.py b/lib/galaxy_test/selenium/test_workflow_management.py
index 87be6676942..b204ef1ed55 100644
--- a/lib/galaxy_test/selenium/test_workflow_management.py
+++ b/lib/galaxy_test/selenium/test_workflow_management.py
@@ -19,7 +19,7 @@ class WorkflowManagementTestCase(SeleniumTestCase):
         assert len(table_elements) == 1
 
         new_workflow = table_elements[0].find_element_by_css_selector(".workflow-dropdown")
-        assert 'TestWorkflow1 (imported from uploaded file)' in new_workflow.text, new_workflow.text
+        assert "TestWorkflow1 (imported from uploaded file)" in new_workflow.text, new_workflow.text
 
     @selenium_test
     def test_view(self):
@@ -40,7 +40,7 @@ class WorkflowManagementTestCase(SeleniumTestCase):
         @retry_assertion_during_transitions
         def check_name():
             name = self.workflow_index_name()
-            assert 'CoolNewName' == name, name
+            assert "CoolNewName" == name, name
 
         check_name()
 
diff --git a/lib/galaxy_test/selenium/test_workflow_run.py b/lib/galaxy_test/selenium/test_workflow_run.py
index a1aeafc6e5e..5f9b4be09a4 100644
--- a/lib/galaxy_test/selenium/test_workflow_run.py
+++ b/lib/galaxy_test/selenium/test_workflow_run.py
@@ -112,7 +112,8 @@ class WorkflowRunTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
     def test_step_parameter_inputs(self):
         self.perform_upload(self.get_filename("1.txt"))
         self.wait_for_history()
-        self.open_in_workflow_run("""
+        self.open_in_workflow_run(
+            """
 class: GalaxyWorkflow
 inputs:
   input_int: integer
@@ -124,7 +125,8 @@ steps:
     in:
       inttest: input_int
       files_0|file: input_data
-""")
+"""
+        )
         workflow_run = self.components.workflow_run
         input_div_element = workflow_run.input_div(label="input_int").wait_for_visible()
         input_element = input_div_element.find_element_by_css_selector("input")
diff --git a/lib/galaxy_test/selenium/test_workflow_sharing.py b/lib/galaxy_test/selenium/test_workflow_sharing.py
index e0366d15ca9..e46ac73591c 100644
--- a/lib/galaxy_test/selenium/test_workflow_sharing.py
+++ b/lib/galaxy_test/selenium/test_workflow_sharing.py
@@ -17,15 +17,15 @@ class WorkflowSharingTestCase(SeleniumTestCase):
         sharing_url = f"workflow/sharing?id={workflow_id}"
         self.get(sharing_url)
         modal = self.components._.messages.error.wait_for_present()
-        assert modal.text == 'You must be logged in to Share or export Galaxy workflows.'
-        login_link = modal.find_element_by_tag_name('a')
-        assert login_link.text == 'logged in'
+        assert modal.text == "You must be logged in to Share or export Galaxy workflows."
+        login_link = modal.find_element_by_tag_name("a")
+        assert login_link.text == "logged in"
         self.sleep_for(self.wait_types.UX_RENDER)
         login_link.click()
         form = self.wait_for_visible(self.navigation.login.selectors.form)
-        self.fill(form, {'login': user_email, 'password': self.default_password})
+        self.fill(form, {"login": user_email, "password": self.default_password})
         self.wait_for_and_click(self.navigation.login.selectors.submit)
         self.wait_for_logged_in()
-        accessible_via_link_button = self.wait_for_selector('.make-accessible')
+        accessible_via_link_button = self.wait_for_selector(".make-accessible")
         accessible_via_link_button.click()
         self.wait_for_xpath('//strong[text()="accessible via link"]')
diff --git a/lib/tool_shed/dependencies/attribute_handlers.py b/lib/tool_shed/dependencies/attribute_handlers.py
index 871534746a9..c3df2ecb2cc 100644
--- a/lib/tool_shed/dependencies/attribute_handlers.py
+++ b/lib/tool_shed/dependencies/attribute_handlers.py
@@ -4,18 +4,21 @@ import logging
 from galaxy.util import asbool
 from galaxy.web import url_for
 from tool_shed.dependencies.tool import tag_attribute_handler
-from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
-from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME
-from tool_shed.util import hg_util
-from tool_shed.util import metadata_util
-from tool_shed.util import repository_util
-from tool_shed.util import xml_util
+from tool_shed.repository_types.util import (
+    REPOSITORY_DEPENDENCY_DEFINITION_FILENAME,
+    TOOL_DEPENDENCY_DEFINITION_FILENAME,
+)
+from tool_shed.util import (
+    hg_util,
+    metadata_util,
+    repository_util,
+    xml_util,
+)
 
 log = logging.getLogger(__name__)
 
 
 class RepositoryDependencyAttributeHandler:
-
     def __init__(self, app, unpopulate):
         self.app = app
         self.file_name = REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
@@ -23,13 +26,13 @@ class RepositoryDependencyAttributeHandler:
 
     def check_tag_attributes(self, elem):
         # <repository name="molecule_datatypes" owner="test" />
-        error_message = ''
-        name = elem.get('name')
+        error_message = ""
+        name = elem.get("name")
         if not name:
-            error_message += 'The tag is missing the required name attribute.  '
-        owner = elem.get('owner')
+            error_message += "The tag is missing the required name attribute.  "
+        owner = elem.get("owner")
         if not owner:
-            error_message += 'The tag is missing the required owner attribute.  '
+            error_message += "The tag is missing the required owner attribute.  "
         log.debug(error_message)
         return error_message
 
@@ -41,7 +44,7 @@ class RepositoryDependencyAttributeHandler:
         # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" />
         altered, new_elem, error_message = self.handle_elem(elem)
         if error_message:
-            error_message += f'  The {TOOL_DEPENDENCY_DEFINITION_FILENAME} file contains an invalid <repository> tag.'
+            error_message += f"  The {TOOL_DEPENDENCY_DEFINITION_FILENAME} file contains an invalid <repository> tag."
         return altered, new_elem, error_message
 
     def handle_elem(self, elem):
@@ -50,22 +53,22 @@ class RepositoryDependencyAttributeHandler:
         # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy">
         #    <package name="xorg_macros" version="1.17.1" />
         # </repository>
-        error_message = ''
-        name = elem.get('name')
-        owner = elem.get('owner')
+        error_message = ""
+        name = elem.get("name")
+        owner = elem.get("owner")
         # The name and owner attributes are always required, so if either are missing, return the error message.
         if not name or not owner:
             error_message = self.check_tag_attributes(elem)
             return False, elem, error_message
         altered = False
-        toolshed = elem.get('toolshed')
-        changeset_revision = elem.get('changeset_revision')
+        toolshed = elem.get("toolshed")
+        changeset_revision = elem.get("changeset_revision")
         # Over a short period of time a bug existed which caused the prior_installation_required attribute
         # to be set to False and included in the <repository> tag when a repository was exported along with
         # its dependencies.  The following will eliminate this problematic attribute upon import.
-        prior_installation_required = elem.get('prior_installation_required')
+        prior_installation_required = elem.get("prior_installation_required")
         if prior_installation_required is not None and not asbool(prior_installation_required):
-            del elem.attrib['prior_installation_required']
+            del elem.attrib["prior_installation_required"]
         sub_elems = [child_elem for child_elem in list(elem)]
         if len(sub_elems) > 0:
             # At this point, a <repository> tag will point only to a package.
@@ -75,11 +78,11 @@ class RepositoryDependencyAttributeHandler:
             packages = []
             for sub_elem in sub_elems:
                 sub_elem_type = sub_elem.tag
-                sub_elem_name = sub_elem.get('name')
-                sub_elem_version = sub_elem.get('version')
+                sub_elem_name = sub_elem.get("name")
+                sub_elem_version = sub_elem.get("version")
                 if sub_elem_type and sub_elem_name and sub_elem_version:
                     packages.append((sub_elem_name, sub_elem_version))
-            sub_elements['packages'] = packages
+            sub_elements["packages"] = packages
         else:
             # Set to None.
             sub_elements = None
@@ -88,19 +91,19 @@ class RepositoryDependencyAttributeHandler:
             # from the <repository> tag.
             if toolshed or changeset_revision:
                 attributes = {}
-                attributes['name'] = name
-                attributes['owner'] = owner
-                prior_installation_required = elem.get('prior_installation_required')
+                attributes["name"] = name
+                attributes["owner"] = owner
+                prior_installation_required = elem.get("prior_installation_required")
                 if asbool(prior_installation_required):
-                    attributes['prior_installation_required'] = 'True'
-                new_elem = xml_util.create_element('repository', attributes=attributes, sub_elements=sub_elements)
+                    attributes["prior_installation_required"] = "True"
+                new_elem = xml_util.create_element("repository", attributes=attributes, sub_elements=sub_elements)
                 altered = True
             return altered, new_elem, error_message
         # From here on we're populating the toolshed and changeset_revision attributes if necessary.
         if not toolshed:
             # Default the setting to the current tool shed.
-            toolshed = str(url_for('/', qualified=True)).rstrip('/')
-            elem.attrib['toolshed'] = toolshed
+            toolshed = str(url_for("/", qualified=True)).rstrip("/")
+            elem.attrib["toolshed"] = toolshed
             altered = True
         if not changeset_revision:
             # Populate the changeset_revision attribute with the latest installable metadata revision for
@@ -108,17 +111,19 @@ class RepositoryDependencyAttributeHandler:
             # revision to ensure that the contents of the revision are valid.
             repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
             if repository:
-                lastest_installable_changeset_revision = \
-                    metadata_util.get_latest_downloadable_changeset_revision(self.app, repository)
+                lastest_installable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(
+                    self.app, repository
+                )
                 if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
-                    elem.attrib['changeset_revision'] = lastest_installable_changeset_revision
+                    elem.attrib["changeset_revision"] = lastest_installable_changeset_revision
                     altered = True
                 else:
-                    error_message = 'Invalid latest installable changeset_revision %s ' % \
-                        str(lastest_installable_changeset_revision)
-                    error_message += f'retrieved for repository {str(name)} owned by {str(owner)}.  '
+                    error_message = "Invalid latest installable changeset_revision %s " % str(
+                        lastest_installable_changeset_revision
+                    )
+                    error_message += f"retrieved for repository {str(name)} owned by {str(owner)}.  "
             else:
-                error_message = f'Unable to locate repository with name {str(name)} and owner {str(owner)}.  '
+                error_message = f"Unable to locate repository with name {str(name)} and owner {str(owner)}.  "
         return altered, elem, error_message
 
     def handle_sub_elem(self, parent_elem, elem_index, elem):
@@ -130,14 +135,16 @@ class RepositoryDependencyAttributeHandler:
         <action type="setup_ruby_environment">
         """
         sub_elem_altered = False
-        error_message = ''
+        error_message = ""
         for sub_index, sub_elem in enumerate(elem):
             # Make sure to skip comments and tags that are not <repository>.
-            if sub_elem.tag == 'repository':
+            if sub_elem.tag == "repository":
                 altered, new_sub_elem, message = self.handle_elem(sub_elem)
                 if message:
-                    error_message += 'The %s file contains an invalid <repository> tag.  %s' % \
-                        (TOOL_DEPENDENCY_DEFINITION_FILENAME, message)
+                    error_message += "The %s file contains an invalid <repository> tag.  %s" % (
+                        TOOL_DEPENDENCY_DEFINITION_FILENAME,
+                        message,
+                    )
                 if altered:
                     if not sub_elem_altered:
                         sub_elem_altered = True
@@ -161,11 +168,11 @@ class RepositoryDependencyAttributeHandler:
         root_altered = False
         new_root = copy.deepcopy(root)
         for index, elem in enumerate(root):
-            if elem.tag == 'repository':
+            if elem.tag == "repository":
                 # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
                 altered, new_elem, error_message = self.handle_elem(elem)
                 if error_message:
-                    error_message = f'The {self.file_name} file contains an invalid <repository> tag.  {error_message}'
+                    error_message = f"The {self.file_name} file contains an invalid <repository> tag.  {error_message}"
                     return False, None, error_message
                 if altered:
                     if not root_altered:
@@ -175,7 +182,6 @@ class RepositoryDependencyAttributeHandler:
 
 
 class ToolDependencyAttributeHandler:
-
     def __init__(self, app, unpopulate):
         self.app = app
         self.file_name = TOOL_DEPENDENCY_DEFINITION_FILENAME
@@ -189,7 +195,7 @@ class ToolDependencyAttributeHandler:
         rdah = RepositoryDependencyAttributeHandler(self.app, self.unpopulate)
         tah = tag_attribute_handler.TagAttributeHandler(self.app, rdah, self.unpopulate)
         altered = False
-        error_message = ''
+        error_message = ""
         # Make sure we're looking at a valid tool_dependencies.xml file.
         tree, error_message = xml_util.parse_xml(tool_dependencies_config)
         if tree is None:
diff --git a/lib/tool_shed/dependencies/repository/relation_builder.py b/lib/tool_shed/dependencies/repository/relation_builder.py
index 46ba3d6677b..49ef4411468 100644
--- a/lib/tool_shed/dependencies/repository/relation_builder.py
+++ b/lib/tool_shed/dependencies/repository/relation_builder.py
@@ -1,19 +1,21 @@
 import logging
 
 import tool_shed.util.repository_util
-from galaxy.util import asbool, listify
+from galaxy.util import (
+    asbool,
+    listify,
+)
 from tool_shed.util import (
     common_util,
     container_util,
     metadata_util,
-    shed_util_common as suc
 )
+from tool_shed.util import shed_util_common as suc
 
 log = logging.getLogger(__name__)
 
 
 class RelationBuilder:
-
     def __init__(self, app, repository, repository_metadata, tool_shed_url):
         self.all_repository_dependencies = {}
         self.app = app
@@ -50,8 +52,14 @@ class RelationBuilder:
         """
         filtered_key_rd_dict = {}
         for rd_key, required_rd_tup in key_rd_dict.items():
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                common_util.parse_repository_dependency_tuple(required_rd_tup)
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = common_util.parse_repository_dependency_tuple(required_rd_tup)
             if not asbool(only_if_compiling_contained_td):
                 filtered_key_rd_dict[rd_key] = required_rd_tup
         return filtered_key_rd_dict
@@ -65,18 +73,24 @@ class RelationBuilder:
         cleaned_toolshed_base_url = common_util.remove_protocol_from_tool_shed_url(self.tool_shed_url)
         if self.all_repository_dependencies:
             for rd_key, rd_tups in self.all_repository_dependencies.items():
-                if rd_key in ['root_key', 'description']:
+                if rd_key in ["root_key", "description"]:
                     continue
                 for rd_tup in rd_tups:
-                    rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
-                        rd_prior_installation_required, \
-                        rd_only_if_compiling_contained_td = \
-                        common_util.parse_repository_dependency_tuple(rd_tup)
+                    (
+                        rd_toolshed,
+                        rd_name,
+                        rd_owner,
+                        rd_changeset_revision,
+                        rd_prior_installation_required,
+                        rd_only_if_compiling_contained_td,
+                    ) = common_util.parse_repository_dependency_tuple(rd_tup)
                     cleaned_rd_toolshed = common_util.remove_protocol_from_tool_shed_url(rd_toolshed)
-                    if cleaned_rd_toolshed == cleaned_toolshed_base_url and \
-                            rd_name == self.repository.name and \
-                            rd_owner == self.repository.user.username and \
-                            rd_changeset_revision == self.repository_metadata.changeset_revision:
+                    if (
+                        cleaned_rd_toolshed == cleaned_toolshed_base_url
+                        and rd_name == self.repository.name
+                        and rd_owner == self.repository.user.username
+                        and rd_changeset_revision == self.repository_metadata.changeset_revision
+                    ):
                         return rd_prior_installation_required, rd_only_if_compiling_contained_td
         elif self.repository_metadata:
             # Get the list of changeset revisions from the tool shed to which self.repository may be updated.
@@ -84,43 +98,55 @@ class RelationBuilder:
             current_changeset_revision = str(self.repository_metadata.changeset_revision)
             # Get the changeset revision to which the current value of required_repository_changeset_revision
             # should be updated if it's not current.
-            text = metadata_util.get_updated_changeset_revisions(self.app,
-                                                                 name=str(self.repository.name),
-                                                                 owner=str(self.repository.user.username),
-                                                                 changeset_revision=current_changeset_revision)
+            text = metadata_util.get_updated_changeset_revisions(
+                self.app,
+                name=str(self.repository.name),
+                owner=str(self.repository.user.username),
+                changeset_revision=current_changeset_revision,
+            )
             if text:
                 valid_changeset_revisions = listify(text)
                 if current_changeset_revision not in valid_changeset_revisions:
                     valid_changeset_revisions.append(current_changeset_revision)
             else:
                 valid_changeset_revisions = [current_changeset_revision]
-            repository_dependencies_dict = metadata['repository_dependencies']
-            rd_tups = repository_dependencies_dict.get('repository_dependencies', [])
+            repository_dependencies_dict = metadata["repository_dependencies"]
+            rd_tups = repository_dependencies_dict.get("repository_dependencies", [])
             for rd_tup in rd_tups:
-                rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
-                    rd_prior_installation_required, \
-                    rd_only_if_compiling_contained_td = \
-                    common_util.parse_repository_dependency_tuple(rd_tup)
+                (
+                    rd_toolshed,
+                    rd_name,
+                    rd_owner,
+                    rd_changeset_revision,
+                    rd_prior_installation_required,
+                    rd_only_if_compiling_contained_td,
+                ) = common_util.parse_repository_dependency_tuple(rd_tup)
                 cleaned_rd_toolshed = common_util.remove_protocol_from_tool_shed_url(rd_toolshed)
-                if cleaned_rd_toolshed == cleaned_toolshed_base_url and \
-                        rd_name == self.repository.name and \
-                        rd_owner == self.repository.user.username and \
-                        rd_changeset_revision in valid_changeset_revisions:
+                if (
+                    cleaned_rd_toolshed == cleaned_toolshed_base_url
+                    and rd_name == self.repository.name
+                    and rd_owner == self.repository.user.username
+                    and rd_changeset_revision in valid_changeset_revisions
+                ):
                     return rd_prior_installation_required, rd_only_if_compiling_contained_td
         # Default both prior_installation_required and only_if_compiling_contained_td to False.
-        return 'False', 'False'
+        return "False", "False"
 
     def get_key_for_repository_changeset_revision(self):
         # The received toolshed_base_url must include the port, but doesn't have to include the protocol.
-        prior_installation_required, only_if_compiling_contained_td = \
-            self.get_prior_installation_required_and_only_if_compiling_contained_td()
+        (
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = self.get_prior_installation_required_and_only_if_compiling_contained_td()
         # Create a key with the value of prior_installation_required defaulted to False.
-        key = container_util.generate_repository_dependencies_key_for_repository(self.tool_shed_url,
-                                                                                 self.repository.name,
-                                                                                 self.repository.user.username,
-                                                                                 self.repository_metadata.changeset_revision,
-                                                                                 prior_installation_required,
-                                                                                 only_if_compiling_contained_td)
+        key = container_util.generate_repository_dependencies_key_for_repository(
+            self.tool_shed_url,
+            self.repository.name,
+            self.repository.user.username,
+            self.repository_metadata.changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        )
         return key
 
     def get_repository_dependencies_for_changeset_revision(self):
@@ -138,16 +164,16 @@ class RelationBuilder:
         if metadata:
             # The value of self.tool_shed_url must include the port, but doesn't have to include
             # the protocol.
-            if 'repository_dependencies' in metadata:
+            if "repository_dependencies" in metadata:
                 current_repository_key = self.get_key_for_repository_changeset_revision()
-                repository_dependencies_dict = metadata['repository_dependencies']
+                repository_dependencies_dict = metadata["repository_dependencies"]
                 if not self.all_repository_dependencies:
                     self.initialize_all_repository_dependencies(current_repository_key, repository_dependencies_dict)
                 # Handle the repository dependencies defined in the current repository, if any, and populate
                 # the various repository dependency objects for this round of processing.
-                current_repository_key_rd_dicts = \
-                    self.populate_repository_dependency_objects_for_processing(current_repository_key,
-                                                                               repository_dependencies_dict)
+                current_repository_key_rd_dicts = self.populate_repository_dependency_objects_for_processing(
+                    current_repository_key, repository_dependencies_dict
+                )
         if current_repository_key:
             if current_repository_key_rd_dicts:
                 # There should be only a single current_repository_key_rd_dict in this list.
@@ -166,32 +192,40 @@ class RelationBuilder:
         return self.all_repository_dependencies
 
     def get_repository_dependency_as_key(self, repository_dependency):
-        tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(repository_dependency)
-        return container_util.generate_repository_dependencies_key_for_repository(tool_shed,
-                                                                                  name,
-                                                                                  owner,
-                                                                                  changeset_revision,
-                                                                                  prior_installation_required,
-                                                                                  only_if_compiling_contained_td)
+        (
+            tool_shed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(repository_dependency)
+        return container_util.generate_repository_dependencies_key_for_repository(
+            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td
+        )
 
     def get_updated_changeset_revisions_for_repository_dependencies(self, key_rd_dicts):
         updated_key_rd_dicts = []
         for key_rd_dict in key_rd_dicts:
             key = next(iter(key_rd_dict))
             repository_dependency = key_rd_dict[key]
-            rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
-                rd_prior_installation_required, \
-                rd_only_if_compiling_contained_td = \
-                common_util.parse_repository_dependency_tuple(repository_dependency)
+            (
+                rd_toolshed,
+                rd_name,
+                rd_owner,
+                rd_changeset_revision,
+                rd_prior_installation_required,
+                rd_only_if_compiling_contained_td,
+            ) = common_util.parse_repository_dependency_tuple(repository_dependency)
             if suc.tool_shed_is_this_tool_shed(rd_toolshed):
-                repository = tool_shed.util.repository_util.get_repository_by_name_and_owner(self.app, rd_name, rd_owner)
+                repository = tool_shed.util.repository_util.get_repository_by_name_and_owner(
+                    self.app, rd_name, rd_owner
+                )
                 if repository:
                     repository_id = self.app.security.encode_id(repository.id)
-                    repository_metadata = \
-                        metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
-                                                                                                  repository_id,
-                                                                                                  rd_changeset_revision)
+                    repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                        self.app, repository_id, rd_changeset_revision
+                    )
                     if repository_metadata:
                         # The repository changeset_revision is installable, so no updates are available.
                         new_key_rd_dict = {}
@@ -199,50 +233,68 @@ class RelationBuilder:
                         updated_key_rd_dicts.append(key_rd_dict)
                     else:
                         # The repository changeset_revision is no longer installable, so see if there's been an update.
-                        changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, rd_changeset_revision)
+                        changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+                            self.app, repository, rd_changeset_revision
+                        )
                         if changeset_revision != rd_changeset_revision:
-                            repository_metadata = \
-                                metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
-                                                                                                          repository_id,
-                                                                                                          changeset_revision)
+                            repository_metadata = (
+                                metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                                    self.app, repository_id, changeset_revision
+                                )
+                            )
                         if repository_metadata:
                             new_key_rd_dict = {}
-                            new_key_rd_dict[key] = \
-                                [rd_toolshed,
-                                 rd_name,
-                                 rd_owner,
-                                 repository_metadata.changeset_revision,
-                                 rd_prior_installation_required,
-                                 rd_only_if_compiling_contained_td]
+                            new_key_rd_dict[key] = [
+                                rd_toolshed,
+                                rd_name,
+                                rd_owner,
+                                repository_metadata.changeset_revision,
+                                rd_prior_installation_required,
+                                rd_only_if_compiling_contained_td,
+                            ]
                             # We have the updated changeset revision.
                             updated_key_rd_dicts.append(new_key_rd_dict)
                         else:
                             repository_components_tuple = container_util.get_components_from_key(key)
-                            components_list = tool_shed.util.repository_util.extract_components_from_tuple(repository_components_tuple)
-                            toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
+                            components_list = tool_shed.util.repository_util.extract_components_from_tuple(
+                                repository_components_tuple
+                            )
+                            (
+                                toolshed,
+                                repository_name,
+                                repository_owner,
+                                repository_changeset_revision,
+                            ) = components_list[0:4]
                             # For backward compatibility to the 12/20/12 Galaxy release.
                             if len(components_list) in (4, 5):
-                                rd_only_if_compiling_contained_td = 'False'
-                            message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
-                                (str(rd_changeset_revision), str(rd_name), str(rd_owner))
+                                rd_only_if_compiling_contained_td = "False"
+                            message = (
+                                "The revision %s defined for repository %s owned by %s is invalid, so repository "
+                                % (str(rd_changeset_revision), str(rd_name), str(rd_owner))
+                            )
                             message += f"dependencies defined for repository {str(repository_name)} will be ignored."
                             log.debug(message)
                 else:
                     repository_components_tuple = container_util.get_components_from_key(key)
-                    components_list = tool_shed.util.repository_util.extract_components_from_tuple(repository_components_tuple)
+                    components_list = tool_shed.util.repository_util.extract_components_from_tuple(
+                        repository_components_tuple
+                    )
                     toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
-                    message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
-                        (str(rd_changeset_revision), str(rd_name), str(rd_owner))
+                    message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % (
+                        str(rd_changeset_revision),
+                        str(rd_name),
+                        str(rd_owner),
+                    )
                     message += f"dependencies defined for repository {str(repository_name)} will be ignored."
                     log.debug(message)
         return updated_key_rd_dicts
 
     def handle_circular_repository_dependency(self, repository_key, repository_dependency):
-        all_repository_dependencies_root_key = self.all_repository_dependencies['root_key']
+        all_repository_dependencies_root_key = self.all_repository_dependencies["root_key"]
         repository_dependency_as_key = self.get_repository_dependency_as_key(repository_dependency)
-        self.update_circular_repository_dependencies(repository_key,
-                                                     repository_dependency,
-                                                     self.all_repository_dependencies[repository_dependency_as_key])
+        self.update_circular_repository_dependencies(
+            repository_key, repository_dependency, self.all_repository_dependencies[repository_dependency_as_key]
+        )
         if all_repository_dependencies_root_key != repository_dependency_as_key:
             self.all_repository_dependencies[repository_key] = [repository_dependency]
 
@@ -260,16 +312,21 @@ class RelationBuilder:
     def handle_key_rd_dicts_for_repository(self, current_repository_key, repository_key_rd_dicts):
         key_rd_dict = repository_key_rd_dicts.pop(0)
         repository_dependency = key_rd_dict[current_repository_key]
-        toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(repository_dependency)
+        (
+            toolshed,
+            name,
+            owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(repository_dependency)
         if suc.tool_shed_is_this_tool_shed(toolshed):
             required_repository = tool_shed.util.repository_util.get_repository_by_name_and_owner(self.app, name, owner)
             self.repository = required_repository
             repository_id = self.app.security.encode_id(required_repository.id)
-            required_repository_metadata = \
-                metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
-                                                                                          repository_id,
-                                                                                          changeset_revision)
+            required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                self.app, repository_id, changeset_revision
+            )
             self.repository_metadata = required_repository_metadata
             if required_repository_metadata:
                 # The required_repository_metadata changeset_revision is installable.
@@ -284,7 +341,9 @@ class RelationBuilder:
                 self.handled_key_rd_dicts.append(key_rd_dict)
             if self.in_key_rd_dicts(key_rd_dict, self.key_rd_dicts_to_be_processed):
                 # Remove the current repository from self.key_rd_dicts_to_be_processed.
-                self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts(key_rd_dict, self.key_rd_dicts_to_be_processed)
+                self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts(
+                    key_rd_dict, self.key_rd_dicts_to_be_processed
+                )
         else:
             # The repository is in a different tool shed, so build an url and send a request.
             error_message = "Repository dependencies are currently supported only within the same Tool Shed.  "
@@ -339,11 +398,11 @@ class RelationBuilder:
     def initialize_all_repository_dependencies(self, current_repository_key, repository_dependencies_dict):
         """Initialize the self.all_repository_dependencies dictionary."""
         # It's safe to assume that current_repository_key in this case will have a value.
-        self.all_repository_dependencies['root_key'] = current_repository_key
+        self.all_repository_dependencies["root_key"] = current_repository_key
         self.all_repository_dependencies[current_repository_key] = []
         # Store the value of the 'description' key only once, the first time through this recursive method.
-        description = repository_dependencies_dict.get('description', None)
-        self.all_repository_dependencies['description'] = description
+        description = repository_dependencies_dict.get("description", None)
+        self.all_repository_dependencies["description"] = description
 
     def is_circular_repository_dependency(self, repository_key, repository_dependency):
         """
@@ -359,7 +418,9 @@ class RelationBuilder:
                 return True
         return False
 
-    def populate_repository_dependency_objects_for_processing(self, current_repository_key, repository_dependencies_dict):
+    def populate_repository_dependency_objects_for_processing(
+        self, current_repository_key, repository_dependencies_dict
+    ):
         """
         The process that discovers all repository dependencies for a specified repository's changeset
         revision uses this method to populate the following items for the current processing loop:
@@ -370,16 +431,18 @@ class RelationBuilder:
         """
         current_repository_key_rd_dicts = []
         filtered_current_repository_key_rd_dicts = []
-        for rd_tup in repository_dependencies_dict['repository_dependencies']:
+        for rd_tup in repository_dependencies_dict["repository_dependencies"]:
             new_key_rd_dict = {}
             new_key_rd_dict[current_repository_key] = rd_tup
             current_repository_key_rd_dicts.append(new_key_rd_dict)
         if current_repository_key_rd_dicts and current_repository_key:
             # Remove all repository dependencies that point to a revision within its own repository.
-            current_repository_key_rd_dicts = \
-                self.remove_repository_dependency_reference_to_self(current_repository_key_rd_dicts)
-        current_repository_key_rd_dicts = \
-            self.get_updated_changeset_revisions_for_repository_dependencies(current_repository_key_rd_dicts)
+            current_repository_key_rd_dicts = self.remove_repository_dependency_reference_to_self(
+                current_repository_key_rd_dicts
+            )
+        current_repository_key_rd_dicts = self.get_updated_changeset_revisions_for_repository_dependencies(
+            current_repository_key_rd_dicts
+        )
         for key_rd_dict in current_repository_key_rd_dicts:
             if self.filter_dependencies_needed_for_compiling:
                 # Filter out repository dependencies that are required only if compiling the dependent
@@ -422,18 +485,18 @@ class RelationBuilder:
         record is not found.
         """
         valid_repository_dependencies = {}
-        description = repository_dependencies.get('description', None)
-        root_key = repository_dependencies.get('root_key', None)
+        description = repository_dependencies.get("description", None)
+        root_key = repository_dependencies.get("root_key", None)
         if root_key is None:
             return valid_repository_dependencies
         for key, value in repository_dependencies.items():
-            if key in ['description', 'root_key']:
+            if key in ["description", "root_key"]:
                 continue
             if value:
                 valid_repository_dependencies[key] = value
         if valid_repository_dependencies:
-            valid_repository_dependencies['description'] = description
-            valid_repository_dependencies['root_key'] = root_key
+            valid_repository_dependencies["description"] = description
+            valid_repository_dependencies["root_key"] = root_key
         return valid_repository_dependencies
 
     def remove_from_key_rd_dicts(self, key_rd_dict, key_rd_dicts):
@@ -454,20 +517,30 @@ class RelationBuilder:
         clean_key_rd_dicts = []
         key = next(iter(key_rd_dicts[0]))
         repository_tup = key.split(container_util.STRSEP)
-        rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
-            rd_prior_installation_required, \
-            rd_only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(repository_tup)
+        (
+            rd_toolshed,
+            rd_name,
+            rd_owner,
+            rd_changeset_revision,
+            rd_prior_installation_required,
+            rd_only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(repository_tup)
         cleaned_rd_toolshed = common_util.remove_protocol_from_tool_shed_url(rd_toolshed)
         for key_rd_dict in key_rd_dicts:
             k = next(iter(key_rd_dict))
             repository_dependency = key_rd_dict[k]
-            toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                common_util.parse_repository_dependency_tuple(repository_dependency)
+            (
+                toolshed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = common_util.parse_repository_dependency_tuple(repository_dependency)
             cleaned_toolshed = common_util.remove_protocol_from_tool_shed_url(toolshed)
             if cleaned_rd_toolshed == cleaned_toolshed and rd_name == name and rd_owner == owner:
                 debug_msg = f"Removing repository dependency for repository {name} owned by {owner} "
-                debug_msg += 'since it refers to a revision within itself.'
+                debug_msg += "since it refers to a revision within itself."
                 log.debug(debug_msg)
             else:
                 new_key_rd_dict = {}
diff --git a/lib/tool_shed/dependencies/tool/tag_attribute_handler.py b/lib/tool_shed/dependencies/tool/tag_attribute_handler.py
index 5dc3bf75c86..baae6d23c3b 100644
--- a/lib/tool_shed/dependencies/tool/tag_attribute_handler.py
+++ b/lib/tool_shed/dependencies/tool/tag_attribute_handler.py
@@ -5,7 +5,6 @@ log = logging.getLogger(__name__)
 
 
 class TagAttributeHandler:
-
     def __init__(self, app, rdd, unpopulate):
         self.app = app
         self.altered = False
@@ -23,13 +22,11 @@ class TagAttributeHandler:
         new_elem = copy.deepcopy(elem)
         for sub_index, sub_elem in enumerate(elem):
             altered = False
-            error_message = ''
-            if sub_elem.tag == 'repository':
-                altered, new_sub_elem, error_message = \
-                    self.process_repository_tag_set(parent_elem=elem,
-                                                    elem_index=sub_index,
-                                                    elem=sub_elem,
-                                                    message=message)
+            error_message = ""
+            if sub_elem.tag == "repository":
+                altered, new_sub_elem, error_message = self.process_repository_tag_set(
+                    parent_elem=elem, elem_index=sub_index, elem=sub_elem, message=message
+                )
             if error_message and error_message not in message:
                 message += error_message
             if altered:
@@ -49,25 +46,24 @@ class TagAttributeHandler:
         new_elem = copy.deepcopy(elem)
         for sub_index, sub_elem in enumerate(elem):
             altered = False
-            error_message = ''
-            if sub_elem.tag == 'package':
-                altered, new_sub_elem, error_message = self.process_package_tag_set(elem=sub_elem,
-                                                                                    message=message,
-                                                                                    skip_actions_tags=skip_actions_tags)
-            elif sub_elem.tag == 'action':
+            error_message = ""
+            if sub_elem.tag == "package":
+                altered, new_sub_elem, error_message = self.process_package_tag_set(
+                    elem=sub_elem, message=message, skip_actions_tags=skip_actions_tags
+                )
+            elif sub_elem.tag == "action":
                 # <action type="set_environment_for_install">
                 #    <repository name="package_readline_6_2" owner="devteam"">
                 #        <package name="readline" version="6.2" />
                 #    </repository>
                 # </action>
-                altered, new_sub_elem, error_message = self.process_action_tag_set(elem=sub_elem,
-                                                                                   message=message)
+                altered, new_sub_elem, error_message = self.process_action_tag_set(elem=sub_elem, message=message)
             else:
                 # Inspect the sub elements of elem to locate all <repository> tags and
                 # populate them with toolshed and changeset_revision attributes if necessary.
-                altered, new_sub_elem, error_message = self.rdd.handle_sub_elem(parent_elem=elem,
-                                                                                elem_index=sub_index,
-                                                                                elem=sub_elem)
+                altered, new_sub_elem, error_message = self.rdd.handle_sub_elem(
+                    parent_elem=elem, elem_index=sub_index, elem=sub_elem
+                )
             if error_message and error_message not in message:
                 message += error_message
             if altered:
@@ -87,18 +83,17 @@ class TagAttributeHandler:
         new_elem = copy.deepcopy(elem)
         for sub_index, sub_elem in enumerate(elem):
             altered = False
-            error_message = ''
-            if sub_elem.tag == 'actions':
+            error_message = ""
+            if sub_elem.tag == "actions":
                 if skip_actions_tags:
                     # Skip all actions tags that include os or architecture attributes.
-                    system = sub_elem.get('os')
-                    architecture = sub_elem.get('architecture')
+                    system = sub_elem.get("os")
+                    architecture = sub_elem.get("architecture")
                     if system or architecture:
                         continue
-                altered, new_sub_elem, error_message = \
-                    self.process_actions_tag_set(elem=sub_elem,
-                                                 message=message,
-                                                 skip_actions_tags=skip_actions_tags)
+                altered, new_sub_elem, error_message = self.process_actions_tag_set(
+                    elem=sub_elem, message=message, skip_actions_tags=skip_actions_tags
+                )
             if error_message and error_message not in message:
                 message += error_message
             if altered:
@@ -110,17 +105,16 @@ class TagAttributeHandler:
         return elem_altered, new_elem, message
 
     def process_config(self, root, skip_actions_tags=True):
-        error_message = ''
+        error_message = ""
         new_root = copy.deepcopy(root)
-        if root.tag == 'tool_dependency':
+        if root.tag == "tool_dependency":
             for elem_index, elem in enumerate(root):
                 altered = False
-                if elem.tag == 'package':
+                if elem.tag == "package":
                     # <package name="eigen" version="2.0.17">
-                    altered, new_elem, error_message = \
-                        self.process_package_tag_set(elem=elem,
-                                                     message=error_message,
-                                                     skip_actions_tags=skip_actions_tags)
+                    altered, new_elem, error_message = self.process_package_tag_set(
+                        elem=elem, message=error_message, skip_actions_tags=skip_actions_tags
+                    )
                 if altered:
                     if not self.altered:
                         self.altered = True
@@ -135,24 +129,24 @@ class TagAttributeHandler:
         new_elem = copy.deepcopy(elem)
         for sub_index, sub_elem in enumerate(elem):
             altered = False
-            error_message = ''
-            if sub_elem.tag == 'actions_group':
-                altered, new_sub_elem, error_message = \
-                    self.process_actions_group_tag_set(elem=sub_elem,
-                                                       message=message,
-                                                       skip_actions_tags=skip_actions_tags)
-            elif sub_elem.tag == 'actions':
-                altered, new_sub_elem, error_message = \
-                    self.process_actions_tag_set(elem=sub_elem,
-                                                 message=message,
-                                                 skip_actions_tags=skip_actions_tags)
+            error_message = ""
+            if sub_elem.tag == "actions_group":
+                altered, new_sub_elem, error_message = self.process_actions_group_tag_set(
+                    elem=sub_elem, message=message, skip_actions_tags=skip_actions_tags
+                )
+            elif sub_elem.tag == "actions":
+                altered, new_sub_elem, error_message = self.process_actions_tag_set(
+                    elem=sub_elem, message=message, skip_actions_tags=skip_actions_tags
+                )
             else:
-                package_name = elem.get('name', '')
-                package_version = elem.get('version', '')
-                error_message += 'Version %s of the %s package cannot be installed because ' % \
-                    (str(package_version), str(package_name))
-                error_message += 'the recipe for installing the package is missing either an '
-                error_message += '&lt;actions&gt; tag set or an &lt;actions_group&gt; tag set.'
+                package_name = elem.get("name", "")
+                package_version = elem.get("version", "")
+                error_message += "Version %s of the %s package cannot be installed because " % (
+                    str(package_version),
+                    str(package_name),
+                )
+                error_message += "the recipe for installing the package is missing either an "
+                error_message += "&lt;actions&gt; tag set or an &lt;actions_group&gt; tag set."
             if error_message and error_message not in message:
                 message += error_message
             if altered:
@@ -168,18 +162,15 @@ class TagAttributeHandler:
         new_elem = copy.deepcopy(elem)
         for sub_index, sub_elem in enumerate(elem):
             altered = False
-            error_message = ''
-            if sub_elem.tag == 'install':
-                altered, new_sub_elem, error_message = \
-                    self.process_install_tag_set(elem=sub_elem,
-                                                 message=message,
-                                                 skip_actions_tags=skip_actions_tags)
-            elif sub_elem.tag == 'repository':
-                altered, new_sub_elem, error_message = \
-                    self.process_repository_tag_set(parent_elem=elem,
-                                                    elem_index=sub_index,
-                                                    elem=sub_elem,
-                                                    message=message)
+            error_message = ""
+            if sub_elem.tag == "install":
+                altered, new_sub_elem, error_message = self.process_install_tag_set(
+                    elem=sub_elem, message=message, skip_actions_tags=skip_actions_tags
+                )
+            elif sub_elem.tag == "repository":
+                altered, new_sub_elem, error_message = self.process_repository_tag_set(
+                    parent_elem=elem, elem_index=sub_index, elem=sub_elem, message=message
+                )
             if error_message and error_message not in message:
                 message += error_message
             if altered:
@@ -192,9 +183,9 @@ class TagAttributeHandler:
 
     def process_repository_tag_set(self, parent_elem, elem_index, elem, message):
         # We have a complex repository dependency.
-        altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem(parent_elem=parent_elem,
-                                                                                   elem_index=elem_index,
-                                                                                   elem=elem)
+        altered, new_elem, error_message = self.rdd.handle_complex_dependency_elem(
+            parent_elem=parent_elem, elem_index=elem_index, elem=elem
+        )
         if error_message and error_message not in message:
             message += error_message
         if altered:
diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index e88f789a930..ffd93158a7d 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -5,18 +5,19 @@ import threading
 
 from galaxy import util
 from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
-from tool_shed.util import common_util
-from tool_shed.util import container_util
-from tool_shed.util import readme_util
-from tool_shed.util import repository_util
-from tool_shed.util import tool_dependency_util
+from tool_shed.util import (
+    common_util,
+    container_util,
+    readme_util,
+    repository_util,
+    tool_dependency_util,
+)
 from tool_shed.utility_containers import utility_container_manager
 
 log = logging.getLogger(__name__)
 
 
 class DependencyDisplayer:
-
     def __init__(self, app):
         self.app = app
 
@@ -30,24 +31,21 @@ class DependencyDisplayer:
         with more than a single repository.
         """
         for dependency_key, requirements_dict in tool_dependencies.items():
-            if dependency_key in ['set_environment']:
+            if dependency_key in ["set_environment"]:
                 continue
-            repository_name = requirements_dict.get('repository_name', 'unknown')
-            repository_owner = requirements_dict.get('repository_owner', 'unknown')
-            changeset_revision = requirements_dict.get('changeset_revision', 'unknown')
-            dependency_name = requirements_dict['name']
-            version = requirements_dict['version']
+            repository_name = requirements_dict.get("repository_name", "unknown")
+            repository_owner = requirements_dict.get("repository_owner", "unknown")
+            changeset_revision = requirements_dict.get("changeset_revision", "unknown")
+            dependency_name = requirements_dict["name"]
+            version = requirements_dict["version"]
             if self.app.tool_dependency_dir:
                 root_dir = self.app.tool_dependency_dir
             else:
-                root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>'
-            install_dir = os.path.join(root_dir,
-                                       dependency_name,
-                                       version,
-                                       repository_owner,
-                                       repository_name,
-                                       changeset_revision)
-            requirements_dict['install_dir'] = install_dir
+                root_dir = "<set your tool_dependency_dir in your Galaxy configuration file>"
+            install_dir = os.path.join(
+                root_dir, dependency_name, version, repository_owner, repository_name, changeset_revision
+            )
+            requirements_dict["install_dir"] = install_dir
             tool_dependencies[dependency_key] = requirements_dict
         return tool_dependencies
 
@@ -55,48 +53,71 @@ class DependencyDisplayer:
         """
         Get or generate and return an error message associated with an invalid repository dependency.
         """
-        message = ''
+        message = ""
         if metadata_dict:
             if error_from_tuple:
                 # Return the error messages associated with a set of one or more invalid repository
                 # dependency tuples.
-                invalid_repository_dependencies_dict = metadata_dict.get('invalid_repository_dependencies', None)
+                invalid_repository_dependencies_dict = metadata_dict.get("invalid_repository_dependencies", None)
                 if invalid_repository_dependencies_dict is not None:
-                    invalid_repository_dependencies = \
-                        invalid_repository_dependencies_dict.get('invalid_repository_dependencies', [])
+                    invalid_repository_dependencies = invalid_repository_dependencies_dict.get(
+                        "invalid_repository_dependencies", []
+                    )
                     for repository_dependency_tup in invalid_repository_dependencies:
-                        toolshed, name, owner, changeset_revision, \
-                            prior_installation_required, \
-                            only_if_compiling_contained_td, error = \
-                            common_util.parse_repository_dependency_tuple(repository_dependency_tup, contains_error=True)
+                        (
+                            toolshed,
+                            name,
+                            owner,
+                            changeset_revision,
+                            prior_installation_required,
+                            only_if_compiling_contained_td,
+                            error,
+                        ) = common_util.parse_repository_dependency_tuple(
+                            repository_dependency_tup, contains_error=True
+                        )
                         if error:
-                            message += f'{str(error)}  '
+                            message += f"{str(error)}  "
             else:
                 # The complete dependency hierarchy could not be determined for a repository being installed into
                 # Galaxy.  This is likely due to invalid repository dependency definitions, so we'll get them from
                 # the metadata and parse them for display in an error message.  This will hopefully communicate the
                 # problem to the user in such a way that a resolution can be determined.
-                message += 'The complete dependency hierarchy could not be determined for this repository, so no required '
-                message += 'repositories will not be installed.  This is likely due to invalid repository dependency definitions.  '
-                repository_dependencies_dict = metadata_dict.get('repository_dependencies', None)
+                message += (
+                    "The complete dependency hierarchy could not be determined for this repository, so no required "
+                )
+                message += "repositories will not be installed.  This is likely due to invalid repository dependency definitions.  "
+                repository_dependencies_dict = metadata_dict.get("repository_dependencies", None)
                 if repository_dependencies_dict is not None:
-                    rd_tups = repository_dependencies_dict.get('repository_dependencies', None)
+                    rd_tups = repository_dependencies_dict.get("repository_dependencies", None)
                     if rd_tups is not None:
-                        message += 'Here are the attributes of the dependencies defined for this repository to help determine the '
-                        message += 'cause of this problem.<br/>'
+                        message += "Here are the attributes of the dependencies defined for this repository to help determine the "
+                        message += "cause of this problem.<br/>"
                         message += '<table cellpadding="2" cellspacing="2">'
-                        message += '<tr><th>Tool shed</th><th>Repository name</th><th>Owner</th><th>Changeset revision</th>'
-                        message += '<th>Prior install required</th></tr>'
+                        message += (
+                            "<tr><th>Tool shed</th><th>Repository name</th><th>Owner</th><th>Changeset revision</th>"
+                        )
+                        message += "<th>Prior install required</th></tr>"
                         for rd_tup in rd_tups:
-                            tool_shed, name, owner, changeset_revision, pir, oicct = \
-                                common_util.parse_repository_dependency_tuple(rd_tup)
+                            (
+                                tool_shed,
+                                name,
+                                owner,
+                                changeset_revision,
+                                pir,
+                                oicct,
+                            ) = common_util.parse_repository_dependency_tuple(rd_tup)
                             if util.asbool(pir):
-                                pir_str = 'True'
+                                pir_str = "True"
                             else:
-                                pir_str = ''
-                            message += '<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>' % \
-                                (tool_shed, name, owner, changeset_revision, pir_str)
-                        message += '</table>'
+                                pir_str = ""
+                            message += "<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>" % (
+                                tool_shed,
+                                name,
+                                owner,
+                                changeset_revision,
+                                pir_str,
+                            )
+                        message += "</table>"
         return message
 
     def generate_message_for_invalid_tool_dependencies(self, metadata_dict):
@@ -106,14 +127,14 @@ class DependencyDisplayer:
         retrieves the error message associated with the invalid tool dependency for display in the
         caller.
         """
-        message = ''
+        message = ""
         if metadata_dict:
-            invalid_tool_dependencies = metadata_dict.get('invalid_tool_dependencies', None)
+            invalid_tool_dependencies = metadata_dict.get("invalid_tool_dependencies", None)
             if invalid_tool_dependencies:
                 for requirement_dict in invalid_tool_dependencies.values():
-                    error = requirement_dict.get('error', None)
+                    error = requirement_dict.get("error", None)
                     if error:
-                        message = f'{str(error)}  '
+                        message = f"{str(error)}  "
         return message
 
     def generate_message_for_orphan_tool_dependencies(self, repository, metadata_dict):
@@ -133,41 +154,46 @@ class DependencyDisplayer:
         """
         has_orphan_package_dependencies = False
         has_orphan_set_environment_dependencies = False
-        message = ''
-        package_orphans_str = ''
-        set_environment_orphans_str = ''
+        message = ""
+        package_orphans_str = ""
+        set_environment_orphans_str = ""
         # Tool dependencies are categorized as orphan only if the repository contains tools.
         if metadata_dict:
-            tools = metadata_dict.get('tools', [])
-            tool_dependencies = metadata_dict.get('tool_dependencies', {})
+            tools = metadata_dict.get("tools", [])
+            tool_dependencies = metadata_dict.get("tool_dependencies", {})
             # The use of the orphan_tool_dependencies category in metadata has been deprecated,
             # but we still need to check in case the metadata is out of date.
-            orphan_tool_dependencies = metadata_dict.get('orphan_tool_dependencies', {})
+            orphan_tool_dependencies = metadata_dict.get("orphan_tool_dependencies", {})
             # Updating should cause no problems here since a tool dependency cannot be included
             # in both dictionaries.
             tool_dependencies.update(orphan_tool_dependencies)
             if tool_dependencies and tools:
                 for td_key, requirements_dict in tool_dependencies.items():
-                    if td_key == 'set_environment':
+                    if td_key == "set_environment":
                         # "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}]
                         for env_requirements_dict in requirements_dict:
-                            name = env_requirements_dict['name']
-                            type = env_requirements_dict['type']
+                            name = env_requirements_dict["name"]
+                            type = env_requirements_dict["type"]
                             if self.tool_dependency_is_orphan(type, name, None, tools):
                                 if not has_orphan_set_environment_dependencies:
                                     has_orphan_set_environment_dependencies = True
-                                set_environment_orphans_str += "<b>* name:</b> %s, <b>type:</b> %s<br/>" % \
-                                    (str(name), str(type))
+                                set_environment_orphans_str += "<b>* name:</b> %s, <b>type:</b> %s<br/>" % (
+                                    str(name),
+                                    str(type),
+                                )
                     else:
                         # "R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1"}
-                        name = requirements_dict['name']
-                        type = requirements_dict['type']
-                        version = requirements_dict['version']
+                        name = requirements_dict["name"]
+                        type = requirements_dict["type"]
+                        version = requirements_dict["version"]
                         if self.tool_dependency_is_orphan(type, name, version, tools):
                             if not has_orphan_package_dependencies:
                                 has_orphan_package_dependencies = True
-                            package_orphans_str += "<b>* name:</b> %s, <b>type:</b> %s, <b>version:</b> %s<br/>" % \
-                                (str(name), str(type), str(version))
+                            package_orphans_str += "<b>* name:</b> %s, <b>type:</b> %s, <b>version:</b> %s<br/>" % (
+                                str(name),
+                                str(type),
+                                str(version),
+                            )
         if has_orphan_package_dependencies:
             message += "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a "
             message += "contained tool configuration file's <b>requirement</b> tag does not match "
@@ -193,46 +219,49 @@ class DependencyDisplayer:
             tool_dependencies = {}
             missing_tool_dependencies = {}
             for td_key, val in all_tool_dependencies.items():
-                if td_key in ['set_environment']:
+                if td_key in ["set_environment"]:
                     for index, td_info_dict in enumerate(val):
-                        name = td_info_dict['name']
+                        name = td_info_dict["name"]
                         version = None
-                        type = td_info_dict['type']
-                        tool_dependency = tool_dependency_util.get_tool_dependency_by_name_type_repository(self.app,
-                                                                                                           repository,
-                                                                                                           name,
-                                                                                                           type)
+                        type = td_info_dict["type"]
+                        tool_dependency = tool_dependency_util.get_tool_dependency_by_name_type_repository(
+                            self.app, repository, name, type
+                        )
                         if tool_dependency:
-                            td_info_dict['repository_id'] = repository.id
-                            td_info_dict['tool_dependency_id'] = tool_dependency.id
+                            td_info_dict["repository_id"] = repository.id
+                            td_info_dict["tool_dependency_id"] = tool_dependency.id
                             if tool_dependency.status:
                                 tool_dependency_status = str(tool_dependency.status)
                             else:
-                                tool_dependency_status = 'Never installed'
-                            td_info_dict['status'] = tool_dependency_status
+                                tool_dependency_status = "Never installed"
+                            td_info_dict["status"] = tool_dependency_status
                             val[index] = td_info_dict
-                            if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED:
+                            if (
+                                tool_dependency.status
+                                == self.app.install_model.ToolDependency.installation_status.INSTALLED
+                            ):
                                 tool_dependencies[td_key] = val
                             else:
                                 missing_tool_dependencies[td_key] = val
                 else:
-                    name = val['name']
-                    version = val['version']
-                    type = val['type']
-                    tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository(self.app,
-                                                                                                               repository,
-                                                                                                               name,
-                                                                                                               version,
-                                                                                                               type)
+                    name = val["name"]
+                    version = val["version"]
+                    type = val["type"]
+                    tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository(
+                        self.app, repository, name, version, type
+                    )
                     if tool_dependency:
-                        val['repository_id'] = repository.id
-                        val['tool_dependency_id'] = tool_dependency.id
+                        val["repository_id"] = repository.id
+                        val["tool_dependency_id"] = tool_dependency.id
                         if tool_dependency.status:
                             tool_dependency_status = str(tool_dependency.status)
                         else:
-                            tool_dependency_status = 'Never installed'
-                        val['status'] = tool_dependency_status
-                        if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED:
+                            tool_dependency_status = "Never installed"
+                        val["status"] = tool_dependency_status
+                        if (
+                            tool_dependency.status
+                            == self.app.install_model.ToolDependency.installation_status.INSTALLED
+                        ):
                             tool_dependencies[td_key] = val
                         else:
                             missing_tool_dependencies[td_key] = val
@@ -250,15 +279,17 @@ class DependencyDisplayer:
         they have previously been merged into the installed dependencies.  This method will merge the
         dependencies entries into a single container and return it for display.
         """
-        new_containers_dict = dict(readme_files=None,
-                                   datatypes=None,
-                                   missing_repository_dependencies=None,
-                                   repository_dependencies=None,
-                                   missing_tool_dependencies=None,
-                                   tool_dependencies=None,
-                                   invalid_tools=None,
-                                   valid_tools=None,
-                                   workflows=None)
+        new_containers_dict = dict(
+            readme_files=None,
+            datatypes=None,
+            missing_repository_dependencies=None,
+            repository_dependencies=None,
+            missing_tool_dependencies=None,
+            tool_dependencies=None,
+            invalid_tools=None,
+            valid_tools=None,
+            workflows=None,
+        )
         if containers_dicts:
             lock = threading.Lock()
             lock.acquire(True)
@@ -269,44 +300,49 @@ class DependencyDisplayer:
                 folder_id = 867
                 for old_container_dict in containers_dicts:
                     # Merge repository_dependencies.
-                    old_container_repository_dependencies_root = old_container_dict['repository_dependencies']
+                    old_container_repository_dependencies_root = old_container_dict["repository_dependencies"]
                     if old_container_repository_dependencies_root:
                         if repository_dependencies_root_folder is None:
-                            repository_dependencies_root_folder = utility_container_manager.Folder(id=folder_id,
-                                                                                                   key='root',
-                                                                                                   label='root',
-                                                                                                   parent=None)
+                            repository_dependencies_root_folder = utility_container_manager.Folder(
+                                id=folder_id, key="root", label="root", parent=None
+                            )
                             folder_id += 1
-                            repository_dependencies_folder = utility_container_manager.Folder(id=folder_id,
-                                                                                              key='merged',
-                                                                                              label='Repository dependencies',
-                                                                                              parent=repository_dependencies_root_folder)
+                            repository_dependencies_folder = utility_container_manager.Folder(
+                                id=folder_id,
+                                key="merged",
+                                label="Repository dependencies",
+                                parent=repository_dependencies_root_folder,
+                            )
                             folder_id += 1
                         # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder.
-                        old_container_repository_dependencies_folder = old_container_repository_dependencies_root.folders[0]
+                        old_container_repository_dependencies_folder = (
+                            old_container_repository_dependencies_root.folders[0]
+                        )
                         # Change the folder id so it won't confict with others being merged.
                         old_container_repository_dependencies_folder.id = folder_id
                         folder_id += 1
-                        repository_components_tuple = \
-                            container_util.get_components_from_key(old_container_repository_dependencies_folder.key)
+                        repository_components_tuple = container_util.get_components_from_key(
+                            old_container_repository_dependencies_folder.key
+                        )
                         components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
                         name = components_list[1]
                         # Generate the label by retrieving the repository name.
                         old_container_repository_dependencies_folder.label = str(name)
                         repository_dependencies_folder.folders.append(old_container_repository_dependencies_folder)
                     # Merge tool_dependencies.
-                    old_container_tool_dependencies_root = old_container_dict['tool_dependencies']
+                    old_container_tool_dependencies_root = old_container_dict["tool_dependencies"]
                     if old_container_tool_dependencies_root:
                         if tool_dependencies_root_folder is None:
-                            tool_dependencies_root_folder = utility_container_manager.Folder(id=folder_id,
-                                                                                             key='root',
-                                                                                             label='root',
-                                                                                             parent=None)
+                            tool_dependencies_root_folder = utility_container_manager.Folder(
+                                id=folder_id, key="root", label="root", parent=None
+                            )
                             folder_id += 1
-                            tool_dependencies_folder = utility_container_manager.Folder(id=folder_id,
-                                                                                        key='merged',
-                                                                                        label='Tool dependencies',
-                                                                                        parent=tool_dependencies_root_folder)
+                            tool_dependencies_folder = utility_container_manager.Folder(
+                                id=folder_id,
+                                key="merged",
+                                label="Tool dependencies",
+                                parent=tool_dependencies_root_folder,
+                            )
                             folder_id += 1
                         else:
                             td_list = [td.listify for td in tool_dependencies_folder.tool_dependencies]
@@ -317,10 +353,10 @@ class DependencyDisplayer:
                                     tool_dependencies_folder.tool_dependencies.append(td)
                 if repository_dependencies_root_folder:
                     repository_dependencies_root_folder.folders.append(repository_dependencies_folder)
-                    new_containers_dict['repository_dependencies'] = repository_dependencies_root_folder
+                    new_containers_dict["repository_dependencies"] = repository_dependencies_root_folder
                 if tool_dependencies_root_folder:
                     tool_dependencies_root_folder.folders.append(tool_dependencies_folder)
-                    new_containers_dict['tool_dependencies'] = tool_dependencies_root_folder
+                    new_containers_dict["tool_dependencies"] = tool_dependencies_root_folder
             except Exception as e:
                 log.debug(f"Exception in merge_containers_dicts_for_new_install: {str(e)}")
             finally:
@@ -332,31 +368,31 @@ class DependencyDisplayer:
         Merge the list of missing repository dependencies into the list of installed
         repository dependencies.
         """
-        missing_rd_container_root = containers_dict.get('missing_repository_dependencies', None)
+        missing_rd_container_root = containers_dict.get("missing_repository_dependencies", None)
         if missing_rd_container_root:
             # The missing_rd_container_root will be a root folder containing a single sub_folder.
             missing_rd_container = missing_rd_container_root.folders[0]
-            installed_rd_container_root = containers_dict.get('repository_dependencies', None)
+            installed_rd_container_root = containers_dict.get("repository_dependencies", None)
             # The installed_rd_container_root will be a root folder containing a single sub_folder.
             if installed_rd_container_root:
                 installed_rd_container = installed_rd_container_root.folders[0]
-                installed_rd_container.label = 'Repository dependencies'
+                installed_rd_container.label = "Repository dependencies"
                 for index, rd in enumerate(missing_rd_container.repository_dependencies):
                     # Skip the header row.
                     if index == 0:
                         continue
                     installed_rd_container.repository_dependencies.append(rd)
                 installed_rd_container_root.folders = [installed_rd_container]
-                containers_dict['repository_dependencies'] = installed_rd_container_root
+                containers_dict["repository_dependencies"] = installed_rd_container_root
             else:
                 # Change the folder label from 'Missing repository dependencies' to be
                 # 'Repository dependencies' for display.
-                root_container = containers_dict['missing_repository_dependencies']
+                root_container = containers_dict["missing_repository_dependencies"]
                 for sub_container in root_container.folders:
                     # There should only be 1 sub-folder.
-                    sub_container.label = 'Repository dependencies'
-                containers_dict['repository_dependencies'] = root_container
-        containers_dict['missing_repository_dependencies'] = None
+                    sub_container.label = "Repository dependencies"
+                containers_dict["repository_dependencies"] = root_container
+        containers_dict["missing_repository_dependencies"] = None
         return containers_dict
 
     def merge_missing_tool_dependencies_to_installed_container(self, containers_dict):
@@ -364,65 +400,75 @@ class DependencyDisplayer:
         Merge the list of missing tool dependencies into the list of installed tool
         dependencies.
         """
-        missing_td_container_root = containers_dict.get('missing_tool_dependencies', None)
+        missing_td_container_root = containers_dict.get("missing_tool_dependencies", None)
         if missing_td_container_root:
             # The missing_td_container_root will be a root folder containing a single sub_folder.
             missing_td_container = missing_td_container_root.folders[0]
-            installed_td_container_root = containers_dict.get('tool_dependencies', None)
+            installed_td_container_root = containers_dict.get("tool_dependencies", None)
             # The installed_td_container_root will be a root folder containing a single sub_folder.
             if installed_td_container_root:
                 installed_td_container = installed_td_container_root.folders[0]
-                installed_td_container.label = 'Tool dependencies'
+                installed_td_container.label = "Tool dependencies"
                 for index, td in enumerate(missing_td_container.tool_dependencies):
                     # Skip the header row.
                     if index == 0:
                         continue
                     installed_td_container.tool_dependencies.append(td)
                 installed_td_container_root.folders = [installed_td_container]
-                containers_dict['tool_dependencies'] = installed_td_container_root
+                containers_dict["tool_dependencies"] = installed_td_container_root
             else:
                 # Change the folder label from 'Missing tool dependencies' to be
                 # 'Tool dependencies' for display.
-                root_container = containers_dict['missing_tool_dependencies']
+                root_container = containers_dict["missing_tool_dependencies"]
                 for sub_container in root_container.folders:
                     # There should only be 1 subfolder.
-                    sub_container.label = 'Tool dependencies'
-                containers_dict['tool_dependencies'] = root_container
-        containers_dict['missing_tool_dependencies'] = None
+                    sub_container.label = "Tool dependencies"
+                containers_dict["tool_dependencies"] = root_container
+        containers_dict["missing_tool_dependencies"] = None
         return containers_dict
 
-    def populate_containers_dict_for_new_install(self, tool_shed_url, tool_path, readme_files_dict,
-                                                 installed_repository_dependencies, missing_repository_dependencies,
-                                                 installed_tool_dependencies, missing_tool_dependencies,
-                                                 updating=False):
+    def populate_containers_dict_for_new_install(
+        self,
+        tool_shed_url,
+        tool_path,
+        readme_files_dict,
+        installed_repository_dependencies,
+        missing_repository_dependencies,
+        installed_tool_dependencies,
+        missing_tool_dependencies,
+        updating=False,
+    ):
         """
         Return the populated containers for a repository being installed for the first time
         or for an installed repository that is being updated and the updates include newly
         defined repository (and possibly tool) dependencies.
         """
-        installed_tool_dependencies, missing_tool_dependencies = \
-            self.populate_tool_dependencies_dicts(tool_shed_url=tool_shed_url,
-                                                  tool_path=tool_path,
-                                                  repository_installed_tool_dependencies=installed_tool_dependencies,
-                                                  repository_missing_tool_dependencies=missing_tool_dependencies,
-                                                  required_repo_info_dicts=None)
+        installed_tool_dependencies, missing_tool_dependencies = self.populate_tool_dependencies_dicts(
+            tool_shed_url=tool_shed_url,
+            tool_path=tool_path,
+            repository_installed_tool_dependencies=installed_tool_dependencies,
+            repository_missing_tool_dependencies=missing_tool_dependencies,
+            required_repo_info_dicts=None,
+        )
         # Most of the repository contents are set to None since we don't yet know what they are.
         gucm = GalaxyUtilityContainerManager(self.app)
-        containers_dict = gucm.build_repository_containers(repository=None,
-                                                           datatypes=None,
-                                                           invalid_tools=None,
-                                                           missing_repository_dependencies=missing_repository_dependencies,
-                                                           missing_tool_dependencies=missing_tool_dependencies,
-                                                           readme_files_dict=readme_files_dict,
-                                                           repository_dependencies=installed_repository_dependencies,
-                                                           tool_dependencies=installed_tool_dependencies,
-                                                           valid_tools=None,
-                                                           workflows=None,
-                                                           valid_data_managers=None,
-                                                           invalid_data_managers=None,
-                                                           data_managers_errors=None,
-                                                           new_install=True,
-                                                           reinstalling=False)
+        containers_dict = gucm.build_repository_containers(
+            repository=None,
+            datatypes=None,
+            invalid_tools=None,
+            missing_repository_dependencies=missing_repository_dependencies,
+            missing_tool_dependencies=missing_tool_dependencies,
+            readme_files_dict=readme_files_dict,
+            repository_dependencies=installed_repository_dependencies,
+            tool_dependencies=installed_tool_dependencies,
+            valid_tools=None,
+            workflows=None,
+            valid_data_managers=None,
+            invalid_data_managers=None,
+            data_managers_errors=None,
+            new_install=True,
+            reinstalling=False,
+        )
         if not updating:
             # If we installing a new repository and not updaing an installed repository, we can merge
             # the missing_repository_dependencies container contents to the installed_repository_dependencies
@@ -433,8 +479,9 @@ class DependencyDisplayer:
             containers_dict = self.merge_missing_tool_dependencies_to_installed_container(containers_dict)
         return containers_dict
 
-    def populate_containers_dict_from_repository_metadata(self, tool_shed_url, tool_path, repository, reinstalling=False,
-                                                          required_repo_info_dicts=None):
+    def populate_containers_dict_from_repository_metadata(
+        self, tool_shed_url, tool_path, repository, reinstalling=False, required_repo_info_dicts=None
+    ):
         """
         Retrieve necessary information from the received repository's metadata to populate the
         containers_dict for display.  This method is called only from Galaxy (not the tool shed)
@@ -444,93 +491,116 @@ class DependencyDisplayer:
         metadata = repository.metadata_
         if metadata:
             # Handle proprietary datatypes.
-            datatypes = metadata.get('datatypes', None)
+            datatypes = metadata.get("datatypes", None)
             # Handle invalid tools.
-            invalid_tools = metadata.get('invalid_tools', None)
+            invalid_tools = metadata.get("invalid_tools", None)
             # Handle README files.
             if repository.has_readme_files:
-                if reinstalling or repository.status not in \
-                    [self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED,
-                     self.app.install_model.ToolShedRepository.installation_status.INSTALLED]:
+                if reinstalling or repository.status not in [
+                    self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED,
+                    self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
+                ]:
                     # Since we're reinstalling, we need to send a request to the tool shed to get the README files.
                     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
-                    params = dict(name=str(repository.name),
-                                  owner=str(repository.owner),
-                                  changeset_revision=str(repository.installed_changeset_revision))
-                    pathspec = ['repository', 'get_readme_files']
-                    raw_text = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+                    params = dict(
+                        name=str(repository.name),
+                        owner=str(repository.owner),
+                        changeset_revision=str(repository.installed_changeset_revision),
+                    )
+                    pathspec = ["repository", "get_readme_files"]
+                    raw_text = util.url_get(
+                        tool_shed_url,
+                        auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
+                        pathspec=pathspec,
+                        params=params,
+                    )
                     readme_files_dict = json.loads(raw_text)
                 else:
-                    readme_files_dict = readme_util.build_readme_files_dict(self.app,
-                                                                            repository,
-                                                                            repository.changeset_revision,
-                                                                            repository.metadata_, tool_path)
+                    readme_files_dict = readme_util.build_readme_files_dict(
+                        self.app, repository, repository.changeset_revision, repository.metadata_, tool_path
+                    )
             else:
                 readme_files_dict = None
             # Handle repository dependencies.
-            installed_repository_dependencies, missing_repository_dependencies = \
-                self.app.installed_repository_manager.get_installed_and_missing_repository_dependencies(repository)
+            (
+                installed_repository_dependencies,
+                missing_repository_dependencies,
+            ) = self.app.installed_repository_manager.get_installed_and_missing_repository_dependencies(repository)
             # Handle the current repository's tool dependencies.
-            repository_tool_dependencies = metadata.get('tool_dependencies', None)
+            repository_tool_dependencies = metadata.get("tool_dependencies", None)
             # Make sure to display missing tool dependencies as well.
-            repository_invalid_tool_dependencies = metadata.get('invalid_tool_dependencies', None)
+            repository_invalid_tool_dependencies = metadata.get("invalid_tool_dependencies", None)
             if repository_invalid_tool_dependencies is not None:
                 if repository_tool_dependencies is None:
                     repository_tool_dependencies = {}
                 repository_tool_dependencies.update(repository_invalid_tool_dependencies)
-            repository_installed_tool_dependencies, repository_missing_tool_dependencies = \
-                self.get_installed_and_missing_tool_dependencies_for_installed_repository(repository,
-                                                                                          repository_tool_dependencies)
+            (
+                repository_installed_tool_dependencies,
+                repository_missing_tool_dependencies,
+            ) = self.get_installed_and_missing_tool_dependencies_for_installed_repository(
+                repository, repository_tool_dependencies
+            )
             if reinstalling:
-                installed_tool_dependencies, missing_tool_dependencies = \
-                    self.populate_tool_dependencies_dicts(tool_shed_url,
-                                                          tool_path,
-                                                          repository_installed_tool_dependencies,
-                                                          repository_missing_tool_dependencies,
-                                                          required_repo_info_dicts)
+                installed_tool_dependencies, missing_tool_dependencies = self.populate_tool_dependencies_dicts(
+                    tool_shed_url,
+                    tool_path,
+                    repository_installed_tool_dependencies,
+                    repository_missing_tool_dependencies,
+                    required_repo_info_dicts,
+                )
             else:
                 installed_tool_dependencies = repository_installed_tool_dependencies
                 missing_tool_dependencies = repository_missing_tool_dependencies
             # Handle valid tools.
-            valid_tools = metadata.get('tools', None)
+            valid_tools = metadata.get("tools", None)
             # Handle workflows.
-            workflows = metadata.get('workflows', None)
+            workflows = metadata.get("workflows", None)
             # Handle Data Managers
             valid_data_managers = None
             invalid_data_managers = None
             data_managers_errors = None
-            if 'data_manager' in metadata:
-                valid_data_managers = metadata['data_manager'].get('data_managers', None)
-                invalid_data_managers = metadata['data_manager'].get('invalid_data_managers', None)
-                data_managers_errors = metadata['data_manager'].get('messages', None)
+            if "data_manager" in metadata:
+                valid_data_managers = metadata["data_manager"].get("data_managers", None)
+                invalid_data_managers = metadata["data_manager"].get("invalid_data_managers", None)
+                data_managers_errors = metadata["data_manager"].get("messages", None)
             gucm = GalaxyUtilityContainerManager(self.app)
-            containers_dict = gucm.build_repository_containers(repository=repository,
-                                                               datatypes=datatypes,
-                                                               invalid_tools=invalid_tools,
-                                                               missing_repository_dependencies=missing_repository_dependencies,
-                                                               missing_tool_dependencies=missing_tool_dependencies,
-                                                               readme_files_dict=readme_files_dict,
-                                                               repository_dependencies=installed_repository_dependencies,
-                                                               tool_dependencies=installed_tool_dependencies,
-                                                               valid_tools=valid_tools,
-                                                               workflows=workflows,
-                                                               valid_data_managers=valid_data_managers,
-                                                               invalid_data_managers=invalid_data_managers,
-                                                               data_managers_errors=data_managers_errors,
-                                                               new_install=False,
-                                                               reinstalling=reinstalling)
+            containers_dict = gucm.build_repository_containers(
+                repository=repository,
+                datatypes=datatypes,
+                invalid_tools=invalid_tools,
+                missing_repository_dependencies=missing_repository_dependencies,
+                missing_tool_dependencies=missing_tool_dependencies,
+                readme_files_dict=readme_files_dict,
+                repository_dependencies=installed_repository_dependencies,
+                tool_dependencies=installed_tool_dependencies,
+                valid_tools=valid_tools,
+                workflows=workflows,
+                valid_data_managers=valid_data_managers,
+                invalid_data_managers=invalid_data_managers,
+                data_managers_errors=data_managers_errors,
+                new_install=False,
+                reinstalling=reinstalling,
+            )
         else:
-            containers_dict = dict(datatypes=None,
-                                   invalid_tools=None,
-                                   readme_files_dict=None,
-                                   repository_dependencies=None,
-                                   tool_dependencies=None,
-                                   valid_tools=None,
-                                   workflows=None)
+            containers_dict = dict(
+                datatypes=None,
+                invalid_tools=None,
+                readme_files_dict=None,
+                repository_dependencies=None,
+                tool_dependencies=None,
+                valid_tools=None,
+                workflows=None,
+            )
         return containers_dict
 
-    def populate_tool_dependencies_dicts(self, tool_shed_url, tool_path, repository_installed_tool_dependencies,
-                                         repository_missing_tool_dependencies, required_repo_info_dicts):
+    def populate_tool_dependencies_dicts(
+        self,
+        tool_shed_url,
+        tool_path,
+        repository_installed_tool_dependencies,
+        repository_missing_tool_dependencies,
+        required_repo_info_dicts,
+    ):
         """
         Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries
         for all repositories defined by entries in the received required_repo_info_dicts.
@@ -541,47 +611,63 @@ class DependencyDisplayer:
             repository_installed_tool_dependencies = {}
         else:
             # Add the install_dir attribute to the tool_dependencies.
-            repository_installed_tool_dependencies = \
-                self.add_installation_directories_to_tool_dependencies(repository_installed_tool_dependencies)
+            repository_installed_tool_dependencies = self.add_installation_directories_to_tool_dependencies(
+                repository_installed_tool_dependencies
+            )
         if repository_missing_tool_dependencies is None:
             repository_missing_tool_dependencies = {}
         else:
             # Add the install_dir attribute to the tool_dependencies.
-            repository_missing_tool_dependencies = \
-                self.add_installation_directories_to_tool_dependencies(repository_missing_tool_dependencies)
+            repository_missing_tool_dependencies = self.add_installation_directories_to_tool_dependencies(
+                repository_missing_tool_dependencies
+            )
         if required_repo_info_dicts:
             # Handle the tool dependencies defined for each of the repository's repository dependencies.
             for rid in required_repo_info_dicts:
                 for name, repo_info_tuple in rid.items():
-                    description, repository_clone_url, changeset_revision, \
-                        ctx_rev, repository_owner, repository_dependencies, \
-                        tool_dependencies = \
-                        repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+                    (
+                        description,
+                        repository_clone_url,
+                        changeset_revision,
+                        ctx_rev,
+                        repository_owner,
+                        repository_dependencies,
+                        tool_dependencies,
+                    ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
                     if tool_dependencies:
                         # Add the install_dir attribute to the tool_dependencies.
                         tool_dependencies = self.add_installation_directories_to_tool_dependencies(tool_dependencies)
                         # The required_repository may have been installed with a different changeset revision.
-                        required_repository, installed_changeset_revision = \
-                            repository_util.repository_was_previously_installed(self.app,
-                                                                                tool_shed_url,
-                                                                                name,
-                                                                                repo_info_tuple,
-                                                                                from_tip=False)
+                        (
+                            required_repository,
+                            installed_changeset_revision,
+                        ) = repository_util.repository_was_previously_installed(
+                            self.app, tool_shed_url, name, repo_info_tuple, from_tip=False
+                        )
                         if required_repository:
-                            required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
-                                self.get_installed_and_missing_tool_dependencies_for_installed_repository(required_repository,
-                                                                                                          tool_dependencies)
+                            (
+                                required_repository_installed_tool_dependencies,
+                                required_repository_missing_tool_dependencies,
+                            ) = self.get_installed_and_missing_tool_dependencies_for_installed_repository(
+                                required_repository, tool_dependencies
+                            )
                             if required_repository_installed_tool_dependencies:
                                 # Add the install_dir attribute to the tool_dependencies.
-                                required_repository_installed_tool_dependencies = \
-                                    self.add_installation_directories_to_tool_dependencies(required_repository_installed_tool_dependencies)
+                                required_repository_installed_tool_dependencies = (
+                                    self.add_installation_directories_to_tool_dependencies(
+                                        required_repository_installed_tool_dependencies
+                                    )
+                                )
                                 for td_key, td_dict in required_repository_installed_tool_dependencies.items():
                                     if td_key not in repository_installed_tool_dependencies:
                                         repository_installed_tool_dependencies[td_key] = td_dict
                             if required_repository_missing_tool_dependencies:
                                 # Add the install_dir attribute to the tool_dependencies.
-                                required_repository_missing_tool_dependencies = \
-                                    self.add_installation_directories_to_tool_dependencies(required_repository_missing_tool_dependencies)
+                                required_repository_missing_tool_dependencies = (
+                                    self.add_installation_directories_to_tool_dependencies(
+                                        required_repository_missing_tool_dependencies
+                                    )
+                                )
                                 for td_key, td_dict in required_repository_missing_tool_dependencies.items():
                                     if td_key not in repository_missing_tool_dependencies:
                                         repository_missing_tool_dependencies[td_key] = td_dict
@@ -597,23 +683,23 @@ class DependencyDisplayer:
         tag for at least one tool in the received list of tools.  If not, the tool dependency defined by the
         combination is considered an orphan in its repository in the tool shed.
         """
-        if type == 'package':
+        if type == "package":
             if name and version:
                 for tool_dict in tools:
-                    requirements = tool_dict.get('requirements', [])
+                    requirements = tool_dict.get("requirements", [])
                     for requirement_dict in requirements:
-                        req_name = requirement_dict.get('name', None)
-                        req_version = requirement_dict.get('version', None)
-                        req_type = requirement_dict.get('type', None)
+                        req_name = requirement_dict.get("name", None)
+                        req_version = requirement_dict.get("version", None)
+                        req_type = requirement_dict.get("type", None)
                         if req_name == name and req_version == version and req_type == type:
                             return False
-        elif type == 'set_environment':
+        elif type == "set_environment":
             if name:
                 for tool_dict in tools:
-                    requirements = tool_dict.get('requirements', [])
+                    requirements = tool_dict.get("requirements", [])
                     for requirement_dict in requirements:
-                        req_name = requirement_dict.get('name', None)
-                        req_type = requirement_dict.get('type', None)
+                        req_name = requirement_dict.get("name", None)
+                        req_type = requirement_dict.get("type", None)
                         if req_name == name and req_type == type:
                             return False
         return True
diff --git a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
index d080a795921..3b9e919e6b7 100644
--- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
+++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
@@ -3,7 +3,10 @@ import logging
 from galaxy import util
 from galaxy.model import tool_shed_install
 from galaxy.web import url_for
-from galaxy.web.framework.helpers import grids, iff
+from galaxy.web.framework.helpers import (
+    grids,
+    iff,
+)
 from tool_shed.util import repository_util
 
 log = logging.getLogger(__name__)
@@ -13,7 +16,7 @@ def generate_deprecated_repository_img_str(include_mouse_over=False):
     if include_mouse_over:
         deprecated_tip_str = 'class="icon-button" title="This repository is deprecated in the Tool Shed"'
     else:
-        deprecated_tip_str = ''
+        deprecated_tip_str = ""
     return f"<img src=\"{url_for('/static')}/images/icon_error_sml.gif\" {deprecated_tip_str}/>"
 
 
@@ -21,31 +24,37 @@ def generate_includes_workflows_img_str(include_mouse_over=False):
     if include_mouse_over:
         deprecated_tip_str = 'class="icon-button" title="This repository contains exported workflows"'
     else:
-        deprecated_tip_str = ''
+        deprecated_tip_str = ""
     return f"<img src=\"{url_for('/static')}/images/fugue/gear.png\" {deprecated_tip_str}/>"
 
 
 def generate_latest_revision_img_str(include_mouse_over=False):
     if include_mouse_over:
-        latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"'
+        latest_revision_tip_str = (
+            'class="icon-button" title="This is the latest installable revision of this repository"'
+        )
     else:
-        latest_revision_tip_str = ''
+        latest_revision_tip_str = ""
     return f"<img src=\"{url_for('/static')}/style/ok_small.png\" {latest_revision_tip_str}/>"
 
 
 def generate_revision_updates_img_str(include_mouse_over=False):
     if include_mouse_over:
-        revision_updates_tip_str = 'class="icon-button" title="Updates are available in the Tool Shed for this revision"'
+        revision_updates_tip_str = (
+            'class="icon-button" title="Updates are available in the Tool Shed for this revision"'
+        )
     else:
-        revision_updates_tip_str = ''
+        revision_updates_tip_str = ""
     return f"<img src=\"{url_for('/static')}/images/icon_warning_sml.gif\" {revision_updates_tip_str}/>"
 
 
 def generate_revision_upgrades_img_str(include_mouse_over=False):
     if include_mouse_over:
-        revision_upgrades_tip_str = 'class="icon-button" title="A newer installable revision is available for this repository"'
+        revision_upgrades_tip_str = (
+            'class="icon-button" title="A newer installable revision is available for this repository"'
+        )
     else:
-        revision_upgrades_tip_str = ''
+        revision_upgrades_tip_str = ""
     return f"<img src=\"{url_for('/static')}/images/up.gif\" {revision_upgrades_tip_str}/>"
 
 
@@ -53,17 +62,15 @@ def generate_unknown_img_str(include_mouse_over=False):
     if include_mouse_over:
         unknown_tip_str = 'class="icon-button" title="Unable to get information from the Tool Shed"'
     else:
-        unknown_tip_str = ''
+        unknown_tip_str = ""
     return f"<img src=\"{url_for('/static')}/style/question-octagon-frame.png\" {unknown_tip_str}/>"
 
 
 class InstalledRepositoryGrid(grids.Grid):
-
     class ToolShedStatusColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             if tool_shed_repository.tool_shed_status:
-                tool_shed_status_str = ''
+                tool_shed_status_str = ""
                 if tool_shed_repository.is_deprecated_in_tool_shed:
                     tool_shed_status_str += generate_deprecated_repository_img_str(include_mouse_over=True)
                 if tool_shed_repository.is_latest_installable_revision:
@@ -79,39 +86,32 @@ class InstalledRepositoryGrid(grids.Grid):
             return tool_shed_status_str
 
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             return str(tool_shed_repository.name)
 
     class DescriptionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             return util.unicodify(tool_shed_repository.description)
 
     class OwnerColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             return str(tool_shed_repository.owner)
 
     class RevisionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             return str(tool_shed_repository.changeset_revision)
 
     class StatusColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             return repository_util.get_tool_shed_repository_status_label(trans.app, tool_shed_repository)
 
     class ToolShedColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, tool_shed_repository):
             return tool_shed_repository.tool_shed
 
     class DeletedColumn(grids.DeletedColumn):
-
         def get_accepted_filters(self):
-            """ Returns a list of accepted filters for this column. """
+            """Returns a list of accepted filters for this column."""
             accepted_filter_labels_and_vals = {"Active": "False", "Deactivated or uninstalled": "True", "All": "All"}
             accepted_filters = []
             for label, val in accepted_filter_labels_and_vals.items():
@@ -125,96 +125,119 @@ class InstalledRepositoryGrid(grids.Grid):
     default_sort_key = "name"
     columns = [
         ToolShedStatusColumn(label=""),
-        NameColumn(label="Name",
-                   key="name",
-                   link=(lambda item: iff(item.status in [tool_shed_install.ToolShedRepository.installation_status.CLONING],
-                                          None,
-                                          dict(controller="admin_toolshed", action="manage_repository", id=item.id))),
-                   target="center",
-                   attach_popup=True),
+        NameColumn(
+            label="Name",
+            key="name",
+            link=(
+                lambda item: iff(
+                    item.status in [tool_shed_install.ToolShedRepository.installation_status.CLONING],
+                    None,
+                    dict(controller="admin_toolshed", action="manage_repository", id=item.id),
+                )
+            ),
+            target="center",
+            attach_popup=True,
+        ),
         DescriptionColumn(label="Description"),
         OwnerColumn(label="Owner"),
         RevisionColumn(label="Revision"),
-        StatusColumn(label="Installation Status",
-                     filterable="advanced"),
+        StatusColumn(label="Installation Status", filterable="advanced"),
         ToolShedColumn(label="Tool shed"),
         # Columns that are valid for filtering but are not visible.
-        DeletedColumn(label="Status",
-                      key="deleted",
-                      visible=False,
-                      filterable="advanced")
+        DeletedColumn(label="Status", key="deleted", visible=False, filterable="advanced"),
+    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    operations = [
+        grids.GridOperation(
+            label="Update tool shed status", condition=(lambda item: not item.deleted), allow_multiple=False
+        ),
+        grids.GridOperation(
+            label="Get updates",
+            condition=(
+                lambda item: not item.deleted
+                and item.revision_update_available
+                and item.status
+                not in [
+                    tool_shed_install.ToolShedRepository.installation_status.ERROR,
+                    tool_shed_install.ToolShedRepository.installation_status.NEW,
+                ]
+            ),
+            allow_multiple=False,
+            target="center",
+            url_args=dict(controller="admin_toolshed", action="check_for_updates"),
+        ),
+        grids.GridOperation(
+            label="Install latest revision",
+            condition=(lambda item: item.upgrade_available),
+            allow_multiple=False,
+            target="center",
+            url_args=dict(controller="admin_toolshed", action="install_latest_repository_revision"),
+        ),
+        grids.GridOperation(
+            label="Install",
+            condition=(
+                lambda item: not item.deleted
+                and item.status == tool_shed_install.ToolShedRepository.installation_status.NEW
+            ),
+            allow_multiple=False,
+            target="center",
+            url_args=dict(controller="admin_toolshed", action="manage_repository", operation="install"),
+        ),
+        grids.GridOperation(
+            label="Deactivate or uninstall",
+            condition=(
+                lambda item: not item.deleted
+                and item.status != tool_shed_install.ToolShedRepository.installation_status.NEW
+            ),
+            allow_multiple=True,
+            target="center",
+            url_args=dict(controller="admin_toolshed", action="deactivate_or_uninstall_repository"),
+        ),
+        grids.GridOperation(
+            label="Activate or reinstall",
+            condition=(lambda item: item.deleted),
+            allow_multiple=False,
+            target="center",
+            url_args=dict(controller="admin_toolshed", action="restore_repository"),
+        ),
+        grids.GridOperation(
+            label="Purge",
+            condition=(lambda item: item.is_new),
+            allow_multiple=False,
+            target="center",
+            url_args=dict(controller="admin_toolshed", action="purge_repository"),
+        ),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    operations = [grids.GridOperation(label="Update tool shed status",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False),
-                  grids.GridOperation(label="Get updates",
-                                      condition=(lambda item:
-                                                 not item.deleted
-                                                 and item.revision_update_available
-                                                 and item.status not in [
-                                                     tool_shed_install.ToolShedRepository.installation_status.ERROR,
-                                                     tool_shed_install.ToolShedRepository.installation_status.NEW]),
-                                      allow_multiple=False,
-                                      target="center",
-                                      url_args=dict(controller='admin_toolshed',
-                                                    action='check_for_updates')),
-                  grids.GridOperation(label="Install latest revision",
-                                      condition=(lambda item: item.upgrade_available),
-                                      allow_multiple=False,
-                                      target="center",
-                                      url_args=dict(controller='admin_toolshed',
-                                                    action='install_latest_repository_revision')),
-                  grids.GridOperation(label="Install",
-                                      condition=(lambda item:
-                                                 not item.deleted
-                                                 and item.status == tool_shed_install.ToolShedRepository.installation_status.NEW),
-                                      allow_multiple=False,
-                                      target='center',
-                                      url_args=dict(controller='admin_toolshed',
-                                                    action='manage_repository',
-                                                    operation='install')),
-                  grids.GridOperation(label="Deactivate or uninstall",
-                                      condition=(lambda item:
-                                                 not item.deleted
-                                                 and item.status != tool_shed_install.ToolShedRepository.installation_status.NEW),
-                                      allow_multiple=True,
-                                      target="center",
-                                      url_args=dict(controller='admin_toolshed',
-                                                    action='deactivate_or_uninstall_repository')),
-                  grids.GridOperation(label="Activate or reinstall",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=False,
-                                      target='center',
-                                      url_args=dict(controller='admin_toolshed',
-                                                    action='restore_repository')),
-                  grids.GridOperation(label="Purge",
-                                      condition=(lambda item: item.is_new),
-                                      allow_multiple=False,
-                                      target='center',
-                                      url_args=dict(controller='admin_toolshed',
-                                                    action='purge_repository'))]
     default_filter = dict(deleted="False")
     num_rows_per_page = 50
     use_paging = False
 
     def build_initial_query(self, trans, **kwd):
-        return trans.install_model.context.query(self.model_class) \
-                                          .order_by(self.model_class.table.c.tool_shed,
-                                                    self.model_class.table.c.name,
-                                                    self.model_class.table.c.owner,
-                                                    self.model_class.table.c.ctx_rev)
+        return trans.install_model.context.query(self.model_class).order_by(
+            self.model_class.table.c.tool_shed,
+            self.model_class.table.c.name,
+            self.model_class.table.c.owner,
+            self.model_class.table.c.ctx_rev,
+        )
 
     @property
     def legend(self):
-        legend_str = f'{generate_revision_updates_img_str()}&nbsp;&nbsp;Updates are available in the Tool Shed for this revision<br/>'
-        legend_str += f'{generate_revision_upgrades_img_str()}&nbsp;&nbsp;A newer installable revision is available for this repository<br/>'
-        legend_str += f'{generate_latest_revision_img_str()}&nbsp;&nbsp;This is the latest installable revision of this repository<br/>'
-        legend_str += f'{generate_deprecated_repository_img_str()}&nbsp;&nbsp;This repository is deprecated in the Tool Shed<br/>'
-        legend_str += f'{generate_includes_workflows_img_str()}&nbsp;&nbsp;This repository contains exported workflows<br/>'
-        legend_str += f'{generate_unknown_img_str()}&nbsp;&nbsp;Unable to get information from the Tool Shed<br/>'
+        legend_str = f"{generate_revision_updates_img_str()}&nbsp;&nbsp;Updates are available in the Tool Shed for this revision<br/>"
+        legend_str += f"{generate_revision_upgrades_img_str()}&nbsp;&nbsp;A newer installable revision is available for this repository<br/>"
+        legend_str += f"{generate_latest_revision_img_str()}&nbsp;&nbsp;This is the latest installable revision of this repository<br/>"
+        legend_str += (
+            f"{generate_deprecated_repository_img_str()}&nbsp;&nbsp;This repository is deprecated in the Tool Shed<br/>"
+        )
+        legend_str += (
+            f"{generate_includes_workflows_img_str()}&nbsp;&nbsp;This repository contains exported workflows<br/>"
+        )
+        legend_str += f"{generate_unknown_img_str()}&nbsp;&nbsp;Unable to get information from the Tool Shed<br/>"
         return legend_str
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index da1547cdd80..131d4bb1020 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -7,30 +7,44 @@ log = logging.getLogger(__name__)
 
 
 class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerManager):
-
     def __init__(self, app):
         self.app = app
 
-    def build_repository_containers(self, repository, datatypes, invalid_tools, missing_repository_dependencies,
-                                    missing_tool_dependencies, readme_files_dict, repository_dependencies,
-                                    tool_dependencies, valid_tools, workflows, valid_data_managers,
-                                    invalid_data_managers, data_managers_errors, new_install=False,
-                                    reinstalling=False):
+    def build_repository_containers(
+        self,
+        repository,
+        datatypes,
+        invalid_tools,
+        missing_repository_dependencies,
+        missing_tool_dependencies,
+        readme_files_dict,
+        repository_dependencies,
+        tool_dependencies,
+        valid_tools,
+        workflows,
+        valid_data_managers,
+        invalid_data_managers,
+        data_managers_errors,
+        new_install=False,
+        reinstalling=False,
+    ):
         """
         Return a dictionary of containers for the received repository's dependencies and readme files for
         display during installation to Galaxy.
         """
-        containers_dict = dict(datatypes=None,
-                               invalid_tools=None,
-                               missing_tool_dependencies=None,
-                               readme_files=None,
-                               repository_dependencies=None,
-                               missing_repository_dependencies=None,
-                               tool_dependencies=None,
-                               valid_tools=None,
-                               workflows=None,
-                               valid_data_managers=None,
-                               invalid_data_managers=None)
+        containers_dict = dict(
+            datatypes=None,
+            invalid_tools=None,
+            missing_tool_dependencies=None,
+            readme_files=None,
+            repository_dependencies=None,
+            missing_repository_dependencies=None,
+            tool_dependencies=None,
+            valid_tools=None,
+            workflows=None,
+            valid_data_managers=None,
+            invalid_data_managers=None,
+        )
         # Some of the tool dependency folders will include links to display tool dependency information, and
         # some of these links require the repository id.  However we need to be careful because sometimes the
         # repository object is None.
@@ -47,96 +61,93 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
             # Datatypes container.
             if datatypes:
                 folder_id, datatypes_root_folder = self.build_datatypes_folder(folder_id, datatypes)
-                containers_dict['datatypes'] = datatypes_root_folder
+                containers_dict["datatypes"] = datatypes_root_folder
             # Invalid tools container.
             if invalid_tools:
-                folder_id, invalid_tools_root_folder = \
-                    self.build_invalid_tools_folder(folder_id,
-                                                    invalid_tools,
-                                                    changeset_revision,
-                                                    repository=repository,
-                                                    label='Invalid tools')
-                containers_dict['invalid_tools'] = invalid_tools_root_folder
+                folder_id, invalid_tools_root_folder = self.build_invalid_tools_folder(
+                    folder_id, invalid_tools, changeset_revision, repository=repository, label="Invalid tools"
+                )
+                containers_dict["invalid_tools"] = invalid_tools_root_folder
             # Readme files container.
             if readme_files_dict:
                 folder_id, readme_files_root_folder = self.build_readme_files_folder(folder_id, readme_files_dict)
-                containers_dict['readme_files'] = readme_files_root_folder
+                containers_dict["readme_files"] = readme_files_root_folder
             # Installed repository dependencies container.
             if repository_dependencies:
                 if new_install:
-                    label = 'Repository dependencies'
+                    label = "Repository dependencies"
                 else:
-                    label = 'Installed repository dependencies'
-                folder_id, repository_dependencies_root_folder = \
-                    self.build_repository_dependencies_folder(folder_id=folder_id,
-                                                              repository_dependencies=repository_dependencies,
-                                                              label=label,
-                                                              installed=True)
-                containers_dict['repository_dependencies'] = repository_dependencies_root_folder
+                    label = "Installed repository dependencies"
+                folder_id, repository_dependencies_root_folder = self.build_repository_dependencies_folder(
+                    folder_id=folder_id, repository_dependencies=repository_dependencies, label=label, installed=True
+                )
+                containers_dict["repository_dependencies"] = repository_dependencies_root_folder
             # Missing repository dependencies container.
             if missing_repository_dependencies:
-                folder_id, missing_repository_dependencies_root_folder = \
-                    self.build_repository_dependencies_folder(folder_id=folder_id,
-                                                              repository_dependencies=missing_repository_dependencies,
-                                                              label='Missing repository dependencies',
-                                                              installed=False)
-                containers_dict['missing_repository_dependencies'] = missing_repository_dependencies_root_folder
+                folder_id, missing_repository_dependencies_root_folder = self.build_repository_dependencies_folder(
+                    folder_id=folder_id,
+                    repository_dependencies=missing_repository_dependencies,
+                    label="Missing repository dependencies",
+                    installed=False,
+                )
+                containers_dict["missing_repository_dependencies"] = missing_repository_dependencies_root_folder
             # Installed tool dependencies container.
             if tool_dependencies:
                 if new_install:
-                    label = 'Tool dependencies'
+                    label = "Tool dependencies"
                 else:
-                    label = 'Installed tool dependencies'
+                    label = "Installed tool dependencies"
                 # We only want to display the Status column if the tool_dependency is missing.
-                folder_id, tool_dependencies_root_folder = \
-                    self.build_tool_dependencies_folder(folder_id,
-                                                        tool_dependencies,
-                                                        label=label,
-                                                        missing=False,
-                                                        new_install=new_install,
-                                                        reinstalling=reinstalling)
-                containers_dict['tool_dependencies'] = tool_dependencies_root_folder
+                folder_id, tool_dependencies_root_folder = self.build_tool_dependencies_folder(
+                    folder_id,
+                    tool_dependencies,
+                    label=label,
+                    missing=False,
+                    new_install=new_install,
+                    reinstalling=reinstalling,
+                )
+                containers_dict["tool_dependencies"] = tool_dependencies_root_folder
             # Missing tool dependencies container.
             if missing_tool_dependencies:
                 # We only want to display the Status column if the tool_dependency is missing.
-                folder_id, missing_tool_dependencies_root_folder = \
-                    self.build_tool_dependencies_folder(folder_id,
-                                                        missing_tool_dependencies,
-                                                        label='Missing tool dependencies',
-                                                        missing=True,
-                                                        new_install=new_install,
-                                                        reinstalling=reinstalling)
-                containers_dict['missing_tool_dependencies'] = missing_tool_dependencies_root_folder
+                folder_id, missing_tool_dependencies_root_folder = self.build_tool_dependencies_folder(
+                    folder_id,
+                    missing_tool_dependencies,
+                    label="Missing tool dependencies",
+                    missing=True,
+                    new_install=new_install,
+                    reinstalling=reinstalling,
+                )
+                containers_dict["missing_tool_dependencies"] = missing_tool_dependencies_root_folder
             # Valid tools container.
             if valid_tools:
-                folder_id, valid_tools_root_folder = self.build_tools_folder(folder_id,
-                                                                             valid_tools,
-                                                                             repository,
-                                                                             changeset_revision,
-                                                                             label='Valid tools')
-                containers_dict['valid_tools'] = valid_tools_root_folder
+                folder_id, valid_tools_root_folder = self.build_tools_folder(
+                    folder_id, valid_tools, repository, changeset_revision, label="Valid tools"
+                )
+                containers_dict["valid_tools"] = valid_tools_root_folder
             # Workflows container.
             if workflows:
-                folder_id, workflows_root_folder = \
-                    self.build_workflows_folder(folder_id=folder_id,
-                                                workflows=workflows,
-                                                repository_metadata_id=None,
-                                                repository_id=repository_id,
-                                                label='Workflows')
-                containers_dict['workflows'] = workflows_root_folder
+                folder_id, workflows_root_folder = self.build_workflows_folder(
+                    folder_id=folder_id,
+                    workflows=workflows,
+                    repository_metadata_id=None,
+                    repository_id=repository_id,
+                    label="Workflows",
+                )
+                containers_dict["workflows"] = workflows_root_folder
             if valid_data_managers:
-                folder_id, valid_data_managers_root_folder = \
-                    self.build_data_managers_folder(folder_id=folder_id,
-                                                    data_managers=valid_data_managers,
-                                                    label='Valid Data Managers')
-                containers_dict['valid_data_managers'] = valid_data_managers_root_folder
+                folder_id, valid_data_managers_root_folder = self.build_data_managers_folder(
+                    folder_id=folder_id, data_managers=valid_data_managers, label="Valid Data Managers"
+                )
+                containers_dict["valid_data_managers"] = valid_data_managers_root_folder
             if invalid_data_managers or data_managers_errors:
-                folder_id, invalid_data_managers_root_folder = \
-                    self.build_invalid_data_managers_folder(folder_id=folder_id,
-                                                            data_managers=invalid_data_managers,
-                                                            error_messages=data_managers_errors,
-                                                            label='Invalid Data Managers')
-                containers_dict['invalid_data_managers'] = invalid_data_managers_root_folder
+                folder_id, invalid_data_managers_root_folder = self.build_invalid_data_managers_folder(
+                    folder_id=folder_id,
+                    data_managers=invalid_data_managers,
+                    error_messages=data_managers_errors,
+                    label="Invalid Data Managers",
+                )
+                containers_dict["invalid_data_managers"] = invalid_data_managers_root_folder
         except Exception as e:
             log.debug(f"Exception in build_repository_containers: {str(e)}")
         finally:
diff --git a/lib/tool_shed/grids/admin_grids.py b/lib/tool_shed/grids/admin_grids.py
index 8e3ac87665e..f38378677b3 100644
--- a/lib/tool_shed/grids/admin_grids.py
+++ b/lib/tool_shed/grids/admin_grids.py
@@ -5,7 +5,10 @@ from sqlalchemy import and_
 
 from galaxy.web.framework.helpers import time_ago
 from galaxy.web.legacy_framework import grids
-from tool_shed.grids.repository_grids import CategoryGrid, RepositoryGrid
+from tool_shed.grids.repository_grids import (
+    CategoryGrid,
+    RepositoryGrid,
+)
 from tool_shed.util import hg_util
 from tool_shed.webapp import model
 
@@ -13,49 +16,41 @@ log = logging.getLogger(__name__)
 
 
 class UserGrid(grids.Grid):
-
     class UserLoginColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, user):
             return escape(user.email)
 
     class UserNameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, user):
             if user.username:
                 return escape(user.username)
-            return 'not set'
+            return "not set"
 
     class GroupsColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, user):
             if user.groups:
                 return len(user.groups)
             return 0
 
     class RolesColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, user):
             if user.roles:
                 return len(user.roles)
             return 0
 
     class ExternalColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, user):
             if user.external:
-                return 'yes'
-            return 'no'
+                return "yes"
+            return "no"
 
     class LastLoginColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, user):
             if user.galaxy_sessions:
                 return self.format(user.galaxy_sessions[0].update_time)
-            return 'never'
+            return "never"
 
     class StatusColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, user):
             if user.purged:
                 return "purged"
@@ -64,61 +59,63 @@ class UserGrid(grids.Grid):
             return ""
 
     class EmailColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
-            return query.filter(and_(model.Tool.table.c.user_id == model.User.table.c.id,
-                                     model.User.table.c.email == column_filter))
+            return query.filter(
+                and_(model.Tool.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter)
+            )
 
     title = "Users"
     model_class = model.User
     default_sort_key = "email"
     columns = [
-        UserLoginColumn("Email",
-                        key="email",
-                        link=(lambda item: dict(operation="information", id=item.id)),
-                        attach_popup=True,
-                        filterable="advanced"),
-        UserNameColumn("User Name",
-                       key="username",
-                       attach_popup=False,
-                       filterable="advanced"),
+        UserLoginColumn(
+            "Email",
+            key="email",
+            link=(lambda item: dict(operation="information", id=item.id)),
+            attach_popup=True,
+            filterable="advanced",
+        ),
+        UserNameColumn("User Name", key="username", attach_popup=False, filterable="advanced"),
         GroupsColumn("Groups", attach_popup=False),
         RolesColumn("Roles", attach_popup=False),
         ExternalColumn("External", attach_popup=False),
         LastLoginColumn("Last Login", format=time_ago),
         StatusColumn("Status", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        EmailColumn("Email",
-                    key="email",
-                    visible=False)
-    ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Create new user",
-                         dict(controller='admin', action='users', operation='create'))
+        EmailColumn("Email", key="email", visible=False),
     ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    global_actions = [grids.GridAction("Create new user", dict(controller="admin", action="users", operation="create"))]
     operations = [
-        grids.GridOperation("Manage Roles and Groups",
-                            condition=(lambda item: not item.deleted),
-                            allow_multiple=False,
-                            url_args=dict(action="manage_roles_and_groups_for_user")),
-        grids.GridOperation("Reset Password",
-                            condition=(lambda item: not item.deleted),
-                            allow_multiple=True,
-                            allow_popup=False,
-                            url_args=dict(action="reset_user_password"))
+        grids.GridOperation(
+            "Manage Roles and Groups",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="manage_roles_and_groups_for_user"),
+        ),
+        grids.GridOperation(
+            "Reset Password",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=True,
+            allow_popup=False,
+            url_args=dict(action="reset_user_password"),
+        ),
     ]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True, purged=False)),
         grids.GridColumnFilter("Purged", args=dict(purged=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
 
     use_paging = False
@@ -128,46 +125,39 @@ class UserGrid(grids.Grid):
 
 
 class RoleGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, role):
             return escape(str(role.name))
 
     class DescriptionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, role):
             if role.description:
                 return str(role.description)
-            return ''
+            return ""
 
     class TypeColumn(grids.TextColumn):
         def get_value(self, trans, grid, role):
             return str(role.type)
 
     class StatusColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, role):
             if role.deleted:
                 return "deleted"
             return ""
 
     class GroupsColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, role):
             if role.groups:
                 return len(role.groups)
             return 0
 
     class RepositoriesColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, role):
             if role.repositories:
                 return len(role.repositories)
             return 0
 
     class UsersColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, role):
             if role.users:
                 return len(role.users)
@@ -177,56 +167,59 @@ class RoleGrid(grids.Grid):
     model_class = model.Role
     default_sort_key = "name"
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   link=(lambda item: dict(operation="Manage role associations", id=item.id)),
-                   attach_popup=True,
-                   filterable="advanced"),
-        DescriptionColumn("Description",
-                          key='description',
-                          attach_popup=False,
-                          filterable="advanced"),
+        NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="Manage role associations", id=item.id)),
+            attach_popup=True,
+            filterable="advanced",
+        ),
+        DescriptionColumn("Description", key="description", attach_popup=False, filterable="advanced"),
         GroupsColumn("Groups", attach_popup=False),
         RepositoriesColumn("Repositories", attach_popup=False),
         UsersColumn("Users", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        grids.DeletedColumn("Deleted",
-                            key="deleted",
-                            visible=False,
-                            filterable="advanced")
-    ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Add new role",
-                         dict(controller='admin', action='roles', operation='create'))
+        grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
     ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard"
+        )
+    )
+    global_actions = [grids.GridAction("Add new role", dict(controller="admin", action="roles", operation="create"))]
     # Repository admin roles currently do not have any operations since they are managed automatically based
     # on other events.  For example, if a repository is renamed, its associated admin role is automatically
     # renamed accordingly and if a repository is deleted its associated admin role is automatically deleted.
-    operations = [grids.GridOperation("Rename",
-                                      condition=(lambda item: not item.deleted and not item.is_repository_admin_role),
-                                      allow_multiple=False,
-                                      url_args=dict(action="rename_role")),
-                  grids.GridOperation("Delete",
-                                      condition=(lambda item: not item.deleted and not item.is_repository_admin_role),
-                                      allow_multiple=True,
-                                      url_args=dict(action="mark_role_deleted")),
-                  grids.GridOperation("Undelete",
-                                      condition=(lambda item: item.deleted and not item.is_repository_admin_role),
-                                      allow_multiple=True,
-                                      url_args=dict(action="undelete_role")),
-                  grids.GridOperation("Purge",
-                                      condition=(lambda item: item.deleted and not item.is_repository_admin_role),
-                                      allow_multiple=True,
-                                      url_args=dict(action="purge_role"))]
+    operations = [
+        grids.GridOperation(
+            "Rename",
+            condition=(lambda item: not item.deleted and not item.is_repository_admin_role),
+            allow_multiple=False,
+            url_args=dict(action="rename_role"),
+        ),
+        grids.GridOperation(
+            "Delete",
+            condition=(lambda item: not item.deleted and not item.is_repository_admin_role),
+            allow_multiple=True,
+            url_args=dict(action="mark_role_deleted"),
+        ),
+        grids.GridOperation(
+            "Undelete",
+            condition=(lambda item: item.deleted and not item.is_repository_admin_role),
+            allow_multiple=True,
+            url_args=dict(action="undelete_role"),
+        ),
+        grids.GridOperation(
+            "Purge",
+            condition=(lambda item: item.deleted and not item.is_repository_admin_role),
+            allow_multiple=True,
+            url_args=dict(action="purge_role"),
+        ),
+    ]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
 
     use_paging = False
@@ -236,28 +229,23 @@ class RoleGrid(grids.Grid):
 
 
 class GroupGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, group):
             return str(group.name)
 
     class StatusColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, group):
             if group.deleted:
                 return "deleted"
             return ""
 
     class RolesColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, group):
             if group.roles:
                 return len(group.roles)
             return 0
 
     class UsersColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, group):
             if group.users:
                 return len(group.users)
@@ -267,48 +255,51 @@ class GroupGrid(grids.Grid):
     model_class = model.Group
     default_sort_key = "name"
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   link=(lambda item: dict(operation="Manage users and roles", id=item.id)),
-                   attach_popup=True),
+        NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="Manage users and roles", id=item.id)),
+            attach_popup=True,
+        ),
         UsersColumn("Users", attach_popup=False),
         RolesColumn("Roles", attach_popup=False),
         StatusColumn("Status", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        grids.DeletedColumn("Deleted",
-                            key="deleted",
-                            visible=False,
-                            filterable="advanced")
+        grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    global_actions = [
-        grids.GridAction("Add new group",
-                         dict(controller='admin', action='groups', operation='create'))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard"
+        )
+    )
+    global_actions = [grids.GridAction("Add new group", dict(controller="admin", action="groups", operation="create"))]
+    operations = [
+        grids.GridOperation(
+            "Rename",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=False,
+            url_args=dict(action="rename_group"),
+        ),
+        grids.GridOperation(
+            "Delete",
+            condition=(lambda item: not item.deleted),
+            allow_multiple=True,
+            url_args=dict(action="mark_group_deleted"),
+        ),
+        grids.GridOperation(
+            "Undelete",
+            condition=(lambda item: item.deleted),
+            allow_multiple=True,
+            url_args=dict(action="undelete_group"),
+        ),
+        grids.GridOperation(
+            "Purge", condition=(lambda item: item.deleted), allow_multiple=True, url_args=dict(action="purge_group")
+        ),
     ]
-    operations = [grids.GridOperation("Rename",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=False,
-                                      url_args=dict(action="rename_group")),
-                  grids.GridOperation("Delete",
-                                      condition=(lambda item: not item.deleted),
-                                      allow_multiple=True,
-                                      url_args=dict(action="mark_group_deleted")),
-                  grids.GridOperation("Undelete",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True,
-                                      url_args=dict(action="undelete_group")),
-                  grids.GridOperation("Purge",
-                                      condition=(lambda item: item.deleted),
-                                      allow_multiple=True,
-                                      url_args=dict(action="purge_group"))]
     standard_filters = [
         grids.GridColumnFilter("Active", args=dict(deleted=False)),
         grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
-        grids.GridColumnFilter("All", args=dict(deleted='All'))
+        grids.GridColumnFilter("All", args=dict(deleted="All")),
     ]
 
     use_paging = False
@@ -317,122 +308,122 @@ class GroupGrid(grids.Grid):
 class ManageCategoryGrid(CategoryGrid):
     columns = [col for col in CategoryGrid.columns]
     # Override the NameColumn to include an Edit link
-    columns[0] = CategoryGrid.NameColumn("Name",
-                                         key="Category.name",
-                                         link=(lambda item: dict(operation="Edit", id=item.id)),
-                                         model_class=model.Category,
-                                         attach_popup=False)
+    columns[0] = CategoryGrid.NameColumn(
+        "Name",
+        key="Category.name",
+        link=(lambda item: dict(operation="Edit", id=item.id)),
+        model_class=model.Category,
+        attach_popup=False,
+    )
     global_actions = [
-        grids.GridAction("Add new category",
-                         dict(controller='admin', action='manage_categories', operation='create'))
+        grids.GridAction("Add new category", dict(controller="admin", action="manage_categories", operation="create"))
     ]
 
 
 class AdminRepositoryGrid(RepositoryGrid):
-
     class DeletedColumn(grids.BooleanColumn):
-
         def get_value(self, trans, grid, repository):
             if repository.deleted:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
-    columns = [RepositoryGrid.NameColumn("Name",
-                                         key="name",
-                                         link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                         attach_popup=True),
-               RepositoryGrid.HeadsColumn("Heads"),
-               RepositoryGrid.UserColumn("Owner",
-                                         model_class=model.User,
-                                         link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                                         attach_popup=False,
-                                         key="User.username"),
-               RepositoryGrid.DeprecatedColumn("Deprecated", key="deprecated", attach_popup=False),
-               # Columns that are valid for filtering but are not visible.
-               DeletedColumn("Deleted", key="deleted", attach_popup=False)]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns = [
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        RepositoryGrid.HeadsColumn("Heads"),
+        RepositoryGrid.UserColumn(
+            "Owner",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+            key="User.username",
+        ),
+        RepositoryGrid.DeprecatedColumn("Deprecated", key="deprecated", attach_popup=False),
+        # Columns that are valid for filtering but are not visible.
+        DeletedColumn("Deleted", key="deleted", attach_popup=False),
+    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
     operations = [operation for operation in RepositoryGrid.operations]
-    operations.append(grids.GridOperation("Delete",
-                                          allow_multiple=False,
-                                          condition=(lambda item: not item.deleted),
-                                          async_compatible=False))
-    operations.append(grids.GridOperation("Undelete",
-                                          allow_multiple=False,
-                                          condition=(lambda item: item.deleted),
-                                          async_compatible=False))
+    operations.append(
+        grids.GridOperation(
+            "Delete", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False
+        )
+    )
+    operations.append(
+        grids.GridOperation(
+            "Undelete", allow_multiple=False, condition=(lambda item: item.deleted), async_compatible=False
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .join(model.User.table)
+        return trans.sa_session.query(model.Repository).join(model.User.table)
 
 
 class RepositoryMetadataGrid(grids.Grid):
-
     class IdColumn(grids.IntegerColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             return repository_metadata.id
 
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             return escape(repository_metadata.repository.name)
 
     class OwnerColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             return escape(repository_metadata.repository.user.username)
 
     class RevisionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             repository = repository_metadata.repository
-            return hg_util.get_revision_label(trans.app,
-                                              repository,
-                                              repository_metadata.changeset_revision,
-                                              include_date=True,
-                                              include_hash=True)
+            return hg_util.get_revision_label(
+                trans.app, repository, repository_metadata.changeset_revision, include_date=True, include_hash=True
+            )
 
     class ToolsColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
-            tools_str = '0'
+            tools_str = "0"
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'tools' in metadata:
+                    if "tools" in metadata:
                         # We used to display the following, but grid was too cluttered.
                         # for tool_metadata_dict in metadata[ 'tools' ]:
                         #    tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] )
-                        return '%d' % len(metadata['tools'])
+                        return "%d" % len(metadata["tools"])
             return tools_str
 
     class DatatypesColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
-            datatypes_str = '0'
+            datatypes_str = "0"
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'datatypes' in metadata:
+                    if "datatypes" in metadata:
                         # We used to display the following, but grid was too cluttered.
                         # for datatype_metadata_dict in metadata[ 'datatypes' ]:
                         #    datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ]
-                        return '%d' % len(metadata['datatypes'])
+                        return "%d" % len(metadata["datatypes"])
             return datatypes_str
 
     class WorkflowsColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
-            workflows_str = '0'
+            workflows_str = "0"
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'workflows' in metadata:
+                    if "workflows" in metadata:
                         # We used to display the following, but grid was too cluttered.
                         # workflows_str += '<b>Workflows:</b><br/>'
                         # metadata[ 'workflows' ] is a list of tuples where each contained tuple is
@@ -441,29 +432,26 @@ class RepositoryMetadataGrid(grids.Grid):
                         # workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ]
                         # for workflow_metadata_dict in workflow_metadata_dicts:
                         #    workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ]
-                        return '%d' % len(metadata['workflows'])
+                        return "%d" % len(metadata["workflows"])
             return workflows_str
 
     class DeletedColumn(grids.BooleanColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.repository.deleted:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class DeprecatedColumn(grids.BooleanColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.repository.deprecated:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class MaliciousColumn(grids.BooleanColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.malicious:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     # Grid definition
     title = "Repository Metadata"
@@ -471,14 +459,14 @@ class RepositoryMetadataGrid(grids.Grid):
     default_sort_key = "name"
     use_hide_message = False
     columns = [
-        IdColumn("Id",
-                 visible=False,
-                 attach_popup=False),
-        NameColumn("Name",
-                   key="name",
-                   model_class=model.Repository,
-                   link=(lambda item: dict(operation="view_or_manage_repository_revision", id=item.id)),
-                   attach_popup=True),
+        IdColumn("Id", visible=False, attach_popup=False),
+        NameColumn(
+            "Name",
+            key="name",
+            model_class=model.Repository,
+            link=(lambda item: dict(operation="view_or_manage_repository_revision", id=item.id)),
+            attach_popup=True,
+        ),
         OwnerColumn("Owner", attach_popup=False),
         RevisionColumn("Revision", attach_popup=False),
         ToolsColumn("Tools", attach_popup=False),
@@ -486,19 +474,26 @@ class RepositoryMetadataGrid(grids.Grid):
         WorkflowsColumn("Workflows", attach_popup=False),
         DeletedColumn("Deleted", attach_popup=False),
         DeprecatedColumn("Deprecated", attach_popup=False),
-        MaliciousColumn("Malicious", attach_popup=False)
+        MaliciousColumn("Malicious", attach_popup=False),
+    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    operations = [
+        grids.GridOperation(
+            "Delete",
+            allow_multiple=False,
+            allow_popup=True,
+            async_compatible=False,
+            confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items.",
+        )
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    operations = [grids.GridOperation("Delete",
-                                      allow_multiple=False,
-                                      allow_popup=True,
-                                      async_compatible=False,
-                                      confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items.")]
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .join(model.Repository.table)
+        return trans.sa_session.query(model.RepositoryMetadata).join(model.Repository.table)
diff --git a/lib/tool_shed/grids/repository_grid_filter_manager.py b/lib/tool_shed/grids/repository_grid_filter_manager.py
index 5b07feb863e..74620883647 100644
--- a/lib/tool_shed/grids/repository_grid_filter_manager.py
+++ b/lib/tool_shed/grids/repository_grid_filter_manager.py
@@ -8,13 +8,15 @@ log = logging.getLogger(__name__)
 class RepositoryGridFilterManager:
     """Provides filtered views of the many Tool SHed repository grids."""
 
-    filters = Bunch(CERTIFIED_LEVEL_ONE='certified_level_one',
-                    CERTIFIED_LEVEL_TWO='certified_level_two',
-                    CERTIFIED_LEVEL_ONE_SUITES='certified_level_one_suites',
-                    CERTIFIED_LEVEL_TWO_SUITES='certified_level_two_suites',
-                    SUITES='suites')
+    filters = Bunch(
+        CERTIFIED_LEVEL_ONE="certified_level_one",
+        CERTIFIED_LEVEL_TWO="certified_level_two",
+        CERTIFIED_LEVEL_ONE_SUITES="certified_level_one_suites",
+        CERTIFIED_LEVEL_TWO_SUITES="certified_level_two_suites",
+        SUITES="suites",
+    )
 
-    def get_grid_title(self, trans, trailing_string='', default=''):
+    def get_grid_title(self, trans, trailing_string="", default=""):
         filter = self.get_filter(trans)
         if filter == self.filters.CERTIFIED_LEVEL_ONE:
             return f"Certified 1 Repositories {trailing_string}"
@@ -29,7 +31,7 @@ class RepositoryGridFilterManager:
         return f"{default} {trailing_string}"
 
     def get_filter(self, trans):
-        filter = trans.get_cookie(name='toolshedrepogridfilter')
+        filter = trans.get_cookie(name="toolshedrepogridfilter")
         return filter or None
 
     def is_valid_filter(self, filter):
@@ -42,8 +44,8 @@ class RepositoryGridFilterManager:
 
     def set_filter(self, trans, **kwd):
         # Set a session cookie value with the selected filter.
-        filter = kwd.get('filter', None)
+        filter = kwd.get("filter", None)
         if filter is not None and self.is_valid_filter(filter):
-            trans.set_cookie(value=filter, name='toolshedrepogridfilter')
+            trans.set_cookie(value=filter, name="toolshedrepogridfilter")
         # if the filter is not valid, expire the cookie.
-        trans.set_cookie(value=filter, name='toolshedrepogridfilter', age=-1)
+        trans.set_cookie(value=filter, name="toolshedrepogridfilter", age=-1)
diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index 501e6e8cb33..017cbb56440 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -2,22 +2,29 @@ import json
 import logging
 
 from markupsafe import escape as escape_html
-from sqlalchemy import and_, false, or_, true
+from sqlalchemy import (
+    and_,
+    false,
+    or_,
+    true,
+)
 
 import tool_shed.grids.util as grids_util
 import tool_shed.repository_types.util as rt_util
 import tool_shed.util.shed_util_common as suc
 from galaxy.web.legacy_framework import grids
-from tool_shed.util import hg_util, metadata_util, repository_util
+from tool_shed.util import (
+    hg_util,
+    metadata_util,
+    repository_util,
+)
 from tool_shed.webapp import model
 
 log = logging.getLogger(__name__)
 
 
 class CategoryGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, category):
             return category.name
 
@@ -26,14 +33,19 @@ class CategoryGrid(grids.Grid):
             return category.description
 
     class RepositoriesColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, category):
             category_name = str(category.name)
             filter = trans.app.repository_grid_filter_manager.get_filter(trans)
             if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
-                return trans.app.repository_registry.certified_level_one_viewable_repositories_and_suites_by_category.get(category_name, 0)
+                return (
+                    trans.app.repository_registry.certified_level_one_viewable_repositories_and_suites_by_category.get(
+                        category_name, 0
+                    )
+                )
             elif filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
-                return trans.app.repository_registry.certified_level_one_viewable_suites_by_category.get(category_name, 0)
+                return trans.app.repository_registry.certified_level_one_viewable_suites_by_category.get(
+                    category_name, 0
+                )
             elif filter == trans.app.repository_grid_filter_manager.filters.SUITES:
                 return trans.app.repository_registry.viewable_suites_by_category.get(category_name, 0)
             else:
@@ -42,39 +54,33 @@ class CategoryGrid(grids.Grid):
 
     title = "Categories"
     model_class = model.Category
-    template = '/webapps/tool_shed/category/grid.mako'
+    template = "/webapps/tool_shed/category/grid.mako"
     default_sort_key = "name"
     columns = [
-        NameColumn("Name",
-                   key="Category.name",
-                   link=(lambda item: dict(operation="repositories_by_category", id=item.id)),
-                   attach_popup=False),
-        DescriptionColumn("Description",
-                          key="Category.description",
-                          attach_popup=False),
-        RepositoriesColumn("Repositories",
-                           model_class=model.Repository,
-                           attach_popup=False)
+        NameColumn(
+            "Name",
+            key="Category.name",
+            link=(lambda item: dict(operation="repositories_by_category", id=item.id)),
+            attach_popup=False,
+        ),
+        DescriptionColumn("Description", key="Category.description", attach_popup=False),
+        RepositoriesColumn("Repositories", model_class=model.Repository, attach_popup=False),
     ]
     # Override these
     num_rows_per_page = 50
 
 
 class RepositoryGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
             return escape_html(repository.name)
 
     class TypeColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
             type_class = repository.get_type_class(trans.app)
             return escape_html(type_class.label)
 
     class HeadsColumn(grids.GridColumn):
-
         def __init__(self, col_name):
             grids.GridColumn.__init__(self, col_name)
 
@@ -86,16 +92,15 @@ class RepositoryGrid(grids.Grid):
             if multiple_heads:
                 heads_str = '<font color="red">'
             else:
-                heads_str = ''
+                heads_str = ""
             for ctx in heads:
-                heads_str += f'{hg_util.get_revision_label_from_ctx(ctx, include_date=True)}<br/>'
-            heads_str.rstrip('<br/>')
+                heads_str += f"{hg_util.get_revision_label_from_ctx(ctx, include_date=True)}<br/>"
+            heads_str.rstrip("<br/>")
             if multiple_heads:
-                heads_str += '</font>'
+                heads_str += "</font>"
             return heads_str
 
     class MetadataRevisionColumn(grids.GridColumn):
-
         def __init__(self, col_name):
             grids.GridColumn.__init__(self, col_name)
 
@@ -111,13 +116,12 @@ class RepositoryGrid(grids.Grid):
                 return tmpl
             elif len(select_field.options) == 1:
                 option_items = select_field.options[0][0]
-                rev_label, rev_date = option_items.split(' ')
+                rev_label, rev_date = option_items.split(" ")
                 rev_date = f'<i><font color="#666666">{rev_date}</font></i>'
-                return f'{rev_label} {rev_date}'
-            return ''
+                return f"{rev_label} {rev_date}"
+            return ""
 
     class LatestInstallableRevisionColumn(grids.GridColumn):
-
         def __init__(self, col_name):
             grids.GridColumn.__init__(self, col_name)
 
@@ -126,10 +130,9 @@ class RepositoryGrid(grids.Grid):
             select_field = grids_util.build_changeset_revision_select_field(trans, repository, downloadable=False)
             if select_field.options:
                 return select_field.options[0][0]
-            return ''
+            return ""
 
     class TipRevisionColumn(grids.GridColumn):
-
         def __init__(self, col_name):
             grids.GridColumn.__init__(self, col_name)
 
@@ -138,25 +141,24 @@ class RepositoryGrid(grids.Grid):
             return escape_html(repository.revision())
 
     class DescriptionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
             return escape_html(repository.description)
 
     class CategoryColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
-            rval = '<ul>'
+            rval = "<ul>"
             if repository.categories:
                 for rca in repository.categories:
-                    rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' \
-                        % (trans.security.encode_id(rca.category.id), rca.category.name)
+                    rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' % (
+                        trans.security.encode_id(rca.category.id),
+                        rca.category.name,
+                    )
             else:
-                rval += '<li>not set</li>'
-            rval += '</ul>'
+                rval += "<li>not set</li>"
+            rval += "</ul>"
             return rval
 
     class RepositoryCategoryColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
             """Modify query to filter by category."""
             if column_filter == "All":
@@ -164,68 +166,67 @@ class RepositoryGrid(grids.Grid):
             return query.filter(model.Category.name == column_filter)
 
     class UserColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
             if repository.user:
                 return escape_html(repository.user.username)
-            return 'no user'
+            return "no user"
 
     class EmailColumn(grids.TextColumn):
-
         def filter(self, trans, user, query, column_filter):
-            if column_filter == 'All':
+            if column_filter == "All":
                 return query
-            return query.filter(and_(model.Repository.table.c.user_id == model.User.table.c.id,
-                                     model.User.table.c.email == column_filter))
+            return query.filter(
+                and_(
+                    model.Repository.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter
+                )
+            )
 
     class EmailAlertsColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
             if trans.user and repository.email_alerts and trans.user.email in json.loads(repository.email_alerts):
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class DeprecatedColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
             if repository.deprecated:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     title = "Repositories"
     model_class = model.Repository
     default_sort_key = "name"
     use_hide_message = False
     columns = [
-        NameColumn("Name",
-                   key="name",
-                   link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                   attach_popup=False),
-        DescriptionColumn("Synopsis",
-                          key="description",
-                          attach_popup=False),
+        NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
+        DescriptionColumn("Synopsis", key="description", attach_popup=False),
         TypeColumn("Type"),
         MetadataRevisionColumn("Metadata<br/>Revisions"),
-        UserColumn("Owner",
-                   model_class=model.User,
-                   link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                   attach_popup=False,
-                   key="User.username"),
+        UserColumn(
+            "Owner",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+            key="User.username",
+        ),
         # Columns that are valid for filtering but are not visible.
-        EmailColumn("Email",
-                    model_class=model.User,
-                    key="email",
-                    visible=False),
-        RepositoryCategoryColumn("Category",
-                                 model_class=model.Category,
-                                 key="Category.name",
-                                 visible=False)
+        EmailColumn("Email", model_class=model.User, key="email", visible=False),
+        RepositoryCategoryColumn("Category", model_class=model.Category, key="Category.name", visible=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
     default_filter = dict(deleted="False")
     num_rows_per_page = 50
     use_paging = True
@@ -234,44 +235,53 @@ class RepositoryGrid(grids.Grid):
     def build_initial_query(self, trans, **kwd):
         filter = trans.app.repository_grid_filter_manager.get_filter(trans)
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
-            return trans.sa_session.query(model.Repository) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
         else:
             # The filter is None.
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deleted == false(),
-                                                model.Repository.table.c.deprecated == false())) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
+                )
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
 
 
 class DockerImageGrid(RepositoryGrid):
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
-        RepositoryGrid.DescriptionColumn("Synopsis",
-                                         key="description",
-                                         attach_popup=False),
-        RepositoryGrid.UserColumn("Owner",
-                                  model_class=model.User,
-                                  link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                                  attach_popup=False,
-                                  key="User.username"),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
+        RepositoryGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
+        RepositoryGrid.UserColumn(
+            "Owner",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+            key="User.username",
+        ),
         RepositoryGrid.EmailAlertsColumn("Alert", attach_popup=False),
     ]
     operations = [grids.GridOperation("Include in Docker image", allow_multiple=True)]
@@ -280,28 +290,27 @@ class DockerImageGrid(RepositoryGrid):
 
 class EmailAlertsRepositoryGrid(RepositoryGrid):
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
-        RepositoryGrid.DescriptionColumn("Synopsis",
-                                         key="description",
-                                         attach_popup=False),
-        RepositoryGrid.UserColumn("Owner",
-                                  model_class=model.User,
-                                  link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                                  attach_popup=False,
-                                  key="User.username"),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
+        RepositoryGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
+        RepositoryGrid.UserColumn(
+            "Owner",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+            key="User.username",
+        ),
         RepositoryGrid.EmailAlertsColumn("Alert", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        grids.DeletedColumn("Deleted",
-                            key="deleted",
-                            visible=False,
-                            filterable="advanced")
+        grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
     ]
     operations = [grids.GridOperation("Receive email alerts", allow_multiple=True)]
     global_actions = [
-        grids.GridAction("User preferences", dict(controller='user', action='index', cntrller='repository'))
+        grids.GridAction("User preferences", dict(controller="user", action="index", cntrller="repository"))
     ]
 
 
@@ -309,26 +318,22 @@ class MatchedRepositoryGrid(grids.Grid):
     # This grid filters out repositories that have been marked as deleted or deprecated.
 
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             return escape_html(repository_metadata.repository.name)
 
     class DescriptionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             return escape_html(repository_metadata.repository.description)
 
     class RevisionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             return repository_metadata.changeset_revision
 
     class UserColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.repository.user:
                 return escape_html(repository_metadata.repository.user.username)
-            return 'no user'
+            return "no user"
 
     # Grid definition
     title = "Matching repositories"
@@ -336,273 +341,328 @@ class MatchedRepositoryGrid(grids.Grid):
     default_sort_key = "Repository.name"
     use_hide_message = False
     columns = [
-        NameColumn("Repository name",
-                   link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                   attach_popup=True),
-        DescriptionColumn("Synopsis",
-                          attach_popup=False),
+        NameColumn(
+            "Repository name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        DescriptionColumn("Synopsis", attach_popup=False),
         RevisionColumn("Revision"),
-        UserColumn("Owner",
-                   model_class=model.User,
-                   attach_popup=False)
+        UserColumn("Owner", model_class=model.User, attach_popup=False),
     ]
     operations = [grids.GridOperation("Install to Galaxy", allow_multiple=True)]
     num_rows_per_page = 50
     use_paging = False
 
     def build_initial_query(self, trans, **kwd):
-        match_tuples = kwd.get('match_tuples', [])
+        match_tuples = kwd.get("match_tuples", [])
         clause_list = []
         if match_tuples:
             for match_tuple in match_tuples:
                 repository_id, changeset_revision = match_tuple
-                clause_list.append(and_(
-                    model.RepositoryMetadata.repository_id == int(repository_id),
-                    model.RepositoryMetadata.changeset_revision == changeset_revision))
-            return trans.sa_session.query(model.RepositoryMetadata) \
-                                   .join(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deleted == false(),
-                                                model.Repository.table.c.deprecated == false())) \
-                                   .join(model.User.table) \
-                                   .filter(or_(*clause_list)) \
-                                   .order_by(model.Repository.name)
+                clause_list.append(
+                    and_(
+                        model.RepositoryMetadata.repository_id == int(repository_id),
+                        model.RepositoryMetadata.changeset_revision == changeset_revision,
+                    )
+                )
+            return (
+                trans.sa_session.query(model.RepositoryMetadata)
+                .join(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
+                )
+                .join(model.User.table)
+                .filter(or_(*clause_list))
+                .order_by(model.Repository.name)
+            )
         # Return an empty query
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .filter(model.RepositoryMetadata.id < 0)
+        return trans.sa_session.query(model.RepositoryMetadata).filter(model.RepositoryMetadata.id < 0)
 
 
 class InstallMatchedRepositoryGrid(MatchedRepositoryGrid):
     columns = [col for col in MatchedRepositoryGrid.columns]
     # Override the NameColumn
-    columns[0] = MatchedRepositoryGrid.NameColumn("Name",
-                                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                  attach_popup=False)
+    columns[0] = MatchedRepositoryGrid.NameColumn(
+        "Name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=False
+    )
 
 
 class MyWritableRepositoriesGrid(RepositoryGrid):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
-    title = 'Repositories I can change'
+    title = "Repositories I can change"
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryGrid.TypeColumn("Type"),
         RepositoryGrid.MetadataRevisionColumn("Metadata<br/>Revisions"),
-        RepositoryGrid.UserColumn("Owner",
-                                  model_class=model.User,
-                                  link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                                  attach_popup=False,
-                                  key="User.username")
+        RepositoryGrid.UserColumn(
+            "Owner",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+            key="User.username",
+        ),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
         # TODO: improve performance by adding a db table associating users with repositories for which they have write access.
         username = trans.user.username
         clause_list = []
-        for repository in trans.sa_session.query(model.Repository) \
-                                          .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                       model.Repository.table.c.deleted == false())):
+        for repository in trans.sa_session.query(model.Repository).filter(
+            and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+        ):
             allow_push = repository.allow_push()
             if allow_push:
-                allow_push_usernames = allow_push.split(',')
+                allow_push_usernames = allow_push.split(",")
                 if username in allow_push_usernames:
                     clause_list.append(model.Repository.table.c.id == repository.id)
         if clause_list:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(or_(*clause_list)) \
-                                   .join(model.User.table)
+            return trans.sa_session.query(model.Repository).filter(or_(*clause_list)).join(model.User.table)
         # Return an empty query.
-        return trans.sa_session.query(model.Repository) \
-                               .filter(model.Repository.table.c.id < 0)
+        return trans.sa_session.query(model.Repository).filter(model.Repository.table.c.id < 0)
 
 
 class RepositoriesByUserGrid(RepositoryGrid):
     title = "Repositories by user"
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
-        RepositoryGrid.DescriptionColumn("Synopsis",
-                                         key="description",
-                                         attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
+        RepositoryGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
         RepositoryGrid.TypeColumn("Type"),
         RepositoryGrid.MetadataRevisionColumn("Metadata<br/>Revisions"),
-        RepositoryGrid.CategoryColumn("Category",
-                                      model_class=model.Category,
-                                      key="Category.name",
-                                      attach_popup=False)
+        RepositoryGrid.CategoryColumn("Category", model_class=model.Category, key="Category.name", attach_popup=False),
     ]
     default_filter = dict(deleted="False")
 
     def build_initial_query(self, trans, **kwd):
-        decoded_user_id = trans.security.decode_id(kwd['user_id'])
+        decoded_user_id = trans.security.decode_id(kwd["user_id"])
         filter = trans.app.repository_grid_filter_manager.get_filter(trans)
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(model.Repository.table.c.user_id == decoded_user_id) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(model.Repository.table.c.user_id == decoded_user_id)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION,
-                                                model.Repository.table.c.user_id == decoded_user_id)) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(
+                        model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION,
+                        model.Repository.table.c.user_id == decoded_user_id,
+                    )
+                )
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
         else:
             # The value of filter is None.
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deleted == false(),
-                                                model.Repository.table.c.deprecated == false(),
-                                                model.Repository.table.c.user_id == decoded_user_id)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(
+                        model.Repository.table.c.deleted == false(),
+                        model.Repository.table.c.deprecated == false(),
+                        model.Repository.table.c.user_id == decoded_user_id,
+                    )
+                )
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
 
 
 class RepositoriesInCategoryGrid(RepositoryGrid):
     title = "Category"
 
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(controller="repository", operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
-        RepositoryGrid.DescriptionColumn("Synopsis",
-                                         key="description",
-                                         attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(controller="repository", operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
+        RepositoryGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
         RepositoryGrid.TypeColumn("Type"),
         RepositoryGrid.MetadataRevisionColumn("Metadata<br/>Revisions"),
-        RepositoryGrid.UserColumn("Owner",
-                                  model_class=model.User,
-                                  link=(lambda item: dict(controller="repository", operation="repositories_by_user", id=item.id)),
-                                  attach_popup=False,
-                                  key="User.username"),
+        RepositoryGrid.UserColumn(
+            "Owner",
+            model_class=model.User,
+            link=(lambda item: dict(controller="repository", operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+            key="User.username",
+        ),
         # Columns that are valid for filtering but are not visible.
-        RepositoryGrid.EmailColumn("Email",
-                                   model_class=model.User,
-                                   key="email",
-                                   visible=False)
+        RepositoryGrid.EmailColumn("Email", model_class=model.User, key="email", visible=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        category_id = kwd.get('id', None)
+        category_id = kwd.get("id", None)
         filter = trans.app.repository_grid_filter_manager.get_filter(trans)
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
             if category_id:
                 category = suc.get_category(trans.app, category_id)
                 if category:
-                    return trans.sa_session.query(model.Repository) \
-                                           .join(model.RepositoryMetadata.table) \
-                                           .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                           .join(model.User.table) \
-                                           .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                           .outerjoin(model.Category.table) \
-                                           .filter(model.Category.table.c.name == category.name)
-            return trans.sa_session.query(model.Repository) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+                    return (
+                        trans.sa_session.query(model.Repository)
+                        .join(model.RepositoryMetadata.table)
+                        .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                        .join(model.User.table)
+                        .outerjoin(model.RepositoryCategoryAssociation.table)
+                        .outerjoin(model.Category.table)
+                        .filter(model.Category.table.c.name == category.name)
+                    )
+            return (
+                trans.sa_session.query(model.Repository)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
             if category_id:
                 category = suc.get_category(trans.app, category_id)
                 if category:
-                    return trans.sa_session.query(model.Repository) \
-                                           .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION) \
-                                           .join(model.RepositoryMetadata.table) \
-                                           .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                           .join(model.User.table) \
-                                           .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                           .outerjoin(model.Category.table) \
-                                           .filter(model.Category.table.c.name == category.name)
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+                    return (
+                        trans.sa_session.query(model.Repository)
+                        .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION)
+                        .join(model.RepositoryMetadata.table)
+                        .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                        .join(model.User.table)
+                        .outerjoin(model.RepositoryCategoryAssociation.table)
+                        .outerjoin(model.Category.table)
+                        .filter(model.Category.table.c.name == category.name)
+                    )
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
         else:
             # The value of filter is None.
             if category_id:
                 category = suc.get_category(trans.app, category_id)
                 if category:
-                    return trans.sa_session.query(model.Repository) \
-                                           .filter(and_(model.Repository.table.c.deleted == false(),
-                                                        model.Repository.table.c.deprecated == false())) \
-                                           .join(model.User.table) \
-                                           .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                           .outerjoin(model.Category.table) \
-                                           .filter(model.Category.table.c.name == category.name)
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deleted == false(),
-                                                model.Repository.table.c.deprecated == false())) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table)
+                    return (
+                        trans.sa_session.query(model.Repository)
+                        .filter(
+                            and_(
+                                model.Repository.table.c.deleted == false(),
+                                model.Repository.table.c.deprecated == false(),
+                            )
+                        )
+                        .join(model.User.table)
+                        .outerjoin(model.RepositoryCategoryAssociation.table)
+                        .outerjoin(model.Category.table)
+                        .filter(model.Category.table.c.name == category.name)
+                    )
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
+                )
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            )
 
 
 class RepositoriesIOwnGrid(RepositoryGrid):
     title = "Repositories I own"
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryGrid.TypeColumn("Type"),
         RepositoryGrid.MetadataRevisionColumn("Metadata<br/>Revisions"),
-        RepositoryGrid.DeprecatedColumn("Deprecated")
+        RepositoryGrid.DeprecatedColumn("Deprecated"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.user_id == trans.user.id)) \
-                               .join(model.User.table) \
-                               .outerjoin(model.RepositoryCategoryAssociation.table) \
-                               .outerjoin(model.Category.table)
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(
+                and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.user_id == trans.user.id)
+            )
+            .join(model.User.table)
+            .outerjoin(model.RepositoryCategoryAssociation.table)
+            .outerjoin(model.Category.table)
+        )
 
 
 class RepositoriesICanAdministerGrid(RepositoryGrid):
     title = "Repositories I can administer"
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryGrid.UserColumn("Owner"),
         RepositoryGrid.MetadataRevisionColumn("Metadata<br/>Revisions"),
-        RepositoryGrid.DeprecatedColumn("Deprecated")
+        RepositoryGrid.DeprecatedColumn("Deprecated"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
         """
@@ -621,57 +681,72 @@ class RepositoriesICanAdministerGrid(RepositoryGrid):
                 clause_list.append(model.Role.table.c.id == gra.role_id)
         # Filter out repositories for which the user does not have the administrative role either directly
         # via a role association or indirectly via a group -> role association.
-        return trans.sa_session.query(model.Repository) \
-                               .filter(model.Repository.table.c.deleted == false()) \
-                               .outerjoin(model.RepositoryRoleAssociation.table) \
-                               .outerjoin(model.Role.table) \
-                               .filter(or_(*clause_list)) \
-                               .join(model.User.table) \
-                               .outerjoin(model.RepositoryCategoryAssociation.table) \
-                               .outerjoin(model.Category.table)
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(model.Repository.table.c.deleted == false())
+            .outerjoin(model.RepositoryRoleAssociation.table)
+            .outerjoin(model.Role.table)
+            .filter(or_(*clause_list))
+            .join(model.User.table)
+            .outerjoin(model.RepositoryCategoryAssociation.table)
+            .outerjoin(model.Category.table)
+        )
 
 
 class RepositoriesMissingToolTestComponentsGrid(RepositoryGrid):
     # This grid displays only the latest installable revision of each repository.
     title = "Repositories with missing tool test components"
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryGrid.LatestInstallableRevisionColumn("Latest Installable Revision"),
-        RepositoryGrid.UserColumn("Owner",
-                                  key="User.username",
-                                  model_class=model.User,
-                                  link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                                  attach_popup=False)
+        RepositoryGrid.UserColumn(
+            "Owner",
+            key="User.username",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+        ),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
         # Filter by latest installable revisions that contain tools with missing tool test components.
         revision_clause_list = []
-        for repository in trans.sa_session.query(model.Repository) \
-                                          .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                       model.Repository.table.c.deleted == false())):
-            changeset_revision = \
-                grids_util.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components(trans, repository)
+        for repository in trans.sa_session.query(model.Repository).filter(
+            and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+        ):
+            changeset_revision = (
+                grids_util.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components(
+                    trans, repository
+                )
+            )
             if changeset_revision:
                 revision_clause_list.append(model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)
         if revision_clause_list:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                model.Repository.table.c.deleted == false())) \
-                                   .join(model.RepositoryMetadata) \
-                                   .filter(or_(*revision_clause_list)) \
-                                   .join(model.User.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+                )
+                .join(model.RepositoryMetadata)
+                .filter(or_(*revision_clause_list))
+                .join(model.User.table)
+            )
         # Return an empty query.
-        return trans.sa_session.query(model.Repository) \
-                               .filter(model.Repository.table.c.id < 0)
+        return trans.sa_session.query(model.Repository).filter(model.Repository.table.c.id < 0)
 
 
 class MyWritableRepositoriesMissingToolTestComponentsGrid(RepositoriesMissingToolTestComponentsGrid):
@@ -683,129 +758,166 @@ class MyWritableRepositoriesMissingToolTestComponentsGrid(RepositoriesMissingToo
         # First get all repositories that the current user is authorized to update.
         username = trans.user.username
         user_clause_list = []
-        for repository in trans.sa_session.query(model.Repository) \
-                                          .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                       model.Repository.table.c.deleted == false())):
+        for repository in trans.sa_session.query(model.Repository).filter(
+            and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+        ):
             allow_push = repository.allow_push()
             if allow_push:
-                allow_push_usernames = allow_push.split(',')
+                allow_push_usernames = allow_push.split(",")
                 if username in allow_push_usernames:
                     user_clause_list.append(model.Repository.table.c.id == repository.id)
         if user_clause_list:
             # We have the list of repositories that the current user is authorized to update, so filter
             # further by latest installable revisions that contain tools with missing tool test components.
             revision_clause_list = []
-            for repository in trans.sa_session.query(model.Repository) \
-                                              .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                           model.Repository.table.c.deleted == false())) \
-                                              .filter(or_(*user_clause_list)):
-                changeset_revision = \
-                    grids_util.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components(trans, repository)
+            for repository in (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+                )
+                .filter(or_(*user_clause_list))
+            ):
+                changeset_revision = (
+                    grids_util.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components(
+                        trans, repository
+                    )
+                )
                 if changeset_revision:
-                    revision_clause_list.append(model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)
+                    revision_clause_list.append(
+                        model.RepositoryMetadata.table.c.changeset_revision == changeset_revision
+                    )
             if revision_clause_list:
-                return trans.sa_session.query(model.Repository) \
-                                       .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                    model.Repository.table.c.deleted == false())) \
-                                       .join(model.User.table) \
-                                       .filter(or_(*user_clause_list)) \
-                                       .join(model.RepositoryMetadata) \
-                                       .filter(or_(*revision_clause_list))
+                return (
+                    trans.sa_session.query(model.Repository)
+                    .filter(
+                        and_(
+                            model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false()
+                        )
+                    )
+                    .join(model.User.table)
+                    .filter(or_(*user_clause_list))
+                    .join(model.RepositoryMetadata)
+                    .filter(or_(*revision_clause_list))
+                )
         # Return an empty query.
-        return trans.sa_session.query(model.Repository) \
-                               .filter(model.Repository.table.c.id < 0)
+        return trans.sa_session.query(model.Repository).filter(model.Repository.table.c.id < 0)
 
 
 class DeprecatedRepositoriesIOwnGrid(RepositoriesIOwnGrid):
     title = "Deprecated repositories I own"
     columns = [
-        RepositoriesIOwnGrid.NameColumn("Name",
-                                        key="name",
-                                        link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                        attach_popup=False),
+        RepositoriesIOwnGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryGrid.TypeColumn("Type"),
         RepositoriesIOwnGrid.MetadataRevisionColumn("Metadata<br/>Revisions"),
-        RepositoriesIOwnGrid.CategoryColumn("Category",
-                                            model_class=model.Category,
-                                            key="Category.name",
-                                            attach_popup=False),
+        RepositoriesIOwnGrid.CategoryColumn(
+            "Category", model_class=model.Category, key="Category.name", attach_popup=False
+        ),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.user_id == trans.user.id,
-                                            model.Repository.table.c.deprecated == true())) \
-                               .join(model.User.table) \
-                               .outerjoin(model.RepositoryCategoryAssociation.table) \
-                               .outerjoin(model.Category.table)
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(
+                and_(
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.user_id == trans.user.id,
+                    model.Repository.table.c.deprecated == true(),
+                )
+            )
+            .join(model.User.table)
+            .outerjoin(model.RepositoryCategoryAssociation.table)
+            .outerjoin(model.Category.table)
+        )
 
 
 class RepositoriesWithInvalidToolsGrid(RepositoryGrid):
     # This grid displays only the latest installable revision of each repository.
 
     class InvalidToolConfigColumn(grids.GridColumn):
-
         def __init__(self, col_name):
             grids.GridColumn.__init__(self, col_name)
 
         def get_value(self, trans, grid, repository):
             # At the time this grid is displayed we know that the received repository will have invalid tools in its latest changeset revision
             # that has associated metadata.
-            val = ''
-            repository_metadata = \
-                grids_util.get_latest_repository_metadata_if_it_includes_invalid_tools(trans, repository)
+            val = ""
+            repository_metadata = grids_util.get_latest_repository_metadata_if_it_includes_invalid_tools(
+                trans, repository
+            )
             metadata = repository_metadata.metadata
-            invalid_tools = metadata.get('invalid_tools', [])
+            invalid_tools = metadata.get("invalid_tools", [])
             if invalid_tools:
                 for invalid_tool_config in invalid_tools:
-                    href_str = '<a href="load_invalid_tool?repository_id=%s&tool_config=%s&changeset_revision=%s">%s</a>' % \
-                        (trans.security.encode_id(repository.id), invalid_tool_config, repository_metadata.changeset_revision, invalid_tool_config)
+                    href_str = (
+                        '<a href="load_invalid_tool?repository_id=%s&tool_config=%s&changeset_revision=%s">%s</a>'
+                        % (
+                            trans.security.encode_id(repository.id),
+                            invalid_tool_config,
+                            repository_metadata.changeset_revision,
+                            invalid_tool_config,
+                        )
+                    )
                     val += href_str
-                    val += '<br/>'
-                val = val.rstrip('<br/>')
+                    val += "<br/>"
+                val = val.rstrip("<br/>")
             return val
 
     title = "Repositories with invalid tools"
     columns = [
         InvalidToolConfigColumn("Tool config"),
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=False),
+        RepositoryGrid.NameColumn(
+            "Name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryGrid.LatestInstallableRevisionColumn("Latest Metadata Revision"),
-        RepositoryGrid.UserColumn("Owner",
-                                  key="User.username",
-                                  model_class=model.User,
-                                  link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
-                                  attach_popup=False)
+        RepositoryGrid.UserColumn(
+            "Owner",
+            key="User.username",
+            model_class=model.User,
+            link=(lambda item: dict(operation="repositories_by_user", id=item.id)),
+            attach_popup=False,
+        ),
     ]
 
     def build_initial_query(self, trans, **kwd):
         # Filter by latest metadata revisions that contain invalid tools.
         revision_clause_list = []
-        for repository in trans.sa_session.query(model.Repository) \
-                                          .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                       model.Repository.table.c.deleted == false())):
-            changeset_revision = \
-                grids_util.filter_by_latest_metadata_changeset_revision_that_has_invalid_tools(trans, repository)
+        for repository in trans.sa_session.query(model.Repository).filter(
+            and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+        ):
+            changeset_revision = grids_util.filter_by_latest_metadata_changeset_revision_that_has_invalid_tools(
+                trans, repository
+            )
             if changeset_revision:
                 revision_clause_list.append(model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)
         if revision_clause_list:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                model.Repository.table.c.deleted == false())) \
-                                   .join(model.RepositoryMetadata) \
-                                   .filter(or_(*revision_clause_list)) \
-                                   .join(model.User.table)
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+                )
+                .join(model.RepositoryMetadata)
+                .filter(or_(*revision_clause_list))
+                .join(model.User.table)
+            )
         # Return an empty query.
-        return trans.sa_session.query(model.Repository) \
-                               .filter(model.Repository.table.c.id < 0)
+        return trans.sa_session.query(model.Repository).filter(model.Repository.table.c.id < 0)
 
 
 class MyWritableRepositoriesWithInvalidToolsGrid(RepositoriesWithInvalidToolsGrid):
@@ -817,231 +929,254 @@ class MyWritableRepositoriesWithInvalidToolsGrid(RepositoriesWithInvalidToolsGri
         # First get all repositories that the current user is authorized to update.
         username = trans.user.username
         user_clause_list = []
-        for repository in trans.sa_session.query(model.Repository) \
-                                          .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                       model.Repository.table.c.deleted == false())):
+        for repository in trans.sa_session.query(model.Repository).filter(
+            and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+        ):
             allow_push = repository.allow_push()
             if allow_push:
-                allow_push_usernames = allow_push.split(',')
+                allow_push_usernames = allow_push.split(",")
                 if username in allow_push_usernames:
                     user_clause_list.append(model.Repository.table.c.id == repository.id)
         if user_clause_list:
             # We have the list of repositories that the current user is authorized to update, so filter
             # further by latest metadata revisions that contain invalid tools.
             revision_clause_list = []
-            for repository in trans.sa_session.query(model.Repository) \
-                                              .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                           model.Repository.table.c.deleted == false())) \
-                                              .filter(or_(*user_clause_list)):
-                changeset_revision = \
-                    grids_util.filter_by_latest_metadata_changeset_revision_that_has_invalid_tools(trans, repository)
+            for repository in (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false())
+                )
+                .filter(or_(*user_clause_list))
+            ):
+                changeset_revision = grids_util.filter_by_latest_metadata_changeset_revision_that_has_invalid_tools(
+                    trans, repository
+                )
                 if changeset_revision:
-                    revision_clause_list.append(model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)
+                    revision_clause_list.append(
+                        model.RepositoryMetadata.table.c.changeset_revision == changeset_revision
+                    )
             if revision_clause_list:
-                return trans.sa_session.query(model.Repository) \
-                                       .filter(and_(model.Repository.table.c.deprecated == false(),
-                                                    model.Repository.table.c.deleted == false())) \
-                                       .join(model.User.table) \
-                                       .filter(or_(*user_clause_list)) \
-                                       .join(model.RepositoryMetadata) \
-                                       .filter(or_(*revision_clause_list))
+                return (
+                    trans.sa_session.query(model.Repository)
+                    .filter(
+                        and_(
+                            model.Repository.table.c.deprecated == false(), model.Repository.table.c.deleted == false()
+                        )
+                    )
+                    .join(model.User.table)
+                    .filter(or_(*user_clause_list))
+                    .join(model.RepositoryMetadata)
+                    .filter(or_(*revision_clause_list))
+                )
         # Return an empty query.
-        return trans.sa_session.query(model.Repository) \
-                               .filter(model.Repository.table.c.id < 0)
+        return trans.sa_session.query(model.Repository).filter(model.Repository.table.c.id < 0)
 
 
 class RepositoryMetadataGrid(grids.Grid):
-
     class RepositoryNameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             repository = repository_metadata.repository
             return escape_html(repository.name)
 
     class RepositoryTypeColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             repository = repository_metadata.repository
             type_class = repository.get_type_class(trans.app)
             return escape_html(type_class.label)
 
     class RepositoryOwnerColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             repository = repository_metadata.repository
             return escape_html(repository.user.username)
 
     class ChangesetRevisionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             repository = repository_metadata.repository
             changeset_revision = repository_metadata.changeset_revision
-            changeset_revision_label = hg_util.get_revision_label(trans.app, repository, changeset_revision, include_date=True)
+            changeset_revision_label = hg_util.get_revision_label(
+                trans.app, repository, changeset_revision, include_date=True
+            )
             return changeset_revision_label
 
     class MaliciousColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.malicious:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class DownloadableColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.downloadable:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class HasRepositoryDependenciesColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.has_repository_dependencies:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class IncludesDatatypesColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.includes_datatypes:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class IncludesToolsColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.includes_tools:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class IncludesToolDependenciesColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.includes_tool_dependencies:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     class IncludesWorkflowsColumn(grids.BooleanColumn):
         def get_value(self, trans, grid, repository_metadata):
             if repository_metadata.includes_workflows:
-                return 'yes'
-            return ''
+                return "yes"
+            return ""
 
     title = "Repository metadata"
     model_class = model.RepositoryMetadata
     default_sort_key = "Repository.name"
     columns = [
-        RepositoryNameColumn("Repository name",
-                             key="Repository.name",
-                             link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                             attach_popup=False),
+        RepositoryNameColumn(
+            "Repository name",
+            key="Repository.name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+        ),
         RepositoryNameColumn("Type"),
-        RepositoryOwnerColumn("Owner",
-                              model_class=model.User,
-                              attach_popup=False,
-                              key="User.username")
+        RepositoryOwnerColumn("Owner", model_class=model.User, attach_popup=False, key="User.username"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
     default_filter = dict(malicious="False")
     num_rows_per_page = 50
     use_paging = True
     allow_fetching_all_results = False
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .join(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.RepositoryMetadata)
+            .join(model.Repository)
+            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
+            .join(model.User.table)
+        )
 
 
 class RepositoryDependenciesGrid(RepositoryMetadataGrid):
-
     class RequiredRepositoryColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             rd_str = []
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    rd_dict = metadata.get('repository_dependencies', {})
+                    rd_dict = metadata.get("repository_dependencies", {})
                     if rd_dict:
-                        rd_tups = rd_dict['repository_dependencies']
+                        rd_tups = rd_dict["repository_dependencies"]
                         # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]]
                         # Sort rd_tups by by required repository name.
                         sorted_rd_tups = sorted(rd_tups, key=lambda rd_tup: rd_tup[1])
                         for rd_tup in sorted_rd_tups:
                             name, owner, changeset_revision = rd_tup[1:4]
-                            rd_line = ''
-                            required_repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
+                            rd_line = ""
+                            required_repository = repository_util.get_repository_by_name_and_owner(
+                                trans.app, name, owner
+                            )
                             if required_repository and not required_repository.deleted:
                                 required_repository_id = trans.security.encode_id(required_repository.id)
-                                required_repository_metadata = \
-                                    metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                                              required_repository_id,
-                                                                                                              changeset_revision)
+                                required_repository_metadata = (
+                                    metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                                        trans.app, required_repository_id, changeset_revision
+                                    )
+                                )
                                 if not required_repository_metadata:
-                                    updated_changeset_revision = \
-                                        metadata_util.get_next_downloadable_changeset_revision(trans.app, required_repository, changeset_revision)
-                                    required_repository_metadata = \
-                                        metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                                                  required_repository_id,
-                                                                                                                  updated_changeset_revision)
-                                required_repository_metadata_id = trans.security.encode_id(required_repository_metadata.id)
+                                    updated_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+                                        trans.app, required_repository, changeset_revision
+                                    )
+                                    required_repository_metadata = (
+                                        metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                                            trans.app, required_repository_id, updated_changeset_revision
+                                        )
+                                    )
+                                required_repository_metadata_id = trans.security.encode_id(
+                                    required_repository_metadata.id
+                                )
                                 rd_line += f'<a href="browse_repository_dependencies?operation=view_or_manage_repository&id={required_repository_metadata_id}">'
-                            rd_line += f'Repository <b>{escape_html(name)}</b> revision <b>{escape_html(owner)}</b> owned by <b>{escape_html(changeset_revision)}</b>'
+                            rd_line += f"Repository <b>{escape_html(name)}</b> revision <b>{escape_html(owner)}</b> owned by <b>{escape_html(changeset_revision)}</b>"
                             if required_repository:
-                                rd_line += '</a>'
+                                rd_line += "</a>"
                             rd_str.append(rd_line)
-            return '<br />'.join(rd_str)
+            return "<br />".join(rd_str)
 
     title = "Valid repository dependency definitions in this tool shed"
     default_sort_key = "Repository.name"
     columns = [
-        RequiredRepositoryColumn("Repository dependency",
-                                 attach_popup=False),
-        RepositoryMetadataGrid.RepositoryNameColumn("Repository name",
-                                                    model_class=model.Repository,
-                                                    link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                    attach_popup=False,
-                                                    key="Repository.name"),
-        RepositoryMetadataGrid.RepositoryOwnerColumn("Owner",
-                                                     model_class=model.User,
-                                                     attach_popup=False,
-                                                     key="User.username"),
-        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision",
-                                                       attach_popup=False)
+        RequiredRepositoryColumn("Repository dependency", attach_popup=False),
+        RepositoryMetadataGrid.RepositoryNameColumn(
+            "Repository name",
+            model_class=model.Repository,
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+            key="Repository.name",
+        ),
+        RepositoryMetadataGrid.RepositoryOwnerColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision", attach_popup=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, owner",
-                                              cols_to_filter=[columns[1], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, owner",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .join(model.Repository) \
-                               .filter(and_(model.RepositoryMetadata.table.c.has_repository_dependencies == true(),
-                                            model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.RepositoryMetadata)
+            .join(model.Repository)
+            .filter(
+                and_(
+                    model.RepositoryMetadata.table.c.has_repository_dependencies == true(),
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.deprecated == false(),
+                )
+            )
+            .join(model.User.table)
+        )
 
 
 class DatatypesGrid(RepositoryMetadataGrid):
-
     class DatatypesColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             datatype_list = []
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    datatype_dicts = metadata.get('datatypes', [])
+                    datatype_dicts = metadata.get("datatypes", [])
                     if datatype_dicts:
                         # Create tuples of the attributes we want so we can sort them by extension.
                         datatype_tups = []
                         for datatype_dict in datatype_dicts:
                             # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"}
-                            extension = datatype_dict.get('extension', '')
-                            dtype = datatype_dict.get('dtype', '')
+                            extension = datatype_dict.get("extension", "")
+                            dtype = datatype_dict.get("dtype", "")
                             # For now we'll just display extension and dtype.
                             if extension and dtype:
                                 datatype_tups.append((extension, dtype))
@@ -1049,129 +1184,143 @@ class DatatypesGrid(RepositoryMetadataGrid):
                         for datatype_tup in sorted_datatype_tups:
                             extension, datatype = datatype_tup[:2]
                             datatype_str = f'<a href="browse_datatypes?operation=view_or_manage_repository&id={trans.security.encode_id(repository_metadata.id)}">'
-                            datatype_str += f'<b>{escape_html(extension)}:</b> {escape_html(datatype)}'
-                            datatype_str += '</a>'
+                            datatype_str += f"<b>{escape_html(extension)}:</b> {escape_html(datatype)}"
+                            datatype_str += "</a>"
                             datatype_list.append(datatype_str)
-            return '<br />'.join(datatype_list)
+            return "<br />".join(datatype_list)
 
     title = "Custom datatypes in this tool shed"
     default_sort_key = "Repository.name"
     columns = [
-        DatatypesColumn("Datatype extension and class",
-                        attach_popup=False),
-        RepositoryMetadataGrid.RepositoryNameColumn("Repository name",
-                                                    model_class=model.Repository,
-                                                    link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                    attach_popup=False,
-                                                    key="Repository.name"),
-        RepositoryMetadataGrid.RepositoryOwnerColumn("Owner",
-                                                     model_class=model.User,
-                                                     attach_popup=False,
-                                                     key="User.username"),
-        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision",
-                                                       attach_popup=False)
+        DatatypesColumn("Datatype extension and class", attach_popup=False),
+        RepositoryMetadataGrid.RepositoryNameColumn(
+            "Repository name",
+            model_class=model.Repository,
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+            key="Repository.name",
+        ),
+        RepositoryMetadataGrid.RepositoryOwnerColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision", attach_popup=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, owner",
-                                              cols_to_filter=[columns[1], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, owner",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .join(model.Repository) \
-                               .filter(and_(model.RepositoryMetadata.table.c.includes_datatypes == true(),
-                                            model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.RepositoryMetadata)
+            .join(model.Repository)
+            .filter(
+                and_(
+                    model.RepositoryMetadata.table.c.includes_datatypes == true(),
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.deprecated == false(),
+                )
+            )
+            .join(model.User.table)
+        )
 
 
 class ToolDependenciesGrid(RepositoryMetadataGrid):
-
     class ToolDependencyColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
-            td_str = ''
+            td_str = ""
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    tds_dict = metadata.get('tool_dependencies', {})
+                    tds_dict = metadata.get("tool_dependencies", {})
                     if tds_dict:
                         # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}}
                         sorted_keys = sorted(tds_dict.keys())
                         num_keys = len(sorted_keys)
                         # Handle environment settings first.
-                        if 'set_environment' in sorted_keys:
+                        if "set_environment" in sorted_keys:
                             # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}]
-                            env_dicts = tds_dict['set_environment']
+                            env_dicts = tds_dict["set_environment"]
                             num_env_dicts = len(env_dicts)
                             if num_env_dicts > 0:
                                 td_str += f'<a href="browse_datatypes?operation=view_or_manage_repository&id={trans.security.encode_id(repository_metadata.id)}">'
-                                td_str += '<b>environment:</b> '
-                                td_str += ', '.join(escape_html(env_dict['name']) for env_dict in env_dicts)
-                                td_str += '</a><br/>'
+                                td_str += "<b>environment:</b> "
+                                td_str += ", ".join(escape_html(env_dict["name"]) for env_dict in env_dicts)
+                                td_str += "</a><br/>"
                         for index, key in enumerate(sorted_keys):
-                            if key == 'set_environment':
+                            if key == "set_environment":
                                 continue
                             td_dict = tds_dict[key]
                             # Example: {"name": "bwa", "type": "package", "version": "0.5.9"}
-                            name = td_dict['name']
-                            version = td_dict['version']
+                            name = td_dict["name"]
+                            version = td_dict["version"]
                             td_str += f'<a href="browse_datatypes?operation=view_or_manage_repository&id={trans.security.encode_id(repository_metadata.id)}">'
-                            td_str += f'<b>{escape_html(name)}</b> version <b>{escape_html(version)}</b>'
-                            td_str += '</a>'
+                            td_str += f"<b>{escape_html(name)}</b> version <b>{escape_html(version)}</b>"
+                            td_str += "</a>"
                             if index < num_keys - 1:
-                                td_str += '<br/>'
+                                td_str += "<br/>"
             return td_str
 
     title = "Tool dependency definitions in this tool shed"
     default_sort_key = "Repository.name"
     columns = [
-        ToolDependencyColumn("Tool dependency",
-                             attach_popup=False),
-        RepositoryMetadataGrid.RepositoryNameColumn("Repository name",
-                                                    model_class=model.Repository,
-                                                    link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                    attach_popup=False,
-                                                    key="Repository.name"),
-        RepositoryMetadataGrid.RepositoryOwnerColumn("Owner",
-                                                     model_class=model.User,
-                                                     attach_popup=False,
-                                                     key="User.username"),
-        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision",
-                                                       attach_popup=False)
+        ToolDependencyColumn("Tool dependency", attach_popup=False),
+        RepositoryMetadataGrid.RepositoryNameColumn(
+            "Repository name",
+            model_class=model.Repository,
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+            key="Repository.name",
+        ),
+        RepositoryMetadataGrid.RepositoryOwnerColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision", attach_popup=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, owner",
-                                              cols_to_filter=[columns[1], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, owner",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .join(model.Repository) \
-                               .filter(and_(model.RepositoryMetadata.table.c.includes_tool_dependencies == true(),
-                                            model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.RepositoryMetadata)
+            .join(model.Repository)
+            .filter(
+                and_(
+                    model.RepositoryMetadata.table.c.includes_tool_dependencies == true(),
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.deprecated == false(),
+                )
+            )
+            .join(model.User.table)
+        )
 
 
 class ToolsGrid(RepositoryMetadataGrid):
-
     class ToolsColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository_metadata):
             tool_line = []
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    tool_dicts = metadata.get('tools', [])
+                    tool_dicts = metadata.get("tools", [])
                     if tool_dicts:
                         # Create tuples of the attributes we want so we can sort them by extension.
                         tool_tups = []
                         for tool_dict in tool_dicts:
-                            tool_id = tool_dict.get('id', '')
-                            version = tool_dict.get('version', '')
+                            tool_id = tool_dict.get("id", "")
+                            version = tool_dict.get("version", "")
                             # For now we'll just display tool id and version.
                             if tool_id and version:
                                 tool_tups.append((tool_id, version))
@@ -1179,76 +1328,89 @@ class ToolsGrid(RepositoryMetadataGrid):
                         for tool_tup in sorted_tool_tups:
                             tool_id, version = tool_tup[:2]
                             tool_str = f'<a href="browse_datatypes?operation=view_or_manage_repository&id={trans.security.encode_id(repository_metadata.id)}">'
-                            tool_str += f'<b>{escape_html(tool_id)}:</b> {escape_html(version)}'
-                            tool_str += '</a>'
+                            tool_str += f"<b>{escape_html(tool_id)}:</b> {escape_html(version)}"
+                            tool_str += "</a>"
                             tool_line.append(tool_str)
-            return '<br />'.join(tool_line)
+            return "<br />".join(tool_line)
 
     title = "Valid tools in this tool shed"
     default_sort_key = "Repository.name"
     columns = [
-        ToolsColumn("Tool id and version",
-                    attach_popup=False),
-        RepositoryMetadataGrid.RepositoryNameColumn("Repository name",
-                                                    model_class=model.Repository,
-                                                    link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                    attach_popup=False,
-                                                    key="Repository.name"),
-        RepositoryMetadataGrid.RepositoryOwnerColumn("Owner",
-                                                     model_class=model.User,
-                                                     attach_popup=False,
-                                                     key="User.username"),
-        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision",
-                                                       attach_popup=False)
+        ToolsColumn("Tool id and version", attach_popup=False),
+        RepositoryMetadataGrid.RepositoryNameColumn(
+            "Repository name",
+            model_class=model.Repository,
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=False,
+            key="Repository.name",
+        ),
+        RepositoryMetadataGrid.RepositoryOwnerColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+        RepositoryMetadataGrid.ChangesetRevisionColumn("Revision", attach_popup=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, owner",
-                                              cols_to_filter=[columns[1], columns[2]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, owner",
+            cols_to_filter=[columns[1], columns[2]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.RepositoryMetadata) \
-                               .join(model.Repository) \
-                               .filter(and_(model.RepositoryMetadata.table.c.includes_tools == true(),
-                                            model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.RepositoryMetadata)
+            .join(model.Repository)
+            .filter(
+                and_(
+                    model.RepositoryMetadata.table.c.includes_tools == true(),
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.deprecated == false(),
+                )
+            )
+            .join(model.User.table)
+        )
 
 
 class ValidCategoryGrid(CategoryGrid):
-
     class RepositoriesColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, category):
             category_name = str(category.name)
             filter = trans.app.repository_grid_filter_manager.get_filter(trans)
             if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
-                return trans.app.repository_registry.certified_level_one_viewable_repositories_and_suites_by_category.get(category_name, 0)
+                return (
+                    trans.app.repository_registry.certified_level_one_viewable_repositories_and_suites_by_category.get(
+                        category_name, 0
+                    )
+                )
             elif filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
-                return trans.app.repository_registry.certified_level_one_viewable_suites_by_category.get(category_name, 0)
+                return trans.app.repository_registry.certified_level_one_viewable_suites_by_category.get(
+                    category_name, 0
+                )
             elif filter == trans.app.repository_grid_filter_manager.filters.SUITES:
                 return trans.app.repository_registry.viewable_valid_suites_by_category.get(category_name, 0)
             else:
                 # The value filter is None.
-                return trans.app.repository_registry.viewable_valid_repositories_and_suites_by_category.get(category_name, 0)
+                return trans.app.repository_registry.viewable_valid_repositories_and_suites_by_category.get(
+                    category_name, 0
+                )
 
     title = "Categories of Valid Repositories"
     model_class = model.Category
-    template = '/webapps/tool_shed/category/valid_grid.mako'
+    template = "/webapps/tool_shed/category/valid_grid.mako"
     default_sort_key = "name"
     columns = [
-        CategoryGrid.NameColumn("Name",
-                                key="Category.name",
-                                link=(lambda item: dict(operation="valid_repositories_by_category", id=item.id)),
-                                attach_popup=False),
-        CategoryGrid.DescriptionColumn("Description",
-                                       key="Category.description",
-                                       attach_popup=False),
+        CategoryGrid.NameColumn(
+            "Name",
+            key="Category.name",
+            link=(lambda item: dict(operation="valid_repositories_by_category", id=item.id)),
+            attach_popup=False,
+        ),
+        CategoryGrid.DescriptionColumn("Description", key="Category.description", attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        RepositoriesColumn("Valid repositories",
-                           model_class=model.Repository,
-                           attach_popup=False)
+        RepositoriesColumn("Valid repositories", model_class=model.Repository, attach_popup=False),
     ]
     # Override these
     num_rows_per_page = 50
@@ -1258,20 +1420,20 @@ class ValidRepositoryGrid(RepositoryGrid):
     # This grid filters out repositories that have been marked as either deleted or deprecated.
 
     class CategoryColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
-            rval = '<ul>'
+            rval = "<ul>"
             if repository.categories:
                 for rca in repository.categories:
-                    rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>' \
+                    rval += (
+                        '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>'
                         % (trans.security.encode_id(rca.category.id), rca.category.name)
+                    )
             else:
-                rval += '<li>not set</li>'
-            rval += '</ul>'
+                rval += "<li>not set</li>"
+            rval += "</ul>"
             return rval
 
     class RepositoryCategoryColumn(grids.GridColumn):
-
         def filter(self, trans, user, query, column_filter):
             """Modify query to filter by category."""
             if column_filter == "All":
@@ -1279,7 +1441,6 @@ class ValidRepositoryGrid(RepositoryGrid):
             return query.filter(model.Category.name == column_filter)
 
     class InstallableRevisionColumn(grids.GridColumn):
-
         def __init__(self, col_name):
             grids.GridColumn.__init__(self, col_name)
 
@@ -1294,93 +1455,116 @@ class ValidRepositoryGrid(RepositoryGrid):
                 return tmpl
             elif len(select_field.options) == 1:
                 return select_field.options[0][0]
-            return ''
+            return ""
 
     title = "Valid Repositories"
     columns = [
-        RepositoryGrid.NameColumn("Name",
-                                  key="name",
-                                  attach_popup=True),
-        RepositoryGrid.DescriptionColumn("Synopsis",
-                                         key="description",
-                                         attach_popup=False),
+        RepositoryGrid.NameColumn("Name", key="name", attach_popup=True),
+        RepositoryGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
         RepositoryGrid.TypeColumn("Type"),
         InstallableRevisionColumn("Installable Revisions"),
-        RepositoryGrid.UserColumn("Owner",
-                                  model_class=model.User,
-                                  attach_popup=False),
+        RepositoryGrid.UserColumn("Owner", model_class=model.User, attach_popup=False),
         # Columns that are valid for filtering but are not visible.
-        RepositoryCategoryColumn("Category",
-                                 model_class=model.Category,
-                                 key="Category.name",
-                                 visible=False)
+        RepositoryCategoryColumn("Category", model_class=model.Category, key="Category.name", visible=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
         filter = trans.app.repository_grid_filter_manager.get_filter(trans)
-        if 'id' in kwd:
+        if "id" in kwd:
             # The user is browsing categories of valid repositories, so filter the request by the received id,
             # which is a category id.
             if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
-                return trans.sa_session.query(model.Repository) \
-                                       .join(model.RepositoryMetadata.table) \
-                                       .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                       .join(model.User.table) \
-                                       .join(model.RepositoryCategoryAssociation.table) \
-                                       .join(model.Category.table) \
-                                       .filter(and_(model.Category.table.c.id == trans.security.decode_id(kwd['id']),
-                                                    model.RepositoryMetadata.table.c.downloadable == true()))
+                return (
+                    trans.sa_session.query(model.Repository)
+                    .join(model.RepositoryMetadata.table)
+                    .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                    .join(model.User.table)
+                    .join(model.RepositoryCategoryAssociation.table)
+                    .join(model.Category.table)
+                    .filter(
+                        and_(
+                            model.Category.table.c.id == trans.security.decode_id(kwd["id"]),
+                            model.RepositoryMetadata.table.c.downloadable == true(),
+                        )
+                    )
+                )
             if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
-                return trans.sa_session.query(model.Repository) \
-                                       .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION) \
-                                       .join(model.RepositoryMetadata.table) \
-                                       .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                       .join(model.User.table) \
-                                       .join(model.RepositoryCategoryAssociation.table) \
-                                       .join(model.Category.table) \
-                                       .filter(and_(model.Category.table.c.id == trans.security.decode_id(kwd['id']),
-                                                    model.RepositoryMetadata.table.c.downloadable == true()))
+                return (
+                    trans.sa_session.query(model.Repository)
+                    .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION)
+                    .join(model.RepositoryMetadata.table)
+                    .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                    .join(model.User.table)
+                    .join(model.RepositoryCategoryAssociation.table)
+                    .join(model.Category.table)
+                    .filter(
+                        and_(
+                            model.Category.table.c.id == trans.security.decode_id(kwd["id"]),
+                            model.RepositoryMetadata.table.c.downloadable == true(),
+                        )
+                    )
+                )
             else:
                 # The value of filter is None.
-                return trans.sa_session.query(model.Repository) \
-                                       .filter(and_(model.Repository.table.c.deleted == false(),
-                                                    model.Repository.table.c.deprecated == false())) \
-                                       .join(model.RepositoryMetadata.table) \
-                                       .join(model.User.table) \
-                                       .join(model.RepositoryCategoryAssociation.table) \
-                                       .join(model.Category.table) \
-                                       .filter(and_(model.Category.table.c.id == trans.security.decode_id(kwd['id']),
-                                                    model.RepositoryMetadata.table.c.downloadable == true()))
+                return (
+                    trans.sa_session.query(model.Repository)
+                    .filter(
+                        and_(
+                            model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()
+                        )
+                    )
+                    .join(model.RepositoryMetadata.table)
+                    .join(model.User.table)
+                    .join(model.RepositoryCategoryAssociation.table)
+                    .join(model.Category.table)
+                    .filter(
+                        and_(
+                            model.Category.table.c.id == trans.security.decode_id(kwd["id"]),
+                            model.RepositoryMetadata.table.c.downloadable == true(),
+                        )
+                    )
+                )
         # The user performed a free text search on the ValidCategoryGrid.
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE:
-            return trans.sa_session.query(model.Repository) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table) \
-                                   .filter(model.RepositoryMetadata.table.c.downloadable == true())
+            return (
+                trans.sa_session.query(model.Repository)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+                .filter(model.RepositoryMetadata.table.c.downloadable == true())
+            )
         if filter == trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE_SUITES:
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list)) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table) \
-                                   .filter(model.RepositoryMetadata.table.c.downloadable == true())
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(model.Repository.type == rt_util.REPOSITORY_SUITE_DEFINITION)
+                .join(model.RepositoryMetadata.table)
+                .filter(or_(*trans.app.repository_registry.certified_level_one_clause_list))
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+                .filter(model.RepositoryMetadata.table.c.downloadable == true())
+            )
         else:
             # The value of filter is None.
-            return trans.sa_session.query(model.Repository) \
-                                   .filter(and_(model.Repository.table.c.deleted == false(),
-                                                model.Repository.table.c.deprecated == false())) \
-                                   .join(model.RepositoryMetadata.table) \
-                                   .join(model.User.table) \
-                                   .outerjoin(model.RepositoryCategoryAssociation.table) \
-                                   .outerjoin(model.Category.table) \
-                                   .filter(model.RepositoryMetadata.table.c.downloadable == true())
+            return (
+                trans.sa_session.query(model.Repository)
+                .filter(
+                    and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
+                )
+                .join(model.RepositoryMetadata.table)
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+                .filter(model.RepositoryMetadata.table.c.downloadable == true())
+            )
diff --git a/lib/tool_shed/grids/repository_review_grids.py b/lib/tool_shed/grids/repository_review_grids.py
index ecac55216b5..f228efd9e5e 100644
--- a/lib/tool_shed/grids/repository_review_grids.py
+++ b/lib/tool_shed/grids/repository_review_grids.py
@@ -1,45 +1,49 @@
 import logging
 
 from markupsafe import escape
-from sqlalchemy import and_, false, null, or_, true
+from sqlalchemy import (
+    and_,
+    false,
+    null,
+    or_,
+    true,
+)
 
 from galaxy.web.legacy_framework import grids
 from tool_shed.grids.repository_grids import RepositoryGrid
-from tool_shed.util import hg_util, metadata_util
+from tool_shed.util import (
+    hg_util,
+    metadata_util,
+)
 from tool_shed.webapp import model
 
 log = logging.getLogger(__name__)
 
 
 class ComponentGrid(grids.Grid):
-
     class NameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, component):
             return escape(component.name)
 
     class DescriptionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, component):
             return escape(component.description)
 
     title = "Repository review components"
     model_class = model.Component
-    template = '/webapps/tool_shed/repository_review/grid.mako'
+    template = "/webapps/tool_shed/repository_review/grid.mako"
     default_sort_key = "name"
     use_hide_message = False
     columns = [
-        NameColumn("Name",
-                   key="Component.name",
-                   link=(lambda item: dict(operation="edit", id=item.id)),
-                   attach_popup=False),
-        DescriptionColumn("Description",
-                          key="Component.description",
-                          attach_popup=False)
+        NameColumn(
+            "Name", key="Component.name", link=(lambda item: dict(operation="edit", id=item.id)), attach_popup=False
+        ),
+        DescriptionColumn("Description", key="Component.description", attach_popup=False),
     ]
     global_actions = [
-        grids.GridAction("Add new component",
-                         dict(controller='repository_review', action='manage_components', operation='create'))
+        grids.GridAction(
+            "Add new component", dict(controller="repository_review", action="manage_components", operation="create")
+        )
     ]
     num_rows_per_page = 50
 
@@ -51,55 +55,55 @@ class RepositoriesWithReviewsGrid(RepositoryGrid):
         def get_value(self, trans, grid, repository):
             # Restrict to revisions that have been reviewed.
             if repository.reviews:
-                rval = ''
+                rval = ""
                 repo = repository.hg_repo
                 for review in repository.reviews:
                     changeset_revision = review.changeset_revision
                     rev, label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision)
-                    rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
-                        (trans.security.encode_id(repository.id), changeset_revision, label)
+                    rval += (
+                        '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>'
+                        % (trans.security.encode_id(repository.id), changeset_revision, label)
+                    )
                 return rval
-            return ''
+            return ""
 
     class WithoutReviewsRevisionColumn(grids.GridColumn):
-
         def get_value(self, trans, grid, repository):
             # Restrict the options to revisions that have not yet been reviewed.
-            repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review(repository, reviewed=False)
+            repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review(
+                repository, reviewed=False
+            )
             if repository_metadata_revisions:
-                rval = ''
+                rval = ""
                 for repository_metadata in repository_metadata_revisions:
-                    rev, label, changeset_revision = \
-                        hg_util.get_rev_label_changeset_revision_from_repository_metadata(trans.app,
-                                                                                          repository_metadata,
-                                                                                          repository=repository,
-                                                                                          include_date=True,
-                                                                                          include_hash=False)
-                    rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \
-                        (trans.security.encode_id(repository.id), changeset_revision, label)
+                    rev, label, changeset_revision = hg_util.get_rev_label_changeset_revision_from_repository_metadata(
+                        trans.app, repository_metadata, repository=repository, include_date=True, include_hash=False
+                    )
+                    rval += (
+                        '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>'
+                        % (trans.security.encode_id(repository.id), changeset_revision, label)
+                    )
                 return rval
-            return ''
+            return ""
 
     class ReviewersColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
-            rval = ''
+            rval = ""
             if repository.reviewers:
                 for user in repository.reviewers:
                     rval += f'<a class="view-info" href="repository_reviews_by_user?id={trans.security.encode_id(user.id)}">'
-                    rval += f'{user.username}</a> | '
-                if rval[-3:] == ' | ':
+                    rval += f"{user.username}</a> | "
+                if rval[-3:] == " | ":
                     rval = rval[:-3]
             return rval
 
     class RatingColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
-            rval = ''
+            rval = ""
             for review in repository.reviews:
                 if review.rating:
                     for index in range(1, 6):
-                        rval += '<input '
+                        rval += "<input "
                         rval += f'name="star1-{trans.security.encode_id(review.id)}" '
                         rval += 'type="radio" '
                         rval += 'class="community_rating_star star" '
@@ -107,92 +111,122 @@ class RepositoriesWithReviewsGrid(RepositoryGrid):
                         rval += f'value="{str(review.rating)}" '
                         if review.rating > (index - 0.5) and review.rating < (index + 0.5):
                             rval += 'checked="checked" '
-                        rval += '/>'
-                rval += '<br/>'
+                        rval += "/>"
+                rval += "<br/>"
             return rval
 
     class ApprovedColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, repository):
-            rval = ''
+            rval = ""
             for review in repository.reviews:
                 if review.approved:
-                    rval += f'{review.approved}<br/>'
+                    rval += f"{review.approved}<br/>"
             return rval
 
     title = "All reviewed repositories"
     model_class = model.Repository
-    template = '/webapps/tool_shed/repository_review/grid.mako'
+    template = "/webapps/tool_shed/repository_review/grid.mako"
     default_sort_key = "Repository.name"
     columns = [
-        RepositoryGrid.NameColumn("Repository name",
-                                  key="name",
-                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                  attach_popup=True),
-        RepositoryGrid.UserColumn("Owner",
-                                  model_class=model.User,
-                                  attach_popup=False,
-                                  key="User.username"),
+        RepositoryGrid.NameColumn(
+            "Repository name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        RepositoryGrid.UserColumn("Owner", model_class=model.User, attach_popup=False, key="User.username"),
         WithReviewsRevisionColumn("Reviewed revisions"),
         ReviewersColumn("Reviewers", attach_popup=False),
         RatingColumn("Rating", attach_popup=False),
-        ApprovedColumn("Approved", attach_popup=False)
+        ApprovedColumn("Approved", attach_popup=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
     operations = [
-        grids.GridOperation("Inspect repository revisions",
-                            allow_multiple=False,
-                            condition=(lambda item: not item.deleted),
-                            async_compatible=False)
+        grids.GridOperation(
+            "Inspect repository revisions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            async_compatible=False,
+        )
     ]
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
-                               .join((model.User.table, model.User.table.c.id == model.Repository.table.c.user_id)) \
-                               .outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \
-                               .outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
+            .join(
+                (
+                    model.RepositoryReview.table,
+                    model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id,
+                )
+            )
+            .join((model.User.table, model.User.table.c.id == model.Repository.table.c.user_id))
+            .outerjoin(
+                (
+                    model.ComponentReview.table,
+                    model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id,
+                )
+            )
+            .outerjoin(
+                (model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id)
+            )
+        )
 
 
 class RepositoriesWithoutReviewsGrid(RepositoriesWithReviewsGrid):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
     title = "Repositories with no reviews"
     columns = [
-        RepositoriesWithReviewsGrid.NameColumn("Repository name",
-                                               key="name",
-                                               link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                               attach_popup=True),
-        RepositoriesWithReviewsGrid.DescriptionColumn("Synopsis",
-                                                      key="description",
-                                                      attach_popup=False),
+        RepositoriesWithReviewsGrid.NameColumn(
+            "Repository name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        RepositoriesWithReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
         RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
-        RepositoriesWithReviewsGrid.UserColumn("Owner",
-                                               model_class=model.User,
-                                               attach_popup=False,
-                                               key="User.username")
+        RepositoriesWithReviewsGrid.UserColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    operations = [
+        grids.GridOperation(
+            "Inspect repository revisions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            async_compatible=False,
+        )
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    operations = [grids.GridOperation("Inspect repository revisions",
-                                      allow_multiple=False,
-                                      condition=(lambda item: not item.deleted),
-                                      async_compatible=False)]
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false(),
-                                            model.Repository.reviews == null())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(
+                and_(
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.deprecated == false(),
+                    model.Repository.reviews == null(),
+                )
+            )
+            .join(model.User.table)
+        )
 
 
 class RepositoriesReadyForReviewGrid(RepositoriesWithoutReviewsGrid):
@@ -202,109 +236,143 @@ class RepositoriesReadyForReviewGrid(RepositoriesWithoutReviewsGrid):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
     title = "Repositories ready for review"
     columns = [
-        RepositoriesWithoutReviewsGrid.NameColumn("Repository name",
-                                                  key="name",
-                                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                  attach_popup=True),
-        RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis",
-                                                         key="description",
-                                                         attach_popup=False),
+        RepositoriesWithoutReviewsGrid.NameColumn(
+            "Repository name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
         RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
-        RepositoriesWithoutReviewsGrid.UserColumn("Owner",
-                                                  model_class=model.User,
-                                                  attach_popup=False,
-                                                  key="User.username")
+        RepositoriesWithoutReviewsGrid.UserColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    operations = [
+        grids.GridOperation(
+            "Inspect repository revisions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            async_compatible=False,
+        )
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    operations = [grids.GridOperation("Inspect repository revisions",
-                                      allow_multiple=False,
-                                      condition=(lambda item: not item.deleted),
-                                      async_compatible=False)]
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false(),
-                                            model.Repository.reviews == null())) \
-                               .join(model.RepositoryMetadata.table) \
-                               .filter(and_(model.RepositoryMetadata.table.c.downloadable == true(),
-                                            or_(model.RepositoryMetadata.table.c.includes_tools == false(),
-                                                and_(model.RepositoryMetadata.table.c.includes_tools == true(),
-                                                     model.RepositoryMetadata.table.c.tools_functionally_correct == true())))) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(
+                and_(
+                    model.Repository.table.c.deleted == false(),
+                    model.Repository.table.c.deprecated == false(),
+                    model.Repository.reviews == null(),
+                )
+            )
+            .join(model.RepositoryMetadata.table)
+            .filter(
+                and_(
+                    model.RepositoryMetadata.table.c.downloadable == true(),
+                    or_(
+                        model.RepositoryMetadata.table.c.includes_tools == false(),
+                        and_(
+                            model.RepositoryMetadata.table.c.includes_tools == true(),
+                            model.RepositoryMetadata.table.c.tools_functionally_correct == true(),
+                        ),
+                    ),
+                )
+            )
+            .join(model.User.table)
+        )
 
 
 class RepositoriesReviewedByMeGrid(RepositoriesWithReviewsGrid):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
 
     columns = [
-        RepositoriesWithReviewsGrid.NameColumn("Repository name",
-                                               key="name",
-                                               link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                               attach_popup=True),
+        RepositoriesWithReviewsGrid.NameColumn(
+            "Repository name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
         RepositoriesWithReviewsGrid.UserColumn("Owner", attach_popup=False),
         RepositoriesWithReviewsGrid.WithReviewsRevisionColumn("Reviewed revisions"),
         RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers", attach_popup=False),
         RepositoriesWithReviewsGrid.RatingColumn("Rating", attach_popup=False),
-        RepositoriesWithReviewsGrid.ApprovedColumn("Approved", attach_popup=False)
+        RepositoriesWithReviewsGrid.ApprovedColumn("Approved", attach_popup=False),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
-                               .filter(model.RepositoryReview.table.c.user_id == trans.user.id) \
-                               .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id)) \
-                               .outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \
-                               .outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
+            .join(
+                (
+                    model.RepositoryReview.table,
+                    model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id,
+                )
+            )
+            .filter(model.RepositoryReview.table.c.user_id == trans.user.id)
+            .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id))
+            .outerjoin(
+                (
+                    model.ComponentReview.table,
+                    model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id,
+                )
+            )
+            .outerjoin(
+                (model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id)
+            )
+        )
 
 
 class RepositoryReviewsByUserGrid(grids.Grid):
     # This grid filters out repositories that have been marked as deprecated.
 
     class RepositoryNameColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, review):
             return escape(review.repository.name)
 
     class RepositoryDescriptionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, review):
             return escape(review.repository.description)
 
     class RevisionColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, review):
             encoded_review_id = trans.security.encode_id(review.id)
             rval = '<a class="action-button" href="'
             if review.user == trans.user:
-                rval += 'edit_review'
+                rval += "edit_review"
             else:
-                rval += 'browse_review'
-            revision_label = hg_util.get_revision_label(trans.app,
-                                                        review.repository,
-                                                        review.changeset_revision,
-                                                        include_date=True,
-                                                        include_hash=False)
+                rval += "browse_review"
+            revision_label = hg_util.get_revision_label(
+                trans.app, review.repository, review.changeset_revision, include_date=True, include_hash=False
+            )
             rval += f'?id={encoded_review_id}">{revision_label}</a>'
             return rval
 
     class RatingColumn(grids.TextColumn):
-
         def get_value(self, trans, grid, review):
             if review.rating:
                 for index in range(1, 6):
-                    rval = '<input '
+                    rval = "<input "
                     rval += f'name="star1-{trans.security.encode_id(review.id)}" '
                     rval += 'type="radio" '
                     rval += 'class="community_rating_star star" '
@@ -312,76 +380,106 @@ class RepositoryReviewsByUserGrid(grids.Grid):
                     rval += f'value="{str(review.rating)}" '
                     if review.rating > (index - 0.5) and review.rating < (index + 0.5):
                         rval += 'checked="checked" '
-                    rval += '/>'
+                    rval += "/>"
                 return rval
-            return ''
+            return ""
 
     title = "Reviews by user"
     model_class = model.RepositoryReview
-    template = '/webapps/tool_shed/repository_review/grid.mako'
-    default_sort_key = 'repository_id'
+    template = "/webapps/tool_shed/repository_review/grid.mako"
+    default_sort_key = "repository_id"
     use_hide_message = False
     columns = [
-        RepositoryNameColumn("Repository Name",
-                             model_class=model.Repository,
-                             key="Repository.name",
-                             link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                             attach_popup=True),
-        RepositoryDescriptionColumn("Description",
-                                    model_class=model.Repository,
-                                    key="Repository.description",
-                                    attach_popup=False),
+        RepositoryNameColumn(
+            "Repository Name",
+            model_class=model.Repository,
+            key="Repository.name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        RepositoryDescriptionColumn(
+            "Description", model_class=model.Repository, key="Repository.description", attach_popup=False
+        ),
         RevisionColumn("Revision", attach_popup=False),
         RatingColumn("Rating", attach_popup=False),
     ]
     operations = [
-        grids.GridOperation("Inspect repository revisions",
-                            allow_multiple=False,
-                            condition=(lambda item: not item.deleted),
-                            async_compatible=False)
+        grids.GridOperation(
+            "Inspect repository revisions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            async_compatible=False,
+        )
     ]
     num_rows_per_page = 50
 
     def build_initial_query(self, trans, **kwd):
-        user_id = trans.security.decode_id(kwd['id'])
-        return trans.sa_session.query(model.RepositoryReview) \
-                               .filter(and_(model.RepositoryReview.table.c.deleted == false(),
-                                            model.RepositoryReview.table.c.user_id == user_id)) \
-                               .join((model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
-                               .filter(model.Repository.table.c.deprecated == false())
+        user_id = trans.security.decode_id(kwd["id"])
+        return (
+            trans.sa_session.query(model.RepositoryReview)
+            .filter(
+                and_(
+                    model.RepositoryReview.table.c.deleted == false(), model.RepositoryReview.table.c.user_id == user_id
+                )
+            )
+            .join((model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id))
+            .filter(model.Repository.table.c.deprecated == false())
+        )
 
 
 class ReviewedRepositoriesIOwnGrid(RepositoriesWithReviewsGrid):
     title = "Reviewed repositories I own"
     columns = [
-        RepositoriesWithReviewsGrid.NameColumn("Repository name",
-                                               key="name",
-                                               link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                               attach_popup=True),
+        RepositoriesWithReviewsGrid.NameColumn(
+            "Repository name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
         RepositoriesWithReviewsGrid.WithReviewsRevisionColumn("Reviewed revisions"),
         RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
         RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers", attach_popup=False),
-        RepositoryGrid.DeprecatedColumn("Deprecated")
+        RepositoryGrid.DeprecatedColumn("Deprecated"),
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name",
-                                              cols_to_filter=[columns[0]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name",
+            cols_to_filter=[columns[0]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
     operations = [
-        grids.GridOperation("Inspect repository revisions",
-                            allow_multiple=False,
-                            condition=(lambda item: not item.deleted),
-                            async_compatible=False)
+        grids.GridOperation(
+            "Inspect repository revisions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            async_compatible=False,
+        )
     ]
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \
-                               .filter(model.Repository.table.c.user_id == trans.user.id) \
-                               .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id)) \
-                               .outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \
-                               .outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
+        return (
+            trans.sa_session.query(model.Repository)
+            .join(
+                (
+                    model.RepositoryReview.table,
+                    model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id,
+                )
+            )
+            .filter(model.Repository.table.c.user_id == trans.user.id)
+            .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id))
+            .outerjoin(
+                (
+                    model.ComponentReview.table,
+                    model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id,
+                )
+            )
+            .outerjoin(
+                (model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id)
+            )
+        )
 
 
 class RepositoriesWithNoToolTestsGrid(RepositoriesWithoutReviewsGrid):
@@ -391,35 +489,47 @@ class RepositoriesWithNoToolTestsGrid(RepositoriesWithoutReviewsGrid):
     # This grid filters out repositories that have been marked as either deprecated or deleted.
     title = "Repositories that contain tools with no tests or test data"
     columns = [
-        RepositoriesWithoutReviewsGrid.NameColumn("Repository name",
-                                                  key="name",
-                                                  link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
-                                                  attach_popup=True),
-        RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis",
-                                                         key="description",
-                                                         attach_popup=False),
+        RepositoriesWithoutReviewsGrid.NameColumn(
+            "Repository name",
+            key="name",
+            link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)),
+            attach_popup=True,
+        ),
+        RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False),
         RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn("Revisions for review"),
-        RepositoriesWithoutReviewsGrid.UserColumn("Owner",
-                                                  model_class=model.User,
-                                                  attach_popup=False,
-                                                  key="User.username")
+        RepositoriesWithoutReviewsGrid.UserColumn(
+            "Owner", model_class=model.User, attach_popup=False, key="User.username"
+        ),
+    ]
+    columns.append(
+        grids.MulticolFilterColumn(
+            "Search repository name, description",
+            cols_to_filter=[columns[0], columns[1]],
+            key="free-text-search",
+            visible=False,
+            filterable="standard",
+        )
+    )
+    operations = [
+        grids.GridOperation(
+            "Inspect repository revisions",
+            allow_multiple=False,
+            condition=(lambda item: not item.deleted),
+            async_compatible=False,
+        )
     ]
-    columns.append(grids.MulticolFilterColumn("Search repository name, description",
-                                              cols_to_filter=[columns[0], columns[1]],
-                                              key="free-text-search",
-                                              visible=False,
-                                              filterable="standard"))
-    operations = [grids.GridOperation("Inspect repository revisions",
-                                      allow_multiple=False,
-                                      condition=(lambda item: not item.deleted),
-                                      async_compatible=False)]
 
     def build_initial_query(self, trans, **kwd):
-        return trans.sa_session.query(model.Repository) \
-                               .filter(and_(model.Repository.table.c.deleted == false(),
-                                            model.Repository.table.c.deprecated == false())) \
-                               .join(model.RepositoryMetadata.table) \
-                               .filter(and_(model.RepositoryMetadata.table.c.downloadable == true(),
-                                            model.RepositoryMetadata.table.c.includes_tools == true(),
-                                            model.RepositoryMetadata.table.c.tools_functionally_correct == false())) \
-                               .join(model.User.table)
+        return (
+            trans.sa_session.query(model.Repository)
+            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
+            .join(model.RepositoryMetadata.table)
+            .filter(
+                and_(
+                    model.RepositoryMetadata.table.c.downloadable == true(),
+                    model.RepositoryMetadata.table.c.includes_tools == true(),
+                    model.RepositoryMetadata.table.c.tools_functionally_correct == false(),
+                )
+            )
+            .join(model.User.table)
+        )
diff --git a/lib/tool_shed/grids/util.py b/lib/tool_shed/grids/util.py
index 5b5d4b6d79f..e80dc717f77 100644
--- a/lib/tool_shed/grids/util.py
+++ b/lib/tool_shed/grids/util.py
@@ -1,16 +1,21 @@
 import logging
 
 from galaxy.web.form_builder import SelectField
-from tool_shed.util import hg_util, metadata_util
+from tool_shed.util import (
+    hg_util,
+    metadata_util,
+)
 
 log = logging.getLogger(__name__)
 
 
 def build_approved_select_field(trans, name, selected_value=None, for_component=True):
-    options = [('No', trans.model.ComponentReview.approved_states.NO),
-               ('Yes', trans.model.ComponentReview.approved_states.YES)]
+    options = [
+        ("No", trans.model.ComponentReview.approved_states.NO),
+        ("Yes", trans.model.ComponentReview.approved_states.YES),
+    ]
     if for_component:
-        options.append(('Not applicable', trans.model.ComponentReview.approved_states.NA))
+        options.append(("Not applicable", trans.model.ComponentReview.approved_states.NA))
         if selected_value is None:
             selected_value = trans.model.ComponentReview.approved_states.NA
     select_field = SelectField(name=name)
@@ -20,8 +25,9 @@ def build_approved_select_field(trans, name, selected_value=None, for_component=
     return select_field
 
 
-def build_changeset_revision_select_field(trans, repository, selected_value=None, add_id_to_name=True,
-                                          downloadable=False, reviewed=False, not_reviewed=False):
+def build_changeset_revision_select_field(
+    trans, repository, selected_value=None, add_id_to_name=True, downloadable=False, reviewed=False, not_reviewed=False
+):
     """
     Build a SelectField whose options are the changeset_rev strings of certain revisions of the
     received repository.
@@ -54,12 +60,9 @@ def build_changeset_revision_select_field(trans, repository, selected_value=None
         # Restrict the options to all revisions that have associated metadata.
         repository_metadata_revisions = repository.metadata_revisions
     for repository_metadata in repository_metadata_revisions:
-        rev, label, changeset_revision = \
-            hg_util.get_rev_label_changeset_revision_from_repository_metadata(trans.app,
-                                                                              repository_metadata,
-                                                                              repository=repository,
-                                                                              include_date=True,
-                                                                              include_hash=False)
+        rev, label, changeset_revision = hg_util.get_rev_label_changeset_revision_from_repository_metadata(
+            trans.app, repository_metadata, repository=repository, include_date=True, include_hash=False
+        )
         changeset_tups.append((rev, label, changeset_revision))
         refresh_on_change_values.append(changeset_revision)
     # Sort options by the revision label.  Even though the downloadable_revisions query sorts by update_time,
@@ -68,9 +71,9 @@ def build_changeset_revision_select_field(trans, repository, selected_value=None
         # Display the latest revision first.
         options.insert(0, (changeset_tup[1], changeset_tup[2]))
     if add_id_to_name:
-        name = 'changeset_revision_%d' % repository.id
+        name = "changeset_revision_%d" % repository.id
     else:
-        name = 'changeset_revision'
+        name = "changeset_revision"
     select_field = SelectField(name=name, refresh_on_change=True)
     for option_tup in options:
         selected = selected_value and option_tup[1] == selected_value
@@ -87,8 +90,7 @@ def filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_
     tool_dependency_definition.
     """
     repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools(trans, repository)
-    if repository_metadata is not None \
-            and repository_metadata.missing_test_components:
+    if repository_metadata is not None and repository_metadata.missing_test_components:
         return repository_metadata.changeset_revision
     return None
 
@@ -116,17 +118,21 @@ def get_latest_downloadable_repository_metadata(trans, repository):
     tip_ctx = str(repo[repo.changelog.tip()])
     repository_metadata = None
     try:
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, tip_ctx)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, encoded_repository_id, tip_ctx
+        )
         if repository_metadata is not None and repository_metadata.downloadable:
             return repository_metadata
         return None
     except Exception:
-        latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, tip_ctx, downloadable=True)
+        latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision(
+            trans.app, repository, tip_ctx, downloadable=True
+        )
         if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
             return None
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                          encoded_repository_id,
-                                                                                          latest_downloadable_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, encoded_repository_id, latest_downloadable_revision
+        )
         if repository_metadata is not None and repository_metadata.downloadable:
             return repository_metadata
         return None
@@ -154,15 +160,19 @@ def get_latest_repository_metadata(trans, repository):
     repo = repository.hg_repo
     tip_ctx = str(repo[repo.changelog.tip()])
     try:
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, encoded_repository_id, tip_ctx)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, encoded_repository_id, tip_ctx
+        )
         return repository_metadata
     except Exception:
-        latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, tip_ctx, downloadable=False)
+        latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision(
+            trans.app, repository, tip_ctx, downloadable=False
+        )
         if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
             return None
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                          encoded_repository_id,
-                                                                                          latest_downloadable_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, encoded_repository_id, latest_downloadable_revision
+        )
         return repository_metadata
 
 
@@ -175,6 +185,6 @@ def get_latest_repository_metadata_if_it_includes_invalid_tools(trans, repositor
     repository_metadata = get_latest_repository_metadata(trans, repository)
     if repository_metadata is not None:
         metadata = repository_metadata.metadata
-        if metadata is not None and 'invalid_tools' in metadata:
+        if metadata is not None and "invalid_tools" in metadata:
             return repository_metadata
     return None
diff --git a/lib/tool_shed/managers/groups.py b/lib/tool_shed/managers/groups.py
index d3a5338bbc1..53cf50337fb 100644
--- a/lib/tool_shed/managers/groups.py
+++ b/lib/tool_shed/managers/groups.py
@@ -3,16 +3,23 @@ Manager and Serializer for TS groups.
 """
 import logging
 
-from sqlalchemy import false, true
-from sqlalchemy.orm.exc import MultipleResultsFound
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy import (
+    false,
+    true,
+)
+from sqlalchemy.orm.exc import (
+    MultipleResultsFound,
+    NoResultFound,
+)
 
-from galaxy.exceptions import Conflict
-from galaxy.exceptions import InconsistentDatabase
-from galaxy.exceptions import InternalServerError
-from galaxy.exceptions import ItemAccessibilityException
-from galaxy.exceptions import ObjectNotFound
-from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import (
+    Conflict,
+    InconsistentDatabase,
+    InternalServerError,
+    ItemAccessibilityException,
+    ObjectNotFound,
+    RequestParameterInvalidException,
+)
 
 log = logging.getLogger(__name__)
 
@@ -37,27 +44,29 @@ class GroupManager:
         :rtype:     tool_shed.model.Group
         """
         if decoded_group_id is None and name is None:
-            raise RequestParameterInvalidException('You must supply either ID or a name of the group.')
+            raise RequestParameterInvalidException("You must supply either ID or a name of the group.")
 
         name_query = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name)
-        id_query = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.id == decoded_group_id)
+        id_query = trans.sa_session.query(trans.app.model.Group).filter(
+            trans.app.model.Group.table.c.id == decoded_group_id
+        )
 
         try:
             group = id_query.one() if decoded_group_id else name_query.one()
         except MultipleResultsFound:
-            raise InconsistentDatabase('Multiple groups found with the same identifier.')
+            raise InconsistentDatabase("Multiple groups found with the same identifier.")
         except NoResultFound:
-            raise ObjectNotFound('No group found with the identifier provided.')
+            raise ObjectNotFound("No group found with the identifier provided.")
         except Exception:
-            raise InternalServerError('Error loading from the database.')
+            raise InternalServerError("Error loading from the database.")
         return group
 
-    def create(self, trans, name, description=''):
+    def create(self, trans, name, description=""):
         """
         Create a new group.
         """
         if not trans.user_is_admin:
-            raise ItemAccessibilityException('Only administrators can create groups.')
+            raise ItemAccessibilityException("Only administrators can create groups.")
         else:
             if self.get(trans, name=name):
                 raise Conflict(f"Group with the given name already exists. Name: {str(name)}")
@@ -73,9 +82,9 @@ class GroupManager:
         """
         changed = False
         if not trans.user_is_admin:
-            raise ItemAccessibilityException('Only administrators can update groups.')
+            raise ItemAccessibilityException("Only administrators can update groups.")
         if group.deleted:
-            raise RequestParameterInvalidException('You cannot modify a deleted group. Undelete it first.')
+            raise RequestParameterInvalidException("You cannot modify a deleted group. Undelete it first.")
         if name is not None:
             group.name = name
             changed = True
@@ -92,7 +101,7 @@ class GroupManager:
         Mark given group deleted/undeleted based on the flag.
         """
         if not trans.user_is_admin:
-            raise ItemAccessibilityException('Only administrators can delete and undelete groups.')
+            raise ItemAccessibilityException("Only administrators can delete and undelete groups.")
         if undelete:
             group.deleted = False
         else:
diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index d1734251c3e..4b26be1ad27 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/lib/tool_shed/managers/repositories.py
@@ -3,10 +3,16 @@ Manager and Serializer for TS repositories.
 """
 import logging
 
-from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound
+from sqlalchemy.orm.exc import (
+    MultipleResultsFound,
+    NoResultFound,
+)
 
-from galaxy.exceptions import (InconsistentDatabase, InternalServerError,
-    RequestParameterInvalidException)
+from galaxy.exceptions import (
+    InconsistentDatabase,
+    InternalServerError,
+    RequestParameterInvalidException,
+)
 
 log = logging.getLogger(__name__)
 
@@ -31,13 +37,17 @@ class RepoManager:
         :rtype:     tool_shed.webapp.model.Repository
         """
         try:
-            repo = trans.sa_session.query(trans.app.model.Repository).filter(trans.app.model.Repository.table.c.id == decoded_repo_id).one()
+            repo = (
+                trans.sa_session.query(trans.app.model.Repository)
+                .filter(trans.app.model.Repository.table.c.id == decoded_repo_id)
+                .one()
+            )
         except MultipleResultsFound:
-            raise InconsistentDatabase('Multiple repositories found with the same id.')
+            raise InconsistentDatabase("Multiple repositories found with the same id.")
         except NoResultFound:
-            raise RequestParameterInvalidException('No repository found with the id provided.')
+            raise RequestParameterInvalidException("No repository found with the id provided.")
         except Exception:
-            raise InternalServerError('Error loading from the database.')
+            raise InternalServerError("Error loading from the database.")
         return repo
 
     def list_by_owner(self, trans, user_id):
@@ -47,10 +57,12 @@ class RepoManager:
         :returns: query that will emit repositories owned by given user
         :rtype:   sqlalchemy query
         """
-        query = trans.sa_session.query(trans.app.model.Repository).filter(trans.app.model.Repository.table.c.user_id == user_id)
+        query = trans.sa_session.query(trans.app.model.Repository).filter(
+            trans.app.model.Repository.table.c.user_id == user_id
+        )
         return query
 
-    def create(self, trans, name, description=''):
+    def create(self, trans, name, description=""):
         """
         Create a new group.
         """
diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py
index 796bed71aa1..06b7720d4a4 100644
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -1,3 +1,3 @@
 from galaxy.tool_shed.metadata.metadata_generator import MetadataGenerator
 
-__all__ = ('MetadataGenerator', )
+__all__ = ("MetadataGenerator",)
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 63b7aba18c6..cf18d3055bc 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -1,7 +1,10 @@
 import logging
 import tempfile
 
-from sqlalchemy import false, or_
+from sqlalchemy import (
+    false,
+    or_,
+)
 
 from galaxy import util
 from galaxy.util import inflector
@@ -9,59 +12,83 @@ from galaxy.web.form_builder import SelectField
 from tool_shed.metadata import metadata_generator
 from tool_shed.repository_types import util as rt_util
 from tool_shed.repository_types.metadata import TipOnly
-from tool_shed.util import (basic_util, common_util, hg_util, metadata_util,
-    repository_util, shed_util_common as suc, tool_util)
+from tool_shed.util import (
+    basic_util,
+    common_util,
+    hg_util,
+    metadata_util,
+    repository_util,
+)
+from tool_shed.util import shed_util_common as suc
+from tool_shed.util import tool_util
 
 log = logging.getLogger(__name__)
 
 
 class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
-
-    def __init__(self, app, user, repository=None, changeset_revision=None, repository_clone_url=None,
-                 shed_config_dict=None, relative_install_dir=None, repository_files_dir=None,
-                 resetting_all_metadata_on_repository=False, updating_installed_repository=False,
-                 persist=False, metadata_dict=None):
-        super().__init__(app, repository, changeset_revision,
-                         repository_clone_url, shed_config_dict,
-                         relative_install_dir, repository_files_dir,
-                         resetting_all_metadata_on_repository,
-                         updating_installed_repository, persist,
-                         metadata_dict=metadata_dict, user=user)
+    def __init__(
+        self,
+        app,
+        user,
+        repository=None,
+        changeset_revision=None,
+        repository_clone_url=None,
+        shed_config_dict=None,
+        relative_install_dir=None,
+        repository_files_dir=None,
+        resetting_all_metadata_on_repository=False,
+        updating_installed_repository=False,
+        persist=False,
+        metadata_dict=None,
+    ):
+        super().__init__(
+            app,
+            repository,
+            changeset_revision,
+            repository_clone_url,
+            shed_config_dict,
+            relative_install_dir,
+            repository_files_dir,
+            resetting_all_metadata_on_repository,
+            updating_installed_repository,
+            persist,
+            metadata_dict=metadata_dict,
+            user=user,
+        )
         self.app = app
         self.user = user
         # Repository metadata comparisons for changeset revisions.
-        self.EQUAL = 'equal'
-        self.NO_METADATA = 'no metadata'
-        self.NOT_EQUAL_AND_NOT_SUBSET = 'not equal and not subset'
-        self.SUBSET = 'subset'
+        self.EQUAL = "equal"
+        self.NO_METADATA = "no metadata"
+        self.NOT_EQUAL_AND_NOT_SUBSET = "not equal and not subset"
+        self.SUBSET = "subset"
         self.SUBSET_VALUES = [self.EQUAL, self.SUBSET]
 
     def add_tool_versions(self, id, repository_metadata, changeset_revisions):
         # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata.
         metadata = repository_metadata.metadata
         tool_versions_dict = {}
-        for tool_dict in metadata.get('tools', []):
+        for tool_dict in metadata.get("tools", []):
             # We have at least 2 changeset revisions to compare tool guids and tool ids.
-            parent_id = self.get_parent_id(id,
-                                           tool_dict['id'],
-                                           tool_dict['version'],
-                                           tool_dict['guid'],
-                                           changeset_revisions)
-            tool_versions_dict[tool_dict['guid']] = parent_id
+            parent_id = self.get_parent_id(
+                id, tool_dict["id"], tool_dict["version"], tool_dict["guid"], changeset_revisions
+            )
+            tool_versions_dict[tool_dict["guid"]] = parent_id
         if tool_versions_dict:
             repository_metadata.tool_versions = tool_versions_dict
             self.sa_session.add(repository_metadata)
             self.sa_session.flush()
 
-    def build_repository_ids_select_field(self, name='repository_ids', multiple=True, display='checkboxes',
-                                          my_writable=False):
+    def build_repository_ids_select_field(
+        self, name="repository_ids", multiple=True, display="checkboxes", my_writable=False
+    ):
         """Generate the current list of repositories for resetting metadata."""
         repositories_select_field = SelectField(name=name, multiple=multiple, display=display)
         query = self.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=True)
         for repository in query:
             owner = str(repository.user.username)
-            option_label = f'{str(repository.name)} ({owner})'
-            option_value = f'{self.app.security.encode_id(repository.id)}'
+            option_label = f"{str(repository.name)} ({owner})"
+            option_value = f"{self.app.security.encode_id(repository.id)}"
             repositories_select_field.add_option(option_label, option_value)
         return repositories_select_field
 
@@ -72,11 +99,14 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         # assume we can delete the older records, so we'll order by update_time descending and
         # delete records that have the same changeset_revision we come across later.
         changeset_revisions_checked = []
-        for repository_metadata in \
-            self.sa_session.query(self.app.model.RepositoryMetadata) \
-                           .filter(self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id) \
-                           .order_by(self.app.model.RepositoryMetadata.table.c.changeset_revision,
-                                     self.app.model.RepositoryMetadata.table.c.update_time.desc()):
+        for repository_metadata in (
+            self.sa_session.query(self.app.model.RepositoryMetadata)
+            .filter(self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id)
+            .order_by(
+                self.app.model.RepositoryMetadata.table.c.changeset_revision,
+                self.app.model.RepositoryMetadata.table.c.update_time.desc(),
+            )
+        ):
             changeset_revision = repository_metadata.changeset_revision
             if changeset_revision in changeset_revisions_checked or changeset_revision not in changeset_revisions:
                 self.sa_session.delete(repository_metadata)
@@ -91,26 +121,26 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         # This changeset_revision is an ancestor of self.changeset_revision which is associated
         # with self.metadata_dict.  A new repository_metadata record will be created only
         # when this method returns the constant value self.NOT_EQUAL_AND_NOT_SUBSET.
-        ancestor_datatypes = ancestor_metadata_dict.get('datatypes', [])
-        ancestor_tools = ancestor_metadata_dict.get('tools', [])
-        ancestor_guids = [tool_dict['guid'] for tool_dict in ancestor_tools]
+        ancestor_datatypes = ancestor_metadata_dict.get("datatypes", [])
+        ancestor_tools = ancestor_metadata_dict.get("tools", [])
+        ancestor_guids = [tool_dict["guid"] for tool_dict in ancestor_tools]
         ancestor_guids.sort()
-        ancestor_readme_files = ancestor_metadata_dict.get('readme_files', [])
-        ancestor_repository_dependencies_dict = ancestor_metadata_dict.get('repository_dependencies', {})
-        ancestor_repository_dependencies = ancestor_repository_dependencies_dict.get('repository_dependencies', [])
-        ancestor_tool_dependencies = ancestor_metadata_dict.get('tool_dependencies', {})
-        ancestor_workflows = ancestor_metadata_dict.get('workflows', [])
-        ancestor_data_manager = ancestor_metadata_dict.get('data_manager', {})
-        current_datatypes = self.metadata_dict.get('datatypes', [])
-        current_tools = self.metadata_dict.get('tools', [])
-        current_guids = [tool_dict['guid'] for tool_dict in current_tools]
+        ancestor_readme_files = ancestor_metadata_dict.get("readme_files", [])
+        ancestor_repository_dependencies_dict = ancestor_metadata_dict.get("repository_dependencies", {})
+        ancestor_repository_dependencies = ancestor_repository_dependencies_dict.get("repository_dependencies", [])
+        ancestor_tool_dependencies = ancestor_metadata_dict.get("tool_dependencies", {})
+        ancestor_workflows = ancestor_metadata_dict.get("workflows", [])
+        ancestor_data_manager = ancestor_metadata_dict.get("data_manager", {})
+        current_datatypes = self.metadata_dict.get("datatypes", [])
+        current_tools = self.metadata_dict.get("tools", [])
+        current_guids = [tool_dict["guid"] for tool_dict in current_tools]
         current_guids.sort()
-        current_readme_files = self.metadata_dict.get('readme_files', [])
-        current_repository_dependencies_dict = self.metadata_dict.get('repository_dependencies', {})
-        current_repository_dependencies = current_repository_dependencies_dict.get('repository_dependencies', [])
-        current_tool_dependencies = self.metadata_dict.get('tool_dependencies', {})
-        current_workflows = self.metadata_dict.get('workflows', [])
-        current_data_manager = self.metadata_dict.get('data_manager', {})
+        current_readme_files = self.metadata_dict.get("readme_files", [])
+        current_repository_dependencies_dict = self.metadata_dict.get("repository_dependencies", {})
+        current_repository_dependencies = current_repository_dependencies_dict.get("repository_dependencies", [])
+        current_tool_dependencies = self.metadata_dict.get("tool_dependencies", {})
+        current_workflows = self.metadata_dict.get("workflows", [])
+        current_data_manager = self.metadata_dict.get("data_manager", {})
         # Handle case where no metadata exists for either changeset.
         no_datatypes = not ancestor_datatypes and not current_datatypes
         no_readme_files = not ancestor_readme_files and not current_readme_files
@@ -119,27 +149,37 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         no_tools = not ancestor_guids and not current_guids
         no_workflows = not ancestor_workflows and not current_workflows
         no_data_manager = not ancestor_data_manager and not current_data_manager
-        if no_datatypes and no_readme_files and no_repository_dependencies and \
-                no_tool_dependencies and no_tools and no_workflows and \
-                no_data_manager:
+        if (
+            no_datatypes
+            and no_readme_files
+            and no_repository_dependencies
+            and no_tool_dependencies
+            and no_tools
+            and no_workflows
+            and no_data_manager
+        ):
             return self.NO_METADATA
         # Uncomment the following if we decide that README files should affect how installable
         # repository revisions are defined.  See the NOTE in self.compare_readme_files().
         # readme_file_comparision = self.compare_readme_files( ancestor_readme_files, current_readme_files )
-        repository_dependency_comparison = self.compare_repository_dependencies(ancestor_repository_dependencies,
-                                                                                current_repository_dependencies)
-        tool_dependency_comparison = self.compare_tool_dependencies(ancestor_tool_dependencies,
-                                                                    current_tool_dependencies)
+        repository_dependency_comparison = self.compare_repository_dependencies(
+            ancestor_repository_dependencies, current_repository_dependencies
+        )
+        tool_dependency_comparison = self.compare_tool_dependencies(
+            ancestor_tool_dependencies, current_tool_dependencies
+        )
         workflow_comparison = self.compare_workflows(ancestor_workflows, current_workflows)
         datatype_comparison = self.compare_datatypes(ancestor_datatypes, current_datatypes)
         data_manager_comparison = self.compare_data_manager(ancestor_data_manager, current_data_manager)
         # Handle case where all metadata is the same.
-        if ancestor_guids == current_guids and \
-                repository_dependency_comparison == self.EQUAL and \
-                tool_dependency_comparison == self.EQUAL and \
-                workflow_comparison == self.EQUAL and \
-                datatype_comparison == self.EQUAL and \
-                data_manager_comparison == self.EQUAL:
+        if (
+            ancestor_guids == current_guids
+            and repository_dependency_comparison == self.EQUAL
+            and tool_dependency_comparison == self.EQUAL
+            and workflow_comparison == self.EQUAL
+            and datatype_comparison == self.EQUAL
+            and data_manager_comparison == self.EQUAL
+        ):
             return self.EQUAL
         # Handle case where ancestor metadata is a subset of current metadata.
         # readme_file_is_subset = readme_file_comparision in [ self.EQUAL, self.SUBSET ]
@@ -148,9 +188,13 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         workflow_dependency_is_subset = workflow_comparison in self.SUBSET_VALUES
         datatype_is_subset = datatype_comparison in self.SUBSET_VALUES
         datamanager_is_subset = data_manager_comparison in self.SUBSET_VALUES
-        if repository_dependency_is_subset and tool_dependency_is_subset and \
-                workflow_dependency_is_subset and datatype_is_subset and \
-                datamanager_is_subset:
+        if (
+            repository_dependency_is_subset
+            and tool_dependency_is_subset
+            and workflow_dependency_is_subset
+            and datatype_is_subset
+            and datamanager_is_subset
+        ):
             is_subset = True
             for guid in ancestor_guids:
                 if guid not in current_guids:
@@ -165,18 +209,23 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
 
         def __data_manager_dict_to_tuple_list(metadata_dict):
             # we do not check tool_guid or tool conf file name
-            return set(sorted((
-                name,
-                tuple(sorted(value.get('data_tables', []))),
-                value.get('guid'),
-                value.get('version'),
-                value.get('name'),
-                value.get('id')
-            ) for name, value in metadata_dict.items()))
+            return set(
+                sorted(
+                    (
+                        name,
+                        tuple(sorted(value.get("data_tables", []))),
+                        value.get("guid"),
+                        value.get("version"),
+                        value.get("name"),
+                        value.get("id"),
+                    )
+                    for name, value in metadata_dict.items()
+                )
+            )
 
         # only compare valid entries, any invalid entries are ignored
-        ancestor_metadata = __data_manager_dict_to_tuple_list(ancestor_metadata.get('data_managers', {}))
-        current_metadata = __data_manager_dict_to_tuple_list(current_metadata.get('data_managers', {}))
+        ancestor_metadata = __data_manager_dict_to_tuple_list(ancestor_metadata.get("data_managers", {}))
+        current_metadata = __data_manager_dict_to_tuple_list(current_metadata.get("data_managers", {}))
         # use set comparisons
         if ancestor_metadata.issubset(current_metadata):
             if ancestor_metadata == current_metadata:
@@ -191,14 +240,16 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         if len(ancestor_datatypes) <= len(current_datatypes):
             for ancestor_datatype in ancestor_datatypes:
                 # Currently the only way to differentiate datatypes is by name.
-                ancestor_datatype_dtype = ancestor_datatype['dtype']
-                ancestor_datatype_extension = ancestor_datatype['extension']
-                ancestor_datatype_mimetype = ancestor_datatype.get('mimetype', None)
+                ancestor_datatype_dtype = ancestor_datatype["dtype"]
+                ancestor_datatype_extension = ancestor_datatype["extension"]
+                ancestor_datatype_mimetype = ancestor_datatype.get("mimetype", None)
                 found_in_current = False
                 for current_datatype in current_datatypes:
-                    if current_datatype['dtype'] == ancestor_datatype_dtype and \
-                            current_datatype['extension'] == ancestor_datatype_extension and \
-                            current_datatype.get('mimetype', None) == ancestor_datatype_mimetype:
+                    if (
+                        current_datatype["dtype"] == ancestor_datatype_dtype
+                        and current_datatype["extension"] == ancestor_datatype_extension
+                        and current_datatype.get("mimetype", None) == ancestor_datatype_mimetype
+                    ):
                         found_in_current = True
                         break
                 if not found_in_current:
@@ -242,30 +293,45 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         # Create a string from each tuple in the list for easier comparison.
         if len(ancestor_repository_dependencies) <= len(current_repository_dependencies):
             for ancestor_tup in ancestor_repository_dependencies:
-                a_tool_shed, a_repo_name, a_repo_owner, a_changeset_revision, \
-                    a_prior_installation_required, \
-                    a_only_if_compiling_contained_td = ancestor_tup
+                (
+                    a_tool_shed,
+                    a_repo_name,
+                    a_repo_owner,
+                    a_changeset_revision,
+                    a_prior_installation_required,
+                    a_only_if_compiling_contained_td,
+                ) = ancestor_tup
                 cleaned_a_tool_shed = common_util.remove_protocol_from_tool_shed_url(a_tool_shed)
                 found_in_current = False
                 for current_tup in current_repository_dependencies:
-                    c_tool_shed, c_repo_name, c_repo_owner, \
-                        c_changeset_revision, c_prior_installation_required, \
-                        c_only_if_compiling_contained_td = current_tup
+                    (
+                        c_tool_shed,
+                        c_repo_name,
+                        c_repo_owner,
+                        c_changeset_revision,
+                        c_prior_installation_required,
+                        c_only_if_compiling_contained_td,
+                    ) = current_tup
                     cleaned_c_tool_shed = common_util.remove_protocol_from_tool_shed_url(c_tool_shed)
-                    if cleaned_c_tool_shed == cleaned_a_tool_shed and \
-                            c_repo_name == a_repo_name and \
-                            c_repo_owner == a_repo_owner and \
-                            c_changeset_revision == a_changeset_revision and \
-                            util.string_as_bool(c_prior_installation_required) == util.string_as_bool(a_prior_installation_required) and \
-                            util.string_as_bool(c_only_if_compiling_contained_td) == util.string_as_bool(a_only_if_compiling_contained_td):
+                    if (
+                        cleaned_c_tool_shed == cleaned_a_tool_shed
+                        and c_repo_name == a_repo_name
+                        and c_repo_owner == a_repo_owner
+                        and c_changeset_revision == a_changeset_revision
+                        and util.string_as_bool(c_prior_installation_required)
+                        == util.string_as_bool(a_prior_installation_required)
+                        and util.string_as_bool(c_only_if_compiling_contained_td)
+                        == util.string_as_bool(a_only_if_compiling_contained_td)
+                    ):
                         found_in_current = True
                         break
                 if not found_in_current:
                     # In some cases, the only difference between a dependency definition in the lists
                     # is the changeset_revision value.  We'll check to see if this is the case, and if
                     # the defined dependency is a repository that has metadata set only on its tip.
-                    if not self.different_revision_defines_tip_only_repository_dependency(ancestor_tup,
-                                                                                          current_repository_dependencies):
+                    if not self.different_revision_defines_tip_only_repository_dependency(
+                        ancestor_tup, current_repository_dependencies
+                    ):
                         return self.NOT_EQUAL_AND_NOT_SUBSET
                     return self.SUBSET
             if len(ancestor_repository_dependencies) == len(current_repository_dependencies):
@@ -308,15 +374,17 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                 # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
                 ancestor_workflow_dict = ancestor_workflow_tup[1]
                 # Currently the only way to differentiate workflows is by name.
-                ancestor_workflow_name = ancestor_workflow_dict['name']
-                num_ancestor_workflow_steps = len(ancestor_workflow_dict['steps'])
+                ancestor_workflow_name = ancestor_workflow_dict["name"]
+                num_ancestor_workflow_steps = len(ancestor_workflow_dict["steps"])
                 found_in_current = False
                 for current_workflow_tup in current_workflows:
                     current_workflow_dict = current_workflow_tup[1]
                     # Assume that if the name and number of steps are euqal, then the workflows
                     # are the same.  Of course, this may not be true...
-                    if current_workflow_dict['name'] == ancestor_workflow_name and \
-                            len(current_workflow_dict['steps']) == num_ancestor_workflow_steps:
+                    if (
+                        current_workflow_dict["name"] == ancestor_workflow_name
+                        and len(current_workflow_dict["steps"]) == num_ancestor_workflow_steps
+                    ):
                         found_in_current = True
                         break
                 if not found_in_current:
@@ -336,28 +404,34 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         includes_tool_dependencies = False
         includes_workflows = False
         if metadata_dict:
-            repository_dependencies_dict = metadata_dict.get('repository_dependencies', {})
-            repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
-            has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
-                repository_util.get_repository_dependency_types(repository_dependencies)
-            if 'datatypes' in metadata_dict:
+            repository_dependencies_dict = metadata_dict.get("repository_dependencies", {})
+            repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
+            (
+                has_repository_dependencies,
+                has_repository_dependencies_only_if_compiling_contained_td,
+            ) = repository_util.get_repository_dependency_types(repository_dependencies)
+            if "datatypes" in metadata_dict:
                 includes_datatypes = True
-            if 'tools' in metadata_dict:
+            if "tools" in metadata_dict:
                 includes_tools = True
-            if 'tool_dependencies' in metadata_dict:
+            if "tool_dependencies" in metadata_dict:
                 includes_tool_dependencies = True
-            if 'workflows' in metadata_dict:
+            if "workflows" in metadata_dict:
                 includes_workflows = True
-        if has_repository_dependencies or \
-                has_repository_dependencies_only_if_compiling_contained_td or \
-                includes_datatypes or includes_tools or \
-                includes_tool_dependencies or includes_workflows:
+        if (
+            has_repository_dependencies
+            or has_repository_dependencies_only_if_compiling_contained_td
+            or includes_datatypes
+            or includes_tools
+            or includes_tool_dependencies
+            or includes_workflows
+        ):
             downloadable = True
         else:
             downloadable = False
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                          self.app.security.encode_id(self.repository.id),
-                                                                                          changeset_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            self.app, self.app.security.encode_id(self.repository.id), changeset_revision
+        )
         if repository_metadata:
             repository_metadata.metadata = metadata_dict
             repository_metadata.downloadable = downloadable
@@ -367,16 +441,17 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
             repository_metadata.includes_tool_dependencies = includes_tool_dependencies
             repository_metadata.includes_workflows = includes_workflows
         else:
-            repository_metadata = \
-                self.app.model.RepositoryMetadata(repository_id=self.repository.id,
-                                                  changeset_revision=changeset_revision,
-                                                  metadata=metadata_dict,
-                                                  downloadable=downloadable,
-                                                  has_repository_dependencies=has_repository_dependencies,
-                                                  includes_datatypes=includes_datatypes,
-                                                  includes_tools=includes_tools,
-                                                  includes_tool_dependencies=includes_tool_dependencies,
-                                                  includes_workflows=includes_workflows)
+            repository_metadata = self.app.model.RepositoryMetadata(
+                repository_id=self.repository.id,
+                changeset_revision=changeset_revision,
+                metadata=metadata_dict,
+                downloadable=downloadable,
+                has_repository_dependencies=has_repository_dependencies,
+                includes_datatypes=includes_datatypes,
+                includes_tools=includes_tools,
+                includes_tool_dependencies=includes_tool_dependencies,
+                includes_workflows=includes_workflows,
+            )
         # Always set the default values for the following columns.  When resetting all metadata
         # on a repository this will reset the values.
         repository_metadata.missing_test_components = False
@@ -390,12 +465,24 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         Determine if the only difference between rd_tup and a dependency definition in the list of
         repository_dependencies is the changeset_revision value.
         """
-        rd_tool_shed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required, rd_only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(rd_tup)
+        (
+            rd_tool_shed,
+            rd_name,
+            rd_owner,
+            rd_changeset_revision,
+            rd_prior_installation_required,
+            rd_only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(rd_tup)
         cleaned_rd_tool_shed = common_util.remove_protocol_from_tool_shed_url(rd_tool_shed)
         for repository_dependency in repository_dependencies:
-            tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                common_util.parse_repository_dependency_tuple(repository_dependency)
+            (
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ) = common_util.parse_repository_dependency_tuple(repository_dependency)
             cleaned_tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed)
             if cleaned_rd_tool_shed == cleaned_tool_shed and rd_name == name and rd_owner == owner:
                 # Determine if the repository represented by the dependency tuple is an instance of the repository type TipOnly.
@@ -409,16 +496,18 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         # Compare from most recent to oldest.
         changeset_revisions.reverse()
         for changeset_revision in changeset_revisions:
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app, id, changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                self.app, id, changeset_revision
+            )
             metadata = repository_metadata.metadata
-            tools_dicts = metadata.get('tools', [])
+            tools_dicts = metadata.get("tools", [])
             for tool_dict in tools_dicts:
-                if tool_dict['guid'] == guid:
+                if tool_dict["guid"] == guid:
                     # The tool has not changed between the compared changeset revisions.
                     continue
-                if tool_dict['id'] == old_id and tool_dict['version'] != version:
+                if tool_dict["id"] == old_id and tool_dict["version"] != version:
                     # The tool version is different, so we've found the parent.
-                    return tool_dict['guid']
+                    return tool_dict["guid"]
         if parent_id is None:
             # The tool did not change through all of the changeset revisions.
             return old_id
@@ -435,8 +524,9 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         if my_writable:
             username = self.user.username
             clause_list = []
-            for repository in self.sa_session.query(self.app.model.Repository) \
-                                             .filter(self.app.model.Repository.table.c.deleted == false()):
+            for repository in self.sa_session.query(self.app.model.Repository).filter(
+                self.app.model.Repository.table.c.deleted == false()
+            ):
                 # Always reset metadata on all repositories of types repository_suite_definition and
                 # tool_dependency_definition.
                 if repository.type in [rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION]:
@@ -445,31 +535,34 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                     allow_push = repository.allow_push()
                     if allow_push:
                         # Include all repositories that are writable by the current user.
-                        allow_push_usernames = allow_push.split(',')
+                        allow_push_usernames = allow_push.split(",")
                         if username in allow_push_usernames:
                             clause_list.append(self.app.model.Repository.table.c.id == repository.id)
             if clause_list:
                 if order:
-                    return self.sa_session.query(self.app.model.Repository) \
-                                          .filter(or_(*clause_list)) \
-                                          .order_by(self.app.model.Repository.table.c.name,
-                                                    self.app.model.Repository.table.c.user_id)
+                    return (
+                        self.sa_session.query(self.app.model.Repository)
+                        .filter(or_(*clause_list))
+                        .order_by(self.app.model.Repository.table.c.name, self.app.model.Repository.table.c.user_id)
+                    )
                 else:
-                    return self.sa_session.query(self.app.model.Repository) \
-                                          .filter(or_(*clause_list))
+                    return self.sa_session.query(self.app.model.Repository).filter(or_(*clause_list))
             else:
                 # Return an empty query.
-                return self.sa_session.query(self.app.model.Repository) \
-                                      .filter(self.app.model.Repository.table.c.id == -1)
+                return self.sa_session.query(self.app.model.Repository).filter(
+                    self.app.model.Repository.table.c.id == -1
+                )
         else:
             if order:
-                return self.sa_session.query(self.app.model.Repository) \
-                                      .filter(self.app.model.Repository.table.c.deleted == false()) \
-                                      .order_by(self.app.model.Repository.table.c.name,
-                                                self.app.model.Repository.table.c.user_id)
+                return (
+                    self.sa_session.query(self.app.model.Repository)
+                    .filter(self.app.model.Repository.table.c.deleted == false())
+                    .order_by(self.app.model.Repository.table.c.name, self.app.model.Repository.table.c.user_id)
+                )
             else:
-                return self.sa_session.query(self.app.model.Repository) \
-                                      .filter(self.app.model.Repository.table.c.deleted == false())
+                return self.sa_session.query(self.app.model.Repository).filter(
+                    self.app.model.Repository.table.c.deleted == false()
+                )
 
     def new_datatypes_metadata_required(self, repository_metadata):
         """
@@ -479,13 +572,13 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         """
         # Datatypes are stored in metadata as a list of dictionaries that looks like:
         # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}]
-        if 'datatypes' in self.metadata_dict:
-            current_datatypes = self.metadata_dict['datatypes']
+        if "datatypes" in self.metadata_dict:
+            current_datatypes = self.metadata_dict["datatypes"]
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'datatypes' in metadata:
-                        ancestor_datatypes = metadata['datatypes']
+                    if "datatypes" in metadata:
+                        ancestor_datatypes = metadata["datatypes"]
                         # The saved metadata must be a subset of the new metadata.
                         datatype_comparison = self.compare_datatypes(ancestor_datatypes, current_datatypes)
                         if datatype_comparison == self.NOT_EQUAL_AND_NOT_SUBSET:
@@ -517,20 +610,24 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         self.repository because one or more Galaxy utilities may have been deleted from self.repository in
         the new tip.
         """
-        repository_metadata = metadata_util.get_latest_repository_metadata(self.app,
-                                                                           self.repository.id,
-                                                                           downloadable=False)
+        repository_metadata = metadata_util.get_latest_repository_metadata(
+            self.app, self.repository.id, downloadable=False
+        )
         datatypes_required = self.new_datatypes_metadata_required(repository_metadata)
         # Uncomment the following if we decide that README files should affect how installable
         # repository revisions are defined.  See the NOTE in the compare_readme_files() method.
         # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata )
-        repository_dependencies_required = \
-            self.new_repository_dependency_metadata_required(repository_metadata)
+        repository_dependencies_required = self.new_repository_dependency_metadata_required(repository_metadata)
         tools_required = self.new_tool_metadata_required(repository_metadata)
         tool_dependencies_required = self.new_tool_dependency_metadata_required(repository_metadata)
         workflows_required = self.new_workflow_metadata_required(repository_metadata)
-        if datatypes_required or repository_dependencies_required or \
-                tools_required or tool_dependencies_required or workflows_required:
+        if (
+            datatypes_required
+            or repository_dependencies_required
+            or tools_required
+            or tool_dependencies_required
+            or workflows_required
+        ):
             return True
         return False
 
@@ -543,16 +640,15 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         # Repository README files are kind of a special case because they have no effect on reproducibility.
         # We'll simply inspect the file names to determine if any that exist in the saved metadata are
         # eliminated from the new metadata in self.metadata_dict.
-        if 'readme_files' in self.metadata_dict:
-            current_readme_files = self.metadata_dict['readme_files']
+        if "readme_files" in self.metadata_dict:
+            current_readme_files = self.metadata_dict["readme_files"]
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'readme_files' in metadata:
-                        ancestor_readme_files = metadata['readme_files']
+                    if "readme_files" in metadata:
+                        ancestor_readme_files = metadata["readme_files"]
                         # The saved metadata must be a subset of the new metadata.
-                        readme_file_comparison = self.compare_readme_files(ancestor_readme_files,
-                                                                           current_readme_files)
+                        readme_file_comparison = self.compare_readme_files(ancestor_readme_files, current_readme_files)
                         if readme_file_comparison == self.NOT_EQUAL_AND_NOT_SUBSET:
                             return True
                         else:
@@ -582,11 +678,13 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         """
         if repository_metadata:
             metadata = repository_metadata.metadata
-            if 'repository_dependencies' in metadata:
-                saved_repository_dependencies = metadata['repository_dependencies']['repository_dependencies']
-                new_repository_dependencies_metadata = self.metadata_dict.get('repository_dependencies', None)
+            if "repository_dependencies" in metadata:
+                saved_repository_dependencies = metadata["repository_dependencies"]["repository_dependencies"]
+                new_repository_dependencies_metadata = self.metadata_dict.get("repository_dependencies", None)
                 if new_repository_dependencies_metadata:
-                    new_repository_dependencies = self.metadata_dict['repository_dependencies']['repository_dependencies']
+                    new_repository_dependencies = self.metadata_dict["repository_dependencies"][
+                        "repository_dependencies"
+                    ]
                     # TODO: We used to include the following here to handle the case where repository
                     # dependency definitions were deleted.  However this erroneously returned True in
                     # cases where is should not have done so.  This usually occurred where multiple single
@@ -602,8 +700,9 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                             # In some cases, the only difference between a dependency definition in the lists
                             # is the changeset_revision value.  We'll check to see if this is the case, and if
                             # the defined dependency is a repository that has metadata set only on its tip.
-                            if not self.different_revision_defines_tip_only_repository_dependency(saved_repository_dependency,
-                                                                                                  new_repository_dependencies):
+                            if not self.different_revision_defines_tip_only_repository_dependency(
+                                saved_repository_dependency, new_repository_dependencies
+                            ):
                                 return True
                     return False
                 else:
@@ -613,7 +712,7 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
             else:
                 return False
         else:
-            if 'repository_dependencies' in self.metadata_dict:
+            if "repository_dependencies" in self.metadata_dict:
                 # There is no saved repository metadata, so we need to create a new repository_metadata record.
                 return True
             else:
@@ -627,29 +726,29 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         self.metadata_dict to determine if a new repository_metadata table record is required, or if
         the last saved metadata record can be updated instead.
         """
-        if 'tools' in self.metadata_dict:
+        if "tools" in self.metadata_dict:
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'tools' in metadata:
+                    if "tools" in metadata:
                         saved_tool_ids = []
                         # The metadata for one or more tools was successfully generated in the past
                         # for this repository, so we first compare the version string for each tool id
                         # in self.metadata_dict with what was previously saved to see if we need to create
                         # a new table record or if we can simply update the existing record.
-                        for new_tool_metadata_dict in self.metadata_dict['tools']:
-                            for saved_tool_metadata_dict in metadata['tools']:
-                                if saved_tool_metadata_dict['id'] not in saved_tool_ids:
-                                    saved_tool_ids.append(saved_tool_metadata_dict['id'])
-                                if new_tool_metadata_dict['id'] == saved_tool_metadata_dict['id']:
-                                    if new_tool_metadata_dict['version'] != saved_tool_metadata_dict['version']:
+                        for new_tool_metadata_dict in self.metadata_dict["tools"]:
+                            for saved_tool_metadata_dict in metadata["tools"]:
+                                if saved_tool_metadata_dict["id"] not in saved_tool_ids:
+                                    saved_tool_ids.append(saved_tool_metadata_dict["id"])
+                                if new_tool_metadata_dict["id"] == saved_tool_metadata_dict["id"]:
+                                    if new_tool_metadata_dict["version"] != saved_tool_metadata_dict["version"]:
                                         return True
                         # So far, a new metadata record is not required, but we still have to check to see if
                         # any new tool ids exist in self.metadata_dict that are not in the saved metadata.  We do
                         # this because if a new tarball was uploaded to a repository that included tools, it
                         # may have removed existing tool files if they were not included in the uploaded tarball.
-                        for new_tool_metadata_dict in self.metadata_dict['tools']:
-                            if new_tool_metadata_dict['id'] not in saved_tool_ids:
+                        for new_tool_metadata_dict in self.metadata_dict["tools"]:
+                            if new_tool_metadata_dict["id"] not in saved_tool_ids:
                                 return True
                         return False
                     else:
@@ -677,9 +776,9 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         if repository_metadata:
             metadata = repository_metadata.metadata
             if metadata:
-                if 'tool_dependencies' in metadata:
-                    saved_tool_dependencies = metadata['tool_dependencies']
-                    new_tool_dependencies = self.metadata_dict.get('tool_dependencies', None)
+                if "tool_dependencies" in metadata:
+                    saved_tool_dependencies = metadata["tool_dependencies"]
+                    new_tool_dependencies = self.metadata_dict.get("tool_dependencies", None)
                     if new_tool_dependencies:
                         # TODO: We used to include the following here to handle the case where
                         # tool dependency definitions were deleted.  However, this erroneously
@@ -708,7 +807,7 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                 # in the repository, so we can update the existing repository metadata.
                 return False
         else:
-            if 'tool_dependencies' in self.metadata_dict:
+            if "tool_dependencies" in self.metadata_dict:
                 # There is no saved repository metadata, so we need to create a new repository_metadata
                 # record.
                 return True
@@ -723,7 +822,7 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         there's no real way to differentiate versions of exported workflows.  If this changes
         at some future time, this method should be enhanced accordingly.
         """
-        if 'workflows' in self.metadata_dict:
+        if "workflows" in self.metadata_dict:
             if repository_metadata:
                 # The repository has metadata, so update the workflows value -
                 # no new record is needed.
@@ -772,7 +871,9 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                         # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current
                         # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current
                         # metadata, so persist ancestor metadata.
-                        comparison = self.compare_changeset_revisions(ancestor_changeset_revision, ancestor_metadata_dict)
+                        comparison = self.compare_changeset_revisions(
+                            ancestor_changeset_revision, ancestor_metadata_dict
+                        )
                         if comparison in [self.NO_METADATA, self.EQUAL, self.SUBSET]:
                             ancestor_changeset_revision = self.changeset_revision
                             ancestor_metadata_dict = self.metadata_dict
@@ -817,38 +918,40 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         changeset_revisions_that_contain_tools = []
         for changeset in repo.changelog:
             changeset_revision = str(repo[changeset])
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                              encoded_repository_id,
-                                                                                              changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                self.app, encoded_repository_id, changeset_revision
+            )
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if metadata.get('tools', None):
+                    if metadata.get("tools", None):
                         changeset_revisions_that_contain_tools.append(changeset_revision)
         # The list of changeset_revisions_that_contain_tools is now filtered to contain only those that
         # are downloadable and contain tools.  If a repository includes tools, build a dictionary of
         # { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision.
         for index, changeset_revision in enumerate(changeset_revisions_that_contain_tools):
             tool_versions_dict = {}
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                              encoded_repository_id,
-                                                                                              changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                self.app, encoded_repository_id, changeset_revision
+            )
             metadata = repository_metadata.metadata
-            tool_dicts = metadata['tools']
+            tool_dicts = metadata["tools"]
             if index == 0:
                 # The first changeset_revision is a special case because it will have no ancestor
                 # changeset_revisions in which to match tools.  The parent tool id for tools in the
                 # first changeset_revision will be the "old_id" in the tool config.
                 for tool_dict in tool_dicts:
-                    tool_versions_dict[tool_dict['guid']] = tool_dict['id']
+                    tool_versions_dict[tool_dict["guid"]] = tool_dict["id"]
             else:
                 for tool_dict in tool_dicts:
-                    parent_id = self.get_parent_id(encoded_repository_id,
-                                                   tool_dict['id'],
-                                                   tool_dict['version'],
-                                                   tool_dict['guid'],
-                                                   changeset_revisions_that_contain_tools[0:index])
-                    tool_versions_dict[tool_dict['guid']] = parent_id
+                    parent_id = self.get_parent_id(
+                        encoded_repository_id,
+                        tool_dict["id"],
+                        tool_dict["version"],
+                        tool_dict["guid"],
+                        changeset_revisions_that_contain_tools[0:index],
+                    )
+                    tool_versions_dict[tool_dict["guid"]] = parent_id
             if tool_versions_dict:
                 repository_metadata.tool_versions = tool_versions_dict
                 self.sa_session.add(repository_metadata)
@@ -859,9 +962,9 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
         Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
         This method is called from both Galaxy and the Tool Shed.
         """
-        repository_ids = util.listify(kwd.get('repository_ids', None))
-        message = ''
-        status = 'done'
+        repository_ids = util.listify(kwd.get("repository_ids", None))
+        message = ""
+        status = "done"
         if repository_ids:
             successful_count = 0
             unsuccessful_count = 0
@@ -872,41 +975,45 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                     self.resetting_all_metadata_on_repository = True
                     self.reset_all_metadata_on_repository_in_tool_shed()
                     if self.invalid_file_tups:
-                        message = tool_util.generate_message_for_invalid_tools(self.app,
-                                                                               self.invalid_file_tups,
-                                                                               repository,
-                                                                               None,
-                                                                               as_html=False)
+                        message = tool_util.generate_message_for_invalid_tools(
+                            self.app, self.invalid_file_tups, repository, None, as_html=False
+                        )
                         log.debug(message)
                         unsuccessful_count += 1
                     else:
-                        log.debug("Successfully reset metadata on repository %s owned by %s" %
-                            (str(repository.name), str(repository.user.username)))
+                        log.debug(
+                            "Successfully reset metadata on repository %s owned by %s"
+                            % (str(repository.name), str(repository.user.username))
+                        )
                         successful_count += 1
                 except Exception:
                     log.exception("Error attempting to reset metadata on repository %s", str(repository.name))
                     unsuccessful_count += 1
-            message = "Successfully reset metadata on %d %s.  " % \
-                (successful_count, inflector.cond_plural(successful_count, "repository"))
+            message = "Successfully reset metadata on %d %s.  " % (
+                successful_count,
+                inflector.cond_plural(successful_count, "repository"),
+            )
             if unsuccessful_count:
-                message += "Error setting metadata on %d %s - see the paster log for details.  " % \
-                    (unsuccessful_count, inflector.cond_plural(unsuccessful_count, "repository"))
+                message += "Error setting metadata on %d %s - see the paster log for details.  " % (
+                    unsuccessful_count,
+                    inflector.cond_plural(unsuccessful_count, "repository"),
+                )
         else:
-            message = 'Select at least one repository to on which to reset all metadata.'
-            status = 'error'
+            message = "Select at least one repository to on which to reset all metadata."
+            status = "error"
         return message, status
 
     def set_repository(self, repository):
         super().set_repository(repository)
         self.repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(self.user, repository)
 
-    def set_repository_metadata(self, host, content_alert_str='', **kwd):
+    def set_repository_metadata(self, host, content_alert_str="", **kwd):
         """
         Set metadata using the self.repository's current disk files, returning specific error
         messages (if any) to alert the repository owner that the changeset has problems.
         """
-        message = ''
-        status = 'done'
+        message = ""
+        status = "done"
         encoded_id = self.app.security.encode_id(self.repository.id)
         repo = self.repository.hg_repo
         self.generate_metadata_for_changeset_revision()
@@ -916,47 +1023,47 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
             tip_only = isinstance(repository_type_class, TipOnly)
             if not tip_only and self.new_metadata_required_for_utilities():
                 # Create a new repository_metadata table row.
-                repository_metadata = self.create_or_update_repository_metadata(self.repository.tip(),
-                                                                                self.metadata_dict)
+                repository_metadata = self.create_or_update_repository_metadata(
+                    self.repository.tip(), self.metadata_dict
+                )
                 # If this is the first record stored for this repository, see if we need to send any email alerts.
                 if len(self.repository.downloadable_revisions) == 1:
-                    suc.handle_email_alerts(self.app,
-                                            host,
-                                            self.repository,
-                                            content_alert_str='',
-                                            new_repo_alert=True,
-                                            admin_only=False)
+                    suc.handle_email_alerts(
+                        self.app, host, self.repository, content_alert_str="", new_repo_alert=True, admin_only=False
+                    )
             else:
                 # Update the latest stored repository metadata with the contents and attributes of self.metadata_dict.
-                repository_metadata = metadata_util.get_latest_repository_metadata(self.app,
-                                                                                   self.repository.id,
-                                                                                   downloadable=False)
+                repository_metadata = metadata_util.get_latest_repository_metadata(
+                    self.app, self.repository.id, downloadable=False
+                )
                 if repository_metadata:
                     downloadable = metadata_util.is_downloadable(self.metadata_dict)
                     # Update the last saved repository_metadata table row.
                     repository_metadata.changeset_revision = self.repository.tip()
                     repository_metadata.metadata = self.metadata_dict
                     repository_metadata.downloadable = downloadable
-                    if 'datatypes' in self.metadata_dict:
+                    if "datatypes" in self.metadata_dict:
                         repository_metadata.includes_datatypes = True
                     else:
                         repository_metadata.includes_datatypes = False
                     # We don't store information about the special type of repository dependency that is needed only for
                     # compiling a tool dependency defined for the dependent repository.
-                    repository_dependencies_dict = self.metadata_dict.get('repository_dependencies', {})
-                    repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
-                    has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
-                        repository_util.get_repository_dependency_types(repository_dependencies)
+                    repository_dependencies_dict = self.metadata_dict.get("repository_dependencies", {})
+                    repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
+                    (
+                        has_repository_dependencies,
+                        has_repository_dependencies_only_if_compiling_contained_td,
+                    ) = repository_util.get_repository_dependency_types(repository_dependencies)
                     repository_metadata.has_repository_dependencies = has_repository_dependencies
-                    if 'tool_dependencies' in self.metadata_dict:
+                    if "tool_dependencies" in self.metadata_dict:
                         repository_metadata.includes_tool_dependencies = True
                     else:
                         repository_metadata.includes_tool_dependencies = False
-                    if 'tools' in self.metadata_dict:
+                    if "tools" in self.metadata_dict:
                         repository_metadata.includes_tools = True
                     else:
                         repository_metadata.includes_tools = False
-                    if 'workflows' in self.metadata_dict:
+                    if "workflows" in self.metadata_dict:
                         repository_metadata.includes_workflows = True
                     else:
                         repository_metadata.includes_workflows = False
@@ -965,28 +1072,31 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
                     self.sa_session.flush()
                 else:
                     # There are no metadata records associated with the repository.
-                    repository_metadata = self.create_or_update_repository_metadata(self.repository.tip(),
-                                                                                    self.metadata_dict)
-            if 'tools' in self.metadata_dict and repository_metadata and status != 'error':
+                    repository_metadata = self.create_or_update_repository_metadata(
+                        self.repository.tip(), self.metadata_dict
+                    )
+            if "tools" in self.metadata_dict and repository_metadata and status != "error":
                 # Set tool versions on the new downloadable change set.  The order of the list of changesets is
                 # critical, so we use the repo's changelog.
                 changeset_revisions = []
                 for changeset in repo.changelog:
                     changeset_revision = str(repo[changeset])
-                    if metadata_util.get_repository_metadata_by_changeset_revision(self.app, encoded_id, changeset_revision):
+                    if metadata_util.get_repository_metadata_by_changeset_revision(
+                        self.app, encoded_id, changeset_revision
+                    ):
                         changeset_revisions.append(changeset_revision)
                 self.add_tool_versions(encoded_id, repository_metadata, changeset_revisions)
         elif len(repo) == 1 and not self.invalid_file_tups:
-            message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % \
-                str(self.repository.tip())
+            message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % str(
+                self.repository.tip()
+            )
             message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
         if self.invalid_file_tups:
-            message = tool_util.generate_message_for_invalid_tools(self.app,
-                                                                   self.invalid_file_tups,
-                                                                   self.repository,
-                                                                   self.metadata_dict)
-            status = 'error'
+            message = tool_util.generate_message_for_invalid_tools(
+                self.app, self.invalid_file_tups, self.repository, self.metadata_dict
+            )
+            status = "error"
         return message, status
 
     def set_repository_metadata_due_to_new_tip(self, host, content_alert_str=None, **kwd):
diff --git a/lib/tool_shed/repository_registry.py b/lib/tool_shed/repository_registry.py
index 304a03ecf48..941bd83285f 100644
--- a/lib/tool_shed/repository_registry.py
+++ b/lib/tool_shed/repository_registry.py
@@ -1,17 +1,22 @@
 import logging
 
-from sqlalchemy import and_, false, or_
+from sqlalchemy import (
+    and_,
+    false,
+    or_,
+)
 
 import tool_shed.repository_types.util as rt_util
-from tool_shed.util import hg_util
-from tool_shed.util import metadata_util
+from tool_shed.util import (
+    hg_util,
+    metadata_util,
+)
 from tool_shed.webapp import model
 
 log = logging.getLogger(__name__)
 
 
 class Registry:
-
     def __init__(self, app):
         log.debug("Loading the repository registry...")
         self.app = app
@@ -140,16 +145,19 @@ class Registry:
     def get_certified_level_one_clause_list(self):
         certified_level_one_tuples = []
         clause_list = []
-        for repository in self.sa_session.query(model.Repository) \
-                                         .filter(and_(model.Repository.table.c.deleted == false(),
-                                                      model.Repository.table.c.deprecated == false())):
+        for repository in self.sa_session.query(model.Repository).filter(
+            and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
+        ):
             certified_level_one_tuple = self.get_certified_level_one_tuple(repository)
             latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple
             if is_level_one_certified:
                 certified_level_one_tuples.append(certified_level_one_tuple)
-                clause_list.append(and_(
-                    model.RepositoryMetadata.table.c.repository_id == repository.id,
-                    model.RepositoryMetadata.table.c.changeset_revision == latest_installable_changeset_revision))
+                clause_list.append(
+                    and_(
+                        model.RepositoryMetadata.table.c.repository_id == repository.id,
+                        model.RepositoryMetadata.table.c.changeset_revision == latest_installable_changeset_revision,
+                    )
+                )
         return clause_list
 
     def get_certified_level_one_tuple(self, repository):
@@ -161,12 +169,14 @@ class Registry:
         if repository.deleted or repository.deprecated:
             return (None, False)
         # Get the latest installable changeset revision since that is all that is currently configured for testing.
-        latest_installable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(self.app, repository)
+        latest_installable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(
+            self.app, repository
+        )
         if latest_installable_changeset_revision not in [None, hg_util.INITIAL_CHANGELOG_HASH]:
             encoded_repository_id = self.app.security.encode_id(repository.id)
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                              encoded_repository_id,
-                                                                                              latest_installable_changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                self.app, encoded_repository_id, latest_installable_changeset_revision
+            )
             if repository_metadata:
                 # No repository_metadata.
                 return (latest_installable_changeset_revision, True)
@@ -180,7 +190,11 @@ class Registry:
             if repository:
                 if repository.deprecated or repository.deleted:
                     return False
-                tuple = (str(repository.name), str(repository.user.username), str(repository_metadata.changeset_revision))
+                tuple = (
+                    str(repository.name),
+                    str(repository.user.username),
+                    str(repository_metadata.changeset_revision),
+                )
                 if repository.type in [rt_util.REPOSITORY_SUITE_DEFINITION]:
                     return tuple in self.certified_level_one_suite_tuples
                 else:
@@ -220,16 +234,19 @@ class Registry:
 
     def load_repository_and_suite_tuples(self):
         # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples.
-        for repository in self.sa_session.query(model.Repository) \
-                                         .join(model.RepositoryMetadata.table) \
-                                         .filter(or_(*self.certified_level_one_clause_list)) \
-                                         .join(model.User.table):
+        for repository in (
+            self.sa_session.query(model.Repository)
+            .join(model.RepositoryMetadata.table)
+            .filter(or_(*self.certified_level_one_clause_list))
+            .join(model.User.table)
+        ):
             self.load_certified_level_one_repository_and_suite_tuple(repository)
         # Load self.repository_and_suite_tuples and self.suite_tuples
-        for repository in self.sa_session.query(model.Repository) \
-                                         .filter(and_(model.Repository.table.c.deleted == false(),
-                                                      model.Repository.table.c.deprecated == false())) \
-                                         .join(model.User.table):
+        for repository in (
+            self.sa_session.query(model.Repository)
+            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
+            .join(model.User.table)
+        ):
             self.load_repository_and_suite_tuple(repository)
 
     def load_viewable_repositories_and_suites_by_category(self):
@@ -262,9 +279,9 @@ class Registry:
                     is_valid = self.is_valid(repository)
                     encoded_repository_id = self.app.security.encode_id(repository.id)
                     tip_changeset_hash = repository.tip()
-                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                                      encoded_repository_id,
-                                                                                                      tip_changeset_hash)
+                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                        self.app, encoded_repository_id, tip_changeset_hash
+                    )
                     self.viewable_repositories_and_suites_by_category[category_name] += 1
                     if is_valid:
                         self.viewable_valid_repositories_and_suites_by_category[category_name] += 1
@@ -327,7 +344,9 @@ class Registry:
                     if is_level_one_certified:
                         if category_name in self.certified_level_one_viewable_repositories_and_suites_by_category:
                             if self.certified_level_one_viewable_repositories_and_suites_by_category[category_name] > 0:
-                                self.certified_level_one_viewable_repositories_and_suites_by_category[category_name] -= 1
+                                self.certified_level_one_viewable_repositories_and_suites_by_category[
+                                    category_name
+                                ] -= 1
                         else:
                             self.certified_level_one_viewable_repositories_and_suites_by_category[category_name] = 0
                         if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION:
diff --git a/lib/tool_shed/repository_types/metadata.py b/lib/tool_shed/repository_types/metadata.py
index 1d9e01f56f0..537600345b9 100644
--- a/lib/tool_shed/repository_types/metadata.py
+++ b/lib/tool_shed/repository_types/metadata.py
@@ -4,7 +4,6 @@ log = logging.getLogger(__name__)
 
 
 class Metadata:
-
     def __init__(self):
         self.type = None
 
@@ -17,7 +16,6 @@ class Metadata:
 
 
 class TipOnly(Metadata):
-
     def __init__(self):
         self.type = None
 
diff --git a/lib/tool_shed/repository_types/registry.py b/lib/tool_shed/repository_types/registry.py
index 83d89eab177..3b1d461698e 100644
--- a/lib/tool_shed/repository_types/registry.py
+++ b/lib/tool_shed/repository_types/registry.py
@@ -3,19 +3,22 @@ import logging
 from . import (
     repository_suite_definition,
     tool_dependency_definition,
-    unrestricted
+    unrestricted,
 )
 
 log = logging.getLogger(__name__)
 
 
 class Registry:
-
     def __init__(self):
         self.repository_types_by_label = {}
-        self.repository_types_by_label['unrestricted'] = unrestricted.Unrestricted()
-        self.repository_types_by_label['repository_suite_definition'] = repository_suite_definition.RepositorySuiteDefinition()
-        self.repository_types_by_label['tool_dependency_definition'] = tool_dependency_definition.ToolDependencyDefinition()
+        self.repository_types_by_label["unrestricted"] = unrestricted.Unrestricted()
+        self.repository_types_by_label[
+            "repository_suite_definition"
+        ] = repository_suite_definition.RepositorySuiteDefinition()
+        self.repository_types_by_label[
+            "tool_dependency_definition"
+        ] = tool_dependency_definition.ToolDependencyDefinition()
 
     def get_class_by_label(self, label):
         return self.repository_types_by_label.get(label, None)
diff --git a/lib/tool_shed/repository_types/repository_suite_definition.py b/lib/tool_shed/repository_types/repository_suite_definition.py
index a891d4605b4..8c1b45fb3d1 100644
--- a/lib/tool_shed/repository_types/repository_suite_definition.py
+++ b/lib/tool_shed/repository_types/repository_suite_definition.py
@@ -9,11 +9,10 @@ log = logging.getLogger(__name__)
 
 
 class RepositorySuiteDefinition(TipOnly):
-
     def __init__(self):
         self.type = rt_util.REPOSITORY_SUITE_DEFINITION
-        self.label = 'Repository suite definition'
-        self.valid_file_names = ['repository_dependencies.xml']
+        self.label = "Repository suite definition"
+        self.valid_file_names = ["repository_dependencies.xml"]
 
     def is_valid_for_type(self, repository, revisions_to_check=None):
         """
diff --git a/lib/tool_shed/repository_types/tool_dependency_definition.py b/lib/tool_shed/repository_types/tool_dependency_definition.py
index 52e30e30252..bd14238e8f1 100644
--- a/lib/tool_shed/repository_types/tool_dependency_definition.py
+++ b/lib/tool_shed/repository_types/tool_dependency_definition.py
@@ -9,11 +9,10 @@ log = logging.getLogger(__name__)
 
 
 class ToolDependencyDefinition(TipOnly):
-
     def __init__(self):
         self.type = rt_util.TOOL_DEPENDENCY_DEFINITION
-        self.label = 'Tool dependency definition'
-        self.valid_file_names = ['tool_dependencies.xml']
+        self.label = "Tool dependency definition"
+        self.valid_file_names = ["tool_dependencies.xml"]
 
     def is_valid_for_type(self, repository, revisions_to_check=None):
         """
diff --git a/lib/tool_shed/repository_types/unrestricted.py b/lib/tool_shed/repository_types/unrestricted.py
index 9ccb55568cc..a9c71fb6f51 100644
--- a/lib/tool_shed/repository_types/unrestricted.py
+++ b/lib/tool_shed/repository_types/unrestricted.py
@@ -7,10 +7,9 @@ log = logging.getLogger(__name__)
 
 
 class Unrestricted(Metadata):
-
     def __init__(self):
         self.type = rt_util.UNRESTRICTED
-        self.label = 'Unrestricted'
+        self.label = "Unrestricted"
 
     def is_valid_for_type(self, repository, revisions_to_check=None):
         """A repository's type can only be changed to the unrestricted type if it is new or has never been installed."""
diff --git a/lib/tool_shed/repository_types/util.py b/lib/tool_shed/repository_types/util.py
index 6c122e02667..dc2751eebc1 100644
--- a/lib/tool_shed/repository_types/util.py
+++ b/lib/tool_shed/repository_types/util.py
@@ -13,7 +13,7 @@ from galaxy.web.form_builder import SelectField
 log = logging.getLogger(__name__)
 
 
-def build_repository_type_select_field(trans, repository=None, name='repository_type'):
+def build_repository_type_select_field(trans, repository=None, name="repository_type"):
     """Called from the Tool Shed to generate the current list of supported repository types."""
     if repository:
         selected_type = str(repository.type)
@@ -38,32 +38,42 @@ def build_repository_type_select_field(trans, repository=None, name='repository_
 
 
 def generate_message_for_repository_type_change(app, repository):
-    message = ''
+    message = ""
     if repository.can_change_type_to(app, REPOSITORY_SUITE_DEFINITION):
-        repository_suite_definition_type_class = \
-            app.repository_types_registry.get_class_by_label(REPOSITORY_SUITE_DEFINITION)
-        message += "This repository currently contains a single file named <b>%s</b>.  If the intent of this repository is " % \
-            REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
+        repository_suite_definition_type_class = app.repository_types_registry.get_class_by_label(
+            REPOSITORY_SUITE_DEFINITION
+        )
+        message += (
+            "This repository currently contains a single file named <b>%s</b>.  If the intent of this repository is "
+            % REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
+        )
         message += "to define relationships to a collection of repositories that contain related Galaxy utilities with "
-        message += "no plans to add additional files, consider setting its type to <b>%s</b>.<br/>" % \
-            repository_suite_definition_type_class.label
+        message += (
+            "no plans to add additional files, consider setting its type to <b>%s</b>.<br/>"
+            % repository_suite_definition_type_class.label
+        )
     elif repository.can_change_type_to(app, TOOL_DEPENDENCY_DEFINITION):
-        tool_dependency_definition_type_class = \
-            app.repository_types_registry.get_class_by_label(TOOL_DEPENDENCY_DEFINITION)
-        message += "This repository currently contains a single file named <b>%s</b>.  If additional files will " % \
-            TOOL_DEPENDENCY_DEFINITION_FILENAME
-        message += "not be added to this repository, consider setting its type to <b>%s</b>.<br/>" % \
-            tool_dependency_definition_type_class.label
+        tool_dependency_definition_type_class = app.repository_types_registry.get_class_by_label(
+            TOOL_DEPENDENCY_DEFINITION
+        )
+        message += (
+            "This repository currently contains a single file named <b>%s</b>.  If additional files will "
+            % TOOL_DEPENDENCY_DEFINITION_FILENAME
+        )
+        message += (
+            "not be added to this repository, consider setting its type to <b>%s</b>.<br/>"
+            % tool_dependency_definition_type_class.label
+        )
     return message
 
 
 __all__ = (
-    'build_repository_type_select_field',
-    'generate_message_for_repository_type_change',
-    'REPOSITORY_DEPENDENCY_DEFINITION_FILENAME',
-    'REPOSITORY_SUITE_DEFINITION',
-    'TOOL_DEPENDENCY_DEFINITION',
-    'TOOL_DEPENDENCY_DEFINITION_FILENAME',
-    'UNRESTRICTED',
-    'types',
+    "build_repository_type_select_field",
+    "generate_message_for_repository_type_change",
+    "REPOSITORY_DEPENDENCY_DEFINITION_FILENAME",
+    "REPOSITORY_SUITE_DEFINITION",
+    "TOOL_DEPENDENCY_DEFINITION",
+    "TOOL_DEPENDENCY_DEFINITION_FILENAME",
+    "UNRESTRICTED",
+    "types",
 )
diff --git a/lib/tool_shed/test/base/common.py b/lib/tool_shed/test/base/common.py
index 2b15cbb7c49..b9694564f90 100644
--- a/lib/tool_shed/test/base/common.py
+++ b/lib/tool_shed/test/base/common.py
@@ -1,35 +1,35 @@
 admin_user = None
 admin_user_private_role = None
-admin_email = 'test@bx.psu.edu'
-admin_username = 'admin-user'
+admin_email = "test@bx.psu.edu"
+admin_username = "admin-user"
 
 test_user_1 = None
 test_user_1_private_role = None
-test_user_1_email = 'test-1@bx.psu.edu'
-test_user_1_name = 'user1'
+test_user_1_email = "test-1@bx.psu.edu"
+test_user_1_name = "user1"
 
 test_user_2 = None
 test_user_2_private_role = None
-test_user_2_email = 'test-2@bx.psu.edu'
-test_user_2_name = 'user2'
+test_user_2_email = "test-2@bx.psu.edu"
+test_user_2_name = "user2"
 
 test_user_3 = None
 test_user_3_private_role = None
-test_user_3_email = 'test-3@bx.psu.edu'
-test_user_3_name = 'user3'
+test_user_3_email = "test-3@bx.psu.edu"
+test_user_3_name = "user3"
 
-complex_repository_dependency_template = '''<?xml version="1.0"?>
+complex_repository_dependency_template = """<?xml version="1.0"?>
 <tool_dependency>
     <package name="${package}" version="${version}">
 ${dependency_lines}
     </package>
 </tool_dependency>
-'''
+"""
 
-new_repository_dependencies_xml = '''<?xml version="1.0"?>
+new_repository_dependencies_xml = """<?xml version="1.0"?>
 <repositories${description}>
 ${dependency_lines}
 </repositories>
-'''
+"""
 
-new_repository_dependencies_line = '''    <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}"${prior_installation_required} />'''
+new_repository_dependencies_line = """    <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}"${prior_installation_required} />"""
diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py
index c128444126e..8b7d3dd6ed3 100644
--- a/lib/tool_shed/test/base/test_db_util.py
+++ b/lib/tool_shed/test/base/test_db_util.py
@@ -1,17 +1,19 @@
 import logging
 
-from sqlalchemy import and_, false, true
+from sqlalchemy import (
+    and_,
+    false,
+    true,
+)
 
 import galaxy.model
 import galaxy.model.tool_shed_install
 import tool_shed.webapp.model as model
-from galaxy_test.driver.driver_util import (
-    galaxy_context as ga_session,
-    install_context as install_session,
-    tool_shed_context as sa_session
-)
+from galaxy_test.driver.driver_util import galaxy_context as ga_session
+from galaxy_test.driver.driver_util import install_context as install_session
+from galaxy_test.driver.driver_util import tool_shed_context as sa_session
 
-log = logging.getLogger('test.tool_shed.test_db_util')
+log = logging.getLogger("test.tool_shed.test_db_util")
 
 
 def delete_obj(obj):
@@ -36,51 +38,71 @@ def get_all_repositories():
 
 def get_all_installed_repositories(actually_installed=False):
     if actually_installed:
-        return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository) \
-                              .filter(and_(galaxy.model.tool_shed_install.ToolShedRepository.table.c.deleted == false(),
-                                           galaxy.model.tool_shed_install.ToolShedRepository.table.c.uninstalled == false(),
-                                           galaxy.model.tool_shed_install.ToolShedRepository.table.c.status == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED)) \
-                              .all()
+        return (
+            install_session.query(galaxy.model.tool_shed_install.ToolShedRepository)
+            .filter(
+                and_(
+                    galaxy.model.tool_shed_install.ToolShedRepository.table.c.deleted == false(),
+                    galaxy.model.tool_shed_install.ToolShedRepository.table.c.uninstalled == false(),
+                    galaxy.model.tool_shed_install.ToolShedRepository.table.c.status
+                    == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED,
+                )
+            )
+            .all()
+        )
     else:
         return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).all()
 
 
 def get_category_by_name(name):
-    return sa_session.query(model.Category) \
-                     .filter(model.Category.table.c.name == name) \
-                     .first()
+    return sa_session.query(model.Category).filter(model.Category.table.c.name == name).first()
 
 
 def get_default_user_permissions_by_role(role):
-    return sa_session.query(model.DefaultUserPermissions) \
-                     .filter(model.DefaultUserPermissions.table.c.role_id == role.id) \
-                     .all()
+    return (
+        sa_session.query(model.DefaultUserPermissions)
+        .filter(model.DefaultUserPermissions.table.c.role_id == role.id)
+        .all()
+    )
 
 
 def get_default_user_permissions_by_user(user):
-    return sa_session.query(model.DefaultUserPermissions) \
-                     .filter(model.DefaultUserPermissions.table.c.user_id == user.id) \
-                     .all()
+    return (
+        sa_session.query(model.DefaultUserPermissions)
+        .filter(model.DefaultUserPermissions.table.c.user_id == user.id)
+        .all()
+    )
 
 
 def get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision):
-    return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository) \
-                          .filter(and_(galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,
-                                       galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner,
-                                       galaxy.model.tool_shed_install.ToolShedRepository.table.c.changeset_revision == changeset_revision)) \
-                          .first()
+    return (
+        install_session.query(galaxy.model.tool_shed_install.ToolShedRepository)
+        .filter(
+            and_(
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner,
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.changeset_revision == changeset_revision,
+            )
+        )
+        .first()
+    )
 
 
 def get_installed_repository_by_id(repository_id):
-    return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository) \
-                          .filter(galaxy.model.tool_shed_install.ToolShedRepository.table.c.id == repository_id) \
-                          .first()
+    return (
+        install_session.query(galaxy.model.tool_shed_install.ToolShedRepository)
+        .filter(galaxy.model.tool_shed_install.ToolShedRepository.table.c.id == repository_id)
+        .first()
+    )
 
 
 def get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False):
-    query = install_session.query(galaxy.model.tool_shed_install.ToolShedRepository) \
-                           .filter(and_(galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,
-                                        galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner))
+    query = install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).filter(
+        and_(
+            galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,
+            galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner,
+        )
+    )
     if return_multiple:
         return query.all()
     return query.first()
@@ -88,7 +110,7 @@ def get_installed_repository_by_name_owner(repository_name, owner, return_multip
 
 def get_private_role(user):
     for role in user.all_roles():
-        if role.name == user.email and role.description == f'Private Role for {user.email}':
+        if role.name == user.email and role.description == f"Private Role for {user.email}":
             return role
     raise AssertionError(f"Private role not found for user '{user.email}'")
 
@@ -101,32 +123,56 @@ def get_role(user, role_name):
 
 
 def get_repository_role_association(repository_id, role_id):
-    rra = sa_session.query(model.RepositoryRoleAssociation) \
-                    .filter(and_(model.RepositoryRoleAssociation.table.c.role_id == role_id,
-                                 model.RepositoryRoleAssociation.table.c.repository_id == repository_id)) \
-                    .first()
+    rra = (
+        sa_session.query(model.RepositoryRoleAssociation)
+        .filter(
+            and_(
+                model.RepositoryRoleAssociation.table.c.role_id == role_id,
+                model.RepositoryRoleAssociation.table.c.repository_id == repository_id,
+            )
+        )
+        .first()
+    )
     return rra
 
 
 def get_repository_reviews(repository_id, reviewer_user_id=None, changeset_revision=None):
     if reviewer_user_id and changeset_revision:
-        reviews = sa_session.query(model.RepositoryReview) \
-                            .filter(and_(model.RepositoryReview.table.c.repository_id == repository_id,
-                                         model.RepositoryReview.table.c.deleted == false(),
-                                         model.RepositoryReview.table.c.changeset_revision == changeset_revision,
-                                         model.RepositoryReview.table.c.user_id == reviewer_user_id)) \
-                            .all()
+        reviews = (
+            sa_session.query(model.RepositoryReview)
+            .filter(
+                and_(
+                    model.RepositoryReview.table.c.repository_id == repository_id,
+                    model.RepositoryReview.table.c.deleted == false(),
+                    model.RepositoryReview.table.c.changeset_revision == changeset_revision,
+                    model.RepositoryReview.table.c.user_id == reviewer_user_id,
+                )
+            )
+            .all()
+        )
     elif reviewer_user_id:
-        reviews = sa_session.query(model.RepositoryReview) \
-                            .filter(and_(model.RepositoryReview.table.c.repository_id == repository_id,
-                                         model.RepositoryReview.table.c.deleted == false(),
-                                         model.RepositoryReview.table.c.user_id == reviewer_user_id)) \
-                            .all()
+        reviews = (
+            sa_session.query(model.RepositoryReview)
+            .filter(
+                and_(
+                    model.RepositoryReview.table.c.repository_id == repository_id,
+                    model.RepositoryReview.table.c.deleted == false(),
+                    model.RepositoryReview.table.c.user_id == reviewer_user_id,
+                )
+            )
+            .all()
+        )
     else:
-        reviews = sa_session.query(model.RepositoryReview) \
-                            .filter(and_(model.RepositoryReview.table.c.repository_id == repository_id,
-                                         model.RepositoryReview.table.c.deleted == false())) \
-                            .all()
+        reviews = (
+            sa_session.query(model.RepositoryReview)
+            .filter(
+                and_(
+                    model.RepositoryReview.table.c.repository_id == repository_id,
+                    model.RepositoryReview.table.c.deleted == false(),
+                )
+            )
+            .all()
+        )
     return reviews
 
 
@@ -141,52 +187,62 @@ def get_reviews_ordered_by_changeset_revision(repository_id, changelog_tuples, r
 
 
 def get_repository_by_id(repository_id):
-    return sa_session.query(model.Repository) \
-                     .filter(model.Repository.table.c.id == repository_id) \
-                     .first()
+    return sa_session.query(model.Repository).filter(model.Repository.table.c.id == repository_id).first()
 
 
 def get_repository_downloadable_revisions(repository_id):
-    revisions = sa_session.query(model.RepositoryMetadata) \
-                          .filter(and_(model.RepositoryMetadata.table.c.repository_id == repository_id,
-                                       model.RepositoryMetadata.table.c.downloadable == true())) \
-                          .all()
+    revisions = (
+        sa_session.query(model.RepositoryMetadata)
+        .filter(
+            and_(
+                model.RepositoryMetadata.table.c.repository_id == repository_id,
+                model.RepositoryMetadata.table.c.downloadable == true(),
+            )
+        )
+        .all()
+    )
     return revisions
 
 
 def get_repository_metadata_for_changeset_revision(repository_id, changeset_revision):
-    repository_metadata = sa_session.query(model.RepositoryMetadata) \
-                                    .filter(and_(model.RepositoryMetadata.table.c.repository_id == repository_id,
-                                                 model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)) \
-                                    .first()
+    repository_metadata = (
+        sa_session.query(model.RepositoryMetadata)
+        .filter(
+            and_(
+                model.RepositoryMetadata.table.c.repository_id == repository_id,
+                model.RepositoryMetadata.table.c.changeset_revision == changeset_revision,
+            )
+        )
+        .first()
+    )
     return repository_metadata
 
 
 def get_repository_review_by_user_id_changeset_revision(user_id, repository_id, changeset_revision):
-    review = sa_session.query(model.RepositoryReview) \
-                       .filter(and_(model.RepositoryReview.table.c.user_id == user_id,
-                                    model.RepositoryReview.table.c.repository_id == repository_id,
-                                    model.RepositoryReview.table.c.changeset_revision == changeset_revision)) \
-                       .first()
+    review = (
+        sa_session.query(model.RepositoryReview)
+        .filter(
+            and_(
+                model.RepositoryReview.table.c.user_id == user_id,
+                model.RepositoryReview.table.c.repository_id == repository_id,
+                model.RepositoryReview.table.c.changeset_revision == changeset_revision,
+            )
+        )
+        .first()
+    )
     return review
 
 
 def get_role_by_name(role_name):
-    return sa_session.query(model.Role) \
-                     .filter(model.Role.table.c.name == role_name) \
-                     .first()
+    return sa_session.query(model.Role).filter(model.Role.table.c.name == role_name).first()
 
 
 def get_user(email):
-    return sa_session.query(model.User) \
-                     .filter(model.User.table.c.email == email) \
-                     .first()
+    return sa_session.query(model.User).filter(model.User.table.c.email == email).first()
 
 
 def get_user_by_name(username):
-    return sa_session.query(model.User) \
-                     .filter(model.User.table.c.username == username) \
-                     .first()
+    return sa_session.query(model.User).filter(model.User.table.c.username == username).first()
 
 
 def mark_obj_deleted(obj):
@@ -205,29 +261,34 @@ def ga_refresh(obj):
 
 def get_galaxy_private_role(user):
     for role in user.all_roles():
-        if role.name == user.email and role.description == f'Private Role for {user.email}':
+        if role.name == user.email and role.description == f"Private Role for {user.email}":
             return role
     raise AssertionError(f"Private role not found for user '{user.email}'")
 
 
 def get_galaxy_user(email):
-    return ga_session.query(galaxy.model.User) \
-                     .filter(galaxy.model.User.table.c.email == email) \
-                     .first()
+    return ga_session.query(galaxy.model.User).filter(galaxy.model.User.table.c.email == email).first()
 
 
 def get_repository_by_name_and_owner(name, owner_username, return_multiple=False):
     owner = get_user_by_name(owner_username)
-    repository = sa_session.query(model.Repository) \
-                           .filter(and_(model.Repository.table.c.name == name,
-                                        model.Repository.table.c.user_id == owner.id)) \
-                           .first()
+    repository = (
+        sa_session.query(model.Repository)
+        .filter(and_(model.Repository.table.c.name == name, model.Repository.table.c.user_id == owner.id))
+        .first()
+    )
     return repository
 
 
 def get_repository_metadata_by_repository_id_changeset_revision(repository_id, changeset_revision):
-    repository_metadata = sa_session.query(model.RepositoryMetadata) \
-                                    .filter(and_(model.RepositoryMetadata.table.c.repository_id == repository_id,
-                                                 model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)) \
-                                    .first()
+    repository_metadata = (
+        sa_session.query(model.RepositoryMetadata)
+        .filter(
+            and_(
+                model.RepositoryMetadata.table.c.repository_id == repository_id,
+                model.RepositoryMetadata.table.c.changeset_revision == changeset_revision,
+            )
+        )
+        .first()
+    )
     return repository_metadata
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index e9c334ecb0c..b69ba442a3e 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -13,7 +13,11 @@ from urllib.parse import (
 
 import requests
 import twill.commands as tc
-from mercurial import commands, hg, ui
+from mercurial import (
+    commands,
+    hg,
+    ui,
+)
 from twill.utils import ResultWrapper
 
 import galaxy.model.tool_shed_install as galaxy_model
@@ -31,7 +35,10 @@ from tool_shed.util import (
     hgweb_config,
     xml_util,
 )
-from . import common, test_db_util
+from . import (
+    common,
+    test_db_util,
+)
 
 # Set a 10 minute timeout for repository installation.
 repository_installation_timeout = 600
@@ -39,7 +46,7 @@ repository_installation_timeout = 600
 # Dial ClientCookie logging down (very noisy)
 logging.getLogger("ClientCookie.cookies").setLevel(logging.WARNING)
 log = logging.getLogger(__name__)
-tc.options['equiv_refresh_interval'] = 0
+tc.options["equiv_refresh_interval"] = 0
 
 
 class ShedTwillTestCase(DrivenFunctionalTestCase):
@@ -47,25 +54,25 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def setUp(self):
         # Security helper
-        self.security = idencoding.IdEncodingHelper(id_secret='changethisinproductiontoo')
+        self.security = idencoding.IdEncodingHelper(id_secret="changethisinproductiontoo")
         self.history_id = None
-        self.hgweb_config_dir = os.environ.get('TEST_HG_WEB_CONFIG_DIR')
+        self.hgweb_config_dir = os.environ.get("TEST_HG_WEB_CONFIG_DIR")
         self.hgweb_config_manager = hgweb_config.hgweb_config_manager
         self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir
-        self.tool_shed_test_tmp_dir = os.environ.get('TOOL_SHED_TEST_TMP_DIR', None)
-        self.host = os.environ.get('TOOL_SHED_TEST_HOST')
-        self.port = os.environ.get('TOOL_SHED_TEST_PORT')
+        self.tool_shed_test_tmp_dir = os.environ.get("TOOL_SHED_TEST_TMP_DIR", None)
+        self.host = os.environ.get("TOOL_SHED_TEST_HOST")
+        self.port = os.environ.get("TOOL_SHED_TEST_PORT")
         self.url = f"http://{self.host}:{self.port}"
-        self.galaxy_host = os.environ.get('GALAXY_TEST_HOST')
-        self.galaxy_port = os.environ.get('GALAXY_TEST_PORT')
+        self.galaxy_host = os.environ.get("GALAXY_TEST_HOST")
+        self.galaxy_port = os.environ.get("GALAXY_TEST_PORT")
         self.galaxy_url = f"http://{self.galaxy_host}:{self.galaxy_port}"
-        self.shed_tool_data_table_conf = os.environ.get('TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF')
-        self.file_dir = os.environ.get('TOOL_SHED_TEST_FILE_DIR', None)
-        self.tool_data_path = os.environ.get('GALAXY_TEST_TOOL_DATA_PATH')
-        self.shed_tool_conf = os.environ.get('GALAXY_TEST_SHED_TOOL_CONF')
+        self.shed_tool_data_table_conf = os.environ.get("TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF")
+        self.file_dir = os.environ.get("TOOL_SHED_TEST_FILE_DIR", None)
+        self.tool_data_path = os.environ.get("GALAXY_TEST_TOOL_DATA_PATH")
+        self.shed_tool_conf = os.environ.get("GALAXY_TEST_SHED_TOOL_CONF")
         self.test_db_util = test_db_util
         # TODO: Figure out a way to alter these attributes during tests.
-        self.galaxy_tool_dependency_dir = os.environ.get('GALAXY_TEST_TOOL_DEPENDENCY_DIR')
+        self.galaxy_tool_dependency_dir = os.environ.get("GALAXY_TEST_TOOL_DEPENDENCY_DIR")
 
     def check_for_strings(self, strings_displayed=None, strings_not_displayed=None):
         strings_displayed = strings_displayed or []
@@ -104,17 +111,17 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     # Functions associated with user accounts
 
-    def create(self, cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect=''):
+    def create(self, cntrller="user", email="test@bx.psu.edu", password="testuser", username="admin-user", redirect=""):
         # HACK: don't use panels because late_javascripts() messes up the twill browser and it
         # can't find form fields (and hence user can't be logged in).
         params = dict(cntrller=cntrller, use_panels=False)
         self.visit_url("/user/create", params)
-        tc.fv('registration', 'email', email)
-        tc.fv('registration', 'redirect', redirect)
-        tc.fv('registration', 'password', password)
-        tc.fv('registration', 'confirm', password)
-        tc.fv('registration', 'username', username)
-        tc.submit('create_user_button')
+        tc.fv("registration", "email", email)
+        tc.fv("registration", "redirect", redirect)
+        tc.fv("registration", "password", password)
+        tc.fv("registration", "confirm", password)
+        tc.fv("registration", "username", username)
+        tc.submit("create_user_button")
         previously_created = False
         username_taken = False
         invalid_username = False
@@ -127,12 +134,12 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
                 previously_created = True
             except AssertionError:
                 try:
-                    self.check_page_for_string('Public name is taken; please choose another')
+                    self.check_page_for_string("Public name is taken; please choose another")
                     username_taken = True
                 except AssertionError:
                     # Note that we're only checking if the usr name is >< 4 chars here...
                     try:
-                        self.check_page_for_string('Public name must be at least 4 characters in length')
+                        self.check_page_for_string("Public name must be at least 4 characters in length")
                         invalid_username = True
                     except AssertionError:
                         pass
@@ -148,22 +155,23 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
     def last_url(self):
         return tc.browser.url
 
-    def login(self, email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True):
+    def login(
+        self, email="test@bx.psu.edu", password="testuser", username="admin-user", redirect="", logout_first=True
+    ):
         # Clear cookies.
         if logout_first:
             self.logout()
         # test@bx.psu.edu is configured as an admin user
-        previously_created, username_taken, invalid_username = \
-            self.create(email=email, password=password, username=username, redirect=redirect)
+        previously_created, username_taken, invalid_username = self.create(
+            email=email, password=password, username=username, redirect=redirect
+        )
         if previously_created:
             # The acount has previously been created, so just login.
             # HACK: don't use panels because late_javascripts() messes up the twill browser and it
             # can't find form fields (and hence user can't be logged in).
-            params = {
-                'use_panels': False
-            }
-            self.visit_url('/user/login', params=params)
-            self.submit_form(button='login_button', login=email, redirect=redirect, password=password)
+            params = {"use_panels": False}
+            self.visit_url("/user/login", params=params)
+            self.submit_form(button="login_button", login=email, redirect=redirect, password=password)
 
     def logout(self):
         self.visit_url("/user/logout")
@@ -184,7 +192,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             except IndexError:
                 raise ValueError("No form to submit found")
         controls = {c.name: c for c in form.inputs}
-        form_name = form.get('name')
+        form_name = form.get("name")
         for control_name, control_value in kwd.items():
             if control_name not in controls:
                 continue  # these cannot be handled safely - cause the test to barf out
@@ -192,7 +200,16 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
                 control_value = [str(control_value)]
             control = controls[control_name]
             control_type = getattr(control, "type", None)
-            if control_type in ("text", "textfield", "submit", "password", "TextareaElement", "checkbox", "radio", None):
+            if control_type in (
+                "text",
+                "textfield",
+                "submit",
+                "password",
+                "TextareaElement",
+                "checkbox",
+                "radio",
+                None,
+            ):
                 for cv in control_value:
                     tc.fv(form_name, control.name, cv)
             else:
@@ -207,210 +224,232 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             params = dict()
         parsed_url = urlparse(url)
         if len(parsed_url.netloc) == 0:
-            url = f'http://{self.host}:{self.port}{parsed_url.path}'
+            url = f"http://{self.host}:{self.port}{parsed_url.path}"
         else:
-            url = f'{parsed_url.scheme}://{parsed_url.netloc}{parsed_url.path}'
+            url = f"{parsed_url.scheme}://{parsed_url.netloc}{parsed_url.path}"
         if parsed_url.query:
-            for query_parameter in parsed_url.query.split('&'):
-                key, value = query_parameter.split('=')
+            for query_parameter in parsed_url.query.split("&"):
+                key, value = query_parameter.split("=")
                 params[key] = value
         if params:
-            url += f'?{urlencode(params, doseq=doseq)}'
+            url += f"?{urlencode(params, doseq=doseq)}"
         new_url = tc.go(url)
         return_code = tc.browser.code
-        assert return_code in allowed_codes, 'Invalid HTTP return code %s, allowed codes: %s' % \
-            (return_code, ', '.join(str(code) for code in allowed_codes))
+        assert return_code in allowed_codes, "Invalid HTTP return code %s, allowed codes: %s" % (
+            return_code,
+            ", ".join(str(code) for code in allowed_codes),
+        )
         return new_url
 
-    def write_temp_file(self, content, suffix='.html'):
-        with tempfile.NamedTemporaryFile(suffix=suffix, prefix='twilltestcase-', delete=False) as fh:
+    def write_temp_file(self, content, suffix=".html"):
+        with tempfile.NamedTemporaryFile(suffix=suffix, prefix="twilltestcase-", delete=False) as fh:
             fh.write(smart_str(content))
         return fh.name
 
     def add_repository_review_component(self, **kwd):
-        params = {
-            'operation': 'create'
-        }
-        self.visit_url('/repository_review/create_component', params=params)
-        self.submit_form(button='create_component_button', **kwd)
+        params = {"operation": "create"}
+        self.visit_url("/repository_review/create_component", params=params)
+        self.submit_form(button="create_component_button", **kwd)
 
     def assign_admin_role(self, repository, user):
         # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript
         # attached to the role selection form. Visit the action url directly with the necessary parameters.
         params = {
-            'id': self.security.encode_id(repository.id),
-            'in_users': user.id,
-            'manage_role_associations_button': 'Save'
+            "id": self.security.encode_id(repository.id),
+            "in_users": user.id,
+            "manage_role_associations_button": "Save",
         }
-        self.visit_url('/repository/manage_repository_admins', params=params)
-        self.check_for_strings(strings_displayed=['Role', 'has been associated'])
+        self.visit_url("/repository/manage_repository_admins", params=params)
+        self.check_for_strings(strings_displayed=["Role", "has been associated"])
 
     def browse_category(self, category, strings_displayed=None, strings_not_displayed=None):
         params = {
-            'sort': 'name',
-            'operation': 'valid_repositories_by_category',
-            'id': self.security.encode_id(category.id)
+            "sort": "name",
+            "operation": "valid_repositories_by_category",
+            "id": self.security.encode_id(category.id),
         }
-        self.visit_url('/repository/browse_valid_categories', params=params)
+        self.visit_url("/repository/browse_valid_categories", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_component_review(self, review, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(review.id)
-        }
-        self.visit_url('/repository_review/browse_review', params=params)
+        params = {"id": self.security.encode_id(review.id)}
+        self.visit_url("/repository_review/browse_review", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_custom_datatypes(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository/browse_datatypes'
+        url = "/repository/browse_datatypes"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_repository(self, repository, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository/browse_repository', params=params)
+        params = {"id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository/browse_repository", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_repository_dependencies(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository/browse_repository_dependencies'
+        url = "/repository/browse_repository_dependencies"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_tool_shed(self, url, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository/browse_valid_categories'
+        url = "/repository/browse_valid_categories"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_tool_dependencies(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository/browse_tool_dependencies'
+        url = "/repository/browse_tool_dependencies"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_tools(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository/browse_tools'
+        url = "/repository/browse_tools"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def check_count_of_metadata_revisions_associated_with_repository(self, repository, metadata_count):
         self.check_repository_changelog(repository)
-        self.check_string_count_in_page('Repository metadata is associated with this change set.', metadata_count)
+        self.check_string_count_in_page("Repository metadata is associated with this change set.", metadata_count)
 
     def check_exported_repository_dependency(self, dependency_filename, repository_name, repository_owner):
         root, error_message = xml_util.parse_xml(dependency_filename)
-        for elem in root.findall('repository'):
-            if 'changeset_revision' in elem:
-                raise AssertionError('Exported repository %s with owner %s has a dependency with a defined changeset revision.' %
-                                     (repository_name, repository_owner))
-            if 'toolshed' in elem:
-                raise AssertionError('Exported repository %s with owner %s has a dependency with a defined tool shed.' %
-                                     (repository_name, repository_owner))
+        for elem in root.findall("repository"):
+            if "changeset_revision" in elem:
+                raise AssertionError(
+                    "Exported repository %s with owner %s has a dependency with a defined changeset revision."
+                    % (repository_name, repository_owner)
+                )
+            if "toolshed" in elem:
+                raise AssertionError(
+                    "Exported repository %s with owner %s has a dependency with a defined tool shed."
+                    % (repository_name, repository_owner)
+                )
 
     def check_for_valid_tools(self, repository, strings_displayed=None, strings_not_displayed=None):
         if strings_displayed is None:
-            strings_displayed = ['Valid tools']
+            strings_displayed = ["Valid tools"]
         else:
-            strings_displayed.append('Valid tools')
+            strings_displayed.append("Valid tools")
         self.display_manage_repository_page(repository, strings_displayed, strings_not_displayed)
 
     def check_galaxy_repository_db_status(self, repository_name, owner, expected_status):
         installed_repository = test_db_util.get_installed_repository_by_name_owner(repository_name, owner)
-        assert installed_repository.status == expected_status, 'Status in database is %s, expected %s' % \
-            (installed_repository.status, expected_status)
+        assert installed_repository.status == expected_status, "Status in database is %s, expected %s" % (
+            installed_repository.status,
+            expected_status,
+        )
 
     def check_galaxy_repository_tool_panel_section(self, repository, expected_tool_panel_section):
         metadata = repository.metadata_
-        assert 'tools' in metadata, f'Tools not found in repository metadata: {metadata}'
+        assert "tools" in metadata, f"Tools not found in repository metadata: {metadata}"
         # If integrated_tool_panel.xml is to be tested, this test method will need to be enhanced to handle tools
         # from the same repository in different tool panel sections. Getting the first tool guid is ok, because
         # currently all tools contained in a single repository will be loaded into the same tool panel section.
-        if repository.status in [galaxy_model.ToolShedRepository.installation_status.UNINSTALLED,
-                                 galaxy_model.ToolShedRepository.installation_status.DEACTIVATED]:
+        if repository.status in [
+            galaxy_model.ToolShedRepository.installation_status.UNINSTALLED,
+            galaxy_model.ToolShedRepository.installation_status.DEACTIVATED,
+        ]:
             tool_panel_section = self.get_tool_panel_section_from_repository_metadata(metadata)
         else:
             tool_panel_section = self.get_tool_panel_section_from_api(metadata)
-        assert tool_panel_section == expected_tool_panel_section, 'Expected to find tool panel section *%s*, but instead found *%s*\nMetadata: %s\n' % \
-            (expected_tool_panel_section, tool_panel_section, metadata)
+        assert (
+            tool_panel_section == expected_tool_panel_section
+        ), "Expected to find tool panel section *%s*, but instead found *%s*\nMetadata: %s\n" % (
+            expected_tool_panel_section,
+            tool_panel_section,
+            metadata,
+        )
 
-    def check_installed_repository_tool_dependencies(self,
-                                                     installed_repository,
-                                                     strings_displayed=None,
-                                                     strings_not_displayed=None,
-                                                     dependencies_installed=False):
+    def check_installed_repository_tool_dependencies(
+        self, installed_repository, strings_displayed=None, strings_not_displayed=None, dependencies_installed=False
+    ):
         # Tool dependencies are not being installed in these functional tests. If this is changed, the test method will also need to be updated.
         if not dependencies_installed:
-            strings_displayed.append('Missing tool dependencies')
+            strings_displayed.append("Missing tool dependencies")
         else:
-            strings_displayed.append('Tool dependencies')
+            strings_displayed.append("Tool dependencies")
         if dependencies_installed:
-            strings_displayed.append('Installed')
+            strings_displayed.append("Installed")
         else:
-            strings_displayed.append('Never installed')
-        params = {
-            'id': self.security.encode_id(installed_repository.id)
-        }
-        self.visit_galaxy_url('/admin_toolshed/manage_repository', params=params)
+            strings_displayed.append("Never installed")
+        params = {"id": self.security.encode_id(installed_repository.id)}
+        self.visit_galaxy_url("/admin_toolshed/manage_repository", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def check_repository_changelog(self, repository, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository/view_changelog', params=params)
+        params = {"id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository/view_changelog", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def check_repository_dependency(self, repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None):
+    def check_repository_dependency(
+        self, repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None
+    ):
         strings_displayed = [depends_on_repository.name, depends_on_repository.user.username]
         if depends_on_changeset_revision:
             strings_displayed.append(depends_on_changeset_revision)
-        self.display_manage_repository_page(repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed)
+        self.display_manage_repository_page(
+            repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed
+        )
 
     def check_repository_metadata(self, repository, tip_only=True):
         if tip_only:
-            assert self.tip_has_metadata(repository) and len(self.get_repository_metadata_revisions(repository)) == 1, \
-                'Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s.'
+            assert (
+                self.tip_has_metadata(repository) and len(self.get_repository_metadata_revisions(repository)) == 1
+            ), "Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s."
         else:
-            assert len(self.get_repository_metadata_revisions(repository)) > 0, \
-                'Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s.' % \
-                (self.get_repository_tip(repository), ', '.join(self.get_repository_metadata_revisions(repository)))
+            assert (
+                len(self.get_repository_metadata_revisions(repository)) > 0
+            ), "Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s." % (
+                self.get_repository_tip(repository),
+                ", ".join(self.get_repository_metadata_revisions(repository)),
+            )
 
-    def check_repository_tools_for_changeset_revision(self, repository, changeset_revision, tool_metadata_strings_displayed=None, tool_page_strings_displayed=None):
-        '''
+    def check_repository_tools_for_changeset_revision(
+        self, repository, changeset_revision, tool_metadata_strings_displayed=None, tool_page_strings_displayed=None
+    ):
+        """
         Loop through each tool dictionary in the repository metadata associated with the received changeset_revision.
         For each of these, check for a tools attribute, and load the tool metadata page if it exists, then display that tool's page.
-        '''
+        """
         test_db_util.refresh(repository)
         repository_metadata = self.get_repository_metadata_by_changeset_revision(repository, changeset_revision)
         metadata = repository_metadata.metadata
-        if 'tools' not in metadata:
-            raise AssertionError(f'No tools in {repository.name} revision {changeset_revision}.')
-        for tool_dict in metadata['tools']:
-            tool_id = tool_dict['id']
-            tool_xml = tool_dict['tool_config']
+        if "tools" not in metadata:
+            raise AssertionError(f"No tools in {repository.name} revision {changeset_revision}.")
+        for tool_dict in metadata["tools"]:
+            tool_id = tool_dict["id"]
+            tool_xml = tool_dict["tool_config"]
             params = {
-                'repository_id': self.security.encode_id(repository.id),
-                'changeset_revision': changeset_revision,
-                'tool_id': tool_id
+                "repository_id": self.security.encode_id(repository.id),
+                "changeset_revision": changeset_revision,
+                "tool_id": tool_id,
             }
-            self.visit_url('/repository/view_tool_metadata', params=params)
+            self.visit_url("/repository/view_tool_metadata", params=params)
             self.check_for_strings(tool_metadata_strings_displayed)
-            self.load_display_tool_page(repository, tool_xml_path=tool_xml,
-                                        changeset_revision=changeset_revision,
-                                        strings_displayed=tool_page_strings_displayed,
-                                        strings_not_displayed=None)
+            self.load_display_tool_page(
+                repository,
+                tool_xml_path=tool_xml,
+                changeset_revision=changeset_revision,
+                strings_displayed=tool_page_strings_displayed,
+                strings_not_displayed=None,
+            )
 
-    def check_repository_invalid_tools_for_changeset_revision(self, repository, changeset_revision, strings_displayed=None, strings_not_displayed=None):
-        '''Load the invalid tool page for each invalid tool associated with this changeset revision and verify the received error messages.'''
+    def check_repository_invalid_tools_for_changeset_revision(
+        self, repository, changeset_revision, strings_displayed=None, strings_not_displayed=None
+    ):
+        """Load the invalid tool page for each invalid tool associated with this changeset revision and verify the received error messages."""
         repository_metadata = self.get_repository_metadata_by_changeset_revision(repository, changeset_revision)
         metadata = repository_metadata.metadata
-        assert 'invalid_tools' in metadata, f'Metadata for changeset revision {changeset_revision} does not define invalid tools'
-        for tool_xml in metadata['invalid_tools']:
-            self.load_invalid_tool_page(repository,
-                                        tool_xml=tool_xml,
-                                        changeset_revision=changeset_revision,
-                                        strings_displayed=strings_displayed,
-                                        strings_not_displayed=strings_not_displayed)
+        assert (
+            "invalid_tools" in metadata
+        ), f"Metadata for changeset revision {changeset_revision} does not define invalid tools"
+        for tool_xml in metadata["invalid_tools"]:
+            self.load_invalid_tool_page(
+                repository,
+                tool_xml=tool_xml,
+                changeset_revision=changeset_revision,
+                strings_displayed=strings_displayed,
+                strings_not_displayed=strings_not_displayed,
+            )
 
     def check_string_count_in_page(self, pattern, min_count, max_count=None):
         """Checks the number of 'pattern' occurrences in the current browser page"""
@@ -423,17 +462,22 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         # than max_count.
         if pattern_count < min_count or pattern_count > max_count:
             fname = self.write_temp_file(page)
-            errmsg = "%i occurrences of '%s' found (min. %i, max. %i).\npage content written to '%s' " % \
-                     (pattern_count, pattern, min_count, max_count, fname)
+            errmsg = "%i occurrences of '%s' found (min. %i, max. %i).\npage content written to '%s' " % (
+                pattern_count,
+                pattern,
+                min_count,
+                max_count,
+                fname,
+            )
             raise AssertionError(errmsg)
 
     def clone_repository(self, repository, destination_path):
-        url = f'{self.url}/repos/{repository.user.username}/{repository.name}'
+        url = f"{self.url}/repos/{repository.user.username}/{repository.name}"
         success, message = hg_util.clone_repository(url, destination_path, self.get_repository_tip(repository))
         assert success is True, message
 
     def commit_and_push(self, repository, hgrepo, options, username, password):
-        url = f'http://{username}:{password}@{self.host}:{self.port}/repos/{repository.user.username}/{repository.name}'
+        url = f"http://{username}:{password}@{self.host}:{self.port}/repos/{repository.user.username}/{repository.name}"
         commands.commit(ui.ui(), hgrepo, **options)
         #  Try pushing multiple times as it transiently fails on Jenkins.
         #  TODO: Figure out why that happens
@@ -441,106 +485,125 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             try:
                 commands.push(ui.ui(), hgrepo, dest=url)
             except Exception as e:
-                if str(e).find('Pushing to Tool Shed is disabled') != -1:
+                if str(e).find("Pushing to Tool Shed is disabled") != -1:
                     return False
             else:
                 return True
         raise
 
     def create_category(self, **kwd):
-        category = test_db_util.get_category_by_name(kwd['name'])
+        category = test_db_util.get_category_by_name(kwd["name"])
         if category is None:
-            params = {
-                'operation': 'create'
-            }
-            self.visit_url('/admin/manage_categories', params=params)
+            params = {"operation": "create"}
+            self.visit_url("/admin/manage_categories", params=params)
             self.submit_form(button="create_category_button", **kwd)
-            category = test_db_util.get_category_by_name(kwd['name'])
+            category = test_db_util.get_category_by_name(kwd["name"])
         return category
 
-    def create_repository_dependency(self,
-                                     repository=None,
-                                     repository_tuples=None,
-                                     filepath=None,
-                                     prior_installation_required=False,
-                                     complex=False,
-                                     package=None,
-                                     version=None,
-                                     strings_displayed=None,
-                                     strings_not_displayed=None):
+    def create_repository_dependency(
+        self,
+        repository=None,
+        repository_tuples=None,
+        filepath=None,
+        prior_installation_required=False,
+        complex=False,
+        package=None,
+        version=None,
+        strings_displayed=None,
+        strings_not_displayed=None,
+    ):
         repository_tuples = repository_tuples or []
         repository_names = []
         if complex:
-            filename = 'tool_dependencies.xml'
-            self.generate_complex_dependency_xml(filename=filename, filepath=filepath, repository_tuples=repository_tuples, package=package, version=version)
+            filename = "tool_dependencies.xml"
+            self.generate_complex_dependency_xml(
+                filename=filename,
+                filepath=filepath,
+                repository_tuples=repository_tuples,
+                package=package,
+                version=version,
+            )
         else:
             for _, name, _, _ in repository_tuples:
                 repository_names.append(name)
             dependency_description = f"{repository.name} depends on {', '.join(repository_names)}."
-            filename = 'repository_dependencies.xml'
-            self.generate_simple_dependency_xml(repository_tuples=repository_tuples,
-                                                filename=filename,
-                                                filepath=filepath,
-                                                dependency_description=dependency_description,
-                                                prior_installation_required=prior_installation_required)
-        self.upload_file(repository,
-                         filename=filename,
-                         filepath=filepath,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message=f"Uploaded dependency on {', '.join(repository_names)}.",
-                         strings_displayed=None,
-                         strings_not_displayed=None)
+            filename = "repository_dependencies.xml"
+            self.generate_simple_dependency_xml(
+                repository_tuples=repository_tuples,
+                filename=filename,
+                filepath=filepath,
+                dependency_description=dependency_description,
+                prior_installation_required=prior_installation_required,
+            )
+        self.upload_file(
+            repository,
+            filename=filename,
+            filepath=filepath,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message=f"Uploaded dependency on {', '.join(repository_names)}.",
+            strings_displayed=None,
+            strings_not_displayed=None,
+        )
 
     def create_repository_review(self, repository, review_contents_dict, changeset_revision=None, copy_from=None):
         strings_displayed = []
         if not copy_from:
-            strings_displayed.append('Begin your review')
+            strings_displayed.append("Begin your review")
         strings_not_displayed = []
         if not changeset_revision:
             changeset_revision = self.get_repository_tip(repository)
-        params = {
-            'changeset_revision': changeset_revision,
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository_review/create_review', params=params)
+        params = {"changeset_revision": changeset_revision, "id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository_review/create_review", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
         strings_displayed = []
         if copy_from:
             old_changeset_revision, review_id = copy_from
-            strings_displayed = ['You have elected to create a new review', 'Select previous revision', changeset_revision]
+            strings_displayed = [
+                "You have elected to create a new review",
+                "Select previous revision",
+                changeset_revision,
+            ]
             self.check_for_strings(strings_displayed)
             strings_displayed = []
             params = {
-                'changeset_revision': self.get_repository_tip(repository),
-                'id': self.security.encode_id(repository.id),
-                'previous_review_id': self.security.encode_id(review_id)
+                "changeset_revision": self.get_repository_tip(repository),
+                "id": self.security.encode_id(repository.id),
+                "previous_review_id": self.security.encode_id(review_id),
             }
-            self.visit_url('/repository_review/create_review', params=params)
+            self.visit_url("/repository_review/create_review", params=params)
         self.fill_review_form(review_contents_dict, strings_displayed, strings_not_displayed)
 
-    def create_user_in_galaxy(self, cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect=''):
+    def create_user_in_galaxy(
+        self, cntrller="user", email="test@bx.psu.edu", password="testuser", username="admin-user", redirect=""
+    ):
         params = {
-            'username': username,
-            'email': email,
-            'password': password,
-            'confirm': password,
-            'session_csrf_token': self.galaxy_token()
+            "username": username,
+            "email": email,
+            "password": password,
+            "confirm": password,
+            "session_csrf_token": self.galaxy_token(),
         }
-        self.visit_galaxy_url('/user/create', params=params, allowed_codes=[200, 400])
+        self.visit_galaxy_url("/user/create", params=params, allowed_codes=[200, 400])
 
     def deactivate_repository(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
         encoded_id = self.security.encode_id(installed_repository.id)
         api_key = get_admin_api_key()
-        response = requests.delete(f"{self.galaxy_url}/api/tool_shed_repositories/{encoded_id}", data={'remove_from_disk': False, 'key': api_key}, timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.delete(
+            f"{self.galaxy_url}/api/tool_shed_repositories/{encoded_id}",
+            data={"remove_from_disk": False, "key": api_key},
+            timeout=DEFAULT_SOCKET_TIMEOUT,
+        )
         assert response.status_code != 403, response.content
 
-    def delete_files_from_repository(self, repository, filenames=None, strings_displayed=None, strings_not_displayed=None):
+    def delete_files_from_repository(
+        self, repository, filenames=None, strings_displayed=None, strings_not_displayed=None
+    ):
         filenames = filenames or []
         files_to_delete = []
         if strings_displayed is None:
-            strings_displayed = ['were deleted from the repository']
+            strings_displayed = ["were deleted from the repository"]
         basepath = self.get_repo_path(repository)
         repository_files = self.get_repository_file_list(repository=repository, base_path=basepath, current_path=None)
         # Verify that the files to delete actually exist in the repository.
@@ -548,112 +611,117 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             if filename in filenames:
                 files_to_delete.append(os.path.join(basepath, filename))
         self.browse_repository(repository)
-        tc.fv("2", "selected_files_to_delete", ','.join(files_to_delete))
-        tc.submit('select_files_to_delete_button')
+        tc.fv("2", "selected_files_to_delete", ",".join(files_to_delete))
+        tc.submit("select_files_to_delete_button")
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def delete_repository(self, repository):
         repository_id = self.security.encode_id(repository.id)
-        self.visit_url('/admin/browse_repositories')
-        params = {
-            'operation': 'Delete',
-            'id': repository_id
-        }
-        self.visit_url('/admin/browse_repositories', params=params)
-        strings_displayed = ['Deleted 1 repository', repository.name]
+        self.visit_url("/admin/browse_repositories")
+        params = {"operation": "Delete", "id": repository_id}
+        self.visit_url("/admin/browse_repositories", params=params)
+        strings_displayed = ["Deleted 1 repository", repository.name]
         strings_not_displayed = []
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def display_galaxy_browse_repositories_page(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/admin_toolshed/browse_repositories'
+        url = "/admin_toolshed/browse_repositories"
         self.visit_galaxy_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def display_installed_jobs_list_page(self, installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None):
-        data_managers = installed_repository.metadata_.get('data_manager', {}).get('data_managers', {})
+    def display_installed_jobs_list_page(
+        self, installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None
+    ):
+        data_managers = installed_repository.metadata_.get("data_manager", {}).get("data_managers", {})
         if data_manager_names:
             if not isinstance(data_manager_names, list):
                 data_manager_names = [data_manager_names]
             for data_manager_name in data_manager_names:
-                assert data_manager_name in data_managers, f"The requested Data Manager '{data_manager_name}' was not found in repository metadata."
+                assert (
+                    data_manager_name in data_managers
+                ), f"The requested Data Manager '{data_manager_name}' was not found in repository metadata."
         else:
             data_manager_name = list(data_managers.keys())
         for data_manager_name in data_manager_names:
-            params = {
-                'id': data_managers[data_manager_name]['guid']
-            }
-            self.visit_galaxy_url('/data_manager/jobs_list', params=params)
+            params = {"id": data_managers[data_manager_name]["guid"]}
+            self.visit_galaxy_url("/data_manager/jobs_list", params=params)
             self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def display_installed_repository_manage_page(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
+    def display_installed_repository_manage_page(
+        self, installed_repository, strings_displayed=None, strings_not_displayed=None
+    ):
         if strings_displayed is None:
             strings_displayed = []
         if strings_not_displayed is None:
             strings_not_displayed = []
-        params = {
-            'id': self.security.encode_id(installed_repository.id)
-        }
-        self.visit_galaxy_url('/admin_toolshed/manage_repository', params=params)
+        params = {"id": self.security.encode_id(installed_repository.id)}
+        self.visit_galaxy_url("/admin_toolshed/manage_repository", params=params)
         strings_displayed.append(str(installed_repository.installed_changeset_revision))
         # Every place Galaxy's XXXX tool appears in attribute - need to quote.
         strings_displayed = [x.replace("'", "&#39;") for x in strings_displayed]
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def display_manage_repository_page(self, repository, changeset_revision=None, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
+    def display_manage_repository_page(
+        self, repository, changeset_revision=None, strings_displayed=None, strings_not_displayed=None
+    ):
+        params = {"id": self.security.encode_id(repository.id)}
         if changeset_revision:
-            params['changeset_revision'] = changeset_revision
-        self.visit_url('/repository/manage_repository', params=params)
+            params["changeset_revision"] = changeset_revision
+        self.visit_url("/repository/manage_repository", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def display_repository_clone_page(self, owner_name, repository_name, strings_displayed=None, strings_not_displayed=None):
-        url = f'/repos/{owner_name}/{repository_name}'
+    def display_repository_clone_page(
+        self, owner_name, repository_name, strings_displayed=None, strings_not_displayed=None
+    ):
+        url = f"/repos/{owner_name}/{repository_name}"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def display_repository_file_contents(self, repository, filename, filepath=None, strings_displayed=None, strings_not_displayed=None):
-        '''Find a file in the repository and display the contents.'''
+    def display_repository_file_contents(
+        self, repository, filename, filepath=None, strings_displayed=None, strings_not_displayed=None
+    ):
+        """Find a file in the repository and display the contents."""
         basepath = self.get_repo_path(repository)
         repository_file_list = []
         if filepath:
             relative_path = os.path.join(basepath, filepath)
         else:
             relative_path = basepath
-        repository_file_list = self.get_repository_file_list(repository=repository, base_path=relative_path, current_path=None)
-        assert filename in repository_file_list, f'File {filename} not found in the repository under {relative_path}.'
-        params = dict(file_path=os.path.join(relative_path, filename), repository_id=self.security.encode_id(repository.id))
-        url = '/repository/get_file_contents'
+        repository_file_list = self.get_repository_file_list(
+            repository=repository, base_path=relative_path, current_path=None
+        )
+        assert filename in repository_file_list, f"File {filename} not found in the repository under {relative_path}."
+        params = dict(
+            file_path=os.path.join(relative_path, filename), repository_id=self.security.encode_id(repository.id)
+        )
+        url = "/repository/get_file_contents"
         self.visit_url(url, params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def display_reviewed_repositories_owned_by_user(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository_review/reviewed_repositories_i_own'
+        url = "/repository_review/reviewed_repositories_i_own"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def display_repository_reviews_by_user(self, user, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(user.id)
-        }
-        self.visit_url('/repository_review/repository_reviews_by_user', params=params)
+        params = {"id": self.security.encode_id(user.id)}
+        self.visit_url("/repository_review/repository_reviews_by_user", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def edit_repository_categories(self, repository, categories_to_add=None, categories_to_remove=None, restore_original=True):
+    def edit_repository_categories(
+        self, repository, categories_to_add=None, categories_to_remove=None, restore_original=True
+    ):
         categories_to_add = categories_to_add or []
         categories_to_remove = categories_to_remove or []
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository/manage_repository', params=params)
+        params = {"id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository/manage_repository", params=params)
         strings_displayed = []
         strings_not_displayed = []
         for category in categories_to_add:
-            tc.fv("2", "category_id", f'+{category}')
+            tc.fv("2", "category_id", f"+{category}")
             strings_displayed.append(f"selected>{category}")
         for category in categories_to_remove:
-            tc.fv("2", "category_id", f'-{category}')
+            tc.fv("2", "category_id", f"-{category}")
             strings_not_displayed.append(f"selected>{category}")
         tc.submit("manage_categories_button")
         self.check_for_strings(strings_displayed, strings_not_displayed)
@@ -661,22 +729,22 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             strings_displayed = []
             strings_not_displayed = []
             for category in categories_to_remove:
-                tc.fv("2", "category_id", f'+{category}')
+                tc.fv("2", "category_id", f"+{category}")
                 strings_displayed.append(f"selected>{category}")
             for category in categories_to_add:
-                tc.fv("2", "category_id", f'-{category}')
+                tc.fv("2", "category_id", f"-{category}")
                 strings_not_displayed.append(f"selected>{category}")
             tc.submit("manage_categories_button")
             self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def edit_repository_information(self, repository, revert=True, **kwd):
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository/manage_repository', params=params)
-        original_information = dict(repo_name=repository.name, description=repository.description, long_description=repository.long_description)
+        params = {"id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository/manage_repository", params=params)
+        original_information = dict(
+            repo_name=repository.name, description=repository.description, long_description=repository.long_description
+        )
         strings_displayed = []
-        for input_elem_name in ['repo_name', 'description', 'long_description', 'repository_type']:
+        for input_elem_name in ["repo_name", "description", "long_description", "repository_type"]:
             if input_elem_name in kwd:
                 tc.fv("edit_repository", input_elem_name, kwd[input_elem_name])
                 strings_displayed.append(self.escape_html(kwd[input_elem_name]))
@@ -684,7 +752,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         self.check_for_strings(strings_displayed)
         if revert:
             strings_displayed = []
-            for input_elem_name in ['repo_name', 'description', 'long_description']:
+            for input_elem_name in ["repo_name", "description", "long_description"]:
                 tc.fv("edit_repository", input_elem_name, original_information[input_elem_name])
                 strings_displayed.append(self.escape_html(original_information[input_elem_name]))
             tc.submit("edit_repository_button")
@@ -692,12 +760,12 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def enable_email_alerts(self, repository, strings_displayed=None, strings_not_displayed=None):
         repository_id = self.security.encode_id(repository.id)
-        params = dict(operation='Receive email alerts', id=repository_id)
-        self.visit_url('/repository/browse_repositories', params)
+        params = dict(operation="Receive email alerts", id=repository_id)
+        self.visit_url("/repository/browse_repositories", params)
         self.check_for_strings(strings_displayed)
 
     def escape_html(self, string, unescape=False):
-        html_entities = [('&', 'X'), ("'", '&#39;'), ('"', '&#34;')]
+        html_entities = [("&", "X"), ("'", "&#39;"), ('"', "&#34;")]
         for character, replacement in html_entities:
             if unescape:
                 string = string.replace(replacement, character)
@@ -707,12 +775,12 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def expect_repo_created_strings(self, name):
         return [
-            f'Repository <b>{name}</b>',
-            f'Repository <b>{name}</b> has been created',
+            f"Repository <b>{name}</b>",
+            f"Repository <b>{name}</b> has been created",
         ]
 
     def fetch_repository_metadata(self, repository, strings_displayed=None, strings_not_displayed=None):
-        url = f'/api/repositories/{self.security.encode_id(repository.id)}/metadata'
+        url = f"/api/repositories/{self.security.encode_id(repository.id)}/metadata"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
@@ -722,17 +790,17 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         for label, contents in review_contents_dict.items():
             if contents:
                 changed = True
-                kwd[f'{label}__ESEP__comment'] = contents['comment']
-                kwd[f'{label}__ESEP__rating'] = contents['rating']
-                if 'private' in contents:
-                    kwd[f'{label}__ESEP__private'] = contents['private']
-                kwd[f'{label}__ESEP__approved'] = contents['approved']
+                kwd[f"{label}__ESEP__comment"] = contents["comment"]
+                kwd[f"{label}__ESEP__rating"] = contents["rating"]
+                if "private" in contents:
+                    kwd[f"{label}__ESEP__private"] = contents["private"]
+                kwd[f"{label}__ESEP__approved"] = contents["approved"]
             else:
-                kwd[f'{label}__ESEP__approved'] = 'not_applicable'
+                kwd[f"{label}__ESEP__approved"] = "not_applicable"
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        self.submit_form(button='Workflows__ESEP__review_button', **kwd)
+        self.submit_form(button="Workflows__ESEP__review_button", **kwd)
         if changed:
-            strings_displayed.append('Reviews were saved')
+            strings_displayed.append("Reviews were saved")
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def galaxy_token(self):
@@ -742,19 +810,17 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         token_sep_index = html.find(":", token_def_index)
         token_quote_start_index = html.find('"', token_sep_index)
         token_quote_end_index = html.find('"', token_quote_start_index + 1)
-        token = html[(token_quote_start_index + 1):token_quote_end_index]
+        token = html[(token_quote_start_index + 1) : token_quote_end_index]
         return token
 
-    def galaxy_login(self, email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True):
+    def galaxy_login(
+        self, email="test@bx.psu.edu", password="testuser", username="admin-user", redirect="", logout_first=True
+    ):
         if logout_first:
             self.galaxy_logout()
         self.create_user_in_galaxy(email=email, password=password, username=username, redirect=redirect)
-        params = {
-            "login": email,
-            "password": password,
-            "session_csrf_token": self.galaxy_token()
-        }
-        self.visit_galaxy_url('/user/login', params=params)
+        params = {"login": email, "password": password, "session_csrf_token": self.galaxy_token()}
+        self.visit_galaxy_url("/user/login", params=params)
 
     def galaxy_logout(self):
         self.visit_galaxy_url("/user/logout", params=dict(session_csrf_token=self.galaxy_token()))
@@ -764,50 +830,64 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         dependency_entries = []
         template = string.Template(common.new_repository_dependencies_line)
         for toolshed_url, name, owner, changeset_revision in repository_tuples:
-            dependency_entries.append(template.safe_substitute(toolshed_url=toolshed_url,
-                                                               owner=owner,
-                                                               repository_name=name,
-                                                               changeset_revision=changeset_revision,
-                                                               prior_installation_required=''))
+            dependency_entries.append(
+                template.safe_substitute(
+                    toolshed_url=toolshed_url,
+                    owner=owner,
+                    repository_name=name,
+                    changeset_revision=changeset_revision,
+                    prior_installation_required="",
+                )
+            )
         if not os.path.exists(filepath):
             os.makedirs(filepath)
         dependency_template = string.Template(common.complex_repository_dependency_template)
-        repository_dependency_xml = dependency_template.safe_substitute(package=package, version=version, dependency_lines='\n'.join(dependency_entries))
+        repository_dependency_xml = dependency_template.safe_substitute(
+            package=package, version=version, dependency_lines="\n".join(dependency_entries)
+        )
         # Save the generated xml to the specified location.
-        open(file_path, 'w').write(repository_dependency_xml)
+        open(file_path, "w").write(repository_dependency_xml)
 
-    def generate_simple_dependency_xml(self,
-                                       repository_tuples,
-                                       filename,
-                                       filepath,
-                                       dependency_description='',
-                                       complex=False,
-                                       package=None,
-                                       version=None,
-                                       prior_installation_required=False):
+    def generate_simple_dependency_xml(
+        self,
+        repository_tuples,
+        filename,
+        filepath,
+        dependency_description="",
+        complex=False,
+        package=None,
+        version=None,
+        prior_installation_required=False,
+    ):
         if not os.path.exists(filepath):
             os.makedirs(filepath)
         dependency_entries = []
         if prior_installation_required:
             prior_installation_value = ' prior_installation_required="True"'
         else:
-            prior_installation_value = ''
+            prior_installation_value = ""
         for toolshed_url, name, owner, changeset_revision in repository_tuples:
             template = string.Template(common.new_repository_dependencies_line)
-            dependency_entries.append(template.safe_substitute(toolshed_url=toolshed_url,
-                                                               owner=owner,
-                                                               repository_name=name,
-                                                               changeset_revision=changeset_revision,
-                                                               prior_installation_required=prior_installation_value))
+            dependency_entries.append(
+                template.safe_substitute(
+                    toolshed_url=toolshed_url,
+                    owner=owner,
+                    repository_name=name,
+                    changeset_revision=changeset_revision,
+                    prior_installation_required=prior_installation_value,
+                )
+            )
         if dependency_description:
             description = f' description="{dependency_description}"'
         else:
             description = dependency_description
         template_parser = string.Template(common.new_repository_dependencies_xml)
-        repository_dependency_xml = template_parser.safe_substitute(description=description, dependency_lines='\n'.join(dependency_entries))
+        repository_dependency_xml = template_parser.safe_substitute(
+            description=description, dependency_lines="\n".join(dependency_entries)
+        )
         # Save the generated xml to the specified location.
         full_path = os.path.join(filepath, filename)
-        open(full_path, 'w').write(repository_dependency_xml)
+        open(full_path, "w").write(repository_dependency_xml)
 
     def generate_temp_path(self, test_script_path, additional_paths=None):
         additional_paths = additional_paths or []
@@ -817,18 +897,17 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         return temp_path
 
     def get_datatypes_count(self):
-        params = {
-            'upload_only': False
-        }
-        self.visit_galaxy_url('/api/datatypes', params=params)
+        params = {"upload_only": False}
+        self.visit_galaxy_url("/api/datatypes", params=params)
         html = self.last_page()
         datatypes = loads(html)
         return len(datatypes)
 
     def get_env_sh_path(self, tool_dependency_name, tool_dependency_version, repository):
-        '''Return the absolute path to an installed repository's env.sh file.'''
-        env_sh_path = os.path.join(self.get_tool_dependency_path(tool_dependency_name, tool_dependency_version, repository),
-                                   'env.sh')
+        """Return the absolute path to an installed repository's env.sh file."""
+        env_sh_path = os.path.join(
+            self.get_tool_dependency_path(tool_dependency_name, tool_dependency_version, repository), "env.sh"
+        )
         return env_sh_path
 
     def get_filename(self, filename, filepath=None):
@@ -838,11 +917,13 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             return os.path.abspath(os.path.join(self.file_dir, filename))
 
     def get_hg_repo(self, path):
-        return hg.repository(ui.ui(), path.encode('utf-8'))
+        return hg.repository(ui.ui(), path.encode("utf-8"))
 
     def get_last_reviewed_revision_by_user(self, user, repository):
         changelog_tuples = self.get_repository_changelog_tuples(repository)
-        reviews = test_db_util.get_reviews_ordered_by_changeset_revision(repository.id, changelog_tuples, reviewer_user_id=user.id)
+        reviews = test_db_util.get_reviews_ordered_by_changeset_revision(
+            repository.id, changelog_tuples, reviewer_user_id=user.id
+        )
         if reviews:
             last_review = reviews[-1]
         else:
@@ -851,32 +932,34 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def get_repositories_category_api(self, categories, strings_displayed=None, strings_not_displayed=None):
         for category in categories:
-            url = f'/api/categories/{self.security.encode_id(category.id)}/repositories'
+            url = f"/api/categories/{self.security.encode_id(category.id)}/repositories"
             self.visit_url(url)
             self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def get_tool_dependency_path(self, tool_dependency_name, tool_dependency_version, repository):
-        '''Return the absolute path for an installed tool dependency.'''
-        return os.path.join(self.galaxy_tool_dependency_dir,
-                            tool_dependency_name,
-                            tool_dependency_version,
-                            repository.owner,
-                            repository.name,
-                            repository.installed_changeset_revision)
+        """Return the absolute path for an installed tool dependency."""
+        return os.path.join(
+            self.galaxy_tool_dependency_dir,
+            tool_dependency_name,
+            tool_dependency_version,
+            repository.owner,
+            repository.name,
+            repository.installed_changeset_revision,
+        )
 
     def get_or_create_repository(self, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd):
         # If not checking for a specific string, it should be safe to assume that
         # we expect repository creation to be successful.
         if strings_displayed is None:
-            strings_displayed = ['Repository', kwd['name'], 'has been created']
+            strings_displayed = ["Repository", kwd["name"], "has been created"]
         if strings_not_displayed is None:
             strings_not_displayed = []
-        repository = test_db_util.get_repository_by_name_and_owner(kwd['name'], owner)
+        repository = test_db_util.get_repository_by_name_and_owner(kwd["name"], owner)
         if repository is None:
-            self.visit_url('/repository/create_repository')
-            self.submit_form(button='create_repository_button', **kwd)
+            self.visit_url("/repository/create_repository")
+            self.submit_form(button="create_repository_button", **kwd)
             self.check_for_strings(strings_displayed, strings_not_displayed)
-            repository = test_db_util.get_repository_by_name_and_owner(kwd['name'], owner)
+            repository = test_db_util.get_repository_by_name_and_owner(kwd["name"], owner)
         return repository
 
     def get_repo_path(self, repository):
@@ -885,7 +968,9 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         try:
             return self.hgweb_config_manager.get_entry(lhs)
         except Exception:
-            raise Exception(f"Entry for repository {lhs} missing in hgweb config file {self.hgweb_config_manager.hgweb_config}.")
+            raise Exception(
+                f"Entry for repository {lhs} missing in hgweb config file {self.hgweb_config_manager.hgweb_config}."
+            )
 
     def get_repository_changelog_tuples(self, repository):
         repo = self.get_hg_repo(self.get_repo_path(repository))
@@ -897,20 +982,20 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def get_repository_datatypes_count(self, repository):
         metadata = self.get_repository_metadata(repository)[0].metadata
-        if 'datatypes' not in metadata:
+        if "datatypes" not in metadata:
             return 0
         else:
-            return len(metadata['datatypes'])
+            return len(metadata["datatypes"])
 
     def get_repository_file_list(self, repository, base_path, current_path=None):
-        '''Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder.'''
+        """Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder."""
         if current_path is None:
             request_param_path = base_path
         else:
             request_param_path = os.path.join(base_path, current_path)
         # Get the current folder's contents.
         params = dict(folder_path=request_param_path, repository_id=self.security.encode_id(repository.id))
-        url = '/repository/open_folder'
+        url = "/repository/open_folder"
         self.visit_url(url, params=params)
         file_list = loads(self.last_page())
         returned_file_list = []
@@ -918,20 +1003,26 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             returned_file_list.append(current_path)
         # Loop through the json dict returned by /repository/open_folder.
         for file_dict in file_list:
-            if file_dict['isFolder']:
+            if file_dict["isFolder"]:
                 # This is a folder. Get the contents of the folder and append it to the list,
                 # prefixed with the path relative to the repository root, if any.
                 if current_path is None:
-                    returned_file_list.extend(self.get_repository_file_list(repository=repository, base_path=base_path, current_path=file_dict['title']))
+                    returned_file_list.extend(
+                        self.get_repository_file_list(
+                            repository=repository, base_path=base_path, current_path=file_dict["title"]
+                        )
+                    )
                 else:
-                    sub_path = os.path.join(current_path, file_dict['title'])
-                    returned_file_list.extend(self.get_repository_file_list(repository=repository, base_path=base_path, current_path=sub_path))
+                    sub_path = os.path.join(current_path, file_dict["title"])
+                    returned_file_list.extend(
+                        self.get_repository_file_list(repository=repository, base_path=base_path, current_path=sub_path)
+                    )
             else:
                 # This is a regular file, prefix the filename with the current path and append it to the list.
                 if current_path is not None:
-                    returned_file_list.append(os.path.join(current_path, file_dict['title']))
+                    returned_file_list.append(os.path.join(current_path, file_dict["title"]))
                 else:
-                    returned_file_list.append(file_dict['title'])
+                    returned_file_list.append(file_dict["title"])
         return returned_file_list
 
     def get_repository_metadata(self, repository):
@@ -948,86 +1039,102 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         return str(repo[repo.changelog.tip()])
 
     def get_sniffers_count(self):
-        url = '/api/datatypes/sniffers'
+        url = "/api/datatypes/sniffers"
         self.visit_galaxy_url(url)
         html = self.last_page()
         sniffers = loads(html)
         return len(sniffers)
 
     def get_tools_from_repository_metadata(self, repository, include_invalid=False):
-        '''Get a list of valid and (optionally) invalid tool dicts from the repository metadata.'''
+        """Get a list of valid and (optionally) invalid tool dicts from the repository metadata."""
         valid_tools = []
         invalid_tools = []
         for repository_metadata in repository.metadata_revisions:
-            if 'tools' in repository_metadata.metadata:
-                valid_tools.append(dict(tools=repository_metadata.metadata['tools'], changeset_revision=repository_metadata.changeset_revision))
-            if include_invalid and 'invalid_tools' in repository_metadata.metadata:
-                invalid_tools.append(dict(tools=repository_metadata.metadata['invalid_tools'], changeset_revision=repository_metadata.changeset_revision))
+            if "tools" in repository_metadata.metadata:
+                valid_tools.append(
+                    dict(
+                        tools=repository_metadata.metadata["tools"],
+                        changeset_revision=repository_metadata.changeset_revision,
+                    )
+                )
+            if include_invalid and "invalid_tools" in repository_metadata.metadata:
+                invalid_tools.append(
+                    dict(
+                        tools=repository_metadata.metadata["invalid_tools"],
+                        changeset_revision=repository_metadata.changeset_revision,
+                    )
+                )
         return valid_tools, invalid_tools
 
     def get_tool_panel_section_from_api(self, metadata):
-        tool_metadata = metadata['tools']
-        tool_guid = quote_plus(tool_metadata[0]['guid'], safe='')
-        api_url = f'/api/tools/{tool_guid}'
+        tool_metadata = metadata["tools"]
+        tool_guid = quote_plus(tool_metadata[0]["guid"], safe="")
+        api_url = f"/api/tools/{tool_guid}"
         self.visit_galaxy_url(api_url)
         tool_dict = loads(self.last_page())
-        tool_panel_section = tool_dict['panel_section_name']
+        tool_panel_section = tool_dict["panel_section_name"]
         return tool_panel_section
 
     def get_tool_panel_section_from_repository_metadata(self, metadata):
-        tool_metadata = metadata['tools']
-        tool_guid = tool_metadata[0]['guid']
-        assert 'tool_panel_section' in metadata, f'Tool panel section not found in metadata: {metadata}'
-        tool_panel_section_metadata = metadata['tool_panel_section']
+        tool_metadata = metadata["tools"]
+        tool_guid = tool_metadata[0]["guid"]
+        assert "tool_panel_section" in metadata, f"Tool panel section not found in metadata: {metadata}"
+        tool_panel_section_metadata = metadata["tool_panel_section"]
         # tool_section_dict = dict( tool_config=guids_and_configs[ guid ],
         #                           id=section_id,
         #                           name=section_name,
         #                           version=section_version )
         # This dict is appended to tool_panel_section_metadata[ tool_guid ]
-        tool_panel_section = tool_panel_section_metadata[tool_guid][0]['name']
+        tool_panel_section = tool_panel_section_metadata[tool_guid][0]["name"]
         return tool_panel_section
 
     def grant_role_to_user(self, user, role):
         strings_displayed = [self.security.encode_id(role.id), role.name]
         strings_not_displayed = []
-        self.visit_url('/admin/roles')
+        self.visit_url("/admin/roles")
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        params = dict(operation='manage users and groups', id=self.security.encode_id(role.id))
-        url = '/admin/roles'
+        params = dict(operation="manage users and groups", id=self.security.encode_id(role.id))
+        url = "/admin/roles"
         self.visit_url(url, params)
         strings_displayed = [common.test_user_1_email, common.test_user_2_email]
         self.check_for_strings(strings_displayed, strings_not_displayed)
         # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript
         # attached to the role selection form. Visit the action url directly with the necessary parameters.
-        params = dict(id=self.security.encode_id(role.id),
-                      in_users=user.id,
-                      operation='manage users and groups',
-                      role_members_edit_button='Save')
-        url = '/admin/manage_users_and_groups_for_role'
+        params = dict(
+            id=self.security.encode_id(role.id),
+            in_users=user.id,
+            operation="manage users and groups",
+            role_members_edit_button="Save",
+        )
+        url = "/admin/manage_users_and_groups_for_role"
         self.visit_url(url, params)
         strings_displayed = [f"Role '{role.name}' has been updated"]
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def grant_write_access(self,
-                           repository,
-                           usernames=None,
-                           strings_displayed=None,
-                           strings_not_displayed=None,
-                           post_submit_strings_displayed=None,
-                           post_submit_strings_not_displayed=None):
+    def grant_write_access(
+        self,
+        repository,
+        usernames=None,
+        strings_displayed=None,
+        strings_not_displayed=None,
+        post_submit_strings_displayed=None,
+        post_submit_strings_not_displayed=None,
+    ):
         usernames = usernames or []
         self.display_manage_repository_page(repository)
         self.check_for_strings(strings_displayed, strings_not_displayed)
         for username in usernames:
-            tc.fv("user_access", "allow_push", f'+{username}')
-        tc.submit('user_access_button')
+            tc.fv("user_access", "allow_push", f"+{username}")
+        tc.submit("user_access_button")
         self.check_for_strings(post_submit_strings_displayed, post_submit_strings_not_displayed)
 
-    def initiate_installation_process(self,
-                                      install_tool_dependencies=False,
-                                      install_repository_dependencies=True,
-                                      no_changes=True,
-                                      new_tool_panel_section_label=None):
+    def initiate_installation_process(
+        self,
+        install_tool_dependencies=False,
+        install_repository_dependencies=True,
+        no_changes=True,
+        new_tool_panel_section_label=None,
+    ):
         html = self.last_page()
         # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the
         # installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in
@@ -1041,22 +1148,34 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             # will handle them correctly. It's safe to pass the cleaned list to manage_repositories, because it can parse
             # comma-separated values.
             repository_ids = str(iri_ids)
-            repository_ids = re.sub('[^a-fA-F0-9,]+', '', repository_ids)
+            repository_ids = re.sub("[^a-fA-F0-9,]+", "", repository_ids)
             encoded_kwd = install_parameters.group(2)
             reinstalling = install_parameters.group(3)
             params = {
-                'tool_shed_repository_ids': ','.join(galaxy.util.listify(repository_ids)),
-                'encoded_kwd': encoded_kwd,
-                'reinstalling': reinstalling
+                "tool_shed_repository_ids": ",".join(galaxy.util.listify(repository_ids)),
+                "encoded_kwd": encoded_kwd,
+                "reinstalling": reinstalling,
             }
-            self.visit_galaxy_url('/admin_toolshed/install_repositories', params=params)
+            self.visit_galaxy_url("/admin_toolshed/install_repositories", params=params)
             return galaxy.util.listify(repository_ids)
 
-    def install_repository(self, name, owner, category_name, install_resolver_dependencies=False, install_tool_dependencies=False,
-                           install_repository_dependencies=True, changeset_revision=None,
-                           strings_displayed=None, strings_not_displayed=None, preview_strings_displayed=None,
-                           post_submit_strings_displayed=None, new_tool_panel_section_label=None, includes_tools_for_display_in_tool_panel=True,
-                           **kwd):
+    def install_repository(
+        self,
+        name,
+        owner,
+        category_name,
+        install_resolver_dependencies=False,
+        install_tool_dependencies=False,
+        install_repository_dependencies=True,
+        changeset_revision=None,
+        strings_displayed=None,
+        strings_not_displayed=None,
+        preview_strings_displayed=None,
+        post_submit_strings_displayed=None,
+        new_tool_panel_section_label=None,
+        includes_tools_for_display_in_tool_panel=True,
+        **kwd,
+    ):
         self.browse_tool_shed(url=self.url)
         self.browse_category(test_db_util.get_category_by_name(category_name))
         self.preview_repository_in_tool_shed(name, owner, strings_displayed=preview_strings_displayed)
@@ -1065,28 +1184,30 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         if changeset_revision is None:
             changeset_revision = self.get_repository_tip(repository)
         params = {
-            'changeset_revisions': changeset_revision,
-            'repository_ids': repository_id,
-            'galaxy_url': self.galaxy_url
+            "changeset_revisions": changeset_revision,
+            "repository_ids": repository_id,
+            "galaxy_url": self.galaxy_url,
         }
-        self.visit_url('/repository/install_repositories_by_revision', params=params)
+        self.visit_url("/repository/install_repositories_by_revision", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        form = tc.browser.form('select_tool_panel_section')
+        form = tc.browser.form("select_tool_panel_section")
         if form is None:
-            form = tc.browser.form('select_shed_tool_panel_config')
-        assert form is not None, 'Could not find form select_shed_tool_panel_config or select_tool_panel_section.'
+            form = tc.browser.form("select_shed_tool_panel_config")
+        assert form is not None, "Could not find form select_shed_tool_panel_config or select_tool_panel_section."
         kwds = {
-            'install_tool_dependencies': install_tool_dependencies,
-            'install_repository_dependencies': install_repository_dependencies,
-            'install_resolver_dependencies': install_resolver_dependencies,
-            'shed_tool_conf': self.shed_tool_conf,
+            "install_tool_dependencies": install_tool_dependencies,
+            "install_repository_dependencies": install_repository_dependencies,
+            "install_resolver_dependencies": install_resolver_dependencies,
+            "shed_tool_conf": self.shed_tool_conf,
         }
         if new_tool_panel_section_label is not None:
-            kwds['new_tool_panel_section_label'] = new_tool_panel_section_label
-        submit_button = [inp.name for inp in form.inputs if getattr(inp, 'type', None) == 'submit']
+            kwds["new_tool_panel_section_label"] = new_tool_panel_section_label
+        submit_button = [inp.name for inp in form.inputs if getattr(inp, "type", None) == "submit"]
         if len(submit_button) == 0:
             # TODO: refactor, use regular TS install API
-            submit_kwargs = {inp.name: inp.value for inp in tc.browser.forms[0].inputs if getattr(inp, 'type', None) == 'submit'}
+            submit_kwargs = {
+                inp.name: inp.value for inp in tc.browser.forms[0].inputs if getattr(inp, "type", None) == "submit"
+            }
             payload = {_: form.inputs[_].value for _ in form.fields.keys()}
             payload.update(kwds)
             payload.update(submit_kwargs)
@@ -1096,156 +1217,155 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             )
             tc.browser.result = ResultWrapper(r)
         else:
-            assert len(submit_button) == 1, f"Expected to find a single submit button, found {len(submit_button)} ({','.join(submit_button)})"
+            assert (
+                len(submit_button) == 1
+            ), f"Expected to find a single submit button, found {len(submit_button)} ({','.join(submit_button)})"
             submit_button = submit_button[0]
             self.submit_form(form=form, button=submit_button, **kwds)
         self.check_for_strings(post_submit_strings_displayed, strings_not_displayed)
         repository_ids = self.initiate_installation_process(new_tool_panel_section_label=new_tool_panel_section_label)
-        log.debug(f'Waiting for the installation of repository IDs: {str(repository_ids)}')
+        log.debug(f"Waiting for the installation of repository IDs: {str(repository_ids)}")
         self.wait_for_repository_installation(repository_ids)
 
-    def load_citable_url(self,
-                         username,
-                         repository_name,
-                         changeset_revision,
-                         encoded_user_id,
-                         encoded_repository_id,
-                         strings_displayed=None,
-                         strings_not_displayed=None,
-                         strings_displayed_in_iframe=None,
-                         strings_not_displayed_in_iframe=None):
+    def load_citable_url(
+        self,
+        username,
+        repository_name,
+        changeset_revision,
+        encoded_user_id,
+        encoded_repository_id,
+        strings_displayed=None,
+        strings_not_displayed=None,
+        strings_displayed_in_iframe=None,
+        strings_not_displayed_in_iframe=None,
+    ):
         strings_displayed_in_iframe = strings_displayed_in_iframe or []
         strings_not_displayed_in_iframe = strings_not_displayed_in_iframe or []
-        url = f'{self.url}/view/{username}'
+        url = f"{self.url}/view/{username}"
         # If repository name is passed in, append that to the url.
         if repository_name:
-            url += f'/{repository_name}'
+            url += f"/{repository_name}"
         if changeset_revision:
             # Changeset revision should never be provided unless repository name also is.
-            assert repository_name is not None, 'Changeset revision is present, but repository name is not - aborting.'
-            url += f'/{changeset_revision}'
+            assert repository_name is not None, "Changeset revision is present, but repository name is not - aborting."
+            url += f"/{changeset_revision}"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
         # Now load the page that should be displayed inside the iframe and check for strings.
         if encoded_repository_id:
-            params = {
-                'id': encoded_repository_id,
-                'operation': 'view_or_manage_repository'
-            }
+            params = {"id": encoded_repository_id, "operation": "view_or_manage_repository"}
             if changeset_revision:
-                params['changeset_revision'] = changeset_revision
-            self.visit_url('/repository/view_repository', params=params)
+                params["changeset_revision"] = changeset_revision
+            self.visit_url("/repository/view_repository", params=params)
             self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe)
         elif encoded_user_id:
-            params = {
-                'user_id': encoded_user_id,
-                'operation': 'repositories_by_user'
-            }
-            self.visit_url('/repository/browse_repositories', params=params)
+            params = {"user_id": encoded_user_id, "operation": "repositories_by_user"}
+            self.visit_url("/repository/browse_repositories", params=params)
             self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe)
 
-    def load_changeset_in_tool_shed(self, repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'ctx_str': changeset_revision,
-            'id': repository_id
-        }
-        self.visit_url('/repository/view_changeset', params=params)
+    def load_changeset_in_tool_shed(
+        self, repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None
+    ):
+        params = {"ctx_str": changeset_revision, "id": repository_id}
+        self.visit_url("/repository/view_changeset", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def load_checkable_revisions(self, strings_displayed=None, strings_not_displayed=None):
         params = {
-            'do_not_test': 'false',
-            'downloadable': 'true',
-            'includes_tools': 'true',
-            'malicious': 'false',
-            'missing_test_components': 'false',
-            'skip_tool_test': 'false'
+            "do_not_test": "false",
+            "downloadable": "true",
+            "includes_tools": "true",
+            "malicious": "false",
+            "missing_test_components": "false",
+            "skip_tool_test": "false",
         }
-        self.visit_url('/api/repository_revisions', params=params)
+        self.visit_url("/api/repository_revisions", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def load_display_tool_page(self, repository, tool_xml_path, changeset_revision, strings_displayed=None, strings_not_displayed=None):
+    def load_display_tool_page(
+        self, repository, tool_xml_path, changeset_revision, strings_displayed=None, strings_not_displayed=None
+    ):
         params = {
-            'repository_id': self.security.encode_id(repository.id),
-            'tool_config': tool_xml_path,
-            'changeset_revision': changeset_revision
+            "repository_id": self.security.encode_id(repository.id),
+            "tool_config": tool_xml_path,
+            "changeset_revision": changeset_revision,
         }
-        self.visit_url('/repository/display_tool', params=params)
+        self.visit_url("/repository/display_tool", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def load_invalid_tool_page(self, repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None):
+    def load_invalid_tool_page(
+        self, repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None
+    ):
         params = {
-            'repository_id': self.security.encode_id(repository.id),
-            'tool_config': tool_xml,
-            'changeset_revision': changeset_revision
+            "repository_id": self.security.encode_id(repository.id),
+            "tool_config": tool_xml,
+            "changeset_revision": changeset_revision,
         }
-        self.visit_url('/repository/load_invalid_tool', params=params)
+        self.visit_url("/repository/load_invalid_tool", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def load_page_for_installed_tool(self, tool_guid, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'tool_id': tool_guid
-        }
-        self.visit_galaxy_url('/tool_runner', params=params)
+        params = {"tool_id": tool_guid}
+        self.visit_galaxy_url("/tool_runner", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def manage_review_components(self, strings_displayed=None, strings_not_displayed=None):
-        url = '/repository_review/manage_components'
+        url = "/repository_review/manage_components"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def preview_repository_in_tool_shed(self, name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None):
+    def preview_repository_in_tool_shed(
+        self, name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None
+    ):
         repository = test_db_util.get_repository_by_name_and_owner(name, owner)
         if not changeset_revision:
             changeset_revision = self.get_repository_tip(repository)
-        params = {
-            'repository_id': self.security.encode_id(repository.id),
-            'changeset_revision': changeset_revision
-        }
-        self.visit_url('/repository/preview_tools_in_changeset', params=params)
+        params = {"repository_id": self.security.encode_id(repository.id), "changeset_revision": changeset_revision}
+        self.visit_url("/repository/preview_tools_in_changeset", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def reactivate_repository(self, installed_repository):
         params = dict(id=self.security.encode_id(installed_repository.id))
-        url = '/admin_toolshed/restore_repository'
+        url = "/admin_toolshed/restore_repository"
         self.visit_galaxy_url(url, params=params)
 
-    def reinstall_repository(self,
-                             installed_repository,
-                             install_repository_dependencies=True,
-                             install_tool_dependencies=False,
-                             no_changes=True,
-                             new_tool_panel_section_label='',
-                             strings_displayed=None,
-                             strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(installed_repository.id)
-        }
-        self.visit_galaxy_url('/admin_toolshed/reselect_tool_panel_section', params=params)
+    def reinstall_repository(
+        self,
+        installed_repository,
+        install_repository_dependencies=True,
+        install_tool_dependencies=False,
+        no_changes=True,
+        new_tool_panel_section_label="",
+        strings_displayed=None,
+        strings_not_displayed=None,
+    ):
+        params = {"id": self.security.encode_id(installed_repository.id)}
+        self.visit_galaxy_url("/admin_toolshed/reselect_tool_panel_section", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed=None)
         # Build the url that will simulate a filled-out form being submitted. Due to a limitation in twill, the reselect_tool_panel_section
         # form doesn't get parsed correctly.
         encoded_repository_id = self.security.encode_id(installed_repository.id)
-        params = dict(id=encoded_repository_id, no_changes=no_changes, new_tool_panel_section_label=new_tool_panel_section_label)
+        params = dict(
+            id=encoded_repository_id, no_changes=no_changes, new_tool_panel_section_label=new_tool_panel_section_label
+        )
         doseq = False
         if install_repository_dependencies:
-            params['install_repository_dependencies'] = True
+            params["install_repository_dependencies"] = True
             doseq = True
         else:
-            params['install_repository_dependencies'] = False
+            params["install_repository_dependencies"] = False
         if install_tool_dependencies:
-            params['install_tool_dependencies'] = True
+            params["install_tool_dependencies"] = True
             doseq = True
         else:
-            params['install_tool_dependencies'] = False
-        url = '/admin_toolshed/reinstall_repository'
+            params["install_tool_dependencies"] = False
+        url = "/admin_toolshed/reinstall_repository"
         self.visit_galaxy_url(url, params=params, doseq=doseq)
         # Manually initiate the install process, as with installing a repository. See comments in the
         # initiate_installation_process method for details.
-        repository_ids = self.initiate_installation_process(install_tool_dependencies,
-                                                            install_repository_dependencies,
-                                                            no_changes,
-                                                            new_tool_panel_section_label)
+        repository_ids = self.initiate_installation_process(
+            install_tool_dependencies, install_repository_dependencies, no_changes, new_tool_panel_section_label
+        )
         # Finally, wait until all repositories are in a final state (either Error or Installed) before returning.
         self.wait_for_repository_installation(repository_ids)
 
@@ -1257,25 +1377,31 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
     def reset_installed_repository_metadata(self, repository):
         encoded_id = self.security.encode_id(repository.id)
         api_key = get_admin_api_key()
-        response = requests.post(f"{self.galaxy_url}/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories", data={'repository_ids': [encoded_id], 'key': api_key}, timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.post(
+            f"{self.galaxy_url}/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories",
+            data={"repository_ids": [encoded_id], "key": api_key},
+            timeout=DEFAULT_SOCKET_TIMEOUT,
+        )
         assert response.status_code != 403, response.content
 
     def reset_metadata_on_selected_repositories(self, repository_ids):
-        self.visit_url('/admin/reset_metadata_on_selected_repositories_in_tool_shed')
+        self.visit_url("/admin/reset_metadata_on_selected_repositories_in_tool_shed")
         kwd = dict(repository_ids=repository_ids)
         self.submit_form(button="reset_metadata_on_selected_repositories_button", **kwd)
 
     def reset_metadata_on_selected_installed_repositories(self, repository_ids):
         api_key = get_admin_api_key()
-        response = requests.post(f"{self.galaxy_url}/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories", data={'repository_ids': repository_ids, 'key': api_key}, timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.post(
+            f"{self.galaxy_url}/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories",
+            data={"repository_ids": repository_ids, "key": api_key},
+            timeout=DEFAULT_SOCKET_TIMEOUT,
+        )
         assert response.status_code != 403, response.content
 
     def reset_repository_metadata(self, repository):
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository/reset_all_metadata', params=params)
-        self.check_for_strings(['All repository metadata has been reset.'])
+        params = {"id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository/reset_all_metadata", params=params)
+        self.check_for_strings(["All repository metadata has been reset."])
 
     def review_repository(self, repository, review_contents_dict, user=None, changeset_revision=None):
         strings_displayed = []
@@ -1283,75 +1409,79 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         if not changeset_revision:
             changeset_revision = self.get_repository_tip(repository)
         if user:
-            review = test_db_util.get_repository_review_by_user_id_changeset_revision(user.id, repository.id, changeset_revision)
-        params = {
-            'id': self.security.encode_id(review.id)
-        }
-        self.visit_url('/repository_review/edit_review', params=params)
+            review = test_db_util.get_repository_review_by_user_id_changeset_revision(
+                user.id, repository.id, changeset_revision
+            )
+        params = {"id": self.security.encode_id(review.id)}
+        self.visit_url("/repository_review/edit_review", params=params)
         self.fill_review_form(review_contents_dict, strings_displayed, strings_not_displayed)
 
     def revoke_write_access(self, repository, username):
-        params = {
-            'user_access_button': 'Remove',
-            'id': self.security.encode_id(repository.id),
-            'remove_auth': username
-        }
-        self.visit_url('/repository/manage_repository', params=params)
+        params = {"user_access_button": "Remove", "id": self.security.encode_id(repository.id), "remove_auth": username}
+        self.visit_url("/repository/manage_repository", params=params)
 
-    def search_for_valid_tools(self, search_fields=None, exact_matches=False, strings_displayed=None, strings_not_displayed=None, from_galaxy=False):
+    def search_for_valid_tools(
+        self,
+        search_fields=None,
+        exact_matches=False,
+        strings_displayed=None,
+        strings_not_displayed=None,
+        from_galaxy=False,
+    ):
         params = {}
         search_fields = search_fields or {}
         if from_galaxy:
-            params['galaxy_url'] = self.galaxy_url
+            params["galaxy_url"] = self.galaxy_url
         for field_name, search_string in search_fields.items():
-            self.visit_url('/repository/find_tools', params=params)
+            self.visit_url("/repository/find_tools", params=params)
             tc.fv("1", "exact_matches", exact_matches)
             tc.fv("1", field_name, search_string)
             tc.submit()
             self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def send_message_to_repository_owner(self,
-                                         repository,
-                                         message,
-                                         strings_displayed=None,
-                                         strings_not_displayed=None,
-                                         post_submit_strings_displayed=None,
-                                         post_submit_strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/repository/contact_owner', params=params)
+    def send_message_to_repository_owner(
+        self,
+        repository,
+        message,
+        strings_displayed=None,
+        strings_not_displayed=None,
+        post_submit_strings_displayed=None,
+        post_submit_strings_not_displayed=None,
+    ):
+        params = {"id": self.security.encode_id(repository.id)}
+        self.visit_url("/repository/contact_owner", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        tc.fv(1, 'message', message)
+        tc.fv(1, "message", message)
         tc.submit()
         self.check_for_strings(post_submit_strings_displayed, post_submit_strings_not_displayed)
 
     def set_form_value(self, form, kwd, field_name, field_value):
-        '''
+        """
         Set the form field field_name to field_value if it exists, and return the provided dict containing that value. If
         the field does not exist in the provided form, return a dict without that index.
-        '''
-        form_id = form.attrib.get('id')
+        """
+        form_id = form.attrib.get("id")
         controls = [control for control in form.inputs if str(control.name) == field_name]
         if len(controls) > 0:
-            log.debug(f'Setting field {field_name} of form {form_id} to {str(field_value)}.')
+            log.debug(f"Setting field {field_name} of form {form_id} to {str(field_value)}.")
             tc.formvalue(form_id, field_name, str(field_value))
             kwd[field_name] = str(field_value)
         else:
             if field_name in kwd:
-                log.debug('No field %s in form %s, discarding from return value.', field_name, form_id)
-                del(kwd[field_name])
+                log.debug("No field %s in form %s, discarding from return value.", field_name, form_id)
+                del kwd[field_name]
         return kwd
 
-    def set_repository_deprecated(self, repository, set_deprecated=True, strings_displayed=None, strings_not_displayed=None):
-        params = {
-            'id': self.security.encode_id(repository.id),
-            'mark_deprecated': set_deprecated
-        }
-        self.visit_url('/repository/deprecate', params=params)
+    def set_repository_deprecated(
+        self, repository, set_deprecated=True, strings_displayed=None, strings_not_displayed=None
+    ):
+        params = {"id": self.security.encode_id(repository.id), "mark_deprecated": set_deprecated}
+        self.visit_url("/repository/deprecate", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def set_repository_malicious(self, repository, set_malicious=True, strings_displayed=None, strings_not_displayed=None):
+    def set_repository_malicious(
+        self, repository, set_malicious=True, strings_displayed=None, strings_not_displayed=None
+    ):
         self.display_manage_repository_page(repository)
         tc.fv("malicious", "malicious", set_malicious)
         tc.submit("malicious_button")
@@ -1362,51 +1492,57 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         return test_db_util.get_repository_metadata_by_repository_id_changeset_revision(repository.id, tip)
 
     def undelete_repository(self, repository):
-        params = {
-            'operation': 'Undelete',
-            'id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/admin/browse_repositories', params=params)
-        strings_displayed = ['Undeleted 1 repository', repository.name]
+        params = {"operation": "Undelete", "id": self.security.encode_id(repository.id)}
+        self.visit_url("/admin/browse_repositories", params=params)
+        strings_displayed = ["Undeleted 1 repository", repository.name]
         strings_not_displayed = []
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def uninstall_repository(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
         encoded_id = self.security.encode_id(installed_repository.id)
         api_key = get_admin_api_key()
-        response = requests.delete(f"{self.galaxy_url}/api/tool_shed_repositories/{encoded_id}", data={'remove_from_disk': True, 'key': api_key}, timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.delete(
+            f"{self.galaxy_url}/api/tool_shed_repositories/{encoded_id}",
+            data={"remove_from_disk": True, "key": api_key},
+            timeout=DEFAULT_SOCKET_TIMEOUT,
+        )
         assert response.status_code != 403, response.content
 
     def update_installed_repository(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
         params = {
-            'name': installed_repository.name,
-            'owner': installed_repository.owner,
-            'changeset_revision': installed_repository.installed_changeset_revision,
-            'galaxy_url': self.galaxy_url
+            "name": installed_repository.name,
+            "owner": installed_repository.owner,
+            "changeset_revision": installed_repository.installed_changeset_revision,
+            "galaxy_url": self.galaxy_url,
         }
-        self.visit_url('/repository/check_for_updates', params=params)
+        self.visit_url("/repository/check_for_updates", params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def update_tool_shed_status(self):
         api_key = get_admin_api_key()
-        response = requests.get(f"{self.galaxy_url}/api/tool_shed_repositories/check_for_updates?key={api_key}", timeout=DEFAULT_SOCKET_TIMEOUT)
+        response = requests.get(
+            f"{self.galaxy_url}/api/tool_shed_repositories/check_for_updates?key={api_key}",
+            timeout=DEFAULT_SOCKET_TIMEOUT,
+        )
         assert response.status_code != 403, response.content
 
-    def upload_file(self,
-                    repository,
-                    filename,
-                    filepath,
-                    valid_tools_only,
-                    uncompress_file,
-                    remove_repo_files_not_in_tar,
-                    commit_message,
-                    strings_displayed=None,
-                    strings_not_displayed=None):
+    def upload_file(
+        self,
+        repository,
+        filename,
+        filepath,
+        valid_tools_only,
+        uncompress_file,
+        remove_repo_files_not_in_tar,
+        commit_message,
+        strings_displayed=None,
+        strings_not_displayed=None,
+    ):
         if strings_displayed is None:
             strings_displayed = []
         if strings_not_displayed is None:
             strings_not_displayed = []
-        removed_message = 'files were removed from the repository'
+        removed_message = "files were removed from the repository"
         if remove_repo_files_not_in_tar:
             if not self.repository_is_new(repository):
                 if removed_message not in strings_displayed:
@@ -1414,23 +1550,21 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         else:
             if removed_message not in strings_not_displayed:
                 strings_not_displayed.append(removed_message)
-        params = {
-            'repository_id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/upload/upload', params=params)
+        params = {"repository_id": self.security.encode_id(repository.id)}
+        self.visit_url("/upload/upload", params=params)
         if valid_tools_only:
-            strings_displayed.extend(['has been successfully', 'uploaded to the repository.'])
+            strings_displayed.extend(["has been successfully", "uploaded to the repository."])
         tc.formfile("1", "file_data", self.get_filename(filename, filepath))
         if uncompress_file:
-            tc.fv(1, 'uncompress_file', 'Yes')
+            tc.fv(1, "uncompress_file", "Yes")
         else:
-            tc.fv(1, 'uncompress_file', 'No')
+            tc.fv(1, "uncompress_file", "No")
         if not self.repository_is_new(repository):
             if remove_repo_files_not_in_tar:
-                tc.fv(1, 'remove_repo_files_not_in_tar', 'Yes')
+                tc.fv(1, "remove_repo_files_not_in_tar", "Yes")
             else:
-                tc.fv(1, 'remove_repo_files_not_in_tar', 'No')
-        tc.fv(1, 'commit_message', commit_message)
+                tc.fv(1, "remove_repo_files_not_in_tar", "No")
+        tc.fv(1, "commit_message", commit_message)
         tc.submit("upload_button")
         self.check_for_strings(strings_displayed, strings_not_displayed)
         # Uncomment this if it becomes necessary to wait for an asynchronous process to complete after submitting an upload.
@@ -1445,17 +1579,19 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         #            time.sleep( 1 )
         #            continue
 
-    def upload_url(self,
-                   repository,
-                   url,
-                   filepath,
-                   valid_tools_only,
-                   uncompress_file,
-                   remove_repo_files_not_in_tar,
-                   commit_message,
-                   strings_displayed=None,
-                   strings_not_displayed=None):
-        removed_message = 'files were removed from the repository'
+    def upload_url(
+        self,
+        repository,
+        url,
+        filepath,
+        valid_tools_only,
+        uncompress_file,
+        remove_repo_files_not_in_tar,
+        commit_message,
+        strings_displayed=None,
+        strings_not_displayed=None,
+    ):
+        removed_message = "files were removed from the repository"
         if remove_repo_files_not_in_tar:
             if not self.repository_is_new(repository):
                 if removed_message not in strings_displayed:
@@ -1463,23 +1599,21 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         else:
             if removed_message not in strings_not_displayed:
                 strings_not_displayed.append(removed_message)
-        params = {
-            'repository_id': self.security.encode_id(repository.id)
-        }
-        self.visit_url('/upload/upload', params=params)
+        params = {"repository_id": self.security.encode_id(repository.id)}
+        self.visit_url("/upload/upload", params=params)
         if valid_tools_only:
-            strings_displayed.extend(['has been successfully', 'uploaded to the repository.'])
+            strings_displayed.extend(["has been successfully", "uploaded to the repository."])
         tc.fv("1", "url", url)
         if uncompress_file:
-            tc.fv(1, 'uncompress_file', 'Yes')
+            tc.fv(1, "uncompress_file", "Yes")
         else:
-            tc.fv(1, 'uncompress_file', 'No')
+            tc.fv(1, "uncompress_file", "No")
         if not self.repository_is_new(repository):
             if remove_repo_files_not_in_tar:
-                tc.fv(1, 'remove_repo_files_not_in_tar', 'Yes')
+                tc.fv(1, "remove_repo_files_not_in_tar", "Yes")
             else:
-                tc.fv(1, 'remove_repo_files_not_in_tar', 'No')
-        tc.fv(1, 'commit_message', commit_message)
+                tc.fv(1, "remove_repo_files_not_in_tar", "No")
+        tc.fv(1, "commit_message", commit_message)
         tc.submit("upload_button")
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
@@ -1489,20 +1623,21 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         for repository_name, repository_owner in installed_repositories:
             galaxy_repository = test_db_util.get_installed_repository_by_name_owner(repository_name, repository_owner)
             if galaxy_repository:
-                assert galaxy_repository.status == 'Installed', \
-                    f'Repository {repository_name} should be installed, but is {galaxy_repository.status}'
+                assert (
+                    galaxy_repository.status == "Installed"
+                ), f"Repository {repository_name} should be installed, but is {galaxy_repository.status}"
 
     def verify_installed_repository_metadata_unchanged(self, name, owner):
         installed_repository = test_db_util.get_installed_repository_by_name_owner(name, owner)
         metadata = installed_repository.metadata_
         self.reset_installed_repository_metadata(installed_repository)
         new_metadata = installed_repository.metadata_
-        assert metadata == new_metadata, f'Metadata for installed repository {name} differs after metadata reset.'
+        assert metadata == new_metadata, f"Metadata for installed repository {name} differs after metadata reset."
 
     def verify_installed_repository_no_tool_panel_section(self, repository):
-        '''Verify that there is no 'tool_panel_section' entry in the repository metadata.'''
+        """Verify that there is no 'tool_panel_section' entry in the repository metadata."""
         metadata = repository.metadata_
-        assert 'tool_panel_section' not in metadata, f'Tool panel section incorrectly found in metadata: {metadata}'
+        assert "tool_panel_section" not in metadata, f"Tool panel section incorrectly found in metadata: {metadata}"
 
     def verify_installed_repository_data_table_entries(self, required_data_table_entries):
         # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ]
@@ -1527,28 +1662,34 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         #     </table>
         # </tables>
         required_data_table_entry = None
-        for table_elem in data_tables.findall('table'):
+        for table_elem in data_tables.findall("table"):
             # The value of table_elem will be something like: <table comment_char="#" name="sam_fa_indexes">
             for required_data_table_entry in required_data_table_entries:
                 # The value of required_data_table_entry will be something like: 'sam_fa_indexes'
-                if 'name' in table_elem.attrib and table_elem.attrib['name'] == required_data_table_entry:
+                if "name" in table_elem.attrib and table_elem.attrib["name"] == required_data_table_entry:
                     found = True
                     # We're processing something like: sam_fa_indexes
-                    file_elem = table_elem.find('file')
+                    file_elem = table_elem.find("file")
                     # We have something like: <file path="tool-data/sam_fa_indices.loc" />
                     # The "path" attribute of the "file" tag is the location that Galaxy always uses because the
                     # Galaxy ToolDataTableManager was implemented in such a way that the hard-coded path is used
                     # rather than allowing the location to be a configurable setting like the tool shed requires.
-                    file_path = file_elem.get('path', None)
+                    file_path = file_elem.get("path", None)
                     # The value of file_path will be something like: "tool-data/all_fasta.loc"
-                    assert file_path is not None, f'The "path" attribute is missing for the {required_data_table_entry} entry.'
+                    assert (
+                        file_path is not None
+                    ), f'The "path" attribute is missing for the {required_data_table_entry} entry.'
                     # The following test is probably not necesary, but the tool-data directory should exist!
                     galaxy_tool_data_dir, loc_file_name = os.path.split(file_path)
-                    assert galaxy_tool_data_dir is not None, f'The hard-coded Galaxy tool-data directory is missing for the {required_data_table_entry} entry.'
-                    assert os.path.exists(galaxy_tool_data_dir), 'The Galaxy tool-data directory does not exist.'
+                    assert (
+                        galaxy_tool_data_dir is not None
+                    ), f"The hard-coded Galaxy tool-data directory is missing for the {required_data_table_entry} entry."
+                    assert os.path.exists(galaxy_tool_data_dir), "The Galaxy tool-data directory does not exist."
                     # Make sure the loc_file_name was correctly copied into the configured directory location.
                     configured_file_location = os.path.join(self.tool_data_path, loc_file_name)
-                    assert os.path.isfile(configured_file_location), f'The expected copied file "{configured_file_location}" is missing.'
+                    assert os.path.isfile(
+                        configured_file_location
+                    ), f'The expected copied file "{configured_file_location}" is missing.'
                     # We've found the value of the required_data_table_entry in data_tables, which is the parsed
                     # shed_tool_data_table_conf.xml, so all is well!
                     break
@@ -1556,7 +1697,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
                 break
         # We better have an entry like: <table comment_char="#" name="sam_fa_indexes"> in our parsed data_tables
         # or we know that the repository was not correctly installed!
-        assert found, f'No entry for {required_data_table_entry} in {self.shed_tool_data_table_conf}.'
+        assert found, f"No entry for {required_data_table_entry} in {self.shed_tool_data_table_conf}."
 
     def verify_repository_reviews(self, repository, reviewer=None, strings_displayed=None, strings_not_displayed=None):
         changeset_revision = self.get_repository_tip(repository)
@@ -1567,20 +1708,24 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         strings_displayed = [repository.name, repository.description]
         self.display_repository_reviews_by_user(reviewer, strings_displayed=strings_displayed)
         # Load the review and check for the components passed in strings_displayed.
-        review = test_db_util.get_repository_review_by_user_id_changeset_revision(reviewer.id, repository.id, changeset_revision)
+        review = test_db_util.get_repository_review_by_user_id_changeset_revision(
+            reviewer.id, repository.id, changeset_revision
+        )
         self.browse_component_review(review, strings_displayed=strings_displayed)
 
-    def verify_tool_metadata_for_installed_repository(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
+    def verify_tool_metadata_for_installed_repository(
+        self, installed_repository, strings_displayed=None, strings_not_displayed=None
+    ):
         if strings_displayed is None:
             strings_displayed = []
         if strings_not_displayed is None:
             strings_not_displayed = []
         repository_id = self.security.encode_id(installed_repository.id)
-        for tool in installed_repository.metadata_['tools']:
+        for tool in installed_repository.metadata_["tools"]:
             strings = list(strings_displayed)
-            strings.extend([tool['id'], tool['description'], tool['version'], tool['guid'], tool['name']])
-            params = dict(repository_id=repository_id, tool_id=tool['id'])
-            url = '/admin_toolshed/view_tool_metadata'
+            strings.extend([tool["id"], tool["description"], tool["version"], tool["guid"], tool["name"]])
+            params = dict(repository_id=repository_id, tool_id=tool["id"])
+            url = "/admin_toolshed/view_tool_metadata"
             self.visit_galaxy_url(url, params)
             self.check_for_strings(strings, strings_not_displayed)
 
@@ -1594,17 +1739,19 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
             new_metadata[metadata.changeset_revision] = metadata.metadata
         # Python's dict comparison recursively compares sorted key => value pairs and returns true if any key or value differs,
         # or if the number of keys differs.
-        assert old_metadata == new_metadata, f'Metadata changed after reset on repository {repository.name}.'
+        assert old_metadata == new_metadata, f"Metadata changed after reset on repository {repository.name}."
 
     def visit_galaxy_url(self, url, params=None, doseq=False, allowed_codes=None):
         if allowed_codes is None:
             allowed_codes = [200]
-        url = f'{self.galaxy_url}{url}'
+        url = f"{self.galaxy_url}{url}"
         self.visit_url(url, params=params, doseq=doseq, allowed_codes=allowed_codes)
 
     def wait_for_repository_installation(self, repository_ids):
-        final_states = [galaxy_model.ToolShedRepository.installation_status.ERROR,
-                        galaxy_model.ToolShedRepository.installation_status.INSTALLED]
+        final_states = [
+            galaxy_model.ToolShedRepository.installation_status.ERROR,
+            galaxy_model.ToolShedRepository.installation_status.INSTALLED,
+        ]
         # Wait until all repositories are in a final state before returning. This ensures that subsequent tests
         # are running against an installed repository, and not one that is still in the process of installing.
         if repository_ids:
@@ -1616,7 +1763,9 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
                     timeout_counter = timeout_counter + 1
                     # This timeout currently defaults to 10 minutes.
                     if timeout_counter > repository_installation_timeout:
-                        raise AssertionError('Repository installation timed out, %d seconds elapsed, repository state is %s.' %
-                                             (timeout_counter, galaxy_repository.status))
+                        raise AssertionError(
+                            "Repository installation timed out, %d seconds elapsed, repository state is %s."
+                            % (timeout_counter, galaxy_repository.status)
+                        )
                         break
                     time.sleep(1)
diff --git a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py
index 63d26e206ca..3525f9684e6 100644
--- a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py
+++ b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py
@@ -1,8 +1,11 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'filtering_0000'
+repository_name = "filtering_0000"
 repository_description = "Galaxy's filtering tool for test 0000"
 repository_long_description = "Long description of Galaxy's filtering tool for test 0000"
 
@@ -10,45 +13,55 @@ log = logging.getLogger(__name__)
 
 
 class TestBasicRepositoryFeatures(ShedTwillTestCase):
-    '''Test core repository features.'''
+    """Test core repository features."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_repository_without_categories(self):
-        '''Verify that a repository cannot be created unless at least one category has been defined.'''
-        strings_displayed = ['No categories have been configured in this instance of the Galaxy Tool Shed']
-        self.visit_url('/repository/create_repository')
+        """Verify that a repository cannot be created unless at least one category has been defined."""
+        strings_displayed = ["No categories have been configured in this instance of the Galaxy Tool Shed"]
+        self.visit_url("/repository/create_repository")
         self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=[])
 
     def test_0010_create_categories(self):
         """Create categories for this test suite"""
-        self.create_category(name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1')
-        self.create_category(name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2')
+        self.create_category(
+            name="Test 0000 Basic Repository Features 1", description="Test 0000 Basic Repository Features 1"
+        )
+        self.create_category(
+            name="Test 0000 Basic Repository Features 2", description="Test 0000 Basic Repository Features 2"
+        )
 
     def test_0015_create_repository(self):
         """Create the filtering repository"""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0000 Basic Repository Features 1')
+        category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
         strings_displayed = self.expect_repo_created_strings(repository_name)
-        self.get_or_create_repository(name=repository_name,
-                                      description=repository_description,
-                                      long_description=repository_long_description,
-                                      owner=common.test_user_1_name,
-                                      category_id=self.security.encode_id(category.id),
-                                      strings_displayed=strings_displayed)
+        self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
 
     def test_0020_edit_repository(self):
         """Edit the repository name, description, and long description"""
@@ -56,17 +69,21 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         new_name = "renamed_filtering"
         new_description = "Edited filtering tool"
         new_long_description = "Edited long description"
-        self.edit_repository_information(repository, repo_name=new_name, description=new_description, long_description=new_long_description)
+        self.edit_repository_information(
+            repository, repo_name=new_name, description=new_description, long_description=new_long_description
+        )
 
     def test_0025_change_repository_category(self):
         """Change the categories associated with the filtering repository"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.edit_repository_categories(repository,
-                                        categories_to_add=["Test 0000 Basic Repository Features 2"],
-                                        categories_to_remove=["Test 0000 Basic Repository Features 1"])
+        self.edit_repository_categories(
+            repository,
+            categories_to_add=["Test 0000 Basic Repository Features 2"],
+            categories_to_remove=["Test 0000 Basic Repository Features 1"],
+        )
 
     def test_0030_grant_write_access(self):
-        '''Grant write access to another user'''
+        """Grant write access to another user"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.grant_write_access(repository, usernames=[common.test_user_2_name])
         self.revoke_write_access(repository, common.test_user_2_name)
@@ -74,216 +91,269 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
     def test_0035_upload_filtering_1_1_0(self):
         """Upload filtering_1.1.0.tar to the repository"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message="Uploaded filtering 1.1.0",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded filtering 1.1.0",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0040_verify_repository(self):
-        '''Display basic repository pages'''
+        """Display basic repository pages"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         latest_changeset_revision = self.get_repository_tip(repository)
-        self.check_for_valid_tools(repository, strings_displayed=['Filter1'])
+        self.check_for_valid_tools(repository, strings_displayed=["Filter1"])
         self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=1)
         tip = self.get_repository_tip(repository)
         tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/filtering_0000/Filter1/1.1.0"
-        tool_metadata_strings_displayed = [tool_guid,
-                                           '1.1.0',  # The tool version.
-                                           'Filter1',  # The tool ID.
-                                           'Filter',  # The tool name.
-                                           'data on any column using simple expressions']  # The tool description.
-        tool_page_strings_displayed = ['Filter (version 1.1.0)']
-        self.check_repository_tools_for_changeset_revision(repository,
-                                                           tip,
-                                                           tool_metadata_strings_displayed=tool_metadata_strings_displayed,
-                                                           tool_page_strings_displayed=tool_page_strings_displayed)
+        tool_metadata_strings_displayed = [
+            tool_guid,
+            "1.1.0",  # The tool version.
+            "Filter1",  # The tool ID.
+            "Filter",  # The tool name.
+            "data on any column using simple expressions",
+        ]  # The tool description.
+        tool_page_strings_displayed = ["Filter (version 1.1.0)"]
+        self.check_repository_tools_for_changeset_revision(
+            repository,
+            tip,
+            tool_metadata_strings_displayed=tool_metadata_strings_displayed,
+            tool_page_strings_displayed=tool_page_strings_displayed,
+        )
         self.check_repository_metadata(repository, tip_only=False)
-        self.browse_repository(repository, strings_displayed=[f"Repository '{repository.name}' revision", '(repository tip)'])
-        self.display_repository_clone_page(common.test_user_1_name,
-                                           repository_name,
-                                           strings_displayed=['Uploaded filtering 1.1.0', latest_changeset_revision])
+        self.browse_repository(
+            repository, strings_displayed=[f"Repository '{repository.name}' revision", "(repository tip)"]
+        )
+        self.display_repository_clone_page(
+            common.test_user_1_name,
+            repository_name,
+            strings_displayed=["Uploaded filtering 1.1.0", latest_changeset_revision],
+        )
 
     def test_0045_alter_repository_states(self):
-        '''Test toggling the malicious and deprecated repository flags.'''
+        """Test toggling the malicious and deprecated repository flags."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.login(email=common.admin_email, username=common.admin_username)
-        self.set_repository_malicious(repository,
-                                      set_malicious=True,
-                                      strings_displayed=['The repository tip has been defined as malicious.'])
-        self.set_repository_malicious(repository,
-                                      set_malicious=False,
-                                      strings_displayed=['The repository tip has been defined as <b>not</b> malicious.'])
+        self.set_repository_malicious(
+            repository, set_malicious=True, strings_displayed=["The repository tip has been defined as malicious."]
+        )
+        self.set_repository_malicious(
+            repository,
+            set_malicious=False,
+            strings_displayed=["The repository tip has been defined as <b>not</b> malicious."],
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        self.set_repository_deprecated(repository,
-                                       strings_displayed=['has been marked as deprecated'])
-        strings_displayed = ['This repository has been marked as deprecated', 'Mark repository as not deprecated']
-        self.display_manage_repository_page(repository,
-                                            strings_displayed=strings_displayed,
-                                            strings_not_displayed=['Upload files', 'Reset all repository metadata'])
-        self.browse_repository(repository, strings_not_displayed=['Upload files'])
-        self.set_repository_deprecated(repository,
-                                       strings_displayed=['has been marked as not deprecated'],
-                                       set_deprecated=False)
-        strings_displayed = ['Mark repository as deprecated', 'Upload files', 'Reset all repository metadata']
+        self.set_repository_deprecated(repository, strings_displayed=["has been marked as deprecated"])
+        strings_displayed = ["This repository has been marked as deprecated", "Mark repository as not deprecated"]
+        self.display_manage_repository_page(
+            repository,
+            strings_displayed=strings_displayed,
+            strings_not_displayed=["Upload files", "Reset all repository metadata"],
+        )
+        self.browse_repository(repository, strings_not_displayed=["Upload files"])
+        self.set_repository_deprecated(
+            repository, strings_displayed=["has been marked as not deprecated"], set_deprecated=False
+        )
+        strings_displayed = ["Mark repository as deprecated", "Upload files", "Reset all repository metadata"]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0050_display_repository_tip_file(self):
-        '''Display the contents of filtering.xml in the repository tip revision'''
+        """Display the contents of filtering.xml in the repository tip revision"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.display_repository_file_contents(repository=repository,
-                                              filename='filtering.xml',
-                                              filepath=None,
-                                              strings_displayed=['1.1.0'],
-                                              strings_not_displayed=[])
+        self.display_repository_file_contents(
+            repository=repository,
+            filename="filtering.xml",
+            filepath=None,
+            strings_displayed=["1.1.0"],
+            strings_not_displayed=[],
+        )
 
     def test_0055_upload_filtering_txt_file(self):
-        '''Upload filtering.txt file associated with tool version 1.1.0.'''
+        """Upload filtering.txt file associated with tool version 1.1.0."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/filtering_0000.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded filtering.txt",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.display_manage_repository_page(repository, strings_displayed=['Readme&nbsp;file&nbsp;for&nbsp;filtering&nbsp;1.1.0'])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_0000.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering.txt",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Readme&nbsp;file&nbsp;for&nbsp;filtering&nbsp;1.1.0"]
+        )
 
     def test_0060_upload_filtering_test_data(self):
-        '''Upload filtering test data.'''
+        """Upload filtering test data."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/filtering_test_data.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded filtering test data",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.display_repository_file_contents(repository=repository,
-                                              filename='1.bed',
-                                              filepath='test-data',
-                                              strings_displayed=[],
-                                              strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_test_data.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering test data",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.display_repository_file_contents(
+            repository=repository,
+            filename="1.bed",
+            filepath="test-data",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         self.check_repository_metadata(repository, tip_only=True)
 
     def test_0065_upload_filtering_2_2_0(self):
-        '''Upload filtering version 2.2.0'''
+        """Upload filtering version 2.2.0"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/filtering_2.2.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded filtering 2.2.0",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_2.2.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 2.2.0",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0070_verify_filtering_repository(self):
-        '''Verify the new tool versions and repository metadata.'''
+        """Verify the new tool versions and repository metadata."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         tip = self.get_repository_tip(repository)
         self.check_for_valid_tools(repository)
-        strings_displayed = ['Select a revision']
+        strings_displayed = ["Select a revision"]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
         self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=2)
         tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/filtering_0000/Filter1/2.2.0"
-        tool_metadata_strings_displayed = [tool_guid,
-                                           '2.2.0',  # The tool version.
-                                           'Filter1',  # The tool ID.
-                                           'Filter',  # The tool name.
-                                           'data on any column using simple expressions']  # The tool description.
-        tool_page_strings_displayed = ['Filter (version 2.2.0)']
-        self.check_repository_tools_for_changeset_revision(repository,
-                                                           tip,
-                                                           tool_metadata_strings_displayed=tool_metadata_strings_displayed,
-                                                           tool_page_strings_displayed=tool_page_strings_displayed)
+        tool_metadata_strings_displayed = [
+            tool_guid,
+            "2.2.0",  # The tool version.
+            "Filter1",  # The tool ID.
+            "Filter",  # The tool name.
+            "data on any column using simple expressions",
+        ]  # The tool description.
+        tool_page_strings_displayed = ["Filter (version 2.2.0)"]
+        self.check_repository_tools_for_changeset_revision(
+            repository,
+            tip,
+            tool_metadata_strings_displayed=tool_metadata_strings_displayed,
+            tool_page_strings_displayed=tool_page_strings_displayed,
+        )
         self.check_repository_metadata(repository, tip_only=False)
 
     def test_0075_upload_readme_txt_file(self):
-        '''Upload readme.txt file associated with tool version 2.2.0.'''
+        """Upload readme.txt file associated with tool version 2.2.0."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded readme.txt",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.display_manage_repository_page(repository, strings_displayed=['This&nbsp;is&nbsp;a&nbsp;readme&nbsp;file.'])
+        self.upload_file(
+            repository,
+            filename="readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded readme.txt",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["This&nbsp;is&nbsp;a&nbsp;readme&nbsp;file."]
+        )
         # Verify that there is a different readme file for each metadata revision.
-        self.display_manage_repository_page(repository,
-                                            strings_displayed=['Readme&nbsp;file&nbsp;for&nbsp;filtering&nbsp;1.1.0',
-                                                               'This&nbsp;is&nbsp;a&nbsp;readme&nbsp;file.'])
+        self.display_manage_repository_page(
+            repository,
+            strings_displayed=[
+                "Readme&nbsp;file&nbsp;for&nbsp;filtering&nbsp;1.1.0",
+                "This&nbsp;is&nbsp;a&nbsp;readme&nbsp;file.",
+            ],
+        )
 
     def test_0080_delete_readme_txt_file(self):
-        '''Delete the readme.txt file.'''
+        """Delete the readme.txt file."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.delete_files_from_repository(repository, filenames=['readme.txt'])
+        self.delete_files_from_repository(repository, filenames=["readme.txt"])
         self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=2)
-        self.display_manage_repository_page(repository, strings_displayed=['Readme&nbsp;file&nbsp;for&nbsp;filtering&nbsp;1.1.0'])
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Readme&nbsp;file&nbsp;for&nbsp;filtering&nbsp;1.1.0"]
+        )
 
     def test_0085_search_for_valid_filter_tool(self):
-        '''Search for the filtering tool by tool ID, name, and version.'''
+        """Search for the filtering tool by tool ID, name, and version."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         tip_changeset = self.get_repository_tip(repository)
-        search_fields = dict(tool_id='Filter1', tool_name='filter', tool_version='2.2.0')
-        self.search_for_valid_tools(search_fields=search_fields, strings_displayed=[tip_changeset], strings_not_displayed=[])
+        search_fields = dict(tool_id="Filter1", tool_name="filter", tool_version="2.2.0")
+        self.search_for_valid_tools(
+            search_fields=search_fields, strings_displayed=[tip_changeset], strings_not_displayed=[]
+        )
 
     def test_0090_verify_repository_metadata(self):
-        '''Verify that resetting the metadata does not change it.'''
+        """Verify that resetting the metadata does not change it."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.verify_unchanged_repository_metadata(repository)
 
     def test_0095_verify_reserved_repository_name_handling(self):
-        '''Check that reserved repository names are handled correctly.'''
-        category = self.test_db_util.get_category_by_name('Test 0000 Basic Repository Features 1')
-        error_message = "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
-        self.get_or_create_repository(name='repos',
-                                      description=repository_description,
-                                      long_description=repository_long_description,
-                                      owner=common.test_user_1_name,
-                                      category_id=self.security.encode_id(category.id),
-                                      strings_displayed=[error_message])
+        """Check that reserved repository names are handled correctly."""
+        category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
+        error_message = (
+            "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
+        )
+        self.get_or_create_repository(
+            name="repos",
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[error_message],
+        )
 
     def test_0100_verify_reserved_username_handling(self):
-        '''Check that reserved usernames are handled correctly.'''
-        self.login(email='baduser@bx.psu.edu', username='repos')
-        test_user_1 = self.test_db_util.get_user('baduser@bx.psu.edu')
+        """Check that reserved usernames are handled correctly."""
+        self.login(email="baduser@bx.psu.edu", username="repos")
+        test_user_1 = self.test_db_util.get_user("baduser@bx.psu.edu")
         assert test_user_1 is None, 'Creating user with public name "repos" succeeded.'
-        error_message = "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a public user name."
+        error_message = (
+            "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a public user name."
+        )
         self.check_for_strings(strings_displayed=[error_message])
 
     def test_0105_contact_repository_owner(self):
-        '''Fill out and submit the form to contact the owner of a repository.
+        """Fill out and submit the form to contact the owner of a repository.
 
         This test should not actually send the email, since functional tests are designed to function without
         any external network connection. The embedded tool shed server these tests are running against has been configured
         with an SMTP server address that will not and should not resolve correctly. However, since the successful sending of
         the email is the last step in the process, this will verify functional correctness of all preceding steps.
-        '''
+        """
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        message = 'This is a test message.'
-        strings_displayed = ['Contact the owner of the repository named', repository.name, 'streamline appropriate communication']
-        post_submit_strings_displayed = ['An error occurred sending your message by email']
-        self.send_message_to_repository_owner(repository=repository,
-                                              message=message,
-                                              strings_displayed=strings_displayed,
-                                              post_submit_strings_displayed=post_submit_strings_displayed)
+        message = "This is a test message."
+        strings_displayed = [
+            "Contact the owner of the repository named",
+            repository.name,
+            "streamline appropriate communication",
+        ]
+        post_submit_strings_displayed = ["An error occurred sending your message by email"]
+        self.send_message_to_repository_owner(
+            repository=repository,
+            message=message,
+            strings_displayed=strings_displayed,
+            post_submit_strings_displayed=post_submit_strings_displayed,
+        )
 
     def test_0110_delete_filtering_repository(self):
-        '''Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions.'''
+        """Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.login(email=common.admin_email, username=common.admin_username)
         self.delete_repository(repository)
@@ -294,7 +364,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         assert True not in [metadata.downloadable for metadata in repository.metadata_revisions]
 
     def test_0115_undelete_filtering_repository(self):
-        '''Undelete the filtering_0000 repository and verify that it now has two downloadable revisions.'''
+        """Undelete the filtering_0000 repository and verify that it now has two downloadable revisions."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.login(email=common.admin_email, username=common.admin_username)
         self.undelete_repository(repository)
@@ -307,38 +377,42 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         assert len(repository.downloadable_revisions) == 2
 
     def test_0120_enable_email_notifications(self):
-        '''Enable email notifications for test user 2 on filtering_0000.'''
+        """Enable email notifications for test user 2 on filtering_0000."""
         # Log in as test_user_2
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         # Get the repository, so we can pass the encoded repository id and browse_repositories method to the set_email_alerts method.
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ['Total alerts added: 1, total alerts removed: 0']
+        strings_displayed = ["Total alerts added: 1, total alerts removed: 0"]
         self.enable_email_alerts(repository, strings_displayed=strings_displayed)
 
     def test_0125_upload_new_readme_file(self):
-        '''Upload a new readme file to the filtering_0000 repository and verify that there is no error.'''
+        """Upload a new readme file to the filtering_0000 repository and verify that there is no error."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         # Upload readme.txt to the filtering_0000 repository and verify that it is now displayed.
-        self.upload_file(repository,
-                         filename='filtering/readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded new readme.txt with invalid ascii characters.",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.display_manage_repository_page(repository, strings_displayed=['These&nbsp;characters&nbsp;should&nbsp;not'])
+        self.upload_file(
+            repository,
+            filename="filtering/readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded new readme.txt with invalid ascii characters.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["These&nbsp;characters&nbsp;should&nbsp;not"]
+        )
 
     def test_0130_verify_handling_of_invalid_characters(self):
-        '''Load the above changeset in the change log and confirm that there is no server error displayed.'''
+        """Load the above changeset in the change log and confirm that there is no server error displayed."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         changeset_revision = self.get_repository_tip(repository)
         repository_id = self.security.encode_id(repository.id)
         changelog_tuples = self.get_repository_changelog_tuples(repository)
         revision_number = -1
-        revision_hash = '000000000000'
+        revision_hash = "000000000000"
         for numeric_changeset, changeset_hash in changelog_tuples:
             if str(changeset_hash) == str(changeset_revision):
                 revision_number = numeric_changeset
@@ -346,21 +420,29 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
                 break
         # Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured
         # unicode decoding error message.
-        strings_displayed = ['%d:%s' % (revision_number, revision_hash), 'filtering_0000', 'user1', 'repos', 'added:',
-                             '+These&nbsp;characters&nbsp;should&nbsp;not']
+        strings_displayed = [
+            "%d:%s" % (revision_number, revision_hash),
+            "filtering_0000",
+            "user1",
+            "repos",
+            "added:",
+            "+These&nbsp;characters&nbsp;should&nbsp;not",
+        ]
         self.load_changeset_in_tool_shed(repository_id, changeset_revision, strings_displayed=strings_displayed)
 
     def test_0135_api_get_repositories_in_category(self):
-        '''Load the api endpoint for repositories in a category.'''
+        """Load the api endpoint for repositories in a category."""
         categories = []
-        categories.append(self.test_db_util.get_category_by_name('Test 0000 Basic Repository Features 1'))
-        categories.append(self.test_db_util.get_category_by_name('Test 0000 Basic Repository Features 2'))
+        categories.append(self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1"))
+        categories.append(self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 2"))
         self.get_repositories_category_api(categories)
 
     def test_0140_view_invalid_changeset(self):
-        '''View repository using an invalid changeset'''
+        """View repository using an invalid changeset"""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         encoded_repository_id = self.security.encode_id(repository.id)
-        strings_displayed = ['Invalid+changeset+revision']
-        self.visit_url(f"/repository/view_repository?id={encoded_repository_id}&changeset_revision=nonsensical_changeset")
+        strings_displayed = ["Invalid+changeset+revision"]
+        self.visit_url(
+            f"/repository/view_repository?id={encoded_repository_id}&changeset_revision=nonsensical_changeset"
+        )
         self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=[])
diff --git a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
index 797baa72fc4..3c767f1bb2a 100644
--- a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
@@ -1,12 +1,15 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'freebayes_0010'
+repository_name = "freebayes_0010"
 repository_description = "Galaxy's freebayes tool"
 repository_long_description = "Long description of Galaxy's freebayes tool"
 
-'''
+"""
 1. Create repository freebayes_0020 and upload only the tool XML.
 2. Upload the tool_data_table_conf.xml.sample file.
 3. Upload sam_fa_indices.loc.sample.
@@ -14,152 +17,179 @@ repository_long_description = "Long description of Galaxy's freebayes tool"
 5. Upload a tool_dependencies.xml file that specifies a version that does not match the tool's requirements.
 6. Upload a valid tool_dependencies.xml file.
 7. Check for the appropriate strings on the manage repository page.
-'''
+"""
 
 
 class TestFreebayesRepository(ShedTwillTestCase):
-    '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.'''
+    """Testing freebayes with tool data table entries, .loc files, and tool dependencies."""
 
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category(self):
         """Create a category for this test suite"""
-        self.create_category(name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.')
+        self.create_category(
+            name="Test 0010 Repository With Tool Dependencies",
+            description="Tests for a repository with tool dependencies.",
+        )
 
     def test_0010_create_freebayes_repository_and_upload_tool_xml(self):
-        '''Create freebayes repository and upload only freebayes.xml.
+        """Create freebayes repository and upload only freebayes.xml.
 
         We are at step 1 - Create repository freebayes_0020 and upload only the tool XML.
         Uploading only the tool XML file should result in an invalid tool and an error message on
         upload, as well as on the manage repository page.
-        '''
+        """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0010 Repository With Tool Dependencies')
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='freebayes/freebayes.xml',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded the tool xml.',
-                         strings_displayed=['Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf'],
-                         strings_not_displayed=[])
-        self.display_manage_repository_page(repository, strings_displayed=['Invalid tools'], strings_not_displayed=['Valid tools'])
+        category = self.test_db_util.get_category_by_name("Test 0010 Repository With Tool Dependencies")
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="freebayes/freebayes.xml",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded the tool xml.",
+            strings_displayed=["Metadata may have been defined", "This file requires an entry", "tool_data_table_conf"],
+            strings_not_displayed=[],
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Invalid tools"], strings_not_displayed=["Valid tools"]
+        )
         tip = self.get_repository_tip(repository)
-        strings_displayed = ['requires an entry', 'tool_data_table_conf.xml']
+        strings_displayed = ["requires an entry", "tool_data_table_conf.xml"]
         self.check_repository_invalid_tools_for_changeset_revision(repository, tip, strings_displayed=strings_displayed)
 
     def test_0015_upload_missing_tool_data_table_conf_file(self):
-        '''Upload the missing tool_data_table_conf.xml.sample file to the repository.
+        """Upload the missing tool_data_table_conf.xml.sample file to the repository.
 
         We are at step 2 - Upload the tool_data_table_conf.xml.sample file.
         Uploading the tool_data_table_conf.xml.sample alone should not make the tool valid, but the error message should change.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='freebayes/tool_data_table_conf.xml.sample',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded the tool data table sample file.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.display_manage_repository_page(repository, strings_displayed=['Invalid tools'], strings_not_displayed=['Valid tools'])
+        self.upload_file(
+            repository,
+            filename="freebayes/tool_data_table_conf.xml.sample",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded the tool data table sample file.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Invalid tools"], strings_not_displayed=["Valid tools"]
+        )
         tip = self.get_repository_tip(repository)
-        strings_displayed = ['refers to a file', 'sam_fa_indices.loc']
+        strings_displayed = ["refers to a file", "sam_fa_indices.loc"]
         self.check_repository_invalid_tools_for_changeset_revision(repository, tip, strings_displayed=strings_displayed)
 
     def test_0020_upload_missing_sample_loc_file(self):
-        '''Upload the missing sam_fa_indices.loc.sample file to the repository.
+        """Upload the missing sam_fa_indices.loc.sample file to the repository.
 
         We are at step 3 - Upload the tool_data_table_conf.xml.sample file.
         Uploading the tool_data_table_conf.xml.sample alone should not make the tool valid, but the error message should change.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='freebayes/sam_fa_indices.loc.sample',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded tool data table .loc file.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="freebayes/sam_fa_indices.loc.sample",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded tool data table .loc file.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_upload_malformed_tool_dependency_xml(self):
-        '''Upload tool_dependencies.xml with bad characters in the readme tag.
+        """Upload tool_dependencies.xml with bad characters in the readme tag.
 
         We are at step 4 - Upload a tool_dependencies.xml file that should not parse correctly.
         Upload a tool_dependencies.xml file that contains <> in the text of the readme tag. This should show an error message about malformed xml.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename=os.path.join('freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml'),
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded malformed tool dependency XML.',
-                         strings_displayed=['Exception attempting to parse', 'invalid element name'],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename=os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml"),
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded malformed tool dependency XML.",
+            strings_displayed=["Exception attempting to parse", "invalid element name"],
+            strings_not_displayed=[],
+        )
 
     def test_0030_upload_invalid_tool_dependency_xml(self):
-        '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.
+        """Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.
 
         We are at step 5 - Upload a tool_dependencies.xml file that specifies a version that does not match the tool's requirements.
         This should result in a message about the tool dependency configuration not matching the tool's requirements.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename=os.path.join('freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml'),
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded invalid tool dependency XML.',
-                         strings_displayed=['The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration'],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename=os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml"),
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded invalid tool dependency XML.",
+            strings_displayed=[
+                "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration"
+            ],
+            strings_not_displayed=[],
+        )
 
     def test_0035_upload_valid_tool_dependency_xml(self):
-        '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.
+        """Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.
 
         We are at step 6 - Upload a valid tool_dependencies.xml file.
         At this stage, there should be no errors on the upload page, as every missing or invalid file has been corrected.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename=os.path.join('freebayes', 'tool_dependencies.xml'),
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded valid tool dependency XML.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename=os.path.join("freebayes", "tool_dependencies.xml"),
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded valid tool dependency XML.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0040_verify_tool_dependencies(self):
-        '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.
+        """Verify that the uploaded tool_dependencies.xml specifies the correct package versions.
 
         We are at step 7 - Check for the appropriate strings on the manage repository page.
         Verify that the manage repository page now displays the valid tool dependencies, and that there are no invalid tools shown on the manage page.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools', 'package']
-        strings_not_displayed = ['Invalid tools']
-        self.display_manage_repository_page(repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Valid tools", "package"]
+        strings_not_displayed = ["Invalid tools"]
+        self.display_manage_repository_page(
+            repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
diff --git a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
index ba85dc69018..14b9ae274cd 100644
--- a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
@@ -1,102 +1,140 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_name = "emboss_datatypes_0020"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0020'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'
+emboss_repository_name = "emboss_0020"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
 
 
 class TestBasicRepositoryDependencies(ShedTwillTestCase):
-    '''Testing emboss 5 with repository dependencies.'''
+    """Testing emboss 5 with repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category(self):
         """Create a category for this test suite"""
-        self.create_category(name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.')
+        self.create_category(
+            name="Test 0020 Basic Repository Dependencies", description="Testing basic repository dependency features."
+        )
 
     def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
-        '''Create and populate the emboss_datatypes repository.'''
+        """Create and populate the emboss_datatypes repository."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0020 Basic Repository Dependencies')
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                             description=datatypes_repository_description,
-                                             long_description=datatypes_repository_long_description,
-                                             owner=common.test_user_1_name,
-                                             category_id=self.security.encode_id(category.id),
-                                             strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded datatypes_conf.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies")
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded datatypes_conf.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_verify_datatypes_in_datatypes_repository(self):
-        '''Verify that the emboss_datatypes repository contains datatype entries.'''
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(repository, strings_displayed=['Datatypes', 'equicktandem', 'hennig86', 'vectorstrip'])
+        """Verify that the emboss_datatypes repository contains datatype entries."""
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Datatypes", "equicktandem", "hennig86", "vectorstrip"]
+        )
 
     def test_0020_create_emboss_5_repository_and_upload_files(self):
-        '''Create and populate the emboss_5_0020 repository.'''
-        category = self.test_db_util.get_category_by_name('Test 0020 Basic Repository Dependencies')
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                             description=emboss_repository_description,
-                                             long_description=emboss_repository_long_description,
-                                             owner=common.test_user_1_name,
-                                             category_id=self.security.encode_id(category.id),
-                                             strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded emboss.tar',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """Create and populate the emboss_5_0020 repository."""
+        category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies")
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded emboss.tar",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_generate_and_upload_repository_dependencies_xml(self):
-        '''Generate and upload the repository_dependencies.xml file'''
+        """Generate and upload the repository_dependencies.xml file"""
         repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0020', additional_paths=['emboss', '5'])
-        repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        self.create_repository_dependency(repository=repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0020", additional_paths=["emboss", "5"])
+        repository_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        self.create_repository_dependency(
+            repository=repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0030_verify_emboss_5_dependencies(self):
-        '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.'''
+        """Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision."""
         repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         changeset_revision = self.get_repository_tip(datatypes_repository)
-        strings_displayed = ['Tool dependencies',
-                             'emboss',
-                             '5.0.0',
-                             'package',
-                             'emboss_datatypes_0020',
-                             'user1',
-                             changeset_revision,
-                             'Repository dependencies']
+        strings_displayed = [
+            "Tool dependencies",
+            "emboss",
+            "5.0.0",
+            "package",
+            "emboss_datatypes_0020",
+            "user1",
+            changeset_revision,
+            "Repository dependencies",
+        ]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0040_verify_repository_metadata(self):
-        '''Verify that resetting the metadata does not change it.'''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
+        """Verify that resetting the metadata does not change it."""
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         self.verify_unchanged_repository_metadata(emboss_repository)
         self.verify_unchanged_repository_metadata(datatypes_repository)
diff --git a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
index 053a2ac0ea0..0f52d50d517 100644
--- a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
+++ b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
@@ -1,163 +1,244 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0030'
+datatypes_repository_name = "emboss_datatypes_0030"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0030'
-emboss_5_repository_name = 'emboss_5_0030'
-emboss_6_repository_name = 'emboss_6_0030'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030'
+emboss_repository_name = "emboss_0030"
+emboss_5_repository_name = "emboss_5_0030"
+emboss_6_repository_name = "emboss_6_0030"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
 
 
 class TestRepositoryDependencyRevisions(ShedTwillTestCase):
-    '''Test dependencies on different revisions of a repository.'''
+    """Test dependencies on different revisions of a repository."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category(self):
         """Create a category for this test suite"""
-        self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
+        self.create_category(
+            name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision."
+        )
 
     def test_0010_create_emboss_5_repository(self):
-        '''Create and populate the emboss_5_0030 repository.'''
+        """Create and populate the emboss_5_0030 repository."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0030 Repository Dependency Revisions')
-        repository = self.get_or_create_repository(name=emboss_5_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
+        repository = self.get_or_create_repository(
+            name=emboss_5_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_emboss_6_repository(self):
-        '''Create and populate the emboss_6_0030 repository.'''
+        """Create and populate the emboss_6_0030 repository."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0030 Repository Dependency Revisions')
-        repository = self.get_or_create_repository(name=emboss_6_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
+        repository = self.get_or_create_repository(
+            name=emboss_6_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_emboss_datatypes_repository(self):
-        '''Create and populate the emboss_datatypes_0030 repository.'''
+        """Create and populate the emboss_datatypes_0030 repository."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0030 Repository Dependency Revisions')
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded datatypes_conf.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded datatypes_conf.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_create_emboss_repository(self):
-        '''Create and populate the emboss_0030 repository.'''
+        """Create and populate the emboss_0030 repository."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.test_db_util.get_category_by_name('Test 0030 Repository Dependency Revisions')
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded the tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded the tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0030_generate_repository_dependencies_for_emboss_5(self):
-        '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.'''
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_5_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss5'])
-        datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
+        """Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository."""
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_5_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss5"])
+        datatypes_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        self.create_repository_dependency(
+            repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0035_generate_repository_dependencies_for_emboss_6(self):
-        '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.'''
-        emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_6_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss6'])
-        datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
+        """Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository."""
+        emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_6_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss6"])
+        datatypes_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        self.create_repository_dependency(
+            repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0040_generate_repository_dependency_on_emboss_5(self):
-        '''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.'''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_5_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss', '5'])
-        emboss_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
-        self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path)
+        """Create and upload repository_dependencies.xml for the emboss_5_0030 repository."""
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_5_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss", "5"])
+        emboss_tuple = (
+            self.url,
+            emboss_5_repository.name,
+            emboss_5_repository.user.username,
+            self.get_repository_tip(emboss_5_repository),
+        )
+        self.create_repository_dependency(
+            repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0045_generate_repository_dependency_on_emboss_6(self):
-        '''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.'''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_6_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss', '5'])
-        emboss_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
-        self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path)
+        """Create and upload repository_dependencies.xml for the emboss_6_0030 repository."""
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_6_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss", "5"])
+        emboss_tuple = (
+            self.url,
+            emboss_6_repository.name,
+            emboss_6_repository.user.username,
+            self.get_repository_tip(emboss_6_repository),
+        )
+        self.create_repository_dependency(
+            repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0050_verify_repository_dependency_revisions(self):
-        '''Verify that different metadata revisions of the emboss repository have different repository dependencies.'''
+        """Verify that different metadata revisions of the emboss repository have different repository dependencies."""
         repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        repository_metadata = [(metadata.metadata, metadata.changeset_revision) for metadata in self.get_repository_metadata(repository)]
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
+        repository_metadata = [
+            (metadata.metadata, metadata.changeset_revision) for metadata in self.get_repository_metadata(repository)
+        ]
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         datatypes_tip = self.get_repository_tip(datatypes_repository)
         strings_displayed = []
         # Iterate through all metadata revisions and check for repository dependencies.
         for _metadata, changeset_revision in repository_metadata:
             # Add the dependency description and datatypes repository details to the strings to check.
-            strings_displayed = ['emboss_datatypes_0030', 'user1', datatypes_tip]
-            strings_displayed.extend(['Tool dependencies', 'emboss', '5.0.0', 'package'])
-            self.display_manage_repository_page(repository,
-                                                changeset_revision=changeset_revision,
-                                                strings_displayed=strings_displayed)
+            strings_displayed = ["emboss_datatypes_0030", "user1", datatypes_tip]
+            strings_displayed.extend(["Tool dependencies", "emboss", "5.0.0", "package"])
+            self.display_manage_repository_page(
+                repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed
+            )
 
     def test_0055_verify_repository_metadata(self):
-        '''Verify that resetting the metadata does not change it.'''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_5_repository_name, common.test_user_1_name)
-        emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_6_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
+        """Verify that resetting the metadata does not change it."""
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_5_repository_name, common.test_user_1_name
+        )
+        emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_6_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         for repository in [emboss_repository, emboss_5_repository, emboss_6_repository, datatypes_repository]:
             self.verify_unchanged_repository_metadata(repository)
diff --git a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
index 6c6c48c7fd4..2fd8f324897 100644
--- a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
@@ -1,116 +1,160 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-freebayes_repository_name = 'freebayes_0040'
+freebayes_repository_name = "freebayes_0040"
 freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
 freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040"
 
-filtering_repository_name = 'filtering_0040'
+filtering_repository_name = "filtering_0040"
 filtering_repository_description = "Galaxy's filtering tool for test 0040"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"
 
 
 class TestRepositoryCircularDependencies(ShedTwillTestCase):
-    '''Verify that the code correctly displays repositories with circular repository dependencies.'''
+    """Verify that the code correctly displays repositories with circular repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category(self):
         """Create a category for this test suite"""
-        self.create_category(name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.')
+        self.create_category(
+            name="test_0040_repository_circular_dependencies",
+            description="Testing handling of circular repository dependencies.",
+        )
 
     def test_0010_create_freebayes_repository(self):
-        '''Create and populate freebayes_0040.'''
+        """Create and populate freebayes_0040."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                   description=freebayes_repository_description,
-                                                   long_description=freebayes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   categories=['test_0040_repository_circular_dependencies'],
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='freebayes/freebayes.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded the tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=freebayes_repository_name,
+            description=freebayes_repository_description,
+            long_description=freebayes_repository_long_description,
+            owner=common.test_user_1_name,
+            categories=["test_0040_repository_circular_dependencies"],
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="freebayes/freebayes.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded the tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_filtering_repository(self):
-        '''Create and populate filtering_0040.'''
+        """Create and populate filtering_0040."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=filtering_repository_name,
-                                                   description=filtering_repository_description,
-                                                   long_description=filtering_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   categories=['test_0040_repository_circular_dependencies'],
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded the tool tarball for filtering 1.1.0.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=filtering_repository_name,
+            description=filtering_repository_description,
+            long_description=filtering_repository_long_description,
+            owner=common.test_user_1_name,
+            categories=["test_0040_repository_circular_dependencies"],
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded the tool tarball for filtering 1.1.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_dependency_on_freebayes(self):
-        '''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.'''
+        """Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository."""
         # The dependency structure should look like:
         # Filtering revision 0 -> freebayes revision 0.
         # Freebayes revision 0 -> filtering revision 1.
         # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
-        repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0040', additional_paths=['filtering'])
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0040", additional_paths=["filtering"])
         repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository))
-        self.create_repository_dependency(repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+        self.create_repository_dependency(
+            repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0025_create_dependency_on_filtering(self):
-        '''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.'''
+        """Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository."""
         # The dependency structure should look like:
         # Filtering revision 0 -> freebayes revision 0.
         # Freebayes revision 0 -> filtering revision 1.
         # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
-        repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0040', additional_paths=['freebayes'])
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0040", additional_paths=["freebayes"])
         repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository))
-        self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+        self.create_repository_dependency(
+            repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0030_verify_repository_dependencies(self):
-        '''Verify that each repository can depend on the other without causing an infinite loop.'''
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
+        """Verify that each repository can depend on the other without causing an infinite loop."""
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
         # The dependency structure should look like:
         # Filtering revision 0 -> freebayes revision 0.
         # Freebayes revision 0 -> filtering revision 1.
         # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
         # In this case, the displayed dependency will specify the tip revision, but this will not always be the case.
-        self.check_repository_dependency(filtering_repository, freebayes_repository, self.get_repository_tip(freebayes_repository))
-        self.check_repository_dependency(freebayes_repository, filtering_repository, self.get_repository_tip(filtering_repository))
+        self.check_repository_dependency(
+            filtering_repository, freebayes_repository, self.get_repository_tip(freebayes_repository)
+        )
+        self.check_repository_dependency(
+            freebayes_repository, filtering_repository, self.get_repository_tip(filtering_repository)
+        )
 
     def test_0035_verify_repository_metadata(self):
-        '''Verify that resetting the metadata does not change it.'''
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
+        """Verify that resetting the metadata does not change it."""
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
         for repository in [freebayes_repository, filtering_repository]:
             self.verify_unchanged_repository_metadata(repository)
 
     def test_0040_verify_tool_dependencies(self):
-        '''Verify that freebayes displays tool dependencies.'''
-        repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(repository,
-                                            strings_displayed=['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools', 'package'],
-                                            strings_not_displayed=['Invalid tools'])
+        """Verify that freebayes displays tool dependencies."""
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        self.display_manage_repository_page(
+            repository,
+            strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Valid tools", "package"],
+            strings_not_displayed=["Invalid tools"],
+        )
diff --git a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
index 79e016d9a8f..1023de824e5 100644
--- a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
+++ b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
@@ -1,218 +1,307 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-emboss_datatypes_repository_name = 'emboss_datatypes_0050'
+emboss_datatypes_repository_name = "emboss_datatypes_0050"
 emboss_datatypes_repository_description = "Datatypes for emboss"
 emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
 
-emboss_repository_name = 'emboss_0050'
+emboss_repository_name = "emboss_0050"
 emboss_repository_description = "Galaxy's emboss tool"
 emboss_repository_long_description = "Long description of Galaxy's emboss tool"
 
-filtering_repository_name = 'filtering_0050'
+filtering_repository_name = "filtering_0050"
 filtering_repository_description = "Galaxy's filtering tool"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool"
 
-freebayes_repository_name = 'freebayes_0050'
+freebayes_repository_name = "freebayes_0050"
 freebayes_repository_description = "Galaxy's freebayes tool"
 freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
 
-column_repository_name = 'column_maker_0050'
+column_repository_name = "column_maker_0050"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0050'
+convert_repository_name = "convert_chars_0050"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-bismark_repository_name = 'bismark_0050'
+bismark_repository_name = "bismark_0050"
 bismark_repository_description = "A flexible aligner."
 bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."
 
-category_name = 'Test 0050 Circular Dependencies 5 Levels'
-category_description = 'Test circular dependency features'
+category_name = "Test 0050 Circular Dependencies 5 Levels"
+category_description = "Test circular dependency features"
 
 
 class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
-    '''Verify that the code correctly handles circular dependencies down to n levels.'''
+    """Verify that the code correctly handles circular dependencies down to n levels."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_convert_repository(self):
-        '''Create and populate convert_chars_0050.'''
+        """Create and populate convert_chars_0050."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='convert_chars/convert_chars.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded convert_chars tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="convert_chars/convert_chars.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded convert_chars tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate convert_chars_0050.'''
+        """Create and populate convert_chars_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column_maker tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column_maker tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_emboss_datatypes_repository(self):
-        '''Create and populate emboss_datatypes_0050.'''
+        """Create and populate emboss_datatypes_0050."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=emboss_datatypes_repository_name,
-                                                   description=emboss_datatypes_repository_description,
-                                                   long_description=emboss_datatypes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded datatypes_conf.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_datatypes_repository_name,
+            description=emboss_datatypes_repository_description,
+            long_description=emboss_datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded datatypes_conf.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_emboss_repository(self):
-        '''Create and populate emboss_0050.'''
+        """Create and populate emboss_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded emboss tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded emboss tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_create_filtering_repository(self):
-        '''Create and populate filtering_0050.'''
+        """Create and populate filtering_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        filtering_repository = self.get_or_create_repository(name=filtering_repository_name,
-                                                             description=filtering_repository_description,
-                                                             long_description=filtering_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
-        self.upload_file(filtering_repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        filtering_repository = self.get_or_create_repository(
+            name=filtering_repository_name,
+            description=filtering_repository_description,
+            long_description=filtering_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            filtering_repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0030_create_freebayes_repository(self):
-        '''Create and populate freebayes_0050.'''
+        """Create and populate freebayes_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                   description=freebayes_repository_description,
-                                                   long_description=freebayes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='freebayes/freebayes.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded freebayes tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=freebayes_repository_name,
+            description=freebayes_repository_description,
+            long_description=freebayes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="freebayes/freebayes.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded freebayes tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0035_create_bismark_repository(self):
-        '''Create and populate bismark_0050.'''
+        """Create and populate bismark_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=bismark_repository_name,
-                                                   description=bismark_repository_description,
-                                                   long_description=bismark_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='bismark/bismark.tar',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded bismark tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bismark_repository_name,
+            description=bismark_repository_description,
+            long_description=bismark_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="bismark/bismark.tar",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded bismark tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0040_create_and_upload_dependency_definitions(self):
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0050', additional_paths=['freebayes'])
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        bismark_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bismark_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0050", additional_paths=["freebayes"])
         # convert_chars depends on column_maker
         # column_maker depends on convert_chars
         # emboss depends on emboss_datatypes
         # emboss_datatypes depends on bismark
         # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker
         # filtering depends on emboss
-        column_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
-        convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-        freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
-        emboss_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository))
-        datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        bismark_tuple = (self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip(bismark_repository))
-        self.create_repository_dependency(repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=freebayes_repository,
-                                          repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
-                                          filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path)
+        column_tuple = (
+            self.url,
+            column_repository.name,
+            column_repository.user.username,
+            self.get_repository_tip(column_repository),
+        )
+        convert_tuple = (
+            self.url,
+            convert_repository.name,
+            convert_repository.user.username,
+            self.get_repository_tip(convert_repository),
+        )
+        freebayes_tuple = (
+            self.url,
+            freebayes_repository.name,
+            freebayes_repository.user.username,
+            self.get_repository_tip(freebayes_repository),
+        )
+        emboss_tuple = (
+            self.url,
+            emboss_repository.name,
+            emboss_repository.user.username,
+            self.get_repository_tip(emboss_repository),
+        )
+        datatypes_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        bismark_tuple = (
+            self.url,
+            bismark_repository.name,
+            bismark_repository.user.username,
+            self.get_repository_tip(bismark_repository),
+        )
+        self.create_repository_dependency(
+            repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=freebayes_repository,
+            repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
+            filepath=dependency_xml_path,
+        )
+        self.create_repository_dependency(
+            repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path
+        )
 
     def test_0045_verify_repository_dependencies(self):
-        '''Verify that the generated dependency circle does not cause an infinite loop.
+        """Verify that the generated dependency circle does not cause an infinite loop.
         Expected structure:
 
         id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b
@@ -229,14 +318,28 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
                  ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0']
              id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04
                  ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507']
-        '''
-        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
+        """
+        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        bismark_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bismark_repository_name, common.test_user_1_name
+        )
         self.check_repository_dependency(convert_repository, column_repository)
         self.check_repository_dependency(column_repository, convert_repository)
         self.check_repository_dependency(emboss_datatypes_repository, bismark_repository)
@@ -244,23 +347,40 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
         self.check_repository_dependency(filtering_repository, emboss_repository)
         for repository in [emboss_datatypes_repository, emboss_repository, column_repository]:
             self.check_repository_dependency(freebayes_repository, repository)
-        strings_displayed = ['freebayes_0050 depends on freebayes_0050, emboss_datatypes_0050, emboss_0050, column_maker_0050.']
-        self.display_manage_repository_page(freebayes_repository,
-                                            strings_displayed=strings_displayed)
+        strings_displayed = [
+            "freebayes_0050 depends on freebayes_0050, emboss_datatypes_0050, emboss_0050, column_maker_0050."
+        ]
+        self.display_manage_repository_page(freebayes_repository, strings_displayed=strings_displayed)
 
     def test_0050_verify_tool_dependencies(self):
-        '''Check that freebayes and emboss display tool dependencies.'''
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(freebayes_repository,
-                                            strings_displayed=['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies', 'package'])
-        self.display_manage_repository_page(emboss_repository, strings_displayed=['Tool dependencies', 'emboss', '5.0.0', 'package'])
+        """Check that freebayes and emboss display tool dependencies."""
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        self.display_manage_repository_page(
+            freebayes_repository,
+            strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Tool dependencies", "package"],
+        )
+        self.display_manage_repository_page(
+            emboss_repository, strings_displayed=["Tool dependencies", "emboss", "5.0.0", "package"]
+        )
 
     def test_0055_verify_repository_metadata(self):
-        '''Verify that resetting the metadata does not change it.'''
-        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
+        """Verify that resetting the metadata does not change it."""
+        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
         for repository in [emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository]:
             self.verify_unchanged_repository_metadata(repository)
diff --git a/lib/tool_shed/test/functional/test_0070_invalid_tool.py b/lib/tool_shed/test/functional/test_0070_invalid_tool.py
index 5ca2fc18690..dba482a7b92 100644
--- a/lib/tool_shed/test/functional/test_0070_invalid_tool.py
+++ b/lib/tool_shed/test/functional/test_0070_invalid_tool.py
@@ -1,67 +1,82 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'bismark_0070'
+repository_name = "bismark_0070"
 repository_description = "Galaxy's bismark wrapper"
 repository_long_description = "Long description of Galaxy's bismark wrapper"
-category_name = 'Test 0070 Invalid Tool Revisions'
-category_description = 'Tests for a repository with invalid tool revisions.'
+category_name = "Test 0070 Invalid Tool Revisions"
+category_description = "Tests for a repository with invalid tool revisions."
 
 
 class TestBismarkRepository(ShedTwillTestCase):
-    '''Testing bismark with valid and invalid tool entries.'''
+    """Testing bismark with valid and invalid tool entries."""
 
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category_and_repository(self):
         """Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='bismark/bismark.tar',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded bismark tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.display_manage_repository_page(repository, strings_displayed=['Invalid tools'])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="bismark/bismark.tar",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded bismark tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.display_manage_repository_page(repository, strings_displayed=["Invalid tools"])
         invalid_revision = self.get_repository_tip(repository)
-        self.upload_file(repository,
-                         filename='bismark/bismark_methylation_extractor.xml',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded an updated tool xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="bismark/bismark_methylation_extractor.xml",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded an updated tool xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         valid_revision = self.get_repository_tip(repository)
         self.test_db_util.refresh(repository)
         tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/bismark_0070/bismark_methylation_extractor/0.7.7.3"
-        tool_metadata_strings_displayed = [tool_guid,
-                                           '0.7.7.3',  # The tool version.
-                                           'bismark_methylation_extractor',  # The tool ID.
-                                           'Bismark',  # The tool name.
-                                           'methylation extractor']  # The tool description.
-        tool_page_strings_displayed = ['Bismark (version 0.7.7.3)']
-        self.check_repository_tools_for_changeset_revision(repository,
-                                                           valid_revision,
-                                                           tool_metadata_strings_displayed=tool_metadata_strings_displayed,
-                                                           tool_page_strings_displayed=tool_page_strings_displayed)
+        tool_metadata_strings_displayed = [
+            tool_guid,
+            "0.7.7.3",  # The tool version.
+            "bismark_methylation_extractor",  # The tool ID.
+            "Bismark",  # The tool name.
+            "methylation extractor",
+        ]  # The tool description.
+        tool_page_strings_displayed = ["Bismark (version 0.7.7.3)"]
+        self.check_repository_tools_for_changeset_revision(
+            repository,
+            valid_revision,
+            tool_metadata_strings_displayed=tool_metadata_strings_displayed,
+            tool_page_strings_displayed=tool_page_strings_displayed,
+        )
         self.check_repository_invalid_tools_for_changeset_revision(repository, invalid_revision)
diff --git a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
index b2ed893bab2..4710b4fd8e4 100644
--- a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
@@ -1,98 +1,145 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-column_repository_name = 'column_maker_0080'
+column_repository_name = "column_maker_0080"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0080'
+convert_repository_name = "convert_chars_0080"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 0080 Advanced Circular Dependencies'
-category_description = 'Test circular dependency features'
+category_name = "Test 0080 Advanced Circular Dependencies"
+category_description = "Test circular dependency features"
 
 
 class TestRepositoryCircularDependencies(ShedTwillTestCase):
-    '''Verify that the code correctly handles circular dependencies.'''
+    """Verify that the code correctly handles circular dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_column_repository(self):
         """Create and populate the column_maker repository."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column_maker tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column_maker tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0005_create_convert_repository(self):
         """Create and populate the convert_chars repository."""
         self.login(email=common.admin_email, username=common.admin_username)
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='convert_chars/convert_chars.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded convert_chars tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="convert_chars/convert_chars.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded convert_chars tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_repository_dependencies(self):
-        '''Upload a repository_dependencies.xml file that specifies the current revision of convert_chars_0080 to the column_maker_0080 repository.'''
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0080', additional_paths=['convert'])
-        repository_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-        self.create_repository_dependency(repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+        """Upload a repository_dependencies.xml file that specifies the current revision of convert_chars_0080 to the column_maker_0080 repository."""
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0080", additional_paths=["convert"])
+        repository_tuple = (
+            self.url,
+            convert_repository.name,
+            convert_repository.user.username,
+            self.get_repository_tip(convert_repository),
+        )
+        self.create_repository_dependency(
+            repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0025_create_dependency_on_filtering(self):
-        '''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.'''
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_0080', additional_paths=['convert'])
-        repository_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
-        self.create_repository_dependency(repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+        """Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository."""
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_0080", additional_paths=["convert"])
+        repository_tuple = (
+            self.url,
+            column_repository.name,
+            column_repository.user.username,
+            self.get_repository_tip(column_repository),
+        )
+        self.create_repository_dependency(
+            repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0030_verify_repository_dependencies(self):
-        '''Verify that each repository can depend on the other without causing an infinite loop.'''
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        self.check_repository_dependency(convert_repository, column_repository, self.get_repository_tip(column_repository))
-        self.check_repository_dependency(column_repository, convert_repository, self.get_repository_tip(convert_repository))
+        """Verify that each repository can depend on the other without causing an infinite loop."""
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        self.check_repository_dependency(
+            convert_repository, column_repository, self.get_repository_tip(column_repository)
+        )
+        self.check_repository_dependency(
+            column_repository, convert_repository, self.get_repository_tip(convert_repository)
+        )
 
     def test_0035_verify_repository_metadata(self):
-        '''Verify that resetting the metadata does not change it.'''
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
+        """Verify that resetting the metadata does not change it."""
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         for repository in [column_repository, convert_repository]:
             self.verify_unchanged_repository_metadata(repository)
diff --git a/lib/tool_shed/test/functional/test_0090_tool_search.py b/lib/tool_shed/test/functional/test_0090_tool_search.py
index a890170135f..c1f0c7c23fc 100644
--- a/lib/tool_shed/test/functional/test_0090_tool_search.py
+++ b/lib/tool_shed/test/functional/test_0090_tool_search.py
@@ -1,190 +1,271 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-emboss_datatypes_repository_name = 'emboss_datatypes_0090'
+emboss_datatypes_repository_name = "emboss_datatypes_0090"
 emboss_datatypes_repository_description = "Datatypes for emboss"
 emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
 
-emboss_repository_name = 'emboss_0090'
+emboss_repository_name = "emboss_0090"
 emboss_repository_description = "Galaxy's emboss tool"
 emboss_repository_long_description = "Long description of Galaxy's emboss tool"
 
-filtering_repository_name = 'filtering_0090'
+filtering_repository_name = "filtering_0090"
 filtering_repository_description = "Galaxy's filtering tool"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool"
 
-freebayes_repository_name = 'freebayes_0090'
+freebayes_repository_name = "freebayes_0090"
 freebayes_repository_description = "Galaxy's freebayes tool"
 freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
 
-bwa_base_repository_name = 'bwa_base_0090'
+bwa_base_repository_name = "bwa_base_0090"
 bwa_base_repository_description = "BWA Base"
 bwa_base_repository_long_description = "NT space mapping with BWA"
 
-bwa_color_repository_name = 'bwa_color_0090'
+bwa_color_repository_name = "bwa_color_0090"
 bwa_color_repository_description = "BWA Color"
 bwa_color_repository_long_description = "Color space mapping with BWA"
 
-category_name = 'Test 0090 Tool Search And Installation'
-category_description = 'Test 0090 Tool Search And Installation'
+category_name = "Test 0090 Tool Search And Installation"
+category_description = "Test 0090 Tool Search And Installation"
 
 
 class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
-    '''Test more features related to repository dependencies.'''
+    """Test more features related to repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_bwa_base_repository(self):
-        '''Create and populate bwa_base_0090.'''
+        """Create and populate bwa_base_0090."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=bwa_base_repository_name,
-                                                   description=bwa_base_repository_description,
-                                                   long_description=bwa_base_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='bwa/bwa_base.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded BWA tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_base_repository_name,
+            description=bwa_base_repository_description,
+            long_description=bwa_base_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/bwa_base.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded BWA tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_bwa_color_repository(self):
-        '''Create and populate bwa_color_0090.'''
+        """Create and populate bwa_color_0090."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=bwa_color_repository_name,
-                                                   description=bwa_color_repository_description,
-                                                   long_description=bwa_color_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='bwa/bwa_color.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded BWA color tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_color_repository_name,
+            description=bwa_color_repository_description,
+            long_description=bwa_color_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/bwa_color.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded BWA color tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_emboss_datatypes_repository(self):
-        '''Create and populate emboss_datatypes_0090.'''
+        """Create and populate emboss_datatypes_0090."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=emboss_datatypes_repository_name,
-                                                   description=emboss_datatypes_repository_description,
-                                                   long_description=emboss_datatypes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded datatypes_conf.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_datatypes_repository_name,
+            description=emboss_datatypes_repository_description,
+            long_description=emboss_datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded datatypes_conf.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_emboss_repository(self):
-        '''Create and populate emboss_0090.'''
+        """Create and populate emboss_0090."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded emboss tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded emboss tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_create_filtering_repository(self):
-        '''Create and populate filtering_0090.'''
+        """Create and populate filtering_0090."""
         category = self.create_category(name=category_name, description=category_description)
-        filtering_repository = self.get_or_create_repository(name=filtering_repository_name,
-                                                             description=filtering_repository_description,
-                                                             long_description=filtering_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
-        self.upload_file(filtering_repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        filtering_repository = self.get_or_create_repository(
+            name=filtering_repository_name,
+            description=filtering_repository_description,
+            long_description=filtering_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            filtering_repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0030_create_freebayes_repository(self):
-        '''Create and populate freebayes_0090.'''
+        """Create and populate freebayes_0090."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                   description=freebayes_repository_description,
-                                                   long_description=freebayes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='freebayes/freebayes.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded freebayes tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=freebayes_repository_name,
+            description=freebayes_repository_description,
+            long_description=freebayes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="freebayes/freebayes.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded freebayes tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0035_create_and_upload_dependency_definitions(self):
-        '''Create and upload repository dependency definitions.'''
-        bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_color_repository_name, common.test_user_1_name)
-        bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0090', additional_paths=['freebayes'])
-        freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
-        emboss_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository))
-        datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        filtering_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository))
-        self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=bwa_base_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path)
-        self.create_repository_dependency(repository=bwa_color_repository, repository_tuples=[filtering_tuple], filepath=dependency_xml_path)
+        """Create and upload repository dependency definitions."""
+        bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_color_repository_name, common.test_user_1_name
+        )
+        bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0090", additional_paths=["freebayes"])
+        freebayes_tuple = (
+            self.url,
+            freebayes_repository.name,
+            freebayes_repository.user.username,
+            self.get_repository_tip(freebayes_repository),
+        )
+        emboss_tuple = (
+            self.url,
+            emboss_repository.name,
+            emboss_repository.user.username,
+            self.get_repository_tip(emboss_repository),
+        )
+        datatypes_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        filtering_tuple = (
+            self.url,
+            filtering_repository.name,
+            filtering_repository.user.username,
+            self.get_repository_tip(filtering_repository),
+        )
+        self.create_repository_dependency(
+            repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=bwa_base_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path
+        )
+        self.create_repository_dependency(
+            repository=bwa_color_repository, repository_tuples=[filtering_tuple], filepath=dependency_xml_path
+        )
 
     def test_0040_verify_repository_dependencies(self):
-        '''Verify the generated dependency structure.'''
-        bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_color_repository_name, common.test_user_1_name)
-        bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
+        """Verify the generated dependency structure."""
+        bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_color_repository_name, common.test_user_1_name
+        )
+        bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
+        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
         self.check_repository_dependency(emboss_repository, emboss_datatypes_repository)
         self.check_repository_dependency(filtering_repository, freebayes_repository)
         self.check_repository_dependency(bwa_base_repository, emboss_repository)
diff --git a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
index e5fa15d2ee2..06e6e59c99d 100644
--- a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
@@ -1,225 +1,279 @@
 import logging
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-bwa_base_repository_name = 'bwa_base_repository_0100'
+bwa_base_repository_name = "bwa_base_repository_0100"
 bwa_base_repository_description = "BWA Base"
-bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
+bwa_base_repository_long_description = (
+    "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
+)
 
-bwa_package_repository_name = 'package_bwa_0_5_9_0100'
+bwa_package_repository_name = "package_bwa_0_5_9_0100"
 bwa_package_repository_description = "BWA Tool"
 bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."
 
-category_name = 'Test 0100 Complex Repository Dependencies'
-category_description = 'Test 0100 Complex Repository Dependencies'
+category_name = "Test 0100 Complex Repository Dependencies"
+category_description = "Test 0100 Complex Repository Dependencies"
 
 
 class TestComplexRepositoryDependencies(ShedTwillTestCase):
-    '''Test features related to complex repository dependencies.'''
+    """Test features related to complex repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_bwa_package_repository(self):
-        '''Create and populate package_bwa_0_5_9_0100.'''
+        """Create and populate package_bwa_0_5_9_0100."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named package_bwa_0_5_9_0100 owned by user1.
-        repository = self.get_or_create_repository(name=bwa_package_repository_name,
-                                                   description=bwa_package_repository_description,
-                                                   long_description=bwa_package_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='bwa/complex/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded tool_dependencies.xml.',
-                         strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_package_repository_name,
+            description=bwa_package_repository_description,
+            long_description=bwa_package_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/complex/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded tool_dependencies.xml.",
+            strings_displayed=["This repository currently contains a single file named <b>tool_dependencies.xml</b>"],
+            strings_not_displayed=[],
+        )
         # Visit the manage repository page for package_bwa_0_5_9_0100.
-        self.display_manage_repository_page(repository, strings_displayed=['Tool dependencies', 'will not be', 'to this repository'])
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"]
+        )
 
     def test_0010_create_bwa_base_repository(self):
-        '''Create and populate bwa_base_0100.'''
+        """Create and populate bwa_base_0100."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named bwa_base_repository_0100 owned by user1.
-        repository = self.get_or_create_repository(name=bwa_base_repository_name,
-                                                   description=bwa_base_repository_description,
-                                                   long_description=bwa_base_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_base_repository_name,
+            description=bwa_base_repository_description,
+            long_description=bwa_base_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive.
-        self.upload_file(repository,
-                         filename='bwa/complex/bwa_base.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="bwa/complex/bwa_base.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_generate_complex_repository_dependency_invalid_shed_url(self):
-        '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.'''
-        dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid'])
+        """Generate and upload a complex repository definition that specifies an invalid tool shed URL."""
+        dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
         # The repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # The repository named package_bwa_0_5_9_0100 is the required repository.
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-        url = 'http://http://this is not an url!'
-        name = 'package_bwa_0_5_9_0100'
-        owner = 'user1'
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
+        url = "http://http://this is not an url!"
+        name = "package_bwa_0_5_9_0100"
+        owner = "user1"
         changeset_revision = self.get_repository_tip(tool_repository)
-        strings_displayed = ['Repository dependencies are currently supported only within the same tool shed']
+        strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"]
         # Populate the dependent repository named bwa_base_repository_0100 with an invalid tool_dependencies.xml file.
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=base_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=True,
-                                          package='bwa',
-                                          version='0.5.9')
+        self.create_repository_dependency(
+            repository=base_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=True,
+            package="bwa",
+            version="0.5.9",
+        )
 
     def test_0020_generate_complex_repository_dependency_invalid_repository_name(self):
-        '''Generate and upload a complex repository definition that specifies an invalid repository name.'''
-        dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid'])
+        """Generate and upload a complex repository definition that specifies an invalid repository name."""
+        dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # The repository named package_bwa_0_5_9_0100 is the required repository.
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
         url = self.url
-        name = 'invalid_repository!?'
-        owner = 'user1'
+        name = "invalid_repository!?"
+        owner = "user1"
         changeset_revision = self.get_repository_tip(tool_repository)
-        strings_displayed = ['because the name is invalid']
+        strings_displayed = ["because the name is invalid"]
         # Populate the dependent base_repository named package_bwa_0_5_9_0100 with an invalid tool_dependencies.xml file.
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=base_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=True,
-                                          package='bwa',
-                                          version='0.5.9')
+        self.create_repository_dependency(
+            repository=base_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=True,
+            package="bwa",
+            version="0.5.9",
+        )
 
     def test_0025_generate_complex_repository_dependency_invalid_owner_name(self):
-        '''Generate and upload a complex repository definition that specifies an invalid owner.'''
-        dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid'])
+        """Generate and upload a complex repository definition that specifies an invalid owner."""
+        dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # The repository named package_bwa_0_5_9_0100 is the required repository.
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
         url = self.url
-        name = 'package_bwa_0_5_9_0100'
-        owner = 'invalid_owner!?'
+        name = "package_bwa_0_5_9_0100"
+        owner = "invalid_owner!?"
         changeset_revision = self.get_repository_tip(tool_repository)
-        strings_displayed = ['because the owner is invalid.']
+        strings_displayed = ["because the owner is invalid."]
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=base_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=True,
-                                          package='bwa',
-                                          version='0.5.9')
+        self.create_repository_dependency(
+            repository=base_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=True,
+            package="bwa",
+            version="0.5.9",
+        )
 
     def test_0030_generate_complex_repository_dependency_invalid_changeset_revision(self):
-        '''Generate and upload a complex repository definition that specifies an invalid changeset revision.'''
-        dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid'])
+        """Generate and upload a complex repository definition that specifies an invalid changeset revision."""
+        dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # The repository named package_bwa_0_5_9_0100 is the required repository.
         url = self.url
-        name = 'package_bwa_0_5_9_0100'
-        owner = 'user1'
-        changeset_revision = '1234abcd'
-        strings_displayed = ['because the changeset revision is invalid.']
+        name = "package_bwa_0_5_9_0100"
+        owner = "user1"
+        changeset_revision = "1234abcd"
+        strings_displayed = ["because the changeset revision is invalid."]
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=base_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=True,
-                                          package='bwa',
-                                          version='0.5.9')
+        self.create_repository_dependency(
+            repository=base_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=True,
+            package="bwa",
+            version="0.5.9",
+        )
 
     def test_0035_generate_complex_repository_dependency(self):
-        '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.'''
+        """Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100."""
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # The repository named package_bwa_0_5_9_0100 is the required repository.
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-        dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex'])
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
+        dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex"])
         url = self.url
-        name = 'package_bwa_0_5_9_0100'
-        owner = 'user1'
+        name = "package_bwa_0_5_9_0100"
+        owner = "user1"
         changeset_revision = self.get_repository_tip(tool_repository)
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=base_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          complex=True,
-                                          package='bwa',
-                                          version='0.5.9')
+        self.create_repository_dependency(
+            repository=base_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            complex=True,
+            package="bwa",
+            version="0.5.9",
+        )
         self.check_repository_dependency(base_repository, depends_on_repository=tool_repository)
-        self.display_manage_repository_page(base_repository, strings_displayed=['bwa', '0.5.9', 'package', changeset_revision])
+        self.display_manage_repository_page(
+            base_repository, strings_displayed=["bwa", "0.5.9", "package", changeset_revision]
+        )
 
     def test_0040_generate_tool_dependency(self):
-        '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.'''
+        """Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision."""
         # The base_repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # The repository named package_bwa_0_5_9_0100 is the required repository.
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
         previous_changeset = self.get_repository_tip(tool_repository)
-        old_tool_dependency = self.get_filename(os.path.join('bwa', 'complex', 'readme', 'tool_dependencies.xml'))
-        new_tool_dependency_path = self.generate_temp_path('test_1100', additional_paths=['tool_dependency'])
-        xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, 'tool_dependencies.xml'))
+        old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "readme", "tool_dependencies.xml"))
+        new_tool_dependency_path = self.generate_temp_path("test_1100", additional_paths=["tool_dependency"])
+        xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, "tool_dependencies.xml"))
         # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem.
-        open(xml_filename, 'w').write(open(old_tool_dependency)
-                                 .read().replace('__PATH__', self.get_filename('bwa/complex')))
-        self.upload_file(tool_repository,
-                         filename=xml_filename,
-                         filepath=new_tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded new tool_dependencies.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        open(xml_filename, "w").write(
+            open(old_tool_dependency).read().replace("__PATH__", self.get_filename("bwa/complex"))
+        )
+        self.upload_file(
+            tool_repository,
+            filename=xml_filename,
+            filepath=new_tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded new tool_dependencies.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
         repository_tip = self.get_repository_tip(tool_repository)
-        strings_displayed = ['bwa', '0.5.9', 'package']
+        strings_displayed = ["bwa", "0.5.9", "package"]
         strings_displayed.append(repository_tip)
         strings_not_displayed = [previous_changeset]
-        self.display_manage_repository_page(tool_repository,
-                                            strings_displayed=strings_displayed,
-                                            strings_not_displayed=strings_not_displayed)
+        self.display_manage_repository_page(
+            tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition.
-        self.display_manage_repository_page(tool_repository,
-                                            strings_displayed=strings_displayed,
-                                            strings_not_displayed=strings_not_displayed)
+        self.display_manage_repository_page(
+            tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition
         # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed
         # as the required repository revision.  The original revision defined in the previously uploaded
         # tool_dependencies.xml file will be updated.
-        self.display_manage_repository_page(base_repository,
-                                            strings_displayed=strings_displayed,
-                                            strings_not_displayed=strings_not_displayed)
+        self.display_manage_repository_page(
+            base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
diff --git a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
index 1b18851e4e5..ece9a2ab67f 100644
--- a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
@@ -1,29 +1,36 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0110'
+datatypes_repository_name = "emboss_datatypes_0110"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0110'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_name = "emboss_0110"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
 
-category_name = 'Test 0110 Invalid Repository Dependencies'
-category_desc = 'Test 0110 Invalid Repository Dependencies'
+category_name = "Test 0110 Invalid Repository Dependencies"
+category_desc = "Test 0110 Invalid Repository Dependencies"
 
 
 class TestBasicRepositoryDependencies(ShedTwillTestCase):
-    '''Testing emboss 5 with repository dependencies.'''
+    """Testing emboss 5 with repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category(self):
@@ -31,113 +38,149 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
         self.create_category(name=category_name, description=category_desc)
 
     def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
-        '''Create and populate the emboss_datatypes repository.'''
+        """Create and populate the emboss_datatypes repository."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                             description=datatypes_repository_description,
-                                             long_description=datatypes_repository_long_description,
-                                             owner=common.test_user_1_name,
-                                             category_id=self.security.encode_id(category.id),
-                                             strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded datatypes_conf.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded datatypes_conf.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_verify_datatypes_in_datatypes_repository(self):
-        '''Verify that the emboss_datatypes repository contains datatype entries.'''
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(repository, strings_displayed=['Datatypes', 'equicktandem', 'hennig86', 'vectorstrip'])
+        """Verify that the emboss_datatypes repository contains datatype entries."""
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Datatypes", "equicktandem", "hennig86", "vectorstrip"]
+        )
 
     def test_0020_create_emboss_5_repository_and_upload_files(self):
-        '''Create and populate the emboss_5_0110 repository.'''
+        """Create and populate the emboss_5_0110 repository."""
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                             description=emboss_repository_description,
-                                             long_description=emboss_repository_long_description,
-                                             owner=common.test_user_1_name,
-                                             category_id=self.security.encode_id(category.id),
-                                             strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded emboss tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded emboss tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_generate_repository_dependency_with_invalid_url(self):
-        '''Generate a repository dependency for emboss 5 with an invalid URL.'''
-        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple'])
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        url = 'http://http://this is not an url!'
+        """Generate a repository dependency for emboss 5 with an invalid URL."""
+        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple"])
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        url = "http://http://this is not an url!"
         name = datatypes_repository.name
         owner = datatypes_repository.user.username
         changeset_revision = self.get_repository_tip(datatypes_repository)
-        strings_displayed = ['Repository dependencies are currently supported only within the same tool shed']
+        strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"]
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=emboss_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=False)
+        self.create_repository_dependency(
+            repository=emboss_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=False,
+        )
 
     def test_0030_generate_repository_dependency_with_invalid_name(self):
-        '''Generate a repository dependency for emboss 5 with an invalid name.'''
-        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple'])
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+        """Generate a repository dependency for emboss 5 with an invalid name."""
+        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple"])
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         url = self.url
-        name = '!?invalid?!'
+        name = "!?invalid?!"
         owner = repository.user.username
         changeset_revision = self.get_repository_tip(repository)
-        strings_displayed = ['because the name is invalid.']
+        strings_displayed = ["because the name is invalid."]
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=emboss_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=False)
+        self.create_repository_dependency(
+            repository=emboss_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=False,
+        )
 
     def test_0035_generate_repository_dependency_with_invalid_owner(self):
-        '''Generate a repository dependency for emboss 5 with an invalid owner.'''
-        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple'])
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+        """Generate a repository dependency for emboss 5 with an invalid owner."""
+        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple"])
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         url = self.url
         name = repository.name
-        owner = '!?invalid?!'
+        owner = "!?invalid?!"
         changeset_revision = self.get_repository_tip(repository)
-        strings_displayed = ['because the owner is invalid.']
+        strings_displayed = ["because the owner is invalid."]
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=emboss_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=False)
+        self.create_repository_dependency(
+            repository=emboss_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=False,
+        )
 
     def test_0040_generate_repository_dependency_with_invalid_changeset_revision(self):
-        '''Generate a repository dependency for emboss 5 with an invalid changeset revision.'''
-        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple', 'invalid'])
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+        """Generate a repository dependency for emboss 5 with an invalid changeset revision."""
+        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple", "invalid"])
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         url = self.url
         name = repository.name
         owner = repository.user.username
-        changeset_revision = '!?invalid?!'
-        strings_displayed = ['because the changeset revision is invalid.']
+        changeset_revision = "!?invalid?!"
+        strings_displayed = ["because the changeset revision is invalid."]
         repository_tuple = (url, name, owner, changeset_revision)
-        self.create_repository_dependency(repository=emboss_repository,
-                                          filepath=dependency_path,
-                                          repository_tuples=[repository_tuple],
-                                          strings_displayed=strings_displayed,
-                                          complex=False)
+        self.create_repository_dependency(
+            repository=emboss_repository,
+            filepath=dependency_path,
+            repository_tuples=[repository_tuple],
+            strings_displayed=strings_displayed,
+            complex=False,
+        )
diff --git a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
index e60ce0a031f..d173222fe72 100644
--- a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
+++ b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
@@ -1,14 +1,17 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'blast_datatypes_0120'
-datatypes_repository_description = 'Galaxy applicable datatypes for BLAST'
-datatypes_repository_long_description = 'Galaxy datatypes for the BLAST top hit descriptons tool'
+datatypes_repository_name = "blast_datatypes_0120"
+datatypes_repository_description = "Galaxy applicable datatypes for BLAST"
+datatypes_repository_long_description = "Galaxy datatypes for the BLAST top hit descriptons tool"
 
-tool_repository_name = 'blastxml_to_top_descr_0120'
-tool_repository_description = 'BLAST top hit descriptions'
-tool_repository_long_description = 'Make a table from BLAST XML'
+tool_repository_name = "blastxml_to_top_descr_0120"
+tool_repository_description = "BLAST top hit descriptions"
+tool_repository_long_description = "Make a table from BLAST XML"
 
-'''
+"""
 Tool shed side:
 
 1) Create and populate blast_datatypes_0120.
@@ -17,14 +20,13 @@ Tool shed side:
 2a) Check for appropriate strings.
 3) Upload repository_dependencies.xml to blastxml_to_top_descr_0120 that defines a relationship to blast_datatypes_0120.
 3a) Check for appropriate strings.
-'''
+"""
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
 
 
 class TestRepositoryMultipleOwners(ShedTwillTestCase):
-
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
 
@@ -33,15 +35,19 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_datatypes_repository(self):
@@ -50,35 +56,50 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
         We are at step 1.
         Create and populate blast_datatypes.
         """
-        category = self.create_category(name='Test 0120', description='Description of test 0120')
+        category = self.create_category(name="Test 0120", description="Description of test 0120")
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         strings_displayed = self.expect_repo_created_strings(datatypes_repository_name)
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                   description=datatypes_repository_description,
-                                                   long_description=datatypes_repository_long_description,
-                                                   owner=common.test_user_2_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='blast/blast_datatypes.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded blast_datatypes tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_2_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="blast/blast_datatypes.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded blast_datatypes tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_verify_datatypes_repository(self):
-        '''Verify the blast_datatypes_0120 repository.
+        """Verify the blast_datatypes_0120 repository.
 
         We are at step 1a.
         Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb,
         the datatypes that are defined in datatypes_conf.xml.
-        '''
+        """
         global repository_datatypes_count
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-        strings_displayed = ['BlastXml', 'BlastNucDb', 'BlastProtDb', 'application/xml', 'text/html', 'blastxml', 'blastdbn', 'blastdbp']
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_2_name
+        )
+        strings_displayed = [
+            "BlastXml",
+            "BlastNucDb",
+            "BlastProtDb",
+            "application/xml",
+            "text/html",
+            "blastxml",
+            "blastdbn",
+            "blastdbp",
+        ]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
         repository_datatypes_count = int(self.get_repository_datatypes_count(repository))
 
@@ -88,54 +109,73 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
         We are at step 2.
         Create and populate blastxml_to_top_descr_0120.
         """
-        category = self.create_category(name='Test 0120', description='Description of test 0120')
+        category = self.create_category(name="Test 0120", description="Description of test 0120")
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(tool_repository_name)
-        repository = self.get_or_create_repository(name=tool_repository_name,
-                                                   description=tool_repository_description,
-                                                   long_description=tool_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='blast/blastxml_to_top_descr.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded blastxml_to_top_descr tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=tool_repository_name,
+            description=tool_repository_description,
+            long_description=tool_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="blast/blastxml_to_top_descr.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded blastxml_to_top_descr tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_verify_tool_repository(self):
-        '''Verify the blastxml_to_top_descr_0120 repository.
+        """Verify the blastxml_to_top_descr_0120 repository.
 
         We are at step 2a.
         Check for appropriate strings, such as tool name, description, and version.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
-        strings_displayed = ['blastxml_to_top_descr_0120', 'BLAST top hit descriptions', 'Make a table from BLAST XML']
-        strings_displayed.extend(['0.0.1', 'Valid tools'])
+        strings_displayed = ["blastxml_to_top_descr_0120", "BLAST top hit descriptions", "Make a table from BLAST XML"]
+        strings_displayed.extend(["0.0.1", "Valid tools"])
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0025_create_repository_dependency(self):
-        '''Create a repository dependency on blast_datatypes_0120.
+        """Create a repository dependency on blast_datatypes_0120.
 
         We are at step 3.
         Create a simple repository dependency for blastxml_to_top_descr_0120 that defines a dependency on blast_datatypes_0120.
-        '''
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0120', additional_paths=['dependencies'])
-        datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        self.create_repository_dependency(repository=tool_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
+        """
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_2_name
+        )
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            tool_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0120", additional_paths=["dependencies"])
+        datatypes_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        self.create_repository_dependency(
+            repository=tool_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+        )
 
     def test_0040_verify_repository_dependency(self):
-        '''Verify the created repository dependency.
+        """Verify the created repository dependency.
 
         We are at step 3a.
         Check the newly created repository dependency to ensure that it was defined and displays correctly.
-        '''
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
+        """
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_2_name
+        )
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            tool_repository_name, common.test_user_1_name
+        )
         self.check_repository_dependency(tool_repository, datatypes_repository)
diff --git a/lib/tool_shed/test/functional/test_0130_datatype_converters.py b/lib/tool_shed/test/functional/test_0130_datatype_converters.py
index 12d634c39e5..bb0e0685760 100644
--- a/lib/tool_shed/test/functional/test_0130_datatype_converters.py
+++ b/lib/tool_shed/test/functional/test_0130_datatype_converters.py
@@ -1,78 +1,91 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'bed_to_gff_0130'
+repository_name = "bed_to_gff_0130"
 repository_description = "Converter: BED to GFF"
 repository_long_description = "Convert bed to gff"
 
-category_name = 'Test 0130 Datatype Converters'
-category_description = 'Test 0130 Datatype Converters'
+category_name = "Test 0130 Datatype Converters"
+category_description = "Test 0130 Datatype Converters"
 
-'''
+"""
 1) Create a populate the bed_to_gff_converter repository
 2) Visit the manage repository page and make sure there is the appropriate valid too and datatype
 3) Visit the view tool metadata page and make sure that "Display in tool panel" is False
-'''
+"""
 
 
 class TestDatatypeConverters(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_bed_to_gff_repository(self):
-        '''Create and populate bed_to_gff_0130.
+        """Create and populate bed_to_gff_0130.
 
         We are at step 1 - Create and populate the bed_to_gff_0130 repository.
         Create the bed_to_gff_0130 repository and populate it with the files needed for this test.
-        '''
+        """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named bed_to_gff_0130 owned by user1.
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload bed_to_gff_converter.tar to the repository.
-        self.upload_file(repository,
-                         filename='bed_to_gff_converter/bed_to_gff_converter.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded bed_to_gff_converter.tar.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="bed_to_gff_converter/bed_to_gff_converter.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded bed_to_gff_converter.tar.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_verify_tool_and_datatype(self):
-        '''Verify that a valid tool and datatype are contained within the repository.
+        """Verify that a valid tool and datatype are contained within the repository.
 
         We are at step 2 - Visit the manage repository page and make sure there is the appropriate valid tool and datatype.
         There should be a 'Convert BED to GFF' tool and a 'galaxy.datatypes.interval:Bed' datatype with extension 'bed'
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ['Convert BED to GFF', 'galaxy.datatypes.interval:Bed', 'bed', 'Valid tools', 'Datatypes']
-        strings_not_displayed = ['Invalid tools']
-        self.display_manage_repository_page(repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["Convert BED to GFF", "galaxy.datatypes.interval:Bed", "bed", "Valid tools", "Datatypes"]
+        strings_not_displayed = ["Invalid tools"]
+        self.display_manage_repository_page(
+            repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0015_verify_tool_panel_display(self):
-        '''Verify that the tool is configured not to be displayed in the tool panel.
+        """Verify that the tool is configured not to be displayed in the tool panel.
 
         We are at step 3
         Datatype converters that are associated with a datatype should have display in tool panel = False in the tool metadata.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        tool_metadata_strings_displayed = '<label>Display in tool panel:</label>\n                    False'
-        self.check_repository_tools_for_changeset_revision(repository,
-                                                           self.get_repository_tip(repository),
-                                                           tool_metadata_strings_displayed=tool_metadata_strings_displayed)
+        tool_metadata_strings_displayed = "<label>Display in tool panel:</label>\n                    False"
+        self.check_repository_tools_for_changeset_revision(
+            repository,
+            self.get_repository_tip(repository),
+            tool_metadata_strings_displayed=tool_metadata_strings_displayed,
+        )
diff --git a/lib/tool_shed/test/functional/test_0140_tool_help_images.py b/lib/tool_shed/test/functional/test_0140_tool_help_images.py
index afcc35fb21a..01115a70a64 100644
--- a/lib/tool_shed/test/functional/test_0140_tool_help_images.py
+++ b/lib/tool_shed/test/functional/test_0140_tool_help_images.py
@@ -1,75 +1,84 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'htseq_count_0140'
+repository_name = "htseq_count_0140"
 repository_description = "Converter: BED to GFF"
 repository_long_description = "Convert bed to gff"
 
-category_name = 'Test 0140 Tool Help Images'
-category_description = 'Test 0140 Tool Help Images'
+category_name = "Test 0140 Tool Help Images"
+category_description = "Test 0140 Tool Help Images"
 
-'''
+"""
 1) Create and populate the htseq_count_0140 repository.
 2) Visit the manage_repository page.
 3) Simulate clicking the htseq_count tool button.
 4) On the resulting display tool page, look for the image string similar to the following string where the encoded repository_id is previously determined:
 
 src="/repository/static/images/<id>/count_modes.png"
-'''
+"""
 
 
 class TestToolHelpImages(ShedTwillTestCase):
-    '''Test features related to tool help images.'''
+    """Test features related to tool help images."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_htseq_count_repository(self):
-        '''Create and populate htseq_count_0140.
+        """Create and populate htseq_count_0140.
 
         We are at step 1 - Create and populate the htseq_count_0140 repository.
         Create the htseq_count_0140 repository and upload the tarball.
-        '''
+        """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named htseq_count_0140 owned by user1.
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload htseq_count.tar to the repository.
-        self.upload_file(repository,
-                         filename='htseq_count/htseq_count.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded htseq_count.tar.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="htseq_count/htseq_count.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded htseq_count.tar.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_load_tool_page(self):
-        '''Load the tool page and check for the image.
+        """Load the tool page and check for the image.
 
         We are at step 2
         Visit the manage_repository page and the tool page, and look for the image url
         similar to the following string:
 
         src="/repository/static/images/<id>/count_modes.png"
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         # Get the repository tip.
         changeset_revision = self.get_repository_tip(repository)
@@ -79,5 +88,7 @@ class TestToolHelpImages(ShedTwillTestCase):
         # The repository uploaded in this test should only have one metadata revision, with one tool defined, which
         # should be the tool that contains a link to the image.
         repository_metadata = repository.metadata_revisions[0].metadata
-        tool_path = repository_metadata['tools'][0]['tool_config']
-        self.load_display_tool_page(repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[])
+        tool_path = repository_metadata["tools"][0]["tool_config"]
+        self.load_display_tool_page(
+            repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[]
+        )
diff --git a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py
index d209c8a5dea..d5c32174faa 100644
--- a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py
@@ -1,17 +1,20 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-column_repository_name = 'column_maker_0150'
+column_repository_name = "column_maker_0150"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0150'
+convert_repository_name = "convert_chars_0150"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 0150 Simple Prior Installation'
-category_description = 'Test 0150 Simple Prior Installation'
+category_name = "Test 0150 Simple Prior Installation"
+category_description = "Test 0150 Simple Prior Installation"
 
-'''
+"""
 Create column_maker and convert_chars.
 
 Column maker repository dependency:
@@ -23,82 +26,109 @@ Galaxy side:
 
 Install column_maker.
 Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
-'''
+"""
 
 
 class TestSimplePriorInstallation(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_convert_repository(self):
-        '''Create and populate convert_chars_0150.'''
+        """Create and populate convert_chars_0150."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='convert_chars/convert_chars.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded convert_chars tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="convert_chars/convert_chars.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded convert_chars tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate convert_chars_0150.'''
+        """Create and populate convert_chars_0150."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column_maker tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column_maker tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_repository_dependency(self):
-        '''Create a repository dependency specifying convert_chars.
+        """Create a repository dependency specifying convert_chars.
 
         Column maker repository dependency:
             <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="<tip>" prior_installation_required="True" />
-        '''
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0150', additional_paths=['column'])
-        convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-        self.create_repository_dependency(repository=column_repository,
-                                          repository_tuples=[convert_tuple],
-                                          filepath=dependency_xml_path,
-                                          prior_installation_required=True)
+        """
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0150", additional_paths=["column"])
+        convert_tuple = (
+            self.url,
+            convert_repository.name,
+            convert_repository.user.username,
+            self.get_repository_tip(convert_repository),
+        )
+        self.create_repository_dependency(
+            repository=column_repository,
+            repository_tuples=[convert_tuple],
+            filepath=dependency_xml_path,
+            prior_installation_required=True,
+        )
 
     def test_0020_verify_repository_dependency(self):
-        '''Verify that the previously generated repositiory dependency displays correctly.'''
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        self.check_repository_dependency(repository=column_repository,
-                                         depends_on_repository=convert_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
+        """Verify that the previously generated repositiory dependency displays correctly."""
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        self.check_repository_dependency(
+            repository=column_repository,
+            depends_on_repository=convert_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
diff --git a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
index 9cdf38a9890..9b230f5b273 100644
--- a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
@@ -1,156 +1,203 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-filter_repository_name = 'filtering_0160'
+filter_repository_name = "filtering_0160"
 filter_repository_description = "Galaxy's filtering tool for test 0160"
 filter_repository_long_description = "Long description of Galaxy's filtering tool for test 0160"
 
-column_repository_name = 'column_maker_0160'
+column_repository_name = "column_maker_0160"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0160'
+convert_repository_name = "convert_chars_0160"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 0160 Simple Prior Installation'
-category_description = 'Test 0160 Simple Prior Installation'
+category_name = "Test 0160 Simple Prior Installation"
+category_description = "Test 0160 Simple Prior Installation"
 
-'''
+"""
 Create column_maker and convert_chars.
 
 Column maker repository dependency:
 <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
 
 Verify display.
-'''
+"""
 
 
 class TestSimplePriorInstallation(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_convert_repository(self):
-        '''Create and populate convert_chars_0160.'''
+        """Create and populate convert_chars_0160."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='convert_chars/convert_chars.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded convert_chars tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="convert_chars/convert_chars.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded convert_chars tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate convert_chars_0160.'''
+        """Create and populate convert_chars_0160."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column_maker tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column_maker tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_filtering_repository(self):
-        '''Create and populate filtering_0160.'''
+        """Create and populate filtering_0160."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=filter_repository_name,
-                                                   description=filter_repository_description,
-                                                   long_description=filter_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=filter_repository_name,
+            description=filter_repository_description,
+            long_description=filter_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_repository_dependency(self):
-        '''Create a repository dependency specifying convert_chars.
+        """Create a repository dependency specifying convert_chars.
 
         Each of the three repositories should depend on the other two, to make this as circular as possible.
-        '''
-        filter_repository = self.test_db_util.get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0160', additional_paths=['column'])
+        """
+        filter_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0160", additional_paths=["column"])
         filter_revision = self.get_repository_tip(filter_repository)
         column_revision = self.get_repository_tip(column_repository)
         convert_revision = self.get_repository_tip(convert_repository)
         column_tuple = (self.url, column_repository.name, column_repository.user.username, column_revision)
         convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, convert_revision)
         filter_tuple = (self.url, filter_repository.name, filter_repository.user.username, filter_revision)
-        self.create_repository_dependency(repository=column_repository,
-                                          repository_tuples=[convert_tuple, filter_tuple],
-                                          filepath=dependency_xml_path,
-                                          prior_installation_required=False)
-        self.create_repository_dependency(repository=convert_repository,
-                                          repository_tuples=[column_tuple, filter_tuple],
-                                          filepath=dependency_xml_path,
-                                          prior_installation_required=False)
-        self.create_repository_dependency(repository=filter_repository,
-                                          repository_tuples=[convert_tuple, column_tuple],
-                                          filepath=dependency_xml_path,
-                                          prior_installation_required=True)
+        self.create_repository_dependency(
+            repository=column_repository,
+            repository_tuples=[convert_tuple, filter_tuple],
+            filepath=dependency_xml_path,
+            prior_installation_required=False,
+        )
+        self.create_repository_dependency(
+            repository=convert_repository,
+            repository_tuples=[column_tuple, filter_tuple],
+            filepath=dependency_xml_path,
+            prior_installation_required=False,
+        )
+        self.create_repository_dependency(
+            repository=filter_repository,
+            repository_tuples=[convert_tuple, column_tuple],
+            filepath=dependency_xml_path,
+            prior_installation_required=True,
+        )
 
     def test_0025_verify_repository_dependency(self):
-        '''Verify that the previously generated repositiory dependency displays correctly.'''
-        filter_repository = self.test_db_util.get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        self.check_repository_dependency(repository=column_repository,
-                                         depends_on_repository=convert_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=column_repository,
-                                         depends_on_repository=filter_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=convert_repository,
-                                         depends_on_repository=column_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=convert_repository,
-                                         depends_on_repository=filter_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=filter_repository,
-                                         depends_on_repository=column_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=filter_repository,
-                                         depends_on_repository=convert_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
+        """Verify that the previously generated repositiory dependency displays correctly."""
+        filter_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        self.check_repository_dependency(
+            repository=column_repository,
+            depends_on_repository=convert_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=column_repository,
+            depends_on_repository=filter_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=convert_repository,
+            depends_on_repository=column_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=convert_repository,
+            depends_on_repository=filter_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=filter_repository,
+            depends_on_repository=column_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=filter_repository,
+            depends_on_repository=convert_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
diff --git a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
index 20e3ad28eca..3d3612a6b18 100644
--- a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
@@ -1,132 +1,163 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-matplotlib_repository_name = 'package_matplotlib_1_2_0170'
+matplotlib_repository_name = "package_matplotlib_1_2_0170"
 matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
-matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+matplotlib_repository_long_description = (
+    "This repository is intended to be defined as a complex repository dependency within a separate repository."
+)
 
-numpy_repository_name = 'package_numpy_1_7_0170'
-numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
-numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+numpy_repository_name = "package_numpy_1_7_0170"
+numpy_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
+)
+numpy_repository_long_description = (
+    "This repository is intended to be defined as a complex repository dependency within a separate repository."
+)
 
-category_name = 'Test 0170 Prior Installation Complex Dependencies'
-category_description = 'Test 0170 Prior Installation Complex Dependencies'
+category_name = "Test 0170 Prior Installation Complex Dependencies"
+category_description = "Test 0170 Prior Installation Complex Dependencies"
 
-'''
+"""
 1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
 2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
 3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
-'''
+"""
 
 
 class TestComplexPriorInstallation(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_matplotlib_repository(self):
-        '''Create and populate the package_matplotlib_1_2_0170 repository.
+        """Create and populate the package_matplotlib_1_2_0170 repository.
 
         This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
-        '''
+        """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=matplotlib_repository_name,
-                                                   description=matplotlib_repository_description,
-                                                   long_description=matplotlib_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='package_matplotlib/package_matplotlib_1_2.tar',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded matplotlib tool dependency tarball.',
-                         strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=matplotlib_repository_name,
+            description=matplotlib_repository_description,
+            long_description=matplotlib_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="package_matplotlib/package_matplotlib_1_2.tar",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded matplotlib tool dependency tarball.",
+            strings_displayed=["This repository currently contains a single file named <b>tool_dependencies.xml</b>"],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_numpy_repository(self):
-        '''Create and populate the package_numpy_1_7_0170 repository.
+        """Create and populate the package_numpy_1_7_0170 repository.
 
         This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
-        '''
+        """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=numpy_repository_name,
-                                                   description=numpy_repository_description,
-                                                   long_description=numpy_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='package_numpy/package_numpy_1_7.tar',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded numpy tool dependency tarball.',
-                         strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=numpy_repository_name,
+            description=numpy_repository_description,
+            long_description=numpy_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="package_numpy/package_numpy_1_7.tar",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded numpy tool dependency tarball.",
+            strings_displayed=["This repository currently contains a single file named <b>tool_dependencies.xml</b>"],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_complex_repository_dependency(self):
-        '''Create a dependency on package_numpy_1_7_0170.
+        """Create a dependency on package_numpy_1_7_0170.
 
         This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
         package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required
         set to True. When matplotlib is selected for installation, the result should be that numpy is compiled
         and installed first.
-        '''
-        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
-        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
+        """
+        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(
+            numpy_repository_name, common.test_user_1_name
+        )
+        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(
+            matplotlib_repository_name, common.test_user_1_name
+        )
         # Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but
         # it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable
         # in this case, because matplotlib already has an additional tool dependency definition that we don't want to
         # overwrite.
         new_xml = '    <package name="numpy" version="1.7">\n'
         new_xml += '        <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n'
-        new_xml += '    </package>\n'
+        new_xml += "    </package>\n"
         url = self.url
         name = numpy_repository.name
         owner = numpy_repository.user.username
         changeset_revision = self.get_repository_tip(numpy_repository)
         processed_xml = new_xml % (url, name, owner, changeset_revision)
-        original_xml = open(self.get_filename('package_matplotlib/tool_dependencies.xml')).read()
-        dependency_xml_path = self.generate_temp_path('test_0170', additional_paths=['matplotlib'])
-        new_xml_file = os.path.join(dependency_xml_path, 'tool_dependencies.xml')
-        open(new_xml_file, 'w').write(original_xml.replace('<!--NUMPY-->', processed_xml))
+        original_xml = open(self.get_filename("package_matplotlib/tool_dependencies.xml")).read()
+        dependency_xml_path = self.generate_temp_path("test_0170", additional_paths=["matplotlib"])
+        new_xml_file = os.path.join(dependency_xml_path, "tool_dependencies.xml")
+        open(new_xml_file, "w").write(original_xml.replace("<!--NUMPY-->", processed_xml))
         # Upload the generated complex repository dependency XML to the matplotlib repository.
-        self.upload_file(matplotlib_repository,
-                         filename='tool_dependencies.xml',
-                         filepath=dependency_xml_path,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded complex repository dependency on numpy 1.7.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            matplotlib_repository,
+            filename="tool_dependencies.xml",
+            filepath=dependency_xml_path,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded complex repository dependency on numpy 1.7.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_verify_generated_dependency(self):
-        '''Verify that matplotlib now has a package tool dependency and a complex repository dependency.
+        """Verify that matplotlib now has a package tool dependency and a complex repository dependency.
 
         This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
                          dependency displays correctly.
         'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
         dependency on the latest revision of package_numpy_1_7_0170.
-        '''
-        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
-        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
+        """
+        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(
+            numpy_repository_name, common.test_user_1_name
+        )
+        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(
+            matplotlib_repository_name, common.test_user_1_name
+        )
         changeset_revision = self.get_repository_tip(numpy_repository)
         self.check_repository_dependency(matplotlib_repository, depends_on_repository=numpy_repository)
-        self.display_manage_repository_page(matplotlib_repository, strings_displayed=['numpy', '1.7', 'package', changeset_revision])
+        self.display_manage_repository_page(
+            matplotlib_repository, strings_displayed=["numpy", "1.7", "package", changeset_revision]
+        )
diff --git a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
index 212f07a11b8..059a04f9bd0 100644
--- a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
@@ -1,591 +1,826 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_name = "emboss_datatypes_0020"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
-workflow_name = 'Workflow for 0060_filter_workflow_repository'
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+workflow_filename = "Workflow_for_0060_filter_workflow_repository.ga"
+workflow_name = "Workflow for 0060_filter_workflow_repository"
 
-emboss_datatypes_repository_name = 'emboss_datatypes_0050'
+emboss_datatypes_repository_name = "emboss_datatypes_0050"
 emboss_datatypes_repository_description = "Datatypes for emboss"
 
-emboss_repository_name = 'emboss_0050'
-emboss_5_repository_name = 'emboss_5_0050'
-emboss_6_repository_name = 'emboss_6_0050'
+emboss_repository_name = "emboss_0050"
+emboss_5_repository_name = "emboss_5_0050"
+emboss_6_repository_name = "emboss_6_0050"
 
-filtering_repository_name = 'filtering_0050'
+filtering_repository_name = "filtering_0050"
 filtering_repository_description = "Galaxy's filtering tool"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool"
 
-freebayes_repository_name = 'freebayes_0050'
+freebayes_repository_name = "freebayes_0050"
 freebayes_repository_description = "Galaxy's freebayes tool"
 freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
 
-column_repository_name = 'column_maker_0050'
+column_repository_name = "column_maker_0050"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0050'
+convert_repository_name = "convert_chars_0050"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-bismark_repository_name = 'bismark_0050'
+bismark_repository_name = "bismark_0050"
 bismark_repository_description = "A flexible aligner."
 bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."
 
-category_0050_name = 'Test 0050 Circular Dependencies 5 Levels'
-category_0050_description = 'Test circular dependency features'
+category_0050_name = "Test 0050 Circular Dependencies 5 Levels"
+category_0050_description = "Test circular dependency features"
 
 running_standalone = False
 
 
 class TestResetAllRepositoryMetadata(ShedTwillTestCase):
-    '''Verify that the "Reset selected metadata" feature works.'''
+    """Verify that the "Reset selected metadata" feature works."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_filtering_repository(self):
-        '''Create and populate the filtering_0000 repository.'''
+        """Create and populate the filtering_0000 repository."""
         global running_standalone
         self.login(email=common.admin_email, username=common.admin_username)
-        category_0000 = self.create_category(name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1')
+        category_0000 = self.create_category(
+            name="Test 0000 Basic Repository Features 1", description="Test 0000 Basic Repository Features 1"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name='filtering_0000',
-                                                   description="Galaxy's filtering tool",
-                                                   long_description="Long description of Galaxy's filtering tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category_0000.id))
+        repository = self.get_or_create_repository(
+            name="filtering_0000",
+            description="Galaxy's filtering tool",
+            long_description="Long description of Galaxy's filtering tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category_0000.id),
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_2.2.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 2.2.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_2.2.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 2.2.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_freebayes_repository(self):
-        '''Create and populate the freebayes_0010 repository.'''
+        """Create and populate the freebayes_0010 repository."""
         global running_standalone
         self.login(email=common.admin_email, username=common.admin_username)
-        category_0010 = self.create_category(name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.')
+        category_0010 = self.create_category(
+            name="Test 0010 Repository With Tool Dependencies",
+            description="Tests for a repository with tool dependencies.",
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name='freebayes_0010',
-                                                   description="Galaxy's freebayes tool",
-                                                   long_description="Long description of Galaxy's freebayes tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category_0010.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name="freebayes_0010",
+            description="Galaxy's freebayes tool",
+            long_description="Long description of Galaxy's freebayes tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category_0010.id),
+            strings_displayed=[],
+        )
         if running_standalone:
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded freebayes.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/tool_data_table_conf.xml.sample',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool_data_table_conf.xml.sample',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/sam_fa_indices.loc.sample',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded sam_fa_indices.loc.sample',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/tool_dependencies.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool_dependencies.xml',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded freebayes.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/tool_data_table_conf.xml.sample",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool_data_table_conf.xml.sample",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/sam_fa_indices.loc.sample",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded sam_fa_indices.loc.sample",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/tool_dependencies.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool_dependencies.xml",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_datatypes_0020_repository(self):
-        '''Create and populate the emboss_datatypes_0020 repository.'''
+        """Create and populate the emboss_datatypes_0020 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0020 = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.')
+            category_0020 = self.create_category(
+                name="Test 0020 Basic Repository Dependencies",
+                description="Testing basic repository dependency features.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name='emboss_datatypes_0020',
-                                                       description=datatypes_repository_description,
-                                                       long_description=datatypes_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category_0020.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name="emboss_datatypes_0020",
+                description=datatypes_repository_description,
+                long_description=datatypes_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0020.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_create_emboss_0020_repository(self):
-        '''Create and populate the emboss_0020 repository.'''
+        """Create and populate the emboss_0020 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0020 = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.')
+            category_0020 = self.create_category(
+                name="Test 0020 Basic Repository Dependencies",
+                description="Testing basic repository dependency features.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name='emboss_0020',
-                                                       description=emboss_repository_long_description,
-                                                       long_description=emboss_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category_0020.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name="emboss_0020",
+                description=emboss_repository_long_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0020.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0025_create_emboss_datatypes_0030_repository(self):
-        '''Create and populate the emboss_0030 repository.'''
+        """Create and populate the emboss_0030 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
+            category_0030 = self.create_category(
+                name="Test 0030 Repository Dependency Revisions",
+                description="Testing repository dependencies by revision.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            datatypes_repository = self.get_or_create_repository(name='emboss_datatypes_0030',
-                                                                 description=datatypes_repository_description,
-                                                                 long_description=datatypes_repository_long_description,
-                                                                 owner=common.test_user_1_name,
-                                                                 category_id=self.security.encode_id(category_0030.id),
-                                                                 strings_displayed=[])
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            datatypes_repository = self.get_or_create_repository(
+                name="emboss_datatypes_0030",
+                description=datatypes_repository_description,
+                long_description=datatypes_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0030.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0030_create_emboss_5_repository(self):
-        '''Create and populate the emboss_5_0030 repository.'''
+        """Create and populate the emboss_5_0030 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
+            category_0030 = self.create_category(
+                name="Test 0030 Repository Dependency Revisions",
+                description="Testing repository dependencies by revision.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            emboss_5_repository = self.get_or_create_repository(name='emboss_5_0030',
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category_0030.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_5_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            emboss_5_repository = self.get_or_create_repository(
+                name="emboss_5_0030",
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0030.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_5_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0035_create_emboss_6_repository(self):
-        '''Create and populate the emboss_6_0030 repository.'''
+        """Create and populate the emboss_6_0030 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
+            category_0030 = self.create_category(
+                name="Test 0030 Repository Dependency Revisions",
+                description="Testing repository dependencies by revision.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            emboss_6_repository = self.get_or_create_repository(name='emboss_6_0030',
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category_0030.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_6_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            emboss_6_repository = self.get_or_create_repository(
+                name="emboss_6_0030",
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0030.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_6_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0040_create_emboss_0030_repository(self):
-        '''Create and populate the emboss_0030 repository.'''
+        """Create and populate the emboss_0030 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
+            category_0030 = self.create_category(
+                name="Test 0030 Repository Dependency Revisions",
+                description="Testing repository dependencies by revision.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            emboss_repository = self.get_or_create_repository(name='emboss_0030',
-                                                              description=emboss_repository_description,
-                                                              long_description=emboss_repository_long_description,
-                                                              owner=common.test_user_1_name,
-                                                              category_id=self.security.encode_id(category_0030.id),
-                                                              strings_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            emboss_repository = self.get_or_create_repository(
+                name="emboss_0030",
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0030.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0045_create_repository_dependencies_for_0030(self):
-        '''Create the dependency structure for test 0030.'''
+        """Create the dependency structure for test 0030."""
         global running_standalone
         if running_standalone:
-            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0030', common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_0030', common.test_user_1_name)
-            emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_5_0030', common.test_user_1_name)
-            emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_6_0030', common.test_user_1_name)
-            repository_dependencies_path = self.generate_temp_path('test_0330', additional_paths=['emboss'])
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            emboss_5_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
-            emboss_6_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
-            self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
-            self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_5_tuple], filepath=repository_dependencies_path)
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_6_tuple], filepath=repository_dependencies_path)
+            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "emboss_datatypes_0030", common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "emboss_0030", common.test_user_1_name
+            )
+            emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "emboss_5_0030", common.test_user_1_name
+            )
+            emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "emboss_6_0030", common.test_user_1_name
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss"])
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            emboss_5_tuple = (
+                self.url,
+                emboss_5_repository.name,
+                emboss_5_repository.user.username,
+                self.get_repository_tip(emboss_5_repository),
+            )
+            emboss_6_tuple = (
+                self.url,
+                emboss_6_repository.name,
+                emboss_6_repository.user.username,
+                self.get_repository_tip(emboss_6_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_5_repository,
+                repository_tuples=[datatypes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            self.create_repository_dependency(
+                repository=emboss_6_repository,
+                repository_tuples=[datatypes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository, repository_tuples=[emboss_5_tuple], filepath=repository_dependencies_path
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository, repository_tuples=[emboss_6_tuple], filepath=repository_dependencies_path
+            )
 
     def test_0050_create_freebayes_repository(self):
-        '''Create and populate the freebayes_0040 repository.'''
+        """Create and populate the freebayes_0040 repository."""
         global running_standalone
         self.login(email=common.admin_email, username=common.admin_username)
-        category_0040 = self.create_category(name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.')
+        category_0040 = self.create_category(
+            name="test_0040_repository_circular_dependencies",
+            description="Testing handling of circular repository dependencies.",
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name='freebayes_0040',
-                                                   description="Galaxy's freebayes tool",
-                                                   long_description="Long description of Galaxy's freebayes tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category_0040.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name="freebayes_0040",
+            description="Galaxy's freebayes tool",
+            long_description="Long description of Galaxy's freebayes tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category_0040.id),
+            strings_displayed=[],
+        )
         if running_standalone:
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded freebayes tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded freebayes tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0055_create_filtering_repository(self):
-        '''Create and populate the filtering_0040 repository.'''
+        """Create and populate the filtering_0040 repository."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
-            category_0040 = self.create_category(name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.')
+            category_0040 = self.create_category(
+                name="test_0040_repository_circular_dependencies",
+                description="Testing handling of circular repository dependencies.",
+            )
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name='filtering_0040',
-                                                       description="Galaxy's filtering tool",
-                                                       long_description="Long description of Galaxy's filtering tool",
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category_0040.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name="filtering_0040",
+                description="Galaxy's filtering tool",
+                long_description="Long description of Galaxy's filtering tool",
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category_0040.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0060_create_dependency_structure(self):
-        '''Create the dependency structure for test 0040.'''
+        """Create the dependency structure for test 0040."""
         global running_standalone
         if running_standalone:
-            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner('freebayes_0040', common.test_user_1_name)
-            filtering_repository = self.test_db_util.get_repository_by_name_and_owner('filtering_0040', common.test_user_1_name)
-            repository_dependencies_path = self.generate_temp_path('test_0340', additional_paths=['dependencies'])
-            freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
-            filtering_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository))
-            self.create_repository_dependency(repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=repository_dependencies_path)
-            self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[filtering_tuple], filepath=repository_dependencies_path)
+            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "freebayes_0040", common.test_user_1_name
+            )
+            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "filtering_0040", common.test_user_1_name
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0340", additional_paths=["dependencies"])
+            freebayes_tuple = (
+                self.url,
+                freebayes_repository.name,
+                freebayes_repository.user.username,
+                self.get_repository_tip(freebayes_repository),
+            )
+            filtering_tuple = (
+                self.url,
+                filtering_repository.name,
+                filtering_repository.user.username,
+                self.get_repository_tip(filtering_repository),
+            )
+            self.create_repository_dependency(
+                repository=filtering_repository,
+                repository_tuples=[freebayes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            self.create_repository_dependency(
+                repository=freebayes_repository,
+                repository_tuples=[filtering_tuple],
+                filepath=repository_dependencies_path,
+            )
 
     def test_0065_create_convert_repository(self):
-        '''Create and populate convert_chars_0050.'''
+        """Create and populate convert_chars_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=convert_repository_name,
-                                                       description=convert_repository_description,
-                                                       long_description=convert_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=convert_repository_name,
+                description=convert_repository_description,
+                long_description=convert_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0070_create_column_repository(self):
-        '''Create and populate convert_chars_0050.'''
+        """Create and populate convert_chars_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=column_repository_name,
-                                                       description=column_repository_description,
-                                                       long_description=column_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=column_repository_name,
+                description=column_repository_description,
+                long_description=column_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0075_create_emboss_datatypes_repository(self):
-        '''Create and populate emboss_datatypes_0050.'''
+        """Create and populate emboss_datatypes_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=emboss_datatypes_repository_name,
-                                                       description=datatypes_repository_description,
-                                                       long_description=datatypes_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=emboss_datatypes_repository_name,
+                description=datatypes_repository_description,
+                long_description=datatypes_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0080_create_emboss_repository(self):
-        '''Create and populate emboss_0050.'''
+        """Create and populate emboss_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                       description=emboss_repository_description,
-                                                       long_description=emboss_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=emboss_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0085_create_filtering_repository(self):
-        '''Create and populate filtering_0050.'''
+        """Create and populate filtering_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            filtering_repository = self.get_or_create_repository(name=filtering_repository_name,
-                                                                 description=filtering_repository_description,
-                                                                 long_description=filtering_repository_long_description,
-                                                                 owner=common.test_user_1_name,
-                                                                 category_id=self.security.encode_id(category.id),
-                                                                 strings_displayed=[])
-            self.upload_file(filtering_repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            filtering_repository = self.get_or_create_repository(
+                name=filtering_repository_name,
+                description=filtering_repository_description,
+                long_description=filtering_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                filtering_repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0090_create_freebayes_repository(self):
-        '''Create and populate freebayes_0050.'''
+        """Create and populate freebayes_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                       description=freebayes_repository_description,
-                                                       long_description=freebayes_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded freebayes tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=freebayes_repository_name,
+                description=freebayes_repository_description,
+                long_description=freebayes_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded freebayes tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0095_create_bismark_repository(self):
-        '''Create and populate bismark_0050.'''
+        """Create and populate bismark_0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.admin_email, username=common.admin_username)
             category = self.create_category(name=category_0050_name, description=category_0050_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=bismark_repository_name,
-                                                       description=bismark_repository_description,
-                                                       long_description=bismark_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='bismark/bismark.tar',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded bismark tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=bismark_repository_name,
+                description=bismark_repository_description,
+                long_description=bismark_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="bismark/bismark.tar",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded bismark tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0100_create_and_upload_dependency_definitions(self):
-        '''Create the dependency structure for test 0050.'''
+        """Create the dependency structure for test 0050."""
         global running_standalone
         if running_standalone:
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-            convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-            bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
-            dependency_xml_path = self.generate_temp_path('test_0050', additional_paths=['freebayes'])
+            column_repository = self.test_db_util.get_repository_by_name_and_owner(
+                column_repository_name, common.test_user_1_name
+            )
+            convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+                convert_repository_name, common.test_user_1_name
+            )
+            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_datatypes_repository_name, common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_repository_name, common.test_user_1_name
+            )
+            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+                filtering_repository_name, common.test_user_1_name
+            )
+            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                freebayes_repository_name, common.test_user_1_name
+            )
+            bismark_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bismark_repository_name, common.test_user_1_name
+            )
+            dependency_xml_path = self.generate_temp_path("test_0050", additional_paths=["freebayes"])
             # convert_chars depends on column_maker
             # column_maker depends on convert_chars
             # emboss depends on emboss_datatypes
             # emboss_datatypes depends on bismark
             # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker
             # filtering depends on emboss
-            column_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
-            convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-            freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
-            emboss_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository))
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            bismark_tuple = (self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip(bismark_repository))
-            self.create_repository_dependency(repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=freebayes_repository,
-                                              repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
-                                              filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path)
+            column_tuple = (
+                self.url,
+                column_repository.name,
+                column_repository.user.username,
+                self.get_repository_tip(column_repository),
+            )
+            convert_tuple = (
+                self.url,
+                convert_repository.name,
+                convert_repository.user.username,
+                self.get_repository_tip(convert_repository),
+            )
+            freebayes_tuple = (
+                self.url,
+                freebayes_repository.name,
+                freebayes_repository.user.username,
+                self.get_repository_tip(freebayes_repository),
+            )
+            emboss_tuple = (
+                self.url,
+                emboss_repository.name,
+                emboss_repository.user.username,
+                self.get_repository_tip(emboss_repository),
+            )
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            bismark_tuple = (
+                self.url,
+                bismark_repository.name,
+                bismark_repository.user.username,
+                self.get_repository_tip(bismark_repository),
+            )
+            self.create_repository_dependency(
+                repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=freebayes_repository,
+                repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
+                filepath=dependency_xml_path,
+            )
+            self.create_repository_dependency(
+                repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path
+            )
 
     def test_0105_create_filtering_repository(self):
-        '''Create and populate the filtering_0060 repository.'''
+        """Create and populate the filtering_0060 repository."""
         self.login(email=common.admin_email, username=common.admin_username)
-        category_0060 = self.create_category(name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features')
+        category_0060 = self.create_category(
+            name="Test 0060 Workflow Features", description="Test 0060 - Workflow Features"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        workflow_repository = self.get_or_create_repository(name='filtering_0060',
-                                                            description="Galaxy's filtering tool",
-                                                            long_description="Long description of Galaxy's filtering tool",
-                                                            owner=common.test_user_1_name,
-                                                            category_id=self.security.encode_id(category_0060.id),
-                                                            strings_displayed=[])
+        workflow_repository = self.get_or_create_repository(
+            name="filtering_0060",
+            description="Galaxy's filtering tool",
+            long_description="Long description of Galaxy's filtering tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category_0060.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(workflow_repository):
-            workflow = open(self.get_filename('filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga')).read()
-            workflow = workflow.replace('__TEST_TOOL_SHED_URL__', self.url.replace('http://', ''))
-            workflow_filepath = self.generate_temp_path('test_0360', additional_paths=['filtering_workflow'])
+            workflow = open(
+                self.get_filename("filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga")
+            ).read()
+            workflow = workflow.replace("__TEST_TOOL_SHED_URL__", self.url.replace("http://", ""))
+            workflow_filepath = self.generate_temp_path("test_0360", additional_paths=["filtering_workflow"])
             if not os.path.exists(workflow_filepath):
                 os.makedirs(workflow_filepath)
-            open(os.path.join(workflow_filepath, workflow_filename), 'w+').write(workflow)
-            self.upload_file(workflow_repository,
-                             filename=workflow_filename,
-                             filepath=workflow_filepath,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering workflow.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(workflow_repository,
-                             filename='filtering/filtering_2.2.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 2.2.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            open(os.path.join(workflow_filepath, workflow_filename), "w+").write(workflow)
+            self.upload_file(
+                workflow_repository,
+                filename=workflow_filename,
+                filepath=workflow_filepath,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering workflow.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                workflow_repository,
+                filename="filtering/filtering_2.2.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 2.2.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0110_reset_metadata_on_all_repositories(self):
-        '''Reset metadata on all repositories, then verify that it has not changed.'''
+        """Reset metadata on all repositories, then verify that it has not changed."""
         self.login(email=common.admin_email, username=common.admin_username)
         old_metadata = dict()
         new_metadata = dict()
@@ -599,5 +834,8 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
             new_metadata[self.security.encode_id(repository.id)] = dict()
             for metadata in self.get_repository_metadata(repository):
                 new_metadata[self.security.encode_id(repository.id)][metadata.changeset_revision] = metadata.metadata
-            if old_metadata[self.security.encode_id(repository.id)] != new_metadata[self.security.encode_id(repository.id)]:
-                raise AssertionError(f'Metadata changed after reset for repository {repository.name}.')
+            if (
+                old_metadata[self.security.encode_id(repository.id)]
+                != new_metadata[self.security.encode_id(repository.id)]
+            ):
+                raise AssertionError(f"Metadata changed after reset for repository {repository.name}.")
diff --git a/lib/tool_shed/test/functional/test_0310_hg_api_features.py b/lib/tool_shed/test/functional/test_0310_hg_api_features.py
index 76e6c907ffb..b41e4c6bcde 100644
--- a/lib/tool_shed/test/functional/test_0310_hg_api_features.py
+++ b/lib/tool_shed/test/functional/test_0310_hg_api_features.py
@@ -1,76 +1,89 @@
 import logging
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'filtering_0310'
+repository_name = "filtering_0310"
 repository_description = "Galaxy's filtering tool for test 0310"
 repository_long_description = "Long description of Galaxy's filtering tool for test 0310"
 
-category_name = 'Test 0310 - HTTP Repo features'
-category_description = 'Test 0310 for verifying the tool shed http interface to mercurial.'
+category_name = "Test 0310 - HTTP Repo features"
+category_description = "Test 0310 for verifying the tool shed http interface to mercurial."
 
-'''
+"""
 1. Create a repository.
 2. Clone the repository to a local path.
-'''
+"""
 
 
 class TestHgWebFeatures(ShedTwillTestCase):
-    '''Test http mercurial interface.'''
+    """Test http mercurial interface."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_filtering_repository(self):
-        '''Create and populate the filtering_0310 repository.
+        """Create and populate the filtering_0310 repository.
 
         We are at step 1 - Create a repository.
         Create and populate the filtering_0310 repository.
-        '''
+        """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message="Uploaded filtering 1.1.0.",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_test_data.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded filtering test data.",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded filtering 1.1.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_test_data.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering test data.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_clone(self):
-        '''Clone the repository to a local path.
+        """Clone the repository to a local path.
 
         We are at step 2 - Clone the repository to a local path.
         The repository should have the following files:
@@ -86,9 +99,9 @@ class TestHgWebFeatures(ShedTwillTestCase):
         test-data/filter1_test2.bed
         test-data/filter1_test3.sam
         test-data/filter1_test4.bed
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        clone_path = self.generate_temp_path('test_0310', additional_paths=['filtering_0310', 'user2'])
+        clone_path = self.generate_temp_path("test_0310", additional_paths=["filtering_0310", "user2"])
         self.clone_repository(repository, clone_path)
         files_in_repository = os.listdir(clone_path)
-        assert 'filtering.py' in files_in_repository, 'File not found in repository: filtering.py'
+        assert "filtering.py" in files_in_repository, "File not found in repository: filtering.py"
diff --git a/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py b/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py
index 9c201670ccf..aceeee96779 100644
--- a/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py
+++ b/lib/tool_shed/test/functional/test_0400_repository_component_reviews.py
@@ -1,8 +1,11 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'filtering_0400'
-repository_description = 'Galaxy filtering tool for test 0400'
-repository_long_description = 'Long description of Galaxy filtering tool for test 0400'
+repository_name = "filtering_0400"
+repository_description = "Galaxy filtering tool for test 0400"
+repository_long_description = "Long description of Galaxy filtering tool for test 0400"
 
 """
 1. Create users.
@@ -47,15 +50,19 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_grant_reviewer_role(self):
@@ -65,7 +72,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         We now have an admin user (admin_user) and two non-admin users (test_user_1 and test_user_2). Grant the repository
         reviewer role to test_user_2, who will not be the owner of the reviewed repositories.
         """
-        reviewer_role = self.test_db_util.get_role_by_name('Repository Reviewer')
+        reviewer_role = self.test_db_util.get_role_by_name("Repository Reviewer")
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
         self.grant_role_to_user(test_user_2, reviewer_role)
 
@@ -76,11 +83,21 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         We now have an admin user (admin_user) and two non-admin users (test_user_1 and test_user_2). Grant the repository
         reviewer role to test_user_2, who will not be the owner of the reviewed repositories.
         """
-        strings_not_displayed = ['Repository dependencies']
+        strings_not_displayed = ["Repository dependencies"]
         self.manage_review_components(strings_not_displayed=strings_not_displayed)
-        self.add_repository_review_component(name='Repository dependencies',
-                                             description='Repository dependencies defined in a file named repository_dependencies.xml included in the repository')
-        strings_displayed = ['Data types', 'Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows']
+        self.add_repository_review_component(
+            name="Repository dependencies",
+            description="Repository dependencies defined in a file named repository_dependencies.xml included in the repository",
+        )
+        strings_displayed = [
+            "Data types",
+            "Functional tests",
+            "README",
+            "Repository dependencies",
+            "Tool dependencies",
+            "Tools",
+            "Workflows",
+        ]
         self.manage_review_components(strings_displayed=strings_displayed)
 
     def test_0015_create_repository(self):
@@ -90,24 +107,30 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         Log in as test_user_1 and create the filtering repository, then upload a basic set of
         components to be reviewed in subsequent tests.
         """
-        category = self.create_category(name='Test 0400 Repository Component Reviews', description='Test 0400 Repository Component Reviews')
+        category = self.create_category(
+            name="Test 0400 Repository Component Reviews", description="Test 0400 Repository Component Reviews"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(repository_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_review_initial_revision_data_types(self):
         """Review the datatypes component for the current tip revision.
@@ -128,7 +151,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Data types': dict()}
+        review_contents_dict = {"Data types": dict()}
         self.create_repository_review(repository, review_contents_dict)
 
     def test_0025_verify_datatype_review(self):
@@ -140,9 +163,18 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Data types', 'not_applicable']
-        strings_not_displayed = ['Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows']
-        self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["Data types", "not_applicable"]
+        strings_not_displayed = [
+            "Functional tests",
+            "README",
+            "Repository dependencies",
+            "Tool dependencies",
+            "Tools",
+            "Workflows",
+        ]
+        self.verify_repository_reviews(
+            repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0030_review_initial_revision_functional_tests(self):
         """Review the functional tests component for the current tip revision.
@@ -166,13 +198,15 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Functional tests': dict(rating=1, comment='Functional tests missing', approved='no', private='yes')}
+        review_contents_dict = {
+            "Functional tests": dict(rating=1, comment="Functional tests missing", approved="no", private="yes")
+        }
         self.review_repository(repository, review_contents_dict, user)
 
-#    def test_0030_verify_review_display( self ):
-#        """Verify that private reviews are restricted to owner and reviewer, and non-private views are viewable by others."""
-#        # Currently not implemented because third parties cannot view reviews whether they are private or not.
-#        self.login( email=common.test_user_3_email, username=common.test_user_3_name )
+    #    def test_0030_verify_review_display( self ):
+    #        """Verify that private reviews are restricted to owner and reviewer, and non-private views are viewable by others."""
+    #        # Currently not implemented because third parties cannot view reviews whether they are private or not.
+    #        self.login( email=common.test_user_3_email, username=common.test_user_3_name )
 
     def test_0035_verify_functional_test_review(self):
         """Verify that the functional tests component review displays correctly.
@@ -185,9 +219,11 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Functional tests', 'Functional tests missing', 'no']
-        strings_not_displayed = ['README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows']
-        self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["Functional tests", "Functional tests missing", "no"]
+        strings_not_displayed = ["README", "Repository dependencies", "Tool dependencies", "Tools", "Workflows"]
+        self.verify_repository_reviews(
+            repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0040_review_readme(self):
         """Review the readme component for the current tip revision.
@@ -211,7 +247,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'README': dict()}
+        review_contents_dict = {"README": dict()}
         self.review_repository(repository, review_contents_dict, user)
 
     def test_0045_verify_readme_review(self):
@@ -223,9 +259,11 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['README', 'not_applicable']
-        strings_not_displayed = ['Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows']
-        self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["README", "not_applicable"]
+        strings_not_displayed = ["Repository dependencies", "Tool dependencies", "Tools", "Workflows"]
+        self.verify_repository_reviews(
+            repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0050_review_repository_dependencies(self):
         """Review the repository dependencies component for the current tip revision.
@@ -250,7 +288,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Repository dependencies': dict()}
+        review_contents_dict = {"Repository dependencies": dict()}
         self.review_repository(repository, review_contents_dict, user)
 
     def test_0055_verify_repository_dependency_review(self):
@@ -263,9 +301,11 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Repository dependencies', 'not_applicable']
-        strings_not_displayed = ['Tool dependencies', 'Tools', 'Workflows']
-        self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["Repository dependencies", "not_applicable"]
+        strings_not_displayed = ["Tool dependencies", "Tools", "Workflows"]
+        self.verify_repository_reviews(
+            repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0060_review_tool_dependencies(self):
         """Review the tool dependencies component for the current tip revision.
@@ -291,7 +331,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Tool dependencies': dict()}
+        review_contents_dict = {"Tool dependencies": dict()}
         self.review_repository(repository, review_contents_dict, user)
 
     def test_0065_verify_tool_dependency_review(self):
@@ -304,9 +344,11 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Tool dependencies', 'not_applicable']
-        strings_not_displayed = ['Tools', 'Workflows']
-        self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["Tool dependencies", "not_applicable"]
+        strings_not_displayed = ["Tools", "Workflows"]
+        self.verify_repository_reviews(
+            repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0070_review_tools(self):
         """Review the tools component for the current tip revision.
@@ -334,7 +376,9 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Tools': dict(rating=5, comment='Excellent tool, easy to use.', approved='yes', private='no')}
+        review_contents_dict = {
+            "Tools": dict(rating=5, comment="Excellent tool, easy to use.", approved="yes", private="no")
+        }
         self.review_repository(repository, review_contents_dict, user)
 
     def test_0075_verify_tools_review(self):
@@ -347,9 +391,11 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Tools', 'yes', 'Excellent tool, easy to use.']
-        strings_not_displayed = ['Workflows']
-        self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["Tools", "yes", "Excellent tool, easy to use."]
+        strings_not_displayed = ["Workflows"]
+        self.verify_repository_reviews(
+            repository, reviewer=user, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0080_review_workflows(self):
         """Review the workflows component for the current tip revision.
@@ -377,7 +423,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Workflows': dict()}
+        review_contents_dict = {"Workflows": dict()}
         self.review_repository(repository, review_contents_dict, user)
 
     def test_0085_verify_workflows_review(self):
@@ -390,7 +436,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Workflows', 'not_applicable']
+        strings_displayed = ["Workflows", "not_applicable"]
         self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed)
 
     def test_0090_upload_readme_file(self):
@@ -402,15 +448,17 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded readme.txt.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded readme.txt.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0095_review_new_changeset_readme_component(self):
         """Update the filtering repository's readme component review to reflect the presence of the readme file.
@@ -427,7 +475,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         # Get the last changeset revision that has a review associated with it.
         last_review = self.get_last_reviewed_revision_by_user(user, repository)
         if last_review is None:
-            raise AssertionError('Previous review expected, none found.')
+            raise AssertionError("Previous review expected, none found.")
         # The create_repository_review method takes a dict( component label=review contents ).
         # If review_contents is empty, it marks that component as not applicable. The review
         # contents dict should have the structure:
@@ -437,11 +485,20 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'README': dict(rating=5, comment='Clear and concise readme file, a true pleasure to read.', approved='yes', private='no')}
-        self.create_repository_review(repository,
-                                      review_contents_dict,
-                                      changeset_revision=self.get_repository_tip(repository),
-                                      copy_from=(str(last_review.changeset_revision), last_review.id))
+        review_contents_dict = {
+            "README": dict(
+                rating=5,
+                comment="Clear and concise readme file, a true pleasure to read.",
+                approved="yes",
+                private="no",
+            )
+        }
+        self.create_repository_review(
+            repository,
+            review_contents_dict,
+            changeset_revision=self.get_repository_tip(repository),
+            copy_from=(str(last_review.changeset_revision), last_review.id),
+        )
 
     def test_0100_verify_readme_review(self):
         """Verify that the readme component review displays correctly.
@@ -453,7 +510,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['README', 'yes', 'Clear and concise readme file, a true pleasure to read.']
+        strings_displayed = ["README", "yes", "Clear and concise readme file, a true pleasure to read."]
         self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed)
 
     def test_0105_upload_test_data(self):
@@ -466,15 +523,17 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         last dowloadable revision hash.
         """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/filtering_test_data.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering test data.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_test_data.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering test data.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0110_review_new_changeset_functional_tests(self):
         """Update the filtering repository's readme component review to reflect the presence of the readme file.
@@ -498,11 +557,15 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Functional tests': dict(rating=5, comment='A good set of functional tests.', approved='yes', private='no')}
-        self.create_repository_review(repository,
-                                      review_contents_dict,
-                                      changeset_revision=self.get_repository_tip(repository),
-                                      copy_from=(str(last_review.changeset_revision), last_review.id))
+        review_contents_dict = {
+            "Functional tests": dict(rating=5, comment="A good set of functional tests.", approved="yes", private="no")
+        }
+        self.create_repository_review(
+            repository,
+            review_contents_dict,
+            changeset_revision=self.get_repository_tip(repository),
+            copy_from=(str(last_review.changeset_revision), last_review.id),
+        )
 
     def test_0115_verify_functional_tests_review(self):
         """Verify that the functional tests component review displays correctly.
@@ -514,7 +577,7 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Functional tests', 'yes', 'A good set of functional tests.']
+        strings_displayed = ["Functional tests", "yes", "A good set of functional tests."]
         self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed)
 
     def test_0120_upload_new_tool_version(self):
@@ -526,15 +589,17 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/filtering_2.2.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 2.2.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_2.2.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 2.2.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0125_review_new_changeset_functional_tests(self):
         """Update the filtering repository's review to apply to the new changeset with filtering 2.2.0.
@@ -557,11 +622,20 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         #   approved: yes/no
         #   private: yes/no
         # }
-        review_contents_dict = {'Tools': dict(rating=5, comment='Version 2.2.0 does the impossible and improves this tool.', approved='yes', private='yes')}
-        self.create_repository_review(repository,
-                                      review_contents_dict,
-                                      changeset_revision=self.get_repository_tip(repository),
-                                      copy_from=(str(last_review.changeset_revision), last_review.id))
+        review_contents_dict = {
+            "Tools": dict(
+                rating=5,
+                comment="Version 2.2.0 does the impossible and improves this tool.",
+                approved="yes",
+                private="yes",
+            )
+        }
+        self.create_repository_review(
+            repository,
+            review_contents_dict,
+            changeset_revision=self.get_repository_tip(repository),
+            copy_from=(str(last_review.changeset_revision), last_review.id),
+        )
 
     def test_0135_verify_review_for_new_version(self):
         """Verify that the reviews display correctly for this changeset revision.
@@ -573,7 +647,20 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Data types', 'Functional tests', 'yes', 'A good set of functional tests.', 'README', 'yes', 'Workflows', 'Tools']
-        strings_displayed.extend(['Clear and concise readme file, a true pleasure to read.', 'Tool dependencies', 'not_applicable'])
-        strings_displayed.extend(['Repository dependencies', 'Version 2.2.0 does the impossible and improves this tool.'])
+        strings_displayed = [
+            "Data types",
+            "Functional tests",
+            "yes",
+            "A good set of functional tests.",
+            "README",
+            "yes",
+            "Workflows",
+            "Tools",
+        ]
+        strings_displayed.extend(
+            ["Clear and concise readme file, a true pleasure to read.", "Tool dependencies", "not_applicable"]
+        )
+        strings_displayed.extend(
+            ["Repository dependencies", "Version 2.2.0 does the impossible and improves this tool."]
+        )
         self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed)
diff --git a/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py b/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py
index 54f0631d7e9..fc6bfa418bc 100644
--- a/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py
+++ b/lib/tool_shed/test/functional/test_0410_repository_component_review_access_control.py
@@ -1,10 +1,13 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'filtering_0410'
-repository_description = 'Galaxy filtering tool for test 0410'
-repository_long_description = 'Long description of Galaxy filtering tool for test 0410'
+repository_name = "filtering_0410"
+repository_description = "Galaxy filtering tool for test 0410"
+repository_long_description = "Long description of Galaxy filtering tool for test 0410"
 
-'''
+"""
 1. Create a repository in the tool shed owned by test_user_1.
 2. Have test_user_2 complete a review of the repository.
 3. Have test_user_1 browse the review.
@@ -12,11 +15,11 @@ repository_long_description = 'Long description of Galaxy filtering tool for tes
 5. Have test_user_1 give write permission on the repository to the test_user_3.
 6. Have test_user_3 browse the repository again and they should now have the ability to browse the review.
 7. Have test_user_3 browse the review.
-'''
+"""
 
 
 class TestRepositoryComponentReviews(ShedTwillTestCase):
-    '''Test repository component review features.'''
+    """Test repository component review features."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
@@ -26,39 +29,55 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_3_email, username=common.test_user_3_name)
         test_user_3 = self.test_db_util.get_user(common.test_user_3_email)
-        assert test_user_3 is not None, f'Problem retrieving user with email {common.test_user_3_email} from the database'
+        assert (
+            test_user_3 is not None
+        ), f"Problem retrieving user with email {common.test_user_3_email} from the database"
         self.test_db_util.get_private_role(test_user_3)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_grant_reviewer_role(self):
-        '''Grant the repository reviewer role to test_user_2.
+        """Grant the repository reviewer role to test_user_2.
 
         We now have an admin user (admin_user) and three non-admin users (test_user_1, test_user_2, and test_user_3). Grant the repository
         reviewer role to test_user_2, who will not be the owner of the reviewed repositories, and do not grant any roles to test_user_3 yet.
-        '''
-        reviewer_role = self.test_db_util.get_role_by_name('Repository Reviewer')
+        """
+        reviewer_role = self.test_db_util.get_role_by_name("Repository Reviewer")
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
         self.grant_role_to_user(test_user_2, reviewer_role)
 
     def test_0010_verify_repository_review_components(self):
-        '''Ensure that the required review components exist.
+        """Ensure that the required review components exist.
 
         Make sure all the components we are to review are recorded in the database.
-        '''
-        self.add_repository_review_component(name='Repository dependencies',
-                                             description='Repository dependencies defined in a file named repository_dependencies.xml included in the repository')
-        strings_displayed = ['Data types', 'Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows']
+        """
+        self.add_repository_review_component(
+            name="Repository dependencies",
+            description="Repository dependencies defined in a file named repository_dependencies.xml included in the repository",
+        )
+        strings_displayed = [
+            "Data types",
+            "Functional tests",
+            "README",
+            "Repository dependencies",
+            "Tool dependencies",
+            "Tools",
+            "Workflows",
+        ]
         self.manage_review_components(strings_displayed=strings_displayed)
 
     def test_0015_create_repository(self):
@@ -68,123 +87,160 @@ class TestRepositoryComponentReviews(ShedTwillTestCase):
         Log in as test_user_1 and create the filtering repository, then upload a basic set of
         components to be reviewed in subsequent tests.
         """
-        category = self.create_category(name='Test 0400 Repository Component Reviews', description='Test 0400 Repository Component Reviews')
+        category = self.create_category(
+            name="Test 0400 Repository Component Reviews", description="Test 0400 Repository Component Reviews"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(repository_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_test_data.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering test data.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.upload_file(repository,
-                         filename='readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded readme.txt.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_test_data.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering test data.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded readme.txt.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_review_repository(self):
-        '''Complete a review of the filtering repository.
+        """Complete a review of the filtering repository.
 
         We are at step 2 - Have test_user_2 complete a review of the repository.
         Review all components of the filtering repository, with the appropriate contents and approved/not approved/not applicable status.
-        '''
+        """
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        review_contents_dict = {'Data types': dict(),
-                                'README': dict(rating=5, comment='Clear and concise readme file, a true pleasure to read.', approved='yes', private='no'),
-                                'Functional tests': dict(rating=5, comment='A good set of functional tests.', approved='yes', private='no'),
-                                'Repository dependencies': dict(),
-                                'Tool dependencies': dict(),
-                                'Tools': dict(rating=5, comment='Excellent tool, easy to use.', approved='yes', private='no'),
-                                'Workflows': dict()}
+        review_contents_dict = {
+            "Data types": dict(),
+            "README": dict(
+                rating=5,
+                comment="Clear and concise readme file, a true pleasure to read.",
+                approved="yes",
+                private="no",
+            ),
+            "Functional tests": dict(rating=5, comment="A good set of functional tests.", approved="yes", private="no"),
+            "Repository dependencies": dict(),
+            "Tool dependencies": dict(),
+            "Tools": dict(rating=5, comment="Excellent tool, easy to use.", approved="yes", private="no"),
+            "Workflows": dict(),
+        }
         self.create_repository_review(repository, review_contents_dict)
 
     def test_0025_verify_repository_review(self):
-        '''Verify that the review was completed and displays properly.
+        """Verify that the review was completed and displays properly.
 
         We are at step 3 - Have test_user_1 browse the review.
         Verify that all the review components were submitted, and that the repository owner can see the review.
-        '''
+        """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['Data types', 'Functional tests', 'yes', 'A good set of functional tests.', 'README', 'yes', 'Workflows', 'Tools']
-        strings_displayed.extend(['Clear and concise readme file, a true pleasure to read.', 'Tool dependencies', 'not_applicable'])
-        strings_displayed.extend(['Repository dependencies', 'Excellent tool, easy to use.'])
-        strings_displayed = ['Browse reviews of this repository']
+        strings_displayed = [
+            "Data types",
+            "Functional tests",
+            "yes",
+            "A good set of functional tests.",
+            "README",
+            "yes",
+            "Workflows",
+            "Tools",
+        ]
+        strings_displayed.extend(
+            ["Clear and concise readme file, a true pleasure to read.", "Tool dependencies", "not_applicable"]
+        )
+        strings_displayed.extend(["Repository dependencies", "Excellent tool, easy to use."])
+        strings_displayed = ["Browse reviews of this repository"]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
         self.verify_repository_reviews(repository, reviewer=user, strings_displayed=strings_displayed)
 
     def test_0030_browse_with_other_user(self):
-        '''Verify that test_user_3 is blocked from browsing the review.
+        """Verify that test_user_3 is blocked from browsing the review.
 
         We are at step 4 - Have test_user_3 browse the repository and make sure they are not allowed to browse the review.
-        '''
+        """
         self.login(email=common.test_user_3_email, username=common.test_user_3_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_not_displayed = ['Browse reviews of this repository']
+        strings_not_displayed = ["Browse reviews of this repository"]
         self.display_manage_repository_page(repository, strings_not_displayed=strings_not_displayed)
-        strings_not_displayed = ['A good set of functional tests.', 'Clear and concise readme file, a true pleasure to read.']
-        strings_not_displayed.append('Excellent tool, easy to use.')
+        strings_not_displayed = [
+            "A good set of functional tests.",
+            "Clear and concise readme file, a true pleasure to read.",
+        ]
+        strings_not_displayed.append("Excellent tool, easy to use.")
         changeset_revision = self.get_repository_tip(repository)
-        review = self.test_db_util.get_repository_review_by_user_id_changeset_revision(user.id, repository.id, changeset_revision)
+        review = self.test_db_util.get_repository_review_by_user_id_changeset_revision(
+            user.id, repository.id, changeset_revision
+        )
         self.browse_component_review(review, strings_not_displayed=strings_not_displayed)
 
     def test_0035_grant_write_access_to_other_user(self):
-        '''Grant write access on the filtering_0410 repository to test_user_3.
+        """Grant write access on the filtering_0410 repository to test_user_3.
 
         We are at step 5 - Have test_user_1 give write permission on the repository to the test_user_3.
-        '''
+        """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.grant_write_access(repository, usernames=[common.test_user_3_name])
 
     def test_0040_verify_test_user_3_can_browse_reviews(self):
-        '''Check that test_user_3 can now browse reviews.
+        """Check that test_user_3 can now browse reviews.
 
         We are at step 6 - Have test_user_3 browse the repository again and they should now have the ability to browse the review.
-        '''
+        """
         self.login(email=common.test_user_3_email, username=common.test_user_3_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ['Browse reviews of this repository']
+        strings_displayed = ["Browse reviews of this repository"]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0045_verify_browse_review_with_write_access(self):
-        '''Check that test_user_3 can now display reviews.
+        """Check that test_user_3 can now display reviews.
 
         We are at step 7 - Have test_user_3 browse the review.
-        '''
+        """
         self.login(email=common.test_user_3_email, username=common.test_user_3_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         user = self.test_db_util.get_user(common.test_user_2_email)
-        strings_displayed = ['A&nbsp;good&nbsp;set&nbsp;of&nbsp;functional&nbsp;tests.',
-                             'Clear&nbsp;and&nbsp;concise&nbsp;readme&nbsp;file',
-                             'a&nbsp;true&nbsp;pleasure&nbsp;to&nbsp;read.',
-                             'Excellent&nbsp;tool,&nbsp;easy&nbsp;to&nbsp;use.']
+        strings_displayed = [
+            "A&nbsp;good&nbsp;set&nbsp;of&nbsp;functional&nbsp;tests.",
+            "Clear&nbsp;and&nbsp;concise&nbsp;readme&nbsp;file",
+            "a&nbsp;true&nbsp;pleasure&nbsp;to&nbsp;read.",
+            "Excellent&nbsp;tool,&nbsp;easy&nbsp;to&nbsp;use.",
+        ]
         changeset_revision = self.get_repository_tip(repository)
-        review = self.test_db_util.get_repository_review_by_user_id_changeset_revision(user.id, repository.id, changeset_revision)
+        review = self.test_db_util.get_repository_review_by_user_id_changeset_revision(
+            user.id, repository.id, changeset_revision
+        )
         self.browse_component_review(review, strings_displayed=strings_displayed)
diff --git a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
index 6aafd4d1cbf..ef5bd589b2b 100644
--- a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
+++ b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
@@ -1,16 +1,19 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'filtering_0420'
-repository_description = 'Galaxy filtering tool for test 0420'
-repository_long_description = 'Long description of Galaxy filtering tool for test 0410'
+repository_name = "filtering_0420"
+repository_description = "Galaxy filtering tool for test 0420"
+repository_long_description = "Long description of Galaxy filtering tool for test 0410"
 
-first_changeset_hash = ''
+first_changeset_hash = ""
 
-'''
+"""
 1. Add and populate a repository to the tool shed with change set revision 0 (assume owner is test).
 2. Add valid change set revision 1.
 3. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1
@@ -21,11 +24,11 @@ first_changeset_hash = ''
 6. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<invalid revision>
 7. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/<invalid repository name>
 8. Visit the following url and check for appropriate strings: <tool shed base url>/view/<invalid owner>
-'''
+"""
 
 
 class TestRepositoryCitableURLs(ShedTwillTestCase):
-    '''Test repository citable url features.'''
+    """Test repository citable url features."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
@@ -35,11 +38,13 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_repository(self):
@@ -49,75 +54,84 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         Add and populate a repository to the tool shed with change set revision 0 (assume owner is test_user_1).
         """
         global first_changeset_hash
-        category = self.create_category(name='Test 0400 Repository Citable URLs',
-                                        description='Test 0400 Repository Citable URLs category')
+        category = self.create_category(
+            name="Test 0400 Repository Citable URLs", description="Test 0400 Repository Citable URLs category"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(repository_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='filtering/filtering_2.2.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 2.2.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_2.2.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 2.2.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         # We'll be checking for this hash later, after uploading another file to the repository, making get_repository_tip() not usable.
         first_changeset_hash = self.get_repository_tip(repository)
 
     def test_0010_upload_new_file_to_repository(self):
-        '''Upload a readme file to the repository in order to create a second changeset revision.
+        """Upload a readme file to the repository in order to create a second changeset revision.
 
         We are at step 2.
         Add valid change set revision 1.
         The repository should now contain two changeset revisions, 0:<revision hash> and 1:<revision hash>.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded readme.txt.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded readme.txt.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_load_user_view_page(self):
-        '''Load the /view/<username> page amd check for strings.
+        """Load the /view/<username> page amd check for strings.
 
         We are at step 3.
         Visit the following url and check for appropriate strings: <tool shed base url>/view/user1
-        '''
+        """
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
         encoded_user_id = self.security.encode_id(test_user_1.id)
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user
-        strings_displayed = ['/repository/browse_repositories', encoded_user_id, 'operation=repositories_by_user']
+        strings_displayed = ["/repository/browse_repositories", encoded_user_id, "operation=repositories_by_user"]
         strings_displayed.append(encoded_user_id)
-        strings_displayed_in_iframe = ['user1', 'filtering_0420', 'Galaxy filtering tool for test 0420']
-        self.load_citable_url(username='user1',
-                              repository_name=None,
-                              changeset_revision=None,
-                              encoded_user_id=encoded_user_id,
-                              encoded_repository_id=None,
-                              strings_displayed=strings_displayed,
-                              strings_displayed_in_iframe=strings_displayed_in_iframe)
+        strings_displayed_in_iframe = ["user1", "filtering_0420", "Galaxy filtering tool for test 0420"]
+        self.load_citable_url(
+            username="user1",
+            repository_name=None,
+            changeset_revision=None,
+            encoded_user_id=encoded_user_id,
+            encoded_repository_id=None,
+            strings_displayed=strings_displayed,
+            strings_displayed_in_iframe=strings_displayed_in_iframe,
+        )
 
     def test_0020_load_repository_view_page(self):
-        '''Load the /view/<user>/<repository> page and check for the appropriate strings.
+        """Load the /view/<user>/<repository> page and check for the appropriate strings.
 
         We are at step 4.
         Visit the following url and check for strings: <tool shed base url>/view/user1/filtering_0420
             Resulting page should contain change set revision 1
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
         encoded_user_id = self.security.encode_id(test_user_1.id)
@@ -125,26 +139,28 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/bview_repository?id=<encoded repository ID>
-        strings_displayed = ['/repository', 'view_repository', 'id=', encoded_repository_id]
-        strings_displayed_in_iframe = ['user1', 'filtering_0420', 'Galaxy filtering tool for test 0420']
+        strings_displayed = ["/repository", "view_repository", "id=", encoded_repository_id]
+        strings_displayed_in_iframe = ["user1", "filtering_0420", "Galaxy filtering tool for test 0420"]
         strings_displayed_in_iframe.append(self.get_repository_tip(repository))
-        strings_displayed_in_iframe.append('Link to this repository:')
-        strings_displayed_in_iframe.append(f'{self.url}/view/user1/filtering_0420')
-        self.load_citable_url(username='user1',
-                              repository_name='filtering_0420',
-                              changeset_revision=None,
-                              encoded_user_id=encoded_user_id,
-                              encoded_repository_id=encoded_repository_id,
-                              strings_displayed=strings_displayed,
-                              strings_displayed_in_iframe=strings_displayed_in_iframe)
+        strings_displayed_in_iframe.append("Link to this repository:")
+        strings_displayed_in_iframe.append(f"{self.url}/view/user1/filtering_0420")
+        self.load_citable_url(
+            username="user1",
+            repository_name="filtering_0420",
+            changeset_revision=None,
+            encoded_user_id=encoded_user_id,
+            encoded_repository_id=encoded_repository_id,
+            strings_displayed=strings_displayed,
+            strings_displayed_in_iframe=strings_displayed_in_iframe,
+        )
 
     def test_0025_load_view_page_for_previous_revision(self):
-        '''Load a citable url for a past changeset revision and verify that strings display.
+        """Load a citable url for a past changeset revision and verify that strings display.
 
         We are at step 5.
         Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<revision 0>
             Resulting page should not contain change set revision 1, but should contain change set revision 0.
-        '''
+        """
         global first_changeset_hash
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
@@ -153,72 +169,89 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/view_repository?id=<encoded repository ID>
-        strings_displayed = ['/repository', 'view_repository', f"id={encoded_repository_id}"]
-        strings_displayed_in_iframe = ['user1', 'filtering_0420', 'Galaxy filtering tool for test 0420', first_changeset_hash]
-        strings_displayed_in_iframe.append('Link to this repository revision:')
-        strings_displayed_in_iframe.append(f'{self.url}/view/user1/filtering_0420/{first_changeset_hash}')
+        strings_displayed = ["/repository", "view_repository", f"id={encoded_repository_id}"]
+        strings_displayed_in_iframe = [
+            "user1",
+            "filtering_0420",
+            "Galaxy filtering tool for test 0420",
+            first_changeset_hash,
+        ]
+        strings_displayed_in_iframe.append("Link to this repository revision:")
+        strings_displayed_in_iframe.append(f"{self.url}/view/user1/filtering_0420/{first_changeset_hash}")
         strings_not_displayed_in_iframe = []
-        self.load_citable_url(username='user1',
-                              repository_name='filtering_0420',
-                              changeset_revision=first_changeset_hash,
-                              encoded_user_id=encoded_user_id,
-                              encoded_repository_id=encoded_repository_id,
-                              strings_displayed=strings_displayed,
-                              strings_displayed_in_iframe=strings_displayed_in_iframe,
-                              strings_not_displayed_in_iframe=strings_not_displayed_in_iframe)
+        self.load_citable_url(
+            username="user1",
+            repository_name="filtering_0420",
+            changeset_revision=first_changeset_hash,
+            encoded_user_id=encoded_user_id,
+            encoded_repository_id=encoded_repository_id,
+            strings_displayed=strings_displayed,
+            strings_displayed_in_iframe=strings_displayed_in_iframe,
+            strings_not_displayed_in_iframe=strings_not_displayed_in_iframe,
+        )
 
     def test_0030_load_sharable_url_with_invalid_changeset_revision(self):
-        '''Load a citable url with an invalid changeset revision specified.'''
+        """Load a citable url with an invalid changeset revision specified."""
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
         encoded_user_id = self.security.encode_id(test_user_1.id)
         encoded_repository_id = self.security.encode_id(repository.id)
-        invalid_changeset_hash = 'invalid'
+        invalid_changeset_hash = "invalid"
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/view_repository?id=<encoded repository ID>&status=error
-        strings_displayed = ['/repository', 'view_repository', f"id={encoded_repository_id}"]
-        strings_displayed.extend(['The+change+log', 'does+not+include+revision', invalid_changeset_hash, 'status=error'])
-        self.load_citable_url(username='user1',
-                              repository_name='filtering_0420',
-                              changeset_revision=invalid_changeset_hash,
-                              encoded_user_id=encoded_user_id,
-                              encoded_repository_id=encoded_repository_id,
-                              strings_displayed=strings_displayed)
+        strings_displayed = ["/repository", "view_repository", f"id={encoded_repository_id}"]
+        strings_displayed.extend(
+            ["The+change+log", "does+not+include+revision", invalid_changeset_hash, "status=error"]
+        )
+        self.load_citable_url(
+            username="user1",
+            repository_name="filtering_0420",
+            changeset_revision=invalid_changeset_hash,
+            encoded_user_id=encoded_user_id,
+            encoded_repository_id=encoded_repository_id,
+            strings_displayed=strings_displayed,
+        )
 
     def test_0035_load_sharable_url_with_invalid_repository_name(self):
-        '''Load a citable url with an invalid changeset revision specified.
+        """Load a citable url with an invalid changeset revision specified.
 
         We are at step 7
         Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/!!invalid!!
-        '''
+        """
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
         encoded_user_id = self.security.encode_id(test_user_1.id)
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user
-        strings_displayed = ['/repository', 'browse_repositories', 'user1']
-        strings_displayed.extend(['list+of+repositories+owned', 'does+not+include+one+named', '%21%21invalid%21%21', 'status=error'])
-        strings_displayed_in_iframe = ['user1', 'filtering_0420']
-        strings_displayed_in_iframe.append('Repositories Owned by user1')
-        self.load_citable_url(username='user1',
-                              repository_name='!!invalid!!',
-                              changeset_revision=None,
-                              encoded_user_id=encoded_user_id,
-                              encoded_repository_id=None,
-                              strings_displayed=strings_displayed,
-                              strings_displayed_in_iframe=strings_displayed_in_iframe)
+        strings_displayed = ["/repository", "browse_repositories", "user1"]
+        strings_displayed.extend(
+            ["list+of+repositories+owned", "does+not+include+one+named", "%21%21invalid%21%21", "status=error"]
+        )
+        strings_displayed_in_iframe = ["user1", "filtering_0420"]
+        strings_displayed_in_iframe.append("Repositories Owned by user1")
+        self.load_citable_url(
+            username="user1",
+            repository_name="!!invalid!!",
+            changeset_revision=None,
+            encoded_user_id=encoded_user_id,
+            encoded_repository_id=None,
+            strings_displayed=strings_displayed,
+            strings_displayed_in_iframe=strings_displayed_in_iframe,
+        )
 
     def test_0040_load_sharable_url_with_invalid_owner(self):
-        '''Load a citable url with an invalid owner.
+        """Load a citable url with an invalid owner.
 
         We are at step 8.
         Visit the following url and check for appropriate strings: <tool shed base url>/view/!!invalid!!
-        '''
-        strings_displayed = ['The tool shed', self.url, 'contains no repositories owned by', '!!invalid!!']
-        self.load_citable_url(username='!!invalid!!',
-                              repository_name=None,
-                              changeset_revision=None,
-                              encoded_user_id=None,
-                              encoded_repository_id=None,
-                              strings_displayed=strings_displayed)
+        """
+        strings_displayed = ["The tool shed", self.url, "contains no repositories owned by", "!!invalid!!"]
+        self.load_citable_url(
+            username="!!invalid!!",
+            repository_name=None,
+            changeset_revision=None,
+            encoded_user_id=None,
+            encoded_repository_id=None,
+            strings_displayed=strings_displayed,
+        )
diff --git a/lib/tool_shed/test/functional/test_0430_browse_utilities.py b/lib/tool_shed/test/functional/test_0430_browse_utilities.py
index 78283ee3bc5..a59a80adc6f 100644
--- a/lib/tool_shed/test/functional/test_0430_browse_utilities.py
+++ b/lib/tool_shed/test/functional/test_0430_browse_utilities.py
@@ -1,31 +1,34 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-datatypes_repository_name = 'emboss_datatypes_0430'
-datatypes_repository_description = 'Galaxy applicable datatypes for EMBOSS for test 0430'
-datatypes_repository_long_description = 'Long description of Galaxy applicable datatypes for EMBOSS for test 0430'
+datatypes_repository_name = "emboss_datatypes_0430"
+datatypes_repository_description = "Galaxy applicable datatypes for EMBOSS for test 0430"
+datatypes_repository_long_description = "Long description of Galaxy applicable datatypes for EMBOSS for test 0430"
 
-emboss_repository_name = 'emboss_0430'
-emboss_repository_description = 'EMBOSS tools for test 0430'
-emboss_repository_long_description = 'Long description of EMBOSS tools for test 0430'
+emboss_repository_name = "emboss_0430"
+emboss_repository_description = "EMBOSS tools for test 0430"
+emboss_repository_long_description = "Long description of EMBOSS tools for test 0430"
 
-freebayes_repository_name = 'freebayes_0430'
-freebayes_repository_description = 'Freebayes tool for test 0430'
-freebayes_repository_long_description = 'Long description of Freebayes tool for test 0430'
-'''
+freebayes_repository_name = "freebayes_0430"
+freebayes_repository_description = "Freebayes tool for test 0430"
+freebayes_repository_long_description = "Long description of Freebayes tool for test 0430"
+"""
 1. Create and populate repositories.
 2. Browse Custom Datatypes.
 3. Browse Tools.
 4. Browse Repository Dependencies.
 5. Browse Tool Dependencies.
-'''
+"""
 
 
 class TestToolShedBrowseUtilities(ShedTwillTestCase):
-    '''Test browsing for Galaxy utilities.'''
+    """Test browsing for Galaxy utilities."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
@@ -35,11 +38,13 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_datatypes_repository(self):
@@ -48,25 +53,30 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
         We are at step 1.
         Create and populate the repository that will contain one or more datatypes.
         """
-        category = self.create_category(name='Test 0430 Galaxy Utilities',
-                                        description='Description of Test 0430 Galaxy Utilities category')
+        category = self.create_category(
+            name="Test 0430 Galaxy Utilities", description="Description of Test 0430 Galaxy Utilities category"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(datatypes_repository_name)
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                   description=datatypes_repository_description,
-                                                   long_description=datatypes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded datatypes_conf.xml.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded datatypes_conf.xml.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_emboss_repository(self):
         """Create and populate the emboss_0430 repository
@@ -74,33 +84,49 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
         We are at step 1.
         Create the emboss_0430 repository, and populate it with tools.
         """
-        category = self.create_category(name='Test 0430 Galaxy Utilities',
-                                        description='Description of Test 0430 Galaxy Utilities category')
+        category = self.create_category(
+            name="Test 0430 Galaxy Utilities", description="Description of Test 0430 Galaxy Utilities category"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(emboss_repository_name)
-        emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                    description=emboss_repository_description,
-                                                    long_description=emboss_repository_long_description,
-                                                    owner=common.test_user_1_name,
-                                                    category_id=self.security.encode_id(category.id),
-                                                    strings_displayed=strings_displayed)
-        self.upload_file(emboss_repository,
-                         filename='emboss/emboss.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded emboss.tar.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        emboss_repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            emboss_repository,
+            filename="emboss/emboss.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded emboss.tar.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_dependency_on_datatypes_repository(self):
-        '''Create a dependency definition file that specifies emboss_datatypes_0430 and upload it to emboss_0430.'''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0430', additional_paths=['dependencies'])
-        datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-        self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
+        """Create a dependency definition file that specifies emboss_datatypes_0430 and upload it to emboss_0430."""
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0430", additional_paths=["dependencies"])
+        datatypes_tuple = (
+            self.url,
+            datatypes_repository.name,
+            datatypes_repository.user.username,
+            self.get_repository_tip(datatypes_repository),
+        )
+        self.create_repository_dependency(
+            repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+        )
         self.check_repository_dependency(emboss_repository, datatypes_repository)
 
     def test_0020_create_tool_dependency_repository(self):
@@ -109,68 +135,103 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
         We are at step 1.
         Create and populate the repository that will have a tool dependency defined.
         """
-        category = self.create_category(name='Test 0430 Galaxy Utilities',
-                                        description='Description of Test 0430 Galaxy Utilities category')
+        category = self.create_category(
+            name="Test 0430 Galaxy Utilities", description="Description of Test 0430 Galaxy Utilities category"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(freebayes_repository_name)
-        repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                   description=freebayes_repository_description,
-                                                   long_description=freebayes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='freebayes/freebayes.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded freebayes.tar.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=freebayes_repository_name,
+            description=freebayes_repository_description,
+            long_description=freebayes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="freebayes/freebayes.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded freebayes.tar.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_browse_custom_datatypes(self):
-        '''Load the page to browse custom datatypes.
+        """Load the page to browse custom datatypes.
 
         We are at step 2.
         Verify that the uploaded emboss datatypes repository has added to the custom datatypes page.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         changeset_revision = self.get_repository_tip(repository)
-        strings_displayed = ['equicktandem', 'est2genome', 'supermatcher', 'galaxy.datatypes.data:Text', changeset_revision, 'user1', 'emboss_datatypes_0430']
+        strings_displayed = [
+            "equicktandem",
+            "est2genome",
+            "supermatcher",
+            "galaxy.datatypes.data:Text",
+            changeset_revision,
+            "user1",
+            "emboss_datatypes_0430",
+        ]
         self.browse_custom_datatypes(strings_displayed=strings_displayed)
 
     def test_0030_browse_tools(self):
-        '''Load the page to browse tools.
+        """Load the page to browse tools.
 
         We are at step 3.
         Verify the existence of emboss tools in the browse tools page.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
         changeset_revision = self.get_repository_tip(repository)
-        strings_displayed = ['EMBOSS', 'antigenic1', '5.0.0', changeset_revision, 'user1', 'emboss_0430']
+        strings_displayed = ["EMBOSS", "antigenic1", "5.0.0", changeset_revision, "user1", "emboss_0430"]
         self.browse_tools(strings_displayed=strings_displayed)
 
     def test_0035_browse_repository_dependencies(self):
-        '''Browse repository dependencies and look for a dependency on emboss_datatypes_0430.
+        """Browse repository dependencies and look for a dependency on emboss_datatypes_0430.
 
         We are at step 3.
         Verify that the browse repository dependencies page shows emboss_datatypes_0430 as a dependency of emboss_0430.
-        '''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
+        """
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         datatypes_changeset_revision = self.get_repository_tip(datatypes_repository)
         emboss_changeset_revision = self.get_repository_tip(emboss_repository)
-        strings_displayed = [datatypes_changeset_revision, emboss_changeset_revision, 'emboss_datatypes_0430', 'user1', 'emboss_0430']
+        strings_displayed = [
+            datatypes_changeset_revision,
+            emboss_changeset_revision,
+            "emboss_datatypes_0430",
+            "user1",
+            "emboss_0430",
+        ]
         self.browse_repository_dependencies(strings_displayed=strings_displayed)
 
     def test_0040_browse_tool_dependencies(self):
-        '''Browse tool dependencies and look for the right versions of freebayes and samtools.
+        """Browse tool dependencies and look for the right versions of freebayes and samtools.
 
         We are at step 4.
         Verify that the browse tool dependencies page shows the correct dependencies defined for freebayes_0430.
-        '''
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
+        """
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
         freebayes_changeset_revision = self.get_repository_tip(freebayes_repository)
-        strings_displayed = [freebayes_changeset_revision, 'freebayes_0430', 'user1', '0.9.4_9696d0ce8a96', 'freebayes', 'samtools', '0.1.18']
+        strings_displayed = [
+            freebayes_changeset_revision,
+            "freebayes_0430",
+            "user1",
+            "0.9.4_9696d0ce8a96",
+            "freebayes",
+            "samtools",
+            "0.1.18",
+        ]
         self.browse_tool_dependencies(strings_displayed=strings_displayed)
diff --git a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
index ae046b9011d..9221ca08d79 100644
--- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
@@ -1,26 +1,29 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-column_repository_name = 'column_maker_0440'
+column_repository_name = "column_maker_0440"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0440'
+convert_repository_name = "convert_chars_0440"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-bwa_package_repository_name = 'bwa_package_0440'
+bwa_package_repository_name = "bwa_package_0440"
 bwa_package_repository_description = "BWA Package Repository"
 bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."
 
-bwa_base_repository_name = 'bwa_base_0440'
+bwa_base_repository_name = "bwa_base_0440"
 bwa_base_repository_description = "BWA Base"
 bwa_base_repository_long_description = "NT space mapping with BWA"
 
-bwa_tool_dependency_repository_name = 'bwa_tool_dependency_0440'
+bwa_tool_dependency_repository_name = "bwa_tool_dependency_0440"
 bwa_tool_dependency_repository_description = "BWA Base"
 bwa_tool_dependency_repository_long_description = "NT space mapping with BWA"
 
-'''
+"""
 Simple repository dependencies:
 
 1. Create and populate column_maker_0440 so that it has an installable revision 0.
@@ -45,11 +48,11 @@ Tool dependencies:
 3. Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440
    still has a single installable revision 0.
 
-'''
+"""
 
 
 class TestDeletedDependencies(ShedTwillTestCase):
-    '''Test metadata setting when dependency definitions are deleted.'''
+    """Test metadata setting when dependency definitions are deleted."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
@@ -59,303 +62,393 @@ class TestDeletedDependencies(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_column_maker_repository(self):
-        '''Create and populate a repository named column_maker_0440.
+        """Create and populate a repository named column_maker_0440.
 
         We are at simple repository dependencies, step 1 - Create and populate column_maker_0440 so that it has an installable revision 0.
-        '''
-        category = self.create_category(name='Test 0440 Deleted Dependency Definitions',
-                                        description='Description of Deleted Dependency Definitions category for test 0440')
+        """
+        category = self.create_category(
+            name="Test 0440 Deleted Dependency Definitions",
+            description="Description of Deleted Dependency Definitions category for test 0440",
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = ["Repository <b>column_maker_0440</b> has been created"]
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column maker tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column maker tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_convert_chars_repository(self):
-        '''Create and populate a repository named convert_chars_0440.
+        """Create and populate a repository named convert_chars_0440.
 
         We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0.
-        '''
-        category = self.test_db_util.get_category_by_name('Test 0440 Deleted Dependency Definitions')
+        """
+        category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = ["Repository <b>convert_chars_0440</b> has been created"]
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='convert_chars/convert_chars.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded convert chars tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="convert_chars/convert_chars.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded convert chars tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_dependency_on_convert_chars(self):
-        '''Create a dependency definition file that specifies column_maker_0440 and upload it to convert_chars_0440.
+        """Create a dependency definition file that specifies column_maker_0440 and upload it to convert_chars_0440.
 
         We are at simple repository dependencies, step 3 - Add a valid simple repository_dependencies.xml to
         convert_chars_0440 that points to the installable revision of column_maker_0440.
-        '''
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        dependency_xml_path = self.generate_temp_path('test_0440', additional_paths=['dependencies'])
-        column_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
+        """
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        dependency_xml_path = self.generate_temp_path("test_0440", additional_paths=["dependencies"])
+        column_tuple = (
+            self.url,
+            column_repository.name,
+            column_repository.user.username,
+            self.get_repository_tip(column_repository),
+        )
         # After this, convert_chars_0440 should depend on column_maker_0440.
-        self.create_repository_dependency(repository=convert_repository,
-                                          repository_tuples=[column_tuple],
-                                          filepath=dependency_xml_path,
-                                          prior_installation_required=True)
+        self.create_repository_dependency(
+            repository=convert_repository,
+            repository_tuples=[column_tuple],
+            filepath=dependency_xml_path,
+            prior_installation_required=True,
+        )
         self.check_repository_dependency(convert_repository, column_repository)
 
     def test_0020_verify_dependency_metadata(self):
-        '''Verify that uploading the dependency moved metadata to the tip.
+        """Verify that uploading the dependency moved metadata to the tip.
 
         We are at simple repository dependencies, step 4 - Make sure the installable revision of convert_chars_0440 is now
         revision 1 (the tip) instead of revision 0.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         tip = self.get_repository_tip(repository)
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, tip)
         # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions.
-        assert metadata_record.downloadable, 'Tip is not downloadable.'
-        assert len(repository.downloadable_revisions) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \
-            (repository.name, len(repository.downloadable_revisions))
+        assert metadata_record.downloadable, "Tip is not downloadable."
+        assert (
+            len(repository.downloadable_revisions) == 1
+        ), "Repository %s has %d downloadable revisions, expected 1." % (
+            repository.name,
+            len(repository.downloadable_revisions),
+        )
 
     def test_0025_delete_repository_dependency(self):
-        '''Delete the repository_dependencies.xml from convert_chars_0440.
+        """Delete the repository_dependencies.xml from convert_chars_0440.
 
         We are at simple repository dependencies, steps 5 and 6 - Delete repository_dependencies.xml from convert_chars_0440.
         Make sure convert_chars_0440 now has two installable revisions: 1 and 2
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         # Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml
         # is deleted and a new downloadable revision is created.
         old_changeset_revision = self.get_repository_tip(repository)
-        self.delete_files_from_repository(repository, filenames=['repository_dependencies.xml'])
+        self.delete_files_from_repository(repository, filenames=["repository_dependencies.xml"])
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, 'The revision of %s that contains repository_dependencies.xml is no longer downloadable.' % \
-            repository.name
+        assert metadata_record.downloadable, (
+            "The revision of %s that contains repository_dependencies.xml is no longer downloadable." % repository.name
+        )
         # Check that the new tip is also downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, 'The revision of %s that does not contain repository_dependencies.xml is not downloadable.' % \
-            repository.name
+        assert metadata_record.downloadable, (
+            "The revision of %s that does not contain repository_dependencies.xml is not downloadable."
+            % repository.name
+        )
         # Explicitly reload the repository instance from the database, to avoid potential caching issues.
         self.test_db_util.refresh(repository)
         # Verify that there are only two downloadable revisions.
-        assert len(repository.downloadable_revisions) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \
-            (repository.name, len(repository.downloadable_revisions))
+        assert (
+            len(repository.downloadable_revisions) == 2
+        ), "Repository %s has %d downloadable revisions, expected 2." % (
+            repository.name,
+            len(repository.downloadable_revisions),
+        )
 
     def test_0030_create_bwa_package_repository(self):
-        '''Create and populate the bwa_package_0440 repository.
+        """Create and populate the bwa_package_0440 repository.
 
         We are at complex repository dependencies, step 1 - Create and populate bwa_package_0440 so that it has a valid
         tool dependency definition and an installable revision 0.
-        '''
-        category = self.test_db_util.get_category_by_name('Test 0440 Deleted Dependency Definitions')
+        """
+        category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = ["Repository <b>bwa_package_0440</b> has been created"]
-        repository = self.get_or_create_repository(name=bwa_package_repository_name,
-                                                   description=bwa_package_repository_description,
-                                                   long_description=bwa_package_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='bwa/complex/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded package tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_package_repository_name,
+            description=bwa_package_repository_description,
+            long_description=bwa_package_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/complex/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded package tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0035_create_bwa_base_repository(self):
-        '''Create and populate the bwa_base_0440 repository.
+        """Create and populate the bwa_base_0440 repository.
 
         We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0.
         This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440.
-        '''
-        category = self.test_db_util.get_category_by_name('Test 0440 Deleted Dependency Definitions')
+        """
+        category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = ["Repository <b>bwa_base_0440</b> has been created"]
-        repository = self.get_or_create_repository(name=bwa_base_repository_name,
-                                                   description=bwa_base_repository_description,
-                                                   long_description=bwa_base_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='bwa/complex/bwa_base.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded BWA nucleotide space mapping tool tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_base_repository_name,
+            description=bwa_base_repository_description,
+            long_description=bwa_base_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/complex/bwa_base.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded BWA nucleotide space mapping tool tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0040_create_dependency_on_bwa_package_repository(self):
-        '''Create a complex repository dependency on bwa_package_0440 and upload it to bwa_tool_0440.
+        """Create a complex repository dependency on bwa_package_0440 and upload it to bwa_tool_0440.
 
         We are at complex repository dependencies, step 3 - Add a valid complex repository dependency tool_dependencies.xml to
         bwa_base_0440 that points to the installable revision 0 of bwa_package_0440.
-        '''
-        bwa_package_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-        bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-        dependency_path = self.generate_temp_path('test_0440', additional_paths=['complex'])
+        """
+        bwa_package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
+        bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
+        dependency_path = self.generate_temp_path("test_0440", additional_paths=["complex"])
         changeset_revision = self.get_repository_tip(bwa_package_repository)
         bwa_tuple = (self.url, bwa_package_repository.name, bwa_package_repository.user.username, changeset_revision)
-        self.create_repository_dependency(repository=bwa_base_repository,
-                                          repository_tuples=[bwa_tuple],
-                                          filepath=dependency_path,
-                                          prior_installation_required=True,
-                                          complex=True,
-                                          package='bwa',
-                                          version='0.5.9')
+        self.create_repository_dependency(
+            repository=bwa_base_repository,
+            repository_tuples=[bwa_tuple],
+            filepath=dependency_path,
+            prior_installation_required=True,
+            complex=True,
+            package="bwa",
+            version="0.5.9",
+        )
 
     def test_0045_verify_dependency_metadata(self):
-        '''Verify that uploading the dependency moved metadata to the tip.
+        """Verify that uploading the dependency moved metadata to the tip.
 
         We are at complex repository dependencies, step 4 - Make sure that bwa_base_0440 installable revision is now revision 1
         instead of revision 0.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         tip = self.get_repository_tip(repository)
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, tip)
         # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions.
-        assert metadata_record.downloadable, 'Tip is not downloadable.'
-        assert len(repository.downloadable_revisions) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \
-            (repository.name, len(repository.downloadable_revisions))
+        assert metadata_record.downloadable, "Tip is not downloadable."
+        assert (
+            len(repository.downloadable_revisions) == 1
+        ), "Repository %s has %d downloadable revisions, expected 1." % (
+            repository.name,
+            len(repository.downloadable_revisions),
+        )
 
     def test_0050_delete_complex_repository_dependency(self):
-        '''Delete the tool_dependencies.xml from bwa_base_0440.
+        """Delete the tool_dependencies.xml from bwa_base_0440.
 
         We are at complex repository dependencies, step 5 - Delete tool_dependencies.xml from bwa_base_0440,
         and make sure bwa_base_0440 now has two installable revisions: 1 and 2
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
         # Record the current tip, so we can verify that it's still a downloadable revision after tool_dependencies.xml
         # is deleted and a new downloadable revision is created.
         old_changeset_revision = self.get_repository_tip(repository)
-        self.delete_files_from_repository(repository, filenames=['tool_dependencies.xml'])
+        self.delete_files_from_repository(repository, filenames=["tool_dependencies.xml"])
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is no longer downloadable.' % \
-            repository.name
+        assert metadata_record.downloadable, (
+            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
+        )
         # Check that the new tip is also downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, 'The revision of %s that does not contain tool_dependencies.xml is not downloadable.' % \
-            repository.name
+        assert metadata_record.downloadable, (
+            "The revision of %s that does not contain tool_dependencies.xml is not downloadable." % repository.name
+        )
         # Verify that there are only two downloadable revisions.
-        assert len(repository.downloadable_revisions) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \
-            (repository.name, len(repository.downloadable_revisions))
+        assert (
+            len(repository.downloadable_revisions) == 2
+        ), "Repository %s has %d downloadable revisions, expected 2." % (
+            repository.name,
+            len(repository.downloadable_revisions),
+        )
 
     def test_0055_create_bwa_tool_dependency_repository(self):
-        '''Create and populate the bwa_tool_dependency_0440 repository.
+        """Create and populate the bwa_tool_dependency_0440 repository.
 
         We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid tool
         dependency definition and an installable revision 0.
-        '''
-        category = self.test_db_util.get_category_by_name('Test 0440 Deleted Dependency Definitions')
+        """
+        category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = ["Repository <b>bwa_tool_dependency_0440</b> has been created"]
-        repository = self.get_or_create_repository(name=bwa_tool_dependency_repository_name,
-                                                   description=bwa_tool_dependency_repository_description,
-                                                   long_description=bwa_tool_dependency_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
-        self.upload_file(repository,
-                         filename='bwa/complex/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded package tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_tool_dependency_repository_name,
+            description=bwa_tool_dependency_repository_description,
+            long_description=bwa_tool_dependency_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/complex/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded package tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0060_delete_bwa_tool_dependency_definition(self):
-        '''Delete the tool_dependencies.xml file from bwa_tool_dependency_0440.
+        """Delete the tool_dependencies.xml file from bwa_tool_dependency_0440.
 
         We are at tool dependencies, step 2 - Delete tool_dependencies.xml from bwa_tool_dependency_0440.
         Make sure bwa_tool_dependency_0440 still has a downloadable changeset revision at the old tip.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(bwa_tool_dependency_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_tool_dependency_repository_name, common.test_user_1_name
+        )
         # Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml
         # is deleted and a new downloadable revision is created.
         old_changeset_revision = self.get_repository_tip(repository)
-        self.delete_files_from_repository(repository, filenames=['tool_dependencies.xml'])
+        self.delete_files_from_repository(repository, filenames=["tool_dependencies.xml"])
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is no longer downloadable.' % \
-            repository.name
+        assert metadata_record.downloadable, (
+            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
+        )
         # Check that the new tip does not have a metadata revision.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
         # If a changeset revision does not have metadata, the above method will return None.
-        assert metadata_record is None, f'The tip revision of {repository.name} should not have metadata, but metadata was found.'
+        assert (
+            metadata_record is None
+        ), f"The tip revision of {repository.name} should not have metadata, but metadata was found."
         # Verify that the new changeset revision is not downloadable.
-        assert len(repository.downloadable_revisions) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \
-            (repository.name, len(repository.downloadable_revisions))
+        assert (
+            len(repository.downloadable_revisions) == 1
+        ), "Repository %s has %d downloadable revisions, expected 1." % (
+            repository.name,
+            len(repository.downloadable_revisions),
+        )
 
     def test_0065_reupload_bwa_tool_dependency_definition(self):
-        '''Reupload the tool_dependencies.xml file to bwa_tool_dependency_0440.
+        """Reupload the tool_dependencies.xml file to bwa_tool_dependency_0440.
 
         We are at tool dependencies, step 3 - Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure
         that bwa_tool_dependency_0440 still has a single installable revision 0.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(bwa_tool_dependency_repository_name, common.test_user_1_name)
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_tool_dependency_repository_name, common.test_user_1_name
+        )
         # Record the current tip, so we can verify that it's still not a downloadable revision after tool_dependencies.xml
         # is re-uploaded and a new downloadable revision is created.
         old_changeset_revision = self.get_repository_tip(repository)
-        self.upload_file(repository,
-                         filename='bwa/complex/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded package tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="bwa/complex/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded package tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record is None, 'The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is.' % \
-            repository.name
+        assert metadata_record is None, (
+            "The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is."
+            % repository.name
+        )
         # Check that the new tip is also downloadable.
         metadata_record = self.get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is not downloadable.' % \
-            repository.name
+        assert metadata_record.downloadable, (
+            "The revision of %s that contains tool_dependencies.xml is not downloadable." % repository.name
+        )
         # Verify that there are only two downloadable revisions.
-        assert len(repository.downloadable_revisions) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \
-            (repository.name, len(repository.downloadable_revisions))
+        assert (
+            len(repository.downloadable_revisions) == 1
+        ), "Repository %s has %d downloadable revisions, expected 1." % (
+            repository.name,
+            len(repository.downloadable_revisions),
+        )
diff --git a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py
index c13f10e75c2..e558f5a59f1 100644
--- a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py
+++ b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py
@@ -1,19 +1,26 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 0460 Automatic repository revision completion'
-category_description = 'Test 0460 Automatic repository revision completion'
-datatypes_repository_name = 'emboss_datatypes_0460'
+category_name = "Test 0460 Automatic repository revision completion"
+category_description = "Test 0460 Automatic repository revision completion"
+datatypes_repository_name = "emboss_datatypes_0460"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
-bwa_repository_name = 'package_bwa_0_5_9_0460'
-bwa_repository_description = "Contains a tool dependency definition that downloads and compiles version 0.5.9 of the BWA package"
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
+bwa_repository_name = "package_bwa_0_5_9_0460"
+bwa_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 0.5.9 of the BWA package"
+)
 bwa_repository_long_description = "bwa (alignment via Burrows-Wheeler transformation) 0.5.9-r16 by Heng Li"
 
-'''
+"""
 For all steps, verify that the generated dependency points to the tip of the specified repository.
 
 1)  Create and populate emboss_datatypes_0460.
@@ -51,75 +58,87 @@ For all steps, verify that the generated dependency points to the tip of the spe
 15) Upload to repository_dependency_test_4_0460 using the url hg://<tool shed url>/repos/user1/hg_repository_dependency_0460.
 
 16) Upload to repository_dependency_test_5_0460 using the url hg://<tool shed url>/repos/user1/hg_repository_dependency_0460.
-'''
+"""
 
 
 class TestAutomaticDependencyRevision(ShedTwillTestCase):
-    '''Test defining repository dependencies without specifying the changeset revision.'''
+    """Test defining repository dependencies without specifying the changeset revision."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_datatypes_repository(self):
-        '''Create and populate the emboss_datatypes_0460 repository
+        """Create and populate the emboss_datatypes_0460 repository
 
         This is step 1 - Create and populate emboss_datatypes_0460.
-        '''
+        """
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                   description=datatypes_repository_description,
-                                                   long_description=datatypes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='emboss/datatypes/datatypes_conf.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate emboss_datatypes_0460 with datatype definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="emboss/datatypes/datatypes_conf.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate emboss_datatypes_0460 with datatype definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_bwa_package_repository(self):
-        '''Create and populate the package_bwa_0_5_9_0460 repository.
+        """Create and populate the package_bwa_0_5_9_0460 repository.
 
         This is step 2 - Create and populate package_bwa_0_5_9_0460.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=bwa_repository_name,
-                                                   description=bwa_repository_description,
-                                                   long_description=bwa_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='bwa/complex/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_bwa_0_5_9_0460 with a tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_repository_name,
+            description=bwa_repository_description,
+            long_description=bwa_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="bwa/complex/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_bwa_0_5_9_0460 with a tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_tool_dependency_repositories(self):
-        '''Create repositories for testing complex dependency generation.
+        """Create repositories for testing complex dependency generation.
 
         This is step 3 - Create complex_dependency_test_1_0460, complex_dependency_test_2_0460, complex_dependency_test_3_0460,
         complex_dependency_test_4_0460, complex_dependency_test_5_0460. Each of these repositories will be populated in a way
@@ -130,176 +149,218 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         - Upload a tool_dependencies.xml in a subfolder within a tarball.
         - Upload via url, with the tool_dependencies.xml in the root of another repository.
         - Upload via url, with the tool_dependencies.xml in a subfolder within another repository.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository_base_name = 'complex_dependency_test_%d_0460'
-        repository_base_description = 'Test #%d for complex repository dependency definitions.'
-        repository_base_long_description = 'Test #%d for complex repository dependency definitions.'
+        repository_base_name = "complex_dependency_test_%d_0460"
+        repository_base_description = "Test #%d for complex repository dependency definitions."
+        repository_base_long_description = "Test #%d for complex repository dependency definitions."
         for number in range(1, 6):
-            self.get_or_create_repository(name=repository_base_name % number,
-                                          description=repository_base_description % number,
-                                          long_description=repository_base_long_description % number,
-                                          owner=common.test_user_1_name,
-                                          category_id=self.security.encode_id(category.id),
-                                          strings_displayed=[])
+            self.get_or_create_repository(
+                name=repository_base_name % number,
+                description=repository_base_description % number,
+                long_description=repository_base_long_description % number,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
 
     def test_0020_populate_complex_dependency_test_1_0460(self):
-        '''Populate complex_dependency_test_1_0460.
+        """Populate complex_dependency_test_1_0460.
 
         This is step 4 - Upload an uncompressed tool_dependencies.xml to complex_dependency_test_1_0460 that specifies
         a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_1_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('package_bwa_0_5_9_0460', common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0460_files/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded complex repository dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "complex_dependency_test_1_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "package_bwa_0_5_9_0460", common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision]
+        strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository, filename='tool_dependencies.xml', strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="tool_dependencies.xml", strings_displayed=[changeset_revision]
+        )
 
     def test_0025_populate_complex_dependency_test_2_0460(self):
-        '''Populate complex_dependency_test_2_0460.
+        """Populate complex_dependency_test_2_0460.
 
         This is step 5 - Upload an tarball with tool_dependencies.xml to complex_dependency_test_2_0460 that specifies
         a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_2_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('package_bwa_0_5_9_0460', common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0460_files/tool_dependencies_in_root.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message='Uploaded complex repository dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "complex_dependency_test_2_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "package_bwa_0_5_9_0460", common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/tool_dependencies_in_root.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision]
+        strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository, filename='tool_dependencies.xml', strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="tool_dependencies.xml", strings_displayed=[changeset_revision]
+        )
 
     def test_0030_populate_complex_dependency_test_3_0460(self):
-        '''Populate complex_dependency_test_3_0460.
+        """Populate complex_dependency_test_3_0460.
 
         This is step 6 - Upload an tarball with tool_dependencies.xml in a subfolder to complex_dependency_test_3_0460 that
         specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_3_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('package_bwa_0_5_9_0460', common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0460_files/tool_dependencies_in_subfolder.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message='Uploaded complex repository dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "complex_dependency_test_3_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "package_bwa_0_5_9_0460", common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/tool_dependencies_in_subfolder.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision]
+        strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository,
-                                              filename='tool_dependencies.xml',
-                                              filepath='subfolder',
-                                              strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="tool_dependencies.xml", filepath="subfolder", strings_displayed=[changeset_revision]
+        )
 
     def test_0035_create_repositories_for_url_upload(self):
-        '''Create and populate hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460.
+        """Create and populate hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460.
 
         This is step 7 - Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with tool dependencies.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name='hg_tool_dependency_0460',
-                                                   description=bwa_repository_description,
-                                                   long_description=bwa_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='0460_files/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate hg_tool_dependency_0460 with a tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        repository = self.get_or_create_repository(name='hg_subfolder_tool_dependency_0460',
-                                                   description=bwa_repository_description,
-                                                   long_description=bwa_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='0460_files/tool_dependencies_in_subfolder.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate hg_subfolder_tool_dependency_0460 with a tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name="hg_tool_dependency_0460",
+            description=bwa_repository_description,
+            long_description=bwa_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate hg_tool_dependency_0460 with a tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        repository = self.get_or_create_repository(
+            name="hg_subfolder_tool_dependency_0460",
+            description=bwa_repository_description,
+            long_description=bwa_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/tool_dependencies_in_subfolder.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate hg_subfolder_tool_dependency_0460 with a tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0040_url_upload_to_complex_test(self):
-        '''Populate complex_dependency_test_4_0460.
+        """Populate complex_dependency_test_4_0460.
 
         This is step 8 - Upload to complex_dependency_test_4_0460 using the url hg://<tool shed url>/repos/user1/hg_tool_dependency_0460.
-        '''
-        url = f'hg://{self.host}:{self.port}/repos/user1/hg_tool_dependency_0460'
-        repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_4_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('package_bwa_0_5_9_0460', common.test_user_1_name)
-        self.upload_url(repository,
-                        url=url,
-                        filepath=None,
-                        valid_tools_only=True,
-                        uncompress_file=False,
-                        remove_repo_files_not_in_tar=True,
-                        commit_message='Uploaded complex repository dependency definition.',
-                        strings_displayed=[],
-                        strings_not_displayed=[])
+        """
+        url = f"hg://{self.host}:{self.port}/repos/user1/hg_tool_dependency_0460"
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "complex_dependency_test_4_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "package_bwa_0_5_9_0460", common.test_user_1_name
+        )
+        self.upload_url(
+            repository,
+            url=url,
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision]
+        strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository,
-                                              filename='tool_dependencies.xml',
-                                              strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="tool_dependencies.xml", strings_displayed=[changeset_revision]
+        )
 
     def test_0045_url_upload_to_complex_test(self):
-        '''Populate complex_dependency_test_4_0460.
+        """Populate complex_dependency_test_4_0460.
 
         This is step 9 - Upload to complex_dependency_test_5_0460 using the url hg://<tool shed url>/repos/user1/hg_subfolder_tool_dependency_0460.
-        '''
-        url = f'hg://{self.host}:{self.port}/repos/user1/hg_subfolder_tool_dependency_0460'
-        repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_5_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('package_bwa_0_5_9_0460', common.test_user_1_name)
-        self.upload_url(repository,
-                        url=url,
-                        filepath=None,
-                        valid_tools_only=True,
-                        uncompress_file=False,
-                        remove_repo_files_not_in_tar=True,
-                        commit_message='Uploaded complex repository dependency definition.',
-                        strings_displayed=[],
-                        strings_not_displayed=[])
+        """
+        url = f"hg://{self.host}:{self.port}/repos/user1/hg_subfolder_tool_dependency_0460"
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "complex_dependency_test_5_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "package_bwa_0_5_9_0460", common.test_user_1_name
+        )
+        self.upload_url(
+            repository,
+            url=url,
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision]
+        strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository,
-                                              filename='tool_dependencies.xml',
-                                              filepath='subfolder',
-                                              strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="tool_dependencies.xml", filepath="subfolder", strings_displayed=[changeset_revision]
+        )
 
     def test_0050_create_repositories_for_simple_dependencies(self):
-        '''Create repositories for testing simple dependency generation.
+        """Create repositories for testing simple dependency generation.
 
         This is step 10 - Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460,
         repository_dependency_test_4_0460, repository_dependency_test_4_0460.. Each of these repositories will be populated in a way
@@ -310,172 +371,220 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         - Upload a repository_dependencies.xml in a subfolder within a tarball.
         - Upload via url, with the repository_dependencies.xml in the root of another repository.
         - Upload via url, with the repository_dependencies.xml in a subfolder within another repository.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository_base_name = 'repository_dependency_test_%d_0460'
-        repository_base_description = 'Test #%d for repository dependency definitions.'
-        repository_base_long_description = 'Test #%d for repository dependency definitions.'
+        repository_base_name = "repository_dependency_test_%d_0460"
+        repository_base_description = "Test #%d for repository dependency definitions."
+        repository_base_long_description = "Test #%d for repository dependency definitions."
         for number in range(1, 6):
-            self.get_or_create_repository(name=repository_base_name % number,
-                                          description=repository_base_description % number,
-                                          long_description=repository_base_long_description % number,
-                                          owner=common.test_user_1_name,
-                                          category_id=self.security.encode_id(category.id),
-                                          strings_displayed=[])
+            self.get_or_create_repository(
+                name=repository_base_name % number,
+                description=repository_base_description % number,
+                long_description=repository_base_long_description % number,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
 
     def test_0055_populate_repository_dependency_test_1_0460(self):
-        '''Populate repository_dependency_test_1_0460.
+        """Populate repository_dependency_test_1_0460.
 
         This is step 11 - Upload an uncompressed repository_dependencies.xml to repository_dependency_test_1_0460 that specifies a
         repository dependency on emboss_datatypes_0460 without a specified changeset revision or tool shed url.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_1_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0460', common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0460_files/repository_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded complex repository dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "repository_dependency_test_1_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "emboss_datatypes_0460", common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/repository_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['emboss_datatypes_0460', 'user1', changeset_revision]
+        strings_displayed = ["emboss_datatypes_0460", "user1", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository, filename='repository_dependencies.xml', strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="repository_dependencies.xml", strings_displayed=[changeset_revision]
+        )
 
     def test_0060_populate_repository_dependency_test_2_0460(self):
-        '''Populate repository_dependency_test_2_0460.
+        """Populate repository_dependency_test_2_0460.
 
         This is step 12 - Upload a tarball to repository_dependency_test_2_0460 with a repository_dependencies.xml in the root of the tarball.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_2_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0460', common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0460_files/repository_dependencies_in_root.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message='Uploaded complex repository dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "repository_dependency_test_2_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "emboss_datatypes_0460", common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/repository_dependencies_in_root.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['emboss_datatypes_0460', 'user1', changeset_revision]
+        strings_displayed = ["emboss_datatypes_0460", "user1", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository, filename='repository_dependencies.xml', strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="repository_dependencies.xml", strings_displayed=[changeset_revision]
+        )
 
     def test_0065_populate_repository_dependency_test_3_0460(self):
-        '''Populate repository_dependency_test_3_0460.
+        """Populate repository_dependency_test_3_0460.
 
         This is step 13 - Upload a tarball to repository_dependency_test_3_0460 with a repository_dependencies.xml in a
         subfolder within the tarball.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_3_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0460', common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0460_files/repository_dependencies_in_subfolder.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message='Uploaded complex repository dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "repository_dependency_test_3_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "emboss_datatypes_0460", common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/repository_dependencies_in_subfolder.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded complex repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['emboss_datatypes_0460', 'user1', changeset_revision]
+        strings_displayed = ["emboss_datatypes_0460", "user1", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository,
-                                              filename='repository_dependencies.xml',
-                                              filepath='subfolder',
-                                              strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository,
+            filename="repository_dependencies.xml",
+            filepath="subfolder",
+            strings_displayed=[changeset_revision],
+        )
 
     def test_0070_create_repositories_for_url_upload(self):
-        '''Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.
+        """Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.
 
         This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate
         with repository dependencies.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name='hg_repository_dependency_0460',
-                                                   description=bwa_repository_description,
-                                                   long_description=bwa_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='0460_files/repository_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate hg_repository_dependency_0460 with a tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        repository = self.get_or_create_repository(name='hg_subfolder_repository_dependency_0460',
-                                                   description=bwa_repository_description,
-                                                   long_description=bwa_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='0460_files/repository_dependencies_in_subfolder.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate hg_subfolder_repository_dependency_0460 with a tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name="hg_repository_dependency_0460",
+            description=bwa_repository_description,
+            long_description=bwa_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/repository_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate hg_repository_dependency_0460 with a tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        repository = self.get_or_create_repository(
+            name="hg_subfolder_repository_dependency_0460",
+            description=bwa_repository_description,
+            long_description=bwa_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="0460_files/repository_dependencies_in_subfolder.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate hg_subfolder_repository_dependency_0460 with a tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0075_url_upload_to_complex_test(self):
-        '''Populate repository_dependency_test_4_0460.
+        """Populate repository_dependency_test_4_0460.
 
         This is step 15 - Upload to repository_dependency_test_4_0460 using the url
         hg://<tool shed url>/repos/user1/hg_repository_dependency_0460.
-        '''
-        url = f'hg://{self.host}:{self.port}/repos/user1/hg_repository_dependency_0460'
-        repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_4_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0460', common.test_user_1_name)
-        self.upload_url(repository,
-                        url=url,
-                        filepath=None,
-                        valid_tools_only=True,
-                        uncompress_file=False,
-                        remove_repo_files_not_in_tar=True,
-                        commit_message='Uploaded repository dependency definition.',
-                        strings_displayed=[],
-                        strings_not_displayed=[])
+        """
+        url = f"hg://{self.host}:{self.port}/repos/user1/hg_repository_dependency_0460"
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "repository_dependency_test_4_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "emboss_datatypes_0460", common.test_user_1_name
+        )
+        self.upload_url(
+            repository,
+            url=url,
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['emboss_datatypes_0460', 'user1', changeset_revision]
+        strings_displayed = ["emboss_datatypes_0460", "user1", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository,
-                                              filename='repository_dependencies.xml',
-                                              strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository, filename="repository_dependencies.xml", strings_displayed=[changeset_revision]
+        )
 
     def test_0080_url_upload_to_complex_test(self):
-        '''Populate repository_dependency_test_4_0460.
+        """Populate repository_dependency_test_4_0460.
 
         This is step 16 - Upload to repository_dependency_test_5_0460 using the url
         hg://<tool shed url>/repos/user1/hg_subfolder_repository_dependency_0460.
-        '''
-        url = f'hg://{self.host}:{self.port}/repos/user1/hg_subfolder_repository_dependency_0460'
-        repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_5_0460', common.test_user_1_name)
-        package_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0460', common.test_user_1_name)
-        self.upload_url(repository,
-                        url=url,
-                        filepath=None,
-                        valid_tools_only=True,
-                        uncompress_file=False,
-                        remove_repo_files_not_in_tar=True,
-                        commit_message='Uploaded repository dependency definition.',
-                        strings_displayed=[],
-                        strings_not_displayed=[])
+        """
+        url = f"hg://{self.host}:{self.port}/repos/user1/hg_subfolder_repository_dependency_0460"
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "repository_dependency_test_5_0460", common.test_user_1_name
+        )
+        package_repository = self.test_db_util.get_repository_by_name_and_owner(
+            "emboss_datatypes_0460", common.test_user_1_name
+        )
+        self.upload_url(
+            repository,
+            url=url,
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded repository dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         changeset_revision = self.get_repository_tip(package_repository)
-        strings_displayed = ['emboss_datatypes_0460', 'user1', changeset_revision]
+        strings_displayed = ["emboss_datatypes_0460", "user1", changeset_revision]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-        self.display_repository_file_contents(repository,
-                                              filename='repository_dependencies.xml',
-                                              filepath='subfolder',
-                                              strings_displayed=[changeset_revision])
+        self.display_repository_file_contents(
+            repository,
+            filename="repository_dependencies.xml",
+            filepath="subfolder",
+            strings_displayed=[changeset_revision],
+        )
diff --git a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
index 8c186cefe93..fce719e6b77 100644
--- a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
+++ b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
@@ -1,25 +1,36 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 0470 Tool dependency repository type'
-category_description = 'Test script 0470 for changing repository types.'
-package_libx11_repository_name = 'package_x11_client_1_5_proto_7_0_0470'
-package_libx11_repository_description = "Contains a tool dependency definition that provides the X11 client libraries and core protocol header files."
-package_libx11_repository_long_description = "Xlib is an X Window System protocol client library written in the C programming language."
-package_emboss_repository_name = 'package_emboss_5_0_0_0470'
-package_emboss_repository_description = "Contains a tool dependency definition that downloads and compiles version 5.0.0 of the EMBOSS tool suite."
+category_name = "Test 0470 Tool dependency repository type"
+category_description = "Test script 0470 for changing repository types."
+package_libx11_repository_name = "package_x11_client_1_5_proto_7_0_0470"
+package_libx11_repository_description = (
+    "Contains a tool dependency definition that provides the X11 client libraries and core protocol header files."
+)
+package_libx11_repository_long_description = (
+    "Xlib is an X Window System protocol client library written in the C programming language."
+)
+package_emboss_repository_name = "package_emboss_5_0_0_0470"
+package_emboss_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 5.0.0 of the EMBOSS tool suite."
+)
 package_emboss_repository_long_description = 'EMBOSS is "The European Molecular Biology Open Software Suite".'
-datatypes_repository_name = 'emboss_datatypes_0470'
-datatypes_repository_description = 'Galaxy applicable data formats used by Emboss tools.'
-datatypes_repository_long_description = 'Galaxy applicable data formats used by Emboss tools.  This repository contains no tools.'
-emboss_repository_name = 'emboss_5_0470'
+datatypes_repository_name = "emboss_datatypes_0470"
+datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
+emboss_repository_name = "emboss_5_0470"
 emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
 emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
 
-'''
+"""
 1. Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml.
    Keep the repository type as the default "Unrestricted".
 
@@ -48,208 +59,258 @@ emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 t
 9. Reset metadata on the package_emboss_5_0_0 repository. It should now have only its tip as the installable revision.
 
 10. Reset metadata on the emboss_5 repository. It should now have only its tip as the installable revision.
-'''
+"""
 
 
 class TestEnvironmentInheritance(ShedTwillTestCase):
-    '''Test referencing environment variables that were defined in a separate tool dependency.'''
+    """Test referencing environment variables that were defined in a separate tool dependency."""
 
     def test_0000_initiate_users_and_category(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
 
     def test_0005_create_libx11_repository(self):
-        '''Create and populate package_x11_client_1_5_proto_7_0_0470.
+        """Create and populate package_x11_client_1_5_proto_7_0_0470.
 
         This is step 1 - Create and populate a repository named package_x11_client_1_5_proto_7_0.
 
         Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml.
         Keep the repository type as the default "Unrestricted".
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_libx11_repository_name,
-                                                   description=package_libx11_repository_description,
-                                                   long_description=package_libx11_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_libx11_repository_name,
+            description=package_libx11_repository_description,
+            long_description=package_libx11_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
-        self.upload_file(repository,
-                         filename='emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_emboss_5_0_0_repository(self):
-        '''Create and populate package_emboss_5_0_0_0470.
+        """Create and populate package_emboss_5_0_0_0470.
 
         This is step 2 - Create a repository named package_emboss_5_0_0 of type "Unrestricted".
 
         Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the
         above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision
         defined so it will get automatically populated.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_emboss_repository_name,
-                                                   description=package_emboss_repository_description,
-                                                   long_description=package_emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_emboss_repository_name,
+            description=package_emboss_repository_description,
+            long_description=package_emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository.
-        self.upload_file(repository,
-                         filename='emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_emboss_5_0_0_0470 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_emboss_5_repository(self):
-        '''Create and populate emboss_5_0470.
+        """Create and populate emboss_5_0470.
 
         This is step 3 - Create a repository named emboss_5 of type "Unrestricted".
 
         Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency
         on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined
         so it will get automatically populated.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Populate emboss_5 with tool and dependency definitions.
-        self.upload_file(repository,
-                         filename='emboss/0470_files/emboss_complex_dependency.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate emboss_5 with tool and dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="emboss/0470_files/emboss_complex_dependency.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate emboss_5 with tool and dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_upload_updated_tool_dependency_to_package_x11(self):
-        '''Upload a new tool_dependencies.xml to package_x11_client_1_5_proto_7_0_0470.
+        """Upload a new tool_dependencies.xml to package_x11_client_1_5_proto_7_0_0470.
 
         This is step 4 - Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating
         a new installable changeset revision at the repository tip.
-        '''
-        package_x11_repository = self.test_db_util.get_repository_by_name_and_owner(package_libx11_repository_name, common.test_user_1_name)
+        """
+        package_x11_repository = self.test_db_util.get_repository_by_name_and_owner(
+            package_libx11_repository_name, common.test_user_1_name
+        )
         # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
-        self.upload_file(package_x11_repository,
-                         filename='emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        assert len(package_x11_repository.metadata_revisions) == 1, \
-            'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found %d' % \
-            len(package_x11_repository.metadata_revisions)
+        self.upload_file(
+            package_x11_repository,
+            filename="emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        assert len(package_x11_repository.metadata_revisions) == 1, (
+            "package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found %d"
+            % len(package_x11_repository.metadata_revisions)
+        )
 
     def test_0025_upload_updated_tool_dependency_to_package_emboss(self):
-        '''Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.
+        """Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.
 
         This is step 5 - Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating
         the change set_revision attribute so that it gets automatically populated when uploaded. After uploading the file,
         the package_emboss_5_0_0 repository should have 2 installable changeset revisions.
-        '''
-        package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner(package_emboss_repository_name, common.test_user_1_name)
+        """
+        package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            package_emboss_repository_name, common.test_user_1_name
+        )
         # Populate package_emboss_5_0_0_0470 with updated tool dependency definition.
-        self.upload_file(package_emboss_repository,
-                         filename='emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        assert len(package_emboss_repository.metadata_revisions) == 2, \
-            'package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found %d' % \
-            len(package_emboss_repository.metadata_revisions)
+        self.upload_file(
+            package_emboss_repository,
+            filename="emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_emboss_5_0_0_0470 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        assert (
+            len(package_emboss_repository.metadata_revisions) == 2
+        ), "package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found %d" % len(
+            package_emboss_repository.metadata_revisions
+        )
 
     def test_0030_upload_updated_tool_dependency_to_emboss_5_repository(self):
-        '''Upload a new tool_dependencies.xml to emboss_5_0470.
+        """Upload a new tool_dependencies.xml to emboss_5_0470.
 
         This is step 6 - Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the
         changeset_revision attribute so that it gets automatically populated when uploaded. After uploading the file,
         the emboss5 repository should have 2 installable metadata revisions.
-        '''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+        """
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         # Populate package_emboss_5_0_0_0470 with updated tool dependency definition.
-        self.upload_file(emboss_repository,
-                         filename='emboss/0470_files/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Upload updated complex repository dependency definition to emboss_5_0470.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        assert len(emboss_repository.metadata_revisions) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions'
+        self.upload_file(
+            emboss_repository,
+            filename="emboss/0470_files/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Upload updated complex repository dependency definition to emboss_5_0470.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        assert (
+            len(emboss_repository.metadata_revisions) == 2
+        ), "package_emboss_5_0_0_0470 has incorrect number of metadata revisions"
 
     def test_0035_modify_package_x11_repository_type(self):
-        '''Set package_x11_client_1_5_proto_7_0 type tool_dependency_definition.
+        """Set package_x11_client_1_5_proto_7_0 type tool_dependency_definition.
 
         This is step 7 - Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition.
-        '''
-        package_x11_repository = self.test_db_util.get_repository_by_name_and_owner(package_libx11_repository_name, common.test_user_1_name)
-        self.edit_repository_information(package_x11_repository, repository_type='tool_dependency_definition')
+        """
+        package_x11_repository = self.test_db_util.get_repository_by_name_and_owner(
+            package_libx11_repository_name, common.test_user_1_name
+        )
+        self.edit_repository_information(package_x11_repository, repository_type="tool_dependency_definition")
 
     def test_0040_modify_package_emboss_repository_type(self):
-        '''Set package_emboss_5_0_0 to type tool_dependency_definition.
+        """Set package_emboss_5_0_0 to type tool_dependency_definition.
 
         This is step 8 - Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition.
-        '''
-        package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner(package_emboss_repository_name, common.test_user_1_name)
-        self.edit_repository_information(package_emboss_repository, repository_type='tool_dependency_definition')
+        """
+        package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            package_emboss_repository_name, common.test_user_1_name
+        )
+        self.edit_repository_information(package_emboss_repository, repository_type="tool_dependency_definition")
 
     def test_0045_reset_repository_metadata(self):
-        '''Reset metadata on package_emboss_5_0_0_0470 and package_x11_client_1_5_proto_7_0.
+        """Reset metadata on package_emboss_5_0_0_0470 and package_x11_client_1_5_proto_7_0.
 
         This is step 9 - Reset metadata on the package_emboss_5_0_0 and package_x11_client_1_5_proto_7_0 repositories. They should
         now have only their tip as the installable revision.
-        '''
-        package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner(package_emboss_repository_name, common.test_user_1_name)
-        package_x11_repository = self.test_db_util.get_repository_by_name_and_owner(package_libx11_repository_name, common.test_user_1_name)
+        """
+        package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            package_emboss_repository_name, common.test_user_1_name
+        )
+        package_x11_repository = self.test_db_util.get_repository_by_name_and_owner(
+            package_libx11_repository_name, common.test_user_1_name
+        )
         self.reset_repository_metadata(package_emboss_repository)
         self.reset_repository_metadata(package_x11_repository)
-        assert len(package_emboss_repository.metadata_revisions) == 1, 'Repository package_emboss_5_0_0 has %d installable revisions, expected 1.' % \
-            len(package_emboss_repository.metadata_revisions)
-        assert len(package_x11_repository.metadata_revisions) == 1, 'Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1.' % \
-            len(package_x11_repository.metadata_revisions)
+        assert (
+            len(package_emboss_repository.metadata_revisions) == 1
+        ), "Repository package_emboss_5_0_0 has %d installable revisions, expected 1." % len(
+            package_emboss_repository.metadata_revisions
+        )
+        assert (
+            len(package_x11_repository.metadata_revisions) == 1
+        ), "Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1." % len(
+            package_x11_repository.metadata_revisions
+        )
 
     def test_0050_reset_emboss_5_metadata(self):
-        '''Reset metadata on emboss_5.
+        """Reset metadata on emboss_5.
 
         This is step 10 - Reset metadata on the emboss_5 repository. It should now have only its tip as the installable revision.
-        '''
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+        """
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.reset_repository_metadata(emboss_repository)
-        assert len(emboss_repository.metadata_revisions) == 1, 'Repository emboss_5 has %d installable revisions, expected 1.' % \
-            len(emboss_repository.metadata_revisions)
+        assert (
+            len(emboss_repository.metadata_revisions) == 1
+        ), "Repository emboss_5 has %d installable revisions, expected 1." % len(emboss_repository.metadata_revisions)
diff --git a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
index ea501c645b8..b51e1944efc 100644
--- a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
+++ b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
@@ -1,71 +1,84 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 0480 Tool dependency definition validation'
-category_description = 'Test script 0480 for validating tool dependency definitions.'
-repository_name = 'package_invalid_tool_dependency_xml_1_0_0'
+category_name = "Test 0480 Tool dependency definition validation"
+category_description = "Test script 0480 for validating tool dependency definitions."
+repository_name = "package_invalid_tool_dependency_xml_1_0_0"
 repository_description = "Contains a tool dependency definition that should return an error."
 repository_long_description = "This repository is in the test suite 0480"
 
-'''
+"""
 
 1. Create a repository package_invalid_tool_dependency_xml_1_0_0
 2. Upload a tool_dependencies.xml file to the repository with no <actions> tags around the <action> tags.
 3. Verify error message is displayed.
 
-'''
+"""
 
 
 class TestDependencyDefinitionValidation(ShedTwillTestCase):
-    '''Test the tool shed's tool dependency XML validation.'''
+    """Test the tool shed's tool dependency XML validation."""
 
     def test_0000_initiate_users_and_category(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
 
     def test_0005_create_tool_dependency_repository(self):
-        '''Create and populate package_invalid_tool_dependency_xml_1_0_0.
+        """Create and populate package_invalid_tool_dependency_xml_1_0_0.
 
         This is step 1 - Create a repository package_invalid_tool_dependency_xml_1_0_0.
 
         Create a repository named package_invalid_tool_dependency_xml_1_0_0 that will contain only a single file named tool_dependencies.xml.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='0480_files/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=False,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_invalid_tool_dependency_xml_1_0_0 with an improperly defined tool dependency.',
-                         strings_displayed=['package cannot be installed because', 'missing either an &lt;actions&gt; tag set'],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="0480_files/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=False,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_invalid_tool_dependency_xml_1_0_0 with an improperly defined tool dependency.",
+            strings_displayed=["package cannot be installed because", "missing either an &lt;actions&gt; tag set"],
+            strings_not_displayed=[],
+        )
 
     def test_0010_populate_tool_dependency_repository(self):
-        '''Verify package_invalid_tool_dependency_xml_1_0_0.
+        """Verify package_invalid_tool_dependency_xml_1_0_0.
 
         This is step 3 - Verify repository. The uploaded tool dependency XML should not have resulted in a new changeset.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        assert self.repository_is_new(repository), 'Uploading an incorrectly defined tool_dependencies.xml resulted in a changeset being generated.'
+        assert self.repository_is_new(
+            repository
+        ), "Uploading an incorrectly defined tool_dependencies.xml resulted in a changeset being generated."
diff --git a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
index d02ced0ad23..a19b6f77b77 100644
--- a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
+++ b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
@@ -1,16 +1,19 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'filtering_0530'
-repository_description = 'Filtering repository for test 0530'
-repository_long_description = 'This is the filtering repository for test 0530.'
-category_name = 'Test 0530 Repository Admin Role'
-category_description = 'Verify the functionality of the code that handles the repository admin role.'
+repository_name = "filtering_0530"
+repository_description = "Filtering repository for test 0530"
+repository_long_description = "This is the filtering repository for test 0530."
+category_name = "Test 0530 Repository Admin Role"
+category_description = "Verify the functionality of the code that handles the repository admin role."
 
-'''
+"""
 1. Create new repository as user user1.
 
 2. Check to make sure a new role was created named <repo_name>_user1_admin.
@@ -27,25 +30,29 @@ category_description = 'Verify the functionality of the code that handles the re
 7. As user user1, add user user2 as a repository admin user.
 
 8. Log into the Tool Shed as user user2 and make sure the repository name and description can now be changed.
-'''
+"""
 
 
 class TestRepositoryAdminRole(ShedTwillTestCase):
-    '''Verify that the code correctly handles the repository admin role.'''
+    """Verify that the code correctly handles the repository admin role."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_filtering_repository(self):
@@ -55,91 +62,105 @@ class TestRepositoryAdminRole(ShedTwillTestCase):
         """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_verify_repository_admin_role_exists(self):
-        '''Verify that the role filtering_0530_user1_admin exists.
+        """Verify that the role filtering_0530_user1_admin exists.
 
         This is step 2 - Check to make sure a new role was created named filtering_0530_user1_admin.
-        '''
+        """
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        repository_admin_role = self.test_db_util.get_role(test_user_1, 'filtering_0530_user1_admin')
-        assert repository_admin_role is not None, 'Admin role for filtering_0530 was not created.'
+        repository_admin_role = self.test_db_util.get_role(test_user_1, "filtering_0530_user1_admin")
+        assert repository_admin_role is not None, "Admin role for filtering_0530 was not created."
 
     def test_0015_verify_repository_role_association(self):
-        '''Verify that the filtering_0530_user1_admin role is associated with the filtering_0530 repository.
+        """Verify that the filtering_0530_user1_admin role is associated with the filtering_0530 repository.
 
         This is step 3 - Check to make sure a new repository_role_association record was created with appropriate repository id and role id.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        repository_admin_role = self.test_db_util.get_role(test_user_1, 'filtering_0530_user1_admin')
-        repository_role_association = self.test_db_util.get_repository_role_association(repository.id, repository_admin_role.id)
-        assert repository_role_association is not None, 'Repository filtering_0530 is not associated with the filtering_0530_user1_admin role.'
+        repository_admin_role = self.test_db_util.get_role(test_user_1, "filtering_0530_user1_admin")
+        repository_role_association = self.test_db_util.get_repository_role_association(
+            repository.id, repository_admin_role.id
+        )
+        assert (
+            repository_role_association is not None
+        ), "Repository filtering_0530 is not associated with the filtering_0530_user1_admin role."
 
     def test_0020_rename_repository(self):
-        '''Rename the repository to renamed_filtering_0530.
+        """Rename the repository to renamed_filtering_0530.
 
         This is step 4 - Change the name of the repository created in step 1 - this can be done as long as the repository has not
         been installed or cloned.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.edit_repository_information(repository, revert=False, repo_name='renamed_filtering_0530')
+        self.edit_repository_information(repository, revert=False, repo_name="renamed_filtering_0530")
         self.test_db_util.refresh(repository)
-        assert repository.name == 'renamed_filtering_0530', 'Repository was not renamed to renamed_filtering_0530.'
+        assert repository.name == "renamed_filtering_0530", "Repository was not renamed to renamed_filtering_0530."
 
     def test_0030_verify_access_denied(self):
-        '''Make sure a non-admin user can't modify the repository.
+        """Make sure a non-admin user can't modify the repository.
 
         This is step 6 - Log into the Tool Shed as a user that is not the repository owner (e.g., user2) and make sure the repository
         name and description cannot be changed.
-        '''
+        """
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
-        repository = self.test_db_util.get_repository_by_name_and_owner('renamed_filtering_0530', common.test_user_1_name)
-        strings_not_displayed = ['Manage repository']
-        strings_displayed = ['View repository']
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "renamed_filtering_0530", common.test_user_1_name
+        )
+        strings_not_displayed = ["Manage repository"]
+        strings_displayed = ["View repository"]
         self.display_manage_repository_page(repository, strings_not_displayed=strings_not_displayed)
-        self.submit_form(form_no=0, button='edit_repository_button', description='This description has been modified.')
-        strings_displayed = ['You are not the owner of this repository, so you cannot administer it.']
-        strings_not_displayed = ['The repository information has been updated.']
+        self.submit_form(form_no=0, button="edit_repository_button", description="This description has been modified.")
+        strings_displayed = ["You are not the owner of this repository, so you cannot administer it."]
+        strings_not_displayed = ["The repository information has been updated."]
         self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
 
     def test_0035_grant_admin_role(self):
-        '''Grant the repository admin role to user2.
+        """Grant the repository admin role to user2.
 
         This is step 7 - As user user1, add user user2 as a repository admin user.
-        '''
+        """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        repository = self.test_db_util.get_repository_by_name_and_owner('renamed_filtering_0530', common.test_user_1_name)
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "renamed_filtering_0530", common.test_user_1_name
+        )
         self.assign_admin_role(repository, test_user_2)
 
     def test_0040_rename_repository_as_repository_admin(self):
-        '''Rename the repository as user2.
+        """Rename the repository as user2.
 
         This is step 8 - Log into the Tool Shed as user user2 and make sure the repository name and description can now be changed.
-        '''
+        """
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
-        repository = self.test_db_util.get_repository_by_name_and_owner('renamed_filtering_0530', common.test_user_1_name)
-        self.edit_repository_information(repository, revert=False, repo_name='filtering_0530')
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            "renamed_filtering_0530", common.test_user_1_name
+        )
+        self.edit_repository_information(repository, revert=False, repo_name="filtering_0530")
         self.test_db_util.refresh(repository)
-        assert repository.name == 'filtering_0530', 'User with admin role failed to rename repository.'
+        assert repository.name == "filtering_0530", "User with admin role failed to rename repository."
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        old_repository_admin_role = self.test_db_util.get_role(test_user_1, 'renamed_filtering_0530_user1_admin')
-        assert old_repository_admin_role is None, 'Admin role renamed_filtering_0530_user1_admin incorrectly exists.'
-        new_repository_admin_role = self.test_db_util.get_role(test_user_1, 'filtering_0530_user1_admin')
-        assert new_repository_admin_role is not None, 'Admin role filtering_0530_user1_admin does not exist.'
+        old_repository_admin_role = self.test_db_util.get_role(test_user_1, "renamed_filtering_0530_user1_admin")
+        assert old_repository_admin_role is None, "Admin role renamed_filtering_0530_user1_admin incorrectly exists."
+        new_repository_admin_role = self.test_db_util.get_role(test_user_1, "filtering_0530_user1_admin")
+        assert new_repository_admin_role is not None, "Admin role filtering_0530_user1_admin does not exist."
diff --git a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
index ac11d04af23..78578ca186e 100644
--- a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
+++ b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
@@ -1,23 +1,34 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repositories = dict(column=dict(name='column_maker_0540',
-                                description='Description for column_maker_0540',
-                                long_description='Long description for column_maker_0540'),
-                    convert=dict(name='convert_chars_0540',
-                                 description='Description for convert_chars_0540',
-                                 long_description='Long description for convert_chars_0540'),
-                    bwa=dict(name='package_bwa_0_5_9_0540',
-                             description='Description for package_bwa_0_5_9_0540',
-                             long_description='Long description for package_bwa_0_5_9_0540'))
+repositories = dict(
+    column=dict(
+        name="column_maker_0540",
+        description="Description for column_maker_0540",
+        long_description="Long description for column_maker_0540",
+    ),
+    convert=dict(
+        name="convert_chars_0540",
+        description="Description for convert_chars_0540",
+        long_description="Long description for convert_chars_0540",
+    ),
+    bwa=dict(
+        name="package_bwa_0_5_9_0540",
+        description="Description for package_bwa_0_5_9_0540",
+        long_description="Long description for package_bwa_0_5_9_0540",
+    ),
+)
 
-category_name = 'Test 0540'
-category_description = 'Verify API endpoint to retrieve all metadata'
+category_name = "Test 0540"
+category_description = "Verify API endpoint to retrieve all metadata"
 
-'''
+"""
 1. Create repository column_maker_0540 as user user1.
 
 2. Create repository convert_chars_0540 with dependency on column_maker_0540.
@@ -27,121 +38,145 @@ category_description = 'Verify API endpoint to retrieve all metadata'
 4. Create dependency on package_bwa_0_5_9_0540 for convert_chars_0540.
 
 5. Load /api/repositories/convert_chars_0540.id/metadata and verify contents.
-'''
+"""
 
 
 class TestGetAllMetadata(ShedTwillTestCase):
-    '''Verify that the code correctly handles the repository admin role.'''
+    """Verify that the code correctly handles the repository admin role."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_bwa_package_repository(self):
-        '''Create and populate package_bwa_0_5_9_0540.'''
+        """Create and populate package_bwa_0_5_9_0540."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named package_bwa_0_5_9_0100 owned by user1.
-        repository = self.get_or_create_repository(name=repositories['bwa']['name'],
-                                                   description=repositories['bwa']['description'],
-                                                   long_description=repositories['bwa']['long_description'],
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repositories["bwa"]["name"],
+            description=repositories["bwa"]["description"],
+            long_description=repositories["bwa"]["long_description"],
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         assert repository is not None, f"Error creating repository {repositories['bwa']['name']}"
-        self.upload_file(repository,
-                         filename='0540_files/package_bwa/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded tool_dependencies.xml.',
-                         strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="0540_files/package_bwa/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded tool_dependencies.xml.",
+            strings_displayed=["This repository currently contains a single file named <b>tool_dependencies.xml</b>"],
+            strings_not_displayed=[],
+        )
         # Visit the manage repository page for package_bwa_0_5_9_0100.
-        self.display_manage_repository_page(repository, strings_displayed=['Tool dependencies', 'will not be', 'to this repository'])
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"]
+        )
 
     def test_0010_create_convert_repository(self):
-        '''Create the convert_chars_0540 repository.'''
+        """Create the convert_chars_0540 repository."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=repositories['convert']['name'],
-                                                   description=repositories['convert']['description'],
-                                                   long_description=repositories['convert']['long_description'],
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repositories["convert"]["name"],
+            description=repositories["convert"]["description"],
+            long_description=repositories["convert"]["long_description"],
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         assert repository is not None, f"Error creating repository {repositories['convert']['name']}"
-        self.upload_file(repository,
-                         filename='0540_files/convert_chars/convert_chars.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column maker 1.0.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="0540_files/convert_chars/convert_chars.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column maker 1.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         # Add a dependency on BWA.
-        self.upload_file(repository,
-                         filename='0540_files/convert_chars/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column maker 1.0.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="0540_files/convert_chars/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column maker 1.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
         # Visit the manage repository page for convert_chars_0540.
-        self.display_manage_repository_page(repository, strings_displayed=[repositories['bwa']['name']])
+        self.display_manage_repository_page(repository, strings_displayed=[repositories["bwa"]["name"]])
 
     def test_0015_create_column_repository(self):
-        '''Create the column_maker_0540 repository.'''
+        """Create the column_maker_0540 repository."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=repositories['column']['name'],
-                                                   description=repositories['column']['description'],
-                                                   long_description=repositories['column']['long_description'],
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repositories["column"]["name"],
+            description=repositories["column"]["description"],
+            long_description=repositories["column"]["long_description"],
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         assert repository is not None, f"Error creating repository {repositories['column']['name']}"
-        self.upload_file(repository,
-                         filename='0540_files/column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column maker 1.0.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="0540_files/column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column maker 1.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_repository_dependency(self):
-        '''Make column_maker depend on convert_chars.'''
-        repository = self.test_db_util.get_repository_by_name_and_owner(repositories['column']['name'],
-                                                                        common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='0540_files/column_maker/repository_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded column maker 2.0.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        """Make column_maker depend on convert_chars."""
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["column"]["name"], common.test_user_1_name
+        )
+        self.upload_file(
+            repository,
+            filename="0540_files/column_maker/repository_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded column maker 2.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_verify_dependency_json(self):
-        '''
+        """
         Load the API endpoint to retrieve all repository metadata and verify
         that all three repository names are displayed.
-        '''
-        repository = self.test_db_util.get_repository_by_name_and_owner(repositories['column']['name'],
-                                                                        common.test_user_1_name)
-        strings_displayed = [repositories['column']['name'],
-                             repositories['convert']['name'],
-                             repositories['bwa']['name']]
+        """
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["column"]["name"], common.test_user_1_name
+        )
+        strings_displayed = [
+            repositories["column"]["name"],
+            repositories["convert"]["name"],
+            repositories["bwa"]["name"],
+        ]
         self.fetch_repository_metadata(repository, strings_displayed=strings_displayed, strings_not_displayed=None)
diff --git a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
index 1c19427eb61..62481139eed 100644
--- a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
@@ -1,23 +1,34 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repositories = dict(freebayes=dict(name='package_freebayes_0550',
-                                   description='Description for package_freebayes_0550',
-                                   long_description='Long description for package_freebayes_0550'),
-                    samtools=dict(name='package_samtools_0550',
-                                  description='Description for package_samtools_0550',
-                                  long_description='Long description for package_samtools_0550'),
-                    filtering=dict(name='filtering_0550',
-                                   description='Description for filtering_0550',
-                                   long_description='Long description for filtering_0550'))
+repositories = dict(
+    freebayes=dict(
+        name="package_freebayes_0550",
+        description="Description for package_freebayes_0550",
+        long_description="Long description for package_freebayes_0550",
+    ),
+    samtools=dict(
+        name="package_samtools_0550",
+        description="Description for package_samtools_0550",
+        long_description="Long description for package_samtools_0550",
+    ),
+    filtering=dict(
+        name="filtering_0550",
+        description="Description for filtering_0550",
+        long_description="Long description for filtering_0550",
+    ),
+)
 
-category_name = 'Test 0550'
-category_description = 'Verify metadata updates'
+category_name = "Test 0550"
+category_description = "Verify metadata updates"
 
-'''
+"""
 1. Create repository package_freebayes_0550.
 
 2. Create repository package_samtools_0550.
@@ -31,127 +42,155 @@ category_description = 'Verify metadata updates'
 6. Update package_freebayes_0550 and package_samtools_0550.
 
 5. Load /api/repositories/{filtering_0550}.id/metadata and verify contents.
-'''
+"""
 
 
 class TestGetUpdatedMetadata(ShedTwillTestCase):
-    '''Verify that updated repositories still have correct dependency links.'''
+    """Verify that updated repositories still have correct dependency links."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_freebayes_repository(self):
-        '''Create and populate package_freebayes_0550.'''
+        """Create and populate package_freebayes_0550."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named package_freebayes_0550 owned by user1.
-        freebayes = self.get_or_create_repository(name=repositories['freebayes']['name'],
-                                                  description=repositories['freebayes']['description'],
-                                                  long_description=repositories['freebayes']['long_description'],
-                                                  owner=common.test_user_1_name,
-                                                  category_id=self.security.encode_id(category.id),
-                                                  strings_displayed=[])
+        freebayes = self.get_or_create_repository(
+            name=repositories["freebayes"]["name"],
+            description=repositories["freebayes"]["description"],
+            long_description=repositories["freebayes"]["long_description"],
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         assert freebayes is not None, f"Error creating freebayes {repositories['freebayes']['name']}"
-        self.upload_file(freebayes,
-                         filename='0550_files/package_freebayes_1_0550.tgz',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded.',
-                         strings_displayed=['has been successfully uploaded to the repository', 'contains a single file'],
-                         strings_not_displayed=None)
+        self.upload_file(
+            freebayes,
+            filename="0550_files/package_freebayes_1_0550.tgz",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded.",
+            strings_displayed=["has been successfully uploaded to the repository", "contains a single file"],
+            strings_not_displayed=None,
+        )
         # Visit the manage repository page for package_freebayes_0_5_9_0100.
-        self.display_manage_repository_page(freebayes, strings_displayed=['Tool dependencies', 'will not be', 'to this repository'])
+        self.display_manage_repository_page(
+            freebayes, strings_displayed=["Tool dependencies", "will not be", "to this repository"]
+        )
 
     def test_0010_create_samtools_repository(self):
-        '''Create and populate the package_samtools_0550 repository.'''
+        """Create and populate the package_samtools_0550 repository."""
         category = self.create_category(name=category_name, description=category_description)
-        samtools = self.get_or_create_repository(name=repositories['samtools']['name'],
-                                                 description=repositories['samtools']['description'],
-                                                 long_description=repositories['samtools']['long_description'],
-                                                 owner=common.test_user_1_name,
-                                                 category_id=self.security.encode_id(category.id),
-                                                 strings_displayed=[])
+        samtools = self.get_or_create_repository(
+            name=repositories["samtools"]["name"],
+            description=repositories["samtools"]["description"],
+            long_description=repositories["samtools"]["long_description"],
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         assert samtools is not None, f"Error creating samtools {repositories['samtools']['name']}"
-        self.upload_file(samtools,
-                         filename='0550_files/package_samtools_1_0550.tgz',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded samtools 1.0.',
-                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
-                         strings_not_displayed=[])
+        self.upload_file(
+            samtools,
+            filename="0550_files/package_samtools_1_0550.tgz",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded samtools 1.0.",
+            strings_displayed=["has been successfully uncompressed and uploaded to the repository"],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_filtering_repository(self):
-        '''Create the filtering_0550 repository.'''
+        """Create the filtering_0550 repository."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=repositories['filtering']['name'],
-                                                   description=repositories['filtering']['description'],
-                                                   long_description=repositories['filtering']['long_description'],
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repositories["filtering"]["name"],
+            description=repositories["filtering"]["description"],
+            long_description=repositories["filtering"]["long_description"],
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         assert repository is not None, f"Error creating repository {repositories['filtering']['name']}"
-        self.upload_file(repository,
-                         filename='0550_files/filtering_1.0.tgz',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.0.',
-                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="0550_files/filtering_1.0.tgz",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.0.",
+            strings_displayed=["has been successfully uncompressed and uploaded to the repository"],
+            strings_not_displayed=[],
+        )
 
     def test_0020_check_repository_dependency(self):
-        '''Make filtering depend on samtools and freebayes.'''
-        freebayes = self.test_db_util.get_repository_by_name_and_owner(repositories['freebayes']['name'],
-                                                                     common.test_user_1_name)
-        samtools = self.test_db_util.get_repository_by_name_and_owner(repositories['samtools']['name'],
-                                                                      common.test_user_1_name)
-        filtering = self.test_db_util.get_repository_by_name_and_owner(repositories['filtering']['name'],
-                                                                       common.test_user_1_name)
+        """Make filtering depend on samtools and freebayes."""
+        freebayes = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["freebayes"]["name"], common.test_user_1_name
+        )
+        samtools = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["samtools"]["name"], common.test_user_1_name
+        )
+        filtering = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["filtering"]["name"], common.test_user_1_name
+        )
         strings_displayed = [self.security.encode_id(freebayes.id), self.security.encode_id(samtools.id)]
         self.display_manage_repository_page(filtering, strings_displayed=strings_displayed)
 
     def test_0025_update_dependent_repositories(self):
-        '''
+        """
         Update freebayes and samtools, load the API endpoint again.
-        '''
-        freebayes = self.test_db_util.get_repository_by_name_and_owner(repositories['freebayes']['name'],
-                                                                     common.test_user_1_name)
-        samtools = self.test_db_util.get_repository_by_name_and_owner(repositories['samtools']['name'],
-                                                                      common.test_user_1_name)
-        filtering = self.test_db_util.get_repository_by_name_and_owner(repositories['filtering']['name'],
-                                                                       common.test_user_1_name)
-        self.upload_file(freebayes,
-                         filename='0550_files/package_freebayes_2_0550.tgz',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded freebayes 2.0.',
-                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
-                         strings_not_displayed=[])
-        self.upload_file(samtools,
-                         filename='0550_files/package_samtools_2_0550.tgz',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded samtools 2.0.',
-                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
-                         strings_not_displayed=[])
-        strings_displayed = [repositories['freebayes']['name'],
-                             repositories['samtools']['name'],
-                             repositories['filtering']['name']]
+        """
+        freebayes = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["freebayes"]["name"], common.test_user_1_name
+        )
+        samtools = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["samtools"]["name"], common.test_user_1_name
+        )
+        filtering = self.test_db_util.get_repository_by_name_and_owner(
+            repositories["filtering"]["name"], common.test_user_1_name
+        )
+        self.upload_file(
+            freebayes,
+            filename="0550_files/package_freebayes_2_0550.tgz",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded freebayes 2.0.",
+            strings_displayed=["has been successfully uncompressed and uploaded to the repository"],
+            strings_not_displayed=[],
+        )
+        self.upload_file(
+            samtools,
+            filename="0550_files/package_samtools_2_0550.tgz",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded samtools 2.0.",
+            strings_displayed=["has been successfully uncompressed and uploaded to the repository"],
+            strings_not_displayed=[],
+        )
+        strings_displayed = [
+            repositories["freebayes"]["name"],
+            repositories["samtools"]["name"],
+            repositories["filtering"]["name"],
+        ]
         self.fetch_repository_metadata(filtering, strings_displayed=strings_displayed, strings_not_displayed=None)
diff --git a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py
index 030ca40f332..38bc1a6268e 100644
--- a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py
+++ b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py
@@ -1,121 +1,161 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 
 class BasicToolShedFeatures(ShedTwillTestCase):
-    '''Test installing a basic repository.'''
+    """Test installing a basic repository."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0000 category and upload the filtering repository to it, if necessary.'''
+        """Create the 0000 category and upload the filtering repository to it, if necessary."""
         self.login(email=common.admin_email, username=common.admin_username)
-        category = self.create_category(name='Test 0000 Basic Repository Features 2', description='Test Description 0000 Basic Repository Features 2')
-        category = self.create_category(name='Test 0000 Basic Repository Features 1', description='Test Description 0000 Basic Repository Features 1')
+        category = self.create_category(
+            name="Test 0000 Basic Repository Features 2",
+            description="Test Description 0000 Basic Repository Features 2",
+        )
+        category = self.create_category(
+            name="Test 0000 Basic Repository Features 1",
+            description="Test Description 0000 Basic Repository Features 1",
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name='filtering_0000',
-                                                   description="Galaxy's filtering tool",
-                                                   long_description="Long description of Galaxy's filtering tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
+        repository = self.get_or_create_repository(
+            name="filtering_0000",
+            description="Galaxy's filtering tool",
+            long_description="Long description of Galaxy's filtering tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_0000.txt',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded readme for 1.1.0',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_2.2.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 2.2.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='readme.txt',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded readme for 2.2.0',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_0000.txt",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded readme for 1.1.0",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_2.2.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 2.2.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="readme.txt",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded readme for 2.2.0",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_browse_tool_sheds(self):
         """Browse the available tool sheds in this Galaxy instance."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.browse_tool_shed(url=self.url, strings_displayed=['Test 0000 Basic Repository Features 1', 'Test 0000 Basic Repository Features 2'])
+        self.browse_tool_shed(
+            url=self.url,
+            strings_displayed=["Test 0000 Basic Repository Features 1", "Test 0000 Basic Repository Features 2"],
+        )
 
     def test_0015_browse_test_0000_category(self):
-        '''Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test.'''
-        category = self.test_db_util.get_category_by_name('Test 0000 Basic Repository Features 1')
-        self.browse_category(category, strings_displayed=['filtering_0000'])
+        """Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test."""
+        category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
+        self.browse_category(category, strings_displayed=["filtering_0000"])
 
     def test_0020_preview_filtering_repository(self):
-        '''Load the preview page for the filtering_0000 repository in the tool shed.'''
-        self.preview_repository_in_tool_shed('filtering_0000', common.test_user_1_name, strings_displayed=['filtering_0000', 'Valid tools'])
+        """Load the preview page for the filtering_0000 repository in the tool shed."""
+        self.preview_repository_in_tool_shed(
+            "filtering_0000", common.test_user_1_name, strings_displayed=["filtering_0000", "Valid tools"]
+        )
 
     def test_0025_install_filtering_repository(self):
-        self.install_repository('filtering_0000',
-                                common.test_user_1_name,
-                                'Test 0000 Basic Repository Features 1',
-                                new_tool_panel_section_label='test_1000')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
-        strings_displayed = ['filtering_0000',
-                             "Galaxy's filtering tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             str(installed_repository.installed_changeset_revision)]
+        self.install_repository(
+            "filtering_0000",
+            common.test_user_1_name,
+            "Test 0000 Basic Repository Features 1",
+            new_tool_panel_section_label="test_1000",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
+        strings_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool",
+            "user1",
+            self.url.replace("http://", ""),
+            str(installed_repository.installed_changeset_revision),
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'Filter1'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "Filter1"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0030_install_filtering_repository_again(self):
-        '''Attempt to install the already installed filtering repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
+        """Attempt to install the already installed filtering repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
         # The page displayed after installation is the ajaxian "Montior installing tool shed repositories" page.  Since the filter
         # repository was already installed, nothing will be in the process of being installed, so the grid will not display 'filtering_0000'.
-        post_submit_strings_not_displayed = ['filtering_0000']
-        self.install_repository('filtering_0000',
-                                common.test_user_1_name,
-                                'Test 0000 Basic Repository Features 1',
-                                post_submit_strings_not_displayed=post_submit_strings_not_displayed)
-        strings_displayed = ['filtering_0000',
-                             "Galaxy's filtering tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             str(installed_repository.installed_changeset_revision)]
+        post_submit_strings_not_displayed = ["filtering_0000"]
+        self.install_repository(
+            "filtering_0000",
+            common.test_user_1_name,
+            "Test 0000 Basic Repository Features 1",
+            post_submit_strings_not_displayed=post_submit_strings_not_displayed,
+        )
+        strings_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool",
+            "user1",
+            self.url.replace("http://", ""),
+            str(installed_repository.installed_changeset_revision),
+        ]
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
 
     def test_0035_verify_installed_repository_metadata(self):
-        '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
-        self.verify_installed_repository_metadata_unchanged('filtering_0000', common.test_user_1_name)
+        """Verify that resetting the metadata on an installed repository does not change the metadata."""
+        self.verify_installed_repository_metadata_unchanged("filtering_0000", common.test_user_1_name)
diff --git a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
index 60d879a9bbb..a3deab4e386 100644
--- a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
@@ -1,97 +1,124 @@
 import logging
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'freebayes_0010'
+repository_name = "freebayes_0010"
 repository_description = "Galaxy's freebayes tool"
 repository_long_description = "Long description of Galaxy's freebayes tool"
-category_name = 'Test 0010 Repository With Tool Dependencies'
+category_name = "Test 0010 Repository With Tool Dependencies"
 log = logging.getLogger(__name__)
 
 
 class ToolWithToolDependencies(ShedTwillTestCase):
-    '''Test installing a repository with tool dependencies.'''
+    """Test installing a repository with tool dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0010 category and upload the freebayes repository to it, if necessary.'''
-        category = self.create_category(name=category_name, description='Tests for a repository with tool dependencies.')
+        """Create the 0010 category and upload the freebayes repository to it, if necessary."""
+        category = self.create_category(
+            name=category_name, description="Tests for a repository with tool dependencies."
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool xml.',
-                             strings_displayed=['Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf'],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/tool_data_table_conf.xml.sample',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool data table sample file.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/sam_fa_indices.loc.sample',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool data table .loc file.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename=os.path.join('freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml'),
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded malformed tool dependency XML.',
-                             strings_displayed=['Exception attempting to parse', 'not well-formed'],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename=os.path.join('freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml'),
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded invalid tool dependency XML.',
-                             strings_displayed=['The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration'],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename=os.path.join('freebayes', 'tool_dependencies.xml'),
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded valid tool dependency XML.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool xml.",
+                strings_displayed=[
+                    "Metadata may have been defined",
+                    "This file requires an entry",
+                    "tool_data_table_conf",
+                ],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/tool_data_table_conf.xml.sample",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool data table sample file.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/sam_fa_indices.loc.sample",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool data table .loc file.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename=os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml"),
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded malformed tool dependency XML.",
+                strings_displayed=["Exception attempting to parse", "not well-formed"],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename=os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml"),
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded invalid tool dependency XML.",
+                strings_displayed=[
+                    "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration"
+                ],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename=os.path.join("freebayes", "tool_dependencies.xml"),
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded valid tool dependency XML.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_browse_tool_shed(self):
         """Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
@@ -99,36 +126,51 @@ class ToolWithToolDependencies(ShedTwillTestCase):
         self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
         category = self.test_db_util.get_category_by_name(category_name)
         self.browse_category(category, strings_displayed=[repository_name])
-        strings_displayed = [repository_name, 'Valid tools', 'Tool dependencies']
-        self.preview_repository_in_tool_shed(repository_name, common.test_user_1_name, strings_displayed=strings_displayed)
+        strings_displayed = [repository_name, "Valid tools", "Tool dependencies"]
+        self.preview_repository_in_tool_shed(
+            repository_name, common.test_user_1_name, strings_displayed=strings_displayed
+        )
 
     def test_0015_install_freebayes_repository(self):
-        '''Install the freebayes repository without installing tool dependencies.'''
-        strings_displayed = ['Never installed', 'install all needed dependencies', 'install Tool Shed managed', 'tool dependencies']
-        strings_displayed.extend(['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18'])
-        self.install_repository(repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                strings_displayed=strings_displayed,
-                                install_tool_dependencies=False,
-                                new_tool_panel_section_label='test_1010')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ['freebayes_0010',
-                             "Galaxy's freebayes tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        """Install the freebayes repository without installing tool dependencies."""
+        strings_displayed = [
+            "Never installed",
+            "install all needed dependencies",
+            "install Tool Shed managed",
+            "tool dependencies",
+        ]
+        strings_displayed.extend(["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"])
+        self.install_repository(
+            repository_name,
+            common.test_user_1_name,
+            category_name,
+            strings_displayed=strings_displayed,
+            install_tool_dependencies=False,
+            new_tool_panel_section_label="test_1010",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "freebayes_0010",
+            "Galaxy's freebayes tool",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'FreeBayes'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "FreeBayes"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
-        strings_displayed = ['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
-        self.check_installed_repository_tool_dependencies(installed_repository, strings_displayed=strings_displayed, dependencies_installed=False)
+        strings_displayed = ["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"]
+        self.check_installed_repository_tool_dependencies(
+            installed_repository, strings_displayed=strings_displayed, dependencies_installed=False
+        )
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0020_verify_installed_repository_metadata(self):
-        '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
+        """Verify that resetting the metadata on an installed repository does not change the metadata."""
         self.verify_installed_repository_metadata_unchanged(repository_name, common.test_user_1_name)
 
     def test_0025_verify_sample_files(self):
-        '''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.'''
-        self.verify_installed_repository_data_table_entries(required_data_table_entries=['sam_fa_indexes'])
+        """Verify that the installed repository populated shed_tool_data_table.xml and the sample files."""
+        self.verify_installed_repository_data_table_entries(required_data_table_entries=["sam_fa_indexes"])
diff --git a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
index 645ac0aff74..1d9bc7c1521 100644
--- a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
@@ -1,74 +1,102 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_name = "emboss_datatypes_0020"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0020'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'
+emboss_repository_name = "emboss_0020"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
 
 
 class ToolWithRepositoryDependencies(ShedTwillTestCase):
-    '''Test installing a repository with repository dependencies.'''
+    """Test installing a repository with repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0020 category and any missing repositories.'''
+        """Create the 0020 category and any missing repositories."""
         global repository_datatypes_count
-        category = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Test 0020 Basic Repository Dependencies')
+        category = self.create_category(
+            name="Test 0020 Basic Repository Dependencies", description="Test 0020 Basic Repository Dependencies"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                             description=datatypes_repository_description,
-                                                             long_description=datatypes_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
+        datatypes_repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(datatypes_repository):
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                              description=emboss_repository_description,
-                                                              long_description=emboss_repository_long_description,
-                                                              owner=common.test_user_1_name,
-                                                              category_id=self.security.encode_id(category.id),
-                                                              strings_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1020', additional_paths=['emboss', '5'])
-            repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            emboss_repository = self.get_or_create_repository(
+                name=emboss_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1020", additional_paths=["emboss", "5"])
+            repository_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
         repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
 
     def test_0010_browse_tool_shed(self):
@@ -76,57 +104,75 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase):
         global base_datatypes_count
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         base_datatypes_count = int(self.get_datatypes_count())
-        self.browse_tool_shed(url=self.url, strings_displayed=['Test 0020 Basic Repository Dependencies'])
-        category = self.test_db_util.get_category_by_name('Test 0020 Basic Repository Dependencies')
-        self.browse_category(category, strings_displayed=['emboss_0020'])
-        self.preview_repository_in_tool_shed('emboss_0020', common.test_user_1_name, strings_displayed=['emboss_0020', 'Valid tools'])
+        self.browse_tool_shed(url=self.url, strings_displayed=["Test 0020 Basic Repository Dependencies"])
+        category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies")
+        self.browse_category(category, strings_displayed=["emboss_0020"])
+        self.preview_repository_in_tool_shed(
+            "emboss_0020", common.test_user_1_name, strings_displayed=["emboss_0020", "Valid tools"]
+        )
 
     def test_0015_install_emboss_repository(self):
-        '''Install the emboss repository without installing tool dependencies.'''
+        """Install the emboss repository without installing tool dependencies."""
         global repository_datatypes_count
         global base_datatypes_count
-        strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
-        self.install_repository('emboss_0020',
-                                common.test_user_1_name,
-                                'Test 0020 Basic Repository Dependencies',
-                                strings_displayed=strings_displayed,
-                                install_tool_dependencies=False,
-                                new_tool_panel_section_label='test_1020')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('emboss_0020', common.test_user_1_name)
-        strings_displayed = ['emboss_0020',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = ["Handle", "Never installed", "tool dependencies", "emboss", "5.0.0", "package"]
+        self.install_repository(
+            "emboss_0020",
+            common.test_user_1_name,
+            "Test 0020 Basic Repository Dependencies",
+            strings_displayed=strings_displayed,
+            install_tool_dependencies=False,
+            new_tool_panel_section_label="test_1020",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "emboss_0020", common.test_user_1_name
+        )
+        strings_displayed = [
+            "emboss_0020",
+            "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'antigenic'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "antigenic"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
-        strings_displayed = ['emboss', '5.0.0', 'package']
-        self.check_installed_repository_tool_dependencies(installed_repository, strings_displayed=strings_displayed, dependencies_installed=False)
+        strings_displayed = ["emboss", "5.0.0", "package"]
+        self.check_installed_repository_tool_dependencies(
+            installed_repository, strings_displayed=strings_displayed, dependencies_installed=False
+        )
         self.verify_tool_metadata_for_installed_repository(installed_repository)
         current_datatypes = int(self.get_datatypes_count())
-        assert current_datatypes > base_datatypes_count, 'Installing emboss did not add new datatypes. Expected: %d. Found: %d' % \
-            (base_datatypes_count + repository_datatypes_count, current_datatypes)
+        assert (
+            current_datatypes > base_datatypes_count
+        ), "Installing emboss did not add new datatypes. Expected: %d. Found: %d" % (
+            base_datatypes_count + repository_datatypes_count,
+            current_datatypes,
+        )
 
     def test_0020_verify_installed_repository_metadata(self):
-        '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
-        self.verify_installed_repository_metadata_unchanged('emboss_0020', common.test_user_1_name)
+        """Verify that resetting the metadata on an installed repository does not change the metadata."""
+        self.verify_installed_repository_metadata_unchanged("emboss_0020", common.test_user_1_name)
 
     def test_0025_deactivate_datatypes_repository(self):
-        '''Deactivate the emboss_datatypes repository without removing it from disk.'''
+        """Deactivate the emboss_datatypes repository without removing it from disk."""
         global repository_datatypes_count
         global base_datatypes_count
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_1_name)
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         old_datatypes_count = int(self.get_datatypes_count())
         self.deactivate_repository(installed_repository)
         current_datatypes = int(self.get_datatypes_count())
-        assert current_datatypes < old_datatypes_count, 'Uninstalling emboss did not remove datatypes.'
+        assert current_datatypes < old_datatypes_count, "Uninstalling emboss did not remove datatypes."
 
     def test_0030_reactivate_datatypes_repository(self):
-        '''Reactivate the datatypes repository and verify that the datatypes are again present.'''
+        """Reactivate the datatypes repository and verify that the datatypes are again present."""
         global repository_datatypes_count
         global base_datatypes_count
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_1_name)
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(installed_repository)
         current_datatypes = int(self.get_datatypes_count())
-        assert current_datatypes > base_datatypes_count, 'Reactivating emboss did not add new datatypes.'
+        assert current_datatypes > base_datatypes_count, "Reactivating emboss did not add new datatypes."
diff --git a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
index 214beef0c07..01f112ec772 100644
--- a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
+++ b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
@@ -1,14 +1,19 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0030'
+datatypes_repository_name = "emboss_datatypes_0030"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0030'
-emboss_5_repository_name = 'emboss_5_0030'
-emboss_6_repository_name = 'emboss_6_0030'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030'
+emboss_repository_name = "emboss_0030"
+emboss_5_repository_name = "emboss_5_0030"
+emboss_6_repository_name = "emboss_6_0030"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
@@ -16,144 +21,214 @@ running_standalone = False
 
 
 class RepositoryWithDependencyRevisions(ShedTwillTestCase):
-    '''Test installing a repository with dependency revisions.'''
+    """Test installing a repository with dependency revisions."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0030 category and add repositories to it, if necessary.'''
+        """Create the 0030 category and add repositories to it, if necessary."""
         global repository_datatypes_count
         global running_standalone
-        category = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Test 0030 Repository Dependency Revisions')
+        category = self.create_category(
+            name="Test 0030 Repository Dependency Revisions", description="Test 0030 Repository Dependency Revisions"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                             description=datatypes_repository_description,
-                                                             long_description=datatypes_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
+        datatypes_repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(datatypes_repository):
             running_standalone = True
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            emboss_5_repository = self.get_or_create_repository(name=emboss_5_repository_name,
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_5_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1030', additional_paths=['emboss', '5'])
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
-            emboss_6_repository = self.get_or_create_repository(name=emboss_6_repository_name,
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_6_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1030', additional_paths=['emboss', '6'])
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
-            emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                              description=emboss_repository_description,
-                                                              long_description=emboss_repository_long_description,
-                                                              owner=common.test_user_1_name,
-                                                              category_id=self.security.encode_id(category.id),
-                                                              strings_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1030', additional_paths=['emboss', '5'])
-            dependency_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            dependency_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            emboss_5_repository = self.get_or_create_repository(
+                name=emboss_5_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_5_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_5_repository,
+                repository_tuples=[datatypes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            emboss_6_repository = self.get_or_create_repository(
+                name=emboss_6_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_6_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "6"])
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_6_repository,
+                repository_tuples=[datatypes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            emboss_repository = self.get_or_create_repository(
+                name=emboss_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
+            dependency_tuple = (
+                self.url,
+                emboss_5_repository.name,
+                emboss_5_repository.user.username,
+                self.get_repository_tip(emboss_5_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            dependency_tuple = (
+                self.url,
+                emboss_6_repository.name,
+                emboss_6_repository.user.username,
+                self.get_repository_tip(emboss_6_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
         repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
 
     def test_0010_browse_tool_shed(self):
         """Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.browse_tool_shed(url=self.url, strings_displayed=['Test 0030 Repository Dependency Revisions'])
-        category = self.test_db_util.get_category_by_name('Test 0030 Repository Dependency Revisions')
-        self.browse_category(category, strings_displayed=['emboss_0030'])
-        self.preview_repository_in_tool_shed('emboss_0030', common.test_user_1_name, strings_displayed=['emboss_0030', 'Valid tools'])
+        self.browse_tool_shed(url=self.url, strings_displayed=["Test 0030 Repository Dependency Revisions"])
+        category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
+        self.browse_category(category, strings_displayed=["emboss_0030"])
+        self.preview_repository_in_tool_shed(
+            "emboss_0030", common.test_user_1_name, strings_displayed=["emboss_0030", "Valid tools"]
+        )
 
     def test_0015_install_emboss_repository(self):
-        '''Install the emboss repository without installing tool dependencies.'''
+        """Install the emboss repository without installing tool dependencies."""
         global repository_datatypes_count
         global base_datatypes_count
         global running_standalone
         base_datatypes_count = int(self.get_datatypes_count())
-        strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
-        self.install_repository('emboss_0030',
-                                common.test_user_1_name,
-                                'Test 0030 Repository Dependency Revisions',
-                                strings_displayed=strings_displayed,
-                                install_tool_dependencies=False,
-                                new_tool_panel_section_label='test_1030')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('emboss_0030', common.test_user_1_name)
-        strings_displayed = ['emboss_0030',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = ["Handle", "Never installed", "tool dependencies", "emboss", "5.0.0", "package"]
+        self.install_repository(
+            "emboss_0030",
+            common.test_user_1_name,
+            "Test 0030 Repository Dependency Revisions",
+            strings_displayed=strings_displayed,
+            install_tool_dependencies=False,
+            new_tool_panel_section_label="test_1030",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "emboss_0030", common.test_user_1_name
+        )
+        strings_displayed = [
+            "emboss_0030",
+            "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'antigenic'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "antigenic"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
-        strings_displayed = ['emboss', '5.0.0', 'package']
-        self.check_installed_repository_tool_dependencies(installed_repository, strings_displayed=strings_displayed, dependencies_installed=False)
+        strings_displayed = ["emboss", "5.0.0", "package"]
+        self.check_installed_repository_tool_dependencies(
+            installed_repository, strings_displayed=strings_displayed, dependencies_installed=False
+        )
         self.verify_tool_metadata_for_installed_repository(installed_repository)
         self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"])
         current_datatypes = int(self.get_datatypes_count())
         if running_standalone:
-            assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
+            assert (
+                current_datatypes == base_datatypes_count + repository_datatypes_count
+            ), "Installing emboss did not add new datatypes."
         else:
-            assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
+            assert current_datatypes == base_datatypes_count, "Installing emboss added new datatypes."
 
     def test_0025_verify_installed_repository_metadata(self):
-        '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
-        self.verify_installed_repository_metadata_unchanged('emboss_0030', common.test_user_1_name)
+        """Verify that resetting the metadata on an installed repository does not change the metadata."""
+        self.verify_installed_repository_metadata_unchanged("emboss_0030", common.test_user_1_name)
diff --git a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
index e2296c7a44f..be9c6173f66 100644
--- a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
@@ -1,155 +1,229 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-freebayes_repository_name = 'freebayes_0040'
+freebayes_repository_name = "freebayes_0040"
 freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
 freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040"
 
-filtering_repository_name = 'filtering_0040'
+filtering_repository_name = "filtering_0040"
 filtering_repository_description = "Galaxy's filtering tool for test 0040"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"
 
-category_name = 'test_0040_repository_circular_dependencies'
+category_name = "test_0040_repository_circular_dependencies"
 
 running_standalone = False
 
 
 class TestInstallingCircularDependencies(ShedTwillTestCase):
-    '''Verify that the code correctly handles installing repositories with circular dependencies.'''
+    """Verify that the code correctly handles installing repositories with circular dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_freebayes_repository(self):
-        '''Create and populate freebayes_0040.'''
+        """Create and populate freebayes_0040."""
         global running_standalone
-        category = self.create_category(name=category_name, description='Testing handling of circular repository dependencies.')
+        category = self.create_category(
+            name=category_name, description="Testing handling of circular repository dependencies."
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                   description=freebayes_repository_description,
-                                                   long_description=freebayes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=freebayes_repository_name,
+            description=freebayes_repository_description,
+            long_description=freebayes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_filtering_repository(self):
-        '''Create and populate filtering_0040.'''
+        """Create and populate filtering_0040."""
         global running_standalone
-        category = self.create_category(name=category_name, description='Testing handling of circular repository dependencies.')
+        category = self.create_category(
+            name=category_name, description="Testing handling of circular repository dependencies."
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=filtering_repository_name,
-                                                   description=filtering_repository_description,
-                                                   long_description=filtering_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=filtering_repository_name,
+            description=filtering_repository_description,
+            long_description=filtering_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool tarball for filtering 1.1.0.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool tarball for filtering 1.1.0.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_create_repository_dependencies(self):
-        '''Set up the filtering and freebayes repository dependencies.'''
+        """Set up the filtering and freebayes repository dependencies."""
         # The dependency structure should look like:
         # Filtering revision 0 -> freebayes revision 0.
         # Freebayes revision 0 -> filtering revision 1.
         # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
         global running_standalone
         if running_standalone:
-            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-            repository_dependencies_path = self.generate_temp_path('test_1040', additional_paths=['circular'])
-            repository_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
-            self.create_repository_dependency(repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
-            repository_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository))
-            self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                freebayes_repository_name, common.test_user_1_name
+            )
+            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+                filtering_repository_name, common.test_user_1_name
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1040", additional_paths=["circular"])
+            repository_tuple = (
+                self.url,
+                freebayes_repository.name,
+                freebayes_repository.user.username,
+                self.get_repository_tip(freebayes_repository),
+            )
+            self.create_repository_dependency(
+                repository=filtering_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
+            repository_tuple = (
+                self.url,
+                filtering_repository.name,
+                filtering_repository.user.username,
+                self.get_repository_tip(filtering_repository),
+            )
+            self.create_repository_dependency(
+                repository=freebayes_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
 
     def test_0025_install_freebayes_repository(self):
-        '''Install freebayes with blank tool panel section, without tool dependencies but with repository dependencies.'''
+        """Install freebayes with blank tool panel section, without tool dependencies but with repository dependencies."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        strings_displayed = ['Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
-        self.install_repository(freebayes_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                strings_displayed=strings_displayed,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True)
+        strings_displayed = ["Handle", "tool dependencies", "freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"]
+        self.install_repository(
+            freebayes_repository_name,
+            common.test_user_1_name,
+            category_name,
+            strings_displayed=strings_displayed,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+        )
 
     def test_0030_uninstall_filtering_repository(self):
-        '''Deactivate filtering, verify tool panel section and missing repository dependency.'''
-        installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name, common.test_user_1_name)
-        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(filtering_repository_name, common.test_user_1_name)
+        """Deactivate filtering, verify tool panel section and missing repository dependency."""
+        installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
         self.display_installed_repository_manage_page(installed_freebayes_repository)
         self.display_installed_repository_manage_page(installed_filtering_repository)
         self.deactivate_repository(installed_filtering_repository)
         self.test_db_util.ga_refresh(installed_filtering_repository)
-        self.check_galaxy_repository_tool_panel_section(installed_filtering_repository, 'Get Data')
-        strings_displayed = ['Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040"]
-        self.display_installed_repository_manage_page(installed_freebayes_repository, strings_displayed=strings_displayed)
-        self.check_galaxy_repository_db_status(filtering_repository_name,
-                                               common.test_user_1_name,
-                                               'Deactivated')
+        self.check_galaxy_repository_tool_panel_section(installed_filtering_repository, "Get Data")
+        strings_displayed = [
+            "Missing repository",
+            "filtering",
+            "freebayes_0040",
+            "user1",
+            "Galaxy's freebayes tool for test 0040",
+        ]
+        self.display_installed_repository_manage_page(
+            installed_freebayes_repository, strings_displayed=strings_displayed
+        )
+        self.check_galaxy_repository_db_status(filtering_repository_name, common.test_user_1_name, "Deactivated")
 
     def test_0035_reactivate_filtering_repository(self):
-        '''Reinstall filtering into 'filtering' tool panel section.'''
-        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name,
-                                                                                            common.test_user_1_name)
-        self.reinstall_repository(installed_filtering_repository,
-                                  install_tool_dependencies=False,
-                                  install_repository_dependencies=True,
-                                  new_tool_panel_section_label='filtering',
-                                  no_changes=False)
+        """Reinstall filtering into 'filtering' tool panel section."""
+        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        self.reinstall_repository(
+            installed_filtering_repository,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="filtering",
+            no_changes=False,
+        )
 
     def test_0040_uninstall_freebayes_repository(self):
-        '''Deactivate freebayes, verify tool panel section and missing repository dependency.'''
-        installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name, common.test_user_1_name)
-        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(filtering_repository_name, common.test_user_1_name)
+        """Deactivate freebayes, verify tool panel section and missing repository dependency."""
+        installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
         self.display_installed_repository_manage_page(installed_freebayes_repository)
         self.display_installed_repository_manage_page(installed_filtering_repository)
         self.deactivate_repository(installed_freebayes_repository)
         self.test_db_util.ga_refresh(installed_freebayes_repository)
-        self.check_galaxy_repository_tool_panel_section(installed_freebayes_repository, 'Get Data')
-        strings_displayed = ['Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040"]
-        self.display_installed_repository_manage_page(installed_filtering_repository, strings_displayed=strings_displayed)
-        self.check_galaxy_repository_db_status('freebayes_0040',
-                                               'user1',
-                                               'Deactivated')
+        self.check_galaxy_repository_tool_panel_section(installed_freebayes_repository, "Get Data")
+        strings_displayed = [
+            "Missing repository",
+            "freebayes",
+            "filtering_0040",
+            "user1",
+            "Galaxy's filtering tool for test 0040",
+        ]
+        self.display_installed_repository_manage_page(
+            installed_filtering_repository, strings_displayed=strings_displayed
+        )
+        self.check_galaxy_repository_db_status("freebayes_0040", "user1", "Deactivated")
 
     def test_0045_deactivate_filtering_repository(self):
-        '''Deactivate filtering, verify tool panel section.'''
-        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(filtering_repository_name, common.test_user_1_name)
-        installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(freebayes_repository_name, common.test_user_1_name)
+        """Deactivate filtering, verify tool panel section."""
+        installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
         self.display_installed_repository_manage_page(installed_freebayes_repository)
         self.display_installed_repository_manage_page(installed_filtering_repository)
         self.deactivate_repository(installed_filtering_repository)
         self.test_db_util.ga_refresh(installed_filtering_repository)
-        strings_displayed = ['Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040"]
-        self.display_installed_repository_manage_page(installed_freebayes_repository, strings_displayed=strings_displayed)
-        self.check_galaxy_repository_db_status(filtering_repository_name,
-                                               common.test_user_1_name,
-                                               'Deactivated')
+        strings_displayed = [
+            "Missing repository",
+            "filtering",
+            "freebayes_0040",
+            "user1",
+            "Galaxy's freebayes tool for test 0040",
+        ]
+        self.display_installed_repository_manage_page(
+            installed_freebayes_repository, strings_displayed=strings_displayed
+        )
+        self.check_galaxy_repository_db_status(filtering_repository_name, common.test_user_1_name, "Deactivated")
diff --git a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
index 25f5c5dd4ec..73fc92cccb5 100644
--- a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
+++ b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
@@ -1,231 +1,320 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-emboss_datatypes_repository_name = 'emboss_datatypes_0050'
+emboss_datatypes_repository_name = "emboss_datatypes_0050"
 emboss_datatypes_repository_description = "Datatypes for emboss"
 emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
 
-emboss_repository_name = 'emboss_0050'
+emboss_repository_name = "emboss_0050"
 emboss_repository_description = "Galaxy's emboss tool"
 emboss_repository_long_description = "Long description of Galaxy's emboss tool"
 
-filtering_repository_name = 'filtering_0050'
+filtering_repository_name = "filtering_0050"
 filtering_repository_description = "Galaxy's filtering tool"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool"
 
-freebayes_repository_name = 'freebayes_0050'
+freebayes_repository_name = "freebayes_0050"
 freebayes_repository_description = "Galaxy's freebayes tool"
 freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
 
-column_repository_name = 'column_maker_0050'
+column_repository_name = "column_maker_0050"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0050'
+convert_repository_name = "convert_chars_0050"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-bismark_repository_name = 'bismark_0050'
+bismark_repository_name = "bismark_0050"
 bismark_repository_description = "A flexible aligner."
 bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."
 
-category_name = 'Test 0050 Circular Dependencies 5 Levels'
-category_description = 'Test circular dependency features'
+category_name = "Test 0050 Circular Dependencies 5 Levels"
+category_description = "Test circular dependency features"
 
 running_standalone = False
 
 
 class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
-    '''Verify that the code correctly handles circular dependencies down to n levels.'''
+    """Verify that the code correctly handles circular dependencies down to n levels."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_convert_repository(self):
-        '''Create and populate convert_chars_0050.'''
+        """Create and populate convert_chars_0050."""
         category = self.create_category(name=category_name, description=category_description)
         global running_standalone
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate convert_chars_0050.'''
+        """Create and populate convert_chars_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_emboss_datatypes_repository(self):
-        '''Create and populate emboss_datatypes_0050.'''
+        """Create and populate emboss_datatypes_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=emboss_datatypes_repository_name,
-                                                   description=emboss_datatypes_repository_description,
-                                                   long_description=emboss_datatypes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_datatypes_repository_name,
+            description=emboss_datatypes_repository_description,
+            long_description=emboss_datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_create_emboss_repository(self):
-        '''Create and populate emboss_0050.'''
+        """Create and populate emboss_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                   description=emboss_repository_description,
-                                                   long_description=emboss_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=emboss_repository_name,
+            description=emboss_repository_description,
+            long_description=emboss_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0025_create_filtering_repository(self):
-        '''Create and populate filtering_0050.'''
+        """Create and populate filtering_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=filtering_repository_name,
-                                                   description=filtering_repository_description,
-                                                   long_description=filtering_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=filtering_repository_name,
+            description=filtering_repository_description,
+            long_description=filtering_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0030_create_freebayes_repository(self):
-        '''Create and populate freebayes_0050.'''
+        """Create and populate freebayes_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=freebayes_repository_name,
-                                                   description=freebayes_repository_description,
-                                                   long_description=freebayes_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=freebayes_repository_name,
+            description=freebayes_repository_description,
+            long_description=freebayes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded freebayes tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded freebayes tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0035_create_bismark_repository(self):
-        '''Create and populate bismark_0050.'''
+        """Create and populate bismark_0050."""
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=bismark_repository_name,
-                                                   description=bismark_repository_description,
-                                                   long_description=bismark_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bismark_repository_name,
+            description=bismark_repository_description,
+            long_description=bismark_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='bismark/bismark.tar',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded bismark tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="bismark/bismark.tar",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded bismark tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0040_create_and_upload_dependency_definitions(self):
-        '''Set up the dependency structure.'''
+        """Set up the dependency structure."""
         global running_standalone
         if running_standalone:
-            column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-            convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-            bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
-            dependency_xml_path = self.generate_temp_path('test_1050', additional_paths=['dependencies'])
+            column_repository = self.test_db_util.get_repository_by_name_and_owner(
+                column_repository_name, common.test_user_1_name
+            )
+            convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+                convert_repository_name, common.test_user_1_name
+            )
+            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_datatypes_repository_name, common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_repository_name, common.test_user_1_name
+            )
+            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+                filtering_repository_name, common.test_user_1_name
+            )
+            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                freebayes_repository_name, common.test_user_1_name
+            )
+            bismark_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bismark_repository_name, common.test_user_1_name
+            )
+            dependency_xml_path = self.generate_temp_path("test_1050", additional_paths=["dependencies"])
             # convert_chars depends on column_maker
             # column_maker depends on convert_chars
             # emboss depends on emboss_datatypes
             # emboss_datatypes depends on bismark
             # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker
             # filtering depends on emboss
-            column_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
-            convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-            freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
-            emboss_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository))
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            bismark_tuple = (self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip(bismark_repository))
-            self.create_repository_dependency(repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=freebayes_repository,
-                                              repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
-                                              filepath=dependency_xml_path)
-            self.create_repository_dependency(repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path)
+            column_tuple = (
+                self.url,
+                column_repository.name,
+                column_repository.user.username,
+                self.get_repository_tip(column_repository),
+            )
+            convert_tuple = (
+                self.url,
+                convert_repository.name,
+                convert_repository.user.username,
+                self.get_repository_tip(convert_repository),
+            )
+            freebayes_tuple = (
+                self.url,
+                freebayes_repository.name,
+                freebayes_repository.user.username,
+                self.get_repository_tip(freebayes_repository),
+            )
+            emboss_tuple = (
+                self.url,
+                emboss_repository.name,
+                emboss_repository.user.username,
+                self.get_repository_tip(emboss_repository),
+            )
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            bismark_tuple = (
+                self.url,
+                bismark_repository.name,
+                bismark_repository.user.username,
+                self.get_repository_tip(bismark_repository),
+            )
+            self.create_repository_dependency(
+                repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+            )
+            self.create_repository_dependency(
+                repository=freebayes_repository,
+                repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
+                filepath=dependency_xml_path,
+            )
+            self.create_repository_dependency(
+                repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path
+            )
 
     def test_0045_verify_repository_dependencies(self):
-        '''Verify that the generated dependency circle does not cause an infinite loop.
+        """Verify that the generated dependency circle does not cause an infinite loop.
         Expected structure:
 
         id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b
@@ -242,14 +331,28 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
                  ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0']
              id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04
                  ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507']
-        '''
-        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
+        """
+        emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filtering_repository_name, common.test_user_1_name
+        )
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        bismark_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bismark_repository_name, common.test_user_1_name
+        )
         self.check_repository_dependency(convert_repository, column_repository)
         self.check_repository_dependency(column_repository, convert_repository)
         self.check_repository_dependency(emboss_datatypes_repository, bismark_repository)
@@ -257,120 +360,196 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
         self.check_repository_dependency(filtering_repository, emboss_repository)
         for repository in [emboss_datatypes_repository, emboss_repository, column_repository]:
             self.check_repository_dependency(freebayes_repository, repository)
-        freebayes_dependencies = [freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository]
-        strings_displayed = [f"{freebayes_repository.name} depends on {', '.join(repo.name for repo in freebayes_dependencies)}."]
+        freebayes_dependencies = [
+            freebayes_repository,
+            emboss_datatypes_repository,
+            emboss_repository,
+            column_repository,
+        ]
+        strings_displayed = [
+            f"{freebayes_repository.name} depends on {', '.join(repo.name for repo in freebayes_dependencies)}."
+        ]
         self.display_manage_repository_page(freebayes_repository, strings_displayed=strings_displayed)
 
     def test_0050_verify_tool_dependencies(self):
-        '''Check that freebayes and emboss display tool dependencies.'''
-        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(freebayes_repository,
-                                            strings_displayed=['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies'])
-        self.display_manage_repository_page(emboss_repository, strings_displayed=['Tool dependencies', 'emboss', '5.0.0', 'package'])
+        """Check that freebayes and emboss display tool dependencies."""
+        freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            freebayes_repository_name, common.test_user_1_name
+        )
+        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        self.display_manage_repository_page(
+            freebayes_repository,
+            strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Tool dependencies"],
+        )
+        self.display_manage_repository_page(
+            emboss_repository, strings_displayed=["Tool dependencies", "emboss", "5.0.0", "package"]
+        )
 
     def test_0055_install_column_repository(self):
-        '''Install column_maker with repository dependencies.'''
+        """Install column_maker with repository dependencies."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository(column_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                new_tool_panel_section_label='column_maker')
+        self.install_repository(
+            column_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="column_maker",
+        )
         # This should result in column_maker and convert_chars being installed, and the rest never installed.
-        installed_repositories = [(column_repository_name, common.test_user_1_name),
-                                  (convert_repository_name, common.test_user_1_name)]
-        strings_displayed = ['column_maker_0050', 'convert_chars_0050']
-        strings_not_displayed = ['emboss_datatypes_0050', 'emboss_0050', 'filtering_0050', 'freebayes_0050', 'bismark_0050']
-        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        installed_repositories = [
+            (column_repository_name, common.test_user_1_name),
+            (convert_repository_name, common.test_user_1_name),
+        ]
+        strings_displayed = ["column_maker_0050", "convert_chars_0050"]
+        strings_not_displayed = [
+            "emboss_datatypes_0050",
+            "emboss_0050",
+            "filtering_0050",
+            "freebayes_0050",
+            "bismark_0050",
+        ]
+        self.display_galaxy_browse_repositories_page(
+            strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         self.verify_installed_repositories(installed_repositories=installed_repositories)
 
     def test_0060_install_emboss_repository(self):
-        '''Install emboss_5 with repository dependencies.'''
+        """Install emboss_5 with repository dependencies."""
         global running_standalone
         original_datatypes = self.get_datatypes_count()
-        self.install_repository(emboss_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                new_tool_panel_section_label='emboss_5_0050')
+        self.install_repository(
+            emboss_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="emboss_5_0050",
+        )
         if running_standalone:
-            assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.'
+            assert (
+                original_datatypes < self.get_datatypes_count()
+            ), "Installing a repository that depends on emboss_datatypes did not add datatypes."
         # Now we have emboss_datatypes, emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed.
-        installed_repositories = [(emboss_datatypes_repository_name, common.test_user_1_name),
-                                  (column_repository_name, common.test_user_1_name),
-                                  (emboss_repository_name, common.test_user_1_name),
-                                  (convert_repository_name, common.test_user_1_name),
-                                  (bismark_repository_name, common.test_user_1_name)]
-        strings_displayed = ['emboss_datatypes_0050', 'emboss_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050']
-        strings_not_displayed = ['filtering_0050', 'freebayes_0050']
-        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        installed_repositories = [
+            (emboss_datatypes_repository_name, common.test_user_1_name),
+            (column_repository_name, common.test_user_1_name),
+            (emboss_repository_name, common.test_user_1_name),
+            (convert_repository_name, common.test_user_1_name),
+            (bismark_repository_name, common.test_user_1_name),
+        ]
+        strings_displayed = [
+            "emboss_datatypes_0050",
+            "emboss_0050",
+            "column_maker_0050",
+            "convert_chars_0050",
+            "bismark_0050",
+        ]
+        strings_not_displayed = ["filtering_0050", "freebayes_0050"]
+        self.display_galaxy_browse_repositories_page(
+            strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         self.verify_installed_repositories(installed_repositories)
 
     def test_0065_deactivate_datatypes_repository(self):
-        '''Deactivate emboss_datatypes and verify that the datatypes count is reduced.'''
+        """Deactivate emboss_datatypes and verify that the datatypes count is reduced."""
         original_datatypes = self.get_datatypes_count()
-        repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_datatypes_repository_name, common.test_user_1_name)
+        repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(repository)
-        assert original_datatypes > self.get_datatypes_count(), 'Deactivating emboss_datatypes did not remove datatypes.'
+        assert (
+            original_datatypes > self.get_datatypes_count()
+        ), "Deactivating emboss_datatypes did not remove datatypes."
         # Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, and emboss_datatypes deactivated.
-        installed_repositories = [(column_repository_name, common.test_user_1_name),
-                                  (emboss_repository_name, common.test_user_1_name),
-                                  (convert_repository_name, common.test_user_1_name),
-                                  (bismark_repository_name, common.test_user_1_name)]
-        strings_displayed = ['emboss_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050']
-        strings_not_displayed = ['emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050']
-        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        installed_repositories = [
+            (column_repository_name, common.test_user_1_name),
+            (emboss_repository_name, common.test_user_1_name),
+            (convert_repository_name, common.test_user_1_name),
+            (bismark_repository_name, common.test_user_1_name),
+        ]
+        strings_displayed = ["emboss_0050", "column_maker_0050", "convert_chars_0050", "bismark_0050"]
+        strings_not_displayed = ["emboss_datatypes_0050", "filtering_0050", "freebayes_0050"]
+        self.display_galaxy_browse_repositories_page(
+            strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         self.verify_installed_repositories(installed_repositories)
 
     def test_0070_uninstall_emboss_repository(self):
-        '''Uninstall the emboss_5 repository.'''
-        repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Uninstall the emboss_5 repository."""
+        repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(repository)
         strings_not_displayed = [repository.name, repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
         self.test_db_util.ga_refresh(repository)
-        self.check_galaxy_repository_tool_panel_section(repository, 'emboss_5_0050')
+        self.check_galaxy_repository_tool_panel_section(repository, "emboss_5_0050")
         # Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated,
         # and emboss uninstalled.
-        installed_repositories = [(column_repository_name, common.test_user_1_name),
-                                  (convert_repository_name, common.test_user_1_name),
-                                  (bismark_repository_name, common.test_user_1_name)]
-        strings_displayed = ['column_maker_0050', 'convert_chars_0050', 'bismark_0050']
-        strings_not_displayed = ['emboss_0050', 'emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050']
-        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        installed_repositories = [
+            (column_repository_name, common.test_user_1_name),
+            (convert_repository_name, common.test_user_1_name),
+            (bismark_repository_name, common.test_user_1_name),
+        ]
+        strings_displayed = ["column_maker_0050", "convert_chars_0050", "bismark_0050"]
+        strings_not_displayed = ["emboss_0050", "emboss_datatypes_0050", "filtering_0050", "freebayes_0050"]
+        self.display_galaxy_browse_repositories_page(
+            strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         self.verify_installed_repositories(installed_repositories)
 
     def test_0075_install_freebayes_repository(self):
-        '''Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5.'''
+        """Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5."""
         original_datatypes = self.get_datatypes_count()
-        strings_displayed = ['Handle', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
-        self.install_repository(freebayes_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                strings_displayed=strings_displayed,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                new_tool_panel_section_label='freebayes')
-        assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.'
-        emboss_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_datatypes_repository_name, common.test_user_1_name)
-        strings_displayed = ['emboss_0050',
-                             'emboss_datatypes_0050',
-                             emboss_repository.installed_changeset_revision,
-                             datatypes_repository.installed_changeset_revision]
+        strings_displayed = ["Handle", "tool dependencies", "freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"]
+        self.install_repository(
+            freebayes_repository_name,
+            common.test_user_1_name,
+            category_name,
+            strings_displayed=strings_displayed,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="freebayes",
+        )
+        assert (
+            original_datatypes < self.get_datatypes_count()
+        ), "Installing a repository that depends on emboss_datatypes did not add datatypes."
+        emboss_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_datatypes_repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "emboss_0050",
+            "emboss_datatypes_0050",
+            emboss_repository.installed_changeset_revision,
+            datatypes_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
         # Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes.
         # Now column_maker, convert_chars, emboss, emboss_datatypes, freebayes, and bismark should be installed.
-        installed_repositories = [(column_repository_name, common.test_user_1_name),
-                                  (emboss_datatypes_repository_name, common.test_user_1_name),
-                                  (emboss_repository_name, common.test_user_1_name),
-                                  (freebayes_repository_name, common.test_user_1_name),
-                                  (convert_repository_name, common.test_user_1_name),
-                                  (bismark_repository_name, common.test_user_1_name)]
-        strings_displayed = ['emboss_0050', 'emboss_datatypes_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050', 'freebayes_0050']
-        strings_not_displayed = ['filtering_0050']
-        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
+        installed_repositories = [
+            (column_repository_name, common.test_user_1_name),
+            (emboss_datatypes_repository_name, common.test_user_1_name),
+            (emboss_repository_name, common.test_user_1_name),
+            (freebayes_repository_name, common.test_user_1_name),
+            (convert_repository_name, common.test_user_1_name),
+            (bismark_repository_name, common.test_user_1_name),
+        ]
+        strings_displayed = [
+            "emboss_0050",
+            "emboss_datatypes_0050",
+            "column_maker_0050",
+            "convert_chars_0050",
+            "bismark_0050",
+            "freebayes_0050",
+        ]
+        strings_not_displayed = ["filtering_0050"]
+        self.display_galaxy_browse_repositories_page(
+            strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
         self.verify_installed_repositories(installed_repositories)
diff --git a/lib/tool_shed/test/functional/test_1070_invalid_tool.py b/lib/tool_shed/test/functional/test_1070_invalid_tool.py
index 47c76e5a67c..47d9f944c99 100644
--- a/lib/tool_shed/test/functional/test_1070_invalid_tool.py
+++ b/lib/tool_shed/test/functional/test_1070_invalid_tool.py
@@ -1,60 +1,73 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'bismark_0070'
+repository_name = "bismark_0070"
 repository_description = "Galaxy's bismark wrapper"
 repository_long_description = "Long description of Galaxy's bismark wrapper"
-category_name = 'Test 0070 Invalid Tool Revisions'
-category_description = 'Test 1070 for a repository with an invalid tool.'
+category_name = "Test 0070 Invalid Tool Revisions"
+category_description = "Test 1070 for a repository with an invalid tool."
 
 
 class TestFreebayesRepository(ShedTwillTestCase):
-    '''Test repository with multiple revisions with invalid tools.'''
+    """Test repository with multiple revisions with invalid tools."""
 
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_ensure_existence_of_repository_and_category(self):
-        '''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.'''
+        """Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool."""
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='bismark/bismark.tar',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded bismark tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='bismark/bismark_methylation_extractor.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded an updated tool xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="bismark/bismark.tar",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded bismark tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="bismark/bismark_methylation_extractor.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded an updated tool xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_browse_tool_shed(self):
         """Browse the available tool sheds in this Galaxy instance and preview the bismark repository."""
@@ -62,27 +75,36 @@ class TestFreebayesRepository(ShedTwillTestCase):
         self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
         category = self.test_db_util.get_category_by_name(category_name)
         self.browse_category(category, strings_displayed=[repository_name])
-        self.preview_repository_in_tool_shed(repository_name, common.test_user_1_name, strings_displayed=[repository_name])
+        self.preview_repository_in_tool_shed(
+            repository_name, common.test_user_1_name, strings_displayed=[repository_name]
+        )
 
     def test_0015_install_freebayes_repository(self):
-        '''Install the test repository without installing tool dependencies.'''
-        self.install_repository(repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                new_tool_panel_section_label='test_1070')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ['bismark_0070',
-                             "Galaxy's bismark wrapper",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        """Install the test repository without installing tool dependencies."""
+        self.install_repository(
+            repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            new_tool_panel_section_label="test_1070",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "bismark_0070",
+            "Galaxy's bismark wrapper",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['methylation extractor', 'Invalid tools'])
-        self.display_installed_repository_manage_page(installed_repository,
-                                                      strings_displayed=strings_displayed,
-                                                      strings_not_displayed=['bisulfite mapper'])
+        strings_displayed.extend(["methylation extractor", "Invalid tools"])
+        self.display_installed_repository_manage_page(
+            installed_repository, strings_displayed=strings_displayed, strings_not_displayed=["bisulfite mapper"]
+        )
         self.verify_tool_metadata_for_installed_repository(installed_repository)
         self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"])
-        assert 'invalid_tools' in installed_repository.metadata_, 'No invalid tools were defined in %s.' % \
-            installed_repository.name
+        assert "invalid_tools" in installed_repository.metadata_, (
+            "No invalid tools were defined in %s." % installed_repository.name
+        )
diff --git a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
index 86836956f43..23e9c64627e 100644
--- a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
+++ b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
@@ -1,17 +1,20 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-column_repository_name = 'column_maker_0080'
+column_repository_name = "column_maker_0080"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0080'
+convert_repository_name = "convert_chars_0080"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 0080 Advanced Circular Dependencies'
-category_description = 'Test circular dependency features'
+category_name = "Test 0080 Advanced Circular Dependencies"
+category_description = "Test circular dependency features"
 
 log = logging.getLogger(__name__)
 
@@ -19,21 +22,25 @@ running_standalone = False
 
 
 class TestRepositoryDependencies(ShedTwillTestCase):
-    '''Testing uninstalling and reinstalling repository dependencies, and setting tool panel sections.'''
+    """Testing uninstalling and reinstalling repository dependencies, and setting tool panel sections."""
 
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_and_populate_column_repository(self):
@@ -41,337 +48,416 @@ class TestRepositoryDependencies(ShedTwillTestCase):
         category = self.create_category(name=category_name, description=category_description)
         global running_standalone
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
             running_standalone = True
 
     def test_0010_create_and_populate_convert_repository(self):
-        '''Create and populate the convert_chars repository.'''
+        """Create and populate the convert_chars repository."""
         global running_standalone
         self.login(email=common.admin_email, username=common.admin_username)
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
             running_standalone = True
 
     def test_0015_upload_dependency_xml_if_needed(self):
-        '''If this test is being run by itself, it will not have repository dependencies configured yet.'''
+        """If this test is being run by itself, it will not have repository dependencies configured yet."""
         global running_standalone
         if running_standalone:
-            convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-            column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-            repository_dependencies_path = self.generate_temp_path('test_1080', additional_paths=['convert'])
-            repository_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-            self.create_repository_dependency(repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
-            repository_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
-            self.create_repository_dependency(repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+            convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+                convert_repository_name, common.test_user_1_name
+            )
+            column_repository = self.test_db_util.get_repository_by_name_and_owner(
+                column_repository_name, common.test_user_1_name
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1080", additional_paths=["convert"])
+            repository_tuple = (
+                self.url,
+                convert_repository.name,
+                convert_repository.user.username,
+                self.get_repository_tip(convert_repository),
+            )
+            self.create_repository_dependency(
+                repository=column_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
+            repository_tuple = (
+                self.url,
+                column_repository.name,
+                column_repository.user.username,
+                self.get_repository_tip(column_repository),
+            )
+            self.create_repository_dependency(
+                repository=convert_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
 
     def test_0020_install_convert_repository(self):
-        '''Install convert_chars without repository dependencies into convert_chars tool panel section.'''
+        """Install convert_chars without repository dependencies into convert_chars tool panel section."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository(convert_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=False,
-                                new_tool_panel_section_label='convert_chars')
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                           common.test_user_1_name)
-        browse_strings_displayed = ['convert_chars_0080',
-                                    'Convert delimiters',
-                                    self.url.replace('http://', ''),
-                                    installed_convert_repository.installed_changeset_revision]
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Missing repository dependencies']
+        self.install_repository(
+            convert_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=False,
+            new_tool_panel_section_label="convert_chars",
+        )
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        browse_strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+        ]
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed)
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     def test_0025_install_column_repository(self):
-        '''Install column maker with repository dependencies into column_maker tool panel section.'''
-        self.install_repository(column_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_repository_dependencies=True,
-                                new_tool_panel_section_label='column_maker',
-                                strings_displayed=['install_repository_dependencies'])
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                           common.test_user_1_name)
-        browse_strings_displayed = ['convert_chars_0080',
-                                    'Convert delimiters',
-                                    self.url.replace('http://', ''),
-                                    installed_convert_repository.installed_changeset_revision,
-                                    'column_maker_0080',
-                                    'Add column',
-                                    installed_column_repository.installed_changeset_revision]
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
+        """Install column maker with repository dependencies into column_maker tool panel section."""
+        self.install_repository(
+            column_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="column_maker",
+            strings_displayed=["install_repository_dependencies"],
+        )
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        browse_strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            "Add column",
+            installed_column_repository.installed_changeset_revision,
+        ]
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed)
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
 
     def test_0030_deactivate_convert_repository(self):
-        '''Deactivate convert_chars, verify that column_maker is installed and missing repository dependencies.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Deactivate convert_chars, verify that column_maker is installed and missing repository dependencies."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_convert_repository)
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Missing repository dependencies',
-                             'Deactivated']
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+            "Deactivated",
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
 
     def test_0035_reactivate_convert_repository(self):
-        '''Reactivate convert_chars, both convert_chars and column_maker should now show as installed.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Reactivate convert_chars, both convert_chars and column_maker should now show as installed."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(installed_convert_repository)
-        strings_displayed = ['convert_chars_0080',
-                             'Compute',
-                             'an expression on every row',
-                             '1.1.0',
-                             'column_maker_0080',
-                             'Installed repository dependencies',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             installed_convert_repository.installed_changeset_revision]
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Compute",
+            "an expression on every row",
+            "1.1.0",
+            "column_maker_0080",
+            "Installed repository dependencies",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            installed_convert_repository.installed_changeset_revision,
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
 
     def test_0040_deactivate_column_repository(self):
-        '''Deactivate column_maker, verify that convert_chars is installed and missing repository dependencies.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Deactivate column_maker, verify that convert_chars is installed and missing repository dependencies."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_column_repository)
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Missing repository dependencies',
-                             'Deactivated']
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+            "Deactivated",
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     def test_0045_deactivate_convert_repository(self):
-        '''Deactivate convert_chars, verify that both convert_chars and column_maker are deactivated.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Deactivate convert_chars, verify that both convert_chars and column_maker are deactivated."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_convert_repository)
-        strings_not_displayed = ['column_maker_0080',
-                                 installed_column_repository.installed_changeset_revision,
-                                 'convert_chars_0080',
-                                 installed_convert_repository.installed_changeset_revision]
+        strings_not_displayed = [
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0050_reactivate_column_repository(self):
-        '''Reactivate column_maker. This should not automatically reactivate convert_chars, so column_maker should be displayed as installed but missing repository dependencies.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Reactivate column_maker. This should not automatically reactivate convert_chars, so column_maker should be displayed as installed but missing repository dependencies."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(installed_column_repository)
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Missing repository dependencies',
-                             'Deactivated']
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+            "Deactivated",
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
 
     def test_0055_reactivate_convert_repository(self):
-        '''Activate convert_chars. Both convert_chars and column_maker should now show as installed.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Activate convert_chars. Both convert_chars and column_maker should now show as installed."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(installed_convert_repository)
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     def test_0060_uninstall_column_repository(self):
-        '''Uninstall column_maker. Verify that convert_chars is installed and missing repository dependencies.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Uninstall column_maker. Verify that convert_chars is installed and missing repository dependencies."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_column_repository)
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Missing repository dependencies',
-                             'Uninstalled']
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+            "Uninstalled",
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
         self.test_db_util.install_session.refresh(installed_column_repository)
 
     def test_0065_reinstall_column_repository(self):
-        '''Reinstall column_maker without repository dependencies, verify both convert_chars and column_maker are installed.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Reinstall column_maker without repository dependencies, verify both convert_chars and column_maker are installed."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.reinstall_repository(installed_column_repository, install_repository_dependencies=False)
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     def test_0070_uninstall_convert_repository(self):
-        '''Uninstall convert_chars, verify column_maker installed but missing repository dependencies.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Uninstall convert_chars, verify column_maker installed but missing repository dependencies."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_convert_repository)
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Missing repository dependencies',
-                             'Deactivated']
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+            "Deactivated",
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
         self.test_db_util.install_session.refresh(installed_convert_repository)
 
     def test_0075_uninstall_column_repository(self):
-        '''Uninstall column_maker, verify that both convert_chars and column_maker are uninstalled.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """Uninstall column_maker, verify that both convert_chars and column_maker are uninstalled."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_column_repository)
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Missing repository dependencies',
-                             'Activate or reinstall repository',
-                             'Deactivated']
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Missing repository dependencies",
+            "Activate or reinstall repository",
+            "Deactivated",
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     def test_0080_reinstall_convert_repository(self):
-        '''Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker.'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
-        self.reinstall_repository(installed_convert_repository,
-                                  install_repository_dependencies=True,
-                                  no_changes=False)
-        strings_displayed = ['column_maker_0080',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision,
-                             'convert_chars_0080',
-                             installed_convert_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
-        strings_displayed = ['convert_chars_0080',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_0080',
-                             installed_column_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        """Reinstall convert_chars with repository dependencies, verify that this installs both convert_chars and column_maker."""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        self.reinstall_repository(installed_convert_repository, install_repository_dependencies=True, no_changes=False)
+        strings_displayed = [
+            "column_maker_0080",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+            "convert_chars_0080",
+            installed_convert_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
+        strings_displayed = [
+            "convert_chars_0080",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_0080",
+            installed_column_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
diff --git a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
index 5f30d4a8eed..e8c0a23f45b 100644
--- a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
+++ b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
@@ -1,168 +1,218 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-column_repository_name = 'column_maker_1085'
+column_repository_name = "column_maker_1085"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_1085'
+convert_repository_name = "convert_chars_1085"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 1085 Advanced Circular Dependencies'
-category_description = 'Test circular dependency features'
+category_name = "Test 1085 Advanced Circular Dependencies"
+category_description = "Test circular dependency features"
 
 log = logging.getLogger(__name__)
 
 
 class TestRepositoryDependencies(ShedTwillTestCase):
-    '''Testing the behavior of repository dependencies with tool panel sections.'''
+    """Testing the behavior of repository dependencies with tool panel sections."""
 
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_and_populate_column_repository(self):
         """Create a category for this test suite and add repositories to it."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_and_populate_convert_repository(self):
         self.login(email=common.admin_email, username=common.admin_username)
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_and_upload_dependency_files(self):
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_1085', additional_paths=['column'])
-        repository_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-        self.create_repository_dependency(repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
-        repository_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
-        self.create_repository_dependency(repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_1085", additional_paths=["column"])
+        repository_tuple = (
+            self.url,
+            convert_repository.name,
+            convert_repository.user.username,
+            self.get_repository_tip(convert_repository),
+        )
+        self.create_repository_dependency(
+            repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
+        repository_tuple = (
+            self.url,
+            column_repository.name,
+            column_repository.user.username,
+            self.get_repository_tip(column_repository),
+        )
+        self.create_repository_dependency(
+            repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0020_install_repositories(self):
-        '''Install column_maker into column_maker tool panel section and install repository dependencies.'''
+        """Install column_maker into column_maker tool panel section and install repository dependencies."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository(column_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                new_tool_panel_section_label='column_maker',
-                                strings_displayed=['install_repository_dependencies'])
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
-        browse_strings_displayed = ['convert_chars_1085',
-                                    'Convert delimiters',
-                                    self.url.replace('http://', ''),
-                                    installed_convert_repository.installed_changeset_revision,
-                                    'column_maker_1085',
-                                    'Add column',
-                                    installed_column_repository.installed_changeset_revision]
-        strings_displayed = ['convert_chars_1085',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision,
-                             'column_maker_1085',
-                             installed_column_repository.installed_changeset_revision,
-                             'Installed repository dependencies']
+        self.install_repository(
+            column_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="column_maker",
+            strings_displayed=["install_repository_dependencies"],
+        )
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        browse_strings_displayed = [
+            "convert_chars_1085",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_1085",
+            "Add column",
+            installed_column_repository.installed_changeset_revision,
+        ]
+        strings_displayed = [
+            "convert_chars_1085",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+            "column_maker_1085",
+            installed_column_repository.installed_changeset_revision,
+            "Installed repository dependencies",
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed)
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     def test_0025_uninstall_column_repository(self):
-        '''uninstall column_maker, verify same section'''
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
+        """uninstall column_maker, verify same section"""
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_column_repository)
         self.test_db_util.ga_refresh(installed_column_repository)
-        self.check_galaxy_repository_tool_panel_section(installed_column_repository, 'column_maker')
+        self.check_galaxy_repository_tool_panel_section(installed_column_repository, "column_maker")
 
     def test_0030_uninstall_convert_repository(self):
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_convert_repository)
         self.test_db_util.ga_refresh(installed_convert_repository)
-        self.check_galaxy_repository_tool_panel_section(installed_convert_repository, 'column_maker')
+        self.check_galaxy_repository_tool_panel_section(installed_convert_repository, "column_maker")
 
     def test_0035_reinstall_column_repository(self):
-        '''reinstall column_maker into new section 'new_column_maker' (no_changes = false), no dependencies'''
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name,
-                                                                                            common.test_user_1_name)
-        self.reinstall_repository(installed_column_repository,
-                                  install_tool_dependencies=False,
-                                  install_repository_dependencies=False,
-                                  new_tool_panel_section_label='new_column_maker',
-                                  no_changes=False)
-        strings_displayed = ['column_maker_1085',
-                             'Add column',
-                             self.url.replace('http://', ''),
-                             installed_column_repository.installed_changeset_revision]
-        self.display_installed_repository_manage_page(installed_column_repository,
-                                                      strings_displayed=strings_displayed)
+        """reinstall column_maker into new section 'new_column_maker' (no_changes = false), no dependencies"""
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        self.reinstall_repository(
+            installed_column_repository,
+            install_tool_dependencies=False,
+            install_repository_dependencies=False,
+            new_tool_panel_section_label="new_column_maker",
+            no_changes=False,
+        )
+        strings_displayed = [
+            "column_maker_1085",
+            "Add column",
+            self.url.replace("http://", ""),
+            installed_column_repository.installed_changeset_revision,
+        ]
+        self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
 
     def test_0040_reinstall_convert_repository(self):
-        '''reinstall convert_chars into new section 'new_convert_chars' (no_changes = false), no dependencies'''
-        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name,
-                                                                                            common.test_user_1_name)
-        self.reinstall_repository(installed_convert_repository,
-                                  install_tool_dependencies=False,
-                                  install_repository_dependencies=False,
-                                  new_tool_panel_section_label='new_convert_chars',
-                                  no_changes=False)
-        strings_displayed = ['convert_chars_1085',
-                             'Convert delimiters',
-                             self.url.replace('http://', ''),
-                             installed_convert_repository.installed_changeset_revision]
-        self.display_installed_repository_manage_page(installed_convert_repository,
-                                                      strings_displayed=strings_displayed)
+        """reinstall convert_chars into new section 'new_convert_chars' (no_changes = false), no dependencies"""
+        installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        self.reinstall_repository(
+            installed_convert_repository,
+            install_tool_dependencies=False,
+            install_repository_dependencies=False,
+            new_tool_panel_section_label="new_convert_chars",
+            no_changes=False,
+        )
+        strings_displayed = [
+            "convert_chars_1085",
+            "Convert delimiters",
+            self.url.replace("http://", ""),
+            installed_convert_repository.installed_changeset_revision,
+        ]
+        self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
 
     # The following check fails somewhere around 5% of the time maybe on Jenkins.
     # https://jenkins.galaxyproject.org/job/docker-toolshed/5578/
diff --git a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
index 825604d7134..62970273c76 100644
--- a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
@@ -1,116 +1,158 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-column_repository_name = 'column_maker_1087'
+column_repository_name = "column_maker_1087"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_1087'
+convert_repository_name = "convert_chars_1087"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 1087 Advanced Circular Dependencies'
-category_description = 'Test circular dependency features'
+category_name = "Test 1087 Advanced Circular Dependencies"
+category_description = "Test circular dependency features"
 
 
 class TestRepositoryDependencies(ShedTwillTestCase):
-    '''Test installing a repository, then updating it to include repository dependencies.'''
+    """Test installing a repository, then updating it to include repository dependencies."""
 
     def test_0000_create_or_login_admin_user(self):
         """Create necessary user accounts and login as an admin user."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_and_populate_column_repository(self):
         """Create a category for this test suite and add repositories to it."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_and_populate_convert_repository(self):
-        '''Create and populate the convert_chars repository.'''
+        """Create and populate the convert_chars repository."""
         self.login(email=common.admin_email, username=common.admin_username)
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_install_and_uninstall_column_repository(self):
-        '''Install and uninstall the column_maker repository.'''
+        """Install and uninstall the column_maker repository."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository(column_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                new_tool_panel_section_label='column_maker',
-                                strings_not_displayed=['install_repository_dependencies'])
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
+        self.install_repository(
+            column_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            new_tool_panel_section_label="column_maker",
+            strings_not_displayed=["install_repository_dependencies"],
+        )
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_column_repository)
 
     def test_0020_upload_dependency_xml(self):
-        '''Upload a repository_dependencies.xml file to column_maker that specifies convert_chars.'''
+        """Upload a repository_dependencies.xml file to column_maker that specifies convert_chars."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        repository_dependencies_path = self.generate_temp_path('test_1085', additional_paths=['column'])
-        convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-        self.create_repository_dependency(repository=column_repository, repository_tuples=[convert_tuple], filepath=repository_dependencies_path)
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        repository_dependencies_path = self.generate_temp_path("test_1085", additional_paths=["column"])
+        convert_tuple = (
+            self.url,
+            convert_repository.name,
+            convert_repository.user.username,
+            self.get_repository_tip(convert_repository),
+        )
+        self.create_repository_dependency(
+            repository=column_repository, repository_tuples=[convert_tuple], filepath=repository_dependencies_path
+        )
 
     def test_0025_verify_repository_dependency(self):
-        '''Verify that the new revision of column_maker now depends on convert_chars.'''
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
+        """Verify that the new revision of column_maker now depends on convert_chars."""
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
         self.check_repository_dependency(column_repository, convert_repository)
 
     def test_0030_reinstall_column_repository(self):
-        '''Reinstall column_maker and verify that it now shows repository dependencies.'''
+        """Reinstall column_maker and verify that it now shows repository dependencies."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        strings_displayed = ['Handle repository dependencies', 'convert_chars_1087', self.get_repository_tip(convert_repository)]
+        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "Handle repository dependencies",
+            "convert_chars_1087",
+            self.get_repository_tip(convert_repository),
+        ]
         # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall.
         params = dict(id=self.security.encode_id(installed_column_repository.id))
-        url = '/admin_toolshed/restore_repository'
+        url = "/admin_toolshed/restore_repository"
         self.visit_galaxy_url(url, params)
         self.check_for_strings(strings_displayed)
-        strings_not_displayed = ['column_maker_1087']
+        strings_not_displayed = ["column_maker_1087"]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
diff --git a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
index 46cab41c50d..888acf969f4 100644
--- a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
@@ -1,282 +1,369 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-bwa_base_repository_name = 'bwa_base_repository_0100'
+bwa_base_repository_name = "bwa_base_repository_0100"
 bwa_base_repository_description = "BWA Base"
-bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
+bwa_base_repository_long_description = (
+    "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
+)
 
-bwa_package_repository_name = 'package_bwa_0_5_9_0100'
+bwa_package_repository_name = "package_bwa_0_5_9_0100"
 bwa_package_repository_description = "BWA Package"
-bwa_package_repository_long_description = "BWA repository with a package tool dependency defined to compile and install BWA 0.5.9."
+bwa_package_repository_long_description = (
+    "BWA repository with a package tool dependency defined to compile and install BWA 0.5.9."
+)
 
-category_name = 'Test 0100 Complex Repository Dependencies'
-category_description = 'Test 0100 Complex Repository Dependencies'
+category_name = "Test 0100 Complex Repository Dependencies"
+category_description = "Test 0100 Complex Repository Dependencies"
 running_standalone = False
 
 
 class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
-    '''Test features related to installing repositories with complex repository dependencies.'''
+    """Test features related to installing repositories with complex repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_bwa_package_repository(self):
-        '''Create and populate package_bwa_0_5_9_0100.'''
+        """Create and populate package_bwa_0_5_9_0100."""
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=bwa_package_repository_name,
-                                                   description=bwa_package_repository_description,
-                                                   long_description=bwa_package_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=bwa_package_repository_name,
+            description=bwa_package_repository_description,
+            long_description=bwa_package_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            old_tool_dependency = self.get_filename(os.path.join('bwa', 'complex', 'tool_dependencies.xml'))
-            new_tool_dependency_path = self.generate_temp_path('test_1100', additional_paths=['tool_dependency'])
-            xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, 'tool_dependencies.xml'))
-            open(xml_filename, 'w').write(open(old_tool_dependency)
-                                     .read().replace('__PATH__', self.get_filename('bwa/complex')))
-            self.upload_file(repository,
-                             filename=xml_filename,
-                             filepath=new_tool_dependency_path,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool_dependencies.xml.',
-                             strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                             strings_not_displayed=[])
-            self.display_manage_repository_page(repository, strings_displayed=['Tool dependencies', 'consider setting its type'])
+            old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "tool_dependencies.xml"))
+            new_tool_dependency_path = self.generate_temp_path("test_1100", additional_paths=["tool_dependency"])
+            xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, "tool_dependencies.xml"))
+            open(xml_filename, "w").write(
+                open(old_tool_dependency).read().replace("__PATH__", self.get_filename("bwa/complex"))
+            )
+            self.upload_file(
+                repository,
+                filename=xml_filename,
+                filepath=new_tool_dependency_path,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool_dependencies.xml.",
+                strings_displayed=[
+                    "This repository currently contains a single file named <b>tool_dependencies.xml</b>"
+                ],
+                strings_not_displayed=[],
+            )
+            self.display_manage_repository_page(
+                repository, strings_displayed=["Tool dependencies", "consider setting its type"]
+            )
 
     def test_0010_create_bwa_base_repository(self):
-        '''Create and populate bwa_base_0100.'''
+        """Create and populate bwa_base_0100."""
         global running_standalone
         if running_standalone:
             category = self.create_category(name=category_name, description=category_description)
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-            repository = self.get_or_create_repository(name=bwa_base_repository_name,
-                                                       description=bwa_base_repository_description,
-                                                       long_description=bwa_base_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
+            repository = self.get_or_create_repository(
+                name=bwa_base_repository_name,
+                description=bwa_base_repository_description,
+                long_description=bwa_base_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
             self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-            self.upload_file(repository,
-                             filename='bwa/complex/bwa_base.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="bwa/complex/bwa_base.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_generate_complex_repository_dependency_invalid_shed_url(self):
-        '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.'''
+        """Generate and upload a complex repository definition that specifies an invalid tool shed URL."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
-            base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-            url = 'http://http://this is not an url!'
+            dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
+            base_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_base_repository_name, common.test_user_1_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_package_repository_name, common.test_user_1_name
+            )
+            url = "http://http://this is not an url!"
             name = tool_repository.name
             owner = tool_repository.user.username
             changeset_revision = self.get_repository_tip(tool_repository)
-            strings_displayed = ['Repository dependencies are currently supported only within the same tool shed']
+            strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=base_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=True,
-                                              package='bwa',
-                                              version='0.5.9')
+            self.create_repository_dependency(
+                repository=base_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=True,
+                package="bwa",
+                version="0.5.9",
+            )
 
     def test_0020_generate_complex_repository_dependency_invalid_repository_name(self):
-        '''Generate and upload a complex repository definition that specifies an invalid repository name.'''
+        """Generate and upload a complex repository definition that specifies an invalid repository name."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
-            base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+            dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
+            base_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_base_repository_name, common.test_user_1_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_package_repository_name, common.test_user_1_name
+            )
             url = self.url
-            name = 'invalid_repository!?'
+            name = "invalid_repository!?"
             owner = tool_repository.user.username
             changeset_revision = self.get_repository_tip(tool_repository)
-            strings_displayed = ['because the name is invalid.']
+            strings_displayed = ["because the name is invalid."]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=base_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=True,
-                                              package='bwa',
-                                              version='0.5.9')
+            self.create_repository_dependency(
+                repository=base_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=True,
+                package="bwa",
+                version="0.5.9",
+            )
 
     def test_0025_generate_complex_repository_dependency_invalid_owner_name(self):
-        '''Generate and upload a complex repository definition that specifies an invalid owner.'''
+        """Generate and upload a complex repository definition that specifies an invalid owner."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
-            base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+            dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
+            base_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_base_repository_name, common.test_user_1_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_package_repository_name, common.test_user_1_name
+            )
             url = self.url
             name = tool_repository.name
-            owner = 'invalid_owner!?'
+            owner = "invalid_owner!?"
             changeset_revision = self.get_repository_tip(tool_repository)
-            strings_displayed = ['because the owner is invalid.']
+            strings_displayed = ["because the owner is invalid."]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=base_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=True,
-                                              package='bwa',
-                                              version='0.5.9')
+            self.create_repository_dependency(
+                repository=base_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=True,
+                package="bwa",
+                version="0.5.9",
+            )
 
     def test_0030_generate_complex_repository_dependency_invalid_changeset_revision(self):
-        '''Generate and upload a complex repository definition that specifies an invalid changeset revision.'''
+        """Generate and upload a complex repository definition that specifies an invalid changeset revision."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
-            base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+            dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
+            base_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_base_repository_name, common.test_user_1_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_package_repository_name, common.test_user_1_name
+            )
             url = self.url
             name = tool_repository.name
             owner = tool_repository.user.username
-            changeset_revision = '1234abcd'
-            strings_displayed = ['because the changeset revision is invalid.']
+            changeset_revision = "1234abcd"
+            strings_displayed = ["because the changeset revision is invalid."]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=base_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=True,
-                                              package='bwa',
-                                              version='0.5.9')
+            self.create_repository_dependency(
+                repository=base_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=True,
+                package="bwa",
+                version="0.5.9",
+            )
 
     def test_0035_generate_valid_complex_repository_dependency(self):
-        '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.'''
+        """Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100."""
         global running_standalone
         if running_standalone:
-            base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-            dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex'])
+            base_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_base_repository_name, common.test_user_1_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_package_repository_name, common.test_user_1_name
+            )
+            dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex"])
             url = self.url
             name = tool_repository.name
             owner = tool_repository.user.username
             changeset_revision = self.get_repository_tip(tool_repository)
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=base_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              complex=True,
-                                              package='bwa',
-                                              version='0.5.9')
+            self.create_repository_dependency(
+                repository=base_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                complex=True,
+                package="bwa",
+                version="0.5.9",
+            )
             self.check_repository_dependency(base_repository, tool_repository)
-            self.display_manage_repository_page(base_repository, strings_displayed=['bwa', '0.5.9', 'package'])
+            self.display_manage_repository_page(base_repository, strings_displayed=["bwa", "0.5.9", "package"])
 
     def test_0040_update_tool_repository(self):
-        '''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.'''
+        """Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset."""
         global running_standalone
         if running_standalone:
-            base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+            base_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_base_repository_name, common.test_user_1_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                bwa_package_repository_name, common.test_user_1_name
+            )
             previous_changeset = self.get_repository_tip(tool_repository)
-            old_tool_dependency = self.get_filename(os.path.join('bwa', 'complex', 'readme', 'tool_dependencies.xml'))
-            new_tool_dependency_path = self.generate_temp_path('test_1100', additional_paths=['tool_dependency'])
-            xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, 'tool_dependencies.xml'))
-            open(xml_filename, 'w').write(open(old_tool_dependency)
-                                     .read().replace('__PATH__', self.get_filename('bwa/complex')))
-            self.upload_file(tool_repository,
-                             filename=xml_filename,
-                             filepath=new_tool_dependency_path,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded new tool_dependencies.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "readme", "tool_dependencies.xml"))
+            new_tool_dependency_path = self.generate_temp_path("test_1100", additional_paths=["tool_dependency"])
+            xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, "tool_dependencies.xml"))
+            open(xml_filename, "w").write(
+                open(old_tool_dependency).read().replace("__PATH__", self.get_filename("bwa/complex"))
+            )
+            self.upload_file(
+                tool_repository,
+                filename=xml_filename,
+                filepath=new_tool_dependency_path,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded new tool_dependencies.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
             # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
-            self.display_manage_repository_page(base_repository,
-                                                strings_displayed=[self.get_repository_tip(tool_repository), 'bwa', '0.5.9', 'package'],
-                                                strings_not_displayed=[previous_changeset])
+            self.display_manage_repository_page(
+                base_repository,
+                strings_displayed=[self.get_repository_tip(tool_repository), "bwa", "0.5.9", "package"],
+                strings_not_displayed=[previous_changeset],
+            )
 
     def test_0045_install_base_repository(self):
-        '''Verify installation of the repository with complex repository dependencies.'''
+        """Verify installation of the repository with complex repository dependencies."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
+        base_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
         preview_strings_displayed = [tool_repository.name, self.get_repository_tip(tool_repository)]
-        self.install_repository(bwa_base_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=True,
-                                preview_strings_displayed=preview_strings_displayed,
-                                post_submit_strings_displayed=[base_repository.name, tool_repository.name, 'New'],
-                                includes_tools_for_display_in_tool_panel=True)
+        self.install_repository(
+            bwa_base_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=True,
+            preview_strings_displayed=preview_strings_displayed,
+            post_submit_strings_displayed=[base_repository.name, tool_repository.name, "New"],
+            includes_tools_for_display_in_tool_panel=True,
+        )
 
     def test_0050_verify_installed_repositories(self):
-        '''Verify that the installed repositories are displayed properly.'''
-        base_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_base_repository_name, common.test_user_1_name)
-        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_package_repository_name, common.test_user_1_name)
-        strings_displayed = ['bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision]
-        strings_displayed.extend(['package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision])
-        strings_displayed.append(self.url.replace('http://', ''))
+        """Verify that the installed repositories are displayed properly."""
+        base_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
+        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
+        strings_displayed = ["bwa_base_repository_0100", "user1", base_repository.installed_changeset_revision]
+        strings_displayed.extend(["package_bwa_0_5_9_0100", "user1", tool_repository.installed_changeset_revision])
+        strings_displayed.append(self.url.replace("http://", ""))
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=[])
-        strings_displayed = ['package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision]
-        strings_not_displayed = ['Missing tool dependencies']
-        self.display_installed_repository_manage_page(tool_repository,
-                                                      strings_displayed=strings_displayed,
-                                                      strings_not_displayed=strings_not_displayed)
-        strings_displayed = ['bwa_base_repository_0100',
-                             'user1',
-                             'package_bwa_0_5_9_0100',
-                             base_repository.installed_changeset_revision,
-                             tool_repository.installed_changeset_revision]
-        strings_not_displayed = ['Missing tool dependencies']
-        self.display_installed_repository_manage_page(base_repository,
-                                                      strings_displayed=strings_displayed,
-                                                      strings_not_displayed=strings_not_displayed)
+        strings_displayed = ["package_bwa_0_5_9_0100", "user1", tool_repository.installed_changeset_revision]
+        strings_not_displayed = ["Missing tool dependencies"]
+        self.display_installed_repository_manage_page(
+            tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
+        strings_displayed = [
+            "bwa_base_repository_0100",
+            "user1",
+            "package_bwa_0_5_9_0100",
+            base_repository.installed_changeset_revision,
+            tool_repository.installed_changeset_revision,
+        ]
+        strings_not_displayed = ["Missing tool dependencies"]
+        self.display_installed_repository_manage_page(
+            base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
 
     def test_0055_verify_complex_tool_dependency(self):
-        '''Verify that the generated env.sh contains the right data.'''
-        base_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_base_repository_name, common.test_user_1_name)
-        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_package_repository_name, common.test_user_1_name)
-        env_sh_path = self.get_env_sh_path(tool_dependency_name='bwa',
-                                           tool_dependency_version='0.5.9',
-                                           repository=base_repository)
-        assert os.path.exists(env_sh_path), f'env.sh was not generated in {env_sh_path} for this dependency.'
+        """Verify that the generated env.sh contains the right data."""
+        base_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            bwa_base_repository_name, common.test_user_1_name
+        )
+        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
+        env_sh_path = self.get_env_sh_path(
+            tool_dependency_name="bwa", tool_dependency_version="0.5.9", repository=base_repository
+        )
+        assert os.path.exists(env_sh_path), f"env.sh was not generated in {env_sh_path} for this dependency."
         contents = open(env_sh_path).read()
         if tool_repository.installed_changeset_revision not in contents:
-            raise AssertionError('Installed changeset revision %s not found in env.sh.\nContents of env.sh: %s' %
-                                 (tool_repository.installed_changeset_revision, contents))
-        if 'package_bwa_0_5_9_0100' not in contents:
-            raise AssertionError(f'Repository name package_bwa_0_5_9_0100 not found in env.sh.\nContents of env.sh: {contents}')
+            raise AssertionError(
+                "Installed changeset revision %s not found in env.sh.\nContents of env.sh: %s"
+                % (tool_repository.installed_changeset_revision, contents)
+            )
+        if "package_bwa_0_5_9_0100" not in contents:
+            raise AssertionError(
+                f"Repository name package_bwa_0_5_9_0100 not found in env.sh.\nContents of env.sh: {contents}"
+            )
 
     def test_0060_verify_tool_dependency_uninstallation(self):
-        '''Uninstall the package_bwa_0_5_9_0100 repository.
+        """Uninstall the package_bwa_0_5_9_0100 repository.
 
         Uninstall the repository that defines a tool dependency relationship on BWA 0.5.9, and verify
         that this results in the compiled binary package also being removed.
-        '''
-        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_package_repository_name, common.test_user_1_name)
+        """
+        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            bwa_package_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(tool_repository)
-        env_sh_path = os.path.join(self.galaxy_tool_dependency_dir,
-                                   'bwa',
-                                   '0.5.9',
-                                   tool_repository.owner,
-                                   tool_repository.name,
-                                   tool_repository.installed_changeset_revision,
-                                   'env.sh')
-        assert os.path.exists(env_sh_path), f'Path {env_sh_path} does not exist after deactivating the repository that generated it.'
+        env_sh_path = os.path.join(
+            self.galaxy_tool_dependency_dir,
+            "bwa",
+            "0.5.9",
+            tool_repository.owner,
+            tool_repository.name,
+            tool_repository.installed_changeset_revision,
+            "env.sh",
+        )
+        assert os.path.exists(
+            env_sh_path
+        ), f"Path {env_sh_path} does not exist after deactivating the repository that generated it."
diff --git a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
index 91ab86e48ad..046febc5863 100644
--- a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
+++ b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
@@ -1,30 +1,37 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0110'
+datatypes_repository_name = "emboss_datatypes_0110"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0110'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_name = "emboss_0110"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
 
-category_name = 'Test 0110 Invalid Repository Dependencies'
-category_desc = 'Test 0110 Invalid Repository Dependencies'
+category_name = "Test 0110 Invalid Repository Dependencies"
+category_desc = "Test 0110 Invalid Repository Dependencies"
 running_standalone = False
 
 
 class TestBasicRepositoryDependencies(ShedTwillTestCase):
-    '''Testing emboss 5 with repository dependencies.'''
+    """Testing emboss 5 with repository dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_category(self):
@@ -32,144 +39,190 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
         self.create_category(name=category_name, description=category_desc)
 
     def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
-        '''Create and populate the emboss_datatypes repository.'''
+        """Create and populate the emboss_datatypes repository."""
         global running_standalone
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                             description=datatypes_repository_description,
-                                             long_description=datatypes_repository_long_description,
-                                             owner=common.test_user_1_name,
-                                             category_id=self.security.encode_id(category.id),
-                                             strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_verify_datatypes_in_datatypes_repository(self):
-        '''Verify that the emboss_datatypes repository contains datatype entries.'''
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(repository, strings_displayed=['Datatypes', 'equicktandem', 'hennig86', 'vectorstrip'])
+        """Verify that the emboss_datatypes repository contains datatype entries."""
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_1_name
+        )
+        self.display_manage_repository_page(
+            repository, strings_displayed=["Datatypes", "equicktandem", "hennig86", "vectorstrip"]
+        )
 
     def test_0020_create_emboss_5_repository_and_upload_files(self):
-        '''Create and populate the emboss_5_0110 repository.'''
+        """Create and populate the emboss_5_0110 repository."""
         global running_standalone
         if running_standalone:
             category = self.test_db_util.get_category_by_name(category_name)
-            repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                 description=emboss_repository_description,
-                                                 long_description=emboss_repository_long_description,
-                                                 owner=common.test_user_1_name,
-                                                 category_id=self.security.encode_id(category.id),
-                                                 strings_displayed=[])
-            self.upload_file(repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=emboss_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0025_generate_repository_dependency_with_invalid_url(self):
-        '''Generate a repository dependency for emboss 5 with an invalid URL.'''
+        """Generate a repository dependency for emboss 5 with an invalid URL."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple'])
-            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-            url = 'http://http://this is not an url!'
+            dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"])
+            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                datatypes_repository_name, common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_repository_name, common.test_user_1_name
+            )
+            url = "http://http://this is not an url!"
             name = datatypes_repository.name
             owner = datatypes_repository.user.username
             changeset_revision = self.get_repository_tip(datatypes_repository)
-            strings_displayed = ['Repository dependencies are currently supported only within the same tool shed']
+            strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=emboss_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=False)
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=False,
+            )
 
     def test_0030_generate_repository_dependency_with_invalid_name(self):
-        '''Generate a repository dependency for emboss 5 with an invalid name.'''
+        """Generate a repository dependency for emboss 5 with an invalid name."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple'])
-            repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+            dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"])
+            repository = self.test_db_util.get_repository_by_name_and_owner(
+                datatypes_repository_name, common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_repository_name, common.test_user_1_name
+            )
             url = self.url
-            name = '!?invalid?!'
+            name = "!?invalid?!"
             owner = repository.user.username
             changeset_revision = self.get_repository_tip(repository)
-            strings_displayed = ['because the name is invalid.']
+            strings_displayed = ["because the name is invalid."]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=emboss_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=False)
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=False,
+            )
 
     def test_0035_generate_repository_dependency_with_invalid_owner(self):
-        '''Generate a repository dependency for emboss 5 with an invalid owner.'''
+        """Generate a repository dependency for emboss 5 with an invalid owner."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple'])
-            repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+            dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"])
+            repository = self.test_db_util.get_repository_by_name_and_owner(
+                datatypes_repository_name, common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_repository_name, common.test_user_1_name
+            )
             url = self.url
             name = repository.name
-            owner = '!?invalid?!'
+            owner = "!?invalid?!"
             changeset_revision = self.get_repository_tip(repository)
-            strings_displayed = ['because the owner is invalid.']
+            strings_displayed = ["because the owner is invalid."]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=emboss_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=False)
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=False,
+            )
 
     def test_0040_generate_repository_dependency_with_invalid_changeset_revision(self):
-        '''Generate a repository dependency for emboss 5 with an invalid changeset revision.'''
+        """Generate a repository dependency for emboss 5 with an invalid changeset revision."""
         global running_standalone
         if running_standalone:
-            dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple', 'invalid'])
-            repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
-            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+            dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple", "invalid"])
+            repository = self.test_db_util.get_repository_by_name_and_owner(
+                datatypes_repository_name, common.test_user_1_name
+            )
+            emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
+                emboss_repository_name, common.test_user_1_name
+            )
             url = self.url
             name = repository.name
             owner = repository.user.username
-            changeset_revision = '!?invalid?!'
-            strings_displayed = ['because the changeset revision is invalid.']
+            changeset_revision = "!?invalid?!"
+            strings_displayed = ["because the changeset revision is invalid."]
             repository_tuple = (url, name, owner, changeset_revision)
-            self.create_repository_dependency(repository=emboss_repository,
-                                              filepath=dependency_path,
-                                              repository_tuples=[repository_tuple],
-                                              strings_displayed=strings_displayed,
-                                              complex=False)
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                filepath=dependency_path,
+                repository_tuples=[repository_tuple],
+                strings_displayed=strings_displayed,
+                complex=False,
+            )
 
     def test_0045_install_repository_with_invalid_repository_dependency(self):
-        '''Install the repository and verify that galaxy detects invalid repository dependencies.'''
+        """Install the repository and verify that galaxy detects invalid repository dependencies."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        preview_strings_displayed = ['emboss_0110', self.get_repository_tip(repository), 'Ignoring repository dependency definition']
-        self.install_repository(emboss_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                preview_strings_displayed=preview_strings_displayed,
-                                post_submit_strings_displayed=[repository.name, repository.name, 'New'],
-                                includes_tools_for_display_in_tool_panel=True)
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
-        self.display_installed_repository_manage_page(installed_repository=installed_repository,
-                                                      strings_displayed=[],
-                                                      strings_not_displayed=['Repository dependencies'])
+        preview_strings_displayed = [
+            "emboss_0110",
+            self.get_repository_tip(repository),
+            "Ignoring repository dependency definition",
+        ]
+        self.install_repository(
+            emboss_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            preview_strings_displayed=preview_strings_displayed,
+            post_submit_strings_displayed=[repository.name, repository.name, "New"],
+            includes_tools_for_display_in_tool_panel=True,
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        self.display_installed_repository_manage_page(
+            installed_repository=installed_repository,
+            strings_displayed=[],
+            strings_not_displayed=["Repository dependencies"],
+        )
diff --git a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
index 06442e4ece2..6298f2bab12 100644
--- a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
+++ b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
@@ -1,14 +1,17 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'blast_datatypes_0120'
-datatypes_repository_description = 'Galaxy applicable datatypes for BLAST'
-datatypes_repository_long_description = 'Galaxy datatypes for the BLAST top hit descriptons tool'
+datatypes_repository_name = "blast_datatypes_0120"
+datatypes_repository_description = "Galaxy applicable datatypes for BLAST"
+datatypes_repository_long_description = "Galaxy datatypes for the BLAST top hit descriptons tool"
 
-tool_repository_name = 'blastxml_to_top_descr_0120'
-tool_repository_description = 'BLAST top hit descriptions'
-tool_repository_long_description = 'Make a table from BLAST XML'
+tool_repository_name = "blastxml_to_top_descr_0120"
+tool_repository_description = "BLAST top hit descriptions"
+tool_repository_long_description = "Make a table from BLAST XML"
 
-'''
+"""
 Tool shed side:
 
 1) Create and populate blast_datatypes_0120.
@@ -21,7 +24,7 @@ Galaxy side:
 
 1) Install blastxml_to_top_descr_0120, with repository dependencies.
 1a) Check for appropriate strings in the installed blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories.
-'''
+"""
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
@@ -29,7 +32,6 @@ running_standalone = False
 
 
 class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
-
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
 
@@ -38,15 +40,19 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_datatypes_repository(self):
@@ -55,36 +61,51 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
         We are at step 1.
         Create and populate blast_datatypes.
         """
-        category = self.create_category(name='Test 0120', description='Description of test 0120')
+        category = self.create_category(name="Test 0120", description="Description of test 0120")
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         strings_displayed = self.expect_repo_created_strings(datatypes_repository_name)
-        repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                   description=datatypes_repository_description,
-                                                   long_description=datatypes_repository_long_description,
-                                                   owner=common.test_user_2_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
+        repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_2_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='blast/blast_datatypes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded blast_datatypes tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="blast/blast_datatypes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded blast_datatypes tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_verify_datatypes_repository(self):
-        '''Verify the blast_datatypes_0120 repository.
+        """Verify the blast_datatypes_0120 repository.
 
         We are at step 1a.
         Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb,
         the datatypes that are defined in datatypes_conf.xml.
-        '''
+        """
         global repository_datatypes_count
-        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-        strings_displayed = ['BlastXml', 'BlastNucDb', 'BlastProtDb', 'application/xml', 'text/html', 'blastxml', 'blastdbn', 'blastdbp']
+        repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_2_name
+        )
+        strings_displayed = [
+            "BlastXml",
+            "BlastNucDb",
+            "BlastProtDb",
+            "application/xml",
+            "text/html",
+            "blastxml",
+            "blastdbn",
+            "blastdbp",
+        ]
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
         repository_datatypes_count = int(self.get_repository_datatypes_count(repository))
 
@@ -95,100 +116,131 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
         Create and populate blastxml_to_top_descr_0120.
         """
         global running_standalone
-        category = self.create_category(name='Test 0120', description='Description of test 0120')
+        category = self.create_category(name="Test 0120", description="Description of test 0120")
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         strings_displayed = self.expect_repo_created_strings(tool_repository_name)
-        repository = self.get_or_create_repository(name=tool_repository_name,
-                                                   description=tool_repository_description,
-                                                   long_description=tool_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=strings_displayed)
+        repository = self.get_or_create_repository(
+            name=tool_repository_name,
+            description=tool_repository_description,
+            long_description=tool_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=strings_displayed,
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='blast/blastxml_to_top_descr.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded blastxml_to_top_descr tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="blast/blastxml_to_top_descr.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded blastxml_to_top_descr tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_verify_tool_repository(self):
-        '''Verify the blastxml_to_top_descr_0120 repository.
+        """Verify the blastxml_to_top_descr_0120 repository.
 
         We are at step 2a.
         Check for appropriate strings, such as tool name, description, and version.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
-        strings_displayed = ['blastxml_to_top_descr_0120', 'BLAST top hit descriptions', 'Make a table from BLAST XML']
-        strings_displayed.extend(['0.0.1', 'Valid tools'])
+        strings_displayed = ["blastxml_to_top_descr_0120", "BLAST top hit descriptions", "Make a table from BLAST XML"]
+        strings_displayed.extend(["0.0.1", "Valid tools"])
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0025_create_repository_dependency(self):
-        '''Create a repository dependency on blast_datatypes_0120.
+        """Create a repository dependency on blast_datatypes_0120.
 
         We are at step 3.
         Create a simple repository dependency for blastxml_to_top_descr_0120 that defines a dependency on blast_datatypes_0120.
-        '''
+        """
         global running_standalone
         if running_standalone:
-            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-            tool_repository = self.test_db_util.get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
-            dependency_xml_path = self.generate_temp_path('test_1120', additional_paths=['dependencies'])
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=tool_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
+            datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                datatypes_repository_name, common.test_user_2_name
+            )
+            tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+                tool_repository_name, common.test_user_1_name
+            )
+            dependency_xml_path = self.generate_temp_path("test_1120", additional_paths=["dependencies"])
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=tool_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
+            )
 
     def test_0040_verify_repository_dependency(self):
-        '''Verify the created repository dependency.
+        """Verify the created repository dependency.
 
         We are at step 3a.
         Check the newly created repository dependency to ensure that it was defined and displays correctly.
-        '''
-        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-        tool_repository = self.test_db_util.get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
+        """
+        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
+            datatypes_repository_name, common.test_user_2_name
+        )
+        tool_repository = self.test_db_util.get_repository_by_name_and_owner(
+            tool_repository_name, common.test_user_1_name
+        )
         self.check_repository_dependency(tool_repository, datatypes_repository)
 
     def test_0045_install_blastxml_to_top_descr(self):
-        '''Install the blastxml_to_top_descr_0120 repository to Galaxy.
+        """Install the blastxml_to_top_descr_0120 repository to Galaxy.
 
         We are at step 1, Galaxy side.
         Install blastxml_to_top_descr_0120 to Galaxy, with repository dependencies, so that the datatypes repository is also installed.
-        '''
+        """
         global base_datatypes_count
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         base_datatypes_count = int(self.get_datatypes_count())
-        post_submit_strings_displayed = ['blastxml_to_top_descr_0120', 'blast_datatypes_0120', 'New']
-        self.install_repository(name='blastxml_to_top_descr_0120',
-                                owner=common.test_user_1_name,
-                                category_name='Test 0120',
-                                install_repository_dependencies=True,
-                                post_submit_strings_displayed=post_submit_strings_displayed,
-                                new_tool_panel_section_label='Test 0120')
+        post_submit_strings_displayed = ["blastxml_to_top_descr_0120", "blast_datatypes_0120", "New"]
+        self.install_repository(
+            name="blastxml_to_top_descr_0120",
+            owner=common.test_user_1_name,
+            category_name="Test 0120",
+            install_repository_dependencies=True,
+            post_submit_strings_displayed=post_submit_strings_displayed,
+            new_tool_panel_section_label="Test 0120",
+        )
 
     def test_0050_verify_repository_installation(self):
-        '''Verify installation of blastxml_to_top_descr_0120 and blast_datatypes_0120.
+        """Verify installation of blastxml_to_top_descr_0120 and blast_datatypes_0120.
 
         We are at step 1a, Galaxy side.
         Check that the blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories installed correctly, and that there
         are now new datatypes in the registry matching the ones defined in blast_datatypes_0120. Also check that
         blast_datatypes_0120 is labeled as an installed repository dependency of blastxml_to_top_descr_0120.
-        '''
+        """
         global repository_datatypes_count
         global base_datatypes_count
-        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(tool_repository_name, common.test_user_1_name)
-        datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_2_name)
+        tool_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            tool_repository_name, common.test_user_1_name
+        )
+        datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            datatypes_repository_name, common.test_user_2_name
+        )
         current_datatypes = int(self.get_datatypes_count())
         expected_count = base_datatypes_count + repository_datatypes_count
         # Once the BLAST datatypes have been included in Galaxy itself, the count won't change
-        assert current_datatypes == base_datatypes_count or current_datatypes == expected_count, \
-            'Installing %s did not add new datatypes. Expected: %d. Found: %d' % \
-            ('blastxml_to_top_descr_0120', expected_count, current_datatypes)
-        strings_displayed = ['Installed repository dependencies', 'user1', 'blast_datatypes_0120']
-        strings_displayed.extend(['Valid tools', 'BLAST top hit', 'Make a table', datatypes_repository.installed_changeset_revision])
+        assert (
+            current_datatypes == base_datatypes_count or current_datatypes == expected_count
+        ), "Installing %s did not add new datatypes. Expected: %d. Found: %d" % (
+            "blastxml_to_top_descr_0120",
+            expected_count,
+            current_datatypes,
+        )
+        strings_displayed = ["Installed repository dependencies", "user1", "blast_datatypes_0120"]
+        strings_displayed.extend(
+            ["Valid tools", "BLAST top hit", "Make a table", datatypes_repository.installed_changeset_revision]
+        )
         self.display_installed_repository_manage_page(tool_repository, strings_displayed=strings_displayed)
-        strings_displayed = ['Datatypes', 'blastxml', 'blastdbp', 'blastdbn', 'BlastXml', 'BlastNucDb', 'BlastProtDb']
-        strings_displayed.extend(['application/xml', 'text/html'])
+        strings_displayed = ["Datatypes", "blastxml", "blastdbp", "blastdbn", "BlastXml", "BlastNucDb", "BlastProtDb"]
+        strings_displayed.extend(["application/xml", "text/html"])
         self.display_installed_repository_manage_page(datatypes_repository, strings_displayed=strings_displayed)
diff --git a/lib/tool_shed/test/functional/test_1150_datatype_converters.py b/lib/tool_shed/test/functional/test_1150_datatype_converters.py
index 061cd037a8f..4b3be1808e2 100644
--- a/lib/tool_shed/test/functional/test_1150_datatype_converters.py
+++ b/lib/tool_shed/test/functional/test_1150_datatype_converters.py
@@ -1,88 +1,101 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'bed_to_gff_0130'
+repository_name = "bed_to_gff_0130"
 repository_description = "Converter: BED to GFF"
 repository_long_description = "Convert bed to gff"
 
-category_name = 'Test 0130 Datatype Converters'
-category_description = 'Test 0130 Datatype Converters'
+category_name = "Test 0130 Datatype Converters"
+category_description = "Test 0130 Datatype Converters"
 
-'''
+"""
 1) Install the bed_to_gff_converter repository.
 2) Make sure the page section to select a tool panel section is NOT displayed since the tool will not be displayed in the Galaxy tool panel.
 3) Make sure the bed_to_gff_converter tool is not displayed in the tool panel.
-'''
+"""
 
 
 class TestDatatypeConverters(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_bed_to_gff_repository(self):
-        '''Create and populate bed_to_gff_0130.'''
+        """Create and populate bed_to_gff_0130."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named bed_to_gff_0130 owned by user1.
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             # Upload bed_to_gff_converter.tar to the repository, if the repository is new.
-            self.upload_file(repository,
-                             filename='bed_to_gff_converter/bed_to_gff_converter.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded bed_to_gff_converter.tar.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="bed_to_gff_converter/bed_to_gff_converter.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded bed_to_gff_converter.tar.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_install_datatype_converter_to_galaxy(self):
-        '''Install bed_to_gff_converter_0130 into the running Galaxy instance.
+        """Install bed_to_gff_converter_0130 into the running Galaxy instance.
 
         We are at step 1 - Install the bed_to_gff_converter repository.
         Install bed_to_gff_converter_0130, checking that the option to select the tool panel section is *not* displayed.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         preview_strings_displayed = [repository.name, self.get_repository_tip(repository)]
-        strings_displayed = ['Your Galaxy instance is configured with', 'shed-related tool configuration file']
-        strings_not_displayed = ['tool panel section']
-        self.install_repository(repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                preview_strings_displayed=preview_strings_displayed,
-                                strings_displayed=strings_displayed,
-                                strings_not_displayed=strings_not_displayed,
-                                post_submit_strings_displayed=[repository.name, 'New'],
-                                includes_tools_for_display_in_tool_panel=False)
+        strings_displayed = ["Your Galaxy instance is configured with", "shed-related tool configuration file"]
+        strings_not_displayed = ["tool panel section"]
+        self.install_repository(
+            repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            preview_strings_displayed=preview_strings_displayed,
+            strings_displayed=strings_displayed,
+            strings_not_displayed=strings_not_displayed,
+            post_submit_strings_displayed=[repository.name, "New"],
+            includes_tools_for_display_in_tool_panel=False,
+        )
 
     def test_0015_uninstall_and_verify_tool_panel_section(self):
-        '''Uninstall bed_to_gff_converter_0130 and verify that the saved tool_panel_section is None.
+        """Uninstall bed_to_gff_converter_0130 and verify that the saved tool_panel_section is None.
 
         We are at step 3 - Make sure the bed_to_gff_converter tool is not displayed in the tool panel.
         The previous tool panel section for a tool is only recorded in the metadata when a repository is uninstalled,
         so we have to uninstall it first, then verify that it was not assigned a tool panel section.
-        '''
+        """
         repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
         self.uninstall_repository(repository)
         self.verify_installed_repository_no_tool_panel_section(repository)
diff --git a/lib/tool_shed/test/functional/test_1160_tool_help_images.py b/lib/tool_shed/test/functional/test_1160_tool_help_images.py
index 91449a893bb..4881a4fa4ca 100644
--- a/lib/tool_shed/test/functional/test_1160_tool_help_images.py
+++ b/lib/tool_shed/test/functional/test_1160_tool_help_images.py
@@ -1,15 +1,18 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'htseq_count_0140'
+repository_name = "htseq_count_0140"
 repository_description = "Converter: BED to GFF"
 repository_long_description = "Convert bed to gff"
 
-category_name = 'Test 0140 Tool Help Images'
-category_description = 'Test 0140 Tool Help Images'
+category_name = "Test 0140 Tool Help Images"
+category_description = "Test 0140 Tool Help Images"
 
 # 1) Create and populate the htseq_count_0140 repository.
 # 2) Visit the manage_repository page, then the tool page, and look for the image string
@@ -18,51 +21,57 @@ category_description = 'Test 0140 Tool Help Images'
 
 
 class TestToolHelpImages(ShedTwillTestCase):
-    '''Test features related to tool help images.'''
+    """Test features related to tool help images."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_htseq_count_repository(self):
-        '''Create and populate htseq_count_0140.
+        """Create and populate htseq_count_0140.
 
         We are at step 1 - Create and populate the htseq_count_0140 repository.
         Create the htseq_count_0140 repository and upload the tarball.
-        '''
+        """
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         # Create a repository named htseq_count_0140 owned by user1.
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             # Upload htseq_count.tar to the repository if it hasn't already been populated.
-            self.upload_file(repository,
-                             filename='htseq_count/htseq_count.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded htseq_count.tar.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="htseq_count/htseq_count.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded htseq_count.tar.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_load_tool_page(self):
-        '''Load the tool page and check for the image URL.
+        """Load the tool page and check for the image URL.
 
         This is a duplicate of test method _0010 in test_0140_tool_help_images.
-        '''
+        """
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         # Get the repository tip.
         changeset_revision = self.get_repository_tip(repository)
@@ -72,5 +81,7 @@ class TestToolHelpImages(ShedTwillTestCase):
         # The repository uploaded in this test should only have one metadata revision, with one tool defined, which
         # should be the tool that contains a link to the image.
         repository_metadata = repository.metadata_revisions[0].metadata
-        tool_path = repository_metadata['tools'][0]['tool_config']
-        self.load_display_tool_page(repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[])
+        tool_path = repository_metadata["tools"][0]["tool_config"]
+        self.load_display_tool_page(
+            repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[]
+        )
diff --git a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py
index 0d3dfb5a3b4..a06e32bac48 100644
--- a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py
@@ -1,21 +1,24 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-column_repository_name = 'column_maker_0150'
+column_repository_name = "column_maker_0150"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0150'
+convert_repository_name = "convert_chars_0150"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 0150 Simple Prior Installation'
-category_description = 'Test 0150 Simple Prior Installation'
+category_name = "Test 0150 Simple Prior Installation"
+category_description = "Test 0150 Simple Prior Installation"
 
-'''
+"""
 Create column_maker and convert_chars.
 
 Column maker repository dependency:
@@ -27,119 +30,158 @@ Galaxy side:
 
 Install column_maker.
 Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
-'''
+"""
 
 running_standalone = False
 
 
 class TestSimplePriorInstallation(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_convert_repository(self):
-        '''Create and populate convert_chars_0150.'''
+        """Create and populate convert_chars_0150."""
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate convert_chars_0150.'''
+        """Create and populate convert_chars_0150."""
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if running_standalone:
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_repository_dependency(self):
-        '''Create a repository dependency specifying convert_chars.
+        """Create a repository dependency specifying convert_chars.
 
         Column maker repository dependency:
             <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="<tip>" prior_installation_required="True" />
-        '''
+        """
         global running_standalone
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         if running_standalone:
-            dependency_xml_path = self.generate_temp_path('test_1150', additional_paths=['column'])
-            convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
-            self.create_repository_dependency(repository=column_repository,
-                                              repository_tuples=[convert_tuple],
-                                              filepath=dependency_xml_path,
-                                              prior_installation_required=True)
+            dependency_xml_path = self.generate_temp_path("test_1150", additional_paths=["column"])
+            convert_tuple = (
+                self.url,
+                convert_repository.name,
+                convert_repository.user.username,
+                self.get_repository_tip(convert_repository),
+            )
+            self.create_repository_dependency(
+                repository=column_repository,
+                repository_tuples=[convert_tuple],
+                filepath=dependency_xml_path,
+                prior_installation_required=True,
+            )
 
     def test_0020_verify_repository_dependency(self):
-        '''Verify that the previously generated repositiory dependency displays correctly.'''
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        self.check_repository_dependency(repository=column_repository,
-                                         depends_on_repository=convert_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
+        """Verify that the previously generated repositiory dependency displays correctly."""
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        self.check_repository_dependency(
+            repository=column_repository,
+            depends_on_repository=convert_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
 
     def test_0025_install_column_repository(self):
-        '''Install column_maker_0150.'''
+        """Install column_maker_0150."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        preview_strings_displayed = ['column_maker_0150', self.get_repository_tip(column_repository)]
-        strings_displayed = ['Choose the tool panel section']
-        self.install_repository(column_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                preview_strings_displayed=preview_strings_displayed,
-                                strings_displayed=strings_displayed,
-                                strings_not_displayed=[],
-                                post_submit_strings_displayed=['column_maker_0150', 'New'],
-                                includes_tools_for_display_in_tool_panel=True)
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        preview_strings_displayed = ["column_maker_0150", self.get_repository_tip(column_repository)]
+        strings_displayed = ["Choose the tool panel section"]
+        self.install_repository(
+            column_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            preview_strings_displayed=preview_strings_displayed,
+            strings_displayed=strings_displayed,
+            strings_not_displayed=[],
+            post_submit_strings_displayed=["column_maker_0150", "New"],
+            includes_tools_for_display_in_tool_panel=True,
+        )
 
     def test_0030_verify_installation_order(self):
-        '''Verify that convert_chars_0150 was installed before column_maker_0150.'''
-        column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name)
+        """Verify that convert_chars_0150 was installed before column_maker_0150."""
+        column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         # Column maker was selected for installation, so convert chars should have been installed first, as reflected by the update_time field.
-        assert column_repository.update_time > convert_repository.update_time, 'Error: column_maker_0150 shows an earlier update time than convert_chars_0150'
+        assert (
+            column_repository.update_time > convert_repository.update_time
+        ), "Error: column_maker_0150 shows an earlier update time than convert_chars_0150"
diff --git a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
index a4b8d015cb3..affea075c83 100644
--- a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
@@ -1,25 +1,28 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-filter_repository_name = 'filtering_0160'
+filter_repository_name = "filtering_0160"
 filter_repository_description = "Galaxy's filtering tool for test 0160"
 filter_repository_long_description = "Long description of Galaxy's filtering tool for test 0160"
 
-column_repository_name = 'column_maker_0160'
+column_repository_name = "column_maker_0160"
 column_repository_description = "Add column"
 column_repository_long_description = "Compute an expression on every row"
 
-convert_repository_name = 'convert_chars_0160'
+convert_repository_name = "convert_chars_0160"
 convert_repository_description = "Convert delimiters"
 convert_repository_long_description = "Convert delimiters to tab"
 
-category_name = 'Test 0160 Simple Prior Installation'
-category_description = 'Test 0160 Simple Prior Installation'
+category_name = "Test 0160 Simple Prior Installation"
+category_description = "Test 0160 Simple Prior Installation"
 
-'''
+"""
 Create column_maker, filtering, and convert_chars.
 
 Column maker repository dependency:
@@ -40,211 +43,291 @@ Galaxy side:
 
 Install filtering.
 Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
-'''
+"""
 
 running_standalone = False
 
 
 class TestSimplePriorInstallation(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_convert_repository(self):
-        '''Create and populate convert_chars_0160.'''
+        """Create and populate convert_chars_0160."""
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=convert_repository_name,
-                                                   description=convert_repository_description,
-                                                   long_description=convert_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=convert_repository_name,
+            description=convert_repository_description,
+            long_description=convert_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='convert_chars/convert_chars.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded convert_chars tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="convert_chars/convert_chars.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded convert_chars tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate convert_chars_0160.'''
+        """Create and populate convert_chars_0160."""
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if running_standalone:
-            self.upload_file(repository,
-                             filename='column_maker/column_maker.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded column_maker tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="column_maker/column_maker.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded column_maker tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_filtering_repository(self):
-        '''Create and populate filtering_0160.'''
+        """Create and populate filtering_0160."""
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
-        repository = self.get_or_create_repository(name=filter_repository_name,
-                                                   description=filter_repository_description,
-                                                   long_description=filter_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=filter_repository_name,
+            description=filter_repository_description,
+            long_description=filter_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if running_standalone:
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_create_repository_dependency(self):
-        '''Create a repository dependency specifying convert_chars.
+        """Create a repository dependency specifying convert_chars.
 
         Each of the three repositories should depend on the other two, to make this as circular as possible.
-        '''
+        """
         global running_standalone
-        filter_repository = self.test_db_util.get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
+        filter_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         filter_revision = self.get_repository_tip(filter_repository)
         column_revision = self.get_repository_tip(column_repository)
         convert_revision = self.get_repository_tip(convert_repository)
         if running_standalone:
-            dependency_xml_path = self.generate_temp_path('test_1160', additional_paths=['column'])
+            dependency_xml_path = self.generate_temp_path("test_1160", additional_paths=["column"])
             column_tuple = (self.url, column_repository.name, column_repository.user.username, column_revision)
             convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, convert_revision)
             filter_tuple = (self.url, filter_repository.name, filter_repository.user.username, filter_revision)
-            self.create_repository_dependency(repository=column_repository,
-                                              repository_tuples=[convert_tuple, filter_tuple],
-                                              filepath=dependency_xml_path,
-                                              prior_installation_required=False)
-            self.create_repository_dependency(repository=convert_repository,
-                                              repository_tuples=[column_tuple, filter_tuple],
-                                              filepath=dependency_xml_path,
-                                              prior_installation_required=False)
-            self.create_repository_dependency(repository=filter_repository,
-                                              repository_tuples=[convert_tuple, column_tuple],
-                                              filepath=dependency_xml_path,
-                                              prior_installation_required=True)
+            self.create_repository_dependency(
+                repository=column_repository,
+                repository_tuples=[convert_tuple, filter_tuple],
+                filepath=dependency_xml_path,
+                prior_installation_required=False,
+            )
+            self.create_repository_dependency(
+                repository=convert_repository,
+                repository_tuples=[column_tuple, filter_tuple],
+                filepath=dependency_xml_path,
+                prior_installation_required=False,
+            )
+            self.create_repository_dependency(
+                repository=filter_repository,
+                repository_tuples=[convert_tuple, column_tuple],
+                filepath=dependency_xml_path,
+                prior_installation_required=True,
+            )
 
     def test_0025_verify_repository_dependency(self):
-        '''Verify that the previously generated repositiory dependency displays correctly.'''
-        filter_repository = self.test_db_util.get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
-        self.check_repository_dependency(repository=column_repository,
-                                         depends_on_repository=convert_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=column_repository,
-                                         depends_on_repository=filter_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=convert_repository,
-                                         depends_on_repository=column_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=convert_repository,
-                                         depends_on_repository=filter_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=filter_repository,
-                                         depends_on_repository=column_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
-        self.check_repository_dependency(repository=filter_repository,
-                                         depends_on_repository=convert_repository,
-                                         depends_on_changeset_revision=None,
-                                         changeset_revision=None)
+        """Verify that the previously generated repositiory dependency displays correctly."""
+        filter_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_repository_by_name_and_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
+            convert_repository_name, common.test_user_1_name
+        )
+        self.check_repository_dependency(
+            repository=column_repository,
+            depends_on_repository=convert_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=column_repository,
+            depends_on_repository=filter_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=convert_repository,
+            depends_on_repository=column_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=convert_repository,
+            depends_on_repository=filter_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=filter_repository,
+            depends_on_repository=column_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
+        self.check_repository_dependency(
+            repository=filter_repository,
+            depends_on_repository=convert_repository,
+            depends_on_changeset_revision=None,
+            changeset_revision=None,
+        )
 
     def test_0030_install_filtering_repository(self):
-        '''Install the filtering_0160 repository.'''
+        """Install the filtering_0160 repository."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        filter_repository = self.test_db_util.get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name)
-        preview_strings_displayed = ['filtering_0160', self.get_repository_tip(filter_repository)]
-        strings_displayed = ['Choose the tool panel section']
-        self.install_repository(filter_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                preview_strings_displayed=preview_strings_displayed,
-                                strings_displayed=strings_displayed,
-                                strings_not_displayed=[],
-                                post_submit_strings_displayed=['filtering_0160', 'New'],
-                                includes_tools_for_display_in_tool_panel=True)
+        filter_repository = self.test_db_util.get_repository_by_name_and_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        preview_strings_displayed = ["filtering_0160", self.get_repository_tip(filter_repository)]
+        strings_displayed = ["Choose the tool panel section"]
+        self.install_repository(
+            filter_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            preview_strings_displayed=preview_strings_displayed,
+            strings_displayed=strings_displayed,
+            strings_not_displayed=[],
+            post_submit_strings_displayed=["filtering_0160", "New"],
+            includes_tools_for_display_in_tool_panel=True,
+        )
 
     def test_0035_verify_installation_order(self):
-        '''Verify that convert_chars_0160 and column_maker_0160 were installed before filtering_0160.'''
-        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name)
+        """Verify that convert_chars_0160 and column_maker_0160 were installed before filtering_0160."""
+        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         # Filtering was selected for installation, so convert chars and column maker should have been installed first.
-        assert filter_repository.update_time > convert_repository.update_time, 'Error: convert_chars_0160 shows a later update time than filtering_0160'
-        assert filter_repository.update_time > column_repository.update_time, 'Error: column_maker_0160 shows a later update time than filtering_0160'
+        assert (
+            filter_repository.update_time > convert_repository.update_time
+        ), "Error: convert_chars_0160 shows a later update time than filtering_0160"
+        assert (
+            filter_repository.update_time > column_repository.update_time
+        ), "Error: column_maker_0160 shows a later update time than filtering_0160"
 
     def test_0040_deactivate_all_repositories(self):
-        '''Uninstall convert_chars_0160, column_maker_0160, and filtering_0160.'''
-        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name)
+        """Uninstall convert_chars_0160, column_maker_0160, and filtering_0160."""
+        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(filter_repository)
         self.deactivate_repository(column_repository)
         self.deactivate_repository(convert_repository)
 
     def test_0045_reactivate_filter_repository(self):
-        '''Reinstall the filtering_0160 repository.'''
-        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(filter_repository_name, common.test_user_1_name)
+        """Reinstall the filtering_0160 repository."""
+        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filter_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(filter_repository)
-        strings_displayed = ['filtering_0160',
-                             "Galaxy's filtering tool for test 0160",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             filter_repository.installed_changeset_revision]
+        strings_displayed = [
+            "filtering_0160",
+            "Galaxy's filtering tool for test 0160",
+            "user1",
+            self.url.replace("http://", ""),
+            filter_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'Filter1'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "Filter1"])
         self.display_installed_repository_manage_page(filter_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(filter_repository)
 
     def test_0050_verify_reinstallation_order(self):
-        '''Verify that convert_chars_0160 and column_maker_0160 were reinstalled before filtering_0160.'''
+        """Verify that convert_chars_0160 and column_maker_0160 were reinstalled before filtering_0160."""
         # Fixme: this test is not covering any important behavior since repositories were only deactivated and not uninstalled.
-        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(filter_repository_name, common.test_user_1_name)
-        column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
-        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name)
+        filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            filter_repository_name, common.test_user_1_name
+        )
+        column_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            column_repository_name, common.test_user_1_name
+        )
+        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            convert_repository_name, common.test_user_1_name
+        )
         # Filtering was selected for reinstallation, so convert chars and column maker should have been installed first.
         for repo in [convert_repository, column_repository, filter_repository]:
             self.test_db_util.install_session.refresh(repo)
-        assert filter_repository.update_time > convert_repository.update_time, 'Prior installed convert_chars_0160 shows a later update time than filtering_0160'
-        assert filter_repository.update_time > column_repository.update_time, 'Prior installed column_maker_0160 shows a later update time than filtering_0160'
+        assert (
+            filter_repository.update_time > convert_repository.update_time
+        ), "Prior installed convert_chars_0160 shows a later update time than filtering_0160"
+        assert (
+            filter_repository.update_time > column_repository.update_time
+        ), "Prior installed column_maker_0160 shows a later update time than filtering_0160"
diff --git a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
index c8c192df17b..ef01b99c158 100644
--- a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
@@ -1,176 +1,220 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-matplotlib_repository_name = 'package_matplotlib_1_2_0170'
+matplotlib_repository_name = "package_matplotlib_1_2_0170"
 matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
-matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+matplotlib_repository_long_description = (
+    "This repository is intended to be defined as a complex repository dependency within a separate repository."
+)
 
-numpy_repository_name = 'package_numpy_1_7_0170'
-numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
-numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
+numpy_repository_name = "package_numpy_1_7_0170"
+numpy_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
+)
+numpy_repository_long_description = (
+    "This repository is intended to be defined as a complex repository dependency within a separate repository."
+)
 
-category_name = 'Test 0170 Prior Installation Complex Dependencies'
-category_description = 'Test 0170 Prior Installation Complex Dependencies'
+category_name = "Test 0170 Prior Installation Complex Dependencies"
+category_description = "Test 0170 Prior Installation Complex Dependencies"
 
-'''
+"""
 1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
 2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
 3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
 4. Install package_matplotlib_1_2_0170 with repository dependencies.
 5. Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first.
-'''
+"""
 
 running_standalone = False
 
 
 class TestComplexPriorInstallation(ShedTwillTestCase):
-    '''Test features related to datatype converters.'''
+    """Test features related to datatype converters."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_matplotlib_repository(self):
-        '''Create and populate the package_matplotlib_1_2_0170 repository.
+        """Create and populate the package_matplotlib_1_2_0170 repository.
 
         This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
-        '''
+        """
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=matplotlib_repository_name,
-                                                   description=matplotlib_repository_description,
-                                                   long_description=matplotlib_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=matplotlib_repository_name,
+            description=matplotlib_repository_description,
+            long_description=matplotlib_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='package_matplotlib/package_matplotlib_1_2.tar',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded matplotlib tool dependency tarball.',
-                             strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="package_matplotlib/package_matplotlib_1_2.tar",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded matplotlib tool dependency tarball.",
+                strings_displayed=[
+                    "This repository currently contains a single file named <b>tool_dependencies.xml</b>"
+                ],
+                strings_not_displayed=[],
+            )
 
     def test_0010_create_numpy_repository(self):
-        '''Create and populate the package_numpy_1_7_0170 repository.
+        """Create and populate the package_numpy_1_7_0170 repository.
 
         This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
-        '''
+        """
         global running_standalone
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         if running_standalone:
-            repository = self.get_or_create_repository(name=numpy_repository_name,
-                                                       description=numpy_repository_description,
-                                                       long_description=numpy_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='package_numpy/package_numpy_1_7.tar',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded numpy tool dependency tarball.',
-                             strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
-                             strings_not_displayed=[])
+            repository = self.get_or_create_repository(
+                name=numpy_repository_name,
+                description=numpy_repository_description,
+                long_description=numpy_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="package_numpy/package_numpy_1_7.tar",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded numpy tool dependency tarball.",
+                strings_displayed=[
+                    "This repository currently contains a single file named <b>tool_dependencies.xml</b>"
+                ],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_complex_repository_dependency(self):
-        '''Create a dependency on package_numpy_1_7_0170.
+        """Create a dependency on package_numpy_1_7_0170.
 
         This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
         package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required
         set to True. When matplotlib is selected for installation, the result should be that numpy is compiled
         and installed first.
-        '''
+        """
         global running_standalone
-        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
-        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
+        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(
+            numpy_repository_name, common.test_user_1_name
+        )
+        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(
+            matplotlib_repository_name, common.test_user_1_name
+        )
         # Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but
         # it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable
         # in this case, because matplotlib already has an additional tool dependency definition that we don't want to
         # overwrite.
         new_xml = '    <package name="numpy" version="1.7">\n'
         new_xml += '        <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n'
-        new_xml += '    </package>\n'
+        new_xml += "    </package>\n"
         url = self.url
         name = numpy_repository.name
         owner = numpy_repository.user.username
         if running_standalone:
             changeset_revision = self.get_repository_tip(numpy_repository)
             processed_xml = new_xml % (url, name, owner, changeset_revision)
-            original_xml = open(self.get_filename('package_matplotlib/tool_dependencies.xml')).read()
-            dependency_xml_path = self.generate_temp_path('test_0170', additional_paths=['matplotlib'])
-            new_xml_file = os.path.join(dependency_xml_path, 'tool_dependencies.xml')
-            open(new_xml_file, 'w').write(original_xml.replace('<!--NUMPY-->', processed_xml))
+            original_xml = open(self.get_filename("package_matplotlib/tool_dependencies.xml")).read()
+            dependency_xml_path = self.generate_temp_path("test_0170", additional_paths=["matplotlib"])
+            new_xml_file = os.path.join(dependency_xml_path, "tool_dependencies.xml")
+            open(new_xml_file, "w").write(original_xml.replace("<!--NUMPY-->", processed_xml))
             # Upload the generated complex repository dependency XML to the matplotlib repository.
-            self.upload_file(matplotlib_repository,
-                             filename='tool_dependencies.xml',
-                             filepath=dependency_xml_path,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded complex repository dependency on numpy 1.7.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                matplotlib_repository,
+                filename="tool_dependencies.xml",
+                filepath=dependency_xml_path,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded complex repository dependency on numpy 1.7.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_verify_generated_dependency(self):
-        '''Verify that matplotlib now has a package tool dependency and a complex repository dependency.
+        """Verify that matplotlib now has a package tool dependency and a complex repository dependency.
 
         This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
                          dependency displays correctly.
         'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
         dependency on the latest revision of package_numpy_1_7_0170.
-        '''
-        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
-        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
+        """
+        numpy_repository = self.test_db_util.get_repository_by_name_and_owner(
+            numpy_repository_name, common.test_user_1_name
+        )
+        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(
+            matplotlib_repository_name, common.test_user_1_name
+        )
         changeset_revision = self.get_repository_tip(numpy_repository)
         self.check_repository_dependency(matplotlib_repository, depends_on_repository=numpy_repository)
-        self.display_manage_repository_page(matplotlib_repository, strings_displayed=['numpy', '1.7', 'package', changeset_revision])
+        self.display_manage_repository_page(
+            matplotlib_repository, strings_displayed=["numpy", "1.7", "package", changeset_revision]
+        )
 
     def test_0025_install_matplotlib_repository(self):
-        '''Install the package_matplotlib_1_2_0170 repository.
+        """Install the package_matplotlib_1_2_0170 repository.
 
         This is step 4 - Install package_matplotlib_1_2_0170 with repository dependencies.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
-        preview_strings_displayed = ['package_matplotlib_1_2_0170', self.get_repository_tip(matplotlib_repository)]
-        strings_displayed = ['Handle repository dependencies', numpy_repository_name, 'Never installed']
-        self.install_repository(matplotlib_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True,
-                                preview_strings_displayed=preview_strings_displayed,
-                                strings_displayed=strings_displayed,
-                                strings_not_displayed=[],
-                                post_submit_strings_displayed=['package_matplotlib_1_2_0170', 'New'],
-                                includes_tools_for_display_in_tool_panel=False)
+        matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(
+            matplotlib_repository_name, common.test_user_1_name
+        )
+        preview_strings_displayed = ["package_matplotlib_1_2_0170", self.get_repository_tip(matplotlib_repository)]
+        strings_displayed = ["Handle repository dependencies", numpy_repository_name, "Never installed"]
+        self.install_repository(
+            matplotlib_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+            preview_strings_displayed=preview_strings_displayed,
+            strings_displayed=strings_displayed,
+            strings_not_displayed=[],
+            post_submit_strings_displayed=["package_matplotlib_1_2_0170", "New"],
+            includes_tools_for_display_in_tool_panel=False,
+        )
 
     def test_0030_verify_installation_order(self):
-        '''Verify that the numpy repository was installed before the matplotlib repository.
+        """Verify that the numpy repository was installed before the matplotlib repository.
 
         This is step 5 - Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first.
         In the previous step, package_matplotlib_1_2_0170 was selected for installation, but package_numpy_1_7_0170 had the
         prior_installation_required attribute set. Confirm that this resulted in package_numpy_1_7_0170 being installed before
         package_matplotlib_1_2_0170.
-        '''
-        matplotlib_repository = self.test_db_util.get_installed_repository_by_name_owner(matplotlib_repository_name, common.test_user_1_name)
-        numpy_repository = self.test_db_util.get_installed_repository_by_name_owner(numpy_repository_name, common.test_user_1_name)
-        assert matplotlib_repository.update_time > numpy_repository.update_time, \
-            'Error: package_numpy_1_7_0170 shows a later update time than package_matplotlib_1_2_0170'
+        """
+        matplotlib_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            matplotlib_repository_name, common.test_user_1_name
+        )
+        numpy_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            numpy_repository_name, common.test_user_1_name
+        )
+        assert (
+            matplotlib_repository.update_time > numpy_repository.update_time
+        ), "Error: package_numpy_1_7_0170 shows a later update time than package_matplotlib_1_2_0170"
diff --git a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
index 931a342cbd3..71756223560 100644
--- a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+++ b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
@@ -1,129 +1,172 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 
 class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
-    '''Test uninstalling and reinstalling a basic repository.'''
+    """Test uninstalling and reinstalling a basic repository."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0000 category and upload the filtering repository to the tool shed, if necessary.'''
-        category = self.create_category(name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1')
-        self.create_category(name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2')
+        """Create the 0000 category and upload the filtering repository to the tool shed, if necessary."""
+        category = self.create_category(
+            name="Test 0000 Basic Repository Features 1", description="Test 0000 Basic Repository Features 1"
+        )
+        self.create_category(
+            name="Test 0000 Basic Repository Features 2", description="Test 0000 Basic Repository Features 2"
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name='filtering_0000',
-                                                   description="Galaxy's filtering tool for test 0000",
-                                                   long_description="Long description of Galaxy's filtering tool for test 0000",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
+        repository = self.get_or_create_repository(
+            name="filtering_0000",
+            description="Galaxy's filtering tool for test 0000",
+            long_description="Long description of Galaxy's filtering tool for test 0000",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_0000.txt',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded readme for 1.1.0',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_2.2.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 2.2.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='readme.txt',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded readme for 2.2.0',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_0000.txt",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded readme for 1.1.0",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_2.2.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 2.2.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="readme.txt",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded readme for 2.2.0",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_install_filtering_repository(self):
-        '''Install the filtering repository into the Galaxy instance.'''
+        """Install the filtering repository into the Galaxy instance."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository('filtering_0000',
-                                common.test_user_1_name,
-                                'Test 0000 Basic Repository Features 1',
-                                new_tool_panel_section_label='test_1000')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
-        strings_displayed = ['filtering_0000',
-                             "Galaxy's filtering tool for test 0000",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        self.install_repository(
+            "filtering_0000",
+            common.test_user_1_name,
+            "Test 0000 Basic Repository Features 1",
+            new_tool_panel_section_label="test_1000",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
+        strings_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool for test 0000",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
 
     def test_0015_uninstall_filtering_repository(self):
-        '''Uninstall the filtering repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
+        """Uninstall the filtering repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
         self.uninstall_repository(installed_repository)
-        strings_not_displayed = ['filtering_0000',
-                                 "Galaxy's filtering tool for test 0000",
-                                 installed_repository.installed_changeset_revision]
+        strings_not_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool for test 0000",
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0020_reinstall_filtering_repository(self):
-        '''Reinstall the filtering repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
+        """Reinstall the filtering repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
         self.reinstall_repository(installed_repository)
-        strings_displayed = ['filtering_0000',
-                             "Galaxy's filtering tool for test 0000",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             str(installed_repository.installed_changeset_revision)]
+        strings_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool for test 0000",
+            "user1",
+            self.url.replace("http://", ""),
+            str(installed_repository.installed_changeset_revision),
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'Filter1'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "Filter1"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0025_deactivate_filtering_repository(self):
-        '''Deactivate the filtering repository without removing it from disk.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
+        """Deactivate the filtering repository without removing it from disk."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
         self.deactivate_repository(installed_repository)
-        strings_not_displayed = ['filtering_0000',
-                                 "Galaxy's filtering tool for test 0000",
-                                 installed_repository.installed_changeset_revision]
+        strings_not_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool for test 0000",
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0030_reactivate_filtering_repository(self):
-        '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
+        """Reactivate the filtering repository and verify that it now shows up in the list of installed repositories."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_0000", common.test_user_1_name
+        )
         self.reactivate_repository(installed_repository)
-        strings_displayed = ['filtering_0000',
-                             "Galaxy's filtering tool for test 0000",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             str(installed_repository.installed_changeset_revision)]
+        strings_displayed = [
+            "filtering_0000",
+            "Galaxy's filtering tool for test 0000",
+            "user1",
+            self.url.replace("http://", ""),
+            str(installed_repository.installed_changeset_revision),
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'Filter1'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "Filter1"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
diff --git a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
index 46e0d75e814..e63f9f47663 100644
--- a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
@@ -1,146 +1,199 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 
 class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
-    '''Test uninstalling and reinstalling a repository with tool dependencies.'''
+    """Test uninstalling and reinstalling a repository with tool dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0010 category and upload the freebayes repository to the tool shed, if necessary.'''
-        category = self.create_category(name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.')
+        """Create the 0010 category and upload the freebayes repository to the tool shed, if necessary."""
+        category = self.create_category(
+            name="Test 0010 Repository With Tool Dependencies",
+            description="Tests for a repository with tool dependencies.",
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name='freebayes_0010',
-                                                   description="Galaxy's freebayes tool",
-                                                   long_description="Long description of Galaxy's freebayes tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
+        repository = self.get_or_create_repository(
+            name="freebayes_0010",
+            description="Galaxy's freebayes tool",
+            long_description="Long description of Galaxy's freebayes tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool xml.',
-                             strings_displayed=['Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf'],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/tool_data_table_conf.xml.sample',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool data table sample file.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/sam_fa_indices.loc.sample',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool data table .loc file.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename=os.path.join('freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml'),
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded malformed tool dependency XML.',
-                             strings_displayed=['Exception attempting to parse', 'not well-formed'],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename=os.path.join('freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml'),
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded invalid tool dependency XML.',
-                             strings_displayed=['The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration'],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename=os.path.join('freebayes', 'tool_dependencies.xml'),
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded valid tool dependency XML.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool xml.",
+                strings_displayed=[
+                    "Metadata may have been defined",
+                    "This file requires an entry",
+                    "tool_data_table_conf",
+                ],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/tool_data_table_conf.xml.sample",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool data table sample file.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/sam_fa_indices.loc.sample",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool data table .loc file.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename=os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml"),
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded malformed tool dependency XML.",
+                strings_displayed=["Exception attempting to parse", "not well-formed"],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename=os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml"),
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded invalid tool dependency XML.",
+                strings_displayed=[
+                    "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration"
+                ],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename=os.path.join("freebayes", "tool_dependencies.xml"),
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded valid tool dependency XML.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0010_install_freebayes_repository(self):
-        '''Install the freebayes repository into the Galaxy instance.'''
+        """Install the freebayes repository into the Galaxy instance."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        strings_displayed = ['install Tool Shed managed', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
-        self.install_repository('freebayes_0010',
-                                common.test_user_1_name,
-                                'Test 0010 Repository With Tool Dependencies',
-                                strings_displayed=strings_displayed,
-                                new_tool_panel_section_label='test_1210')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name)
-        strings_displayed = ['freebayes_0010',
-                             "Galaxy's freebayes tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "install Tool Shed managed",
+            "tool dependencies",
+            "freebayes",
+            "0.9.4_9696d0ce8a9",
+            "samtools",
+            "0.1.18",
+        ]
+        self.install_repository(
+            "freebayes_0010",
+            common.test_user_1_name,
+            "Test 0010 Repository With Tool Dependencies",
+            strings_displayed=strings_displayed,
+            new_tool_panel_section_label="test_1210",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "freebayes_0010", common.test_user_1_name
+        )
+        strings_displayed = [
+            "freebayes_0010",
+            "Galaxy's freebayes tool",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
 
     def test_0015_uninstall_freebayes_repository(self):
-        '''Uninstall the freebayes repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name)
+        """Uninstall the freebayes repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "freebayes_0010", common.test_user_1_name
+        )
         self.uninstall_repository(installed_repository)
         strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0020_reinstall_freebayes_repository(self):
-        '''Reinstall the freebayes repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name)
+        """Reinstall the freebayes repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "freebayes_0010", common.test_user_1_name
+        )
         self.reinstall_repository(installed_repository)
-        strings_displayed = ['freebayes_0010',
-                             "Galaxy's freebayes tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "freebayes_0010",
+            "Galaxy's freebayes tool",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'FreeBayes'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "FreeBayes"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0025_deactivate_freebayes_repository(self):
-        '''Deactivate the freebayes repository without removing it from disk.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name)
+        """Deactivate the freebayes repository without removing it from disk."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "freebayes_0010", common.test_user_1_name
+        )
         self.deactivate_repository(installed_repository)
         strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0030_reactivate_freebayes_repository(self):
-        '''Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('freebayes_0010', common.test_user_1_name)
+        """Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "freebayes_0010", common.test_user_1_name
+        )
         self.reactivate_repository(installed_repository)
-        strings_displayed = ['freebayes_0010',
-                             "Galaxy's freebayes tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "freebayes_0010",
+            "Galaxy's freebayes tool",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'FreeBayes'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "FreeBayes"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
diff --git a/lib/tool_shed/test/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py b/lib/tool_shed/test/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
index da514480d1b..b3e6aed5cc2 100644
--- a/lib/tool_shed/test/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
@@ -1,12 +1,17 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_name = "emboss_datatypes_0020"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0020'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_name = "emboss_0020"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
@@ -14,133 +19,175 @@ running_standalone = False
 
 
 class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
-    '''Test uninstalling and reinstalling a repository with tool dependencies.'''
+    """Test uninstalling and reinstalling a repository with tool dependencies."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0020 category and upload the emboss repository to the tool shed, if necessary.'''
+        """Create the 0020 category and upload the emboss repository to the tool shed, if necessary."""
         global repository_datatypes_count
         global running_standalone
-        category = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Tests for a repository with tool dependencies.')
+        category = self.create_category(
+            name="Test 0020 Basic Repository Dependencies", description="Tests for a repository with tool dependencies."
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                             description=datatypes_repository_description,
-                                                             long_description=datatypes_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
+        datatypes_repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(datatypes_repository):
             running_standalone = True
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                              description=emboss_repository_description,
-                                                              long_description=emboss_repository_long_description,
-                                                              owner=common.test_user_1_name,
-                                                              category_id=self.security.encode_id(category.id),
-                                                              strings_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1020', additional_paths=['emboss', '5'])
-            repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            emboss_repository = self.get_or_create_repository(
+                name=emboss_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1020", additional_paths=["emboss", "5"])
+            repository_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
         repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
 
     def test_0010_install_emboss_repository(self):
-        '''Install the emboss repository into the Galaxy instance.'''
+        """Install the emboss repository into the Galaxy instance."""
         global repository_datatypes_count
         global base_datatypes_count
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         base_datatypes_count = int(self.get_datatypes_count())
-        strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
-        self.install_repository(emboss_repository_name,
-                                common.test_user_1_name,
-                                'Test 0020 Basic Repository Dependencies',
-                                strings_displayed=strings_displayed,
-                                new_tool_panel_section_label='test_1210')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
-        strings_displayed = ['emboss_0020',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = ["Handle", "Never installed", "tool dependencies", "emboss", "5.0.0", "package"]
+        self.install_repository(
+            emboss_repository_name,
+            common.test_user_1_name,
+            "Test 0020 Basic Repository Dependencies",
+            strings_displayed=strings_displayed,
+            new_tool_panel_section_label="test_1210",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "emboss_0020",
+            "Galaxy wrappers for Emboss version 5.0.0 tools",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
         current_datatypes = int(self.get_datatypes_count())
         # If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
         # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
         # have been added, otherwise verify that the count is unchanged.
         if running_standalone:
-            assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
+            assert (
+                current_datatypes == base_datatypes_count + repository_datatypes_count
+            ), "Installing emboss did not add new datatypes."
         else:
-            assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
+            assert current_datatypes == base_datatypes_count, "Installing emboss added new datatypes."
 
     def test_0015_uninstall_emboss_repository(self):
-        '''Uninstall the emboss repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Uninstall the emboss repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_repository)
         strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0020_reinstall_emboss_repository(self):
-        '''Reinstall the emboss repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Reinstall the emboss repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.reinstall_repository(installed_repository)
-        strings_displayed = ['emboss_0020',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "emboss_0020",
+            "Galaxy wrappers for Emboss version 5.0.0 tools",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "emboss"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0025_deactivate_emboss_repository(self):
-        '''Deactivate the emboss repository without removing it from disk.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Deactivate the emboss repository without removing it from disk."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_repository)
-        strings_not_displayed = ['emboss_0020',
-                                 installed_repository.installed_changeset_revision]
+        strings_not_displayed = ["emboss_0020", installed_repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0030_reactivate_emboss_repository(self):
-        '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Reactivate the emboss repository and verify that it now shows up in the list of installed repositories."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(installed_repository)
-        strings_displayed = ['emboss_0020',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "emboss_0020",
+            "Galaxy wrappers for Emboss version 5.0.0 tools",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "emboss"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
diff --git a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
index 8c8756d95b8..9f987463788 100644
--- a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
+++ b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
@@ -1,14 +1,19 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0030'
+datatypes_repository_name = "emboss_datatypes_0030"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
 
-emboss_repository_name = 'emboss_0030'
-emboss_5_repository_name = 'emboss_5_0030'
-emboss_6_repository_name = 'emboss_6_0030'
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_name = "emboss_0030"
+emboss_5_repository_name = "emboss_5_0030"
+emboss_6_repository_name = "emboss_6_0030"
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
@@ -16,166 +21,248 @@ running_standalone = False
 
 
 class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
-    '''Test uninstalling and reinstalling a repository with repository dependency revisions.'''
+    """Test uninstalling and reinstalling a repository with repository dependency revisions."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(admin_user)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 0030 category and upload the emboss repository to the tool shed, if necessary.'''
+        """Create the 0030 category and upload the emboss repository to the tool shed, if necessary."""
         global repository_datatypes_count
         global running_standalone
-        category = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Tests for a repository with tool dependencies.')
+        category = self.create_category(
+            name="Test 0030 Repository Dependency Revisions",
+            description="Tests for a repository with tool dependencies.",
+        )
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name,
-                                                             description=datatypes_repository_description,
-                                                             long_description=datatypes_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
+        datatypes_repository = self.get_or_create_repository(
+            name=datatypes_repository_name,
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(datatypes_repository):
             running_standalone = True
-            emboss_5_repository = self.get_or_create_repository(name=emboss_5_repository_name,
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category.id),
-                                                                strings_displayed=[])
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1030', additional_paths=['emboss', '5'])
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
-            emboss_6_repository = self.get_or_create_repository(name=emboss_6_repository_name,
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_6_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1030', additional_paths=['emboss', '6'])
-            datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
-            emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
-                                                              description=emboss_repository_description,
-                                                              long_description=emboss_repository_long_description,
-                                                              owner=common.test_user_1_name,
-                                                              category_id=self.security.encode_id(category.id),
-                                                              strings_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_1030', additional_paths=['emboss', '5'])
-            dependency_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            dependency_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
+            emboss_5_repository = self.get_or_create_repository(
+                name=emboss_5_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_5_repository,
+                repository_tuples=[datatypes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            emboss_6_repository = self.get_or_create_repository(
+                name=emboss_6_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_6_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "6"])
+            datatypes_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_6_repository,
+                repository_tuples=[datatypes_tuple],
+                filepath=repository_dependencies_path,
+            )
+            emboss_repository = self.get_or_create_repository(
+                name=emboss_repository_name,
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
+            dependency_tuple = (
+                self.url,
+                emboss_5_repository.name,
+                emboss_5_repository.user.username,
+                self.get_repository_tip(emboss_5_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            dependency_tuple = (
+                self.url,
+                emboss_6_repository.name,
+                emboss_6_repository.user.username,
+                self.get_repository_tip(emboss_6_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
         repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
 
     def test_0010_install_emboss_repository(self):
-        '''Install the emboss repository into the Galaxy instance.'''
+        """Install the emboss repository into the Galaxy instance."""
         global repository_datatypes_count
         global base_datatypes_count
         global running_standalone
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         base_datatypes_count = int(self.get_datatypes_count())
-        strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
-        self.install_repository(emboss_repository_name,
-                                common.test_user_1_name,
-                                'Test 0030 Repository Dependency Revisions',
-                                strings_displayed=strings_displayed,
-                                new_tool_panel_section_label='test_1210')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
-        strings_displayed = ['emboss_0030',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = ["Handle", "Never installed", "tool dependencies", "emboss", "5.0.0", "package"]
+        self.install_repository(
+            emboss_repository_name,
+            common.test_user_1_name,
+            "Test 0030 Repository Dependency Revisions",
+            strings_displayed=strings_displayed,
+            new_tool_panel_section_label="test_1210",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "emboss_0030",
+            "Galaxy wrappers for Emboss version 5.0.0 tools",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
         current_datatypes = int(self.get_datatypes_count())
         # If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
         # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
         # have been added, otherwise verify that the count is unchanged.
         if running_standalone:
-            assert current_datatypes == base_datatypes_count + repository_datatypes_count, \
-                'Installing emboss resulted in unexpected count in datatypes registry, expected: %s, actual: %s, original: %s, added from repo: %s' % \
-                (str(base_datatypes_count + repository_datatypes_count), str(current_datatypes), str(base_datatypes_count), str(repository_datatypes_count))
+            assert current_datatypes == base_datatypes_count + repository_datatypes_count, (
+                "Installing emboss resulted in unexpected count in datatypes registry, expected: %s, actual: %s, original: %s, added from repo: %s"
+                % (
+                    str(base_datatypes_count + repository_datatypes_count),
+                    str(current_datatypes),
+                    str(base_datatypes_count),
+                    str(repository_datatypes_count),
+                )
+            )
         else:
-            assert current_datatypes == base_datatypes_count, \
-                'Installing emboss added new datatypes, current datatypes: %s, original datatypes: %s' % \
-                (str(current_datatypes), str(base_datatypes_count))
+            assert (
+                current_datatypes == base_datatypes_count
+            ), "Installing emboss added new datatypes, current datatypes: %s, original datatypes: %s" % (
+                str(current_datatypes),
+                str(base_datatypes_count),
+            )
 
     def test_0015_uninstall_emboss_repository(self):
-        '''Uninstall the emboss repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Uninstall the emboss repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_repository)
         strings_not_displayed = [installed_repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0020_reinstall_emboss_repository(self):
-        '''Reinstall the emboss repository.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Reinstall the emboss repository."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.reinstall_repository(installed_repository)
-        strings_displayed = ['emboss_0030',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "emboss_0030",
+            "Galaxy wrappers for Emboss version 5.0.0 tools",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "emboss"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0025_deactivate_emboss_repository(self):
-        '''Deactivate the emboss repository without removing it from disk.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Deactivate the emboss repository without removing it from disk."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.deactivate_repository(installed_repository)
         strings_not_displayed = [installed_repository.installed_changeset_revision]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
 
     def test_0030_reactivate_emboss_repository(self):
-        '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.'''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
+        """Reactivate the emboss repository and verify that it now shows up in the list of installed repositories."""
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            emboss_repository_name, common.test_user_1_name
+        )
         self.reactivate_repository(installed_repository)
-        strings_displayed = ['emboss_0030',
-                             'Galaxy wrappers for Emboss version 5.0.0 tools',
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = [
+            "emboss_0030",
+            "Galaxy wrappers for Emboss version 5.0.0 tools",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "emboss"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
diff --git a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
index 17178d96cc2..eecf3f81602 100644
--- a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
@@ -1,27 +1,32 @@
 import os
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_name = "emboss_datatypes_0020"
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
-datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
-emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
-workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
-workflow_name = 'Workflow for 0060_filter_workflow_repository'
+datatypes_repository_long_description = (
+    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+)
+emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
+workflow_filename = "Workflow_for_0060_filter_workflow_repository.ga"
+workflow_name = "Workflow for 0060_filter_workflow_repository"
 filtering_repository_description = "Galaxy's filtering tool for test 0040"
 filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"
 
-category_0000_name = 'Test 0000 Basic Repository Features 1'
-category_0001_name = 'Test 0000 Basic Repository Features 2'
-category_0010_name = 'Test 0010 Repository With Tool Dependencies'
-category_0020_name = 'Test 0020 Basic Repository Dependencies'
-category_0030_name = 'Test 0030 Repository Dependency Revisions'
-category_0040_name = 'test_0040_repository_circular_dependencies'
-category_0050_name = 'test_0050_repository_n_level_circular_dependencies'
-category_0060_name = 'Test 0060 Workflow Features'
+category_0000_name = "Test 0000 Basic Repository Features 1"
+category_0001_name = "Test 0000 Basic Repository Features 2"
+category_0010_name = "Test 0010 Repository With Tool Dependencies"
+category_0020_name = "Test 0020 Basic Repository Dependencies"
+category_0030_name = "Test 0030 Repository Dependency Revisions"
+category_0040_name = "test_0040_repository_circular_dependencies"
+category_0050_name = "test_0050_repository_n_level_circular_dependencies"
+category_0060_name = "Test 0060 Workflow Features"
 
-'''
+"""
 This script will run in one of two possible ways:
 
 1. Directly, by calling sh run_functional_tests.sh -toolshed test/tool_shed/functional/test_1300_reset_all_metadata.py. -or-
@@ -30,7 +35,7 @@ This script will run in one of two possible ways:
 In the first case, it is desirable to have the Galaxy database in a state that is as close as possible to the state it would
 be in following the second case. This means explicitly installing whatever repositories would be in an installed state following
 the previous test scripts.
-'''
+"""
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
@@ -38,406 +43,597 @@ running_standalone = False
 
 
 class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
-    '''Verify that the "Reset selected metadata" feature works.'''
+    """Verify that the "Reset selected metadata" feature works."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_categories(self):
-        '''Create the categories for the repositories in this test script.'''
+        """Create the categories for the repositories in this test script."""
         self.login(email=common.admin_email, username=common.admin_username)
-        self.create_category(name=category_0000_name, description='Test 0000 Basic Repository Features 1')
-        self.create_category(name=category_0001_name, description='Test 0000 Basic Repository Features 2')
-        self.create_category(name=category_0010_name, description='Tests for a repository with tool dependencies.')
-        self.create_category(name=category_0020_name, description='Testing basic repository dependency features.')
-        self.create_category(name=category_0030_name, description='Testing repository dependencies by revision.')
-        self.create_category(name=category_0040_name, description='Testing handling of circular repository dependencies.')
-        self.create_category(name=category_0050_name, description='Testing handling of circular repository dependencies to n levels.')
-        self.create_category(name=category_0060_name, description='Test 0060 - Workflow Features')
+        self.create_category(name=category_0000_name, description="Test 0000 Basic Repository Features 1")
+        self.create_category(name=category_0001_name, description="Test 0000 Basic Repository Features 2")
+        self.create_category(name=category_0010_name, description="Tests for a repository with tool dependencies.")
+        self.create_category(name=category_0020_name, description="Testing basic repository dependency features.")
+        self.create_category(name=category_0030_name, description="Testing repository dependencies by revision.")
+        self.create_category(
+            name=category_0040_name, description="Testing handling of circular repository dependencies."
+        )
+        self.create_category(
+            name=category_0050_name, description="Testing handling of circular repository dependencies to n levels."
+        )
+        self.create_category(name=category_0060_name, description="Test 0060 - Workflow Features")
 
     def test_0010_create_repositories_from_0000_series(self):
-        '''Create repository filtering_0000 if necessary.'''
+        """Create repository filtering_0000 if necessary."""
         global running_standalone
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        category = self.create_category(name=category_0000_name, description='')
-        repository = self.get_or_create_repository(name='filtering_0000',
-                                                   description="Galaxy's filtering tool",
-                                                   long_description="Long description of Galaxy's filtering tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
+        category = self.create_category(name=category_0000_name, description="")
+        repository = self.get_or_create_repository(
+            name="filtering_0000",
+            description="Galaxy's filtering tool",
+            long_description="Long description of Galaxy's filtering tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
         if self.repository_is_new(repository):
             running_standalone = True
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_2.2.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 2.2.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_2.2.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 2.2.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0015_create_repositories_from_0010_series(self):
-        '''Create repository freebayes_0010.'''
-        category = self.create_category(name=category_0010_name, description='')
-        repository = self.get_or_create_repository(name='freebayes_0010',
-                                                   description="Galaxy's freebayes tool",
-                                                   long_description="Long description of Galaxy's freebayes tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        """Create repository freebayes_0010."""
+        category = self.create_category(name=category_0010_name, description="")
+        repository = self.get_or_create_repository(
+            name="freebayes_0010",
+            description="Galaxy's freebayes tool",
+            long_description="Long description of Galaxy's freebayes tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded freebayes.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/tool_data_table_conf.xml.sample',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool_data_table_conf.xml.sample',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/sam_fa_indices.loc.sample',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded sam_fa_indices.loc.sample',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(repository,
-                             filename='freebayes/tool_dependencies.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded tool_dependencies.xml',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded freebayes.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/tool_data_table_conf.xml.sample",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool_data_table_conf.xml.sample",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/sam_fa_indices.loc.sample",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded sam_fa_indices.loc.sample",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="freebayes/tool_dependencies.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded tool_dependencies.xml",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0020_create_repositories_from_0020_series(self):
-        '''Create repositories emboss_0020 and emboss_datatypes_0020 if necessary.'''
-        category = self.create_category(name=category_0020_name, description='')
-        repository = self.get_or_create_repository(name='emboss_datatypes_0020',
-                                                   description="Galaxy applicable data formats used by Emboss tools.",
-                                                   long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        """Create repositories emboss_0020 and emboss_datatypes_0020 if necessary."""
+        category = self.create_category(name=category_0020_name, description="")
+        repository = self.get_or_create_repository(
+            name="emboss_datatypes_0020",
+            description="Galaxy applicable data formats used by Emboss tools.",
+            long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository = self.get_or_create_repository(name='emboss_0020',
-                                                 description='Galaxy wrappers for Emboss version 5.0.0 tools',
-                                                 long_description='Galaxy wrappers for Emboss version 5.0.0 tools',
-                                                 owner=common.test_user_1_name,
-                                                 category_id=self.security.encode_id(category.id),
-                                                 strings_displayed=[])
-            self.upload_file(repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository = self.get_or_create_repository(
+                name="emboss_0020",
+                description="Galaxy wrappers for Emboss version 5.0.0 tools",
+                long_description="Galaxy wrappers for Emboss version 5.0.0 tools",
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_0025_create_repositories_from_0030_series(self):
-        '''Create repositories emboss_0030, emboss_5_0030, emboss_6_0030, and emboss_datatypes_0030.'''
+        """Create repositories emboss_0030, emboss_5_0030, emboss_6_0030, and emboss_datatypes_0030."""
         global repository_datatypes_count
-        category = self.create_category(name=category_0030_name, description='')
-        datatypes_repository = self.get_or_create_repository(name='emboss_datatypes_0030',
-                                                             description=datatypes_repository_description,
-                                                             long_description=datatypes_repository_long_description,
-                                                             owner=common.test_user_1_name,
-                                                             category_id=self.security.encode_id(category.id),
-                                                             strings_displayed=[])
+        category = self.create_category(name=category_0030_name, description="")
+        datatypes_repository = self.get_or_create_repository(
+            name="emboss_datatypes_0030",
+            description=datatypes_repository_description,
+            long_description=datatypes_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(datatypes_repository):
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
             repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
-            emboss_5_repository = self.get_or_create_repository(name='emboss_5_0030',
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_5_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_0330', additional_paths=['emboss', '5'])
-            dependency_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            emboss_6_repository = self.get_or_create_repository(name='emboss_6_0030',
-                                                                description=emboss_repository_description,
-                                                                long_description=emboss_repository_long_description,
-                                                                owner=common.test_user_1_name,
-                                                                category_id=self.security.encode_id(category.id),
-                                                                strings_displayed=[])
-            self.upload_file(emboss_6_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_0330', additional_paths=['emboss', '6'])
-            dependency_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            emboss_repository = self.get_or_create_repository(name='emboss_0030',
-                                                              description=emboss_repository_description,
-                                                              long_description=emboss_repository_long_description,
-                                                              owner=common.test_user_1_name,
-                                                              category_id=self.security.encode_id(category.id),
-                                                              strings_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_0330', additional_paths=['emboss', '5'])
-            dependency_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            dependency_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
+            emboss_5_repository = self.get_or_create_repository(
+                name="emboss_5_0030",
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_5_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss", "5"])
+            dependency_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_5_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            emboss_6_repository = self.get_or_create_repository(
+                name="emboss_6_0030",
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_6_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss", "6"])
+            dependency_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_6_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            emboss_repository = self.get_or_create_repository(
+                name="emboss_0030",
+                description=emboss_repository_description,
+                long_description=emboss_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss", "5"])
+            dependency_tuple = (
+                self.url,
+                emboss_5_repository.name,
+                emboss_5_repository.user.username,
+                self.get_repository_tip(emboss_5_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            dependency_tuple = (
+                self.url,
+                emboss_6_repository.name,
+                emboss_6_repository.user.username,
+                self.get_repository_tip(emboss_6_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
 
     def test_0030_create_repositories_from_0040_series(self):
-        '''Create repositories freebayes_0040 and filtering_0040.'''
-        category = self.create_category(name=category_0040_name, description='')
-        repository = self.get_or_create_repository(name='freebayes_0040',
-                                                   description="Galaxy's freebayes tool",
-                                                   long_description="Long description of Galaxy's freebayes tool",
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        """Create repositories freebayes_0040 and filtering_0040."""
+        category = self.create_category(name=category_0040_name, description="")
+        repository = self.get_or_create_repository(
+            name="freebayes_0040",
+            description="Galaxy's freebayes tool",
+            long_description="Long description of Galaxy's freebayes tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='freebayes/freebayes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository = self.get_or_create_repository(name='filtering_0040',
-                                                       description=filtering_repository_description,
-                                                       long_description=filtering_repository_long_description,
-                                                       owner=common.test_user_1_name,
-                                                       category_id=self.security.encode_id(category.id),
-                                                       strings_displayed=[])
-            self.upload_file(repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded the tool tarball for filtering 1.1.0.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository = self.test_db_util.get_repository_by_name_and_owner('freebayes_0040', common.test_user_1_name)
-            filtering_repository = self.test_db_util.get_repository_by_name_and_owner('filtering_0040', common.test_user_1_name)
-            repository_dependencies_path = self.generate_temp_path('test_1340', additional_paths=['filtering'])
-            repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository))
-            self.create_repository_dependency(repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
-            repository = self.test_db_util.get_repository_by_name_and_owner('filtering_0040', common.test_user_1_name)
-            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner('freebayes_0040', common.test_user_1_name)
-            repository_dependencies_path = self.generate_temp_path('test_1340', additional_paths=['freebayes'])
-            repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository))
-            self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
+            self.upload_file(
+                repository,
+                filename="freebayes/freebayes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository = self.get_or_create_repository(
+                name="filtering_0040",
+                description=filtering_repository_description,
+                long_description=filtering_repository_long_description,
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded the tool tarball for filtering 1.1.0.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository = self.test_db_util.get_repository_by_name_and_owner("freebayes_0040", common.test_user_1_name)
+            filtering_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "filtering_0040", common.test_user_1_name
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1340", additional_paths=["filtering"])
+            repository_tuple = (
+                self.url,
+                repository.name,
+                repository.user.username,
+                self.get_repository_tip(repository),
+            )
+            self.create_repository_dependency(
+                repository=filtering_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
+            repository = self.test_db_util.get_repository_by_name_and_owner("filtering_0040", common.test_user_1_name)
+            freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(
+                "freebayes_0040", common.test_user_1_name
+            )
+            repository_dependencies_path = self.generate_temp_path("test_1340", additional_paths=["freebayes"])
+            repository_tuple = (
+                self.url,
+                repository.name,
+                repository.user.username,
+                self.get_repository_tip(repository),
+            )
+            self.create_repository_dependency(
+                repository=freebayes_repository,
+                repository_tuples=[repository_tuple],
+                filepath=repository_dependencies_path,
+            )
 
     def test_0035_create_repositories_from_0050_series(self):
-        '''Create repositories emboss_0050, emboss_datatypes_0050, filtering_0050, freebayes_0050.'''
-        category = self.create_category(name=category_0050_name, description='')
-        datatypes_repository = self.get_or_create_repository(name='emboss_datatypes_0050',
-                                                    description="Datatypes for emboss",
-                                                    long_description="Long description of Emboss' datatypes",
-                                                    owner=common.test_user_1_name,
-                                                    category_id=self.security.encode_id(category.id),
-                                                    strings_displayed=[])
+        """Create repositories emboss_0050, emboss_datatypes_0050, filtering_0050, freebayes_0050."""
+        category = self.create_category(name=category_0050_name, description="")
+        datatypes_repository = self.get_or_create_repository(
+            name="emboss_datatypes_0050",
+            description="Datatypes for emboss",
+            long_description="Long description of Emboss' datatypes",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(datatypes_repository):
-            emboss_repository = self.get_or_create_repository(name='emboss_0050',
-                                                        description="Galaxy's emboss tool",
-                                                        long_description="Long description of Galaxy's emboss tool",
-                                                        owner=common.test_user_1_name,
-                                                        category_id=self.security.encode_id(category.id),
-                                                        strings_displayed=[])
-            filtering_repository = self.get_or_create_repository(name='filtering_0050',
-                                                                 description="Galaxy's filtering tool",
-                                                                 long_description="Long description of Galaxy's filtering tool",
-                                                                 owner=common.test_user_1_name,
-                                                                 category_id=self.security.encode_id(category.id),
-                                                                 strings_displayed=[])
-            freebayes_repository = self.get_or_create_repository(name='freebayes_0050',
-                                                                 description="Galaxy's freebayes tool",
-                                                                 long_description="Long description of Galaxy's freebayes tool",
-                                                                 owner=common.test_user_1_name,
-                                                                 category_id=self.security.encode_id(category.id),
-                                                                 strings_displayed=[])
-            self.upload_file(datatypes_repository,
-                             filename='emboss/datatypes/datatypes_conf.xml',
-                             filepath=None,
-                             valid_tools_only=False,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatypes_conf.xml.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(emboss_repository,
-                             filename='emboss/emboss.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded emboss.tar',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(freebayes_repository,
-                             filename='freebayes/freebayes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded freebayes tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(filtering_repository,
-                             filename='filtering/filtering_1.1.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 1.1.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            repository_dependencies_path = self.generate_temp_path('test_0350', additional_paths=['emboss'])
-            dependency_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            repository_dependencies_path = self.generate_temp_path('test_0350', additional_paths=['filtering'])
-            dependency_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository))
-            self.create_repository_dependency(repository=filtering_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            repository_dependencies_path = self.generate_temp_path('test_0350', additional_paths=['freebayes'])
-            dependency_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository))
-            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path)
-            dependency_tuples = [(self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository)),
-                                 (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository)),
-                                 (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository)),
-                                 (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))]
-            self.create_repository_dependency(repository=freebayes_repository, repository_tuples=dependency_tuples, filepath=repository_dependencies_path)
+            emboss_repository = self.get_or_create_repository(
+                name="emboss_0050",
+                description="Galaxy's emboss tool",
+                long_description="Long description of Galaxy's emboss tool",
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            filtering_repository = self.get_or_create_repository(
+                name="filtering_0050",
+                description="Galaxy's filtering tool",
+                long_description="Long description of Galaxy's filtering tool",
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            freebayes_repository = self.get_or_create_repository(
+                name="freebayes_0050",
+                description="Galaxy's freebayes tool",
+                long_description="Long description of Galaxy's freebayes tool",
+                owner=common.test_user_1_name,
+                category_id=self.security.encode_id(category.id),
+                strings_displayed=[],
+            )
+            self.upload_file(
+                datatypes_repository,
+                filename="emboss/datatypes/datatypes_conf.xml",
+                filepath=None,
+                valid_tools_only=False,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatypes_conf.xml.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                emboss_repository,
+                filename="emboss/emboss.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded emboss.tar",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                freebayes_repository,
+                filename="freebayes/freebayes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded freebayes tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                filtering_repository,
+                filename="filtering/filtering_1.1.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 1.1.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0350", additional_paths=["emboss"])
+            dependency_tuple = (
+                self.url,
+                datatypes_repository.name,
+                datatypes_repository.user.username,
+                self.get_repository_tip(datatypes_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0350", additional_paths=["filtering"])
+            dependency_tuple = (
+                self.url,
+                emboss_repository.name,
+                emboss_repository.user.username,
+                self.get_repository_tip(emboss_repository),
+            )
+            self.create_repository_dependency(
+                repository=filtering_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            repository_dependencies_path = self.generate_temp_path("test_0350", additional_paths=["freebayes"])
+            dependency_tuple = (
+                self.url,
+                filtering_repository.name,
+                filtering_repository.user.username,
+                self.get_repository_tip(filtering_repository),
+            )
+            self.create_repository_dependency(
+                repository=emboss_repository,
+                repository_tuples=[dependency_tuple],
+                filepath=repository_dependencies_path,
+            )
+            dependency_tuples = [
+                (
+                    self.url,
+                    datatypes_repository.name,
+                    datatypes_repository.user.username,
+                    self.get_repository_tip(datatypes_repository),
+                ),
+                (
+                    self.url,
+                    emboss_repository.name,
+                    emboss_repository.user.username,
+                    self.get_repository_tip(emboss_repository),
+                ),
+                (
+                    self.url,
+                    filtering_repository.name,
+                    filtering_repository.user.username,
+                    self.get_repository_tip(filtering_repository),
+                ),
+                (
+                    self.url,
+                    freebayes_repository.name,
+                    freebayes_repository.user.username,
+                    self.get_repository_tip(freebayes_repository),
+                ),
+            ]
+            self.create_repository_dependency(
+                repository=freebayes_repository,
+                repository_tuples=dependency_tuples,
+                filepath=repository_dependencies_path,
+            )
 
     def test_0035_create_repositories_from_0060_series(self):
-        category = self.create_category(name=category_0060_name, description='')
-        workflow_repository = self.get_or_create_repository(name='filtering_0060',
-                                                            description="Galaxy's filtering tool",
-                                                            long_description="Long description of Galaxy's filtering tool",
-                                                            owner=common.test_user_1_name,
-                                                            category_id=self.security.encode_id(category.id),
-                                                            strings_displayed=[])
+        category = self.create_category(name=category_0060_name, description="")
+        workflow_repository = self.get_or_create_repository(
+            name="filtering_0060",
+            description="Galaxy's filtering tool",
+            long_description="Long description of Galaxy's filtering tool",
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(workflow_repository):
-            workflow = open(self.get_filename('filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga')).read()
-            workflow = workflow.replace('__TEST_TOOL_SHED_URL__', self.url.replace('http://', ''))
-            workflow_filepath = self.generate_temp_path('test_0360', additional_paths=['filtering_workflow'])
+            workflow = open(
+                self.get_filename("filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga")
+            ).read()
+            workflow = workflow.replace("__TEST_TOOL_SHED_URL__", self.url.replace("http://", ""))
+            workflow_filepath = self.generate_temp_path("test_0360", additional_paths=["filtering_workflow"])
             if not os.path.exists(workflow_filepath):
                 os.makedirs(workflow_filepath)
-            open(os.path.join(workflow_filepath, workflow_filename), 'w+').write(workflow)
-            self.upload_file(workflow_repository,
-                             filename=workflow_filename,
-                             filepath=workflow_filepath,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering workflow.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
-            self.upload_file(workflow_repository,
-                             filename='filtering/filtering_2.2.0.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=True,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded filtering 2.2.0 tarball.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            open(os.path.join(workflow_filepath, workflow_filename), "w+").write(workflow)
+            self.upload_file(
+                workflow_repository,
+                filename=workflow_filename,
+                filepath=workflow_filepath,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering workflow.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
+            self.upload_file(
+                workflow_repository,
+                filename="filtering/filtering_2.2.0.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=True,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded filtering 2.2.0 tarball.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
 
     def test_9900_install_all_missing_repositories(self):
-        '''Call the install_repository method to ensure that all required repositories are installed.'''
+        """Call the install_repository method to ensure that all required repositories are installed."""
         global repository_datatypes_count
         global base_datatypes_count
         global running_standalone
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         base_datatypes_count = int(self.get_datatypes_count())
-        self.install_repository('filtering_0000', common.test_user_1_name, category_0000_name, strings_displayed=[])
-        self.install_repository('freebayes_0010', common.test_user_1_name, category_0010_name, strings_displayed=[])
-        self.install_repository('emboss_0020', common.test_user_1_name, category_0020_name, strings_displayed=[])
-        self.install_repository('emboss_5_0030', common.test_user_1_name, category_0030_name, strings_displayed=[])
-        self.install_repository('freebayes_0050', common.test_user_1_name, category_0050_name, strings_displayed=[])
-        self.install_repository('filtering_0060', common.test_user_1_name, category_0060_name, strings_displayed=[])
+        self.install_repository("filtering_0000", common.test_user_1_name, category_0000_name, strings_displayed=[])
+        self.install_repository("freebayes_0010", common.test_user_1_name, category_0010_name, strings_displayed=[])
+        self.install_repository("emboss_0020", common.test_user_1_name, category_0020_name, strings_displayed=[])
+        self.install_repository("emboss_5_0030", common.test_user_1_name, category_0030_name, strings_displayed=[])
+        self.install_repository("freebayes_0050", common.test_user_1_name, category_0050_name, strings_displayed=[])
+        self.install_repository("filtering_0060", common.test_user_1_name, category_0060_name, strings_displayed=[])
         current_datatypes = int(self.get_datatypes_count())
         # If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
         # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
         # have been added, otherwise verify that the count is unchanged.
         if running_standalone:
-            message = 'Installing emboss did not add new datatypes.\nFound: %d\nExpected: %d' % \
-                (current_datatypes, base_datatypes_count + repository_datatypes_count)
+            message = "Installing emboss did not add new datatypes.\nFound: %d\nExpected: %d" % (
+                current_datatypes,
+                base_datatypes_count + repository_datatypes_count,
+            )
             assert current_datatypes > base_datatypes_count, message
         else:
-            assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
+            assert current_datatypes == base_datatypes_count, "Installing emboss added new datatypes."
 
     def test_9905_reset_metadata_on_all_repositories(self):
-        '''Reset metadata on all repositories, then verify that it has not changed.'''
+        """Reset metadata on all repositories, then verify that it has not changed."""
         repository_metadata = dict()
         repositories = self.test_db_util.get_all_installed_repositories(actually_installed=True)
         for repository in repositories:
@@ -452,7 +648,13 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
             # is normal and expected behavior, the functional tests assume that repository metadata will not change
             # in any way after a reset. A workaround is to remove the tool panel section from the stored repository
             # metadata dict, in order to eliminate the misleading detection of changed metadata.
-            if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata_:
-                del old_metadata['tool_panel_section']
-            assert repository.metadata_ == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \
-                (repository.status, repository.name, old_metadata, repository.metadata_)
+            if "tool_panel_section" in old_metadata and "tool_panel_section" not in repository.metadata_:
+                del old_metadata["tool_panel_section"]
+            assert (
+                repository.metadata_ == old_metadata
+            ), "Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s" % (
+                repository.status,
+                repository.name,
+                old_metadata,
+                repository.metadata_,
+            )
diff --git a/lib/tool_shed/test/functional/test_1410_update_manager.py b/lib/tool_shed/test/functional/test_1410_update_manager.py
index c1b54c7fd7c..e75198762a3 100644
--- a/lib/tool_shed/test/functional/test_1410_update_manager.py
+++ b/lib/tool_shed/test/functional/test_1410_update_manager.py
@@ -1,27 +1,30 @@
 import logging
 import time
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'filtering_1410'
+repository_name = "filtering_1410"
 repository_description = "Galaxy's filtering tool"
 repository_long_description = "Long description of Galaxy's filtering repository"
 
-category_name = 'Test 1410 - Galaxy Update Manager'
-category_description = 'Functional test suite to test the update manager.'
+category_name = "Test 1410 - Galaxy Update Manager"
+category_description = "Functional test suite to test the update manager."
 
-'''
+"""
 1. Create and populate the filtering_1410 repository.
 2. Install filtering_1410 to Galaxy.
 3. Upload a readme file.
 4. Verify that the browse page now shows an update available.
-'''
+"""
 
 
 class TestUpdateManager(ShedTwillTestCase):
-    '''Test the Galaxy update manager.'''
+    """Test the Galaxy update manager."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts and login as an admin user.
@@ -31,94 +34,107 @@ class TestUpdateManager(ShedTwillTestCase):
         """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
 
     def test_0005_create_filtering_repository(self):
-        '''Create and populate the filtering_1410 repository.
+        """Create and populate the filtering_1410 repository.
 
         We are at step 1 - Create and populate the filtering_1410 repository.
         Create filtering_1410 and upload the tool tarball to it.
-        '''
+        """
         self.login(email=common.admin_email, username=common.admin_username)
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id))
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=True,
-                         commit_message="Uploaded filtering 1.1.0",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=True,
+            commit_message="Uploaded filtering 1.1.0",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_install_filtering_repository(self):
-        '''Install the filtering_1410 repository.
+        """Install the filtering_1410 repository.
 
         We are at step 2 - Install filtering_1410 to Galaxy.
         Install the filtering repository to Galaxy.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository('filtering_1410',
-                                common.test_user_1_name,
-                                category_name,
-                                new_tool_panel_section_label='test_1410')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_1410', common.test_user_1_name)
-        strings_displayed = ['filtering_1410',
-                             "Galaxy's filtering tool",
-                             'user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        self.install_repository(
+            "filtering_1410", common.test_user_1_name, category_name, new_tool_panel_section_label="test_1410"
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filtering_1410", common.test_user_1_name
+        )
+        strings_displayed = [
+            "filtering_1410",
+            "Galaxy's filtering tool",
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'Filter1'])
+        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "Filter1"])
         self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
         self.verify_tool_metadata_for_installed_repository(installed_repository)
 
     def test_0015_upload_readme_file(self):
-        '''Upload readme.txt to filtering_1410.
+        """Upload readme.txt to filtering_1410.
 
         We are at step 3 - Upload a readme file.
         Upload readme.txt. This will have the effect of making the installed changeset revision not be the most recent downloadable revision,
         but without generating a second downloadable revision. Then sleep for 3 seconds to make sure the update manager picks up the new
         revision.
-        '''
+        """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message="Uploaded readme.txt",
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded readme.txt",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_check_for_displayed_update(self):
-        '''Browse installed repositories and verify update.
+        """Browse installed repositories and verify update.
 
         We are at step 4 - Verify that the browse page now shows an update available.
         The browse page should now show filtering_1410 as installed, but with a yellow box indicating that there is an update available.
-        '''
+        """
         # Wait 3 seconds, just to be sure we're past hours_between_check.
         time.sleep(3)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         self.update_tool_shed_status()
-        ok_title = r'title=\"Updates are available in the Tool Shed for this revision\"'
-        updates_icon = '/static/images/icon_warning_sml.gif'
+        ok_title = r"title=\"Updates are available in the Tool Shed for this revision\""
+        updates_icon = "/static/images/icon_warning_sml.gif"
         strings_displayed = [ok_title, updates_icon]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
diff --git a/lib/tool_shed/test/functional/test_1420_tool_dependency_environment_inheritance.py b/lib/tool_shed/test/functional/test_1420_tool_dependency_environment_inheritance.py
index b3bfbea9e5e..319a91678e4 100644
--- a/lib/tool_shed/test/functional/test_1420_tool_dependency_environment_inheritance.py
+++ b/lib/tool_shed/test/functional/test_1420_tool_dependency_environment_inheritance.py
@@ -1,31 +1,42 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 1420 Tool dependency environment variable inheritance'
-category_description = 'Test script 1420 for interpolation of inherited environment variables.'
-package_atlas_repository_name = 'package_atlas_3_10_1420'
-package_bzlib_repository_name = 'package_bzlib_1_0_1420'
-package_boost_repository_name = 'package_boost_1_53_1420'
-package_numpy_repository_name = 'package_numpy_1_7_1420'
-package_rdkit_repository_name = 'package_rdkit_2012_12_1420'
-package_lapack_repository_name = 'package_lapack_3_4_1420'
-package_atlas_repository_description = 'Automatically Tuned Linear Algebra Software'
-package_bzlib_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.0 of the bzlib library.'
-package_boost_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.53 of the boost C++ libraries'
-package_numpy_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package'
-package_rdkit_repository_description = 'Contains a tool dependency definition that downloads and compiles version 2012-12 of the RDKit cheminformatics and machine-learning package.'
-package_lapack_repository_description = 'Linear Algebra PACKage'
-package_atlas_repository_long_description = f'{package_atlas_repository_name}: {package_atlas_repository_description}'
-package_bzlib_repository_long_description = f'{package_bzlib_repository_name}: {package_bzlib_repository_description}'
-package_boost_repository_long_description = f'{package_boost_repository_name}: {package_boost_repository_description}'
-package_numpy_repository_long_description = f'{package_numpy_repository_name}: {package_numpy_repository_description}'
-package_rdkit_repository_long_description = f'{package_rdkit_repository_name}: {package_rdkit_repository_description}'
-package_lapack_repository_long_description = f'{package_lapack_repository_name}: {package_lapack_repository_description}'
+category_name = "Test 1420 Tool dependency environment variable inheritance"
+category_description = "Test script 1420 for interpolation of inherited environment variables."
+package_atlas_repository_name = "package_atlas_3_10_1420"
+package_bzlib_repository_name = "package_bzlib_1_0_1420"
+package_boost_repository_name = "package_boost_1_53_1420"
+package_numpy_repository_name = "package_numpy_1_7_1420"
+package_rdkit_repository_name = "package_rdkit_2012_12_1420"
+package_lapack_repository_name = "package_lapack_3_4_1420"
+package_atlas_repository_description = "Automatically Tuned Linear Algebra Software"
+package_bzlib_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.0 of the bzlib library."
+)
+package_boost_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.53 of the boost C++ libraries"
+)
+package_numpy_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package"
+)
+package_rdkit_repository_description = "Contains a tool dependency definition that downloads and compiles version 2012-12 of the RDKit cheminformatics and machine-learning package."
+package_lapack_repository_description = "Linear Algebra PACKage"
+package_atlas_repository_long_description = f"{package_atlas_repository_name}: {package_atlas_repository_description}"
+package_bzlib_repository_long_description = f"{package_bzlib_repository_name}: {package_bzlib_repository_description}"
+package_boost_repository_long_description = f"{package_boost_repository_name}: {package_boost_repository_description}"
+package_numpy_repository_long_description = f"{package_numpy_repository_name}: {package_numpy_repository_description}"
+package_rdkit_repository_long_description = f"{package_rdkit_repository_name}: {package_rdkit_repository_description}"
+package_lapack_repository_long_description = (
+    f"{package_lapack_repository_name}: {package_lapack_repository_description}"
+)
 
-'''
+"""
 1. Create repository package_lapack_3_4_1420
 
 2. Create repository package_atlas_3_10_1420
@@ -49,234 +60,298 @@ Repository dependency structure should be as follows:
 8. Install package_rdkit_2012_12 into Galaxy.
 
 9. Verify that the env.sh file for package_rdkit_2012_12_1420 also defines the variables inherited from package_numpy_1_7_1420 and package_boost_1_53_1420.
-'''
+"""
 
 
 class TestEnvironmentInheritance(ShedTwillTestCase):
-    '''Test referencing environment variables that were defined in a separate tool dependency.'''
+    """Test referencing environment variables that were defined in a separate tool dependency."""
 
     def test_0000_initiate_users_and_category(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
 
     def test_0005_create_lapack_repository(self):
-        '''Create and populate package_lapack_3_4_1420.
+        """Create and populate package_lapack_3_4_1420.
 
         This is step 1 - Create repository package_lapack_3_4_1420.
 
         All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
         filesystem and install them into the path specified by $INSTALL_DIR.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_lapack_repository_name,
-                                                   description=package_lapack_repository_description,
-                                                   long_description=package_lapack_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_lapack_repository_name,
+            description=package_lapack_repository_description,
+            long_description=package_lapack_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
         # actual system path where the binary tarball is found.
-        tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_lapack_3_4_1420'])
-        precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/lapack.tar')
-        edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
-        original_tool_dependency = self.get_filename('1420_files/package_lapack_3_4_1420/tool_dependencies.xml')
-        tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
-        open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
+        tool_dependency_path = self.generate_temp_path(
+            "1420_tool_dependency", additional_paths=["package_lapack_3_4_1420"]
+        )
+        precompiled_binary_tarball = self.get_filename("1420_files/binary_tarballs/lapack.tar")
+        edited_tool_dependency_filename = self.get_filename(
+            filepath=tool_dependency_path, filename="tool_dependencies.xml"
+        )
+        original_tool_dependency = self.get_filename("1420_files/package_lapack_3_4_1420/tool_dependencies.xml")
+        tool_dependency_definition = (
+            open(original_tool_dependency).read().replace("__PATH__", precompiled_binary_tarball)
+        )
+        open(edited_tool_dependency_filename, "w").write(tool_dependency_definition)
         # Upload the edited tool dependency definition to the package_lapack_3_4_1420 repository.
-        self.upload_file(repository,
-                         filename='tool_dependencies.xml',
-                         filepath=tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_lapack_3_4_1420 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="tool_dependencies.xml",
+            filepath=tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_lapack_3_4_1420 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_atlas_repository(self):
-        '''Create and populate package_atlas_3_10_1420.
+        """Create and populate package_atlas_3_10_1420.
 
         This is step 1 - Create repository package_atlas_3_10_1420.
 
         All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
         filesystem and install them into the path specified by $INSTALL_DIR.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_atlas_repository_name,
-                                                   description=package_atlas_repository_description,
-                                                   long_description=package_atlas_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_atlas_repository_name,
+            description=package_atlas_repository_description,
+            long_description=package_atlas_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
         # actual system path where the binary tarball is found.
-        tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_atlas_3_10_1420'])
-        precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/atlas.tar')
-        edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
-        original_tool_dependency = self.get_filename('1420_files/package_atlas_3_10_1420/tool_dependencies.xml')
-        tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
-        open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
+        tool_dependency_path = self.generate_temp_path(
+            "1420_tool_dependency", additional_paths=["package_atlas_3_10_1420"]
+        )
+        precompiled_binary_tarball = self.get_filename("1420_files/binary_tarballs/atlas.tar")
+        edited_tool_dependency_filename = self.get_filename(
+            filepath=tool_dependency_path, filename="tool_dependencies.xml"
+        )
+        original_tool_dependency = self.get_filename("1420_files/package_atlas_3_10_1420/tool_dependencies.xml")
+        tool_dependency_definition = (
+            open(original_tool_dependency).read().replace("__PATH__", precompiled_binary_tarball)
+        )
+        open(edited_tool_dependency_filename, "w").write(tool_dependency_definition)
         # Upload the edited tool dependency definition to the package_atlas_3_10_1420 repository.
-        self.upload_file(repository,
-                         filename='tool_dependencies.xml',
-                         filepath=tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_atlas_3_10_1420 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="tool_dependencies.xml",
+            filepath=tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_atlas_3_10_1420 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_bzlib_repository(self):
-        '''Create and populate package_bzlib_1_0_1420.
+        """Create and populate package_bzlib_1_0_1420.
 
         This is step 1 - Create repository package_bzlib_1_0_1420.
 
         All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
         filesystem and install them into the path specified by $INSTALL_DIR.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_bzlib_repository_name,
-                                                   description=package_bzlib_repository_description,
-                                                   long_description=package_bzlib_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_bzlib_repository_name,
+            description=package_bzlib_repository_description,
+            long_description=package_bzlib_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
         # actual system path where the binary tarball is found.
-        tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_bzlib_1_0_1420'])
-        precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/bzlib.tar')
-        edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
-        original_tool_dependency = self.get_filename('1420_files/package_bzlib_1_0_1420/tool_dependencies.xml')
-        tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
-        open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
+        tool_dependency_path = self.generate_temp_path(
+            "1420_tool_dependency", additional_paths=["package_bzlib_1_0_1420"]
+        )
+        precompiled_binary_tarball = self.get_filename("1420_files/binary_tarballs/bzlib.tar")
+        edited_tool_dependency_filename = self.get_filename(
+            filepath=tool_dependency_path, filename="tool_dependencies.xml"
+        )
+        original_tool_dependency = self.get_filename("1420_files/package_bzlib_1_0_1420/tool_dependencies.xml")
+        tool_dependency_definition = (
+            open(original_tool_dependency).read().replace("__PATH__", precompiled_binary_tarball)
+        )
+        open(edited_tool_dependency_filename, "w").write(tool_dependency_definition)
         # Upload the edited tool dependency definition to the package_bzlib_1_0_1420 repository.
-        self.upload_file(repository,
-                         filename='tool_dependencies.xml',
-                         filepath=tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_bzlib_1_0_1420 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="tool_dependencies.xml",
+            filepath=tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_bzlib_1_0_1420 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_create_boost_repository(self):
-        '''Create and populate package_boost_1_53_1420.
+        """Create and populate package_boost_1_53_1420.
 
         This is step 1 - Create repository package_boost_1_53_1420.
 
         All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
         filesystem and install them into the path specified by $INSTALL_DIR.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_boost_repository_name,
-                                                   description=package_boost_repository_description,
-                                                   long_description=package_boost_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_boost_repository_name,
+            description=package_boost_repository_description,
+            long_description=package_boost_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
         # actual system path where the binary tarball is found.
-        tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_boost_1_53_1420'])
-        precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/boost.tar')
-        edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
-        original_tool_dependency = self.get_filename('1420_files/package_boost_1_53_1420/tool_dependencies.xml')
-        tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
-        open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
+        tool_dependency_path = self.generate_temp_path(
+            "1420_tool_dependency", additional_paths=["package_boost_1_53_1420"]
+        )
+        precompiled_binary_tarball = self.get_filename("1420_files/binary_tarballs/boost.tar")
+        edited_tool_dependency_filename = self.get_filename(
+            filepath=tool_dependency_path, filename="tool_dependencies.xml"
+        )
+        original_tool_dependency = self.get_filename("1420_files/package_boost_1_53_1420/tool_dependencies.xml")
+        tool_dependency_definition = (
+            open(original_tool_dependency).read().replace("__PATH__", precompiled_binary_tarball)
+        )
+        open(edited_tool_dependency_filename, "w").write(tool_dependency_definition)
         # Upload the edited tool dependency definition to the package_boost_1_53_1420 repository.
-        self.upload_file(repository,
-                         filename='tool_dependencies.xml',
-                         filepath=tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_boost_1_53_1420 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="tool_dependencies.xml",
+            filepath=tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_boost_1_53_1420 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0025_create_numpy_repository(self):
-        '''Create and populate package_numpy_1_7_1420.
+        """Create and populate package_numpy_1_7_1420.
 
         This is step 1 - Create repository package_numpy_1_7_1420.
 
         All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
         filesystem and install them into the path specified by $INSTALL_DIR.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_numpy_repository_name,
-                                                   description=package_numpy_repository_description,
-                                                   long_description=package_numpy_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_numpy_repository_name,
+            description=package_numpy_repository_description,
+            long_description=package_numpy_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
         # actual system path where the binary tarball is found.
-        tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_numpy_1_7_1420'])
-        precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/numpy.tar')
-        edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
-        original_tool_dependency = self.get_filename('1420_files/package_numpy_1_7_1420/tool_dependencies.xml')
-        tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
-        open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
+        tool_dependency_path = self.generate_temp_path(
+            "1420_tool_dependency", additional_paths=["package_numpy_1_7_1420"]
+        )
+        precompiled_binary_tarball = self.get_filename("1420_files/binary_tarballs/numpy.tar")
+        edited_tool_dependency_filename = self.get_filename(
+            filepath=tool_dependency_path, filename="tool_dependencies.xml"
+        )
+        original_tool_dependency = self.get_filename("1420_files/package_numpy_1_7_1420/tool_dependencies.xml")
+        tool_dependency_definition = (
+            open(original_tool_dependency).read().replace("__PATH__", precompiled_binary_tarball)
+        )
+        open(edited_tool_dependency_filename, "w").write(tool_dependency_definition)
         # Upload the edited tool dependency definition to the package_numpy_1_7_1420 repository.
-        self.upload_file(repository,
-                         filename='tool_dependencies.xml',
-                         filepath=tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_numpy_1_7_1420 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="tool_dependencies.xml",
+            filepath=tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_numpy_1_7_1420 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0030_create_rdkit_repository(self):
-        '''Create and populate package_rdkit_2012_12_1420.
+        """Create and populate package_rdkit_2012_12_1420.
 
         This is step 1 - Create repository package_rdkit_2012_12_1420.
 
         All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
         filesystem and install them into the path specified by $INSTALL_DIR.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_rdkit_repository_name,
-                                                   description=package_rdkit_repository_description,
-                                                   long_description=package_rdkit_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_rdkit_repository_name,
+            description=package_rdkit_repository_description,
+            long_description=package_rdkit_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
         # actual system path where the binary tarball is found.
-        tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_rdkit_2012_12_1420'])
-        precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/rdkit.tar')
-        edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
-        original_tool_dependency = self.get_filename('1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml')
-        tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
-        open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
+        tool_dependency_path = self.generate_temp_path(
+            "1420_tool_dependency", additional_paths=["package_rdkit_2012_12_1420"]
+        )
+        precompiled_binary_tarball = self.get_filename("1420_files/binary_tarballs/rdkit.tar")
+        edited_tool_dependency_filename = self.get_filename(
+            filepath=tool_dependency_path, filename="tool_dependencies.xml"
+        )
+        original_tool_dependency = self.get_filename("1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml")
+        tool_dependency_definition = (
+            open(original_tool_dependency).read().replace("__PATH__", precompiled_binary_tarball)
+        )
+        open(edited_tool_dependency_filename, "w").write(tool_dependency_definition)
         # Upload the edited tool dependency definition to the package_rdkit_2012_12_1420 repository.
-        self.upload_file(repository,
-                         filename='tool_dependencies.xml',
-                         filepath=tool_dependency_path,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_rdkit_2012_12_1420 with tool dependency definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="tool_dependencies.xml",
+            filepath=tool_dependency_path,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_rdkit_2012_12_1420 with tool dependency definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0035_install_rdkit_2012_12_repository(self):
-        '''Install the package_rdkit_2012_12_1420 repository into Galaxy.
+        """Install the package_rdkit_2012_12_1420 repository into Galaxy.
 
         This is step 4 - Install package_rdkit_2012_12_1420 into Galaxy.
 
@@ -284,36 +359,53 @@ class TestEnvironmentInheritance(ShedTwillTestCase):
         package_atlas_3_10_1420, package_bzlib_1_0_1420, package_boost_1_53_1420, package_numpy_1_7_1420, package_rdkit_2012_12_1420,
         and package_lapack_3_4_1420 being installed, and an env.sh generated for package_rdkit_2012_12_1420 that
         contains environment variables defined in package_boost_1_53_1420 and package_numpy_1_7_1420.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        post_submit_strings_displayed = ['package_rdkit_2012_12_1420', 'package_atlas_3_10_1420', 'package_bzlib_1_0_1420',
-                                         'package_numpy_1_7_1420', 'package_lapack_3_4_1420', 'package_boost_1_53_1420']
-        self.install_repository('package_rdkit_2012_12_1420',
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=True,
-                                post_submit_strings_displayed=post_submit_strings_displayed)
+        post_submit_strings_displayed = [
+            "package_rdkit_2012_12_1420",
+            "package_atlas_3_10_1420",
+            "package_bzlib_1_0_1420",
+            "package_numpy_1_7_1420",
+            "package_lapack_3_4_1420",
+            "package_boost_1_53_1420",
+        ]
+        self.install_repository(
+            "package_rdkit_2012_12_1420",
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=True,
+            post_submit_strings_displayed=post_submit_strings_displayed,
+        )
 
     def test_0040_verify_env_sh_contents(self):
-        '''Check the env.sh file for the appropriate contents.
+        """Check the env.sh file for the appropriate contents.
 
         This is step 5 - Verify that the env.sh file for package_rdkit_2012_12_1420 also defines the variables inherited from package_numpy_1_7_1420
         and package_boost_1_53_1420. Test for the numpy and boost tool dependency paths.
-        '''
-        package_rdkit_repository = self.test_db_util.get_installed_repository_by_name_owner('package_rdkit_2012_12_1420', common.test_user_1_name)
-        package_numpy_repository = self.test_db_util.get_installed_repository_by_name_owner('package_numpy_1_7_1420', common.test_user_1_name)
-        package_boost_repository = self.test_db_util.get_installed_repository_by_name_owner('package_boost_1_53_1420', common.test_user_1_name)
-        rdkit_env_sh = self.get_env_sh_path(tool_dependency_name='rdkit',
-                                            tool_dependency_version='2012_12_1',
-                                            repository=package_rdkit_repository)
-        numpy_tool_dependency_path = self.get_tool_dependency_path(tool_dependency_name='numpy',
-                                                                   tool_dependency_version='1.7.1',
-                                                                   repository=package_numpy_repository)
-        boost_tool_dependency_path = self.get_tool_dependency_path(tool_dependency_name='boost',
-                                                                   tool_dependency_version='1.53.0',
-                                                                   repository=package_boost_repository)
+        """
+        package_rdkit_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "package_rdkit_2012_12_1420", common.test_user_1_name
+        )
+        package_numpy_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "package_numpy_1_7_1420", common.test_user_1_name
+        )
+        package_boost_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "package_boost_1_53_1420", common.test_user_1_name
+        )
+        rdkit_env_sh = self.get_env_sh_path(
+            tool_dependency_name="rdkit", tool_dependency_version="2012_12_1", repository=package_rdkit_repository
+        )
+        numpy_tool_dependency_path = self.get_tool_dependency_path(
+            tool_dependency_name="numpy", tool_dependency_version="1.7.1", repository=package_numpy_repository
+        )
+        boost_tool_dependency_path = self.get_tool_dependency_path(
+            tool_dependency_name="boost", tool_dependency_version="1.53.0", repository=package_boost_repository
+        )
         rdkit_env_file_contents = open(rdkit_env_sh).read()
-        if numpy_tool_dependency_path not in rdkit_env_file_contents or boost_tool_dependency_path not in rdkit_env_file_contents:
-            message = 'Environment file for package_rdkit_2012_12_1420 does not contain expected path.'
-            message += f'\nExpected:\n{numpy_tool_dependency_path}\n{boost_tool_dependency_path}\nContents:\n{rdkit_env_file_contents}'
+        if (
+            numpy_tool_dependency_path not in rdkit_env_file_contents
+            or boost_tool_dependency_path not in rdkit_env_file_contents
+        ):
+            message = "Environment file for package_rdkit_2012_12_1420 does not contain expected path."
+            message += f"\nExpected:\n{numpy_tool_dependency_path}\n{boost_tool_dependency_path}\nContents:\n{rdkit_env_file_contents}"
             raise AssertionError(message)
diff --git a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
index a6da968666e..6f3258a46b9 100644
--- a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
+++ b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
@@ -1,19 +1,22 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 1430 Repair installed repository'
-category_description = 'Test script 1430 for repairing an installed repository.'
-filter_repository_name = 'filter_1430'
-column_repository_name = 'column_1430'
+category_name = "Test 1430 Repair installed repository"
+category_description = "Test script 1430 for repairing an installed repository."
+filter_repository_name = "filter_1430"
+column_repository_name = "column_1430"
 filter_repository_description = "Galaxy's filter tool for test 1430"
-column_repository_description = 'Add a value as a new column'
-filter_repository_long_description = f'{filter_repository_name}: {filter_repository_description}'
-column_repository_long_description = f'{column_repository_name}: {column_repository_description}'
+column_repository_description = "Add a value as a new column"
+filter_repository_long_description = f"{filter_repository_name}: {filter_repository_description}"
+column_repository_long_description = f"{column_repository_name}: {column_repository_description}"
 
-'''
+"""
 In the Tool Shed:
 
 1) Create and populate the filter_1430 repository
@@ -28,121 +31,139 @@ In Galaxy:
    repository is also installed. Make sure to install the repositories in a specified section of the tool panel.
 
 2) Uninstall the filter_1430 repository.
-'''
+"""
 
 
 class TestRepairRepository(ShedTwillTestCase):
-    '''Test repairing an installed repository.'''
+    """Test repairing an installed repository."""
 
     def test_0000_initiate_users_and_category(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
 
     def test_0005_create_filter_repository(self):
-        '''Create and populate the filter_1430 repository.
+        """Create and populate the filter_1430 repository.
 
         This is step 1 - Create and populate the filter_1430 repository.
 
         This repository will be depended on by the column_1430 repository.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=filter_repository_name,
-                                                   description=filter_repository_description,
-                                                   long_description=filter_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate filter_1430 with version 1.1.0.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=filter_repository_name,
+            description=filter_repository_description,
+            long_description=filter_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate filter_1430 with version 1.1.0.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_column_repository(self):
-        '''Create and populate the column_1430 repository.
+        """Create and populate the column_1430 repository.
 
         This is step 2 - Create and populate the column_1430 repository.
 
         This repository will depend on the filter_1430 repository.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=column_repository_name,
-                                                   description=column_repository_description,
-                                                   long_description=column_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='column_maker/column_maker.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate column_1430 with tool definitions.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=column_repository_name,
+            description=column_repository_description,
+            long_description=column_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="column_maker/column_maker.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate column_1430 with tool definitions.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_create_repository_dependency(self):
-        '''Create a dependency on filter_1430.
+        """Create a dependency on filter_1430.
 
         This is step 3 - Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository
         dependency on the filter_1430 repository.
-        '''
-        column_repository = self.test_db_util.get_repository_by_name_and_owner('column_1430', common.test_user_1_name)
-        filter_repository = self.test_db_util.get_repository_by_name_and_owner('filter_1430', common.test_user_1_name)
+        """
+        column_repository = self.test_db_util.get_repository_by_name_and_owner("column_1430", common.test_user_1_name)
+        filter_repository = self.test_db_util.get_repository_by_name_and_owner("filter_1430", common.test_user_1_name)
         tool_shed_url = self.url
         name = filter_repository.name
         owner = filter_repository.user.username
         changeset_revision = self.get_repository_tip(filter_repository)
         repository_dependency_tuple = (tool_shed_url, name, owner, changeset_revision)
-        filepath = self.generate_temp_path('1430_repository_dependency')
+        filepath = self.generate_temp_path("1430_repository_dependency")
         self.create_repository_dependency(column_repository, [repository_dependency_tuple], filepath=filepath)
 
     def test_0020_install_column_repository(self):
-        '''Install the column_1430 repository into Galaxy.
+        """Install the column_1430 repository into Galaxy.
 
         This is step 1 (galaxy side) - Install the column_1430 repository, making sure to check the checkbox to
         handle repository dependencies so that the filter_1430 repository is also installed. Make sure to install
         the repositories in a specified section of the tool panel.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        post_submit_strings_displayed = ['column_1430', 'filter_1430']
-        self.install_repository('column_1430',
-                                common.test_user_1_name,
-                                category_name,
-                                new_tool_panel_section_label='repair',
-                                post_submit_strings_displayed=post_submit_strings_displayed,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=True)
+        post_submit_strings_displayed = ["column_1430", "filter_1430"]
+        self.install_repository(
+            "column_1430",
+            common.test_user_1_name,
+            category_name,
+            new_tool_panel_section_label="repair",
+            post_submit_strings_displayed=post_submit_strings_displayed,
+            install_tool_dependencies=False,
+            install_repository_dependencies=True,
+        )
 
     def test_0025_uninstall_filter_repository(self):
-        '''Uninstall the filter_1430 repository from Galaxy.
+        """Uninstall the filter_1430 repository from Galaxy.
 
         This is step 2 - Uninstall the filter_1430 repository.
-        '''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filter_1430', common.test_user_1_name)
-        strings_displayed = ['Uninstalling this repository will result in the following']
+        """
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "filter_1430", common.test_user_1_name
+        )
+        strings_displayed = ["Uninstalling this repository will result in the following"]
         strings_not_displayed = []
-        self.uninstall_repository(installed_repository,
-                                  strings_displayed=strings_displayed,
-                                  strings_not_displayed=strings_not_displayed)
-        strings_not_displayed = ['filter_1430',
-                                 "Galaxy's filter tool for test 1430",
-                                 installed_repository.installed_changeset_revision]
+        self.uninstall_repository(
+            installed_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
+        )
+        strings_not_displayed = [
+            "filter_1430",
+            "Galaxy's filter tool for test 1430",
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
diff --git a/lib/tool_shed/test/functional/test_1440_missing_env_sh_files.py b/lib/tool_shed/test/functional/test_1440_missing_env_sh_files.py
index 93821fd5562..4c9415c7f47 100644
--- a/lib/tool_shed/test/functional/test_1440_missing_env_sh_files.py
+++ b/lib/tool_shed/test/functional/test_1440_missing_env_sh_files.py
@@ -1,19 +1,22 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 1440 Tool dependency missing env.sh'
-category_description = 'Test script 1440 for detection of missing environment settings.'
-package_repository_name = 'package_env_sh_1_0_1440'
-tool_repository_name = 'filter_1440'
-package_repository_description = 'Repository that should result in an env.sh file, but does not.'
-tool_repository_description = 'Galaxy filtering tool.'
-package_repository_long_description = f'{package_repository_name}: {package_repository_description}'
-tool_repository_long_description = f'{tool_repository_name}: {tool_repository_description}'
+category_name = "Test 1440 Tool dependency missing env.sh"
+category_description = "Test script 1440 for detection of missing environment settings."
+package_repository_name = "package_env_sh_1_0_1440"
+tool_repository_name = "filter_1440"
+package_repository_description = "Repository that should result in an env.sh file, but does not."
+tool_repository_description = "Galaxy filtering tool."
+package_repository_long_description = f"{package_repository_name}: {package_repository_description}"
+tool_repository_long_description = f"{tool_repository_name}: {tool_repository_description}"
 
-'''
+"""
 1. Create a tool dependency type repository that reliably fails to install successfully. This repository should define
    an action that would have created an env.sh file on success, resulting in an env.sh file that should exist, but is missing.
 
@@ -22,104 +25,122 @@ tool_repository_long_description = f'{tool_repository_name}: {tool_repository_de
 
 3. Attempt to install the second repository into a galaxy instance, verify that it is installed but missing tool dependencies.
 
-'''
+"""
 
 
 class TestMissingEnvSh(ShedTwillTestCase):
-    '''Test installing a repository that should create an env.sh file, but does not.'''
+    """Test installing a repository that should create an env.sh file, but does not."""
 
     def test_0000_initiate_users_and_category(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
 
     def test_0005_create_package_repository(self):
-        '''Create and populate package_env_sh_1_0_1440.
+        """Create and populate package_env_sh_1_0_1440.
 
         This is step 1 - Create repository package_env_sh_1_0_1440.
 
         Create and populate a repository that is designed to fail a tool dependency installation. This tool dependency should
         also define one or more environment variables.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=package_repository_name,
-                                                   description=package_repository_description,
-                                                   long_description=package_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=package_repository_name,
+            description=package_repository_description,
+            long_description=package_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload the edited tool dependency definition to the package_lapack_3_4_1440 repository.
-        self.upload_file(repository,
-                         filename='1440_files/dependency_definition/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate package_env_sh_1_0_1440 with a broken tool dependency definition.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="1440_files/dependency_definition/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate package_env_sh_1_0_1440 with a broken tool dependency definition.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_create_filter_repository(self):
-        '''Create and populate filter_1440.
+        """Create and populate filter_1440.
 
         This is step 2 - Create a repository that defines a complex repository dependency on the repository created in
         step 1, with prior_install_required and set_environment_for_install.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=tool_repository_name,
-                                                   description=tool_repository_description,
-                                                   long_description=tool_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=tool_repository_name,
+            description=tool_repository_description,
+            long_description=tool_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload the edited tool dependency definition to the package_lapack_3_4_1440 repository.
-        self.upload_file(repository,
-                         filename='filtering/filtering_2.2.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate filter_1440 with the filtering tool.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
-        self.upload_file(repository,
-                         filename='1440_files/complex_dependency/tool_dependencies.xml',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Populate filter_1440 with a dependency on package_env_sh_1_0_1440.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_2.2.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate filter_1440 with the filtering tool.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="1440_files/complex_dependency/tool_dependencies.xml",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Populate filter_1440 with a dependency on package_env_sh_1_0_1440.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0015_install_filter_repository(self):
-        '''Install the filter_1440 repository to galaxy.
+        """Install the filter_1440 repository to galaxy.
 
         This is step 3 - Attempt to install the second repository into a galaxy instance, verify that it is installed but
         missing tool dependencies.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        post_submit_strings_displayed = ['filter_1440', 'package_env_sh_1_0_1440']
-        self.install_repository('filter_1440',
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=True,
-                                post_submit_strings_displayed=post_submit_strings_displayed)
+        post_submit_strings_displayed = ["filter_1440", "package_env_sh_1_0_1440"]
+        self.install_repository(
+            "filter_1440",
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=True,
+            post_submit_strings_displayed=post_submit_strings_displayed,
+        )
 
     def test_0020_verify_missing_tool_dependency(self):
-        '''Verify that the filter_1440 repository is installed and missing tool dependencies.'''
-        repository = self.test_db_util.get_installed_repository_by_name_owner('filter_1440', common.test_user_1_name)
-        strings_displayed = ['Missing tool dependencies']
+        """Verify that the filter_1440 repository is installed and missing tool dependencies."""
+        repository = self.test_db_util.get_installed_repository_by_name_owner("filter_1440", common.test_user_1_name)
+        strings_displayed = ["Missing tool dependencies"]
         self.display_installed_repository_manage_page(repository, strings_displayed=strings_displayed)
-        assert len(repository.missing_tool_dependencies) == 1, 'filter_1440 should have a missing tool dependency, but does not.'
+        assert (
+            len(repository.missing_tool_dependencies) == 1
+        ), "filter_1440 should have a missing tool dependency, but does not."
diff --git a/lib/tool_shed/test/functional/test_1450_installing_datatypes_sniffers.py b/lib/tool_shed/test/functional/test_1450_installing_datatypes_sniffers.py
index 7c56cd42f1d..8bd4ec1004f 100644
--- a/lib/tool_shed/test/functional/test_1450_installing_datatypes_sniffers.py
+++ b/lib/tool_shed/test/functional/test_1450_installing_datatypes_sniffers.py
@@ -1,12 +1,15 @@
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
-repository_name = 'proteomics_datatypes_1450'
+repository_name = "proteomics_datatypes_1450"
 repository_description = "Proteomics datatypes"
 repository_long_description = "Datatypes used in proteomics"
 
-category_name = 'Test 1450 Datatype Sniffers'
-category_description = 'Test 1450 - Installing Datatype Sniffers'
-'''
+category_name = "Test 1450 Datatype Sniffers"
+category_description = "Test 1450 - Installing Datatype Sniffers"
+"""
 1. Get a count of datatypes and sniffers.
 2. Install proteomics_datatypes_1450.
 3. Verify the count of datatypes and sniffers is the previous count + the datatypes contained within proteomics_datatypes_1450.
@@ -14,7 +17,7 @@ category_description = 'Test 1450 - Installing Datatype Sniffers'
 5. Reactivate proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository.
 6. Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1.
 7. Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository.
-'''
+"""
 
 base_datatypes_count = 0
 repository_datatypes_count = 0
@@ -22,156 +25,194 @@ base_sniffers_count = 0
 
 
 class TestInstallDatatypesSniffers(ShedTwillTestCase):
-    '''Test installing a repository that defines datatypes and datatype sniffers.'''
+    """Test installing a repository that defines datatypes and datatype sniffers."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
-        assert galaxy_admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert (
+            galaxy_admin_user is not None
+        ), f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
 
     def test_0005_ensure_repositories_and_categories_exist(self):
-        '''Create the 1450 category and proteomics_datatypes_1450 repository.'''
+        """Create the 1450 category and proteomics_datatypes_1450 repository."""
         global repository_datatypes_count
         self.login(email=common.admin_email, username=common.admin_username)
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         if self.repository_is_new(repository):
-            self.upload_file(repository,
-                             filename='proteomics_datatypes/proteomics_datatypes.tar',
-                             filepath=None,
-                             valid_tools_only=True,
-                             uncompress_file=False,
-                             remove_repo_files_not_in_tar=False,
-                             commit_message='Uploaded datatype and sniffer definitions.',
-                             strings_displayed=[],
-                             strings_not_displayed=[])
+            self.upload_file(
+                repository,
+                filename="proteomics_datatypes/proteomics_datatypes.tar",
+                filepath=None,
+                valid_tools_only=True,
+                uncompress_file=False,
+                remove_repo_files_not_in_tar=False,
+                commit_message="Uploaded datatype and sniffer definitions.",
+                strings_displayed=[],
+                strings_not_displayed=[],
+            )
         repository_datatypes_count = self.get_repository_datatypes_count(repository)
 
     def test_0010_install_datatypes_repository(self):
-        '''Install the proteomics_datatypes_1450 repository into the Galaxy instance.
+        """Install the proteomics_datatypes_1450 repository into the Galaxy instance.
 
         This includes steps 1 and 2 - Get a count of datatypes and sniffers.
         Store a count of the current datatypes registry and sniffers in global variables, to compare with the updated count
         after changing the installation status of the proteomics_datatypes_1450 repository.
-        '''
+        """
         global base_datatypes_count
         global base_sniffers_count
         base_datatypes_count = self.get_datatypes_count()
         base_sniffers_count = self.get_sniffers_count()
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        strings_displayed = ['proteomics']
-        self.install_repository('proteomics_datatypes_1450',
-                                common.test_user_1_name,
-                                category_name,
-                                strings_displayed=strings_displayed,
-                                new_tool_panel_section_label='test_1450')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('proteomics_datatypes_1450', common.test_user_1_name)
-        strings_displayed = ['user1',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision]
+        strings_displayed = ["proteomics"]
+        self.install_repository(
+            "proteomics_datatypes_1450",
+            common.test_user_1_name,
+            category_name,
+            strings_displayed=strings_displayed,
+            new_tool_panel_section_label="test_1450",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            "proteomics_datatypes_1450", common.test_user_1_name
+        )
+        strings_displayed = [
+            "user1",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
 
     def test_0015_verify_datatypes_count(self):
-        '''Verify that datatypes were added in the previous step.
+        """Verify that datatypes were added in the previous step.
 
         This is step 3 - Verify the count of datatypes and sniffers is the previous count + the datatypes
                          contained within proteomics_datatypes_1450.
         Compare the current datatypes registry and sniffers with the values that were retrieved in the previous step.
-        '''
+        """
         current_datatypes = self.get_datatypes_count()
-        assert current_datatypes == base_datatypes_count + repository_datatypes_count, \
-            'Found %d datatypes, expected %d.' % (current_datatypes, base_datatypes_count + repository_datatypes_count)
+        assert (
+            current_datatypes == base_datatypes_count + repository_datatypes_count
+        ), "Found %d datatypes, expected %d." % (current_datatypes, base_datatypes_count + repository_datatypes_count)
         current_sniffers = self.get_sniffers_count()
-        assert current_sniffers > base_sniffers_count, \
-            'Sniffer count after installing proteomics_datatypes_1450 is %d, which is not greater than %d' % \
-            (current_sniffers, base_sniffers_count)
+        assert (
+            current_sniffers > base_sniffers_count
+        ), "Sniffer count after installing proteomics_datatypes_1450 is %d, which is not greater than %d" % (
+            current_sniffers,
+            base_sniffers_count,
+        )
 
     def test_0020_deactivate_datatypes_repository(self):
-        '''Deactivate the installed proteomics_datatypes_1450 repository.
+        """Deactivate the installed proteomics_datatypes_1450 repository.
 
         This is step 4 - Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to
                          the count determined in step 1.
         Deactivate proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values
         determined in the first step.
-        '''
+        """
         repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
         global base_datatypes_count
         global base_sniffers_count
         self.deactivate_repository(repository)
         new_datatypes_count = self.get_datatypes_count()
-        assert new_datatypes_count == base_datatypes_count, 'Expected %d datatypes, got %d' % (base_datatypes_count, new_datatypes_count)
+        assert new_datatypes_count == base_datatypes_count, "Expected %d datatypes, got %d" % (
+            base_datatypes_count,
+            new_datatypes_count,
+        )
         current_sniffers = self.get_sniffers_count()
-        assert current_sniffers == base_sniffers_count, \
-            'Sniffer count after deactivating proteomics_datatypes_1450 is %d, expected %d' % \
-            (current_sniffers, base_sniffers_count)
+        assert (
+            current_sniffers == base_sniffers_count
+        ), "Sniffer count after deactivating proteomics_datatypes_1450 is %d, expected %d" % (
+            current_sniffers,
+            base_sniffers_count,
+        )
 
     def test_0025_reactivate_datatypes_repository(self):
-        '''Reactivate the deactivated proteomics_datatypes_1450 repository.
+        """Reactivate the deactivated proteomics_datatypes_1450 repository.
 
         This is step 5 - Reactivate proteomics_datatypes, verify that the count of datatypes and sniffers has been
                          increased by the contents of the repository.
-        '''
+        """
         repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
         global repository_datatypes_count
         global base_datatypes_count
         global base_sniffers_count
         self.reactivate_repository(repository)
         new_datatypes_count = self.get_datatypes_count()
-        assert new_datatypes_count == base_datatypes_count + repository_datatypes_count, \
-            'Found %d datatypes, expected %d.' % (new_datatypes_count, base_datatypes_count + repository_datatypes_count)
+        assert (
+            new_datatypes_count == base_datatypes_count + repository_datatypes_count
+        ), "Found %d datatypes, expected %d." % (new_datatypes_count, base_datatypes_count + repository_datatypes_count)
         current_sniffers = self.get_sniffers_count()
-        assert current_sniffers > base_sniffers_count, \
-            'Sniffer count after reactivating proteomics_datatypes_1450 is %d, which is not greater than %d' % \
-            (current_sniffers, base_sniffers_count)
+        assert (
+            current_sniffers > base_sniffers_count
+        ), "Sniffer count after reactivating proteomics_datatypes_1450 is %d, which is not greater than %d" % (
+            current_sniffers,
+            base_sniffers_count,
+        )
 
     def test_0030_uninstall_datatypes_repository(self):
-        '''Uninstall the installed proteomics_datatypes_1450 repository.
+        """Uninstall the installed proteomics_datatypes_1450 repository.
 
         This is step 6 - Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal
                          to the count determined in step 1.
         Uninstall proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values
         determined in the first step.
-        '''
+        """
         repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
         global base_datatypes_count
         self.uninstall_repository(repository)
         new_datatypes_count = self.get_datatypes_count()
-        assert new_datatypes_count == base_datatypes_count, 'Expected %d datatypes, got %d' % (base_datatypes_count, new_datatypes_count)
+        assert new_datatypes_count == base_datatypes_count, "Expected %d datatypes, got %d" % (
+            base_datatypes_count,
+            new_datatypes_count,
+        )
         current_sniffers = self.get_sniffers_count()
-        assert current_sniffers == base_sniffers_count, \
-            'Sniffer count after uninstalling proteomics_datatypes_1450 is %d, expected %d' % \
-            (current_sniffers, base_sniffers_count)
+        assert (
+            current_sniffers == base_sniffers_count
+        ), "Sniffer count after uninstalling proteomics_datatypes_1450 is %d, expected %d" % (
+            current_sniffers,
+            base_sniffers_count,
+        )
 
     def test_0035_reinstall_datatypes_repository(self):
-        '''Reinstall the uninstalled proteomics_datatypes_1450 repository.
+        """Reinstall the uninstalled proteomics_datatypes_1450 repository.
 
         This is step 7 - Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been
                          increased by the contents of the repository.
-        '''
+        """
         repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
         global repository_datatypes_count
         global base_datatypes_count
         self.reinstall_repository(repository)
         new_datatypes_count = self.get_datatypes_count()
-        assert new_datatypes_count == base_datatypes_count + repository_datatypes_count, \
-            'Found %d datatypes, expected %d.' % (new_datatypes_count, base_datatypes_count + repository_datatypes_count)
+        assert (
+            new_datatypes_count == base_datatypes_count + repository_datatypes_count
+        ), "Found %d datatypes, expected %d." % (new_datatypes_count, base_datatypes_count + repository_datatypes_count)
         current_sniffers = self.get_sniffers_count()
-        assert current_sniffers > base_sniffers_count, \
-            'Sniffer count after reinstalling proteomics_datatypes_1450 is %d, which is not greater than %d' % \
-            (current_sniffers, base_sniffers_count)
+        assert (
+            current_sniffers > base_sniffers_count
+        ), "Sniffer count after reinstalling proteomics_datatypes_1450 is %d, which is not greater than %d" % (
+            current_sniffers,
+            base_sniffers_count,
+        )
diff --git a/lib/tool_shed/test/functional/test_1460_data_managers.py b/lib/tool_shed/test/functional/test_1460_data_managers.py
index 60333de63ec..f93d03bffbc 100644
--- a/lib/tool_shed/test/functional/test_1460_data_managers.py
+++ b/lib/tool_shed/test/functional/test_1460_data_managers.py
@@ -1,92 +1,111 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-category_name = 'Test 1460 Data Manager'
-category_description = 'Test script 1460 for testing Data Managers'
-data_manager_repository_name = 'data_manager_1460'
-data_manager_repository_description = 'Repository that contains a Data Manager'
-data_manager_repository_long_description = f'{data_manager_repository_name}: {data_manager_repository_description}'
-data_manager_name = 'testing_data_manager'
-data_manager_tar_file = '1460_files/data_manager_files/test_data_manager.tar'
+category_name = "Test 1460 Data Manager"
+category_description = "Test script 1460 for testing Data Managers"
+data_manager_repository_name = "data_manager_1460"
+data_manager_repository_description = "Repository that contains a Data Manager"
+data_manager_repository_long_description = f"{data_manager_repository_name}: {data_manager_repository_description}"
+data_manager_name = "testing_data_manager"
+data_manager_tar_file = "1460_files/data_manager_files/test_data_manager.tar"
 
-'''
+"""
 1. Add a Data Manager to toolshed
 
 2. install Data Manager
 
 3. Check that Data Manager tool
 
-'''
+"""
 
 # TODO: Allow testing actual Execution of installed Data Manager Tool.
 
 
 class TestDataManagers(ShedTwillTestCase):
-    '''Test installing a repository containing a Data Manager.'''
+    """Test installing a repository containing a Data Manager."""
 
     def test_0000_initiate_users_and_category(self):
         """Create necessary user accounts and login as an admin user."""
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
         self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
-        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
+        assert (
+            test_user_2 is not None
+        ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
         self.test_db_util.get_private_role(test_user_2)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
 
     def test_0010_create_data_manager_repository(self):
-        '''Create and populate data_manager_1460.
+        """Create and populate data_manager_1460.
 
         This is step 1 - Create repository data_manager_1460.
 
         Create and populate a repository that contains a Data manager.
-        '''
+        """
         category = self.test_db_util.get_category_by_name(category_name)
-        repository = self.get_or_create_repository(name=data_manager_repository_name,
-                                                   description=data_manager_repository_description,
-                                                   long_description=data_manager_repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
+        repository = self.get_or_create_repository(
+            name=data_manager_repository_name,
+            description=data_manager_repository_description,
+            long_description=data_manager_repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
         # Upload the data manager files to the repository.
-        self.upload_file(repository,
-                         filename=data_manager_tar_file,
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message=f'Populate {data_manager_repository_name} with a data manager configuration.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename=data_manager_tar_file,
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message=f"Populate {data_manager_repository_name} with a data manager configuration.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_install_data_manager_repository(self):
-        '''Install the data_manager_1460 repository to galaxy.
+        """Install the data_manager_1460 repository to galaxy.
 
         This is step 3 - Attempt to install the repository into a galaxy instance, verify that it is installed.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
         post_submit_strings_displayed = [data_manager_repository_name]
-        self.install_repository(data_manager_repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=True,
-                                post_submit_strings_displayed=post_submit_strings_displayed)
+        self.install_repository(
+            data_manager_repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=True,
+            post_submit_strings_displayed=post_submit_strings_displayed,
+        )
 
     def test_0030_verify_data_manager_tool(self):
-        '''Verify that the data_manager_1460 repository is installed and Data Manager tool appears in list in Galaxy.'''
-        repository = self.test_db_util.get_installed_repository_by_name_owner(data_manager_repository_name, common.test_user_1_name)
-        strings_displayed = ['status', 'jobs', data_manager_name]
-        self.display_installed_jobs_list_page(repository, data_manager_names=data_manager_name, strings_displayed=strings_displayed)
+        """Verify that the data_manager_1460 repository is installed and Data Manager tool appears in list in Galaxy."""
+        repository = self.test_db_util.get_installed_repository_by_name_owner(
+            data_manager_repository_name, common.test_user_1_name
+        )
+        strings_displayed = ["status", "jobs", data_manager_name]
+        self.display_installed_jobs_list_page(
+            repository, data_manager_names=data_manager_name, strings_displayed=strings_displayed
+        )
 
     def test_0040_verify_data_manager_data_table(self):
-        '''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.'''
-        self.verify_installed_repository_data_table_entries(required_data_table_entries=['data_manager_test_data_table'])
+        """Verify that the installed repository populated shed_tool_data_table.xml and the sample files."""
+        self.verify_installed_repository_data_table_entries(
+            required_data_table_entries=["data_manager_test_data_table"]
+        )
diff --git a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
index 216759c52e9..862a6d27030 100644
--- a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
+++ b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
@@ -1,136 +1,158 @@
 import logging
 
-from ..base.twilltestcase import common, ShedTwillTestCase
+from ..base.twilltestcase import (
+    common,
+    ShedTwillTestCase,
+)
 
 log = logging.getLogger(__name__)
 
-repository_name = 'filtering_1470'
+repository_name = "filtering_1470"
 repository_description = "Galaxy's filtering tool"
 repository_long_description = "Long description of Galaxy's filtering tool"
 
-category_name = 'Test 1470 - Updating Installed Repositories'
-category_description = 'Functional test suite to ensure that updating installed repositories does not create white ghosts.'
+category_name = "Test 1470 - Updating Installed Repositories"
+category_description = (
+    "Functional test suite to ensure that updating installed repositories does not create white ghosts."
+)
 
-'''
+"""
 1. Install a repository into Galaxy.
 2. In the Tool Shed, update the repository from Step 1.
 3. In Galaxy, get updates to the repository.
 4. In Galaxy, uninstall the repository.
 5. In Galaxy, reinstall the repository.
 6. Make sure step 5 created no white ghosts.
-'''
+"""
 
 
 class TestUpdateInstalledRepository(ShedTwillTestCase):
-    '''Verify that the code correctly handles updating an installed repository, then uninstalling and reinstalling.'''
+    """Verify that the code correctly handles updating an installed repository, then uninstalling and reinstalling."""
 
     def test_0000_initiate_users(self):
         """Create necessary user accounts."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
-        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
+        assert (
+            test_user_1 is not None
+        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
         self.test_db_util.get_private_role(test_user_1)
         self.login(email=common.admin_email, username=common.admin_username)
         admin_user = self.test_db_util.get_user(common.admin_email)
-        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
+        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
         self.test_db_util.get_private_role(admin_user)
 
     def test_0005_create_filtering_repository(self):
         """Create and populate the filtering_0530 repository."""
         category = self.create_category(name=category_name, description=category_description)
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        repository = self.get_or_create_repository(name=repository_name,
-                                                   description=repository_description,
-                                                   long_description=repository_long_description,
-                                                   owner=common.test_user_1_name,
-                                                   category_id=self.security.encode_id(category.id),
-                                                   strings_displayed=[])
-        self.upload_file(repository,
-                         filename='filtering/filtering_1.1.0.tar',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=True,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded filtering 1.1.0 tarball.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        repository = self.get_or_create_repository(
+            name=repository_name,
+            description=repository_description,
+            long_description=repository_long_description,
+            owner=common.test_user_1_name,
+            category_id=self.security.encode_id(category.id),
+            strings_displayed=[],
+        )
+        self.upload_file(
+            repository,
+            filename="filtering/filtering_1.1.0.tar",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=True,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded filtering 1.1.0 tarball.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0010_install_filtering_to_galaxy(self):
-        '''Install the filtering_1470 repository to galaxy.
+        """Install the filtering_1470 repository to galaxy.
 
         This is step 1 - Install a repository into Galaxy.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        self.install_repository(repository_name,
-                                common.test_user_1_name,
-                                category_name,
-                                install_tool_dependencies=False,
-                                install_repository_dependencies=False,
-                                new_tool_panel_section_label='Filtering')
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name,
-                                                                                        common.test_user_1_name)
-        strings_displayed = ['filtering_1470',
-                             self.url.replace('http://', ''),
-                             installed_repository.installed_changeset_revision,
-                             installed_repository.changeset_revision]
+        self.install_repository(
+            repository_name,
+            common.test_user_1_name,
+            category_name,
+            install_tool_dependencies=False,
+            install_repository_dependencies=False,
+            new_tool_panel_section_label="Filtering",
+        )
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name
+        )
+        strings_displayed = [
+            "filtering_1470",
+            self.url.replace("http://", ""),
+            installed_repository.installed_changeset_revision,
+            installed_repository.changeset_revision,
+        ]
         self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
-        self.display_installed_repository_manage_page(installed_repository,
-                                                      strings_displayed=strings_displayed)
+        self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
 
     def test_0015_update_repository(self):
-        '''Upload a readme file to the filtering_1470 repository.
+        """Upload a readme file to the filtering_1470 repository.
 
         This is step 2 - In the Tool Shed, update the repository from Step 1.
 
         Importantly, this update should *not* create a new installable changeset revision, because that would
         eliminate the process we're testing in this script. So, we upload a readme file.
-        '''
+        """
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.upload_file(repository,
-                         filename='filtering/readme.txt',
-                         filepath=None,
-                         valid_tools_only=True,
-                         uncompress_file=False,
-                         remove_repo_files_not_in_tar=False,
-                         commit_message='Uploaded readme.',
-                         strings_displayed=[],
-                         strings_not_displayed=[])
+        self.upload_file(
+            repository,
+            filename="filtering/readme.txt",
+            filepath=None,
+            valid_tools_only=True,
+            uncompress_file=False,
+            remove_repo_files_not_in_tar=False,
+            commit_message="Uploaded readme.",
+            strings_displayed=[],
+            strings_not_displayed=[],
+        )
 
     def test_0020_get_repository_updates(self):
-        '''Get updates to the installed repository.
+        """Get updates to the installed repository.
 
         This is step 3 - In Galaxy, get updates to the repository.
-        '''
+        """
         self.galaxy_login(email=common.admin_email, username=common.admin_username)
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name,
-                                                                                        common.test_user_1_name)
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name
+        )
         self.update_installed_repository(installed_repository)
 
     def test_0025_uninstall_repository(self):
-        '''Uninstall the filtering_1470 repository.
+        """Uninstall the filtering_1470 repository.
 
         This is step 4 - In Galaxy, uninstall the repository.
-        '''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name,
-                                                                                        common.test_user_1_name)
+        """
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name
+        )
         self.uninstall_repository(installed_repository)
 
     def test_0030_reinstall_repository(self):
-        '''Reinstall the filtering_1470 repository.
+        """Reinstall the filtering_1470 repository.
 
         This is step 5 - In Galaxy, reinstall the repository.
-        '''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name,
-                                                                                        common.test_user_1_name)
+        """
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name
+        )
         self.reinstall_repository(installed_repository)
 
     def test_0035_verify_absence_of_ghosts(self):
-        '''Check the count of repositories in the database named filtering_1470 and owned by user1.
+        """Check the count of repositories in the database named filtering_1470 and owned by user1.
 
         This is step 6 - Make sure step 5 created no white ghosts.
-        '''
-        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name,
-                                                                                        common.test_user_1_name,
-                                                                                        return_multiple=True)
-        assert len(installed_repository) == 1, 'Multiple filtering repositories found in the Galaxy database, possibly indicating a "white ghost" scenario.'
+        """
+        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
+            repository_name, common.test_user_1_name, return_multiple=True
+        )
+        assert (
+            len(installed_repository) == 1
+        ), 'Multiple filtering repositories found in the Galaxy database, possibly indicating a "white ghost" scenario.'
diff --git a/lib/tool_shed/test/functional_tests.py b/lib/tool_shed/test/functional_tests.py
index 5bc08abc79a..4856de28b63 100644
--- a/lib/tool_shed/test/functional_tests.py
+++ b/lib/tool_shed/test/functional_tests.py
@@ -20,28 +20,28 @@ from tool_shed.webapp import buildapp as toolshedbuildapp
 
 log = driver_util.build_logger()
 
-tool_sheds_conf_xml_template = '''<?xml version="1.0"?>
+tool_sheds_conf_xml_template = """<?xml version="1.0"?>
 <tool_sheds>
     <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/>
     <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/>
     <tool_shed name="Embedded tool shed for functional tests" url="http://${shed_url}:${shed_port}/"/>
 </tool_sheds>
-'''
+"""
 
-shed_tool_conf_xml_template = '''<?xml version="1.0"?>
+shed_tool_conf_xml_template = """<?xml version="1.0"?>
 <toolbox tool_path="${shed_tool_path}">
 </toolbox>
-'''
+"""
 
-tool_data_table_conf_xml_template = '''<?xml version="1.0"?>
+tool_data_table_conf_xml_template = """<?xml version="1.0"?>
 <tables>
 </tables>
-'''
+"""
 
-shed_data_manager_conf_xml_template = '''<?xml version="1.0"?>
+shed_data_manager_conf_xml_template = """<?xml version="1.0"?>
 <data_managers>
 </data_managers>
-'''
+"""
 
 
 class ToolShedTestDriver(driver_util.TestDriver):
@@ -55,56 +55,68 @@ class ToolShedTestDriver(driver_util.TestDriver):
             os.mkdir(tool_shed_test_tmp_dir)
         self.temp_directories.append(tool_shed_test_tmp_dir)
         shed_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir, prefix="TOOL_SHED")
-        shed_tool_data_table_conf_file = os.environ.get('TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join(tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml'))
-        galaxy_shed_data_manager_conf_file = os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_shed_data_manager_conf.xml'))
-        default_tool_data_table_config_path = os.path.join(tool_shed_test_tmp_dir, 'tool_data_table_conf.xml')
-        galaxy_shed_tool_conf_file = os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml'))
-        galaxy_migrated_tool_conf_file = os.environ.get('GALAXY_TEST_MIGRATED_TOOL_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_migrated_tool_conf.xml'))
-        galaxy_tool_sheds_conf_file = os.environ.get('GALAXY_TEST_TOOL_SHEDS_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_sheds_conf.xml'))
-        if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
-            tool_data_path = os.environ.get('GALAXY_TEST_TOOL_DATA_PATH')
+        shed_tool_data_table_conf_file = os.environ.get(
+            "TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF", os.path.join(tool_shed_test_tmp_dir, "shed_tool_data_table_conf.xml")
+        )
+        galaxy_shed_data_manager_conf_file = os.environ.get(
+            "GALAXY_SHED_DATA_MANAGER_CONF", os.path.join(tool_shed_test_tmp_dir, "test_shed_data_manager_conf.xml")
+        )
+        default_tool_data_table_config_path = os.path.join(tool_shed_test_tmp_dir, "tool_data_table_conf.xml")
+        galaxy_shed_tool_conf_file = os.environ.get(
+            "GALAXY_TEST_SHED_TOOL_CONF", os.path.join(tool_shed_test_tmp_dir, "test_shed_tool_conf.xml")
+        )
+        galaxy_migrated_tool_conf_file = os.environ.get(
+            "GALAXY_TEST_MIGRATED_TOOL_CONF", os.path.join(tool_shed_test_tmp_dir, "test_migrated_tool_conf.xml")
+        )
+        galaxy_tool_sheds_conf_file = os.environ.get(
+            "GALAXY_TEST_TOOL_SHEDS_CONF", os.path.join(tool_shed_test_tmp_dir, "test_sheds_conf.xml")
+        )
+        if "GALAXY_TEST_TOOL_DATA_PATH" in os.environ:
+            tool_data_path = os.environ.get("GALAXY_TEST_TOOL_DATA_PATH")
         else:
             tool_data_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
-            os.environ['GALAXY_TEST_TOOL_DATA_PATH'] = tool_data_path
+            os.environ["GALAXY_TEST_TOOL_DATA_PATH"] = tool_data_path
         galaxy_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir)
-        shed_file_path = os.path.join(shed_db_path, 'files')
+        shed_file_path = os.path.join(shed_db_path, "files")
         hgweb_config_file_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         new_repos_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         galaxy_shed_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         galaxy_migrated_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         hgweb_config_dir = hgweb_config_file_path
-        os.environ['TEST_HG_WEB_CONFIG_DIR'] = hgweb_config_dir
+        os.environ["TEST_HG_WEB_CONFIG_DIR"] = hgweb_config_dir
         print("Directory location for hgweb.config:", hgweb_config_dir)
         toolshed_database_conf = driver_util.database_conf(shed_db_path, prefix="TOOL_SHED")
-        kwargs = dict(admin_users='test@bx.psu.edu',
-                      allow_user_creation=True,
-                      allow_user_deletion=True,
-                      datatype_converters_config_file='datatype_converters_conf.xml.sample',
-                      file_path=shed_file_path,
-                      hgweb_config_dir=hgweb_config_dir,
-                      id_secret='changethisinproductiontoo',
-                      log_destination="stdout",
-                      new_file_path=new_repos_path,
-                      running_functional_tests=True,
-                      shed_tool_data_table_config=shed_tool_data_table_conf_file,
-                      smtp_server='smtp.dummy.string.tld',
-                      email_from='functional@localhost',
-                      tool_parse_help=False,
-                      use_heartbeat=False)
+        kwargs = dict(
+            admin_users="test@bx.psu.edu",
+            allow_user_creation=True,
+            allow_user_deletion=True,
+            datatype_converters_config_file="datatype_converters_conf.xml.sample",
+            file_path=shed_file_path,
+            hgweb_config_dir=hgweb_config_dir,
+            id_secret="changethisinproductiontoo",
+            log_destination="stdout",
+            new_file_path=new_repos_path,
+            running_functional_tests=True,
+            shed_tool_data_table_config=shed_tool_data_table_conf_file,
+            smtp_server="smtp.dummy.string.tld",
+            email_from="functional@localhost",
+            tool_parse_help=False,
+            use_heartbeat=False,
+        )
         kwargs.update(toolshed_database_conf)
         # Generate the tool_data_table_conf.xml file.
-        with open(default_tool_data_table_config_path, 'w') as fh:
+        with open(default_tool_data_table_config_path, "w") as fh:
             fh.write(tool_data_table_conf_xml_template)
         # Generate the shed_tool_data_table_conf.xml file.
-        with open(shed_tool_data_table_conf_file, 'w') as fh:
+        with open(shed_tool_data_table_conf_file, "w") as fh:
             fh.write(tool_data_table_conf_xml_template)
-        os.environ['TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF'] = shed_tool_data_table_conf_file
+        os.environ["TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF"] = shed_tool_data_table_conf_file
         # ---- Build Tool Shed Application --------------------------------------------------
         toolshedapp = driver_util.build_shed_app(kwargs)
 
         # ---- Run tool shed webserver ------------------------------------------------------
         # TODO: Needed for hg middleware ('lib/galaxy/webapps/tool_shed/framework/middleware/hg.py')
-        kwargs['global_conf']['database_connection'] = kwargs["database_connection"]
+        kwargs["global_conf"]["database_connection"] = kwargs["database_connection"]
         tool_shed_server_wrapper = driver_util.launch_server(
             toolshedapp,
             toolshedbuildapp.app_factory,
@@ -117,31 +129,37 @@ class ToolShedTestDriver(driver_util.TestDriver):
         log.info(f"Functional tests will be run against {tool_shed_test_host}:{tool_shed_test_port}")
 
         # ---- Optionally start up a Galaxy instance ------------------------------------------------------
-        if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ:
+        if "TOOL_SHED_TEST_OMIT_GALAXY" not in os.environ:
             # Generate the shed_tool_conf.xml file.
             tool_sheds_conf_template_parser = string.Template(tool_sheds_conf_xml_template)
-            tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute(shed_url=tool_shed_test_host, shed_port=tool_shed_test_port)
-            with open(galaxy_tool_sheds_conf_file, 'w') as fh:
+            tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute(
+                shed_url=tool_shed_test_host, shed_port=tool_shed_test_port
+            )
+            with open(galaxy_tool_sheds_conf_file, "w") as fh:
                 fh.write(tool_sheds_conf_xml)
             # Generate the tool_sheds_conf.xml file.
             shed_tool_conf_template_parser = string.Template(shed_tool_conf_xml_template)
             shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_shed_tool_path)
-            with open(galaxy_shed_tool_conf_file, 'w') as fh:
+            with open(galaxy_shed_tool_conf_file, "w") as fh:
                 fh.write(shed_tool_conf_xml)
             # Generate the migrated_tool_conf.xml file.
-            migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_migrated_tool_path)
-            with open(galaxy_migrated_tool_conf_file, 'w') as fh:
+            migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(
+                shed_tool_path=galaxy_migrated_tool_path
+            )
+            with open(galaxy_migrated_tool_conf_file, "w") as fh:
                 fh.write(migrated_tool_conf_xml)
-            os.environ['GALAXY_TEST_SHED_TOOL_CONF'] = galaxy_shed_tool_conf_file
+            os.environ["GALAXY_TEST_SHED_TOOL_CONF"] = galaxy_shed_tool_conf_file
             # Generate shed_data_manager_conf.xml
-            if not os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF'):
-                with open(galaxy_shed_data_manager_conf_file, 'w') as fh:
+            if not os.environ.get("GALAXY_SHED_DATA_MANAGER_CONF"):
+                with open(galaxy_shed_data_manager_conf_file, "w") as fh:
                     fh.write(shed_data_manager_conf_xml_template)
-            kwargs = dict(migrated_tools_config=galaxy_migrated_tool_conf_file,
-                          shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
-                          shed_tool_path=galaxy_shed_tool_path,
-                          tool_data_path=tool_data_path,
-                          tool_sheds_config_file=galaxy_tool_sheds_conf_file)
+            kwargs = dict(
+                migrated_tools_config=galaxy_migrated_tool_conf_file,
+                shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
+                shed_tool_path=galaxy_shed_tool_path,
+                tool_data_path=tool_data_path,
+                tool_sheds_config_file=galaxy_tool_sheds_conf_file,
+            )
             kwargs.update(
                 driver_util.setup_galaxy_config(
                     galaxy_db_path,
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
index d609a8ffc90..1ed90229a70 100644
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -11,14 +11,13 @@ from tool_shed.util import (
     hg_util,
     repository_util,
     tool_util,
-    xml_util
+    xml_util,
 )
 
 log = logging.getLogger(__name__)
 
 
 class ToolValidator(GalaxyToolValidator):
-
     def can_use_tool_config_disk_file(self, repository, repo, file_path, changeset_revision):
         """
         Determine if repository's tool config file on disk can be used.  This method
@@ -33,8 +32,9 @@ class ToolValidator(GalaxyToolValidator):
         if changeset_revision == repository.tip():
             return True
         file_name = basic_util.strip_path(file_path)
-        latest_version_of_file = \
-            self.get_latest_tool_config_revision_from_repository_manifest(repo, file_name, changeset_revision)
+        latest_version_of_file = self.get_latest_tool_config_revision_from_repository_manifest(
+            repo, file_name, changeset_revision
+        )
         can_use_disk_file = filecmp.cmp(file_path, latest_version_of_file)
         try:
             os.unlink(latest_version_of_file)
@@ -45,13 +45,13 @@ class ToolValidator(GalaxyToolValidator):
     def concat_messages(self, msg1, msg2):
         if msg1:
             if msg2:
-                message = f'{msg1}  {msg2}'
+                message = f"{msg1}  {msg2}"
             else:
                 message = msg1
         elif msg2:
             message = msg2
         else:
-            message = ''
+            message = ""
         return message
 
     def copy_disk_sample_files_to_dir(self, repo_files_dir, dest_path):
@@ -61,9 +61,9 @@ class ToolValidator(GalaxyToolValidator):
         """
         sample_files = []
         for root, _dirs, files in os.walk(repo_files_dir):
-            if root.find('.hg') < 0:
+            if root.find(".hg") < 0:
                 for name in files:
-                    if name.endswith('.sample'):
+                    if name.endswith(".sample"):
                         relative_path = os.path.join(root, name)
                         tool_util.copy_sample_file(self.app, relative_path, dest_path=dest_path)
                         sample_files.append(name)
@@ -89,10 +89,10 @@ class ToolValidator(GalaxyToolValidator):
                         # 'ncbi_blastp_wrapper.xml' was moved to 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml',
                         # so keep looking for the file until we find the new location.
                         continue
-                    fh = tempfile.NamedTemporaryFile('wb', prefix="tmp-toolshed-gltcrfrm")
+                    fh = tempfile.NamedTemporaryFile("wb", prefix="tmp-toolshed-gltcrfrm")
                     tmp_filename = fh.name
                     fh.close()
-                    fh = open(tmp_filename, 'wb')
+                    fh = open(tmp_filename, "wb")
                     fh.write(fctx.data())
                     fh.close()
                     return tmp_filename
@@ -117,9 +117,9 @@ class ToolValidator(GalaxyToolValidator):
                 # If we decide in the future that files deleted later in the changelog should
                 # not be used, we can use the following if statement. if ctx_file_name.endswith( '.sample' )
                 # and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files:
-                if ctx_file_name.endswith('.sample') and ctx_file_name not in sample_files:
+                if ctx_file_name.endswith(".sample") and ctx_file_name not in sample_files:
                     fctx = hg_util.get_file_context_from_ctx(changeset_ctx, ctx_file)
-                    if fctx in ['DELETED']:
+                    if fctx in ["DELETED"]:
                         # Since the possibly future used if statement above is commented out, the
                         # same file that was initially added will be discovered in an earlier changeset
                         # in the change log and fall through to the else block below.  In other words,
@@ -132,45 +132,54 @@ class ToolValidator(GalaxyToolValidator):
                             deleted_sample_files.append(ctx_file_name)
                     else:
                         sample_files.append(ctx_file_name)
-                        tmp_ctx_file_name = os.path.join(dir, ctx_file_name.replace('.sample', ''))
-                        with open(tmp_ctx_file_name, 'wb') as fh:
+                        tmp_ctx_file_name = os.path.join(dir, ctx_file_name.replace(".sample", ""))
+                        with open(tmp_ctx_file_name, "wb") as fh:
                             fh.write(fctx.data())
         return sample_files, deleted_sample_files
 
-    def handle_sample_files_and_load_tool_from_disk(self, repo_files_dir, repository_id, tool_config_filepath, work_dir):
+    def handle_sample_files_and_load_tool_from_disk(
+        self, repo_files_dir, repository_id, tool_config_filepath, work_dir
+    ):
         """
         Copy all sample files from disk to a temporary directory since the sample files may
         be in multiple directories.
         """
-        message = ''
+        message = ""
         sample_files = self.copy_disk_sample_files_to_dir(repo_files_dir, work_dir)
         if sample_files:
-            if 'tool_data_table_conf.xml.sample' in sample_files:
+            if "tool_data_table_conf.xml.sample" in sample_files:
                 # Load entries into the tool_data_tables if the tool requires them.
-                tool_data_table_config = os.path.join(work_dir, 'tool_data_table_conf.xml')
-                error, message = self.stdtm.handle_sample_tool_data_table_conf_file(tool_data_table_config,
-                                                                                   persist=False)
+                tool_data_table_config = os.path.join(work_dir, "tool_data_table_conf.xml")
+                error, message = self.stdtm.handle_sample_tool_data_table_conf_file(
+                    tool_data_table_config, persist=False
+                )
         tool, valid, message2 = self.load_tool_from_config(repository_id, tool_config_filepath)
         message = self.concat_messages(message, message2)
         return tool, valid, message, sample_files
 
-    def handle_sample_files_and_load_tool_from_tmp_config(self, repo, repository_id, changeset_revision,
-                                                          tool_config_filename, work_dir):
+    def handle_sample_files_and_load_tool_from_tmp_config(
+        self, repo, repository_id, changeset_revision, tool_config_filename, work_dir
+    ):
         tool = None
         valid = False
-        message = ''
+        message = ""
         # We're not currently doing anything with the returned list of deleted_sample_files here.  It is
         # intended to help handle sample files that are in the manifest, but have been deleted from disk.
-        sample_files, deleted_sample_files = self.get_list_of_copied_sample_files(repo, changeset_revision, dir=work_dir)
+        sample_files, deleted_sample_files = self.get_list_of_copied_sample_files(
+            repo, changeset_revision, dir=work_dir
+        )
         if sample_files:
-            if 'tool_data_table_conf.xml.sample' in sample_files:
+            if "tool_data_table_conf.xml.sample" in sample_files:
                 # Load entries into the tool_data_tables if the tool requires them.
-                tool_data_table_config = os.path.join(work_dir, 'tool_data_table_conf.xml')
-                error, message = self.stdtm.handle_sample_tool_data_table_conf_file(tool_data_table_config,
-                                                                                    persist=False)
+                tool_data_table_config = os.path.join(work_dir, "tool_data_table_conf.xml")
+                error, message = self.stdtm.handle_sample_tool_data_table_conf_file(
+                    tool_data_table_config, persist=False
+                )
         manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest(tool_config_filename, repo, changeset_revision)
         if manifest_ctx and ctx_file:
-            tool, valid, message2 = self.load_tool_from_tmp_config(repo, repository_id, manifest_ctx, ctx_file, work_dir)
+            tool, valid, message2 = self.load_tool_from_tmp_config(
+                repo, repository_id, manifest_ctx, ctx_file, work_dir
+            )
             message = self.concat_messages(message, message2)
         return tool, valid, message, sample_files
 
@@ -185,39 +194,35 @@ class ToolValidator(GalaxyToolValidator):
         repository = repository_util.get_repository_in_tool_shed(self.app, repository_id)
         repo_files_dir = repository.repo_path(self.app)
         repo = repository.hg_repo
-        tool_config_filepath = repository_util.get_absolute_path_to_file_in_repository(repo_files_dir, tool_config_filename)
+        tool_config_filepath = repository_util.get_absolute_path_to_file_in_repository(
+            repo_files_dir, tool_config_filename
+        )
         work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-ltfcr")
-        can_use_disk_file = self.can_use_tool_config_disk_file(repository,
-                                                               repo,
-                                                               tool_config_filepath,
-                                                               changeset_revision)
+        can_use_disk_file = self.can_use_tool_config_disk_file(
+            repository, repo, tool_config_filepath, changeset_revision
+        )
         if can_use_disk_file:
-            tool, valid, message, sample_files = \
-                self.handle_sample_files_and_load_tool_from_disk(repo_files_dir,
-                                                                 repository_id,
-                                                                 tool_config_filepath,
-                                                                 work_dir)
+            tool, valid, message, sample_files = self.handle_sample_files_and_load_tool_from_disk(
+                repo_files_dir, repository_id, tool_config_filepath, work_dir
+            )
             if tool is not None:
-                invalid_files_and_errors_tups = \
-                    self.check_tool_input_params(repo_files_dir,
-                                                 tool_config_filename,
-                                                 tool,
-                                                 sample_files)
+                invalid_files_and_errors_tups = self.check_tool_input_params(
+                    repo_files_dir, tool_config_filename, tool, sample_files
+                )
                 if invalid_files_and_errors_tups:
-                    message2 = tool_util.generate_message_for_invalid_tools(self.app,
-                                                                            invalid_files_and_errors_tups,
-                                                                            repository,
-                                                                            metadata_dict=None,
-                                                                            as_html=True,
-                                                                            displaying_invalid_tool=True)
+                    message2 = tool_util.generate_message_for_invalid_tools(
+                        self.app,
+                        invalid_files_and_errors_tups,
+                        repository,
+                        metadata_dict=None,
+                        as_html=True,
+                        displaying_invalid_tool=True,
+                    )
                     message = self.concat_messages(message, message2)
         else:
-            tool, valid, message, sample_files = \
-                self.handle_sample_files_and_load_tool_from_tmp_config(repo,
-                                                                       repository_id,
-                                                                       changeset_revision,
-                                                                       tool_config_filename,
-                                                                       work_dir)
+            tool, valid, message, sample_files = self.handle_sample_files_and_load_tool_from_tmp_config(
+                repo, repository_id, changeset_revision, tool_config_filename, work_dir
+            )
         basic_util.remove_dir(work_dir)
         # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
         self.stdtm.reset_tool_data_tables()
@@ -226,7 +231,7 @@ class ToolValidator(GalaxyToolValidator):
     def load_tool_from_tmp_config(self, repo, repository_id, ctx, ctx_file, work_dir):
         tool = None
         valid = False
-        message = ''
+        message = ""
         tmp_tool_config = hg_util.get_named_tmpfile_from_ctx(ctx, ctx_file, work_dir)
         if tmp_tool_config:
             tool_element, error_message = xml_util.parse_xml(tmp_tool_config)
diff --git a/lib/tool_shed/tools/tool_version_manager.py b/lib/tool_shed/tools/tool_version_manager.py
index acfb64a4542..c5f4a2ee1ed 100644
--- a/lib/tool_shed/tools/tool_version_manager.py
+++ b/lib/tool_shed/tools/tool_version_manager.py
@@ -2,23 +2,26 @@ import logging
 
 from sqlalchemy import and_
 
-from tool_shed.util import hg_util
-from tool_shed.util import metadata_util
-from tool_shed.util import repository_util
+from tool_shed.util import (
+    hg_util,
+    metadata_util,
+    repository_util,
+)
 
 log = logging.getLogger(__name__)
 
 
 class ToolVersionManager:
-
     def __init__(self, app):
         self.app = app
 
     def get_tool_version(self, tool_id):
         context = self.app.install_model.context
-        return context.query(self.app.install_model.ToolVersion) \
-                      .filter(self.app.install_model.ToolVersion.table.c.tool_id == tool_id) \
-                      .first()
+        return (
+            context.query(self.app.install_model.ToolVersion)
+            .filter(self.app.install_model.ToolVersion.table.c.tool_id == tool_id)
+            .first()
+        )
 
     def get_tool_version_association(self, parent_tool_version, tool_version):
         """
@@ -26,10 +29,16 @@ class ToolVersionManager:
         received tool_versions. This function is called only from Galaxy.
         """
         context = self.app.install_model.context
-        return context.query(self.app.install_model.ToolVersionAssociation) \
-                      .filter(and_(self.app.install_model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id,
-                                   self.app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id)) \
-                      .first()
+        return (
+            context.query(self.app.install_model.ToolVersionAssociation)
+            .filter(
+                and_(
+                    self.app.install_model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id,
+                    self.app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id,
+                )
+            )
+            .first()
+        )
 
     def get_version_lineage_for_tool(self, repository_id, repository_metadata, guid):
         """
@@ -53,9 +62,9 @@ class ToolVersionManager:
                     current_child_guid = parent_guid
         # Get all descendant guids of the received guid.
         current_parent_guid = guid
-        for changeset in hg_util.reversed_lower_upper_bounded_changelog(repo,
-                                                                        repository_metadata.changeset_revision,
-                                                                        repository.tip()):
+        for changeset in hg_util.reversed_lower_upper_bounded_changelog(
+            repo, repository_metadata.changeset_revision, repository.tip()
+        ):
             ctx = repo[changeset]
             rm = metadata_util.get_repository_metadata_by_changeset_revision(self.app, repository_id, str(ctx))
             if rm:
diff --git a/lib/tool_shed/util/admin_util.py b/lib/tool_shed/util/admin_util.py
index 79adee0339b..3e8eca90341 100644
--- a/lib/tool_shed/util/admin_util.py
+++ b/lib/tool_shed/util/admin_util.py
@@ -2,18 +2,27 @@ import logging
 import time
 from typing import Optional
 
-from sqlalchemy import false, func
+from sqlalchemy import (
+    false,
+    func,
+)
 
-from galaxy import util, web
+from galaxy import (
+    util,
+    web,
+)
 from galaxy.security.validate_user_input import validate_password
 from galaxy.util import inflector
 from galaxy.util.hash_util import new_secure_hash
 from galaxy.web.form_builder import CheckboxField
-from galaxy.web.legacy_framework.grids import Grid, GridOperation
+from galaxy.web.legacy_framework.grids import (
+    Grid,
+    GridOperation,
+)
 from tool_shed.util.web_util import escape
 
 log = logging.getLogger(__name__)
-compliance_log = logging.getLogger('COMPLIANCE')
+compliance_log = logging.getLogger("COMPLIANCE")
 
 
 class Admin:
@@ -28,26 +37,22 @@ class Admin:
     @web.expose
     @web.require_admin
     def index(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        return trans.fill_template('/webapps/tool_shed/admin/index.mako',
-                                   message=message,
-                                   status=status)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        return trans.fill_template("/webapps/tool_shed/admin/index.mako", message=message, status=status)
 
     @web.expose
     @web.require_admin
     def center(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        return trans.fill_template('/webapps/tool_shed/admin/center.mako',
-                                   message=message,
-                                   status=status)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        return trans.fill_template("/webapps/tool_shed/admin/center.mako", message=message, status=status)
 
     @web.expose
     @web.require_admin
     def roles(self, trans, **kwargs):
-        if 'operation' in kwargs:
-            operation = kwargs['operation'].lower().replace('+', ' ')
+        if "operation" in kwargs:
+            operation = kwargs["operation"].lower().replace("+", " ")
             if operation == "roles":
                 return self.role(trans, **kwargs)
             if operation == "create":
@@ -72,25 +77,25 @@ class Admin:
     @web.require_admin
     def create_role(self, trans, **kwd):
         params = util.Params(kwd)
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        name = util.restore_text(params.get('name', ''))
-        description = util.restore_text(params.get('description', ''))
-        in_users = util.listify(params.get('in_users', []))
-        out_users = util.listify(params.get('out_users', []))
-        in_groups = util.listify(params.get('in_groups', []))
-        out_groups = util.listify(params.get('out_groups', []))
-        create_group_for_role = params.get('create_group_for_role', '')
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        name = util.restore_text(params.get("name", ""))
+        description = util.restore_text(params.get("description", ""))
+        in_users = util.listify(params.get("in_users", []))
+        out_users = util.listify(params.get("out_users", []))
+        in_groups = util.listify(params.get("in_groups", []))
+        out_groups = util.listify(params.get("out_groups", []))
+        create_group_for_role = params.get("create_group_for_role", "")
         create_group_for_role_checked = CheckboxField.is_checked(create_group_for_role)
         ok = True
-        if params.get('create_role_button', False):
+        if params.get("create_role_button", False):
             if not name or not description:
                 message = "Enter a valid name and a description."
-                status = 'error'
+                status = "error"
                 ok = False
             elif trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first():
                 message = "Role names must be unique and a role with that name already exists, so choose another name."
-                status = 'error'
+                status = "error"
                 ok = False
             else:
                 # Create the role
@@ -115,60 +120,73 @@ class Admin:
                 else:
                     num_in_groups = len(in_groups)
                 trans.sa_session.flush()
-                message = "Role '%s' has been created with %d associated users and %d associated groups.  " \
-                    % (role.name, len(in_users), num_in_groups)
+                message = "Role '%s' has been created with %d associated users and %d associated groups.  " % (
+                    role.name,
+                    len(in_users),
+                    num_in_groups,
+                )
                 if create_group_for_role_checked:
-                    message += 'One of the groups associated with this role is the newly created group with the same name.'
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='roles',
-                                                         message=util.sanitize_text(message),
-                                                         status='done'))
+                    message += (
+                        "One of the groups associated with this role is the newly created group with the same name."
+                    )
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="done")
+                )
         if ok:
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 out_users.append((user.id, user.email))
-            for group in trans.sa_session.query(trans.app.model.Group) \
-                                         .filter(trans.app.model.Group.table.c.deleted == false()) \
-                                         .order_by(trans.app.model.Group.table.c.name):
+            for group in (
+                trans.sa_session.query(trans.app.model.Group)
+                .filter(trans.app.model.Group.table.c.deleted == false())
+                .order_by(trans.app.model.Group.table.c.name)
+            ):
                 out_groups.append((group.id, group.name))
-        return trans.fill_template('/webapps/tool_shed/admin/dataset_security/role/role_create.mako',
-                                   name=name,
-                                   description=description,
-                                   in_users=in_users,
-                                   out_users=out_users,
-                                   in_groups=in_groups,
-                                   out_groups=out_groups,
-                                   create_group_for_role_checked=create_group_for_role_checked,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/dataset_security/role/role_create.mako",
+            name=name,
+            description=description,
+            in_users=in_users,
+            out_users=out_users,
+            in_groups=in_groups,
+            out_groups=out_groups,
+            create_group_for_role_checked=create_group_for_role_checked,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def rename_role(self, trans, **kwd):
         params = util.Params(kwd)
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        id = params.get('id', None)
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        id = params.get("id", None)
         if not id:
             message = "No role ids received for renaming"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='roles',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="roles", message=message, status="error")
+            )
         role = get_role(trans, id)
-        if params.get('rename_role_button', False):
+        if params.get("rename_role_button", False):
             old_name = role.name
             new_name = util.restore_text(params.name)
             new_description = util.restore_text(params.description)
             if not new_name:
-                message = 'Enter a valid name'
-                status = 'error'
+                message = "Enter a valid name"
+                status = "error"
             else:
-                existing_role = trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == new_name).first()
+                existing_role = (
+                    trans.sa_session.query(trans.app.model.Role)
+                    .filter(trans.app.model.Role.table.c.name == new_name)
+                    .first()
+                )
                 if existing_role and existing_role.id != role.id:
-                    message = 'A role with that name already exists'
-                    status = 'error'
+                    message = "A role with that name already exists"
+                    status = "error"
                 else:
                     if not (role.name == new_name and role.description == new_description):
                         role.name = new_name
@@ -176,32 +194,31 @@ class Admin:
                         trans.sa_session.add(role)
                         trans.sa_session.flush()
                         message = f"Role '{old_name}' has been renamed to '{new_name}'"
-                    return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                    action='roles',
-                                                                    message=util.sanitize_text(message),
-                                                                    status='done'))
-        return trans.fill_template('/webapps/tool_shed/admin/dataset_security/role/role_rename.mako',
-                                   role=role,
-                                   message=message,
-                                   status=status)
+                    return trans.response.send_redirect(
+                        web.url_for(
+                            controller="admin", action="roles", message=util.sanitize_text(message), status="done"
+                        )
+                    )
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/dataset_security/role/role_rename.mako", role=role, message=message, status=status
+        )
 
     @web.expose
     @web.require_admin
     def manage_users_and_groups_for_role(self, trans, **kwd):
         params = util.Params(kwd)
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        id = params.get('id', None)
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        id = params.get("id", None)
         if not id:
             message = "No role ids received for managing users and groups"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='roles',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="roles", message=message, status="error")
+            )
         role = get_role(trans, id)
-        if params.get('role_members_edit_button', False):
+        if params.get("role_members_edit_button", False):
             in_users = [trans.sa_session.query(trans.app.model.User).get(x) for x in util.listify(params.in_users)]
-            if trans.webapp.name == 'galaxy':
+            if trans.webapp.name == "galaxy":
                 for ura in role.users:
                     user = trans.sa_session.query(trans.app.model.User).get(ura.user_id)
                     if user not in in_users:
@@ -218,50 +235,60 @@ class Admin:
             in_groups = [trans.sa_session.query(trans.app.model.Group).get(x) for x in util.listify(params.in_groups)]
             trans.app.security_agent.set_entity_role_associations(roles=[role], users=in_users, groups=in_groups)
             trans.sa_session.refresh(role)
-            message = "Role '%s' has been updated with %d associated users and %d associated groups" % (role.name, len(in_users), len(in_groups))
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='roles',
-                                                     message=util.sanitize_text(message),
-                                                     status=status))
+            message = "Role '%s' has been updated with %d associated users and %d associated groups" % (
+                role.name,
+                len(in_users),
+                len(in_groups),
+            )
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status=status)
+            )
         in_users = []
         out_users = []
         in_groups = []
         out_groups = []
-        for user in trans.sa_session.query(trans.app.model.User) \
-                                    .filter(trans.app.model.User.table.c.deleted == false()) \
-                                    .order_by(trans.app.model.User.table.c.email):
+        for user in (
+            trans.sa_session.query(trans.app.model.User)
+            .filter(trans.app.model.User.table.c.deleted == false())
+            .order_by(trans.app.model.User.table.c.email)
+        ):
             if user in [x.user for x in role.users]:
                 in_users.append((user.id, user.email))
             else:
                 out_users.append((user.id, user.email))
-        for group in trans.sa_session.query(trans.app.model.Group) \
-                                     .filter(trans.app.model.Group.table.c.deleted == false()) \
-                                     .order_by(trans.app.model.Group.table.c.name):
+        for group in (
+            trans.sa_session.query(trans.app.model.Group)
+            .filter(trans.app.model.Group.table.c.deleted == false())
+            .order_by(trans.app.model.Group.table.c.name)
+        ):
             if group in [x.group for x in role.groups]:
                 in_groups.append((group.id, group.name))
             else:
                 out_groups.append((group.id, group.name))
         library_dataset_actions = {}
-        if trans.webapp.name == 'galaxy' and len(role.dataset_actions) < 25:
+        if trans.webapp.name == "galaxy" and len(role.dataset_actions) < 25:
             # Build a list of tuples that are LibraryDatasetDatasetAssociationss followed by a list of actions
             # whose DatasetPermissions is associated with the Role
             # [ ( LibraryDatasetDatasetAssociation [ action, action ] ) ]
             for dp in role.dataset_actions:
-                for ldda in trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation) \
-                                            .filter(trans.app.model.LibraryDatasetDatasetAssociation.dataset_id == dp.dataset_id):
+                for ldda in trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).filter(
+                    trans.app.model.LibraryDatasetDatasetAssociation.dataset_id == dp.dataset_id
+                ):
                     root_found = False
-                    folder_path = ''
+                    folder_path = ""
                     folder = ldda.library_dataset.folder
                     while not root_found:
-                        folder_path = f'{folder.name} / {folder_path}'
+                        folder_path = f"{folder.name} / {folder_path}"
                         if not folder.parent:
                             root_found = True
                         else:
                             folder = folder.parent
-                    folder_path = f'{folder_path} {ldda.name}'
-                    library = trans.sa_session.query(trans.app.model.Library) \
-                                              .filter(trans.app.model.Library.table.c.root_folder_id == folder.id) \
-                                              .first()
+                    folder_path = f"{folder_path} {ldda.name}"
+                    library = (
+                        trans.sa_session.query(trans.app.model.Library)
+                        .filter(trans.app.model.Library.table.c.root_folder_id == folder.id)
+                        .first()
+                    )
                     if library not in library_dataset_actions:
                         library_dataset_actions[library] = {}
                     try:
@@ -270,27 +297,28 @@ class Admin:
                         library_dataset_actions[library][folder_path] = [dp.action]
         else:
             message = "Not showing associated datasets, there are too many."
-            status = 'info'
-        return trans.fill_template('/webapps/tool_shed/admin/dataset_security/role/role.mako',
-                                   role=role,
-                                   in_users=in_users,
-                                   out_users=out_users,
-                                   in_groups=in_groups,
-                                   out_groups=out_groups,
-                                   library_dataset_actions=library_dataset_actions,
-                                   message=message,
-                                   status=status)
+            status = "info"
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/dataset_security/role/role.mako",
+            role=role,
+            in_users=in_users,
+            out_users=out_users,
+            in_groups=in_groups,
+            out_groups=out_groups,
+            library_dataset_actions=library_dataset_actions,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def mark_role_deleted(self, trans, **kwd):
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No role ids received for deleting"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='roles',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="roles", message=message, status="error")
+            )
         ids = util.listify(id)
         message = "Deleted %d roles: " % len(ids)
         for role_id in ids:
@@ -299,21 +327,19 @@ class Admin:
             trans.sa_session.add(role)
             trans.sa_session.flush()
             message += f" {role.name} "
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='roles',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def undelete_role(self, trans, **kwd):
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No role ids received for undeleting"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='roles',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="roles", message=message, status="error")
+            )
         ids = util.listify(id)
         count = 0
         undeleted_roles = ""
@@ -321,20 +347,18 @@ class Admin:
             role = get_role(trans, role_id)
             if not role.deleted:
                 message = f"Role '{role.name}' has not been deleted, so it cannot be undeleted."
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='roles',
-                                                         message=util.sanitize_text(message),
-                                                         status='error'))
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="error")
+                )
             role.deleted = False
             trans.sa_session.add(role)
             trans.sa_session.flush()
             count += 1
             undeleted_roles += f" {role.name}"
         message = "Undeleted %d roles: %s" % (count, undeleted_roles)
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='roles',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
@@ -346,23 +370,21 @@ class Admin:
         # - DefaultHistoryPermissions where role_id == Role.id
         # - GroupRoleAssociations where role_id == Role.id
         # - DatasetPermissionss where role_id == Role.id
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No role ids received for purging"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='roles',
-                                                     message=util.sanitize_text(message),
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="error")
+            )
         ids = util.listify(id)
         message = "Purged %d roles: " % len(ids)
         for role_id in ids:
             role = get_role(trans, role_id)
             if not role.deleted:
                 message = f"Role '{role.name}' has not been deleted, so it cannot be purged."
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='roles',
-                                                         message=util.sanitize_text(message),
-                                                         status='error'))
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="error")
+                )
             # Delete UserRoleAssociations
             for ura in role.users:
                 user = trans.sa_session.query(trans.app.model.User).get(ura.user_id)
@@ -384,16 +406,15 @@ class Admin:
                 trans.sa_session.delete(dp)
             trans.sa_session.flush()
             message += f" {role.name} "
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='roles',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="roles", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def groups(self, trans, **kwargs):
-        if 'operation' in kwargs:
-            operation = kwargs['operation'].lower().replace('+', ' ')
+        if "operation" in kwargs:
+            operation = kwargs["operation"].lower().replace("+", " ")
             if operation == "groups":
                 return self.group(trans, **kwargs)
             if operation == "create":
@@ -415,109 +436,132 @@ class Admin:
     @web.require_admin
     def rename_group(self, trans, **kwd):
         params = util.Params(kwd)
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        id = params.get('id', None)
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        id = params.get("id", None)
         if not id:
             message = "No group ids received for renaming"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='groups',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="groups", message=message, status="error")
+            )
         group = get_group(trans, id)
-        if params.get('rename_group_button', False):
+        if params.get("rename_group_button", False):
             old_name = group.name
             new_name = util.restore_text(params.name)
             if not new_name:
-                message = 'Enter a valid name'
-                status = 'error'
+                message = "Enter a valid name"
+                status = "error"
             else:
-                existing_group = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == new_name).first()
+                existing_group = (
+                    trans.sa_session.query(trans.app.model.Group)
+                    .filter(trans.app.model.Group.table.c.name == new_name)
+                    .first()
+                )
                 if existing_group and existing_group.id != group.id:
-                    message = 'A group with that name already exists'
-                    status = 'error'
+                    message = "A group with that name already exists"
+                    status = "error"
                 else:
                     if group.name != new_name:
                         group.name = new_name
                         trans.sa_session.add(group)
                         trans.sa_session.flush()
                         message = f"Group '{old_name}' has been renamed to '{new_name}'"
-                    return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                    action='groups',
-                                                                    message=util.sanitize_text(message),
-                                                                    status='done'))
-        return trans.fill_template('/webapps/tool_shed/admin/dataset_security/group/group_rename.mako',
-                                   group=group,
-                                   message=message,
-                                   status=status)
+                    return trans.response.send_redirect(
+                        web.url_for(
+                            controller="admin", action="groups", message=util.sanitize_text(message), status="done"
+                        )
+                    )
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/dataset_security/group/group_rename.mako",
+            group=group,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def manage_users_and_roles_for_group(self, trans, **kwd):
         params = util.Params(kwd)
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
         group = get_group(trans, params.id)
-        if params.get('group_roles_users_edit_button', False):
+        if params.get("group_roles_users_edit_button", False):
             in_roles = [trans.sa_session.query(trans.app.model.Role).get(x) for x in util.listify(params.in_roles)]
             in_users = [trans.sa_session.query(trans.app.model.User).get(x) for x in util.listify(params.in_users)]
             trans.app.security_agent.set_entity_group_associations(groups=[group], roles=in_roles, users=in_users)
             trans.sa_session.refresh(group)
-            message += "Group '%s' has been updated with %d associated roles and %d associated users" % (group.name, len(in_roles), len(in_users))
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='groups',
-                                                     message=util.sanitize_text(message),
-                                                     status=status))
+            message += "Group '%s' has been updated with %d associated roles and %d associated users" % (
+                group.name,
+                len(in_roles),
+                len(in_users),
+            )
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="groups", message=util.sanitize_text(message), status=status)
+            )
         in_roles = []
         out_roles = []
         in_users = []
         out_users = []
-        for role in trans.sa_session.query(trans.app.model.Role) \
-                                    .filter(trans.app.model.Role.table.c.deleted == false()) \
-                                    .order_by(trans.app.model.Role.table.c.name):
+        for role in (
+            trans.sa_session.query(trans.app.model.Role)
+            .filter(trans.app.model.Role.table.c.deleted == false())
+            .order_by(trans.app.model.Role.table.c.name)
+        ):
             if role in [x.role for x in group.roles]:
                 in_roles.append((role.id, role.name))
             else:
                 out_roles.append((role.id, role.name))
-        for user in trans.sa_session.query(trans.app.model.User) \
-                                    .filter(trans.app.model.User.table.c.deleted == false()) \
-                                    .order_by(trans.app.model.User.table.c.email):
+        for user in (
+            trans.sa_session.query(trans.app.model.User)
+            .filter(trans.app.model.User.table.c.deleted == false())
+            .order_by(trans.app.model.User.table.c.email)
+        ):
             if user in [x.user for x in group.users]:
                 in_users.append((user.id, user.email))
             else:
                 out_users.append((user.id, user.email))
-        message += 'Group %s is currently associated with %d roles and %d users' % (group.name, len(in_roles), len(in_users))
-        return trans.fill_template('/webapps/tool_shed/admin/dataset_security/group/group.mako',
-                                   group=group,
-                                   in_roles=in_roles,
-                                   out_roles=out_roles,
-                                   in_users=in_users,
-                                   out_users=out_users,
-                                   message=message,
-                                   status=status)
+        message += "Group %s is currently associated with %d roles and %d users" % (
+            group.name,
+            len(in_roles),
+            len(in_users),
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/dataset_security/group/group.mako",
+            group=group,
+            in_roles=in_roles,
+            out_roles=out_roles,
+            in_users=in_users,
+            out_users=out_users,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def create_group(self, trans, **kwd):
         params = util.Params(kwd)
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        name = util.restore_text(params.get('name', ''))
-        in_users = util.listify(params.get('in_users', []))
-        out_users = util.listify(params.get('out_users', []))
-        in_roles = util.listify(params.get('in_roles', []))
-        out_roles = util.listify(params.get('out_roles', []))
-        create_role_for_group = params.get('create_role_for_group', '')
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        name = util.restore_text(params.get("name", ""))
+        in_users = util.listify(params.get("in_users", []))
+        out_users = util.listify(params.get("out_users", []))
+        in_roles = util.listify(params.get("in_roles", []))
+        out_roles = util.listify(params.get("out_roles", []))
+        create_role_for_group = params.get("create_role_for_group", "")
         create_role_for_group_checked = CheckboxField.is_checked(create_role_for_group)
         ok = True
-        if params.get('create_group_button', False):
+        if params.get("create_group_button", False):
             if not name:
                 message = "Enter a valid name."
-                status = 'error'
+                status = "error"
                 ok = False
-            elif trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first():
-                message = "Group names must be unique and a group with that name already exists, so choose another name."
-                status = 'error'
+            elif (
+                trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first()
+            ):
+                message = (
+                    "Group names must be unique and a group with that name already exists, so choose another name."
+                )
+                status = "error"
                 ok = False
             else:
                 # Create the group
@@ -534,7 +578,7 @@ class Admin:
                     trans.sa_session.add(gra)
                 if create_role_for_group_checked:
                     # Create the role
-                    role = trans.app.model.Role(name=name, description=f'Role for group {name}')
+                    role = trans.app.model.Role(name=name, description=f"Role for group {name}")
                     trans.sa_session.add(role)
                     # Associate the role with the group
                     gra = trans.model.GroupRoleAssociation(group, role)
@@ -543,44 +587,53 @@ class Admin:
                 else:
                     num_in_roles = len(in_roles)
                 trans.sa_session.flush()
-                message = "Group '%s' has been created with %d associated users and %d associated roles.  " \
-                    % (group.name, len(in_users), num_in_roles)
+                message = "Group '%s' has been created with %d associated users and %d associated roles.  " % (
+                    group.name,
+                    len(in_users),
+                    num_in_roles,
+                )
                 if create_role_for_group_checked:
-                    message += 'One of the roles associated with this group is the newly created role with the same name.'
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='groups',
-                                                         message=util.sanitize_text(message),
-                                                         status='done'))
+                    message += (
+                        "One of the roles associated with this group is the newly created role with the same name."
+                    )
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="groups", message=util.sanitize_text(message), status="done")
+                )
         if ok:
-            for user in trans.sa_session.query(trans.app.model.User) \
-                                        .filter(trans.app.model.User.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.User.table.c.email):
+            for user in (
+                trans.sa_session.query(trans.app.model.User)
+                .filter(trans.app.model.User.table.c.deleted == false())
+                .order_by(trans.app.model.User.table.c.email)
+            ):
                 out_users.append((user.id, user.email))
-            for role in trans.sa_session.query(trans.app.model.Role) \
-                                        .filter(trans.app.model.Role.table.c.deleted == false()) \
-                                        .order_by(trans.app.model.Role.table.c.name):
+            for role in (
+                trans.sa_session.query(trans.app.model.Role)
+                .filter(trans.app.model.Role.table.c.deleted == false())
+                .order_by(trans.app.model.Role.table.c.name)
+            ):
                 out_roles.append((role.id, role.name))
-        return trans.fill_template('/webapps/tool_shed/admin/dataset_security/group/group_create.mako',
-                                   name=name,
-                                   in_users=in_users,
-                                   out_users=out_users,
-                                   in_roles=in_roles,
-                                   out_roles=out_roles,
-                                   create_role_for_group_checked=create_role_for_group_checked,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/dataset_security/group/group_create.mako",
+            name=name,
+            in_users=in_users,
+            out_users=out_users,
+            in_roles=in_roles,
+            out_roles=out_roles,
+            create_role_for_group_checked=create_role_for_group_checked,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def mark_group_deleted(self, trans, **kwd):
         params = util.Params(kwd)
-        id = params.get('id', None)
+        id = params.get("id", None)
         if not id:
             message = "No group ids received for marking deleted"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='groups',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="groups", message=message, status="error")
+            )
         ids = util.listify(id)
         message = "Deleted %d groups: " % len(ids)
         for group_id in ids:
@@ -589,21 +642,19 @@ class Admin:
             trans.sa_session.add(group)
             trans.sa_session.flush()
             message += f" {group.name} "
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='groups',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="groups", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def undelete_group(self, trans, **kwd):
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No group ids received for undeleting"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='groups',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="groups", message=message, status="error")
+            )
         ids = util.listify(id)
         count = 0
         undeleted_groups = ""
@@ -611,33 +662,32 @@ class Admin:
             group = get_group(trans, group_id)
             if not group.deleted:
                 message = f"Group '{group.name}' has not been deleted, so it cannot be undeleted."
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='groups',
-                                                         message=util.sanitize_text(message),
-                                                         status='error'))
+                trans.response.send_redirect(
+                    web.url_for(
+                        controller="admin", action="groups", message=util.sanitize_text(message), status="error"
+                    )
+                )
             group.deleted = False
             trans.sa_session.add(group)
             trans.sa_session.flush()
             count += 1
             undeleted_groups += f" {group.name}"
         message = "Undeleted %d groups: %s" % (count, undeleted_groups)
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='groups',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="groups", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def purge_group(self, trans, **kwd):
         # This method should only be called for a Group that has previously been deleted.
         # Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations.
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No group ids received for purging"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='groups',
-                                                     message=util.sanitize_text(message),
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="groups", message=util.sanitize_text(message), status="error")
+            )
         ids = util.listify(id)
         message = "Purged %d groups: " % len(ids)
         for group_id in ids:
@@ -645,10 +695,11 @@ class Admin:
             if not group.deleted:
                 # We should never reach here, but just in case there is a bug somewhere...
                 message = f"Group '{group.name}' has not been deleted, so it cannot be purged."
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='groups',
-                                                         message=util.sanitize_text(message),
-                                                         status='error'))
+                trans.response.send_redirect(
+                    web.url_for(
+                        controller="admin", action="groups", message=util.sanitize_text(message), status="error"
+                    )
+                )
             # Delete UserGroupAssociations
             for uga in group.users:
                 trans.sa_session.delete(uga)
@@ -657,83 +708,77 @@ class Admin:
                 trans.sa_session.delete(gra)
             trans.sa_session.flush()
             message += f" {group.name} "
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='groups',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="groups", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def create_new_user(self, trans, **kwd):
-        return trans.response.send_redirect(web.url_for(controller='user',
-                                                        action='create',
-                                                        cntrller='admin'))
+        return trans.response.send_redirect(web.url_for(controller="user", action="create", cntrller="admin"))
 
     @web.expose
     @web.require_admin
     def reset_user_password(self, trans, **kwd):
-        user_id = kwd.get('id', None)
+        user_id = kwd.get("id", None)
         if not user_id:
             message = "No users received for resetting passwords."
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='users',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="users", message=message, status="error")
+            )
         user_ids = util.listify(user_id)
-        if 'reset_user_password_button' in kwd:
-            message = ''
-            status = ''
+        if "reset_user_password_button" in kwd:
+            message = ""
+            status = ""
             for user_id in user_ids:
                 user = get_user(trans, user_id)
-                password = kwd.get('password', None)
-                confirm = kwd.get('confirm', None)
+                password = kwd.get("password", None)
+                confirm = kwd.get("confirm", None)
                 message = validate_password(trans, password, confirm)
                 if message:
-                    status = 'error'
+                    status = "error"
                     break
                 else:
                     user.set_password_cleartext(password)
                     trans.sa_session.add(user)
                     trans.sa_session.flush()
             if not message and not status:
-                message = "Passwords reset for %d %s." % (len(user_ids), inflector.cond_plural(len(user_ids), 'user'))
-                status = 'done'
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='users',
-                                                     message=util.sanitize_text(message),
-                                                     status=status))
+                message = "Passwords reset for %d %s." % (len(user_ids), inflector.cond_plural(len(user_ids), "user"))
+                status = "done"
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status=status)
+            )
         users = [get_user(trans, user_id) for user_id in user_ids]
         if len(user_ids) > 1:
-            user_id = ','.join(user_ids)
-        return trans.fill_template('/webapps/tool_shed/admin/user/reset_password.mako',
-                                   id=user_id,
-                                   users=users,
-                                   password='',
-                                   confirm='')
+            user_id = ",".join(user_ids)
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/user/reset_password.mako", id=user_id, users=users, password="", confirm=""
+        )
 
     @web.expose
     @web.require_admin
     def mark_user_deleted(self, trans, **kwd):
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No user ids received for deleting"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='users',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="users", message=message, status="error")
+            )
         ids = util.listify(id)
         message = "Deleted %d users: " % len(ids)
         for user_id in ids:
             user = get_user(trans, user_id)
             user.deleted = True
 
-            compliance_log.info(f'delete-user-event: {user_id}')
+            compliance_log.info(f"delete-user-event: {user_id}")
             # See lib/galaxy/webapps/tool_shed/controllers/admin.py
             pseudorandom_value = str(int(time.time()))
             email_hash = new_secure_hash(user.email + pseudorandom_value)
             uname_hash = new_secure_hash(user.username + pseudorandom_value)
             for role in user.all_roles():
-                print(role, self.app.config.redact_username_during_deletion, self.app.config.redact_email_during_deletion)
+                print(
+                    role, self.app.config.redact_username_during_deletion, self.app.config.redact_email_during_deletion
+                )
                 if self.app.config.redact_username_during_deletion:
                     role.name = role.name.replace(user.username, uname_hash)
                     role.description = role.description.replace(user.username, uname_hash)
@@ -750,21 +795,19 @@ class Admin:
             trans.sa_session.add(user)
             trans.sa_session.flush()
             message += f" {user.email} "
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='users',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def undelete_user(self, trans, **kwd):
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No user ids received for undeleting"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='users',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="users", message=message, status="error")
+            )
         ids = util.listify(id)
         count = 0
         undeleted_users = ""
@@ -772,20 +815,18 @@ class Admin:
             user = get_user(trans, user_id)
             if not user.deleted:
                 message = f"User '{user.email}' has not been deleted, so it cannot be undeleted."
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='users',
-                                                         message=util.sanitize_text(message),
-                                                         status='error'))
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="error")
+                )
             user.deleted = False
             trans.sa_session.add(user)
             trans.sa_session.flush()
             count += 1
             undeleted_users += f" {user.email}"
         message = "Undeleted %d users: %s" % (count, undeleted_users)
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='users',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
@@ -802,13 +843,12 @@ class Admin:
         # - UserRoleAssociation where user_id == User.id EXCEPT FOR THE PRIVATE ROLE
         # - UserAddress where user_id == User.id
         # Purging Histories and Datasets must be handled via the cleanup_datasets.py script
-        id = kwd.get('id', None)
+        id = kwd.get("id", None)
         if not id:
             message = "No user ids received for purging"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='users',
-                                                     message=util.sanitize_text(message),
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="error")
+            )
         ids = util.listify(id)
         message = "Purged %d users: " % len(ids)
         for user_id in ids:
@@ -816,10 +856,9 @@ class Admin:
             if not user.deleted:
                 # We should never reach here, but just in case there is a bug somewhere...
                 message = f"User '{user.email}' has not been deleted, so it cannot be purged."
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='users',
-                                                         message=util.sanitize_text(message),
-                                                         status='error'))
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="error")
+                )
             private_role = trans.app.security_agent.get_private_user_role(user)
             # Delete History
             for h in user.active_histories:
@@ -850,16 +889,15 @@ class Admin:
             trans.sa_session.add(user)
             trans.sa_session.flush()
             message += f"{user.email} "
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='users',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="done")
+        )
 
     @web.expose
     @web.require_admin
     def users(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "roles":
                 return self.user(trans, **kwd)
             elif operation == "reset password":
@@ -890,56 +928,63 @@ class Admin:
     def name_autocomplete_data(self, trans, q=None, limit=None, timestamp=None):
         """Return autocomplete data for user emails"""
         ac_data = ""
-        for user in trans.sa_session.query(trans.app.model.User).filter_by(deleted=False).filter(func.lower(trans.app.model.User.email).like(f"{q.lower()}%")):
+        for user in (
+            trans.sa_session.query(trans.app.model.User)
+            .filter_by(deleted=False)
+            .filter(func.lower(trans.app.model.User.email).like(f"{q.lower()}%"))
+        ):
             ac_data = f"{ac_data + user.email}\n"
         return ac_data
 
     @web.expose
     @web.require_admin
     def manage_roles_and_groups_for_user(self, trans, **kwd):
-        user_id = kwd.get('id', None)
-        message = ''
-        status = ''
+        user_id = kwd.get("id", None)
+        message = ""
+        status = ""
         if not user_id:
             message += f"Invalid user id ({str(user_id)}) received"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='users',
-                                                     message=util.sanitize_text(message),
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="error")
+            )
         user = get_user(trans, user_id)
         private_role = trans.app.security_agent.get_private_user_role(user)
-        if kwd.get('user_roles_groups_edit_button', False):
+        if kwd.get("user_roles_groups_edit_button", False):
             # Make sure the user is not dis-associating himself from his private role
-            out_roles = kwd.get('out_roles', [])
+            out_roles = kwd.get("out_roles", [])
             if out_roles:
                 out_roles = [trans.sa_session.query(trans.app.model.Role).get(x) for x in util.listify(out_roles)]
             if private_role in out_roles:
                 message += "You cannot eliminate a user's private role association.  "
-                status = 'error'
-            in_roles = kwd.get('in_roles', [])
+                status = "error"
+            in_roles = kwd.get("in_roles", [])
             if in_roles:
                 in_roles = [trans.sa_session.query(trans.app.model.Role).get(x) for x in util.listify(in_roles)]
-            out_groups = kwd.get('out_groups', [])
+            out_groups = kwd.get("out_groups", [])
             if out_groups:
                 out_groups = [trans.sa_session.query(trans.app.model.Group).get(x) for x in util.listify(out_groups)]
-            in_groups = kwd.get('in_groups', [])
+            in_groups = kwd.get("in_groups", [])
             if in_groups:
                 in_groups = [trans.sa_session.query(trans.app.model.Group).get(x) for x in util.listify(in_groups)]
             if in_roles:
                 trans.app.security_agent.set_entity_user_associations(users=[user], roles=in_roles, groups=in_groups)
                 trans.sa_session.refresh(user)
-                message += "User '%s' has been updated with %d associated roles and %d associated groups (private roles are not displayed)" % \
-                    (user.email, len(in_roles), len(in_groups))
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='users',
-                                                         message=util.sanitize_text(message),
-                                                         status='done'))
+                message += (
+                    "User '%s' has been updated with %d associated roles and %d associated groups (private roles are not displayed)"
+                    % (user.email, len(in_roles), len(in_groups))
+                )
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="users", message=util.sanitize_text(message), status="done")
+                )
         in_roles = []
         out_roles = []
         in_groups = []
         out_groups = []
-        for role in trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.deleted == false()) \
-                .order_by(trans.app.model.Role.table.c.name):
+        for role in (
+            trans.sa_session.query(trans.app.model.Role)
+            .filter(trans.app.model.Role.table.c.deleted == false())
+            .order_by(trans.app.model.Role.table.c.name)
+        ):
             if role in [x.role for x in user.roles]:
                 in_roles.append((role.id, role.name))
             elif role.type != trans.app.model.Role.types.PRIVATE:
@@ -948,24 +993,32 @@ class Admin:
                 # role, which should always be in in_roles.  The check above is added as an additional
                 # precaution, since for a period of time we were including private roles in the form fields.
                 out_roles.append((role.id, role.name))
-        for group in trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.deleted == false()) \
-                .order_by(trans.app.model.Group.table.c.name):
+        for group in (
+            trans.sa_session.query(trans.app.model.Group)
+            .filter(trans.app.model.Group.table.c.deleted == false())
+            .order_by(trans.app.model.Group.table.c.name)
+        ):
             if group in [x.group for x in user.groups]:
                 in_groups.append((group.id, group.name))
             else:
                 out_groups.append((group.id, group.name))
-        message += "User '%s' is currently associated with %d roles and is a member of %d groups" % \
-            (user.email, len(in_roles), len(in_groups))
+        message += "User '%s' is currently associated with %d roles and is a member of %d groups" % (
+            user.email,
+            len(in_roles),
+            len(in_groups),
+        )
         if not status:
-            status = 'done'
-        return trans.fill_template('/webapps/tool_shed/admin/user/user.mako',
-                                   user=user,
-                                   in_roles=in_roles,
-                                   out_roles=out_roles,
-                                   in_groups=in_groups,
-                                   out_groups=out_groups,
-                                   message=message,
-                                   status=status)
+            status = "done"
+        return trans.fill_template(
+            "/webapps/tool_shed/admin/user/user.mako",
+            user=user,
+            in_roles=in_roles,
+            out_roles=out_roles,
+            in_groups=in_groups,
+            out_groups=out_groups,
+            message=message,
+            status=status,
+        )
 
 
 # ---- Utility methods -------------------------------------------------------
diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py
index fcc9e988def..25a1d6dc127 100644
--- a/lib/tool_shed/util/commit_util.py
+++ b/lib/tool_shed/util/commit_util.py
@@ -13,12 +13,16 @@ import tool_shed.repository_types.util as rt_util
 from galaxy.util import checkers
 from galaxy.util.path import safe_relpath
 from tool_shed.tools.data_table_manager import ShedToolDataTableManager
-from tool_shed.util import basic_util, hg_util, shed_util_common as suc
+from tool_shed.util import (
+    basic_util,
+    hg_util,
+)
+from tool_shed.util import shed_util_common as suc
 
 log = logging.getLogger(__name__)
 
-UNDESIRABLE_DIRS = ['.hg', '.svn', '.git', '.cvs', '.idea']
-UNDESIRABLE_FILES = ['.hg_archival.txt', 'hgrc', '.DS_Store', 'tool_test_output.html', 'tool_test_output.json']
+UNDESIRABLE_DIRS = [".hg", ".svn", ".git", ".cvs", ".idea"]
+UNDESIRABLE_FILES = [".hg_archival.txt", "hgrc", ".DS_Store", "tool_test_output.html", "tool_test_output.json"]
 
 
 def check_archive(repository, archive):
@@ -30,7 +34,9 @@ def check_archive(repository, archive):
     for member in archive.getmembers():
         # Allow regular files and directories only
         if not (member.isdir() or member.isfile() or member.islnk()):
-            errors.append("Uploaded archives can only include regular directories and files (no symbolic links, devices, etc).")
+            errors.append(
+                "Uploaded archives can only include regular directories and files (no symbolic links, devices, etc)."
+            )
             invalid.append(member)
             continue
         if not safe_relpath(member.name):
@@ -50,16 +56,28 @@ def check_archive(repository, archive):
                 break
         if found_undesirable_dir:
             continue
-        if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION and member.name != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
-            errors.append('Repositories of type <b>Repository suite definition</b> can contain only a single file named <b>repository_dependencies.xml</b>.')
+        if (
+            repository.type == rt_util.REPOSITORY_SUITE_DEFINITION
+            and member.name != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
+        ):
+            errors.append(
+                "Repositories of type <b>Repository suite definition</b> can contain only a single file named <b>repository_dependencies.xml</b>."
+            )
             invalid.append(member)
             continue
-        if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and member.name != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
-            errors.append('Repositories of type <b>Tool dependency definition</b> can contain only a single file named <b>tool_dependencies.xml</b>.')
+        if (
+            repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION
+            and member.name != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME
+        ):
+            errors.append(
+                "Repositories of type <b>Tool dependency definition</b> can contain only a single file named <b>tool_dependencies.xml</b>."
+            )
             invalid.append(member)
             continue
         valid.append(member)
-    ArchiveCheckResults = namedtuple('ArchiveCheckResults', ['valid', 'invalid', 'undesirable_files', 'undesirable_dirs', 'errors'])
+    ArchiveCheckResults = namedtuple(
+        "ArchiveCheckResults", ["valid", "invalid", "undesirable_files", "undesirable_dirs", "errors"]
+    )
     return ArchiveCheckResults(valid, invalid, undesirable_files, undesirable_dirs, errors)
 
 
@@ -70,8 +88,9 @@ def check_file_contents_for_email_alerts(app):
     """
     sa_session = app.model.session
     admin_users = app.config.get("admin_users", "").split(",")
-    for repository in sa_session.query(app.model.Repository) \
-                                .filter(app.model.Repository.table.c.email_alerts != null()):
+    for repository in sa_session.query(app.model.Repository).filter(
+        app.model.Repository.table.c.email_alerts != null()
+    ):
         email_alerts = json.loads(repository.email_alerts)
         for user_email in email_alerts:
             if user_email in admin_users:
@@ -80,7 +99,7 @@ def check_file_contents_for_email_alerts(app):
 
 
 def check_file_content_for_html_and_images(file_path):
-    message = ''
+    message = ""
     if checkers.check_html(file_path):
         message = f'The file "{str(file_path)}" contains HTML content.\n'
     elif checkers.check_image(file_path):
@@ -95,10 +114,10 @@ def get_change_lines_in_file_for_tag(tag, change_dict):
     and returns appropriate lines for inspection.
     """
     cleaned_lines = []
-    data_list = change_dict.get('data', [])
+    data_list = change_dict.get("data", [])
     for data_dict in data_list:
-        block = data_dict.get('block', '')
-        lines = block.split('\\n')
+        block = data_dict.get("block", "")
+        lines = block.split("\\n")
         for line in lines:
             index = line.find(tag)
             if index > -1:
@@ -108,7 +127,7 @@ def get_change_lines_in_file_for_tag(tag, change_dict):
 
 
 def get_upload_point(repository, **kwd):
-    upload_point = kwd.get('upload_point', None)
+    upload_point = kwd.get("upload_point", None)
     if upload_point is not None:
         # The value of upload_point will be something like: database/community_files/000/repo_12/1.bed
         if os.path.exists(upload_point):
@@ -116,12 +135,12 @@ def get_upload_point(repository, **kwd):
                 # Get the parent directory
                 upload_point, not_needed = os.path.split(upload_point)
                 # Now the value of uplaod_point will be something like: database/community_files/000/repo_12/
-            upload_point = upload_point.split('repo_%d' % repository.id)[1]
+            upload_point = upload_point.split("repo_%d" % repository.id)[1]
             if upload_point:
-                upload_point = upload_point.lstrip('/')
-                upload_point = upload_point.rstrip('/')
+                upload_point = upload_point.lstrip("/")
+                upload_point = upload_point.rstrip("/")
             # Now the value of uplaod_point will be something like: /
-            if upload_point == '/':
+            if upload_point == "/":
                 upload_point = None
         else:
             # Must have been an error selecting something that didn't exist, so default to repository root
@@ -131,11 +150,11 @@ def get_upload_point(repository, **kwd):
 
 def handle_bz2(repository, uploaded_file_name):
     with tempfile.NamedTemporaryFile(
-        mode='wb',
-        prefix=f'repo_{repository.id}_upload_bunzip2_',
+        mode="wb",
+        prefix=f"repo_{repository.id}_upload_bunzip2_",
         dir=os.path.dirname(uploaded_file_name),
         delete=False,
-    ) as uncompressed, bz2.BZ2File(uploaded_file_name, 'rb') as bzipped_file:
+    ) as uncompressed, bz2.BZ2File(uploaded_file_name, "rb") as bzipped_file:
         while 1:
             try:
                 chunk = bzipped_file.read(basic_util.CHUNK_SIZE)
@@ -149,17 +168,28 @@ def handle_bz2(repository, uploaded_file_name):
     shutil.move(uncompressed.name, uploaded_file_name)
 
 
-def handle_directory_changes(app, host, username, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar,
-                             new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed):
+def handle_directory_changes(
+    app,
+    host,
+    username,
+    repository,
+    full_path,
+    filenames_in_archive,
+    remove_repo_files_not_in_tar,
+    new_repo_alert,
+    commit_message,
+    undesirable_dirs_removed,
+    undesirable_files_removed,
+):
     repo_path = repository.repo_path(app)
-    content_alert_str = ''
+    content_alert_str = ""
     files_to_remove = []
     filenames_in_archive = [os.path.join(full_path, name) for name in filenames_in_archive]
     if remove_repo_files_not_in_tar and not repository.is_new():
         # We have a repository that is not new (it contains files), so discover those files that are in the
         # repository, but not in the uploaded archive.
         for root, dirs, files in os.walk(full_path):
-            if root.find('.hg') < 0 and root.find('hgrc') < 0:
+            if root.find(".hg") < 0 and root.find("hgrc") < 0:
                 for undesirable_dir in UNDESIRABLE_DIRS:
                     if undesirable_dir in dirs:
                         dirs.remove(undesirable_dir)
@@ -178,9 +208,9 @@ def handle_directory_changes(app, host, username, repository, full_path, filenam
             try:
                 hg_util.remove_path(repo_path, repo_file)
             except Exception as e:
-                error_message = (f"Error removing file {repo_file} in mercurial repo:\n{e}")
+                error_message = f"Error removing file {repo_file} in mercurial repo:\n{e}"
                 log.debug(error_message)
-                return 'error', error_message, files_to_remove, content_alert_str, 0, 0
+                return "error", error_message, files_to_remove, content_alert_str, 0, 0
     # See if any admin users have chosen to receive email alerts when a repository is updated.
     # If so, check every uploaded file to ensure content is appropriate.
     check_contents = check_file_contents_for_email_alerts(app)
@@ -189,35 +219,33 @@ def handle_directory_changes(app, host, username, repository, full_path, filenam
         if check_contents and os.path.isfile(filename_in_archive):
             content_alert_str += check_file_content_for_html_and_images(filename_in_archive)
         hg_util.add_changeset(repo_path, filename_in_archive)
-        if filename_in_archive.endswith('tool_data_table_conf.xml.sample'):
+        if filename_in_archive.endswith("tool_data_table_conf.xml.sample"):
             # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded
             # by parsing the file and adding new entries to the in-memory app.tool_data_tables
             # dictionary.
             stdtm = ShedToolDataTableManager(app)
             error, message = stdtm.handle_sample_tool_data_table_conf_file(filename_in_archive, persist=False)
             if error:
-                return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
-    hg_util.commit_changeset(repo_path,
-                             full_path_to_changeset=full_path,
-                             username=username,
-                             message=commit_message)
+                return (
+                    False,
+                    message,
+                    files_to_remove,
+                    content_alert_str,
+                    undesirable_dirs_removed,
+                    undesirable_files_removed,
+                )
+    hg_util.commit_changeset(repo_path, full_path_to_changeset=full_path, username=username, message=commit_message)
     admin_only = len(repository.downloadable_revisions) != 1
-    suc.handle_email_alerts(app,
-                            host,
-                            repository,
-                            content_alert_str=content_alert_str,
-                            new_repo_alert=new_repo_alert,
-                            admin_only=admin_only)
-    return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
+    suc.handle_email_alerts(
+        app, host, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only
+    )
+    return True, "", files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
 
 
 def handle_gzip(repository, uploaded_file_name):
     with tempfile.NamedTemporaryFile(
-        mode='wb',
-        prefix=f'repo_{repository.id}_upload_gunzip_',
-        dir=os.path.dirname(uploaded_file_name),
-        delete=False
-    ) as uncompressed, gzip.GzipFile(uploaded_file_name, 'rb') as gzipped_file:
+        mode="wb", prefix=f"repo_{repository.id}_upload_gunzip_", dir=os.path.dirname(uploaded_file_name), delete=False
+    ) as uncompressed, gzip.GzipFile(uploaded_file_name, "rb") as gzipped_file:
         while 1:
             try:
                 chunk = gzipped_file.read(basic_util.CHUNK_SIZE)
@@ -234,7 +262,7 @@ def handle_gzip(repository, uploaded_file_name):
 def uncompress(repository, uploaded_file_name, uploaded_file_filename, isgzip=False, isbz2=False):
     if isgzip:
         handle_gzip(repository, uploaded_file_name)
-        return uploaded_file_filename.rstrip('.gz')
+        return uploaded_file_filename.rstrip(".gz")
     if isbz2:
         handle_bz2(repository, uploaded_file_name)
-        return uploaded_file_filename.rstrip('.bz2')
+        return uploaded_file_filename.rstrip(".bz2")
diff --git a/lib/tool_shed/util/container_util.py b/lib/tool_shed/util/container_util.py
index c61bb40c0c8..6d2f7b20b70 100644
--- a/lib/tool_shed/util/container_util.py
+++ b/lib/tool_shed/util/container_util.py
@@ -4,9 +4,8 @@ from galaxy.tool_shed.util.container_util import (
     STRSEP,
 )
 
-
 __all__ = (
-    'generate_repository_dependencies_key_for_repository',
-    'get_components_from_key',
-    'STRSEP',
+    "generate_repository_dependencies_key_for_repository",
+    "get_components_from_key",
+    "STRSEP",
 )
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index 82c8feb2bd4..34aa49587ac 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -23,12 +23,12 @@ from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
-INITIAL_CHANGELOG_HASH = '000000000000'
+INITIAL_CHANGELOG_HASH = "000000000000"
 
 
 def add_changeset(repo_path, path_to_filename_in_archive):
     try:
-        subprocess.check_output(['hg', 'add', path_to_filename_in_archive], stderr=subprocess.STDOUT, cwd=repo_path)
+        subprocess.check_output(["hg", "add", path_to_filename_in_archive], stderr=subprocess.STDOUT, cwd=repo_path)
     except Exception as e:
         error_message = f"Error adding '{path_to_filename_in_archive}' to repository: {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
@@ -37,10 +37,12 @@ def add_changeset(repo_path, path_to_filename_in_archive):
 
 
 def archive_repository_revision(app, repository, archive_dir, changeset_revision):
-    '''Create an un-versioned archive of a repository.'''
+    """Create an un-versioned archive of a repository."""
     repo_path = repository.repo_path(app)
     try:
-        subprocess.check_output(['hg', 'archive', '-r', changeset_revision, archive_dir], stderr=subprocess.STDOUT, cwd=repo_path)
+        subprocess.check_output(
+            ["hg", "archive", "-r", changeset_revision, archive_dir], stderr=subprocess.STDOUT, cwd=repo_path
+        )
     except Exception as e:
         error_message = f"Error attempting to archive revision '{changeset_revision}' of repository '{repository.name}': {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
@@ -51,18 +53,22 @@ def archive_repository_revision(app, repository, archive_dir, changeset_revision
 
 def commit_changeset(repo_path, full_path_to_changeset, username, message):
     try:
-        subprocess.check_output(['hg', 'commit', '-u', username, '-m', message, full_path_to_changeset], stderr=subprocess.STDOUT, cwd=repo_path)
+        subprocess.check_output(
+            ["hg", "commit", "-u", username, "-m", message, full_path_to_changeset],
+            stderr=subprocess.STDOUT,
+            cwd=repo_path,
+        )
     except Exception as e:
         error_message = f"Error committing '{full_path_to_changeset}' to repository: {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
-            if e.returncode == 1 and 'nothing changed' in unicodify(e.output):
+            if e.returncode == 1 and "nothing changed" in unicodify(e.output):
                 return
             error_message += f"\nOutput was:\n{unicodify(e.output)}"
         raise Exception(error_message)
 
 
 def get_hgrc_path(repo_path):
-    return os.path.join(repo_path, '.hg', 'hgrc')
+    return os.path.join(repo_path, ".hg", "hgrc")
 
 
 def create_hgrc_file(app, repository):
@@ -74,16 +80,16 @@ def create_hgrc_file(app, repository):
     # in the Mercurial API.
     repo_path = repository.repo_path(app)
     hgrc_path = get_hgrc_path(repo_path)
-    with open(hgrc_path, 'w') as fp:
-        fp.write('[paths]\n')
-        fp.write('default = .\n')
-        fp.write('default-push = .\n')
-        fp.write('[web]\n')
-        fp.write(f'allow_push = {repository.user.username}\n')
-        fp.write(f'name = {repository.name}\n')
-        fp.write('push_ssl = false\n')
-        fp.write('[extensions]\n')
-        fp.write('hgext.purge=')
+    with open(hgrc_path, "w") as fp:
+        fp.write("[paths]\n")
+        fp.write("default = .\n")
+        fp.write("default-push = .\n")
+        fp.write("[web]\n")
+        fp.write(f"allow_push = {repository.user.username}\n")
+        fp.write(f"name = {repository.name}\n")
+        fp.write("push_ssl = false\n")
+        fp.write("[extensions]\n")
+        fp.write("hgext.purge=")
 
 
 def get_named_tmpfile_from_ctx(ctx, filename, dir):
@@ -103,10 +109,10 @@ def get_named_tmpfile_from_ctx(ctx, filename, dir):
                 fctx = None
                 continue
             if fctx:
-                fh = tempfile.NamedTemporaryFile('wb', prefix="tmp-toolshed-gntfc", dir=dir)
+                fh = tempfile.NamedTemporaryFile("wb", prefix="tmp-toolshed-gntfc", dir=dir)
                 tmp_filename = fh.name
                 fh.close()
-                fh = open(tmp_filename, 'wb')
+                fh = open(tmp_filename, "wb")
                 fh.write(fctx.data())
                 fh.close()
                 return tmp_filename
@@ -151,15 +157,16 @@ def get_revision_label(app, repository, changeset_revision, include_date=True, i
             return "-1"
 
 
-def get_rev_label_changeset_revision_from_repository_metadata(app, repository_metadata, repository=None,
-                                                              include_date=True, include_hash=True):
+def get_rev_label_changeset_revision_from_repository_metadata(
+    app, repository_metadata, repository=None, include_date=True, include_hash=True
+):
     if repository is None:
         repository = repository_metadata.repository
     repo = repository.hg_repo
     changeset_revision = repository_metadata.changeset_revision
     ctx = get_changectx_for_changeset(repo, changeset_revision)
     if ctx:
-        rev = '%04d' % ctx.rev()
+        rev = "%04d" % ctx.rev()
         if include_date:
             changeset_revision_date = get_readable_ctx_date(ctx)
             if include_hash:
@@ -172,7 +179,7 @@ def get_rev_label_changeset_revision_from_repository_metadata(app, repository_me
             else:
                 label = f"{str(ctx.rev())}"
     else:
-        rev = '-1'
+        rev = "-1"
         if include_hash:
             label = f"-1:{changeset_revision}"
         else:
@@ -183,14 +190,16 @@ def get_rev_label_changeset_revision_from_repository_metadata(app, repository_me
 def get_revision_label_from_ctx(ctx, include_date=True, include_hash=True):
     if include_date:
         if include_hash:
-            return '%s:%s <i><font color="#666666">(%s)</font></i>' % \
-                (str(ctx.rev()), str(ctx), str(get_readable_ctx_date(ctx)))
+            return '%s:%s <i><font color="#666666">(%s)</font></i>' % (
+                str(ctx.rev()),
+                str(ctx),
+                str(get_readable_ctx_date(ctx)),
+            )
         else:
-            return '%s <i><font color="#666666">(%s)</font></i>' % \
-                (str(ctx.rev()), str(get_readable_ctx_date(ctx)))
+            return '%s <i><font color="#666666">(%s)</font></i>' % (str(ctx.rev()), str(get_readable_ctx_date(ctx)))
     else:
         if include_hash:
-            return f'{str(ctx.rev())}:{str(ctx)}'
+            return f"{str(ctx.rev())}:{str(ctx)}"
         else:
             return str(ctx.rev())
 
@@ -202,23 +211,23 @@ def get_rev_label_from_changeset_revision(repo, changeset_revision, include_date
     """
     ctx = get_changectx_for_changeset(repo, changeset_revision)
     if ctx:
-        rev = '%04d' % ctx.rev()
+        rev = "%04d" % ctx.rev()
         label = get_revision_label_from_ctx(ctx, include_date=include_date)
     else:
-        rev = '-1'
+        rev = "-1"
         label = f"-1:{changeset_revision}"
     return rev, label
 
 
 def remove_path(repo_path, selected_file):
-    cmd = ['hg', 'remove', '--force', selected_file]
+    cmd = ["hg", "remove", "--force", selected_file]
     try:
         subprocess.check_output(cmd, stderr=subprocess.STDOUT, cwd=repo_path)
     except Exception as e:
         error_message = f"Error removing path '{selected_file}': {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
             output = unicodify(e.output)
-            if 'is untracked' in output:
+            if "is untracked" in output:
                 # That's ok, happens if we add a new file or directory via tarball upload,
                 # just delete the file or dir on disk
                 selected_file_path = os.path.join(repo_path, selected_file)
@@ -236,9 +245,9 @@ def init_repository(repo_path):
     Create a new Mercurial repository in the given directory.
     """
     try:
-        subprocess.check_output(['hg', 'init'], stderr=subprocess.STDOUT, cwd=repo_path)
+        subprocess.check_output(["hg", "init"], stderr=subprocess.STDOUT, cwd=repo_path)
     except Exception as e:
-        error_message = f'Error initializing repository: {unicodify(e)}'
+        error_message = f"Error initializing repository: {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
             error_message += f"\nOutput was:\n{unicodify(e.output)}"
         raise Exception(error_message)
@@ -249,7 +258,9 @@ def changeset2rev(repo_path, changeset_revision):
     Return the revision number (as an int) corresponding to a specified changeset revision.
     """
     try:
-        rev = subprocess.check_output(['hg', 'id', '-r', changeset_revision, '-n'], stderr=subprocess.STDOUT, cwd=repo_path)
+        rev = subprocess.check_output(
+            ["hg", "id", "-r", changeset_revision, "-n"], stderr=subprocess.STDOUT, cwd=repo_path
+        )
     except Exception as e:
         error_message = f"Error looking for changeset '{changeset_revision}': {unicodify(e)}"
         if isinstance(e, subprocess.CalledProcessError):
@@ -259,29 +270,29 @@ def changeset2rev(repo_path, changeset_revision):
 
 
 __all__ = (
-    'add_changeset',
-    'archive_repository_revision',
-    'clone_repository',
-    'commit_changeset',
-    'copy_file_from_manifest',
-    'create_hgrc_file',
-    'get_changectx_for_changeset',
-    'get_config_from_disk',
-    'get_ctx_file_path_from_manifest',
-    'get_file_context_from_ctx',
-    'get_named_tmpfile_from_ctx',
-    'get_readable_ctx_date',
-    'get_repository_heads',
-    'get_reversed_changelog_changesets',
-    'get_revision_label',
-    'get_rev_label_changeset_revision_from_repository_metadata',
-    'get_revision_label_from_ctx',
-    'get_rev_label_from_changeset_revision',
-    'pull_repository',
-    'remove_path',
-    'reversed_lower_upper_bounded_changelog',
-    'reversed_upper_bounded_changelog',
-    'update_repository',
-    'init_repository',
-    'changeset2rev',
+    "add_changeset",
+    "archive_repository_revision",
+    "clone_repository",
+    "commit_changeset",
+    "copy_file_from_manifest",
+    "create_hgrc_file",
+    "get_changectx_for_changeset",
+    "get_config_from_disk",
+    "get_ctx_file_path_from_manifest",
+    "get_file_context_from_ctx",
+    "get_named_tmpfile_from_ctx",
+    "get_readable_ctx_date",
+    "get_repository_heads",
+    "get_reversed_changelog_changesets",
+    "get_revision_label",
+    "get_rev_label_changeset_revision_from_repository_metadata",
+    "get_revision_label_from_ctx",
+    "get_rev_label_from_changeset_revision",
+    "pull_repository",
+    "remove_path",
+    "reversed_lower_upper_bounded_changelog",
+    "reversed_upper_bounded_changelog",
+    "update_repository",
+    "init_repository",
+    "changeset2rev",
 )
diff --git a/lib/tool_shed/util/hgweb_config.py b/lib/tool_shed/util/hgweb_config.py
index 870dadf7ae7..f39d9abcc3d 100644
--- a/lib/tool_shed/util/hgweb_config.py
+++ b/lib/tool_shed/util/hgweb_config.py
@@ -28,11 +28,11 @@ class HgWebConfigManager:
             # Since we're changing the config, make sure the latest is loaded into memory.
             self.read_config(force_read=True)
             # An entry looks something like: repos/test/mira_assembler = database/community_files/000/repo_123.
-            if rhs.startswith('./'):
-                rhs = rhs.replace('./', '', 1)
+            if rhs.startswith("./"):
+                rhs = rhs.replace("./", "", 1)
             self.make_backup()
             # Add the new entry into memory.
-            self.in_memory_config.set('paths', lhs, rhs)
+            self.in_memory_config.set("paths", lhs, rhs)
             # Persist our in-memory configuration.
             self.write_config()
         except Exception as e:
@@ -47,9 +47,9 @@ class HgWebConfigManager:
         try:
             self.make_backup()
             # Remove the old entry.
-            self.in_memory_config.remove_option('paths', old_lhs)
+            self.in_memory_config.remove_option("paths", old_lhs)
             # Add the new entry.
-            self.in_memory_config.set('paths', new_lhs, new_rhs)
+            self.in_memory_config.set("paths", new_lhs, new_rhs)
             # Persist our in-memory configuration.
             self.write_config()
         except Exception as e:
@@ -61,25 +61,27 @@ class HgWebConfigManager:
         """Return an entry in the hgweb.config file for a repository"""
         self.read_config()
         try:
-            entry = self.in_memory_config.get('paths', lhs)
+            entry = self.in_memory_config.get("paths", lhs)
         except configparser.NoOptionError:
             try:
                 # We have a multi-threaded front-end, so one of the threads may not have the latest version of the hgweb.config file.
                 self.read_config(force_read=True)
-                entry = self.in_memory_config.get('paths', lhs)
+                entry = self.in_memory_config.get("paths", lhs)
             except configparser.NoOptionError:
                 raise Exception(f"Entry for repository {lhs} missing in file {self.hgweb_config}.")
         return entry
 
     @property
     def hgweb_config(self):
-        hgweb_config = os.path.join(self.hgweb_config_dir, 'hgweb.config')
+        hgweb_config = os.path.join(self.hgweb_config_dir, "hgweb.config")
         if not os.path.exists(hgweb_config):
             # We used to raise an exception here...
             # raise Exception( "Required file %s does not exist - check config setting for hgweb_config_dir." % hgweb_config )
             # ...but now we just log the missing file and create a new empty one.
-            log.debug(f"Required file {hgweb_config} does not exist, so creating a new, empty file.  Check your config setting for hgweb_config_dir.")
-            with open(hgweb_config, 'w') as hgweb_config_file:
+            log.debug(
+                f"Required file {hgweb_config} does not exist, so creating a new, empty file.  Check your config setting for hgweb_config_dir."
+            )
+            with open(hgweb_config, "w") as hgweb_config_file:
                 hgweb_config_file.write(new_hgweb_config_template)
         return os.path.abspath(hgweb_config)
 
@@ -87,7 +89,7 @@ class HgWebConfigManager:
         # Make a backup of the hgweb.config file.
         today = date.today()
         backup_date = today.strftime("%Y_%m_%d")
-        hgweb_config_backup_filename = f'hgweb.config_{backup_date}_backup'
+        hgweb_config_backup_filename = f"hgweb.config_{backup_date}_backup"
         hgweb_config_copy = os.path.join(self.hgweb_config_dir, hgweb_config_backup_filename)
         shutil.copy(os.path.abspath(self.hgweb_config), os.path.abspath(hgweb_config_copy))
 
@@ -99,7 +101,7 @@ class HgWebConfigManager:
 
     def write_config(self):
         """Writing the in-memory configuration to the hgweb.config file on disk."""
-        with open(self.hgweb_config, 'w') as config_file:
+        with open(self.hgweb_config, "w") as config_file:
             self.in_memory_config.write(config_file)
 
 
diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
index 6719ee24d46..e6f77309836 100644
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -17,48 +17,52 @@ log = logging.getLogger(__name__)
 def get_all_dependencies(app, metadata_entry, processed_dependency_links=None):
     processed_dependency_links = processed_dependency_links or []
     encoder = app.security.encode_id
-    value_mapper = {'repository_id': encoder, 'id': encoder, 'user_id': encoder}
-    metadata = metadata_entry.to_dict(value_mapper=value_mapper, view='element')
+    value_mapper = {"repository_id": encoder, "id": encoder, "user_id": encoder}
+    metadata = metadata_entry.to_dict(value_mapper=value_mapper, view="element")
     db = app.model.session
     returned_dependencies = []
     required_metadata = get_dependencies_for_metadata_revision(app, metadata)
     if required_metadata is None:
         return metadata
     for dependency_metadata in required_metadata:
-        dependency_dict = dependency_metadata.to_dict(value_mapper=value_mapper, view='element')
-        dependency_link = (metadata['id'], dependency_dict['id'])
+        dependency_dict = dependency_metadata.to_dict(value_mapper=value_mapper, view="element")
+        dependency_link = (metadata["id"], dependency_dict["id"])
         if dependency_link in processed_dependency_links:
             continue
         processed_dependency_links.append(dependency_link)
-        repository = db.query(app.model.Repository).get(app.security.decode_id(dependency_dict['repository_id']))
-        dependency_dict['repository'] = repository.to_dict(value_mapper=value_mapper)
+        repository = db.query(app.model.Repository).get(app.security.decode_id(dependency_dict["repository_id"]))
+        dependency_dict["repository"] = repository.to_dict(value_mapper=value_mapper)
         if dependency_metadata.includes_tools:
-            dependency_dict['tools'] = dependency_metadata.metadata['tools']
-        dependency_dict['repository_dependencies'] = []
-        if dependency_dict['includes_tool_dependencies']:
-            dependency_dict['tool_dependencies'] = repository.get_tool_dependencies(app, dependency_dict['changeset_revision'])
-        if dependency_dict['has_repository_dependencies']:
-            dependency_dict['repository_dependencies'] = get_all_dependencies(app, dependency_metadata, processed_dependency_links)
+            dependency_dict["tools"] = dependency_metadata.metadata["tools"]
+        dependency_dict["repository_dependencies"] = []
+        if dependency_dict["includes_tool_dependencies"]:
+            dependency_dict["tool_dependencies"] = repository.get_tool_dependencies(
+                app, dependency_dict["changeset_revision"]
+            )
+        if dependency_dict["has_repository_dependencies"]:
+            dependency_dict["repository_dependencies"] = get_all_dependencies(
+                app, dependency_metadata, processed_dependency_links
+            )
         else:
-            dependency_dict['repository_dependencies'] = []
+            dependency_dict["repository_dependencies"] = []
         returned_dependencies.append(dependency_dict)
     return returned_dependencies
 
 
 def get_current_repository_metadata_for_changeset_revision(app, repository, changeset_revision):
     encoded_repository_id = app.security.encode_id(repository.id)
-    repository_metadata = get_repository_metadata_by_changeset_revision(app,
-                                                                        encoded_repository_id,
-                                                                        changeset_revision)
+    repository_metadata = get_repository_metadata_by_changeset_revision(app, encoded_repository_id, changeset_revision)
     if repository_metadata:
         return repository_metadata
     # The installable changeset_revision may have been changed because it was "moved ahead"
     # in the repository changelog.
-    updated_changeset_revision = get_next_downloadable_changeset_revision(app, repository, after_changeset_revision=changeset_revision)
+    updated_changeset_revision = get_next_downloadable_changeset_revision(
+        app, repository, after_changeset_revision=changeset_revision
+    )
     if updated_changeset_revision and updated_changeset_revision != changeset_revision:
-        repository_metadata = get_repository_metadata_by_changeset_revision(app,
-                                                                            encoded_repository_id,
-                                                                            updated_changeset_revision)
+        repository_metadata = get_repository_metadata_by_changeset_revision(
+            app, encoded_repository_id, updated_changeset_revision
+        )
         if repository_metadata:
             return repository_metadata
     return None
@@ -66,21 +70,23 @@ def get_current_repository_metadata_for_changeset_revision(app, repository, chan
 
 def get_dependencies_for_metadata_revision(app, metadata):
     dependencies = []
-    for _shed, name, owner, changeset, _prior, _ in metadata['repository_dependencies']:
+    for _shed, name, owner, changeset, _prior, _ in metadata["repository_dependencies"]:
         required_repository = get_repository_by_name_and_owner(app, name, owner)
         updated_changeset = get_next_downloadable_changeset_revision(app, required_repository, changeset)
         if updated_changeset is None:
             continue
-        metadata_entry = get_repository_metadata_by_changeset_revision(app, app.security.encode_id(required_repository.id), updated_changeset)
+        metadata_entry = get_repository_metadata_by_changeset_revision(
+            app, app.security.encode_id(required_repository.id), updated_changeset
+        )
         dependencies.append(metadata_entry)
     return dependencies
 
 
 def get_latest_changeset_revision(app, repository):
     repository_tip = repository.tip()
-    repository_metadata = get_repository_metadata_by_changeset_revision(app,
-                                                                        app.security.encode_id(repository.id),
-                                                                        repository_tip)
+    repository_metadata = get_repository_metadata_by_changeset_revision(
+        app, app.security.encode_id(repository.id), repository_tip
+    )
     if repository_metadata and repository_metadata.downloadable:
         return repository_tip
     changeset_revisions = [revision[1] for revision in get_metadata_revisions(app, repository)]
@@ -91,7 +97,9 @@ def get_latest_changeset_revision(app, repository):
 
 def get_latest_downloadable_changeset_revision(app, repository):
     repository_tip = repository.tip()
-    repository_metadata = get_repository_metadata_by_changeset_revision(app, app.security.encode_id(repository.id), repository_tip)
+    repository_metadata = get_repository_metadata_by_changeset_revision(
+        app, app.security.encode_id(repository.id), repository_tip
+    )
     if repository_metadata and repository_metadata.downloadable:
         return repository_tip
     changeset_revisions = [revision[1] for revision in get_metadata_revisions(app, repository)]
@@ -108,9 +116,7 @@ def get_latest_repository_metadata(app, decoded_repository_id, downloadable=Fals
         changeset_revision = get_latest_downloadable_changeset_revision(app, repository)
     else:
         changeset_revision = get_latest_changeset_revision(app, repository)
-    return get_repository_metadata_by_changeset_revision(app,
-                                                         app.security.encode_id(repository.id),
-                                                         changeset_revision)
+    return get_repository_metadata_by_changeset_revision(app, app.security.encode_id(repository.id), changeset_revision)
 
 
 def get_metadata_revisions(app, repository, sort_revisions=True, reverse=False, downloadable=True):
@@ -198,15 +204,16 @@ def get_repository_dependency_tups_from_repository_metadata(app, repository_meta
     if repository_metadata is not None:
         metadata = repository_metadata.metadata
         if metadata:
-            repository_dependencies_dict = metadata.get('repository_dependencies', None)
+            repository_dependencies_dict = metadata.get("repository_dependencies", None)
             if repository_dependencies_dict is not None:
-                repository_dependency_tups = repository_dependencies_dict.get('repository_dependencies', None)
+                repository_dependency_tups = repository_dependencies_dict.get("repository_dependencies", None)
                 if repository_dependency_tups is not None:
                     # The value of repository_dependency_tups is a list of repository dependency tuples like this:
                     # ['http://localhost:9009', 'package_samtools_0_1_18', 'devteam', 'ef37fc635cb9', 'False', 'False']
                     for repository_dependency_tup in repository_dependency_tups:
-                        toolshed, name, owner, changeset_revision, pir, oicct = \
-                            parse_repository_dependency_tuple(repository_dependency_tup)
+                        toolshed, name, owner, changeset_revision, pir, oicct = parse_repository_dependency_tuple(
+                            repository_dependency_tup
+                        )
                         repository = get_repository_by_name_and_owner(app, name, owner)
                         if repository:
                             if deprecated_only:
@@ -215,8 +222,10 @@ def get_repository_dependency_tups_from_repository_metadata(app, repository_meta
                             else:
                                 dependency_tups.append(repository_dependency_tup)
                         else:
-                            log.debug("Cannot locate repository %s owned by %s for inclusion in repository dependency tups." %
-                                (name, owner))
+                            log.debug(
+                                "Cannot locate repository %s owned by %s for inclusion in repository dependency tups."
+                                % (name, owner)
+                            )
     return dependency_tups
 
 
@@ -226,10 +235,16 @@ def get_repository_metadata_by_changeset_revision(app, id, changeset_revision):
     # Duplicate records were somehow created in the past.  The cause of this issue has been resolved, but we'll
     # leave this method as is for a while longer to ensure all duplicate records are removed.
     sa_session = app.model.session
-    all_metadata_records = sa_session.query(app.model.RepositoryMetadata) \
-                                     .filter(and_(app.model.RepositoryMetadata.table.c.repository_id == app.security.decode_id(id),
-                                                  app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision)) \
-                                     .all()
+    all_metadata_records = (
+        sa_session.query(app.model.RepositoryMetadata)
+        .filter(
+            and_(
+                app.model.RepositoryMetadata.table.c.repository_id == app.security.decode_id(id),
+                app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision,
+            )
+        )
+        .all()
+    )
     if len(all_metadata_records) > 1:
         # Delete all records older than the last one updated.
         for repository_metadata in all_metadata_records[1:]:
@@ -295,28 +310,28 @@ def get_updated_changeset_revisions(app, name, owner, changeset_revision):
         if changeset != upper_bound_changeset_revision:
             changeset_hashes.append(str(repo[changeset]))
     if changeset_hashes:
-        changeset_hashes_str = ','.join(changeset_hashes)
+        changeset_hashes_str = ",".join(changeset_hashes)
         return changeset_hashes_str
-    return ''
+    return ""
 
 
 def is_downloadable(metadata_dict):
     # NOTE: although repository README files are considered Galaxy utilities, they have no
     # effect on determining if a revision is installable.  See the comments in the
     # compare_readme_files() method.
-    if 'datatypes' in metadata_dict:
+    if "datatypes" in metadata_dict:
         # We have proprietary datatypes.
         return True
-    if 'repository_dependencies' in metadata_dict:
+    if "repository_dependencies" in metadata_dict:
         # We have repository_dependencies.
         return True
-    if 'tools' in metadata_dict:
+    if "tools" in metadata_dict:
         # We have tools.
         return True
-    if 'tool_dependencies' in metadata_dict:
+    if "tool_dependencies" in metadata_dict:
         # We have tool dependencies, and perhaps only tool dependencies!
         return True
-    if 'workflows' in metadata_dict:
+    if "workflows" in metadata_dict:
         # We have exported workflows.
         return True
     return False
diff --git a/lib/tool_shed/util/readme_util.py b/lib/tool_shed/util/readme_util.py
index 629d3052c9b..e573f4bd6cd 100644
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -28,45 +28,56 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
     received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
     file contents may not be available on disk.  This method is used by both Galaxy and the Tool Shed.
     """
-    if app.name == 'galaxy':
+    if app.name == "galaxy":
         can_use_disk_files = True
     else:
-        latest_downloadable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(app, repository)
+        latest_downloadable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(
+            app, repository
+        )
         can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
     readme_files_dict = {}
     if metadata:
-        if 'readme_files' in metadata:
-            for relative_path_to_readme_file in metadata['readme_files']:
+        if "readme_files" in metadata:
+            for relative_path_to_readme_file in metadata["readme_files"]:
                 readme_file_name = os.path.split(relative_path_to_readme_file)[1]
                 if can_use_disk_files:
                     if tool_path:
-                        full_path_to_readme_file = os.path.abspath(os.path.join(tool_path, relative_path_to_readme_file))
+                        full_path_to_readme_file = os.path.abspath(
+                            os.path.join(tool_path, relative_path_to_readme_file)
+                        )
                     else:
                         full_path_to_readme_file = os.path.abspath(relative_path_to_readme_file)
                     text = None
                     try:
-                        with open(full_path_to_readme_file, encoding='utf-8') as f:
+                        with open(full_path_to_readme_file, encoding="utf-8") as f:
                             text = f.read()
                     except Exception:
                         log.exception("Error reading README file '%s' from disk", relative_path_to_readme_file)
                         text = None
                     if text:
                         text_of_reasonable_length = basic_util.size_string(text)
-                        if text_of_reasonable_length.find('.. image:: ') >= 0:
+                        if text_of_reasonable_length.find(".. image:: ") >= 0:
                             # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
                             try:
-                                text_of_reasonable_length = suc.set_image_paths(app,
-                                                                                text_of_reasonable_length,
-                                                                                encoded_repository_id=app.security.encode_id(repository.id))
+                                text_of_reasonable_length = suc.set_image_paths(
+                                    app,
+                                    text_of_reasonable_length,
+                                    encoded_repository_id=app.security.encode_id(repository.id),
+                                )
                             except Exception:
-                                log.exception("Exception in build_readme_files_dict, so images may not be properly displayed")
-                        if readme_file_name.endswith('.rst'):
-                            text_of_reasonable_length = Template(rst_to_html(text_of_reasonable_length),
-                                                                 input_encoding='utf-8',
-                                                                 default_filters=['decode.utf8'],
-                                                                 encoding_errors='replace')
-                            text_of_reasonable_length = text_of_reasonable_length.render(static_path=web.url_for('/static'),
-                                                                                         host_url=web.url_for('/', qualified=True))
+                                log.exception(
+                                    "Exception in build_readme_files_dict, so images may not be properly displayed"
+                                )
+                        if readme_file_name.endswith(".rst"):
+                            text_of_reasonable_length = Template(
+                                rst_to_html(text_of_reasonable_length),
+                                input_encoding="utf-8",
+                                default_filters=["decode.utf8"],
+                                encoding_errors="replace",
+                            )
+                            text_of_reasonable_length = text_of_reasonable_length.render(
+                                static_path=web.url_for("/static"), host_url=web.url_for("/", qualified=True)
+                            )
                             text_of_reasonable_length = unicodify(text_of_reasonable_length)
                         else:
                             text_of_reasonable_length = basic_util.to_html_string(text_of_reasonable_length)
@@ -77,12 +88,15 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                     ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
                     if ctx:
                         fctx = hg_util.get_file_context_from_ctx(ctx, readme_file_name)
-                        if fctx and fctx not in ['DELETED']:
+                        if fctx and fctx not in ["DELETED"]:
                             try:
                                 text = unicodify(fctx.data())
                                 readme_files_dict[readme_file_name] = basic_util.size_string(text)
                             except Exception:
-                                log.exception("Error reading README file '%s' from repository manifest", relative_path_to_readme_file)
+                                log.exception(
+                                    "Error reading README file '%s' from repository manifest",
+                                    relative_path_to_readme_file,
+                                )
     return readme_files_dict
 
 
@@ -93,12 +107,21 @@ def get_readme_files_dict_for_display(app, tool_shed_url, repo_info_dict):
     """
     name = next(iter(repo_info_dict))
     repo_info_tuple = repo_info_dict[name]
-    description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
-        repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+    (
+        description,
+        repository_clone_url,
+        changeset_revision,
+        ctx_rev,
+        repository_owner,
+        repository_dependencies,
+        installed_td,
+    ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
     # Handle changing HTTP protocols over time.
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
     params = dict(name=name, owner=repository_owner, changeset_revision=changeset_revision)
-    pathspec = ['repository', 'get_readme_files']
-    raw_text = url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+    pathspec = ["repository", "get_readme_files"]
+    raw_text = url_get(
+        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+    )
     readme_files_dict = json.loads(raw_text)
     return readme_files_dict
diff --git a/lib/tool_shed/util/repository_content_util.py b/lib/tool_shed/util/repository_content_util.py
index d12e349fde2..a08fd3d32cd 100644
--- a/lib/tool_shed/util/repository_content_util.py
+++ b/lib/tool_shed/util/repository_content_util.py
@@ -8,8 +8,18 @@ from tool_shed.util import (
 )
 
 
-def upload_tar(trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar,
-               commit_message, new_repo_alert):
+def upload_tar(
+    trans,
+    rdah,
+    tdah,
+    repository,
+    tar,
+    uploaded_file,
+    upload_point,
+    remove_repo_files_not_in_tar,
+    commit_message,
+    new_repo_alert,
+):
     # Upload a tar archive of files.
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
@@ -17,9 +27,8 @@ def upload_tar(trans, rdah, tdah, repository, tar, uploaded_file, upload_point,
     if check_results.invalid:
         tar.close()
         uploaded_file.close()
-        message = '{} Invalid paths were: {}'.format(
-            ' '.join(check_results.errors), ', '.join(check_results.invalid))
-        return False, message, [], '', undesirable_dirs_removed, undesirable_files_removed
+        message = "{} Invalid paths were: {}".format(" ".join(check_results.errors), ", ".join(check_results.invalid))
+        return False, message, [], "", undesirable_dirs_removed, undesirable_files_removed
     else:
         repository.hg_repo
         repo_dir = repository.repo_path(trans.app)
@@ -41,7 +50,7 @@ def upload_tar(trans, rdah, tdah, repository, tar, uploaded_file, upload_point,
                 # are missing and if so, set them appropriately.
                 altered, root_elem, error_message = rdah.handle_tag_attributes(uploaded_file_name)
                 if error_message:
-                    return False, error_message, [], '', [], []
+                    return False, error_message, [], "", [], []
                 elif altered:
                     tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                     shutil.move(tmp_filename, uploaded_file_name)
@@ -50,18 +59,20 @@ def upload_tar(trans, rdah, tdah, repository, tar, uploaded_file, upload_point,
                 # attributes are missing and if so, set them appropriately.
                 altered, root_elem, error_message = tdah.handle_tag_attributes(uploaded_file_name)
                 if error_message:
-                    return False, error_message, [], '', [], []
+                    return False, error_message, [], "", [], []
                 if altered:
                     tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                     shutil.move(tmp_filename, uploaded_file_name)
-        return commit_util.handle_directory_changes(trans.app,
-                                                    trans.request.host,
-                                                    trans.user.username,
-                                                    repository,
-                                                    full_path,
-                                                    filenames_in_archive,
-                                                    remove_repo_files_not_in_tar,
-                                                    new_repo_alert,
-                                                    commit_message,
-                                                    undesirable_dirs_removed,
-                                                    undesirable_files_removed)
+        return commit_util.handle_directory_changes(
+            trans.app,
+            trans.request.host,
+            trans.user.username,
+            repository,
+            full_path,
+            filenames_in_archive,
+            remove_repo_files_not_in_tar,
+            new_repo_alert,
+            commit_message,
+            undesirable_dirs_removed,
+            undesirable_files_removed,
+        )
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 2b0418e389a..132051e5979 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -8,8 +8,10 @@ from sqlalchemy import false
 from sqlalchemy.sql import select
 
 import tool_shed.dependencies.repository
-from galaxy import util
-from galaxy import web
+from galaxy import (
+    util,
+    web,
+)
 from galaxy.tool_shed.util.repository_util import (
     check_for_updates,
     check_or_update_tool_shed_status_for_installed_repository,
@@ -59,8 +61,18 @@ log = logging.getLogger(__name__)
 VALID_REPOSITORYNAME_RE = re.compile(r"^[a-z0-9\_]+$")
 
 
-def create_repo_info_dict(app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None,
-                          repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None):
+def create_repo_info_dict(
+    app,
+    repository_clone_url,
+    changeset_revision,
+    ctx_rev,
+    repository_owner,
+    repository_name=None,
+    repository=None,
+    repository_metadata=None,
+    tool_dependencies=None,
+    repository_dependencies=None,
+):
     """
     Return a dictionary that includes all of the information needed to install a repository into a local
     Galaxy instance.  The dictionary will also contain the recursive list of repository dependencies defined
@@ -85,43 +97,47 @@ def create_repo_info_dict(app, repository_clone_url, changeset_revision, ctx_rev
     """
     repo_info_dict = {}
     repository = get_repository_by_name_and_owner(app, repository_name, repository_owner)
-    if app.name == 'tool_shed':
+    if app.name == "tool_shed":
         # We're in the tool shed.
-        repository_metadata = get_repository_metadata_by_changeset_revision(app,
-                                                                            app.security.encode_id(repository.id),
-                                                                            changeset_revision)
+        repository_metadata = get_repository_metadata_by_changeset_revision(
+            app, app.security.encode_id(repository.id), changeset_revision
+        )
         if repository_metadata:
             metadata = repository_metadata.metadata
             if metadata:
-                tool_shed_url = web.url_for('/', qualified=True).rstrip('/')
-                rb = tool_shed.dependencies.repository.relation_builder.RelationBuilder(app, repository, repository_metadata, tool_shed_url)
+                tool_shed_url = web.url_for("/", qualified=True).rstrip("/")
+                rb = tool_shed.dependencies.repository.relation_builder.RelationBuilder(
+                    app, repository, repository_metadata, tool_shed_url
+                )
                 # Get a dictionary of all repositories upon which the contents of the received repository depends.
                 repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
-                tool_dependencies = metadata.get('tool_dependencies', {})
+                tool_dependencies = metadata.get("tool_dependencies", {})
     if tool_dependencies:
         new_tool_dependencies = {}
         for dependency_key, requirements_dict in tool_dependencies.items():
-            if dependency_key in ['set_environment']:
+            if dependency_key in ["set_environment"]:
                 new_set_environment_dict_list = []
                 for set_environment_dict in requirements_dict:
-                    set_environment_dict['repository_name'] = repository_name
-                    set_environment_dict['repository_owner'] = repository_owner
-                    set_environment_dict['changeset_revision'] = changeset_revision
+                    set_environment_dict["repository_name"] = repository_name
+                    set_environment_dict["repository_owner"] = repository_owner
+                    set_environment_dict["changeset_revision"] = changeset_revision
                     new_set_environment_dict_list.append(set_environment_dict)
                 new_tool_dependencies[dependency_key] = new_set_environment_dict_list
             else:
-                requirements_dict['repository_name'] = repository_name
-                requirements_dict['repository_owner'] = repository_owner
-                requirements_dict['changeset_revision'] = changeset_revision
+                requirements_dict["repository_name"] = repository_name
+                requirements_dict["repository_owner"] = repository_owner
+                requirements_dict["changeset_revision"] = changeset_revision
                 new_tool_dependencies[dependency_key] = requirements_dict
         tool_dependencies = new_tool_dependencies
-    repo_info_dict[repository.name] = (repository.description,
-                                       repository_clone_url,
-                                       changeset_revision,
-                                       ctx_rev,
-                                       repository_owner,
-                                       repository_dependencies,
-                                       tool_dependencies)
+    repo_info_dict[repository.name] = (
+        repository.description,
+        repository_clone_url,
+        changeset_revision,
+        ctx_rev,
+        repository_owner,
+        repository_dependencies,
+        tool_dependencies,
+    )
     return repo_info_dict
 
 
@@ -132,7 +148,7 @@ def create_repository_admin_role(app, repository):
     """
     sa_session = app.model.session
     name = get_repository_admin_role_name(str(repository.name), str(repository.user.username))
-    description = 'A user or group member with this role can administer this repository.'
+    description = "A user or group member with this role can administer this repository."
     role = app.model.Role(name=name, description=description, type=app.model.Role.types.SYSTEM)
     sa_session.add(role)
     sa_session.flush()
@@ -145,18 +161,30 @@ def create_repository_admin_role(app, repository):
     return role
 
 
-def create_repository(app, name, type, description, long_description, user_id, category_ids=None, remote_repository_url=None, homepage_url=None):
+def create_repository(
+    app,
+    name,
+    type,
+    description,
+    long_description,
+    user_id,
+    category_ids=None,
+    remote_repository_url=None,
+    homepage_url=None,
+):
     """Create a new ToolShed repository"""
     category_ids = category_ids or []
     sa_session = app.model.session
     # Add the repository record to the database.
-    repository = app.model.Repository(name=name,
-                                      type=type,
-                                      remote_repository_url=remote_repository_url,
-                                      homepage_url=homepage_url,
-                                      description=description,
-                                      long_description=long_description,
-                                      user_id=user_id)
+    repository = app.model.Repository(
+        name=name,
+        type=type,
+        remote_repository_url=remote_repository_url,
+        homepage_url=homepage_url,
+        description=description,
+        long_description=long_description,
+        user_id=user_id,
+    )
     # Flush to get the id.
     sa_session.add(repository)
     sa_session.flush()
@@ -183,8 +211,7 @@ def create_repository(app, name, type, description, long_description, user_id, c
     if category_ids:
         # Create category associations
         for category_id in category_ids:
-            category = sa_session.query(app.model.Category) \
-                                 .get(app.security.decode_id(category_id))
+            category = sa_session.query(app.model.Category).get(app.security.decode_id(category_id))
             rca = app.model.RepositoryCategoryAssociation(repository, category)
             sa_session.add(rca)
             flush_needed = True
@@ -198,44 +225,45 @@ def create_repository(app, name, type, description, long_description, user_id, c
 
 def generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=None):
     """Generate the URL for sharing a repository that is in the tool shed."""
-    base_url = web.url_for('/', qualified=True).rstrip('/')
-    sharable_url = f'{base_url}/view/{repository.user.username}/{repository.name}'
+    base_url = web.url_for("/", qualified=True).rstrip("/")
+    sharable_url = f"{base_url}/view/{repository.user.username}/{repository.name}"
     if changeset_revision:
-        sharable_url += f'/{changeset_revision}'
+        sharable_url += f"/{changeset_revision}"
     return sharable_url
 
 
 def get_repo_info_dict(app, user, repository_id, changeset_revision):
     repository = get_repository_in_tool_shed(app, repository_id)
     repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(user, repository)
-    repository_metadata = get_repository_metadata_by_changeset_revision(app,
-                                                                        repository_id,
-                                                                        changeset_revision)
+    repository_metadata = get_repository_metadata_by_changeset_revision(app, repository_id, changeset_revision)
     if not repository_metadata:
         # The received changeset_revision is no longer installable, so get the next changeset_revision
         # in the repository's changelog.  This generally occurs only with repositories of type
         # repository_suite_definition or tool_dependency_definition.
-        next_downloadable_changeset_revision = \
-            get_next_downloadable_changeset_revision(app, repository, changeset_revision)
+        next_downloadable_changeset_revision = get_next_downloadable_changeset_revision(
+            app, repository, changeset_revision
+        )
         if next_downloadable_changeset_revision and next_downloadable_changeset_revision != changeset_revision:
-            repository_metadata = get_repository_metadata_by_changeset_revision(app,
-                                                                                repository_id,
-                                                                                next_downloadable_changeset_revision)
+            repository_metadata = get_repository_metadata_by_changeset_revision(
+                app, repository_id, next_downloadable_changeset_revision
+            )
     if repository_metadata:
         # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
         # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
         # returned repo_info_dict.
         metadata = repository_metadata.metadata
-        if 'tools' in metadata:
+        if "tools" in metadata:
             includes_tools = True
         else:
             includes_tools = False
         includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
-        repository_dependencies_dict = metadata.get('repository_dependencies', {})
-        repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
-        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
-            get_repository_dependency_types(repository_dependencies)
-        if 'tool_dependencies' in metadata:
+        repository_dependencies_dict = metadata.get("repository_dependencies", {})
+        repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
+        (
+            has_repository_dependencies,
+            has_repository_dependencies_only_if_compiling_contained_td,
+        ) = get_repository_dependency_types(repository_dependencies)
+        if "tool_dependencies" in metadata:
             includes_tool_dependencies = True
         else:
             includes_tool_dependencies = False
@@ -248,33 +276,56 @@ def get_repo_info_dict(app, user, repository_id, changeset_revision):
         includes_tools_for_display_in_tool_panel = False
     repo_path = repository.repo_path(app)
     ctx_rev = str(changeset2rev(repo_path, changeset_revision))
-    repo_info_dict = create_repo_info_dict(app=app,
-                                           repository_clone_url=repository_clone_url,
-                                           changeset_revision=changeset_revision,
-                                           ctx_rev=ctx_rev,
-                                           repository_owner=repository.user.username,
-                                           repository_name=repository.name,
-                                           repository=repository,
-                                           repository_metadata=repository_metadata,
-                                           tool_dependencies=None,
-                                           repository_dependencies=None)
-    return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
-        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
+    repo_info_dict = create_repo_info_dict(
+        app=app,
+        repository_clone_url=repository_clone_url,
+        changeset_revision=changeset_revision,
+        ctx_rev=ctx_rev,
+        repository_owner=repository.user.username,
+        repository_name=repository.name,
+        repository=repository,
+        repository_metadata=repository_metadata,
+        tool_dependencies=None,
+        repository_dependencies=None,
+    )
+    return (
+        repo_info_dict,
+        includes_tools,
+        includes_tool_dependencies,
+        includes_tools_for_display_in_tool_panel,
+        has_repository_dependencies,
+        has_repository_dependencies_only_if_compiling_contained_td,
+    )
 
 
-def get_repositories_by_category(app, category_id, installable=False, sort_order='asc', sort_key='name', page=None, per_page=25):
+def get_repositories_by_category(
+    app, category_id, installable=False, sort_order="asc", sort_key="name", page=None, per_page=25
+):
     sa_session = app.model.session
-    query = sa_session.query(app.model.Repository) \
-                      .join(app.model.RepositoryCategoryAssociation, app.model.Repository.id == app.model.RepositoryCategoryAssociation.repository_id) \
-                      .join(app.model.User, app.model.User.id == app.model.Repository.user_id) \
-                      .filter(app.model.RepositoryCategoryAssociation.category_id == category_id)
+    query = (
+        sa_session.query(app.model.Repository)
+        .join(
+            app.model.RepositoryCategoryAssociation,
+            app.model.Repository.id == app.model.RepositoryCategoryAssociation.repository_id,
+        )
+        .join(app.model.User, app.model.User.id == app.model.Repository.user_id)
+        .filter(app.model.RepositoryCategoryAssociation.category_id == category_id)
+    )
     if installable:
         subquery = select([app.model.RepositoryMetadata.table.c.repository_id])
         query = query.filter(app.model.Repository.id.in_(subquery))
-    if sort_key == 'owner':
-        query = query.order_by(app.model.User.username) if sort_order == 'asc' else query.order_by(app.model.User.username.desc())
+    if sort_key == "owner":
+        query = (
+            query.order_by(app.model.User.username)
+            if sort_order == "asc"
+            else query.order_by(app.model.User.username.desc())
+        )
     else:
-        query = query.order_by(app.model.Repository.name) if sort_order == 'asc' else query.order_by(app.model.Repository.name.desc())
+        query = (
+            query.order_by(app.model.Repository.name)
+            if sort_order == "asc"
+            else query.order_by(app.model.Repository.name.desc())
+        )
     if page is not None:
         page = int(page)
         query = query.limit(per_page)
@@ -283,13 +334,19 @@ def get_repositories_by_category(app, category_id, installable=False, sort_order
     resultset = query.all()
     repositories = []
     for repository in resultset:
-        default_value_mapper = {'id': app.security.encode_id, 'user_id': app.security.encode_id, 'repository_id': app.security.encode_id}
+        default_value_mapper = {
+            "id": app.security.encode_id,
+            "user_id": app.security.encode_id,
+            "repository_id": app.security.encode_id,
+        }
         repository_dict = repository.to_dict(value_mapper=default_value_mapper)
-        repository_dict['metadata'] = {}
+        repository_dict["metadata"] = {}
         for changeset, changehash in repository.installable_revisions(app):
             encoded_id = app.security.encode_id(repository.id)
             metadata = get_repository_metadata_by_changeset_revision(app, encoded_id, changehash)
-            repository_dict['metadata'][f'{changeset}:{changehash}'] = metadata.to_dict(value_mapper=default_value_mapper)
+            repository_dict["metadata"][f"{changeset}:{changehash}"] = metadata.to_dict(
+                value_mapper=default_value_mapper
+            )
         if installable:
             if len(repository.installable_revisions(app)):
                 repositories.append(repository_dict)
@@ -298,26 +355,30 @@ def get_repositories_by_category(app, category_id, installable=False, sort_order
     return repositories
 
 
-def get_tool_shed_repository_status_label(app, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None):
+def get_tool_shed_repository_status_label(
+    app, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None
+):
     """Return a color-coded label for the status of the received tool-shed_repository installed into Galaxy."""
     if tool_shed_repository is None:
         if name is not None and owner is not None and repository_clone_url is not None:
             tool_shed = get_tool_shed_from_clone_url(repository_clone_url)
-            tool_shed_repository = get_installed_repository(app,
-                                                            tool_shed=tool_shed,
-                                                            name=name,
-                                                            owner=owner,
-                                                            installed_changeset_revision=changeset_revision)
+            tool_shed_repository = get_installed_repository(
+                app, tool_shed=tool_shed, name=name, owner=owner, installed_changeset_revision=changeset_revision
+            )
     if tool_shed_repository:
         status_label = tool_shed_repository.status
-        if tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.CLONING,
-                                           app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
-                                           app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
-                                           app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
-                                           app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
+        if tool_shed_repository.status in [
+            app.install_model.ToolShedRepository.installation_status.CLONING,
+            app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
+            app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
+            app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
+            app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES,
+        ]:
             bgcolor = app.install_model.ToolShedRepository.states.INSTALLING
-        elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.NEW,
-                                             app.install_model.ToolShedRepository.installation_status.UNINSTALLED]:
+        elif tool_shed_repository.status in [
+            app.install_model.ToolShedRepository.installation_status.NEW,
+            app.install_model.ToolShedRepository.installation_status.UNINSTALLED,
+        ]:
             bgcolor = app.install_model.ToolShedRepository.states.UNINSTALLED
         elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.ERROR]:
             bgcolor = app.install_model.ToolShedRepository.states.ERROR
@@ -326,35 +387,38 @@ def get_tool_shed_repository_status_label(app, tool_shed_repository=None, name=N
         elif tool_shed_repository.status in [app.install_model.ToolShedRepository.installation_status.INSTALLED]:
             if tool_shed_repository.repository_dependencies_being_installed:
                 bgcolor = app.install_model.ToolShedRepository.states.WARNING
-                status_label = '{}, {}'.format(status_label,
-                                           app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES)
+                status_label = "{}, {}".format(
+                    status_label,
+                    app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
+                )
             elif tool_shed_repository.missing_repository_dependencies:
                 bgcolor = app.install_model.ToolShedRepository.states.WARNING
-                status_label = f'{status_label}, missing repository dependencies'
+                status_label = f"{status_label}, missing repository dependencies"
             elif tool_shed_repository.tool_dependencies_being_installed:
                 bgcolor = app.install_model.ToolShedRepository.states.WARNING
-                status_label = '{}, {}'.format(status_label,
-                                           app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
+                status_label = "{}, {}".format(
+                    status_label, app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES
+                )
             elif tool_shed_repository.missing_tool_dependencies:
                 bgcolor = app.install_model.ToolShedRepository.states.WARNING
-                status_label = f'{status_label}, missing tool dependencies'
+                status_label = f"{status_label}, missing tool dependencies"
             else:
                 bgcolor = app.install_model.ToolShedRepository.states.OK
         else:
             bgcolor = app.install_model.ToolShedRepository.states.ERROR
     else:
         bgcolor = app.install_model.ToolShedRepository.states.WARNING
-        status_label = 'unknown status'
+        status_label = "unknown status"
     return f'<div class="count-box state-color-{bgcolor}">{status_label}</div>'
 
 
 def handle_role_associations(app, role, repository, **kwd):
     sa_session = app.model.session
-    message = escape(kwd.get('message', ''))
-    status = kwd.get('status', 'done')
+    message = escape(kwd.get("message", ""))
+    status = kwd.get("status", "done")
     repository_owner = repository.user
-    if kwd.get('manage_role_associations_button', False):
-        in_users_list = util.listify(kwd.get('in_users', []))
+    if kwd.get("manage_role_associations_button", False):
+        in_users_list = util.listify(kwd.get("in_users", []))
         in_users = [sa_session.query(app.model.User).get(x) for x in in_users_list]
         # Make sure the repository owner is always associated with the repostory's admin role.
         owner_associated = False
@@ -365,49 +429,58 @@ def handle_role_associations(app, role, repository, **kwd):
         if not owner_associated:
             in_users.append(repository_owner)
             message += "The repository owner must always be associated with the repository's administrator role.  "
-            status = 'error'
-        in_groups_list = util.listify(kwd.get('in_groups', []))
+            status = "error"
+        in_groups_list = util.listify(kwd.get("in_groups", []))
         in_groups = [sa_session.query(app.model.Group).get(x) for x in in_groups_list]
         in_repositories = [repository]
-        app.security_agent.set_entity_role_associations(roles=[role],
-                                                        users=in_users,
-                                                        groups=in_groups,
-                                                        repositories=in_repositories)
+        app.security_agent.set_entity_role_associations(
+            roles=[role], users=in_users, groups=in_groups, repositories=in_repositories
+        )
         sa_session.refresh(role)
-        message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories.  " % \
-            (escape(str(role.name)), len(in_users), len(in_groups), len(in_repositories))
+        message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories.  " % (
+            escape(str(role.name)),
+            len(in_users),
+            len(in_groups),
+            len(in_repositories),
+        )
     in_users = []
     out_users = []
     in_groups = []
     out_groups = []
-    for user in sa_session.query(app.model.User) \
-                          .filter(app.model.User.table.c.deleted == false()) \
-                          .order_by(app.model.User.table.c.email):
+    for user in (
+        sa_session.query(app.model.User)
+        .filter(app.model.User.table.c.deleted == false())
+        .order_by(app.model.User.table.c.email)
+    ):
         if user in [x.user for x in role.users]:
             in_users.append((user.id, user.email))
         else:
             out_users.append((user.id, user.email))
-    for group in sa_session.query(app.model.Group) \
-                           .filter(app.model.Group.table.c.deleted == false()) \
-                           .order_by(app.model.Group.table.c.name):
+    for group in (
+        sa_session.query(app.model.Group)
+        .filter(app.model.Group.table.c.deleted == false())
+        .order_by(app.model.Group.table.c.name)
+    ):
         if group in [x.group for x in role.groups]:
             in_groups.append((group.id, group.name))
         else:
             out_groups.append((group.id, group.name))
-    associations_dict = dict(in_users=in_users,
-                             out_users=out_users,
-                             in_groups=in_groups,
-                             out_groups=out_groups,
-                             message=message,
-                             status=status)
+    associations_dict = dict(
+        in_users=in_users,
+        out_users=out_users,
+        in_groups=in_groups,
+        out_groups=out_groups,
+        message=message,
+        status=status,
+    )
     return associations_dict
 
 
 def change_repository_name_in_hgrc_file(hgrc_file, new_name):
     config = configparser.ConfigParser()
     config.read(hgrc_file)
-    config.set('web', 'name', new_name)
-    with open(hgrc_file, 'w') as fh:
+    config.set("web", "name", new_name)
+    with open(hgrc_file, "w") as fh:
         config.write(fh)
 
 
@@ -420,30 +493,29 @@ def update_repository(app, trans, id, **kwds):
     if repository is None:
         return None, "Unknown repository ID"
 
-    if not (trans.user_is_admin
-            or trans.app.security_agent.user_can_administer_repository(trans.user, repository)):
+    if not (trans.user_is_admin or trans.app.security_agent.user_can_administer_repository(trans.user, repository)):
         message = "You are not the owner of this repository, so you cannot administer it."
         return None, message
 
     # Allowlist properties that can be changed via this method
-    for key in ('type', 'description', 'long_description', 'remote_repository_url', 'homepage_url'):
+    for key in ("type", "description", "long_description", "remote_repository_url", "homepage_url"):
         # If that key is available, not None and different than what's in the model
         if key in kwds and kwds[key] is not None and kwds[key] != getattr(repository, key):
             setattr(repository, key, kwds[key])
             flush_needed = True
 
-    if 'category_ids' in kwds and isinstance(kwds['category_ids'], list):
+    if "category_ids" in kwds and isinstance(kwds["category_ids"], list):
         # Get existing category associations
-        category_associations = sa_session.query(app.model.RepositoryCategoryAssociation) \
-                                          .filter(app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id))
+        category_associations = sa_session.query(app.model.RepositoryCategoryAssociation).filter(
+            app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id)
+        )
         # Remove all of them
         for rca in category_associations:
             sa_session.delete(rca)
 
         # Then (re)create category associations
-        for category_id in kwds['category_ids']:
-            category = sa_session.query(app.model.Category) \
-                                 .get(app.security.decode_id(category_id))
+        for category_id in kwds["category_ids"]:
+            category = sa_session.query(app.model.Category).get(app.security.decode_id(category_id))
             if category:
                 rca = app.model.RepositoryCategoryAssociation(repository, category)
                 sa_session.add(rca)
@@ -452,11 +524,11 @@ def update_repository(app, trans, id, **kwds):
         flush_needed = True
 
     # However some properties are special, like 'name'
-    if 'name' in kwds and kwds['name'] is not None and repository.name != kwds['name']:
+    if "name" in kwds and kwds["name"] is not None and repository.name != kwds["name"]:
         if repository.times_downloaded != 0:
             message = "Repository names cannot be changed if the repository has been cloned."
         else:
-            message = validate_repository_name(trans.app, kwds['name'], trans.user)
+            message = validate_repository_name(trans.app, kwds["name"], trans.user)
         if message:
             return None, message
 
@@ -468,13 +540,13 @@ def update_repository(app, trans, id, **kwds):
 
         # Change the entry in the repository's hgrc file.
         hgrc_file = get_hgrc_path(repo_dir)
-        change_repository_name_in_hgrc_file(hgrc_file, kwds['name'])
+        change_repository_name_in_hgrc_file(hgrc_file, kwds["name"])
 
         # Rename the repository's admin role to match the new repository name.
         repository_admin_role = repository.admin_role
-        repository_admin_role.name = get_repository_admin_role_name(str(kwds['name']), str(repository.user.username))
+        repository_admin_role.name = get_repository_admin_role_name(str(kwds["name"]), str(repository.user.username))
         trans.sa_session.add(repository_admin_role)
-        repository.name = kwds['name']
+        repository.name = kwds["name"]
         flush_needed = True
 
     if flush_needed:
@@ -492,65 +564,65 @@ def validate_repository_name(app, name, user):
     Repository names must be unique for each user, must be at least two characters
     in length and must contain only lower-case letters, numbers, and the '_' character.
     """
-    if name in ['None', None, '']:
-        return 'Enter the required repository name.'
-    if name in ['repos']:
+    if name in ["None", None, ""]:
+        return "Enter the required repository name."
+    if name in ["repos"]:
         return f"The term '{name}' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
     check_existing = get_repository_by_name_and_owner(app, name, user.username)
     if check_existing is not None:
         if check_existing.deleted:
-            return f'You own a deleted repository named <b>{escape(name)}</b>, please choose a different name.'
+            return f"You own a deleted repository named <b>{escape(name)}</b>, please choose a different name."
         else:
             return f"You already own a repository named <b>{escape(name)}</b>, please choose a different name."
     if len(name) < 2:
         return "Repository names must be at least 2 characters in length."
     if len(name) > 80:
         return "Repository names cannot be more than 80 characters in length."
-    if not(VALID_REPOSITORYNAME_RE.match(name)):
+    if not (VALID_REPOSITORYNAME_RE.match(name)):
         return "Repository names must contain only lower-case letters, numbers and underscore."
-    return ''
+    return ""
 
 
 __all__ = (
-    'change_repository_name_in_hgrc_file',
-    'check_for_updates',
-    'check_or_update_tool_shed_status_for_installed_repository',
-    'create_or_update_tool_shed_repository',
-    'create_repo_info_dict',
-    'create_repository_admin_role',
-    'create_repository',
-    'extract_components_from_tuple',
-    'generate_sharable_link_for_repository_in_tool_shed',
-    'generate_tool_shed_repository_install_dir',
-    'get_absolute_path_to_file_in_repository',
-    'get_ids_of_tool_shed_repositories_being_installed',
-    'get_installed_repository',
-    'get_installed_tool_shed_repository',
-    'get_prior_import_or_install_required_dict',
-    'get_repo_info_dict',
-    'get_repo_info_tuple_contents',
-    'get_repositories_by_category',
-    'get_repository_admin_role_name',
-    'get_repository_and_repository_dependencies_from_repo_info_dict',
-    'get_repository_by_id',
-    'get_repository_by_name',
-    'get_repository_by_name_and_owner',
-    'get_repository_dependency_types',
-    'get_repository_for_dependency_relationship',
-    'get_repository_ids_requiring_prior_import_or_install',
-    'get_repository_in_tool_shed',
-    'get_repository_owner',
-    'get_repository_owner_from_clone_url',
-    'get_repository_query',
-    'get_role_by_id',
-    'get_tool_shed_from_clone_url',
-    'get_tool_shed_repository_by_id',
-    'get_tool_shed_repository_status_label',
-    'get_tool_shed_status_for_installed_repository',
-    'handle_role_associations',
-    'is_tool_shed_client',
-    'repository_was_previously_installed',
-    'set_repository_attributes',
-    'update_repository',
-    'validate_repository_name',
+    "change_repository_name_in_hgrc_file",
+    "check_for_updates",
+    "check_or_update_tool_shed_status_for_installed_repository",
+    "create_or_update_tool_shed_repository",
+    "create_repo_info_dict",
+    "create_repository_admin_role",
+    "create_repository",
+    "extract_components_from_tuple",
+    "generate_sharable_link_for_repository_in_tool_shed",
+    "generate_tool_shed_repository_install_dir",
+    "get_absolute_path_to_file_in_repository",
+    "get_ids_of_tool_shed_repositories_being_installed",
+    "get_installed_repository",
+    "get_installed_tool_shed_repository",
+    "get_prior_import_or_install_required_dict",
+    "get_repo_info_dict",
+    "get_repo_info_tuple_contents",
+    "get_repositories_by_category",
+    "get_repository_admin_role_name",
+    "get_repository_and_repository_dependencies_from_repo_info_dict",
+    "get_repository_by_id",
+    "get_repository_by_name",
+    "get_repository_by_name_and_owner",
+    "get_repository_dependency_types",
+    "get_repository_for_dependency_relationship",
+    "get_repository_ids_requiring_prior_import_or_install",
+    "get_repository_in_tool_shed",
+    "get_repository_owner",
+    "get_repository_owner_from_clone_url",
+    "get_repository_query",
+    "get_role_by_id",
+    "get_tool_shed_from_clone_url",
+    "get_tool_shed_repository_by_id",
+    "get_tool_shed_repository_status_label",
+    "get_tool_shed_status_for_installed_repository",
+    "handle_role_associations",
+    "is_tool_shed_client",
+    "repository_was_previously_installed",
+    "set_repository_attributes",
+    "update_repository",
+    "validate_repository_name",
 )
diff --git a/lib/tool_shed/util/review_util.py b/lib/tool_shed/util/review_util.py
index fe5c5088518..7c745620aa7 100644
--- a/lib/tool_shed/util/review_util.py
+++ b/lib/tool_shed/util/review_util.py
@@ -15,9 +15,7 @@ def can_browse_repository_reviews(app, user, repository):
     if user:
         for review in repository.reviews:
             for component_review in review.component_reviews:
-                if app.security_agent.user_can_browse_component_review(app,
-                                                                       repository,
-                                                                       component_review, user):
+                if app.security_agent.user_can_browse_component_review(app, repository, component_review, user):
                     return True
     return False
 
@@ -45,25 +43,27 @@ def get_component_review(app, id):
 def get_component_by_name(app, name):
     """Get a component from the database via a name."""
     sa_session = app.model.session
-    return sa_session.query(app.model.Component) \
-                     .filter(app.model.Component.table.c.name == name) \
-                     .first()
+    return sa_session.query(app.model.Component).filter(app.model.Component.table.c.name == name).first()
 
 
 def get_component_review_by_repository_review_id_component_id(app, repository_review_id, component_id):
     """Get a component_review from the database via repository_review_id and component_id."""
     sa_session = app.model.session
-    return sa_session.query(app.model.ComponentReview) \
-                     .filter(and_(app.model.ComponentReview.table.c.repository_review_id == app.security.decode_id(repository_review_id),
-                                  app.model.ComponentReview.table.c.component_id == app.security.decode_id(component_id))) \
-                     .first()
+    return (
+        sa_session.query(app.model.ComponentReview)
+        .filter(
+            and_(
+                app.model.ComponentReview.table.c.repository_review_id == app.security.decode_id(repository_review_id),
+                app.model.ComponentReview.table.c.component_id == app.security.decode_id(component_id),
+            )
+        )
+        .first()
+    )
 
 
 def get_components(app):
     sa_session = app.model.session
-    return sa_session.query(app.model.Component) \
-                     .order_by(app.model.Component.name) \
-                     .all()
+    return sa_session.query(app.model.Component).order_by(app.model.Component.name).all()
 
 
 def get_previous_repository_reviews(app, repository, changeset_revision):
@@ -77,14 +77,15 @@ def get_previous_repository_reviews(app, repository, changeset_revision):
     for changeset in hg_util.reversed_upper_bounded_changelog(repo, changeset_revision):
         previous_changeset_revision = str(repo[changeset])
         if previous_changeset_revision in reviewed_revision_hashes:
-            previous_rev, previous_changeset_revision_label = \
-                hg_util.get_rev_label_from_changeset_revision(repo, previous_changeset_revision)
-            revision_reviews = get_reviews_by_repository_id_changeset_revision(app,
-                                                                               app.security.encode_id(repository.id),
-                                                                               previous_changeset_revision)
-            previous_reviews_dict[previous_changeset_revision] = \
-                dict(changeset_revision_label=previous_changeset_revision_label,
-                     reviews=revision_reviews)
+            previous_rev, previous_changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(
+                repo, previous_changeset_revision
+            )
+            revision_reviews = get_reviews_by_repository_id_changeset_revision(
+                app, app.security.encode_id(repository.id), previous_changeset_revision
+            )
+            previous_reviews_dict[previous_changeset_revision] = dict(
+                changeset_revision_label=previous_changeset_revision_label, reviews=revision_reviews
+            )
     return previous_reviews_dict
 
 
@@ -100,20 +101,32 @@ def get_review_by_repository_id_changeset_revision_user_id(app, repository_id, c
     and user_id.
     """
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryReview) \
-                     .filter(and_(app.model.RepositoryReview.repository_id == app.security.decode_id(repository_id),
-                                  app.model.RepositoryReview.changeset_revision == changeset_revision,
-                                  app.model.RepositoryReview.user_id == app.security.decode_id(user_id))) \
-                     .first()
+    return (
+        sa_session.query(app.model.RepositoryReview)
+        .filter(
+            and_(
+                app.model.RepositoryReview.repository_id == app.security.decode_id(repository_id),
+                app.model.RepositoryReview.changeset_revision == changeset_revision,
+                app.model.RepositoryReview.user_id == app.security.decode_id(user_id),
+            )
+        )
+        .first()
+    )
 
 
 def get_reviews_by_repository_id_changeset_revision(app, repository_id, changeset_revision):
     """Get all repository_reviews from the database via repository id and changeset_revision."""
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryReview) \
-                     .filter(and_(app.model.RepositoryReview.repository_id == app.security.decode_id(repository_id),
-                                  app.model.RepositoryReview.changeset_revision == changeset_revision)) \
-                     .all()
+    return (
+        sa_session.query(app.model.RepositoryReview)
+        .filter(
+            and_(
+                app.model.RepositoryReview.repository_id == app.security.decode_id(repository_id),
+                app.model.RepositoryReview.changeset_revision == changeset_revision,
+            )
+        )
+        .all()
+    )
 
 
 def has_previous_repository_reviews(app, repository, changeset_revision):
diff --git a/lib/tool_shed/util/search_util.py b/lib/tool_shed/util/search_util.py
index 5a9eef5ca54..ee0898b1a14 100644
--- a/lib/tool_shed/util/search_util.py
+++ b/lib/tool_shed/util/search_util.py
@@ -1,6 +1,10 @@
 import logging
 
-from sqlalchemy import and_, false, true
+from sqlalchemy import (
+    and_,
+    false,
+    true,
+)
 
 log = logging.getLogger(__name__)
 
@@ -8,50 +12,62 @@ log = logging.getLogger(__name__)
 def in_tool_dict(tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None):
     found = False
     if tool_id and not tool_name and not tool_version:
-        tool_dict_tool_id = tool_dict['id'].lower()
-        found = (tool_id == tool_dict_tool_id) or \
-                (not exact_matches_checked and tool_dict_tool_id.find(tool_id) >= 0)
+        tool_dict_tool_id = tool_dict["id"].lower()
+        found = (tool_id == tool_dict_tool_id) or (not exact_matches_checked and tool_dict_tool_id.find(tool_id) >= 0)
     elif tool_name and not tool_id and not tool_version:
-        tool_dict_tool_name = tool_dict['name'].lower()
-        found = (tool_name == tool_dict_tool_name) or \
-                (not exact_matches_checked and tool_dict_tool_name.find(tool_name) >= 0)
+        tool_dict_tool_name = tool_dict["name"].lower()
+        found = (tool_name == tool_dict_tool_name) or (
+            not exact_matches_checked and tool_dict_tool_name.find(tool_name) >= 0
+        )
     elif tool_version and not tool_id and not tool_name:
-        tool_dict_tool_version = tool_dict['version'].lower()
-        found = (tool_version == tool_dict_tool_version) or \
-                (not exact_matches_checked and tool_dict_tool_version.find(tool_version) >= 0)
+        tool_dict_tool_version = tool_dict["version"].lower()
+        found = (tool_version == tool_dict_tool_version) or (
+            not exact_matches_checked and tool_dict_tool_version.find(tool_version) >= 0
+        )
     elif tool_id and tool_name and not tool_version:
-        tool_dict_tool_id = tool_dict['id'].lower()
-        tool_dict_tool_name = tool_dict['name'].lower()
-        found = (tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name) or \
-                (not exact_matches_checked and tool_dict_tool_id.find(tool_id) >= 0 and tool_dict_tool_name.find(tool_name) >= 0)
+        tool_dict_tool_id = tool_dict["id"].lower()
+        tool_dict_tool_name = tool_dict["name"].lower()
+        found = (tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name) or (
+            not exact_matches_checked
+            and tool_dict_tool_id.find(tool_id) >= 0
+            and tool_dict_tool_name.find(tool_name) >= 0
+        )
     elif tool_id and tool_version and not tool_name:
-        tool_dict_tool_id = tool_dict['id'].lower()
-        tool_dict_tool_version = tool_dict['version'].lower()
-        found = (tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version) or \
-                (not exact_matches_checked and tool_dict_tool_id.find(tool_id) >= 0 and tool_dict_tool_version.find(tool_version) >= 0)
+        tool_dict_tool_id = tool_dict["id"].lower()
+        tool_dict_tool_version = tool_dict["version"].lower()
+        found = (tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version) or (
+            not exact_matches_checked
+            and tool_dict_tool_id.find(tool_id) >= 0
+            and tool_dict_tool_version.find(tool_version) >= 0
+        )
     elif tool_version and tool_name and not tool_id:
-        tool_dict_tool_version = tool_dict['version'].lower()
-        tool_dict_tool_name = tool_dict['name'].lower()
-        found = (tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name) or \
-                (not exact_matches_checked and tool_dict_tool_version.find(tool_version) >= 0 and tool_dict_tool_name.find(tool_name) >= 0)
+        tool_dict_tool_version = tool_dict["version"].lower()
+        tool_dict_tool_name = tool_dict["name"].lower()
+        found = (tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name) or (
+            not exact_matches_checked
+            and tool_dict_tool_version.find(tool_version) >= 0
+            and tool_dict_tool_name.find(tool_name) >= 0
+        )
     elif tool_version and tool_name and tool_id:
-        tool_dict_tool_version = tool_dict['version'].lower()
-        tool_dict_tool_name = tool_dict['name'].lower()
-        tool_dict_tool_id = tool_dict['id'].lower()
-        found = (tool_version == tool_dict_tool_version
-                 and tool_name == tool_dict_tool_name
-                 and tool_id == tool_dict_tool_id) or \
-                (not exact_matches_checked
-                 and tool_dict_tool_version.find(tool_version) >= 0
-                 and tool_dict_tool_name.find(tool_name) >= 0
-                 and tool_dict_tool_id.find(tool_id) >= 0)
+        tool_dict_tool_version = tool_dict["version"].lower()
+        tool_dict_tool_name = tool_dict["name"].lower()
+        tool_dict_tool_id = tool_dict["id"].lower()
+        found = (
+            tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name and tool_id == tool_dict_tool_id
+        ) or (
+            not exact_matches_checked
+            and tool_dict_tool_version.find(tool_version) >= 0
+            and tool_dict_tool_name.find(tool_name) >= 0
+            and tool_dict_tool_id.find(tool_id) >= 0
+        )
     return found
 
 
 def in_workflow_dict(workflow_dict, exact_matches_checked, workflow_name):
-    workflow_dict_workflow_name = workflow_dict['name'].lower()
-    return (workflow_name == workflow_dict_workflow_name) or \
-           (not exact_matches_checked and workflow_dict_workflow_name.find(workflow_name) >= 0)
+    workflow_dict_workflow_name = workflow_dict["name"].lower()
+    return (workflow_name == workflow_dict_workflow_name) or (
+        not exact_matches_checked and workflow_dict_workflow_name.find(workflow_name) >= 0
+    )
 
 
 def make_same_length(list1, list2):
@@ -81,7 +97,9 @@ def search_ids_versions(tool_dict, exact_matches_checked, match_tuples, reposito
     return match_tuples
 
 
-def search_names_versions(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions):
+def search_names_versions(
+    tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions
+):
     for i, tool_name in enumerate(tool_names):
         tool_version = tool_versions[i]
         if in_tool_dict(tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version):
@@ -89,55 +107,109 @@ def search_names_versions(tool_dict, exact_matches_checked, match_tuples, reposi
     return match_tuples
 
 
-def search_repository_metadata(app, exact_matches_checked, tool_ids='', tool_names='', tool_versions='',
-                               workflow_names='', all_workflows=False):
+def search_repository_metadata(
+    app, exact_matches_checked, tool_ids="", tool_names="", tool_versions="", workflow_names="", all_workflows=False
+):
     sa_session = app.model.session
     match_tuples = []
     ok = True
     if tool_ids or tool_names or tool_versions:
-        for repository_metadata in sa_session.query(app.model.RepositoryMetadata) \
-                                             .filter(app.model.RepositoryMetadata.table.c.includes_tools == true()) \
-                                             .join(app.model.Repository) \
-                                             .filter(and_(app.model.Repository.table.c.deleted == false(),
-                                                          app.model.Repository.table.c.deprecated == false())):
+        for repository_metadata in (
+            sa_session.query(app.model.RepositoryMetadata)
+            .filter(app.model.RepositoryMetadata.table.c.includes_tools == true())
+            .join(app.model.Repository)
+            .filter(
+                and_(
+                    app.model.Repository.table.c.deleted == false(), app.model.Repository.table.c.deprecated == false()
+                )
+            )
+        ):
             metadata = repository_metadata.metadata
             if metadata:
-                tools = metadata.get('tools', [])
+                tools = metadata.get("tools", [])
                 for tool_dict in tools:
                     if tool_ids and not tool_names and not tool_versions:
                         for tool_id in tool_ids:
                             if in_tool_dict(tool_dict, exact_matches_checked, tool_id=tool_id):
-                                match_tuples.append((repository_metadata.repository_id, repository_metadata.changeset_revision))
+                                match_tuples.append(
+                                    (repository_metadata.repository_id, repository_metadata.changeset_revision)
+                                )
                     elif tool_names and not tool_ids and not tool_versions:
                         for tool_name in tool_names:
                             if in_tool_dict(tool_dict, exact_matches_checked, tool_name=tool_name):
-                                match_tuples.append((repository_metadata.repository_id, repository_metadata.changeset_revision))
+                                match_tuples.append(
+                                    (repository_metadata.repository_id, repository_metadata.changeset_revision)
+                                )
                     elif tool_versions and not tool_ids and not tool_names:
                         for tool_version in tool_versions:
                             if in_tool_dict(tool_dict, exact_matches_checked, tool_version=tool_version):
-                                match_tuples.append((repository_metadata.repository_id, repository_metadata.changeset_revision))
+                                match_tuples.append(
+                                    (repository_metadata.repository_id, repository_metadata.changeset_revision)
+                                )
                     elif tool_ids and tool_names and not tool_versions:
                         if len(tool_ids) == len(tool_names):
-                            match_tuples = search_ids_names(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names)
+                            match_tuples = search_ids_names(
+                                tool_dict,
+                                exact_matches_checked,
+                                match_tuples,
+                                repository_metadata,
+                                tool_ids,
+                                tool_names,
+                            )
                         elif len(tool_ids) == 1 or len(tool_names) == 1:
                             tool_ids, tool_names = make_same_length(tool_ids, tool_names)
-                            match_tuples = search_ids_names(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names)
+                            match_tuples = search_ids_names(
+                                tool_dict,
+                                exact_matches_checked,
+                                match_tuples,
+                                repository_metadata,
+                                tool_ids,
+                                tool_names,
+                            )
                         else:
                             ok = False
                     elif tool_ids and tool_versions and not tool_names:
                         if len(tool_ids) == len(tool_versions):
-                            match_tuples = search_ids_versions(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions)
+                            match_tuples = search_ids_versions(
+                                tool_dict,
+                                exact_matches_checked,
+                                match_tuples,
+                                repository_metadata,
+                                tool_ids,
+                                tool_versions,
+                            )
                         elif len(tool_ids) == 1 or len(tool_versions) == 1:
                             tool_ids, tool_versions = make_same_length(tool_ids, tool_versions)
-                            match_tuples = search_ids_versions(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions)
+                            match_tuples = search_ids_versions(
+                                tool_dict,
+                                exact_matches_checked,
+                                match_tuples,
+                                repository_metadata,
+                                tool_ids,
+                                tool_versions,
+                            )
                         else:
                             ok = False
                     elif tool_versions and tool_names and not tool_ids:
                         if len(tool_versions) == len(tool_names):
-                            match_tuples = search_names_versions(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions)
+                            match_tuples = search_names_versions(
+                                tool_dict,
+                                exact_matches_checked,
+                                match_tuples,
+                                repository_metadata,
+                                tool_names,
+                                tool_versions,
+                            )
                         elif len(tool_versions) == 1 or len(tool_names) == 1:
                             tool_versions, tool_names = make_same_length(tool_versions, tool_names)
-                            match_tuples = search_names_versions(tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions)
+                            match_tuples = search_names_versions(
+                                tool_dict,
+                                exact_matches_checked,
+                                match_tuples,
+                                repository_metadata,
+                                tool_names,
+                                tool_versions,
+                            )
                         else:
                             ok = False
                     elif tool_versions and tool_names and tool_ids:
@@ -145,27 +217,42 @@ def search_repository_metadata(app, exact_matches_checked, tool_ids='', tool_nam
                             for i, tool_version in enumerate(tool_versions):
                                 tool_name = tool_names[i]
                                 tool_id = tool_ids[i]
-                                if in_tool_dict(tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version):
-                                    match_tuples.append((repository_metadata.repository_id, repository_metadata.changeset_revision))
+                                if in_tool_dict(
+                                    tool_dict,
+                                    exact_matches_checked,
+                                    tool_id=tool_id,
+                                    tool_name=tool_name,
+                                    tool_version=tool_version,
+                                ):
+                                    match_tuples.append(
+                                        (repository_metadata.repository_id, repository_metadata.changeset_revision)
+                                    )
                         else:
                             ok = False
     elif workflow_names or all_workflows:
-        for repository_metadata in sa_session.query(app.model.RepositoryMetadata) \
-                                             .filter(app.model.RepositoryMetadata.table.c.includes_workflows == true()) \
-                                             .join(app.model.Repository) \
-                                             .filter(and_(app.model.Repository.table.c.deleted == false(),
-                                                          app.model.Repository.table.c.deprecated == false())):
+        for repository_metadata in (
+            sa_session.query(app.model.RepositoryMetadata)
+            .filter(app.model.RepositoryMetadata.table.c.includes_workflows == true())
+            .join(app.model.Repository)
+            .filter(
+                and_(
+                    app.model.Repository.table.c.deleted == false(), app.model.Repository.table.c.deprecated == false()
+                )
+            )
+        ):
             metadata = repository_metadata.metadata
             if metadata:
                 # metadata[ 'workflows' ] is a list of tuples where each contained tuple is
                 # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
                 if workflow_names:
-                    workflow_tups = metadata.get('workflows', [])
+                    workflow_tups = metadata.get("workflows", [])
                     workflows = [workflow_tup[1] for workflow_tup in workflow_tups]
                     for workflow_dict in workflows:
                         for workflow_name in workflow_names:
                             if in_workflow_dict(workflow_dict, exact_matches_checked, workflow_name):
-                                match_tuples.append((repository_metadata.repository_id, repository_metadata.changeset_revision))
+                                match_tuples.append(
+                                    (repository_metadata.repository_id, repository_metadata.changeset_revision)
+                                )
                 elif all_workflows:
                     match_tuples.append((repository_metadata.repository_id, repository_metadata.changeset_revision))
     return ok, match_tuples
diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 26afd1bc18c..e90f5c27c42 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -1,7 +1,10 @@
 import logging
 import os
 
-from mercurial import hg, ui
+from mercurial import (
+    hg,
+    ui,
+)
 from whoosh.writing import AsyncWriter
 
 import tool_shed.webapp.model.mapping as ts_mapping
@@ -11,7 +14,7 @@ from galaxy.util import (
     directory_hash_id,
     ExecutionTimer,
     pretty_print_time_interval,
-    unicodify
+    unicodify,
 )
 from tool_shed.util.hgweb_config import hgweb_config_manager
 from tool_shed.webapp import model
@@ -22,7 +25,7 @@ log = logging.getLogger(__name__)
 
 
 def _get_or_create_index(whoosh_index_dir):
-    tool_index_dir = os.path.join(whoosh_index_dir, 'tools')
+    tool_index_dir = os.path.join(whoosh_index_dir, "tools")
     if not os.path.exists(whoosh_index_dir):
         os.makedirs(whoosh_index_dir)
     if not os.path.exists(tool_index_dir):
@@ -49,16 +52,16 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
     execution_timer = ExecutionTimer()
     with repo_index.searcher() as searcher:
         for repo in get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
-            tools_list = repo.pop('tools_list')
-            repo_id = repo['id']
+            tools_list = repo.pop("tools_list")
+            repo_id = repo["id"]
             indexed_document = searcher.document(id=repo_id)
             if indexed_document:
-                if indexed_document['full_last_updated'] == repo.get('full_last_updated'):
+                if indexed_document["full_last_updated"] == repo.get("full_last_updated"):
                     # We're done, since we sorted repos by update time
                     break
                 else:
                     # Got an update, delete the previous document
-                    repo_index_writer.delete_by_term('id', repo_id)
+                    repo_index_writer.delete_by_term("id", repo_id)
 
             repo_index_writer.add_document(**repo)
 
@@ -84,11 +87,18 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
     hgwcm = hgweb_config_manager
     hgwcm.hgweb_config_dir = hgweb_config_dir
     # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
-    q = sa_session.query(model.Repository).filter_by(deleted=False).filter_by(deprecated=False).order_by(model.Repository.update_time.desc())
-    q = q.filter(model.Repository.type != 'tool_dependency_definition')
+    q = (
+        sa_session.query(model.Repository)
+        .filter_by(deleted=False)
+        .filter_by(deprecated=False)
+        .order_by(model.Repository.update_time.desc())
+    )
+    q = q.filter(model.Repository.type != "tool_dependency_definition")
     for repo in q:
         category_names = []
-        for rca in sa_session.query(model.RepositoryCategoryAssociation).filter(model.RepositoryCategoryAssociation.repository_id == repo.id):
+        for rca in sa_session.query(model.RepositoryCategoryAssociation).filter(
+            model.RepositoryCategoryAssociation.repository_id == repo.id
+        ):
             for category in sa_session.query(model.Category).filter(model.Category.id == rca.category.id):
                 category_names.append(category.name.lower())
         categories = (",").join(category_names)
@@ -101,23 +111,25 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
 
         times_downloaded = repo.times_downloaded or 0
 
-        repo_owner_username = ''
+        repo_owner_username = ""
         if repo.user_id is not None:
             user = sa_session.query(model.User).filter(model.User.id == repo.user_id).one()
             repo_owner_username = user.username.lower()
 
-        approved = 'no'
+        approved = "no"
         for review in repo.reviews:
-            if review.approved == 'yes':
-                approved = 'yes'
+            if review.approved == "yes":
+                approved = "yes"
                 break
 
         last_updated = pretty_print_time_interval(repo.update_time)
         full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
 
         # Load all changesets of the repo for lineage.
-        repo_path = os.path.join(hgweb_config_dir, hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name)))
-        hg_repo = hg.repository(ui.ui(), repo_path.encode('utf-8'))
+        repo_path = os.path.join(
+            hgweb_config_dir, hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
+        )
+        hg_repo = hg.repository(ui.ui(), repo_path.encode("utf-8"))
         lineage = []
         for changeset in hg_repo.changelog:
             lineage.append(f"{unicodify(changeset)}:{unicodify(hg_repo[changeset])}")
@@ -130,26 +142,30 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
         if os.path.exists(path):
             tools_list.extend(load_one_dir(path))
             for root, dirs, _files in os.walk(path):
-                if '.hg' in dirs:
-                    dirs.remove('.hg')
+                if ".hg" in dirs:
+                    dirs.remove(".hg")
                 for dirname in dirs:
                     tools_in_dir = load_one_dir(os.path.join(root, dirname))
                     tools_list.extend(tools_in_dir)
 
-        yield (dict(id=unicodify(repo_id),
-                    name=unicodify(name),
-                    description=unicodify(description),
-                    long_description=unicodify(long_description),
-                    homepage_url=unicodify(homepage_url),
-                    remote_repository_url=unicodify(remote_repository_url),
-                    repo_owner_username=unicodify(repo_owner_username),
-                    times_downloaded=unicodify(times_downloaded),
-                    approved=unicodify(approved),
-                    last_updated=unicodify(last_updated),
-                    full_last_updated=unicodify(full_last_updated),
-                    tools_list=tools_list,
-                    repo_lineage=unicodify(repo_lineage),
-                    categories=unicodify(categories)))
+        yield (
+            dict(
+                id=unicodify(repo_id),
+                name=unicodify(name),
+                description=unicodify(description),
+                long_description=unicodify(long_description),
+                homepage_url=unicodify(homepage_url),
+                remote_repository_url=unicodify(remote_repository_url),
+                repo_owner_username=unicodify(repo_owner_username),
+                times_downloaded=unicodify(times_downloaded),
+                approved=unicodify(approved),
+                last_updated=unicodify(last_updated),
+                full_last_updated=unicodify(full_last_updated),
+                tools_list=tools_list,
+                repo_lineage=unicodify(repo_lineage),
+                categories=unicodify(categories),
+            )
+        )
 
 
 def debug_handler(path, exc_info):
@@ -166,14 +182,18 @@ def load_one_dir(path):
     if tool_elems:
         for elem in tool_elems:
             root = elem[1].getroot()
-            if root.tag == 'tool':
+            if root.tag == "tool":
                 tool = {}
-                if root.find('help') is not None:
-                    tool.update(dict(help=unicodify(root.find('help').text)))
-                if root.find('description') is not None:
-                    tool.update(dict(description=unicodify(root.find('description').text)))
-                tool.update(dict(id=unicodify(root.attrib.get('id')),
-                                 name=unicodify(root.attrib.get('name')),
-                                 version=unicodify(root.attrib.get('version'))))
+                if root.find("help") is not None:
+                    tool.update(dict(help=unicodify(root.find("help").text)))
+                if root.find("description") is not None:
+                    tool.update(dict(description=unicodify(root.find("description").text)))
+                tool.update(
+                    dict(
+                        id=unicodify(root.attrib.get("id")),
+                        name=unicodify(root.attrib.get("name")),
+                        version=unicodify(root.attrib.get("version")),
+                    )
+                )
                 tools_in_dir.append(tool)
     return tools_in_dir
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 3e3c222b70e..4e1f6827203 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -5,7 +5,11 @@ import socket
 import string
 
 import sqlalchemy.orm.exc
-from sqlalchemy import and_, false, true
+from sqlalchemy import (
+    and_,
+    false,
+    true,
+)
 
 import galaxy.tool_util.deps.requirements
 from galaxy import util
@@ -30,14 +34,14 @@ from tool_shed.util import (
     basic_util,
     common_util,
     hg_util,
-    repository_util
+    repository_util,
 )
 
 log = logging.getLogger(__name__)
 
 MAX_CONTENT_SIZE = 1048576
-DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml'
-REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml'
+DATATYPES_CONFIG_FILENAME = "datatypes_conf.xml"
+REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = "data_manager_conf.xml"
 
 new_repo_email_alert_template = """
 Sharable link:         ${sharable_link}
@@ -98,18 +102,22 @@ This message was sent from the Galaxy Tool Shed instance hosted on the server
 
 def count_repositories_in_category(app, category_id):
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryCategoryAssociation) \
-                     .filter(app.model.RepositoryCategoryAssociation.table.c.category_id == app.security.decode_id(category_id)) \
-                     .count()
+    return (
+        sa_session.query(app.model.RepositoryCategoryAssociation)
+        .filter(app.model.RepositoryCategoryAssociation.table.c.category_id == app.security.decode_id(category_id))
+        .count()
+    )
 
 
 def get_categories(app):
     """Get all categories from the database."""
     sa_session = app.model.session
-    return sa_session.query(app.model.Category) \
-                     .filter(app.model.Category.table.c.deleted == false()) \
-                     .order_by(app.model.Category.table.c.name) \
-                     .all()
+    return (
+        sa_session.query(app.model.Category)
+        .filter(app.model.Category.table.c.deleted == false())
+        .order_by(app.model.Category.table.c.name)
+        .all()
+    )
 
 
 def get_category(app, id):
@@ -137,9 +145,10 @@ def get_tool_shed_repo_requirements(app, tool_shed_url, repositories=None, repo_
     if repositories:
         if not isinstance(repositories, list):
             repositories = [repositories]
-        repository_params = [{'name': repository.name,
-                             'owner': repository.owner,
-                             'changeset_revision': repository.changeset_revision} for repository in repositories]
+        repository_params = [
+            {"name": repository.name, "owner": repository.owner, "changeset_revision": repository.changeset_revision}
+            for repository in repositories
+        ]
     else:
         if not isinstance(repo_info_dicts, list):
             repo_info_dicts = [repo_info_dicts]
@@ -149,82 +158,86 @@ def get_tool_shed_repo_requirements(app, tool_shed_url, repositories=None, repo_
                 # repo_info_tuple is a list, but keep terminology
                 owner = repo_info_tuple[4]
                 changeset_revision = repo_info_tuple[2]
-                repository_params.append({'name': name,
-                                          'owner': owner,
-                                          'changeset_revision': changeset_revision})
+                repository_params.append({"name": name, "owner": owner, "changeset_revision": changeset_revision})
     pathspec = ["api", "repositories", "get_repository_revision_install_info"]
     tools = []
     for params in repository_params:
-        response = util.url_get(tool_shed_url,
-                                auth=app.tool_shed_registry.url_auth(tool_shed_url),
-                                pathspec=pathspec,
-                                params=params
-                                )
+        response = util.url_get(
+            tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+        )
         json_response = json.loads(response)
-        valid_tools = json_response[1].get('valid_tools', [])
+        valid_tools = json_response[1].get("valid_tools", [])
         if valid_tools:
             tools.extend(valid_tools)
     return get_requirements_from_tools(tools)
 
 
 def get_requirements_from_tools(tools):
-    return {tool['id']: galaxy.tool_util.deps.requirements.ToolRequirements.from_list(tool['requirements']) for tool in tools}
+    return {
+        tool["id"]: galaxy.tool_util.deps.requirements.ToolRequirements.from_list(tool["requirements"])
+        for tool in tools
+    }
 
 
 def get_requirements_from_repository(repository):
     if not repository.includes_tools:
         return {}
     else:
-        return get_requirements_from_tools(repository.metadata_.get('tools', []))
+        return get_requirements_from_tools(repository.metadata_.get("tools", []))
 
 
 def get_repository_categories(app, id):
     """Get categories of a repository on the tool shed side from the database via id"""
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryCategoryAssociation) \
-        .filter(app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id))
+    return sa_session.query(app.model.RepositoryCategoryAssociation).filter(
+        app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id)
+    )
 
 
 def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
     """Return the display-safe contents of a repository file for display in a browser."""
-    safe_str = ''
+    safe_str = ""
     if not is_path_browsable(app, file_path, repository_id, is_admin):
-        log.warning('Request tries to access a file outside of the repository location. File path: %s', file_path)
-        return 'Invalid file path'
+        log.warning("Request tries to access a file outside of the repository location. File path: %s", file_path)
+        return "Invalid file path"
     # Symlink targets are checked by is_path_browsable
     if os.path.islink(file_path):
         safe_str = f"link to: {basic_util.to_html_string(os.readlink(file_path))}"
         return safe_str
     elif checkers.is_gzip(file_path):
-        return '<br/>gzip compressed file<br/>'
+        return "<br/>gzip compressed file<br/>"
     elif checkers.is_bz2(file_path):
-        return '<br/>bz2 compressed file<br/>'
+        return "<br/>bz2 compressed file<br/>"
     elif checkers.is_zip(file_path):
-        return '<br/>zip compressed file<br/>'
+        return "<br/>zip compressed file<br/>"
     elif checkers.check_binary(file_path):
-        return '<br/>Binary file<br/>'
+        return "<br/>Binary file<br/>"
     else:
         for line in open(file_path):
-            safe_str = f'{safe_str}{basic_util.to_html_string(line)}'
+            safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
             # Stop reading after string is larger than MAX_CONTENT_SIZE.
             if len(safe_str) > MAX_CONTENT_SIZE:
-                large_str = \
-                    '<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \
-                    util.nice_size(MAX_CONTENT_SIZE)
-                safe_str = f'{safe_str}{large_str}'
+                large_str = (
+                    "<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
+                    % util.nice_size(MAX_CONTENT_SIZE)
+                )
+                safe_str = f"{safe_str}{large_str}"
                 break
 
         if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
             # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
             # This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
-            join_by_str = \
-                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \
-                util.nice_size(basic_util.MAX_DISPLAY_SIZE)
-            safe_str = util.shrink_string_by_size(safe_str,
-                                                  basic_util.MAX_DISPLAY_SIZE,
-                                                  join_by=join_by_str,
-                                                  left_larger=True,
-                                                  beginning_on_size_error=True)
+            join_by_str = (
+                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>"
+                % util.nice_size(basic_util.MAX_DISPLAY_SIZE)
+            )
+            safe_str = util.shrink_string_by_size(
+                safe_str,
+                basic_util.MAX_DISPLAY_SIZE,
+                join_by=join_by_str,
+                left_larger=True,
+                beginning_on_size_error=True,
+            )
         return safe_str
 
 
@@ -233,7 +246,7 @@ def get_repository_files(folder_path):
     contents = []
     for item in os.listdir(folder_path):
         # Skip .hg directories
-        if item.startswith('.hg'):
+        if item.startswith(".hg"):
             continue
         contents.append(item)
     if contents:
@@ -249,7 +262,7 @@ def get_repository_from_refresh_on_change(app, **kwd):
     repository_id = None
     v = None
     for k, v in kwd.items():
-        changeset_revision_str = 'changeset_revision_'
+        changeset_revision_str = "changeset_revision_"
         if k.startswith(changeset_revision_str):
             repository_id = app.security.encode_id(int(k.lstrip(changeset_revision_str)))
             repository = repository_util.get_repository_in_tool_shed(app, repository_id)
@@ -266,8 +279,10 @@ def get_repository_type_from_tool_shed(app, tool_shed_url, name, owner):
     """
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
     params = dict(name=name, owner=owner)
-    pathspec = ['repository', 'get_repository_type']
-    repository_type = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+    pathspec = ["repository", "get_repository_type"]
+    repository_type = util.url_get(
+        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+    )
     return repository_type
 
 
@@ -279,8 +294,10 @@ def get_tool_dependency_definition_metadata_from_tool_shed(app, tool_shed_url, n
     """
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
     params = dict(name=name, owner=owner)
-    pathspec = ['repository', 'get_tool_dependency_definition_metadata']
-    metadata = util.url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
+    pathspec = ["repository", "get_tool_dependency_definition_metadata"]
+    metadata = util.url_get(
+        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
+    )
     return metadata
 
 
@@ -290,17 +307,17 @@ def get_tool_path_by_shed_tool_conf_filename(app, shed_tool_conf):
     dictionary whose config_filename key has a value matching the received shed_tool_conf.
     """
     for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
-        config_filename = shed_tool_conf_dict['config_filename']
+        config_filename = shed_tool_conf_dict["config_filename"]
         if config_filename == shed_tool_conf:
-            return shed_tool_conf_dict['tool_path']
+            return shed_tool_conf_dict["tool_path"]
         else:
             file_name = basic_util.strip_path(config_filename)
             if file_name == shed_tool_conf:
-                return shed_tool_conf_dict['tool_path']
+                return shed_tool_conf_dict["tool_path"]
     return None
 
 
-def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_alert=False, admin_only=False):
+def handle_email_alerts(app, host, repository, content_alert_str="", new_repo_alert=False, admin_only=False):
     """
     There are 2 complementary features that enable a tool shed user to receive email notification:
 
@@ -328,13 +345,15 @@ def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_al
     """
     sa_session = app.model.session
     repo = repository.hg_repo
-    sharable_link = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=None)
+    sharable_link = repository_util.generate_sharable_link_for_repository_in_tool_shed(
+        repository, changeset_revision=None
+    )
     smtp_server = app.config.smtp_server
     if smtp_server and (new_repo_alert or repository.email_alerts):
         # Send email alert to users that want them.
         if app.config.email_from is not None:
             email_from = app.config.email_from
-        elif host.split(':')[0] in ['localhost', '127.0.0.1', '0.0.0.0']:
+        elif host.split(":")[0] in ["localhost", "127.0.0.1", "0.0.0.0"]:
             email_from = f"galaxy-no-reply@{socket.getfqdn()}"
         else:
             email_from = f"galaxy-no-reply@{host.split(':')[0]}"
@@ -352,32 +371,36 @@ def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_al
             template = email_alert_template
         display_date = hg_util.get_readable_ctx_date(ctx)
         description = unicodify(ctx.description())
-        revision = f'{ctx.rev()}:{ctx}'
-        admin_body = string.Template(template).safe_substitute(host=host,
-                                                               sharable_link=sharable_link,
-                                                               repository_name=repository.name,
-                                                               revision=revision,
-                                                               display_date=display_date,
-                                                               description=description,
-                                                               username=username,
-                                                               content_alert_str=content_alert_str)
-        body = string.Template(template).safe_substitute(host=host,
-                                                         sharable_link=sharable_link,
-                                                         repository_name=repository.name,
-                                                         revision=revision,
-                                                         display_date=display_date,
-                                                         description=description,
-                                                         username=username,
-                                                         content_alert_str='')
+        revision = f"{ctx.rev()}:{ctx}"
+        admin_body = string.Template(template).safe_substitute(
+            host=host,
+            sharable_link=sharable_link,
+            repository_name=repository.name,
+            revision=revision,
+            display_date=display_date,
+            description=description,
+            username=username,
+            content_alert_str=content_alert_str,
+        )
+        body = string.Template(template).safe_substitute(
+            host=host,
+            sharable_link=sharable_link,
+            repository_name=repository.name,
+            revision=revision,
+            display_date=display_date,
+            description=description,
+            username=username,
+            content_alert_str="",
+        )
         admin_users = app.config.get("admin_users", "").split(",")
         frm = email_from
         if new_repo_alert:
             subject = f"Galaxy tool shed alert for new repository named {str(repository.name)}"
             subject = subject[:80]
             email_alerts = []
-            for user in sa_session.query(app.model.User) \
-                                  .filter(and_(app.model.User.table.c.deleted == false(),
-                                               app.model.User.table.c.new_repo_alert == true())):
+            for user in sa_session.query(app.model.User).filter(
+                and_(app.model.User.table.c.deleted == false(), app.model.User.table.c.new_repo_alert == true())
+            ):
                 if admin_only:
                     if user.email in admin_users:
                         email_alerts.append(user.email)
@@ -416,7 +439,7 @@ def is_path_within_dependency_dir(app, path):
     """
     allowed = False
     resolved_path = os.path.realpath(path)
-    tool_dependency_dir = app.config.get('tool_dependency_dir', None)
+    tool_dependency_dir = app.config.get("tool_dependency_dir", None)
     if tool_dependency_dir:
         dependency_path = os.path.abspath(tool_dependency_dir)
         allowed = os.path.commonprefix([dependency_path, resolved_path]) == dependency_path
@@ -439,12 +462,12 @@ def open_repository_files_folder(app, folder_path, repository_id, is_admin=False
     within a directory in a repository file hierarchy.
     """
     if not is_path_browsable(app, folder_path, repository_id, is_admin):
-        log.warning('Request tries to access a folder outside of the allowed locations. Folder path: %s', folder_path)
+        log.warning("Request tries to access a folder outside of the allowed locations. Folder path: %s", folder_path)
         return []
     try:
         files_list = get_repository_files(folder_path)
     except OSError as e:
-        if str(e).find('No such file or directory') >= 0:
+        if str(e).find("No such file or directory") >= 0:
             # We have a repository with no contents.
             return []
     folder_contents = []
@@ -454,49 +477,53 @@ def open_repository_files_folder(app, folder_path, repository_id, is_admin=False
         is_link = os.path.islink(full_path)
         path_is_browsable = is_path_browsable(app, full_path, repository_id)
         if is_link and not path_is_browsable:
-            log.warning(f"Valid folder contains a symlink outside of the repository location. Link found in: {str(full_path)}")
+            log.warning(
+                f"Valid folder contains a symlink outside of the repository location. Link found in: {str(full_path)}"
+            )
         if filename:
             if os.path.isdir(full_path) and path_is_browsable:
                 # Append a '/' character so that our jquery dynatree will function properly.
-                filename = f'{filename}/'
-                full_path = f'{full_path}/'
+                filename = f"{filename}/"
+                full_path = f"{full_path}/"
                 is_folder = True
-            node = {"title": filename,
-                    "isFolder": is_folder,
-                    "isLazy": is_folder,
-                    "tooltip": full_path,
-                    "key": full_path}
+            node = {
+                "title": filename,
+                "isFolder": is_folder,
+                "isLazy": is_folder,
+                "tooltip": full_path,
+                "key": full_path,
+            }
             folder_contents.append(node)
     return folder_contents
 
 
 __all__ = (
-    'can_eliminate_repository_dependency',
-    'can_eliminate_tool_dependency',
-    'clean_dependency_relationships',
-    'count_repositories_in_category',
-    'generate_tool_guid',
-    'get_categories',
-    'get_category',
-    'get_category_by_name',
-    'get_requirements_from_tools',
-    'get_requirements_from_repository',
-    'get_tool_shed_repo_requirements',
-    'get_ctx_rev',
-    'get_next_prior_import_or_install_required_dict_entry',
-    'get_repository_categories',
-    'get_repository_file_contents',
-    'get_repository_type_from_tool_shed',
-    'get_tool_dependency_definition_metadata_from_tool_shed',
-    'get_tool_panel_config_tool_path_install_dir',
-    'get_tool_path_by_shed_tool_conf_filename',
-    'get_user',
-    'handle_email_alerts',
-    'have_shed_tool_conf_for_install',
-    'is_path_browsable',
-    'is_path_within_dependency_dir',
-    'is_path_within_repo',
-    'open_repository_files_folder',
-    'set_image_paths',
-    'tool_shed_is_this_tool_shed',
+    "can_eliminate_repository_dependency",
+    "can_eliminate_tool_dependency",
+    "clean_dependency_relationships",
+    "count_repositories_in_category",
+    "generate_tool_guid",
+    "get_categories",
+    "get_category",
+    "get_category_by_name",
+    "get_requirements_from_tools",
+    "get_requirements_from_repository",
+    "get_tool_shed_repo_requirements",
+    "get_ctx_rev",
+    "get_next_prior_import_or_install_required_dict_entry",
+    "get_repository_categories",
+    "get_repository_file_contents",
+    "get_repository_type_from_tool_shed",
+    "get_tool_dependency_definition_metadata_from_tool_shed",
+    "get_tool_panel_config_tool_path_install_dir",
+    "get_tool_path_by_shed_tool_conf_filename",
+    "get_user",
+    "handle_email_alerts",
+    "have_shed_tool_conf_for_install",
+    "is_path_browsable",
+    "is_path_within_dependency_dir",
+    "is_path_within_repo",
+    "open_repository_files_folder",
+    "set_image_paths",
+    "tool_shed_is_this_tool_shed",
 )
diff --git a/lib/tool_shed/util/web_util.py b/lib/tool_shed/util/web_util.py
index 0d5e2ac992f..b25e747ce2d 100644
--- a/lib/tool_shed/util/web_util.py
+++ b/lib/tool_shed/util/web_util.py
@@ -5,7 +5,7 @@ ALLOWED_MAP = {x: raw_escape(x) for x in ALLOWED_ELEMENTS}
 
 
 def escape(string):
-    """ A tool shed variant of markupsafe.escape that allows a select few
+    """A tool shed variant of markupsafe.escape that allows a select few
     HTML elements that are repeatedly used in messages created deep
     in the toolshed components. Ideally abstract things would be produced
     in these components and messages in the views or client side - this is
diff --git a/lib/tool_shed/utility_containers/__init__.py b/lib/tool_shed/utility_containers/__init__.py
index 13327535656..79482e27fab 100644
--- a/lib/tool_shed/utility_containers/__init__.py
+++ b/lib/tool_shed/utility_containers/__init__.py
@@ -5,7 +5,7 @@ from galaxy import util
 from tool_shed.util import (
     common_util,
     container_util,
-    readme_util
+    readme_util,
 )
 from . import utility_container_manager
 
@@ -27,8 +27,17 @@ class FailedTest:
 class InvalidRepositoryDependency:
     """Invalid repository dependency definition object"""
 
-    def __init__(self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None,
-                 prior_installation_required=False, only_if_compiling_contained_td=False, error=None):
+    def __init__(
+        self,
+        id=None,
+        toolshed=None,
+        repository_name=None,
+        repository_owner=None,
+        changeset_revision=None,
+        prior_installation_required=False,
+        only_if_compiling_contained_td=False,
+        error=None,
+    ):
         self.id = id
         self.toolshed = toolshed
         self.repository_name = repository_name
@@ -125,53 +134,61 @@ class ToolDependencySuccessfulInstallation:
 
 
 class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainerManager):
-
     def __init__(self, app):
         self.app = app
 
     def build_invalid_repository_dependencies_root_folder(self, folder_id, invalid_repository_dependencies_dict):
         """Return a folder hierarchy containing invalid repository dependencies."""
-        label = 'Invalid repository dependencies'
+        label = "Invalid repository dependencies"
         if invalid_repository_dependencies_dict:
             invalid_repository_dependency_id = 0
             folder_id += 1
-            invalid_repository_dependencies_root_folder = \
-                utility_container_manager.Folder(id=folder_id,
-                                                 key='root',
-                                                 label='root',
-                                                 parent=None)
+            invalid_repository_dependencies_root_folder = utility_container_manager.Folder(
+                id=folder_id, key="root", label="root", parent=None
+            )
             folder_id += 1
-            invalid_repository_dependencies_folder = \
-                utility_container_manager.Folder(id=folder_id,
-                                                 key='invalid_repository_dependencies',
-                                                 label=label,
-                                                 parent=invalid_repository_dependencies_root_folder)
+            invalid_repository_dependencies_folder = utility_container_manager.Folder(
+                id=folder_id,
+                key="invalid_repository_dependencies",
+                label=label,
+                parent=invalid_repository_dependencies_root_folder,
+            )
             invalid_repository_dependencies_root_folder.folders.append(invalid_repository_dependencies_folder)
-            invalid_repository_dependencies = invalid_repository_dependencies_dict['repository_dependencies']
+            invalid_repository_dependencies = invalid_repository_dependencies_dict["repository_dependencies"]
             for invalid_repository_dependency in invalid_repository_dependencies:
                 folder_id += 1
                 invalid_repository_dependency_id += 1
-                toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
-                    common_util.parse_repository_dependency_tuple(invalid_repository_dependency, contains_error=True)
-                key = container_util.generate_repository_dependencies_key_for_repository(toolshed,
-                                                                                         name,
-                                                                                         owner,
-                                                                                         changeset_revision,
-                                                                                         prior_installation_required,
-                                                                                         only_if_compiling_contained_td)
+                (
+                    toolshed,
+                    name,
+                    owner,
+                    changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                    error,
+                ) = common_util.parse_repository_dependency_tuple(invalid_repository_dependency, contains_error=True)
+                key = container_util.generate_repository_dependencies_key_for_repository(
+                    toolshed,
+                    name,
+                    owner,
+                    changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                )
                 label = f"Repository <b>{name}</b> revision <b>{changeset_revision}</b> owned by <b>{owner}</b>"
-                folder = utility_container_manager.Folder(id=folder_id,
-                                                          key=key,
-                                                          label=label,
-                                                          parent=invalid_repository_dependencies_folder)
-                ird = InvalidRepositoryDependency(id=invalid_repository_dependency_id,
-                                                  toolshed=toolshed,
-                                                  repository_name=name,
-                                                  repository_owner=owner,
-                                                  changeset_revision=changeset_revision,
-                                                  prior_installation_required=util.asbool(prior_installation_required),
-                                                  only_if_compiling_contained_td=util.asbool(only_if_compiling_contained_td),
-                                                  error=error)
+                folder = utility_container_manager.Folder(
+                    id=folder_id, key=key, label=label, parent=invalid_repository_dependencies_folder
+                )
+                ird = InvalidRepositoryDependency(
+                    id=invalid_repository_dependency_id,
+                    toolshed=toolshed,
+                    repository_name=name,
+                    repository_owner=owner,
+                    changeset_revision=changeset_revision,
+                    prior_installation_required=util.asbool(prior_installation_required),
+                    only_if_compiling_contained_td=util.asbool(only_if_compiling_contained_td),
+                    error=error,
+                )
                 folder.invalid_repository_dependencies.append(ird)
                 invalid_repository_dependencies_folder.folders.append(folder)
         else:
@@ -182,65 +199,64 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
         """Return a folder hierarchy containing invalid tool dependencies."""
         # # INvalid tool dependencies are always packages like:
         # {"R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1" "error" : "some sting" }
-        label = 'Invalid tool dependencies'
+        label = "Invalid tool dependencies"
         if invalid_tool_dependencies_dict:
             invalid_tool_dependency_id = 0
             folder_id += 1
-            invalid_tool_dependencies_root_folder = \
-                utility_container_manager.Folder(id=folder_id, key='root', label='root', parent=None)
+            invalid_tool_dependencies_root_folder = utility_container_manager.Folder(
+                id=folder_id, key="root", label="root", parent=None
+            )
             folder_id += 1
-            invalid_tool_dependencies_folder = \
-                utility_container_manager.Folder(id=folder_id,
-                                                 key='invalid_tool_dependencies',
-                                                 label=label,
-                                                 parent=invalid_tool_dependencies_root_folder)
+            invalid_tool_dependencies_folder = utility_container_manager.Folder(
+                id=folder_id, key="invalid_tool_dependencies", label=label, parent=invalid_tool_dependencies_root_folder
+            )
             invalid_tool_dependencies_root_folder.folders.append(invalid_tool_dependencies_folder)
             for requirements_dict in invalid_tool_dependencies_dict.values():
                 folder_id += 1
                 invalid_tool_dependency_id += 1
                 try:
-                    name = requirements_dict['name']
-                    type = requirements_dict['type']
-                    version = requirements_dict['version']
-                    error = requirements_dict['error']
+                    name = requirements_dict["name"]
+                    type = requirements_dict["type"]
+                    version = requirements_dict["version"]
+                    error = requirements_dict["error"]
                 except Exception as e:
-                    name = 'unknown'
-                    type = 'unknown'
-                    version = 'unknown'
+                    name = "unknown"
+                    type = "unknown"
+                    version = "unknown"
                     error = str(e)
                 key = self.generate_tool_dependencies_key(name, version, type)
                 label = f"Version <b>{version}</b> of the <b>{name}</b> <b>{type}</b>"
-                folder = utility_container_manager.Folder(id=folder_id,
-                                                          key=key,
-                                                          label=label,
-                                                          parent=invalid_tool_dependencies_folder)
-                itd = InvalidToolDependency(id=invalid_tool_dependency_id,
-                                            name=name,
-                                            version=version,
-                                            type=type,
-                                            error=error)
+                folder = utility_container_manager.Folder(
+                    id=folder_id, key=key, label=label, parent=invalid_tool_dependencies_folder
+                )
+                itd = InvalidToolDependency(
+                    id=invalid_tool_dependency_id, name=name, version=version, type=type, error=error
+                )
                 folder.invalid_tool_dependencies.append(itd)
                 invalid_tool_dependencies_folder.folders.append(folder)
         else:
             invalid_tool_dependencies_root_folder = None
         return folder_id, invalid_tool_dependencies_root_folder
 
-    def build_repository_containers(self, repository, changeset_revision, repository_dependencies, repository_metadata,
-                                    exclude=None):
+    def build_repository_containers(
+        self, repository, changeset_revision, repository_dependencies, repository_metadata, exclude=None
+    ):
         """
         Return a dictionary of containers for the received repository's dependencies and
         contents for display in the Tool Shed.
         """
         if exclude is None:
             exclude = []
-        containers_dict = dict(datatypes=None,
-                               invalid_tools=None,
-                               readme_files=None,
-                               repository_dependencies=None,
-                               tool_dependencies=None,
-                               valid_tools=None,
-                               workflows=None,
-                               valid_data_managers=None)
+        containers_dict = dict(
+            datatypes=None,
+            invalid_tools=None,
+            readme_files=None,
+            repository_dependencies=None,
+            tool_dependencies=None,
+            valid_tools=None,
+            workflows=None,
+            valid_data_managers=None,
+        )
         if repository_metadata:
             metadata = repository_metadata.metadata
             lock = threading.Lock()
@@ -249,107 +265,116 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
                 folder_id = 0
                 # Datatypes container.
                 if metadata:
-                    if 'datatypes' not in exclude and 'datatypes' in metadata:
-                        datatypes = metadata['datatypes']
+                    if "datatypes" not in exclude and "datatypes" in metadata:
+                        datatypes = metadata["datatypes"]
                         folder_id, datatypes_root_folder = self.build_datatypes_folder(folder_id, datatypes)
-                        containers_dict['datatypes'] = datatypes_root_folder
+                        containers_dict["datatypes"] = datatypes_root_folder
                 # Invalid repository dependencies container.
                 if metadata:
-                    if 'invalid_repository_dependencies' not in exclude and 'invalid_repository_dependencies' in metadata:
-                        invalid_repository_dependencies = metadata['invalid_repository_dependencies']
-                        folder_id, invalid_repository_dependencies_root_folder = \
-                            self.build_invalid_repository_dependencies_root_folder(folder_id,
-                                                                                   invalid_repository_dependencies)
-                        containers_dict['invalid_repository_dependencies'] = invalid_repository_dependencies_root_folder
+                    if (
+                        "invalid_repository_dependencies" not in exclude
+                        and "invalid_repository_dependencies" in metadata
+                    ):
+                        invalid_repository_dependencies = metadata["invalid_repository_dependencies"]
+                        (
+                            folder_id,
+                            invalid_repository_dependencies_root_folder,
+                        ) = self.build_invalid_repository_dependencies_root_folder(
+                            folder_id, invalid_repository_dependencies
+                        )
+                        containers_dict["invalid_repository_dependencies"] = invalid_repository_dependencies_root_folder
                 # Invalid tool dependencies container.
                 if metadata:
-                    if 'invalid_tool_dependencies' not in exclude and 'invalid_tool_dependencies' in metadata:
-                        invalid_tool_dependencies = metadata['invalid_tool_dependencies']
-                        folder_id, invalid_tool_dependencies_root_folder = \
-                            self.build_invalid_tool_dependencies_root_folder(folder_id,
-                                                                             invalid_tool_dependencies)
-                        containers_dict['invalid_tool_dependencies'] = invalid_tool_dependencies_root_folder
+                    if "invalid_tool_dependencies" not in exclude and "invalid_tool_dependencies" in metadata:
+                        invalid_tool_dependencies = metadata["invalid_tool_dependencies"]
+                        (
+                            folder_id,
+                            invalid_tool_dependencies_root_folder,
+                        ) = self.build_invalid_tool_dependencies_root_folder(folder_id, invalid_tool_dependencies)
+                        containers_dict["invalid_tool_dependencies"] = invalid_tool_dependencies_root_folder
                 # Invalid tools container.
                 if metadata:
-                    if 'invalid_tools' not in exclude and 'invalid_tools' in metadata:
-                        invalid_tool_configs = metadata['invalid_tools']
-                        folder_id, invalid_tools_root_folder = \
-                            self.build_invalid_tools_folder(folder_id,
-                                                            invalid_tool_configs,
-                                                            changeset_revision,
-                                                            repository=repository,
-                                                            label='Invalid tools')
-                        containers_dict['invalid_tools'] = invalid_tools_root_folder
+                    if "invalid_tools" not in exclude and "invalid_tools" in metadata:
+                        invalid_tool_configs = metadata["invalid_tools"]
+                        folder_id, invalid_tools_root_folder = self.build_invalid_tools_folder(
+                            folder_id,
+                            invalid_tool_configs,
+                            changeset_revision,
+                            repository=repository,
+                            label="Invalid tools",
+                        )
+                        containers_dict["invalid_tools"] = invalid_tools_root_folder
                 # Readme files container.
                 if metadata:
-                    if 'readme_files' not in exclude and 'readme_files' in metadata:
-                        readme_files_dict = readme_util.build_readme_files_dict(self.app, repository, changeset_revision, metadata)
-                        folder_id, readme_files_root_folder = self.build_readme_files_folder(folder_id, readme_files_dict)
-                        containers_dict['readme_files'] = readme_files_root_folder
-                if 'repository_dependencies' not in exclude:
+                    if "readme_files" not in exclude and "readme_files" in metadata:
+                        readme_files_dict = readme_util.build_readme_files_dict(
+                            self.app, repository, changeset_revision, metadata
+                        )
+                        folder_id, readme_files_root_folder = self.build_readme_files_folder(
+                            folder_id, readme_files_dict
+                        )
+                        containers_dict["readme_files"] = readme_files_root_folder
+                if "repository_dependencies" not in exclude:
                     # Repository dependencies container.
-                    folder_id, repository_dependencies_root_folder = \
-                        self.build_repository_dependencies_folder(folder_id=folder_id,
-                                                                  repository_dependencies=repository_dependencies,
-                                                                  label='Repository dependencies',
-                                                                  installed=False)
+                    folder_id, repository_dependencies_root_folder = self.build_repository_dependencies_folder(
+                        folder_id=folder_id,
+                        repository_dependencies=repository_dependencies,
+                        label="Repository dependencies",
+                        installed=False,
+                    )
                     if repository_dependencies_root_folder:
-                        containers_dict['repository_dependencies'] = repository_dependencies_root_folder
+                        containers_dict["repository_dependencies"] = repository_dependencies_root_folder
                 # Tool dependencies container.
                 if metadata:
-                    if 'tool_dependencies' not in exclude and 'tool_dependencies' in metadata:
-                        tool_dependencies = metadata['tool_dependencies']
-                        if 'orphan_tool_dependencies' in metadata:
+                    if "tool_dependencies" not in exclude and "tool_dependencies" in metadata:
+                        tool_dependencies = metadata["tool_dependencies"]
+                        if "orphan_tool_dependencies" in metadata:
                             # The use of the orphan_tool_dependencies category in metadata has been deprecated,
                             # but we still need to check in case the metadata is out of date.
-                            orphan_tool_dependencies = metadata['orphan_tool_dependencies']
+                            orphan_tool_dependencies = metadata["orphan_tool_dependencies"]
                             tool_dependencies.update(orphan_tool_dependencies)
                         # Tool dependencies can be categorized as orphans only if the repository contains tools.
-                        if 'tools' not in exclude:
-                            tools = metadata.get('tools', [])
-                            tools.extend(metadata.get('invalid_tools', []))
-                        folder_id, tool_dependencies_root_folder = \
-                            self.build_tool_dependencies_folder(folder_id,
-                                                                tool_dependencies,
-                                                                missing=False,
-                                                                new_install=False)
-                        containers_dict['tool_dependencies'] = tool_dependencies_root_folder
+                        if "tools" not in exclude:
+                            tools = metadata.get("tools", [])
+                            tools.extend(metadata.get("invalid_tools", []))
+                        folder_id, tool_dependencies_root_folder = self.build_tool_dependencies_folder(
+                            folder_id, tool_dependencies, missing=False, new_install=False
+                        )
+                        containers_dict["tool_dependencies"] = tool_dependencies_root_folder
                 # Valid tools container.
                 if metadata:
-                    if 'tools' not in exclude and 'tools' in metadata:
-                        valid_tools = metadata['tools']
-                        folder_id, valid_tools_root_folder = self.build_tools_folder(folder_id,
-                                                                                     valid_tools,
-                                                                                     repository,
-                                                                                     changeset_revision,
-                                                                                     label='Valid tools')
-                        containers_dict['valid_tools'] = valid_tools_root_folder
+                    if "tools" not in exclude and "tools" in metadata:
+                        valid_tools = metadata["tools"]
+                        folder_id, valid_tools_root_folder = self.build_tools_folder(
+                            folder_id, valid_tools, repository, changeset_revision, label="Valid tools"
+                        )
+                        containers_dict["valid_tools"] = valid_tools_root_folder
                 # Workflows container.
                 if metadata:
-                    if 'workflows' not in exclude and 'workflows' in metadata:
-                        workflows = metadata['workflows']
-                        folder_id, workflows_root_folder = \
-                            self.build_workflows_folder(folder_id=folder_id,
-                                                        workflows=workflows,
-                                                        repository_metadata_id=repository_metadata.id,
-                                                        repository_id=None,
-                                                        label='Workflows')
-                        containers_dict['workflows'] = workflows_root_folder
+                    if "workflows" not in exclude and "workflows" in metadata:
+                        workflows = metadata["workflows"]
+                        folder_id, workflows_root_folder = self.build_workflows_folder(
+                            folder_id=folder_id,
+                            workflows=workflows,
+                            repository_metadata_id=repository_metadata.id,
+                            repository_id=None,
+                            label="Workflows",
+                        )
+                        containers_dict["workflows"] = workflows_root_folder
                 # Valid Data Managers container
                 if metadata:
-                    if 'data_manager' not in exclude and 'data_manager' in metadata:
-                        data_managers = metadata['data_manager'].get('data_managers', None)
-                        folder_id, data_managers_root_folder = \
-                            self.build_data_managers_folder(folder_id, data_managers, label="Data Managers")
-                        containers_dict['valid_data_managers'] = data_managers_root_folder
-                        error_messages = metadata['data_manager'].get('error_messages', None)
-                        data_managers = metadata['data_manager'].get('invalid_data_managers', None)
-                        folder_id, data_managers_root_folder = \
-                            self.build_invalid_data_managers_folder(folder_id,
-                                                                    data_managers,
-                                                                    error_messages,
-                                                                    label="Invalid Data Managers")
-                        containers_dict['invalid_data_managers'] = data_managers_root_folder
+                    if "data_manager" not in exclude and "data_manager" in metadata:
+                        data_managers = metadata["data_manager"].get("data_managers", None)
+                        folder_id, data_managers_root_folder = self.build_data_managers_folder(
+                            folder_id, data_managers, label="Data Managers"
+                        )
+                        containers_dict["valid_data_managers"] = data_managers_root_folder
+                        error_messages = metadata["data_manager"].get("error_messages", None)
+                        data_managers = metadata["data_manager"].get("invalid_data_managers", None)
+                        folder_id, data_managers_root_folder = self.build_invalid_data_managers_folder(
+                            folder_id, data_managers, error_messages, label="Invalid Data Managers"
+                        )
+                        containers_dict["invalid_data_managers"] = data_managers_root_folder
             except Exception:
                 log.exception("Exception in build_repository_containers")
             finally:
@@ -357,4 +382,4 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
         return containers_dict
 
     def generate_tool_dependencies_key(self, name, version, type):
-        return f'{str(name)}{container_util.STRSEP}{str(version)}{container_util.STRSEP}{str(type)}'
+        return f"{str(name)}{container_util.STRSEP}{str(version)}{container_util.STRSEP}{str(type)}"
diff --git a/lib/tool_shed/utility_containers/utility_container_manager.py b/lib/tool_shed/utility_containers/utility_container_manager.py
index df0a75c52f9..5db3f1294b0 100644
--- a/lib/tool_shed/utility_containers/utility_container_manager.py
+++ b/lib/tool_shed/utility_containers/utility_container_manager.py
@@ -1,9 +1,11 @@
 import logging
 
 from galaxy import util
-from tool_shed.util import common_util
-from tool_shed.util import container_util
-from tool_shed.util import repository_util
+from tool_shed.util import (
+    common_util,
+    container_util,
+    repository_util,
+)
 
 log = logging.getLogger(__name__)
 
@@ -69,7 +71,16 @@ class DataManager:
 class Datatype:
     """Datatype object"""
 
-    def __init__(self, id=None, extension=None, type=None, mimetype=None, subclass=None, converters=None, display_app_containers=None):
+    def __init__(
+        self,
+        id=None,
+        extension=None,
+        type=None,
+        mimetype=None,
+        subclass=None,
+        converters=None,
+        display_app_containers=None,
+    ):
         self.id = id
         self.extension = extension
         self.type = type
@@ -91,7 +102,14 @@ class InvalidDataManager:
 class InvalidTool:
     """Invalid tool object"""
 
-    def __init__(self, id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None):
+    def __init__(
+        self,
+        id=None,
+        tool_config=None,
+        repository_id=None,
+        changeset_revision=None,
+        repository_installation_status=None,
+    ):
         self.id = id
         self.tool_config = tool_config
         self.repository_id = repository_id
@@ -111,8 +129,18 @@ class ReadMe:
 class RepositoryDependency:
     """Repository dependency object"""
 
-    def __init__(self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False,
-                 only_if_compiling_contained_td=False, installation_status=None, tool_shed_repository_id=None):
+    def __init__(
+        self,
+        id=None,
+        toolshed=None,
+        repository_name=None,
+        repository_owner=None,
+        changeset_revision=None,
+        prior_installation_required=False,
+        only_if_compiling_contained_td=False,
+        installation_status=None,
+        tool_shed_repository_id=None,
+    ):
         self.id = id
         self.toolshed = toolshed
         self.repository_name = repository_name
@@ -125,19 +153,33 @@ class RepositoryDependency:
 
     @property
     def listify(self):
-        return [self.toolshed,
-                self.repository_name,
-                self.repository_owner,
-                self.changeset_revision,
-                self.prior_installation_required,
-                self.only_if_compiling_contained_td]
+        return [
+            self.toolshed,
+            self.repository_name,
+            self.repository_owner,
+            self.changeset_revision,
+            self.prior_installation_required,
+            self.only_if_compiling_contained_td,
+        ]
 
 
 class Tool:
     """Tool object"""
 
-    def __init__(self, id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, profile=None, requirements=None,
-                 repository_id=None, changeset_revision=None, repository_installation_status=None):
+    def __init__(
+        self,
+        id=None,
+        tool_config=None,
+        tool_id=None,
+        name=None,
+        description=None,
+        version=None,
+        profile=None,
+        requirements=None,
+        repository_id=None,
+        changeset_revision=None,
+        repository_installation_status=None,
+    ):
         self.id = id
         self.tool_config = tool_config
         self.tool_id = tool_id
@@ -154,8 +196,17 @@ class Tool:
 class ToolDependency:
     """Tool dependency object"""
 
-    def __init__(self, id=None, name=None, version=None, type=None, readme=None, installation_status=None, repository_id=None,
-                 tool_dependency_id=None):
+    def __init__(
+        self,
+        id=None,
+        name=None,
+        version=None,
+        type=None,
+        readme=None,
+        installation_status=None,
+        repository_id=None,
+        tool_dependency_id=None,
+    ):
         self.id = id
         self.name = name
         self.version = version
@@ -173,8 +224,16 @@ class ToolDependency:
 class Workflow:
     """Workflow object."""
 
-    def __init__(self, id=None, workflow_name=None, steps=None, format_version=None, annotation=None,
-                 repository_metadata_id=None, repository_id=None):
+    def __init__(
+        self,
+        id=None,
+        workflow_name=None,
+        steps=None,
+        format_version=None,
+        annotation=None,
+        repository_metadata_id=None,
+        repository_id=None,
+    ):
         """
         When rendered in the tool shed, repository_metadata_id will have a value and repository_id will
         be None.  When rendered in Galaxy, repository_id will have a value and repository_metadata_id will
@@ -190,7 +249,6 @@ class Workflow:
 
 
 class UtilityContainerManager:
-
     def __init__(self, app):
         self.app = app
 
@@ -201,53 +259,45 @@ class UtilityContainerManager:
                 label = "Data Managers"
             data_manager_id = 0
             folder_id += 1
-            data_managers_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            data_managers_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
             key = "valid_data_managers"
             folder = Folder(id=folder_id, key=key, label=label, parent=data_managers_root_folder)
             data_managers_root_folder.folders.append(folder)
             # Insert a header row.
             data_manager_id += 1
-            data_manager = DataManager(id=data_manager_id,
-                                       name='Name',
-                                       version='Version',
-                                       data_tables='Data Tables')
+            data_manager = DataManager(id=data_manager_id, name="Name", version="Version", data_tables="Data Tables")
             folder.valid_data_managers.append(data_manager)
             for data_manager_dict in data_managers.values():
                 data_manager_id += 1
                 try:
-                    name = data_manager_dict.get('name', '')
-                    version = data_manager_dict.get('version', '')
-                    data_tables = ", ".join(data_manager_dict.get('data_tables', ''))
+                    name = data_manager_dict.get("name", "")
+                    version = data_manager_dict.get("version", "")
+                    data_tables = ", ".join(data_manager_dict.get("data_tables", ""))
                 except Exception as e:
                     name = str(e)
-                    version = 'unknown'
-                    data_tables = 'unknown'
-                data_manager = DataManager(id=data_manager_id,
-                                           name=name,
-                                           version=version,
-                                           data_tables=data_tables)
+                    version = "unknown"
+                    data_tables = "unknown"
+                data_manager = DataManager(id=data_manager_id, name=name, version=version, data_tables=data_tables)
                 folder.valid_data_managers.append(data_manager)
         else:
             data_managers_root_folder = None
         return folder_id, data_managers_root_folder
 
-    def build_datatypes_folder(self, folder_id, datatypes, label='Datatypes'):
+    def build_datatypes_folder(self, folder_id, datatypes, label="Datatypes"):
         """Return a folder hierarchy containing datatypes."""
         if datatypes:
             datatype_id = 0
             folder_id += 1
-            datatypes_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            datatypes_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
-            folder = Folder(id=folder_id, key='datatypes', label=label, parent=datatypes_root_folder)
+            folder = Folder(id=folder_id, key="datatypes", label=label, parent=datatypes_root_folder)
             datatypes_root_folder.folders.append(folder)
             # Insert a header row.
             datatype_id += 1
-            datatype = Datatype(id=datatype_id,
-                                extension='extension',
-                                type='type',
-                                mimetype='mimetype',
-                                subclass='subclass')
+            datatype = Datatype(
+                id=datatype_id, extension="extension", type="type", mimetype="mimetype", subclass="subclass"
+            )
             folder.datatypes.append(datatype)
             for datatypes_dict in datatypes:
                 # {"converters":
@@ -259,39 +309,41 @@ class UtilityContainerManager:
                 # "extension": "bed"}
                 # TODO: converters and display_app information is not currently rendered.  Should it be?
                 # Handle defined converters, if any.
-                converters = datatypes_dict.get('converters', None)
+                converters = datatypes_dict.get("converters", None)
                 if converters:
                     num_converters = len(converters)
                 else:
                     num_converters = 0
                 # Handle defined display applications, if any.
-                display_app_containers = datatypes_dict.get('display_app_containers', None)
+                display_app_containers = datatypes_dict.get("display_app_containers", None)
                 if display_app_containers:
                     num_display_app_containers = len(display_app_containers)
                 else:
                     num_display_app_containers = 0
                 datatype_id += 1
                 try:
-                    extension = datatypes_dict.get('extension', '')
-                    type = datatypes_dict.get('dtype', '')
-                    mimetype = datatypes_dict.get('mimetype', '')
-                    subclass = datatypes_dict.get('subclass', '')
+                    extension = datatypes_dict.get("extension", "")
+                    type = datatypes_dict.get("dtype", "")
+                    mimetype = datatypes_dict.get("mimetype", "")
+                    subclass = datatypes_dict.get("subclass", "")
                     converters = num_converters
                     display_app_containers = num_display_app_containers
                 except Exception as e:
                     extension = str(e)
-                    type = 'unknown'
-                    mimetype = 'unknown'
-                    subclass = 'unknown'
-                    converters = 'unknown'
-                    display_app_containers = 'unknown'
-                datatype = Datatype(id=datatype_id,
-                                    extension=extension,
-                                    type=type,
-                                    mimetype=mimetype,
-                                    subclass=subclass,
-                                    converters=converters,
-                                    display_app_containers=display_app_containers)
+                    type = "unknown"
+                    mimetype = "unknown"
+                    subclass = "unknown"
+                    converters = "unknown"
+                    display_app_containers = "unknown"
+                datatype = Datatype(
+                    id=datatype_id,
+                    extension=extension,
+                    type=type,
+                    mimetype=mimetype,
+                    subclass=subclass,
+                    converters=converters,
+                    display_app_containers=display_app_containers,
+                )
                 folder.datatypes.append(datatype)
         else:
             datatypes_root_folder = None
@@ -304,75 +356,76 @@ class UtilityContainerManager:
                 label = "Invalid Data Managers"
             data_manager_id = 0
             folder_id += 1
-            data_managers_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            data_managers_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
             key = "invalid_data_managers"
             folder = Folder(id=folder_id, key=key, label=label, parent=data_managers_root_folder)
             data_managers_root_folder.folders.append(folder)
             # Insert a header row.
             data_manager_id += 1
-            data_manager = InvalidDataManager(id=data_manager_id,
-                                              index='Element Index',
-                                              error='Error')
+            data_manager = InvalidDataManager(id=data_manager_id, index="Element Index", error="Error")
             folder.invalid_data_managers.append(data_manager)
             if error_messages:
                 for error_message in error_messages:
                     data_manager_id += 1
-                    data_manager = InvalidDataManager(id=data_manager_id,
-                                                      index=0,
-                                                      error=error_message)
+                    data_manager = InvalidDataManager(id=data_manager_id, index=0, error=error_message)
                     folder.invalid_data_managers.append(data_manager)
             for data_manager_dict in data_managers:
                 data_manager_id += 1
-                data_manager = InvalidDataManager(id=data_manager_id,
-                                                  index=data_manager_dict.get('index', 0) + 1,
-                                                  error=data_manager_dict.get('error_message', ''))
+                data_manager = InvalidDataManager(
+                    id=data_manager_id,
+                    index=data_manager_dict.get("index", 0) + 1,
+                    error=data_manager_dict.get("error_message", ""),
+                )
                 folder.invalid_data_managers.append(data_manager)
         else:
             data_managers_root_folder = None
         return folder_id, data_managers_root_folder
 
-    def build_invalid_tools_folder(self, folder_id, invalid_tool_configs, changeset_revision, repository=None,
-                                   label='Invalid tools'):
+    def build_invalid_tools_folder(
+        self, folder_id, invalid_tool_configs, changeset_revision, repository=None, label="Invalid tools"
+    ):
         """Return a folder hierarchy containing invalid tools."""
         # TODO: Should we display invalid tools on the tool panel selection page when installing the
         # repository into Galaxy?
         if invalid_tool_configs:
             invalid_tool_id = 0
             folder_id += 1
-            invalid_tools_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            invalid_tools_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
-            folder = Folder(id=folder_id, key='invalid_tools', label=label, parent=invalid_tools_root_folder)
+            folder = Folder(id=folder_id, key="invalid_tools", label=label, parent=invalid_tools_root_folder)
             invalid_tools_root_folder.folders.append(folder)
             for invalid_tool_config in invalid_tool_configs:
                 invalid_tool_id += 1
                 if repository:
                     repository_id = repository.id
-                    if self.app.name == 'galaxy':
+                    if self.app.name == "galaxy":
                         repository_installation_status = repository.status
                     else:
                         repository_installation_status = None
                 else:
                     repository_id = None
                     repository_installation_status = None
-                invalid_tool = InvalidTool(id=invalid_tool_id,
-                                           tool_config=invalid_tool_config,
-                                           repository_id=repository_id,
-                                           changeset_revision=changeset_revision,
-                                           repository_installation_status=repository_installation_status)
+                invalid_tool = InvalidTool(
+                    id=invalid_tool_id,
+                    tool_config=invalid_tool_config,
+                    repository_id=repository_id,
+                    changeset_revision=changeset_revision,
+                    repository_installation_status=repository_installation_status,
+                )
                 folder.invalid_tools.append(invalid_tool)
         else:
             invalid_tools_root_folder = None
         return folder_id, invalid_tools_root_folder
 
-    def build_readme_files_folder(self, folder_id, readme_files_dict, label='Readme files'):
+    def build_readme_files_folder(self, folder_id, readme_files_dict, label="Readme files"):
         """Return a folder hierarchy containing readme text files."""
         if readme_files_dict:
             readme_id = 0
             folder_id += 1
-            readme_files_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            readme_files_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
-            readme_files_folder = Folder(id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder)
+            readme_files_folder = Folder(id=folder_id, key="readme_files", label=label, parent=readme_files_root_folder)
             multiple_readme_files = len(readme_files_dict) > 1
             readme_files_root_folder.folders.append(readme_files_folder)
             for readme_file_name, readme_file_text in readme_files_dict.items():
@@ -380,7 +433,9 @@ class UtilityContainerManager:
                 readme = ReadMe(id=readme_id, name=readme_file_name, text=readme_file_text)
                 if multiple_readme_files:
                     folder_id += 1
-                    folder = Folder(id=folder_id, key=readme_file_name, label=readme_file_name, parent=readme_files_folder)
+                    folder = Folder(
+                        id=folder_id, key=readme_file_name, label=readme_file_name, parent=readme_files_folder
+                    )
                     folder.readme_files.append(readme)
                     readme_files_folder.folders.append(folder)
                 else:
@@ -389,64 +444,73 @@ class UtilityContainerManager:
             readme_files_root_folder = None
         return folder_id, readme_files_root_folder
 
-    def build_repository_dependencies_folder(self, folder_id, repository_dependencies, label='Repository dependencies',
-                                             installed=False):
+    def build_repository_dependencies_folder(
+        self, folder_id, repository_dependencies, label="Repository dependencies", installed=False
+    ):
         """Return a folder hierarchy containing repository dependencies."""
         if repository_dependencies:
             repository_dependency_id = 0
             folder_id += 1
             # Create the root folder.
-            repository_dependencies_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            repository_dependencies_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
             # Create the Repository dependencies folder and add it to the root folder.
-            repository_dependencies_folder_key = repository_dependencies['root_key']
-            repository_dependencies_folder = Folder(id=folder_id,
-                                                    key=repository_dependencies_folder_key,
-                                                    label=label,
-                                                    parent=repository_dependencies_root_folder)
-            del repository_dependencies['root_key']
+            repository_dependencies_folder_key = repository_dependencies["root_key"]
+            repository_dependencies_folder = Folder(
+                id=folder_id,
+                key=repository_dependencies_folder_key,
+                label=label,
+                parent=repository_dependencies_root_folder,
+            )
+            del repository_dependencies["root_key"]
             # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more
             # repository_dependency keys.  We want the description value associated with the repository_dependencies_folder.
-            repository_dependencies_folder.description = repository_dependencies.get('description', None)
+            repository_dependencies_folder.description = repository_dependencies.get("description", None)
             repository_dependencies_root_folder.folders.append(repository_dependencies_folder)
-            del repository_dependencies['description']
-            repository_dependencies_folder, folder_id, repository_dependency_id = \
-                self.populate_repository_dependencies_container(repository_dependencies_folder,
-                                                                repository_dependencies,
-                                                                folder_id,
-                                                                repository_dependency_id)
+            del repository_dependencies["description"]
+            (
+                repository_dependencies_folder,
+                folder_id,
+                repository_dependency_id,
+            ) = self.populate_repository_dependencies_container(
+                repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id
+            )
             repository_dependencies_folder = self.prune_repository_dependencies(repository_dependencies_folder)
         else:
             repository_dependencies_root_folder = None
         return folder_id, repository_dependencies_root_folder
 
-    def build_tools_folder(self, folder_id, tool_dicts, repository, changeset_revision, valid=True, label='Valid tools'):
+    def build_tools_folder(
+        self, folder_id, tool_dicts, repository, changeset_revision, valid=True, label="Valid tools"
+    ):
         """Return a folder hierarchy containing valid tools."""
         if tool_dicts:
             container_object_tool_id = 0
             folder_id += 1
-            tools_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            tools_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
-            folder = Folder(id=folder_id, key='tools', label=label, parent=tools_root_folder)
-            if self.app.name == 'galaxy':
-                folder.description = 'click the name to inspect the tool metadata'
+            folder = Folder(id=folder_id, key="tools", label=label, parent=tools_root_folder)
+            if self.app.name == "galaxy":
+                folder.description = "click the name to inspect the tool metadata"
             tools_root_folder.folders.append(folder)
             # Insert a header row.
             container_object_tool_id += 1
-            tool = Tool(id=container_object_tool_id,
-                        tool_config='',
-                        tool_id='',
-                        name='Name',
-                        description='Description',
-                        version='Version',
-                        profile='Minimum Galaxy Version',
-                        requirements='',
-                        repository_id='',
-                        changeset_revision='')
+            tool = Tool(
+                id=container_object_tool_id,
+                tool_config="",
+                tool_id="",
+                name="Name",
+                description="Description",
+                version="Version",
+                profile="Minimum Galaxy Version",
+                requirements="",
+                repository_id="",
+                changeset_revision="",
+            )
             folder.valid_tools.append(tool)
             if repository:
                 repository_id = repository.id
-                if self.app.name == 'galaxy':
+                if self.app.name == "galaxy":
                     repository_installation_status = repository.status
                 else:
                     repository_installation_status = None
@@ -460,52 +524,61 @@ class UtilityContainerManager:
                     # list of supposedly valid tools:  'rgPicardASMetrics.xml', 'rgPicardGCBiasMetrics.xml'.
                     continue
                 container_object_tool_id += 1
-                requirements = tool_dict.get('requirements', None)
+                requirements = tool_dict.get("requirements", None)
                 if requirements is not None:
                     # 'requirements': [{'version': '1.56.0', 'type': 'package', 'name': 'picard'}],
-                    requirements_str = ''
+                    requirements_str = ""
                     for requirement_dict in requirements:
                         try:
-                            requirement_name = str(requirement_dict.get('name', 'unknown'))
-                            requirement_type = str(requirement_dict.get('type', 'unknown'))
+                            requirement_name = str(requirement_dict.get("name", "unknown"))
+                            requirement_type = str(requirement_dict.get("type", "unknown"))
                         except Exception as e:
                             requirement_name = str(e)
-                            requirement_type = 'unknown'
-                        requirements_str += f'{requirement_name} ({requirement_type}), '
-                    requirements_str = requirements_str.rstrip(', ')
+                            requirement_type = "unknown"
+                        requirements_str += f"{requirement_name} ({requirement_type}), "
+                    requirements_str = requirements_str.rstrip(", ")
                 else:
-                    requirements_str = 'none'
+                    requirements_str = "none"
                 try:
-                    tool_config = str(tool_dict.get('tool_config', 'missing'))
-                    tool_id = str(tool_dict.get('id', 'unknown'))
-                    name = str(tool_dict.get('name', 'unknown'))
-                    description = str(tool_dict.get('description', ''))
-                    version = str(tool_dict.get('version', 'unknown'))
-                    profile = str(tool_dict.get('profile', 'any'))
+                    tool_config = str(tool_dict.get("tool_config", "missing"))
+                    tool_id = str(tool_dict.get("id", "unknown"))
+                    name = str(tool_dict.get("name", "unknown"))
+                    description = str(tool_dict.get("description", ""))
+                    version = str(tool_dict.get("version", "unknown"))
+                    profile = str(tool_dict.get("profile", "any"))
                 except Exception as e:
                     tool_config = str(e)
-                    tool_id = 'unknown'
-                    name = 'unknown'
-                    description = ''
-                    version = 'unknown'
-                tool = Tool(id=container_object_tool_id,
-                            tool_config=tool_config,
-                            tool_id=tool_id,
-                            name=name,
-                            description=description,
-                            version=version,
-                            profile=profile,
-                            requirements=requirements_str,
-                            repository_id=repository_id,
-                            changeset_revision=changeset_revision,
-                            repository_installation_status=repository_installation_status)
+                    tool_id = "unknown"
+                    name = "unknown"
+                    description = ""
+                    version = "unknown"
+                tool = Tool(
+                    id=container_object_tool_id,
+                    tool_config=tool_config,
+                    tool_id=tool_id,
+                    name=name,
+                    description=description,
+                    version=version,
+                    profile=profile,
+                    requirements=requirements_str,
+                    repository_id=repository_id,
+                    changeset_revision=changeset_revision,
+                    repository_installation_status=repository_installation_status,
+                )
                 folder.valid_tools.append(tool)
         else:
             tools_root_folder = None
         return folder_id, tools_root_folder
 
-    def build_tool_dependencies_folder(self, folder_id, tool_dependencies, label='Tool dependencies', missing=False,
-                                       new_install=False, reinstalling=False):
+    def build_tool_dependencies_folder(
+        self,
+        folder_id,
+        tool_dependencies,
+        label="Tool dependencies",
+        missing=False,
+        new_install=False,
+        reinstalling=False,
+    ):
         """Return a folder hierarchy containing tool dependencies."""
         # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state,
         # they are considered missing.  The tool dependency status will be displayed only if a record exists for the tool
@@ -515,103 +588,112 @@ class UtilityContainerManager:
         if tool_dependencies:
             tool_dependency_id = 0
             folder_id += 1
-            tool_dependencies_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            tool_dependencies_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
-            folder = Folder(id=folder_id, key='tool_dependencies', label=label, parent=tool_dependencies_root_folder)
-            if self.app.name == 'galaxy':
+            folder = Folder(id=folder_id, key="tool_dependencies", label=label, parent=tool_dependencies_root_folder)
+            if self.app.name == "galaxy":
                 if new_install or reinstalling:
                     folder.description = "repository tools require handling of these dependencies"
                 elif missing and not new_install and not reinstalling:
-                    folder.description = 'click the name to install the missing dependency'
+                    folder.description = "click the name to install the missing dependency"
                 else:
-                    folder.description = 'click the name to browse the dependency installation directory'
+                    folder.description = "click the name to browse the dependency installation directory"
             tool_dependencies_root_folder.folders.append(folder)
             # Insert a header row.
             tool_dependency_id += 1
-            if self.app.name == 'galaxy':
-                tool_dependency = ToolDependency(id=tool_dependency_id,
-                                                 name='Name',
-                                                 version='Version',
-                                                 type='Type',
-                                                 readme=None,
-                                                 installation_status='Installation status',
-                                                 repository_id=None,
-                                                 tool_dependency_id=None)
+            if self.app.name == "galaxy":
+                tool_dependency = ToolDependency(
+                    id=tool_dependency_id,
+                    name="Name",
+                    version="Version",
+                    type="Type",
+                    readme=None,
+                    installation_status="Installation status",
+                    repository_id=None,
+                    tool_dependency_id=None,
+                )
             else:
-                tool_dependency = ToolDependency(id=tool_dependency_id,
-                                                 name='Name',
-                                                 version='Version',
-                                                 type='Type',
-                                                 readme=None,
-                                                 installation_status=None,
-                                                 repository_id=None,
-                                                 tool_dependency_id=None)
+                tool_dependency = ToolDependency(
+                    id=tool_dependency_id,
+                    name="Name",
+                    version="Version",
+                    type="Type",
+                    readme=None,
+                    installation_status=None,
+                    repository_id=None,
+                    tool_dependency_id=None,
+                )
             folder.tool_dependencies.append(tool_dependency)
             for dependency_key, requirements_dict in tool_dependencies.items():
                 tool_dependency_id += 1
-                if dependency_key in ['set_environment']:
+                if dependency_key in ["set_environment"]:
                     for set_environment_dict in requirements_dict:
                         try:
-                            name = set_environment_dict.get('name', None)
-                            type = set_environment_dict['type']
-                            repository_id = set_environment_dict.get('repository_id', None)
-                            td_id = set_environment_dict.get('tool_dependency_id', None)
+                            name = set_environment_dict.get("name", None)
+                            type = set_environment_dict["type"]
+                            repository_id = set_environment_dict.get("repository_id", None)
+                            td_id = set_environment_dict.get("tool_dependency_id", None)
                         except Exception as e:
                             name = str(e)
-                            type = 'unknown'
-                            repository_id = 'unknown'
-                            td_id = 'unknown'
-                        if self.app.name == 'galaxy':
+                            type = "unknown"
+                            repository_id = "unknown"
+                            td_id = "unknown"
+                        if self.app.name == "galaxy":
                             try:
-                                installation_status = set_environment_dict.get('status', 'Never installed')
+                                installation_status = set_environment_dict.get("status", "Never installed")
                             except Exception as e:
                                 installation_status = str(e)
                         else:
                             installation_status = None
-                        tool_dependency = ToolDependency(id=tool_dependency_id,
-                                                         name=name,
-                                                         version=None,
-                                                         type=type,
-                                                         readme=None,
-                                                         installation_status=installation_status,
-                                                         repository_id=repository_id,
-                                                         tool_dependency_id=td_id)
+                        tool_dependency = ToolDependency(
+                            id=tool_dependency_id,
+                            name=name,
+                            version=None,
+                            type=type,
+                            readme=None,
+                            installation_status=installation_status,
+                            repository_id=repository_id,
+                            tool_dependency_id=td_id,
+                        )
                         folder.tool_dependencies.append(tool_dependency)
                 else:
                     try:
-                        name = requirements_dict['name']
-                        version = requirements_dict['version']
-                        type = requirements_dict['type']
-                        repository_id = requirements_dict.get('repository_id', None)
-                        td_id = requirements_dict.get('tool_dependency_id', None)
+                        name = requirements_dict["name"]
+                        version = requirements_dict["version"]
+                        type = requirements_dict["type"]
+                        repository_id = requirements_dict.get("repository_id", None)
+                        td_id = requirements_dict.get("tool_dependency_id", None)
                     except Exception as e:
                         name = str(e)
-                        version = 'unknown'
-                        type = 'unknown'
-                        repository_id = 'unknown'
-                        td_id = 'unknown'
-                    if self.app.name == 'galaxy':
+                        version = "unknown"
+                        type = "unknown"
+                        repository_id = "unknown"
+                        td_id = "unknown"
+                    if self.app.name == "galaxy":
                         try:
-                            installation_status = requirements_dict.get('status', 'Never installed')
+                            installation_status = requirements_dict.get("status", "Never installed")
                         except Exception as e:
                             installation_status = str(e)
                     else:
                         installation_status = None
-                    tool_dependency = ToolDependency(id=tool_dependency_id,
-                                                     name=name,
-                                                     version=version,
-                                                     type=type,
-                                                     readme=None,
-                                                     installation_status=installation_status,
-                                                     repository_id=repository_id,
-                                                     tool_dependency_id=td_id)
+                    tool_dependency = ToolDependency(
+                        id=tool_dependency_id,
+                        name=name,
+                        version=version,
+                        type=type,
+                        readme=None,
+                        installation_status=installation_status,
+                        repository_id=repository_id,
+                        tool_dependency_id=td_id,
+                    )
                     folder.tool_dependencies.append(tool_dependency)
         else:
             tool_dependencies_root_folder = None
         return folder_id, tool_dependencies_root_folder
 
-    def build_workflows_folder(self, folder_id, workflows, repository_metadata_id=None, repository_id=None,
-                               label='Workflows'):
+    def build_workflows_folder(
+        self, folder_id, workflows, repository_metadata_id=None, repository_id=None, label="Workflows"
+    ):
         """
         Return a folder hierarchy containing workflow objects for each workflow dictionary in the
         received workflows list.  When this method is called from the tool shed, repository_metadata_id
@@ -622,56 +704,74 @@ class UtilityContainerManager:
         if workflows:
             workflow_id = 0
             folder_id += 1
-            workflows_root_folder = Folder(id=folder_id, key='root', label='root', parent=None)
+            workflows_root_folder = Folder(id=folder_id, key="root", label="root", parent=None)
             folder_id += 1
-            folder = Folder(id=folder_id, key='workflows', label=label, parent=workflows_root_folder)
+            folder = Folder(id=folder_id, key="workflows", label=label, parent=workflows_root_folder)
             workflows_root_folder.folders.append(folder)
             # Insert a header row.
             workflow_id += 1
-            workflow = Workflow(id=workflow_id,
-                                workflow_name='Name',
-                                steps='steps',
-                                format_version='format-version',
-                                annotation='annotation',
-                                repository_metadata_id=repository_metadata_id,
-                                repository_id=repository_id)
+            workflow = Workflow(
+                id=workflow_id,
+                workflow_name="Name",
+                steps="steps",
+                format_version="format-version",
+                annotation="annotation",
+                repository_metadata_id=repository_metadata_id,
+                repository_id=repository_id,
+            )
             folder.workflows.append(workflow)
             for workflow_tup in workflows:
                 workflow_dict = workflow_tup[1]
-                steps = workflow_dict.get('steps', [])
+                steps = workflow_dict.get("steps", [])
                 if steps:
                     steps = str(len(steps))
                 else:
-                    steps = 'unknown'
+                    steps = "unknown"
                 workflow_id += 1
-                workflow = Workflow(id=workflow_id,
-                                    workflow_name=workflow_dict.get('name', ''),
-                                    steps=steps,
-                                    format_version=workflow_dict.get('format-version', ''),
-                                    annotation=workflow_dict.get('annotation', ''),
-                                    repository_metadata_id=repository_metadata_id,
-                                    repository_id=repository_id)
+                workflow = Workflow(
+                    id=workflow_id,
+                    workflow_name=workflow_dict.get("name", ""),
+                    steps=steps,
+                    format_version=workflow_dict.get("format-version", ""),
+                    annotation=workflow_dict.get("annotation", ""),
+                    repository_metadata_id=repository_metadata_id,
+                    repository_id=repository_id,
+                )
                 folder.workflows.append(workflow)
         else:
             workflows_root_folder = None
         return folder_id, workflows_root_folder
 
-    def generate_repository_dependencies_folder_label_from_key(self, repository_name, repository_owner, changeset_revision,
-                                                               prior_installation_required, only_if_compiling_contained_td, key):
+    def generate_repository_dependencies_folder_label_from_key(
+        self,
+        repository_name,
+        repository_owner,
+        changeset_revision,
+        prior_installation_required,
+        only_if_compiling_contained_td,
+        key,
+    ):
         """Return a repository dependency label based on the repository dependency key."""
-        if self.key_is_current_repositorys_key(repository_name,
-                                               repository_owner,
-                                               changeset_revision,
-                                               prior_installation_required,
-                                               only_if_compiling_contained_td, key):
-            label = 'Repository dependencies'
+        if self.key_is_current_repositorys_key(
+            repository_name,
+            repository_owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+            key,
+        ):
+            label = "Repository dependencies"
         else:
             if util.asbool(prior_installation_required):
                 prior_installation_required_str = " <i>(prior install required)</i>"
             else:
                 prior_installation_required_str = ""
-            label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>%s" % \
-                (repository_name, changeset_revision, repository_owner, prior_installation_required_str)
+            label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>%s" % (
+                repository_name,
+                changeset_revision,
+                repository_owner,
+                prior_installation_required_str,
+            )
         return label
 
     def get_components_from_repository_dependency_for_installed_repository(self, repository_dependency):
@@ -680,21 +780,34 @@ class UtilityContainerManager:
         in Galaxy on the Manage repository page.
         """
         # Default prior_installation_required and only_if_compiling_contained_td to False.
-        prior_installation_required = 'False'
-        only_if_compiling_contained_td = 'False'
+        prior_installation_required = "False"
+        only_if_compiling_contained_td = "False"
         if len(repository_dependency) == 6:
             # Metadata should have been reset on this installed repository, but it wasn't.
             tool_shed_repository_id = repository_dependency[4]
             installation_status = repository_dependency[5]
             tool_shed, name, owner, changeset_revision = repository_dependency[0:4]
-            repository_dependency = [tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td]
+            repository_dependency = [
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ]
         elif len(repository_dependency) == 7:
             # We have a repository dependency tuple that includes a prior_installation_required value but not a only_if_compiling_contained_td value.
             tool_shed_repository_id = repository_dependency[5]
             installation_status = repository_dependency[6]
             tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency[0:5]
-            repository_dependency = \
-                [tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td]
+            repository_dependency = [
+                tool_shed,
+                name,
+                owner,
+                changeset_revision,
+                prior_installation_required,
+                only_if_compiling_contained_td,
+            ]
         elif len(repository_dependency) == 8:
             # We have a repository dependency tuple that includes both a prior_installation_required value
             # and a only_if_compiling_contained_td value.
@@ -703,15 +816,16 @@ class UtilityContainerManager:
             repository_dependency = repository_dependency[0:6]
         else:
             tool_shed_repository_id = None
-            installation_status = 'unknown'
+            installation_status = "unknown"
         if tool_shed_repository_id:
-            tool_shed_repository = repository_util.get_tool_shed_repository_by_id(self.app,
-                                                                                  self.app.security.encode_id(tool_shed_repository_id))
+            tool_shed_repository = repository_util.get_tool_shed_repository_by_id(
+                self.app, self.app.security.encode_id(tool_shed_repository_id)
+            )
             if tool_shed_repository:
                 if tool_shed_repository.missing_repository_dependencies:
-                    installation_status = f'{installation_status}, missing repository dependencies'
+                    installation_status = f"{installation_status}, missing repository dependencies"
                 elif tool_shed_repository.missing_tool_dependencies:
-                    installation_status = f'{installation_status}, missing tool dependencies'
+                    installation_status = f"{installation_status}, missing tool dependencies"
         return tool_shed_repository_id, installation_status, repository_dependency
 
     def get_folder(self, folder, key):
@@ -721,28 +835,31 @@ class UtilityContainerManager:
             return self.get_folder(sub_folder, key)
         return None
 
-    def handle_repository_dependencies_container_entry(self, repository_dependencies_folder, rd_key, rd_value, folder_id,
-                                                       repository_dependency_id, folder_keys):
+    def handle_repository_dependencies_container_entry(
+        self, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys
+    ):
         repository_components_tuple = container_util.get_components_from_key(rd_key)
         components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
         toolshed, repository_name, repository_owner, changeset_revision = components_list[0:4]
         # For backward compatibility to the 12/20/12 Galaxy release.
         if len(components_list) == 4:
-            prior_installation_required = 'False'
-            only_if_compiling_contained_td = 'False'
+            prior_installation_required = "False"
+            only_if_compiling_contained_td = "False"
         elif len(components_list) == 5:
             prior_installation_required = components_list[4]
-            only_if_compiling_contained_td = 'False'
+            only_if_compiling_contained_td = "False"
         elif len(components_list) == 6:
             prior_installation_required = components_list[4]
             only_if_compiling_contained_td = components_list[5]
         folder = self.get_folder(repository_dependencies_folder, rd_key)
-        label = self.generate_repository_dependencies_folder_label_from_key(repository_name,
-                                                                            repository_owner,
-                                                                            changeset_revision,
-                                                                            prior_installation_required,
-                                                                            only_if_compiling_contained_td,
-                                                                            repository_dependencies_folder.key)
+        label = self.generate_repository_dependencies_folder_label_from_key(
+            repository_name,
+            repository_owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+            repository_dependencies_folder.key,
+        )
         if folder:
             if rd_key not in folder_keys:
                 folder_id += 1
@@ -754,92 +871,123 @@ class UtilityContainerManager:
             folder_id += 1
             sub_folder = Folder(id=folder_id, key=rd_key, label=label, parent=repository_dependencies_folder)
             repository_dependencies_folder.folders.append(sub_folder)
-        if self.app.name == 'galaxy':
+        if self.app.name == "galaxy":
             # Insert a header row.
             repository_dependency_id += 1
-            repository_dependency = RepositoryDependency(id=repository_dependency_id,
-                                                         repository_name='Name',
-                                                         changeset_revision='Revision',
-                                                         repository_owner='Owner',
-                                                         installation_status='Installation status')
+            repository_dependency = RepositoryDependency(
+                id=repository_dependency_id,
+                repository_name="Name",
+                changeset_revision="Revision",
+                repository_owner="Owner",
+                installation_status="Installation status",
+            )
             # Insert the header row into the folder.
             sub_folder.repository_dependencies.append(repository_dependency)
         for repository_dependency in rd_value:
-            if self.app.name == 'galaxy':
-                tool_shed_repository_id, installation_status, repository_dependency = \
-                    self.get_components_from_repository_dependency_for_installed_repository(repository_dependency)
+            if self.app.name == "galaxy":
+                (
+                    tool_shed_repository_id,
+                    installation_status,
+                    repository_dependency,
+                ) = self.get_components_from_repository_dependency_for_installed_repository(repository_dependency)
             else:
                 tool_shed_repository_id = None
                 installation_status = None
             can_create_dependency = not self.is_subfolder_of(sub_folder, repository_dependency)
             if can_create_dependency:
-                toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                    common_util.parse_repository_dependency_tuple(repository_dependency)
+                (
+                    toolshed,
+                    repository_name,
+                    repository_owner,
+                    changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                ) = common_util.parse_repository_dependency_tuple(repository_dependency)
                 repository_dependency_id += 1
-                repository_dependency = RepositoryDependency(id=repository_dependency_id,
-                                                             toolshed=toolshed,
-                                                             repository_name=repository_name,
-                                                             repository_owner=repository_owner,
-                                                             changeset_revision=changeset_revision,
-                                                             prior_installation_required=util.asbool(prior_installation_required),
-                                                             only_if_compiling_contained_td=util.asbool(only_if_compiling_contained_td),
-                                                             installation_status=installation_status,
-                                                             tool_shed_repository_id=tool_shed_repository_id)
+                repository_dependency = RepositoryDependency(
+                    id=repository_dependency_id,
+                    toolshed=toolshed,
+                    repository_name=repository_name,
+                    repository_owner=repository_owner,
+                    changeset_revision=changeset_revision,
+                    prior_installation_required=util.asbool(prior_installation_required),
+                    only_if_compiling_contained_td=util.asbool(only_if_compiling_contained_td),
+                    installation_status=installation_status,
+                    tool_shed_repository_id=tool_shed_repository_id,
+                )
                 # Insert the repository_dependency into the folder.
                 sub_folder.repository_dependencies.append(repository_dependency)
         return repository_dependencies_folder, folder_id, repository_dependency_id
 
     def is_subfolder_of(self, folder, repository_dependency):
-        toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-            common_util.parse_repository_dependency_tuple(repository_dependency)
-        key = container_util.generate_repository_dependencies_key_for_repository(toolshed,
-                                                                                 repository_name,
-                                                                                 repository_owner,
-                                                                                 changeset_revision,
-                                                                                 prior_installation_required,
-                                                                                 only_if_compiling_contained_td)
+        (
+            toolshed,
+            repository_name,
+            repository_owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        ) = common_util.parse_repository_dependency_tuple(repository_dependency)
+        key = container_util.generate_repository_dependencies_key_for_repository(
+            toolshed,
+            repository_name,
+            repository_owner,
+            changeset_revision,
+            prior_installation_required,
+            only_if_compiling_contained_td,
+        )
         for sub_folder in folder.folders:
             if key == sub_folder.key:
                 return True
         return False
 
-    def key_is_current_repositorys_key(self, repository_name, repository_owner, changeset_revision,
-                                       prior_installation_required, only_if_compiling_contained_td, key):
+    def key_is_current_repositorys_key(
+        self,
+        repository_name,
+        repository_owner,
+        changeset_revision,
+        prior_installation_required,
+        only_if_compiling_contained_td,
+        key,
+    ):
         repository_components_tuple = container_util.get_components_from_key(key)
         components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
         toolshed, key_name, key_owner, key_changeset_revision = components_list[0:4]
         # For backward compatibility to the 12/20/12 Galaxy release.
         if len(components_list) == 4:
-            key_prior_installation_required = 'False'
-            key_only_if_compiling_contained_td = 'False'
+            key_prior_installation_required = "False"
+            key_only_if_compiling_contained_td = "False"
         elif len(components_list) == 5:
             key_prior_installation_required = components_list[4]
-            key_only_if_compiling_contained_td = 'False'
+            key_only_if_compiling_contained_td = "False"
         elif len(components_list) == 6:
             key_prior_installation_required = components_list[4]
             key_only_if_compiling_contained_td = components_list[5]
-        if (repository_name == key_name
-                and repository_owner == key_owner
-                and changeset_revision == key_changeset_revision
-                and prior_installation_required == key_prior_installation_required
-                and only_if_compiling_contained_td == key_only_if_compiling_contained_td):
+        if (
+            repository_name == key_name
+            and repository_owner == key_owner
+            and changeset_revision == key_changeset_revision
+            and prior_installation_required == key_prior_installation_required
+            and only_if_compiling_contained_td == key_only_if_compiling_contained_td
+        ):
             return True
         return False
 
-    def populate_repository_dependencies_container(self, repository_dependencies_folder, repository_dependencies, folder_id,
-                                                   repository_dependency_id):
+    def populate_repository_dependencies_container(
+        self, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id
+    ):
         folder_keys = []
         for key in repository_dependencies.keys():
             if key not in folder_keys:
                 folder_keys.append(key)
         for key, value in repository_dependencies.items():
-            repository_dependencies_folder, folder_id, repository_dependency_id = \
-                self.handle_repository_dependencies_container_entry(repository_dependencies_folder,
-                                                                    key,
-                                                                    value,
-                                                                    folder_id,
-                                                                    repository_dependency_id,
-                                                                    folder_keys)
+            (
+                repository_dependencies_folder,
+                folder_id,
+                repository_dependency_id,
+            ) = self.handle_repository_dependencies_container_entry(
+                repository_dependencies_folder, key, value, folder_id, repository_dependency_id, folder_keys
+            )
         return repository_dependencies_folder, folder_id, repository_dependency_id
 
     def prune_folder(self, folder, repository_dependency):
diff --git a/lib/tool_shed/webapp/__init__.py b/lib/tool_shed/webapp/__init__.py
index 1e1338b2b95..863e5e94667 100644
--- a/lib/tool_shed/webapp/__init__.py
+++ b/lib/tool_shed/webapp/__init__.py
@@ -3,4 +3,4 @@
 from galaxy.web.framework import url_for
 from galaxy.web.framework.decorators import expose
 
-__all__ = ('url_for', 'expose')
+__all__ = ("url_for", "expose")
diff --git a/lib/tool_shed/webapp/api/authenticate.py b/lib/tool_shed/webapp/api/authenticate.py
index e1a7bb865d6..853004ce6fd 100644
--- a/lib/tool_shed/webapp/api/authenticate.py
+++ b/lib/tool_shed/webapp/api/authenticate.py
@@ -24,7 +24,6 @@ log = logging.getLogger(__name__)
 
 
 class ToolShedAuthenticationController(AuthenticationController):
-
     @expose_api_raw_anonymous_and_sessionless
     def get_tool_shed_api_key(self, trans, **kwd):
         """
diff --git a/lib/tool_shed/webapp/api/categories.py b/lib/tool_shed/webapp/api/categories.py
index 707dc967b89..d8e2b2f9e82 100644
--- a/lib/tool_shed/webapp/api/categories.py
+++ b/lib/tool_shed/webapp/api/categories.py
@@ -4,13 +4,13 @@ import tool_shed.util.shed_util_common as suc
 from galaxy import (
     exceptions,
     util,
-    web
+    web,
 )
 from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
-    require_admin as require_admin
 )
+from galaxy.web import require_admin as require_admin
 from galaxy.webapps.base.controller import BaseAPIController
 from tool_shed.util import repository_util
 
@@ -24,7 +24,7 @@ class CategoriesController(BaseAPIController):
         return self.app.repository_registry.viewable_repositories_and_suites_by_category.get(category_name, 0)
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id': trans.security.encode_id}
+        value_mapper = {"id": trans.security.encode_id}
         return value_mapper
 
     @expose_api
@@ -42,26 +42,25 @@ class CategoriesController(BaseAPIController):
         Content-Disposition: form-data; name="name" Category_Name
         Content-Disposition: form-data; name="description" Category_Description
         """
-        category_dict = dict(message='', status='ok')
-        name = payload.get('name', '')
+        category_dict = dict(message="", status="ok")
+        name = payload.get("name", "")
         if name:
-            description = payload.get('description', '')
+            description = payload.get("description", "")
             if not description:
                 # Default the description to the name.
                 description = name
             if suc.get_category_by_name(self.app, name):
-                raise exceptions.Conflict('A category with that name already exists.')
+                raise exceptions.Conflict("A category with that name already exists.")
             else:
                 # Create the category
                 category = self.app.model.Category(name=name, description=description)
                 trans.sa_session.add(category)
                 trans.sa_session.flush()
-                category_dict = category.to_dict(view='element',
-                                                 value_mapper=self.__get_value_mapper(trans))
-                category_dict['message'] = f"Category '{str(category.name)}' has been created"
-                category_dict['url'] = web.url_for(controller='categories',
-                                                   action='show',
-                                                   id=trans.security.encode_id(category.id))
+                category_dict = category.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+                category_dict["message"] = f"Category '{str(category.name)}' has been created"
+                category_dict["url"] = web.url_for(
+                    controller="categories", action="show", id=trans.security.encode_id(category.id)
+                )
         else:
             raise exceptions.RequestParameterMissingException('Missing required parameter "name".')
         return category_dict
@@ -79,28 +78,23 @@ class CategoriesController(BaseAPIController):
 
         Example: GET localhost:9009/api/categories/f9cad7b01a472135/repositories
         """
-        installable = util.asbool(kwd.get('installable', 'false'))
-        sort_key = kwd.get('sort_key', 'name')
-        sort_order = kwd.get('sort_order', 'asc')
-        page = kwd.get('page', None)
+        installable = util.asbool(kwd.get("installable", "false"))
+        sort_key = kwd.get("sort_key", "name")
+        sort_order = kwd.get("sort_order", "asc")
+        page = kwd.get("page", None)
         category = suc.get_category(self.app, category_id)
         if category is None:
-            category_dict = dict(message=f'Unable to locate category record for id {str(id)}.',
-                                 status='error')
+            category_dict = dict(message=f"Unable to locate category record for id {str(id)}.", status="error")
             return category_dict
-        category_dict = category.to_dict(view='element',
-                                         value_mapper=self.__get_value_mapper(trans))
-        category_dict['repository_count'] = suc.count_repositories_in_category(self.app, category_id)
-        category_dict['url'] = web.url_for(controller='categories',
-                                           action='show',
-                                           id=trans.security.encode_id(category.id))
-        repositories = repository_util.get_repositories_by_category(self.app,
-                                                                    category.id,
-                                                                    installable=installable,
-                                                                    sort_order=sort_order,
-                                                                    sort_key=sort_key,
-                                                                    page=page)
-        category_dict['repositories'] = repositories
+        category_dict = category.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+        category_dict["repository_count"] = suc.count_repositories_in_category(self.app, category_id)
+        category_dict["url"] = web.url_for(
+            controller="categories", action="show", id=trans.security.encode_id(category.id)
+        )
+        repositories = repository_util.get_repositories_by_category(
+            self.app, category.id, installable=installable, sort_order=sort_order, sort_key=sort_key, page=page
+        )
+        category_dict["repositories"] = repositories
         return category_dict
 
     @expose_api_anonymous_and_sessionless
@@ -116,16 +110,19 @@ class CategoriesController(BaseAPIController):
         category_dicts = []
         deleted = util.asbool(deleted)
         if deleted and not trans.user_is_admin:
-            raise exceptions.AdminRequiredException('Only administrators can query deleted categories.')
-        for category in trans.sa_session.query(self.app.model.Category) \
-                                        .filter(self.app.model.Category.table.c.deleted == deleted) \
-                                        .order_by(self.app.model.Category.table.c.name):
-            category_dict = category.to_dict(view='collection',
-                                             value_mapper=self.__get_value_mapper(trans))
-            category_dict['url'] = web.url_for(controller='categories',
-                                               action='show',
-                                               id=trans.security.encode_id(category.id))
-            category_dict['repositories'] = self.app.repository_registry.viewable_repositories_and_suites_by_category.get(category.name, 0)
+            raise exceptions.AdminRequiredException("Only administrators can query deleted categories.")
+        for category in (
+            trans.sa_session.query(self.app.model.Category)
+            .filter(self.app.model.Category.table.c.deleted == deleted)
+            .order_by(self.app.model.Category.table.c.name)
+        ):
+            category_dict = category.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
+            category_dict["url"] = web.url_for(
+                controller="categories", action="show", id=trans.security.encode_id(category.id)
+            )
+            category_dict[
+                "repositories"
+            ] = self.app.repository_registry.viewable_repositories_and_suites_by_category.get(category.name, 0)
             category_dicts.append(category_dict)
         return category_dicts
 
@@ -141,12 +138,10 @@ class CategoriesController(BaseAPIController):
         """
         category = suc.get_category(self.app, id)
         if category is None:
-            category_dict = dict(message=f'Unable to locate category record for id {str(id)}.',
-                                 status='error')
+            category_dict = dict(message=f"Unable to locate category record for id {str(id)}.", status="error")
             return category_dict
-        category_dict = category.to_dict(view='element',
-                                         value_mapper=self.__get_value_mapper(trans))
-        category_dict['url'] = web.url_for(controller='categories',
-                                           action='show',
-                                           id=trans.security.encode_id(category.id))
+        category_dict = category.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+        category_dict["url"] = web.url_for(
+            controller="categories", action="show", id=trans.security.encode_id(category.id)
+        )
         return category_dict
diff --git a/lib/tool_shed/webapp/api/configuration.py b/lib/tool_shed/webapp/api/configuration.py
index f4b657575d7..fb449597607 100644
--- a/lib/tool_shed/webapp/api/configuration.py
+++ b/lib/tool_shed/webapp/api/configuration.py
@@ -11,7 +11,6 @@ log = logging.getLogger(__name__)
 
 
 class ConfigurationController(BaseAPIController):
-
     def __init__(self, app):
         super().__init__(app)
 
diff --git a/lib/tool_shed/webapp/api/groups.py b/lib/tool_shed/webapp/api/groups.py
index a7479ca93a6..bc7a72f01f0 100644
--- a/lib/tool_shed/webapp/api/groups.py
+++ b/lib/tool_shed/webapp/api/groups.py
@@ -2,19 +2,19 @@ import logging
 
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.exceptions import (
     AdminRequiredException,
     ObjectNotFound,
-    RequestParameterMissingException
+    RequestParameterMissingException,
 )
 from galaxy.util import pretty_print_time_interval
 from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
-    require_admin as require_admin
 )
+from galaxy.web import require_admin as require_admin
 from galaxy.webapps.base.controller import BaseAPIController
 from tool_shed.managers import groups
 
@@ -29,7 +29,7 @@ class GroupsController(BaseAPIController):
         self.group_manager = groups.GroupManager()
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id': trans.security.encode_id}
+        value_mapper = {"id": trans.security.encode_id}
         return value_mapper
 
     @expose_api_anonymous_and_sessionless
@@ -45,7 +45,7 @@ class GroupsController(BaseAPIController):
         group_dicts = []
         deleted = util.asbool(deleted)
         if deleted and not trans.user_is_admin:
-            raise AdminRequiredException('Only administrators can query deleted groups.')
+            raise AdminRequiredException("Only administrators can query deleted groups.")
         for group in self.group_manager.list(trans, deleted):
             group_dicts.append(self._populate(trans, group))
         return group_dicts
@@ -65,15 +65,17 @@ class GroupsController(BaseAPIController):
         Content-Disposition: form-data; name="name" Group_Name
         Content-Disposition: form-data; name="description" Group_Description
         """
-        group_dict = dict(message='', status='ok')
-        name = payload.get('name', '')
+        group_dict = dict(message="", status="ok")
+        name = payload.get("name", "")
         if name:
-            description = payload.get('description', '')
+            description = payload.get("description", "")
             if not description:
-                description = ''
+                description = ""
             else:
                 # TODO add description field to the model
-                group_dict = self.group_manager.create(trans, name=name).to_dict(view='element', value_mapper=self.__get_value_mapper(trans))
+                group_dict = self.group_manager.create(trans, name=name).to_dict(
+                    view="element", value_mapper=self.__get_value_mapper(trans)
+                )
         else:
             raise RequestParameterMissingException('Missing required parameter "name".')
         return group_dict
@@ -91,7 +93,7 @@ class GroupsController(BaseAPIController):
         decoded_id = trans.security.decode_id(encoded_id)
         group = self.group_manager.get(trans, decoded_id)
         if group is None:
-            raise ObjectNotFound(f'Unable to locate group record for id {str(encoded_id)}.')
+            raise ObjectNotFound(f"Unable to locate group record for id {str(encoded_id)}.")
         return self._populate(trans, group)
 
     def _populate(self, trans, group):
@@ -100,19 +102,21 @@ class GroupsController(BaseAPIController):
         and add other characteristics like members and repositories.
         """
         model = trans.app.model
-        group_dict = group.to_dict(view='collection', value_mapper=self.__get_value_mapper(trans))
+        group_dict = group.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
         group_members = []
         group_repos = []
         total_downloads = 0
         for uga in group.users:
             user = trans.sa_session.query(model.User).filter(model.User.table.c.id == uga.user_id).one()
             user_repos_count = 0
-            for repo in trans.sa_session.query(model.Repository) \
-                    .filter(model.Repository.table.c.user_id == uga.user_id) \
-                    .join(model.RepositoryMetadata.table) \
-                    .join(model.User.table) \
-                    .outerjoin(model.RepositoryCategoryAssociation.table) \
-                    .outerjoin(model.Category.table):
+            for repo in (
+                trans.sa_session.query(model.Repository)
+                .filter(model.Repository.table.c.user_id == uga.user_id)
+                .join(model.RepositoryMetadata.table)
+                .join(model.User.table)
+                .outerjoin(model.RepositoryCategoryAssociation.table)
+                .outerjoin(model.Category.table)
+            ):
                 categories = []
                 for rca in repo.categories:
                     cat_dict = dict(name=rca.category.name, id=trans.app.security.encode_id(rca.category.id))
@@ -121,36 +125,49 @@ class GroupsController(BaseAPIController):
                 time_repo_updated_full = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
                 time_repo_created = pretty_print_time_interval(repo.create_time, True)
                 time_repo_updated = pretty_print_time_interval(repo.update_time, True)
-                approved = ''
+                approved = ""
                 ratings = []
                 for review in repo.reviews:
                     if review.rating:
                         ratings.append(review.rating)
-                    if review.approved == 'yes':
-                        approved = 'yes'
+                    if review.approved == "yes":
+                        approved = "yes"
                 # TODO add user ratings
-                ratings_mean = str(float(sum(ratings)) / len(ratings)) if len(ratings) > 0 else ''
+                ratings_mean = str(float(sum(ratings)) / len(ratings)) if len(ratings) > 0 else ""
                 total_downloads += repo.times_downloaded
-                group_repos.append({'name': repo.name,
-                                    'times_downloaded': repo.times_downloaded,
-                                    'owner': repo.user.username,
-                                    'time_created_full': time_repo_created_full,
-                                    'time_created': time_repo_created,
-                                    'time_updated_full': time_repo_updated_full,
-                                    'time_updated': time_repo_updated,
-                                    'description': repo.description,
-                                    'approved': approved,
-                                    'ratings_mean': ratings_mean,
-                                    'categories': categories})
+                group_repos.append(
+                    {
+                        "name": repo.name,
+                        "times_downloaded": repo.times_downloaded,
+                        "owner": repo.user.username,
+                        "time_created_full": time_repo_created_full,
+                        "time_created": time_repo_created,
+                        "time_updated_full": time_repo_updated_full,
+                        "time_updated": time_repo_updated,
+                        "description": repo.description,
+                        "approved": approved,
+                        "ratings_mean": ratings_mean,
+                        "categories": categories,
+                    }
+                )
                 user_repos_count += 1
             encoded_user_id = trans.app.security.encode_id(user.id)
-            user_repos_url = web.url_for(controller='repository', action='browse_repositories_by_user', user_id=encoded_user_id)
+            user_repos_url = web.url_for(
+                controller="repository", action="browse_repositories_by_user", user_id=encoded_user_id
+            )
             time_created = pretty_print_time_interval(user.create_time, True)
-            member_dict = {'id': encoded_user_id, 'username': user.username, 'user_repos_url': user_repos_url, 'user_repos_count': user_repos_count, 'user_tools_count': 'unknown', 'time_created': time_created}
+            member_dict = {
+                "id": encoded_user_id,
+                "username": user.username,
+                "user_repos_url": user_repos_url,
+                "user_repos_count": user_repos_count,
+                "user_tools_count": "unknown",
+                "time_created": time_created,
+            }
             group_members.append(member_dict)
-        group_dict['members'] = group_members
-        group_dict['total_members'] = len(group_members)
-        group_dict['repositories'] = group_repos
-        group_dict['total_repos'] = len(group_repos)
-        group_dict['total_downloads'] = total_downloads
+        group_dict["members"] = group_members
+        group_dict["total_members"] = len(group_members)
+        group_dict["repositories"] = group_repos
+        group_dict["total_repos"] = len(group_repos)
+        group_dict["total_downloads"] = total_downloads
         return group_dict
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index ba4bc97a2a9..8bd824fba4e 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -6,12 +6,15 @@ from collections import namedtuple
 from io import StringIO
 from time import strftime
 
-from sqlalchemy import and_, false
+from sqlalchemy import (
+    and_,
+    false,
+)
 from webob.compat import cgi_FieldStorage
 
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.exceptions import (
     ActionInputError,
@@ -19,17 +22,17 @@ from galaxy.exceptions import (
     InsufficientPermissionsException,
     ObjectNotFound,
     RequestParameterInvalidException,
-    RequestParameterMissingException
+    RequestParameterMissingException,
 )
 from galaxy.util import checkers
 from galaxy.web import (
     expose_api,
     expose_api_anonymous_and_sessionless,
-    expose_api_raw_anonymous_and_sessionless
+    expose_api_raw_anonymous_and_sessionless,
 )
 from galaxy.webapps.base.controller import (
     BaseAPIController,
-    HTTPBadRequest
+    HTTPBadRequest,
 )
 from tool_shed.dependencies import attribute_handlers
 from tool_shed.metadata import repository_metadata_manager
@@ -41,7 +44,7 @@ from tool_shed.util import (
     metadata_util,
     repository_content_util,
     repository_util,
-    tool_util
+    tool_util,
 )
 from tool_shed.webapp.search.repo_search import RepoSearch
 
@@ -66,31 +69,35 @@ class RepositoriesController(BaseAPIController):
         """
         response_dict = {}
         if not trans.user_is_admin:
-            response_dict['status'] = 'error'
-            response_dict['message'] = "You are not authorized to add entries to this Tool Shed's repository registry."
+            response_dict["status"] = "error"
+            response_dict["message"] = "You are not authorized to add entries to this Tool Shed's repository registry."
             return response_dict
-        tool_shed_url = payload.get('tool_shed_url', '')
+        tool_shed_url = payload.get("tool_shed_url", "")
         if not tool_shed_url:
             raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
-        tool_shed_url = tool_shed_url.rstrip('/')
-        name = payload.get('name', '')
+        tool_shed_url = tool_shed_url.rstrip("/")
+        name = payload.get("name", "")
         if not name:
             raise HTTPBadRequest(detail="Missing required parameter 'name'.")
-        owner = payload.get('owner', '')
+        owner = payload.get("owner", "")
         if not owner:
             raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
         repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
         if repository is None:
-            error_message = f'Cannot locate repository with name {str(name)} and owner {str(owner)},'
+            error_message = f"Cannot locate repository with name {str(name)} and owner {str(owner)},"
             log.debug(error_message)
-            response_dict['status'] = 'error'
-            response_dict['message'] = error_message
+            response_dict["status"] = "error"
+            response_dict["message"] = error_message
             return response_dict
         # Update the repository registry.
         self.app.repository_registry.add_entry(repository)
-        response_dict['status'] = 'ok'
-        response_dict['message'] = 'Entries for repository %s owned by %s have been added to the Tool Shed repository registry.' \
-            % (name, owner)
+        response_dict["status"] = "ok"
+        response_dict[
+            "message"
+        ] = "Entries for repository %s owned by %s have been added to the Tool Shed repository registry." % (
+            name,
+            owner,
+        )
         return response_dict
 
     @web.legacy_expose_api_anonymous
@@ -106,19 +113,23 @@ class RepositoriesController(BaseAPIController):
         """
         # Example URL: http://localhost:9009/api/repositories/get_ordered_installable_revisions?name=add_column&owner=test
         if name is None:
-            name = kwd.get('name', None)
+            name = kwd.get("name", None)
         if owner is None:
-            owner = kwd.get('owner', None)
-        tsr_id = kwd.get('tsr_id', None)
-        eagerload_columns = ['downloadable_revisions']
+            owner = kwd.get("owner", None)
+        tsr_id = kwd.get("tsr_id", None)
+        eagerload_columns = ["downloadable_revisions"]
         if None not in [name, owner]:
             # Get the repository information.
-            repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner, eagerload_columns=eagerload_columns)
+            repository = repository_util.get_repository_by_name_and_owner(
+                self.app, name, owner, eagerload_columns=eagerload_columns
+            )
             if repository is None:
                 trans.response.status = 404
-                return {'status': 'error', 'message': f'No repository named {name} found with owner {owner}'}
+                return {"status": "error", "message": f"No repository named {name} found with owner {owner}"}
         elif tsr_id is not None:
-            repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id, eagerload_columns=eagerload_columns)
+            repository = repository_util.get_repository_in_tool_shed(
+                self.app, tsr_id, eagerload_columns=eagerload_columns
+            )
         else:
             error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
             error_message += "invalid parameters received."
@@ -204,57 +215,62 @@ class RepositoriesController(BaseAPIController):
         # http://<xyz>/api/repositories/get_repository_revision_install_info?name=<n>&owner=<o>&changeset_revision=<cr>
         if name and owner and changeset_revision:
             # Get the repository information.
-            repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner, eagerload_columns=['downloadable_revisions'])
+            repository = repository_util.get_repository_by_name_and_owner(
+                self.app, name, owner, eagerload_columns=["downloadable_revisions"]
+            )
             if repository is None:
-                log.debug(f'Cannot locate repository {str(name)} owned by {str(owner)}')
+                log.debug(f"Cannot locate repository {str(name)} owned by {str(owner)}")
                 return {}, {}, {}
             encoded_repository_id = trans.security.encode_id(repository.id)
-            repository_dict = repository.to_dict(view='element',
-                                                 value_mapper=self.__get_value_mapper(trans))
-            repository_dict['url'] = web.url_for(controller='repositories',
-                                                 action='show',
-                                                 id=encoded_repository_id)
+            repository_dict = repository.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+            repository_dict["url"] = web.url_for(controller="repositories", action="show", id=encoded_repository_id)
             # Get the repository_metadata information.
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                              encoded_repository_id,
-                                                                                              changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                self.app, encoded_repository_id, changeset_revision
+            )
             if repository_metadata is None:
                 # The changeset_revision column in the repository_metadata table has been updated with a new
                 # value value, so find the changeset_revision to which we need to update.
-                new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, changeset_revision)
-                repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                                  encoded_repository_id,
-                                                                                                  new_changeset_revision)
+                new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+                    self.app, repository, changeset_revision
+                )
+                repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                    self.app, encoded_repository_id, new_changeset_revision
+                )
                 changeset_revision = new_changeset_revision
             if repository_metadata is not None:
                 encoded_repository_metadata_id = trans.security.encode_id(repository_metadata.id)
-                repository_metadata_dict = repository_metadata.to_dict(view='collection',
-                                                                       value_mapper=self.__get_value_mapper(trans))
-                repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
-                                                              action='show',
-                                                              id=encoded_repository_metadata_id)
-                if 'tools' in repository_metadata.metadata:
-                    repository_metadata_dict['valid_tools'] = repository_metadata.metadata['tools']
+                repository_metadata_dict = repository_metadata.to_dict(
+                    view="collection", value_mapper=self.__get_value_mapper(trans)
+                )
+                repository_metadata_dict["url"] = web.url_for(
+                    controller="repository_revisions", action="show", id=encoded_repository_metadata_id
+                )
+                if "tools" in repository_metadata.metadata:
+                    repository_metadata_dict["valid_tools"] = repository_metadata.metadata["tools"]
                 # Get the repo_info_dict for installing the repository.
-                repo_info_dict, \
-                    includes_tools, \
-                    includes_tool_dependencies, \
-                    includes_tools_for_display_in_tool_panel, \
-                    has_repository_dependencies, \
-                    has_repository_dependencies_only_if_compiling_contained_td = \
-                    repository_util.get_repo_info_dict(self.app,
-                                                       trans.user,
-                                                       encoded_repository_id,
-                                                       changeset_revision)
+                (
+                    repo_info_dict,
+                    includes_tools,
+                    includes_tool_dependencies,
+                    includes_tools_for_display_in_tool_panel,
+                    has_repository_dependencies,
+                    has_repository_dependencies_only_if_compiling_contained_td,
+                ) = repository_util.get_repo_info_dict(self.app, trans.user, encoded_repository_id, changeset_revision)
                 return repository_dict, repository_metadata_dict, repo_info_dict
             else:
-                log.debug("Unable to locate repository_metadata record for repository id %s and changeset_revision %s" %
-                          (str(repository.id), str(changeset_revision)))
+                log.debug(
+                    "Unable to locate repository_metadata record for repository id %s and changeset_revision %s"
+                    % (str(repository.id), str(changeset_revision))
+                )
                 return repository_dict, {}, {}
         else:
             debug_msg = "Error in the Tool Shed repositories API in get_repository_revision_install_info: "
-            debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % \
-                (str(name), str(owner), str(changeset_revision))
+            debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % (
+                str(name),
+                str(owner),
+                str(changeset_revision),
+            )
             log.debug(debug_msg)
             return {}, {}, {}
 
@@ -268,9 +284,11 @@ class RepositoriesController(BaseAPIController):
         Returns a list of lists of changesets, in the format [ [ 0, fbb391dc803c ], [ 1, 9d9ec4d9c03e ], [ 2, 9b5b20673b89 ], [ 3, e8c99ce51292 ] ].
         """
         # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?tsr_id=9d37e53072ff9fa4
-        tsr_id = kwd.get('tsr_id', None)
+        tsr_id = kwd.get("tsr_id", None)
         if tsr_id is not None:
-            repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id, eagerload_columns=['downloadable_revisions'])
+            repository = repository_util.get_repository_in_tool_shed(
+                self.app, tsr_id, eagerload_columns=["downloadable_revisions"]
+            )
         else:
             error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
             error_message += "missing or invalid parameter received."
@@ -279,9 +297,11 @@ class RepositoriesController(BaseAPIController):
         return repository.installable_revisions(self.app)
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id': trans.security.encode_id,
-                        'repository_id': trans.security.encode_id,
-                        'user_id': trans.security.encode_id}
+        value_mapper = {
+            "id": trans.security.encode_id,
+            "repository_id": trans.security.encode_id,
+            "user_id": trans.security.encode_id,
+        }
         return value_mapper
 
     @expose_api_raw_anonymous_and_sessionless
@@ -326,79 +346,99 @@ class RepositoriesController(BaseAPIController):
         """
         repository_dicts = []
         deleted = util.asbool(deleted)
-        q = kwd.get('q', '')
+        q = kwd.get("q", "")
         if q:
-            page = kwd.get('page', 1)
-            page_size = kwd.get('page_size', 10)
+            page = kwd.get("page", 1)
+            page_size = kwd.get("page_size", 10)
             try:
                 page = int(page)
                 page_size = int(page_size)
             except ValueError:
                 raise RequestParameterInvalidException('The "page" and "page_size" parameters have to be integers.')
-            return_jsonp = util.asbool(kwd.get('jsonp', False))
-            callback = kwd.get('callback', 'callback')
+            return_jsonp = util.asbool(kwd.get("jsonp", False))
+            callback = kwd.get("callback", "callback")
             search_results = self._search(trans, q, page, page_size)
             if return_jsonp:
-                response = str(f'{callback}({json.dumps(search_results)});')
+                response = str(f"{callback}({json.dumps(search_results)});")
             else:
                 response = json.dumps(search_results)
             return response
-        tool_ids = kwd.get('tool_ids', None)
+        tool_ids = kwd.get("tool_ids", None)
         if tool_ids is not None:
             tool_ids = util.listify(tool_ids)
             repository_found = []
             all_metadata = dict()
             for tool_id in tool_ids:
                 # A valid GUID looks like toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.1.0
-                shed, _, owner, name, tool, version = tool_id.split('/')
-                clause_list = [and_(self.app.model.Repository.table.c.deprecated == false(),
-                                    self.app.model.Repository.table.c.deleted == false(),
-                                    self.app.model.Repository.table.c.name == name,
-                                    self.app.model.User.table.c.username == owner,
-                                    self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id)]
+                shed, _, owner, name, tool, version = tool_id.split("/")
+                clause_list = [
+                    and_(
+                        self.app.model.Repository.table.c.deprecated == false(),
+                        self.app.model.Repository.table.c.deleted == false(),
+                        self.app.model.Repository.table.c.name == name,
+                        self.app.model.User.table.c.username == owner,
+                        self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id,
+                    )
+                ]
                 repository = trans.sa_session.query(self.app.model.Repository).filter(*clause_list).first()
                 for changeset, changehash in repository.installable_revisions(self.app):
-                    metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
-                    tools = metadata.metadata['tools']
+                    metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(
+                        self.app, repository, changehash
+                    )
+                    tools = metadata.metadata["tools"]
                     for tool in tools:
-                        if tool['guid'] in tool_ids:
-                            repository_found.append('%d:%s' % (int(changeset), changehash))
-                    metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
+                        if tool["guid"] in tool_ids:
+                            repository_found.append("%d:%s" % (int(changeset), changehash))
+                    metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(
+                        self.app, repository, changehash
+                    )
                     if metadata is None:
                         continue
-                    metadata_dict = metadata.to_dict(value_mapper={'id': self.app.security.encode_id, 'repository_id': self.app.security.encode_id})
-                    metadata_dict['repository'] = repository.to_dict(value_mapper={'id': self.app.security.encode_id})
+                    metadata_dict = metadata.to_dict(
+                        value_mapper={"id": self.app.security.encode_id, "repository_id": self.app.security.encode_id}
+                    )
+                    metadata_dict["repository"] = repository.to_dict(value_mapper={"id": self.app.security.encode_id})
                     if metadata.has_repository_dependencies:
-                        metadata_dict['repository_dependencies'] = metadata_util.get_all_dependencies(self.app, metadata, processed_dependency_links=[])
+                        metadata_dict["repository_dependencies"] = metadata_util.get_all_dependencies(
+                            self.app, metadata, processed_dependency_links=[]
+                        )
                     else:
-                        metadata_dict['repository_dependencies'] = []
+                        metadata_dict["repository_dependencies"] = []
                     if metadata.includes_tool_dependencies:
-                        metadata_dict['tool_dependencies'] = repository.get_tool_dependencies(self.app, changehash)
+                        metadata_dict["tool_dependencies"] = repository.get_tool_dependencies(self.app, changehash)
                     else:
-                        metadata_dict['tool_dependencies'] = {}
+                        metadata_dict["tool_dependencies"] = {}
                     if metadata.includes_tools:
-                        metadata_dict['tools'] = metadata.metadata['tools']
-                    all_metadata[f'{int(changeset)}:{changehash}'] = metadata_dict
+                        metadata_dict["tools"] = metadata.metadata["tools"]
+                    all_metadata[f"{int(changeset)}:{changehash}"] = metadata_dict
             if repository_found:
-                all_metadata['current_changeset'] = repository_found[0]
+                all_metadata["current_changeset"] = repository_found[0]
                 # all_metadata[ 'found_changesets' ] = repository_found
                 return json.dumps(all_metadata)
-            return '{}'
+            return "{}"
 
-        clause_list = [and_(self.app.model.Repository.table.c.deprecated == false(),
-                            self.app.model.Repository.table.c.deleted == deleted)]
+        clause_list = [
+            and_(
+                self.app.model.Repository.table.c.deprecated == false(),
+                self.app.model.Repository.table.c.deleted == deleted,
+            )
+        ]
         if owner is not None:
-            clause_list.append(and_(self.app.model.User.table.c.username == owner,
-                                    self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id))
+            clause_list.append(
+                and_(
+                    self.app.model.User.table.c.username == owner,
+                    self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id,
+                )
+            )
         if name is not None:
             clause_list.append(self.app.model.Repository.table.c.name == name)
-        for repository in trans.sa_session.query(self.app.model.Repository) \
-                                          .filter(*clause_list) \
-                                          .order_by(self.app.model.Repository.table.c.name):
-            repository_dict = repository.to_dict(view='collection',
-                                                 value_mapper=self.__get_value_mapper(trans))
-            repository_dict['category_ids'] = \
-                [trans.security.encode_id(x.category.id) for x in repository.categories]
+        for repository in (
+            trans.sa_session.query(self.app.model.Repository)
+            .filter(*clause_list)
+            .order_by(self.app.model.Repository.table.c.name)
+        ):
+            repository_dict = repository.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
+            repository_dict["category_ids"] = [trans.security.encode_id(x.category.id) for x in repository.categories]
             repository_dicts.append(repository_dict)
         return json.dumps(repository_dicts)
 
@@ -412,36 +452,41 @@ class RepositoriesController(BaseAPIController):
         """
         conf = self.app.config
         if not conf.toolshed_search_on:
-            raise ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.')
+            raise ConfigDoesNotAllowException("Searching the TS through the API is turned off for this instance.")
         if not conf.whoosh_index_dir:
-            raise ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
+            raise ConfigDoesNotAllowException(
+                "There is no directory for the search index specified. Please contact the administrator."
+            )
         search_term = q.strip()
         if len(search_term) < 1:
-            raise RequestParameterInvalidException('The search term has to be at least one character long.')
+            raise RequestParameterInvalidException("The search term has to be at least one character long.")
 
         repo_search = RepoSearch()
 
-        Boosts = namedtuple('Boosts', ['repo_name_boost',
-                                       'repo_description_boost',
-                                       'repo_long_description_boost',
-                                       'repo_homepage_url_boost',
-                                       'repo_remote_repository_url_boost',
-                                       'categories_boost',
-                                       'repo_owner_username_boost'])
-        boosts = Boosts(float(conf.get('repo_name_boost', 0.9)),
-                        float(conf.get('repo_description_boost', 0.6)),
-                        float(conf.get('repo_long_description_boost', 0.5)),
-                        float(conf.get('repo_homepage_url_boost', 0.3)),
-                        float(conf.get('repo_remote_repository_url_boost', 0.2)),
-                        float(conf.get('categories_boost', 0.5)),
-                        float(conf.get('repo_owner_username_boost', 0.3)))
+        Boosts = namedtuple(
+            "Boosts",
+            [
+                "repo_name_boost",
+                "repo_description_boost",
+                "repo_long_description_boost",
+                "repo_homepage_url_boost",
+                "repo_remote_repository_url_boost",
+                "categories_boost",
+                "repo_owner_username_boost",
+            ],
+        )
+        boosts = Boosts(
+            float(conf.get("repo_name_boost", 0.9)),
+            float(conf.get("repo_description_boost", 0.6)),
+            float(conf.get("repo_long_description_boost", 0.5)),
+            float(conf.get("repo_homepage_url_boost", 0.3)),
+            float(conf.get("repo_remote_repository_url_boost", 0.2)),
+            float(conf.get("categories_boost", 0.5)),
+            float(conf.get("repo_owner_username_boost", 0.3)),
+        )
 
-        results = repo_search.search(trans,
-                                     search_term,
-                                     page,
-                                     page_size,
-                                     boosts)
-        results['hostname'] = web.url_for('/', qualified=True)
+        results = repo_search.search(trans, search_term, page, page_size, boosts)
+        results["hostname"] = web.url_for("/", qualified=True)
         return results
 
     @web.legacy_expose_api
@@ -459,31 +504,37 @@ class RepositoriesController(BaseAPIController):
         """
         response_dict = {}
         if not trans.user_is_admin:
-            response_dict['status'] = 'error'
-            response_dict['message'] = "You are not authorized to remove entries from this Tool Shed's repository registry."
+            response_dict["status"] = "error"
+            response_dict[
+                "message"
+            ] = "You are not authorized to remove entries from this Tool Shed's repository registry."
             return response_dict
-        tool_shed_url = payload.get('tool_shed_url', '')
+        tool_shed_url = payload.get("tool_shed_url", "")
         if not tool_shed_url:
             raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
-        tool_shed_url = tool_shed_url.rstrip('/')
-        name = payload.get('name', '')
+        tool_shed_url = tool_shed_url.rstrip("/")
+        name = payload.get("name", "")
         if not name:
             raise HTTPBadRequest(detail="Missing required parameter 'name'.")
-        owner = payload.get('owner', '')
+        owner = payload.get("owner", "")
         if not owner:
             raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
         repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
         if repository is None:
-            error_message = f'Cannot locate repository with name {str(name)} and owner {str(owner)},'
+            error_message = f"Cannot locate repository with name {str(name)} and owner {str(owner)},"
             log.debug(error_message)
-            response_dict['status'] = 'error'
-            response_dict['message'] = error_message
+            response_dict["status"] = "error"
+            response_dict["message"] = error_message
             return response_dict
         # Update the repository registry.
         self.app.repository_registry.remove_entry(repository)
-        response_dict['status'] = 'ok'
-        response_dict['message'] = 'Entries for repository %s owned by %s have been removed from the Tool Shed repository registry.' \
-            % (name, owner)
+        response_dict["status"] = "ok"
+        response_dict[
+            "message"
+        ] = "Entries for repository %s owned by %s have been removed from the Tool Shed repository registry." % (
+            name,
+            owner,
+        )
         return response_dict
 
     @web.legacy_expose_api
@@ -549,47 +600,50 @@ class RepositoriesController(BaseAPIController):
                 rmm.reset_all_metadata_on_repository_in_tool_shed()
                 rmm_invalid_file_tups = rmm.get_invalid_file_tups()
                 if rmm_invalid_file_tups:
-                    message = tool_util.generate_message_for_invalid_tools(self.app,
-                                                                           rmm_invalid_file_tups,
-                                                                           repository,
-                                                                           None,
-                                                                           as_html=False)
-                    results['unsuccessful_count'] += 1
+                    message = tool_util.generate_message_for_invalid_tools(
+                        self.app, rmm_invalid_file_tups, repository, None, as_html=False
+                    )
+                    results["unsuccessful_count"] += 1
                 else:
-                    message = "Successfully reset metadata on repository %s owned by %s" % \
-                        (str(repository.name), str(repository.user.username))
-                    results['successful_count'] += 1
+                    message = "Successfully reset metadata on repository %s owned by %s" % (
+                        str(repository.name),
+                        str(repository.user.username),
+                    )
+                    results["successful_count"] += 1
             except Exception as e:
-                message = "Error resetting metadata on repository %s owned by %s: %s" % \
-                    (str(repository.name), str(repository.user.username), util.unicodify(e))
-                results['unsuccessful_count'] += 1
-            status = f'{str(repository.name)} : {message}'
-            results['repository_status'].append(status)
+                message = "Error resetting metadata on repository %s owned by %s: %s" % (
+                    str(repository.name),
+                    str(repository.user.username),
+                    util.unicodify(e),
+                )
+                results["unsuccessful_count"] += 1
+            status = f"{str(repository.name)} : {message}"
+            results["repository_status"].append(status)
             return results
-        rmm = repository_metadata_manager.RepositoryMetadataManager(app=self.app,
-                                                                    user=trans.user,
-                                                                    resetting_all_metadata_on_repository=True,
-                                                                    updating_installed_repository=False,
-                                                                    persist=False)
+
+        rmm = repository_metadata_manager.RepositoryMetadataManager(
+            app=self.app,
+            user=trans.user,
+            resetting_all_metadata_on_repository=True,
+            updating_installed_repository=False,
+            persist=False,
+        )
         start_time = strftime("%Y-%m-%d %H:%M:%S")
-        results = dict(start_time=start_time,
-                       repository_status=[],
-                       successful_count=0,
-                       unsuccessful_count=0)
+        results = dict(start_time=start_time, repository_status=[], successful_count=0, unsuccessful_count=0)
         handled_repository_ids = []
-        encoded_ids_to_skip = payload.get('encoded_ids_to_skip', [])
-        skip_file = payload.get('skip_file', None)
+        encoded_ids_to_skip = payload.get("encoded_ids_to_skip", [])
+        skip_file = payload.get("skip_file", None)
         if skip_file and os.path.exists(skip_file) and not encoded_ids_to_skip:
             # Load the list of encoded_ids_to_skip from the skip_file.
             # Contents of file must be 1 encoded repository id per line.
-            lines = open(skip_file, 'rb').readlines()
+            lines = open(skip_file, "rb").readlines()
             for line in lines:
-                if line.startswith('#'):
+                if line.startswith("#"):
                     # Skip comments.
                     continue
-                encoded_ids_to_skip.append(line.rstrip('\n'))
+                encoded_ids_to_skip.append(line.rstrip("\n"))
         if trans.user_is_admin:
-            my_writable = util.asbool(payload.get('my_writable', False))
+            my_writable = util.asbool(payload.get("my_writable", False))
         else:
             my_writable = True
         query = rmm.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=False)
@@ -597,20 +651,24 @@ class RepositoriesController(BaseAPIController):
         for repository in query:
             encoded_id = trans.security.encode_id(repository.id)
             if encoded_id in encoded_ids_to_skip:
-                log.debug("Skipping repository with id %s because it is in encoded_ids_to_skip %s" %
-                          (str(repository.id), str(encoded_ids_to_skip)))
+                log.debug(
+                    "Skipping repository with id %s because it is in encoded_ids_to_skip %s"
+                    % (str(repository.id), str(encoded_ids_to_skip))
+                )
             elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
                 results = handle_repository(trans, rmm, repository, results)
         # Now reset metadata on all remaining repositories.
         for repository in query:
             encoded_id = trans.security.encode_id(repository.id)
             if encoded_id in encoded_ids_to_skip:
-                log.debug("Skipping repository with id %s because it is in encoded_ids_to_skip %s" %
-                          (str(repository.id), str(encoded_ids_to_skip)))
+                log.debug(
+                    "Skipping repository with id %s because it is in encoded_ids_to_skip %s"
+                    % (str(repository.id), str(encoded_ids_to_skip))
+                )
             elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
                 results = handle_repository(trans, rmm, repository, results)
         stop_time = strftime("%Y-%m-%d %H:%M:%S")
-        results['stop_time'] = stop_time
+        results["stop_time"] = stop_time
         return json.dumps(results, sort_keys=True, indent=4)
 
     @web.legacy_expose_api
@@ -627,44 +685,48 @@ class RepositoriesController(BaseAPIController):
         """
 
         def handle_repository(trans, start_time, repository):
-            results = dict(start_time=start_time,
-                           repository_status=[])
+            results = dict(start_time=start_time, repository_status=[])
             try:
-                rmm = repository_metadata_manager.RepositoryMetadataManager(app=self.app,
-                                                                            user=trans.user,
-                                                                            repository=repository,
-                                                                            resetting_all_metadata_on_repository=True,
-                                                                            updating_installed_repository=False,
-                                                                            persist=False)
+                rmm = repository_metadata_manager.RepositoryMetadataManager(
+                    app=self.app,
+                    user=trans.user,
+                    repository=repository,
+                    resetting_all_metadata_on_repository=True,
+                    updating_installed_repository=False,
+                    persist=False,
+                )
                 rmm.reset_all_metadata_on_repository_in_tool_shed()
                 rmm_invalid_file_tups = rmm.get_invalid_file_tups()
                 if rmm_invalid_file_tups:
-                    message = tool_util.generate_message_for_invalid_tools(self.app,
-                                                                           rmm_invalid_file_tups,
-                                                                           repository,
-                                                                           None,
-                                                                           as_html=False)
-                    results['status'] = 'warning'
+                    message = tool_util.generate_message_for_invalid_tools(
+                        self.app, rmm_invalid_file_tups, repository, None, as_html=False
+                    )
+                    results["status"] = "warning"
                 else:
-                    message = "Successfully reset metadata on repository %s owned by %s" % \
-                        (str(repository.name), str(repository.user.username))
-                    results['status'] = 'ok'
+                    message = "Successfully reset metadata on repository %s owned by %s" % (
+                        str(repository.name),
+                        str(repository.user.username),
+                    )
+                    results["status"] = "ok"
             except Exception as e:
-                message = "Error resetting metadata on repository %s owned by %s: %s" % \
-                    (str(repository.name), str(repository.user.username), util.unicodify(e))
-                results['status'] = 'error'
-            status = f'{str(repository.name)} : {message}'
-            results['repository_status'].append(status)
+                message = "Error resetting metadata on repository %s owned by %s: %s" % (
+                    str(repository.name),
+                    str(repository.user.username),
+                    util.unicodify(e),
+                )
+                results["status"] = "error"
+            status = f"{str(repository.name)} : {message}"
+            results["repository_status"].append(status)
             return results
 
-        repository_id = payload.get('repository_id', None)
+        repository_id = payload.get("repository_id", None)
         if repository_id is not None:
             repository = repository_util.get_repository_in_tool_shed(self.app, repository_id)
             start_time = strftime("%Y-%m-%d %H:%M:%S")
             log.debug(f"{start_time}...resetting metadata on repository {str(repository.name)}")
             results = handle_repository(trans, start_time, repository)
             stop_time = strftime("%Y-%m-%d %H:%M:%S")
-            results['stop_time'] = stop_time
+            results["stop_time"] = stop_time
         return results
 
     @expose_api_anonymous_and_sessionless
@@ -685,12 +747,10 @@ class RepositoriesController(BaseAPIController):
         """
         repository = repository_util.get_repository_in_tool_shed(self.app, id)
         if repository is None:
-            raise ObjectNotFound('Unable to locate repository for the given id.')
-        repository_dict = repository.to_dict(view='element',
-                                             value_mapper=self.__get_value_mapper(trans))
+            raise ObjectNotFound("Unable to locate repository for the given id.")
+        repository_dict = repository.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
         # TODO the following property would be better suited in the to_dict method
-        repository_dict['category_ids'] = \
-            [trans.security.encode_id(x.category.id) for x in repository.categories]
+        repository_dict["category_ids"] = [trans.security.encode_id(x.category.id) for x in repository.categories]
         return repository_dict
 
     @expose_api_raw_anonymous_and_sessionless
@@ -713,76 +773,87 @@ class RepositoriesController(BaseAPIController):
         :returns:   information about repository deprecations, updates, and upgrades
         :rtype:     dict
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
-        hexlify_this = util.asbool(kwd.get('hexlify', True))
-        repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner, eagerload_columns=['downloadable_revisions'])
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
+        hexlify_this = util.asbool(kwd.get("hexlify", True))
+        repository = repository_util.get_repository_by_name_and_owner(
+            trans.app, name, owner, eagerload_columns=["downloadable_revisions"]
+        )
         if repository and repository.downloadable_revisions:
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                              trans.security.encode_id(repository.id),
-                                                                                              changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                trans.app, trans.security.encode_id(repository.id), changeset_revision
+            )
             tool_shed_status_dict = {}
             # Handle repository deprecation.
-            tool_shed_status_dict['repository_deprecated'] = str(repository.deprecated)
+            tool_shed_status_dict["repository_deprecated"] = str(repository.deprecated)
             tip_revision = repository.downloadable_revisions[0]
             # Handle latest installable revision.
             if changeset_revision == tip_revision:
-                tool_shed_status_dict['latest_installable_revision'] = 'True'
+                tool_shed_status_dict["latest_installable_revision"] = "True"
             else:
-                next_installable_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
+                next_installable_revision = metadata_util.get_next_downloadable_changeset_revision(
+                    trans.app, repository, changeset_revision
+                )
                 if repository_metadata is None:
                     if next_installable_revision and next_installable_revision != changeset_revision:
-                        tool_shed_status_dict['latest_installable_revision'] = 'True'
+                        tool_shed_status_dict["latest_installable_revision"] = "True"
                     else:
-                        tool_shed_status_dict['latest_installable_revision'] = 'False'
+                        tool_shed_status_dict["latest_installable_revision"] = "False"
                 else:
                     if next_installable_revision and next_installable_revision != changeset_revision:
-                        tool_shed_status_dict['latest_installable_revision'] = 'False'
+                        tool_shed_status_dict["latest_installable_revision"] = "False"
                     else:
-                        tool_shed_status_dict['latest_installable_revision'] = 'True'
+                        tool_shed_status_dict["latest_installable_revision"] = "True"
             # Handle revision updates.
             if changeset_revision == tip_revision:
-                tool_shed_status_dict['revision_update'] = 'False'
+                tool_shed_status_dict["revision_update"] = "False"
             else:
                 if repository_metadata is None:
-                    tool_shed_status_dict['revision_update'] = 'True'
+                    tool_shed_status_dict["revision_update"] = "True"
                 else:
-                    tool_shed_status_dict['revision_update'] = 'False'
+                    tool_shed_status_dict["revision_update"] = "False"
             # Handle revision upgrades.
-            metadata_revisions = [revision[1] for revision in metadata_util.get_metadata_revisions(trans.app, repository)]
+            metadata_revisions = [
+                revision[1] for revision in metadata_util.get_metadata_revisions(trans.app, repository)
+            ]
             num_metadata_revisions = len(metadata_revisions)
             for index, metadata_revision in enumerate(metadata_revisions):
                 if index == num_metadata_revisions:
-                    tool_shed_status_dict['revision_upgrade'] = 'False'
+                    tool_shed_status_dict["revision_upgrade"] = "False"
                     break
                 if metadata_revision == changeset_revision:
                     if num_metadata_revisions - index > 1:
-                        tool_shed_status_dict['revision_upgrade'] = 'True'
+                        tool_shed_status_dict["revision_upgrade"] = "True"
                     else:
-                        tool_shed_status_dict['revision_upgrade'] = 'False'
+                        tool_shed_status_dict["revision_upgrade"] = "False"
                     break
-            return encoding_util.tool_shed_encode(tool_shed_status_dict) if hexlify_this else json.dumps(tool_shed_status_dict)
+            return (
+                encoding_util.tool_shed_encode(tool_shed_status_dict)
+                if hexlify_this
+                else json.dumps(tool_shed_status_dict)
+            )
         return encoding_util.tool_shed_encode({}) if hexlify_this else json.dumps({})
 
     @expose_api_anonymous_and_sessionless
     def show_tools(self, trans, id, changeset, **kwd):
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
-                                                                                          id,
-                                                                                          changeset)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app, id, changeset)
         if repository_metadata is not None:
             encoded_repository_metadata_id = trans.security.encode_id(repository_metadata.id)
-            repository_metadata_dict = repository_metadata.to_dict(view='collection',
-                                                                   value_mapper=self.__get_value_mapper(trans))
-            repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
-                                                          action='show',
-                                                          id=encoded_repository_metadata_id)
-            if 'tools' in repository_metadata.metadata:
-                repository_metadata_dict['valid_tools'] = repository_metadata.metadata['tools']
+            repository_metadata_dict = repository_metadata.to_dict(
+                view="collection", value_mapper=self.__get_value_mapper(trans)
+            )
+            repository_metadata_dict["url"] = web.url_for(
+                controller="repository_revisions", action="show", id=encoded_repository_metadata_id
+            )
+            if "tools" in repository_metadata.metadata:
+                repository_metadata_dict["valid_tools"] = repository_metadata.metadata["tools"]
             return repository_metadata_dict
         else:
-            log.debug("Unable to locate repository_metadata record for repository id %s and changeset_revision %s" %
-                      (str(id), str(changeset)))
+            log.debug(
+                "Unable to locate repository_metadata record for repository id %s and changeset_revision %s"
+                % (str(id), str(changeset))
+            )
             return {}
 
     @expose_api_anonymous_and_sessionless
@@ -800,26 +871,34 @@ class RepositoriesController(BaseAPIController):
 
         :not found:  Empty dictionary.
         """
-        recursive = util.asbool(kwd.get('recursive', 'True'))
+        recursive = util.asbool(kwd.get("recursive", "True"))
         all_metadata = {}
-        repository = repository_util.get_repository_in_tool_shed(self.app, id, eagerload_columns=['downloadable_revisions'])
+        repository = repository_util.get_repository_in_tool_shed(
+            self.app, id, eagerload_columns=["downloadable_revisions"]
+        )
         for changeset, changehash in repository.installable_revisions(self.app):
-            metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(self.app, repository, changehash)
+            metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(
+                self.app, repository, changehash
+            )
             if metadata is None:
                 continue
-            metadata_dict = metadata.to_dict(value_mapper={'id': self.app.security.encode_id, 'repository_id': self.app.security.encode_id})
-            metadata_dict['repository'] = repository.to_dict(value_mapper={'id': self.app.security.encode_id})
+            metadata_dict = metadata.to_dict(
+                value_mapper={"id": self.app.security.encode_id, "repository_id": self.app.security.encode_id}
+            )
+            metadata_dict["repository"] = repository.to_dict(value_mapper={"id": self.app.security.encode_id})
             if metadata.has_repository_dependencies and recursive:
-                metadata_dict['repository_dependencies'] = metadata_util.get_all_dependencies(self.app, metadata, processed_dependency_links=[])
+                metadata_dict["repository_dependencies"] = metadata_util.get_all_dependencies(
+                    self.app, metadata, processed_dependency_links=[]
+                )
             else:
-                metadata_dict['repository_dependencies'] = []
+                metadata_dict["repository_dependencies"] = []
             if metadata.includes_tool_dependencies and recursive:
-                metadata_dict['tool_dependencies'] = repository.get_tool_dependencies(self.app, changehash)
+                metadata_dict["tool_dependencies"] = repository.get_tool_dependencies(self.app, changehash)
             else:
-                metadata_dict['tool_dependencies'] = {}
+                metadata_dict["tool_dependencies"] = {}
             if metadata.includes_tools:
-                metadata_dict['tools'] = metadata.metadata['tools']
-            all_metadata[f'{int(changeset)}:{changehash}'] = metadata_dict
+                metadata_dict["tools"] = metadata.metadata["tools"]
+            all_metadata[f"{int(changeset)}:{changehash}"] = metadata_dict
         return all_metadata
 
     @expose_api
@@ -846,16 +925,16 @@ class RepositoriesController(BaseAPIController):
 
         :raises: RequestParameterInvalidException, InsufficientPermissionsException
         """
-        payload = kwd.get('payload', None)
+        payload = kwd.get("payload", None)
         if not payload:
             raise RequestParameterMissingException("You did not specify any payload.")
 
-        name = payload.get('name', None)
-        synopsis = payload.get('synopsis', None)
-        description = payload.get('description', None)
-        remote_repository_url = payload.get('remote_repository_url', None)
-        homepage_url = payload.get('homepage_url', None)
-        category_ids = payload.get('category_ids', None)
+        name = payload.get("name", None)
+        synopsis = payload.get("synopsis", None)
+        description = payload.get("description", None)
+        remote_repository_url = payload.get("remote_repository_url", None)
+        homepage_url = payload.get("homepage_url", None)
+        category_ids = payload.get("category_ids", None)
         if category_ids is not None:
             # We need to know if it was actually passed, and listify turns None into []
             category_ids = util.listify(category_ids)
@@ -876,9 +955,8 @@ class RepositoriesController(BaseAPIController):
             else:
                 raise ActionInputError(message)
 
-        repository_dict = repo.to_dict(view='element', value_mapper=self.__get_value_mapper(trans))
-        repository_dict['category_ids'] = \
-            [trans.security.encode_id(x.category.id) for x in repo.categories]
+        repository_dict = repo.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+        repository_dict["category_ids"] = [trans.security.encode_id(x.category.id) for x in repo.categories]
         return repository_dict
 
     @expose_api
@@ -906,42 +984,43 @@ class RepositoriesController(BaseAPIController):
 
         :raises: RequestParameterMissingException, RequestParameterInvalidException
         """
-        payload = kwd.get('payload', None)
+        payload = kwd.get("payload", None)
         if not payload:
             raise RequestParameterMissingException("You did not specify any payload.")
-        name = payload.get('name', None)
+        name = payload.get("name", None)
         if not name:
             raise RequestParameterMissingException("Missing required parameter 'name'.")
-        synopsis = payload.get('synopsis', None)
+        synopsis = payload.get("synopsis", None)
         if not synopsis:
             raise RequestParameterMissingException("Missing required parameter 'synopsis'.")
 
-        description = payload.get('description', '')
-        remote_repository_url = payload.get('remote_repository_url', '')
-        homepage_url = payload.get('homepage_url', '')
-        category_ids = util.listify(payload.get('category_ids[]', ''))
+        description = payload.get("description", "")
+        remote_repository_url = payload.get("remote_repository_url", "")
+        homepage_url = payload.get("homepage_url", "")
+        category_ids = util.listify(payload.get("category_ids[]", ""))
 
-        repo_type = payload.get('type', rt_util.UNRESTRICTED)
+        repo_type = payload.get("type", rt_util.UNRESTRICTED)
         if repo_type not in rt_util.types:
-            raise RequestParameterInvalidException('This repository type is not valid')
+            raise RequestParameterInvalidException("This repository type is not valid")
 
         invalid_message = repository_util.validate_repository_name(self.app, name, trans.user)
         if invalid_message:
             raise RequestParameterInvalidException(invalid_message)
 
-        repo, message = repository_util.create_repository(app=self.app,
-                                                          name=name,
-                                                          type=repo_type,
-                                                          description=synopsis,
-                                                          long_description=description,
-                                                          user_id=trans.user.id,
-                                                          category_ids=category_ids,
-                                                          remote_repository_url=remote_repository_url,
-                                                          homepage_url=homepage_url)
+        repo, message = repository_util.create_repository(
+            app=self.app,
+            name=name,
+            type=repo_type,
+            description=synopsis,
+            long_description=description,
+            user_id=trans.user.id,
+            category_ids=category_ids,
+            remote_repository_url=remote_repository_url,
+            homepage_url=homepage_url,
+        )
 
-        repository_dict = repo.to_dict(view='element', value_mapper=self.__get_value_mapper(trans))
-        repository_dict['category_ids'] = \
-            [trans.security.encode_id(x.category.id) for x in repo.categories]
+        repository_dict = repo.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+        repository_dict["category_ids"] = [trans.security.encode_id(x.category.id) for x in repo.categories]
         return repository_dict
 
     @web.legacy_expose_api
@@ -966,9 +1045,11 @@ class RepositoriesController(BaseAPIController):
 
         repository = repository_util.get_repository_in_tool_shed(self.app, id)
 
-        if not (trans.user_is_admin
-                or self.app.security_agent.user_can_administer_repository(trans.user, repository)
-                or self.app.security_agent.can_push(self.app, trans.user, repository)):
+        if not (
+            trans.user_is_admin
+            or self.app.security_agent.user_can_administer_repository(trans.user, repository)
+            or self.app.security_agent.can_push(self.app, trans.user, repository)
+        ):
             trans.response.status = 400
             return {
                 "err_msg": "You do not have permission to update this repository.",
@@ -979,66 +1060,70 @@ class RepositoriesController(BaseAPIController):
         upload_point = commit_util.get_upload_point(repository, **kwd)
         tip = repository.tip()
 
-        file_data = payload.get('file')
+        file_data = payload.get("file")
         # Code stolen from gx's upload_common.py
         if isinstance(file_data, cgi_FieldStorage):
             assert not isinstance(file_data.file, StringIO)
-            assert file_data.file.name != '<fdopen>'
-            local_filename = util.mkstemp_ln(file_data.file.name, 'upload_file_data_')
+            assert file_data.file.name != "<fdopen>"
+            local_filename = util.mkstemp_ln(file_data.file.name, "upload_file_data_")
             file_data.file.close()
-            file_data = dict(filename=file_data.filename,
-                             local_filename=local_filename)
-        elif type(file_data) == dict and 'local_filename' not in file_data:
-            raise Exception('Uploaded file was encoded in a way not understood.')
+            file_data = dict(filename=file_data.filename, local_filename=local_filename)
+        elif type(file_data) == dict and "local_filename" not in file_data:
+            raise Exception("Uploaded file was encoded in a way not understood.")
 
-        commit_message = kwd.get('commit_message', 'Uploaded')
+        commit_message = kwd.get("commit_message", "Uploaded")
 
-        uploaded_file = open(file_data['local_filename'], 'rb')
-        uploaded_file_name = file_data['local_filename']
+        uploaded_file = open(file_data["local_filename"], "rb")
+        uploaded_file_name = file_data["local_filename"]
 
         isgzip = False
         isbz2 = False
         isgzip = checkers.is_gzip(uploaded_file_name)
         if not isgzip:
             isbz2 = checkers.is_bz2(uploaded_file_name)
-        if (isgzip or isbz2):
+        if isgzip or isbz2:
             # Open for reading with transparent compression.
-            tar = tarfile.open(uploaded_file_name, 'r:*')
+            tar = tarfile.open(uploaded_file_name, "r:*")
         else:
             tar = tarfile.open(uploaded_file_name)
 
         new_repo_alert = False
         remove_repo_files_not_in_tar = True
 
-        ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
-            repository_content_util.upload_tar(
-                trans,
-                rdah,
-                tdah,
-                repository,
-                tar,
-                uploaded_file,
-                upload_point,
-                remove_repo_files_not_in_tar,
-                commit_message,
-                new_repo_alert
-            )
+        (
+            ok,
+            message,
+            files_to_remove,
+            content_alert_str,
+            undesirable_dirs_removed,
+            undesirable_files_removed,
+        ) = repository_content_util.upload_tar(
+            trans,
+            rdah,
+            tdah,
+            repository,
+            tar,
+            uploaded_file,
+            upload_point,
+            remove_repo_files_not_in_tar,
+            commit_message,
+            new_repo_alert,
+        )
         if ok:
             # Update the repository files for browsing.
             hg_util.update_repository(repo_dir)
             # Get the new repository tip.
             if tip == repository.tip():
                 trans.response.status = 400
-                message = 'No changes to repository.'
+                message = "No changes to repository."
                 ok = False
             else:
-                rmm = repository_metadata_manager.RepositoryMetadataManager(app=self.app,
-                                                                            user=trans.user,
-                                                                            repository=repository)
-                status, error_message = \
-                    rmm.set_repository_metadata_due_to_new_tip(trans.request.host,
-                                                               content_alert_str=content_alert_str,
-                                                               **kwd)
+                rmm = repository_metadata_manager.RepositoryMetadataManager(
+                    app=self.app, user=trans.user, repository=repository
+                )
+                status, error_message = rmm.set_repository_metadata_due_to_new_tip(
+                    trans.request.host, content_alert_str=content_alert_str, **kwd
+                )
                 if error_message:
                     ok = False
                     trans.response.status = 500
@@ -1048,10 +1133,6 @@ class RepositoriesController(BaseAPIController):
         if os.path.exists(uploaded_file_name):
             os.remove(uploaded_file_name)
         if not ok:
-            return {
-                "err_msg": message
-            }
+            return {"err_msg": message}
         else:
-            return {
-                "message": message
-            }
+            return {"message": message}
diff --git a/lib/tool_shed/webapp/api/repository_revisions.py b/lib/tool_shed/webapp/api/repository_revisions.py
index 9ba52661d2d..591b07d8d6c 100644
--- a/lib/tool_shed/webapp/api/repository_revisions.py
+++ b/lib/tool_shed/webapp/api/repository_revisions.py
@@ -2,11 +2,18 @@ import logging
 
 from sqlalchemy import and_
 
-from galaxy import util
-from galaxy import web
-from galaxy.webapps.base.controller import BaseAPIController, HTTPBadRequest
-from tool_shed.util import metadata_util
-from tool_shed.util import repository_util
+from galaxy import (
+    util,
+    web,
+)
+from galaxy.webapps.base.controller import (
+    BaseAPIController,
+    HTTPBadRequest,
+)
+from tool_shed.util import (
+    metadata_util,
+    repository_util,
+)
 
 log = logging.getLogger(__name__)
 
@@ -15,9 +22,11 @@ class RepositoryRevisionsController(BaseAPIController):
     """RESTful controller for interactions with tool shed repository revisions."""
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id': trans.security.encode_id,
-                        'repository_id': trans.security.encode_id,
-                        'user_id': trans.security.encode_id}
+        value_mapper = {
+            "id": trans.security.encode_id,
+            "repository_id": trans.security.encode_id,
+            "user_id": trans.security.encode_id,
+        }
         return value_mapper
 
     @web.legacy_expose_api_anonymous
@@ -31,29 +40,34 @@ class RepositoryRevisionsController(BaseAPIController):
         # Build up an anded clause list of filters.
         clause_list = []
         # Filter by downloadable if received.
-        downloadable = kwd.get('downloadable', None)
+        downloadable = kwd.get("downloadable", None)
         if downloadable is not None:
             clause_list.append(trans.model.RepositoryMetadata.table.c.downloadable == util.asbool(downloadable))
         # Filter by malicious if received.
-        malicious = kwd.get('malicious', None)
+        malicious = kwd.get("malicious", None)
         if malicious is not None:
             clause_list.append(trans.model.RepositoryMetadata.table.c.malicious == util.asbool(malicious))
         # Filter by missing_test_components if received.
-        missing_test_components = kwd.get('missing_test_components', None)
+        missing_test_components = kwd.get("missing_test_components", None)
         if missing_test_components is not None:
-            clause_list.append(trans.model.RepositoryMetadata.table.c.missing_test_components == util.asbool(missing_test_components))
+            clause_list.append(
+                trans.model.RepositoryMetadata.table.c.missing_test_components == util.asbool(missing_test_components)
+            )
         # Filter by includes_tools if received.
-        includes_tools = kwd.get('includes_tools', None)
+        includes_tools = kwd.get("includes_tools", None)
         if includes_tools is not None:
             clause_list.append(trans.model.RepositoryMetadata.table.c.includes_tools == util.asbool(includes_tools))
-        for repository_metadata in trans.sa_session.query(trans.app.model.RepositoryMetadata) \
-                                                   .filter(and_(*clause_list)) \
-                                                   .order_by(trans.app.model.RepositoryMetadata.table.c.repository_id.desc()):
-            repository_metadata_dict = repository_metadata.to_dict(view='collection',
-                                                                   value_mapper=self.__get_value_mapper(trans))
-            repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
-                                                          action='show',
-                                                          id=trans.security.encode_id(repository_metadata.id))
+        for repository_metadata in (
+            trans.sa_session.query(trans.app.model.RepositoryMetadata)
+            .filter(and_(*clause_list))
+            .order_by(trans.app.model.RepositoryMetadata.table.c.repository_id.desc())
+        ):
+            repository_metadata_dict = repository_metadata.to_dict(
+                view="collection", value_mapper=self.__get_value_mapper(trans)
+            )
+            repository_metadata_dict["url"] = web.url_for(
+                controller="repository_revisions", action="show", id=trans.security.encode_id(repository_metadata.id)
+            )
             repository_metadata_dicts.append(repository_metadata_dict)
         return repository_metadata_dicts
 
@@ -74,46 +88,55 @@ class RepositoryRevisionsController(BaseAPIController):
         repository_dependencies_dicts = []
         repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
         if repository_metadata is None:
-            log.debug(f'Invalid repository_metadata id received: {str(id)}')
+            log.debug(f"Invalid repository_metadata id received: {str(id)}")
             return repository_dependencies_dicts
         metadata = repository_metadata.metadata
         if metadata is None:
-            log.debug(f'The repository_metadata record with id {str(id)} has no metadata.')
+            log.debug(f"The repository_metadata record with id {str(id)} has no metadata.")
             return repository_dependencies_dicts
-        if 'repository_dependencies' in metadata:
-            rd_tups = metadata['repository_dependencies']['repository_dependencies']
+        if "repository_dependencies" in metadata:
+            rd_tups = metadata["repository_dependencies"]["repository_dependencies"]
             for rd_tup in rd_tups:
                 tool_shed, name, owner, changeset_revision = rd_tup[0:4]
                 repository_dependency = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
                 if repository_dependency is None:
-                    log.dbug(f'Cannot locate repository dependency {name} owned by {owner}.')
+                    log.dbug(f"Cannot locate repository dependency {name} owned by {owner}.")
                     continue
                 repository_dependency_id = trans.security.encode_id(repository_dependency.id)
-                repository_dependency_repository_metadata = \
-                    metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_dependency_id, changeset_revision)
+                repository_dependency_repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                    trans.app, repository_dependency_id, changeset_revision
+                )
                 if repository_dependency_repository_metadata is None:
                     # The changeset_revision column in the repository_metadata table has been updated with a new
                     # value value, so find the changeset_revision to which we need to update.
-                    new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository_dependency, changeset_revision)
+                    new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+                        trans.app, repository_dependency, changeset_revision
+                    )
                     if new_changeset_revision != changeset_revision:
-                        repository_dependency_repository_metadata = \
-                            metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                        repository_dependency_id,
-                                                                                        new_changeset_revision)
+                        repository_dependency_repository_metadata = (
+                            metadata_util.get_repository_metadata_by_changeset_revision(
+                                trans.app, repository_dependency_id, new_changeset_revision
+                            )
+                        )
                         changeset_revision = new_changeset_revision
                     else:
                         decoded_repository_dependency_id = trans.security.decode_id(repository_dependency_id)
-                        debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
-                            (decoded_repository_dependency_id, str(name), str(owner))
-                        debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
-                            (str(changeset_revision), str(new_changeset_revision))
+                        debug_msg = (
+                            "Cannot locate repository_metadata with id %d for repository dependency %s owned by %s "
+                            % (decoded_repository_dependency_id, str(name), str(owner))
+                        )
+                        debug_msg += "using either of these changeset_revisions: %s, %s." % (
+                            str(changeset_revision),
+                            str(new_changeset_revision),
+                        )
                         log.debug(debug_msg)
                         continue
-                repository_dependency_metadata_dict = \
-                    repository_dependency_repository_metadata.to_dict(view='element',
-                                                                      value_mapper=self.__get_value_mapper(trans))
-                repository_dependency_dict = repository_dependency.to_dict(view='element',
-                                                                           value_mapper=self.__get_value_mapper(trans))
+                repository_dependency_metadata_dict = repository_dependency_repository_metadata.to_dict(
+                    view="element", value_mapper=self.__get_value_mapper(trans)
+                )
+                repository_dependency_dict = repository_dependency.to_dict(
+                    view="element", value_mapper=self.__get_value_mapper(trans)
+                )
                 # We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
                 # controller is working with repository_metadata records.  The above to_dict() method returns a dictionary
                 # with an id entry for the repository record.  However, all of the other methods in this controller have
@@ -123,9 +146,9 @@ class RepositoryRevisionsController(BaseAPIController):
                 for k, v in repository_dependency_dict.items():
                     if k not in repository_dependency_metadata_dict:
                         repository_dependency_metadata_dict[k] = v
-                repository_dependency_metadata_dict['url'] = web.url_for(controller='repositories',
-                                                                         action='show',
-                                                                         id=repository_dependency_id)
+                repository_dependency_metadata_dict["url"] = web.url_for(
+                    controller="repositories", action="show", id=repository_dependency_id
+                )
                 repository_dependencies_dicts.append(repository_dependency_metadata_dict)
         return repository_dependencies_dicts
 
@@ -140,14 +163,15 @@ class RepositoryRevisionsController(BaseAPIController):
         # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
         repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
         if repository_metadata is None:
-            log.debug(f'Cannot locate repository_metadata with id {str(id)}')
+            log.debug(f"Cannot locate repository_metadata with id {str(id)}")
             return {}
         encoded_repository_id = trans.security.encode_id(repository_metadata.repository_id)
-        repository_metadata_dict = repository_metadata.to_dict(view='element',
-                                                               value_mapper=self.__get_value_mapper(trans))
-        repository_metadata_dict['url'] = web.url_for(controller='repositories',
-                                                      action='show',
-                                                      id=encoded_repository_id)
+        repository_metadata_dict = repository_metadata.to_dict(
+            view="element", value_mapper=self.__get_value_mapper(trans)
+        )
+        repository_metadata_dict["url"] = web.url_for(
+            controller="repositories", action="show", id=encoded_repository_id
+        )
         return repository_metadata_dict
 
     @web.legacy_expose_api
@@ -158,13 +182,13 @@ class RepositoryRevisionsController(BaseAPIController):
 
         :param id: the encoded id of the `RepositoryMetadata` object
         """
-        repository_metadata_id = kwd.get('id', None)
+        repository_metadata_id = kwd.get("id", None)
         if repository_metadata_id is None:
             raise HTTPBadRequest(detail="Missing required parameter 'id'.")
         repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
         if repository_metadata is None:
             decoded_repository_metadata_id = trans.security.decode_id(repository_metadata_id)
-            log.debug(f'Cannot locate repository_metadata with id {str(decoded_repository_metadata_id)}')
+            log.debug(f"Cannot locate repository_metadata with id {str(decoded_repository_metadata_id)}")
             return {}
         else:
             decoded_repository_metadata_id = repository_metadata.id
@@ -172,20 +196,25 @@ class RepositoryRevisionsController(BaseAPIController):
         for key, new_value in payload.items():
             if hasattr(repository_metadata, key):
                 # log information when setting attributes associated with the Tool Shed's install and test framework.
-                if key in ['includes_tools', 'missing_test_components']:
-                    log.debug('Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.' %
-                              (str(key), str(new_value), str(repository_metadata.changeset_revision)))
+                if key in ["includes_tools", "missing_test_components"]:
+                    log.debug(
+                        "Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API."
+                        % (str(key), str(new_value), str(repository_metadata.changeset_revision))
+                    )
                 setattr(repository_metadata, key, new_value)
                 flush_needed = True
         if flush_needed:
-            log.debug('Updating repository_metadata record with id %s and changeset_revision %s.' %
-                      (str(decoded_repository_metadata_id), str(repository_metadata.changeset_revision)))
+            log.debug(
+                "Updating repository_metadata record with id %s and changeset_revision %s."
+                % (str(decoded_repository_metadata_id), str(repository_metadata.changeset_revision))
+            )
             trans.sa_session.add(repository_metadata)
             trans.sa_session.flush()
             trans.sa_session.refresh(repository_metadata)
-        repository_metadata_dict = repository_metadata.to_dict(view='element',
-                                                               value_mapper=self.__get_value_mapper(trans))
-        repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
-                                                      action='show',
-                                                      id=repository_metadata_id)
+        repository_metadata_dict = repository_metadata.to_dict(
+            view="element", value_mapper=self.__get_value_mapper(trans)
+        )
+        repository_metadata_dict["url"] = web.url_for(
+            controller="repository_revisions", action="show", id=repository_metadata_id
+        )
         return repository_metadata_dict
diff --git a/lib/tool_shed/webapp/api/tools.py b/lib/tool_shed/webapp/api/tools.py
index e0097ab4cd2..8bb8d4f5845 100644
--- a/lib/tool_shed/webapp/api/tools.py
+++ b/lib/tool_shed/webapp/api/tools.py
@@ -5,7 +5,7 @@ from collections import namedtuple
 from galaxy import (
     exceptions,
     util,
-    web
+    web,
 )
 from galaxy.tools.parameters import params_to_strings
 from galaxy.tools.repositories import ValidationContext
@@ -17,8 +17,8 @@ from tool_shed.util import (
     common_util,
     metadata_util,
     repository_util,
-    shed_util_common as suc
 )
+from tool_shed.util import shed_util_common as suc
 from tool_shed.utility_containers import ToolShedUtilityContainerManager
 from tool_shed.webapp.search.tool_search import ToolSearch
 
@@ -56,22 +56,24 @@ class ToolsController(BaseAPIController):
             GET http://localhost:9009/api/tools
             GET http://localhost:9009/api/tools?q=fastq
         """
-        q = kwd.get('q', '')
+        q = kwd.get("q", "")
         if not q:
-            raise exceptions.NotImplemented('Listing of all the tools is not implemented. Provide parameter "q" to search instead.')
+            raise exceptions.NotImplemented(
+                'Listing of all the tools is not implemented. Provide parameter "q" to search instead.'
+            )
         else:
-            page = kwd.get('page', 1)
-            page_size = kwd.get('page_size', 10)
+            page = kwd.get("page", 1)
+            page_size = kwd.get("page_size", 10)
             try:
                 page = int(page)
                 page_size = int(page_size)
             except ValueError:
                 raise exceptions.RequestParameterInvalidException('The "page" and "page_size" have to be integers.')
-            return_jsonp = util.asbool(kwd.get('jsonp', False))
-            callback = kwd.get('callback', 'callback')
+            return_jsonp = util.asbool(kwd.get("jsonp", False))
+            callback = kwd.get("callback", "callback")
             search_results = self._search(trans, q, page, page_size)
             if return_jsonp:
-                response = str(f'{callback}({json.dumps(search_results)});')
+                response = str(f"{callback}({json.dumps(search_results)});")
             else:
                 response = json.dumps(search_results)
             return response
@@ -86,30 +88,31 @@ class ToolsController(BaseAPIController):
         """
         conf = self.app.config
         if not conf.toolshed_search_on:
-            raise exceptions.ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.')
+            raise exceptions.ConfigDoesNotAllowException(
+                "Searching the TS through the API is turned off for this instance."
+            )
         if not conf.whoosh_index_dir:
-            raise exceptions.ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
+            raise exceptions.ConfigDoesNotAllowException(
+                "There is no directory for the search index specified. Please contact the administrator."
+            )
         search_term = q.strip()
         if len(search_term) < 1:
-            raise exceptions.RequestParameterInvalidException('The search term has to be at least one character long.')
+            raise exceptions.RequestParameterInvalidException("The search term has to be at least one character long.")
 
         tool_search = ToolSearch()
 
-        Boosts = namedtuple('Boosts', ['tool_name_boost',
-                                       'tool_description_boost',
-                                       'tool_help_boost',
-                                       'tool_repo_owner_username_boost'])
-        boosts = Boosts(float(conf.get('tool_name_boost', 1.2)),
-                        float(conf.get('tool_description_boost', 0.6)),
-                        float(conf.get('tool_help_boost', 0.4)),
-                        float(conf.get('tool_repo_owner_username_boost', 0.3)))
+        Boosts = namedtuple(
+            "Boosts", ["tool_name_boost", "tool_description_boost", "tool_help_boost", "tool_repo_owner_username_boost"]
+        )
+        boosts = Boosts(
+            float(conf.get("tool_name_boost", 1.2)),
+            float(conf.get("tool_description_boost", 0.6)),
+            float(conf.get("tool_help_boost", 0.4)),
+            float(conf.get("tool_repo_owner_username_boost", 0.3)),
+        )
 
-        results = tool_search.search(trans,
-                                     search_term,
-                                     page,
-                                     page_size,
-                                     boosts)
-        results['hostname'] = web.url_for('/', qualified=True)
+        results = tool_search.search(trans, search_term, page, page_size, boosts)
+        results["hostname"] = web.url_for("/", qualified=True)
         return results
 
     @expose_api_raw_anonymous_and_sessionless
@@ -128,27 +131,26 @@ class ToolsController(BaseAPIController):
         :param changeset:     the changeset at which to load the tool json
         :param changeset:     str
         """
-        guid = kwd.get('guid', None)
-        tsr_id = kwd.get('tsr_id', None)
-        changeset = kwd.get('changeset', None)
+        guid = kwd.get("guid", None)
+        tsr_id = kwd.get("tsr_id", None)
+        changeset = kwd.get("changeset", None)
         if None in [changeset, tsr_id, guid]:
-            message = 'Changeset, repository ID, and tool GUID are all required parameters.'
+            message = "Changeset, repository ID, and tool GUID are all required parameters."
             trans.response.status = 400
-            return {'status': 'error', 'message': message}
+            return {"status": "error", "message": message}
         tsucm = ToolShedUtilityContainerManager(trans.app)
         repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
         repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(repository.user, repository)
         repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, tsr_id, changeset)
-        toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
+        toolshed_base_url = str(web.url_for("/", qualified=True)).rstrip("/")
         rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
         repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
-        containers_dict = tsucm.build_repository_containers(repository,
-                                                            changeset,
-                                                            repository_dependencies,
-                                                            repository_metadata)
+        containers_dict = tsucm.build_repository_containers(
+            repository, changeset, repository_dependencies, repository_metadata
+        )
         found_tool = None
-        for folder in containers_dict['valid_tools'].folders:
-            if hasattr(folder, 'valid_tools'):
+        for folder in containers_dict["valid_tools"].folders:
+            if hasattr(folder, "valid_tools"):
                 for tool in folder.valid_tools:
                     tool.id = tool.tool_id
                     tool_guid = suc.generate_tool_guid(repository_clone_url, tool)
@@ -156,33 +158,35 @@ class ToolsController(BaseAPIController):
                         found_tool = tool
                         break
         if found_tool is None:
-            message = f'Unable to find tool with guid {guid} in repository {repository.name}.'
+            message = f"Unable to find tool with guid {guid} in repository {repository.name}."
             trans.response.status = 404
-            return {'status': 'error', 'message': message}
+            return {"status": "error", "message": message}
 
         with ValidationContext.from_app(trans.app) as validation_context:
             tv = tool_validator.ToolValidator(validation_context)
-            repository, tool, valid, message = tv.load_tool_from_changeset_revision(tsr_id,
-                                                                                    changeset,
-                                                                                    found_tool.tool_config)
+            repository, tool, valid, message = tv.load_tool_from_changeset_revision(
+                tsr_id, changeset, found_tool.tool_config
+            )
         if message or not valid:
-            status = 'error'
+            status = "error"
             return dict(message=message, status=status)
-        tool_help = ''
+        tool_help = ""
         if tool.help:
-            tool_help = tool.help.render(static_path=web.url_for('/static'), host_url=web.url_for('/', qualified=True))
-            tool_help = util.unicodify(tool_help, 'utf-8')
+            tool_help = tool.help.render(static_path=web.url_for("/static"), host_url=web.url_for("/", qualified=True))
+            tool_help = util.unicodify(tool_help, "utf-8")
         tool_dict = tool.to_dict(trans)
-        tool_dict['inputs'] = {}
-        tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
-        tool_dict.update({
-            'help': tool_help,
-            'citations': bool(tool.citations),
-            'requirements': [{'name': r.name, 'version': r.version} for r in tool.requirements],
-            'state_inputs': params_to_strings(tool.inputs, {}, trans.app),
-            'display': tool.display_interface,
-            'action': web.url_for(tool.action),
-            'method': tool.method,
-            'enctype': tool.enctype
-        })
+        tool_dict["inputs"] = {}
+        tool.populate_model(trans, tool.inputs, {}, tool_dict["inputs"])
+        tool_dict.update(
+            {
+                "help": tool_help,
+                "citations": bool(tool.citations),
+                "requirements": [{"name": r.name, "version": r.version} for r in tool.requirements],
+                "state_inputs": params_to_strings(tool.inputs, {}, trans.app),
+                "display": tool.display_interface,
+                "action": web.url_for(tool.action),
+                "method": tool.method,
+                "enctype": tool.enctype,
+            }
+        )
         return json.dumps(tool_dict)
diff --git a/lib/tool_shed/webapp/api/users.py b/lib/tool_shed/webapp/api/users.py
index 556aee34dfa..822b215b6ac 100644
--- a/lib/tool_shed/webapp/api/users.py
+++ b/lib/tool_shed/webapp/api/users.py
@@ -3,12 +3,12 @@ import logging
 import tool_shed.util.shed_util_common as suc
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_password,
-    validate_publicname
+    validate_publicname,
 )
 from galaxy.webapps.base.controller import BaseAPIController
 
@@ -22,40 +22,32 @@ class UsersController(BaseAPIController):
     @web.require_admin
     def create(self, trans, payload, **kwd):
         """
-        POST /api/users
-        Returns a dictionary of information about the created user.
+                POST /api/users
+                Returns a dictionary of information about the created user.
 
-:       param key: the current Galaxy admin user's API key
+        :       param key: the current Galaxy admin user's API key
 
-        The following parameters are included in the payload.
-        :param email (required): the email address of the user
-        :param password (required): the password of the user
-        :param username (required): the public username of the user
+                The following parameters are included in the payload.
+                :param email (required): the email address of the user
+                :param password (required): the password of the user
+                :param username (required): the public username of the user
         """
-        user_dict = dict(message='',
-                         status='ok')
+        user_dict = dict(message="", status="ok")
         # Get the information about the user to be created from the payload.
-        email = payload.get('email', '')
-        password = payload.get('password', '')
-        username = payload.get('username', '')
-        message = self.__validate(trans,
-                                  email=email,
-                                  password=password,
-                                  confirm=password,
-                                  username=username)
+        email = payload.get("email", "")
+        password = payload.get("password", "")
+        username = payload.get("username", "")
+        message = self.__validate(trans, email=email, password=password, confirm=password, username=username)
         if message:
-            message = f'email: {email}, username: {username} - {message}'
-            user_dict['message'] = message
-            user_dict['status'] = 'error'
+            message = f"email: {email}, username: {username} - {message}"
+            user_dict["message"] = message
+            user_dict["status"] = "error"
         else:
             # Create the user.
             user = self.__create_user(trans, email, username, password)
-            user_dict = user.to_dict(view='element',
-                                     value_mapper=self.__get_value_mapper(trans))
-            user_dict['message'] = f"User '{str(user.username)}' has been created."
-            user_dict['url'] = web.url_for(controller='users',
-                                           action='show',
-                                           id=trans.security.encode_id(user.id))
+            user_dict = user.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+            user_dict["message"] = f"User '{str(user.username)}' has been created."
+            user_dict["url"] = web.url_for(controller="users", action="show", id=trans.security.encode_id(user.id))
         return user_dict
 
     def __create_user(self, trans, email, username, password):
@@ -72,7 +64,7 @@ class UsersController(BaseAPIController):
         return user
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id': trans.security.encode_id}
+        value_mapper = {"id": trans.security.encode_id}
         return value_mapper
 
     @web.legacy_expose_api_anonymous
@@ -84,14 +76,13 @@ class UsersController(BaseAPIController):
         # Example URL: http://localhost:9009/api/users
         user_dicts = []
         deleted = util.asbool(deleted)
-        for user in trans.sa_session.query(trans.app.model.User) \
-                                    .filter(trans.app.model.User.table.c.deleted == deleted) \
-                                    .order_by(trans.app.model.User.table.c.username):
-            user_dict = user.to_dict(view='collection',
-                                     value_mapper=self.__get_value_mapper(trans))
-            user_dict['url'] = web.url_for(controller='users',
-                                           action='show',
-                                           id=trans.security.encode_id(user.id))
+        for user in (
+            trans.sa_session.query(trans.app.model.User)
+            .filter(trans.app.model.User.table.c.deleted == deleted)
+            .order_by(trans.app.model.User.table.c.username)
+        ):
+            user_dict = user.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
+            user_dict["url"] = web.url_for(controller="users", action="show", id=trans.security.encode_id(user.id))
             user_dicts.append(user_dict)
         return user_dicts
 
@@ -106,22 +97,22 @@ class UsersController(BaseAPIController):
         """
         user = None
         # user is requesting data about themselves
-        user = trans.user if id == 'current' else suc.get_user(trans.app, id)
+        user = trans.user if id == "current" else suc.get_user(trans.app, id)
         if user is None:
-            user_dict = dict(message=f'Unable to locate user record for id {str(id)}.',
-                             status='error')
+            user_dict = dict(message=f"Unable to locate user record for id {str(id)}.", status="error")
             return user_dict
-        user_dict = user.to_dict(view='element',
-                                 value_mapper=self.__get_value_mapper(trans))
-        user_dict['url'] = web.url_for(controller='users',
-                                       action='show',
-                                       id=trans.security.encode_id(user.id))
+        user_dict = user.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
+        user_dict["url"] = web.url_for(controller="users", action="show", id=trans.security.encode_id(user.id))
         return user_dict
 
     def __validate(self, trans, email, password, confirm, username):
-        if username in ['repos']:
+        if username in ["repos"]:
             return f"The term '{username}' is a reserved word in the Tool Shed, so it cannot be used as a public user name."
-        message = "\n".join((validate_email(trans, email),
-                             validate_password(trans, password, confirm),
-                             validate_publicname(trans, username))).rstrip()
+        message = "\n".join(
+            (
+                validate_email(trans, email),
+                validate_password(trans, password, confirm),
+                validate_publicname(trans, username),
+            )
+        ).rstrip()
         return message
diff --git a/lib/tool_shed/webapp/app.py b/lib/tool_shed/webapp/app.py
index bf0ac7c8cb3..9f1c1671632 100644
--- a/lib/tool_shed/webapp/app.py
+++ b/lib/tool_shed/webapp/app.py
@@ -17,7 +17,10 @@ from galaxy.managers.citations import CitationsManager
 from galaxy.managers.users import UserManager
 from galaxy.model.base import SharedModelMapping
 from galaxy.model.tags import CommunityTagHandler
-from galaxy.quota import NoQuotaAgent, QuotaAgent
+from galaxy.quota import (
+    NoQuotaAgent,
+    QuotaAgent,
+)
 from galaxy.security import idencoding
 from galaxy.structured_app import BasicSharedApp
 from galaxy.util.dbkeys import GenomeBuilds
@@ -58,13 +61,13 @@ class UniverseApplication(BasicSharedApp, SentryClientMixin):
             db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE"
         # Initialize the Tool Shed database and check for appropriate schema version.
         from tool_shed.webapp.model.migrate.check import create_or_verify_database
+
         create_or_verify_database(db_url, self.config.database_engine_options)
         # Set up the Tool Shed database engine and ORM.
         from tool_shed.webapp.model import mapping
+
         model: mapping.ToolShedModelMapping = mapping.init(
-            self.config.file_path,
-            db_url,
-            self.config.database_engine_options
+            self.config.file_path, db_url, self.config.database_engine_options
         )
         self.model = model
         self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
diff --git a/lib/tool_shed/webapp/buildapp.py b/lib/tool_shed/webapp/buildapp.py
index 48ab3dee0ac..1c165d32ef5 100644
--- a/lib/tool_shed/webapp/buildapp.py
+++ b/lib/tool_shed/webapp/buildapp.py
@@ -29,8 +29,9 @@ def add_ui_controllers(webapp, app):
     Search for controllers in the 'galaxy.webapps.controllers' module and add
     them to the webapp.
     """
-    from galaxy.webapps.base.controller import BaseUIController
     import tool_shed.webapp.controllers
+    from galaxy.webapps.base.controller import BaseUIController
+
     controller_dir = tool_shed.webapp.controllers.__path__[0]
     for fname in os.listdir(controller_dir):
         if not fname.startswith("_") and fname.endswith(".py"):
@@ -50,145 +51,158 @@ def app_factory(global_conf, load_app_kwds=None, **kwargs):
     """Return a wsgi application serving the root object"""
     # Create the Galaxy tool shed application unless passed in
     load_app_kwds = load_app_kwds or {}
-    kwargs = load_app_properties(
-        kwds=kwargs,
-        config_prefix='TOOL_SHED_CONFIG_',
-        **load_app_kwds
-    )
-    if 'app' in kwargs:
-        app = kwargs.pop('app')
+    kwargs = load_app_properties(kwds=kwargs, config_prefix="TOOL_SHED_CONFIG_", **load_app_kwds)
+    if "app" in kwargs:
+        app = kwargs.pop("app")
     else:
         try:
             from tool_shed.webapp.app import UniverseApplication
+
             app = UniverseApplication(global_conf=global_conf, **kwargs)
         except Exception:
-            import traceback
             import sys
+            import traceback
+
             traceback.print_exc()
             sys.exit(1)
     atexit.register(app.shutdown)
     # Create the universe WSGI application
-    webapp = CommunityWebApplication(app, session_cookie='galaxycommunitysession', name="tool_shed")
+    webapp = CommunityWebApplication(app, session_cookie="galaxycommunitysession", name="tool_shed")
     add_ui_controllers(webapp, app)
-    webapp.add_route('/view/{owner}', controller='repository', action='sharable_owner')
-    webapp.add_route('/view/{owner}/{name}', controller='repository', action='sharable_repository')
-    webapp.add_route('/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision')
+    webapp.add_route("/view/{owner}", controller="repository", action="sharable_owner")
+    webapp.add_route("/view/{owner}/{name}", controller="repository", action="sharable_repository")
+    webapp.add_route(
+        "/view/{owner}/{name}/{changeset_revision}", controller="repository", action="sharable_repository_revision"
+    )
     # Handle displaying tool help images and README file images for tools contained in repositories.
-    webapp.add_route('/repository/static/images/{repository_id}/{image_file:.+?}',
-                     controller='repository',
-                     action='display_image_in_repository',
-                     repository_id=None,
-                     image_file=None)
-    webapp.add_route('/{controller}/{action}', action='index')
-    webapp.add_route('/{action}', controller='repository', action='index')
+    webapp.add_route(
+        "/repository/static/images/{repository_id}/{image_file:.+?}",
+        controller="repository",
+        action="display_image_in_repository",
+        repository_id=None,
+        image_file=None,
+    )
+    webapp.add_route("/{controller}/{action}", action="index")
+    webapp.add_route("/{action}", controller="repository", action="index")
     # Enable 'hg clone' functionality on repos by letting hgwebapp handle the request
-    webapp.add_route('/repos/*path_info', controller='hg', action='handle_request', path_info='/')
+    webapp.add_route("/repos/*path_info", controller="hg", action="handle_request", path_info="/")
     # Add the web API.  # A good resource for RESTful services - https://routes.readthedocs.io/en/latest/restful.html
-    webapp.add_api_controllers('tool_shed.webapp.api', app)
-    webapp.mapper.connect('api_key_retrieval',
-                          '/api/authenticate/baseauth/',
-                          controller='authenticate',
-                          action='get_tool_shed_api_key',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('group',
-                          '/api/groups/',
-                          controller='groups',
-                          action='index',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('group',
-                          '/api/groups/',
-                          controller='groups',
-                          action='create',
-                          conditions=dict(method=["POST"]))
-    webapp.mapper.connect('group',
-                          '/api/groups/{encoded_id}',
-                          controller='groups',
-                          action='show',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.resource('category',
-                           'categories',
-                           controller='categories',
-                           name_prefix='category_',
-                           path_prefix='/api',
-                           parent_resources=dict(member_name='category', collection_name='categories'))
-    webapp.mapper.connect('repositories_in_category',
-                          '/api/categories/{category_id}/repositories',
-                          controller='categories',
-                          action='get_repositories',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('show_updates_for_repository',
-                          '/api/repositories/updates',
-                          controller='repositories',
-                          action='updates',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.resource('repository',
-                           'repositories',
-                           controller='repositories',
-                           collection={'add_repository_registry_entry': 'POST',
-                                       'get_repository_revision_install_info': 'GET',
-                                       'get_ordered_installable_revisions': 'GET',
-                                       'get_installable_revisions': 'GET',
-                                       'remove_repository_registry_entry': 'POST',
-                                       'repository_ids_for_setting_metadata': 'GET',
-                                       'reset_metadata_on_repositories': 'POST',
-                                       'reset_metadata_on_repository': 'POST'},
-                           name_prefix='repository_',
-                           path_prefix='/api',
-                           parent_resources=dict(member_name='repository', collection_name='repositories'))
-    webapp.mapper.resource('repository_revision',
-                           'repository_revisions',
-                           member={'repository_dependencies': 'GET',
-                                   'export': 'POST'},
-                           controller='repository_revisions',
-                           name_prefix='repository_revision_',
-                           path_prefix='/api',
-                           parent_resources=dict(member_name='repository_revision', collection_name='repository_revisions'))
-    webapp.mapper.resource('user',
-                           'users',
-                           controller='users',
-                           name_prefix='user_',
-                           path_prefix='/api',
-                           parent_resources=dict(member_name='user', collection_name='users'))
-    webapp.mapper.connect('update_repository',
-                          '/api/repositories/{id}',
-                          controller='repositories',
-                          action='update',
-                          conditions=dict(method=["PATCH", "PUT"]))
-    webapp.mapper.connect('repository_create_changeset_revision',
-                          '/api/repositories/{id}/changeset_revision',
-                          controller='repositories',
-                          action='create_changeset_revision',
-                          conditions=dict(method=["POST"]))
-    webapp.mapper.connect('repository_get_metadata',
-                          '/api/repositories/{id}/metadata',
-                          controller='repositories',
-                          action='metadata',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('repository_show_tools',
-                          '/api/repositories/{id}/{changeset}/show_tools',
-                          controller='repositories',
-                          action='show_tools',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('create_repository',
-                          '/api/repositories',
-                          controller='repositories',
-                          action='create',
-                          conditions=dict(method=["POST"]))
-    webapp.mapper.connect('tools',
-                          '/api/tools',
-                          controller='tools',
-                          action='index',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect('json',
-                          '/api/tools/json',
-                          controller='tools',
-                          action='json',
-                          conditions=dict(method=["GET"]))
-    webapp.mapper.connect("version", "/api/version", controller="configuration", action="version", conditions=dict(method=["GET"]))
+    webapp.add_api_controllers("tool_shed.webapp.api", app)
+    webapp.mapper.connect(
+        "api_key_retrieval",
+        "/api/authenticate/baseauth/",
+        controller="authenticate",
+        action="get_tool_shed_api_key",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect("group", "/api/groups/", controller="groups", action="index", conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "group", "/api/groups/", controller="groups", action="create", conditions=dict(method=["POST"])
+    )
+    webapp.mapper.connect(
+        "group", "/api/groups/{encoded_id}", controller="groups", action="show", conditions=dict(method=["GET"])
+    )
+    webapp.mapper.resource(
+        "category",
+        "categories",
+        controller="categories",
+        name_prefix="category_",
+        path_prefix="/api",
+        parent_resources=dict(member_name="category", collection_name="categories"),
+    )
+    webapp.mapper.connect(
+        "repositories_in_category",
+        "/api/categories/{category_id}/repositories",
+        controller="categories",
+        action="get_repositories",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "show_updates_for_repository",
+        "/api/repositories/updates",
+        controller="repositories",
+        action="updates",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.resource(
+        "repository",
+        "repositories",
+        controller="repositories",
+        collection={
+            "add_repository_registry_entry": "POST",
+            "get_repository_revision_install_info": "GET",
+            "get_ordered_installable_revisions": "GET",
+            "get_installable_revisions": "GET",
+            "remove_repository_registry_entry": "POST",
+            "repository_ids_for_setting_metadata": "GET",
+            "reset_metadata_on_repositories": "POST",
+            "reset_metadata_on_repository": "POST",
+        },
+        name_prefix="repository_",
+        path_prefix="/api",
+        parent_resources=dict(member_name="repository", collection_name="repositories"),
+    )
+    webapp.mapper.resource(
+        "repository_revision",
+        "repository_revisions",
+        member={"repository_dependencies": "GET", "export": "POST"},
+        controller="repository_revisions",
+        name_prefix="repository_revision_",
+        path_prefix="/api",
+        parent_resources=dict(member_name="repository_revision", collection_name="repository_revisions"),
+    )
+    webapp.mapper.resource(
+        "user",
+        "users",
+        controller="users",
+        name_prefix="user_",
+        path_prefix="/api",
+        parent_resources=dict(member_name="user", collection_name="users"),
+    )
+    webapp.mapper.connect(
+        "update_repository",
+        "/api/repositories/{id}",
+        controller="repositories",
+        action="update",
+        conditions=dict(method=["PATCH", "PUT"]),
+    )
+    webapp.mapper.connect(
+        "repository_create_changeset_revision",
+        "/api/repositories/{id}/changeset_revision",
+        controller="repositories",
+        action="create_changeset_revision",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect(
+        "repository_get_metadata",
+        "/api/repositories/{id}/metadata",
+        controller="repositories",
+        action="metadata",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "repository_show_tools",
+        "/api/repositories/{id}/{changeset}/show_tools",
+        controller="repositories",
+        action="show_tools",
+        conditions=dict(method=["GET"]),
+    )
+    webapp.mapper.connect(
+        "create_repository",
+        "/api/repositories",
+        controller="repositories",
+        action="create",
+        conditions=dict(method=["POST"]),
+    )
+    webapp.mapper.connect("tools", "/api/tools", controller="tools", action="index", conditions=dict(method=["GET"]))
+    webapp.mapper.connect("json", "/api/tools/json", controller="tools", action="json", conditions=dict(method=["GET"]))
+    webapp.mapper.connect(
+        "version", "/api/version", controller="configuration", action="version", conditions=dict(method=["GET"])
+    )
 
     webapp.finalize_config()
     # Wrap the webapp in some useful middleware
-    if kwargs.get('middleware', True):
+    if kwargs.get("middleware", True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
     return webapp
 
@@ -199,11 +213,11 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     # Merge the global and local configurations
     conf = global_conf.copy()
     conf.update(local_conf)
-    debug = asbool(conf.get('debug', False))
+    debug = asbool(conf.get("debug", False))
     # First put into place httpexceptions, which must be most closely
     # wrapped around the application (it can interact poorly with
     # other middleware):
-    app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,))
+    app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name="paste.httpexceptions", args=(conf,))
     # Create a separate mapper for redirects to prevent conflicts.
     redirect_mapper = routes.Mapper()
     redirect_mapper = _map_redirects(redirect_mapper)
@@ -212,49 +226,62 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     # If we're using remote_user authentication, add middleware that
     # protects Galaxy from improperly configured authentication in the
     # upstream server
-    if asbool(conf.get('use_remote_user', False)):
+    if asbool(conf.get("use_remote_user", False)):
         from tool_shed.webapp.framework.middleware.remoteuser import RemoteUser
-        app = wrap_if_allowed(app, stack, RemoteUser,
-                              kwargs=dict(
-                                  maildomain=conf.get('remote_user_maildomain', None),
-                                  display_servers=util.listify(conf.get('display_servers', '')),
-                                  admin_users=conf.get('admin_users', '').split(','),
-                                  remote_user_header=conf.get('remote_user_header', 'HTTP_REMOTE_USER'),
-                                  remote_user_secret_header=conf.get('remote_user_secret', None),
-                                  normalize_remote_user_email=conf.get('normalize_remote_user_email', False)))
+
+        app = wrap_if_allowed(
+            app,
+            stack,
+            RemoteUser,
+            kwargs=dict(
+                maildomain=conf.get("remote_user_maildomain", None),
+                display_servers=util.listify(conf.get("display_servers", "")),
+                admin_users=conf.get("admin_users", "").split(","),
+                remote_user_header=conf.get("remote_user_header", "HTTP_REMOTE_USER"),
+                remote_user_secret_header=conf.get("remote_user_secret", None),
+                normalize_remote_user_email=conf.get("normalize_remote_user_email", False),
+            ),
+        )
     # The recursive middleware allows for including requests in other
     # requests or forwarding of requests, all on the server side.
-    if asbool(conf.get('use_recursive', True)):
+    if asbool(conf.get("use_recursive", True)):
         from paste import recursive
+
         app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
     # Transaction logging (apache access.log style)
-    if asbool(conf.get('use_translogger', True)):
+    if asbool(conf.get("use_translogger", True)):
         from paste.translogger import TransLogger
+
         app = wrap_if_allowed(app, stack, TransLogger)
     # If sentry logging is enabled, log here before propogating up to
     # the error middleware
     # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
-    sentry_dsn = conf.get('sentry_dsn', None)
+    sentry_dsn = conf.get("sentry_dsn", None)
     if sentry_dsn:
         from sentry_sdk.integrations.wsgi import SentryWsgiMiddleware
+
         app = wrap_if_allowed(app, stack, SentryWsgiMiddleware)
     # X-Forwarded-Host handling
     from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
+
     app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
     # Various debug middleware that can only be turned on if the debug
     # flag is set, either because they are insecure or greatly hurt
     # performance.
     if debug:
         # Middleware to check for WSGI compliance
-        if asbool(conf.get('use_lint', True)):
+        if asbool(conf.get("use_lint", True)):
             from paste import lint
-            app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
+
+            app = wrap_if_allowed(app, stack, lint.make_middleware, name="paste.lint", args=(conf,))
         # Middleware to run the python profiler on each request
-        if asbool(conf.get('use_profile', False)):
+        if asbool(conf.get("use_profile", False)):
             from paste.debug import profile
+
             app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
     # Error middleware
     import galaxy.web.framework.middleware.error
+
     app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
     return app
 
@@ -265,13 +292,19 @@ def _map_redirects(mapper):
     Subsequently when the redirect is triggered in Routes middleware the request
     will not even reach the webapp.
     """
+
     def forward_qs(environ, result):
-        qs_dict = parse_qs(environ['QUERY_STRING'])
+        qs_dict = parse_qs(environ["QUERY_STRING"])
         for qs in qs_dict:
             result[qs] = qs_dict[qs]
         return True
 
-    mapper.redirect("/repository/status_for_installed_repository", "/api/repositories/updates/", _redirect_code="301 Moved Permanently", conditions=dict(function=forward_qs))
+    mapper.redirect(
+        "/repository/status_for_installed_repository",
+        "/api/repositories/updates/",
+        _redirect_code="301 Moved Permanently",
+        conditions=dict(function=forward_qs),
+    )
     return mapper
 
 
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 094186b431b..d9b7fac51bb 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -15,7 +15,11 @@ from galaxy.config import (
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 from galaxy.util import string_as_bool
-from galaxy.version import VERSION, VERSION_MAJOR, VERSION_MINOR
+from galaxy.version import (
+    VERSION,
+    VERSION_MAJOR,
+    VERSION_MINOR,
+)
 from galaxy.web.formatting import expand_pretty_datetime_format
 
 try:
@@ -26,14 +30,14 @@ except ImportError:
 
 log = logging.getLogger(__name__)
 
-TOOLSHED_APP_NAME = 'tool_shed'
-TOOLSHED_CONFIG_SCHEMA_PATH = files('tool_shed.webapp') / 'config_schema.yml'
+TOOLSHED_APP_NAME = "tool_shed"
+TOOLSHED_CONFIG_SCHEMA_PATH = files("tool_shed.webapp") / "config_schema.yml"
 
 
 class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
-    default_config_file_name = 'tool_shed.yml'
+    default_config_file_name = "tool_shed.yml"
 
-    add_sample_file_to_defaults = {'datatypes_config_file'}
+    add_sample_file_to_defaults = {"datatypes_config_file"}
 
     def _load_schema(self):
         return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
@@ -53,13 +57,13 @@ class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.hgweb_config_dir,
             self.tool_data_path,
             self.template_cache_path,
-            os.path.join(self.tool_data_path, 'shared', 'jars'),
+            os.path.join(self.tool_data_path, "shared", "jars"),
         ]
         for path in paths_to_check:
             self._ensure_directory(path)
         # Check that required files exist.
         if not os.path.isfile(self.datatypes_config):
-            raise ConfigurationError(f'File not found: {self.datatypes_config}')
+            raise ConfigurationError(f"File not found: {self.datatypes_config}")
 
     def _process_config(self, kwargs):
         # Backwards compatibility for names used in too many places to fix
@@ -75,58 +79,70 @@ class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         if not self.database_connection:  # Provide default if not supplied by user
             self.database_connection = f"sqlite:///{self._in_data_dir('community.sqlite')}?isolation_level=IMMEDIATE"
         self.database_engine_options = get_database_engine_options(kwargs)
-        self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
+        self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True"))
         # Where dataset files are stored
         self.file_path = self._in_root_dir(self.file_path)
         self.new_file_path = self._in_root_dir(self.new_file_path)
-        self.cookie_path = kwargs.get('cookie_path')
-        self.cookie_domain = kwargs.get('cookie_domain')
-        self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
+        self.cookie_path = kwargs.get("cookie_path")
+        self.cookie_domain = kwargs.get("cookie_domain")
+        self.enable_quotas = string_as_bool(kwargs.get("enable_quotas", False))
         # Tool stuff
-        self.tool_path = self._in_root_dir(kwargs.get('tool_path', 'tools'))
-        self.tool_secret = kwargs.get('tool_secret', '')
-        self.tool_data_path = os.path.join(os.getcwd(), kwargs.get('tool_data_path', 'shed-tool-data'))
+        self.tool_path = self._in_root_dir(kwargs.get("tool_path", "tools"))
+        self.tool_secret = kwargs.get("tool_secret", "")
+        self.tool_data_path = os.path.join(os.getcwd(), kwargs.get("tool_data_path", "shed-tool-data"))
         self.tool_data_table_config_path = None
-        self.integrated_tool_panel_config = self._in_root_dir(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'))
-        self.builds_file_path = self._in_root_dir(kwargs.get('builds_file_path', os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')))
-        self.len_file_path = self._in_root_dir(kwargs.get('len_file_path', os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')))
-        self.ftp_upload_dir = kwargs.get('ftp_upload_dir')
+        self.integrated_tool_panel_config = self._in_root_dir(
+            kwargs.get("integrated_tool_panel_config", "integrated_tool_panel.xml")
+        )
+        self.builds_file_path = self._in_root_dir(
+            kwargs.get("builds_file_path", os.path.join(self.tool_data_path, "shared", "ucsc", "builds.txt"))
+        )
+        self.len_file_path = self._in_root_dir(
+            kwargs.get("len_file_path", os.path.join(self.tool_data_path, "shared", "ucsc", "chrom"))
+        )
+        self.ftp_upload_dir = kwargs.get("ftp_upload_dir")
         self.update_integrated_tool_panel = False
         # Galaxy flavor Docker Image
         self.user_activation_on = None
-        self.registration_warning_message = kwargs.get('registration_warning_message')
+        self.registration_warning_message = kwargs.get("registration_warning_message")
         self.email_domain_blocklist_content = None
         self.email_domain_allowlist_content = None
-        self.template_cache_path = self._in_root_dir(kwargs.get('template_cache_path', 'database/compiled_templates/community'))
-        self.error_email_to = kwargs.get('error_email_to')
+        self.template_cache_path = self._in_root_dir(
+            kwargs.get("template_cache_path", "database/compiled_templates/community")
+        )
+        self.error_email_to = kwargs.get("error_email_to")
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         # Configuration for the message box directly below the masthead.
-        self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
-        self.blog_url = kwargs.get('blog_url')
-        self.screencasts_url = kwargs.get('screencasts_url')
+        self.wiki_url = kwargs.get("wiki_url", "https://galaxyproject.org/")
+        self.blog_url = kwargs.get("blog_url")
+        self.screencasts_url = kwargs.get("screencasts_url")
         self.log_events = False
         self.cloud_controller_instance = False
-        self.server_name = ''
+        self.server_name = ""
         # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
         self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir) or self.root
         # Proxy features
-        self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script')
+        self.drmaa_external_runjob_script = kwargs.get("drmaa_external_runjob_script")
         # Parse global_conf and save the parser
-        global_conf = kwargs.get('global_conf')
+        global_conf = kwargs.get("global_conf")
         global_conf_parser = configparser.ConfigParser()
         self.global_conf_parser = global_conf_parser
-        if global_conf and '__file__' in global_conf and '.yml' not in global_conf['__file__']:
-            global_conf_parser.read(global_conf['__file__'])
-        self.running_functional_tests = string_as_bool(kwargs.get('running_functional_tests', False))
-        self.citation_cache_data_dir = self._in_root_dir(kwargs.get('citation_cache_data_dir', 'database/tool_shed_citations/data'))
-        self.citation_cache_lock_dir = self._in_root_dir(kwargs.get('citation_cache_lock_dir', 'database/tool_shed_citations/locks'))
+        if global_conf and "__file__" in global_conf and ".yml" not in global_conf["__file__"]:
+            global_conf_parser.read(global_conf["__file__"])
+        self.running_functional_tests = string_as_bool(kwargs.get("running_functional_tests", False))
+        self.citation_cache_data_dir = self._in_root_dir(
+            kwargs.get("citation_cache_data_dir", "database/tool_shed_citations/data")
+        )
+        self.citation_cache_lock_dir = self._in_root_dir(
+            kwargs.get("citation_cache_lock_dir", "database/tool_shed_citations/locks")
+        )
         self.password_expiration_period = timedelta(days=int(self.password_expiration_period))
 
         # Security/Policy Compliance
         self.redact_username_during_deletion = False
         self.redact_email_during_deletion = False
         self.redact_username_in_logs = False
-        self.enable_beta_gdpr = string_as_bool(kwargs.get('enable_beta_gdpr', False))
+        self.enable_beta_gdpr = string_as_bool(kwargs.get("enable_beta_gdpr", False))
         if self.enable_beta_gdpr:
             self.redact_username_during_deletion = True
             self.redact_email_during_deletion = True
diff --git a/lib/tool_shed/webapp/controllers/admin.py b/lib/tool_shed/webapp/controllers/admin.py
index 71d79df638b..3c1e9f75bc6 100644
--- a/lib/tool_shed/webapp/controllers/admin.py
+++ b/lib/tool_shed/webapp/controllers/admin.py
@@ -3,7 +3,7 @@ import logging
 import tool_shed.grids.admin_grids as admin_grids
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.util import inflector
 from galaxy.web.legacy_framework import grids
@@ -12,8 +12,8 @@ from tool_shed.metadata import repository_metadata_manager
 from tool_shed.util import (
     metadata_util,
     repository_util,
-    shed_util_common as suc
 )
+from tool_shed.util import shed_util_common as suc
 from tool_shed.util.admin_util import Admin
 from tool_shed.util.web_util import escape
 
@@ -30,8 +30,12 @@ class AdminController(BaseUIController, Admin):
     repository_metadata_grid = admin_grids.RepositoryMetadataGrid()
 
     delete_operation = grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True)
-    undelete_operation = grids.GridOperation("Undelete", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True)
-    purge_operation = grids.GridOperation("Purge", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True)
+    undelete_operation = grids.GridOperation(
+        "Undelete", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True
+    )
+    purge_operation = grids.GridOperation(
+        "Purge", condition=(lambda item: item.deleted and not item.purged), allow_multiple=True
+    )
 
     @web.expose
     @web.require_admin
@@ -39,48 +43,48 @@ class AdminController(BaseUIController, Admin):
         # We add parameters to the keyword dict in this method in order to rename the param
         # with an "f-" prefix, simulating filtering by clicking a search link.  We have
         # to take this approach because the "-" character is illegal in HTTP requests.
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repositories',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_repositories", **kwd)
+                )
             elif operation == "edit_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='edit_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="edit_repository", **kwd)
+                )
             elif operation == "repositories_by_user":
                 # Eliminate the current filters if any exist.
                 for k in list(kwd.keys()):
-                    if k.startswith('f-'):
+                    if k.startswith("f-"):
                         del kwd[k]
-                if 'user_id' in kwd:
-                    user = suc.get_user(trans.app, kwd['user_id'])
-                    kwd['f-email'] = user.email
-                    del kwd['user_id']
+                if "user_id" in kwd:
+                    user = suc.get_user(trans.app, kwd["user_id"])
+                    kwd["f-email"] = user.email
+                    del kwd["user_id"]
                 else:
                     # The received id is the repository id, so we need to get the id of the user
                     # that uploaded the repository.
-                    repository_id = kwd.get('id', None)
+                    repository_id = kwd.get("id", None)
                     repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-                    kwd['f-email'] = repository.user.email
+                    kwd["f-email"] = repository.user.email
             elif operation == "repositories_by_category":
                 # Eliminate the current filters if any exist.
                 for k in list(kwd.keys()):
-                    if k.startswith('f-'):
+                    if k.startswith("f-"):
                         del kwd[k]
-                category_id = kwd.get('id', None)
+                category_id = kwd.get("id", None)
                 category = suc.get_category(trans.app, category_id)
-                kwd['f-Category.name'] = category.name
+                kwd["f-Category.name"] = category.name
             elif operation == "receive email alerts":
-                if kwd['id']:
-                    kwd['caller'] = 'browse_repositories'
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action='set_email_alerts',
-                                                                    **kwd))
+                if kwd["id"]:
+                    kwd["caller"] = "browse_repositories"
+                    return trans.response.send_redirect(
+                        web.url_for(controller="repository", action="set_email_alerts", **kwd)
+                    )
                 else:
-                    del kwd['operation']
-            elif operation == 'delete':
+                    del kwd["operation"]
+            elif operation == "delete":
                 return self.delete_repository(trans, **kwd)
             elif operation == "undelete":
                 return self.undelete_repository(trans, **kwd)
@@ -91,54 +95,58 @@ class AdminController(BaseUIController, Admin):
         # know the refresh_on_change occurred, and we have the necessary repository id and change set
         # revision to pass on.
         for k, v in kwd.items():
-            changeset_revision_str = 'changeset_revision_'
+            changeset_revision_str = "changeset_revision_"
             if k.startswith(changeset_revision_str):
                 repository_id = trans.security.encode_id(int(k.lstrip(changeset_revision_str)))
                 repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
                 if repository.tip() != v:
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action='browse_repositories',
-                                                                    operation='view_or_manage_repository',
-                                                                    id=trans.security.encode_id(repository.id),
-                                                                    changeset_revision=v))
+                    return trans.response.send_redirect(
+                        web.url_for(
+                            controller="repository",
+                            action="browse_repositories",
+                            operation="view_or_manage_repository",
+                            id=trans.security.encode_id(repository.id),
+                            changeset_revision=v,
+                        )
+                    )
         # Render the list view
         return self.repository_grid(trans, **kwd)
 
     @web.expose
     @web.require_admin
     def browse_repository_metadata(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "delete":
                 return self.delete_repository_metadata(trans, **kwd)
             if operation == "view_or_manage_repository_revision":
                 # The received id is a RepositoryMetadata object id, so we need to get the
                 # associated Repository and redirect to view_or_manage_repository with the
                 # changeset_revision.
-                repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, kwd['id'])
+                repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, kwd["id"])
                 repository = repository_metadata.repository
-                kwd['id'] = trans.security.encode_id(repository.id)
-                kwd['changeset_revision'] = repository_metadata.changeset_revision
-                kwd['operation'] = 'view_or_manage_repository'
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repositories',
-                                                                **kwd))
+                kwd["id"] = trans.security.encode_id(repository.id)
+                kwd["changeset_revision"] = repository_metadata.changeset_revision
+                kwd["operation"] = "view_or_manage_repository"
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_repositories", **kwd)
+                )
         return self.repository_metadata_grid(trans, **kwd)
 
     @web.expose
     @web.require_admin
     def create_category(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        name = kwd.get('name', '').strip()
-        description = kwd.get('description', '').strip()
-        if kwd.get('create_category_button', False):
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        name = kwd.get("name", "").strip()
+        description = kwd.get("description", "").strip()
+        if kwd.get("create_category_button", False):
             if not name or not description:
-                message = 'Enter a valid name and a description'
-                status = 'error'
+                message = "Enter a valid name and a description"
+                status = "error"
             elif suc.get_category_by_name(trans.app, name):
-                message = 'A category with that name already exists'
-                status = 'error'
+                message = "A category with that name already exists"
+                status = "error"
             else:
                 # Create the category
                 category = trans.app.model.Category(name=name, description=description)
@@ -147,23 +155,24 @@ class AdminController(BaseUIController, Admin):
                 # Update the Tool Shed's repository registry.
                 trans.app.repository_registry.add_category_entry(category)
                 message = f"Category '{escape(category.name)}' has been created"
-                status = 'done'
-                trans.response.send_redirect(web.url_for(controller='admin',
-                                                         action='manage_categories',
-                                                         message=message,
-                                                         status=status))
-        return trans.fill_template('/webapps/tool_shed/category/create_category.mako',
-                                   name=name,
-                                   description=description,
-                                   message=message,
-                                   status=status)
+                status = "done"
+                trans.response.send_redirect(
+                    web.url_for(controller="admin", action="manage_categories", message=message, status=status)
+                )
+        return trans.fill_template(
+            "/webapps/tool_shed/category/create_category.mako",
+            name=name,
+            description=description,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def delete_repository(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        id = kwd.get("id", None)
         if id:
             # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
             ids = util.listify(id)
@@ -190,23 +199,28 @@ class AdminController(BaseUIController, Admin):
                         count += 1
                         deleted_repositories += f" {repository.name} "
             if count:
-                message = "Deleted %d %s: %s" % (count, inflector.cond_plural(len(ids), "repository"), escape(deleted_repositories))
+                message = "Deleted %d %s: %s" % (
+                    count,
+                    inflector.cond_plural(len(ids), "repository"),
+                    escape(deleted_repositories),
+                )
             else:
                 message = "All selected repositories were already marked deleted."
         else:
             message = "No repository ids received for deleting."
-            status = 'error'
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='browse_repositories',
-                                                 message=util.sanitize_text(message),
-                                                 status=status))
+            status = "error"
+        trans.response.send_redirect(
+            web.url_for(
+                controller="admin", action="browse_repositories", message=util.sanitize_text(message), status=status
+            )
+        )
 
     @web.expose
     @web.require_admin
     def delete_repository_metadata(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        id = kwd.get("id", None)
         if id:
             ids = util.listify(id)
             count = 0
@@ -219,39 +233,42 @@ class AdminController(BaseUIController, Admin):
                 message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record"))
         else:
             message = "No repository metadata ids received for deleting."
-            status = 'error'
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='browse_repository_metadata',
-                                                 message=util.sanitize_text(message),
-                                                 status=status))
+            status = "error"
+        trans.response.send_redirect(
+            web.url_for(
+                controller="admin",
+                action="browse_repository_metadata",
+                message=util.sanitize_text(message),
+                status=status,
+            )
+        )
 
     @web.expose
     @web.require_admin
     def edit_category(self, trans, **kwd):
-        '''Handle requests to edit TS category name or description'''
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        id = kwd.get('id', None)
+        """Handle requests to edit TS category name or description"""
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        id = kwd.get("id", None)
         if not id:
             message = "No category ids received for editing"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='manage_categories',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="manage_categories", message=message, status="error")
+            )
         category = suc.get_category(trans.app, id)
         original_category_name = str(category.name)
         original_category_description = str(category.description)
-        if kwd.get('edit_category_button', False):
+        if kwd.get("edit_category_button", False):
             flush_needed = False
-            new_name = kwd.get('name', '').strip()
-            new_description = kwd.get('description', '').strip()
+            new_name = kwd.get("name", "").strip()
+            new_description = kwd.get("description", "").strip()
             if original_category_name != new_name:
                 if not new_name:
-                    message = 'Enter a valid name'
-                    status = 'error'
+                    message = "Enter a valid name"
+                    status = "error"
                 elif original_category_name != new_name and suc.get_category_by_name(trans.app, new_name):
-                    message = 'A category with that name already exists'
-                    status = 'error'
+                    message = "A category with that name already exists"
+                    status = "error"
                 else:
                     category.name = new_name
                     flush_needed = True
@@ -266,116 +283,102 @@ class AdminController(BaseUIController, Admin):
                     # Update the Tool Shed's repository registry.
                     trans.app.repository_registry.edit_category_entry(original_category_name, new_name)
                 message = f"The information has been saved for category '{escape(category.name)}'"
-                status = 'done'
-                return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                action='manage_categories',
-                                                                message=message,
-                                                                status=status))
-        return trans.fill_template('/webapps/tool_shed/category/edit_category.mako',
-                                   category=category,
-                                   message=message,
-                                   status=status)
+                status = "done"
+                return trans.response.send_redirect(
+                    web.url_for(controller="admin", action="manage_categories", message=message, status=status)
+                )
+        return trans.fill_template(
+            "/webapps/tool_shed/category/edit_category.mako", category=category, message=message, status=status
+        )
 
     @web.expose
     @web.require_admin
     def manage_categories(self, trans, **kwd):
-        if 'f-free-text-search' in kwd:
+        if "f-free-text-search" in kwd:
             # Trick to enable searching repository name, description from the CategoryGrid.
             # What we've done is rendered the search box for the RepositoryGrid on the grid.mako
             # template for the CategoryGrid.  See ~/templates/webapps/tool_shed/category/grid.mako.
             # Since we are searching repositories and not categories, redirect to browse_repositories().
-            return trans.response.send_redirect(web.url_for(controller='admin',
-                                                            action='browse_repositories',
-                                                            **kwd))
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+            return trans.response.send_redirect(web.url_for(controller="admin", action="browse_repositories", **kwd))
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "create":
-                return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                action='create_category',
-                                                                **kwd))
+                return trans.response.send_redirect(web.url_for(controller="admin", action="create_category", **kwd))
             elif operation == "delete":
-                return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                action='mark_category_deleted',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="admin", action="mark_category_deleted", **kwd)
+                )
             elif operation == "undelete":
-                return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                action='undelete_category',
-                                                                **kwd))
+                return trans.response.send_redirect(web.url_for(controller="admin", action="undelete_category", **kwd))
             elif operation == "purge":
-                return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                action='purge_category',
-                                                                **kwd))
+                return trans.response.send_redirect(web.url_for(controller="admin", action="purge_category", **kwd))
             elif operation == "edit":
-                return trans.response.send_redirect(web.url_for(controller='admin',
-                                                                action='edit_category',
-                                                                **kwd))
+                return trans.response.send_redirect(web.url_for(controller="admin", action="edit_category", **kwd))
         return self.manage_category_grid(trans, **kwd)
 
     @web.expose
     @web.require_admin
     def regenerate_statistics(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        if 'regenerate_statistics_button' in kwd:
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        if "regenerate_statistics_button" in kwd:
             trans.app.shed_counter.generate_statistics()
             message = "Successfully regenerated statistics"
-        return trans.fill_template('/webapps/tool_shed/admin/statistics.mako',
-                                   message=message,
-                                   status=status)
+        return trans.fill_template("/webapps/tool_shed/admin/statistics.mako", message=message, status=status)
 
     @web.expose
     @web.require_admin
     def manage_role_associations(self, trans, **kwd):
         """Manage users, groups and repositories associated with a role."""
-        role_id = kwd.get('id', None)
+        role_id = kwd.get("id", None)
         role = repository_util.get_role_by_id(trans.app, role_id)
         # We currently only have a single role associated with a repository, the repository admin role.
         repository_role_association = role.repositories[0]
         repository = repository_role_association.repository
-        associations_dict = repository_util.handle_role_associations(trans.app,
-                                                                     role,
-                                                                     repository,
-                                                                     **kwd)
-        in_users = associations_dict.get('in_users', [])
-        out_users = associations_dict.get('out_users', [])
-        in_groups = associations_dict.get('in_groups', [])
-        out_groups = associations_dict.get('out_groups', [])
-        message = associations_dict.get('message', '')
-        status = associations_dict.get('status', 'done')
-        return trans.fill_template('/webapps/tool_shed/role/role.mako',
-                                   in_admin_controller=True,
-                                   repository=repository,
-                                   role=role,
-                                   in_users=in_users,
-                                   out_users=out_users,
-                                   in_groups=in_groups,
-                                   out_groups=out_groups,
-                                   message=message,
-                                   status=status)
+        associations_dict = repository_util.handle_role_associations(trans.app, role, repository, **kwd)
+        in_users = associations_dict.get("in_users", [])
+        out_users = associations_dict.get("out_users", [])
+        in_groups = associations_dict.get("in_groups", [])
+        out_groups = associations_dict.get("out_groups", [])
+        message = associations_dict.get("message", "")
+        status = associations_dict.get("status", "done")
+        return trans.fill_template(
+            "/webapps/tool_shed/role/role.mako",
+            in_admin_controller=True,
+            repository=repository,
+            role=role,
+            in_users=in_users,
+            out_users=out_users,
+            in_groups=in_groups,
+            out_groups=out_groups,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def reset_metadata_on_selected_repositories_in_tool_shed(self, trans, **kwd):
         rmm = repository_metadata_manager.RepositoryMetadataManager(trans.app, trans.user)
-        if 'reset_metadata_on_selected_repositories_button' in kwd:
+        if "reset_metadata_on_selected_repositories_button" in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories(**kwd)
         else:
-            message = escape(util.restore_text(kwd.get('message', '')))
-            status = kwd.get('status', 'done')
-        repositories_select_field = rmm.build_repository_ids_select_field(name='repository_ids',
-                                                                          multiple=True,
-                                                                          display='checkboxes',
-                                                                          my_writable=False)
-        return trans.fill_template('/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako',
-                                   repositories_select_field=repositories_select_field,
-                                   message=message,
-                                   status=status)
+            message = escape(util.restore_text(kwd.get("message", "")))
+            status = kwd.get("status", "done")
+        repositories_select_field = rmm.build_repository_ids_select_field(
+            name="repository_ids", multiple=True, display="checkboxes", my_writable=False
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako",
+            repositories_select_field=repositories_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @web.require_admin
     def undelete_repository(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        id = kwd.get("id", None)
         if id:
             # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
             ids = util.listify(id)
@@ -407,15 +410,20 @@ class AdminController(BaseUIController, Admin):
                         count += 1
                         undeleted_repositories += f" {repository.name}"
             if count:
-                message = "Undeleted %d %s: %s" % (count, inflector.cond_plural(count, "repository"), undeleted_repositories)
+                message = "Undeleted %d %s: %s" % (
+                    count,
+                    inflector.cond_plural(count, "repository"),
+                    undeleted_repositories,
+                )
             else:
                 message = "No selected repositories were marked deleted, so they could not be undeleted."
         else:
             message = "No repository ids received for undeleting."
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='browse_repositories',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(
+                controller="admin", action="browse_repositories", message=util.sanitize_text(message), status="done"
+            )
+        )
 
     @web.expose
     @web.require_admin
@@ -423,8 +431,8 @@ class AdminController(BaseUIController, Admin):
         # TODO: We should probably eliminate the Category.deleted column since it really makes no
         # sense to mark a category as deleted (category names and descriptions can be changed instead).
         # If we do this, and the following 2 methods can be eliminated.
-        message = escape(kwd.get('message', ''))
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        id = kwd.get("id", None)
         if id:
             ids = util.listify(id)
             message = "Deleted %d categories: " % len(ids)
@@ -438,10 +446,11 @@ class AdminController(BaseUIController, Admin):
                 message += f" {escape(category.name)} "
         else:
             message = "No category ids received for deleting."
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='manage_categories',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(
+                controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done"
+            )
+        )
 
     @web.expose
     @web.require_admin
@@ -449,8 +458,8 @@ class AdminController(BaseUIController, Admin):
         # This method should only be called for a Category that has previously been deleted.
         # Purging a deleted Category deletes all of the following from the database:
         # - RepoitoryCategoryAssociations where category_id == Category.id
-        message = escape(kwd.get('message', ''))
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        id = kwd.get("id", None)
         if id:
             ids = util.listify(id)
             count = 0
@@ -467,16 +476,17 @@ class AdminController(BaseUIController, Admin):
             message = "Purged %d categories: %s" % (count, escape(purged_categories))
         else:
             message = "No category ids received for purging."
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='manage_categories',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(
+                controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done"
+            )
+        )
 
     @web.expose
     @web.require_admin
     def undelete_category(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        id = kwd.get("id", None)
         if id:
             ids = util.listify(id)
             count = 0
@@ -494,7 +504,8 @@ class AdminController(BaseUIController, Admin):
             message = "Undeleted %d categories: %s" % (count, escape(undeleted_categories))
         else:
             message = "No category ids received for undeleting."
-        trans.response.send_redirect(web.url_for(controller='admin',
-                                                 action='manage_categories',
-                                                 message=util.sanitize_text(message),
-                                                 status='done'))
+        trans.response.send_redirect(
+            web.url_for(
+                controller="admin", action="manage_categories", message=util.sanitize_text(message), status="done"
+            )
+        )
diff --git a/lib/tool_shed/webapp/controllers/groups.py b/lib/tool_shed/webapp/controllers/groups.py
index 2fbbef9e5bb..84e1e632fed 100644
--- a/lib/tool_shed/webapp/controllers/groups.py
+++ b/lib/tool_shed/webapp/controllers/groups.py
@@ -7,14 +7,10 @@ log = logging.getLogger(__name__)
 
 
 class Group(BaseUIController):
-
     @web.expose
     def index(self, trans, **kwd):
         # define app configuration for generic mako template
-        app = {
-            'jscript': "../toolshed/scripts/toolshed.groups"
-        }
-        return trans.fill_template('/webapps/tool_shed/group/index.mako',
-                                   config={
-                                       'title': 'Tool Shed Groups',
-                                       'app': app})
+        app = {"jscript": "../toolshed/scripts/toolshed.groups"}
+        return trans.fill_template(
+            "/webapps/tool_shed/group/index.mako", config={"title": "Tool Shed Groups", "app": app}
+        )
diff --git a/lib/tool_shed/webapp/controllers/hg.py b/lib/tool_shed/webapp/controllers/hg.py
index d61d43ff6b1..c07e2c665bb 100644
--- a/lib/tool_shed/webapp/controllers/hg.py
+++ b/lib/tool_shed/webapp/controllers/hg.py
@@ -19,20 +19,20 @@ class HgController(BaseUIController):
         hgweb_config = trans.app.hgweb_config_manager.hgweb_config
 
         def make_web_app():
-            hgwebapp = hgwebdir(hgweb_config.encode('utf-8'))
+            hgwebapp = hgwebdir(hgweb_config.encode("utf-8"))
             return hgwebapp
 
         wsgi_app = wsgiapplication(make_web_app)
         repository = None
-        path_info = kwd.get('path_info', None)
-        if path_info and len(path_info.split('/')) == 2:
-            owner, name = path_info.split('/')
+        path_info = kwd.get("path_info", None)
+        if path_info and len(path_info.split("/")) == 2:
+            owner, name = path_info.split("/")
             repository = get_repository_by_name_and_owner(trans.app, name, owner)
         if repository:
             if repository.deprecated:
                 raise ObjectNotFound("Requested repository not found or deprecated.")
-            cmd = kwd.get('cmd', None)
-            if cmd == 'getbundle':
+            cmd = kwd.get("cmd", None)
+            if cmd == "getbundle":
                 times_downloaded = repository.times_downloaded
                 times_downloaded += 1
                 repository.times_downloaded = times_downloaded
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 83b49dbcbee..386cef33c9f 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -9,19 +9,26 @@ from mercurial import (
     cmdutil,
     commands,
     mdiff,
-    patch
+    patch,
+)
+from sqlalchemy import (
+    and_,
+    false,
+    null,
 )
-from sqlalchemy import and_, false, null
 
 import tool_shed.grids.repository_grids as repository_grids
 import tool_shed.grids.util as grids_util
 import tool_shed.repository_types.util as rt_util
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.tools.repositories import ValidationContext
-from galaxy.web.form_builder import CheckboxField, SelectField
+from galaxy.web.form_builder import (
+    CheckboxField,
+    SelectField,
+)
 from galaxy.web.legacy_framework import grids
 from galaxy.webapps.base.controller import BaseUIController
 from tool_shed.dependencies.repository import relation_builder
@@ -29,7 +36,7 @@ from tool_shed.galaxy_install import dependency_display
 from tool_shed.metadata import repository_metadata_manager
 from tool_shed.tools import (
     tool_validator,
-    tool_version_manager
+    tool_version_manager,
 )
 from tool_shed.util import (
     basic_util,
@@ -40,9 +47,9 @@ from tool_shed.util import (
     readme_util,
     repository_util,
     search_util,
-    shed_util_common as suc,
-    tool_util
 )
+from tool_shed.util import shed_util_common as suc
+from tool_shed.util import tool_util
 from tool_shed.util.web_util import escape
 from tool_shed.utility_containers import ToolShedUtilityContainerManager
 from tool_shed.webapp.framework.decorators import require_login
@@ -55,14 +62,14 @@ malicious_error_can_push = "  Correct this changeset as soon as possible, it pot
 
 
 def get_mercurial_default_options_dict(command):
-    '''Borrowed from repoman - get default parameters for a mercurial command.'''
+    """Borrowed from repoman - get default parameters for a mercurial command."""
     possible = cmdutil.findpossible(command, commands.table)
     # Mercurial >= 3.4 returns a tuple whose first element is the old return dict
     if type(possible) is tuple:
         possible = possible[0]
     if len(possible) != 1:
         raise Exception(f'unable to find mercurial command "{command}"')
-    return {r[1].replace(b'-', b'_'): r[2] for r in next(iter(possible.values()))[1][1]}
+    return {r[1].replace(b"-", b"_"): r[2] for r in next(iter(possible.values()))[1][1]}
 
 
 class RepositoryController(BaseUIController, ratings_util.ItemRatings):
@@ -75,7 +82,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
     install_matched_repository_grid = repository_grids.InstallMatchedRepositoryGrid()
     matched_repository_grid = repository_grids.MatchedRepositoryGrid()
     my_writable_repositories_grid = repository_grids.MyWritableRepositoriesGrid()
-    my_writable_repositories_missing_tool_test_components_grid = repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid()
+    my_writable_repositories_missing_tool_test_components_grid = (
+        repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid()
+    )
     my_writable_repositories_with_invalid_tools_grid = repository_grids.MyWritableRepositoriesWithInvalidToolsGrid()
     repositories_by_user_grid = repository_grids.RepositoriesByUserGrid()
     repositories_i_own_grid = repository_grids.RepositoriesIOwnGrid()
@@ -93,90 +102,91 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
     valid_repository_grid = repository_grids.ValidRepositoryGrid()
 
     def _redirect_if_necessary(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **kwd)
+                )
             elif operation == "repositories_by_user":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repositories_by_user',
-                                                                **kwd))
-            elif operation in ['mark as deprecated', 'mark as not deprecated']:
-                kwd['mark_deprecated'] = operation == 'mark as deprecated'
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='deprecate',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_repositories_by_user", **kwd)
+                )
+            elif operation in ["mark as deprecated", "mark as not deprecated"]:
+                kwd["mark_deprecated"] = operation == "mark as deprecated"
+                return trans.response.send_redirect(web.url_for(controller="repository", action="deprecate", **kwd))
 
     @web.expose
     def browse_categories(self, trans, **kwd):
         # The request came from the tool shed.
-        if 'f-free-text-search' in kwd:
+        if "f-free-text-search" in kwd:
             # Trick to enable searching repository name, description from the CategoryGrid.
             # What we've done is rendered the search box for the RepositoryGrid on the grid.mako
             # template for the CategoryGrid.  See ~/templates/webapps/tool_shed/category/grid.mako.
             # Since we are searching repositories and not categories, redirect to browse_repositories().
-            if 'id' in kwd and 'f-free-text-search' in kwd and kwd['id'] == kwd['f-free-text-search']:
+            if "id" in kwd and "f-free-text-search" in kwd and kwd["id"] == kwd["f-free-text-search"]:
                 # The value of 'id' has been set to the search string, which is a repository name.
                 # We'll try to get the desired encoded repository id to pass on.
                 try:
-                    repository_name = kwd['id']
+                    repository_name = kwd["id"]
                     repository = repository_util.get_repository_by_name(trans.app, repository_name)
-                    kwd['id'] = trans.security.encode_id(repository.id)
+                    kwd["id"] = trans.security.encode_id(repository.id)
                 except Exception:
                     pass
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            **kwd))
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+            return trans.response.send_redirect(
+                web.url_for(controller="repository", action="browse_repositories", **kwd)
+            )
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation in ["repositories_by_category", "repositories_by_user"]:
                 # Eliminate the current filters if any exist.
                 for k in list(kwd.keys()):
-                    if k.startswith('f-'):
+                    if k.startswith("f-"):
                         del kwd[k]
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repositories',
-                                                                **kwd))
-        title = trans.app.repository_grid_filter_manager.get_grid_title(trans,
-                                                                        trailing_string='by Category',
-                                                                        default='Repositories')
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_repositories", **kwd)
+                )
+        title = trans.app.repository_grid_filter_manager.get_grid_title(
+            trans, trailing_string="by Category", default="Repositories"
+        )
         self.category_grid.title = title
         return self.category_grid(trans, **kwd)
 
     @web.expose
     def browse_datatypes(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             # The received id is a RepositoryMetadata id.
-            repository_metadata_id = kwd['id']
+            repository_metadata_id = kwd["id"]
             repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
             repository_id = trans.security.encode_id(repository_metadata.repository_id)
             changeset_revision = repository_metadata.changeset_revision
-            new_kwd = dict(id=repository_id,
-                           changeset_revision=changeset_revision)
+            new_kwd = dict(id=repository_id, changeset_revision=changeset_revision)
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **new_kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **new_kwd)
+                )
         return self.datatypes_grid(trans, **kwd)
 
     @web.expose
     def browse_deprecated_repositories_i_own(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **kwd)
+                )
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            operation='view_or_manage_repository',
-                                                            id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    operation="view_or_manage_repository",
+                    id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
         return self.deprecated_repositories_i_own_grid(trans, **kwd)
 
     @web.expose
@@ -187,11 +197,15 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
 
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            operation='view_or_manage_repository',
-                                                            id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    operation="view_or_manage_repository",
+                    id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
         return self.my_writable_repositories_grid(trans, **kwd)
 
     @web.expose
@@ -200,15 +214,17 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         if _redir is not None:
             return _redir
 
-        if 'message' not in kwd:
-            message = 'This list contains repositories that match the following criteria:<br>'
-            message += '<ul>'
-            message += '<li>you are authorized to update them</li>'
-            message += '<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>'
-            message += '<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>'
-            message += '</ul>'
-            kwd['message'] = message
-            kwd['status'] = 'warning'
+        if "message" not in kwd:
+            message = "This list contains repositories that match the following criteria:<br>"
+            message += "<ul>"
+            message += "<li>you are authorized to update them</li>"
+            message += (
+                "<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>"
+            )
+            message += "<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>"
+            message += "</ul>"
+            kwd["message"] = message
+            kwd["status"] = "warning"
         return self.my_writable_repositories_missing_tool_test_components_grid(trans, **kwd)
 
     @web.expose
@@ -217,15 +233,15 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         if _redir is not None:
             return _redir
 
-        if 'message' not in kwd:
-            message = 'This list contains repositories that match the following criteria:<br>'
-            message += '<ul>'
-            message += '<li>you are authorized to update them</li>'
-            message += '<li>the latest metadata revision contains at least 1 invalid tool</li>'
-            message += '</ul>'
-            message += 'Click the tool config file name to see why the tool is invalid.'
-            kwd['message'] = message
-            kwd['status'] = 'warning'
+        if "message" not in kwd:
+            message = "This list contains repositories that match the following criteria:<br>"
+            message += "<ul>"
+            message += "<li>you are authorized to update them</li>"
+            message += "<li>the latest metadata revision contains at least 1 invalid tool</li>"
+            message += "</ul>"
+            message += "Click the tool config file name to see why the tool is invalid."
+            kwd["message"] = message
+            kwd["status"] = "warning"
         return self.my_writable_repositories_with_invalid_tools_grid(trans, **kwd)
 
     @web.expose
@@ -233,53 +249,62 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix,
         # simulating filtering by clicking a search link.  We have to take this approach because the "-"
         # character is illegal in HTTP requests.
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **kwd)
+                )
             elif operation == "edit_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='edit_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="edit_repository", **kwd)
+                )
             elif operation == "repositories_by_user":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repositories_by_user',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_repositories_by_user", **kwd)
+                )
             elif operation == "reviewed_repositories_i_own":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='reviewed_repositories_i_own'))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="reviewed_repositories_i_own")
+                )
             elif operation == "repositories_by_category":
-                category_id = kwd.get('id', None)
-                message = escape(kwd.get('message', ''))
-                status = kwd.get('status', 'done')
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repositories_in_category',
-                                                                id=category_id,
-                                                                message=message,
-                                                                status=status))
+                category_id = kwd.get("id", None)
+                message = escape(kwd.get("message", ""))
+                status = kwd.get("status", "done")
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository",
+                        action="browse_repositories_in_category",
+                        id=category_id,
+                        message=message,
+                        status=status,
+                    )
+                )
             elif operation == "receive email alerts":
                 if trans.user:
-                    if kwd['id']:
-                        kwd['caller'] = 'browse_repositories'
-                        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                        action='set_email_alerts',
-                                                                        **kwd))
+                    if kwd["id"]:
+                        kwd["caller"] = "browse_repositories"
+                        return trans.response.send_redirect(
+                            web.url_for(controller="repository", action="set_email_alerts", **kwd)
+                        )
                 else:
-                    kwd['message'] = 'You must be logged in to set email alerts.'
-                    kwd['status'] = 'error'
-                    del kwd['operation']
+                    kwd["message"] = "You must be logged in to set email alerts."
+                    kwd["status"] = "error"
+                    del kwd["operation"]
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            operation='view_or_manage_repository',
-                                                            id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
-        title = trans.app.repository_grid_filter_manager.get_grid_title(trans,
-                                                                        trailing_string='',
-                                                                        default='Repositories')
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    operation="view_or_manage_repository",
+                    id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
+        title = trans.app.repository_grid_filter_manager.get_grid_title(
+            trans, trailing_string="", default="Repositories"
+        )
         self.repository_grid.title = title
         return self.repository_grid(trans, **kwd)
 
@@ -288,40 +313,44 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         """Display the list of repositories owned by a specified user."""
         # Eliminate the current search filters if any exist.
         for k in list(kwd.keys()):
-            if k.startswith('f-'):
+            if k.startswith("f-"):
                 del kwd[k]
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
-        user_id = kwd.get('user_id', None)
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **kwd)
+                )
+        user_id = kwd.get("user_id", None)
         if user_id is None:
             # The received id is the repository id, so we need to get the id of the user that owns the repository.
-            repository_id = kwd.get('id', None)
+            repository_id = kwd.get("id", None)
             if repository_id:
                 repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
                 user_id = trans.security.encode_id(repository.user.id)
-                kwd['user_id'] = user_id
+                kwd["user_id"] = user_id
             else:
                 # The user selected a repository revision which results in a refresh_on_change.
                 selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
                 if repository:
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action='view_or_manage_repository',
-                                                                    id=trans.security.encode_id(repository.id),
-                                                                    changeset_revision=selected_changeset_revision))
+                    return trans.response.send_redirect(
+                        web.url_for(
+                            controller="repository",
+                            action="view_or_manage_repository",
+                            id=trans.security.encode_id(repository.id),
+                            changeset_revision=selected_changeset_revision,
+                        )
+                    )
         if user_id:
             user = suc.get_user(trans.app, user_id)
-            trailing_string = ''
-            default = f'Repositories Owned by {str(user.username)}'
+            trailing_string = ""
+            default = f"Repositories Owned by {str(user.username)}"
         else:
-            trailing_string = ''
-            default = 'Repositories'
-        title = trans.app.repository_grid_filter_manager.get_grid_title(trans,
-                                                                        trailing_string=trailing_string,
-                                                                        default=default)
+            trailing_string = ""
+            default = "Repositories"
+        title = trans.app.repository_grid_filter_manager.get_grid_title(
+            trans, trailing_string=trailing_string, default=default
+        )
         self.repositories_by_user_grid.title = title
         return self.repositories_by_user_grid(trans, **kwd)
 
@@ -333,11 +362,15 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
 
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            operation='view_or_manage_repository',
-                                                            id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    operation="view_or_manage_repository",
+                    id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
         return self.repositories_i_can_administer_grid(trans, **kwd)
 
     @web.expose
@@ -348,52 +381,60 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
 
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            operation='view_or_manage_repository',
-                                                            id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    operation="view_or_manage_repository",
+                    id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
         return self.repositories_i_own_grid(trans, **kwd)
 
     @web.expose
     def browse_repositories_in_category(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
-            if operation == 'repositories_by_user':
-                user_id = kwd.get('user_id', None)
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **kwd)
+                )
+            if operation == "repositories_by_user":
+                user_id = kwd.get("user_id", None)
                 if user_id is None:
                     # The received id is the repository id, so we need to get the id of the user that owns the repository.
-                    repository_id = kwd.get('id', None)
+                    repository_id = kwd.get("id", None)
                     if repository_id:
                         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
                         user_id = trans.security.encode_id(repository.user.id)
                         user = suc.get_user(trans.app, user_id)
                         self.repositories_by_user_grid.title = f"Repositories owned by {user.username}"
-                        kwd['user_id'] = user_id
+                        kwd["user_id"] = user_id
                         return self.repositories_by_user_grid(trans, **kwd)
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
             # The user selected a repository revision which results in a refresh_on_change.
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='view_or_manage_repository',
-                                                            id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
-        category_id = kwd.get('id', None)
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="view_or_manage_repository",
+                    id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
+        category_id = kwd.get("id", None)
         if category_id:
             category = suc.get_category(trans.app, category_id)
             if category:
-                trailing_string = f'in Category {str(category.name)}'
+                trailing_string = f"in Category {str(category.name)}"
             else:
-                trailing_string = 'in Category'
+                trailing_string = "in Category"
         else:
-            trailing_string = 'in Category'
-        title = trans.app.repository_grid_filter_manager.get_grid_title(trans,
-                                                                        trailing_string=trailing_string,
-                                                                        default='Repositories')
+            trailing_string = "in Category"
+        title = trans.app.repository_grid_filter_manager.get_grid_title(
+            trans, trailing_string=trailing_string, default="Repositories"
+        )
         self.repositories_in_category_grid.title = title
         return self.repositories_in_category_grid(trans, **kwd)
 
@@ -403,14 +444,16 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         if _redir is not None:
             return _redir
 
-        if 'message' not in kwd:
-            message = 'This list contains repositories that match the following criteria:<br>'
-            message += '<ul>'
-            message += '<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>'
-            message += '<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>'
-            message += '</ul>'
-            kwd['message'] = message
-            kwd['status'] = 'warning'
+        if "message" not in kwd:
+            message = "This list contains repositories that match the following criteria:<br>"
+            message += "<ul>"
+            message += (
+                "<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>"
+            )
+            message += "<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>"
+            message += "</ul>"
+            kwd["message"] = message
+            kwd["status"] = "warning"
         return self.repositories_missing_tool_test_components_grid(trans, **kwd)
 
     @web.expose
@@ -419,93 +462,91 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         if _redir is not None:
             return _redir
 
-        if 'message' not in kwd:
-            message = 'This list contains repositories that match the following criteria:<br>'
-            message += '<ul>'
-            message += '<li>the latest metadata revision contains at least 1 invalid tool</li>'
-            message += '</ul>'
-            message += 'Click the tool config file name to see why the tool is invalid.'
-            kwd['message'] = message
-            kwd['status'] = 'warning'
+        if "message" not in kwd:
+            message = "This list contains repositories that match the following criteria:<br>"
+            message += "<ul>"
+            message += "<li>the latest metadata revision contains at least 1 invalid tool</li>"
+            message += "</ul>"
+            message += "Click the tool config file name to see why the tool is invalid."
+            kwd["message"] = message
+            kwd["status"] = "warning"
         return self.repositories_with_invalid_tools_grid(trans, **kwd)
 
     @web.expose
     def browse_repository(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        commit_message = escape(kwd.get('commit_message', 'Deleted selected files'))
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        commit_message = escape(kwd.get("commit_message", "Deleted selected files"))
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo_path = repository.repo_path(trans.app)
         # Update repository files for browsing.
         hg_util.update_repository(repo_path)
         changeset_revision = repository.tip()
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             id,
-                                                                                             changeset_revision,
-                                                                                             metadata_only=True)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, id, changeset_revision, metadata_only=True
+        )
         repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
-        return trans.fill_template('/webapps/tool_shed/repository/browse_repository.mako',
-                                   repository=repository,
-                                   changeset_revision=changeset_revision,
-                                   metadata=metadata,
-                                   commit_message=commit_message,
-                                   repository_type_select_field=repository_type_select_field,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/browse_repository.mako",
+            repository=repository,
+            changeset_revision=changeset_revision,
+            metadata=metadata,
+            commit_message=commit_message,
+            repository_type_select_field=repository_type_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def browse_repository_dependencies(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             # The received id is a RepositoryMetadata id.
-            repository_metadata_id = kwd['id']
+            repository_metadata_id = kwd["id"]
             repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
             repository_id = trans.security.encode_id(repository_metadata.repository_id)
             changeset_revision = repository_metadata.changeset_revision
-            new_kwd = dict(id=repository_id,
-                           changeset_revision=changeset_revision)
+            new_kwd = dict(id=repository_id, changeset_revision=changeset_revision)
             if operation == "browse_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_repository',
-                                                                **new_kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_repository", **new_kwd)
+                )
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **new_kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **new_kwd)
+                )
         return self.repository_dependencies_grid(trans, **kwd)
 
     @web.expose
     def browse_tools(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             # The received id is a RepositoryMetadata id.
-            repository_metadata_id = kwd['id']
+            repository_metadata_id = kwd["id"]
             repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
             repository_id = trans.security.encode_id(repository_metadata.repository_id)
             changeset_revision = repository_metadata.changeset_revision
-            new_kwd = dict(id=repository_id,
-                           changeset_revision=changeset_revision)
+            new_kwd = dict(id=repository_id, changeset_revision=changeset_revision)
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **new_kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **new_kwd)
+                )
         return self.tools_grid(trans, **kwd)
 
     @web.expose
     def browse_tool_dependencies(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             # The received id is a RepositoryMetadata id.
-            repository_metadata_id = kwd['id']
+            repository_metadata_id = kwd["id"]
             repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
             repository_id = trans.security.encode_id(repository_metadata.repository_id)
             changeset_revision = repository_metadata.changeset_revision
-            new_kwd = dict(id=repository_id,
-                           changeset_revision=changeset_revision)
+            new_kwd = dict(id=repository_id, changeset_revision=changeset_revision)
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **new_kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **new_kwd)
+                )
         return self.tool_dependencies_grid(trans, **kwd)
 
     @web.expose
@@ -514,36 +555,36 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions.
         galaxy_url = common_util.handle_galaxy_url(trans, **kwd)
         if galaxy_url:
-            kwd['galaxy_url'] = galaxy_url
-        if 'f-free-text-search' in kwd:
-            if kwd['f-free-text-search'] == 'All':
+            kwd["galaxy_url"] = galaxy_url
+        if "f-free-text-search" in kwd:
+            if kwd["f-free-text-search"] == "All":
                 # The user performed a search, then clicked the "x" to eliminate the search criteria.
                 new_kwd = {}
                 return self.valid_category_grid(trans, **new_kwd)
             # Since we are searching valid repositories and not categories, redirect to browse_valid_repositories().
-            if 'id' in kwd and 'f-free-text-search' in kwd and kwd['id'] == kwd['f-free-text-search']:
+            if "id" in kwd and "f-free-text-search" in kwd and kwd["id"] == kwd["f-free-text-search"]:
                 # The value of 'id' has been set to the search string, which is a repository name.
                 # We'll try to get the desired encoded repository id to pass on.
                 try:
-                    name = kwd['id']
+                    name = kwd["id"]
                     repository = repository_util.get_repository_by_name(trans.app, name)
-                    kwd['id'] = trans.security.encode_id(repository.id)
+                    kwd["id"] = trans.security.encode_id(repository.id)
                 except Exception:
                     pass
             return self.browse_valid_repositories(trans, **kwd)
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation in ["valid_repositories_by_category", "valid_repositories_by_user"]:
                 # Eliminate the current filters if any exist.
                 for k in list(kwd.keys()):
-                    if k.startswith('f-'):
+                    if k.startswith("f-"):
                         del kwd[k]
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='browse_valid_repositories',
-                                                                **kwd))
-        title = trans.app.repository_grid_filter_manager.get_grid_title(trans,
-                                                                        trailing_string='by Category',
-                                                                        default='Categories of Valid Repositories')
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="browse_valid_repositories", **kwd)
+                )
+        title = trans.app.repository_grid_filter_manager.get_grid_title(
+            trans, trailing_string="by Category", default="Categories of Valid Repositories"
+        )
         self.valid_category_grid.title = title
         return self.valid_category_grid(trans, **kwd)
 
@@ -552,80 +593,91 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         """Filter repositories to those that are installable into Galaxy."""
         galaxy_url = common_util.handle_galaxy_url(trans, **kwd)
         if galaxy_url:
-            kwd['galaxy_url'] = galaxy_url
-        repository_id = kwd.get('id', None)
-        if 'f-free-text-search' in kwd:
-            if 'f-Category.name' in kwd:
+            kwd["galaxy_url"] = galaxy_url
+        repository_id = kwd.get("id", None)
+        if "f-free-text-search" in kwd:
+            if "f-Category.name" in kwd:
                 # The user browsed to a category and then entered a search string, so get the category associated with its value.
-                category_name = kwd['f-Category.name']
+                category_name = kwd["f-Category.name"]
                 category = suc.get_category_by_name(trans.app, category_name)
                 # Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method.
-                kwd['id'] = trans.security.encode_id(category.id)
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+                kwd["id"] = trans.security.encode_id(category.id)
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "preview_tools_in_changeset":
                 repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-                repository_metadata = metadata_util.get_latest_repository_metadata(trans.app, repository.id, downloadable=True)
+                repository_metadata = metadata_util.get_latest_repository_metadata(
+                    trans.app, repository.id, downloadable=True
+                )
                 latest_installable_changeset_revision = repository_metadata.changeset_revision
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='preview_tools_in_changeset',
-                                                                repository_id=repository_id,
-                                                                changeset_revision=latest_installable_changeset_revision))
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository",
+                        action="preview_tools_in_changeset",
+                        repository_id=repository_id,
+                        changeset_revision=latest_installable_changeset_revision,
+                    )
+                )
             elif operation == "valid_repositories_by_category":
                 # Eliminate the current filters if any exist.
                 for k in list(kwd.keys()):
-                    if k.startswith('f-'):
+                    if k.startswith("f-"):
                         del kwd[k]
-                category_id = kwd.get('id', None)
+                category_id = kwd.get("id", None)
                 category = suc.get_category(trans.app, category_id)
-                kwd['f-Category.name'] = category.name
+                kwd["f-Category.name"] = category.name
         selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change(trans.app, **kwd)
         if repository:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='preview_tools_in_changeset',
-                                                            repository_id=trans.security.encode_id(repository.id),
-                                                            changeset_revision=selected_changeset_revision))
-        url_args = dict(action='browse_valid_repositories',
-                        operation='preview_tools_in_changeset',
-                        repository_id=repository_id)
-        self.valid_repository_grid.operations = [grids.GridOperation("Preview and install",
-                                                                     url_args=url_args,
-                                                                     allow_multiple=False,
-                                                                     async_compatible=False)]
-        title = trans.app.repository_grid_filter_manager.get_grid_title(trans,
-                                                                        trailing_string='',
-                                                                        default='Valid Repositories')
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="preview_tools_in_changeset",
+                    repository_id=trans.security.encode_id(repository.id),
+                    changeset_revision=selected_changeset_revision,
+                )
+            )
+        url_args = dict(
+            action="browse_valid_repositories", operation="preview_tools_in_changeset", repository_id=repository_id
+        )
+        self.valid_repository_grid.operations = [
+            grids.GridOperation("Preview and install", url_args=url_args, allow_multiple=False, async_compatible=False)
+        ]
+        title = trans.app.repository_grid_filter_manager.get_grid_title(
+            trans, trailing_string="", default="Valid Repositories"
+        )
         self.valid_repository_grid.title = title
         return self.valid_repository_grid(trans, **kwd)
 
     @web.expose
     def check_for_updates(self, trans, **kwd):
         """Handle a request from a local Galaxy instance."""
-        message = escape(kwd.get('message', ''))
+        message = escape(kwd.get("message", ""))
         # If the request originated with the UpdateRepositoryManager, it will not include a galaxy_url.
         galaxy_url = common_util.handle_galaxy_url(trans, **kwd)
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         repo = repository.hg_repo
         # Default to the current changeset revision.
         update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
         latest_changeset_revision = changeset_revision
-        from_update_manager = kwd.get('from_update_manager', False)
+        from_update_manager = kwd.get("from_update_manager", False)
         if from_update_manager:
-            update = 'true'
-            no_update = 'false'
+            update = "true"
+            no_update = "false"
         elif galaxy_url:
             # Start building up the url to redirect back to the calling Galaxy instance.
-            params = dict(tool_shed_url=web.url_for('/', qualified=True),
-                          name=str(repository.name),
-                          owner=str(repository.user.username),
-                          changeset_revision=changeset_revision)
-            pathspec = ['admin_toolshed', 'update_to_changeset_revision']
+            params = dict(
+                tool_shed_url=web.url_for("/", qualified=True),
+                name=str(repository.name),
+                owner=str(repository.user.username),
+                changeset_revision=changeset_revision,
+            )
+            pathspec = ["admin_toolshed", "update_to_changeset_revision"]
         else:
-            message = f'Unable to check for updates due to an invalid Galaxy URL: <b>{galaxy_url}</b>.  '
-            message += 'You may need to enable third-party cookies in your browser.  '
+            message = f"Unable to check for updates due to an invalid Galaxy URL: <b>{galaxy_url}</b>.  "
+            message += "You may need to enable third-party cookies in your browser.  "
             return trans.show_error_message(message)
         if changeset_revision == repository.tip():
             # If changeset_revision is the repository tip, there are no additional updates.
@@ -633,9 +685,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 return no_update
             # Return the same value for changeset_revision and latest_changeset_revision.
         else:
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                              trans.security.encode_id(repository.id),
-                                                                                              changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                trans.app, trans.security.encode_id(repository.id), changeset_revision
+            )
             if repository_metadata:
                 # If changeset_revision is in the repository_metadata table for this repository, there are no
                 # additional updates.
@@ -656,9 +708,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                             latest_changeset_revision = changeset_hash
                             break
                         else:
-                            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                                              trans.security.encode_id(repository.id),
-                                                                                                              changeset_hash)
+                            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                                trans.app, trans.security.encode_id(repository.id), changeset_hash
+                            )
                             if repository_metadata:
                                 # We found a RepositoryMetadata record.
                                 update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_hash)
@@ -674,74 +726,77 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     if latest_changeset_revision == changeset_revision:
                         return no_update
                     return update
-        params['latest_changeset_revision'] = str(latest_changeset_revision)
-        params['latest_ctx_rev'] = str(update_to_ctx.rev())
+        params["latest_changeset_revision"] = str(latest_changeset_revision)
+        params["latest_ctx_rev"] = str(update_to_ctx.rev())
         url = util.build_url(galaxy_url, pathspec=pathspec, params=params)
         return trans.response.send_redirect(url)
 
     @web.expose
     def contact_owner(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             id,
-                                                                                             repository.tip(),
-                                                                                             metadata_only=True)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, id, repository.tip(), metadata_only=True
+        )
         if trans.user and trans.user.email:
-            return trans.fill_template("/webapps/tool_shed/repository/contact_owner.mako",
-                                       repository=repository,
-                                       metadata=metadata,
-                                       message=message,
-                                       status=status)
+            return trans.fill_template(
+                "/webapps/tool_shed/repository/contact_owner.mako",
+                repository=repository,
+                metadata=metadata,
+                message=message,
+                status=status,
+            )
         else:
             # Do all we can to eliminate spam.
             return trans.show_error_message("You must be logged in to contact the owner of a repository.")
 
     @web.expose
     def create_galaxy_docker_image(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_ids = util.listify(kwd.get('id', ''))
-        if 'operation' in kwd:
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_ids = util.listify(kwd.get("id", ""))
+        if "operation" in kwd:
             if repository_ids:
-                operation = kwd['operation'].lower()
+                operation = kwd["operation"].lower()
                 if operation == "include in docker image":
                     repository_tups = []
                     for repository_id in repository_ids:
                         repository = repository_util.get_repository_by_id(trans.app, repository_id)
-                        repository_tups.append((str(repository.name),
-                                                str(repository.user.username),
-                                                str(repository.type)))
-                    return trans.fill_template("/webapps/tool_shed/repository/docker_image_repositories.mako",
-                                               id=','.join(repository_ids),
-                                               repository_tups=repository_tups,
-                                               message=message,
-                                               status=status)
+                        repository_tups.append(
+                            (str(repository.name), str(repository.user.username), str(repository.type))
+                        )
+                    return trans.fill_template(
+                        "/webapps/tool_shed/repository/docker_image_repositories.mako",
+                        id=",".join(repository_ids),
+                        repository_tups=repository_tups,
+                        message=message,
+                        status=status,
+                    )
             else:
                 # This can only occur when there is a multi-select grid with check boxes and an operation,
                 # and the user clicked the operation button without checking any of the check boxes.
-                kwd['message'] = "No items were selected."
-                kwd['status'] = 'error'
-        elif kwd.get('create_docker_image_button', False):
+                kwd["message"] = "No items were selected."
+                kwd["status"] = "error"
+        elif kwd.get("create_docker_image_button", False):
             tmp_image_dir = tempfile.mkdtemp(prefix="tmp-toolshed-cdidir")
-            docker_file_name = 'Dockerfile'
+            docker_file_name = "Dockerfile"
             docker_file_path = os.path.join(tmp_image_dir, docker_file_name)
-            tool_shed_url = tool_shed_url = web.url_for('/', qualified=True)
-            repository_string = ''
+            tool_shed_url = tool_shed_url = web.url_for("/", qualified=True)
+            repository_string = ""
             for repository_id in repository_ids:
                 repository = repository_util.get_repository_by_id(trans.app, repository_id)
                 template = basic_util.SELECTED_REPOSITORIES_TEMPLATE
-                repository_template = \
-                    string.Template(template).safe_substitute(tool_shed_url=tool_shed_url,
-                                                              repository_owner=str(repository.user.username),
-                                                              repository_name=str(repository.name))
-                repository_string = f'{repository_string}\n{repository_template}'
+                repository_template = string.Template(template).safe_substitute(
+                    tool_shed_url=tool_shed_url,
+                    repository_owner=str(repository.user.username),
+                    repository_name=str(repository.name),
+                )
+                repository_string = f"{repository_string}\n{repository_template}"
             template = basic_util.DOCKER_IMAGE_TEMPLATE
-            docker_image_template = \
-                string.Template(template).safe_substitute(selected_repositories=repository_string)
+            docker_image_template = string.Template(template).safe_substitute(selected_repositories=repository_string)
             docker_image_string = docker_image_template
-            trans.response.set_content_type('application/text/plain')
+            trans.response.set_content_type("application/text/plain")
             trans.response.headers["Content-Disposition"] = f'attachment; filename="{docker_file_name}"'
             opened_file = open(docker_file_path, "w")
             opened_file.write(docker_image_string)
@@ -756,61 +811,68 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
 
     @web.expose
     def create_repository(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         categories = suc.get_categories(trans)
         if not categories:
-            message = 'No categories have been configured in this instance of the Galaxy Tool Shed.  '
-            message += 'An administrator needs to create some via the Administrator control panel before creating repositories.'
-            status = 'error'
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            message=message,
-                                                            status=status))
-        name = kwd.get('name', '').strip()
-        remote_repository_url = kwd.get('remote_repository_url', '')
-        homepage_url = kwd.get('homepage_url', '')
-        description = kwd.get('description', '')
-        long_description = kwd.get('long_description', '')
-        category_ids = util.listify(kwd.get('category_id', ''))
+            message = "No categories have been configured in this instance of the Galaxy Tool Shed.  "
+            message += "An administrator needs to create some via the Administrator control panel before creating repositories."
+            status = "error"
+            return trans.response.send_redirect(
+                web.url_for(controller="repository", action="browse_repositories", message=message, status=status)
+            )
+        name = kwd.get("name", "").strip()
+        remote_repository_url = kwd.get("remote_repository_url", "")
+        homepage_url = kwd.get("homepage_url", "")
+        description = kwd.get("description", "")
+        long_description = kwd.get("long_description", "")
+        category_ids = util.listify(kwd.get("category_id", ""))
         selected_categories = [trans.security.decode_id(id) for id in category_ids]
-        repository_type = kwd.get('repository_type', rt_util.UNRESTRICTED)
-        if kwd.get('create_repository_button', False):
+        repository_type = kwd.get("repository_type", rt_util.UNRESTRICTED)
+        if kwd.get("create_repository_button", False):
             error = False
             message = repository_util.validate_repository_name(trans.app, name, trans.user)
             if message:
                 error = True
             if not description:
-                message = 'Enter a description.'
+                message = "Enter a description."
                 error = True
             if error:
-                status = 'error'
+                status = "error"
             else:
-                repository, message = repository_util.create_repository(trans.app,
-                                                                        name,
-                                                                        repository_type,
-                                                                        description,
-                                                                        long_description,
-                                                                        user_id=trans.user.id,
-                                                                        category_ids=category_ids,
-                                                                        remote_repository_url=remote_repository_url,
-                                                                        homepage_url=homepage_url)
-                trans.response.send_redirect(web.url_for(controller='repository',
-                                                         action='manage_repository',
-                                                         message=message,
-                                                         id=trans.security.encode_id(repository.id)))
+                repository, message = repository_util.create_repository(
+                    trans.app,
+                    name,
+                    repository_type,
+                    description,
+                    long_description,
+                    user_id=trans.user.id,
+                    category_ids=category_ids,
+                    remote_repository_url=remote_repository_url,
+                    homepage_url=homepage_url,
+                )
+                trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository",
+                        action="manage_repository",
+                        message=message,
+                        id=trans.security.encode_id(repository.id),
+                    )
+                )
         repository_type_select_field = rt_util.build_repository_type_select_field(trans)
-        return trans.fill_template('/webapps/tool_shed/repository/create_repository.mako',
-                                   name=name,
-                                   remote_repository_url=remote_repository_url,
-                                   homepage_url=homepage_url,
-                                   description=description,
-                                   long_description=long_description,
-                                   selected_categories=selected_categories,
-                                   categories=categories,
-                                   repository_type_select_field=repository_type_select_field,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/create_repository.mako",
+            name=name,
+            remote_repository_url=remote_repository_url,
+            homepage_url=homepage_url,
+            description=description,
+            long_description=long_description,
+            selected_categories=selected_categories,
+            categories=categories,
+            repository_type_select_field=repository_type_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("deprecate repository")
@@ -819,27 +881,31 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset
         # revisions that may be associated with the repository.  Revisions are not marked as not downlaodable
         # because those that have installed the repository must be allowed to get updates.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_id = kwd.get("id", None)
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-        mark_deprecated = util.string_as_bool(kwd.get('mark_deprecated', False))
+        mark_deprecated = util.string_as_bool(kwd.get("mark_deprecated", False))
         repository.deprecated = mark_deprecated
         trans.sa_session.add(repository)
         trans.sa_session.flush()
         if mark_deprecated:
             # Update the repository registry.
             trans.app.repository_registry.remove_entry(repository)
-            message = f'The repository <b>{escape(repository.name)}</b> has been marked as deprecated.'
+            message = f"The repository <b>{escape(repository.name)}</b> has been marked as deprecated."
         else:
             # Update the repository registry.
             trans.app.repository_registry.add_entry(repository)
-            message = f'The repository <b>{escape(repository.name)}</b> has been marked as not deprecated.'
-        trans.response.send_redirect(web.url_for(controller='repository',
-                                                 action='browse_repositories',
-                                                 operation='repositories_i_own',
-                                                 message=message,
-                                                 status=status))
+            message = f"The repository <b>{escape(repository.name)}</b> has been marked as not deprecated."
+        trans.response.send_redirect(
+            web.url_for(
+                controller="repository",
+                action="browse_repositories",
+                operation="repositories_i_own",
+                message=message,
+                status=status,
+            )
+        )
 
     @web.expose
     def display_image_in_repository(self, trans, **kwd):
@@ -853,68 +919,79 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         .. image:: some_image.jpg
         .. image:: /deep/some_image.png
         """
-        repository_id = kwd.get('repository_id', None)
-        relative_path_to_image_file = kwd.get('image_file', None)
+        repository_id = kwd.get("repository_id", None)
+        relative_path_to_image_file = kwd.get("image_file", None)
         if repository_id and relative_path_to_image_file:
             repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
             if repository:
                 repo_files_dir = repository.repo_path(trans.app)
-                path_to_file = repository_util.get_absolute_path_to_file_in_repository(repo_files_dir, relative_path_to_image_file)
+                path_to_file = repository_util.get_absolute_path_to_file_in_repository(
+                    repo_files_dir, relative_path_to_image_file
+                )
                 if os.path.exists(path_to_file):
                     file_name = os.path.basename(relative_path_to_image_file)
                     try:
-                        extension = file_name.split('.')[-1]
+                        extension = file_name.split(".")[-1]
                     except Exception:
                         extension = None
                     if extension:
                         mimetype = trans.app.datatypes_registry.get_mimetype_by_extension(extension)
                         if mimetype:
                             trans.response.set_content_type(mimetype)
-                    return open(path_to_file, 'rb')
+                    return open(path_to_file, "rb")
         return None
 
     @web.expose
     def display_tool(self, trans, repository_id, tool_config, changeset_revision, **kwd):
-        status = kwd.get('status', 'done')
-        render_repository_actions_for = kwd.get('render_repository_actions_for', 'tool_shed')
+        status = kwd.get("status", "done")
+        render_repository_actions_for = kwd.get("render_repository_actions_for", "tool_shed")
         with ValidationContext.from_app(trans.app) as validation_context:
             tv = tool_validator.ToolValidator(validation_context)
-            repository, tool, valid, message = tv.load_tool_from_changeset_revision(repository_id,
-                                                                                    changeset_revision,
-                                                                                    tool_config)
+            repository, tool, valid, message = tv.load_tool_from_changeset_revision(
+                repository_id, changeset_revision, tool_config
+            )
         if message or not valid:
-            status = 'error'
+            status = "error"
         tool_state = tool_util.new_state(trans, tool, invalid=not valid)
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             repository_id,
-                                                                                             changeset_revision,
-                                                                                             metadata_only=True)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, repository_id, changeset_revision, metadata_only=True
+        )
         try:
-            return trans.fill_template("/webapps/tool_shed/repository/tool_form.mako",
-                                       repository=repository,
-                                       render_repository_actions_for=render_repository_actions_for,
-                                       metadata=metadata,
-                                       changeset_revision=changeset_revision,
-                                       tool=tool,
-                                       tool_state=tool_state,
-                                       message=message,
-                                       status=status)
+            return trans.fill_template(
+                "/webapps/tool_shed/repository/tool_form.mako",
+                repository=repository,
+                render_repository_actions_for=render_repository_actions_for,
+                metadata=metadata,
+                changeset_revision=changeset_revision,
+                tool=tool,
+                tool_state=tool_state,
+                message=message,
+                status=status,
+            )
         except Exception as e:
             message = f"Error displaying tool, probably due to a problem in the tool config.  The exception is: {util.unicodify(e)}."
-        if trans.webapp.name == 'galaxy' or render_repository_actions_for == 'galaxy':
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='preview_tools_in_changeset',
-                                                            repository_id=repository_id,
-                                                            changeset_revision=changeset_revision,
-                                                            message=message,
-                                                            status='error'))
-        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                        action='browse_repositories',
-                                                        operation='view_or_manage_repository',
-                                                        id=repository_id,
-                                                        changeset_revision=changeset_revision,
-                                                        message=message,
-                                                        status='error'))
+        if trans.webapp.name == "galaxy" or render_repository_actions_for == "galaxy":
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="preview_tools_in_changeset",
+                    repository_id=repository_id,
+                    changeset_revision=changeset_revision,
+                    message=message,
+                    status="error",
+                )
+            )
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="repository",
+                action="browse_repositories",
+                operation="view_or_manage_repository",
+                id=repository_id,
+                changeset_revision=changeset_revision,
+                message=message,
+                status="error",
+            )
+        )
 
     @web.expose
     def download(self, trans, repository_id, changeset_revision, file_type, **kwd):
@@ -930,177 +1007,197 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         repository.times_downloaded += 1
         trans.sa_session.add(repository)
         trans.sa_session.flush()
-        tool_shed_url = web.url_for('/', qualified=True)
-        pathspec = ['repos', str(repository.user.username), str(repository.name), 'archive', file_type_str]
+        tool_shed_url = web.url_for("/", qualified=True)
+        pathspec = ["repos", str(repository.user.username), str(repository.name), "archive", file_type_str]
         download_url = util.build_url(tool_shed_url, pathspec=pathspec)
         return trans.response.send_redirect(download_url)
 
     @web.expose
     def export_via_api(self, trans, **kwd):
         """Return an exported gzip compressed repository archive file opened for reading."""
-        encoded_repositories_archive_name = kwd.get('encoded_repositories_archive_name', None)
+        encoded_repositories_archive_name = kwd.get("encoded_repositories_archive_name", None)
         if encoded_repositories_archive_name:
             repositories_archive_name = encoding_util.tool_shed_decode(encoded_repositories_archive_name)
             opened_archive = open(repositories_archive_name)
             # Make sure the file is removed from disk after the contents have been downloaded.
             os.unlink(repositories_archive_name)
             return opened_archive
-        return ''
+        return ""
 
     @web.expose
     def find_tools(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         common_util.handle_galaxy_url(trans, **kwd)
-        if 'operation' in kwd:
-            item_id = kwd.get('id', '')
+        if "operation" in kwd:
+            item_id = kwd.get("id", "")
             if item_id:
-                operation = kwd['operation'].lower()
+                operation = kwd["operation"].lower()
                 is_admin = trans.user_is_admin
                 if operation == "view_or_manage_repository":
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
                     repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, item_id)
                     repository_id = trans.security.encode_id(repository_metadata.repository.id)
                     repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-                    kwd['id'] = repository_id
-                    kwd['changeset_revision'] = repository_metadata.changeset_revision
-                    if trans.webapp.name == 'tool_shed' and (is_admin or repository.user == trans.user):
-                        a = 'manage_repository'
+                    kwd["id"] = repository_id
+                    kwd["changeset_revision"] = repository_metadata.changeset_revision
+                    if trans.webapp.name == "tool_shed" and (is_admin or repository.user == trans.user):
+                        a = "manage_repository"
                     else:
-                        a = 'view_repository'
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action=a,
-                                                                    **kwd))
+                        a = "view_repository"
+                    return trans.response.send_redirect(web.url_for(controller="repository", action=a, **kwd))
                 if operation == "install to galaxy":
                     # We've received a list of RepositoryMetadata ids, so we need to build a list of associated Repository ids.
                     encoded_repository_ids = []
                     changeset_revisions = []
                     for repository_metadata_id in util.listify(item_id):
-                        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
+                        repository_metadata = metadata_util.get_repository_metadata_by_id(
+                            trans.app, repository_metadata_id
+                        )
                         encoded_repository_ids.append(trans.security.encode_id(repository_metadata.repository.id))
                         changeset_revisions.append(repository_metadata.changeset_revision)
                     new_kwd = {}
-                    new_kwd['repository_ids'] = encoded_repository_ids
-                    new_kwd['changeset_revisions'] = changeset_revisions
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action='install_repositories_by_revision',
-                                                                    **new_kwd))
+                    new_kwd["repository_ids"] = encoded_repository_ids
+                    new_kwd["changeset_revisions"] = changeset_revisions
+                    return trans.response.send_redirect(
+                        web.url_for(controller="repository", action="install_repositories_by_revision", **new_kwd)
+                    )
             else:
                 # This can only occur when there is a multi-select grid with check boxes and an operation,
                 # and the user clicked the operation button without checking any of the check boxes.
                 return trans.show_error_message("No items were selected.")
-        tool_ids = [item.lower() for item in util.listify(kwd.get('tool_id', ''))]
-        tool_names = [item.lower() for item in util.listify(kwd.get('tool_name', ''))]
-        tool_versions = [item.lower() for item in util.listify(kwd.get('tool_version', ''))]
-        exact_matches = kwd.get('exact_matches', '')
+        tool_ids = [item.lower() for item in util.listify(kwd.get("tool_id", ""))]
+        tool_names = [item.lower() for item in util.listify(kwd.get("tool_name", ""))]
+        tool_versions = [item.lower() for item in util.listify(kwd.get("tool_version", ""))]
+        exact_matches = kwd.get("exact_matches", "")
         exact_matches_checked = CheckboxField.is_checked(exact_matches)
         match_tuples = []
         ok = True
         if tool_ids or tool_names or tool_versions:
-            ok, match_tuples = search_util.search_repository_metadata(trans.app,
-                                                                      exact_matches_checked,
-                                                                      tool_ids=tool_ids,
-                                                                      tool_names=tool_names,
-                                                                      tool_versions=tool_versions)
+            ok, match_tuples = search_util.search_repository_metadata(
+                trans.app, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions
+            )
             if ok:
-                kwd['match_tuples'] = match_tuples
+                kwd["match_tuples"] = match_tuples
                 # Render the list view
-                if trans.webapp.name == 'galaxy':
+                if trans.webapp.name == "galaxy":
                     # Our initial request originated from a Galaxy instance.
-                    global_actions = [grids.GridAction("Browse valid repositories",
-                                                       dict(controller='repository', action='browse_valid_categories')),
-                                      grids.GridAction("Search for valid tools",
-                                                       dict(controller='repository', action='find_tools'))]
+                    global_actions = [
+                        grids.GridAction(
+                            "Browse valid repositories", dict(controller="repository", action="browse_valid_categories")
+                        ),
+                        grids.GridAction("Search for valid tools", dict(controller="repository", action="find_tools")),
+                    ]
                     self.install_matched_repository_grid.global_actions = global_actions
-                    install_url_args = dict(controller='repository', action='find_tools')
-                    operations = [grids.GridOperation("Install", url_args=install_url_args, allow_multiple=True, async_compatible=False)]
+                    install_url_args = dict(controller="repository", action="find_tools")
+                    operations = [
+                        grids.GridOperation(
+                            "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False
+                        )
+                    ]
                     self.install_matched_repository_grid.operations = operations
                     return self.install_matched_repository_grid(trans, **kwd)
                 else:
-                    kwd['message'] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
-                        (basic_util.stringify(tool_ids),
-                         escape(basic_util.stringify(tool_names)),
-                         escape(basic_util.stringify(tool_versions)),
-                         str(exact_matches_checked))
+                    kwd["message"] = (
+                        "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>"
+                        % (
+                            basic_util.stringify(tool_ids),
+                            escape(basic_util.stringify(tool_names)),
+                            escape(basic_util.stringify(tool_versions)),
+                            str(exact_matches_checked),
+                        )
+                    )
                     self.matched_repository_grid.title = "Repositories with matching tools"
                     return self.matched_repository_grid(trans, **kwd)
             else:
                 message = "No search performed - each field must contain the same number of comma-separated items."
                 status = "error"
-        exact_matches_check_box = CheckboxField('exact_matches', value=exact_matches_checked)
-        return trans.fill_template('/webapps/tool_shed/repository/find_tools.mako',
-                                   tool_id=basic_util.stringify(tool_ids),
-                                   tool_name=basic_util.stringify(tool_names),
-                                   tool_version=basic_util.stringify(tool_versions),
-                                   exact_matches_check_box=exact_matches_check_box,
-                                   message=message,
-                                   status=status)
+        exact_matches_check_box = CheckboxField("exact_matches", value=exact_matches_checked)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/find_tools.mako",
+            tool_id=basic_util.stringify(tool_ids),
+            tool_name=basic_util.stringify(tool_names),
+            tool_version=basic_util.stringify(tool_versions),
+            exact_matches_check_box=exact_matches_check_box,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def get_changeset_revision_and_ctx_rev(self, trans, **kwd):
         """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated."""
+
         def has_galaxy_utilities(repository_metadata):
-            has_galaxy_utilities_dict = dict(includes_data_managers=False,
-                                             includes_datatypes=False,
-                                             includes_tools=False,
-                                             includes_tools_for_display_in_tool_panel=False,
-                                             has_repository_dependencies=False,
-                                             has_repository_dependencies_only_if_compiling_contained_td=False,
-                                             includes_tool_dependencies=False,
-                                             includes_workflows=False)
+            has_galaxy_utilities_dict = dict(
+                includes_data_managers=False,
+                includes_datatypes=False,
+                includes_tools=False,
+                includes_tools_for_display_in_tool_panel=False,
+                has_repository_dependencies=False,
+                has_repository_dependencies_only_if_compiling_contained_td=False,
+                includes_tool_dependencies=False,
+                includes_workflows=False,
+            )
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    if 'data_manager' in metadata:
-                        has_galaxy_utilities_dict['includes_data_managers'] = True
-                    if 'datatypes' in metadata:
-                        has_galaxy_utilities_dict['includes_datatypes'] = True
-                    if 'tools' in metadata:
-                        has_galaxy_utilities_dict['includes_tools'] = True
-                    if 'tool_dependencies' in metadata:
-                        has_galaxy_utilities_dict['includes_tool_dependencies'] = True
-                    repository_dependencies_dict = metadata.get('repository_dependencies', {})
-                    repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
-                    has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
-                        repository_util.get_repository_dependency_types(repository_dependencies)
-                    has_galaxy_utilities_dict['has_repository_dependencies'] = has_repository_dependencies
-                    has_galaxy_utilities_dict['has_repository_dependencies_only_if_compiling_contained_td'] = \
-                        has_repository_dependencies_only_if_compiling_contained_td
-                    if 'workflows' in metadata:
-                        has_galaxy_utilities_dict['includes_workflows'] = True
+                    if "data_manager" in metadata:
+                        has_galaxy_utilities_dict["includes_data_managers"] = True
+                    if "datatypes" in metadata:
+                        has_galaxy_utilities_dict["includes_datatypes"] = True
+                    if "tools" in metadata:
+                        has_galaxy_utilities_dict["includes_tools"] = True
+                    if "tool_dependencies" in metadata:
+                        has_galaxy_utilities_dict["includes_tool_dependencies"] = True
+                    repository_dependencies_dict = metadata.get("repository_dependencies", {})
+                    repository_dependencies = repository_dependencies_dict.get("repository_dependencies", [])
+                    (
+                        has_repository_dependencies,
+                        has_repository_dependencies_only_if_compiling_contained_td,
+                    ) = repository_util.get_repository_dependency_types(repository_dependencies)
+                    has_galaxy_utilities_dict["has_repository_dependencies"] = has_repository_dependencies
+                    has_galaxy_utilities_dict[
+                        "has_repository_dependencies_only_if_compiling_contained_td"
+                    ] = has_repository_dependencies_only_if_compiling_contained_td
+                    if "workflows" in metadata:
+                        has_galaxy_utilities_dict["includes_workflows"] = True
             return has_galaxy_utilities_dict
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                 trans.security.encode_id(repository.id),
-                                                                                 changeset_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, trans.security.encode_id(repository.id), changeset_revision
+        )
         has_galaxy_utilities_dict = has_galaxy_utilities(repository_metadata)
-        includes_data_managers = has_galaxy_utilities_dict['includes_data_managers']
-        includes_datatypes = has_galaxy_utilities_dict['includes_datatypes']
-        includes_tools = has_galaxy_utilities_dict['includes_tools']
-        includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict['includes_tools_for_display_in_tool_panel']
-        includes_tool_dependencies = has_galaxy_utilities_dict['includes_tool_dependencies']
-        has_repository_dependencies = has_galaxy_utilities_dict['has_repository_dependencies']
-        has_repository_dependencies_only_if_compiling_contained_td = \
-            has_galaxy_utilities_dict['has_repository_dependencies_only_if_compiling_contained_td']
-        includes_workflows = has_galaxy_utilities_dict['includes_workflows']
+        includes_data_managers = has_galaxy_utilities_dict["includes_data_managers"]
+        includes_datatypes = has_galaxy_utilities_dict["includes_datatypes"]
+        includes_tools = has_galaxy_utilities_dict["includes_tools"]
+        includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict["includes_tools_for_display_in_tool_panel"]
+        includes_tool_dependencies = has_galaxy_utilities_dict["includes_tool_dependencies"]
+        has_repository_dependencies = has_galaxy_utilities_dict["has_repository_dependencies"]
+        has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[
+            "has_repository_dependencies_only_if_compiling_contained_td"
+        ]
+        includes_workflows = has_galaxy_utilities_dict["includes_workflows"]
         repo = repository.hg_repo
         # Default to the received changeset revision and ctx_rev.
         update_to_ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
         ctx_rev = str(update_to_ctx.rev())
         latest_changeset_revision = changeset_revision
-        update_dict = dict(changeset_revision=changeset_revision,
-                           ctx_rev=ctx_rev,
-                           includes_data_managers=includes_data_managers,
-                           includes_datatypes=includes_datatypes,
-                           includes_tools=includes_tools,
-                           includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                           includes_tool_dependencies=includes_tool_dependencies,
-                           has_repository_dependencies=has_repository_dependencies,
-                           has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
-                           includes_workflows=includes_workflows)
+        update_dict = dict(
+            changeset_revision=changeset_revision,
+            ctx_rev=ctx_rev,
+            includes_data_managers=includes_data_managers,
+            includes_datatypes=includes_datatypes,
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            includes_tool_dependencies=includes_tool_dependencies,
+            has_repository_dependencies=has_repository_dependencies,
+            has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
+            includes_workflows=includes_workflows,
+        )
         if changeset_revision == repository.tip():
             # If changeset_revision is the repository tip, there are no additional updates.
             return encoding_util.tool_shed_encode(update_dict)
@@ -1118,19 +1215,23 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     has_repository_dependencies_only_if_compiling_contained_td = False
                     changeset_hash = str(repo[changeset])
                     if update_to_changeset_hash:
-                        update_to_repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                                                    trans.security.encode_id(repository.id),
-                                                                                                                    changeset_hash)
+                        update_to_repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                            trans.app, trans.security.encode_id(repository.id), changeset_hash
+                        )
                         if update_to_repository_metadata:
                             has_galaxy_utilities_dict = has_galaxy_utilities(repository_metadata)
-                            includes_data_managers = has_galaxy_utilities_dict['includes_data_managers']
-                            includes_datatypes = has_galaxy_utilities_dict['includes_datatypes']
-                            includes_tools = has_galaxy_utilities_dict['includes_tools']
-                            includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict['includes_tools_for_display_in_tool_panel']
-                            includes_tool_dependencies = has_galaxy_utilities_dict['includes_tool_dependencies']
-                            has_repository_dependencies = has_galaxy_utilities_dict['has_repository_dependencies']
-                            has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict['has_repository_dependencies_only_if_compiling_contained_td']
-                            includes_workflows = has_galaxy_utilities_dict['includes_workflows']
+                            includes_data_managers = has_galaxy_utilities_dict["includes_data_managers"]
+                            includes_datatypes = has_galaxy_utilities_dict["includes_datatypes"]
+                            includes_tools = has_galaxy_utilities_dict["includes_tools"]
+                            includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict[
+                                "includes_tools_for_display_in_tool_panel"
+                            ]
+                            includes_tool_dependencies = has_galaxy_utilities_dict["includes_tool_dependencies"]
+                            has_repository_dependencies = has_galaxy_utilities_dict["has_repository_dependencies"]
+                            has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[
+                                "has_repository_dependencies_only_if_compiling_contained_td"
+                            ]
+                            includes_workflows = has_galaxy_utilities_dict["includes_workflows"]
                             # We found a RepositoryMetadata record.
                             if changeset_hash == repository.tip():
                                 # The current ctx is the repository tip, so use it.
@@ -1143,30 +1244,32 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     elif not update_to_changeset_hash and changeset_hash == changeset_revision:
                         # We've found the changeset in the changelog for which we need to get the next update.
                         update_to_changeset_hash = changeset_hash
-                update_dict['includes_data_managers'] = includes_data_managers
-                update_dict['includes_datatypes'] = includes_datatypes
-                update_dict['includes_tools'] = includes_tools
-                update_dict['includes_tools_for_display_in_tool_panel'] = includes_tools_for_display_in_tool_panel
-                update_dict['includes_tool_dependencies'] = includes_tool_dependencies
-                update_dict['includes_workflows'] = includes_workflows
-                update_dict['has_repository_dependencies'] = has_repository_dependencies
-                update_dict['has_repository_dependencies_only_if_compiling_contained_td'] = has_repository_dependencies_only_if_compiling_contained_td
-                update_dict['changeset_revision'] = str(latest_changeset_revision)
-        update_dict['ctx_rev'] = str(update_to_ctx.rev())
+                update_dict["includes_data_managers"] = includes_data_managers
+                update_dict["includes_datatypes"] = includes_datatypes
+                update_dict["includes_tools"] = includes_tools
+                update_dict["includes_tools_for_display_in_tool_panel"] = includes_tools_for_display_in_tool_panel
+                update_dict["includes_tool_dependencies"] = includes_tool_dependencies
+                update_dict["includes_workflows"] = includes_workflows
+                update_dict["has_repository_dependencies"] = has_repository_dependencies
+                update_dict[
+                    "has_repository_dependencies_only_if_compiling_contained_td"
+                ] = has_repository_dependencies_only_if_compiling_contained_td
+                update_dict["changeset_revision"] = str(latest_changeset_revision)
+        update_dict["ctx_rev"] = str(update_to_ctx.rev())
         return encoding_util.tool_shed_encode(update_dict)
 
     @web.expose
     def get_ctx_rev(self, trans, **kwd):
         """Given a repository and changeset_revision, return the correct ctx.rev() value."""
-        repository_name = kwd['name']
-        repository_owner = kwd['owner']
-        changeset_revision = kwd['changeset_revision']
+        repository_name = kwd["name"]
+        repository_owner = kwd["owner"]
+        changeset_revision = kwd["changeset_revision"]
         repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
         repo = repository.hg_repo
         ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
         if ctx:
             return str(ctx.rev())
-        return ''
+        return ""
 
     @web.json
     @web.do_not_cache
@@ -1181,8 +1284,8 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         name and owner.  This method is called from Galaxy when attempting to install the latest revision
         of an installed repository.
         """
-        repository_name = kwd.get('name', None)
-        repository_owner = kwd.get('owner', None)
+        repository_name = kwd.get("name", None)
+        repository_owner = kwd.get("owner", None)
         if repository_name is not None and repository_owner is not None:
             repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
             if repository:
@@ -1195,23 +1298,21 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         This method is called when installing or re-installing a single repository into a Galaxy instance.
         If the received changeset_revision includes one or more readme files, return them in a dictionary.
         """
-        repository_name = kwd.get('name', None)
-        repository_owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        repository_name = kwd.get("name", None)
+        repository_owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         if repository_name is not None and repository_owner is not None and changeset_revision is not None:
             repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
             if repository:
-                repository_metadata = \
-                    metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                trans.security.encode_id(repository.id),
-                                                                                changeset_revision)
+                repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                    trans.app, trans.security.encode_id(repository.id), changeset_revision
+                )
                 if repository_metadata:
                     metadata = repository_metadata.metadata
                     if metadata:
-                        return readme_util.build_readme_files_dict(trans.app,
-                                                                   repository,
-                                                                   changeset_revision,
-                                                                   repository_metadata.metadata)
+                        return readme_util.build_readme_files_dict(
+                            trans.app, repository, changeset_revision, repository_metadata.metadata
+                        )
         return {}
 
     @web.json
@@ -1220,25 +1321,27 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         Return an encoded dictionary of all repositories upon which the contents of the received repository
         depends.
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         # get_repository_dependencies( self, app, changeset, toolshed_url )
-        dependencies = repository.get_repository_dependencies(trans.app, changeset_revision, web.url_for('/', qualified=True))
+        dependencies = repository.get_repository_dependencies(
+            trans.app, changeset_revision, web.url_for("/", qualified=True)
+        )
         if dependencies:
             return encoding_util.tool_shed_encode(dependencies)
-        return ''
+        return ""
 
     @web.expose
     def get_repository_id(self, trans, **kwd):
         """Given a repository name and owner, return the encoded repository id."""
-        repository_name = kwd['name']
-        repository_owner = kwd['owner']
+        repository_name = kwd["name"]
+        repository_owner = kwd["owner"]
         repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
         if repository:
             return trans.security.encode_id(repository.id)
-        return ''
+        return ""
 
     @web.json
     def get_repository_information(self, trans, repository_ids, changeset_revisions, **kwd):
@@ -1254,12 +1357,20 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         repo_info_dicts = []
         for tup in zip(util.listify(repository_ids), util.listify(changeset_revisions)):
             repository_id, changeset_revision = tup
-            repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \
-                cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \
-                repository_util.get_repo_info_dict(trans.app, trans.user, repository_id, changeset_revision)
+            (
+                repo_info_dict,
+                cur_includes_tools,
+                cur_includes_tool_dependencies,
+                cur_includes_tools_for_display_in_tool_panel,
+                cur_has_repository_dependencies,
+                cur_has_repository_dependencies_only_if_compiling_contained_td,
+            ) = repository_util.get_repo_info_dict(trans.app, trans.user, repository_id, changeset_revision)
             if cur_has_repository_dependencies and not has_repository_dependencies:
                 has_repository_dependencies = True
-            if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td:
+            if (
+                cur_has_repository_dependencies_only_if_compiling_contained_td
+                and not has_repository_dependencies_only_if_compiling_contained_td
+            ):
                 has_repository_dependencies_only_if_compiling_contained_td = True
             if cur_includes_tools and not includes_tools:
                 includes_tools = True
@@ -1268,18 +1379,20 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             if cur_includes_tools_for_display_in_tool_panel and not includes_tools_for_display_in_tool_panel:
                 includes_tools_for_display_in_tool_panel = True
             repo_info_dicts.append(encoding_util.tool_shed_encode(repo_info_dict))
-        return dict(includes_tools=includes_tools,
-                    includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                    has_repository_dependencies=has_repository_dependencies,
-                    has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
-                    includes_tool_dependencies=includes_tool_dependencies,
-                    repo_info_dicts=repo_info_dicts)
+        return dict(
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            has_repository_dependencies=has_repository_dependencies,
+            has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
+            includes_tool_dependencies=includes_tool_dependencies,
+            repo_info_dicts=repo_info_dicts,
+        )
 
     @web.expose
     def get_repository_type(self, trans, **kwd):
         """Given a repository name and owner, return the type."""
-        repository_name = kwd['name']
-        repository_owner = kwd['owner']
+        repository_name = kwd["name"]
+        repository_owner = kwd["owner"]
         repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
         return str(repository.type)
 
@@ -1295,17 +1408,27 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             encoded_required_repository_tups = encoded_required_repository_str.split(encoding_util.encoding_sep2)
             decoded_required_repository_tups = []
             for encoded_required_repository_tup in encoded_required_repository_tups:
-                decoded_required_repository_tups.append(encoded_required_repository_tup.split(encoding_util.encoding_sep))
+                decoded_required_repository_tups.append(
+                    encoded_required_repository_tup.split(encoding_util.encoding_sep)
+                )
             encoded_repository_ids = []
             changeset_revisions = []
             for required_repository_tup in decoded_required_repository_tups:
-                tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                    common_util.parse_repository_dependency_tuple(required_repository_tup)
+                (
+                    tool_shed,
+                    name,
+                    owner,
+                    changeset_revision,
+                    prior_installation_required,
+                    only_if_compiling_contained_td,
+                ) = common_util.parse_repository_dependency_tuple(required_repository_tup)
                 repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
                 encoded_repository_ids.append(trans.security.encode_id(repository.id))
                 changeset_revisions.append(changeset_revision)
             if encoded_repository_ids and changeset_revisions:
-                repo_info_dict = json.loads(self.get_repository_information(trans, encoded_repository_ids, changeset_revisions))
+                repo_info_dict = json.loads(
+                    self.get_repository_information(trans, encoded_repository_ids, changeset_revisions)
+                )
         return repo_info_dict
 
     @web.expose
@@ -1314,14 +1437,14 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         Handle a request from a Galaxy instance to get the tool_dependencies entry from the metadata
         for a specified changeset revision.
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         dependencies = repository.get_tool_dependencies(trans.app, changeset_revision)
         if len(dependencies) > 0:
             return encoding_util.tool_shed_encode(dependencies)
-        return ''
+        return ""
 
     @web.expose
     def get_tool_dependencies_config_contents(self, trans, **kwd):
@@ -1329,8 +1452,8 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         Handle a request from a Galaxy instance to get the tool_dependencies.xml file contents for a
         specified changeset revision.
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         # TODO: We're currently returning the tool_dependencies.xml file that is available on disk.  We need
         # to enhance this process to retrieve older versions of the tool-dependencies.xml file from the repository
@@ -1340,11 +1463,11 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         tool_dependencies_config = hg_util.get_config_from_disk(rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, repo_dir)
         # Return the encoded contents of the tool_dependencies.xml file.
         if tool_dependencies_config:
-            tool_dependencies_config_file = open(tool_dependencies_config, 'rb')
+            tool_dependencies_config_file = open(tool_dependencies_config, "rb")
             contents = tool_dependencies_config_file.read()
             tool_dependencies_config_file.close()
             return contents
-        return ''
+        return ""
 
     @web.json
     def get_tool_dependency_definition_metadata(self, trans, **kwd):
@@ -1352,14 +1475,14 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         Given a repository name and ownerof a repository whose type is
         tool_dependency_definition, return the current metadata.
         """
-        repository_name = kwd['name']
-        repository_owner = kwd['owner']
+        repository_name = kwd["name"]
+        repository_owner = kwd["owner"]
         repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
         encoded_id = trans.app.security.encode_id(repository.id)
         repository_tip = repository.tip()
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                          encoded_id,
-                                                                                          repository_tip)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, encoded_id, repository_tip
+        )
         return repository_metadata.metadata
 
     @web.expose
@@ -1368,24 +1491,24 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         For each valid /downloadable change set (up to the received changeset_revision) in the repository's
         change log, append the changeset tool_versions dictionary to the list that will be returned.
         """
-        name = kwd['name']
-        owner = kwd['owner']
-        changeset_revision = kwd['changeset_revision']
+        name = kwd["name"]
+        owner = kwd["owner"]
+        changeset_revision = kwd["changeset_revision"]
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         repo = repository.hg_repo
         tool_version_dicts = []
         for changeset in repo.changelog:
             current_changeset_revision = str(repo[changeset])
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                              trans.security.encode_id(repository.id),
-                                                                                              current_changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                trans.app, trans.security.encode_id(repository.id), current_changeset_revision
+            )
             if repository_metadata and repository_metadata.tool_versions:
                 tool_version_dicts.append(repository_metadata.tool_versions)
                 if current_changeset_revision == changeset_revision:
                     break
         if tool_version_dicts:
             return json.dumps(tool_version_dicts)
-        return ''
+        return ""
 
     @web.json
     def get_updated_repository_information(self, trans, name, owner, changeset_revision, **kwd):
@@ -1396,24 +1519,32 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         repository_id = trans.security.encode_id(repository.id)
         repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, repository_id, changeset_revision
+        )
         if not repository_metadata:
             # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository
             # changelog that is associated with metadata.
-            changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, after_changeset_revision=changeset_revision)
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
+            changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+                trans.app, repository, after_changeset_revision=changeset_revision
+            )
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                trans.app, repository_id, changeset_revision
+            )
         repo_path = repository.repo_path(trans.app)
         ctx_rev = str(hg_util.changeset2rev(repo_path, changeset_revision))
-        repo_info_dict = repository_util.create_repo_info_dict(app=trans.app,
-                                                               repository_clone_url=repository_clone_url,
-                                                               changeset_revision=changeset_revision,
-                                                               ctx_rev=ctx_rev,
-                                                               repository_owner=repository.user.username,
-                                                               repository_name=repository.name,
-                                                               repository=repository,
-                                                               repository_metadata=repository_metadata,
-                                                               tool_dependencies=None,
-                                                               repository_dependencies=None)
+        repo_info_dict = repository_util.create_repo_info_dict(
+            app=trans.app,
+            repository_clone_url=repository_clone_url,
+            changeset_revision=changeset_revision,
+            ctx_rev=ctx_rev,
+            repository_owner=repository.user.username,
+            repository_name=repository.name,
+            repository=repository,
+            repository_metadata=repository_metadata,
+            tool_dependencies=None,
+            repository_dependencies=None,
+        )
         includes_data_managers = False
         includes_datatypes = False
         includes_tools = False
@@ -1422,19 +1553,19 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         readme_files_dict = None
         metadata = repository_metadata.metadata
         if metadata:
-            if 'data_manager' in metadata:
+            if "data_manager" in metadata:
                 includes_data_managers = True
-            if 'datatypes' in metadata:
+            if "datatypes" in metadata:
                 includes_datatypes = True
-            if 'tools' in metadata:
+            if "tools" in metadata:
                 includes_tools = True
                 # Handle includes_tools_for_display_in_tool_panel.
-                tool_dicts = metadata['tools']
+                tool_dicts = metadata["tools"]
                 for tool_dict in tool_dicts:
-                    if tool_dict.get('includes_tools_for_display_in_tool_panel', False):
+                    if tool_dict.get("includes_tools_for_display_in_tool_panel", False):
                         includes_tools_for_display_in_tool_panel = True
                         break
-            if 'workflows' in metadata:
+            if "workflows" in metadata:
                 includes_workflows = True
             readme_files_dict = readme_util.build_readme_files_dict(trans.app, repository, changeset_revision, metadata)
         # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies.
@@ -1442,41 +1573,59 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         has_repository_dependencies_only_if_compiling_contained_td = False
         includes_tool_dependencies = False
         for repo_info_tuple in repo_info_dict.values():
-            if not has_repository_dependencies or not has_repository_dependencies_only_if_compiling_contained_td or not includes_tool_dependencies:
-                description, reposectory_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
-                    repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+            if (
+                not has_repository_dependencies
+                or not has_repository_dependencies_only_if_compiling_contained_td
+                or not includes_tool_dependencies
+            ):
+                (
+                    description,
+                    reposectory_clone_url,
+                    changeset_revision,
+                    ctx_rev,
+                    repository_owner,
+                    repository_dependencies,
+                    tool_dependencies,
+                ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
                 for rd_key, rd_tups in repository_dependencies.items():
-                    if rd_key in ['root_key', 'description']:
+                    if rd_key in ["root_key", "description"]:
                         continue
-                    curr_has_repository_dependencies, curr_has_repository_dependencies_only_if_compiling_contained_td = \
-                        repository_util.get_repository_dependency_types(rd_tups)
+                    (
+                        curr_has_repository_dependencies,
+                        curr_has_repository_dependencies_only_if_compiling_contained_td,
+                    ) = repository_util.get_repository_dependency_types(rd_tups)
                     if curr_has_repository_dependencies and not has_repository_dependencies:
                         has_repository_dependencies = True
-                    if curr_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td:
+                    if (
+                        curr_has_repository_dependencies_only_if_compiling_contained_td
+                        and not has_repository_dependencies_only_if_compiling_contained_td
+                    ):
                         has_repository_dependencies_only_if_compiling_contained_td = True
                 if tool_dependencies and not includes_tool_dependencies:
                     includes_tool_dependencies = True
-        return dict(includes_data_managers=includes_data_managers,
-                    includes_datatypes=includes_datatypes,
-                    includes_tools=includes_tools,
-                    includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-                    has_repository_dependencies=has_repository_dependencies,
-                    has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
-                    includes_tool_dependencies=includes_tool_dependencies,
-                    includes_workflows=includes_workflows,
-                    readme_files_dict=readme_files_dict,
-                    repo_info_dict=repo_info_dict)
+        return dict(
+            includes_data_managers=includes_data_managers,
+            includes_datatypes=includes_datatypes,
+            includes_tools=includes_tools,
+            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
+            has_repository_dependencies=has_repository_dependencies,
+            has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
+            includes_tool_dependencies=includes_tool_dependencies,
+            includes_workflows=includes_workflows,
+            readme_files_dict=readme_files_dict,
+            repo_info_dict=repo_info_dict,
+        )
 
     @web.expose
     def help(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        return trans.fill_template('/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        return trans.fill_template("/webapps/tool_shed/repository/help.mako", message=message, status=status, **kwd)
 
     @web.expose
     def index(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         # See if there are any RepositoryMetadata records since menu items require them.
         repository_metadata = trans.sa_session.query(trans.model.RepositoryMetadata).first()
         current_user = trans.user
@@ -1501,27 +1650,30 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 if current_user.active_repositories:
                     can_administer_repositories = True
                 else:
-                    for repository in trans.sa_session.query(trans.model.Repository) \
-                                                      .filter(trans.model.Repository.table.c.deleted == false()):
+                    for repository in trans.sa_session.query(trans.model.Repository).filter(
+                        trans.model.Repository.table.c.deleted == false()
+                    ):
                         if trans.app.security_agent.user_can_administer_repository(current_user, repository):
                             can_administer_repositories = True
                             break
         # Route in may have been from a sharable URL, in whcih case we'll have a user_id and possibly a name
         # The received user_id will be the id of the repository owner.
-        user_id = kwd.get('user_id', None)
-        repository_id = kwd.get('repository_id', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        user_id = kwd.get("user_id", None)
+        repository_id = kwd.get("repository_id", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         self.validate_changeset_revision(trans, changeset_revision, repository_id)
-        return trans.fill_template('/webapps/tool_shed/index.mako',
-                                   repository_metadata=repository_metadata,
-                                   can_administer_repositories=can_administer_repositories,
-                                   has_reviewed_repositories=has_reviewed_repositories,
-                                   has_deprecated_repositories=has_deprecated_repositories,
-                                   user_id=user_id,
-                                   repository_id=repository_id,
-                                   changeset_revision=changeset_revision,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/index.mako",
+            repository_metadata=repository_metadata,
+            can_administer_repositories=can_administer_repositories,
+            has_reviewed_repositories=has_reviewed_repositories,
+            has_deprecated_repositories=has_deprecated_repositories,
+            user_id=user_id,
+            repository_id=repository_id,
+            changeset_revision=changeset_revision,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def install_repositories_by_revision(self, trans, **kwd):
@@ -1530,143 +1682,158 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         process.  If the value of repository_ids is not received, then the name and owner of a single repository
         must be received to install a single repository.
         """
-        repository_ids = kwd.get('repository_ids', None)
-        changeset_revisions = kwd.get('changeset_revisions', None)
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
+        repository_ids = kwd.get("repository_ids", None)
+        changeset_revisions = kwd.get("changeset_revisions", None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
         if not repository_ids:
             repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
             repository_ids = trans.security.encode_id(repository.id)
         galaxy_url = common_util.handle_galaxy_url(trans, **kwd)
         if galaxy_url:
             # Redirect back to local Galaxy to perform install.
-            params = dict(tool_shed_url=web.url_for('/', qualified=True),
-                          repository_ids=','.join(util.listify(repository_ids)),
-                          changeset_revisions=','.join(util.listify(changeset_revisions)))
-            pathspec = ['admin_toolshed', 'prepare_for_install']
+            params = dict(
+                tool_shed_url=web.url_for("/", qualified=True),
+                repository_ids=",".join(util.listify(repository_ids)),
+                changeset_revisions=",".join(util.listify(changeset_revisions)),
+            )
+            pathspec = ["admin_toolshed", "prepare_for_install"]
             url = util.build_url(galaxy_url, pathspec=pathspec, params=params)
             return trans.response.send_redirect(url)
         else:
-            message = f'Repository installation is not possible due to an invalid Galaxy URL: <b>{galaxy_url}</b>.  '
-            message += 'You may need to enable third-party cookies in your browser.  '
-            status = 'error'
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_valid_categories',
-                                                            message=message,
-                                                            status=status))
+            message = f"Repository installation is not possible due to an invalid Galaxy URL: <b>{galaxy_url}</b>.  "
+            message += "You may need to enable third-party cookies in your browser.  "
+            status = "error"
+            return trans.response.send_redirect(
+                web.url_for(controller="repository", action="browse_valid_categories", message=message, status=status)
+            )
 
     @web.expose
     def load_invalid_tool(self, trans, repository_id, tool_config, changeset_revision, **kwd):
-        message = escape(kwd.get('message', ''))
-        render_repository_actions_for = kwd.get('render_repository_actions_for', 'tool_shed')
+        message = escape(kwd.get("message", ""))
+        render_repository_actions_for = kwd.get("render_repository_actions_for", "tool_shed")
 
         with ValidationContext.from_app(trans.app) as validation_context:
             tv = tool_validator.ToolValidator(validation_context)
-            repository, tool, valid, error_message = tv.load_tool_from_changeset_revision(repository_id,
-                                                                                          changeset_revision,
-                                                                                          tool_config)
+            repository, tool, valid, error_message = tv.load_tool_from_changeset_revision(
+                repository_id, changeset_revision, tool_config
+            )
             tool_state = tool_util.new_state(trans, tool, invalid=True)
             invalid_file_tups = []
             if tool:
-                invalid_file_tups = tv.check_tool_input_params(repository.repo_path(trans.app),
-                                                               tool_config,
-                                                               tool,
-                                                               [])
+                invalid_file_tups = tv.check_tool_input_params(repository.repo_path(trans.app), tool_config, tool, [])
         if invalid_file_tups:
-            message = tool_util.generate_message_for_invalid_tools(trans.app,
-                                                                   invalid_file_tups,
-                                                                   repository,
-                                                                   {},
-                                                                   as_html=True,
-                                                                   displaying_invalid_tool=True)
+            message = tool_util.generate_message_for_invalid_tools(
+                trans.app, invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True
+            )
         elif error_message:
             message = error_message
         try:
-            return trans.fill_template("/webapps/tool_shed/repository/tool_form.mako",
-                                       repository=repository,
-                                       render_repository_actions_for=render_repository_actions_for,
-                                       changeset_revision=changeset_revision,
-                                       tool=tool,
-                                       tool_state=tool_state,
-                                       message=message,
-                                       status='error')
+            return trans.fill_template(
+                "/webapps/tool_shed/repository/tool_form.mako",
+                repository=repository,
+                render_repository_actions_for=render_repository_actions_for,
+                changeset_revision=changeset_revision,
+                tool=tool,
+                tool_state=tool_state,
+                message=message,
+                status="error",
+            )
         except Exception as e:
             message = f"Exception thrown attempting to display tool: {util.unicodify(e)}."
-        if trans.webapp.name == 'galaxy':
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='preview_tools_in_changeset',
-                                                            repository_id=repository_id,
-                                                            changeset_revision=changeset_revision,
-                                                            message=message,
-                                                            status='error'))
-        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                        action='browse_repositories',
-                                                        operation='view_or_manage_repository',
-                                                        id=repository_id,
-                                                        changeset_revision=changeset_revision,
-                                                        message=message,
-                                                        status='error'))
+        if trans.webapp.name == "galaxy":
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="preview_tools_in_changeset",
+                    repository_id=repository_id,
+                    changeset_revision=changeset_revision,
+                    message=message,
+                    status="error",
+                )
+            )
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="repository",
+                action="browse_repositories",
+                operation="view_or_manage_repository",
+                id=repository_id,
+                changeset_revision=changeset_revision,
+                message=message,
+                status="error",
+            )
+        )
 
     @web.expose
     @require_login("manage email alerts")
     def manage_email_alerts(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        new_repo_alert = kwd.get('new_repo_alert', '')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        new_repo_alert = kwd.get("new_repo_alert", "")
         new_repo_alert_checked = CheckboxField.is_checked(new_repo_alert)
         user = trans.user
-        if kwd.get('new_repo_alert_button', False):
+        if kwd.get("new_repo_alert_button", False):
             user.new_repo_alert = new_repo_alert_checked
             trans.sa_session.add(user)
             trans.sa_session.flush()
             if new_repo_alert_checked:
-                message = 'You will receive email alerts for all new valid tool shed repositories.'
+                message = "You will receive email alerts for all new valid tool shed repositories."
             else:
-                message = 'You will not receive any email alerts for new valid tool shed repositories.'
+                message = "You will not receive any email alerts for new valid tool shed repositories."
         checked = new_repo_alert_checked or (user and user.new_repo_alert)
-        new_repo_alert_check_box = CheckboxField('new_repo_alert', value=checked)
+        new_repo_alert_check_box = CheckboxField("new_repo_alert", value=checked)
         email_alert_repositories = []
-        for repository in trans.sa_session.query(trans.model.Repository) \
-                                          .filter(and_(trans.model.Repository.table.c.deleted == false(),
-                                                       trans.model.Repository.table.c.email_alerts != null())) \
-                                          .order_by(trans.model.Repository.table.c.name):
+        for repository in (
+            trans.sa_session.query(trans.model.Repository)
+            .filter(
+                and_(
+                    trans.model.Repository.table.c.deleted == false(),
+                    trans.model.Repository.table.c.email_alerts != null(),
+                )
+            )
+            .order_by(trans.model.Repository.table.c.name)
+        ):
             if user.email in repository.email_alerts:
                 email_alert_repositories.append(repository)
-        return trans.fill_template("/webapps/tool_shed/user/manage_email_alerts.mako",
-                                   new_repo_alert_check_box=new_repo_alert_check_box,
-                                   email_alert_repositories=email_alert_repositories,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/user/manage_email_alerts.mako",
+            new_repo_alert_check_box=new_repo_alert_check_box,
+            email_alert_repositories=email_alert_repositories,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("manage repository")
     def manage_repository(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        repository_type = kwd.get('repository_type', str(repository.type))
+        repository_type = kwd.get("repository_type", str(repository.type))
         repo = repository.hg_repo
-        repo_name = kwd.get('repo_name', repository.name)
-        changeset_revision = kwd.get('changeset_revision', repository.tip())
-        repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=changeset_revision)
+        repo_name = kwd.get("repo_name", repository.name)
+        changeset_revision = kwd.get("changeset_revision", repository.tip())
+        repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(
+            repository, changeset_revision=changeset_revision
+        )
         repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
-        remote_repository_url = kwd.get('remote_repository_url', repository.remote_repository_url)
-        homepage_url = kwd.get('homepage_url', repository.homepage_url)
-        description = kwd.get('description', repository.description)
-        long_description = kwd.get('long_description', repository.long_description)
+        remote_repository_url = kwd.get("remote_repository_url", repository.remote_repository_url)
+        homepage_url = kwd.get("homepage_url", repository.homepage_url)
+        description = kwd.get("description", repository.description)
+        long_description = kwd.get("long_description", repository.long_description)
         avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model)
-        display_reviews = util.string_as_bool(kwd.get('display_reviews', False))
-        alerts = kwd.get('alerts', '')
+        display_reviews = util.string_as_bool(kwd.get("display_reviews", False))
+        alerts = kwd.get("alerts", "")
         alerts_checked = CheckboxField.is_checked(alerts)
-        category_ids = util.listify(kwd.get('category_id', ''))
+        category_ids = util.listify(kwd.get("category_id", ""))
         if repository.email_alerts:
             email_alerts = json.loads(repository.email_alerts)
         else:
             email_alerts = []
-        allow_push = kwd.get('allow_push', '')
+        allow_push = kwd.get("allow_push", "")
         error = False
         user = trans.user
-        if kwd.get('edit_repository_button', False):
+        if kwd.get("edit_repository_button", False):
             update_kwds = dict(
                 name=repo_name,
                 description=description,
@@ -1678,13 +1845,13 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
 
             repository, message = repository_util.update_repository(app=trans.app, trans=trans, id=id, **update_kwds)
             if repository is None:
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_repository',
-                                                                id=id,
-                                                                message=message,
-                                                                status='error'))
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository", action="view_repository", id=id, message=message, status="error"
+                    )
+                )
 
-        elif kwd.get('manage_categories_button', False):
+        elif kwd.get("manage_categories_button", False):
             flush_needed = False
             # Delete all currently existing categories.
             for rca in repository.categories:
@@ -1698,21 +1865,21 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     trans.sa_session.add(rca)
                     trans.sa_session.flush()
             message = "The repository information has been updated."
-        elif kwd.get('user_access_button', False):
-            if allow_push not in ['none']:
-                remove_auth = kwd.get('remove_auth', '')
+        elif kwd.get("user_access_button", False):
+            if allow_push not in ["none"]:
+                remove_auth = kwd.get("remove_auth", "")
                 if remove_auth:
-                    usernames = ''
+                    usernames = ""
                 else:
                     user_ids = util.listify(allow_push)
                     usernames = []
                     for user_id in user_ids:
                         user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
                         usernames.append(user.username)
-                    usernames = ','.join(usernames)
+                    usernames = ",".join(usernames)
                 repository.set_allow_push(usernames, remove_auth=remove_auth)
             message = "The repository information has been updated."
-        elif kwd.get('receive_email_alerts_button', False):
+        elif kwd.get("receive_email_alerts_button", False):
             flush_needed = False
             if alerts_checked:
                 if user.email not in email_alerts:
@@ -1729,12 +1896,11 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 trans.sa_session.flush()
             message = "The repository information has been updated."
         if error:
-            status = 'error'
-        allow_push_select_field = SelectField(name='allow_push',
-                                              multiple=True)
+            status = "error"
+        allow_push_select_field = SelectField(name="allow_push", multiple=True)
         current_allow_push = repository.allow_push()
         if current_allow_push:
-            current_allow_push_list = current_allow_push.split(',')
+            current_allow_push_list = current_allow_push.split(",")
         else:
             current_allow_push_list = []
         options = []
@@ -1745,185 +1911,196 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             label = obj.username
             allow_push_select_field.add_option(label, trans.security.encode_id(obj.id))
         checked = alerts_checked or user.email in email_alerts
-        alerts_check_box = CheckboxField('alerts', value=checked)
-        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
-                                                                                           repository,
-                                                                                           selected_value=changeset_revision,
-                                                                                           add_id_to_name=False,
-                                                                                           downloadable=False)
+        alerts_check_box = CheckboxField("alerts", value=checked)
+        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(
+            trans, repository, selected_value=changeset_revision, add_id_to_name=False, downloadable=False
+        )
         revision_label = hg_util.get_revision_label(trans.app, repository, repository.tip(), include_date=False)
         repository_metadata = None
         metadata = None
         is_malicious = False
         repository_dependencies = None
         if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                trans.app, id, changeset_revision
+            )
             if repository_metadata:
-                revision_label = hg_util.get_revision_label(trans.app, repository, changeset_revision, include_date=False)
+                revision_label = hg_util.get_revision_label(
+                    trans.app, repository, changeset_revision, include_date=False
+                )
                 metadata = repository_metadata.metadata
                 is_malicious = repository_metadata.malicious
             else:
                 # There is no repository_metadata defined for the changeset_revision, so see if it was defined in a previous
                 # changeset in the changelog.
-                previous_changeset_revision = \
-                    metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=False)
+                previous_changeset_revision = metadata_util.get_previous_metadata_changeset_revision(
+                    trans.app, repository, changeset_revision, downloadable=False
+                )
                 if previous_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
-                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, previous_changeset_revision)
+                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                        trans.app, id, previous_changeset_revision
+                    )
                     if repository_metadata:
-                        revision_label = hg_util.get_revision_label(trans.app, repository, previous_changeset_revision, include_date=False)
+                        revision_label = hg_util.get_revision_label(
+                            trans.app, repository, previous_changeset_revision, include_date=False
+                        )
                         metadata = repository_metadata.metadata
                         is_malicious = repository_metadata.malicious
                         changeset_revision = previous_changeset_revision
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
-                toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
+                toolshed_base_url = str(web.url_for("/", qualified=True)).rstrip("/")
                 rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
                 repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
                 if str(repository.type) != rt_util.REPOSITORY_SUITE_DEFINITION:
                     # Handle messaging for resetting repository type to the optimal value.
-                    change_repository_type_message = rt_util.generate_message_for_repository_type_change(trans.app,
-                                                                                                         repository)
+                    change_repository_type_message = rt_util.generate_message_for_repository_type_change(
+                        trans.app, repository
+                    )
                     if change_repository_type_message:
                         message += change_repository_type_message
-                        status = 'warning'
+                        status = "warning"
                 elif str(repository.type) != rt_util.TOOL_DEPENDENCY_DEFINITION:
                     # Handle messaging for resetting repository type to the optimal value.
-                    change_repository_type_message = rt_util.generate_message_for_repository_type_change(trans.app,
-                                                                                                         repository)
+                    change_repository_type_message = rt_util.generate_message_for_repository_type_change(
+                        trans.app, repository
+                    )
                     if change_repository_type_message:
                         message += change_repository_type_message
-                        status = 'warning'
+                        status = "warning"
                     else:
                         # Handle messaging for orphan tool dependency definitions.
                         dd = dependency_display.DependencyDisplayer(trans.app)
                         orphan_message = dd.generate_message_for_orphan_tool_dependencies(repository, metadata)
                         if orphan_message:
                             message += orphan_message
-                            status = 'warning'
+                            status = "warning"
         if is_malicious:
             if trans.app.security_agent.can_push(trans.app, trans.user, repository):
                 message += malicious_error_can_push
             else:
                 message += malicious_error
-            status = 'error'
+            status = "error"
         repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
-        malicious_check_box = CheckboxField('malicious', value=is_malicious)
+        malicious_check_box = CheckboxField("malicious", value=is_malicious)
         categories = suc.get_categories(trans.app)
         selected_categories = [_rca.category_id for _rca in repository.categories]
         tsucm = ToolShedUtilityContainerManager(trans.app)
-        containers_dict = tsucm.build_repository_containers(repository,
-                                                            changeset_revision,
-                                                            repository_dependencies,
-                                                            repository_metadata)
+        containers_dict = tsucm.build_repository_containers(
+            repository, changeset_revision, repository_dependencies, repository_metadata
+        )
         heads = hg_util.get_repository_heads(repo)
-        deprecated_repository_dependency_tups = \
-            metadata_util.get_repository_dependency_tups_from_repository_metadata(trans.app,
-                                                                                  repository_metadata,
-                                                                                  deprecated_only=True)
-        return trans.fill_template('/webapps/tool_shed/repository/manage_repository.mako',
-                                   repo_name=repo_name,
-                                   remote_repository_url=remote_repository_url,
-                                   homepage_url=homepage_url,
-                                   description=description,
-                                   long_description=long_description,
-                                   current_allow_push_list=current_allow_push_list,
-                                   allow_push_select_field=allow_push_select_field,
-                                   deprecated_repository_dependency_tups=deprecated_repository_dependency_tups,
-                                   repo=repo,
-                                   heads=heads,
-                                   repository=repository,
-                                   containers_dict=containers_dict,
-                                   repository_metadata=repository_metadata,
-                                   changeset_revision=changeset_revision,
-                                   changeset_revision_select_field=changeset_revision_select_field,
-                                   revision_label=revision_label,
-                                   selected_categories=selected_categories,
-                                   categories=categories,
-                                   metadata=metadata,
-                                   avg_rating=avg_rating,
-                                   display_reviews=display_reviews,
-                                   num_ratings=num_ratings,
-                                   alerts_check_box=alerts_check_box,
-                                   malicious_check_box=malicious_check_box,
-                                   repository_type_select_field=repository_type_select_field,
-                                   message=message,
-                                   status=status)
+        deprecated_repository_dependency_tups = metadata_util.get_repository_dependency_tups_from_repository_metadata(
+            trans.app, repository_metadata, deprecated_only=True
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/manage_repository.mako",
+            repo_name=repo_name,
+            remote_repository_url=remote_repository_url,
+            homepage_url=homepage_url,
+            description=description,
+            long_description=long_description,
+            current_allow_push_list=current_allow_push_list,
+            allow_push_select_field=allow_push_select_field,
+            deprecated_repository_dependency_tups=deprecated_repository_dependency_tups,
+            repo=repo,
+            heads=heads,
+            repository=repository,
+            containers_dict=containers_dict,
+            repository_metadata=repository_metadata,
+            changeset_revision=changeset_revision,
+            changeset_revision_select_field=changeset_revision_select_field,
+            revision_label=revision_label,
+            selected_categories=selected_categories,
+            categories=categories,
+            metadata=metadata,
+            avg_rating=avg_rating,
+            display_reviews=display_reviews,
+            num_ratings=num_ratings,
+            alerts_check_box=alerts_check_box,
+            malicious_check_box=malicious_check_box,
+            repository_type_select_field=repository_type_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("manage repository administrators")
     def manage_repository_admins(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        changeset_revision = kwd.get('changeset_revision', repository.tip())
+        changeset_revision = kwd.get("changeset_revision", repository.tip())
         metadata = None
         if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
-            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                trans.app, id, changeset_revision
+            )
             if repository_metadata:
                 metadata = repository_metadata.metadata
             else:
                 # There is no repository_metadata defined for the changeset_revision, so see if it was defined
                 # in a previous changeset in the changelog.
-                previous_changeset_revision = \
-                    metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=False)
+                previous_changeset_revision = metadata_util.get_previous_metadata_changeset_revision(
+                    trans.app, repository, changeset_revision, downloadable=False
+                )
                 if previous_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
-                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
-                                                                                                      id,
-                                                                                                      previous_changeset_revision)
+                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                        trans.app, id, previous_changeset_revision
+                    )
                     if repository_metadata:
                         metadata = repository_metadata.metadata
         role = repository.admin_role
-        associations_dict = repository_util.handle_role_associations(trans.app,
-                                                                     role,
-                                                                     repository,
-                                                                     **kwd)
-        in_users = associations_dict.get('in_users', [])
-        out_users = associations_dict.get('out_users', [])
-        in_groups = associations_dict.get('in_groups', [])
-        out_groups = associations_dict.get('out_groups', [])
-        message = associations_dict.get('message', '')
-        status = associations_dict.get('status', 'done')
-        return trans.fill_template('/webapps/tool_shed/role/role.mako',
-                                   in_admin_controller=False,
-                                   repository=repository,
-                                   metadata=metadata,
-                                   changeset_revision=changeset_revision,
-                                   role=role,
-                                   in_users=in_users,
-                                   out_users=out_users,
-                                   in_groups=in_groups,
-                                   out_groups=out_groups,
-                                   message=message,
-                                   status=status)
+        associations_dict = repository_util.handle_role_associations(trans.app, role, repository, **kwd)
+        in_users = associations_dict.get("in_users", [])
+        out_users = associations_dict.get("out_users", [])
+        in_groups = associations_dict.get("in_groups", [])
+        out_groups = associations_dict.get("out_groups", [])
+        message = associations_dict.get("message", "")
+        status = associations_dict.get("status", "done")
+        return trans.fill_template(
+            "/webapps/tool_shed/role/role.mako",
+            in_admin_controller=False,
+            repository=repository,
+            metadata=metadata,
+            changeset_revision=changeset_revision,
+            role=role,
+            in_users=in_users,
+            out_users=out_users,
+            in_groups=in_groups,
+            out_groups=out_groups,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("review repository revision")
     def manage_repository_reviews_of_revision(self, trans, **kwd):
-        return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                        action='manage_repository_reviews_of_revision',
-                                                        **kwd))
+        return trans.response.send_redirect(
+            web.url_for(controller="repository_review", action="manage_repository_reviews_of_revision", **kwd)
+        )
 
     @web.expose
     @require_login("multi select email alerts")
     def multi_select_email_alerts(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "receive email alerts":
                 if trans.user:
-                    if kwd['id']:
-                        kwd['caller'] = 'multi_select_email_alerts'
-                        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                        action='set_email_alerts',
-                                                                        **kwd))
+                    if kwd["id"]:
+                        kwd["caller"] = "multi_select_email_alerts"
+                        return trans.response.send_redirect(
+                            web.url_for(controller="repository", action="set_email_alerts", **kwd)
+                        )
                 else:
-                    kwd['message'] = 'You must be logged in to set email alerts.'
-                    kwd['status'] = 'error'
-                    del kwd['operation']
+                    kwd["message"] = "You must be logged in to set email alerts."
+                    kwd["status"] = "error"
+                    del kwd["operation"]
             elif operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository", action="view_or_manage_repository", **kwd)
+                )
         self.email_alerts_repository_grid.title = "Set email alerts for repository changes"
         return self.email_alerts_repository_grid(trans, **kwd)
 
@@ -1934,15 +2111,17 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         in a dependency definition file is older than the changeset_revision associated with the installed
         repository.
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         # Get the next installable changeset_revision beyond the received changeset_revision.
-        next_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
+        next_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+            trans.app, repository, changeset_revision
+        )
         if next_changeset_revision and next_changeset_revision != changeset_revision:
             return next_changeset_revision
-        return ''
+        return ""
 
     @web.json
     @web.do_not_cache
@@ -1952,67 +2131,70 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
 
     @web.expose
     def preview_tools_in_changeset(self, trans, repository_id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-        changeset_revision = kwd.get('changeset_revision', repository.tip())
+        changeset_revision = kwd.get("changeset_revision", repository.tip())
         self.validate_changeset_revision(trans, changeset_revision, repository_id)
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, repository_id, changeset_revision
+        )
         if repository_metadata:
-            repository_metadata_id = trans.security.encode_id(repository_metadata.id),
+            repository_metadata_id = (trans.security.encode_id(repository_metadata.id),)
             metadata = repository_metadata.metadata
             # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
-            toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
+            toolshed_base_url = str(web.url_for("/", qualified=True)).rstrip("/")
             rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
             repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
             if metadata:
-                if 'repository_dependencies' in metadata and not repository_dependencies:
+                if "repository_dependencies" in metadata and not repository_dependencies:
                     # See if we have an invalid repository dependency definition or if the repository dependency is required
                     # only for compiling the repository's tool dependency.
                     invalid = False
-                    repository_dependencies_dict = metadata['repository_dependencies']
-                    rd_tups = repository_dependencies_dict.get('repository_dependencies', [])
+                    repository_dependencies_dict = metadata["repository_dependencies"]
+                    rd_tups = repository_dependencies_dict.get("repository_dependencies", [])
                     for rd_tup in rd_tups:
-                        rdtool_shed, \
-                            rd_name, \
-                            rd_owner, \
-                            rd_changeset_revision, \
-                            rd_prior_installation_required, \
-                            rd_only_if_compiling_contained_td = \
-                            common_util.parse_repository_dependency_tuple(rd_tup)
+                        (
+                            rdtool_shed,
+                            rd_name,
+                            rd_owner,
+                            rd_changeset_revision,
+                            rd_prior_installation_required,
+                            rd_only_if_compiling_contained_td,
+                        ) = common_util.parse_repository_dependency_tuple(rd_tup)
                         if not util.asbool(rd_only_if_compiling_contained_td):
                             invalid = True
                             break
                     if invalid:
                         dd = dependency_display.DependencyDisplayer(trans.app)
-                        message = dd.generate_message_for_invalid_repository_dependencies(metadata,
-                                                                                          error_from_tuple=False)
-                        status = 'error'
+                        message = dd.generate_message_for_invalid_repository_dependencies(
+                            metadata, error_from_tuple=False
+                        )
+                        status = "error"
         else:
             repository_metadata_id = None
             metadata = None
             repository_dependencies = None
         revision_label = hg_util.get_revision_label(trans.app, repository, changeset_revision, include_date=True)
-        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
-                                                                                           repository,
-                                                                                           selected_value=changeset_revision,
-                                                                                           add_id_to_name=False,
-                                                                                           downloadable=False)
+        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(
+            trans, repository, selected_value=changeset_revision, add_id_to_name=False, downloadable=False
+        )
         tsucm = ToolShedUtilityContainerManager(trans.app)
-        containers_dict = tsucm.build_repository_containers(repository,
-                                                            changeset_revision,
-                                                            repository_dependencies,
-                                                            repository_metadata)
-        return trans.fill_template('/webapps/tool_shed/repository/preview_tools_in_changeset.mako',
-                                   repository=repository,
-                                   containers_dict=containers_dict,
-                                   repository_metadata_id=repository_metadata_id,
-                                   changeset_revision=changeset_revision,
-                                   revision_label=revision_label,
-                                   changeset_revision_select_field=changeset_revision_select_field,
-                                   metadata=metadata,
-                                   message=message,
-                                   status=status)
+        containers_dict = tsucm.build_repository_containers(
+            repository, changeset_revision, repository_dependencies, repository_metadata
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/preview_tools_in_changeset.mako",
+            repository=repository,
+            containers_dict=containers_dict,
+            repository_metadata_id=repository_metadata_id,
+            changeset_revision=changeset_revision,
+            revision_label=revision_label,
+            changeset_revision_select_field=changeset_revision_select_field,
+            metadata=metadata,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def previous_changeset_revisions(self, trans, from_tip=False, **kwd):
@@ -2028,187 +2210,198 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         due to the behavior of "Tool dependency definition" repositories, whose metadata is always the tip),
         so the complete list of changset hashes in the changelog must be returned.
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
         if name is not None and owner is not None:
             repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
             from_tip = util.string_as_bool(from_tip)
             if from_tip:
                 changeset_revision = repository.tip()
             else:
-                changeset_revision = kwd.get('changeset_revision', None)
+                changeset_revision = kwd.get("changeset_revision", None)
             if changeset_revision is not None:
                 repo = repository.hg_repo
                 # Get the lower bound changeset revision.
-                lower_bound_changeset_revision = \
-                    metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=True)
+                lower_bound_changeset_revision = metadata_util.get_previous_metadata_changeset_revision(
+                    trans.app, repository, changeset_revision, downloadable=True
+                )
                 # Build the list of changeset revision hashes.
                 changeset_hashes = []
-                for changeset in hg_util.reversed_lower_upper_bounded_changelog(repo,
-                                                                                lower_bound_changeset_revision,
-                                                                                changeset_revision):
+                for changeset in hg_util.reversed_lower_upper_bounded_changelog(
+                    repo, lower_bound_changeset_revision, changeset_revision
+                ):
                     changeset_hashes.append(str(repo[changeset]))
                 if changeset_hashes:
-                    changeset_hashes_str = ','.join(changeset_hashes)
+                    changeset_hashes_str = ",".join(changeset_hashes)
                     return changeset_hashes_str
-        return ''
+        return ""
 
     @web.expose
     @require_login("rate repositories")
     def rate_repository(self, trans, **kwd):
-        """ Rate a repository and return updated rating data. """
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        id = kwd.get('id', None)
+        """Rate a repository and return updated rating data."""
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        id = kwd.get("id", None)
         if not id:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            message='Select a repository to rate',
-                                                            status='error'))
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    message="Select a repository to rate",
+                    status="error",
+                )
+            )
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         changeset_revision = repository.tip()
         if repository.user == trans.user:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='browse_repositories',
-                                                            message="You are not allowed to rate your own repository",
-                                                            status='error'))
-        if kwd.get('rate_button', False):
-            rating = int(kwd.get('rating', '0'))
-            comment = kwd.get('comment', '')
+            return trans.response.send_redirect(
+                web.url_for(
+                    controller="repository",
+                    action="browse_repositories",
+                    message="You are not allowed to rate your own repository",
+                    status="error",
+                )
+            )
+        if kwd.get("rate_button", False):
+            rating = int(kwd.get("rating", "0"))
+            comment = kwd.get("comment", "")
             rating = self.rate_item(trans, trans.user, repository, rating, comment)
         avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model)
-        display_reviews = util.string_as_bool(kwd.get('display_reviews', False))
+        display_reviews = util.string_as_bool(kwd.get("display_reviews", False))
         rra = self.get_user_item_rating(trans.sa_session, trans.user, repository, webapp_model=trans.model)
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             id,
-                                                                                             changeset_revision,
-                                                                                             metadata_only=True)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, id, changeset_revision, metadata_only=True
+        )
         repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
         revision_label = hg_util.get_revision_label(trans.app, repository, changeset_revision, include_date=True)
-        return trans.fill_template('/webapps/tool_shed/repository/rate_repository.mako',
-                                   repository=repository,
-                                   metadata=metadata,
-                                   revision_label=revision_label,
-                                   avg_rating=avg_rating,
-                                   display_reviews=display_reviews,
-                                   num_ratings=num_ratings,
-                                   rra=rra,
-                                   repository_type_select_field=repository_type_select_field,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/rate_repository.mako",
+            repository=repository,
+            metadata=metadata,
+            revision_label=revision_label,
+            avg_rating=avg_rating,
+            display_reviews=display_reviews,
+            num_ratings=num_ratings,
+            rra=rra,
+            repository_type_select_field=repository_type_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def reset_all_metadata(self, trans, id, **kwd):
         """Reset all metadata on the complete changelog for a single repository in the tool shed."""
         # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template.
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
-                                                                    user=trans.user,
-                                                                    repository=repository,
-                                                                    resetting_all_metadata_on_repository=True)
+        rmm = repository_metadata_manager.RepositoryMetadataManager(
+            app=trans.app, user=trans.user, repository=repository, resetting_all_metadata_on_repository=True
+        )
         rmm.reset_all_metadata_on_repository_in_tool_shed()
         rmm_metadata_dict = rmm.get_metadata_dict()
         rmm_invalid_file_tups = rmm.get_invalid_file_tups()
         if rmm_invalid_file_tups:
-            message = tool_util.generate_message_for_invalid_tools(trans.app,
-                                                                   rmm_invalid_file_tups,
-                                                                   repository,
-                                                                   rmm_metadata_dict)
-            status = 'error'
+            message = tool_util.generate_message_for_invalid_tools(
+                trans.app, rmm_invalid_file_tups, repository, rmm_metadata_dict
+            )
+            status = "error"
         else:
             message = "All repository metadata has been reset.  "
-            status = 'done'
-        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                        action='manage_repository',
-                                                        id=id,
-                                                        message=message,
-                                                        status=status))
+            status = "done"
+        return trans.response.send_redirect(
+            web.url_for(controller="repository", action="manage_repository", id=id, message=message, status=status)
+        )
 
     @web.expose
     def reset_metadata_on_my_writable_repositories_in_tool_shed(self, trans, **kwd):
-        rmm = repository_metadata_manager.RepositoryMetadataManager(trans.app, trans.user, resetting_all_metadata_on_repository=True)
-        if 'reset_metadata_on_selected_repositories_button' in kwd:
+        rmm = repository_metadata_manager.RepositoryMetadataManager(
+            trans.app, trans.user, resetting_all_metadata_on_repository=True
+        )
+        if "reset_metadata_on_selected_repositories_button" in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories(**kwd)
         else:
-            message = escape(kwd.get('message', ''))
-            status = kwd.get('status', 'done')
-        repositories_select_field = rmm.build_repository_ids_select_field(name='repository_ids',
-                                                                          multiple=True,
-                                                                          display='checkboxes',
-                                                                          my_writable=True)
-        return trans.fill_template('/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako',
-                                   repositories_select_field=repositories_select_field,
-                                   message=message,
-                                   status=status)
+            message = escape(kwd.get("message", ""))
+            status = kwd.get("status", "done")
+        repositories_select_field = rmm.build_repository_ids_select_field(
+            name="repository_ids", multiple=True, display="checkboxes", my_writable=True
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako",
+            repositories_select_field=repositories_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def select_files_to_delete(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        commit_message = escape(kwd.get('commit_message', 'Deleted selected files'))
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        commit_message = escape(kwd.get("commit_message", "Deleted selected files"))
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo_dir = repository.repo_path(trans.app)
         repo = repository.hg_repo
-        selected_files_to_delete = kwd.get('selected_files_to_delete', '')
-        if kwd.get('select_files_to_delete_button', False):
+        selected_files_to_delete = kwd.get("selected_files_to_delete", "")
+        if kwd.get("select_files_to_delete_button", False):
             if selected_files_to_delete:
-                selected_files_to_delete = selected_files_to_delete.split(',')
+                selected_files_to_delete = selected_files_to_delete.split(",")
                 # Get the current repository tip.
                 tip = repository.tip()
                 for selected_file in selected_files_to_delete:
                     try:
                         hg_util.remove_path(repo_dir, selected_file)
                     except Exception as e:
-                        status = 'error'
+                        status = "error"
                         message = f"Error removing file {selected_file} in mercurial repo:\n{e}"
                         log.debug(message)
                 # Commit the change set.
                 if not commit_message:
-                    commit_message = 'Deleted selected files'
-                hg_util.commit_changeset(repo_dir,
-                                         full_path_to_changeset=repo_dir,
-                                         username=trans.user.username,
-                                         message=commit_message)
+                    commit_message = "Deleted selected files"
+                hg_util.commit_changeset(
+                    repo_dir, full_path_to_changeset=repo_dir, username=trans.user.username, message=commit_message
+                )
                 suc.handle_email_alerts(trans.app, trans.request.host, repository)
                 # Update the repository files for browsing.
                 hg_util.update_repository(repo_dir)
                 # Get the new repository tip.
                 if tip == repository.tip():
-                    message += 'No changes to repository.  '
+                    message += "No changes to repository.  "
                 else:
-                    rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
-                                                                                user=trans.user,
-                                                                                repository=repository)
+                    rmm = repository_metadata_manager.RepositoryMetadataManager(
+                        app=trans.app, user=trans.user, repository=repository
+                    )
                     status, error_message = rmm.set_repository_metadata_due_to_new_tip(trans.request.host, **kwd)
                     if error_message:
                         message = error_message
                     else:
-                        message += 'The selected files were deleted from the repository.  '
+                        message += "The selected files were deleted from the repository.  "
             else:
-                message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>."
+                message = (
+                    "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>."
+                )
                 status = "error"
         repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
         changeset_revision = repository.tip()
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             id,
-                                                                                             changeset_revision,
-                                                                                             metadata_only=True)
-        return trans.fill_template('/webapps/tool_shed/repository/browse_repository.mako',
-                                   repo=repo,
-                                   repository=repository,
-                                   changeset_revision=changeset_revision,
-                                   metadata=metadata,
-                                   commit_message=commit_message,
-                                   repository_type_select_field=repository_type_select_field,
-                                   message=message,
-                                   status=status)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, id, changeset_revision, metadata_only=True
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/browse_repository.mako",
+            repo=repo,
+            repository=repository,
+            changeset_revision=changeset_revision,
+            metadata=metadata,
+            commit_message=commit_message,
+            repository_type_select_field=repository_type_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
-    def send_to_owner(self, trans, id, message=''):
+    def send_to_owner(self, trans, id, message=""):
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         if not message:
-            message = 'Enter a message'
-            status = 'error'
+            message = "Enter a message"
+            status = "error"
         elif trans.user and trans.user.email:
             smtp_server = trans.app.config.smtp_server
             from_address = trans.app.config.email_from
@@ -2218,12 +2411,13 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             # Get the name of the server hosting the tool shed instance.
             host = trans.request.host
             # Build the email message
-            body = string.Template(suc.contact_owner_template) \
-                .safe_substitute(username=trans.user.username,
-                                 repository_name=repository.name,
-                                 email=trans.user.email,
-                                 message=message,
-                                 host=host)
+            body = string.Template(suc.contact_owner_template).safe_substitute(
+                username=trans.user.username,
+                repository_name=repository.name,
+                email=trans.user.email,
+                message=message,
+                host=host,
+            )
             subject = f"Regarding your tool shed repository named {repository.name}"
             # Send it
             try:
@@ -2236,21 +2430,19 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         else:
             # Do all we can to eliminate spam.
             return trans.show_error_message("You must be logged in to contact the owner of a repository.")
-        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                        action='contact_owner',
-                                                        id=id,
-                                                        message=message,
-                                                        status=status))
+        return trans.response.send_redirect(
+            web.url_for(controller="repository", action="contact_owner", id=id, message=message, status=status)
+        )
 
     @web.expose
     @require_login("set email alerts")
     def set_email_alerts(self, trans, **kwd):
         """Set email alerts for selected repositories."""
         # This method is called from multiple grids, so the caller must be passed.
-        caller = kwd['caller']
+        caller = kwd["caller"]
         user = trans.user
         if user:
-            repository_ids = util.listify(kwd.get('id', ''))
+            repository_ids = util.listify(kwd.get("id", ""))
             total_alerts_added = 0
             total_alerts_removed = 0
             flush_needed = False
@@ -2274,19 +2466,17 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     total_alerts_added += 1
             if flush_needed:
                 trans.sa_session.flush()
-            message = 'Total alerts added: %d, total alerts removed: %d' % (total_alerts_added, total_alerts_removed)
-            kwd['message'] = message
-            kwd['status'] = 'done'
-        del kwd['operation']
-        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                        action=caller,
-                                                        **kwd))
+            message = "Total alerts added: %d, total alerts removed: %d" % (total_alerts_added, total_alerts_removed)
+            kwd["message"] = message
+            kwd["status"] = "done"
+        del kwd["operation"]
+        return trans.response.send_redirect(web.url_for(controller="repository", action=caller, **kwd))
 
     @web.expose
     @require_login("set repository as malicious")
     def set_malicious(self, trans, id, ctx_str, **kwd):
-        malicious = kwd.get('malicious', '')
-        if kwd.get('malicious_button', False):
+        malicious = kwd.get("malicious", "")
+        if kwd.get("malicious_button", False):
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, ctx_str)
             malicious_checked = CheckboxField.is_checked(malicious)
             repository_metadata.malicious = malicious_checked
@@ -2296,14 +2486,18 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 message = "The repository tip has been defined as malicious."
             else:
                 message = "The repository tip has been defined as <b>not</b> malicious."
-            status = 'done'
-        return trans.response.send_redirect(web.url_for(controller='repository',
-                                                        action='manage_repository',
-                                                        id=id,
-                                                        changeset_revision=ctx_str,
-                                                        malicious=malicious,
-                                                        message=message,
-                                                        status=status))
+            status = "done"
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="repository",
+                action="manage_repository",
+                id=id,
+                changeset_revision=ctx_str,
+                malicious=malicious,
+                message=message,
+                status=status,
+            )
+        )
 
     @web.expose
     def sharable_owner(self, trans, owner):
@@ -2314,12 +2508,12 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             user = None
         if user:
             user_id = trans.security.encode_id(user.id)
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='index',
-                                                            user_id=user_id))
+            return trans.response.send_redirect(web.url_for(controller="repository", action="index", user_id=user_id))
         else:
-            return trans.show_error_message("The tool shed <b>%s</b> contains no repositories owned by <b>%s</b>." %
-                                            (web.url_for('/', qualified=True).rstrip('/'), str(owner)))
+            return trans.show_error_message(
+                "The tool shed <b>%s</b> contains no repositories owned by <b>%s</b>."
+                % (web.url_for("/", qualified=True).rstrip("/"), str(owner))
+            )
 
     @web.expose
     def sharable_repository(self, trans, owner, name):
@@ -2330,9 +2524,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             repository = None
         if repository:
             repository_id = trans.security.encode_id(repository.id)
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='index',
-                                                            repository_id=repository_id))
+            return trans.response.send_redirect(
+                web.url_for(controller="repository", action="index", repository_id=repository_id)
+            )
         else:
             # If the owner is valid, then show all of their repositories.
             try:
@@ -2342,14 +2536,16 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             if user:
                 user_id = trans.security.encode_id(user.id)
                 message = f"This list of repositories owned by <b>{str(owner)}</b>, does not include one named <b>{str(name)}</b>."
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='index',
-                                                                user_id=user_id,
-                                                                message=message,
-                                                                status='error'))
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository", action="index", user_id=user_id, message=message, status="error"
+                    )
+                )
             else:
-                return trans.show_error_message("The tool shed <b>%s</b> contains no repositories named <b>%s</b> with owner <b>%s</b>." %
-                                                (web.url_for('/', qualified=True).rstrip('/'), str(name), str(owner)))
+                return trans.show_error_message(
+                    "The tool shed <b>%s</b> contains no repositories named <b>%s</b> with owner <b>%s</b>."
+                    % (web.url_for("/", qualified=True).rstrip("/"), str(name), str(owner))
+                )
 
     @web.expose
     def sharable_repository_revision(self, trans, owner, name, changeset_revision):
@@ -2360,35 +2556,47 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             repository = None
         if repository:
             repository_id = trans.security.encode_id(repository.id)
-            repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                                            repository_id,
-                                                                                                            changeset_revision)
+            repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                trans.app, repository_id, changeset_revision
+            )
             if not repository_metadata:
                 # Get updates to the received changeset_revision if any exist.
-                upper_bound_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
+                upper_bound_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
+                    trans.app, repository, changeset_revision
+                )
                 if upper_bound_changeset_revision and upper_bound_changeset_revision != changeset_revision:
                     changeset_revision = upper_bound_changeset_revision
-                    repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                                                    repository_id,
-                                                                                                                    changeset_revision)
+                    repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+                        trans.app, repository_id, changeset_revision
+                    )
             if repository_metadata:
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='index',
-                                                                repository_id=repository_id,
-                                                                changeset_revision=changeset_revision))
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository",
+                        action="index",
+                        repository_id=repository_id,
+                        changeset_revision=changeset_revision,
+                    )
+                )
             else:
-                message = "The change log for the repository named <b>%s</b> owned by <b>%s</b> does not include revision <b>%s</b>." % \
-                    (escape(str(name)), escape(str(owner)), escape(str(changeset_revision)))
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='index',
-                                                                repository_id=repository_id,
-                                                                message=message,
-                                                                status='error'))
+                message = (
+                    "The change log for the repository named <b>%s</b> owned by <b>%s</b> does not include revision <b>%s</b>."
+                    % (escape(str(name)), escape(str(owner)), escape(str(changeset_revision)))
+                )
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository",
+                        action="index",
+                        repository_id=repository_id,
+                        message=message,
+                        status="error",
+                    )
+                )
         else:
             # See if the owner is valid.
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='sharable_owner',
-                                                            owner=owner))
+            return trans.response.send_redirect(
+                web.url_for(controller="repository", action="sharable_owner", owner=owner)
+            )
 
     @web.expose
     def updated_changeset_revisions(self, trans, **kwd):
@@ -2401,17 +2609,17 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         revision is older than the current changeset revision for the required repository, making it impossible to
         discover the repository without knowledge of revisions to which it could have been updated.
         """
-        name = kwd.get('name', None)
-        owner = kwd.get('owner', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        name = kwd.get("name", None)
+        owner = kwd.get("owner", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         if name and owner and changeset_revision:
             return metadata_util.get_updated_changeset_revisions(trans.app, name, owner, changeset_revision)
-        return ''
+        return ""
 
     @web.expose
     def view_changelog(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo = repository.hg_repo
         changesets = []
@@ -2421,43 +2629,44 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 has_metadata = True
             else:
                 has_metadata = False
-            change_dict = {'ctx': ctx,
-                           'rev': str(ctx.rev()),
-                           'date': date,
-                           'display_date': hg_util.get_readable_ctx_date(ctx),
-                           'description': ctx.description(),
-                           'files': ctx.files(),
-                           'user': ctx.user(),
-                           'parent': ctx.parents()[0],
-                           'has_metadata': has_metadata}
+            change_dict = {
+                "ctx": ctx,
+                "rev": str(ctx.rev()),
+                "date": date,
+                "display_date": hg_util.get_readable_ctx_date(ctx),
+                "description": ctx.description(),
+                "files": ctx.files(),
+                "user": ctx.user(),
+                "parent": ctx.parents()[0],
+                "has_metadata": has_metadata,
+            }
             # Make sure we'll view latest changeset first.
             changesets.insert(0, change_dict)
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             id,
-                                                                                             repository.tip(),
-                                                                                             metadata_only=True)
-        return trans.fill_template('/webapps/tool_shed/repository/view_changelog.mako',
-                                   repository=repository,
-                                   metadata=metadata,
-                                   changesets=changesets,
-                                   message=message,
-                                   status=status)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, id, repository.tip(), metadata_only=True
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/view_changelog.mako",
+            repository=repository,
+            metadata=metadata,
+            changesets=changesets,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def view_changeset(self, trans, id, ctx_str, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo = repository.hg_repo
         ctx = hg_util.get_changectx_for_changeset(repo, ctx_str)
         if ctx is None:
             message = f"Repository does not include changeset revision '{str(ctx_str)}'."
-            status = 'error'
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='view_changelog',
-                                                            id=id,
-                                                            message=message,
-                                                            status=status))
+            status = "error"
+            return trans.response.send_redirect(
+                web.url_for(controller="repository", action="view_changelog", id=id, message=message, status=status)
+            )
         ctx_parent = ctx.parents()[0]
         if ctx.children():
             ctx_child = ctx.children()[0]
@@ -2468,20 +2677,21 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         # Not quite sure if the following settings make any difference, but with a combination of them and the size check on each
         # diff, we don't run out of memory when viewing the changelog of the cisortho2 repository on the test tool shed.
         options_dict = {util.unicodify(k): util.unicodify(v) for k, v in options_dict.items()}
-        options_dict['maxfile'] = basic_util.MAXDIFFSIZE
-        options_dict['maxtotal'] = basic_util.MAXDIFFSIZE
+        options_dict["maxfile"] = basic_util.MAXDIFFSIZE
+        options_dict["maxtotal"] = basic_util.MAXDIFFSIZE
         diffopts = mdiff.diffopts(**options_dict)
         for diff in patch.diff(repo, node1=ctx_parent.node(), node2=ctx.node(), opts=diffopts):
             if len(diff) > basic_util.MAXDIFFSIZE:
                 diff = util.shrink_string_by_size(diff, basic_util.MAXDIFFSIZE)
             diffs.append(basic_util.to_html_string(diff))
-        modified, added, removed, deleted, unknown, ignored, clean = repo.status(node1=ctx_parent.node(), node2=ctx.node())
+        modified, added, removed, deleted, unknown, ignored, clean = repo.status(
+            node1=ctx_parent.node(), node2=ctx.node()
+        )
         anchors = modified + added + removed + deleted + unknown + ignored + clean
         anchors = util.unicodify(anchors)
-        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
-                                                                                             id,
-                                                                                             ctx_str,
-                                                                                             metadata_only=True)
+        metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(
+            trans.app, id, ctx_str, metadata_only=True
+        )
         # For rendering the prev button.
         if ctx_parent:
             ctx_parent_date = hg_util.get_readable_ctx_date(ctx_parent)
@@ -2498,58 +2708,63 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             next = f"<b>{ctx_child_rev}:{ctx_child}</b> <i>({ctx_child_date})</i>"
         else:
             next = None
-        return trans.fill_template('/webapps/tool_shed/repository/view_changeset.mako',
-                                   repository=repository,
-                                   metadata=metadata,
-                                   prev=prev,
-                                   next=next,
-                                   ctx=ctx,
-                                   ctx_parent=ctx_parent,
-                                   ctx_child=ctx_child,
-                                   anchors=anchors,
-                                   modified=modified,
-                                   added=added,
-                                   removed=removed,
-                                   deleted=deleted,
-                                   unknown=unknown,
-                                   ignored=ignored,
-                                   clean=clean,
-                                   diffs=diffs,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/view_changeset.mako",
+            repository=repository,
+            metadata=metadata,
+            prev=prev,
+            next=next,
+            ctx=ctx,
+            ctx_parent=ctx_parent,
+            ctx_child=ctx_child,
+            anchors=anchors,
+            modified=modified,
+            added=added,
+            removed=removed,
+            deleted=deleted,
+            unknown=unknown,
+            ignored=ignored,
+            clean=clean,
+            diffs=diffs,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def view_or_manage_repository(self, trans, **kwd):
-        repository_id = kwd.get('id', None)
+        repository_id = kwd.get("id", None)
         if repository_id:
             repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
             user = trans.user
             if repository:
-                if user is not None and (trans.user_is_admin
-                                         or trans.app.security_agent.user_can_administer_repository(user, repository)):
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action='manage_repository',
-                                                                    **kwd))
+                if user is not None and (
+                    trans.user_is_admin or trans.app.security_agent.user_can_administer_repository(user, repository)
+                ):
+                    return trans.response.send_redirect(
+                        web.url_for(controller="repository", action="manage_repository", **kwd)
+                    )
                 else:
-                    return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                    action='view_repository',
-                                                                    **kwd))
+                    return trans.response.send_redirect(
+                        web.url_for(controller="repository", action="view_repository", **kwd)
+                    )
             return trans.show_error_message(f"Invalid repository id '{repository_id}' received.")
         return trans.show_error_message("The repository id was not received.")
 
     @web.expose
     def view_repository(self, trans, id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
         repo = repository.hg_repo
         avg_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, repository, webapp_model=trans.model)
-        changeset_revision = kwd.get('changeset_revision', repository.tip())
+        changeset_revision = kwd.get("changeset_revision", repository.tip())
         self.validate_changeset_revision(trans, changeset_revision, id)
-        repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(repository, changeset_revision=changeset_revision)
+        repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed(
+            repository, changeset_revision=changeset_revision
+        )
         repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
-        display_reviews = kwd.get('display_reviews', False)
-        alerts = kwd.get('alerts', '')
+        display_reviews = kwd.get("display_reviews", False)
+        alerts = kwd.get("alerts", "")
         alerts_checked = CheckboxField.is_checked(alerts)
         if repository.email_alerts:
             email_alerts = json.loads(repository.email_alerts)
@@ -2557,7 +2772,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             email_alerts = []
         repository_dependencies = None
         user = trans.user
-        if user and kwd.get('receive_email_alerts_button', False):
+        if user and kwd.get("receive_email_alerts_button", False):
             flush_needed = False
             if alerts_checked:
                 if user.email not in email_alerts:
@@ -2573,18 +2788,18 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 trans.sa_session.add(repository)
                 trans.sa_session.flush()
         checked = alerts_checked or (user and user.email in email_alerts)
-        alerts_check_box = CheckboxField('alerts', value=checked)
-        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
-                                                                                           repository,
-                                                                                           selected_value=changeset_revision,
-                                                                                           add_id_to_name=False,
-                                                                                           downloadable=False)
+        alerts_check_box = CheckboxField("alerts", value=checked)
+        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(
+            trans, repository, selected_value=changeset_revision, add_id_to_name=False, downloadable=False
+        )
         revision_label = hg_util.get_revision_label(trans.app, repository, changeset_revision, include_date=False)
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, changeset_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, id, changeset_revision
+        )
         if repository_metadata:
             metadata = repository_metadata.metadata
             # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
-            toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
+            toolshed_base_url = str(web.url_for("/", qualified=True)).rstrip("/")
             rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
             repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
             if str(repository.type) != rt_util.TOOL_DEPENDENCY_DEFINITION:
@@ -2593,7 +2808,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 orphan_message = dd.generate_message_for_orphan_tool_dependencies(repository, metadata)
                 if orphan_message:
                     message += orphan_message
-                    status = 'warning'
+                    status = "warning"
         else:
             metadata = None
         is_malicious = metadata_util.is_malicious(trans.app, id, repository.tip())
@@ -2602,37 +2817,38 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 message += malicious_error_can_push
             else:
                 message += malicious_error
-            status = 'error'
+            status = "error"
         tsucm = ToolShedUtilityContainerManager(trans.app)
-        containers_dict = tsucm.build_repository_containers(repository,
-                                                            changeset_revision,
-                                                            repository_dependencies,
-                                                            repository_metadata)
+        containers_dict = tsucm.build_repository_containers(
+            repository, changeset_revision, repository_dependencies, repository_metadata
+        )
         repository_type_select_field = rt_util.build_repository_type_select_field(trans, repository=repository)
         heads = hg_util.get_repository_heads(repo)
-        return trans.fill_template('/webapps/tool_shed/repository/view_repository.mako',
-                                   repo=repo,
-                                   heads=heads,
-                                   repository=repository,
-                                   repository_metadata=repository_metadata,
-                                   metadata=metadata,
-                                   containers_dict=containers_dict,
-                                   avg_rating=avg_rating,
-                                   display_reviews=display_reviews,
-                                   num_ratings=num_ratings,
-                                   alerts_check_box=alerts_check_box,
-                                   changeset_revision=changeset_revision,
-                                   changeset_revision_select_field=changeset_revision_select_field,
-                                   revision_label=revision_label,
-                                   repository_type_select_field=repository_type_select_field,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/view_repository.mako",
+            repo=repo,
+            heads=heads,
+            repository=repository,
+            repository_metadata=repository_metadata,
+            metadata=metadata,
+            containers_dict=containers_dict,
+            avg_rating=avg_rating,
+            display_reviews=display_reviews,
+            num_ratings=num_ratings,
+            alerts_check_box=alerts_check_box,
+            changeset_revision=changeset_revision,
+            changeset_revision_select_field=changeset_revision_select_field,
+            revision_label=revision_label,
+            repository_type_select_field=repository_type_select_field,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def view_tool_metadata(self, trans, repository_id, changeset_revision, tool_id, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        render_repository_actions_for = kwd.get('render_repository_actions_for', 'tool_shed')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        render_repository_actions_for = kwd.get("render_repository_actions_for", "tool_shed")
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
         repo_files_dir = repository.repo_path(trans.app)
         repo = repository.hg_repo
@@ -2642,70 +2858,69 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
         guid = None
         self.validate_changeset_revision(trans, changeset_revision, repository_id)
         revision_label = hg_util.get_revision_label(trans.app, repository, changeset_revision, include_date=False)
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
+        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+            trans.app, repository_id, changeset_revision
+        )
         if repository_metadata:
             repository_metadata_id = trans.security.encode_id(repository_metadata.id)
             metadata = repository_metadata.metadata
             if metadata:
-                if 'tools' in metadata:
+                if "tools" in metadata:
                     with ValidationContext.from_app(trans.app) as validation_context:
                         tv = tool_validator.ToolValidator(validation_context)
-                        for tool_metadata_dict in metadata['tools']:
-                            if tool_metadata_dict['id'] == tool_id:
+                        for tool_metadata_dict in metadata["tools"]:
+                            if tool_metadata_dict["id"] == tool_id:
                                 work_dir = tempfile.mkdtemp()
-                                relative_path_to_tool_config = tool_metadata_dict['tool_config']
-                                guid = tool_metadata_dict['guid']
+                                relative_path_to_tool_config = tool_metadata_dict["tool_config"]
+                                guid = tool_metadata_dict["guid"]
                                 full_path_to_tool_config = os.path.abspath(relative_path_to_tool_config)
                                 full_path_to_dir, tool_config_filename = os.path.split(full_path_to_tool_config)
-                                can_use_disk_file = tv.can_use_tool_config_disk_file(repository,
-                                                                                     repo,
-                                                                                     full_path_to_tool_config,
-                                                                                     changeset_revision)
+                                can_use_disk_file = tv.can_use_tool_config_disk_file(
+                                    repository, repo, full_path_to_tool_config, changeset_revision
+                                )
                                 if can_use_disk_file:
-                                    tool, valid, message, sample_files = \
-                                        tv.handle_sample_files_and_load_tool_from_disk(repo_files_dir,
-                                                                                       repository_id,
-                                                                                       full_path_to_tool_config,
-                                                                                       work_dir)
+                                    tool, valid, message, sample_files = tv.handle_sample_files_and_load_tool_from_disk(
+                                        repo_files_dir, repository_id, full_path_to_tool_config, work_dir
+                                    )
                                     if message:
-                                        status = 'error'
+                                        status = "error"
                                 else:
-                                    tool, valid, message, sample_files = \
-                                        tv.handle_sample_files_and_load_tool_from_tmp_config(repo,
-                                                                                             repository_id,
-                                                                                             changeset_revision,
-                                                                                             tool_config_filename,
-                                                                                             work_dir)
+                                    (
+                                        tool,
+                                        valid,
+                                        message,
+                                        sample_files,
+                                    ) = tv.handle_sample_files_and_load_tool_from_tmp_config(
+                                        repo, repository_id, changeset_revision, tool_config_filename, work_dir
+                                    )
                                     if message:
-                                        status = 'error'
+                                        status = "error"
                                 basic_util.remove_dir(work_dir)
                                 break
                         if guid:
                             tvm = tool_version_manager.ToolVersionManager(trans.app)
-                            tool_lineage = tvm.get_version_lineage_for_tool(repository_id,
-                                                                            repository_metadata,
-                                                                            guid)
+                            tool_lineage = tvm.get_version_lineage_for_tool(repository_id, repository_metadata, guid)
         else:
             repository_metadata_id = None
             metadata = None
-        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(trans,
-                                                                                           repository,
-                                                                                           selected_value=changeset_revision,
-                                                                                           add_id_to_name=False,
-                                                                                           downloadable=False)
-        return trans.fill_template("/webapps/tool_shed/repository/view_tool_metadata.mako",
-                                   render_repository_actions_for=render_repository_actions_for,
-                                   repository=repository,
-                                   repository_metadata_id=repository_metadata_id,
-                                   metadata=metadata,
-                                   tool=tool,
-                                   tool_metadata_dict=tool_metadata_dict,
-                                   tool_lineage=tool_lineage,
-                                   changeset_revision=changeset_revision,
-                                   revision_label=revision_label,
-                                   changeset_revision_select_field=changeset_revision_select_field,
-                                   message=message,
-                                   status=status)
+        changeset_revision_select_field = grids_util.build_changeset_revision_select_field(
+            trans, repository, selected_value=changeset_revision, add_id_to_name=False, downloadable=False
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/view_tool_metadata.mako",
+            render_repository_actions_for=render_repository_actions_for,
+            repository=repository,
+            repository_metadata_id=repository_metadata_id,
+            metadata=metadata,
+            tool=tool,
+            tool_metadata_dict=tool_metadata_dict,
+            tool_lineage=tool_lineage,
+            changeset_revision=changeset_revision,
+            revision_label=revision_label,
+            changeset_revision_select_field=changeset_revision_select_field,
+            message=message,
+            status=status,
+        )
 
     def validate_changeset_revision(self, trans, changeset_revision, repository_id):
         """In case changeset revision is invalid send them to the repository page"""
@@ -2713,9 +2928,13 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
             repo = repository.hg_repo
             if not hg_util.get_changectx_for_changeset(repo, changeset_revision):
-                message = 'Invalid changeset revision'
-                return trans.response.send_redirect(web.url_for(controller='repository',
-                                                                action='index',
-                                                                repository_id=repository_id,
-                                                                message=message,
-                                                                status='error'))
+                message = "Invalid changeset revision"
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository",
+                        action="index",
+                        repository_id=repository_id,
+                        message=message,
+                        status="error",
+                    )
+                )
diff --git a/lib/tool_shed/webapp/controllers/repository_review.py b/lib/tool_shed/webapp/controllers/repository_review.py
index 0c4059173a4..adf8ebba3c2 100644
--- a/lib/tool_shed/webapp/controllers/repository_review.py
+++ b/lib/tool_shed/webapp/controllers/repository_review.py
@@ -3,14 +3,14 @@ import logging
 from sqlalchemy import (
     and_,
     false,
-    func
+    func,
 )
 
 import tool_shed.grids.repository_review_grids as repository_review_grids
 import tool_shed.grids.util as grids_util
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.web.form_builder import CheckboxField
 from galaxy.webapps.base.controller import BaseUIController
@@ -19,8 +19,8 @@ from tool_shed.util import (
     metadata_util,
     repository_util,
     review_util,
-    shed_util_common as suc
 )
+from tool_shed.util import shed_util_common as suc
 from tool_shed.util.container_util import STRSEP
 from tool_shed.util.web_util import escape
 from tool_shed.webapp.framework.decorators import require_login
@@ -44,61 +44,69 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
     @require_login("approve repository review")
     def approve_repository_review(self, trans, **kwd):
         # The value of the received id is the encoded review id.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        encoded_review_id = kwd['id']
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        encoded_review_id = kwd["id"]
         review = review_util.get_review(trans.app, encoded_review_id)
-        if kwd.get('approve_repository_review_button', False):
-            approved_select_field_name = f'{encoded_review_id}{STRSEP}approved'
+        if kwd.get("approve_repository_review_button", False):
+            approved_select_field_name = f"{encoded_review_id}{STRSEP}approved"
             approved_select_field_value = str(kwd[approved_select_field_name])
             review.approved = approved_select_field_value
             trans.sa_session.add(review)
             trans.sa_session.flush()
-            message = f'Approved value <b>{escape(approved_select_field_value)}</b> saved for this revision.'
+            message = f"Approved value <b>{escape(approved_select_field_value)}</b> saved for this revision."
         repository_id = trans.security.encode_id(review.repository_id)
         changeset_revision = review.changeset_revision
-        return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                        action='manage_repository_reviews_of_revision',
-                                                        id=repository_id,
-                                                        changeset_revision=changeset_revision,
-                                                        message=message,
-                                                        status=status))
+        return trans.response.send_redirect(
+            web.url_for(
+                controller="repository_review",
+                action="manage_repository_reviews_of_revision",
+                id=repository_id,
+                changeset_revision=changeset_revision,
+                message=message,
+                status=status,
+            )
+        )
 
     @web.expose
     @require_login("browse components")
     def browse_components(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "create":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='create_component',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="create_component", **kwd)
+                )
         return self.component_grid(trans, **kwd)
 
     @web.expose
     @require_login("browse review")
     def browse_review(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        review = review_util.get_review(trans.app, kwd['id'])
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        review = review_util.get_review(trans.app, kwd["id"])
         repository = review.repository
         repo = repository.hg_repo
         rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, review.changeset_revision)
-        return trans.fill_template('/webapps/tool_shed/repository_review/browse_review.mako',
-                                   repository=repository,
-                                   changeset_revision_label=changeset_revision_label,
-                                   review=review,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/browse_review.mako",
+            repository=repository,
+            changeset_revision_label=changeset_revision_label,
+            review=review,
+            message=message,
+            status=status,
+        )
 
     def copy_review(self, trans, review_to_copy, review):
         for component_review in review_to_copy.component_reviews:
-            copied_component_review = trans.model.ComponentReview(repository_review_id=review.id,
-                                                                  component_id=component_review.component.id,
-                                                                  comment=component_review.comment,
-                                                                  private=component_review.private,
-                                                                  approved=component_review.approved,
-                                                                  rating=component_review.rating)
+            copied_component_review = trans.model.ComponentReview(
+                repository_review_id=review.id,
+                component_id=component_review.component.id,
+                comment=component_review.comment,
+                private=component_review.private,
+                approved=component_review.approved,
+                rating=component_review.rating,
+            )
             trans.sa_session.add(copied_component_review)
             trans.sa_session.flush()
         review.approved = review_to_copy.approved
@@ -109,136 +117,157 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
     @web.expose
     @require_login("create component")
     def create_component(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        name = kwd.get('name', '')
-        description = kwd.get('description', '')
-        if kwd.get('create_component_button', False):
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        name = kwd.get("name", "")
+        description = kwd.get("description", "")
+        if kwd.get("create_component_button", False):
             if not name or not description:
-                message = 'Enter a valid name and a description'
-                status = 'error'
+                message = "Enter a valid name and a description"
+                status = "error"
             elif review_util.get_component_by_name(trans.app, name):
-                message = 'A component with that name already exists'
-                status = 'error'
+                message = "A component with that name already exists"
+                status = "error"
             else:
                 component = trans.app.model.Component(name=name, description=description)
                 trans.sa_session.add(component)
                 trans.sa_session.flush()
                 message = f"Component '{escape(component.name)}' has been created"
-                status = 'done'
-                trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                         action='manage_components',
-                                                         message=message,
-                                                         status=status))
-        return trans.fill_template('/webapps/tool_shed/repository_review/create_component.mako',
-                                   name=name,
-                                   description=description,
-                                   message=message,
-                                   status=status)
+                status = "done"
+                trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository_review", action="manage_components", message=message, status=status
+                    )
+                )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/create_component.mako",
+            name=name,
+            description=description,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("create review")
     def create_review(self, trans, **kwd):
         # The value of the received id is the encoded repository id.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_id = kwd.get('id', None)
-        changeset_revision = kwd.get('changeset_revision', None)
-        previous_review_id = kwd.get('previous_review_id', None)
-        create_without_copying = 'create_without_copying' in kwd
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_id = kwd.get("id", None)
+        changeset_revision = kwd.get("changeset_revision", None)
+        previous_review_id = kwd.get("previous_review_id", None)
+        create_without_copying = "create_without_copying" in kwd
         if repository_id:
             if changeset_revision:
                 # Make sure there is not already a review of the revision by the user.
                 repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
-                if review_util.get_review_by_repository_id_changeset_revision_user_id(app=trans.app,
-                                                                                      repository_id=repository_id,
-                                                                                      changeset_revision=changeset_revision,
-                                                                                      user_id=trans.security.encode_id(trans.user.id)):
+                if review_util.get_review_by_repository_id_changeset_revision_user_id(
+                    app=trans.app,
+                    repository_id=repository_id,
+                    changeset_revision=changeset_revision,
+                    user_id=trans.security.encode_id(trans.user.id),
+                ):
                     message = f"You have already created a review for revision <b>{changeset_revision}</b> of repository <b>{escape(repository.name)}</b>."
                     status = "error"
                 else:
                     # See if there are any reviews for previous changeset revisions that the user can copy.
-                    if not create_without_copying and \
-                            not previous_review_id and \
-                            review_util.has_previous_repository_reviews(trans.app, repository, changeset_revision):
-                        return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                        action='select_previous_review',
-                                                                        **kwd))
+                    if (
+                        not create_without_copying
+                        and not previous_review_id
+                        and review_util.has_previous_repository_reviews(trans.app, repository, changeset_revision)
+                    ):
+                        return trans.response.send_redirect(
+                            web.url_for(controller="repository_review", action="select_previous_review", **kwd)
+                        )
                     # A review can be initially performed only on an installable revision of a repository, so make sure we have metadata associated
                     # with the received changeset_revision.
-                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
+                    repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                        trans.app, repository_id, changeset_revision
+                    )
                     if repository_metadata:
                         metadata = repository_metadata.metadata
                         if metadata:
-                            review = trans.app.model.RepositoryReview(repository_id=repository_metadata.repository_id,
-                                                                      changeset_revision=changeset_revision,
-                                                                      user_id=trans.user.id,
-                                                                      rating=None,
-                                                                      deleted=False)
+                            review = trans.app.model.RepositoryReview(
+                                repository_id=repository_metadata.repository_id,
+                                changeset_revision=changeset_revision,
+                                user_id=trans.user.id,
+                                rating=None,
+                                deleted=False,
+                            )
                             trans.sa_session.add(review)
                             trans.sa_session.flush()
                             if previous_review_id:
                                 review_to_copy = review_util.get_review(trans.app, previous_review_id)
                                 self.copy_review(trans, review_to_copy, review)
                             review_id = trans.security.encode_id(review.id)
-                            message = "Begin your review of revision <b>%s</b> of repository <b>%s</b>." \
-                                % (changeset_revision, repository.name)
-                            status = 'done'
-                            trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                     action='edit_review',
-                                                                     id=review_id,
-                                                                     message=message,
-                                                                     status=status))
+                            message = "Begin your review of revision <b>%s</b> of repository <b>%s</b>." % (
+                                changeset_revision,
+                                repository.name,
+                            )
+                            status = "done"
+                            trans.response.send_redirect(
+                                web.url_for(
+                                    controller="repository_review",
+                                    action="edit_review",
+                                    id=review_id,
+                                    message=message,
+                                    status=status,
+                                )
+                            )
                     else:
-                        message = "A new review cannot be created for revision <b>%s</b> of repository <b>%s</b>.  Select a valid revision and try again." \
+                        message = (
+                            "A new review cannot be created for revision <b>%s</b> of repository <b>%s</b>.  Select a valid revision and try again."
                             % (changeset_revision, escape(repository.name))
-                        kwd['message'] = message
-                        kwd['status'] = 'error'
+                        )
+                        kwd["message"] = message
+                        kwd["status"] = "error"
             else:
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='manage_repository_reviews',
-                                                                **kwd))
-        return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                        action='view_or_manage_repository',
-                                                        **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="manage_repository_reviews", **kwd)
+                )
+        return trans.response.send_redirect(
+            web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+        )
 
     @web.expose
     @require_login("edit component")
     def edit_component(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        id = kwd.get("id", None)
         if not id:
             message = "No component ids received for editing"
-            trans.response.send_redirect(web.url_for(controller='admin',
-                                                     action='manage_categories',
-                                                     message=message,
-                                                     status='error'))
+            trans.response.send_redirect(
+                web.url_for(controller="admin", action="manage_categories", message=message, status="error")
+            )
         component = review_util.get_component(trans.app, id)
-        if kwd.get('edit_component_button', False):
-            new_description = kwd.get('description', '').strip()
+        if kwd.get("edit_component_button", False):
+            new_description = kwd.get("description", "").strip()
             if component.description != new_description:
                 component.description = new_description
                 trans.sa_session.add(component)
                 trans.sa_session.flush()
                 message = f"The information has been saved for the component named <b>{escape(component.name)}</b>"
-                status = 'done'
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='manage_components',
-                                                                message=message,
-                                                                status=status))
-        return trans.fill_template('/webapps/tool_shed/repository_review/edit_component.mako',
-                                   component=component,
-                                   message=message,
-                                   status=status)
+                status = "done"
+                return trans.response.send_redirect(
+                    web.url_for(
+                        controller="repository_review", action="manage_components", message=message, status=status
+                    )
+                )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/edit_component.mako",
+            component=component,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("edit review")
     def edit_review(self, trans, **kwd):
         # The value of the received id is the encoded review id.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        review_id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        review_id = kwd.get("id", None)
         review = review_util.get_review(trans.app, review_id)
         components_dict = {}
         for component in review_util.get_components(trans.app):
@@ -250,19 +279,19 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
                 component_name = component_review.component.name
                 if component_name in components_dict:
                     component_review_dict = components_dict[component_name]
-                    component_review_dict['component_review'] = component_review
+                    component_review_dict["component_review"] = component_review
                     components_dict[component_name] = component_review_dict
         # Handle a Save button click.
         save_button_clicked = False
-        save_buttons = [f'{comp_name}{STRSEP}review_button' for comp_name in components_dict.keys()]
-        save_buttons.append('revision_approved_button')
+        save_buttons = [f"{comp_name}{STRSEP}review_button" for comp_name in components_dict.keys()]
+        save_buttons.append("revision_approved_button")
         for save_button in save_buttons:
             if save_button in kwd:
                 save_button_clicked = True
                 break
         if save_button_clicked:
             # Handle the revision_approved_select_field value.
-            revision_approved = kwd.get('revision_approved', None)
+            revision_approved = kwd.get("revision_approved", None)
             revision_approved_setting_changed = False
             if revision_approved:
                 revision_approved = str(revision_approved)
@@ -280,29 +309,30 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
                 rating = 0
                 private = False
                 for k, v in kwd.items():
-                    if k.startswith(f'{component_name}{STRSEP}'):
-                        component_review_attr = k.replace(f'{component_name}{STRSEP}', '')
-                        if component_review_attr == 'component_id':
+                    if k.startswith(f"{component_name}{STRSEP}"):
+                        component_review_attr = k.replace(f"{component_name}{STRSEP}", "")
+                        if component_review_attr == "component_id":
                             component_id = str(v)
-                        elif component_review_attr == 'comment':
+                        elif component_review_attr == "comment":
                             comment = str(v)
-                        elif component_review_attr == 'private':
+                        elif component_review_attr == "private":
                             private = CheckboxField.is_checked(v)
-                        elif component_review_attr == 'approved':
+                        elif component_review_attr == "approved":
                             approved = str(v)
-                        elif component_review_attr == 'rating':
+                        elif component_review_attr == "rating":
                             rating = int(str(v))
                 component = review_util.get_component(trans.app, component_id)
-                component_review = \
-                    review_util.get_component_review_by_repository_review_id_component_id(trans.app,
-                                                                                          review_id,
-                                                                                          component_id)
+                component_review = review_util.get_component_review_by_repository_review_id_component_id(
+                    trans.app, review_id, component_id
+                )
                 if component_review:
                     # See if the existing component review should be updated.
-                    if component_review.comment != comment or \
-                            component_review.private != private or \
-                            component_review.approved != approved or \
-                            component_review.rating != rating:
+                    if (
+                        component_review.comment != comment
+                        or component_review.private != private
+                        or component_review.approved != approved
+                        or component_review.rating != rating
+                    ):
                         component_review.comment = comment
                         component_review.private = private
                         component_review.approved = approved
@@ -314,22 +344,31 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
                 else:
                     # See if a new component_review should be created.
                     if comment or private or approved != trans.model.ComponentReview.approved_states.NO or rating:
-                        component_review = trans.model.ComponentReview(repository_review_id=review.id,
-                                                                       component_id=component.id,
-                                                                       comment=comment,
-                                                                       approved=approved,
-                                                                       rating=rating)
+                        component_review = trans.model.ComponentReview(
+                            repository_review_id=review.id,
+                            component_id=component.id,
+                            comment=comment,
+                            approved=approved,
+                            rating=rating,
+                        )
                         trans.sa_session.add(component_review)
                         trans.sa_session.flush()
                         flushed = True
                         saved_component_names.append(component_name)
                 if flushed:
                     # Update the repository rating value to be the average of all component review ratings.
-                    average_rating = trans.sa_session.query(func.avg(trans.model.ComponentReview.table.c.rating)) \
-                                                     .filter(and_(trans.model.ComponentReview.table.c.repository_review_id == review.id,
-                                                                  trans.model.ComponentReview.table.c.deleted == false(),
-                                                                  trans.model.ComponentReview.table.c.approved != trans.model.ComponentReview.approved_states.NA)) \
-                                                     .scalar()
+                    average_rating = (
+                        trans.sa_session.query(func.avg(trans.model.ComponentReview.table.c.rating))
+                        .filter(
+                            and_(
+                                trans.model.ComponentReview.table.c.repository_review_id == review.id,
+                                trans.model.ComponentReview.table.c.deleted == false(),
+                                trans.model.ComponentReview.table.c.approved
+                                != trans.model.ComponentReview.approved_states.NA,
+                            )
+                        )
+                        .scalar()
+                    )
                     if average_rating is not None:
                         review.rating = int(average_rating)
                     trans.sa_session.add(review)
@@ -337,51 +376,52 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
                     # Update the information in components_dict.
                     if component_name in components_dict:
                         component_review_dict = components_dict[component_name]
-                        component_review_dict['component_review'] = component_review
+                        component_review_dict["component_review"] = component_review
                         components_dict[component_name] = component_review_dict
             if revision_approved_setting_changed:
-                message += f'Approved value <b>{review.approved}</b> saved for this revision.<br/>'
+                message += f"Approved value <b>{review.approved}</b> saved for this revision.<br/>"
             if saved_component_names:
                 message += f"Reviews were saved for components: {', '.join(saved_component_names)}"
             if not revision_approved_setting_changed and not saved_component_names:
-                message += 'No changes were made to this review, so nothing was saved.'
+                message += "No changes were made to this review, so nothing was saved."
         if review and review.approved:
             selected_value = review.approved
         else:
             selected_value = trans.model.ComponentReview.approved_states.NO
-        revision_approved_select_field = grids_util.build_approved_select_field(trans,
-                                                                                name='revision_approved',
-                                                                                selected_value=selected_value,
-                                                                                for_component=False)
+        revision_approved_select_field = grids_util.build_approved_select_field(
+            trans, name="revision_approved", selected_value=selected_value, for_component=False
+        )
         rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, review.changeset_revision)
-        return trans.fill_template('/webapps/tool_shed/repository_review/edit_review.mako',
-                                   repository=repository,
-                                   review=review,
-                                   changeset_revision_label=changeset_revision_label,
-                                   revision_approved_select_field=revision_approved_select_field,
-                                   components_dict=components_dict,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/edit_review.mako",
+            repository=repository,
+            review=review,
+            changeset_revision_label=changeset_revision_label,
+            revision_approved_select_field=revision_approved_select_field,
+            components_dict=components_dict,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("manage components")
     def manage_components(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "create":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='create_component',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="create_component", **kwd)
+                )
             elif operation == "edit":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='edit_component',
-                                                                **kwd))
-        if 'message' not in kwd:
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="edit_component", **kwd)
+                )
+        if "message" not in kwd:
             message = "This is a list of repository components (features) that can be reviewed.  You can add new components or change "
             message += "the description of an existing component if appropriate.  Click on the name link to change the description."
             status = "warning"
-            kwd['message'] = message
-            kwd['status'] = status
+            kwd["message"] = message
+            kwd["status"] = status
         return self.component_grid(trans, **kwd)
 
     @web.expose
@@ -394,32 +434,32 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
         2) It contains tools the tools_functionally_correct flag is set to True.  This implies that the repository metadata revision was installed and tested
            by the Tool Shed's install and test framework.
         """
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "inspect repository revisions":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='create_review',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="create_review", **kwd)
+                )
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
-        message = 'Any of these repositories that contain tools have been installed into Galaxy and proven to be functionally correct by executing the tests defined '
-        message += 'for each tool.  Repositories that do not contain tools have not been installed into Galaxy. '
-        kwd['message'] = message
-        kwd['status'] = 'warning'
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+                )
+        message = "Any of these repositories that contain tools have been installed into Galaxy and proven to be functionally correct by executing the tests defined "
+        message += "for each tool.  Repositories that do not contain tools have not been installed into Galaxy. "
+        kwd["message"] = message
+        kwd["status"] = "warning"
         return self.repositories_ready_for_review_grid(trans, **kwd)
 
     @web.expose
     @require_login("manage repositories reviewed by me")
     def manage_repositories_reviewed_by_me(self, trans, **kwd):
         # The value of the received id is the encoded repository id.
-        if 'operation' in kwd:
-            kwd['mine'] = True
-            return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                            action='manage_repositories_with_reviews',
-                                                            **kwd))
-        self.repositories_reviewed_by_me_grid.title = 'Repositories reviewed by me'
+        if "operation" in kwd:
+            kwd["mine"] = True
+            return trans.response.send_redirect(
+                web.url_for(controller="repository_review", action="manage_repositories_with_reviews", **kwd)
+            )
+        self.repositories_reviewed_by_me_grid.title = "Repositories reviewed by me"
         return self.repositories_reviewed_by_me_grid(trans, **kwd)
 
     @web.expose
@@ -429,78 +469,85 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
         Display a list of repositories that contain tools, have not yet been reviewed, and have invalid functional tests.  Tests are defined as
         invalid if they are missing from the tool config or if defined test data is not included in the repository.
         """
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "inspect repository revisions":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='create_review',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="create_review", **kwd)
+                )
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
-        message = 'These repositories contain tools with missing functional tests or test data.  '
-        kwd['message'] = message
-        kwd['status'] = 'warning'
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+                )
+        message = "These repositories contain tools with missing functional tests or test data.  "
+        kwd["message"] = message
+        kwd["status"] = "warning"
         return self.repositories_with_no_tool_tests_grid(trans, **kwd)
 
     @web.expose
     @require_login("manage repositories with reviews")
     def manage_repositories_with_reviews(self, trans, **kwd):
         # The value of the received id is the encoded repository id.
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "inspect repository revisions":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='manage_repository_reviews',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="manage_repository_reviews", **kwd)
+                )
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+                )
         return self.repositories_with_reviews_grid(trans, **kwd)
 
     @web.expose
     @require_login("manage repositories without reviews")
     def manage_repositories_without_reviews(self, trans, **kwd):
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "inspect repository revisions":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='create_review',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="create_review", **kwd)
+                )
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+                )
         return self.repositories_without_reviews_grid(trans, **kwd)
 
     @web.expose
     @require_login("manage repository reviews")
     def manage_repository_reviews(self, trans, mine=False, **kwd):
         # The value of the received id is the encoded repository id.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_id = kwd.get('id', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_id = kwd.get("id", None)
         if repository_id:
             repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
             repo = repository.hg_repo
-            metadata_revision_hashes = [metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions]
+            metadata_revision_hashes = [
+                metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions
+            ]
             reviewed_revision_hashes = [review.changeset_revision for review in repository.reviews]
             reviews_dict = {}
             for changeset in hg_util.get_reversed_changelog_changesets(repo):
                 changeset_revision = str(repo[changeset])
                 if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes:
-                    rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision)
+                    rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(
+                        repo, changeset_revision
+                    )
                     if changeset_revision in reviewed_revision_hashes:
                         # Find the review for this changeset_revision
-                        repository_reviews = \
-                            review_util.get_reviews_by_repository_id_changeset_revision(trans.app,
-                                                                                        repository_id,
-                                                                                        changeset_revision)
+                        repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision(
+                            trans.app, repository_id, changeset_revision
+                        )
                         # Determine if the current user can add a review to this revision.
-                        can_add_review = trans.user not in [repository_review.user for repository_review in repository_reviews]
-                        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
+                        can_add_review = trans.user not in [
+                            repository_review.user for repository_review in repository_reviews
+                        ]
+                        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
+                            trans.app, repository_id, changeset_revision
+                        )
                         if repository_metadata:
                             repository_metadata_reviews = util.listify(repository_metadata.reviews)
                         else:
@@ -510,64 +557,72 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
                         repository_metadata_reviews = []
                         can_add_review = True
                     installable = changeset_revision in metadata_revision_hashes
-                    revision_dict = dict(changeset_revision_label=changeset_revision_label,
-                                         repository_reviews=repository_reviews,
-                                         repository_metadata_reviews=repository_metadata_reviews,
-                                         installable=installable,
-                                         can_add_review=can_add_review)
+                    revision_dict = dict(
+                        changeset_revision_label=changeset_revision_label,
+                        repository_reviews=repository_reviews,
+                        repository_metadata_reviews=repository_metadata_reviews,
+                        installable=installable,
+                        can_add_review=can_add_review,
+                    )
                     reviews_dict[changeset_revision] = revision_dict
-        return trans.fill_template('/webapps/tool_shed/repository_review/reviews_of_repository.mako',
-                                   repository=repository,
-                                   reviews_dict=reviews_dict,
-                                   mine=mine,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/reviews_of_repository.mako",
+            repository=repository,
+            reviews_dict=reviews_dict,
+            mine=mine,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("manage repository reviews of revision")
     def manage_repository_reviews_of_revision(self, trans, **kwd):
         # The value of the received id is the encoded repository id.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository_id = kwd.get('id', None)
-        changeset_revision = kwd.get('changeset_revision', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository_id = kwd.get("id", None)
+        changeset_revision = kwd.get("changeset_revision", None)
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
         repo = repository.hg_repo
-        installable = changeset_revision in [metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions]
+        installable = changeset_revision in [
+            metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions
+        ]
         rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision)
-        reviews = review_util.get_reviews_by_repository_id_changeset_revision(trans.app,
-                                                                              repository_id,
-                                                                              changeset_revision)
-        return trans.fill_template('/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako',
-                                   repository=repository,
-                                   changeset_revision=changeset_revision,
-                                   changeset_revision_label=changeset_revision_label,
-                                   reviews=reviews,
-                                   installable=installable,
-                                   message=message,
-                                   status=status)
+        reviews = review_util.get_reviews_by_repository_id_changeset_revision(
+            trans.app, repository_id, changeset_revision
+        )
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako",
+            repository=repository,
+            changeset_revision=changeset_revision,
+            changeset_revision_label=changeset_revision_label,
+            reviews=reviews,
+            installable=installable,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("repository reviews by user")
     def repository_reviews_by_user(self, trans, **kwd):
 
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             # The value of the received id is the encoded review id.
-            review = review_util.get_review(trans.app, kwd['id'])
+            review = review_util.get_review(trans.app, kwd["id"])
             repository = review.repository
-            kwd['id'] = trans.security.encode_id(repository.id)
+            kwd["id"] = trans.security.encode_id(repository.id)
             if operation == "inspect repository revisions":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='manage_repository_reviews',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="manage_repository_reviews", **kwd)
+                )
             if operation == "view_or_manage_repository":
-                kwd['changeset_revision'] = review.changeset_revision
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                kwd["changeset_revision"] = review.changeset_revision
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+                )
         # The user may not be the current user.  The value of the received id is the encoded user id.
-        user = suc.get_user(trans.app, kwd['id'])
+        user = suc.get_user(trans.app, kwd["id"])
         self.repository_reviews_by_user_grid.title = f"All repository revision reviews for user '{user.username}'"
         return self.repository_reviews_by_user_grid(trans, **kwd)
 
@@ -575,48 +630,44 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
     @require_login("reviewed repositories i own")
     def reviewed_repositories_i_own(self, trans, **kwd):
         # The value of the received id is the encoded repository id.
-        if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+        if "operation" in kwd:
+            operation = kwd["operation"].lower()
             if operation == "inspect repository revisions":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='manage_repository_reviews',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="manage_repository_reviews", **kwd)
+                )
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect(web.url_for(controller='repository_review',
-                                                                action='view_or_manage_repository',
-                                                                **kwd))
+                return trans.response.send_redirect(
+                    web.url_for(controller="repository_review", action="view_or_manage_repository", **kwd)
+                )
         return self.reviewed_repositories_i_own_grid(trans, **kwd)
 
     @web.expose
     @require_login("select previous review")
     def select_previous_review(self, trans, **kwd):
         # The value of the received id is the encoded repository id.
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        repository = repository_util.get_repository_in_tool_shed(trans.app, kwd['id'])
-        changeset_revision = kwd.get('changeset_revision', None)
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        repository = repository_util.get_repository_in_tool_shed(trans.app, kwd["id"])
+        changeset_revision = kwd.get("changeset_revision", None)
         repo = repository.hg_repo
-        previous_reviews_dict = review_util.get_previous_repository_reviews(trans.app,
-                                                                            repository,
-                                                                            changeset_revision)
+        previous_reviews_dict = review_util.get_previous_repository_reviews(trans.app, repository, changeset_revision)
         rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(repo, changeset_revision)
-        return trans.fill_template('/webapps/tool_shed/repository_review/select_previous_review.mako',
-                                   repository=repository,
-                                   changeset_revision=changeset_revision,
-                                   changeset_revision_label=changeset_revision_label,
-                                   previous_reviews_dict=previous_reviews_dict,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository_review/select_previous_review.mako",
+            repository=repository,
+            changeset_revision=changeset_revision,
+            changeset_revision_label=changeset_revision_label,
+            previous_reviews_dict=previous_reviews_dict,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login("view or manage repository")
     def view_or_manage_repository(self, trans, **kwd):
-        repository = repository_util.get_repository_in_tool_shed(trans.app, kwd['id'])
+        repository = repository_util.get_repository_in_tool_shed(trans.app, kwd["id"])
         if trans.user_is_admin or repository.user == trans.user:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='manage_repository',
-                                                            **kwd))
+            return trans.response.send_redirect(web.url_for(controller="repository", action="manage_repository", **kwd))
         else:
-            return trans.response.send_redirect(web.url_for(controller='repository',
-                                                            action='view_repository',
-                                                            **kwd))
+            return trans.response.send_redirect(web.url_for(controller="repository", action="view_repository", **kwd))
diff --git a/lib/tool_shed/webapp/controllers/upload.py b/lib/tool_shed/webapp/controllers/upload.py
index cefa6ae993a..5b635be5e33 100644
--- a/lib/tool_shed/webapp/controllers/upload.py
+++ b/lib/tool_shed/webapp/controllers/upload.py
@@ -8,7 +8,7 @@ import requests
 
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.util import checkers
 from galaxy.webapps.base.controller import BaseUIController
@@ -23,9 +23,9 @@ from tool_shed.util import (
     hg_util,
     repository_content_util,
     repository_util,
-    shed_util_common as suc,
-    xml_util
 )
+from tool_shed.util import shed_util_common as suc
+from tool_shed.util import xml_util
 from tool_shed.util.web_util import escape
 from tool_shed.webapp.framework.decorators import require_login
 
@@ -33,41 +33,40 @@ log = logging.getLogger(__name__)
 
 
 class UploadController(BaseUIController):
-
     @web.expose
-    @require_login('upload', use_panels=True)
+    @require_login("upload", use_panels=True)
     def upload(self, trans, **kwd):
-        message = escape(kwd.get('message', ''))
-        status = kwd.get('status', 'done')
-        commit_message = escape(kwd.get('commit_message', 'Uploaded'))
-        repository_id = kwd.get('repository_id', '')
+        message = escape(kwd.get("message", ""))
+        status = kwd.get("status", "done")
+        commit_message = escape(kwd.get("commit_message", "Uploaded"))
+        repository_id = kwd.get("repository_id", "")
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
         repo_dir = repository.repo_path(trans.app)
-        uncompress_file = util.string_as_bool(kwd.get('uncompress_file', 'true'))
-        remove_repo_files_not_in_tar = util.string_as_bool(kwd.get('remove_repo_files_not_in_tar', 'true'))
+        uncompress_file = util.string_as_bool(kwd.get("uncompress_file", "true"))
+        remove_repo_files_not_in_tar = util.string_as_bool(kwd.get("remove_repo_files_not_in_tar", "true"))
         uploaded_file = None
         upload_point = commit_util.get_upload_point(repository, **kwd)
         tip = repository.tip()
-        file_data = kwd.get('file_data', '')
-        url = kwd.get('url', '')
+        file_data = kwd.get("file_data", "")
+        url = kwd.get("url", "")
         # Part of the upload process is sending email notification to those that have registered to
         # receive them.  One scenario occurs when the first change set is produced for the repository.
         # See the suc.handle_email_alerts() method for the definition of the scenarios.
         new_repo_alert = repository.is_new()
         uploaded_directory = None
-        if kwd.get('upload_button', False):
-            if file_data == '' and url == '':
-                message = 'No files were entered on the upload form.'
-                status = 'error'
+        if kwd.get("upload_button", False):
+            if file_data == "" and url == "":
+                message = "No files were entered on the upload form."
+                status = "error"
                 uploaded_file = None
-            elif url and url.startswith('hg'):
+            elif url and url.startswith("hg"):
                 # Use mercurial clone to fetch repository, contents will then be copied over.
                 uploaded_directory = tempfile.mkdtemp()
                 repo_url = f"http{url[len('hg'):]}"
                 cloned_ok, error_message = hg_util.clone_repository(repo_url, uploaded_directory)
                 if not cloned_ok:
-                    message = f'Error uploading via mercurial clone: {error_message}'
-                    status = 'error'
+                    message = f"Error uploading via mercurial clone: {error_message}"
+                    status = "error"
                     basic_util.remove_dir(uploaded_directory)
                     uploaded_directory = None
             elif url:
@@ -76,19 +75,19 @@ class UploadController(BaseUIController):
                     stream = requests.get(url, stream=True, timeout=util.DEFAULT_SOCKET_TIMEOUT)
                 except Exception as e:
                     valid_url = False
-                    message = f'Error uploading file via http: {util.unicodify(e)}'
-                    status = 'error'
+                    message = f"Error uploading file via http: {util.unicodify(e)}"
+                    status = "error"
                     uploaded_file = None
                 if valid_url:
-                    with tempfile.NamedTemporaryFile(mode='wb', delete=False) as uploaded_file:
+                    with tempfile.NamedTemporaryFile(mode="wb", delete=False) as uploaded_file:
                         uploaded_file_name = uploaded_file.name
                         for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
                             if chunk:
                                 uploaded_file.write(chunk)
                         uploaded_file.flush()
-                    uploaded_file_filename = url.split('/')[-1]
+                    uploaded_file_filename = url.split("/")[-1]
                     isempty = os.path.getsize(os.path.abspath(uploaded_file_name)) == 0
-            elif file_data not in ('', None):
+            elif file_data not in ("", None):
                 uploaded_file = file_data.file
                 uploaded_file_name = uploaded_file.name
                 uploaded_file_filename = os.path.split(file_data.filename)[-1]
@@ -113,7 +112,7 @@ class UploadController(BaseUIController):
                         try:
                             if (isgzip or isbz2) and uncompress_file:
                                 # Open for reading with transparent compression.
-                                tar = tarfile.open(uploaded_file_name, 'r:*')
+                                tar = tarfile.open(uploaded_file_name, "r:*")
                             else:
                                 tar = tarfile.open(uploaded_file_name)
                             istar = True
@@ -124,47 +123,63 @@ class UploadController(BaseUIController):
                     # Uploaded directory
                     istar = False
                 if istar:
-                    ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
-                        repository_content_util.upload_tar(
-                            trans,
-                            rdah,
-                            tdah,
-                            repository,
-                            tar,
-                            uploaded_file,
-                            upload_point,
-                            remove_repo_files_not_in_tar,
-                            commit_message,
-                            new_repo_alert
-                        )
+                    (
+                        ok,
+                        message,
+                        files_to_remove,
+                        content_alert_str,
+                        undesirable_dirs_removed,
+                        undesirable_files_removed,
+                    ) = repository_content_util.upload_tar(
+                        trans,
+                        rdah,
+                        tdah,
+                        repository,
+                        tar,
+                        uploaded_file,
+                        upload_point,
+                        remove_repo_files_not_in_tar,
+                        commit_message,
+                        new_repo_alert,
+                    )
                 elif uploaded_directory:
-                    ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
-                        self.upload_directory(trans,
-                                              rdah,
-                                              tdah,
-                                              repository,
-                                              uploaded_directory,
-                                              upload_point,
-                                              remove_repo_files_not_in_tar,
-                                              commit_message,
-                                              new_repo_alert)
+                    (
+                        ok,
+                        message,
+                        files_to_remove,
+                        content_alert_str,
+                        undesirable_dirs_removed,
+                        undesirable_files_removed,
+                    ) = self.upload_directory(
+                        trans,
+                        rdah,
+                        tdah,
+                        repository,
+                        uploaded_directory,
+                        upload_point,
+                        remove_repo_files_not_in_tar,
+                        commit_message,
+                        new_repo_alert,
+                    )
                 else:
                     if (isgzip or isbz2) and uncompress_file:
-                        uploaded_file_filename = commit_util.uncompress(repository,
-                                                                        uploaded_file_name,
-                                                                        uploaded_file_filename,
-                                                                        isgzip=isgzip,
-                                                                        isbz2=isbz2)
-                    if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION and \
-                            uploaded_file_filename != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
+                        uploaded_file_filename = commit_util.uncompress(
+                            repository, uploaded_file_name, uploaded_file_filename, isgzip=isgzip, isbz2=isbz2
+                        )
+                    if (
+                        repository.type == rt_util.REPOSITORY_SUITE_DEFINITION
+                        and uploaded_file_filename != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
+                    ):
                         ok = False
-                        message = 'Repositories of type <b>Repository suite definition</b> can only contain a single file named '
-                        message += '<b>repository_dependencies.xml</b>.'
-                    elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and \
-                            uploaded_file_filename != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
+                        message = "Repositories of type <b>Repository suite definition</b> can only contain a single file named "
+                        message += "<b>repository_dependencies.xml</b>."
+                    elif (
+                        repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION
+                        and uploaded_file_filename != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME
+                    ):
                         ok = False
-                        message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named '
-                        message += '<b>tool_dependencies.xml</b>.'
+                        message = "Repositories of type <b>Tool dependency definition</b> can only contain a single file named "
+                        message += "<b>tool_dependencies.xml</b>."
                     if ok:
                         if upload_point is not None:
                             full_path = os.path.abspath(os.path.join(repo_dir, upload_point, uploaded_file_filename))
@@ -178,7 +193,7 @@ class UploadController(BaseUIController):
                             if error_message:
                                 ok = False
                                 message = error_message
-                                status = 'error'
+                                status = "error"
                             elif altered:
                                 tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                                 shutil.move(tmp_filename, full_path)
@@ -191,7 +206,7 @@ class UploadController(BaseUIController):
                             if error_message:
                                 ok = False
                                 message = error_message
-                                status = 'error'
+                                status = "error"
                             if ok:
                                 if altered:
                                     tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
@@ -207,67 +222,80 @@ class UploadController(BaseUIController):
                             if check_contents and os.path.isfile(full_path):
                                 content_alert_str = commit_util.check_file_content_for_html_and_images(full_path)
                             else:
-                                content_alert_str = ''
+                                content_alert_str = ""
                             hg_util.add_changeset(repo_dir, full_path)
-                            hg_util.commit_changeset(repo_dir,
-                                                     full_path_to_changeset=full_path,
-                                                     username=trans.user.username,
-                                                     message=commit_message)
-                            if full_path.endswith('tool_data_table_conf.xml.sample'):
+                            hg_util.commit_changeset(
+                                repo_dir,
+                                full_path_to_changeset=full_path,
+                                username=trans.user.username,
+                                message=commit_message,
+                            )
+                            if full_path.endswith("tool_data_table_conf.xml.sample"):
                                 # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded
                                 # by parsing the file and adding new entries to the in-memory trans.app.tool_data_tables
                                 # dictionary.
-                                error, error_message = stdtm.handle_sample_tool_data_table_conf_file(full_path, persist=False)
+                                error, error_message = stdtm.handle_sample_tool_data_table_conf_file(
+                                    full_path, persist=False
+                                )
                                 if error:
-                                    message = f'{message}<br/>{error_message}'
+                                    message = f"{message}<br/>{error_message}"
                             # See if the content of the change set was valid.
                             admin_only = len(repository.downloadable_revisions) != 1
-                            suc.handle_email_alerts(trans.app,
-                                                    trans.request.host,
-                                                    repository,
-                                                    content_alert_str=content_alert_str,
-                                                    new_repo_alert=new_repo_alert,
-                                                    admin_only=admin_only)
+                            suc.handle_email_alerts(
+                                trans.app,
+                                trans.request.host,
+                                repository,
+                                content_alert_str=content_alert_str,
+                                new_repo_alert=new_repo_alert,
+                                admin_only=admin_only,
+                            )
                 if ok:
                     # Update the repository files for browsing.
                     hg_util.update_repository(repo_dir)
                     # Get the new repository tip.
                     if tip == repository.tip():
-                        message = 'No changes to repository.  '
-                        status = 'warning'
+                        message = "No changes to repository.  "
+                        status = "warning"
                     else:
                         if (isgzip or isbz2) and uncompress_file:
-                            uncompress_str = ' uncompressed and '
+                            uncompress_str = " uncompressed and "
                         else:
-                            uncompress_str = ' '
+                            uncompress_str = " "
                         if uploaded_directory:
                             source_type = "repository"
                             source = url
                         else:
                             source_type = "file"
                             source = uploaded_file_filename
-                        message = "The %s <b>%s</b> has been successfully%suploaded to the repository.  " % \
-                            (source_type, escape(source), uncompress_str)
+                        message = "The %s <b>%s</b> has been successfully%suploaded to the repository.  " % (
+                            source_type,
+                            escape(source),
+                            uncompress_str,
+                        )
                         if istar and (undesirable_dirs_removed or undesirable_files_removed):
                             items_removed = undesirable_dirs_removed + undesirable_files_removed
-                            message += "  %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) " % items_removed
+                            message += (
+                                "  %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) "
+                                % items_removed
+                            )
                             message += "were removed from the archive.  "
                         if istar and remove_repo_files_not_in_tar and files_to_remove:
                             if upload_point is not None:
-                                message += "  %d files were removed from the repository relative to the selected upload point '%s'.  " % \
-                                    (len(files_to_remove), upload_point)
+                                message += (
+                                    "  %d files were removed from the repository relative to the selected upload point '%s'.  "
+                                    % (len(files_to_remove), upload_point)
+                                )
                             else:
                                 message += "  %d files were removed from the repository root.  " % len(files_to_remove)
-                        rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
-                                                                                    user=trans.user,
-                                                                                    repository=repository)
-                        status, error_message = \
-                            rmm.set_repository_metadata_due_to_new_tip(trans.request.host,
-                                                                       content_alert_str=content_alert_str,
-                                                                       **kwd)
+                        rmm = repository_metadata_manager.RepositoryMetadataManager(
+                            app=trans.app, user=trans.user, repository=repository
+                        )
+                        status, error_message = rmm.set_repository_metadata_due_to_new_tip(
+                            trans.request.host, content_alert_str=content_alert_str, **kwd
+                        )
                         if error_message:
                             message = error_message
-                        kwd['message'] = message
+                        kwd["message"] = message
                     if repository.metadata_revisions:
                         # A repository's metadata revisions are order descending by update_time, so the zeroth revision
                         # will be the tip just after an upload.
@@ -275,13 +303,16 @@ class UploadController(BaseUIController):
                     else:
                         metadata_dict = {}
                     dd = dependency_display.DependencyDisplayer(trans.app)
-                    if str(repository.type) not in [rt_util.REPOSITORY_SUITE_DEFINITION,
-                                                    rt_util.TOOL_DEPENDENCY_DEFINITION]:
-                        change_repository_type_message = rt_util.generate_message_for_repository_type_change(trans.app,
-                                                                                                             repository)
+                    if str(repository.type) not in [
+                        rt_util.REPOSITORY_SUITE_DEFINITION,
+                        rt_util.TOOL_DEPENDENCY_DEFINITION,
+                    ]:
+                        change_repository_type_message = rt_util.generate_message_for_repository_type_change(
+                            trans.app, repository
+                        )
                         if change_repository_type_message:
                             message += change_repository_type_message
-                            status = 'warning'
+                            status = "warning"
                         else:
                             # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies
                             # weren't loaded due to a requirement tag mismatch or some other problem.  Tool dependency
@@ -292,47 +323,63 @@ class UploadController(BaseUIController):
                             orphan_message = dd.generate_message_for_orphan_tool_dependencies(repository, metadata_dict)
                             if orphan_message:
                                 message += orphan_message
-                                status = 'warning'
+                                status = "warning"
                     # Handle messaging for invalid tool dependencies.
                     invalid_tool_dependencies_message = dd.generate_message_for_invalid_tool_dependencies(metadata_dict)
                     if invalid_tool_dependencies_message:
                         message += invalid_tool_dependencies_message
-                        status = 'error'
+                        status = "error"
                     # Handle messaging for invalid repository dependencies.
-                    invalid_repository_dependencies_message = \
-                        dd.generate_message_for_invalid_repository_dependencies(metadata_dict,
-                                                                                error_from_tuple=True)
+                    invalid_repository_dependencies_message = dd.generate_message_for_invalid_repository_dependencies(
+                        metadata_dict, error_from_tuple=True
+                    )
                     if invalid_repository_dependencies_message:
                         message += invalid_repository_dependencies_message
-                        status = 'error'
+                        status = "error"
                     # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
                     stdtm.reset_tool_data_tables()
                     if uploaded_directory:
                         basic_util.remove_dir(uploaded_directory)
-                    trans.response.send_redirect(web.url_for(controller='repository',
-                                                             action='browse_repository',
-                                                             id=repository_id,
-                                                             commit_message='Deleted selected files',
-                                                             message=message,
-                                                             status=status))
+                    trans.response.send_redirect(
+                        web.url_for(
+                            controller="repository",
+                            action="browse_repository",
+                            id=repository_id,
+                            commit_message="Deleted selected files",
+                            message=message,
+                            status=status,
+                        )
+                    )
                 else:
                     if uploaded_directory:
                         basic_util.remove_dir(uploaded_directory)
-                    status = 'error'
+                    status = "error"
                 # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
                 stdtm.reset_tool_data_tables()
-        return trans.fill_template('/webapps/tool_shed/repository/upload.mako',
-                                   repository=repository,
-                                   changeset_revision=tip,
-                                   url=url,
-                                   commit_message=commit_message,
-                                   uncompress_file=uncompress_file,
-                                   remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/repository/upload.mako",
+            repository=repository,
+            changeset_revision=tip,
+            url=url,
+            commit_message=commit_message,
+            uncompress_file=uncompress_file,
+            remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
+            message=message,
+            status=status,
+        )
 
-    def upload_directory(self, trans, rdah, tdah, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar,
-                         commit_message, new_repo_alert):
+    def upload_directory(
+        self,
+        trans,
+        rdah,
+        tdah,
+        repository,
+        uploaded_directory,
+        upload_point,
+        remove_repo_files_not_in_tar,
+        commit_message,
+        new_repo_alert,
+    ):
         repo_dir = repository.repo_path(trans.app)
         undesirable_dirs_removed = 0
         undesirable_files_removed = 0
@@ -351,7 +398,7 @@ class UploadController(BaseUIController):
                 else:
                     ok = os.path.basename(uploaded_file) not in commit_util.UNDESIRABLE_FILES
                 if ok:
-                    for file_path_item in relative_path.split('/'):
+                    for file_path_item in relative_path.split("/"):
                         if file_path_item in commit_util.UNDESIRABLE_DIRS:
                             undesirable_dirs_removed += 1
                             ok = False
@@ -365,7 +412,7 @@ class UploadController(BaseUIController):
                         # attributes are missing and if so, set them appropriately.
                         altered, root_elem, error_message = rdah.handle_tag_attributes(uploaded_file_name)
                         if error_message:
-                            return False, error_message, [], '', [], []
+                            return False, error_message, [], "", [], []
                         elif altered:
                             tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                             shutil.move(tmp_filename, uploaded_file_name)
@@ -374,7 +421,7 @@ class UploadController(BaseUIController):
                         # attributes are missing and if so, set them appropriately.
                         altered, root_elem, error_message = tdah.handle_tag_attributes(uploaded_file_name)
                         if error_message:
-                            return False, error_message, [], '', [], []
+                            return False, error_message, [], "", [], []
                         if altered:
                             tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                             shutil.move(tmp_filename, uploaded_file_name)
@@ -389,14 +436,16 @@ class UploadController(BaseUIController):
                             os.remove(repo_path)
                     shutil.move(os.path.join(uploaded_directory, relative_path), repo_path)
                     filenames_in_archive.append(relative_path)
-        return commit_util.handle_directory_changes(trans.app,
-                                                    trans.request.host,
-                                                    trans.user.username,
-                                                    repository,
-                                                    full_path,
-                                                    filenames_in_archive,
-                                                    remove_repo_files_not_in_tar,
-                                                    new_repo_alert,
-                                                    commit_message,
-                                                    undesirable_dirs_removed,
-                                                    undesirable_files_removed)
+        return commit_util.handle_directory_changes(
+            trans.app,
+            trans.request.host,
+            trans.user.username,
+            repository,
+            full_path,
+            filenames_in_archive,
+            remove_repo_files_not_in_tar,
+            new_repo_alert,
+            commit_message,
+            undesirable_dirs_removed,
+            undesirable_files_removed,
+        )
diff --git a/lib/tool_shed/webapp/controllers/user.py b/lib/tool_shed/webapp/controllers/user.py
index a6bec978cad..45649b05fb6 100644
--- a/lib/tool_shed/webapp/controllers/user.py
+++ b/lib/tool_shed/webapp/controllers/user.py
@@ -6,12 +6,12 @@ from sqlalchemy import func
 
 from galaxy import (
     util,
-    web
+    web,
 )
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_password,
-    validate_publicname
+    validate_publicname,
 )
 from galaxy.web import url_for
 from galaxy.web.form_builder import CheckboxField
@@ -41,38 +41,39 @@ can also copy and paste it into your browser.
 
 
 class User(BaseUser):
-
     @web.expose
-    def index(self, trans, cntrller='user', **kwd):
-        return trans.fill_template('/webapps/tool_shed/user/index.mako', cntrller=cntrller)
+    def index(self, trans, cntrller="user", **kwd):
+        return trans.fill_template("/webapps/tool_shed/user/index.mako", cntrller=cntrller)
 
     @web.expose
     def login(self, trans, refresh_frames=None, **kwd):
-        '''Handle Galaxy Log in'''
+        """Handle Galaxy Log in"""
         refresh_frames = refresh_frames or []
-        referer = trans.request.referer or ''
-        redirect = self.__get_redirect_url(kwd.get('redirect', referer).strip())
-        redirect_url = ''  # always start with redirect_url being empty
-        use_panels = util.string_as_bool(kwd.get('use_panels', False))
-        message = kwd.get('message', '')
-        status = kwd.get('status', 'done')
-        header = ''
+        referer = trans.request.referer or ""
+        redirect = self.__get_redirect_url(kwd.get("redirect", referer).strip())
+        redirect_url = ""  # always start with redirect_url being empty
+        use_panels = util.string_as_bool(kwd.get("use_panels", False))
+        message = kwd.get("message", "")
+        status = kwd.get("status", "done")
+        header = ""
         user = trans.user
         success = False
-        login = kwd.get('login', '')
+        login = kwd.get("login", "")
         if user:
             # Already logged in.
             redirect_url = redirect
-            message = 'You are already logged in.'
-            status = 'info'
-        elif kwd.get('login_button', False):
+            message = "You are already logged in."
+            status = "info"
+        elif kwd.get("login_button", False):
             response = self.__validate_login(trans, **kwd)
             if trans.response.status == 400:
                 trans.response.status = 200
                 message = response.get("err_msg")
                 status = "error"
             elif response.get("expired_user"):
-                change_password_url = url_for(controller='user', action='change_password', id=response.get("expired_user"))
+                change_password_url = url_for(
+                    controller="user", action="change_password", id=response.get("expired_user")
+                )
                 message = f"{response.get('message')}<br>Click <a href='{change_password_url}'>here</a> to change your password."
                 status = "warning"
             else:
@@ -81,64 +82,72 @@ class User(BaseUser):
                 redirect_url = redirect
         if not success and not user and trans.app.config.require_login:
             if trans.app.config.allow_user_creation:
-                create_account_str = "  If you don't already have an account, <a href='%s'>you may create one</a>." % \
-                    web.url_for(controller='user', action='create', cntrller='user')
+                create_account_str = (
+                    "  If you don't already have an account, <a href='%s'>you may create one</a>."
+                    % web.url_for(controller="user", action="create", cntrller="user")
+                )
                 header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", create_account_str)
             else:
                 header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", "")
-        return trans.fill_template('/webapps/tool_shed/user/login.mako',
-                                   login=login,
-                                   header=header,
-                                   use_panels=use_panels,
-                                   redirect_url=redirect_url,
-                                   redirect=redirect,
-                                   refresh_frames=refresh_frames,
-                                   message=message,
-                                   status=status,
-                                   form_input_auto_focus=True,
-                                   active_view="user")
+        return trans.fill_template(
+            "/webapps/tool_shed/user/login.mako",
+            login=login,
+            header=header,
+            use_panels=use_panels,
+            redirect_url=redirect_url,
+            redirect=redirect,
+            refresh_frames=refresh_frames,
+            message=message,
+            status=status,
+            form_input_auto_focus=True,
+            active_view="user",
+        )
 
     @web.expose
-    def create(self, trans, cntrller='user', redirect_url='', refresh_frames=None, **kwd):
+    def create(self, trans, cntrller="user", redirect_url="", refresh_frames=None, **kwd):
         refresh_frames = refresh_frames or []
         params = util.Params(kwd)
         # If the honeypot field is not empty we are dealing with a bot.
-        honeypot_field = params.get('bear_field', '')
-        if honeypot_field != '':
-            return trans.show_error_message("You've been flagged as a possible bot. If you are not, please try registering again and fill the form out carefully. <a target=\"_top\" href=\"%s\">Go to the home page</a>.") % url_for('/')
+        honeypot_field = params.get("bear_field", "")
+        if honeypot_field != "":
+            return trans.show_error_message(
+                'You\'ve been flagged as a possible bot. If you are not, please try registering again and fill the form out carefully. <a target="_top" href="%s">Go to the home page</a>.'
+            ) % url_for("/")
 
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        use_panels = util.string_as_bool(kwd.get('use_panels', True))
-        email = util.restore_text(params.get('email', ''))
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        use_panels = util.string_as_bool(kwd.get("use_panels", True))
+        email = util.restore_text(params.get("email", ""))
         # Do not sanitize passwords, so take from kwd
         # instead of params ( which were sanitized )
-        password = kwd.get('password', '')
-        confirm = kwd.get('confirm', '')
-        username = util.restore_text(params.get('username', ''))
-        subscribe = params.get('subscribe', '')
+        password = kwd.get("password", "")
+        confirm = kwd.get("confirm", "")
+        username = util.restore_text(params.get("username", ""))
+        subscribe = params.get("subscribe", "")
         subscribe_checked = CheckboxField.is_checked(subscribe)
-        referer = trans.request.referer or ''
-        redirect = kwd.get('redirect', referer).strip()
+        referer = trans.request.referer or ""
+        redirect = kwd.get("redirect", referer).strip()
         is_admin = trans.user_is_admin
         success = False
         show_user_prepopulate_form = False
         if not trans.app.config.allow_user_creation and not trans.user_is_admin:
-            message = 'User registration is disabled.  Please contact your local Galaxy administrator for an account.'
+            message = "User registration is disabled.  Please contact your local Galaxy administrator for an account."
             if trans.app.config.error_email_to is not None:
-                message += f' Contact: {trans.app.config.error_email_to}'
-            status = 'error'
+                message += f" Contact: {trans.app.config.error_email_to}"
+            status = "error"
         else:
             # check user is allowed to register
             message, status = trans.app.auth_manager.check_registration_allowed(email, username, password)
             if not message:
                 # Create the user, save all the user info and login to Galaxy
-                if params.get('create_user_button', False):
+                if params.get("create_user_button", False):
                     # Check email and password validity
                     message = self.__validate(trans, email, password, confirm, username)
                     if not message:
                         # All the values are valid
-                        message, status, user, success = self.__register(trans, subscribe_checked=subscribe_checked, **kwd)
+                        message, status, user, success = self.__register(
+                            trans, subscribe_checked=subscribe_checked, **kwd
+                        )
                         if success and not is_admin:
                             # The handle_user_login() method has a call to the history_set_default_permissions() method
                             # (needed when logging in with a history), user needs to have default permissions set before logging in
@@ -146,26 +155,28 @@ class User(BaseUser):
                             trans.log_event("User created a new account")
                             trans.log_event("User logged in")
                     else:
-                        status = 'error'
+                        status = "error"
         registration_warning_message = trans.app.config.registration_warning_message
         if success:
             if is_admin:
-                redirect_url = web.url_for('/admin/users?status=success&message=Created new user account.')
+                redirect_url = web.url_for("/admin/users?status=success&message=Created new user account.")
             else:
-                redirect_url = web.url_for('/')
-        return trans.fill_template('/webapps/tool_shed/user/register.mako',
-                                   cntrller=cntrller,
-                                   email=email,
-                                   username=username,
-                                   subscribe_checked=subscribe_checked,
-                                   show_user_prepopulate_form=show_user_prepopulate_form,
-                                   use_panels=use_panels,
-                                   redirect=redirect,
-                                   redirect_url=redirect_url,
-                                   refresh_frames=refresh_frames,
-                                   registration_warning_message=registration_warning_message,
-                                   message=message,
-                                   status=status)
+                redirect_url = web.url_for("/")
+        return trans.fill_template(
+            "/webapps/tool_shed/user/register.mako",
+            cntrller=cntrller,
+            email=email,
+            username=username,
+            subscribe_checked=subscribe_checked,
+            show_user_prepopulate_form=show_user_prepopulate_form,
+            use_panels=use_panels,
+            redirect=redirect,
+            redirect_url=redirect_url,
+            refresh_frames=refresh_frames,
+            registration_warning_message=registration_warning_message,
+            message=message,
+            status=status,
+        )
 
     def __register(self, trans, email=None, username=None, password=None, subscribe_checked=False, **kwd):
         """Registers a new user."""
@@ -181,14 +192,14 @@ class User(BaseUser):
                 status = "error"
                 message = f"Now logged in as {user.email}. However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance. <br>Please contact your local Galaxy administrator."
             else:
-                body = 'Join Mailing list.\n'
+                body = "Join Mailing list.\n"
                 to = trans.app.config.mailing_join_addr
                 frm = email
-                subject = 'Join Mailing List'
+                subject = "Join Mailing List"
                 try:
                     util.send_mail(frm, to, subject, body, trans.app.config)
                 except Exception:
-                    log.exception('Subscribing to the mailing list has failed.')
+                    log.exception("Subscribing to the mailing list has failed.")
                     status = "warning"
                     message = f"Now logged in as {user.email}. However, subscribing to the mailing list has failed."
         if status != "error":
@@ -204,9 +215,9 @@ class User(BaseUser):
                     message = f"Now logged in as {escape(user.email)}.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.<br><a target=\"_top\" href=\"{url_for('/')}\">Return to the home page.</a>"
                 else:
                     status = "error"
-                    message = 'Unable to send activation email, please contact your local Galaxy administrator.'
+                    message = "Unable to send activation email, please contact your local Galaxy administrator."
                     if trans.app.config.error_email_to is not None:
-                        message += f' Contact: {trans.app.config.error_email_to}'
+                        message += f" Contact: {trans.app.config.error_email_to}"
         else:
             # User activation is OFF, proceed without sending the activation email.
             message = f"Now logged in as {escape(user.email)}.<br><a target=\"_top\" href=\"{url_for('/')}\">Return to the home page.</a>"
@@ -216,118 +227,131 @@ class User(BaseUser):
     def reset_password(self, trans, email=None, **kwd):
         """Reset the user's password. Send an email with token that allows a password change."""
         if trans.app.config.smtp_server is None:
-            return trans.show_error_message("Mail is not configured for this Galaxy instance "
-                                            "and password reset information cannot be sent. "
-                                            "Please contact your local Galaxy administrator.")
+            return trans.show_error_message(
+                "Mail is not configured for this Galaxy instance "
+                "and password reset information cannot be sent. "
+                "Please contact your local Galaxy administrator."
+            )
         message = None
-        status = 'done'
-        if kwd.get('reset_password_button', False):
+        status = "done"
+        if kwd.get("reset_password_button", False):
             message = validate_email(trans, email, check_dup=False)
             if not message:
                 # Default to a non-userinfo-leaking response message
-                message = ("Your reset request for %s has been received.  "
-                           "Please check your email account for more instructions.  "
-                           "If you do not receive an email shortly, please contact an administrator." % (escape(email)))
-                reset_user = trans.sa_session.query(trans.app.model.User).filter(trans.app.model.User.table.c.email == email).first()
+                message = (
+                    "Your reset request for %s has been received.  "
+                    "Please check your email account for more instructions.  "
+                    "If you do not receive an email shortly, please contact an administrator." % (escape(email))
+                )
+                reset_user = (
+                    trans.sa_session.query(trans.app.model.User)
+                    .filter(trans.app.model.User.table.c.email == email)
+                    .first()
+                )
                 if not reset_user:
                     # Perform a case-insensitive check only if the user wasn't found
-                    reset_user = trans.sa_session.query(trans.app.model.User).filter(func.lower(trans.app.model.User.table.c.email) == func.lower(email)).first()
+                    reset_user = (
+                        trans.sa_session.query(trans.app.model.User)
+                        .filter(func.lower(trans.app.model.User.table.c.email) == func.lower(email))
+                        .first()
+                    )
                 if reset_user:
                     prt = trans.app.model.PasswordResetToken(reset_user)
                     trans.sa_session.add(prt)
                     trans.sa_session.flush()
-                    host = trans.request.host.split(':')[0]
-                    if host in ['localhost', '127.0.0.1', '0.0.0.0']:
+                    host = trans.request.host.split(":")[0]
+                    if host in ["localhost", "127.0.0.1", "0.0.0.0"]:
                         host = socket.getfqdn()
-                    reset_url = url_for(controller='user',
-                                        action="change_password",
-                                        token=prt.token, qualified=True)
-                    body = PASSWORD_RESET_TEMPLATE % (host, prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
-                                                      reset_url)
+                    reset_url = url_for(controller="user", action="change_password", token=prt.token, qualified=True)
+                    body = PASSWORD_RESET_TEMPLATE % (
+                        host,
+                        prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
+                        reset_url,
+                    )
                     frm = trans.app.config.email_from or f"galaxy-no-reply@{host}"
-                    subject = 'Galaxy Password Reset'
+                    subject = "Galaxy Password Reset"
                     try:
                         util.send_mail(frm, email, subject, body, trans.app.config)
                         trans.sa_session.add(reset_user)
                         trans.sa_session.flush()
                         trans.log_event(f"User reset password: {email}")
                     except Exception:
-                        log.exception('Unable to reset password.')
-        return trans.fill_template('/webapps/tool_shed/user/reset_password.mako',
-                                   message=message,
-                                   status=status)
+                        log.exception("Unable to reset password.")
+        return trans.fill_template("/webapps/tool_shed/user/reset_password.mako", message=message, status=status)
 
     @web.expose
     def manage_user_info(self, trans, cntrller, **kwd):
-        '''Manage a user's login, password, public username, type, addresses, etc.'''
+        """Manage a user's login, password, public username, type, addresses, etc."""
         params = util.Params(kwd)
-        user_id = params.get('id', None)
+        user_id = params.get("id", None)
         if user_id:
             user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
         else:
             user = trans.user
         if not user:
             raise AssertionError(f"The user id ({str(user_id)}) is not valid")
-        email = util.restore_text(params.get('email', user.email))
-        username = util.restore_text(params.get('username', ''))
+        email = util.restore_text(params.get("email", user.email))
+        username = util.restore_text(params.get("username", ""))
         if not username:
             username = user.username
-        message = escape(util.restore_text(params.get('message', '')))
-        status = params.get('status', 'done')
-        return trans.fill_template('/webapps/tool_shed/user/manage_info.mako',
-                                   cntrller=cntrller,
-                                   user=user,
-                                   email=email,
-                                   username=username,
-                                   message=message,
-                                   status=status)
+        message = escape(util.restore_text(params.get("message", "")))
+        status = params.get("status", "done")
+        return trans.fill_template(
+            "/webapps/tool_shed/user/manage_info.mako",
+            cntrller=cntrller,
+            user=user,
+            email=email,
+            username=username,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     @require_login()
     def api_keys(self, trans, cntrller, **kwd):
         params = util.Params(kwd)
-        message = escape(util.restore_text(params.get('message', '')))
-        status = params.get('status', 'done')
-        if params.get('new_api_key_button', False):
+        message = escape(util.restore_text(params.get("message", "")))
+        status = params.get("status", "done")
+        if params.get("new_api_key_button", False):
             self.create_api_key(trans, trans.user)
             message = "Generated a new web API key"
             status = "done"
-        return trans.fill_template('/webapps/tool_shed/user/api_keys.mako',
-                                   cntrller=cntrller,
-                                   user=trans.user,
-                                   message=message,
-                                   status=status)
+        return trans.fill_template(
+            "/webapps/tool_shed/user/api_keys.mako", cntrller=cntrller, user=trans.user, message=message, status=status
+        )
 
     # For REMOTE_USER, we need the ability to just edit the username
     @web.expose
     @require_login("to manage the public name")
     def edit_username(self, trans, cntrller, **kwd):
         params = util.Params(kwd)
-        is_admin = cntrller == 'admin' and trans.user_is_admin
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        user_id = params.get('user_id', None)
+        is_admin = cntrller == "admin" and trans.user_is_admin
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        user_id = params.get("user_id", None)
         if user_id and is_admin:
             user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
         else:
             user = trans.user
-        if user and params.get('change_username_button', False):
-            username = kwd.get('username', '')
+        if user and params.get("change_username_button", False):
+            username = kwd.get("username", "")
             if username:
                 message = validate_publicname(trans, username, user)
             if message:
-                status = 'error'
+                status = "error"
             else:
                 user.username = username
                 trans.sa_session.add(user)
                 trans.sa_session.flush()
-                message = 'The username has been updated with the changes.'
-        return trans.fill_template('/webapps/tool_shed/user/username.mako',
-                                   cntrller=cntrller,
-                                   user=user,
-                                   username=user.username,
-                                   message=message,
-                                   status=status)
+                message = "The username has been updated with the changes."
+        return trans.fill_template(
+            "/webapps/tool_shed/user/username.mako",
+            cntrller=cntrller,
+            user=user,
+            username=user.username,
+            message=message,
+            status=status,
+        )
 
     @web.expose
     def edit_info(self, trans, cntrller, **kwd):
@@ -335,31 +359,31 @@ class User(BaseUser):
         Edit user information = username, email or password.
         """
         params = util.Params(kwd)
-        is_admin = cntrller == 'admin' and trans.user_is_admin
-        message = util.restore_text(params.get('message', ''))
-        status = params.get('status', 'done')
-        user_id = params.get('user_id', None)
+        is_admin = cntrller == "admin" and trans.user_is_admin
+        message = util.restore_text(params.get("message", ""))
+        status = params.get("status", "done")
+        user_id = params.get("user_id", None)
         if user_id and is_admin:
             user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
         elif user_id and (not trans.user or trans.user.id != trans.security.decode_id(user_id)):
-            message = 'Invalid user id'
-            status = 'error'
+            message = "Invalid user id"
+            status = "error"
             user = None
         else:
             user = trans.user
-        if user and params.get('login_info_button', False):
+        if user and params.get("login_info_button", False):
             # Editing email and username
-            email = util.restore_text(params.get('email', ''))
-            username = util.restore_text(params.get('username', '')).lower()
+            email = util.restore_text(params.get("email", ""))
+            username = util.restore_text(params.get("username", "")).lower()
 
             # Validate the new values for email and username
             message = validate_email(trans, email, user)
             if not message and username:
                 message = validate_publicname(trans, username, user)
             if message:
-                status = 'error'
+                status = "error"
             else:
-                if (user.email != email):
+                if user.email != email:
                     # The user's private role name must match the user's login ( email )
                     private_role = trans.app.security_agent.get_private_user_role(user)
                     private_role.name = email
@@ -368,27 +392,29 @@ class User(BaseUser):
                     user.email = email
                     trans.sa_session.add_all((user, private_role))
                     trans.sa_session.flush()
-                    if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on:
+                    if trans.webapp.name == "galaxy" and trans.app.config.user_activation_on:
                         user.active = False
                         trans.sa_session.add(user)
                         trans.sa_session.flush()
                         is_activation_sent = self.user_manager.send_activation_email(trans, user.email, user.username)
                         if is_activation_sent:
-                            message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.'
+                            message = "The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message."
                         else:
-                            message = 'Unable to send activation email, please contact your local Galaxy administrator.'
+                            message = "Unable to send activation email, please contact your local Galaxy administrator."
                             if trans.app.config.error_email_to is not None:
-                                message += f' Contact: {trans.app.config.error_email_to}'
-                if (user.username != username):
+                                message += f" Contact: {trans.app.config.error_email_to}"
+                if user.username != username:
                     user.username = username
                     trans.sa_session.add(user)
                     trans.sa_session.flush()
-                message = 'The login information has been updated with the changes.'
-        elif user and params.get('edit_user_info_button', False):
+                message = "The login information has been updated with the changes."
+        elif user and params.get("edit_user_info_button", False):
             # Edit user information - webapp MUST BE 'galaxy'
-            user_type_fd_id = params.get('user_type_fd_id', 'none')
-            if user_type_fd_id not in ['none']:
-                user_type_form_definition = trans.sa_session.query(trans.app.model.FormDefinition).get(trans.security.decode_id(user_type_fd_id))
+            user_type_fd_id = params.get("user_type_fd_id", "none")
+            if user_type_fd_id not in ["none"]:
+                user_type_form_definition = trans.sa_session.query(trans.app.model.FormDefinition).get(
+                    trans.security.decode_id(user_type_fd_id)
+                )
             elif user.values:
                 user_type_form_definition = user.values.form_definition
             else:
@@ -413,17 +439,16 @@ class User(BaseUser):
                 trans.sa_session.add(user)
                 trans.sa_session.flush()
             message = "The user information has been updated with the changes."
-        if user and trans.webapp.name == 'galaxy' and is_admin:
-            kwd['user_id'] = trans.security.encode_id(user.id)
-        kwd['id'] = user_id
+        if user and trans.webapp.name == "galaxy" and is_admin:
+            kwd["user_id"] = trans.security.encode_id(user.id)
+        kwd["id"] = user_id
         if message:
-            kwd['message'] = util.sanitize_text(message)
+            kwd["message"] = util.sanitize_text(message)
         if status:
-            kwd['status'] = status
-        return trans.response.send_redirect(web.url_for(controller='user',
-                                                        action='manage_user_info',
-                                                        cntrller=cntrller,
-                                                        **kwd))
+            kwd["status"] = status
+        return trans.response.send_redirect(
+            web.url_for(controller="user", action="manage_user_info", cntrller=cntrller, **kwd)
+        )
 
     @web.expose
     def change_password(self, trans, token=None, id=None, **kwd):
@@ -431,35 +456,45 @@ class User(BaseUser):
         Provides a form with which one can change their password.  If token is
         provided, don't require current password.
         """
-        if kwd.get('change_password_button', False):
-            password = kwd.get('password', '')
-            confirm = kwd.get('confirm', '')
-            current = kwd.get('current', '')
-            user, message = self.user_manager.change_password(trans, password=password,
-                current=current, token=token, confirm=confirm, id=id)
+        if kwd.get("change_password_button", False):
+            password = kwd.get("password", "")
+            confirm = kwd.get("confirm", "")
+            current = kwd.get("current", "")
+            user, message = self.user_manager.change_password(
+                trans, password=password, current=current, token=token, confirm=confirm, id=id
+            )
             if not user:
                 return trans.show_error_message(message)
-            return trans.show_ok_message('The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted).')
-        return trans.fill_template('/webapps/tool_shed/user/change_password.mako', token=token, id=id)
+            return trans.show_ok_message(
+                "The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted)."
+            )
+        return trans.fill_template("/webapps/tool_shed/user/change_password.mako", token=token, id=id)
 
     @web.expose
     def logout(self, trans, logout_all=False, **kwd):
         trans.handle_user_logout(logout_all=logout_all)
-        message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % \
-            (url_for('/'))
+        message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % (
+            url_for("/")
+        )
         if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href:
             trans.response.send_redirect(trans.app.config.remote_user_logout_href)
         else:
-            return trans.fill_template('/webapps/tool_shed/user/logout.mako',
-                                       refresh_frames=['masthead'],
-                                       message=message,
-                                       status='done',
-                                       active_view="user")
+            return trans.fill_template(
+                "/webapps/tool_shed/user/logout.mako",
+                refresh_frames=["masthead"],
+                message=message,
+                status="done",
+                active_view="user",
+            )
 
     def __validate(self, trans, email, password, confirm, username):
-        if username in ['repos']:
+        if username in ["repos"]:
             return f"The term '{username}' is a reserved word in the Tool Shed, so it cannot be used as a public user name."
-        message = "\n".join((validate_email(trans, email),
-                             validate_password(trans, password, confirm),
-                             validate_publicname(trans, username))).rstrip()
+        message = "\n".join(
+            (
+                validate_email(trans, email),
+                validate_password(trans, password, confirm),
+                validate_publicname(trans, username),
+            )
+        ).rstrip()
         return message
diff --git a/lib/tool_shed/webapp/fast_app.py b/lib/tool_shed/webapp/fast_app.py
index 2d0c70d4d97..488b7c6de7a 100644
--- a/lib/tool_shed/webapp/fast_app.py
+++ b/lib/tool_shed/webapp/fast_app.py
@@ -11,14 +11,12 @@ from galaxy.webapps.base.api import (
 def initialize_fast_app(gx_webapp):
     app = FastAPI(
         title="Galaxy Tool Shed API",
-        description=(
-            "This API allows you to manage the Tool Shed repositories."
-        ),
+        description=("This API allows you to manage the Tool Shed repositories."),
         docs_url="/api/docs",
     )
     add_exception_handler(app)
     add_request_id_middleware(app)
-    include_all_package_routers(app, 'tool_shed.webapp.api')
+    include_all_package_routers(app, "tool_shed.webapp.api")
     wsgi_handler = WSGIMiddleware(gx_webapp)
-    app.mount('/', wsgi_handler)
+    app.mount("/", wsgi_handler)
     return app
diff --git a/lib/tool_shed/webapp/fast_factory.py b/lib/tool_shed/webapp/fast_factory.py
index e8cf8480f90..6b7285dc0e1 100644
--- a/lib/tool_shed/webapp/fast_factory.py
+++ b/lib/tool_shed/webapp/fast_factory.py
@@ -36,7 +36,7 @@ with the following command-line.
 
 from galaxy.main_config import (
     WebappConfigResolver,
-    WebappSetupProps
+    WebappSetupProps,
 )
 from tool_shed.webapp.buildapp import app_factory
 from tool_shed.webapp.config import TOOLSHED_APP_NAME
@@ -47,9 +47,11 @@ def factory():
     props = WebappSetupProps(
         app_name=TOOLSHED_APP_NAME,
         default_section_name=TOOLSHED_APP_NAME,
-        env_config_file='TOOL_SHED_CONFIG_FILE',
+        env_config_file="TOOL_SHED_CONFIG_FILE",
     )
     config_provider = WebappConfigResolver(props)
     config = config_provider.resolve_config()
-    gx_webapp = app_factory(global_conf=config.global_conf, load_app_kwds=config.load_app_kwds, wsgi_preflight=config.wsgi_preflight)
+    gx_webapp = app_factory(
+        global_conf=config.global_conf, load_app_kwds=config.load_app_kwds, wsgi_preflight=config.wsgi_preflight
+    )
     return initialize_fast_app(gx_webapp)
diff --git a/lib/tool_shed/webapp/framework/decorators.py b/lib/tool_shed/webapp/framework/decorators.py
index 755f3036a58..c66ed2a55b9 100644
--- a/lib/tool_shed/webapp/framework/decorators.py
+++ b/lib/tool_shed/webapp/framework/decorators.py
@@ -15,6 +15,10 @@ def require_login(verb="perform this action", use_panels=False):
             else:
                 return trans.show_error_message(
                     'You must be <a target="galaxy_main" href="%s">logged in</a> to %s.'
-                    % (url_for(controller='user', action='login'), verb), use_panels=use_panels)
+                    % (url_for(controller="user", action="login"), verb),
+                    use_panels=use_panels,
+                )
+
         return decorator
+
     return argcatcher
diff --git a/lib/tool_shed/webapp/framework/middleware/remoteuser.py b/lib/tool_shed/webapp/framework/middleware/remoteuser.py
index f0f9db25d36..d2c5bc67893 100644
--- a/lib/tool_shed/webapp/framework/middleware/remoteuser.py
+++ b/lib/tool_shed/webapp/framework/middleware/remoteuser.py
@@ -46,16 +46,16 @@ class RemoteUser:
         self.config_secret_header = remote_user_secret_header
 
     def __call__(self, environ, start_response):
-        environ['webapp'] = 'tool_shed'
+        environ["webapp"] = "tool_shed"
         # Allow display servers
-        if self.display_servers and 'REMOTE_ADDR' in environ:
+        if self.display_servers and "REMOTE_ADDR" in environ:
             try:
-                host = socket.gethostbyaddr(environ['REMOTE_ADDR'])[0]
-            except(OSError, socket.herror, socket.gaierror, socket.timeout):
+                host = socket.gethostbyaddr(environ["REMOTE_ADDR"])[0]
+            except (OSError, socket.herror, socket.gaierror, socket.timeout):
                 # in the event of a lookup failure, deny access
                 host = None
             if host in self.display_servers:
-                environ['HTTP_REMOTE_USER'] = 'remote_display_server@%s' % (self.maildomain or 'example.org')
+                environ["HTTP_REMOTE_USER"] = "remote_display_server@%s" % (self.maildomain or "example.org")
                 return self.app(environ, start_response)
 
         # If the secret header is enabled, we expect upstream to send along some key
@@ -71,7 +71,7 @@ class RemoteUser:
         # Galaxy would not have access to Galaxy itself, and be attempting to
         # attack the system
         if self.config_secret_header is not None:
-            if not safe_str_cmp(environ.get('HTTP_GX_SECRET'), self.config_secret_header):
+            if not safe_str_cmp(environ.get("HTTP_GX_SECRET"), self.config_secret_header):
                 title = "Access to Galaxy is denied"
                 message = """
                 Galaxy is configured to authenticate users via an external
@@ -87,11 +87,11 @@ class RemoteUser:
 
         # Apache sets REMOTE_USER to the string '(null)' when using the Rewrite* method for passing REMOTE_USER and a user is
         # un-authenticated.  Any other possible values need to go here as well.
-        path_info = environ.get('PATH_INFO', '')
-        if 'HTTP_REMOTE_USER' in environ and environ['HTTP_REMOTE_USER'] != '(null)':
-            if not environ['HTTP_REMOTE_USER'].count('@'):
+        path_info = environ.get("PATH_INFO", "")
+        if "HTTP_REMOTE_USER" in environ and environ["HTTP_REMOTE_USER"] != "(null)":
+            if not environ["HTTP_REMOTE_USER"].count("@"):
                 if self.maildomain is not None:
-                    environ['HTTP_REMOTE_USER'] += f"@{self.maildomain}"
+                    environ["HTTP_REMOTE_USER"] += f"@{self.maildomain}"
                 else:
                     title = "Access to this Galaxy tool shed is denied"
                     message = """
@@ -104,10 +104,10 @@ class RemoteUser:
                     """
                     return self.error(start_response, title, message)
             return self.app(environ, start_response)
-        elif path_info.startswith('/api/'):
+        elif path_info.startswith("/api/"):
             # The API handles its own authentication via keys
             return self.app(environ, start_response)
-        elif path_info.startswith('/user/api_keys'):
+        elif path_info.startswith("/user/api_keys"):
             # api_keys can be managed when remote_user is in use.
             pass
         else:
@@ -121,6 +121,8 @@ class RemoteUser:
             """
             return self.error(start_response, title, message)
 
-    def error(self, start_response, title="Access denied", message="Contact your local Galaxy tool shed administrator."):
-        start_response('403 Forbidden', [('Content-type', 'text/html')])
+    def error(
+        self, start_response, title="Access denied", message="Contact your local Galaxy tool shed administrator."
+    ):
+        start_response("403 Forbidden", [("Content-type", "text/html")])
         return [errorpage % (title, message)]
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 596417fa17f..9a0fac17c5e 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -3,9 +3,13 @@ import os
 import weakref
 from datetime import (
     datetime,
-    timedelta
+    timedelta,
+)
+from typing import (
+    Any,
+    Mapping,
+    TYPE_CHECKING,
 )
-from typing import Any, Mapping, TYPE_CHECKING
 
 from sqlalchemy import (
     Boolean,
@@ -30,7 +34,10 @@ from sqlalchemy.orm.decl_api import DeclarativeMeta
 
 import tool_shed.repository_types.util as rt_util
 from galaxy import util
-from galaxy.model.custom_types import MutableJSONType, TrimmedString
+from galaxy.model.custom_types import (
+    MutableJSONType,
+    TrimmedString,
+)
 from galaxy.model.orm.now import now
 from galaxy.security.validate_user_input import validate_password_str
 from galaxy.util import unique_id
@@ -40,17 +47,19 @@ from galaxy.util.hash_util import new_secure_hash
 from tool_shed.dependencies.repository import relation_builder
 from tool_shed.util import (
     hg_util,
-    metadata_util
+    metadata_util,
 )
 from tool_shed.util.hgweb_config import hgweb_config_manager
 
 log = logging.getLogger(__name__)
 
-WEAK_HG_REPO_CACHE: Mapping['Repository', Any] = weakref.WeakKeyDictionary()
+WEAK_HG_REPO_CACHE: Mapping["Repository", Any] = weakref.WeakKeyDictionary()
 
 if TYPE_CHECKING:
+
     class _HasTable:
         table: Table
+
 else:
     _HasTable = object
 
@@ -70,17 +79,17 @@ class Base(metaclass=DeclarativeMeta):
 
 
 class APIKeys(Base, _HasTable):
-    __tablename__ = 'api_keys'
+    __tablename__ = "api_keys"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
-    user_id = Column(ForeignKey('galaxy_user.id'), index=True)
+    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
     key = Column(TrimmedString(32), index=True, unique=True)
-    user = relationship('User', back_populates='api_keys')
+    user = relationship("User", back_populates="api_keys")
 
 
 class User(Base, Dictifiable, _HasTable):
-    __tablename__ = 'galaxy_user'
+    __tablename__ = "galaxy_user"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -92,33 +101,33 @@ class User(Base, Dictifiable, _HasTable):
     new_repo_alert = Column(Boolean, default=False)
     deleted = Column(Boolean, index=True, default=False)
     purged = Column(Boolean, index=True, default=False)
-    active_repositories = relationship('Repository',
+    active_repositories = relationship(
+        "Repository",
         primaryjoin=(lambda: (Repository.user_id == User.id) & (not_(Repository.deleted))),  # type: ignore[has-type]
-        back_populates='user',
-        order_by=lambda: desc(Repository.name))  # type: ignore[has-type]
-    galaxy_sessions = relationship('GalaxySession',
-        back_populates='user',
-        order_by=lambda: desc(GalaxySession.update_time))  # type: ignore[has-type]
-    api_keys = relationship(
-        'APIKeys',
-        back_populates='user',
-        order_by=lambda: desc(APIKeys.create_time))
-    reset_tokens = relationship('PasswordResetToken', back_populates='user')
-    groups = relationship('UserGroupAssociation', back_populates='user')
+        back_populates="user",
+        order_by=lambda: desc(Repository.name),
+    )  # type: ignore[has-type]
+    galaxy_sessions = relationship(
+        "GalaxySession", back_populates="user", order_by=lambda: desc(GalaxySession.update_time)
+    )  # type: ignore[has-type]
+    api_keys = relationship("APIKeys", back_populates="user", order_by=lambda: desc(APIKeys.create_time))
+    reset_tokens = relationship("PasswordResetToken", back_populates="user")
+    groups = relationship("UserGroupAssociation", back_populates="user")
 
-    dict_collection_visible_keys = ['id', 'username']
-    dict_element_visible_keys = ['id', 'username']
+    dict_collection_visible_keys = ["id", "username"]
+    dict_element_visible_keys = ["id", "username"]
     bootstrap_admin_user = False
-    roles = relationship('UserRoleAssociation', back_populates='user')
+    roles = relationship("UserRoleAssociation", back_populates="user")
     non_private_roles = relationship(
-        'UserRoleAssociation',
+        "UserRoleAssociation",
         viewonly=True,
-        primaryjoin=(lambda:
-            (User.id == UserRoleAssociation.user_id)  # type: ignore[has-type]
+        primaryjoin=(
+            lambda: (User.id == UserRoleAssociation.user_id)  # type: ignore[has-type]
             & (UserRoleAssociation.role_id == Role.id)  # type: ignore[has-type]
-            & not_(Role.name == User.email))  # type: ignore[has-type]
+            & not_(Role.name == User.email)
+        ),  # type: ignore[has-type]
     )
-    repository_reviews = relationship('RepositoryReview', back_populates='user')
+    repository_reviews = relationship("RepositoryReview", back_populates="user")
 
     def __init__(self, email=None, password=None):
         self.email = email
@@ -161,12 +170,12 @@ class User(Base, Dictifiable, _HasTable):
 
 
 class PasswordResetToken(Base, _HasTable):
-    __tablename__ = 'password_reset_token'
+    __tablename__ = "password_reset_token"
 
     token = Column(String(32), primary_key=True, unique=True, index=True)
     expiration_time = Column(DateTime)
-    user_id = Column(ForeignKey('galaxy_user.id'), index=True)
-    user = relationship('User', back_populates='reset_tokens')
+    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
+    user = relationship("User", back_populates="reset_tokens")
 
     def __init__(self, user, token=None):
         if token:
@@ -178,18 +187,18 @@ class PasswordResetToken(Base, _HasTable):
 
 
 class Group(Base, Dictifiable, _HasTable):
-    __tablename__ = 'galaxy_group'
+    __tablename__ = "galaxy_group"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     name = Column(String(255), index=True, unique=True)
     deleted = Column(Boolean, index=True, default=False)
-    roles = relationship('GroupRoleAssociation', back_populates='group')
-    users = relationship('UserGroupAssociation', back_populates='group')
+    roles = relationship("GroupRoleAssociation", back_populates="group")
+    users = relationship("UserGroupAssociation", back_populates="group")
 
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'name']
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = ["id", "name"]
 
     def __init__(self, name=None):
         self.name = name
@@ -197,7 +206,7 @@ class Group(Base, Dictifiable, _HasTable):
 
 
 class Role(Base, Dictifiable, _HasTable):
-    __tablename__ = 'role'
+    __tablename__ = "role"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -206,18 +215,14 @@ class Role(Base, Dictifiable, _HasTable):
     description = Column(TEXT)
     type = Column(String(40), index=True)
     deleted = Column(Boolean, index=True, default=False)
-    repositories = relationship('RepositoryRoleAssociation', back_populates='role')
-    groups = relationship('GroupRoleAssociation', back_populates='role')
-    users = relationship('UserRoleAssociation', back_populates='role')
+    repositories = relationship("RepositoryRoleAssociation", back_populates="role")
+    groups = relationship("GroupRoleAssociation", back_populates="role")
+    users = relationship("UserRoleAssociation", back_populates="role")
 
-    dict_collection_visible_keys = ['id', 'name']
-    dict_element_visible_keys = ['id', 'name', 'description', 'type']
+    dict_collection_visible_keys = ["id", "name"]
+    dict_element_visible_keys = ["id", "name", "description", "type"]
     private_id = None
-    types = Bunch(PRIVATE='private',
-                  SYSTEM='system',
-                  USER='user',
-                  ADMIN='admin',
-                  SHARING='sharing')
+    types = Bunch(PRIVATE="private", SYSTEM="system", USER="user", ADMIN="admin", SHARING="sharing")
 
     def __init__(self, name=None, description=None, type=types.SYSTEM, deleted=False):
         self.name = name
@@ -236,15 +241,15 @@ class Role(Base, Dictifiable, _HasTable):
 
 
 class UserGroupAssociation(Base, _HasTable):
-    __tablename__ = 'user_group_association'
+    __tablename__ = "user_group_association"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(ForeignKey('galaxy_user.id'), index=True)
-    group_id = Column(ForeignKey('galaxy_group.id'), index=True)
+    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
+    group_id = Column(ForeignKey("galaxy_group.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user = relationship('User', back_populates='groups')
-    group = relationship('Group', back_populates='users')
+    user = relationship("User", back_populates="groups")
+    group = relationship("Group", back_populates="users")
 
     def __init__(self, user, group):
         self.user = user
@@ -252,15 +257,15 @@ class UserGroupAssociation(Base, _HasTable):
 
 
 class UserRoleAssociation(Base, _HasTable):
-    __tablename__ = 'user_role_association'
+    __tablename__ = "user_role_association"
 
     id = Column(Integer, primary_key=True)
-    user_id = Column(ForeignKey('galaxy_user.id'), index=True)
-    role_id = Column(ForeignKey('role.id'), index=True)
+    user_id = Column(ForeignKey("galaxy_user.id"), index=True)
+    role_id = Column(ForeignKey("role.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    user = relationship('User', back_populates='roles')
-    role = relationship('Role', back_populates='users')
+    user = relationship("User", back_populates="roles")
+    role = relationship("Role", back_populates="users")
 
     def __init__(self, user, role):
         self.user = user
@@ -268,15 +273,15 @@ class UserRoleAssociation(Base, _HasTable):
 
 
 class GroupRoleAssociation(Base, _HasTable):
-    __tablename__ = 'group_role_association'
+    __tablename__ = "group_role_association"
 
     id = Column(Integer, primary_key=True)
     group_id = Column(ForeignKey("galaxy_group.id"), index=True)
     role_id = Column(ForeignKey("role.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    group = relationship('Group', back_populates='roles')
-    role = relationship('Role', back_populates='groups')
+    group = relationship("Group", back_populates="roles")
+    role = relationship("Role", back_populates="groups")
 
     def __init__(self, group, role):
         self.group = group
@@ -284,15 +289,15 @@ class GroupRoleAssociation(Base, _HasTable):
 
 
 class RepositoryRoleAssociation(Base, _HasTable):
-    __tablename__ = 'repository_role_association'
+    __tablename__ = "repository_role_association"
 
     id = Column(Integer, primary_key=True)
     repository_id = Column(ForeignKey("repository.id"), index=True)
     role_id = Column(ForeignKey("role.id"), index=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    repository = relationship('Repository', back_populates='roles')
-    role = relationship('Role', back_populates='repositories')
+    repository = relationship("Repository", back_populates="roles")
+    role = relationship("Role", back_populates="repositories")
 
     def __init__(self, repository, role):
         self.repository = repository
@@ -300,7 +305,7 @@ class RepositoryRoleAssociation(Base, _HasTable):
 
 
 class GalaxySession(Base, _HasTable):
-    __tablename__ = 'galaxy_session'
+    __tablename__ = "galaxy_session"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -315,7 +320,7 @@ class GalaxySession(Base, _HasTable):
     # saves a reference to the previous session so we have a way to chain them together
     prev_session_id = Column(Integer)
     last_action = Column(DateTime)
-    user = relationship('User', back_populates='galaxy_sessions')
+    user = relationship("User", back_populates="galaxy_sessions")
 
     def __init__(self, is_valid=False, **kwd):
         super().__init__(**kwd)
@@ -324,7 +329,7 @@ class GalaxySession(Base, _HasTable):
 
 
 class Repository(Base, Dictifiable, _HasTable):
-    __tablename__ = 'repository'
+    __tablename__ = "repository"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -341,30 +346,58 @@ class Repository(Base, Dictifiable, _HasTable):
     email_alerts = Column(MutableJSONType, nullable=True)
     times_downloaded = Column(Integer)
     deprecated = Column(Boolean, default=False)
-    categories = relationship('RepositoryCategoryAssociation', back_populates='repository')
-    ratings = relationship('RepositoryRatingAssociation',
-        order_by=lambda: desc(RepositoryRatingAssociation.update_time), back_populates='repository')
-    user = relationship('User', back_populates='active_repositories')
-    downloadable_revisions = relationship('RepositoryMetadata',
+    categories = relationship("RepositoryCategoryAssociation", back_populates="repository")
+    ratings = relationship(
+        "RepositoryRatingAssociation",
+        order_by=lambda: desc(RepositoryRatingAssociation.update_time),
+        back_populates="repository",
+    )
+    user = relationship("User", back_populates="active_repositories")
+    downloadable_revisions = relationship(
+        "RepositoryMetadata",
         primaryjoin=lambda: (Repository.id == RepositoryMetadata.repository_id) & (RepositoryMetadata.downloadable == true()),  # type: ignore[attr-defined,has-type]
         viewonly=True,
-        order_by=lambda: desc(RepositoryMetadata.update_time))  # type: ignore[attr-defined]
-    metadata_revisions = relationship('RepositoryMetadata',
+        order_by=lambda: desc(RepositoryMetadata.update_time),
+    )  # type: ignore[attr-defined]
+    metadata_revisions = relationship(
+        "RepositoryMetadata",
         order_by=lambda: desc(RepositoryMetadata.update_time),  # type: ignore[attr-defined]
-        back_populates='repository')
-    roles = relationship('RepositoryRoleAssociation', back_populates='repository')
-    reviews = relationship('RepositoryReview', back_populates='repository')
-    reviewers = relationship('User', secondary=lambda: RepositoryReview.__table__, viewonly=True)  # type: ignore
+        back_populates="repository",
+    )
+    roles = relationship("RepositoryRoleAssociation", back_populates="repository")
+    reviews = relationship("RepositoryReview", back_populates="repository")
+    reviewers = relationship("User", secondary=lambda: RepositoryReview.__table__, viewonly=True)  # type: ignore
 
-    dict_collection_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'user_id', 'private', 'deleted',
-                                    'times_downloaded', 'deprecated', 'create_time']
-    dict_element_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'long_description', 'user_id', 'private',
-                                 'deleted', 'times_downloaded', 'deprecated', 'create_time']
-    file_states = Bunch(NORMAL='n',
-                        NEEDS_MERGING='m',
-                        MARKED_FOR_REMOVAL='r',
-                        MARKED_FOR_ADDITION='a',
-                        NOT_TRACKED='?')
+    dict_collection_visible_keys = [
+        "id",
+        "name",
+        "type",
+        "remote_repository_url",
+        "homepage_url",
+        "description",
+        "user_id",
+        "private",
+        "deleted",
+        "times_downloaded",
+        "deprecated",
+        "create_time",
+    ]
+    dict_element_visible_keys = [
+        "id",
+        "name",
+        "type",
+        "remote_repository_url",
+        "homepage_url",
+        "description",
+        "long_description",
+        "user_id",
+        "private",
+        "deleted",
+        "times_downloaded",
+        "deprecated",
+        "create_time",
+    ]
+    file_states = Bunch(NORMAL="n", NEEDS_MERGING="m", MARKED_FOR_REMOVAL="r", MARKED_FOR_ADDITION="a", NOT_TRACKED="?")
 
     def __init__(self, private=False, times_downloaded=0, deprecated=False, **kwd):
         super().__init__(**kwd)
@@ -377,29 +410,32 @@ class Repository(Base, Dictifiable, _HasTable):
     def hg_repo(self):
         from mercurial import (
             hg,
-            ui
+            ui,
         )
+
         if not WEAK_HG_REPO_CACHE.get(self):
-            WEAK_HG_REPO_CACHE[self] = hg.cachedlocalrepo(hg.repository(ui.ui(), self.repo_path().encode('utf-8')))
+            WEAK_HG_REPO_CACHE[self] = hg.cachedlocalrepo(hg.repository(ui.ui(), self.repo_path().encode("utf-8")))
         return WEAK_HG_REPO_CACHE[self].fetch()[0]
 
     @property
     def admin_role(self):
-        admin_role_name = f'{str(self.name)}_{str(self.user.username)}_admin'
+        admin_role_name = f"{str(self.name)}_{str(self.user.username)}_admin"
         for rra in self.roles:
             role = rra.role
             if str(role.name) == admin_role_name:
                 return role
-        raise Exception('Repository %s owned by %s is not associated with a required administrative role.' %
-                        (str(self.name), str(self.user.username)))
+        raise Exception(
+            "Repository %s owned by %s is not associated with a required administrative role."
+            % (str(self.name), str(self.user.username))
+        )
 
     def allow_push(self):
         hgrc_file = hg_util.get_hgrc_path(self.repo_path())
         with open(hgrc_file) as fh:
             for line in fh.read().splitlines():
-                if line.startswith('allow_push = '):
-                    return line[len('allow_push = '):]
-        return ''
+                if line.startswith("allow_push = "):
+                    return line[len("allow_push = ") :]
+        return ""
 
     def can_change_type(self):
         # Allow changing the type only if the repository has no contents, has never been installed, or has
@@ -431,9 +467,7 @@ class Repository(Base, Dictifiable, _HasTable):
         # have repository dependencies. However, if a readme file is uploaded, or some other change
         # is made that does not create a new downloadable changeset revision but updates the existing
         # one, we still want to be able to get repository dependencies.
-        repository_metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(app,
-                                                                                                   self,
-                                                                                                   changeset)
+        repository_metadata = metadata_util.get_current_repository_metadata_for_changeset_revision(app, self, changeset)
         if repository_metadata:
             metadata = repository_metadata.metadata
             if metadata:
@@ -450,7 +484,7 @@ class Repository(Base, Dictifiable, _HasTable):
         changeset_revision = metadata_util.get_next_downloadable_changeset_revision(app, self, changeset_revision)
         for downloadable_revision in self.downloadable_revisions:
             if downloadable_revision.changeset_revision == changeset_revision:
-                return downloadable_revision.metadata.get('tool_dependencies', {})
+                return downloadable_revision.metadata.get("tool_dependencies", {})
         return {}
 
     def installable_revisions(self, app, sort_revisions=True):
@@ -469,7 +503,7 @@ class Repository(Base, Dictifiable, _HasTable):
         tip_ctx = repo[repo.changelog.tip()]
         return f"{str(tip_ctx.rev())}:{str(tip_ctx)}"
 
-    def set_allow_push(self, usernames, remove_auth=''):
+    def set_allow_push(self, usernames, remove_auth=""):
         allow_push = util.listify(self.allow_push())
         if remove_auth:
             allow_push.remove(remove_auth)
@@ -484,10 +518,10 @@ class Repository(Base, Dictifiable, _HasTable):
         hgrc_file = hg_util.get_hgrc_path(repo_dir)
         with open(hgrc_file) as fh:
             lines = fh.readlines()
-        with open(hgrc_file, 'w') as fh:
+        with open(hgrc_file, "w") as fh:
             for line in lines:
-                if line.startswith('allow_push'):
-                    fh.write(f'allow_push = {allow_push}')
+                if line.startswith("allow_push"):
+                    fh.write(f"allow_push = {allow_push}")
                 else:
                     fh.write(line)
 
@@ -495,51 +529,64 @@ class Repository(Base, Dictifiable, _HasTable):
         repo = self.hg_repo
         return str(repo[repo.changelog.tip()])
 
-    def to_dict(self, view='collection', value_mapper=None):
+    def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
-        if 'user_id' in rval:
-            rval['owner'] = self.user.username
+        if "user_id" in rval:
+            rval["owner"] = self.user.username
         return rval
 
 
 class RepositoryReview(Base, Dictifiable, _HasTable):
-    __tablename__ = 'repository_review'
+    __tablename__ = "repository_review"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    repository_id = Column(ForeignKey('repository.id'), index=True)
+    repository_id = Column(ForeignKey("repository.id"), index=True)
     changeset_revision = Column(TrimmedString(255), index=True)
-    user_id = Column(ForeignKey('galaxy_user.id'), index=True, nullable=False)
+    user_id = Column(ForeignKey("galaxy_user.id"), index=True, nullable=False)
     approved = Column(TrimmedString(255))
     rating = Column(Integer, index=True)
     deleted = Column(Boolean, index=True, default=False)
-    repository = relationship('Repository', back_populates='reviews')
+    repository = relationship("Repository", back_populates="reviews")
     # Take care when using the mapper below!  It should be used only when a new review is being created for a repository change set revision.
     # Keep in mind that repository_metadata records can be removed from the database for certain change set revisions when metadata is being
     # reset on a repository!
-    repository_metadata = relationship('RepositoryMetadata',
+    repository_metadata = relationship(
+        "RepositoryMetadata",
         viewonly=True,
         foreign_keys=lambda: [RepositoryReview.repository_id, RepositoryReview.changeset_revision],
-        primaryjoin=lambda: ((RepositoryReview.repository_id == RepositoryMetadata.repository_id)  # type: ignore[has-type]
-            & (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision)),  # type: ignore[has-type]
-        back_populates='reviews')
-    user = relationship('User', back_populates='repository_reviews')
+        primaryjoin=lambda: (
+            (RepositoryReview.repository_id == RepositoryMetadata.repository_id)  # type: ignore[has-type]
+            & (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision)
+        ),  # type: ignore[has-type]
+        back_populates="reviews",
+    )
+    user = relationship("User", back_populates="repository_reviews")
 
-    component_reviews = relationship('ComponentReview',
+    component_reviews = relationship(
+        "ComponentReview",
         viewonly=True,
-        primaryjoin=lambda: ((RepositoryReview.id == ComponentReview.repository_review_id)  # type: ignore[has-type]
-            & (ComponentReview.deleted == false())),  # type: ignore[has-type]
-        back_populates='repository_review')
+        primaryjoin=lambda: (
+            (RepositoryReview.id == ComponentReview.repository_review_id)  # type: ignore[has-type]
+            & (ComponentReview.deleted == false())
+        ),  # type: ignore[has-type]
+        back_populates="repository_review",
+    )
 
-    private_component_reviews = relationship('ComponentReview',
+    private_component_reviews = relationship(
+        "ComponentReview",
         viewonly=True,
-        primaryjoin=lambda: ((RepositoryReview.id == ComponentReview.repository_review_id)  # type: ignore[has-type]
-            & (ComponentReview.deleted == false()) & (ComponentReview.private == true())))  # type: ignore[has-type]
+        primaryjoin=lambda: (
+            (RepositoryReview.id == ComponentReview.repository_review_id)  # type: ignore[has-type]
+            & (ComponentReview.deleted == false())
+            & (ComponentReview.private == true())
+        ),
+    )  # type: ignore[has-type]
 
-    dict_collection_visible_keys = ['id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted']
-    dict_element_visible_keys = ['id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted']
-    approved_states = Bunch(NO='no', YES='yes')
+    dict_collection_visible_keys = ["id", "repository_id", "changeset_revision", "user_id", "rating", "deleted"]
+    dict_element_visible_keys = ["id", "repository_id", "changeset_revision", "user_id", "rating", "deleted"]
+    approved_states = Bunch(NO="no", YES="yes")
 
     def __init__(self, deleted=False, **kwd):
         super().__init__(**kwd)
@@ -547,7 +594,7 @@ class RepositoryReview(Base, Dictifiable, _HasTable):
 
 
 class ComponentReview(Base, Dictifiable, _HasTable):
-    __tablename__ = 'component_review'
+    __tablename__ = "component_review"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -559,12 +606,28 @@ class ComponentReview(Base, Dictifiable, _HasTable):
     approved = Column(TrimmedString(255))
     rating = Column(Integer)
     deleted = Column(Boolean, index=True, default=False)
-    repository_review = relationship('RepositoryReview', back_populates='component_reviews')
-    component = relationship('Component')
+    repository_review = relationship("RepositoryReview", back_populates="component_reviews")
+    component = relationship("Component")
 
-    dict_collection_visible_keys = ['id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted']
-    dict_element_visible_keys = ['id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted']
-    approved_states = Bunch(NO='no', YES='yes', NA='not_applicable')
+    dict_collection_visible_keys = [
+        "id",
+        "repository_review_id",
+        "component_id",
+        "private",
+        "approved",
+        "rating",
+        "deleted",
+    ]
+    dict_element_visible_keys = [
+        "id",
+        "repository_review_id",
+        "component_id",
+        "private",
+        "approved",
+        "rating",
+        "deleted",
+    ]
+    approved_states = Bunch(NO="no", YES="yes", NA="not_applicable")
 
     def __init__(self, private=False, approved=False, deleted=False, **kwd):
         super().__init__(**kwd)
@@ -574,7 +637,7 @@ class ComponentReview(Base, Dictifiable, _HasTable):
 
 
 class Component(Base, _HasTable):
-    __tablename__ = 'component'
+    __tablename__ = "component"
 
     id = Column(Integer, primary_key=True)
     name = Column(TrimmedString(255))
@@ -582,8 +645,7 @@ class Component(Base, _HasTable):
 
 
 class ItemRatingAssociation(_HasTable):
-
-    def __init__(self, id=None, user=None, item=None, rating=0, comment=''):
+    def __init__(self, id=None, user=None, item=None, rating=0, comment=""):
         self.id = id
         self.user = user
         self.item = item
@@ -591,11 +653,11 @@ class ItemRatingAssociation(_HasTable):
         self.comment = comment
 
     def set_item(self, item):
-        """ Set association's item. """
+        """Set association's item."""
 
 
 class RepositoryRatingAssociation(Base, ItemRatingAssociation, _HasTable):
-    __tablename__ = 'repository_rating_association'
+    __tablename__ = "repository_rating_association"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -604,15 +666,15 @@ class RepositoryRatingAssociation(Base, ItemRatingAssociation, _HasTable):
     user_id = Column(ForeignKey("galaxy_user.id"), index=True)
     rating = Column(Integer, index=True)
     comment = Column(TEXT)
-    repository = relationship('Repository', back_populates='ratings')
-    user = relationship('User')
+    repository = relationship("Repository", back_populates="ratings")
+    user = relationship("User")
 
     def set_item(self, repository):
         self.repository = repository
 
 
 class Category(Base, Dictifiable, _HasTable):
-    __tablename__ = 'category'
+    __tablename__ = "category"
 
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
@@ -620,10 +682,10 @@ class Category(Base, Dictifiable, _HasTable):
     name = Column(TrimmedString(255), index=True, unique=True)
     description = Column(TEXT)
     deleted = Column(Boolean, index=True, default=False)
-    repositories = relationship('RepositoryCategoryAssociation', back_populates='category')
+    repositories = relationship("RepositoryCategoryAssociation", back_populates="category")
 
-    dict_collection_visible_keys = ['id', 'name', 'description', 'deleted']
-    dict_element_visible_keys = ['id', 'name', 'description', 'deleted']
+    dict_collection_visible_keys = ["id", "name", "description", "deleted"]
+    dict_element_visible_keys = ["id", "name", "description", "deleted"]
 
     def __init__(self, deleted=False, **kwd):
         super().__init__(**kwd)
@@ -631,13 +693,13 @@ class Category(Base, Dictifiable, _HasTable):
 
 
 class RepositoryCategoryAssociation(Base, _HasTable):
-    __tablename__ = 'repository_category_association'
+    __tablename__ = "repository_category_association"
 
     id = Column(Integer, primary_key=True)
-    repository_id = Column(ForeignKey('repository.id'), index=True)
-    category_id = Column(ForeignKey('category.id'), index=True)
-    category = relationship('Category', back_populates='repositories')
-    repository = relationship('Repository', back_populates='categories')
+    repository_id = Column(ForeignKey("repository.id"), index=True)
+    category_id = Column(ForeignKey("category.id"), index=True)
+    category = relationship("Category", back_populates="repositories")
+    repository = relationship("Repository", back_populates="categories")
 
     def __init__(self, repository=None, category=None):
         self.repository = repository
@@ -645,17 +707,15 @@ class RepositoryCategoryAssociation(Base, _HasTable):
 
 
 class Tag(Base, _HasTable):
-    __tablename__ = 'tag'
-    __table_args__ = (
-        UniqueConstraint('name'),
-    )
+    __tablename__ = "tag"
+    __table_args__ = (UniqueConstraint("name"),)
 
     id = Column(Integer, primary_key=True)
     type = Column(Integer)
-    parent_id = Column(ForeignKey('tag.id'))
+    parent_id = Column(ForeignKey("tag.id"))
     name = Column(TrimmedString(255))
-    children = relationship('Tag', back_populates='parent')
-    parent = relationship('Tag', back_populates='children', remote_side=[id])
+    children = relationship("Tag", back_populates="parent")
+    parent = relationship("Tag", back_populates="children", remote_side=[id])
 
     def __str__(self):
         return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % (self.id, self.type, self.parent_id, self.name)
@@ -664,38 +724,82 @@ class Tag(Base, _HasTable):
 # The RepositoryMetadata model is mapped imperatively (for details see discussion in PR #12064).
 # TLDR: a declaratively-mapped class cannot have a .metadata attribute (it is used by SQLAlchemy's DeclarativeBase).
 
+
 class RepositoryMetadata(Dictifiable, _HasTable):
     # Once the class has been mapped, all Column items in this table will be available
     # as instrumented class attributes on RepositoryMetadata.
-    table = Table('repository_metadata', mapper_registry.metadata,
-        Column('id', Integer, primary_key=True),
-        Column('create_time', DateTime, default=now),
-        Column('update_time', DateTime, default=now, onupdate=now),
-        Column('repository_id', ForeignKey('repository.id'), index=True),
-        Column('changeset_revision', TrimmedString(255), index=True),
-        Column('numeric_revision', Integer, index=True),
-        Column('metadata', MutableJSONType, nullable=True),
-        Column('tool_versions', MutableJSONType, nullable=True),
-        Column('malicious', Boolean, default=False),
-        Column('downloadable', Boolean, default=True),
-        Column('missing_test_components', Boolean, default=False, index=True),
-        Column('has_repository_dependencies', Boolean, default=False, index=True),
-        Column('includes_datatypes', Boolean, default=False, index=True),
-        Column('includes_tools', Boolean, default=False, index=True),
-        Column('includes_tool_dependencies', Boolean, default=False, index=True),
-        Column('includes_workflows', Boolean, default=False, index=True))
+    table = Table(
+        "repository_metadata",
+        mapper_registry.metadata,
+        Column("id", Integer, primary_key=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("repository_id", ForeignKey("repository.id"), index=True),
+        Column("changeset_revision", TrimmedString(255), index=True),
+        Column("numeric_revision", Integer, index=True),
+        Column("metadata", MutableJSONType, nullable=True),
+        Column("tool_versions", MutableJSONType, nullable=True),
+        Column("malicious", Boolean, default=False),
+        Column("downloadable", Boolean, default=True),
+        Column("missing_test_components", Boolean, default=False, index=True),
+        Column("has_repository_dependencies", Boolean, default=False, index=True),
+        Column("includes_datatypes", Boolean, default=False, index=True),
+        Column("includes_tools", Boolean, default=False, index=True),
+        Column("includes_tool_dependencies", Boolean, default=False, index=True),
+        Column("includes_workflows", Boolean, default=False, index=True),
+    )
 
-    dict_collection_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components',
-                                    'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies',
-                                    'includes_tools_for_display_in_tool_panel', 'includes_workflows']
-    dict_element_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components',
-                                 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies',
-                                 'includes_tools_for_display_in_tool_panel', 'includes_workflows', 'repository_dependencies']
+    dict_collection_visible_keys = [
+        "id",
+        "repository_id",
+        "numeric_revision",
+        "changeset_revision",
+        "malicious",
+        "downloadable",
+        "missing_test_components",
+        "has_repository_dependencies",
+        "includes_datatypes",
+        "includes_tools",
+        "includes_tool_dependencies",
+        "includes_tools_for_display_in_tool_panel",
+        "includes_workflows",
+    ]
+    dict_element_visible_keys = [
+        "id",
+        "repository_id",
+        "numeric_revision",
+        "changeset_revision",
+        "malicious",
+        "downloadable",
+        "missing_test_components",
+        "has_repository_dependencies",
+        "includes_datatypes",
+        "includes_tools",
+        "includes_tool_dependencies",
+        "includes_tools_for_display_in_tool_panel",
+        "includes_workflows",
+        "repository_dependencies",
+    ]
 
-    def __init__(self, id=None, repository_id=None, numeric_revision=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False,
-                 downloadable=False, missing_test_components=None, tools_functionally_correct=False, test_install_error=False,
-                 has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False,
-                 includes_workflows=False):
+    def __init__(
+        self,
+        id=None,
+        repository_id=None,
+        numeric_revision=None,
+        changeset_revision=None,
+        metadata=None,
+        tool_versions=None,
+        malicious=False,
+        downloadable=False,
+        missing_test_components=None,
+        tools_functionally_correct=False,
+        test_install_error=False,
+        has_repository_dependencies=False,
+        includes_datatypes=False,
+        includes_tools=False,
+        includes_tool_dependencies=False,
+        includes_workflows=False,
+    ):
         self.id = id
         self.repository_id = repository_id
         self.numeric_revision = numeric_revision
@@ -715,30 +819,42 @@ class RepositoryMetadata(Dictifiable, _HasTable):
     @property
     def includes_tools_for_display_in_tool_panel(self):
         if self.metadata:
-            tool_dicts = self.metadata.get('tools', [])
+            tool_dicts = self.metadata.get("tools", [])
             for tool_dict in tool_dicts:
-                if tool_dict.get('add_to_tool_panel', True):
+                if tool_dict.get("add_to_tool_panel", True):
                     return True
         return False
 
     @property
     def repository_dependencies(self):
         if self.has_repository_dependencies:
-            return [repository_dependency for repository_dependency in self.metadata['repository_dependencies']['repository_dependencies']]
+            return [
+                repository_dependency
+                for repository_dependency in self.metadata["repository_dependencies"]["repository_dependencies"]
+            ]
         return []
 
 
 # After the map_imperatively statement has been executed, the members of the
 # properties dictionary (repository, reviews) will be available as instrumented
 # class attributes on RepositoryMetadata.
-mapper_registry.map_imperatively(RepositoryMetadata, RepositoryMetadata.table, properties=dict(
-    repository=relationship(Repository, back_populates='metadata_revisions'),
-    reviews=relationship(RepositoryReview,
-        viewonly=True,
-        foreign_keys=lambda: [RepositoryReview.repository_id, RepositoryReview.changeset_revision],
-        primaryjoin=lambda: ((RepositoryReview.repository_id == RepositoryMetadata.repository_id)
-            & (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision)),
-        back_populates='repository_metadata')))
+mapper_registry.map_imperatively(
+    RepositoryMetadata,
+    RepositoryMetadata.table,
+    properties=dict(
+        repository=relationship(Repository, back_populates="metadata_revisions"),
+        reviews=relationship(
+            RepositoryReview,
+            viewonly=True,
+            foreign_keys=lambda: [RepositoryReview.repository_id, RepositoryReview.changeset_revision],
+            primaryjoin=lambda: (
+                (RepositoryReview.repository_id == RepositoryMetadata.repository_id)
+                & (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision)
+            ),
+            back_populates="repository_metadata",
+        ),
+    ),
+)
 
 
 # Utility methods
diff --git a/lib/tool_shed/webapp/model/migrate/check.py b/lib/tool_shed/webapp/model/migrate/check.py
index ccb65ec6038..10df4878017 100644
--- a/lib/tool_shed/webapp/model/migrate/check.py
+++ b/lib/tool_shed/webapp/model/migrate/check.py
@@ -2,16 +2,26 @@ import logging
 import os.path
 import sys
 
-from migrate.versioning import repository, schema
-from sqlalchemy import create_engine, MetaData, Table
+from migrate.versioning import (
+    repository,
+    schema,
+)
+from sqlalchemy import (
+    create_engine,
+    MetaData,
+    Table,
+)
 from sqlalchemy.exc import NoSuchTableError
 
-from galaxy.model.database_utils import create_database, database_exists
+from galaxy.model.database_utils import (
+    create_database,
+    database_exists,
+)
 
 log = logging.getLogger(__name__)
 
 # path relative to galaxy
-migrate_repository_directory = os.path.dirname(__file__).replace(os.getcwd() + os.path.sep, '', 1)
+migrate_repository_directory = os.path.dirname(__file__).replace(os.getcwd() + os.path.sep, "", 1)
 migrate_repository = repository.Repository(migrate_repository_directory)
 
 
@@ -66,7 +76,10 @@ def create_or_verify_database(url, engine_options=None):
     # Verify that the code and the DB are in sync
     db_schema = schema.ControlledSchema(engine, migrate_repository)
     if migrate_repository.versions.latest != db_schema.version:
-        exception_msg = "Your database has version '%d' but this code expects version '%d'.  " % (db_schema.version, migrate_repository.versions.latest)
+        exception_msg = "Your database has version '%d' but this code expects version '%d'.  " % (
+            db_schema.version,
+            migrate_repository.versions.latest,
+        )
         exception_msg += "Back up your database and then migrate the schema by running the following from your Galaxy installation directory:"
         exception_msg += "\n\nsh manage_db.sh upgrade tool_shed\n"
         raise Exception(exception_msg)
@@ -79,7 +92,7 @@ def migrate_to_current_version(engine, schema):
     changeset = schema.changeset(None)
     for ver, change in changeset:
         nextver = ver + changeset.step
-        log.info(f'Migrating {ver} -> {nextver}... ')
+        log.info(f"Migrating {ver} -> {nextver}... ")
         old_stdout = sys.stdout
 
         class FakeStdout:
@@ -91,6 +104,7 @@ def migrate_to_current_version(engine, schema):
 
             def flush(self):
                 pass
+
         sys.stdout = FakeStdout()
         try:
             schema.runchange(ver, change, changeset.step)
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0001_initial_tables.py b/lib/tool_shed/webapp/model/migrate/versions/0001_initial_tables.py
index d865aa843eb..1d6161425b3 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0001_initial_tables.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0001_initial_tables.py
@@ -6,7 +6,19 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Index, Integer, MetaData, String, Table, TEXT, UniqueConstraint
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Index,
+    Integer,
+    MetaData,
+    String,
+    Table,
+    TEXT,
+    UniqueConstraint,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
@@ -22,134 +34,183 @@ log.addHandler(handler)
 
 metadata = MetaData()
 
-User_table = Table("galaxy_user", metadata,
-                   Column("id", Integer, primary_key=True),
-                   Column("create_time", DateTime, default=now),
-                   Column("update_time", DateTime, default=now, onupdate=now),
-                   Column("email", TrimmedString(255), nullable=False),
-                   Column("username", String(255), index=True),
-                   Column("password", TrimmedString(40), nullable=False),
-                   Column("external", Boolean, default=False),
-                   Column("deleted", Boolean, index=True, default=False),
-                   Column("purged", Boolean, index=True, default=False))
+User_table = Table(
+    "galaxy_user",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("email", TrimmedString(255), nullable=False),
+    Column("username", String(255), index=True),
+    Column("password", TrimmedString(40), nullable=False),
+    Column("external", Boolean, default=False),
+    Column("deleted", Boolean, index=True, default=False),
+    Column("purged", Boolean, index=True, default=False),
+)
 
-Group_table = Table("galaxy_group", metadata,
-                    Column("id", Integer, primary_key=True),
-                    Column("create_time", DateTime, default=now),
-                    Column("update_time", DateTime, default=now, onupdate=now),
-                    Column("name", String(255), index=True, unique=True),
-                    Column("deleted", Boolean, index=True, default=False))
+Group_table = Table(
+    "galaxy_group",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", String(255), index=True, unique=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-Role_table = Table("role", metadata,
-                   Column("id", Integer, primary_key=True),
-                   Column("create_time", DateTime, default=now),
-                   Column("update_time", DateTime, default=now, onupdate=now),
-                   Column("name", String(255), index=True, unique=True),
-                   Column("description", TEXT),
-                   Column("type", String(40), index=True),
-                   Column("deleted", Boolean, index=True, default=False))
+Role_table = Table(
+    "role",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", String(255), index=True, unique=True),
+    Column("description", TEXT),
+    Column("type", String(40), index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-UserGroupAssociation_table = Table("user_group_association", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                   Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
-                                   Column("create_time", DateTime, default=now),
-                                   Column("update_time", DateTime, default=now, onupdate=now))
+UserGroupAssociation_table = Table(
+    "user_group_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-UserRoleAssociation_table = Table("user_role_association", metadata,
-                                  Column("id", Integer, primary_key=True),
-                                  Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                  Column("role_id", Integer, ForeignKey("role.id"), index=True),
-                                  Column("create_time", DateTime, default=now),
-                                  Column("update_time", DateTime, default=now, onupdate=now))
+UserRoleAssociation_table = Table(
+    "user_role_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-GroupRoleAssociation_table = Table("group_role_association", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
-                                   Column("role_id", Integer, ForeignKey("role.id"), index=True),
-                                   Column("create_time", DateTime, default=now),
-                                   Column("update_time", DateTime, default=now, onupdate=now))
+GroupRoleAssociation_table = Table(
+    "group_role_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+)
 
-GalaxySession_table = Table("galaxy_session", metadata,
-                            Column("id", Integer, primary_key=True),
-                            Column("create_time", DateTime, default=now),
-                            Column("update_time", DateTime, default=now, onupdate=now),
-                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True),
-                            Column("remote_host", String(255)),
-                            Column("remote_addr", String(255)),
-                            Column("referer", TEXT),
-                            Column("session_key", TrimmedString(255), index=True, unique=True),  # unique 128 bit random number coerced to a string
-                            Column("is_valid", Boolean, default=False),
-                            Column("prev_session_id", Integer))  # saves a reference to the previous session so we have a way to chain them together
+GalaxySession_table = Table(
+    "galaxy_session",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True),
+    Column("remote_host", String(255)),
+    Column("remote_addr", String(255)),
+    Column("referer", TEXT),
+    Column(
+        "session_key", TrimmedString(255), index=True, unique=True
+    ),  # unique 128 bit random number coerced to a string
+    Column("is_valid", Boolean, default=False),
+    Column("prev_session_id", Integer),
+)  # saves a reference to the previous session so we have a way to chain them together
 
-Tool_table = Table("tool", metadata,
-                   Column("id", Integer, primary_key=True),
-                   Column("guid", TrimmedString(255), index=True, unique=True),
-                   Column("tool_id", TrimmedString(255), index=True),
-                   Column("create_time", DateTime, default=now),
-                   Column("update_time", DateTime, default=now, onupdate=now),
-                   Column("newer_version_id", Integer, ForeignKey("tool.id"), nullable=True),
-                   Column("name", TrimmedString(255), index=True),
-                   Column("description", TEXT),
-                   Column("user_description", TEXT),
-                   Column("version", TrimmedString(255)),
-                   Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                   Column("external_filename", TEXT),
-                   Column("deleted", Boolean, index=True, default=False))
+Tool_table = Table(
+    "tool",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("guid", TrimmedString(255), index=True, unique=True),
+    Column("tool_id", TrimmedString(255), index=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("newer_version_id", Integer, ForeignKey("tool.id"), nullable=True),
+    Column("name", TrimmedString(255), index=True),
+    Column("description", TEXT),
+    Column("user_description", TEXT),
+    Column("version", TrimmedString(255)),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("external_filename", TEXT),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-Event_table = Table('event', metadata,
-                    Column("id", Integer, primary_key=True),
-                    Column("create_time", DateTime, default=now),
-                    Column("update_time", DateTime, default=now, onupdate=now),
-                    Column("state", TrimmedString(255), index=True),
-                    Column("comment", TEXT))
+Event_table = Table(
+    "event",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("state", TrimmedString(255), index=True),
+    Column("comment", TEXT),
+)
 
-ToolEventAssociation_table = Table("tool_event_association", metadata,
-                                   Column("id", Integer, primary_key=True),
-                                   Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                   Column("event_id", Integer, ForeignKey("event.id"), index=True))
+ToolEventAssociation_table = Table(
+    "tool_event_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+    Column("event_id", Integer, ForeignKey("event.id"), index=True),
+)
 
-Category_table = Table("category", metadata,
-                       Column("id", Integer, primary_key=True),
-                       Column("create_time", DateTime, default=now),
-                       Column("update_time", DateTime, default=now, onupdate=now),
-                       Column("name", TrimmedString(255), index=True, unique=True),
-                       Column("description", TEXT),
-                       Column("deleted", Boolean, index=True, default=False))
+Category_table = Table(
+    "category",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), index=True, unique=True),
+    Column("description", TEXT),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-ToolCategoryAssociation_table = Table("tool_category_association", metadata,
-                                      Column("id", Integer, primary_key=True),
-                                      Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                      Column("category_id", Integer, ForeignKey("category.id"), index=True))
+ToolCategoryAssociation_table = Table(
+    "tool_category_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+    Column("category_id", Integer, ForeignKey("category.id"), index=True),
+)
 
-Tag_table = Table("tag", metadata,
-                  Column("id", Integer, primary_key=True),
-                  Column("type", Integer),
-                  Column("parent_id", Integer, ForeignKey("tag.id")),
-                  Column("name", TrimmedString(255)),
-                  UniqueConstraint("name"))
+Tag_table = Table(
+    "tag",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("type", Integer),
+    Column("parent_id", Integer, ForeignKey("tag.id")),
+    Column("name", TrimmedString(255)),
+    UniqueConstraint("name"),
+)
 
-ToolTagAssociation_table = Table("tool_tag_association", metadata,
-                                 Column("id", Integer, primary_key=True),
-                                 Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                 Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                 Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                 Column("user_tname", TrimmedString(255), index=True),
-                                 Column("value", TrimmedString(255), index=True),
-                                 Column("user_value", TrimmedString(255), index=True))
+ToolTagAssociation_table = Table(
+    "tool_tag_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("user_tname", TrimmedString(255), index=True),
+    Column("value", TrimmedString(255), index=True),
+    Column("user_value", TrimmedString(255), index=True),
+)
 
-ToolAnnotationAssociation_table = Table("tool_annotation_association", metadata,
-                                        Column("id", Integer, primary_key=True),
-                                        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                        Column("annotation", TEXT))
+ToolAnnotationAssociation_table = Table(
+    "tool_annotation_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("annotation", TEXT),
+)
 
 
 def upgrade(migrate_engine):
     print(__doc__)
     metadata.bind = migrate_engine
     metadata.create_all()
-    Index('ix_tool_annotation_association_annotation', ToolAnnotationAssociation_table.c.annotation, mysql_length=767).create()
+    Index(
+        "ix_tool_annotation_association_annotation", ToolAnnotationAssociation_table.c.annotation, mysql_length=767
+    ).create()
 
 
 def downgrade(migrate_engine):
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0002_add_tool_suite_column.py b/lib/tool_shed/webapp/model/migrate/versions/0002_add_tool_suite_column.py
index 9223379e520..f54984c2aae 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0002_add_tool_suite_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0002_add_tool_suite_column.py
@@ -5,7 +5,12 @@ Migration script to add the suite column to the tool table.
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -27,12 +32,12 @@ def upgrade(migrate_engine):
     c = Column("suite", Boolean, default=False, index=True)
     try:
         # Create
-        c.create(Tool_table, index_name='ix_tool_suite')
+        c.create(Tool_table, index_name="ix_tool_suite")
         assert c is Tool_table.c.suite
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_false = "0"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_false = "false"
         migrate_engine.execute(f"UPDATE tool SET suite={default_false}")
     except Exception:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0003_review_and_review_association_tables.py b/lib/tool_shed/webapp/model/migrate/versions/0003_review_and_review_association_tables.py
index 02450f344c6..7003b8d4894 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0003_review_and_review_association_tables.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0003_review_and_review_association_tables.py
@@ -6,7 +6,15 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -19,14 +27,17 @@ log.addHandler(handler)
 
 metadata = MetaData()
 
-ToolRatingAssociation_table = Table("tool_rating_association", metadata,
-                                    Column("id", Integer, primary_key=True),
-                                    Column("create_time", DateTime, default=now),
-                                    Column("update_time", DateTime, default=now, onupdate=now),
-                                    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                    Column("rating", Integer, index=True),
-                                    Column("comment", TEXT))
+ToolRatingAssociation_table = Table(
+    "tool_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+    Column("comment", TEXT),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0004_repository_tables.py b/lib/tool_shed/webapp/model/migrate/versions/0004_repository_tables.py
index e0287565ca8..529015a2cd8 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0004_repository_tables.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0004_repository_tables.py
@@ -6,7 +6,16 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
@@ -22,29 +31,38 @@ log.addHandler(handler)
 
 metadata = MetaData()
 
-Repository_table = Table("repository", metadata,
-                         Column("id", Integer, primary_key=True),
-                         Column("create_time", DateTime, default=now),
-                         Column("update_time", DateTime, default=now, onupdate=now),
-                         Column("name", TrimmedString(255), index=True),
-                         Column("description", TEXT),
-                         Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                         Column("private", Boolean, default=False),
-                         Column("deleted", Boolean, index=True, default=False))
+Repository_table = Table(
+    "repository",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("name", TrimmedString(255), index=True),
+    Column("description", TEXT),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("private", Boolean, default=False),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-RepositoryRatingAssociation_table = Table("repository_rating_association", metadata,
-                                          Column("id", Integer, primary_key=True),
-                                          Column("create_time", DateTime, default=now),
-                                          Column("update_time", DateTime, default=now, onupdate=now),
-                                          Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
-                                          Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                          Column("rating", Integer, index=True),
-                                          Column("comment", TEXT))
+RepositoryRatingAssociation_table = Table(
+    "repository_rating_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("rating", Integer, index=True),
+    Column("comment", TEXT),
+)
 
-RepositoryCategoryAssociation_table = Table("repository_category_association", metadata,
-                                            Column("id", Integer, primary_key=True),
-                                            Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
-                                            Column("category_id", Integer, ForeignKey("category.id"), index=True))
+RepositoryCategoryAssociation_table = Table(
+    "repository_category_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
+    Column("category_id", Integer, ForeignKey("category.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0005_drop_tool_related_tables.py b/lib/tool_shed/webapp/model/migrate/versions/0005_drop_tool_related_tables.py
index 8988410afc3..a6fb2ebecbb 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0005_drop_tool_related_tables.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0005_drop_tool_related_tables.py
@@ -8,7 +8,16 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 from sqlalchemy.exc import NoSuchTableError
 
 # Need our custom types, but don't import anything else from model
@@ -102,62 +111,83 @@ def downgrade(migrate_engine):
     metadata.reflect()
     # We've lost all of our data, so downgrading is useless. However, we'll
     # at least re-create the dropped tables.
-    Event_table = Table('event', metadata,
-                        Column("id", Integer, primary_key=True),
-                        Column("create_time", DateTime, default=now),
-                        Column("update_time", DateTime, default=now, onupdate=now),
-                        Column("state", TrimmedString(255), index=True),
-                        Column("comment", TEXT))
+    Event_table = Table(
+        "event",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("state", TrimmedString(255), index=True),
+        Column("comment", TEXT),
+    )
 
-    Tool_table = Table("tool", metadata,
-                       Column("id", Integer, primary_key=True),
-                       Column("guid", TrimmedString(255), index=True, unique=True),
-                       Column("tool_id", TrimmedString(255), index=True),
-                       Column("create_time", DateTime, default=now),
-                       Column("update_time", DateTime, default=now, onupdate=now),
-                       Column("newer_version_id", Integer, ForeignKey("tool.id"), nullable=True),
-                       Column("name", TrimmedString(255), index=True),
-                       Column("description", TEXT),
-                       Column("user_description", TEXT),
-                       Column("version", TrimmedString(255)),
-                       Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                       Column("external_filename", TEXT),
-                       Column("deleted", Boolean, index=True, default=False),
-                       Column("suite", Boolean, default=False, index=True))
+    Tool_table = Table(
+        "tool",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("guid", TrimmedString(255), index=True, unique=True),
+        Column("tool_id", TrimmedString(255), index=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("newer_version_id", Integer, ForeignKey("tool.id"), nullable=True),
+        Column("name", TrimmedString(255), index=True),
+        Column("description", TEXT),
+        Column("user_description", TEXT),
+        Column("version", TrimmedString(255)),
+        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+        Column("external_filename", TEXT),
+        Column("deleted", Boolean, index=True, default=False),
+        Column("suite", Boolean, default=False, index=True),
+    )
 
-    ToolCategoryAssociation_table = Table("tool_category_association", metadata,
-                                          Column("id", Integer, primary_key=True),
-                                          Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                          Column("category_id", Integer, ForeignKey("category.id"), index=True))
+    ToolCategoryAssociation_table = Table(
+        "tool_category_association",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+        Column("category_id", Integer, ForeignKey("category.id"), index=True),
+    )
 
-    ToolEventAssociation_table = Table("tool_event_association", metadata,
-                                       Column("id", Integer, primary_key=True),
-                                       Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                       Column("event_id", Integer, ForeignKey("event.id"), index=True))
+    ToolEventAssociation_table = Table(
+        "tool_event_association",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+        Column("event_id", Integer, ForeignKey("event.id"), index=True),
+    )
 
-    ToolRatingAssociation_table = Table("tool_rating_association", metadata,
-                                        Column("id", Integer, primary_key=True),
-                                        Column("create_time", DateTime, default=now),
-                                        Column("update_time", DateTime, default=now, onupdate=now),
-                                        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                        Column("rating", Integer, index=True),
-                                        Column("comment", TEXT))
+    ToolRatingAssociation_table = Table(
+        "tool_rating_association",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("create_time", DateTime, default=now),
+        Column("update_time", DateTime, default=now, onupdate=now),
+        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+        Column("rating", Integer, index=True),
+        Column("comment", TEXT),
+    )
 
-    ToolTagAssociation_table = Table("tool_tag_association", metadata,
-                                     Column("id", Integer, primary_key=True),
-                                     Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                     Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-                                     Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                     Column("user_tname", TrimmedString(255), index=True),
-                                     Column("value", TrimmedString(255), index=True),
-                                     Column("user_value", TrimmedString(255), index=True))
+    ToolTagAssociation_table = Table(
+        "tool_tag_association",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+        Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
+        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+        Column("user_tname", TrimmedString(255), index=True),
+        Column("value", TrimmedString(255), index=True),
+        Column("user_value", TrimmedString(255), index=True),
+    )
 
-    ToolAnnotationAssociation_table = Table("tool_annotation_association", metadata,
-                                            Column("id", Integer, primary_key=True),
-                                            Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
-                                            Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                                            Column("annotation", TEXT, index=True))
+    ToolAnnotationAssociation_table = Table(
+        "tool_annotation_association",
+        metadata,
+        Column("id", Integer, primary_key=True),
+        Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
+        Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+        Column("annotation", TEXT, index=True),
+    )
 
     # Create the event table
     try:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0006_add_email_alerts_column.py b/lib/tool_shed/webapp/model/migrate/versions/0006_add_email_alerts_column.py
index 4301bb366e1..c9ca96fd44e 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0006_add_email_alerts_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0006_add_email_alerts_column.py
@@ -5,7 +5,11 @@ Migration script to add the email_alerts column to the repository table.
 import logging
 import sys
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import JSONType
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py b/lib/tool_shed/webapp/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
index d8555b61e0e..0be164296f3 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
@@ -5,7 +5,13 @@ Migration script to add the long_description and times_downloaded columns to the
 import logging
 import sys
 
-from sqlalchemy import Column, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0008_add_repository_metadata_table.py b/lib/tool_shed/webapp/model/migrate/versions/0008_add_repository_metadata_table.py
index 57f385b66b9..4aa01361d1e 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0008_add_repository_metadata_table.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0008_add_repository_metadata_table.py
@@ -6,10 +6,20 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
-from galaxy.model.custom_types import JSONType, TrimmedString
+from galaxy.model.custom_types import (
+    JSONType,
+    TrimmedString,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
@@ -22,13 +32,16 @@ log.addHandler(handler)
 
 metadata = MetaData()
 
-RepositoryMetadata_table = Table("repository_metadata", metadata,
-                                 Column("id", Integer, primary_key=True),
-                                 Column("create_time", DateTime, default=now),
-                                 Column("update_time", DateTime, default=now, onupdate=now),
-                                 Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
-                                 Column("changeset_revision", TrimmedString(255), index=True),
-                                 Column("metadata", JSONType, nullable=True))
+RepositoryMetadata_table = Table(
+    "repository_metadata",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
+    Column("changeset_revision", TrimmedString(255), index=True),
+    Column("metadata", JSONType, nullable=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0009_add_malicious_column.py b/lib/tool_shed/webapp/model/migrate/versions/0009_add_malicious_column.py
index 9ee235260ee..ed029b567cd 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0009_add_malicious_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0009_add_malicious_column.py
@@ -5,7 +5,12 @@ Migration script to add the malicious column to the repository_metadata table.
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -30,9 +35,9 @@ def upgrade(migrate_engine):
         c.create(Repository_metadata_table, index_name="ix_repository_metadata_malicious")
         assert c is Repository_metadata_table.c.malicious
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_false = "0"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_false = "false"
         migrate_engine.execute(f"UPDATE repository_metadata SET malicious={default_false}")
     except Exception:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0010_add_new_repo_alert_column.py b/lib/tool_shed/webapp/model/migrate/versions/0010_add_new_repo_alert_column.py
index 73ee33252ab..39ceff28a28 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0010_add_new_repo_alert_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0010_add_new_repo_alert_column.py
@@ -5,7 +5,12 @@ Migration script to add the new_repo_alert column to the galaxy_user table.
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -30,9 +35,9 @@ def upgrade(migrate_engine):
         c.create(User_table, index_name="ix_galaxy_user_new_repo_alert")
         assert c is User_table.c.new_repo_alert
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_false = "0"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_false = "false"
         else:
             log.debug("unknown migrate_engine dialect")
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0011_add_tool_versions_column.py b/lib/tool_shed/webapp/model/migrate/versions/0011_add_tool_versions_column.py
index c668accfa3c..5b0e23ee84f 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0011_add_tool_versions_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0011_add_tool_versions_column.py
@@ -6,7 +6,11 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import JSONType
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0012_add_downloadable_column.py b/lib/tool_shed/webapp/model/migrate/versions/0012_add_downloadable_column.py
index f84f236d567..4fe97a081af 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0012_add_downloadable_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0012_add_downloadable_column.py
@@ -5,7 +5,12 @@ Migration script to add the downloadable column to the repository_metadata table
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -30,9 +35,9 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table)
         assert c is RepositoryMetadata_table.c.downloadable
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_true = "1"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_true = "true"
         migrate_engine.execute(f"UPDATE repository_metadata SET downloadable={default_true}")
     except Exception:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0013_add_review_tables.py b/lib/tool_shed/webapp/model/migrate/versions/0013_add_review_tables.py
index 5d8a8fcef8f..98bdd67d430 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0013_add_review_tables.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0013_add_review_tables.py
@@ -6,7 +6,16 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
@@ -21,66 +30,75 @@ log.addHandler(handler)
 
 metadata = MetaData()
 
-IUC = 'Intergalactic Utilities Commission'
+IUC = "Intergalactic Utilities Commission"
 NOW = datetime.datetime.utcnow
-REVIEWER = 'Repository Reviewer'
-ROLE_TYPE = 'system'
+REVIEWER = "Repository Reviewer"
+ROLE_TYPE = "system"
 
 
-def nextval(migrate_engine, table, col='id'):
-    if migrate_engine.name in ['postgresql', 'postgres']:
+def nextval(migrate_engine, table, col="id"):
+    if migrate_engine.name in ["postgresql", "postgres"]:
         return f"nextval('{table}_{col}_seq')"
-    elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+    elif migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
         return "null"
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def localtimestamp(migrate_engine):
-    if migrate_engine.name in ['postgresql', 'postgres'] or migrate_engine.name == 'mysql':
+    if migrate_engine.name in ["postgresql", "postgres"] or migrate_engine.name == "mysql":
         return "LOCALTIMESTAMP"
-    elif migrate_engine.name == 'sqlite':
+    elif migrate_engine.name == "sqlite":
         return "current_date || ' ' || current_time"
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def boolean_false(migrate_engine):
-    if migrate_engine.name in ['postgresql', 'postgres'] or migrate_engine.name == 'mysql':
+    if migrate_engine.name in ["postgresql", "postgres"] or migrate_engine.name == "mysql":
         return False
-    elif migrate_engine.name == 'sqlite':
+    elif migrate_engine.name == "sqlite":
         return 0
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
-RepositoryReview_table = Table("repository_review", metadata,
-                               Column("id", Integer, primary_key=True),
-                               Column("create_time", DateTime, default=NOW),
-                               Column("update_time", DateTime, default=NOW, onupdate=NOW),
-                               Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
-                               Column("changeset_revision", TrimmedString(255), index=True),
-                               Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
-                               Column("approved", TrimmedString(255)),
-                               Column("rating", Integer, index=True),
-                               Column("deleted", Boolean, index=True, default=False))
+RepositoryReview_table = Table(
+    "repository_review",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=NOW),
+    Column("update_time", DateTime, default=NOW, onupdate=NOW),
+    Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
+    Column("changeset_revision", TrimmedString(255), index=True),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
+    Column("approved", TrimmedString(255)),
+    Column("rating", Integer, index=True),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-ComponentReview_table = Table("component_review", metadata,
-                              Column("id", Integer, primary_key=True),
-                              Column("create_time", DateTime, default=NOW),
-                              Column("update_time", DateTime, default=NOW, onupdate=NOW),
-                              Column("repository_review_id", Integer, ForeignKey("repository_review.id"), index=True),
-                              Column("component_id", Integer, ForeignKey("component.id"), index=True),
-                              Column("comment", TEXT),
-                              Column("private", Boolean, default=False),
-                              Column("approved", TrimmedString(255)),
-                              Column("rating", Integer),
-                              Column("deleted", Boolean, index=True, default=False))
+ComponentReview_table = Table(
+    "component_review",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=NOW),
+    Column("update_time", DateTime, default=NOW, onupdate=NOW),
+    Column("repository_review_id", Integer, ForeignKey("repository_review.id"), index=True),
+    Column("component_id", Integer, ForeignKey("component.id"), index=True),
+    Column("comment", TEXT),
+    Column("private", Boolean, default=False),
+    Column("approved", TrimmedString(255)),
+    Column("rating", Integer),
+    Column("deleted", Boolean, index=True, default=False),
+)
 
-Component_table = Table("component", metadata,
-                        Column("id", Integer, primary_key=True),
-                        Column("name", TrimmedString(255)),
-                        Column("description", TEXT))
+Component_table = Table(
+    "component",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("name", TrimmedString(255)),
+    Column("description", TEXT),
+)
 
 
 def upgrade(migrate_engine):
@@ -101,13 +119,15 @@ def upgrade(migrate_engine):
     except Exception:
         log.exception("Creating component_review table failed.")
     # Insert default Component values.
-    names = ['Data types', 'Functional tests', 'README', 'Tool dependencies', 'Tools', 'Workflows']
-    descriptions = ['Proprietary datatypes defined in a file named datatypes_conf.xml included in the repository',
-                    'Functional tests defined in each tool config included in the repository along with test data files',
-                    'An appropriately named file included in the repository that contains installation information or 3rd-party tool dependency licensing information',
-                    'Tool dependencies defined in a file named tool_dependencies.xml included in the repository for contained tools',
-                    'Galaxy tools included in the repository',
-                    'Exported Galaxy workflows included in the repository']
+    names = ["Data types", "Functional tests", "README", "Tool dependencies", "Tools", "Workflows"]
+    descriptions = [
+        "Proprietary datatypes defined in a file named datatypes_conf.xml included in the repository",
+        "Functional tests defined in each tool config included in the repository along with test data files",
+        "An appropriately named file included in the repository that contains installation information or 3rd-party tool dependency licensing information",
+        "Tool dependencies defined in a file named tool_dependencies.xml included in the repository for contained tools",
+        "Galaxy tools included in the repository",
+        "Exported Galaxy workflows included in the repository",
+    ]
     for tup in zip(names, descriptions):
         name, description = tup
         cmd = "INSERT INTO component VALUES ("
@@ -205,7 +225,10 @@ def downgrade(migrate_engine):
             cmd = "DELETE FROM user_group_association WHERE group_id = %d;" % int(group_id)
             migrate_engine.execute(cmd)
             # Delete all GroupRoleAssociations for the IUC group and the REVIEWER role.
-            cmd = "DELETE FROM group_role_association WHERE group_id = %d and role_id = %d;" % (int(group_id), int(role_id))
+            cmd = "DELETE FROM group_role_association WHERE group_id = %d and role_id = %d;" % (
+                int(group_id),
+                int(role_id),
+            )
             migrate_engine.execute(cmd)
             # Delete the IUC group from the galaxy_group table.
             cmd = "DELETE FROM galaxy_group WHERE id = %d;" % int(group_id)
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0014_add_deprecated_column.py b/lib/tool_shed/webapp/model/migrate/versions/0014_add_deprecated_column.py
index e9db03e1d31..01810d8c110 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0014_add_deprecated_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0014_add_deprecated_column.py
@@ -5,7 +5,12 @@ Migration script to add the deprecated column to the repository table.
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -30,9 +35,9 @@ def upgrade(migrate_engine):
         c.create(Repository_table)
         assert c is Repository_table.c.deprecated
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_false = "0"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_false = "false"
         migrate_engine.execute(f"UPDATE repository SET deprecated={default_false}")
     except Exception:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0015_add_api_keys_table.py b/lib/tool_shed/webapp/model/migrate/versions/0015_add_api_keys_table.py
index 10170e12e34..311be966c8e 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0015_add_api_keys_table.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0015_add_api_keys_table.py
@@ -6,7 +6,14 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
@@ -23,11 +30,14 @@ now = datetime.datetime.utcnow
 
 metadata = MetaData()
 
-APIKeys_table = Table("api_keys", metadata,
-                      Column("id", Integer, primary_key=True),
-                      Column("create_time", DateTime, default=now),
-                      Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-                      Column("key", TrimmedString(32), index=True, unique=True))
+APIKeys_table = Table(
+    "api_keys",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+    Column("key", TrimmedString(32), index=True, unique=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py b/lib/tool_shed/webapp/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
index 7610c58a0cc..0cfd8551015 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
@@ -5,7 +5,13 @@ Migration script to add the tool_test_errors, do_not_test, tools_functionally_co
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, DateTime, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import JSONType
@@ -33,9 +39,9 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tfc")
         assert c is RepositoryMetadata_table.c.tools_functionally_correct
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_false = "0"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_false = "false"
         migrate_engine.execute(f"UPDATE repository_metadata SET tools_functionally_correct={default_false}")
     except Exception:
@@ -46,9 +52,9 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_dnt")
         assert c is RepositoryMetadata_table.c.do_not_test
         # Initialize.
-        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+        if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
             default_false = "0"
-        elif migrate_engine.name in ['postgresql', 'postgres']:
+        elif migrate_engine.name in ["postgresql", "postgres"]:
             default_false = "false"
         migrate_engine.execute(f"UPDATE repository_metadata SET do_not_test={default_false}")
     except Exception:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py b/lib/tool_shed/webapp/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
index e2252df0ccf..87ec8211861 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
@@ -6,7 +6,12 @@ columns to the repository_metadata table.
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -24,9 +29,9 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     # Initialize.
-    if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+    if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
         default_false = "0"
-    elif migrate_engine.name in ['postgres', 'postgresql']:
+    elif migrate_engine.name in ["postgres", "postgresql"]:
         default_false = "false"
     # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table.
     RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0018_add_repository_metadata_flag_columns.py b/lib/tool_shed/webapp/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
index 78c1839cce7..de27705f350 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
@@ -6,7 +6,12 @@ tool_test_results, missing_test_components.
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, MetaData, Table
+from sqlalchemy import (
+    Boolean,
+    Column,
+    MetaData,
+    Table,
+)
 from sqlalchemy.exc import NoSuchTableError
 
 # Need our custom types, but don't import anything else from model
@@ -28,9 +33,9 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     # Initialize.
-    if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+    if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
         default_false = "0"
-    elif migrate_engine.name in ['postgresql', 'postgres']:
+    elif migrate_engine.name in ["postgresql", "postgres"]:
         default_false = "false"
 
     try:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py b/lib/tool_shed/webapp/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
index 5b4bdea2509..8803fdc47c5 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
@@ -6,7 +6,16 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+)
 from sqlalchemy.exc import NoSuchTableError
 
 # Need our custom types, but don't import anything else from model
@@ -24,13 +33,16 @@ now = datetime.datetime.utcnow
 
 metadata = MetaData()
 
-SkipToolTest_table = Table("skip_tool_test", metadata,
-                           Column("id", Integer, primary_key=True),
-                           Column("create_time", DateTime, default=now),
-                           Column("update_time", DateTime, default=now, onupdate=now),
-                           Column("repository_metadata_id", Integer, ForeignKey("repository_metadata.id"), index=True),
-                           Column("initial_changeset_revision", TrimmedString(255), index=True),
-                           Column("comment", TEXT))
+SkipToolTest_table = Table(
+    "skip_tool_test",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("create_time", DateTime, default=now),
+    Column("update_time", DateTime, default=now, onupdate=now),
+    Column("repository_metadata_id", Integer, ForeignKey("repository_metadata.id"), index=True),
+    Column("initial_changeset_revision", TrimmedString(255), index=True),
+    Column("comment", TEXT),
+)
 
 
 def upgrade(migrate_engine):
@@ -38,9 +50,9 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
     # Initialize.
-    if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+    if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite":
         default_false = "0"
-    elif migrate_engine.name in ['postgresql', 'postgres']:
+    elif migrate_engine.name in ["postgresql", "postgres"]:
         default_false = "false"
 
     try:
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0020_add_repository_type_column.py b/lib/tool_shed/webapp/model/migrate/versions/0020_add_repository_type_column.py
index 26963a1a0f1..e59f772738c 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0020_add_repository_type_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0020_add_repository_type_column.py
@@ -3,7 +3,11 @@
 import logging
 import sys
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 # Need our custom types, but don't import anything else from model
 from galaxy.model.custom_types import TrimmedString
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0022_add_repository_admin_roles.py b/lib/tool_shed/webapp/model/migrate/versions/0022_add_repository_admin_roles.py
index edc5ac493aa..d0482912e7d 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0022_add_repository_admin_roles.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0022_add_repository_admin_roles.py
@@ -8,7 +8,14 @@ import datetime
 import logging
 import sys
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+)
 from sqlalchemy.exc import NoSuchTableError
 
 log = logging.getLogger(__name__)
@@ -22,41 +29,44 @@ log.addHandler(handler)
 metadata = MetaData()
 
 NOW = datetime.datetime.utcnow
-ROLE_TYPE = 'system'
+ROLE_TYPE = "system"
 
-RepositoryRoleAssociation_table = Table("repository_role_association", metadata,
-                                        Column("id", Integer, primary_key=True),
-                                        Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
-                                        Column("role_id", Integer, ForeignKey("role.id"), index=True),
-                                        Column("create_time", DateTime, default=NOW),
-                                        Column("update_time", DateTime, default=NOW, onupdate=NOW))
+RepositoryRoleAssociation_table = Table(
+    "repository_role_association",
+    metadata,
+    Column("id", Integer, primary_key=True),
+    Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
+    Column("role_id", Integer, ForeignKey("role.id"), index=True),
+    Column("create_time", DateTime, default=NOW),
+    Column("update_time", DateTime, default=NOW, onupdate=NOW),
+)
 
 
-def nextval(migrate_engine, table, col='id'):
-    if migrate_engine.name in ['postgresql', 'postgres']:
+def nextval(migrate_engine, table, col="id"):
+    if migrate_engine.name in ["postgresql", "postgres"]:
         return f"nextval('{table}_{col}_seq')"
-    elif migrate_engine.name in ['mysql', 'sqlite']:
+    elif migrate_engine.name in ["mysql", "sqlite"]:
         return "null"
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def localtimestamp(migrate_engine):
-    if migrate_engine.name in ['postgresql', 'postgres', 'mysql']:
+    if migrate_engine.name in ["postgresql", "postgres", "mysql"]:
         return "LOCALTIMESTAMP"
-    elif migrate_engine.name == 'sqlite':
+    elif migrate_engine.name == "sqlite":
         return "current_date || ' ' || current_time"
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def boolean_false(migrate_engine):
-    if migrate_engine.name in ['postgresql', 'postgres', 'mysql']:
+    if migrate_engine.name in ["postgresql", "postgres", "mysql"]:
         return False
-    elif migrate_engine.name == 'sqlite':
+    elif migrate_engine.name == "sqlite":
         return 0
     else:
-        raise Exception(f'Unable to convert data for unknown database type: {migrate_engine.name}')
+        raise Exception(f"Unable to convert data for unknown database type: {migrate_engine.name}")
 
 
 def upgrade(migrate_engine):
@@ -72,14 +82,14 @@ def upgrade(migrate_engine):
     user_ids = []
     repository_ids = []
     role_names = []
-    cmd = 'SELECT repository.id, repository.name, repository.user_id, galaxy_user.username FROM repository, galaxy_user WHERE repository.user_id = galaxy_user.id;'
+    cmd = "SELECT repository.id, repository.name, repository.user_id, galaxy_user.username FROM repository, galaxy_user WHERE repository.user_id = galaxy_user.id;"
     for row in migrate_engine.execute(cmd):
         repository_id = row[0]
         name = row[1]
         user_id = row[2]
         username = row[3]
         repository_ids.append(int(repository_id))
-        role_names.append(f'{str(name)}_{str(username)}_admin')
+        role_names.append(f"{str(name)}_{str(username)}_admin")
         user_ids.append(int(user_id))
     # Insert a new record into the role table for each new role.
     for tup in zip(repository_ids, user_ids, role_names):
@@ -128,11 +138,11 @@ def downgrade(migrate_engine):
     # Determine the list of roles to delete by first selecting the list of repositories and associated
     # public user names for their owners.
     role_names = []
-    cmd = 'SELECT name, username FROM repository, galaxy_user WHERE repository.user_id = galaxy_user.id;'
+    cmd = "SELECT name, username FROM repository, galaxy_user WHERE repository.user_id = galaxy_user.id;"
     for row in migrate_engine.execute(cmd):
         name = row[0]
         username = row[1]
-        role_names.append(f'{str(name)}_{str(username)}_admin')
+        role_names.append(f"{str(name)}_{str(username)}_admin")
     # Delete each role as well as all users associated with each role.
     for role_name in role_names:
         # Select the id of the record associated with the current role_name from the role table.
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py b/lib/tool_shed/webapp/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
index e4435209e4d..ba283917251 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
@@ -6,7 +6,11 @@ columns to the repository table.
 import logging
 import sys
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import (
+    Column,
+    MetaData,
+    Table,
+)
 
 from galaxy.model.custom_types import TrimmedString
 
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0024_password_reset.py b/lib/tool_shed/webapp/model/migrate/versions/0024_password_reset.py
index 2b585b0c419..f13f502e4df 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0024_password_reset.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0024_password_reset.py
@@ -5,16 +5,27 @@ Migration script for the password reset table
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
 metadata = MetaData()
 
-PasswordResetToken_table = Table("password_reset_token", metadata,
-                                 Column("token", String(32), primary_key=True, unique=True, index=True),
-                                 Column("expiration_time", DateTime),
-                                 Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
+PasswordResetToken_table = Table(
+    "password_reset_token",
+    metadata,
+    Column("token", String(32), primary_key=True, unique=True, index=True),
+    Column("expiration_time", DateTime),
+    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
+)
 
 
 def upgrade(migrate_engine):
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0025_session_timeout.py b/lib/tool_shed/webapp/model/migrate/versions/0025_session_timeout.py
index 20197ab6172..146a02352ed 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0025_session_timeout.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0025_session_timeout.py
@@ -5,7 +5,12 @@ Migration script to add session update time (used for timeouts)
 import datetime
 import logging
 
-from sqlalchemy import Column, DateTime, MetaData, Table
+from sqlalchemy import (
+    Column,
+    DateTime,
+    MetaData,
+    Table,
+)
 
 now = datetime.datetime.utcnow
 log = logging.getLogger(__name__)
diff --git a/lib/tool_shed/webapp/model/migrate/versions/0026_add_numeric_revision_column.py b/lib/tool_shed/webapp/model/migrate/versions/0026_add_numeric_revision_column.py
index 8d5185bb7c7..a5721cd7d1e 100644
--- a/lib/tool_shed/webapp/model/migrate/versions/0026_add_numeric_revision_column.py
+++ b/lib/tool_shed/webapp/model/migrate/versions/0026_add_numeric_revision_column.py
@@ -3,7 +3,12 @@
 import logging
 import sys
 
-from sqlalchemy import Column, Integer, MetaData, Table
+from sqlalchemy import (
+    Column,
+    Integer,
+    MetaData,
+    Table,
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
diff --git a/lib/tool_shed/webapp/search/repo_search.py b/lib/tool_shed/webapp/search/repo_search.py
index fcfb01a3947..aaf0aaa2045 100644
--- a/lib/tool_shed/webapp/search/repo_search.py
+++ b/lib/tool_shed/webapp/search/repo_search.py
@@ -3,9 +3,19 @@ import logging
 
 import whoosh.index
 from whoosh import scoring
-from whoosh.fields import KEYWORD, NUMERIC, Schema, STORED, TEXT
+from whoosh.fields import (
+    KEYWORD,
+    NUMERIC,
+    Schema,
+    STORED,
+    TEXT,
+)
 from whoosh.qparser import MultifieldParser
-from whoosh.query import And, Every, Term
+from whoosh.query import (
+    And,
+    Every,
+    Term,
+)
 
 from galaxy import exceptions
 from galaxy.exceptions import ObjectNotFound
@@ -26,7 +36,8 @@ schema = Schema(
     approved=STORED,
     last_updated=STORED,
     repo_lineage=STORED,
-    full_last_updated=STORED)
+    full_last_updated=STORED,
+)
 
 
 class RepoWeighting(scoring.BM25F):
@@ -34,6 +45,7 @@ class RepoWeighting(scoring.BM25F):
     Affect the BM25G scoring model through the final method.
     source: https://groups.google.com/forum/#!msg/whoosh/1AKNbW8R_l8/XySW0OecH6gJ
     """
+
     use_final = True
 
     def final(self, searcher, docnum, score):
@@ -48,9 +60,9 @@ class RepoWeighting(scoring.BM25F):
         # Add 1 to prevent 0 being divided
         if times_downloaded == 0:
             times_downloaded = 1
-        popularity_modifier = (times_downloaded / reasonable_hits)
+        popularity_modifier = times_downloaded / reasonable_hits
 
-        cert_modifier = 2 if searcher.stored_fields(docnum)["approved"] == 'yes' else 1
+        cert_modifier = 2 if searcher.stored_fields(docnum)["approved"] == "yes" else 1
 
         # Adjust the computed score for this document by the popularity
         # and by the certification level.
@@ -59,7 +71,6 @@ class RepoWeighting(scoring.BM25F):
 
 
 class RepoSearch:
-
     def search(self, trans, search_term, page, page_size, boosts):
         """
         Perform the search on the given search_term
@@ -85,63 +96,73 @@ class RepoSearch:
                 # http://trec.nist.gov/pubs/trec13/papers/microsoft-cambridge.web.hard.pdf
                 # http://en.wikipedia.org/wiki/Okapi_BM25
                 # __Basically__ the higher number the bigger weight.
-                repo_weighting = RepoWeighting(field_B={'name_B': boosts.repo_name_boost,
-                                                        'description_B': boosts.repo_description_boost,
-                                                        'long_description_B': boosts.repo_long_description_boost,
-                                                        'homepage_url_B': boosts.repo_homepage_url_boost,
-                                                        'remote_repository_url_B': boosts.repo_remote_repository_url_boost,
-                                                        'repo_owner_username_B': boosts.repo_owner_username_boost,
-                                                        'categories_B': boosts.categories_boost})
+                repo_weighting = RepoWeighting(
+                    field_B={
+                        "name_B": boosts.repo_name_boost,
+                        "description_B": boosts.repo_description_boost,
+                        "long_description_B": boosts.repo_long_description_boost,
+                        "homepage_url_B": boosts.repo_homepage_url_boost,
+                        "remote_repository_url_B": boosts.repo_remote_repository_url_boost,
+                        "repo_owner_username_B": boosts.repo_owner_username_boost,
+                        "categories_B": boosts.categories_boost,
+                    }
+                )
                 searcher = index.searcher(weighting=repo_weighting)
-                parser = MultifieldParser([
-                    'name',
-                    'description',
-                    'long_description',
-                    'homepage_url',
-                    'remote_repository_url',
-                    'repo_owner_username',
-                    'categories'], schema=schema)
+                parser = MultifieldParser(
+                    [
+                        "name",
+                        "description",
+                        "long_description",
+                        "homepage_url",
+                        "remote_repository_url",
+                        "repo_owner_username",
+                        "categories",
+                    ],
+                    schema=schema,
+                )
 
                 # If user query has just filters prevent wildcard search.
                 if len(search_term_without_filters) < 1:
-                    user_query = Every('name')
-                    sortedby = 'name'
+                    user_query = Every("name")
+                    sortedby = "name"
                 else:
                     user_query = parser.parse(f"*{search_term_without_filters}*")
-                    sortedby = ''
+                    sortedby = ""
                 try:
-                    hits = searcher.search_page(user_query, page, pagelen=page_size, filter=allow_query, terms=True, sortedby=sortedby)
+                    hits = searcher.search_page(
+                        user_query, page, pagelen=page_size, filter=allow_query, terms=True, sortedby=sortedby
+                    )
                     log.debug(f"total hits: {str(len(hits))}")
                     log.debug(f"scored hits: {str(hits.scored_length())}")
                 except ValueError:
-                    raise ObjectNotFound('The requested page does not exist.')
+                    raise ObjectNotFound("The requested page does not exist.")
                 results = {}
-                results['total_results'] = str(len(hits))
-                results['page'] = str(page)
-                results['page_size'] = str(page_size)
-                results['hits'] = []
+                results["total_results"] = str(len(hits))
+                results["page"] = str(page)
+                results["page_size"] = str(page_size)
+                results["hits"] = []
                 for hit in hits:
                     log.debug(f"matched terms: {str(hit.matched_terms())}")
                     hit_dict = {}
-                    hit_dict['id'] = trans.security.encode_id(hit.get('id'))
-                    hit_dict['repo_owner_username'] = hit.get('repo_owner_username')
-                    hit_dict['name'] = hit.get('name')
-                    hit_dict['long_description'] = hit.get('long_description')
-                    hit_dict['remote_repository_url'] = hit.get('remote_repository_url')
-                    hit_dict['homepage_url'] = hit.get('homepage_url')
-                    hit_dict['description'] = hit.get('description')
-                    hit_dict['last_updated'] = hit.get('last_updated')
-                    hit_dict['full_last_updated'] = hit.get('full_last_updated')
-                    hit_dict['repo_lineage'] = hit.get('repo_lineage')
-                    hit_dict['categories'] = hit.get('categories')
-                    hit_dict['approved'] = hit.get('approved')
-                    hit_dict['times_downloaded'] = hit.get('times_downloaded')
-                    results['hits'].append({'repository': hit_dict, 'score': hit.score})
+                    hit_dict["id"] = trans.security.encode_id(hit.get("id"))
+                    hit_dict["repo_owner_username"] = hit.get("repo_owner_username")
+                    hit_dict["name"] = hit.get("name")
+                    hit_dict["long_description"] = hit.get("long_description")
+                    hit_dict["remote_repository_url"] = hit.get("remote_repository_url")
+                    hit_dict["homepage_url"] = hit.get("homepage_url")
+                    hit_dict["description"] = hit.get("description")
+                    hit_dict["last_updated"] = hit.get("last_updated")
+                    hit_dict["full_last_updated"] = hit.get("full_last_updated")
+                    hit_dict["repo_lineage"] = hit.get("repo_lineage")
+                    hit_dict["categories"] = hit.get("categories")
+                    hit_dict["approved"] = hit.get("approved")
+                    hit_dict["times_downloaded"] = hit.get("times_downloaded")
+                    results["hits"].append({"repository": hit_dict, "score": hit.score})
                 return results
             finally:
                 searcher.close()
         else:
-            raise exceptions.InternalServerError('The search index file is missing.')
+            raise exceptions.InternalServerError("The search index file is missing.")
 
     def _parse_reserved_filters(self, search_term):
         """
@@ -187,5 +208,7 @@ class RepoSearch:
             "o": "repo_owner_username",
         }
         allow_query, search_term_without_filters = parse_filters(search_term, filters)
-        allow_query = And([Term(t, v) for (t, v) in allow_query] if len(allow_query) > 0 else None) if allow_query else None
+        allow_query = (
+            And([Term(t, v) for (t, v) in allow_query] if len(allow_query) > 0 else None) if allow_query else None
+        )
         return allow_query, search_term_without_filters
diff --git a/lib/tool_shed/webapp/search/tool_search.py b/lib/tool_shed/webapp/search/tool_search.py
index f325b022683..93d7676a3f1 100644
--- a/lib/tool_shed/webapp/search/tool_search.py
+++ b/lib/tool_shed/webapp/search/tool_search.py
@@ -7,7 +7,7 @@ from whoosh import scoring
 from whoosh.fields import (
     Schema,
     STORED,
-    TEXT
+    TEXT,
 )
 from whoosh.qparser import MultifieldParser
 
@@ -26,11 +26,11 @@ schema = Schema(
     version=TEXT(stored=True),
     repo_name=TEXT(stored=True),
     repo_owner_username=TEXT(stored=True),
-    repo_id=STORED)
+    repo_id=STORED,
+)
 
 
 class ToolSearch:
-
     def search(self, trans, search_term, page, page_size, boosts):
         """
         Perform the search on the given search_term
@@ -39,7 +39,7 @@ class ToolSearch:
 
         :returns results: dictionary containing number of hits, hits themselves and matched terms for each
         """
-        tool_index_dir = os.path.join(trans.app.config.whoosh_index_dir, 'tools')
+        tool_index_dir = os.path.join(trans.app.config.whoosh_index_dir, "tools")
         index_exists = whoosh.index.exists_in(tool_index_dir)
         if index_exists:
             index = whoosh.index.open_dir(tool_index_dir)
@@ -48,45 +48,44 @@ class ToolSearch:
                 # http://trec.nist.gov/pubs/trec13/papers/microsoft-cambridge.web.hard.pdf
                 # http://en.wikipedia.org/wiki/Okapi_BM25
                 # __Basically__ the higher number the bigger weight.
-                tool_weighting = scoring.BM25F(field_B={
-                                               'name_B': boosts.tool_name_boost,
-                                               'description_B': boosts.tool_description_boost,
-                                               'help_B': boosts.tool_help_boost,
-                                               'repo_owner_username_B': boosts.tool_repo_owner_username_boost})
+                tool_weighting = scoring.BM25F(
+                    field_B={
+                        "name_B": boosts.tool_name_boost,
+                        "description_B": boosts.tool_description_boost,
+                        "help_B": boosts.tool_help_boost,
+                        "repo_owner_username_B": boosts.tool_repo_owner_username_boost,
+                    }
+                )
                 searcher = index.searcher(weighting=tool_weighting)
 
-                parser = MultifieldParser([
-                    'name',
-                    'description',
-                    'help',
-                    'repo_owner_username'], schema=schema)
+                parser = MultifieldParser(["name", "description", "help", "repo_owner_username"], schema=schema)
 
                 user_query = parser.parse(f"*{search_term}*")
 
                 try:
                     hits = searcher.search_page(user_query, page, pagelen=page_size, terms=True)
                 except ValueError:
-                    raise ObjectNotFound('The requested page does not exist.')
+                    raise ObjectNotFound("The requested page does not exist.")
 
                 log.debug(f"searching tools for: #{str(search_term)}")
                 log.debug(f"total hits: {str(len(hits))}")
                 log.debug(f"scored hits: {str(hits.scored_length())}")
                 results = {}
-                results['total_results'] = str(len(hits))
-                results['page'] = str(page)
-                results['page_size'] = str(page_size)
-                results['hits'] = []
+                results["total_results"] = str(len(hits))
+                results["page"] = str(page)
+                results["page_size"] = str(page_size)
+                results["hits"] = []
                 for hit in hits:
                     hit_dict = {}
-                    hit_dict['id'] = hit.get('id')
-                    hit_dict['repo_owner_username'] = hit.get('repo_owner_username')
-                    hit_dict['repo_name'] = hit.get('repo_name')
-                    hit_dict['name'] = hit.get('name')
-                    hit_dict['description'] = hit.get('description')
+                    hit_dict["id"] = hit.get("id")
+                    hit_dict["repo_owner_username"] = hit.get("repo_owner_username")
+                    hit_dict["repo_name"] = hit.get("repo_name")
+                    hit_dict["name"] = hit.get("name")
+                    hit_dict["description"] = hit.get("description")
                     matched_terms = {k: unicodify(v) for k, v in hit.matched_terms()}
-                    results['hits'].append({'tool': hit_dict, 'matched_terms': matched_terms, 'score': hit.score})
+                    results["hits"].append({"tool": hit_dict, "matched_terms": matched_terms, "score": hit.score})
                 return results
             finally:
                 searcher.close()
         else:
-            raise exceptions.InternalServerError('The search index file is missing.')
+            raise exceptions.InternalServerError("The search index file is missing.")
diff --git a/lib/tool_shed/webapp/security/__init__.py b/lib/tool_shed/webapp/security/__init__.py
index c5ba9486aa5..bd6c12acb82 100644
--- a/lib/tool_shed/webapp/security/__init__.py
+++ b/lib/tool_shed/webapp/security/__init__.py
@@ -1,7 +1,10 @@
 """Tool Shed Security"""
 import logging
 
-from sqlalchemy import and_, false
+from sqlalchemy import (
+    and_,
+    false,
+)
 
 from galaxy.util import listify
 from galaxy.util.bunch import Bunch
@@ -10,7 +13,6 @@ log = logging.getLogger(__name__)
 
 
 class Action:
-
     def __init__(self, action, description, model):
         self.action = action
         self.description = description
@@ -19,20 +21,25 @@ class Action:
 
 class RBACAgent:
     """Handle Galaxy Tool Shed security"""
+
     permitted_actions = Bunch()
 
     def associate_components(self, **kwd):
-        raise Exception(f'No valid method of associating provided components: {kwd}')
+        raise Exception(f"No valid method of associating provided components: {kwd}")
 
     def associate_user_role(self, user, role):
-        raise Exception('No valid method of associating a user with a role')
+        raise Exception("No valid method of associating a user with a role")
 
     def convert_permitted_action_strings(self, permitted_action_strings):
         """
         When getting permitted actions from an untrusted source like a
         form, ensure that they match our actual permitted actions.
         """
-        return [x for x in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings] if x is not None]
+        return [
+            x
+            for x in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings]
+            if x is not None
+        ]
 
     def create_user_role(self, user, app):
         raise Exception("Unimplemented Method")
@@ -52,14 +59,13 @@ class RBACAgent:
         return list(self.permitted_actions.__dict__.values())
 
     def get_item_actions(self, action, item):
-        raise Exception(f'No valid method of retrieving action ({action}) for item {item}.')
+        raise Exception(f"No valid method of retrieving action ({action}) for item {item}.")
 
     def get_private_user_role(self, user):
         raise Exception("Unimplemented Method")
 
 
 class CommunityRBACAgent(RBACAgent):
-
     def __init__(self, model, permitted_actions=None):
         self.model = model
         if permitted_actions:
@@ -77,7 +83,7 @@ class CommunityRBACAgent(RBACAgent):
         """
         item_actions = self.get_item_actions(action, item)
         if not item_actions:
-            return action.model == 'restrict'
+            return action.model == "restrict"
         ret_val = False
         for item_action in item_actions:
             if item_action.role in roles:
@@ -86,17 +92,17 @@ class CommunityRBACAgent(RBACAgent):
         return ret_val
 
     def associate_components(self, **kwd):
-        if 'user' in kwd:
-            if 'group' in kwd:
-                return self.associate_user_group(kwd['user'], kwd['group'])
-            elif 'role' in kwd:
-                return self.associate_user_role(kwd['user'], kwd['role'])
-        elif 'role' in kwd:
-            if 'group' in kwd:
-                return self.associate_group_role(kwd['group'], kwd['role'])
-        elif 'repository' in kwd:
-            return self.associate_repository_category(kwd['repository'], kwd['category'])
-        raise Exception(f'No valid method of associating provided components: {kwd}')
+        if "user" in kwd:
+            if "group" in kwd:
+                return self.associate_user_group(kwd["user"], kwd["group"])
+            elif "role" in kwd:
+                return self.associate_user_role(kwd["user"], kwd["role"])
+        elif "role" in kwd:
+            if "group" in kwd:
+                return self.associate_group_role(kwd["group"], kwd["role"])
+        elif "repository" in kwd:
+            return self.associate_repository_category(kwd["repository"], kwd["category"])
+        raise Exception(f"No valid method of associating provided components: {kwd}")
 
     def associate_group_role(self, group, role):
         assoc = self.model.GroupRoleAssociation(group, role)
@@ -124,7 +130,9 @@ class CommunityRBACAgent(RBACAgent):
 
     def create_private_user_role(self, user):
         # Create private role
-        role = self.model.Role(name=user.email, description=f"Private Role for {user.email}", type=self.model.Role.types.PRIVATE)
+        role = self.model.Role(
+            name=user.email, description=f"Private Role for {user.email}", type=self.model.Role.types.PRIVATE
+        )
         self.sa_session.add(role)
         self.sa_session.flush()
         # Add user to role
@@ -139,10 +147,16 @@ class CommunityRBACAgent(RBACAgent):
         return [permission for permission in item.actions if permission.action == action.action]
 
     def get_private_user_role(self, user, auto_create=False):
-        role = self.sa_session.query(self.model.Role) \
-                              .filter(and_(self.model.Role.table.c.name == user.email,
-                                           self.model.Role.table.c.type == self.model.Role.types.PRIVATE)) \
-                              .first()
+        role = (
+            self.sa_session.query(self.model.Role)
+            .filter(
+                and_(
+                    self.model.Role.table.c.name == user.email,
+                    self.model.Role.table.c.type == self.model.Role.types.PRIVATE,
+                )
+            )
+            .first()
+        )
         if not role:
             if auto_create:
                 return self.create_private_user_role(user)
@@ -151,10 +165,16 @@ class CommunityRBACAgent(RBACAgent):
         return role
 
     def get_repository_reviewer_role(self):
-        return self.sa_session.query(self.model.Role) \
-                              .filter(and_(self.model.Role.table.c.name == 'Repository Reviewer',
-                                           self.model.Role.table.c.type == self.model.Role.types.SYSTEM)) \
-                              .first()
+        return (
+            self.sa_session.query(self.model.Role)
+            .filter(
+                and_(
+                    self.model.Role.table.c.name == "Repository Reviewer",
+                    self.model.Role.table.c.type == self.model.Role.types.SYSTEM,
+                )
+            )
+            .first()
+        )
 
     def set_entity_group_associations(self, groups=None, users=None, roles=None, delete_existing_assocs=True):
         if groups is None:
@@ -173,7 +193,9 @@ class CommunityRBACAgent(RBACAgent):
             for user in users:
                 self.associate_components(group=group, user=user)
 
-    def set_entity_role_associations(self, roles=None, users=None, groups=None, repositories=None, delete_existing_assocs=True):
+    def set_entity_role_associations(
+        self, roles=None, users=None, groups=None, repositories=None, delete_existing_assocs=True
+    ):
         if roles is None:
             roles = []
         if users is None:
@@ -245,10 +267,16 @@ class CommunityRBACAgent(RBACAgent):
         if user.username == archive_owner:
             return True
         # A member of the IUC is authorized to create new repositories that are owned by another user.
-        iuc_group = self.sa_session.query(self.model.Group) \
-                                   .filter(and_(self.model.Group.table.c.name == 'Intergalactic Utilities Commission',
-                                                self.model.Group.table.c.deleted == false())) \
-                                   .first()
+        iuc_group = (
+            self.sa_session.query(self.model.Group)
+            .filter(
+                and_(
+                    self.model.Group.table.c.name == "Intergalactic Utilities Commission",
+                    self.model.Group.table.c.deleted == false(),
+                )
+            )
+            .first()
+        )
         if iuc_group is not None:
             for uga in iuc_group.users:
                 if uga.user.id == user.id:
@@ -277,7 +305,7 @@ class CommunityRBACAgent(RBACAgent):
 
 
 def get_permitted_actions(filter=None):
-    '''Utility method to return a subset of RBACAgent's permitted actions'''
+    """Utility method to return a subset of RBACAgent's permitted actions"""
     if filter is None:
         return RBACAgent.permitted_actions
     tmp_bunch = Bunch()
diff --git a/lib/tool_shed/webapp/util/ratings_util.py b/lib/tool_shed/webapp/util/ratings_util.py
index 8a4e848bbf7..477a3e68a09 100644
--- a/lib/tool_shed/webapp/util/ratings_util.py
+++ b/lib/tool_shed/webapp/util/ratings_util.py
@@ -8,8 +8,8 @@ log = logging.getLogger(__name__)
 class ItemRatings(UsesItemRatings):
     """Overrides rate_item method since we also allow for comments"""
 
-    def rate_item(self, trans, user, item, rating, comment=''):
-        """ Rate an item. Return type is <item_class>RatingAssociation. """
+    def rate_item(self, trans, user, item, rating, comment=""):
+        """Rate an item. Return type is <item_class>RatingAssociation."""
         item_rating = self.get_user_item_rating(trans.sa_session, user, item, webapp_model=trans.model)
         if not item_rating:
             # User has not yet rated item; create rating.
diff --git a/lib/tool_shed/webapp/util/shed_statistics.py b/lib/tool_shed/webapp/util/shed_statistics.py
index aa68b573753..2b2ae9db2d2 100644
--- a/lib/tool_shed/webapp/util/shed_statistics.py
+++ b/lib/tool_shed/webapp/util/shed_statistics.py
@@ -1,5 +1,7 @@
-from time import gmtime
-from time import strftime
+from time import (
+    gmtime,
+    strftime,
+)
 
 
 class ShedCounter:
@@ -57,35 +59,35 @@ class ShedCounter:
                 # repository_metadata.downloadable column.
                 for metadata_revision in repository.metadata_revisions:
                     metadata = metadata_revision.metadata
-                    if 'tools' in metadata:
-                        tool_dicts = metadata['tools']
+                    if "tools" in metadata:
+                        tool_dicts = metadata["tools"]
                         for tool_dict in tool_dicts:
-                            if 'guid' in tool_dict:
-                                guid = tool_dict['guid']
+                            if "guid" in tool_dict:
+                                guid = tool_dict["guid"]
                                 if guid not in processed_guids:
                                     self.valid_versions_of_tools += 1
                                     processed_guids.append(guid)
-                            if 'id' in tool_dict:
-                                tool_id = tool_dict['id']
+                            if "id" in tool_dict:
+                                tool_id = tool_dict["id"]
                                 if tool_id not in processed_tool_ids:
                                     self.unique_valid_tools += 1
                                     processed_tool_ids.append(tool_id)
-                    if 'invalid_tools' in metadata:
-                        invalid_tool_configs = metadata['invalid_tools']
+                    if "invalid_tools" in metadata:
+                        invalid_tool_configs = metadata["invalid_tools"]
                         for invalid_tool_config in invalid_tool_configs:
                             if invalid_tool_config not in processed_invalid_tool_configs:
                                 self.invalid_versions_of_tools += 1
                                 processed_invalid_tool_configs.append(invalid_tool_config)
-                    if 'datatypes' in metadata:
-                        datatypes = metadata['datatypes']
+                    if "datatypes" in metadata:
+                        datatypes = metadata["datatypes"]
                         for datatypes_dict in datatypes:
-                            if 'extension' in datatypes_dict:
-                                extension = datatypes_dict['extension']
+                            if "extension" in datatypes_dict:
+                                extension = datatypes_dict["extension"]
                                 if extension not in processed_datatypes:
                                     self.custom_datatypes += 1
                                     processed_datatypes.append(extension)
-                    if 'workflows' in metadata:
-                        workflows = metadata['workflows']
+                    if "workflows" in metadata:
+                        workflows = metadata["workflows"]
                         for workflow_tup in workflows:
                             relative_path, exported_workflow_dict = workflow_tup
                             if relative_path not in processed_relative_workflow_paths:
diff --git a/packages/app/setup.py b/packages/app/setup.py
index b07f8886ee7..82a1140d56c 100644
--- a/packages/app/setup.py
+++ b/packages/app/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/auth/setup.py b/packages/auth/setup.py
index 2eafa480d0a..5c431dddbf1 100644
--- a/packages/auth/setup.py
+++ b/packages/auth/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/build_scripts/commit_version.py b/packages/build_scripts/commit_version.py
index ae5872d190b..1552384b8d6 100644
--- a/packages/build_scripts/commit_version.py
+++ b/packages/build_scripts/commit_version.py
@@ -6,7 +6,6 @@ import re
 import subprocess
 import sys
 
-
 DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
 PROJECT_DIRECTORY = os.getcwd()
 PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
diff --git a/packages/build_scripts/new_version.py b/packages/build_scripts/new_version.py
index 74f294abc3f..d61db5a1c36 100644
--- a/packages/build_scripts/new_version.py
+++ b/packages/build_scripts/new_version.py
@@ -6,7 +6,6 @@ import subprocess
 import sys
 from distutils.version import StrictVersion
 
-
 DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
 PROJECT_DIRECTORY = os.getcwd()
 PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
diff --git a/packages/containers/setup.py b/packages/containers/setup.py
index 399aae00a47..8f940b9a92d 100644
--- a/packages/containers/setup.py
+++ b/packages/containers/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/data/setup.py b/packages/data/setup.py
index 6eb9d0f66c7..461fd311076 100644
--- a/packages/data/setup.py
+++ b/packages/data/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/files/setup.py b/packages/files/setup.py
index bb48f5fec00..99e69ebd1b9 100644
--- a/packages/files/setup.py
+++ b/packages/files/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/job_execution/setup.py b/packages/job_execution/setup.py
index 313826fa094..6d2c638dc34 100644
--- a/packages/job_execution/setup.py
+++ b/packages/job_execution/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/job_metrics/setup.py b/packages/job_metrics/setup.py
index 6aaa5c24640..d86ff05db93 100644
--- a/packages/job_metrics/setup.py
+++ b/packages/job_metrics/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/meta/setup.py b/packages/meta/setup.py
index 69886c2feb5..86a022b6b5f 100644
--- a/packages/meta/setup.py
+++ b/packages/meta/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/objectstore/setup.py b/packages/objectstore/setup.py
index d7487978fbd..d14e54382a5 100644
--- a/packages/objectstore/setup.py
+++ b/packages/objectstore/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/selenium/setup.py b/packages/selenium/setup.py
index e0ce6ffb455..b9f015016a1 100644
--- a/packages/selenium/setup.py
+++ b/packages/selenium/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/test_api/setup.py b/packages/test_api/setup.py
index 05e75f2eba3..7453980a0c3 100644
--- a/packages/test_api/setup.py
+++ b/packages/test_api/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/test_base/setup.py b/packages/test_base/setup.py
index d36b39f8ea7..43423a68298 100644
--- a/packages/test_base/setup.py
+++ b/packages/test_base/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/test_driver/setup.py b/packages/test_driver/setup.py
index 097c348490c..50da11e1c29 100644
--- a/packages/test_driver/setup.py
+++ b/packages/test_driver/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/test_selenium/setup.py b/packages/test_selenium/setup.py
index ed5946425bc..11834eb8eae 100644
--- a/packages/test_selenium/setup.py
+++ b/packages/test_selenium/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py
index 4527dfbe009..b8329af7b0e 100644
--- a/packages/tool_util/setup.py
+++ b/packages/tool_util/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/util/setup.py b/packages/util/setup.py
index e5cbb7ff406..636427edb1e 100644
--- a/packages/util/setup.py
+++ b/packages/util/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/web_framework/setup.py b/packages/web_framework/setup.py
index ebcecb09ff6..3a3dd0286ec 100644
--- a/packages/web_framework/setup.py
+++ b/packages/web_framework/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/web_stack/setup.py b/packages/web_stack/setup.py
index e3020e83fb6..1d3ff9ac01b 100644
--- a/packages/web_stack/setup.py
+++ b/packages/web_stack/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/packages/webapps/setup.py b/packages/webapps/setup.py
index 2cba3c31293..ed5dbab0238 100644
--- a/packages/webapps/setup.py
+++ b/packages/webapps/setup.py
@@ -3,6 +3,7 @@
 import ast
 import os
 import re
+
 try:
     from setuptools import setup
 except ImportError:
diff --git a/scripts/api/common.py b/scripts/api/common.py
index c99cdf6f486..1a99d4af6c3 100644
--- a/scripts/api/common.py
+++ b/scripts/api/common.py
@@ -20,12 +20,12 @@ def make_url(api_key, url, args=None):
     """
     if args is None:
         args = []
-    argsep = '&'
-    if '?' not in url:
-        argsep = '?'
-    if '?key=' not in url and '&key=' not in url:
-        args.insert(0, ('key', api_key))
-    return url + argsep + '&'.join('='.join(t) for t in args)
+    argsep = "&"
+    if "?" not in url:
+        argsep = "?"
+    if "?key=" not in url and "&key=" not in url:
+        args.insert(0, ("key", api_key))
+    return url + argsep + "&".join("=".join(t) for t in args)
 
 
 def get(api_key, url):
@@ -45,7 +45,7 @@ def post(api_key, url, data):
     Do the actual POST.
     """
     url = make_url(api_key, url)
-    req = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
+    req = Request(url, headers={"Content-Type": "application/json"}, data=json.dumps(data))
     return json.loads(urlopen(req).read())
 
 
@@ -54,8 +54,8 @@ def put(api_key, url, data):
     Do the actual PUT
     """
     url = make_url(api_key, url)
-    req = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
-    req.get_method = lambda: 'PUT'
+    req = Request(url, headers={"Content-Type": "application/json"}, data=json.dumps(data))
+    req.get_method = lambda: "PUT"
     return json.loads(urlopen(req).read())
 
 
@@ -64,8 +64,8 @@ def __del(api_key, url, data):
     Do the actual DELETE
     """
     url = make_url(api_key, url)
-    req = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
-    req.get_method = lambda: 'DELETE'
+    req = Request(url, headers={"Content-Type": "application/json"}, data=json.dumps(data))
+    req.get_method = lambda: "DELETE"
     return json.loads(urlopen(req).read())
 
 
@@ -83,36 +83,36 @@ def display(api_key, url, return_formatted=True):
         return r
     elif type(r) == list:
         # Response is a collection as defined in the REST style.
-        print('Collection Members')
-        print('------------------')
+        print("Collection Members")
+        print("------------------")
         for n, i in enumerate(r):
             if isinstance(i, str):
-                print('  %s' % i)
+                print("  %s" % i)
             else:
                 # All collection members should have a name in the response.
                 # url is optional
-                if 'url' in i:
-                    print('#%d: %s' % (n + 1, i.pop('url')))
-                if 'name' in i:
-                    print('  name: %s' % i.pop('name'))
+                if "url" in i:
+                    print("#%d: %s" % (n + 1, i.pop("url")))
+                if "name" in i:
+                    print("  name: %s" % i.pop("name"))
                 try:
                     for k, v in i.items():
-                        print(f'  {k}: {v}')
+                        print(f"  {k}: {v}")
                 except AttributeError:
                     for item in i:
                         print(item)
-        print('')
-        print('%d element(s) in collection' % len(r))
+        print("")
+        print("%d element(s) in collection" % len(r))
     elif type(r) == dict:
         # Response is an element as defined in the REST style.
-        print('Member Information')
-        print('------------------')
+        print("Member Information")
+        print("------------------")
         for k, v in r.items():
-            print(f'{k}: {v}')
+            print(f"{k}: {v}")
     elif type(r) == str:
         print(r)
     else:
-        print('response is unknown type: %s' % type(r))
+        print("response is unknown type: %s" % type(r))
 
 
 def submit(api_key, url, data, return_formatted=True):
@@ -128,24 +128,24 @@ def submit(api_key, url, data, return_formatted=True):
             print(e.read(1024))
             sys.exit(1)
         else:
-            return 'Error. ' + str(e.read(1024))
+            return "Error. " + str(e.read(1024))
     if not return_formatted:
         return r
-    print('Response')
-    print('--------')
+    print("Response")
+    print("--------")
     if type(r) == list:
         # Currently the only implemented responses are lists of dicts, because
         # submission creates some number of collection elements.
         for i in r:
             if type(i) == dict:
-                if 'url' in i:
-                    print(i.pop('url'))
+                if "url" in i:
+                    print(i.pop("url"))
                 else:
-                    print('----')
-                if 'name' in i:
-                    print('  name: %s' % i.pop('name'))
+                    print("----")
+                if "name" in i:
+                    print("  name: %s" % i.pop("name"))
                 for k, v in i.items():
-                    print(f'  {k}: {v}')
+                    print(f"  {k}: {v}")
             else:
                 print(i)
     else:
@@ -165,11 +165,11 @@ def update(api_key, url, data, return_formatted=True):
             print(e.read(1024))
             sys.exit(1)
         else:
-            return 'Error. ' + str(e.read(1024))
+            return "Error. " + str(e.read(1024))
     if not return_formatted:
         return r
-    print('Response')
-    print('--------')
+    print("Response")
+    print("--------")
     print(r)
 
 
@@ -186,9 +186,9 @@ def delete(api_key, url, data, return_formatted=True):
             print(e.read(1024))
             sys.exit(1)
         else:
-            return 'Error. ' + str(e.read(1024))
+            return "Error. " + str(e.read(1024))
     if not return_formatted:
         return r
-    print('Response')
-    print('--------')
+    print("Response")
+    print("--------")
     print(r)
diff --git a/scripts/api/copy_hda_to_library_folder.py b/scripts/api/copy_hda_to_library_folder.py
index 722e078f2f2..e997c330e6f 100755
--- a/scripts/api/copy_hda_to_library_folder.py
+++ b/scripts/api/copy_hda_to_library_folder.py
@@ -7,12 +7,12 @@ from common import submit
 usage = "USAGE: copy_hda_to_library_folder.py <base url> <api key> <hda id> <library id> <folder id> [ message ]"
 
 
-def copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, message=''):
-    url = f'http://{base_url}/api/libraries/{library_id}/contents'
+def copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, message=""):
+    url = f"http://{base_url}/api/libraries/{library_id}/contents"
     payload = {
-        'folder_id': folder_id,
-        'create_type': 'file',
-        'from_hda_id': hda_id,
+        "folder_id": folder_id,
+        "create_type": "file",
+        "from_hda_id": hda_id,
     }
     if message:
         payload.update(dict(ldda_message=message))
@@ -20,7 +20,7 @@ def copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, mes
     return submit(key, url, payload)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     num_args = len(sys.argv)
     if num_args < 6:
         print(usage, file=sys.stderr)
@@ -28,7 +28,7 @@ if __name__ == '__main__':
 
     (base_url, key, hda_id, library_id, folder_id) = sys.argv[1:6]
 
-    message = ''
+    message = ""
     if num_args >= 7:
         message = sys.argv[6]
 
diff --git a/scripts/api/create.py b/scripts/api/create.py
index 685aa7feea5..378d3cb52fa 100644
--- a/scripts/api/create.py
+++ b/scripts/api/create.py
@@ -9,7 +9,7 @@ import sys
 from common import submit
 
 data = {}
-for k, v in [kwarg.split('=', 1) for kwarg in sys.argv[3:]]:
+for k, v in [kwarg.split("=", 1) for kwarg in sys.argv[3:]]:
     data[k] = v
 
 submit(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/data_manager_example_execute.py b/scripts/api/data_manager_example_execute.py
index 02c62604716..5e7e7dc2884 100644
--- a/scripts/api/data_manager_example_execute.py
+++ b/scripts/api/data_manager_example_execute.py
@@ -8,30 +8,35 @@ import optparse
 import time
 from urllib.parse import urljoin
 
-from common import get, post  # noqa: I100,I202
+from common import (  # noqa: I100,I202
+    get,
+    post,
+)
 
 DEFAULT_SLEEP_TIME = 3
-FETCH_GENOME_TOOL_ID = 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1'
-BUILD_INDEX_TOOLS_ID = ['testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_index_builder_data_manager/0.0.1',
-                        'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_color_space_index_builder_data_manager/0.0.1']
+FETCH_GENOME_TOOL_ID = "testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1"
+BUILD_INDEX_TOOLS_ID = [
+    "testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_index_builder_data_manager/0.0.1",
+    "testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder/bwa_color_space_index_builder_data_manager/0.0.1",
+]
 
 
 def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_time=None, **kwargs):
     sleep_time = sleep_time or DEFAULT_SLEEP_TIME
-    tools_url = urljoin(galaxy_url, 'api/tools')
+    tools_url = urljoin(galaxy_url, "api/tools")
     payload = {
-        'tool_id': tool_id,
+        "tool_id": tool_id,
     }
     if history_id:
-        payload['history_id'] = history_id
-    payload['inputs'] = params
+        payload["history_id"] = history_id
+    payload["inputs"] = params
     rval = post(api_key, tools_url, payload)
     if wait:
-        outputs = list(rval['outputs'])
+        outputs = list(rval["outputs"])
         while outputs:
             finished_datasets = []
             for i, dataset_dict in enumerate(outputs):
-                if dataset_is_terminal(dataset_dict['id'], api_key=api_key, galaxy_url=galaxy_url):
+                if dataset_is_terminal(dataset_dict["id"], api_key=api_key, galaxy_url=galaxy_url):
                     finished_datasets.append(i)
             for _ in reversed(finished_datasets):
                 outputs.pop(0)
@@ -42,64 +47,105 @@ def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_
 
 
 def get_dataset_state(hda_id, api_key, galaxy_url):
-    datasets_url = urljoin(galaxy_url, 'api/datasets/%s' % hda_id)
+    datasets_url = urljoin(galaxy_url, "api/datasets/%s" % hda_id)
     dataset_info = get(api_key, datasets_url)
-    return dataset_info['state']
+    return dataset_info["state"]
 
 
 def dataset_is_terminal(hda_id, api_key, galaxy_url):
     dataset_state = get_dataset_state(hda_id, api_key, galaxy_url)
-    return dataset_state in ['ok', 'error']
+    return dataset_state in ["ok", "error"]
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = optparse.OptionParser()
-    parser.add_option('-k', '--key', dest='api_key', action='store', type="string", default=None, help='API Key.')
-    parser.add_option('-u', '--url', dest='base_url', action='store', type="string", default='http://localhost:8080', help='Base URL of Galaxy Server')
-    parser.add_option('-d', '--dbkey', dest='dbkeys', action='append', type="string", default=[], help='List of dbkeys to download and Index')
-    parser.add_option('-s', '--sleep_time', dest='sleep_time', action='store', type="int", default=DEFAULT_SLEEP_TIME, help='How long to sleep between check loops')
+    parser.add_option("-k", "--key", dest="api_key", action="store", type="string", default=None, help="API Key.")
+    parser.add_option(
+        "-u",
+        "--url",
+        dest="base_url",
+        action="store",
+        type="string",
+        default="http://localhost:8080",
+        help="Base URL of Galaxy Server",
+    )
+    parser.add_option(
+        "-d",
+        "--dbkey",
+        dest="dbkeys",
+        action="append",
+        type="string",
+        default=[],
+        help="List of dbkeys to download and Index",
+    )
+    parser.add_option(
+        "-s",
+        "--sleep_time",
+        dest="sleep_time",
+        action="store",
+        type="int",
+        default=DEFAULT_SLEEP_TIME,
+        help="How long to sleep between check loops",
+    )
     (options, args) = parser.parse_args()
 
     # check options
-    assert options.api_key is not None, ValueError('You must specify an API key.')
-    assert options.dbkeys, ValueError('You must specify at least one dbkey to use.')
+    assert options.api_key is not None, ValueError("You must specify an API key.")
+    assert options.dbkeys, ValueError("You must specify at least one dbkey to use.")
 
     # check user is admin
-    configuration_options = get(options.api_key, urljoin(options.base_url, 'api/configuration'))
-    if 'library_import_dir' not in configuration_options:  # hack to check if is admin user
-        print("Warning: Data Managers are only available to admin users. The API Key provided does not appear to belong to an admin user. Will attempt to run anyway.")
+    configuration_options = get(options.api_key, urljoin(options.base_url, "api/configuration"))
+    if "library_import_dir" not in configuration_options:  # hack to check if is admin user
+        print(
+            "Warning: Data Managers are only available to admin users. The API Key provided does not appear to belong to an admin user. Will attempt to run anyway."
+        )
 
     # Fetch Genomes
     dbkeys = {}
     for dbkey in options.dbkeys:
         if dbkey not in dbkeys:
-            dbkeys[dbkey] = run_tool(FETCH_GENOME_TOOL_ID, None, {'dbkey': dbkey, 'reference_source|reference_source_selector': 'ucsc', 'reference_source|requested_dbkey': dbkey}, options.api_key, options.base_url, wait=False)
+            dbkeys[dbkey] = run_tool(
+                FETCH_GENOME_TOOL_ID,
+                None,
+                {
+                    "dbkey": dbkey,
+                    "reference_source|reference_source_selector": "ucsc",
+                    "reference_source|requested_dbkey": dbkey,
+                },
+                options.api_key,
+                options.base_url,
+                wait=False,
+            )
         else:
             "dbkey (%s) was specified more than once, skipping additional specification." % (dbkey)
 
-    print('Genomes Queued for downloading.')
+    print("Genomes Queued for downloading.")
 
     # Start indexers
     indexing_tools = []
     while dbkeys:
         for dbkey, value in dbkeys.items():
-            if dataset_is_terminal(value['outputs'][0]['id'], options.api_key, options.base_url):
+            if dataset_is_terminal(value["outputs"][0]["id"], options.api_key, options.base_url):
                 del dbkeys[dbkey]
                 for tool_id in BUILD_INDEX_TOOLS_ID:
-                    indexing_tools.append(run_tool(tool_id, None, {'all_fasta_source': dbkey}, options.api_key, options.base_url, wait=False))
+                    indexing_tools.append(
+                        run_tool(
+                            tool_id, None, {"all_fasta_source": dbkey}, options.api_key, options.base_url, wait=False
+                        )
+                    )
         if dbkeys:
             time.sleep(options.sleep_time)
 
-    print('All genomes downloaded and indexers now queued.')
+    print("All genomes downloaded and indexers now queued.")
 
     # Wait for indexers to finish
     while indexing_tools:
         for i, indexing_tool_value in enumerate(indexing_tools):
-            if dataset_is_terminal(indexing_tool_value['outputs'][0]['id'], options.api_key, options.base_url):
-                print('Finished:', indexing_tool_value)
+            if dataset_is_terminal(indexing_tool_value["outputs"][0]["id"], options.api_key, options.base_url):
+                print("Finished:", indexing_tool_value)
                 del indexing_tools[i]
                 break
         if indexing_tools:
             time.sleep(options.sleep_time)
 
-    print('All indexers have been run, please check results.')
+    print("All indexers have been run, please check results.")
diff --git a/scripts/api/delete.py b/scripts/api/delete.py
index 6467befd535..5780f3f723d 100644
--- a/scripts/api/delete.py
+++ b/scripts/api/delete.py
@@ -9,7 +9,7 @@ import sys
 from common import delete
 
 data = {}
-for k, v in [kwarg.split('=', 1) for kwarg in sys.argv[3:]]:
+for k, v in [kwarg.split("=", 1) for kwarg in sys.argv[3:]]:
     data[k] = v
 
 delete(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/display.py b/scripts/api/display.py
index 25aad53d0c6..d46266c2a9c 100755
--- a/scripts/api/display.py
+++ b/scripts/api/display.py
@@ -9,7 +9,7 @@ from common import display  # noqa: I100,I202
 try:
     display(*sys.argv[1:3])
 except TypeError as e:
-    print('usage: %s key url' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url" % os.path.basename(sys.argv[0]))
     print(e)
     sys.exit(1)
 except URLError as e:
diff --git a/scripts/api/example_watch_folder.py b/scripts/api/example_watch_folder.py
index 152443aae82..dd11c594022 100755
--- a/scripts/api/example_watch_folder.py
+++ b/scripts/api/example_watch_folder.py
@@ -16,25 +16,28 @@ import shutil
 import sys
 import time
 
-from common import display, submit
+from common import (
+    display,
+    submit,
+)
 
 
 def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
     # Find/Create data library with the above name.  Assume we're putting datasets in the root folder '/'
-    libs = display(api_key, api_url + 'libraries', return_formatted=False)
+    libs = display(api_key, api_url + "libraries", return_formatted=False)
     library_id = None
     for library in libs:
-        if library['name'] == data_library:
-            library_id = library['id']
+        if library["name"] == data_library:
+            library_id = library["id"]
     if not library_id:
-        lib_create_data = {'name': data_library}
-        library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False)
-        library_id = library[0]['id']
+        lib_create_data = {"name": data_library}
+        library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
+        library_id = library[0]["id"]
     folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
     for f in folders:
-        if f['name'] == "/":
-            library_folder_id = f['id']
-    workflow = display(api_key, api_url + 'workflows/%s' % workflow, return_formatted=False)
+        if f["name"] == "/":
+            library_folder_id = f["id"]
+    workflow = display(api_key, api_url + "workflows/%s" % workflow, return_formatted=False)
     if not workflow:
         print("Workflow %s not found, terminating.")
         sys.exit(1)
@@ -48,27 +51,27 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
             fullpath = os.path.join(in_folder, fname)
             if os.path.isfile(fullpath):
                 data = {}
-                data['folder_id'] = library_folder_id
-                data['file_type'] = 'auto'
-                data['dbkey'] = ''
-                data['upload_option'] = 'upload_paths'
-                data['filesystem_paths'] = fullpath
-                data['create_type'] = 'file'
+                data["folder_id"] = library_folder_id
+                data["file_type"] = "auto"
+                data["dbkey"] = ""
+                data["upload_option"] = "upload_paths"
+                data["filesystem_paths"] = fullpath
+                data["create_type"] = "file"
                 libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=False)
                 # TODO Handle this better, but the datatype isn't always
                 # set for the followup workflow execution without this
                 # pause.
                 time.sleep(5)
                 for ds in libset:
-                    if 'id' in ds:
+                    if "id" in ds:
                         # Successful upload of dataset, we have the ldda now.  Run the workflow.
                         wf_data = {}
-                        wf_data['workflow_id'] = workflow['id']
-                        wf_data['history'] = "{} - {}".format(fname, workflow['name'])
-                        wf_data['ds_map'] = {}
-                        for step_id in workflow['inputs'].keys():
-                            wf_data['ds_map'][step_id] = {'src': 'ld', 'id': ds['id']}
-                        res = submit(api_key, api_url + 'workflows', wf_data, return_formatted=False)
+                        wf_data["workflow_id"] = workflow["id"]
+                        wf_data["history"] = "{} - {}".format(fname, workflow["name"])
+                        wf_data["ds_map"] = {}
+                        for step_id in workflow["inputs"].keys():
+                            wf_data["ds_map"][step_id] = {"src": "ld", "id": ds["id"]}
+                        res = submit(api_key, api_url + "workflows", wf_data, return_formatted=False)
                         if res:
                             print(res)
                             # Successful workflow execution, safe to move dataset.
@@ -76,7 +79,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
         time.sleep(10)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     try:
         api_key = sys.argv[1]
         api_url = sys.argv[2]
@@ -85,6 +88,6 @@ if __name__ == '__main__':
         data_library = sys.argv[5]
         workflow = sys.argv[6]
     except IndexError:
-        print('usage: %s key url in_folder out_folder data_library workflow' % os.path.basename(sys.argv[0]))
+        print("usage: %s key url in_folder out_folder data_library workflow" % os.path.basename(sys.argv[0]))
         sys.exit(1)
     main(api_key, api_url, in_folder, out_folder, data_library, workflow)
diff --git a/scripts/api/fetch_to_library.py b/scripts/api/fetch_to_library.py
index 678d56425e7..c291762edfa 100644
--- a/scripts/api/fetch_to_library.py
+++ b/scripts/api/fetch_to_library.py
@@ -6,28 +6,23 @@ import yaml
 
 
 def main():
-    parser = argparse.ArgumentParser(description='Upload a directory into a data library')
+    parser = argparse.ArgumentParser(description="Upload a directory into a data library")
     parser.add_argument("-u", "--url", dest="url", required=True, help="Galaxy URL")
     parser.add_argument("-a", "--api", dest="api_key", required=True, help="API Key")
-    parser.add_argument('target', metavar='FILE', type=str,
-                        help='file describing data library to fetch')
+    parser.add_argument("target", metavar="FILE", type=str, help="file describing data library to fetch")
     args = parser.parse_args()
     with open(args.target) as f:
         target = yaml.safe_load(f)
 
     histories_url = args.url + "/api/histories"
-    new_history_response = requests.post(histories_url, data={'key': args.api_key})
+    new_history_response = requests.post(histories_url, data={"key": args.api_key})
 
-    fetch_url = args.url + '/api/tools/fetch'
-    payload = {
-        'key': args.api_key,
-        'targets': json.dumps([target]),
-        'history_id': new_history_response.json()["id"]
-    }
+    fetch_url = args.url + "/api/tools/fetch"
+    payload = {"key": args.api_key, "targets": json.dumps([target]), "history_id": new_history_response.json()["id"]}
 
     response = requests.post(fetch_url, data=payload)
     print(response.content)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/scripts/api/filter_failed_datasets_from_collection.py b/scripts/api/filter_failed_datasets_from_collection.py
index 9eaa913506c..659e7fc6c2d 100644
--- a/scripts/api/filter_failed_datasets_from_collection.py
+++ b/scripts/api/filter_failed_datasets_from_collection.py
@@ -9,13 +9,14 @@ python filter_failed_datasets_from_collection.py <GalaxyUrl> <ApiKey> MySpecialH
 
 import sys
 
-from bioblend.galaxy import (
-    dataset_collections as collections,
-    GalaxyInstance
-)
+from bioblend.galaxy import dataset_collections as collections
+from bioblend.galaxy import GalaxyInstance
 
 if len(sys.argv) < 5:
-    print("Usage: %s <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>" % sys.argv[0])
+    print(
+        "Usage: %s <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
+        % sys.argv[0]
+    )
     exit(0)
 
 galaxyUrl = sys.argv[1]
@@ -26,13 +27,13 @@ collectionHistoryId = int(sys.argv[4])
 gi = GalaxyInstance(url=galaxyUrl, key=galaxyApiKey)
 
 historyMatches = gi.histories.get_histories(name=historyName)
-if (len(historyMatches) > 1):
+if len(historyMatches) > 1:
     print("Error: more than one history matches that name.")
     exit(1)
 
-historyId = historyMatches[0]['id']
+historyId = historyMatches[0]["id"]
 historyContents = gi.histories.show_history(historyId, contents=True, deleted=False, visible=True, details=False)
-matchingCollections = [x for x in historyContents if x['hid'] == collectionHistoryId]
+matchingCollections = [x for x in historyContents if x["hid"] == collectionHistoryId]
 
 if len(matchingCollections) == 0:
     print("Error: no collections matching that id found.")
@@ -42,21 +43,27 @@ if len(matchingCollections) > 1:
     print("Error: more than one collection matching that id found (WTF?)")
     exit(1)
 
-collectionId = matchingCollections[0]['id']
+collectionId = matchingCollections[0]["id"]
 failedCollection = gi.histories.show_dataset_collection(historyId, collectionId)
-okDatasets = [d for d in failedCollection['elements'] if d['object']['state'] == 'ok' and d['object']['file_size'] > 0]
-notOkDatasets = [d for d in failedCollection['elements'] if d['object']['state'] != 'ok' or d['object']['file_size'] == 0]
-okCollectionName = failedCollection['name'] + " (ok)"
-notOkCollectionName = failedCollection['name'] + " (not ok)"
+okDatasets = [d for d in failedCollection["elements"] if d["object"]["state"] == "ok" and d["object"]["file_size"] > 0]
+notOkDatasets = [
+    d for d in failedCollection["elements"] if d["object"]["state"] != "ok" or d["object"]["file_size"] == 0
+]
+okCollectionName = failedCollection["name"] + " (ok)"
+notOkCollectionName = failedCollection["name"] + " (not ok)"
 
 gi.histories.create_dataset_collection(
     history_id=historyId,
     collection_description=collections.CollectionDescription(
         name=okCollectionName,
-        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in okDatasets]))
+        elements=[collections.HistoryDatasetElement(d["object"]["name"], d["object"]["id"]) for d in okDatasets],
+    ),
+)
 
 gi.histories.create_dataset_collection(
     history_id=historyId,
     collection_description=collections.CollectionDescription(
         name=notOkCollectionName,
-        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in notOkDatasets]))
+        elements=[collections.HistoryDatasetElement(d["object"]["name"], d["object"]["id"]) for d in notOkDatasets],
+    ),
+)
diff --git a/scripts/api/history_create_history.py b/scripts/api/history_create_history.py
index 4f8b0dac1f4..210311324e6 100644
--- a/scripts/api/history_create_history.py
+++ b/scripts/api/history_create_history.py
@@ -8,11 +8,11 @@ from common import submit
 try:
     assert sys.argv[2]
 except IndexError:
-    print('usage: %s key url [name] ' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
     sys.exit(1)
 try:
     data = {}
-    data['name'] = sys.argv[3]
+    data["name"] = sys.argv[3]
 except IndexError:
     pass
 
diff --git a/scripts/api/history_delete_history.py b/scripts/api/history_delete_history.py
index b460a38e613..2c48d5a4533 100644
--- a/scripts/api/history_delete_history.py
+++ b/scripts/api/history_delete_history.py
@@ -8,11 +8,11 @@ from common import delete
 try:
     assert sys.argv[2]
 except IndexError:
-    print('usage: %s key url [purge (true/false)] ' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
     sys.exit(1)
 try:
     data = {}
-    data['purge'] = sys.argv[3]
+    data["purge"] = sys.argv[3]
 except IndexError:
     pass
 
diff --git a/scripts/api/import_library_dataset_to_history.py b/scripts/api/import_library_dataset_to_history.py
index 9cefea965de..75d0e8a9095 100644
--- a/scripts/api/import_library_dataset_to_history.py
+++ b/scripts/api/import_library_dataset_to_history.py
@@ -8,10 +8,10 @@ from common import submit
 try:
     assert sys.argv[3]
     data = {}
-    data['from_ld_id'] = sys.argv[3]
+    data["from_ld_id"] = sys.argv[3]
 except IndexError:
-    print('usage: %s key url library_file_id' % os.path.basename(sys.argv[0]))
-    print('    library_file_id is from /api/libraries/<library_id>/contents/<library_file_id>')
+    print("usage: %s key url library_file_id" % os.path.basename(sys.argv[0]))
+    print("    library_file_id is from /api/libraries/<library_id>/contents/<library_file_id>")
     sys.exit(1)
 
 submit(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/import_workflows_from_installed_tool_shed_repository.py b/scripts/api/import_workflows_from_installed_tool_shed_repository.py
index 418cfc4ce32..f78e6e684ef 100644
--- a/scripts/api/import_workflows_from_installed_tool_shed_repository.py
+++ b/scripts/api/import_workflows_from_installed_tool_shed_repository.py
@@ -8,36 +8,46 @@ python ./import_workflows_from_installed_tool_shed_repository.py -a 22be3b -l ht
 
 import argparse
 
-from common import display, submit
+from common import (
+    display,
+    submit,
+)
 
 
 def clean_url(url):
-    if url.find('//') > 0:
+    if url.find("//") > 0:
         # We have an url that includes a protocol, something like: http://localhost:9009
-        items = url.split('//')
-        return items[1].rstrip('/')
-    return url.rstrip('/')
+        items = url.split("//")
+        return items[1].rstrip("/")
+    return url.rstrip("/")
 
 
 def main(options):
     api_key = options.api
-    base_galaxy_url = options.local_url.rstrip('/')
-    base_tool_shed_url = options.tool_shed_url.rstrip('/')
+    base_galaxy_url = options.local_url.rstrip("/")
+    base_tool_shed_url = options.tool_shed_url.rstrip("/")
     cleaned_tool_shed_url = clean_url(base_tool_shed_url)
-    installed_tool_shed_repositories_url = '%s/api/tool_shed_repositories' % base_galaxy_url
+    installed_tool_shed_repositories_url = "%s/api/tool_shed_repositories" % base_galaxy_url
     tool_shed_repository_id = None
     installed_tool_shed_repositories = display(api_key, installed_tool_shed_repositories_url, return_formatted=False)
     for installed_tool_shed_repository in installed_tool_shed_repositories:
-        tool_shed = str(installed_tool_shed_repository['tool_shed'])
-        name = str(installed_tool_shed_repository['name'])
-        owner = str(installed_tool_shed_repository['owner'])
-        changeset_revision = str(installed_tool_shed_repository['changeset_revision'])
-        if tool_shed == cleaned_tool_shed_url and name == options.name and owner == options.owner and changeset_revision == options.changeset_revision:
-            tool_shed_repository_id = installed_tool_shed_repository['id']
+        tool_shed = str(installed_tool_shed_repository["tool_shed"])
+        name = str(installed_tool_shed_repository["name"])
+        owner = str(installed_tool_shed_repository["owner"])
+        changeset_revision = str(installed_tool_shed_repository["changeset_revision"])
+        if (
+            tool_shed == cleaned_tool_shed_url
+            and name == options.name
+            and owner == options.owner
+            and changeset_revision == options.changeset_revision
+        ):
+            tool_shed_repository_id = installed_tool_shed_repository["id"]
             break
     if tool_shed_repository_id:
         # Get the list of exported workflows contained in the installed repository.
-        url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/exported_workflows' % str(tool_shed_repository_id))
+        url = "{}{}".format(
+            base_galaxy_url, "/api/tool_shed_repositories/%s/exported_workflows" % str(tool_shed_repository_id)
+        )
         exported_workflows = display(api_key, url, return_formatted=False)
         if exported_workflows:
             # Import all of the workflows in the list of exported workflows.
@@ -46,14 +56,18 @@ def main(options):
             # data[ 'index' ] = 0
             # and change the url to be ~/import_workflow (singular).  For example,
             # url = '%s%s' % ( base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflow' % str( tool_shed_repository_id ) )
-            url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/import_workflows' % str(tool_shed_repository_id))
+            url = "{}{}".format(
+                base_galaxy_url, "/api/tool_shed_repositories/%s/import_workflows" % str(tool_shed_repository_id)
+            )
             submit(options.api, url, data)
     else:
         print("Invalid tool_shed / name / owner / changeset_revision.")
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Import workflows contained in an installed tool shed repository via the Galaxy API.')
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Import workflows contained in an installed tool shed repository via the Galaxy API."
+    )
     parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
     parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
     parser.add_argument("-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance.")
diff --git a/scripts/api/install_tool_shed_repositories.py b/scripts/api/install_tool_shed_repositories.py
index 08538c6180d..672181e42f0 100644
--- a/scripts/api/install_tool_shed_repositories.py
+++ b/scripts/api/install_tool_shed_repositories.py
@@ -24,45 +24,68 @@ from common import submit
 def main(options):
     """Collect all user data and install the tools via the Galaxy API."""
     data = {}
-    data['tool_shed_url'] = options.tool_shed_url
-    data['name'] = options.name
-    data['owner'] = options.owner
+    data["tool_shed_url"] = options.tool_shed_url
+    data["name"] = options.name
+    data["owner"] = options.owner
     if options.changeset_revision:
-        data['changeset_revision'] = options.changeset_revision
+        data["changeset_revision"] = options.changeset_revision
     else:
         # If the changeset_revision is not specified, default to the latest installable revision.
         revision_data = {}
-        revision_data['tool_shed_url'] = options.tool_shed_url.rstrip('/')
-        revision_data['name'] = options.name
-        revision_data['owner'] = options.owner
-        revision_url = '{}{}'.format(options.local_url.rstrip('/'), '/api/tool_shed_repositories/get_latest_installable_revision')
-        latest_installable_revision = submit(options.api,
-                                             revision_url,
-                                             revision_data,
-                                             return_formatted=False)
-        data['changeset_revision'] = latest_installable_revision
+        revision_data["tool_shed_url"] = options.tool_shed_url.rstrip("/")
+        revision_data["name"] = options.name
+        revision_data["owner"] = options.owner
+        revision_url = "{}{}".format(
+            options.local_url.rstrip("/"), "/api/tool_shed_repositories/get_latest_installable_revision"
+        )
+        latest_installable_revision = submit(options.api, revision_url, revision_data, return_formatted=False)
+        data["changeset_revision"] = latest_installable_revision
     if options.tool_panel_section_id:
-        data['tool_panel_section_id'] = options.tool_panel_section_id
+        data["tool_panel_section_id"] = options.tool_panel_section_id
     elif options.new_tool_panel_section_label:
-        data['new_tool_panel_section_label'] = options.new_tool_panel_section_label
+        data["new_tool_panel_section_label"] = options.new_tool_panel_section_label
     if options.install_repository_dependencies:
-        data['install_repository_dependencies'] = options.install_repository_dependencies
+        data["install_repository_dependencies"] = options.install_repository_dependencies
     if options.install_tool_dependencies:
-        data['install_tool_dependencies'] = options.install_tool_dependencies
-    submit(options.api, '{}{}'.format(options.local_url.rstrip('/'), '/api/tool_shed_repositories/new/install_repository_revision'), data)
+        data["install_tool_dependencies"] = options.install_tool_dependencies
+    submit(
+        options.api,
+        "{}{}".format(options.local_url.rstrip("/"), "/api/tool_shed_repositories/new/install_repository_revision"),
+        data,
+    )
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Installation of tool shed repositories via the Galaxy API.')
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Installation of tool shed repositories via the Galaxy API.")
     parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
     parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
     parser.add_argument("-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance.")
     parser.add_argument("-n", "--name", required=True, help="Repository name.")
     parser.add_argument("-o", "--owner", required=True, help="Repository owner.")
     parser.add_argument("-r", "--revision", dest="changeset_revision", help="Repository revision.")
-    parser.add_argument("--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section.")
-    parser.add_argument("--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created.")
-    parser.add_argument("--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]")
-    parser.add_argument("--tool-deps", dest="install_tool_dependencies", action="store_true", default=False, help="Install tool dependencies. [False]")
+    parser.add_argument(
+        "--panel-section-id",
+        dest="tool_panel_section_id",
+        help="Tool panel section id if you want to add your repository to an existing tool section.",
+    )
+    parser.add_argument(
+        "--panel-section-name",
+        dest="new_tool_panel_section_label",
+        help="New tool panel section label. If specified a new tool section will be created.",
+    )
+    parser.add_argument(
+        "--repository-deps",
+        dest="install_repository_dependencies",
+        action="store_true",
+        default=False,
+        help="Install repository dependencies. [False]",
+    )
+    parser.add_argument(
+        "--tool-deps",
+        dest="install_tool_dependencies",
+        action="store_true",
+        default=False,
+        help="Install tool dependencies. [False]",
+    )
     options = parser.parse_args()
     main(options)
diff --git a/scripts/api/library_create_folder.py b/scripts/api/library_create_folder.py
index c356453ff48..8df85a5f46d 100755
--- a/scripts/api/library_create_folder.py
+++ b/scripts/api/library_create_folder.py
@@ -7,16 +7,16 @@ from common import submit
 
 try:
     data = {}
-    data['folder_id'] = sys.argv[3]
-    data['name'] = sys.argv[4]
-    data['create_type'] = 'folder'
+    data["folder_id"] = sys.argv[3]
+    data["name"] = sys.argv[4]
+    data["create_type"] = "folder"
 except IndexError:
-    print('usage: %s key url folder_id name [description]' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url folder_id name [description]" % os.path.basename(sys.argv[0]))
     sys.exit(1)
 try:
-    data['description'] = sys.argv[5]
+    data["description"] = sys.argv[5]
 except IndexError:
     print("Unable to set description; using empty description in its place")
-    data['description'] = ''
+    data["description"] = ""
 
 submit(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/library_create_library.py b/scripts/api/library_create_library.py
index 01f28ea1ffd..b9485c2b155 100755
--- a/scripts/api/library_create_library.py
+++ b/scripts/api/library_create_library.py
@@ -7,13 +7,13 @@ from common import submit
 
 try:
     data = {}
-    data['name'] = sys.argv[3]
+    data["name"] = sys.argv[3]
 except IndexError:
-    print('usage: %s key url name [description] [synopsys]' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url name [description] [synopsys]" % os.path.basename(sys.argv[0]))
     sys.exit(1)
 try:
-    data['description'] = sys.argv[4]
-    data['synopsis'] = sys.argv[5]
+    data["description"] = sys.argv[4]
+    data["synopsis"] = sys.argv[5]
 except IndexError:
     pass
 
diff --git a/scripts/api/library_upload_dir.py b/scripts/api/library_upload_dir.py
index 6862b57118b..9a5f89ca78b 100644
--- a/scripts/api/library_upload_dir.py
+++ b/scripts/api/library_upload_dir.py
@@ -8,9 +8,7 @@ from bioblend import galaxy
 
 
 class Uploader:
-
-    def __init__(self, url, api, library_id, folder_id, should_link,
-                 non_local):
+    def __init__(self, url, api, library_id, folder_id, should_link, non_local):
         self.gi = galaxy.GalaxyInstance(url=url, key=api)
         self.library_id = library_id
         self.folder_id = folder_id
@@ -35,22 +33,21 @@ class Uploader:
         """
         existing = self.gi.libraries.show_library(self.library_id, contents=True)
 
-        uploading_to = [x for x in existing if x['id'] == self.folder_id]
+        uploading_to = [x for x in existing if x["id"] == self.folder_id]
         if len(uploading_to) == 0:
-            raise Exception("Unknown folder [%s] in library [%s]" %
-                            (self.folder_id, self.library_id))
+            raise Exception("Unknown folder [%s] in library [%s]" % (self.folder_id, self.library_id))
         else:
             uploading_to = uploading_to[0]
 
         for x in existing:
             # We only care if it's a subdirectory of where we're uploading to
-            if not x['name'].startswith(uploading_to['name']):
+            if not x["name"].startswith(uploading_to["name"]):
                 continue
 
-            name_part = x['name'].split(uploading_to['name'], 1)[-1]
-            if name_part.startswith('/'):
+            name_part = x["name"].split(uploading_to["name"], 1)[-1]
+            if name_part.startswith("/"):
                 name_part = name_part[1:]
-            self.memo_path[name_part] = x['id']
+            self.memo_path[name_part] = x["id"]
 
     def memoized_path(self, path_parts, base_folder=None):
         """Get the folder ID for a given folder path specified by path_parts.
@@ -65,21 +62,21 @@ class Uploader:
             base_folder = self.folder_id
         dropped_prefix = []
 
-        fk = '/'.join(path_parts)
+        fk = "/".join(path_parts)
         if fk in self.memo_path:
             return self.memo_path[fk]
         else:
             for i in reversed(range(len(path_parts))):
-                fk = '/'.join(path_parts[0:i + 1])
+                fk = "/".join(path_parts[0 : i + 1])
                 if fk in self.memo_path:
-                    dropped_prefix = path_parts[0:i + 1]
-                    path_parts = path_parts[i + 1:]
+                    dropped_prefix = path_parts[0 : i + 1]
+                    path_parts = path_parts[i + 1 :]
                     base_folder = self.memo_path[fk]
                     break
 
         nfk = []
         for i in range(len(path_parts)):
-            nfk.append('/'.join(list(dropped_prefix) + list(path_parts[0:i + 1])))
+            nfk.append("/".join(list(dropped_prefix) + list(path_parts[0 : i + 1])))
 
         # Recursively create the path from our base_folder starting points,
         # getting the IDs of each folder per path component
@@ -99,19 +96,19 @@ class Uploader:
             return ids
         else:
             pf = self.gi.libraries.create_folder(self.library_id, path_parts[0], base_folder_id=parent_folder_id)
-            ids.append(pf[0]['id'])
-            return self.recursively_build_path(path_parts[1:], pf[0]['id'], ids=ids)
+            ids.append(pf[0]["id"])
+            return self.recursively_build_path(path_parts[1:], pf[0]["id"], ids=ids)
 
     # http://stackoverflow.com/questions/13505819/python-split-path-recursively/13505966#13505966
     def rec_split(self, s):
-        if s == '/':
+        if s == "/":
             return ()
 
         rest, tail = os.path.split(s)
-        if tail == '.':
+        if tail == ".":
             return ()
-        if rest == '':
-            return tail,
+        if rest == "":
+            return (tail,)
         return self.rec_split(rest) + (tail,)
 
     def upload(self):
@@ -131,7 +128,7 @@ class Uploader:
             # So that we can check if it really needs to be uploaded.
             already_uploaded = memo_key in self.memo_path.keys()
             fid = self.memoized_path(basepath, base_folder=self.folder_id)
-            print(f'[{idx + 1}/{len(all_files)}] {fid}/{fname} uploaded={already_uploaded}')
+            print(f"[{idx + 1}/{len(all_files)}] {fid}/{fname} uploaded={already_uploaded}")
 
             if not already_uploaded:
                 if self.non_local:
@@ -145,22 +142,34 @@ class Uploader:
                         self.library_id,
                         os.path.join(dirName, fname),
                         folder_id=fid,
-                        link_data_only='link_to_files' if self.should_link else 'copy_files',
+                        link_data_only="link_to_files" if self.should_link else "copy_files",
                     )
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Upload a directory into a data library')
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Upload a directory into a data library")
     parser.add_argument("-u", "--url", dest="url", required=True, help="Galaxy URL")
     parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
 
     parser.add_argument("-l", "--lib", dest="library_id", required=True, help="Library ID")
-    parser.add_argument("-f", "--folder", dest="folder_id", help="Folder ID. If not specified, will go to root of library.")
+    parser.add_argument(
+        "-f", "--folder", dest="folder_id", help="Folder ID. If not specified, will go to root of library."
+    )
 
-    parser.add_argument("--nonlocal", dest="non_local", action="store_true", default=False,
-                        help="Set this flag if you are NOT running this script on your Galaxy head node with access to the full filesystem")
-    parser.add_argument("--link", dest="should_link", action="store_true", default=False,
-                        help="Link datasets only, do not upload to Galaxy. ONLY Avaialble if you run 'locally' relative to your Galaxy head node/filesystem ")
+    parser.add_argument(
+        "--nonlocal",
+        dest="non_local",
+        action="store_true",
+        default=False,
+        help="Set this flag if you are NOT running this script on your Galaxy head node with access to the full filesystem",
+    )
+    parser.add_argument(
+        "--link",
+        dest="should_link",
+        action="store_true",
+        default=False,
+        help="Link datasets only, do not upload to Galaxy. ONLY Avaialble if you run 'locally' relative to your Galaxy head node/filesystem ",
+    )
     args = parser.parse_args()
 
     u = Uploader(**vars(args))
diff --git a/scripts/api/library_upload_from_import_dir.py b/scripts/api/library_upload_from_import_dir.py
index ce23929d92b..09a42a91d12 100755
--- a/scripts/api/library_upload_from_import_dir.py
+++ b/scripts/api/library_upload_from_import_dir.py
@@ -11,14 +11,14 @@ from common import submit
 
 try:
     data = {}
-    data['folder_id'] = sys.argv[3]
-    data['file_type'] = sys.argv[4]
-    data['server_dir'] = sys.argv[5]
-    data['dbkey'] = sys.argv[6]
-    data['upload_option'] = 'upload_directory'
-    data['create_type'] = 'file'
+    data["folder_id"] = sys.argv[3]
+    data["file_type"] = sys.argv[4]
+    data["server_dir"] = sys.argv[5]
+    data["dbkey"] = sys.argv[6]
+    data["upload_option"] = "upload_directory"
+    data["create_type"] = "file"
 except IndexError:
-    print('usage: %s key url folder_id file_type server_dir dbkey' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url folder_id file_type server_dir dbkey" % os.path.basename(sys.argv[0]))
     sys.exit(1)
 
 submit(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/load_data_with_metadata.py b/scripts/api/load_data_with_metadata.py
index 6a670aaaf79..47e6a7080f1 100755
--- a/scripts/api/load_data_with_metadata.py
+++ b/scripts/api/load_data_with_metadata.py
@@ -15,26 +15,29 @@ import json
 import os
 import sys
 
-from common import display, submit
+from common import (
+    display,
+    submit,
+)
 
 
 def load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_field=None):
     data = {}
-    data['folder_id'] = library_folder_id
-    data['file_type'] = 'auto'
-    data['dbkey'] = ''
-    data['upload_option'] = 'upload_paths'
-    data['filesystem_paths'] = fullpath
-    data['create_type'] = 'file'
-    data['link_data_only'] = 'link_to_files'
+    data["folder_id"] = library_folder_id
+    data["file_type"] = "auto"
+    data["dbkey"] = ""
+    data["upload_option"] = "upload_paths"
+    data["filesystem_paths"] = fullpath
+    data["create_type"] = "file"
+    data["link_data_only"] = "link_to_files"
 
     handle = open(fullpath + ".json")
     smeta = handle.read()
     handle.close()
     ext_meta = json.loads(smeta)
-    data['extended_metadata'] = ext_meta
+    data["extended_metadata"] = ext_meta
     if uuid_field is not None and uuid_field in ext_meta:
-        data['uuid'] = ext_meta[uuid_field]
+        data["uuid"] = ext_meta[uuid_field]
 
     libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=True)
     print(libset)
@@ -42,19 +45,19 @@ def load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_fi
 
 def main(api_key, api_url, in_folder, data_library, uuid_field=None):
     # Find/Create data library with the above name.  Assume we're putting datasets in the root folder '/'
-    libs = display(api_key, api_url + 'libraries', return_formatted=False)
+    libs = display(api_key, api_url + "libraries", return_formatted=False)
     library_id = None
     for library in libs:
-        if library['name'] == data_library:
-            library_id = library['id']
+        if library["name"] == data_library:
+            library_id = library["id"]
     if not library_id:
-        lib_create_data = {'name': data_library}
-        library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False)
-        library_id = library['id']
+        lib_create_data = {"name": data_library}
+        library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
+        library_id = library["id"]
     folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
     for f in folders:
-        if f['name'] == "/":
-            library_folder_id = f['id']
+        if f["name"] == "/":
+            library_folder_id = f["id"]
     if not library_id or not library_folder_id:
         print("Failure to configure library destination.")
         sys.exit(1)
@@ -72,10 +75,10 @@ def main(api_key, api_url, in_folder, data_library, uuid_field=None):
                 load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_field)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument("api_key", help="API KEY")
-    parser.add_argument('api_url', help='API URL')
+    parser.add_argument("api_url", help="API URL")
     parser.add_argument("in_folder", help="Input Folder")
     parser.add_argument("data_library", help="Data Library")
     parser.add_argument("--uuid_field", help="UUID Field", default=None)
diff --git a/scripts/api/repair_tool_shed_repository.py b/scripts/api/repair_tool_shed_repository.py
index 6e816ba9017..dca07e6a372 100644
--- a/scripts/api/repair_tool_shed_repository.py
+++ b/scripts/api/repair_tool_shed_repository.py
@@ -8,48 +8,58 @@ Here is a working example of how to use this script to repair a repository insta
 
 import argparse
 
-from common import display, submit
+from common import (
+    display,
+    submit,
+)
 
 
 def clean_url(url):
-    if url.find('//') > 0:
+    if url.find("//") > 0:
         # We have an url that includes a protocol, something like: http://localhost:9009
-        items = url.split('//')
-        return items[1].rstrip('/')
-    return url.rstrip('/')
+        items = url.split("//")
+        return items[1].rstrip("/")
+    return url.rstrip("/")
 
 
 def main(options):
     """Collect all user data and install the tools via the Galaxy API."""
     api_key = options.api
-    base_galaxy_url = options.local_url.rstrip('/')
-    base_tool_shed_url = options.tool_shed_url.rstrip('/')
+    base_galaxy_url = options.local_url.rstrip("/")
+    base_tool_shed_url = options.tool_shed_url.rstrip("/")
     cleaned_tool_shed_url = clean_url(base_tool_shed_url)
-    installed_tool_shed_repositories_url = '{}/api/{}'.format(base_galaxy_url, 'tool_shed_repositories')
+    installed_tool_shed_repositories_url = "{}/api/{}".format(base_galaxy_url, "tool_shed_repositories")
     data = {}
-    data['tool_shed_url'] = cleaned_tool_shed_url
-    data['name'] = options.name
-    data['owner'] = options.owner
-    data['changeset_revision'] = options.changeset_revision
+    data["tool_shed_url"] = cleaned_tool_shed_url
+    data["name"] = options.name
+    data["owner"] = options.owner
+    data["changeset_revision"] = options.changeset_revision
     tool_shed_repository_id = None
     installed_tool_shed_repositories = display(api_key, installed_tool_shed_repositories_url, return_formatted=False)
     for installed_tool_shed_repository in installed_tool_shed_repositories:
-        tool_shed = str(installed_tool_shed_repository['tool_shed'])
-        name = str(installed_tool_shed_repository['name'])
-        owner = str(installed_tool_shed_repository['owner'])
-        changeset_revision = str(installed_tool_shed_repository['changeset_revision'])
-        if tool_shed == cleaned_tool_shed_url and name == options.name and owner == options.owner and changeset_revision == options.changeset_revision:
-            tool_shed_repository_id = installed_tool_shed_repository['id']
+        tool_shed = str(installed_tool_shed_repository["tool_shed"])
+        name = str(installed_tool_shed_repository["name"])
+        owner = str(installed_tool_shed_repository["owner"])
+        changeset_revision = str(installed_tool_shed_repository["changeset_revision"])
+        if (
+            tool_shed == cleaned_tool_shed_url
+            and name == options.name
+            and owner == options.owner
+            and changeset_revision == options.changeset_revision
+        ):
+            tool_shed_repository_id = installed_tool_shed_repository["id"]
             break
     if tool_shed_repository_id:
-        url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/repair_repository_revision' % str(tool_shed_repository_id))
+        url = "{}{}".format(
+            base_galaxy_url, "/api/tool_shed_repositories/%s/repair_repository_revision" % str(tool_shed_repository_id)
+        )
         submit(options.api, url, data)
     else:
         print("Invalid tool_shed / name / owner / changeset_revision.")
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Installation of tool shed repositories via the Galaxy API.')
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Installation of tool shed repositories via the Galaxy API.")
     parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
     parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
     parser.add_argument("-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance.")
diff --git a/scripts/api/reset_metadata_on_installed_repositories.py b/scripts/api/reset_metadata_on_installed_repositories.py
index 86c546cd2a0..150f809c0a4 100644
--- a/scripts/api/reset_metadata_on_installed_repositories.py
+++ b/scripts/api/reset_metadata_on_installed_repositories.py
@@ -14,13 +14,15 @@ from common import submit
 
 
 def main(options):
-    base_galaxy_url = options.galaxy_url.rstrip('/')
-    url = '%s/api/tool_shed_repositories/reset_metadata_on_installed_repositories' % base_galaxy_url
+    base_galaxy_url = options.galaxy_url.rstrip("/")
+    url = "%s/api/tool_shed_repositories/reset_metadata_on_installed_repositories" % base_galaxy_url
     submit(options.api, url, {})
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Reset metadata on all Tool Shed repositories installed into Galaxy via the Galaxy API.')
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Reset metadata on all Tool Shed repositories installed into Galaxy via the Galaxy API."
+    )
     parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
     parser.add_argument("-u", "--url", dest="galaxy_url", required=True, help="Galaxy URL")
     options = parser.parse_args()
diff --git a/scripts/api/search.py b/scripts/api/search.py
index fce32407d3d..14e30f1866a 100644
--- a/scripts/api/search.py
+++ b/scripts/api/search.py
@@ -9,7 +9,6 @@ import requests
 
 
 class RemoteGalaxy:
-
     def __init__(self, url, api_key):
         self.url = url
         self.api_key = api_key
@@ -17,15 +16,17 @@ class RemoteGalaxy:
     def get(self, path):
         c_url = self.url + path
         params = {}
-        params['key'] = self.api_key
+        params["key"] = self.api_key
         req = requests.get(c_url, params=params)
         return req.json()
 
     def post(self, path, payload):
         c_url = self.url + path
         params = {}
-        params['key'] = self.api_key
-        req = requests.post(c_url, data=json.dumps(payload), params=params, headers={'Content-Type': 'application/json'})
+        params["key"] = self.api_key
+        req = requests.post(
+            c_url, data=json.dumps(payload), params=params, headers={"Content-Type": "application/json"}
+        )
         return req.json()
 
 
diff --git a/scripts/api/update.py b/scripts/api/update.py
index a0a552d7c05..cd21e139298 100644
--- a/scripts/api/update.py
+++ b/scripts/api/update.py
@@ -9,7 +9,7 @@ import sys
 from common import update
 
 data = {}
-for k, v in [kwarg.split('=', 1) for kwarg in sys.argv[3:]]:
+for k, v in [kwarg.split("=", 1) for kwarg in sys.argv[3:]]:
     data[k] = v
 
 update(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/upload_to_history.py b/scripts/api/upload_to_history.py
index 0c073644810..e3c71e09144 100755
--- a/scripts/api/upload_to_history.py
+++ b/scripts/api/upload_to_history.py
@@ -10,44 +10,48 @@ import sys
 try:
     import requests
 except ImportError:
-    print("Could not import the requests module. See http://docs.python-requests.org/en/latest/"
-          + " or install with 'pip install requests'")
+    print(
+        "Could not import the requests module. See http://docs.python-requests.org/en/latest/"
+        + " or install with 'pip install requests'"
+    )
     raise
 
 
 def upload_file(base_url, api_key, history_id, filepath, **kwargs):
-    full_url = base_url + '/api/tools'
+    full_url = base_url + "/api/tools"
 
     payload = {
-        'key': api_key,
-        'tool_id': 'upload1',
-        'history_id': history_id,
+        "key": api_key,
+        "tool_id": "upload1",
+        "history_id": history_id,
     }
     inputs = {
-        'files_0|NAME': kwargs.get('filename', os.path.basename(filepath)),
-        'files_0|type': 'upload_dataset',
+        "files_0|NAME": kwargs.get("filename", os.path.basename(filepath)),
+        "files_0|type": "upload_dataset",
         # TODO: the following doesn't work with tools.py
-        'dbkey': '?',
-        'file_type': kwargs.get('file_type', 'auto'),
-        'ajax_upload': 'true',
+        "dbkey": "?",
+        "file_type": kwargs.get("file_type", "auto"),
+        "ajax_upload": "true",
     }
-    payload['inputs'] = json.dumps(inputs)
+    payload["inputs"] = json.dumps(inputs)
 
     response = None
-    with open(filepath, 'rb') as file_to_upload:
-        files = {'files_0|file_data': file_to_upload}
+    with open(filepath, "rb") as file_to_upload:
+        files = {"files_0|file_data": file_to_upload}
         response = requests.post(full_url, data=payload, files=files)
     return response.json()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     if len(sys.argv) < 5:
-        print("history_upload.py <api key> <galaxy base url> <history id> <filepath to upload>\n"
-              + "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')")
+        print(
+            "history_upload.py <api key> <galaxy base url> <history id> <filepath to upload>\n"
+            + "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')"
+        )
         sys.exit(1)
 
     api_key, base_url, history_id, filepath = sys.argv[1:5]
-    kwargs = dict([kwarg.split('=', 1) for kwarg in sys.argv[5:]])
+    kwargs = dict([kwarg.split("=", 1) for kwarg in sys.argv[5:]])
 
     response = upload_file(base_url, api_key, history_id, filepath, **kwargs)
     print(response, file=sys.stderr)
diff --git a/scripts/api/workflow_delete.py b/scripts/api/workflow_delete.py
index 944a2428fd8..9972a9b1359 100644
--- a/scripts/api/workflow_delete.py
+++ b/scripts/api/workflow_delete.py
@@ -17,11 +17,11 @@ from common import delete
 try:
     assert sys.argv[2]
 except IndexError:
-    print('usage: %s key url [purge (true/false)] ' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
     sys.exit(1)
 try:
     data = {}
-    data['purge'] = sys.argv[3]
+    data["purge"] = sys.argv[3]
 except IndexError:
     pass
 
diff --git a/scripts/api/workflow_execute.py b/scripts/api/workflow_execute.py
index 6b7b55cac07..18824704d92 100755
--- a/scripts/api/workflow_execute.py
+++ b/scripts/api/workflow_execute.py
@@ -15,19 +15,19 @@ from common import submit
 def main():
     try:
         data = {}
-        data['workflow_id'] = sys.argv[3]
-        data['history'] = sys.argv[4]
-        data['ds_map'] = {}
+        data["workflow_id"] = sys.argv[3]
+        data["history"] = sys.argv[4]
+        data["ds_map"] = {}
         # DBTODO If only one input is given, don't require a step
         # mapping, just use it for everything?
         for v in sys.argv[5:]:
-            step, src, ds_id = v.split('=')
-            data['ds_map'][step] = {'src': src, 'id': ds_id}
+            step, src, ds_id = v.split("=")
+            data["ds_map"][step] = {"src": src, "id": ds_id}
     except IndexError:
-        print('usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0]))
+        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/scripts/api/workflow_execute_parameters.py b/scripts/api/workflow_execute_parameters.py
index bd5c119bb53..280976f8d3f 100644
--- a/scripts/api/workflow_execute_parameters.py
+++ b/scripts/api/workflow_execute_parameters.py
@@ -20,12 +20,12 @@ def main():
     try:
         print("workflow_execute:py:")
         data = {}
-        data['workflow_id'] = sys.argv[3]
-        data['history'] = sys.argv[4]
-        data['ds_map'] = {}
+        data["workflow_id"] = sys.argv[3]
+        data["history"] = sys.argv[4]
+        data["ds_map"] = {}
 
         # Trying to pass in parameter for my own dictionary
-        data['parameters'] = {}
+        data["parameters"] = {}
 
         # DBTODO If only one input is given, don't require a step
         # mapping, just use it for everything?
@@ -34,22 +34,22 @@ def main():
             print(v)
 
             try:
-                step, src, ds_id = v.split('=')
-                data['ds_map'][step] = {'src': src, 'id': ds_id}
+                step, src, ds_id = v.split("=")
+                data["ds_map"][step] = {"src": src, "id": ds_id}
 
             except ValueError:
                 print("VALUE ERROR:")
-                wtype, wtool, wparam, wvalue = v.split('=')
+                wtype, wtool, wparam, wvalue = v.split("=")
                 try:
-                    data['parameters'][wtool] = {'param': wparam, 'value': wvalue}
+                    data["parameters"][wtool] = {"param": wparam, "value": wvalue}
                 except ValueError:
                     print("TOOL ID ERROR:")
 
     except IndexError:
-        print('usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0]))
+        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/scripts/api/workflow_import.py b/scripts/api/workflow_import.py
index 21a1abc2f0f..1f78d956751 100755
--- a/scripts/api/workflow_import.py
+++ b/scripts/api/workflow_import.py
@@ -17,14 +17,14 @@ def main():
     api_url = "%s/api/workflows" % api_base_url
     try:
         data = {}
-        data['installed_repository_file'] = sys.argv[3]
+        data["installed_repository_file"] = sys.argv[3]
         if len(sys.argv) > 4 and sys.argv[4] == "--add_to_menu":
-            data['add_to_menu'] = True
+            data["add_to_menu"] = True
     except IndexError:
-        print('usage: %s key galaxy_url workflow_file' % os.path.basename(sys.argv[0]))
+        print("usage: %s key galaxy_url workflow_file" % os.path.basename(sys.argv[0]))
         sys.exit(1)
     submit(api_key, api_url, data, return_formatted=False)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/scripts/api/workflow_import_from_file_rpark.py b/scripts/api/workflow_import_from_file_rpark.py
index 9d4fdb66db3..31242d8b25d 100644
--- a/scripts/api/workflow_import_from_file_rpark.py
+++ b/scripts/api/workflow_import_from_file_rpark.py
@@ -20,12 +20,12 @@ def openWorkflow(in_file):
 try:
     assert sys.argv[2]
 except IndexError:
-    print('usage: %s key url [name] ' % os.path.basename(sys.argv[0]))
+    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
     sys.exit(1)
 try:
     data = {}
     workflow_dict = openWorkflow(sys.argv[3])
-    data['workflow'] = workflow_dict
+    data["workflow"] = workflow_dict
 except IndexError:
     pass
 
diff --git a/scripts/apply_tags.py b/scripts/apply_tags.py
index 1d118f19db0..50ee61e3098 100644
--- a/scripts/apply_tags.py
+++ b/scripts/apply_tags.py
@@ -7,7 +7,6 @@ from bioblend.galaxy import GalaxyInstance
 
 
 class ApplyTagsHistory:
-
     @classmethod
     def __init__(self, galaxy_url, galaxy_api_key, history_id=None):
         self.galaxy_url = galaxy_url
@@ -54,7 +53,7 @@ class ApplyTagsHistory:
         print("Total datasets: %d. Updating their tags may take a while..." % len(all_datasets))
         for dataset in all_datasets:
             try:
-                if dataset["deleted"] is False and dataset["state"] == 'ok':
+                if dataset["deleted"] is False and dataset["state"] == "ok":
                     parent_ids = list()
                     child_dataset_id = dataset["id"]
                     own_tags[child_dataset_id] = dataset["tags"]
@@ -89,7 +88,9 @@ class ApplyTagsHistory:
             parent_dataset_ids = all_parents[dataset_id]
             # update history tags for a dataset taking all from its parents if there is a parent
             if len(parent_dataset_ids) > 0:
-                is_updated = self.propagate_tags(history, history_id, parent_dataset_ids, dataset_id, parent_tags, own_tags)
+                is_updated = self.propagate_tags(
+                    history, history_id, parent_dataset_ids, dataset_id, parent_tags, own_tags
+                )
                 if is_updated is True:
                     count_datasets_updated += 1
         print("Tags of %d datasets updated" % count_datasets_updated)
@@ -111,6 +112,7 @@ class ApplyTagsHistory:
                     recursive_parents.extend(dataset_parents)
                     for parent in dataset_parents:
                         find_parent_recursive(parent)
+
             find_parent_recursive(item)
             # take unique parents
             recursive_parent_ids[item] = list(set(recursive_parents))
@@ -138,7 +140,7 @@ class ApplyTagsHistory:
         # find unique tags from all parents
         all_tags = set(all_tags)
         self_tags_set = set(self_tags)
-        is_same = (all_tags == self_tags_set)
+        is_same = all_tags == self_tags_set
         # update tags if there are new tags from parents
         if is_same is False:
             is_subset = all_tags.issubset(self_tags_set)
diff --git a/scripts/auth/pam_auth_helper.py b/scripts/auth/pam_auth_helper.py
index 815708445c2..cbffd00d77d 100755
--- a/scripts/auth/pam_auth_helper.py
+++ b/scripts/auth/pam_auth_helper.py
@@ -11,7 +11,7 @@ TIMEOUT = 5
 try:
     import pam
 except ImportError:
-    log.debug('PAM auth helper: Could not import pam module')
+    log.debug("PAM auth helper: Could not import pam module")
     sys.exit(1)
 
 
@@ -32,10 +32,10 @@ signal.alarm(0)
 p_auth = pam.pam()
 authenticated = p_auth.authenticate(pam_username, pam_password, service=pam_service)
 if authenticated:
-    log.debug(f'PAM auth helper: authentication successful for {pam_username}')
-    sys.stdout.write('True\n')
+    log.debug(f"PAM auth helper: authentication successful for {pam_username}")
+    sys.stdout.write("True\n")
     sys.exit(0)
 else:
-    log.debug(f'PAM auth helper: authentication failed for {pam_username}')
-    sys.stdout.write('False\n')
+    log.debug(f"PAM auth helper: authentication failed for {pam_username}")
+    sys.stdout.write("False\n")
     sys.exit(1)
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 06168001014..2c37e4adf84 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -36,12 +36,25 @@ RELEASE_DELTA_MONTHS = 4  # Number of months between releases.
 
 # Uncredit pull requestors... kind of arbitrary at this point.
 DEVTEAM = [
-    "afgane", "dannon", "blankenberg",
-    "davebx", "martenson", "jmchilton",
-    "tnabtaf", "natefoo", "jgoecks",
-    "guerler", "jennaj", "nekrut", "jxtx",
-    "VJalili", "WilliamHolden", "Nerdinacan",
-    "ic4f", "mvdbeek", "galaxyproject"
+    "afgane",
+    "dannon",
+    "blankenberg",
+    "davebx",
+    "martenson",
+    "jmchilton",
+    "tnabtaf",
+    "natefoo",
+    "jgoecks",
+    "guerler",
+    "jennaj",
+    "nekrut",
+    "jxtx",
+    "VJalili",
+    "WilliamHolden",
+    "Nerdinacan",
+    "ic4f",
+    "mvdbeek",
+    "galaxyproject",
 ]
 
 TEMPLATE = """
@@ -79,7 +92,8 @@ Fixes
 
 """
 
-ANNOUNCE_TEMPLATE = string.Template("""
+ANNOUNCE_TEMPLATE = string.Template(
+    """
 ===========================================================
 ${month_name} 20${year} Galaxy Release (v ${release})
 ===========================================================
@@ -124,9 +138,11 @@ Release Notes
    :start-after: announce_start
 
 .. include:: _thanks.rst
-""")
+"""
+)
 
-ANNOUNCE_USER_TEMPLATE = string.Template("""
+ANNOUNCE_USER_TEMPLATE = string.Template(
+    """
 ===========================================================
 ${month_name} 20${year} Galaxy Release (v ${release})
 ===========================================================
@@ -176,9 +192,11 @@ Please see the `full release notes <${release}_announce.html>`_ for more details
 .. include:: ${release}_prs.rst
 
 .. include:: _thanks.rst
-""")
+"""
+)
 
-NEXT_TEMPLATE = string.Template("""
+NEXT_TEMPLATE = string.Template(
+    """
 :orphan:
 
 ===========================================================
@@ -190,13 +208,15 @@ Schedule
 ===========================================================
  * Planned Freeze Date: ${freeze_date}
  * Planned Release Date: ${release_date}
-""")
+"""
+)
 
 PRS_TEMPLATE = """
 .. github_links
 """
 
-RELEASE_ISSUE_TEMPLATE = string.Template("""
+RELEASE_ISSUE_TEMPLATE = string.Template(
+    """
 
 - [X] **Prep**
 
@@ -301,17 +321,20 @@ RELEASE_ISSUE_TEMPLATE = string.Template("""
     - [ ] Create release issue for next version ``make release-issue``.
     - [ ] Schedule committer meeting to discuss re-alignment of priorities.
     - [ ] Close this issue.
-""")
+"""
+)
 
-GROUPPED_TAGS = OrderedDict([
-    ('area/visualizations', 'viz'),
-    ('area/datatypes', 'datatypes'),
-    ('area/tools', 'tools'),
-    ('area/workflows', 'workflows'),
-    ('area/client', 'ui'),
-    ('area/jobs', 'jobs'),
-    ('area/admin', 'admin'),
-])
+GROUPPED_TAGS = OrderedDict(
+    [
+        ("area/visualizations", "viz"),
+        ("area/datatypes", "datatypes"),
+        ("area/tools", "tools"),
+        ("area/workflows", "workflows"),
+        ("area/client", "ui"),
+        ("area/jobs", "jobs"),
+        ("area/admin", "admin"),
+    ]
+)
 
 # https://api.github.com/repos/galaxyproject/galaxy/pulls?base=dev&state=closed
 # https://api.github.com/repos/galaxyproject/galaxy/pulls?base=release_15.07&state=closed
@@ -354,19 +377,11 @@ def do_release(argv):
     month_name = calendar.month_name[month]
     year = release_name.split(".")[0]
 
-    announce_info = ANNOUNCE_TEMPLATE.substitute(
-        month_name=month_name,
-        year=year,
-        release=release_name
-    )
+    announce_info = ANNOUNCE_TEMPLATE.substitute(month_name=month_name, year=year, release=release_name)
     announce_file = _release_file(release_name + "_announce.rst")
     _write_file(announce_file, announce_info, skip_if_exists=True)
 
-    announce_user_info = ANNOUNCE_USER_TEMPLATE.substitute(
-        month_name=month_name,
-        year=year,
-        release=release_name
-    )
+    announce_user_info = ANNOUNCE_USER_TEMPLATE.substitute(month_name=month_name, year=year, release=release_name)
     announce_user_file = _release_file(release_name + "_announce_user.rst")
     _write_file(announce_user_file, announce_user_info, skip_if_exists=True)
 
@@ -374,7 +389,7 @@ def do_release(argv):
     seen_prs = set()
     try:
         with open(prs_file) as fh:
-            seen_prs = set(re.findall(r'\.\. _Pull Request (\d*): https', fh.read()))
+            seen_prs = set(re.findall(r"\.\. _Pull Request (\d*): https", fh.read()))
     except FileNotFoundError:
         pass
     _write_file(prs_file, PRS_TEMPLATE, skip_if_exists=True)
@@ -387,7 +402,9 @@ def do_release(argv):
     open(next_release_file, "w").write(next_announce)
     releases_index = _release_file("index.rst")
     releases_index_contents = _read_file(releases_index)
-    releases_index_contents = releases_index_contents.replace(".. announcements\n", ".. announcements\n   " + next_version + "_announce\n")
+    releases_index_contents = releases_index_contents.replace(
+        ".. announcements\n", ".. announcements\n   " + next_version + "_announce\n"
+    )
     _write_file(releases_index, releases_index_contents, skip_if_exists=True)
 
     for pr in _get_prs(release_name):
@@ -398,7 +415,10 @@ def do_release(argv):
             "head": pr.head,
             "labels": _pr_to_labels(pr),
         }
-        main([argv[0], "--release_file", "%s.rst" % release_name, "--request", as_dict, "pr" + str(pr.number)], seen_prs=seen_prs)
+        main(
+            [argv[0], "--release_file", "%s.rst" % release_name, "--request", as_dict, "pr" + str(pr.number)],
+            seen_prs=seen_prs,
+        )
 
 
 def check_release(argv):
@@ -421,10 +441,14 @@ def check_blocking_issues(argv):
     release_name = argv[2]
     block = 0
     github = _github_client()
-    repo = github.get_repo('galaxyproject/galaxy')
-    issues = repo.get_issues(state='open')
+    repo = github.get_repo("galaxyproject/galaxy")
+    issues = repo.get_issues(state="open")
     for issue in issues:
-        if issue.milestone and issue.milestone.title == release_name and "Publication of Galaxy Release" not in issue.title:
+        if (
+            issue.milestone
+            and issue.milestone.title == release_name
+            and "Publication of Galaxy Release" not in issue.title
+        ):
             print("WARN: Blocking issue| %s" % _issue_to_str(issue))
             block = 1
 
@@ -529,8 +553,8 @@ def main(argv, seen_prs=None):
     if newest_release is None:
         newest_release = sorted(os.listdir(RELEASES_PATH))[-1]
     history_path = os.path.join(RELEASES_PATH, newest_release)
-    user_announce_path = history_path[0:-len(".rst")] + "_announce_user.rst"
-    prs_path = history_path[0:-len(".rst")] + "_prs.rst"
+    user_announce_path = history_path[0 : -len(".rst")] + "_announce_user.rst"
+    prs_path = history_path[0 : -len(".rst")] + "_prs.rst"
 
     history = _read_file(history_path)
     user_announce = _read_file(user_announce_path)
@@ -557,13 +581,13 @@ def main(argv, seen_prs=None):
         message = commit["message"]
         message = get_first_sentence(message)
     elif ident.startswith("pr"):
-        pull_request = ident[len("pr"):]
+        pull_request = ident[len("pr") :]
         api_url = urljoin(PROJECT_API, "pulls/%s" % pull_request)
         if req is None:
             req = requests.get(api_url).json()
         message = req["title"]
     elif ident.startswith("issue"):
-        issue = ident[len("issue"):]
+        issue = ident[len("issue") :]
         api_url = urljoin(PROJECT_API, "issues/%s" % issue)
         if req is None:
             req = requests.get(api_url).json()
@@ -576,7 +600,7 @@ def main(argv, seen_prs=None):
 
     owner = None
     if ident.startswith("pr"):
-        pull_request = ident[len("pr"):]
+        pull_request = ident[len("pr") :]
         if pull_request in seen_prs:
             to_doc = None
         else:
@@ -588,15 +612,16 @@ def main(argv, seen_prs=None):
             prs_content = extend_target("github_links", text, prs_content)
             if owner:
                 to_doc += "\n(thanks to `@{} <https://github.com/{}>`__).".format(
-                    owner, owner,
+                    owner,
+                    owner,
                 )
             to_doc += f"\n`Pull Request {pull_request}`_"
             labels = None
-            if req and 'labels' in req:
-                labels = req['labels']
+            if req and "labels" in req:
+                labels = req["labels"]
             text_target = _text_target(pull_request, labels=labels)
     elif ident.startswith("issue"):
-        issue = ident[len("issue"):]
+        issue = ident[len("issue") :]
         text = ".. _Issue {0}: {1}/issues/{0}".format(issue, PROJECT_URL)
         prs_content = extend_target("github_links", text, prs_content)
         to_doc += f"`Issue {issue}`_"
@@ -610,13 +635,13 @@ def main(argv, seen_prs=None):
         to_doc = wrap(to_doc)
         if text_target is not None:
             history = extend_target(text_target, to_doc, history)
-        if req and req['labels']:
-            labels = req['labels']
-            if 'area/datatypes' in labels:
+        if req and req["labels"]:
+            labels = req["labels"]
+            if "area/datatypes" in labels:
                 user_announce = extend_target("datatypes", to_doc, user_announce)
-            if 'area/visualizations' in labels:
+            if "area/visualizations" in labels:
                 user_announce = extend_target("visualizations", to_doc, user_announce)
-            if 'area/tools' in labels:
+            if "area/tools" in labels:
                 user_announce = extend_target("tools", to_doc, user_announce)
         _write_file(history_path, history)
         _write_file(prs_path, prs_content)
@@ -652,7 +677,7 @@ def _text_target(pull_request, labels=None):
             print(e)
     is_bug = is_enhancement = is_feature = is_minor = is_major = is_merge = is_small_enhancement = False
     if len(labels) == 0:
-        print('No labels found for %s' % pr_number)
+        print("No labels found for %s" % pr_number)
         return None
     for label_name in labels:
         if label_name == "minor":
@@ -675,7 +700,7 @@ def _text_target(pull_request, labels=None):
 
     is_some_kind_of_enhancement = is_enhancement or is_feature or is_small_enhancement
 
-    if not(is_bug or is_some_kind_of_enhancement or is_minor or is_merge):
+    if not (is_bug or is_some_kind_of_enhancement or is_minor or is_merge):
         print("No 'kind/*' or 'minor' or 'merge' or 'procedures' label found for %s" % _pr_to_str(pull_request))
         text_target = None
 
@@ -732,7 +757,7 @@ def _releases():
     all_files = sorted(os.listdir(RELEASES_PATH))
     release_note_file_pattern = re.compile(r"\d+\.\d+.rst")
     release_note_files = [f for f in all_files if release_note_file_pattern.match(f)]
-    return sorted(f.rstrip('.rst') for f in release_note_files)
+    return sorted(f.rstrip(".rst") for f in release_note_files)
 
 
 def _github_client():
@@ -765,14 +790,14 @@ def process_sentence(message):
     message = re.sub(r"^\s*\[.*\]\s*", r"", message)
     # Link issues and pull requests...
     issue_url = f"https://github.com/{PROJECT_OWNER}/{PROJECT_NAME}/issues"
-    message = re.sub(r'#(\d+)', r'`#\1 <%s/\1>`__' % issue_url, message)
+    message = re.sub(r"#(\d+)", r"`#\1 <%s/\1>`__" % issue_url, message)
     return message
 
 
 def wrap(message):
     message = process_sentence(message)
     wrapper = textwrap.TextWrapper(initial_indent="* ")
-    wrapper.subsequent_indent = '  '
+    wrapper.subsequent_indent = "  "
     wrapper.width = 160
     message_lines = message.splitlines()
     first_lines = "\n".join(wrapper.wrap(message_lines[0]))
@@ -782,7 +807,7 @@ def wrap(message):
 
 
 def next_weekday(d, weekday):
-    """ Return the next week day (0 for Monday, 6 for Sunday) starting from ``d``. """
+    """Return the next week day (0 for Monday, 6 for Sunday) starting from ``d``."""
     days_ahead = weekday - d.weekday()
     if days_ahead <= 0:  # Target day already happened this week
         days_ahead += 7
diff --git a/scripts/build_toolbox.py b/scripts/build_toolbox.py
index 6309f4d85df..d471bc9b8d7 100644
--- a/scripts/build_toolbox.py
+++ b/scripts/build_toolbox.py
@@ -5,9 +5,9 @@ from xml.etree import ElementTree as ET
 
 
 def prettify(elem):
-    rough_string = ET.tostring(elem, 'utf-8')
+    rough_string = ET.tostring(elem, "utf-8")
     repaired = minidom.parseString(rough_string)
-    return repaired.toprettyxml(indent='  ')
+    return repaired.toprettyxml(indent="  ")
 
 
 # Build a list of all toolconf xml files in the tools directory
@@ -16,9 +16,9 @@ def getfilenamelist(startdir):
     for root, _dirs, files in os.walk(startdir):
         for fn in files:
             fullfn = os.path.join(root, fn)
-            if fn.endswith('toolconf.xml'):
+            if fn.endswith("toolconf.xml"):
                 filenamelist.append(fullfn)
-            elif fn.endswith('.xml'):
+            elif fn.endswith(".xml"):
                 try:
                     doc = ET.parse(fullfn)
                 except Exception:
@@ -27,8 +27,8 @@ def getfilenamelist(startdir):
                 rootelement = doc.getroot()
                 # Only interpret those 'tool' XML files that have
                 # the 'section' element.
-                if rootelement.tag == 'tool':
-                    if rootelement.findall('toolboxposition'):
+                if rootelement.tag == "tool":
+                    if rootelement.findall("toolboxposition"):
                         filenamelist.append(fullfn)
                     else:
                         print("DBG> tool config does not have a <section>:", fullfn)
@@ -41,10 +41,10 @@ class ToolBox:
         self.sectionorders = {}
 
     def add(self, toolelement, toolboxpositionelement):
-        section = toolboxpositionelement.attrib.get('section', '')
-        label = toolboxpositionelement.attrib.get('label', '')
-        order = int(toolboxpositionelement.attrib.get('order', '0'))
-        sectionorder = int(toolboxpositionelement.attrib.get('sectionorder', '0'))
+        section = toolboxpositionelement.attrib.get("section", "")
+        label = toolboxpositionelement.attrib.get("label", "")
+        order = int(toolboxpositionelement.attrib.get("order", "0"))
+        sectionorder = int(toolboxpositionelement.attrib.get("sectionorder", "0"))
 
         # If this is the first time we encounter the section, store its order
         # number. If we have seen it before, ignore the given order and use
@@ -62,9 +62,9 @@ class ToolBox:
         toolkeys.sort()
 
         # Initialize the loop: IDs to zero, current section and label to ''
-        currentsection = ''
+        currentsection = ""
         sectionnumber = 0
-        currentlabel = ''
+        currentlabel = ""
         labelnumber = 0
         for toolkey in toolkeys:
             section = toolkey[3]
@@ -74,12 +74,11 @@ class ToolBox:
             if currentsection != section:
                 currentsection = section
                 # Start the section with empty label
-                currentlabel = ''
+                currentlabel = ""
                 if section:
                     sectionnumber += 1
-                    attrib = {'name': section,
-                              'id': "section%d" % sectionnumber}
-                    sectionelement = ET.Element('section', attrib)
+                    attrib = {"name": section, "id": "section%d" % sectionnumber}
+                    sectionelement = ET.Element("section", attrib)
                     rootelement.append(sectionelement)
                     currentelement = sectionelement
                 else:
@@ -91,9 +90,8 @@ class ToolBox:
                 currentlabel = label
                 if label:
                     labelnumber += 1
-                    attrib = {'text': label,
-                              'id': "label%d" % labelnumber}
-                    labelelement = ET.Element('label', attrib)
+                    attrib = {"text": label, "id": "label%d" % labelnumber}
+                    labelelement = ET.Element("label", attrib)
                     currentelement.append(labelelement)
 
             # Add the tools that are in this place
@@ -112,38 +110,36 @@ def scanfiles(filenamelist):
         doc = ET.parse(fn)
         root = doc.getroot()
 
-        if root.tag == 'tool':
+        if root.tag == "tool":
             toolelements = [root]
         else:
-            toolelements = doc.findall('tool')
+            toolelements = doc.findall("tool")
 
         for toolelement in toolelements:
             # Figure out where the tool XML file is, absolute path.
-            if 'file' in toolelement.attrib:
+            if "file" in toolelement.attrib:
                 # It is mentioned, we need to make it absolute
-                fileattrib = os.path.join(os.getcwd(),
-                                          os.path.dirname(fn),
-                                          toolelement.attrib['file'])
+                fileattrib = os.path.join(os.getcwd(), os.path.dirname(fn), toolelement.attrib["file"])
             else:
                 # It is the current file
                 fileattrib = os.path.join(os.getcwd(), fn)
 
             # Store the file in the attibutes of the new tool element
-            attrib = {'file': fileattrib}
+            attrib = {"file": fileattrib}
 
             # Add the tags into the attributes
-            tags = toolelement.find('tags')
+            tags = toolelement.find("tags")
             if tags:
                 tagarray = []
-                for tag in tags.findall('tag'):
+                for tag in tags.findall("tag"):
                     tagarray.append(tag.text)
-                attrib['tags'] = ",".join(tagarray)
+                attrib["tags"] = ",".join(tagarray)
             else:
                 print("DBG> No tags in", fn)
 
             # Build the tool element
-            newtoolelement = ET.Element('tool', attrib)
-            toolboxpositionelements = toolelement.findall('toolboxposition')
+            newtoolelement = ET.Element("tool", attrib)
+            toolboxpositionelements = toolelement.findall("toolboxposition")
             if not toolboxpositionelements:
                 print("DBG> %s has no toolboxposition" % fn)
             else:
@@ -154,13 +150,13 @@ def scanfiles(filenamelist):
 
 def assemble():
     filenamelist = []
-    for directorytree in ['tools']:
+    for directorytree in ["tools"]:
         filenamelist.extend(getfilenamelist(directorytree))
     filenamelist.sort()
 
     toolbox = scanfiles(filenamelist)
 
-    toolboxelement = ET.Element('toolbox')
+    toolboxelement = ET.Element("toolbox")
 
     toolbox.addElementsTo(toolboxelement)
 
diff --git a/scripts/celery_shell.py b/scripts/celery_shell.py
index 9df3cb8b1f9..bd4fc23e881 100644
--- a/scripts/celery_shell.py
+++ b/scripts/celery_shell.py
@@ -7,16 +7,17 @@ ipython -i scripts/celery_shell.py -- -c config/galaxy.yml
 import logging
 import os
 
-WARNING_MODULES = ['parso', 'asyncio', 'galaxy.datatypes']
+WARNING_MODULES = ["parso", "asyncio", "galaxy.datatypes"]
 for mod in WARNING_MODULES:
     logger = logging.getLogger(mod)
-    logger.setLevel('WARNING')
+    logger.setLevel("WARNING")
 
 from scripts.db_shell import config
-os.environ['GALAXY_CONFIG_FILE'] = os.environ.get('GALAXY_CONFIG_FILE', config['config_file'])
 
-from galaxy.celery import get_galaxy_app
+os.environ["GALAXY_CONFIG_FILE"] = os.environ.get("GALAXY_CONFIG_FILE", config["config_file"])
+
 from galaxy.celery import tasks  # noqa: F401
+from galaxy.celery import get_galaxy_app
 
 HELP = """
 ============
diff --git a/scripts/check_model.py b/scripts/check_model.py
index 0a2e3cb3615..58819421495 100644
--- a/scripts/check_model.py
+++ b/scripts/check_model.py
@@ -8,14 +8,17 @@ import os
 import sys
 from collections import namedtuple
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
-from sqlalchemy import create_engine, MetaData
+from sqlalchemy import (
+    create_engine,
+    MetaData,
+)
 
 from galaxy.model import mapping
 from galaxy.model.orm.scripts import get_config
 
-IndexTuple = namedtuple('IndexTuple', 'table column_names')
+IndexTuple = namedtuple("IndexTuple", "table column_names")
 
 
 def tuple_from_index(index):
@@ -26,7 +29,6 @@ def tuple_from_index(index):
 
 
 def find_missing_indexes():
-
     def load_indexes(metadata):
         indexes = {}
         for t in metadata.tables.values():
@@ -40,7 +42,7 @@ def find_missing_indexes():
     mapping_indexes = load_indexes(metadata)
 
     # create EMPTY metadata, then load from database
-    db_url = get_config(sys.argv)['db_url']
+    db_url = get_config(sys.argv)["db_url"]
     metadata = MetaData(bind=create_engine(db_url))
     metadata.reflect()
     indexes_in_db = load_indexes(metadata)
@@ -50,7 +52,7 @@ def find_missing_indexes():
         return [(mapping_indexes[index], index.table, index.column_names) for index in missing_indexes]
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     indexes = find_missing_indexes()
     if indexes:
         print(json.dumps(indexes, indent=4, sort_keys=True))
diff --git a/scripts/check_python.py b/scripts/check_python.py
index 085f9019122..3ab8f8f7173 100644
--- a/scripts/check_python.py
+++ b/scripts/check_python.py
@@ -11,19 +11,22 @@ def check_python():
         # supported
         return
     else:
-        version_string = '.'.join(str(_) for _ in sys.version_info[:3])
-        msg = """\
+        version_string = ".".join(str(_) for _ in sys.version_info[:3])
+        msg = (
+            """\
 ERROR: Your Python version is: %s
 Galaxy is currently supported on Python >=3.7 .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
-on how to force Galaxy to use a different version.""" % version_string
+on how to force Galaxy to use a different version."""
+            % version_string
+        )
         print(msg, file=sys.stderr)
         raise Exception(msg)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     try:
         check_python()
     except Exception:
diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index f93afed6e53..36cd444845d 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -44,21 +44,30 @@ import shutil
 import sys
 import time
 from collections import defaultdict
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from time import strftime
 
 import sqlalchemy as sa
 from mako.template import Template
-from sqlalchemy import and_, false
+from sqlalchemy import (
+    and_,
+    false,
+)
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
+
+from cleanup_datasets import CleanupDatasetsApplication  # noqa: I100
 
 import galaxy.config
 import galaxy.model.mapping
 import galaxy.util
-from galaxy.util.script import app_properties_from_args, populate_config_args
-
-from cleanup_datasets import CleanupDatasetsApplication  # noqa: I100
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 log = logging.getLogger()
 log.setLevel(logging.INFO)
@@ -74,34 +83,48 @@ def main():
     the user will be notified by email using the specified template file.
     """
     parser = argparse.ArgumentParser()
-    parser.add_argument('legacy_config', metavar='CONFIG', type=str,
-                        default=None,
-                        nargs='?',
-                        help='config file (legacy, use --config instead)')
-    parser.add_argument("-d", "--days", dest="days", action="store",
-                        type=int, help="number of days (60)", default=60)
-    parser.add_argument("--tool_id", default=None,
-                        help="Text to match against tool_id"
-                        "Default: match all")
-    parser.add_argument("--template", default=None,
-                        help="Mako Template file to use as email "
-                        "Variables are 'cutoff' for the cutoff in days, "
-                        "'email' for users email and "
-                        "'datasets' which is a list of tuples "
-                        "containing 'dataset' and 'history' names. "
-                        "Default: admin_cleanup_deletion_template.txt")
-    parser.add_argument("-i", "--info_only", action="store_true",
-                        dest="info_only", help="info about the requested action",
-                        default=False)
-    parser.add_argument("-e", "--email_only", action="store_true",
-                        dest="email_only", help="Send emails only, don't delete",
-                        default=False)
-    parser.add_argument("--smtp", default=None,
-                        help="SMTP Server to use to send email. "
-                        "Default: [read from galaxy ini file]")
-    parser.add_argument("--fromaddr", default=None,
-                        help="From address to use to send email. "
-                        "Default: [read from galaxy ini file]")
+    parser.add_argument(
+        "legacy_config",
+        metavar="CONFIG",
+        type=str,
+        default=None,
+        nargs="?",
+        help="config file (legacy, use --config instead)",
+    )
+    parser.add_argument("-d", "--days", dest="days", action="store", type=int, help="number of days (60)", default=60)
+    parser.add_argument("--tool_id", default=None, help="Text to match against tool_id" "Default: match all")
+    parser.add_argument(
+        "--template",
+        default=None,
+        help="Mako Template file to use as email "
+        "Variables are 'cutoff' for the cutoff in days, "
+        "'email' for users email and "
+        "'datasets' which is a list of tuples "
+        "containing 'dataset' and 'history' names. "
+        "Default: admin_cleanup_deletion_template.txt",
+    )
+    parser.add_argument(
+        "-i",
+        "--info_only",
+        action="store_true",
+        dest="info_only",
+        help="info about the requested action",
+        default=False,
+    )
+    parser.add_argument(
+        "-e",
+        "--email_only",
+        action="store_true",
+        dest="email_only",
+        help="Send emails only, don't delete",
+        default=False,
+    )
+    parser.add_argument(
+        "--smtp", default=None, help="SMTP Server to use to send email. " "Default: [read from galaxy ini file]"
+    )
+    parser.add_argument(
+        "--fromaddr", default=None, help="From address to use to send email. " "Default: [read from galaxy ini file]"
+    )
     populate_config_args(parser)
 
     args = parser.parse_args()
@@ -112,23 +135,21 @@ def main():
     app_properties = app_properties_from_args(args, legacy_config_override=config_override)
 
     if args.smtp is not None:
-        app_properties['smtp_server'] = args.smtp
-    if app_properties.get('smtp_server') is None:
-        parser.error("SMTP Server must be specified as an option (--smtp) "
-                     "or in the config file (smtp_server)")
+        app_properties["smtp_server"] = args.smtp
+    if app_properties.get("smtp_server") is None:
+        parser.error("SMTP Server must be specified as an option (--smtp) " "or in the config file (smtp_server)")
 
     if args.fromaddr is not None:
-        app_properties['email_from'] = args.fromaddr
-    if app_properties.get('email_from') is None:
-        parser.error("From address must be specified as an option "
-                     "(--fromaddr) or in the config file "
-                     "(email_from)")
+        app_properties["email_from"] = args.fromaddr
+    if app_properties.get("email_from") is None:
+        parser.error(
+            "From address must be specified as an option " "(--fromaddr) or in the config file " "(email_from)"
+        )
 
     scriptdir = os.path.dirname(os.path.abspath(__file__))
     template_file = args.template
     if template_file is None:
-        default_template = os.path.join(scriptdir,
-                                        'admin_cleanup_deletion_template.txt')
+        default_template = os.path.join(scriptdir, "admin_cleanup_deletion_template.txt")
         sample_template_file = "%s.sample" % default_template
         if os.path.exists(default_template):
             template_file = default_template
@@ -137,10 +158,12 @@ def main():
             shutil.copyfile(sample_template_file, default_template)
             template_file = default_template
         else:
-            parser.error("Default template (%s) or sample template (%s) not "
-                         "found, please specify template as an option "
-                         "(--template)." % default_template,
-                         sample_template_file)
+            parser.error(
+                "Default template (%s) or sample template (%s) not "
+                "found, please specify template as an option "
+                "(--template)." % default_template,
+                sample_template_file,
+            )
     elif not os.path.exists(template_file):
         parser.error("Specified template file (%s) not found." % template_file)
 
@@ -159,37 +182,40 @@ def main():
         print("# Sending emails only, not deleting ( --email_only )\n")
 
     administrative_delete_datasets(
-        app, cutoff_time, args.days, tool_id=args.tool_id,
-        template_file=template_file, config=config,
-        email_only=args.email_only, info_only=args.info_only)
+        app,
+        cutoff_time,
+        args.days,
+        tool_id=args.tool_id,
+        template_file=template_file,
+        config=config,
+        email_only=args.email_only,
+        info_only=args.info_only,
+    )
     app.shutdown()
     sys.exit(0)
 
 
-def administrative_delete_datasets(app, cutoff_time, cutoff_days,
-                                   tool_id, template_file,
-                                   config, email_only=False,
-                                   info_only=False):
+def administrative_delete_datasets(
+    app, cutoff_time, cutoff_days, tool_id, template_file, config, email_only=False, info_only=False
+):
     # Marks dataset history association deleted and email users
     start = time.time()
     # Get HDAs older than cutoff time (ignore tool_id at this point)
     # We really only need the id column here, but sqlalchemy barfs when
     # trying to select only 1 column
     hda_ids_query = sa.select(
-        (app.model.HistoryDatasetAssociation.table.c.id,
-         app.model.HistoryDatasetAssociation.table.c.deleted),
+        (app.model.HistoryDatasetAssociation.table.c.id, app.model.HistoryDatasetAssociation.table.c.deleted),
         whereclause=and_(
             app.model.Dataset.table.c.deleted == false(),
             app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
-            app.model.HistoryDatasetAssociation.table.c.deleted == false()),
-        from_obj=[sa.outerjoin(
-                  app.model.Dataset.table,
-                  app.model.HistoryDatasetAssociation.table)])
+            app.model.HistoryDatasetAssociation.table.c.deleted == false(),
+        ),
+        from_obj=[sa.outerjoin(app.model.Dataset.table, app.model.HistoryDatasetAssociation.table)],
+    )
 
     # Add all datasets associated with Histories to our list
     hda_ids = []
-    hda_ids.extend(
-        [row.id for row in app.sa_session.execute(hda_ids_query)])
+    hda_ids.extend([row.id for row in app.sa_session.execute(hda_ids_query)])
 
     # Now find the tool_id that generated the dataset (even if it was copied)
     tool_matched_ids = []
@@ -206,39 +232,32 @@ def administrative_delete_datasets(app, cutoff_time, cutoff_days,
     # Process each of the Dataset objects
     for hda_id in hda_ids:
         user_query = sa.select(
-            [app.model.HistoryDatasetAssociation.table,
-             app.model.History.table,
-             app.model.User.table],
-            whereclause=and_(
-                app.model.HistoryDatasetAssociation.table.c.id == hda_id),
-            from_obj=[sa.join(app.model.User.table,
-                              app.model.History.table)
-                      .join(app.model.HistoryDatasetAssociation.table)],
-            use_labels=True)
+            [app.model.HistoryDatasetAssociation.table, app.model.History.table, app.model.User.table],
+            whereclause=and_(app.model.HistoryDatasetAssociation.table.c.id == hda_id),
+            from_obj=[
+                sa.join(app.model.User.table, app.model.History.table).join(app.model.HistoryDatasetAssociation.table)
+            ],
+            use_labels=True,
+        )
         for result in app.sa_session.execute(user_query):
             user_notifications[result[app.model.User.table.c.email]].append(
-                (result[app.model.HistoryDatasetAssociation.table.c.name],
-                 result[app.model.History.table.c.name]))
+                (result[app.model.HistoryDatasetAssociation.table.c.name], result[app.model.History.table.c.name])
+            )
             deleted_instance_count += 1
             if not info_only and not email_only:
                 # Get the HistoryDatasetAssociation objects
-                hda = app.sa_session.query(
-                    app.model.HistoryDatasetAssociation).get(hda_id)
+                hda = app.sa_session.query(app.model.HistoryDatasetAssociation).get(hda_id)
                 if not hda.deleted:
                     # Mark the HistoryDatasetAssociation as deleted
                     hda.deleted = True
                     app.sa_session.add(hda)
-                    print("Marked HistoryDatasetAssociation id %d as "
-                          "deleted" % hda.id)
+                    print("Marked HistoryDatasetAssociation id %d as " "deleted" % hda.id)
                 app.sa_session.flush()
 
     emailtemplate = Template(filename=template_file)
     for (email, dataset_list) in user_notifications.items():
-        msgtext = emailtemplate.render(email=email,
-                                       datasets=dataset_list,
-                                       cutoff=cutoff_days)
-        subject = "Galaxy Server Cleanup " \
-            "- %d datasets DELETED" % len(dataset_list)
+        msgtext = emailtemplate.render(email=email, datasets=dataset_list, cutoff=cutoff_days)
+        subject = "Galaxy Server Cleanup " "- %d datasets DELETED" % len(dataset_list)
         fromaddr = config.email_from
         print()
         print("From: %s" % fromaddr)
@@ -247,8 +266,7 @@ def administrative_delete_datasets(app, cutoff_time, cutoff_days,
         print("----------")
         print(msgtext)
         if not info_only:
-            galaxy.util.send_mail(fromaddr, email, subject,
-                                  msgtext, config)
+            galaxy.util.send_mail(fromaddr, email, subject, msgtext, config)
 
     stop = time.time()
     print()
@@ -261,17 +279,17 @@ def _get_tool_id_for_hda(app, hda_id):
     # TODO Some datasets don't seem to have an entry in jtod or a copied_from
     if hda_id is None:
         return None
-    job = app.sa_session.query(app.model.Job).\
-        join(app.model.JobToOutputDatasetAssociation).\
-        filter(app.model.JobToOutputDatasetAssociation.table.c.dataset_id
-               == hda_id).first()
+    job = (
+        app.sa_session.query(app.model.Job)
+        .join(app.model.JobToOutputDatasetAssociation)
+        .filter(app.model.JobToOutputDatasetAssociation.table.c.dataset_id == hda_id)
+        .first()
+    )
     if job is not None:
         return job.tool_id
     else:
-        hda = app.sa_session.query(app.model.HistoryDatasetAssociation).\
-            get(hda_id)
-        return _get_tool_id_for_hda(app, hda.
-                                    copied_from_history_dataset_association_id)
+        hda = app.sa_session.query(app.model.HistoryDatasetAssociation).get(hda_id)
+        return _get_tool_id_for_hda(app, hda.copied_from_history_dataset_association_id)
 
 
 if __name__ == "__main__":
diff --git a/scripts/cleanup_datasets/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py
index ac858881d44..2b5abe9c808 100755
--- a/scripts/cleanup_datasets/cleanup_datasets.py
+++ b/scripts/cleanup_datasets/cleanup_datasets.py
@@ -6,21 +6,32 @@ import os
 import shutil
 import sys
 import time
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from time import strftime
 
 import sqlalchemy as sa
-from sqlalchemy import and_, false, null, true
+from sqlalchemy import (
+    and_,
+    false,
+    null,
+    true,
+)
 from sqlalchemy.orm import eagerload
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
 import galaxy.config
 from galaxy.datatypes.registry import Registry
 from galaxy.exceptions import ObjectNotFound
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.util import unicodify
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 log = logging.getLogger()
 log.setLevel(logging.INFO)
@@ -68,20 +79,87 @@ def main():
     and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects.
     """
     parser = argparse.ArgumentParser()
-    parser.add_argument('legacy_config', metavar='CONFIG', type=str,
-                        default=None,
-                        nargs='?',
-                        help='config file (legacy, use --config instead)')
+    parser.add_argument(
+        "legacy_config",
+        metavar="CONFIG",
+        type=str,
+        default=None,
+        nargs="?",
+        help="config file (legacy, use --config instead)",
+    )
     parser.add_argument("-d", "--days", dest="days", action="store", type=int, help="number of days (60)", default=60)
-    parser.add_argument("-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False)
-    parser.add_argument("-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False)
-    parser.add_argument("-f", "--force_retry", action="store_true", dest="force_retry", help="performs the requested actions, but ignores whether it might have been done before. Useful when -r wasn't used, but should have been", default=False)
-    parser.add_argument("-1", "--delete_userless_histories", action="store_true", dest="delete_userless_histories", default=False, help="delete userless histories and datasets")
-    parser.add_argument("-2", "--purge_histories", action="store_true", dest="purge_histories", default=False, help="purge deleted histories")
-    parser.add_argument("-3", "--purge_datasets", action="store_true", dest="purge_datasets", default=False, help="purge deleted datasets")
-    parser.add_argument("-4", "--purge_libraries", action="store_true", dest="purge_libraries", default=False, help="purge deleted libraries")
-    parser.add_argument("-5", "--purge_folders", action="store_true", dest="purge_folders", default=False, help="purge deleted library folders")
-    parser.add_argument("-6", "--delete_datasets", action="store_true", dest="delete_datasets", default=False, help="mark deletable datasets as deleted and purge associated dataset instances")
+    parser.add_argument(
+        "-r",
+        "--remove_from_disk",
+        action="store_true",
+        dest="remove_from_disk",
+        help="remove datasets from disk when purged",
+        default=False,
+    )
+    parser.add_argument(
+        "-i",
+        "--info_only",
+        action="store_true",
+        dest="info_only",
+        help="info about the requested action",
+        default=False,
+    )
+    parser.add_argument(
+        "-f",
+        "--force_retry",
+        action="store_true",
+        dest="force_retry",
+        help="performs the requested actions, but ignores whether it might have been done before. Useful when -r wasn't used, but should have been",
+        default=False,
+    )
+    parser.add_argument(
+        "-1",
+        "--delete_userless_histories",
+        action="store_true",
+        dest="delete_userless_histories",
+        default=False,
+        help="delete userless histories and datasets",
+    )
+    parser.add_argument(
+        "-2",
+        "--purge_histories",
+        action="store_true",
+        dest="purge_histories",
+        default=False,
+        help="purge deleted histories",
+    )
+    parser.add_argument(
+        "-3",
+        "--purge_datasets",
+        action="store_true",
+        dest="purge_datasets",
+        default=False,
+        help="purge deleted datasets",
+    )
+    parser.add_argument(
+        "-4",
+        "--purge_libraries",
+        action="store_true",
+        dest="purge_libraries",
+        default=False,
+        help="purge deleted libraries",
+    )
+    parser.add_argument(
+        "-5",
+        "--purge_folders",
+        action="store_true",
+        dest="purge_folders",
+        default=False,
+        help="purge deleted library folders",
+    )
+    parser.add_argument(
+        "-6",
+        "--delete_datasets",
+        action="store_true",
+        dest="delete_datasets",
+        default=False,
+        help="mark deletable datasets as deleted and purge associated dataset instances",
+    )
     populate_config_args(parser)
 
     args = parser.parse_args()
@@ -89,9 +167,14 @@ def main():
     if args.legacy_config:
         config_override = args.legacy_config
 
-    if not (args.purge_folders ^ args.delete_userless_histories
-            ^ args.purge_libraries ^ args.purge_histories
-            ^ args.purge_datasets ^ args.delete_datasets):
+    if not (
+        args.purge_folders
+        ^ args.delete_userless_histories
+        ^ args.purge_libraries
+        ^ args.purge_histories
+        ^ args.purge_datasets
+        ^ args.delete_datasets
+    ):
         parser.print_help()
         sys.exit(0)
 
@@ -138,14 +221,17 @@ def delete_userless_histories(app, cutoff_time, info_only=False, force_retry=Fal
     history_count = 0
     start = time.time()
     if force_retry:
-        histories = app.sa_session.query(app.model.History) \
-                                  .filter(and_(app.model.History.table.c.user_id == null(),
-                                               app.model.History.update_time < cutoff_time))
+        histories = app.sa_session.query(app.model.History).filter(
+            and_(app.model.History.table.c.user_id == null(), app.model.History.update_time < cutoff_time)
+        )
     else:
-        histories = app.sa_session.query(app.model.History) \
-                                  .filter(and_(app.model.History.table.c.user_id == null(),
-                                               app.model.History.table.c.deleted == false(),
-                                               app.model.History.update_time < cutoff_time))
+        histories = app.sa_session.query(app.model.History).filter(
+            and_(
+                app.model.History.table.c.user_id == null(),
+                app.model.History.table.c.deleted == false(),
+                app.model.History.update_time < cutoff_time,
+            )
+        )
     for history in histories:
         if not info_only:
             log.info("Deleting history id %d", history.id)
@@ -168,20 +254,29 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
     history_count = 0
     start = time.time()
     if force_retry:
-        histories = app.sa_session.query(app.model.History) \
-                                  .filter(and_(app.model.History.table.c.deleted == true(),
-                                               app.model.History.update_time < cutoff_time)) \
-                                  .options(eagerload('datasets'))
+        histories = (
+            app.sa_session.query(app.model.History)
+            .filter(and_(app.model.History.table.c.deleted == true(), app.model.History.update_time < cutoff_time))
+            .options(eagerload("datasets"))
+        )
     else:
-        histories = app.sa_session.query(app.model.History) \
-                                  .filter(and_(app.model.History.table.c.deleted == true(),
-                                               app.model.History.table.c.purged == false(),
-                                               app.model.History.update_time < cutoff_time)) \
-                                  .options(eagerload('datasets'))
+        histories = (
+            app.sa_session.query(app.model.History)
+            .filter(
+                and_(
+                    app.model.History.table.c.deleted == true(),
+                    app.model.History.table.c.purged == false(),
+                    app.model.History.update_time < cutoff_time,
+                )
+            )
+            .options(eagerload("datasets"))
+        )
     for history in histories:
         log.info("### Processing history id %d (%s)", history.id, unicodify(history.name))
         for dataset_assoc in history.datasets:
-            _purge_dataset_instance(dataset_assoc, app, remove_from_disk, info_only=info_only)  # mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
+            _purge_dataset_instance(
+                dataset_assoc, app, remove_from_disk, info_only=info_only
+            )  # mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
         if not info_only:
             # TODO: should the Delete DefaultHistoryPermissions be deleted here?  This was incorrectly
             # done in the _list_delete() method of the history controller, so copied it here.  Not sure
@@ -196,7 +291,7 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
             log.info("History id %d will be purged (without 'info_only' mode)", history.id)
         history_count += 1
     stop = time.time()
-    log.info('Purged %d histories.', history_count)
+    log.info("Purged %d histories.", history_count)
     log.info("Elapsed time: %f", stop - start)
     log.info("##########################################")
 
@@ -210,14 +305,17 @@ def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_r
     library_count = 0
     start = time.time()
     if force_retry:
-        libraries = app.sa_session.query(app.model.Library) \
-                                  .filter(and_(app.model.Library.table.c.deleted == true(),
-                                               app.model.Library.table.c.update_time < cutoff_time))
+        libraries = app.sa_session.query(app.model.Library).filter(
+            and_(app.model.Library.table.c.deleted == true(), app.model.Library.table.c.update_time < cutoff_time)
+        )
     else:
-        libraries = app.sa_session.query(app.model.Library) \
-                                  .filter(and_(app.model.Library.table.c.deleted == true(),
-                                               app.model.Library.table.c.purged == false(),
-                                               app.model.Library.table.c.update_time < cutoff_time))
+        libraries = app.sa_session.query(app.model.Library).filter(
+            and_(
+                app.model.Library.table.c.deleted == true(),
+                app.model.Library.table.c.purged == false(),
+                app.model.Library.table.c.update_time < cutoff_time,
+            )
+        )
     for library in libraries:
         _purge_folder(library.root_folder, app, remove_from_disk, info_only=info_only)
         if not info_only:
@@ -227,7 +325,7 @@ def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_r
             app.sa_session.flush()
         library_count += 1
     stop = time.time()
-    log.info('# Purged %d libraries .', library_count)
+    log.info("# Purged %d libraries .", library_count)
     log.info("Elapsed time: %f", stop - start)
     log.info("##########################################")
 
@@ -241,19 +339,25 @@ def purge_folders(app, cutoff_time, remove_from_disk, info_only=False, force_ret
     folder_count = 0
     start = time.time()
     if force_retry:
-        folders = app.sa_session.query(app.model.LibraryFolder) \
-                                .filter(and_(app.model.LibraryFolder.table.c.deleted == true(),
-                                             app.model.LibraryFolder.table.c.update_time < cutoff_time))
+        folders = app.sa_session.query(app.model.LibraryFolder).filter(
+            and_(
+                app.model.LibraryFolder.table.c.deleted == true(),
+                app.model.LibraryFolder.table.c.update_time < cutoff_time,
+            )
+        )
     else:
-        folders = app.sa_session.query(app.model.LibraryFolder) \
-                                .filter(and_(app.model.LibraryFolder.table.c.deleted == true(),
-                                             app.model.LibraryFolder.table.c.purged == false(),
-                                             app.model.LibraryFolder.table.c.update_time < cutoff_time))
+        folders = app.sa_session.query(app.model.LibraryFolder).filter(
+            and_(
+                app.model.LibraryFolder.table.c.deleted == true(),
+                app.model.LibraryFolder.table.c.purged == false(),
+                app.model.LibraryFolder.table.c.update_time < cutoff_time,
+            )
+        )
     for folder in folders:
         _purge_folder(folder, app, remove_from_disk, info_only=info_only)
         folder_count += 1
     stop = time.time()
-    log.info('# Purged %d folders.', folder_count)
+    log.info("# Purged %d folders.", folder_count)
     log.info("Elapsed time: %f", stop - start)
     log.info("##########################################")
 
@@ -262,30 +366,36 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
     # Marks datasets as deleted if associated items are all deleted.
     start = time.time()
     if force_retry:
-        history_dataset_ids_query = sa.select((app.model.Dataset.table.c.id,
-                                               app.model.Dataset.table.c.state),
-                                              whereclause=app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
-                                              from_obj=[sa.outerjoin(app.model.Dataset.table,
-                                                                     app.model.HistoryDatasetAssociation.table)])
-        library_dataset_ids_query = sa.select((app.model.LibraryDataset.table.c.id,
-                                               app.model.LibraryDataset.table.c.deleted),
-                                              whereclause=app.model.LibraryDataset.table.c.update_time < cutoff_time,
-                                              from_obj=[app.model.LibraryDataset.table])
+        history_dataset_ids_query = sa.select(
+            (app.model.Dataset.table.c.id, app.model.Dataset.table.c.state),
+            whereclause=app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
+            from_obj=[sa.outerjoin(app.model.Dataset.table, app.model.HistoryDatasetAssociation.table)],
+        )
+        library_dataset_ids_query = sa.select(
+            (app.model.LibraryDataset.table.c.id, app.model.LibraryDataset.table.c.deleted),
+            whereclause=app.model.LibraryDataset.table.c.update_time < cutoff_time,
+            from_obj=[app.model.LibraryDataset.table],
+        )
     else:
         # We really only need the id column here, but sqlalchemy barfs when trying to select only 1 column
-        history_dataset_ids_query = sa.select((app.model.Dataset.table.c.id,
-                                               app.model.Dataset.table.c.state),
-                                              whereclause=and_(app.model.Dataset.table.c.deleted == false(),
-                                                               app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
-                                                               app.model.HistoryDatasetAssociation.table.c.deleted == true()),
-                                              from_obj=[sa.outerjoin(app.model.Dataset.table,
-                                                                     app.model.HistoryDatasetAssociation.table)])
-        library_dataset_ids_query = sa.select((app.model.LibraryDataset.table.c.id,
-                                               app.model.LibraryDataset.table.c.deleted),
-                                              whereclause=and_(app.model.LibraryDataset.table.c.deleted == true(),
-                                                               app.model.LibraryDataset.table.c.purged == false(),
-                                                               app.model.LibraryDataset.table.c.update_time < cutoff_time),
-                                              from_obj=[app.model.LibraryDataset.table])
+        history_dataset_ids_query = sa.select(
+            (app.model.Dataset.table.c.id, app.model.Dataset.table.c.state),
+            whereclause=and_(
+                app.model.Dataset.table.c.deleted == false(),
+                app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
+                app.model.HistoryDatasetAssociation.table.c.deleted == true(),
+            ),
+            from_obj=[sa.outerjoin(app.model.Dataset.table, app.model.HistoryDatasetAssociation.table)],
+        )
+        library_dataset_ids_query = sa.select(
+            (app.model.LibraryDataset.table.c.id, app.model.LibraryDataset.table.c.deleted),
+            whereclause=and_(
+                app.model.LibraryDataset.table.c.deleted == true(),
+                app.model.LibraryDataset.table.c.purged == false(),
+                app.model.LibraryDataset.table.c.update_time < cutoff_time,
+            ),
+            from_obj=[app.model.LibraryDataset.table],
+        )
     deleted_dataset_count = 0
     deleted_instance_count = 0
     skip = []
@@ -331,7 +441,9 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
         skip.append(dataset.id)
         log.info("######### Processing dataset id: %d", dataset_id)
         if not _dataset_is_deletable(dataset):
-            log.info("Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)")
+            log.info(
+                "Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)"
+            )
             continue
         deleted_dataset_count += 1
         for dataset_instance in dataset.history_associations + dataset.library_associations:
@@ -339,7 +451,12 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
             _purge_dataset_instance(dataset_instance, app, remove_from_disk, info_only=info_only, is_deletable=True)
             deleted_instance_count += 1
     stop = time.time()
-    log.info("Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted", len(skip), deleted_dataset_count, deleted_instance_count)
+    log.info(
+        "Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted",
+        len(skip),
+        deleted_dataset_count,
+        deleted_instance_count,
+    )
     log.info("Total elapsed time: %f", stop - start)
     log.info("##########################################")
 
@@ -351,16 +468,22 @@ def purge_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_re
     disk_space = 0
     start = time.time()
     if force_retry:
-        datasets = app.sa_session.query(app.model.Dataset) \
-                                 .filter(and_(app.model.Dataset.table.c.deleted == true(),
-                                              app.model.Dataset.table.c.purgable == true(),
-                                              app.model.Dataset.table.c.update_time < cutoff_time))
+        datasets = app.sa_session.query(app.model.Dataset).filter(
+            and_(
+                app.model.Dataset.table.c.deleted == true(),
+                app.model.Dataset.table.c.purgable == true(),
+                app.model.Dataset.table.c.update_time < cutoff_time,
+            )
+        )
     else:
-        datasets = app.sa_session.query(app.model.Dataset) \
-                                 .filter(and_(app.model.Dataset.table.c.deleted == true(),
-                                              app.model.Dataset.table.c.purgable == true(),
-                                              app.model.Dataset.table.c.purged == false(),
-                                              app.model.Dataset.table.c.update_time < cutoff_time))
+        datasets = app.sa_session.query(app.model.Dataset).filter(
+            and_(
+                app.model.Dataset.table.c.deleted == true(),
+                app.model.Dataset.table.c.purgable == true(),
+                app.model.Dataset.table.c.purged == false(),
+                app.model.Dataset.table.c.update_time < cutoff_time,
+            )
+        )
     for dataset in datasets:
         file_size = dataset.file_size
         _purge_dataset(app, dataset, remove_from_disk, info_only=info_only)
@@ -370,7 +493,7 @@ def purge_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_re
         except Exception:
             pass
     stop = time.time()
-    log.info('Purged %d datasets', dataset_count)
+    log.info("Purged %d datasets", dataset_count)
     if remove_from_disk:
         log.info("Freed disk space: %d", disk_space)
     log.info("Elapsed time: %f", stop - start)
@@ -381,24 +504,38 @@ def _purge_dataset_instance(dataset_instance, app, remove_from_disk, info_only=F
     # A dataset_instance is either a HDA or an LDDA.  Purging a dataset instance marks the instance as deleted,
     # and marks the associated dataset as deleted if it is not associated with another active DatsetInstance.
     if not info_only:
-        log.info("Marking as deleted: %s id %d (for dataset id %d)",
-              dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id)
+        log.info(
+            "Marking as deleted: %s id %d (for dataset id %d)",
+            dataset_instance.__class__.__name__,
+            dataset_instance.id,
+            dataset_instance.dataset.id,
+        )
         dataset_instance.mark_deleted()
         dataset_instance.clear_associated_files()
         app.sa_session.add(dataset_instance)
         app.sa_session.flush()
         app.sa_session.refresh(dataset_instance.dataset)
     else:
-        log.info("%s id %d (for dataset id %d) will be marked as deleted (without 'info_only' mode)",
-              dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id)
+        log.info(
+            "%s id %d (for dataset id %d) will be marked as deleted (without 'info_only' mode)",
+            dataset_instance.__class__.__name__,
+            dataset_instance.id,
+            dataset_instance.dataset.id,
+        )
     if is_deletable or _dataset_is_deletable(dataset_instance.dataset):
         # Calling methods may have already checked _dataset_is_deletable, if so, is_deletable should be True
         _delete_dataset(dataset_instance.dataset, app, remove_from_disk, info_only=info_only, is_deletable=is_deletable)
     else:
         if info_only:
-            log.info("Not deleting dataset %d, (will be possibly deleted without 'info_only' mode)", dataset_instance.dataset.id)
+            log.info(
+                "Not deleting dataset %d, (will be possibly deleted without 'info_only' mode)",
+                dataset_instance.dataset.id,
+            )
         else:
-            log.info("Not deleting dataset %d (shared between multiple histories/libraries, at least one not deleted)", dataset_instance.dataset.id)
+            log.info(
+                "Not deleting dataset %d (shared between multiple histories/libraries, at least one not deleted)",
+                dataset_instance.dataset.id,
+            )
 
 
 def _dataset_is_deletable(dataset):
@@ -416,27 +553,41 @@ def _delete_dataset(dataset, app, remove_from_disk, info_only=False, is_deletabl
         metadata_files = []
         # lets create a list of metadata files, then perform actions on them
         for hda in dataset.history_associations:
-            for metadata_file in app.sa_session.query(app.model.MetadataFile) \
-                                               .filter(app.model.MetadataFile.table.c.hda_id == hda.id):
+            for metadata_file in app.sa_session.query(app.model.MetadataFile).filter(
+                app.model.MetadataFile.table.c.hda_id == hda.id
+            ):
                 metadata_files.append(metadata_file)
         for ldda in dataset.library_associations:
-            for metadata_file in app.sa_session.query(app.model.MetadataFile) \
-                                               .filter(app.model.MetadataFile.table.c.lda_id == ldda.id):
+            for metadata_file in app.sa_session.query(app.model.MetadataFile).filter(
+                app.model.MetadataFile.table.c.lda_id == ldda.id
+            ):
                 metadata_files.append(metadata_file)
         for metadata_file in metadata_files:
             op_description = "marked as deleted"
             if remove_from_disk:
                 op_description = op_description + " and purged from disk"
             if info_only:
-                log.info("The following metadata files attached to associations of Dataset '%d' will be %s (without 'info_only' mode):", dataset.id, op_description)
+                log.info(
+                    "The following metadata files attached to associations of Dataset '%d' will be %s (without 'info_only' mode):",
+                    dataset.id,
+                    op_description,
+                )
             else:
-                log.info("The following metadata files attached to associations of Dataset '%d' have been %s:", dataset.id, op_description)
+                log.info(
+                    "The following metadata files attached to associations of Dataset '%d' have been %s:",
+                    dataset.id,
+                    op_description,
+                )
                 if remove_from_disk:
                     try:
                         log.info("Removing disk file %s", metadata_file.file_name)
                         os.unlink(metadata_file.file_name)
                     except Exception as e:
-                        log.info("Error, exception: %s caught attempting to purge metadata file %s\n", unicodify(e), metadata_file.file_name)
+                        log.info(
+                            "Error, exception: %s caught attempting to purge metadata file %s\n",
+                            unicodify(e),
+                            metadata_file.file_name,
+                        )
                     metadata_file.purged = True
                     app.sa_session.add(metadata_file)
                     app.sa_session.flush()
@@ -465,7 +616,9 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
                         os.unlink(dataset.file_name)
                         # Remove associated extra files from disk if they exist
                         if dataset.extra_files_path and os.path.exists(dataset.extra_files_path):
-                            shutil.rmtree(dataset.extra_files_path)  # we need to delete the directory and its contents; os.unlink would always fail on a directory
+                            shutil.rmtree(
+                                dataset.extra_files_path
+                            )  # we need to delete the directory and its contents; os.unlink would always fail on a directory
                         usage_users = []
                         for hda in dataset.history_associations:
                             if not hda.purged:
@@ -482,7 +635,11 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
                 else:
                     log.info("Dataset %d will be purged (without 'info_only' mode)", dataset.id)
             else:
-                log.info("This dataset (%d) is not purgable, the file (%s) will not be removed.\n", dataset.id, dataset.file_name)
+                log.info(
+                    "This dataset (%d) is not purgable, the file (%s) will not be removed.\n",
+                    dataset.id,
+                    dataset.file_name,
+                )
         except OSError as exc:
             log.error("Error, dataset file has already been removed: %s", unicodify(exc))
             log.error("Purging dataset id %d", dataset.id)
@@ -503,7 +660,9 @@ def _purge_folder(folder, app, remove_from_disk, info_only=False):
         log.info("Deleting library dataset id %d", ld.id)
         ld.deleted = True
         for ldda in [ld.library_dataset_dataset_association] + ld.expired_datasets:
-            _purge_dataset_instance(ldda, app, remove_from_disk, info_only=info_only)  # mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
+            _purge_dataset_instance(
+                ldda, app, remove_from_disk, info_only=info_only
+            )  # mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
     for sub_folder in folder.folders:
         _purge_folder(sub_folder, app, remove_from_disk, info_only=info_only)
     if not info_only:
@@ -516,6 +675,7 @@ def _purge_folder(folder, app, remove_from_disk, info_only=False):
 
 class CleanupDatasetsApplication:
     """Encapsulates the state of a Universe application"""
+
     def __init__(self, config):
         self.object_store = build_object_store_from_config(config)
         # Setup the database engine and ORM
diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index b20ca097a46..b7183d3aa29 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -21,7 +21,7 @@ from psycopg2.extras import NamedTupleCursor
 from sqlalchemy.engine.url import make_url
 
 galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
-sys.path.insert(1, os.path.join(galaxy_root, 'lib'))
+sys.path.insert(1, os.path.join(galaxy_root, "lib"))
 
 import galaxy.config
 from galaxy.exceptions import ObjectNotFound
@@ -32,7 +32,7 @@ from galaxy.util.script import (
     set_log_handler,
 )
 
-DEFAULT_LOG_DIR = os.path.join(galaxy_root, 'scripts', 'cleanup_datasets')
+DEFAULT_LOG_DIR = os.path.join(galaxy_root, "scripts", "cleanup_datasets")
 
 log = logging.getLogger(__name__)
 
@@ -51,7 +51,7 @@ class LevelFormatter(logging.Formatter):
             fmt = self.warn_fmt
         else:
             fmt = self.def_fmt
-        if hasattr(self, '_style'):  # py3
+        if hasattr(self, "_style"):  # py3
             self._style._fmt = fmt
         else:
             self._fmt = fmt
@@ -74,6 +74,7 @@ class Action:
     Generally you should set at least ``_action_sql`` in subclasses (although it's possible to just override ``sql``
     directly.)
     """
+
     update_time_sql = ", update_time = NOW() AT TIME ZONE 'utc'"
     force_retry_sql = " AND NOT purged"
     primary_key = None
@@ -86,18 +87,18 @@ class Action:
     @classmethod
     def name_c(cls):
         # special case - for more complex stuff you can always implement name_c() on subclasses
-        clsname = cls.__name__.replace('HDA', 'Hda')
+        clsname = cls.__name__.replace("HDA", "Hda")
         actname = [clsname[0].lower()]
         for c in clsname[1:]:
             if c in string.ascii_uppercase:
-                c = '_' + c.lower()
+                c = "_" + c.lower()
             actname.append(c)
-        return ''.join(actname)
+        return "".join(actname)
 
     @classmethod
     def doc_iter(cls):
         for line in cls.__doc__.splitlines():
-            yield line.replace(' ', '', 4)
+            yield line.replace(" ", "", 4)
 
     def __init__(self, app):
         self._log_dir = app.args.log_dir
@@ -129,24 +130,24 @@ class Action:
         if self._log_file:
             logf = os.path.join(self._log_dir, self._log_file)
         else:
-            logf = os.path.join(self._log_dir, self.name + '.log')
+            logf = os.path.join(self._log_dir, self.name + ".log")
         if self._dry_run:
-            log.info('--dry-run specified, logging changes to stderr instead of log file: %s' % logf)
+            log.info("--dry-run specified, logging changes to stderr instead of log file: %s" % logf)
             h = set_log_handler()
         else:
-            log.info('Opening log file: %s' % logf)
+            log.info("Opening log file: %s" % logf)
             h = set_log_handler(filename=logf)
         h.setLevel(logging.DEBUG if self._debug else logging.INFO)
         h.setFormatter(LevelFormatter())
         self.__log = logging.getLogger(self.name)
         self.__log.addHandler(h)
         self.__log.propagate = False
-        m = ('==== Log opened: %s ' % datetime.datetime.now().isoformat()).ljust(72, '=')
+        m = ("==== Log opened: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
         self.__log.info(m)
-        self.__log.info(f'Epoch time for this action: {self._epoch_time}')
+        self.__log.info(f"Epoch time for this action: {self._epoch_time}")
 
     def __close_log(self):
-        m = ('==== Log closed: %s ' % datetime.datetime.now().isoformat()).ljust(72, '=')
+        m = ("==== Log closed: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
         self.log.info(m)
         self.__log = None
 
@@ -197,8 +198,8 @@ class Action:
     @property
     def sql_args(self):
         args = self._action_sql_args.copy()
-        if 'days' not in args:
-            args['days'] = self._days
+        if "days" not in args:
+            args["days"] = self._days
         return args
 
     def _collect_row_results(self, row, results, primary_key):
@@ -214,11 +215,11 @@ class Action:
 
     def _log_results(self, results, primary_key):
         for primary in sorted(results.keys()):
-            self.log.info(f'{primary_key}: {primary}')
+            self.log.info(f"{primary_key}: {primary}")
             for causal, s in zip(self.causals, results[primary]):
                 for r in sorted(s):
-                    secondaries = ', '.join('%s: %s' % x for x in zip(causal[1:], r[1:]))
-                    self.log.info(f'{causal[0]} {r[0]} caused {secondaries}')
+                    secondaries = ", ".join("%s: %s" % x for x in zip(causal[1:], r[1:]))
+                    self.log.info(f"{causal[0]} {r[0]} caused {secondaries}")
 
     def handle_results(self, cur):
         results = {}
@@ -244,11 +245,11 @@ class Action:
 
 
 class RemovesObjects:
-    """Base class for mixins that remove objects from object stores.
-    """
+    """Base class for mixins that remove objects from object stores."""
+
     def _init(self):
         self.objects_to_remove = set()
-        log.info('Initializing object store for action %s', self.name)
+        log.info("Initializing object store for action %s", self.name)
         self.object_store = build_object_store_from_config(self._config)
         self._register_row_method(self.collect_removed_object_info)
         self._register_post_method(self.remove_objects)
@@ -273,13 +274,13 @@ class RemovesObjects:
             # identifier" which in the case of Disk would be the path
             if not check_exists or self.object_store.exists(object_to_remove, **object_store_kwargs):
                 filename = self.object_store.get_filename(object_to_remove, **object_store_kwargs)
-                self.log.info('removing %s at: %s', object_to_remove, filename)
+                self.log.info("removing %s at: %s", object_to_remove, filename)
                 if not self._dry_run:
                     self.object_store.delete(object_to_remove, entire_dir=entire_dir, **object_store_kwargs)
         except ObjectNotFound as e:
-            [log_.warning('object store failure: %s: %s', object_to_remove, e) for log_ in loggers]
+            [log_.warning("object store failure: %s: %s", object_to_remove, e) for log_ in loggers]
         except Exception as e:
-            [log_.error('delete failure: %s: %s', object_to_remove, e) for log_ in loggers]
+            [log_.error("delete failure: %s: %s", object_to_remove, e) for log_ in loggers]
 
     def remove_object(self, object_to_remove):
         raise NotImplementedError()
@@ -296,6 +297,7 @@ class PurgesHDAs:
     To use, place ``{purge_hda_dependencies_sql}`` somewhere in your CTEs after a ``purged_hda_ids`` CTE returning HDA
     ids. If you have additional CTEs after the template point, be sure to append a ``,``.
     """
+
     _purge_hda_dependencies_sql = """deleted_metadata_file_ids
           AS (     UPDATE metadata_file
                       SET deleted = true{update_time_sql}
@@ -353,6 +355,7 @@ class RequiresDiskUsageRecalculation:
 
     To use, ensure your query returns a ``recalculate_disk_usage_user_id`` column.
     """
+
     def _init(self):
         self.__recalculate_disk_usage_user_ids = set()
         self._register_row_method(self.collect_recalculate_disk_usage_user_id)
@@ -371,7 +374,7 @@ class RequiresDiskUsageRecalculation:
 
         This could probably be done more efficiently.
         """
-        log.info('Recalculating disk usage for users whose data were purged')
+        log.info("Recalculating disk usage for users whose data were purged")
         for user_id in sorted(self.__recalculate_disk_usage_user_ids):
             # TODO: h.purged = false should be unnecessary once all hdas in purged histories are purged.
             sql = """
@@ -392,11 +395,11 @@ class RequiresDiskUsageRecalculation:
                     WHERE id = %(user_id)s
                 RETURNING disk_usage;
             """
-            args = {'user_id': user_id}
+            args = {"user_id": user_id}
             cur = self._update(sql, args, add_event=False)
             for row in cur:
                 # disk_usage might be None (e.g. user has purged all data)
-                self.log.info('recalculate_disk_usage user_id %i to %s bytes' % (user_id, row.disk_usage))
+                self.log.info("recalculate_disk_usage user_id %i to %s bytes" % (user_id, row.disk_usage))
 
 
 class RemovesMetadataFiles(RemovesObjects):
@@ -404,16 +407,15 @@ class RemovesMetadataFiles(RemovesObjects):
 
     To use, ensure your query returns ``deleted_metadata_file_id`` and ``object_store_id`` columns.
     """
-    object_class = namedtuple('MetadataFile', ['id', 'object_store_id'])
-    id_column = 'deleted_metadata_file_id'
+
+    object_class = namedtuple("MetadataFile", ["id", "object_store_id"])
+    id_column = "deleted_metadata_file_id"
 
     def remove_object(self, metadata_file):
         self.remove_from_object_store(
             metadata_file,
-            dict(
-                extra_dir='_metadata_files',
-                extra_dir_at_root=True,
-                alt_name="metadata_%d.dat" % metadata_file.id))
+            dict(extra_dir="_metadata_files", extra_dir_at_root=True, alt_name="metadata_%d.dat" % metadata_file.id),
+        )
 
 
 class RemovesDatasets(RemovesObjects):
@@ -421,18 +423,15 @@ class RemovesDatasets(RemovesObjects):
 
     To use, ensure your query returns ``purged_dataset_id`` and ``object_store_id`` columns.
     """
-    object_class = namedtuple('Dataset', ['id', 'object_store_id'])
-    id_column = 'purged_dataset_id'
+
+    object_class = namedtuple("Dataset", ["id", "object_store_id"])
+    id_column = "purged_dataset_id"
 
     def remove_object(self, dataset):
         self.remove_from_object_store(dataset, dict())
         self.remove_from_object_store(
-            dataset,
-            dict(
-                dir_only=True,
-                extra_dir="dataset_%d_files" % dataset.id),
-            entire_dir=True,
-            check_exists=True)
+            dataset, dict(dir_only=True, extra_dir="dataset_%d_files" % dataset.id), entire_dir=True, check_exists=True
+        )
 
 
 #
@@ -445,6 +444,7 @@ class UpdateHDAPurgedFlag(Action):
     The old cleanup script does not mark HistoryDatasetAssociations as purged when deleted Histories
     are purged.  This action can be used to rectify that situation.
     """
+
     # update_time is intentionally left unmodified.
     _action_sql = """
         WITH purged_hda_ids
@@ -471,6 +471,7 @@ class DeleteUserlessHistories(Action):
     - Mark deleted all "anonymous" Histories (not owned by a registered user) that are older than
       the specified number of days.
     """
+
     _action_sql = """
         WITH deleted_history_ids
           AS (     UPDATE history
@@ -495,6 +496,7 @@ class DeleteInactiveUsers(Action):
     - Mark deleted all users that are older than the specified number of days.
     - Mark deleted (state = 'deleted') all Jobs whose user_ids are deleted in this step.
     """
+
     force_retry_sql = " AND NOT deleted"
     _action_sql = """
         WITH deleted_user_ids
@@ -523,9 +525,7 @@ class DeleteInactiveUsers(Action):
                              ON deleted_job_ids.user_id = deleted_user_ids.id
     ORDER BY deleted_user_ids.id
     """
-    causals = (
-        ('purged_user_id', 'purged_job_id'),
-    )
+    causals = (("purged_user_id", "purged_job_id"),)
 
 
 class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
@@ -539,6 +539,7 @@ class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
       ROLE.
     - Delete all UserAddresses whose user_ids are purged in this step.
     """
+
     _action_sql = """
         WITH purged_user_ids
           AS (     UPDATE galaxy_user
@@ -629,13 +630,13 @@ class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
     ORDER BY purged_user_ids.id
     """
     causals = (
-        ('purged_user_id', 'purged_history_id'),
-        ('purged_history_id', 'purged_hda_id'),
-        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
-        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
-        ('purged_user_id', 'deleted_uga_id'),
-        ('purged_user_id', 'deleted_ura_id'),
-        ('purged_user_id', 'deleted_ua_id'),
+        ("purged_user_id", "purged_history_id"),
+        ("purged_history_id", "purged_hda_id"),
+        ("purged_hda_id", "deleted_metadata_file_id", "object_store_id"),
+        ("purged_hda_id", "deleted_icda_id", "deleted_icda_hda_id"),
+        ("purged_user_id", "deleted_uga_id"),
+        ("purged_user_id", "deleted_ura_id"),
+        ("purged_user_id", "deleted_ua_id"),
     )
 
     def _init(self):
@@ -650,16 +651,16 @@ class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
     def zero_disk_usage(self):
         if not self.__zero_disk_usage_user_ids:
             return
-        log.info('Zeroing disk usage for users who were purged')
+        log.info("Zeroing disk usage for users who were purged")
         sql = """
             UPDATE galaxy_user
                SET disk_usage = 0
              WHERE id IN %(user_ids)s
         """
         user_ids = sorted(self.__zero_disk_usage_user_ids)
-        args = {'user_ids': tuple(user_ids)}
+        args = {"user_ids": tuple(user_ids)}
         self._update(sql, args, add_event=False)
-        self.log.info('zero_disk_usage user_ids: %s', ' '.join(str(i) for i in user_ids))
+        self.log.info("zero_disk_usage user_ids: %s", " ".join(str(i) for i in user_ids))
 
 
 class PurgeDeletedUsersGDPR(PurgesHDAs, RemovesMetadataFiles, Action):
@@ -670,6 +671,7 @@ class PurgeDeletedUsersGDPR(PurgesHDAs, RemovesMetadataFiles, Action):
     NOTE: Your database must have the pgcrypto extension installed e.g. with:
       CREATE EXTENSION IF NOT EXISTS pgcrypto;
     """
+
     _action_sql = """
         WITH purged_user_ids
           AS (     UPDATE galaxy_user
@@ -763,18 +765,18 @@ class PurgeDeletedUsersGDPR(PurgesHDAs, RemovesMetadataFiles, Action):
     ORDER BY purged_user_ids.id
     """
     causals = (
-        ('purged_user_id', 'purged_history_id'),
-        ('purged_history_id', 'purged_hda_id'),
-        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
-        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
-        ('purged_user_id', 'deleted_uga_id'),
-        ('purged_user_id', 'deleted_ura_id'),
-        ('purged_user_id', 'deleted_ua_id'),
+        ("purged_user_id", "purged_history_id"),
+        ("purged_history_id", "purged_hda_id"),
+        ("purged_hda_id", "deleted_metadata_file_id", "object_store_id"),
+        ("purged_hda_id", "deleted_icda_id", "deleted_icda_hda_id"),
+        ("purged_user_id", "deleted_uga_id"),
+        ("purged_user_id", "deleted_ura_id"),
+        ("purged_user_id", "deleted_ua_id"),
     )
 
     @classmethod
     def name_c(cls):
-        return 'purge_deleted_users_gdpr'
+        return "purge_deleted_users_gdpr"
 
 
 class PurgeDeletedHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRecalculation, Action):
@@ -787,6 +789,7 @@ class PurgeDeletedHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRecalc
     - Mark purged all HistoryDatasetAssociations for which an ImplicitlyConvertedDatasetAssociation
       with matching hda_id is deleted in this step.
     """
+
     _action_sql = """
         WITH purged_hda_ids
           AS (     UPDATE history_dataset_association
@@ -817,8 +820,8 @@ class PurgeDeletedHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRecalc
     ORDER BY purged_hda_ids.id
     """
     causals = (
-        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
-        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
+        ("purged_hda_id", "deleted_metadata_file_id", "object_store_id"),
+        ("purged_hda_id", "deleted_icda_id", "deleted_icda_hda_id"),
     )
 
 
@@ -826,6 +829,7 @@ class PurgeHistorylessHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRe
     """
     - Mark purged all HistoryDatasetAssociations whose history_id is null.
     """
+
     _action_sql = """
         WITH purged_hda_ids
           AS (     UPDATE history_dataset_association
@@ -852,8 +856,8 @@ class PurgeHistorylessHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRe
     ORDER BY purged_hda_ids.id
     """
     causals = (
-        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
-        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
+        ("purged_hda_id", "deleted_metadata_file_id", "object_store_id"),
+        ("purged_hda_id", "deleted_icda_id", "deleted_icda_hda_id"),
     )
 
 
@@ -862,6 +866,7 @@ class PurgeErrorHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRecalcul
     - Mark purged all HistoryDatasetAssociations whose dataset_id is state = 'error' that are older
       than the specified number of days.
     """
+
     force_retry_sql = " AND NOT history_dataset_association.purged"
     _action_sql = """
         WITH purged_hda_ids
@@ -895,8 +900,8 @@ class PurgeErrorHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRecalcul
     ORDER BY purged_hda_ids.id
     """
     causals = (
-        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
-        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
+        ("purged_hda_id", "deleted_metadata_file_id", "object_store_id"),
+        ("purged_hda_id", "deleted_icda_id", "deleted_icda_hda_id"),
     )
 
 
@@ -905,6 +910,7 @@ class PurgeHDAsOfPurgedHistories(PurgesHDAs, RequiresDiskUsageRecalculation, Act
     - Mark purged all HistoryDatasetAssociations in histories that are purged and older than the
       specified number of days.
     """
+
     force_retry_sql = " AND NOT history_dataset_association.purged"
     _action_sql = """
         WITH purged_hda_ids
@@ -945,6 +951,7 @@ class PurgeDeletedHistories(PurgesHDAs, RequiresDiskUsageRecalculation, Action):
     - Mark purged all HistoryDatasetAssociations in Histories marked purged in this step (if not
       already purged).
     """
+
     _action_sql = """
         WITH purged_history_ids
           AS (     UPDATE history
@@ -989,9 +996,9 @@ class PurgeDeletedHistories(PurgesHDAs, RequiresDiskUsageRecalculation, Action):
     ORDER BY purged_history_ids.id
     """
     causals = (
-        ('purged_history_id', 'purged_hda_id'),
-        ('purged_hda_id', 'deleted_metadata_file_id', 'object_store_id'),
-        ('purged_hda_id', 'deleted_icda_id', 'deleted_icda_hda_id'),
+        ("purged_history_id", "purged_hda_id"),
+        ("purged_hda_id", "deleted_metadata_file_id", "object_store_id"),
+        ("purged_hda_id", "deleted_icda_id", "deleted_icda_hda_id"),
     )
 
 
@@ -1000,6 +1007,7 @@ class DeleteExportedHistories(Action):
     - Mark deleted all Datasets that are derivative of JobExportHistoryArchives that are older than
       the specified number of days.
     """
+
     _action_sql = """
         WITH deleted_dataset_ids
           AS (     UPDATE dataset
@@ -1027,6 +1035,7 @@ class DeleteDatasets(Action):
     - JobExportHistoryArchives have no deleted column, so the datasets for these will simply be
       deleted after the specified number of days
     """
+
     _action_sql = """
         WITH deleted_dataset_ids
           AS (     UPDATE dataset
@@ -1060,6 +1069,7 @@ class PurgeDatasets(RemovesDatasets, Action):
     """
     - Mark purged all Datasets marked deleted that are older than the specified number of days.
     """
+
     _action_sql = """
         WITH purged_dataset_ids
           AS (     UPDATE dataset
@@ -1105,7 +1115,12 @@ class Cleanup:
         if self.__actions is None:
             self.__actions = {}
             for name, value in inspect.getmembers(sys.modules[__name__]):
-                if not name.startswith('_') and inspect.isclass(value) and value != Action and issubclass(value, Action):
+                if (
+                    not name.startswith("_")
+                    and inspect.isclass(value)
+                    and value != Action
+                    and issubclass(value, Action)
+                ):
                     self.__actions[value.name_c()] = value
         return self.__actions
 
@@ -1113,76 +1128,63 @@ class Cleanup:
     def conn(self):
         if self.__conn is None:
             url = make_url(galaxy.config.get_database_url(self.config))
-            log.info(f'Connecting to database with URL: {url}')
-            args = url.translate_connect_args(username='user')
+            log.info(f"Connecting to database with URL: {url}")
+            args = url.translate_connect_args(username="user")
             args.update(url.query)
-            assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
+            assert url.get_dialect().name == "postgresql", "This script can only be used with PostgreSQL."
             self.__conn = psycopg2.connect(cursor_factory=NamedTupleCursor, **args)
             # TODO: is this per session or cursor?
             if self.args.work_mem is not None:
-                log.info('Setting work_mem to %s' % self.args.work_mem)
-                self.__conn.cursor().execute('SET work_mem TO %s', (self.args.work_mem,))
+                log.info("Setting work_mem to %s" % self.args.work_mem)
+                self.__conn.cursor().execute("SET work_mem TO %s", (self.args.work_mem,))
         return self.__conn
 
     def __parse_args(self):
         parser = argparse.ArgumentParser()
         populate_config_args(parser)
         parser.add_argument(
-            '-d', '--debug',
-            action='store_true',
-            default=False,
-            help='Enable debug logging (SQL queries)')
+            "-d", "--debug", action="store_true", default=False, help="Enable debug logging (SQL queries)"
+        )
+        parser.add_argument("--dry-run", action="store_true", default=False, help="Dry run (rollback all transactions)")
         parser.add_argument(
-            '--dry-run',
-            action='store_true',
-            default=False,
-            help="Dry run (rollback all transactions)")
+            "--force-retry", action="store_true", default=False, help="Retry file removals (on applicable actions)"
+        )
         parser.add_argument(
-            '--force-retry',
-            action='store_true',
-            default=False,
-            help="Retry file removals (on applicable actions)")
-        parser.add_argument(
-            '-o', '--older-than',
-            dest='days',
+            "-o",
+            "--older-than",
+            dest="days",
             type=int,
             default=14,
-            help='Only perform action(s) on objects that have not been updated since the specified number of days')
+            help="Only perform action(s) on objects that have not been updated since the specified number of days",
+        )
         parser.add_argument(
-            '-U', '--no-update-time',
-            action='store_false',
-            dest='update_time',
+            "-U",
+            "--no-update-time",
+            action="store_false",
+            dest="update_time",
             default=True,
-            help="Don't set update_time on updated objects")
+            help="Don't set update_time on updated objects",
+        )
         parser.add_argument(
-            '-s', '--sequence',
-            dest='sequence',
-            default='',
-            help='DEPRECATED: Comma-separated sequence of actions')
+            "-s", "--sequence", dest="sequence", default="", help="DEPRECATED: Comma-separated sequence of actions"
+        )
         parser.add_argument(
-            '-w', '--work-mem',
-            dest='work_mem',
-            default=None,
-            help='Set PostgreSQL work_mem for this connection')
+            "-w", "--work-mem", dest="work_mem", default=None, help="Set PostgreSQL work_mem for this connection"
+        )
+        parser.add_argument("-l", "--log-dir", default=DEFAULT_LOG_DIR, help="Log file directory")
+        parser.add_argument("-g", "--log-file", default=None, help="Log file name")
         parser.add_argument(
-            '-l', '--log-dir',
-            default=DEFAULT_LOG_DIR,
-            help='Log file directory')
-        parser.add_argument(
-            '-g', '--log-file',
-            default=None,
-            help='Log file name')
-        parser.add_argument(
-            'actions',
-            nargs='*',
-            metavar='ACTION',
+            "actions",
+            nargs="*",
+            metavar="ACTION",
             default=[],
-            help='Action(s) to perform, chosen from: %s' % ', '.join(sorted(self.actions.keys())))
+            help="Action(s) to perform, chosen from: %s" % ", ".join(sorted(self.actions.keys())),
+        )
         self.args = parser.parse_args()
 
         # add deprecated sequence arg to actions
-        self.args.sequence = [x.strip() for x in self.args.sequence.split(',')]
-        if self.args.sequence != ['']:
+        self.args.sequence = [x.strip() for x in self.args.sequence.split(",")]
+        if self.args.sequence != [""]:
             self.args.actions.extend(self.args.sequence)
         if not self.args.actions:
             parser.error("Please specify one or more actions")
@@ -1190,16 +1192,17 @@ class Cleanup:
     def __setup_logging(self):
         logging.basicConfig(
             level=logging.DEBUG if self.args.debug else logging.INFO,
-            format="%(asctime)s %(levelname)-5s %(funcName)s(): %(message)s")
+            format="%(asctime)s %(levelname)-5s %(funcName)s(): %(message)s",
+        )
 
     def __validate_actions(self):
         ok = True
         for name in self.args.actions:
             if name not in self.actions.keys():
-                log.error('Unknown action in sequence: %s' % name)
+                log.error("Unknown action in sequence: %s" % name)
                 ok = False
         if not ok:
-            log.critical('Exiting due to previous error(s)')
+            log.critical("Exiting due to previous error(s)")
             sys.exit(1)
 
     def __load_config(self):
@@ -1219,17 +1222,19 @@ class Cleanup:
             self.conn.commit()
             log.info("An event must exist for the subsequent query to succeed, so a dummy event has been created")
         else:
-            log.info("Not executing event creation (increments sequence even when rolling back), using an old "
-                     "event ID (%i) for dry run" % max_id)
+            log.info(
+                "Not executing event creation (increments sequence even when rolling back), using an old "
+                "event ID (%i) for dry run" % max_id
+            )
         return max_id
 
     def _execute(self, sql, args):
         cur = self.conn.cursor()
-        sql_str = cur.mogrify(sql, args).decode('utf-8')
+        sql_str = cur.mogrify(sql, args).decode("utf-8")
         log.debug(f"SQL is: {sql_str}")
         log.info("Executing SQL")
         cur.execute(sql, args)
-        log.info('Database status: %s', cur.statusmessage)
+        log.info("Database status: %s", cur.statusmessage)
         return cur
 
     def _create_event(self, message=None):
@@ -1246,20 +1251,20 @@ class Cleanup:
               RETURNING id;
         """
         message = message or self.__current_action
-        args = {'message': message}
+        args = {"message": message}
         event_id = self._execute(sql, args).fetchone()[0]
         log.info("Created event %s for action: %s", event_id, self.__current_action)
         return event_id
 
     def _update(self, sql, args, add_event=True, event_message=None):
-        if add_event and 'event_id' not in args:
-            args['event_id'] = self._create_event(message=event_message)
+        if add_event and "event_id" not in args:
+            args["event_id"] = self._create_event(message=event_message)
         cur = self._execute(sql, args)
         if cur.rowcount <= 0:
             log.info("Update resulted in no changes, rolling back transaction")
             self.conn.rollback()
         else:
-            log.info('Flushing transaction')
+            log.info("Flushing transaction")
             self._flush()
         return cur
 
@@ -1283,12 +1288,12 @@ class Cleanup:
             self.__current_action = name
             with cls(self) as action:
                 self._run_action(action)
-            log.info('Finished %s' % name)
+            log.info("Finished %s" % name)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     with Cleanup() as app:
         try:
             app.run()
         except Exception:
-            log.exception('Caught exception in run sequence:')
+            log.exception("Caught exception in run sequence:")
diff --git a/scripts/cleanup_datasets/populate_uuid.py b/scripts/cleanup_datasets/populate_uuid.py
index da262653a41..597cd0e849d 100755
--- a/scripts/cleanup_datasets/populate_uuid.py
+++ b/scripts/cleanup_datasets/populate_uuid.py
@@ -12,10 +12,13 @@ import os
 import sys
 import uuid
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
 import galaxy.config
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 DESCRIPTION = """
 Populates blank uuid fields in datasets with randomly generated values.
diff --git a/scripts/config_sample_to_kwalify.py b/scripts/config_sample_to_kwalify.py
index 5ab80170dbc..5ced81c081f 100644
--- a/scripts/config_sample_to_kwalify.py
+++ b/scripts/config_sample_to_kwalify.py
@@ -12,7 +12,7 @@ def main():
         sample = "config/galaxy.ini.sample"
 
     for line in open(sample):
-        is_app_main = line.startswith('[app:main]')
+        is_app_main = line.startswith("[app:main]")
         if not found_app_main and not is_app_main:
             continue
         if is_app_main:
@@ -37,6 +37,7 @@ def main():
 def _dump_option(option, current_section_desc):
     def print_line(line):
         print((" " * 6) + line)
+
     if "=" not in option:
         print(option)
     key, default = (s.strip() for s in option.split("=", 1))
diff --git a/scripts/create_db.py b/scripts/create_db.py
index 39d808c8065..c3e986c8cfb 100755
--- a/scripts/create_db.py
+++ b/scripts/create_db.py
@@ -19,7 +19,7 @@ import logging
 import os.path
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.model.migrate.check import create_or_verify_database as create_db
 from galaxy.model.orm.scripts import get_config
@@ -32,12 +32,12 @@ log = logging.getLogger(__name__)
 
 def invoke_create():
     config = get_config(sys.argv)
-    if config['database'] == 'galaxy':
-        create_db(config['db_url'], config['config_file'], map_install_models=not config['install_database_connection'])
-    elif config['database'] == 'tool_shed':
-        create_tool_shed_db(config['db_url'])
-    elif config['database'] == 'install':
-        create_install_db(config['db_url'])
+    if config["database"] == "galaxy":
+        create_db(config["db_url"], config["config_file"], map_install_models=not config["install_database_connection"])
+    elif config["database"] == "tool_shed":
+        create_tool_shed_db(config["db_url"])
+    elif config["database"] == "install":
+        create_install_db(config["db_url"])
 
 
 if __name__ == "__main__":
diff --git a/scripts/cwl_conformance_to_test_cases.py b/scripts/cwl_conformance_to_test_cases.py
index 710ae275dbd..a11833942a1 100644
--- a/scripts/cwl_conformance_to_test_cases.py
+++ b/scripts/cwl_conformance_to_test_cases.py
@@ -8,7 +8,8 @@ THIS_DIRECTORY = os.path.dirname(os.path.realpath(__file__))
 GALAXY_ROOT_DIR = os.path.abspath(os.path.join(THIS_DIRECTORY, os.pardir))
 CWL_API_TESTS_DIRECTORY = os.path.join(GALAXY_ROOT_DIR, "lib", "galaxy_test", "api", "cwl")
 
-TEST_FILE_TEMPLATE = string.Template('''"""Test CWL conformance for version ${version}."""
+TEST_FILE_TEMPLATE = string.Template(
+    '''"""Test CWL conformance for version ${version}."""
 
 import pytest
 
@@ -17,9 +18,11 @@ from ..test_workflows_cwl import BaseCwlWorkflowTestCase
 
 class CwlConformanceTestCase(BaseCwlWorkflowTestCase):
     """Test case mapping to CWL conformance tests for version ${version}."""
-$tests''')
+$tests'''
+)
 
-TEST_TEMPLATE = string.Template('''
+TEST_TEMPLATE = string.Template(
+    '''
 ${marks}    def test_conformance_${version_simple}_${label}(self):
         """${doc}
 
@@ -28,7 +31,8 @@ ${marks}    def test_conformance_${version_simple}_${label}(self):
 ${cwl_test_def}
         """  # noqa: W293
         self.cwl_populator.run_conformance_test("""${version}""", """${doc}""")
-''')
+'''
+)
 
 RED_TESTS = {
     "v1.0": [
@@ -356,7 +360,7 @@ def main():
 
     for i, conformance_test in enumerate(conformance_tests_gen(os.path.join(conformance_tests_dir, version))):
         test_with_doc = conformance_test.copy()
-        if 'doc' not in test_with_doc:
+        if "doc" not in test_with_doc:
             raise Exception(f"No doc in test [{test_with_doc}]")
         del test_with_doc["doc"]
         cwl_test_def = yaml.dump(test_with_doc, default_flow_style=False)
@@ -375,15 +379,18 @@ def main():
             marks += "    @pytest.mark.green\n"
 
         if not {"command_line_tool", "expression_tool", "workflow"}.intersection(tags):
-            print(f"PROBLEM - test [{label}] tagged with neither command_line_tool, expression_tool, nor workflow", file=sys.stderr)
+            print(
+                f"PROBLEM - test [{label}] tagged with neither command_line_tool, expression_tool, nor workflow",
+                file=sys.stderr,
+            )
 
         template_kwargs = {
-            'version_simple': version_simple,
-            'version': version,
-            'doc': conformance_test['doc'],
-            'cwl_test_def': cwl_test_def,
-            'label': label.replace("-", "_"),
-            'marks': marks,
+            "version_simple": version_simple,
+            "version": version,
+            "doc": conformance_test["doc"],
+            "cwl_test_def": cwl_test_def,
+            "label": label.replace("-", "_"),
+            "marks": marks,
         }
         test_body = TEST_TEMPLATE.safe_substitute(template_kwargs)
         tests += test_body
@@ -394,11 +401,13 @@ def main():
         if is_red:
             red_tests_found.add(label)
 
-    test_file_contents = TEST_FILE_TEMPLATE.safe_substitute({
-        'version': version,
-        'version_simple': version_simple,
-        'tests': tests,
-    })
+    test_file_contents = TEST_FILE_TEMPLATE.safe_substitute(
+        {
+            "version": version,
+            "version_simple": version_simple,
+            "tests": tests,
+        }
+    )
 
     test_file = os.path.join(CWL_API_TESTS_DIRECTORY, f"test_cwl_conformance_{version_simple}.py")
     with open(test_file, "w") as f:
diff --git a/scripts/db_shell.py b/scripts/db_shell.py
index 07ac89956bb..a74bce329aa 100644
--- a/scripts/db_shell.py
+++ b/scripts/db_shell.py
@@ -21,11 +21,11 @@ import sys
 
 # Setup DB scripting environment
 from sqlalchemy import *  # noqa
-from sqlalchemy.orm import *  # noqa
 from sqlalchemy.exc import *  # noqa
+from sqlalchemy.orm import *  # noqa
 from sqlalchemy.sql import label  # noqa
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.datatypes.registry import Registry
 from galaxy.model import *  # noqa
@@ -37,8 +37,8 @@ registry = Registry()
 registry.load_datatypes()
 set_datatypes_registry(registry)
 config = get_config(sys.argv)
-db_url = config['db_url']
-sa_session = init('/tmp/', db_url).context
+db_url = config["db_url"]
+sa_session = init("/tmp/", db_url).context
 
 
 # Helper function for debugging sqlalchemy queries...
@@ -51,6 +51,7 @@ def printquery(statement, bind=None):
     please also note that this function is quite slow
     """
     import sqlalchemy.orm
+
     if isinstance(statement, sqlalchemy.orm.Query):
         if bind is None:
             bind = statement.session.get_bind()
@@ -62,15 +63,9 @@ def printquery(statement, bind=None):
     compiler = statement._compiler(dialect)
 
     class LiteralCompiler(compiler.__class__):
-        def visit_bindparam(
-                self, bindparam, within_columns_clause=False,
-                literal_binds=False, **kwargs
-        ):
+        def visit_bindparam(self, bindparam, within_columns_clause=False, literal_binds=False, **kwargs):
             return super().render_literal_bindparam(
-                bindparam,
-                within_columns_clause=within_columns_clause,
-                literal_binds=literal_binds,
-                **kwargs
+                bindparam, within_columns_clause=within_columns_clause, literal_binds=literal_binds, **kwargs
             )
 
         def render_literal_value(self, value, type_):
@@ -96,9 +91,7 @@ def printquery(statement, bind=None):
                 return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S")
 
             else:
-                raise NotImplementedError(
-                    "Don't know how to literal-quote value %r" % value
-                )
+                raise NotImplementedError("Don't know how to literal-quote value %r" % value)
 
     compiler = LiteralCompiler(dialect, statement)
     print(compiler.process(statement))
diff --git a/scripts/docker_swarm_manager.py b/scripts/docker_swarm_manager.py
index 1383cd75ab4..5ba7b9c5191 100644
--- a/scripts/docker_swarm_manager.py
+++ b/scripts/docker_swarm_manager.py
@@ -16,11 +16,13 @@ try:
     import daemon.pidfile
     import lockfile
 except ImportError:
-    print('ERROR: The daemon module is required to use the swarm manager, '
-          'install it with `pip install python-daemon`', file=sys.stderr)
+    print(
+        "ERROR: The daemon module is required to use the swarm manager, " "install it with `pip install python-daemon`",
+        file=sys.stderr,
+    )
     sys.exit(1)
 
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.containers import (
     build_container_interfaces,
@@ -33,32 +35,30 @@ from galaxy.containers.docker_model import (
     IMAGE_CONSTRAINT,
 )
 
-
 DESCRIPTION = "Daemon to manage a Docker Swarm (running in Docker Swarm mode)."
 SWARM_MANAGER_CONF_DEFAULTS = {
-    'pid_file': '{xdg_data_home}/galaxy_swarm_manager.pid',
-    'log_file': '{xdg_data_home}/galaxy_swarm_manager.log',
-    'service_wait_count_limit': 0,
-    'service_wait_time_limit': 5,
-    'slots_min_limit': 0,
-    'slots_max_limit': sys.maxsize,
-    'slots_min_spare': 0,
-    'node_idle_limit': 120,
-    'limits': [],
-    'spawn_wait_time': 30,
-    'spawn_command': '/bin/true',
-    'destroy_command': '/bin/true',
-    'command_failure_command': '/bin/true',
-    'command_retries': 0,
-    'command_retry_wait': 10,
-    'terminate_when_idle': True,
-    'log_environment_variables': [],
+    "pid_file": "{xdg_data_home}/galaxy_swarm_manager.pid",
+    "log_file": "{xdg_data_home}/galaxy_swarm_manager.log",
+    "service_wait_count_limit": 0,
+    "service_wait_time_limit": 5,
+    "slots_min_limit": 0,
+    "slots_max_limit": sys.maxsize,
+    "slots_min_spare": 0,
+    "node_idle_limit": 120,
+    "limits": [],
+    "spawn_wait_time": 30,
+    "spawn_command": "/bin/true",
+    "destroy_command": "/bin/true",
+    "command_failure_command": "/bin/true",
+    "command_retries": 0,
+    "command_retry_wait": 10,
+    "terminate_when_idle": True,
+    "log_environment_variables": [],
 }
 log = logging.getLogger(__name__)
 
 
 class SwarmManager:
-
     def __init__(self, conf, docker_interface):
         self._conf = conf
         self._cpus = docker_interface._conf.cpus
@@ -85,7 +85,7 @@ class SwarmManager:
         if returncodes:
             allowed_returncodes = returncodes
         raw_cmd = command.format(**kwargs)
-        log.debug('running command: %s', raw_cmd)
+        log.debug("running command: %s", raw_cmd)
         success = False
         while not success and attempt < command_retries + 1:
             attempt += 1
@@ -94,13 +94,15 @@ class SwarmManager:
             if p.returncode not in allowed_returncodes:
                 msg = f"error running '{raw_cmd}': returned {p.returncode}"
                 if attempt < command_retries + 1:
-                    msg += ', waiting %s seconds' % self._conf.command_retry_wait
+                    msg += ", waiting %s seconds" % self._conf.command_retry_wait
                     time.sleep(self._conf.command_retry_wait)
                     log.warning(msg + "\nstdout: %s\nstderr: %s\n", stdout, stderr)
                 else:
-                    msg += ' (final attempt)'
+                    msg += " (final attempt)"
                     log.error(msg + "\nstdout: %s\nstderr: %s\n", stdout, stderr)
-                    self._run_command(self._conf.command_failure_command.format(failed_command=raw_cmd), command_retries=0)
+                    self._run_command(
+                        self._conf.command_failure_command.format(failed_command=raw_cmd), command_retries=0
+                    )
                 stdout = None
             else:
                 stdout = stdout.strip()
@@ -116,9 +118,9 @@ class SwarmManager:
         waiting = self._docker_interface.services_waiting_by_constraints()
         active = self._docker_interface.nodes_active_by_constraints()
         for constraints, needed_dict in self._state.slots_needed(waiting, active).items():
-            services = needed_dict['services']
-            nodes = needed_dict['nodes']
-            slots_needed = needed_dict['slots_needed']
+            services = needed_dict["services"]
+            nodes = needed_dict["nodes"]
+            slots_needed = needed_dict["slots_needed"]
             if slots_needed > 0:
                 self._spawn_nodes(constraints, services, slots_needed)
             elif slots_needed < 0:
@@ -127,17 +129,24 @@ class SwarmManager:
     def _check_for_new_nodes(self):
         nodes = None
         for node_state in self._state.spawning_nodes():
-            name = node_state['name']
-            elapsed = node_state['elapsed']
-            constraints = node_state['constraints']
-            state = node_state['state']
+            name = node_state["name"]
+            elapsed = node_state["elapsed"]
+            constraints = node_state["constraints"]
+            state = node_state["state"]
             if not nodes:
                 nodes = self._docker_interface.nodes()
             node = ([x for x in nodes if x.name == name] + [None])[0]
             if not node:
                 if elapsed > self._conf.spawn_wait_time:
-                    log.warning("spawning node '%s' not found in `docker node ls` and spawn_wait_time exceeded! %d seconds have elapsed", name, elapsed)
-                    self._run_command(self._conf.command_failure_command.format(failed_command='wait_for_spawning_node %s' % name), command_retries=0)
+                    log.warning(
+                        "spawning node '%s' not found in `docker node ls` and spawn_wait_time exceeded! %d seconds have elapsed",
+                        name,
+                        elapsed,
+                    )
+                    self._run_command(
+                        self._conf.command_failure_command.format(failed_command="wait_for_spawning_node %s" % name),
+                        command_retries=0,
+                    )
                     self.mark_spawning_node_timeout(name)
             elif node.is_ok():
                 node.set_labels_for_constraints(constraints)
@@ -154,13 +163,13 @@ class SwarmManager:
         cleaned_services = self._docker_interface.services_clean()
         if cleaned_services:
             self._state.clean_services(cleaned_services)
-            log.info("cleaned services: %s", ', '.join(x.id for x in cleaned_services))
+            log.info("cleaned services: %s", ", ".join(x.id for x in cleaned_services))
 
     @staticmethod
     def _env_str(envs, service):
         if envs.get(service.id):
-            return ' [' + ', '.join(envs.get(service.id, [])) + ']'
-        return ''
+            return " [" + ", ".join(envs.get(service.id, [])) + "]"
+        return ""
 
     def _log_state(self, now=False):
         if not now and not (self._last_log < (time.time() - self._log_interval)):
@@ -171,28 +180,58 @@ class SwarmManager:
         node_task_ids = [t.id for nt in [n.tasks for n in nodes] for t in nt]
         envs = {}
         for service in services:
-            envs[service.id] = ['{}={}'.format(k, service.env.get(k, 'unset')) for k in self._conf.log_environment_variables]
-        log.info('%s nodes, %s services (%s terminal)', len(nodes), len(services), len(terminal))
+            envs[service.id] = [
+                "{}={}".format(k, service.env.get(k, "unset")) for k in self._conf.log_environment_variables
+            ]
+        log.info("%s nodes, %s services (%s terminal)", len(nodes), len(services), len(terminal))
         if terminal:
-            service_strs = [f'{s.name} (state: {s.state})' for s in terminal]
-            log.info('terminal services: %s', ', '.join(service_strs) or 'none')
+            service_strs = [f"{s.name} (state: {s.state})" for s in terminal]
+            log.info("terminal services: %s", ", ".join(service_strs) or "none")
         for service in services:
             unassigned_tasks = [t for t in service.tasks if t.id not in node_task_ids]
             if service not in terminal and unassigned_tasks:
                 task = unassigned_tasks[0]
-                log.info('service %s (%s)%s is not assigned to a node; state: %s %s', service.name, service.id,
-                         self._env_str(envs, service), service.state, task.current_state_time)
+                log.info(
+                    "service %s (%s)%s is not assigned to a node; state: %s %s",
+                    service.name,
+                    service.id,
+                    self._env_str(envs, service),
+                    service.state,
+                    task.current_state_time,
+                )
         for node in nodes:
-            log.info('node %s (%s) state: %s, %s tasks (%s terminal)', node.name, node.id, node.state,
-                     len(node.tasks), len([t for t in node.tasks if t.terminal]))
+            log.info(
+                "node %s (%s) state: %s, %s tasks (%s terminal)",
+                node.name,
+                node.id,
+                node.state,
+                len(node.tasks),
+                len([t for t in node.tasks if t.terminal]),
+            )
             for task in node.tasks:
                 if not task.service:
-                    log.warning('node %s (%s) task %s (%s) has no service! state: %s %s', node.name, node.id,
-                                task.slot, task.id, task.state, task.current_state_time)
+                    log.warning(
+                        "node %s (%s) task %s (%s) has no service! state: %s %s",
+                        node.name,
+                        node.id,
+                        task.slot,
+                        task.id,
+                        task.state,
+                        task.current_state_time,
+                    )
                 else:
-                    log.info('node %s (%s) service %s (%s) task %s (%s)%s state: %s %s', node.name, node.id,
-                             task.service.name, task.service.id, task.slot, task.id,
-                             self._env_str(envs, task.service), task.state, task.current_state_time)
+                    log.info(
+                        "node %s (%s) service %s (%s) task %s (%s)%s state: %s %s",
+                        node.name,
+                        node.id,
+                        task.service.name,
+                        task.service.id,
+                        task.slot,
+                        task.id,
+                        self._env_str(envs, task.service),
+                        task.state,
+                        task.current_state_time,
+                    )
         self._last_log = time.time()
 
     def _terminate_if_idle(self):
@@ -211,13 +250,13 @@ class SwarmManager:
                 return  # services are waiting
             if needed < 0:
                 extra_slots = max(
-                    self._state.get_limit(constraints, 'slots_min_limit'),
-                    self._state.get_limit(constraints, 'slots_min_spare')
+                    self._state.get_limit(constraints, "slots_min_limit"),
+                    self._state.get_limit(constraints, "slots_min_spare"),
                 )
                 if total + needed != extra_slots:
                     return  # otherwise, nodes remaining are for configured minimums
         # FIXME: there's a race condition here
-        log.info('nothing to manage, shutting down')
+        log.info("nothing to manage, shutting down")
         sys.exit(0)
 
     # other methods
@@ -237,23 +276,30 @@ class SwarmManager:
     def _spawn_nodes(self, constraints, services, slots_needed):
         service_ids = [x.id for x in services]
         if service_ids:
-            log.info("requesting node(s) for services needing %s slots with constraints [%s]: %s",
-                     slots_needed, constraints, ', '.join(service_ids))
+            log.info(
+                "requesting node(s) for services needing %s slots with constraints [%s]: %s",
+                slots_needed,
+                constraints,
+                ", ".join(service_ids),
+            )
         else:
-            log.info("requesting node(s) for %s slots (due to minimum limits with constraints [%s]",
-                     slots_needed, constraints)
+            log.info(
+                "requesting node(s) for %s slots (due to minimum limits with constraints [%s]",
+                slots_needed,
+                constraints,
+            )
         command = self._conf.spawn_command.format(
-            service_ids=','.join(service_ids),
+            service_ids=",".join(service_ids),
             service_count=len(services),
-            image=self._get_spawn_property(constraints, IMAGE_CONSTRAINT, services) or '',
-            cpus=self._get_spawn_property(constraints, CPUS_CONSTRAINT, services) or '',
+            image=self._get_spawn_property(constraints, IMAGE_CONSTRAINT, services) or "",
+            cpus=self._get_spawn_property(constraints, CPUS_CONSTRAINT, services) or "",
             slots=slots_needed,
         )
         rc, output = self._run_command(command, returncodes=(0, 2))
         if rc == 2:
-            log.info('spawn_command indicated that spawning should be retried: %s', output)
+            log.info("spawn_command indicated that spawning should be retried: %s", output)
         elif not output:
-            log.warning('spawn_command returned no new nodes, cannot manage nodes')
+            log.warning("spawn_command returned no new nodes, cannot manage nodes")
             self._state.mark_services_handled(services)
         else:
             log.info("node allocator will spawn: %s", output)
@@ -271,11 +317,10 @@ class SwarmManager:
                 destroy_nodes.append(node)
                 destroyed_slots += node_slots
         if destroy_nodes:
-            command = self._conf.destroy_command.format(
-                nodes=' '.join(x.name for x in destroy_nodes))
+            command = self._conf.destroy_command.format(nodes=" ".join(x.name for x in destroy_nodes))
             destroyed_nodes = self._run_command(command)
             if not destroyed_nodes:
-                log.warning('destroy_command returned no destroyed nodes')
+                log.warning("destroy_command returned no destroyed nodes")
             else:
                 log.info("destroyed nodes: %s", destroyed_nodes)
 
@@ -291,10 +336,9 @@ class SwarmManager:
 
 
 class SwarmState:
-
     def __init__(self, conf, interface_conf):
         self._conf = conf
-        self._cpus = interface_conf.cpus   # this is effectively the slot size
+        self._cpus = interface_conf.cpus  # this is effectively the slot size
         self._service_create_image_constraint = interface_conf.service_create_image_constraint
         self._service_create_cpus_constraint = interface_conf.service_create_cpus_constraint
         self._handled_services = set()
@@ -303,15 +347,15 @@ class SwarmState:
         self._surplus_nodes = {}
         self._limits = {}
         for limit in conf.limits:
-            constraints = DockerServiceConstraints.from_constraint_string_list(limit.get('constraints', []))
+            constraints = DockerServiceConstraints.from_constraint_string_list(limit.get("constraints", []))
             self._limits[constraints] = self._make_limit_dict(limit)
 
     def _make_limit_dict(self, limit):
         return {
-            'slots_min_limit': limit.get('slots_min_limit', self._conf.slots_min_limit),
-            'slots_max_limit': limit.get('slots_max_limit', self._conf.slots_max_limit),
-            'slots_min_spare': limit.get('slots_min_spare', self._conf.slots_min_spare),
-            'node_idle_limit': limit.get('node_idle_limit', self._conf.node_idle_limit),
+            "slots_min_limit": limit.get("slots_min_limit", self._conf.slots_min_limit),
+            "slots_max_limit": limit.get("slots_max_limit", self._conf.slots_max_limit),
+            "slots_min_spare": limit.get("slots_min_spare", self._conf.slots_min_spare),
+            "node_idle_limit": limit.get("node_idle_limit", self._conf.node_idle_limit),
         }
 
     def slots_needed(self, waiting_services, active_nodes):
@@ -326,11 +370,13 @@ class SwarmState:
         all_constraints = services_constraints.union(nodes_constraints).union(limits_constraints)
         if not all_constraints and (self._conf.slots_min_spare or self._conf.slots_min_limit):
             if self._service_create_image_constraint or self._service_create_cpus_constraint:
-                raise Exception("Global 'slots_min_limit' and/or 'slots_min_spare' are set and "
+                raise Exception(
+                    "Global 'slots_min_limit' and/or 'slots_min_spare' are set and "
                     "'service_create_image_constraint' and/or 'service_create_cpus_constraint' are set but "
                     "constraint-specific limits are unset, minimum nodes cannot be started since the constraints are not "
                     "known until service creation time. Either disable 'service_create_*_constraint' or create "
-                    "constraint-specific limits in the 'limits' section of 'manager_conf' in containers_conf.yml")
+                    "constraint-specific limits in the 'limits' section of 'manager_conf' in containers_conf.yml"
+                )
             all_constraints.add(DockerServiceConstraints.from_constraint_string_list([]))
         for constraints in all_constraints:
             services = waiting_services.get(constraints, [])
@@ -345,9 +391,9 @@ class SwarmState:
             elif not services and constraints in self._waiting_since:
                 del self._waiting_since[constraints]
             rval[constraints] = {
-                'services': services,
-                'nodes': nodes,
-                'slots_needed': slots_needed,
+                "services": services,
+                "nodes": nodes,
+                "slots_needed": slots_needed,
             }
         return rval
 
@@ -361,17 +407,19 @@ class SwarmState:
             used += sum(t.cpus for t in node.non_terminal_tasks) / self._cpus
             total += node.cpus / self._cpus
         # need at least this many slots
-        needed = used + self.get_limit(constraints, 'slots_min_spare')
-        if (len(services) > self._conf.service_wait_count_limit
-                and time.time() - self._waiting_since.get(constraints, time.time()) > self._conf.service_wait_time_limit):
+        needed = used + self.get_limit(constraints, "slots_min_spare")
+        if (
+            len(services) > self._conf.service_wait_count_limit
+            and time.time() - self._waiting_since.get(constraints, time.time()) > self._conf.service_wait_time_limit
+        ):
             # add slots for waiting services that have exceeded limits
             needed += sum(s.cpus for s in services) / self._cpus
         # subtract slots for spawning nodes
-        needed -= sum(n.get('slots', 0) for n in self._spawning_nodes.get(constraints, {}))
+        needed -= sum(n.get("slots", 0) for n in self._spawning_nodes.get(constraints, {}))
         # ensure no less than slots_min_limit slots will exist (free or used)
-        needed = max(needed, self.get_limit(constraints, 'slots_min_limit'))
+        needed = max(needed, self.get_limit(constraints, "slots_min_limit"))
         # ensure no more than slots_max_limit slots will exist
-        needed = min(needed, self.get_limit(constraints, 'slots_max_limit'))
+        needed = min(needed, self.get_limit(constraints, "slots_max_limit"))
         # need to add/remove this many slots
         return int(needed - total), total
 
@@ -384,9 +432,9 @@ class SwarmState:
         for constraints in self._spawning_nodes.keys():
             for name, node in self._spawning_nodes[constraints].items():
                 yval = {
-                    'name': name,
-                    'elapsed': now - node['time_requested'],
-                    'constraints': constraints,
+                    "name": name,
+                    "elapsed": now - node["time_requested"],
+                    "constraints": constraints,
                 }
                 yval.update(node)
                 yield yval
@@ -395,15 +443,15 @@ class SwarmState:
         if constraints not in self._spawning_nodes:
             self._spawning_nodes[constraints] = {}
         for node in nodes:
-            name = node.split(':')[0]
+            name = node.split(":")[0]
             try:
-                slots = int(node.split(':')[1])
+                slots = int(node.split(":")[1])
             except IndexError:
                 slots = int(1 / self._cpus)
             self._spawning_nodes[constraints][name] = {
-                'state': 'requested',
-                'time_requested': time.time(),
-                'slots': slots,
+                "state": "requested",
+                "time_requested": time.time(),
+                "slots": slots,
             }
 
     def mark_services_handled(self, services):
@@ -423,11 +471,11 @@ class SwarmState:
     def mark_spawning_node_state(self, node_name, state):
         for constraints in self._spawning_nodes.keys():
             if node_name in self._spawning_nodes[constraints]:
-                self._spawning_nodes[constraints][node_name]['state'] = state
+                self._spawning_nodes[constraints][node_name]["state"] = state
 
     def is_destruction_time(self, node):
         now = time.time()
-        limit = self.get_limit(node.labels_as_constraints, 'node_idle_limit')
+        limit = self.get_limit(node.labels_as_constraints, "node_idle_limit")
         return now - self._surplus_nodes.get(node.name, now) > limit
 
     def mark_node_idle(self, node_name):
@@ -456,8 +504,7 @@ def _arg_parser():
     parser.add_argument("-c", "--containers-config-file", default=None)
     parser.add_argument("-f", "--foreground", action="store_true", default=False)
     parser.add_argument("-d", "--debug", action="store_true", default=False)
-    parser.add_argument("-s", "--swarm", default="_default_",
-                        help='Swarm name in containers config to manage')
+    parser.add_argument("-s", "--swarm", default="_default_", help="Swarm name in containers config to manage")
     return parser
 
 
@@ -471,11 +518,11 @@ def _run_swarm_manager(args):
     pidfile = _swarm_manager_pidfile(swarm_manager_conf)
 
     if not args.foreground:
-        _swarm_manager_daemon(pidfile, swarm_manager_conf['log_file'], swarm_manager_conf, docker_interface)
+        _swarm_manager_daemon(pidfile, swarm_manager_conf["log_file"], swarm_manager_conf, docker_interface)
     else:
-        if swarm_manager_conf['terminate_when_idle']:
-            log.info('running in the foreground, disabling automatic swarm manager termination')
-            swarm_manager_conf['terminate_when_idle'] = False
+        if swarm_manager_conf["terminate_when_idle"]:
+            log.info("running in the foreground, disabling automatic swarm manager termination")
+            swarm_manager_conf["terminate_when_idle"] = False
         else:
             log.info("running in the foreground")
         try:
@@ -499,32 +546,32 @@ def _run_swarm_manager(args):
 def _containers_config_file(args):
     containers_config_file = args.containers_config_file
     if not containers_config_file:
-        for path in ('./config', '.'):
-            testf = os.path.join(path, 'containers_conf.yml')
+        for path in ("./config", "."):
+            testf = os.path.join(path, "containers_conf.yml")
             if os.path.exists(testf):
                 containers_config_file = testf
-    assert containers_config_file, \
-        "containers_conf.yml cannot be found, please set with '-c' or '--containers-config-file'"
+    assert (
+        containers_config_file
+    ), "containers_conf.yml cannot be found, please set with '-c' or '--containers-config-file'"
     return containers_config_file
 
 
 def _container_conf(containers_conf, swarm):
-    assert swarm in containers_conf, \
-        "invalid container configuration name: %s" % swarm
-    assert containers_conf[swarm]['type'] == 'docker_swarm', \
+    assert swarm in containers_conf, "invalid container configuration name: %s" % swarm
+    assert containers_conf[swarm]["type"] == "docker_swarm", (
         "'%s' container configuration is not 'docker_swarm' type" % swarm
-    assert containers_conf[swarm].get('managed', True), \
-        "'%s' swarm is not managed" % swarm
+    )
+    assert containers_conf[swarm].get("managed", True), "'%s' swarm is not managed" % swarm
     return containers_conf[swarm]
 
 
 def _swarm_manager_conf(new_conf):
     conf = ContainerInterfaceConfig()
     conf.update(SWARM_MANAGER_CONF_DEFAULTS)
-    conf.update(new_conf.get('manager_conf', {}))
+    conf.update(new_conf.get("manager_conf", {}))
     xdg_env = _load_xdg_environment()
-    for opt in ('pid_file', 'log_file'):
-        conf[opt] = conf[opt].format(xdg_data_home=xdg_env['data_home'])
+    for opt in ("pid_file", "log_file"):
+        conf[opt] = conf[opt].format(xdg_data_home=xdg_env["data_home"])
     return conf
 
 
@@ -533,13 +580,13 @@ def _configure_logging(args, conf):
     if args and args.debug:
         log_level = logging.DEBUG
     else:
-        log_level = logging.getLevelName(conf.get('log_level', 'INFO').upper())
-        assert int(log_level), 'invalid log level: %s' % conf['log_level']
+        log_level = logging.getLevelName(conf.get("log_level", "INFO").upper())
+        assert int(log_level), "invalid log level: %s" % conf["log_level"]
     log = logging.getLogger(__name__)
-    gxlog = logging.getLogger('galaxy')
+    gxlog = logging.getLogger("galaxy")
     log.setLevel(log_level)
     gxlog.setLevel(log_level)
-    log_format = conf.get('log_format', '%(name)s %(levelname)s %(asctime)s %(message)s')
+    log_format = conf.get("log_format", "%(name)s %(levelname)s %(asctime)s %(message)s")
     formatter = logging.Formatter(log_format)
     # file logging is handled by daemon
     handler = logging.StreamHandler(sys.stdout)
@@ -550,22 +597,22 @@ def _configure_logging(args, conf):
 
 def _load_xdg_environment():
     return dict(
-        data_home=os.path.expanduser(os.environ.get('XDG_DATA_HOME', '~/.local/share')),
+        data_home=os.path.expanduser(os.environ.get("XDG_DATA_HOME", "~/.local/share")),
     )
 
 
 def _swarm_manager_pidfile(conf):
     try:
-        os.makedirs(os.path.dirname(conf['pid_file']))
+        os.makedirs(os.path.dirname(conf["pid_file"]))
     except OSError as exc:
         if exc.errno != errno.EEXIST:
             raise
-    return daemon.pidfile.PIDLockFile(conf['pid_file'])
+    return daemon.pidfile.PIDLockFile(conf["pid_file"])
 
 
 def _swarm_manager_daemon(pidfile, logfile, swarm_manager_conf, docker_interface):
     log.info("daemonizing, logs will be written to '%s'", logfile)
-    with open(logfile, 'a') as logfh:
+    with open(logfile, "a") as logfh:
         try:
             with daemon.DaemonContext(
                 pidfile=pidfile,
@@ -588,6 +635,6 @@ def _swarm_manager(conf, docker_interface):
             log.error("restarting due to fatal error")
 
 
-if __name__ == '__main__':
-    __name__ = 'swarm_manager'
+if __name__ == "__main__":
+    __name__ = "swarm_manager"
     main()
diff --git a/scripts/drmaa_external_killer.py b/scripts/drmaa_external_killer.py
index dfe6a1a89b2..e7c53b18df0 100755
--- a/scripts/drmaa_external_killer.py
+++ b/scripts/drmaa_external_killer.py
@@ -29,15 +29,21 @@ def set_user(uid):
         os.setuid(uid)
     except OSError as e:
         if e.errno == errno.EPERM:
-            sys.stderr.write("error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid)
+            sys.stderr.write(
+                "error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid
+            )
             exit(1)
         else:
             pass
     if os.getuid() == 0:
-        sys.stderr.write("error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n")
+        sys.stderr.write(
+            "error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n"
+        )
         exit(1)
     if os.geteuid() == 0:
-        sys.stderr.write("error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n")
+        sys.stderr.write(
+            "error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n"
+        )
         exit(1)
 
 
diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py
index 621950ea9e0..17bbf18fea4 100755
--- a/scripts/drmaa_external_runner.py
+++ b/scripts/drmaa_external_runner.py
@@ -14,8 +14,17 @@ import sys
 
 import drmaa
 
-DRMAA_jobTemplate_attributes = ['args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification',
-                                'workingDirectory', 'jobName', 'email', 'project']
+DRMAA_jobTemplate_attributes = [
+    "args",
+    "remoteCommand",
+    "outputPath",
+    "errorPath",
+    "nativeSpecification",
+    "workingDirectory",
+    "jobName",
+    "email",
+    "project",
+]
 
 
 def load_job_template(jt, data):
@@ -86,6 +95,7 @@ def set_user(uid, assign_all_groups):
         # Solves issue with permission denied for JSON files
         gid = pwd.getpwuid(uid).pw_gid
         import grp
+
         os.setgid(gid)
         if assign_all_groups:
             # Added lines to assure read/write permission for groups
@@ -97,17 +107,23 @@ def set_user(uid, assign_all_groups):
 
     except OSError as e:
         if e.errno == errno.EPERM:
-            sys.stderr.write("error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid)
+            sys.stderr.write(
+                "error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid
+            )
             exit(1)
         else:
             pass
 
     if os.getuid() == 0:
-        sys.stderr.write("error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n")
+        sys.stderr.write(
+            "error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n"
+        )
         exit(1)
 
     if os.geteuid() == 0:
-        sys.stderr.write("error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n")
+        sys.stderr.write(
+            "error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n"
+        )
         exit(1)
 
 
@@ -122,7 +138,7 @@ def main():
     set_user(userid, assign_all_groups)
     # Added to disable LSF generated messages that would interfer with this
     # script. Fix thank to Chong Chen at IBM.
-    os.environ['BSUB_QUIET'] = 'Y'
+    os.environ["BSUB_QUIET"] = "Y"
     s = drmaa.Session()
     s.initialize()
     jt = s.createJobTemplate()
diff --git a/scripts/dump_library_paths.py b/scripts/dump_library_paths.py
index 4c9360650a6..f3080c5118f 100644
--- a/scripts/dump_library_paths.py
+++ b/scripts/dump_library_paths.py
@@ -15,9 +15,12 @@ import logging
 import os
 import sys
 
-from sqlalchemy import false, not_
+from sqlalchemy import (
+    false,
+    not_,
+)
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy.config
 import galaxy.model.mapping
@@ -27,41 +30,37 @@ from galaxy.util.script import main_factory
 DESCRIPTION = "Locate all datasets in libraries."
 ARGUMENTS = (
     (
-        ('-v', '--verbose'),
+        ("-v", "--verbose"),
         dict(
-            action='store_true',
+            action="store_true",
             default=False,
-            help='Verbose logging output',
+            help="Verbose logging output",
         ),
     ),
     (
-        ('-o', '--output'),
+        ("-o", "--output"),
         dict(
-            default='stdout',
-            help='Write output to file',
+            default="stdout",
+            help="Write output to file",
         ),
     ),
     (
-        ('-p', '--public'),
-        dict(
-            action='store_true',
-            default=False,
-            help='Only dump files in "public" libraries'
-        ),
+        ("-p", "--public"),
+        dict(action="store_true", default=False, help='Only dump files in "public" libraries'),
     ),
     (
-        ('--relative',),
+        ("--relative",),
         dict(
             default=None,
-            help='Write paths relative to the given directory',
+            help="Write paths relative to the given directory",
         ),
     ),
     (
-        ('--exists',),
+        ("--exists",),
         dict(
-            action='store_true',
+            action="store_true",
             default=False,
-            help='Check for dataset existence, warn if it does not exist',
+            help="Check for dataset existence, warn if it does not exist",
         ),
     ),
 )
@@ -76,15 +75,19 @@ def _config_logging(args):
 
 
 def _get_libraries(args, model):
-    log.debug('Setting up query')
+    log.debug("Setting up query")
     library_access_action = model.security_agent.permitted_actions.LIBRARY_ACCESS.action
     query = model.context.query(model.Library)
     query = query.filter(model.Library.table.c.deleted == false())
     if args.public:
-        restricted_library_ids = {lp.library_id for lp in (
-            model.context.query(model.LibraryPermissions).filter(
-                model.LibraryPermissions.table.c.action == library_access_action
-            ).distinct())}
+        restricted_library_ids = {
+            lp.library_id
+            for lp in (
+                model.context.query(model.LibraryPermissions)
+                .filter(model.LibraryPermissions.table.c.action == library_access_action)
+                .distinct()
+            )
+        }
         if restricted_library_ids:
             query = query.filter(not_(model.Library.table.c.id.in_(restricted_library_ids)))
     query = query.order_by(model.Library.table.c.name)
@@ -107,10 +110,10 @@ def _walk_libraries(args, model):
 
 
 def _open_output(args):
-    if args.output == 'stdout':
+    if args.output == "stdout":
         return sys.stdout
     else:
-        return open(args.output, 'w')
+        return open(args.output, "w")
 
 
 def _path(path, args):
@@ -124,21 +127,21 @@ def _get_library_dataset_paths(args, kwargs):
     _config_logging(args)
     config = galaxy.config.Configuration(**kwargs)
     object_store = build_object_store_from_config(config)
-    model = galaxy.model.mapping.init('/tmp/', kwargs.get('database_connection'), object_store=object_store)
+    model = galaxy.model.mapping.init("/tmp/", kwargs.get("database_connection"), object_store=object_store)
     output = _open_output(args)
     last_library = None
-    log.debug('Beginning library walk')
+    log.debug("Beginning library walk")
     for library, dataset in _walk_libraries(args, model):
         if library != last_library:
-            log.info('Library: %s', library.name)
+            log.info("Library: %s", library.name)
         filename = object_store.get_filename(dataset)
         files_dir = dataset.get_extra_files_path()
         if (args.exists and object_store.exists(dataset)) or not args.exists:
-            output.write('%s\n' % _path(filename, args))
+            output.write("%s\n" % _path(filename, args))
         elif args.exists:
-            log.warning('Missing %s', filename)
+            log.warning("Missing %s", filename)
         if files_dir and os.path.exists(files_dir):
-            output.write('%s\n' % _path(files_dir, args))
+            output.write("%s\n" % _path(files_dir, args))
         last_library = library
     output.close()
 
@@ -148,11 +151,8 @@ ACTIONS = {
 }
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main = main_factory(
-        description=DESCRIPTION,
-        actions=ACTIONS,
-        arguments=ARGUMENTS,
-        default_action="get_library_dataset_paths"
+        description=DESCRIPTION, actions=ACTIONS, arguments=ARGUMENTS, default_action="get_library_dataset_paths"
     )
     main()
diff --git a/scripts/edam_mapping.py b/scripts/edam_mapping.py
index d164bae5087..817765a6957 100644
--- a/scripts/edam_mapping.py
+++ b/scripts/edam_mapping.py
@@ -18,7 +18,7 @@ from xml import etree
 
 import requests
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy.datatypes.registry
 import galaxy.model
@@ -30,7 +30,9 @@ CONFIG_FILE = os.path.join(PROJECT_DIR, "config", "datatypes_conf.xml.sample")
 datatypes_registry = galaxy.datatypes.registry.Registry()
 datatypes_registry.load_datatypes(root_dir=PROJECT_DIR, config=CONFIG_FILE)
 
-EDAM_OWL_URL = "http://data.bioontology.org/ontologies/EDAM/submissions/25/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb"
+EDAM_OWL_URL = (
+    "http://data.bioontology.org/ontologies/EDAM/submissions/25/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb"
+)
 
 
 if not os.path.exists("/tmp/edam.owl"):
@@ -39,13 +41,13 @@ if not os.path.exists("/tmp/edam.owl"):
 
 owl_xml_tree = etree.ElementTree.parse("/tmp/edam.owl")
 format_info = {}
-for child in owl_xml_tree.getroot().findall('{http://www.w3.org/2002/07/owl#}Class'):
+for child in owl_xml_tree.getroot().findall("{http://www.w3.org/2002/07/owl#}Class"):
     about = child.attrib.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about")
     if not about:
         continue
     if not about.startswith("http://edamontology.org/format_"):
         continue
-    the_format = about[len("http://edamontology.org/"):]
+    the_format = about[len("http://edamontology.org/") :]
     label = child.find("{http://www.w3.org/2000/01/rdf-schema#}label").text
     definition = ""
     def_el = child.find("{http://www.geneontology.org/formats/oboInOwl#}hasDefinition")
diff --git a/scripts/external_chown_script.py b/scripts/external_chown_script.py
index 829bb6a3d2b..2032e5dd90c 100755
--- a/scripts/external_chown_script.py
+++ b/scripts/external_chown_script.py
@@ -39,7 +39,7 @@ def validate_parameters():
 
 def main():
     path, galaxy_user_name, gid = validate_parameters()
-    for cmd in [['chown', '-Rh', galaxy_user_name, path], ['chgrp', '-Rh', gid, path]]:
+    for cmd in [["chown", "-Rh", galaxy_user_name, path], ["chgrp", "-Rh", gid, path]]:
         p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         (stdoutdata, stderrdata) = p.communicate()
         exitcode = p.returncode
diff --git a/scripts/extract_dataset_part.py b/scripts/extract_dataset_part.py
index 57449565b8b..82d05b544d5 100644
--- a/scripts/extract_dataset_part.py
+++ b/scripts/extract_dataset_part.py
@@ -11,7 +11,7 @@ import logging
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 # This junk is here to prevent loading errors
 import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
@@ -32,13 +32,13 @@ def __main__():
         sys.exit(0)
     data = json.load(open(file_path))
     try:
-        class_name_parts = data['class_name'].split('.')
-        module_name = '.'.join(class_name_parts[:-1])
+        class_name_parts = data["class_name"].split(".")
+        module_name = ".".join(class_name_parts[:-1])
         class_name = class_name_parts[-1]
         mod = __import__(module_name, globals(), locals(), [class_name])
         cls = getattr(mod, class_name)
         if not cls.process_split_file(data):
-            sys.stderr.write('Writing split file failed\n')
+            sys.stderr.write("Writing split file failed\n")
             sys.exit(1)
     except Exception as e:
         sys.stderr.write(str(e))
diff --git a/scripts/extract_toolbox_sections.py b/scripts/extract_toolbox_sections.py
index b7f7b67b2f4..f729e706d24 100644
--- a/scripts/extract_toolbox_sections.py
+++ b/scripts/extract_toolbox_sections.py
@@ -18,24 +18,24 @@ def main():
 
     for rootchild in root:
         currentsectionlabel = ""
-        if (rootchild.tag == "section"):
-            sectionname = rootchild.attrib['name']
+        if rootchild.tag == "section":
+            sectionname = rootchild.attrib["name"]
             # per section tool index range 1-1000, current labels/tools
             # divided between 20 and 750
             toolindex = 250
             toolfactor = int(500 / len(rootchild))
             currentlabel = ""
             for sectionchild in rootchild:
-                if (sectionchild.tag == "tool"):
+                if sectionchild.tag == "tool":
                     addToToolDict(sectionchild, sectionname, sectionindex, toolindex, currentlabel)
                     toolindex += toolfactor
-                elif (sectionchild.tag == "label"):
+                elif sectionchild.tag == "label":
                     currentlabel = sectionchild.attrib["text"]
             sectionindex += sectionfactor
-        elif (rootchild.tag == "tool"):
+        elif rootchild.tag == "tool":
             addToToolDict(rootchild, "", sectionindex, None, currentsectionlabel)
             sectionindex += sectionfactor
-        elif (rootchild.tag == "label"):
+        elif rootchild.tag == "label":
             currentsectionlabel = rootchild.attrib["text"]
             sectionindex += sectionfactor
 
@@ -57,14 +57,14 @@ def main():
         tooldocroot = tooldoc.getroot()
         # check tags element, set flag
         tagselement = tooldocroot.find("tags")
-        if (tagselement):
+        if tagselement:
             hastags = True
         # check if toolboxposition element already exists in this tooconfig file
         toolboxposelement = tooldocroot.find("toolboxposition")
-        if (toolboxposelement):
+        if toolboxposelement:
             hastoolboxpos = True
 
-        if (not (hastags and hastoolboxpos)):
+        if not (hastags and hastoolboxpos):
             original = open(toolconffile)
             contents = original.readlines()
             original.close()
@@ -72,27 +72,26 @@ def main():
             # the new elements will be added directly below the root tool element
             addelementsatposition = 1
             # but what's on the first line? Root or not?
-            if (contents[0].startswith("<?")):
+            if contents[0].startswith("<?"):
                 addelementsatposition = 2
             newelements = []
-            if (not hastoolboxpos):
-                if (toolconffile in tooldict):
+            if not hastoolboxpos:
+                if toolconffile in tooldict:
                     for attributes in tooldict[toolconffile]:
                         # create toolboxposition element
                         sectionelement = ET.Element("toolboxposition")
                         sectionelement.attrib = attributes
                         sectionelement.tail = "\n  "
-                        newelements.append(ET.tostring(sectionelement, 'utf-8'))
+                        newelements.append(ET.tostring(sectionelement, "utf-8"))
 
-            if (not hastags):
+            if not hastags:
                 # create empty tags element
                 newelements.append("<tags/>\n  ")
 
-            contents = (contents[0:addelementsatposition] + newelements
-                        + contents[addelementsatposition:])
+            contents = contents[0:addelementsatposition] + newelements + contents[addelementsatposition:]
 
             # add .new for testing/safety purposes :P
-            newtoolconffile = open(toolconffile, 'w')
+            newtoolconffile = open(toolconffile, "w")
             newtoolconffile.writelines(contents)
             newtoolconffile.close()
 
@@ -103,13 +102,13 @@ def addToToolDict(tool, sectionname, sectionindex, toolindex, currentlabel):
 
     # define attributes for the toolboxposition xml-tag
     attribdict = {}
-    if (sectionname):
+    if sectionname:
         attribdict["section"] = sectionname
-    if (currentlabel):
+    if currentlabel:
         attribdict["label"] = currentlabel
-    if (sectionindex):
+    if sectionindex:
         attribdict["sectionorder"] = str(sectionindex)
-    if (toolindex):
+    if toolindex:
         attribdict["order"] = str(toolindex)
     tooldict[realtoolfile].append(attribdict)
 
@@ -120,14 +119,14 @@ def getfnl(startdir):
     for root, _dirs, files in os.walk(startdir):
         for fn in files:
             fullfn = os.path.join(root, fn)
-            if fn.endswith('.xml'):
+            if fn.endswith(".xml"):
                 try:
                     doc = ET.parse(fullfn)
                 except Exception as e:
                     raise Exception(f"Oops, bad XML in '{fullfn}': {e}")
                 rootelement = doc.getroot()
                 # here we check if this xml file actually is a tool conf xml!
-                if rootelement.tag == 'tool':
+                if rootelement.tag == "tool":
                     filenamelist.append(fullfn)
     return filenamelist
 
diff --git a/scripts/fetch_eggs.py b/scripts/fetch_eggs.py
index 55a9af7db97..1dfa5f4dccb 100755
--- a/scripts/fetch_eggs.py
+++ b/scripts/fetch_eggs.py
@@ -4,7 +4,7 @@ from os import pardir
 from os.path import (
     abspath,
     dirname,
-    join
+    join,
 )
 from sys import exit
 
@@ -30,7 +30,6 @@ cd {dir} && ./scripts/common_startup.sh --skip-venv
 """
 
 galaxy = abspath(join(dirname(__file__), pardir))
-venv = join(galaxy, '.venv')
-print(msg.format(dir=abspath(join(dirname(__file__), pardir)),
-                 venv=venv))
+venv = join(galaxy, ".venv")
+print(msg.format(dir=abspath(join(dirname(__file__), pardir)), venv=venv))
 exit(1)
diff --git a/scripts/fix_dm_versions.py b/scripts/fix_dm_versions.py
index 0983e305505..4578cabf8b8 100755
--- a/scripts/fix_dm_versions.py
+++ b/scripts/fix_dm_versions.py
@@ -26,15 +26,18 @@ need to be corrected manually.
 """
 
 parser = argparse.ArgumentParser(description=desc)
-parser.add_argument('shed_data_manager_conf', metavar='CONFIG_FILE', type=str,
-                    default="config/shed_data_manager_conf.xml",
-                    help='an integer for the accumulator')
-parser.add_argument('--all-entries', action='store_true',
-                    help='modify all entries (default only those with duplicated guid)')
-parser.add_argument('--add-version', action='store_true',
-                    help='also add version attribute if absent')
-parser.add_argument('--dry-run', action='store_true',
-                    help='do not write resulting config file')
+parser.add_argument(
+    "shed_data_manager_conf",
+    metavar="CONFIG_FILE",
+    type=str,
+    default="config/shed_data_manager_conf.xml",
+    help="an integer for the accumulator",
+)
+parser.add_argument(
+    "--all-entries", action="store_true", help="modify all entries (default only those with duplicated guid)"
+)
+parser.add_argument("--add-version", action="store_true", help="also add version attribute if absent")
+parser.add_argument("--dry-run", action="store_true", help="do not write resulting config file")
 args = parser.parse_args()
 
 with open(args.shed_data_manager_conf) as fh:
@@ -42,7 +45,7 @@ with open(args.shed_data_manager_conf) as fh:
 root = tree.getroot()
 
 guid_mapping = dict()
-for dm in root.iter('data_manager'):
+for dm in root.iter("data_manager"):
     guid = dm.attrib["guid"]
     if guid not in guid_mapping:
         guid_mapping[guid] = [dm]
@@ -51,7 +54,7 @@ for dm in root.iter('data_manager'):
 
 for guid in guid_mapping:
     if len(guid_mapping[guid]) > 1:
-        print(f'{guid} found {len(guid_mapping[guid])}x')
+        print(f"{guid} found {len(guid_mapping[guid])}x")
     elif not args.all_entries:
         continue
 
@@ -60,14 +63,14 @@ for guid in guid_mapping:
         tool_version = tool_version.text
 
         new_guid = f"{guid[:guid.rfind('/')]}/{tool_version}"
-        dm.attrib['guid'] = new_guid
+        dm.attrib["guid"] = new_guid
         print(f"changing guid: {guid} -> {new_guid}")
         if "version" in dm.attrib:
             print(f"changing version: {dm.attrib['version']} -> {tool_version}")
-            dm.attrib['version'] = tool_version
+            dm.attrib["version"] = tool_version
         elif args.add_version:
             print(f"adding version: {tool_version}")
-            dm.attrib['version'] = tool_version
+            dm.attrib["version"] = tool_version
 
 if not args.dry_run:
     nfn = args.shed_data_manager_conf + datetime.now().isoformat()
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 18ad65c8ff6..8bad3e2736e 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -13,7 +13,10 @@ galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pa
 sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")]
 
 from galaxy.util import classproperty
-from galaxy_test.base.api_util import get_admin_api_key, get_user_api_key
+from galaxy_test.base.api_util import (
+    get_admin_api_key,
+    get_user_api_key,
+)
 from galaxy_test.driver import driver_util
 
 log = driver_util.build_logger()
@@ -65,6 +68,7 @@ class SeleniumGalaxyTestDriver(driver_util.GalaxyTestDriver):
     @classproperty
     def default_web_host(cls):
         from galaxy_test.selenium.framework import default_web_host_for_selenium_tests
+
         return default_web_host_for_selenium_tests()
 
 
@@ -82,6 +86,7 @@ class DataManagersGalaxyTestDriver(driver_util.GalaxyTestDriver):
     def build_tests(self):
         """Build data manager test methods."""
         import functional.test_data_managers
+
         functional.test_data_managers.data_managers = self.app.data_managers
         functional.test_data_managers.build_tests(
             tmp_dir=self.galaxy_test_tmp_dir,
@@ -94,11 +99,11 @@ class DataManagersGalaxyTestDriver(driver_util.GalaxyTestDriver):
 
 
 TEST_DRIVERS = {
-    '-migrated': MigratedToolsGalaxyTestDriver,
-    '-installed': InstalledToolsGalaxyTestDriver,
-    '-framework': FrameworkToolsGalaxyTestDriver,
-    '-data_managers': DataManagersGalaxyTestDriver,
-    '-selenium': SeleniumGalaxyTestDriver,
+    "-migrated": MigratedToolsGalaxyTestDriver,
+    "-installed": InstalledToolsGalaxyTestDriver,
+    "-framework": FrameworkToolsGalaxyTestDriver,
+    "-data_managers": DataManagersGalaxyTestDriver,
+    "-selenium": SeleniumGalaxyTestDriver,
 }
 
 
diff --git a/scripts/galaxy_main.py b/scripts/galaxy_main.py
index cb0595baa19..6afaa3a0115 100755
--- a/scripts/galaxy_main.py
+++ b/scripts/galaxy_main.py
@@ -46,7 +46,7 @@ log = logging.getLogger(__name__)
 
 real_file = os.path.realpath(__file__)
 GALAXY_ROOT_DIR_ = os.path.abspath(os.path.join(os.path.dirname(real_file), os.pardir))
-if not os.path.exists(os.path.join(GALAXY_ROOT_DIR_, 'run.sh')):
+if not os.path.exists(os.path.join(GALAXY_ROOT_DIR_, "run.sh")):
     # Galaxy is installed
     GALAXY_ROOT_DIR = None
 else:
@@ -73,20 +73,14 @@ DEFAULT_PID = "galaxy.pid"
 DEFAULT_VERBOSE = True
 DESCRIPTION = "Daemonized entry point for Galaxy."
 
-SHUTDOWN_MSG = '__SHUTDOWN__'
-UWSGI_FARMS_VAR = '_GALAXY_UWSGI_FARM_NAMES'
+SHUTDOWN_MSG = "__SHUTDOWN__"
+UWSGI_FARMS_VAR = "_GALAXY_UWSGI_FARM_NAMES"
 
 
 exit = threading.Event()
 
 
-def load_galaxy_app(
-    config_builder,
-    config_env=False,
-    log=None,
-    attach_to_pools=None,
-    **kwds
-):
+def load_galaxy_app(config_builder, config_env=False, log=None, attach_to_pools=None, **kwds):
     # Allow specification of log so daemon can reuse properly configured one.
     if log is None:
         log = logging.getLogger(__name__)
@@ -102,25 +96,23 @@ def load_galaxy_app(
 
     config_builder.setup_logging()
     from galaxy.util.properties import load_app_properties
+
     kwds = config_builder.app_kwds()
     kwds = load_app_properties(**kwds)
     from galaxy.app import UniverseApplication
-    app = UniverseApplication(
-        global_conf=config_builder.global_conf(),
-        attach_to_pools=attach_to_pools,
-        **kwds
-    )
+
+    app = UniverseApplication(global_conf=config_builder.global_conf(), attach_to_pools=attach_to_pools, **kwds)
     app.database_heartbeat.start()
     app.application_stack.log_startup()
     return app
 
 
 def handle_signal(signum, frame):
-    log.info('Received signal %d, exiting', signum)
-    if uwsgi and 'mule_id' in dir(uwsgi) and uwsgi.mule_id() > 0:
+    log.info("Received signal %d, exiting", signum)
+    if uwsgi and "mule_id" in dir(uwsgi) and uwsgi.mule_id() > 0:
         farms = os.environ.get(UWSGI_FARMS_VAR, None)
         if farms:
-            for farm in farms.split(','):
+            for farm in farms.split(","):
                 uwsgi.farm_msg(farm, SHUTDOWN_MSG)
         else:
             uwsgi.mule_msg(SHUTDOWN_MSG, uwsgi.mule_id())
@@ -128,8 +120,8 @@ def handle_signal(signum, frame):
 
 
 def register_signals():
-    for name in ('TERM', 'INT', 'HUP'):
-        sig = getattr(signal, f'SIG{name}')
+    for name in ("TERM", "INT", "HUP"):
+        sig = getattr(signal, f"SIG{name}")
         signal.signal(sig, handle_signal)
 
 
@@ -160,8 +152,7 @@ def app_loop(args, log):
 
 
 class GalaxyConfigBuilder:
-    """ Generate paste-like configuration from supplied command-line arguments.
-    """
+    """Generate paste-like configuration from supplied command-line arguments."""
 
     def __init__(self, args=None, **kwds):
         self.config_file = None
@@ -170,8 +161,8 @@ class GalaxyConfigBuilder:
         config_file = kwds.get("config_file", None) or (args and args.config_file)
         # If given app_conf_path - use that - else we need to ensure we have a
         # config file path.
-        if not config_file and 'config_file' in self.app_kwds():
-            config_file = self.app_kwds()['config_file']
+        if not config_file and "config_file" in self.app_kwds():
+            config_file = self.app_kwds()["config_file"]
         if not config_file:
             galaxy_root = kwds.get("galaxy_root", GALAXY_ROOT_DIR)
             config_file = find_config(config_file, galaxy_root)
@@ -182,19 +173,32 @@ class GalaxyConfigBuilder:
             self.config_section = f"app:{unicodify(kwds.get('app') or args and args.app or DEFAULT_INI_APP)}"
         else:
             self.config_section = self.app_name
-        self.log_file = (args and args.log_file)
+        self.log_file = args and args.log_file
 
     @classmethod
     def populate_options(cls, arg_parser):
-        arg_parser.add_argument("-c", "--config-file", default=None, help="Galaxy config file (defaults to config/galaxy.ini)")
+        arg_parser.add_argument(
+            "-c", "--config-file", default=None, help="Galaxy config file (defaults to config/galaxy.ini)"
+        )
         arg_parser.add_argument("--ini-path", default=None, help="DEPRECATED: use -c/--config-file")
-        arg_parser.add_argument("--app", default=None, help="app section in config file (defaults to 'galaxy' for YAML/JSON, 'main' (w/ 'app:' prepended) for INI")
+        arg_parser.add_argument(
+            "--app",
+            default=None,
+            help="app section in config file (defaults to 'galaxy' for YAML/JSON, 'main' (w/ 'app:' prepended) for INI",
+        )
         arg_parser.add_argument("-d", "--daemonize", default=False, help="Daemonize process", action="store_true")
         arg_parser.add_argument("--daemon-log-file", default=None, help="log file for daemon script ")
-        arg_parser.add_argument("--log-file", default=None, help="Galaxy log file (overrides log configuration in config_file if set)")
+        arg_parser.add_argument(
+            "--log-file", default=None, help="Galaxy log file (overrides log configuration in config_file if set)"
+        )
         arg_parser.add_argument("--pid-file", default=DEFAULT_PID, help=f"pid file (default is {DEFAULT_PID})")
         arg_parser.add_argument("--server-name", default=None, help="set a galaxy server name")
-        arg_parser.add_argument("--attach-to-pool", action="append", default=None, help="attach to asynchronous worker pool (specify multiple times for multiple pools)")
+        arg_parser.add_argument(
+            "--attach-to-pool",
+            action="append",
+            default=None,
+            help="attach to asynchronous worker pool (specify multiple times for multiple pools)",
+        )
 
     @property
     def config_is_ini(self):
@@ -202,10 +206,10 @@ class GalaxyConfigBuilder:
 
     def app_kwds(self):
         kwds = get_app_kwds(self.app_name, app_name=self.app_name)
-        if 'config_file' not in kwds:
-            kwds['config_file'] = self.config_file
-        if 'config_section' not in kwds:
-            kwds['config_section'] = self.config_section
+        if "config_file" not in kwds:
+            kwds["config_file"] = self.config_file
+        if "config_section" not in kwds:
+            kwds["config_section"] = self.config_section
         return kwds
 
     def global_conf(self):
@@ -223,12 +227,9 @@ class GalaxyConfigBuilder:
         if self.config_is_ini:
             raw_config = ConfigParser()
             raw_config.read([self.config_file])
-            if raw_config.has_section('loggers'):
+            if raw_config.has_section("loggers"):
                 config_file = os.path.abspath(self.config_file)
-                fileConfig(
-                    config_file,
-                    dict(__file__=config_file, here=os.path.dirname(config_file))
-                )
+                fileConfig(config_file, dict(__file__=config_file, here=os.path.dirname(config_file)))
 
 
 def main(func=app_loop):
diff --git a/scripts/galaxy_schemadisp.py b/scripts/galaxy_schemadisp.py
index 5410a92f8e6..0130f8c5ae5 100644
--- a/scripts/galaxy_schemadisp.py
+++ b/scripts/galaxy_schemadisp.py
@@ -4,37 +4,43 @@ import sys
 from db_shell import *  # noqa
 from sqlalchemy import MetaData
 from sqlalchemy.orm import class_mapper
+
 try:
-    from sqlalchemy_schemadisplay import create_schema_graph, create_uml_graph
+    from sqlalchemy_schemadisplay import (
+        create_schema_graph,
+        create_uml_graph,
+    )
 except ImportError:
     print("please install sqlalchemy_schemadisplay to use this script (pip install sqlalchemy_schemadisplay)")
     raise
 
 
 gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
-sys.path.insert(1, os.path.abspath(os.path.join(gxy_root, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(gxy_root, "lib")))
 
 from galaxy import model
 
 if __name__ == "__main__":
     gxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
-    sqlitedb = os.path.join(gxy_root, 'database/universe.sqlite')
+    sqlitedb = os.path.join(gxy_root, "database/universe.sqlite")
     # Try to build a representation of what's in the sqlite database
     if os.path.exists(sqlitedb):
-        graph = create_schema_graph(metadata=MetaData('sqlite:///' + sqlitedb),
-                                    show_datatypes=False,
-                                    show_indexes=False,
-                                    rankdir='LR',
-                                    concentrate=False)
+        graph = create_schema_graph(
+            metadata=MetaData("sqlite:///" + sqlitedb),
+            show_datatypes=False,
+            show_indexes=False,
+            rankdir="LR",
+            concentrate=False,
+        )
         print(f"Writing galaxy_universe.png, built from {sqlitedb}")
-        graph.write_png('galaxy_universe.png')
+        graph.write_png("galaxy_universe.png")
     else:
         print(f"No sqlitedb available at {sqlitedb}, skipping rendering")
 
     # Build UML graph from loaded mapper
     mappers = []
     for attr in dir(model):
-        if attr[0] == '_':
+        if attr[0] == "_":
             continue
         try:
             cls = getattr(model, attr)
@@ -47,4 +53,4 @@ if __name__ == "__main__":
         show_operations=False,
     )
     print("Writing galaxy_uml.png")
-    graph.write_png('galaxy_uml.png')  # write out the file
+    graph.write_png("galaxy_uml.png")  # write out the file
diff --git a/scripts/get_platforms.py b/scripts/get_platforms.py
index a4d3733798f..13f0d88e140 100755
--- a/scripts/get_platforms.py
+++ b/scripts/get_platforms.py
@@ -9,4 +9,5 @@ lib = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib"))
 sys.path.insert(1, lib)
 
 import pkg_resources
+
 print(pkg_resources.get_platform())
diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index 80fe80319ba..486bee14861 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -2,32 +2,44 @@ import os
 import shlex
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.util.path import get_ext
-from galaxy.util.properties import load_app_properties, nice_config_parser
+from galaxy.util.properties import (
+    load_app_properties,
+    nice_config_parser,
+)
 from galaxy.util.script import main_factory
 
-
 DESCRIPTION = "Script to determine uWSGI command line arguments"
 # socket is not an alias for http, but it is assumed that if you configure a socket in your uwsgi config you do not
 # want to run the default http server (or you can configure it yourself)
 ALIASES = {
-    'virtualenv': ('home', 'venv', 'pyhome'),
-    'pythonpath': ('python-path', 'pp'),
-    'http': ('httprouter', 'socket', 'uwsgi-socket', 'suwsgi-socket', 'ssl-socket'),
-    'module': ('mount',),   # mount is not actually an alias for module, but we don't want to set module if mount is set
+    "virtualenv": ("home", "venv", "pyhome"),
+    "pythonpath": ("python-path", "pp"),
+    "http": ("httprouter", "socket", "uwsgi-socket", "suwsgi-socket", "ssl-socket"),
+    "module": ("mount",),  # mount is not actually an alias for module, but we don't want to set module if mount is set
 }
 DEFAULT_ARGS = {
-    '_all_': ('pythonpath', 'threads', 'buffer-size', 'http', 'static-map', 'die-on-term', 'hook-master-start', 'enable-threads', 'umask'),
-    'galaxy': ('py-call-osafterfork',),
-    'reports': (),
-    'tool_shed': ('cron',),
+    "_all_": (
+        "pythonpath",
+        "threads",
+        "buffer-size",
+        "http",
+        "static-map",
+        "die-on-term",
+        "hook-master-start",
+        "enable-threads",
+        "umask",
+    ),
+    "galaxy": ("py-call-osafterfork",),
+    "reports": (),
+    "tool_shed": ("cron",),
 }
 DEFAULT_PORTS = {
-    'galaxy': 8080,
-    'reports': 9001,
-    'tool_shed': 9009,
+    "galaxy": 8080,
+    "reports": 9001,
+    "tool_shed": 9009,
 }
 
 
@@ -41,13 +53,13 @@ def __arg_set(arg, kwargs):
 
 
 def __add_arg(args, arg, value):
-    optarg = '--%s' % arg
+    optarg = "--%s" % arg
     if isinstance(value, bool):
         if value is True:
             args.append(optarg)
     elif isinstance(value, str):
         # the = in --optarg=value is usually, but not always, optional
-        if value.startswith('='):
+        if value.startswith("="):
             args.append(shlex.quote(optarg + value))
         else:
             args.append(optarg)
@@ -60,65 +72,64 @@ def __add_config_file_arg(args, config_file, app):
     ext = None
     if config_file:
         ext = get_ext(config_file)
-    if ext in ('yaml', 'json'):
+    if ext in ("yaml", "json"):
         __add_arg(args, ext, config_file)
-    elif ext == 'ini':
+    elif ext == "ini":
         config = nice_config_parser(config_file)
-        has_logging = config.has_section('loggers')
-        if config.has_section('app:main'):
+        has_logging = config.has_section("loggers")
+        if config.has_section("app:main"):
             # uWSGI does not have any way to set the app name when loading with paste.deploy:loadapp(), so hardcoding
             # the name to `main` is fine
-            __add_arg(args, 'ini-paste' if not has_logging else 'ini-paste-logged', config_file)
+            __add_arg(args, "ini-paste" if not has_logging else "ini-paste-logged", config_file)
             return  # do not add --module
         else:
             __add_arg(args, ext, config_file)
             if has_logging:
-                __add_arg(args, 'paste-logger', True)
+                __add_arg(args, "paste-logger", True)
 
 
 def _get_uwsgi_args(cliargs, kwargs):
     # it'd be nice if we didn't have to reparse here but we need things out of more than one section
-    config_file = cliargs.config_file or kwargs.get('__file__')
-    uwsgi_kwargs = load_app_properties(config_file=config_file, config_section='uwsgi')
+    config_file = cliargs.config_file or kwargs.get("__file__")
+    uwsgi_kwargs = load_app_properties(config_file=config_file, config_section="uwsgi")
     args = []
-    ts_cron_config_option = '' if config_file is None else '-c %s' % config_file
+    ts_cron_config_option = "" if config_file is None else "-c %s" % config_file
     defaults = {
-        'pythonpath': 'lib',
-        'threads': '4',
-        'buffer-size': '16384',  # https://github.com/galaxyproject/galaxy/issues/1530
-        'http': f'localhost:{DEFAULT_PORTS[cliargs.app]}',
-        'static-map': (f'/static={os.getcwd()}/static',
-                       f'/favicon.ico={os.getcwd()}/static/favicon.ico'),
-        'die-on-term': True,
-        'enable-threads': True,
-        'hook-master-start': ('unix_signal:2 gracefully_kill_them_all',
-                              'unix_signal:15 gracefully_kill_them_all'),
-        'py-call-osafterfork': True,
-        'cron': '0 -1 -1 -1 -1 python scripts/tool_shed/build_ts_whoosh_index.py %s --config-section tool_shed -d' % ts_cron_config_option,
-        'umask': '027',
+        "pythonpath": "lib",
+        "threads": "4",
+        "buffer-size": "16384",  # https://github.com/galaxyproject/galaxy/issues/1530
+        "http": f"localhost:{DEFAULT_PORTS[cliargs.app]}",
+        "static-map": (f"/static={os.getcwd()}/static", f"/favicon.ico={os.getcwd()}/static/favicon.ico"),
+        "die-on-term": True,
+        "enable-threads": True,
+        "hook-master-start": ("unix_signal:2 gracefully_kill_them_all", "unix_signal:15 gracefully_kill_them_all"),
+        "py-call-osafterfork": True,
+        "cron": "0 -1 -1 -1 -1 python scripts/tool_shed/build_ts_whoosh_index.py %s --config-section tool_shed -d"
+        % ts_cron_config_option,
+        "umask": "027",
     }
     __add_config_file_arg(args, config_file, cliargs.app)
-    if not __arg_set('module', uwsgi_kwargs):
+    if not __arg_set("module", uwsgi_kwargs):
         if cliargs.app in ["tool_shed"]:
-            __add_arg(args, 'module', 'tool_shed.webapp.buildapp:uwsgi_app()')
+            __add_arg(args, "module", "tool_shed.webapp.buildapp:uwsgi_app()")
         else:
-            __add_arg(args, 'module', f'galaxy.webapps.{cliargs.app}.buildapp:uwsgi_app()')
+            __add_arg(args, "module", f"galaxy.webapps.{cliargs.app}.buildapp:uwsgi_app()")
     # only include virtualenv if it's set/exists, otherwise this breaks conda-env'd Galaxy
-    if not __arg_set('virtualenv', uwsgi_kwargs) and ('VIRTUAL_ENV' in os.environ or os.path.exists('.venv')):
-        __add_arg(args, 'virtualenv', os.environ.get('VIRTUAL_ENV', '.venv'))
+    if not __arg_set("virtualenv", uwsgi_kwargs) and ("VIRTUAL_ENV" in os.environ or os.path.exists(".venv")):
+        __add_arg(args, "virtualenv", os.environ.get("VIRTUAL_ENV", ".venv"))
 
     # We always want to append client/src/assets as static-safe.
-    __add_arg(args, 'static-safe', f'{os.getcwd()}/client/src/assets')
+    __add_arg(args, "static-safe", f"{os.getcwd()}/client/src/assets")
 
     # Do not let uwsgi remap stdin to /dev/null if galaxy is in debug mode
-    galaxy_kwargs = load_app_properties(config_file=config_file, config_section='galaxy')
-    if __arg_set('debug', galaxy_kwargs) and not __arg_set('honour-stdin', uwsgi_kwargs):
-        __add_arg(args, 'honour-stdin', True)
+    galaxy_kwargs = load_app_properties(config_file=config_file, config_section="galaxy")
+    if __arg_set("debug", galaxy_kwargs) and not __arg_set("honour-stdin", uwsgi_kwargs):
+        __add_arg(args, "honour-stdin", True)
 
-    for arg in DEFAULT_ARGS['_all_'] + DEFAULT_ARGS[cliargs.app]:
+    for arg in DEFAULT_ARGS["_all_"] + DEFAULT_ARGS[cliargs.app]:
         if not __arg_set(arg, uwsgi_kwargs):
             __add_arg(args, arg, defaults[arg])
-    print(' '.join(args))
+    print(" ".join(args))
 
 
 ACTIONS = {
@@ -126,6 +137,6 @@ ACTIONS = {
 }
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main = main_factory(description=DESCRIPTION, actions=ACTIONS, default_action="get_uwsgi_args")
     main()
diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index 3b586d2da07..f2194a8376e 100644
--- a/scripts/grt/export.py
+++ b/scripts/grt/export.py
@@ -14,19 +14,22 @@ from collections import defaultdict
 
 import yaml
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 import galaxy
 import galaxy.app
 import galaxy.config
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.util import (
     hash_util,
-    unicodify
+    unicodify,
+)
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
 )
-from galaxy.util.script import app_properties_from_args, populate_config_args
 
-sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml.sample'))
-default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml'))
+sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), "grt.yml.sample"))
+default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), "grt.yml"))
 
 
 def _init(args):
@@ -34,7 +37,9 @@ def _init(args):
     config = galaxy.config.Configuration(**properties)
     object_store = build_object_store_from_config(config)
     if not config.database_connection:
-        logging.warning("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
+        logging.warning(
+            "The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml"
+        )
 
     model = galaxy.config.init_models_from_config(config, object_store=object_store)
     return (
@@ -45,31 +50,40 @@ def _init(args):
 
 
 def kw_metrics(job):
-    return {
-        f'{metric.plugin}_{metric.metric_name}': metric.metric_value
-        for metric in job.metrics
-    }
+    return {f"{metric.plugin}_{metric.metric_name}": metric.metric_value for metric in job.metrics}
 
 
 def round_to_2sd(number):
     if number:
-        return str(int(float('%.2g' % number)))
+        return str(int(float("%.2g" % number)))
     else:
-        return '-1'
+        return "-1"
 
 
 def main(argv):
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('-r', '--report-directory', help='Directory to store reports in',
-                        default=os.path.abspath(os.path.join('.', 'reports')))
-    parser.add_argument('-g', '--grt-config', help='Path to GRT config file',
-                        default=default_config)
-    parser.add_argument("-l", "--loglevel", choices=['debug', 'info', 'warning', 'error', 'critical'],
-                        help="Set the logging level", default='warning')
-    parser.add_argument("-b", "--batch-size", type=int, default=1000,
-                        help="Batch size for sql queries")
-    parser.add_argument("-m", "--max-records", type=int, default=5000000,
-                        help="Maximum number of records to include in a single report. This option should ONLY be used when reporting historical data. Setting this may require running GRT multiple times to capture all historical logs.")
+    parser.add_argument(
+        "-r",
+        "--report-directory",
+        help="Directory to store reports in",
+        default=os.path.abspath(os.path.join(".", "reports")),
+    )
+    parser.add_argument("-g", "--grt-config", help="Path to GRT config file", default=default_config)
+    parser.add_argument(
+        "-l",
+        "--loglevel",
+        choices=["debug", "info", "warning", "error", "critical"],
+        help="Set the logging level",
+        default="warning",
+    )
+    parser.add_argument("-b", "--batch-size", type=int, default=1000, help="Batch size for sql queries")
+    parser.add_argument(
+        "-m",
+        "--max-records",
+        type=int,
+        default=5000000,
+        help="Maximum number of records to include in a single report. This option should ONLY be used when reporting historical data. Setting this may require running GRT multiple times to capture all historical logs.",
+    )
     populate_config_args(parser)
 
     args = parser.parse_args()
@@ -83,18 +97,18 @@ def main(argv):
             logging.info(human_label)
         _times.append((label, time.time() - _start_time))
 
-    annotate('init_start', 'Loading GRT configuration...')
+    annotate("init_start", "Loading GRT configuration...")
     try:
         with open(args.grt_config) as handle:
             config = yaml.safe_load(handle)
     except Exception:
-        logging.info('Using default GRT configuration')
+        logging.info("Using default GRT configuration")
         with open(sample_config) as handle:
             config = yaml.safe_load(handle)
-    annotate('init_end')
+    annotate("init_end")
 
     REPORT_DIR = args.report_directory
-    CHECK_POINT_FILE = os.path.join(REPORT_DIR, '.checkpoint')
+    CHECK_POINT_FILE = os.path.join(REPORT_DIR, ".checkpoint")
     REPORT_IDENTIFIER = str(time.time())
     REPORT_BASE = os.path.join(REPORT_DIR, REPORT_IDENTIFIER)
 
@@ -104,13 +118,13 @@ def main(argv):
     else:
         last_job_sent = -1
 
-    annotate('galaxy_init', 'Loading Galaxy...')
+    annotate("galaxy_init", "Loading Galaxy...")
     model, object_store, gxconfig = _init(args)
 
     # Galaxy overrides our logging level.
     logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
     sa_session = model.context.current
-    annotate('galaxy_end')
+    annotate("galaxy_end")
 
     # Fetch jobs COMPLETED with status OK that have not yet been sent.
 
@@ -122,17 +136,15 @@ def main(argv):
         os.makedirs(REPORT_DIR)
 
     # Pick an end point so our queries can return uniform data.
-    annotate('endpoint_start', 'Identifying a safe endpoint for SQL queries')
-    end_job_id = sa_session.query(model.Job.id) \
-        .order_by(model.Job.id.desc()) \
-        .first()[0]
+    annotate("endpoint_start", "Identifying a safe endpoint for SQL queries")
+    end_job_id = sa_session.query(model.Job.id).order_by(model.Job.id.desc()).first()[0]
 
     # Allow users to only report N records at once.
     if args.max_records > 0:
         if end_job_id - last_job_sent > args.max_records:
             end_job_id = last_job_sent + args.max_records
 
-    annotate('endpoint_end', f'Processing jobs ({last_job_sent}, {end_job_id}]')
+    annotate("endpoint_end", f"Processing jobs ({last_job_sent}, {end_job_id}]")
 
     # Remember the last job sent.
     if end_job_id == last_job_sent:
@@ -142,17 +154,26 @@ def main(argv):
 
     # Unfortunately we have to keep this mapping for the sanitizer to work properly.
     job_tool_map = {}
-    blacklisted_tools = config['sanitization']['tools']
+    blacklisted_tools = config["sanitization"]["tools"]
 
-    annotate('export_jobs_start', 'Exporting Jobs')
-    with open(REPORT_BASE + '.jobs.tsv', 'w', encoding='utf-8') as handle_job:
-        handle_job.write('\t'.join(('id', 'tool_id', 'tool_version', 'state', 'create_time')) + '\n')
+    annotate("export_jobs_start", "Exporting Jobs")
+    with open(REPORT_BASE + ".jobs.tsv", "w", encoding="utf-8") as handle_job:
+        handle_job.write("\t".join(("id", "tool_id", "tool_version", "state", "create_time")) + "\n")
         for offset_start in range(last_job_sent, end_job_id, args.batch_size):
             logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
-            for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
-                    .filter(model.Job.id > offset_start) \
-                    .filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
-                    .all():
+            for job in (
+                sa_session.query(
+                    model.Job.id,
+                    model.Job.user_id,
+                    model.Job.tool_id,
+                    model.Job.tool_version,
+                    model.Job.state,
+                    model.Job.create_time,
+                )
+                .filter(model.Job.id > offset_start)
+                .filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size))
+                .all()
+            ):
                 # If the tool is blacklisted, exclude everywhere
                 if job[2] in blacklisted_tools:
                     continue
@@ -163,9 +184,9 @@ def main(argv):
                         job[2],  # tool_id
                         job[3],  # tool_version
                         job[4],  # state
-                        str(job[5])  # create_time
+                        str(job[5]),  # create_time
                     ]
-                    cline = unicodify('\t'.join(line) + '\n')
+                    cline = unicodify("\t".join(line) + "\n")
                     handle_job.write(cline)
                 except Exception:
                     logging.warning("Unable to write out a 'handle_job' row. Ignoring the row.", exc_info=True)
@@ -174,46 +195,67 @@ def main(argv):
                 job_state_data[job[4]] += 1
                 active_users[job[1]] += 1
                 job_tool_map[job[0]] = job[2]
-    annotate('export_jobs_end')
+    annotate("export_jobs_end")
 
-    annotate('export_datasets_start', 'Exporting Datasets')
-    with open(REPORT_BASE + '.datasets.tsv', 'w', encoding='utf-8') as handle_datasets:
-        handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
+    annotate("export_datasets_start", "Exporting Datasets")
+    with open(REPORT_BASE + ".datasets.tsv", "w", encoding="utf-8") as handle_datasets:
+        handle_datasets.write(
+            "\t".join(("job_id", "dataset_id", "extension", "file_size", "param_name", "type")) + "\n"
+        )
         for offset_start in range(last_job_sent, end_job_id, args.batch_size):
             logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
 
             # four queries: JobToInputDatasetAssociation, JobToOutputDatasetAssociation, HistoryDatasetAssociation, Dataset
 
-            job_to_input_hda_ids = sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
-                model.JobToInputDatasetAssociation.name) \
-                .filter(model.JobToInputDatasetAssociation.job_id > offset_start) \
-                .filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
+            job_to_input_hda_ids = (
+                sa_session.query(
+                    model.JobToInputDatasetAssociation.job_id,
+                    model.JobToInputDatasetAssociation.dataset_id,
+                    model.JobToInputDatasetAssociation.name,
+                )
+                .filter(model.JobToInputDatasetAssociation.job_id > offset_start)
+                .filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size))
                 .all()
+            )
 
-            job_to_output_hda_ids = sa_session.query(model.JobToOutputDatasetAssociation.job_id, model.JobToOutputDatasetAssociation.dataset_id,
-                model.JobToOutputDatasetAssociation.name) \
-                .filter(model.JobToOutputDatasetAssociation.job_id > offset_start) \
-                .filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
+            job_to_output_hda_ids = (
+                sa_session.query(
+                    model.JobToOutputDatasetAssociation.job_id,
+                    model.JobToOutputDatasetAssociation.dataset_id,
+                    model.JobToOutputDatasetAssociation.name,
+                )
+                .filter(model.JobToOutputDatasetAssociation.job_id > offset_start)
+                .filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size))
                 .all()
+            )
 
             # add type and concat
-            job_to_hda_ids = [[list(i), "input"] for i in job_to_input_hda_ids] + [[list(i), "output"] for i in job_to_output_hda_ids]
+            job_to_hda_ids = [[list(i), "input"] for i in job_to_input_hda_ids] + [
+                [list(i), "output"] for i in job_to_output_hda_ids
+            ]
 
             # put all of the hda_ids into a list
             hda_ids = [i[0][1] for i in job_to_hda_ids]
 
-            hdas = sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
-                model.HistoryDatasetAssociation.extension) \
-                .filter(model.HistoryDatasetAssociation.id.in_(hda_ids)) \
+            hdas = (
+                sa_session.query(
+                    model.HistoryDatasetAssociation.id,
+                    model.HistoryDatasetAssociation.dataset_id,
+                    model.HistoryDatasetAssociation.extension,
+                )
+                .filter(model.HistoryDatasetAssociation.id.in_(hda_ids))
                 .all()
+            )
 
             # put all the dataset ids into a list
             dataset_ids = [i[1] for i in hdas]
 
             # get the sizes of the datasets
-            datasets = sa_session.query(model.Dataset.id, model.Dataset.total_size) \
-                .filter(model.Dataset.id.in_(dataset_ids)) \
+            datasets = (
+                sa_session.query(model.Dataset.id, model.Dataset.total_size)
+                .filter(model.Dataset.id.in_(dataset_ids))
                 .all()
+            )
 
             # datasets to dictionay for easy search
             hdas = {i[0]: i[1:] for i in hdas}
@@ -247,24 +289,31 @@ def main(argv):
                         str(hdas[hda_id][1]),  # Extension
                         round_to_2sd(datasets[dataset_id][0]),  # File size
                         job[2],  # Parameter name
-                        str(filetype)  # input/output
+                        str(filetype),  # input/output
                     ]
-                    cline = unicodify('\t'.join(line) + '\n')
+                    cline = unicodify("\t".join(line) + "\n")
                     handle_datasets.write(cline)
                 except Exception:
                     logging.warning("Unable to write out a 'handle_datasets' row. Ignoring the row.", exc_info=True)
                     continue
-    annotate('export_datasets_end')
+    annotate("export_datasets_end")
 
-    annotate('export_metric_num_start', 'Exporting Metrics (Numeric)')
-    with open(REPORT_BASE + '.metric_num.tsv', 'w', encoding='utf-8') as handle_metric_num:
-        handle_metric_num.write('\t'.join(('job_id', 'plugin', 'name', 'value')) + '\n')
+    annotate("export_metric_num_start", "Exporting Metrics (Numeric)")
+    with open(REPORT_BASE + ".metric_num.tsv", "w", encoding="utf-8") as handle_metric_num:
+        handle_metric_num.write("\t".join(("job_id", "plugin", "name", "value")) + "\n")
         for offset_start in range(last_job_sent, end_job_id, args.batch_size):
             logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
-            for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \
-                    .filter(model.JobMetricNumeric.job_id > offset_start) \
-                    .filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size)) \
-                    .all():
+            for metric in (
+                sa_session.query(
+                    model.JobMetricNumeric.job_id,
+                    model.JobMetricNumeric.plugin,
+                    model.JobMetricNumeric.metric_name,
+                    model.JobMetricNumeric.metric_value,
+                )
+                .filter(model.JobMetricNumeric.job_id > offset_start)
+                .filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size))
+                .all()
+            ):
                 # No associated job
                 if metric[0] not in job_tool_map:
                     continue
@@ -273,57 +322,55 @@ def main(argv):
                     continue
 
                 try:
-                    line = [
-                        str(metric[0]),  # job id
-                        metric[1],  # plugin
-                        metric[2],  # name
-                        str(metric[3])  # value
-                    ]
+                    line = [str(metric[0]), metric[1], metric[2], str(metric[3])]  # job id  # plugin  # name  # value
 
-                    cline = unicodify('\t'.join(line) + '\n')
+                    cline = unicodify("\t".join(line) + "\n")
                     handle_metric_num.write(cline)
                 except Exception:
                     logging.warning("Unable to write out a 'handle_metric_num' row. Ignoring the row.", exc_info=True)
                     continue
-    annotate('export_metric_num_end')
+    annotate("export_metric_num_end")
 
     # Now on to outputs.
-    with tarfile.open(REPORT_BASE + '.tar.gz', 'w:gz') as handle:
-        for name in ('jobs', 'metric_num', 'datasets'):
-            path = REPORT_BASE + '.' + name + '.tsv'
+    with tarfile.open(REPORT_BASE + ".tar.gz", "w:gz") as handle:
+        for name in ("jobs", "metric_num", "datasets"):
+            path = REPORT_BASE + "." + name + ".tsv"
             if os.path.exists(path):
                 handle.add(path)
 
-    for name in ('jobs', 'metric_num', 'datasets'):
-        path = REPORT_BASE + '.' + name + '.tsv'
+    for name in ("jobs", "metric_num", "datasets"):
+        path = REPORT_BASE + "." + name + ".tsv"
         if os.path.exists(path):
-            os.unlink(REPORT_BASE + '.' + name + '.tsv')
+            os.unlink(REPORT_BASE + "." + name + ".tsv")
 
-    _times.append(('job_finish', time.time() - _start_time))
+    _times.append(("job_finish", time.time() - _start_time))
     sha = hash_util.memory_bound_hexdigest(hash_func=hash_util.sha256, path=REPORT_BASE + ".tar.gz")
-    _times.append(('hash_finish', time.time() - _start_time))
+    _times.append(("hash_finish", time.time() - _start_time))
 
     # Now serialize the individual report data.
-    with open(REPORT_BASE + '.json', 'w') as handle:
-        json.dump({
-            "version": 3,
-            "galaxy_version": gxconfig.version_major,
-            "generated": REPORT_IDENTIFIER,
-            "report_hash": "sha256:" + sha,
-            "metrics": {
-                "_times": _times,
+    with open(REPORT_BASE + ".json", "w") as handle:
+        json.dump(
+            {
+                "version": 3,
+                "galaxy_version": gxconfig.version_major,
+                "generated": REPORT_IDENTIFIER,
+                "report_hash": "sha256:" + sha,
+                "metrics": {
+                    "_times": _times,
+                },
+                "users": {
+                    "active": len(active_users.keys()),
+                    "total": sa_session.query(model.User.id).count(),
+                },
+                "jobs": job_state_data,
             },
-            "users": {
-                "active": len(active_users.keys()),
-                "total": sa_session.query(model.User.id).count(),
-            },
-            "jobs": job_state_data,
-        }, handle)
+            handle,
+        )
 
     # Write our checkpoint file so we know where to start next time.
-    with open(CHECK_POINT_FILE, 'w') as handle:
+    with open(CHECK_POINT_FILE, "w") as handle:
         handle.write(str(end_job_id))
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main(sys.argv)
diff --git a/scripts/grt/upload.py b/scripts/grt/upload.py
index 807ac6f25a3..7f732cf1a97 100644
--- a/scripts/grt/upload.py
+++ b/scripts/grt/upload.py
@@ -11,64 +11,68 @@ import sys
 import requests
 import yaml
 
-sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml.sample'))
-default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml'))
+sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), "grt.yml.sample"))
+default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), "grt.yml"))
 
 
 def main(argv):
     parser = argparse.ArgumentParser()
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('-r', '--report-directory', help='Directory in which reports are stored',
-                        default=os.path.abspath(os.path.join('.', 'reports')))
-    parser.add_argument('-g', '--grt-config', help='Path to GRT config file',
-                        default=default_config)
-    parser.add_argument("-l", "--loglevel", choices=['debug', 'info', 'warning', 'error', 'critical'],
-                        help="Set the logging level", default='warning')
+    parser.add_argument(
+        "-r",
+        "--report-directory",
+        help="Directory in which reports are stored",
+        default=os.path.abspath(os.path.join(".", "reports")),
+    )
+    parser.add_argument("-g", "--grt-config", help="Path to GRT config file", default=default_config)
+    parser.add_argument(
+        "-l",
+        "--loglevel",
+        choices=["debug", "info", "warning", "error", "critical"],
+        help="Set the logging level",
+        default="warning",
+    )
 
     args = parser.parse_args()
     logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
 
-    logging.info('Loading GRT configuration...')
+    logging.info("Loading GRT configuration...")
     try:
         with open(args.grt_config) as handle:
             config = yaml.safe_load(handle)
     except Exception:
-        logging.exception('Could not parse GRT configuration')
+        logging.exception("Could not parse GRT configuration")
         sys.exit(1)
 
     REPORT_DIR = args.report_directory
-    GRT_URL = config['grt']['url'].rstrip('/') + '/'
-    GRT_INSTANCE_ID = config['grt']['instance_id']
-    GRT_API_KEY = config['grt']['api_key']
+    GRT_URL = config["grt"]["url"].rstrip("/") + "/"
+    GRT_INSTANCE_ID = config["grt"]["instance_id"]
+    GRT_API_KEY = config["grt"]["api_key"]
 
     # Contact the server and check auth details.
-    headers = {
-        'AUTHORIZATION': f'{GRT_INSTANCE_ID}:{GRT_API_KEY}'
-    }
-    r = requests.post(GRT_URL + 'api/whoami', headers=headers)
+    headers = {"AUTHORIZATION": f"{GRT_INSTANCE_ID}:{GRT_API_KEY}"}
+    r = requests.post(GRT_URL + "api/whoami", headers=headers)
     data = r.json()
     # Get back some information about which reports had previously been uploaded.
-    remote_reports = data['uploaded_reports']
+    remote_reports = data["uploaded_reports"]
     logging.debug("Remote reports: %s", remote_reports)
-    local_reports = [x.strip('.json') for x in os.listdir(REPORT_DIR) if x.endswith('.json')]
+    local_reports = [x.strip(".json") for x in os.listdir(REPORT_DIR) if x.endswith(".json")]
     logging.debug("Local reports: %s", local_reports)
     # Now we know which to send.
     for report_id in local_reports:
         if report_id not in remote_reports:
             logging.info("Uploading %s", report_id)
             files = {
-                'meta': open(os.path.join(REPORT_DIR, report_id + '.json'), 'rb'),
-                'data': open(os.path.join(REPORT_DIR, report_id + '.tar.gz'), 'rb')
+                "meta": open(os.path.join(REPORT_DIR, report_id + ".json"), "rb"),
+                "data": open(os.path.join(REPORT_DIR, report_id + ".tar.gz"), "rb"),
             }
-            data = {
-                'identifier': report_id
-            }
-            r = requests.post(GRT_URL + 'api/v2/upload', files=files, headers=headers, data=data)
+            data = {"identifier": report_id}
+            r = requests.post(GRT_URL + "api/v2/upload", files=files, headers=headers, data=data)
             if r.ok:
                 logging.info("Uploaded successfully %s", report_id)
             else:
                 logging.critical("Non-OK response: %s", r.status_code)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main(sys.argv)
diff --git a/scripts/helper.py b/scripts/helper.py
index 97b3e394f1d..2f15a681941 100644
--- a/scripts/helper.py
+++ b/scripts/helper.py
@@ -9,23 +9,26 @@ import argparse
 import os
 import sys
 
-sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))
+sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, "lib"))
 
 import galaxy.config
 from galaxy.security import idencoding
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 parser = argparse.ArgumentParser()
 populate_config_args(parser)
-parser.add_argument('-e', '--encode-id', dest='encode_id', help='Encode an ID')
-parser.add_argument('-d', '--decode-id', dest='decode_id', help='Decode an ID')
-parser.add_argument('--hda', dest='hda_id', help='Display HistoryDatasetAssociation info')
-parser.add_argument('--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info')
+parser.add_argument("-e", "--encode-id", dest="encode_id", help="Encode an ID")
+parser.add_argument("-d", "--decode-id", dest="decode_id", help="Decode an ID")
+parser.add_argument("--hda", dest="hda_id", help="Display HistoryDatasetAssociation info")
+parser.add_argument("--ldda", dest="ldda_id", help="Display LibraryDatasetDatasetAssociation info")
 args = parser.parse_args()
 
 app_properties = app_properties_from_args(args)
 config = galaxy.config.Configuration(**app_properties)
-helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
+helper = idencoding.IdEncodingHelper(id_secret=app_properties.get("id_secret"))
 model = galaxy.config.init_models_from_config(config)
 
 if args.encode_id:
diff --git a/scripts/interactivetools/key_type_token_mapping.py b/scripts/interactivetools/key_type_token_mapping.py
index 0a236c4f8f6..edfdbabd9d9 100644
--- a/scripts/interactivetools/key_type_token_mapping.py
+++ b/scripts/interactivetools/key_type_token_mapping.py
@@ -5,14 +5,13 @@ from time import time
 
 import uwsgi
 
-
-realtime_db_file = uwsgi.opt["interactivetools_map"].decode('utf-8')
+realtime_db_file = uwsgi.opt["interactivetools_map"].decode("utf-8")
 db_conn = sqlite3.connect(realtime_db_file)
 
-DATABASE_TABLE_NAME = 'gxitproxy'
+DATABASE_TABLE_NAME = "gxitproxy"
 
 
-class CacheEntry():
+class CacheEntry:
     def __init__(self, key, value, ttl=20):
         self.key = key
         self.value = value
@@ -21,12 +20,12 @@ class CacheEntry():
 
     def expired(self):
         if self._expired is False:
-            return (self.expires_at < time())
+            return self.expires_at < time()
         else:
             return self._expired
 
 
-class CacheList():
+class CacheList:
     def __init__(self):
         self.entries = []
         self.lock = RLock()
@@ -53,8 +52,9 @@ key_type_token_mapped_cache = CacheList()
 
 def args_as_unicode(func):
     def wrap_args(*args):
-        args = (arg.decode('utf-8') if isinstance(arg, bytes) else arg for arg in args)
+        args = (arg.decode("utf-8") if isinstance(arg, bytes) else arg for arg in args)
         return func(*args)
+
     return wrap_args
 
 
@@ -81,9 +81,13 @@ def key_type_token_mapper(key, key_type, token, route_extra, url):
         for _ in range(2):
             # Order by rowid gives us the last row added
             try:
-                row = db_conn.execute("SELECT host, port FROM %s WHERE key=? AND key_type=? AND token=? ORDER BY rowid DESC LIMIT 1" % (DATABASE_TABLE_NAME), (key, key_type, token)).fetchone()
+                row = db_conn.execute(
+                    "SELECT host, port FROM %s WHERE key=? AND key_type=? AND token=? ORDER BY rowid DESC LIMIT 1"
+                    % (DATABASE_TABLE_NAME),
+                    (key, key_type, token),
+                ).fetchone()
                 if row:
-                    rval = '%s:%s' % (tuple(row))
+                    rval = "%s:%s" % (tuple(row))
                     return rval.encode()
                 break
             except sqlite3.ProgrammingError:
@@ -93,5 +97,5 @@ def key_type_token_mapper(key, key_type, token, route_extra, url):
     return None
 
 
-uwsgi.register_rpc('rtt_key_type_token_mapper', key_type_token_mapper)
-uwsgi.register_rpc('rtt_key_type_token_mapper_cached', key_type_token_mapper_cached)
+uwsgi.register_rpc("rtt_key_type_token_mapper", key_type_token_mapper)
+uwsgi.register_rpc("rtt_key_type_token_mapper_cached", key_type_token_mapper_cached)
diff --git a/scripts/loc_files/create_all_fasta_loc.py b/scripts/loc_files/create_all_fasta_loc.py
index 9c6387de2f7..e785b01509c 100644
--- a/scripts/loc_files/create_all_fasta_loc.py
+++ b/scripts/loc_files/create_all_fasta_loc.py
@@ -29,152 +29,236 @@ import os
 import sys
 from xml.etree.ElementTree import parse
 
-DEFAULT_TOOL_DATA_TABLE_CONF = 'tool_data_table_conf.xml'
-DEFAULT_ALL_FASTA_LOC_BASE = 'all_fasta'
-DEFAULT_BASE_GENOME_DIR = '/afs/bx.psu.edu/depot/data/genome'
-EXEMPTIONS = 'bin,tmp,lengths,equCab2_chrM,microbes'
+DEFAULT_TOOL_DATA_TABLE_CONF = "tool_data_table_conf.xml"
+DEFAULT_ALL_FASTA_LOC_BASE = "all_fasta"
+DEFAULT_BASE_GENOME_DIR = "/afs/bx.psu.edu/depot/data/genome"
+EXEMPTIONS = "bin,tmp,lengths,equCab2_chrM,microbes"
 INSPECT_DIR = None
-FASTA_EXTS = '.fa,.fasta,.fna'
-VARIANTS = 'chrM,chr21,full,canon,female,male,haps,nohaps'
+FASTA_EXTS = ".fa,.fasta,.fna"
+VARIANTS = "chrM,chr21,full,canon,female,male,haps,nohaps"
 
-VARIANT_EXCLUSIONS = ':full'
+VARIANT_EXCLUSIONS = ":full"
 
-DBKEY_DESCRIPTION_MAP = {'AaegL1': 'Mosquito (Aedes aegypti): AaegL1',
-                         'AgamP3': 'Mosquito (Anopheles gambiae): AgamP3',
-                         'anoCar1': 'Lizard (Anolis carolinensis): anoCar1',
-                         'anoGam1': 'Mosquito (Anopheles gambiae): anoGam1',
-                         'apiMel1': 'Honeybee (Apis mellifera): apiMel1',
-                         'apiMel2': 'Honeybee (Apis mellifera): apiMel2',
-                         'apiMel3': 'Honeybee (Apis mellifera): apiMel3',
-                         'Arabidopsis_thaliana_TAIR9': '',
-                         'borEut13': 'Boreoeutherian: borEut13',
-                         'bosTau2': 'Cow (Bos taurus): bosTau2',
-                         'bosTau3': 'Cow (Bos taurus): bosTau3',
-                         'bosTau4': 'Cow (Bos taurus): bosTau4',
-                         'bosTauMd3': 'Cow (Bos taurus): bosTauMd3',
-                         'calJac1': 'Marmoset (Callithrix jacchus): calJac1',
-                         'canFam1': 'Dog (Canis lupus familiaris): canFam1',
-                         'canFam2': 'Dog (Canis lupus familiaris): canFam2',
-                         'cavPor3': 'Guinea Pig (Cavia porcellus): cavPor3',
-                         'ce2': 'Caenorhabditis elegans: ce2',
-                         'ce4': 'Caenorhabditis elegans: ce4',
-                         'ce5': 'Caenorhabditis elegans: ce5',
-                         'ce6': 'Caenorhabditis elegans: ce6',
-                         'CpipJ1': 'Mosquito (Culex quinquefasciatus): CpipJ1',
-                         'danRer2': 'Zebrafish (Danio rerio): danRer2',
-                         'danRer3': 'Zebrafish (Danio rerio): danRer3',
-                         'danRer4': 'Zebrafish (Danio rerio): danRer4',
-                         'danRer5': 'Zebrafish (Danio rerio): danRer5',
-                         'danRer6': 'Zebrafish (Danio rerio): danRer6',
-                         'dm1': 'Fruit Fly (Drosophila melanogaster): dm1',
-                         'dm2': 'Fruit Fly (Drosophila melanogaster): dm2',
-                         'dm3': 'Fruit Fly (Drosophila melanogaster): dm3',
-                         'dm4': 'Fruit Fly (Drosophila melanogaster): dm',
-                         'dp3': 'Fruit Fly (Drosophila pseudoobscura): dp3',
-                         'dp4': 'Fruit Fly (Drosophila pseudoobscura): dp4',
-                         'droAna1': 'Fruit Fly (Drosophila ananassae): droAna1',
-                         'droAna2': 'Fruit Fly (Drosophila ananassae): droAna2',
-                         'droAna3': 'Fruit Fly (Drosophila ananassae): droAna3',
-                         'droEre1': 'Fruit Fly (Drosophila erecta): droEre1',
-                         'droEre2': 'Fruit Fly (Drosophila erecta): droEre2',
-                         'droGri1': 'Fruit Fly (Drosophila grimshawi): droGri1',
-                         'droGri2': 'Fruit Fly (Drosophila grimshawi): droGri2',
-                         'droMoj1': 'Fruit Fly (Drosophila mojavensis): droMoj1',
-                         'droMoj2': 'Fruit Fly (Drosophila mojavensis): droMoj2',
-                         'droMoj3': 'Fruit Fly (Drosophila mojavensis): droMoj3',
-                         'droPer1': 'Fruit Fly (Drosophila persimilis): droPer1',
-                         'droSec1': 'Fruit Fly (Drosophila sechellia): droSec1',
-                         'droSim1': 'Fruit Fly (Drosophila simulans): droSim1',
-                         'droVir1': 'Fruit Fly (Drosophila virilis): droVir1',
-                         'droVir2': 'Fruit Fly (Drosophila virilis): droVir2',
-                         'droVir3': 'Fruit Fly (Drosophila virilis): droVir3',
-                         'droYak1': 'Fruit Fly (Drosophila yakuba): droYak1',
-                         'droYak2': 'Fruit Fly (Drosophila yakuba): droYak2',
-                         'echTel1': 'Tenrec (Echinops telfairi): echTel1',
-                         'equCab1': 'Horse (Equus caballus): equCab1',
-                         'equCab2': 'Horse (Equus caballus): equCab2',
-                         'eriEur1': 'Hedgehog (Erinaceus europaeus): eriEur1',
-                         'felCat3': 'Cat (Felis catus): felCat3',
-                         'fr1': 'Fugu (Takifugu rubripes): fr1',
-                         'fr2': 'Fugu (Takifugu rubripes): fr2',
-                         'galGal2': 'Chicken (Gallus gallus): galGal2',
-                         'galGal3': 'Chicken (Gallus gallus): galGal3',
-                         'gasAcu1': 'Stickleback (Gasterosteus aculeatus): gasAcu1',
-                         'hg16': 'Human (Homo sapiens): hg16',
-                         'hg17': 'Human (Homo sapiens): hg17',
-                         'hg18': 'Human (Homo sapiens): hg18',
-                         'hg19': 'Human (Homo sapiens): hg19',
-                         'IscaW1': 'Deer Tick (Ixodes scapularis): IscaW1',
-                         'lMaj5': 'Leishmania major: lMaj5',
-                         'mm5': 'Mouse (Mus musculus): mm5',
-                         'mm6': 'Mouse (Mus musculus): mm6',
-                         'mm7': 'Mouse (Mus musculus): mm7',
-                         'mm8': 'Mouse (Mus musculus): mm8',
-                         'mm9': 'Mouse (Mus musculus): mm9',
-                         'monDom4': 'Opossum (Monodelphis domestica): monDom4',
-                         'monDom5': 'Opossum (Monodelphis domestica): monDom5',
-                         'ornAna1': 'Platypus (Ornithorhynchus anatinus): ornAna1',
-                         'oryCun1': 'Rabbit (Oryctolagus cuniculus): oryCun1',
-                         'oryLat1': 'Medaka (Oryzias latipes): oryLat1',
-                         'oryLat2': 'Medaka (Oryzias latipes): oryLat2',
-                         'oryza_sativa_japonica_nipponbare_IRGSP4.0': 'Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0',
-                         'otoGar1': 'Bushbaby (Otolemur garnetti): otoGar1',
-                         'panTro1': 'Chimpanzee (Pan troglodytes): panTro1',
-                         'panTro2': 'Chimpanzee (Pan troglodytes): panTro2',
-                         'petMar1': 'Lamprey (Petromyzon marinus): petMar1',
-                         'phiX': 'phiX174 (AF176034)',
-                         'PhumU1': 'Head Louse (Pediculus humanus): PhumU1',
-                         'ponAbe2': 'Orangutan (Pongo pygmaeus abelii): ponAbe2',
-                         'pUC18': 'pUC18 (L09136)',
-                         'rheMac2': 'Rhesus Macaque (Macaca mulatta): rheMac2',
-                         'rn3': 'Rat (Rattus norvegicus): rn3',
-                         'rn4': 'Rat (Rattus norvegicus): rn4',
-                         'sacCer1': 'Yeast (Saccharomyces cerevisiae): sacCer1',
-                         'sacCer2': 'Yeast (Saccharomyces cerevisiae): sacCer2',
-                         'sorAra1': 'Common Shrew (Sorex araneus): sorAra1',
-                         'Sscrofa9.58': 'Pig (Sus scrofa): Sscrofa9.58',
-                         'strPur2': 'Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2',
-                         'susScr2': 'Pig (Sus scrofa): susScr2',
-                         'taeGut1': 'Zebra Finch (Taeniopygia guttata): taeGut1',
-                         'tetNig1': 'Tetraodon (Tetraodon nigroviridis): tetNig1',
-                         'tetNig2': 'Tetraodon (Tetraodon nigroviridis): tetNig2',
-                         'tupBel1': 'Tree Shrew (Tupaia belangeri): tupBel1',
-                         'venter1': 'Human (J. Craig Venter): venter1',
-                         'xenTro2': 'Frog (Xenopus tropicalis): xenTro2'}
+DBKEY_DESCRIPTION_MAP = {
+    "AaegL1": "Mosquito (Aedes aegypti): AaegL1",
+    "AgamP3": "Mosquito (Anopheles gambiae): AgamP3",
+    "anoCar1": "Lizard (Anolis carolinensis): anoCar1",
+    "anoGam1": "Mosquito (Anopheles gambiae): anoGam1",
+    "apiMel1": "Honeybee (Apis mellifera): apiMel1",
+    "apiMel2": "Honeybee (Apis mellifera): apiMel2",
+    "apiMel3": "Honeybee (Apis mellifera): apiMel3",
+    "Arabidopsis_thaliana_TAIR9": "",
+    "borEut13": "Boreoeutherian: borEut13",
+    "bosTau2": "Cow (Bos taurus): bosTau2",
+    "bosTau3": "Cow (Bos taurus): bosTau3",
+    "bosTau4": "Cow (Bos taurus): bosTau4",
+    "bosTauMd3": "Cow (Bos taurus): bosTauMd3",
+    "calJac1": "Marmoset (Callithrix jacchus): calJac1",
+    "canFam1": "Dog (Canis lupus familiaris): canFam1",
+    "canFam2": "Dog (Canis lupus familiaris): canFam2",
+    "cavPor3": "Guinea Pig (Cavia porcellus): cavPor3",
+    "ce2": "Caenorhabditis elegans: ce2",
+    "ce4": "Caenorhabditis elegans: ce4",
+    "ce5": "Caenorhabditis elegans: ce5",
+    "ce6": "Caenorhabditis elegans: ce6",
+    "CpipJ1": "Mosquito (Culex quinquefasciatus): CpipJ1",
+    "danRer2": "Zebrafish (Danio rerio): danRer2",
+    "danRer3": "Zebrafish (Danio rerio): danRer3",
+    "danRer4": "Zebrafish (Danio rerio): danRer4",
+    "danRer5": "Zebrafish (Danio rerio): danRer5",
+    "danRer6": "Zebrafish (Danio rerio): danRer6",
+    "dm1": "Fruit Fly (Drosophila melanogaster): dm1",
+    "dm2": "Fruit Fly (Drosophila melanogaster): dm2",
+    "dm3": "Fruit Fly (Drosophila melanogaster): dm3",
+    "dm4": "Fruit Fly (Drosophila melanogaster): dm",
+    "dp3": "Fruit Fly (Drosophila pseudoobscura): dp3",
+    "dp4": "Fruit Fly (Drosophila pseudoobscura): dp4",
+    "droAna1": "Fruit Fly (Drosophila ananassae): droAna1",
+    "droAna2": "Fruit Fly (Drosophila ananassae): droAna2",
+    "droAna3": "Fruit Fly (Drosophila ananassae): droAna3",
+    "droEre1": "Fruit Fly (Drosophila erecta): droEre1",
+    "droEre2": "Fruit Fly (Drosophila erecta): droEre2",
+    "droGri1": "Fruit Fly (Drosophila grimshawi): droGri1",
+    "droGri2": "Fruit Fly (Drosophila grimshawi): droGri2",
+    "droMoj1": "Fruit Fly (Drosophila mojavensis): droMoj1",
+    "droMoj2": "Fruit Fly (Drosophila mojavensis): droMoj2",
+    "droMoj3": "Fruit Fly (Drosophila mojavensis): droMoj3",
+    "droPer1": "Fruit Fly (Drosophila persimilis): droPer1",
+    "droSec1": "Fruit Fly (Drosophila sechellia): droSec1",
+    "droSim1": "Fruit Fly (Drosophila simulans): droSim1",
+    "droVir1": "Fruit Fly (Drosophila virilis): droVir1",
+    "droVir2": "Fruit Fly (Drosophila virilis): droVir2",
+    "droVir3": "Fruit Fly (Drosophila virilis): droVir3",
+    "droYak1": "Fruit Fly (Drosophila yakuba): droYak1",
+    "droYak2": "Fruit Fly (Drosophila yakuba): droYak2",
+    "echTel1": "Tenrec (Echinops telfairi): echTel1",
+    "equCab1": "Horse (Equus caballus): equCab1",
+    "equCab2": "Horse (Equus caballus): equCab2",
+    "eriEur1": "Hedgehog (Erinaceus europaeus): eriEur1",
+    "felCat3": "Cat (Felis catus): felCat3",
+    "fr1": "Fugu (Takifugu rubripes): fr1",
+    "fr2": "Fugu (Takifugu rubripes): fr2",
+    "galGal2": "Chicken (Gallus gallus): galGal2",
+    "galGal3": "Chicken (Gallus gallus): galGal3",
+    "gasAcu1": "Stickleback (Gasterosteus aculeatus): gasAcu1",
+    "hg16": "Human (Homo sapiens): hg16",
+    "hg17": "Human (Homo sapiens): hg17",
+    "hg18": "Human (Homo sapiens): hg18",
+    "hg19": "Human (Homo sapiens): hg19",
+    "IscaW1": "Deer Tick (Ixodes scapularis): IscaW1",
+    "lMaj5": "Leishmania major: lMaj5",
+    "mm5": "Mouse (Mus musculus): mm5",
+    "mm6": "Mouse (Mus musculus): mm6",
+    "mm7": "Mouse (Mus musculus): mm7",
+    "mm8": "Mouse (Mus musculus): mm8",
+    "mm9": "Mouse (Mus musculus): mm9",
+    "monDom4": "Opossum (Monodelphis domestica): monDom4",
+    "monDom5": "Opossum (Monodelphis domestica): monDom5",
+    "ornAna1": "Platypus (Ornithorhynchus anatinus): ornAna1",
+    "oryCun1": "Rabbit (Oryctolagus cuniculus): oryCun1",
+    "oryLat1": "Medaka (Oryzias latipes): oryLat1",
+    "oryLat2": "Medaka (Oryzias latipes): oryLat2",
+    "oryza_sativa_japonica_nipponbare_IRGSP4.0": "Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0",
+    "otoGar1": "Bushbaby (Otolemur garnetti): otoGar1",
+    "panTro1": "Chimpanzee (Pan troglodytes): panTro1",
+    "panTro2": "Chimpanzee (Pan troglodytes): panTro2",
+    "petMar1": "Lamprey (Petromyzon marinus): petMar1",
+    "phiX": "phiX174 (AF176034)",
+    "PhumU1": "Head Louse (Pediculus humanus): PhumU1",
+    "ponAbe2": "Orangutan (Pongo pygmaeus abelii): ponAbe2",
+    "pUC18": "pUC18 (L09136)",
+    "rheMac2": "Rhesus Macaque (Macaca mulatta): rheMac2",
+    "rn3": "Rat (Rattus norvegicus): rn3",
+    "rn4": "Rat (Rattus norvegicus): rn4",
+    "sacCer1": "Yeast (Saccharomyces cerevisiae): sacCer1",
+    "sacCer2": "Yeast (Saccharomyces cerevisiae): sacCer2",
+    "sorAra1": "Common Shrew (Sorex araneus): sorAra1",
+    "Sscrofa9.58": "Pig (Sus scrofa): Sscrofa9.58",
+    "strPur2": "Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2",
+    "susScr2": "Pig (Sus scrofa): susScr2",
+    "taeGut1": "Zebra Finch (Taeniopygia guttata): taeGut1",
+    "tetNig1": "Tetraodon (Tetraodon nigroviridis): tetNig1",
+    "tetNig2": "Tetraodon (Tetraodon nigroviridis): tetNig2",
+    "tupBel1": "Tree Shrew (Tupaia belangeri): tupBel1",
+    "venter1": "Human (J. Craig Venter): venter1",
+    "xenTro2": "Frog (Xenopus tropicalis): xenTro2",
+}
 
-VARIANT_MAP = {'canon': 'Canonical',
-               'full': 'Full',
-               'female': 'Female',
-               'male': 'Male'}
+VARIANT_MAP = {"canon": "Canonical", "full": "Full", "female": "Female", "male": "Male"}
 
 
 def __main__():
     # command line variables
     parser = optparse.OptionParser()
-    parser.add_option('-d', '--data-table-xml', dest='data_table_xml', type='string', default=DEFAULT_TOOL_DATA_TABLE_CONF, help='The name of the data table configuration file to get format of loc file')
-    parser.add_option('-t', '--data-table', dest='data_table_name', type='string', default=DEFAULT_ALL_FASTA_LOC_BASE, help='The name of the data table listed in the data table XML file')
-    parser.add_option('-g', '--genome_dir', dest='genome_dir', type='string', default=DEFAULT_BASE_GENOME_DIR, help='Genome directory to look in')
-    parser.add_option('-e', '--exemptions', dest='exemptions', type='string', default=EXEMPTIONS, help='Comma-separated list of subdirectories in genome dir to not look in')
-    parser.add_option('-i', '--inspect-dir', dest='inspect_dir', type='string', default=INSPECT_DIR, help='Comma-separated list of subdirectories inside genome dirs to look in (default is all)')
-    parser.add_option('-x', '--fasta_exts', dest='fasta_exts', type='string', default=FASTA_EXTS, help='Comma-separated list of all fasta extensions to list')
-    parser.add_option('-s', '--loc-sample', dest='loc_sample_name', type='string', help='The name of the sample loc file (to copy text into top of output loc file)')
-    parser.add_option('-f', '--unmatching-fasta', dest='unmatching_fasta', type='string', default=None, help='Name of file to output non-matching fasta files to')
-    parser.add_option('-v', '--variants', dest='variants', type='string', default=VARIANTS, help='Comma-separated list of recognized variants of fasta file names')
-    parser.add_option('-n', '--variant-exclusions', dest='variant_exclusions', type='string', default=VARIANT_EXCLUSIONS, help="List of files to exclude because they're duplicated by a variants; of the format: '<variant_to_keep_1>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]][;<variant_to_keep_2>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]]]'; default ':(full)' (if non-variant version present (like 'hg19'), full version (like 'hg19full') will be thrown out)")
-    parser.add_option('-a', '--append', dest='append', action='store_true', default=False, help='Append to existing all_fasta.loc file rather than create new')
-    parser.add_option('-p', '--sample-text', dest='sample_text', action='store_true', default='True', help='Copy over text from all_fasta.loc.sample file (false if set to append)')
+    parser.add_option(
+        "-d",
+        "--data-table-xml",
+        dest="data_table_xml",
+        type="string",
+        default=DEFAULT_TOOL_DATA_TABLE_CONF,
+        help="The name of the data table configuration file to get format of loc file",
+    )
+    parser.add_option(
+        "-t",
+        "--data-table",
+        dest="data_table_name",
+        type="string",
+        default=DEFAULT_ALL_FASTA_LOC_BASE,
+        help="The name of the data table listed in the data table XML file",
+    )
+    parser.add_option(
+        "-g",
+        "--genome_dir",
+        dest="genome_dir",
+        type="string",
+        default=DEFAULT_BASE_GENOME_DIR,
+        help="Genome directory to look in",
+    )
+    parser.add_option(
+        "-e",
+        "--exemptions",
+        dest="exemptions",
+        type="string",
+        default=EXEMPTIONS,
+        help="Comma-separated list of subdirectories in genome dir to not look in",
+    )
+    parser.add_option(
+        "-i",
+        "--inspect-dir",
+        dest="inspect_dir",
+        type="string",
+        default=INSPECT_DIR,
+        help="Comma-separated list of subdirectories inside genome dirs to look in (default is all)",
+    )
+    parser.add_option(
+        "-x",
+        "--fasta_exts",
+        dest="fasta_exts",
+        type="string",
+        default=FASTA_EXTS,
+        help="Comma-separated list of all fasta extensions to list",
+    )
+    parser.add_option(
+        "-s",
+        "--loc-sample",
+        dest="loc_sample_name",
+        type="string",
+        help="The name of the sample loc file (to copy text into top of output loc file)",
+    )
+    parser.add_option(
+        "-f",
+        "--unmatching-fasta",
+        dest="unmatching_fasta",
+        type="string",
+        default=None,
+        help="Name of file to output non-matching fasta files to",
+    )
+    parser.add_option(
+        "-v",
+        "--variants",
+        dest="variants",
+        type="string",
+        default=VARIANTS,
+        help="Comma-separated list of recognized variants of fasta file names",
+    )
+    parser.add_option(
+        "-n",
+        "--variant-exclusions",
+        dest="variant_exclusions",
+        type="string",
+        default=VARIANT_EXCLUSIONS,
+        help="List of files to exclude because they're duplicated by a variants; of the format: '<variant_to_keep_1>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]][;<variant_to_keep_2>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]]]'; default ':(full)' (if non-variant version present (like 'hg19'), full version (like 'hg19full') will be thrown out)",
+    )
+    parser.add_option(
+        "-a",
+        "--append",
+        dest="append",
+        action="store_true",
+        default=False,
+        help="Append to existing all_fasta.loc file rather than create new",
+    )
+    parser.add_option(
+        "-p",
+        "--sample-text",
+        dest="sample_text",
+        action="store_true",
+        default="True",
+        help="Copy over text from all_fasta.loc.sample file (false if set to append)",
+    )
     (options, args) = parser.parse_args()
 
-    exemptions = [e.strip() for e in options.exemptions.split(',')]
-    fasta_exts = [x.strip() for x in options.fasta_exts.split(',')]
-    variants = [v.strip() for v in options.variants.split(',')]
+    exemptions = [e.strip() for e in options.exemptions.split(",")]
+    fasta_exts = [x.strip() for x in options.fasta_exts.split(",")]
+    variants = [v.strip() for v in options.variants.split(",")]
     variant_exclusions = {}
     try:
-        for ve in options.variant_exclusions.split(';'):
-            v, e = ve.split(':')
-            variant_exclusions[v] = e.split(',')
+        for ve in options.variant_exclusions.split(";"):
+            v, e = ve.split(":")
+            variant_exclusions[v] = e.split(",")
     except Exception:
-        sys.stderr.write('Problem parsing the variant exclusion parameter (-n/--variant-exclusion). Make sure it follows the expected format\n')
+        sys.stderr.write(
+            "Problem parsing the variant exclusion parameter (-n/--variant-exclusion). Make sure it follows the expected format\n"
+        )
         sys.exit(1)
     if options.append:
         sample_text = False
@@ -183,21 +267,21 @@ def __main__():
 
     # all paths to look in
     if options.inspect_dir:
-        paths_to_look_in = [os.path.join(options.genome_dir, '%s', id) for id in options.inspect_dir.split(',')]
+        paths_to_look_in = [os.path.join(options.genome_dir, "%s", id) for id in options.inspect_dir.split(",")]
     else:
-        paths_to_look_in = [os.path.join(options.genome_dir, '%s')]
+        paths_to_look_in = [os.path.join(options.genome_dir, "%s")]
 
     # say what we're looking in
-    print('\nLooking in:\n\t%s' % '\n\t'.join(p % '<build_name>' for p in paths_to_look_in))
-    poss_names = ['<build_name>%s' % _ for _ in variants]
-    print('for files that are named %s' % ', '.join(poss_names[:-1]), end=' ')
+    print("\nLooking in:\n\t%s" % "\n\t".join(p % "<build_name>" for p in paths_to_look_in))
+    poss_names = ["<build_name>%s" % _ for _ in variants]
+    print("for files that are named %s" % ", ".join(poss_names[:-1]), end=" ")
     if len(poss_names) > 1:
-        print('or %s' % poss_names[-1], end=' ')
+        print("or %s" % poss_names[-1], end=" ")
     if len(options.fasta_exts) == 1:
-        print('with the extension %s.' % ', '.join(fasta_exts[:-1]))
+        print("with the extension %s." % ", ".join(fasta_exts[:-1]))
     else:
-        print('with the extension {} or {}.'.format(', '.join(fasta_exts[:-1]), fasta_exts[-1]))
-    print('\nSkipping the following:\n\t%s' % '\n\t'.join(exemptions))
+        print("with the extension {} or {}.".format(", ".join(fasta_exts[:-1]), fasta_exts[-1]))
+    print("\nSkipping the following:\n\t%s" % "\n\t".join(exemptions))
 
     # get column names
     col_values = []
@@ -205,18 +289,20 @@ def __main__():
     tree = parse(options.data_table_xml)
     tables = tree.getroot()
     for table in tables.iter():
-        name = table.attrib.get('name')
+        name = table.attrib.get("name")
         if name == options.data_table_name:
             cols = None
             for node in table.iter():
-                if node.tag == 'columns':
+                if node.tag == "columns":
                     cols = node.text
-                elif node.tag == 'file':
-                    loc_path = node.attrib.get('path')
+                elif node.tag == "file":
+                    loc_path = node.attrib.get("path")
             if cols:
-                col_values = [col.strip() for col in cols.split(',')]
+                col_values = [col.strip() for col in cols.split(",")]
     if not col_values or not loc_path:
-        raise Exception(f'No columns can be found for this data table ({options.data_table}) in {options.data_table_xml}')
+        raise Exception(
+            f"No columns can be found for this data table ({options.data_table}) in {options.data_table_xml}"
+        )
 
     # get all fasta paths under genome directory
     fasta_locs = {}
@@ -224,7 +310,7 @@ def __main__():
     genome_subdirs = [dr for dr in os.listdir(options.genome_dir) if dr not in exemptions]
     for genome_subdir in genome_subdirs:
         possible_names = [genome_subdir]
-        possible_names.extend([f'{genome_subdir}{_}' for _ in variants])
+        possible_names.extend([f"{genome_subdir}{_}" for _ in variants])
         # get paths to all fasta files
         for path_to_look_in in paths_to_look_in:
             for dirpath, _dirnames, filenames in os.walk(path_to_look_in % genome_subdir):
@@ -237,40 +323,53 @@ def __main__():
                                 name = DBKEY_DESCRIPTION_MAP[genome_subdir]
                             else:
                                 try:
-                                    name = '{} {}'.format(DBKEY_DESCRIPTION_MAP[genome_subdir], VARIANT_MAP[fasta_base.replace(genome_subdir, '')])
+                                    name = "{} {}".format(
+                                        DBKEY_DESCRIPTION_MAP[genome_subdir],
+                                        VARIANT_MAP[fasta_base.replace(genome_subdir, "")],
+                                    )
                                 except KeyError:
-                                    name = '{} {}'.format(DBKEY_DESCRIPTION_MAP[genome_subdir], fasta_base.replace(genome_subdir, ''))
-                            fasta_locs[fasta_base] = {'value': fasta_base, 'dbkey': genome_subdir, 'name': name, 'path': os.path.join(dirpath, fn)}
+                                    name = "{} {}".format(
+                                        DBKEY_DESCRIPTION_MAP[genome_subdir], fasta_base.replace(genome_subdir, "")
+                                    )
+                            fasta_locs[fasta_base] = {
+                                "value": fasta_base,
+                                "dbkey": genome_subdir,
+                                "name": name,
+                                "path": os.path.join(dirpath, fn),
+                            }
                         else:
                             unmatching_fasta_paths.append(os.path.join(dirpath, fn))
         # remove redundant fasta files
         for k, v in variant_exclusions.items():
-            leave_in = f'{genome_subdir}{k}'
+            leave_in = f"{genome_subdir}{k}"
             if leave_in in fasta_locs:
-                to_remove = [f'{genome_subdir}{_}' for _ in v]
+                to_remove = [f"{genome_subdir}{_}" for _ in v]
                 for tr in to_remove:
                     if tr in fasta_locs:
                         del fasta_locs[tr]
 
     # output results
-    print('\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len(unmatching_fasta_paths))
-    print('%s fasta files were found and listed.\n' % len(fasta_locs.keys()))
+    print(
+        "\nThere were %s fasta files found that were not included because they did not have the expected file names."
+        % len(unmatching_fasta_paths)
+    )
+    print("%s fasta files were found and listed.\n" % len(fasta_locs.keys()))
 
     # output unmatching fasta files
     if options.unmatching_fasta and unmatching_fasta_paths:
-        open(options.unmatching_fasta, 'wb').write('%s\n' % '\n'.join(unmatching_fasta_paths))
+        open(options.unmatching_fasta, "wb").write("%s\n" % "\n".join(unmatching_fasta_paths))
 
     # output loc file
     if options.append:
-        all_fasta_loc = open(loc_path, 'ab')
+        all_fasta_loc = open(loc_path, "ab")
     else:
-        all_fasta_loc = open(loc_path, 'wb')
+        all_fasta_loc = open(loc_path, "wb")
     # put sample loc file text at top of file if appropriate
     if sample_text:
         if options.loc_sample_name:
-            all_fasta_loc.write('%s\n' % open(options.loc_sample_name, 'rb').read().strip())
+            all_fasta_loc.write("%s\n" % open(options.loc_sample_name, "rb").read().strip())
         else:
-            all_fasta_loc.write('%s\n' % open('%s.sample' % loc_path, 'rb').read().strip())
+            all_fasta_loc.write("%s\n" % open("%s.sample" % loc_path, "rb").read().strip())
     # output list of fasta files in alphabetical order
     fasta_bases = list(fasta_locs.keys())
     fasta_bases.sort(key=str.upper)
@@ -280,12 +379,12 @@ def __main__():
             try:
                 out_line.append(fasta_locs[fb][col])
             except KeyError:
-                raise Exception('Unexpected column (%s) encountered' % col)
+                raise Exception("Unexpected column (%s) encountered" % col)
         if out_line:
-            all_fasta_loc.write('%s\n' % '\t'.join(out_line))
+            all_fasta_loc.write("%s\n" % "\t".join(out_line))
     # close up output loc file
     all_fasta_loc.close()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     __main__()
diff --git a/scripts/manage_db.py b/scripts/manage_db.py
index e55d3a13daa..4bbf2eb4abf 100644
--- a/scripts/manage_db.py
+++ b/scripts/manage_db.py
@@ -7,7 +7,7 @@ import sys
 
 from migrate.versioning.shell import main
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.model.orm.scripts import get_config
 
@@ -18,8 +18,8 @@ log = logging.getLogger(__name__)
 def invoke_migrate_main():
     # Migrate has its own args, so cannot use argparse
     config = get_config(sys.argv, use_argparse=False, cwd=os.getcwd())
-    db_url = config['db_url']
-    repo = config['repo']
+    db_url = config["db_url"]
+    repo = config["repo"]
 
     main(repository=repo, url=db_url)
 
diff --git a/scripts/manage_tool_dependencies.py b/scripts/manage_tool_dependencies.py
index 72dba77e92f..32f082acba9 100644
--- a/scripts/manage_tool_dependencies.py
+++ b/scripts/manage_tool_dependencies.py
@@ -1,7 +1,7 @@
 import os.path
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.config import configure_logging
 from galaxy.tool_util.deps import build_dependency_manager
@@ -23,10 +23,14 @@ def _build_dependency_manager_no_config(kwargs):
     which we do not have available in this script (an optimization).
     """
     configure_logging(kwargs)
-    base, ext = os.path.splitext(kwargs.get('dependency_resolvers_config_file', 'dependency_resolvers_conf.xml'))
-    dependency_resolvers_config_file = find_config_file(base, exts=[ext.lstrip('.')])
+    base, ext = os.path.splitext(kwargs.get("dependency_resolvers_config_file", "dependency_resolvers_conf.xml"))
+    dependency_resolvers_config_file = find_config_file(base, exts=[ext.lstrip(".")])
     # FIXME: default is wrong for installed Galaxy
-    dependency_manager = build_dependency_manager(app_config_dict=kwargs, conf_file=dependency_resolvers_config_file, default_tool_dependency_dir="database/dependencies")
+    dependency_manager = build_dependency_manager(
+        app_config_dict=kwargs,
+        conf_file=dependency_resolvers_config_file,
+        default_tool_dependency_dir="database/dependencies",
+    )
     return dependency_manager
 
 
@@ -35,6 +39,6 @@ ACTIONS = {
 }
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main = main_factory(description=DESCRIPTION, actions=ACTIONS)
     main()
diff --git a/scripts/metagenomics/convert_title.py b/scripts/metagenomics/convert_title.py
index 58f203290e3..4beafbc056d 100644
--- a/scripts/metagenomics/convert_title.py
+++ b/scripts/metagenomics/convert_title.py
@@ -6,26 +6,26 @@ run formatdb in the command line: gunzip -c nt.gz |formatdb -i stdin -p F -n "nt
 
 import sys
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     seq = []
     len_seq = 0
     invalid_lines = 0
     gi = None
 
     for line in sys.stdin:
-        line = line.rstrip('\r\n')
-        if line.startswith('>'):
+        line = line.rstrip("\r\n")
+        if line.startswith(">"):
             if len_seq > 0:
                 if gi is None:
-                    raise Exception('The first sequence does not have an header.')
+                    raise Exception("The first sequence does not have an header.")
                 print(">%s_%d" % (gi, len_seq))
                 print("\n".join(seq))
             title = line
-            fields = title.split('|')
-            if len(fields) >= 2 and fields[0] == '>gi':
+            fields = title.split("|")
+            if len(fields) >= 2 and fields[0] == ">gi":
                 gi = fields[1]
             else:
-                gi = 'giunknown'
+                gi = "giunknown"
                 invalid_lines += 1
             len_seq = 0
             seq = []
@@ -36,4 +36,7 @@ if __name__ == '__main__':
         print(">%s_%d" % (gi, len_seq))
         print("\n".join(seq))
 
-    print("Unable to find gi number for %d sequences, the title is replaced as giunknown" % (invalid_lines), file=sys.stderr)
+    print(
+        "Unable to find gi number for %d sequences, the title is replaced as giunknown" % (invalid_lines),
+        file=sys.stderr,
+    )
diff --git a/scripts/microbes/create_bacteria_loc_file.py b/scripts/microbes/create_bacteria_loc_file.py
index bddcace6024..f9dae93dbd1 100644
--- a/scripts/microbes/create_bacteria_loc_file.py
+++ b/scripts/microbes/create_bacteria_loc_file.py
@@ -26,47 +26,120 @@ def __main__():
                 for line in info:
                     fields = line.replace("\n", "").split("=")
                     tmp_dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in tmp_dict.keys():
-                    name = tmp_dict['genome project id']
-                    if 'build' in tmp_dict.keys():
-                        name = tmp_dict['build']
+                if "genome project id" in tmp_dict.keys():
+                    name = tmp_dict["genome project id"]
+                    if "build" in tmp_dict.keys():
+                        name = tmp_dict["build"]
                     if name not in organisms.keys():
-                        organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
+                        organisms[name] = {"chrs": {}, "base_dir": this_base_dir}
                     for key in tmp_dict.keys():
                         organisms[name][key] = tmp_dict[key]
                 else:
-                    if tmp_dict['organism'] not in organisms.keys():
-                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
+                    if tmp_dict["organism"] not in organisms.keys():
+                        organisms[tmp_dict["organism"]] = {"chrs": {}, "base_dir": this_base_dir}
+                    organisms[tmp_dict["organism"]]["chrs"][tmp_dict["chromosome"]] = tmp_dict
     for org in organisms:
         org = organisms[org]
         # if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
         try:
-            build = org['genome project id']
+            build = org["genome project id"]
         except KeyError:
             continue
-        if 'build' in org:
-            build = org['build']
-            print("ORG\t{}\t{}\t{}\t{}\t{}\t{}\tUCSC".format(build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
+        if "build" in org:
+            build = org["build"]
+            print(
+                "ORG\t{}\t{}\t{}\t{}\t{}\t{}\tUCSC".format(
+                    build, org["name"], org["kingdom"], org["group"], org["chromosomes"], org["info url"]
+                )
+            )
         else:
-            print("ORG\t{}\t{}\t{}\t{}\t{}\t{}\tNone".format(build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
+            print(
+                "ORG\t{}\t{}\t{}\t{}\t{}\t{}\tNone".format(
+                    build, org["name"], org["kingdom"], org["group"], org["chromosomes"], org["info url"]
+                )
+            )
 
-        for chr in org['chrs']:
-            chr = org['chrs'][chr]
-            print("CHR\t{}\t{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr['refseq']))
-            for feature in ['CDS', 'tRNA', 'rRNA']:
-                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join(org['base_dir'], "{}.{}.bed".format(chr['chromosome'], feature))))
+        for chr in org["chrs"]:
+            chr = org["chrs"][chr]
+            print(
+                "CHR\t{}\t{}\t{}\t{}\t{}\t{}\t{}".format(
+                    build,
+                    chr["chromosome"],
+                    chr["name"],
+                    chr["length"],
+                    chr["gi"],
+                    chr["gb"],
+                    "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr["refseq"],
+                )
+            )
+            for feature in ["CDS", "tRNA", "rRNA"]:
+                print(
+                    "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
+                        build,
+                        chr["chromosome"],
+                        feature,
+                        build,
+                        chr["chromosome"],
+                        feature,
+                        "bed",
+                        os.path.join(org["base_dir"], "{}.{}.bed".format(chr["chromosome"], feature)),
+                    )
+                )
             # FASTA
-            print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])))
+            print(
+                "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
+                    build,
+                    chr["chromosome"],
+                    "seq",
+                    build,
+                    chr["chromosome"],
+                    "sequence",
+                    "fasta",
+                    os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"]),
+                )
+            )
             # GeneMark
-            if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])):
-                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])))
+            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"])):
+                print(
+                    "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
+                        build,
+                        chr["chromosome"],
+                        "GeneMark",
+                        build,
+                        chr["chromosome"],
+                        "GeneMark",
+                        "bed",
+                        os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"]),
+                    )
+                )
             # GenMarkHMM
-            if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])):
-                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])))
+            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"])):
+                print(
+                    "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
+                        build,
+                        chr["chromosome"],
+                        "GeneMarkHMM",
+                        build,
+                        chr["chromosome"],
+                        "GeneMarkHMM",
+                        "bed",
+                        os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"]),
+                    )
+                )
             # Glimmer3
-            if os.path.exists(os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])):
-                print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])))
+            if os.path.exists(os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"])):
+                print(
+                    "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
+                        build,
+                        chr["chromosome"],
+                        "Glimmer3",
+                        build,
+                        chr["chromosome"],
+                        "Glimmer3",
+                        "bed",
+                        os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"]),
+                    )
+                )
 
 
 if __name__ == "__main__":
diff --git a/scripts/microbes/create_bacteria_table.py b/scripts/microbes/create_bacteria_table.py
index 6211cf4b91f..b3a3252cb5a 100644
--- a/scripts/microbes/create_bacteria_table.py
+++ b/scripts/microbes/create_bacteria_table.py
@@ -26,21 +26,21 @@ def __main__():
                 for line in info:
                     fields = line.replace("\n", "").split("=")
                     tmp_dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in tmp_dict.keys():
-                    name = tmp_dict['genome project id']
-                    if 'build' in tmp_dict.keys():
-                        name = tmp_dict['build']
+                if "genome project id" in tmp_dict.keys():
+                    name = tmp_dict["genome project id"]
+                    if "build" in tmp_dict.keys():
+                        name = tmp_dict["build"]
                     if name not in organisms.keys():
-                        organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
+                        organisms[name] = {"chrs": {}, "base_dir": this_base_dir}
                     for key in tmp_dict.keys():
                         organisms[name][key] = tmp_dict[key]
                 else:
-                    if tmp_dict['organism'] not in organisms.keys():
-                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
+                    if tmp_dict["organism"] not in organisms.keys():
+                        organisms[tmp_dict["organism"]] = {"chrs": {}, "base_dir": this_base_dir}
+                    organisms[tmp_dict["organism"]]["chrs"][tmp_dict["chromosome"]] = tmp_dict
 
     for org_name, org in list(organisms.items()):
-        if 'name' not in org:
+        if "name" not in org:
             del organisms[org_name]
 
     orgs = list(organisms.keys())
@@ -48,7 +48,7 @@ def __main__():
     swap_test = False
     for i in range(0, len(orgs) - 1):
         for j in range(0, len(orgs) - i - 1):
-            if organisms[orgs[j]]['name'] > organisms[orgs[j + 1]]['name']:
+            if organisms[orgs[j]]["name"] > organisms[orgs[j + 1]]["name"]:
                 orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
             swap_test = True
         if swap_test is False:
@@ -60,13 +60,13 @@ def __main__():
         at_ucsc = False
         # if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
         try:
-            org['genome project id']
+            org["genome project id"]
         except KeyError:
             continue
-        if 'build' in org:
+        if "build" in org:
             at_ucsc = True
 
-        out_str = "||" + org['name'] + "||" + org['kingdom'] + "||" + org['group'] + "||"
+        out_str = "||" + org["name"] + "||" + org["kingdom"] + "||" + org["group"] + "||"
         if at_ucsc:
             out_str = out_str + "Yes"
         out_str = out_str + "||"
diff --git a/scripts/microbes/create_nib_seq_loc_file.py b/scripts/microbes/create_nib_seq_loc_file.py
index 255dbcf0a2c..3a79d9b84e5 100644
--- a/scripts/microbes/create_nib_seq_loc_file.py
+++ b/scripts/microbes/create_nib_seq_loc_file.py
@@ -22,7 +22,7 @@ def __main__():
 
     organisms = {}
 
-    loc_out = open(loc_out, 'wb')
+    loc_out = open(loc_out, "wb")
 
     for result in os.walk(base_dir):
         this_base_dir, sub_dirs, files = result
@@ -35,29 +35,29 @@ def __main__():
                 for line in info:
                     fields = line.replace("\n", "").split("=")
                     tmp_dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in tmp_dict.keys():
-                    name = tmp_dict['genome project id']
-                    if 'build' in tmp_dict.keys():
-                        name = tmp_dict['build']
+                if "genome project id" in tmp_dict.keys():
+                    name = tmp_dict["genome project id"]
+                    if "build" in tmp_dict.keys():
+                        name = tmp_dict["build"]
                     if name not in organisms.keys():
-                        organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
+                        organisms[name] = {"chrs": {}, "base_dir": this_base_dir}
                     for key in tmp_dict.keys():
                         organisms[name][key] = tmp_dict[key]
                 else:
-                    if tmp_dict['organism'] not in organisms.keys():
-                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
+                    if tmp_dict["organism"] not in organisms.keys():
+                        organisms[tmp_dict["organism"]] = {"chrs": {}, "base_dir": this_base_dir}
+                    organisms[tmp_dict["organism"]]["chrs"][tmp_dict["chromosome"]] = tmp_dict
 
     for org in organisms:
         org = organisms[org]
         try:
-            build = org['genome project id']
+            build = org["genome project id"]
         except KeyError:
             continue
-        if 'build' in org:
-            build = org['build']
+        if "build" in org:
+            build = org["build"]
 
-        seq_path = os.path.join(org['base_dir'], "seq")
+        seq_path = os.path.join(org["base_dir"], "seq")
 
         # create seq dir, if exists go to next org
         # TODO: add better checking, i.e. for updating
@@ -71,11 +71,11 @@ def __main__():
 
         # Print org info
 
-        for chr in org['chrs']:
-            chr = org['chrs'][chr]
+        for chr in org["chrs"]:
+            chr = org["chrs"][chr]
 
-            fasta_file = os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])
-            nib_out_file = os.path.join(seq_path, "%s.nib " % chr['chromosome'])
+            fasta_file = os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"])
+            nib_out_file = os.path.join(seq_path, "%s.nib " % chr["chromosome"])
             # create nibs using faToNib binary
             # TODO: when bx supports writing nib, use it here instead
             command = f"faToNib {fasta_file} {nib_out_file}"
diff --git a/scripts/microbes/get_builds_lengths.py b/scripts/microbes/get_builds_lengths.py
index ed61e4c7121..5d0f8284aed 100644
--- a/scripts/microbes/get_builds_lengths.py
+++ b/scripts/microbes/get_builds_lengths.py
@@ -26,34 +26,34 @@ def __main__():
                 for line in info:
                     fields = line.replace("\n", "").split("=")
                     tmp_dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in tmp_dict.keys():
-                    name = tmp_dict['genome project id']
-                    if 'build' in tmp_dict.keys():
-                        name = tmp_dict['build']
+                if "genome project id" in tmp_dict.keys():
+                    name = tmp_dict["genome project id"]
+                    if "build" in tmp_dict.keys():
+                        name = tmp_dict["build"]
                     if name not in organisms.keys():
-                        organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
+                        organisms[name] = {"chrs": {}, "base_dir": this_base_dir}
                     for key in tmp_dict.keys():
                         organisms[name][key] = tmp_dict[key]
                 else:
-                    if tmp_dict['organism'] not in organisms.keys():
-                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
+                    if tmp_dict["organism"] not in organisms.keys():
+                        organisms[tmp_dict["organism"]] = {"chrs": {}, "base_dir": this_base_dir}
+                    organisms[tmp_dict["organism"]]["chrs"][tmp_dict["chromosome"]] = tmp_dict
     for org in organisms:
         org = organisms[org]
         # if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
         try:
-            build = org['genome project id']
+            build = org["genome project id"]
         except KeyError:
             continue
 
-        if 'build' in org:
-            build = org['build']
+        if "build" in org:
+            build = org["build"]
 
         chrs = []
-        for chrom in org['chrs']:
-            chrom = org['chrs'][chrom]
-            chrs.append("{}={}".format(chrom['chromosome'], chrom['length']))
-        print("{}\t{}\t{}".format(build, org['name'], ",".join(chrs)))
+        for chrom in org["chrs"]:
+            chrom = org["chrs"][chrom]
+            chrs.append("{}={}".format(chrom["chromosome"], chrom["length"]))
+        print("{}\t{}\t{}".format(build, org["name"], ",".join(chrs)))
 
 
 if __name__ == "__main__":
diff --git a/scripts/microbes/harvest_bacteria.py b/scripts/microbes/harvest_bacteria.py
index f069e44f2d6..4aaacf725e0 100644
--- a/scripts/microbes/harvest_bacteria.py
+++ b/scripts/microbes/harvest_bacteria.py
@@ -12,6 +12,7 @@ from ftplib import FTP
 from urllib.request import urlretrieve
 
 import requests
+
 try:
     from bs4 import BeautifulSoup
 except ImportError:
@@ -21,44 +22,49 @@ from util import (  # noqa: I202
     get_bed_from_genbank,
     get_bed_from_GeneMark,
     get_bed_from_GeneMarkHMM,
-    get_bed_from_glimmer3
+    get_bed_from_glimmer3,
 )
 
 assert sys.version_info[:2] >= (2, 6)
 
 # this defines the types of ftp files we are interested in, and how to process/convert them to a form for our use
-desired_ftp_files = {'GeneMark': {'ext': 'GeneMark-2.5f', 'parser': 'process_GeneMark'},
-                    'GeneMarkHMM': {'ext': 'GeneMarkHMM-2.6m', 'parser': 'process_GeneMarkHMM'},
-                    'Glimmer3': {'ext': 'Glimmer3', 'parser': 'process_Glimmer3'},
-                    'fna': {'ext': 'fna', 'parser': 'process_FASTA'},
-                    'gbk': {'ext': 'gbk', 'parser': 'process_Genbank'}}
+desired_ftp_files = {
+    "GeneMark": {"ext": "GeneMark-2.5f", "parser": "process_GeneMark"},
+    "GeneMarkHMM": {"ext": "GeneMarkHMM-2.6m", "parser": "process_GeneMarkHMM"},
+    "Glimmer3": {"ext": "Glimmer3", "parser": "process_Glimmer3"},
+    "fna": {"ext": "fna", "parser": "process_FASTA"},
+    "gbk": {"ext": "gbk", "parser": "process_Genbank"},
+}
 
 
 # number, name, chroms, kingdom, group, genbank, refseq, info_url, ftp_url
-def iter_genome_projects(url="http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1", info_url_base="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids="):
-    for row in BeautifulSoup(requests.get(url).text).findAll(name='tr', bgcolor=["#EEFFDD", "#E8E8DD"]):
+def iter_genome_projects(
+    url="http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1",
+    info_url_base="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=",
+):
+    for row in BeautifulSoup(requests.get(url).text).findAll(name="tr", bgcolor=["#EEFFDD", "#E8E8DD"]):
         row = str(row).replace("\n", "").replace("\r", "")
 
         fields = row.split("</td>")
 
-        org_num = fields[0].split("list_uids=")[-1].split("\"")[0]
+        org_num = fields[0].split("list_uids=")[-1].split('"')[0]
 
-        name = fields[1].split("\">")[-1].split("<")[0]
+        name = fields[1].split('">')[-1].split("<")[0]
 
         kingdom = "archaea"
-        if "<td class=\"bacteria\" align=\"center\">B" in fields[2]:
+        if '<td class="bacteria" align="center">B' in fields[2]:
             kingdom = "bacteria"
 
         group = fields[3].split(">")[-1]
 
         info_url = f"{info_url_base}{org_num}"
 
-        org_genbank = fields[7].split("\">")[-1].split("<")[0].split(".")[0]
-        org_refseq = fields[8].split("\">")[-1].split("<")[0].split(".")[0]
+        org_genbank = fields[7].split('">')[-1].split("<")[0].split(".")[0]
+        org_refseq = fields[8].split('">')[-1].split("<")[0].split(".")[0]
 
         # seems some things donot have an ftp url, try and except it here:
         try:
-            ftp_url = fields[22].split("href=\"")[1].split("\"")[0]
+            ftp_url = fields[22].split('href="')[1].split('"')[0]
         except Exception:
             print("FAILED TO AQUIRE FTP ADDRESS:", org_num, info_url)
             ftp_url = None
@@ -68,7 +74,9 @@ def iter_genome_projects(url="http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?vie
         yield org_num, name, chroms, kingdom, group, org_genbank, org_refseq, info_url, ftp_url
 
 
-def get_chroms_by_project_id(org_num, base_url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids="):
+def get_chroms_by_project_id(
+    org_num, base_url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids="
+):
     html_count = 0
     html = None
     while html_count < 500 and html is None:
@@ -114,7 +122,7 @@ def get_ftp_contents(ftp_url):
 
 def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
     for file_type, items in desired_ftp_files.items():
-        ext = items['ext']
+        ext = items["ext"]
         ftp_filename = f"{refseq}.{ext}"
         target_filename = os.path.join(org_dir, f"{refseq}.{ext}")
         if ftp_filename in ftp_contents:
@@ -133,8 +141,8 @@ def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
                 return
 
             # do special processing for each file type:
-            if items['parser'] is not None:
-                globals()[items['parser']](target_filename, org_num, refseq)
+            if items["parser"] is not None:
+                globals()[items["parser"]](target_filename, org_num, refseq)
         else:
             print("FTP filetype:", file_type, "not found for", org_num, refseq)
     # FTP Files have been Loaded
@@ -142,7 +150,7 @@ def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
 
 def process_FASTA(filename, org_num, refseq):
     fasta = []
-    fasta = [line.strip() for line in open(filename, 'rb').readlines()]
+    fasta = [line.strip() for line in open(filename, "rb").readlines()]
     fasta_header = fasta.pop(0)[1:]
     fasta_header_split = fasta_header.split("|")
     chr_name = fasta_header_split.pop(-1).strip()
@@ -150,14 +158,14 @@ def process_FASTA(filename, org_num, refseq):
     fasta = "".join(fasta)
 
     # Create Chrom Info File:
-    chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), 'wb+')
+    chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), "wb+")
     chrom_info_file.write(f"chromosome={refseq}\nname={chr_name}\nlength={len(fasta)}\norganism={org_num}\n")
     try:
-        chrom_info_file.write("gi=%s\n" % accesions['gi'])
+        chrom_info_file.write("gi=%s\n" % accesions["gi"])
     except Exception:
         chrom_info_file.write("gi=None\n")
     try:
-        chrom_info_file.write("gb=%s\n" % accesions['gb'])
+        chrom_info_file.write("gb=%s\n" % accesions["gb"])
     except Exception:
         chrom_info_file.write("gb=None\n")
     try:
@@ -169,10 +177,10 @@ def process_FASTA(filename, org_num, refseq):
 
 def process_Genbank(filename, org_num, refseq):
     # extracts 'CDS', 'tRNA', 'rRNA' features from genbank file
-    features = get_bed_from_genbank(filename, refseq, ['CDS', 'tRNA', 'rRNA'])
+    features = get_bed_from_genbank(filename, refseq, ["CDS", "tRNA", "rRNA"])
     for feature, values in features.items():
-        feature_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.{feature}.bed"), 'wb+')
-        feature_file.write('\n'.join(values))
+        feature_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.{feature}.bed"), "wb+")
+        feature_file.write("\n".join(values))
         feature_file.close()
     print("Genbank extraction finished for chrom:", refseq, "file:", filename)
 
@@ -183,8 +191,8 @@ def process_Glimmer3(filename, org_num, refseq):
     except Exception as e:
         print("Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e)
         glimmer3_bed = []
-    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.Glimmer3.bed" % refseq), 'wb+')
-    glimmer3_bed_file.write('\n'.join(glimmer3_bed))
+    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.Glimmer3.bed" % refseq), "wb+")
+    glimmer3_bed_file.write("\n".join(glimmer3_bed))
     glimmer3_bed_file.close()
 
 
@@ -194,8 +202,8 @@ def process_GeneMarkHMM(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMarkHMM_bed = []
-    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMarkHMM.bed" % refseq), 'wb+')
-    geneMarkHMM_bed_bed_file.write('\n'.join(geneMarkHMM_bed))
+    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMarkHMM.bed" % refseq), "wb+")
+    geneMarkHMM_bed_bed_file.write("\n".join(geneMarkHMM_bed))
     geneMarkHMM_bed_bed_file.close()
 
 
@@ -205,8 +213,8 @@ def process_GeneMark(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMark_bed = []
-    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMark.bed" % refseq), 'wb+')
-    geneMark_bed_bed_file.write('\n'.join(geneMark_bed))
+    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMark.bed" % refseq), "wb+")
+    geneMark_bed_bed_file.write("\n".join(geneMark_bed))
     geneMark_bed_bed_file.close()
 
 
@@ -246,7 +254,7 @@ def __main__():
                 print("Org:", org_num, "chrom:", refseq, "[", time.time() - start_time, "seconds elapsed. ]")
 
         # Create org info file
-        info_file = open(os.path.join(org_dir, "%s.info" % org_num), 'wb+')
+        info_file = open(os.path.join(org_dir, "%s.info" % org_num), "wb+")
         info_file.write("genome project id=%s\n" % org_num)
         info_file.write("name=%s\n" % name)
         info_file.write("kingdom=%s\n" % kingdom)
diff --git a/scripts/microbes/ncbi_to_ucsc.py b/scripts/microbes/ncbi_to_ucsc.py
index 148be9950b9..8723b313aaa 100644
--- a/scripts/microbes/ncbi_to_ucsc.py
+++ b/scripts/microbes/ncbi_to_ucsc.py
@@ -30,15 +30,15 @@ def __main__():
                 for line in info:
                     fields = line.replace("\n", "").split("=")
                     tmp_dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in tmp_dict.keys():
-                    if tmp_dict['genome project id'] not in organisms.keys():
-                        organisms[tmp_dict['genome project id']] = {'chrs': {}, 'base_dir': this_base_dir}
+                if "genome project id" in tmp_dict.keys():
+                    if tmp_dict["genome project id"] not in organisms.keys():
+                        organisms[tmp_dict["genome project id"]] = {"chrs": {}, "base_dir": this_base_dir}
                     for key in tmp_dict.keys():
-                        organisms[tmp_dict['genome project id']][key] = tmp_dict[key]
+                        organisms[tmp_dict["genome project id"]][key] = tmp_dict[key]
                 else:
-                    if tmp_dict['organism'] not in organisms.keys():
-                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
+                    if tmp_dict["organism"] not in organisms.keys():
+                        organisms[tmp_dict["organism"]] = {"chrs": {}, "base_dir": this_base_dir}
+                    organisms[tmp_dict["organism"]]["chrs"][tmp_dict["chromosome"]] = tmp_dict
 
     # get UCSC data
 
@@ -62,9 +62,16 @@ def __main__():
     builds = {}
 
     for dsn in tree:
-        build = dsn.find("SOURCE").attrib['id']
+        build = dsn.find("SOURCE").attrib["id"]
         try:
-            org_page = urlopen("http://archaea.ucsc.edu/cgi-bin/hgGateway?db=" + build).read().replace("\n", "").split("<table border=2 cellspacing=2 cellpadding=2>")[1].split("</table>")[0].split("</tr>")
+            org_page = (
+                urlopen("http://archaea.ucsc.edu/cgi-bin/hgGateway?db=" + build)
+                .read()
+                .replace("\n", "")
+                .split("<table border=2 cellspacing=2 cellpadding=2>")[1]
+                .split("</table>")[0]
+                .split("</tr>")
+            )
         except Exception:
             print("NO CHROMS FOR", build)
             continue
@@ -76,36 +83,39 @@ def __main__():
             chr = row.split("</a>")[0].split(">")[-1]
             refseq = row.split("</a>")[-2].split(">")[-1]
             for org in organisms:
-                for org_chr in organisms[org]['chrs']:
-                    if organisms[org]['chrs'][org_chr]['chromosome'] == refseq:
+                for org_chr in organisms[org]["chrs"]:
+                    if organisms[org]["chrs"][org_chr]["chromosome"] == refseq:
                         if org not in builds:
-                            builds[org] = {'chrs': {}, 'build': build}
-                        builds[org]['chrs'][refseq] = chr
+                            builds[org] = {"chrs": {}, "build": build}
+                        builds[org]["chrs"][refseq] = chr
 
     print()
-    ext_to_edit = ['bed', 'info', ]
+    ext_to_edit = [
+        "bed",
+        "info",
+    ]
     for org in builds:
-        print(org, "changed to", builds[org]['build'])
+        print(org, "changed to", builds[org]["build"])
 
         # org info file
         info_file_old = os.path.join(base_dir + org, org + ".info")
-        info_file_new = os.path.join(base_dir + org, builds[org]['build'] + ".info")
+        info_file_new = os.path.join(base_dir + org, builds[org]["build"] + ".info")
 
         old_dir = base_dir + org
-        new_dir = base_dir + builds[org]['build']
+        new_dir = base_dir + builds[org]["build"]
 
         # open and edit org info file
         info_file_contents = open(info_file_old).read()
-        info_file_contents = info_file_contents + "build=" + builds[org]['build'] + "\n"
-        for chrom in builds[org]['chrs']:
-            info_file_contents = info_file_contents.replace(chrom, builds[org]['chrs'][chrom])
+        info_file_contents = info_file_contents + "build=" + builds[org]["build"] + "\n"
+        for chrom in builds[org]["chrs"]:
+            info_file_contents = info_file_contents.replace(chrom, builds[org]["chrs"][chrom])
             for result in os.walk(base_dir + org):
                 this_base_dir, sub_dirs, files = result
                 for file in files:
-                    if file[0:len(chrom)] == chrom:
+                    if file[0 : len(chrom)] == chrom:
                         # rename file
                         old_name = os.path.join(this_base_dir, file)
-                        new_name = os.path.join(this_base_dir, builds[org]['chrs'][chrom] + file[len(chrom):])
+                        new_name = os.path.join(this_base_dir, builds[org]["chrs"][chrom] + file[len(chrom) :])
                         move(old_name, new_name)
 
                         # edit contents of file, skiping those in list
@@ -113,20 +123,22 @@ def __main__():
                             continue
 
                         file_contents = open(new_name).read()
-                        file_contents = file_contents.replace(chrom, builds[org]['chrs'][chrom])
+                        file_contents = file_contents.replace(chrom, builds[org]["chrs"][chrom])
 
                         # special case fixes...
                         if file[-5:] == ".info":
-                            file_contents = file_contents.replace("organism=" + org, "organism=" + builds[org]['build'])
-                            file_contents = file_contents.replace("refseq=" + builds[org]['chrs'][chrom], "refseq=" + chrom)
+                            file_contents = file_contents.replace("organism=" + org, "organism=" + builds[org]["build"])
+                            file_contents = file_contents.replace(
+                                "refseq=" + builds[org]["chrs"][chrom], "refseq=" + chrom
+                            )
 
                         # write out new file
-                        file_out = open(new_name, 'w')
+                        file_out = open(new_name, "w")
                         file_out.write(file_contents)
                         file_out.close()
 
         # write out org info file and remove old file
-        org_info_out = open(info_file_new, 'w')
+        org_info_out = open(info_file_new, "w")
         org_info_out.write(info_file_contents)
         org_info_out.close()
         os.unlink(info_file_old)
diff --git a/scripts/microbes/util.py b/scripts/microbes/util.py
index 3a3715046c8..78aad82fa64 100644
--- a/scripts/microbes/util.py
+++ b/scripts/microbes/util.py
@@ -12,21 +12,21 @@ class Region:
         self.qualifiers = {}
         self.start = None
         self.end = None
-        self.strand = '+'
+        self.strand = "+"
 
     def set_coordinates_by_location(self, location):
-        location = location.strip().lower().replace('..', ',')
+        location = location.strip().lower().replace("..", ",")
         if "complement(" in location:  # if part of the sequence is on the negative strand, it all is?
-            self.strand = '-'  # default of + strand
+            self.strand = "-"  # default of + strand
         for remove_text in ["join(", "order(", "complement(", ")"]:
             location = location.replace(remove_text, "")
-        for number in location.split(','):
-            number = number.strip('\n\r\t <>,()')
+        for number in location.split(","):
+            number = number.strip("\n\r\t <>,()")
             if number:
                 if "^" in number:
                     # a single point
                     # check that this is correct for points, ie: 413/NC_005027.gbk:     misc_feature    6636286^6636287  ===> 6636285,6636286
-                    end = int(number.split('^')[0])
+                    end = int(number.split("^")[0])
                     start = end - 1
                 else:
                     end = int(number)
@@ -39,6 +39,7 @@ class Region:
 
 class GenBankFeatureParser:
     """Parses Features from Single Locus GenBank file"""
+
     def __init__(self, fh):
         self.fh = fh
         self.features = {}
@@ -48,7 +49,7 @@ class GenBankFeatureParser:
         base_indent = 0
         last_attr_name = None
         for line in fh:
-            if not in_features and line.startswith('FEATURES'):
+            if not in_features and line.startswith("FEATURES"):
                 in_features = True
                 continue
             if in_features:
@@ -71,8 +72,8 @@ class GenBankFeatureParser:
                 else:
                     # add info to last known feature
                     line = line.strip()
-                    if line.startswith('/'):
-                        fields = line[1:].split('=', 1)
+                    if line.startswith("/"):
+                        fields = line[1:].split("=", 1)
                         if len(fields) == 2:
                             last_attr_name, content = fields
                         else:
@@ -88,10 +89,14 @@ class GenBankFeatureParser:
                         self.features[last_feature_name][-1].set_coordinates_by_location(line)
                     else:
                         # continuation of multi-line qualifier content
-                        if last_feature_name.lower() in ['translation']:
-                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{}{}".format(self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
+                        if last_feature_name.lower() in ["translation"]:
+                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{}{}".format(
+                                self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"')
+                            )
                         else:
-                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{} {}".format(self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
+                            self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{} {}".format(
+                                self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"')
+                            )
 
     def get_features_by_type(self, feature_type):
         if feature_type not in self.features:
@@ -108,7 +113,7 @@ def get_bed_from_genbank(gb_file, chrom, feature_list):
         features[feature_type] = []
         for feature in genbank_parser.get_features_by_type(feature_type):
             name = ""
-            for name_tag in ['gene', 'locus_tag', 'db_xref']:
+            for name_tag in ["gene", "locus_tag", "db_xref"]:
                 if name_tag in feature.qualifiers:
                     if name:
                         name = name + ";"
@@ -116,7 +121,9 @@ def get_bed_from_genbank(gb_file, chrom, feature_list):
             if not name:
                 name = "unknown"
 
-            features[feature_type].append(f"{chrom}\t{feature.start}\t{feature.end}\t{name}\t{0}\t{feature.strand}")  # append new bed field here
+            features[feature_type].append(
+                f"{chrom}\t{feature.start}\t{feature.end}\t{name}\t{0}\t{feature.strand}"
+            )  # append new bed field here
     return features
 
 
@@ -136,7 +143,14 @@ def get_bed_from_GeneMark(geneMark_filename, chr):
     for block in orfs.split("\n\n"):
         if block.startswith("List of Regions of interest"):
             break
-        best_block = {'start': 0, 'end': 0, 'strand': '+', 'avg_prob': -sys.maxsize, 'start_prob': -sys.maxsize, 'name': 'DNE'}
+        best_block = {
+            "start": 0,
+            "end": 0,
+            "strand": "+",
+            "avg_prob": -sys.maxsize,
+            "start_prob": -sys.maxsize,
+            "name": "DNE",
+        }
         ctr += 1
         ctr2 = 0
         for line in block.split("\n"):
@@ -145,7 +159,7 @@ def get_bed_from_GeneMark(geneMark_filename, chr):
             start = int(fields.pop(0)) - 1
             end = int(fields.pop(0))
             strand = fields.pop(0)
-            if strand == 'complement':
+            if strand == "complement":
                 strand = "-"
             else:
                 strand = "+"
@@ -157,9 +171,28 @@ def get_bed_from_GeneMark(geneMark_filename, chr):
             except Exception:
                 start_prob = 0
             name = "orf_" + str(ctr) + "_" + str(ctr2)
-            if avg_prob >= best_block['avg_prob'] and start_prob > best_block['start_prob']:
-                best_block = {'start': start, 'end': end, 'strand': strand, 'avg_prob': avg_prob, 'start_prob': start_prob, 'name': name}
-        regions.append(chr + "\t" + str(best_block['start']) + "\t" + str(best_block['end']) + "\t" + best_block['name'] + "\t" + str(int(best_block['avg_prob'] * 1000)) + "\t" + best_block['strand'])
+            if avg_prob >= best_block["avg_prob"] and start_prob > best_block["start_prob"]:
+                best_block = {
+                    "start": start,
+                    "end": end,
+                    "strand": strand,
+                    "avg_prob": avg_prob,
+                    "start_prob": start_prob,
+                    "name": name,
+                }
+        regions.append(
+            chr
+            + "\t"
+            + str(best_block["start"])
+            + "\t"
+            + str(best_block["end"])
+            + "\t"
+            + best_block["name"]
+            + "\t"
+            + str(int(best_block["avg_prob"] * 1000))
+            + "\t"
+            + best_block["strand"]
+        )
     return regions
 
 
@@ -214,7 +247,7 @@ def get_bed_from_glimmer3(glimmer3_filename, chr):
         else:
             strand = "+"
         start = start - 1
-        score = (float(fields.pop(0)))
+        score = float(fields.pop(0))
         if score > max_score:
             max_score = score
         if score < min_score:
diff --git a/scripts/nosetests.py b/scripts/nosetests.py
index 49b0b0a2780..4f65208a02e 100755
--- a/scripts/nosetests.py
+++ b/scripts/nosetests.py
@@ -7,5 +7,5 @@ from pkg_resources import load_entry_point
 
 assert sys.version_info[:2] >= (2, 7)
 
-nose_core_TestProgram = load_entry_point('nose', 'console_scripts', 'nosetests')
+nose_core_TestProgram = load_entry_point("nose", "console_scripts", "nosetests")
 nose_core_TestProgram()
diff --git a/scripts/objectstore/copy_files_to_irods.py b/scripts/objectstore/copy_files_to_irods.py
index 1d88faf4c1f..d0240a6d567 100644
--- a/scripts/objectstore/copy_files_to_irods.py
+++ b/scripts/objectstore/copy_files_to_irods.py
@@ -7,8 +7,11 @@ import uuid
 from datetime import datetime
 
 import irods.keywords as kw
-from irods.exception import (CollectionDoesNotExist, DataObjectDoesNotExist,
-                             NetworkException)
+from irods.exception import (
+    CollectionDoesNotExist,
+    DataObjectDoesNotExist,
+    NetworkException,
+)
 from irods.session import iRODSSession
 from psycopg2 import connect
 
@@ -48,7 +51,9 @@ last_accessed_sql_statement = """SELECT iq.dataset_id, MAX(iq.create_time) AS ma
                                  """
 
 
-def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file, irods_info_file, db_connection_info_file, copy_or_checksum):
+def copy_files_to_irods(
+    start_dataset_id, end_dataset_id, object_store_info_file, irods_info_file, db_connection_info_file, copy_or_checksum
+):
     conn = None
     session = None
     osi_keys = None
@@ -97,7 +102,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
             dbname=db_connection_info["dbname"],
             user=db_connection_info["user"],
             host=db_connection_info["host"],
-            password=db_connection_info["password"]
+            password=db_connection_info["password"],
         )
         conn.cursor()
 
@@ -105,7 +110,13 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
         print(e)
         return
 
-    session = iRODSSession(host=irods_info["host"], port=irods_info["port"], user=irods_info["user"], password=irods_info["password"], zone=irods_info["zone"])
+    session = iRODSSession(
+        host=irods_info["host"],
+        port=irods_info["port"],
+        user=irods_info["user"],
+        password=irods_info["password"],
+        zone=irods_info["zone"],
+    )
     session.connection_timeout = int(irods_info["timeout"])
 
     osi_keys = tuple(object_store_info.keys())
@@ -124,7 +135,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
 
     try:
         read_cursor = conn.cursor()
-        args = ('ok', start_dataset_id, end_dataset_id, osi_keys)
+        args = ("ok", start_dataset_id, end_dataset_id, osi_keys)
         read_cursor.execute(read_sql_statement, args)
         rows = read_cursor.fetchall()
         for row in rows:
@@ -144,16 +155,20 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
             irods_sub_folder = os.path.join(*directory_hash_id(uuid_with_dash))
             disk_file_path = os.path.join(object_store_path, disk_sub_folder, "dataset_" + str(objectid) + ".dat")
             disk_folder_path = os.path.join(object_store_path, disk_sub_folder, "dataset_" + str(objectid) + "_files")
-            irods_file_path = os.path.join(irods_info["home"], irods_sub_folder, "dataset_" + str(uuid_with_dash) + ".dat")
+            irods_file_path = os.path.join(
+                irods_info["home"], irods_sub_folder, "dataset_" + str(uuid_with_dash) + ".dat"
+            )
             irods_file_collection_path = os.path.join(irods_info["home"], irods_sub_folder)
-            irods_folder_collection_path = os.path.join(irods_file_collection_path, "dataset_" + str(uuid_with_dash) + "_files")
+            irods_folder_collection_path = os.path.join(
+                irods_file_collection_path, "dataset_" + str(uuid_with_dash) + "_files"
+            )
 
             if copy_or_checksum == "copy":
                 # Create the collection
                 session.collections.create(irods_file_collection_path)
 
                 # Add disk file to collection
-                options = {kw.REG_CHKSUM_KW: '', kw.RESC_NAME_KW: irods_resc}
+                options = {kw.REG_CHKSUM_KW: "", kw.RESC_NAME_KW: irods_resc}
                 session.data_objects.put(disk_file_path, irods_file_path, **options)
                 print(f"Copied disk file {disk_file_path} to irods {irods_file_path}")
 
@@ -163,7 +178,14 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                     # Create the collection
                     session.collections.create(irods_folder_collection_path)
 
-                    iput_command = "iput -R " + irods_resc + " -rk " + disk_folder_path_all_files + " " + irods_folder_collection_path
+                    iput_command = (
+                        "iput -R "
+                        + irods_resc
+                        + " -rk "
+                        + disk_folder_path_all_files
+                        + " "
+                        + irods_folder_collection_path
+                    )
                     subprocess.call(iput_command, shell=True)
                     print(f"Copied disk folder {disk_folder_path} to irods {irods_folder_collection_path}")
 
@@ -177,7 +199,9 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                     # obj.checksum is prepended with 'sha2:'. Remove that so we can compare it to disk file checksum
                     irods_file_checksum = obj.checksum[5:]
                     if irods_file_checksum != disk_file_checksum:
-                        print(f"Error: irods file checksum {irods_file_checksum} does not match disk file checksum {disk_file_checksum} for irods file {irods_file_path} and disk file {disk_file_path}")
+                        print(
+                            f"Error: irods file checksum {irods_file_checksum} does not match disk file checksum {disk_file_checksum} for irods file {irods_file_path} and disk file {disk_file_path}"
+                        )
                         continue
                 except (DataObjectDoesNotExist, CollectionDoesNotExist) as e:
                     print(e)
@@ -207,7 +231,9 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                                 # obj.checksum is prepended with 'sha2:'. Remove that so we can compare it to disk file checksum
                                 an_irods_file_checksum = obj.checksum[5:]
                                 if an_irods_file_checksum != a_disk_file_checksum:
-                                    print(f"Error: irods file checksum {an_irods_file_checksum} does not match disk file checksum {a_disk_file_checksum} for irods file {an_irods_file_path} and disk file {a_disk_file_path}")
+                                    print(
+                                        f"Error: irods file checksum {an_irods_file_checksum} does not match disk file checksum {a_disk_file_checksum} for irods file {an_irods_file_path} and disk file {a_disk_file_path}"
+                                    )
                                     continue
                             except (DataObjectDoesNotExist, CollectionDoesNotExist) as e:
                                 print(e)
@@ -225,9 +251,17 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                 update_cursor.execute(update_sql_statement, (irods_info["object_store_id"], objectid))
                 updated_rows = update_cursor.rowcount
                 if updated_rows == 1:
-                    print("Updated object store ID to {} in dataset table for object ID {}".format(irods_info["object_store_id"], objectid))
+                    print(
+                        "Updated object store ID to {} in dataset table for object ID {}".format(
+                            irods_info["object_store_id"], objectid
+                        )
+                    )
                 else:
-                    print("Error: Failed to update object store ID to {} in dataset table for object ID {}".format(irods_info["object_store_id"], objectid))
+                    print(
+                        "Error: Failed to update object store ID to {} in dataset table for object ID {}".format(
+                            irods_info["object_store_id"], objectid
+                        )
+                    )
                 update_cursor.close()
 
                 # Delete file on disk
@@ -257,16 +291,20 @@ def get_irods_resource(conn, objectid, object_store_id, irods_info):
         irods_tape_resc_cuttoff_dt = datetime.strptime(irods_tape_resc_cuttoff, "%m/%d/%Y")
 
         read_cursor = conn.cursor()
-        args = ('ok', objectid, objectid, (object_store_id, ), 'ok', objectid, objectid, (object_store_id, ))
+        args = ("ok", objectid, objectid, (object_store_id,), "ok", objectid, objectid, (object_store_id,))
         read_cursor.execute(last_accessed_sql_statement, args)
         row = read_cursor.fetchone()
         if row is None:
-            print(f"Could not find the last access time for dataset with id {objectid}. Returning the default resc {irods_resc}.")
+            print(
+                f"Could not find the last access time for dataset with id {objectid}. Returning the default resc {irods_resc}."
+            )
             return irods_resc
 
         dataset_id = row[0]
         if int(dataset_id) != objectid:
-            print(f"The returned dataset id {dataset_id} does not match the passed in datsetid {objectid}. Returning the default resc {irods_resc}.")
+            print(
+                f"The returned dataset id {dataset_id} does not match the passed in datsetid {objectid}. Returning the default resc {irods_resc}."
+            )
             return irods_resc
 
         max_create_time = row[1]
@@ -274,10 +312,14 @@ def get_irods_resource(conn, objectid, object_store_id, irods_info):
         max_create_time_dt = max_create_time.replace(tzinfo=None)
         # If the last time a dataset was accessed was prior to a cuttoff date, use the tape resource. Otherwise, use the regular (non-tape) resource
         if max_create_time_dt < irods_tape_resc_cuttoff_dt:
-            print(f"The last time dataset with id {objectid} was accessed {max_create_time_dt} is prior to tape resource cuttoff {irods_tape_resc_cuttoff_dt}. Using tape resource in irods.")
+            print(
+                f"The last time dataset with id {objectid} was accessed {max_create_time_dt} is prior to tape resource cuttoff {irods_tape_resc_cuttoff_dt}. Using tape resource in irods."
+            )
             return irods_tape_resc
 
-        print(f"The last time dataset with id {objectid} was accessed {max_create_time_dt} is after the tape resource cuttoff {irods_tape_resc_cuttoff_dt}. Using regular (non-tape) resource in irods.")
+        print(
+            f"The last time dataset with id {objectid} was accessed {max_create_time_dt} is after the tape resource cuttoff {irods_tape_resc_cuttoff_dt}. Using regular (non-tape) resource in irods."
+        )
         return irods_resc
 
     except Exception as e:
@@ -291,7 +333,7 @@ def get_file_checksum(disk_file_path):
     disk_file_checksum = subprocess.check_output(checksum_cmd, shell=True)
     # remove '\n' from the end of disk_file_checksum
     disk_file_checksum_len = len(disk_file_checksum)
-    disk_file_checksum_trimmed = disk_file_checksum[0:(disk_file_checksum_len - 1)]
+    disk_file_checksum_trimmed = disk_file_checksum[0 : (disk_file_checksum_len - 1)]
     # Return Unicode string
     return disk_file_checksum_trimmed.decode("utf-8")
 
@@ -336,15 +378,15 @@ def print_help_msg():
     print(help_msg)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
 
-    parser.add_argument('-s', '--start_dataset_id', type=int, required=True)
-    parser.add_argument('-e', '--end_dataset_id', type=int, required=True)
-    parser.add_argument('-o', '--object_store_info_file', type=str, required=True)
-    parser.add_argument('-i', '--irods_info_file', type=str, required=True)
-    parser.add_argument('-d', '--db_connection_info_file', type=str, required=True)
-    parser.add_argument('-c', '--copy_or_checksum', type=str, required=True, choices=['copy', 'checksum'])
+    parser.add_argument("-s", "--start_dataset_id", type=int, required=True)
+    parser.add_argument("-e", "--end_dataset_id", type=int, required=True)
+    parser.add_argument("-o", "--object_store_info_file", type=str, required=True)
+    parser.add_argument("-i", "--irods_info_file", type=str, required=True)
+    parser.add_argument("-d", "--db_connection_info_file", type=str, required=True)
+    parser.add_argument("-c", "--copy_or_checksum", type=str, required=True, choices=["copy", "checksum"])
 
     args = parser.parse_args()
     print(args)
@@ -356,4 +398,11 @@ if __name__ == '__main__':
     db_connection_info_file = args.db_connection_info_file
     copy_or_checksum = args.copy_or_checksum
 
-    copy_files_to_irods(start_dataset_id=start_dataset_id, end_dataset_id=end_dataset_id, object_store_info_file=object_store_info_file, irods_info_file=irods_info_file, db_connection_info_file=db_connection_info_file, copy_or_checksum=copy_or_checksum)
+    copy_files_to_irods(
+        start_dataset_id=start_dataset_id,
+        end_dataset_id=end_dataset_id,
+        object_store_info_file=object_store_info_file,
+        irods_info_file=irods_info_file,
+        db_connection_info_file=db_connection_info_file,
+        copy_or_checksum=copy_or_checksum,
+    )
diff --git a/scripts/pages_identifier_conversion.py b/scripts/pages_identifier_conversion.py
index b9cec401071..256df5d3cd5 100644
--- a/scripts/pages_identifier_conversion.py
+++ b/scripts/pages_identifier_conversion.py
@@ -4,23 +4,29 @@ import logging
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy
 import galaxy.app
 import galaxy.config
-from galaxy.managers.pages import PageContentProcessor, placeholderRenderForSave
+from galaxy.managers.pages import (
+    PageContentProcessor,
+    placeholderRenderForSave,
+)
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 
 def main(argv):
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('-k', '--secret-key', help='Key to convert pages with', default='')
-    parser.add_argument('-d', '--dry-run', help='No changes, just test it.', action='store_true')
+    parser.add_argument("-k", "--secret-key", help="Key to convert pages with", default="")
+    parser.add_argument("-d", "--dry-run", help="No changes, just test it.", action="store_true")
     populate_config_args(parser)
     args = parser.parse_args()
     properties = app_properties_from_args(args)
@@ -29,7 +35,9 @@ def main(argv):
     security_helper = IdEncodingHelper(id_secret=secret)
     object_store = build_object_store_from_config(config)
     if not config.database_connection:
-        print("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
+        print(
+            "The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml"
+        )
 
     model = galaxy.config.init_models_from_config(config, object_store=object_store)
     session = model.context.current
@@ -39,19 +47,21 @@ def main(argv):
         try:
             processor = PageContentProcessor(mock_trans, placeholderRenderForSave)
             processor.feed(p.content)
-            newcontent = unicodify(processor.output(), 'utf-8')
+            newcontent = unicodify(processor.output(), "utf-8")
             if p.content != newcontent:
                 if not args.dry_run:
-                    p.content = unicodify(processor.output(), 'utf-8')
+                    p.content = unicodify(processor.output(), "utf-8")
                     session.add(p)
                     session.flush()
                 else:
                     print("Modifying revision %s." % p.id)
                     print(difflib.unified_diff(p.content, newcontent))
         except Exception:
-            logging.exception("Error parsing page, rolling changes back and skipping revision %s.  Please report this error." % p.id)
+            logging.exception(
+                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error." % p.id
+            )
             session.rollback()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main(sys.argv)
diff --git a/scripts/paster.py b/scripts/paster.py
index 12fe39da16f..1734fcab583 100755
--- a/scripts/paster.py
+++ b/scripts/paster.py
@@ -8,10 +8,11 @@ top level directly.
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
+
+from check_python import check_python  # noqa: I100, I201
 
 from galaxy.util.pastescript import serve
-from check_python import check_python  # noqa: I100, I201
 
 # ensure supported version
 try:
diff --git a/scripts/plugin_staging.py b/scripts/plugin_staging.py
index 57623bf1648..3d0703ea4c6 100644
--- a/scripts/plugin_staging.py
+++ b/scripts/plugin_staging.py
@@ -6,8 +6,8 @@ GXY_ROOT = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file_
 
 
 def stage_static(f):
-    src = os.path.join(GXY_ROOT, 'config/plugins', f)
-    dest = os.path.join(GXY_ROOT, 'static/plugins', f)
+    src = os.path.join(GXY_ROOT, "config/plugins", f)
+    dest = os.path.join(GXY_ROOT, "static/plugins", f)
     dest_parent = os.path.abspath(os.path.join(dest, os.pardir))
     if os.path.lexists(dest):
         # We have to clear out the old staged or linked static to relink.
@@ -29,6 +29,8 @@ def stage_static(f):
 
 if __name__ == "__main__":
     # This is not awesome, but it's temporary, and it supports two-tier plugin static.
-    for f in glob.glob(os.path.join(GXY_ROOT, 'config/plugins/*/*/static')) + glob.glob(os.path.join(GXY_ROOT, 'config/plugins/*/*/*/static')):
-        f = os.path.relpath(f, os.path.join(GXY_ROOT, 'config/plugins'))
+    for f in glob.glob(os.path.join(GXY_ROOT, "config/plugins/*/*/static")) + glob.glob(
+        os.path.join(GXY_ROOT, "config/plugins/*/*/*/static")
+    ):
+        f = os.path.relpath(f, os.path.join(GXY_ROOT, "config/plugins"))
         stage_static(f)
diff --git a/scripts/release-diff.py b/scripts/release-diff.py
index 240faa90dc7..2d545562a6b 100644
--- a/scripts/release-diff.py
+++ b/scripts/release-diff.py
@@ -45,8 +45,8 @@ def diff_files(old, new):
     new_k = set(new_kv.keys())
 
     added = []
-    for item in (new_k - old_k):
-        parent = '.'.join(item.split('.')[0:-1])
+    for item in new_k - old_k:
+        parent = ".".join(item.split(".")[0:-1])
         if parent in new_k and parent not in old_k:
             added.append(item)
         else:
@@ -54,8 +54,8 @@ def diff_files(old, new):
     added = set(added)
 
     removed = []
-    for item in (old_k - new_k):
-        parent = '.'.join(item.split('.')[0:-1])
+    for item in old_k - new_k:
+        parent = ".".join(item.split(".")[0:-1])
         if parent in old_k and parent not in new_k:
             removed.append(item)
         else:
@@ -85,7 +85,7 @@ def _report_dict(title, subheading, data, mapper):
 
 
 def _indent(s, by=4):
-    whitespace = ' ' * by
+    whitespace = " " * by
     s = s if isinstance(s, list) else s.splitlines()
     return "\n".join((f"{whitespace}{line}" for line in s))
 
@@ -98,27 +98,19 @@ def report_diff(added, changed, removed, new_files):
         print()
 
     if added:
-        _report_dict(
-            "Added",
-            "The following configuration options are new",
-            added,
-            lambda x: f"-  {x}"
-        )
+        _report_dict("Added", "The following configuration options are new", added, lambda x: f"-  {x}")
 
     if changed:
         _report_dict(
             "Changed",
             "The following configuration options have been changed",
             changed,
-            lambda x: f"-  {x[0]} has changed from\n\n   ::\n\n{_indent(x[1])}\n\n   to\n\n   ::\n\n{_indent(x[2])}\n\n"
+            lambda x: f"-  {x[0]} has changed from\n\n   ::\n\n{_indent(x[1])}\n\n   to\n\n   ::\n\n{_indent(x[2])}\n\n",
         )
 
     if removed:
         _report_dict(
-            "Removed",
-            "The following configuration options have been completely removed",
-            removed,
-            lambda x: f"-  {x}"
+            "Removed", "The following configuration options have been completely removed", removed, lambda x: f"-  {x}"
         )
 
     if new_files:
@@ -133,9 +125,7 @@ def report_diff(added, changed, removed, new_files):
 
 def load_at_time(path, revision=None):
     if revision is not None:
-        return subprocess.check_output(
-            ["git", "show", f"{revision}:{path}"], stderr=subprocess.STDOUT
-        )
+        return subprocess.check_output(["git", "show", f"{revision}:{path}"], stderr=subprocess.STDOUT)
     else:
         with open(path) as handle:
             return handle.read()
@@ -156,19 +146,15 @@ def main(old_revision, new_revision=None):
 
     for file in files_to_diff:
         filename = file
-        if 'config_schema.yml' in file:
-            filename = 'config/galaxy.yml.sample:galaxy'
-        elif 'uwsgi_schema.yml' in file:
-            filename = 'config/galaxy.yml.sample:uwsgi'
+        if "config_schema.yml" in file:
+            filename = "config/galaxy.yml.sample:galaxy"
+        elif "uwsgi_schema.yml" in file:
+            filename = "config/galaxy.yml.sample:uwsgi"
 
         real_path = Path(file).resolve().relative_to(Path.cwd())
         try:
-            old_contents = yaml.load(
-                load_at_time(real_path, old_revision), Loader=MockOrderedLoader
-            )
-            new_contents = yaml.load(
-                load_at_time(real_path, new_revision), Loader=MockOrderedLoader
-            )
+            old_contents = yaml.load(load_at_time(real_path, old_revision), Loader=MockOrderedLoader)
+            new_contents = yaml.load(load_at_time(real_path, new_revision), Loader=MockOrderedLoader)
 
             (a, r, c) = diff_files(old_contents, new_contents)
             if a:
@@ -187,9 +173,7 @@ def main(old_revision, new_revision=None):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Diff yaml configuration files between two points in time."
-    )
+    parser = argparse.ArgumentParser(description="Diff yaml configuration files between two points in time.")
     parser.add_argument("old_revision", help="Old revision")
     parser.add_argument(
         "--new_revision",
diff --git a/scripts/resumable_upload.py b/scripts/resumable_upload.py
index eb2bc8e3377..8ffd694c592 100644
--- a/scripts/resumable_upload.py
+++ b/scripts/resumable_upload.py
@@ -6,30 +6,29 @@ import requests
 from tusclient import client
 from tusclient.storage import filestorage
 
-
-UPLOAD_ENDPOINT = '/api/upload/resumable_upload'
-SUBMISSION_ENDPOINT = '/api/tools/fetch'
-CHUNK_SIZE = 10 ** 7
+UPLOAD_ENDPOINT = "/api/upload/resumable_upload"
+SUBMISSION_ENDPOINT = "/api/tools/fetch"
+CHUNK_SIZE = 10**7
 
 
 @click.command()
-@click.option("--url", default='http://localhost:8080', help="URL of Galaxy instance")
+@click.option("--url", default="http://localhost:8080", help="URL of Galaxy instance")
 @click.option("--api_key", envvar="GALAXY_API_KEY", required=True, help="API key for Galaxy instance")
-@click.option('--history_id', type=str, required=True, help="Target History ID")
-@click.option('--file_type', default="auto", type=str, help="Galaxy file type to use")
-@click.option('--dbkey', default="?", type=str, help="Genome Build for dataset")
-@click.option('--filename', type=str, help="Filename to use in Galaxy history, if different from path")
-@click.option('--storage', type=click.Path(), required=False, help="Store URLs to resume here")
-@click.argument('path', type=click.Path())
-def upload_file(url, path, api_key, history_id, file_type='auto', dbkey='?', filename=None, storage=None):
-    headers = {'x-api-key': api_key}
+@click.option("--history_id", type=str, required=True, help="Target History ID")
+@click.option("--file_type", default="auto", type=str, help="Galaxy file type to use")
+@click.option("--dbkey", default="?", type=str, help="Genome Build for dataset")
+@click.option("--filename", type=str, help="Filename to use in Galaxy history, if different from path")
+@click.option("--storage", type=click.Path(), required=False, help="Store URLs to resume here")
+@click.argument("path", type=click.Path())
+def upload_file(url, path, api_key, history_id, file_type="auto", dbkey="?", filename=None, storage=None):
+    headers = {"x-api-key": api_key}
     my_client = client.TusClient(f"{url}{UPLOAD_ENDPOINT}", headers=headers)
     filename = filename or os.path.basename(path)
     metadata = {
-        'filename': filename,
-        'history_id': history_id,
-        'file_type': file_type,
-        'dbkey': dbkey,
+        "filename": filename,
+        "history_id": history_id,
+        "file_type": file_type,
+        "dbkey": dbkey,
     }
 
     # Upload a file to a tus server.
@@ -40,26 +39,26 @@ def upload_file(url, path, api_key, history_id, file_type='auto', dbkey='?', fil
     uploader.upload()
 
     # Extract session from created upload URL
-    session_id = uploader.url.rsplit('/', 1)[1]
+    session_id = uploader.url.rsplit("/", 1)[1]
     payload = {
-        'history_id': history_id,
-        'targets': json.dumps([
-            {
-                "destination": {"type": "hdas"},
-                "elements": [
-                    {
-                        "src": "files",
-                        "ext": file_type,
-                        "dbkey": dbkey,
-                        "name": filename
-                    }
-                ]
-            }
-        ]),
+        "history_id": history_id,
+        "targets": json.dumps(
+            [
+                {
+                    "destination": {"type": "hdas"},
+                    "elements": [{"src": "files", "ext": file_type, "dbkey": dbkey, "name": filename}],
+                }
+            ]
+        ),
     }
-    response = requests.post(f"{url}{SUBMISSION_ENDPOINT}", data=payload, files={'files_0|file_data': json.dumps({"session_id": session_id})}, headers=headers)
+    response = requests.post(
+        f"{url}{SUBMISSION_ENDPOINT}",
+        data=payload,
+        files={"files_0|file_data": json.dumps({"session_id": session_id})},
+        headers=headers,
+    )
     response.raise_for_status()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     upload_file()
diff --git a/scripts/rst2html.py b/scripts/rst2html.py
index 3c66a2bd1c7..5e825c5badd 100755
--- a/scripts/rst2html.py
+++ b/scripts/rst2html.py
@@ -12,16 +12,16 @@ A minimal front end to the Docutils Publisher, producing HTML.
 
 try:
     import locale
-    locale.setlocale(locale.LC_ALL, '')
+
+    locale.setlocale(locale.LC_ALL, "")
 except Exception:
     pass
 
 from docutils.core import (
     default_description,
-    publish_cmdline
+    publish_cmdline,
 )
 
-description = ('Generates (X)HTML documents from standalone reStructuredText '
-               'sources.  ' + default_description)
+description = "Generates (X)HTML documents from standalone reStructuredText " "sources.  " + default_description
 
-publish_cmdline(writer_name='html', description=description)
+publish_cmdline(writer_name="html", description=description)
diff --git a/scripts/runtime_stats.py b/scripts/runtime_stats.py
index 4e358d278dd..a746f267adf 100755
--- a/scripts/runtime_stats.py
+++ b/scripts/runtime_stats.py
@@ -40,13 +40,15 @@ import psycopg2
 from sqlalchemy.engine import url
 
 galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
-sys.path.insert(1, os.path.join(galaxy_root, 'lib'))
+sys.path.insert(1, os.path.join(galaxy_root, "lib"))
 
 import galaxy.config
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
-
-DATA_SOURCES = ('metrics', 'history')
+DATA_SOURCES = ("metrics", "history")
 METRICS_SQL = """
     SELECT metric_value
     FROM job_metric_numeric jmn
@@ -74,68 +76,54 @@ HISTORY_SQL = """
 
 
 def parse_arguments():
-    parser = argparse.ArgumentParser(
-        description='Generate walltime statistics')
-    parser.add_argument('tool_id', help='Tool (by ID) to collect stats about')
-    parser.add_argument('--like',
-                        action='store_true',
-                        default=False,
-                        help='Use SQL `LIKE` operator to find '
-                             'a shed-installed tool using the tool\'s '
-                             '"short" id')
+    parser = argparse.ArgumentParser(description="Generate walltime statistics")
+    parser.add_argument("tool_id", help="Tool (by ID) to collect stats about")
+    parser.add_argument(
+        "--like",
+        action="store_true",
+        default=False,
+        help="Use SQL `LIKE` operator to find " "a shed-installed tool using the tool's " '"short" id',
+    )
     populate_config_args(parser)
-    parser.add_argument('-d', '--debug',
-                        action='store_true',
-                        default=False,
-                        help='Print extra info')
-    parser.add_argument('-m', '--min',
-                        type=int,
-                        default=-1,
-                        help='Ignore runtimes less than MIN seconds')
-    parser.add_argument('-M', '--max',
-                        type=int,
-                        default=-1,
-                        help='Ignore runtimes greater than MAX seconds')
-    parser.add_argument('-u', '--user',
-                        help='Return stats for only this user (id, email, '
-                             'or username)')
-    parser.add_argument('-s', '--source',
-                        default='metrics',
-                        help='Runtime data source (SOURCES: %s)'
-                             % ', '.join(DATA_SOURCES))
+    parser.add_argument("-d", "--debug", action="store_true", default=False, help="Print extra info")
+    parser.add_argument("-m", "--min", type=int, default=-1, help="Ignore runtimes less than MIN seconds")
+    parser.add_argument("-M", "--max", type=int, default=-1, help="Ignore runtimes greater than MAX seconds")
+    parser.add_argument("-u", "--user", help="Return stats for only this user (id, email, " "or username)")
+    parser.add_argument(
+        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: %s)" % ", ".join(DATA_SOURCES)
+    )
     args = parser.parse_args()
 
-    if args.like and '/' in args.tool_id:
-        print('ERROR: Do not use --like with a tool shed tool id (the tool '
-              'id should not contain `/` characters)')
+    if args.like and "/" in args.tool_id:
+        print("ERROR: Do not use --like with a tool shed tool id (the tool " "id should not contain `/` characters)")
         sys.exit(2)
 
     args.source = args.source.lower()
-    if args.source not in ('metrics', 'history'):
-        print('ERROR: Data source `%s` unknown, valid source are: %s'
-              % (args.source, ', '.join(DATA_SOURCES)))
+    if args.source not in ("metrics", "history"):
+        print("ERROR: Data source `%s` unknown, valid source are: %s" % (args.source, ", ".join(DATA_SOURCES)))
 
     app_properties = app_properties_from_args(args)
     config = galaxy.config.Configuration(**app_properties)
     uri = args.config.get_database_url(config)
 
-    names = {'database': 'dbname', 'username': 'user'}
+    names = {"database": "dbname", "username": "user"}
     args.connect_args = url.make_url(uri).translate_connect_args(**names)
 
     if args.debug:
-        print('Got options:')
+        print("Got options:")
         for i in vars(args).items():
-            print('%s: %s' % i)
+            print("%s: %s" % i)
 
     return args
 
 
-def query(tool_id=None, user=None, like=None, source='metrics',
-          connect_args=None, debug=False, min=-1, max=-1, **kwargs):
+def query(
+    tool_id=None, user=None, like=None, source="metrics", connect_args=None, debug=False, min=-1, max=-1, **kwargs
+):
 
-    connect_arg_str = ''
+    connect_arg_str = ""
     for k, v in connect_args.items():
-        connect_arg_str += f'{k}={v}'
+        connect_arg_str += f"{k}={v}"
 
     pc = psycopg2.connect(connect_arg_str)
     cur = pc.cursor()
@@ -144,26 +132,26 @@ def query(tool_id=None, user=None, like=None, source='metrics',
         try:
             user_id = int(user)
         except ValueError:
-            if '@' not in user:
-                field = 'username'
+            if "@" not in user:
+                field = "username"
             else:
-                field = 'email'
-            sql = 'SELECT id FROM galaxy_user WHERE {} = {}'.format(field, '%s')
+                field = "email"
+            sql = "SELECT id FROM galaxy_user WHERE {} = {}".format(field, "%s")
             cur.execute(sql, (user,))
             if debug:
-                print('Executed:')
+                print("Executed:")
                 print(cur.query)
             row = cur.fetchone()
             if row:
                 user_id = row[0]
             else:
-                print('Invalid user: %s' % user)
+                print("Invalid user: %s" % user)
                 sys.exit(1)
 
     if like:
-        query_tool_id = '%%/%s/%%' % tool_id
-    elif '/' in tool_id and not re.match(r'\d+\.\d+', tool_id.split('/')[-1]):
-        query_tool_id = '%s%%' % tool_id
+        query_tool_id = "%%/%s/%%" % tool_id
+    elif "/" in tool_id and not re.match(r"\d+\.\d+", tool_id.split("/")[-1]):
+        query_tool_id = "%s%%" % tool_id
         like = True
     else:
         query_tool_id = tool_id
@@ -181,7 +169,7 @@ def query(tool_id=None, user=None, like=None, source='metrics',
     else:
         user_clause = ""
 
-    if source == 'metrics':
+    if source == "metrics":
         if min > 0 and max > 0:
             time_clause = """AND metric_value > %s
           AND metric_value < %s"""
@@ -196,56 +184,57 @@ def query(tool_id=None, user=None, like=None, source='metrics',
         else:
             time_clause = ""
         sql = METRICS_SQL
-    elif source == 'history':
+    elif source == "history":
         if min > 0 and max > 0:
             time_clause = """WHERE ctimes[1] - ctimes[2] > interval %s
           AND ctimes[1] - ctimes[2] < interval %s"""
-            sql_args.append('%s seconds' % min)
-            sql_args.append('%s seconds' % max)
+            sql_args.append("%s seconds" % min)
+            sql_args.append("%s seconds" % max)
         elif min > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] > interval %s"
-            sql_args.append('%s seconds' % min)
+            sql_args.append("%s seconds" % min)
         elif max > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] < interval %s"
-            sql_args.append('%s seconds' % max)
+            sql_args.append("%s seconds" % max)
         else:
             time_clause = ""
         sql = HISTORY_SQL
 
-    sql = sql.format(tool_clause=tool_clause, user_clause=user_clause,
-                     time_clause=time_clause)
+    sql = sql.format(tool_clause=tool_clause, user_clause=user_clause, time_clause=time_clause)
 
     cur.execute(sql, sql_args)
     if debug:
-        print('Executed:')
+        print("Executed:")
         print(cur.query)
-    print('Query returned %d rows' % cur.rowcount)
+    print("Query returned %d rows" % cur.rowcount)
 
-    if source == 'metrics':
+    if source == "metrics":
         times = numpy.array([r[0] for r in cur if r[0]])
-    elif source == 'history':
+    elif source == "history":
         times = numpy.array([r[0].total_seconds() for r in cur if r[0]])
 
-    print('Collected %d times' % times.size)
+    print("Collected %d times" % times.size)
 
     if times.size == 0:
         return
 
     if user:
-        print('Displaying statistics for user %s' % user)
+        print("Displaying statistics for user %s" % user)
 
-    stats = (('Mean runtime', numpy.mean(times)),
-             ('Standard deviation', numpy.std(times)),
-             ('Minimum runtime', times.min()),
-             ('Maximum runtime', times.max()))
+    stats = (
+        ("Mean runtime", numpy.mean(times)),
+        ("Standard deviation", numpy.std(times)),
+        ("Minimum runtime", times.min()),
+        ("Maximum runtime", times.max()),
+    )
 
     for name, seconds in stats:
         hours, minutes = nice_times(seconds)
-        msg = name + ' is %0.0f seconds' % seconds
+        msg = name + " is %0.0f seconds" % seconds
         if minutes:
-            msg += ' (=%0.2f minutes)' % minutes
+            msg += " (=%0.2f minutes)" % minutes
         if hours:
-            msg += ' (=%0.2f hours)' % hours
+            msg += " (=%0.2f hours)" % hours
         print(msg)
 
 
@@ -267,5 +256,5 @@ def main():
     query(**vars(args))
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/scripts/secret_decoder_ring.py b/scripts/secret_decoder_ring.py
index a70dd711b66..8b14d23900b 100644
--- a/scripts/secret_decoder_ring.py
+++ b/scripts/secret_decoder_ring.py
@@ -7,22 +7,21 @@ import logging
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import unicodify
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 logging.basicConfig()
 log = logging.getLogger(__name__)
 
 parser = argparse.ArgumentParser()
-parser.add_argument('action', metavar='ACTION', type=str,
-                    default=None,
-                    help='decode|encode')
-parser.add_argument('value', metavar='VALUE', type=str,
-                    default=None,
-                    help='value to encode or decode')
+parser.add_argument("action", metavar="ACTION", type=str, default=None, help="decode|encode")
+parser.add_argument("value", metavar="VALUE", type=str, default=None, help="value to encode or decode")
 populate_config_args(parser)
 args = parser.parse_args()
 
@@ -33,16 +32,16 @@ app_properties = app_properties_from_args(args)
 if "id_secret" not in app_properties:
     log.warning('No ID_SECRET specified. Please set the "id_secret" in your galaxy.yml.')
 
-id_secret = app_properties.get('id_secret', 'dangerous_default')
+id_secret = app_properties.get("id_secret", "dangerous_default")
 
 security_helper = IdEncodingHelper(id_secret=id_secret)
 # And get access to the models
 # Login manager to manage current_user functionality
 
-if args.action == 'decode':
-    sys.stdout.write(security_helper.decode_guid(args.value.lstrip('F')))
-elif args.action == 'encode':
+if args.action == "decode":
+    sys.stdout.write(security_helper.decode_guid(args.value.lstrip("F")))
+elif args.action == "encode":
     sys.stdout.write(unicodify(security_helper.encode_guid(args.value)))
 else:
     sys.stdout.write("Unknown argument")
-sys.stdout.write('\n')
+sys.stdout.write("\n")
diff --git a/scripts/set_dataset_sizes.py b/scripts/set_dataset_sizes.py
index d3a6e355478..8d1f070d5eb 100644
--- a/scripts/set_dataset_sizes.py
+++ b/scripts/set_dataset_sizes.py
@@ -4,11 +4,14 @@ import argparse
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy.config
 from galaxy.objectstore import build_object_store_from_config
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
 parser = argparse.ArgumentParser()
 populate_config_args(parser)
@@ -24,16 +27,16 @@ def init():
     return model, object_store
 
 
-if __name__ == '__main__':
-    print('Loading Galaxy model...')
+if __name__ == "__main__":
+    print("Loading Galaxy model...")
     model, object_store = init()
     sa_session = model.context.current
 
     set = 0
     dataset_count = sa_session.query(model.Dataset).count()
-    print('Processing %i datasets...' % dataset_count)
+    print("Processing %i datasets..." % dataset_count)
     percent = 0
-    print('Completed %i%%' % percent, end=' ')
+    print("Completed %i%%" % percent, end=" ")
     sys.stdout.flush()
     for i, dataset in enumerate(sa_session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
         if dataset.total_size is None:
@@ -44,8 +47,8 @@ if __name__ == '__main__':
         new_percent = int(float(i) / dataset_count * 100)
         if new_percent != percent:
             percent = new_percent
-            print('\rCompleted %i%%' % percent, end=' ')
+            print("\rCompleted %i%%" % percent, end=" ")
             sys.stdout.flush()
     sa_session.flush()
-    print('\rCompleted 100%')
+    print("\rCompleted 100%")
     object_store.shutdown()
diff --git a/scripts/set_user_disk_usage.py b/scripts/set_user_disk_usage.py
index bfd1f3d394e..ca0d401a780 100755
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -4,28 +4,37 @@ import argparse
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy.config
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.util import nice_size
-from galaxy.util.script import app_properties_from_args, populate_config_args
+from galaxy.util.script import (
+    app_properties_from_args,
+    populate_config_args,
+)
 
-default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'config/galaxy.ini'))
+default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "config/galaxy.ini"))
 
 parser = argparse.ArgumentParser()
-parser.add_argument('-u', '--username', dest='username', help='Username of user to update', default='all')
-parser.add_argument('-e', '--email', dest='email', help='Email address of user to update', default='all')
-parser.add_argument('--dry-run', dest='dryrun', help='Dry run (show changes but do not save to database)', action='store_true', default=False)
+parser.add_argument("-u", "--username", dest="username", help="Username of user to update", default="all")
+parser.add_argument("-e", "--email", dest="email", help="Email address of user to update", default="all")
+parser.add_argument(
+    "--dry-run",
+    dest="dryrun",
+    help="Dry run (show changes but do not save to database)",
+    action="store_true",
+    default=False,
+)
 populate_config_args(parser)
 args = parser.parse_args()
 
 
 def init():
 
-    if args.username == 'all':
+    if args.username == "all":
         args.username = None
-    if args.email == 'all':
+    if args.email == "all":
         args.email = None
 
     app_properties = app_properties_from_args(args)
@@ -38,7 +47,7 @@ def init():
 def quotacheck(sa_session, users, engine):
     sa_session.refresh(user)
     current = user.get_disk_usage()
-    print(user.username, '<' + user.email + '>:', end=' ')
+    print(user.username, "<" + user.email + ">:", end=" ")
 
     if not args.dryrun:
         # Apply new disk usage
@@ -48,28 +57,28 @@ def quotacheck(sa_session, users, engine):
     else:
         new = user.calculate_disk_usage()
 
-    print('old usage:', nice_size(current), 'change:', end=' ')
+    print("old usage:", nice_size(current), "change:", end=" ")
     if new in (current, None):
-        print('none')
+        print("none")
     else:
         if new > current:
-            print('+%s' % (nice_size(new - current)))
+            print("+%s" % (nice_size(new - current)))
         else:
-            print('-%s' % (nice_size(current - new)))
+            print("-%s" % (nice_size(current - new)))
 
 
-if __name__ == '__main__':
-    print('Loading Galaxy model...')
+if __name__ == "__main__":
+    print("Loading Galaxy model...")
     model, object_store, engine = init()
     sa_session = model.context.current
 
     if not args.username and not args.email:
         user_count = sa_session.query(model.User).count()
-        print('Processing %i users...' % user_count)
+        print("Processing %i users..." % user_count)
         for i, user in enumerate(sa_session.query(model.User).enable_eagerloads(False).yield_per(1000)):
-            print('%3i%%' % int(float(i) / user_count * 100), end=' ')
+            print("%3i%%" % int(float(i) / user_count * 100), end=" ")
             quotacheck(sa_session, user, engine)
-        print('100% complete')
+        print("100% complete")
         object_store.shutdown()
         sys.exit(0)
     elif args.username:
@@ -77,7 +86,7 @@ if __name__ == '__main__':
     elif args.email:
         user = sa_session.query(model.User).enable_eagerloads(False).filter_by(email=args.email).first()
     if not user:
-        print('User not found')
+        print("User not found")
         sys.exit(1)
     object_store.shutdown()
     quotacheck(sa_session, user, engine)
diff --git a/scripts/slideshow/build_slideshow.py b/scripts/slideshow/build_slideshow.py
index e8f2d7c7f98..0eb411239b6 100644
--- a/scripts/slideshow/build_slideshow.py
+++ b/scripts/slideshow/build_slideshow.py
@@ -2,7 +2,6 @@ import os
 import string
 import sys
 
-
 SCRIPTS_DIRECTORY = os.path.dirname(__file__)
 TEMPLATE_PATH = os.path.join(SCRIPTS_DIRECTORY, "slideshow_template.html")
 TEMPLATE = string.Template(open(TEMPLATE_PATH).read())
@@ -13,13 +12,15 @@ def main(argv=None):
         argv = sys.argv
     title = argv[1]
     markdown_source = argv[2]
-    output = os.path.splitext(markdown_source)[0] + '.html'
+    output = os.path.splitext(markdown_source)[0] + ".html"
     with open(markdown_source) as s:
         content = s.read()
-    html = TEMPLATE.safe_substitute(**{
-        'title': title,
-        'content': content,
-    })
+    html = TEMPLATE.safe_substitute(
+        **{
+            "title": title,
+            "content": content,
+        }
+    )
     print(html)
     open(output, "w").write(html)
 
diff --git a/scripts/summarize_timings.py b/scripts/summarize_timings.py
index 3d1a7ae5306..5c96a3648fc 100644
--- a/scripts/summarize_timings.py
+++ b/scripts/summarize_timings.py
@@ -5,7 +5,6 @@ from argparse import ArgumentParser
 
 import numpy
 
-
 DESCRIPTION = ""
 
 TIMING_LINE_PATTERN = re.compile(r"\((\d+.\d+) ms\)")
@@ -36,13 +35,7 @@ def main(argv=None):
             print(line.strip())
 
     template = "Summary (ms) - Mean: %f, Median: %f, Max: %f, Min: %f, StdDev: %f"
-    message = template % (
-        numpy.mean(times),
-        numpy.median(times),
-        numpy.max(times),
-        numpy.min(times),
-        numpy.std(times)
-    )
+    message = template % (numpy.mean(times), numpy.median(times), numpy.max(times), numpy.min(times), numpy.std(times))
     print(message)
 
 
diff --git a/scripts/tests_markdown.py b/scripts/tests_markdown.py
index e9b4d95f5af..41cd1afe9aa 100644
--- a/scripts/tests_markdown.py
+++ b/scripts/tests_markdown.py
@@ -8,15 +8,12 @@ import sys
 import jinja2
 from mir import html_report
 
-
 DESCRIPTION = "Script to generate (potentially merged) HTML summary of Galaxy Test Performance"
 templateLoader = jinja2.FileSystemLoader(searchpath="./scripts")
 template_env = jinja2.Environment(loader=templateLoader)
 TEMPLATE_FILE = "tests_markdown.tpl"
 TEMPLATE_COMPARE_FILE = "tests_markdown_compare.tpl"
-LINKS = [
-    {"href": "https://github.com/galaxyproject/galaxy", "title": "Galaxy"}
-]
+LINKS = [{"href": "https://github.com/galaxyproject/galaxy", "title": "Galaxy"}]
 
 
 def main(argv=None):
@@ -71,20 +68,22 @@ def _merge_summarizes(raw_data_dicts):
     all_labels = set()
 
     for raw_data_dict in raw_data_dicts:
-        these_api_endpoints = raw_data_dict['raw_data']['api_endpoint_metrics']
+        these_api_endpoints = raw_data_dict["raw_data"]["api_endpoint_metrics"]
         for api_endpoint in these_api_endpoints.keys():
             all_api_endpoints.add(api_endpoint)
-        these_internal_endpoints = raw_data_dict['raw_data']['internals_metrics']
+        these_internal_endpoints = raw_data_dict["raw_data"]["internals_metrics"]
         for internal_endpoint in these_internal_endpoints.keys():
             all_internal_metrics.add(internal_endpoint)
-        these_tests = raw_data_dict['raw_data']['tests']
+        these_tests = raw_data_dict["raw_data"]["tests"]
         for test in these_tests:
-            all_tests.add(test['nodeid'])
+            all_tests.add(test["nodeid"])
         all_labels.add(raw_data_dict["label"])
 
     for label in all_labels:
         for api_endpoint in all_api_endpoints:
-            _ensure_has_dict_at_key(api_endpoints, api_endpoint,
+            _ensure_has_dict_at_key(
+                api_endpoints,
+                api_endpoint,
                 total_time={},
                 sql_time={},
                 sql_queries={},
@@ -92,7 +91,9 @@ def _merge_summarizes(raw_data_dicts):
             api_endpoints[api_endpoint]["total_time"][label] = _empty_statistics()
             api_endpoints[api_endpoint]["sql_time"][label] = _empty_statistics()
         for internal_endpoint in all_internal_metrics:
-            _ensure_has_dict_at_key(internals, internal_endpoint,
+            _ensure_has_dict_at_key(
+                internals,
+                internal_endpoint,
                 total_time={},
             )
             internals[internal_endpoint]["total_time"][label] = _empty_statistics()
@@ -102,10 +103,10 @@ def _merge_summarizes(raw_data_dicts):
             tests[test][label] = {"outcome": "absent"}
 
     for raw_data_dict in raw_data_dicts:
-        ab_label = raw_data_dict['label']
-        these_api_endpoints = raw_data_dict['raw_data']['api_endpoint_metrics']
-        these_internals = raw_data_dict['raw_data']['internals_metrics']
-        these_tests = raw_data_dict['raw_data']['tests']
+        ab_label = raw_data_dict["label"]
+        these_api_endpoints = raw_data_dict["raw_data"]["api_endpoint_metrics"]
+        these_internals = raw_data_dict["raw_data"]["internals_metrics"]
+        these_tests = raw_data_dict["raw_data"]["tests"]
 
         for api_endpoint, endpoint_metrics in these_api_endpoints.items():
             api_endpoints[api_endpoint]["label"] = endpoint_metrics["label"]
@@ -114,16 +115,18 @@ def _merge_summarizes(raw_data_dicts):
 
         for endpoint, endpoint_metrics in these_internals.items():
             internals[endpoint]["label"] = endpoint_metrics["label"]
-            internals[endpoint]['total_time'][ab_label].update(endpoint_metrics["total_time"])
+            internals[endpoint]["total_time"][ab_label].update(endpoint_metrics["total_time"])
 
         for test in these_tests:
-            tests[test["nodeid"]][ab_label]["outcome"] = test.get('outcome')
+            tests[test["nodeid"]][ab_label]["outcome"] = test.get("outcome")
 
-    return {"raw_data": {
-        "api_endpoint_metrics": api_endpoints,
-        "internals_metrics": internals,
-        "tests": tests,
-    }}
+    return {
+        "raw_data": {
+            "api_endpoint_metrics": api_endpoints,
+            "internals_metrics": internals,
+            "tests": tests,
+        }
+    }
 
 
 def _prepare_raw_data(path):
@@ -138,11 +141,11 @@ def _prepare_raw_data(path):
 
 
 def __inject_api_timing_summary_environment(environment):
-    for test in environment['raw_data']['tests']:
-        if 'metadata' not in test:
+    for test in environment["raw_data"]["tests"]:
+        if "metadata" not in test:
             continue
 
-        if 'local_metrics' in test['metadata']:
+        if "local_metrics" in test["metadata"]:
             __inject_api_timing_summary_test(test)
 
 
@@ -150,58 +153,62 @@ def __inject_api_timing_summary_across_tests(environment):
     api_endpoints = {}
     internals = {}
 
-    for test in environment['raw_data']['tests']:
-        if 'metadata' not in test:
+    for test in environment["raw_data"]["tests"]:
+        if "metadata" not in test:
             continue
 
-        test_endpoints = test['api_endpoint_metrics']
+        test_endpoints = test["api_endpoint_metrics"]
         for api_endpoint, endpoint_metrics in test_endpoints.items():
-            _ensure_has_dict_at_key(api_endpoints, api_endpoint,
-                total_time={'raw': []},
-                sql_time={'raw': []},
-                sql_queries={'raw': []},
+            _ensure_has_dict_at_key(
+                api_endpoints,
+                api_endpoint,
+                total_time={"raw": []},
+                sql_time={"raw": []},
+                sql_queries={"raw": []},
             )
-            api_endpoints[api_endpoint]['label'] = endpoint_metrics['label']
-            api_endpoints[api_endpoint]['total_time']['raw'].extend(endpoint_metrics['total_time']['raw'])
-            api_endpoints[api_endpoint]['sql_time']['raw'].extend(endpoint_metrics['sql_time']['raw'])
-            api_endpoints[api_endpoint]['sql_queries']['raw'].extend(endpoint_metrics['sql_queries']['raw'])
+            api_endpoints[api_endpoint]["label"] = endpoint_metrics["label"]
+            api_endpoints[api_endpoint]["total_time"]["raw"].extend(endpoint_metrics["total_time"]["raw"])
+            api_endpoints[api_endpoint]["sql_time"]["raw"].extend(endpoint_metrics["sql_time"]["raw"])
+            api_endpoints[api_endpoint]["sql_queries"]["raw"].extend(endpoint_metrics["sql_queries"]["raw"])
 
-        test_endpoints = test['internals_metrics']
+        test_endpoints = test["internals_metrics"]
         for api_endpoint, endpoint_metrics in test_endpoints.items():
-            _ensure_has_dict_at_key(internals, api_endpoint,
-                total_time={'raw': []},
+            _ensure_has_dict_at_key(
+                internals,
+                api_endpoint,
+                total_time={"raw": []},
             )
-            internals[api_endpoint]['label'] = endpoint_metrics['label']
-            internals[api_endpoint]['total_time']['raw'].extend(endpoint_metrics['total_time']['raw'])
+            internals[api_endpoint]["label"] = endpoint_metrics["label"]
+            internals[api_endpoint]["total_time"]["raw"].extend(endpoint_metrics["total_time"]["raw"])
 
     for endpoint_metrics in api_endpoints.values():
-        __inject_statistics(endpoint_metrics['total_time'])
-        __inject_statistics(endpoint_metrics['sql_time'])
-        __inject_statistics(endpoint_metrics['sql_queries'])
+        __inject_statistics(endpoint_metrics["total_time"])
+        __inject_statistics(endpoint_metrics["sql_time"])
+        __inject_statistics(endpoint_metrics["sql_queries"])
 
     for endpoint_metrics in internals.values():
-        __inject_statistics(endpoint_metrics['total_time'])
+        __inject_statistics(endpoint_metrics["total_time"])
 
-    environment['raw_data']['api_endpoint_metrics'] = api_endpoints
-    environment['raw_data']['internals_metrics'] = internals
+    environment["raw_data"]["api_endpoint_metrics"] = api_endpoints
+    environment["raw_data"]["internals_metrics"] = internals
 
 
 def __inject_raw_timings(environment):
     all_timings = []
 
-    for test in environment['raw_data']['tests']:
-        if 'metadata' not in test or 'local_metrics' not in test['metadata']:
+    for test in environment["raw_data"]["tests"]:
+        if "metadata" not in test or "local_metrics" not in test["metadata"]:
             continue
 
-        metrics = test['metadata']['local_metrics']
-        timing = metrics['timing']
+        metrics = test["metadata"]["local_metrics"]
+        timing = metrics["timing"]
 
         for endpoint, timings in timing.items():
             recording = timings[0].copy()
-            recording['endpoint'] = endpoint
+            recording["endpoint"] = endpoint
             all_timings.append(recording)
 
-    environment['raw_data']['all_timings'] = all_timings
+    environment["raw_data"]["all_timings"] = all_timings
 
 
 def _ensure_has_dict_at_key(the_dict, key, **kwd):
@@ -210,64 +217,62 @@ def _ensure_has_dict_at_key(the_dict, key, **kwd):
 
 
 def __inject_api_timing_summary_test(test):
-    metrics = test['metadata']['local_metrics']
-    timing = metrics['timing']
-    counter = metrics['counter']
+    metrics = test["metadata"]["local_metrics"]
+    timing = metrics["timing"]
+    counter = metrics["counter"]
     api_endpoints = {}
     internal_timings = {}
 
     def summarize_times(timings):
-        times = list(map(lambda t: t['time'], timings))
-        return __inject_statistics({
-            'raw': times,
-        })
+        times = list(map(lambda t: t["time"], timings))
+        return __inject_statistics(
+            {
+                "raw": times,
+            }
+        )
 
     def summarize_counter(c):
-        counters = list(map(lambda t: t['n'], c))
-        return __inject_statistics({
-            'raw': counters,
-        })
+        counters = list(map(lambda t: t["n"], c))
+        return __inject_statistics(
+            {
+                "raw": counters,
+            }
+        )
 
     for endpoint, timings in timing.items():
         if not endpoint.startswith("api"):
             continue
 
-        endpoint_summary = {
-            'total_time': summarize_times(timings),
-            'label': endpoint[len("api."):]
-        }
+        endpoint_summary = {"total_time": summarize_times(timings), "label": endpoint[len("api.") :]}
         sql_times = "sql.%s" % endpoint
         if sql_times in timing:
-            endpoint_summary['sql_time'] = summarize_times(timing[sql_times])
+            endpoint_summary["sql_time"] = summarize_times(timing[sql_times])
         sql_queries = "sqlqueries.%s" % endpoint
         if sql_queries in counter:
-            endpoint_summary['sql_queries'] = summarize_counter(counter[sql_queries])
+            endpoint_summary["sql_queries"] = summarize_counter(counter[sql_queries])
         api_endpoints[endpoint] = endpoint_summary
 
     for endpoint, timings in timing.items():
         if not endpoint.startswith("internals"):
             continue
 
-        internal_summary = {
-            'total_time': summarize_times(timings),
-            'label': endpoint[len("internals."):]
-        }
+        internal_summary = {"total_time": summarize_times(timings), "label": endpoint[len("internals.") :]}
         internal_timings[endpoint] = internal_summary
 
-    test['api_endpoint_metrics'] = api_endpoints
-    test['internals_metrics'] = internal_timings
+    test["api_endpoint_metrics"] = api_endpoints
+    test["internals_metrics"] = internal_timings
 
 
 def __inject_statistics(from_dict):
-    raw_values = from_dict['raw']
-    from_dict['sum'] = sum(raw_values)
-    from_dict['median'] = f"{statistics.median(raw_values):.2f}"
+    raw_values = from_dict["raw"]
+    from_dict["sum"] = sum(raw_values)
+    from_dict["median"] = f"{statistics.median(raw_values):.2f}"
     if len(raw_values) > 1:
-        from_dict['stdev'] = f"{statistics.stdev(raw_values):.4f}"
+        from_dict["stdev"] = f"{statistics.stdev(raw_values):.4f}"
     else:
-        from_dict['stdev'] = "n/a"
-    from_dict['mean'] = f"{statistics.mean(raw_values):.2f}"
-    from_dict['count'] = len(raw_values)
+        from_dict["stdev"] = "n/a"
+    from_dict["mean"] = f"{statistics.mean(raw_values):.2f}"
+    from_dict["count"] = len(raw_values)
     return from_dict
 
 
@@ -275,29 +280,26 @@ def __inject_summary(environment):
     total = 0
     failures = 0
     skips = 0
-    for test in environment['raw_data']['tests']:
+    for test in environment["raw_data"]["tests"]:
         total += 1
-        status = test.get('outcome')
-        if status == 'failed':
+        status = test.get("outcome")
+        if status == "failed":
             failures += 1
-        elif status == 'skipped':
+        elif status == "skipped":
             skips += 1
-    environment['raw_data']['results'] = {
-        'total': total,
-        'failures': failures,
-        'skips': skips,
+    environment["raw_data"]["results"] = {
+        "total": total,
+        "failures": failures,
+        "skips": skips,
     }
 
 
 def _parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
-    parser.add_argument('input_path', metavar='INPUT', type=str, nargs="+",
-                        help='structured input path (.json)')
-    parser.add_argument('--output_path', type=str, default="test.html",
-                        help='output path (.html)')
-    parser.add_argument('--title', type=str, default="Test Performance Summary",
-                        help='Performance Test Results')
-    parser.add_argument('--include_raw_metrics', action="store_true", default=False)
+    parser.add_argument("input_path", metavar="INPUT", type=str, nargs="+", help="structured input path (.json)")
+    parser.add_argument("--output_path", type=str, default="test.html", help="output path (.html)")
+    parser.add_argument("--title", type=str, default="Test Performance Summary", help="Performance Test Results")
+    parser.add_argument("--include_raw_metrics", action="store_true", default=False)
 
     return parser
 
diff --git a/scripts/tool_shed/api/common.py b/scripts/tool_shed/api/common.py
index 8513188bccc..df594cafccb 100644
--- a/scripts/tool_shed/api/common.py
+++ b/scripts/tool_shed/api/common.py
@@ -7,35 +7,36 @@ from urllib.request import (
     HTTPRedirectHandler,
     install_opener,
     Request,
-    urlopen
+    urlopen,
 )
 
-sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
+sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "lib"))
 
 from galaxy import util
 from tool_shed.util import hg_util
 
 
 class HTTPRedirectWithDataHandler(HTTPRedirectHandler):
-
     def __init__(self, method):
-        '''
+        """
         Upon first inspection, it would seem that this shouldn't be necessary, but for some reason
         not having a constructor explicitly set the request method breaks PUT requests.
-        '''
-        self.valid_methods = ['GET', 'HEAD', 'POST', 'PUT', 'DELETE']
-        self.redirect_codes = ['301', '302', '303', '307']
+        """
+        self.valid_methods = ["GET", "HEAD", "POST", "PUT", "DELETE"]
+        self.redirect_codes = ["301", "302", "303", "307"]
         self.method = method
 
     def redirect_request(self, request, fp, code, msg, headers, new_url):
         request_method = request.get_method()
         if str(code) in self.redirect_codes and request_method in self.valid_methods:
-            new_url = new_url.replace(' ', '%20')
-            request = Request(new_url,
-                              data=request.data,
-                              headers=request.headers,
-                              origin_req_host=request.get_origin_req_host(),
-                              unverifiable=True)
+            new_url = new_url.replace(" ", "%20")
+            request = Request(
+                new_url,
+                data=request.data,
+                headers=request.headers,
+                origin_req_host=request.get_origin_req_host(),
+                unverifiable=True,
+            )
             if self.method in self.valid_methods:
                 if request.get_method() != self.method:
                     request.get_method = lambda: self.method
@@ -50,7 +51,7 @@ def build_request_with_data(url, data, api_key, method):
     opener = build_opener(http_redirect_with_data_handler)
     install_opener(opener)
     url = make_url(url, api_key=api_key, args=None)
-    request = Request(url, headers={'Content-Type': 'application/json'}, data=json.dumps(data))
+    request = Request(url, headers={"Content-Type": "application/json"}, data=json.dumps(data))
     request_method = request.get_method()
     if request_method != method:
         request.get_method = lambda: method
@@ -63,7 +64,7 @@ def delete(api_key, url, data, return_formatted=True):
     'data' will become the JSON payload read by the Tool Shed.
     """
     try:
-        opener, request = build_request_with_data(url, data, api_key, 'DELETE')
+        opener, request = build_request_with_data(url, data, api_key, "DELETE")
         delete_request = opener.open(request)
         response = json.loads(delete_request.read())
     except HTTPError as e:
@@ -72,10 +73,10 @@ def delete(api_key, url, data, return_formatted=True):
             print(e.read(1024))
             sys.exit(1)
         else:
-            return dict(status='error', message=str(e.read(1024)))
+            return dict(status="error", message=str(e.read(1024)))
     if return_formatted:
-        print('Response')
-        print('--------')
+        print("Response")
+        print("--------")
         print(response)
     else:
         return response
@@ -91,33 +92,33 @@ def display(url, api_key=None, return_formatted=True):
         print(e.read(1024))
         sys.exit(1)
     if isinstance(r, str):
-        print('error: %s' % r)
+        print("error: %s" % r)
         return None
     if not return_formatted:
         return r
     elif isinstance(r, list):
         # Response is a collection as defined in the REST style.
-        print('Collection Members')
-        print('------------------')
+        print("Collection Members")
+        print("------------------")
         for n, i in enumerate(r):
             # All collection members should have a name in the response.
             # url is optional
-            if 'url' in i:
-                print('#%d: %s' % (n + 1, i.pop('url')))
-            if 'name' in i:
-                print('  name: %s' % i.pop('name'))
+            if "url" in i:
+                print("#%d: %s" % (n + 1, i.pop("url")))
+            if "name" in i:
+                print("  name: %s" % i.pop("name"))
             for k, v in i.items():
-                print(f'  {k}: {v}')
+                print(f"  {k}: {v}")
         print()
-        print('%d element(s) in collection' % len(r))
+        print("%d element(s) in collection" % len(r))
     elif isinstance(r, dict):
         # Response is an element as defined in the REST style.
-        print('Member Information')
-        print('------------------')
+        print("Member Information")
+        print("------------------")
         for k, v in r.items():
-            print(f'{k}: {v}')
+            print(f"{k}: {v}")
     else:
-        print('response is unknown type: %s' % type(r))
+        print("response is unknown type: %s" % type(r))
 
 
 def get(url, api_key=None):
@@ -131,11 +132,11 @@ def get(url, api_key=None):
 
 def get_api_url(base, parts, params=None):
     """Compose and return a URL for the Tool Shed API."""
-    if 'api' in parts and parts.index('api') != 0:
-        parts.pop(parts.index('api'))
-        parts.insert(0, 'api')
-    elif 'api' not in parts:
-        parts.insert(0, 'api')
+    if "api" in parts and parts.index("api") != 0:
+        parts.pop(parts.index("api"))
+        parts.insert(0, "api")
+    elif "api" not in parts:
+        parts.insert(0, "api")
     url = util.build_url(base, pathspec=parts, params=params)
     return url
 
@@ -145,8 +146,8 @@ def get_latest_downloadable_changeset_revision_via_api(url, name, owner):
     Return the latest downloadable changeset revision for the repository defined by the received
     name and owner.
     """
-    error_message = ''
-    parts = ['api', 'repositories', 'get_ordered_installable_revisions']
+    error_message = ""
+    parts = ["api", "repositories", "get_ordered_installable_revisions"]
     params = dict(name=name, owner=owner)
     api_url = get_api_url(base=url, parts=parts, params=params)
     changeset_revisions, error_message = json_from_url(api_url)
@@ -162,44 +163,44 @@ def get_repository_dict(url, repository_dict):
     Send a request to the Tool Shed to get additional information about the repository defined
     by the received repository_dict.  Add the information to the repository_dict and return it.
     """
-    error_message = ''
+    error_message = ""
     if not isinstance(repository_dict, dict):
-        error_message = 'Invalid repository_dict received: %s' % str(repository_dict)
+        error_message = "Invalid repository_dict received: %s" % str(repository_dict)
         return None, error_message
-    repository_id = repository_dict.get('repository_id', None)
+    repository_id = repository_dict.get("repository_id", None)
     if repository_id is None:
-        error_message = 'Invalid repository_dict does not contain a repository_id entry: %s' % str(repository_dict)
+        error_message = "Invalid repository_dict does not contain a repository_id entry: %s" % str(repository_dict)
         return None, error_message
-    parts = ['api', 'repositories', repository_id]
+    parts = ["api", "repositories", repository_id]
     api_url = get_api_url(base=url, parts=parts)
     extended_dict, error_message = json_from_url(api_url)
     if extended_dict is None or error_message:
         return None, error_message
-    name = extended_dict.get('name', None)
-    owner = extended_dict.get('owner', None)
+    name = extended_dict.get("name", None)
+    owner = extended_dict.get("owner", None)
     if name is not None and owner is not None:
         name = str(name)
         owner = str(owner)
         latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision_via_api(url, name, owner)
         if latest_changeset_revision is None or error_message:
             return None, error_message
-        extended_dict['latest_revision'] = str(latest_changeset_revision)
+        extended_dict["latest_revision"] = str(latest_changeset_revision)
         return extended_dict, error_message
     else:
-        error_message = 'Invalid extended_dict does not contain name or owner entries: %s' % str(extended_dict)
+        error_message = "Invalid extended_dict does not contain name or owner entries: %s" % str(extended_dict)
         return None, error_message
 
 
 def json_from_url(url):
     """Send a request to the Tool Shed via the Tool Shed API and handle the response."""
-    error_message = ''
+    error_message = ""
     url_handle = urlopen(url)
     url_contents = url_handle.read()
     try:
         parsed_json = json.loads(url_contents)
     except Exception as e:
         error_message = str(url_contents)
-        print('Error parsing JSON data in json_from_url():', e)
+        print("Error parsing JSON data in json_from_url():", e)
         return None, error_message
     return parsed_json, error_message
 
@@ -208,33 +209,33 @@ def make_url(url, api_key=None, args=None):
     """Adds the API Key to the URL if it's not already there."""
     if args is None:
         args = []
-    argsep = '&'
-    if '?' not in url:
-        argsep = '?'
+    argsep = "&"
+    if "?" not in url:
+        argsep = "?"
     if api_key:
-        if '?key=' not in url and '&key=' not in url:
-            args.insert(0, ('key', api_key))
-    return url + argsep + '&'.join('='.join(t) for t in args)
+        if "?key=" not in url and "&key=" not in url:
+            args.insert(0, ("key", api_key))
+    return url + argsep + "&".join("=".join(t) for t in args)
 
 
 def post(url, data, api_key=None):
     """Do the POST."""
     try:
-        opener, request = build_request_with_data(url, data, api_key, 'POST')
+        opener, request = build_request_with_data(url, data, api_key, "POST")
         post_request = opener.open(request)
         return json.loads(post_request.read())
     except HTTPError as e:
-        return dict(status='error', message=str(e.read(1024)))
+        return dict(status="error", message=str(e.read(1024)))
 
 
 def put(url, data, api_key=None):
     """Do the PUT."""
     try:
-        opener, request = build_request_with_data(url, data, api_key, 'PUT')
+        opener, request = build_request_with_data(url, data, api_key, "PUT")
         put_request = opener.open(request)
         return json.loads(put_request.read())
     except HTTPError as e:
-        return dict(status='error', message=str(e.read(1024)))
+        return dict(status="error", message=str(e.read(1024)))
 
 
 def submit(url, data, api_key=None, return_formatted=True):
@@ -250,24 +251,24 @@ def submit(url, data, api_key=None, return_formatted=True):
             print(e.read(1024))
             sys.exit(1)
         else:
-            return dict(status='error', message=str(e.read(1024)))
+            return dict(status="error", message=str(e.read(1024)))
     if not return_formatted:
         return response
-    print('Response')
-    print('--------')
+    print("Response")
+    print("--------")
     if isinstance(response, list):
         # Currently the only implemented responses are lists of dicts, because submission creates
         # some number of collection elements.
         for i in response:
             if isinstance(i, dict):
-                if 'url' in i:
-                    print(i.pop('url'))
+                if "url" in i:
+                    print(i.pop("url"))
                 else:
-                    print('----')
-                if 'name' in i:
-                    print('  name: %s' % i.pop('name'))
+                    print("----")
+                if "name" in i:
+                    print("  name: %s" % i.pop("name"))
                 for k, v in i.items():
-                    print(f'  {k}: {v}')
+                    print(f"  {k}: {v}")
             else:
                 print(i)
     else:
@@ -287,10 +288,10 @@ def update(api_key, url, data, return_formatted=True):
             print(e.read(1024))
             sys.exit(1)
         else:
-            return dict(status='error', message=str(e.read(1024)))
+            return dict(status="error", message=str(e.read(1024)))
     if return_formatted:
-        print('Response')
-        print('--------')
+        print("Response")
+        print("--------")
         print(response)
     else:
         return response
diff --git a/scripts/tool_shed/api/create_categories.py b/scripts/tool_shed/api/create_categories.py
index 4b2b7fd8984..86c76a1200f 100644
--- a/scripts/tool_shed/api/create_categories.py
+++ b/scripts/tool_shed/api/create_categories.py
@@ -20,24 +20,26 @@ available in the test public Tool Shed and create each of them in a local develo
 
 import argparse
 
-from common import get, submit
+from common import (
+    get,
+    submit,
+)
 
 
 def main(options):
     api_key = options.api
-    from_tool_shed = options.from_tool_shed.rstrip('/')
-    to_tool_shed = options.to_tool_shed.rstrip('/')
+    from_tool_shed = options.from_tool_shed.rstrip("/")
+    to_tool_shed = options.to_tool_shed.rstrip("/")
     # Get the categories from the specified Tool Shed.
-    url = '%s/api/categories' % from_tool_shed
+    url = "%s/api/categories" % from_tool_shed
     category_dicts = get(url)
     create_response_dicts = []
     for category_dict in category_dicts:
-        name = category_dict.get('name', None)
-        description = category_dict.get('description', None)
+        name = category_dict.get("name", None)
+        description = category_dict.get("description", None)
         if name is not None and description is not None:
-            data = dict(name=name,
-                        description=description)
-            url = '%s/api/categories' % to_tool_shed
+            data = dict(name=name, description=description)
+            url = "%s/api/categories" % to_tool_shed
             try:
                 response = submit(url, data, api_key)
             except Exception as e:
@@ -47,10 +49,26 @@ def main(options):
             create_response_dicts.append(create_response_dict)
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Retrieve a list of categories from a Tool Shed and create them in another Tool Shed.')
-    parser.add_argument("-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which categories will be created")
-    parser.add_argument("-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the categories")
-    parser.add_argument("-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the categories")
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Retrieve a list of categories from a Tool Shed and create them in another Tool Shed."
+    )
+    parser.add_argument(
+        "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which categories will be created"
+    )
+    parser.add_argument(
+        "-f",
+        "--from_tool_shed",
+        dest="from_tool_shed",
+        required=True,
+        help="URL of Tool Shed from which to retrieve the categories",
+    )
+    parser.add_argument(
+        "-t",
+        "--to_tool_shed",
+        dest="to_tool_shed",
+        required=True,
+        help="URL of Tool Shed in which to create the categories",
+    )
     options = parser.parse_args()
     main(options)
diff --git a/scripts/tool_shed/api/create_users.py b/scripts/tool_shed/api/create_users.py
index 09267e27c01..dea8adef38f 100644
--- a/scripts/tool_shed/api/create_users.py
+++ b/scripts/tool_shed/api/create_users.py
@@ -21,26 +21,27 @@ are available in the test public Tool Shed and create each of them in a local de
 
 import argparse
 
-from common import get, submit
+from common import (
+    get,
+    submit,
+)
 
 
 def main(options):
     api_key = options.api
-    from_tool_shed = options.from_tool_shed.rstrip('/')
-    to_tool_shed = options.to_tool_shed.rstrip('/')
+    from_tool_shed = options.from_tool_shed.rstrip("/")
+    to_tool_shed = options.to_tool_shed.rstrip("/")
     # Get the users from the specified Tool Shed.
-    url = '%s/api/users' % from_tool_shed
+    url = "%s/api/users" % from_tool_shed
     user_dicts = get(url)
     create_response_dicts = []
     for user_dict in user_dicts:
-        username = user_dict.get('username', None)
+        username = user_dict.get("username", None)
         if username is not None:
-            email = '%s@test.org' % username
-            password = 'testuser'
-            data = dict(email=email,
-                        password=password,
-                        username=username)
-            url = '%s/api/users' % to_tool_shed
+            email = "%s@test.org" % username
+            password = "testuser"
+            data = dict(email=email, password=password, username=username)
+            url = "%s/api/users" % to_tool_shed
             try:
                 response = submit(url, data, api_key)
             except Exception as e:
@@ -50,10 +51,22 @@ def main(options):
             create_response_dicts.append(create_response_dict)
 
 
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Retrieve a list of users from a Tool Shed and create them in another Tool Shed.')
-    parser.add_argument("-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which users will be created")
-    parser.add_argument("-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the users")
-    parser.add_argument("-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the users")
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Retrieve a list of users from a Tool Shed and create them in another Tool Shed."
+    )
+    parser.add_argument(
+        "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which users will be created"
+    )
+    parser.add_argument(
+        "-f",
+        "--from_tool_shed",
+        dest="from_tool_shed",
+        required=True,
+        help="URL of Tool Shed from which to retrieve the users",
+    )
+    parser.add_argument(
+        "-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the users"
+    )
     options = parser.parse_args()
     main(options)
diff --git a/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py b/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
index 2e60f3fe5e6..8c5b382fd27 100755
--- a/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
+++ b/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
@@ -5,9 +5,12 @@ import os
 import sys
 from configparser import ConfigParser
 
-from sqlalchemy.exc import OperationalError, ProgrammingError
+from sqlalchemy.exc import (
+    OperationalError,
+    ProgrammingError,
+)
 
-sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
+sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "lib"))
 
 import tool_shed.webapp.model.mapping as tool_shed_model
 from tool_shed.util import xml_util
@@ -16,21 +19,27 @@ from tool_shed.util import xml_util
 def check_db(config_parser):
     dburi = None
 
-    if config_parser.has_option('app:main', 'database_connection'):
-        dburi = config_parser.get('app:main', 'database_connection')
-    elif config_parser.has_option('app:main', 'database_file'):
-        db_file = config_parser.get('app:main', 'database_file')
+    if config_parser.has_option("app:main", "database_connection"):
+        dburi = config_parser.get("app:main", "database_connection")
+    elif config_parser.has_option("app:main", "database_file"):
+        db_file = config_parser.get("app:main", "database_file")
         dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file
     else:
-        sys.exit('The database configuration setting is missing from the tool_shed.ini file.  Add this setting before attempting to bootstrap.')
+        sys.exit(
+            "The database configuration setting is missing from the tool_shed.ini file.  Add this setting before attempting to bootstrap."
+        )
 
     sa_session = None
 
-    database_exists_message = 'The database configured for this Tool Shed is not new, so bootstrapping is not allowed.  '
-    database_exists_message += 'Create a new database that has not been migrated before attempting to bootstrap.'
+    database_exists_message = (
+        "The database configured for this Tool Shed is not new, so bootstrapping is not allowed.  "
+    )
+    database_exists_message += "Create a new database that has not been migrated before attempting to bootstrap."
 
     try:
-        model = tool_shed_model.init(config_parser.get('app:main', 'file_path'), dburi, engine_options={}, create_tables=False)
+        model = tool_shed_model.init(
+            config_parser.get("app:main", "file_path"), dburi, engine_options={}, create_tables=False
+        )
         sa_session = model.context.current
         sys.exit(database_exists_message)
     except ProgrammingError:
@@ -40,7 +49,7 @@ def check_db(config_parser):
 
     try:
         if sa_session is not None:
-            result = sa_session.execute('SELECT version FROM migrate_version').first()
+            result = sa_session.execute("SELECT version FROM migrate_version").first()
             if result[0] >= 2:
                 sys.exit(database_exists_message)
             else:
@@ -48,14 +57,14 @@ def check_db(config_parser):
     except ProgrammingError:
         pass
 
-    if config_parser.has_option('app:main', 'hgweb_config_dir'):
+    if config_parser.has_option("app:main", "hgweb_config_dir"):
         hgweb_config_parser = ConfigParser()
-        hgweb_dir = config_parser.get('app:main', 'hgweb_config_dir')
-        hgweb_config_file = os.path.join(hgweb_dir, 'hgweb.config')
+        hgweb_dir = config_parser.get("app:main", "hgweb_config_dir")
+        hgweb_config_file = os.path.join(hgweb_dir, "hgweb.config")
         if not os.path.exists(hgweb_config_file):
             sys.exit(0)
         hgweb_config_parser.read(hgweb_config_file)
-        configured_repos = hgweb_config_parser.items('paths')
+        configured_repos = hgweb_config_parser.items("paths")
         if len(configured_repos) >= 1:
             message = "This Tool Shed's hgweb.config file contains entries, so bootstrapping is not allowed.  Delete"
             message += " the current hgweb.config file along with all associated repositories in the configured "
@@ -70,35 +79,37 @@ def check_db(config_parser):
 
 
 def admin_user_info():
-    user_info_config = os.path.abspath(os.path.join(os.getcwd(), 'scripts/tool_shed/bootstrap_tool_shed', 'user_info.xml'))
+    user_info_config = os.path.abspath(
+        os.path.join(os.getcwd(), "scripts/tool_shed/bootstrap_tool_shed", "user_info.xml")
+    )
     tree, error_message = xml_util.parse_xml(user_info_config)
     username = None
     email = None
     password = None
     if tree is None:
         print("The XML file ", user_info_config, " seems to be invalid, using defaults.")
-        email = 'admin@test.org'
-        password = 'testuser'
-        username = 'admin'
+        email = "admin@test.org"
+        password = "testuser"
+        username = "admin"
     else:
         root = tree.getroot()
         for elem in root:
-            if elem.tag == 'email':
+            if elem.tag == "email":
                 email = elem.text
-            elif elem.tag == 'password':
+            elif elem.tag == "password":
                 password = elem.text
-            elif elem.tag == 'username':
+            elif elem.tag == "username":
                 username = elem.text
     return (username, email, password)
 
 
 def get_local_tool_shed_url(config_parser):
-    port = '9009'
-    if config_parser.has_section('server:main'):
-        if config_parser.has_option('server:main', 'port'):
-            port = config_parser.get('server:main', 'port')
-    host = '127.0.0.1'
-    print(f'http://{host}:{port}')
+    port = "9009"
+    if config_parser.has_section("server:main"):
+        if config_parser.has_option("server:main", "port"):
+            port = config_parser.get("server:main", "port")
+    host = "127.0.0.1"
+    print(f"http://{host}:{port}")
     return 0
 
 
@@ -110,22 +121,22 @@ def main(args):
     else:
         return 1
 
-    if args.method == 'check_db':
+    if args.method == "check_db":
         return check_db(config_parser)
-    elif args.method == 'admin_user_info':
+    elif args.method == "admin_user_info":
         (username, email, password) = admin_user_info()
-        print(f'{username}__SEP__{email}__SEP__{password}')
+        print(f"{username}__SEP__{email}__SEP__{password}")
         return 0
-    elif args.method == 'get_url':
+    elif args.method == "get_url":
         return get_local_tool_shed_url(config_parser)
     else:
         return 1
 
 
 parser = optparse.OptionParser()
-parser.add_option('-c', '--config_file', dest='config', action='store', default='config/tool_shed.yml.sample')
-parser.add_option('-e', '--execute', dest='method', action='store', default='check_db')
+parser.add_option("-c", "--config_file", dest="config", action="store", default="config/tool_shed.yml.sample")
+parser.add_option("-e", "--execute", dest="method", action="store", default="check_db")
 (args, options) = parser.parse_args()
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     sys.exit(main(args))
diff --git a/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py b/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
index 06b85bfd7d4..6a6850d43bc 100644
--- a/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
+++ b/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
@@ -6,18 +6,19 @@ import os
 import sys
 from configparser import ConfigParser
 
-sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
+sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "lib"))
 sys.path.insert(1, os.path.join(os.path.dirname(__file__)))
 
+from bootstrap_util import admin_user_info  # noqa: I100,I201
+
 import tool_shed.webapp.config as tool_shed_config
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.security.validate_user_input import (
     validate_email_str,
     validate_password_str,
-    validate_publicname_str
+    validate_publicname_str,
 )
 from tool_shed.webapp.model import mapping
-from bootstrap_util import admin_user_info  # noqa: I100,I201
 
 log = logging.getLogger(__name__)
 
@@ -32,16 +33,15 @@ class BootstrapApplication:
         self.config = config
         if not self.config.database_connection:
             self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str(config.database)
-        print('Using database connection: ', self.config.database_connection)
+        print("Using database connection: ", self.config.database_connection)
         # Setup the database engine and ORM
-        self.model = mapping.init(self.config.file_path,
-                                  self.config.database_connection,
-                                  engine_options={},
-                                  create_tables=False)
+        self.model = mapping.init(
+            self.config.file_path, self.config.database_connection, engine_options={}, create_tables=False
+        )
         self.security = IdEncodingHelper(id_secret=self.config.id_secret)
         self.hgweb_config_manager = self.model.hgweb_config_manager
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
-        print('Using hgweb.config file: ', self.hgweb_config_manager.hgweb_config)
+        print("Using hgweb.config file: ", self.hgweb_config_manager.hgweb_config)
 
     @property
     def sa_session(self):
@@ -82,18 +82,18 @@ def create_user(app):
 
 
 def validate(email, password, username):
-    message = "\n".join([validate_email_str(email),
-                         validate_password_str(password),
-                         validate_publicname_str(username)]).rstrip()
+    message = "\n".join(
+        [validate_email_str(email), validate_password_str(password), validate_publicname_str(username)]
+    ).rstrip()
     return message
 
 
 if __name__ == "__main__":
-    parser = optparse.OptionParser(description='Create a user with API key.')
-    parser.add_option('-c', dest='config', action='store', help='.ini file to retrieve toolshed configuration from')
+    parser = optparse.OptionParser(description="Create a user with API key.")
+    parser.add_option("-c", dest="config", action="store", help=".ini file to retrieve toolshed configuration from")
     (args, options) = parser.parse_args()
     ini_file = args.config
-    config_parser = ConfigParser({'here': os.getcwd()})
+    config_parser = ConfigParser({"here": os.getcwd()})
     print("Reading ini file: ", ini_file)
     config_parser.read(ini_file)
     config_dict = {}
@@ -104,7 +104,11 @@ if __name__ == "__main__":
     user = create_user(app)
     if user is not None:
         api_key = create_api_key(app, user)
-        print("Created new user with public username '", user.username, ".  An API key was also created and associated with the user.")
+        print(
+            "Created new user with public username '",
+            user.username,
+            ".  An API key was also created and associated with the user.",
+        )
         sys.exit(0)
     else:
         sys.exit("Problem creating a new user and an associated API key.")
diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index dfd9f68f580..f2088f8ee60 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -16,11 +16,11 @@ import logging
 import os
 import sys
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
 from galaxy.util.script import (
     app_properties_from_args,
-    populate_config_args
+    populate_config_args,
 )
 from tool_shed.util.shed_index import build_index
 from tool_shed.webapp import config as ts_config
@@ -30,12 +30,11 @@ log.addHandler(logging.StreamHandler(sys.stdout))
 
 
 def parse_arguments():
-    parser = argparse.ArgumentParser(description='Build a disk-backed Toolshed repository index and tool index for searching.')
+    parser = argparse.ArgumentParser(
+        description="Build a disk-backed Toolshed repository index and tool index for searching."
+    )
     populate_config_args(parser)
-    parser.add_argument('-d', '--debug',
-                        action='store_true',
-                        default=False,
-                        help='Print extra info')
+    parser.add_argument("-d", "--debug", action="store_true", default=False, help="Print extra info")
     args = parser.parse_args()
     app_properties = app_properties_from_args(args)
     config = ts_config.ToolShedAppConfiguration(**app_properties)
@@ -45,9 +44,9 @@ def parse_arguments():
     args.file_path = config.file_path
     if args.debug:
         log.setLevel(logging.DEBUG)
-        log.debug('Full options:')
+        log.debug("Full options:")
         for i in vars(args).items():
-            log.debug('%s: %s' % i)
+            log.debug("%s: %s" % i)
     return args
 
 
diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py
index aea2db985c1..5987aaba187 100644
--- a/scripts/tool_shed/deprecate_repositories_without_metadata.py
+++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py
@@ -7,21 +7,27 @@ import string
 import sys
 import textwrap
 import time
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from optparse import OptionParser
 from time import strftime
 
 import sqlalchemy as sa
-from sqlalchemy import and_, distinct, false, not_
+from sqlalchemy import (
+    and_,
+    distinct,
+    false,
+    not_,
+)
 
-sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib'))
+sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib"))
 
 import tool_shed.webapp.config as tool_shed_config
 import tool_shed.webapp.model.mapping
-from galaxy.util import (
-    build_url,
-    send_mail as galaxy_send_mail
-)
+from galaxy.util import build_url
+from galaxy.util import send_mail as galaxy_send_mail
 
 log = logging.getLogger()
 log.setLevel(10)
@@ -30,23 +36,37 @@ assert sys.version_info[:2] >= (2, 6)
 
 
 def build_citable_url(host, repository):
-    return build_url(host, pathspec=['view', repository.user.username, repository.name])
+    return build_url(host, pathspec=["view", repository.user.username, repository.name])
 
 
 def main():
-    '''
+    """
     Script to deprecate any repositories that are older than n days, and have been empty since creation.
-    '''
+    """
     parser = OptionParser()
     parser.add_option("-d", "--days", dest="days", action="store", type="int", help="number of days (14)", default=14)
-    parser.add_option("-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False)
-    parser.add_option("-v", "--verbose", action="store_true", dest="verbose", help="verbose mode, print the name of each repository", default=False)
+    parser.add_option(
+        "-i",
+        "--info_only",
+        action="store_true",
+        dest="info_only",
+        help="info about the requested action",
+        default=False,
+    )
+    parser.add_option(
+        "-v",
+        "--verbose",
+        action="store_true",
+        dest="verbose",
+        help="verbose mode, print the name of each repository",
+        default=False,
+    )
     (options, args) = parser.parse_args()
     try:
         ini_file = args[0]
     except IndexError:
         sys.exit("Usage: python %s <tool shed .ini file> [options]" % sys.argv[0])
-    config_parser = configparser.ConfigParser({'here': os.getcwd()})
+    config_parser = configparser.ConfigParser({"here": os.getcwd()})
     config_parser.read(ini_file)
     config_dict = {}
     for key, value in config_parser.items("app:main"):
@@ -66,32 +86,38 @@ def main():
 
 
 def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
-    '''
+    """
     Sends an email to the owner of the provided repository.
-    '''
-    smtp_server = app.config.get('smtp_server', None)
-    from_address = app.config.get('email_from', None)
+    """
+    smtp_server = app.config.get("smtp_server", None)
+    from_address = app.config.get("email_from", None)
     # Since there is no way to programmatically determine the URL for the tool shed from the .ini file, this method requires that
     # an environment variable named TOOL_SHED_CANONICAL_URL be set, pointing to the tool shed that is being checked.
-    url = os.environ.get('TOOL_SHED_CANONICAL_URL', None)
+    url = os.environ.get("TOOL_SHED_CANONICAL_URL", None)
     if None in [smtp_server, from_address]:
-        print('# Mail not configured, not sending email to repository owner.')
+        print("# Mail not configured, not sending email to repository owner.")
         return
     elif url is None:
-        print('# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.')
+        print("# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.")
         return
     subject = "Regarding your tool shed repositories at %s" % url
-    message_body_template = 'The tool shed automated repository checker has discovered that one or more of your repositories hosted ' + \
-        'at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans ' + \
-        'for these repositories, you can mark them as un-deprecated at any time.'
+    message_body_template = (
+        "The tool shed automated repository checker has discovered that one or more of your repositories hosted "
+        + "at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans "
+        + "for these repositories, you can mark them as un-deprecated at any time."
+    )
     message_template = string.Template(message_body_template)
-    body = '\n'.join(textwrap.wrap(message_template.safe_substitute(days=days, url=url), width=95))
-    body += '\n\n'
-    body += 'Repositories that were deprecated:\n'
-    body += '\n'.join(build_citable_url(url, repository) for repository in repositories_deprecated)
+    body = "\n".join(textwrap.wrap(message_template.safe_substitute(days=days, url=url), width=95))
+    body += "\n\n"
+    body += "Repositories that were deprecated:\n"
+    body += "\n".join(build_citable_url(url, repository) for repository in repositories_deprecated)
     try:
         galaxy_send_mail(from_address, email, subject, body, app.config)
-        print("# An email has been sent to {}, the owner of {}.".format(owner, ', '.join(repository.name for repository in repositories_deprecated)))
+        print(
+            "# An email has been sent to {}, the owner of {}.".format(
+                owner, ", ".join(repository.name for repository in repositories_deprecated)
+            )
+        )
         return True
     except Exception as e:
         print("# An error occurred attempting to send email: %s" % e)
@@ -106,8 +132,11 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
     repository_ids_to_not_check = []
     # Get a unique list of repository ids from the repository_metadata table. Any repository ID found in this table is not
     # empty, and will not be checked.
-    metadata_records = app.sa_session.execute(sa.select([distinct(app.model.RepositoryMetadata.table.c.repository_id)],
-                                 from_obj=app.model.RepositoryMetadata.table))
+    metadata_records = app.sa_session.execute(
+        sa.select(
+            [distinct(app.model.RepositoryMetadata.table.c.repository_id)], from_obj=app.model.RepositoryMetadata.table
+        )
+    )
     for metadata_record in metadata_records:
         repository_ids_to_not_check.append(metadata_record.repository_id)
     # Get the repositories that are A) not present in the above list, and b) older than the specified time.
@@ -129,39 +158,47 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
     repository_ids = [row.id for row in query_result]
     # Iterate through the list of repository ids for empty repositories and deprecate them unless info_only is set.
     for repository_id in repository_ids:
-        repository = app.sa_session.query(app.model.Repository) \
-            .filter(app.model.Repository.table.c.id == repository_id).one()
+        repository = (
+            app.sa_session.query(app.model.Repository).filter(app.model.Repository.table.c.id == repository_id).one()
+        )
         owner = repository.user
         if info_only:
-            print(f'# Repository {repository.name} owned by {repository.user.username} would have been deprecated, but info_only was set.')
+            print(
+                f"# Repository {repository.name} owned by {repository.user.username} would have been deprecated, but info_only was set."
+            )
         else:
             if verbose:
-                print(f'# Deprecating repository {repository.name} owned by {owner.username}.')
+                print(f"# Deprecating repository {repository.name} owned by {owner.username}.")
             if owner.username not in repositories_by_owner:
                 repositories_by_owner[owner.username] = dict(owner=owner, repositories=[])
-            repositories_by_owner[owner.username]['repositories'].append(repository)
+            repositories_by_owner[owner.username]["repositories"].append(repository)
             repositories.append(repository)
     # Send an email to each repository owner, listing the repositories that were deprecated.
     for repository_owner in repositories_by_owner:
-        for repository in repositories_by_owner[repository_owner]['repositories']:
+        for repository in repositories_by_owner[repository_owner]["repositories"]:
             repository.deprecated = True
             app.sa_session.add(repository)
             app.sa_session.flush()
-        owner = repositories_by_owner[repository_owner]['owner']
-        send_mail_to_owner(app, owner.username, owner.email, repositories_by_owner[repository_owner]['repositories'], days)
+        owner = repositories_by_owner[repository_owner]["owner"]
+        send_mail_to_owner(
+            app, owner.username, owner.email, repositories_by_owner[repository_owner]["repositories"], days
+        )
     stop = time.time()
-    print('# Deprecated %d repositories.' % len(repositories))
+    print("# Deprecated %d repositories." % len(repositories))
     print("# Elapsed time: ", stop - start)
     print("####################################################################################")
 
 
 class DeprecateRepositoriesApplication:
     """Encapsulates the state of a Universe application"""
+
     def __init__(self, config):
         if config.database_connection is False:
             config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database
         # Setup the database engine and ORM
-        self.model = tool_shed.webapp.model.mapping.init(config.file_path, config.database_connection, engine_options={}, create_tables=False)
+        self.model = tool_shed.webapp.model.mapping.init(
+            config.file_path, config.database_connection, engine_options={}, create_tables=False
+        )
         self.config = config
 
     @property
diff --git a/scripts/tools/maf/check_loc_file.py b/scripts/tools/maf/check_loc_file.py
index e0bf632c18a..ad66b8cc7ad 100644
--- a/scripts/tools/maf/check_loc_file.py
+++ b/scripts/tools/maf/check_loc_file.py
@@ -15,12 +15,12 @@ def __main__():
     index_location_file = sys.argv[1]
     for i, line in enumerate(open(index_location_file)):
         try:
-            if line.startswith('#'):
+            if line.startswith("#"):
                 continue
-            display_name, uid, indexed_for_species, species_exist, maf_files = line.rstrip().split('\t')
-            indexed_for_species = indexed_for_species.split(',')
-            species_exist = species_exist.split(',')
-            maf_files = maf_files.split(',')
+            display_name, uid, indexed_for_species, species_exist, maf_files = line.rstrip().split("\t")
+            indexed_for_species = indexed_for_species.split(",")
+            species_exist = species_exist.split(",")
+            maf_files = maf_files.split(",")
             species_indexed_in_maf = []
             species_found_in_maf = []
             for maf_file in maf_files:
diff --git a/scripts/tools/re_escape_output.py b/scripts/tools/re_escape_output.py
index 987ff6a7310..9deab8c743c 100644
--- a/scripts/tools/re_escape_output.py
+++ b/scripts/tools/re_escape_output.py
@@ -11,21 +11,23 @@ import re
 
 def __main__():
     parser = optparse.OptionParser()
-    parser.add_option("-m", "--multiline", action="store_true", dest="multiline", default=False, help="Use Multiline Matching")
+    parser.add_option(
+        "-m", "--multiline", action="store_true", dest="multiline", default=False, help="Use Multiline Matching"
+    )
     (options, args) = parser.parse_args()
-    input = open(args[0], 'rb')
+    input = open(args[0], "rb")
     if len(args) > 1:
-        output = open(args[1], 'wb')
+        output = open(args[1], "wb")
     else:
         if options.multiline:
-            suffix = 're_match_multiline'
+            suffix = "re_match_multiline"
         else:
-            suffix = 're_match'
-        output = open(f"{args[0]}.{suffix}", 'wb')
+            suffix = "re_match"
+        output = open(f"{args[0]}.{suffix}", "wb")
     if options.multiline:
         lines = [re.escape(input.read())]
     else:
-        lines = ["%s\n" % re.escape(line.rstrip('\n\r')) for line in input]
+        lines = ["%s\n" % re.escape(line.rstrip("\n\r")) for line in input]
     output.writelines(lines)
     output.close()
 
diff --git a/scripts/update_shed_config_path.py b/scripts/update_shed_config_path.py
index ee911f7fc44..fab013b9fe2 100644
--- a/scripts/update_shed_config_path.py
+++ b/scripts/update_shed_config_path.py
@@ -3,22 +3,28 @@ import os
 import sys
 from configparser import ConfigParser
 
-from sqlalchemy import create_engine, MetaData
-from sqlalchemy.orm import scoped_session, sessionmaker
+from sqlalchemy import (
+    create_engine,
+    MetaData,
+)
+from sqlalchemy.orm import (
+    scoped_session,
+    sessionmaker,
+)
 
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy.model.tool_shed_install.mapping as mapping
 
 
 def main(opts, session, model):
-    '''
+    """
     Find all tool shed repositories with the bad path and update with the correct path.
-    '''
+    """
     for row in session.query(model.ToolShedRepository).all():
-        if 'shed_config_filename' in row.metadata_:
-            if row.metadata_['shed_config_filename'] == opts.bad_filename:
-                row.metadata_['shed_config_filename'] = opts.good_filename
+        if "shed_config_filename" in row.metadata_:
+            if row.metadata_["shed_config_filename"] == opts.bad_filename:
+                row.metadata_["shed_config_filename"] = opts.good_filename
                 session.add(row)
                 session.flush()
     return 0
@@ -28,13 +34,13 @@ def create_database(config_file):
     parser = ConfigParser()
     parser.read(config_file)
     # Determine which database connection to use.
-    database_connection = parser.get('app:main', 'install_database_connection')
+    database_connection = parser.get("app:main", "install_database_connection")
     if database_connection is None:
-        database_connection = parser.get('app:main', 'database_connection')
+        database_connection = parser.get("app:main", "database_connection")
     if database_connection is None:
-        database_connection = 'sqlite:///%s' % parser.get('app:main', 'database_file')
+        database_connection = "sqlite:///%s" % parser.get("app:main", "database_file")
     if database_connection is None:
-        print('Unable to determine correct database connection.')
+        print("Unable to determine correct database connection.")
         exit(1)
 
     # Initialize the database connection.
@@ -45,15 +51,32 @@ def create_database(config_file):
     return install_session, model
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('--config_file', dest='config_file', required=True, help="The path to your Galaxy configuration .ini file.")
-    parser.add_argument('--from', dest='bad_filename', required=True, help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file.")
-    parser.add_argument('--to', dest='good_filename', required=True, help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file.")
-    parser.add_argument('--force', dest='force', action='store_true', help="Use this flag to set the new path even if the file does not (yet) exist there.")
+    parser.add_argument(
+        "--config_file", dest="config_file", required=True, help="The path to your Galaxy configuration .ini file."
+    )
+    parser.add_argument(
+        "--from",
+        dest="bad_filename",
+        required=True,
+        help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file.",
+    )
+    parser.add_argument(
+        "--to",
+        dest="good_filename",
+        required=True,
+        help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file.",
+    )
+    parser.add_argument(
+        "--force",
+        dest="force",
+        action="store_true",
+        help="Use this flag to set the new path even if the file does not (yet) exist there.",
+    )
     opts = parser.parse_args()
     if not os.path.exists(opts.good_filename) and not opts.force:
-        print('The file %s does not exist, use the --force option to proceed.' % opts.good_filename)
+        print("The file %s does not exist, use the --force option to proceed." % opts.good_filename)
         exit(1)
     session, model = create_database(opts.config_file)
     exit(main(opts, session, model))
diff --git a/test/functional/conftest.py b/test/functional/conftest.py
index 51cc4c2e78e..76c1603839e 100644
--- a/test/functional/conftest.py
+++ b/test/functional/conftest.py
@@ -2,6 +2,7 @@ def pytest_unconfigure(config):
     try:
         # This needs to be run if no test were run.
         from .test_toolbox_pytest import DRIVER
+
         DRIVER.tear_down()
         print("Galaxy test driver shutdown successful")
     except Exception:
diff --git a/test/functional/test_data_managers.py b/test/functional/test_data_managers.py
index 65d14697c5b..cf48323e0ee 100644
--- a/test/functional/test_data_managers.py
+++ b/test/functional/test_data_managers.py
@@ -1,16 +1,16 @@
 import logging
 
-from .test_toolbox import (
-    build_tests as _build_tests,
-    ToolTestCase,
-)
+from .test_toolbox import build_tests as _build_tests
+from .test_toolbox import ToolTestCase
 
 try:
     from nose.tools import nottest
 except ImportError:
+
     def nottest(x):
         return x
 
+
 log = logging.getLogger(__name__)
 data_managers = None
 
@@ -20,7 +20,9 @@ class DataManagerToolTestCase(ToolTestCase):
 
 
 @nottest
-def build_tests(tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None, create_admin=False, user_email=None):
+def build_tests(
+    tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None, create_admin=False, user_email=None
+):
     """
     If the module level variable `data_managers` is set, generate `DataManagerToolTestCase`
     classes for all of its tests and put them into this modules globals() so
@@ -28,17 +30,19 @@ def build_tests(tmp_dir=None, testing_shed_tools=False, master_api_key=None, use
     """
 
     if data_managers is None:
-        log.warning('data_managers was not set for Data Manager functional testing. Will not test.')
+        log.warning("data_managers was not set for Data Manager functional testing. Will not test.")
         return
 
     G = globals()
 
-    _build_tests(testing_shed_tools=testing_shed_tools,
-                 master_api_key=master_api_key,
-                 user_api_key=user_api_key,
-                 name_prefix="TestForDataManagerTool_",
-                 baseclass=DataManagerToolTestCase,
-                 user_email=user_email,
-                 create_admin=create_admin,
-                 G=G,
-                 contains='data_manager')
+    _build_tests(
+        testing_shed_tools=testing_shed_tools,
+        master_api_key=master_api_key,
+        user_api_key=user_api_key,
+        name_prefix="TestForDataManagerTool_",
+        baseclass=DataManagerToolTestCase,
+        user_email=user_email,
+        create_admin=create_admin,
+        G=G,
+        contains="data_manager",
+    )
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index f7d701be18b..4266e5d0953 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -3,12 +3,20 @@ import logging
 try:
     from nose.tools import nottest
 except ImportError:
+
     def nottest(x):
         return x
 
-from galaxy.tool_util.verify.interactor import GalaxyInteractorApi, verify_tool
+
+from galaxy.tool_util.verify.interactor import (
+    GalaxyInteractorApi,
+    verify_tool,
+)
 from galaxy.tools import DataManagerTool
-from galaxy_test.base.env import setup_keep_outdir, target_url_parts
+from galaxy_test.base.env import (
+    setup_keep_outdir,
+    target_url_parts,
+)
 from galaxy_test.base.instrument import register_job_data
 from galaxy_test.driver.testcase import DrivenFunctionalTestCase
 
@@ -17,7 +25,7 @@ log = logging.getLogger(__name__)
 toolbox = None
 
 # Do not test Data Managers as part of the standard Tool Test Framework.
-TOOL_TYPES_NO_TEST = (DataManagerTool, )
+TOOL_TYPES_NO_TEST = (DataManagerTool,)
 
 
 class ToolTestCase(DrivenFunctionalTestCase):
@@ -32,20 +40,29 @@ class ToolTestCase(DrivenFunctionalTestCase):
             tool_id = self.tool_id
         assert tool_id
 
-        verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
+        verify_tool(
+            tool_id,
+            self.galaxy_interactor,
+            resource_parameters=resource_parameters,
+            test_index=test_index,
+            tool_version=tool_version,
+            register_job_data=register_job_data,
+        )
 
 
 @nottest
-def build_tests(app=None,
-                testing_shed_tools=False,
-                master_api_key=None,
-                user_api_key=None,
-                name_prefix="TestForTool_",
-                baseclass=ToolTestCase,
-                create_admin=False,
-                user_email=None,
-                G=None,
-                contains=None):
+def build_tests(
+    app=None,
+    testing_shed_tools=False,
+    master_api_key=None,
+    user_api_key=None,
+    name_prefix="TestForTool_",
+    baseclass=ToolTestCase,
+    create_admin=False,
+    user_email=None,
+    G=None,
+    contains=None,
+):
     """
     If the module level variable `toolbox` is set, generate `ToolTestCase`
     classes for all of its tests and put them into this modules globals() so
@@ -64,7 +81,7 @@ def build_tests(app=None,
         "user_api_key_is_admin_key": True,
     }
     if create_admin and not user_api_key:
-        galaxy_interactor_kwds['test_user'] = user_email
+        galaxy_interactor_kwds["test_user"] = user_email
     galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
 
     if not G:
@@ -73,7 +90,7 @@ def build_tests(app=None,
 
     # Eliminate all previous tests from G.
     for key in G.copy().keys():
-        if key.startswith('TestForTool_'):
+        if key.startswith("TestForTool_"):
             del G[key]
 
     tests_summary = galaxy_interactor.get_tests_summary()
@@ -82,8 +99,8 @@ def build_tests(app=None,
         # named test_tool_XXX that run each test defined in the tool config.
         if contains and contains not in tool_id:
             continue
-        name = name_prefix + tool_id.replace(' ', '_')
-        baseclasses = (baseclass, )
+        name = name_prefix + tool_id.replace(" ", "_")
+        baseclasses = (baseclass,)
         namespace = dict()
 
         all_versions_test_count = 0
@@ -91,11 +108,12 @@ def build_tests(app=None,
         for tool_version, version_summary in tool_summary.items():
             count = version_summary["count"]
             for i in range(count):
-                test_function_name = 'test_tool_%06d' % all_versions_test_count
+                test_function_name = "test_tool_%06d" % all_versions_test_count
 
                 def make_test_method(tool_version, test_index):
                     def test_tool(self):
                         self.do_it(tool_version=tool_version, test_index=test_index)
+
                     test_tool.__name__ = test_function_name
 
                     return test_tool
@@ -103,11 +121,11 @@ def build_tests(app=None,
                 test_method = make_test_method(tool_version, i)
                 test_method.__doc__ = "( %s ) > Test-%d" % (tool_id, all_versions_test_count + 1)
                 namespace[test_function_name] = test_method
-                namespace['tool_id'] = tool_id
+                namespace["tool_id"] = tool_id
                 namespace["galaxy_interactor"] = galaxy_interactor
-                namespace['master_api_key'] = master_api_key
-                namespace['user_api_key'] = user_api_key or galaxy_interactor.api_key
-                namespace['test_count'] = count
+                namespace["master_api_key"] = master_api_key
+                namespace["user_api_key"] = user_api_key or galaxy_interactor.api_key
+                namespace["test_count"] = count
 
                 all_versions_test_count += 1
 
diff --git a/test/functional/test_toolbox_pytest.py b/test/functional/test_toolbox_pytest.py
index 0b31344c99a..36114dd47cd 100644
--- a/test/functional/test_toolbox_pytest.py
+++ b/test/functional/test_toolbox_pytest.py
@@ -1,15 +1,15 @@
 import os
 import sys
 
-galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir + '/' + os.path.pardir))
+galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir + "/" + os.path.pardir))
 sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")]
 
 import pytest
 
 from galaxy_test.driver import driver_util
 
-SKIPTEST = os.path.join(os.path.dirname(__file__), 'known_broken_tools.txt')
-TEST_PREFIX = 'TestForTool_'
+SKIPTEST = os.path.join(os.path.dirname(__file__), "known_broken_tools.txt")
+TEST_PREFIX = "TestForTool_"
 
 
 class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
@@ -18,6 +18,7 @@ class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
     Just populate non-shed tool tests and run tests. Works
     for tool tests, regular twill tests, and API testing.
     """
+
     conda_auto_init = True
     conda_auto_install = True
 
@@ -28,7 +29,7 @@ class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
 
 def get_skiplist():
     with open(SKIPTEST) as skiptest:
-        skiplist = [line.strip() for line in skiptest if line.strip() and not line.startswith('#')]
+        skiplist = [line.strip() for line in skiptest if line.strip() and not line.startswith("#")]
         return skiplist
 
 
@@ -38,7 +39,7 @@ def galaxy_driver():
     return driver
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def driver(request):
     request.addfinalizer(DRIVER.tear_down)
     return DRIVER
@@ -67,7 +68,7 @@ def cases():
             test = (test_instance.tool_id + "_test_%d" % (index + 1), test_instance, index)
             marks = []
             marks.append(pytest.mark.skipif(test_instance.tool_id in skiplist, reason="tool in skiplist"))
-            if 'data_manager_' in test_instance.tool_id:
+            if "data_manager_" in test_instance.tool_id:
                 marks.append(pytest.mark.data_manager(test))
             else:
                 marks.append(pytest.mark.tool(test))
diff --git a/test/functional/tools/code_file.py b/test/functional/tools/code_file.py
index a2c03fdd137..3de0b30920c 100644
--- a/test/functional/tools/code_file.py
+++ b/test/functional/tools/code_file.py
@@ -1,8 +1,8 @@
 def validate_input(trans, error_map, param_values, page_param_map):
     """
-        Validates the user input, before execution.
+    Validates the user input, before execution.
     """
-    first = param_values['name1']
-    second = param_values['name2']
+    first = param_values["name1"]
+    second = param_values["name2"]
     if first == second:
-        error_map['name1'] = "The value names should be different."
+        error_map["name1"] = "The value names should be different."
diff --git a/test/functional/tools/directory_uri_copy_to.py b/test/functional/tools/directory_uri_copy_to.py
index 487a8a6c1f6..7bc067bae9b 100644
--- a/test/functional/tools/directory_uri_copy_to.py
+++ b/test/functional/tools/directory_uri_copy_to.py
@@ -28,16 +28,15 @@ def main(argv=None):
         target_uri = directory_uri + "/helloworld"
     file_source_path = file_sources.get_file_source_path(target_uri)
     file_source = file_source_path.file_source
-    with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
-        f.write('hello world!\n')
+    with tempfile.NamedTemporaryFile(mode="w", delete=False) as f:
+        f.write("hello world!\n")
     file_source.write_from(file_source_path.path, f.name)
 
 
 def _parser():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--directory_uri', type=str,
-                        help='directory target URI')
-    parser.add_argument('--file_sources', type=str, help='file sources json')
+    parser.add_argument("--directory_uri", type=str, help="directory target URI")
+    parser.add_argument("--file_sources", type=str, help="file sources json")
     return parser
 
 
diff --git a/test/functional/tools/python_environment_problem.py b/test/functional/tools/python_environment_problem.py
index 19bc7305b01..2638e9632e0 100644
--- a/test/functional/tools/python_environment_problem.py
+++ b/test/functional/tools/python_environment_problem.py
@@ -8,5 +8,5 @@ def main():
         f.write("out_file1")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/test/functional/webhooks/phdcomics/__init__.py b/test/functional/webhooks/phdcomics/__init__.py
index a5979760d66..275a03b0eb1 100644
--- a/test/functional/webhooks/phdcomics/__init__.py
+++ b/test/functional/webhooks/phdcomics/__init__.py
@@ -7,8 +7,8 @@ log = logging.getLogger(__name__)
 
 
 def main(trans, webhook, params):
-    error = ''
-    comic_src = ''
+    error = ""
+    comic_src = ""
 
     try:
         # Third-party dependencies
@@ -16,33 +16,31 @@ def main(trans, webhook, params):
             from bs4 import BeautifulSoup
         except ImportError as e:
             log.exception(e)
-            return {'success': False, 'error': str(e)}
+            return {"success": False, "error": str(e)}
 
         # Get latest id
-        if 'latest_id' not in webhook.config.keys():
-            url = 'http://phdcomics.com/gradfeed.php'
+        if "latest_id" not in webhook.config.keys():
+            url = "http://phdcomics.com/gradfeed.php"
             content = urlopen(url).read()
-            soap = BeautifulSoup(content, 'html.parser')
-            pattern = r'(?:http://www\.phdcomics\.com/comics\.php\?f=)(\d+)'
-            webhook.config['latest_id'] = max(
-                int(re.search(pattern, link.text).group(1))
-                for link in soap.find_all('link', text=re.compile(pattern))
+            soap = BeautifulSoup(content, "html.parser")
+            pattern = r"(?:http://www\.phdcomics\.com/comics\.php\?f=)(\d+)"
+            webhook.config["latest_id"] = max(
+                int(re.search(pattern, link.text).group(1)) for link in soap.find_all("link", text=re.compile(pattern))
             )
 
-        random_id = random.randint(1, webhook.config['latest_id'])
-        url = 'http://www.phdcomics.com/comics/archive.php?comicid=%d' % \
-            random_id
+        random_id = random.randint(1, webhook.config["latest_id"])
+        url = "http://www.phdcomics.com/comics/archive.php?comicid=%d" % random_id
         content = urlopen(url).read()
-        soup = BeautifulSoup(content, 'html.parser')
-        comic_img = soup.find_all('img', id='comic2')
+        soup = BeautifulSoup(content, "html.parser")
+        comic_img = soup.find_all("img", id="comic2")
 
         try:
-            comic_src = comic_img[0].attrs.get('src')
+            comic_src = comic_img[0].attrs.get("src")
         except IndexError:
-            pattern = r'<img id=comic2 name=comic2 src=([\w:\/\.]+)'
+            pattern = r"<img id=comic2 name=comic2 src=([\w:\/\.]+)"
             comic_src = re.search(pattern, content).group(1)
 
     except Exception as e:
         error = str(e)
 
-    return {'success': not error, 'error': error, 'src': comic_src}
+    return {"success": not error, "error": error, "src": comic_src}
diff --git a/test/functional/webhooks/trans_object/__init__.py b/test/functional/webhooks/trans_object/__init__.py
index dafa10e7d62..172d407c863 100644
--- a/test/functional/webhooks/trans_object/__init__.py
+++ b/test/functional/webhooks/trans_object/__init__.py
@@ -2,5 +2,5 @@ def main(trans, webhook, params):
     if trans.user:
         user = trans.user.username
     else:
-        user = 'No user is logged in.'
-    return {'username': user}
+        user = "No user is logged in."
+    return {"username": user}
diff --git a/test/integration/chained_dyndest_rules/module2/rules.py b/test/integration/chained_dyndest_rules/module2/rules.py
index afe0d6dcc0c..1d7ea5c6eab 100644
--- a/test/integration/chained_dyndest_rules/module2/rules.py
+++ b/test/integration/chained_dyndest_rules/module2/rules.py
@@ -11,10 +11,13 @@ def dyndest_chain_2(tmp_dir_prefix):
     # Chain to yet a third
     return JobDestination(
         runner="dynamic",
-        params={'type': 'python',
-                'function': 'dyndest_chain_3',
-                'rules_module': 'integration.chained_dyndest_rules.module3',
-                'tmp_dir_prefix_two': '%sand2' % tmp_dir_prefix})
+        params={
+            "type": "python",
+            "function": "dyndest_chain_3",
+            "rules_module": "integration.chained_dyndest_rules.module3",
+            "tmp_dir_prefix_two": "%sand2" % tmp_dir_prefix,
+        },
+    )
 
 
 def dyndest_chain_3():
diff --git a/test/integration/chained_dyndest_rules/module3/rules.py b/test/integration/chained_dyndest_rules/module3/rules.py
index 61fd78aba41..f329428f24e 100644
--- a/test/integration/chained_dyndest_rules/module3/rules.py
+++ b/test/integration/chained_dyndest_rules/module3/rules.py
@@ -14,6 +14,5 @@ def dyndest_chain_2():
 
 
 def dyndest_chain_3(tmp_dir_prefix_two):
-    tmp_dir = '$(mktemp -d -p $(pwd) %sand3XXXXXXXXXXXX)' % tmp_dir_prefix_two
-    return JobDestination(runner="local",
-                          params={'tmp_dir': tmp_dir})
+    tmp_dir = "$(mktemp -d -p $(pwd) %sand3XXXXXXXXXXXX)" % tmp_dir_prefix_two
+    return JobDestination(runner="local", params={"tmp_dir": tmp_dir})
diff --git a/test/integration/cloudauthz/test_cloudauthz.py b/test/integration/cloudauthz/test_cloudauthz.py
index 49a23c383b3..d3dda565b69 100644
--- a/test/integration/cloudauthz/test_cloudauthz.py
+++ b/test/integration/cloudauthz/test_cloudauthz.py
@@ -26,11 +26,7 @@ class DefineCloudAuthzTestCase(integration_util.IntegrationTestCase):
             # The payload for the POST API.
             payload = {
                 "provider": provider,
-                "config": json.dumps({
-                    "tenant_id": tenant_id,
-                    "client_id": client_id,
-                    "client_secret": client_secret
-                })
+                "config": json.dumps({"tenant_id": tenant_id, "client_id": client_id, "client_secret": client_secret}),
             }
 
             response = self._post(path="cloud/authz", data=payload)
diff --git a/test/integration/conftest.py b/test/integration/conftest.py
index f1b9e2923ca..a20c1038f61 100644
--- a/test/integration/conftest.py
+++ b/test/integration/conftest.py
@@ -9,6 +9,7 @@ def pytest_collection_finish(session):
     try:
         # This needs to be run after test collection
         from .test_config_defaults import DRIVER
+
         DRIVER.tear_down()
         print("Galaxy test driver shutdown successful")
     except Exception:
@@ -17,5 +18,5 @@ def pytest_collection_finish(session):
 
 @pytest.fixture
 def temp_file():
-    with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh:
+    with tempfile.NamedTemporaryFile(delete=True, mode="wb") as fh:
         yield fh
diff --git a/test/integration/objectstore/_base.py b/test/integration/objectstore/_base.py
index 9f2282dbf13..521c33d172e 100644
--- a/test/integration/objectstore/_base.py
+++ b/test/integration/objectstore/_base.py
@@ -3,17 +3,15 @@ import re
 import string
 import subprocess
 
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
-
-OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_HOST', '127.0.0.1')
-OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_PORT', 9000))
-OBJECT_STORE_ACCESS_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_ACCESS_KEY', 'minioadmin')
-OBJECT_STORE_SECRET_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_SECRET_KEY', 'minioadmin')
-OBJECT_STORE_CONFIG = string.Template("""
+OBJECT_STORE_HOST = os.environ.get("GALAXY_INTEGRATION_OBJECT_STORE_HOST", "127.0.0.1")
+OBJECT_STORE_PORT = int(os.environ.get("GALAXY_INTEGRATION_OBJECT_STORE_PORT", 9000))
+OBJECT_STORE_ACCESS_KEY = os.environ.get("GALAXY_INTEGRATION_OBJECT_STORE_ACCESS_KEY", "minioadmin")
+OBJECT_STORE_SECRET_KEY = os.environ.get("GALAXY_INTEGRATION_OBJECT_STORE_SECRET_KEY", "minioadmin")
+OBJECT_STORE_CONFIG = string.Template(
+    """
 <object_store type="hierarchical" id="primary">
     <backends>
         <object_store id="swifty" type="swift" weight="1" order="0">
@@ -26,27 +24,29 @@ OBJECT_STORE_CONFIG = string.Template("""
         </object_store>
     </backends>
 </object_store>
-""")
+"""
+)
 
 
 def start_minio(container_name):
     minio_start_args = [
-        'docker',
-        'run',
-        '-p',
-        f'{OBJECT_STORE_PORT}:9000',
-        '-d',
-        '--name',
+        "docker",
+        "run",
+        "-p",
+        f"{OBJECT_STORE_PORT}:9000",
+        "-d",
+        "--name",
         container_name,
-        '--rm',
-        'minio/minio:latest',
-        'server',
-        '/tmp/data']
+        "--rm",
+        "minio/minio:latest",
+        "server",
+        "/tmp/data",
+    ]
     subprocess.check_call(minio_start_args)
 
 
 def stop_minio(container_name):
-    subprocess.check_call(['docker', 'rm', '-f', container_name])
+    subprocess.check_call(["docker", "rm", "-f", container_name])
 
 
 class BaseObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
diff --git a/test/integration/objectstore/test_jobs.py b/test/integration/objectstore/test_jobs.py
index 559e4f813d5..4bafed5c965 100644
--- a/test/integration/objectstore/test_jobs.py
+++ b/test/integration/objectstore/test_jobs.py
@@ -3,9 +3,13 @@
 import os
 import string
 
-from ._base import BaseObjectStoreIntegrationTestCase, files_count
+from ._base import (
+    BaseObjectStoreIntegrationTestCase,
+    files_count,
+)
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
+    """<?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>
         <object_store type="distributed" id="primary" order="0">
@@ -29,7 +33,8 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0
         </object_store>
     </backends>
 </object_store>
-""")
+"""
+)
 
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
diff --git a/test/integration/objectstore/test_mixed_store_by.py b/test/integration/objectstore/test_mixed_store_by.py
index e976cdd4f87..b11e9751a52 100644
--- a/test/integration/objectstore/test_mixed_store_by.py
+++ b/test/integration/objectstore/test_mixed_store_by.py
@@ -5,9 +5,13 @@ import re
 import string
 
 from galaxy.util import is_uuid
-from ._base import BaseObjectStoreIntegrationTestCase, files_count
+from ._base import (
+    BaseObjectStoreIntegrationTestCase,
+    files_count,
+)
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
+    """<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="files1" type="disk" weight="1" store_by="uuid">
@@ -22,7 +26,8 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0
         </backend>
     </backends>
 </object_store>
-""")
+"""
+)
 
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
@@ -37,8 +42,7 @@ class MixedStoreByObjectStoreIntegrationTestCase(BaseObjectStoreIntegrationTestC
         cls._configure_object_store(DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE, config)
 
     def test_both_types(self):
-        """Test each object store configures files correctly.
-        """
+        """Test each object store configures files correctly."""
         i = 0
         with self.dataset_populator.test_history() as history_id:
             # Loop breaks once each object store has at least once file of each type.
@@ -52,10 +56,12 @@ class MixedStoreByObjectStoreIntegrationTestCase(BaseObjectStoreIntegrationTestC
                     break
                 i += 1
                 if i > 50:
-                    raise Exception("Problem with logic of test, randomly each object store should have at least one file by now")
+                    raise Exception(
+                        "Problem with logic of test, randomly each object store should have at least one file by now"
+                    )
 
             def strip_to_id(x):
-                match = re.match(r'dataset_(.*)\.dat', os.path.basename(x))
+                match = re.match(r"dataset_(.*)\.dat", os.path.basename(x))
                 assert match
                 return match.group(1)
 
diff --git a/test/integration/objectstore/test_objectstore_datatype_upload.py b/test/integration/objectstore/test_objectstore_datatype_upload.py
index de0a24a2091..0230c587cd8 100644
--- a/test/integration/objectstore/test_objectstore_datatype_upload.py
+++ b/test/integration/objectstore/test_objectstore_datatype_upload.py
@@ -11,21 +11,22 @@ from galaxy_test.driver import integration_util
 from ..test_datatype_upload import (
     TEST_CASES,
     upload_datatype_helper,
-    UploadTestDatatypeDataTestCase
+    UploadTestDatatypeDataTestCase,
 )
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-IRODS_OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_HOST', 'localhost')
-IRODS_OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PORT', 1247))
-IRODS_OBJECT_STORE_TIMEOUT = int(os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_TIMEOUT', 30))
-IRODS_OBJECT_STORE_POOLSIZE = int(os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_POOLSIZE', 3))
-IRODS_OBJECT_STORE_USERNAME = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_USERNAME', 'rods')
-IRODS_OBJECT_STORE_PASSWORD = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PASSWORD', 'rods')
-IRODS_OBJECT_STORE_RESOURCE = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_RESOURCE', 'demoResc')
-IRODS_OBJECT_STORE_ZONE = os.environ.get('GALAXY_INTEGRATION_IRODS_OBJECT_STORE_ZONE', 'tempZone')
+IRODS_OBJECT_STORE_HOST = os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_HOST", "localhost")
+IRODS_OBJECT_STORE_PORT = int(os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PORT", 1247))
+IRODS_OBJECT_STORE_TIMEOUT = int(os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_TIMEOUT", 30))
+IRODS_OBJECT_STORE_POOLSIZE = int(os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_POOLSIZE", 3))
+IRODS_OBJECT_STORE_USERNAME = os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_USERNAME", "rods")
+IRODS_OBJECT_STORE_PASSWORD = os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_PASSWORD", "rods")
+IRODS_OBJECT_STORE_RESOURCE = os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_RESOURCE", "demoResc")
+IRODS_OBJECT_STORE_ZONE = os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_ZONE", "tempZone")
 # Run test for only the first 10 test files
 TEST_CASES = dict(list(TEST_CASES.items())[0:10])
-DISTRIBUTED_OBJECT_STORE_CONFIG = string.Template("""
+DISTRIBUTED_OBJECT_STORE_CONFIG = string.Template(
+    """
 <object_store type="distributed">
     <backends>
         <backend id="files1" type="disk" weight="1">
@@ -40,8 +41,10 @@ DISTRIBUTED_OBJECT_STORE_CONFIG = string.Template("""
         </backend>
     </backends>
 </object_store>
-""")
-DISTRIBUTED_IRODS_OBJECT_STORE_CONFIG = string.Template("""
+"""
+)
+DISTRIBUTED_IRODS_OBJECT_STORE_CONFIG = string.Template(
+    """
 <object_store type="distributed">
     <backends>
         <backend id="files1" type="disk" weight="1">
@@ -60,8 +63,10 @@ DISTRIBUTED_IRODS_OBJECT_STORE_CONFIG = string.Template("""
         </backend>
     </backends>
 </object_store>
-""")
-IRODS_OBJECT_STORE_CONFIG = string.Template("""<object_store type="irods">
+"""
+)
+IRODS_OBJECT_STORE_CONFIG = string.Template(
+    """<object_store type="irods">
     <auth username="${username}" password="${password}"/>
     <resource name="${resource}"/>
     <zone name="${zone}"/>
@@ -70,30 +75,26 @@ IRODS_OBJECT_STORE_CONFIG = string.Template("""<object_store type="irods">
     <extra_dir type="job_work" path="${temp_directory}/job_working_directory_irods"/>
     <extra_dir type="temp" path="${temp_directory}/tmp_irods"/>
 </object_store>
-""")
+"""
+)
 
 
 def check_container_active(container_name):
-    return subprocess.call([
-        'docker',
-        'inspect',
-        '-f',
-        '{{.State.Running}}',
-        container_name
-    ]) == 0
+    return subprocess.call(["docker", "inspect", "-f", "{{.State.Running}}", container_name]) == 0
 
 
 def start_irods(container_name):
     if not check_container_active(container_name):
         irods_start_args = [
-            'docker',
-            'run',
-            '-p',
-            '1247:1247',
-            '-d',
-            '--name',
+            "docker",
+            "run",
+            "-p",
+            "1247:1247",
+            "-d",
+            "--name",
             container_name,
-            'kxk302/irods-server:0.1']
+            "kxk302/irods-server:0.1",
+        ]
         subprocess.check_call(irods_start_args)
 
         # Sleep so integration test's iRODS instance is up and running
@@ -102,7 +103,7 @@ def start_irods(container_name):
 
 def stop_irods(container_name):
     if check_container_active(container_name):
-        subprocess.check_call(['docker', 'rm', '-f', container_name])
+        subprocess.check_call(["docker", "rm", "-f", container_name])
 
 
 class BaseObjectstoreUploadTest(UploadTestDatatypeDataTestCase):
@@ -153,7 +154,7 @@ class IrodsUploadTestDatatypeDataTestCase(BaseObjectstoreUploadTest):
             "username": IRODS_OBJECT_STORE_USERNAME,
             "password": IRODS_OBJECT_STORE_PASSWORD,
             "resource": IRODS_OBJECT_STORE_RESOURCE,
-            "zone": IRODS_OBJECT_STORE_ZONE
+            "zone": IRODS_OBJECT_STORE_ZONE,
         }
 
 
@@ -163,7 +164,7 @@ class UploadTestDosDiskAndDiskTestCase(BaseObjectstoreUploadTest):
 
     @classmethod
     def get_object_store_kwargs(cls):
-        return {'temp_directory': cls.object_stores_parent}
+        return {"temp_directory": cls.object_stores_parent}
 
 
 class UploadTestDosIrodsAndDiskTestCase(IrodsUploadTestDatatypeDataTestCase):
@@ -176,16 +177,16 @@ irods_instance = integration_util.integration_module_instance(IrodsUploadTestDat
 distributed_and_irods_instance = integration_util.integration_module_instance(UploadTestDosIrodsAndDiskTestCase)
 
 
-@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+@pytest.mark.parametrize("test_data", TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_dos_disk_and_disk(distributed_instance, test_data, temp_file):
     upload_datatype_helper(distributed_instance, test_data, temp_file)
 
 
-@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+@pytest.mark.parametrize("test_data", TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_irods(irods_instance, test_data, temp_file):
     upload_datatype_helper(irods_instance, test_data, temp_file, True)
 
 
-@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+@pytest.mark.parametrize("test_data", TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_dos_irods_and_disk(distributed_and_irods_instance, test_data, temp_file):
     upload_datatype_helper(distributed_and_irods_instance, test_data, temp_file)
diff --git a/test/integration/objectstore/test_remote_objectstore_cache_operations.py b/test/integration/objectstore/test_remote_objectstore_cache_operations.py
index f922989370d..8e7d396c398 100644
--- a/test/integration/objectstore/test_remote_objectstore_cache_operations.py
+++ b/test/integration/objectstore/test_remote_objectstore_cache_operations.py
@@ -10,7 +10,6 @@ from ._base import (
 
 
 class CacheOperationTestCase(BaseSwiftObjectStoreIntegrationTestCase):
-
     def tearDown(self):
         shutil.rmtree(self.object_store_cache_path)
         os.mkdir(self.object_store_cache_path)
@@ -18,7 +17,7 @@ class CacheOperationTestCase(BaseSwiftObjectStoreIntegrationTestCase):
 
     def upload_dataset(self):
         history_id = self.dataset_populator.new_history()
-        hda = self.dataset_populator.new_dataset(history_id, content='123', wait=True)
+        hda = self.dataset_populator.new_dataset(history_id, content="123", wait=True)
         return hda
 
     def test_cache_populated(self):
@@ -31,8 +30,8 @@ class CacheOperationTestCase(BaseSwiftObjectStoreIntegrationTestCase):
         shutil.rmtree(self.object_store_cache_path)
         os.mkdir(self.object_store_cache_path)
         assert files_count(self.object_store_cache_path) == 0
-        content = self.dataset_populator.get_history_dataset_content(hda['history_id'], content_id=hda['id'])
-        assert content == '123\n'
+        content = self.dataset_populator.get_history_dataset_content(hda["history_id"], content_id=hda["id"])
+        assert content == "123\n"
         assert files_count(self.object_store_cache_path) == 1
 
     def test_delete_item_not_in_cache(self):
@@ -41,8 +40,10 @@ class CacheOperationTestCase(BaseSwiftObjectStoreIntegrationTestCase):
         shutil.rmtree(self.object_store_cache_path)
         os.mkdir(self.object_store_cache_path)
         assert files_count(self.object_store_cache_path) == 0
-        self.dataset_populator.delete_dataset(hda['history_id'], hda['id'], purge=True)
+        self.dataset_populator.delete_dataset(hda["history_id"], hda["id"], purge=True)
         # Don't wait for dataset, this uses the history state, which is new if there is no dataset ...
         with pytest.raises(AssertionError) as excinfo:
-            self.dataset_populator.get_history_dataset_content(hda['history_id'], content_id=hda['id'], wait=False, assert_ok=False)
+            self.dataset_populator.get_history_dataset_content(
+                hda["history_id"], content_id=hda["id"], wait=False, assert_ok=False
+            )
             assert "File Not Found" in str(excinfo.value)
diff --git a/test/integration/objectstore/test_selection.py b/test/integration/objectstore/test_selection.py
index fa296303209..762b0bc378b 100644
--- a/test/integration/objectstore/test_selection.py
+++ b/test/integration/objectstore/test_selection.py
@@ -3,13 +3,17 @@
 import os
 import string
 
-from ._base import BaseObjectStoreIntegrationTestCase, files_count
+from ._base import (
+    BaseObjectStoreIntegrationTestCase,
+    files_count,
+)
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_conf.xml")
 JOB_RESOURCE_PARAMETERS_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_resource_parameters_conf.xml")
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
+    """<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="default" type="disk" weight="1" name="Default Store">
@@ -35,7 +39,8 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0
         </backend>
     </backends>
 </object_store>
-""")
+"""
+)
 
 
 class ObjectStoreSelectionIntegrationTestCase(BaseObjectStoreIntegrationTestCase):
diff --git a/test/integration/objectstore_selection_rules/rules.py b/test/integration/objectstore_selection_rules/rules.py
index ded02fc33fe..8ce46d2b43f 100644
--- a/test/integration/objectstore_selection_rules/rules.py
+++ b/test/integration/objectstore_selection_rules/rules.py
@@ -10,5 +10,5 @@ def the_destination(resource_params):
     object_store_id = "dynamic_ebs"
     if how_store == "slow":
         object_store_id = "dynamic_s3"
-    job_destination.params['object_store_id'] = object_store_id
+    job_destination.params["object_store_id"] = object_store_id
     return job_destination
diff --git a/test/integration/resubmission_rules/rules.py b/test/integration/resubmission_rules/rules.py
index ec98b0e56d5..3a4b477ceaa 100644
--- a/test/integration/resubmission_rules/rules.py
+++ b/test/integration/resubmission_rules/rules.py
@@ -11,10 +11,12 @@ def dynamic_resubmit_once(resource_params):
     """Build environment that always fails first time and always re-routes to passing environment."""
     job_destination = JobDestination()
     # Always fail on the first attempt.
-    job_destination['runner'] = "failure_runner"
+    job_destination["runner"] = "failure_runner"
     # Resubmit to a valid environment.
-    job_destination['resubmit'] = [dict(
-        condition="any_failure",
-        environment="local",
-    )]
+    job_destination["resubmit"] = [
+        dict(
+            condition="any_failure",
+            environment="local",
+        )
+    ]
     return job_destination
diff --git a/test/integration/resubmission_runners.py b/test/integration/resubmission_runners.py
index ece06942a44..73da3c2e1e7 100644
--- a/test/integration/resubmission_runners.py
+++ b/test/integration/resubmission_runners.py
@@ -2,9 +2,7 @@ import time
 from typing import List
 
 from galaxy import model
-from galaxy.jobs.runners import (
-    JobState
-)
+from galaxy.jobs.runners import JobState
 from galaxy.jobs.runners.local import LocalJobRunner
 from galaxy.model.orm.now import now
 
@@ -25,10 +23,7 @@ class FailsJobRunner(LocalJobRunner):
             if run_for > 0:
                 time.sleep(run_for)
 
-        job_state = JobState(
-            job_wrapper,
-            job_wrapper.job_destination
-        )
+        job_state = JobState(job_wrapper, job_wrapper.job_destination)
         if failure_state is not None:
             job_state.runner_state = failure_state
         job_state.stop_job = False
@@ -84,4 +79,4 @@ class FailOnlyFirstJobRunner(LocalJobRunner):
             self._fail_job_local(job_wrapper, "Failing first attempt")
 
 
-__all__ = ('FailsJobRunner', 'AssertionJobRunner')
+__all__ = ("FailsJobRunner", "AssertionJobRunner")
diff --git a/test/integration/test_celery_tasks.py b/test/integration/test_celery_tasks.py
index 39700142ed4..ca8c7cc82e3 100644
--- a/test/integration/test_celery_tasks.py
+++ b/test/integration/test_celery_tasks.py
@@ -1,10 +1,19 @@
 from celery import shared_task
 
-from galaxy.celery.tasks import galaxy_task, purge_hda
+from galaxy.celery.tasks import (
+    galaxy_task,
+    purge_hda,
+)
 from galaxy.model import HistoryDatasetAssociation
 from galaxy.schema.schema import CreatePagePayload
-from galaxy_test.base.populators import DatasetPopulator, wait_on
-from galaxy_test.driver.integration_util import IntegrationTestCase, UsesCeleryTasks
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    wait_on,
+)
+from galaxy_test.driver.integration_util import (
+    IntegrationTestCase,
+    UsesCeleryTasks,
+)
 
 
 @shared_task
@@ -19,7 +28,6 @@ def process_page(request: CreatePagePayload):
 
 
 class CeleryTasksIntegrationTestCase(IntegrationTestCase, UsesCeleryTasks):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -34,7 +42,10 @@ class CeleryTasksIntegrationTestCase(IntegrationTestCase, UsesCeleryTasks):
             slug="my-cool-title",
             annotation="my cool annotation",
         )
-        assert process_page.delay(request).get(timeout=10) == "content_format is markdown with annotation my cool annotation"
+        assert (
+            process_page.delay(request).get(timeout=10)
+            == "content_format is markdown with annotation my cool annotation"
+        )
 
     def test_galaxy_task(self):
         history_id = self.dataset_populator.new_history()
@@ -43,7 +54,9 @@ class CeleryTasksIntegrationTestCase(IntegrationTestCase, UsesCeleryTasks):
         assert hda
 
         def hda_purged():
-            latest_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=dataset, assert_ok=False, wait=False)
+            latest_details = self.dataset_populator.get_history_dataset_details(
+                history_id, dataset=dataset, assert_ok=False, wait=False
+            )
             return True if latest_details["purged"] else None
 
         assert not hda_purged()
@@ -55,5 +68,9 @@ class CeleryTasksIntegrationTestCase(IntegrationTestCase, UsesCeleryTasks):
 
     @property
     def _latest_hda(self):
-        latest_hda = self._app.model.session.query(HistoryDatasetAssociation).order_by(HistoryDatasetAssociation.table.c.id.desc()).first()
+        latest_hda = (
+            self._app.model.session.query(HistoryDatasetAssociation)
+            .order_by(HistoryDatasetAssociation.table.c.id.desc())
+            .first()
+        )
         return latest_hda
diff --git a/test/integration/test_chained_dynamic_destinations.py b/test/integration/test_chained_dynamic_destinations.py
index c684bc2533b..60a82edd776 100644
--- a/test/integration/test_chained_dynamic_destinations.py
+++ b/test/integration/test_chained_dynamic_destinations.py
@@ -3,9 +3,7 @@
 import os
 import tempfile
 
-from galaxy_test.base.populators import (
-    skip_without_tool,
-)
+from galaxy_test.base.populators import skip_without_tool
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
@@ -13,7 +11,6 @@ CHAINED_DYNDESTS_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "chained_dyndest_jo
 
 
 class ChainedDynamicDestinationIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = tempfile.mkdtemp()
diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index d621a1c2175..abadc70fe03 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -6,7 +6,10 @@ import sys
 import tempfile
 import time
 import unittest
-from typing import ClassVar, NamedTuple
+from typing import (
+    ClassVar,
+    NamedTuple,
+)
 
 from galaxy.security.ssh_util import generate_ssh_keys
 from galaxy_test.base.populators import skip_without_tool
@@ -24,44 +27,47 @@ class RemoteConnection(NamedTuple):
     public_key: str
 
 
-def start_ssh_docker(container_name, jobs_directory, port=10022, image='agaveapi/slurm') -> RemoteConnection:
+def start_ssh_docker(container_name, jobs_directory, port=10022, image="agaveapi/slurm") -> RemoteConnection:
     ssh_keys = generate_ssh_keys()
-    START_SLURM_DOCKER = ['docker',
-                          'run',
-                          '-h',
-                          'localhost',
-                          '-p',
-                          f'{port}:22',
-                          '-d',
-                          '--name',
-                          container_name,
-                          '--rm',
-                          '--privileged',  # for torque
-                          '-v',
-                          "{jobs_directory}:{jobs_directory}".format(jobs_directory=jobs_directory),
-                          "-v",
-                          f"{ssh_keys.public_key_file}:/home/testuser/.ssh/authorized_keys",
-                          '--ulimit',
-                          'nofile=2048:2048',
-                          image]
+    START_SLURM_DOCKER = [
+        "docker",
+        "run",
+        "-h",
+        "localhost",
+        "-p",
+        f"{port}:22",
+        "-d",
+        "--name",
+        container_name,
+        "--rm",
+        "--privileged",  # for torque
+        "-v",
+        "{jobs_directory}:{jobs_directory}".format(jobs_directory=jobs_directory),
+        "-v",
+        f"{ssh_keys.public_key_file}:/home/testuser/.ssh/authorized_keys",
+        "--ulimit",
+        "nofile=2048:2048",
+        image,
+    ]
     subprocess.check_call(START_SLURM_DOCKER)
-    if 'openpbs' in image:
+    if "openpbs" in image:
         time.sleep(PBS_STARTUP_DELAY)
-    if sys.platform != 'darwin':
+    if sys.platform != "darwin":
         # Change testuser's uid to match current user id. This ensures that /home/testuser/.ssh/authorized_keys
         # is owned by the right user and that job outputs can be cleaned up.
-        subprocess.check_call(['docker', 'exec', container_name, 'usermod', '-u', str(os.getuid()), 'testuser'])
-    return RemoteConnection('localhost', 'testuser', port, ssh_keys.private_key_file, ssh_keys.public_key_file)
+        subprocess.check_call(["docker", "exec", container_name, "usermod", "-u", str(os.getuid()), "testuser"])
+    return RemoteConnection("localhost", "testuser", port, ssh_keys.private_key_file, ssh_keys.public_key_file)
 
 
 def stop_ssh_docker(container_name, remote_connection):
-    subprocess.check_call(['docker', 'rm', '-f', container_name])
+    subprocess.check_call(["docker", "rm", "-f", container_name])
     os.remove(remote_connection.private_key)
     os.remove(remote_connection.public_key)
 
 
-def cli_job_config(remote_connection, shell_plugin='ParamikoShell', job_plugin='Slurm'):
-    job_conf_template = string.Template("""<job_conf>
+def cli_job_config(remote_connection, shell_plugin="ParamikoShell", job_plugin="Slurm"):
+    job_conf_template = string.Template(
+        """<job_conf>
     <plugins>
         <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="1"/>
     </plugins>
@@ -79,10 +85,11 @@ def cli_job_config(remote_connection, shell_plugin='ParamikoShell', job_plugin='
         </destination>
     </destinations>
 </job_conf>
-""")
-    job_conf_str = job_conf_template.substitute(shell_plugin=shell_plugin,
-                                                job_plugin=job_plugin,
-                                                **remote_connection._asdict())
+"""
+    )
+    job_conf_str = job_conf_template.substitute(
+        shell_plugin=shell_plugin, job_plugin=job_plugin, **remote_connection._asdict()
+    )
     with tempfile.NamedTemporaryFile(suffix="_slurm_integration_job_conf.xml", mode="w", delete=False) as job_conf:
         job_conf.write(job_conf_str)
     return job_conf.name
@@ -103,9 +110,9 @@ class BaseCliIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
             raise unittest.SkipTest("Base class")
         cls.container_name = "%s_container" % cls.__name__
         cls.jobs_directory = tempfile.mkdtemp()
-        cls.remote_connection = start_ssh_docker(container_name=cls.container_name,
-                                                 jobs_directory=cls.jobs_directory,
-                                                 image=cls.image)
+        cls.remote_connection = start_ssh_docker(
+            container_name=cls.container_name, jobs_directory=cls.jobs_directory, image=cls.image
+        )
         super().setUpClass()
 
     @classmethod
@@ -117,32 +124,32 @@ class BaseCliIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
     def handle_galaxy_config_kwds(cls, config):
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
-        config["job_config_file"] = cli_job_config(remote_connection=cls.remote_connection,
-                                                   shell_plugin=cls.shell_plugin,
-                                                   job_plugin=cls.job_plugin)
+        config["job_config_file"] = cli_job_config(
+            remote_connection=cls.remote_connection, shell_plugin=cls.shell_plugin, job_plugin=cls.job_plugin
+        )
 
     @skip_without_tool("job_environment_default")
     def test_running_cli_job(self):
         job_env = self._run_and_get_environment_properties()
-        assert job_env.some_env == '42'
+        assert job_env.some_env == "42"
 
 
 class OpenPBSSetup:
-    job_plugin = 'OpenPBS'
-    image = 'mvdbeek/galaxy-integration-docker-images:openpbs-22.01'
+    job_plugin = "OpenPBS"
+    image = "mvdbeek/galaxy-integration-docker-images:openpbs-22.01"
 
 
 class SlurmSetup:
-    job_plugin = 'Slurm'
-    image = 'mvdbeek/galaxy-integration-docker-images:slurm-22.01'
+    job_plugin = "Slurm"
+    image = "mvdbeek/galaxy-integration-docker-images:slurm-22.01"
 
 
 class ParamikoShell:
-    shell_plugin = 'ParamikoShell'
+    shell_plugin = "ParamikoShell"
 
 
 class SecureShell:
-    shell_plugin = 'SecureShell'
+    shell_plugin = "SecureShell"
 
 
 class ParamikoCliSlurmIntegrationTestCase(SlurmSetup, ParamikoShell, BaseCliIntegrationTestCase):
diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index 5938e6957ce..fde3adc5212 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -35,69 +35,69 @@ import pytest
 from galaxy.util import listify
 from galaxy_test.driver.driver_util import GalaxyTestDriver
 
-OptionData = namedtuple('OptionData', ('key', 'expected', 'loaded'))
+OptionData = namedtuple("OptionData", ("key", "expected", "loaded"))
 
 driver_created = False
 
 # Configuration properties that are paths should be absolute paths, by default resolved w.r.t root.
 PATH_CONFIG_PROPERTIES = [
     # For now, these include base config properties
-    'root',
-    'config_file',
-    'config_dir',
-    'managed_config_dir',
-    'cache_dir',
-    'data_dir',
-    'auth_config_file',
-    'email_domain_blocklist_file',
-    'builds_file_path',
-    'citation_cache_data_dir',
-    'citation_cache_lock_dir',
-    'cluster_files_directory',
-    'container_resolvers_config_file',
-    'data_manager_config_file',
-    'datatypes_config_file',
-    'dependency_resolvers_config_file',
-    'file_path',
-    'file_sources_config_file',
-    'ftp_upload_dir',
-    'galaxy_data_manager_data_path',
-    'integrated_tool_panel_config',
-    'interactive_environment_plugins_directory',
-    'involucro_path',
-    'job_config_file',
-    'job_resource_params_file',
-    'job_working_directory',
-    'len_file_path',
-    'library_import_dir',
-    'markdown_export_css',
-    'markdown_export_css_pages',
-    'markdown_export_css_invocation_reports',
-    'migrated_tools_config',
-    'new_file_path',
-    'nginx_upload_job_files_path',
-    'nginx_upload_job_files_store',
-    'nginx_upload_path',
-    'object_store_config_file',
-    'oidc_backends_config_file',
-    'oidc_config_file',
-    'sanitize_allowlist_file',
-    'shed_data_manager_config_file',
-    'shed_tool_config_file',
-    'shed_tool_data_path',
-    'shed_tool_data_table_config',
-    'template_cache_path',
-    'tool_data_path',
-    'tool_dependency_cache_dir',
-    'tool_path',
-    'tool_sheds_config_file',
-    'trs_servers_config_file',
-    'user_preferences_extra_conf_path',
-    'vault_config_file',
-    'webhooks_dir',
-    'workflow_resource_params_file',
-    'workflow_resource_params_mapper',
-    'workflow_schedulers_config_file',
+    "root",
+    "config_file",
+    "config_dir",
+    "managed_config_dir",
+    "cache_dir",
+    "data_dir",
+    "auth_config_file",
+    "email_domain_blocklist_file",
+    "builds_file_path",
+    "citation_cache_data_dir",
+    "citation_cache_lock_dir",
+    "cluster_files_directory",
+    "container_resolvers_config_file",
+    "data_manager_config_file",
+    "datatypes_config_file",
+    "dependency_resolvers_config_file",
+    "file_path",
+    "file_sources_config_file",
+    "ftp_upload_dir",
+    "galaxy_data_manager_data_path",
+    "integrated_tool_panel_config",
+    "interactive_environment_plugins_directory",
+    "involucro_path",
+    "job_config_file",
+    "job_resource_params_file",
+    "job_working_directory",
+    "len_file_path",
+    "library_import_dir",
+    "markdown_export_css",
+    "markdown_export_css_pages",
+    "markdown_export_css_invocation_reports",
+    "migrated_tools_config",
+    "new_file_path",
+    "nginx_upload_job_files_path",
+    "nginx_upload_job_files_store",
+    "nginx_upload_path",
+    "object_store_config_file",
+    "oidc_backends_config_file",
+    "oidc_config_file",
+    "sanitize_allowlist_file",
+    "shed_data_manager_config_file",
+    "shed_tool_config_file",
+    "shed_tool_data_path",
+    "shed_tool_data_table_config",
+    "template_cache_path",
+    "tool_data_path",
+    "tool_dependency_cache_dir",
+    "tool_path",
+    "tool_sheds_config_file",
+    "trs_servers_config_file",
+    "user_preferences_extra_conf_path",
+    "vault_config_file",
+    "webhooks_dir",
+    "workflow_resource_params_file",
+    "workflow_resource_params_mapper",
+    "workflow_schedulers_config_file",
 ]
 # TODO: fix or mark as not absolute (2 are lists):
 # - 'tool_config_file',
@@ -110,118 +110,118 @@ PATH_CONFIG_PROPERTIES = [
 
 # Most of these (except root_dir) will go away once path_resolves_to is set in the schema
 RESOLVE = {
-    'auth_config_file': 'config_dir',
-    'builds_file_path': 'tool_data_path',
-    'dependency_resolvers_config_file': 'config_dir',
-    'integrated_tool_panel_config': 'managed_config_dir',
-    'involucro_path': 'root_dir',
-    'file_sources_config_file': 'config_dir',
-    'job_resource_params_file': 'config_dir',
-    'len_file_path': 'tool_data_path',
-    'object_store_config_file': 'config_dir',
-    'oidc_backends_config_file': 'config_dir',
-    'oidc_config_file': 'config_dir',
-    'trs_servers_config_file': 'config_dir',
-    'sanitize_allowlist_file': 'managed_config_dir',
-    'shed_data_manager_config_file': 'managed_config_dir',
-    'shed_tool_config_file': 'managed_config_dir',
-    'shed_tool_data_path': 'tool_data_path',
-    'shed_tool_data_table_config': 'managed_config_dir',
-    'tool_data_path': 'root_dir',
-    'tool_path': 'root_dir',
-    'tool_sheds_config_file': 'config_dir',
-    'user_preferences_extra_conf_path': 'config_dir',
-    'vault_config_file': 'config_dir',
-    'workflow_resource_params_file': 'config_dir',
-    'workflow_schedulers_config_file': 'config_dir',
+    "auth_config_file": "config_dir",
+    "builds_file_path": "tool_data_path",
+    "dependency_resolvers_config_file": "config_dir",
+    "integrated_tool_panel_config": "managed_config_dir",
+    "involucro_path": "root_dir",
+    "file_sources_config_file": "config_dir",
+    "job_resource_params_file": "config_dir",
+    "len_file_path": "tool_data_path",
+    "object_store_config_file": "config_dir",
+    "oidc_backends_config_file": "config_dir",
+    "oidc_config_file": "config_dir",
+    "trs_servers_config_file": "config_dir",
+    "sanitize_allowlist_file": "managed_config_dir",
+    "shed_data_manager_config_file": "managed_config_dir",
+    "shed_tool_config_file": "managed_config_dir",
+    "shed_tool_data_path": "tool_data_path",
+    "shed_tool_data_table_config": "managed_config_dir",
+    "tool_data_path": "root_dir",
+    "tool_path": "root_dir",
+    "tool_sheds_config_file": "config_dir",
+    "user_preferences_extra_conf_path": "config_dir",
+    "vault_config_file": "config_dir",
+    "workflow_resource_params_file": "config_dir",
+    "workflow_schedulers_config_file": "config_dir",
 }
 
 
 def expected_default_config_dir(value):
     # expected absolute path to the default config dir (when NO galaxy.yml provided)
-    return os.path.join(DRIVER.app.config.root, 'lib', 'galaxy', 'config', 'sample')
+    return os.path.join(DRIVER.app.config.root, "lib", "galaxy", "config", "sample")
 
 
 CUSTOM = {
-    'config_dir': expected_default_config_dir,
-    'password_expiration_period': timedelta,
-    'toolbox_filter_base_modules': listify,
-    'mulled_channels': listify,
-    'user_library_import_symlink_allowlist': listify,
-    'tool_filters': listify,
-    'tool_label_filters': listify,
-    'tool_section_filters': listify,
+    "config_dir": expected_default_config_dir,
+    "password_expiration_period": timedelta,
+    "toolbox_filter_base_modules": listify,
+    "mulled_channels": listify,
+    "user_library_import_symlink_allowlist": listify,
+    "tool_filters": listify,
+    "tool_label_filters": listify,
+    "tool_section_filters": listify,
 }
 
 
 # TODO: split into (1) do not test; and (2) todo: fix and test
 DO_NOT_TEST = [
-    'admin_users',  # may or may not be testable: special test value assigned
-    'allow_user_deletion',  # broken: default overridden
-    'amqp_internal_connection',  # may or may not be testable; refactor config/
-    'api_allow_run_as',  # may or may not be testable: test value assigned
-    'build_sites_config_file',  # broken: remove 'config/' prefix from schema
-    'chunk_upload_size',  # broken: default overridden
-    'cleanup_job',  # broken: default overridden
-    'conda_auto_init',  # broken: default overridden
-    'config_dir',  # value overridden for testing
-    'data_dir',  # value overridden for testing
-    'data_manager_config_file',  # broken: remove 'config/' prefix from schema
-    'database_connection',  # untestable; refactor config/__init__ to test
-    'database_engine_option_max_overflow',  # overridden for tests running on non-sqlite databases
-    'database_engine_option_pool_size',  # overridden for tests runnign on non-sqlite databases
-    'database_log_query_counts',  # overridden for tests
-    'database_template',  # default value set for tests
-    'datatypes_config_file',  # broken
-    'default_locale',  # broken
-    'dependency_resolution',  # nested properties
-    'disable_library_comptypes',  # broken: default overridden with empty string
-    'enable_per_request_sql_debugging',  # overridden for tests
-    'expose_dataset_path',  # broken: default overridden
-    'ftp_upload_purge',  # broken: default overridden
-    'ftp_upload_dir_template',  # dynamically sets os.path.sep
-    'galaxy_data_manager_data_path',  # broken: review config/, possibly refactor
-    'galaxy_infrastructure_url',  # broken
-    'galaxy_infrastructure_web_port',  # broken
-    'heartbeat_log',  # untestable; refactor config/__init__ to test
-    'id_secret',  # broken: default overridden
-    'job_config',  # no obvious testable defaults
-    'job_config_file',  # broken: remove 'config/' prefix from schema
-    'job_metrics_config_file',
-    'job_working_directory',  # broken; may or may not be able to test
-    'library_import_dir',  # broken: default overridden
-    'logging',  # mapping loaded in config/
-    'managed_config_dir',  # depends on config_dir: see note above
-    'markdown_export_css',  # default not used?
-    'markdown_export_css_pages',  # default not used?
-    'markdown_export_css_invocation_reports',  # default not used?
-    'master_api_key',  # broken: default value assigned outside of config/
-    'migrated_tools_config',  # needs more work (should work)
-    'monitor_thread_join_timeout',  # broken: default overridden
-    'new_file_path',  # value overridden for testing
-    'object_store_store_by',  # broken: default overridden
-    'pretty_datetime_format',  # untestable; refactor config/__init__ to test
-    'retry_metadata_internally',  # broken: default overridden
-    'simplified_workflow_run_ui',  # set to off in testing
-    'statsd_host',  # broken: default overridden with empty string
-    'statsd_influxdb',  # overridden for tests
-    'template_cache_path',  # may or may not be able to test; may be broken
-    'tool_config_file',  # default not used; may or may not be testable
-    'tool_data_table_config_path',  # broken: remove 'config/' prefix from schema
-    'tool_test_data_directories',  # untestable; refactor config/__init__ to test
-    'trs_servers_config_file',  # default not used?
-    'use_remote_user',  # broken: default overridden
-    'use_tasked_jobs',  # broken: default overridden
-    'user_library_import_dir',  # broken: default overridden
-    'user_tool_filters',  # broken: default overridden
-    'user_tool_label_filters',  # broken: default overridden
-    'user_tool_section_filters',  # broken: default overridden
-    'webhooks_dir',  # broken; also remove 'config/' prefix from schema
-    'workflow_resource_params_mapper',  # broken: remove 'config/' prefix from schema
+    "admin_users",  # may or may not be testable: special test value assigned
+    "allow_user_deletion",  # broken: default overridden
+    "amqp_internal_connection",  # may or may not be testable; refactor config/
+    "api_allow_run_as",  # may or may not be testable: test value assigned
+    "build_sites_config_file",  # broken: remove 'config/' prefix from schema
+    "chunk_upload_size",  # broken: default overridden
+    "cleanup_job",  # broken: default overridden
+    "conda_auto_init",  # broken: default overridden
+    "config_dir",  # value overridden for testing
+    "data_dir",  # value overridden for testing
+    "data_manager_config_file",  # broken: remove 'config/' prefix from schema
+    "database_connection",  # untestable; refactor config/__init__ to test
+    "database_engine_option_max_overflow",  # overridden for tests running on non-sqlite databases
+    "database_engine_option_pool_size",  # overridden for tests runnign on non-sqlite databases
+    "database_log_query_counts",  # overridden for tests
+    "database_template",  # default value set for tests
+    "datatypes_config_file",  # broken
+    "default_locale",  # broken
+    "dependency_resolution",  # nested properties
+    "disable_library_comptypes",  # broken: default overridden with empty string
+    "enable_per_request_sql_debugging",  # overridden for tests
+    "expose_dataset_path",  # broken: default overridden
+    "ftp_upload_purge",  # broken: default overridden
+    "ftp_upload_dir_template",  # dynamically sets os.path.sep
+    "galaxy_data_manager_data_path",  # broken: review config/, possibly refactor
+    "galaxy_infrastructure_url",  # broken
+    "galaxy_infrastructure_web_port",  # broken
+    "heartbeat_log",  # untestable; refactor config/__init__ to test
+    "id_secret",  # broken: default overridden
+    "job_config",  # no obvious testable defaults
+    "job_config_file",  # broken: remove 'config/' prefix from schema
+    "job_metrics_config_file",
+    "job_working_directory",  # broken; may or may not be able to test
+    "library_import_dir",  # broken: default overridden
+    "logging",  # mapping loaded in config/
+    "managed_config_dir",  # depends on config_dir: see note above
+    "markdown_export_css",  # default not used?
+    "markdown_export_css_pages",  # default not used?
+    "markdown_export_css_invocation_reports",  # default not used?
+    "master_api_key",  # broken: default value assigned outside of config/
+    "migrated_tools_config",  # needs more work (should work)
+    "monitor_thread_join_timeout",  # broken: default overridden
+    "new_file_path",  # value overridden for testing
+    "object_store_store_by",  # broken: default overridden
+    "pretty_datetime_format",  # untestable; refactor config/__init__ to test
+    "retry_metadata_internally",  # broken: default overridden
+    "simplified_workflow_run_ui",  # set to off in testing
+    "statsd_host",  # broken: default overridden with empty string
+    "statsd_influxdb",  # overridden for tests
+    "template_cache_path",  # may or may not be able to test; may be broken
+    "tool_config_file",  # default not used; may or may not be testable
+    "tool_data_table_config_path",  # broken: remove 'config/' prefix from schema
+    "tool_test_data_directories",  # untestable; refactor config/__init__ to test
+    "trs_servers_config_file",  # default not used?
+    "use_remote_user",  # broken: default overridden
+    "use_tasked_jobs",  # broken: default overridden
+    "user_library_import_dir",  # broken: default overridden
+    "user_tool_filters",  # broken: default overridden
+    "user_tool_label_filters",  # broken: default overridden
+    "user_tool_section_filters",  # broken: default overridden
+    "webhooks_dir",  # broken; also remove 'config/' prefix from schema
+    "workflow_resource_params_mapper",  # broken: remove 'config/' prefix from schema
 ]
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def driver(request):
     request.addfinalizer(DRIVER.tear_down)
     return DRIVER
@@ -249,20 +249,20 @@ def get_config_data():
 
     def load_parent_dirs():
         return {
-            'root_dir': DRIVER.app.config.root,
-            'config_dir': DRIVER.app.config.config_dir,
-            'managed_config_dir': DRIVER.app.config.managed_config_dir,
-            'data_dir': DRIVER.app.config.data_dir,
-            'tool_data_path': DRIVER.app.config.tool_data_path,
-            'cache_dir': DRIVER.app.config.cache_dir
+            "root_dir": DRIVER.app.config.root,
+            "config_dir": DRIVER.app.config.config_dir,
+            "managed_config_dir": DRIVER.app.config.managed_config_dir,
+            "data_dir": DRIVER.app.config.data_dir,
+            "tool_data_path": DRIVER.app.config.tool_data_path,
+            "cache_dir": DRIVER.app.config.cache_dir,
         }
 
     def resolve(parent, child):
         return os.path.join(parent, child) if child else parent
 
     def get_expected(key, data, parent_dirs):
-        value = data.get('default')
-        parent = data.get('path_resolves_to')
+        value = data.get("default")
+        parent = data.get("path_resolves_to")
         if parent:
             value = resolve(parent_dirs[parent], value)
         if key in RESOLVE:
@@ -294,12 +294,12 @@ def get_key(option_data):
     return option_data.key
 
 
-@pytest.mark.parametrize('data', get_config_data(), ids=get_key)
+@pytest.mark.parametrize("data", get_config_data(), ids=get_key)
 def test_config_option(data, driver):
     assert data.expected == data.loaded
 
 
-@pytest.mark.parametrize('data', get_path_data())
+@pytest.mark.parametrize("data", get_path_data())
 def test_is_path_absolute(data, driver):
     global DRIVER
     path = getattr(DRIVER.app.config, data)
diff --git a/test/integration/test_config_options_users.py b/test/integration/test_config_options_users.py
index abfe952cf7a..951da6087ac 100644
--- a/test/integration/test_config_options_users.py
+++ b/test/integration/test_config_options_users.py
@@ -4,7 +4,6 @@ from galaxy_test.driver import integration_util
 
 
 class _BaseUserExposeIntegerationTestCase(integration_util.IntegrationTestCase):
-
     def original_user_ids(self):
         return [u["id"] for u in self.galaxy_interactor.get("users").json()]
 
@@ -14,7 +13,6 @@ class _BaseUserExposeIntegerationTestCase(integration_util.IntegrationTestCase):
 
 
 class DefaultUserExposeIntegrationTestCase(_BaseUserExposeIntegerationTestCase):
-
     def test_defaults(self):
         original_user_ids = self.original_user_ids()
         self.galaxy_interactor.ensure_user_with_email("defaultuserexposetest@galaxyproject.org")
@@ -25,7 +23,6 @@ class DefaultUserExposeIntegrationTestCase(_BaseUserExposeIntegerationTestCase):
 
 
 class EmailUserExposeIntegrationTestCase(_BaseUserExposeIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["expose_user_email"] = True
@@ -42,7 +39,6 @@ class EmailUserExposeIntegrationTestCase(_BaseUserExposeIntegerationTestCase):
 
 
 class UsernameUserExposeIntegrationTestCase(_BaseUserExposeIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["expose_user_name"] = True
diff --git a/test/integration/test_config_schema.py b/test/integration/test_config_schema.py
index 8766c91f660..71a43f80646 100644
--- a/test/integration/test_config_schema.py
+++ b/test/integration/test_config_schema.py
@@ -2,7 +2,6 @@ from galaxy_test.driver import integration_util
 
 
 class ConfigSchemaTestCase(integration_util.IntegrationTestCase):
-
     def test_schema_path_resolution_graph(self):
         # Run schema's validation method; throws error if schema invalid
         schema = self._app.config.schema
diff --git a/test/integration/test_configuration_decode.py b/test/integration/test_configuration_decode.py
index 3b346053b42..4a54feba0a0 100644
--- a/test/integration/test_configuration_decode.py
+++ b/test/integration/test_configuration_decode.py
@@ -1,23 +1,20 @@
-from galaxy_test.base.populators import (
-    LibraryPopulator
-)
+from galaxy_test.base.populators import LibraryPopulator
 from galaxy_test.driver import integration_util
 
 
 class ConfigurationDecodeIntegrationTestCase(integration_util.IntegrationTestCase):
-
     def setUp(self):
         super().setUp()
         self.library_populator = LibraryPopulator(self.galaxy_interactor)
 
     def test_admin_decode_id(self):
-        new_lib = self.library_populator.new_library('DecodeTestLibrary')
+        new_lib = self.library_populator.new_library("DecodeTestLibrary")
         decode_response = self._get("configuration/decode/" + new_lib["id"], admin=True)
         response_id = decode_response.json()["decoded_id"]
         decoded_library_id = self._app.security.decode_id(new_lib["id"])
         assert decoded_library_id == response_id
         # fake valid folder id by prepending F
-        valid_encoded_folder_id = 'F' + new_lib["id"]
+        valid_encoded_folder_id = "F" + new_lib["id"]
         folder_decode_response = self._get("configuration/decode/" + valid_encoded_folder_id, admin=True)
         folder_response_id = folder_decode_response.json()["decoded_id"]
         assert decoded_library_id == folder_response_id
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 10acbf3e4a2..78db28f2a0f 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -5,9 +5,7 @@ import os
 import unittest
 
 from galaxy.util.commands import which
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
 
@@ -38,7 +36,6 @@ class MulledJobTestCases:
 
 
 class ContainerizedIntegrationTestCase(integration_util.IntegrationTestCase):
-
     @classmethod
     def setUpClass(cls):
         skip_if_container_type_unavailable(cls)
@@ -65,8 +62,8 @@ def skip_if_container_type_unavailable(cls):
 class DockerizedJobsIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
 
     job_config_file = DOCKERIZED_JOB_CONFIG_FILE
-    build_mulled_resolver = 'build_mulled'
-    container_type = 'docker'
+    build_mulled_resolver = "build_mulled"
+    container_type = "docker"
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -107,44 +104,58 @@ class DockerizedJobsIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
         assert job_env.group_id == str(egid), job_env.group_id
         assert job_env.pwd.startswith(self.jobs_directory)
         assert job_env.pwd.endswith("/working")
-        assert not job_env.home.endswith('/home')
+        assert not job_env.home.endswith("/home")
 
     def test_container_job_environment_explicit_shared_home(self):
         job_env = self._run_and_get_environment_properties("job_environment_explicit_shared_home")
 
         assert job_env.pwd.startswith(self.jobs_directory)
         assert job_env.pwd.endswith("/working")
-        assert not job_env.home.endswith('/home')
+        assert not job_env.home.endswith("/home")
 
     def test_container_job_environment_explicit_isolated_home(self):
         job_env = self._run_and_get_environment_properties("job_environment_explicit_isolated_home")
 
         assert job_env.pwd.startswith(self.jobs_directory)
         assert job_env.pwd.endswith("/working")
-        assert job_env.home.endswith('/home')
+        assert job_env.home.endswith("/home")
 
     def test_build_mulled(self):
-        if not which('docker'):
+        if not which("docker"):
             raise unittest.SkipTest("Docker not found on PATH, required for building images via involucro")
         resolver_type = self.build_mulled_resolver
-        tool_ids = ['mulled_example_multi_1']
+        tool_ids = ["mulled_example_multi_1"]
         endpoint = "dependency_resolvers/toolbox/install"
-        data = {'tool_ids': json.dumps(tool_ids), 'resolver_type': resolver_type, 'container_type': self.container_type, 'include_containers': True}
+        data = {
+            "tool_ids": json.dumps(tool_ids),
+            "resolver_type": resolver_type,
+            "container_type": self.container_type,
+            "include_containers": True,
+        }
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
-        create_response = self._get("dependency_resolvers/toolbox", data={'tool_ids': tool_ids, 'container_type': self.container_type, 'include_containers': True, 'index_by': 'tools'}, admin=True)
+        create_response = self._get(
+            "dependency_resolvers/toolbox",
+            data={
+                "tool_ids": tool_ids,
+                "container_type": self.container_type,
+                "include_containers": True,
+                "index_by": "tools",
+            },
+            admin=True,
+        )
         response = create_response.json()
         assert len(response) == 1
-        status = response[0]['status']
-        assert status[0]['model_class'] == 'ContainerDependency'
-        assert status[0]['dependency_type'] == self.container_type
-        assert status[0]['container_description']['identifier'].startswith('quay.io/local/mulled-v2-')
+        status = response[0]["status"]
+        assert status[0]["model_class"] == "ContainerDependency"
+        assert status[0]["dependency_type"] == self.container_type
+        assert status[0]["container_description"]["identifier"].startswith("quay.io/local/mulled-v2-")
 
 
 class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
 
     framework_tool_and_types = True
-    container_type = 'docker'
+    container_type = "docker"
     job_config_file = DOCKERIZED_JOB_CONFIG_FILE
 
     @classmethod
@@ -155,13 +166,15 @@ class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
         disable_dependency_resolution(config)
         container_resolvers_config_path = os.path.join(cls.jobs_directory, "container_resolvers.yml")
         with open(container_resolvers_config_path, "w") as f:
-            f.write("""
+            f.write(
+                """
 - type: mapping
   mappings:
     - container_type: docker
       tool_id: mulled_example_broken_no_requirements
       identifier: 'quay.io/biocontainers/bwa:0.7.15--0'
-""")
+"""
+            )
         config["container_resolvers_config_file"] = container_resolvers_config_path
 
     @classmethod
@@ -182,28 +195,31 @@ class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
 
 
 class InlineContainerConfigurationTestCase(MappingContainerResolverTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = cls._test_driver.mkdtemp()
         config["jobs_directory"] = cls.jobs_directory
         config["job_config_file"] = cls.job_config_file
         disable_dependency_resolution(config)
-        container_resolvers_config = [{
-            'type': 'mapping',
-            'mappings': [{
-                'container_type': 'docker',
-                'tool_id': 'mulled_example_broken_no_requirements',
-                'identifier': 'quay.io/biocontainers/bwa:0.7.15--0',
-            }],
-        }]
+        container_resolvers_config = [
+            {
+                "type": "mapping",
+                "mappings": [
+                    {
+                        "container_type": "docker",
+                        "tool_id": "mulled_example_broken_no_requirements",
+                        "identifier": "quay.io/biocontainers/bwa:0.7.15--0",
+                    }
+                ],
+            }
+        ]
         config["container_resolvers"] = container_resolvers_config
 
 
 class InlineJobEnvironmentContainerResolverTestCase(integration_util.IntegrationTestCase):
 
     framework_tool_and_types = True
-    container_type = 'docker'
+    container_type = "docker"
     job_config_file = DOCKERIZED_JOB_CONFIG_FILE
 
     @classmethod
@@ -237,5 +253,5 @@ class InlineJobEnvironmentContainerResolverTestCase(integration_util.Integration
 class SingularityJobsIntegrationTestCase(DockerizedJobsIntegrationTestCase):
 
     job_config_file = SINGULARITY_JOB_CONFIG_FILE
-    build_mulled_resolver = 'build_mulled_singularity'
-    container_type = 'singularity'
+    build_mulled_resolver = "build_mulled_singularity"
+    container_type = "singularity"
diff --git a/test/integration/test_data_manager.py b/test/integration/test_data_manager.py
index 14225a1234b..41aaab91c08 100644
--- a/test/integration/test_data_manager.py
+++ b/test/integration/test_data_manager.py
@@ -4,11 +4,17 @@ import string
 import pytest
 from nose.plugins.skip import SkipTest
 
-from galaxy_test.base.populators import DatasetPopulator, skip_if_toolshed_down
-from galaxy_test.base.uses_shed import CONDA_AUTO_INSTALL_JOB_TIMEOUT, UsesShed
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    skip_if_toolshed_down,
+)
+from galaxy_test.base.uses_shed import (
+    CONDA_AUTO_INSTALL_JOB_TIMEOUT,
+    UsesShed,
+)
 from galaxy_test.driver import integration_util
 
-FETCH_TOOL_ID = 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3'
+FETCH_TOOL_ID = "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3"
 FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {
     "dbkey_source|dbkey_source_selector": "new",
     "dbkey_source|dbkey": "NC_001617.1",
@@ -17,11 +23,11 @@ FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {
     "sequence_id": "NC_001617.1",
     "reference_source|reference_source_selector": "url",
     "reference_source|user_url": "https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/master/NC_001617.1.fasta",
-    "sorting|sort_selector": "as_is"
+    "sorting|sort_selector": "as_is",
 }
 SAM_FASTA_ID = "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.3"
 SAM_FASTA_INPUT = {"all_fasta_source": "NC_001617.1", "sequence_name": "", "sequence_id": ""}
-DATA_MANAGER_MANUAL_ID = 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_manual/data_manager_manual/0.0.2'
+DATA_MANAGER_MANUAL_ID = "toolshed.g2.bx.psu.edu/repos/iuc/data_manager_manual/data_manager_manual/0.0.2"
 DATA_MANAGER_MANUAL_INPUT = {
     "data_tables_0|data_table_name": "all_fasta",
     "data_tables_0|columns_0|data_table_column_name": "value",
@@ -53,7 +59,7 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
         except ImportError:
             raise SkipTest("watchdog library is not available")
         cls.configure_shed_and_conda(config)
-        config['metadata_strategy'] = 'extended'
+        config["metadata_strategy"] = "extended"
         config["tool_evaluation_strategy"] = "remote"
         config["tool_data_path"] = cls.shed_tool_data_dir
         config["watch_tool_data_dir"] = True
@@ -74,21 +80,25 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     inputs=FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
                 run_response = self.dataset_populator.run_tool_raw(
                     tool_id=SAM_FASTA_ID,
                     inputs=SAM_FASTA_INPUT,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
 
     @skip_if_toolshed_down
     def test_data_manager_hook_can_fail(self):
         self.install_repository("devteam", "data_manager_fetch_genome_dbkeys_all_fasta", "14eb0fc65c62")
         inputs = FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT.copy()
-        keys = ['dbkey_source|dbkey', 'dbkey_source|dbkey_name', 'sequence_id', 'sequence_name']
+        keys = ["dbkey_source|dbkey", "dbkey_source|dbkey_name", "sequence_id", "sequence_name"]
         for key in keys:
-            inputs[key] = 'unique_dbkey_value'
+            inputs[key] = "unique_dbkey_value"
         with self._different_user(email="%s@galaxy.org" % self.username):
             with self.dataset_populator.test_history() as history_id:
                 # First run should work
@@ -97,7 +107,9 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     inputs=inputs,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
                 # Second run should fail
                 run_response = self.dataset_populator.run_tool_raw(
                     tool_id=FETCH_TOOL_ID,
@@ -105,13 +117,15 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     history_id=history_id,
                 )
                 with pytest.raises(AssertionError):
-                    self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                    self.dataset_populator.wait_for_tool_run(
+                        history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                    )
 
     def test_data_manager_manual(self):
         """
         Test that data_manager_manual works, which uses a significant amount of Galaxy-internal code
         """
-        self.install_repository('iuc', 'data_manager_manual', '1ed87dee9e68')
+        self.install_repository("iuc", "data_manager_manual", "1ed87dee9e68")
         with self._different_user(email="%s@galaxy.org" % self.username):
             with self.dataset_populator.test_history() as history_id:
                 run_response = self.dataset_populator.run_tool_raw(
@@ -119,15 +133,19 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     inputs=DATA_MANAGER_MANUAL_INPUT,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
 
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'dm6', 'dbkey')
-        assert 'dm6' in entries
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("dbkey", "dm6", "dbkey")
+        assert "dm6" in entries
 
-        table_content = {line[0]: line for line in self._app.tool_data_tables.get("all_fasta").to_dict(view="element")['fields']}
+        table_content = {
+            line[0]: line for line in self._app.tool_data_tables.get("all_fasta").to_dict(view="element")["fields"]
+        }
 
-        self._app.tool_data_tables.get("all_fasta").remove_entry(table_content['dm6'])
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'dm6', 'dbkey')
+        self._app.tool_data_tables.get("all_fasta").remove_entry(table_content["dm6"])
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("dbkey", "dm6", "dbkey")
         assert entries is None
 
     def test_data_manager_manual_multiple(self):
@@ -135,9 +153,9 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
         Test adding/removing on the same data table with multiple data managers
         """
         self.install_repository("devteam", "data_manager_fetch_genome_dbkeys_all_fasta", "14eb0fc65c62")
-        self.install_repository('iuc', 'data_manager_manual', '1ed87dee9e68')
+        self.install_repository("iuc", "data_manager_manual", "1ed87dee9e68")
         inputs = FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT.copy()
-        inputs['dbkey_source|dbkey'] = 'another_unique_dbkey_value'
+        inputs["dbkey_source|dbkey"] = "another_unique_dbkey_value"
         with self._different_user(email="%s@galaxy.org" % self.username):
             with self.dataset_populator.test_history() as history_id:
                 run_response = self.dataset_populator.run_tool_raw(
@@ -145,32 +163,42 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     inputs=inputs,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
                 run_response = self.dataset_populator.run_tool_raw(
                     tool_id=DATA_MANAGER_MANUAL_ID,
                     inputs=DATA_MANAGER_MANUAL_INPUT,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
 
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'another_unique_dbkey_value', 'dbkey')
-        assert 'another_unique_dbkey_value' in entries
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries(
+            "dbkey", "another_unique_dbkey_value", "dbkey"
+        )
+        assert "another_unique_dbkey_value" in entries
 
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'dm6', 'dbkey')
-        assert 'dm6' in entries
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("dbkey", "dm6", "dbkey")
+        assert "dm6" in entries
 
-        table_content = {line[0]: line for line in self._app.tool_data_tables.get("all_fasta").to_dict(view="element")['fields']}
+        table_content = {
+            line[0]: line for line in self._app.tool_data_tables.get("all_fasta").to_dict(view="element")["fields"]
+        }
 
-        self._app.tool_data_tables.get("all_fasta").remove_entry(table_content['dm6'])
+        self._app.tool_data_tables.get("all_fasta").remove_entry(table_content["dm6"])
 
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'dm6', 'dbkey')
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("dbkey", "dm6", "dbkey")
         assert entries is None
 
-        self._app.tool_data_tables.get("all_fasta").remove_entry(table_content['NC_001617.1'])
+        self._app.tool_data_tables.get("all_fasta").remove_entry(table_content["NC_001617.1"])
 
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'another_unique_dbkey_value', 'dbkey')
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries(
+            "dbkey", "another_unique_dbkey_value", "dbkey"
+        )
         assert entries is None
 
     @classmethod
     def get_secure_ascii_digits(cls, n=12):
-        return ''.join(random.SystemRandom().choice(string.ascii_lowercase + string.digits) for _ in range(12))
+        return "".join(random.SystemRandom().choice(string.ascii_lowercase + string.digits) for _ in range(12))
diff --git a/test/integration/test_data_manager_refgenie.py b/test/integration/test_data_manager_refgenie.py
index 7b4de7a87cd..ca79c901a05 100644
--- a/test/integration/test_data_manager_refgenie.py
+++ b/test/integration/test_data_manager_refgenie.py
@@ -5,10 +5,13 @@ import string
 from nose.plugins.skip import SkipTest
 
 from galaxy_test.base.populators import DatasetPopulator
-from galaxy_test.base.uses_shed import CONDA_AUTO_INSTALL_JOB_TIMEOUT, UsesShed
+from galaxy_test.base.uses_shed import (
+    CONDA_AUTO_INSTALL_JOB_TIMEOUT,
+    UsesShed,
+)
 from galaxy_test.driver import integration_util
 
-FETCH_TOOL_ID = 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3'
+FETCH_TOOL_ID = "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3"
 FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {
     "dbkey_source|dbkey_source_selector": "new",
     "dbkey_source|dbkey": "NC_001617.1",
@@ -17,11 +20,11 @@ FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {
     "sequence_id": "NC_001617.1",
     "reference_source|reference_source_selector": "url",
     "reference_source|user_url": "https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/master/NC_001617.1.fasta",
-    "sorting|sort_selector": "as_is"
+    "sorting|sort_selector": "as_is",
 }
 SAM_FASTA_ID = "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.3"
 SAM_FASTA_INPUT = {"all_fasta_source": "NC_001617.1", "sequence_name": "", "sequence_id": ""}
-DATA_MANAGER_MANUAL_ID = 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_manual/data_manager_manual/0.0.2'
+DATA_MANAGER_MANUAL_ID = "toolshed.g2.bx.psu.edu/repos/iuc/data_manager_manual/data_manager_manual/0.0.2"
 DATA_MANAGER_MANUAL_INPUT = {
     "data_tables_0|data_table_name": "all_fasta",
     "data_tables_0|columns_0|data_table_column_name": "value",
@@ -74,7 +77,7 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
         """
         Test that data_manager_manual works with refgenie enabled, which uses a significant amount of Galaxy-internal code
         """
-        self.install_repository('iuc', 'data_manager_manual', '1ed87dee9e68')
+        self.install_repository("iuc", "data_manager_manual", "1ed87dee9e68")
         with self._different_user(email="%s@galaxy.org" % self.username):
             with self.dataset_populator.test_history() as history_id:
                 run_response = self.dataset_populator.run_tool_raw(
@@ -82,20 +85,24 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     inputs=DATA_MANAGER_MANUAL_INPUT,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
 
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'dm6', 'dbkey')
-        assert 'dm6' in entries
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("dbkey", "dm6", "dbkey")
+        assert "dm6" in entries
 
-        self._app.tool_data_tables.get("all_fasta").remove_entry(self._app.tool_data_tables.get("all_fasta").to_dict(view="element")['fields'][0])
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('dbkey', 'dm6', 'dbkey')
+        self._app.tool_data_tables.get("all_fasta").remove_entry(
+            self._app.tool_data_tables.get("all_fasta").to_dict(view="element")["fields"][0]
+        )
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("dbkey", "dm6", "dbkey")
         assert entries is None
 
     def test_data_manager_manual_refgenie_dbkeys(self):
         """
         Test that data_manager_manual works with refgenie enabled, with a table defined first by refgenie
         """
-        self.install_repository('iuc', 'data_manager_manual', '1ed87dee9e68')
+        self.install_repository("iuc", "data_manager_manual", "1ed87dee9e68")
         with self._different_user(email="%s@galaxy.org" % self.username):
             with self.dataset_populator.test_history() as history_id:
                 run_response = self.dataset_populator.run_tool_raw(
@@ -103,15 +110,19 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase, UsesS
                     inputs=DATA_MANAGER_MANUAL_INPUT_DBKEY,
                     history_id=history_id,
                 )
-                self.dataset_populator.wait_for_tool_run(history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT)
+                self.dataset_populator.wait_for_tool_run(
+                    history_id=history_id, run_response=run_response, timeout=CONDA_AUTO_INSTALL_JOB_TIMEOUT
+                )
 
-        entries = self._app.tool_data_tables.get("__dbkeys__").get_entries('name', 'dm7', 'name')
-        assert 'dm7' in entries
+        entries = self._app.tool_data_tables.get("__dbkeys__").get_entries("name", "dm7", "name")
+        assert "dm7" in entries
 
-        self._app.tool_data_tables.get("__dbkeys__").remove_entry(self._app.tool_data_tables.get("__dbkeys__").to_dict(view="element")['fields'][0])
-        entries = self._app.tool_data_tables.get("all_fasta").get_entries('name', 'dm7', 'name')
+        self._app.tool_data_tables.get("__dbkeys__").remove_entry(
+            self._app.tool_data_tables.get("__dbkeys__").to_dict(view="element")["fields"][0]
+        )
+        entries = self._app.tool_data_tables.get("all_fasta").get_entries("name", "dm7", "name")
         assert entries is None
 
     @classmethod
     def get_secure_ascii_digits(cls, n=12):
-        return ''.join(random.SystemRandom().choice(string.ascii_lowercase + string.digits) for _ in range(12))
+        return "".join(random.SystemRandom().choice(string.ascii_lowercase + string.digits) for _ in range(12))
diff --git a/test/integration/test_datatype_upload.py b/test/integration/test_datatype_upload.py
index 2e2a0485ed6..da4347cb1e8 100644
--- a/test/integration/test_datatype_upload.py
+++ b/test/integration/test_datatype_upload.py
@@ -8,18 +8,18 @@ from galaxy.datatypes.registry import Registry
 from galaxy.util.checkers import (
     is_bz2,
     is_gzip,
-    is_zip
+    is_zip,
 )
 from galaxy.util.hash_util import md5_hash_file
 from galaxy_test.driver import integration_util
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-TEST_FILE_DIR = '%s/../../lib/galaxy/datatypes/test' % SCRIPT_DIRECTORY
-TestData = collections.namedtuple('TestData', 'path datatype uploadable')
-GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
-DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'lib/galaxy/config/sample/datatypes_conf.xml.sample')
-PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
+TEST_FILE_DIR = "%s/../../lib/galaxy/datatypes/test" % SCRIPT_DIRECTORY
+TestData = collections.namedtuple("TestData", "path datatype uploadable")
+GALAXY_ROOT = os.path.abspath("%s/../../" % SCRIPT_DIRECTORY)
+DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, "lib/galaxy/config/sample/datatypes_conf.xml.sample")
+PARENT_SNIFFER_MAP = {"fastqsolexa": "fastq"}
 
 
 def find_datatype(registry, filename):
@@ -55,7 +55,7 @@ registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
 TEST_CASES = collect_test_data(registry)
 
 
-@pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
+@pytest.mark.parametrize("test_data", TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
     upload_datatype_helper(instance, test_data, temp_file)
 
@@ -66,27 +66,31 @@ def upload_datatype_helper(instance, test_data, temp_file, delete_cache_dir=Fals
         is_compressed = is_method(test_data.path)
         if is_compressed:
             break
-    with open(test_data.path, 'rb') as content:
-        if hasattr(test_data.datatype, 'sniff') or 'false' in test_data.path:
-            file_type = 'auto'
+    with open(test_data.path, "rb") as content:
+        if hasattr(test_data.datatype, "sniff") or "false" in test_data.path:
+            file_type = "auto"
         else:
             file_type = test_data.datatype.file_ext
-        dataset = instance.dataset_populator.new_dataset(instance.history_id, content=content, wait=False, file_type=file_type)
-    dataset = instance.dataset_populator.get_history_dataset_details(instance.history_id, dataset=dataset, assert_ok=False)
+        dataset = instance.dataset_populator.new_dataset(
+            instance.history_id, content=content, wait=False, file_type=file_type
+        )
+    dataset = instance.dataset_populator.get_history_dataset_details(
+        instance.history_id, dataset=dataset, assert_ok=False
+    )
     expected_file_ext = test_data.datatype.file_ext
     # State might be error if the datatype can't be uploaded
-    if dataset['state'] == 'error' and not test_data.uploadable:
+    if dataset["state"] == "error" and not test_data.uploadable:
         # Some things can't be uploaded, if attempting to upload these datasets we mention why
-        assert 'invalid' in dataset['misc_info'] or 'unsupported' in dataset['misc_info']
+        assert "invalid" in dataset["misc_info"] or "unsupported" in dataset["misc_info"]
         return
-    elif dataset['state'] == 'error' and 'empty' in dataset['misc_info']:
+    elif dataset["state"] == "error" and "empty" in dataset["misc_info"]:
         return
     else:
         # state should be OK
-        assert dataset['state'] == 'ok'
+        assert dataset["state"] == "ok"
     # Check that correct datatype has been detected
-    file_ext = dataset['file_ext']
-    if 'false' in test_data.path:
+    file_ext = dataset["file_ext"]
+    if "false" in test_data.path:
         # datasets with false in their name are not of a specific datatype
         assert file_ext != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
     else:
@@ -97,16 +101,16 @@ def upload_datatype_helper(instance, test_data, temp_file, delete_cache_dir=Fals
         if delete_cache_dir:
             # Delete cache directory and then re-create it. This way we confirm
             # that dataset is fetched from the object store, not from the cache
-            temp_dir = instance.get_object_store_kwargs()['temp_directory']
-            cache_dir = temp_dir + '/object_store_cache'
+            temp_dir = instance.get_object_store_kwargs()["temp_directory"]
+            cache_dir = temp_dir + "/object_store_cache"
             shutil.rmtree(cache_dir)
             os.mkdir(cache_dir)
 
         # download file and verify it hasn't been manipulated
-        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
-                                                                               dataset=dataset,
-                                                                               type='bytes',
-                                                                               assert_ok=False,
-                                                                               raw=True))
+        temp_file.write(
+            instance.dataset_populator.get_history_dataset_content(
+                history_id=instance.history_id, dataset=dataset, type="bytes", assert_ok=False, raw=True
+            )
+        )
         temp_file.flush()
         assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)
diff --git a/test/integration/test_default_permissions.py b/test/integration/test_default_permissions.py
index cf6287b0b74..08c1de5c427 100644
--- a/test/integration/test_default_permissions.py
+++ b/test/integration/test_default_permissions.py
@@ -1,6 +1,4 @@
-from galaxy_test.base.populators import (
-    DatasetPopulator
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 
diff --git a/test/integration/test_dynamic_edam_loading.py b/test/integration/test_dynamic_edam_loading.py
index 40b2c31dcec..0be53aa399d 100644
--- a/test/integration/test_dynamic_edam_loading.py
+++ b/test/integration/test_dynamic_edam_loading.py
@@ -1,8 +1,6 @@
 import os
 
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
diff --git a/test/integration/test_extended_metadata.py b/test/integration/test_extended_metadata.py
index 64334b0e770..78e0815e6a6 100644
--- a/test/integration/test_extended_metadata.py
+++ b/test/integration/test_extended_metadata.py
@@ -3,6 +3,7 @@ import json
 
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
+
 TEST_TOOL_IDS = [
     "job_properties",
     "multi_output",
@@ -41,7 +42,6 @@ TEST_TOOL_IDS = [
 
 
 class ExtendedMetadataIntegrationTestCase(integration_util.IntegrationTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -61,17 +61,13 @@ class ExtendedMetadataIntegrationTestCase(integration_util.IntegrationTestCase):
             "elements": [element],
         }
         targets = json.dumps([target])
-        upload_content = 'abcdef'
-        payload = {
-            "history_id": history_id,
-            "targets": targets,
-            "__files": {"files_0|file_data": upload_content}
-        }
+        upload_content = "abcdef"
+        payload = {"history_id": history_id, "targets": targets, "__files": {"files_0|file_data": upload_content}}
         new_dataset = self.dataset_populator.fetch(payload, assert_ok=True).json()["outputs"][0]
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         content = self.dataset_populator.get_history_dataset_content(
             history_id=history_id,
-            dataset_id=new_dataset['id'],
+            dataset_id=new_dataset["id"],
         )
         assert content == upload_content
 
diff --git a/test/integration/test_extended_metadata_mapping.py b/test/integration/test_extended_metadata_mapping.py
index cc3e93730fd..8efe4a0cf7e 100644
--- a/test/integration/test_extended_metadata_mapping.py
+++ b/test/integration/test_extended_metadata_mapping.py
@@ -27,6 +27,6 @@ class ExtendedMetadataMappingIntegrationTestCase(integration_util.IntegrationTes
     def test_map_over_collection(self, history_id):
         hdca_id = self._build_pair(history_id, ["123", "456"])
         inputs = {
-            "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         self._run_and_check_simple_collection_mapping(history_id, inputs)
diff --git a/test/integration/test_extended_metadata_outputs_to_working_directory.py b/test/integration/test_extended_metadata_outputs_to_working_directory.py
index 6e2b8a4f7a1..6df5e042d18 100644
--- a/test/integration/test_extended_metadata_outputs_to_working_directory.py
+++ b/test/integration/test_extended_metadata_outputs_to_working_directory.py
@@ -3,7 +3,7 @@
 from galaxy_test.driver import integration_util
 from .test_extended_metadata import (
     ExtendedMetadataIntegrationInstance,
-    TEST_TOOL_IDS
+    TEST_TOOL_IDS,
 )
 
 
diff --git a/test/integration/test_fail_job_tool_unavailable.py b/test/integration/test_fail_job_tool_unavailable.py
index d2fa210a950..464b78d1b71 100644
--- a/test/integration/test_fail_job_tool_unavailable.py
+++ b/test/integration/test_fail_job_tool_unavailable.py
@@ -18,13 +18,17 @@ class FailJobWhenToolUnavailableTestCase(integration_util.IntegrationTestCase):
         self.history_id = self.dataset_populator.new_history()
 
     @classmethod
-    def handle_galaxy_config_kwds(cls, config, ):
+    def handle_galaxy_config_kwds(
+        cls,
+        config,
+    ):
         # config["jobs_directory"] = cls.jobs_directory
         # Disable tool dependency resolution.
         config["tool_dependency_dir"] = "none"
 
     def test_fail_job_when_tool_unavailable(self):
-        self.workflow_populator.run_workflow("""
+        self.workflow_populator.run_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   sleep:
@@ -42,16 +46,22 @@ steps:
       queries:
         input2:
           $link: sleep/output1
-""", history_id=self.history_id, assert_ok=False, wait=False)
+""",
+            history_id=self.history_id,
+            assert_ok=False,
+            wait=False,
+        )
         # Wait until workflow is fully scheduled, otherwise can't test effect of removing tool from queued job
         time.sleep(10)
-        self._app.toolbox.remove_tool_by_id('cat1')
+        self._app.toolbox.remove_tool_by_id("cat1")
         self.dataset_populator.wait_for_history(self.history_id, assert_ok=False)
-        state_details = self.galaxy_interactor.get('histories/%s' % self.history_id).json()['state_details']
-        assert state_details['running'] == 0
-        assert state_details['ok'] == 1
-        assert state_details['error'] == 1
-        failed_hda = self.dataset_populator.get_history_dataset_details(history_id=self.history_id, assert_ok=False, details=True)
-        assert failed_hda['state'] == 'error'
-        job = self.galaxy_interactor.get("jobs/%s" % failed_hda['creating_job']).json()
-        assert job['state'] == 'error'
+        state_details = self.galaxy_interactor.get("histories/%s" % self.history_id).json()["state_details"]
+        assert state_details["running"] == 0
+        assert state_details["ok"] == 1
+        assert state_details["error"] == 1
+        failed_hda = self.dataset_populator.get_history_dataset_details(
+            history_id=self.history_id, assert_ok=False, details=True
+        )
+        assert failed_hda["state"] == "error"
+        job = self.galaxy_interactor.get("jobs/%s" % failed_hda["creating_job"]).json()
+        assert job["state"] == "error"
diff --git a/test/integration/test_fluent_metrics.py b/test/integration/test_fluent_metrics.py
index 3552a4c8be2..394c2b93d4b 100644
--- a/test/integration/test_fluent_metrics.py
+++ b/test/integration/test_fluent_metrics.py
@@ -5,7 +5,6 @@ from galaxy_test.driver import integration_util
 
 
 class FluentMetricsIntegrationTestCase(integration_util.IntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["fluent_log"] = True
@@ -14,9 +13,7 @@ class FluentMetricsIntegrationTestCase(integration_util.IntegrationTestCase):
 
     def test_create(self):
         metrics = self._get_test_metrics()
-        payload = {
-            "metrics": metrics
-        }
+        payload = {"metrics": metrics}
         response = self._post("metrics", payload, json=True)
         self._assert_status_code_is(response, 200)
 
@@ -33,9 +30,7 @@ class FluentMetricsIntegrationTestCase(integration_util.IntegrationTestCase):
                 "namespace": "api-test",
                 "time": f"{datetime.utcnow().isoformat()}Z",
                 "level": 1,
-                "args": json.dumps({
-                    "arg01": "test"
-                }),
+                "args": json.dumps({"arg01": "test"}),
             }
         ]
         return metrics
diff --git a/test/integration/test_flush_per_n_datasets.py b/test/integration/test_flush_per_n_datasets.py
index 8568f9a8776..e371b3677ac 100644
--- a/test/integration/test_flush_per_n_datasets.py
+++ b/test/integration/test_flush_per_n_datasets.py
@@ -13,7 +13,6 @@ class FlushPerNDatasetsTestCase(integration_util.IntegrationInstance):
 
 
 instance = integration_util.integration_module_instance(FlushPerNDatasetsTestCase)
-test_tools = integration_util.integration_tool_runner([
-    'collection_creates_dynamic_nested',
-    'collection_creates_dynamic_list_of_pairs'
-])
+test_tools = integration_util.integration_tool_runner(
+    ["collection_creates_dynamic_nested", "collection_creates_dynamic_list_of_pairs"]
+)
diff --git a/test/integration/test_galaxy_interactor.py b/test/integration/test_galaxy_interactor.py
index 950b6c64db6..ef68b7cacbb 100644
--- a/test/integration/test_galaxy_interactor.py
+++ b/test/integration/test_galaxy_interactor.py
@@ -12,10 +12,12 @@ class GalaxyInteractorTestCase(integration_util.IntegrationTestCase):
     def test_local_test_data_download(self):
         self.galaxy_interactor._target_galaxy_version = Version("18.09")
         assert self.galaxy_interactor.supports_test_data_download is False
-        assert self.galaxy_interactor.test_data_download(tool_id='cat1', filename='1.bed').startswith(b'chr1\t147962192\t147962580')
+        assert self.galaxy_interactor.test_data_download(tool_id="cat1", filename="1.bed").startswith(
+            b"chr1\t147962192\t147962580"
+        )
 
     def test_run_test_select_version(self):
-        self._run_tool_test(tool_id='multiple_versions', tool_version="0.1")
+        self._run_tool_test(tool_id="multiple_versions", tool_version="0.1")
 
     def test_get_tool_tests(self):
         # test that get_tool_tests will return the right tests when the tool_version has a '+' in it
@@ -24,9 +26,11 @@ class GalaxyInteractorTestCase(integration_util.IntegrationTestCase):
         assert isinstance(test_data, list)
         assert len(test_data) > 0
         assert isinstance(test_data[0], dict)
-        assert test_data[0].get('tool_version') == "0.1+galaxy6"
+        assert test_data[0].get("tool_version") == "0.1+galaxy6"
 
-        test_data = self.galaxy_interactor.get_tool_tests(tool_id="multiple_versions")  # test that tool_version=None does not break it
+        test_data = self.galaxy_interactor.get_tool_tests(
+            tool_id="multiple_versions"
+        )  # test that tool_version=None does not break it
         assert isinstance(test_data, list)
         assert len(test_data) > 0
         assert isinstance(test_data[0], dict)
diff --git a/test/integration/test_genomes.py b/test/integration/test_genomes.py
index 50556ebee0b..c033f2c7fd8 100644
--- a/test/integration/test_genomes.py
+++ b/test/integration/test_genomes.py
@@ -9,25 +9,24 @@ from galaxy.exceptions import (
 from galaxy_test.driver import integration_util
 
 BUILDS_DATA = (
-    '?\tunspecified (?)',
-    'hg_test\tdescription of hg_test',
-    'hg_test_nolen\tdescription of hg_test_nolen',
+    "?\tunspecified (?)",
+    "hg_test\tdescription of hg_test",
+    "hg_test_nolen\tdescription of hg_test_nolen",
 )
 
 LEN_DATA = (
-    'chr1\t248956422',
-    'chr2\t242193529',
-    'chr3\t198295559',
+    "chr1\t248956422",
+    "chr2\t242193529",
+    "chr3\t198295559",
 )
 
 
 def get_key(has_len_file=True):
     pos = 1 if has_len_file else 2
-    return BUILDS_DATA[pos].split('\t')[0]
+    return BUILDS_DATA[pos].split("\t")[0]
 
 
 class GenomesTestCase(integration_util.IntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         genomes_dir = cls.temp_config_dir("test_genomes")
@@ -38,74 +37,74 @@ class GenomesTestCase(integration_util.IntegrationTestCase):
     @classmethod
     def _setup_builds_file(cls, config, genomes_dir):
         """Create builds file + set config option."""
-        builds_file_path = os.path.join(genomes_dir, 'builds.txt')
-        config['builds_file_path'] = builds_file_path
-        with open(builds_file_path, 'w') as f:
-            f.write('\n'.join(BUILDS_DATA))
+        builds_file_path = os.path.join(genomes_dir, "builds.txt")
+        config["builds_file_path"] = builds_file_path
+        with open(builds_file_path, "w") as f:
+            f.write("\n".join(BUILDS_DATA))
 
     @classmethod
     def _setup_len_file(cls, config, genomes_dir):
         """Create len file + set config option."""
-        config['len_file_path'] = genomes_dir  # the config option is a dir
+        config["len_file_path"] = genomes_dir  # the config option is a dir
         key = get_key()
-        len_file_path = os.path.join(genomes_dir, f'{key}.len')
-        with open(len_file_path, 'w') as f:
-            f.write('\n'.join(LEN_DATA))
+        len_file_path = os.path.join(genomes_dir, f"{key}.len")
+        with open(len_file_path, "w") as f:
+            f.write("\n".join(LEN_DATA))
 
     def test_index(self):
-        response = self._get('genomes')
+        response = self._get("genomes")
         self._assert_status_code_is(response, 200)
         rval = response.json()
-        expected_data = [item.split('\t')[::-1] for item in BUILDS_DATA]
+        expected_data = [item.split("\t")[::-1] for item in BUILDS_DATA]
         assert rval == expected_data
 
     def test_show_valid(self):
         key = get_key()
-        response = self._get(f'genomes/{key}')
+        response = self._get(f"genomes/{key}")
         self._assert_status_code_is(response, 200)
         rval = response.json()
-        assert rval['id'] == key
-        assert len(rval['chrom_info']) == len(LEN_DATA)
+        assert rval["id"] == key
+        assert len(rval["chrom_info"]) == len(LEN_DATA)
 
     def test_show_valid_no_refdata(self):
         key = get_key(has_len_file=False)
-        response = self._get(f'genomes/{key}')
+        response = self._get(f"genomes/{key}")
         self._assert_status_code_is(response, 500)
-        assert response.json()['err_code'] == ReferenceDataError.err_code.code
+        assert response.json()["err_code"] == ReferenceDataError.err_code.code
 
     def test_show_invalid(self):
-        response = self._get('genomes/invalid')
+        response = self._get("genomes/invalid")
         self._assert_status_code_is(response, 404)
-        assert response.json()['err_code'] == ObjectNotFound.err_code.code
+        assert response.json()["err_code"] == ObjectNotFound.err_code.code
 
     def test_sequences(self):
-
         class RefDataMock:
-            sequence = 'test-value'
+            sequence = "test-value"
 
         key = get_key()
-        with patch.object(self._app.genomes, 'has_reference_data', return_value=True), \
-                patch.object(self._app.genomes, '_get_reference_data', return_value=RefDataMock()):
-            response = self._get(f'genomes/{key}/sequences')
+        with patch.object(self._app.genomes, "has_reference_data", return_value=True), patch.object(
+            self._app.genomes, "_get_reference_data", return_value=RefDataMock()
+        ):
+            response = self._get(f"genomes/{key}/sequences")
             self._assert_status_code_is(response, 200)
-            assert response.content == bytes(RefDataMock.sequence, 'utf-8')
+            assert response.content == bytes(RefDataMock.sequence, "utf-8")
 
     def test_sequences_no_data(self):
         key = get_key()
-        with patch.object(self._app.genomes, 'has_reference_data', return_value=False):
-            response = self._get(f'genomes/{key}/sequences')
+        with patch.object(self._app.genomes, "has_reference_data", return_value=False):
+            response = self._get(f"genomes/{key}/sequences")
             self._assert_status_code_is(response, 500)
-            assert response.json()['err_code'] == ReferenceDataError.err_code.code
+            assert response.json()["err_code"] == ReferenceDataError.err_code.code
 
     def test_indexes(self):
-        mock_key, mock_content, index_type, suffix = 'mykey', 'mydata', 'fasta_indexes', '.fai'
+        mock_key, mock_content, index_type, suffix = "mykey", "mydata", "fasta_indexes", ".fai"
         # write some data to a tempfile
         with tempfile.NamedTemporaryFile(dir=self._tempdir, suffix=suffix, mode="w", delete=False) as tf:
             tf.write(mock_content)
         # make a mock containing the path to the tempfile
-        tmpfile_path = tf.name[:-len(suffix)]  # chop off the extention
+        tmpfile_path = tf.name[: -len(suffix)]  # chop off the extention
         mock_data = [[mock_key, tmpfile_path]]
-        with patch.object(self._app.tool_data_tables.data_tables[index_type], 'data', new=mock_data):
-            response = self._get(f'genomes/{mock_key}/indexes?type={index_type}')
+        with patch.object(self._app.tool_data_tables.data_tables[index_type], "data", new=mock_data):
+            response = self._get(f"genomes/{mock_key}/indexes?type={index_type}")
             self._assert_status_code_is(response, 200)
-            assert response.content == bytes(mock_content, 'utf-8')
+            assert response.content == bytes(mock_content, "utf-8")
diff --git a/test/integration/test_handler_assignment_methods.py b/test/integration/test_handler_assignment_methods.py
index 8608194f1d5..4196b0e0aa7 100644
--- a/test/integration/test_handler_assignment_methods.py
+++ b/test/integration/test_handler_assignment_methods.py
@@ -9,17 +9,15 @@ HANDLER_TEMPLATE_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "handler_templ
 
 
 class WritesConfig:
-
     def _with_handlers_config(self, assign_with=None, default=None, handlers=None):
         handlers = handlers or []
         template = {
-            'assign_with': ' assign_with="%s"' % assign_with if assign_with is not None else '',
-            'default': ' default="%s"' % default if default is not None else '',
-            'handlers': '\n'.join(
-                '<handler id="{id}"{tags}/>'.format(
-                    id=x['id'],
-                    tags=' tags="%s"' % x['tags'] if 'tags' in x else ''
-                ) for x in handlers),
+            "assign_with": ' assign_with="%s"' % assign_with if assign_with is not None else "",
+            "default": ' default="%s"' % default if default is not None else "",
+            "handlers": "\n".join(
+                '<handler id="{id}"{tags}/>'.format(id=x["id"], tags=' tags="%s"' % x["tags"] if "tags" in x else "")
+                for x in handlers
+            ),
         }
         self.__write_config_from(HANDLER_TEMPLATE_JOB_CONFIG_FILE, template=template)
 
@@ -46,35 +44,32 @@ class BaseHandlerAssignmentMethodIntegrationTestCase(integration_util.Integratio
 
 
 class DBPreassignHandlerAssignmentMethodIntegrationTestCase(BaseHandlerAssignmentMethodIntegrationTestCase):
-
     def setUp(self):
-        self._with_handlers_config(assign_with='db-preassign', handlers=[{'id': 'main'}])
+        self._with_handlers_config(assign_with="db-preassign", handlers=[{"id": "main"}])
         super().setUp()
 
     def test_handler_assignment(self):
-        tool_id = 'config_vars'
+        tool_id = "config_vars"
         self._run_tool_test(tool_id)
 
 
 class DBTransactionIsolationHandlerAssignmentMethodIntegrationTestCase(BaseHandlerAssignmentMethodIntegrationTestCase):
-
     def setUp(self):
-        self._with_handlers_config(assign_with='db-transaction-isolation', handlers=[{'id': 'main'}])
+        self._with_handlers_config(assign_with="db-transaction-isolation", handlers=[{"id": "main"}])
         super().setUp()
 
     def test_handler_assignment(self):
         self._skip_unless_postgres()
-        tool_id = 'config_vars'
+        tool_id = "config_vars"
         self._run_tool_test(tool_id)
 
 
 class DBSkipLockedHandlerAssignmentMethodIntegrationTestCase(BaseHandlerAssignmentMethodIntegrationTestCase):
-
     def setUp(self):
-        self._with_handlers_config(assign_with='db-skip-locked', handlers=[{'id': 'main'}])
+        self._with_handlers_config(assign_with="db-skip-locked", handlers=[{"id": "main"}])
         super().setUp()
 
     def test_handler_assignment(self):
         self._skip_unless_postgres()
-        tool_id = 'config_vars'
+        tool_id = "config_vars"
         self._run_tool_test(tool_id)
diff --git a/test/integration/test_history_import_export.py b/test/integration/test_history_import_export.py
index b29f87f53bf..5aba1fb585f 100644
--- a/test/integration/test_history_import_export.py
+++ b/test/integration/test_history_import_export.py
@@ -11,5 +11,5 @@ class ImportExportHistoryOutputsToWorkingDirTestCase(ImportExportTests, Integrat
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
-        config['metadata_strategy'] = 'extended'
-        config['outputs_to_working_directory'] = True
+        config["metadata_strategy"] = "extended"
+        config["outputs_to_working_directory"] = True
diff --git a/test/integration/test_interactivetools_api.py b/test/integration/test_interactivetools_api.py
index 18979a8fbaa..06c63c1b224 100644
--- a/test/integration/test_interactivetools_api.py
+++ b/test/integration/test_interactivetools_api.py
@@ -70,7 +70,7 @@ class BaseInteractiveToolsIntegrationTestCase(ContainerizedIntegrationTestCase):
                 return None
             elif any(not e["active"] for e in entry_points):
                 job_json = self._get(f"jobs/{job_id}?full=true").json()
-                if job_json['state'] == 'error':
+                if job_json["state"] == "error":
                     raise Exception(f"Interactive tool job {job_id} failed: {job_json}")
                 return None
             else:
@@ -87,7 +87,6 @@ class BaseInteractiveToolsIntegrationTestCase(ContainerizedIntegrationTestCase):
 
 
 class RunsInterativeToolTests:
-
     def test_simple_execution(self):
         response_dict = self.dataset_populator.run_tool("interactivetool_simple", {}, self.history_id)
         assert "jobs" in response_dict, response_dict
@@ -122,16 +121,18 @@ class RunsInterativeToolTests:
         assert content1 == "moo cow\n", content1
         stop_response = self.dataset_populator._delete(f'entry_points/{entry_point0["id"]}')
         stop_response.raise_for_status()
-        self.dataset_populator.wait_for_job(job0['id'], assert_ok=True)
-        job_details = self.dataset_populator.get_job_details(job0['id'], full=True)
+        self.dataset_populator.wait_for_job(job0["id"], assert_ok=True)
+        job_details = self.dataset_populator.get_job_details(job0["id"], full=True)
         job_details.raise_for_status()
         job_details = job_details.json()
-        assert job_details['state'] == 'ok'
-        it_output_details = self.dataset_populator.get_history_dataset_details_raw(self.history_id, dataset_id=job_details['outputs']['test_output']['id'])
+        assert job_details["state"] == "ok"
+        it_output_details = self.dataset_populator.get_history_dataset_details_raw(
+            self.history_id, dataset_id=job_details["outputs"]["test_output"]["id"]
+        )
         it_output_details.raise_for_status()
         it_output_details = it_output_details.json()
-        assert it_output_details['state'] == 'ok'
-        assert not it_output_details['deleted']
+        assert it_output_details["state"] == "ok"
+        assert not it_output_details["deleted"]
 
 
 class InteractiveToolsIntegrationTestCase(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
@@ -139,11 +140,10 @@ class InteractiveToolsIntegrationTestCase(BaseInteractiveToolsIntegrationTestCas
 
 
 class InteractiveToolsPulsarIntegrationTestCase(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE_DOCKER
-        config["galaxy_infrastructure_url"] = 'http://localhost:$UWSGI_PORT'
+        config["galaxy_infrastructure_url"] = "http://localhost:$UWSGI_PORT"
         disable_dependency_resolution(config)
 
 
@@ -155,12 +155,15 @@ class InteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsIntegra
     $ # Need to create new DB for each test I think, duplicate IDs are the problem I think because each test starts at 1
     $ GALAXY_TEST_EXTERNAL_PROXY_HOST="localhost:9001" GALAXY_TEST_EXTERNAL_PROXY_MAP="$HOME/gxitexproxy.sqlite" pytest -s test/integration/test_interactivetools_api.py::InteractiveToolsRemoteProxyIntegrationTestCase
     """
+
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         interactivetools_map = os.environ.get("GALAXY_TEST_EXTERNAL_PROXY_MAP")
         interactivetools_proxy_host = os.environ.get("GALAXY_TEST_EXTERNAL_PROXY_HOST")
         if not interactivetools_map or not interactivetools_proxy_host:
-            pytest.skip(f"External proxy not configured for test [map={interactivetools_map},host={interactivetools_proxy_host}]")
+            pytest.skip(
+                f"External proxy not configured for test [map={interactivetools_map},host={interactivetools_proxy_host}]"
+            )
         config["job_config_file"] = DOCKERIZED_JOB_CONFIG_FILE
         config["interactivetools_proxy_host"] = interactivetools_proxy_host
         config["interactivetools_map"] = interactivetools_map
@@ -170,7 +173,9 @@ class InteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsIntegra
 @integration_util.skip_unless_kubernetes()
 @integration_util.skip_unless_amqp()
 @integration_util.skip_if_github_workflow()
-class KubeInteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
+class KubeInteractiveToolsRemoteProxyIntegrationTestCase(
+    BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests
+):
     """
     $ git clone https://github.com/galaxyproject/gx-it-proxy.git $HOME/gx-it-proxy
     $ cd $HOME/gx-it-proxy/docker/k8s
@@ -184,6 +189,7 @@ class KubeInteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsInt
     $ cd back/to/galaxy
     $ GALAXY_TEST_K8S_EXTERNAL_PROXY_HOST="localhost:9002" GALAXY_TEST_K8S_EXTERNAL_PROXY_MAP="$HOME/gxitk8proxy.sqlite" pytest -s test/integration/test_interactivetools_api.py::KubeInteractiveToolsRemoteProxyIntegrationTestCase
     """
+
     require_uwsgi = True
 
     @classmethod
@@ -197,7 +203,9 @@ class KubeInteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsInt
         interactivetools_map = os.environ.get("GALAXY_TEST_K8S_EXTERNAL_PROXY_MAP")
         interactivetools_proxy_host = os.environ.get("GALAXY_TEST_K8S_EXTERNAL_PROXY_HOST")
         if not interactivetools_map or not interactivetools_proxy_host:
-            pytest.skip(f"External proxy not configured for test [map={interactivetools_map},host={interactivetools_proxy_host}]")
+            pytest.skip(
+                f"External proxy not configured for test [map={interactivetools_map},host={interactivetools_proxy_host}]"
+            )
 
         config["interactivetools_proxy_host"] = interactivetools_proxy_host
         config["interactivetools_map"] = interactivetools_map
@@ -205,7 +213,7 @@ class KubeInteractiveToolsRemoteProxyIntegrationTestCase(BaseInteractiveToolsInt
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
         config["job_config_file"] = job_config(CONTAINERIZED_TEMPLATE, cls.jobs_directory)
-        config["default_job_shell"] = '/bin/sh'
+        config["default_job_shell"] = "/bin/sh"
 
         set_infrastucture_url(config)
         disable_dependency_resolution(config)
diff --git a/test/integration/test_job_environments.py b/test/integration/test_job_environments.py
index 1e619d81409..5997bf7d852 100644
--- a/test/integration/test_job_environments.py
+++ b/test/integration/test_job_environments.py
@@ -17,14 +17,17 @@ SETS_TMP_DIR_TO_TRUE_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_t
 SETS_TMP_DIR_AS_EXPRESSION_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_expression_job_conf.xml")
 EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
 
-JobEnvironmentProperties = collections.namedtuple("JobEnvironmentProperties", [
-    "user_id",
-    "group_id",
-    "pwd",
-    "home",
-    "tmp",
-    "some_env",
-])
+JobEnvironmentProperties = collections.namedtuple(
+    "JobEnvironmentProperties",
+    [
+        "user_id",
+        "group_id",
+        "pwd",
+        "home",
+        "tmp",
+        "some_env",
+    ],
+)
 
 
 class BaseJobEnvironmentIntegrationTestCase(integration_util.IntegrationTestCase):
@@ -64,7 +67,6 @@ class BaseJobEnvironmentIntegrationTestCase(integration_util.IntegrationTestCase
 
 
 class DefaultJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = tempfile.mkdtemp()
@@ -132,7 +134,7 @@ class EmbeddedPulsarDefaultJobEnvironmentIntegrationTestCase(BaseJobEnvironmentI
 
         assert job_env.user_id == str(euid), job_env.user_id
         assert job_env.group_id == str(egid), job_env.group_id
-        assert 'pulsar_staging' in job_env.pwd
+        assert "pulsar_staging" in job_env.pwd
         assert job_env.pwd.endswith("/working")
         # job ran in embedded pulsar, not local job dir
         assert self.jobs_directory not in job_env.pwd
@@ -146,7 +148,6 @@ class EmbeddedPulsarDefaultJobEnvironmentIntegrationTestCase(BaseJobEnvironmentI
 
 
 class TmpDirToTrueJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = tempfile.mkdtemp()
@@ -164,7 +165,6 @@ class TmpDirToTrueJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegratio
 
 
 class TmpDirAsShellCommandJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = tempfile.mkdtemp()
@@ -182,7 +182,6 @@ class TmpDirAsShellCommandJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIn
 
 
 class SharedHomeJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = tempfile.mkdtemp()
@@ -219,7 +218,6 @@ class SharedHomeJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationT
 
 
 class JobIOEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         cls.jobs_directory = tempfile.mkdtemp()
@@ -236,7 +234,7 @@ class JobIOEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase)
         job = jobs[0]
         job_details = self.dataset_populator.get_job_details(job["id"], full=True)
         job_details = job_details.json()
-        assert 'moo std cow' in job_details['job_stdout']
-        assert 'moo err cow' in job_details['job_stderr']
-        assert 'Writing environment properties to output files.' in job_details['tool_stdout']
-        assert 'Example tool stderr output.' in job_details['tool_stderr']
+        assert "moo std cow" in job_details["job_stdout"]
+        assert "moo err cow" in job_details["job_stderr"]
+        assert "Writing environment properties to output files." in job_details["tool_stdout"]
+        assert "Example tool stderr output." in job_details["tool_stderr"]
diff --git a/test/integration/test_job_outputs_to_working_directory.py b/test/integration/test_job_outputs_to_working_directory.py
index 7e9cbeb063e..a8f574a5dc1 100644
--- a/test/integration/test_job_outputs_to_working_directory.py
+++ b/test/integration/test_job_outputs_to_working_directory.py
@@ -15,4 +15,6 @@ class JobOutputsToWorkingDirectoryIntegrationInstance(integration_util.Integrati
 
 instance = integration_util.integration_module_instance(JobOutputsToWorkingDirectoryIntegrationInstance)
 
-test_tools = integration_util.integration_tool_runner(["output_format", "output_empty_work_dir", "collection_creates_pair_from_work_dir"])
+test_tools = integration_util.integration_tool_runner(
+    ["output_format", "output_empty_work_dir", "collection_creates_pair_from_work_dir"]
+)
diff --git a/test/integration/test_job_recovery.py b/test/integration/test_job_recovery.py
index c3771043b26..1f624e0ccad 100644
--- a/test/integration/test_job_recovery.py
+++ b/test/integration/test_job_recovery.py
@@ -2,9 +2,7 @@
 
 import os
 
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
diff --git a/test/integration/test_job_resubmission.py b/test/integration/test_job_resubmission.py
index 809eac31a4f..943c09b7685 100644
--- a/test/integration/test_job_resubmission.py
+++ b/test/integration/test_job_resubmission.py
@@ -9,10 +9,18 @@ JOB_RESUBMISSION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_
 JOB_RESUBMISSION_DEFAULT_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_default_job_conf.xml")
 JOB_RESUBMISSION_DYNAMIC_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_dynamic_job_conf.xml")
 JOB_RESUBMISSION_SMALL_MEMORY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_small_memory_job_conf.xml")
-JOB_RESUBMISSION_SMALL_MEMORY_RESUBMISSION_TO_LARGE_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_small_memory_resubmission_to_large_job_conf.xml")
-JOB_RESUBMISSION_TOOL_DETECTED_ALWAYS_ERROR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_tool_detected_always_error_job_conf.xml")
-JOB_RESUBMISSION_TOOL_DETECTED_RESUBMIT_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_tool_detected_resubmit_job_conf.xml")
-JOB_RESUBMISSION_JOB_RESOURCES_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_job_resource_parameters_conf.xml")
+JOB_RESUBMISSION_SMALL_MEMORY_RESUBMISSION_TO_LARGE_JOB_CONFIG_FILE = os.path.join(
+    SCRIPT_DIRECTORY, "resubmission_small_memory_resubmission_to_large_job_conf.xml"
+)
+JOB_RESUBMISSION_TOOL_DETECTED_ALWAYS_ERROR_JOB_CONFIG_FILE = os.path.join(
+    SCRIPT_DIRECTORY, "resubmission_tool_detected_always_error_job_conf.xml"
+)
+JOB_RESUBMISSION_TOOL_DETECTED_RESUBMIT_JOB_CONFIG_FILE = os.path.join(
+    SCRIPT_DIRECTORY, "resubmission_tool_detected_resubmit_job_conf.xml"
+)
+JOB_RESUBMISSION_JOB_RESOURCES_CONFIG_FILE = os.path.join(
+    SCRIPT_DIRECTORY, "resubmission_job_resource_parameters_conf.xml"
+)
 JOB_RESUBMISSION_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_pulsar_job_conf.xml")
 
 
@@ -51,64 +59,117 @@ class JobResubmissionIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
 
     def test_job_resources(self):
         """Test initial environment dynamic rule used by remaining re-submission test case works."""
-        self._assert_job_passes(resource_parameters={"test_name": "test_job_resources", "initial_target_environment": "local"})
+        self._assert_job_passes(
+            resource_parameters={"test_name": "test_job_resources", "initial_target_environment": "local"}
+        )
 
     def test_failure_runner(self):
         """Test FailsJobRunner used by remaining re-submission test cases."""
-        self._assert_job_fails(resource_parameters={"test_name": "test_failure_runner", "initial_target_environment": "fails_without_resubmission"})
+        self._assert_job_fails(
+            resource_parameters={
+                "test_name": "test_failure_runner",
+                "initial_target_environment": "fails_without_resubmission",
+            }
+        )
 
     def test_walltime_resubmission(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_walltime_resubmission", "failure_state": "walltime_reached"})
+        self._assert_job_passes(
+            resource_parameters={"test_name": "test_walltime_resubmission", "failure_state": "walltime_reached"}
+        )
 
     def test_memory_resubmission(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_memory_resubmission", "failure_state": "memory_limit_reached"})
+        self._assert_job_passes(
+            resource_parameters={"test_name": "test_memory_resubmission", "failure_state": "memory_limit_reached"}
+        )
 
     def test_unknown_error(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_unknown_error", "failure_state": "unknown_error"})
+        self._assert_job_passes(
+            resource_parameters={"test_name": "test_unknown_error", "failure_state": "unknown_error"}
+        )
 
     def test_condition_expressions(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_condition_expressions_0",
-                                                     "initial_target_environment": "fail_first_if_memory_or_walltime",
-                                                     "failure_state": "memory_limit_reached"})
-        self._assert_job_passes(resource_parameters={"test_name": "test_condition_expressions_1",
-                                                     "initial_target_environment": "fail_first_if_memory_or_walltime",
-                                                     "failure_state": "walltime_reached"})
-        self._assert_job_fails(resource_parameters={"test_name": "test_condition_expressions_2",
-                                                    "initial_target_environment": "fail_first_if_memory_or_walltime",
-                                                    "failure_state": "unknown_error"})
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_condition_expressions_0",
+                "initial_target_environment": "fail_first_if_memory_or_walltime",
+                "failure_state": "memory_limit_reached",
+            }
+        )
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_condition_expressions_1",
+                "initial_target_environment": "fail_first_if_memory_or_walltime",
+                "failure_state": "walltime_reached",
+            }
+        )
+        self._assert_job_fails(
+            resource_parameters={
+                "test_name": "test_condition_expressions_2",
+                "initial_target_environment": "fail_first_if_memory_or_walltime",
+                "failure_state": "unknown_error",
+            }
+        )
 
     def test_condition_any_failure(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_condition_any_failure",
-                                                     "initial_target_environment": "fail_first_any_failure",
-                                                     "failure_state": "unknown_error"})
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_condition_any_failure",
+                "initial_target_environment": "fail_first_any_failure",
+                "failure_state": "unknown_error",
+            }
+        )
 
     def test_condition_attempt(self):
-        self._assert_job_fails(resource_parameters={"test_name": "test_condition_attempt",
-                                                    "initial_target_environment": "fail_two_attempts",
-                                                    "failure_state": "unknown_error"})
-        self._assert_job_passes(resource_parameters={"test_name": "test_condition_attempt",
-                                                     "initial_target_environment": "fail_two_attempts",
-                                                     "failure_state": "walltime_reached"})
+        self._assert_job_fails(
+            resource_parameters={
+                "test_name": "test_condition_attempt",
+                "initial_target_environment": "fail_two_attempts",
+                "failure_state": "unknown_error",
+            }
+        )
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_condition_attempt",
+                "initial_target_environment": "fail_two_attempts",
+                "failure_state": "walltime_reached",
+            }
+        )
 
     def test_condition_seconds_running(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_condition_seconds_running",
-                                                     "initial_target_environment": "resubmit_if_short",
-                                                     "failure_state": "walltime_reached",
-                                                     "run_for": "1"})
-        self._assert_job_fails(resource_parameters={"test_name": "test_condition_seconds_running",
-                                                    "initial_target_environment": "resubmit_if_short",
-                                                    "failure_state": "walltime_reached",
-                                                    "run_for": "15"})
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_condition_seconds_running",
+                "initial_target_environment": "resubmit_if_short",
+                "failure_state": "walltime_reached",
+                "run_for": "1",
+            }
+        )
+        self._assert_job_fails(
+            resource_parameters={
+                "test_name": "test_condition_seconds_running",
+                "initial_target_environment": "resubmit_if_short",
+                "failure_state": "walltime_reached",
+                "run_for": "15",
+            }
+        )
 
     def test_resubmission_after_delay(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_resubmission_after_delay",
-                                                     "initial_target_environment": "resubmit_after_delay",
-                                                     "failure_state": "unknown_error"})
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_resubmission_after_delay",
+                "initial_target_environment": "resubmit_after_delay",
+                "failure_state": "unknown_error",
+            }
+        )
 
     def test_resubmission_after_delay_expression(self):
-        self._assert_job_passes(resource_parameters={"test_name": "test_resubmission_after_delay_expression",
-                                                     "initial_target_environment": "resubmit_after_two_delays",
-                                                     "failure_state": "unknown_error"})
+        self._assert_job_passes(
+            resource_parameters={
+                "test_name": "test_resubmission_after_delay_expression",
+                "initial_target_environment": "resubmit_after_two_delays",
+                "failure_state": "unknown_error",
+            }
+        )
 
 
 class JobResubmissionDefaultIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
@@ -139,7 +200,6 @@ class JobResubmissionDynamicIntegrationTestCase(_BaseResubmissionIntegerationTes
 
 # Verify the test tool fails if only a small amount of memory is allocated.
 class JobResubmissionSmallMemoryIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = JOB_RESUBMISSION_SMALL_MEMORY_JOB_CONFIG_FILE
@@ -151,7 +211,6 @@ class JobResubmissionSmallMemoryIntegrationTestCase(_BaseResubmissionIntegeratio
 # Verify the test tool will resubmit on failure tested above and will then pass with
 # proper resubmission condition.
 class JobResubmissionSmallMemoryResubmitsToLargeIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = JOB_RESUBMISSION_SMALL_MEMORY_RESUBMISSION_TO_LARGE_JOB_CONFIG_FILE
@@ -162,7 +221,6 @@ class JobResubmissionSmallMemoryResubmitsToLargeIntegrationTestCase(_BaseResubmi
 
 # Verify the test tool fails with an exit code issue.
 class JobResubmissionToolDetectedErrorIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = JOB_RESUBMISSION_TOOL_DETECTED_ALWAYS_ERROR_JOB_CONFIG_FILE
@@ -174,7 +232,6 @@ class JobResubmissionToolDetectedErrorIntegrationTestCase(_BaseResubmissionInteg
 # Verify the test tool will resubmit on failure tested above and will then pass in
 # an environment without a tool indicated error.
 class JobResubmissionToolDetectedErrorResubmitsIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = JOB_RESUBMISSION_TOOL_DETECTED_RESUBMIT_JOB_CONFIG_FILE
@@ -185,7 +242,6 @@ class JobResubmissionToolDetectedErrorResubmitsIntegrationTestCase(_BaseResubmis
 
 # Verify that a failure to connect to pulsar can trigger a resubmit
 class JobResubmissionPulsarIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = JOB_RESUBMISSION_PULSAR_JOB_CONFIG_FILE
diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index 81c767ffd5e..0ebba84c3d4 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -20,23 +20,23 @@ from galaxy_test.driver import integration_util
 from .test_containerized_jobs import MulledJobTestCases
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
 
-PERSISTENT_VOLUME_NAME = 'pv-galaxy-integration-test'
-PERSISTENT_VOLUME_CLAIM_NAME = 'galaxy-pvc-integration-test'
-Config = collections.namedtuple('Config', 'path')
-TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'tools'))
+PERSISTENT_VOLUME_NAME = "pv-galaxy-integration-test"
+PERSISTENT_VOLUME_CLAIM_NAME = "galaxy-pvc-integration-test"
+Config = collections.namedtuple("Config", "path")
+TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "tools"))
 
 
 class KubeSetupConfigTuple(Config):
-
     def setup(self):
-        subprocess.check_call(['kubectl', 'create', '-f', self.path])
+        subprocess.check_call(["kubectl", "create", "-f", self.path])
 
     def teardown(self):
-        subprocess.check_call(['kubectl', 'delete', '-f', self.path])
+        subprocess.check_call(["kubectl", "delete", "-f", self.path])
 
 
 def persistent_volume(path, persistent_volume_name):
-    volume_yaml = string.Template("""
+    volume_yaml = string.Template(
+        """
 kind: PersistentVolume
 apiVersion: v1
 metadata:
@@ -60,15 +60,16 @@ spec:
           operator: NotIn
           values:
             - 'i-do-not-exist'
-    """).substitute(path=path,
-                    persistent_volume_name=persistent_volume_name)
+    """
+    ).substitute(path=path, persistent_volume_name=persistent_volume_name)
     with tempfile.NamedTemporaryFile(suffix="_persistent_volume.yml", mode="w", delete=False) as volume:
         volume.write(volume_yaml)
     return KubeSetupConfigTuple(path=volume.name)
 
 
 def persistent_volume_claim(persistent_volume_name, persistent_volum_claim_name):
-    peristent_volume_claim_yaml = string.Template("""
+    peristent_volume_claim_yaml = string.Template(
+        """
 kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
@@ -81,15 +82,18 @@ spec:
     requests:
       storage: 2Gi
   storageClassName: manual
-""").substitute(persistent_volume_name=persistent_volume_name,
-                persistent_volume_claim_name=persistent_volum_claim_name)
+"""
+    ).substitute(
+        persistent_volume_name=persistent_volume_name, persistent_volume_claim_name=persistent_volum_claim_name
+    )
     with tempfile.NamedTemporaryFile(suffix="_persistent_volume_claim.yml", mode="w", delete=False) as volume_claim:
         volume_claim.write(peristent_volume_claim_yaml)
     return KubeSetupConfigTuple(path=volume_claim.name)
 
 
 def job_config(jobs_directory):
-    job_conf_template = string.Template("""<job_conf>
+    job_conf_template = string.Template(
+        """<job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
         <plugin id="k8s" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
@@ -144,29 +148,29 @@ def job_config(jobs_directory):
         <tool id="galaxy_slots_and_memory" destination="k8s_destination_no_cleanup"/>
     </tools>
 </job_conf>
-""")
-    job_conf_str = job_conf_template.substitute(jobs_directory=jobs_directory,
-                                                tool_directory=TOOL_DIR,
-                                                k8s_config_path=integration_util.k8s_config_path(),
-                                                )
+"""
+    )
+    job_conf_str = job_conf_template.substitute(
+        jobs_directory=jobs_directory,
+        tool_directory=TOOL_DIR,
+        k8s_config_path=integration_util.k8s_config_path(),
+    )
     with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf.xml", mode="w", delete=False) as job_conf:
         job_conf.write(job_conf_str)
     return Config(job_conf.name)
 
 
 class KubernetesDatasetPopulator(DatasetPopulator):
-
     def wait_for_history(self, *args, **kwargs):
         try:
             super().wait_for_history(*args, **kwargs)
         except AssertionError:
-            print("Kubernetes status:\n %s" % unicodify(subprocess.check_output(['kubectl', 'describe', 'nodes'])))
+            print("Kubernetes status:\n %s" % unicodify(subprocess.check_output(["kubectl", "describe", "nodes"])))
             raise
 
 
 @integration_util.skip_unless_kubernetes()
 class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = KubernetesDatasetPopulator(self.galaxy_interactor)
@@ -177,8 +181,8 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
         # realpath for docker deployed in a VM on Mac, also done in driver_util.
         cls.jobs_directory = os.path.realpath(tempfile.mkdtemp())
         cls.volumes = [
-            [cls.jobs_directory, 'jobs-directory-volume', 'jobs-directory-claim'],
-            [TOOL_DIR, 'tool-directory-volume', 'tool-directory-claim'],
+            [cls.jobs_directory, "jobs-directory-volume", "jobs-directory-claim"],
+            [TOOL_DIR, "tool-directory-volume", "tool-directory-claim"],
         ]
         cls.persistent_volumes = []
         cls.persistent_volume_claims = []
@@ -203,18 +207,18 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         # TODO: implement metadata setting as separate job, as service or side-car
-        config['retry_metadata_internally'] = True
+        config["retry_metadata_internally"] = True
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
         config["job_config_file"] = cls.job_config.path
-        config["default_job_shell"] = '/bin/sh'
+        config["default_job_shell"] = "/bin/sh"
         # Disable tool dependency resolution.
         config["tool_dependency_dir"] = "none"
 
     @skip_without_tool("job_environment_default")
     def test_job_environment(self):
         job_env = self._run_and_get_environment_properties()
-        assert job_env.some_env == '42'
+        assert job_env.some_env == "42"
 
     @staticmethod
     def _wait_for_external_state(sa_session, job, expected):
@@ -227,7 +231,7 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
             time.sleep(1)
             max_tries -= 1
 
-    @skip_without_tool('cat_data_and_sleep')
+    @skip_without_tool("cat_data_and_sleep")
     def test_kill_process(self):
         with self.dataset_populator.test_history() as history_id:
             hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
@@ -250,9 +254,9 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
             assert not job.finished
 
             external_id = job.job_runner_external_id
-            output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
+            output = unicodify(subprocess.check_output(["kubectl", "get", "job", external_id, "-o", "json"]))
             status = json.loads(output)
-            assert status['status']['active'] == 1
+            assert status["status"]["active"] == 1
 
             delete_response = self.dataset_populator.cancel_job(job_dict["id"])
             assert delete_response.json() is True
@@ -261,10 +265,10 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
             time.sleep(2)
             # The default job config removes jobs, didn't find a better way to check that the job doesn't exist anymore
             with pytest.raises(subprocess.CalledProcessError) as excinfo:
-                subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json'], stderr=subprocess.STDOUT)
+                subprocess.check_output(["kubectl", "get", "job", external_id, "-o", "json"], stderr=subprocess.STDOUT)
             assert "not found" in unicodify(excinfo.value.output)
 
-    @skip_without_tool('cat_data_and_sleep')
+    @skip_without_tool("cat_data_and_sleep")
     def test_external_job_delete(self):
         with self.dataset_populator.test_history() as history_id:
             hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
@@ -286,80 +290,80 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
             self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
 
             external_id = job.job_runner_external_id
-            output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
+            output = unicodify(subprocess.check_output(["kubectl", "get", "job", external_id, "-o", "json"]))
             status = json.loads(output)
-            assert status['status']['active'] == 1
+            assert status["status"]["active"] == 1
 
-            output = unicodify(subprocess.check_output(['kubectl', 'delete', 'job', external_id, '-o', 'name']))
-            assert 'job.batch/%s' % external_id in output
+            output = unicodify(subprocess.check_output(["kubectl", "delete", "job", external_id, "-o", "name"]))
+            assert "job.batch/%s" % external_id in output
 
-            result = self.dataset_populator.wait_for_tool_run(run_response=running_response, history_id=history_id,
-                                                              assert_ok=False).json()
-            details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
+            result = self.dataset_populator.wait_for_tool_run(
+                run_response=running_response, history_id=history_id, assert_ok=False
+            ).json()
+            details = self.dataset_populator.get_job_details(result["jobs"][0]["id"], full=True).json()
 
-            assert details['state'] == app.model.Job.states.ERROR, details
+            assert details["state"] == app.model.Job.states.ERROR, details
 
-    @skip_without_tool('job_properties')
+    @skip_without_tool("job_properties")
     def test_exit_code_127(self):
-        inputs = {
-            'failbool': True
-        }
+        inputs = {"failbool": True}
         running_response = self.dataset_populator.run_tool_raw(
             "job_properties",
             inputs,
             self.history_id,
         )
-        result = self.dataset_populator.wait_for_tool_run(run_response=running_response, history_id=self.history_id, assert_ok=False).json()
-        details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
+        result = self.dataset_populator.wait_for_tool_run(
+            run_response=running_response, history_id=self.history_id, assert_ok=False
+        ).json()
+        details = self.dataset_populator.get_job_details(result["jobs"][0]["id"], full=True).json()
 
-        assert details['state'] == 'error', details
-        assert details['stdout'].strip() == 'The bool is not true', details
-        assert details['stderr'].strip() == 'The bool is very not true', details
-        assert details['exit_code'] == 127, details
+        assert details["state"] == "error", details
+        assert details["stdout"].strip() == "The bool is not true", details
+        assert details["stderr"].strip() == "The bool is very not true", details
+        assert details["exit_code"] == 127, details
 
-    @skip_without_tool('Count1')
+    @skip_without_tool("Count1")
     def test_python_dep(self):
         with self.dataset_populator.test_history() as history_id:
-            hda1 = self.dataset_populator.new_dataset(history_id, content="1\t2\t3", file_type='tabular', wait=True)
+            hda1 = self.dataset_populator.new_dataset(history_id, content="1\t2\t3", file_type="tabular", wait=True)
             self.dataset_populator.run_tool(
-                'Count1',
-                {'input': {"src": "hda", "id": hda1["id"]},
-                 'column': [1]},
+                "Count1",
+                {"input": {"src": "hda", "id": hda1["id"]}, "column": [1]},
                 self.history_id,
             )
 
-    @skip_without_tool('galaxy_slots_and_memory')
+    @skip_without_tool("galaxy_slots_and_memory")
     def test_slots_and_memory(self):
         running_response = self.dataset_populator.run_tool(
-            'galaxy_slots_and_memory',
+            "galaxy_slots_and_memory",
             {},
             self.history_id,
         )
         dataset_content = self.dataset_populator.get_history_dataset_content(self.history_id, hid=1).strip()
-        CPU = '2'
-        MEM = '10'
-        MEM_PER_SLOT = '5'
-        assert [CPU, MEM, MEM_PER_SLOT] == dataset_content.split('\n'), dataset_content
+        CPU = "2"
+        MEM = "10"
+        MEM_PER_SLOT = "5"
+        assert [CPU, MEM, MEM_PER_SLOT] == dataset_content.split("\n"), dataset_content
 
         # Tool is mapped to destination without cleanup, make sure job still exists in kubernetes API
         job_dict = running_response["jobs"][0]
-        job = self.galaxy_interactor.get("jobs/%s" % job_dict['id'], admin=True).json()
-        external_id = job['external_id']
-        output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
+        job = self.galaxy_interactor.get("jobs/%s" % job_dict["id"], admin=True).json()
+        external_id = job["external_id"]
+        output = unicodify(subprocess.check_output(["kubectl", "get", "job", external_id, "-o", "json"]))
         status = json.loads(output)
-        assert 'active' not in status['status']
+        assert "active" not in status["status"]
 
-    @skip_without_tool('create_2')
+    @skip_without_tool("create_2")
     def test_walltime_limit(self):
         running_response = self.dataset_populator.run_tool_raw(
-            'create_2',
-            {'sleep_time': 60},
+            "create_2",
+            {"sleep_time": 60},
             self.history_id,
         )
-        result = self.dataset_populator.wait_for_tool_run(run_response=running_response,
-                                                          history_id=self.history_id,
-                                                          assert_ok=False).json()
-        details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
-        assert details['state'] == 'error'
+        result = self.dataset_populator.wait_for_tool_run(
+            run_response=running_response, history_id=self.history_id, assert_ok=False
+        ).json()
+        details = self.dataset_populator.get_job_details(result["jobs"][0]["id"], full=True).json()
+        assert details["state"] == "error"
         hda_details = self.dataset_populator.get_history_dataset_details(self.history_id, assert_ok=False)
-        assert hda_details['misc_info'] == 'Job was active longer than specified deadline'
+        assert hda_details["misc_info"] == "Job was active longer than specified deadline"
diff --git a/test/integration/test_kubernetes_staging.py b/test/integration/test_kubernetes_staging.py
index 0c98674c63e..f923db679f2 100644
--- a/test/integration/test_kubernetes_staging.py
+++ b/test/integration/test_kubernetes_staging.py
@@ -25,13 +25,18 @@ from galaxy.jobs.runners.util.pykube_util import (
 )
 from galaxy_test.base.populators import skip_without_tool
 from galaxy_test.driver import integration_util
-from .test_containerized_jobs import EXTENDED_TIMEOUT, MulledJobTestCases
+from .test_containerized_jobs import (
+    EXTENDED_TIMEOUT,
+    MulledJobTestCases,
+)
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
 from .test_kubernetes_runner import KubernetesDatasetPopulator
 from .test_local_job_cancellation import CancelsJob
 
-TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'tools'))
-GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST = os.environ.get("GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST", "host.docker.internal")
+TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "tools"))
+GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST = os.environ.get(
+    "GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST", "host.docker.internal"
+)
 AMQP_URL = integration_util.AMQP_URL
 GALAXY_TEST_KUBERNETES_NAMESPACE = os.environ.get("GALAXY_TEST_K8S_NAMESPACE", "default")
 
@@ -101,15 +106,16 @@ tools:
 def job_config(template_str, jobs_directory):
     job_conf_template = string.Template(template_str)
     container_amqp_url = to_infrastructure_uri(AMQP_URL)
-    instance_id = ''.join(random.choice(string.ascii_lowercase) for i in range(8))
-    job_conf_str = job_conf_template.substitute(jobs_directory=jobs_directory,
-                                                tool_directory=TOOL_DIR,
-                                                instance_id=instance_id,
-                                                k8s_config_path=integration_util.k8s_config_path(),
-                                                k8s_namespace=GALAXY_TEST_KUBERNETES_NAMESPACE,
-                                                amqp_url=AMQP_URL,
-                                                container_amqp_url=container_amqp_url,
-                                                )
+    instance_id = "".join(random.choice(string.ascii_lowercase) for i in range(8))
+    job_conf_str = job_conf_template.substitute(
+        jobs_directory=jobs_directory,
+        tool_directory=TOOL_DIR,
+        instance_id=instance_id,
+        k8s_config_path=integration_util.k8s_config_path(),
+        k8s_namespace=GALAXY_TEST_KUBERNETES_NAMESPACE,
+        amqp_url=AMQP_URL,
+        container_amqp_url=container_amqp_url,
+    )
     with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf.yml", mode="w", delete=False) as job_conf:
         job_conf.write(job_conf_str)
     return job_conf.name
@@ -119,7 +125,6 @@ def job_config(template_str, jobs_directory):
 @integration_util.skip_unless_amqp()
 @integration_util.skip_if_github_workflow()
 class BaseKubernetesStagingTest(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = KubernetesDatasetPopulator(self.galaxy_interactor)
@@ -133,14 +138,13 @@ class BaseKubernetesStagingTest(BaseJobEnvironmentIntegrationTestCase, MulledJob
 
 
 class KubernetesStagingContainerIntegrationTestCase(CancelsJob, BaseKubernetesStagingTest):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
         cls.job_config_file = job_config(CONTAINERIZED_TEMPLATE, cls.jobs_directory)
         config["job_config_file"] = cls.job_config_file
-        config["default_job_shell"] = '/bin/sh'
+        config["default_job_shell"] = "/bin/sh"
         # Disable local tool dependency resolution.
         config["tool_dependency_dir"] = "none"
         set_infrastucture_url(config)
@@ -169,7 +173,7 @@ class KubernetesStagingContainerIntegrationTestCase(CancelsJob, BaseKubernetesSt
     @skip_without_tool("job_environment_default")
     def test_job_environment(self):
         job_env = self._run_and_get_environment_properties()
-        assert job_env.some_env == '42'
+        assert job_env.some_env == "42"
 
     @property
     def _active_kubernetes_jobs(self):
@@ -186,14 +190,13 @@ class KubernetesStagingContainerIntegrationTestCase(CancelsJob, BaseKubernetesSt
 
 
 class KubernetesDependencyResolutionIntegrationTestCase(BaseKubernetesStagingTest):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["jobs_directory"] = cls.jobs_directory
         config["file_path"] = cls.jobs_directory
         config["job_config_file"] = job_config(DEPENDENCY_RESOLUTION_TEMPLATE, cls.jobs_directory)
 
-        config["default_job_shell"] = '/bin/sh'
+        config["default_job_shell"] = "/bin/sh"
         # Disable tool dependency resolution.
         config["tool_dependency_dir"] = "none"
         set_infrastucture_url(config)
diff --git a/test/integration/test_local_job_cancellation.py b/test/integration/test_local_job_cancellation.py
index 83768eac131..1e79a555f33 100644
--- a/test/integration/test_local_job_cancellation.py
+++ b/test/integration/test_local_job_cancellation.py
@@ -4,14 +4,11 @@ import time
 
 import psutil
 
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 
 class CancelsJob:
-
     def _setup_cat_data_and_sleep(self, history_id):
         hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
         running_inputs = {
@@ -27,9 +24,11 @@ class CancelsJob:
         return job_dict["id"]
 
     def _wait_for_job_running(self, job_id):
-        self.galaxy_interactor.wait_for(lambda: self._get("jobs/%s" % job_id).json()['state'] != 'running',
-                                        what="Wait for job to start running",
-                                        maxseconds=60)
+        self.galaxy_interactor.wait_for(
+            lambda: self._get("jobs/%s" % job_id).json()["state"] != "running",
+            what="Wait for job to start running",
+            maxseconds=60,
+        )
 
 
 class LocalJobCancellationTestCase(CancelsJob, integration_util.IntegrationTestCase):
@@ -49,17 +48,18 @@ class LocalJobCancellationTestCase(CancelsJob, integration_util.IntegrationTestC
             Job = app.model.Job
             job = sa_session.query(Job).filter_by(tool_id="cat_data_and_sleep").order_by(Job.create_time.desc()).first()
             # This is how the admin controller code cancels a job
-            job.job_stderr = 'admin cancelled job'
+            job.job_stderr = "admin cancelled job"
             job.set_state(app.model.Job.states.DELETED_NEW)
             sa_session.add(job)
             sa_session.flush()
-            self.galaxy_interactor.wait_for(lambda: self._get("jobs/%s" % job_id).json()['state'] != 'error',
-                                            what="Wait for job to end in error",
-                                            maxseconds=60)
+            self.galaxy_interactor.wait_for(
+                lambda: self._get("jobs/%s" % job_id).json()["state"] != "error",
+                what="Wait for job to end in error",
+                maxseconds=60,
+            )
 
     def test_kill_process(self):
-        """
-        """
+        """ """
         with self.dataset_populator.test_history() as history_id:
             job_id = self._setup_cat_data_and_sleep(history_id)
 
@@ -95,14 +95,14 @@ class LocalJobCancellationTestCase(CancelsJob, integration_util.IntegrationTestC
                 state = job.state
                 if state == app.model.Job.states.DELETED:
                     break
-                time.sleep(.1)
+                time.sleep(0.1)
 
             # Now make sure the pid is actually killed.
             for _ in range(100):
                 if not pid_exists:
                     break
                 pid_exists = psutil.pid_exists(external_id)
-                time.sleep(.1)
+                time.sleep(0.1)
 
             final_state = f"pid exists? {pid_exists}, final db job state {state}"
             assert state == app.model.Job.states.DELETED, final_state
diff --git a/test/integration/test_max_discovered_files.py b/test/integration/test_max_discovered_files.py
index 979685213ee..06735442d3d 100644
--- a/test/integration/test_max_discovered_files.py
+++ b/test/integration/test_max_discovered_files.py
@@ -20,17 +20,19 @@ class MaxDiscoveredFilesTestCase(integration_util.IntegrationTestCase):
     def test_discover(self):
         with self.dataset_populator.test_history() as history_id:
             response = self.dataset_populator.run_tool("discover_sort_by", inputs={}, history_id=history_id)
-            job_id = response["jobs"][0]['id']
+            job_id = response["jobs"][0]["id"]
             self.dataset_populator.wait_for_job(job_id, assert_ok=False)
             job_details_response = self.dataset_populator.get_job_details(job_id, full=True)
             job_details_response.raise_for_status()
             job_details = job_details_response.json()
-            assert job_details['state'] == 'error'
-            assert f"Job generated more than maximum number ({self.max_discovered_files}) of output datasets" in job_details['job_messages']
+            assert job_details["state"] == "error"
+            assert (
+                f"Job generated more than maximum number ({self.max_discovered_files}) of output datasets"
+                in job_details["job_messages"]
+            )
 
 
 class ExtendedMetadataMaxDiscoveredFilesTestCase(MaxDiscoveredFilesTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["max_discovered_files"] = cls.max_discovered_files
diff --git a/test/integration/test_mules_as_job_handlers.py b/test/integration/test_mules_as_job_handlers.py
index e55d51b98c0..d639b15588e 100644
--- a/test/integration/test_mules_as_job_handlers.py
+++ b/test/integration/test_mules_as_job_handlers.py
@@ -13,51 +13,55 @@ class _BaseMulesIntegrationTestCase(integration_util.IntegrationTestCase):
 
     framework_tool_and_types = True
     require_uwsgi = True
-    expected_server_name = 'main.web'
+    expected_server_name = "main.web"
 
     def test_runs_on_mule(self):
-        tool_id = 'config_vars'
+        tool_id = "config_vars"
         expect_server_name = self.expected_server_name
         dataset_populator = DatasetPopulator(self.galaxy_interactor)
         history_id = dataset_populator.new_history()
         payload = dataset_populator.run_tool(
             tool_id=tool_id,
-            inputs={'var': 'server_name'},
+            inputs={"var": "server_name"},
             history_id=history_id,
         )
-        dataset_id = payload['outputs'][0]['id']
+        dataset_id = payload["outputs"][0]["id"]
         dataset_populator.wait_for_dataset(history_id, dataset_id, assert_ok=True)
         output = dataset_populator.get_history_dataset_content(history_id, dataset_id=dataset_id).strip()
-        assert output.startswith(expect_server_name), (
-            "Job handler's server name '{output}' does not start with expected string '{expected}'".format(
-                output=output,
-                expected=expect_server_name,
-            )
+        assert output.startswith(
+            expect_server_name
+        ), "Job handler's server name '{output}' does not start with expected string '{expected}'".format(
+            output=output,
+            expected=expect_server_name,
         )
 
 
 class SingleMuleAsJobHandlersIntegrationTestCase(_BaseMulesIntegrationTestCase):
 
-    expected_server_name = 'main.job-handlers'
+    expected_server_name = "main.job-handlers"
 
     @classmethod
     def handle_uwsgi_cli_command(cls, command):
-        command.extend([
-            "--py-call-osafterfork",
-            "--mule=lib/galaxy/main.py",
-            "--farm=job-handlers:1",
-        ])
+        command.extend(
+            [
+                "--py-call-osafterfork",
+                "--mule=lib/galaxy/main.py",
+                "--farm=job-handlers:1",
+            ]
+        )
 
 
 class MultipleMulesAsJobHandlersIntegrationTestCase(_BaseMulesIntegrationTestCase):
 
-    expected_server_name = 'main.job-handlers'
+    expected_server_name = "main.job-handlers"
 
     @classmethod
     def handle_uwsgi_cli_command(cls, command):
-        command.extend([
-            "--py-call-osafterfork",
-            "--mule=lib/galaxy/main.py",
-            "--mule=lib/galaxy/main.py",
-            "--farm=job-handlers:1,2",
-        ])
+        command.extend(
+            [
+                "--py-call-osafterfork",
+                "--mule=lib/galaxy/main.py",
+                "--mule=lib/galaxy/main.py",
+                "--farm=job-handlers:1,2",
+            ]
+        )
diff --git a/test/integration/test_page_revision_json_encoding.py b/test/integration/test_page_revision_json_encoding.py
index 6ac0667fb9a..2d77dfe21a7 100644
--- a/test/integration/test_page_revision_json_encoding.py
+++ b/test/integration/test_page_revision_json_encoding.py
@@ -7,14 +7,11 @@ exported API values are encoded though.
 
 from galaxy import model
 from galaxy_test.base import api_asserts
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 
 class PageJsonEncodingIntegrationTestCase(integration_util.IntegrationTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -24,7 +21,7 @@ class PageJsonEncodingIntegrationTestCase(integration_util.IntegrationTestCase):
         request = dict(
             slug="mypage",
             title="MY PAGE",
-            content='''<p>Page!<div class="embedded-item" id="History-%s"></div></p>''' % self.history_id,
+            content="""<p>Page!<div class="embedded-item" id="History-%s"></div></p>""" % self.history_id,
         )
         page_response = self._post("pages", request, json=True)
         api_asserts.assert_status_code_is_ok(page_response)
@@ -45,26 +42,39 @@ class PageJsonEncodingIntegrationTestCase(integration_util.IntegrationTestCase):
         request = dict(
             slug="mypage-markdown",
             title="MY PAGE",
-            content='''```galaxy
+            content="""```galaxy
 history_dataset_display(history_dataset_id=%s)
-```''' % dataset["id"],
+```"""
+            % dataset["id"],
             content_format="markdown",
         )
         page_response = self._post("pages", request, json=True)
         api_asserts.assert_status_code_is_ok(page_response)
         sa_session = self._app.model.context
         page_revision = sa_session.query(model.PageRevision).filter_by(content_format="markdown").all()[0]
-        assert '''```galaxy
+        assert (
+            """```galaxy
 history_dataset_display(history_dataset_id=1)
-```''' in page_revision.content, page_revision.content
-        assert '''::: history_dataset_display history_dataset_id=%s''' % dataset_id not in page_revision.content, page_revision.content
+```"""
+            in page_revision.content
+        ), page_revision.content
+        assert (
+            """::: history_dataset_display history_dataset_id=%s""" % dataset_id not in page_revision.content
+        ), page_revision.content
 
         show_page_response = self._get("pages/%s" % page_response.json()["id"])
         api_asserts.assert_status_code_is_ok(show_page_response)
         content = show_page_response.json()["content"]
-        assert '''```galaxy
+        assert (
+            """```galaxy
 history_dataset_display(history_dataset_id=1)
-```''' not in content, content
-        assert '''```galaxy
+```"""
+            not in content
+        ), content
+        assert (
+            """```galaxy
 history_dataset_display(history_dataset_id=%s)
-```''' % dataset_id in content, content
+```"""
+            % dataset_id
+            in content
+        ), content
diff --git a/test/integration/test_panel_views.py b/test/integration/test_panel_views.py
index 1082dd35a30..7ba1d348067 100644
--- a/test/integration/test_panel_views.py
+++ b/test/integration/test_panel_views.py
@@ -126,19 +126,23 @@ class PanelViewsFromConfigIntegrationTestCase(integration_util.IntegrationTestCa
                     {
                         "type": "label",
                         "text": "The Start",
-                    }, {
+                    },
+                    {
                         "type": "tool",
                         "id": "empty_list",
-                    }, {
+                    },
+                    {
                         "type": "label",
                         "text": "The Middle",
-                    }, {
+                    },
+                    {
                         "type": "tool",
                         "id": "count_list",
-                    }, {
+                    },
+                    {
                         "type": "label",
                         "text": "The End",
-                    }
+                    },
                 ],
             }
         ]
@@ -171,7 +175,13 @@ def verify_custom_embed(index):
     section_elems = section["elems"]
     assert len(section_elems) == 5, model_classes(section_elems)
     assert model_classes(section_elems) == ["Tool", "Tool", "Tool", "Tool", "Tool"]
-    assert element_ids(section_elems) == ["multi_data_optional", "paths_as_file", "param_text_option", "column_param", "Filter1"]
+    assert element_ids(section_elems) == [
+        "multi_data_optional",
+        "paths_as_file",
+        "param_text_option",
+        "column_param",
+        "Filter1",
+    ]
 
 
 def verify_custom_regex_filtered(index):
diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py
index 75d1df29276..9e14fa2df00 100644
--- a/test/integration/test_pulsar_embedded.py
+++ b/test/integration/test_pulsar_embedded.py
@@ -20,15 +20,17 @@ class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance):
 
 instance = integration_util.integration_module_instance(EmbeddedPulsarIntegrationInstance)
 
-test_tools = integration_util.integration_tool_runner([
-    "collection_creates_dynamic_nested_from_json",
-    "composite",
-    "simple_constructs",
-    "multi_data_param",
-    "output_filter",
-    "vcf_bgzip_test",
-    "environment_variables",
-    "multi_output_assign_primary_ext_dbkey",
-    "strict_shell",
-    "tool_provided_metadata_9",
-])
+test_tools = integration_util.integration_tool_runner(
+    [
+        "collection_creates_dynamic_nested_from_json",
+        "composite",
+        "simple_constructs",
+        "multi_data_param",
+        "output_filter",
+        "vcf_bgzip_test",
+        "environment_variables",
+        "multi_output_assign_primary_ext_dbkey",
+        "strict_shell",
+        "tool_provided_metadata_9",
+    ]
+)
diff --git a/test/integration/test_pulsar_embedded_containers.py b/test/integration/test_pulsar_embedded_containers.py
index 08c2dfe8339..e697ac5482b 100644
--- a/test/integration/test_pulsar_embedded_containers.py
+++ b/test/integration/test_pulsar_embedded_containers.py
@@ -1,8 +1,6 @@
 import os
 
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 from .test_containerized_jobs import (
     disable_dependency_resolution,
@@ -38,18 +36,20 @@ class BaseEmbeddedPulsarContainerIntegrationTestCase(integration_util.Integratio
 
 class EmbeddedSingularityPulsarIntegrationTestCase(BaseEmbeddedPulsarContainerIntegrationTestCase, MulledJobTestCases):
     # singularity passes $HOME by default
-    default_container_home_dir = os.environ.get('HOME', '/')
+    default_container_home_dir = os.environ.get("HOME", "/")
     job_config_file = EMBEDDED_PULSAR_JOB_CONFIG_FILE_SINGULARITY
-    container_type = 'singularity'
+    container_type = "singularity"
 
 
 class EmbeddedDockerPulsarIntegrationTestCase(BaseEmbeddedPulsarContainerIntegrationTestCase, MulledJobTestCases):
     job_config_file = EMBEDDED_PULSAR_JOB_CONFIG_FILE_DOCKER
-    container_type = 'docker'
+    container_type = "docker"
 
 
 instance = integration_util.integration_module_instance(EmbeddedSingularityPulsarIntegrationTestCase)
 
-test_tools = integration_util.integration_tool_runner([
-    "tool_directory_docker",
-])
+test_tools = integration_util.integration_tool_runner(
+    [
+        "tool_directory_docker",
+    ]
+)
diff --git a/test/integration/test_pulsar_embedded_extended_metadata.py b/test/integration/test_pulsar_embedded_extended_metadata.py
index 2be7482a154..2a332b19eb2 100644
--- a/test/integration/test_pulsar_embedded_extended_metadata.py
+++ b/test/integration/test_pulsar_embedded_extended_metadata.py
@@ -16,9 +16,9 @@ class EmbeddedAndExtendedMetadataPulsarIntegrationInstance(integration_util.Inte
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE
-        config['object_store_store_by'] = 'uuid'
-        config['metadata_strategy'] = 'extended'
-        config['retry_metadata_internally'] = False
+        config["object_store_store_by"] = "uuid"
+        config["metadata_strategy"] = "extended"
+        config["retry_metadata_internally"] = False
 
 
 instance = integration_util.integration_module_instance(EmbeddedAndExtendedMetadataPulsarIntegrationInstance)
@@ -28,6 +28,6 @@ test_tools = integration_util.integration_tool_runner(
         "simple_constructs",
         "metadata_bam",
         # "job_properties",  # https://github.com/galaxyproject/galaxy/issues/11813
-        "from_work_dir_glob"
+        "from_work_dir_glob",
     ]
 )
diff --git a/test/integration/test_pulsar_embedded_mq.py b/test/integration/test_pulsar_embedded_mq.py
index 3e8e0bfa276..f92b2c2eb90 100644
--- a/test/integration/test_pulsar_embedded_mq.py
+++ b/test/integration/test_pulsar_embedded_mq.py
@@ -65,9 +65,7 @@ class EmbeddedMessageQueuePulsarIntegrationInstance(integration_util.Integration
         safe_makedirs(jobs_directory)
         job_conf_template = string.Template(JOB_CONF_TEMPLATE)
         job_conf_str = job_conf_template.substitute(
-            amqp_url=AMQP_URL,
-            jobs_directory=jobs_directory,
-            galaxy_home=os.path.join(SCRIPT_DIRECTORY, os.pardir)
+            amqp_url=AMQP_URL, jobs_directory=jobs_directory, galaxy_home=os.path.join(SCRIPT_DIRECTORY, os.pardir)
         )
         with tempfile.NamedTemporaryFile(suffix="_mq_job_conf.yml", mode="w", delete=False) as job_conf:
             job_conf.write(job_conf_str)
diff --git a/test/integration/test_pulsar_embedded_remote_metadata.py b/test/integration/test_pulsar_embedded_remote_metadata.py
index a331e30ff6b..970d6d64f7a 100644
--- a/test/integration/test_pulsar_embedded_remote_metadata.py
+++ b/test/integration/test_pulsar_embedded_remote_metadata.py
@@ -16,8 +16,8 @@ class EmbeddedMetadataPulsarIntegrationInstance(integration_util.IntegrationInst
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE
-        config['object_store_store_by'] = 'uuid'
-        config['retry_metadata_internally'] = False
+        config["object_store_store_by"] = "uuid"
+        config["retry_metadata_internally"] = False
 
 
 instance = integration_util.integration_module_instance(EmbeddedMetadataPulsarIntegrationInstance)
diff --git a/test/integration/test_quota.py b/test/integration/test_quota.py
index 3e4b49e2a95..88ee8d1a51c 100644
--- a/test/integration/test_quota.py
+++ b/test/integration/test_quota.py
@@ -1,6 +1,4 @@
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 
@@ -62,7 +60,7 @@ class QuotaIntegrationTestCase(integration_util.IntegrationTestCase):
 
         new_quota_name = "updated-quota-name"
         update_payload = {
-            'name': new_quota_name,
+            "name": new_quota_name,
         }
         put_response = self._put(f"quotas/{quota_id}", data=update_payload, json=True)
         put_response.raise_for_status()
@@ -158,19 +156,17 @@ class QuotaIntegrationTestCase(integration_util.IntegrationTestCase):
     def _build_quota_payload_with_name(self, quota_name: str, is_default: bool = False):
         default = "registered" if is_default else "no"
         return {
-            'name': quota_name,
-            'description': f'Quota {quota_name} description',
-            'amount': '100MB',
-            'operation': '=',
-            'default': default,
-            'in_users': [],
-            'in_groups': []
+            "name": quota_name,
+            "description": f"Quota {quota_name} description",
+            "amount": "100MB",
+            "operation": "=",
+            "default": default,
+            "in_users": [],
+            "in_groups": [],
         }
 
     def _delete_and_purge(self, quota_id):
-        data = {
-            'purge': 'true'
-        }
+        data = {"purge": "true"}
         return self._delete(f"quotas/{quota_id}", data=data, admin=True, json=True)
 
     def _assert_quota_is_deleted(self, quota_id: str):
diff --git a/test/integration/test_remote_files.py b/test/integration/test_remote_files.py
index 157dd8a0d08..e854f9df57e 100644
--- a/test/integration/test_remote_files.py
+++ b/test/integration/test_remote_files.py
@@ -6,16 +6,22 @@ from tempfile import mkdtemp
 from typing import ClassVar
 
 from galaxy.exceptions import error_codes
-from galaxy_test.base.api_asserts import assert_error_code_is, assert_error_message_contains
-from galaxy_test.base.populators import DatasetCollectionPopulator, DatasetPopulator
+from galaxy_test.base.api_asserts import (
+    assert_error_code_is,
+    assert_error_message_contains,
+)
+from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+)
 from galaxy_test.driver import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_JOB_CONF = os.path.join(SCRIPT_DIRECTORY, "file_sources_conf.yml")
-VCF_GZ_PATH = os.path.join(SCRIPT_DIRECTORY, os.path.pardir, os.path.pardir, 'test-data', 'test.vcf.gz')
+VCF_GZ_PATH = os.path.join(SCRIPT_DIRECTORY, os.path.pardir, os.path.pardir, "test-data", "test.vcf.gz")
 
-USERNAME = 'user--bx--psu--edu'
-USER_EMAIL = 'user@bx.psu.edu'
+USERNAME = "user--bx--psu--edu"
+USER_EMAIL = "user@bx.psu.edu"
 
 
 class ConfiguresRemoteFilesIntegrationTestCase(integration_util.IntegrationTestCase):
@@ -41,7 +47,7 @@ class ConfiguresRemoteFilesIntegrationTestCase(integration_util.IntegrationTestC
         # driver_util sets this to False, though the Galaxy default is True.
         # Restore default for these tests.
         config["ftp_upload_purge"] = True
-        config['metadata_strategy'] = 'extended'
+        config["metadata_strategy"] = "extended"
         config["tool_evaluation_strategy"] = "remote"
 
     def setUp(self):
@@ -63,7 +69,6 @@ class ConfiguresRemoteFilesIntegrationTestCase(integration_util.IntegrationTestC
 
 
 class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
-
     def test_index(self):
         index = self.galaxy_interactor.get("remote_files?target=importdir").json()
         self._assert_index_empty(index)
@@ -74,7 +79,7 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
 
         # Get a 404 if the directory doesn't exist.
         index = self.galaxy_interactor.get("remote_files?target=userdir").json()
-        assert_error_code_is(index, error_codes.error_codes_by_name['USER_OBJECT_NOT_FOUND'])
+        assert_error_code_is(index, error_codes.error_codes_by_name["USER_OBJECT_NOT_FOUND"])
 
         users_dir = os.path.join(self.user_library_dir, USER_EMAIL)
         os.mkdir(users_dir)
@@ -139,9 +144,9 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
             }
             response = dataset_populator.run_tool("directory_uri", inputs, history_id)
             dataset_populator.wait_for_job(response["jobs"][0]["id"])
-            assert 'helloworld' in os.listdir(ftp_dir)
-            with open(os.path.join(ftp_dir, 'helloworld')) as f:
-                assert 'hello world!\n' == f.read()
+            assert "helloworld" in os.listdir(ftp_dir)
+            with open(os.path.join(ftp_dir, "helloworld")) as f:
+                assert "hello world!\n" == f.read()
 
     def test_export_remote_tool_default(self):
         dataset_populator = self.dataset_populator
@@ -149,10 +154,7 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
         _write_file_fixtures(self.root, ftp_dir)
         with dataset_populator.test_history() as history_id:
             dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo")
-            infile = {
-                "src": "hda",
-                "id": dataset["id"]
-            }
+            infile = {"src": "hda", "id": dataset["id"]}
             inputs = {
                 "d_uri": "gxftp://",
                 "export_type|export_type_selector": "datasets_named",
@@ -161,8 +163,8 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
             }
             response = dataset_populator.run_tool("export_remote", inputs, history_id)
             dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
-            with open(os.path.join(ftp_dir, 'my_cool', 'utf8_name_😻.txt')) as f:
-                assert 'example content\n' == f.read()
+            with open(os.path.join(ftp_dir, "my_cool", "utf8_name_😻.txt")) as f:
+                assert "example content\n" == f.read()
 
     def test_export_remote_tool_default_duplicate_name_fails(self):
         dataset_populator = self.dataset_populator
@@ -170,10 +172,7 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
         _write_file_fixtures(self.root, ftp_dir)
         with dataset_populator.test_history() as history_id:
             dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo")
-            infile = {
-                "src": "hda",
-                "id": dataset["id"]
-            }
+            infile = {"src": "hda", "id": dataset["id"]}
             inputs = {
                 "d_uri": "gxftp://",
                 "export_type|export_type_selector": "datasets_named",
@@ -186,21 +185,20 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
             job_id = response["jobs"][0]["id"]
             dataset_populator.wait_for_job(job_id, assert_ok=False)
             job = self.dataset_populator.get_job_details(job_id, full=True).json()
-            assert job['state'] == 'error'
-            assert 'Duplicate export filenames given' in job['tool_stderr']
-            assert not os.path.exists(os.path.join(ftp_dir, 'name.txt'))
+            assert job["state"] == "error"
+            assert "Duplicate export filenames given" in job["tool_stderr"]
+            assert not os.path.exists(os.path.join(ftp_dir, "name.txt"))
 
     def test_export_remote_tool_with_metadata_file_auto_name(self):
         dataset_populator = self.dataset_populator
         ftp_dir = self.user_ftp_dir
         _write_file_fixtures(self.root, ftp_dir)
         with dataset_populator.test_history() as history_id:
-            with open(VCF_GZ_PATH, 'rb') as vcf_gz:
-                dataset = dataset_populator.new_dataset(history_id, content=vcf_gz, file_type="vcf_bgzip", wait=True, name="foo/1")
-            infile = {
-                "src": "hda",
-                "id": dataset["id"]
-            }
+            with open(VCF_GZ_PATH, "rb") as vcf_gz:
+                dataset = dataset_populator.new_dataset(
+                    history_id, content=vcf_gz, file_type="vcf_bgzip", wait=True, name="foo/1"
+                )
+            infile = {"src": "hda", "id": dataset["id"]}
             inputs = {
                 "d_uri": "gxftp://",
                 "export_type|export_type_selector": "datasets_auto",
@@ -208,26 +206,23 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
             }
             response = dataset_populator.run_tool("export_remote", inputs, history_id)
             dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
-            with open(os.path.join(ftp_dir, 'foo_1.vcf.gz'), 'rb') as export, open(VCF_GZ_PATH, 'rb') as vcf_gz:
+            with open(os.path.join(ftp_dir, "foo_1.vcf.gz"), "rb") as export, open(VCF_GZ_PATH, "rb") as vcf_gz:
                 assert export.read() == vcf_gz.read()
-            assert os.path.exists(os.path.join(ftp_dir, 'foo_1.vcf.gz.tbi'))
+            assert os.path.exists(os.path.join(ftp_dir, "foo_1.vcf.gz.tbi"))
 
     def test_export_remote_tool_collection_structure(self):
         dataset_populator = self.dataset_populator
         ftp_dir = self.user_ftp_dir
-        assert 'test0' not in os.listdir(ftp_dir)
+        assert "test0" not in os.listdir(ftp_dir)
         _write_file_fixtures(self.root, ftp_dir)
         with dataset_populator.test_history() as history_id:
             hdca = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
-            outer_elements = hdca['elements'][0]
-            assert outer_elements['element_identifier'] == 'test0'
+            outer_elements = hdca["elements"][0]
+            assert outer_elements["element_identifier"] == "test0"
             for i in range(2):
-                assert outer_elements['object']['elements'][i]['element_identifier'] == f'data{i + 1}'
-                assert outer_elements['object']['elements'][i]['object']['file_ext'] == 'txt'
-            incollection = {
-                "src": "hdca",
-                "id": hdca['id']
-            }
+                assert outer_elements["object"]["elements"][i]["element_identifier"] == f"data{i + 1}"
+                assert outer_elements["object"]["elements"][i]["object"]["file_ext"] == "txt"
+            incollection = {"src": "hdca", "id": hdca["id"]}
             inputs = {
                 "d_uri": "gxftp://",
                 "export_type|export_type_selector": "collection_auto",
@@ -235,9 +230,9 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
             }
             response = dataset_populator.run_tool("export_remote", inputs, history_id)
             dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
-            assert 'test0' in os.listdir(ftp_dir)
-            subdir_content = os.listdir(os.path.join(ftp_dir, 'test0'))
-            assert sorted(subdir_content) == ['data1.txt', 'data2.txt', 'data3.txt']
+            assert "test0" in os.listdir(ftp_dir)
+            subdir_content = os.listdir(os.path.join(ftp_dir, "test0"))
+            assert sorted(subdir_content) == ["data1.txt", "data2.txt", "data3.txt"]
 
     def _assert_index_empty(self, index):
         assert len(index) == 0
@@ -261,7 +256,6 @@ class RemoteFilesIntegrationTestCase(ConfiguresRemoteFilesIntegrationTestCase):
 
 
 class RemoteFilesNotConfiguredIntegrationTestCase(integration_util.IntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["library_import_dir"] = None
@@ -270,20 +264,20 @@ class RemoteFilesNotConfiguredIntegrationTestCase(integration_util.IntegrationTe
 
     def test_configuration_statuses(self):
         importfiles = self.galaxy_interactor.get("remote_files?target=importdir")
-        assert_error_code_is(importfiles, error_codes.error_codes_by_name['CONFIG_DOES_NOT_ALLOW'])
-        assert_error_message_contains(importfiles, 'import directory')
+        assert_error_code_is(importfiles, error_codes.error_codes_by_name["CONFIG_DOES_NOT_ALLOW"])
+        assert_error_message_contains(importfiles, "import directory")
 
         importfiles = self.galaxy_interactor.get("remote_files?target=ftpdir")
-        assert_error_code_is(importfiles, error_codes.error_codes_by_name['CONFIG_DOES_NOT_ALLOW'])
-        assert_error_message_contains(importfiles, 'FTP directories')
+        assert_error_code_is(importfiles, error_codes.error_codes_by_name["CONFIG_DOES_NOT_ALLOW"])
+        assert_error_message_contains(importfiles, "FTP directories")
 
         importfiles = self.galaxy_interactor.get("remote_files?target=userdir")
-        assert_error_code_is(importfiles, error_codes.error_codes_by_name['CONFIG_DOES_NOT_ALLOW'])
-        assert_error_message_contains(importfiles, 'user directories')
+        assert_error_code_is(importfiles, error_codes.error_codes_by_name["CONFIG_DOES_NOT_ALLOW"])
+        assert_error_message_contains(importfiles, "user directories")
 
         # invalid request parameter waitwhat...
         importfiles = self.galaxy_interactor.get("remote_files?target=waitwhat")
-        assert_error_code_is(importfiles, error_codes.error_codes_by_name['USER_REQUEST_INVALID_PARAMETER'])
+        assert_error_code_is(importfiles, error_codes.error_codes_by_name["USER_REQUEST_INVALID_PARAMETER"])
 
 
 def _write_file_fixtures(tmp, root):
diff --git a/test/integration/test_remote_files_histories.py b/test/integration/test_remote_files_histories.py
index 06425fa8df9..c4509341fcf 100644
--- a/test/integration/test_remote_files_histories.py
+++ b/test/integration/test_remote_files_histories.py
@@ -9,9 +9,9 @@ class RemoteFilesHistoryImportExportIntegrationTestCase(ConfiguresRemoteFilesInt
     framework_tool_and_types = True
 
     def test_history_import_from_library_dir(self):
-        f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), 'rb')
+        f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), "rb")
         import_path = os.path.join(self.library_dir, "to_import.tgz")
-        with open(import_path, 'wb') as out:
+        with open(import_path, "wb") as out:
             out.write(f.read())
         import_uri = "gximport://to_import.tgz"
         import_data = dict(archive_source=import_uri, archive_type="url")
@@ -20,9 +20,9 @@ class RemoteFilesHistoryImportExportIntegrationTestCase(ConfiguresRemoteFilesInt
         self.dataset_populator.delete_history(imported_history_id)
 
     def test_history_import_from_ftp_dir(self):
-        f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), 'rb')
+        f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), "rb")
         import_path = os.path.join(self.user_ftp_dir, "to_import.tgz")
-        with open(import_path, 'wb') as out:
+        with open(import_path, "wb") as out:
             out.write(f.read())
         import_uri = "gxftp://to_import.tgz"
         # Consider distinguishing between url and uri...
diff --git a/test/integration/test_remote_files_posix.py b/test/integration/test_remote_files_posix.py
index 9cd1168cbab..93d2fbb396b 100644
--- a/test/integration/test_remote_files_posix.py
+++ b/test/integration/test_remote_files_posix.py
@@ -13,7 +13,6 @@ REQUIRED_GROUP = "fs_test_group"
 
 
 class PosixFileSourceIntegrationTestCase(PosixFileSourceSetup, integration_util.IntegrationTestCase):
-
     def setUp(self):
         super().setUp()
         self._write_file_fixtures()
diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index 2060c047978..8682b103d11 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -6,14 +6,14 @@ from galaxy_test.base.uses_shed import UsesShed
 from galaxy_test.driver import integration_util
 from tool_shed.util import hg_util
 
-REPO_TYPE = namedtuple('REPO_TYPE', 'name owner changeset')
+REPO_TYPE = namedtuple("REPO_TYPE", "name owner changeset")
 REPO = REPO_TYPE(
-    'collection_column_join',
-    'iuc',
-    'dfde09461b1e',  # revision 2, a known installable revision
+    "collection_column_join",
+    "iuc",
+    "dfde09461b1e",  # revision 2, a known installable revision
 )
-REVISION_3 = '58228a4d58fe'
-REVISION_4 = '071084070619'
+REVISION_3 = "58228a4d58fe"
+REVISION_4 = "071084070619"
 
 
 class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestCase, UsesShed):
@@ -45,35 +45,35 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         self._uninstall_repository()
 
     def test_datatype_uninstall(self):
-        repo = ('devteam', 'blast_datatypes', '01b38f20197e')
+        repo = ("devteam", "blast_datatypes", "01b38f20197e")
         self.install_repository(*repo)
         self.uninstall_repository(*repo)
 
     def test_package_uninstall(self):
-        repo = ('iuc', 'package_fastqc_0_11_4', 'a8f485b2efd9')
+        repo = ("iuc", "package_fastqc_0_11_4", "a8f485b2efd9")
         self.install_repository(*repo)
         self.uninstall_repository(*repo)
 
     def test_tool_with_package_dependency_uninstall(self):
-        repo = ('devteam', 'fastqc', 'e7b2202befea')
+        repo = ("devteam", "fastqc", "e7b2202befea")
         self.install_repository(*repo)
         self.uninstall_repository(*repo)
 
     def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3")[0]
-        assert int(response['ctx_rev']) >= 4
-        latest_revision = response['changeset_revision']
-        repo_response = self._get("/api/tool_shed_repositories/%s" % response['id']).json()
-        assert repo_response['tool_shed_status']['revision_update'] == 'False'  # that should really be a boolean
+        assert int(response["ctx_rev"]) >= 4
+        latest_revision = response["changeset_revision"]
+        repo_response = self._get("/api/tool_shed_repositories/%s" % response["id"]).json()
+        assert repo_response["tool_shed_status"]["revision_update"] == "False"  # that should really be a boolean
         # now checkout revision 3 and attempt an update
         path_components = [
             os.path.dirname(self._app.config.shed_tool_config_file),
-            'toolshed.g2.bx.psu.edu',
-            'repos',
+            "toolshed.g2.bx.psu.edu",
+            "repos",
             REPO.owner,
             REPO.name,
             REVISION_3,
-            REPO.name
+            REPO.name,
         ]
         revision_3_path = os.path.join(*path_components[:6])
         latest_revision_path = os.path.join(*path_components[:5] + [latest_revision])
@@ -81,51 +81,47 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         # Move repo to location expected before minor update
         os.rename(latest_revision_path, revision_3_path)
         # Checkout revision 3
-        hg_util.update_repository(repository_path, ctx_rev='3')
+        hg_util.update_repository(repository_path, ctx_rev="3")
         # change repo to revision 3 in database
         model = self._app.install_model
         tsr = model.context.query(model.ToolShedRepository).first()
         assert tsr.name == REPO.name
         assert tsr.changeset_revision == latest_revision
         assert int(tsr.ctx_rev) >= 4
-        tsr.ctx_rev = '3'
+        tsr.ctx_rev = "3"
         tsr.installed_changeset_revision = REVISION_3
         tsr.changeset_revision = REVISION_3
         model.context.flush()
         # update shed_tool_conf.xml to look like revision 3 was the installed_changeset_revision
         with open(self._app.config.shed_tool_config_file) as shed_config:
             shed_text = shed_config.read().replace(latest_revision, REVISION_3)
-        with open(self._app.config.shed_tool_config_file, 'w') as shed_config:
+        with open(self._app.config.shed_tool_config_file, "w") as shed_config:
             shed_config.write(shed_text)
-        self._get(
-            '/api/tool_shed_repositories/check_for_updates',
-            data={'id': response['id']},
-            admin=True
-        ).json()
+        self._get("/api/tool_shed_repositories/check_for_updates", data={"id": response["id"]}, admin=True).json()
         # At this point things should look like there is minor update available
-        repo_response = self._get("/api/tool_shed_repositories/%s" % response['id']).json()
-        assert repo_response['tool_shed_status']['revision_update'] == 'True'
-        assert repo_response['changeset_revision'] == REVISION_3
-        assert repo_response['ctx_rev'] == '3'
+        repo_response = self._get("/api/tool_shed_repositories/%s" % response["id"]).json()
+        assert repo_response["tool_shed_status"]["revision_update"] == "True"
+        assert repo_response["changeset_revision"] == REVISION_3
+        assert repo_response["ctx_rev"] == "3"
         # now install revision 4 (or newer) (a.k.a a minor update)
         response = self._install_repository(revision=REVISION_4, version="0.0.3", verify_tool_absent=False)[0]
-        assert response['changeset_revision'] == latest_revision
-        assert response['installed_changeset_revision'] == REVISION_3
+        assert response["changeset_revision"] == latest_revision
+        assert response["installed_changeset_revision"] == REVISION_3
         # should be 4 or newer
-        assert int(response['ctx_rev']) >= 4
+        assert int(response["ctx_rev"]) >= 4
 
     def _uninstall_repository(self):
-        tool = self._get('/api/tools/collection_column_join').json()
-        assert tool['version'] == "0.0.2"
+        tool = self._get("/api/tools/collection_column_join").json()
+        assert tool["version"] == "0.0.2"
         self.uninstall_repository(REPO.owner, REPO.name, REPO.changeset)
-        response = self._get('/api/tools/collection_column_join').json()
-        assert response['err_msg']
+        response = self._get("/api/tools/collection_column_join").json()
+        assert response["err_msg"]
 
     def _install_repository(self, revision=None, version="0.0.2", verify_tool_absent=True):
         if verify_tool_absent:
-            response = self._get('/api/tools/collection_column_join').json()
-            assert response['err_msg']
+            response = self._get("/api/tools/collection_column_join").json()
+            assert response["err_msg"]
         install_response = self.install_repository(REPO.owner, REPO.name, revision or REPO.changeset)
-        tool = self._get('/api/tools/collection_column_join').json()
-        assert tool['version'] == version
+        tool = self._get("/api/tools/collection_column_join").json()
+        assert tool["version"] == version
         return install_response
diff --git a/test/integration/test_resolvers.py b/test/integration/test_resolvers.py
index 5dfae3c24dd..7a4d760375e 100644
--- a/test/integration/test_resolvers.py
+++ b/test/integration/test_resolvers.py
@@ -3,12 +3,10 @@ import os
 from tempfile import mkdtemp
 from typing import ClassVar
 
-from galaxy_test.base.populators import (
-    DatasetPopulator,
-)
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
-GNUPLOT = {'version': '4.6', 'type': 'package', 'name': 'gnuplot'}
+GNUPLOT = {"version": "4.6", "type": "package", "name": "gnuplot"}
 
 
 class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
@@ -24,7 +22,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         cls._test_driver.temp_directories.append(cls.conda_tmp_prefix)
         config["use_cached_dependency_manager"] = True
         config["conda_auto_init"] = True
-        config["conda_prefix"] = os.path.join(cls.conda_tmp_prefix, 'conda')
+        config["conda_prefix"] = os.path.join(cls.conda_tmp_prefix, "conda")
 
     def test_dependency_before_install(self):
         """
@@ -34,7 +32,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         create_response = self._get("dependency_resolvers/dependency", data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert response['dependency_type'] is None and response['exact']
+        assert response["dependency_type"] is None and response["exact"]
 
     def test_dependency_install(self):
         """
@@ -56,7 +54,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         Test installation of gnuplot with a version that does not exist.
         """
         data = GNUPLOT.copy()
-        data['version'] = '4.9999'
+        data["version"] = "4.9999"
         create_response = self._post("dependency_resolvers/dependency", data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
@@ -68,13 +66,12 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         self._assert_dependency_type(response, exact=False)
 
     def test_legacy_r_mapping(self):
-        """
-        """
+        """ """
         tool_id = "legacy_R"
         dataset_populator = DatasetPopulator(self.galaxy_interactor)
         history_id = dataset_populator.new_history()
         endpoint = "tools/%s/install_dependencies" % tool_id
-        data = {'id': tool_id}
+        data = {"id": tool_id}
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         payload = dataset_populator.run_tool_payload(
@@ -87,66 +84,66 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         dataset_populator.wait_for_history(history_id, assert_ok=True)
 
     def test_conda_install_through_tools_api(self):
-        tool_id = 'mulled_example_multi_1'
+        tool_id = "mulled_example_multi_1"
         endpoint = "tools/%s/install_dependencies" % tool_id
-        data = {'id': tool_id}
+        data = {"id": tool_id}
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert any(True for d in response if d['dependency_type'] == 'conda')
+        assert any(True for d in response if d["dependency_type"] == "conda")
         endpoint = "tools/%s/build_dependency_cache" % tool_id
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
 
     def test_uninstall_through_tools_api(self):
-        tool_id = 'mulled_example_multi_1'
+        tool_id = "mulled_example_multi_1"
         endpoint = "tools/%s/dependencies" % tool_id
-        data = {'id': tool_id}
+        data = {"id": tool_id}
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert any(True for d in response if d['dependency_type'] == 'conda')
+        assert any(True for d in response if d["dependency_type"] == "conda")
         endpoint = "tools/%s/dependencies" % tool_id
         create_response = self._delete(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert not [True for d in response if d['dependency_type'] == 'conda']
+        assert not [True for d in response if d["dependency_type"] == "conda"]
 
     def _uninstall_mulled_example_multi_1(self, resolver_type=None):
-        tool_id = 'mulled_example_multi_1'
+        tool_id = "mulled_example_multi_1"
         endpoint = "tools/%s/dependencies" % tool_id
-        data = {'id': tool_id, 'resolver_type': resolver_type}
+        data = {"id": tool_id, "resolver_type": resolver_type}
         create_response = self._delete(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert not [True for d in response if d['dependency_type'] == 'conda']
+        assert not [True for d in response if d["dependency_type"] == "conda"]
 
     def test_conda_install_with_resolver_type_via_tools_api(self):
         # Makes sure dependency is not already installed
-        self._uninstall_mulled_example_multi_1(resolver_type='conda')
+        self._uninstall_mulled_example_multi_1(resolver_type="conda")
         # Now do the actual test
-        tool_id = 'mulled_example_multi_1'
+        tool_id = "mulled_example_multi_1"
         endpoint = "tools/%s/dependencies" % tool_id
-        data = {'id': tool_id, 'resolver_type': 'conda'}
+        data = {"id": tool_id, "resolver_type": "conda"}
         create_response = self._post(endpoint, data=data, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
-        assert any(True for d in response if d['dependency_type'] == 'conda')
+        assert any(True for d in response if d["dependency_type"] == "conda")
         # Now that we know install was successfullt we can also doube check that the uninstall works
-        self._uninstall_mulled_example_multi_1(resolver_type='conda')
+        self._uninstall_mulled_example_multi_1(resolver_type="conda")
 
     def test_conda_clean(self):
-        endpoint = 'dependency_resolvers/clean'
+        endpoint = "dependency_resolvers/clean"
         create_response = self._post(endpoint, data={}, admin=True)
         self._assert_status_code_is(create_response, 200)
         response = create_response.json()
         assert response == "OK"
 
-    def _assert_dependency_type(self, response, type='conda', exact=True):
-        if 'dependency_type' not in response:
+    def _assert_dependency_type(self, response, type="conda", exact=True):
+        if "dependency_type" not in response:
             raise Exception("Response [%s] did not contain key 'dependency_type'" % response)
-        dependency_type = response['dependency_type']
+        dependency_type = response["dependency_type"]
         assert dependency_type == type, f"Dependency type [{dependency_type}] not the expected value [{type}]"
-        if 'exact' not in response:
+        if "exact" not in response:
             raise Exception("Response [%s] did not contain key 'exact'" % response)
-        assert response['exact'] is exact
+        assert response["exact"] is exact
diff --git a/test/integration/test_save_job_id_on_datasets.py b/test/integration/test_save_job_id_on_datasets.py
index aea2e311acc..8b59a0a4a52 100644
--- a/test/integration/test_save_job_id_on_datasets.py
+++ b/test/integration/test_save_job_id_on_datasets.py
@@ -18,9 +18,9 @@ class TestConfig:
 
 
 TEST_TOOL_IDS = [
-    'boolean_conditional',  # 1 job >> 1 dataset
-    'color_param',          # 1 job >> multiple datasets
-    'multi_output',         # 1 job >> 1 dataset + 1 discovered dataset
+    "boolean_conditional",  # 1 job >> 1 dataset
+    "color_param",  # 1 job >> multiple datasets
+    "multi_output",  # 1 job >> 1 dataset + 1 discovered dataset
     # test upload?            # not implemented
 ]
 
@@ -35,14 +35,14 @@ def test_driver():
         driver.tear_down()
 
 
-@pytest.mark.parametrize('tool_id', TEST_TOOL_IDS)
+@pytest.mark.parametrize("tool_id", TEST_TOOL_IDS)
 def test_tool_datasets(tool_id, test_driver):
     test_driver.run_tool_test(tool_id)
     session = test_driver.app.model.context.current
     job = session.query(model.Job).order_by(model.Job.id.desc()).first()
     datasets = session.query(model.Dataset).filter(model.Dataset.job_id == job.id).all()
 
-    if tool_id == 'boolean_conditional':
+    if tool_id == "boolean_conditional":
         assert len(datasets) == 1
-    elif tool_id in ('color_param', 'multi_output'):
+    elif tool_id in ("color_param", "multi_output"):
         assert len(datasets) == 2
diff --git a/test/integration/test_scripts.py b/test/integration/test_scripts.py
index 19c1ce239ca..4837e2ec0ac 100644
--- a/test/integration/test_scripts.py
+++ b/test/integration/test_scripts.py
@@ -11,7 +11,7 @@ import yaml
 
 from galaxy.util import (
     galaxy_directory,
-    unicodify
+    unicodify,
 )
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
@@ -30,7 +30,6 @@ def skip_unless_module(module):
 
 
 class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -77,7 +76,9 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
         assert delete_response.status_code == 200
         assert delete_response.json()["purged"] is False
         config_file = self.write_config_file()
-        output = self._scripts_check_output(script, ["-c", config_file, "--older-than", "0", "--sequence", "purge_deleted_histories"])
+        output = self._scripts_check_output(
+            script, ["-c", config_file, "--older-than", "0", "--sequence", "purge_deleted_histories"]
+        )
         print(output)
         history_response = self.dataset_populator._get("histories/%s" % history_id)
         assert history_response.status_code == 200
@@ -187,7 +188,7 @@ class ScriptsIntegrationTestCase(integration_util.IntegrationTestCase):
         self._test_driver.temp_directories.extend([config_dir])
         config = self._raw_config
         # Update config dict with database_connection, which might be set through env variables
-        config['database_connection'] = self._app.config.database_connection
+        config["database_connection"] = self._app.config.database_connection
         with open(path, "w") as f:
             yaml.dump({"galaxy": config}, f)
 
diff --git a/test/integration/test_tool_data_delete.py b/test/integration/test_tool_data_delete.py
index fde8477a8e5..66353afa2c3 100644
--- a/test/integration/test_tool_data_delete.py
+++ b/test/integration/test_tool_data_delete.py
@@ -13,7 +13,6 @@ import time
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
-
 THIS_DIR = os.path.dirname(__file__)
 SOURCE_TOOL_DATA_DIRECTORY = os.path.join(THIS_DIR, os.pardir, "functional", "tool-data")
 
diff --git a/test/integration/test_upload_configuration_options.py b/test/integration/test_upload_configuration_options.py
index f5d37c54111..8eafc8d71e6 100644
--- a/test/integration/test_upload_configuration_options.py
+++ b/test/integration/test_upload_configuration_options.py
@@ -25,11 +25,13 @@ import re
 import shutil
 import tempfile
 import unittest
-from typing import Dict, TextIO, Union
-
-from galaxy_test.base.api_util import (
-    TEST_USER,
+from typing import (
+    Dict,
+    TextIO,
+    Union,
 )
+
+from galaxy_test.base.api_util import TEST_USER
 from galaxy_test.base.constants import (
     ONE_TO_SIX_ON_WINDOWS,
     ONE_TO_SIX_WITH_SPACES,
@@ -42,7 +44,6 @@ from galaxy_test.base.populators import (
 )
 from galaxy_test.driver import integration_util
 
-
 SCRIPT_DIR = os.path.normpath(os.path.dirname(__file__))
 TEST_DATA_DIRECTORY = os.path.join(SCRIPT_DIR, os.pardir, os.pardir, "test-data")
 
@@ -86,7 +87,6 @@ class BaseUploadContentConfigurationTestCase(BaseUploadContentConfigurationInsta
 
 
 class InvalidFetchRequestsTestCase(BaseUploadContentConfigurationTestCase):
-
     def test_in_place_not_allowed(self):
         elements = [{"src": "files", "in_place": False}]
         target = {
@@ -96,7 +96,7 @@ class InvalidFetchRequestsTestCase(BaseUploadContentConfigurationTestCase):
         }
         response = self.fetch_target(target, attach_test_file=True)
         self._assert_status_code_is(response, 400)
-        assert 'in_place' in response.json()["err_msg"]
+        assert "in_place" in response.json()["err_msg"]
 
     def test_files_not_attached(self):
         elements = [{"src": "files"}]
@@ -107,18 +107,17 @@ class InvalidFetchRequestsTestCase(BaseUploadContentConfigurationTestCase):
         }
         response = self.fetch_target(target)
         self._assert_status_code_is(response, 400)
-        assert 'Failed to find uploaded file matching target' in response.json()["err_msg"]
+        assert "Failed to find uploaded file matching target" in response.json()["err_msg"]
 
 
 class NonAdminsCannotPasteFilePathTestCase(BaseUploadContentConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["allow_path_paste"] = True
 
     def test_disallowed_for_primary_file(self):
         payload = self.dataset_populator.upload_payload(
-            self.history_id, 'file://%s/1.RData' % TEST_DATA_DIRECTORY, file_type="binary"
+            self.history_id, "file://%s/1.RData" % TEST_DATA_DIRECTORY, file_type="binary"
         )
         create_response = self.dataset_populator.tools_post(payload)
         # Ideally this would be 403 but the tool API endpoint isn't using
@@ -150,7 +149,9 @@ class NonAdminsCannotPasteFilePathTestCase(BaseUploadContentConfigurationTestCas
         path = os.path.join(TEST_DATA_DIRECTORY, "1.txt")
         assert os.path.exists(path)
         library = self.library_populator.new_private_library("pathpastedisallowedlibraries")
-        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_paths", paths=path)
+        payload, files = self.library_populator.create_dataset_request(
+            library, upload_option="upload_paths", paths=path
+        )
         response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
         assert response.status_code == 403, response.json()
         assert os.path.exists(path)
@@ -192,7 +193,8 @@ class AdminsCanPasteFilePathsTestCase(BaseUploadContentConfigurationTestCase):
 
     def test_admin_path_paste(self):
         payload = self.dataset_populator.upload_payload(
-            self.history_id, 'file://%s/random-file' % TEST_DATA_DIRECTORY,
+            self.history_id,
+            "file://%s/random-file" % TEST_DATA_DIRECTORY,
         )
         create_response = self.dataset_populator.tools_post(payload)
         # Is admin - so this should work fine!
@@ -202,7 +204,9 @@ class AdminsCanPasteFilePathsTestCase(BaseUploadContentConfigurationTestCase):
         library = self.library_populator.new_private_library("pathpasteallowedlibraries")
         path = "%s/1.txt" % TEST_DATA_DIRECTORY
         assert os.path.exists(path)
-        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_paths", paths=path)
+        payload, files = self.library_populator.create_dataset_request(
+            library, upload_option="upload_paths", paths=path
+        )
         response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
         # Was 403 for non-admin above.
         assert response.status_code == 200
@@ -213,7 +217,9 @@ class AdminsCanPasteFilePathsTestCase(BaseUploadContentConfigurationTestCase):
         library = self.library_populator.new_private_library("pathpasteallowedlibraries")
         path = "%s/1.txt" % TEST_DATA_DIRECTORY
         assert os.path.exists(path)
-        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_paths", paths=path, link_data=True)
+        payload, files = self.library_populator.create_dataset_request(
+            library, upload_option="upload_paths", paths=path, link_data=True
+        )
         response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
         assert response.status_code == 200
         dataset = response.json()[0]
@@ -256,14 +262,14 @@ class DefaultBinaryContentFiltersTestCase(BaseUploadContentConfigurationTestCase
 
     def test_random_binary_allowed(self):
         dataset = self.dataset_populator.new_dataset(
-            self.history_id, 'file://%s/random-file' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+            self.history_id, "file://%s/random-file" % TEST_DATA_DIRECTORY, file_type="auto", wait=True
         )
         dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
         assert dataset["file_ext"] == "binary", dataset
 
     def test_gzipped_html_content_blocked_by_default(self):
         dataset = self.dataset_populator.new_dataset(
-            self.history_id, 'file://%s/bad.html.gz' % TEST_DATA_DIRECTORY, file_type="auto", wait=True, assert_ok=False
+            self.history_id, "file://%s/bad.html.gz" % TEST_DATA_DIRECTORY, file_type="auto", wait=True, assert_ok=False
         )
         dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset, assert_ok=False)
         assert dataset["file_size"] == 0
@@ -280,7 +286,7 @@ class DisableContentCheckingTestCase(BaseUploadContentConfigurationTestCase):
 
     def test_gzipped_html_content_now_allowed(self):
         dataset = self.dataset_populator.new_dataset(
-            self.history_id, 'file://%s/bad.html.gz' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+            self.history_id, "file://%s/bad.html.gz" % TEST_DATA_DIRECTORY, file_type="auto", wait=True
         )
         dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
         # Same file was empty above!
@@ -297,25 +303,26 @@ class AutoDecompressTestCase(BaseUploadContentConfigurationTestCase):
 
     def test_auto_decompress_off(self):
         dataset = self.dataset_populator.new_dataset(
-            self.history_id, 'file://%s/1.sam.gz' % TEST_DATA_DIRECTORY, file_type="auto", auto_decompress=False, wait=True
+            self.history_id,
+            "file://%s/1.sam.gz" % TEST_DATA_DIRECTORY,
+            file_type="auto",
+            auto_decompress=False,
+            wait=True,
         )
         dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
         assert dataset["file_ext"] == "binary", dataset
 
     def test_auto_decompress_on(self):
         dataset = self.dataset_populator.new_dataset(
-            self.history_id, 'file://%s/1.sam.gz' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+            self.history_id, "file://%s/1.sam.gz" % TEST_DATA_DIRECTORY, file_type="auto", wait=True
         )
         dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
         assert dataset["file_ext"] == "sam", dataset
 
 
 class LocalAddressWhitelisting(BaseUploadContentConfigurationTestCase):
-
     def test_blocked_url_for_primary_file(self):
-        payload = self.dataset_populator.upload_payload(
-            self.history_id, 'http://localhost/', file_type="txt"
-        )
+        payload = self.dataset_populator.upload_payload(self.history_id, "http://localhost/", file_type="txt")
         create_response = self.dataset_populator.tools_post(payload)
         # Ideally this would be 403 but the tool API endpoint isn't using
         # the newer API decorator that handles those details.
@@ -351,7 +358,6 @@ class LocalAddressWhitelisting(BaseUploadContentConfigurationTestCase):
 
 
 class BaseFtpUploadConfigurationTestCase(BaseUploadContentConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         ftp_dir = cls.ftp_dir()
@@ -406,7 +412,6 @@ class BaseFtpUploadConfigurationTestCase(BaseUploadContentConfigurationTestCase)
 
 
 class SimpleFtpUploadConfigurationTestCase(BaseFtpUploadConfigurationTestCase):
-
     def test_ftp_upload(self):
         content = "hello world\n"
         ftp_path = self._write_ftp_file(content)
@@ -445,25 +450,22 @@ class SimpleFtpUploadConfigurationTestCase(BaseFtpUploadConfigurationTestCase):
 
 
 class ExplicitEmailAsIdentifierFtpUploadConfigurationTestCase(SimpleFtpUploadConfigurationTestCase):
-
     @classmethod
     def handle_extra_ftp_config(cls, config):
         config["ftp_upload_dir_identifier"] = "email"
 
 
 class PerUsernameFtpUploadConfigurationTestCase(SimpleFtpUploadConfigurationTestCase):
-
     @classmethod
     def handle_extra_ftp_config(cls, config):
         config["ftp_upload_dir_identifier"] = "username"
 
     def _get_user_ftp_path(self):
-        username = re.sub('[^a-z-]', '--', TEST_USER.lower())
+        username = re.sub("[^a-z-]", "--", TEST_USER.lower())
         return os.path.join(self.ftp_dir(), username)
 
 
 class TemplatedFtpDirectoryUploadConfigurationTestCase(SimpleFtpUploadConfigurationTestCase):
-
     @classmethod
     def handle_extra_ftp_config(cls, config):
         config["ftp_upload_dir_template"] = "${ftp_upload_dir}/moo_${ftp_upload_dir_identifier}_cow"
@@ -473,7 +475,6 @@ class TemplatedFtpDirectoryUploadConfigurationTestCase(SimpleFtpUploadConfigurat
 
 
 class DisableFtpPurgeUploadConfigurationTestCase(BaseFtpUploadConfigurationTestCase):
-
     @classmethod
     def handle_extra_ftp_config(cls, config):
         config["ftp_upload_purge"] = "False"
@@ -485,7 +486,6 @@ class DisableFtpPurgeUploadConfigurationTestCase(BaseFtpUploadConfigurationTestC
 
 
 class EnableFtpPurgeUploadConfigurationTestCase(BaseFtpUploadConfigurationTestCase):
-
     @classmethod
     def handle_extra_ftp_config(cls, config):
         config["ftp_upload_purge"] = "True"
@@ -496,7 +496,6 @@ class EnableFtpPurgeUploadConfigurationTestCase(BaseFtpUploadConfigurationTestCa
 
 
 class AdvancedFtpUploadFetchTestCase(BaseFtpUploadConfigurationTestCase):
-
     def test_fetch_ftp_directory(self):
         dir_path = self._get_user_ftp_path()
         self._write_file(os.path.join(dir_path, "subdir"), "content 1", filename="1")
@@ -522,8 +521,20 @@ class AdvancedFtpUploadFetchTestCase(BaseFtpUploadConfigurationTestCase):
         self._write_file(os.path.join(dir_path, "subdir1"), "content 22", filename="2")
         self._write_file(os.path.join(dir_path, "subdir2"), "content 333", filename="3")
         elements = [
-            {"name": "subdirel1", "src": "ftp_import", "ftp_path": "subdir1", "elements_from": "directory", "collection_type": "list"},
-            {"name": "subdirel2", "src": "ftp_import", "ftp_path": "subdir2", "elements_from": "directory", "collection_type": "list"},
+            {
+                "name": "subdirel1",
+                "src": "ftp_import",
+                "ftp_path": "subdir1",
+                "elements_from": "directory",
+                "collection_type": "list",
+            },
+            {
+                "name": "subdirel2",
+                "src": "ftp_import",
+                "ftp_path": "subdir2",
+                "elements_from": "directory",
+                "collection_type": "list",
+            },
         ]
         target = {
             "destination": {"type": "hdca"},
@@ -531,20 +542,22 @@ class AdvancedFtpUploadFetchTestCase(BaseFtpUploadConfigurationTestCase):
             "collection_type": "list:list",
         }
         self.fetch_target(target, assert_ok=True, wait=True)
-        hdca = self.dataset_populator.get_history_collection_details(self.history_id, history_content_type='dataset_collection')
+        hdca = self.dataset_populator.get_history_collection_details(
+            self.history_id, history_content_type="dataset_collection"
+        )
         assert len(hdca["elements"]) == 2, hdca
         element0 = hdca["elements"][0]
         assert element0["element_identifier"] == "subdirel1"
 
 
 class UploadOptionsFtpUploadConfigurationTestCase(BaseFtpUploadConfigurationTestCase):
-
     def test_upload_api_option_space_to_tab(self):
         self._write_user_ftp_file("0.txt", ONE_TO_SIX_WITH_SPACES)
         self._write_user_ftp_file("1.txt", ONE_TO_SIX_WITH_SPACES)
         self._write_user_ftp_file("2.txt", ONE_TO_SIX_WITH_SPACES)
 
-        payload = self.dataset_populator.upload_payload(self.history_id,
+        payload = self.dataset_populator.upload_payload(
+            self.history_id,
             ftp_files="0.txt",
             file_type="tabular",
             dbkey="hg19",
@@ -559,7 +572,7 @@ class UploadOptionsFtpUploadConfigurationTestCase(BaseFtpUploadConfigurationTest
                 "files_2|file_type": "txt",
                 "files_2|space_to_tab": "Yes",
                 "file_count": "3",
-            }
+            },
         )
         run_response = self.dataset_populator.tools_post(payload)
         self.dataset_populator.wait_for_tool_run(self.history_id, run_response)
@@ -580,7 +593,8 @@ class UploadOptionsFtpUploadConfigurationTestCase(BaseFtpUploadConfigurationTest
         self._write_user_ftp_file("1.txt", ONE_TO_SIX_ON_WINDOWS)
         self._write_user_ftp_file("2.txt", ONE_TO_SIX_ON_WINDOWS)
 
-        payload = self.dataset_populator.upload_payload(self.history_id,
+        payload = self.dataset_populator.upload_payload(
+            self.history_id,
             ftp_files="0.txt",
             file_type="tabular",
             dbkey="hg19",
@@ -595,7 +609,7 @@ class UploadOptionsFtpUploadConfigurationTestCase(BaseFtpUploadConfigurationTest
                 "files_2|NAME": "ThirdOutputName",
                 "files_2|file_type": "txt",
                 "file_count": "3",
-            }
+            },
         )
         run_response = self.dataset_populator.tools_post(payload)
         self.dataset_populator.wait_for_tool_run(self.history_id, run_response)
@@ -658,7 +672,9 @@ class ServerDirectoryOffByDefaultTestCase(BaseUploadContentConfigurationTestCase
 
     def test_server_dir_uploads_403_if_dir_not_set(self):
         library = self.library_populator.new_private_library("serverdiroffbydefault")
-        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_directory", server_dir="foobar")
+        payload, files = self.library_populator.create_dataset_request(
+            library, upload_option="upload_directory", server_dir="foobar"
+        )
         response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
         assert response.status_code == 403, response.json()
         assert '"library_import_dir" is not set' in response.json()["err_msg"]
@@ -677,15 +693,17 @@ class ServerDirectoryValidUsageTestCase(BaseUploadContentConfigurationTestCase):
         config["library_import_dir"] = server_dir
 
     def test_valid_server_dir_uploads_okay(self):
-        dir_to_import = 'library'
+        dir_to_import = "library"
         full_dir_path = os.path.join(self.server_dir(), dir_to_import)
         os.makedirs(full_dir_path)
         file_content = "hello world\n"
-        with tempfile.NamedTemporaryFile(mode='w', dir=full_dir_path, delete=False) as fh:
+        with tempfile.NamedTemporaryFile(mode="w", dir=full_dir_path, delete=False) as fh:
             fh.write(file_content)
             file_to_import = fh.name
 
-        library_dataset = self.library_populator.new_library_dataset("serverdirupload", upload_option="upload_directory", server_dir=dir_to_import)
+        library_dataset = self.library_populator.new_library_dataset(
+            "serverdirupload", upload_option="upload_directory", server_dir=dir_to_import
+        )
         # Check the file is still there and was not modified
         with open(file_to_import) as fh:
             read_content = fh.read()
@@ -699,7 +717,9 @@ class ServerDirectoryValidUsageTestCase(BaseUploadContentConfigurationTestCase):
         file_path = self._write_file(dir_path, content)
         library = self.library_populator.new_private_library("serverdirupload")
         # upload $GALAXY_ROOT/test-data/library
-        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_directory", server_dir="lib1", link_data=True)
+        payload, files = self.library_populator.create_dataset_request(
+            library, upload_option="upload_directory", server_dir="lib1", link_data=True
+        )
         response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
         assert response.status_code == 200, response.json()
         dataset = response.json()[0]
@@ -713,7 +733,6 @@ class ServerDirectoryValidUsageTestCase(BaseUploadContentConfigurationTestCase):
 
 
 class UserServerDirectoryOffByDefaultTestCase(BaseUploadContentConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["user_library_import_dir"] = None
@@ -721,13 +740,14 @@ class UserServerDirectoryOffByDefaultTestCase(BaseUploadContentConfigurationTest
     def test_library_import_dir_not_available_to_non_admins(self):
         # same test case above works for admins
         library = self.library_populator.new_private_library("serverdirupload")
-        payload, files = self.library_populator.create_dataset_request(library, upload_option="upload_directory", server_dir="library")
+        payload, files = self.library_populator.create_dataset_request(
+            library, upload_option="upload_directory", server_dir="library"
+        )
         response = self.library_populator.raw_library_contents_create(library["id"], payload, files=files)
         assert response.status_code == 403, response.json()
 
 
 class UserServerDirectoryValidUsageTestCase(BaseUploadContentConfigurationTestCase):
-
     @classmethod
     def user_server_dir(cls):
         return cls.temp_config_dir("user_library_import_dir")
@@ -739,15 +759,17 @@ class UserServerDirectoryValidUsageTestCase(BaseUploadContentConfigurationTestCa
         config["user_library_import_dir"] = os.path.join(user_server_dir)
 
     def test_valid_user_server_dir_uploads_okay(self):
-        dir_to_import = 'library'
+        dir_to_import = "library"
         full_dir_path = os.path.join(self.user_server_dir(), TEST_USER, dir_to_import)
         os.makedirs(full_dir_path)
         file_content = "hello world\n"
-        with tempfile.NamedTemporaryFile(mode='w', dir=full_dir_path, delete=False) as fh:
+        with tempfile.NamedTemporaryFile(mode="w", dir=full_dir_path, delete=False) as fh:
             fh.write(file_content)
             file_to_import = fh.name
 
-        library_dataset = self.library_populator.new_library_dataset("serverdirupload", upload_option="upload_directory", server_dir=dir_to_import)
+        library_dataset = self.library_populator.new_library_dataset(
+            "serverdirupload", upload_option="upload_directory", server_dir=dir_to_import
+        )
         # Check the file is still there and was not modified
         with open(file_to_import) as fh:
             read_content = fh.read()
@@ -769,10 +791,7 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
         bed_test_data_path = self.test_data_resolver.get_filename("4.bed")
         assert os.path.exists(bed_test_data_path)
         items = [{"src": "path", "path": bed_test_data_path, "info": "my cool bed"}]
-        targets = [{
-            "destination": destination,
-            "items": items
-        }]
+        targets = [{"destination": destination, "items": items}]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -787,10 +806,7 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
         bed_test_data_path = self.test_data_resolver.get_filename("4.bed")
         assert os.path.exists(bed_test_data_path)
         items = [{"src": "path", "path": bed_test_data_path, "info": "my cool bed", "link_data_only": True}]
-        targets = [{
-            "destination": destination,
-            "items": items
-        }]
+        targets = [{"destination": destination, "items": items}]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -804,10 +820,14 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
     def test_fetch_recursive_archive(self):
         history_id, library, destination = self.library_populator.setup_fetch_to_folder("recursive_archive")
         archive_test_data_path = self.test_data_resolver.get_filename("testdir1.zip")
-        targets = [{
-            "destination": destination,
-            "items_from": "archive", "src": "path", "path": archive_test_data_path,
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items_from": "archive",
+                "src": "path",
+                "path": archive_test_data_path,
+            }
+        ]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -825,10 +845,12 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
     def test_fetch_history_compressed_type(self):
         destination = {"type": "hdas"}
         archive = self.test_data_resolver.get_filename("1.fastqsanger.gz")
-        targets = [{
-            "destination": destination,
-            "items": [{"src": "path", "path": archive, "ext": "fastqsanger.gz"}],
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items": [{"src": "path", "path": archive, "ext": "fastqsanger.gz"}],
+            }
+        ]
         payload = {
             "history_id": self.history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -850,10 +872,14 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
     def test_fetch_recursive_archive_history(self):
         destination = {"type": "hdas"}
         archive = self.test_data_resolver.get_filename("testdir1.zip")
-        targets = [{
-            "destination": destination,
-            "items_from": "archive", "src": "path", "path": archive,
-        }]
+        targets = [
+            {
+                "destination": destination,
+                "items_from": "archive",
+                "src": "path",
+                "path": archive,
+            }
+        ]
         payload = {
             "history_id": self.history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -866,10 +892,14 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
 
     def test_fetch_recursive_archive_to_library(self):
         bed_test_data_path = self.test_data_resolver.get_filename("testdir1.zip")
-        targets = [{
-            "destination": {"type": "library", "name": "My Cool Library"},
-            "items_from": "archive", "src": "path", "path": bed_test_data_path,
-        }]
+        targets = [
+            {
+                "destination": {"type": "library", "name": "My Cool Library"},
+                "items_from": "archive",
+                "src": "path",
+                "path": bed_test_data_path,
+            }
+        ]
         payload = {
             "history_id": self.history_id,  # TODO: Shouldn't be needed :(
             "targets": json.dumps(targets),
@@ -893,7 +923,11 @@ class TestDirectoryAndCompressedTypes(BaseUploadContentConfigurationTestCase):
 
     def test_tar_to_directory(self):
         dataset = self.dataset_populator.new_dataset(
-            self.history_id, 'file://%s/testdir.tar' % TEST_DATA_DIRECTORY, file_type="tar", auto_decompress=False, wait=True
+            self.history_id,
+            "file://%s/testdir.tar" % TEST_DATA_DIRECTORY,
+            file_type="tar",
+            auto_decompress=False,
+            wait=True,
         )
         dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
         assert dataset["file_ext"] == "tar", dataset
diff --git a/test/integration/test_vault_extra_prefs.py b/test/integration/test_vault_extra_prefs.py
index 62706ed0be8..6e1cabfee17 100644
--- a/test/integration/test_vault_extra_prefs.py
+++ b/test/integration/test_vault_extra_prefs.py
@@ -1,10 +1,13 @@
 import json
 import os
-from typing import Any, cast
+from typing import (
+    Any,
+    cast,
+)
 
 from requests import (
     get,
-    put
+    put,
 )
 
 from galaxy_test.driver import integration_util
@@ -13,87 +16,115 @@ TEST_USER_EMAIL = "vault_test_user@bx.psu.edu"
 
 
 class ExtraUserPreferencesTestCase(integration_util.IntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["vault_config_file"] = os.path.join(os.path.dirname(__file__), "vault_conf.yml")
-        config["user_preferences_extra_conf_path"] = os.path.join(os.path.dirname(__file__), "user_preferences_extra_conf.yml")
+        config["user_preferences_extra_conf_path"] = os.path.join(
+            os.path.dirname(__file__), "user_preferences_extra_conf.yml"
+        )
 
     def test_extra_prefs_vault_storage(self):
         user = self._setup_user(TEST_USER_EMAIL)
         url = self.__url("information/inputs", user)
         app = cast(Any, self._test_driver.app if self._test_driver else None)
-        db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user['email']).first()
+        db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user["email"]).first()
 
         # create some initial data
-        put(url, data=json.dumps({
-            "vaulttestsection|client_id": "hello_client_id",
-            "vaulttestsection|client_secret": "hello_client_secret",
-            "vaulttestsection|refresh_token": "a_super_secret_value",
-        }))
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "vaulttestsection|client_id": "hello_client_id",
+                    "vaulttestsection|client_secret": "hello_client_secret",
+                    "vaulttestsection|refresh_token": "a_super_secret_value",
+                }
+            ),
+        )
 
         # retrieve saved data
         response = get(url).json()
 
         def get_input_by_name(inputs, name):
-            return [input for input in inputs if input['name'] == name][0]
+            return [input for input in inputs if input["name"] == name][0]
 
-        inputs = [section for section in response["inputs"] if section['name'] == 'vaulttestsection'][0]["inputs"]
+        inputs = [section for section in response["inputs"] if section["name"] == "vaulttestsection"][0]["inputs"]
 
         # value should be what we saved
-        input_client_id = get_input_by_name(inputs, 'client_id')
-        self.assertEqual(input_client_id['value'], "hello_client_id")
+        input_client_id = get_input_by_name(inputs, "client_id")
+        self.assertEqual(input_client_id["value"], "hello_client_id")
 
         # however, this value should not be in the vault
         self.assertIsNone(app.vault.read_secret(f"user/{db_user.id}/preferences/vaulttestsection/client_id"))
         # it should be in the user preferences model
-        self.assertEqual(db_user.extra_preferences['vaulttestsection|client_id'], "hello_client_id")
+        self.assertEqual(db_user.extra_preferences["vaulttestsection|client_id"], "hello_client_id")
 
         # the secret however, was configured to be stored in the vault
-        input_client_secret = get_input_by_name(inputs, 'client_secret')
-        self.assertEqual(input_client_secret['value'], "hello_client_secret")
-        self.assertEqual(app.vault.read_secret(
-            f"user/{db_user.id}/preferences/vaulttestsection/client_secret"), "hello_client_secret")
+        input_client_secret = get_input_by_name(inputs, "client_secret")
+        self.assertEqual(input_client_secret["value"], "hello_client_secret")
+        self.assertEqual(
+            app.vault.read_secret(f"user/{db_user.id}/preferences/vaulttestsection/client_secret"),
+            "hello_client_secret",
+        )
         # it should not be stored in the user preferences model
-        self.assertIsNone(db_user.extra_preferences['vaulttestsection|client_secret'])
+        self.assertIsNone(db_user.extra_preferences["vaulttestsection|client_secret"])
 
         # secret type values should not be retrievable by the client
-        input_refresh_token = get_input_by_name(inputs, 'refresh_token')
-        self.assertNotEqual(input_refresh_token['value'], "a_super_secret_value")
-        self.assertEqual(input_refresh_token['value'], "__SECRET_PLACEHOLDER__")
+        input_refresh_token = get_input_by_name(inputs, "refresh_token")
+        self.assertNotEqual(input_refresh_token["value"], "a_super_secret_value")
+        self.assertEqual(input_refresh_token["value"], "__SECRET_PLACEHOLDER__")
 
         # however, that secret value should be correctly stored on the server
-        self.assertEqual(app.vault.read_secret(
-            f"user/{db_user.id}/preferences/vaulttestsection/refresh_token"), "a_super_secret_value")
+        self.assertEqual(
+            app.vault.read_secret(f"user/{db_user.id}/preferences/vaulttestsection/refresh_token"),
+            "a_super_secret_value",
+        )
 
     def test_extra_prefs_vault_storage_update_secret(self):
         user = self._setup_user(TEST_USER_EMAIL)
         url = self.__url("information/inputs", user)
         app = cast(Any, self._test_driver.app if self._test_driver else None)
-        db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user['email']).first()
+        db_user = app.model.context.query(app.model.User).filter(app.model.User.email == user["email"]).first()
 
         # write the initial secret value
-        put(url, data=json.dumps({
-            "vaulttestsection|refresh_token": "a_new_secret_value",
-        }))
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "vaulttestsection|refresh_token": "a_new_secret_value",
+                }
+            ),
+        )
 
         # attempt to overwrite it with placeholder
-        put(url, data=json.dumps({
-            "vaulttestsection|refresh_token": "__SECRET_PLACEHOLDER__",
-        }))
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "vaulttestsection|refresh_token": "__SECRET_PLACEHOLDER__",
+                }
+            ),
+        )
 
         # value should not have been overwritten
-        self.assertEqual(app.vault.read_secret(
-            f"user/{db_user.id}/preferences/vaulttestsection/refresh_token"), "a_new_secret_value")
+        self.assertEqual(
+            app.vault.read_secret(f"user/{db_user.id}/preferences/vaulttestsection/refresh_token"), "a_new_secret_value"
+        )
 
         # write a new value
-        put(url, data=json.dumps({
-            "vaulttestsection|refresh_token": "an_updated_secret_value",
-        }))
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "vaulttestsection|refresh_token": "an_updated_secret_value",
+                }
+            ),
+        )
 
         # value should now be overwritten
-        self.assertEqual(app.vault.read_secret(
-            f"user/{db_user.id}/preferences/vaulttestsection/refresh_token"), "an_updated_secret_value")
+        self.assertEqual(
+            app.vault.read_secret(f"user/{db_user.id}/preferences/vaulttestsection/refresh_token"),
+            "an_updated_secret_value",
+        )
 
     def __url(self, action, user):
         return self._api_url(f"users/{user['id']}/{action}", params=dict(key=self.master_api_key))
diff --git a/test/integration/test_vault_file_source.py b/test/integration/test_vault_file_source.py
index f8f6a9c330d..d362bf969f7 100644
--- a/test/integration/test_vault_file_source.py
+++ b/test/integration/test_vault_file_source.py
@@ -7,7 +7,6 @@ from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
-
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_VAULT_CONF = os.path.join(SCRIPT_DIRECTORY, "file_sources_conf_vault.yml")
 VAULT_CONF = os.path.join(SCRIPT_DIRECTORY, "vault_conf.yml")
@@ -34,11 +33,14 @@ class VaultFileSourceIntegrationTestCase(integration_util.IntegrationTestCase):
         """
         with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
             app = self._app
-            user = app.model.context.query(app.model.User).filter(
-                app.model.User.email == self.USER_1_APP_VAULT_ENTRY).first()
+            user = (
+                app.model.context.query(app.model.User)
+                .filter(app.model.User.email == self.USER_1_APP_VAULT_ENTRY)
+                .first()
+            )
             user_vault = UserVaultWrapper(self._app.vault, user)
             # use a valid symlink path so the posix list succeeds
-            user_vault.write_secret('posix/root_path', app.config.user_library_import_symlink_allowlist[0])
+            user_vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
 
             data = {"target": "gxfiles://test_user_vault"}
             list_response = self.galaxy_interactor.get("remote_files", data)
@@ -48,11 +50,14 @@ class VaultFileSourceIntegrationTestCase(integration_util.IntegrationTestCase):
 
         with self._different_user(email=self.USER_2_APP_VAULT_ENTRY):
             app = self._app
-            user = app.model.context.query(app.model.User).filter(
-                app.model.User.email == self.USER_2_APP_VAULT_ENTRY).first()
+            user = (
+                app.model.context.query(app.model.User)
+                .filter(app.model.User.email == self.USER_2_APP_VAULT_ENTRY)
+                .first()
+            )
             user_vault = UserVaultWrapper(self._app.vault, user)
             # use an invalid symlink path so the posix list fails
-            user_vault.write_secret('posix/root_path', '/invalid/root')
+            user_vault.write_secret("posix/root_path", "/invalid/root")
 
             data = {"target": "gxfiles://test_user_vault"}
             list_response = self.galaxy_interactor.get("remote_files", data)
@@ -67,14 +72,17 @@ class VaultFileSourceIntegrationTestCase(integration_util.IntegrationTestCase):
         # write app level secret
         app = self._app
         # use a valid symlink path so the posix list succeeds
-        app.vault.write_secret('posix/root_path', app.config.user_library_import_symlink_allowlist[0])
+        app.vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
 
         with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
-            user = app.model.context.query(app.model.User).filter(
-                app.model.User.email == self.USER_1_APP_VAULT_ENTRY).first()
+            user = (
+                app.model.context.query(app.model.User)
+                .filter(app.model.User.email == self.USER_1_APP_VAULT_ENTRY)
+                .first()
+            )
             user_vault = UserVaultWrapper(self._app.vault, user)
             # use a valid symlink path so the posix list succeeds
-            user_vault.write_secret('posix/root_path', app.config.user_library_import_symlink_allowlist[0])
+            user_vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
 
             data = {"target": "gxfiles://test_app_vault"}
             list_response = self.galaxy_interactor.get("remote_files", data)
@@ -83,11 +91,14 @@ class VaultFileSourceIntegrationTestCase(integration_util.IntegrationTestCase):
             print(remote_files)
 
         with self._different_user(email=self.USER_2_APP_VAULT_ENTRY):
-            user = app.model.context.query(app.model.User).filter(
-                app.model.User.email == self.USER_2_APP_VAULT_ENTRY).first()
+            user = (
+                app.model.context.query(app.model.User)
+                .filter(app.model.User.email == self.USER_2_APP_VAULT_ENTRY)
+                .first()
+            )
             user_vault = UserVaultWrapper(self._app.vault, user)
             # use an invalid symlink path so the posix list would fail if used
-            user_vault.write_secret('posix/root_path', '/invalid/root')
+            user_vault.write_secret("posix/root_path", "/invalid/root")
 
             data = {"target": "gxfiles://test_app_vault"}
             list_response = self.galaxy_interactor.get("remote_files", data)
@@ -98,14 +109,17 @@ class VaultFileSourceIntegrationTestCase(integration_util.IntegrationTestCase):
     def test_upload_file_from_remote_source(self):
         with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
             app = self._app
-            user = app.model.context.query(app.model.User).filter(
-                app.model.User.email == self.USER_1_APP_VAULT_ENTRY).first()
+            user = (
+                app.model.context.query(app.model.User)
+                .filter(app.model.User.email == self.USER_1_APP_VAULT_ENTRY)
+                .first()
+            )
             user_vault = UserVaultWrapper(self._app.vault, user)
             # use a valid symlink path so the posix list succeeds
-            user_vault.write_secret('posix/root_path', app.config.user_library_import_symlink_allowlist[0])
+            user_vault.write_secret("posix/root_path", app.config.user_library_import_symlink_allowlist[0])
             data = {"target": "gxfiles://test_user_vault"}
-            with open(os.path.join(app.config.user_library_import_symlink_allowlist[0], 'a_file'), 'w') as fh:
-                fh.write('I require access to the vault')
+            with open(os.path.join(app.config.user_library_import_symlink_allowlist[0], "a_file"), "w") as fh:
+                fh.write("I require access to the vault")
             list_response = self.galaxy_interactor.get("remote_files", data)
             api_asserts.assert_status_code_is_ok(list_response)
             remote_files = list_response.json()
diff --git a/test/integration/test_web_framework_config.py b/test/integration/test_web_framework_config.py
index 6892fc98e36..b9d00b1f441 100644
--- a/test/integration/test_web_framework_config.py
+++ b/test/integration/test_web_framework_config.py
@@ -5,7 +5,6 @@ from galaxy_test.driver import integration_util
 
 
 class BaseWebFrameworkTestCase(integration_util.IntegrationTestCase):
-
     def _options(self, headers=None):
         url = self._api_url("licenses")
         options_response = options(url, headers=headers or {})
@@ -22,7 +21,7 @@ class CorsDefaultIntegrationTestCase(BaseWebFrameworkTestCase):
         }
         options_response = self._options(headers)
         assert options_response.status_code == 200
-        assert 'access-control-allow-origin' not in options_response.headers
+        assert "access-control-allow-origin" not in options_response.headers
 
     def test_origin_not_allowed_default(self):
         headers = {
@@ -32,7 +31,7 @@ class CorsDefaultIntegrationTestCase(BaseWebFrameworkTestCase):
         }
         options_response = self._options(headers)
         assert options_response.status_code == 200
-        assert 'access-control-allow-origin' not in options_response.headers
+        assert "access-control-allow-origin" not in options_response.headers
 
 
 class AllowOriginIntegrationTestCase(BaseWebFrameworkTestCase):
@@ -50,9 +49,9 @@ class AllowOriginIntegrationTestCase(BaseWebFrameworkTestCase):
         }
         options_response = self._options(headers)
         options_response.raise_for_status()
-        assert 'access-control-allow-origin' in options_response.headers
-        assert options_response.headers['access-control-allow-origin'] == "http://192.168.0.101:8083"
-        assert options_response.headers['access-control-max-age'] == "600"
+        assert "access-control-allow-origin" in options_response.headers
+        assert options_response.headers["access-control-allow-origin"] == "http://192.168.0.101:8083"
+        assert options_response.headers["access-control-max-age"] == "600"
 
     def test_origin_allowed_if_configured_via_regex(self):
         headers = {
@@ -62,9 +61,9 @@ class AllowOriginIntegrationTestCase(BaseWebFrameworkTestCase):
         }
         options_response = self._options(headers)
         options_response.raise_for_status()
-        assert 'access-control-allow-origin' in options_response.headers
-        assert options_response.headers['access-control-allow-origin'] == "http://rna.galaxyproject.org"
-        assert options_response.headers['access-control-max-age'] == "600"
+        assert "access-control-allow-origin" in options_response.headers
+        assert options_response.headers["access-control-allow-origin"] == "http://rna.galaxyproject.org"
+        assert options_response.headers["access-control-max-age"] == "600"
 
     def test_origin_not_allowed_if_not_in_configured_list(self):
         headers = {
diff --git a/test/integration/test_webdav.py b/test/integration/test_webdav.py
index ba4036d8b03..363f72531a0 100644
--- a/test/integration/test_webdav.py
+++ b/test/integration/test_webdav.py
@@ -11,19 +11,14 @@ from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
-
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_JOB_CONF = os.path.join(SCRIPT_DIRECTORY, "file_sources_conf.yml")
 
-skip_if_no_webdav = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_WEBDAV'),
-    reason="GALAXY_TEST_WEBDAV not set"
-)
+skip_if_no_webdav = pytest.mark.skipif(not os.environ.get("GALAXY_TEST_WEBDAV"), reason="GALAXY_TEST_WEBDAV not set")
 
 
 @skip_if_no_webdav
 class WebDavIntegrationTestCase(integration_util.IntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["file_sources_config_file"] = FILE_SOURCES_JOB_CONF
diff --git a/test/integration/test_work_queue_put_failure.py b/test/integration/test_work_queue_put_failure.py
index 7e97d14fefe..d832c344eef 100644
--- a/test/integration/test_work_queue_put_failure.py
+++ b/test/integration/test_work_queue_put_failure.py
@@ -17,16 +17,18 @@ execution:
 
 
 class WorkQueuePutFailureTestCase(integration_util.IntegrationTestCase):
-
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
         self.history_id = self.dataset_populator.new_history()
 
     @classmethod
-    def handle_galaxy_config_kwds(cls, config, ):
+    def handle_galaxy_config_kwds(
+        cls,
+        config,
+    ):
         # config["jobs_directory"] = cls.jobs_directory
-        with tempfile.NamedTemporaryFile(mode='w', suffix='job_conf.yml', delete=False) as job_conf:
+        with tempfile.NamedTemporaryFile(mode="w", suffix="job_conf.yml", delete=False) as job_conf:
             job_conf.write(job_conf_yaml)
         config["job_config_file"] = job_conf.name
         # Disable tool dependency resolution.
@@ -35,6 +37,6 @@ class WorkQueuePutFailureTestCase(integration_util.IntegrationTestCase):
     def test_job_fails(self):
         self.dataset_populator.new_dataset(self.history_id, content="1 2 3")
         self.dataset_populator.wait_for_history(self.history_id, assert_ok=False)
-        state_details = self.galaxy_interactor.get('histories/%s' % self.history_id).json()['state_details']
-        assert state_details['running'] == 0
-        assert state_details['error'] == 1
+        state_details = self.galaxy_interactor.get("histories/%s" % self.history_id).json()["state_details"]
+        assert state_details["running"] == 0
+        assert state_details["error"] == 1
diff --git a/test/integration/test_workflow_handler_configuration.py b/test/integration/test_workflow_handler_configuration.py
index 0b3fda5a922..a26f98ac1c0 100644
--- a/test/integration/test_workflow_handler_configuration.py
+++ b/test/integration/test_workflow_handler_configuration.py
@@ -16,7 +16,8 @@ from galaxy_test.driver import integration_util
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 WORKFLOW_HANDLER_CONFIGURATION_JOB_CONF = os.path.join(SCRIPT_DIRECTORY, "workflow_handler_configuration_job_conf.xml")
 
-WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template("""
+WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template(
+    """
 <job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
@@ -40,9 +41,11 @@ WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template("""
         </destination>
     </destinations>
 </job_conf>
-""")
+"""
+)
 
-POOL_JOB_CONFIG_TEMPLATE = string.Template("""<job_conf>
+POOL_JOB_CONFIG_TEMPLATE = string.Template(
+    """<job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
     </plugins>
@@ -53,9 +56,11 @@ POOL_JOB_CONFIG_TEMPLATE = string.Template("""<job_conf>
         </destination>
     </destinations>
 </job_conf>
-""")
+"""
+)
 
-WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template("""
+WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template(
+    """
 <workflow_schedulers default="core">
   <core id="core" />
   <handlers default="workflow_handlers" $assign_with>
@@ -63,7 +68,8 @@ WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template("""
     <handler id="work2" tags="workflow_handlers" />
   </handlers>
 </workflow_schedulers>
-""")
+"""
+)
 JOB_HANDLER_PATTERN = re.compile(r"handler\d")
 WORKFLOW_SCHEDULER_HANDLER_PATTERN = re.compile(r"work\d")
 
@@ -80,8 +86,10 @@ steps:
 """
 
 
-def config_file(template, assign_with=''):
-    with tempfile.NamedTemporaryFile(mode='w', suffix=".xml", prefix="workflow_handler_config_", delete=False) as config:
+def config_file(template, assign_with=""):
+    with tempfile.NamedTemporaryFile(
+        mode="w", suffix=".xml", prefix="workflow_handler_config_", delete=False
+    ) as config:
         if assign_with:
             assign_with = f'assign_with="{assign_with}"'
         config.write(template.substitute(assign_with=assign_with))
@@ -107,13 +115,11 @@ class BaseWorkflowHandlerConfigurationTestCase(integration_util.IntegrationTestC
         workflow_id = self.workflow_populator.upload_yaml_workflow(PAUSE_WORKFLOW)
         history_id = self.history_id
         hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
-        index_map = {
-            '0': dict(src="hda", id=hda1["id"])
-        }
+        index_map = {"0": dict(src="hda", id=hda1["id"])}
         request = {}
         request["history"] = "hist_id=%s" % history_id
         request["inputs"] = dumps(index_map)
-        request["inputs_by"] = 'step_index'
+        request["inputs_by"] = "step_index"
         url = "workflows/%s/invocations" % (workflow_id)
         for _ in range(n):
             self._post(url, data=request)
@@ -136,7 +142,7 @@ class BaseWorkflowHandlerConfigurationTestCase(integration_util.IntegrationTestC
 class HistoryRestrictionConfigurationTestCase(BaseWorkflowHandlerConfigurationTestCase):
 
     # Assign with db-preassign. Would also work with grabbing assignment, but we don't start grabber.
-    assign_with = 'db-preassign'
+    assign_with = "db-preassign"
 
     def test_history_to_handler_restriction(self):
         self._invoke_n_workflows(10)
@@ -153,7 +159,7 @@ class HistoryRestrictionConfigurationTestCase(BaseWorkflowHandlerConfigurationTe
 class HistoryParallelConfigurationTestCase(BaseWorkflowHandlerConfigurationTestCase):
 
     # Assign with db-preassign. Would also work with grabbing assignment, but we don't start grabber.
-    assign_with = 'db-preassign'
+    assign_with = "db-preassign"
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -177,12 +183,14 @@ class HistoryParallelConfigurationTestCase(BaseWorkflowHandlerConfigurationTestC
 class WorkflowSchedulerHandlerAssignment(BaseWorkflowHandlerConfigurationTestCase):
 
     # Assign with db-preassign. Would also work with grabbing assignment, but we don't start grabber.
-    assign_with = 'db-preassign'
+    assign_with = "db-preassign"
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        config["workflow_schedulers_config_file"] = config_file(WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with)
+        config["workflow_schedulers_config_file"] = config_file(
+            WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with
+        )
 
     def test_handler_assignment(self):
         self._invoke_n_workflows(1)
@@ -200,7 +208,6 @@ class WorkflowSchedulerHandlerAssignment(BaseWorkflowHandlerConfigurationTestCas
 #  - If a workflow scheduler conf is defined and assign_with is set to db-transaction-isolation, invocation handler is correctly set
 #  - If a workflow scheduler conf is defined and the process is not listed as a handler, it is not workflow scheduler.
 class DefaultWorkflowHandlerOnTestCase(BaseWorkflowHandlerConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         # Override so we don't setup a job conf like in the base class.
@@ -211,7 +218,6 @@ class DefaultWorkflowHandlerOnTestCase(BaseWorkflowHandlerConfigurationTestCase)
 
 
 class DefaultWorkflowHandlerIfJobHandlerOnTestCase(BaseWorkflowHandlerConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
@@ -223,7 +229,7 @@ class DefaultWorkflowHandlerIfJobHandlerOnTestCase(BaseWorkflowHandlerConfigurat
 
 class JobHandlerAsWorkflowHandlerWithDbSkipLocked(BaseWorkflowHandlerConfigurationTestCase):
 
-    assign_with = 'db-skip-locked'
+    assign_with = "db-skip-locked"
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -241,7 +247,6 @@ class JobHandlerAsWorkflowHandlerWithDbSkipLocked(BaseWorkflowHandlerConfigurati
 
 
 class JobHandlerAsWorkflowHandlerWithDbSkipLockedAttachToPool(JobHandlerAsWorkflowHandlerWithDbSkipLocked):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = config_file(POOL_JOB_CONFIG_TEMPLATE, assign_with=cls.assign_with)
@@ -250,7 +255,6 @@ class JobHandlerAsWorkflowHandlerWithDbSkipLockedAttachToPool(JobHandlerAsWorkfl
 
 
 class DefaultWorkflowHandlerIfJobHandlerOffTestCase(BaseWorkflowHandlerConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
@@ -267,7 +271,9 @@ class ExplicitWorkflowHandlersOnTestCase(BaseWorkflowHandlerConfigurationTestCas
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        config["workflow_schedulers_config_file"] = config_file(WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with)
+        config["workflow_schedulers_config_file"] = config_file(
+            WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with
+        )
         config["server_name"] = "work1"
 
     def test_app_is_workflow_scheduler(self):
@@ -277,7 +283,7 @@ class ExplicitWorkflowHandlersOnTestCase(BaseWorkflowHandlerConfigurationTestCas
 @integration_util.skip_unless_postgres()
 class WorkflowSchedulerHandlerAssignmentDbSkipLocked(ExplicitWorkflowHandlersOnTestCase):
 
-    assign_with = 'db-skip-locked'
+    assign_with = "db-skip-locked"
 
     def test_handler_assignment(self):
         self._invoke_n_workflows(1)
@@ -289,15 +295,16 @@ class WorkflowSchedulerHandlerAssignmentDbSkipLocked(ExplicitWorkflowHandlersOnT
 @integration_util.skip_unless_postgres()
 class WorkflowSchedulerHandlerAssignmentDbTransactionIsolation(WorkflowSchedulerHandlerAssignmentDbSkipLocked):
 
-    assign_with = 'db-transaction-isolation'
+    assign_with = "db-transaction-isolation"
 
 
 class ExplicitWorkflowHandlersOffTestCase(BaseWorkflowHandlerConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        config["workflow_schedulers_config_file"] = config_file(WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with)
+        config["workflow_schedulers_config_file"] = config_file(
+            WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with
+        )
         config["server_name"] = "handler0"  # Configured as a job handler but not a workflow handler.
 
     def test_app_is_not_workflow_scheduler(self):
@@ -305,11 +312,12 @@ class ExplicitWorkflowHandlersOffTestCase(BaseWorkflowHandlerConfigurationTestCa
 
 
 class ExplicitWorkflowHandlersOffPoolTestCase(BaseWorkflowHandlerConfigurationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        config["workflow_schedulers_config_file"] = config_file(WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with)
+        config["workflow_schedulers_config_file"] = config_file(
+            WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE, assign_with=cls.assign_with
+        )
         config["server_name"] = "handler0"  # Configured as a job handler but not a workflow handler.
         config["attach_to_pools"] = ["job-handlers"]
 
diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index 719d7f87f0b..8007aa8674f 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -13,15 +13,9 @@ from galaxy.model import (
     WorkflowStep,
     WorkflowStepConnection,
 )
-from galaxy.workflow.refactor.schema import (
-    RefactorActionExecutionMessageTypeEnum,
-)
-from galaxy_test.base.populators import (
-    WorkflowPopulator,
-)
-from galaxy_test.base.uses_shed import (
-    UsesShed
-)
+from galaxy.workflow.refactor.schema import RefactorActionExecutionMessageTypeEnum
+from galaxy_test.base.populators import WorkflowPopulator
+from galaxy_test.base.uses_shed import UsesShed
 from galaxy_test.base.workflow_fixtures import (
     WORKFLOW_NESTED_RUNTIME_PARAMETER,
     WORKFLOW_NESTED_SIMPLE,
@@ -29,7 +23,6 @@ from galaxy_test.base.workflow_fixtures import (
 )
 from galaxy_test.driver import integration_util
 
-
 REFACTORING_SIMPLE_TEST = """
 class: GalaxyWorkflow
 inputs:
@@ -81,9 +74,7 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
         assert self._latest_workflow.creator_metadata[0]["class"] == "Person"
         assert self._latest_workflow.creator_metadata[0]["name"] == "Mary"
 
-        actions = [
-            {"action_type": "update_report", "report": {"markdown": "my report..."}}
-        ]
+        actions = [{"action_type": "update_report", "report": {"markdown": "my report..."}}]
         self._refactor(actions)
         assert self._latest_workflow.reports_config["markdown"] == "my report..."
 
@@ -104,7 +95,13 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
 
         # Build raw steps...
         actions = [
-            {"action_type": "add_step", "type": "parameter_input", "label": "new_param", "tool_state": {"parameter_type": "text"}, "position": {"left": 10, "top": 50}},
+            {
+                "action_type": "add_step",
+                "type": "parameter_input",
+                "label": "new_param",
+                "tool_state": {"parameter_type": "text"},
+                "position": {"left": 10, "top": 50},
+            },
         ]
         self._refactor(actions)
         assert self._latest_workflow.step_by_label("new_param").label == "new_param"
@@ -114,7 +111,13 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
 
         # Cleaner syntax for defining inputs...
         actions = [
-            {"action_type": "add_input", "type": "text", "label": "new_param2", "optional": True, "position": {"top": 1, "left": 2}},
+            {
+                "action_type": "add_input",
+                "type": "text",
+                "label": "new_param2",
+                "optional": True,
+                "position": {"top": 1, "left": 2},
+            },
         ]
         self._refactor(actions)
         assert self._latest_workflow.step_by_label("new_param2").label == "new_param2"
@@ -206,14 +209,18 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
         assert creator["class"] == "Person"
         assert creator["name"] == "Mary"
 
-        actions = [
-            {"action_type": "update_report", "report": {"markdown": "my report..."}}
-        ]
+        actions = [{"action_type": "update_report", "report": {"markdown": "my report..."}}]
         response = self._dry_run(actions)
         assert response.workflow["report"]["markdown"] == "my report..."
 
         actions = [
-            {"action_type": "add_step", "type": "parameter_input", "label": "new_param", "tool_state": {"parameter_type": "text"}, "position": {"left": 10, "top": 50}},
+            {
+                "action_type": "add_step",
+                "type": "parameter_input",
+                "label": "new_param",
+                "tool_state": {"parameter_type": "text"},
+                "position": {"left": 10, "top": 50},
+            },
         ]
         response = self._dry_run(actions)
         workflow_dict = response.workflow
@@ -246,7 +253,7 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
         num_lines = random_lines_state["num_lines"]
         assert isinstance(num_lines, dict)
         assert "__class__" in num_lines
-        assert num_lines["__class__"] == 'ConnectedValue'
+        assert num_lines["__class__"] == "ConnectedValue"
         assert "seed_source" in random_lines_state
         seed_source = random_lines_state["seed_source"]
         assert isinstance(seed_source, dict)
@@ -254,7 +261,7 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
         seed = seed_source["seed"]
         assert isinstance(seed, dict)
         assert "__class__" in seed
-        assert seed["__class__"] == 'ConnectedValue'
+        assert seed["__class__"] == "ConnectedValue"
 
         # cannot handle mixed, incompatible types on the inputs though
         wf = self.workflow_populator.load_workflow_from_resource("test_workflow_randomlines_legacy_params_mixed_types")
@@ -274,7 +281,8 @@ class WorkflowRefactoringIntegrationTestCase(integration_util.IntegrationTestCas
         # test parameters used in PJA without being used in tool state.
         # These will work fine with the simplified workflow UI, but should probably
         # be formalized and assigned a unique label and informative annotation.
-        self.workflow_populator.upload_yaml_workflow("""
+        self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -286,7 +294,8 @@ steps:
     outputs:
       out_file1:
         rename: "${pja_only_param} name"
-""")
+"""
+        )
         actions = [
             {"action_type": "extract_untyped_parameter", "name": "pja_only_param"},
         ]
@@ -295,7 +304,8 @@ steps:
 
     def test_refactoring_legacy_parameters_without_tool_state_dry_run(self):
         # same as above but dry run...
-        self.workflow_populator.upload_yaml_workflow("""
+        self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -307,7 +317,8 @@ steps:
     outputs:
       out_file1:
         rename: "${pja_only_param} name"
-""")
+"""
+        )
         actions = [
             {"action_type": "extract_untyped_parameter", "name": "pja_only_param"},
         ]
@@ -319,7 +330,8 @@ steps:
 
     def test_refactoring_legacy_parameters_without_tool_state_relabel(self):
         # same thing as above, but apply relabeling and ensure PJA gets updated.
-        self.workflow_populator.upload_yaml_workflow("""
+        self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -331,7 +343,8 @@ steps:
     outputs:
       out_file1:
         rename: "${pja_only_param} name"
-""")
+"""
+        )
         actions = [
             {"action_type": "extract_untyped_parameter", "name": "pja_only_param", "label": "new_label"},
         ]
@@ -485,7 +498,8 @@ steps:
         assert message.input_name == "num_lines"
 
     def test_tool_version_upgrade_no_state_change(self):
-        self.workflow_populator.upload_yaml_workflow("""
+        self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   the_step:
@@ -493,7 +507,8 @@ steps:
     tool_version: '0.1'
     state:
       inttest: 0
-""")
+"""
+        )
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
         actions = [
             {"action_type": "upgrade_tool", "step": {"label": "the_step"}},
@@ -507,7 +522,8 @@ steps:
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.2"
 
     def test_tool_version_upgrade_state_added(self):
-        self.workflow_populator.upload_yaml_workflow("""
+        self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   the_step:
@@ -515,7 +531,8 @@ steps:
     tool_version: '0.1'
     state:
       inttest: 0
-""")
+"""
+        )
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
         actions = [
             {"action_type": "upgrade_tool", "step": {"label": "the_step"}, "tool_version": "0.2"},
@@ -539,11 +556,7 @@ steps:
         nested_stored_workflow = self._recent_stored_workflow(2)
         assert len(nested_stored_workflow.workflows) == 1
 
-        self._increment_nested_workflow_version(
-            nested_stored_workflow,
-            num_lines_from="1",
-            num_lines_to="2"
-        )
+        self._increment_nested_workflow_version(nested_stored_workflow, num_lines_from="1", num_lines_to="2")
         self._app.model.session.expunge(nested_stored_workflow)
         # ensure subworkflow updated properly...
         nested_stored_workflow = self._recent_stored_workflow(2)
@@ -577,23 +590,19 @@ steps:
         nested_stored_workflow = self._recent_stored_workflow(2)
 
         # create two versions so we can test jumping to the middle one...
-        self._increment_nested_workflow_version(
-            nested_stored_workflow,
-            num_lines_from="1",
-            num_lines_to="20"
-        )
-        self._increment_nested_workflow_version(
-            nested_stored_workflow,
-            num_lines_from="20",
-            num_lines_to="30"
-        )
+        self._increment_nested_workflow_version(nested_stored_workflow, num_lines_from="1", num_lines_to="20")
+        self._increment_nested_workflow_version(nested_stored_workflow, num_lines_from="20", num_lines_to="30")
         self._app.model.session.expunge(nested_stored_workflow)
         # ensure subworkflow updated properly...
         nested_stored_workflow = self._recent_stored_workflow(2)
         assert len(nested_stored_workflow.workflows) == 3
         middle_workflow_id = self._app.security.encode_id(nested_stored_workflow.workflows[1].id)
         actions = [
-            {"action_type": "upgrade_subworkflow", "step": {"label": "nested_workflow"}, "content_id": middle_workflow_id},
+            {
+                "action_type": "upgrade_subworkflow",
+                "step": {"label": "nested_workflow"},
+                "content_id": middle_workflow_id,
+            },
         ]
         action_executions = self._dry_run(actions).action_executions
         assert len(action_executions) == 1
@@ -704,11 +713,7 @@ steps:
         updated_nested_step = nested_stored_workflow.latest_workflow.step_by_label("random_lines")
         assert updated_nested_step.tool_inputs["num_lines"] == "1"
 
-        self._increment_nested_workflow_version(
-            nested_stored_workflow,
-            num_lines_from="1",
-            num_lines_to="2"
-        )
+        self._increment_nested_workflow_version(nested_stored_workflow, num_lines_from="1", num_lines_to="2")
         self._app.model.session.expunge(nested_stored_workflow)
         # ensure subworkflow updated properly...
         nested_stored_workflow = self._recent_stored_workflow(2)
@@ -721,8 +726,11 @@ steps:
         nested_stored_workflow = self._recent_stored_workflow(2)
         updated_nested_step = nested_stored_workflow.latest_workflow.step_by_label("random_lines")
         assert updated_nested_step.tool_inputs["num_lines"] == "2"
-        assert self._latest_workflow.step_by_label("compose_text_param").tool_version == '0.1.1'
-        assert self._latest_workflow.step_by_label("compose_text_param").tool_id == 'toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1'
+        assert self._latest_workflow.step_by_label("compose_text_param").tool_version == "0.1.1"
+        assert (
+            self._latest_workflow.step_by_label("compose_text_param").tool_id
+            == "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1"
+        )
 
         assert len(action_executions) == 1
         messages = action_executions[0].messages
@@ -752,16 +760,14 @@ steps:
         original_url_for = app.url_for
 
         def url_for(*args, **kwd):
-            return ''
+            return ""
 
         app.url_for = url_for
         try:
             return self._manager.refactor(
                 mock_trans,
                 stored_workflow or self._most_recent_stored_workflow,
-                RefactorRequest(
-                    actions=actions, dry_run=dry_run, style=style
-                )
+                RefactorRequest(actions=actions, dry_run=dry_run, style=style),
             )
         finally:
             app = url_for = original_url_for
@@ -862,11 +868,10 @@ def _step_with_label(native_dict, label):
     for step_dict in native_dict["steps"].values():
         if step_dict.get("label") == label:
             return step_dict
-    raise AssertionError(f'Failed to find step with label {label}')
+    raise AssertionError(f"Failed to find step with label {label}")
 
 
 class MockTrans(ProvidesAppContext):
-
     def __init__(self, app, user):
         self._app = app
         self.user = user
diff --git a/test/integration/test_workflow_scheduling_options.py b/test/integration/test_workflow_scheduling_options.py
index af282b43d1c..06ac2f9a3eb 100644
--- a/test/integration/test_workflow_scheduling_options.py
+++ b/test/integration/test_workflow_scheduling_options.py
@@ -29,13 +29,11 @@ class MaximumWorkflowInvocationDurationTestCase(integration_util.IntegrationTest
         workflow_id = self.workflow_populator.create_workflow(workflow)
         history_id = self.dataset_populator.new_history()
         hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
-        index_map = {
-            '0': dict(src="hda", id=hda1["id"])
-        }
+        index_map = {"0": dict(src="hda", id=hda1["id"])}
         request = {}
         request["history"] = "hist_id=%s" % history_id
         request["inputs"] = dumps(index_map)
-        request["inputs_by"] = 'step_index'
+        request["inputs_by"] = "step_index"
         url = "workflows/%s/invocations" % (workflow_id)
         invocation_response = self._post(url, data=request)
         invocation_url = url + "/" + invocation_response.json()["id"]
@@ -62,7 +60,8 @@ class MaximumWorkflowJobsPerSchedulingIterationTestCase(integration_util.Integra
         config["maximum_workflow_jobs_per_scheduling_iteration"] = 1
 
     def test_collection_explicit_and_implicit(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow("""
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
 class: GalaxyWorkflow
 steps:
   - type: input_collection
@@ -78,21 +77,27 @@ steps:
     state:
       input1:
         $link: 2/out1
-""")
+"""
+        )
         with self.dataset_populator.test_history() as history_id:
-            hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]).json()
+            hdca1 = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]
+            ).json()
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             inputs = {
-                '0': {"src": "hdca", "id": hdca1["id"]},
+                "0": {"src": "hdca", "id": hdca1["id"]},
             }
             invocation_id = self.workflow_populator.invoke_workflow(history_id, workflow_id, inputs)
             self.workflow_populator.wait_for_workflow(history_id, workflow_id, invocation_id)
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-            self.assertEqual("a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0))
+            self.assertEqual(
+                "a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0)
+            )
 
     def test_scheduling_rounds(self):
         with self.dataset_populator.test_history() as history_id:
-            invocation_response = self.workflow_populator.run_workflow("""
+            invocation_response = self.workflow_populator.run_workflow(
+                """
 class: GalaxyWorkflow
 inputs:
   input1: data
@@ -117,12 +122,15 @@ steps:
 outputs:
   wf_output_1:
     outputSource: collection_creates_dynamic_list_of_pairs/list_output
-""", test_data="""
+""",
+                test_data="""
 input1:
   value: 1.fasta
   type: File
   name: fasta1
 text_input: foo
-""", history_id=history_id)
+""",
+                history_id=history_id,
+            )
             invocation = self._get(f"invocations/{invocation_response.invocation_id}").json()
-            assert 'wf_output_1' in invocation['output_collections']
+            assert "wf_output_1" in invocation["output_collections"]
diff --git a/test/integration_selenium/framework.py b/test/integration_selenium/framework.py
index c2b72fa6a51..cf5add8de5f 100644
--- a/test/integration_selenium/framework.py
+++ b/test/integration_selenium/framework.py
@@ -1,13 +1,12 @@
 from galaxy_test.driver import integration_util
-from galaxy_test.selenium import (
-    framework
-)
+from galaxy_test.selenium import framework
 
 selenium_test = framework.selenium_test
 
 
-class SeleniumIntegrationTestCase(integration_util.IntegrationTestCase, framework.TestWithSeleniumMixin, framework.UsesLibraryAssertions):
-
+class SeleniumIntegrationTestCase(
+    integration_util.IntegrationTestCase, framework.TestWithSeleniumMixin, framework.UsesLibraryAssertions
+):
     def setUp(self):
         super().setUp()
         self.setup_selenium()
@@ -22,6 +21,6 @@ class SeleniumIntegrationTestCase(integration_util.IntegrationTestCase, framewor
 
 
 __all__ = (
-    'selenium_test',
-    'SeleniumIntegrationTestCase',
+    "selenium_test",
+    "SeleniumIntegrationTestCase",
 )
diff --git a/test/integration_selenium/test_admin_dependencies.py b/test/integration_selenium/test_admin_dependencies.py
index 652aebf7bdd..f6fbc0a1ed0 100644
--- a/test/integration_selenium/test_admin_dependencies.py
+++ b/test/integration_selenium/test_admin_dependencies.py
@@ -1,6 +1,6 @@
 from .framework import (
     selenium_test,
-    SeleniumIntegrationTestCase
+    SeleniumIntegrationTestCase,
 )
 
 
@@ -16,9 +16,9 @@ class AdminDependencyContainersTestCase(SeleniumIntegrationTestCase):
         admin_component.index.dependencies.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         # Make sure the tabs are visible
-        self.driver.find_element_by_link_text('Dependencies')
-        self.driver.find_element_by_link_text('Unused')
-        containers_link = self.driver.find_element_by_link_text('Containers')
+        self.driver.find_element_by_link_text("Dependencies")
+        self.driver.find_element_by_link_text("Unused")
+        containers_link = self.driver.find_element_by_link_text("Containers")
         # Ensure that #manage-resolver-type is visible.
         admin_component.manage_dependencies.resolver_type.wait_for_visible()
         self.screenshot("admin_dependencies_landing")
diff --git a/test/integration_selenium/test_dataset_details_source_transforms.py b/test/integration_selenium/test_dataset_details_source_transforms.py
index d2bc3fed6c9..d9d44f9bcd6 100644
--- a/test/integration_selenium/test_dataset_details_source_transforms.py
+++ b/test/integration_selenium/test_dataset_details_source_transforms.py
@@ -1,6 +1,4 @@
-from galaxy_test.driver.integration_setup import (
-    PosixFileSourceSetup,
-)
+from galaxy_test.driver.integration_setup import PosixFileSourceSetup
 from .framework import (
     selenium_test,
     SeleniumIntegrationTestCase,
@@ -20,10 +18,10 @@ class DatasetSourceTransformSeleniumIntegrationTestCase(PosixFileSourceSetup, Se
             "ext": "txt",
             "to_posix_lines": True,
         }
-        output = self.dataset_populator.fetch_hda(
-            history_id, item
+        output = self.dataset_populator.fetch_hda(history_id, item)
+        actions = self.dataset_populator.get_history_dataset_source_transform_actions(
+            history_id, dataset=output, assert_ok=True
         )
-        actions = self.dataset_populator.get_history_dataset_source_transform_actions(history_id, dataset=output, assert_ok=True)
         assert actions == {"to_posix_lines"}
         details = self._display_first_hid_details()
         transform_element = details.transform_action(action="to_posix_lines").wait_for_visible()
@@ -40,10 +38,10 @@ class DatasetSourceTransformSeleniumIntegrationTestCase(PosixFileSourceSetup, Se
             "to_posix_lines": True,
             "space_to_tab": True,
         }
-        output = self.dataset_populator.fetch_hda(
-            history_id, item
+        output = self.dataset_populator.fetch_hda(history_id, item)
+        actions = self.dataset_populator.get_history_dataset_source_transform_actions(
+            history_id, dataset=output, assert_ok=True
         )
-        actions = self.dataset_populator.get_history_dataset_source_transform_actions(history_id, dataset=output, assert_ok=True)
         assert actions == {"spaces_to_tabs", "to_posix_lines"}
         details = self._display_first_hid_details()
         transform_element = details.transform_action(action="spaces_to_tabs").wait_for_visible()
@@ -58,17 +56,19 @@ class DatasetSourceTransformSeleniumIntegrationTestCase(PosixFileSourceSetup, Se
             "url": "gxfiles://testdatafiles/qname_sorted.bam",
             "ext": "bam",
         }
-        output = self.dataset_populator.fetch_hda(
-            history_id, item
+        output = self.dataset_populator.fetch_hda(history_id, item)
+        actions = self.dataset_populator.get_history_dataset_source_transform_actions(
+            history_id, dataset=output, assert_ok=True
         )
-        actions = self.dataset_populator.get_history_dataset_source_transform_actions(history_id, dataset=output, assert_ok=True)
         assert actions == {"datatype_groom"}
         details = self._display_first_hid_details()
         transform_element = details.transform_action(action="datatype_groom").wait_for_visible()
         self.assert_tooltip_text_contains(transform_element, "sorted", click_away=False)
         self.screenshot("dataset_details_source_transform_bam_grooming")
         self.click_center()
-        self.assert_tooltip_text_contains(transform_element, "Galaxy applied datatype specific cleaning of the supplied data", click_away=False)
+        self.assert_tooltip_text_contains(
+            transform_element, "Galaxy applied datatype specific cleaning of the supplied data", click_away=False
+        )
 
     def _display_first_hid_details(self):
         self.home()
diff --git a/test/integration_selenium/test_edam_tool_panel_views.py b/test/integration_selenium/test_edam_tool_panel_views.py
index e982c717a35..859e8994185 100644
--- a/test/integration_selenium/test_edam_tool_panel_views.py
+++ b/test/integration_selenium/test_edam_tool_panel_views.py
@@ -1,7 +1,7 @@
 from galaxy.selenium.navigates_galaxy import retry_during_transitions
 from .framework import (
     selenium_test,
-    SeleniumIntegrationTestCase
+    SeleniumIntegrationTestCase,
 )
 
 
diff --git a/test/integration_selenium/test_history_import_export_ftp.py b/test/integration_selenium/test_history_import_export_ftp.py
index b278ee5649b..3792b3e8966 100644
--- a/test/integration_selenium/test_history_import_export_ftp.py
+++ b/test/integration_selenium/test_history_import_export_ftp.py
@@ -2,7 +2,7 @@ import os
 
 from .framework import (
     selenium_test,
-    SeleniumIntegrationTestCase
+    SeleniumIntegrationTestCase,
 )
 
 
diff --git a/test/integration_selenium/test_toolbox_filters.py b/test/integration_selenium/test_toolbox_filters.py
index 4c3286d23c5..ce66426ffa0 100644
--- a/test/integration_selenium/test_toolbox_filters.py
+++ b/test/integration_selenium/test_toolbox_filters.py
@@ -2,15 +2,14 @@ from selenium.common.exceptions import NoSuchElementException
 
 from .framework import (
     selenium_test,
-    SeleniumIntegrationTestCase
+    SeleniumIntegrationTestCase,
 )
 
-TEST_FILTER_MODULES = 'galaxy.selenium.toolbox'
-TEST_SECTION_FILTERS = 'filters:restrict_test'
+TEST_FILTER_MODULES = "galaxy.selenium.toolbox"
+TEST_SECTION_FILTERS = "filters:restrict_test"
 
 
 class ToolboxFiltersSeleniumIntegrationTestCase(SeleniumIntegrationTestCase):
-
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["user_tool_section_filters"] = TEST_SECTION_FILTERS
@@ -18,20 +17,20 @@ class ToolboxFiltersSeleniumIntegrationTestCase(SeleniumIntegrationTestCase):
 
     @selenium_test
     def test_toolbox_filters(self):
-        '''
+        """
         Test applying and removing a toolbox filter.
 
         This test applies the filter galaxy.selenium.filters.toolbox:restrict_test and confirms that
         the specified section is no longer displayed in the browser.
-        '''
+        """
         self.register()
         # The tool panel section should be visible and clickable at this stage
-        section = self.driver.find_element_by_link_text('Test Section')
+        section = self.driver.find_element_by_link_text("Test Section")
         self.action_chains().move_to_element(section).click().perform()
         self.navigate_to_user_preferences()
         self.components.preferences.toolbox_filters.wait_for_and_click()
         self.screenshot("toolbox_filters_landing")
-        sibling_text = 'This tool filter will disable the Test Section section.'
+        sibling_text = "This tool filter will disable the Test Section section."
         component = self.components.toolbox_filters.input(description=sibling_text)
         filter_upload = component.wait_for_visible()
         self.action_chains().move_to_element(filter_upload).click().perform()
@@ -41,4 +40,4 @@ class ToolboxFiltersSeleniumIntegrationTestCase(SeleniumIntegrationTestCase):
         self.sleep_for(self.wait_types.UX_RENDER)
         self.home()
         # But now it should raise NoSuchElementException
-        self.assertRaises(NoSuchElementException, lambda: self.driver.find_element_by_link_text('Test Section'))
+        self.assertRaises(NoSuchElementException, lambda: self.driver.find_element_by_link_text("Test Section"))
diff --git a/test/integration_selenium/test_trs_import.py b/test/integration_selenium/test_trs_import.py
index 51d405387ff..5aa57ec2cb6 100644
--- a/test/integration_selenium/test_trs_import.py
+++ b/test/integration_selenium/test_trs_import.py
@@ -15,12 +15,14 @@ TRS_CONFIG = """
   label: workflowhub
   link_url: https://workflowhub.eu
 """
-TRS_ID_DOCKSTORE = "workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA"
+TRS_ID_DOCKSTORE = (
+    "workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA"
+)
 TRS_NAME = "sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA"
-TRS_VERSION_DOCKSTORE = 'v0.4'
+TRS_VERSION_DOCKSTORE = "v0.4"
 TRS_ID_WORKFLOWHUB = "110"
 TRS_VERSION_WORKFLOWHUB = "4"
-WORKFLOW_NAME = 'COVID-19: variation analysis on ARTIC PE data'
+WORKFLOW_NAME = "COVID-19: variation analysis on ARTIC PE data"
 
 
 class TrsImportTestCase(SeleniumIntegrationTestCase):
@@ -31,7 +33,7 @@ class TrsImportTestCase(SeleniumIntegrationTestCase):
         trs_config_dir = cls.trs_config_dir()
         os.makedirs(trs_config_dir)
         trs_config_file = os.path.join(trs_config_dir, "trs_config.yml")
-        with open(trs_config_file, 'w') as trs_config:
+        with open(trs_config_file, "w") as trs_config:
             trs_config.write(TRS_CONFIG)
         config["trs_servers_config_file"] = trs_config_file
 
@@ -59,8 +61,10 @@ class TrsImportTestCase(SeleniumIntegrationTestCase):
 
     def test_import_by_search_dockstore(self):
         self.trs_search()
-        self.components.trs_search.search.wait_for_and_send_keys('This is the documentation for the workflow.')
-        self.components.trs_search.search_result(workflow_name='galaxy-workflow-dockstore-example-1').wait_for_and_click()
+        self.components.trs_search.search.wait_for_and_send_keys("This is the documentation for the workflow.")
+        self.components.trs_search.search_result(
+            workflow_name="galaxy-workflow-dockstore-example-1"
+        ).wait_for_and_click()
         self.components.trs_search.import_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
@@ -68,7 +72,7 @@ class TrsImportTestCase(SeleniumIntegrationTestCase):
 
     def test_import_by_organization_search_dockstore(self):
         self.trs_search()
-        self.components.trs_search.search.wait_for_and_send_keys('organization: iwc-workflows')
+        self.components.trs_search.search.wait_for_and_send_keys("organization: iwc-workflows")
         self.components.trs_search.search_result(workflow_name=TRS_NAME).wait_for_and_click()
         self.components.trs_search.import_version(version="v0.4").wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
@@ -78,7 +82,7 @@ class TrsImportTestCase(SeleniumIntegrationTestCase):
     def test_import_by_search_workflowhub(self):
         self.trs_search()
         self.components.trs_search.select_server_button.wait_for_and_click()
-        self.components.trs_search.select_server(server='workflowhub').wait_for_and_click()
+        self.components.trs_search.select_server(server="workflowhub").wait_for_and_click()
         self.components.trs_search.search.wait_for_and_send_keys(WORKFLOW_NAME)
         self.components.trs_search.search_result(workflow_name=WORKFLOW_NAME).wait_for_and_click()
         self.components.trs_search.import_button.wait_for_and_click()
@@ -87,10 +91,10 @@ class TrsImportTestCase(SeleniumIntegrationTestCase):
         self.assert_workflow_imported(WORKFLOW_NAME)
 
     def test_import_by_id_dockstore(self):
-        self._import_by_id(f"#{TRS_ID_DOCKSTORE}", server='dockstore')
+        self._import_by_id(f"#{TRS_ID_DOCKSTORE}", server="dockstore")
 
     def test_import_by_id_workflowhub(self):
-        self._import_by_id(TRS_ID_WORKFLOWHUB, server='workflowhub')
+        self._import_by_id(TRS_ID_WORKFLOWHUB, server="workflowhub")
 
     def _import_by_id(self, trs_id, server):
         self.trs_by_id()
diff --git a/test/integration_selenium/test_upload_file_sources.py b/test/integration_selenium/test_upload_file_sources.py
index b7d4d5d7b7e..23291352fb1 100644
--- a/test/integration_selenium/test_upload_file_sources.py
+++ b/test/integration_selenium/test_upload_file_sources.py
@@ -1,6 +1,4 @@
-from galaxy_test.driver.integration_setup import (
-    PosixFileSourceSetup,
-)
+from galaxy_test.driver.integration_setup import PosixFileSourceSetup
 from .framework import (
     selenium_test,
     SeleniumIntegrationTestCase,
@@ -16,8 +14,8 @@ class PosixFileSourceSeleniumIntegrationTestCase(PosixFileSourceSetup, SeleniumI
         self.admin_login()
         self.components.upload.start.wait_for_and_click()
         self.components.upload.ftp_add.wait_for_and_click()
-        self.components.upload.file_source_selector(path='gxfiles://posix_test').wait_for_and_click()
-        self.components.upload.file_source_selector(path='gxfiles://posix_test/a').wait_for_and_click()
+        self.components.upload.file_source_selector(path="gxfiles://posix_test").wait_for_and_click()
+        self.components.upload.file_source_selector(path="gxfiles://posix_test/a").wait_for_and_click()
         self.components.upload.file_dialog_ok.wait_for_and_click()
         self.upload_start()
         self.sleep_for(self.wait_types.UX_RENDER)
diff --git a/test/integration_selenium/test_upload_ftp.py b/test/integration_selenium/test_upload_ftp.py
index ac7b2002382..1f21b7bf142 100644
--- a/test/integration_selenium/test_upload_ftp.py
+++ b/test/integration_selenium/test_upload_ftp.py
@@ -2,7 +2,7 @@ import os
 
 from .framework import (
     selenium_test,
-    SeleniumIntegrationTestCase
+    SeleniumIntegrationTestCase,
 )
 
 
diff --git a/test/integration_selenium/test_user_library_permissions.py b/test/integration_selenium/test_user_library_permissions.py
index e346418f2de..7ed9d0dea23 100644
--- a/test/integration_selenium/test_user_library_permissions.py
+++ b/test/integration_selenium/test_user_library_permissions.py
@@ -26,7 +26,7 @@ class TestUserLibraryImport(SeleniumIntegrationTestCase):
         current_user_import_dir = os.path.join(self.user_import_dir(), email)
         os.makedirs(current_user_import_dir)
         random_filename = self._get_random_name()
-        file = open(f'{current_user_import_dir}/{random_filename}', "w")
+        file = open(f"{current_user_import_dir}/{random_filename}", "w")
         file.write(random_filename)
         file.close()
 
diff --git a/test/integration_selenium/test_workflow_repository_tool_update.py b/test/integration_selenium/test_workflow_repository_tool_update.py
index 214697de515..a0233215318 100644
--- a/test/integration_selenium/test_workflow_repository_tool_update.py
+++ b/test/integration_selenium/test_workflow_repository_tool_update.py
@@ -1,7 +1,7 @@
 from galaxy_test.base.uses_shed import UsesShed
 from .framework import (
     selenium_test,
-    SeleniumIntegrationTestCase
+    SeleniumIntegrationTestCase,
 )
 
 
@@ -18,22 +18,28 @@ class WorkflowEditorToolUpgradeWithToolShedToolTestCase(SeleniumIntegrationTestC
         self.install_repository("iuc", "compose_text_param", "e188c9826e0f")  # 0.1.1
         self.login()
         workflow_populator = self.workflow_populator
-        workflow_id = workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
+        workflow_id = workflow_populator.upload_yaml_workflow(
+            """class: GalaxyWorkflow
 inputs: []
 steps:
   - tool_id: compose_text_param
     tool_version: 0.1.0
     label: compose_text_param
-        """, exact_tools=True)
+        """,
+            exact_tools=True,
+        )
         self.workflow_index_open()
         self.workflow_index_click_option("Edit")
         editor = self.components.workflow_editor
         editor.node._(label="compose_text_param").wait_for_and_click()
         editor.tool_version_button.wait_for_and_click()
-        assert self.select_dropdown_item('Switch to 0.1.1'), 'Switch to tool version dropdown item not found'
+        assert self.select_dropdown_item("Switch to 0.1.1"), "Switch to tool version dropdown item not found"
         self.screenshot("workflow_editor_version_update_tool_shed")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(workflow_id)
-        assert workflow['steps']['0']['tool_version'] == '0.1.1'
-        assert workflow['steps']['0']['tool_id'] == 'toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1'
+        assert workflow["steps"]["0"]["tool_version"] == "0.1.1"
+        assert (
+            workflow["steps"]["0"]["tool_id"]
+            == "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1"
+        )
diff --git a/test/manual/gen_history_export_test_artifacts.py b/test/manual/gen_history_export_test_artifacts.py
index 3ad0a82a3f7..1d971678e3a 100644
--- a/test/manual/gen_history_export_test_artifacts.py
+++ b/test/manual/gen_history_export_test_artifacts.py
@@ -8,9 +8,7 @@ from bioblend import galaxy
 galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
 sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")]
 
-from galaxy_test.base.populators import (
-    GiDatasetPopulator,
-)
+from galaxy_test.base.populators import GiDatasetPopulator
 
 DESCRIPTION = "Script to generate history export test artifacts."
 
diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py
index 914e21cfac9..f1b88332ba5 100644
--- a/test/manual/workflows_scaling.py
+++ b/test/manual/workflows_scaling.py
@@ -124,38 +124,34 @@ def _workflow_struct(args, input_uuid):
 def _workflow_struct_simple(args, input_uuid):
     workflow_struct = [
         {"tool_id": "create_input_collection", "state": {"collection_size": args.collection_size}},
-        {"tool_id": "cat", "state": {"input1": _link(0, "output")}}
+        {"tool_id": "cat", "state": {"input1": _link(0, "output")}},
     ]
 
     workflow_depth = args.workflow_depth
     for i in range(workflow_depth):
         link = str(i + 1) + "#out_file1"
-        workflow_struct.append(
-            {"tool_id": "cat", "state": {"input1": _link(link)}}
-        )
+        workflow_struct.append({"tool_id": "cat", "state": {"input1": _link(link)}})
     return workflow_struct
 
 
 def _workflow_struct_two_outputs(args, input_uuid):
     workflow_struct = [
         {"type": "input_collection", "uuid": input_uuid},
-        {"tool_id": "cat", "state": {"input1": _link(0), "input2": _link(0)}}
+        {"tool_id": "cat", "state": {"input1": _link(0), "input2": _link(0)}},
     ]
 
     workflow_depth = args.workflow_depth
     for i in range(workflow_depth):
         link1 = str(i + 1) + "#out_file1"
         link2 = str(i + 1) + "#out_file2"
-        workflow_struct.append(
-            {"tool_id": "cat", "state": {"input1": _link(link1), "input2": _link(link2)}}
-        )
+        workflow_struct.append({"tool_id": "cat", "state": {"input1": _link(link1), "input2": _link(link2)}})
     return workflow_struct
 
 
 def _workflow_struct_wave(args, input_uuid):
     workflow_struct = [
         {"tool_id": "create_input_collection", "state": {"collection_size": args.collection_size}},
-        {"tool_id": "cat_list", "state": {"input1": _link(0, "output")}}
+        {"tool_id": "cat_list", "state": {"input1": _link(0, "output")}},
     ]
 
     workflow_depth = args.workflow_depth
diff --git a/test/unit/app/authnz/test_custos_authnz.py b/test/unit/app/authnz/test_custos_authnz.py
index 2430d10a57e..f0f35ab43b0 100644
--- a/test/unit/app/authnz/test_custos_authnz.py
+++ b/test/unit/app/authnz/test_custos_authnz.py
@@ -3,7 +3,10 @@ import json
 import os
 import unittest
 import uuid
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from urllib.parse import (
     parse_qs,
     quote,
@@ -15,7 +18,10 @@ import requests
 
 from galaxy.app_unittest_utils.galaxy_mock import MockTrans
 from galaxy.authnz import custos_authnz
-from galaxy.model import CustosAuthnzToken, User
+from galaxy.model import (
+    CustosAuthnzToken,
+    User,
+)
 from galaxy.util import unicodify
 
 
@@ -29,7 +35,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
     def _get_idp_url(self):
         # it would be ideal is we can use a URI as the following:
         # https://test_base_uri/auth
-        return 'https://iam.scigap.org/auth'
+        return "https://iam.scigap.org/auth"
 
     def _get_credential_url(self):
         return f"{self._get_idp_url()}/credentials"
@@ -78,7 +84,9 @@ class CustosAuthnzTestCase(unittest.TestCase):
         self.test_refresh_expires_in = 1800
         self.test_user_id = str(uuid.uuid4())
         self.test_alt_user_id = str(uuid.uuid4())
-        self.trans.request.url = f"https://localhost:8000/authnz/custos/oidc/callback?state={self.test_state}&code={self.test_code}"
+        self.trans.request.url = (
+            f"https://localhost:8000/authnz/custos/oidc/callback?state={self.test_state}&code={self.test_code}"
+        )
 
     def setupMocks(self):
         self.mock_fetch_token(self.custos_authnz)
@@ -102,6 +110,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
             self._create_oauth2_session_called = True
             assert state == self.test_state
             return orig_create_oauth2_session(state)
+
         custos_authnz._create_oauth2_session = create_oauth2_session
 
     def mock_fetch_token(self, custos_authnz):
@@ -112,9 +121,10 @@ class CustosAuthnzTestCase(unittest.TestCase):
                 "id_token": self.test_id_token,
                 "refresh_token": self.test_refresh_token,
                 "expires_in": self.test_expires_in,
-                "refresh_expires_in": self.test_refresh_expires_in
+                "refresh_expires_in": self.test_refresh_expires_in,
             }
             return self._raw_token
+
         custos_authnz._fetch_token = fetch_token
 
     def mock_get_userinfo(self, custos_authnz):
@@ -126,13 +136,14 @@ class CustosAuthnzTestCase(unittest.TestCase):
                 "sub": self.test_user_id,
                 "alt_username": self.test_alt_username,
                 "alt_email": self.test_alt_email,
-                "alt_id": self.test_alt_user_id
+                "alt_id": self.test_alt_user_id,
             }
+
         custos_authnz._get_userinfo = get_userinfo
 
     def mockRequest(self, request_dict):
         def get(x, **kwargs):
-            assert(x in request_dict)
+            assert x in request_dict
             return Response(request_dict[x])
 
         class Response:
@@ -145,7 +156,6 @@ class CustosAuthnzTestCase(unittest.TestCase):
         return get
 
     def mockTrans(self):
-
         class Request:
             url = None
 
@@ -206,7 +216,6 @@ class CustosAuthnzTestCase(unittest.TestCase):
                 return self._query
 
         class Trans(MockTrans):
-
             def __init__(self, app=None, user=None, history=None, **kwargs):
                 super().__init__(app, user, history, **kwargs)
                 self.cookies = {}
@@ -229,26 +238,26 @@ class CustosAuthnzTestCase(unittest.TestCase):
         requests.get = self.orig_requests_get
 
     def test_parse_config(self):
-        self.assertTrue(self.custos_authnz.config['verify_ssl'])
-        self.assertEqual(self.custos_authnz.config['client_id'], 'test-client-id')
-        self.assertEqual(self.custos_authnz.config['client_secret'], 'test-client-secret')
-        self.assertEqual(self.custos_authnz.config['redirect_uri'], 'https://test-redirect-uri')
-        self.assertEqual(self.custos_authnz.config['authorization_endpoint'], 'https://test-auth-endpoint')
-        self.assertEqual(self.custos_authnz.config['token_endpoint'], 'https://test-token-endpoint')
-        self.assertEqual(self.custos_authnz.config['userinfo_endpoint'], 'https://test-userinfo-endpoint')
+        self.assertTrue(self.custos_authnz.config["verify_ssl"])
+        self.assertEqual(self.custos_authnz.config["client_id"], "test-client-id")
+        self.assertEqual(self.custos_authnz.config["client_secret"], "test-client-secret")
+        self.assertEqual(self.custos_authnz.config["redirect_uri"], "https://test-redirect-uri")
+        self.assertEqual(self.custos_authnz.config["authorization_endpoint"], "https://test-auth-endpoint")
+        self.assertEqual(self.custos_authnz.config["token_endpoint"], "https://test-token-endpoint")
+        self.assertEqual(self.custos_authnz.config["userinfo_endpoint"], "https://test-userinfo-endpoint")
 
     def test_authenticate_set_state_cookie(self):
         """Verify that authenticate() sets a state cookie."""
         authorization_url = self.custos_authnz.authenticate(self.trans)
         parsed = urlparse(authorization_url)
-        state = parse_qs(parsed.query)['state'][0]
+        state = parse_qs(parsed.query)["state"][0]
         self.assertEqual(state, self.trans.cookies[custos_authnz.STATE_COOKIE_NAME])
 
     def test_authenticate_set_nonce_cookie(self):
         """Verify that authenticate() sets a nonce cookie."""
         authorization_url = self.custos_authnz.authenticate(self.trans)
         parsed = urlparse(authorization_url)
-        hashed_nonce_in_url = parse_qs(parsed.query)['nonce'][0]
+        hashed_nonce_in_url = parse_qs(parsed.query)["nonce"][0]
         nonce_in_cookie = self.trans.cookies[custos_authnz.NONCE_COOKIE_NAME]
         hashed_nonce = self.custos_authnz._hash_nonce(nonce_in_cookie)
         self.assertEqual(hashed_nonce, hashed_nonce_in_url)
@@ -257,30 +266,32 @@ class CustosAuthnzTestCase(unittest.TestCase):
         """Verify that authenticate() adds configured extra params."""
         authorization_url = self.custos_authnz.authenticate(self.trans)
         parsed = urlparse(authorization_url)
-        param1_value = parse_qs(parsed.query)['kc_idp_hint'][0]
-        self.assertEqual(param1_value, 'oidc')
+        param1_value = parse_qs(parsed.query)["kc_idp_hint"][0]
+        self.assertEqual(param1_value, "oidc")
 
     def test_authenticate_sets_env_var_when_localhost_redirect(self):
         """Verify that OAUTHLIB_INSECURE_TRANSPORT var is set with localhost redirect."""
-        self.custos_authnz = custos_authnz.CustosAuthnz('Custos', {
-            'VERIFY_SSL': True
-        }, {
-            'url': self._get_idp_url(),
-            'client_id': 'test-client-id',
-            'client_secret': 'test-client-secret',
-            'redirect_uri': 'http://localhost/auth/callback',
-            'realm': 'test-realm'
-        })
+        self.custos_authnz = custos_authnz.CustosAuthnz(
+            "Custos",
+            {"VERIFY_SSL": True},
+            {
+                "url": self._get_idp_url(),
+                "client_id": "test-client-id",
+                "client_secret": "test-client-secret",
+                "redirect_uri": "http://localhost/auth/callback",
+                "realm": "test-realm",
+            },
+        )
         self.setupMocks()
-        self.assertIsNone(os.environ.get('OAUTHLIB_INSECURE_TRANSPORT', None))
+        self.assertIsNone(os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None))
         self.custos_authnz.authenticate(self.trans)
-        self.assertEqual("1", os.environ['OAUTHLIB_INSECURE_TRANSPORT'])
+        self.assertEqual("1", os.environ["OAUTHLIB_INSECURE_TRANSPORT"])
 
     def test_authenticate_does_not_set_env_var_when_https_redirect(self):
-        self.assertTrue(self.custos_authnz.config['redirect_uri'].startswith("https:"))
-        self.assertIsNone(os.environ.get('OAUTHLIB_INSECURE_TRANSPORT', None))
+        self.assertTrue(self.custos_authnz.config["redirect_uri"].startswith("https:"))
+        self.assertIsNone(os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None))
         self.custos_authnz.authenticate(self.trans)
-        self.assertIsNone(os.environ.get('OAUTHLIB_INSECURE_TRANSPORT', None))
+        self.assertIsNone(os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None))
 
     def test_callback_verify_with_state_cookie(self):
         """Verify that state from cookie is passed to OAuth2Session constructor."""
@@ -294,7 +305,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
         existing_custos_authnz_token = CustosAuthnzToken(
             user=User(email=self.test_email, username=self.test_username),
             external_user_id=self.test_user_id,
-            provider=self.custos_authnz.config['provider'],
+            provider=self.custos_authnz.config["provider"],
             access_token=old_access_token,
             id_token=old_id_token,
             refresh_token=old_refresh_token,
@@ -305,9 +316,8 @@ class CustosAuthnzTestCase(unittest.TestCase):
         self.trans.sa_session._query.custos_authnz_token = existing_custos_authnz_token
         self.assertIsNotNone(
             self.trans.sa_session.query(CustosAuthnzToken)
-                .filter_by(external_user_id=self.test_user_id,
-                           provider=self.custos_authnz.config['provider'])
-                .one_or_none()
+            .filter_by(external_user_id=self.test_user_id, provider=self.custos_authnz.config["provider"])
+            .one_or_none()
         )
         self.trans.sa_session._query.user = User(email=self.test_email, username=self.test_username)
 
@@ -317,9 +327,8 @@ class CustosAuthnzTestCase(unittest.TestCase):
         # Intentionally passing a bad state_token to make sure that code under
         # test uses the state cookie instead when creating the OAuth2Session
         login_redirect_url, user = self.custos_authnz.callback(
-            state_token="xxx",
-            authz_code=self.test_code, trans=self.trans,
-            login_redirect_url="http://localhost:8000/")
+            state_token="xxx", authz_code=self.test_code, trans=self.trans, login_redirect_url="http://localhost:8000/"
+        )
         self.assertTrue(self._create_oauth2_session_called)
         self.assertTrue(self._fetch_token_called)
         self.assertTrue(self._get_userinfo_called)
@@ -340,7 +349,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
                 state_token="xxx",
                 authz_code=self.test_code,
                 trans=self.trans,
-                login_redirect_url="http://localhost:8000/"
+                login_redirect_url="http://localhost:8000/",
             )
         self.assertTrue(self._fetch_token_called)
         self.assertFalse(self._get_userinfo_called)
@@ -351,15 +360,13 @@ class CustosAuthnzTestCase(unittest.TestCase):
 
         self.assertIsNone(
             self.trans.sa_session.query(CustosAuthnzToken)
-                .filter_by(external_user_id=self.test_user_id,
-                           provider=self.custos_authnz.config['provider'])
-                .one_or_none()
+            .filter_by(external_user_id=self.test_user_id, provider=self.custos_authnz.config["provider"])
+            .one_or_none()
         )
         self.assertEqual(0, len(self.trans.sa_session.items))
         login_redirect_url, user = self.custos_authnz.callback(
-            state_token="xxx",
-            authz_code=self.test_code, trans=self.trans,
-            login_redirect_url="http://localhost:8000/")
+            state_token="xxx", authz_code=self.test_code, trans=self.trans, login_redirect_url="http://localhost:8000/"
+        )
         self.assertIsNone(user)
         self.assertTrue("http://localhost:8000/root/login?confirm=true&custos_token=" in login_redirect_url)
         self.assertTrue(self._fetch_token_called)
@@ -367,9 +374,8 @@ class CustosAuthnzTestCase(unittest.TestCase):
     def test_create_user(self):
         self.assertIsNone(
             self.trans.sa_session.query(CustosAuthnzToken)
-                .filter_by(external_user_id=self.test_user_id,
-                           provider=self.custos_authnz.config['provider'])
-                .one_or_none()
+            .filter_by(external_user_id=self.test_user_id, provider=self.custos_authnz.config["provider"])
+            .one_or_none()
         )
         self.assertEqual(0, len(self.trans.sa_session.items))
 
@@ -392,12 +398,11 @@ class CustosAuthnzTestCase(unittest.TestCase):
             "id_token": test_id_token,
             "refresh_token": self.test_refresh_token,
             "expires_in": self.test_expires_in,
-            "refresh_expires_in": self.test_refresh_expires_in
+            "refresh_expires_in": self.test_refresh_expires_in,
         }
         login_redirect_url, user = self.custos_authnz.create_user(
-            token=json.dumps(self._raw_token),
-            trans=self.trans,
-            login_redirect_url="http://localhost:8000/")
+            token=json.dumps(self._raw_token), trans=self.trans, login_redirect_url="http://localhost:8000/"
+        )
         self.assertEqual(login_redirect_url, "http://localhost:8000/")
         self.trans.set_user(user)
         self.assertEqual(2, len(self.trans.sa_session.items), "Session has new User & new CustosAuthnzToken")
@@ -417,9 +422,11 @@ class CustosAuthnzTestCase(unittest.TestCase):
         expiration_timedelta = expected_expiration_time - added_custos_authnz_token.expiration_time
         self.assertTrue(expiration_timedelta.total_seconds() < 1)
         expected_refresh_expiration_time = datetime.now() + timedelta(seconds=self.test_refresh_expires_in)
-        refresh_expiration_timedelta = expected_refresh_expiration_time - added_custos_authnz_token.refresh_expiration_time
+        refresh_expiration_timedelta = (
+            expected_refresh_expiration_time - added_custos_authnz_token.refresh_expiration_time
+        )
         self.assertTrue(refresh_expiration_timedelta.total_seconds() < 1)
-        self.assertEqual(self.custos_authnz.config['provider'], added_custos_authnz_token.provider)
+        self.assertEqual(self.custos_authnz.config["provider"], added_custos_authnz_token.provider)
         self.assertTrue(self.trans.sa_session.flush_called)
 
     def test_callback_galaxy_user_not_created_when_user_logged_in_and_no_custos_authnz_token_exists(self):
@@ -433,15 +440,13 @@ class CustosAuthnzTestCase(unittest.TestCase):
 
         self.assertIsNone(
             self.trans.sa_session.query(CustosAuthnzToken)
-                .filter_by(external_user_id=self.test_user_id,
-                           provider=self.custos_authnz.config['provider'])
-                .one_or_none()
+            .filter_by(external_user_id=self.test_user_id, provider=self.custos_authnz.config["provider"])
+            .one_or_none()
         )
         self.assertEqual(0, len(self.trans.sa_session.items))
         login_redirect_url, user = self.custos_authnz.callback(
-            state_token="xxx",
-            authz_code=self.test_code, trans=self.trans,
-            login_redirect_url="http://localhost:8000/")
+            state_token="xxx", authz_code=self.test_code, trans=self.trans, login_redirect_url="http://localhost:8000/"
+        )
         self.assertTrue(self._fetch_token_called)
         self.assertTrue(self._get_userinfo_called)
         self.assertEqual(1, len(self.trans.sa_session.items), "Session has new CustosAuthnzToken")
@@ -463,7 +468,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
         existing_custos_authnz_token = CustosAuthnzToken(
             user=User(email=self.test_email, username=self.test_username),
             external_user_id=self.test_user_id,
-            provider=self.custos_authnz.config['provider'],
+            provider=self.custos_authnz.config["provider"],
             access_token=old_access_token,
             id_token=old_id_token,
             refresh_token=old_refresh_token,
@@ -475,24 +480,24 @@ class CustosAuthnzTestCase(unittest.TestCase):
 
         self.assertIsNotNone(
             self.trans.sa_session.query(CustosAuthnzToken)
-                .filter_by(external_user_id=self.test_user_id,
-                           provider=self.custos_authnz.config['provider'])
-                .one_or_none()
+            .filter_by(external_user_id=self.test_user_id, provider=self.custos_authnz.config["provider"])
+            .one_or_none()
         )
         self.assertEqual(0, len(self.trans.sa_session.items))
         login_redirect_url, user = self.custos_authnz.callback(
-            state_token="xxx",
-            authz_code=self.test_code, trans=self.trans,
-            login_redirect_url="http://localhost:8000/")
+            state_token="xxx", authz_code=self.test_code, trans=self.trans, login_redirect_url="http://localhost:8000/"
+        )
         self.assertTrue(self._fetch_token_called)
         self.assertTrue(self._get_userinfo_called)
         # Make sure query was called with correct parameters
         self.assertEqual(self.test_user_id, self.trans.sa_session._query.external_user_id)
-        self.assertEqual(self.custos_authnz.config['provider'], self.trans.sa_session._query.provider)
+        self.assertEqual(self.custos_authnz.config["provider"], self.trans.sa_session._query.provider)
         self.assertEqual(1, len(self.trans.sa_session.items), "Session has updated CustosAuthnzToken")
         session_custos_authnz_token = self.trans.sa_session.items[0]
         self.assertIsInstance(session_custos_authnz_token, CustosAuthnzToken)
-        self.assertIs(existing_custos_authnz_token, session_custos_authnz_token, "existing CustosAuthnzToken should be updated")
+        self.assertIs(
+            existing_custos_authnz_token, session_custos_authnz_token, "existing CustosAuthnzToken should be updated"
+        )
         # Verify both that existing CustosAuthnzToken has the correct values and different values than before
         self.assertEqual(self.test_access_token, session_custos_authnz_token.access_token)
         self.assertNotEqual(old_access_token, session_custos_authnz_token.access_token)
@@ -505,7 +510,9 @@ class CustosAuthnzTestCase(unittest.TestCase):
         self.assertTrue(expiration_timedelta.total_seconds() < 1)
         self.assertNotEqual(old_expiration_time, session_custos_authnz_token.expiration_time)
         expected_refresh_expiration_time = datetime.now() + timedelta(seconds=self.test_refresh_expires_in)
-        refresh_expiration_timedelta = expected_refresh_expiration_time - session_custos_authnz_token.refresh_expiration_time
+        refresh_expiration_timedelta = (
+            expected_refresh_expiration_time - session_custos_authnz_token.refresh_expiration_time
+        )
         self.assertTrue(refresh_expiration_timedelta.total_seconds() < 1)
         self.assertNotEqual(old_refresh_expiration_time, session_custos_authnz_token.refresh_expiration_time)
         self.assertTrue(self.trans.sa_session.flush_called)
@@ -514,7 +521,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
         custos_authnz_token = CustosAuthnzToken(
             user=User(email=self.test_email, username=self.test_username),
             external_user_id=self.test_user_id,
-            provider=self.custos_authnz.config['provider'],
+            provider=self.custos_authnz.config["provider"],
             access_token=self.test_access_token,
             id_token=self.test_id_token,
             refresh_token=self.test_refresh_token,
@@ -550,7 +557,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
         custos_authnz_token1 = CustosAuthnzToken(
             user=self.trans.user,
             external_user_id=self.test_user_id + "1",
-            provider=self.custos_authnz.config['provider'],
+            provider=self.custos_authnz.config["provider"],
             access_token=self.test_access_token,
             id_token=self.test_id_token,
             refresh_token=self.test_refresh_token,
@@ -560,7 +567,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
         custos_authnz_token2 = CustosAuthnzToken(
             user=self.trans.user,
             external_user_id=self.test_user_id + "2",
-            provider=self.custos_authnz.config['provider'],
+            provider=self.custos_authnz.config["provider"],
             access_token=self.test_access_token,
             id_token=self.test_id_token,
             refresh_token=self.test_refresh_token,
diff --git a/test/unit/app/dependencies/test_deps.py b/test/unit/app/dependencies/test_deps.py
index 216cd0308b7..13ce79e7bc8 100644
--- a/test/unit/app/dependencies/test_deps.py
+++ b/test/unit/app/dependencies/test_deps.py
@@ -5,7 +5,6 @@ from tempfile import mkdtemp
 
 from galaxy.dependencies import ConditionalDependencies
 
-
 AZURE_BLOB_TEST_CONFIG = """<object_store type="azure_blob">
     blah...
 </object_store>
@@ -98,7 +97,7 @@ def test_yaml_jobconf_runners():
             "job_config_file": job_conf_file,
         }
         cds = cc.get_cond_deps(config=config)
-        assert 'job_runner_A' in cds.job_runners
+        assert "job_runner_A" in cds.job_runners
 
 
 def test_vault_custos_configured():
@@ -133,7 +132,6 @@ def _config_context():
 
 
 class ConfigContext:
-
     def __init__(self, directory):
         self.tempdir = directory
 
diff --git a/test/unit/app/jobs/dynamic_tool_destination/mockGalaxy.py b/test/unit/app/jobs/dynamic_tool_destination/mockGalaxy.py
index 65547c23d22..e6e8e67bc5f 100644
--- a/test/unit/app/jobs/dynamic_tool_destination/mockGalaxy.py
+++ b/test/unit/app/jobs/dynamic_tool_destination/mockGalaxy.py
@@ -38,7 +38,7 @@ class Dataset:
         self.datatype = Datatype(file_ext)
         self.ext = file_ext
         self.metadata = dict()
-        self.metadata['sequences'] = value
+        self.metadata["sequences"] = value
 
     def get_metadata(self):
         return self.metadata
@@ -87,15 +87,24 @@ class JobConfig:
         self.default_id = "cluster_default"
         self.defNativeSpec = "-q test.q"
         self.defRunner = "drmaa"
-        self.keys = {tool_id: Info(self.tool_id, self.nativeSpec, self.defRunner),
-                     "cluster_default": Info(self.default_id, self.defNativeSpec, self.defRunner), }
+        self.keys = {
+            tool_id: Info(self.tool_id, self.nativeSpec, self.defRunner),
+            "cluster_default": Info(self.default_id, self.defNativeSpec, self.defRunner),
+        }
 
     def get_destination(self, tool_id):
-        invalid_destinations = ["cluster-kow", "destinationf", "thig",
-                                "not_true_destination", "cluster_kow",
-                                "Destination_3_med", "fake_destination",
-                                "cluster_defaut", "even_lamerr_cluster",
-                                "no_such_dest"]
+        invalid_destinations = [
+            "cluster-kow",
+            "destinationf",
+            "thig",
+            "not_true_destination",
+            "cluster_kow",
+            "Destination_3_med",
+            "fake_destination",
+            "cluster_defaut",
+            "even_lamerr_cluster",
+            "no_such_dest",
+        ]
         if tool_id in invalid_destinations:
             return None
         else:
@@ -110,6 +119,6 @@ class JobMappingException(Exception):
 class JobDestination:
     def __init__(self, params=None, **kwd):
         params = params or {}
-        self.id = kwd.get('id')
-        self.nativeSpec = params['nativeSpecification']
-        self.runner = kwd.get('runner')
+        self.id = kwd.get("id")
+        self.nativeSpec = params["nativeSpecification"]
+        self.runner = kwd.get("runner")
diff --git a/test/unit/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py b/test/unit/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
index 4cea416e3ce..8b62b33978e 100644
--- a/test/unit/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
+++ b/test/unit/app/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
@@ -46,24 +46,24 @@ dbcountJob = mg.Job()
 dbcountJob.add_input_dataset(mg.InputDataset("input1", mg.Dataset((script_dir + "/data/test.fasta"), "fasta", None)))
 
 # ======================Tools===================================
-vanillaTool = mg.Tool('test')
+vanillaTool = mg.Tool("test")
 
-unTool = mg.Tool('unregistered')
+unTool = mg.Tool("unregistered")
 
-overlapTool = mg.Tool('test_overlap')
+overlapTool = mg.Tool("test_overlap")
 
-defaultTool = mg.Tool('test_tooldefault')
+defaultTool = mg.Tool("test_tooldefault")
 
-dbTool = mg.Tool('test_db')
-dbinfTool = mg.Tool('test_db_high')
+dbTool = mg.Tool("test_db")
+dbinfTool = mg.Tool("test_db_high")
 
-argTool = mg.Tool('test_arguments')
+argTool = mg.Tool("test_arguments")
 
-noVBTool = mg.Tool('test_no_verbose')
+noVBTool = mg.Tool("test_no_verbose")
 
-usersTool = mg.Tool('test_users')
+usersTool = mg.Tool("test_users")
 
-numinputsTool = mg.Tool('test_num_input_datasets')
+numinputsTool = mg.Tool("test_num_input_datasets")
 
 # =======================Configuration files================================
 path = script_dir + "/data/tool_destination.yml"
@@ -95,236 +95,380 @@ class TestDynamicToolDestination(unittest.TestCase):
 
     @log_capture()
     def test_brokenDestYML(self, lc):
-        self.assertRaises(JobMappingException, map_tool_to_destination, runJob, theApp, vanillaTool, "user@email.com", True, broken_default_dest_path, job_conf_path)
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            runJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            broken_default_dest_path,
+            job_conf_path,
+        )
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "No global default destination specified in config!"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test3.full"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 3.23 KB"),
         )
 
     @log_capture()
     def test_filesize_empty(self, lc):
-        self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
-        self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            emptyJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            path,
+            job_conf_path,
+        )
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            emptyJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            priority_path,
+            job_conf_path,
+        )
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test.empty"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 0.00 B"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 1"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test.empty"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 0.00 B"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 1"),
         )
 
     @log_capture()
     def test_filesize_zero(self, lc):
-        self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
-        self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            zeroJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            path,
+            job_conf_path,
+        )
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            zeroJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            priority_path,
+            job_conf_path,
+        )
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 0'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 0')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 0.00 B"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 0"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 0.00 B"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 0"),
         )
 
     @log_capture()
     def test_filesize_fail(self, lc):
-        self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
-        self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            failJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            path,
+            job_conf_path,
+        )
+        self.assertRaises(
+            JobMappingException,
+            map_tool_to_destination,
+            failJob,
+            theApp,
+            vanillaTool,
+            "user@email.com",
+            True,
+            priority_path,
+            job_conf_path,
+        )
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 293.00 B'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 293.00 B'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test1.full"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 293.00 B"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 1"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test1.full"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 293.00 B"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 1"),
         )
 
     @log_capture()
     def test_filesize_run(self, lc):
         job = map_tool_to_destination(runJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'Destination1')
-        priority_job = map_tool_to_destination(runJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'Destination1_high')
+        self.assertEqual(job, "Destination1")
+        priority_job = map_tool_to_destination(
+            runJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "Destination1_high")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test' with 'Destination1'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 3.23 KB'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total number of files: 1'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test' with 'Destination1_high'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test3.full"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 3.23 KB"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 1"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test' with 'Destination1'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test3.full"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total size: 3.23 KB"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total number of files: 1"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test' with 'Destination1_high'."),
         )
 
     @log_capture()
     def test_default_tool(self, lc):
         job = map_tool_to_destination(runJob, theApp, defaultTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'cluster_default')
-        priority_job = map_tool_to_destination(runJob, theApp, defaultTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'cluster_default_high')
+        self.assertEqual(job, "cluster_default")
+        priority_job = map_tool_to_destination(
+            runJob, theApp, defaultTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "cluster_default_high")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_tooldefault' with 'cluster_default'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_tooldefault' with 'cluster_default_high'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'test_tooldefault' not specified in config. Using default destination.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_tooldefault' with 'cluster_default'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'test_tooldefault' not specified in config. Using default destination.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Running 'test_tooldefault' with 'cluster_default_high'.",
+            ),
         )
 
     @log_capture()
     def test_arguments_tool(self, lc):
         job = map_tool_to_destination(argJob, theApp, argTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'Destination6')
-        priority_job = map_tool_to_destination(argJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'Destination6_med')
+        self.assertEqual(job, "Destination6")
+        priority_job = map_tool_to_destination(
+            argJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "Destination6_med")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6_med'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_arguments' with 'Destination6'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_arguments' with 'Destination6_med'."),
         )
 
     @log_capture()
     def test_arguments_arg_not_found(self, lc):
         job = map_tool_to_destination(argNotFoundJob, theApp, argTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'cluster_default')
-        priority_job = map_tool_to_destination(argNotFoundJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'cluster_default_high')
+        self.assertEqual(job, "cluster_default")
+        priority_job = map_tool_to_destination(
+            argNotFoundJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "cluster_default_high")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'cluster_default'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'cluster_default_high'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_arguments' with 'cluster_default'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_arguments' with 'cluster_default_high'."),
         )
 
     @log_capture()
     def test_tool_not_found(self, lc):
         job = map_tool_to_destination(runJob, theApp, unTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'cluster_default')
-        priority_job = map_tool_to_destination(runJob, theApp, unTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'cluster_default_high')
+        self.assertEqual(job, "cluster_default")
+        priority_job = map_tool_to_destination(
+            runJob, theApp, unTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "cluster_default_high")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'unregistered' with 'cluster_default'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'unregistered' with 'cluster_default_high'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'unregistered' not specified in config. Using default destination.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'unregistered' with 'cluster_default'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'unregistered' not specified in config. Using default destination.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'unregistered' with 'cluster_default_high'."),
         )
 
     @log_capture()
     def test_fasta(self, lc):
         job = map_tool_to_destination(dbJob, theApp, dbTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'Destination4')
-        priority_job = map_tool_to_destination(dbJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'Destination4_high')
+        self.assertEqual(job, "Destination4")
+        priority_job = map_tool_to_destination(
+            dbJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "Destination4_high")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 10'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 10'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4_high'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test.fasta"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total amount of records: 10"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_db' with 'Destination4'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test.fasta"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total amount of records: 10"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_db' with 'Destination4_high'."),
         )
 
     @log_capture()
     def test_fasta_count(self, lc):
         job = map_tool_to_destination(dbcountJob, theApp, dbTool, "user@email.com", True, path, job_conf_path)
-        self.assertEqual(job, 'Destination4')
-        priority_job = map_tool_to_destination(dbcountJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path)
-        self.assertEqual(priority_job, 'Destination4_high')
+        self.assertEqual(job, "Destination4")
+        priority_job = map_tool_to_destination(
+            dbcountJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path
+        )
+        self.assertEqual(priority_job, "Destination4_high")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 6'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total amount of records: 6'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_db' with 'Destination4_high'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test.fasta"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total amount of records: 6"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_db' with 'Destination4'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Loading file: input1" + script_dir + "/data/test.fasta"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Total amount of records: 6"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_db' with 'Destination4_high'."),
         )
 
     @log_capture()
     def test_no_verbose(self, lc):
         job = map_tool_to_destination(runJob, theApp, noVBTool, "user@email.com", True, no_verbose_path, job_conf_path)
-        self.assertEqual(job, 'Destination1')
+        self.assertEqual(job, "Destination1")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_no_verbose' with 'Destination1'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_no_verbose' with 'Destination1'.")
         )
 
     @log_capture()
     def test_authorized_user(self, lc):
         job = map_tool_to_destination(runJob, theApp, usersTool, "user@email.com", True, users_test_path, job_conf_path)
-        self.assertEqual(job, 'special_cluster')
+        self.assertEqual(job, "special_cluster")
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'special_cluster'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_users' with 'special_cluster'."),
         )
 
     @log_capture()
     def test_unauthorized_user(self, lc):
-        job = map_tool_to_destination(runJob, theApp, usersTool, "userblah@email.com", True, users_test_path, job_conf_path)
-        self.assertEqual(job, 'lame_cluster')
-
-        lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'lame_cluster'.")
+        job = map_tool_to_destination(
+            runJob, theApp, usersTool, "userblah@email.com", True, users_test_path, job_conf_path
         )
+        self.assertEqual(job, "lame_cluster")
 
-# ================================Invalid yaml files==============================
+        lc.check_present(("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running 'test_users' with 'lame_cluster'."))
+
+    # ================================Invalid yaml files==============================
     @log_capture()
     def test_no_file(self, lc):
         self.assertRaises(IOError, dt.parse_yaml, path="")
@@ -334,11 +478,13 @@ class TestDynamicToolDestination(unittest.TestCase):
     def test_bad_nice(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest11, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
-             "Running config validation..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
-             "nice_value goes from -20 to 20; rule 1 in 'spades' has a nice_value of '-21'. Setting nice_value to 0."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "nice_value goes from -20 to 20; rule 1 in 'spades' has a nice_value of '-21'. Setting nice_value to 0.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
@@ -349,538 +495,818 @@ class TestDynamicToolDestination(unittest.TestCase):
     def test_no_tool_name(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest3, job_conf_path=job_conf_path, test=True), yt.iv3dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Malformed YML; expected job name, but found a list instead!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_no_rule_type(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest4, job_conf_path=job_conf_path, test=True), yt.ivDict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "No rule_type found for rule 1 in 'spades'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_no_rule_lower_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest51, job_conf_path=job_conf_path, test=True), yt.ivDict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_no_rule_upper_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest52, job_conf_path=job_conf_path, test=True), yt.ivDict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_no_rule_arg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest53, job_conf_path=job_conf_path, test=True), yt.ivDict53)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_bad_rule_type(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest6, job_conf_path=job_conf_path, test=True), yt.ivDict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_no_err_msg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest91, job_conf_path=job_conf_path, test=True), yt.iv91dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No nice_value found for rule 1 in 'spades'. Setting nice_value to 0."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No nice_value found for rule 1 in 'spades'. Setting nice_value to 0.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_no_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest7, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "No global default destination specified in config!"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_invalid_category(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest8, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "No global default destination specified in config!"),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Unrecognized category 'ice_cream' found in config file!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_arguments_no_err_msg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest12, job_conf_path=job_conf_path, test=True), yt.iv12dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
-             "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_arguments_no_args(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest131, job_conf_path=job_conf_path, test=True), yt.iv131dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
-             "No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_arguments_no_arg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest132, job_conf_path=job_conf_path, test=True), yt.iv132dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_multiple_jobs(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest133, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Missing a fail_message for rule 1 in 'smalt'.")
         )
 
     @log_capture()
     def test_return_rule_for_multiple_jobs(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest133, job_conf_path=job_conf_path, test=True), yt.iv133dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_no_destination(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest134, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'.")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "No destination specified for rule 1 in 'spades'.")
         )
 
     @log_capture()
     def test_return_rule_for_no_destination(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest134, job_conf_path=job_conf_path, test=True), yt.iv134dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No destination specified for rule 1 in 'spades'. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_rule_for_reversed_bounds(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest135, job_conf_path=job_conf_path, test=True), yt.iv135dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_missing_tool_fields(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest136, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!")
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'spades' does not have rules nor a default_destination!",
+            )
         )
 
     @log_capture()
     def test_return_rule_for_missing_tool_fields(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest136, job_conf_path=job_conf_path, test=True), yt.iv136dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'spades' does not have rules nor a default_destination!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_blank_tool(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest137, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!")
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Config section for tool 'spades' is blank!")
         )
 
     @log_capture()
     def test_return_rule_for_blank_tool(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest137, job_conf_path=job_conf_path, test=True), yt.iv137dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Config section for tool 'spades' is blank!"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_malformed_users(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest138, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!")
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!",
+            ),
         )
 
     @log_capture()
     def test_return_rule_for_malformed_users(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest138, job_conf_path=job_conf_path, test=True), yt.iv138dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_no_users(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest139, job_conf_path=job_conf_path, test=True, return_bool=True))
-        lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!")
-        )
+        lc.check_present(("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Couldn't find a list under 'users:'!"))
 
     @log_capture()
     def test_return_rule_for_no_users(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest139, job_conf_path=job_conf_path, test=True), yt.iv139dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Couldn't find a list under 'users:'! Ignoring rule."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_malformed_user_email(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest140, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No valid user emails were specified for rule 2 in tool 'spades'!",
+            ),
         )
 
     @log_capture()
     def test_return_rule_for_malformed_user_email(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest140, job_conf_path=job_conf_path, test=True), yt.iv140dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_empty_users(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest141, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No valid user emails were specified for rule 2 in tool 'spades'!",
+            ),
         )
 
     @log_capture()
     def test_return_rule_for_empty_users(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest141, job_conf_path=job_conf_path, test=True), yt.iv141dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_bad_num_input_datasets_bounds(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest142, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'smalt'.")
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Error: lower_bound is set to Infinity, but must be lower than upper_bound!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "lower_bound exceeds upper_bound for rule 1 in 'smalt'."),
         )
 
     @log_capture()
     def test_return_rule_for_bad_num_input_datasets_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest142, job_conf_path=job_conf_path, test=True), yt.iv142dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_return_bool_for_worse_num_input_datasets_bounds(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest143, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!")
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Error: lower_bound is set to Infinity, but must be lower than upper_bound!",
+            )
         )
 
     @log_capture()
     def test_return_rule_for_worse_num_input_datasets_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest143, job_conf_path=job_conf_path, test=True), yt.iv143dict)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_without_low_default_destination(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest146, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'low' for rule 1 in 'smalt'. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Invalid priority 'low' for rule 1 in 'smalt'. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_with_invalid_priority_destination(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest147, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'mine' for rule 1 in 'smalt'. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Invalid priority 'mine' for rule 1 in 'smalt'. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_not_all_priorities_in_tool(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest149, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_rule_destination_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest150, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_default_destination_not_in_job_conf_with_no_rules(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest151, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'blah' does not have rules nor a default_destination!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'blah' does not have rules nor a default_destination!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_default_destination_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest152, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'no_such_dest' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination 'no_such_dest' does not appear in the job configuration.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_rule_destination_without_priority_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest153, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_default_destination_without_priority_not_in_job_conf_with_no_rules(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest154, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'blah' does not have rules nor a default_destination!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'blah' does not have rules nor a default_destination!",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_default_destination_without_priority_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest155, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'no_such_dest' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination 'no_such_dest' does not appear in the job configuration.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_rule_priority_does_not_exist(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest156, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'notAPriority' for rule 1 in 'aTool'. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Invalid priority 'notAPriority' for rule 1 in 'aTool'. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_default_destination_priority_does_not_exist(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest157, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default destination priority 'notAPriority' for 'aTool'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Invalid default destination priority 'notAPriority' for 'aTool'.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_default_destination_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest158, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_tool_default_destination_without_priority_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest159, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_empty_priority_dict(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest163, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No global default destinations specified in config!"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "No global default destinations specified in config!"),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_default_dest_is_string_but_priorities_used_in_rule(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest161, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'med' for rule 1 in 'blah'. Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Invalid priority 'med' for rule 1 in 'blah'. Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_default_dest_is_string_but_priorities_used_in_tool_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest162, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default destination priority 'med' for 'blah'."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Invalid default destination priority 'med' for 'blah'."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_str_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest164, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'cluster-kow' does not appear in the job configuration. Did you mean 'cluster_low'?"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination 'cluster-kow' does not appear in the job configuration. Did you mean 'cluster_low'?",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_dict_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest165, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'cluster_kow' does not appear in the job configuration. Did you mean 'cluster_low'?"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination 'cluster_kow' does not appear in the job configuration. Did you mean 'cluster_low'?",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_dict_tool_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest166, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'cluster_defaut' does not appear in the job configuration. Did you mean 'cluster_default'?"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'cluster_defaut' does not appear in the job configuration. Did you mean 'cluster_default'?",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_str_tool_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest167, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'Destination_3_med' does not appear in the job configuration. Did you mean 'Destination3_med'?"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'Destination_3_med' does not appear in the job configuration. Did you mean 'Destination3_med'?",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_str_tool_rule_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest168, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blah', rule 1: 'thig' does not exist in job configuration. Did you mean 'things'? Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Destination for 'blah', rule 1: 'thig' does not exist in job configuration. Did you mean 'things'? Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_dict_tool_rule_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest169, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blah', rule 1: 'even_lamerr_cluster' does not exist in job configuration. Did you mean 'even_lamer_cluster'? Ignoring..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Destination for 'blah', rule 1: 'even_lamerr_cluster' does not exist in job configuration. Did you mean 'even_lamer_cluster'? Ignoring...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_typo_in_case(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest170, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'destinationf' does not appear in the job configuration. Did you mean 'DestinationF'?"),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination 'destinationf' does not appear in the job configuration. Did you mean 'DestinationF'?",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_invalid_verbose_value(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest171, job_conf_path=job_conf_path, test=True)
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Verbose value 'notavalue' is not True or False! Falling back to verbose..."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Verbose value 'notavalue' is not True or False! Falling back to verbose...",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
     @log_capture()
     def test_invalid_default_dest_valid_tool_default_dest_bool(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest172, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'fake_destination' does not appear in the job configuration."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination 'fake_destination' does not appear in the job configuration.",
+            ),
         )
 
     @log_capture()
     def test_valid_default_dest_invalid_tool_default_dest_bool(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest173, job_conf_path=job_conf_path, test=True, return_bool=True))
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'fake_destination' does not appear in the job configuration."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'blah' does not have rules nor a default_destination!"),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Default destination for 'blah': 'fake_destination' does not appear in the job configuration.",
+            ),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "Tool 'blah' does not have rules nor a default_destination!",
+            ),
         )
 
-# ================================Valid yaml files==============================
+    # ================================Valid yaml files==============================
     @log_capture()
     def test_parse_valid_yml(self, lc):
         self.assertEqual(dt.parse_yaml(yt.vYMLTest1, job_conf_path=job_conf_path, test=True), yt.vdictTest1_yml)
@@ -900,29 +1326,37 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertEqual(dt.parse_yaml(yt.vYMLTest164, job_conf_path=job_conf_path, test=True), yt.vdictTest164_yml)
 
         lc.check_present(
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
-            ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            (
+                "galaxy.jobs.dynamic_tool_destination",
+                "DEBUG",
+                "No default_priority section found in config. Setting 'med' as default priority.",
+            ),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Running config validation..."),
+            ("galaxy.jobs.dynamic_tool_destination", "DEBUG", "Finished config validation."),
         )
 
-# ================================Testing str_to_bytes==========================
+    # ================================Testing str_to_bytes==========================
     def test_str_to_bytes_invalid(self):
         self.assertRaises(dt.MalformedYMLException, dt.str_to_bytes, "1d")
         self.assertRaises(dt.MalformedYMLException, dt.str_to_bytes, "1 d")
@@ -941,7 +1375,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertEqual(dt.str_to_bytes("1 ZB"), valueZ)
         self.assertEqual(dt.str_to_bytes("1 YB"), valueY)
 
-# ==============================Testing bytes_to_str=============================
+    # ==============================Testing bytes_to_str=============================
     def test_bytes_to_str_invalid(self):
         testValue = ""
         self.assertRaises(ValueError, dt.bytes_to_str, testValue)
@@ -987,5 +1421,5 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertEqual(dt.bytes_to_str(1024, "fda"), "1.00 KB")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/app/jobs/dynamic_tool_destination/ymltests.py b/test/unit/app/jobs/dynamic_tool_destination/ymltests.py
index 0c73b3bb569..2cf6e9cfc0f 100644
--- a/test/unit/app/jobs/dynamic_tool_destination/ymltests.py
+++ b/test/unit/app/jobs/dynamic_tool_destination/ymltests.py
@@ -22,16 +22,16 @@ vdictTest1_yml = {
                     "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": 100000000,
-                    "destination": "things"
+                    "destination": "things",
                 },
             ]
         }
     },
-    'default_destination': "cluster_default"
+    "default_destination": "cluster_default",
 }
 
 # Multiple jobs, multiple rules
-vYMLTest2 = '''
+vYMLTest2 = """
     tools:
       spades:
         default_destination: cluster_default
@@ -51,38 +51,37 @@ vYMLTest2 = '''
             destination: fail
     default_destination: cluster_low
     verbose: True
-'''
+"""
 
 vdictTest2_yml = {
     "tools": {
-        "spades": {
-            "default_destination": "cluster_default"
-        },
+        "spades": {"default_destination": "cluster_default"},
         "smalt": {
             "rules": [
                 {
                     "rule_type": "file_size",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": 100000000,
                     "fail_message": "Too few reads for smalt to work",
-                    "destination": "fail"
-                }, {
+                    "destination": "fail",
+                },
+                {
                     "rule_type": "file_size",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 100000000,
                     "upper_bound": "Infinity",
                     "fail_message": "Too few reads for smalt to work",
-                    "destination": "fail"
-                }
+                    "destination": "fail",
+                },
             ]
-        }
+        },
     },
-    'default_destination': "cluster_low"
+    "default_destination": "cluster_low",
 }
 
 # Rule with extra attribute
-vYMLTest3 = '''
+vYMLTest3 = """
     tools:
       spades:
         rules:
@@ -95,7 +94,7 @@ vYMLTest3 = '''
             destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 vdictTest3_yml = {
     "tools": {
@@ -103,17 +102,17 @@ vdictTest3_yml = {
             "rules": [
                 {
                     "rule_type": "file_size",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "hax": 1337,
                     "lower_bound": 0,
                     "upper_bound": 100000000,
                     "fail_message": "Whats hax",
-                    "destination": "fail"
+                    "destination": "fail",
                 }
             ]
         }
     },
-    'default_destination': "cluster_default"
+    "default_destination": "cluster_default",
 }
 
 # Arguments type
@@ -137,21 +136,21 @@ vdictTest4_yml = {
             "rules": [
                 {
                     "rule_type": "arguments",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "arguments": {
                         "careful": True,
                     },
                     "fail_message": "Failure",
-                    "destination": "fail"
+                    "destination": "fail",
                 }
             ]
         }
     },
-    'default_destination': "cluster_default"
+    "default_destination": "cluster_default",
 }
 
 # Records type
-vYMLTest5 = '''
+vYMLTest5 = """
     tools:
       spades:
         rules:
@@ -162,7 +161,7 @@ vYMLTest5 = '''
             destination: cluster_low_4
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 vdictTest5_yml = {
     "tools": {
@@ -170,19 +169,19 @@ vdictTest5_yml = {
             "rules": [
                 {
                     "rule_type": "records",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": 100000000,
-                    "destination": "cluster_low_4"
+                    "destination": "cluster_low_4",
                 }
             ]
         }
     },
-    'default_destination': "cluster_default"
+    "default_destination": "cluster_default",
 }
 
 # Num_input_datasets type
-vYMLTest6 = '''
+vYMLTest6 = """
     tools:
       spades:
         default_destination: cluster_default
@@ -200,32 +199,31 @@ vYMLTest6 = '''
             destination: cluster_high_32
     default_destination: cluster_low
     verbose: True
-'''
+"""
 
 vdictTest6_yml = {
     "tools": {
-        "spades": {
-            "default_destination": "cluster_default"
-        },
+        "spades": {"default_destination": "cluster_default"},
         "smalt": {
             "rules": [
                 {
                     "rule_type": "num_input_datasets",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": 200,
-                    "destination": "cluster_low_4"
-                }, {
+                    "destination": "cluster_low_4",
+                },
+                {
                     "rule_type": "num_input_datasets",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 200,
                     "upper_bound": "Infinity",
-                    "destination": "cluster_high_32"
-                }
+                    "destination": "cluster_high_32",
+                },
             ]
-        }
+        },
     },
-    'default_destination': "cluster_low"
+    "default_destination": "cluster_low",
 }
 
 # One job, one rule, and priority destinations
@@ -258,30 +256,18 @@ vdictTest7_yml = {
                     "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": 100000000,
-                    "destination": {
-                        'priority': {
-                            'med': 'things'
-                        }
-                    }
+                    "destination": {"priority": {"med": "things"}},
                 },
             ]
         }
     },
-    'default_destination': {
-        'priority': {
-            'med': 'cluster_default'
-        }
-    },
-    'default_priority': 'med',
-    'users': {
-        'user@example.com': {
-            'priority': 'med'
-        }
-    }
+    "default_destination": {"priority": {"med": "cluster_default"}},
+    "default_priority": "med",
+    "users": {"user@example.com": {"priority": "med"}},
 }
 
 # No valid priorities but the tool doesn't require one
-vYMLTest160 = '''
+vYMLTest160 = """
     default_destination: cluster_low
     default_priority: med
     tools:
@@ -294,7 +280,7 @@ vYMLTest160 = '''
             destination: cluster_default
         default_destination: cluster_high
     verbose: True
-'''
+"""
 
 vdictTest160_yml = {
     "tools": {
@@ -305,17 +291,17 @@ vdictTest160_yml = {
                     "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": "Infinity",
-                    "destination": "cluster_default"
+                    "destination": "cluster_default",
                 }
             ],
-            "default_destination": "cluster_high"
+            "default_destination": "cluster_high",
         }
     },
-    'default_destination': 'cluster_low',
+    "default_destination": "cluster_low",
 }
 
 # No valid priorities but the tool doesn't require one
-vYMLTest164 = '''
+vYMLTest164 = """
     default_destination:
       priority:
         good: Destination1_med
@@ -336,7 +322,7 @@ vYMLTest164 = '''
             good: cluster_med_4
             fast: cluster_high
     verbose: True
-'''
+"""
 
 vdictTest164_yml = {
     "tools": {
@@ -347,28 +333,14 @@ vdictTest164_yml = {
                     "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": "Infinity",
-                    "destination": {
-                        "priority": {
-                            "fast": "lame_cluster"
-                        }
-                    }
+                    "destination": {"priority": {"fast": "lame_cluster"}},
                 }
             ],
-            "default_destination": {
-                "priority": {
-                    "good": "cluster_med_4",
-                    "fast": "cluster_high"
-                }
-            }
+            "default_destination": {"priority": {"good": "cluster_med_4", "fast": "cluster_high"}},
         }
     },
-    'default_destination': {
-        "priority": {
-            "good": "Destination1_med",
-            "fast": "Destination1_high"
-        }
-    },
-    'default_priority': 'good'
+    "default_destination": {"priority": {"good": "Destination1_med", "fast": "Destination1_high"}},
+    "default_priority": "good",
 }
 
 # =====================================================Invalid XML tests==========================================================
@@ -377,7 +349,7 @@ vdictTest164_yml = {
 ivYMLTest2 = ""
 
 # Job without name
-ivYMLTest3 = '''
+ivYMLTest3 = """
     tools:
       rules:
         - rule_type: file_size
@@ -387,14 +359,12 @@ ivYMLTest3 = '''
           destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
-iv3dict = {
-    'default_destination': "cluster_default"
-}
+iv3dict = {"default_destination": "cluster_default"}
 
 # Rule missing type
-ivYMLTest4 = '''
+ivYMLTest4 = """
     tools:
       spades:
         rules:
@@ -405,10 +375,10 @@ ivYMLTest4 = '''
             destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 # Rule missing attribute
-ivYMLTest51 = '''
+ivYMLTest51 = """
     tools:
       spades:
         rules:
@@ -419,10 +389,10 @@ ivYMLTest51 = '''
             destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 # Rule missing attribute
-ivYMLTest52 = '''
+ivYMLTest52 = """
     tools:
       spades:
         rules:
@@ -433,10 +403,10 @@ ivYMLTest52 = '''
             destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 # Rule missing attribute
-ivYMLTest53 = '''
+ivYMLTest53 = """
     tools:
       spades:
         rules:
@@ -447,30 +417,28 @@ ivYMLTest53 = '''
             fail_message: No type...
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 ivDict53 = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'upper_bound': 0,
-                    'rule_type':
-                    'file_size',
-                    'fail_message':
-                    'No type...',
-                    'nice_value': 0,
-                    'lower_bound': 0,
-                    'destination': 'fail'
+                    "upper_bound": 0,
+                    "rule_type": "file_size",
+                    "fail_message": "No type...",
+                    "nice_value": 0,
+                    "lower_bound": 0,
+                    "destination": "fail",
                 }
             ]
         }
-    }
+    },
 }
 
 # Rule unknown type
-ivYMLTest6 = '''
+ivYMLTest6 = """
     tools:
       spades:
         rules:
@@ -482,26 +450,24 @@ ivYMLTest6 = '''
             destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 # No default destination
-ivYMLTest7 = '''
+ivYMLTest7 = """
     default_destination:
     verbose: True
-'''
+"""
 
-ivDict = {
-    'default_destination': "cluster_default"
-}
+ivDict = {"default_destination": "cluster_default"}
 
 # Invalid category
-ivYMLTest8 = '''
+ivYMLTest8 = """
     ice_cream:
     verbose: True
-'''
+"""
 
 # Tool rule fail no fail_message and apparently no nice_value
-ivYMLTest91 = '''
+ivYMLTest91 = """
     tools:
       spades:
         rules:
@@ -511,28 +477,28 @@ ivYMLTest91 = '''
             destination: fail
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 iv91dict = {
-    'tools': {
-        'spades': {
-            'rules': [
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'lower_bound': 0,
-                    'nice_value': 0,
-                    'rule_type': 'file_size',
-                    'upper_bound': 0,
-                    'destination': 'fail',
-                    'fail_message': "Invalid parameters for rule 1 in 'spades'."
+                    "lower_bound": 0,
+                    "nice_value": 0,
+                    "rule_type": "file_size",
+                    "upper_bound": 0,
+                    "destination": "fail",
+                    "fail_message": "Invalid parameters for rule 1 in 'spades'.",
                 }
             ]
         }
     },
-    'default_destination': "cluster_default"
+    "default_destination": "cluster_default",
 }
 
 # Tool default fail no destination
-ivYMLTest11 = '''
+ivYMLTest11 = """
     tools:
       spades:
         rules:
@@ -544,7 +510,7 @@ ivYMLTest11 = '''
         default_destination: cluster_low
     default_destination: cluster_default
     verbose: True
-'''
+"""
 
 # Arguments fail no fail_message
 ivYMLTest12 = """
@@ -566,17 +532,17 @@ iv12dict = {
             "rules": [
                 {
                     "rule_type": "arguments",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "arguments": {
                         "careful": True,
                     },
                     "destination": "fail",
-                    "fail_message": "Invalid parameters for rule 1 in 'spades'."
+                    "fail_message": "Invalid parameters for rule 1 in 'spades'.",
                 }
             ]
         }
     },
-    'default_destination': "cluster_default"
+    "default_destination": "cluster_default",
 }
 
 # Arguments fail no arguments
@@ -592,9 +558,7 @@ ivYMLTest131 = """
     verbose: True
 """
 
-iv131dict = {
-    'default_destination': "cluster_default"
-}
+iv131dict = {"default_destination": "cluster_default"}
 
 # Arguments fail no destination
 ivYMLTest132 = """
@@ -611,26 +575,24 @@ ivYMLTest132 = """
 """
 
 iv132dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'arguments': {
-                        'careful': True
-                    },
-                    'rule_type': 'arguments',
-                    'destination': 'fail',
-                    'fail_message': 'Something went wrong',
-                    'nice_value': 0
+                    "arguments": {"careful": True},
+                    "rule_type": "arguments",
+                    "destination": "fail",
+                    "fail_message": "Something went wrong",
+                    "nice_value": 0,
                 }
             ]
         }
-    }
+    },
 }
 
 # Multiple rules in 1 job, first one failing
-ivYMLTest133 = '''
+ivYMLTest133 = """
     tools:
       smalt:
         rules:
@@ -646,7 +608,7 @@ ivYMLTest133 = '''
             destination: cluster_low_4
     default_destination: cluster_low
     verbose: True
-'''
+"""
 
 iv133dict = {
     "tools": {
@@ -654,22 +616,23 @@ iv133dict = {
             "rules": [
                 {
                     "rule_type": "file_size",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 0,
                     "upper_bound": 100000000,
                     "fail_message": "Invalid parameters for rule 1 in 'smalt'.",
-                    "destination": "fail"
-                }, {
+                    "destination": "fail",
+                },
+                {
                     "rule_type": "file_size",
-                    'nice_value': 0,
+                    "nice_value": 0,
                     "lower_bound": 100000000,
                     "upper_bound": "Infinity",
-                    "destination": "cluster_low_4"
-                }
+                    "destination": "cluster_low_4",
+                },
             ]
         }
     },
-    'default_destination': "cluster_low"
+    "default_destination": "cluster_low",
 }
 
 # No destination and no fail_message
@@ -686,19 +649,10 @@ ivYMLTest134 = """
 """
 
 iv134dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
-                {
-                    'rule_type': 'file_size',
-                    'upper_bound': 10000,
-                    'lower_bound': 0,
-                    'nice_value': 0
-                }
-            ]
-        }
-    }
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {"rules": [{"rule_type": "file_size", "upper_bound": 10000, "lower_bound": 0, "nice_value": 0}]}
+    },
 }
 
 # Reversed upper and lower bounds
@@ -716,20 +670,20 @@ ivYMLTest135 = """
 """
 
 iv135dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'rule_type': 'file_size',
-                    'upper_bound': 200,
-                    'lower_bound': 100,
-                    'nice_value': 0,
-                    'destination': 'cluster_low_4'
+                    "rule_type": "file_size",
+                    "upper_bound": 200,
+                    "lower_bound": 100,
+                    "nice_value": 0,
+                    "destination": "cluster_low_4",
                 }
             ]
         }
-    }
+    },
 }
 
 # Tool has rules category but no rules, and no tool-specific default destination
@@ -742,9 +696,7 @@ ivYMLTest136 = """
     verbose: True
 """
 
-iv136dict = {
-    'default_destination': 'cluster_default'
-}
+iv136dict = {"default_destination": "cluster_default"}
 
 # Tool is blank; no tool-specific default destination, no rules category
 ivYMLTest137 = """
@@ -755,9 +707,7 @@ ivYMLTest137 = """
     verbose: True
 """
 
-iv137dict = {
-    'default_destination': 'cluster_default'
-}
+iv137dict = {"default_destination": "cluster_default"}
 
 # Tool specifies authorized users with an invalid entry
 ivYMLTest138 = """
@@ -778,23 +728,21 @@ ivYMLTest138 = """
 """
 
 iv138dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'rule_type': 'file_size',
-                    'upper_bound': 200,
-                    'lower_bound': 100,
-                    'nice_value': 0,
-                    'destination': 'cluster_low_4',
-                    'users': [
-                        'validuser@email.com'
-                    ]
+                    "rule_type": "file_size",
+                    "upper_bound": 200,
+                    "lower_bound": 100,
+                    "nice_value": 0,
+                    "destination": "cluster_low_4",
+                    "users": ["validuser@email.com"],
                 }
             ]
         }
-    }
+    },
 }
 
 # Tool does not specify list under users
@@ -818,20 +766,20 @@ ivYMLTest139 = """
 """
 
 iv139dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'rule_type': 'file_size',
-                    'upper_bound': 600,
-                    'lower_bound': 200,
-                    'nice_value': 0,
-                    'destination': 'cluster_high'
+                    "rule_type": "file_size",
+                    "upper_bound": 600,
+                    "lower_bound": 200,
+                    "nice_value": 0,
+                    "destination": "cluster_high",
                 }
             ]
         }
-    }
+    },
 }
 
 # Tool supplies only invalid users
@@ -857,20 +805,20 @@ ivYMLTest140 = """
 """
 
 iv140dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'rule_type': 'file_size',
-                    'upper_bound': 600,
-                    'lower_bound': 200,
-                    'nice_value': 0,
-                    'destination': 'cluster_high'
+                    "rule_type": "file_size",
+                    "upper_bound": 600,
+                    "lower_bound": 200,
+                    "nice_value": 0,
+                    "destination": "cluster_high",
                 }
             ]
         }
-    }
+    },
 }
 
 # Tool supplies users list, but empty
@@ -896,24 +844,24 @@ ivYMLTest141 = """
 """
 
 iv141dict = {
-    'default_destination': 'cluster_default',
-    'tools': {
-        'spades': {
-            'rules': [
+    "default_destination": "cluster_default",
+    "tools": {
+        "spades": {
+            "rules": [
                 {
-                    'rule_type': 'file_size',
-                    'upper_bound': 600,
-                    'lower_bound': 200,
-                    'nice_value': 0,
-                    'destination': 'cluster_high'
+                    "rule_type": "file_size",
+                    "upper_bound": 600,
+                    "lower_bound": 200,
+                    "nice_value": 0,
+                    "destination": "cluster_high",
                 }
             ]
         }
-    }
+    },
 }
 
 # Bad bounds setup for num_input_datasets
-ivYMLTest142 = '''
+ivYMLTest142 = """
     tools:
       smalt:
         rules:
@@ -924,27 +872,27 @@ ivYMLTest142 = '''
             destination: cluster_low_4
     default_destination: cluster_low
     verbose: True
-'''
+"""
 
 iv142dict = {
-    'default_destination': 'cluster_low',
-    'tools': {
-        'smalt': {
-            'rules': [
+    "default_destination": "cluster_low",
+    "tools": {
+        "smalt": {
+            "rules": [
                 {
-                    'rule_type': 'num_input_datasets',
-                    'upper_bound': 200,
-                    'lower_bound': 0,
-                    'nice_value': 0,
-                    'destination': 'cluster_low_4'
+                    "rule_type": "num_input_datasets",
+                    "upper_bound": 200,
+                    "lower_bound": 0,
+                    "nice_value": 0,
+                    "destination": "cluster_low_4",
                 }
             ]
         }
-    }
+    },
 }
 
 # Even worse bounds setup for num_input_datasets
-ivYMLTest143 = '''
+ivYMLTest143 = """
     tools:
       smalt:
         rules:
@@ -955,44 +903,44 @@ ivYMLTest143 = '''
             destination: cluster_low_4
     default_destination: cluster_low
     verbose: True
-'''
+"""
 
 iv143dict = {
-    'default_destination': 'cluster_low',
-    'tools': {
-        'smalt': {
-            'rules': [
+    "default_destination": "cluster_low",
+    "tools": {
+        "smalt": {
+            "rules": [
                 {
-                    'rule_type': 'num_input_datasets',
-                    'upper_bound': 'Infinity',
-                    'lower_bound': 0,
-                    'nice_value': 0,
-                    'destination': 'cluster_low_4'
+                    "rule_type": "num_input_datasets",
+                    "upper_bound": "Infinity",
+                    "lower_bound": 0,
+                    "nice_value": 0,
+                    "destination": "cluster_low_4",
                 }
             ]
         }
-    }
+    },
 }
 
 # No med priority destination in default destination
-ivYMLTest144 = '''
+ivYMLTest144 = """
     default_destination:
       priority:
         low: cluster_low
     verbose: True
-'''
+"""
 
 # invalid priority destination in default destination
-ivYMLTest145 = '''
+ivYMLTest145 = """
     default_destination:
       priority:
         med: cluster_low
         mine: cluster_low
     verbose: True
-'''
+"""
 
 # No med priority destination in tool config
-ivYMLTest146 = '''
+ivYMLTest146 = """
     tools:
       smalt:
         rules:
@@ -1007,10 +955,10 @@ ivYMLTest146 = '''
       priority:
         med: cluster_low
     verbose: True
-'''
+"""
 
 # Invalid priority destination in tool config
-ivYMLTest147 = '''
+ivYMLTest147 = """
     tools:
       smalt:
         rules:
@@ -1026,10 +974,10 @@ ivYMLTest147 = '''
       priority:
         med: cluster_low
     verbose: True
-'''
+"""
 
 # invalid priority in users section
-ivYMLTest148 = '''
+ivYMLTest148 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1037,10 +985,10 @@ ivYMLTest148 = '''
       user@email.com:
         priority: mine
     verbose: True
-'''
+"""
 
 # not all priorities in tool destinations
-ivYMLTest149 = '''
+ivYMLTest149 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1054,10 +1002,10 @@ ivYMLTest149 = '''
             med: cluster_default
             high: cluster_high
     verbose: True
-'''
+"""
 
 # rule destination not in job config
-ivYMLTest150 = '''
+ivYMLTest150 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1072,10 +1020,10 @@ ivYMLTest150 = '''
               priority:
                 med: fake_destination
     verbose: True
-'''
+"""
 
 # tool default destination not in job config and no rules
-ivYMLTest151 = '''
+ivYMLTest151 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1085,18 +1033,18 @@ ivYMLTest151 = '''
           priority:
             med: not_true_destination
     verbose: True
-'''
+"""
 
 # default destination not in job config
-ivYMLTest152 = '''
+ivYMLTest152 = """
     default_destination:
       priority:
         med: no_such_dest
     verbose: True
-'''
+"""
 
 # rule destination not in job config (without priority dict)
-ivYMLTest153 = '''
+ivYMLTest153 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1109,10 +1057,10 @@ ivYMLTest153 = '''
             upper_bound: Infinity
             destination: fake_destination
     verbose: True
-'''
+"""
 
 # tool default destination not in job config (without priority dict) and no rules
-ivYMLTest154 = '''
+ivYMLTest154 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1120,16 +1068,16 @@ ivYMLTest154 = '''
       blah:
         default_destination: not_true_destination
     verbose: True
-'''
+"""
 
 # default destination not in job config (without priority dict)
-ivYMLTest155 = '''
+ivYMLTest155 = """
     default_destination: no_such_dest
     verbose: True
-'''
+"""
 
 # tool rule destination priority doesn't exist
-ivYMLTest156 = '''
+ivYMLTest156 = """
     default_destination:
       priority:
         med: cluster_default
@@ -1147,10 +1095,10 @@ ivYMLTest156 = '''
               priority:
                 notAPriority: cluster_default
     verbose: True
-'''
+"""
 
 # tool default destination priority doesn't exist
-ivYMLTest157 = '''
+ivYMLTest157 = """
     default_destination:
       priority:
         med: cluster_default
@@ -1161,10 +1109,10 @@ ivYMLTest157 = '''
             notAPriority: cluster_low
             med: cluster_low
     verbose: True
-'''
+"""
 
 # tool default destination not in job config
-ivYMLTest158 = '''
+ivYMLTest158 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1182,10 +1130,10 @@ ivYMLTest158 = '''
           priority:
             med: not_true_destination
     verbose: True
-'''
+"""
 
 # tool default destination not in job config (without priority dict)
-ivYMLTest159 = '''
+ivYMLTest159 = """
     default_destination: cluster_low
     tools:
       blah:
@@ -1197,10 +1145,10 @@ ivYMLTest159 = '''
             destination: cluster_default
         default_destination: not_true_destination
     verbose: True
-'''
+"""
 
 # No valid priorities and the tool rule requires them
-ivYMLTest161 = '''
+ivYMLTest161 = """
     default_destination: cluster_low
     tools:
       blah:
@@ -1214,10 +1162,10 @@ ivYMLTest161 = '''
                 med: cluster_default
         default_destination: cluster_high
     verbose: True
-'''
+"""
 
 # No valid priorities and the tool default_destination requires them
-ivYMLTest162 = '''
+ivYMLTest162 = """
     default_destination: cluster_low
     tools:
       blah:
@@ -1231,31 +1179,31 @@ ivYMLTest162 = '''
           priority:
             med: cluster_default
     verbose: True
-'''
+"""
 # Nothing in the priority dict
-ivYMLTest163 = '''
+ivYMLTest163 = """
     default_destination:
       priority:
     verbose: True
-'''
+"""
 
 # Typo in str default destination
-ivYMLTest164 = '''
+ivYMLTest164 = """
     default_destination: cluster-kow
     verbose: True
-'''
+"""
 
 # Typo in dict default destination
-ivYMLTest165 = '''
+ivYMLTest165 = """
     default_destination:
       priority:
         pr: cluster_kow
     default_priority: pr
     verbose: True
-'''
+"""
 
 # Typo in dict tool default destination
-ivYMLTest166 = '''
+ivYMLTest166 = """
     default_destination:
       priority:
         med: cluster_low
@@ -1272,10 +1220,10 @@ ivYMLTest166 = '''
             upper_bound: Infinity
             destination: DestinationF
     verbose: True
-'''
+"""
 
 # Typo in str tool default destination
-ivYMLTest167 = '''
+ivYMLTest167 = """
     default_destination: cluster_low
     default_priority: cluster_low
     tools:
@@ -1288,10 +1236,10 @@ ivYMLTest167 = '''
             upper_bound: Infinity
             destination: DestinationF
     verbose: True
-'''
+"""
 
 # Typo in dict tool rule destination
-ivYMLTest168 = '''
+ivYMLTest168 = """
     default_destination:
       priority:
         med: cluster_default
@@ -1307,10 +1255,10 @@ ivYMLTest168 = '''
               priority:
                 med: thig
     verbose: True
-'''
+"""
 
 # Typo in str tool rule destination
-ivYMLTest169 = '''
+ivYMLTest169 = """
     default_destination:
       priority:
         med: cluster_default
@@ -1327,40 +1275,40 @@ ivYMLTest169 = '''
           priority:
             med: cluster_default
     verbose: True
-'''
+"""
 
 # Typo in str tool rule destination
-ivYMLTest170 = '''
+ivYMLTest170 = """
     default_destination:
       priority:
         med: destinationf
     default_priority: med
     verbose: True
-'''
+"""
 
 # Invalid verbose setting
-ivYMLTest171 = '''
+ivYMLTest171 = """
     default_destination:
       priority:
         med: DestinationF
     default_priority: med
     verbose: notavalue
-'''
+"""
 
 # invalid default destination and valid tool default destination
-ivYMLTest172 = '''
+ivYMLTest172 = """
     default_destination: fake_destination
     tools:
       blah:
         default_destination: cluster_default
     verbose: True
-'''
+"""
 
 # valid default destination and invalid tool default destination
-ivYMLTest173 = '''
+ivYMLTest173 = """
     default_destination: cluster_default
     tools:
       blah:
         default_destination: fake_destination
     verbose: True
-'''
+"""
diff --git a/test/unit/app/jobs/test_command_factory.py b/test/unit/app/jobs/test_command_factory.py
index 6abc3225703..d5a49530ac1 100644
--- a/test/unit/app/jobs/test_command_factory.py
+++ b/test/unit/app/jobs/test_command_factory.py
@@ -2,7 +2,10 @@ import os
 import shutil
 from os import getcwd
 from tempfile import mkdtemp
-from typing import List, Tuple
+from typing import (
+    List,
+    Tuple,
+)
 from unittest import TestCase
 
 from galaxy.jobs.command_factory import (
@@ -18,7 +21,6 @@ TEST_FILES_PATH = "file_path"
 
 
 class TestCommandFactory(TestCase):
-
     def setUp(self):
         self.job_dir = mkdtemp()
         self.job_wrapper = MockJobWrapper(self.job_dir)
@@ -28,7 +30,9 @@ class TestCommandFactory(TestCase):
             assert job_wrapper == self.job_wrapper
             return self.workdir_outputs
 
-        self.runner = Bunch(app=Bunch(model=Bunch(Dataset=Bunch(file_path=TEST_FILES_PATH))), get_work_dir_outputs=workdir_outputs)
+        self.runner = Bunch(
+            app=Bunch(model=Bunch(Dataset=Bunch(file_path=TEST_FILES_PATH))), get_work_dir_outputs=workdir_outputs
+        )
         self.include_metadata = False
         self.include_work_dir_outputs = True
 
@@ -50,25 +54,33 @@ class TestCommandFactory(TestCase):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command(
-            "{} {}/tool_script.sh > ../outputs/tool_stdout 2> ../outputs/tool_stderr; return_code=$?".format(
-                self.job_wrapper.shell,
-                self.job_wrapper.working_directory,
-            )))
+        self.__assert_command_is(
+            _surround_command(
+                "{} {}/tool_script.sh > ../outputs/tool_stdout 2> ../outputs/tool_stderr; return_code=$?".format(
+                    self.job_wrapper.shell,
+                    self.job_wrapper.working_directory,
+                )
+            )
+        )
         self.__assert_tool_script_is(f"#!/bin/sh\n{dep_commands[0]}; {MOCK_COMMAND_LINE}")
 
     def test_remote_dependency_resolution(self):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command(MOCK_COMMAND_LINE + "; return_code=$?"), remote_command_params=dict(dependency_resolution="remote"))
+        self.__assert_command_is(
+            _surround_command(MOCK_COMMAND_LINE + "; return_code=$?"),
+            remote_command_params=dict(dependency_resolution="remote"),
+        )
 
     def test_explicit_local_dependency_resolution(self):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command(f"{dep_commands[0]}; {MOCK_COMMAND_LINE}; return_code=$?"),
-                                 remote_command_params=dict(dependency_resolution="local"))
+        self.__assert_command_is(
+            _surround_command(f"{dep_commands[0]}; {MOCK_COMMAND_LINE}; return_code=$?"),
+            remote_command_params=dict(dependency_resolution="local"),
+        )
 
     def test_task_prepare_inputs(self):
         self.include_work_dir_outputs = False
@@ -78,13 +90,18 @@ class TestCommandFactory(TestCase):
     def test_workdir_outputs(self):
         self.include_work_dir_outputs = True
         self.workdir_outputs = [("foo", "bar")]
-        self.__assert_command_is(_surround_command('%s; return_code=$?; \nif [ -f "foo" ] ; then cp "foo" "bar" ; fi' % MOCK_COMMAND_LINE))
+        self.__assert_command_is(
+            _surround_command('%s; return_code=$?; \nif [ -f "foo" ] ; then cp "foo" "bar" ; fi' % MOCK_COMMAND_LINE)
+        )
 
     def test_workdir_outputs_with_glob(self):
         self.include_work_dir_outputs = True
         self.workdir_outputs = [("foo*bar", "foo_x_bar")]
-        self.__assert_command_is(_surround_command(
-            '%s; return_code=$?; \nif [ -f "foo"*"bar" ] ; then cp "foo"*"bar" "foo_x_bar" ; fi' % MOCK_COMMAND_LINE))
+        self.__assert_command_is(
+            _surround_command(
+                '%s; return_code=$?; \nif [ -f "foo"*"bar" ] ; then cp "foo"*"bar" "foo_x_bar" ; fi' % MOCK_COMMAND_LINE
+            )
+        )
 
     def test_set_metadata_skipped_if_unneeded(self):
         self.include_metadata = True
@@ -102,7 +119,9 @@ class TestCommandFactory(TestCase):
         self.include_metadata = True
         self.include_work_dir_outputs = False
         self.job_wrapper.metadata_line = TEST_METADATA_LINE
-        expected_command = _surround_command(f"{MOCK_COMMAND_LINE}; return_code=$?; cd '{self.job_dir}'; {SETUP_GALAXY_FOR_METADATA}{TEST_METADATA_LINE}")
+        expected_command = _surround_command(
+            f"{MOCK_COMMAND_LINE}; return_code=$?; cd '{self.job_dir}'; {SETUP_GALAXY_FOR_METADATA}{TEST_METADATA_LINE}"
+        )
         self.__assert_command_is(expected_command)
 
     def test_empty_metadata(self):
@@ -111,29 +130,29 @@ class TestCommandFactory(TestCase):
         """
         self.include_metadata = True
         self.include_work_dir_outputs = False
-        self.job_wrapper.metadata_line = ' '
+        self.job_wrapper.metadata_line = " "
         # Empty metadata command do not touch command line.
         expected_command = _surround_command(f"{MOCK_COMMAND_LINE}; return_code=$?; cd '{self.job_dir}'")
         self.__assert_command_is(expected_command)
 
     def test_metadata_kwd_defaults(self):
         configured_kwds = self.__set_metadata_with_kwds()
-        assert configured_kwds['exec_dir'] == getcwd()
-        assert configured_kwds['tmp_dir'] == self.job_wrapper.working_directory
-        assert configured_kwds['dataset_files_path'] == TEST_FILES_PATH
-        assert configured_kwds['output_fnames'] == ['output1']
+        assert configured_kwds["exec_dir"] == getcwd()
+        assert configured_kwds["tmp_dir"] == self.job_wrapper.working_directory
+        assert configured_kwds["dataset_files_path"] == TEST_FILES_PATH
+        assert configured_kwds["output_fnames"] == ["output1"]
 
     def test_metadata_kwds_overrride(self):
         configured_kwds = self.__set_metadata_with_kwds(
             exec_dir="/path/to/remote/galaxy",
             tmp_dir="/path/to/remote/staging/directory/job1",
             dataset_files_path="/path/to/remote/datasets/",
-            output_fnames=['/path/to/remote_output1'],
+            output_fnames=["/path/to/remote_output1"],
         )
-        assert configured_kwds['exec_dir'] == "/path/to/remote/galaxy"
-        assert configured_kwds['tmp_dir'] == "/path/to/remote/staging/directory/job1"
-        assert configured_kwds['dataset_files_path'] == "/path/to/remote/datasets/"
-        assert configured_kwds['output_fnames'] == ['/path/to/remote_output1']
+        assert configured_kwds["exec_dir"] == "/path/to/remote/galaxy"
+        assert configured_kwds["tmp_dir"] == "/path/to/remote/staging/directory/job1"
+        assert configured_kwds["dataset_files_path"] == "/path/to/remote/datasets/"
+        assert configured_kwds["output_fnames"] == ["/path/to/remote_output1"]
 
     def __set_metadata_with_kwds(self, **kwds):
         self.include_metadata = True
@@ -162,7 +181,7 @@ class TestCommandFactory(TestCase):
             job_wrapper=self.job_wrapper,
             include_metadata=self.include_metadata,
             include_work_dir_outputs=self.include_work_dir_outputs,
-            **extra_kwds
+            **extra_kwds,
         )
         return build_command(**kwds)
 
@@ -172,7 +191,6 @@ def _surround_command(command):
 
 
 class MockJobWrapper:
-
     def __init__(self, job_dir):
         self.strict_shell = False
         self.command_line = MOCK_COMMAND_LINE
@@ -206,4 +224,4 @@ class MockJobWrapper:
 
     @property
     def job_io(self):
-        return Bunch(get_output_fnames=lambda: ['output1'], check_job_script_integrity=False)
+        return Bunch(get_output_fnames=lambda: ["output1"], check_job_script_integrity=False)
diff --git a/test/unit/app/jobs/test_expression_run.py b/test/unit/app/jobs/test_expression_run.py
index 08e79bfcd21..56e0347bc44 100644
--- a/test/unit/app/jobs/test_expression_run.py
+++ b/test/unit/app/jobs/test_expression_run.py
@@ -15,11 +15,9 @@ def test_run_simple():
     try:
         environment_path = os.path.join(test_directory, "env.json")
         environment = {
-            'job': {'input1': '7'},
-            'outputs': [
-                {'name': 'out1', 'from_expression': "output1", 'path': 'moo'}
-            ],
-            'script': "{return {'output1': parseInt($job.input1)};}",
+            "job": {"input1": "7"},
+            "outputs": [{"name": "out1", "from_expression": "output1", "path": "moo"}],
+            "script": "{return {'output1': parseInt($job.input1)};}",
         }
         with open(environment_path, "w") as f:
             json.dump(environment, f)
@@ -28,18 +26,18 @@ def test_run_simple():
         )
         new_env = os.environ.copy()
         if "PYTHONPATH" in new_env:
-            new_env['PYTHONPATH'] = "{}:{}".format(LIB_DIRECTORY, new_env["PYTHONPATH"])
+            new_env["PYTHONPATH"] = "{}:{}".format(LIB_DIRECTORY, new_env["PYTHONPATH"])
         else:
-            new_env['PYTHONPATH'] = LIB_DIRECTORY
-        new_env['GALAXY_EXPRESSION_INPUTS'] = environment_path
+            new_env["PYTHONPATH"] = LIB_DIRECTORY
+        new_env["GALAXY_EXPRESSION_INPUTS"] = environment_path
         subprocess.check_call(
             args=expressions.EXPRESSION_SCRIPT_CALL,
             shell=True,
             cwd=test_directory,
             env=new_env,
         )
-        with open(os.path.join(test_directory, 'moo')) as f:
+        with open(os.path.join(test_directory, "moo")) as f:
             out_content = f.read()
-        assert out_content == '7', out_content
+        assert out_content == "7", out_content
     finally:
         shutil.rmtree(test_directory)
diff --git a/test/unit/app/jobs/test_job_configuration.py b/test/unit/app/jobs/test_job_configuration.py
index a4dde99ca53..3235b201cc9 100644
--- a/test/unit/app/jobs/test_job_configuration.py
+++ b/test/unit/app/jobs/test_job_configuration.py
@@ -10,8 +10,14 @@ from pykwalify.core import Core
 from galaxy.config import GALAXY_SCHEMAS_PATH
 from galaxy.job_metrics import JobMetrics
 from galaxy.jobs import JobConfiguration
-from galaxy.util import galaxy_directory, galaxy_samples_directory
-from galaxy.web_stack import ApplicationStack, UWSGIApplicationStack
+from galaxy.util import (
+    galaxy_directory,
+    galaxy_samples_directory,
+)
+from galaxy.web_stack import (
+    ApplicationStack,
+    UWSGIApplicationStack,
+)
 from galaxy.web_stack.handlers import HANDLER_ASSIGNMENT_METHODS
 
 # File would be slightly more readable if contents were embedded directly, but
@@ -24,13 +30,11 @@ HANDLER_TEMPLATE_JOB_CONF = os.path.join(os.path.dirname(__file__), "handler_tem
 
 
 class TestApplicationStack(ApplicationStack):
-
     def get_preferred_handler_assignment_method(self):
         return HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED
 
 
 class TestUWSGIApplicationStack(UWSGIApplicationStack):
-
     def get_preferred_handler_assignment_method(self):
         return HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED
 
@@ -65,9 +69,7 @@ class BaseJobConfXmlParserTestCase(unittest.TestCase):
     def app(self):
         if not self._app:
             self._app = mock.Mock(
-                config=self.config,
-                job_metrics=JobMetrics(),
-                application_stack=self.application_stack
+                config=self.config, job_metrics=JobMetrics(), application_stack=self.application_stack
             )
         return self._app
 
@@ -83,9 +85,9 @@ class BaseJobConfXmlParserTestCase(unittest.TestCase):
             base_handler_pools = self._job_configuration_base_pools or JobConfiguration.DEFAULT_BASE_HANDLER_POOLS
             mock_uwsgi = mock.Mock()
             mock_uwsgi.mule_id = lambda: 1
-            with mock.patch('galaxy.web_stack.uwsgi', mock_uwsgi), \
-                    mock.patch('galaxy.web_stack.uwsgi.opt', self._uwsgi_opt), \
-                    mock.patch('galaxy.jobs.JobConfiguration.DEFAULT_BASE_HANDLER_POOLS', base_handler_pools):
+            with mock.patch("galaxy.web_stack.uwsgi", mock_uwsgi), mock.patch(
+                "galaxy.web_stack.uwsgi.opt", self._uwsgi_opt
+            ), mock.patch("galaxy.jobs.JobConfiguration.DEFAULT_BASE_HANDLER_POOLS", base_handler_pools):
                 self._job_configuration = JobConfiguration(self.app)
         return self._job_configuration
 
@@ -96,13 +98,12 @@ class BaseJobConfXmlParserTestCase(unittest.TestCase):
     def _with_handlers_config(self, assign_with=None, default=None, handlers=None, base_pools=None):
         handlers = handlers or []
         template = {
-            'assign_with': ' assign_with="%s"' % assign_with if assign_with is not None else '',
-            'default': ' default="%s"' % default if default is not None else '',
-            'handlers': '\n'.join(
-                '<handler id="{id}"{tags}/>'.format(
-                    id=x['id'],
-                    tags=' tags="%s"' % x['tags'] if 'tags' in x else ''
-                ) for x in handlers),
+            "assign_with": ' assign_with="%s"' % assign_with if assign_with is not None else "",
+            "default": ' default="%s"' % default if default is not None else "",
+            "handlers": "\n".join(
+                '<handler id="{id}"{tags}/>'.format(id=x["id"], tags=' tags="%s"' % x["tags"] if "tags" in x else "")
+                for x in handlers
+            ),
         }
         self._job_configuration_base_pools = base_pools
         self._write_config_from(HANDLER_TEMPLATE_JOB_CONF, template=template)
@@ -121,7 +122,9 @@ class BaseJobConfXmlParserTestCase(unittest.TestCase):
                 while not os.path.exists(dir_that_exists):
                     dir_that_exists = os.path.dirname(dir_that_exists)
                 dir_contents = os.listdir(dir_that_exists)
-                raise Exception(f"Failed to find file {path}, directory {dir_path} does not exist - {dir_that_exists} is the first root that exists and contains {dir_contents}.")
+                raise Exception(
+                    f"Failed to find file {path}, directory {dir_path} does not exist - {dir_that_exists} is the first root that exists and contains {dir_contents}."
+                )
         if template:
             contents = contents.format(**template)
         self._write_config(contents)
@@ -158,107 +161,108 @@ class SimpleJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
 
     def test_explicit_handler_default(self):
         self._with_handlers_config(
-            handlers=[{'id': 'handler0', 'tags': 'handlers'}, {'id': 'handler1', 'tags': 'handlers'}],
-            default='handlers'
+            handlers=[{"id": "handler0", "tags": "handlers"}, {"id": "handler1", "tags": "handlers"}],
+            default="handlers",
         )
         assert self.job_config.default_handler_id == "handlers"
 
     def test_handler_tag_parsing(self):
         self._with_handlers_config(
-            handlers=[{'id': 'handler0', 'tags': 'handlers'}, {'id': 'handler1', 'tags': 'handlers'}],
-            default='handlers'
+            handlers=[{"id": "handler0", "tags": "handlers"}, {"id": "handler1", "tags": "handlers"}],
+            default="handlers",
         )
         assert "handler0" in self.job_config.handlers["handlers"]
         assert "handler1" in self.job_config.handlers["handlers"]
 
     def test_implict_db_self_handler_assign(self):
-        assert self.job_config.handler_assignment_methods == ['db-skip-locked']
+        assert self.job_config.handler_assignment_methods == ["db-skip-locked"]
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
 
     def test_implicit_db_assign_handler_assign_with_explicit_handlers(self):
-        self._with_handlers_config(handlers=[{'id': 'handler0'}, {'id': 'handler1'}])
-        assert self.job_config.handler_assignment_methods == ['db-skip-locked']
+        self._with_handlers_config(handlers=[{"id": "handler0"}, {"id": "handler1"}])
+        assert self.job_config.handler_assignment_methods == ["db-skip-locked"]
         assert self.job_config.default_handler_id is None
-        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'handler1']
+        assert sorted(self.job_config.handlers["_default_"]) == ["handler0", "handler1"]
 
     def test_implict_uwsgi_mule_message_handler_assign(self):
-        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
-        assert self.job_config.handler_assignment_methods == ['uwsgi-mule-message', 'db-skip-locked']
+        self._with_uwsgi_application_stack(mule="lib/galaxy/main.py", farm="job-handlers:1")
+        assert self.job_config.handler_assignment_methods == ["uwsgi-mule-message", "db-skip-locked"]
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['main.job-handlers.1']
+        assert self.job_config.handlers["_default_"] == ["main.job-handlers.1"]
 
     def test_implict_uwsgi_mule_message_handler_assign_with_explicit_handlers(self):
-        self._with_handlers_config(handlers=[{'id': 'handler0'}, {'id': 'handler1'}])
-        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
-        assert self.job_config.handler_assignment_methods == ['uwsgi-mule-message', 'db-skip-locked'], self.job_config.handler_assignment_methods
+        self._with_handlers_config(handlers=[{"id": "handler0"}, {"id": "handler1"}])
+        self._with_uwsgi_application_stack(mule="lib/galaxy/main.py", farm="job-handlers:1")
+        assert self.job_config.handler_assignment_methods == [
+            "uwsgi-mule-message",
+            "db-skip-locked",
+        ], self.job_config.handler_assignment_methods
         assert self.job_config.default_handler_id is None
-        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'handler1', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers["_default_"]) == ["handler0", "handler1", "main.job-handlers.1"]
 
     def test_explicit_mem_self_handler_assign(self):
-        self._with_handlers_config(assign_with='mem-self')
-        assert self.job_config.handler_assignment_methods == ['mem-self']
+        self._with_handlers_config(assign_with="mem-self")
+        assert self.job_config.handler_assignment_methods == ["mem-self"]
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
         assert not self.config.track_jobs_in_database
 
     def test_explicit_mem_self_handler_assign_with_handlers(self):
-        self._with_handlers_config(assign_with='mem-self', handlers=[{'id': 'handler0'}])
-        assert self.job_config.handler_assignment_methods == ['mem-self']
+        self._with_handlers_config(assign_with="mem-self", handlers=[{"id": "handler0"}])
+        assert self.job_config.handler_assignment_methods == ["mem-self"]
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['handler0']
+        assert self.job_config.handlers["_default_"] == ["handler0"]
 
     def test_explicit_db_preassign_handler_assign_with_uwsgi(self):
-        self._with_handlers_config(assign_with='db-preassign', handlers=[{'id': 'handler0'}])
-        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
-        assert self.job_config.handler_assignment_methods == ['db-preassign']
+        self._with_handlers_config(assign_with="db-preassign", handlers=[{"id": "handler0"}])
+        self._with_uwsgi_application_stack(mule="lib/galaxy/main.py", farm="job-handlers:1")
+        assert self.job_config.handler_assignment_methods == ["db-preassign"]
         assert self.job_config.default_handler_id is None
-        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers["_default_"]) == ["handler0", "main.job-handlers.1"]
 
     def test_explicit_db_transaction_isolation_handler_assign(self):
-        self._with_handlers_config(assign_with='db-transaction-isolation')
-        assert self.job_config.handler_assignment_methods == ['db-transaction-isolation']
+        self._with_handlers_config(assign_with="db-transaction-isolation")
+        assert self.job_config.handler_assignment_methods == ["db-transaction-isolation"]
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
 
     def test_explicit_db_transaction_isolation_handler_assign_with_uwsgi(self):
-        self._with_handlers_config(assign_with='db-transaction-isolation', handlers=[{'id': 'handler0'}])
-        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
-        assert self.job_config.handler_assignment_methods == ['db-transaction-isolation']
+        self._with_handlers_config(assign_with="db-transaction-isolation", handlers=[{"id": "handler0"}])
+        self._with_uwsgi_application_stack(mule="lib/galaxy/main.py", farm="job-handlers:1")
+        assert self.job_config.handler_assignment_methods == ["db-transaction-isolation"]
         assert self.job_config.default_handler_id is None
-        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers["_default_"]) == ["handler0", "main.job-handlers.1"]
 
     def test_explicit_db_skip_locked_handler_assign(self):
-        self._with_handlers_config(assign_with='db-skip-locked')
-        assert self.job_config.handler_assignment_methods == ['db-skip-locked']
+        self._with_handlers_config(assign_with="db-skip-locked")
+        assert self.job_config.handler_assignment_methods == ["db-skip-locked"]
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
 
     def test_explicit_db_skip_locked_handler_assign_with_uwsgi(self):
-        self._with_handlers_config(assign_with='db-skip-locked', handlers=[{'id': 'handler0'}])
-        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
-        assert self.job_config.handler_assignment_methods == ['db-skip-locked']
+        self._with_handlers_config(assign_with="db-skip-locked", handlers=[{"id": "handler0"}])
+        self._with_uwsgi_application_stack(mule="lib/galaxy/main.py", farm="job-handlers:1")
+        assert self.job_config.handler_assignment_methods == ["db-skip-locked"]
         assert self.job_config.default_handler_id is None
-        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers["_default_"]) == ["handler0", "main.job-handlers.1"]
 
     def test_uwsgi_farms_as_handler_tags(self):
         self._with_uwsgi_application_stack(
-            mule=['lib/galaxy/main.py'] * 2,
-            farm=['job-handlers:1', 'job-handlers.foo:2']
+            mule=["lib/galaxy/main.py"] * 2, farm=["job-handlers:1", "job-handlers.foo:2"]
         )
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['main.job-handlers.1']
-        assert self.job_config.handlers['foo'] == ['main.job-handlers.foo.1']
+        assert self.job_config.handlers["_default_"] == ["main.job-handlers.1"]
+        assert self.job_config.handlers["foo"] == ["main.job-handlers.foo.1"]
 
     def test_uwsgi_overlapping_pools(self):
-        self._with_handlers_config(base_pools=('workflow-schedulers', 'job-handlers'))
+        self._with_handlers_config(base_pools=("workflow-schedulers", "job-handlers"))
         self._with_uwsgi_application_stack(
-            mule=['lib/galaxy/main.py'] * 3,
-            farm=['job-handlers:1', 'workflow-schedulers:2', 'job-handlers.foo:3']
+            mule=["lib/galaxy/main.py"] * 3, farm=["job-handlers:1", "workflow-schedulers:2", "job-handlers.foo:3"]
         )
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['main.workflow-schedulers.1']
-        assert self.job_config.handlers['foo'] == ['main.job-handlers.foo.1']
+        assert self.job_config.handlers["_default_"] == ["main.workflow-schedulers.1"]
+        assert self.job_config.handlers["foo"] == ["main.job-handlers.foo.1"]
 
     def test_load_simple_destination(self):
         local_dest = self.job_config.destinations["local"][0]
@@ -307,7 +311,6 @@ class SimpleJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
 
 
 class AdvancedJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
-
     def test_disable_job_metrics(self):
         self._with_advanced_config()
         self.job_config.destinations["multicore_local"]
@@ -362,7 +365,7 @@ class AdvancedJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
         env_dest = self.job_config.destinations["java_cluster"][0]
         assert len(env_dest.env) == 4, len(env_dest.env)
         assert env_dest.env[0]["name"] == "_JAVA_OPTIONS"
-        assert env_dest.env[0]["value"] == '-Xmx6G'
+        assert env_dest.env[0]["value"] == "-Xmx6G"
 
         assert env_dest.env[1]["name"] == "ANOTHER_OPTION"
         assert env_dest.env[1]["raw"] is True
@@ -423,7 +426,7 @@ class AdvancedJobConfYamlParserTestCase(AdvancedJobConfXmlParserTestCase):
 
 
 def test_yaml_advanced_validation():
-    schema = GALAXY_SCHEMAS_PATH / 'job_config_schema.yml'
+    schema = GALAXY_SCHEMAS_PATH / "job_config_schema.yml"
     integration_tests_dir = os.path.join(galaxy_directory(), "test", "integration")
     valid_files = [
         ADVANCED_JOB_CONF_YAML,
diff --git a/test/unit/app/jobs/test_job_context.py b/test/unit/app/jobs/test_job_context.py
index 7e0821bd081..9d65c5a5703 100644
--- a/test/unit/app/jobs/test_job_context.py
+++ b/test/unit/app/jobs/test_job_context.py
@@ -12,7 +12,6 @@ from ..tools.test_history_imp_exp import _mock_app
 
 
 class PermissionProvider:
-
     def __init__(self):
         self.permissions = []
 
@@ -24,13 +23,11 @@ class PermissionProvider:
 
 
 class MetadataSourceProvider:
-
     def get_metadata_source(self, input_name):
         return None
 
 
 class Tool:
-
     def __init__(self, app):
         self.app = app
         self.sa_session = app.model.context
@@ -38,7 +35,7 @@ class Tool:
 
 def setup_data(job_working_directory):
     for i in range(10):
-        with open(os.path.join(job_working_directory, f'datasets_{i}.txt'), 'w') as out:
+        with open(os.path.join(job_working_directory, f"datasets_{i}.txt"), "w") as out:
             out.write(str(i))
 
 
@@ -61,24 +58,35 @@ def test_job_context_discover_outputs_flushes_once(mocker):
     permission_provider = PermissionProvider()
     metadata_source_provider = MetadataSourceProvider()
     object_store = app.object_store
-    input_dbkey = '?'
-    final_job_state = 'ok'
+    input_dbkey = "?"
+    final_job_state = "ok"
     collection_description = FilePatternDatasetCollectionDescription(pattern="__name__")
-    collection = model.DatasetCollection(collection_type='list', populated=False)
+    collection = model.DatasetCollection(collection_type="list", populated=False)
     sa_session.add(collection)
-    job_context = JobContext(tool, tool_provided_metadata, job, job_working_directory, permission_provider, metadata_source_provider, input_dbkey, object_store, final_job_state, max_discovered_files=100)
+    job_context = JobContext(
+        tool,
+        tool_provided_metadata,
+        job,
+        job_working_directory,
+        permission_provider,
+        metadata_source_provider,
+        input_dbkey,
+        object_store,
+        final_job_state,
+        max_discovered_files=100,
+    )
     collection_builder = builder.BoundCollectionBuilder(collection)
     dataset_collectors = [dataset_collector(collection_description)]
-    output_name = 'output'
+    output_name = "output"
     filenames = job_context.find_files(output_name, collection, dataset_collectors)
     assert len(filenames) == 10
-    spy = mocker.spy(sa_session, 'flush')
+    spy = mocker.spy(sa_session, "flush")
     job_context.populate_collection_elements(
         collection,
         collection_builder,
         filenames,
         name=output_name,
-        metadata_source_name='',
+        metadata_source_name="",
         final_job_state=job_context.final_job_state,
     )
     collection_builder.populate()
diff --git a/test/unit/app/jobs/test_job_wrapper.py b/test/unit/app/jobs/test_job_wrapper.py
index ba9cb55ca74..a03bb35b3d2 100644
--- a/test/unit/app/jobs/test_job_wrapper.py
+++ b/test/unit/app/jobs/test_job_wrapper.py
@@ -1,19 +1,22 @@
 import abc
 import os
 from contextlib import contextmanager
-from typing import Dict, Type
+from typing import (
+    Dict,
+    Type,
+)
 from unittest import TestCase
 
 from galaxy.app_unittest_utils.tools_support import UsesApp
 from galaxy.jobs import (
     JobWrapper,
-    TaskWrapper
+    TaskWrapper,
 )
 from galaxy.model import (
     Base,
     Job,
     Task,
-    User
+    User,
 )
 from galaxy.util.bunch import Bunch
 
@@ -24,7 +27,6 @@ TEST_COMMAND = ""
 
 
 class BaseWrapperTestCase(UsesApp):
-
     def setUp(self):
         self.setup_app()
         job = Job()
@@ -72,13 +74,11 @@ class BaseWrapperTestCase(UsesApp):
 
 
 class JobWrapperTestCase(BaseWrapperTestCase, TestCase):
-
     def _wrapper(self):
         return JobWrapper(self.job, self.queue)  # type: ignore[arg-type]
 
 
 class TaskWrapperTestCase(BaseWrapperTestCase, TestCase):
-
     def setUp(self):
         super().setUp()
         self.task = Task(self.job, self.working_directory, "prepare_bwa_job.sh")
@@ -90,7 +90,6 @@ class TaskWrapperTestCase(BaseWrapperTestCase, TestCase):
 
 
 class MockEvaluator:
-
     def __init__(self, app, tool, job, local_working_directory):
         self.app = app
         self.tool = tool
@@ -109,14 +108,12 @@ class MockEvaluator:
 
 
 class MockJobQueue:
-
     def __init__(self, app):
         self.app = app
         self.dispatcher = MockJobDispatcher(app)
 
 
 class MockJobDispatcher:
-
     def __init__(self, app):
         pass
 
@@ -125,7 +122,6 @@ class MockJobDispatcher:
 
 
 class MockContext:
-
     def __init__(self, model_objects):
         self.expunged_all = False
         self.flushed = False
@@ -146,7 +142,6 @@ class MockContext:
 
 
 class MockQuery:
-
     def __init__(self, class_objects):
         self.class_objects = class_objects
 
@@ -158,26 +153,24 @@ class MockQuery:
 
 
 class MockTool:
-
     def __init__(self, app):
         self.version_string_cmd = TEST_VERSION_COMMAND
         self.tool_dir = "/path/to/tools"
         self.dependencies = []
         self.requires_galaxy_python_environment = False
-        self.id = 'mock_id'
+        self.id = "mock_id"
         self.home_target = None
         self.tmp_target = None
-        self.tool_source = Bunch(to_string=lambda: '')
+        self.tool_source = Bunch(to_string=lambda: "")
 
     def get_job_destination(self, params):
-        return Bunch(runner='local', id='local', params={})
+        return Bunch(runner="local", id="local", params={})
 
     def build_dependency_shell_commands(self, job_directory):
         return TEST_DEPENDENCIES_COMMANDS
 
 
 class MockToolbox:
-
     def __init__(self, test_tool):
         self.test_tool = test_tool
 
@@ -191,7 +184,6 @@ class MockToolbox:
 
 
 class MockObjectStore:
-
     def __init__(self, working_directory):
         self.working_directory = working_directory
         os.makedirs(working_directory)
diff --git a/test/unit/app/jobs/test_mapper.py b/test/unit/app/jobs/test_mapper.py
index 05db11212fb..bf49b262c98 100644
--- a/test/unit/app/jobs/test_mapper.py
+++ b/test/unit/app/jobs/test_mapper.py
@@ -10,8 +10,10 @@ from galaxy.jobs.mapper import (
     JobRunnerMapper,
 )
 from galaxy.util import bunch
-from . import test_rules
-from . import test_rules_override
+from . import (
+    test_rules,
+    test_rules_override,
+)
 
 WORKFLOW_UUID = uuid.uuid1().hex
 TOOL_JOB_DESTINATION = JobDestination()
@@ -97,8 +99,9 @@ def test_dynamic_mapping_missing_function():
 
 
 def test_dynamic_mapping_rule_module_override():
-    mapper = __mapper(__dynamic_destination(dict(function="rule_module_override",
-                                                 rules_module=test_rules_override.__name__)))
+    mapper = __mapper(
+        __dynamic_destination(dict(function="rule_module_override", rules_module=test_rules_override.__name__))
+    )
     assert mapper.get_job_destination({}) is DYNAMICALLY_GENERATED_DESTINATION
     assert mapper.job_config.rule_response == "new_rules_package"
 
@@ -106,7 +109,7 @@ def test_dynamic_mapping_rule_module_override():
 def test_dynamic_mapping_externally_set_job_destination():
     mapper = __mapper(__dynamic_destination(dict(function="upload")))
     # Initially, the mapper should not have a cached destination
-    assert not hasattr(mapper, 'cached_job_destination')
+    assert not hasattr(mapper, "cached_job_destination")
     # Overwrite with an externally set job destination
     manually_set_destination = JobDestination(runner="dynamic")
     mapper.cached_job_destination = manually_set_destination
@@ -134,11 +137,7 @@ def __mapper(tool_job_destination=TOOL_JOB_DESTINATION):
     job_wrapper = MockJobWrapper(tool_job_destination)
     job_config = MockJobConfig()
 
-    mapper = JobRunnerMapper(
-        job_wrapper,
-        {},
-        job_config
-    )
+    mapper = JobRunnerMapper(job_wrapper, {}, job_config)
     mapper.rules_module = test_rules
     return mapper
 
@@ -149,7 +148,6 @@ def __dynamic_destination(params=None):
 
 
 class MockJobConfig:
-
     def __init__(self):
         self.rule_response = None
         self.dynamic_params = None
@@ -162,7 +160,6 @@ class MockJobConfig:
 
 
 class MockJobWrapper(HasResourceParameters):
-
     def __init__(self, tool_job_destination):
         self.tool = MockTool(tool_job_destination)
         self.job_id = 12345
@@ -180,24 +177,17 @@ class MockJobWrapper(HasResourceParameters):
         def get_param_values(app, ignore_errors):
             assert app == self.app
             params = raw_params.copy()
-            params["__job_resource"] = {
-                "__job_resource__select": "True",
-                "memory": "8gb"
-            }
+            params["__job_resource"] = {"__job_resource__select": "True", "memory": "8gb"}
             return params
 
         return bunch.Bunch(
-            user=bunch.Bunch(
-                id=6789,
-                email="test@example.com"
-            ),
+            user=bunch.Bunch(id=6789, email="test@example.com"),
             raw_param_dict=lambda: raw_params,
-            get_param_values=get_param_values
+            get_param_values=get_param_values,
         )
 
 
 class MockTool:
-
     def __init__(self, tool_job_destination):
         self.id = "testtoolshed/devteam/tool1/23abcd13123"
         self.call_count = 0
diff --git a/test/unit/app/jobs/test_rule_helper.py b/test/unit/app/jobs/test_rule_helper.py
index 82b51c30304..c4a4df3a0ad 100644
--- a/test/unit/app/jobs/test_rule_helper.py
+++ b/test/unit/app/jobs/test_rule_helper.py
@@ -36,10 +36,22 @@ def test_job_count():
     __assert_job_count_is(0, rule_helper, for_destination="local", for_user_email=USER_EMAIL_2)
 
     # Test per user, per state destination counts
-    __assert_job_count_is(3, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["queued"])
-    __assert_job_count_is(2, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["running"])
-    __assert_job_count_is(0, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["error"])
-    __assert_job_count_is(5, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["queued", "running", "error"])
+    __assert_job_count_is(
+        3, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["queued"]
+    )
+    __assert_job_count_is(
+        2, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["running"]
+    )
+    __assert_job_count_is(
+        0, rule_helper, for_destination="cluster1", for_user_email=USER_EMAIL_1, for_job_states=["error"]
+    )
+    __assert_job_count_is(
+        5,
+        rule_helper,
+        for_destination="cluster1",
+        for_user_email=USER_EMAIL_1,
+        for_job_states=["queued", "running", "error"],
+    )
 
 
 def __assert_job_count_is(expected_count, rule_helper, **kwds):
@@ -78,9 +90,9 @@ def test_choose_one_unhashed():
 
     # Random choices if hash not set.
     chosen_ones = set()
-    __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'])))
+    __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(["a", "b"])))
 
-    assert chosen_ones == {'a', 'b'}
+    assert chosen_ones == {"a", "b"}
 
 
 def test_choose_one_hashed():
@@ -88,12 +100,12 @@ def test_choose_one_hashed():
 
     # Hashed, so all choosen ones should be the same...
     chosen_ones = set()
-    __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'], hash_value=1234)))
+    __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(["a", "b"], hash_value=1234)))
     assert len(chosen_ones) == 1
 
     # ... also can verify hashing on strings
     chosen_ones = set()
-    __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(['a', 'b'], hash_value="i am a string")))
+    __do_a_bunch(lambda: chosen_ones.add(rule_helper.choose_one(["a", "b"], hash_value="i am a string")))
 
     assert len(chosen_ones) == 1
 
@@ -181,14 +193,9 @@ def __rule_helper():
 
 
 class MockApp:
-
     def __init__(self):
         self.config = bunch.Bunch()
-        self.model = mapping.init(
-            "/tmp",
-            "sqlite:///:memory:",
-            create_tables=True
-        )
+        self.model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True)
 
     def add(self, *args):
         for arg in args:
diff --git a/test/unit/app/jobs/test_rules/10_site.py b/test/unit/app/jobs/test_rules/10_site.py
index 8b2ac476869..89b140600fb 100644
--- a/test/unit/app/jobs/test_rules/10_site.py
+++ b/test/unit/app/jobs/test_rules/10_site.py
@@ -2,26 +2,25 @@ from galaxy.jobs import JobDestination
 
 
 def upload():
-    return 'local_runner'
+    return "local_runner"
 
 
 def tophat():
-    return 'site_dest_id'
+    return "site_dest_id"
 
 
 def tool1():
     # tool1 is id to test tool mocked out in test_mapper.py, without specify
     # function name in dynamic destination - this function should be used by
     # default.
-    return 'tool1_dest_id'
+    return "tool1_dest_id"
 
 
 def dynamic_chain_1():
     # Check whether chaining dynamic job destinations work
-    return JobDestination(runner="dynamic",
-                          params={'type': 'python',
-                                  'function': 'dynamic_chain_2',
-                                  'test_param': 'my_test_param'})
+    return JobDestination(
+        runner="dynamic", params={"type": "python", "function": "dynamic_chain_2", "test_param": "my_test_param"}
+    )
 
 
 def dynamic_chain_2(test_param):
@@ -49,7 +48,7 @@ def check_rule_params(
     assert app == job_wrapper.app
     assert rule_helper is not None
     assert isinstance(referrer, JobDestination)
-    assert referrer.params['param1'] == "referrer_param"
+    assert referrer.params["param1"] == "referrer_param"
 
     assert job.user == user
     assert user.id == 6789
diff --git a/test/unit/app/jobs/test_rules/20_instance.py b/test/unit/app/jobs/test_rules/20_instance.py
index 0638d4b0e6b..f35033728a1 100644
--- a/test/unit/app/jobs/test_rules/20_instance.py
+++ b/test/unit/app/jobs/test_rules/20_instance.py
@@ -1,3 +1,3 @@
 def tophat():
     # This should override definition in 10_site.py
-    return 'instance_dest_id'
+    return "instance_dest_id"
diff --git a/test/unit/app/jobs/test_rules_override/10_rule.py b/test/unit/app/jobs/test_rules_override/10_rule.py
index 7cccd3dfc27..1cf1e70d53b 100644
--- a/test/unit/app/jobs/test_rules_override/10_rule.py
+++ b/test/unit/app/jobs/test_rules_override/10_rule.py
@@ -1,3 +1,3 @@
 def rule_module_override():
     # Dummy rule for testing rule module overrides
-    return 'new_rules_package'
+    return "new_rules_package"
diff --git a/test/unit/app/jobs/test_runner_local.py b/test/unit/app/jobs/test_runner_local.py
index d9e98cf3a53..04a23d968a9 100644
--- a/test/unit/app/jobs/test_runner_local.py
+++ b/test/unit/app/jobs/test_runner_local.py
@@ -6,15 +6,16 @@ from unittest import TestCase
 
 import psutil
 
-from galaxy import job_metrics
-from galaxy import model
+from galaxy import (
+    job_metrics,
+    model,
+)
 from galaxy.app_unittest_utils.tools_support import UsesTools
 from galaxy.jobs.runners import local
 from galaxy.util import bunch
 
 
 class TestLocalJobRunner(TestCase, UsesTools):
-
     def setUp(self):
         self.setup_app()
         self._init_tool()
@@ -37,7 +38,7 @@ class TestLocalJobRunner(TestCase, UsesTools):
         assert self.job_wrapper.exit_code == 0
 
     def test_default_slots(self):
-        self.job_wrapper.command_line = '''echo $GALAXY_SLOTS'''
+        self.job_wrapper.command_line = """echo $GALAXY_SLOTS"""
         runner = local.LocalJobRunner(self.app, 1)
         runner.queue_job(self.job_wrapper)
         assert self.job_wrapper.stdout.strip() == "1"
@@ -46,7 +47,7 @@ class TestLocalJobRunner(TestCase, UsesTools):
         # Set local_slots in job destination to specify slots for
         # local job runner.
         self.job_wrapper.job_destination.params["local_slots"] = 3
-        self.job_wrapper.command_line = '''echo $GALAXY_SLOTS'''
+        self.job_wrapper.command_line = """echo $GALAXY_SLOTS"""
         runner = local.LocalJobRunner(self.app, 1)
         runner.queue_job(self.job_wrapper)
         assert self.job_wrapper.stdout.strip() == "3"
@@ -114,7 +115,6 @@ class TestLocalJobRunner(TestCase, UsesTools):
 
 
 class MockJobWrapper:
-
     def __init__(self, app, test_directory, tool):
         working_directory = os.path.join(test_directory, "workdir")
         tool_working_directory = os.path.join(working_directory, "working")
@@ -136,7 +136,7 @@ class MockJobWrapper:
         self.job = model.Job()
         self.job_id = 1
         self.job.id = 1
-        self.output_paths = ['/tmp/output1.dat']
+        self.output_paths = ["/tmp/output1.dat"]
         self.mock_metadata_path = os.path.abspath(os.path.join(test_directory, "METADATA_SET"))
         self.metadata_command = "touch %s" % self.mock_metadata_path
         self.galaxy_virtual_env = None
@@ -150,9 +150,7 @@ class MockJobWrapper:
         self.external_output_metadata: Optional[bunch.Bunch] = bunch.Bunch(
             set_job_runner_external_pid=lambda pid, session: None
         )
-        self.app.datatypes_registry.set_external_metadata_tool = bunch.Bunch(
-            build_dependency_shell_commands=lambda: []
-        )
+        self.app.datatypes_registry.set_external_metadata_tool = bunch.Bunch(build_dependency_shell_commands=lambda: [])
 
     def check_tool_output(*args, **kwds):
         return "ok"
@@ -164,7 +162,7 @@ class MockJobWrapper:
             external_id = self.job.job_runner_external_id
             if external_id:
                 break
-            time.sleep(.1)
+            time.sleep(0.1)
         return external_id
 
     def prepare(self):
diff --git a/test/unit/app/jobs/test_runner_params.py b/test/unit/app/jobs/test_runner_params.py
index 96a73b8c400..83921a362a4 100644
--- a/test/unit/app/jobs/test_runner_params.py
+++ b/test/unit/app/jobs/test_runner_params.py
@@ -3,7 +3,9 @@ from galaxy.jobs import runners
 
 def test_default_specs():
     # recheck_missing_job_retries is integer >= 0
-    params = runners.RunnerParams(specs=runners.BaseJobRunner.DEFAULT_SPECS, params=dict(recheck_missing_job_retries="1"))
+    params = runners.RunnerParams(
+        specs=runners.BaseJobRunner.DEFAULT_SPECS, params=dict(recheck_missing_job_retries="1")
+    )
     assert params.recheck_missing_job_retries == 1
     assert params["recheck_missing_job_retries"] == 1
 
diff --git a/test/unit/app/managers/base.py b/test/unit/app/managers/base.py
index 439f1a6df41..d456c455e00 100644
--- a/test/unit/app/managers/base.py
+++ b/test/unit/app/managers/base.py
@@ -10,30 +10,29 @@ from galaxy.app_unittest_utils import galaxy_mock
 from galaxy.managers.users import UserManager
 
 # =============================================================================
-admin_email = 'admin@admin.admin'
+admin_email = "admin@admin.admin"
 admin_users = admin_email
-default_password = '123456'
+default_password = "123456"
 
 
 # =============================================================================
 class BaseTestCase(unittest.TestCase):
-
     @classmethod
     def setUpClass(cls):
-        print('\n', '-' * 20, 'begin class', cls)
+        print("\n", "-" * 20, "begin class", cls)
 
     @classmethod
     def tearDownClass(cls):
-        print('\n', '-' * 20, 'end class', cls)
+        print("\n", "-" * 20, "end class", cls)
 
     def setUp(self):
-        self.log('.' * 20, 'begin test', self)
+        self.log("." * 20, "begin test", self)
         self.set_up_mocks()
         self.set_up_managers()
         self.set_up_trans()
 
     def set_up_mocks(self):
-        admin_users_list = [u for u in admin_users.split(',') if u]
+        admin_users_list = [u for u in admin_users.split(",") if u]
         self.trans = galaxy_mock.MockTrans(admin_users=admin_users, admin_users_list=admin_users_list)
         self.app = self.trans.app
 
@@ -41,12 +40,12 @@ class BaseTestCase(unittest.TestCase):
         self.user_manager = self.app[UserManager]
 
     def set_up_trans(self):
-        self.admin_user = self.user_manager.create(email=admin_email, username='admin', password=default_password)
+        self.admin_user = self.user_manager.create(email=admin_email, username="admin", password=default_password)
         self.trans.set_user(self.admin_user)
         self.trans.set_history(None)
 
     def tearDown(self):
-        self.log('.' * 20, 'end test', self, '\n')
+        self.log("." * 20, "end test", self, "\n")
 
     def log(self, *args, **kwargs):
         print(*args, **kwargs)
@@ -60,54 +59,56 @@ class BaseTestCase(unittest.TestCase):
     def assertHasKeys(self, obj, key_list):
         for key in key_list:
             if key not in obj:
-                self.fail('Missing key: ' + key)
+                self.fail("Missing key: " + key)
         else:
-            self.assertTrue(True, 'keys found in object')
+            self.assertTrue(True, "keys found in object")
 
     def assertNullableBasestring(self, item):
         if not isinstance(item, (str, type(None))):
-            self.fail('Non-nullable basestring: ' + str(type(item)))
+            self.fail("Non-nullable basestring: " + str(type(item)))
         # TODO: len mod 8 and hex re
-        self.assertTrue(True, 'is nullable basestring: ' + str(item))
+        self.assertTrue(True, "is nullable basestring: " + str(item))
 
     def assertEncodedId(self, item):
         if not isinstance(item, str):
-            self.fail('Non-string: ' + str(type(item)))
+            self.fail("Non-string: " + str(type(item)))
         # TODO: len mod 8 and hex re
-        self.assertTrue(True, 'is id: ' + item)
+        self.assertTrue(True, "is id: " + item)
 
     def assertNullableEncodedId(self, item):
         if item is None:
-            self.assertTrue(True, 'nullable id is None')
+            self.assertTrue(True, "nullable id is None")
         else:
             self.assertEncodedId(item)
 
     def assertDate(self, item):
         if not isinstance(item, str):
-            self.fail('Non-string: ' + str(type(item)))
+            self.fail("Non-string: " + str(type(item)))
         # TODO: no great way to parse this fully (w/o python-dateutil)
         # TODO: re?
-        self.assertTrue(True, 'is date: ' + item)
+        self.assertTrue(True, "is date: " + item)
 
     def assertUUID(self, item):
         if not isinstance(item, str):
-            self.fail('Non-string: ' + str(type(item)))
+            self.fail("Non-string: " + str(type(item)))
         # TODO: re for d4d76d69-80d4-4ed7-80c7-211ebcc1a358
-        self.assertTrue(True, 'is uuid: ' + item)
+        self.assertTrue(True, "is uuid: " + item)
 
     def assertORMFilter(self, item, msg=None):
-        if not isinstance(item.filter, (sqlalchemy.sql.elements.BinaryExpression, sqlalchemy.sql.elements.BooleanClauseList)):
-            self.fail('Not an orm filter: ' + str(type(item.filter)))
-        self.assertTrue(True, msg or ('is an orm filter: ' + str(item.filter)))
+        if not isinstance(
+            item.filter, (sqlalchemy.sql.elements.BinaryExpression, sqlalchemy.sql.elements.BooleanClauseList)
+        ):
+            self.fail("Not an orm filter: " + str(type(item.filter)))
+        self.assertTrue(True, msg or ("is an orm filter: " + str(item.filter)))
 
     def assertORMFunctionFilter(self, item, msg=None):
-        assert item.filter_type == 'orm_function'
+        assert item.filter_type == "orm_function"
         assert callable(item.filter)
 
     def assertFnFilter(self, item, msg=None):
         if not item.filter or not callable(item.filter):
-            self.fail('Not a fn filter: ' + str(type(item.filter)))
-        self.assertTrue(True, msg or ('is a fn filter: ' + str(item.filter)))
+            self.fail("Not a fn filter: " + str(type(item.filter)))
+        self.assertTrue(True, msg or ("is a fn filter: " + str(item.filter)))
 
     def assertIsJsonifyable(self, item):
         # TODO: use galaxy's override
@@ -120,7 +121,7 @@ class CreatesCollectionsMixin:
     def build_element_identifiers(self, elements):
         identifier_list = []
         for element in elements:
-            src = 'hda'
+            src = "hda"
             # if isinstance( element, model.DatasetCollection ):
             #    src = 'collection'#?
             # elif isinstance( element, model.LibraryDatasetDatasetAssociation ):
@@ -131,6 +132,6 @@ class CreatesCollectionsMixin:
 
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_CollectionManager.py b/test/unit/app/managers/test_CollectionManager.py
index a6f6a7d47e0..d26cf8a8315 100644
--- a/test/unit/app/managers/test_CollectionManager.py
+++ b/test/unit/app/managers/test_CollectionManager.py
@@ -8,17 +8,19 @@ from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.histories import HistoryManager
-from .base import BaseTestCase, CreatesCollectionsMixin
+from .base import (
+    BaseTestCase,
+    CreatesCollectionsMixin,
+)
 
 # =============================================================================
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
 
 
 # =============================================================================
 class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.dataset_manager = self.app[DatasetManager]
@@ -29,21 +31,19 @@ class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
     def test_create_simple_list(self):
         owner = self.user_manager.create(**user2_data)
 
-        history = self.history_manager.create(name='history1', user=owner)
+        history = self.history_manager.create(name="history1", user=owner)
 
-        hda1 = self.hda_manager.create(name='one',
-            history=history, dataset=self.dataset_manager.create())
-        hda2 = self.hda_manager.create(name='two',
-            history=history, dataset=self.dataset_manager.create())
-        hda3 = self.hda_manager.create(name='three',
-            history=history, dataset=self.dataset_manager.create())
+        hda1 = self.hda_manager.create(name="one", history=history, dataset=self.dataset_manager.create())
+        hda2 = self.hda_manager.create(name="two", history=history, dataset=self.dataset_manager.create())
+        hda3 = self.hda_manager.create(name="three", history=history, dataset=self.dataset_manager.create())
 
         self.log("should be able to create a new Collection via ids")
         element_identifiers = self.build_element_identifiers([hda1, hda2, hda3])
-        hdca = self.collection_manager.create(self.trans, history, 'test collection', 'list',
-                                           element_identifiers=element_identifiers)
+        hdca = self.collection_manager.create(
+            self.trans, history, "test collection", "list", element_identifiers=element_identifiers
+        )
         self.assertIsInstance(hdca, model.HistoryDatasetCollectionAssociation)
-        self.assertEqual(hdca.name, 'test collection')
+        self.assertEqual(hdca.name, "test collection")
         self.assertEqual(hdca.hid, 4)
         self.assertFalse(hdca.deleted)
         self.assertTrue(hdca.visible)
@@ -51,65 +51,66 @@ class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
         self.log("should contain an underlying, well-formed DatasetCollection")
         self.assertIsInstance(hdca.collection, model.DatasetCollection)
         collection = hdca.collection
-        self.assertEqual(collection.collection_type, 'list')
-        self.assertEqual(collection.state, 'ok')
+        self.assertEqual(collection.collection_type, "list")
+        self.assertEqual(collection.state, "ok")
         self.assertEqual(len(collection.dataset_instances), 3)
         self.assertEqual(len(collection.elements), 3)
 
         self.log("and that collection should have three well-formed Elements")
         self.assertIsInstance(collection.elements[0], model.DatasetCollectionElement)
-        self.assertEqual(collection.elements[0].element_identifier, 'one')
+        self.assertEqual(collection.elements[0].element_identifier, "one")
         self.assertEqual(collection.elements[0].element_index, 0)
-        self.assertEqual(collection.elements[0].element_type, 'hda')
+        self.assertEqual(collection.elements[0].element_type, "hda")
         self.assertEqual(collection.elements[0].element_object, hda1)
 
         self.assertIsInstance(collection.elements[1], model.DatasetCollectionElement)
-        self.assertEqual(collection.elements[1].element_identifier, 'two')
+        self.assertEqual(collection.elements[1].element_identifier, "two")
         self.assertEqual(collection.elements[1].element_index, 1)
-        self.assertEqual(collection.elements[1].element_type, 'hda')
+        self.assertEqual(collection.elements[1].element_type, "hda")
         self.assertEqual(collection.elements[1].element_object, hda2)
 
         self.assertIsInstance(collection.elements[2], model.DatasetCollectionElement)
-        self.assertEqual(collection.elements[2].element_identifier, 'three')
+        self.assertEqual(collection.elements[2].element_identifier, "three")
         self.assertEqual(collection.elements[2].element_index, 2)
-        self.assertEqual(collection.elements[2].element_type, 'hda')
+        self.assertEqual(collection.elements[2].element_type, "hda")
         self.assertEqual(collection.elements[2].element_object, hda3)
 
         self.log("should be able to create a new Collection via objects")
         elements = dict(one=hda1, two=hda2, three=hda3)
-        hdca2 = self.collection_manager.create(self.trans, history, 'test collection 2', 'list', elements=elements)
+        hdca2 = self.collection_manager.create(self.trans, history, "test collection 2", "list", elements=elements)
         self.assertIsInstance(hdca2, model.HistoryDatasetCollectionAssociation)
 
     def test_update_from_dict(self):
         owner = self.user_manager.create(**user2_data)
 
-        history = self.history_manager.create(name='history1', user=owner)
+        history = self.history_manager.create(name="history1", user=owner)
 
-        hda1 = self.hda_manager.create(name='one',
-            history=history, dataset=self.dataset_manager.create())
-        hda2 = self.hda_manager.create(name='two',
-            history=history, dataset=self.dataset_manager.create())
-        hda3 = self.hda_manager.create(name='three',
-            history=history, dataset=self.dataset_manager.create())
+        hda1 = self.hda_manager.create(name="one", history=history, dataset=self.dataset_manager.create())
+        hda2 = self.hda_manager.create(name="two", history=history, dataset=self.dataset_manager.create())
+        hda3 = self.hda_manager.create(name="three", history=history, dataset=self.dataset_manager.create())
 
         elements = dict(one=hda1, two=hda2, three=hda3)
-        hdca = self.collection_manager.create(self.trans, history, 'test collection', 'list', elements=elements)
+        hdca = self.collection_manager.create(self.trans, history, "test collection", "list", elements=elements)
 
         self.log("should be set from a dictionary")
-        self.collection_manager._set_from_dict(self.trans, hdca, {
-            'deleted': True,
-            'visible': False,
-            'name': 'New Name',
-            'tags': ['name:one', 'group:two', 'three']
-            # TODO: doesn't work
-            # 'annotations'      : [?]
-        })
-        self.assertEqual(hdca.name, 'New Name')
+        self.collection_manager._set_from_dict(
+            self.trans,
+            hdca,
+            {
+                "deleted": True,
+                "visible": False,
+                "name": "New Name",
+                "tags": ["name:one", "group:two", "three"]
+                # TODO: doesn't work
+                # 'annotations'      : [?]
+            },
+        )
+        self.assertEqual(hdca.name, "New Name")
         self.assertTrue(hdca.deleted)
         self.assertFalse(hdca.visible)
 
         tag_names = hdca.make_tag_string_list()
-        self.assertEqual(tag_names, ['name:one', 'group:two', 'three'])
+        self.assertEqual(tag_names, ["name:one", "group:two", "three"])
         # self.assertEqual( hdca.annotations, [ 'one', 'two', 'three' ] )
 
     # def test_validation( self ):
@@ -120,6 +121,6 @@ class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
 
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_DatasetManager.py b/test/unit/app/managers/test_DatasetManager.py
index c070b3583f5..4ff56d8a1a0 100644
--- a/test/unit/app/managers/test_DatasetManager.py
+++ b/test/unit/app/managers/test_DatasetManager.py
@@ -6,25 +6,24 @@ import sqlalchemy
 
 from galaxy import (
     exceptions,
-    model
+    model,
 )
 from galaxy.managers.base import SkipAttribute
 from galaxy.managers.datasets import (
     DatasetManager,
-    DatasetSerializer
+    DatasetSerializer,
 )
 from galaxy.managers.roles import RoleManager
 from .base import BaseTestCase
 
 # =============================================================================
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
 
 
 # =============================================================================
 class DatasetManagerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.dataset_manager = DatasetManager(self.app)
@@ -55,8 +54,9 @@ class DatasetManagerTestCase(BaseTestCase):
         self.assertEqual(self.dataset_manager.list(offset=3), [])
 
         self.log("should be able to order")
-        self.assertEqual(self.dataset_manager.list(order_by=sqlalchemy.desc(model.Dataset.create_time)),
-            [dataset2, dataset1])
+        self.assertEqual(
+            self.dataset_manager.list(order_by=sqlalchemy.desc(model.Dataset.create_time)), [dataset2, dataset1]
+        )
 
     def test_delete(self):
         item1 = self.dataset_manager.create()
@@ -117,8 +117,10 @@ class DatasetManagerTestCase(BaseTestCase):
         self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, None))
 
     def test_create_public_dataset(self):
-        self.log("should be able to create a new Dataset and give it some permissions that actually, you know, "
-            "might work if there's any justice in this universe")
+        self.log(
+            "should be able to create a new Dataset and give it some permissions that actually, you know, "
+            "might work if there's any justice in this universe"
+        )
         owner = self.user_manager.create(**user2_data)
         owner_private_role = self.user_manager.private_role(owner)
         dataset = self.dataset_manager.create(manage_roles=[owner_private_role])
@@ -153,8 +155,7 @@ class DatasetManagerTestCase(BaseTestCase):
         self.log("should be able to create a new Dataset and give it private permissions")
         owner = self.user_manager.create(**user2_data)
         owner_private_role = self.user_manager.private_role(owner)
-        dataset = self.dataset_manager.create(
-            manage_roles=[owner_private_role], access_roles=[owner_private_role])
+        dataset = self.dataset_manager.create(manage_roles=[owner_private_role], access_roles=[owner_private_role])
 
         permissions = self.dataset_manager.permissions.get(dataset)
         self.assertIsInstance(permissions, tuple)
@@ -189,7 +190,6 @@ class DatasetManagerTestCase(BaseTestCase):
 
 # =============================================================================
 class DatasetRBACPermissionsTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.dataset_manager = DatasetManager(self.app)
@@ -205,14 +205,13 @@ class DatasetRBACPermissionsTestCase(BaseTestCase):
 # =============================================================================
 # web.url_for doesn't work well in the framework
 def testable_url_for(*a, **k):
-    return f'(fake url): {a}, {k}'
+    return f"(fake url): {a}, {k}"
 
 
 DatasetSerializer.url_for = staticmethod(testable_url_for)
 
 
 class DatasetSerializerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.dataset_manager = DatasetManager(self.app)
@@ -222,51 +221,54 @@ class DatasetSerializerTestCase(BaseTestCase):
     def test_views(self):
         dataset = self.dataset_manager.create()
 
-        self.log('should have a summary view')
-        summary_view = self.dataset_serializer.serialize_to_view(dataset, view='summary')
-        self.assertKeys(summary_view, self.dataset_serializer.views['summary'])
+        self.log("should have a summary view")
+        summary_view = self.dataset_serializer.serialize_to_view(dataset, view="summary")
+        self.assertKeys(summary_view, self.dataset_serializer.views["summary"])
 
-        self.log('should have the summary view as default view')
-        self.dataset_serializer.serialize_to_view(dataset, default_view='summary')
-        self.assertKeys(summary_view, self.dataset_serializer.views['summary'])
+        self.log("should have the summary view as default view")
+        self.dataset_serializer.serialize_to_view(dataset, default_view="summary")
+        self.assertKeys(summary_view, self.dataset_serializer.views["summary"])
 
-        self.log('should have a serializer for all serializable keys')
+        self.log("should have a serializer for all serializable keys")
         for key in self.dataset_serializer.serializable_keyset:
             instantiated_attribute = getattr(dataset, key, None)
-            if not ((key in self.dataset_serializer.serializers)
-                    or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
-                self.fail(f'no serializer for: {key} ({instantiated_attribute})')
+            if not (
+                (key in self.dataset_serializer.serializers)
+                or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
+            ):
+                self.fail(f"no serializer for: {key} ({instantiated_attribute})")
         else:
-            self.assertTrue(True, 'all serializable keys have a serializer')
+            self.assertTrue(True, "all serializable keys have a serializer")
 
     def test_views_and_keys(self):
         dataset = self.dataset_manager.create()
 
-        self.log('should be able to use keys with views')
-        serialized = self.dataset_serializer.serialize_to_view(dataset,
+        self.log("should be able to use keys with views")
+        serialized = self.dataset_serializer.serialize_to_view(
+            dataset,
             # file_name is exposed using app.config.expose_dataset_path = True
-            view='summary', keys=['file_name'])
-        self.assertKeys(serialized,
-            self.dataset_serializer.views['summary'] + ['file_name'])
+            view="summary",
+            keys=["file_name"],
+        )
+        self.assertKeys(serialized, self.dataset_serializer.views["summary"] + ["file_name"])
 
-        self.log('should be able to use keys on their own')
-        serialized = self.dataset_serializer.serialize_to_view(dataset,
-            keys=['purgable', 'file_size'])
-        self.assertKeys(serialized, ['purgable', 'file_size'])
+        self.log("should be able to use keys on their own")
+        serialized = self.dataset_serializer.serialize_to_view(dataset, keys=["purgable", "file_size"])
+        self.assertKeys(serialized, ["purgable", "file_size"])
 
     def test_serialize_permissions(self):
         dataset = self.dataset_manager.create()
         who_manages = self.user_manager.create(**user2_data)
         self.dataset_manager.permissions.manage.grant(dataset, who_manages)
 
-        self.log('serialized permissions should be returned for the user who can manage and be well formed')
-        permissions = self.dataset_serializer.serialize_permissions(dataset, 'perms', user=who_manages)
+        self.log("serialized permissions should be returned for the user who can manage and be well formed")
+        permissions = self.dataset_serializer.serialize_permissions(dataset, "perms", user=who_manages)
         self.assertIsInstance(permissions, dict)
-        self.assertKeys(permissions, ['manage', 'access'])
-        self.assertIsInstance(permissions['manage'], list)
-        self.assertIsInstance(permissions['access'], list)
+        self.assertKeys(permissions, ["manage", "access"])
+        self.assertIsInstance(permissions["manage"], list)
+        self.assertIsInstance(permissions["access"], list)
 
-        manage_perms = permissions['manage']
+        manage_perms = permissions["manage"]
         self.assertTrue(len(manage_perms) == 1)
         role_id = manage_perms[0]
         self.assertEncodedId(role_id)
@@ -274,19 +276,19 @@ class DatasetSerializerTestCase(BaseTestCase):
         role = self.role_manager.get(self.trans, role_id)
         self.assertTrue(who_manages in [user_role.user for user_role in role.users])
 
-        self.log('permissions should be not returned for non-managing users')
+        self.log("permissions should be not returned for non-managing users")
         not_my_supervisor = self.user_manager.create(**user3_data)
-        self.assertRaises(SkipAttribute, self.dataset_serializer.serialize_permissions,
-            dataset, 'perms', user=not_my_supervisor)
+        self.assertRaises(
+            SkipAttribute, self.dataset_serializer.serialize_permissions, dataset, "perms", user=not_my_supervisor
+        )
 
-        self.log('permissions should not be returned for anon users')
-        self.assertRaises(SkipAttribute, self.dataset_serializer.serialize_permissions,
-            dataset, 'perms', user=None)
+        self.log("permissions should not be returned for anon users")
+        self.assertRaises(SkipAttribute, self.dataset_serializer.serialize_permissions, dataset, "perms", user=None)
 
-        self.log('permissions should be returned for admin users')
-        permissions = self.dataset_serializer.serialize_permissions(dataset, 'perms', user=self.admin_user)
+        self.log("permissions should be returned for admin users")
+        permissions = self.dataset_serializer.serialize_permissions(dataset, "perms", user=self.admin_user)
         self.assertIsInstance(permissions, dict)
-        self.assertKeys(permissions, ['manage', 'access'])
+        self.assertKeys(permissions, ["manage", "access"])
 
     def test_serializers(self):
         # self.user_manager.create( **user2_data )
@@ -294,22 +296,22 @@ class DatasetSerializerTestCase(BaseTestCase):
         all_keys = list(self.dataset_serializer.serializable_keyset)
         serialized = self.dataset_serializer.serialize(dataset, all_keys)
 
-        self.log('everything serialized should be of the proper type')
-        self.assertEncodedId(serialized['id'])
-        self.assertDate(serialized['create_time'])
-        self.assertDate(serialized['update_time'])
+        self.log("everything serialized should be of the proper type")
+        self.assertEncodedId(serialized["id"])
+        self.assertDate(serialized["create_time"])
+        self.assertDate(serialized["update_time"])
 
-        self.assertUUID(serialized['uuid'])
-        self.assertIsInstance(serialized['state'], str)
-        self.assertIsInstance(serialized['deleted'], bool)
-        self.assertIsInstance(serialized['purged'], bool)
-        self.assertIsInstance(serialized['purgable'], bool)
+        self.assertUUID(serialized["uuid"])
+        self.assertIsInstance(serialized["state"], str)
+        self.assertIsInstance(serialized["deleted"], bool)
+        self.assertIsInstance(serialized["purged"], bool)
+        self.assertIsInstance(serialized["purgable"], bool)
 
         # # TODO: no great way to do these with mocked dataset
         # self.assertIsInstance( serialized[ 'file_size' ], int )
         # self.assertIsInstance( serialized[ 'total_size' ], int )
 
-        self.log('serialized should jsonify well')
+        self.log("serialized should jsonify well")
         self.assertIsJsonifyable(serialized)
 
 
@@ -322,6 +324,6 @@ class DatasetSerializerTestCase(BaseTestCase):
 #   DatasetAssociationFilterParser
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_HDAManager.py b/test/unit/app/managers/test_HDAManager.py
index bdf491c1de1..b3377c7f026 100644
--- a/test/unit/app/managers/test_HDAManager.py
+++ b/test/unit/app/managers/test_HDAManager.py
@@ -2,21 +2,23 @@ import unittest
 
 import sqlalchemy
 
-from galaxy import exceptions, model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.managers import hdas
 from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.histories import HistoryManager
 from .base import BaseTestCase
 
 # =============================================================================
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
 
 
 # =============================================================================
 class HDATestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.hda_manager = self.app[hdas.HDAManager]
@@ -26,18 +28,17 @@ class HDATestCase(BaseTestCase):
     def _create_vanilla_hda(self, user_data=None):
         user_data = user_data or user2_data
         owner = self.user_manager.create(**user_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         return self.hda_manager.create(history=history1, dataset=dataset1)
 
 
 # =============================================================================
 class HDAManagerTestCase(HDATestCase):
-
     def test_base(self):
         hda_model = model.HistoryDatasetAssociation
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         hda1 = self.hda_manager.create(history=history1, hid=1)
         hda2 = self.hda_manager.create(history=history1, hid=2)
         hda3 = self.hda_manager.create(history=history1, hid=3)
@@ -58,13 +59,12 @@ class HDAManagerTestCase(HDATestCase):
         self.assertEqual(self.hda_manager.list(offset=3), [])
 
         self.log("should be able to order")
-        self.assertEqual(self.hda_manager.list(order_by=sqlalchemy.desc(hda_model.create_time)),
-            [hda3, hda2, hda1])
+        self.assertEqual(self.hda_manager.list(order_by=sqlalchemy.desc(hda_model.create_time)), [hda3, hda2, hda1])
 
     def test_create(self):
         owner = self.user_manager.create(**user2_data)
 
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
 
         self.log("should be able to create a new HDA with a specified history and dataset")
@@ -91,30 +91,30 @@ class HDAManagerTestCase(HDATestCase):
 
     def test_hda_tags(self):
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         hda1 = self.hda_manager.create(history=history1, dataset=dataset1)
 
         self.log("should be able to set tags on an hda")
-        tags_to_set = ['tag-one', 'tag-two']
+        tags_to_set = ["tag-one", "tag-two"]
         self.hda_manager.set_tags(hda1, tags_to_set, user=owner)
         tag_str_array = self.hda_manager.get_tags(hda1)
         self.assertEqual(sorted(tags_to_set), sorted(tag_str_array))
 
     def test_hda_annotation(self):
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         hda1 = self.hda_manager.create(history=history1, dataset=dataset1)
 
         self.log("should be able to set annotation on an hda")
-        annotation = 'an annotation or анотація'
+        annotation = "an annotation or анотація"
         self.hda_manager.annotate(hda1, annotation, user=owner)
         self.assertEqual(self.hda_manager.annotation(hda1), annotation)
 
     def test_copy_from_hda(self):
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         hda1 = self.hda_manager.create(history=history1, dataset=dataset1)
 
@@ -129,7 +129,7 @@ class HDAManagerTestCase(HDATestCase):
 
         self.log("tags should be copied between HDAs")
         tagged = self.hda_manager.create(history=history1, dataset=self.dataset_manager.create())
-        tags_to_set = ['tag-one', 'tag-two']
+        tags_to_set = ["tag-one", "tag-two"]
         self.hda_manager.set_tags(tagged, tags_to_set, user=owner)
 
         hda2 = self.hda_manager.copy(tagged, history=history1)
@@ -138,7 +138,7 @@ class HDAManagerTestCase(HDATestCase):
 
         self.log("annotations should be copied between HDAs")
         annotated = self.hda_manager.create(history=history1, dataset=self.dataset_manager.create())
-        annotation = '( ͡° ͜ʖ ͡°)'
+        annotation = "( ͡° ͜ʖ ͡°)"
         self.hda_manager.annotate(annotated, annotation, user=owner)
 
         hda3 = self.hda_manager.copy(annotated, history=history1)
@@ -154,7 +154,7 @@ class HDAManagerTestCase(HDATestCase):
 
     def test_delete(self):
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history=history1, dataset=dataset1)
 
@@ -169,7 +169,7 @@ class HDAManagerTestCase(HDATestCase):
         self.trans.app.config.allow_user_dataset_purge = True
 
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history=history1, dataset=dataset1)
 
@@ -183,7 +183,7 @@ class HDAManagerTestCase(HDATestCase):
         self.trans.app.config.allow_user_dataset_purge = False
 
         owner = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history=history1, dataset=dataset1)
 
@@ -197,7 +197,7 @@ class HDAManagerTestCase(HDATestCase):
         owner = self.user_manager.create(**user2_data)
         non_owner = self.user_manager.create(**user3_data)
 
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history1, dataset1)
 
@@ -206,12 +206,10 @@ class HDAManagerTestCase(HDATestCase):
         self.assertFalse(self.hda_manager.is_owner(item1, non_owner))
 
         self.log("should raise an error when checking ownership with non-owner")
-        self.assertRaises(exceptions.ItemOwnershipException,
-            self.hda_manager.error_unless_owner, item1, non_owner)
+        self.assertRaises(exceptions.ItemOwnershipException, self.hda_manager.error_unless_owner, item1, non_owner)
 
         self.log("should raise an error when checking ownership with anonymous")
-        self.assertRaises(exceptions.ItemOwnershipException,
-            self.hda_manager.error_unless_owner, item1, None)
+        self.assertRaises(exceptions.ItemOwnershipException, self.hda_manager.error_unless_owner, item1, None)
 
         self.log("should not raise an error when checking ownership with owner")
         self.assertEqual(self.hda_manager.error_unless_owner(item1, owner), item1)
@@ -223,7 +221,7 @@ class HDAManagerTestCase(HDATestCase):
         owner = self.user_manager.create(**user2_data)
         non_owner = self.user_manager.create(**user3_data)
 
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history1, dataset1)
 
@@ -238,33 +236,52 @@ class HDAManagerTestCase(HDATestCase):
         accessible = self.hda_manager.get_accessible(item1.id, owner, current_history=self.trans.history)
         self.assertEqual(accessible, item1)
 
-        self.log("after setting a dataset to private (one user) permissions, "
-            + "access should be not allowed for other users")
-        self.assertRaises(exceptions.ItemAccessibilityException,
-            self.hda_manager.get_accessible, item1.id, non_owner, current_history=self.trans.history)
+        self.log(
+            "after setting a dataset to private (one user) permissions, "
+            + "access should be not allowed for other users"
+        )
+        self.assertRaises(
+            exceptions.ItemAccessibilityException,
+            self.hda_manager.get_accessible,
+            item1.id,
+            non_owner,
+            current_history=self.trans.history,
+        )
 
-        self.log("a copy of a restricted dataset in another users history should be inaccessible even to "
-            + "the histories owner")
-        history2 = self.history_manager.create(name='history2', user=non_owner)
+        self.log(
+            "a copy of a restricted dataset in another users history should be inaccessible even to "
+            + "the histories owner"
+        )
+        history2 = self.history_manager.create(name="history2", user=non_owner)
         self.trans.set_history(history2)
         item2 = self.hda_manager.copy(item1, history=history2)
         self.assertIsInstance(item2, model.HistoryDatasetAssociation)
-        self.assertRaises(exceptions.ItemAccessibilityException,
-            self.hda_manager.get_accessible, item2.id, non_owner, current_history=self.trans.history)
+        self.assertRaises(
+            exceptions.ItemAccessibilityException,
+            self.hda_manager.get_accessible,
+            item2.id,
+            non_owner,
+            current_history=self.trans.history,
+        )
 
         self.log("a restricted dataset cannot be accessed by anonymous users")
         anon_user = None
         self.trans.set_user(anon_user)
-        history3 = self.history_manager.create(name='anon_history', user=anon_user)
+        history3 = self.history_manager.create(name="anon_history", user=anon_user)
         self.trans.set_history(history3)
-        self.assertRaises(exceptions.ItemAccessibilityException,
-            self.hda_manager.get_accessible, item1.id, anon_user, current_history=self.trans.history)
+        self.assertRaises(
+            exceptions.ItemAccessibilityException,
+            self.hda_manager.get_accessible,
+            item1.id,
+            anon_user,
+            current_history=self.trans.history,
+        )
 
     def test_anon_ownership(self):
         anon_user = None
         self.trans.set_user(anon_user)
 
-        history1 = self.history_manager.create(name='anon_history', user=anon_user)
+        history1 = self.history_manager.create(name="anon_history", user=anon_user)
         self.trans.set_history(history1)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history1, dataset1)
@@ -280,16 +297,14 @@ class HDAManagerTestCase(HDATestCase):
         self.log("should raise an error when checking ownership on anonymous' dataset with other user")
         non_owner = self.user_manager.create(**user3_data)
         self.assertFalse(self.hda_manager.is_owner(item1, non_owner))
-        self.assertRaises(exceptions.ItemOwnershipException,
-            self.hda_manager.error_unless_owner, item1, non_owner)
-        self.assertRaises(exceptions.ItemOwnershipException,
-            self.hda_manager.get_owned, item1.id, non_owner)
+        self.assertRaises(exceptions.ItemOwnershipException, self.hda_manager.error_unless_owner, item1, non_owner)
+        self.assertRaises(exceptions.ItemOwnershipException, self.hda_manager.get_owned, item1.id, non_owner)
 
     def test_anon_accessibility(self):
         anon_user = None
         self.trans.set_user(anon_user)
 
-        history1 = self.history_manager.create(name='anon_history', user=anon_user)
+        history1 = self.history_manager.create(name="anon_history", user=anon_user)
         self.trans.set_history(history1)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history1, dataset1)
@@ -300,14 +315,19 @@ class HDAManagerTestCase(HDATestCase):
         dataset_owner = self.user_manager.create(**user3_data)
         self.dataset_manager.permissions.set_private_to_one_user(dataset1, dataset_owner)
 
-        self.log("anonymous users should not be able to access datasets within their own histories if "
-            + "permissions do not allow")
+        self.log(
+            "anonymous users should not be able to access datasets within their own histories if "
+            + "permissions do not allow"
+        )
         self.assertFalse(self.hda_manager.is_accessible(item1, anon_user))
-        self.assertRaises(exceptions.ItemAccessibilityException,
-            self.hda_manager.error_unless_accessible, item1, anon_user)
+        self.assertRaises(
+            exceptions.ItemAccessibilityException, self.hda_manager.error_unless_accessible, item1, anon_user
+        )
 
-        self.log("those users with access permissions should still be allowed access to datasets "
-            + "within anon users' histories")
+        self.log(
+            "those users with access permissions should still be allowed access to datasets "
+            + "within anon users' histories"
+        )
         self.assertTrue(self.hda_manager.is_accessible(item1, dataset_owner))
 
     def test_error_if_uploading(self):
@@ -319,21 +339,17 @@ class HDAManagerTestCase(HDATestCase):
 
         hda.state = model.Dataset.states.UPLOAD
         self.log("should raise an error when calling error_if_uploading and in the uploading state")
-        self.assertRaises(exceptions.Conflict,
-            self.hda_manager.error_if_uploading, hda)
+        self.assertRaises(exceptions.Conflict, self.hda_manager.error_if_uploading, hda)
 
     def test_data_conversion_status(self):
         hda = self._create_vanilla_hda()
 
         self.log("data conversion status should reflect state")
-        self.assertEqual(self.hda_manager.data_conversion_status(None),
-            hda.conversion_messages.NO_DATA)
+        self.assertEqual(self.hda_manager.data_conversion_status(None), hda.conversion_messages.NO_DATA)
         hda.state = model.Dataset.states.ERROR
-        self.assertEqual(self.hda_manager.data_conversion_status(hda),
-            hda.conversion_messages.ERROR)
+        self.assertEqual(self.hda_manager.data_conversion_status(hda), hda.conversion_messages.ERROR)
         hda.state = model.Dataset.states.QUEUED
-        self.assertEqual(self.hda_manager.data_conversion_status(hda),
-            hda.conversion_messages.PENDING)
+        self.assertEqual(self.hda_manager.data_conversion_status(hda), hda.conversion_messages.PENDING)
         hda.state = model.Dataset.states.OK
         self.assertEqual(self.hda_manager.data_conversion_status(hda), None)
 
@@ -343,14 +359,13 @@ class HDAManagerTestCase(HDATestCase):
 # =============================================================================
 # web.url_for doesn't work well in the framework
 def testable_url_for(*a, **k):
-    return f'(fake url): {a}, {k}'
+    return f"(fake url): {a}, {k}"
 
 
 hdas.HDASerializer.url_for = staticmethod(testable_url_for)
 
 
 class HDASerializerTestCase(HDATestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.hda_serializer = hdas.HDASerializer(self.app)
@@ -358,13 +373,13 @@ class HDASerializerTestCase(HDATestCase):
     def test_views(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should have a summary view')
-        summary_view = self.hda_serializer.serialize_to_view(hda, view='summary')
-        self.assertKeys(summary_view, self.hda_serializer.views['summary'])
+        self.log("should have a summary view")
+        summary_view = self.hda_serializer.serialize_to_view(hda, view="summary")
+        self.assertKeys(summary_view, self.hda_serializer.views["summary"])
 
-        self.log('should have the summary view as default view')
-        default_view = self.hda_serializer.serialize_to_view(hda, default_view='summary')
-        self.assertKeys(default_view, self.hda_serializer.views['summary'])
+        self.log("should have the summary view as default view")
+        default_view = self.hda_serializer.serialize_to_view(hda, default_view="summary")
+        self.assertKeys(default_view, self.hda_serializer.views["summary"])
 
         # self.log( 'should have a detailed view' )
         # detailed_view = self.hda_serializer.serialize_to_view( hda, view='detailed' )
@@ -374,144 +389,143 @@ class HDASerializerTestCase(HDATestCase):
         # extended_view = self.hda_serializer.serialize_to_view( hda, view='extended' )
         # self.assertKeys( extended_view, self.hda_serializer.views[ 'extended' ] )
 
-        self.log('should have a inaccessible view')
-        inaccessible_view = self.hda_serializer.serialize_to_view(hda, view='inaccessible')
-        self.assertKeys(inaccessible_view, self.hda_serializer.views['inaccessible'])
+        self.log("should have a inaccessible view")
+        inaccessible_view = self.hda_serializer.serialize_to_view(hda, view="inaccessible")
+        self.assertKeys(inaccessible_view, self.hda_serializer.views["inaccessible"])
 
         # skip metadata for this test
         def is_metadata(key):
-            return (key == 'metadata'
-                or key.startswith('metadata_'))
+            return key == "metadata" or key.startswith("metadata_")
 
-        self.log('should have a serializer for all serializable keys')
+        self.log("should have a serializer for all serializable keys")
         for key in self.hda_serializer.serializable_keyset:
             instantiated_attribute = getattr(hda, key, None)
-            if not ((key in self.hda_serializer.serializers)
-                   or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
-                   or (is_metadata(key))):
-                self.fail(f'no serializer for: {key} ({instantiated_attribute})')
+            if not (
+                (key in self.hda_serializer.serializers)
+                or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
+                or (is_metadata(key))
+            ):
+                self.fail(f"no serializer for: {key} ({instantiated_attribute})")
         else:
-            self.assertTrue(True, 'all serializable keys have a serializer')
+            self.assertTrue(True, "all serializable keys have a serializer")
 
     def test_views_and_keys(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should be able to use keys with views')
-        serialized = self.hda_serializer.serialize_to_view(hda,
-            view='summary', keys=['uuid'])
-        self.assertKeys(serialized,
-            self.hda_serializer.views['summary'] + ['uuid'])
+        self.log("should be able to use keys with views")
+        serialized = self.hda_serializer.serialize_to_view(hda, view="summary", keys=["uuid"])
+        self.assertKeys(serialized, self.hda_serializer.views["summary"] + ["uuid"])
 
-        self.log('should be able to use keys on their own')
-        serialized = self.hda_serializer.serialize_to_view(hda,
-            keys=['file_path', 'visualizations'])
-        self.assertKeys(serialized, ['file_path', 'visualizations'])
+        self.log("should be able to use keys on their own")
+        serialized = self.hda_serializer.serialize_to_view(hda, keys=["file_path", "visualizations"])
+        self.assertKeys(serialized, ["file_path", "visualizations"])
 
     def test_serializers(self):
         hda = self._create_vanilla_hda()
         all_keys = list(self.hda_serializer.serializable_keyset)
         serialized = self.hda_serializer.serialize(hda, all_keys, user=hda.history.user)
 
-        self.log('everything serialized should be of the proper type')
+        self.log("everything serialized should be of the proper type")
         # base
-        self.assertEncodedId(serialized['id'])
-        self.assertDate(serialized['create_time'])
-        self.assertDate(serialized['update_time'])
+        self.assertEncodedId(serialized["id"])
+        self.assertDate(serialized["create_time"])
+        self.assertDate(serialized["update_time"])
 
         # dataset association
-        self.assertIsInstance(serialized['dataset'], dict)
-        self.assertEncodedId(serialized['dataset_id'])
-        self.assertUUID(serialized['uuid'])
-        self.assertIsInstance(serialized['file_name'], str)
-        self.assertIsInstance(serialized['extra_files_path'], str)
-        self.assertIsInstance(serialized['size'], int)
-        self.assertIsInstance(serialized['file_size'], int)
-        self.assertIsInstance(serialized['nice_size'], str)
+        self.assertIsInstance(serialized["dataset"], dict)
+        self.assertEncodedId(serialized["dataset_id"])
+        self.assertUUID(serialized["uuid"])
+        self.assertIsInstance(serialized["file_name"], str)
+        self.assertIsInstance(serialized["extra_files_path"], str)
+        self.assertIsInstance(serialized["size"], int)
+        self.assertIsInstance(serialized["file_size"], int)
+        self.assertIsInstance(serialized["nice_size"], str)
         # TODO: these should be tested w/copy
-        self.assertNullableEncodedId(serialized['copied_from_history_dataset_association_id'])
-        self.assertNullableEncodedId(serialized['copied_from_library_dataset_dataset_association_id'])
-        self.assertNullableBasestring(serialized['info'])
-        self.assertNullableBasestring(serialized['blurb'])
-        self.assertNullableBasestring(serialized['peek'])
-        self.assertIsInstance(serialized['meta_files'], list)
-        self.assertNullableEncodedId(serialized['parent_id'])
-        self.assertEqual(serialized['designation'], None)
-        self.assertIsInstance(serialized['genome_build'], str)
-        self.assertIsInstance(serialized['data_type'], str)
+        self.assertNullableEncodedId(serialized["copied_from_history_dataset_association_id"])
+        self.assertNullableEncodedId(serialized["copied_from_library_dataset_dataset_association_id"])
+        self.assertNullableBasestring(serialized["info"])
+        self.assertNullableBasestring(serialized["blurb"])
+        self.assertNullableBasestring(serialized["peek"])
+        self.assertIsInstance(serialized["meta_files"], list)
+        self.assertNullableEncodedId(serialized["parent_id"])
+        self.assertEqual(serialized["designation"], None)
+        self.assertIsInstance(serialized["genome_build"], str)
+        self.assertIsInstance(serialized["data_type"], str)
 
         # hda
-        self.assertEncodedId(serialized['history_id'])
-        self.assertEqual(serialized['type_id'], 'dataset-' + serialized['id'])
+        self.assertEncodedId(serialized["history_id"])
+        self.assertEqual(serialized["type_id"], "dataset-" + serialized["id"])
 
-        self.assertIsInstance(serialized['resubmitted'], bool)
-        self.assertIsInstance(serialized['display_apps'], list)
-        self.assertIsInstance(serialized['display_types'], list)
-        self.assertIsInstance(serialized['visualizations'], list)
+        self.assertIsInstance(serialized["resubmitted"], bool)
+        self.assertIsInstance(serialized["display_apps"], list)
+        self.assertIsInstance(serialized["display_types"], list)
+        self.assertIsInstance(serialized["visualizations"], list)
 
         # remapped
-        self.assertNullableBasestring(serialized['misc_info'])
-        self.assertNullableBasestring(serialized['misc_blurb'])
-        self.assertNullableBasestring(serialized['file_ext'])
-        self.assertNullableBasestring(serialized['file_path'])
+        self.assertNullableBasestring(serialized["misc_info"])
+        self.assertNullableBasestring(serialized["misc_blurb"])
+        self.assertNullableBasestring(serialized["file_ext"])
+        self.assertNullableBasestring(serialized["file_path"])
 
         # identities
-        self.assertEqual(serialized['model_class'], 'HistoryDatasetAssociation')
-        self.assertEqual(serialized['history_content_type'], 'dataset')
-        self.assertEqual(serialized['hda_ldda'], 'hda')
-        self.assertEqual(serialized['accessible'], True)
-        self.assertEqual(serialized['api_type'], 'file')
-        self.assertEqual(serialized['type'], 'file')
+        self.assertEqual(serialized["model_class"], "HistoryDatasetAssociation")
+        self.assertEqual(serialized["history_content_type"], "dataset")
+        self.assertEqual(serialized["hda_ldda"], "hda")
+        self.assertEqual(serialized["accessible"], True)
+        self.assertEqual(serialized["api_type"], "file")
+        self.assertEqual(serialized["type"], "file")
 
-        self.assertIsInstance(serialized['url'], str)
-        self.assertIsInstance(serialized['urls'], dict)
-        self.assertIsInstance(serialized['download_url'], str)
+        self.assertIsInstance(serialized["url"], str)
+        self.assertIsInstance(serialized["urls"], dict)
+        self.assertIsInstance(serialized["download_url"], str)
 
-        self.log('serialized should jsonify well')
+        self.log("serialized should jsonify well")
         self.assertIsJsonifyable(serialized)
 
     def test_file_name_serializers(self):
         hda = self._create_vanilla_hda()
         owner = hda.history.user
-        keys = ['file_name']
+        keys = ["file_name"]
 
-        self.log('file_name should be included if app configured to do so')
+        self.log("file_name should be included if app configured to do so")
         # this is on by default in galaxy_mock
         self.assertTrue(self.app.config.expose_dataset_path)
         # ... so non-admin user CAN get file_name
         serialized = self.hda_serializer.serialize(hda, keys, user=None)
-        self.assertTrue('file_name' in serialized)
+        self.assertTrue("file_name" in serialized)
         serialized = self.hda_serializer.serialize(hda, keys, user=owner)
-        self.assertTrue('file_name' in serialized)
+        self.assertTrue("file_name" in serialized)
 
-        self.log('file_name should be skipped for non-admin when not exposed by config')
+        self.log("file_name should be skipped for non-admin when not exposed by config")
         self.app.config.expose_dataset_path = False
         serialized = self.hda_serializer.serialize(hda, keys, user=None)
-        self.assertFalse('file_name' in serialized)
+        self.assertFalse("file_name" in serialized)
         serialized = self.hda_serializer.serialize(hda, keys, user=owner)
-        self.assertFalse('file_name' in serialized)
+        self.assertFalse("file_name" in serialized)
 
-        self.log('file_name should be sent for admin in either case')
+        self.log("file_name should be sent for admin in either case")
         serialized = self.hda_serializer.serialize(hda, keys, user=self.admin_user)
-        self.assertTrue('file_name' in serialized)
+        self.assertTrue("file_name" in serialized)
         self.app.config.expose_dataset_path = True
         serialized = self.hda_serializer.serialize(hda, keys, user=self.admin_user)
-        self.assertTrue('file_name' in serialized)
+        self.assertTrue("file_name" in serialized)
 
     def test_serializing_inaccessible(self):
         owner = self.user_manager.create(**user2_data)
         non_owner = self.user_manager.create(**user3_data)
 
-        history1 = self.history_manager.create(name='history1', user=owner)
+        history1 = self.history_manager.create(name="history1", user=owner)
         dataset1 = self.dataset_manager.create()
         item1 = self.hda_manager.create(history1, dataset1)
 
-        keys_in_inaccessible_view = self.hda_serializer._view_to_keys('inaccessible')
+        keys_in_inaccessible_view = self.hda_serializer._view_to_keys("inaccessible")
 
-        self.log('file_name should be included if app configured to do so')
+        self.log("file_name should be included if app configured to do so")
         self.dataset_manager.permissions.set_private_to_one_user(dataset1, owner)
         # request random crap
-        serialized = self.hda_serializer.serialize_to_view(item1, view='detailed',
-            keys=['file_path', 'visualizations'], user=non_owner)
+        serialized = self.hda_serializer.serialize_to_view(
+            item1, view="detailed", keys=["file_path", "visualizations"], user=non_owner
+        )
         self.assertEqual(sorted(keys_in_inaccessible_view), sorted(serialized.keys()))
 
     # TODO: test extra_files_path as well
@@ -519,7 +533,6 @@ class HDASerializerTestCase(HDATestCase):
 
 # =============================================================================
 class HDADeserializerTestCase(HDATestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.hda_deserializer = hdas.HDADeserializer(self.app)
@@ -527,46 +540,49 @@ class HDADeserializerTestCase(HDATestCase):
     def test_deserialize_delete(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should raise when deserializing deleted from non-bool')
+        self.log("should raise when deserializing deleted from non-bool")
         self.assertFalse(hda.deleted)
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'deleted': None})
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"deleted": None}
+        )
         self.assertFalse(hda.deleted)
-        self.log('should be able to deserialize deleted from True')
-        self.hda_deserializer.deserialize(hda, {'deleted': True})
+        self.log("should be able to deserialize deleted from True")
+        self.hda_deserializer.deserialize(hda, {"deleted": True})
         self.assertTrue(hda.deleted)
-        self.log('should be able to reverse by deserializing deleted from False')
-        self.hda_deserializer.deserialize(hda, {'deleted': False})
+        self.log("should be able to reverse by deserializing deleted from False")
+        self.hda_deserializer.deserialize(hda, {"deleted": False})
         self.assertFalse(hda.deleted)
 
     def test_deserialize_purge(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should raise when deserializing purged from non-bool')
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'purged': None})
+        self.log("should raise when deserializing purged from non-bool")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"purged": None}
+        )
         self.assertFalse(hda.purged)
-        self.log('should be able to deserialize purged from True')
-        self.hda_deserializer.deserialize(hda, {'purged': True})
+        self.log("should be able to deserialize purged from True")
+        self.hda_deserializer.deserialize(hda, {"purged": True})
         self.assertTrue(hda.purged)
         # TODO: should this raise an error?
-        self.log('should NOT be able to deserialize purged from False (will remain True)')
-        self.hda_deserializer.deserialize(hda, {'purged': False})
+        self.log("should NOT be able to deserialize purged from False (will remain True)")
+        self.hda_deserializer.deserialize(hda, {"purged": False})
         self.assertTrue(hda.purged)
 
     def test_deserialize_visible(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should raise when deserializing from non-bool')
+        self.log("should raise when deserializing from non-bool")
         self.assertTrue(hda.visible)
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'visible': 'None'})
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"visible": "None"}
+        )
         self.assertTrue(hda.visible)
-        self.log('should be able to deserialize from False')
-        self.hda_deserializer.deserialize(hda, {'visible': False})
+        self.log("should be able to deserialize from False")
+        self.hda_deserializer.deserialize(hda, {"visible": False})
         self.assertFalse(hda.visible)
-        self.log('should be able to reverse by deserializing from True')
-        self.hda_deserializer.deserialize(hda, {'visible': True})
+        self.log("should be able to reverse by deserializing from True")
+        self.hda_deserializer.deserialize(hda, {"visible": True})
         self.assertTrue(hda.visible)
 
     def test_deserialize_genome_build(self):
@@ -574,95 +590,100 @@ class HDADeserializerTestCase(HDATestCase):
 
         self.assertIsInstance(hda.dbkey, str)
         self.log('should deserialize to "?" from None')
-        self.hda_deserializer.deserialize(hda, {'genome_build': None})
-        self.assertEqual(hda.dbkey, '?')
-        self.log('should raise when deserializing from non-string')
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'genome_build': 12})
-        self.log('should be able to deserialize from unicode')
-        date_palm = 'نخيل التمر'
-        self.hda_deserializer.deserialize(hda, {'genome_build': date_palm})
+        self.hda_deserializer.deserialize(hda, {"genome_build": None})
+        self.assertEqual(hda.dbkey, "?")
+        self.log("should raise when deserializing from non-string")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"genome_build": 12}
+        )
+        self.log("should be able to deserialize from unicode")
+        date_palm = "نخيل التمر"
+        self.hda_deserializer.deserialize(hda, {"genome_build": date_palm})
         self.assertEqual(hda.dbkey, date_palm)
-        self.log('should be deserializable from empty string')
-        self.hda_deserializer.deserialize(hda, {'genome_build': ''})
-        self.assertEqual(hda.dbkey, '')
+        self.log("should be deserializable from empty string")
+        self.hda_deserializer.deserialize(hda, {"genome_build": ""})
+        self.assertEqual(hda.dbkey, "")
 
     def test_deserialize_name(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should raise when deserializing from non-string')
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'name': True})
-        self.log('should raise when deserializing from None')
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'name': None})
+        self.log("should raise when deserializing from non-string")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"name": True}
+        )
+        self.log("should raise when deserializing from None")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"name": None}
+        )
         # self.log( 'should deserialize to empty string from None' )
         # self.hda_deserializer.deserialize( hda, { 'name': None } )
         # self.assertEqual( hda.name, '' )
-        self.log('should be able to deserialize from unicode')
-        olive = 'ελιά'
-        self.hda_deserializer.deserialize(hda, {'name': olive})
+        self.log("should be able to deserialize from unicode")
+        olive = "ελιά"
+        self.hda_deserializer.deserialize(hda, {"name": olive})
         self.assertEqual(hda.name, olive)
-        self.log('should be deserializable from empty string')
-        self.hda_deserializer.deserialize(hda, {'name': ''})
-        self.assertEqual(hda.name, '')
+        self.log("should be deserializable from empty string")
+        self.hda_deserializer.deserialize(hda, {"name": ""})
+        self.assertEqual(hda.name, "")
 
     def test_deserialize_info(self):
         hda = self._create_vanilla_hda()
 
-        self.log('should raise when deserializing from non-string')
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'info': True})
-        self.log('should raise when deserializing from None')
-        self.assertRaises(exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, hda, {'info': None})
-        self.log('should be able to deserialize from unicode')
-        rice = '飯'
-        self.hda_deserializer.deserialize(hda, {'info': rice})
+        self.log("should raise when deserializing from non-string")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"info": True}
+        )
+        self.log("should raise when deserializing from None")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException, self.hda_deserializer.deserialize, hda, {"info": None}
+        )
+        self.log("should be able to deserialize from unicode")
+        rice = "飯"
+        self.hda_deserializer.deserialize(hda, {"info": rice})
         self.assertEqual(hda.info, rice)
-        self.log('should be deserializable from empty string')
-        self.hda_deserializer.deserialize(hda, {'info': ''})
-        self.assertEqual(hda.info, '')
+        self.log("should be deserializable from empty string")
+        self.hda_deserializer.deserialize(hda, {"info": ""})
+        self.assertEqual(hda.info, "")
 
 
 # =============================================================================
 class HDAFilterParserTestCase(HDATestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.filter_parser = hdas.HDAFilterParser(self.app)
 
     def test_parsable(self):
-        self.log('the following filters should be parsable')
+        self.log("the following filters should be parsable")
         # base
-        self.assertORMFilter(self.filter_parser.parse_filter('id', 'in', [1, 2]))
-        encoded_id_string = ','.join(self.app.security.encode_id(id_) for id_ in [1, 2])
-        self.assertORMFilter(self.filter_parser.parse_filter('encoded_id', 'in', encoded_id_string))
-        self.assertORMFilter(self.filter_parser.parse_filter('create_time', 'le', '2015-03-15'))
-        self.assertORMFilter(self.filter_parser.parse_filter('create_time', 'ge', '2015-03-15'))
-        self.assertORMFilter(self.filter_parser.parse_filter('update_time', 'le', '2015-03-15'))
-        self.assertORMFilter(self.filter_parser.parse_filter('update_time', 'ge', '2015-03-15'))
+        self.assertORMFilter(self.filter_parser.parse_filter("id", "in", [1, 2]))
+        encoded_id_string = ",".join(self.app.security.encode_id(id_) for id_ in [1, 2])
+        self.assertORMFilter(self.filter_parser.parse_filter("encoded_id", "in", encoded_id_string))
+        self.assertORMFilter(self.filter_parser.parse_filter("create_time", "le", "2015-03-15"))
+        self.assertORMFilter(self.filter_parser.parse_filter("create_time", "ge", "2015-03-15"))
+        self.assertORMFilter(self.filter_parser.parse_filter("update_time", "le", "2015-03-15"))
+        self.assertORMFilter(self.filter_parser.parse_filter("update_time", "ge", "2015-03-15"))
         # purgable
-        self.assertORMFilter(self.filter_parser.parse_filter('deleted', 'eq', True))
-        self.assertORMFilter(self.filter_parser.parse_filter('purged', 'eq', True))
+        self.assertORMFilter(self.filter_parser.parse_filter("deleted", "eq", True))
+        self.assertORMFilter(self.filter_parser.parse_filter("purged", "eq", True))
         # dataset asociation
-        self.assertORMFilter(self.filter_parser.parse_filter('name', 'eq', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('name', 'contains', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('name', 'like', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('state', 'eq', 'ok'))
-        self.assertORMFilter(self.filter_parser.parse_filter('state', 'in', ['queued', 'running']))
-        self.assertORMFilter(self.filter_parser.parse_filter('visible', 'eq', True))
+        self.assertORMFilter(self.filter_parser.parse_filter("name", "eq", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("name", "contains", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("name", "like", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("state", "eq", "ok"))
+        self.assertORMFilter(self.filter_parser.parse_filter("state", "in", ["queued", "running"]))
+        self.assertORMFilter(self.filter_parser.parse_filter("visible", "eq", True))
         # taggable
-        self.assertORMFunctionFilter(self.filter_parser.parse_filter('tag', 'eq', 'wot'))
-        self.assertORMFunctionFilter(self.filter_parser.parse_filter('tag', 'has', 'wot'))
+        self.assertORMFunctionFilter(self.filter_parser.parse_filter("tag", "eq", "wot"))
+        self.assertORMFunctionFilter(self.filter_parser.parse_filter("tag", "has", "wot"))
         # genomebuild
-        self.assertFnFilter(self.filter_parser.parse_filter('genome_build', 'eq', 'wot'))
-        self.assertFnFilter(self.filter_parser.parse_filter('genome_build', 'contains', 'wot'))
+        self.assertFnFilter(self.filter_parser.parse_filter("genome_build", "eq", "wot"))
+        self.assertFnFilter(self.filter_parser.parse_filter("genome_build", "contains", "wot"))
         # data_type
-        self.assertFnFilter(self.filter_parser.parse_filter('data_type', 'eq', 'wot'))
-        self.assertFnFilter(self.filter_parser.parse_filter('data_type', 'isinstance', 'wot'))
+        self.assertFnFilter(self.filter_parser.parse_filter("data_type", "eq", "wot"))
+        self.assertFnFilter(self.filter_parser.parse_filter("data_type", "isinstance", "wot"))
         # annotatable
-        self.assertFnFilter(self.filter_parser.parse_filter('annotation', 'has', 'wot'))
+        self.assertFnFilter(self.filter_parser.parse_filter("annotation", "has", "wot"))
+
 
 #     def test_genome_build_filters( self ):
 #         pass
@@ -672,6 +693,6 @@ class HDAFilterParserTestCase(HDATestCase):
 
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_HDCAManager.py b/test/unit/app/managers/test_HDCAManager.py
index c9a3f250e8b..6566e978e4c 100644
--- a/test/unit/app/managers/test_HDCAManager.py
+++ b/test/unit/app/managers/test_HDCAManager.py
@@ -3,24 +3,23 @@ import unittest
 from galaxy.managers import (
     collections,
     hdas,
-    hdcas
+    hdcas,
 )
 from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.histories import HistoryManager
 from .base import (
     BaseTestCase,
-    CreatesCollectionsMixin
+    CreatesCollectionsMixin,
 )
 
 # =============================================================================
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
 
 
 # =============================================================================
 class HDCATestCase(BaseTestCase, CreatesCollectionsMixin):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.hdca_manager = self.app[hdcas.HDCAManager]
@@ -40,77 +39,75 @@ class HDCATestCase(BaseTestCase, CreatesCollectionsMixin):
         hda = self.hda_manager.create(history=history, dataset=dataset, **kwargs)
         return hda
 
-    def _create_list_hdca(self, hdas, history=None, name='test collection', **kwargs):
+    def _create_list_hdca(self, hdas, history=None, name="test collection", **kwargs):
         if not history:
             history = history or self._create_history()
         for i, hda in enumerate(hdas):
             if not isinstance(hdas, self.hda_manager.model_class):
                 hdas[i] = self._create_hda(history, **hda)
-        hdca = self.collection_manager.create(self.trans, history, name, 'list',
-            element_identifiers=self.build_element_identifiers(hdas))
+        hdca = self.collection_manager.create(
+            self.trans, history, name, "list", element_identifiers=self.build_element_identifiers(hdas)
+        )
         return hdca
 
 
 # =============================================================================
 # web.url_for doesn't work well in the framework
 def testable_url_for(*a, **k):
-    return f'(fake url): {a}, {k}'
+    return f"(fake url): {a}, {k}"
 
 
 hdcas.HDCASerializer.url_for = staticmethod(testable_url_for)
 
 
 class HDCASerializerTestCase(HDCATestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.hdca_serializer = hdcas.HDCASerializer(self.app)
 
     def test_views(self):
         serializer = self.hdca_serializer
-        item = self._create_list_hdca([
-            dict(name=(f"hda-{i}"), hid=i) for i in range(5)
-        ])
+        item = self._create_list_hdca([dict(name=(f"hda-{i}"), hid=i) for i in range(5)])
 
-        self.log('should have a summary view')
-        summary_view = serializer.serialize_to_view(item, view='summary')
-        self.assertKeys(summary_view, serializer.views['summary'])
+        self.log("should have a summary view")
+        summary_view = serializer.serialize_to_view(item, view="summary")
+        self.assertKeys(summary_view, serializer.views["summary"])
 
-        self.log('should have the summary view as default view')
-        default_view = serializer.serialize_to_view(item, default_view='summary')
-        self.assertKeys(default_view, serializer.views['summary'])
+        self.log("should have the summary view as default view")
+        default_view = serializer.serialize_to_view(item, default_view="summary")
+        self.assertKeys(default_view, serializer.views["summary"])
 
-        self.log('should have a detailed view')
-        detailed_view = serializer.serialize_to_view(item, view='detailed')
-        self.assertKeys(detailed_view, serializer.views['detailed'])
+        self.log("should have a detailed view")
+        detailed_view = serializer.serialize_to_view(item, view="detailed")
+        self.assertKeys(detailed_view, serializer.views["detailed"])
 
-        self.log('should have a serializer for all serializable keys')
+        self.log("should have a serializer for all serializable keys")
         for key in serializer.serializable_keyset:
             instantiated_attribute = getattr(item, key, None)
-            if not ((key in serializer.serializers)
-                   or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
-                self.fail(f'no serializer for: {key} ({instantiated_attribute})')
+            if not (
+                (key in serializer.serializers)
+                or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
+            ):
+                self.fail(f"no serializer for: {key} ({instantiated_attribute})")
         else:
-            self.assertTrue(True, 'all serializable keys have a serializer')
+            self.assertTrue(True, "all serializable keys have a serializer")
 
     def test_views_and_keys(self):
         serializer = self.hdca_serializer
-        item = self._create_list_hdca([
-            dict(name=(f"hda-{i}"), hid=i) for i in range(5)
-        ])
-        summary_plus_key = ['elements']
-        only_keys = ['id', 'populated_state_message']
+        item = self._create_list_hdca([dict(name=(f"hda-{i}"), hid=i) for i in range(5)])
+        summary_plus_key = ["elements"]
+        only_keys = ["id", "populated_state_message"]
 
-        self.log('should be able to use keys with views')
-        serialized = serializer.serialize_to_view(item, view='summary', keys=summary_plus_key)
-        self.assertKeys(serialized, serializer.views['summary'] + summary_plus_key)
+        self.log("should be able to use keys with views")
+        serialized = serializer.serialize_to_view(item, view="summary", keys=summary_plus_key)
+        self.assertKeys(serialized, serializer.views["summary"] + summary_plus_key)
 
-        self.log('should be able to use keys on their own')
+        self.log("should be able to use keys on their own")
         serialized = serializer.serialize_to_view(item, keys=only_keys)
         self.assertKeys(serialized, only_keys)
 
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_HistoryContentsManager.py b/test/unit/app/managers/test_HistoryContentsManager.py
index e43ba2d06e2..a3f7313b2dd 100644
--- a/test/unit/app/managers/test_HistoryContentsManager.py
+++ b/test/unit/app/managers/test_HistoryContentsManager.py
@@ -4,23 +4,34 @@ import datetime
 import random
 import unittest
 
-from sqlalchemy import column, desc, false, true
+from sqlalchemy import (
+    column,
+    desc,
+    false,
+    true,
+)
 
-from galaxy.managers import base, collections, hdas, history_contents
+from galaxy.managers import (
+    base,
+    collections,
+    hdas,
+    history_contents,
+)
 from galaxy.managers.histories import HistoryManager
-from .base import BaseTestCase
-from .base import CreatesCollectionsMixin
+from .base import (
+    BaseTestCase,
+    CreatesCollectionsMixin,
+)
 
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
-user4_data = dict(email='user4@user4.user4', username='user4', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
+user4_data = dict(email="user4@user4.user4", username="user4", password=default_password)
 parsed_filter = base.ModelFilterParser.parsed_filter
 
 
 # =============================================================================
 class HistoryAsContainerBaseTestCase(BaseTestCase, CreatesCollectionsMixin):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.history_manager = self.app[HistoryManager]
@@ -34,26 +45,24 @@ class HistoryAsContainerBaseTestCase(BaseTestCase, CreatesCollectionsMixin):
         hda = self.hda_manager.create(history=history, dataset=dataset, **kwargs)
         return hda
 
-    def add_list_collection_to_history(self, history, hdas, name='test collection', **kwargs):
-        hdca = self.collection_manager.create(self.trans,
-                                              history, name, 'list',
-                                              element_identifiers=self.build_element_identifiers(hdas),
-                                              **kwargs)
+    def add_list_collection_to_history(self, history, hdas, name="test collection", **kwargs):
+        hdca = self.collection_manager.create(
+            self.trans, history, name, "list", element_identifiers=self.build_element_identifiers(hdas), **kwargs
+        )
         return hdca
 
 
 # =============================================================================
 class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
-
     def test_contents(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
 
         self.log("calling contents on an empty history should return an empty list")
         self.assertEqual([], list(self.contents_manager.contents(history)))
 
         self.log("calling contents on an history with hdas should return those in order of their hids")
-        hdas = [self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)]
+        hdas = [self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)]
         random.shuffle(hdas)
         ordered_hda_contents = list(self.contents_manager.contents(history))
         self.assertEqual([hda.hid for hda in ordered_hda_contents], [1, 2, 3])
@@ -65,20 +74,20 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
 
     def test_contained(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
 
         self.log("calling contained on an empty history should return an empty list")
         self.assertEqual([], list(self.contents_manager.contained(history)))
 
         self.log("calling contained on an history with both hdas and collections should return only hdas")
-        hdas = [self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)]
+        hdas = [self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)]
         self.add_list_collection_to_history(history, hdas)
         self.assertEqual(list(self.contents_manager.contained(history)), hdas)
 
     def test_copy_elements_on_collection_creation(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
-        hdas = [self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)]
+        history = self.history_manager.create(name="history", user=user2)
+        hdas = [self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)]
         hdca = self.add_list_collection_to_history(history, hdas)
         self.assertEqual(hdas, hdca.dataset_instances)
 
@@ -87,24 +96,24 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
 
     def test_subcontainers(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
 
         self.log("calling subcontainers on an empty history should return an empty list")
         self.assertEqual([], list(self.contents_manager.subcontainers(history)))
 
         self.log("calling subcontainers on an history with both hdas and collections should return only collections")
-        hdas = [self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)]
+        hdas = [self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)]
         hdca = self.add_list_collection_to_history(history, hdas)
         subcontainers = list(self.contents_manager.subcontainers(history))
         self.assertEqual(subcontainers, [hdca])
 
     def test_limit_and_offset(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         contents = []
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)])
         contents.append(self.add_list_collection_to_history(history, contents[:3]))
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(4, 6)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(4, 6)])
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should be able to limit and offset")
@@ -121,11 +130,11 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
     def test_orm_filtering(self):
         parse_filter = self.history_contents_filters.parse_filter
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         contents = []
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)])
         contents.append(self.add_list_collection_to_history(history, contents[:3]))
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(4, 6)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(4, 6)])
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should allow filter on deleted")
@@ -136,15 +145,17 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         self.app.model.context.flush()
 
         # TODO: cross db compat?
-        filters = [parse_filter('deleted', 'eq', 'True')]
+        filters = [parse_filter("deleted", "eq", "True")]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), deleted)
 
         # even stranger that sqlalx can use the first model in the union (HDA) for columns across the union
         HDA = self.hda_manager.model_class
-        self.assertEqual(self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.deleted == true())]), deleted)
-        filter_limited_contents = self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.deleted == true())], limit=2, offset=1)
+        self.assertEqual(
+            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.deleted == true())]), deleted
+        )
+        filter_limited_contents = self.contents_manager.contents(
+            history, filters=[parsed_filter("orm", HDA.deleted == true())], limit=2, offset=1
+        )
         self.assertEqual(filter_limited_contents, deleted[1:])
 
         self.log("should allow filter on visible")
@@ -154,115 +165,133 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         invisible = [contents[2], contents[5], contents[6]]
         self.app.model.context.flush()
 
-        filters = [parse_filter('visible', 'eq', 'False')]
+        filters = [parse_filter("visible", "eq", "False")]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), invisible)
-        self.assertEqual(self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.visible == false())]), invisible)
-        filter_limited_contents = self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.visible == false())], limit=2, offset=1)
+        self.assertEqual(
+            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.visible == false())]), invisible
+        )
+        filter_limited_contents = self.contents_manager.contents(
+            history, filters=[parsed_filter("orm", HDA.visible == false())], limit=2, offset=1
+        )
         self.assertEqual(filter_limited_contents, invisible[1:])
 
         self.log("should allow filtering more than one attribute")
         deleted_and_invisible = [contents[6]]
-        filters = [
-            parse_filter('deleted', 'eq', 'True'),
-            parse_filter('visible', 'eq', 'False')
-        ]
+        filters = [parse_filter("deleted", "eq", "True"), parse_filter("visible", "eq", "False")]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), deleted_and_invisible)
-        self.assertEqual(self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())]), deleted_and_invisible)
-        offset_too_far = self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())], limit=2, offset=1)
+        self.assertEqual(
+            self.contents_manager.contents(
+                history,
+                filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())],
+            ),
+            deleted_and_invisible,
+        )
+        offset_too_far = self.contents_manager.contents(
+            history,
+            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())],
+            limit=2,
+            offset=1,
+        )
         self.assertEqual(offset_too_far, [])
 
         self.log("should allow filtering more than one attribute")
         deleted_and_invisible = [contents[6]]
         # note the two syntaxes both work
-        filters = [
-            parse_filter('deleted', 'eq', 'True'),
-            parse_filter('visible', 'eq', 'False')
-        ]
-        self.assertEqual(self.contents_manager.contents(history,
-            filters=filters), deleted_and_invisible)
-        self.assertEqual(self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())]), deleted_and_invisible)
-        offset_too_far = self.contents_manager.contents(history,
-            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())], limit=2, offset=1)
+        filters = [parse_filter("deleted", "eq", "True"), parse_filter("visible", "eq", "False")]
+        self.assertEqual(self.contents_manager.contents(history, filters=filters), deleted_and_invisible)
+        self.assertEqual(
+            self.contents_manager.contents(
+                history,
+                filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())],
+            ),
+            deleted_and_invisible,
+        )
+        offset_too_far = self.contents_manager.contents(
+            history,
+            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())],
+            limit=2,
+            offset=1,
+        )
         self.assertEqual(offset_too_far, [])
 
         self.log("should allow filtering using like")
         # find 'hda-4'
-        self.assertEqual([contents[4]],
-            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.name.like('%-4'))]))
+        self.assertEqual(
+            [contents[4]], self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.name.like("%-4"))])
+        )
         # the collections added above have the default name 'test collection'
-        self.assertEqual(self.contents_manager.subcontainers(history),
-            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.name.like('%collect%'))]))
+        self.assertEqual(
+            self.contents_manager.subcontainers(history),
+            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.name.like("%collect%"))]),
+        )
 
     def test_order_by(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         contents = []
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)])
         contents.append(self.add_list_collection_to_history(history, contents[:3]))
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(4, 6)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(4, 6)])
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should default to hid order_by")
         self.assertEqual(self.contents_manager.contents(history), contents)
 
         self.log("should allow asc, desc order_by")
-        self.assertEqual(self.contents_manager.contents(history, order_by=desc('hid')), contents[::-1])
+        self.assertEqual(self.contents_manager.contents(history, order_by=desc("hid")), contents[::-1])
 
         def get_create_time(item):
-            create_time = getattr(item, 'create_time', None)
+            create_time = getattr(item, "create_time", None)
             if not create_time:
                 create_time = item.collection.create_time
             return create_time
 
         self.log("should allow create_time order_by")
         newest_first = sorted(contents, key=get_create_time, reverse=True)
-        results = self.contents_manager.contents(history, order_by=desc('create_time'))
+        results = self.contents_manager.contents(history, order_by=desc("create_time"))
         self.assertEqual(newest_first, results)
 
         self.log("should allow update_time order_by")
         # change the oldest created to update the update_time
-        contents[0].name = 'zany and/or wacky'
+        contents[0].name = "zany and/or wacky"
         self.app.model.context.flush()
-        results = self.contents_manager.contents(history, order_by=desc('update_time'))
+        results = self.contents_manager.contents(history, order_by=desc("update_time"))
         self.assertEqual(contents[0], results[0])
 
     def test_update_time_filter(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         contents = []
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)])
         contents.append(self.add_list_collection_to_history(history, contents[:3]))
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(4, 6)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(4, 6)])
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should allow filtering by update_time")
         # change the update_time by updating the name
-        contents[3].name = 'big ball of mud'
+        contents[3].name = "big ball of mud"
         self.app.model.context.flush()
         update_time = contents[3].update_time
 
         def get_update_time(item):
-            update_time = getattr(item, 'update_time', None)
+            update_time = getattr(item, "update_time", None)
             if not update_time:
                 update_time = item.update_time
             return update_time
 
-        results = self.contents_manager.contents(history, filters=[parsed_filter("orm", column('update_time') >= update_time)])
+        results = self.contents_manager.contents(
+            history, filters=[parsed_filter("orm", column("update_time") >= update_time)]
+        )
         self.assertEqual(results, [contents[3]])
 
     def test_filtered_counting(self):
         parse_filter = self.history_contents_filters.parse_filter
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         contents = []
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)])
         contents.append(self.add_list_collection_to_history(history, contents[:3]))
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(4, 6)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(4, 6)])
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should show correct count with filters")
@@ -277,80 +306,81 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         self.app.model.context.flush()
 
         HDA = self.hda_manager.model_class
-        self.assertEqual(self.contents_manager.contents_count(history, filters=[parsed_filter("orm", HDA.deleted == true())]), 3)
-        filters = [parse_filter('visible', 'eq', 'False')]
+        self.assertEqual(
+            self.contents_manager.contents_count(history, filters=[parsed_filter("orm", HDA.deleted == true())]), 3
+        )
+        filters = [parse_filter("visible", "eq", "False")]
         self.assertEqual(self.contents_manager.contents_count(history, filters=filters), 3)
 
-        filters = [
-            parse_filter('deleted', 'eq', 'True'),
-            parse_filter('visible', 'eq', 'False')
-        ]
+        filters = [parse_filter("deleted", "eq", "True"), parse_filter("visible", "eq", "False")]
         self.assertEqual(self.contents_manager.contents_count(history, filters=filters), 1)
 
     def test_type_id(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         contents = []
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(3)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(3)])
         contents.append(self.add_list_collection_to_history(history, contents[:3]))
-        contents.extend([self.add_hda_to_history(history, name=('hda-' + str(x))) for x in range(4, 6)])
+        contents.extend([self.add_hda_to_history(history, name=("hda-" + str(x))) for x in range(4, 6)])
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should be able to use eq and in with hybrid type_id")
-        filters = [parsed_filter("orm", column('type_id') == 'dataset-2')]
+        filters = [parsed_filter("orm", column("type_id") == "dataset-2")]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[1]])
-        filters = [parsed_filter("orm", column('type_id').in_(['dataset-1', 'dataset-3']))]
+        filters = [parsed_filter("orm", column("type_id").in_(["dataset-1", "dataset-3"]))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[0], contents[2]])
-        filters = [parsed_filter("orm", column('type_id') == 'dataset_collection-1')]
+        filters = [parsed_filter("orm", column("type_id") == "dataset_collection-1")]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[3]])
-        filters = [parsed_filter("orm", column('type_id').in_(['dataset-2', 'dataset_collection-2']))]
+        filters = [parsed_filter("orm", column("type_id").in_(["dataset-2", "dataset_collection-2"]))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[1], contents[6]])
 
 
 class HistoryContentsFilterParserTestCase(HistoryAsContainerBaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.filter_parser = history_contents.HistoryContentsFilters(self.app)
 
     def test_date_parser(self):
         # -- seconds and milliseconds from epoch
-        self.log('should be able to parse epoch seconds')
-        self.assertEqual(self.filter_parser.parse_date('1234567890'),
-            datetime.datetime.fromtimestamp(1234567890).isoformat(sep=' '))
+        self.log("should be able to parse epoch seconds")
+        self.assertEqual(
+            self.filter_parser.parse_date("1234567890"), datetime.datetime.fromtimestamp(1234567890).isoformat(sep=" ")
+        )
 
-        self.log('should be able to parse floating point epoch seconds.milliseconds')
-        self.assertEqual(self.filter_parser.parse_date('1234567890.123'),
-            datetime.datetime.fromtimestamp(1234567890.123).isoformat(sep=' '))
+        self.log("should be able to parse floating point epoch seconds.milliseconds")
+        self.assertEqual(
+            self.filter_parser.parse_date("1234567890.123"),
+            datetime.datetime.fromtimestamp(1234567890.123).isoformat(sep=" "),
+        )
 
-        self.log('should error if bad epoch is used')
-        self.assertRaises(ValueError, self.filter_parser.parse_date, '0x000234')
+        self.log("should error if bad epoch is used")
+        self.assertRaises(ValueError, self.filter_parser.parse_date, "0x000234")
 
         # -- datetime strings
-        self.log('should allow date alone')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13'), '2009-02-13')
+        self.log("should allow date alone")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13"), "2009-02-13")
 
-        self.log('should allow date and time')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13 18:13:00'), '2009-02-13 18:13:00')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13T18:13:00'), '2009-02-13 18:13:00')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13T18:13:00Z'), '2009-02-13 18:13:00')
+        self.log("should allow date and time")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13 18:13:00"), "2009-02-13 18:13:00")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13T18:13:00"), "2009-02-13 18:13:00")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13T18:13:00Z"), "2009-02-13 18:13:00")
 
-        self.log('should allow date and time with milliseconds')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13 18:13:00.123'), '2009-02-13 18:13:00.123')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13T18:13:00.123'), '2009-02-13 18:13:00.123')
-        self.assertEqual(self.filter_parser.parse_date('2009-02-13T18:13:00.123Z'), '2009-02-13 18:13:00.123')
+        self.log("should allow date and time with milliseconds")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13 18:13:00.123"), "2009-02-13 18:13:00.123")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13T18:13:00.123"), "2009-02-13 18:13:00.123")
+        self.assertEqual(self.filter_parser.parse_date("2009-02-13T18:13:00.123Z"), "2009-02-13 18:13:00.123")
 
-        self.log('should error if timezone is added')
-        self.assertRaises(ValueError, self.filter_parser.parse_date, '2009-02-13T18:13:00.123+0700')
+        self.log("should error if timezone is added")
+        self.assertRaises(ValueError, self.filter_parser.parse_date, "2009-02-13T18:13:00.123+0700")
 
-        self.log('should error if locale is used')
-        self.assertRaises(ValueError, self.filter_parser.parse_date, 'Fri Feb 13 18:31:30 2009')
+        self.log("should error if locale is used")
+        self.assertRaises(ValueError, self.filter_parser.parse_date, "Fri Feb 13 18:31:30 2009")
 
-        self.log('should error if wrong milliseconds format is used')
-        self.assertRaises(ValueError, self.filter_parser.parse_date, '2009-02-13 18:13:00.')
-        self.assertRaises(ValueError, self.filter_parser.parse_date, '2009-02-13 18:13:00.1234567')
+        self.log("should error if wrong milliseconds format is used")
+        self.assertRaises(ValueError, self.filter_parser.parse_date, "2009-02-13 18:13:00.")
+        self.assertRaises(ValueError, self.filter_parser.parse_date, "2009-02-13 18:13:00.1234567")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_HistoryManager.py b/test/unit/app/managers/test_HistoryManager.py
index 9dcb1a9c85b..73fe8eb6226 100644
--- a/test/unit/app/managers/test_HistoryManager.py
+++ b/test/unit/app/managers/test_HistoryManager.py
@@ -8,29 +8,28 @@ from sqlalchemy import true
 
 from galaxy import (
     exceptions,
-    model
+    model,
 )
 from galaxy.managers import (
     base,
-    hdas
+    hdas,
 )
 from galaxy.managers.histories import (
     HistoryDeserializer,
     HistoryFilters,
     HistoryManager,
-    HistorySerializer
+    HistorySerializer,
 )
 from .base import BaseTestCase
 
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
-user4_data = dict(email='user4@user4.user4', username='user4', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
+user4_data = dict(email="user4@user4.user4", username="user4", password=default_password)
 parsed_filter = base.ModelFilterParser.parsed_filter
 
 
 class HistoryManagerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.history_manager = self.app[HistoryManager]
@@ -46,15 +45,15 @@ class HistoryManagerTestCase(BaseTestCase):
         user3 = self.user_manager.create(**user3_data)
 
         self.log("should be able to create a new history")
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
         self.assertIsInstance(history1, model.History)
-        self.assertEqual(history1.name, 'history1')
+        self.assertEqual(history1.name, "history1")
         self.assertEqual(history1.user, user2)
         self.assertEqual(history1, self.trans.sa_session.query(model.History).get(history1.id))
-        self.assertEqual(history1,
-            self.trans.sa_session.query(model.History).filter(model.History.name == 'history1').one())
-        self.assertEqual(history1,
-            self.trans.sa_session.query(model.History).filter(model.History.user == user2).one())
+        self.assertEqual(
+            history1, self.trans.sa_session.query(model.History).filter(model.History.name == "history1").one()
+        )
+        self.assertEqual(history1, self.trans.sa_session.query(model.History).filter(model.History.user == user2).one())
 
         history2 = self.history_manager.copy(history1, user=user3)
 
@@ -76,23 +75,22 @@ class HistoryManagerTestCase(BaseTestCase):
         self.log("should be able to order")
         history3 = self.history_manager.create(name="history3", user=user2)
         name_first_then_time = (model.History.name, sqlalchemy.desc(model.History.create_time))
-        self.assertEqual(self.history_manager.list(order_by=name_first_then_time),
-            [history2, history1, history3])
+        self.assertEqual(self.history_manager.list(order_by=name_first_then_time), [history2, history1, history3])
 
     def test_copy(self):
         user2 = self.user_manager.create(**user2_data)
         user3 = self.user_manager.create(**user3_data)
 
         self.log("should be able to copy a history (and it's hdas)")
-        history1 = self.history_manager.create(name='history1', user=user2)
-        tags = ['tag-one']
-        annotation = 'history annotation'
+        history1 = self.history_manager.create(name="history1", user=user2)
+        tags = ["tag-one"]
+        annotation = "history annotation"
         self.history_manager.set_tags(history1, tags, user=user2)
         self.history_manager.annotate(history1, annotation, user=user2)
 
-        hda = self.add_hda_to_history(history1, name='wat')
-        hda_tags = ['tag-one', 'tag-two']
-        hda_annotation = 'annotation'
+        hda = self.add_hda_to_history(history1, name="wat")
+        hda_tags = ["tag-one", "tag-two"]
+        hda_annotation = "annotation"
         self.hda_manager.set_tags(hda, hda_tags, user=user2)
         self.hda_manager.annotate(hda, hda_annotation, user=user2)
 
@@ -132,10 +130,8 @@ class HistoryManagerTestCase(BaseTestCase):
         self.assertFalse(self.history_manager.is_owner(item1, non_owner))
 
         self.log("should raise an error when checking ownership with non-owner")
-        self.assertRaises(exceptions.ItemOwnershipException,
-            self.history_manager.error_unless_owner, item1, non_owner)
-        self.assertRaises(exceptions.ItemOwnershipException,
-            self.history_manager.get_owned, item1.id, non_owner)
+        self.assertRaises(exceptions.ItemOwnershipException, self.history_manager.error_unless_owner, item1, non_owner)
+        self.assertRaises(exceptions.ItemOwnershipException, self.history_manager.get_owned, item1.id, non_owner)
 
         self.log("should not raise an error when checking ownership with owner")
         self.assertEqual(self.history_manager.error_unless_owner(item1, owner), item1)
@@ -158,10 +154,12 @@ class HistoryManagerTestCase(BaseTestCase):
         self.assertFalse(self.history_manager.is_accessible(item1, non_owner))
 
         self.log("should raise an error when checking accessibility with non-owner")
-        self.assertRaises(exceptions.ItemAccessibilityException,
-            self.history_manager.error_unless_accessible, item1, non_owner)
-        self.assertRaises(exceptions.ItemAccessibilityException,
-            self.history_manager.get_accessible, item1.id, non_owner)
+        self.assertRaises(
+            exceptions.ItemAccessibilityException, self.history_manager.error_unless_accessible, item1, non_owner
+        )
+        self.assertRaises(
+            exceptions.ItemAccessibilityException, self.history_manager.get_accessible, item1.id, non_owner
+        )
 
         self.log("should not raise an error when checking ownership with owner")
         self.assertEqual(self.history_manager.error_unless_accessible(item1, owner), item1)
@@ -255,10 +253,8 @@ class HistoryManagerTestCase(BaseTestCase):
         share_assoc = self.history_manager.share_with(item1, non_owner)
         self.assertIsInstance(share_assoc, model.HistoryUserShareAssociation)
         self.assertTrue(self.history_manager.is_accessible(item1, non_owner))
-        self.assertEqual(
-            len(self.history_manager.get_share_assocs(item1)), 1)
-        self.assertEqual(
-            len(self.history_manager.get_share_assocs(item1, user=non_owner)), 1)
+        self.assertEqual(len(self.history_manager.get_share_assocs(item1)), 1)
+        self.assertEqual(len(self.history_manager.get_share_assocs(item1, user=non_owner)), 1)
         self.assertIsInstance(item1.slug, str)
 
         self.log("should be able to unshare with specific users")
@@ -266,8 +262,7 @@ class HistoryManagerTestCase(BaseTestCase):
         self.assertIsInstance(share_assoc, model.HistoryUserShareAssociation)
         self.assertFalse(self.history_manager.is_accessible(item1, non_owner))
         self.assertEqual(self.history_manager.get_share_assocs(item1), [])
-        self.assertEqual(
-            self.history_manager.get_share_assocs(item1, user=non_owner), [])
+        self.assertEqual(self.history_manager.get_share_assocs(item1, user=non_owner), [])
 
     # TODO: test slug formation
 
@@ -279,31 +274,41 @@ class HistoryManagerTestCase(BaseTestCase):
         anon_history1 = self.history_manager.create(user=None)
         # do not set the trans.history!
         self.assertFalse(self.history_manager.is_owner(anon_history1, anon_user, current_history=self.trans.history))
-        self.assertFalse(self.history_manager.is_accessible(anon_history1, anon_user, current_history=self.trans.history))
+        self.assertFalse(
+            self.history_manager.is_accessible(anon_history1, anon_user, current_history=self.trans.history)
+        )
 
         self.log("should allow access and owner for anon user on a history if it's the session's current history")
         anon_history2 = self.history_manager.create(user=anon_user)
         self.trans.set_history(anon_history2)
         self.assertTrue(self.history_manager.is_owner(anon_history2, anon_user, current_history=self.trans.history))
-        self.assertTrue(self.history_manager.is_accessible(anon_history2, anon_user, current_history=self.trans.history))
+        self.assertTrue(
+            self.history_manager.is_accessible(anon_history2, anon_user, current_history=self.trans.history)
+        )
 
         self.log("should not allow owner or access for anon user on someone elses history")
         owner = self.user_manager.create(**user2_data)
         someone_elses = self.history_manager.create(user=owner)
         self.assertFalse(self.history_manager.is_owner(someone_elses, anon_user, current_history=self.trans.history))
-        self.assertFalse(self.history_manager.is_accessible(someone_elses, anon_user, current_history=self.trans.history))
+        self.assertFalse(
+            self.history_manager.is_accessible(someone_elses, anon_user, current_history=self.trans.history)
+        )
 
         self.log("should allow access for anon user if the history is published or importable")
         self.history_manager.make_importable(someone_elses)
-        self.assertTrue(self.history_manager.is_accessible(someone_elses, anon_user, current_history=self.trans.history))
+        self.assertTrue(
+            self.history_manager.is_accessible(someone_elses, anon_user, current_history=self.trans.history)
+        )
         self.history_manager.publish(someone_elses)
-        self.assertTrue(self.history_manager.is_accessible(someone_elses, anon_user, current_history=self.trans.history))
+        self.assertTrue(
+            self.history_manager.is_accessible(someone_elses, anon_user, current_history=self.trans.history)
+        )
 
     def test_delete_and_purge(self):
         user2 = self.user_manager.create(**user2_data)
         self.trans.set_user(user2)
 
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
         self.trans.set_history(history1)
 
         self.log("should allow deletion and undeletion")
@@ -316,7 +321,7 @@ class HistoryManagerTestCase(BaseTestCase):
         self.assertFalse(history1.deleted)
 
         self.log("should allow purging")
-        history2 = self.history_manager.create(name='history2', user=user2)
+        history2 = self.history_manager.create(name="history2", user=user2)
         self.history_manager.purge(history2)
         self.assertTrue(history2.deleted)
         self.assertTrue(history2.purged)
@@ -325,9 +330,9 @@ class HistoryManagerTestCase(BaseTestCase):
         user2 = self.user_manager.create(**user2_data)
         self.trans.set_user(user2)
 
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
         self.trans.set_history(history1)
-        history2 = self.history_manager.create(name='history2', user=user2)
+        history2 = self.history_manager.create(name="history2", user=user2)
 
         self.log("should be able to set or get the current history for a user")
         self.assertEqual(self.history_manager.get_current(self.trans), history1)
@@ -340,19 +345,19 @@ class HistoryManagerTestCase(BaseTestCase):
         user2 = self.user_manager.create(**user2_data)
         self.trans.set_user(user2)
 
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
         self.trans.set_history(history1)
-        history2 = self.history_manager.create(name='history2', user=user2)
+        history2 = self.history_manager.create(name="history2", user=user2)
 
         self.log("should be able to get the most recently used (updated) history for a given user")
         self.assertEqual(self.history_manager.most_recent(user2), history2)
-        self.history_manager.update(history1, {'name': 'new name'})
+        self.history_manager.update(history1, {"name": "new name"})
         self.assertEqual(self.history_manager.most_recent(user2), history1)
 
     def test_rating(self):
         user2 = self.user_manager.create(**user2_data)
         manager = self.history_manager
-        item = manager.create(name='history1', user=user2)
+        item = manager.create(name="history1", user=user2)
 
         self.log("should properly handle no ratings")
         self.assertEqual(manager.rating(item, user2), None)
@@ -387,7 +392,7 @@ class HistoryManagerTestCase(BaseTestCase):
 # =============================================================================
 # web.url_for doesn't work well in the framework
 def testable_url_for(*a, **k):
-    return f'(fake url): {a}, {k}'
+    return f"(fake url): {a}, {k}"
 
 
 HistorySerializer.url_for = staticmethod(testable_url_for)
@@ -395,7 +400,6 @@ hdas.HDASerializer.url_for = staticmethod(testable_url_for)
 
 
 class HistorySerializerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.history_manager = self.app[HistoryManager]
@@ -404,106 +408,105 @@ class HistorySerializerTestCase(BaseTestCase):
 
     def test_views(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
 
-        self.log('should have a summary view')
-        summary_view = self.history_serializer.serialize_to_view(history1, view='summary')
-        self.assertKeys(summary_view, self.history_serializer.views['summary'])
+        self.log("should have a summary view")
+        summary_view = self.history_serializer.serialize_to_view(history1, view="summary")
+        self.assertKeys(summary_view, self.history_serializer.views["summary"])
 
-        self.log('should have a detailed view')
-        detailed_view = self.history_serializer.serialize_to_view(history1, view='detailed')
-        self.assertKeys(detailed_view, self.history_serializer.views['detailed'])
+        self.log("should have a detailed view")
+        detailed_view = self.history_serializer.serialize_to_view(history1, view="detailed")
+        self.assertKeys(detailed_view, self.history_serializer.views["detailed"])
 
-        self.log('should have the summary view as default view')
-        default_view = self.history_serializer.serialize_to_view(history1, default_view='summary')
-        self.assertKeys(default_view, self.history_serializer.views['summary'])
+        self.log("should have the summary view as default view")
+        default_view = self.history_serializer.serialize_to_view(history1, default_view="summary")
+        self.assertKeys(default_view, self.history_serializer.views["summary"])
 
-        self.log('should have a serializer for all serializable keys')
+        self.log("should have a serializer for all serializable keys")
         for key in self.history_serializer.serializable_keyset:
             instantiated_attribute = getattr(history1, key, None)
-            if not ((key in self.history_serializer.serializers)
-                    or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
-                self.fail(f'no serializer for: {key} ({instantiated_attribute})')
+            if not (
+                (key in self.history_serializer.serializers)
+                or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
+            ):
+                self.fail(f"no serializer for: {key} ({instantiated_attribute})")
         else:
-            self.assertTrue(True, 'all serializable keys have a serializer')
+            self.assertTrue(True, "all serializable keys have a serializer")
 
     def test_views_and_keys(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
 
-        self.log('should be able to use keys with views')
-        serialized = self.history_serializer.serialize_to_view(history1,
-            view='summary', keys=['state_ids', 'user_id'])
-        self.assertKeys(serialized,
-            self.history_serializer.views['summary'] + ['state_ids', 'user_id'])
+        self.log("should be able to use keys with views")
+        serialized = self.history_serializer.serialize_to_view(history1, view="summary", keys=["state_ids", "user_id"])
+        self.assertKeys(serialized, self.history_serializer.views["summary"] + ["state_ids", "user_id"])
 
-        self.log('should be able to use keys on their own')
-        serialized = self.history_serializer.serialize_to_view(history1,
-            keys=['state_ids', 'user_id'])
-        self.assertKeys(serialized, ['state_ids', 'user_id'])
+        self.log("should be able to use keys on their own")
+        serialized = self.history_serializer.serialize_to_view(history1, keys=["state_ids", "user_id"])
+        self.assertKeys(serialized, ["state_ids", "user_id"])
 
     def test_sharable(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
 
-        self.log('should have a serializer for all SharableModel keys')
-        sharable_attrs = ['user_id', 'username_and_slug', 'importable', 'published', 'slug']
+        self.log("should have a serializer for all SharableModel keys")
+        sharable_attrs = ["user_id", "username_and_slug", "importable", "published", "slug"]
         serialized = self.history_serializer.serialize(history1, sharable_attrs)
         self.assertKeys(serialized, sharable_attrs)
 
-        self.log('should return user_id for user with whom it\'s been shared if the requester is the owner')
+        self.log("should return user_id for user with whom it's been shared if the requester is the owner")
         non_owner = self.user_manager.create(**user3_data)
         self.history_manager.share_with(history1, non_owner)
-        serialized = self.history_serializer.serialize(history1, ['users_shared_with'], user=user2)
-        self.assertKeys(serialized, ['users_shared_with'])
-        self.assertIsInstance(serialized['users_shared_with'], list)
-        self.assertEqual(serialized['users_shared_with'][0], self.app.security.encode_id(non_owner.id))
+        serialized = self.history_serializer.serialize(history1, ["users_shared_with"], user=user2)
+        self.assertKeys(serialized, ["users_shared_with"])
+        self.assertIsInstance(serialized["users_shared_with"], list)
+        self.assertEqual(serialized["users_shared_with"][0], self.app.security.encode_id(non_owner.id))
 
-        self.log('should not return users_shared_with if the requester is not the owner')
-        serialized = self.history_serializer.serialize(history1, ['users_shared_with'], user=non_owner)
-        self.assertFalse(hasattr(serialized, 'users_shared_with'))
+        self.log("should not return users_shared_with if the requester is not the owner")
+        serialized = self.history_serializer.serialize(history1, ["users_shared_with"], user=non_owner)
+        self.assertFalse(hasattr(serialized, "users_shared_with"))
 
     def test_purgable(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
 
-        self.log('deleted and purged should be returned in their default states')
-        keys = ['deleted', 'purged']
+        self.log("deleted and purged should be returned in their default states")
+        keys = ["deleted", "purged"]
         serialized = self.history_serializer.serialize(history1, keys)
-        self.assertEqual(serialized['deleted'], False)
-        self.assertEqual(serialized['purged'], False)
+        self.assertEqual(serialized["deleted"], False)
+        self.assertEqual(serialized["purged"], False)
 
-        self.log('deleted and purged should return their current state')
+        self.log("deleted and purged should return their current state")
         self.history_manager.delete(history1)
         serialized = self.history_serializer.serialize(history1, keys)
-        self.assertEqual(serialized['deleted'], True)
-        self.assertEqual(serialized['purged'], False)
+        self.assertEqual(serialized["deleted"], True)
+        self.assertEqual(serialized["purged"], False)
 
         self.history_manager.purge(history1)
         serialized = self.history_serializer.serialize(history1, keys)
-        self.assertEqual(serialized['deleted'], True)
-        self.assertEqual(serialized['purged'], True)
+        self.assertEqual(serialized["deleted"], True)
+        self.assertEqual(serialized["purged"], True)
 
     def test_history_serializers(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
         all_keys = list(self.history_serializer.serializable_keyset)
         serialized = self.history_serializer.serialize(history1, all_keys, user=user2)
 
-        self.log('everything serialized should be of the proper type')
-        self.assertIsInstance(serialized['size'], int)
-        self.assertIsInstance(serialized['nice_size'], str)
+        self.log("everything serialized should be of the proper type")
+        self.assertIsInstance(serialized["size"], int)
+        self.assertIsInstance(serialized["nice_size"], str)
 
-        self.log('serialized should jsonify well')
+        self.log("serialized should jsonify well")
         self.assertIsJsonifyable(serialized)
 
     def test_history_resume(self):
         user2 = self.user_manager.create(**user2_data)
-        history = self.history_manager.create(name='history', user=user2)
+        history = self.history_manager.create(name="history", user=user2)
         # No running jobs
         history.resume_paused_jobs()
         # Mock running jobs
-        with mock.patch('galaxy.model.History.paused_jobs', new_callable=mock.PropertyMock) as mock_paused_jobs:
+        with mock.patch("galaxy.model.History.paused_jobs", new_callable=mock.PropertyMock) as mock_paused_jobs:
             job = model.Job()
             job.state = model.Job.states.PAUSED
             jobs = [job]
@@ -516,11 +519,11 @@ class HistorySerializerTestCase(BaseTestCase):
             assert job.state == model.Job.states.NEW, job.state
 
     def _history_state_from_states_and_deleted(self, user, hda_state_and_deleted_tuples):
-        history = self.history_manager.create(name='name', user=user)
+        history = self.history_manager.create(name="name", user=user)
         for state, deleted in hda_state_and_deleted_tuples:
             hda = self.hda_manager.create(history=history)
             hda = self.hda_manager.update(hda, dict(state=state, deleted=deleted))
-        history_state = self.history_serializer.serialize(history, ['state'])['state']
+        history_state = self.history_serializer.serialize(history, ["state"])["state"]
         return history_state
 
     def test_state(self):
@@ -529,62 +532,78 @@ class HistorySerializerTestCase(BaseTestCase):
 
         ready_states = [(state, False) for state in [dataset_states.OK, dataset_states.OK]]
 
-        self.log('a history\'s serialized state should be running if any of its datasets are running')
-        self.assertEqual('running', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.RUNNING, False)]))
-        self.assertEqual('running', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.SETTING_METADATA, False)]))
-        self.assertEqual('running', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.UPLOAD, False)]))
+        self.log("a history's serialized state should be running if any of its datasets are running")
+        self.assertEqual(
+            "running",
+            self._history_state_from_states_and_deleted(user2, ready_states + [(dataset_states.RUNNING, False)]),
+        )
+        self.assertEqual(
+            "running",
+            self._history_state_from_states_and_deleted(
+                user2, ready_states + [(dataset_states.SETTING_METADATA, False)]
+            ),
+        )
+        self.assertEqual(
+            "running",
+            self._history_state_from_states_and_deleted(user2, ready_states + [(dataset_states.UPLOAD, False)]),
+        )
 
-        self.log('a history\'s serialized state should be queued if any of its datasets are queued')
-        self.assertEqual('queued', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.QUEUED, False)]))
+        self.log("a history's serialized state should be queued if any of its datasets are queued")
+        self.assertEqual(
+            "queued",
+            self._history_state_from_states_and_deleted(user2, ready_states + [(dataset_states.QUEUED, False)]),
+        )
 
-        self.log('a history\'s serialized state should be error if any of its datasets are errored')
-        self.assertEqual('error', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.ERROR, False)]))
-        self.assertEqual('error', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.FAILED_METADATA, False)]))
+        self.log("a history's serialized state should be error if any of its datasets are errored")
+        self.assertEqual(
+            "error", self._history_state_from_states_and_deleted(user2, ready_states + [(dataset_states.ERROR, False)])
+        )
+        self.assertEqual(
+            "error",
+            self._history_state_from_states_and_deleted(
+                user2, ready_states + [(dataset_states.FAILED_METADATA, False)]
+            ),
+        )
 
-        self.log('a history\'s serialized state should be ok if *all* of its datasets are ok')
-        self.assertEqual('ok', self._history_state_from_states_and_deleted(user2, ready_states))
+        self.log("a history's serialized state should be ok if *all* of its datasets are ok")
+        self.assertEqual("ok", self._history_state_from_states_and_deleted(user2, ready_states))
 
-        self.log('a history\'s serialized state should be not be affected by deleted datasets')
-        self.assertEqual('ok', self._history_state_from_states_and_deleted(user2,
-            ready_states + [(dataset_states.RUNNING, True)]))
+        self.log("a history's serialized state should be not be affected by deleted datasets")
+        self.assertEqual(
+            "ok", self._history_state_from_states_and_deleted(user2, ready_states + [(dataset_states.RUNNING, True)])
+        )
 
     def test_contents(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
 
-        self.log('a history with no contents should be properly reflected in empty, etc.')
-        keys = ['empty', 'count', 'state_ids', 'state_details', 'state', 'hdas']
+        self.log("a history with no contents should be properly reflected in empty, etc.")
+        keys = ["empty", "count", "state_ids", "state_details", "state", "hdas"]
         serialized = self.history_serializer.serialize(history1, keys)
-        self.assertEqual(serialized['state'], 'new')
-        self.assertEqual(serialized['empty'], True)
-        self.assertEqual(serialized['count'], 0)
-        self.assertEqual(sum(serialized['state_details'].values()), 0)
-        self.assertEqual(serialized['state_ids']['ok'], [])
-        self.assertIsInstance(serialized['hdas'], list)
+        self.assertEqual(serialized["state"], "new")
+        self.assertEqual(serialized["empty"], True)
+        self.assertEqual(serialized["count"], 0)
+        self.assertEqual(sum(serialized["state_details"].values()), 0)
+        self.assertEqual(serialized["state_ids"]["ok"], [])
+        self.assertIsInstance(serialized["hdas"], list)
 
-        self.log('a history with contents should be properly reflected in empty, etc.')
+        self.log("a history with contents should be properly reflected in empty, etc.")
         hda1 = self.hda_manager.create(history=history1)
-        self.hda_manager.update(hda1, dict(state='ok'))
+        self.hda_manager.update(hda1, dict(state="ok"))
 
         serialized = self.history_serializer.serialize(history1, keys)
-        self.assertEqual(serialized['state'], 'ok')
-        self.assertEqual(serialized['empty'], False)
-        self.assertEqual(serialized['count'], 1)
-        self.assertEqual(serialized['state_details']['ok'], 1)
-        self.assertIsInstance(serialized['state_ids']['ok'], list)
-        self.assertIsInstance(serialized['hdas'], list)
-        self.assertIsInstance(serialized['hdas'][0], str)
+        self.assertEqual(serialized["state"], "ok")
+        self.assertEqual(serialized["empty"], False)
+        self.assertEqual(serialized["count"], 1)
+        self.assertEqual(serialized["state_details"]["ok"], 1)
+        self.assertIsInstance(serialized["state_ids"]["ok"], list)
+        self.assertIsInstance(serialized["hdas"], list)
+        self.assertIsInstance(serialized["hdas"][0], str)
 
-        serialized = self.history_serializer.serialize(history1, ['contents'])
-        self.assertHasKeys(serialized['contents'][0], ['id', 'name', 'state', 'create_time'])
+        serialized = self.history_serializer.serialize(history1, ["contents"])
+        self.assertHasKeys(serialized["contents"][0], ["id", "name", "state", "create_time"])
 
-        self.log('serialized should jsonify well')
+        self.log("serialized should jsonify well")
         self.assertIsJsonifyable(serialized)
 
     def test_ratings(self):
@@ -592,31 +611,29 @@ class HistorySerializerTestCase(BaseTestCase):
         user3 = self.user_manager.create(**user3_data)
         manager = self.history_manager
         serializer = self.history_serializer
-        item = manager.create(name='history1', user=user2)
+        item = manager.create(name="history1", user=user2)
 
-        self.log('serialization should reflect no ratings')
-        serialized = serializer.serialize(item, ['user_rating', 'community_rating'], user=user2)
-        self.assertEqual(serialized['user_rating'], None)
-        self.assertEqual(serialized['community_rating']['count'], 0)
-        self.assertEqual(serialized['community_rating']['average'], 0.0)
+        self.log("serialization should reflect no ratings")
+        serialized = serializer.serialize(item, ["user_rating", "community_rating"], user=user2)
+        self.assertEqual(serialized["user_rating"], None)
+        self.assertEqual(serialized["community_rating"]["count"], 0)
+        self.assertEqual(serialized["community_rating"]["average"], 0.0)
 
-        self.log('serialization should reflect ratings')
+        self.log("serialization should reflect ratings")
         manager.rate(item, user2, 1)
         manager.rate(item, user3, 4)
-        serialized = serializer.serialize(item, ['user_rating', 'community_rating'], user=user2)
-        self.assertEqual(serialized['user_rating'], 1)
-        self.assertEqual(serialized['community_rating']['count'], 2)
-        self.assertEqual(serialized['community_rating']['average'], 2.5)
+        serialized = serializer.serialize(item, ["user_rating", "community_rating"], user=user2)
+        self.assertEqual(serialized["user_rating"], 1)
+        self.assertEqual(serialized["community_rating"]["count"], 2)
+        self.assertEqual(serialized["community_rating"]["average"], 2.5)
         self.assertIsJsonifyable(serialized)
 
-        self.log('serialization of user_rating without user should error')
-        self.assertRaises(base.ModelSerializingError,
-            serializer.serialize, item, ['user_rating'])
+        self.log("serialization of user_rating without user should error")
+        self.assertRaises(base.ModelSerializingError, serializer.serialize, item, ["user_rating"])
 
 
 # =============================================================================
 class HistoryDeserializerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.history_manager = self.app[HistoryManager]
@@ -626,17 +643,17 @@ class HistoryDeserializerTestCase(BaseTestCase):
         user2 = self.user_manager.create(**user2_data)
         manager = self.history_manager
         deserializer = self.history_deserializer
-        item = manager.create(name='history1', user=user2)
+        item = manager.create(name="history1", user=user2)
 
-        self.log('deserialization should allow ratings change')
-        deserializer.deserialize(item, {'user_rating': 4}, user=user2)
+        self.log("deserialization should allow ratings change")
+        deserializer.deserialize(item, {"user_rating": 4}, user=user2)
         self.assertEqual(manager.rating(item, user2), 4)
         self.assertEqual(manager.ratings(item), [4])
         self.assertEqual(manager.ratings_avg(item), 4)
         self.assertEqual(manager.ratings_count(item), 1)
 
-        self.log('deserialization should fail silently on community_rating')
-        deserializer.deserialize(item, {'community_rating': 4}, user=user2)
+        self.log("deserialization should fail silently on community_rating")
+        deserializer.deserialize(item, {"community_rating": 4}, user=user2)
         self.assertEqual(manager.ratings_count(item), 1)
 
     def test_sharable(self):
@@ -644,41 +661,41 @@ class HistoryDeserializerTestCase(BaseTestCase):
         deserializer = self.history_deserializer
 
         user2 = self.user_manager.create(**user2_data)
-        item = manager.create(name='history1', user=user2)
+        item = manager.create(name="history1", user=user2)
         non_owner = self.user_manager.create(**user3_data)
 
-        self.log('should allow adding a share by adding a user id to users_shared_with')
+        self.log("should allow adding a share by adding a user id to users_shared_with")
         non_owner_id = self.app.security.encode_id(non_owner.id)
-        deserializer.deserialize(item, {'users_shared_with': [non_owner_id]}, user=user2)
+        deserializer.deserialize(item, {"users_shared_with": [non_owner_id]}, user=user2)
         user_shares = manager.get_share_assocs(item)
         self.assertEqual(len(user_shares), 1)
         self.assertEqual(user_shares[0].user_id, non_owner.id)
 
-        self.log('re-adding an existing user id should do nothing')
-        deserializer.deserialize(item, {'users_shared_with': [non_owner_id, non_owner_id]}, user=user2)
+        self.log("re-adding an existing user id should do nothing")
+        deserializer.deserialize(item, {"users_shared_with": [non_owner_id, non_owner_id]}, user=user2)
         user_shares = manager.get_share_assocs(item)
         self.assertEqual(len(user_shares), 1)
         self.assertEqual(user_shares[0].user_id, non_owner.id)
 
-        self.log('should allow removing a share by not having it in users_shared_with')
-        deserializer.deserialize(item, {'users_shared_with': []}, user=user2)
+        self.log("should allow removing a share by not having it in users_shared_with")
+        deserializer.deserialize(item, {"users_shared_with": []}, user=user2)
         user_shares = manager.get_share_assocs(item)
         self.assertEqual(len(user_shares), 0)
 
-        self.log('adding a bad user id should error')
-        self.assertRaises(exceptions.MalformedId,
-            deserializer.deserialize, item, {'users_shared_with': [None]}, user=user2)
+        self.log("adding a bad user id should error")
+        self.assertRaises(
+            exceptions.MalformedId, deserializer.deserialize, item, {"users_shared_with": [None]}, user=user2
+        )
 
-        self.log('adding a non-existing user id should do nothing')
+        self.log("adding a non-existing user id should do nothing")
         non_user_id = self.app.security.encode_id(99)
-        deserializer.deserialize(item, {'users_shared_with': [non_user_id]}, user=user2)
+        deserializer.deserialize(item, {"users_shared_with": [non_user_id]}, user=user2)
         user_shares = manager.get_share_assocs(item)
         self.assertEqual(len(user_shares), 0)
 
 
 # =============================================================================
 class HistoryFiltersTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.history_manager = self.app[HistoryManager]
@@ -686,81 +703,123 @@ class HistoryFiltersTestCase(BaseTestCase):
 
     # ---- functional and orm filter splitting and resolution
     def test_parse_filters(self):
-        filters = self.filter_parser.parse_filters([
-            ('name', 'eq', 'wot'),
-            ('deleted', 'eq', 'True'),
-            ('annotation', 'has', 'hrrmm')
-        ])
-        self.log('both orm and fn filters should be parsed and returned')
+        filters = self.filter_parser.parse_filters(
+            [("name", "eq", "wot"), ("deleted", "eq", "True"), ("annotation", "has", "hrrmm")]
+        )
+        self.log("both orm and fn filters should be parsed and returned")
         self.assertEqual(len(filters), 3)
 
-        self.log('values should be parsed')
+        self.log("values should be parsed")
         self.assertIsInstance(filters[1].filter.right, sqlalchemy.sql.elements.True_)
 
     def test_parse_filters_invalid_filters(self):
-        self.log('should error on non-column attr')
-        self.assertRaises(exceptions.RequestParameterInvalidException, self.filter_parser.parse_filters, [
-            ('merp', 'eq', 'wot'),
-        ])
-        self.log('should error on non-allowlisted attr')
-        self.assertRaises(exceptions.RequestParameterInvalidException, self.filter_parser.parse_filters, [
-            ('user_id', 'eq', 'wot'),
-        ])
-        self.log('should error on non-allowlisted op')
-        self.assertRaises(exceptions.RequestParameterInvalidException, self.filter_parser.parse_filters, [
-            ('name', 'lt', 'wot'),
-        ])
-        self.log('should error on non-listed fn op')
-        self.assertRaises(exceptions.RequestParameterInvalidException, self.filter_parser.parse_filters, [
-            ('annotation', 'like', 'wot'),
-        ])
-        self.log('should error on val parsing error')
-        self.assertRaises(exceptions.RequestParameterInvalidException, self.filter_parser.parse_filters, [
-            ('deleted', 'eq', 'true'),
-        ])
+        self.log("should error on non-column attr")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException,
+            self.filter_parser.parse_filters,
+            [
+                ("merp", "eq", "wot"),
+            ],
+        )
+        self.log("should error on non-allowlisted attr")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException,
+            self.filter_parser.parse_filters,
+            [
+                ("user_id", "eq", "wot"),
+            ],
+        )
+        self.log("should error on non-allowlisted op")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException,
+            self.filter_parser.parse_filters,
+            [
+                ("name", "lt", "wot"),
+            ],
+        )
+        self.log("should error on non-listed fn op")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException,
+            self.filter_parser.parse_filters,
+            [
+                ("annotation", "like", "wot"),
+            ],
+        )
+        self.log("should error on val parsing error")
+        self.assertRaises(
+            exceptions.RequestParameterInvalidException,
+            self.filter_parser.parse_filters,
+            [
+                ("deleted", "eq", "true"),
+            ],
+        )
 
     def test_orm_filter_parsing(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
-        history2 = self.history_manager.create(name='history2', user=user2)
-        history3 = self.history_manager.create(name='history3', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
+        history2 = self.history_manager.create(name="history2", user=user2)
+        history3 = self.history_manager.create(name="history3", user=user2)
 
-        filters = self.filter_parser.parse_filters([
-            ('name', 'like', 'history%'),
-        ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("name", "like", "history%"),
+            ]
+        )
         histories = self.history_manager.list(filters=filters)
         self.assertEqual(histories, [history1, history2, history3])
 
-        filters = self.filter_parser.parse_filters([('name', 'like', '%2'), ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("name", "like", "%2"),
+            ]
+        )
         self.assertEqual(self.history_manager.list(filters=filters), [history2])
 
-        filters = self.filter_parser.parse_filters([('name', 'eq', 'history2'), ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("name", "eq", "history2"),
+            ]
+        )
         self.assertEqual(self.history_manager.list(filters=filters), [history2])
 
         self.history_manager.update(history1, dict(deleted=True))
-        filters = self.filter_parser.parse_filters([('deleted', 'eq', 'True'), ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("deleted", "eq", "True"),
+            ]
+        )
         self.assertEqual(self.history_manager.list(filters=filters), [history1])
-        filters = self.filter_parser.parse_filters([('deleted', 'eq', 'False'), ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("deleted", "eq", "False"),
+            ]
+        )
         self.assertEqual(self.history_manager.list(filters=filters), [history2, history3])
         self.assertEqual(self.history_manager.list(), [history1, history2, history3])
 
         self.history_manager.update(history3, dict(deleted=True))
         self.history_manager.update(history1, dict(importable=True))
         self.history_manager.update(history2, dict(importable=True))
-        filters = self.filter_parser.parse_filters([
-            ('deleted', 'eq', 'True'),
-            ('importable', 'eq', 'True'),
-        ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("deleted", "eq", "True"),
+                ("importable", "eq", "True"),
+            ]
+        )
         self.assertEqual(self.history_manager.list(filters=filters), [history1])
         self.assertEqual(self.history_manager.list(), [history1, history2, history3])
 
     def test_fn_filter_parsing(self):
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
-        history2 = self.history_manager.create(name='history2', user=user2)
-        history3 = self.history_manager.create(name='history3', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
+        history2 = self.history_manager.create(name="history2", user=user2)
+        history3 = self.history_manager.create(name="history3", user=user2)
 
-        filters = self.filter_parser.parse_filters([('annotation', 'has', 'no play'), ])
+        filters = self.filter_parser.parse_filters(
+            [
+                ("annotation", "has", "no play"),
+            ]
+        )
         anno_filter = filters[0].filter
 
         history3.add_item_annotation(self.trans.sa_session, user2, history3, "All work and no play")
@@ -771,37 +830,37 @@ class HistoryFiltersTestCase(BaseTestCase):
 
         self.assertEqual(self.history_manager.list(filters=filters), [history3])
 
-        self.log('should allow combinations of orm and fn filters')
+        self.log("should allow combinations of orm and fn filters")
         self.history_manager.update(history3, dict(importable=True))
         self.history_manager.update(history2, dict(importable=True))
         history1.add_item_annotation(self.trans.sa_session, user2, history1, "All work and no play")
         self.trans.sa_session.flush()
 
-        shining_examples = self.history_manager.list(filters=self.filter_parser.parse_filters([
-            ('importable', 'eq', 'True'),
-            ('annotation', 'has', 'no play'),
-        ]))
+        shining_examples = self.history_manager.list(
+            filters=self.filter_parser.parse_filters(
+                [
+                    ("importable", "eq", "True"),
+                    ("annotation", "has", "no play"),
+                ]
+            )
+        )
         self.assertEqual(shining_examples, [history3])
 
     def test_fn_filter_currying(self):
-        self.filter_parser.fn_filter_parsers = {
-            'name_len': {'op': {'lt': lambda i, v: len(i.name) < v}, 'val': int}
-        }
-        self.log('should be 2 filters now')
+        self.filter_parser.fn_filter_parsers = {"name_len": {"op": {"lt": lambda i, v: len(i.name) < v}, "val": int}}
+        self.log("should be 2 filters now")
         self.assertEqual(len(self.filter_parser.fn_filter_parsers), 1)
-        filters = self.filter_parser.parse_filters([
-            ('name_len', 'lt', '4')
-        ])
-        self.log('should have parsed out a single filter')
+        filters = self.filter_parser.parse_filters([("name_len", "lt", "4")])
+        self.log("should have parsed out a single filter")
         self.assertEqual(len(filters), 1)
 
         filter_ = filters[0].filter
         fake = mock.Mock()
-        fake.name = '123'
-        self.log('123 should return true through the filter')
+        fake.name = "123"
+        self.log("123 should return true through the filter")
         self.assertTrue(filter_(fake))
-        fake.name = '1234'
-        self.log('1234 should return false through the filter')
+        fake.name = "1234"
+        self.log("1234 should return false through the filter")
         self.assertFalse(filter_(fake))
 
     def test_list(self):
@@ -809,10 +868,10 @@ class HistoryFiltersTestCase(BaseTestCase):
         Test limit and offset in conjunction with both orm and fn filtering.
         """
         user2 = self.user_manager.create(**user2_data)
-        history1 = self.history_manager.create(name='history1', user=user2)
-        history2 = self.history_manager.create(name='history2', user=user2)
-        history3 = self.history_manager.create(name='history3', user=user2)
-        history4 = self.history_manager.create(name='history4', user=user2)
+        history1 = self.history_manager.create(name="history1", user=user2)
+        history2 = self.history_manager.create(name="history2", user=user2)
+        history3 = self.history_manager.create(name="history3", user=user2)
+        history4 = self.history_manager.create(name="history4", user=user2)
 
         self.history_manager.delete(history1)
         self.history_manager.delete(history2)
@@ -862,7 +921,7 @@ class HistoryFiltersTestCase(BaseTestCase):
         found = self.history_manager.list(filters=filters, offset=1, limit=1)
         self.assertEqual(found, [history2])
 
-        filters = self.filter_parser.parse_filters([('annotation', 'has', test_annotation)])
+        filters = self.filter_parser.parse_filters([("annotation", "has", test_annotation)])
         self.log("fn filtered, no offset, no limit should work")
         found = self.history_manager.list(filters=filters)
         self.assertEqual(found, [history2, history3, history4])
@@ -876,10 +935,7 @@ class HistoryFiltersTestCase(BaseTestCase):
         found = self.history_manager.list(filters=filters, offset=1, limit=1)
         self.assertEqual(found, [history3])
 
-        filters = self.filter_parser.parse_filters([
-            ('deleted', 'eq', 'True'),
-            ('annotation', 'has', test_annotation)
-        ])
+        filters = self.filter_parser.parse_filters([("deleted", "eq", "True"), ("annotation", "has", test_annotation)])
         self.log("orm and fn filtered, no offset, no limit should work")
         found = self.history_manager.list(filters=filters)
         self.assertEqual(found, [history2, history3])
@@ -912,6 +968,6 @@ class HistoryFiltersTestCase(BaseTestCase):
 
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     # or more generally, nosetests test_resourcemanagers.py -s -v
     unittest.main()
diff --git a/test/unit/app/managers/test_TagHandler.py b/test/unit/app/managers/test_TagHandler.py
index 118edddfaa6..65ca95811ff 100644
--- a/test/unit/app/managers/test_TagHandler.py
+++ b/test/unit/app/managers/test_TagHandler.py
@@ -6,13 +6,12 @@ from galaxy.util import unicodify
 from .base import BaseTestCase
 
 # =============================================================================
-default_password = '123456'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
+default_password = "123456"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
 
 
 # =============================================================================
 class TagHandlerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.app.hda_manager = self.app[hdas.HDAManager]
@@ -23,7 +22,7 @@ class TagHandlerTestCase(BaseTestCase):
 
     def _create_vanilla_hda(self, user=None):
         owner = user or self.user
-        history1 = self.app.history_manager.create(name='history1', user=owner)
+        history1 = self.app.history_manager.create(name="history1", user=owner)
         dataset1 = self.app.dataset_manager.create()
         return self.app.hda_manager.create(history=history1, dataset=dataset1)
 
@@ -41,26 +40,26 @@ class TagHandlerTestCase(BaseTestCase):
 
     def test_apply_item_tags(self):
         tag_strings = [
-            'tag1',
-            'tag1:value1',
-            'tag1:value1:value11',
-            '\x00tag1',
-            'tag1:\x00value1',
-            'tag1,tag2',
-            '...',
-            '.test',
-            'test.a.b',
+            "tag1",
+            "tag1:value1",
+            "tag1:value1:value11",
+            "\x00tag1",
+            "tag1:\x00value1",
+            "tag1,tag2",
+            "...",
+            ".test",
+            "test.a.b",
         ]
         expected_tags = [
-            ['tag1'],
-            ['tag1:value1'],
-            ['tag1:value1:value11'],
-            ['tag1'],
-            ['tag1:value1'],
-            ['tag1', 'tag2'],
+            ["tag1"],
+            ["tag1:value1"],
+            ["tag1:value1:value11"],
+            ["tag1"],
+            ["tag1:value1"],
+            ["tag1", "tag2"],
             [],
-            ['test'],
-            ['test.a.b'],
+            ["test"],
+            ["test.a.b"],
         ]
         for tag_string, expected_tag in zip(tag_strings, expected_tags):
             hda = self._create_vanilla_hda()
@@ -69,50 +68,50 @@ class TagHandlerTestCase(BaseTestCase):
 
     def test_set_tag_from_list(self):
         hda = self._create_vanilla_hda()
-        tags = ['tag1', 'tag2']
+        tags = ["tag1", "tag2"]
         self.tag_handler.set_tags_from_list(self.user, hda, tags)
         self._check_tag_list(hda.tags, tags)
         # Setting tags should erase previous tags
-        self.tag_handler.set_tags_from_list(self.user, hda, ['tag1'])
-        self._check_tag_list(hda.tags, expected_tags=['tag1'])
+        self.tag_handler.set_tags_from_list(self.user, hda, ["tag1"])
+        self._check_tag_list(hda.tags, expected_tags=["tag1"])
 
     def test_add_tag_from_list(self):
         hda = self._create_vanilla_hda()
-        tags = ['tag1', 'tag2']
+        tags = ["tag1", "tag2"]
         self.tag_handler.add_tags_from_list(self.user, hda, tags)
         self._check_tag_list(tags=hda.tags, expected_tags=tags)
         # Adding tags should keep previous tags
-        self.tag_handler.add_tags_from_list(self.user, hda, ['tag3'])
-        self._check_tag_list(hda.tags, expected_tags=['tag1', 'tag2', 'tag3'])
+        self.tag_handler.add_tags_from_list(self.user, hda, ["tag3"])
+        self._check_tag_list(hda.tags, expected_tags=["tag1", "tag2", "tag3"])
 
     def test_remove_tag_from_list(self):
         hda = self._create_vanilla_hda()
-        tags = ['tag1', 'tag2', 'tag3']
+        tags = ["tag1", "tag2", "tag3"]
         self.tag_handler.set_tags_from_list(self.user, hda, tags)
         self._check_tag_list(hda.tags, tags)
-        self.tag_handler.remove_tags_from_list(self.user, hda, ['tag1', 'tag3'])
-        self._check_tag_list(hda.tags, ['tag2'])
+        self.tag_handler.remove_tags_from_list(self.user, hda, ["tag1", "tag3"])
+        self._check_tag_list(hda.tags, ["tag2"])
 
     def test_delete_item_tags(self):
         hda = self._create_vanilla_hda()
-        tags = ['tag1']
+        tags = ["tag1"]
         self.tag_handler.set_tags_from_list(self.user, hda, tags)
         self.tag_handler.delete_item_tags(user=self.user, item=hda)
         self.assertEqual(hda.tags, [])
 
     def test_unique_constraint_applied(self):
-        tag_name = 'abc'
+        tag_name = "abc"
         tag = self.tag_handler._create_tag_instance(tag_name)
         same_tag = self.tag_handler._create_tag_instance(tag_name)
         assert tag.id == same_tag.id
 
     def test_item_has_tag(self):
         hda = self._create_vanilla_hda()
-        tags = ['tag1']
+        tags = ["tag1"]
         self.tag_handler.set_tags_from_list(self.user, hda, tags)
-        self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag='tag1'))
+        self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag="tag1"))
         # ItemTagAssociation
         self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag=hda.tags[0]))
         # Tag
         self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag=hda.tags[0].tag))
-        self.assertFalse(self.tag_handler.item_has_tag(self.user, item=hda, tag='tag2'))
+        self.assertFalse(self.tag_handler.item_has_tag(self.user, item=hda, tag="tag2"))
diff --git a/test/unit/app/managers/test_UserManager.py b/test/unit/app/managers/test_UserManager.py
index 05f16869687..8269164d7dc 100644
--- a/test/unit/app/managers/test_UserManager.py
+++ b/test/unit/app/managers/test_UserManager.py
@@ -8,26 +8,30 @@ from datetime import datetime
 
 from sqlalchemy import desc
 
-from galaxy import exceptions, model
+from galaxy import (
+    exceptions,
+    model,
+)
 from galaxy.managers import base as base_manager
-from galaxy.managers import histories, users
+from galaxy.managers import (
+    histories,
+    users,
+)
 from galaxy.security.passwords import check_password
 from .base import BaseTestCase
 
-
 # =============================================================================
-default_password = '123456'
-changed_password = '654321'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
-user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
-user4_data = dict(email='user4@user4.user4', username='user4', password=default_password)
-uppercase_email_user = dict(email='USER5@USER5.USER5', username='USER5', password=default_password)
-lowercase_email_user = dict(email='user5@user5.user5', username='user5', password=default_password)
+default_password = "123456"
+changed_password = "654321"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
+user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
+user4_data = dict(email="user4@user4.user4", username="user4", password=default_password)
+uppercase_email_user = dict(email="USER5@USER5.USER5", username="USER5", password=default_password)
+lowercase_email_user = dict(email="user5@user5.user5", username="user5", password=default_password)
 
 
 # =============================================================================
 class UserManagerTestCase(BaseTestCase):
-
     def test_framework(self):
         self.log("(for testing) should have admin_user, and admin_user is current")
         self.assertEqual(self.trans.user, self.admin_user)
@@ -37,7 +41,7 @@ class UserManagerTestCase(BaseTestCase):
         user2 = self.user_manager.create(**user2_data)
         self.assertIsInstance(user2, model.User)
         self.assertIsNotNone(user2.id)
-        self.assertEqual(user2.email, user2_data['email'])
+        self.assertEqual(user2.email, user2_data["email"])
         self.assertTrue(check_password(default_password, user2.password))
 
         user3 = self.user_manager.create(**user3_data)
@@ -58,24 +62,31 @@ class UserManagerTestCase(BaseTestCase):
         self.assertEqual(self.user_manager.list(offset=3), [])
 
         self.log("should be able to order")
-        self.assertEqual(self.user_manager.list(order_by=(desc(model.User.create_time))),
-            [user3, user2, self.admin_user])
+        self.assertEqual(
+            self.user_manager.list(order_by=(desc(model.User.create_time))), [user3, user2, self.admin_user]
+        )
 
     def test_invalid_create(self):
         self.user_manager.create(**user2_data)
 
         self.log("emails must be unique")
-        self.assertRaises(exceptions.Conflict, self.user_manager.create,
-            **dict(email='user2@user2.user2', username='user2a', password=default_password))
+        self.assertRaises(
+            exceptions.Conflict,
+            self.user_manager.create,
+            **dict(email="user2@user2.user2", username="user2a", password=default_password),
+        )
         self.log("usernames must be unique")
-        self.assertRaises(exceptions.Conflict, self.user_manager.create,
-            **dict(email='user2a@user2.user2', username='user2', password=default_password))
+        self.assertRaises(
+            exceptions.Conflict,
+            self.user_manager.create,
+            **dict(email="user2a@user2.user2", username="user2", password=default_password),
+        )
 
     def test_email_queries(self):
         user2 = self.user_manager.create(**user2_data)
 
         self.log("should be able to query by email")
-        self.assertEqual(self.user_manager.by_email(user2_data['email']), user2)
+        self.assertEqual(self.user_manager.by_email(user2_data["email"]), user2)
 
     def test_admin(self):
         user2 = self.user_manager.create(**user2_data)
@@ -114,19 +125,29 @@ class UserManagerTestCase(BaseTestCase):
         self.assertEqual(message, "Please provide a token or a user and password.")
         user, message = self.user_manager.change_password(self.trans, id=encoded_id, current=changed_password)
         self.assertEqual(message, "Invalid current password.")
-        user, message = self.user_manager.change_password(self.trans, id=encoded_id, current=default_password, password=changed_password, confirm=default_password)
+        user, message = self.user_manager.change_password(
+            self.trans, id=encoded_id, current=default_password, password=changed_password, confirm=default_password
+        )
         self.assertEqual(message, "Passwords do not match.")
-        user, message = self.user_manager.change_password(self.trans, id=encoded_id, current=default_password, password=default_password, confirm=changed_password)
+        user, message = self.user_manager.change_password(
+            self.trans, id=encoded_id, current=default_password, password=default_password, confirm=changed_password
+        )
         self.assertEqual(message, "Passwords do not match.")
-        user, message = self.user_manager.change_password(self.trans, id=encoded_id, current=default_password, password=changed_password, confirm=changed_password)
+        user, message = self.user_manager.change_password(
+            self.trans, id=encoded_id, current=default_password, password=changed_password, confirm=changed_password
+        )
         self.assertFalse(check_password(default_password, user2.password))
         self.assertTrue(check_password(changed_password, user2.password))
         reset_user, prt = self.user_manager.get_reset_token(self.trans, user2.email)
-        user, message = self.user_manager.change_password(self.trans, token=prt.token, password=default_password, confirm=default_password)
+        user, message = self.user_manager.change_password(
+            self.trans, token=prt.token, password=default_password, confirm=default_password
+        )
         self.assertTrue(check_password(default_password, user2.password))
         self.assertFalse(check_password(changed_password, user2.password))
         prt.expiration_time = datetime.utcnow()
-        user, message = self.user_manager.change_password(self.trans, token=prt.token, password=default_password, confirm=default_password)
+        user, message = self.user_manager.change_password(
+            self.trans, token=prt.token, password=default_password, confirm=default_password
+        )
         self.assertEqual(message, "Invalid or expired password reset token, please request a new one.")
 
     def test_login(self):
@@ -140,7 +161,7 @@ class UserManagerTestCase(BaseTestCase):
 
     def test_empty_password(self):
         self.log("should be able to create a user with no password")
-        user = self.user_manager.create(email='user@nopassword.com', username='nopassword')
+        user = self.user_manager.create(email="user@nopassword.com", username="nopassword")
         self.assertIsNotNone(user.id)
         self.assertIsNotNone(user.password)
         # should not be able to login with a null or empty password
@@ -149,18 +170,18 @@ class UserManagerTestCase(BaseTestCase):
 
     def test_get_user_by_identity(self):
         # return None if username/email not found
-        assert self.user_manager.get_user_by_identity('xyz') is None
+        assert self.user_manager.get_user_by_identity("xyz") is None
         uppercase_user = self.user_manager.create(**uppercase_email_user)
-        assert uppercase_user.email == uppercase_email_user['email']
-        assert uppercase_user.username == uppercase_email_user['username']
+        assert uppercase_user.email == uppercase_email_user["email"]
+        assert uppercase_user.username == uppercase_email_user["username"]
         assert self.user_manager.get_user_by_identity(uppercase_user.email) == uppercase_user
         assert self.user_manager.get_user_by_identity(uppercase_user.username) == uppercase_user
         # Create another user with the same email just differently capitalized.
         # This is not normally allowed now, since registration goes through user_manager.register(),
         # which checks for that, but was possible in earlier releases of Galaxy
         lowercase_user = self.user_manager.create(**lowercase_email_user)
-        assert lowercase_user.email == lowercase_email_user['email']
-        assert lowercase_user.username == lowercase_email_user['username']
+        assert lowercase_user.email == lowercase_email_user["email"]
+        assert lowercase_user.username == lowercase_email_user["username"]
         assert self.user_manager.get_user_by_identity(lowercase_user.email) == lowercase_user
         assert self.user_manager.get_user_by_identity(lowercase_user.username) == lowercase_user
         # assert uppercase user can still be retrieved
@@ -169,13 +190,17 @@ class UserManagerTestCase(BaseTestCase):
         # username matches need to be exact
         assert self.user_manager.get_user_by_identity(uppercase_user.username.capitalize()) is None
         # email matches can ignore capitalization
-        ignore_email_capitalization_user = self.user_manager.create(email='user123@nopassword.com', username='someusername123')
-        assert self.user_manager.get_user_by_identity(ignore_email_capitalization_user.email.capitalize()) == ignore_email_capitalization_user
+        ignore_email_capitalization_user = self.user_manager.create(
+            email="user123@nopassword.com", username="someusername123"
+        )
+        assert (
+            self.user_manager.get_user_by_identity(ignore_email_capitalization_user.email.capitalize())
+            == ignore_email_capitalization_user
+        )
 
 
 # =============================================================================
 class UserSerializerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.user_serializer = users.UserSerializer(self.app)
@@ -183,36 +208,35 @@ class UserSerializerTestCase(BaseTestCase):
     def test_views(self):
         user = self.user_manager.create(**user2_data)
 
-        self.log('should have a summary view')
-        summary_view = self.user_serializer.serialize_to_view(user, view='summary')
-        self.assertKeys(summary_view, self.user_serializer.views['summary'])
+        self.log("should have a summary view")
+        summary_view = self.user_serializer.serialize_to_view(user, view="summary")
+        self.assertKeys(summary_view, self.user_serializer.views["summary"])
 
-        self.log('should have the summary view as default view')
-        default_view = self.user_serializer.serialize_to_view(user, default_view='summary')
-        self.assertKeys(default_view, self.user_serializer.views['summary'])
+        self.log("should have the summary view as default view")
+        default_view = self.user_serializer.serialize_to_view(user, default_view="summary")
+        self.assertKeys(default_view, self.user_serializer.views["summary"])
 
-        self.log('should have a serializer for all serializable keys')
+        self.log("should have a serializer for all serializable keys")
         for key in self.user_serializer.serializable_keyset:
             instantiated_attribute = getattr(user, key, None)
-            if not ((key in self.user_serializer.serializers)
-                    or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
-                self.fail(f'no serializer for: {key} ({instantiated_attribute})')
+            if not (
+                (key in self.user_serializer.serializers)
+                or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
+            ):
+                self.fail(f"no serializer for: {key} ({instantiated_attribute})")
         else:
-            self.assertTrue(True, 'all serializable keys have a serializer')
+            self.assertTrue(True, "all serializable keys have a serializer")
 
     def test_views_and_keys(self):
         user = self.user_manager.create(**user2_data)
 
-        self.log('should be able to use keys with views')
-        serialized = self.user_serializer.serialize_to_view(user,
-            view='summary', keys=['create_time'])
-        self.assertKeys(serialized,
-            self.user_serializer.views['summary'] + ['create_time'])
+        self.log("should be able to use keys with views")
+        serialized = self.user_serializer.serialize_to_view(user, view="summary", keys=["create_time"])
+        self.assertKeys(serialized, self.user_serializer.views["summary"] + ["create_time"])
 
-        self.log('should be able to use keys on their own')
-        serialized = self.user_serializer.serialize_to_view(user,
-            keys=['tags_used', 'is_admin'])
-        self.assertKeys(serialized, ['tags_used', 'is_admin'])
+        self.log("should be able to use keys on their own")
+        serialized = self.user_serializer.serialize_to_view(user, keys=["tags_used", "is_admin"])
+        self.assertKeys(serialized, ["tags_used", "is_admin"])
 
     def test_serializers(self):
         user = self.user_manager.create(**user2_data)
@@ -220,26 +244,25 @@ class UserSerializerTestCase(BaseTestCase):
         serialized = self.user_serializer.serialize(user, all_keys, trans=self.trans)
         # pprint.pprint( serialized )
 
-        self.log('everything serialized should be of the proper type')
-        self.assertEncodedId(serialized['id'])
-        self.assertDate(serialized['create_time'])
-        self.assertDate(serialized['update_time'])
-        self.assertIsInstance(serialized['deleted'], bool)
-        self.assertIsInstance(serialized['purged'], bool)
+        self.log("everything serialized should be of the proper type")
+        self.assertEncodedId(serialized["id"])
+        self.assertDate(serialized["create_time"])
+        self.assertDate(serialized["update_time"])
+        self.assertIsInstance(serialized["deleted"], bool)
+        self.assertIsInstance(serialized["purged"], bool)
 
         # self.assertIsInstance( serialized[ 'active' ], bool )
-        self.assertIsInstance(serialized['is_admin'], bool)
-        self.assertIsInstance(serialized['total_disk_usage'], float)
-        self.assertIsInstance(serialized['nice_total_disk_usage'], str)
-        self.assertIsInstance(serialized['quota_percent'], (type(None), float))
-        self.assertIsInstance(serialized['tags_used'], list)
+        self.assertIsInstance(serialized["is_admin"], bool)
+        self.assertIsInstance(serialized["total_disk_usage"], float)
+        self.assertIsInstance(serialized["nice_total_disk_usage"], str)
+        self.assertIsInstance(serialized["quota_percent"], (type(None), float))
+        self.assertIsInstance(serialized["tags_used"], list)
 
-        self.log('serialized should jsonify well')
+        self.log("serialized should jsonify well")
         self.assertIsJsonifyable(serialized)
 
 
 class CurrentUserSerializerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.history_manager = self.app[histories.HistoryManager]
@@ -250,25 +273,23 @@ class CurrentUserSerializerTestCase(BaseTestCase):
         # need a history here for total_disk_usage
         self.trans.set_history(self.history_manager.create())
 
-        self.log('should be able to serialize anonymous user')
-        serialized = self.user_serializer.serialize_to_view(anonym, view='detailed', trans=self.trans)
-        self.assertKeys(serialized,
-            ['id', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent'])
+        self.log("should be able to serialize anonymous user")
+        serialized = self.user_serializer.serialize_to_view(anonym, view="detailed", trans=self.trans)
+        self.assertKeys(serialized, ["id", "total_disk_usage", "nice_total_disk_usage", "quota_percent"])
 
-        self.log('anonymous\'s id should be None')
-        self.assertEqual(serialized['id'], None)
-        self.log('everything serialized should be of the proper type')
-        self.assertIsInstance(serialized['total_disk_usage'], float)
-        self.assertIsInstance(serialized['nice_total_disk_usage'], str)
-        self.assertIsInstance(serialized['quota_percent'], (type(None), float))
+        self.log("anonymous's id should be None")
+        self.assertEqual(serialized["id"], None)
+        self.log("everything serialized should be of the proper type")
+        self.assertIsInstance(serialized["total_disk_usage"], float)
+        self.assertIsInstance(serialized["nice_total_disk_usage"], str)
+        self.assertIsInstance(serialized["quota_percent"], (type(None), float))
 
-        self.log('serialized should jsonify well')
+        self.log("serialized should jsonify well")
         self.assertIsJsonifyable(serialized)
 
 
 # =============================================================================
 class UserDeserializerTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.deserializer = users.UserDeserializer(self.app)
@@ -279,7 +300,7 @@ class UserDeserializerTestCase(BaseTestCase):
         except exception_class as exception:
             self.assertTrue(True)
             return exception
-        raise AssertionError(f'{exception_class.__name__} not raised')
+        raise AssertionError(f"{exception_class.__name__} not raised")
 
     def test_username_validation(self):
         user = self.user_manager.create(**user2_data)
@@ -288,43 +309,57 @@ class UserDeserializerTestCase(BaseTestCase):
         # self.deserializer.deserialize( user, { 'username': 'Σίσυφος' }, trans=self.trans )
 
         self.log("usernames must be long enough and with no non-hyphen punctuation")
-        exception = self._assertRaises_and_return_raised(base_manager.ModelDeserializingError,
-            self.deserializer.deserialize, user, {'username': 'ed'}, trans=self.trans)
-        self.assertTrue('Public name must be at least' in str(exception))
-        self.assertRaises(base_manager.ModelDeserializingError, self.deserializer.deserialize,
-            user, {'username': 'f,d,r,'}, trans=self.trans)
+        exception = self._assertRaises_and_return_raised(
+            base_manager.ModelDeserializingError,
+            self.deserializer.deserialize,
+            user,
+            {"username": "ed"},
+            trans=self.trans,
+        )
+        self.assertTrue("Public name must be at least" in str(exception))
+        self.assertRaises(
+            base_manager.ModelDeserializingError,
+            self.deserializer.deserialize,
+            user,
+            {"username": "f,d,r,"},
+            trans=self.trans,
+        )
 
         self.log("usernames must be unique")
         self.user_manager.create(**user3_data)
-        self.assertRaises(base_manager.ModelDeserializingError, self.deserializer.deserialize,
-            user, {'username': 'user3'}, trans=self.trans)
+        self.assertRaises(
+            base_manager.ModelDeserializingError,
+            self.deserializer.deserialize,
+            user,
+            {"username": "user3"},
+            trans=self.trans,
+        )
 
         self.log("username should be updatable")
-        new_name = 'double-plus-good'
-        self.deserializer.deserialize(user, {'username': new_name}, trans=self.trans)
+        new_name = "double-plus-good"
+        self.deserializer.deserialize(user, {"username": new_name}, trans=self.trans)
         self.assertEqual(self.user_manager.by_id(user.id).username, new_name)
 
 
 # =============================================================================
 class AdminUserFilterParserTestCase(BaseTestCase):
-
     def set_up_managers(self):
         super().set_up_managers()
         self.filter_parser = users.AdminUserFilterParser(self.app)
 
     def test_parsable(self):
-        self.log('the following filters should be parsable')
-        self.assertORMFilter(self.filter_parser.parse_filter('email', 'eq', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('email', 'contains', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('email', 'like', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('username', 'eq', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('username', 'contains', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('username', 'like', 'wot'))
-        self.assertORMFilter(self.filter_parser.parse_filter('active', 'eq', True))
-        self.assertORMFilter(self.filter_parser.parse_filter('disk_usage', 'le', 500000.00))
-        self.assertORMFilter(self.filter_parser.parse_filter('disk_usage', 'ge', 500000.00))
+        self.log("the following filters should be parsable")
+        self.assertORMFilter(self.filter_parser.parse_filter("email", "eq", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("email", "contains", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("email", "like", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("username", "eq", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("username", "contains", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("username", "like", "wot"))
+        self.assertORMFilter(self.filter_parser.parse_filter("active", "eq", True))
+        self.assertORMFilter(self.filter_parser.parse_filter("disk_usage", "le", 500000.00))
+        self.assertORMFilter(self.filter_parser.parse_filter("disk_usage", "ge", 500000.00))
 
 
 # =============================================================================
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/app/managers/test_markdown_export.py b/test/unit/app/managers/test_markdown_export.py
index 45b94b8e192..6b591f13980 100644
--- a/test/unit/app/managers/test_markdown_export.py
+++ b/test/unit/app/managers/test_markdown_export.py
@@ -14,7 +14,6 @@ from .base import BaseTestCase
 
 
 class BaseExportTestCase(BaseTestCase):
-
     def setUp(self):
         super().setUp()
         self.app.hda_manager = mock.MagicMock()
@@ -86,7 +85,6 @@ class BaseExportTestCase(BaseTestCase):
 
 
 class ToBasicMarkdownTestCase(BaseExportTestCase):
-
     def setUp(self):
         super().setUp()
         self.test_dataset_path = None
@@ -127,7 +125,7 @@ history_dataset_peek(history_dataset_id=1)
 """
         with self._expect_get_hda(hda):
             result = self._to_basic(example)
-        assert '\n    My Cool Peek\n\n' in result
+        assert "\n    My Cool Peek\n\n" in result
 
     def test_history_dataset_peek_empty(self):
         hda = self._new_hda()
@@ -138,7 +136,7 @@ history_dataset_peek(history_dataset_id=1)
 """
         with self._expect_get_hda(hda):
             result = self._to_basic(example)
-        assert '\n*No Dataset Peek Available*\n' in result
+        assert "\n*No Dataset Peek Available*\n" in result
 
     def test_history_link(self):
         history = self._new_history()
@@ -149,11 +147,11 @@ history_link(history_id=1)
 """
         with self._expect_get_history(history):
             result = self._to_basic(example)
-        assert '\n    New History\n\n' in result
+        assert "\n    New History\n\n" in result
 
     def test_history_display_binary(self):
         hda = self._new_hda()
-        hda.extension = 'ab1'
+        hda.extension = "ab1"
         example = """# Example
 ```galaxy
 history_dataset_display(history_dataset_id=1)
@@ -165,7 +163,7 @@ history_dataset_display(history_dataset_id=1)
 
     def test_history_display_text(self):
         hda = self._new_hda(contents="MooCow")
-        hda.extension = 'txt'
+        hda.extension = "txt"
         example = """# Example
 ```galaxy
 history_dataset_display(history_dataset_id=1)
@@ -186,12 +184,13 @@ history_dataset_display(history_dataset_id=1)
 ```
 """
         hda = self._new_hda(contents=gtf)
-        hda.extension = 'gtf'
+        hda.extension = "gtf"
         from galaxy.datatypes.tabular import Tabular
+
         assert isinstance(hda.datatype, Tabular)
         with self._expect_get_hda(hda):
             result = self._to_basic(example)
-        assert '<table' in result
+        assert "<table" in result
 
     def test_dataset_name(self):
         hda = self._new_hda()
@@ -203,7 +202,7 @@ history_dataset_name(history_dataset_id=1)
 """
         with self._expect_get_hda(hda):
             result = self._to_basic(example)
-        assert '\n    cool name' in result
+        assert "\n    cool name" in result
 
     def test_dataset_extension(self):
         hda = self._new_hda()
@@ -215,7 +214,7 @@ history_dataset_type(history_dataset_id=1)
 """
         with self._expect_get_hda(hda):
             result = self._to_basic(example)
-        assert '\n    gtf' in result
+        assert "\n    gtf" in result
 
     def test_history_collection_paired(self):
         hdca = model.HistoryDatasetCollectionAssociation()
@@ -297,7 +296,7 @@ job_parameters(job_id=1)
             {"text": "Input Dataset", "value": [{"src": "hda", "hid": 5, "name": "Cool Data"}], "depth": 1},
         ]
         response = {"parameters": parameters}
-        with mock.patch.object(JobManager, 'get_accessible_job', return_value=job):
+        with mock.patch.object(JobManager, "get_accessible_job", return_value=job):
             with mock.patch("galaxy.managers.markdown_util.summarize_job_parameters", return_value=response):
                 result = self._to_basic(example)
         assert "| Num Lines |" in result
@@ -318,7 +317,7 @@ job_metrics(job_id=1)
             {"plugin": "core", "title": "Job Start Time", "value": "2019-12-17 11:53:13"},
             {"plugin": "env", "title": "GALAXY_HOME", "value": "/path/to/home"},
         ]
-        with mock.patch.object(JobManager, 'get_accessible_job', return_value=job):
+        with mock.patch.object(JobManager, "get_accessible_job", return_value=job):
             with mock.patch("galaxy.managers.markdown_util.summarize_job_metrics", return_value=metrics):
                 result = self._to_basic(example)
         assert "**core**\n" in result
@@ -331,7 +330,6 @@ job_metrics(job_id=1)
 
 
 class ReadyExportTestCase(BaseExportTestCase):
-
     def test_ready_dataset_display(self):
         hda = self._new_hda()
         example = """
@@ -378,7 +376,8 @@ history_dataset_collection_display(history_dataset_collection_id=1)
 """
         # Patch out url_for since we haven't initialized an app.
         from galaxy.managers.hdcas import HDCASerializer
-        with mock.patch.object(HDCASerializer, 'url_for', return_value="http://google.com"):
+
+        with mock.patch.object(HDCASerializer, "url_for", return_value="http://google.com"):
             export, extra_data = self._ready_export(example)
         assert "history_dataset_collections" in extra_data
         assert len(extra_data.get("history_dataset_collections")) == 1
diff --git a/test/unit/app/managers/test_markdown_to_html.py b/test/unit/app/managers/test_markdown_to_html.py
index a02a3c29c51..36cd2313168 100644
--- a/test/unit/app/managers/test_markdown_to_html.py
+++ b/test/unit/app/managers/test_markdown_to_html.py
@@ -8,7 +8,8 @@ from galaxy.managers.markdown_util import to_html
 
 
 def test_basics():
-    as_html = to_html("""
+    as_html = to_html(
+        """
 # My header!
 
 My cool document. **Bold** text.
@@ -16,43 +17,52 @@ My cool document. **Bold** text.
 ## My sub header
 
 Less important content.
-""")
+"""
+    )
     assert "<h1>My header!</h1>" in as_html
     assert "<strong>Bold</strong>" in as_html
 
 
 def test_indent_code_blocks():
-    as_html = to_html("""
+    as_html = to_html(
+        """
 A Code Block Follows:
 
     This is code right?
     Here is another line.
-""")
+"""
+    )
     assert "<pre><code>This is code right?\nHere is another line." in as_html
 
 
 def test_tables():
-    as_html = to_html("""
+    as_html = to_html(
+        """
 |animal|sound|
 |------|-----|
 |dog   |bark |
 |cat   |meow |
-""")
+"""
+    )
     assert "<table>" in as_html, as_html
 
 
 def test_tags_escaped():
-    as_html = to_html("""
+    as_html = to_html(
+        """
 Bad block approaches <br>
 
 <script>window.location.href = "bad_place";</script>
-""")
+"""
+    )
     assert "<script>" not in as_html, as_html
 
 
 def test_embed_img_tags():
-    as_html = to_html("""
+    as_html = to_html(
+        """
 ![Red dot](data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAUAAAAFCAYAAACNbyblAAAAHElEQVQI12P4//8/w38GIAXDIBKE0DHxgljNBAAO9TXL0Y4OHwAAAABJRU5ErkJggg==)
-""")
+"""
+    )
     assert "img" in as_html, as_html
     assert "iVBORw0KGgoAAAANSUhEUgAAAAUAAA" in as_html, as_html
diff --git a/test/unit/app/queue_worker/conftest.py b/test/unit/app/queue_worker/conftest.py
index 89131ba7613..d5aceae46c6 100644
--- a/test/unit/app/queue_worker/conftest.py
+++ b/test/unit/app/queue_worker/conftest.py
@@ -23,24 +23,22 @@ def create_base_test(connection, amqp_type, amqp_connection=None):
 @pytest.fixture()
 def sqlite_connection(request):
     with tempfile.NamedTemporaryFile() as temp:
-        yield f'sqlite:////{temp.name}'
+        yield f"sqlite:////{temp.name}"
 
 
 @pytest.fixture()
 def sqlite_rabbitmq_app(sqlite_connection):
-
     def create_app():
-        amqp_connection = os.environ.get('GALAXY_TEST_AMQP_INTERNAL_CONNECTION')
-        return create_base_test(sqlite_connection, amqp_type='rabbitmq', amqp_connection=amqp_connection)
+        amqp_connection = os.environ.get("GALAXY_TEST_AMQP_INTERNAL_CONNECTION")
+        return create_base_test(sqlite_connection, amqp_type="rabbitmq", amqp_connection=amqp_connection)
 
     return create_app
 
 
 @pytest.fixture()
 def sqlite_app(sqlite_connection):
-
     def create_app():
-        return create_base_test(sqlite_connection, amqp_type='sqlite')
+        return create_base_test(sqlite_connection, amqp_type="sqlite")
 
     return create_app
 
@@ -50,19 +48,19 @@ def postgres_app(postgresql_proc):
     connection = "postgresql://{p.user}@{p.host}:{p.port}/".format(p=postgresql_proc)
 
     def create_app():
-        return create_base_test(connection, amqp_type='postgres')
+        return create_base_test(connection, amqp_type="postgres")
 
     return create_app
 
 
-@pytest.fixture(params=['postgres_app', 'sqlite_app', 'sqlite_rabbitmq_app'])
+@pytest.fixture(params=["postgres_app", "sqlite_app", "sqlite_rabbitmq_app"])
 def database_app(request):
-    if request.param == 'postgres_app':
-        if not which('initdb'):
+    if request.param == "postgres_app":
+        if not which("initdb"):
             pytest.skip("initdb must be on PATH for postgresql fixture")
         if not psycopg2:
             pytest.skip("psycopg2 must be installed for postgresql fixture")
-    if request.param == 'sqlite_rabbitmq_app':
-        if not os.environ.get('GALAXY_TEST_AMQP_INTERNAL_CONNECTION'):
+    if request.param == "sqlite_rabbitmq_app":
+        if not os.environ.get("GALAXY_TEST_AMQP_INTERNAL_CONNECTION"):
             pytest.skip("rabbitmq tests will be skipped if GALAXY_TEST_AMQP_INTERNAL_CONNECTION env var is unset")
     return request.getfixturevalue(request.param)
diff --git a/test/unit/app/queue_worker/test_database_heartbeat.py b/test/unit/app/queue_worker/test_database_heartbeat.py
index 8ecb1f31d0c..ff58df5fcb9 100644
--- a/test/unit/app/queue_worker/test_database_heartbeat.py
+++ b/test/unit/app/queue_worker/test_database_heartbeat.py
@@ -9,9 +9,7 @@ import galaxy.web_stack as stack
 
 @pytest.fixture
 def heartbeat_app(database_app):
-
     class QueueWorker:
-
         def send_control_task(self, *args, **kwargs):
             return
 
@@ -22,10 +20,12 @@ def heartbeat_app(database_app):
 
 @contextlib.contextmanager
 def setup_heartbeat_app(app):
-    app.config.server_name = 'test_heartbeat'
+    app.config.server_name = "test_heartbeat"
     app.config.attach_to_pools = False
     app.application_stack = stack.application_stack_instance(app=app)
-    app.database_heartbeat = heartbeat.DatabaseHeartbeat(application_stack=app.application_stack, heartbeat_interval=0.1)
+    app.database_heartbeat = heartbeat.DatabaseHeartbeat(
+        application_stack=app.application_stack, heartbeat_interval=0.1
+    )
     yield app
     app.database_heartbeat.shutdown()
 
@@ -65,7 +65,7 @@ def wait_for_assertion(assert_f):
             return v
         except AssertionError as e:
             assertion_error = e
-        time.sleep(.2)
+        time.sleep(0.2)
 
     if assertion_error:
         raise assertion_error
diff --git a/test/unit/app/queue_worker/test_queue_worker.py b/test/unit/app/queue_worker/test_queue_worker.py
index b6cbd395ce9..5e4e9a49be7 100644
--- a/test/unit/app/queue_worker/test_queue_worker.py
+++ b/test/unit/app/queue_worker/test_queue_worker.py
@@ -1,10 +1,11 @@
 import datetime
 import time
+
 try:
     from math import inf
 except ImportError:
     # python 2 doesn't have math.inf, but can use float('inf')
-    inf = float('inf')
+    inf = float("inf")
 
 import pytest
 
@@ -19,17 +20,16 @@ from galaxy.web_stack import application_stack_instance
 
 
 def bar(app, **kwargs):
-    app.some_var = 'bar'
-    app.tasks_executed.append('echo')
-    return 'bar'
+    app.some_var = "bar"
+    app.tasks_executed.append("echo")
+    return "bar"
 
 
-control_message_to_task = {'echo': bar}
+control_message_to_task = {"echo": bar}
 
 
 @pytest.fixture()
 def queue_worker_factory(request, database_app):
-
     def app_factory():
         app = setup_queue_worker_test(database_app())
         request.addfinalizer(app.queue_worker.shutdown)
@@ -40,7 +40,7 @@ def queue_worker_factory(request, database_app):
 
 
 def setup_queue_worker_test(app):
-    app.some_var = 'foo'
+    app.some_var = "foo"
     app.tasks_executed = []
     server_name = f"{app.amqp_type}.{datetime.datetime.now()}"
     app.config.server_name = server_name
@@ -59,8 +59,8 @@ def setup_queue_worker_test(app):
 
 def test_send_control_task(queue_worker_factory):
     app = queue_worker_factory()
-    send_control_task(app=app, task='echo')
-    wait_for_var(app, 'some_var', 'bar')
+    send_control_task(app=app, task="echo")
+    wait_for_var(app, "some_var", "bar")
     assert len(app.tasks_executed) == 1
 
 
@@ -70,52 +70,52 @@ def test_send_control_task_to_many_listeners(queue_worker_factory):
     app3 = queue_worker_factory()
     app4 = queue_worker_factory()
     app5 = queue_worker_factory()
-    send_control_task(app=app1, task='echo')
+    send_control_task(app=app1, task="echo")
     for app in [app1, app2, app3, app4, app5]:
-        wait_for_var(app, 'some_var', 'bar')
+        wait_for_var(app, "some_var", "bar")
         assert len(app.tasks_executed) == 1
 
 
 def test_send_control_task_get_result(queue_worker_factory):
     app = queue_worker_factory()
-    response = send_control_task(app=app, task='echo', get_response=True)
-    assert response == 'bar'
-    assert app.some_var == 'bar'
+    response = send_control_task(app=app, task="echo", get_response=True)
+    assert response == "bar"
+    assert app.some_var == "bar"
     assert len(app.tasks_executed) == 1
 
 
 def test_send_local_control_task(queue_worker_factory):
     app = queue_worker_factory()
-    send_local_control_task(app=app, task='echo')
-    wait_for_var(app, 'some_var', 'bar')
+    send_local_control_task(app=app, task="echo")
+    wait_for_var(app, "some_var", "bar")
     assert len(app.tasks_executed) == 1
 
 
 def test_send_local_control_task_with_past_message(queue_worker_factory):
     app = queue_worker_factory()
     app.queue_worker.epoch = inf
-    response = send_local_control_task(app=app, task='echo', get_response=True)
+    response = send_local_control_task(app=app, task="echo", get_response=True)
     assert len(app.tasks_executed) == 0
-    assert response == 'NO_OP'
+    assert response == "NO_OP"
 
 
 def test_send_local_control_task_with_non_target_listeners(queue_worker_factory):
     app1 = queue_worker_factory()
     app2 = queue_worker_factory()
-    assert app2.some_var == 'foo'
-    send_local_control_task(app=app1, task='echo')
-    wait_for_var(app1, 'some_var', 'bar')
-    assert app2.some_var == 'foo'
+    assert app2.some_var == "foo"
+    send_local_control_task(app=app1, task="echo")
+    wait_for_var(app1, "some_var", "bar")
+    assert app2.some_var == "foo"
     assert len(app1.tasks_executed) == 1
     assert len(app2.tasks_executed) == 0
 
 
 def test_send_control_task_noop_self(queue_worker_factory):
     app = queue_worker_factory()
-    assert app.some_var == 'foo'
-    response = send_control_task(app=app, task='echo', noop_self=True, get_response=True)
-    assert response == 'NO_OP'
-    assert app.some_var == 'foo'
+    assert app.some_var == "foo"
+    response = send_control_task(app=app, task="echo", noop_self=True, get_response=True)
+    assert response == "NO_OP"
+    assert app.some_var == "foo"
     assert len(app.tasks_executed) == 0
 
 
diff --git a/test/unit/app/test_markdown_validate.py b/test/unit/app/test_markdown_validate.py
index 4cce819f547..a1fbb048711 100644
--- a/test/unit/app/test_markdown_validate.py
+++ b/test/unit/app/test_markdown_validate.py
@@ -17,10 +17,13 @@ def assert_markdown_invalid(markdown, at_line=None):
 
 
 def test_markdown_validation():
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 hello world
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 hello ``world``
 
 Here is some more text.
@@ -29,15 +32,19 @@ Here is some more text.
 import <stdio>
 printf('hello')
 ```
-""")
+"""
+    )
     # assert valid container is fine.
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 job_metrics(job_id=THISFAKEID)
 ```
-""")
+"""
+    )
     # assert multiple valid container is fine.
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 job_metrics(job_id=THISFAKEID)
 ```
@@ -48,178 +55,250 @@ Markdown between directives.
 job_metrics(job_id=THISFAKEID)
 ```
 
-""")
+"""
+    )
 
     # assert valid container is fine at end of document.
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 job_metrics(job_id=THISFAKEID)
-```""")
+```"""
+    )
     # assert valid containers require container close
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(job_id=THISFAKEID)
-""", at_line=1)
+""",
+        at_line=1,
+    )
     # assert valid containers require container close, even at end...
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
-job_metrics(job_id=THISFAKEID)""")
+job_metrics(job_id=THISFAKEID)"""
+    )
     # assert only one command allowed
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(job_id=THISFAKEID)
 job_metrics(job_id=THISFAKEID2)
 ```
-""")
+"""
+    )
     # assert command paren is closed
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(job_id=THISFAKEID
 ```
-""")
+"""
+    )
     # assert command arg is named.
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(THISFAKEID)
 ```
-""")
+"""
+    )
     # assert quotes are fine
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 job_metrics(step="Moo Cow")
 ```
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 ```galaxy
 job_metrics(step='Moo Cow')
 ```
-""")
+"""
+    )
     # assert spaces require quotes
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(output=Moo Cow)
 ```
-""")
+"""
+    )
     # assert unmatched quotes invalid
-    assert_markdown_invalid("""
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(output="Moo Cow)
 ```
-""")
-    assert_markdown_invalid("""
+"""
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(output=Moo Cow")
 ```
-""")
-    assert_markdown_invalid("""
+"""
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(output='Moo Cow)
 ```
-""")
-    assert_markdown_invalid("""
+"""
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 job_metrics(output=Moo Cow')
 ```
-""")
+"""
+    )
 
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 workflow_display()
 ```
-""")
+"""
+    )
 
     # Test image with a composite path (param needs to be closed, can't be misnamed i.e. pathx)
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 
 ```galaxy
 history_dataset_as_image(output="cow", path="foo/bar.png")
 ```
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 
 ```galaxy
 history_dataset_as_image(output=cow, path="foo/bar.png")
 ```
-""")
-    assert_markdown_invalid("""
+"""
+    )
+    assert_markdown_invalid(
+        """
 
 ```galaxy
 history_dataset_as_image(output="cow", path="foo/bar.png)
 ```
-""", at_line=3)
-    assert_markdown_invalid("""
+""",
+        at_line=3,
+    )
+    assert_markdown_invalid(
+        """
 
 ```galaxy
 history_dataset_as_image(output="cow", pathx="foo/bar.png")
 ```
-""", at_line=3)
+""",
+        at_line=3,
+    )
 
     # Test validation of three arguments
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 history_dataset_link(output=moo, path="cow.png", label="my label")
 ```
-""")
-    assert_markdown_invalid("""
+"""
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 history_dataset_link(outputx=moo, path="cow.png", label="my label")
 ```
-""", at_line=2)
-    assert_markdown_invalid("""
+""",
+        at_line=2,
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 history_dataset_link(output=moo, pathx="cow.png", label="my label")
 ```
-""", at_line=2)
-    assert_markdown_invalid("""
+""",
+        at_line=2,
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 history_dataset_link(output=moo, path="cow.png", labelx="my label")
 ```
-""", at_line=2)
+""",
+        at_line=2,
+    )
 
     # Test validation of arguments with different whitespaces
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 history_dataset_link(output= moo, path= "cow.png", label= "my label")
 ```
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 ```galaxy
 history_dataset_link(output = moo, path = "cow.png", label = "my label")
 ```
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 ```galaxy
 history_dataset_link(output = moo, path ="cow.png", label= "my label" )
 ```
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 ```galaxy
 history_dataset_link(  output = moo, path ="cow.png", label= "my label" )
 ```
-""")
-    assert_markdown_invalid("""
+"""
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 history_dataset_link(  outputx = moo, path ="cow.png", label= "my label" )
 ```
-""", at_line=2)
-    assert_markdown_invalid("""
+""",
+        at_line=2,
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 history_dataset_link(  output = moo, pathx ="cow.png", label= "my label" )
 ```
-""", at_line=2)
-    assert_markdown_invalid("""
+""",
+        at_line=2,
+    )
+    assert_markdown_invalid(
+        """
 ```galaxy
 history_dataset_link(  output = moo, path ="cow.png", labelx= "my label" )
 ```
-""", at_line=2)
+""",
+        at_line=2,
+    )
 
-    assert_markdown_valid("""
+    assert_markdown_valid(
+        """
 ```galaxy
 visualization(id=1)
 ```
-""")
-    assert_markdown_valid("""
+"""
+    )
+    assert_markdown_valid(
+        """
 ```galaxy
 visualization(foo|bar=hello)
 ```
-""")
+"""
+    )
diff --git a/test/unit/app/test_remote_shell.py b/test/unit/app/test_remote_shell.py
index dc5e49ccce7..bae05ddd421 100644
--- a/test/unit/app/test_remote_shell.py
+++ b/test/unit/app/test_remote_shell.py
@@ -1,6 +1,9 @@
 import os
 import unittest
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 try:
     import mockssh
@@ -8,7 +11,10 @@ except ImportError:
     raise unittest.SkipTest("Skipping tests that require mockssh")
 
 from galaxy.jobs.runners.cli import CliInterface
-from galaxy.security.ssh_util import generate_ssh_keys, SSHKeys
+from galaxy.security.ssh_util import (
+    generate_ssh_keys,
+    SSHKeys,
+)
 
 
 class TestCliInterface(unittest.TestCase):
@@ -25,33 +31,35 @@ class TestCliInterface(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.ssh_keys = generate_ssh_keys()
-        cls.username = 'testuser'
-        cls.shell_params = {'username': cls.username,
-                            'private_key': cls.ssh_keys.private_key_file,
-                            'strict_host_key_checking': False,
-                            'hostname': 'localhost'}
+        cls.username = "testuser"
+        cls.shell_params = {
+            "username": cls.username,
+            "private_key": cls.ssh_keys.private_key_file,
+            "strict_host_key_checking": False,
+            "hostname": "localhost",
+        }
         cls.cli_interface = CliInterface()
 
     def test_secure_shell_plugin_without_strict(self):
         with mockssh.Server(users={self.username: self.ssh_keys.private_key_file}) as server:
-            self.shell_params['port'] = server.port
-            self.shell_params['plugin'] = 'SecureShell'
-            self.shell_params['strict_host_key_checking'] = False
+            self.shell_params["port"] = server.port
+            self.shell_params["plugin"] = "SecureShell"
+            self.shell_params["strict_host_key_checking"] = False
             self.shell = self.cli_interface.get_shell_plugin(self.shell_params)
-            result = self.shell.execute(cmd='echo hello')
-        assert result.stdout.strip() == 'hello'
+            result = self.shell.execute(cmd="echo hello")
+        assert result.stdout.strip() == "hello"
 
     def test_get_shell_plugin(self):
         with mockssh.Server(users={self.username: self.ssh_keys.private_key_file}) as server:
-            self.shell_params['port'] = server.port
-            self.shell_params['plugin'] = 'ParamikoShell'
+            self.shell_params["port"] = server.port
+            self.shell_params["plugin"] = "ParamikoShell"
             self.shell = self.cli_interface.get_shell_plugin(self.shell_params)
         assert self.shell.username == self.username
 
     def test_paramiko_shell_plugin(self):
         with mockssh.Server(users={self.username: self.ssh_keys.private_key_file}) as server:
-            self.shell_params['port'] = server.port
-            self.shell_params['plugin'] = 'ParamikoShell'
+            self.shell_params["port"] = server.port
+            self.shell_params["plugin"] = "ParamikoShell"
             self.shell = self.cli_interface.get_shell_plugin(self.shell_params)
-            result = self.shell.execute(cmd='echo hello')
-        assert result.stdout.strip() == 'hello'
+            result = self.shell.execute(cmd="echo hello")
+        assert result.stdout.strip() == "hello"
diff --git a/test/unit/app/tools/conftest.py b/test/unit/app/tools/conftest.py
index 9d645a728ec..3c150e9b44f 100644
--- a/test/unit/app/tools/conftest.py
+++ b/test/unit/app/tools/conftest.py
@@ -24,7 +24,9 @@ def tool_shed_repository_cache(mock_app):
 
 @pytest.fixture
 def repos(mock_app):
-    repositories = [create_repo(mock_app.install_model.context, changeset=i + 1, installed_changeset=i) for i in range(10)]
+    repositories = [
+        create_repo(mock_app.install_model.context, changeset=i + 1, installed_changeset=i) for i in range(10)
+    ]
     mock_app.install_model.context.flush()
     return repositories
 
@@ -33,14 +35,14 @@ def repos(mock_app):
 def tool_conf_repos(tool_shed_repository_cache):
     for i in range(10, 20):
         repo = ToolConfRepository(
-            'github.com',
-            'example',
-            'galaxyproject',
+            "github.com",
+            "example",
+            "galaxyproject",
             str(i),
             str(i + 1),
             None,
-            repository_path=mkdtemp(prefix='repository_path'),
-            tool_path='../shed_tools',
+            repository_path=mkdtemp(prefix="repository_path"),
+            tool_path="../shed_tools",
         )
         tool_shed_repository_cache.add_local_repository(repo)
     return tool_shed_repository_cache.local_repositories
@@ -48,14 +50,16 @@ def tool_conf_repos(tool_shed_repository_cache):
 
 def create_repo(session, changeset, installed_changeset, config_filename=None):
     metadata = {
-        'tools': [{
-            'add_to_tool_panel': False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
-            'guid': "github.com/galaxyproject/example/test_tool/0.%s" % changeset,
-            'tool_config': 'tool.xml'
-        }],
+        "tools": [
+            {
+                "add_to_tool_panel": False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
+                "guid": "github.com/galaxyproject/example/test_tool/0.%s" % changeset,
+                "tool_config": "tool.xml",
+            }
+        ],
     }
     if config_filename:
-        metadata['shed_config_filename'] = config_filename
+        metadata["shed_config_filename"] = config_filename
     repository = tool_shed_install.ToolShedRepository(metadata_=metadata)
     repository.tool_shed = "github.com"
     repository.owner = "galaxyproject"
@@ -67,10 +71,10 @@ def create_repo(session, changeset, installed_changeset, config_filename=None):
     session.add(repository)
     session.flush()
     tool_dependency = tool_shed_install.ToolDependency(
-        name='Name',
-        version='100',
-        type='package',
-        status='ok',
+        name="Name",
+        version="100",
+        type="package",
+        status="ok",
         tool_shed_repository_id=repository.id,
     )
     session.add(tool_dependency)
diff --git a/test/unit/app/tools/test_actions.py b/test/unit/app/tools/test_actions.py
index 3af9965926b..b522d5e093b 100644
--- a/test/unit/app/tools/test_actions.py
+++ b/test/unit/app/tools/test_actions.py
@@ -8,15 +8,14 @@ from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.actions import (
     DefaultToolAction,
     determine_output_format,
-    on_text_for_names
+    on_text_for_names,
 )
 from galaxy.util import XML
 
-
 # I cannot think of a saner way to test if data is being wrapped than use a
 # data param in the output label - though you would probably never want to do
 # this.
-DATA_IN_LABEL_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
+DATA_IN_LABEL_TOOL_CONTENTS = """<tool id="test_tool" name="Test Tool">
     <command>echo "$param1" &lt; $out1</command>
     <inputs>
         <repeat name="repeat1" label="The Repeat">
@@ -27,11 +26,11 @@ DATA_IN_LABEL_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
         <data name="out1" format="data" label="Output (${repeat1[0].param1})" />
     </outputs>
 </tool>
-'''
+"""
 
 # Tool with two outputs - used to verify all datasets within same job get same
 # object store id.
-TWO_OUTPUTS = '''<tool id="test_tool" name="Test Tool">
+TWO_OUTPUTS = """<tool id="test_tool" name="Test Tool">
     <command>echo "$param1" &lt; $out1</command>
     <inputs>
         <param type="text" name="param1" value="" />
@@ -41,7 +40,7 @@ TWO_OUTPUTS = '''<tool id="test_tool" name="Test Tool">
         <data name="out2" format="data" label="Output 2 ($param1)" />
     </outputs>
 </tool>
-'''
+"""
 
 
 def test_on_text_for_names():
@@ -58,15 +57,11 @@ def test_on_text_for_names():
 
 
 class DefaultToolActionTestCase(unittest.TestCase, tools_support.UsesTools):
-
     def setUp(self):
         self.setup_app()
         history = model.History()
         self.history = history
-        self.trans = MockTrans(
-            self.app,
-            self.history
-        )
+        self.trans = MockTrans(self.app, self.history)
         self.app.model.context.add(history)
         self.app.model.context.flush()
         self.action = DefaultToolAction()
@@ -89,7 +84,7 @@ class DefaultToolActionTestCase(unittest.TestCase, tools_support.UsesTools):
             "param1": hda1,
             "repeat1": [
                 {"param2": hda2},
-            ]
+            ],
         }
         job, output = self._simple_execute(
             tools_support.SIMPLE_CAT_TOOL_CONTENTS,
@@ -119,10 +114,10 @@ class DefaultToolActionTestCase(unittest.TestCase, tools_support.UsesTools):
             return
         raise AssertionError("Tool execution succeeded for inactive user!")
 
-    def __add_dataset(self, state='ok'):
+    def __add_dataset(self, state="ok"):
         hda = model.HistoryDatasetAssociation()
         hda.dataset = model.Dataset()
-        hda.dataset.state = 'ok'
+        hda.dataset.state = "ok"
         hda.dataset.external_filename = "/tmp/datasets/dataset_001.dat"
         self.history.add_dataset(hda)
         self.app.model.context.flush()
@@ -175,20 +170,24 @@ def test_determine_output_format():
 
     change_format_output = quick_output("fastq", change_format_xml=change_format_xml)
     # Test maching a change_format when.
-    __assert_output_format_is("fastqillumina", change_format_output, param_context={"options_type": {"output_type": "illumina"}})
+    __assert_output_format_is(
+        "fastqillumina", change_format_output, param_context={"options_type": {"output_type": "illumina"}}
+    )
     # Test change_format but no match
     __assert_output_format_is("fastq", change_format_output, param_context={"options_type": {"output_type": "sanger"}})
 
-    change_on_metadata_xml_template = string.Template("""<data><change_format>
+    change_on_metadata_xml_template = string.Template(
+        """<data><change_format>
         <when input_dataset="${input}" attribute="random_field" value="1" format="fastqsolexa" />
         <when input_dataset="${input}" attribute="random_field" value="2" format="fastqillumina" />
-    </change_format></data>""")
+    </change_format></data>"""
+    )
 
-    change_on_metadata_illumina = change_on_metadata_xml_template.safe_substitute({'input': "i2"})
+    change_on_metadata_illumina = change_on_metadata_xml_template.safe_substitute({"input": "i2"})
     change_on_metadata_output = quick_output("fastq", change_format_xml=change_on_metadata_illumina)
     __assert_output_format_is("fastqillumina", change_on_metadata_output, [("i1", "txt"), ("i2", "txt")])
 
-    change_on_metadata_solexa = change_on_metadata_xml_template.safe_substitute({'input': "i1"})
+    change_on_metadata_solexa = change_on_metadata_xml_template.safe_substitute({"input": "i1"})
     change_on_metadata_output = quick_output("fastq", change_format_xml=change_on_metadata_solexa)
     __assert_output_format_is("fastqsolexa", change_on_metadata_output, [("i1", "txt"), ("i2", "txt")])
 
@@ -213,8 +212,12 @@ def __assert_output_format_is(expected, output, input_extensions=None, param_con
         c1 = model.DatasetCollection(collection_type="pair")
         hc1 = model.HistoryDatasetCollectionAssociation(collection=c1, name="HistoryCollectionTest1")
 
-        dce1 = model.DatasetCollectionElement(collection=c1, element=hda_forward, element_identifier="forward", element_index=0)
-        dce2 = model.DatasetCollectionElement(collection=c1, element=hda_reverse, element_identifier="reverse", element_index=1)
+        dce1 = model.DatasetCollectionElement(
+            collection=c1, element=hda_forward, element_identifier="forward", element_index=0
+        )
+        dce2 = model.DatasetCollectionElement(
+            collection=c1, element=hda_reverse, element_identifier="reverse", element_index=1
+        )
         c1.elements = [dce1, dce2]
 
         input_collections["hdcai"] = [(hc1, False)]
@@ -235,7 +238,6 @@ def quick_output(format, format_source=None, change_format_xml=None):
 
 
 class MockTrans:
-
     def __init__(self, app, history, user=None):
         self.app = app
         self.history = history
@@ -271,7 +273,6 @@ class MockTrans:
 
 
 class MockObjectStore:
-
     def __init__(self):
         self.created_datasets = []
         self.first_create = True
diff --git a/test/unit/app/tools/test_citations.py b/test/unit/app/tools/test_citations.py
index 8e5371b4cd9..ab6b79292ee 100644
--- a/test/unit/app/tools/test_citations.py
+++ b/test/unit/app/tools/test_citations.py
@@ -37,6 +37,5 @@ def test_citation_collection():
 
 
 class QuickBibtexCitation(BibtexCitation):
-
     def __init__(self, raw_bibtex):
         self.raw_bibtex = raw_bibtex
diff --git a/test/unit/app/tools/test_collect_primary_datasets.py b/test/unit/app/tools/test_collect_primary_datasets.py
index 05b2816d3de..82697984a80 100644
--- a/test/unit/app/tools/test_collect_primary_datasets.py
+++ b/test/unit/app/tools/test_collect_primary_datasets.py
@@ -4,7 +4,7 @@ import unittest
 
 from galaxy import (
     model,
-    util
+    util,
 )
 from galaxy.app_unittest_utils import tools_support
 from galaxy.tool_util.parser import output_collection_def
@@ -19,7 +19,6 @@ DEFAULT_EXTRA_NAME = "test1"
 
 
 class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools):
-
     def setUp(self):
         self.setup_app()
         object_store = MockObjectStore()
@@ -61,10 +60,12 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         assert created_hda_1.dbkey == "?"
 
     def test_collect_multiple_recurse(self):
-        self._replace_output_collectors('''<output>
+        self._replace_output_collectors(
+            """<output>
             <discover_datasets pattern="__name__" directory="subdir1" recurse="true" ext="txt" />
             <discover_datasets pattern="__name__" directory="subdir2" recurse="true" ext="txt" />
-        </output>''')
+        </output>"""
+        )
         path1 = self._setup_extra_file(filename="test1", subdir="subdir1")
         path2 = self._setup_extra_file(filename="test2", subdir="subdir2/nested1/")
         path3 = self._setup_extra_file(filename="test3", subdir="subdir2")
@@ -86,18 +87,23 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         self.app.object_store.assert_created_with_path(created_hda_3.dataset, path3)
 
     def test_collect_multiple_recurse_dict(self):
-        self._replace_output_collectors_from_dict({
-            "discover_datasets": [{
-                "pattern": "__name__",
-                "directory": "subdir1",
-                "recurse": True,
-                "format": "txt",
-            }, {
-                "pattern": "__name__",
-                "directory": "subdir2",
-                "recurse": True,
-                "format": "txt",
-            }]}
+        self._replace_output_collectors_from_dict(
+            {
+                "discover_datasets": [
+                    {
+                        "pattern": "__name__",
+                        "directory": "subdir1",
+                        "recurse": True,
+                        "format": "txt",
+                    },
+                    {
+                        "pattern": "__name__",
+                        "directory": "subdir2",
+                        "recurse": True,
+                        "format": "txt",
+                    },
+                ]
+            }
         )
         path1 = self._setup_extra_file(filename="test1", subdir="subdir1")
         path2 = self._setup_extra_file(filename="test2", subdir="subdir2/nested1/")
@@ -120,9 +126,11 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         self.app.object_store.assert_created_with_path(created_hda_3.dataset, path3)
 
     def test_collect_sorted_reverse(self):
-        self._replace_output_collectors('''<output>
+        self._replace_output_collectors(
+            """<output>
             <discover_datasets pattern="__name__" directory="subdir_for_name_discovery" sort_by="reverse_filename" ext="txt" />
-        </output>''')
+        </output>"""
+        )
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test2")
 
@@ -133,9 +141,11 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         assert list(datasets[DEFAULT_TOOL_OUTPUT].keys()) == ["test2", "test1"]
 
     def test_collect_sorted_name(self):
-        self._replace_output_collectors('''<output>
+        self._replace_output_collectors(
+            """<output>
             <discover_datasets pattern="[abc](?P&lt;name&gt;.*)" directory="subdir_for_name_discovery" sort_by="name" ext="txt" />
-        </output>''')
+        </output>"""
+        )
         # Setup filenames in reverse order and ensure name is used as key.
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="ctest1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="btest2")
@@ -148,9 +158,11 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         assert list(datasets[DEFAULT_TOOL_OUTPUT].keys()) == ["test1", "test2", "test3"]
 
     def test_collect_sorted_numeric(self):
-        self._replace_output_collectors('''<output>
+        self._replace_output_collectors(
+            """<output>
             <discover_datasets pattern="[abc](?P&lt;name&gt;.*)" directory="subdir_for_name_discovery" sort_by="numeric_name" ext="txt" />
-        </output>''')
+        </output>"""
+        )
         # Setup filenames in reverse order and ensure name is used as key.
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="c1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="b10")
@@ -222,7 +234,9 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         assert extra_job_assoc.name == "__new_primary_file_out1|test1__"
 
     def test_pattern_override_designation(self):
-        self._replace_output_collectors('''<output><discover_datasets pattern="__designation__" directory="subdir" ext="txt" /></output>''')
+        self._replace_output_collectors(
+            """<output><discover_datasets pattern="__designation__" directory="subdir" ext="txt" /></output>"""
+        )
         self._setup_extra_file(subdir="subdir", filename="foo.txt")
         primary_outputs = self._collect()[DEFAULT_TOOL_OUTPUT]
         assert len(primary_outputs) == 1
@@ -233,7 +247,9 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         assert created_hda.dbkey == "btau"
 
     def test_name_and_ext_pattern(self):
-        self._replace_output_collectors('''<output><discover_datasets pattern="__name_and_ext__" directory="subdir" /></output>''')
+        self._replace_output_collectors(
+            """<output><discover_datasets pattern="__name_and_ext__" directory="subdir" /></output>"""
+        )
         self._setup_extra_file(subdir="subdir", filename="foo1.txt")
         self._setup_extra_file(subdir="subdir", filename="foo2.tabular")
         primary_outputs = self._collect()[DEFAULT_TOOL_OUTPUT]
@@ -247,7 +263,9 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         # Hypothetical oral metagenomic classifier that populates a directory
         # of files based on name and genome. Use custom regex pattern to grab
         # and classify these files.
-        self._replace_output_collectors('''<output><discover_datasets pattern="(?P&lt;designation&gt;.*)__(?P&lt;dbkey&gt;.*).fasta" directory="genome_breakdown" ext="fasta" /></output>''')
+        self._replace_output_collectors(
+            """<output><discover_datasets pattern="(?P&lt;designation&gt;.*)__(?P&lt;dbkey&gt;.*).fasta" directory="genome_breakdown" ext="fasta" /></output>"""
+        )
         self._setup_extra_file(subdir="genome_breakdown", filename="samp1__hg19.fasta")
         self._setup_extra_file(subdir="genome_breakdown", filename="samp2__lactLact.fasta")
         self._setup_extra_file(subdir="genome_breakdown", filename="samp3__hg19.fasta")
@@ -265,13 +283,15 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
             assert hda.dbkey == genomes[key]
 
     def test_custom_pattern_dict(self):
-        self._replace_output_collectors_from_dict({
-            "discover_datasets": {
-                "pattern": "(?P<designation>.*)__(?P<dbkey>.*).fasta",
-                "directory": "genome_breakdown",
-                "format": "fasta",
+        self._replace_output_collectors_from_dict(
+            {
+                "discover_datasets": {
+                    "pattern": "(?P<designation>.*)__(?P<dbkey>.*).fasta",
+                    "directory": "genome_breakdown",
+                    "format": "fasta",
+                }
             }
-        })
+        )
 
         self._setup_extra_file(subdir="genome_breakdown", filename="samp1__hg19.fasta")
         self._setup_extra_file(subdir="genome_breakdown", filename="samp2__lactLact.fasta")
@@ -290,14 +310,16 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
             assert hda.dbkey == genomes[key]
 
     def test_name_versus_designation(self):
-        """ This test demonstrates the difference between name and desgination
+        """This test demonstrates the difference between name and desgination
         in grouping patterns and named patterns such as __designation__,
         __name__, __designation_and_ext__, and __name_and_ext__.
         """
-        self._replace_output_collectors('''<output>
+        self._replace_output_collectors(
+            """<output>
             <discover_datasets pattern="__name_and_ext__" directory="subdir_for_name_discovery" />
             <discover_datasets pattern="__designation_and_ext__" directory="subdir_for_designation_discovery" />
-        </output>''')
+        </output>"""
+        )
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="example1.txt")
         self._setup_extra_file(subdir="subdir_for_designation_discovery", filename="example2.txt")
         primary_outputs = self._collect()[DEFAULT_TOOL_OUTPUT]
@@ -309,9 +331,11 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         assert designation_output.name == "{} ({})".format(self.hda.name, "example2")
 
     def test_cannot_read_files_outside_job_directory(self):
-        self._replace_output_collectors('''<output>
+        self._replace_output_collectors(
+            """<output>
             <discover_datasets pattern="__name_and_ext__" directory="../../secrets" />
-        </output>''')
+        </output>"""
+        )
         exception_thrown = False
         try:
             self._collect()
@@ -336,16 +360,30 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         else:
             tool_provided_metadata = LegacyToolProvidedMetadata(meta_file)
 
-        return self.tool.discover_outputs(self.outputs, {}, tool_provided_metadata, job_working_directory, job=self.job, input_ext="txt", input_dbkey="btau")
+        return self.tool.discover_outputs(
+            self.outputs,
+            {},
+            tool_provided_metadata,
+            job_working_directory,
+            job=self.job,
+            input_ext="txt",
+            input_dbkey="btau",
+        )
 
     def _replace_output_collectors(self, xml_str):
         # Rewrite tool as if it had been created with output containing
         # supplied dataset_collector elem.
         elem = util.parse_xml_string(xml_str)
-        self.tool.outputs[DEFAULT_TOOL_OUTPUT].dataset_collector_descriptions = output_collection_def.dataset_collector_descriptions_from_elem(elem)
+        self.tool.outputs[
+            DEFAULT_TOOL_OUTPUT
+        ].dataset_collector_descriptions = output_collection_def.dataset_collector_descriptions_from_elem(elem)
 
     def _replace_output_collectors_from_dict(self, output_dict):
-        self.tool.outputs[DEFAULT_TOOL_OUTPUT].dataset_collector_descriptions = output_collection_def.dataset_collector_descriptions_from_output_dict(output_dict)
+        self.tool.outputs[
+            DEFAULT_TOOL_OUTPUT
+        ].dataset_collector_descriptions = output_collection_def.dataset_collector_descriptions_from_output_dict(
+            output_dict
+        )
 
     def _append_job_json(self, object, output_path=None, line_type="new_primary_dataset"):
         object["type"] = line_type
@@ -402,7 +440,6 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
 
 
 class MockObjectStore:
-
     def __init__(self):
         self.created_datasets = {}
 
diff --git a/test/unit/app/tools/test_column_parameters.py b/test/unit/app/tools/test_column_parameters.py
index 5ef38893cb6..fbead80450c 100644
--- a/test/unit/app/tools/test_column_parameters.py
+++ b/test/unit/app/tools/test_column_parameters.py
@@ -8,7 +8,6 @@ from .util import BaseParameterTestCase
 
 
 class DataColumnParameterTestCase(BaseParameterTestCase):
-
     def test_not_optional_by_default(self):
         assert not self.__param_optional()
 
@@ -43,19 +42,19 @@ class DataColumnParameterTestCase(BaseParameterTestCase):
         assert value == ["1", "2", "3"]
 
     def test_get_initial_value_default(self):
-        self.assertEqual('1', self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
+        self.assertEqual("1", self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
 
     def test_get_initial_value_override_legacy(self):
         self.other_attributes = "default_value='2'"
-        self.assertEqual('2', self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
+        self.assertEqual("2", self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
 
     def test_get_initial_value_override_newstyle(self):
         self.other_attributes = "value='2'"
-        self.assertEqual('2', self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
+        self.assertEqual("2", self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
 
     def test_get_initial_value_override_newstyle_strips_c(self):
         self.other_attributes = "value='c2'"
-        self.assertEqual('2', self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
+        self.assertEqual("2", self.param.get_initial_value(self.trans, {"input_tsv": self.build_ready_hda()}))
 
     def setUp(self):
         super().setUp()
@@ -80,8 +79,12 @@ class DataColumnParameterTestCase(BaseParameterTestCase):
     def build_ready_hda(self):
         hist = model.History()
         self.app.model.context.add(hist)
-        ready_hda = hist.add_dataset(model.HistoryDatasetAssociation(extension='interval', create_dataset=True, sa_session=self.app.model.context))
-        ready_hda.set_dataset_state('ok')
+        ready_hda = hist.add_dataset(
+            model.HistoryDatasetAssociation(
+                extension="interval", create_dataset=True, sa_session=self.app.model.context
+            )
+        )
+        ready_hda.set_dataset_state("ok")
         return ready_hda
 
     @property
@@ -96,7 +99,7 @@ class DataColumnParameterTestCase(BaseParameterTestCase):
             data_ref_text = ""
             if self.set_data_ref:
                 data_ref_text = 'data_ref="input_tsv"'
-            template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>'''
+            template_xml = """<param name="my_name" type="%s" %s %s %s %s></param>"""
             param_str = template_xml % (self.type, data_ref_text, multi_text, optional_text, self.other_attributes)
             self._param = self._parameter_for(xml=param_str)
             self._param.ref_input = bunch.Bunch(formats=[datatypes_registry.get_datatype_by_extension("tabular")])
diff --git a/test/unit/app/tools/test_data_fetch.py b/test/unit/app/tools/test_data_fetch.py
index c5b75e3b508..332b0bd7037 100644
--- a/test/unit/app/tools/test_data_fetch.py
+++ b/test/unit/app/tools/test_data_fetch.py
@@ -10,8 +10,7 @@ import pytest
 from galaxy.tools.data_fetch import main
 
 github_fetch = pytest.mark.skipif(
-    not environ.get('GALAXY_TEST_INCLUDE_SLOW'),
-    reason="GALAXY_TEST_INCLUDE_SLOW not set"
+    not environ.get("GALAXY_TEST_INCLUDE_SLOW"), reason="GALAXY_TEST_INCLUDE_SLOW not set"
 )
 
 
@@ -27,12 +26,7 @@ def test_simple_path_get():
                     "destination": {
                         "type": "hdas",
                     },
-                    "elements": [
-                        {
-                            "src": "path",
-                            "path": example_path
-                        }
-                    ]
+                    "elements": [{"src": "path", "path": example_path}],
                 }
             ]
         }
@@ -54,12 +48,7 @@ def test_simple_list_path_get():
                         "type": "hdca",
                         "object_id": 76,
                     },
-                    "elements": [
-                        {
-                            "src": "path",
-                            "path": example_path
-                        }
-                    ]
+                    "elements": [{"src": "path", "path": example_path}],
                 }
             ]
         }
@@ -86,15 +75,12 @@ def test_hdas_single_url_error():
                         "type": "hdas",
                     },
                     "elements": [
-                        {
-                            "src": "path",
-                            "path": example_path
-                        },
+                        {"src": "path", "path": example_path},
                         {
                             "src": "url",
-                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed"
-                        }
-                    ]
+                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed",
+                        },
+                    ],
                 }
             ]
         }
@@ -108,7 +94,9 @@ def test_hdas_single_url_error():
         assert "error_message" not in elements[0]
         assert "error_message" in elements[1]
         error = elements[1]["error_message"]
-        assert "Failed to fetch url https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed" in error
+        assert (
+            "Failed to fetch url https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed" in error
+        )
 
 
 @github_fetch
@@ -125,15 +113,12 @@ def test_hdca_collection_element_failed():
                         "type": "hdca",
                     },
                     "elements": [
-                        {
-                            "src": "path",
-                            "path": example_path
-                        },
+                        {"src": "path", "path": example_path},
                         {
                             "src": "url",
-                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed"
-                        }
-                    ]
+                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed",
+                        },
+                    ],
                 }
             ]
         }
@@ -143,7 +128,9 @@ def test_hdca_collection_element_failed():
         output = galaxy_json.get("__unnamed_outputs")[0]
         assert "error_message" in output
         error = output["error_message"]
-        assert "Failed to fetch url https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed" in error
+        assert (
+            "Failed to fetch url https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed" in error
+        )
 
 
 @github_fetch
@@ -161,17 +148,14 @@ def test_hdca_allow_failed_collections():
                         "type": "hdca",
                     },
                     "elements": [
-                        {
-                            "src": "path",
-                            "path": example_path
-                        },
+                        {"src": "path", "path": example_path},
                         {
                             "src": "url",
-                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed"
-                        }
-                    ]
+                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed",
+                        },
+                    ],
                 }
-            ]
+            ],
         }
         execute_context.execute_request(request)
         galaxy_json = execute_context.galaxy_json
@@ -184,7 +168,9 @@ def test_hdca_allow_failed_collections():
         assert "error_message" not in elements[0]
         assert "error_message" in elements[1]
         error = elements[1]["error_message"]
-        assert "Failed to fetch url https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed" in error
+        assert (
+            "Failed to fetch url https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/12.bed" in error
+        )
 
 
 def test_hdca_failed_expansion():
@@ -227,7 +213,6 @@ def _execute_context():
 
 
 class ExecuteContext:
-
     def __init__(self, directory):
         self.job_directory = directory
         self.galaxy_json_path = os.path.join(directory, "galaxy.json")
diff --git a/test/unit/app/tools/test_data_parameters.py b/test/unit/app/tools/test_data_parameters.py
index 10e44752910..6a08da1e334 100644
--- a/test/unit/app/tools/test_data_parameters.py
+++ b/test/unit/app/tools/test_data_parameters.py
@@ -1,4 +1,8 @@
-from typing import Any, Optional, Tuple
+from typing import (
+    Any,
+    Optional,
+    Tuple,
+)
 
 from galaxy import model
 from galaxy.app_unittest_utils import galaxy_mock
@@ -6,11 +10,10 @@ from .util import BaseParameterTestCase
 
 
 class DataToolParameterTestCase(BaseParameterTestCase):
-
     def test_to_python_none_values(self):
         assert self.param.to_python(None, self.app) is None
-        assert self.param.to_python('None', self.app) is None
-        assert self.param.to_python('', self.app) is None
+        assert self.param.to_python("None", self.app) is None
+        assert self.param.to_python("", self.app) is None
 
     def test_to_python_hda(self):
         hda = self._new_hda()
@@ -29,22 +32,22 @@ class DataToolParameterTestCase(BaseParameterTestCase):
         # Selection is Optional. may be selected with other stuff,
         # not sure the UI should really allow this but easy enough
         # to just filter it out.
-        self.assertEqual([hda], self.param.to_python('%s,None' % hda.id, self.app))
+        self.assertEqual([hda], self.param.to_python("%s,None" % hda.id, self.app))
 
     def test_field_filter_on_types(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
         hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
         self.stub_active_datasets(hda1, hda2)
         field = self._simple_field()
-        assert len(field['options']['hda']) == 2
-        assert field['options']['hda'][0]['name'] == "hda2"
-        assert field['options']['hda'][1]['name'] == "hda1"
+        assert len(field["options"]["hda"]) == 2
+        assert field["options"]["hda"][0]["name"] == "hda2"
+        assert field["options"]["hda"][1]["name"] == "hda1"
 
-        hda2.extension = 'data'
+        hda2.extension = "data"
         hda2.conversion_destination = (False, None, None)
         field = self._simple_field()
-        assert len(field['options']['hda']) == 1, field
-        assert field['options']['hda'][0]['name'] == "hda1"
+        assert len(field["options"]["hda"]) == 1, field
+        assert field["options"]["hda"][0]["name"] == "hda1"
 
     def test_field_display_hidden_hdas_only_if_selected(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
@@ -53,8 +56,8 @@ class DataToolParameterTestCase(BaseParameterTestCase):
         hda2.visible = False
         self.stub_active_datasets(hda1, hda2)
         field = self._simple_field(other_values={"data2": hda2})
-        assert len(field['options']['hda']) == 1  # hda1 not an option, not visible or selected
-        assert field['options']['hda'][0]['name'] == "(hidden) hda2"
+        assert len(field["options"]["hda"]) == 1  # hda1 not an option, not visible or selected
+        assert field["options"]["hda"][0]["name"] == "(hidden) hda2"
 
     def test_field_display_deleted_hdas_only_if_selected(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
@@ -63,45 +66,45 @@ class DataToolParameterTestCase(BaseParameterTestCase):
         hda2.deleted = True
         self.stub_active_datasets(hda1, hda2)
         field = self._simple_field(other_values={"data2": hda2})
-        assert len(field['options']['hda']) == 1  # hda1 not an option, not visible or selected
-        assert field['options']['hda'][0]['name'] == "(deleted) hda2"
+        assert len(field["options"]["hda"]) == 1  # hda1 not an option, not visible or selected
+        assert field["options"]["hda"][0]["name"] == "(deleted) hda2"
 
     def test_field_implicit_conversion_new(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
-        hda1.extension = 'data'
+        hda1.extension = "data"
         hda1.conversion_destination = (False, "tabular", None)
         self.stub_active_datasets(hda1)
         field = self._simple_field()
-        assert len(field['options']['hda']) == 1
-        assert field['options']['hda'][0]['name'] == "hda1 (as tabular)"
-        assert field['options']['hda'][0]['hid'] == 1
+        assert len(field["options"]["hda"]) == 1
+        assert field["options"]["hda"][0]["name"] == "hda1 (as tabular)"
+        assert field["options"]["hda"][0]["hid"] == 1
 
     def test_field_implicit_conversion_existing(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
-        hda1.extension = 'data'
+        hda1.extension = "data"
         hda1.conversion_destination = (False, "tabular", MockHistoryDatasetAssociation(name="hda1converted", id=2))
         self.stub_active_datasets(hda1)
         field = self._simple_field()
-        assert len(field['options']['hda']) == 1
-        assert field['options']['hda'][0]['name'] == "hda1 (as tabular)"
+        assert len(field["options"]["hda"]) == 1
+        assert field["options"]["hda"][0]["name"] == "hda1 (as tabular)"
         # This is difference with previous test, value is existing
         # hda id not new one.
-        assert field['options']['hda'][0]['hid'] == 2
+        assert field["options"]["hda"][0]["hid"] == 2
 
     def test_field_multiple(self):
         self.multiple = True
         field = self._simple_field()
-        assert field['multiple']
+        assert field["multiple"]
 
     def test_field_empty_selection(self):
         field = self._simple_field()
-        assert len(field['options']['hda']) == 0
-        assert len(field['options']['hdca']) == 0
+        assert len(field["options"]["hda"]) == 0
+        assert len(field["options"]["hdca"]) == 0
 
     def test_field_empty_selection_optional(self):
         self.optional = True
         field = self._simple_field()
-        assert field['optional']
+        assert field["optional"]
 
     def test_get_initial_value(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
@@ -126,7 +129,7 @@ class DataToolParameterTestCase(BaseParameterTestCase):
 
     def test_get_initial_with_previously_converted_data(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
-        hda1.extension = 'data'
+        hda1.extension = "data"
         converted = MockHistoryDatasetAssociation(name="hda1converted", id=2)
         hda1.conversion_destination = (False, "tabular", converted)
         self.stub_active_datasets(hda1)
@@ -134,7 +137,7 @@ class DataToolParameterTestCase(BaseParameterTestCase):
 
     def test_get_initial_with_to_be_converted_data(self):
         hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
-        hda1.extension = 'data'
+        hda1.extension = "data"
         hda1.conversion_destination = (False, "tabular", None)
         self.stub_active_datasets(hda1)
         assert hda1 == self.param.get_initial_value(self.trans, {}), hda1
@@ -173,7 +176,7 @@ class DataToolParameterTestCase(BaseParameterTestCase):
             optional_text = ""
             if self.optional:
                 optional_text = 'optional="True"'
-            template_xml = '''<param name="data2" type="data" format="txt" %s %s></param>'''
+            template_xml = """<param name="data2" type="data" format="txt" %s %s></param>"""
             param_str = template_xml % (multi_text, optional_text)
             self._param = self._parameter_for(tool=self.mock_tool, xml=param_str)
 
@@ -181,7 +184,7 @@ class DataToolParameterTestCase(BaseParameterTestCase):
 
 
 class MockHistoryDatasetAssociation:
-    """ Fake HistoryDatasetAssociation stubbed out for testing matching and
+    """Fake HistoryDatasetAssociation stubbed out for testing matching and
     stuff like that.
     """
 
diff --git a/test/unit/app/tools/test_dataset_matcher.py b/test/unit/app/tools/test_dataset_matcher.py
index e403906a204..fde2f9baae5 100644
--- a/test/unit/app/tools/test_dataset_matcher.py
+++ b/test/unit/app/tools/test_dataset_matcher.py
@@ -4,7 +4,7 @@ from galaxy import model
 from galaxy.app_unittest_utils.tools_support import UsesApp
 from galaxy.tools.parameters import (
     basic,
-    dataset_matcher
+    dataset_matcher,
 )
 from galaxy.util import (
     bunch,
@@ -13,8 +13,7 @@ from galaxy.util import (
 from .test_data_parameters import MockHistoryDatasetAssociation
 
 
-class MockTool():
-
+class MockTool:
     def __init__(self, app):
         self.app = app
         self.tool_type = "default"
@@ -22,7 +21,6 @@ class MockTool():
 
 
 class DatasetMatcherTestCase(TestCase, UsesApp):
-
     def test_hda_mismatches(self):
         # Datasets not visible are not "valid" for param.
         self.mock_hda.visible = False
@@ -30,14 +28,14 @@ class DatasetMatcherTestCase(TestCase, UsesApp):
 
         # Datasets that don't match datatype are not valid.
         self.mock_hda.visible = True
-        self.mock_hda.extension = 'data'
+        self.mock_hda.extension = "data"
         self.mock_hda.conversion_destination = (False, None, None)
         assert not self.test_context.hda_match(self.mock_hda)
 
     def test_valid_hda_direct_match(self):
         # Datasets that visible and matching are valid
         self.mock_hda.visible = True
-        self.mock_hda.extension = 'txt'
+        self.mock_hda.extension = "txt"
         hda_match = self.test_context.hda_match(self.mock_hda, check_implicit_conversions=False)
         assert hda_match
 
@@ -49,7 +47,7 @@ class DatasetMatcherTestCase(TestCase, UsesApp):
     def test_valid_hda_implicit_convered(self):
         # Find conversion returns an HDA to an already implicitly converted
         # dataset.
-        self.mock_hda.extension = 'data'
+        self.mock_hda.extension = "data"
         converted_hda = model.HistoryDatasetAssociation()
         self.mock_hda.conversion_destination = (False, "tabular", converted_hda)
         hda_match = self.test_context.hda_match(self.mock_hda)
@@ -62,7 +60,7 @@ class DatasetMatcherTestCase(TestCase, UsesApp):
     def test_hda_match_implicit_can_convert(self):
         # Find conversion returns a target extension to convert to, but not
         # a previously implicitly converted dataset.
-        self.mock_hda.extension = 'data'
+        self.mock_hda.extension = "data"
         self.mock_hda.conversion_destination = (False, "tabular", None)
         hda_match = self.test_context.hda_match(self.mock_hda)
 
@@ -72,7 +70,7 @@ class DatasetMatcherTestCase(TestCase, UsesApp):
         assert hda_match.target_ext == "tabular"
 
     def test_hda_match_properly_skips_conversion(self):
-        self.mock_hda.extension = 'data'
+        self.mock_hda.extension = "data"
         self.mock_hda.conversion_destination = (False, "tabular", bunch.Bunch())
         hda_match = self.test_context.hda_match(self.mock_hda, check_implicit_conversions=False)
         assert not hda_match
@@ -163,14 +161,14 @@ class DatasetMatcherTestCase(TestCase, UsesApp):
         if self._test_context is None:
             option_xml = ""
             if self.filtered_param:
-                option_xml = '''<options><filter type="data_meta" ref="data1" key="dbkey" /></options>'''
+                option_xml = """<options><filter type="data_meta" ref="data1" key="dbkey" /></options>"""
             if self.metadata_filtered_param:
-                option_xml = '''
+                option_xml = """
                     <options options_filter_attribute="metadata.foo">
                       <filter type="add_value" value="bar" />
                       <filter type="add_value" value="baz" />
-                    </options>'''
-            param_xml = XML('''<param name="data2" type="data" format="txt">%s</param>''' % option_xml)
+                    </options>"""
+            param_xml = XML("""<param name="data2" type="data" format="txt">%s</param>""" % option_xml)
             self.param = basic.DataToolParameter(
                 self.tool,
                 param_xml,
@@ -181,8 +179,7 @@ class DatasetMatcherTestCase(TestCase, UsesApp):
                 workflow_building_mode=True,
             )
             self._test_context = dataset_matcher.get_dataset_matcher_factory(trans).dataset_matcher(
-                param=self.param,
-                other_values=self.other_values
+                param=self.param, other_values=self.other_values
             )
 
         return self._test_context
diff --git a/test/unit/app/tools/test_evaluation.py b/test/unit/app/tools/test_evaluation.py
index b6b0ce484c2..d2937fa1db1 100644
--- a/test/unit/app/tools/test_evaluation.py
+++ b/test/unit/app/tools/test_evaluation.py
@@ -15,17 +15,18 @@ from galaxy.model import (
 )
 from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.evaluation import ToolEvaluator
+
 # For MockTool
 from galaxy.tools.parameters import params_from_strings
 from galaxy.tools.parameters.basic import (
     DataToolParameter,
     IntegerToolParameter,
-    SelectToolParameter
+    SelectToolParameter,
 )
 from galaxy.tools.parameters.grouping import (
     Conditional,
     ConditionalWhen,
-    Repeat
+    Repeat,
 )
 from galaxy.util import XML
 from galaxy.util.bunch import Bunch
@@ -37,7 +38,6 @@ TEST_GALAXY_URL = "http://mycool.galaxyproject.org:8456"
 
 
 class ToolEvaluatorTestCase(TestCase, UsesApp):
-
     def setUp(self):
         self.setup_app()
         self.tool = MockTool(self.app)
@@ -54,14 +54,18 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         self._setup_test_bwa_job()
         self._set_compute_environment()
         command_line, extra_filenames, _ = self.evaluator.build()
-        self.assertEqual(command_line, "bwa --thresh=4 --in=/galaxy/files/dataset_1.dat --out=/galaxy/files/dataset_2.dat")
+        self.assertEqual(
+            command_line, "bwa --thresh=4 --in=/galaxy/files/dataset_1.dat --out=/galaxy/files/dataset_2.dat"
+        )
 
     def test_repeat_evaluation(self):
         repeat = Repeat()
         repeat.name = "r"
         repeat.inputs = {"thresh": self.tool.test_thresh_param()}
         self.tool.set_params({"r": repeat})
-        self.job.parameters = [JobParameter(name="r", value='''[{"thresh": 4, "__index__": 0},{"thresh": 5, "__index__": 1}]''')]
+        self.job.parameters = [
+            JobParameter(name="r", value="""[{"thresh": 4, "__index__": 0},{"thresh": 5, "__index__": 1}]""")
+        ]
         self.tool._command_line = "prog1 #for $r_i in $r # $r_i.thresh#end for#"
         self._set_compute_environment()
         command_line, extra_filenames, _ = self.evaluator.build()
@@ -80,7 +84,7 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         self.assertEqual(command_line, "prog1 '%s'" % self.app.security.encode_id(42))
 
     def test_conditional_evaluation(self):
-        select_xml = XML('''<param name="always_true" type="select"><option value="true">True</option></param>''')
+        select_xml = XML("""<param name="always_true" type="select"><option value="true">True</option></param>""")
         parameter = SelectToolParameter(self.tool, select_xml)
 
         conditional = Conditional()
@@ -91,7 +95,9 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         when.value = "true"
         conditional.cases = [when]
         self.tool.set_params({"c": conditional})
-        self.job.parameters = [JobParameter(name="c", value='''{"thresh": 4, "always_true": "true", "__current_case__": 0}''')]
+        self.job.parameters = [
+            JobParameter(name="c", value="""{"thresh": 4, "always_true": "true", "__current_case__": 0}""")
+        ]
         self.tool._command_line = "prog1 --thresh=${c.thresh} --test_param=${c.always_true}"
         self._set_compute_environment()
         command_line, extra_filenames, _ = self.evaluator.build()
@@ -100,9 +106,9 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
     def test_evaluation_of_optional_datasets(self):
         # Make sure optional dataset don't cause evaluation to break and
         # evaluate in cheetah templates as 'None'.
-        select_xml = XML('''<param name="input1" type="data" optional="true"></param>''')
+        select_xml = XML("""<param name="input1" type="data" optional="true"></param>""")
         parameter = DataToolParameter(self.tool, select_xml)
-        self.job.parameters = [JobParameter(name="input1", value='null')]
+        self.job.parameters = [JobParameter(name="input1", value="null")]
         self.tool.set_params({"input1": parameter})
         self.tool._command_line = "prog1 --opt_input='${input1}'"
         self._set_compute_environment()
@@ -125,8 +131,8 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         job_path_1 = "%s/dataset_1.dat" % self.test_directory
         job_path_2 = "%s/dataset_2.dat" % self.test_directory
         self._set_compute_environment(
-            input_paths=[DatasetPath(1, '/galaxy/files/dataset_1.dat', false_path=job_path_1)],
-            output_paths=[DatasetPath(2, '/galaxy/files/dataset_2.dat', false_path=job_path_2)],
+            input_paths=[DatasetPath(1, "/galaxy/files/dataset_1.dat", false_path=job_path_1)],
+            output_paths=[DatasetPath(2, "/galaxy/files/dataset_2.dat", false_path=job_path_2)],
         )
         command_line, extra_filenames, _ = self.evaluator.build()
         self.assertEqual(command_line, f"bwa --thresh=4 --in={job_path_1} --out={job_path_2}")
@@ -154,11 +160,13 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         self.__test_arbitrary_path_rewriting()
 
     def __test_arbitrary_path_rewriting(self):
-        self.job.parameters = [JobParameter(name="index_path", value="\"/old/path/human\"")]
-        xml = XML('''<param name="index_path" type="select">
+        self.job.parameters = [JobParameter(name="index_path", value='"/old/path/human"')]
+        xml = XML(
+            """<param name="index_path" type="select">
             <option value="/old/path/human">Human</option>
             <option value="/old/path/mouse">Mouse</option>
-        </param>''')
+        </param>"""
+        )
         parameter = SelectToolParameter(self.tool, xml)
 
         def get_field_by_name_for_value(name, value, trans, other_values):
@@ -170,9 +178,7 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
             return [["", "/old/path/human", ""]]
 
         parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value, get_options=get_options)
-        self.tool.set_params({
-            "index_path": parameter
-        })
+        self.tool.set_params({"index_path": parameter})
         self.tool._command_line = "prog1 $index_path.fields.path"
         self._set_compute_environment(unstructured_path_rewrites={"/old": "/new"})
         command_line, extra_filenames, _ = self.evaluator.build()
@@ -214,40 +220,32 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         assert "exec_before_job" in self.tool.hooks_called
 
     def _setup_test_bwa_job(self):
-
         def hda(id, name, path):
             hda = HistoryDatasetAssociation(name=name, metadata=dict())
             hda.dataset = Dataset(id=id, external_filename=path)
             return hda
 
-        id, name, path = 111, 'input1', '/galaxy/files/dataset_1.dat'
+        id, name, path = 111, "input1", "/galaxy/files/dataset_1.dat"
         self.job.input_datasets = [JobToInputDatasetAssociation(name=name, dataset=hda(id, name, path))]
 
-        id, name, path = 112, 'output1', '/galaxy/files/dataset_2.dat'
+        id, name, path = 112, "output1", "/galaxy/files/dataset_2.dat"
         self.job.output_datasets = [JobToOutputDatasetAssociation(name=name, dataset=hda(id, name, path))]
 
 
 class MockHistoryDatasetAssociation(HistoryDatasetAssociation):
-
     def __init__(self, **kwds):
         self._metadata = dict()
         super().__init__(**kwds)
 
 
 class ComputeEnvironment(SimpleComputeEnvironment):
-
     def __init__(
-        self,
-        new_file_path,
-        working_directory,
-        input_paths=None,
-        output_paths=None,
-        unstructured_path_rewrites=None
+        self, new_file_path, working_directory, input_paths=None, output_paths=None, unstructured_path_rewrites=None
     ):
         if input_paths is None:
-            input_paths = ['/galaxy/files/dataset_1.dat']
+            input_paths = ["/galaxy/files/dataset_1.dat"]
         if output_paths is None:
-            output_paths = ['/galaxy/files/dataset_2.dat']
+            output_paths = ["/galaxy/files/dataset_2.dat"]
         self._new_file_path = new_file_path
         self._working_directory = working_directory
         self._input_paths = input_paths
@@ -300,10 +298,9 @@ class ComputeEnvironment(SimpleComputeEnvironment):
 
 
 class MockTool:
-
     def __init__(self, app):
         self.profile = 16.01
-        self.python_template_version = '2.7'
+        self.python_template_version = "2.7"
         self.app = app
         self.hooks_called = []
         self.environment_variables = []
diff --git a/test/unit/app/tools/test_execution.py b/test/unit/app/tools/test_execution.py
index a82e468a5ce..0f22d7471ee 100644
--- a/test/unit/app/tools/test_execution.py
+++ b/test/unit/app/tools/test_execution.py
@@ -9,7 +9,7 @@ import galaxy.model
 from galaxy.app_unittest_utils import tools_support
 from galaxy.util.bunch import Bunch
 
-BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
+BASE_REPEAT_TOOL_CONTENTS = """<tool id="test_tool" name="Test Tool">
     <command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# &lt; $out1</command>
     <inputs>
         <param type="text" name="param1" value="" />
@@ -21,15 +21,17 @@ BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
         <data name="out1" format="data" />
     </outputs>
 </tool>
-'''
+"""
 
 # Tool with a repeat parameter, to test state update.
-REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="text" name="param2" value="" />'''
-REPEAT_COLLECTION_PARAM_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="data_collection" name="param2" collection_type="paired" />'''
+REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % """<param type="text" name="param2" value="" />"""
+REPEAT_COLLECTION_PARAM_CONTENTS = (
+    BASE_REPEAT_TOOL_CONTENTS % """<param type="data_collection" name="param2" collection_type="paired" />"""
+)
 
 
 class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
-    tool_action: 'MockAction'
+    tool_action: "MockAction"
 
     def setUp(self):
         self.setup_app()
@@ -60,7 +62,7 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
         try:
             self.__handle_with_incoming(param1="moo")
         except Exception as e:
-            assert 'Error executing tool' in str(e)
+            assert "Error executing tool" in str(e)
 
     def test_execute_errors(self):
         self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
@@ -68,7 +70,7 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
         try:
             self.__handle_with_incoming(param1="moo")
         except Exception as e:
-            assert 'Test Error Message' in str(e)
+            assert "Test Error Message" in str(e)
 
     def test_redirect(self):
         self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
@@ -89,9 +91,9 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
     def test_invalid_remap_job(self):
         self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
         try:
-            self.__handle_with_incoming(param1="moo", rerun_remap_job_id='123')
+            self.__handle_with_incoming(param1="moo", rerun_remap_job_id="123")
         except Exception as e:
-            assert 'invalid job' in str(e)
+            assert "invalid job" in str(e)
 
     def test_data_param_execute(self):
         self._init_tool(tools_support.SIMPLE_CAT_TOOL_CONTENTS)
@@ -112,16 +114,16 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
         assert hda == state["param1"]
 
     def __handle_with_incoming(self, **kwds):
-        """ Execute tool.handle_input with incoming specified by kwds
+        """Execute tool.handle_input with incoming specified by kwds
         (optionally extending a previous state).
         """
         return self.tool.handle_input(trans=self.trans, incoming=kwds)
 
-    def __add_dataset(self, id, state='ok'):
+    def __add_dataset(self, id, state="ok"):
         hda = galaxy.model.HistoryDatasetAssociation()
         hda.id = id
         hda.dataset = galaxy.model.Dataset()
-        hda.dataset.state = 'ok'
+        hda.dataset.state = "ok"
 
         self.trans.sa_session.add(hda)
         self.history.datasets.append(hda)
@@ -145,7 +147,7 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
 
     def __assert_executed(self, vars):
         self.__assert_no_errors(vars)
-        assert len(vars['jobs']) > 0
+        assert len(vars["jobs"]) > 0
 
     def __assert_no_errors(self, vars):
         assert "job_errors" in vars
@@ -153,7 +155,6 @@ class ToolExecutionTestCase(TestCase, tools_support.UsesTools):
 
 
 class MockAction(tools_support.MockActionI):
-
     def __init__(self, expected_trans):
         self.expected_trans = expected_trans
         self.execution_call_args = []
@@ -184,12 +185,15 @@ class MockAction(tools_support.MockActionI):
 
 
 class MockTrans:
-
     def __init__(self, app, history):
         self.app = app
         self.history = history
         self.user = None
-        self.history._active_datasets_and_roles = [hda for hda in self.app.model.context.query(galaxy.model.HistoryDatasetAssociation).all() if hda.active and hda.history == history]
+        self.history._active_datasets_and_roles = [
+            hda
+            for hda in self.app.model.context.query(galaxy.model.HistoryDatasetAssociation).all()
+            if hda.active and hda.history == history
+        ]
         self.workflow_building_mode = False
         self.webapp = Bunch(name="galaxy")
         self.sa_session = self.app.model.context
@@ -206,7 +210,6 @@ class MockTrans:
 
 
 class MockCollectionService:
-
     def __init__(self):
         self.collection_info = object()
 
diff --git a/test/unit/app/tools/test_expression_basics.py b/test/unit/app/tools/test_expression_basics.py
index 51c7293ac3f..96245b49a08 100644
--- a/test/unit/app/tools/test_expression_basics.py
+++ b/test/unit/app/tools/test_expression_basics.py
@@ -2,7 +2,5 @@ from galaxy.tools.expressions import evaluate
 
 
 def test_evaluate():
-    input = {
-        "script": "{return 5;}"
-    }
+    input = {"script": "{return 5;}"}
     assert evaluate(None, input) == 5
diff --git a/test/unit/app/tools/test_history_imp_exp.py b/test/unit/app/tools/test_history_imp_exp.py
index b35cbeddfce..6a087fc46e3 100644
--- a/test/unit/app/tools/test_history_imp_exp.py
+++ b/test/unit/app/tools/test_history_imp_exp.py
@@ -8,20 +8,21 @@ from unittest.mock import Mock
 from galaxy import model
 from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.exceptions import MalformedContents
-from galaxy.objectstore.unittest_utils import (
-    Config as TestConfig,
+from galaxy.objectstore.unittest_utils import Config as TestConfig
+from galaxy.tools.imp_exp import (
+    JobExportHistoryArchiveWrapper,
+    JobImportHistoryArchiveWrapper,
+    unpack_tar_gz_archive,
 )
-from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper, JobImportHistoryArchiveWrapper, unpack_tar_gz_archive
 from galaxy.tools.imp_exp.export_history import create_archive
 from galaxy.util import galaxy_directory
 
-
 # good enough for the very specific tests we're writing as of now...
-DATASETS_ATTRS = '''[{{"info": "\\nuploaded txt file", "peek": "foo\\n\\n\\n\\n\\n\\n", "update_time": "2016-02-08 18:39:22.937474", "name": "Pasted Entry", "extension": "txt", "tags": {{}}, "__HistoryDatasetAssociation__": true, "file_name": "{file_name}", "deleted": false, "designation": null, "visible": true, "create_time": "2016-02-08 18:38:38.682087", "hid": 1, "parent_id": null, "extra_files_path": "", "uuid": "406d913e-925d-4ccd-800d-06c9b32df309", "metadata": {{"dbkey": "?", "data_lines": 1}}, "annotation": null, "blurb": "1 line", "exported": true}}]'''
-DATASETS_ATTRS_EXPORT = '''[{{"info": "\\nuploaded txt file", "peek": "foo\\n\\n\\n\\n\\n\\n", "update_time": "2016-02-08 18:39:22.937474", "name": "Pasted Entry", "extension": "txt", "tags": {{}}, "__HistoryDatasetAssociation__": true, "file_name": "{file_name}", "deleted": false, "designation": null, "visible": true, "create_time": "2016-02-08 18:38:38.682087", "hid": 1, "parent_id": null, "_extra_files_path": "", "uuid": "406d913e-925d-4ccd-800d-06c9b32df309", "metadata": {{"dbkey": "?", "data_lines": 1}}, "annotation": null, "blurb": "1 line"}}]'''
-DATASETS_ATTRS_PROVENANCE = '''[]'''
-HISTORY_ATTRS = '''{"hid_counter": 2, "update_time": "2016-02-08 18:38:38.705058", "create_time": "2016-02-08 18:38:20.790057", "name": "paste", "tags": {}, "genome_build": "?", "annotation": null}'''
-JOBS_ATTRS = '''[{"info": null, "tool_id": "upload1", "update_time": "2016-02-08T18:39:23.356482", "stdout": "", "input_mapping": {}, "tool_version": "1.1.4", "traceback": null, "command_line": "python /galaxy/tools/data_source/upload.py /galaxy /scratch/tmppwU9rD /scratch/tmpP4_45Y 1:/scratch/jobs/000/dataset_1_files:/data/000/dataset_1.dat", "exit_code": 0, "output_datasets": [1], "state": "ok", "create_time": "2016-02-08T18:38:39.153873", "params": {"files": [{"to_posix_lines": "Yes", "NAME": "None", "file_data": null, "space_to_tab": null, "url_paste": "/scratch/strio_url_paste_o6nrv8", "__index__": 0, "ftp_files": "", "uuid": "None"}], "paramfile": "/scratch/tmpP4_45Y", "file_type": "auto", "files_metadata": {"file_type": "auto", "__current_case__": 41}, "async_datasets": "None", "dbkey": "?"}, "stderr": ""}]'''
+DATASETS_ATTRS = """[{{"info": "\\nuploaded txt file", "peek": "foo\\n\\n\\n\\n\\n\\n", "update_time": "2016-02-08 18:39:22.937474", "name": "Pasted Entry", "extension": "txt", "tags": {{}}, "__HistoryDatasetAssociation__": true, "file_name": "{file_name}", "deleted": false, "designation": null, "visible": true, "create_time": "2016-02-08 18:38:38.682087", "hid": 1, "parent_id": null, "extra_files_path": "", "uuid": "406d913e-925d-4ccd-800d-06c9b32df309", "metadata": {{"dbkey": "?", "data_lines": 1}}, "annotation": null, "blurb": "1 line", "exported": true}}]"""
+DATASETS_ATTRS_EXPORT = """[{{"info": "\\nuploaded txt file", "peek": "foo\\n\\n\\n\\n\\n\\n", "update_time": "2016-02-08 18:39:22.937474", "name": "Pasted Entry", "extension": "txt", "tags": {{}}, "__HistoryDatasetAssociation__": true, "file_name": "{file_name}", "deleted": false, "designation": null, "visible": true, "create_time": "2016-02-08 18:38:38.682087", "hid": 1, "parent_id": null, "_extra_files_path": "", "uuid": "406d913e-925d-4ccd-800d-06c9b32df309", "metadata": {{"dbkey": "?", "data_lines": 1}}, "annotation": null, "blurb": "1 line"}}]"""
+DATASETS_ATTRS_PROVENANCE = """[]"""
+HISTORY_ATTRS = """{"hid_counter": 2, "update_time": "2016-02-08 18:38:38.705058", "create_time": "2016-02-08 18:38:20.790057", "name": "paste", "tags": {}, "genome_build": "?", "annotation": null}"""
+JOBS_ATTRS = """[{"info": null, "tool_id": "upload1", "update_time": "2016-02-08T18:39:23.356482", "stdout": "", "input_mapping": {}, "tool_version": "1.1.4", "traceback": null, "command_line": "python /galaxy/tools/data_source/upload.py /galaxy /scratch/tmppwU9rD /scratch/tmpP4_45Y 1:/scratch/jobs/000/dataset_1_files:/data/000/dataset_1.dat", "exit_code": 0, "output_datasets": [1], "state": "ok", "create_time": "2016-02-08T18:38:39.153873", "params": {"files": [{"to_posix_lines": "Yes", "NAME": "None", "file_data": null, "space_to_tab": null, "url_paste": "/scratch/strio_url_paste_o6nrv8", "__index__": 0, "ftp_files": "", "uuid": "None"}], "paramfile": "/scratch/tmpP4_45Y", "file_type": "auto", "files_metadata": {"file_type": "auto", "__current_case__": 41}, "async_datasets": "None", "dbkey": "?"}, "stderr": ""}]"""
 
 
 def t_data_path(name):
@@ -31,8 +32,8 @@ def t_data_path(name):
 def _run_jihaw_cleanup(archive_dir, app=None):
     app = app or _mock_app()
     job = model.Job()
-    job.user = model.User(email="test@test.org", password='test')
-    job.tool_stderr = ''
+    job.user = model.User(email="test@test.org", password="test")
+    job.tool_stderr = ""
     jiha = model.JobImportHistoryArchive(job=job, archive_dir=archive_dir)
     app.model.context.current.add_all([job, jiha])
     app.model.context.flush()
@@ -61,53 +62,51 @@ def test_create_archive():
     tempdir = tempfile.mkdtemp()
     with tempfile.NamedTemporaryFile() as temp:
         out_file = temp.name
-        dataset = os.path.join(tempdir, 'datasets/Pasted_Entry_1.txt')
-        history_attrs_file = os.path.join(tempdir, 'history_attrs.txt')
-        datasets_attrs_file = os.path.join(tempdir, 'datasets_attrs.txt')
-        jobs_attrs_file = os.path.join(tempdir, 'jobs_attrs.txt')
-        os.makedirs(os.path.join(tempdir, 'datasets'))
-        with open(dataset, 'w') as out:
-            out.write('Hello\n')
-        with open(history_attrs_file, 'w') as out:
+        dataset = os.path.join(tempdir, "datasets/Pasted_Entry_1.txt")
+        history_attrs_file = os.path.join(tempdir, "history_attrs.txt")
+        datasets_attrs_file = os.path.join(tempdir, "datasets_attrs.txt")
+        jobs_attrs_file = os.path.join(tempdir, "jobs_attrs.txt")
+        os.makedirs(os.path.join(tempdir, "datasets"))
+        with open(dataset, "w") as out:
+            out.write("Hello\n")
+        with open(history_attrs_file, "w") as out:
             out.write(HISTORY_ATTRS)
-        with open(datasets_attrs_file, 'w') as out:
+        with open(datasets_attrs_file, "w") as out:
             out.write(DATASETS_ATTRS_EXPORT.format(file_name=dataset))
-        with open(jobs_attrs_file, 'w') as out:
+        with open(jobs_attrs_file, "w") as out:
             out.write(JOBS_ATTRS)
         create_archive(tempdir, out_file, gzip=True)
         with tarfile.open(out_file) as t:
-            assert sorted(t.getnames()) == sorted(['datasets', 'datasets/Pasted_Entry_1.txt', 'history_attrs.txt', 'datasets_attrs.txt', 'jobs_attrs.txt']), t.getnames()
+            assert sorted(t.getnames()) == sorted(
+                ["datasets", "datasets/Pasted_Entry_1.txt", "history_attrs.txt", "datasets_attrs.txt", "jobs_attrs.txt"]
+            ), t.getnames()
 
 
 def test_history_import_symlink():
-    """ Ensure a history containing a dataset that is a symlink cannot be imported
-    """
+    """Ensure a history containing a dataset that is a symlink cannot be imported"""
     with HistoryArchive() as history_archive:
         history_archive.write_metafiles()
-        history_archive.write_link('datasets/Pasted_Entry_1.txt', '../target.txt')
-        history_archive.write_file('target.txt', 'insecure')
-        _run_jihaw_cleanup_check_secure(history_archive, 'Symlink dataset in import archive allowed')
+        history_archive.write_link("datasets/Pasted_Entry_1.txt", "../target.txt")
+        history_archive.write_file("target.txt", "insecure")
+        _run_jihaw_cleanup_check_secure(history_archive, "Symlink dataset in import archive allowed")
 
 
 def test_history_import_relpath_in_metadata():
-    """ Ensure that dataset_attrs.txt cannot contain a relative path outside the archive
-    """
+    """Ensure that dataset_attrs.txt cannot contain a relative path outside the archive"""
     with HistoryArchive() as history_archive:
-        history_archive.write_metafiles(dataset_file_name='../outside.txt')
-        history_archive.write_file('datasets/Pasted_Entry_1.txt', 'foo')
+        history_archive.write_metafiles(dataset_file_name="../outside.txt")
+        history_archive.write_file("datasets/Pasted_Entry_1.txt", "foo")
         history_archive.write_outside()
-        _run_jihaw_cleanup_check_secure(history_archive, 'Relative parent path in datasets_attrs.txt allowed')
+        _run_jihaw_cleanup_check_secure(history_archive, "Relative parent path in datasets_attrs.txt allowed")
 
 
 def test_history_import_abspath_in_metadata():
-    """ Ensure that dataset_attrs.txt cannot contain a absolute path outside the archive
-    """
+    """Ensure that dataset_attrs.txt cannot contain a absolute path outside the archive"""
     with HistoryArchive() as history_archive:
-        history_archive.write_metafiles(
-            dataset_file_name=os.path.join(history_archive.temp_directory, 'outside.txt'))
-        history_archive.write_file('datasets/Pasted_Entry_1.txt', 'foo')
+        history_archive.write_metafiles(dataset_file_name=os.path.join(history_archive.temp_directory, "outside.txt"))
+        history_archive.write_file("datasets/Pasted_Entry_1.txt", "foo")
         history_archive.write_outside()
-        _run_jihaw_cleanup_check_secure(history_archive, 'Absolute path in datasets_attrs.txt allowed')
+        _run_jihaw_cleanup_check_secure(history_archive, "Absolute path in datasets_attrs.txt allowed")
 
 
 def test_export_dataset():
@@ -123,12 +122,12 @@ def test_export_dataset():
     d1_source.source_uri = "http://google.com/mycooldata.txt"
     d1.dataset.sources.append(d1_source)
 
-    d1.state = d2.state = 'ok'
+    d1.state = d2.state = "ok"
 
     j = model.Job()
     j.user = h.user
     j.tool_id = "cat1"
-    j.state = 'ok'
+    j.state = "ok"
 
     j.add_input_dataset("input1", d1)
     j.add_output_dataset("out_file1", d2)
@@ -154,8 +153,8 @@ def test_export_dataset():
     assert imported_job.input_datasets
     assert imported_job.input_datasets[0].dataset == datasets[0]
 
-    assert datasets[0].state == 'ok'
-    assert datasets[1].state == 'ok'
+    assert datasets[0].state == "ok"
+    assert datasets[1].state == "ok"
     assert len(datasets[0].dataset.hashes) == 1
     dataset_hash = datasets[0].dataset.hashes[0]
     assert dataset_hash.hash_function == "MD5"
@@ -215,7 +214,7 @@ def test_export_dataset_with_deleted_and_purged():
     datasets = list(imported_history.contents_iter(types=["dataset"]))
     assert len(datasets) == 1
 
-    assert datasets[0].state == 'discarded'
+    assert datasets[0].state == "discarded"
     assert datasets[0].deleted
     assert datasets[0].dataset.deleted
     assert datasets[0].creating_job
@@ -288,8 +287,12 @@ def test_export_collection_history():
     hc2 = model.HistoryDatasetCollectionAssociation(history=h, hid=2, collection=c2, name="HistoryCollectionTest2")
 
     cleaf = model.DatasetCollection(collection_type="paired")
-    dce2leaf1 = model.DatasetCollectionElement(collection=cleaf, element=d3, element_identifier="forward", element_index=0)
-    dce2leaf2 = model.DatasetCollectionElement(collection=cleaf, element=d4, element_identifier="reverse", element_index=1)
+    dce2leaf1 = model.DatasetCollectionElement(
+        collection=cleaf, element=d3, element_identifier="forward", element_index=0
+    )
+    dce2leaf2 = model.DatasetCollectionElement(
+        collection=cleaf, element=d4, element_identifier="reverse", element_index=1
+    )
 
     dce21 = model.DatasetCollectionElement(collection=c2, element=cleaf, element_identifier="listel", element_index=0)
 
@@ -622,7 +625,12 @@ def _assert_distinct(list_):
 
 
 def _create_datasets(sa_session, history, n, extension="txt"):
-    return [model.HistoryDatasetAssociation(extension=extension, history=history, create_dataset=True, sa_session=sa_session, hid=i + 1) for i in range(n)]
+    return [
+        model.HistoryDatasetAssociation(
+            extension=extension, history=history, create_dataset=True, sa_session=sa_session, hid=i + 1
+        )
+        for i in range(n)
+    ]
 
 
 def _setup_history_for_export(history_name):
@@ -651,6 +659,7 @@ def _import_export(app, h, dest_export=None):
     wrapper.setup_job(h, jeha.temp_directory)
 
     from galaxy.tools.imp_exp import export_history
+
     ret = export_history.main(["--gzip", jeha.temp_directory, dest_export])
     assert ret == 0, ret
 
@@ -660,7 +669,7 @@ def _import_export(app, h, dest_export=None):
 
 
 def test_import_1901_default():
-    app, new_history = import_archive(t_data_path('exports/1901_two_datasets.tgz'))
+    app, new_history = import_archive(t_data_path("exports/1901_two_datasets.tgz"))
     assert new_history
 
     datasets = new_history.datasets
@@ -672,11 +681,10 @@ def test_import_1901_default():
     # There was a deleted dataset so skip to 3
     assert dataset1.hid == 3, dataset1.hid
 
-    jobs = app.model.context.query(model.Job) \
-        .filter_by(history_id=new_history.id).order_by(model.Job.table.c.id).all()
+    jobs = app.model.context.query(model.Job).filter_by(history_id=new_history.id).order_by(model.Job.table.c.id).all()
     assert len(jobs) == 2
-    assert jobs[0].tool_id == 'upload1'
-    assert jobs[1].tool_id == 'cat'
+    assert jobs[0].tool_id == "upload1"
+    assert jobs[1].tool_id == "cat"
 
     cat_job = jobs[1]
     assert len(cat_job.input_datasets) == 2
@@ -690,18 +698,18 @@ def test_import_1901_default():
     # Not sure these shouldn't be {"values": [{"src": "hda", "id": dataset0.id}]}
     # but parameter processing for pre-19.05 exports/imports didn't work anyway so
     # perhaps not a problem?
-    input1_param = json.loads(param_dict['input1'])
+    input1_param = json.loads(param_dict["input1"])
     assert input1_param["src"] == "hda"
     assert input1_param["id"] == dataset0.id
 
-    input2_param = json.loads(param_dict['queries'])[0]['input2']
+    input2_param = json.loads(param_dict["queries"])[0]["input2"]
     assert input2_param["src"] == "hda"
     assert input2_param["id"] == dataset0.id
 
 
 def import_archive(archive_path, app=None):
     dest_parent = tempfile.mkdtemp()
-    dest_dir = os.path.join(dest_parent, 'dest')
+    dest_dir = os.path.join(dest_parent, "dest")
 
     options = Mock()
     options.is_url = False
@@ -715,8 +723,8 @@ def import_archive(archive_path, app=None):
 
 
 def _run_unpack(history_archive, dest_parent, msg):
-    dest_dir = os.path.join(dest_parent, 'dest')
-    insecure_dir = os.path.join(dest_parent, 'insecure')
+    dest_dir = os.path.join(dest_parent, "dest")
+    insecure_dir = os.path.join(dest_parent, "insecure")
     os.makedirs(dest_dir)
     options = Mock()
     options.is_url = False
@@ -731,39 +739,39 @@ def _run_unpack(history_archive, dest_parent, msg):
 
 
 def test_history_import_relpath_in_archive():
-    """ Ensure that a history import archive cannot reference a relative path
+    """Ensure that a history import archive cannot reference a relative path
     outside the archive
     """
     dest_parent = tempfile.mkdtemp()
-    with HistoryArchive(arcname_prefix='../insecure') as history_archive:
+    with HistoryArchive(arcname_prefix="../insecure") as history_archive:
 
         history_archive.write_metafiles()
-        history_archive.write_file('datasets/Pasted_Entry_1.txt', 'foo')
+        history_archive.write_file("datasets/Pasted_Entry_1.txt", "foo")
         history_archive.finalize()
-        _run_unpack(history_archive, dest_parent, 'Relative parent path in import archive allowed')
+        _run_unpack(history_archive, dest_parent, "Relative parent path in import archive allowed")
 
 
 def test_history_import_abspath_in_archive():
-    """ Ensure that a history import archive cannot reference a absolute path
+    """Ensure that a history import archive cannot reference a absolute path
     outside the archive
     """
     dest_parent = tempfile.mkdtemp()
-    arcname_prefix = os.path.abspath(os.path.join(dest_parent, 'insecure'))
+    arcname_prefix = os.path.abspath(os.path.join(dest_parent, "insecure"))
 
     with HistoryArchive(arcname_prefix=arcname_prefix) as history_archive:
         history_archive.write_metafiles()
-        history_archive.write_file('datasets/Pasted_Entry_1.txt', 'foo')
+        history_archive.write_file("datasets/Pasted_Entry_1.txt", "foo")
         history_archive.finalize()
-        _run_unpack(history_archive, dest_parent, 'Absolute path in import archive allowed')
+        _run_unpack(history_archive, dest_parent, "Absolute path in import archive allowed")
 
 
 class HistoryArchive:
     def __init__(self, arcname_prefix=None):
         self.temp_directory = tempfile.mkdtemp()
-        self.arc_directory = os.path.join(self.temp_directory, 'archive')
+        self.arc_directory = os.path.join(self.temp_directory, "archive")
         self.arcname_prefix = arcname_prefix
-        self.tar_file_path = os.path.join(self.temp_directory, 'archive.tar.gz')
-        self.tar_file = tarfile.open(self.tar_file_path, 'w:gz')
+        self.tar_file_path = os.path.join(self.temp_directory, "archive.tar.gz")
+        self.tar_file = tarfile.open(self.tar_file_path, "w:gz")
         os.makedirs(self.arc_directory)
 
     def __enter__(self):
@@ -782,27 +790,26 @@ class HistoryArchive:
             path = os.path.join(self.arcname_prefix, path)
         return path
 
-    def write_metafiles(self, dataset_file_name='datasets/Pasted_Entry_1.txt'):
-        self.write_file('datasets_attrs.txt',
-                        DATASETS_ATTRS.format(file_name=dataset_file_name))
-        self.write_file('datasets_attrs.txt.provenance', DATASETS_ATTRS_PROVENANCE)
-        self.write_file('history_attrs.txt', HISTORY_ATTRS)
-        self.write_file('jobs_attrs.txt', JOBS_ATTRS)
+    def write_metafiles(self, dataset_file_name="datasets/Pasted_Entry_1.txt"):
+        self.write_file("datasets_attrs.txt", DATASETS_ATTRS.format(file_name=dataset_file_name))
+        self.write_file("datasets_attrs.txt.provenance", DATASETS_ATTRS_PROVENANCE)
+        self.write_file("history_attrs.txt", HISTORY_ATTRS)
+        self.write_file("jobs_attrs.txt", JOBS_ATTRS)
 
-    def write_outside(self, fname='outside.txt', contents='invalid'):
-        with open(os.path.join(self.temp_directory, fname), 'w') as f:
+    def write_outside(self, fname="outside.txt", contents="invalid"):
+        with open(os.path.join(self.temp_directory, fname), "w") as f:
             f.write(contents)
 
     def write_file(self, fname, contents):
         self._create_parent(fname)
         path = os.path.join(self.arc_directory, fname)
-        with open(path, 'w') as f:
+        with open(path, "w") as f:
             f.write(contents)
         # TarFile.add() (via TarFile.gettarinfo()) strips leading '/' and is
         # unsuitable for our purposes
-        ti = self.tar_file.gettarinfo(fileobj=open(path, 'rb'))
+        ti = self.tar_file.gettarinfo(fileobj=open(path, "rb"))
         ti.name = self._arcname(fname)
-        self.tar_file.addfile(ti, fileobj=open(path, 'rb'))
+        self.tar_file.addfile(ti, fileobj=open(path, "rb"))
 
     def write_link(self, fname, target):
         self._create_parent(fname)
diff --git a/test/unit/app/tools/test_metadata.py b/test/unit/app/tools/test_metadata.py
index 25240d43798..29e417ffb81 100644
--- a/test/unit/app/tools/test_metadata.py
+++ b/test/unit/app/tools/test_metadata.py
@@ -7,11 +7,13 @@ from galaxy.app_unittest_utils import tools_support
 from galaxy.job_execution.datasets import DatasetPath
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.objectstore import ObjectStorePopulator
-from galaxy.util import galaxy_directory, safe_makedirs
+from galaxy.util import (
+    galaxy_directory,
+    safe_makedirs,
+)
 
 
 class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
-
     def setUp(self):
         super().setUp()
         self.setup_app()
@@ -57,9 +59,13 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
         self._write_job_files()
         self.exec_metadata_command(command)
         assert self.metadata_compute_strategy
-        metadata_set_successfully = self.metadata_compute_strategy.external_metadata_set_successfully(output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory)
+        metadata_set_successfully = self.metadata_compute_strategy.external_metadata_set_successfully(
+            output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory
+        )
         assert metadata_set_successfully
-        self.metadata_compute_strategy.load_metadata(output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory)
+        self.metadata_compute_strategy.load_metadata(
+            output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory
+        )
         assert output_dataset.metadata.data_lines == 2
         assert output_dataset.metadata.sequences == 1
 
@@ -81,15 +87,22 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
             "out_file1": output_dataset,
         }
         command = self.metadata_command(output_datasets)
-        self._write_galaxy_json("""{"type": "dataset", "dataset_id": "%s", "name": "my dynamic name", "ext": "fasta", "info": "my dynamic info"}""" % output_dataset.dataset.id)
+        self._write_galaxy_json(
+            """{"type": "dataset", "dataset_id": "%s", "name": "my dynamic name", "ext": "fasta", "info": "my dynamic info"}"""
+            % output_dataset.dataset.id
+        )
         self._write_output_dataset_contents(output_dataset, ">seq1\nGCTGCATG\n")
         self._write_job_files()
         self.exec_metadata_command(command)
         assert self.metadata_compute_strategy
-        metadata_set_successfully = self.metadata_compute_strategy.external_metadata_set_successfully(output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory)
+        metadata_set_successfully = self.metadata_compute_strategy.external_metadata_set_successfully(
+            output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory
+        )
         assert metadata_set_successfully
         output_dataset.extension = "fasta"  # gets done in job finish...
-        self.metadata_compute_strategy.load_metadata(output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory)
+        self.metadata_compute_strategy.load_metadata(
+            output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory
+        )
         assert output_dataset.metadata.data_lines == 2
         assert output_dataset.metadata.sequences == 1
 
@@ -113,15 +126,22 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
             "out_file1": output_dataset,
         }
         command = self.metadata_command(output_datasets)
-        self._write_galaxy_json("""{"type": "dataset", "dataset_id": "%s", "name": "my dynamic name", "ext": "fasta", "info": "my dynamic info", "metadata": {"sequences": 42}}""" % output_dataset.dataset.id)
+        self._write_galaxy_json(
+            """{"type": "dataset", "dataset_id": "%s", "name": "my dynamic name", "ext": "fasta", "info": "my dynamic info", "metadata": {"sequences": 42}}"""
+            % output_dataset.dataset.id
+        )
         self._write_output_dataset_contents(output_dataset, ">seq1\nGCTGCATG\n")
         self._write_job_files()
         self.exec_metadata_command(command)
         assert self.metadata_compute_strategy
-        metadata_set_successfully = self.metadata_compute_strategy.external_metadata_set_successfully(output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory)
+        metadata_set_successfully = self.metadata_compute_strategy.external_metadata_set_successfully(
+            output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory
+        )
         assert metadata_set_successfully
         output_dataset.extension = "fasta"  # get done in job finish...
-        self.metadata_compute_strategy.load_metadata(output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory)
+        self.metadata_compute_strategy.load_metadata(
+            output_dataset, "out_file1", sa_session, working_directory=self.job_working_directory
+        )
         assert output_dataset.metadata.data_lines == 2
         assert output_dataset.metadata.sequences == 42
 
@@ -143,9 +163,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
         # Emulate job stuff here...
 
     def _create_output_dataset_collection(self, **kwd):
-        output_dataset_collection = model.HistoryDatasetCollectionAssociation(
-            **kwd
-        )
+        output_dataset_collection = model.HistoryDatasetCollectionAssociation(**kwd)
         self.history.add_dataset_collection(output_dataset_collection)
         assert output_dataset_collection.collection
         self.app.model.session.add(output_dataset_collection)
@@ -154,10 +172,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
 
     def _create_output_dataset(self, **kwd):
         output_dataset = model.HistoryDatasetAssociation(
-            sa_session=self.app.model.session,
-            create_dataset=True,
-            flush=True,
-            **kwd
+            sa_session=self.app.model.session, create_dataset=True, flush=True, **kwd
         )
         self.history.add_dataset(output_dataset)
         ObjectStorePopulator(self.app, user=self.job.user).set_object_store_id(output_dataset)
@@ -177,7 +192,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
             f.write(contents)
 
     def _write_job_files(self, stdout="tool stdout", stderr="tool stderr"):
-        with open(os.path.join(self.job_working_directory, "tool_script.sh"), 'w') as f:
+        with open(os.path.join(self.job_working_directory, "tool_script.sh"), "w") as f:
             f.write("echo hi")
         with open(os.path.join(self.job_working_directory, "tool_stdout"), "w") as f:
             f.write(stdout)
@@ -193,38 +208,42 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesTools):
         dataset_files_path = self.app.model.Dataset.file_path
         config_root = self.app.config.root
         config_file = None
-        datatypes_config = os.path.join(self.job_working_directory, 'metadata', 'registry.xml')
-        safe_makedirs(os.path.join(self.job_working_directory, 'metadata'))
+        datatypes_config = os.path.join(self.job_working_directory, "metadata", "registry.xml")
+        safe_makedirs(os.path.join(self.job_working_directory, "metadata"))
         self.app.datatypes_registry.to_xml_file(path=datatypes_config)
         job_metadata = os.path.join(self.tool_working_directory, self.tool.provided_metadata_file)
         output_fnames = [DatasetPath(o.dataset.id, o.dataset.file_name, None) for o in output_datasets.values()]
-        command = metadata_compute_strategy.setup_external_metadata(output_datasets,
-                                                                    output_collections,
-                                                                    self.app.model.session,
-                                                                    exec_dir=exec_dir,
-                                                                    tmp_dir=self.job_working_directory,  # set in jobs/runners.py - better if was default.
-                                                                    dataset_files_path=dataset_files_path,
-                                                                    config_root=config_root,
-                                                                    config_file=config_file,
-                                                                    datatypes_config=datatypes_config,
-                                                                    job_metadata=job_metadata,
-                                                                    output_fnames=output_fnames,
-                                                                    tool=self.tool,
-                                                                    job=self.job,
-                                                                    object_store_conf=self.app.object_store.to_dict(),
-                                                                    max_metadata_value_size=10000)
+        command = metadata_compute_strategy.setup_external_metadata(
+            output_datasets,
+            output_collections,
+            self.app.model.session,
+            exec_dir=exec_dir,
+            tmp_dir=self.job_working_directory,  # set in jobs/runners.py - better if was default.
+            dataset_files_path=dataset_files_path,
+            config_root=config_root,
+            config_file=config_file,
+            datatypes_config=datatypes_config,
+            job_metadata=job_metadata,
+            output_fnames=output_fnames,
+            tool=self.tool,
+            job=self.job,
+            object_store_conf=self.app.object_store.to_dict(),
+            max_metadata_value_size=10000,
+        )
         return command
 
     def exec_metadata_command(self, command):
         with open(self.stdout_path, "wb") as stdout_file, open(self.stderr_path, "wb") as stderr_file:
             _environ = os.environ.copy()
             _environ["PYTHONPATH"] = os.path.abspath("lib")
-            proc = subprocess.Popen(args=command,
-                                    shell=True,
-                                    cwd=self.job_working_directory,
-                                    env=_environ,
-                                    stdout=stdout_file,
-                                    stderr=stderr_file)
+            proc = subprocess.Popen(
+                args=command,
+                shell=True,
+                cwd=self.job_working_directory,
+                env=_environ,
+                stdout=stdout_file,
+                stderr=stderr_file,
+            )
             ret = proc.wait()
         self.print_command_output()
         assert ret == 0
diff --git a/test/unit/app/tools/test_parameter_parsing.py b/test/unit/app/tools/test_parameter_parsing.py
index 7f7283c883f..6d47d7694ff 100644
--- a/test/unit/app/tools/test_parameter_parsing.py
+++ b/test/unit/app/tools/test_parameter_parsing.py
@@ -1,4 +1,7 @@
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 from unittest import TestCase
 
 from galaxy.tools.parameters.meta import process_key
@@ -6,21 +9,20 @@ from .util import BaseParameterTestCase
 
 
 class ProcessKeyTestCase(TestCase):
-
     def test_process_key(self):
         nested_dict: Dict[str, Any] = {}
         d = {
-            'repeat_1|inner_repeat_1|data_table_column_value': 'bla4',
-            'repeat_0|inner_repeat_1|data_table_column_value': 'bla2',
-            'repeat_1|inner_repeat_0|data_table_column_value': 'bla3',
-            'repeat_0|inner_repeat_0|data_table_column_value': 'bla1',
+            "repeat_1|inner_repeat_1|data_table_column_value": "bla4",
+            "repeat_0|inner_repeat_1|data_table_column_value": "bla2",
+            "repeat_1|inner_repeat_0|data_table_column_value": "bla3",
+            "repeat_0|inner_repeat_0|data_table_column_value": "bla1",
         }
         for key, value in d.items():
             process_key(key, value, nested_dict)
         expected_dict = {
-            'repeat': [
-                {'inner_repeat': [{'data_table_column_value': 'bla1'}, {'data_table_column_value': 'bla2'}]},
-                {'inner_repeat': [{'data_table_column_value': 'bla3'}, {'data_table_column_value': 'bla4'}]},
+            "repeat": [
+                {"inner_repeat": [{"data_table_column_value": "bla1"}, {"data_table_column_value": "bla2"}]},
+                {"inner_repeat": [{"data_table_column_value": "bla3"}, {"data_table_column_value": "bla4"}]},
             ]
         }
         self.assertEqual(nested_dict, expected_dict)
@@ -28,23 +30,21 @@ class ProcessKeyTestCase(TestCase):
     def test_process_key_2(self):
         nested_dict: Dict[str, Any] = {}
         d = {
-            'data_tables_0|columns_0|data_table_column_value': 'Amel_HAv3.1',
-            'data_tables': [],
-            'directory_content': [],
+            "data_tables_0|columns_0|data_table_column_value": "Amel_HAv3.1",
+            "data_tables": [],
+            "directory_content": [],
         }
         for key, value in d.items():
             process_key(key, value, nested_dict)
         expected_dict = {
-            'data_tables': [
-                {'columns': [{'data_table_column_value': 'Amel_HAv3.1'}]}
-            ],
-            'directory_content': []
+            "data_tables": [{"columns": [{"data_table_column_value": "Amel_HAv3.1"}]}],
+            "directory_content": [],
         }
         self.assertEqual(nested_dict, expected_dict)
 
 
 class ParameterParsingTestCase(BaseParameterTestCase):
-    """ Test the parsing of XML for most parameter types - in many
+    """Test the parsing of XML for most parameter types - in many
     ways these are not very good tests since they break the abstraction
     established by the tools. The docs tests in basic.py are better but
     largely rely on HTML stuff we are moving to the client side so they
@@ -55,73 +55,91 @@ class ParameterParsingTestCase(BaseParameterTestCase):
     """
 
     def test_parse_help_and_label(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault" label="x" help="y" />
-        """)
+        """
+        )
         assert param.label == "x"
         assert param.help == "y"
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault">
                 <label>x2</label>
                 <help>y2</help>
             </param>
-        """)
+        """
+        )
         assert param.label == "x2"
         assert param.help == "y2"
 
     def test_parse_sanitizers(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault">
               <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=","/> </valid>
               </sanitizer>
             </param>
-        """)
+        """
+        )
         sanitizer = param.sanitizer
         assert sanitizer is not None
         assert sanitizer.sanitize_param("a") == ""
         assert sanitizer.sanitize_param(",") == ","
 
     def test_parse_optional(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault" />
-        """)
+        """
+        )
         assert param.optional is False
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault" optional="true" />
-        """)
+        """
+        )
         assert param.optional is True
 
     def test_parse_validators(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault">
                 <validator type="unspecified_build" message="no genome?" />
             </param>
-        """)
+        """
+        )
         assert param.validators[0].message == "no genome?"
 
     def test_text_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="texti" value="mydefault" />
-        """)
+        """
+        )
         assert param.value == "mydefault"
         assert param.type == "text"
         assert not param.area
 
     def test_text_area_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="text" name="textarea" area="true" />
-        """)
+        """
+        )
         assert param.value is None
         assert param.type == "text"
         assert param.area
 
     def test_integer_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="integer" name="intp" min="8" max="9" value="9" />
-        """)
+        """
+        )
         assert param.name == "intp"
         assert param.value == "9"
         assert param.type == "integer"
@@ -129,9 +147,11 @@ class ParameterParsingTestCase(BaseParameterTestCase):
         self.assertRaises(Exception, lambda: param.validate(10))
 
     def test_float_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="float" name="floatp" min="7.8" max="9.5" value="9" />
-        """)
+        """
+        )
         assert param.name == "floatp"
         assert param.value == "9"
         assert param.type == "float"
@@ -139,62 +159,78 @@ class ParameterParsingTestCase(BaseParameterTestCase):
         self.assertRaises(Exception, lambda: param.validate(10.0))
 
     def test_boolean_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="boolean" name="boolp" />
-        """)
+        """
+        )
         assert param.name == "boolp"
         assert param.truevalue == "true"
         assert param.falsevalue == "false"
         assert param.type == "boolean"
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="boolean" name="boolp" truevalue="t" falsevalue="f" />
-        """)
+        """
+        )
         assert param.truevalue == "t"
         assert param.falsevalue == "f"
 
     def test_file_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="file" name="filep" />
-        """)
+        """
+        )
         assert param.name == "filep"
         assert param.type == "file"
 
     def test_ftpfile_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param type="ftpfile" name="ftpfilep" />
-        """)
+        """
+        )
         assert param.name == "ftpfilep"
         assert param.type == "ftpfile"
 
     def test_hidden(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="hiddenp" type="hidden" value="a hidden value" />
-        """)
+        """
+        )
         assert param.name == "hiddenp"
         assert param.type == "hidden"
         assert param.value == "a hidden value"
 
     def test_base_url(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="urlp" type="baseurl" value="http://twitter.com/" />
-        """)
+        """
+        )
         assert param.name == "urlp"
         assert param.type == "baseurl"
         assert param.value == "http://twitter.com/"
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="urlp" type="baseurl" />
-        """)
+        """
+        )
         assert param.value == ""
 
     def test_select_static(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="selectp" type="select" multiple="true">
                 <option value="a">A</option>
                 <option value="b" selected="true">B</option>
             </param>
-        """)
+        """
+        )
         assert param.display is None
         assert param.multiple is True
         assert param.name == "selectp"
@@ -215,10 +251,12 @@ class ParameterParsingTestCase(BaseParameterTestCase):
         assert options[1][2]
 
     def test_select_dynamic(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="selectp" type="select" dynamic_options="cow" display="checkboxes" separator="moo">
             </param>
-        """)
+        """
+        )
         assert param.multiple is False
         assert param.options is None
         assert param.dynamic_options == "cow"
@@ -230,12 +268,14 @@ class ParameterParsingTestCase(BaseParameterTestCase):
         assert param.separator == "moo"
 
     def test_select_options_from(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="selectp" type="select">
                 <options from_data_table="cow">
                 </options>
             </param>
-        """)
+        """
+        )
         assert param.dynamic_options is None
         assert param.is_dynamic
 
@@ -244,89 +284,110 @@ class ParameterParsingTestCase(BaseParameterTestCase):
         assert param.options.missing_tool_data_table_name == "cow"
 
     def test_genome_build(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="genomep" type="genomebuild">
             </param>
-        """)
+        """
+        )
         assert param.type == "genomebuild"
         assert param.name == "genomep"
         assert param.static_options
 
     def test_column_params(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="col1" type="data_column" data_ref="input1">
             </param>
-        """)
+        """
+        )
         assert param.data_ref == "input1"
         assert param.usecolnames is False
         assert param.optional is False
         assert param.numerical is False
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="col1" type="data_column" data_ref="input1" use_header_names="true" numerical="true" force_select="false">
             </param>
-        """)
+        """
+        )
         assert param.data_ref == "input1"
         assert param.usecolnames is True
         assert param.optional is True
         assert param.numerical is True
 
     def test_data_param_no_validation(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data">
             </param>
-        """)
+        """
+        )
         assert len(param.validators) == 1
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data" no_validation="true">
             </param>
-        """)
+        """
+        )
         assert len(param.validators) == 0
 
     def test_data_param_dynamic_options(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data" />
-        """)
+        """
+        )
         assert param.options is None
         assert param.options_filter_attribute is None
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data">
                 <options from_data_table="cow">
                 </options>
             </param>
-        """)
+        """
+        )
         assert param.options is not None
         assert param.options_filter_attribute is None
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data">
                 <options from_data_table="cow" options_filter_attribute="cow">
                 </options>
             </param>
-        """)
+        """
+        )
         assert param.options is not None
         assert param.options_filter_attribute == "cow"
 
     def test_conversions(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data" />
-        """)
+        """
+        )
         assert param.conversions == []
 
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="input" type="data">
                 <conversion name="foo" type="txt" />
                 <conversion name="foo2" type="bam" />
             </param>
-        """)
+        """
+        )
         assert param.conversions[0][0] == "foo"
         assert param.conversions[0][1] == "txt"
         assert param.conversions[1][0] == "foo2"
         assert param.conversions[1][1] == "bam"
 
     def test_drilldown(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
               <options>
                <option name="Heading 1" value="heading1">
@@ -340,7 +401,8 @@ class ParameterParsingTestCase(BaseParameterTestCase):
                <option name="Option 5" value="option5"/>
               </options>
             </param>
-        """)
+        """
+        )
         assert param.type == "drill_down"
         assert param.name == "some_name"
         assert param.options
@@ -361,17 +423,21 @@ class ParameterParsingTestCase(BaseParameterTestCase):
         assert len(option5["options"]) == 0
 
     def test_tool_collection(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="datac" type="data_collection" collection_type="list,list:paired" format="txt">
             </param>
-        """)
+        """
+        )
         assert param.type == "data_collection"
         assert param.collection_types == ["list", "list:paired"]
 
     def test_library(self):
-        param = self._parameter_for(xml="""
+        param = self._parameter_for(
+            xml="""
             <param name="libraryp" type="library_data">
             </param>
-        """)
+        """
+        )
         assert param.type == "library_data"
         assert param.name == "libraryp"
diff --git a/test/unit/app/tools/test_select_parameters.py b/test/unit/app/tools/test_select_parameters.py
index 0365271857d..ed86102b88f 100644
--- a/test/unit/app/tools/test_select_parameters.py
+++ b/test/unit/app/tools/test_select_parameters.py
@@ -8,44 +8,46 @@ from .util import BaseParameterTestCase
 
 
 class SelectToolParameterTestCase(BaseParameterTestCase):
-
     def test_validated_values(self):
-        self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
+        self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
         with pytest.raises(ValueError) as exc_info:
             self.param.from_json("42", self.trans, {"input_bam": model.HistoryDatasetAssociation()})
             assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
 
     def test_validated_values_missing_dependency(self):
-        self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
+        self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
         with pytest.raises(ValueError) as exc_info:
             self.param.from_json("42", self.trans)
             assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
 
     def test_unvalidated_values(self):
-        self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
+        self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
         self.trans.workflow_building_mode = True
         assert self.param.from_json("42", self.trans) == "42"
 
     def test_validated_datasets(self):
-        self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
+        self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
         with pytest.raises(ValueError) as exc_info:
             self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": None})
             assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
 
     def test_unvalidated_datasets(self):
-        self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
+        self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
         self.trans.workflow_building_mode = True
-        assert isinstance(self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": basic.RuntimeValue()}), model.HistoryDatasetAssociation)
+        assert isinstance(
+            self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": basic.RuntimeValue()}),
+            model.HistoryDatasetAssociation,
+        )
 
     def test_filter_param_value(self):
-        self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>'''
+        self.options_xml = """<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>"""
         assert ("testname1", "testpath1", False) in self.param.get_options(self.trans, {"input_bam": "testname1"})
         assert ("testname2", "testpath2", False) in self.param.get_options(self.trans, {"input_bam": "testname2"})
         assert len(self.param.get_options(self.trans, {"input_bam": "testname3"})) == 0
 
     def test_filter_param_value2(self):
         # Same test as above, but filtering on a different column.
-        self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>'''
+        self.options_xml = """<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>"""
         assert ("testname1", "testpath1", False) in self.param.get_options(self.trans, {"input_bam": "testpath1"})
         assert ("testname2", "testpath2", False) in self.param.get_options(self.trans, {"input_bam": "testpath2"})
         assert len(self.param.get_options(self.trans, {"input_bam": "testpath3"})) == 0
@@ -85,7 +87,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
             data_ref_text = ""
             if self.set_data_ref:
                 data_ref_text = 'data_ref="input_bam"'
-            template_xml = '''<param name="my_name" type="%s" %s %s %s>%s</param>'''
+            template_xml = """<param name="my_name" type="%s" %s %s %s>%s</param>"""
             param_str = template_xml % (self.type, data_ref_text, multi_text, optional_text, options_text)
             self._param = self._parameter_for(xml=param_str)
 
@@ -93,7 +95,6 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
 
 
 class MockToolDataTable:
-
     def __init__(self):
         self.columns = dict(
             name=0,
diff --git a/test/unit/app/tools/test_tool_dependency_description.py b/test/unit/app/tools/test_tool_dependency_description.py
index 6425a003b1c..6e82ff83b1a 100644
--- a/test/unit/app/tools/test_tool_dependency_description.py
+++ b/test/unit/app/tools/test_tool_dependency_description.py
@@ -1,7 +1,7 @@
 from galaxy.model import tool_shed_install
 from galaxy.tool_util.deps import (
     dependencies,
-    requirements
+    requirements,
 )
 
 
@@ -27,9 +27,7 @@ def test_serialization():
         requirements=[tool_requirement],
         installed_tool_dependencies=[dependency],
     )
-    result_descript = dependencies.DependenciesDescription.from_dict(
-        descript.to_dict()
-    )
+    result_descript = dependencies.DependenciesDescription.from_dict(descript.to_dict())
     result_requirement = result_descript.requirements[0]
     assert result_requirement.name == "tophat"
     assert result_requirement.version == "2.0"
diff --git a/test/unit/app/tools/test_tool_deserialization.py b/test/unit/app/tools/test_tool_deserialization.py
index 3c0577bf81d..2aca4bb8b3f 100644
--- a/test/unit/app/tools/test_tool_deserialization.py
+++ b/test/unit/app/tools/test_tool_deserialization.py
@@ -39,7 +39,7 @@ outputs:
 
 
 class ToolApp(GalaxyDataTestApp):
-    name = 'galaxy'
+    name = "galaxy"
     biotools_metadata_source = None
     job_search = None
 
@@ -57,18 +57,18 @@ def _deserialize(app, tool_source_class, raw_tool_source):
 
 def test_deserialize_xml_tool(tool_app):
 
-    tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL)
-    assert tool.id == 'tool_id'
-    assert tool.name == 'xml tool'
+    tool = _deserialize(tool_app, tool_source_class="XmlToolSource", raw_tool_source=XML_TOOL)
+    assert tool.id == "tool_id"
+    assert tool.name == "xml tool"
 
 
 def test_deserialize_yaml_tool(tool_app):
-    tool = _deserialize(tool_app, tool_source_class='YamlToolSource', raw_tool_source=YAML_TOOL)
-    assert tool.id == 'simple_constructs_y'
-    assert tool.name == 'simple_constructs_y'
+    tool = _deserialize(tool_app, tool_source_class="YamlToolSource", raw_tool_source=YAML_TOOL)
+    assert tool.id == "simple_constructs_y"
+    assert tool.name == "simple_constructs_y"
 
 
 def test_deserialize_cwl_tool(tool_app):
     # Can't verify much about cwl tools at this point
-    tool_source = get_tool_source(tool_app, tool_source_class='CwlToolSource', raw_tool_source=CWL_TOOL)
+    tool_source = get_tool_source(tool_app, tool_source_class="CwlToolSource", raw_tool_source=CWL_TOOL)
     assert isinstance(tool_source, CwlToolSource)
diff --git a/test/unit/app/tools/test_tool_shed_repository_cache.py b/test/unit/app/tools/test_tool_shed_repository_cache.py
index 436147303ca..920e52fdf5c 100644
--- a/test/unit/app/tools/test_tool_shed_repository_cache.py
+++ b/test/unit/app/tools/test_tool_shed_repository_cache.py
@@ -14,33 +14,49 @@ def test_add_repository_to_repository_cache(tool_shed_repository_cache, repos):
     assert len(tool_shed_repository_cache.local_repositories) == 0
 
 
-def test_add_repository_and_tool_conf_repository_to_repository_cache(tool_shed_repository_cache, repos, tool_conf_repos):
+def test_add_repository_and_tool_conf_repository_to_repository_cache(
+    tool_shed_repository_cache, repos, tool_conf_repos
+):
     tool_shed_repository_cache._build()
     assert len(tool_shed_repository_cache.repositories) == 10
     assert len(tool_shed_repository_cache.local_repositories) == 10
     tool_shed_repository_cache._build()
     assert len(tool_shed_repository_cache.repositories) == 10
     assert len(tool_shed_repository_cache.local_repositories) == 10
-    create_repo(tool_shed_repository_cache.session, '21', '20')
+    create_repo(tool_shed_repository_cache.session, "21", "20")
     tool_shed_repository_cache.session.flush()
     tool_shed_repository_cache._build()
     assert len(tool_shed_repository_cache.repositories) == 11
     assert len(tool_shed_repository_cache.local_repositories) == 10
 
 
-@pytest.mark.parametrize('tool_shed,name,owner,changeset_revision,installed_changeset_revision,repository_id,repo_exists', [
-    ('github.com', 'example', 'galaxyproject', None, None, None, True),
-    ('github.com', 'example', 'noone', None, None, None, False),
-    ('github.com', 'example', 'galaxyproject', '1', None, None, True),
-    ('github.com', 'example', 'galaxyproject', None, '1', None, True),
-    ('github.com', 'example', 'galaxyproject', '2', '1', None, True),
-    ('github.com', 'example', 'galaxyproject', '500', '1', None, False),
-    ('github.com', 'example', 'galaxyproject', '1', '500', None, False),
-    ('github.com', 'example', 'galaxyproject', '2', '1', 1, True),
-    ('github.com', 'example', 'galaxyproject', '2', '1', 500, False),
-    ('github.com', 'example', 'galaxyproject', '19', '18', None, True),
-])
-def test_get_installed_repository(tool_shed_repository_cache, repos, tool_conf_repos, tool_shed, name, owner, changeset_revision, installed_changeset_revision, repository_id, repo_exists):
+@pytest.mark.parametrize(
+    "tool_shed,name,owner,changeset_revision,installed_changeset_revision,repository_id,repo_exists",
+    [
+        ("github.com", "example", "galaxyproject", None, None, None, True),
+        ("github.com", "example", "noone", None, None, None, False),
+        ("github.com", "example", "galaxyproject", "1", None, None, True),
+        ("github.com", "example", "galaxyproject", None, "1", None, True),
+        ("github.com", "example", "galaxyproject", "2", "1", None, True),
+        ("github.com", "example", "galaxyproject", "500", "1", None, False),
+        ("github.com", "example", "galaxyproject", "1", "500", None, False),
+        ("github.com", "example", "galaxyproject", "2", "1", 1, True),
+        ("github.com", "example", "galaxyproject", "2", "1", 500, False),
+        ("github.com", "example", "galaxyproject", "19", "18", None, True),
+    ],
+)
+def test_get_installed_repository(
+    tool_shed_repository_cache,
+    repos,
+    tool_conf_repos,
+    tool_shed,
+    name,
+    owner,
+    changeset_revision,
+    installed_changeset_revision,
+    repository_id,
+    repo_exists,
+):
     tool_shed_repository_cache._build()
     repo = tool_shed_repository_cache.get_installed_repository(
         tool_shed=tool_shed,
@@ -48,7 +64,7 @@ def test_get_installed_repository(tool_shed_repository_cache, repos, tool_conf_r
         owner=owner,
         installed_changeset_revision=installed_changeset_revision,
         changeset_revision=changeset_revision,
-        repository_id=repository_id
+        repository_id=repository_id,
     )
     if repo_exists:
         assert repo
diff --git a/test/unit/app/tools/test_toolbox.py b/test/unit/app/tools/test_toolbox.py
index 9af7f9f9bb5..7ef73e80f3d 100644
--- a/test/unit/app/tools/test_toolbox.py
+++ b/test/unit/app/tools/test_toolbox.py
@@ -16,7 +16,10 @@ from galaxy.config_watchers import ConfigWatchers
 from galaxy.model import tool_shed_install
 from galaxy.model.tool_shed_install import mapping
 from galaxy.tool_util.unittest_utils import mock_trans
-from galaxy.tool_util.unittest_utils.sample_data import SIMPLE_MACRO, SIMPLE_TOOL_WITH_MACRO
+from galaxy.tool_util.unittest_utils.sample_data import (
+    SIMPLE_MACRO,
+    SIMPLE_TOOL_WITH_MACRO,
+)
 from galaxy.tools import ToolBox
 from galaxy.tools.cache import ToolCache
 
@@ -38,22 +41,21 @@ CONFIG_TEST_TOOL_VERSION_1 = CONFIG_TEST_TOOL_VERSION_TEMPLATE.safe_substitute(d
 CONFIG_TEST_TOOL_VERSION_2 = CONFIG_TEST_TOOL_VERSION_TEMPLATE.safe_substitute(dict(version="2"))
 
 REPO_TYPE = collections.namedtuple(
-    'REPO_TYPE',
-    'tool_shed owner name changeset_revision installed_changeset_revision description status',
+    "REPO_TYPE",
+    "tool_shed owner name changeset_revision installed_changeset_revision description status",
 )
-DEFAULT_TEST_REPO = REPO_TYPE('github.com', 'galaxyproject', 'example', '1', '1', 'description', 'OK')
+DEFAULT_TEST_REPO = REPO_TYPE("github.com", "galaxyproject", "example", "1", "1", "description", "OK")
 
 
 class SimplifiedToolBox(ToolBox):
-
     def __init__(self, test_case):
         app = test_case.app
         app.watchers.tool_config_watcher.reload_callback = lambda: reload_callback(test_case)
         # Handle app/config stuff needed by toolbox but not by tools.
-        app.tool_cache = ToolCache() if not hasattr(app, 'tool_cache') else app.tool_cache
+        app.tool_cache = ToolCache() if not hasattr(app, "tool_cache") else app.tool_cache
         app.job_config.get_tool_resource_parameters = lambda tool_id: None
         app.config.update_integrated_tool_panel = True
-        app.config.schema.defaults = {'tool_dependency_dir': 'dependencies'}
+        app.config.schema.defaults = {"tool_dependency_dir": "dependencies"}
         config_files = test_case.config_files
         tool_root_dir = test_case.test_directory
         super().__init__(
@@ -103,14 +105,16 @@ class BaseToolBoxTestCase(unittest.TestCase, UsesTools):
 
     def _repo_install(self, changeset, config_filename=None):
         metadata = {
-            'tools': [{
-                'add_to_tool_panel': False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
-                'guid': "github.com/galaxyproject/example/test_tool/0.%s" % changeset,
-                'tool_config': 'tool.xml'
-            }],
+            "tools": [
+                {
+                    "add_to_tool_panel": False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
+                    "guid": "github.com/galaxyproject/example/test_tool/0.%s" % changeset,
+                    "tool_config": "tool.xml",
+                }
+            ],
         }
         if config_filename:
-            metadata['shed_config_filename'] = config_filename
+            metadata["shed_config_filename"] = config_filename
         repository = tool_shed_install.ToolShedRepository(metadata_=metadata)
         repository.tool_shed = DEFAULT_TEST_REPO.tool_shed
         repository.owner = DEFAULT_TEST_REPO.owner
@@ -187,7 +191,6 @@ class BaseToolBoxTestCase(unittest.TestCase, UsesTools):
 
 
 class ToolBoxTestCase(BaseToolBoxTestCase):
-
     def test_load_file(self):
         self._init_tool()
         self._add_config("""<toolbox><tool file="tool.xml" /></toolbox>""")
@@ -198,10 +201,12 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
 
     def test_record_macros(self):
         self._init_tool()
-        self._init_tool(filename="tool_with_macro.xml",
-                        tool_contents=SIMPLE_TOOL_WITH_MACRO,
-                        extra_file_contents=SIMPLE_MACRO.substitute(tool_version="2.0"),
-                        extra_file_path="external.xml")
+        self._init_tool(
+            filename="tool_with_macro.xml",
+            tool_contents=SIMPLE_TOOL_WITH_MACRO,
+            extra_file_contents=SIMPLE_MACRO.substitute(tool_version="2.0"),
+            extra_file_path="external.xml",
+        )
         self._add_config("""<toolbox><tool file="tool_with_macro.xml"/><tool file="tool.xml" /></toolbox>""")
         toolbox = self.toolbox
         tool = toolbox.get_tool("test_tool")
@@ -213,17 +218,19 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
 
     @pytest.mark.xfail(raises=AssertionError)
     def test_tool_reload_when_macro_is_altered(self):
-        self._init_tool(filename="tool_with_macro.xml",
-                        tool_contents=SIMPLE_TOOL_WITH_MACRO,
-                        extra_file_contents=SIMPLE_MACRO.substitute(tool_version="2.0"),
-                        extra_file_path="external.xml")
+        self._init_tool(
+            filename="tool_with_macro.xml",
+            tool_contents=SIMPLE_TOOL_WITH_MACRO,
+            extra_file_contents=SIMPLE_MACRO.substitute(tool_version="2.0"),
+            extra_file_path="external.xml",
+        )
         self._add_config("""<toolbox><tool file="tool_with_macro.xml"/></toolbox>""")
         toolbox = self.toolbox
         tool = toolbox.get_tool("tool_with_macro")
         assert tool is not None
         assert len(tool._macro_paths) == 1
         macro_path = tool._macro_paths[0]
-        with open(macro_path, 'w') as macro_out:
+        with open(macro_path, "w") as macro_out:
             macro_out.write(SIMPLE_MACRO.substitute(tool_version="3.0"))
 
         def check_tool_macro():
@@ -237,20 +244,20 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         self._init_tool(filename="simple_tool.xml", version="1.0")
         self._add_config("""<toolbox><tool file="simple_tool.xml"/></toolbox>""")
         toolbox = self.toolbox
-        tool = toolbox.get_tool('test_tool')
+        tool = toolbox.get_tool("test_tool")
         assert tool is not None
         assert tool.version == "1.0"
         assert tool.tool_errors is None
         # Tool is loaded, now let's break it
         tool_path = tool.config_file
-        with open(tool.config_file, 'w') as out:
-            out.write('certainly not a valid tool')
+        with open(tool.config_file, "w") as out:
+            out.write("certainly not a valid tool")
 
         def check_tool_errors():
             tool = self.toolbox.get_tool("test_tool")
             assert tool is not None
             assert tool.version == "1.0"
-            assert tool.tool_errors == 'Current on-disk tool is not valid'
+            assert tool.tool_errors == "Current on-disk tool is not valid"
 
         self._try_until_no_errors(check_tool_errors)
 
@@ -274,7 +281,7 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
                 return
             except AssertionError as error:
                 e = error
-                time.sleep(.25)
+                time.sleep(0.25)
 
         if e:
             raise e
@@ -359,14 +366,14 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         self._setup_two_versions()
 
         test_tool = self.toolbox.get_tool("test_tool", tool_version="0.1")
-        assert test_tool.version == '0.1'
+        assert test_tool.version == "0.1"
 
         test_tool = self.toolbox.get_tool("test_tool", tool_version="0.2")
-        assert test_tool.version == '0.2'
+        assert test_tool.version == "0.2"
 
         # there is no version 3, return newest version
         test_tool = self.toolbox.get_tool("test_tool", tool_version="3")
-        assert test_tool.version == '0.2'
+        assert test_tool.version == "0.2"
 
     def test_load_file_in_section(self):
         self._init_tool_in_section()
@@ -410,12 +417,15 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
 
     def test_get_section_by_label(self):
         self._add_config(
-            """<toolbox><section id="tid" name="Completely unrelated"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>""")
+            """<toolbox><section id="tid" name="Completely unrelated"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>"""
+        )
         assert len(self.toolbox._tool_panel) == 1
-        section = self.toolbox._tool_panel['tid']
-        tool_panel_section_key, section_by_label = self.toolbox.get_section(section_id='nope', new_label='Completely unrelated', create_if_needed=True)
+        section = self.toolbox._tool_panel["tid"]
+        tool_panel_section_key, section_by_label = self.toolbox.get_section(
+            section_id="nope", new_label="Completely unrelated", create_if_needed=True
+        )
         assert section_by_label is section
-        assert tool_panel_section_key == 'tid'
+        assert tool_panel_section_key == "tid"
 
     def test_get_tool(self):
         self._init_tool()
@@ -423,11 +433,20 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         self._setup_two_versions()
         assert self.toolbox.get_tool("test_tool").id in [
             "github.com/galaxyproject/example/test_tool/0.1",
-            "github.com/galaxyproject/example/test_tool/0.2"
+            "github.com/galaxyproject/example/test_tool/0.2",
         ]
-        assert self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.1").id == "github.com/galaxyproject/example/test_tool/0.1"
-        assert self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.2").id == "github.com/galaxyproject/example/test_tool/0.2"
-        assert self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.3").id != "github.com/galaxyproject/example/test_tool/0.3"
+        assert (
+            self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.1").id
+            == "github.com/galaxyproject/example/test_tool/0.1"
+        )
+        assert (
+            self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.2").id
+            == "github.com/galaxyproject/example/test_tool/0.2"
+        )
+        assert (
+            self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.3").id
+            != "github.com/galaxyproject/example/test_tool/0.3"
+        )
 
     def test_tool_dir(self):
         self._init_tool()
@@ -455,9 +474,11 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
     def test_workflow_in_section(self):
         stored_workflow = self.__test_workflow()
         encoded_id = self.app.security.encode_id(stored_workflow.id)
-        self._add_config("""<toolbox><section id="tid" name="TID"><workflow id="%s" /></section></toolbox>""" % encoded_id)
+        self._add_config(
+            """<toolbox><section id="tid" name="TID"><workflow id="%s" /></section></toolbox>""" % encoded_id
+        )
         assert len(self.toolbox._tool_panel) == 1
-        section = self.toolbox._tool_panel['tid']
+        section = self.toolbox._tool_panel["tid"]
         assert len(section.elems) == 1
         panel_workflow = next(iter(section.elems.values()))
         assert panel_workflow == stored_workflow.latest_workflow
@@ -468,9 +489,11 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         self.__check_test_labels(self.toolbox._tool_panel)
 
     def test_label_in_section(self):
-        self._add_config("""<toolbox><section id="tid" name="TID"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>""")
+        self._add_config(
+            """<toolbox><section id="tid" name="TID"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>"""
+        )
         assert len(self.toolbox._tool_panel) == 1
-        section = self.toolbox._tool_panel['tid']
+        section = self.toolbox._tool_panel["tid"]
         self.__check_test_labels(section.elems)
 
     def _init_tool_in_section(self, json=False):
@@ -482,8 +505,7 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
                 "type": "section",
                 "id": "t",
                 "name": "test",
-                "items": [{"type": "tool",
-                           "file": "tool.xml"}],
+                "items": [{"type": "tool", "file": "tool.xml"}],
             }
             self._add_config({"items": [section]}, name="tool_conf.json")
 
@@ -524,8 +546,14 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
             assert lineage_ids[1] == "github.com/galaxyproject/example/test_tool/0.2"
 
         # Test tool_version attribute.
-        assert self.toolbox.get_tool("test_tool", tool_version="0.1").guid == "github.com/galaxyproject/example/test_tool/0.1"
-        assert self.toolbox.get_tool("test_tool", tool_version="0.2").guid == "github.com/galaxyproject/example/test_tool/0.2"
+        assert (
+            self.toolbox.get_tool("test_tool", tool_version="0.1").guid
+            == "github.com/galaxyproject/example/test_tool/0.1"
+        )
+        assert (
+            self.toolbox.get_tool("test_tool", tool_version="0.2").guid
+            == "github.com/galaxyproject/example/test_tool/0.2"
+        )
 
     def test_default_lineage(self):
         self.__init_versioned_tools()
diff --git a/test/unit/app/tools/test_wrappers.py b/test/unit/app/tools/test_wrappers.py
index 257cbf3a1c3..5932a1fbe6e 100644
--- a/test/unit/app/tools/test_wrappers.py
+++ b/test/unit/app/tools/test_wrappers.py
@@ -22,7 +22,7 @@ from galaxy.tools.wrappers import (
     DatasetFilenameWrapper,
     InputValueWrapper,
     RawObjectWrapper,
-    SelectToolParameterWrapper
+    SelectToolParameterWrapper,
 )
 from galaxy.util import XML
 
@@ -33,18 +33,23 @@ def with_mock_tool(func):
         app = MockApp(test_directory)
         tool = MockTool(app)
         return func(tool)
+
     call.__name__ = func.__name__
     return call
 
 
 def selectwrapper(tool, value, multiple=False, optional=False):
-    optional = 'optional="true"' if optional else ''
-    multiple = 'multiple="true"' if multiple else ''
-    xml = XML('''<param name="blah" type="select" {} {}>
+    optional = 'optional="true"' if optional else ""
+    multiple = 'multiple="true"' if multiple else ""
+    xml = XML(
+        """<param name="blah" type="select" {} {}>
         <option value="x">I am X</option>
         <option value="y" selected="true">I am Y</option>
         <option value="z">I am Z</option>
-    </param>'''.format(multiple, optional))
+    </param>""".format(
+            multiple, optional
+        )
+    )
     parameter = SelectToolParameter(tool, xml)
     return SelectToolParameterWrapper(parameter, value)
 
@@ -105,7 +110,9 @@ def test_select_wrapper_multiple(tool):
 def test_select_wrapper_with_path_rewritting(tool):
     parameter = _setup_blast_tool(tool, multiple=True)
     compute_environment = cast(ComputeEnvironment, MockComputeEnvironment(None))
-    wrapper = SelectToolParameterWrapper(parameter, ["val1", "val2"], other_values={}, compute_environment=compute_environment)
+    wrapper = SelectToolParameterWrapper(
+        parameter, ["val1", "val2"], other_values={}, compute_environment=compute_environment
+    )
     assert wrapper.fields.path == "Rewrite<path1>,Rewrite<path2>"
 
 
@@ -132,7 +139,9 @@ def valuewrapper(tool, value, paramtype, optional=False):
         parameter = FloatToolParameter(tool, XML('<param name="blah" type="float" %s/>' % optional))
     elif paramtype == "boolean":
         optional = 'optional="true"' if optional else 'value=""'
-        parameter = BooleanToolParameter(tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" %s/>' % optional))
+        parameter = BooleanToolParameter(
+            tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" %s/>' % optional)
+        )
     return InputValueWrapper(parameter, value)
 
 
@@ -159,24 +168,26 @@ def test_input_value_wrapper_comparison(tool):
 
 @with_mock_tool
 def test_input_value_wrapper_comparison_optional(tool):
-    wrapper = valuewrapper(tool, None, 'integer', optional=True)
+    wrapper = valuewrapper(tool, None, "integer", optional=True)
     assert not wrapper
     with pytest.raises(ValueError):
         int(wrapper)
     assert str(wrapper) == ""
     assert wrapper == ""  # for backward-compatibility
-    wrapper = valuewrapper(tool, 0, 'integer', optional=True)
+    wrapper = valuewrapper(tool, 0, "integer", optional=True)
     assert wrapper == 0
     assert int(wrapper) == 0
     assert str(wrapper)
-    assert wrapper != ""  # for backward-compatibility, the correct way to check if an optional integer param is not empty is to use str(wrapper)
-    wrapper = valuewrapper(tool, None, 'integer', optional=True)
+    assert (
+        wrapper != ""
+    )  # for backward-compatibility, the correct way to check if an optional integer param is not empty is to use str(wrapper)
+    wrapper = valuewrapper(tool, None, "integer", optional=True)
     assert wrapper != 1
     assert str(wrapper) == ""
     assert wrapper == None  # noqa: E711
     wrapper = valuewrapper(tool, None, "boolean")
     assert bool(wrapper) is False, wrapper
-    assert str(wrapper) == 'falsevalue'
+    assert str(wrapper) == "falsevalue"
 
 
 @with_mock_tool
@@ -204,13 +215,14 @@ def test_dataset_wrapper():
 def test_dataset_wrapper_false_path():
     dataset = cast(DatasetInstance, MockDataset())
     new_path = "/new/path/dataset_123.dat"
-    wrapper = DatasetFilenameWrapper(dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(false_path=new_path)))
+    wrapper = DatasetFilenameWrapper(
+        dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(false_path=new_path))
+    )
     assert str(wrapper) == new_path
     assert wrapper.file_name == new_path
 
 
 class MockComputeEnvironment:
-
     def __init__(self, false_path, false_extra_files_path=None):
         self.false_path = false_path
         self.false_extra_files_path = false_extra_files_path
@@ -233,17 +245,25 @@ def test_dataset_false_extra_files_path():
 
     new_path = "/new/path/dataset_123.dat"
     dataset_path = DatasetPath(123, MOCK_DATASET_PATH, false_path=new_path)
-    wrapper = DatasetFilenameWrapper(dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(dataset_path)))
+    wrapper = DatasetFilenameWrapper(
+        dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(dataset_path))
+    )
     # Setting false_path is not enough to override
     assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
 
     new_files_path = "/new/path/dataset_123_files"
-    wrapper = DatasetFilenameWrapper(dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(false_path=new_path, false_extra_files_path=new_files_path)))
+    wrapper = DatasetFilenameWrapper(
+        dataset,
+        compute_environment=cast(
+            ComputeEnvironment, MockComputeEnvironment(false_path=new_path, false_extra_files_path=new_files_path)
+        ),
+    )
     assert wrapper.extra_files_path == new_files_path
 
 
 def _drilldown_parameter(tool):
-    xml = XML('''<param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
+    xml = XML(
+        """<param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
         <options>
             <option name="Heading 1" value="heading1">
                 <option name="Option 1" value="option1"/>
@@ -255,20 +275,24 @@ def _drilldown_parameter(tool):
             </option>
            <option name="Option 5" value="option5"/>
       </options>
-    </param>''')
+    </param>"""
+    )
     parameter = DrillDownSelectToolParameter(tool, xml)
     return parameter
 
 
 def _setup_blast_tool(tool, multiple=False):
     tool.app.write_test_tool_data("blastdb.loc", "val1\tname1\tpath1\nval2\tname2\tpath2\n")
-    xml = XML('''<param name="database" type="select" label="Nucleotide BLAST database" multiple="%s">
+    xml = XML(
+        """<param name="database" type="select" label="Nucleotide BLAST database" multiple="%s">
         <options from_file="blastdb.loc">
             <column name="value" index="0"/>
             <column name="name" index="1"/>
             <column name="path" index="2"/>
         </options>
-    </param>''' % multiple)
+    </param>"""
+        % multiple
+    )
     parameter = SelectToolParameter(tool, xml)
     return parameter
 
@@ -279,7 +303,6 @@ MOCK_DATASET_EXT = "bam"
 
 
 class MockDataset:
-
     def __init__(self):
         self.metadata = MetadataSpecCollection({})
         self.file_name = MOCK_DATASET_PATH
@@ -289,14 +312,12 @@ class MockDataset:
 
 
 class MockTool:
-
     def __init__(self, app):
         self.app = app
         self.options = Mock(sanitize=False)
 
 
 class MockApp:
-
     def __init__(self, test_directory):
         self.config = Mock(tool_data_path=test_directory)
 
diff --git a/test/unit/app/tools/util.py b/test/unit/app/tools/util.py
index 8c2c5f80675..711e785981d 100644
--- a/test/unit/app/tools/util.py
+++ b/test/unit/app/tools/util.py
@@ -10,7 +10,6 @@ from galaxy.util import (
 
 
 class BaseParameterTestCase(TestCase, UsesApp):
-
     def setUp(self):
         self.setup_app()
         self.mock_tool = bunch.Bunch(
diff --git a/test/unit/app/visualizations/plugins/__init__.py b/test/unit/app/visualizations/plugins/__init__.py
index 650dd6c5d74..5aa9f3bf67f 100644
--- a/test/unit/app/visualizations/plugins/__init__.py
+++ b/test/unit/app/visualizations/plugins/__init__.py
@@ -4,7 +4,6 @@ import routes
 
 
 class VisualizationsBase_TestCase(unittest.TestCase):
-
     @classmethod
     def setUpClass(cls):
         routes.Mapper()
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
index 943ddf1430d..ead81ab0834 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
@@ -5,11 +5,9 @@ import unittest
 
 from galaxy.app_unittest_utils import galaxy_mock
 from galaxy.util import clean_multiline_string
-from galaxy.visualization.plugins import (
-    plugin as vis_plugin,
-    resource_parser,
-    utils as vis_utils
-)
+from galaxy.visualization.plugins import plugin as vis_plugin
+from galaxy.visualization.plugins import resource_parser
+from galaxy.visualization.plugins import utils as vis_utils
 from . import VisualizationsBase_TestCase
 
 
@@ -20,23 +18,22 @@ class VisualizationsPlugin_TestCase(VisualizationsBase_TestCase):
         """
         A plugin with no context passed in should have sane defaults.
         """
-        vis_dir = galaxy_mock.MockDir({
-            'config': {
-                'vis1.xml': ''
-            },
-            'static': {},
-            'templates': {},
-        })
-        plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path,
-            'myvis', {})
-        self.assertEqual(plugin.name, 'myvis')
+        vis_dir = galaxy_mock.MockDir(
+            {
+                "config": {"vis1.xml": ""},
+                "static": {},
+                "templates": {},
+            }
+        )
+        plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path, "myvis", {})
+        self.assertEqual(plugin.name, "myvis")
         self.assertEqual(plugin.path, vis_dir.root_path)
         self.assertEqual(plugin.config, {})
-        self.assertEqual(plugin.base_url, 'myvis')
+        self.assertEqual(plugin.base_url, "myvis")
         # template
         self.assertTrue(plugin.serves_templates)
-        self.assertEqual(plugin.template_path, vis_dir.root_path + '/templates')
-        self.assertEqual(plugin.template_lookup.__class__.__name__, 'TemplateLookup')
+        self.assertEqual(plugin.template_path, vis_dir.root_path + "/templates")
+        self.assertEqual(plugin.template_lookup.__class__.__name__, "TemplateLookup")
         # resource parser
         self.assertIsInstance(plugin.resource_parser, resource_parser.ResourceParser)
 
@@ -44,34 +41,24 @@ class VisualizationsPlugin_TestCase(VisualizationsBase_TestCase):
         """
         A plugin with context passed in should use those in it's set up.
         """
-        vis_dir = galaxy_mock.MockDir({
-            'config': {
-                'vis1.xml': ''
-            },
-            'static': {},
-            'templates': {},
-        })
-        context = dict(
-            base_url='u/wot/m8',
-            template_cache_dir='template_cache',
-            additional_template_paths=['one']
+        vis_dir = galaxy_mock.MockDir(
+            {
+                "config": {"vis1.xml": ""},
+                "static": {},
+                "templates": {},
+            }
         )
-        plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path,
-            'myvis', {}, context=context)
-        self.assertEqual(plugin.base_url, 'u/wot/m8/myvis')
-        self.assertEqual(plugin.template_lookup.__class__.__name__, 'TemplateLookup')
+        context = dict(base_url="u/wot/m8", template_cache_dir="template_cache", additional_template_paths=["one"])
+        plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path, "myvis", {}, context=context)
+        self.assertEqual(plugin.base_url, "u/wot/m8/myvis")
+        self.assertEqual(plugin.template_lookup.__class__.__name__, "TemplateLookup")
 
     def test_init_without_static_or_templates(self):
         """
         A plugin that has neither template or static directory should serve neither.
         """
-        vis_dir = galaxy_mock.MockDir({
-            'config': {
-                'vis1.xml': ''
-            }
-        })
-        plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path,
-            'myvis', dict())
+        vis_dir = galaxy_mock.MockDir({"config": {"vis1.xml": ""}})
+        plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path, "myvis", dict())
         self.assertFalse(plugin.serves_templates)
         # not sure what this would do, but...
 
@@ -80,40 +67,37 @@ class VisualizationsPlugin_TestCase(VisualizationsBase_TestCase):
         Render vars passed to render should default properly.
         """
         # well, that's kind of a lot of typing to say nothing new
-        config = dict(
-            name='Cat Fancy Magazine\'s Genomic Visualization'
-        )
-        plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis', config)
+        config = dict(name="Cat Fancy Magazine's Genomic Visualization")
+        plugin = self.plugin_class(galaxy_mock.MockApp(), "", "myvis", config)
 
         render_vars = plugin._build_render_vars(config)
-        self.assertEqual(render_vars['visualization_name'], plugin.name)
-        self.assertEqual(render_vars['visualization_display_name'], plugin.config['name'])
-        self.assertEqual(render_vars['title'], None)
-        self.assertEqual(render_vars['saved_visualization'], None)
-        self.assertEqual(render_vars['visualization_id'], None)
-        self.assertEqual(render_vars['query'], {})
-        self.assertIsInstance(render_vars['config'], vis_utils.OpenObject)
-        self.assertEqual(render_vars['config'].__dict__, {})
+        self.assertEqual(render_vars["visualization_name"], plugin.name)
+        self.assertEqual(render_vars["visualization_display_name"], plugin.config["name"])
+        self.assertEqual(render_vars["title"], None)
+        self.assertEqual(render_vars["saved_visualization"], None)
+        self.assertEqual(render_vars["visualization_id"], None)
+        self.assertEqual(render_vars["query"], {})
+        self.assertIsInstance(render_vars["config"], vis_utils.OpenObject)
+        self.assertEqual(render_vars["config"].__dict__, {})
 
     def test_build_config(self):
-        """
-        """
+        """ """
         plugin_config: dict = dict()
-        plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis', plugin_config)
+        plugin = self.plugin_class(galaxy_mock.MockApp(), "", "myvis", plugin_config)
         config = plugin._build_config({})
         self.assertIsInstance(config, vis_utils.OpenObject)
         self.assertEqual(config.__dict__, {})
 
         # existing should flow through
         plugin_config = dict()
-        plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis', plugin_config)
+        plugin = self.plugin_class(galaxy_mock.MockApp(), "", "myvis", plugin_config)
         existing_config = dict(wat=1)
         config = plugin._build_config(existing_config)
         self.assertEqual(config.wat, 1)
 
         # unlisted/non-param kwargs should NOT overwrite existing
         plugin_config = dict()
-        plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis', plugin_config)
+        plugin = self.plugin_class(galaxy_mock.MockApp(), "", "myvis", plugin_config)
         existing_config = dict(wat=1)
         config = plugin._build_config(existing_config, wat=2)
         self.assertEqual(config.wat, 1)
@@ -121,26 +105,21 @@ class VisualizationsPlugin_TestCase(VisualizationsBase_TestCase):
         # listed/param kwargs *should* overwrite existing
         plugin_config = dict(
             params=dict(
-                wat={
-                    'csv': False,
-                    'required': False,
-                    'type': 'int',
-                    'var_name_in_template': 'wot'
-                },
+                wat={"csv": False, "required": False, "type": "int", "var_name_in_template": "wot"},
             )
         )
-        plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis', plugin_config)
+        plugin = self.plugin_class(galaxy_mock.MockApp(), "", "myvis", plugin_config)
         existing_config = dict(wat=1)
         # send as string like a query would - should be parsed
-        config = plugin._build_config(existing_config, wat='2')
+        config = plugin._build_config(existing_config, wat="2")
         self.assertEqual(config.wat, 2)
 
     def test_render(self):
-        """
-        """
+        """ """
         # use the python in a template to test for variables that should be there
         # TODO: gotta be a better way
-        testing_template = clean_multiline_string("""\
+        testing_template = clean_multiline_string(
+            """\
         <%
             found_all = True
             should_have = [
@@ -158,19 +137,15 @@ class VisualizationsPlugin_TestCase(VisualizationsBase_TestCase):
                     break
         %>
         ${ found_all }
-        """)
+        """
+        )
 
-        mock_app_dir = galaxy_mock.MockDir({
-            'cache': {},
-            'template.mako': testing_template
-        })
+        mock_app_dir = galaxy_mock.MockDir({"cache": {}, "template.mako": testing_template})
         mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
-        plugin = self.plugin_class(mock_app, '', 'myvis', {
-            "name": "Vlad News Bears"
-        })
+        plugin = self.plugin_class(mock_app, "", "myvis", {"name": "Vlad News Bears"})
 
         # somewhat easier to set this up by hand
-        plugin.config['entry_point'] = {'file': 'template.mako'}
+        plugin.config["entry_point"] = {"file": "template.mako"}
         plugin.template_path = mock_app_dir.root_path
         plugin.template_lookup = plugin._build_template_lookup(mock_app_dir.root_path)
 
@@ -182,5 +157,5 @@ class VisualizationsPlugin_TestCase(VisualizationsBase_TestCase):
 # -----------------------------------------------------------------------------
 # TODO: config parser tests (in separate file)
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
index 9534d8b480a..1a3d0b61c38 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
@@ -8,15 +8,18 @@ from typing import Dict
 
 from galaxy import model
 from galaxy.app_unittest_utils import galaxy_mock
-from galaxy.util import clean_multiline_string, galaxy_directory
+from galaxy.util import (
+    clean_multiline_string,
+    galaxy_directory,
+)
 from galaxy.visualization.plugins import plugin
 from galaxy.visualization.plugins.registry import VisualizationsRegistry
 from . import VisualizationsBase_TestCase
 
 glx_dir = galaxy_directory()
-template_cache_dir = os.path.join(glx_dir, 'database', 'compiled_templates')
-addtional_templates_dir = os.path.join(glx_dir, 'config', 'plugins', 'visualizations', 'common', 'templates')
-vis_reg_path = 'config/plugins/visualizations'
+template_cache_dir = os.path.join(glx_dir, "database", "compiled_templates")
+addtional_templates_dir = os.path.join(glx_dir, "config", "plugins", "visualizations", "common", "templates")
+vis_reg_path = "config/plugins/visualizations"
 
 config1 = """\
 <?xml version="1.0" encoding="UTF-8"?>
@@ -38,102 +41,89 @@ config1 = """\
 
 
 class VisualizationsRegistry_TestCase(VisualizationsBase_TestCase):
-
     def test_plugin_load_from_repo(self):
         """should attempt load if criteria met"""
         mock_app = galaxy_mock.MockApp(root=glx_dir)
-        plugin_mgr = VisualizationsRegistry(mock_app,
-            directories_setting=vis_reg_path,
-            template_cache_dir=None)
+        plugin_mgr = VisualizationsRegistry(mock_app, directories_setting=vis_reg_path, template_cache_dir=None)
 
         expected_plugins_path = os.path.join(glx_dir, vis_reg_path)
-        self.assertEqual(plugin_mgr.base_url, 'visualizations')
+        self.assertEqual(plugin_mgr.base_url, "visualizations")
         self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
 
-        scatterplot = plugin_mgr.plugins['scatterplot']
-        self.assertEqual(scatterplot.name, 'scatterplot')
-        self.assertEqual(scatterplot.path, os.path.join(expected_plugins_path, 'scatterplot'))
-        self.assertEqual(scatterplot.base_url, '/'.join((plugin_mgr.base_url, scatterplot.name)))
+        scatterplot = plugin_mgr.plugins["scatterplot"]
+        self.assertEqual(scatterplot.name, "scatterplot")
+        self.assertEqual(scatterplot.path, os.path.join(expected_plugins_path, "scatterplot"))
+        self.assertEqual(scatterplot.base_url, "/".join((plugin_mgr.base_url, scatterplot.name)))
         self.assertTrue(scatterplot.serves_templates)
-        self.assertEqual(scatterplot.template_path, os.path.join(scatterplot.path, 'templates'))
-        self.assertEqual(scatterplot.template_lookup.__class__.__name__, 'TemplateLookup')
+        self.assertEqual(scatterplot.template_path, os.path.join(scatterplot.path, "templates"))
+        self.assertEqual(scatterplot.template_lookup.__class__.__name__, "TemplateLookup")
 
-        trackster = plugin_mgr.plugins['trackster']
-        self.assertEqual(trackster.name, 'trackster')
-        self.assertEqual(trackster.path, os.path.join(expected_plugins_path, 'trackster'))
-        self.assertEqual(trackster.base_url, '/'.join((plugin_mgr.base_url, trackster.name)))
+        trackster = plugin_mgr.plugins["trackster"]
+        self.assertEqual(trackster.name, "trackster")
+        self.assertEqual(trackster.path, os.path.join(expected_plugins_path, "trackster"))
+        self.assertEqual(trackster.base_url, "/".join((plugin_mgr.base_url, trackster.name)))
         self.assertFalse(trackster.serves_templates)
 
     def test_plugin_load(self):
         """"""
-        mock_app_dir = galaxy_mock.MockDir({
-            'plugins': {
-                'vis1': {
-                    'config': {
-                        'vis1.xml': config1
+        mock_app_dir = galaxy_mock.MockDir(
+            {
+                "plugins": {
+                    "vis1": {
+                        "config": {"vis1.xml": config1},
+                        "static": {},
+                        "templates": {},
                     },
-                    'static': {},
-                    'templates': {},
-                },
-                'vis2': {
-                    'config': {
-                        'vis2.xml': config1
-                    }
-                },
-                'not_a_vis1': {
-                    'config': {
-                        'vis1.xml': 'blerbler'
+                    "vis2": {"config": {"vis2.xml": config1}},
+                    "not_a_vis1": {
+                        "config": {"vis1.xml": "blerbler"},
                     },
-                },
-                # empty
-                'not_a_vis2': {},
-                'not_a_vis3': 'blerbler',
-                # bad config
-                'not_a_vis4': {
-                    'config': {
-                        'not_a_vis4.xml': 'blerbler'
-                    }
-                },
-                'not_a_vis5': {
-                    # no config
-                    'static': {},
-                    'templates': {},
-                },
+                    # empty
+                    "not_a_vis2": {},
+                    "not_a_vis3": "blerbler",
+                    # bad config
+                    "not_a_vis4": {"config": {"not_a_vis4.xml": "blerbler"}},
+                    "not_a_vis5": {
+                        # no config
+                        "static": {},
+                        "templates": {},
+                    },
+                }
             }
-        })
+        )
         mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
-        plugin_mgr = VisualizationsRegistry(mock_app,
-            directories_setting='plugins',
-            template_cache_dir=template_cache_dir)
+        plugin_mgr = VisualizationsRegistry(
+            mock_app, directories_setting="plugins", template_cache_dir=template_cache_dir
+        )
 
-        expected_plugins_path = os.path.join(mock_app_dir.root_path, 'plugins')
-        expected_plugin_names = ['vis1', 'vis2']
+        expected_plugins_path = os.path.join(mock_app_dir.root_path, "plugins")
+        expected_plugin_names = ["vis1", "vis2"]
 
-        self.assertEqual(plugin_mgr.base_url, 'visualizations')
+        self.assertEqual(plugin_mgr.base_url, "visualizations")
         self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
         self.assertEqual(sorted(plugin_mgr.plugins.keys()), expected_plugin_names)
 
-        vis1 = plugin_mgr.plugins['vis1']
-        self.assertEqual(vis1.name, 'vis1')
-        self.assertEqual(vis1.path, os.path.join(expected_plugins_path, 'vis1'))
-        self.assertEqual(vis1.base_url, '/'.join((plugin_mgr.base_url, vis1.name)))
+        vis1 = plugin_mgr.plugins["vis1"]
+        self.assertEqual(vis1.name, "vis1")
+        self.assertEqual(vis1.path, os.path.join(expected_plugins_path, "vis1"))
+        self.assertEqual(vis1.base_url, "/".join((plugin_mgr.base_url, vis1.name)))
         self.assertTrue(vis1.serves_templates)
-        self.assertEqual(vis1.template_path, os.path.join(vis1.path, 'templates'))
-        self.assertEqual(vis1.template_lookup.__class__.__name__, 'TemplateLookup')
+        self.assertEqual(vis1.template_path, os.path.join(vis1.path, "templates"))
+        self.assertEqual(vis1.template_lookup.__class__.__name__, "TemplateLookup")
 
-        vis2 = plugin_mgr.plugins['vis2']
-        self.assertEqual(vis2.name, 'vis2')
-        self.assertEqual(vis2.path, os.path.join(expected_plugins_path, 'vis2'))
-        self.assertEqual(vis2.base_url, '/'.join((plugin_mgr.base_url, vis2.name)))
+        vis2 = plugin_mgr.plugins["vis2"]
+        self.assertEqual(vis2.name, "vis2")
+        self.assertEqual(vis2.path, os.path.join(expected_plugins_path, "vis2"))
+        self.assertEqual(vis2.base_url, "/".join((plugin_mgr.base_url, vis2.name)))
         self.assertFalse(vis2.serves_templates)
 
         mock_app_dir.remove()
         template_cache_dir
 
     def test_interactive_environ_plugin_load(self):
-        """
-        """
-        jupyter_config = clean_multiline_string("""\
+        """ """
+        jupyter_config = clean_multiline_string(
+            """\
         <?xml version="1.0" encoding="UTF-8"?>
         <!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
         <interactive_environment name="Jupyter">
@@ -150,63 +140,62 @@ class VisualizationsRegistry_TestCase(VisualizationsBase_TestCase):
             </params>
             <template>jupyter.mako</template>
         </interactive_environment>
-        """)
+        """
+        )
 
         templates: Dict[str, str] = {}
         mock_app_dir_config = {
-            'plugins': {
-                'jupyter': {
-                    'config': {
-                        'jupyter.xml': jupyter_config
-                    },
-                    'templates': templates,
+            "plugins": {
+                "jupyter": {
+                    "config": {"jupyter.xml": jupyter_config},
+                    "templates": templates,
                 },
             },
         }
 
         # going to use a fake template here to simplify testing
         jupyter_template = "${ ie_request }-${ get_api_key() }"
-        templates['jupyter.mako'] = jupyter_template
+        templates["jupyter.mako"] = jupyter_template
         # so that we don't create a cached version of that fake template in the real mako caches
         #   we'll set up a cache in the temp dir
-        mock_app_dir_config['caches'] = {}
+        mock_app_dir_config["caches"] = {}
         # and make sure the vis reg uses that
         mock_app_dir = galaxy_mock.MockDir(mock_app_dir_config)
         mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
-        plugin_mgr = VisualizationsRegistry(mock_app,
-            directories_setting='plugins',
-            template_cache_dir=os.path.join(mock_app_dir.root_path, 'caches'))
+        plugin_mgr = VisualizationsRegistry(
+            mock_app, directories_setting="plugins", template_cache_dir=os.path.join(mock_app_dir.root_path, "caches")
+        )
 
         # ...then start testing
-        expected_plugins_path = os.path.join(mock_app_dir.root_path, 'plugins')
-        expected_plugin_names = ['jupyter']
+        expected_plugins_path = os.path.join(mock_app_dir.root_path, "plugins")
+        expected_plugin_names = ["jupyter"]
 
-        self.assertEqual(plugin_mgr.base_url, 'visualizations')
+        self.assertEqual(plugin_mgr.base_url, "visualizations")
         self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
         self.assertEqual(sorted(plugin_mgr.plugins.keys()), expected_plugin_names)
 
-        jupyter = plugin_mgr.plugins['jupyter']
+        jupyter = plugin_mgr.plugins["jupyter"]
         config = jupyter.config
 
-        self.assertEqual(jupyter.name, 'jupyter')
-        self.assertEqual(config.get('plugin_type'), 'interactive_environment')
+        self.assertEqual(jupyter.name, "jupyter")
+        self.assertEqual(config.get("plugin_type"), "interactive_environment")
 
         # get_api_key needs a user, fill_template a trans
         user = model.User(email="blah@bler.blah", password="dockerDockerDOCKER")
         trans = galaxy_mock.MockTrans(user=user)
         # use a mock request factory - this will be written into the filled template to show it was used
-        jupyter.INTENV_REQUEST_FACTORY = lambda t, p: 'mock'
+        jupyter.INTENV_REQUEST_FACTORY = lambda t, p: "mock"
 
         # should return the (new) api key for the above user (see the template above)
         response = jupyter._render({}, trans=trans)
         response.strip()
         self.assertIsInstance(response, str)
-        self.assertTrue('-' in response)
-        ie_request, api_key = response.split('-')
+        self.assertTrue("-" in response)
+        ie_request, api_key = response.split("-")
 
-        self.assertEqual(ie_request, 'mock')
+        self.assertEqual(ie_request, "mock")
 
-        match = re.match(r'[a-f0-9]{32}', api_key)
+        match = re.match(r"[a-f0-9]{32}", api_key)
         assert match
         self.assertEqual(match.span(), (0, 32))
 
@@ -214,7 +203,8 @@ class VisualizationsRegistry_TestCase(VisualizationsBase_TestCase):
 
     def test_script_entry(self):
         """"""
-        script_entry_config = clean_multiline_string("""\
+        script_entry_config = clean_multiline_string(
+            """\
         <?xml version="1.0" encoding="UTF-8"?>
         <visualization name="js-test">
             <data_sources>
@@ -224,26 +214,24 @@ class VisualizationsRegistry_TestCase(VisualizationsBase_TestCase):
             </data_sources>
             <entry_point entry_point_type="script" data-main="one" src="bler"></entry_point>
         </visualization>
-        """)
+        """
+        )
 
-        mock_app_dir = galaxy_mock.MockDir({
-            'plugins': {
-                'jstest': {
-                    'config': {
-                        'jstest.xml': script_entry_config
-                    },
-                    'static': {}
-                },
+        mock_app_dir = galaxy_mock.MockDir(
+            {
+                "plugins": {
+                    "jstest": {"config": {"jstest.xml": script_entry_config}, "static": {}},
+                }
             }
-        })
+        )
         mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
-        plugin_mgr = VisualizationsRegistry(mock_app,
-            directories_setting='plugins',
-            template_cache_dir=template_cache_dir)
-        script_entry = plugin_mgr.plugins['jstest']
+        plugin_mgr = VisualizationsRegistry(
+            mock_app, directories_setting="plugins", template_cache_dir=template_cache_dir
+        )
+        script_entry = plugin_mgr.plugins["jstest"]
 
         self.assertIsInstance(script_entry, plugin.ScriptVisualizationPlugin)
-        self.assertEqual(script_entry.name, 'jstest')
+        self.assertEqual(script_entry.name, "jstest")
         self.assertTrue(script_entry.serves_templates)
 
         trans = galaxy_mock.MockTrans()
@@ -258,5 +246,5 @@ class VisualizationsRegistry_TestCase(VisualizationsBase_TestCase):
 # -----------------------------------------------------------------------------
 # TODO: config parser tests (in separate file)
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/auth/test_auth.py b/test/unit/auth/test_auth.py
index c9b20bc9a7b..9b3820ca903 100644
--- a/test/unit/auth/test_auth.py
+++ b/test/unit/auth/test_auth.py
@@ -5,20 +5,20 @@ from galaxy.model import User
 
 def test_alwaysreject():
     t = AlwaysReject()
-    assert t.authenticate('testmail', 'testuser', 'secret', dict()) == (None, '', '')
+    assert t.authenticate("testmail", "testuser", "secret", dict()) == (None, "", "")
 
 
 def test_localdb():
-    user = User(email='testmail', username='tester')
-    user.set_password_cleartext('test123')
+    user = User(email="testmail", username="tester")
+    user.set_password_cleartext("test123")
     t = LocalDB()
-    reject = t.authenticate_user(user, 'wrong', {'redact_username_in_logs': False})
-    accept = t.authenticate_user(user, 'test123', {'redact_username_in_logs': False})
+    reject = t.authenticate_user(user, "wrong", {"redact_username_in_logs": False})
+    accept = t.authenticate_user(user, "test123", {"redact_username_in_logs": False})
     assert reject is False
     assert accept is True
     # Password must conform to policy (length etc)
     try:
-        user.set_password_cleartext('test')
+        user.set_password_cleartext("test")
     except Exception:
         pass
     else:
diff --git a/test/unit/config/config_manage/test_config_manage.py b/test/unit/config/config_manage/test_config_manage.py
index 536309e67e4..4024e562a08 100644
--- a/test/unit/config/config_manage/test_config_manage.py
+++ b/test/unit/config/config_manage/test_config_manage.py
@@ -91,7 +91,6 @@ def test_validate_embedded_config():
 
 
 class _TestConfigDirectory:
-
     def __init__(self, base_name):
         temp_directory = tempfile.mkdtemp()
         os.removedirs(temp_directory)
diff --git a/test/unit/config/test_config_dataset_storage.py b/test/unit/config/test_config_dataset_storage.py
index 8c455c83126..292c1665a74 100644
--- a/test/unit/config/test_config_dataset_storage.py
+++ b/test/unit/config/test_config_dataset_storage.py
@@ -11,44 +11,46 @@ def mock_config_file(monkeypatch):
     # Patch this; otherwise tempfile.tempdir will be set, which is a global variable that
     # defines the value of the default `dir` argument to the functions in Python's
     # tempfile module - which breaks multiple tests.
-    monkeypatch.setattr(config.GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
+    monkeypatch.setattr(config.GalaxyAppConfiguration, "_override_tempdir", lambda a, b: None)
 
 
 def test_object_store_store_by_set(mock_config_file, monkeypatch):
     # object_store_store_by set by admin
-    appconfig = config.GalaxyAppConfiguration(object_store_store_by='id')
-    assert appconfig.object_store_store_by == 'id'
+    appconfig = config.GalaxyAppConfiguration(object_store_store_by="id")
+    assert appconfig.object_store_store_by == "id"
 
 
 def test_uuid_1(mock_config_file, monkeypatch):
     # object_store_store_by not set
     # file_path set by admin to `objects` (no need for the dir to exist)
-    appconfig = config.GalaxyAppConfiguration(file_path='objects')
+    appconfig = config.GalaxyAppConfiguration(file_path="objects")
 
-    assert appconfig.object_store_store_by == 'uuid'
+    assert appconfig.object_store_store_by == "uuid"
 
 
 def test_uuid_2(mock_config_file, monkeypatch):
     # object_store_store_by not set
     # file_path not set, `files` dir doesn't exist
-    monkeypatch.setattr(BaseAppConfiguration, '_path_exists', lambda self, path: False)
+    monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda self, path: False)
     appconfig = config.GalaxyAppConfiguration()
 
-    assert appconfig.object_store_store_by == 'uuid'
+    assert appconfig.object_store_store_by == "uuid"
 
 
 def test_id_1(mock_config_file, monkeypatch):
     # object_store_store_by not set
     # file_path set by admin to `not_objects` (no need for the dir to exist)
-    appconfig = config.GalaxyAppConfiguration(file_path='not_objects')
+    appconfig = config.GalaxyAppConfiguration(file_path="not_objects")
 
-    assert appconfig.object_store_store_by == 'id'
+    assert appconfig.object_store_store_by == "id"
 
 
 def test_id_2(mock_config_file, monkeypatch):
     # object_store_store_by not set
     # file_path not set, `files` dir exists
-    monkeypatch.setattr(BaseAppConfiguration, '_path_exists', lambda self, path: True if os.path.basename(path) == 'files' else False)
+    monkeypatch.setattr(
+        BaseAppConfiguration, "_path_exists", lambda self, path: True if os.path.basename(path) == "files" else False
+    )
     appconfig = config.GalaxyAppConfiguration()
 
-    assert appconfig.object_store_store_by == 'id'
+    assert appconfig.object_store_store_by == "id"
diff --git a/test/unit/config/test_config_values.py b/test/unit/config/test_config_values.py
index 6a4306be3c9..c5b7be1abed 100644
--- a/test/unit/config/test_config_values.py
+++ b/test/unit/config/test_config_values.py
@@ -8,10 +8,10 @@ from galaxy import config
 from galaxy.util import listify
 from galaxy.web.formatting import expand_pretty_datetime_format
 
-TestData = namedtuple('TestData', ('key', 'expected', 'loaded'))
+TestData = namedtuple("TestData", ("key", "expected", "loaded"))
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def appconfig():
     return config.GalaxyAppConfiguration()
 
@@ -21,39 +21,39 @@ def mock_config_file(monkeypatch):
     # Patch this; otherwise tempfile.tempdir will be set, which is a global variable that
     # defines the value of the default `dir` argument to the functions in Python's
     # tempfile module - which breaks multiple tests.
-    monkeypatch.setattr(config.GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
+    monkeypatch.setattr(config.GalaxyAppConfiguration, "_override_tempdir", lambda a, b: None)
     # Set this to return None to force the creation of base config directories
     # in _set_config_directories(). Used to test the values of these directories only.
-    monkeypatch.setattr(config, 'find_config_file', lambda x: None)
+    monkeypatch.setattr(config, "find_config_file", lambda x: None)
 
 
 def test_root(appconfig):
-    assert appconfig.root == os.path.abspath('.')
+    assert appconfig.root == os.path.abspath(".")
 
 
 def test_common_base_config(appconfig):
-    assert appconfig.shed_tools_dir == os.path.join(appconfig.data_dir, 'shed_tools')
-    assert appconfig.sample_config_dir == os.path.join(appconfig.root, 'lib', 'galaxy', 'config', 'sample')
+    assert appconfig.shed_tools_dir == os.path.join(appconfig.data_dir, "shed_tools")
+    assert appconfig.sample_config_dir == os.path.join(appconfig.root, "lib", "galaxy", "config", "sample")
 
 
 def test_base_config_if_running_from_source(monkeypatch, mock_config_file):
     # Simulated condition: running from source, config_file is None.
-    monkeypatch.setattr(config, 'running_from_source', True)
+    monkeypatch.setattr(config, "running_from_source", True)
     appconfig = config.GalaxyAppConfiguration()
     assert not appconfig.config_file
-    assert appconfig.config_dir == os.path.join(appconfig.root, 'config')
-    assert appconfig.data_dir == os.path.join(appconfig.root, 'database')
+    assert appconfig.config_dir == os.path.join(appconfig.root, "config")
+    assert appconfig.data_dir == os.path.join(appconfig.root, "database")
     assert appconfig.managed_config_dir == appconfig.config_dir
 
 
 def test_base_config_if_running_not_from_source(monkeypatch, mock_config_file):
     # Simulated condition: running not from source, config_file is None.
-    monkeypatch.setattr(config, 'running_from_source', False)
+    monkeypatch.setattr(config, "running_from_source", False)
     appconfig = config.GalaxyAppConfiguration()
     assert not appconfig.config_file
     assert appconfig.config_dir == os.getcwd()
-    assert appconfig.data_dir == os.path.join(appconfig.config_dir, 'data')
-    assert appconfig.managed_config_dir == os.path.join(appconfig.data_dir, 'config')
+    assert appconfig.data_dir == os.path.join(appconfig.config_dir, "data")
+    assert appconfig.managed_config_dir == os.path.join(appconfig.data_dir, "config")
 
 
 def listify_strip(value):
@@ -61,7 +61,6 @@ def listify_strip(value):
 
 
 class ExpectedValues:
-
     def __init__(self, config):
         self._config = config
         self._load_resolvers()
@@ -69,27 +68,27 @@ class ExpectedValues:
 
     def _load_resolvers(self):
         self._resolvers = {
-            'amqp_internal_connection': self.get_expected_amqp_internal_connection,
-            'database_connection': self.get_expected_database_connection,
-            'disable_library_comptypes': [''],  # TODO: we can do better
-            'file_path': self.get_expected_file_path,
-            'ftp_upload_dir_template': self.get_expected_ftp_upload_dir_template,
-            'mulled_channels': listify_strip,
-            'object_store_store_by': self.get_expected_object_store_store_by,
-            'password_expiration_period': timedelta,
-            'pretty_datetime_format': expand_pretty_datetime_format,
-            'statsd_host': '',  # TODO: do we need '' as the default?
-            'tool_config_file': listify_strip,
-            'tool_data_table_config_path': listify_strip,
-            'tool_filters': listify_strip,
-            'tool_label_filters': listify_strip,
-            'tool_section_filters': listify_strip,
-            'toolbox_filter_base_modules': listify_strip,
-            'use_remote_user': None,  # TODO: should be False (config logic incorrect)
-            'user_library_import_symlink_allowlist': listify_strip,
-            'user_tool_filters': listify_strip,
-            'user_tool_label_filters': listify_strip,
-            'user_tool_section_filters': listify_strip,
+            "amqp_internal_connection": self.get_expected_amqp_internal_connection,
+            "database_connection": self.get_expected_database_connection,
+            "disable_library_comptypes": [""],  # TODO: we can do better
+            "file_path": self.get_expected_file_path,
+            "ftp_upload_dir_template": self.get_expected_ftp_upload_dir_template,
+            "mulled_channels": listify_strip,
+            "object_store_store_by": self.get_expected_object_store_store_by,
+            "password_expiration_period": timedelta,
+            "pretty_datetime_format": expand_pretty_datetime_format,
+            "statsd_host": "",  # TODO: do we need '' as the default?
+            "tool_config_file": listify_strip,
+            "tool_data_table_config_path": listify_strip,
+            "tool_filters": listify_strip,
+            "tool_label_filters": listify_strip,
+            "tool_section_filters": listify_strip,
+            "toolbox_filter_base_modules": listify_strip,
+            "use_remote_user": None,  # TODO: should be False (config logic incorrect)
+            "user_library_import_symlink_allowlist": listify_strip,
+            "user_tool_filters": listify_strip,
+            "user_tool_label_filters": listify_strip,
+            "user_tool_section_filters": listify_strip,
         }
         # _resolvers provides expected values for config options.
         # - key: config option
@@ -98,67 +97,67 @@ class ExpectedValues:
 
     def _load_paths(self):
         self._expected_paths = {
-            'admin_tool_recommendations_path': self._in_config_dir('tool_recommendations_overwrite.yml'),
-            'auth_config_file': self._in_config_dir('auth_conf.xml'),
-            'biotools_service_cache_data_dir': self._in_cache_dir('biotools/data'),
-            'biotools_service_cache_lock_dir': self._in_cache_dir('biotools/locks'),
-            'build_sites_config_file': self._in_sample_dir('build_sites.yml.sample'),
-            'builds_file_path': self._in_root_dir('tool-data/shared/ucsc/builds.txt'),
-            'cache_dir': self._in_data_dir('cache'),
-            'citation_cache_data_dir': self._in_cache_dir('citations/data'),
-            'citation_cache_lock_dir': self._in_cache_dir('citations/locks'),
-            'cluster_files_directory': self._in_data_dir('pbs'),
-            'config_dir': self._in_config_dir(),
-            'containers_config_file': self._in_config_dir('containers_conf.yml'),
-            'data_dir': self._in_data_dir(),
-            'data_manager_config_file': self._in_config_dir('data_manager_conf.xml'),
-            'datatypes_config_file': self._in_sample_dir('datatypes_conf.xml.sample'),
-            'dependency_resolvers_config_file': self._in_config_dir('dependency_resolvers_conf.xml'),
-            'dynamic_proxy_session_map': self._in_data_dir('session_map.sqlite'),
-            'edam_toolbox_ontology_path': self._in_data_dir('EDAM.tsv'),
-            'error_report_file': self._in_config_dir('error_report.yml'),
-            'file_sources_config_file': self._in_config_dir('file_sources_conf.yml'),
-            'galaxy_data_manager_data_path': self._in_root_dir('tool-data'),
-            'integrated_tool_panel_config': self._in_managed_config_dir('integrated_tool_panel.xml'),
-            'interactivetools_map': self._in_data_dir('interactivetools_map.sqlite'),
-            'involucro_path': self._in_root_dir('involucro'),
-            'job_config_file': self._in_config_dir('job_conf.xml'),
-            'job_metrics_config_file': self._in_sample_dir('job_metrics_conf.xml.sample'),
-            'job_resource_params_file': self._in_config_dir('job_resource_params_conf.xml'),
-            'len_file_path': self._in_root_dir('tool-data/shared/ucsc/chrom'),
-            'local_conda_mapping_file': self._in_config_dir('local_conda_mapping.yml'),
-            'managed_config_dir': self._in_managed_config_dir(),
-            'markdown_export_css': self._in_config_dir('markdown_export.css'),
-            'markdown_export_css_invocation_reports': self._in_config_dir('markdown_export_invocation_reports.css'),
-            'markdown_export_css_pages': self._in_config_dir('markdown_export_pages.css'),
-            'migrated_tools_config': self._in_managed_config_dir('migrated_tools_conf.xml'),
-            'modules_mapping_files': self._in_config_dir('environment_modules_mapping.yml'),
-            'mulled_resolution_cache_data_dir': self._in_cache_dir('mulled/data'),
-            'mulled_resolution_cache_lock_dir': self._in_cache_dir('mulled/locks'),
-            'new_file_path': self._in_data_dir('tmp'),
-            'object_store_config_file': self._in_config_dir('object_store_conf.xml'),
-            'oidc_backends_config_file': self._in_config_dir('oidc_backends_config.xml'),
-            'oidc_config_file': self._in_config_dir('oidc_config.xml'),
-            'sanitize_allowlist_file': self._in_managed_config_dir('sanitize_allowlist.txt'),
-            'shed_data_manager_config_file': self._in_managed_config_dir('shed_data_manager_conf.xml'),
-            'shed_tool_config_file': self._in_managed_config_dir('shed_tool_conf.xml'),
-            'shed_tool_data_path': self._in_root_dir('tool-data'),
-            'shed_tool_data_table_config': self._in_managed_config_dir('shed_tool_data_table_conf.xml'),
-            'template_cache_path': self._in_cache_dir('compiled_templates'),
-            'tool_cache_data_dir': self._in_cache_dir('tool_cache'),
-            'tool_config_file': self._in_sample_dir('tool_conf.xml.sample'),
-            'tool_data_path': self._in_root_dir('tool-data'),
-            'tool_data_table_config_path': self._in_sample_dir('tool_data_table_conf.xml.sample'),
-            'tool_destinations_config_file': self._in_config_dir('tool_destinations.yml'),
-            'tool_path': self._in_root_dir('tools'),
-            'tool_search_index_dir': self._in_data_dir('tool_search_index'),
-            'tool_sheds_config_file': self._in_config_dir('tool_sheds_conf.xml'),
-            'tool_test_data_directories': self._in_root_dir('test-data'),
-            'trs_servers_config_file': self._in_config_dir('trs_servers_conf.yml'),
-            'user_preferences_extra_conf_path': self._in_config_dir('user_preferences_extra_conf.yml'),
-            'vault_config_file': self._in_config_dir('vault_conf.yml'),
-            'workflow_resource_params_file': self._in_config_dir('workflow_resource_params_conf.xml'),
-            'workflow_schedulers_config_file': self._in_config_dir('workflow_schedulers_conf.xml'),
+            "admin_tool_recommendations_path": self._in_config_dir("tool_recommendations_overwrite.yml"),
+            "auth_config_file": self._in_config_dir("auth_conf.xml"),
+            "biotools_service_cache_data_dir": self._in_cache_dir("biotools/data"),
+            "biotools_service_cache_lock_dir": self._in_cache_dir("biotools/locks"),
+            "build_sites_config_file": self._in_sample_dir("build_sites.yml.sample"),
+            "builds_file_path": self._in_root_dir("tool-data/shared/ucsc/builds.txt"),
+            "cache_dir": self._in_data_dir("cache"),
+            "citation_cache_data_dir": self._in_cache_dir("citations/data"),
+            "citation_cache_lock_dir": self._in_cache_dir("citations/locks"),
+            "cluster_files_directory": self._in_data_dir("pbs"),
+            "config_dir": self._in_config_dir(),
+            "containers_config_file": self._in_config_dir("containers_conf.yml"),
+            "data_dir": self._in_data_dir(),
+            "data_manager_config_file": self._in_config_dir("data_manager_conf.xml"),
+            "datatypes_config_file": self._in_sample_dir("datatypes_conf.xml.sample"),
+            "dependency_resolvers_config_file": self._in_config_dir("dependency_resolvers_conf.xml"),
+            "dynamic_proxy_session_map": self._in_data_dir("session_map.sqlite"),
+            "edam_toolbox_ontology_path": self._in_data_dir("EDAM.tsv"),
+            "error_report_file": self._in_config_dir("error_report.yml"),
+            "file_sources_config_file": self._in_config_dir("file_sources_conf.yml"),
+            "galaxy_data_manager_data_path": self._in_root_dir("tool-data"),
+            "integrated_tool_panel_config": self._in_managed_config_dir("integrated_tool_panel.xml"),
+            "interactivetools_map": self._in_data_dir("interactivetools_map.sqlite"),
+            "involucro_path": self._in_root_dir("involucro"),
+            "job_config_file": self._in_config_dir("job_conf.xml"),
+            "job_metrics_config_file": self._in_sample_dir("job_metrics_conf.xml.sample"),
+            "job_resource_params_file": self._in_config_dir("job_resource_params_conf.xml"),
+            "len_file_path": self._in_root_dir("tool-data/shared/ucsc/chrom"),
+            "local_conda_mapping_file": self._in_config_dir("local_conda_mapping.yml"),
+            "managed_config_dir": self._in_managed_config_dir(),
+            "markdown_export_css": self._in_config_dir("markdown_export.css"),
+            "markdown_export_css_invocation_reports": self._in_config_dir("markdown_export_invocation_reports.css"),
+            "markdown_export_css_pages": self._in_config_dir("markdown_export_pages.css"),
+            "migrated_tools_config": self._in_managed_config_dir("migrated_tools_conf.xml"),
+            "modules_mapping_files": self._in_config_dir("environment_modules_mapping.yml"),
+            "mulled_resolution_cache_data_dir": self._in_cache_dir("mulled/data"),
+            "mulled_resolution_cache_lock_dir": self._in_cache_dir("mulled/locks"),
+            "new_file_path": self._in_data_dir("tmp"),
+            "object_store_config_file": self._in_config_dir("object_store_conf.xml"),
+            "oidc_backends_config_file": self._in_config_dir("oidc_backends_config.xml"),
+            "oidc_config_file": self._in_config_dir("oidc_config.xml"),
+            "sanitize_allowlist_file": self._in_managed_config_dir("sanitize_allowlist.txt"),
+            "shed_data_manager_config_file": self._in_managed_config_dir("shed_data_manager_conf.xml"),
+            "shed_tool_config_file": self._in_managed_config_dir("shed_tool_conf.xml"),
+            "shed_tool_data_path": self._in_root_dir("tool-data"),
+            "shed_tool_data_table_config": self._in_managed_config_dir("shed_tool_data_table_conf.xml"),
+            "template_cache_path": self._in_cache_dir("compiled_templates"),
+            "tool_cache_data_dir": self._in_cache_dir("tool_cache"),
+            "tool_config_file": self._in_sample_dir("tool_conf.xml.sample"),
+            "tool_data_path": self._in_root_dir("tool-data"),
+            "tool_data_table_config_path": self._in_sample_dir("tool_data_table_conf.xml.sample"),
+            "tool_destinations_config_file": self._in_config_dir("tool_destinations.yml"),
+            "tool_path": self._in_root_dir("tools"),
+            "tool_search_index_dir": self._in_data_dir("tool_search_index"),
+            "tool_sheds_config_file": self._in_config_dir("tool_sheds_conf.xml"),
+            "tool_test_data_directories": self._in_root_dir("test-data"),
+            "trs_servers_config_file": self._in_config_dir("trs_servers_conf.yml"),
+            "user_preferences_extra_conf_path": self._in_config_dir("user_preferences_extra_conf.yml"),
+            "vault_config_file": self._in_config_dir("vault_conf.yml"),
+            "workflow_resource_params_file": self._in_config_dir("workflow_resource_params_conf.xml"),
+            "workflow_schedulers_config_file": self._in_config_dir("workflow_schedulers_conf.xml"),
         }
         # _expected_paths provides expected values for config options that are paths. Each value is
         # wrapped in a function that ensures that the path (a) is resolved w.r.t. its parent as per
@@ -190,7 +189,7 @@ class ExpectedValues:
         return os.path.join(_dir, path) if path else _dir
 
     def get_value(self, key, data):
-        value = data.get('default')
+        value = data.get("default")
         # 1. If this is a path, resolve it
         if key in self._expected_paths:
             value = self._expected_paths[key]
@@ -204,25 +203,25 @@ class ExpectedValues:
         return value
 
     def get_expected_database_connection(self, value):
-        return f'sqlite:///{self._config.data_dir}/universe.sqlite?isolation_level=IMMEDIATE'
+        return f"sqlite:///{self._config.data_dir}/universe.sqlite?isolation_level=IMMEDIATE"
 
     def get_expected_ftp_upload_dir_template(self, value):
-        return '${ftp_upload_dir}%s${ftp_upload_dir_identifier}' % os.path.sep
+        return "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep
 
     def get_expected_amqp_internal_connection(self, value):
-        return f'sqlalchemy+sqlite:///{self._config.data_dir}/control.sqlite?isolation_level=IMMEDIATE'
+        return f"sqlalchemy+sqlite:///{self._config.data_dir}/control.sqlite?isolation_level=IMMEDIATE"
 
     def get_expected_file_path(self, value):
-        for dir in ('files', 'objects'):
+        for dir in ("files", "objects"):
             dir_path = self._in_data_dir(dir)
             if os.path.exists(dir_path):
                 return dir_path
         return dir_path
 
     def get_expected_object_store_store_by(self, value):
-        if os.path.exists(self._in_data_dir('files')):
-            return 'id'
-        return 'uuid'
+        if os.path.exists(self._in_data_dir("files")):
+            return "id"
+        return "uuid"
 
 
 def get_config_data():
@@ -241,7 +240,8 @@ def get_key(test_data):
     return test_data.key
 
 
-@pytest.mark.parametrize('test_data', get_config_data(), ids=get_key)
+@pytest.mark.parametrize("test_data", get_config_data(), ids=get_key)
 def test_config_defaults(test_data):
-    assert test_data.expected == test_data.loaded, \
-        f"Default value of option [{test_data.key}] is [{test_data.loaded}] instead of expected [{test_data.expected}]"
+    assert (
+        test_data.expected == test_data.loaded
+    ), f"Default value of option [{test_data.key}] is [{test_data.loaded}] instead of expected [{test_data.expected}]"
diff --git a/test/unit/config/test_load_config.py b/test/unit/config/test_load_config.py
index ce0bb90df07..f481661793c 100644
--- a/test/unit/config/test_load_config.py
+++ b/test/unit/config/test_load_config.py
@@ -4,98 +4,103 @@ from galaxy.config import BaseAppConfiguration
 from galaxy.config.schema import AppSchema
 
 MOCK_SCHEMA = {
-    'property1': {'default': 'a', 'type': 'str'},  # str
-    'property2': {'default': 1, 'type': 'int'},  # int
-    'property3': {'default': 1.0, 'type': 'float'},  # float
-    'property4': {'default': True, 'type': 'bool'},  # bool
-    'property5': {'something_else': 'b', 'type': 'invalid'},
-    'property6': {'something_else': 'b'},  # no type
+    "property1": {"default": "a", "type": "str"},  # str
+    "property2": {"default": 1, "type": "int"},  # int
+    "property3": {"default": 1.0, "type": "float"},  # float
+    "property4": {"default": True, "type": "bool"},  # bool
+    "property5": {"something_else": "b", "type": "invalid"},
+    "property6": {"something_else": "b"},  # no type
 }
 
 
 MOCK_SCHEMA_DBURL = {
-    'database_connection': {'type': 'str'},
-    'install_database_connection': {'type': 'str'},
+    "database_connection": {"type": "str"},
+    "install_database_connection": {"type": "str"},
 }
 
 
 def get_schema(app_mapping):
-    return {'mapping': {'_': {'mapping': app_mapping}}}
+    return {"mapping": {"_": {"mapping": app_mapping}}}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
-    monkeypatch.setattr(BaseAppConfiguration, '_load_schema', lambda a: AppSchema(None, '_'))
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(None, "_"))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(MOCK_SCHEMA))
 
 
 @pytest.fixture
 def mock_init_dburl(mock_init, monkeypatch):
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA_DBURL))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(MOCK_SCHEMA_DBURL))
 
 
 def test_load_config_from_schema(mock_init):
     config = BaseAppConfiguration()
 
     assert len(config._raw_config) == 6
-    assert config._raw_config['property1'] == 'a'
-    assert config._raw_config['property2'] == 1
-    assert config._raw_config['property3'] == 1.0
-    assert config._raw_config['property4'] is True
-    assert config._raw_config['property5'] is None
-    assert config._raw_config['property6'] is None
+    assert config._raw_config["property1"] == "a"
+    assert config._raw_config["property2"] == 1
+    assert config._raw_config["property3"] == 1.0
+    assert config._raw_config["property4"] is True
+    assert config._raw_config["property5"] is None
+    assert config._raw_config["property6"] is None
 
-    assert type(config._raw_config['property1']) is str
-    assert type(config._raw_config['property2']) is int
-    assert type(config._raw_config['property3']) is float
-    assert type(config._raw_config['property4']) is bool
+    assert type(config._raw_config["property1"]) is str
+    assert type(config._raw_config["property2"]) is int
+    assert type(config._raw_config["property3"]) is float
+    assert type(config._raw_config["property4"]) is bool
 
 
 def test_update_raw_config_from_kwargs(mock_init):
     config = BaseAppConfiguration(property2=2, property3=2.0, another_key=66)
 
-    assert len(config._raw_config) == 6   # no change: another_key NOT added
-    assert config._raw_config['property1'] == 'a'  # no change
-    assert config._raw_config['property2'] == 2  # updated
-    assert config._raw_config['property3'] == 2.0  # updated
-    assert config._raw_config['property4'] is True  # no change
-    assert config._raw_config['property5'] is None  # no change
-    assert config._raw_config['property6'] is None  # no change
+    assert len(config._raw_config) == 6  # no change: another_key NOT added
+    assert config._raw_config["property1"] == "a"  # no change
+    assert config._raw_config["property2"] == 2  # updated
+    assert config._raw_config["property3"] == 2.0  # updated
+    assert config._raw_config["property4"] is True  # no change
+    assert config._raw_config["property5"] is None  # no change
+    assert config._raw_config["property6"] is None  # no change
 
-    assert type(config._raw_config['property1']) is str
-    assert type(config._raw_config['property2']) is int
-    assert type(config._raw_config['property3']) is float
-    assert type(config._raw_config['property4']) is bool
+    assert type(config._raw_config["property1"]) is str
+    assert type(config._raw_config["property2"]) is int
+    assert type(config._raw_config["property3"]) is float
+    assert type(config._raw_config["property4"]) is bool
 
 
 def test_update_raw_config_from_string_kwargs(mock_init):
     # kwargs may be passed as strings: property data types should not be affected
-    config = BaseAppConfiguration(property1='b', property2='2', property3='2.0', property4='false')
+    config = BaseAppConfiguration(property1="b", property2="2", property3="2.0", property4="false")
 
     assert len(config._raw_config) == 6  # no change
-    assert config._raw_config['property1'] == 'b'  # updated
-    assert config._raw_config['property2'] == 2  # updated
-    assert config._raw_config['property3'] == 2.0  # updated
-    assert config._raw_config['property4'] is False  # updated
+    assert config._raw_config["property1"] == "b"  # updated
+    assert config._raw_config["property2"] == 2  # updated
+    assert config._raw_config["property3"] == 2.0  # updated
+    assert config._raw_config["property4"] is False  # updated
 
-    assert type(config._raw_config['property1']) is str
-    assert type(config._raw_config['property2']) is int
-    assert type(config._raw_config['property3']) is float
-    assert type(config._raw_config['property4']) is bool
+    assert type(config._raw_config["property1"]) is str
+    assert type(config._raw_config["property2"]) is int
+    assert type(config._raw_config["property3"]) is float
+    assert type(config._raw_config["property4"]) is bool
 
 
 def test_update_raw_config_from_kwargs_with_none(mock_init):
     # should be able to set to null regardless of property's datatype
     config = BaseAppConfiguration(
-        property1=None, property2=None, property3=None, property4=None, property5=None, property6=None,
+        property1=None,
+        property2=None,
+        property3=None,
+        property4=None,
+        property5=None,
+        property6=None,
     )
 
-    assert config._raw_config['property1'] is None
-    assert config._raw_config['property2'] is None
-    assert config._raw_config['property3'] is None
-    assert config._raw_config['property4'] is None
-    assert config._raw_config['property5'] is None
-    assert config._raw_config['property6'] is None
+    assert config._raw_config["property1"] is None
+    assert config._raw_config["property2"] is None
+    assert config._raw_config["property3"] is None
+    assert config._raw_config["property4"] is None
+    assert config._raw_config["property5"] is None
+    assert config._raw_config["property6"] is None
 
 
 def test_update_raw_config_from_kwargs_falsy_not_none(mock_init):
@@ -103,21 +108,21 @@ def test_update_raw_config_from_kwargs_falsy_not_none(mock_init):
     # (ensures code is 'if value is not None' vs. 'if value')
     config = BaseAppConfiguration(property1=0)
 
-    assert config._raw_config['property1'] == '0'  # updated
-    assert type(config._raw_config['property1']) is str  # and converted to str
+    assert config._raw_config["property1"] == "0"  # updated
+    assert type(config._raw_config["property1"]) is str  # and converted to str
 
 
 def test_unset_renamed_option_set_by_old_option(mock_init, monkeypatch):
-    monkeypatch.setattr(BaseAppConfiguration, 'renamed_options', {'old_property1': 'property1'})
-    config = BaseAppConfiguration(old_property1='b')
+    monkeypatch.setattr(BaseAppConfiguration, "renamed_options", {"old_property1": "property1"})
+    config = BaseAppConfiguration(old_property1="b")
 
-    assert config._raw_config['property1'] == 'b'
+    assert config._raw_config["property1"] == "b"
 
 
 def test_set_renamed_option_not_overridden_by_old_option(mock_init):
-    config = BaseAppConfiguration(old_property1='b', property1='c')
+    config = BaseAppConfiguration(old_property1="b", property1="c")
 
-    assert config._raw_config['property1'] == 'c'
+    assert config._raw_config["property1"] == "c"
 
 
 def test_is_set(mock_init):
@@ -127,43 +132,45 @@ def test_is_set(mock_init):
 
     # First, test that none are set
     config = BaseAppConfiguration()
-    assert not config.is_set('property1')
-    assert not config.is_set('property2')
-    assert not config.is_set('property3')
-    assert not config.is_set('property4')
-    assert not config.is_set('property5')
-    assert not config.is_set('property6')
+    assert not config.is_set("property1")
+    assert not config.is_set("property2")
+    assert not config.is_set("property3")
+    assert not config.is_set("property4")
+    assert not config.is_set("property5")
+    assert not config.is_set("property6")
 
     # Now set all values, including setting to None and setting to the schema default
     config = BaseAppConfiguration(
-        property1='b',    # default = 'a'  (overwrites default w/'a')
-        property2=None,   # default = 1    (overwrites default w/None)
-        property3=1.0,    # default = 1.0  (same as default: 1.0)
-        property4=True,   # default = True (same as default: True)
-        property5=None,   # default = None (same as default: None)
-        property6=1)      # default = None (overwrites default w/None)
+        property1="b",  # default = 'a'  (overwrites default w/'a')
+        property2=None,  # default = 1    (overwrites default w/None)
+        property3=1.0,  # default = 1.0  (same as default: 1.0)
+        property4=True,  # default = True (same as default: True)
+        property5=None,  # default = None (same as default: None)
+        property6=1,
+    )  # default = None (overwrites default w/None)
 
-    assert config.is_set('property1')
-    assert config.is_set('property2')
-    assert config.is_set('property3')
-    assert config.is_set('property4')
-    assert config.is_set('property4')
-    assert config.is_set('property6')
+    assert config.is_set("property1")
+    assert config.is_set("property2")
+    assert config.is_set("property3")
+    assert config.is_set("property4")
+    assert config.is_set("property4")
+    assert config.is_set("property6")
 
 
 def test_deprecated_postgres_urls_are_fixed(mock_init_dburl):
     error_message = '"postgres" prefix should become "postgresql"'
 
     config = BaseAppConfiguration(
-        database_connection='postgres://foo',  # incorrect
-        install_database_connection='postgresql://foo')  # correct
+        database_connection="postgres://foo", install_database_connection="postgresql://foo"  # incorrect
+    )  # correct
 
-    assert config.database_connection == 'postgresql://foo', error_message
-    assert config.install_database_connection == 'postgresql://foo'
+    assert config.database_connection == "postgresql://foo", error_message
+    assert config.install_database_connection == "postgresql://foo"
 
     config = BaseAppConfiguration(
-        database_connection='postgresql+psycopg2://foo',  # correct
-        install_database_connection='postgres+psycopg2://foo')  # incorrect
+        database_connection="postgresql+psycopg2://foo",  # correct
+        install_database_connection="postgres+psycopg2://foo",
+    )  # incorrect
 
-    assert config.database_connection == 'postgresql+psycopg2://foo', error_message
-    assert config.install_database_connection == 'postgresql+psycopg2://foo'
+    assert config.database_connection == "postgresql+psycopg2://foo", error_message
+    assert config.install_database_connection == "postgresql+psycopg2://foo"
diff --git a/test/unit/config/test_path_graph.py b/test/unit/config/test_path_graph.py
index 1a49e93d5e4..f05bc347771 100644
--- a/test/unit/config/test_path_graph.py
+++ b/test/unit/config/test_path_graph.py
@@ -4,7 +4,6 @@ from galaxy.config import BaseAppConfiguration
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 
-
 # When a config property 'foo' has an attribute 'path_resolves_to', that attribute is a reference to
 # another property 'bar'. Together, these two properties form a graph where 'foo' and 'bar are
 # vertices and the reference from 'foo' to 'bar' is a directed edge.
@@ -17,150 +16,150 @@ from galaxy.exceptions import ConfigurationError
 
 
 def get_schema(app_mapping):
-    return {'mapping': {'_': {'mapping': app_mapping}}}
+    return {"mapping": {"_": {"mapping": app_mapping}}}
 
 
 def test_basecase(monkeypatch):
     # Check that a valid graph is loaded correctly (this graph has 2 components)
     mock_schema = {
-        'component1_path0': {
-            'type': 'str',
-            'default': 'value0',
+        "component1_path0": {
+            "type": "str",
+            "default": "value0",
         },
-        'component1_path1': {
-            'type': 'str',
-            'default': 'value1',
-            'path_resolves_to': 'component1_path0',
+        "component1_path1": {
+            "type": "str",
+            "default": "value1",
+            "path_resolves_to": "component1_path0",
         },
-        'component1_path2': {
-            'type': 'str',
-            'default': 'value2',
-            'path_resolves_to': 'component1_path1',
+        "component1_path2": {
+            "type": "str",
+            "default": "value2",
+            "path_resolves_to": "component1_path1",
         },
-        'component2_path0': {
-            'type': 'str',
-            'default': 'value3',
+        "component2_path0": {
+            "type": "str",
+            "default": "value3",
         },
-        'component2_path1': {
-            'type': 'str',
-            'default': 'value4',
-            'path_resolves_to': 'component2_path0',
+        "component2_path1": {
+            "type": "str",
+            "default": "value4",
+            "path_resolves_to": "component2_path0",
         },
     }
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
-    monkeypatch.setattr(BaseAppConfiguration, '_load_schema', lambda a: AppSchema(None, '_'))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(None, "_"))
 
     config = BaseAppConfiguration()
-    assert config.component1_path0 == 'value0'
-    assert config.component1_path1 == 'value0/value1'
-    assert config.component1_path2 == 'value0/value1/value2'
-    assert config.component2_path0 == 'value3'
-    assert config.component2_path1 == 'value3/value4'
+    assert config.component1_path0 == "value0"
+    assert config.component1_path1 == "value0/value1"
+    assert config.component1_path2 == "value0/value1/value2"
+    assert config.component2_path0 == "value3"
+    assert config.component2_path1 == "value3/value4"
 
 
 def test_resolves_to_invalid_property(monkeypatch):
     # 'path_resolves_to' should point to an existing property in the schema
     mock_schema = {
-        'path0': {
-            'type': 'str',
-            'default': 'value0',
+        "path0": {
+            "type": "str",
+            "default": "value0",
         },
-        'path1': {
-            'type': 'str',
-            'default': 'value1',
-            'path_resolves_to': 'invalid',  # invalid
+        "path1": {
+            "type": "str",
+            "default": "value1",
+            "path_resolves_to": "invalid",  # invalid
         },
     }
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        AppSchema(None, '_').validate_path_resolution_graph()
+        AppSchema(None, "_").validate_path_resolution_graph()
 
 
 def test_path_resolution_cycle(monkeypatch):
     # Must be a DAG, but this one has a cycle
     mock_schema = {
-        'path0': {
-            'type': 'str',
-            'default': 'value0',
-            'path_resolves_to': 'path2',
+        "path0": {
+            "type": "str",
+            "default": "value0",
+            "path_resolves_to": "path2",
         },
-        'path1': {
-            'type': 'str',
-            'default': 'value1',
-            'path_resolves_to': 'path0',
+        "path1": {
+            "type": "str",
+            "default": "value1",
+            "path_resolves_to": "path0",
         },
-        'path2': {
-            'type': 'str',
-            'default': 'value2',
-            'path_resolves_to': 'path1',
+        "path2": {
+            "type": "str",
+            "default": "value2",
+            "path_resolves_to": "path1",
         },
     }
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        AppSchema(None, '_').validate_path_resolution_graph()
+        AppSchema(None, "_").validate_path_resolution_graph()
 
 
 def test_path_invalid_type(monkeypatch):
     # Paths should be strings
     mock_schema = {
-        'path0': {
-            'type': 'str',
-            'default': 'value0',
+        "path0": {
+            "type": "str",
+            "default": "value0",
         },
-        'path1': {
-            'type': 'float',  # invalid
-            'default': 'value1',
-            'path_resolves_to': 'path0',
+        "path1": {
+            "type": "float",  # invalid
+            "default": "value1",
+            "path_resolves_to": "path0",
         },
     }
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        AppSchema(None, '_').validate_path_resolution_graph()
+        AppSchema(None, "_").validate_path_resolution_graph()
 
 
 def test_resolves_to_invalid_type(monkeypatch):
     # Paths should be strings
     mock_schema = {
-        'path0': {
-            'type': 'int',  # invalid
-            'default': 'value0',
+        "path0": {
+            "type": "int",  # invalid
+            "default": "value0",
         },
-        'path1': {
-            'type': 'str',
-            'default': 'value1',
-            'path_resolves_to': 'path0',
+        "path1": {
+            "type": "str",
+            "default": "value1",
+            "path_resolves_to": "path0",
         },
     }
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        AppSchema(None, '_').validate_path_resolution_graph()
+        AppSchema(None, "_").validate_path_resolution_graph()
 
 
 def test_resolves_with_empty_component(monkeypatch):
     # A path can be None (root path is never None; may be asigned elsewhere)
     mock_schema = {
-        'path0': {
-            'type': 'str',
-            'default': 'value0',
+        "path0": {
+            "type": "str",
+            "default": "value0",
         },
-        'path1': {
-            'type': 'str',
-            'path_resolves_to': 'path0',
+        "path1": {
+            "type": "str",
+            "path_resolves_to": "path0",
         },
-        'path2': {
-            'type': 'str',
-            'default': 'value2',
-            'path_resolves_to': 'path1',
+        "path2": {
+            "type": "str",
+            "default": "value2",
+            "path_resolves_to": "path1",
         },
     }
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
-    monkeypatch.setattr(BaseAppConfiguration, '_load_schema', lambda a: AppSchema(None, '_'))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(None, "_"))
 
     config = BaseAppConfiguration()
-    assert config.path0 == 'value0'
-    assert config.path1 == 'value0'
-    assert config.path2 == 'value0/value2'
+    assert config.path0 == "value0"
+    assert config.path1 == "value0"
+    assert config.path2 == "value0/value2"
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index abbf3f22e57..eb280c3f852 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -3,138 +3,139 @@ import pytest
 from galaxy.config import BaseAppConfiguration
 from galaxy.config.schema import AppSchema
 
-
 MOCK_DEPRECATED_DIRS = {
-    'my_config_dir': 'old-config',
-    'my_data_dir': 'old-database',
+    "my_config_dir": "old-config",
+    "my_data_dir": "old-database",
 }
 
 # Mock properties loaded from schema (all options represent paths)
 MOCK_SCHEMA = {
-    'my_config_dir': {
-        'type': 'str',
-        'default': 'my-config',
+    "my_config_dir": {
+        "type": "str",
+        "default": "my-config",
     },
-    'my_data_dir': {
-        'type': 'str',
-        'default': 'my-data',
+    "my_data_dir": {
+        "type": "str",
+        "default": "my-data",
     },
-    'path1': {
-        'type': 'str',
-        'default': 'my-config-files',
-        'path_resolves_to': 'my_config_dir',
+    "path1": {
+        "type": "str",
+        "default": "my-config-files",
+        "path_resolves_to": "my_config_dir",
     },
-    'path2': {
-        'type': 'str',
-        'default': 'my-data-files',
-        'path_resolves_to': 'my_data_dir',
+    "path2": {
+        "type": "str",
+        "default": "my-data-files",
+        "path_resolves_to": "my_data_dir",
     },
-    'path3': {
-        'type': 'str',
-        'default': 'my-other-files',
+    "path3": {
+        "type": "str",
+        "default": "my-other-files",
     },
-    'path4': {
-        'type': 'str',
-        'default': 'conf1, conf2, conf3',
-        'path_resolves_to': 'my_config_dir',
+    "path4": {
+        "type": "str",
+        "default": "conf1, conf2, conf3",
+        "path_resolves_to": "my_config_dir",
     },
 }
 
 
 def get_schema(app_mapping):
-    return {'mapping': {'_': {'mapping': app_mapping}}}
+    return {"mapping": {"_": {"mapping": app_mapping}}}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
-    monkeypatch.setattr(BaseAppConfiguration, '_load_schema', lambda a: AppSchema(None, '_'))
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
-    monkeypatch.setattr(BaseAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
-    monkeypatch.setattr(BaseAppConfiguration, 'listify_options', {'path4'})
+    monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(None, "_"))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(BaseAppConfiguration, "deprecated_dirs", MOCK_DEPRECATED_DIRS)
+    monkeypatch.setattr(BaseAppConfiguration, "listify_options", {"path4"})
 
 
 def test_mock_schema_is_loaded(mock_init):
     # Check that mock is loaded as expected
     config = BaseAppConfiguration()
     assert len(config._raw_config) == 6
-    assert config._raw_config['my_config_dir'] == 'my-config'
-    assert config._raw_config['my_data_dir'] == 'my-data'
-    assert config._raw_config['path1'] == 'my-config-files'
-    assert config._raw_config['path2'] == 'my-data-files'
-    assert config._raw_config['path3'] == 'my-other-files'
-    assert config._raw_config['path4'] == 'conf1, conf2, conf3'
+    assert config._raw_config["my_config_dir"] == "my-config"
+    assert config._raw_config["my_data_dir"] == "my-data"
+    assert config._raw_config["path1"] == "my-config-files"
+    assert config._raw_config["path2"] == "my-data-files"
+    assert config._raw_config["path3"] == "my-other-files"
+    assert config._raw_config["path4"] == "conf1, conf2, conf3"
 
 
 def test_no_kwargs(mock_init):
     # Expected: use default from schema, then resolve
     config = BaseAppConfiguration()
-    assert config.path1 == 'my-config/my-config-files'  # resolved
-    assert config.path2 == 'my-data/my-data-files'  # resolved
-    assert config.path3 == 'my-other-files'  # no change
-    assert config.path4 == ['my-config/conf3']  # last value resolved and listified; others dropped as files do not exist
+    assert config.path1 == "my-config/my-config-files"  # resolved
+    assert config.path2 == "my-data/my-data-files"  # resolved
+    assert config.path3 == "my-other-files"  # no change
+    assert config.path4 == [
+        "my-config/conf3"
+    ]  # last value resolved and listified; others dropped as files do not exist
 
 
 def test_kwargs_relative_path(mock_init):
     # Expected: use value from kwargs, then resolve
-    new_path1 = 'foo1/bar'
-    new_path2 = 'foo2/bar'
+    new_path1 = "foo1/bar"
+    new_path2 = "foo2/bar"
     config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
 
-    assert config.path1 == 'my-config/' + new_path1  # resolved
-    assert config.path2 == 'my-data/' + new_path2  # resolved
-    assert config.path3 == 'my-other-files'  # no change
+    assert config.path1 == "my-config/" + new_path1  # resolved
+    assert config.path2 == "my-data/" + new_path2  # resolved
+    assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_absolute_path(mock_init):
     # Expected: use value from kwargs, do NOT resolve
-    new_path1 = '/foo1/bar'
-    new_path2 = '/foo2/bar'
+    new_path1 = "/foo1/bar"
+    new_path2 = "/foo2/bar"
     config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
 
     assert config.path1 == new_path1  # NOT resolved
     assert config.path2 == new_path2  # NOT resolved
-    assert config.path3 == 'my-other-files'  # no change
+    assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_relative_path_old_prefix(mock_init):
     # Expect: use value from kwargs, strip old prefix, then resolve
-    new_path1 = 'old-config/foo1/bar'
-    new_path2 = 'old-database/foo2/bar'
+    new_path1 = "old-config/foo1/bar"
+    new_path2 = "old-database/foo2/bar"
     config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
 
-    assert config.path1 == 'my-config/foo1/bar'  # stripped of old prefix, resolved
-    assert config.path2 == 'my-data/foo2/bar'  # stripped of old prefix, resolved
-    assert config.path3 == 'my-other-files'  # no change
+    assert config.path1 == "my-config/foo1/bar"  # stripped of old prefix, resolved
+    assert config.path2 == "my-data/foo2/bar"  # stripped of old prefix, resolved
+    assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_relative_path_old_prefix_csv_value(mock_init):
     # Expect: use value from kwargs, split at commas, then for each path strip
     # spaces, strip old prefix if needed, and resolve if needed
-    config = BaseAppConfiguration(path4='old-config/foo/file1 , /foo1/bar,  foo/file3')
-    assert config.path4 == ['my-config/foo/file1', '/foo1/bar', 'my-config/foo/file3']
+    config = BaseAppConfiguration(path4="old-config/foo/file1 , /foo1/bar,  foo/file3")
+    assert config.path4 == ["my-config/foo/file1", "/foo1/bar", "my-config/foo/file3"]
 
 
 def test_kwargs_relative_path_old_prefix_for_other_option(mock_init):
     # Expect: use value from kwargs, do NOT strip old prefix, then resolve
     # Reason: deprecated dirs are option-specific: we don't want to strip 'old-config'
     # (deprecated for the config_dir option) if it's used for another option
-    new_path1 = 'old-database/foo1/bar'
-    new_path2 = 'old-config/foo2/bar'
+    new_path1 = "old-database/foo1/bar"
+    new_path2 = "old-config/foo2/bar"
     config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
 
-    assert config.path1 == 'my-config/' + new_path1  # resolved
-    assert config.path2 == 'my-data/' + new_path2  # resolved
-    assert config.path3 == 'my-other-files'  # no change
+    assert config.path1 == "my-config/" + new_path1  # resolved
+    assert config.path2 == "my-data/" + new_path2  # resolved
+    assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init):
     # Expect: use value from kwargs, strip old prefix, then resolve
-    new_path1 = 'old-config'
+    new_path1 = "old-config"
     config = BaseAppConfiguration(path1=new_path1)
 
-    assert config.path1 == 'my-config/'  # stripped of old prefix, then resolved
-    assert config.path2 == 'my-data/my-data-files'  # stripped of old prefix, then resolved
-    assert config.path3 == 'my-other-files'  # no change
+    assert config.path1 == "my-config/"  # stripped of old prefix, then resolved
+    assert config.path2 == "my-data/my-data-files"  # stripped of old prefix, then resolved
+    assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_set_to_null(mock_init):
@@ -143,9 +144,9 @@ def test_kwargs_set_to_null(mock_init):
     # `job_config` set to `None` when testing
     config = BaseAppConfiguration(path1=None)
 
-    assert config.path1 == 'my-config'  # resolved
-    assert config.path2 == 'my-data/my-data-files'  # resolved
-    assert config.path3 == 'my-other-files'  # no change
+    assert config.path1 == "my-config"  # resolved
+    assert config.path2 == "my-data/my-data-files"  # resolved
+    assert config.path3 == "my-other-files"  # no change
 
 
 def test_add_sample_file(mock_init, monkeypatch):
@@ -153,80 +154,79 @@ def test_add_sample_file(mock_init, monkeypatch):
     # - resolved w.r.t sample-dir (_in_sample_dir mocked)
     # - has ".sample" suffix
     # Last value (sample file) resolved and listified; others dropped as files do not exist
-    monkeypatch.setattr(BaseAppConfiguration, 'add_sample_file_to_defaults', {'path1', 'path4'})
-    monkeypatch.setattr(BaseAppConfiguration, '_in_sample_dir', lambda a, path: '/sample-dir/%s' % path)
+    monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1", "path4"})
+    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: "/sample-dir/%s" % path)
     config = BaseAppConfiguration()
 
-    assert config._raw_config['path1'] == 'my-config-files'
-    assert config.path1 == '/sample-dir/my-config-files.sample'
-    assert config._raw_config['path4'] == 'conf1, conf2, conf3'
-    assert config.path4 == ['/sample-dir/conf3.sample']
+    assert config._raw_config["path1"] == "my-config-files"
+    assert config.path1 == "/sample-dir/my-config-files.sample"
+    assert config._raw_config["path4"] == "conf1, conf2, conf3"
+    assert config.path4 == ["/sample-dir/conf3.sample"]
 
 
 def test_select_one_path_from_list(mock_init, monkeypatch):
     # Expected: files do not exist, so use last file in list (would be sample file); value is not a list
-    monkeypatch.setattr(BaseAppConfiguration, 'add_sample_file_to_defaults', {'path1'})
-    monkeypatch.setattr(BaseAppConfiguration, '_in_sample_dir', lambda a, path: '/sample-dir/%s' % path)
+    monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"})
+    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: "/sample-dir/%s" % path)
     config = BaseAppConfiguration()
 
-    assert config._raw_config['path1'] == 'my-config-files'
-    assert config.path1 == '/sample-dir/my-config-files.sample'
+    assert config._raw_config["path1"] == "my-config-files"
+    assert config.path1 == "/sample-dir/my-config-files.sample"
 
 
 def test_select_one_path_from_list_all_files_exist(mock_init, monkeypatch):
     # Expected: all files exist, so use first file in list; value is not a list
-    monkeypatch.setattr(BaseAppConfiguration, 'add_sample_file_to_defaults', {'path1'})
-    monkeypatch.setattr(BaseAppConfiguration, '_path_exists', lambda a, b: True)
+    monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"})
+    monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda a, b: True)
     config = BaseAppConfiguration()
 
-    assert config._raw_config['path1'] == 'my-config-files'
-    assert config.path1 == 'my-config/my-config-files'
+    assert config._raw_config["path1"] == "my-config-files"
+    assert config.path1 == "my-config/my-config-files"
 
 
 def test_no_kwargs_listify(mock_init, monkeypatch):
     # Expected: last value resolved and listified; others dropped as files do not exist
     config = BaseAppConfiguration()
 
-    assert config._raw_config['path4'] == 'conf1, conf2, conf3'
-    assert config.path4 == ['my-config/conf3']
+    assert config._raw_config["path4"] == "conf1, conf2, conf3"
+    assert config.path4 == ["my-config/conf3"]
 
 
 def test_no_kwargs_listify_all_files_exist(mock_init, monkeypatch):
     # Expected: each value resolved and listified (mock: all files exist)
-    monkeypatch.setattr(BaseAppConfiguration, '_path_exists', lambda a, b: True)
+    monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda a, b: True)
     config = BaseAppConfiguration()
 
-    assert config._raw_config['path4'] == 'conf1, conf2, conf3'
-    assert config.path4 == ['my-config/conf1', 'my-config/conf2', 'my-config/conf3']
+    assert config._raw_config["path4"] == "conf1, conf2, conf3"
+    assert config.path4 == ["my-config/conf1", "my-config/conf2", "my-config/conf3"]
 
 
 def test_kwargs_listify(mock_init, monkeypatch):
     # Expected: use values from kwargs; each value resolved and listified
-    new_path4 = 'new1, new2'
+    new_path4 = "new1, new2"
     config = BaseAppConfiguration(path4=new_path4)
 
-    assert config._raw_config['path4'] == 'new1,new2'
-    assert config.path4 == ['my-config/new1', 'my-config/new2']
+    assert config._raw_config["path4"] == "new1,new2"
+    assert config.path4 == ["my-config/new1", "my-config/new2"]
 
 
 def test_kwargs_as_list_listify(mock_init, monkeypatch):
     # Expected: use values from kwargs; each value resolved and listified
-    new_path4 = ['new1', 'new2']
+    new_path4 = ["new1", "new2"]
     config = BaseAppConfiguration(path4=new_path4)
 
-    assert config._raw_config['path4'] == ['new1', 'new2']
-    assert config.path4 == ['my-config/new1', 'my-config/new2']
+    assert config._raw_config["path4"] == ["new1", "new2"]
+    assert config.path4 == ["my-config/new1", "my-config/new2"]
 
 
 @pytest.fixture
 def mock_check_against_root(mock_init, monkeypatch):
-
     def path_exists(_, path):
-        return True if path == 'root/foo' else False
+        return True if path == "root/foo" else False
 
-    monkeypatch.setattr(BaseAppConfiguration, '_path_exists', path_exists)
-    monkeypatch.setattr(BaseAppConfiguration, '_in_root_dir', lambda _, path: 'root/%s' % path)
-    monkeypatch.setattr(BaseAppConfiguration, 'paths_to_check_against_root', {'path1', 'path4'})
+    monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: "root/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "paths_to_check_against_root", {"path1", "path4"})
 
 
 def test_check_against_root_single_path(mock_check_against_root):
@@ -235,9 +235,9 @@ def test_check_against_root_single_path(mock_check_against_root):
     # 3. path1 is in paths to check against root
     # 4. 'my-config/foo' does not exist, so 'foo' is re-resolved w.r.t root
     # 5. 'root/foo' exists, so config.path1 is set to 'root/foo'
-    config = BaseAppConfiguration(path1='foo')
+    config = BaseAppConfiguration(path1="foo")
 
-    assert config.path1 == 'root/foo'
+    assert config.path1 == "root/foo"
 
 
 def test_check_against_root_list_of_paths(mock_check_against_root):
@@ -246,34 +246,33 @@ def test_check_against_root_list_of_paths(mock_check_against_root):
     # 3. path4 is in paths to check against root
     # 4. both paths do not exist, so both are re-resolved w.r.t root
     # 5. 'root/foo' exists, so config.path4 is set to ['root/foo', 'my-config/bar']
-    config = BaseAppConfiguration(path4='foo, bar')
+    config = BaseAppConfiguration(path4="foo, bar")
 
-    assert config.path4 == ['root/foo', 'my-config/bar']
+    assert config.path4 == ["root/foo", "my-config/bar"]
 
 
 def test_set_alt_paths(mock_init, monkeypatch):
-
     def path_exists(_, path):
-        return True if path == 'foo' else False
+        return True if path == "foo" else False
 
-    monkeypatch.setattr(BaseAppConfiguration, '_path_exists', path_exists)
+    monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists)
 
     def reset_to_initial_default():
-        config.path1 = 'my-config/my-config-files'
+        config.path1 = "my-config/my-config-files"
 
     config = BaseAppConfiguration()
 
     # default does not exist, one alt path exists
-    assert config.path1 == 'my-config/my-config-files'
-    config._set_alt_paths('path1', 'foo')
-    assert config.path1 == 'foo'
+    assert config.path1 == "my-config/my-config-files"
+    config._set_alt_paths("path1", "foo")
+    assert config.path1 == "foo"
 
     # default does not exist, 2 alt paths passed, second exists
     reset_to_initial_default()
-    config._set_alt_paths('path1', 'invalid', 'foo')
-    assert config.path1 == 'foo'
+    config._set_alt_paths("path1", "invalid", "foo")
+    assert config.path1 == "foo"
 
     # default does not exist, alt paths do not exist
     reset_to_initial_default()
-    config._set_alt_paths('path1', 'invalid', 'invalid-2')
-    assert config.path1 == 'my-config/my-config-files'
+    config._set_alt_paths("path1", "invalid", "invalid-2")
+    assert config.path1 == "my-config/my-config-files"
diff --git a/test/unit/config/test_reload_config.py b/test/unit/config/test_reload_config.py
index f6441ed0e3c..30211768fbe 100644
--- a/test/unit/config/test_reload_config.py
+++ b/test/unit/config/test_reload_config.py
@@ -1,29 +1,30 @@
 import pytest
 
 from galaxy import config
-from galaxy.config import BaseAppConfiguration
-from galaxy.config import reload_config_options
+from galaxy.config import (
+    BaseAppConfiguration,
+    reload_config_options,
+)
 from galaxy.config.schema import AppSchema
 
-
-R1, R2, N1, N2 = 'reloadable1', 'reloadable2', 'nonrelodable1', 'nonreloadable2'  # config options
+R1, R2, N1, N2 = "reloadable1", "reloadable2", "nonrelodable1", "nonreloadable2"  # config options
 
 MOCK_SCHEMA = {
-    R1: {'reloadable': True, 'default': 1},
-    R2: {'reloadable': True, 'default': 2},
-    N1: {'default': 3},
-    N2: {'default': 4},
+    R1: {"reloadable": True, "default": 1},
+    R2: {"reloadable": True, "default": 2},
+    N1: {"default": 3},
+    N2: {"default": 4},
 }
 
 
 def get_schema(app_mapping):
-    return {'mapping': {'_': {'mapping': app_mapping}}}
+    return {"mapping": {"_": {"mapping": app_mapping}}}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
-    monkeypatch.setattr(BaseAppConfiguration, '_load_schema', lambda a: AppSchema(None, '_'))
-    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(None, "_"))
+    monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(MOCK_SCHEMA))
 
 
 def test_update_property(mock_init, monkeypatch):
@@ -32,7 +33,7 @@ def test_update_property(mock_init, monkeypatch):
     # to the config file, it's the same as modifying that property's value.
 
     # edits to config file: R2, N1 modified
-    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, R2: 42, N1: 99})
+    monkeypatch.setattr(config, "read_properties_from_file", lambda _: {R1: 1, R2: 42, N1: 99})
 
     appconfig = BaseAppConfiguration()
 
@@ -57,7 +58,7 @@ def test_overwrite_reloadable_attribute(mock_init, monkeypatch):
     # to the `_raw_config` dict. This test ensures this works correctly.
 
     # edits to config file: R2 modified
-    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, R2: 42})
+    monkeypatch.setattr(config, "read_properties_from_file", lambda _: {R1: 1, R2: 42})
 
     appconfig = BaseAppConfiguration()
 
@@ -79,7 +80,7 @@ def test_cant_delete_property(mock_init, monkeypatch):
     # is removed from the config file, it will not be modified or deleted.
 
     # edits to config file: R2, N2 deleted
-    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, N1: 3})
+    monkeypatch.setattr(config, "read_properties_from_file", lambda _: {R1: 1, N1: 3})
 
     appconfig = BaseAppConfiguration()
 
diff --git a/test/unit/config/test_schema.py b/test/unit/config/test_schema.py
index c727d0e4a00..1b6b11b4c86 100644
--- a/test/unit/config/test_schema.py
+++ b/test/unit/config/test_schema.py
@@ -4,7 +4,7 @@ from galaxy.util.yaml_util import (
     OrderedLoader,
 )
 
-MOCK_YAML = '''
+MOCK_YAML = """
     type: map
     desc: mocked schema
     foo: bar
@@ -33,43 +33,42 @@ MOCK_YAML = '''
             type: invalid
           property6:
             something_else: b
-    '''
+    """
 
 
 def test_schema_is_loaded(monkeypatch):
-
     def mock_read_schema(self, path):
         return ordered_load(MOCK_YAML)
 
     def mock_init(self, stream):
         super(OrderedLoader, self).__init__(stream)
 
-    monkeypatch.setattr(AppSchema, '_read_schema', mock_read_schema)
-    monkeypatch.setattr(OrderedLoader, '__init__', mock_init)
+    monkeypatch.setattr(AppSchema, "_read_schema", mock_read_schema)
+    monkeypatch.setattr(OrderedLoader, "__init__", mock_init)
 
-    schema = AppSchema('no path', 'mockgalaxy')
+    schema = AppSchema("no path", "mockgalaxy")
     data = ordered_load(MOCK_YAML)
 
-    assert schema.description == data['desc']
-    assert schema.raw_schema['foo'] == 'bar'
+    assert schema.description == data["desc"]
+    assert schema.raw_schema["foo"] == "bar"
 
     assert len(schema.defaults) == 6
-    assert schema.defaults['property1'] == 'a'
-    assert schema.defaults['property2'] == 1
-    assert schema.defaults['property3'] == 1.0
-    assert schema.defaults['property4'] is True
-    assert schema.defaults['property5'] is None
-    assert schema.defaults['property6'] is None
+    assert schema.defaults["property1"] == "a"
+    assert schema.defaults["property2"] == 1
+    assert schema.defaults["property3"] == 1.0
+    assert schema.defaults["property4"] is True
+    assert schema.defaults["property5"] is None
+    assert schema.defaults["property6"] is None
 
-    assert type(schema.defaults['property1']) is str
-    assert type(schema.defaults['property2']) is int
-    assert type(schema.defaults['property3']) is float
-    assert type(schema.defaults['property4']) is bool
+    assert type(schema.defaults["property1"]) is str
+    assert type(schema.defaults["property2"]) is int
+    assert type(schema.defaults["property3"]) is float
+    assert type(schema.defaults["property4"]) is bool
 
     assert len(schema.reloadable_options) == 2
-    assert 'property2' in schema.reloadable_options
-    assert 'property3' in schema.reloadable_options
+    assert "property2" in schema.reloadable_options
+    assert "property3" in schema.reloadable_options
 
     assert len(schema.paths_to_resolve) == 2
-    assert 'property1' in schema.paths_to_resolve
-    assert 'property4' in schema.paths_to_resolve
+    assert "property1" in schema.paths_to_resolve
+    assert "property4" in schema.paths_to_resolve
diff --git a/test/unit/containers/test_containers.py b/test/unit/containers/test_containers.py
index 5bfb271a62f..ec8b9f7c794 100644
--- a/test/unit/containers/test_containers.py
+++ b/test/unit/containers/test_containers.py
@@ -3,7 +3,7 @@ import galaxy.containers.docker_model
 
 
 def test_dummy():
-    t = galaxy.containers.parse_containers_config('')
-    assert t == {'_default_': {'type': 'docker'}}
+    t = galaxy.containers.parse_containers_config("")
+    assert t == {"_default_": {"type": "docker"}}
     s = galaxy.containers.docker_model.DockerAttributeContainer()
     assert s.members == frozenset()
diff --git a/test/unit/data/dataset_collections/test_matching.py b/test/unit/data/dataset_collections/test_matching.py
index 777593f1057..8637304e9a1 100644
--- a/test/unit/data/dataset_collections/test_matching.py
+++ b/test/unit/data/dataset_collections/test_matching.py
@@ -87,10 +87,13 @@ def pair_element(element_identifier):
 
 
 def pair_instance():
-    paired_collection_instance = collection_instance(collection_type="paired", elements=[
-        hda_element("left"),
-        hda_element("right"),
-    ])
+    paired_collection_instance = collection_instance(
+        collection_type="paired",
+        elements=[
+            hda_element("left"),
+            hda_element("right"),
+        ],
+    )
     return paired_collection_instance
 
 
@@ -99,21 +102,16 @@ def list_instance(collection_type="list", elements=None, ids=None):
         if ids is None:
             ids = ["data1", "data2"]
         elements = [hda_element(_) for _ in ids]
-    list_collection_instance = collection_instance(
-        collection_type=collection_type,
-        elements=elements
-    )
+    list_collection_instance = collection_instance(collection_type=collection_type, elements=elements)
     return list_collection_instance
 
 
 class MockCollectionInstance:
-
     def __init__(self, collection_type, elements):
         self.collection = MockCollection(collection_type, elements)
 
 
 class MockCollection:
-
     def __init__(self, collection_type, elements):
         self.collection_type = collection_type
         self.elements = elements
@@ -121,7 +119,6 @@ class MockCollection:
 
 
 class MockCollectionElement:
-
     def __init__(self, element_identifier, collection):
         self.element_identifier = element_identifier
         self.child_collection = collection
@@ -129,7 +126,6 @@ class MockCollectionElement:
 
 
 class MockHDAElement:
-
     def __init__(self, element_identifier):
         self.element_identifier = element_identifier
         self.child_collection = False
diff --git a/test/unit/data/datatypes/converters/test_interval_to_tabix.py b/test/unit/data/datatypes/converters/test_interval_to_tabix.py
index 574de716ed5..b1ce9570d67 100644
--- a/test/unit/data/datatypes/converters/test_interval_to_tabix.py
+++ b/test/unit/data/datatypes/converters/test_interval_to_tabix.py
@@ -3,15 +3,13 @@ import pysam
 from galaxy.datatypes.converters.interval_to_tabix_converter import to_tabix
 from ..util import (
     get_input_files,
-    get_tmp_path
+    get_tmp_path,
 )
 
 
 def test_to_tabix():
-    with get_input_files('1.vcf') as input_files:
-        with get_tmp_path(suffix='.tbi') as index:
-            bgzip_fname = to_tabix(input_files[0],
-                                   index,
-                                   preset='vcf')
+    with get_input_files("1.vcf") as input_files:
+        with get_tmp_path(suffix=".tbi") as index:
+            bgzip_fname = to_tabix(input_files[0], index, preset="vcf")
             f = pysam.TabixFile(bgzip_fname, index=index)
             f.close()
diff --git a/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py b/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py
index ee439f1bd82..52a5baa3c6d 100644
--- a/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py
+++ b/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py
@@ -9,7 +9,10 @@ import unittest
 from io import StringIO
 from typing import Type
 
-from galaxy.datatypes.dataproviders import base, exceptions
+from galaxy.datatypes.dataproviders import (
+    base,
+    exceptions,
+)
 from galaxy.util import clean_multiline_string
 
 log = logging.getLogger(__name__)
@@ -28,40 +31,39 @@ class BaseTestCase(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
-        log.debug('CLASS %s %s', ('_' * 40), cls.__name__)
+        log.debug("CLASS %s %s", ("_" * 40), cls.__name__)
 
     @classmethod
     def tearDownClass(cls):
-        log.debug('CLASS %s %s\n\n', ('_' * 40), cls.__name__)
+        log.debug("CLASS %s %s\n\n", ("_" * 40), cls.__name__)
 
     def __init__(self, *args):
         unittest.TestCase.__init__(self, *args)
         self.tmpfiles = TempFileCache()
 
     def setUp(self):
-        log.debug('BEGIN %s %s', ('.' * 40), self._testMethodName)
+        log.debug("BEGIN %s %s", ("." * 40), self._testMethodName)
         if self._testMethodDoc:
             log.debug(' """%s"""', self._testMethodDoc.strip())
 
     def tearDown(self):
         self.tmpfiles.clear()
-        log.debug('END\n')
+        log.debug("END\n")
 
     def format_tmpfile_contents(self, contents=None):
         contents = contents or self.default_file_contents
         contents = clean_multiline_string(contents)
-        log.debug('file contents:\n%s', contents)
+        log.debug("file contents:\n%s", contents)
         return contents
 
     def parses_default_content_as(self):
-        return ['One\n', 'Two\n', 'Three\n']
+        return ["One\n", "Two\n", "Three\n"]
 
 
 class Test_BaseDataProvider(BaseTestCase):
     provider_class: Type[base.DataProvider] = base.DataProvider
 
-    def contents_provider_and_data(self,
-            filename=None, contents=None, source=None, *provider_args, **provider_kwargs):
+    def contents_provider_and_data(self, filename=None, contents=None, source=None, *provider_args, **provider_kwargs):
         # to remove boiler plate
         # returns file content string, provider used, and data list
         if not filename:
@@ -71,44 +73,42 @@ class Test_BaseDataProvider(BaseTestCase):
         if not source:
             source = open(filename)
         provider = self.provider_class(source, *provider_args, **provider_kwargs)
-        log.debug('provider: %s', provider)
+        log.debug("provider: %s", provider)
         data = list(provider)
-        log.debug('data: %s', str(data))
+        log.debug("data: %s", str(data))
         return (contents, provider, data)
 
     def test_iterators(self):
         source = (str(x) for x in range(1, 10))
         provider = self.provider_class(source)
         data = list(provider)
-        log.debug('data: %s', str(data))
+        log.debug("data: %s", str(data))
         self.assertEqual(data, [str(x) for x in range(1, 10)])
 
         source = (str(x) for x in range(1, 10))
         provider = self.provider_class(source)
         data = list(provider)
-        log.debug('data: %s', str(data))
+        log.debug("data: %s", str(data))
         self.assertEqual(data, [str(x) for x in range(1, 10)])
 
         source = (str(x) for x in range(1, 10))
         provider = self.provider_class(source)
         data = list(provider)
-        log.debug('data: %s', str(data))
+        log.debug("data: %s", str(data))
         self.assertEqual(data, [str(x) for x in range(1, 10)])
 
     def test_validate_source(self):
-        """validate_source should throw an error if the source doesn't have attr '__iter__'
-        """
+        """validate_source should throw an error if the source doesn't have attr '__iter__'"""
+
         def non_iterator_dprov(source):
             return self.provider_class(source)
+
         # two objects without __iter__ method: build in function and int
-        self.assertRaises(exceptions.InvalidDataProviderSource,
-            non_iterator_dprov, sum)
-        self.assertRaises(exceptions.InvalidDataProviderSource,
-            non_iterator_dprov, 40)
+        self.assertRaises(exceptions.InvalidDataProviderSource, non_iterator_dprov, sum)
+        self.assertRaises(exceptions.InvalidDataProviderSource, non_iterator_dprov, 40)
 
     def test_writemethods(self):
-        """should throw an error if any write methods are called
-        """
+        """should throw an error if any write methods are called"""
         source = (str(x) for x in range(1, 10))
         provider = self.provider_class(source)
 
@@ -117,42 +117,41 @@ class Test_BaseDataProvider(BaseTestCase):
             method = getattr(provider, method_name)
             return method(*args)
 
-        self.assertRaises(NotImplementedError, call_method, provider, 'truncate', 20)
-        self.assertRaises(NotImplementedError, call_method, provider, 'write', 'bler')
-        self.assertRaises(NotImplementedError, call_method, provider, 'writelines', ['one', 'two'])
+        self.assertRaises(NotImplementedError, call_method, provider, "truncate", 20)
+        self.assertRaises(NotImplementedError, call_method, provider, "write", "bler")
+        self.assertRaises(NotImplementedError, call_method, provider, "writelines", ["one", "two"])
 
     def test_readlines(self):
-        """readlines should return all the data in list form
-        """
+        """readlines should return all the data in list form"""
         source = (str(x) for x in range(1, 10))
         provider = self.provider_class(source)
         data = provider.readlines()
-        log.debug('data: %s', str(data))
+        log.debug("data: %s", str(data))
         self.assertEqual(data, [str(x) for x in range(1, 10)])
 
     def test_stringio(self):
-        """should work with StringIO
-        """
-        contents = clean_multiline_string("""
+        """should work with StringIO"""
+        contents = clean_multiline_string(
+            """
             One
             Two
             Three
-        """)
+        """
+        )
         source = StringIO(contents)
         provider = self.provider_class(source)
         data = list(provider)
-        log.debug('data: %s', str(data))
+        log.debug("data: %s", str(data))
         # provider should call close on file
         self.assertEqual(data, self.parses_default_content_as())
         self.assertTrue(source.closed)
 
     def test_file(self):
-        """should work with files
-        """
+        """should work with files"""
         (contents, provider, data) = self.contents_provider_and_data()
         self.assertEqual(data, self.parses_default_content_as())
         # provider should call close on file
-        self.assertTrue(hasattr(provider.source, 'read'))
+        self.assertTrue(hasattr(provider.source, "read"))
         self.assertTrue(provider.source.closed)
 
 
@@ -165,8 +164,7 @@ class Test_FilteredDataProvider(Test_BaseDataProvider):
         self.assertEqual(provider.num_data_returned, returned)
 
     def test_counters(self):
-        """should count: lines read, lines that passed the filter, lines returned
-        """
+        """should count: lines read, lines that passed the filter, lines returned"""
         (contents, provider, data) = self.contents_provider_and_data()
         self.assertCounters(provider, 3, 3, 3)
 
@@ -174,10 +172,12 @@ class Test_FilteredDataProvider(Test_BaseDataProvider):
         """should filter out lines using filter_fn and set counters properly
         based on filter
         """
+
         def filter_ts(string):
-            if string.lower().startswith('t'):
+            if string.lower().startswith("t"):
                 return None
             return string
+
         (contents, provider, data) = self.contents_provider_and_data(filter_fn=filter_ts)
         self.assertCounters(provider, 3, 1, 1)
 
@@ -186,57 +186,49 @@ class Test_LimitedOffsetDataProvider(Test_FilteredDataProvider):
     provider_class: Type[base.DataProvider] = base.LimitedOffsetDataProvider
 
     def test_offset_1(self):
-        """when offset is 1, should skip first
-        """
+        """when offset is 1, should skip first"""
         (contents, provider, data) = self.contents_provider_and_data(offset=1)
         self.assertEqual(data, self.parses_default_content_as()[1:])
         self.assertCounters(provider, 3, 3, 2)
 
     def test_offset_all(self):
-        """when offset >= num lines, should return empty list
-        """
+        """when offset >= num lines, should return empty list"""
         (contents, provider, data) = self.contents_provider_and_data(offset=4)
         self.assertEqual(data, [])
         self.assertCounters(provider, 3, 3, 0)
 
     def test_offset_none(self):
-        """when offset is 0, should return all
-        """
+        """when offset is 0, should return all"""
         (contents, provider, data) = self.contents_provider_and_data(offset=0)
         self.assertEqual(data, self.parses_default_content_as())
         self.assertCounters(provider, 3, 3, 3)
 
     def test_offset_negative(self):
-        """when offset is negative, should return all
-        """
+        """when offset is negative, should return all"""
         (contents, provider, data) = self.contents_provider_and_data(offset=-1)
         self.assertEqual(data, self.parses_default_content_as())
         self.assertCounters(provider, 3, 3, 3)
 
     def test_limit_1(self):
-        """when limit is one, should return first
-        """
+        """when limit is one, should return first"""
         (contents, provider, data) = self.contents_provider_and_data(limit=1)
         self.assertEqual(data, self.parses_default_content_as()[:1])
         self.assertCounters(provider, 1, 1, 1)
 
     def test_limit_all(self):
-        """when limit >= num lines, should return all
-        """
+        """when limit >= num lines, should return all"""
         (contents, provider, data) = self.contents_provider_and_data(limit=4)
         self.assertEqual(data, self.parses_default_content_as())
         self.assertCounters(provider, 3, 3, 3)
 
     def test_limit_zero(self):
-        """when limit >= num lines, should return empty list
-        """
+        """when limit >= num lines, should return empty list"""
         (contents, provider, data) = self.contents_provider_and_data(limit=0)
         self.assertEqual(data, [])
         self.assertCounters(provider, 0, 0, 0)
 
     def test_limit_none(self):
-        """when limit is None, should return all
-        """
+        """when limit is None, should return all"""
         (contents, provider, data) = self.contents_provider_and_data(limit=None)
         self.assertEqual(data, self.parses_default_content_as())
         self.assertCounters(provider, 3, 3, 3)
@@ -247,6 +239,7 @@ class Test_LimitedOffsetDataProvider(Test_FilteredDataProvider):
             (contents, provider, data) = self.contents_provider_and_data(limit=limit, offset=offset)
             self.assertEqual(data, data_should_be)
             # self.assertCounters( provider, read, valid, returned )
+
         result_data = self.parses_default_content_as()
         test_data = [
             (0, 0, [], 0, 0, 0),
@@ -261,20 +254,21 @@ class Test_LimitedOffsetDataProvider(Test_FilteredDataProvider):
             (3, 2, result_data[2:3], 1, 1, 1),
         ]
         for test in test_data:
-            log.debug('limit_offset_combo: %s', ', '.join(str(e) for e in test))
+            log.debug("limit_offset_combo: %s", ", ".join(str(e) for e in test))
             limit_offset_combo(*test)
 
     def test_limit_with_offset_and_filter(self):
         def limit_offset_combo(limit, offset, data_should_be, read, valid, returned):
             def only_ts(string):
-                if not string.lower().startswith('t'):
+                if not string.lower().startswith("t"):
                     return None
                 return string
-            (contents, provider, data) = self.contents_provider_and_data(
-                limit=limit, offset=offset, filter_fn=only_ts)
+
+            (contents, provider, data) = self.contents_provider_and_data(limit=limit, offset=offset, filter_fn=only_ts)
             self.assertEqual(data, data_should_be)
             # self.assertCounters( provider, read, valid, returned )
-        result_data = [c for c in self.parses_default_content_as() if c.lower().startswith('t')]
+
+        result_data = [c for c in self.parses_default_content_as() if c.lower().startswith("t")]
         test_data = [
             (0, 0, [], 0, 0, 0),
             (1, 0, result_data[:1], 1, 1, 1),
@@ -285,7 +279,7 @@ class Test_LimitedOffsetDataProvider(Test_FilteredDataProvider):
             (1, 2, result_data[2:3], 0, 0, 0),
         ]
         for test in test_data:
-            log.debug('limit_offset_combo: %s', ', '.join(str(e) for e in test))
+            log.debug("limit_offset_combo: %s", ", ".join(str(e) for e in test))
             limit_offset_combo(*test)
 
 
@@ -319,16 +313,16 @@ class Test_MultiSourceDataProvider(BaseTestCase):
             """
                 Eleven
                 Twelve! (<-- http://youtu.be/JZshZp-cxKg)
-            """
+            """,
         ]
         contents = [clean_multiline_string(c) for c in contents]
         source_list = [open(self.tmpfiles.create_tmpfile(c)) for c in contents]
 
         provider = self.provider_class(source_list)
-        log.debug('provider: %s', provider)
+        log.debug("provider: %s", provider)
         data = list(provider)
-        log.debug('data: %s', str(data))
-        self.assertEqual(''.join(data), ''.join(contents))
+        log.debug("data: %s", str(data))
+        self.assertEqual("".join(data), "".join(contents))
 
     def test_multiple_compound_sources(self):
         # clean the following contents, write them to tmpfiles, open them,
@@ -351,16 +345,16 @@ class Test_MultiSourceDataProvider(BaseTestCase):
             """
                 Eleven
                 Twelve! (<-- http://youtu.be/JZshZp-cxKg)
-            """
+            """,
         ]
         contents = [clean_multiline_string(c) for c in contents]
         source_list_f = [open(self.tmpfiles.create_tmpfile(c)) for c in contents]
 
         def no_Fs(string):
-            return None if string.startswith('F') else string
+            return None if string.startswith("F") else string
 
         def no_youtube(string):
-            return None if ('youtu.be' in string) else string
+            return None if ("youtu.be" in string) else string
 
         source_list = [
             base.LimitedOffsetDataProvider(source_list_f[0], filter_fn=no_Fs, limit=2, offset=1),
@@ -368,10 +362,10 @@ class Test_MultiSourceDataProvider(BaseTestCase):
             base.FilteredDataProvider(source_list_f[2], filter_fn=no_youtube),
         ]
         provider = self.provider_class(source_list)
-        log.debug('provider: %s', provider)
+        log.debug("provider: %s", provider)
         data = list(provider)
-        log.debug('data: %s', str(data))
-        self.assertEqual(''.join(data), 'Two\nThree\nNine\nEleven\n')
+        log.debug("data: %s", str(data))
+        self.assertEqual("".join(data), "Two\nThree\nNine\nEleven\n")
 
 
 class TempFileCache:
@@ -385,23 +379,23 @@ class TempFileCache:
     def create_tmpfile(self, contents):
         if contents not in self._content_dict:
             # create a named tmp and write contents to it, return filename
-            with tempfile.NamedTemporaryFile(delete=False, mode='w+') as tmpfile:
+            with tempfile.NamedTemporaryFile(delete=False, mode="w+") as tmpfile:
                 tmpfile.write(contents)
                 tmpfile_name = tmpfile.name
-            log.debug('created tmpfile.name: %s', tmpfile_name)
+            log.debug("created tmpfile.name: %s", tmpfile_name)
             self._content_dict[contents] = tmpfile_name
 
         else:
-            log.debug('(cached): %s', self._content_dict[contents])
+            log.debug("(cached): %s", self._content_dict[contents])
         return self._content_dict[contents]
 
     def clear(self):
         for tmpfile in self._content_dict.values():
             if os.path.exists(tmpfile):
-                log.debug('unlinking tmpfile: %s', tmpfile)
+                log.debug("unlinking tmpfile: %s", tmpfile)
                 os.unlink(tmpfile)
         self._content_dict = {}
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py b/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py
index 60b6cfdee7e..a9170c05c21 100644
--- a/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py
+++ b/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py
@@ -6,8 +6,10 @@ import logging
 import unittest
 from typing import Type
 
-from galaxy.datatypes.dataproviders import base
-from galaxy.datatypes.dataproviders import line
+from galaxy.datatypes.dataproviders import (
+    base,
+    line,
+)
 from . import test_base_dataproviders
 
 log = logging.getLogger(__name__)
@@ -27,11 +29,10 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
         """
 
     def parses_default_content_as(self):
-        return ['One', 'Two', 'Three']
+        return ["One", "Two", "Three"]
 
     def test_counters(self):
-        """should count: lines read, lines that passed the filter, lines returned
-        """
+        """should count: lines read, lines that passed the filter, lines returned"""
         (contents, provider, data) = self.contents_provider_and_data()
         self.assertCounters(provider, 7, 3, 3)
 
@@ -39,10 +40,12 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
         """should filter out lines using filter_fn and set counters properly
         based on filter
         """
+
         def filter_ts(string):
-            if string.lower().startswith('t'):
+            if string.lower().startswith("t"):
                 return None
             return string
+
         (contents, provider, data) = self.contents_provider_and_data(filter_fn=filter_ts)
         self.assertCounters(provider, 7, 1, 1)
 
@@ -51,6 +54,7 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
             (contents, provider, data) = self.contents_provider_and_data(limit=limit, offset=offset)
             self.assertEqual(data, data_should_be)
             # self.assertCounters( provider, read, valid, returned )
+
         result_data = self.parses_default_content_as()
         test_data = [
             (0, 0, [], 0, 0, 0),
@@ -65,29 +69,28 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
             (3, 2, result_data[2:3], 1, 1, 1),
         ]
         for test in test_data:
-            log.debug('limit_offset_combo: %s', ', '.join(str(e) for e in test))
+            log.debug("limit_offset_combo: %s", ", ".join(str(e) for e in test))
             limit_offset_combo(*test)
 
     def test_provide_blank(self):
-        """should return blank lines if ``provide_blank`` is true.
-        """
+        """should return blank lines if ``provide_blank`` is true."""
         (contents, provider, data) = self.contents_provider_and_data(provide_blank=True)
-        self.assertEqual(data, ['One', '', 'Two', 'Three'])
+        self.assertEqual(data, ["One", "", "Two", "Three"])
         self.assertCounters(provider, 7, 4, 4)
 
     def test_strip_lines(self):
-        """should return unstripped lines if ``strip_lines`` is false.
-        """
+        """should return unstripped lines if ``strip_lines`` is false."""
         (contents, provider, data) = self.contents_provider_and_data(strip_lines=False)
-        self.assertEqual(data, ['One\n', '\n', '    Two\n', 'Three\n'])
+        self.assertEqual(data, ["One\n", "\n", "    Two\n", "Three\n"])
         self.assertCounters(provider, 7, 4, 4)
 
     def test_comment_char(self):
-        """should return unstripped lines if ``strip_lines`` is false.
-        """
-        (contents, provider, data) = self.contents_provider_and_data(comment_char='T')
-        self.assertEqual(data, ['# this should be stripped out', 'One',
-                                '# as should blank lines', '# preceding/trailing whitespace too'])
+        """should return unstripped lines if ``strip_lines`` is false."""
+        (contents, provider, data) = self.contents_provider_and_data(comment_char="T")
+        self.assertEqual(
+            data,
+            ["# this should be stripped out", "One", "# as should blank lines", "# preceding/trailing whitespace too"],
+        )
         self.assertCounters(provider, 7, 4, 4)
 
 
@@ -104,43 +107,38 @@ class Test_RegexLineDataProvider(Test_FilteredLineDataProvider):
         """
 
     def test_regex(self):
-        """should return lines matching regex (AFTER strip, comments, blanks).
-        """
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r'^O'])
-        self.assertEqual(data, ['One'])
+        """should return lines matching regex (AFTER strip, comments, blanks)."""
+        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^O"])
+        self.assertEqual(data, ["One"])
         self.assertCounters(provider, 7, 1, 1)
 
     def test_regex_list(self):
-        """should return regex matches using more than one regex by ORing them.
-        """
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r'^O', r'T'])
-        self.assertEqual(data, ['One', 'Two', 'Three'])
+        """should return regex matches using more than one regex by ORing them."""
+        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^O", r"T"])
+        self.assertEqual(data, ["One", "Two", "Three"])
         self.assertCounters(provider, 7, 3, 3)
 
     def test_inverse(self):
-        """should return inverse matches when ``invert`` is true.
-        """
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r'^O'], invert=True)
-        self.assertEqual(data, ['Two', 'Three'])
+        """should return inverse matches when ``invert`` is true."""
+        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^O"], invert=True)
+        self.assertEqual(data, ["Two", "Three"])
         self.assertCounters(provider, 7, 2, 2)
 
     def test_regex_no_match(self):
-        """should return empty if no regex matches.
-        """
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r'^Z'])
+        """should return empty if no regex matches."""
+        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^Z"])
         self.assertEqual(data, [])
         self.assertCounters(provider, 7, 0, 0)
 
     def test_regex_w_limit_offset(self):
-        """regex should play well with limit and offset
-        """
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r'^T'], limit=1)
-        self.assertEqual(data, ['Two'])
+        """regex should play well with limit and offset"""
+        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^T"], limit=1)
+        self.assertEqual(data, ["Two"])
         # TODO: once again, valid data, returned data is off
         self.assertCounters(provider, 6, 1, 1)
 
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r'^T'], limit=1, offset=1)
-        self.assertEqual(data, ['Three'])
+        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^T"], limit=1, offset=1)
+        self.assertEqual(data, ["Three"])
         self.assertCounters(provider, 7, 2, 1)
 
 
@@ -156,7 +154,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
     """
 
     def parses_default_content_as(self):
-        return [['One'], ['ABCD'], ['Two'], ['ABCD'], ['EFGH'], ['Three']]
+        return [["One"], ["ABCD"], ["Two"], ["ABCD"], ["EFGH"], ["Three"]]
 
     # TODO: well, this is ham-handed...
     def test_stringio(self):
@@ -169,18 +167,16 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
         pass
 
     def test_file(self):
-        """should work with files
-        """
+        """should work with files"""
         (contents, provider, data) = self.contents_provider_and_data()
         self.assertEqual(data, self.parses_default_content_as())
         self.assertTrue(isinstance(provider.source, line.FilteredLineDataProvider))
-        self.assertTrue(hasattr(provider.source.source, 'read'))
+        self.assertTrue(hasattr(provider.source.source, "read"))
         # provider should call close on file
         self.assertTrue(provider.source.source.closed)
 
     def test_counters(self):
-        """should count: lines read, lines that passed the filter, lines returned
-        """
+        """should count: lines read, lines that passed the filter, lines returned"""
         (contents, provider, data) = self.contents_provider_and_data()
         self.assertCounters(provider, 6, 6, 6)
 
@@ -188,46 +184,52 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
         """should filter out lines using filter_fn and set counters properly
         based on filter
         """
+
         def filter_ts(string):
-            if string.lower().startswith('t'):
+            if string.lower().startswith("t"):
                 return None
             return string
+
         (contents, provider, data) = self.contents_provider_and_data(filter_fn=filter_ts)
         # no block fns here, so will parse as lines
-        self.assertEqual(data, [['One'], ['ABCD'], ['ABCD'], ['EFGH']])
+        self.assertEqual(data, [["One"], ["ABCD"], ["ABCD"], ["EFGH"]])
         self.assertCounters(provider, 4, 4, 4)
 
     def test_new_block_delim_fn(self):
-        """should return blocks based on ``new_block_delim_fn``
-        """
+        """should return blocks based on ``new_block_delim_fn``"""
+
         def is_not_indented(line):
             strip_diff = len(line) - len(line.lstrip())
-            return (strip_diff == 0)
+            return strip_diff == 0
+
         # in order to use indentation as a delimiter, we need to strip the newlines only
-        (contents, provider, data) = self.contents_provider_and_data(strip_lines=False, strip_newlines=True,
-            new_block_delim_fn=is_not_indented)
-        self.assertEqual(data, [['One', '    ABCD'], ['Two', '    ABCD', '    EFGH'], ['Three']])
+        (contents, provider, data) = self.contents_provider_and_data(
+            strip_lines=False, strip_newlines=True, new_block_delim_fn=is_not_indented
+        )
+        self.assertEqual(data, [["One", "    ABCD"], ["Two", "    ABCD", "    EFGH"], ["Three"]])
         self.assertCounters(provider, 3, 3, 3)
 
     def test_block_filter_fn(self):
-        """should return blocks only blocks that pass ``block_filter_fn``
-        """
+        """should return blocks only blocks that pass ``block_filter_fn``"""
+
         def is_not_indented(line):
             strip_diff = len(line) - len(line.lstrip())
-            return (strip_diff == 0)
+            return strip_diff == 0
+
         # def empty_block( block ):
         #    if len( block ) <= 1:
         #        return None
         #    return block
 
         def no_tw(block):
-            if block[0].startswith('Tw'):
+            if block[0].startswith("Tw"):
                 return None
             return block
 
-        (contents, provider, data) = self.contents_provider_and_data(strip_lines=False, strip_newlines=True,
-            new_block_delim_fn=is_not_indented, block_filter_fn=no_tw)
-        self.assertEqual(data, [['One', '    ABCD'], ['Three']])
+        (contents, provider, data) = self.contents_provider_and_data(
+            strip_lines=False, strip_newlines=True, new_block_delim_fn=is_not_indented, block_filter_fn=no_tw
+        )
+        self.assertEqual(data, [["One", "    ABCD"], ["Three"]])
         self.assertCounters(provider, 3, 2, 2)
 
     def test_hack_block_filter_fn(self):
@@ -235,46 +237,56 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
 
         Although, it would be better to subclass and override assemble_current_block
         """
+
         def is_not_indented(line):
             strip_diff = len(line) - len(line.lstrip())
-            return (strip_diff == 0)
+            return strip_diff == 0
 
         def empty_block(block):
             if len(block) <= 1:
                 return None
-            return {'header': block[0].strip(), 'data': [b.strip() for b in block[1:] if b.strip()]}
+            return {"header": block[0].strip(), "data": [b.strip() for b in block[1:] if b.strip()]}
 
         (contents, provider, data) = self.contents_provider_and_data(
-            strip_lines=False, strip_newlines=True,
-            new_block_delim_fn=is_not_indented, block_filter_fn=empty_block)
-        self.assertEqual(data, [{'header': 'One', 'data': ['ABCD']},
-                                {'header': 'Two', 'data': ['ABCD', 'EFGH']}])
+            strip_lines=False, strip_newlines=True, new_block_delim_fn=is_not_indented, block_filter_fn=empty_block
+        )
+        self.assertEqual(data, [{"header": "One", "data": ["ABCD"]}, {"header": "Two", "data": ["ABCD", "EFGH"]}])
         self.assertCounters(provider, 3, 2, 2)
 
     def test_block_filter_fn_w_limit_offset(self):
-        """should allow both block fns and limit, offset
-        """
+        """should allow both block fns and limit, offset"""
+
         def is_not_indented(line):
             strip_diff = len(line) - len(line.lstrip())
-            return (strip_diff == 0)
+            return strip_diff == 0
 
         def empty_block(block):
             if len(block) <= 1:
                 return None
             return block
 
-        (contents, provider, data) = self.contents_provider_and_data(strip_lines=False, strip_newlines=True,
-            new_block_delim_fn=is_not_indented, block_filter_fn=empty_block, limit=1)
-        self.assertEqual(data, [['One', '    ABCD']])
+        (contents, provider, data) = self.contents_provider_and_data(
+            strip_lines=False,
+            strip_newlines=True,
+            new_block_delim_fn=is_not_indented,
+            block_filter_fn=empty_block,
+            limit=1,
+        )
+        self.assertEqual(data, [["One", "    ABCD"]])
         self.assertCounters(provider, 1, 1, 1)
-        (contents, provider, data) = self.contents_provider_and_data(strip_lines=False, strip_newlines=True,
-            new_block_delim_fn=is_not_indented, block_filter_fn=empty_block, limit=2, offset=1)
-        self.assertEqual(data, [['Two', '    ABCD', '    EFGH']])
+        (contents, provider, data) = self.contents_provider_and_data(
+            strip_lines=False,
+            strip_newlines=True,
+            new_block_delim_fn=is_not_indented,
+            block_filter_fn=empty_block,
+            limit=2,
+            offset=1,
+        )
+        self.assertEqual(data, [["Two", "    ABCD", "    EFGH"]])
         self.assertCounters(provider, 3, 2, 1)
 
     def test_simple_example(self):
-        """
-        """
+        """ """
         file_contents = """
             >One
             ABCD
@@ -286,16 +298,17 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
             """
 
         def fasta_header(line):
-            return line.startswith('>')
+            return line.startswith(">")
 
         def id_seq(block):
-            return {'id': block[0][1:], 'seq': (''.join(block[1:]))}
+            return {"id": block[0][1:], "seq": ("".join(block[1:]))}
 
-        (contents, provider, data) = self.contents_provider_and_data(contents=file_contents,
-            new_block_delim_fn=fasta_header, block_filter_fn=id_seq)
-        self.assertEqual(data, [{'id': 'One', 'seq': 'ABCD'}, {'id': 'Two', 'seq': 'ABCDEFGH'}])
+        (contents, provider, data) = self.contents_provider_and_data(
+            contents=file_contents, new_block_delim_fn=fasta_header, block_filter_fn=id_seq
+        )
+        self.assertEqual(data, [{"id": "One", "seq": "ABCD"}, {"id": "Two", "seq": "ABCDEFGH"}])
         self.assertCounters(provider, 2, 2, 2)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/data/datatypes/test_bam.py b/test/unit/data/datatypes/test_bam.py
index 06ccf924bf4..4e14285b892 100644
--- a/test/unit/data/datatypes/test_bam.py
+++ b/test/unit/data/datatypes/test_bam.py
@@ -4,21 +4,21 @@ from galaxy.datatypes.binary import Bam
 from .util import (
     get_dataset,
     get_input_files,
-    get_tmp_path
+    get_tmp_path,
 )
 
 
 def test_merge_bam():
-    with get_input_files('1.bam', '1.bam') as input_files, get_tmp_path() as outpath:
+    with get_input_files("1.bam", "1.bam") as input_files, get_tmp_path() as outpath:
         Bam.merge(input_files, outpath)
-        alignment_count_output = int(pysam.view('-c', outpath).strip())
-        alignment_count_input = int(pysam.view('-c', input_files[0]).strip()) * 2
+        alignment_count_output = int(pysam.view("-c", outpath).strip())
+        alignment_count_input = int(pysam.view("-c", input_files[0]).strip()) * 2
         assert alignment_count_input == alignment_count_output
 
 
 def test_dataset_content_needs_grooming():
     b = Bam()
-    with get_input_files('1.bam', '2.shuffled.unsorted.bam') as input_files:
+    with get_input_files("1.bam", "2.shuffled.unsorted.bam") as input_files:
         sorted_bam, shuffled_bam = input_files
         assert b.dataset_content_needs_grooming(sorted_bam) is False
         assert b.dataset_content_needs_grooming(shuffled_bam) is True
@@ -27,24 +27,25 @@ def test_dataset_content_needs_grooming():
 def test_groom_dataset_content():
     b = Bam()
     try:
-        with get_input_files('2.shuffled.unsorted.bam') as input_files:
+        with get_input_files("2.shuffled.unsorted.bam") as input_files:
             b.groom_dataset_content(input_files[0])
             assert b.dataset_content_needs_grooming(input_files[0]) is False
     except AssertionError as e:
         # Grooming modifies files in-place, so the md5 hash comparison has to fail
-        assert 'Unexpected change' in str(e)
+        assert "Unexpected change" in str(e)
         return
     # should not reach this part of the test
-    raise Exception('Bam grooming did not occur in-place')
+    raise Exception("Bam grooming did not occur in-place")
 
 
 def test_set_meta_presorted():
     b = Bam()
-    with get_dataset('1.bam') as dataset:
+    with get_dataset("1.bam") as dataset:
         b.set_meta(dataset=dataset)
-        assert dataset.metadata.sort_order == 'coordinate'
-        bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb',
-                                       index_filename=dataset.metadata.bam_index.file_name)
+        assert dataset.metadata.sort_order == "coordinate"
+        bam_file = pysam.AlignmentFile(
+            dataset.file_name, mode="rb", index_filename=dataset.metadata.bam_index.file_name
+        )
         assert bam_file.has_index() is True
 
 
@@ -54,7 +55,10 @@ def test_set_meta_header_info():
     as metadata
     """
     b = Bam()
-    with get_dataset('bam_from_sam.bam') as dataset:
+    with get_dataset("bam_from_sam.bam") as dataset:
         b.set_meta(dataset=dataset)
-        assert dataset.metadata.bam_header == {'HD': {'VN': '1.3', 'SO': 'coordinate'}, 'SQ': [{'SN': 'ref', 'LN': 45}, {'SN': 'ref2', 'LN': 40}]}
-        assert dataset.metadata.reference_names == ['ref', 'ref2']
+        assert dataset.metadata.bam_header == {
+            "HD": {"VN": "1.3", "SO": "coordinate"},
+            "SQ": [{"SN": "ref", "LN": 45}, {"SN": "ref2", "LN": 40}],
+        }
+        assert dataset.metadata.reference_names == ["ref", "ref2"]
diff --git a/test/unit/data/datatypes/test_bcf.py b/test/unit/data/datatypes/test_bcf.py
index f455a50f670..2390f648f35 100644
--- a/test/unit/data/datatypes/test_bcf.py
+++ b/test/unit/data/datatypes/test_bcf.py
@@ -1,6 +1,6 @@
 from galaxy.datatypes.binary import (
     Bcf,
-    BcfUncompressed
+    BcfUncompressed,
 )
 from .util import (
     get_dataset,
@@ -11,7 +11,7 @@ from .util import (
 def test_bcf_sniff():
     bcf = Bcf()
     bcfu = BcfUncompressed()
-    with get_input_files('1.bcf', '1.bcf_uncompressed') as input_files:
+    with get_input_files("1.bcf", "1.bcf_uncompressed") as input_files:
         compressed, uncompressed = input_files
         assert bcf.sniff(compressed) is True
         assert bcf.sniff(uncompressed) is False
@@ -21,5 +21,5 @@ def test_bcf_sniff():
 
 def test_bcf_set_meta():
     bcf = Bcf()
-    with get_input_files('1.bcf') as input_files, get_dataset(input_files[0], index_attr='bcf_index') as dataset:
+    with get_input_files("1.bcf") as input_files, get_dataset(input_files[0], index_attr="bcf_index") as dataset:
         bcf.set_meta(dataset)
diff --git a/test/unit/data/datatypes/test_cram.py b/test/unit/data/datatypes/test_cram.py
index c117ff785d2..a2908d9b45b 100644
--- a/test/unit/data/datatypes/test_cram.py
+++ b/test/unit/data/datatypes/test_cram.py
@@ -11,10 +11,10 @@ from .util import (
 
 def test_cram():
     c = CRAM()
-    with get_input_files('2.cram') as input_files, get_dataset(input_files[0], index_attr='cram_index') as dataset:
+    with get_input_files("2.cram") as input_files, get_dataset(input_files[0], index_attr="cram_index") as dataset:
         assert os.path.exists(dataset.metadata.cram_index.file_name) is False
         c.set_index_file(dataset=dataset, index_file=dataset.metadata.cram_index)
         assert os.path.exists(dataset.metadata.cram_index.file_name) is True
         c.set_meta(dataset)
         pysam.AlignmentFile(dataset.file_name, index_filename=dataset.metadata.cram_index.file_name)
-    assert dataset.metadata.cram_version == '3.0'
+    assert dataset.metadata.cram_version == "3.0"
diff --git a/test/unit/data/datatypes/test_data.py b/test/unit/data/datatypes/test_data.py
index aead12719e9..26c5bc3d2cf 100644
--- a/test/unit/data/datatypes/test_data.py
+++ b/test/unit/data/datatypes/test_data.py
@@ -11,14 +11,17 @@ from galaxy.datatypes.data import (
 )
 from galaxy.datatypes.interval import (
     Bed,
-    BedStrict
+    BedStrict,
 )
 from galaxy.util import galaxy_directory
 
 
 def test_get_file_peek():
     # should get the first 5 lines of the file without a trailing newline character
-    assert get_file_peek(os.path.join(galaxy_directory(), 'test-data/1.tabular'), line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11\n'
+    assert (
+        get_file_peek(os.path.join(galaxy_directory(), "test-data/1.tabular"), line_wrap=False)
+        == "chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11\n"
+    )
 
 
 def test_is_datatype_change_allowed():
diff --git a/test/unit/data/datatypes/test_datatypes_registry.py b/test/unit/data/datatypes/test_datatypes_registry.py
index 606afca295b..1504a0a28b3 100644
--- a/test/unit/data/datatypes/test_datatypes_registry.py
+++ b/test/unit/data/datatypes/test_datatypes_registry.py
@@ -4,16 +4,16 @@ from galaxy.datatypes.registry import example_datatype_registry_for_sample
 
 def test_matches_any():
     datatypes_registry = example_datatype_registry_for_sample()
-    data_datatype = datatypes_registry.get_datatype_by_extension('data')
-    fasta_datatype = datatypes_registry.get_datatype_by_extension('fasta')
-    fastq_datatype = datatypes_registry.get_datatype_by_extension('fastq')
-    fastqsanger_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger')
-    fastqgz_datatype = datatypes_registry.get_datatype_by_extension('fastq.gz')
-    fastqbz2_datatype = datatypes_registry.get_datatype_by_extension('fastq.bz2')
-    fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger.gz')
-    fastqsangerbz2_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger.bz2')
-    h5_datatype = datatypes_registry.get_datatype_by_extension('h5')
-    mz5_datatype = datatypes_registry.get_datatype_by_extension('mz5')
+    data_datatype = datatypes_registry.get_datatype_by_extension("data")
+    fasta_datatype = datatypes_registry.get_datatype_by_extension("fasta")
+    fastq_datatype = datatypes_registry.get_datatype_by_extension("fastq")
+    fastqsanger_datatype = datatypes_registry.get_datatype_by_extension("fastqsanger")
+    fastqgz_datatype = datatypes_registry.get_datatype_by_extension("fastq.gz")
+    fastqbz2_datatype = datatypes_registry.get_datatype_by_extension("fastq.bz2")
+    fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension("fastqsanger.gz")
+    fastqsangerbz2_datatype = datatypes_registry.get_datatype_by_extension("fastqsanger.bz2")
+    h5_datatype = datatypes_registry.get_datatype_by_extension("h5")
+    mz5_datatype = datatypes_registry.get_datatype_by_extension("mz5")
 
     # Test empty list behavior.
     assert not fasta_datatype.matches_any([])
@@ -88,15 +88,15 @@ def test_sniff_compressed_dynamic_datatypes_default_on():
     # when coming from guess_ext.
     datatypes_registry = example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=True)
 
-    fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger.gz')
-    fname = sniff.get_test_fname('1.fastqsanger.gz')
+    fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension("fastqsanger.gz")
+    fname = sniff.get_test_fname("1.fastqsanger.gz")
     assert fastqsangergz_datatype.sniff(fname)
 
     sniff_order = datatypes_registry.sniff_order
-    fname = sniff.get_test_fname('1.fastqsanger.gz')
-    assert sniff.guess_ext(fname, sniff_order) == 'fastqsanger.gz'
-    fname = sniff.get_test_fname('1.fastqsanger.bz2')
-    assert sniff.guess_ext(fname, sniff_order) == 'fastqsanger.bz2'
+    fname = sniff.get_test_fname("1.fastqsanger.gz")
+    assert sniff.guess_ext(fname, sniff_order) == "fastqsanger.gz"
+    fname = sniff.get_test_fname("1.fastqsanger.bz2")
+    assert sniff.guess_ext(fname, sniff_order) == "fastqsanger.bz2"
 
 
 def test_sniff_compressed_dynamic_datatypes_default_off():
@@ -104,13 +104,13 @@ def test_sniff_compressed_dynamic_datatypes_default_off():
     datatypes_registry = example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=False)
 
     # sniffer still returns True for these files...
-    fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger.gz')
-    fname = sniff.get_test_fname('1.fastqsanger.gz')
+    fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension("fastqsanger.gz")
+    fname = sniff.get_test_fname("1.fastqsanger.gz")
     assert fastqsangergz_datatype.sniff(fname)
 
     # but they don't report as matching the specified sniff_order.
     sniff_order = datatypes_registry.sniff_order
-    fname = sniff.get_test_fname('1.fastqsanger.gz')
-    assert 'fastq' not in sniff.guess_ext(fname, sniff_order)
-    fname = sniff.get_test_fname('1.fastqsanger.bz2')
-    assert 'fastq' not in sniff.guess_ext(fname, sniff_order)
+    fname = sniff.get_test_fname("1.fastqsanger.gz")
+    assert "fastq" not in sniff.guess_ext(fname, sniff_order)
+    fname = sniff.get_test_fname("1.fastqsanger.bz2")
+    assert "fastq" not in sniff.guess_ext(fname, sniff_order)
diff --git a/test/unit/data/datatypes/test_sniff.py b/test/unit/data/datatypes/test_sniff.py
index 42c794ac3fd..c45fc2e60f8 100644
--- a/test/unit/data/datatypes/test_sniff.py
+++ b/test/unit/data/datatypes/test_sniff.py
@@ -10,8 +10,8 @@ from galaxy.datatypes.sniff import (
 )
 
 
-def assert_converts_to_1234_convert_sep2tabs(content, expected='1\t2\n3\t4\n'):
-    with tempfile.NamedTemporaryFile(delete=False, mode='w') as tf:
+def assert_converts_to_1234_convert_sep2tabs(content, expected="1\t2\n3\t4\n"):
+    with tempfile.NamedTemporaryFile(delete=False, mode="w") as tf:
         tf.write(content)
     rval = convert_newlines_sep2tabs(tf.name, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
     assert expected == open(tf.name).read()
@@ -19,41 +19,44 @@ def assert_converts_to_1234_convert_sep2tabs(content, expected='1\t2\n3\t4\n'):
 
 
 def assert_converts_to_1234_convert(content, block_size=1024):
-    with tempfile.NamedTemporaryFile(delete=False, mode='w') as tf:
+    with tempfile.NamedTemporaryFile(delete=False, mode="w") as tf:
         tf.write(content)
     rval = convert_newlines(tf.name, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir(), block_size=block_size)
     actual_contents = open(tf.name).read()
-    assert '1 2\n3 4\n' == actual_contents, actual_contents
+    assert "1 2\n3 4\n" == actual_contents, actual_contents
     assert rval[0:2] == (2, None), f"rval != {rval} for {content}"
 
 
 def assert_converts_to_1234_convert_sep2tabs_only(content: bytes, expected: bytes):
-    with tempfile.NamedTemporaryFile(delete=False, mode='wb') as tf:
+    with tempfile.NamedTemporaryFile(delete=False, mode="wb") as tf:
         tf.write(content)
     convert_sep2tabs(tf.name, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
     assert expected == open(tf.name, "rb").read()
 
 
-@pytest.mark.parametrize('source,block_size', [
-    ("1 2\r3 4", None),
-    ("1 2\n3 4", None),
-    ("1 2\r\n3 4", None),
-    ("1 2\r3 4\r", None),
-    ("1 2\n3 4\n", None),
-    ("1 2\r\n3 4\r\n", None),
-    ("1 2\r3 4", 2),
-    ("1 2\n3 4", 2),
-    ("1 2\r\n3 4", 2),
-    ("1 2\r3 4\r", 2),
-    ("1 2\n3 4\n", 2),
-    ("1 2\r\n3 4\r\n", 2),
-    ("1 2\r3 4", 3),
-    ("1 2\n3 4", 3),
-    ("1 2\r\n3 4", 3),
-    ("1 2\r3 4\r", 3),
-    ("1 2\n3 4\n", 3),
-    ("1 2\r\n3 4\r\n", 3),
-])
+@pytest.mark.parametrize(
+    "source,block_size",
+    [
+        ("1 2\r3 4", None),
+        ("1 2\n3 4", None),
+        ("1 2\r\n3 4", None),
+        ("1 2\r3 4\r", None),
+        ("1 2\n3 4\n", None),
+        ("1 2\r\n3 4\r\n", None),
+        ("1 2\r3 4", 2),
+        ("1 2\n3 4", 2),
+        ("1 2\r\n3 4", 2),
+        ("1 2\r3 4\r", 2),
+        ("1 2\n3 4\n", 2),
+        ("1 2\r\n3 4\r\n", 2),
+        ("1 2\r3 4", 3),
+        ("1 2\n3 4", 3),
+        ("1 2\r\n3 4", 3),
+        ("1 2\r3 4\r", 3),
+        ("1 2\n3 4\n", 3),
+        ("1 2\r\n3 4\r\n", 3),
+    ],
+)
 def test_convert_newlines(source, block_size):
     # Verify ends with newline - with or without that on inputs - for any of
     # \r \\n or \\r\\n newlines.
@@ -71,15 +74,18 @@ def test_convert_newlines_non_utf():
     assert open(new_file, "rb").read() == open(get_test_fname("1imzml"), "rb").read()
 
 
-@pytest.mark.parametrize('source,expected', [
-    ("1 2\n3 4\n", None),
-    ("1    2\n3    4\n", None),
-    ("1\t2\n3\t4\n", None),
-    ("1\t2\r3\t4\r", None),
-    ("1\t2\r\n3\t4\r\n", None),
-    ("1    2\r\n3       4\r\n", None),
-    ("1 2     \n3 4 \n", '1\t2\t\n3\t4\t\n'),
-])
+@pytest.mark.parametrize(
+    "source,expected",
+    [
+        ("1 2\n3 4\n", None),
+        ("1    2\n3    4\n", None),
+        ("1\t2\n3\t4\n", None),
+        ("1\t2\r3\t4\r", None),
+        ("1\t2\r\n3\t4\r\n", None),
+        ("1    2\r\n3       4\r\n", None),
+        ("1 2     \n3 4 \n", "1\t2\t\n3\t4\t\n"),
+    ],
+)
 def test_convert_sep2tabs(source, expected):
     if expected:
         assert_converts_to_1234_convert_sep2tabs(source, expected=expected)
diff --git a/test/unit/data/datatypes/test_tabular.py b/test/unit/data/datatypes/test_tabular.py
index 3875e94f674..a41d8333e31 100644
--- a/test/unit/data/datatypes/test_tabular.py
+++ b/test/unit/data/datatypes/test_tabular.py
@@ -8,7 +8,7 @@ from .util import MockDataset
 
 
 def test_tabular_set_meta_large_file():
-    with tempfile.NamedTemporaryFile(mode='w') as test_file:
+    with tempfile.NamedTemporaryFile(mode="w") as test_file:
         for _ in range(MAX_DATA_LINES + 1):
             test_file.write("A\tB\n")
         test_file.flush()
diff --git a/test/unit/data/datatypes/test_validation.py b/test/unit/data/datatypes/test_validation.py
index 850bb8c1395..6640e7c1991 100644
--- a/test/unit/data/datatypes/test_validation.py
+++ b/test/unit/data/datatypes/test_validation.py
@@ -56,7 +56,6 @@ def _run_validation(extension, file_name):
 
 
 class MockDataset:
-
     def __init__(self, file_name, datatype):
         self.file_name = file_name
         self.datatype = datatype
diff --git a/test/unit/data/datatypes/test_vcf.py b/test/unit/data/datatypes/test_vcf.py
index f068591f229..0723013eead 100644
--- a/test/unit/data/datatypes/test_vcf.py
+++ b/test/unit/data/datatypes/test_vcf.py
@@ -13,7 +13,7 @@ from .util import (
 def test_vcf_sniff():
     vcf_datatype = Vcf()
     vcf_bgzip_datatype = VcfGz()
-    with get_input_files('1.vcf_bgzip', '1.vcf', 'vcf_gzipped.vcf.gz') as input_files:
+    with get_input_files("1.vcf_bgzip", "1.vcf", "vcf_gzipped.vcf.gz") as input_files:
         vcf_bgzip, uncompressed, compressed = input_files
         assert vcf_bgzip_datatype.sniff(vcf_bgzip) is True
         assert vcf_bgzip_datatype.sniff(uncompressed) is False
@@ -26,7 +26,9 @@ def test_vcf_sniff():
 
 def test_vcf_bgzip_set_meta():
     vcf_bgzip_datatype = VcfGz()
-    with get_input_files('1.vcf_bgzip') as input_files, get_dataset(input_files[0], index_attr='tabix_index') as dataset:
+    with get_input_files("1.vcf_bgzip") as input_files, get_dataset(
+        input_files[0], index_attr="tabix_index"
+    ) as dataset:
         vcf_bgzip_datatype.set_meta(dataset)
         f = pysam.VariantFile(dataset.file_name, index_filename=dataset.metadata.tabix_index.file_name)
         assert isinstance(f.index, pysam.libcbcf.TabixIndex) is True
diff --git a/test/unit/data/datatypes/util.py b/test/unit/data/datatypes/util.py
index d5d8b86a84a..87a66a027c5 100644
--- a/test/unit/data/datatypes/util.py
+++ b/test/unit/data/datatypes/util.py
@@ -28,7 +28,7 @@ class MockDataset:
 
 
 @contextmanager
-def get_dataset(filename, index_attr='bam_index', dataset_id=1, has_data=True):
+def get_dataset(filename, index_attr="bam_index", dataset_id=1, has_data=True):
     dataset = MockDataset(dataset_id)
     with get_input_files(filename) as input_files, get_tmp_path() as index_path:
         dataset.file_name = input_files[0]
@@ -39,7 +39,7 @@ def get_dataset(filename, index_attr='bam_index', dataset_id=1, has_data=True):
 
 
 @contextmanager
-def get_tmp_path(should_exist=False, suffix=''):
+def get_tmp_path(should_exist=False, suffix=""):
     with tempfile.NamedTemporaryFile(suffix=suffix) as temp:
         if not should_exist:
             os.remove(temp.name)
@@ -58,6 +58,6 @@ def get_input_files(*args):
         yield test_files
         new_md5_sums = [md5_hash_file(f) for f in test_files]
         for old_hash, new_hash, f in zip(md5_sums, new_md5_sums, test_files):
-            assert old_hash == new_hash, 'Unexpected change of content for file %s' % f
+            assert old_hash == new_hash, "Unexpected change of content for file %s" % f
     finally:
         shutil.rmtree(temp_dir, ignore_errors=True)
diff --git a/test/unit/data/model/common.py b/test/unit/data/model/common.py
index 3f9386b5fe8..20dcdbdf1fc 100644
--- a/test/unit/data/model/common.py
+++ b/test/unit/data/model/common.py
@@ -8,14 +8,12 @@ from galaxy.model.database_utils import sqlalchemy_engine
 
 # GALAXY_TEST_CONNECT_POSTGRES_URI='postgresql://postgres@localhost:5432/postgres' pytest test/unit/model
 skip_if_not_postgres_uri = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_CONNECT_POSTGRES_URI'),
-    reason="GALAXY_TEST_CONNECT_POSTGRES_URI not set"
+    not os.environ.get("GALAXY_TEST_CONNECT_POSTGRES_URI"), reason="GALAXY_TEST_CONNECT_POSTGRES_URI not set"
 )
 
 # GALAXY_TEST_CONNECT_MYSQL_URI='mysql+mysqldb://root@localhost/mysql' pytest test/unit/model
 skip_if_not_mysql_uri = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_CONNECT_MYSQL_URI'),
-    reason="GALAXY_TEST_CONNECT_MYSQL_URI not set"
+    not os.environ.get("GALAXY_TEST_CONNECT_MYSQL_URI"), reason="GALAXY_TEST_CONNECT_MYSQL_URI not set"
 )
 
 
@@ -26,8 +24,8 @@ def replace_database_in_url(url, database_name):
     Example: replace_database_in_url('foo/db1', 'db2') returns 'foo/db2'
     This will not work for unix domain connections.
     """
-    i = url.rfind('/')
-    return f'{url[:i]}/{database_name}'
+    i = url.rfind("/")
+    return f"{url[:i]}/{database_name}"
 
 
 def drop_database(db_url, database):
@@ -35,12 +33,12 @@ def drop_database(db_url, database):
 
     Used only for test purposes to cleanup after creating a test database.
     """
-    if db_url.startswith('postgresql') or db_url.startswith('mysql'):
+    if db_url.startswith("postgresql") or db_url.startswith("mysql"):
         with sqlalchemy_engine(db_url) as engine:
             preparer = IdentifierPreparer(engine.dialect)
             database = preparer.quote(database)
-            stmt = f'DROP DATABASE IF EXISTS {database}'
-            with engine.connect().execution_options(isolation_level='AUTOCOMMIT') as conn:
+            stmt = f"DROP DATABASE IF EXISTS {database}"
+            with engine.connect().execution_options(isolation_level="AUTOCOMMIT") as conn:
                 conn.execute(stmt)
     else:
         url = make_url(db_url)
diff --git a/test/unit/data/model/conftest.py b/test/unit/data/model/conftest.py
index 02f5252c7b1..4d780e0f3d4 100644
--- a/test/unit/data/model/conftest.py
+++ b/test/unit/data/model/conftest.py
@@ -6,19 +6,19 @@ import pytest
 
 @pytest.fixture
 def database_name():
-    return f'galaxytest_{uuid.uuid4().hex}'
+    return f"galaxytest_{uuid.uuid4().hex}"
 
 
 @pytest.fixture
 def postgres_url():
-    return os.environ.get('GALAXY_TEST_CONNECT_POSTGRES_URI')
+    return os.environ.get("GALAXY_TEST_CONNECT_POSTGRES_URI")
 
 
 @pytest.fixture
 def mysql_url():
-    return os.environ.get('GALAXY_TEST_CONNECT_MYSQL_URI')
+    return os.environ.get("GALAXY_TEST_CONNECT_MYSQL_URI")
 
 
 @pytest.fixture
 def sqlite_memory_url():
-    return 'sqlite:///:memory:'
+    return "sqlite:///:memory:"
diff --git a/test/unit/data/model/mapping/common.py b/test/unit/data/model/mapping/common.py
index b941e493bd7..bd672f3d54e 100644
--- a/test/unit/data/model/mapping/common.py
+++ b/test/unit/data/model/mapping/common.py
@@ -1,4 +1,7 @@
-from abc import ABC, abstractmethod
+from abc import (
+    ABC,
+    abstractmethod,
+)
 from contextlib import contextmanager
 from uuid import uuid4
 
@@ -117,7 +120,7 @@ def collection_consists_of_objects(collection, *objects):
     """
     if len(collection) != len(objects):  # False if lengths are different
         return False
-    if not collection:   # True if both are empty
+    if not collection:  # True if both are empty
         return True
 
     # Sort, then compare each member by its 'id' attribute, which must be its primary key.
diff --git a/test/unit/data/model/mapping/conftest.py b/test/unit/data/model/mapping/conftest.py
index 5f4ad43c8e7..0bdb28e6abc 100644
--- a/test/unit/data/model/mapping/conftest.py
+++ b/test/unit/data/model/mapping/conftest.py
@@ -1,11 +1,14 @@
 import pytest
 from sqlalchemy import create_engine
-from sqlalchemy.orm import scoped_session, sessionmaker
+from sqlalchemy.orm import (
+    scoped_session,
+    sessionmaker,
+)
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def engine():
-    db_uri = 'sqlite:///:memory:'
+    db_uri = "sqlite:///:memory:"
     return create_engine(db_uri)
 
 
diff --git a/test/unit/data/model/mapping/test_common.py b/test/unit/data/model/mapping/test_common.py
index 4389b22e9df..ced80427fdc 100644
--- a/test/unit/data/model/mapping/test_common.py
+++ b/test/unit/data/model/mapping/test_common.py
@@ -11,10 +11,13 @@ from sqlalchemy import (
     Index,
     Integer,
     select,
-    UniqueConstraint
+    UniqueConstraint,
 )
 from sqlalchemy.exc import NoResultFound
-from sqlalchemy.orm import registry, Session
+from sqlalchemy.orm import (
+    registry,
+    Session,
+)
 
 from galaxy.model import _HasTable
 from .common import (
@@ -50,7 +53,7 @@ def test_get_stored_obj_must_have_obj_id_xor_where_clause():
     Verify that function must be called with either obj_id or where_clause, but not both.
     """
     with pytest.raises(AssertionError):
-        get_stored_obj(None, None, obj_id=1, where_clause='a')
+        get_stored_obj(None, None, obj_id=1, where_clause="a")
     with pytest.raises(AssertionError):
         get_stored_obj(None, None, obj_id=None, where_clause=None)
 
@@ -136,6 +139,7 @@ def test_dbcleanup_wrapper(session):
     Verify dbcleanup_wrapper has same effect as dbcleanup context manager,
     and yields the object instance.
     """
+
     @contextmanager  # we need a context manager to similate scope
     def managed(a, b):
         yield from dbcleanup_wrapper(a, b)
@@ -153,13 +157,13 @@ def test_dbcleanup_wrapper(session):
 
 
 def test_has_index(session):
-    assert has_index(Bar.__table__, ('field1',))
-    assert not has_index(Foo.__table__, ('field1',))
+    assert has_index(Bar.__table__, ("field1",))
+    assert not has_index(Foo.__table__, ("field1",))
 
 
 def test_has_unique_constraint(session):
-    assert has_unique_constraint(Bar.__table__, ('field2',))
-    assert not has_unique_constraint(Foo.__table__, ('field1',))
+    assert has_unique_constraint(Bar.__table__, ("field2",))
+    assert not has_unique_constraint(Foo.__table__, ("field1",))
 
 
 def test_collection_consists_of_objects(session):
@@ -204,31 +208,31 @@ mapper_registry = registry()
 
 @mapper_registry.mapped
 class Foo(_HasTable):
-    __tablename__ = 'foo'
+    __tablename__ = "foo"
     id = Column(Integer, primary_key=True)
     field1 = Column(Integer)
 
 
 @mapper_registry.mapped
 class Bar(_HasTable):
-    __tablename__ = 'bar'
+    __tablename__ = "bar"
     id = Column(Integer, primary_key=True)
     field1 = Column(Integer)
     field2 = Column(Integer)
     __table_args__ = (
-        Index('ix', 'field1'),
-        UniqueConstraint('field2'),
+        Index("ix", "field1"),
+        UniqueConstraint("field2"),
     )
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def engine():
     """Create connection engine. (Fixture is module-scoped)."""
-    db_uri = 'sqlite:///:memory:'  # We only need sqlite for these tests
+    db_uri = "sqlite:///:memory:"  # We only need sqlite for these tests
     return create_engine(db_uri)
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def init(engine):
     """Create database objects. (Fixture is module-scoped)."""
     mapper_registry.metadata.create_all(engine)
diff --git a/test/unit/data/model/mapping/test_install_model_mapping.py b/test/unit/data/model/mapping/test_install_model_mapping.py
index ec167c4dc58..e873b19949a 100644
--- a/test/unit/data/model/mapping/test_install_model_mapping.py
+++ b/test/unit/data/model/mapping/test_install_model_mapping.py
@@ -2,7 +2,10 @@
 See documentation + annotated examples for these tests in test_model_mapping.py.
 """
 
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 
 import pytest
 
@@ -18,34 +21,32 @@ from .common import (
 
 
 class BaseTest(AbstractBaseTest):
-
     def get_model(self):
         return model
 
 
 class TestToolShedRepository(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'tool_shed_repository'
+        assert cls_.__tablename__ == "tool_shed_repository"
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        tool_shed = 'a'
-        name = 'b'
-        description = 'c'
-        owner = 'd'
-        installed_changeset_revision = 'e'
-        changeset_revision = 'f'
-        ctx_rev = 'g'
-        metadata_ = 'h'
+        tool_shed = "a"
+        name = "b"
+        description = "c"
+        owner = "d"
+        installed_changeset_revision = "e"
+        changeset_revision = "f"
+        ctx_rev = "g"
+        metadata_ = "h"
         includes_datatypes = True
-        tool_shed_status = 'i'
+        tool_shed_status = "i"
         deleted = True
         uninstalled = True
         dist_to_shed = True
-        status = 'j'
-        error_message = 'k'
+        status = "j"
+        error_message = "k"
 
         obj = cls_()
         obj.create_time = create_time
@@ -89,7 +90,8 @@ class TestToolShedRepository(BaseTest):
 
     def test_relationships(
         self,
-        session, cls_,
+        session,
+        cls_,
         repository,
         tool_version,
         tool_dependency,
@@ -105,13 +107,13 @@ class TestToolShedRepository(BaseTest):
             assert collection_consists_of_objects(stored_obj.tool_versions, tool_version)
             assert collection_consists_of_objects(stored_obj.tool_dependencies, tool_dependency)
             assert collection_consists_of_objects(
-                stored_obj.required_repositories, repository_repository_dependency_association)
+                stored_obj.required_repositories, repository_repository_dependency_association
+            )
 
 
 class TestRepositoryRepositoryDependencyAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository_repository_dependency_association'
+        assert cls_.__tablename__ == "repository_repository_dependency_association"
 
     def test_columns(self, session, cls_, repository, repository_dependency):
         create_time = datetime.now()
@@ -142,9 +144,8 @@ class TestRepositoryRepositoryDependencyAssociation(BaseTest):
 
 
 class TestRepositoryDependency(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository_dependency'
+        assert cls_.__tablename__ == "repository_dependency"
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()
@@ -171,14 +172,13 @@ class TestRepositoryDependency(BaseTest):
 
 
 class TestToolDependency(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'tool_dependency'
+        assert cls_.__tablename__ == "tool_dependency"
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        name, version, type, status, error_message = 'a', 'b', 'c', 'd', 'e'
+        name, version, type, status, error_message = "a", "b", "c", "d", "e"
         obj = cls_()
         obj.create_time = create_time
         obj.update_time = update_time
@@ -204,7 +204,7 @@ class TestToolDependency(BaseTest):
     def test_relationships(self, session, cls_, repository):
         obj = cls_()
         obj.tool_shed_repository = repository
-        obj.status = 'a'
+        obj.status = "a"
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
@@ -212,14 +212,13 @@ class TestToolDependency(BaseTest):
 
 
 class TestToolVersion(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'tool_version'
+        assert cls_.__tablename__ == "tool_version"
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        tool_id = 'a'
+        tool_id = "a"
         obj = cls_()
         obj.create_time = create_time
         obj.update_time = update_time
@@ -265,9 +264,8 @@ class TestToolVersion(BaseTest):
 
 
 class TestToolVersionAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'tool_version_association'
+        assert cls_.__tablename__ == "tool_version_association"
 
     def test_columns(self, session, cls_, tool_version_factory):
         tool_version = tool_version_factory()
@@ -292,13 +290,15 @@ class TestToolVersionAssociation(BaseTest):
 
 # Misc. helper fixtures.
 
-@pytest.fixture(scope='module')
+
+@pytest.fixture(scope="module")
 def init_model(engine):
     model.mapper_registry.metadata.create_all(engine)
 
 
 # Fixtures yielding persisted instances of models, deleted from the database on test exit.
 
+
 @pytest.fixture
 def repository(session):
     instance = model.ToolShedRepository()
@@ -322,7 +322,7 @@ def repository_dependency(session, repository):
 def tool_dependency(session, repository):
     instance = model.ToolDependency()
     instance.tool_shed_repository = repository
-    instance.status = 'a'
+    instance.status = "a"
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -334,10 +334,12 @@ def tool_version(session):
 
 # Fixtures yielding factory functions.
 
+
 @pytest.fixture
 def tool_version_association_factory():
     def make_instance(*args, **kwds):
         return model.ToolVersionAssociation(*args, **kwds)
+
     return make_instance
 
 
@@ -345,4 +347,5 @@ def tool_version_association_factory():
 def tool_version_factory():
     def make_instance(*args, **kwds):
         return model.ToolVersion(*args, **kwds)
+
     return make_instance
diff --git a/test/unit/data/model/mapping/test_model_mapping.py b/test/unit/data/model/mapping/test_model_mapping.py
index 8793c46df29..8db4c8eae9e 100644
--- a/test/unit/data/model/mapping/test_model_mapping.py
+++ b/test/unit/data/model/mapping/test_model_mapping.py
@@ -60,11 +60,20 @@ class TestPlanet(BaseTest):  # BaseTest is a base class; we need it to get the t
 See other model tests in this module for examples of more complex setups.
 """
 
-from datetime import datetime, timedelta
-from uuid import UUID, uuid4
+from datetime import (
+    datetime,
+    timedelta,
+)
+from uuid import (
+    UUID,
+    uuid4,
+)
 
 import pytest
-from sqlalchemy import func, select
+from sqlalchemy import (
+    func,
+    select,
+)
 
 from galaxy import model
 from .common import (
@@ -82,7 +91,6 @@ from .common import (
 
 
 class BaseTest(AbstractBaseTest):
-
     def get_model(self):
         return model
 
@@ -189,9 +197,7 @@ class TestCleanupEventImplicitlyConvertedDatasetAssociationAssociation(BaseTest)
     def test_table(self, cls_):
         assert cls_.__tablename__ == "cleanup_event_icda_association"
 
-    def test_columns(
-        self, session, cls_, cleanup_event, implicitly_converted_dataset_association
-    ):
+    def test_columns(self, session, cls_, cleanup_event, implicitly_converted_dataset_association):
         create_time = datetime.now()
         obj = cls_(
             create_time=create_time,
@@ -251,9 +257,7 @@ class TestCleanupEventLibraryDatasetDatasetAssociationAssociation(BaseTest):
     def test_table(self, cls_):
         assert cls_.__tablename__ == "cleanup_event_ldda_association"
 
-    def test_columns(
-        self, session, cls_, cleanup_event, library_dataset_dataset_association
-    ):
+    def test_columns(self, session, cls_, cleanup_event, library_dataset_dataset_association):
         create_time = datetime.now()
         obj = cls_(
             create_time=create_time,
@@ -311,9 +315,7 @@ class TestCleanupEventMetadataFileAssociation(BaseTest):
 class TestCustosAuthnzToken(BaseTest):
     def test_table(self, cls_):
         assert cls_.__tablename__ == "custos_authnz_token"
-        assert has_unique_constraint(
-            cls_.__table__, ("user_id", "external_user_id", "provider")
-        )
+        assert has_unique_constraint(cls_.__table__, ("user_id", "external_user_id", "provider"))
         assert has_unique_constraint(cls_.__table__, ("external_user_id", "provider"))
 
     def test_columns(self, session, cls_, user):
@@ -529,12 +531,8 @@ class TestDataset(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.job.id == job.id
-            assert collection_consists_of_objects(
-                stored_obj.actions, dataset_permission
-            )
-            assert collection_consists_of_objects(
-                stored_obj.active_history_associations, history_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.actions, dataset_permission)
+            assert collection_consists_of_objects(stored_obj.active_history_associations, history_dataset_association)
             assert stored_obj.purged_history_associations[0].id == hda.id
             assert collection_consists_of_objects(
                 stored_obj.active_library_associations,
@@ -542,12 +540,8 @@ class TestDataset(BaseTest):
             )
             assert collection_consists_of_objects(stored_obj.hashes, dataset_hash)
             assert collection_consists_of_objects(stored_obj.sources, dataset_source)
-            assert collection_consists_of_objects(
-                stored_obj.library_associations, library_dataset_dataset_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.history_associations, hda, history_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.library_associations, library_dataset_dataset_association)
+            assert collection_consists_of_objects(stored_obj.history_associations, hda, history_dataset_association)
 
         delete_from_database(session, hda)
 
@@ -594,9 +588,7 @@ class TestDatasetCollection(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert collection_consists_of_objects(
-                stored_obj.elements, dataset_collection_element
-            )
+            assert collection_consists_of_objects(stored_obj.elements, dataset_collection_element)
 
 
 class TestDatasetCollectionElement(BaseTest):
@@ -613,9 +605,7 @@ class TestDatasetCollectionElement(BaseTest):
         dataset_collection_factory,
     ):
         element_index, element_identifier = 1, "a"
-        obj = cls_(
-            element=history_dataset_association
-        )  # using hda is sufficient for this test
+        obj = cls_(element=history_dataset_association)  # using hda is sufficient for this test
         obj.element_index = element_index
         obj.element_identifier = element_identifier
         obj.hda = history_dataset_association
@@ -647,17 +637,13 @@ class TestDatasetCollectionElement(BaseTest):
         library_dataset_dataset_association,
         dataset_collection_factory,
     ):
-        obj = cls_(
-            element=history_dataset_association
-        )  # using hda is sufficient for this test
+        obj = cls_(element=history_dataset_association)  # using hda is sufficient for this test
         obj.hda = history_dataset_association
         obj.ldda = library_dataset_dataset_association
         obj.child_collection = dataset_collection
 
         parent_collection = dataset_collection_factory()
-        obj.collection = (
-            parent_collection  # same as parent_collection.elements.append(obj)
-        )
+        obj.collection = parent_collection  # same as parent_collection.elements.append(obj)
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
@@ -755,9 +741,7 @@ class TestDatasetSource(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.dataset.id == dataset.id
-            assert collection_consists_of_objects(
-                stored_obj.hashes, dataset_source_hash
-            )
+            assert collection_consists_of_objects(stored_obj.hashes, dataset_source_hash)
 
 
 class TestDatasetSourceHash(BaseTest):
@@ -984,9 +968,7 @@ class TestExtendedMetadata(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert collection_consists_of_objects(
-                stored_obj.children, extended_metadata_index
-            )
+            assert collection_consists_of_objects(stored_obj.children, extended_metadata_index)
 
 
 class TestExtendedMetadataIndex(BaseTest):
@@ -1128,9 +1110,7 @@ class TestGalaxySession(BaseTest):
         disk_usage = 9
         last_action = update_time + timedelta(hours=1)
 
-        obj = cls_(
-            user=user, current_history=history, prev_session_id=galaxy_session.id
-        )
+        obj = cls_(user=user, current_history=history, prev_session_id=galaxy_session.id)
 
         obj.create_time = create_time
         obj.update_time = update_time
@@ -1158,9 +1138,7 @@ class TestGalaxySession(BaseTest):
             assert stored_obj.disk_usage == disk_usage
             assert stored_obj.last_action == last_action
 
-    def test_relationships(
-        self, session, cls_, user, history, galaxy_session_history_association
-    ):
+    def test_relationships(self, session, cls_, user, history, galaxy_session_history_association):
         obj = cls_(user=user, current_history=history)
         obj.session_key = get_unique_value()
         obj.histories.append(galaxy_session_history_association)
@@ -1169,9 +1147,7 @@ class TestGalaxySession(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.user.id == user.id
             assert stored_obj.current_history.id == history.id
-            assert collection_consists_of_objects(
-                stored_obj.histories, galaxy_session_history_association
-            )
+            assert collection_consists_of_objects(stored_obj.histories, galaxy_session_history_association)
 
 
 class TestGalaxySessionToHistoryAssociation(BaseTest):
@@ -1281,15 +1257,9 @@ class TestGroup(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert collection_consists_of_objects(
-                stored_obj.quotas, group_quota_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.roles, group_role_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.users, user_group_association
-            )
+            assert collection_consists_of_objects(stored_obj.quotas, group_quota_association)
+            assert collection_consists_of_objects(stored_obj.roles, group_role_association)
+            assert collection_consists_of_objects(stored_obj.users, user_group_association)
 
 
 class TestGroupQuotaAssociation(BaseTest):
@@ -1426,58 +1396,32 @@ class TestHistory(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.user.id == user.id
-            assert collection_consists_of_objects(
-                stored_obj.datasets, history_dataset_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.exports, job_export_history_archive
-            )
-            assert collection_consists_of_objects(
-                stored_obj.active_datasets, history_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.datasets, history_dataset_association)
+            assert collection_consists_of_objects(stored_obj.exports, job_export_history_archive)
+            assert collection_consists_of_objects(stored_obj.active_datasets, history_dataset_association)
             assert collection_consists_of_objects(
                 stored_obj.active_dataset_collections,
                 history_dataset_collection_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.visible_datasets, history_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.visible_datasets, history_dataset_association)
             assert collection_consists_of_objects(
                 stored_obj.visible_dataset_collections,
                 history_dataset_collection_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.tags, history_tag_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.annotations, history_annotation_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, history_rating_association
-            )
+            assert collection_consists_of_objects(stored_obj.tags, history_tag_association)
+            assert collection_consists_of_objects(stored_obj.annotations, history_annotation_association)
+            assert collection_consists_of_objects(stored_obj.ratings, history_rating_association)
             # This doesn't test the average amount, just the mapping.
             assert stored_obj.average_rating == history_rating_association.rating
             assert stored_obj.users_shared_with_count == 1
-            assert collection_consists_of_objects(
-                stored_obj.users_shared_with, history_user_share_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.default_permissions, default_history_permissions
-            )
-            assert collection_consists_of_objects(
-                stored_obj.galaxy_sessions, galaxy_session_history_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.workflow_invocations, workflow_invocation
-            )
+            assert collection_consists_of_objects(stored_obj.users_shared_with, history_user_share_association)
+            assert collection_consists_of_objects(stored_obj.default_permissions, default_history_permissions)
+            assert collection_consists_of_objects(stored_obj.galaxy_sessions, galaxy_session_history_association)
+            assert collection_consists_of_objects(stored_obj.workflow_invocations, workflow_invocation)
             assert collection_consists_of_objects(stored_obj.jobs, job)
 
-    def test_average_rating(
-        self, session, history, user, history_rating_association_factory
-    ):
-        _run_average_rating_test(
-            session, history, user, history_rating_association_factory
-        )
+    def test_average_rating(self, session, history, user, history_rating_association_factory):
+        _run_average_rating_test(session, history, user, history_rating_association_factory)
 
 
 class TestHistoryAnnotationAssociation(BaseTest):
@@ -1555,9 +1499,7 @@ class TestHistoryDatasetAssociation(BaseTest):
         obj.update_time = update_time
         obj.state = state
         obj.copied_from_history_dataset_association = copied_from_hda
-        obj.copied_from_library_dataset_dataset_association = (
-            library_dataset_dataset_association
-        )
+        obj.copied_from_library_dataset_dataset_association = library_dataset_dataset_association
         obj.name = name
         obj.info = info
         obj.blurb = blurb
@@ -1585,13 +1527,9 @@ class TestHistoryDatasetAssociation(BaseTest):
             assert stored_obj.create_time == create_time
             assert stored_obj.update_time == update_time
             assert stored_obj.state == state
+            assert stored_obj.copied_from_history_dataset_association_id == copied_from_hda.id
             assert (
-                stored_obj.copied_from_history_dataset_association_id
-                == copied_from_hda.id
-            )
-            assert (
-                stored_obj.copied_from_library_dataset_dataset_association_id
-                == library_dataset_dataset_association.id
+                stored_obj.copied_from_library_dataset_dataset_association_id == library_dataset_dataset_association.id
             )
             assert stored_obj.name == name
             assert stored_obj.info == info
@@ -1610,10 +1548,7 @@ class TestHistoryDatasetAssociation(BaseTest):
             assert stored_obj.purged == purged
             assert stored_obj.validated_state == validated_state
             assert stored_obj.validated_state_message == validated_state_message
-            assert (
-                stored_obj.hidden_beneath_collection_instance_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.hidden_beneath_collection_instance_id == history_dataset_collection_association.id
 
         delete_from_database(session, [copied_from_hda, parent])
 
@@ -1672,57 +1607,34 @@ class TestHistoryDatasetAssociation(BaseTest):
             assert stored_obj.id == obj_id
             assert stored_obj.history.id == history.id
             assert stored_obj.dataset.id == dataset.id
-            assert (
-                stored_obj.copied_from_history_dataset_association.id
-                == copied_from_hda.id
-            )
-            assert (
-                stored_obj.copied_from_library_dataset_dataset_association.id
-                == copied_from_ldda.id
-            )
+            assert stored_obj.copied_from_history_dataset_association.id == copied_from_hda.id
+            assert stored_obj.copied_from_library_dataset_dataset_association.id == copied_from_ldda.id
             assert stored_obj.extended_metadata.id == extended_metadata.id
-            assert (
-                stored_obj.hidden_beneath_collection_instance.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.hidden_beneath_collection_instance.id == history_dataset_collection_association.id
             assert collection_consists_of_objects(
                 stored_obj.copied_to_library_dataset_dataset_associations,
                 copied_to_ldda,
             )
-            assert collection_consists_of_objects(
-                stored_obj.copied_to_history_dataset_associations, copied_to_hda
-            )
-            assert collection_consists_of_objects(
-                stored_obj.tags, history_dataset_association_tag_association
-            )
+            assert collection_consists_of_objects(stored_obj.copied_to_history_dataset_associations, copied_to_hda)
+            assert collection_consists_of_objects(stored_obj.tags, history_dataset_association_tag_association)
             assert collection_consists_of_objects(
                 stored_obj.annotations,
                 history_dataset_association_annotation_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, history_dataset_association_rating_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.dependent_jobs, job_to_input_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.ratings, history_dataset_association_rating_association)
+            assert collection_consists_of_objects(stored_obj.dependent_jobs, job_to_input_dataset_association)
             assert collection_consists_of_objects(
                 stored_obj.creating_job_associations, job_to_output_dataset_association
             )
-            assert collection_consists_of_objects(
-                stored_obj.implicitly_converted_datasets, icda
-            )
-            assert collection_consists_of_objects(
-                stored_obj.implicitly_converted_parent_datasets, icpda
-            )
+            assert collection_consists_of_objects(stored_obj.implicitly_converted_datasets, icda)
+            assert collection_consists_of_objects(stored_obj.implicitly_converted_parent_datasets, icpda)
 
         delete_from_database(session, persisted)
 
 
 class TestHistoryDatasetAssociationAnnotationAssociation(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__ == "history_dataset_association_annotation_association"
-        )
+        assert cls_.__tablename__ == "history_dataset_association_annotation_association"
         assert has_index(cls_.__table__, ("annotation",))
 
     def test_columns(self, session, cls_, history_dataset_association, user):
@@ -1735,10 +1647,7 @@ class TestHistoryDatasetAssociationAnnotationAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_association_id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association_id == history_dataset_association.id
             assert stored_obj.user_id == user.id
             assert stored_obj.annotation == annotation
 
@@ -1755,9 +1664,7 @@ class TestHistoryDatasetAssociationAnnotationAssociation(BaseTest):
 
 class TestHistoryDatasetAssociationDisplayAtAuthorization(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__ == "history_dataset_association_display_at_authorization"
-        )
+        assert cls_.__tablename__ == "history_dataset_association_display_at_authorization"
 
     def test_columns(self, session, cls_, history_dataset_association, user):
         create_time = datetime.now()
@@ -1770,10 +1677,7 @@ class TestHistoryDatasetAssociationDisplayAtAuthorization(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_association_id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association_id == history_dataset_association.id
             assert stored_obj.user_id == user.id
             assert stored_obj.site == site
 
@@ -1782,10 +1686,7 @@ class TestHistoryDatasetAssociationDisplayAtAuthorization(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.history_dataset_association.id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association.id == history_dataset_association.id
             assert stored_obj.user.id == user.id
 
 
@@ -1793,9 +1694,7 @@ class TestHistoryDatasetAssociationHistory(BaseTest):
     def test_table(self, cls_):
         assert cls_.__tablename__ == "history_dataset_association_history"
 
-    def test_columns(
-        self, session, cls_, history_dataset_association, extended_metadata
-    ):
+    def test_columns(self, session, cls_, history_dataset_association, extended_metadata):
         name, update_time, version, extension, metadata = (
             "a",
             datetime.now(),
@@ -1817,10 +1716,7 @@ class TestHistoryDatasetAssociationHistory(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_association_id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association_id == history_dataset_association.id
             assert stored_obj.name == name
             assert stored_obj.update_time == update_time
             assert stored_obj.version == version
@@ -1848,10 +1744,7 @@ class TestHistoryDatasetAssociationRatingAssociation(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.history_dataset_association.id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association.id == history_dataset_association.id
             assert stored_obj.user.id == user.id
 
 
@@ -1875,10 +1768,7 @@ class TestHistoryDatasetAssociationSubset(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_association_id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association_id == history_dataset_association.id
             assert stored_obj.history_dataset_association_subset_id == hda_subset.id
             assert stored_obj.location == location
 
@@ -1922,10 +1812,7 @@ class TestHistoryDatasetAssociationTagAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_association_id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association_id == history_dataset_association.id
             assert stored_obj.tag_id == tag.id
             assert stored_obj.user_id == user.id
             assert stored_obj.user_tname == user_tname
@@ -1938,10 +1825,7 @@ class TestHistoryDatasetAssociationTagAssociation(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.history_dataset_association.id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association.id == history_dataset_association.id
             assert stored_obj.tag.id == tag.id
             assert stored_obj.user.id == user.id
 
@@ -1975,9 +1859,7 @@ class TestHistoryDatasetCollectionAssociation(BaseTest):
         obj.hid = hid
         obj.visible = visible
         obj.deleted = deleted
-        obj.copied_from_history_dataset_collection_association = (
-            history_dataset_collection_association
-        )
+        obj.copied_from_history_dataset_collection_association = history_dataset_collection_association
         obj.implicit_output_name = implicit_output_name
         obj.job = job
         obj.implicit_collection_jobs = implicit_collection_jobs
@@ -2024,15 +1906,11 @@ class TestHistoryDatasetCollectionAssociation(BaseTest):
         obj = cls_()
         obj.collection = dataset_collection
         obj.history = history
-        obj.copied_from_history_dataset_collection_association = (
-            history_dataset_collection_association
-        )
+        obj.copied_from_history_dataset_collection_association = history_dataset_collection_association
         obj.copied_to_history_dataset_collection_association.append(copied_to_hdca)
         obj.job = job
         obj.implicit_collection_jobs = implicit_collection_jobs
-        obj.implicit_input_collections.append(
-            implicitly_created_dataset_collection_input
-        )
+        obj.implicit_input_collections.append(implicitly_created_dataset_collection_input)
         obj.tags.append(history_dataset_collection_tag_association)
         obj.annotations.append(history_dataset_collection_annotation_association)
         obj.ratings.append(history_dataset_collection_rating_association)
@@ -2055,16 +1933,12 @@ class TestHistoryDatasetCollectionAssociation(BaseTest):
                 stored_obj.implicit_input_collections,
                 implicitly_created_dataset_collection_input,
             )
-            assert collection_consists_of_objects(
-                stored_obj.tags, history_dataset_collection_tag_association
-            )
+            assert collection_consists_of_objects(stored_obj.tags, history_dataset_collection_tag_association)
             assert collection_consists_of_objects(
                 stored_obj.annotations,
                 history_dataset_collection_annotation_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, history_dataset_collection_rating_association
-            )
+            assert collection_consists_of_objects(stored_obj.ratings, history_dataset_collection_rating_association)
             # stored_obj.job_state_summary is a view: can't test in this setup.
 
         delete_from_database(session, copied_to_hdca)
@@ -2084,26 +1958,18 @@ class TestHistoryDatasetCollectionAssociationAnnotationAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.history_dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.user_id == user.id
             assert stored_obj.annotation == annotation
 
-    def test_relationships(
-        self, session, cls_, history_dataset_collection_association, user
-    ):
+    def test_relationships(self, session, cls_, history_dataset_collection_association, user):
         obj = cls_()
         obj.user = user
         obj.history_dataset_collection = history_dataset_collection_association
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.history_dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.history_dataset_collection.id == history_dataset_collection_association.id
             assert stored_obj.user.id == user.id
 
 
@@ -2118,24 +1984,16 @@ class TestHistoryDatasetCollectionRatingAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.history_dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.user.id == user.id
             assert stored_obj.rating == rating
 
-    def test_relationships(
-        self, session, cls_, history_dataset_collection_association, user
-    ):
+    def test_relationships(self, session, cls_, history_dataset_collection_association, user):
         obj = cls_(user, history_dataset_collection_association, 1)
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == history_dataset_collection_association.id
             assert stored_obj.user.id == user.id
 
 
@@ -2143,9 +2001,7 @@ class TestHistoryDatasetCollectionTagAssociation(BaseTest):
     def test_table(self, cls_):
         assert cls_.__tablename__ == "history_dataset_collection_tag_association"
 
-    def test_columns(
-        self, session, cls_, history_dataset_collection_association, tag, user
-    ):
+    def test_columns(self, session, cls_, history_dataset_collection_association, tag, user):
         user_tname, value, user_value = "a", "b", "c"
         obj = cls_(
             user=user,
@@ -2159,28 +2015,20 @@ class TestHistoryDatasetCollectionTagAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.history_dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.history_dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.tag_id == tag.id
             assert stored_obj.user_id == user.id
             assert stored_obj.user_tname == user_tname
             assert stored_obj.value == value
             assert stored_obj.user_value == user_value
 
-    def test_relationships(
-        self, session, cls_, history_dataset_collection_association, tag, user
-    ):
+    def test_relationships(self, session, cls_, history_dataset_collection_association, tag, user):
         obj = cls_(user=user, tag=tag)
         obj.dataset_collection = history_dataset_collection_association
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == history_dataset_collection_association.id
             assert stored_obj.tag.id == tag.id
             assert stored_obj.user.id == user.id
 
@@ -2291,9 +2139,7 @@ class TestImplicitCollectionJobs(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert collection_consists_of_objects(
-                stored_obj.jobs, implicit_collection_jobs_job_association
-            )
+            assert collection_consists_of_objects(stored_obj.jobs, implicit_collection_jobs_job_association)
 
 
 class TestImplicitCollectionJobsJobAssociation(BaseTest):
@@ -2412,10 +2258,7 @@ class TestImplicitlyCreatedDatasetCollectionInput(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.input_dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.input_dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.dataset_collection_id == hdca2.id
             assert stored_obj.name == name
 
@@ -2431,10 +2274,7 @@ class TestImplicitlyCreatedDatasetCollectionInput(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.input_dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.input_dataset_collection.id == history_dataset_collection_association.id
 
 
 class TestInteractiveToolEntryPoint(BaseTest):
@@ -2649,18 +2489,10 @@ class TestJob(BaseTest):
         obj.user = user
         obj.parameters.append(job_parameter)
         obj.input_datasets.append(job_to_input_dataset_association)
-        obj.input_dataset_collections.append(
-            job_to_input_dataset_collection_association
-        )
-        obj.input_dataset_collection_elements.append(
-            job_to_input_dataset_collection_element_association
-        )
-        obj.output_dataset_collection_instances.append(
-            job_to_output_dataset_collection_association
-        )
-        obj.output_dataset_collections.append(
-            job_to_implicit_output_dataset_collection_association
-        )
+        obj.input_dataset_collections.append(job_to_input_dataset_collection_association)
+        obj.input_dataset_collection_elements.append(job_to_input_dataset_collection_element_association)
+        obj.output_dataset_collection_instances.append(job_to_output_dataset_collection_association)
+        obj.output_dataset_collections.append(job_to_implicit_output_dataset_collection_association)
         obj.post_job_actions.append(post_job_action_association)
         obj.input_library_datasets.append(job_to_input_library_dataset_association)
         obj.output_library_datasets.append(job_to_output_library_dataset_association)
@@ -2671,14 +2503,10 @@ class TestJob(BaseTest):
         obj.text_metrics.append(job_metric_text)
         obj.numeric_metrics.append(job_metric_numeric)
         obj.interactivetool_entry_points.append(interactive_tool_entry_point)
-        obj.implicit_collection_jobs_association = (
-            implicit_collection_jobs_job_association
-        )
+        obj.implicit_collection_jobs_association = implicit_collection_jobs_job_association
         obj.container = job_container_association
         obj.data_manager_association = data_manager_job_association
-        obj.history_dataset_collection_associations.append(
-            history_dataset_collection_association
-        )
+        obj.history_dataset_collection_associations.append(history_dataset_collection_association)
         obj.workflow_invocation_step = workflow_invocation_step
 
         with dbcleanup(session, obj) as obj_id:
@@ -2688,9 +2516,7 @@ class TestJob(BaseTest):
             assert stored_obj.session_id == galaxy_session.id
             assert stored_obj.user_id == user.id
             assert collection_consists_of_objects(stored_obj.parameters, job_parameter)
-            assert collection_consists_of_objects(
-                stored_obj.input_datasets, job_to_input_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.input_datasets, job_to_input_dataset_association)
             assert collection_consists_of_objects(
                 stored_obj.input_dataset_collections,
                 job_to_input_dataset_collection_association,
@@ -2707,9 +2533,7 @@ class TestJob(BaseTest):
                 stored_obj.output_dataset_collections,
                 job_to_implicit_output_dataset_collection_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.post_job_actions, post_job_action_association
-            )
+            assert collection_consists_of_objects(stored_obj.post_job_actions, post_job_action_association)
             assert collection_consists_of_objects(
                 stored_obj.input_library_datasets,
                 job_to_input_library_dataset_association,
@@ -2718,27 +2542,14 @@ class TestJob(BaseTest):
                 stored_obj.output_library_datasets,
                 job_to_output_library_dataset_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.external_output_metadata, job_external_output_metadata
-            )
+            assert collection_consists_of_objects(stored_obj.external_output_metadata, job_external_output_metadata)
             assert collection_consists_of_objects(stored_obj.tasks, task)
-            assert collection_consists_of_objects(
-                stored_obj.output_datasets, job_to_output_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.output_datasets, job_to_output_dataset_association)
             assert job_state_history in stored_obj.state_history  # sufficient for test
-            assert collection_consists_of_objects(
-                stored_obj.text_metrics, job_metric_text
-            )
-            assert collection_consists_of_objects(
-                stored_obj.numeric_metrics, job_metric_numeric
-            )
-            assert collection_consists_of_objects(
-                stored_obj.interactivetool_entry_points, interactive_tool_entry_point
-            )
-            assert (
-                stored_obj.implicit_collection_jobs_association
-                == implicit_collection_jobs_job_association
-            )
+            assert collection_consists_of_objects(stored_obj.text_metrics, job_metric_text)
+            assert collection_consists_of_objects(stored_obj.numeric_metrics, job_metric_numeric)
+            assert collection_consists_of_objects(stored_obj.interactivetool_entry_points, interactive_tool_entry_point)
+            assert stored_obj.implicit_collection_jobs_association == implicit_collection_jobs_job_association
             assert stored_obj.container == job_container_association
             assert stored_obj.data_manager_association == data_manager_job_association
             assert collection_consists_of_objects(
@@ -2858,10 +2669,7 @@ class TestJobExternalOutputMetadata(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
             assert stored_obj.job_id == job.id
-            assert (
-                stored_obj.history_dataset_association_id
-                == history_dataset_association.id
-            )
+            assert stored_obj.history_dataset_association_id == history_dataset_association.id
             assert stored_obj.is_valid == is_valid
             assert stored_obj.filename_in == filename_in
             assert stored_obj.filename_out == filename_out
@@ -2878,10 +2686,7 @@ class TestJobExternalOutputMetadata(BaseTest):
         obj = cls_(job, library_dataset_dataset_association)
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.library_dataset_dataset_association_id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association_id == library_dataset_dataset_association.id
 
     def test_relationships(
         self,
@@ -3071,25 +2876,17 @@ class TestJobToInputDatasetCollectionAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
             assert stored_obj.job_id == job.id
-            assert (
-                stored_obj.dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.name == name
 
-    def test_relationships(
-        self, session, cls_, history_dataset_collection_association, job
-    ):
+    def test_relationships(self, session, cls_, history_dataset_collection_association, job):
         obj = cls_(None, history_dataset_collection_association)
         obj.job = job
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.job.id == job.id
-            assert (
-                stored_obj.dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == history_dataset_collection_association.id
 
 
 class TestJobToInputDatasetCollectionElementAssociation(BaseTest):
@@ -3105,10 +2902,7 @@ class TestJobToInputDatasetCollectionElementAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
             assert stored_obj.job_id == job.id
-            assert (
-                stored_obj.dataset_collection_element_id
-                == dataset_collection_element.id
-            )
+            assert stored_obj.dataset_collection_element_id == dataset_collection_element.id
             assert stored_obj.name == name
 
     def test_relationships(self, session, cls_, dataset_collection_element, job):
@@ -3118,10 +2912,7 @@ class TestJobToInputDatasetCollectionElementAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.job.id == job.id
-            assert (
-                stored_obj.dataset_collection_element.id
-                == dataset_collection_element.id
-            )
+            assert stored_obj.dataset_collection_element.id == dataset_collection_element.id
 
 
 class TestJobToInputLibraryDatasetAssociation(BaseTest):
@@ -3140,9 +2931,7 @@ class TestJobToInputLibraryDatasetAssociation(BaseTest):
             assert stored_obj.ldda_id == library_dataset_dataset_association.id
             assert stored_obj.name == name
 
-    def test_relationships(
-        self, session, cls_, library_dataset_dataset_association, job
-    ):
+    def test_relationships(self, session, cls_, library_dataset_dataset_association, job):
         obj = cls_(None, library_dataset_dataset_association)
         obj.job = job
 
@@ -3191,25 +2980,17 @@ class TestJobToOutputDatasetCollectionAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
             assert stored_obj.job_id == job.id
-            assert (
-                stored_obj.dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.name == name
 
-    def test_relationships(
-        self, session, cls_, history_dataset_collection_association, job
-    ):
+    def test_relationships(self, session, cls_, history_dataset_collection_association, job):
         obj = cls_(None, history_dataset_collection_association)
         obj.job = job
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.job.id == job.id
-            assert (
-                stored_obj.dataset_collection_instance.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection_instance.id == history_dataset_collection_association.id
 
 
 class TestJobToOutputLibraryDatasetAssociation(BaseTest):
@@ -3228,9 +3009,7 @@ class TestJobToOutputLibraryDatasetAssociation(BaseTest):
             assert stored_obj.ldda_id == library_dataset_dataset_association.id
             assert stored_obj.name == name
 
-    def test_relationships(
-        self, session, cls_, library_dataset_dataset_association, job
-    ):
+    def test_relationships(self, session, cls_, library_dataset_dataset_association, job):
         obj = cls_(None, library_dataset_dataset_association)
         obj.job = job
 
@@ -3279,9 +3058,7 @@ class TestLibrary(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.root_folder.id == library_folder.id
-            assert collection_consists_of_objects(
-                stored_obj.actions, library_permission
-            )
+            assert collection_consists_of_objects(stored_obj.actions, library_permission)
 
 
 class TestLibraryDataset(BaseTest):
@@ -3340,15 +3117,10 @@ class TestLibraryDataset(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.library_dataset_dataset_association.id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association.id == library_dataset_dataset_association.id
             assert stored_obj.folder.id == library_folder.id
             assert stored_obj.expired_datasets[0].id == ldda.id
-            assert collection_consists_of_objects(
-                stored_obj.actions, library_dataset_permission
-            )
+            assert collection_consists_of_objects(stored_obj.actions, library_dataset_permission)
 
         delete_from_database(session, ldda)
 
@@ -3367,26 +3139,18 @@ class TestLibraryDatasetCollectionAnnotationAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.library_dataset_collection_id
-                == library_dataset_collection_association.id
-            )
+            assert stored_obj.library_dataset_collection_id == library_dataset_collection_association.id
             assert stored_obj.user_id == user.id
             assert stored_obj.annotation == annotation
 
-    def test_relationships(
-        self, session, cls_, library_dataset_collection_association, user
-    ):
+    def test_relationships(self, session, cls_, library_dataset_collection_association, user):
         obj = cls_()
         obj.user = user
         obj.dataset_collection = library_dataset_collection_association
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.dataset_collection.id
-                == library_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == library_dataset_collection_association.id
             assert stored_obj.user.id == user.id
 
 
@@ -3432,16 +3196,12 @@ class TestLibraryDatasetCollectionAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.collection.id == dataset_collection.id
             assert stored_obj.folder.id == library_folder.id
-            assert collection_consists_of_objects(
-                stored_obj.tags, library_dataset_collection_tag_association
-            )
+            assert collection_consists_of_objects(stored_obj.tags, library_dataset_collection_tag_association)
             assert collection_consists_of_objects(
                 stored_obj.annotations,
                 library_dataset_collection_annotation_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, library_dataset_collection_rating_association
-            )
+            assert collection_consists_of_objects(stored_obj.ratings, library_dataset_collection_rating_association)
 
 
 class TestLibraryDatasetCollectionRatingAssociation(BaseTest):
@@ -3455,24 +3215,16 @@ class TestLibraryDatasetCollectionRatingAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.library_dataset_collection_id
-                == library_dataset_collection_association.id
-            )
+            assert stored_obj.library_dataset_collection_id == library_dataset_collection_association.id
             assert stored_obj.user_id == user.id
             assert stored_obj.rating == rating
 
-    def test_relationships(
-        self, session, cls_, library_dataset_collection_association, user
-    ):
+    def test_relationships(self, session, cls_, library_dataset_collection_association, user):
         obj = cls_(user, library_dataset_collection_association, 1)
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.dataset_collection.id
-                == library_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == library_dataset_collection_association.id
             assert stored_obj.user.id == user.id
 
 
@@ -3480,9 +3232,7 @@ class TestLibraryDatasetCollectionTagAssociation(BaseTest):
     def test_table(self, cls_):
         assert cls_.__tablename__ == "library_dataset_collection_tag_association"
 
-    def test_columns(
-        self, session, cls_, library_dataset_collection_association, tag, user
-    ):
+    def test_columns(self, session, cls_, library_dataset_collection_association, tag, user):
         user_tname, value, user_value = "a", "b", "c"
         obj = cls_(user=user, tag=tag, user_tname=user_tname, value=value)
         obj.user_value = user_value
@@ -3491,28 +3241,20 @@ class TestLibraryDatasetCollectionTagAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.library_dataset_collection_id
-                == library_dataset_collection_association.id
-            )
+            assert stored_obj.library_dataset_collection_id == library_dataset_collection_association.id
             assert stored_obj.tag_id == tag.id
             assert stored_obj.user_id == user.id
             assert stored_obj.user_tname == user_tname
             assert stored_obj.value == value
             assert stored_obj.user_value == user_value
 
-    def test_relationships(
-        self, session, cls_, library_dataset_collection_association, tag, user
-    ):
+    def test_relationships(self, session, cls_, library_dataset_collection_association, tag, user):
         obj = cls_(user=user, tag=tag)
         obj.dataset_collection = library_dataset_collection_association
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.dataset_collection.id
-                == library_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == library_dataset_collection_association.id
             assert stored_obj.tag.id == tag.id
             assert stored_obj.user.id == user.id
 
@@ -3583,17 +3325,9 @@ class TestLibraryDatasetDatasetAssociation(BaseTest):
             assert stored_obj.library_dataset_id == library_dataset.id
             assert stored_obj.dataset_id == dataset.id
             assert stored_obj.create_time == create_time
-            assert (
-                stored_obj.update_time >= create_time
-            )  # this is sufficient for testing
-            assert (
-                stored_obj.copied_from_history_dataset_association_id
-                == history_dataset_association.id
-            )
-            assert (
-                stored_obj.copied_from_library_dataset_dataset_association_id
-                == copied_from_ldda.id
-            )
+            assert stored_obj.update_time >= create_time  # this is sufficient for testing
+            assert stored_obj.copied_from_history_dataset_association_id == history_dataset_association.id
+            assert stored_obj.copied_from_library_dataset_dataset_association_id == copied_from_ldda.id
             assert stored_obj.state == state
             assert stored_obj.name == name
             assert stored_obj.info == info
@@ -3669,38 +3403,20 @@ class TestLibraryDatasetDatasetAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.library_dataset.id == library_dataset.id
             assert stored_obj.dataset.id == dataset.id
-            assert (
-                stored_obj.copied_from_history_dataset_association.id
-                == history_dataset_association.id
-            )
-            assert (
-                stored_obj.copied_from_library_dataset_dataset_association.id
-                == copied_from_ldda.id
-            )
+            assert stored_obj.copied_from_history_dataset_association.id == history_dataset_association.id
+            assert stored_obj.copied_from_library_dataset_dataset_association.id == copied_from_ldda.id
             assert stored_obj.extended_metadata.id == extended_metadata.id
             assert stored_obj.user.id == user.id
-            assert collection_consists_of_objects(
-                stored_obj.tags, library_dataset_dataset_association_tag_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.actions, library_dataset_dataset_association_permission
-            )
-            assert collection_consists_of_objects(
-                stored_obj.copied_to_history_dataset_associations, copied_to_hda
-            )
+            assert collection_consists_of_objects(stored_obj.tags, library_dataset_dataset_association_tag_association)
+            assert collection_consists_of_objects(stored_obj.actions, library_dataset_dataset_association_permission)
+            assert collection_consists_of_objects(stored_obj.copied_to_history_dataset_associations, copied_to_hda)
             assert collection_consists_of_objects(
                 stored_obj.copied_to_library_dataset_dataset_associations,
                 copied_to_ldda,
             )
-            assert collection_consists_of_objects(
-                stored_obj.implicitly_converted_datasets, icda
-            )
-            assert collection_consists_of_objects(
-                stored_obj.implicitly_converted_parent_datasets, icpda
-            )
-            assert collection_consists_of_objects(
-                stored_obj.dependent_jobs, job_to_input_library_dataset_association
-            )
+            assert collection_consists_of_objects(stored_obj.implicitly_converted_datasets, icda)
+            assert collection_consists_of_objects(stored_obj.implicitly_converted_parent_datasets, icpda)
+            assert collection_consists_of_objects(stored_obj.dependent_jobs, job_to_input_library_dataset_association)
             assert collection_consists_of_objects(
                 stored_obj.creating_job_associations,
                 job_to_output_library_dataset_association,
@@ -3727,35 +3443,23 @@ class TestLibraryDatasetDatasetAssociationPermissions(BaseTest):
             assert stored_obj.create_time == create_time
             assert stored_obj.update_time == update_time
             assert stored_obj.action == action
-            assert (
-                stored_obj.library_dataset_dataset_association_id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association_id == library_dataset_dataset_association.id
             assert stored_obj.role_id == role.id
 
-    def test_relationships(
-        self, session, cls_, library_dataset_dataset_association, role
-    ):
+    def test_relationships(self, session, cls_, library_dataset_dataset_association, role):
         obj = cls_(None, library_dataset_dataset_association, role)
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.library_dataset_dataset_association.id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association.id == library_dataset_dataset_association.id
             assert stored_obj.role.id == role.id
 
 
 class TestLibraryDatasetDatasetAssociationTagAssociation(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__ == "library_dataset_dataset_association_tag_association"
-        )
+        assert cls_.__tablename__ == "library_dataset_dataset_association_tag_association"
 
-    def test_columns(
-        self, session, cls_, library_dataset_dataset_association, tag, user
-    ):
+    def test_columns(self, session, cls_, library_dataset_dataset_association, tag, user):
         user_tname, value, user_value = "a", "b", "c"
         obj = cls_(user=user, tag=tag, user_tname=user_tname, value=value)
         obj.user_value = user_value
@@ -3764,28 +3468,20 @@ class TestLibraryDatasetDatasetAssociationTagAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.library_dataset_dataset_association_id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association_id == library_dataset_dataset_association.id
             assert stored_obj.tag_id == tag.id
             assert stored_obj.user_id == user.id
             assert stored_obj.user_tname == user_tname
             assert stored_obj.value == value
             assert stored_obj.user_value == user_value
 
-    def test_relationships(
-        self, session, cls_, library_dataset_dataset_association, tag, user
-    ):
+    def test_relationships(self, session, cls_, library_dataset_dataset_association, tag, user):
         obj = cls_(user=user, tag=tag)
         obj.library_dataset_dataset_association = library_dataset_dataset_association
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.library_dataset_dataset_association.id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association.id == library_dataset_dataset_association.id
             assert stored_obj.tag.id == tag.id
             assert stored_obj.user.id == user.id
 
@@ -3809,10 +3505,7 @@ class TestLibraryDatasetDatasetInfoAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.id == obj_id
-            assert (
-                stored_obj.library_dataset_dataset_association_id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association_id == library_dataset_dataset_association.id
             assert stored_obj.form_definition_id == form_definition.id
             assert stored_obj.form_values_id == form_values.id
             assert stored_obj.deleted == deleted
@@ -3829,10 +3522,7 @@ class TestLibraryDatasetDatasetInfoAssociation(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert (
-                stored_obj.library_dataset_dataset_association.id
-                == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset_dataset_association.id == library_dataset_dataset_association.id
             assert stored_obj.template.id == form_definition.id
             assert stored_obj.info.id == form_values.id
 
@@ -3937,9 +3627,7 @@ class TestLibraryFolder(BaseTest):
             assert collection_consists_of_objects(stored_obj.folders, folder1)
             assert collection_consists_of_objects(stored_obj.active_folders, folder1)
             assert collection_consists_of_objects(stored_obj.library_root, library)
-            assert collection_consists_of_objects(
-                stored_obj.actions, library_folder_permission
-            )
+            assert collection_consists_of_objects(stored_obj.actions, library_folder_permission)
             # use identity equality instread of object equality.
             assert stored_obj.datasets[0].id == library_dataset.id
             assert stored_obj.active_datasets[0].id == library_dataset.id
@@ -3965,9 +3653,7 @@ class TestLibraryFolderInfoAssociation(BaseTest):
             assert stored_obj.inheritable == inheritable
             assert stored_obj.deleted == deleted
 
-    def test_relationships(
-        self, session, cls_, library_folder, form_definition, form_values
-    ):
+    def test_relationships(self, session, cls_, library_folder, form_definition, form_values):
         obj = cls_(library_folder, form_definition, form_values)
 
         with dbcleanup(session, obj) as obj_id:
@@ -4122,9 +3808,7 @@ class TestMetadataFile(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.history_dataset.id == history_dataset_association.id
-            assert (
-                stored_obj.library_dataset.id == library_dataset_dataset_association.id
-            )
+            assert stored_obj.library_dataset.id == library_dataset_dataset_association.id
 
 
 class TestPSAAssociation(BaseTest):
@@ -4269,15 +3953,9 @@ class TestPage(BaseTest):
             assert collection_consists_of_objects(stored_obj.revisions, page_revision)
             assert stored_obj.latest_revision.id == page_revision.id
             assert collection_consists_of_objects(stored_obj.tags, page_tag_association)
-            assert collection_consists_of_objects(
-                stored_obj.annotations, page_annotation_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, page_rating_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.users_shared_with, page_user_share_association
-            )
+            assert collection_consists_of_objects(stored_obj.annotations, page_annotation_association)
+            assert collection_consists_of_objects(stored_obj.ratings, page_rating_association)
+            assert collection_consists_of_objects(stored_obj.users_shared_with, page_user_share_association)
             # This doesn't test the average amount, just the mapping.
             assert stored_obj.average_rating == page_rating_association.rating
 
@@ -4362,9 +4040,7 @@ class TestPageRevision(BaseTest):
             assert stored_obj.page_id == page.id
             assert stored_obj.title == title
             assert stored_obj.content == content
-            assert (
-                stored_obj.content_format == model.PageRevision.DEFAULT_CONTENT_FORMAT
-            )
+            assert stored_obj.content_format == model.PageRevision.DEFAULT_CONTENT_FORMAT
 
     def test_relationships(self, session, cls_, page):
         obj = cls_()
@@ -4545,15 +4221,9 @@ class TestQuota(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert collection_consists_of_objects(
-                stored_obj.default, default_quota_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.groups, group_quota_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.users, user_quota_association
-            )
+            assert collection_consists_of_objects(stored_obj.default, default_quota_association)
+            assert collection_consists_of_objects(stored_obj.groups, group_quota_association)
+            assert collection_consists_of_objects(stored_obj.users, user_quota_association)
 
 
 class TestRole(BaseTest):
@@ -4599,15 +4269,9 @@ class TestRole(BaseTest):
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert collection_consists_of_objects(
-                stored_obj.dataset_actions, dataset_permission
-            )
-            assert collection_consists_of_objects(
-                stored_obj.groups, group_role_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.users, user_role_association
-            )
+            assert collection_consists_of_objects(stored_obj.dataset_actions, dataset_permission)
+            assert collection_consists_of_objects(stored_obj.groups, group_role_association)
+            assert collection_consists_of_objects(stored_obj.users, user_role_association)
 
 
 class TestStoredWorkflow(BaseTest):
@@ -4689,32 +4353,18 @@ class TestStoredWorkflow(BaseTest):
             assert stored_obj.user.id == user.id
             assert stored_obj.latest_workflow.id == workflow.id
             assert stored_obj.workflows[0].id == wf.id
-            assert collection_consists_of_objects(
-                stored_obj.annotations, stored_workflow_annotation_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, stored_workflow_rating_association
-            )
+            assert collection_consists_of_objects(stored_obj.annotations, stored_workflow_annotation_association)
+            assert collection_consists_of_objects(stored_obj.ratings, stored_workflow_rating_association)
             # This doesn't test the average amount, just the mapping.
-            assert (
-                stored_obj.average_rating == stored_workflow_rating_association.rating
-            )
-            assert collection_consists_of_objects(
-                stored_obj.tags, stored_workflow_tag_association, tag_assoc2
-            )
+            assert stored_obj.average_rating == stored_workflow_rating_association.rating
+            assert collection_consists_of_objects(stored_obj.tags, stored_workflow_tag_association, tag_assoc2)
             assert collection_consists_of_objects(stored_obj.owner_tags, tag_assoc2)
-            assert collection_consists_of_objects(
-                stored_obj.users_shared_with, stored_workflow_user_share_association
-            )
+            assert collection_consists_of_objects(stored_obj.users_shared_with, stored_workflow_user_share_association)
 
         delete_from_database(session, [wf, tag_assoc2])
 
-    def test_average_rating(
-        self, session, stored_workflow, user, stored_workflow_rating_association_factory
-    ):
-        _run_average_rating_test(
-            session, stored_workflow, user, stored_workflow_rating_association_factory
-        )
+    def test_average_rating(self, session, stored_workflow, user, stored_workflow_rating_association_factory):
+        _run_average_rating_test(session, stored_workflow, user, stored_workflow_rating_association_factory)
 
 
 class TestStoredWorkflowAnnotationAssociation(BaseTest):
@@ -4965,9 +4615,7 @@ class TestTask(BaseTest):
             assert stored_obj.task_runner_name == task_runner_name
             assert stored_obj.task_runner_external_id == task_runner_external_id
 
-    def test_relationships(
-        self, session, cls_, job, task_metric_numeric, task_metric_text
-    ):
+    def test_relationships(self, session, cls_, job, task_metric_numeric, task_metric_text):
         obj = cls_(job, None, None)
         obj.numeric_metrics.append(task_metric_numeric)
         obj.text_metrics.append(task_metric_text)
@@ -4975,12 +4623,8 @@ class TestTask(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.job.id == job.id
-            assert collection_consists_of_objects(
-                stored_obj.numeric_metrics, task_metric_numeric
-            )
-            assert collection_consists_of_objects(
-                stored_obj.text_metrics, task_metric_text
-            )
+            assert collection_consists_of_objects(stored_obj.numeric_metrics, task_metric_numeric)
+            assert collection_consists_of_objects(stored_obj.text_metrics, task_metric_text)
 
 
 class TestTaskMetricNumeric(BaseTest):
@@ -5150,7 +4794,7 @@ class TestUser(BaseTest):
 
         obj.roles.append(private_user_role)
 
-        _non_private_role = role_factory(name='a')
+        _non_private_role = role_factory(name="a")
         cleanup.append(_non_private_role)
 
         non_private_user_role = user_role_association_factory(obj, _non_private_role)
@@ -5176,45 +4820,21 @@ class TestUser(BaseTest):
             assert stored_obj.values.id == form_values.id
             assert collection_consists_of_objects(stored_obj.addresses, user_address)
             assert collection_consists_of_objects(stored_obj.cloudauthz, cloud_authz)
-            assert collection_consists_of_objects(
-                stored_obj.custos_auth, custos_authnz_token
-            )
-            assert collection_consists_of_objects(
-                stored_obj.default_permissions, default_user_permissions
-            )
-            assert collection_consists_of_objects(
-                stored_obj.groups, user_group_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.histories, history1, history2
-            )
+            assert collection_consists_of_objects(stored_obj.custos_auth, custos_authnz_token)
+            assert collection_consists_of_objects(stored_obj.default_permissions, default_user_permissions)
+            assert collection_consists_of_objects(stored_obj.groups, user_group_association)
+            assert collection_consists_of_objects(stored_obj.histories, history1, history2)
             assert collection_consists_of_objects(stored_obj.active_histories, history1)
-            assert collection_consists_of_objects(
-                stored_obj.galaxy_sessions, galaxy_session
-            )
-            assert collection_consists_of_objects(
-                stored_obj.quotas, user_quota_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.social_auth, user_authnz_token
-            )
-            assert collection_consists_of_objects(
-                stored_obj.stored_workflow_menu_entries, swme
-            )
+            assert collection_consists_of_objects(stored_obj.galaxy_sessions, galaxy_session)
+            assert collection_consists_of_objects(stored_obj.quotas, user_quota_association)
+            assert collection_consists_of_objects(stored_obj.social_auth, user_authnz_token)
+            assert collection_consists_of_objects(stored_obj.stored_workflow_menu_entries, swme)
             assert user_preference in stored_obj._preferences.values()
             assert collection_consists_of_objects(stored_obj.api_keys, api_keys)
-            assert collection_consists_of_objects(
-                stored_obj.data_manager_histories, data_manager_history_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.roles, private_user_role, non_private_user_role
-            )
-            assert collection_consists_of_objects(
-                stored_obj.non_private_roles, non_private_user_role
-            )
-            assert collection_consists_of_objects(
-                stored_obj.stored_workflows, stored_workflow
-            )
+            assert collection_consists_of_objects(stored_obj.data_manager_histories, data_manager_history_association)
+            assert collection_consists_of_objects(stored_obj.roles, private_user_role, non_private_user_role)
+            assert collection_consists_of_objects(stored_obj.non_private_roles, non_private_user_role)
+            assert collection_consists_of_objects(stored_obj.stored_workflows, stored_workflow)
 
         delete_from_database(session, cleanup)
 
@@ -5453,9 +5073,9 @@ class TestVault(BaseTest):
 
     def test_columns(self, session, cls_):
         create_time = update_time = datetime.now()
-        key = '/some/path'
-        parent_key = '/some'
-        value = 'helloworld'
+        key = "/some/path"
+        parent_key = "/some"
+        value = "helloworld"
         obj = cls_(create_time=create_time, update_time=update_time, key=key, parent_key=parent_key, value=value)
 
         with dbcleanup(session, obj, where_clause=cls_.key == key):
@@ -5541,29 +5161,17 @@ class TestVisualization(BaseTest):
             assert stored_obj.user.id == user.id
             assert stored_obj.latest_revision.id == visualization_revision.id
             assert collection_consists_of_objects(stored_obj.revisions, revision2)
-            assert collection_consists_of_objects(
-                stored_obj.tags, visualization_tag_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.annotations, visualization_annotation_association
-            )
-            assert collection_consists_of_objects(
-                stored_obj.ratings, visualization_rating_association
-            )
+            assert collection_consists_of_objects(stored_obj.tags, visualization_tag_association)
+            assert collection_consists_of_objects(stored_obj.annotations, visualization_annotation_association)
+            assert collection_consists_of_objects(stored_obj.ratings, visualization_rating_association)
             # This doesn't test the average amount, just the mapping.
             assert stored_obj.average_rating == visualization_rating_association.rating
-            assert collection_consists_of_objects(
-                stored_obj.users_shared_with, visualization_user_share_association
-            )
+            assert collection_consists_of_objects(stored_obj.users_shared_with, visualization_user_share_association)
 
         delete_from_database(session, revision2)
 
-    def test_average_rating(
-        self, session, visualization, user, visualization_rating_association_factory
-    ):
-        _run_average_rating_test(
-            session, visualization, user, visualization_rating_association_factory
-        )
+    def test_average_rating(self, session, visualization, user, visualization_rating_association_factory):
+        _run_average_rating_test(session, visualization, user, visualization_rating_association_factory)
 
 
 class TestVisualizationAnnotationAssociation(BaseTest):
@@ -5778,9 +5386,7 @@ class TestWorkflow(BaseTest):
             assert stored_obj.license == license
             assert stored_obj.uuid == uuid
 
-    def test_relationships(
-        self, session, cls_, stored_workflow, workflow, workflow_step_factory
-    ):
+    def test_relationships(self, session, cls_, stored_workflow, workflow, workflow_step_factory):
         obj = cls_()
         obj.stored_workflow = stored_workflow
         obj.parent_workflow_id = workflow.id
@@ -5851,9 +5457,7 @@ class TestWorkflowInvocation(BaseTest):
         workflow_request_to_input_dataset_collection_association,
         workflow_invocation_output_value,
     ):
-        subworkflow_invocation_assoc = (
-            workflow_invocation_to_subworkflow_invocation_association_factory()
-        )
+        subworkflow_invocation_assoc = workflow_invocation_to_subworkflow_invocation_association_factory()
 
         obj = cls_()
         obj.workflow = workflow
@@ -5862,14 +5466,10 @@ class TestWorkflowInvocation(BaseTest):
         obj.step_states.append(workflow_request_step_state)
         obj.input_step_parameters.append(workflow_request_input_step_parameter)
         obj.input_datasets.append(workflow_request_to_input_dataset_association)
-        obj.input_dataset_collections.append(
-            workflow_request_to_input_dataset_collection_association
-        )
+        obj.input_dataset_collections.append(workflow_request_to_input_dataset_collection_association)
         obj.subworkflow_invocations.append(subworkflow_invocation_assoc)
         obj.steps.append(workflow_invocation_step)
-        obj.output_dataset_collections.append(
-            workflow_invocation_output_dataset_collection_association
-        )
+        obj.output_dataset_collections.append(workflow_invocation_output_dataset_collection_association)
         obj.output_datasets.append(workflow_invocation_output_dataset_association)
         obj.output_values.append(workflow_invocation_output_value)
 
@@ -5878,12 +5478,8 @@ class TestWorkflowInvocation(BaseTest):
             assert stored_obj.workflow.id == workflow.id
             assert stored_obj.history.id == history.id
 
-            assert collection_consists_of_objects(
-                stored_obj.input_parameters, workflow_request_input_parameter
-            )
-            assert collection_consists_of_objects(
-                stored_obj.step_states, workflow_request_step_state
-            )
+            assert collection_consists_of_objects(stored_obj.input_parameters, workflow_request_input_parameter)
+            assert collection_consists_of_objects(stored_obj.step_states, workflow_request_step_state)
             assert collection_consists_of_objects(
                 stored_obj.input_step_parameters, workflow_request_input_step_parameter
             )
@@ -5894,12 +5490,8 @@ class TestWorkflowInvocation(BaseTest):
                 stored_obj.input_dataset_collections,
                 workflow_request_to_input_dataset_collection_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.subworkflow_invocations, subworkflow_invocation_assoc
-            )
-            assert collection_consists_of_objects(
-                stored_obj.steps, workflow_invocation_step
-            )
+            assert collection_consists_of_objects(stored_obj.subworkflow_invocations, subworkflow_invocation_assoc)
+            assert collection_consists_of_objects(stored_obj.steps, workflow_invocation_step)
             assert collection_consists_of_objects(
                 stored_obj.output_dataset_collections,
                 workflow_invocation_output_dataset_collection_association,
@@ -5908,9 +5500,7 @@ class TestWorkflowInvocation(BaseTest):
                 stored_obj.output_datasets,
                 workflow_invocation_output_dataset_association,
             )
-            assert collection_consists_of_objects(
-                stored_obj.output_values, workflow_invocation_output_value
-            )
+            assert collection_consists_of_objects(stored_obj.output_values, workflow_invocation_output_value)
 
         delete_from_database(session, subworkflow_invocation_assoc)
 
@@ -5967,10 +5557,7 @@ class TestWorkflowInvocationOutputDatasetAssociation(BaseTest):
 
 class TestWorkflowInvocationOutputDatasetCollectionAssociation(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__
-            == "workflow_invocation_output_dataset_collection_association"
-        )
+        assert cls_.__tablename__ == "workflow_invocation_output_dataset_collection_association"
 
     def test_columns(
         self,
@@ -5992,10 +5579,7 @@ class TestWorkflowInvocationOutputDatasetCollectionAssociation(BaseTest):
             assert stored_obj.id == obj_id
             assert stored_obj.workflow_invocation_id == workflow_invocation.id
             assert stored_obj.workflow_step_id == workflow_step.id
-            assert (
-                stored_obj.dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.workflow_output_id == workflow_output.id
 
     def test_relationships(
@@ -6017,10 +5601,7 @@ class TestWorkflowInvocationOutputDatasetCollectionAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.workflow_invocation.id == workflow_invocation.id
             assert stored_obj.workflow_step.id == workflow_step.id
-            assert (
-                stored_obj.dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == history_dataset_collection_association.id
             assert stored_obj.workflow_output.id == workflow_output.id
 
 
@@ -6075,9 +5656,7 @@ class TestWorkflowInvocationOutputValue(BaseTest):
             assert stored_obj.workflow_invocation.id == workflow_invocation.id
             assert stored_obj.workflow_step.id == workflow_step.id
             assert stored_obj.workflow_output.id == workflow_output.id
-            assert (
-                stored_obj.workflow_invocation_step[0].id == workflow_invocation_step.id
-            )
+            assert stored_obj.workflow_invocation_step[0].id == workflow_invocation_step.id
 
         delete_from_database(session, [workflow_invocation_step])
 
@@ -6100,9 +5679,7 @@ class TestWorkflowInvocationStep(BaseTest):
         state, action = "a", "b"
 
         session.add(job)  # must be bound to a session for lazy load of attributes
-        session.add(
-            implicit_collection_jobs
-        )  # must be bound to a session for lazy load of attributes
+        session.add(implicit_collection_jobs)  # must be bound to a session for lazy load of attributes
 
         obj = cls_()
         obj.create_time = create_time
@@ -6139,9 +5716,7 @@ class TestWorkflowInvocationStep(BaseTest):
         workflow_invocation_output_value,
     ):
         session.add(job)  # must be bound to a session for lazy load of attributes
-        session.add(
-            implicit_collection_jobs
-        )  # must be bound to a session for lazy load of attributes
+        session.add(implicit_collection_jobs)  # must be bound to a session for lazy load of attributes
 
         # setup workflow_invocation_output_value to test the output_value attribute
         output_value = workflow_invocation_output_value
@@ -6154,9 +5729,7 @@ class TestWorkflowInvocationStep(BaseTest):
         obj.workflow_step = workflow_step
         obj.job = job
         obj.implicit_collection_jobs = implicit_collection_jobs
-        obj.output_dataset_collections.append(
-            workflow_invocation_step_output_dataset_collection_association
-        )
+        obj.output_dataset_collections.append(workflow_invocation_step_output_dataset_collection_association)
         obj.output_datasets.append(workflow_invocation_step_output_dataset_association)
 
         with dbcleanup(session, obj) as obj_id:
@@ -6185,9 +5758,7 @@ class TestWorkflowInvocationStep(BaseTest):
     ):
         # use defaults to create 2 workflows
         workflow_invocation1 = workflow_invocation_factory()
-        workflow_invocation2 = (
-            workflow_invocation_factory()
-        )  # this is the subworkflow invocation
+        workflow_invocation2 = workflow_invocation_factory()  # this is the subworkflow invocation
 
         # store to retrieve object ids
         persist(session, workflow_invocation1)
@@ -6217,13 +5788,9 @@ class TestWorkflowInvocationStep(BaseTest):
 
 class TestWorkflowInvocationStepOutputDatasetAssociation(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__ == "workflow_invocation_step_output_dataset_association"
-        )
+        assert cls_.__tablename__ == "workflow_invocation_step_output_dataset_association"
 
-    def test_columns(
-        self, session, cls_, workflow_invocation_step, history_dataset_association
-    ):
+    def test_columns(self, session, cls_, workflow_invocation_step, history_dataset_association):
         output_name = "a"
         obj = cls_()
         obj.workflow_invocation_step = workflow_invocation_step
@@ -6237,9 +5804,7 @@ class TestWorkflowInvocationStepOutputDatasetAssociation(BaseTest):
             assert stored_obj.dataset_id == history_dataset_association.id
             assert stored_obj.output_name == output_name
 
-    def test_relationships(
-        self, session, cls_, workflow_invocation_step, history_dataset_association
-    ):
+    def test_relationships(self, session, cls_, workflow_invocation_step, history_dataset_association):
         obj = cls_()
         obj.workflow_invocation_step = workflow_invocation_step
         obj.dataset = history_dataset_association
@@ -6252,10 +5817,7 @@ class TestWorkflowInvocationStepOutputDatasetAssociation(BaseTest):
 
 class TestWorkflowInvocationStepOutputDatasetCollectionAssociation(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__
-            == "workflow_invocation_step_output_dataset_collection_association"
-        )
+        assert cls_.__tablename__ == "workflow_invocation_step_output_dataset_collection_association"
 
     def test_columns(
         self,
@@ -6277,10 +5839,7 @@ class TestWorkflowInvocationStepOutputDatasetCollectionAssociation(BaseTest):
             assert stored_obj.id == obj_id
             assert stored_obj.workflow_invocation_step_id == workflow_invocation_step.id
             assert stored_obj.workflow_step_id == workflow_step.id
-            assert (
-                stored_obj.dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection_id == history_dataset_collection_association.id
             assert stored_obj.output_name == output_name
 
     def test_relationships(
@@ -6297,18 +5856,12 @@ class TestWorkflowInvocationStepOutputDatasetCollectionAssociation(BaseTest):
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.workflow_invocation_step.id == workflow_invocation_step.id
-            assert (
-                stored_obj.dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == history_dataset_collection_association.id
 
 
 class TestWorkflowInvocationToSubworkflowInvocationAssociation(BaseTest):
     def test_table(self, cls_):
-        assert (
-            cls_.__tablename__
-            == "workflow_invocation_to_subworkflow_invocation_association"
-        )
+        assert cls_.__tablename__ == "workflow_invocation_to_subworkflow_invocation_association"
 
     def test_columns(
         self,
@@ -6349,9 +5902,7 @@ class TestWorkflowInvocationToSubworkflowInvocationAssociation(BaseTest):
         persist(session, parent_workflow_invocation)
 
         obj = cls_()
-        obj.subworkflow_invocation = (
-            workflow_invocation  # We need only 1 instance, so we use the fixture
-        )
+        obj.subworkflow_invocation = workflow_invocation  # We need only 1 instance, so we use the fixture
         obj.workflow_step = workflow_step
         obj.parent_workflow_invocation = parent_workflow_invocation
 
@@ -6359,10 +5910,7 @@ class TestWorkflowInvocationToSubworkflowInvocationAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.subworkflow_invocation.id == workflow_invocation.id
             assert stored_obj.workflow_step.id == workflow_step.id
-            assert (
-                stored_obj.parent_workflow_invocation.id
-                == parent_workflow_invocation.id
-            )
+            assert stored_obj.parent_workflow_invocation.id == parent_workflow_invocation.id
 
         delete_from_database(session, parent_workflow_invocation)
 
@@ -6548,10 +6096,7 @@ class TestWorkflowRequestToInputDatasetCollectionAssociation(BaseTest):
             assert stored_obj.id == obj_id
             assert stored_obj.workflow_invocation_id == workflow_invocation.id
             assert stored_obj.workflow_step_id == workflow_step.id
-            assert (
-                stored_obj.dataset_collection_id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection_id == history_dataset_collection_association.id
 
     def test_relationships(
         self,
@@ -6570,10 +6115,7 @@ class TestWorkflowRequestToInputDatasetCollectionAssociation(BaseTest):
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.workflow_invocation.id == workflow_invocation.id
             assert stored_obj.workflow_step.id == workflow_step.id
-            assert (
-                stored_obj.dataset_collection.id
-                == history_dataset_collection_association.id
-            )
+            assert stored_obj.dataset_collection.id == history_dataset_collection_association.id
 
 
 class TestWorkflowStep(BaseTest):
@@ -6662,9 +6204,7 @@ class TestWorkflowStep(BaseTest):
             assert stored_obj.workflow.id == workflow.id
             assert stored_obj.subworkflow.id == subworkflow.id
             assert stored_obj.dynamic_tool.id == dynamic_tool.id
-            assert collection_consists_of_objects(
-                stored_obj.output_connections, workflow_step_connection_out
-            )
+            assert collection_consists_of_objects(stored_obj.output_connections, workflow_step_connection_out)
 
         persisted = [
             subworkflow,
@@ -6804,18 +6344,14 @@ class TestWorkflowStepInput(BaseTest):
             assert stored_obj.default_value_set == default_value_set
             assert stored_obj.runtime_value == runtime_value
 
-    def test_relationships(
-        self, session, cls_, workflow_step, workflow_step_connection
-    ):
+    def test_relationships(self, session, cls_, workflow_step, workflow_step_connection):
         obj = cls_(workflow_step)
         obj.connections.append(workflow_step_connection)
 
         with dbcleanup(session, obj) as obj_id:
             stored_obj = get_stored_obj(session, cls_, obj_id)
             assert stored_obj.workflow_step_id == workflow_step.id
-            assert collection_consists_of_objects(
-                stored_obj.connections, workflow_step_connection
-            )
+            assert collection_consists_of_objects(stored_obj.connections, workflow_step_connection)
 
 
 class TestWorkflowStepTagAssociation(BaseTest):
@@ -6873,9 +6409,8 @@ def ensure_database_is_empty(session):
     https://docs.pytest.org/en/6.2.x/fixture.html#fixture-instantiation-order
     """
     # Created indirectrly (via db trigger and at Job instantiation): can't cleanup up automatically
-    exclude = ['HistoryAudit', 'JobStateHistory']
-    models = (cls_ for cls_ in model.__dict__.values()
-        if hasattr(cls_, '__mapper__') and cls_.__name__ not in exclude)
+    exclude = ["HistoryAudit", "JobStateHistory"]
+    models = (cls_ for cls_ in model.__dict__.values() if hasattr(cls_, "__mapper__") and cls_.__name__ not in exclude)
     # For each mapped class, check that the database table to which it is mapped is empty
     for m in models:
         stmt = select(func.count()).select_from(m)
@@ -6885,13 +6420,15 @@ def ensure_database_is_empty(session):
 
 # Misc. helper fixtures.
 
-@pytest.fixture(scope='module')
+
+@pytest.fixture(scope="module")
 def init_model(engine):
     model.mapper_registry.metadata.create_all(engine)
 
 
 # Fixtures yielding persisted instances of models, deleted from the database on test exit.
 
+
 @pytest.fixture
 def api_keys(session):
     instance = model.APIKeys(key=get_unique_value())
@@ -6941,12 +6478,8 @@ def dataset_collection(session):
 
 
 @pytest.fixture
-def dataset_collection_element(
-    session, dataset_collection, history_dataset_association
-):
-    instance = model.DatasetCollectionElement(
-        collection=dataset_collection, element=history_dataset_association
-    )
+def dataset_collection_element(session, dataset_collection, history_dataset_association):
+    instance = model.DatasetCollectionElement(collection=dataset_collection, element=history_dataset_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7013,9 +6546,7 @@ def extended_metadata_index(session, extended_metadata):
 
 @pytest.fixture
 def form_definition(session, form_definition_current):
-    instance = model.FormDefinition(
-        name="a", form_definition_current=form_definition_current
-    )
+    instance = model.FormDefinition(name="a", form_definition_current=form_definition_current)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7115,9 +6646,7 @@ def history_dataset_collection_rating_association(
     user,
     history_dataset_collection_association,
 ):
-    instance = model.HistoryDatasetCollectionRatingAssociation(
-        user, history_dataset_collection_association
-    )
+    instance = model.HistoryDatasetCollectionRatingAssociation(user, history_dataset_collection_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7159,9 +6688,7 @@ def implicit_collection_jobs_job_association(session):
 
 
 @pytest.fixture
-def implicitly_converted_dataset_association(
-    session, history_dataset_association
-):
+def implicitly_converted_dataset_association(session, history_dataset_association):
     instance = model.ImplicitlyConvertedDatasetAssociation(
         dataset=history_dataset_association,
         parent=history_dataset_association,  # using the same dataset; should work here.
@@ -7170,12 +6697,8 @@ def implicitly_converted_dataset_association(
 
 
 @pytest.fixture
-def implicitly_created_dataset_collection_input(
-    session, history_dataset_collection_association
-):
-    instance = model.ImplicitlyCreatedDatasetCollectionInput(
-        None, history_dataset_collection_association
-    )
+def implicitly_created_dataset_collection_input(session, history_dataset_collection_association):
+    instance = model.ImplicitlyCreatedDatasetCollectionInput(None, history_dataset_collection_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7234,12 +6757,8 @@ def job_state_history(session, job):
 
 
 @pytest.fixture
-def job_to_implicit_output_dataset_collection_association(
-    session, dataset_collection
-):
-    instance = model.JobToImplicitOutputDatasetCollectionAssociation(
-        None, dataset_collection
-    )
+def job_to_implicit_output_dataset_collection_association(session, dataset_collection):
+    instance = model.JobToImplicitOutputDatasetCollectionAssociation(None, dataset_collection)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7250,32 +6769,20 @@ def job_to_input_dataset_association(session, history_dataset_association):
 
 
 @pytest.fixture
-def job_to_input_dataset_collection_association(
-    session, history_dataset_collection_association
-):
-    instance = model.JobToInputDatasetCollectionAssociation(
-        None, history_dataset_collection_association
-    )
+def job_to_input_dataset_collection_association(session, history_dataset_collection_association):
+    instance = model.JobToInputDatasetCollectionAssociation(None, history_dataset_collection_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
 @pytest.fixture
-def job_to_input_dataset_collection_element_association(
-    session, dataset_collection_element
-):
-    instance = model.JobToInputDatasetCollectionElementAssociation(
-        None, dataset_collection_element
-    )
+def job_to_input_dataset_collection_element_association(session, dataset_collection_element):
+    instance = model.JobToInputDatasetCollectionElementAssociation(None, dataset_collection_element)
     yield from dbcleanup_wrapper(session, instance)
 
 
 @pytest.fixture
-def job_to_input_library_dataset_association(
-    session, library_dataset_dataset_association
-):
-    instance = model.JobToInputLibraryDatasetAssociation(
-        None, library_dataset_dataset_association
-    )
+def job_to_input_library_dataset_association(session, library_dataset_dataset_association):
+    instance = model.JobToInputLibraryDatasetAssociation(None, library_dataset_dataset_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7286,22 +6793,14 @@ def job_to_output_dataset_association(session, history_dataset_association):
 
 
 @pytest.fixture
-def job_to_output_dataset_collection_association(
-    session, history_dataset_collection_association
-):
-    instance = model.JobToOutputDatasetCollectionAssociation(
-        None, history_dataset_collection_association
-    )
+def job_to_output_dataset_collection_association(session, history_dataset_collection_association):
+    instance = model.JobToOutputDatasetCollectionAssociation(None, history_dataset_collection_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
 @pytest.fixture
-def job_to_output_library_dataset_association(
-    session, library_dataset_dataset_association
-):
-    instance = model.JobToOutputLibraryDatasetAssociation(
-        None, library_dataset_dataset_association
-    )
+def job_to_output_library_dataset_association(session, library_dataset_dataset_association):
+    instance = model.JobToOutputLibraryDatasetAssociation(None, library_dataset_dataset_association)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7348,12 +6847,8 @@ def library_dataset_dataset_association(session):
 
 
 @pytest.fixture
-def library_dataset_dataset_association_permission(
-    session, library_dataset_dataset_association, role
-):
-    instance = model.LibraryDatasetDatasetAssociationPermissions(
-        "a", library_dataset_dataset_association, role
-    )
+def library_dataset_dataset_association_permission(session, library_dataset_dataset_association, role):
+    instance = model.LibraryDatasetDatasetAssociationPermissions("a", library_dataset_dataset_association, role)
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -7720,6 +7215,7 @@ def workflow_step_tag_association(session):
 # how to construct the model it is testing, so instead of constructing an object directly,
 # a test calls a factory function, passed to it as a fixture.
 
+
 @pytest.fixture
 def dataset_collection_factory():
     def make_instance(*args, **kwds):
@@ -7766,9 +7262,7 @@ def history_rating_association_factory():
 
 
 @pytest.fixture
-def implicitly_converted_dataset_association_factory(
-    history_dataset_association
-):
+def implicitly_converted_dataset_association_factory(history_dataset_association):
     def make_instance(*args, **kwds):
         instance = model.ImplicitlyConvertedDatasetAssociation(
             dataset=history_dataset_association,
diff --git a/test/unit/data/model/test_database_utils.py b/test/unit/data/model/test_database_utils.py
index 72cbf17c860..6f1ea94c290 100644
--- a/test/unit/data/model/test_database_utils.py
+++ b/test/unit/data/model/test_database_utils.py
@@ -72,4 +72,4 @@ def test_create_exists_mysql_database(database_name, mysql_url):
 
 def make_sqlite_url(tmp_dir, database_name):
     path = os.path.join(tmp_dir, database_name)
-    return f'sqlite:///{path}'
+    return f"sqlite:///{path}"
diff --git a/test/unit/data/model/test_model.py b/test/unit/data/model/test_model.py
index 287fa507a95..c5326c6e204 100644
--- a/test/unit/data/model/test_model.py
+++ b/test/unit/data/model/test_model.py
@@ -1,4 +1,7 @@
-from uuid import UUID, uuid4
+from uuid import (
+    UUID,
+    uuid4,
+)
 
 from galaxy import model
 
diff --git a/test/unit/data/model/test_model_discovery.py b/test/unit/data/model/test_model_discovery.py
index f3fe2091fca..d59fc9b1c55 100644
--- a/test/unit/data/model/test_model_discovery.py
+++ b/test/unit/data/model/test_model_discovery.py
@@ -15,13 +15,15 @@ def test_model_create_context_persist_hdas():
         "destination": {
             "type": "hdas",
         },
-        "elements": [{
-            "filename": "file1.txt",
-            "ext": "txt",
-            "dbkey": "hg19",
-            "name": "my file",
-            "md5": "e5d21b1ea57fc9a31f8ea0110531bf3d",
-        }],
+        "elements": [
+            {
+                "filename": "file1.txt",
+                "ext": "txt",
+                "dbkey": "hg19",
+                "name": "my file",
+                "md5": "e5d21b1ea57fc9a31f8ea0110531bf3d",
+            }
+        ],
     }
     app = _mock_app()
     temp_directory = mkdtemp()
@@ -50,9 +52,11 @@ def test_model_create_context_persist_error_hda():
         "destination": {
             "type": "hdas",
         },
-        "elements": [{
-            "error_message": "Failed to download some URL I guess",
-        }],
+        "elements": [
+            {
+                "error_message": "Failed to download some URL I guess",
+            }
+        ],
     }
     app = _mock_app()
     temp_directory = mkdtemp()
@@ -78,12 +82,14 @@ def test_persist_target_library_dataset():
             "description": "Example Library Description",
             "synopsis": "Example Library Synopsis",
         },
-        "elements": [{
-            "filename": "file1.txt",
-            "ext": "txt",
-            "dbkey": "hg19",
-            "name": "my file",
-        }],
+        "elements": [
+            {
+                "filename": "file1.txt",
+                "ext": "txt",
+                "dbkey": "hg19",
+                "name": "my file",
+            }
+        ],
     }
     sa_session = _import_library_target(target, work_directory)
     new_library = _assert_one_library_created(sa_session)
@@ -114,17 +120,21 @@ def test_persist_target_library_folder():
             "description": "Example Library Description",
             "synopsis": "Example Library Synopsis",
         },
-        "items": [{
-            "name": "Folder 1",
-            "description": "Folder 1 Description",
-            "items": [{
-                "filename": "file1.txt",
-                "ext": "txt",
-                "dbkey": "hg19",
-                "info": "dataset info",
-                "name": "my file",
-            }]
-        }],
+        "items": [
+            {
+                "name": "Folder 1",
+                "description": "Folder 1 Description",
+                "items": [
+                    {
+                        "filename": "file1.txt",
+                        "ext": "txt",
+                        "dbkey": "hg19",
+                        "info": "dataset info",
+                        "name": "my file",
+                    }
+                ],
+            }
+        ],
     }
     sa_session = _import_library_target(target, work_directory)
     new_library = _assert_one_library_created(sa_session)
@@ -156,19 +166,22 @@ def test_persist_target_hdca():
         },
         "name": "My HDCA",
         "collection_type": "list",
-        "elements": [{
-            "filename": "file1.txt",
-            "ext": "txt",
-            "dbkey": "hg19",
-            "info": "dataset info",
-            "name": "my file",
-        }, {
-            "filename": "file2.txt",
-            "ext": "txt",
-            "dbkey": "hg18",
-            "info": "dataset info 2",
-            "name": "my file 2",
-        }]
+        "elements": [
+            {
+                "filename": "file1.txt",
+                "ext": "txt",
+                "dbkey": "hg19",
+                "info": "dataset info",
+                "name": "my file",
+            },
+            {
+                "filename": "file2.txt",
+                "ext": "txt",
+                "dbkey": "hg18",
+                "info": "dataset info 2",
+                "name": "my file 2",
+            },
+        ],
     }
 
     app = _mock_app()
@@ -208,7 +221,9 @@ def _import_library_target(target, work_directory):
     u = model.User(email="library@example.com", password="password")
 
     import_options = store.ImportOptions(allow_dataset_object_edit=True, allow_library_creation=True)
-    import_model_store = store.get_import_model_store_for_directory(temp_directory, app=app, user=u, import_options=import_options)
+    import_model_store = store.get_import_model_store_for_directory(
+        temp_directory, app=app, user=u, import_options=import_options
+    )
     import_model_store.perform_import()
 
     sa_session = app.model.context
@@ -228,7 +243,9 @@ def _import_directory_to_history(app, target, work_directory):
     assert len(import_history.datasets) == 0
 
     import_options = store.ImportOptions(allow_dataset_object_edit=True)
-    import_model_store = store.get_import_model_store_for_directory(target, app=app, user=u, import_options=import_options)
+    import_model_store = store.get_import_model_store_for_directory(
+        target, app=app, user=u, import_options=import_options
+    )
     with import_model_store.target_history(default_history=import_history):
         import_model_store.perform_import(import_history)
 
diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
index fa5514c1811..0605e4b93fb 100644
--- a/test/unit/data/model/test_model_store.py
+++ b/test/unit/data/model/test_model_store.py
@@ -3,7 +3,10 @@ import json
 import os
 import pathlib
 import shutil
-from tempfile import mkdtemp, NamedTemporaryFile
+from tempfile import (
+    mkdtemp,
+    NamedTemporaryFile,
+)
 
 import pytest
 
@@ -15,8 +18,8 @@ from galaxy.objectstore.unittest_utils import Config as TestConfig
 from galaxy.util.compression_utils import CompressedFile
 
 TESTCASE_DIRECTORY = pathlib.Path(__file__).parent
-TEST_PATH_1 = TESTCASE_DIRECTORY / '1.txt'
-TEST_PATH_2 = TESTCASE_DIRECTORY / '2.bed'
+TEST_PATH_1 = TESTCASE_DIRECTORY / "1.txt"
+TEST_PATH_2 = TESTCASE_DIRECTORY / "2.bed"
 
 
 def test_import_export_history():
@@ -34,11 +37,11 @@ def test_import_export_history_failed_job():
     """Test a simple job import/export, make sure state is maintained correctly."""
     app = _mock_app()
 
-    u, h, d1, d2, j = _setup_simple_cat_job(app, state='error')
+    u, h, d1, d2, j = _setup_simple_cat_job(app, state="error")
 
     imported_history = _import_export_history(app, h, export_files="copy")
 
-    _assert_simple_cat_job_imported(imported_history, state='error')
+    _assert_simple_cat_job_imported(imported_history, state="error")
 
 
 def test_import_export_bag_archive():
@@ -50,7 +53,9 @@ def test_import_export_bag_archive():
 
     u, h, d1, d2, j = _setup_simple_cat_job(app)
 
-    with store.BagArchiveModelExportStore(dest_export, app=app, bag_archiver="tgz", export_files="copy") as export_store:
+    with store.BagArchiveModelExportStore(
+        dest_export, app=app, bag_archiver="tgz", export_files="copy"
+    ) as export_store:
         export_store.export_history(h)
 
     model_store = store.BagArchiveImportModelStore(dest_export, app=app, user=u)
@@ -86,7 +91,7 @@ def test_import_library_require_permissions():
     u = model.User(email="collection@example.com", password="password")
 
     library = model.Library(name="my library 1", description="my library description", synopsis="my synopsis")
-    root_folder = model.LibraryFolder(name="my library 1", description='folder description')
+    root_folder = model.LibraryFolder(name="my library 1", description="folder description")
     library.root_folder = root_folder
     sa_session.add_all((library, root_folder))
     sa_session.flush()
@@ -114,7 +119,7 @@ def test_import_export_library():
     u = model.User(email="collection@example.com", password="password")
 
     library = model.Library(name="my library 1", description="my library description", synopsis="my synopsis")
-    root_folder = model.LibraryFolder(name="my library 1", description='folder description')
+    root_folder = model.LibraryFolder(name="my library 1", description="folder description")
     library.root_folder = root_folder
     sa_session.add_all((library, root_folder))
     sa_session.flush()
@@ -124,9 +129,7 @@ def test_import_export_library():
     sa_session.add(subfolder)
 
     ld = model.LibraryDataset(folder=root_folder, name="my name", info="my library dataset")
-    ldda = model.LibraryDatasetDatasetAssociation(
-        create_dataset=True, flush=False
-    )
+    ldda = model.LibraryDatasetDatasetAssociation(create_dataset=True, flush=False)
     ld.library_dataset_dataset_association = ldda
     root_folder.add_library_dataset(ld)
 
@@ -141,7 +144,9 @@ def test_import_export_library():
     with store.DirectoryModelExportStore(temp_directory, app=app) as export_store:
         export_store.export_library(library)
 
-    import_model_store = store.get_import_model_store_for_directory(temp_directory, app=app, user=u, import_options=store.ImportOptions(allow_library_creation=True))
+    import_model_store = store.get_import_model_store_for_directory(
+        temp_directory, app=app, user=u, import_options=store.ImportOptions(allow_library_creation=True)
+    )
     import_model_store.perform_import()
 
     all_libraries = sa_session.query(model.Library).all()
@@ -273,8 +278,10 @@ def test_import_export_edit_collection():
     d2 = model.HistoryDatasetAssociation(extension="txt", create_dataset=True, flush=False)
     d2.hid = 2
     serialization_options = model.SerializationOptions(for_edit=True)
-    dataset_list = [d1.serialize(app.security, serialization_options),
-                    d2.serialize(app.security, serialization_options)]
+    dataset_list = [
+        d1.serialize(app.security, serialization_options),
+        d2.serialize(app.security, serialization_options),
+    ]
 
     dc = model.DatasetCollection(
         id=collection_metadata["id"],
@@ -322,12 +329,7 @@ def test_import_export_composite_datasets():
     primary = NamedTemporaryFile("w")
     primary.write("cool primary file")
     primary.flush()
-    app.object_store.update_from_file(
-        d1.dataset,
-        file_name=primary.name,
-        create=True,
-        preserve_symlinks=True
-    )
+    app.object_store.update_from_file(d1.dataset, file_name=primary.name, create=True, preserve_symlinks=True)
 
     composite1 = NamedTemporaryFile("w")
     composite1.write("cool composite file")
@@ -339,7 +341,7 @@ def test_import_export_composite_datasets():
         alt_name="child_file",
         file_name=composite1.name,
         create=True,
-        preserve_symlinks=True
+        preserve_symlinks=True,
     )
 
     temp_directory = mkdtemp()
@@ -381,7 +383,9 @@ def test_edit_metadata_files():
     assert isinstance(d1.metadata.bam_index, model.MetadataFile)
 
     temp_directory = mkdtemp()
-    with store.DirectoryModelExportStore(temp_directory, app=app, for_edit=True, strip_metadata_files=False) as export_store:
+    with store.DirectoryModelExportStore(
+        temp_directory, app=app, for_edit=True, strip_metadata_files=False
+    ) as export_store:
         export_store.add_dataset(d1)
 
     import_history = model.History(name="Test History for Import", user=u)
@@ -393,7 +397,9 @@ def test_edit_metadata_files():
 def test_sessionless_import_edit_datasets():
     app, h, temp_directory, import_history = _setup_simple_export({"for_edit": True})
     # Create a model store without a session and import it.
-    import_model_store = store.get_import_model_store_for_directory(temp_directory, import_options=store.ImportOptions(allow_dataset_object_edit=True, allow_edit=True))
+    import_model_store = store.get_import_model_store_for_directory(
+        temp_directory, import_options=store.ImportOptions(allow_dataset_object_edit=True, allow_edit=True)
+    )
     import_model_store.perform_import()
     # Not using app.sa_session but a session mock that has a query/find pattern emulating usage
     # of real sa_session.
@@ -435,7 +441,7 @@ def _setup_simple_export(export_kwds):
     return app, h, temp_directory, import_history
 
 
-def _assert_simple_cat_job_imported(imported_history, state='ok'):
+def _assert_simple_cat_job_imported(imported_history, state="ok"):
     assert imported_history.name == "imported from archive: Test History"
 
     datasets = imported_history.datasets
@@ -456,7 +462,7 @@ def _assert_simple_cat_job_imported(imported_history, state='ok'):
         assert f.read().startswith("chr1\t147962192\t147962580\tNM_005997_cds_0_0_chr1_147962193_r\t0\t-")
 
 
-def _setup_simple_cat_job(app, state='ok'):
+def _setup_simple_cat_job(app, state="ok"):
     sa_session = app.model.context
 
     u = model.User(email="collection@example.com", password="password")
@@ -496,13 +502,20 @@ def _import_export_history(app, h, dest_export=None, export_files=None):
 
 
 def _perform_import_from_directory(directory, app, user, import_history, import_options=None):
-    import_model_store = store.get_import_model_store_for_directory(directory, app=app, user=user, import_options=import_options)
+    import_model_store = store.get_import_model_store_for_directory(
+        directory, app=app, user=user, import_options=import_options
+    )
     with import_model_store.target_history(default_history=import_history):
         import_model_store.perform_import(import_history)
 
 
 def _create_datasets(sa_session, history, n, extension="txt"):
-    return [model.HistoryDatasetAssociation(extension=extension, history=history, create_dataset=True, sa_session=sa_session, hid=i + 1) for i in range(n)]
+    return [
+        model.HistoryDatasetAssociation(
+            extension=extension, history=history, create_dataset=True, sa_session=sa_session, hid=i + 1
+        )
+        for i in range(n)
+    ]
 
 
 def _mock_app(store_by="id"):
diff --git a/test/unit/data/model/test_views.py b/test/unit/data/model/test_views.py
index 27203dddcd7..284e5d74a60 100644
--- a/test/unit/data/model/test_views.py
+++ b/test/unit/data/model/test_views.py
@@ -30,12 +30,9 @@ from .common import (
 def view():
     # A View class we would add to galaxy.model.view
     class TestView(View):
-        name = 'testview'
-        __view__ = text('SELECT id, foo FROM testfoo').columns(
-            column('id', Integer),
-            column('foo', Integer)
-        )
-        pkeys = {'id'}
+        name = "testview"
+        __view__ = text("SELECT id, foo FROM testfoo").columns(column("id", Integer), column("foo", Integer))
+        pkeys = {"id"}
         View._make_table(name, __view__, pkeys)
 
     return TestView
@@ -72,10 +69,8 @@ def test_mysql_create_view(database_name, mysql_url, view):
 
 
 def make_table(metadata):
-    users = Table('testfoo', metadata,
-        Column('id', Integer, primary_key=True),
-        Column('foo', Integer),
-        Column('bar', Integer)
+    users = Table(
+        "testfoo", metadata, Column("id", Integer, primary_key=True), Column("foo", Integer), Column("bar", Integer)
     )
     return users
 
diff --git a/test/unit/data/security/test_id_encode_decode.py b/test/unit/data/security/test_id_encode_decode.py
index 55422c28aac..7b9ffc8f839 100644
--- a/test/unit/data/security/test_id_encode_decode.py
+++ b/test/unit/data/security/test_id_encode_decode.py
@@ -1,6 +1,5 @@
 from galaxy.security import idencoding
 
-
 test_helper_1 = idencoding.IdEncodingHelper(id_secret="secu1")
 test_helper_2 = idencoding.IdEncodingHelper(id_secret="secu2")
 
diff --git a/test/unit/data/security/test_passwords.py b/test/unit/data/security/test_passwords.py
index baaa588a292..06ad2e585c7 100644
--- a/test/unit/data/security/test_passwords.py
+++ b/test/unit/data/security/test_passwords.py
@@ -28,16 +28,16 @@ def test_hash_consistent():
     complex_pass = "à strange ünicode ڃtring"
 
     # Check hashes built in Python 2 for 18.05.
-    simple_pass_hash = 'PBKDF2$sha256$10000$LlkhoImT15LZAcFB$/afKJrFX9GXt6VEpB+omae19A2S4kBEY'
-    complex_pass_hash = 'PBKDF2$sha256$10000$rg2gPThkJycziB0s$/BJ7AfuaYjpo5hhUvCMhf4TTrhsrOIH1'
+    simple_pass_hash = "PBKDF2$sha256$10000$LlkhoImT15LZAcFB$/afKJrFX9GXt6VEpB+omae19A2S4kBEY"
+    complex_pass_hash = "PBKDF2$sha256$10000$rg2gPThkJycziB0s$/BJ7AfuaYjpo5hhUvCMhf4TTrhsrOIH1"
 
     # Check hashes built in Python 3 for 18.05.
-    simple_pass_hash_2 = 'PBKDF2$sha256$10000$vOIv7wGXS2/rGhDu$wS/5NwGSZm1ECv/vSEZb7jKjYSzXWZDL'
-    complex_pass_hash_2 = 'PBKDF2$sha256$10000$q1av/Clyujm5Fdc6$Dh7o1KTMn/YQYc5NurN+aVaF3uaI8iOv'
+    simple_pass_hash_2 = "PBKDF2$sha256$10000$vOIv7wGXS2/rGhDu$wS/5NwGSZm1ECv/vSEZb7jKjYSzXWZDL"
+    complex_pass_hash_2 = "PBKDF2$sha256$10000$q1av/Clyujm5Fdc6$Dh7o1KTMn/YQYc5NurN+aVaF3uaI8iOv"
 
     # Check older sha1 passwords that may still be the database as well.
-    simple_pass_hash_old = '58f17339ffdb71050734d2fbdd41b870423fe433'
-    complex_pass_hash_old = 'b567602039213afc0db026eedd72bd3ee2e57092'
+    simple_pass_hash_old = "58f17339ffdb71050734d2fbdd41b870423fe433"
+    complex_pass_hash_old = "b567602039213afc0db026eedd72bd3ee2e57092"
 
     assert passwords.check_password(simple_pass, simple_pass_hash)
     assert passwords.check_password(complex_pass, complex_pass_hash)
diff --git a/test/unit/data/test_galaxy_mapping.py b/test/unit/data/test_galaxy_mapping.py
index 0ddf699195e..4a16c2dcafb 100644
--- a/test/unit/data/test_galaxy_mapping.py
+++ b/test/unit/data/test_galaxy_mapping.py
@@ -7,7 +7,10 @@ from tempfile import NamedTemporaryFile
 from typing import List
 
 import pytest
-from sqlalchemy import inspect, select
+from sqlalchemy import (
+    inspect,
+    select,
+)
 
 import galaxy.datatypes.registry
 import galaxy.model
@@ -25,8 +28,8 @@ DB_URI = "sqlite:///:memory:"
 # docker run -e POSTGRES_USER=galaxy -p 5432:5432 -d postgres
 # GALAXY_TEST_UNIT_MAPPING_URI_POSTGRES_BASE='postgresql://galaxy@localhost:5432/' pytest test/unit/data/test_galaxy_mapping.py
 skip_if_not_postgres_base = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_UNIT_MAPPING_URI_POSTGRES_BASE'),
-    reason="GALAXY_TEST_UNIT_MAPPING_URI_POSTGRES_BASE not set"
+    not os.environ.get("GALAXY_TEST_UNIT_MAPPING_URI_POSTGRES_BASE"),
+    reason="GALAXY_TEST_UNIT_MAPPING_URI_POSTGRES_BASE not set",
 )
 
 
@@ -50,12 +53,12 @@ class BaseModelTestCase(unittest.TestCase):
     @classmethod
     def persist(cls, *args, **kwargs):
         session = cls.session()
-        flush = kwargs.get('flush', True)
+        flush = kwargs.get("flush", True)
         for arg in args:
             session.add(arg)
             if flush:
                 session.flush()
-        if kwargs.get('expunge', not flush):
+        if kwargs.get("expunge", not flush):
             cls.expunge()
         return arg  # Return last or only arg.
 
@@ -70,7 +73,6 @@ class BaseModelTestCase(unittest.TestCase):
 
 
 class MappingTests(BaseModelTestCase):
-
     def test_annotations(self):
         u = model.User(email="annotator@example.com", password="password")
         self.persist(u)
@@ -105,7 +107,9 @@ class MappingTests(BaseModelTestCase):
         self.persist(h)
         persist_and_check_annotation(model.HistoryAnnotationAssociation, history=h)
 
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(d1)
         persist_and_check_annotation(model.HistoryDatasetAssociationAnnotationAssociation, hda=d1)
 
@@ -122,11 +126,16 @@ class MappingTests(BaseModelTestCase):
         dataset_collection = model.DatasetCollection(collection_type="paired")
         history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
         self.persist(history_dataset_collection)
-        persist_and_check_annotation(model.HistoryDatasetCollectionAssociationAnnotationAssociation, history_dataset_collection=history_dataset_collection)
+        persist_and_check_annotation(
+            model.HistoryDatasetCollectionAssociationAnnotationAssociation,
+            history_dataset_collection=history_dataset_collection,
+        )
 
         library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
         self.persist(library_dataset_collection)
-        persist_and_check_annotation(model.LibraryDatasetCollectionAnnotationAssociation, library_dataset_collection=library_dataset_collection)
+        persist_and_check_annotation(
+            model.LibraryDatasetCollectionAnnotationAssociation, library_dataset_collection=library_dataset_collection
+        )
 
     def test_ratings(self):
         user_email = "rater@example.com"
@@ -151,7 +160,9 @@ class MappingTests(BaseModelTestCase):
         self.persist(h)
         persist_and_check_rating(model.HistoryRatingAssociation, h)
 
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(d1)
         persist_and_check_rating(model.HistoryDatasetAssociationRatingAssociation, d1)
 
@@ -175,40 +186,37 @@ class MappingTests(BaseModelTestCase):
         persist_and_check_rating(model.LibraryDatasetCollectionRatingAssociation, library_dataset_collection)
 
     def test_display_name(self):
-
         def assert_display_name_converts_to_unicode(item, name):
             assert isinstance(item.get_display_name(), str)
             assert item.get_display_name() == name
 
-        ldda = model.LibraryDatasetDatasetAssociation(name='ldda_name')
-        assert_display_name_converts_to_unicode(ldda, 'ldda_name')
+        ldda = model.LibraryDatasetDatasetAssociation(name="ldda_name")
+        assert_display_name_converts_to_unicode(ldda, "ldda_name")
 
-        hda = model.HistoryDatasetAssociation(name='hda_name')
-        assert_display_name_converts_to_unicode(hda, 'hda_name')
+        hda = model.HistoryDatasetAssociation(name="hda_name")
+        assert_display_name_converts_to_unicode(hda, "hda_name")
 
-        history = model.History(name='history_name')
-        assert_display_name_converts_to_unicode(history, 'history_name')
+        history = model.History(name="history_name")
+        assert_display_name_converts_to_unicode(history, "history_name")
 
-        library = model.Library(name='library_name')
-        assert_display_name_converts_to_unicode(library, 'library_name')
+        library = model.Library(name="library_name")
+        assert_display_name_converts_to_unicode(library, "library_name")
 
-        library_folder = model.LibraryFolder(name='library_folder')
-        assert_display_name_converts_to_unicode(library_folder, 'library_folder')
+        library_folder = model.LibraryFolder(name="library_folder")
+        assert_display_name_converts_to_unicode(library_folder, "library_folder")
 
-        history = model.History(
-            name='Hello₩◎ґʟⅾ'
-        )
+        history = model.History(name="Hello₩◎ґʟⅾ")
 
         assert isinstance(history.name, str)
         assert isinstance(history.get_display_name(), str)
-        assert history.get_display_name() == 'Hello₩◎ґʟⅾ'
+        assert history.get_display_name() == "Hello₩◎ґʟⅾ"
 
     def test_hda_to_library_dataset_dataset_association(self):
         u = model.User(email="mary@example.com", password="password")
-        hda = model.HistoryDatasetAssociation(name='hda_name')
+        hda = model.HistoryDatasetAssociation(name="hda_name")
         self.persist(hda)
-        trans = collections.namedtuple('trans', 'user')
-        target_folder = model.LibraryFolder(name='library_folder')
+        trans = collections.namedtuple("trans", "user")
+        target_folder = model.LibraryFolder(name="library_folder")
         ldda = hda.to_library_dataset_dataset_association(
             trans=trans(user=u),
             target_folder=target_folder,
@@ -222,9 +230,7 @@ class MappingTests(BaseModelTestCase):
         library_dataset_id = ldda.library_dataset_id
         replace_dataset = ldda.library_dataset
         new_ldda = hda.to_library_dataset_dataset_association(
-            trans=trans(user=u),
-            target_folder=target_folder,
-            replace_dataset=replace_dataset
+            trans=trans(user=u), target_folder=target_folder, replace_dataset=replace_dataset
         )
         assert new_ldda.id != ldda.id
         assert new_ldda.library_dataset_id == library_dataset_id
@@ -234,7 +240,7 @@ class MappingTests(BaseModelTestCase):
         assert target_folder.item_count == 1
 
     def test_tags(self):
-        TAG_NAME = 'Test Tag'
+        TAG_NAME = "Test Tag"
         my_tag = model.Tag(name=TAG_NAME)
         u = model.User(email="tagger@example.com", password="password")
         self.persist(my_tag, u)
@@ -257,7 +263,9 @@ class MappingTests(BaseModelTestCase):
         h = model.History(name="History for Tagging", user=u)
         tag_and_test(h, model.HistoryTagAssociation)
 
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         tag_and_test(d1, model.HistoryDatasetAssociationTagAssociation)
 
         page = model.Page(user=u)
@@ -276,10 +284,15 @@ class MappingTests(BaseModelTestCase):
     def test_collection_get_interface(self):
         u = model.User(email="mary@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h1, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
+        )
         c1 = model.DatasetCollection(collection_type="list")
         elements = 100
-        dces = [model.DatasetCollectionElement(collection=c1, element=d1, element_identifier=f"{i}", element_index=i) for i in range(elements)]
+        dces = [
+            model.DatasetCollectionElement(collection=c1, element=d1, element_identifier=f"{i}", element_index=i)
+            for i in range(elements)
+        ]
         self.persist(u, h1, d1, c1, *dces, flush=False, expunge=False)
         self.model.session.flush()
         for i in range(elements):
@@ -292,10 +305,18 @@ class MappingTests(BaseModelTestCase):
         list_pair = model.DatasetCollection(collection_type="list:paired")
         for i in range(20):
             pair = model.DatasetCollection(collection_type="pair")
-            forward = model.HistoryDatasetAssociation(extension="txt", history=h1, name=f"forward_{i}", create_dataset=True, sa_session=self.model.session)
-            reverse = model.HistoryDatasetAssociation(extension="bam", history=h1, name=f"reverse_{i}", create_dataset=True, sa_session=self.model.session)
-            dce1 = model.DatasetCollectionElement(collection=pair, element=forward, element_identifier=f"forward_{i}", element_index=1)
-            dce2 = model.DatasetCollectionElement(collection=pair, element=reverse, element_identifier=f"reverse_{i}", element_index=2)
+            forward = model.HistoryDatasetAssociation(
+                extension="txt", history=h1, name=f"forward_{i}", create_dataset=True, sa_session=self.model.session
+            )
+            reverse = model.HistoryDatasetAssociation(
+                extension="bam", history=h1, name=f"reverse_{i}", create_dataset=True, sa_session=self.model.session
+            )
+            dce1 = model.DatasetCollectionElement(
+                collection=pair, element=forward, element_identifier=f"forward_{i}", element_index=1
+            )
+            dce2 = model.DatasetCollectionElement(
+                collection=pair, element=reverse, element_identifier=f"reverse_{i}", element_index=2
+            )
             to_persist = [(forward, reverse), (dce1, dce2)]
             self.persist(pair)
             for pair_item in to_persist:
@@ -305,7 +326,11 @@ class MappingTests(BaseModelTestCase):
                 else:
                     self.persist(pair_item[1])
                     self.persist(pair_item[0])
-            elements.append(model.DatasetCollectionElement(collection=list_pair, element=pair, element_index=i, element_identifier=str(i)))
+            elements.append(
+                model.DatasetCollectionElement(
+                    collection=list_pair, element=pair, element_index=i, element_identifier=str(i)
+                )
+            )
         self.persist(list_pair)
         random.shuffle(elements)
         for item in elements:
@@ -323,8 +348,12 @@ class MappingTests(BaseModelTestCase):
     def test_collections_in_histories(self):
         u = model.User(email="mary@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h1, create_dataset=True, sa_session=self.model.session)
-        d2 = model.HistoryDatasetAssociation(extension="txt", history=h1, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
+        )
+        d2 = model.HistoryDatasetAssociation(
+            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
+        )
 
         c1 = model.DatasetCollection(collection_type="pair")
         hc1 = model.HistoryDatasetCollectionAssociation(history=h1, collection=c1, name="HistoryCollectionTest1")
@@ -334,7 +363,12 @@ class MappingTests(BaseModelTestCase):
 
         self.persist(u, h1, d1, d2, c1, hc1, dce1, dce2)
 
-        loaded_dataset_collection = self.query(model.HistoryDatasetCollectionAssociation).filter(model.HistoryDatasetCollectionAssociation.name == "HistoryCollectionTest1").first().collection
+        loaded_dataset_collection = (
+            self.query(model.HistoryDatasetCollectionAssociation)
+            .filter(model.HistoryDatasetCollectionAssociation.name == "HistoryCollectionTest1")
+            .first()
+            .collection
+        )
         self.assertEqual(len(loaded_dataset_collection.elements), 2)
         assert loaded_dataset_collection.collection_type == "pair"
         assert loaded_dataset_collection["left"] == dce1
@@ -363,32 +397,48 @@ class MappingTests(BaseModelTestCase):
     def test_nested_collection_attributes(self):
         u = model.User(email="mary2@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(extension="bam", history=h1, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="bam", history=h1, create_dataset=True, sa_session=self.model.session
+        )
         index = NamedTemporaryFile("w")
         index.write("cool bam index")
         index2 = NamedTemporaryFile("w")
         index2.write("cool bam index 2")
-        metadata_dict = {"bam_index": MetadataTempFile.from_JSON({"kwds": {}, "filename": index.name}), "bam_csi_index": MetadataTempFile.from_JSON({"kwds": {}, "filename": index2.name})}
+        metadata_dict = {
+            "bam_index": MetadataTempFile.from_JSON({"kwds": {}, "filename": index.name}),
+            "bam_csi_index": MetadataTempFile.from_JSON({"kwds": {}, "filename": index2.name}),
+        }
         d1.metadata.from_JSON_dict(json_dict=metadata_dict)
         assert d1.metadata.bam_index
         assert d1.metadata.bam_csi_index
         assert isinstance(d1.metadata.bam_index, model.MetadataFile)
         assert isinstance(d1.metadata.bam_csi_index, model.MetadataFile)
-        d2 = model.HistoryDatasetAssociation(extension="txt", history=h1, create_dataset=True, sa_session=self.model.session)
-        c1 = model.DatasetCollection(collection_type='paired')
+        d2 = model.HistoryDatasetAssociation(
+            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
+        )
+        c1 = model.DatasetCollection(collection_type="paired")
         dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
         dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
         c2 = model.DatasetCollection(collection_type="list:paired")
-        dce3 = model.DatasetCollectionElement(collection=c2, element=c1, element_identifier="inner_list", element_index=0)
+        dce3 = model.DatasetCollectionElement(
+            collection=c2, element=c1, element_identifier="inner_list", element_index=0
+        )
         c3 = model.DatasetCollection(collection_type="list:list")
         c4 = model.DatasetCollection(collection_type="list:list:paired")
-        dce4 = model.DatasetCollectionElement(collection=c4, element=c2, element_identifier="outer_list", element_index=0)
+        dce4 = model.DatasetCollectionElement(
+            collection=c4, element=c2, element_identifier="outer_list", element_index=0
+        )
         self.model.session.add_all([d1, d2, c1, dce1, dce2, c2, dce3, c3, c4, dce4])
         self.model.session.flush()
-        q = c2._get_nested_collection_attributes(element_attributes=('element_identifier',), hda_attributes=('extension',), dataset_attributes=('state',))
-        assert [(r.keys()) for r in q] == [['element_identifier_0', 'element_identifier_1', 'extension', 'state'], ['element_identifier_0', 'element_identifier_1', 'extension', 'state']]
-        assert q.all() == [('inner_list', 'forward', 'bam', 'new'), ('inner_list', 'reverse', 'txt', 'new')]
-        q = c2._get_nested_collection_attributes(return_entities=(model.HistoryDatasetAssociation, ))
+        q = c2._get_nested_collection_attributes(
+            element_attributes=("element_identifier",), hda_attributes=("extension",), dataset_attributes=("state",)
+        )
+        assert [(r.keys()) for r in q] == [
+            ["element_identifier_0", "element_identifier_1", "extension", "state"],
+            ["element_identifier_0", "element_identifier_1", "extension", "state"],
+        ]
+        assert q.all() == [("inner_list", "forward", "bam", "new"), ("inner_list", "reverse", "txt", "new")]
+        q = c2._get_nested_collection_attributes(return_entities=(model.HistoryDatasetAssociation,))
         assert q.all() == [d1, d2]
         q = c2._get_nested_collection_attributes(return_entities=(model.HistoryDatasetAssociation, model.Dataset))
         assert q.all() == [(d1, d1.dataset), (d2, d2.dataset)]
@@ -397,22 +447,37 @@ class MappingTests(BaseModelTestCase):
         assert c2.dataset_elements == [dce1, dce2]
         assert c2.dataset_action_tuples == []
         assert c2.populated_optimized
-        assert c2.dataset_states_and_extensions_summary == ({'new'}, {'txt', 'bam'})
-        assert c2.element_identifiers_extensions_paths_and_metadata_files == [[('inner_list', 'forward'), 'bam', 'mock_dataset_14.dat', [('bai', 'mock_dataset_14.dat'), ('bam.csi', 'mock_dataset_14.dat')]], [('inner_list', 'reverse'), 'txt', 'mock_dataset_14.dat', []]]
+        assert c2.dataset_states_and_extensions_summary == ({"new"}, {"txt", "bam"})
+        assert c2.element_identifiers_extensions_paths_and_metadata_files == [
+            [
+                ("inner_list", "forward"),
+                "bam",
+                "mock_dataset_14.dat",
+                [("bai", "mock_dataset_14.dat"), ("bam.csi", "mock_dataset_14.dat")],
+            ],
+            [("inner_list", "reverse"), "txt", "mock_dataset_14.dat", []],
+        ]
         assert c3.dataset_instances == []
         assert c3.dataset_elements == []
         assert c3.dataset_states_and_extensions_summary == (set(), set())
-        q = c4._get_nested_collection_attributes(element_attributes=('element_identifier',))
-        assert q.all() == [('outer_list', 'inner_list', 'forward'), ('outer_list', 'inner_list', 'reverse')]
+        q = c4._get_nested_collection_attributes(element_attributes=("element_identifier",))
+        assert q.all() == [("outer_list", "inner_list", "forward"), ("outer_list", "inner_list", "reverse")]
         assert c4.dataset_elements == [dce1, dce2]
-        assert c4.element_identifiers_extensions_and_paths == [(('outer_list', 'inner_list', 'forward'), 'bam', 'mock_dataset_14.dat'), (('outer_list', 'inner_list', 'reverse'), 'txt', 'mock_dataset_14.dat')]
+        assert c4.element_identifiers_extensions_and_paths == [
+            (("outer_list", "inner_list", "forward"), "bam", "mock_dataset_14.dat"),
+            (("outer_list", "inner_list", "reverse"), "txt", "mock_dataset_14.dat"),
+        ]
 
     def test_dataset_dbkeys_and_extensions_summary(self):
         u = model.User(email="mary2@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(extension="bam", dbkey="hg19", history=h1, create_dataset=True, sa_session=self.model.session)
-        d2 = model.HistoryDatasetAssociation(extension="txt", dbkey="hg19", history=h1, create_dataset=True, sa_session=self.model.session)
-        c1 = model.DatasetCollection(collection_type='paired')
+        d1 = model.HistoryDatasetAssociation(
+            extension="bam", dbkey="hg19", history=h1, create_dataset=True, sa_session=self.model.session
+        )
+        d2 = model.HistoryDatasetAssociation(
+            extension="txt", dbkey="hg19", history=h1, create_dataset=True, sa_session=self.model.session
+        )
+        c1 = model.DatasetCollection(collection_type="paired")
         dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
         dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
         hdca = model.HistoryDatasetCollectionAssociation(collection=c1, history=h1)
@@ -424,9 +489,13 @@ class MappingTests(BaseModelTestCase):
     def test_populated_optimized_ok(self):
         u = model.User(email="mary2@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h1, create_dataset=True, sa_session=self.model.session)
-        d2 = model.HistoryDatasetAssociation(extension="txt", history=h1, create_dataset=True, sa_session=self.model.session)
-        c1 = model.DatasetCollection(collection_type='paired')
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
+        )
+        d2 = model.HistoryDatasetAssociation(
+            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
+        )
+        c1 = model.DatasetCollection(collection_type="paired")
         dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
         dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
         self.model.session.add_all([d1, d2, c1, dce1, dce2])
@@ -435,9 +504,11 @@ class MappingTests(BaseModelTestCase):
         assert c1.populated_optimized
 
     def test_populated_optimized_empty_list_list_ok(self):
-        c1 = model.DatasetCollection(collection_type='list')
-        c2 = model.DatasetCollection(collection_type='list:list')
-        dce1 = model.DatasetCollectionElement(collection=c2, element=c1, element_identifier="empty_list", element_index=0)
+        c1 = model.DatasetCollection(collection_type="list")
+        c2 = model.DatasetCollection(collection_type="list:list")
+        dce1 = model.DatasetCollectionElement(
+            collection=c2, element=c1, element_identifier="empty_list", element_index=0
+        )
         self.model.session.add_all([c1, c2, dce1])
         self.model.session.flush()
         assert c1.populated
@@ -446,10 +517,12 @@ class MappingTests(BaseModelTestCase):
         assert c2.populated_optimized
 
     def test_populated_optimized_list_list_not_populated(self):
-        c1 = model.DatasetCollection(collection_type='list')
+        c1 = model.DatasetCollection(collection_type="list")
         c1.populated_state = False
-        c2 = model.DatasetCollection(collection_type='list:list')
-        dce1 = model.DatasetCollectionElement(collection=c2, element=c1, element_identifier="empty_list", element_index=0)
+        c2 = model.DatasetCollection(collection_type="list:list")
+        dce1 = model.DatasetCollectionElement(
+            collection=c2, element=c1, element_identifier="empty_list", element_index=0
+        )
         self.model.session.add_all([c1, c2, dce1])
         self.model.session.flush()
         assert not c1.populated
@@ -479,7 +552,9 @@ class MappingTests(BaseModelTestCase):
         self.persist(u, h1, h2)
         # q1 = model.Query( "h2->q1" )
         metadata = dict(chromCol=1, startCol=2, endCol=3)
-        d1 = model.HistoryDatasetAssociation(extension="interval", metadata=metadata, history=h2, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="interval", metadata=metadata, history=h2, create_dataset=True, sa_session=self.model.session
+        )
         # h2.queries.append( q1 )
         # h2.queries.append( model.Query( "h2->q2" ) )
         self.persist(d1)
@@ -518,7 +593,7 @@ class MappingTests(BaseModelTestCase):
         d = model.HistoryDatasetAssociation(extension="interval", metadata=metadata, sa_session=self.model.session)
         assert d.metadata.chromCol == 1
         assert d.metadata.anyAttribute is None
-        assert 'items' not in d.metadata
+        assert "items" not in d.metadata
 
     def test_dataset_job_relationship(self):
         dataset = model.Dataset()
@@ -585,9 +660,9 @@ class MappingTests(BaseModelTestCase):
         self.session().flush()
 
         def contents_iter_names(**kwds):
-            history = self.model.context.query(model.History).filter(
-                model.History.name == "HistoryContentsHistory1"
-            ).first()
+            history = (
+                self.model.context.query(model.History).filter(model.History.name == "HistoryContentsHistory1").first()
+            )
             return list(map(lambda hda: hda.name, history.contents_iter(**kwds)))
 
         self.assertEqual(contents_iter_names(), ["1", "2", "3", "4"])
@@ -607,8 +682,12 @@ class MappingTests(BaseModelTestCase):
         h2 = model.History(name="HistoryAuditHistory", user=u)
 
         def get_audit_table_entries(history):
-            return self.session().query(model.HistoryAudit.table).filter(
-                model.HistoryAudit.table.c.history_id == history.id).all()
+            return (
+                self.session()
+                .query(model.HistoryAudit.table)
+                .filter(model.HistoryAudit.table.c.history_id == history.id)
+                .all()
+            )
 
         def get_latest_entry(entries):
             # key ensures result is correct if new columns are added
@@ -651,10 +730,7 @@ class MappingTests(BaseModelTestCase):
         # states and flushing in SQL Alchemy is very subtle and it is good to have a executable
         # reference for how it behaves in the context of Galaxy objects.
         model = self.model
-        user = model.User(
-            email="testworkflows@bx.psu.edu",
-            password="password"
-        )
+        user = model.User(email="testworkflows@bx.psu.edu", password="password")
         galaxy_session = model.GalaxySession()
         galaxy_session_other = model.GalaxySession()
         galaxy_session.user = user
@@ -668,25 +744,25 @@ class MappingTests(BaseModelTestCase):
         expected_id = galaxy_model_object.id
 
         # id loaded as part of the object query, could be any non-deferred attribute.
-        assert 'id' not in inspect(galaxy_model_object).unloaded
+        assert "id" not in inspect(galaxy_model_object).unloaded
 
         # Perform an empty flush, verify empty flush doesn't reload all attributes.
         session.flush()
-        assert 'id' not in inspect(galaxy_model_object).unloaded
+        assert "id" not in inspect(galaxy_model_object).unloaded
 
         # However, flushing anything non-empty - even unrelated object will invalidate
         # the session ID.
         self._non_empty_flush()
-        assert 'id' in inspect(galaxy_model_object).unloaded
+        assert "id" in inspect(galaxy_model_object).unloaded
 
         # Fetch the ID loads the value from the database
         assert expected_id == galaxy_model_object.id
-        assert 'id' not in inspect(galaxy_model_object).unloaded
+        assert "id" not in inspect(galaxy_model_object).unloaded
 
         # Using cached_id instead does not exhibit this behavior.
         self._non_empty_flush()
         assert expected_id == galaxy.model.cached_id(galaxy_model_object)
-        assert 'id' in inspect(galaxy_model_object).unloaded
+        assert "id" in inspect(galaxy_model_object).unloaded
 
         # Keeping the following failed experiments here for future reference,
         # I probed the internals of the attribute tracking and couldn't find an
@@ -712,19 +788,16 @@ class MappingTests(BaseModelTestCase):
         session.add(galaxy_model_object_new)
         session.flush()
         assert galaxy.model.cached_id(galaxy_model_object_new)
-        assert 'id' in inspect(galaxy_model_object_new).unloaded
+        assert "id" in inspect(galaxy_model_object_new).unloaded
 
         # Verify a targeted flush prevent expiring unrelated objects.
         galaxy_model_object_new.id
-        assert 'id' not in inspect(galaxy_model_object_new).unloaded
+        assert "id" not in inspect(galaxy_model_object_new).unloaded
         session.flush(model.GalaxySession())
-        assert 'id' not in inspect(galaxy_model_object_new).unloaded
+        assert "id" not in inspect(galaxy_model_object_new).unloaded
 
     def test_workflows(self):
-        user = model.User(
-            email="testworkflows@bx.psu.edu",
-            password="password"
-        )
+        user = model.User(email="testworkflows@bx.psu.edu", password="password")
 
         def workflow_from_steps(steps):
             stored_workflow = model.StoredWorkflow()
@@ -857,7 +930,9 @@ class MappingTests(BaseModelTestCase):
         u_from, u_to, u_other = self._three_users("private_share_role")
 
         h = model.History(name="History for Annotation", user=u_from)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(h, d1)
 
         security_agent.privately_share_dataset(d1.dataset, [u_to])
@@ -869,7 +944,9 @@ class MappingTests(BaseModelTestCase):
         u_from, u_to, u_other = self._three_users("make_dataset_public")
 
         h = model.History(name="History for Annotation", user=u_from)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(h, d1)
 
         security_agent.privately_share_dataset(d1.dataset, [u_to])
@@ -883,7 +960,9 @@ class MappingTests(BaseModelTestCase):
         u_from, _, u_other = self._three_users("set_all_perms")
 
         h = model.History(name="History for Annotation", user=u_from)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(h, d1)
 
         role = security_agent.get_private_user_role(u_from, auto_create=True)
@@ -892,7 +971,9 @@ class MappingTests(BaseModelTestCase):
         permissions = {access_action: [role], manage_action: [role]}
         assert security_agent.can_access_dataset(u_other.all_roles(), d1.dataset)
         security_agent.set_all_dataset_permissions(d1.dataset, permissions)
-        assert not security_agent.allow_action(u_other.all_roles(), security_agent.permitted_actions.DATASET_ACCESS, d1.dataset)
+        assert not security_agent.allow_action(
+            u_other.all_roles(), security_agent.permitted_actions.DATASET_ACCESS, d1.dataset
+        )
         assert not security_agent.can_access_dataset(u_other.all_roles(), d1.dataset)
 
     def test_can_manage_privately_shared_dataset(self):
@@ -900,7 +981,9 @@ class MappingTests(BaseModelTestCase):
         u_from, u_to, u_other = self._three_users("can_manage_dataset")
 
         h = model.History(name="History for Prevent Sharing", user=u_from)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(h, d1)
 
         self._make_owned(security_agent, u_from, d1)
@@ -913,7 +996,9 @@ class MappingTests(BaseModelTestCase):
         u_from, _, u_other = self._three_users("can_manage_dataset_ps")
 
         h = model.History(name="History for Prevent Sharing", user=u_from)
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         self.persist(h, d1)
 
         self._make_private(security_agent, u_from, d1)
@@ -926,13 +1011,13 @@ class MappingTests(BaseModelTestCase):
         self.persist(u, h)
         state = inspect(h)
         assert h.hid_counter == 1
-        assert 'hid_counter' not in state.unloaded
-        assert 'id' not in state.unloaded
+        assert "hid_counter" not in state.unloaded
+        assert "id" not in state.unloaded
 
         h._next_hid()
 
-        assert 'hid_counter' in state.unloaded  # this attribute has been expired
-        assert 'id' not in state.unloaded  # but other attributes have NOT been expired
+        assert "hid_counter" in state.unloaded  # this attribute has been expired
+        assert "id" not in state.unloaded  # but other attributes have NOT been expired
         assert h.hid_counter == 2  # check this last: this causes thie hid_counter to be reloaded
 
     def test_next_hid(self):
@@ -970,12 +1055,13 @@ class MappingTests(BaseModelTestCase):
         security_agent.set_all_dataset_permissions(hda.dataset, permissions)
 
     def new_hda(self, history, **kwds):
-        return history.add_dataset(model.HistoryDatasetAssociation(create_dataset=True, sa_session=self.model.session, **kwds))
+        return history.add_dataset(
+            model.HistoryDatasetAssociation(create_dataset=True, sa_session=self.model.session, **kwds)
+        )
 
 
 @skip_if_not_postgres_base
 class PostgresMappingTests(MappingTests):
-
     @classmethod
     def _db_uri(cls):
         base = os.environ.get("GALAXY_TEST_UNIT_MAPPING_URI_POSTGRES_BASE")
@@ -987,7 +1073,6 @@ class PostgresMappingTests(MappingTests):
 
 
 class MockObjectStore:
-
     def __init__(self):
         pass
 
@@ -1001,7 +1086,7 @@ class MockObjectStore:
         return "mock_dataset_14.dat"
 
     def get_store_by(self, *args, **kwds):
-        return 'id'
+        return "id"
 
     def update_from_file(self, *arg, **kwds):
         pass
diff --git a/test/unit/data/test_model_copy.py b/test/unit/data/test_model_copy.py
index e453cce6569..f1bcec97691 100644
--- a/test/unit/data/test_model_copy.py
+++ b/test/unit/data/test_model_copy.py
@@ -11,13 +11,10 @@ from galaxy.model import (
     User,
 )
 from galaxy.model.metadata import MetadataTempFile
-from galaxy.objectstore.unittest_utils import (
-    Config as TestConfig,
-    DISK_TEST_CONFIG,
-)
+from galaxy.objectstore.unittest_utils import Config as TestConfig
+from galaxy.objectstore.unittest_utils import DISK_TEST_CONFIG
 from galaxy.util import ExecutionTimer
 
-
 datatypes_registry = galaxy.datatypes.registry.Registry()
 datatypes_registry.load_datatypes()
 galaxy.model.set_datatypes_registry(datatypes_registry)
@@ -56,7 +53,9 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
             hdas = []
             for i in range(list_size * 2):
                 hda_path = test_config.write("moo", "test_metadata_original_%d" % i)
-                hda = _create_hda(model, object_store, old_history, hda_path, visible=False, include_metadata_file=False)
+                hda = _create_hda(
+                    model, object_store, old_history, hda_path, visible=False, include_metadata_file=False
+                )
                 hdas.append(hda)
 
             list_elements = []
@@ -65,7 +64,9 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
                 paired_collection = model.DatasetCollection(collection_type="paired")
                 forward_dce = model.DatasetCollectionElement(collection=paired_collection, element=hdas[j * 2])
                 reverse_dce = model.DatasetCollectionElement(collection=paired_collection, element=hdas[j * 2 + 1])
-                paired_collection_element = model.DatasetCollectionElement(collection=list_collection, element=paired_collection)
+                paired_collection_element = model.DatasetCollectionElement(
+                    collection=list_collection, element=paired_collection
+                )
                 list_elements.append(paired_collection_element)
                 model.context.add_all([forward_dce, reverse_dce, paired_collection_element])
             history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=list_collection)
@@ -74,10 +75,17 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
 
             model.context.flush()
             old_history.add_dataset_collection(history_dataset_collection)
-            history_dataset_collection.add_item_annotation(model.context, old_history.user, history_dataset_collection, "annotation #%d" % history_dataset_collection.hid)
+            history_dataset_collection.add_item_annotation(
+                model.context,
+                old_history.user,
+                history_dataset_collection,
+                "annotation #%d" % history_dataset_collection.hid,
+            )
 
         model.context.flush()
-        annotation_str = history_dataset_collection.get_item_annotation_str(model.context, old_history.user, history_dataset_collection)
+        annotation_str = history_dataset_collection.get_item_annotation_str(
+            model.context, old_history.user, history_dataset_collection
+        )
 
         # Saving magic SA invocations for detecting full flushes that may harm performance.
         # from sqlalchemy import event
@@ -107,7 +115,14 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
 def _setup_mapping_and_user():
     with TestConfig(DISK_TEST_CONFIG) as (test_config, object_store):
         # Start the database and connect the mapping
-        model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=object_store, slow_query_log_threshold=SLOW_QUERY_LOG_THRESHOLD, thread_local_log=THREAD_LOCAL_LOG)
+        model = mapping.init(
+            "/tmp",
+            "sqlite:///:memory:",
+            create_tables=True,
+            object_store=object_store,
+            slow_query_log_threshold=SLOW_QUERY_LOG_THRESHOLD,
+            thread_local_log=THREAD_LOCAL_LOG,
+        )
 
         u = User(email="historycopy@example.com", password="password")
         h1 = History(name="HistoryCopyHistory1", user=u)
diff --git a/test/unit/data/test_mutable_json_column.py b/test/unit/data/test_mutable_json_column.py
index 380a619b587..95a36ec7934 100644
--- a/test/unit/data/test_mutable_json_column.py
+++ b/test/unit/data/test_mutable_json_column.py
@@ -5,7 +5,6 @@ from .test_galaxy_mapping import BaseModelTestCase
 
 
 class MutableColumnTest(BaseModelTestCase):
-
     def persist_and_reload(self, item):
         item_id = item.id
         self.model.session.flush()
@@ -16,16 +15,16 @@ class MutableColumnTest(BaseModelTestCase):
         w = model.Workflow()
         self.model.session.add(w)
         self.model.session.flush()
-        w.reports_config = {'x': 'z'}
+        w.reports_config = {"x": "z"}
         persisted = self.persist_and_reload(w)
-        assert persisted.reports_config == {'x': 'z'}
-        persisted.reports_config['x'] = '1'
+        assert persisted.reports_config == {"x": "z"}
+        persisted.reports_config["x"] = "1"
         persisted = self.persist_and_reload(persisted)
-        assert persisted.reports_config['x'] == '1'
+        assert persisted.reports_config["x"] == "1"
         # test string
-        persisted.reports_config = 'abcdefg'
+        persisted.reports_config = "abcdefg"
         persisted = self.persist_and_reload(persisted)
-        assert persisted.reports_config == 'abcdefg'
+        assert persisted.reports_config == "abcdefg"
         # test int
         persisted.reports_config = 1
         persisted = self.persist_and_reload(persisted)
@@ -39,22 +38,22 @@ class MutableColumnTest(BaseModelTestCase):
         persisted = self.persist_and_reload(persisted)
         assert persisted.reports_config is True
         # Test nested dict/list
-        persisted.reports_config = {'list': [[1, 2, 3]]}
+        persisted.reports_config = {"list": [[1, 2, 3]]}
         persisted = self.persist_and_reload(persisted)
-        assert persisted.reports_config == {'list': [[1, 2, 3]]}
+        assert persisted.reports_config == {"list": [[1, 2, 3]]}
         copy.deepcopy(persisted.reports_config)
-        assert persisted.reports_config.pop('list') == [[1, 2, 3]]
+        assert persisted.reports_config.pop("list") == [[1, 2, 3]]
         persisted = self.persist_and_reload(persisted)
         assert persisted.reports_config == {}
-        persisted.reports_config.update({'x': 'z'})
+        persisted.reports_config.update({"x": "z"})
         persisted = self.persist_and_reload(persisted)
-        assert persisted.reports_config == {'x': 'z'}
-        del persisted.reports_config['x']
+        assert persisted.reports_config == {"x": "z"}
+        del persisted.reports_config["x"]
         persisted = self.persist_and_reload(persisted)
         assert persisted.reports_config == {}
-        persisted.reports_config = {'x': {'y': 'z'}}
+        persisted.reports_config = {"x": {"y": "z"}}
         persisted = self.persist_and_reload(persisted)
-        assert persisted.reports_config == {'x': {'y': 'z'}}
+        assert persisted.reports_config == {"x": {"y": "z"}}
         # These tests are failing ... at least since 20.09,
         # but nested mutable change tracking might have
         # never worked
diff --git a/test/unit/data/test_quota.py b/test/unit/data/test_quota.py
index 48772cafe18..b3c07af047a 100644
--- a/test/unit/data/test_quota.py
+++ b/test/unit/data/test_quota.py
@@ -4,7 +4,6 @@ from .test_galaxy_mapping import BaseModelTestCase
 
 
 class CalculateUsageTestCase(BaseModelTestCase):
-
     def test_calculate_usage(self):
         u = model.User(email="calc_usage@example.com", password="password")
         self.persist(u)
@@ -12,7 +11,9 @@ class CalculateUsageTestCase(BaseModelTestCase):
         h = model.History(name="History for Usage", user=u)
         self.persist(h)
 
-        d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=self.model.session)
+        d1 = model.HistoryDatasetAssociation(
+            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
+        )
         d1.dataset.total_size = 10
         self.persist(d1)
 
@@ -35,7 +36,6 @@ class CalculateUsageTestCase(BaseModelTestCase):
 
 
 class QuotaTestCase(BaseModelTestCase):
-
     def setUp(self):
         super().setUp()
         model = self.model
diff --git a/test/unit/data/test_sniff_file_sources.py b/test/unit/data/test_sniff_file_sources.py
index 05f752b68c2..84b81ee963d 100644
--- a/test/unit/data/test_sniff_file_sources.py
+++ b/test/unit/data/test_sniff_file_sources.py
@@ -2,7 +2,11 @@ import os
 
 from galaxy.datatypes import sniff
 from galaxy.files import ConfiguredFileSourcesConfig
-from galaxy.files.unittest_utils import setup_root, TestConfiguredFileSources, write_file_fixtures
+from galaxy.files.unittest_utils import (
+    setup_root,
+    TestConfiguredFileSources,
+    write_file_fixtures,
+)
 
 
 def test_posix():
@@ -28,9 +32,9 @@ def _configured_file_sources() -> TestConfiguredFileSources:
     tmp, root = setup_root()
     file_sources_config = ConfiguredFileSourcesConfig()
     plugin = {
-        'type': 'posix',
+        "type": "posix",
     }
-    plugin['root'] = root
+    plugin["root"] = root
     write_file_fixtures(tmp, root)
     file_sources = TestConfiguredFileSources(file_sources_config, conf_dict={"test1": plugin}, test_root=root)
     return file_sources
diff --git a/test/unit/files/_util.py b/test/unit/files/_util.py
index 8e7e59499af..2b96536f097 100644
--- a/test/unit/files/_util.py
+++ b/test/unit/files/_util.py
@@ -54,23 +54,23 @@ def user_context_fixture(user_ftp_dir=None, role_names=None, group_names=None, i
         email=TEST_EMAIL,
         user_ftp_dir=user_ftp_dir,
         preferences={
-            'webdav|password': 'secret1234',
-            'dropbox|access_token': os.environ.get('GALAXY_TEST_DROPBOX_ACCESS_TOKEN'),
-            'googledrive|client_id': os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_ID'),
-            'googledrive|client_secret': os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_SECRET'),
-            'googledrive|access_token': os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN'),
-            'googledrive|refresh_token': os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN'),
-            'googlecloudstorage|project': os.environ.get('GALAXY_TEST_GCS_PROJECT'),
-            'googlecloudstorage|bucket_name': os.environ.get('GALAXY_TEST_GCS_BUCKET'),
-            'googlecloudstorage|client_id': os.environ.get('GALAXY_TEST_GCS_CLIENT_ID'),
-            'googlecloudstorage|client_secret': os.environ.get('GALAXY_TEST_GCS_CLIENT_SECRET'),
-            'googlecloudstorage|access_token': os.environ.get('GALAXY_TEST_GCS_ACCESS_TOKEN'),
-            'googlecloudstorage|refresh_token': os.environ.get('GALAXY_TEST_GCS_REFRESH_TOKEN'),
-            'onedata|provider_host': os.environ.get('GALAXY_TEST_ONEDATA_PROVIDER_HOST'),
-            'onedata|access_token': os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
-            'basespace|client_id': os.environ.get('GALAXY_TEST_ONEDATA_CLIENT_ID'),
-            'basespace|client_secret': os.environ.get('GALAXY_TEST_ONEDATA_CLIENT_SECRET'),
-            'basespace|access_token': os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
+            "webdav|password": "secret1234",
+            "dropbox|access_token": os.environ.get("GALAXY_TEST_DROPBOX_ACCESS_TOKEN"),
+            "googledrive|client_id": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_CLIENT_ID"),
+            "googledrive|client_secret": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_CLIENT_SECRET"),
+            "googledrive|access_token": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN"),
+            "googledrive|refresh_token": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN"),
+            "googlecloudstorage|project": os.environ.get("GALAXY_TEST_GCS_PROJECT"),
+            "googlecloudstorage|bucket_name": os.environ.get("GALAXY_TEST_GCS_BUCKET"),
+            "googlecloudstorage|client_id": os.environ.get("GALAXY_TEST_GCS_CLIENT_ID"),
+            "googlecloudstorage|client_secret": os.environ.get("GALAXY_TEST_GCS_CLIENT_SECRET"),
+            "googlecloudstorage|access_token": os.environ.get("GALAXY_TEST_GCS_ACCESS_TOKEN"),
+            "googlecloudstorage|refresh_token": os.environ.get("GALAXY_TEST_GCS_REFRESH_TOKEN"),
+            "onedata|provider_host": os.environ.get("GALAXY_TEST_ONEDATA_PROVIDER_HOST"),
+            "onedata|access_token": os.environ.get("GALAXY_TEST_ONEDATA_ACCESS_TOKEN"),
+            "basespace|client_id": os.environ.get("GALAXY_TEST_ONEDATA_CLIENT_ID"),
+            "basespace|client_secret": os.environ.get("GALAXY_TEST_ONEDATA_CLIENT_SECRET"),
+            "basespace|access_token": os.environ.get("GALAXY_TEST_ONEDATA_ACCESS_TOKEN"),
         },
         role_names=role_names or set(),
         group_names=group_names or set(),
@@ -81,7 +81,7 @@ def user_context_fixture(user_ftp_dir=None, role_names=None, group_names=None, i
 
 def realize_to_temp_file(file_sources, uri, user_context=None):
     file_source_path = file_sources.get_file_source_path(uri)
-    with tempfile.NamedTemporaryFile(mode='r') as temp:
+    with tempfile.NamedTemporaryFile(mode="r") as temp:
         file_source_path.file_source.realize_to(file_source_path.path, temp.name, user_context=user_context)
         with open(temp.name) as f:
             realized_contents = f.read()
@@ -122,7 +122,7 @@ def assert_realizes_throws_exception(file_sources, uri, user_context=None) -> Ex
 
 def write_from(file_sources, uri, content, user_context=None):
     file_source_path = file_sources.get_file_source_path(uri)
-    with tempfile.NamedTemporaryFile(mode='w') as f:
+    with tempfile.NamedTemporaryFile(mode="w") as f:
         f.write(content)
         f.flush()
         file_source_path.file_source.write_from(file_source_path.path, f.name, user_context=user_context)
diff --git a/test/unit/files/test_basespace.py b/test/unit/files/test_basespace.py
index 85719d8d1f0..75592aa95fe 100644
--- a/test/unit/files/test_basespace.py
+++ b/test/unit/files/test_basespace.py
@@ -8,15 +8,16 @@ from ._util import (
     find,
     user_context_fixture,
 )
+
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "basespace_file_sources_conf.yml")
 
 skip_if_no_basespace_access_token = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_BASESPACE_CLIENT_ID')
-    or not os.environ.get('GALAXY_TEST_BASESPACE_CLIENT_SECRET')
-    or not os.environ.get('GALAXY_TEST_BASESPACE_ACCESS_TOKEN')
-    or not os.environ.get('GALAXY_TEST_BASESPACE_TEST_FILE_PATH'),
-    reason="GALAXY_TEST_BASESPACE_CLIENT_ID and related vars not set"
+    not os.environ.get("GALAXY_TEST_BASESPACE_CLIENT_ID")
+    or not os.environ.get("GALAXY_TEST_BASESPACE_CLIENT_SECRET")
+    or not os.environ.get("GALAXY_TEST_BASESPACE_ACCESS_TOKEN")
+    or not os.environ.get("GALAXY_TEST_BASESPACE_TEST_FILE_PATH"),
+    reason="GALAXY_TEST_BASESPACE_CLIENT_ID and related vars not set",
 )
 
 
@@ -28,9 +29,9 @@ def test_file_source():
 
     assert file_source_pair.path == "/"
     file_source = file_source_pair.file_source
-    test_file = os.environ.get('GALAXY_TEST_BASESPACE_TEST_FILE_PATH', "")
+    test_file = os.environ.get("GALAXY_TEST_BASESPACE_TEST_FILE_PATH", "")
     res = file_source.list(os.path.dirname(test_file), recursive=False, user_context=user_context)
     a_file = find(res, class_="File", name=os.path.basename(test_file))
     assert a_file
 
-    assert_realizes_as(file_sources, a_file['uri'], "a\n", user_context=user_context)
+    assert_realizes_as(file_sources, a_file["uri"], "a\n", user_context=user_context)
diff --git a/test/unit/files/test_dropbox.py b/test/unit/files/test_dropbox.py
index 7bee738d288..111612ea495 100644
--- a/test/unit/files/test_dropbox.py
+++ b/test/unit/files/test_dropbox.py
@@ -8,8 +8,7 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "dropbox_file_sources_conf.yml")
 
 skip_if_no_dropbox_access_token = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_DROPBOX_ACCESS_TOKEN'),
-    reason="GALAXY_TEST_DROPBOX_ACCESS_TOKEN not set"
+    not os.environ.get("GALAXY_TEST_DROPBOX_ACCESS_TOKEN"), reason="GALAXY_TEST_DROPBOX_ACCESS_TOKEN not set"
 )
 
 
diff --git a/test/unit/files/test_gcsfs.py b/test/unit/files/test_gcsfs.py
index 8ad3a46cca5..94a11371783 100644
--- a/test/unit/files/test_gcsfs.py
+++ b/test/unit/files/test_gcsfs.py
@@ -14,12 +14,12 @@ FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "gcsfs_file_sources_conf.yml"
 
 
 skip_if_no_gcsfs_libs = pytest.mark.skipif(
-    not GCSFS,
-    reason="Required lib to run gcs file source test: fs_gcsfs is not available"
+    not GCSFS, reason="Required lib to run gcs file source test: fs_gcsfs is not available"
 )
 
 
 @skip_if_no_gcsfs_libs
 def test_file_source():
-    assert_simple_file_realize(FILE_SOURCES_CONF, recursive=False, filename="README", contents="1000genomes",
-                               contains=True)
+    assert_simple_file_realize(
+        FILE_SOURCES_CONF, recursive=False, filename="README", contents="1000genomes", contains=True
+    )
diff --git a/test/unit/files/test_googledrive.py b/test/unit/files/test_googledrive.py
index 8fc39c1136b..2661713ee62 100644
--- a/test/unit/files/test_googledrive.py
+++ b/test/unit/files/test_googledrive.py
@@ -8,9 +8,9 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "googledrive_file_sources_conf.yml")
 
 skip_if_no_google_drive_access_token = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN')
-    or not os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN'),
-    reason="GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN and related vars not set"
+    not os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN")
+    or not os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN"),
+    reason="GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN and related vars not set",
 )
 
 
diff --git a/test/unit/files/test_onedata.py b/test/unit/files/test_onedata.py
index d78dad707c4..b4a5813699f 100644
--- a/test/unit/files/test_onedata.py
+++ b/test/unit/files/test_onedata.py
@@ -8,9 +8,8 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "onedata_file_sources_conf.yml")
 
 skip_if_no_onedata_access_token = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_ONEDATA_PROVIDER_HOST')
-    or not os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
-    reason="GALAXY_TEST_ONEDATA_PROVIDER_HOST and GALAXY_TEST_ONEDATA_ACCESS_TOKEN not set"
+    not os.environ.get("GALAXY_TEST_ONEDATA_PROVIDER_HOST") or not os.environ.get("GALAXY_TEST_ONEDATA_ACCESS_TOKEN"),
+    reason="GALAXY_TEST_ONEDATA_PROVIDER_HOST and GALAXY_TEST_ONEDATA_ACCESS_TOKEN not set",
 )
 
 
diff --git a/test/unit/files/test_posix.py b/test/unit/files/test_posix.py
index dc0e75eef1c..a190bfa5955 100644
--- a/test/unit/files/test_posix.py
+++ b/test/unit/files/test_posix.py
@@ -24,7 +24,7 @@ from ._util import (
     write_from,
 )
 
-EMAIL = 'alice@galaxyproject.org'
+EMAIL = "alice@galaxyproject.org"
 
 
 def test_posix():
@@ -98,7 +98,9 @@ def test_posix_disable_link_security():
 
 
 def test_posix_nonexistent_parent_write():
-    file_sources = _configured_file_sources(include_allowlist=True, writable=True, plugin_extra_config={'allow_subdir_creation': False})
+    file_sources = _configured_file_sources(
+        include_allowlist=True, writable=True, plugin_extra_config={"allow_subdir_creation": False}
+    )
     e = None
     try:
         write_from(file_sources, "gxfiles://test1/notreal/myfile", "my test content")
@@ -147,7 +149,7 @@ def test_user_ftp_explicit_config():
         ftp_upload_purge=False,
     )
     plugin = {
-        'type': 'gxftp',
+        "type": "gxftp",
     }
     tmp, root = setup_root()
     file_sources = ConfiguredFileSources(file_sources_config, conf_dict=[plugin])
@@ -215,7 +217,7 @@ def test_import_dir_explicit_config():
         library_import_dir=root,
     )
     plugin = {
-        'type': 'gximport',
+        "type": "gximport",
     }
     file_sources = ConfiguredFileSources(file_sources_config, conf_dict=[plugin])
     write_file_fixtures(tmp, root)
@@ -315,34 +317,19 @@ def test_posix_user_access_using_boolean_rules():
     }
     file_sources = _configured_file_sources(writable=True, plugin_extra_config=plugin_extra_config)
 
-    user_context = user_context_fixture(
-        role_names=set(),
-        group_names=set()
-    )
+    user_context = user_context_fixture(role_names=set(), group_names=set())
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(
-        role_names={"role1"},
-        group_names={"group1", "group2"}
-    )
+    user_context = user_context_fixture(role_names={"role1"}, group_names={"group1", "group2"})
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(
-        role_names={"role1", "role3"},
-        group_names={"group1", "group2", "group3"}
-    )
+    user_context = user_context_fixture(role_names={"role1", "role3"}, group_names={"group1", "group2", "group3"})
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(
-        role_names={"role1", "role2"},
-        group_names={"group3", "group5"}
-    )
+    user_context = user_context_fixture(role_names={"role1", "role2"}, group_names={"group3", "group5"})
     _assert_user_access_prohibited(file_sources, user_context)
 
-    user_context = user_context_fixture(
-        role_names={"role1", "role3"},
-        group_names={"group1", "group2"}
-    )
+    user_context = user_context_fixture(role_names={"role1", "role3"}, group_names={"group1", "group2"})
     _assert_user_access_granted(file_sources, user_context)
 
 
@@ -370,24 +357,26 @@ def _assert_user_access_granted(file_sources, user_context):
     assert_realizes_as(file_sources, "gxfiles://test1/a", "a\n", user_context=user_context)
 
 
-def _configured_file_sources(include_allowlist=False, plugin_extra_config=None, per_user=False, writable=None, allow_subdir_creation=True) -> TestConfiguredFileSources:
+def _configured_file_sources(
+    include_allowlist=False, plugin_extra_config=None, per_user=False, writable=None, allow_subdir_creation=True
+) -> TestConfiguredFileSources:
     tmp, root = setup_root()
     config_kwd = {}
     if include_allowlist:
         config_kwd["symlink_allowlist"] = [tmp]
     file_sources_config = ConfiguredFileSourcesConfig(**config_kwd)
     plugin = {
-        'type': 'posix',
+        "type": "posix",
     }
     if writable is not None:
-        plugin['writable'] = writable
+        plugin["writable"] = writable
     if per_user:
-        plugin['root'] = "%s/${user.username}" % root
+        plugin["root"] = "%s/${user.username}" % root
         # setup files just for alice
         root = os.path.join(root, "alice")
         os.mkdir(root)
     else:
-        plugin['root'] = root
+        plugin["root"] = root
     plugin.update(plugin_extra_config or {})
     write_file_fixtures(tmp, root)
     file_sources = TestConfiguredFileSources(file_sources_config, conf_dict={"test1": plugin}, test_root=root)
diff --git a/test/unit/files/test_s3.py b/test/unit/files/test_s3.py
index f88d7905401..7f9f835f66d 100644
--- a/test/unit/files/test_s3.py
+++ b/test/unit/files/test_s3.py
@@ -8,12 +8,16 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "s3_file_sources_conf.yml")
 
 skip_if_not_slow = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_INCLUDE_SLOW'),
-    reason="GALAXY_TEST_INCLUDE_SLOW not set"
+    not os.environ.get("GALAXY_TEST_INCLUDE_SLOW"), reason="GALAXY_TEST_INCLUDE_SLOW not set"
 )
 
 
 @skip_if_not_slow
 def test_file_source():
-    assert_simple_file_realize(FILE_SOURCES_CONF, recursive=False, filename="data_use_policies.txt",
-                               contents="DATA USE POLICIES", contains=True)
+    assert_simple_file_realize(
+        FILE_SOURCES_CONF,
+        recursive=False,
+        filename="data_use_policies.txt",
+        contents="DATA USE POLICIES",
+        contains=True,
+    )
diff --git a/test/unit/files/test_webdav.py b/test/unit/files/test_webdav.py
index 30909b99e65..4c0632bbc6e 100644
--- a/test/unit/files/test_webdav.py
+++ b/test/unit/files/test_webdav.py
@@ -19,10 +19,7 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "webdav_file_sources_conf.yml")
 USER_FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "webdav_user_file_sources_conf.yml")
 
-skip_if_no_webdav = pytest.mark.skipif(
-    not os.environ.get('GALAXY_TEST_WEBDAV'),
-    reason="GALAXY_TEST_WEBDAV not set"
-)
+skip_if_no_webdav = pytest.mark.skipif(not os.environ.get("GALAXY_TEST_WEBDAV"), reason="GALAXY_TEST_WEBDAV not set")
 
 
 @skip_if_no_webdav
diff --git a/test/unit/job_execution/test_datasets.py b/test/unit/job_execution/test_datasets.py
index 1a920d83bfa..4a3ca32687c 100644
--- a/test/unit/job_execution/test_datasets.py
+++ b/test/unit/job_execution/test_datasets.py
@@ -9,7 +9,9 @@ def test_dataset_path():
     assert dataset_path_1.mutable
     assert str(dataset_path_1) == "/galaxy/database/files/dataset_1.dat"
 
-    dataset_path_2 = DatasetPath(2, "/galaxy/database/files/dataset_2.dat", false_path="/mnt/galaxyData/files/dataset_2.dat", mutable=False)
+    dataset_path_2 = DatasetPath(
+        2, "/galaxy/database/files/dataset_2.dat", false_path="/mnt/galaxyData/files/dataset_2.dat", mutable=False
+    )
     assert dataset_path_2.dataset_id == 2
     assert dataset_path_2.real_path == "/galaxy/database/files/dataset_2.dat"
     assert dataset_path_2.false_path == "/mnt/galaxyData/files/dataset_2.dat"
diff --git a/test/unit/job_execution/test_job_io.py b/test/unit/job_execution/test_job_io.py
index 4369dd196d8..83c8e8cd544 100644
--- a/test/unit/job_execution/test_job_io.py
+++ b/test/unit/job_execution/test_job_io.py
@@ -11,23 +11,21 @@ from galaxy.job_execution.setup import JobIO
 from galaxy.model import Job
 from galaxy.model.unittest_utils import GalaxyDataTestApp
 
-
-WORKING_DIRECTORY = '/tmp'
-VERSION_PATH = '/tmp/version'
-GALAXY_URL = 'http://galaxy'
+WORKING_DIRECTORY = "/tmp"
+VERSION_PATH = "/tmp/version"
+GALAXY_URL = "http://galaxy"
 USER_CONTEXT = {
-    'email': 'test@email.com',
-    'username': 'user',
-    'ftp_dir': 'tmp/ftp_dir',
-    'preferences': {'a': 'b'},
-    'role_names': ['role1'],
-    'group_names': ['group1'],
-    'is_admin': False,
+    "email": "test@email.com",
+    "username": "user",
+    "ftp_dir": "tmp/ftp_dir",
+    "preferences": {"a": "b"},
+    "role_names": ["role1"],
+    "group_names": ["group1"],
+    "is_admin": False,
 }
 
 
 class FileSourcesMockApp(GalaxyDataTestApp):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.file_sources = ConfiguredFileSources(ConfiguredFileSourcesConfig.from_app_config(self.config))  # type: ignore[assignment]
@@ -78,8 +76,8 @@ def job_io(app: FileSourcesMockApp, job: Job) -> JobIO:
 def test_job_io_serialization(job_io: JobIO):
     job_io_dict = job_io.to_dict()
     assert isinstance(job_io_dict, dict)
-    assert isinstance(job_io_dict['file_sources_dict'], dict)
-    assert isinstance(job_io_dict['user_context'], dict)
+    assert isinstance(job_io_dict["file_sources_dict"], dict)
+    assert isinstance(job_io_dict["user_context"], dict)
 
 
 def test_job_io_deserialization(job_io: JobIO):
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index 6942b7cd24f..72cb917e1a7 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -7,13 +7,13 @@ from galaxy.util import parse_xml
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
-CONFIG_FILE_NAME = 'irods_object_store_conf.xml'
+CONFIG_FILE_NAME = "irods_object_store_conf.xml"
 CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME)
 
-CONFIG_FILE_NAME_NO_EXTRA_DIR = 'irods_object_store_conf_no_extra_dir.xml'
+CONFIG_FILE_NAME_NO_EXTRA_DIR = "irods_object_store_conf_no_extra_dir.xml"
 CONFIG_FILE_NO_EXTRA_DIR = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_EXTRA_DIR)
 
-CONFIG_FILE_NAME_NO_AUTH = 'irods_object_store_conf_no_auth.xml'
+CONFIG_FILE_NAME_NO_AUTH = "irods_object_store_conf_no_auth.xml"
 CONFIG_FILE_NO_AUTH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_AUTH)
 
 
@@ -22,30 +22,30 @@ def test_parse_valid_config_xml():
     root = tree.getroot()
     config = parse_config_xml(root)
 
-    assert config['auth']['username'] == 'rods'
-    assert config['auth']['password'] == 'rods'
-    assert config['resource']['name'] == 'demoResc'
-    assert config['zone']['name'] == 'tempZone'
-    assert config['connection']['host'] == 'localhost'
-    assert config['connection']['port'] == 1247
-    assert config['connection']['timeout'] == 30
-    assert config['cache']['path'] == 'database/object_store_cache'
-    assert config['cache']['size'] == 1000
-    assert config['extra_dirs'][0]['type'] == 'job_work'
-    assert config['extra_dirs'][0]['path'] == 'database/job_working_directory_irods'
-    assert config['extra_dirs'][1]['type'] == 'temp'
-    assert config['extra_dirs'][1]['path'] == 'database/tmp_irods'
+    assert config["auth"]["username"] == "rods"
+    assert config["auth"]["password"] == "rods"
+    assert config["resource"]["name"] == "demoResc"
+    assert config["zone"]["name"] == "tempZone"
+    assert config["connection"]["host"] == "localhost"
+    assert config["connection"]["port"] == 1247
+    assert config["connection"]["timeout"] == 30
+    assert config["cache"]["path"] == "database/object_store_cache"
+    assert config["cache"]["size"] == 1000
+    assert config["extra_dirs"][0]["type"] == "job_work"
+    assert config["extra_dirs"][0]["path"] == "database/job_working_directory_irods"
+    assert config["extra_dirs"][1]["type"] == "temp"
+    assert config["extra_dirs"][1]["path"] == "database/tmp_irods"
 
 
 def test_parse_config_xml_no_extra_dir():
     tree = parse_xml(CONFIG_FILE_NO_EXTRA_DIR)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No extra_dir element in config XML tree'):
+    with pytest.raises(Exception, match="No extra_dir element in config XML tree"):
         parse_config_xml(root)
 
 
 def test_parse_config_xml_no_auth():
     tree = parse_xml(CONFIG_FILE_NO_AUTH)
     root = tree.getroot()
-    with pytest.raises(Exception, match='No auth element in config XML tree'):
+    with pytest.raises(Exception, match="No auth element in config XML tree"):
         parse_config_xml(root)
diff --git a/test/unit/objectstore/test_objectstore.py b/test/unit/objectstore/test_objectstore.py
index 83e5306a257..19ab416902d 100644
--- a/test/unit/objectstore/test_objectstore.py
+++ b/test/unit/objectstore/test_objectstore.py
@@ -12,8 +12,8 @@ from galaxy.objectstore.azure_blob import AzureBlobObjectStore
 from galaxy.objectstore.cloud import Cloud
 from galaxy.objectstore.pithos import PithosObjectStore
 from galaxy.objectstore.s3 import S3ObjectStore
+from galaxy.objectstore.unittest_utils import Config as TestConfig
 from galaxy.objectstore.unittest_utils import (
-    Config as TestConfig,
     DISK_TEST_CONFIG,
     DISK_TEST_CONFIG_YAML,
 )
@@ -119,7 +119,10 @@ def test_disk_store_by_uuid():
 
             # Write non-empty dataset in backend 1, test it is not emtpy & exists.
             hello_world_dataset = MockDataset(3)
-            directory.write("Hello World!", f"files1/{hello_world_dataset.rel_path_for_uuid_test()}/dataset_{hello_world_dataset.uuid}.dat")
+            directory.write(
+                "Hello World!",
+                f"files1/{hello_world_dataset.rel_path_for_uuid_test()}/dataset_{hello_world_dataset.uuid}.dat",
+            )
             assert object_store.exists(hello_world_dataset)
             assert not object_store.empty(hello_world_dataset)
 
@@ -145,7 +148,12 @@ def test_disk_store_by_uuid():
 
             # Test update_from_file test
             output_dataset = MockDataset(4)
-            output_real_path = os.path.join(directory.temp_directory, "files1", output_dataset.rel_path_for_uuid_test(), "dataset_%s.dat" % output_dataset.uuid)
+            output_real_path = os.path.join(
+                directory.temp_directory,
+                "files1",
+                output_dataset.rel_path_for_uuid_test(),
+                "dataset_%s.dat" % output_dataset.uuid,
+            )
             assert not os.path.exists(output_real_path)
             output_working_path = directory.write("NEW CONTENTS", "job_working_directory1/example_output")
             object_store.update_from_file(output_dataset, file_name=output_working_path, create=True)
@@ -153,7 +161,10 @@ def test_disk_store_by_uuid():
 
             # Test delete
             to_delete_dataset = MockDataset(5)
-            to_delete_real_path = directory.write("content to be deleted!", f"files1/{to_delete_dataset.rel_path_for_uuid_test()}/dataset_{to_delete_dataset.uuid}.dat")
+            to_delete_real_path = directory.write(
+                "content to be deleted!",
+                f"files1/{to_delete_dataset.rel_path_for_uuid_test()}/dataset_{to_delete_dataset.uuid}.dat",
+            )
             assert object_store.exists(to_delete_dataset)
             assert object_store.delete(to_delete_dataset)
             assert not object_store.exists(to_delete_dataset)
@@ -161,7 +172,7 @@ def test_disk_store_by_uuid():
 
 
 def test_disk_store_alt_name_relpath():
-    """ Test that alt_name cannot be used to access arbitrary paths using a
+    """Test that alt_name cannot be used to access arbitrary paths using a
     relative path
     """
     with TestConfig(DISK_TEST_CONFIG) as (directory, object_store):
@@ -169,29 +180,25 @@ def test_disk_store_alt_name_relpath():
         directory.write("", "files1/000/dataset_1.dat")
         directory.write("foo", "foo.txt")
         try:
-            assert object_store.get_data(
-                empty_dataset,
-                extra_dir='dataset_1_files',
-                alt_name='../../../foo.txt') != 'foo'
+            assert (
+                object_store.get_data(empty_dataset, extra_dir="dataset_1_files", alt_name="../../../foo.txt") != "foo"
+            )
         except ObjectInvalid:
             pass
 
 
 def test_disk_store_alt_name_abspath():
-    """ Test that alt_name cannot be used to access arbitrary paths using a
+    """Test that alt_name cannot be used to access arbitrary paths using a
     absolute path
     """
     with TestConfig(DISK_TEST_CONFIG) as (directory, object_store):
         empty_dataset = MockDataset(1)
         directory.write("", "files1/000/dataset_1.dat")
         absfoo = os.path.abspath(os.path.join(directory.temp_directory, "foo.txt"))
-        with open(absfoo, 'w') as f:
+        with open(absfoo, "w") as f:
             f.write("foo")
         try:
-            assert object_store.get_data(
-                empty_dataset,
-                extra_dir='dataset_1_files',
-                alt_name=absfoo) != 'foo'
+            assert object_store.get_data(empty_dataset, extra_dir="dataset_1_files", alt_name=absfoo) != "foo"
         except ObjectInvalid:
             pass
 
@@ -397,25 +404,21 @@ def test_distributed_store():
 # we can at least stub out initializing and test the configuration of these things from
 # XML and dicts.
 class UnitializedPithosObjectStore(PithosObjectStore):
-
     def _initialize(self):
         pass
 
 
 class UnitializeS3ObjectStore(S3ObjectStore):
-
     def _initialize(self):
         pass
 
 
 class UnitializedAzureBlobObjectStore(AzureBlobObjectStore):
-
     def _initialize(self):
         pass
 
 
 class UnitializedCloudObjectStore(Cloud):
-
     def _initialize(self):
         pass
 
@@ -664,9 +667,14 @@ extra_dirs:
 
 
 def test_config_parse_cloud():
-    for config_str in [CLOUD_AWS_TEST_CONFIG, CLOUD_AWS_TEST_CONFIG_YAML,
-                       CLOUD_AZURE_TEST_CONFIG, CLOUD_AZURE_TEST_CONFIG_YAML,
-                       CLOUD_GOOGLE_TEST_CONFIG, CLOUD_GOOGLE_TEST_CONFIG_YAML]:
+    for config_str in [
+        CLOUD_AWS_TEST_CONFIG,
+        CLOUD_AWS_TEST_CONFIG_YAML,
+        CLOUD_AZURE_TEST_CONFIG,
+        CLOUD_AZURE_TEST_CONFIG_YAML,
+        CLOUD_GOOGLE_TEST_CONFIG,
+        CLOUD_GOOGLE_TEST_CONFIG_YAML,
+    ]:
         if "google" in config_str:
             tmpdir = mkdtemp()
             if not os.path.exists(tmpdir):
@@ -857,7 +865,6 @@ def test_config_parse_azure():
 
 
 class MockDataset:
-
     def __init__(self, id):
         self.id = id
         self.object_store_id = None
diff --git a/test/unit/security/test_vault.py b/test/unit/security/test_vault.py
index 6b694472c12..f56574bd6ff 100644
--- a/test/unit/security/test_vault.py
+++ b/test/unit/security/test_vault.py
@@ -6,8 +6,15 @@ from abc import ABC
 
 from cryptography.fernet import InvalidToken
 
-from galaxy.model.unittest_utils.data_app import GalaxyDataTestApp, GalaxyDataTestConfig
-from galaxy.security.vault import InvalidVaultKeyException, Vault, VaultFactory
+from galaxy.model.unittest_utils.data_app import (
+    GalaxyDataTestApp,
+    GalaxyDataTestConfig,
+)
+from galaxy.security.vault import (
+    InvalidVaultKeyException,
+    Vault,
+    VaultFactory,
+)
 
 
 class VaultTestBase(ABC):
@@ -37,16 +44,18 @@ class VaultTestBase(ABC):
 VAULT_CONF_HASHICORP = os.path.join(os.path.dirname(__file__), "fixtures/vault_conf_hashicorp.yml")
 
 
-@unittest.skipIf(not os.environ.get('VAULT_ADDRESS') or not os.environ.get('VAULT_TOKEN'),
-                 "VAULT_ADDRESS and VAULT_TOKEN env vars not set")
+@unittest.skipIf(
+    not os.environ.get("VAULT_ADDRESS") or not os.environ.get("VAULT_TOKEN"),
+    "VAULT_ADDRESS and VAULT_TOKEN env vars not set",
+)
 class TestHashicorpVault(VaultTestBase, unittest.TestCase):
-
     def setUp(self) -> None:
-        with tempfile.NamedTemporaryFile(
-                mode="w", prefix="vault_hashicorp", delete=False) as tempconf, open(VAULT_CONF_HASHICORP) as f:
+        with tempfile.NamedTemporaryFile(mode="w", prefix="vault_hashicorp", delete=False) as tempconf, open(
+            VAULT_CONF_HASHICORP
+        ) as f:
             content = string.Template(f.read()).safe_substitute(
-                vault_address=os.environ.get('VAULT_ADDRESS'),
-                vault_token=os.environ.get('VAULT_TOKEN'))
+                vault_address=os.environ.get("VAULT_ADDRESS"), vault_token=os.environ.get("VAULT_TOKEN")
+            )
             tempconf.write(content)
             self.vault_temp_conf = tempconf.name
         config = GalaxyDataTestConfig(vault_config_file=self.vault_temp_conf)
@@ -63,7 +72,6 @@ VAULT_CONF_DATABASE_INVALID = os.path.join(os.path.dirname(__file__), "fixtures/
 
 
 class TestDatabaseVault(VaultTestBase, unittest.TestCase):
-
     def setUp(self) -> None:
         config = GalaxyDataTestConfig(vault_config_file=VAULT_CONF_DATABASE)
         app = GalaxyDataTestApp(config=config)
@@ -96,16 +104,19 @@ class TestDatabaseVault(VaultTestBase, unittest.TestCase):
 VAULT_CONF_CUSTOS = os.path.join(os.path.dirname(__file__), "fixtures/vault_conf_custos.yml")
 
 
-@unittest.skipIf(not os.environ.get('CUSTOS_CLIENT_ID') or not os.environ.get('CUSTOS_CLIENT_SECRET'),
-                 "CUSTOS_CLIENT_ID and CUSTOS_CLIENT_SECRET env vars not set")
+@unittest.skipIf(
+    not os.environ.get("CUSTOS_CLIENT_ID") or not os.environ.get("CUSTOS_CLIENT_SECRET"),
+    "CUSTOS_CLIENT_ID and CUSTOS_CLIENT_SECRET env vars not set",
+)
 class TestCustosVault(VaultTestBase, unittest.TestCase):
-
     def setUp(self) -> None:
-        with tempfile.NamedTemporaryFile(
-                mode="w", prefix="vault_custos", delete=False) as tempconf, open(VAULT_CONF_CUSTOS) as f:
+        with tempfile.NamedTemporaryFile(mode="w", prefix="vault_custos", delete=False) as tempconf, open(
+            VAULT_CONF_CUSTOS
+        ) as f:
             content = string.Template(f.read()).safe_substitute(
-                custos_client_id=os.environ.get('CUSTOS_CLIENT_ID'),
-                custos_client_secret=os.environ.get('CUSTOS_CLIENT_SECRET'))
+                custos_client_id=os.environ.get("CUSTOS_CLIENT_ID"),
+                custos_client_secret=os.environ.get("CUSTOS_CLIENT_SECRET"),
+            )
             tempconf.write(content)
             self.vault_temp_conf = tempconf.name
         config = GalaxyDataTestConfig(vault_config_file=self.vault_temp_conf)
diff --git a/test/unit/shed_unit/model/test_mapping.py b/test/unit/shed_unit/model/test_mapping.py
index e329d1c9186..2eb27150407 100644
--- a/test/unit/shed_unit/model/test_mapping.py
+++ b/test/unit/shed_unit/model/test_mapping.py
@@ -1,5 +1,8 @@
 from contextlib import contextmanager
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from uuid import uuid4
 
 import pytest
@@ -21,15 +24,14 @@ class BaseTest:
         Assumptions: if the class under test is Foo, then the class grouping
         the tests should be a subclass of BaseTest, named TestFoo.
         """
-        prefix = len('Test')
+        prefix = len("Test")
         class_name = self.__class__.__name__[prefix:]
         return getattr(model, class_name)
 
 
 class TestAPIKeys(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'api_keys'
+        assert cls_.__tablename__ == "api_keys"
 
     def test_columns(self, session, cls_, user):
         create_time, user_id, key = datetime.now(), user.id, get_unique_value()
@@ -51,14 +53,13 @@ class TestAPIKeys(BaseTest):
 
 
 class TestCategory(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'category'
+        assert cls_.__tablename__ == "category"
 
     def test_columns(self, session, cls_):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        name, description, deleted = get_unique_value(), 'b', True
+        name, description, deleted = get_unique_value(), "b", True
 
         obj = cls_()
         obj.create_time = create_time
@@ -87,12 +88,11 @@ class TestCategory(BaseTest):
 
 
 class TestComponent(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'component'
+        assert cls_.__tablename__ == "component"
 
     def test_columns(self, session, cls_):
-        name, description = 'a', 'b'
+        name, description = "a", "b"
         obj = cls_(name=name, description=description)
 
         with dbcleanup(session, obj) as obj_id:
@@ -103,16 +103,15 @@ class TestComponent(BaseTest):
 
 
 class TestComponentReview(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'component_review'
+        assert cls_.__tablename__ == "component_review"
 
     def test_columns(self, session, cls_, repository_review, component):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        comment = 'a'
+        comment = "a"
         private = True
-        approved = 'b'
+        approved = "b"
         rating = 1
         deleted = True
 
@@ -152,17 +151,16 @@ class TestComponentReview(BaseTest):
 
 
 class TestGalaxySession(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'galaxy_session'
+        assert cls_.__tablename__ == "galaxy_session"
 
     def test_columns(self, session, cls_, user, galaxy_session):
 
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        remote_host = 'a'
-        remote_addr = 'b'
-        referer = 'c'
+        remote_host = "a"
+        remote_addr = "b"
+        referer = "c"
         session_key = get_unique_value()
         is_valid = True
         last_action = update_time + timedelta(hours=1)
@@ -202,9 +200,8 @@ class TestGalaxySession(BaseTest):
 
 
 class TestGroup(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'galaxy_group'
+        assert cls_.__tablename__ == "galaxy_group"
 
     def test_columns(self, session, cls_):
         create_time = datetime.now()
@@ -245,9 +242,8 @@ class TestGroup(BaseTest):
 
 
 class TestGroupRoleAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'group_role_association'
+        assert cls_.__tablename__ == "group_role_association"
 
     def test_columns(self, session, cls_, group, role):
         obj = cls_(group, role)
@@ -274,9 +270,8 @@ class TestGroupRoleAssociation(BaseTest):
 
 
 class TestPasswordResetToken(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'password_reset_token'
+        assert cls_.__tablename__ == "password_reset_token"
 
     def test_columns_and_relationships(self, session, cls_, user):
         token = get_unique_value()
@@ -297,19 +292,18 @@ class TestPasswordResetToken(BaseTest):
 
 
 class TestRepository(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository'
+        assert cls_.__tablename__ == "repository"
 
     def test_columns(self, session, cls_, user):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        name = 'a'
-        type = 'b'
-        remote_repository_url = 'c'
-        homepage_url = 'd'
-        description = 'e'
-        long_description = 'f'
+        name = "a"
+        type = "b"
+        remote_repository_url = "c"
+        homepage_url = "d"
+        description = "e"
+        long_description = "f"
         private = True
         deleted = True
         email_alerts = False
@@ -408,9 +402,8 @@ class TestRepository(BaseTest):
 
 
 class TestRepositoryCategoryAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository_category_association'
+        assert cls_.__tablename__ == "repository_category_association"
 
     def test_columns(self, session, cls_, repository, category):
         obj = cls_(repository=repository, category=category)
@@ -431,17 +424,16 @@ class TestRepositoryCategoryAssociation(BaseTest):
 
 
 class TestRepositoryMetadata(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.table.name == 'repository_metadata'
+        assert cls_.table.name == "repository_metadata"
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        changeset_revision = 'a'
+        changeset_revision = "a"
         numeric_revision = 1
-        metadata = 'b'
-        tool_versions = 'c'
+        metadata = "b"
+        tool_versions = "c"
         malicious = True
         downloadable = False
         missing_test_components = True
@@ -498,7 +490,7 @@ class TestRepositoryMetadata(BaseTest):
 
         obj = cls_()
         obj.repository = repository
-        obj.changeset_revision = 'nonempty'
+        obj.changeset_revision = "nonempty"
 
         # create 3 reviews
         review1 = repository_review_factory()
@@ -518,7 +510,7 @@ class TestRepositoryMetadata(BaseTest):
         # set the same changeset for reviews 1,2
         review1.changeset_revision = obj.changeset_revision
         review2.changeset_revision = obj.changeset_revision
-        review3.changeset_revision = 'something else'  # this won't be in reviews for this metadata
+        review3.changeset_revision = "something else"  # this won't be in reviews for this metadata
 
         # add to session
         session.add(review1)
@@ -534,15 +526,14 @@ class TestRepositoryMetadata(BaseTest):
 
 
 class TestRepositoryRatingAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository_rating_association'
+        assert cls_.__tablename__ == "repository_rating_association"
 
     def test_columns(self, session, cls_, repository, user):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
         rating = 1
-        comment = 'a'
+        comment = "a"
 
         obj = cls_()
         obj.create_time = create_time
@@ -574,15 +565,14 @@ class TestRepositoryRatingAssociation(BaseTest):
 
 
 class TestRepositoryReview(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository_review'
+        assert cls_.__tablename__ == "repository_review"
 
     def test_columns(self, session, cls_, repository, user):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
-        changeset_revision = 'a'
-        approved = 'b'
+        changeset_revision = "a"
+        approved = "b"
         rating = 1
         deleted = True
 
@@ -609,16 +599,10 @@ class TestRepositoryReview(BaseTest):
             assert stored_obj.deleted == deleted
 
     def test_relationships(
-        self,
-        session,
-        cls_,
-        repository,
-        user,
-        repository_metadata_factory,
-        component_review_factory
+        self, session, cls_, repository, user, repository_metadata_factory, component_review_factory
     ):
         obj = cls_()
-        changeset = 'nonempty'
+        changeset = "nonempty"
         obj.changeset_revision = changeset
         obj.repository = repository
         obj.user = user
@@ -628,7 +612,7 @@ class TestRepositoryReview(BaseTest):
         metadata1.repository = repository
         metadata2.repository = repository
         metadata1.changeset_revision = changeset
-        metadata2.changeset_revision = 'something else'
+        metadata2.changeset_revision = "something else"
 
         component_review1 = component_review_factory()
         component_review1.repository_review = obj
@@ -653,9 +637,8 @@ class TestRepositoryReview(BaseTest):
 
 
 class TestRepositoryRoleAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'repository_role_association'
+        assert cls_.__tablename__ == "repository_role_association"
 
     def test_columns(self, session, cls_, repository, role):
         create_time = datetime.now()
@@ -682,12 +665,11 @@ class TestRepositoryRoleAssociation(BaseTest):
 
 
 class TestRole(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'role'
+        assert cls_.__tablename__ == "role"
 
     def test_columns(self, session, cls_):
-        name, description, type_, deleted = get_unique_value(), 'b', cls_.types.SYSTEM, True
+        name, description, type_, deleted = get_unique_value(), "b", cls_.types.SYSTEM, True
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
         obj = cls_(name, description, type_, deleted)
@@ -713,7 +695,7 @@ class TestRole(BaseTest):
         group_role_association_factory,
         group,
     ):
-        name, description, type_ = get_unique_value(), 'b', cls_.types.SYSTEM
+        name, description, type_ = get_unique_value(), "b", cls_.types.SYSTEM
         obj = cls_(name, description, type_)
         obj.repositories.append(repository_role_association)
         obj.users.append(user_role_association)
@@ -731,10 +713,9 @@ class TestRole(BaseTest):
 
 
 class TestTag(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'tag'
-        assert has_unique_constraint(cls_.table, ('name',))
+        assert cls_.__tablename__ == "tag"
+        assert has_unique_constraint(cls_.table, ("name",))
 
     def test_columns(self, session, cls_):
         parent_tag = cls_()
@@ -775,16 +756,15 @@ class TestTag(BaseTest):
 
 
 class TestUser(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'galaxy_user'
+        assert cls_.__tablename__ == "galaxy_user"
 
     def test_columns(self, session, cls_):
         create_time = datetime.now()
         update_time = create_time + timedelta(hours=1)
         email = get_unique_value()
         username = get_unique_value()
-        password = 'c'
+        password = "c"
         external = True
         new_repo_alert = True
         deleted = True
@@ -828,11 +808,11 @@ class TestUser(BaseTest):
         user_group_association,
         user_role_association,
         role_factory,
-        user_role_association_factory
+        user_role_association_factory,
     ):
         obj = cls_()
         obj.email = get_unique_value()
-        obj.password = 'a'
+        obj.password = "a"
         obj.active_repositories.append(repository)
         obj.galaxy_sessions.append(galaxy_session)
         obj.api_keys.append(api_keys)
@@ -844,7 +824,7 @@ class TestUser(BaseTest):
         private_user_role = user_role_association_factory(obj, _private_role)
         obj.roles.append(private_user_role)
 
-        _non_private_role = role_factory(name='a')
+        _non_private_role = role_factory(name="a")
         non_private_user_role = user_role_association_factory(obj, _non_private_role)
         obj.roles.append(non_private_user_role)
 
@@ -863,9 +843,8 @@ class TestUser(BaseTest):
 
 
 class TestUserGroupAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'user_group_association'
+        assert cls_.__tablename__ == "user_group_association"
 
     def test_columns(self, session, cls_, user, group):
         create_time = datetime.now()
@@ -892,9 +871,8 @@ class TestUserGroupAssociation(BaseTest):
 
 
 class TestUserRoleAssociation(BaseTest):
-
     def test_table(self, cls_):
-        assert cls_.__tablename__ == 'user_role_association'
+        assert cls_.__tablename__ == "user_role_association"
 
     def test_columns(self, session, cls_, user, role):
         create_time = datetime.now()
@@ -930,7 +908,7 @@ def ensure_database_is_empty(session, model):
     For fixture instantiation order, see:
     https://docs.pytest.org/en/6.2.x/fixture.html#fixture-instantiation-order
     """
-    models = (cls_ for cls_ in model.__dict__.values() if hasattr(cls_, '__mapper__'))
+    models = (cls_ for cls_ in model.__dict__.values() if hasattr(cls_, "__mapper__"))
     # For each mapped class, check that the database table to which it is mapped is empty
     for m in models:
         stmt = select(func.count()).select_from(m)
@@ -938,10 +916,10 @@ def ensure_database_is_empty(session, model):
         assert result == 0
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def model():
-    db_uri = 'sqlite:///:memory:'
-    return mapping.init('/tmp', db_uri, create_tables=True)
+    db_uri = "sqlite:///:memory:"
+    return mapping.init("/tmp", db_uri, create_tables=True)
 
 
 @pytest.fixture
@@ -1040,7 +1018,7 @@ def role(model, session):
 
 @pytest.fixture
 def user(model, session):
-    instance = model.User(email=get_unique_value(), password='password')
+    instance = model.User(email=get_unique_value(), password="password")
     yield from dbcleanup_wrapper(session, instance)
 
 
@@ -1058,10 +1036,12 @@ def user_role_association(model, session, user, role):
 
 # Fixtures yielding factory functions.
 
+
 @pytest.fixture
 def component_review_factory(model):
     def make_instance(*args, **kwds):
         return model.ComponentReview(*args, **kwds)
+
     return make_instance
 
 
@@ -1069,6 +1049,7 @@ def component_review_factory(model):
 def group_role_association_factory(model):
     def make_instance(*args, **kwds):
         return model.GroupRoleAssociation(*args, **kwds)
+
     return make_instance
 
 
@@ -1076,6 +1057,7 @@ def group_role_association_factory(model):
 def repository_metadata_factory(model):
     def make_instance(*args, **kwds):
         return model.RepositoryMetadata(*args, **kwds)
+
     return make_instance
 
 
@@ -1083,6 +1065,7 @@ def repository_metadata_factory(model):
 def repository_review_factory(model):
     def make_instance(*args, **kwds):
         return model.RepositoryReview(*args, **kwds)
+
     return make_instance
 
 
@@ -1090,6 +1073,7 @@ def repository_review_factory(model):
 def role_factory(model):
     def make_instance(*args, **kwds):
         return model.Role(*args, **kwds)
+
     return make_instance
 
 
@@ -1098,8 +1082,9 @@ def user_factory(model):
     def make_instance(*args, **kwds):
         user = model.User(*args, **kwds)
         user.email = get_unique_value()
-        user.password = 'a'
+        user.password = "a"
         return user
+
     return make_instance
 
 
@@ -1107,11 +1092,13 @@ def user_factory(model):
 def user_role_association_factory(model):
     def make_instance(*args, **kwds):
         return model.UserRoleAssociation(*args, **kwds)
+
     return make_instance
 
 
 # Test utilities
 
+
 def dbcleanup_wrapper(session, obj, where_clause=None):
     with dbcleanup(session, obj, where_clause):
         yield obj
diff --git a/test/unit/shed_unit/test_hg_util.py b/test/unit/shed_unit/test_hg_util.py
index b5d2f88b165..db6d009e84a 100644
--- a/test/unit/shed_unit/test_hg_util.py
+++ b/test/unit/shed_unit/test_hg_util.py
@@ -5,31 +5,31 @@ from tool_shed.util import hg_util
 
 def test_init_repository(tmpdir):
     hg_util.init_repository(str(tmpdir))
-    assert (tmpdir / '.hg').exists()
+    assert (tmpdir / ".hg").exists()
 
 
 def test_init_repository_fails(tmpdir):
     test_init_repository(tmpdir)
     with pytest.raises(Exception) as exc_info:
         test_init_repository(tmpdir)
-    assert 'Error initializing repository' in str(exc_info.value)
+    assert "Error initializing repository" in str(exc_info.value)
 
 
 def test_add_file_and_commmit_changeset(tmpdir):
     test_init_repository(tmpdir)
-    path_to_add = (tmpdir / 'test.txt')
-    path_to_add.write('test')
+    path_to_add = tmpdir / "test.txt"
+    path_to_add.write("test")
     hg_util.add_changeset(str(tmpdir), str(path_to_add))
-    hg_util.commit_changeset(str(tmpdir), str(path_to_add), 'testuser', 'testcommit')
+    hg_util.commit_changeset(str(tmpdir), str(path_to_add), "testuser", "testcommit")
     return path_to_add
 
 
 def test_add_dir_and_commit_changeset(tmpdir):
     test_init_repository(tmpdir)
-    path_to_add = tmpdir.mkdir('abc')
-    (path_to_add / 'test.txt').write('bla')
+    path_to_add = tmpdir.mkdir("abc")
+    (path_to_add / "test.txt").write("bla")
     hg_util.add_changeset(str(tmpdir), str(path_to_add))
-    hg_util.commit_changeset(str(tmpdir), str(path_to_add), 'testuser', 'testcommit')
+    hg_util.commit_changeset(str(tmpdir), str(path_to_add), "testuser", "testcommit")
     return path_to_add
 
 
@@ -40,8 +40,8 @@ def test_remove_tracked_file(tmpdir):
 
 def test_remove_untracked_file(tmpdir):
     test_init_repository(tmpdir)
-    untracked_path = tmpdir / 'untracked.txt'
-    untracked_path.write('bla')
+    untracked_path = tmpdir / "untracked.txt"
+    untracked_path.write("bla")
     hg_util.remove_path(str(tmpdir), str(untracked_path))
 
 
@@ -53,5 +53,5 @@ def test_remove_tracked_dir(tmpdir):
 def test_remove_nonexistant_file_fails(tmpdir):
     test_init_repository(tmpdir)
     with pytest.raises(Exception) as exc_info:
-        hg_util.remove_path(str(tmpdir), str(tmpdir / 'some path'))
-    assert 'Error removing path' in str(exc_info.value)
+        hg_util.remove_path(str(tmpdir), str(tmpdir / "some path"))
+    assert "Error removing path" in str(exc_info.value)
diff --git a/test/unit/shed_unit/test_installed_repository_manager.py b/test/unit/shed_unit/test_installed_repository_manager.py
index 5085adbfb1b..2a0f5b21eb2 100644
--- a/test/unit/shed_unit/test_installed_repository_manager.py
+++ b/test/unit/shed_unit/test_installed_repository_manager.py
@@ -1,5 +1,8 @@
 import os
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 from unittest.mock import MagicMock
 
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
@@ -12,12 +15,11 @@ from galaxy.tool_shed.util import (
 from galaxy.util.tool_shed import common_util
 from ..app.tools.test_toolbox import (
     BaseToolBoxTestCase,
-    DEFAULT_TEST_REPO
+    DEFAULT_TEST_REPO,
 )
 
 
 class ToolShedRepoBaseTestCase(BaseToolBoxTestCase):
-
     def setUp(self):
         super().setUp()
         self._init_dynamic_tool_conf()
@@ -26,11 +28,10 @@ class ToolShedRepoBaseTestCase(BaseToolBoxTestCase):
         self.app.toolbox = self.toolbox
 
     def _setup_repository(self):
-        return self._repo_install(changeset='1', config_filename=self.config_files[0])
+        return self._repo_install(changeset="1", config_filename=self.config_files[0])
 
 
 class InstallRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
-
     def setUp(self):
         super().setUp()
         self.irm = InstallRepositoryManager(self.app)
@@ -39,39 +40,47 @@ class InstallRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
 
     def test_tool_shed_repository_install(self):
         hg_util.clone_repository = MagicMock(return_value=(True, None))
-        self._install_tool_shed_repository(start_status='New', end_status='Installed', changeset_revision='1')
+        self._install_tool_shed_repository(start_status="New", end_status="Installed", changeset_revision="1")
         hg_util.clone_repository.assert_called_with(
-            'github.com/repos/galaxyproject/example',
-            os.path.abspath(os.path.join('../shed_tools', 'github.com/repos/galaxyproject/example/1/example')),
-            '1',
+            "github.com/repos/galaxyproject/example",
+            os.path.abspath(os.path.join("../shed_tools", "github.com/repos/galaxyproject/example/1/example")),
+            "1",
         )
 
     def test_tool_shed_repository_update(self):
-        common_util.get_tool_shed_url_from_tool_shed_registry = MagicMock(return_value='https://github.com')
-        repository_util.get_tool_shed_status_for_installed_repository = MagicMock(return_value={'revision_update': 'false'})
+        common_util.get_tool_shed_url_from_tool_shed_registry = MagicMock(return_value="https://github.com")
+        repository_util.get_tool_shed_status_for_installed_repository = MagicMock(
+            return_value={"revision_update": "false"}
+        )
         hg_util.pull_repository = MagicMock()
         hg_util.update_repository = MagicMock(return_value=(True, None))
-        self._install_tool_shed_repository(start_status='Installed', end_status='Installed', changeset_revision='2')
-        assert hg_util.pull_repository.call_args[0][0].endswith('github.com/repos/galaxyproject/example/1/example')
-        assert hg_util.pull_repository.call_args[0][1] == 'https://github.com/repos/galaxyproject/example'
-        assert hg_util.pull_repository.call_args[0][2] == '2'
-        assert hg_util.update_repository.call_args[0][0].endswith('github.com/repos/galaxyproject/example/1/example')
-        assert hg_util.update_repository.call_args[0][1] == '2'
+        self._install_tool_shed_repository(start_status="Installed", end_status="Installed", changeset_revision="2")
+        assert hg_util.pull_repository.call_args[0][0].endswith("github.com/repos/galaxyproject/example/1/example")
+        assert hg_util.pull_repository.call_args[0][1] == "https://github.com/repos/galaxyproject/example"
+        assert hg_util.pull_repository.call_args[0][2] == "2"
+        assert hg_util.update_repository.call_args[0][0].endswith("github.com/repos/galaxyproject/example/1/example")
+        assert hg_util.update_repository.call_args[0][1] == "2"
 
     def _install_tool_shed_repository(self, start_status, end_status, changeset_revision):
         repository = self._setup_repository()
         repository.status = start_status
         repo_info_dict: Dict[str, Any] = {
-            'example': (
-                'description', 'github.com/repos/galaxyproject/example', changeset_revision, changeset_revision, 'galaxyproject', [], [],
+            "example": (
+                "description",
+                "github.com/repos/galaxyproject/example",
+                changeset_revision,
+                changeset_revision,
+                "galaxyproject",
+                [],
+                [],
             )
         }
         self.irm.install_tool_shed_repository(
             repository,
             repo_info_dict,
-            'section_key',
+            "section_key",
             self.app.config.tool_configs[0],
-            '../shed_tools',
+            "../shed_tools",
             False,
             False,
             reinstalling=False,
@@ -81,7 +90,6 @@ class InstallRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
 
 
 class InstalledRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
-
     def setUp(self):
         super().setUp()
         self.irm = InstalledRepositoryManager(self.app)
@@ -102,12 +110,12 @@ class InstalledRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
 
     def test_create_or_update_tool_shed_repository_update(self):
         repository = self._setup_repository()
-        self._create_or_update_tool_shed_repository(repository=repository, changeset_revision='2')
+        self._create_or_update_tool_shed_repository(repository=repository, changeset_revision="2")
 
     def test_create_or_update_tool_shed_repository_create(self):
-        self._create_or_update_tool_shed_repository(repository=None, changeset_revision='2')
+        self._create_or_update_tool_shed_repository(repository=None, changeset_revision="2")
 
-    def _create_or_update_tool_shed_repository(self, repository=None, changeset_revision='2'):
+    def _create_or_update_tool_shed_repository(self, repository=None, changeset_revision="2"):
         if repository is None:
             repository = DEFAULT_TEST_REPO
         new_repository = repository_util.create_or_update_tool_shed_repository(
@@ -116,12 +124,13 @@ class InstalledRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
             description=repository.description,
             installed_changeset_revision=repository.installed_changeset_revision,
             ctx_rev=repository.changeset_revision,
-            repository_clone_url='https://github.com/galaxyproject/example/test_tool/0.%s' % repository.installed_changeset_revision,  # not needed if owner is given
+            repository_clone_url="https://github.com/galaxyproject/example/test_tool/0.%s"
+            % repository.installed_changeset_revision,  # not needed if owner is given
             status=repository.status,
             metadata_dict=None,
             current_changeset_revision=str(int(repository.changeset_revision) + 1),
             owner=repository.owner,
-            dist_to_shed=False
+            dist_to_shed=False,
         )
         assert new_repository.changeset_revision == changeset_revision
 
diff --git a/test/unit/shed_unit/test_shed_index.py b/test/unit/shed_unit/test_shed_index.py
index 82f7ab238d1..b589dc74fd8 100644
--- a/test/unit/shed_unit/test_shed_index.py
+++ b/test/unit/shed_unit/test_shed_index.py
@@ -11,19 +11,19 @@ from whoosh import index
 
 from tool_shed.util.shed_index import build_index
 
-URL = 'https://github.com/mvdbeek/toolshed-test-data/blob/master/toolshed_community_files.tgz?raw=true'
+URL = "https://github.com/mvdbeek/toolshed-test-data/blob/master/toolshed_community_files.tgz?raw=true"
 
 
 @pytest.fixture
 def whoosh_index_dir():
     try:
-        whoosh_index_dir = tempfile.mkdtemp(suffix='_whoosh_index_test')
+        whoosh_index_dir = tempfile.mkdtemp(suffix="_whoosh_index_test")
         yield whoosh_index_dir
     finally:
         shutil.rmtree(whoosh_index_dir)
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def community_file_dir():
     extracted_archive_dir = tempfile.mkdtemp()
     b = BytesIO(requests.get(URL).content)
@@ -36,30 +36,45 @@ def community_file_dir():
 
 @pytest.fixture()
 def community_file_structure(community_file_dir):
-    community = namedtuple('community', 'file_path hgweb_config_dir dburi')
+    community = namedtuple("community", "file_path hgweb_config_dir dburi")
     return community(
-        file_path=os.path.join(community_file_dir, 'database', 'community_files'),
+        file_path=os.path.join(community_file_dir, "database", "community_files"),
         hgweb_config_dir=community_file_dir,
-        dburi="sqlite:///%s" % os.path.join(community_file_dir, 'database', 'community.sqlite')
+        dburi="sqlite:///%s" % os.path.join(community_file_dir, "database", "community.sqlite"),
     )
 
 
 def test_build_index(whoosh_index_dir, community_file_structure):
-    repos_indexed, tools_indexed = build_index(whoosh_index_dir, community_file_structure.file_path, community_file_structure.hgweb_config_dir, community_file_structure.dburi)
+    repos_indexed, tools_indexed = build_index(
+        whoosh_index_dir,
+        community_file_structure.file_path,
+        community_file_structure.hgweb_config_dir,
+        community_file_structure.dburi,
+    )
     assert repos_indexed == 1
     assert tools_indexed == 1
     idx = index.open_dir(whoosh_index_dir)
     assert idx.doc_count() == 1
-    repos_indexed, tools_indexed = build_index(whoosh_index_dir, community_file_structure.file_path, community_file_structure.hgweb_config_dir, community_file_structure.dburi)
+    repos_indexed, tools_indexed = build_index(
+        whoosh_index_dir,
+        community_file_structure.file_path,
+        community_file_structure.hgweb_config_dir,
+        community_file_structure.dburi,
+    )
     assert repos_indexed == 0
     assert tools_indexed == 0
     idx = index.open_dir(whoosh_index_dir)
     assert idx.doc_count() == 1
     writer = idx.writer()
-    writer.delete_by_term('id', 1)
+    writer.delete_by_term("id", 1)
     writer.commit()
     idx = index.open_dir(whoosh_index_dir)
     assert idx.doc_count() == 0
-    repos_indexed, tools_indexed = build_index(whoosh_index_dir, community_file_structure.file_path, community_file_structure.hgweb_config_dir, community_file_structure.dburi)
+    repos_indexed, tools_indexed = build_index(
+        whoosh_index_dir,
+        community_file_structure.file_path,
+        community_file_structure.hgweb_config_dir,
+        community_file_structure.dburi,
+    )
     assert repos_indexed == 1
     assert tools_indexed == 1
diff --git a/test/unit/shed_unit/test_td_common_util.py b/test/unit/shed_unit/test_td_common_util.py
index 7189944c6cb..ad212f9ae50 100644
--- a/test/unit/shed_unit/test_td_common_util.py
+++ b/test/unit/shed_unit/test_td_common_util.py
@@ -1,6 +1,9 @@
 from contextlib import contextmanager
 from os.path import join
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 from galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
@@ -11,7 +14,6 @@ TEST_INSTALL_DIR = "%s/test_install_dir" % TEST_DEPENDENCIES_DIR
 
 
 class MockApp:
-
     def __init__(self):
         pass
 
@@ -19,19 +21,27 @@ class MockApp:
 def test_create_or_update_env_shell_file():
     test_path = "/usr/share/R/libs"
     env_file_builder = EnvFileBuilder(test_path)
-    line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="append_to", name="R_LIBS", value=test_path))
+    line, path = env_file_builder.create_or_update_env_shell_file(
+        TEST_INSTALL_DIR, dict(action="append_to", name="R_LIBS", value=test_path)
+    )
     assert path == join(TEST_INSTALL_DIR, "env.sh")
     assert line == "R_LIBS=$R_LIBS:/usr/share/R/libs; export R_LIBS"
 
-    line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="prepend_to", name="R_LIBS", value=test_path))
+    line, path = env_file_builder.create_or_update_env_shell_file(
+        TEST_INSTALL_DIR, dict(action="prepend_to", name="R_LIBS", value=test_path)
+    )
     assert path == join(TEST_INSTALL_DIR, "env.sh")
     assert line == "R_LIBS=/usr/share/R/libs:$R_LIBS; export R_LIBS"
 
-    line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="set_to", name="R_LIBS", value=test_path))
+    line, path = env_file_builder.create_or_update_env_shell_file(
+        TEST_INSTALL_DIR, dict(action="set_to", name="R_LIBS", value=test_path)
+    )
     assert path == join(TEST_INSTALL_DIR, "env.sh")
     assert line == "R_LIBS=/usr/share/R/libs; export R_LIBS"
 
-    line, path = env_file_builder.create_or_update_env_shell_file(TEST_INSTALL_DIR, dict(action="source", value=test_path))
+    line, path = env_file_builder.create_or_update_env_shell_file(
+        TEST_INSTALL_DIR, dict(action="source", value=test_path)
+    )
     assert path == join(TEST_INSTALL_DIR, "env.sh")
     assert line == "if [ -f /usr/share/R/libs ] ; then . /usr/share/R/libs ; fi"
 
@@ -48,15 +58,15 @@ def test_get_env_shell_file_paths_from_setup_environment_elem():
     """
     mock_app = MockApp()
     action_elem = parse_xml_string(xml)
-    required_for_install_env_sh = '/path/to/existing.sh'
+    required_for_install_env_sh = "/path/to/existing.sh"
     all_env_paths = [required_for_install_env_sh]
     action_dict: Dict[str, Any] = {}
     env_manager = EnvManager(mock_app)
 
-    r_env_sh = '/path/to/go/env.sh'
+    r_env_sh = "/path/to/go/env.sh"
 
     def mock_get_env_shell_file_paths(elem):
-        assert elem.get('name') in ["package_r_3_0_1", "package_zlib_1_2_8"]
+        assert elem.get("name") in ["package_r_3_0_1", "package_zlib_1_2_8"]
         return [r_env_sh]
 
     with __mock_common_util_method(env_manager, "get_env_shell_file_paths", mock_get_env_shell_file_paths):
@@ -66,15 +76,15 @@ def test_get_env_shell_file_paths_from_setup_environment_elem():
         # Verify new ones added.
         assert r_env_sh in all_env_paths
         # env_shell_file_paths includes everything
-        assert all(env in action_dict['env_shell_file_paths'] for env in all_env_paths)
+        assert all(env in action_dict["env_shell_file_paths"] for env in all_env_paths)
         # for every given repository there should be one env
         # file + the required_for_install_env_sh file
-        assert len(action_dict['env_shell_file_paths']) == 3
+        assert len(action_dict["env_shell_file_paths"]) == 3
 
         # action_shell_file_paths includes only env files defined
         # inside the setup_ action element.
-        assert required_for_install_env_sh in action_dict['action_shell_file_paths']
-        assert r_env_sh in action_dict['action_shell_file_paths']
+        assert required_for_install_env_sh in action_dict["action_shell_file_paths"]
+        assert r_env_sh in action_dict["action_shell_file_paths"]
 
 
 # Poor man's mocking. Need to get a real mocking library as real Galaxy development
diff --git a/test/unit/shed_unit/test_tool_panel_manager.py b/test/unit/shed_unit/test_tool_panel_manager.py
index 420e5ea12e2..1314506332c 100644
--- a/test/unit/shed_unit/test_tool_panel_manager.py
+++ b/test/unit/shed_unit/test_tool_panel_manager.py
@@ -5,14 +5,13 @@ from galaxy.util import parse_xml
 from tool_shed.tools import tool_version_manager
 from ..app.tools.test_toolbox import (
     BaseToolBoxTestCase,
-    SimplifiedToolBox
+    SimplifiedToolBox,
 )
 
 DEFAULT_GUID = "123456"
 
 
 class ToolPanelManagerTestCase(BaseToolBoxTestCase):
-
     def get_new_toolbox(self):
         return SimplifiedToolBox(self)
 
@@ -116,16 +115,24 @@ class ToolPanelManagerTestCase(BaseToolBoxTestCase):
         self._setup_two_versions_remove_one(section=True, uninstall=True)
         self._verify_version_2_removed_from_panel()
         # Not in tool conf because it was uninstalled.
-        assert "github.com/galaxyproject/example/test_tool/0.2" not in open(os.path.join(self.test_directory, "tool_conf.xml")).read()
+        assert (
+            "github.com/galaxyproject/example/test_tool/0.2"
+            not in open(os.path.join(self.test_directory, "tool_conf.xml")).read()
+        )
         new_toolbox = self.get_new_toolbox()
-        assert "tool_github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel["tid"].elems
+        assert (
+            "tool_github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel["tid"].elems
+        )
         self._verify_tool_confs()
 
     def test_uninstall_outside_section(self):
         self._setup_two_versions_remove_one(section=False, uninstall=True)
         self._verify_version_2_removed_from_panel(section=False)
         # Still in tool conf since not uninstalled only deactivated...
-        assert "github.com/galaxyproject/example/test_tool/0.2" not in open(os.path.join(self.test_directory, "tool_conf.xml")).read()
+        assert (
+            "github.com/galaxyproject/example/test_tool/0.2"
+            not in open(os.path.join(self.test_directory, "tool_conf.xml")).read()
+        )
         self._verify_tool_confs()
 
         self._remove_repository_contents("github.com/galaxyproject/example/test_tool/0.1", uninstall=True)
@@ -154,7 +161,9 @@ class ToolPanelManagerTestCase(BaseToolBoxTestCase):
             assert len(section.elems) == 1
             assert next(iter(section.elems.values())).id == "github.com/galaxyproject/example/test_tool/0.1"
 
-            assert "github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel["tid"].elems
+            assert (
+                "github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel["tid"].elems
+            )
         else:
             assert next(iter(new_toolbox._tool_panel.values())).id == "github.com/galaxyproject/example/test_tool/0.1"
             assert "github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel
@@ -183,7 +192,7 @@ class ToolPanelManagerTestCase(BaseToolBoxTestCase):
     def _init_ts_tool(self, guid=DEFAULT_GUID, **kwds):
         tool = self._init_tool(**kwds)
         tool.guid = guid
-        tool.version = kwds.get('version', '1.0')
+        tool.version = kwds.get("version", "1.0")
         return tool
 
     @property
diff --git a/test/unit/test_galaxy_transactions.py b/test/unit/test_galaxy_transactions.py
index 17e9a402570..a5b330dd2a1 100644
--- a/test/unit/test_galaxy_transactions.py
+++ b/test/unit/test_galaxy_transactions.py
@@ -7,21 +7,15 @@ from galaxy.util import bunch
 
 
 class App:
-
     def __init__(self):
         self.config = bunch.Bunch(
             log_events=False,
             log_actions=False,
         )
-        self.model = mapping.init(
-            "/tmp",
-            "sqlite:///:memory:",
-            create_tables=True
-        )
+        self.model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True)
 
 
 class Transaction(context.ProvidesAppContext):
-
     def __init__(self):
         self._app = App()
 
diff --git a/test/unit/tool_util/biotools/test_edam_parsing.py b/test/unit/tool_util/biotools/test_edam_parsing.py
index ec5c77fe053..58473f60b02 100644
--- a/test/unit/tool_util/biotools/test_edam_parsing.py
+++ b/test/unit/tool_util/biotools/test_edam_parsing.py
@@ -1,6 +1,4 @@
-from galaxy.tool_util.biotools.source import (
-    GitContentBiotoolsMetadataSource,
-)
+from galaxy.tool_util.biotools.source import GitContentBiotoolsMetadataSource
 from ._util import content_dir
 
 
diff --git a/test/unit/tool_util/mulled/test_get_tests.py b/test/unit/tool_util/mulled/test_get_tests.py
index 39fa4f381eb..9c346ce638d 100644
--- a/test/unit/tool_util/mulled/test_get_tests.py
+++ b/test/unit/tool_util/mulled/test_get_tests.py
@@ -1,4 +1,16 @@
-from galaxy.tool_util.deps.mulled.get_tests import deep_test_search, find_anaconda_versions, get_alternative_versions, get_anaconda_url, get_commands_from_yaml, get_run_test, get_test_from_anaconda, hashed_test_search, main_test_search, open_recipe_file, prepend_anaconda_url
+from galaxy.tool_util.deps.mulled.get_tests import (
+    deep_test_search,
+    find_anaconda_versions,
+    get_alternative_versions,
+    get_anaconda_url,
+    get_commands_from_yaml,
+    get_run_test,
+    get_test_from_anaconda,
+    hashed_test_search,
+    main_test_search,
+    open_recipe_file,
+    prepend_anaconda_url,
+)
 from galaxy.util import smart_str
 from ..util import external_dependency_management
 
@@ -20,72 +32,79 @@ test:
 
 def test_get_commands_from_yaml():
     commands = get_commands_from_yaml(smart_str(TEST_RECIPE))
-    assert commands['imports'] == ['eagle']
-    assert commands['commands'] == ['eagle --help']
-    assert commands['import_lang'] == 'python -c'
+    assert commands["imports"] == ["eagle"]
+    assert commands["commands"] == ["eagle --help"]
+    assert commands["import_lang"] == "python -c"
 
 
 def test_get_run_test():
     commands = get_run_test(' #!/bin/bash\npslScore 2> /dev/null || [[ "$?" == 255 ]]')
-    assert commands['commands'] == [' #!/bin/bash && pslScore 2> /dev/null || [[ "$?" == 255 ]]']
+    assert commands["commands"] == [' #!/bin/bash && pslScore 2> /dev/null || [[ "$?" == 255 ]]']
 
 
 @external_dependency_management
 def test_get_anaconda_url():
-    url = get_anaconda_url('samtools:1.7--1')
-    assert url == 'https://anaconda.org/bioconda/samtools/1.7/download/linux-64/samtools-1.7-1.tar.bz2'
+    url = get_anaconda_url("samtools:1.7--1")
+    assert url == "https://anaconda.org/bioconda/samtools/1.7/download/linux-64/samtools-1.7-1.tar.bz2"
 
 
 def test_prepend_anaconda_url():
-    url = prepend_anaconda_url('/bioconda/samtools/0.1.12/download/linux-64/samtools-0.1.12-2.tar.bz2')
-    assert url == 'https://anaconda.org/bioconda/samtools/0.1.12/download/linux-64/samtools-0.1.12-2.tar.bz2'
+    url = prepend_anaconda_url("/bioconda/samtools/0.1.12/download/linux-64/samtools-0.1.12-2.tar.bz2")
+    assert url == "https://anaconda.org/bioconda/samtools/0.1.12/download/linux-64/samtools-0.1.12-2.tar.bz2"
 
 
 @external_dependency_management
 def test_get_test_from_anaconda():
-    tests = get_test_from_anaconda('https://anaconda.org/bioconda/samtools/1.3.1/download/linux-64/samtools-1.3.1-5.tar.bz2')
-    assert tests['commands'] == ['samtools --help']
-    assert tests['import_lang'] == 'python -c'
+    tests = get_test_from_anaconda(
+        "https://anaconda.org/bioconda/samtools/1.3.1/download/linux-64/samtools-1.3.1-5.tar.bz2"
+    )
+    assert tests["commands"] == ["samtools --help"]
+    assert tests["import_lang"] == "python -c"
 
 
 @external_dependency_management
 def test_find_anaconda_versions():
-    versions = find_anaconda_versions('2pg_cartesian')
-    assert '/bioconda/2pg_cartesian/1.0.1/download/linux-64/2pg_cartesian-1.0.1-0.tar.bz2' in versions
+    versions = find_anaconda_versions("2pg_cartesian")
+    assert "/bioconda/2pg_cartesian/1.0.1/download/linux-64/2pg_cartesian-1.0.1-0.tar.bz2" in versions
 
 
 @external_dependency_management
 def test_open_recipe_file():
-    recipe = open_recipe_file('recipes/samtools/1.1/meta.yaml')
-    assert b'samtools' in recipe
+    recipe = open_recipe_file("recipes/samtools/1.1/meta.yaml")
+    assert b"samtools" in recipe
 
 
 @external_dependency_management
 def test_get_alternative_versions():
-    versions = get_alternative_versions('recipes/bamtools', 'meta.yaml')
-    assert versions == ['recipes/bamtools/2.3.0/meta.yaml']
+    versions = get_alternative_versions("recipes/bamtools", "meta.yaml")
+    assert versions == ["recipes/bamtools/2.3.0/meta.yaml"]
 
 
 @external_dependency_management
 def test_deep_test_search():
-    tests = deep_test_search('abundancebin:1.0.1--0')
-    assert tests['commands'] == ['command -v abundancebin', 'abundancebin &> /dev/null || [[ "$?" == "255" ]]']
-    assert tests['container'] == 'abundancebin:1.0.1--0'
-    assert tests['import_lang'] == 'python -c'
+    tests = deep_test_search("abundancebin:1.0.1--0")
+    assert tests["commands"] == ["command -v abundancebin", 'abundancebin &> /dev/null || [[ "$?" == "255" ]]']
+    assert tests["container"] == "abundancebin:1.0.1--0"
+    assert tests["import_lang"] == "python -c"
 
 
 @external_dependency_management
 def test_main_test_search():
-    tests = main_test_search('abundancebin:1.0.1--0')
-    assert tests['commands'] == ['command -v abundancebin', 'abundancebin &> /dev/null || [[ "$?" == "255" ]]']
-    assert tests['container'] == 'abundancebin:1.0.1--0'
-    assert tests['import_lang'] == 'python -c'
+    tests = main_test_search("abundancebin:1.0.1--0")
+    assert tests["commands"] == ["command -v abundancebin", 'abundancebin &> /dev/null || [[ "$?" == "255" ]]']
+    assert tests["container"] == "abundancebin:1.0.1--0"
+    assert tests["import_lang"] == "python -c"
 
 
 @external_dependency_management
 def test_hashed_test_search():
-    tests = hashed_test_search('mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:c17ce694dd57ab0ac1a2b86bb214e65fedef760e-0')
-    assert tests['commands'] == ['bamtools --help', 'samtools --help']
-    assert tests['container'] == 'mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:c17ce694dd57ab0ac1a2b86bb214e65fedef760e-0'
-    assert tests['import_lang'] == 'python -c'
-    assert tests['imports'] == []
+    tests = hashed_test_search(
+        "mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:c17ce694dd57ab0ac1a2b86bb214e65fedef760e-0"
+    )
+    assert tests["commands"] == ["bamtools --help", "samtools --help"]
+    assert (
+        tests["container"]
+        == "mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:c17ce694dd57ab0ac1a2b86bb214e65fedef760e-0"
+    )
+    assert tests["import_lang"] == "python -c"
+    assert tests["imports"] == []
diff --git a/test/unit/tool_util/mulled/test_mulled_build.py b/test/unit/tool_util/mulled/test_mulled_build.py
index 8bd9d6284cc..64f4e2bfa59 100644
--- a/test/unit/tool_util/mulled/test_mulled_build.py
+++ b/test/unit/tool_util/mulled/test_mulled_build.py
@@ -6,16 +6,19 @@ from galaxy.tool_util.deps.mulled.mulled_build import (
     DEFAULT_BASE_IMAGE,
     DEFAULT_EXTENDED_BASE_IMAGE,
     mull_targets,
-    target_str_to_targets
+    target_str_to_targets,
 )
 from ..util import external_dependency_management
 
 
-@pytest.mark.parametrize("target,version,base_image", [
-    ('maker', None, DEFAULT_EXTENDED_BASE_IMAGE),
-    ('qiime', '1.9.1', DEFAULT_EXTENDED_BASE_IMAGE),
-    ('samtools', None, DEFAULT_BASE_IMAGE),
-])
+@pytest.mark.parametrize(
+    "target,version,base_image",
+    [
+        ("maker", None, DEFAULT_EXTENDED_BASE_IMAGE),
+        ("qiime", "1.9.1", DEFAULT_EXTENDED_BASE_IMAGE),
+        ("samtools", None, DEFAULT_BASE_IMAGE),
+    ],
+)
 @external_dependency_management
 def test_base_image_for_targets(target, version, base_image):
     target = build_target(target, version=version)
@@ -24,14 +27,14 @@ def test_base_image_for_targets(target, version, base_image):
 
 @external_dependency_management
 def test_mulled_build_files_cli(tmpdir):
-    singularity_image_dir = tmpdir.mkdir('singularity image dir')
-    target = build_target('zlib')
-    mull_targets([target], command='build-and-test', singularity=True, singularity_image_dir=singularity_image_dir)
-    assert singularity_image_dir.join('zlib').exists()
+    singularity_image_dir = tmpdir.mkdir("singularity image dir")
+    target = build_target("zlib")
+    mull_targets([target], command="build-and-test", singularity=True, singularity_image_dir=singularity_image_dir)
+    assert singularity_image_dir.join("zlib").exists()
 
 
 def test_target_str_to_targets():
-    target_str = 'samtools=1.3.1--4,bedtools=2.22'
+    target_str = "samtools=1.3.1--4,bedtools=2.22"
     targets = target_str_to_targets(target_str)
-    assert (targets[0].package, targets[0].version, targets[0].build) == ('samtools', '1.3.1', '4')
-    assert (targets[1].package, targets[1].version, targets[1].build) == ('bedtools', '2.22', None)
+    assert (targets[0].package, targets[0].version, targets[0].build) == ("samtools", "1.3.1", "4")
+    assert (targets[1].package, targets[1].version, targets[1].build) == ("bedtools", "2.22", None)
diff --git a/test/unit/tool_util/mulled/test_mulled_build_files.py b/test/unit/tool_util/mulled/test_mulled_build_files.py
index ed8b22f4e56..dc3f7ffd13a 100644
--- a/test/unit/tool_util/mulled/test_mulled_build_files.py
+++ b/test/unit/tool_util/mulled/test_mulled_build_files.py
@@ -9,8 +9,8 @@ from galaxy.tool_util.deps.mulled.mulled_build_files import (
     generate_targets,
 )
 
-
-TESTCASES = yaml.safe_load(r"""
+TESTCASES = yaml.safe_load(
+    r"""
 - test_legacy_files_package_only:
     content: samtools
     equals:
@@ -53,15 +53,18 @@ TESTCASES = yaml.safe_load(r"""
       image_build: '10'
       name_override: image_name
       targets: samtools
-""")
+"""
+)
 TEST_IDS = [next(iter(k.keys())) for k in TESTCASES]
 
 
-@pytest.mark.parametrize('content, equals', [(d[k]['content'], d[k]['equals']) for k, d in zip(TEST_IDS, TESTCASES)], ids=TEST_IDS)
+@pytest.mark.parametrize(
+    "content, equals", [(d[k]["content"], d[k]["equals"]) for k, d in zip(TEST_IDS, TESTCASES)], ids=TEST_IDS
+)
 def test_generate_targets(content, equals):
-    equals['targets'] = target_str_to_targets(equals['targets'])
+    equals["targets"] = target_str_to_targets(equals["targets"])
     equals = FALLBACK_LINE_TUPLE(**equals)
-    with tempfile.NamedTemporaryFile(mode='w') as tmpfile:
+    with tempfile.NamedTemporaryFile(mode="w") as tmpfile:
         tmpfile.write(content)
         tmpfile.flush()
         generated_target = next(generate_targets(tmpfile.name))
diff --git a/test/unit/tool_util/mulled/test_mulled_list.py b/test/unit/tool_util/mulled/test_mulled_list.py
index 0f6a95d3080..07e71905a31 100644
--- a/test/unit/tool_util/mulled/test_mulled_list.py
+++ b/test/unit/tool_util/mulled/test_mulled_list.py
@@ -1,7 +1,11 @@
 import shutil
 import tempfile
 
-from galaxy.tool_util.deps.mulled.mulled_list import get_missing_containers, get_missing_envs, get_singularity_containers
+from galaxy.tool_util.deps.mulled.mulled_list import (
+    get_missing_containers,
+    get_missing_envs,
+    get_singularity_containers,
+)
 from ..util import external_dependency_management
 
 # def test_get_quay_containers():
@@ -14,18 +18,20 @@ from ..util import external_dependency_management
 @external_dependency_management
 def test_get_singularity_containers():
     lst = get_singularity_containers()
-    assert 'aragorn:1.2.36--1' in lst
-    assert 'znc:latest' not in lst
+    assert "aragorn:1.2.36--1" in lst
+    assert "znc:latest" not in lst
 
 
 def test_get_missing_containers():
     test_dir = tempfile.mkdtemp()
     try:
-        exclude_list = '%s/blocklist.txt' % test_dir
-        with open(exclude_list, 'w') as f:
-            f.write('a\n\nb\nc\nd')
-        containers = get_missing_containers(quay_list=['1', '2', '3', 'a', 'b', 'z'], singularity_list=['3', '4', '5'], blocklist_file=exclude_list)
-        assert containers == ['1', '2', 'z']
+        exclude_list = "%s/blocklist.txt" % test_dir
+        with open(exclude_list, "w") as f:
+            f.write("a\n\nb\nc\nd")
+        containers = get_missing_containers(
+            quay_list=["1", "2", "3", "a", "b", "z"], singularity_list=["3", "4", "5"], blocklist_file=exclude_list
+        )
+        assert containers == ["1", "2", "z"]
     finally:
         shutil.rmtree(test_dir)
 
@@ -33,10 +39,12 @@ def test_get_missing_containers():
 def test_get_missing_envs():
     test_dir = tempfile.mkdtemp()
     try:
-        exclude_list = '%s/blocklist.txt' % test_dir
-        with open(exclude_list, 'w') as f:
-            f.write('a\n\nb\nc\nd')
-        envs = get_missing_envs(quay_list=['1', '2', '3', 'a', 'b--2', 'z--1'], conda_list=['3', '4', '5'], blocklist_file=exclude_list)
-        assert envs == ['1', '2', 'z--1']
+        exclude_list = "%s/blocklist.txt" % test_dir
+        with open(exclude_list, "w") as f:
+            f.write("a\n\nb\nc\nd")
+        envs = get_missing_envs(
+            quay_list=["1", "2", "3", "a", "b--2", "z--1"], conda_list=["3", "4", "5"], blocklist_file=exclude_list
+        )
+        assert envs == ["1", "2", "z--1"]
     finally:
         shutil.rmtree(test_dir)
diff --git a/test/unit/tool_util/mulled/test_mulled_search.py b/test/unit/tool_util/mulled/test_mulled_search.py
index 9524a5e954d..5bc52c43331 100644
--- a/test/unit/tool_util/mulled/test_mulled_search.py
+++ b/test/unit/tool_util/mulled/test_mulled_search.py
@@ -6,7 +6,7 @@ from galaxy.tool_util.deps.mulled.mulled_search import (
     GitHubSearch,
     QuaySearch,
     run_command,
-    singularity_search
+    singularity_search,
 )
 from ..util import external_dependency_management
 
@@ -18,19 +18,19 @@ def test_quay_search():
     search1 = t.search_repository("adsfasdf", True)
     search2 = t.search_repository("bioconductor-gosemsim", True)
     assert search1 == []
-    assert {'version': '2.2.0--0', 'package': 'bioconductor-gosemsim'} in search2
+    assert {"version": "2.2.0--0", "package": "bioconductor-gosemsim"} in search2
 
 
 @external_dependency_management
 @pytest.mark.skipif(run_command is None, reason="requires import from conda library")
 def test_conda_search():
-    t = CondaSearch('bioconda')
+    t = CondaSearch("bioconda")
     search1 = t.get_json("asdfasdf")
     search2 = t.get_json("bioconductor-gosemsim")
     assert search1 == []
-    assert search2['version'] == '2.2.0'
-    assert search2['package'] == 'bioconductor-gosemsim'
-    assert search2['build'] == '0'
+    assert search2["version"] == "2.2.0"
+    assert search2["package"] == "bioconductor-gosemsim"
+    assert search2["build"] == "0"
 
 
 @external_dependency_management
@@ -39,28 +39,29 @@ def test_github_search():
     search1 = t.process_json(t.get_json("adsfasdf"), "adsfasdf")
     search2 = t.process_json(t.get_json("bioconductor-gosemsim"), "bioconductor-gosemsim")
     assert search1 == []
-    assert {'path': 'recipes/bioconductor-gosemsim/meta.yaml', 'name': 'meta.yaml'} in search2
+    assert {"path": "recipes/bioconductor-gosemsim/meta.yaml", "name": "meta.yaml"} in search2
 
 
 @external_dependency_management
 def test_get_package_hash():
-    package_hash1 = get_package_hash(['bamtools', 'samtools'], {})
-    package_hash2 = get_package_hash(['bamtools', 'samtools'], {'bamtools': '2.4.0', 'samtools': '1.3.1'})
-    package_hash3 = get_package_hash(['abricate', 'abyss'], {'abricate': '0.4', 'abyss': '2.0.1'})
-    assert package_hash1['package_hash'] == 'mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa'
-    assert package_hash2['version_hash'] == 'c17ce694dd57ab0ac1a2b86bb214e65fedef760e'
-    assert package_hash2['package_hash'] == 'mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa'
-    assert package_hash3['version_hash'] == 'e21d1262f064e1e01b6b9fad5bea117928f31b38'
-    assert package_hash3['package_hash'] == 'mulled-v2-cde36934a4704f448af44bf01deeae8d2832ca2e'
+    package_hash1 = get_package_hash(["bamtools", "samtools"], {})
+    package_hash2 = get_package_hash(["bamtools", "samtools"], {"bamtools": "2.4.0", "samtools": "1.3.1"})
+    package_hash3 = get_package_hash(["abricate", "abyss"], {"abricate": "0.4", "abyss": "2.0.1"})
+    assert package_hash1["package_hash"] == "mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa"
+    assert package_hash2["version_hash"] == "c17ce694dd57ab0ac1a2b86bb214e65fedef760e"
+    assert package_hash2["package_hash"] == "mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa"
+    assert package_hash3["version_hash"] == "e21d1262f064e1e01b6b9fad5bea117928f31b38"
+    assert package_hash3["package_hash"] == "mulled-v2-cde36934a4704f448af44bf01deeae8d2832ca2e"
 
 
 @external_dependency_management
 def test_singularity_search():
-    sing1 = singularity_search('mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa')
-    sing1_versions = {result['version'] for result in sing1}
+    sing1 = singularity_search("mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa")
+    sing1_versions = {result["version"] for result in sing1}
     assert {
-        'c17ce694dd57ab0ac1a2b86bb214e65fedef760e-0',
-        'f471ba33d45697daad10614c5bd25a67693f67f1-0',
-        'fc33176431a4b9ef3213640937e641d731db04f1-0'}.issubset(sing1_versions)
-    sing2 = singularity_search('mulled-v2-19fa9431f5863b2be81ff13791f1b00160ed0852')
+        "c17ce694dd57ab0ac1a2b86bb214e65fedef760e-0",
+        "f471ba33d45697daad10614c5bd25a67693f67f1-0",
+        "fc33176431a4b9ef3213640937e641d731db04f1-0",
+    }.issubset(sing1_versions)
+    sing2 = singularity_search("mulled-v2-19fa9431f5863b2be81ff13791f1b00160ed0852")
     assert sing2 == []
diff --git a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
index 0bf25c44fcf..d03de6aa7bb 100644
--- a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
+++ b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
@@ -4,7 +4,11 @@ import tempfile
 
 import pytest
 
-from galaxy.tool_util.deps.mulled.mulled_update_singularity_containers import docker_to_singularity, get_list_from_file, singularity_container_test
+from galaxy.tool_util.deps.mulled.mulled_update_singularity_containers import (
+    docker_to_singularity,
+    get_list_from_file,
+    singularity_container_test,
+)
 from galaxy.util import which
 from ..util import external_dependency_management
 
@@ -12,32 +16,56 @@ from ..util import external_dependency_management
 def test_get_list_from_file():
     test_dir = tempfile.mkdtemp()
     try:
-        list_file = os.path.join(test_dir, 'list_file.txt')
-        with open(list_file, 'w') as f:
-            f.write('bbmap:36.84--0\nbiobambam:2.0.42--0\nconnor:0.5.1--py35_0\ndiamond:0.8.26--0\nedd:1.1.18--py27_0')
-        assert get_list_from_file(list_file) == ['bbmap:36.84--0', 'biobambam:2.0.42--0', 'connor:0.5.1--py35_0', 'diamond:0.8.26--0', 'edd:1.1.18--py27_0']
+        list_file = os.path.join(test_dir, "list_file.txt")
+        with open(list_file, "w") as f:
+            f.write("bbmap:36.84--0\nbiobambam:2.0.42--0\nconnor:0.5.1--py35_0\ndiamond:0.8.26--0\nedd:1.1.18--py27_0")
+        assert get_list_from_file(list_file) == [
+            "bbmap:36.84--0",
+            "biobambam:2.0.42--0",
+            "connor:0.5.1--py35_0",
+            "diamond:0.8.26--0",
+            "edd:1.1.18--py27_0",
+        ]
     finally:
         shutil.rmtree(test_dir)
 
 
 @external_dependency_management
-@pytest.mark.skipif(not which('singularity'), reason="requires singularity but singularity not on PATH")
+@pytest.mark.skipif(not which("singularity"), reason="requires singularity but singularity not on PATH")
 def test_docker_to_singularity(tmp_path):
     tmp_dir = str(tmp_path)
-    docker_to_singularity('abundancebin:1.0.1--0', 'singularity', tmp_dir, no_sudo=True)
-    assert tmp_path.joinpath('abundancebin:1.0.1--0').exists()
+    docker_to_singularity("abundancebin:1.0.1--0", "singularity", tmp_dir, no_sudo=True)
+    assert tmp_path.joinpath("abundancebin:1.0.1--0").exists()
 
 
 @external_dependency_management
-@pytest.mark.skipif(not which('singularity'), reason="requires singularity but singularity not on PATH")
+@pytest.mark.skipif(not which("singularity"), reason="requires singularity but singularity not on PATH")
 def test_singularity_container_test(tmp_path):
     test_dir = tempfile.mkdtemp()
     try:
-        for n in ['pybigwig:0.1.11--py36_0', 'samtools:1.0--1', 'yasm:1.3.0--0']:
-            docker_to_singularity(n, 'singularity', test_dir, no_sudo=True)
-        results = singularity_container_test({'pybigwig:0.1.11--py36_0': {'imports': ['pyBigWig'], 'commands': ['python -c "import pyBigWig; assert(pyBigWig.numpy == 1); assert(pyBigWig.remote == 1)"'], 'import_lang': 'python -c'}, 'samtools:1.0--1': {'commands': ['samtools --help'], 'import_lang': 'python -c', 'container': 'samtools:1.0--1'}, 'yasm:1.3.0--0': {}}, 'singularity', test_dir)
-        assert 'samtools:1.0--1' in results['passed']
-        assert results['failed'][0]['imports'] == ['pyBigWig']
-        assert 'yasm:1.3.0--0' in results['notest']
+        for n in ["pybigwig:0.1.11--py36_0", "samtools:1.0--1", "yasm:1.3.0--0"]:
+            docker_to_singularity(n, "singularity", test_dir, no_sudo=True)
+        results = singularity_container_test(
+            {
+                "pybigwig:0.1.11--py36_0": {
+                    "imports": ["pyBigWig"],
+                    "commands": [
+                        'python -c "import pyBigWig; assert(pyBigWig.numpy == 1); assert(pyBigWig.remote == 1)"'
+                    ],
+                    "import_lang": "python -c",
+                },
+                "samtools:1.0--1": {
+                    "commands": ["samtools --help"],
+                    "import_lang": "python -c",
+                    "container": "samtools:1.0--1",
+                },
+                "yasm:1.3.0--0": {},
+            },
+            "singularity",
+            test_dir,
+        )
+        assert "samtools:1.0--1" in results["passed"]
+        assert results["failed"][0]["imports"] == ["pyBigWig"]
+        assert "yasm:1.3.0--0" in results["notest"]
     finally:
         shutil.rmtree(test_dir)
diff --git a/test/unit/tool_util/mulled/test_mulled_util.py b/test/unit/tool_util/mulled/test_mulled_util.py
index da67e6807b4..9aa9c81fda4 100644
--- a/test/unit/tool_util/mulled/test_mulled_util.py
+++ b/test/unit/tool_util/mulled/test_mulled_util.py
@@ -3,11 +3,17 @@ import pytest
 from galaxy.tool_util.deps.mulled.util import version_sorted
 
 
-@pytest.mark.parametrize("tags,tag", [
-    (["2.22--he941832_1", "2.22--he860b03_2", "2.22--hdbcaa40_3"], "2.22--hdbcaa40_3"),
-    (["1.1.2--py27_0", "1.1.2--py36_0", "1.1.2--py35_0"], "1.1.2--py36_0"),
-    (["6725cda82000b8e514baddcbf8c2dce054e3f797-1", "6725cda82000b8e514baddcbf8c2dce054e3f797-0"], "6725cda82000b8e514baddcbf8c2dce054e3f797-1"),
-    (["python:3.5", "python:3.7", "python:3.7--2"], "python:3.7--2")
-])
+@pytest.mark.parametrize(
+    "tags,tag",
+    [
+        (["2.22--he941832_1", "2.22--he860b03_2", "2.22--hdbcaa40_3"], "2.22--hdbcaa40_3"),
+        (["1.1.2--py27_0", "1.1.2--py36_0", "1.1.2--py35_0"], "1.1.2--py36_0"),
+        (
+            ["6725cda82000b8e514baddcbf8c2dce054e3f797-1", "6725cda82000b8e514baddcbf8c2dce054e3f797-0"],
+            "6725cda82000b8e514baddcbf8c2dce054e3f797-1",
+        ),
+        (["python:3.5", "python:3.7", "python:3.7--2"], "python:3.7--2"),
+    ],
+)
 def test_version_sorted(tags, tag):
     assert version_sorted(tags)[0] == tag
diff --git a/test/unit/tool_util/test_conda_resolution.py b/test/unit/tool_util/test_conda_resolution.py
index 18fdca874ea..52ea9ec8db1 100644
--- a/test/unit/tool_util/test_conda_resolution.py
+++ b/test/unit/tool_util/test_conda_resolution.py
@@ -4,7 +4,7 @@ from tempfile import mkdtemp
 
 from galaxy.tool_util.deps import (
     conda_util,
-    DependencyManager
+    DependencyManager,
 )
 from galaxy.tool_util.deps.requirements import ToolRequirement
 from galaxy.tool_util.deps.resolvers.conda import CondaDependencyResolver
@@ -40,7 +40,7 @@ def test_conda_resolution():
 def test_against_conda_prefix_regression():
     """Test that would fail if https://github.com/rtfd/readthedocs.org/issues/1902 regressed."""
 
-    base_path = mkdtemp(prefix='x' * 80)  # a ridiculously long prefix
+    base_path = mkdtemp(prefix="x" * 80)  # a ridiculously long prefix
     try:
         job_dir = os.path.join(base_path, "000")
         dependency_manager = DependencyManager(base_path)
diff --git a/test/unit/tool_util/test_container_resolution.py b/test/unit/tool_util/test_container_resolution.py
index af2aac64144..1332e4b1257 100644
--- a/test/unit/tool_util/test_container_resolution.py
+++ b/test/unit/tool_util/test_container_resolution.py
@@ -8,80 +8,97 @@ from galaxy.tool_util.deps.container_resolvers.mulled import (
 from galaxy.tool_util.deps.dependencies import ToolInfo
 from galaxy.tool_util.deps.requirements import ToolRequirement
 
-
-SINGULARITY_IMAGES = ('foo:1.0--bar', 'baz:2.22', 'mulled-v2-fe8a3b846bc50d24e5df78fa0b562c43477fe9ce:9f946d13f673ab2903cb0da849ad42916d619d18-0')
+SINGULARITY_IMAGES = (
+    "foo:1.0--bar",
+    "baz:2.22",
+    "mulled-v2-fe8a3b846bc50d24e5df78fa0b562c43477fe9ce:9f946d13f673ab2903cb0da849ad42916d619d18-0",
+)
 
 
 def test_docker_container_resolver_detects_docker_cli_absent(mocker):
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled.which", return_value=None)
     resolver = CachedMulledDockerContainerResolver()
     assert resolver._cli_available is False
 
 
 def test_docker_container_resolver_detects_docker_cli(mocker):
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled', return_value='/bin/docker')
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled", return_value="/bin/docker")
     resolver = CachedMulledDockerContainerResolver()
     assert resolver.cli_available
 
 
 def test_cached_docker_container_docker_cli_absent_resolve(mocker):
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled.which", return_value=None)
     resolver = CachedMulledDockerContainerResolver()
     assert resolver.cli_available is False
     assert resolver.resolve(enabled_container_types=[], tool_info={}) is None
 
 
 def test_docker_container_docker_cli_absent_resolve(mocker):
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled.which", return_value=None)
     resolver = MulledDockerContainerResolver()
     assert resolver.cli_available is False
     requirement = ToolRequirement(name="samtools", version="1.10", type="package")
     tool_info = ToolInfo(requirements=[requirement])
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
-    container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info)
-    assert container_description.type == 'docker'
-    assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
+    mocker.patch(
+        "galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name",
+        return_value="samtools:1.10--h2e538c0_3",
+    )
+    container_description = resolver.resolve(enabled_container_types=["docker"], tool_info=tool_info)
+    assert container_description.type == "docker"
+    assert container_description.identifier == "quay.io/biocontainers/samtools:1.10--h2e538c0_3"
 
 
 def test_docker_container_docker_cli_exception_resolve(mocker):
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value='/bin/docker')
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled.which", return_value="/bin/docker")
     resolver = MulledDockerContainerResolver()
     assert resolver.cli_available is True
     requirement = ToolRequirement(name="samtools", version="1.10", type="package")
     tool_info = ToolInfo(requirements=[requirement])
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.docker_cached_container_description', side_effect=CalledProcessError(1, 'bla'))
-    container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info, install=True)
+    mocker.patch(
+        "galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name",
+        return_value="samtools:1.10--h2e538c0_3",
+    )
+    mocker.patch(
+        "galaxy.tool_util.deps.container_resolvers.mulled.docker_cached_container_description",
+        side_effect=CalledProcessError(1, "bla"),
+    )
+    container_description = resolver.resolve(enabled_container_types=["docker"], tool_info=tool_info, install=True)
     assert resolver.cli_available is True
-    assert container_description.type == 'docker'
-    assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
+    assert container_description.type == "docker"
+    assert container_description.identifier == "quay.io/biocontainers/samtools:1.10--h2e538c0_3"
 
 
 def test_cached_singularity_container_resolver_uncached(mocker):
-    mocker.patch('os.listdir', return_value=SINGULARITY_IMAGES)
-    mocker.patch('os.path.exists', return_value=True)
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.safe_makedirs')
-    resolver = CachedMulledSingularityContainerResolver(app_info=mocker.Mock(container_image_cache_path='/'))
+    mocker.patch("os.listdir", return_value=SINGULARITY_IMAGES)
+    mocker.patch("os.path.exists", return_value=True)
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled.safe_makedirs")
+    resolver = CachedMulledSingularityContainerResolver(app_info=mocker.Mock(container_image_cache_path="/"))
     requirement = ToolRequirement(name="foo", version="1.0", type="package")
     tool_info = ToolInfo(requirements=[requirement])
-    container_description = resolver.resolve(enabled_container_types=['singularity'], tool_info=tool_info)
-    assert container_description.type == 'singularity'
-    assert container_description.identifier == '/singularity/mulled/foo:1.0--bar'
+    container_description = resolver.resolve(enabled_container_types=["singularity"], tool_info=tool_info)
+    assert container_description.type == "singularity"
+    assert container_description.identifier == "/singularity/mulled/foo:1.0--bar"
 
 
 def test_cached_singularity_container_resolver_dir_mtime_cached(mocker):
-    mocker.patch('os.listdir', return_value=SINGULARITY_IMAGES)
-    mocker.patch('os.path.exists', return_value=True)
-    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.safe_makedirs')
-    mocker.patch('os.stat', return_value=mocker.Mock(st_mtime=42))
-    resolver = CachedMulledSingularityContainerResolver(app_info=mocker.Mock(container_image_cache_path='/'), cache_directory_cacher_type='dir_mtime')
+    mocker.patch("os.listdir", return_value=SINGULARITY_IMAGES)
+    mocker.patch("os.path.exists", return_value=True)
+    mocker.patch("galaxy.tool_util.deps.container_resolvers.mulled.safe_makedirs")
+    mocker.patch("os.stat", return_value=mocker.Mock(st_mtime=42))
+    resolver = CachedMulledSingularityContainerResolver(
+        app_info=mocker.Mock(container_image_cache_path="/"), cache_directory_cacher_type="dir_mtime"
+    )
     requirement = ToolRequirement(name="baz", version="2.22", type="package")
     tool_info = ToolInfo(requirements=[requirement])
-    container_description = resolver.resolve(enabled_container_types=['singularity'], tool_info=tool_info)
-    assert container_description.type == 'singularity'
-    assert container_description.identifier == '/singularity/mulled/baz:2.22'
+    container_description = resolver.resolve(enabled_container_types=["singularity"], tool_info=tool_info)
+    assert container_description.type == "singularity"
+    assert container_description.identifier == "/singularity/mulled/baz:2.22"
     requirement = ToolRequirement(name="foo", version="1.0", type="package")
     tool_info.requirements.append(requirement)
-    container_description = resolver.resolve(enabled_container_types=['singularity'], tool_info=tool_info)
-    assert container_description.type == 'singularity'
-    assert container_description.identifier == '/singularity/mulled/mulled-v2-fe8a3b846bc50d24e5df78fa0b562c43477fe9ce:9f946d13f673ab2903cb0da849ad42916d619d18-0'
+    container_description = resolver.resolve(enabled_container_types=["singularity"], tool_info=tool_info)
+    assert container_description.type == "singularity"
+    assert (
+        container_description.identifier
+        == "/singularity/mulled/mulled-v2-fe8a3b846bc50d24e5df78fa0b562c43477fe9ce:9f946d13f673ab2903cb0da849ad42916d619d18-0"
+    )
diff --git a/test/unit/tool_util/test_edam_util.py b/test/unit/tool_util/test_edam_util.py
index 96d340972b1..e982e1c3b37 100644
--- a/test/unit/tool_util/test_edam_util.py
+++ b/test/unit/tool_util/test_edam_util.py
@@ -1,5 +1,8 @@
 import tempfile
-from typing import Any, Dict
+from typing import (
+    Any,
+    Dict,
+)
 
 from edam_ontology.streams import tabular_stream
 
@@ -24,6 +27,9 @@ def _verify_tree(tree: Dict[str, Any]):
     assert "operation_0004" in tree
     assert "topic_3974" in tree
     assert tree["topic_3974"]["label"] == "Epistasis"
-    assert tree["topic_3974"]["parents"] == ['topic_0622', 'topic_3295']
-    assert tree["topic_3974"]["path"] == [['topic_3391', 'topic_0003'], ['topic_3070', 'topic_0003']]
-    assert tree["topic_3974"]["definition"] == "The study of the epigenetic modifications of a whole cell, tissue, organism etc."
+    assert tree["topic_3974"]["parents"] == ["topic_0622", "topic_3295"]
+    assert tree["topic_3974"]["path"] == [["topic_3391", "topic_0003"], ["topic_3070", "topic_0003"]]
+    assert (
+        tree["topic_3974"]["definition"]
+        == "The study of the epigenetic modifications of a whole cell, tissue, organism etc."
+    )
diff --git a/test/unit/tool_util/test_output_checker.py b/test/unit/tool_util/test_output_checker.py
index 62659e456e7..b08808f61dd 100644
--- a/test/unit/tool_util/test_output_checker.py
+++ b/test/unit/tool_util/test_output_checker.py
@@ -1,8 +1,10 @@
 from unittest import TestCase
 from unittest.mock import Mock
 
-
-from galaxy.tool_util.output_checker import check_output, DETECTED_JOB_STATE
+from galaxy.tool_util.output_checker import (
+    check_output,
+    DETECTED_JOB_STATE,
+)
 from galaxy.tool_util.parser.stdio import (
     StdioErrorLevel,
     ToolStdioRegex,
@@ -10,21 +12,20 @@ from galaxy.tool_util.parser.stdio import (
 
 
 class OutputCheckerTestCase(TestCase):
-
     def setUp(self):
         self.tool = Mock(
             stdio_regexes=[],
             stdio_exit_codes=[],
         )
-        self.stdout = ''
-        self.stderr = ''
+        self.stdout = ""
+        self.stderr = ""
         self.tool_exit_code = None
 
     def test_default_no_stderr_success(self):
         self.__assertSuccessful()
 
     def test_default_stderr_failure(self):
-        self.stderr = 'foo'
+        self.stderr = "foo"
         self.__assertNotSuccessful()
 
     def test_exit_code_error(self):
@@ -40,14 +41,18 @@ class OutputCheckerTestCase(TestCase):
         self.__assertSuccessful()
 
     def test_problematic_strings_matching(self):
-        problematic_str = '\x80abc'
-        self.__add_regex(Mock(match=r'.abc', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None))
+        problematic_str = "\x80abc"
+        self.__add_regex(
+            Mock(match=r".abc", stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None)
+        )
         self.stderr = problematic_str
         self.__assertNotSuccessful()
 
     def test_problematic_strings_not_matching(self):
-        problematic_str = '\x80abc'
-        self.__add_regex(Mock(match=r'.abcd', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None))
+        problematic_str = "\x80abc"
+        self.__add_regex(
+            Mock(match=r".abcd", stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None)
+        )
         self.stderr = problematic_str
         self.__assertSuccessful()
 
@@ -93,4 +98,6 @@ class OutputCheckerTestCase(TestCase):
         assert self.__check_output()[0] != DETECTED_JOB_STATE.OK
 
     def __check_output(self):
-        return check_output(self.tool.stdio_regexes, self.tool.stdio_exit_codes, self.stdout, self.stderr, self.tool_exit_code, "job_id")
+        return check_output(
+            self.tool.stdio_regexes, self.tool.stdio_exit_codes, self.stdout, self.stderr, self.tool_exit_code, "job_id"
+        )
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
index 5d806b45ee4..09a76d7d6e0 100644
--- a/test/unit/tool_util/test_parsing.py
+++ b/test/unit/tool_util/test_parsing.py
@@ -9,7 +9,6 @@ from typing import Optional
 from galaxy.tool_util.parser.factory import get_tool_source
 from galaxy.util import galaxy_directory
 
-
 TOOL_XML_1 = """
 <tool name="BWA Mapper" id="bwa" version="1.0.1" display_interface="true" require_login="true" hidden="true">
     <description>The BWA Mapper</description>
@@ -219,7 +218,7 @@ class BaseLoaderTestCase(unittest.TestCase):
             with open(path, "w") as out:
                 out.write(source_contents)
             if macro_contents:
-                macro_path = os.path.join(self.temp_directory, 'macros.xml')
+                macro_path = os.path.join(self.temp_directory, "macros.xml")
                 with open(macro_path, "w") as out:
                     out.write(macro_contents)
 
@@ -332,8 +331,8 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
         outputs = test_dict["outputs"]
         assert len(outputs) == 1
         output1 = outputs[0]
-        assert output1["name"] == 'out1'
-        assert output1["value"] == 'moo.txt'
+        assert output1["name"] == "out1"
+        assert output1["value"] == "moo.txt"
         attributes1 = output1["attributes"]
         assert attributes1["compare"] == "diff"
         assert attributes1["lines_diff"] == 0
@@ -342,7 +341,7 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
         outputs = test2["outputs"]
         assert len(outputs) == 1
         output2 = outputs[0]
-        assert output2["name"] == 'out1'
+        assert output2["name"] == "out1"
         assert output2["value"] is None
         attributes1 = output2["attributes"]
         assert attributes1["compare"] == "sim_size"
@@ -350,25 +349,29 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs == [{'value': 'bwa', 'reftype': 'bio.tools'}]
+        assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
 
     def test_exit_code(self):
-        tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
+        tool_source = self._get_tool_source(
+            source_contents="""<tool id="bwa" name="bwa">
             <command detect_errors="exit_code">
                 ls
             </command>
         </tool>
-        """)
+        """
+        )
         exit, regexes = tool_source.parse_stdio()
         assert len(exit) == 2, exit
         assert len(regexes) == 0, regexes
 
-        tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
+        tool_source = self._get_tool_source(
+            source_contents="""<tool id="bwa" name="bwa">
             <command detect_errors="aggressive">
                 ls
             </command>
         </tool>
-        """)
+        """
+        )
         exit, regexes = tool_source.parse_stdio()
         assert len(exit) == 2, exit
         # error:, exception: various memory exception...
@@ -384,13 +387,15 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
         tool_source = self._get_tool_source(source_contents=TOOL_WITH_TOKEN)
         command = tool_source.parse_command()
         assert command
-        assert '@' not in command
+        assert "@" not in command
 
     def test_token_significant_whitespace(self):
-        tool_source = self._get_tool_source(source_contents=TOOL_WTIH_TOKEN_FROM_MACRO_FILE, macro_contents=MACRO_CONTENTS)
+        tool_source = self._get_tool_source(
+            source_contents=TOOL_WTIH_TOKEN_FROM_MACRO_FILE, macro_contents=MACRO_CONTENTS
+        )
         command = tool_source.parse_command()
-        assert command == 'cat   '
-        assert '@' not in command
+        assert command == "cat   "
+        assert "@" not in command
 
     def test_recursive_token(self):
         with self.assertRaisesRegex(Exception, "^Token '@NESTED_TOKEN@' cannot contain itself$"):
@@ -507,8 +512,8 @@ class YamlLoaderTestCase(BaseLoaderTestCase):
         outputs = test_dict["outputs"]
         assert len(outputs) == 1
         output1 = outputs[0]
-        assert output1["name"] == 'out1'
-        assert output1["value"] == 'moo.txt'
+        assert output1["name"] == "out1"
+        assert output1["value"] == "moo.txt"
         attributes1 = output1["attributes"]
         assert attributes1["compare"] == "diff"
         assert attributes1["lines_diff"] == 0
@@ -517,7 +522,7 @@ class YamlLoaderTestCase(BaseLoaderTestCase):
         outputs = test2["outputs"]
         assert len(outputs) == 1
         output2 = outputs[0]
-        assert output2["name"] == 'out1'
+        assert output2["name"] == "out1"
         assert output2["value"] is None
         attributes1 = output2["attributes"]
         assert attributes1["compare"] == "sim_size"
@@ -525,7 +530,7 @@ class YamlLoaderTestCase(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs == [{'value': 'bwa', 'reftype': 'bio.tools'}]
+        assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
 
     def test_sanitize(self):
         assert self._tool_source.parse_sanitize() is True
@@ -611,28 +616,28 @@ class ExpressionTestToolLoaderTestCase(BaseLoaderTestCase):
     source_contents = None
 
     def test_test(self):
-        test_dicts = self._tool_source.parse_tests_to_dict()['tests']
+        test_dicts = self._tool_source.parse_tests_to_dict()["tests"]
         assert len(test_dicts) == 3
         test_dict_0 = test_dicts[0]
-        assert 'outputs' in test_dict_0, test_dict_0
-        outputs = test_dict_0['outputs']
+        assert "outputs" in test_dict_0, test_dict_0
+        outputs = test_dict_0["outputs"]
         output0 = outputs[0]
-        assert 'object' in output0['attributes']
-        assert output0['attributes']['object'] is True
+        assert "object" in output0["attributes"]
+        assert output0["attributes"]["object"] is True
 
         test_dict_1 = test_dicts[1]
-        assert 'outputs' in test_dict_1, test_dict_1
-        outputs = test_dict_1['outputs']
+        assert "outputs" in test_dict_1, test_dict_1
+        outputs = test_dict_1["outputs"]
         output0 = outputs[0]
-        assert 'object' in output0['attributes']
-        assert output0['attributes']['object'] is False
+        assert "object" in output0["attributes"]
+        assert output0["attributes"]["object"] is False
 
         test_dict_2 = test_dicts[2]
-        assert 'outputs' in test_dict_2, test_dict_2
-        outputs = test_dict_2['outputs']
+        assert "outputs" in test_dict_2, test_dict_2
+        outputs = test_dict_2["outputs"]
         output0 = outputs[0]
-        assert 'object' in output0['attributes']
-        assert output0['attributes']['object'] is None
+        assert "object" in output0["attributes"]
+        assert output0["attributes"]["object"] is None
 
 
 class ExpressionOutputDataToolLoaderTestCase(BaseLoaderTestCase):
@@ -641,8 +646,8 @@ class ExpressionOutputDataToolLoaderTestCase(BaseLoaderTestCase):
 
     def test_output_parsing(self):
         outputs, _ = self._tool_source.parse_outputs(None)
-        assert 'larger_file' in outputs
-        tool_output = outputs['larger_file']
+        assert "larger_file" in outputs
+        tool_output = outputs["larger_file"]
         assert tool_output.format == "data"
         assert tool_output.from_expression == "output"
 
diff --git a/test/unit/tool_util/test_tool_deps.py b/test/unit/tool_util/test_tool_deps.py
index 47a34f36352..9cfd3c95182 100644
--- a/test/unit/tool_util/test_tool_deps.py
+++ b/test/unit/tool_util/test_tool_deps.py
@@ -9,18 +9,33 @@ from os import (
 )
 from shutil import rmtree
 from stat import S_IXUSR
-from subprocess import PIPE, Popen
-from typing import Any, Dict
+from subprocess import (
+    PIPE,
+    Popen,
+)
+from typing import (
+    Any,
+    Dict,
+)
 
-from galaxy.tool_util.deps import build_dependency_manager, DependencyManager
+from galaxy.tool_util.deps import (
+    build_dependency_manager,
+    DependencyManager,
+)
 from galaxy.tool_util.deps.requirements import (
     ToolRequirement,
-    ToolRequirements
+    ToolRequirements,
 )
 from galaxy.tool_util.deps.resolvers import NullDependency
 from galaxy.tool_util.deps.resolvers.galaxy_packages import GalaxyPackageDependency
-from galaxy.tool_util.deps.resolvers.lmod import LmodDependency, LmodDependencyResolver
-from galaxy.tool_util.deps.resolvers.modules import ModuleDependency, ModuleDependencyResolver
+from galaxy.tool_util.deps.resolvers.lmod import (
+    LmodDependency,
+    LmodDependencyResolver,
+)
+from galaxy.tool_util.deps.resolvers.modules import (
+    ModuleDependency,
+    ModuleDependencyResolver,
+)
 from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
 from .util import modify_environ
@@ -47,16 +62,16 @@ def test_tool_dependencies():
 
         dm = __dependency_manager_for_base_path(default_base_path=base_path)
         dependency = dm.find_dep("dep1", "1.0")
-        assert dependency.script == os.path.join(base_path, 'dep1', '1.0', 'env.sh')
-        assert dependency.path == os.path.join(base_path, 'dep1', '1.0')
+        assert dependency.script == os.path.join(base_path, "dep1", "1.0", "env.sh")
+        assert dependency.path == os.path.join(base_path, "dep1", "1.0")
         assert dependency.version == "1.0"
         dependency = dm.find_dep("dep1", "2.0")
         assert dependency.script is None
-        assert dependency.path == os.path.join(base_path, 'dep1', '2.0')
+        assert dependency.path == os.path.join(base_path, "dep1", "2.0")
         assert dependency.version == "2.0"
 
         # Test default versions
-        symlink(os.path.join(base_path, 'dep1', '2.0'), os.path.join(base_path, 'dep1', 'default'))
+        symlink(os.path.join(base_path, "dep1", "2.0"), os.path.join(base_path, "dep1", "default"))
         dependency = dm.find_dep("dep1", None)
         assert dependency.version == "2.0"
 
@@ -74,21 +89,27 @@ TEST_VERSION = "0.5.9"
 
 def test_toolshed_set_enviornment_requiremetns():
     with __test_base_path() as base_path:
-        test_repo = __build_test_repo('set_environment')
+        test_repo = __build_test_repo("set_environment")
         dm = __dependency_manager_for_base_path(default_base_path=base_path)
-        env_settings_dir = os.path.join(base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET)
+        env_settings_dir = os.path.join(
+            base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET
+        )
         os.makedirs(env_settings_dir)
-        dependency = dm.find_dep(TEST_REPO_NAME, version=None, type='set_environment', installed_tool_dependencies=[test_repo])
+        dependency = dm.find_dep(
+            TEST_REPO_NAME, version=None, type="set_environment", installed_tool_dependencies=[test_repo]
+        )
         assert dependency.version is None
         assert dependency.script == os.path.join(env_settings_dir, "env.sh")
 
 
 def test_toolshed_package_requirements():
     with __test_base_path() as base_path:
-        test_repo = __build_test_repo('package', version=TEST_VERSION)
+        test_repo = __build_test_repo("package", version=TEST_VERSION)
         dm = __dependency_manager_for_base_path(default_base_path=base_path)
         package_dir = __build_ts_test_package(base_path)
-        dependency = dm.find_dep(TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo])
+        dependency = dm.find_dep(
+            TEST_REPO_NAME, version=TEST_VERSION, type="package", installed_tool_dependencies=[test_repo]
+        )
         assert dependency.version == TEST_VERSION
         assert dependency.script == os.path.join(package_dir, "env.sh")
 
@@ -96,9 +117,9 @@ def test_toolshed_package_requirements():
 def test_toolshed_tools_fallback_on_manual_dependencies():
     with __test_base_path() as base_path:
         dm = __dependency_manager_for_base_path(default_base_path=base_path)
-        test_repo = __build_test_repo('package', version=TEST_VERSION)
+        test_repo = __build_test_repo("package", version=TEST_VERSION)
         env_path = __setup_galaxy_package_dep(base_path, "dep1", "1.0")
-        dependency = dm.find_dep("dep1", version="1.0", type='package', installed_tool_dependencies=[test_repo])
+        dependency = dm.find_dep("dep1", version="1.0", type="package", installed_tool_dependencies=[test_repo])
         assert dependency.version == "1.0"
         assert dependency.script == env_path
 
@@ -106,26 +127,28 @@ def test_toolshed_tools_fallback_on_manual_dependencies():
 def test_toolshed_greater_precendence():
     with __test_base_path() as base_path:
         dm = __dependency_manager_for_base_path(default_base_path=base_path)
-        test_repo = __build_test_repo('package', version=TEST_VERSION)
+        test_repo = __build_test_repo("package", version=TEST_VERSION)
         ts_package_dir = __build_ts_test_package(base_path)
         gx_env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION)
         ts_env_path = os.path.join(ts_package_dir, "env.sh")
-        dependency = dm.find_dep(TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo])
+        dependency = dm.find_dep(
+            TEST_REPO_NAME, version=TEST_VERSION, type="package", installed_tool_dependencies=[test_repo]
+        )
         assert dependency.script != gx_env_path  # Not the galaxy path, it should be the tool shed path used.
         assert dependency.script == ts_env_path
 
 
-def __build_ts_test_package(base_path, script_contents=''):
-    package_dir = os.path.join(base_path, TEST_REPO_NAME, TEST_VERSION, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET)
-    __touch(os.path.join(package_dir, 'env.sh'), script_contents)
+def __build_ts_test_package(base_path, script_contents=""):
+    package_dir = os.path.join(
+        base_path, TEST_REPO_NAME, TEST_VERSION, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET
+    )
+    __touch(os.path.join(package_dir, "env.sh"), script_contents)
     return package_dir
 
 
-REQUIREMENT_A = {'name': 'gnuplot',
-                 'type': 'package',
-                 'version': '4.6'}
+REQUIREMENT_A = {"name": "gnuplot", "type": "package", "version": "4.6"}
 REQUIREMENT_B = REQUIREMENT_A.copy()
-REQUIREMENT_B['version'] = '4.7'
+REQUIREMENT_B["version"] = "4.7"
 
 
 def test_tool_requirement_equality():
@@ -147,7 +170,9 @@ def test_tool_requirements():
 
 def test_module_dependency_resolver():
     with __test_base_path() as temp_directory:
-        module_script = _setup_module_command(temp_directory, '''
+        module_script = _setup_module_command(
+            temp_directory,
+            """
 -------------------------- /soft/modules/modulefiles ---------------------------
 JAGS/3.2.0-gcc45
 JAGS/3.3.0-gcc4.7.2
@@ -166,7 +191,8 @@ abokia-blast/2.0.2-130630/ompi_intel
 advisor/2013/update1    intel/11.1.075          mkl/10.2.1.017
 advisor/2013/update2    intel/11.1.080          mkl/10.2.5.035
 advisor/2013/update3    intel/12.0              mkl/10.2.7.041
-''')
+""",
+        )
         resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script)
         module = resolver.resolve(ToolRequirement(name="R", version=None, type="package"))
         assert module.module_name == "R"
@@ -182,18 +208,25 @@ advisor/2013/update3    intel/12.0              mkl/10.2.7.041
 
 def test_module_resolver_with_mapping():
     with __test_base_path() as temp_directory:
-        module_script = _setup_module_command(temp_directory, '''
+        module_script = _setup_module_command(
+            temp_directory,
+            """
 -------------------------- /soft/modules/modulefiles ---------------------------
 blast/2.24
-''')
+""",
+        )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write('''
+            f.write(
+                """
 - from: blast+
   to: blast
-''')
+"""
+            )
 
-        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        resolver = ModuleDependencyResolver(
+            _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
+        )
         module = resolver.resolve(ToolRequirement(name="blast+", version="2.24", type="package"))
         assert module.module_name == "blast"
         assert module.module_version == "2.24", module.module_version
@@ -204,40 +237,55 @@ def test_module_resolver_with_mapping_specificity_rules():
     # do not map to a different version when the version
     # has not been specified explicitly
     with __test_base_path() as temp_directory:
-        module_script = _setup_module_command(temp_directory, '''
+        module_script = _setup_module_command(
+            temp_directory,
+            """
 -------------------------- /soft/modules/modulefiles ---------------------------
 blast/2.24
-''')
+""",
+        )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write('''
+            f.write(
+                """
 - from:
     name: blast
     unversioned: true
   to:
     name: blast
     version: 2.24
-''')
+"""
+            )
 
-        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        resolver = ModuleDependencyResolver(
+            _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
+        )
         module = resolver.resolve(ToolRequirement(name="blast", type="package"))
         assert module.module_name == "blast"
-        assert module.module_version == "2.24", module.module_version  # successful resolution, because Requirement does not ask for a specific version
+        assert (
+            module.module_version == "2.24"
+        ), module.module_version  # successful resolution, because Requirement does not ask for a specific version
         module = resolver.resolve(ToolRequirement(name="blast", version="2.22", type="package"))
-        assert isinstance(module, NullDependency)  # NullDependency, because we don't map `version: Null` over a Requirement that asks for a specific version
+        assert isinstance(
+            module, NullDependency
+        )  # NullDependency, because we don't map `version: Null` over a Requirement that asks for a specific version
 
 
 def test_module_resolver_with_mapping_versions():
     with __test_base_path() as temp_directory:
-        module_script = _setup_module_command(temp_directory, '''
+        module_script = _setup_module_command(
+            temp_directory,
+            """
 -------------------------- /soft/modules/modulefiles ---------------------------
 blast/2.22.0-mpi
 blast/2.23
 blast/2.24.0-mpi
-''')
+""",
+        )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write('''
+            f.write(
+                """
 - from:
     name: blast+
     version: 2.24
@@ -249,14 +297,19 @@ blast/2.24.0-mpi
     version: 2.22
   to:
     version: 2.22.0-mpi
-''')
+"""
+            )
 
-        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        resolver = ModuleDependencyResolver(
+            _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
+        )
         module = resolver.resolve(ToolRequirement(name="blast+", version="2.24", type="package"))
         assert module.module_name == "blast"
         assert module.module_version == "2.24.0-mpi", module.module_version
 
-        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        resolver = ModuleDependencyResolver(
+            _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
+        )
         module = resolver.resolve(ToolRequirement(name="blast+", version="2.23", type="package"))
         assert isinstance(module, NullDependency)
 
@@ -267,9 +320,13 @@ blast/2.24.0-mpi
 
 def _setup_module_command(temp_directory, contents):
     module_script = os.path.join(temp_directory, "modulecmd")
-    __write_script(module_script, '''#!/bin/sh
+    __write_script(
+        module_script,
+        """#!/bin/sh
 cat %s/example_output 1>&2;
-''' % temp_directory)
+"""
+        % temp_directory,
+    )
     with open(os.path.join(temp_directory, "example_output"), "w") as f:
         # Subset of module avail from MSI cluster.
         f.write(contents)
@@ -281,22 +338,27 @@ def test_module_dependency():
         # Create mock modulecmd script that just exports a variable
         # the way modulecmd sh load would, but also validate correct
         # module name and version are coming through.
-        mock_modulecmd = os.path.join(temp_directory, 'modulecmd')
-        __write_script(mock_modulecmd, '''#!/bin/sh
+        mock_modulecmd = os.path.join(temp_directory, "modulecmd")
+        __write_script(
+            mock_modulecmd,
+            """#!/bin/sh
 if [ $3 != "foomodule/1.0" ];
 then
     exit 1
 fi
 echo 'FOO="bar"'
-''')
-        resolver = Bunch(modulecmd=mock_modulecmd, modulepath='/something')
+""",
+        )
+        resolver = Bunch(modulecmd=mock_modulecmd, modulepath="/something")
         dependency = ModuleDependency(resolver, "foomodule", "1.0")
         __assert_foo_exported(dependency.shell_commands())
 
 
 def test_lmod_dependency_resolver():
     with __test_base_path() as temp_directory:
-        lmod_script = _setup_lmod_command(temp_directory, '''
+        lmod_script = _setup_lmod_command(
+            temp_directory,
+            """
 /opt/apps/modulefiles:
 BlastPlus/
 BlastPlus/2.2.31+
@@ -307,8 +369,11 @@ Mothur/
 Mothur/1.33.3
 Mothur/1.36.1
 Mothur/1.38.1.1
-''')
-        resolver = LmodDependencyResolver(_SimpleDependencyManager(), lmodexec=lmod_script, modulepath='/path/to/modulefiles')
+""",
+        )
+        resolver = LmodDependencyResolver(
+            _SimpleDependencyManager(), lmodexec=lmod_script, modulepath="/path/to/modulefiles"
+        )
 
         lmod = resolver.resolve(ToolRequirement(name="Infernal", version=None, type="package"))
         assert lmod.module_name == "Infernal"
@@ -324,13 +389,18 @@ Mothur/1.38.1.1
 
 def test_lmod_dependency_resolver_versionless():
     with __test_base_path() as temp_directory:
-        lmod_script = _setup_lmod_command(temp_directory, '''
+        lmod_script = _setup_lmod_command(
+            temp_directory,
+            """
 /opt/apps/modulefiles:
 BlastPlus/2.4.0+
 Infernal/1.1.2
 Mothur/1.36.1
-''')
-        resolver = LmodDependencyResolver(_SimpleDependencyManager(), lmodexec=lmod_script, versionless='true', modulepath='/path/to/modulefiles')
+""",
+        )
+        resolver = LmodDependencyResolver(
+            _SimpleDependencyManager(), lmodexec=lmod_script, versionless="true", modulepath="/path/to/modulefiles"
+        )
 
         lmod = resolver.resolve(ToolRequirement(name="Infernal", version=None, type="package"))
         assert lmod.module_name == "Infernal"
@@ -350,7 +420,9 @@ Mothur/1.36.1
 
 def test_lmod_dependency_resolver_with_mapping_file():
     with __test_base_path() as temp_directory:
-        lmod_script = _setup_lmod_command(temp_directory, '''
+        lmod_script = _setup_lmod_command(
+            temp_directory,
+            """
 /opt/apps/modulefiles:
 BlastPlus/
 BlastPlus/2.2.31+
@@ -361,10 +433,12 @@ Mothur/
 Mothur/1.33.3
 Mothur/1.36.1
 Mothur/1.38.1.1
-''')
+""",
+        )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write('''
+            f.write(
+                """
 - from:
     name: blast+
     unversioned: true
@@ -376,9 +450,15 @@ Mothur/1.38.1.1
     version: 1.38
   to:
     version: 1.38.1.1
-''')
+"""
+            )
 
-        resolver = LmodDependencyResolver(_SimpleDependencyManager(), lmodexec=lmod_script, mapping_files=mapping_file, modulepath='/path/to/modulefiles')
+        resolver = LmodDependencyResolver(
+            _SimpleDependencyManager(),
+            lmodexec=lmod_script,
+            mapping_files=mapping_file,
+            modulepath="/path/to/modulefiles",
+        )
 
         lmod = resolver.resolve(ToolRequirement(name="BlastPlus", version="2.2.31+", type="package"))
         assert lmod.module_name == "BlastPlus"
@@ -401,9 +481,13 @@ Mothur/1.38.1.1
 
 def _setup_lmod_command(temp_directory, contents):
     lmod_script = os.path.join(temp_directory, "lmod")
-    __write_script(lmod_script, '''#!/bin/sh
+    __write_script(
+        lmod_script,
+        """#!/bin/sh
 cat %s/lmod_example_output 1>&2;
-''' % temp_directory)
+"""
+        % temp_directory,
+    )
     with open(os.path.join(temp_directory, "lmod_example_output"), "w") as f:
         # Subset of a "lmod -t avail" command of the LMOD environment module system.
         f.write(contents)
@@ -415,20 +499,23 @@ def test_lmod_dependency():
         # Create mock lmod script that just exports a variable
         # the way "lmod load" would, but also validate correct
         # module name and version are coming through.
-        mock_lmodexec = os.path.join(temp_directory, 'pouet')
-        __write_script(mock_lmodexec, '''#!/bin/sh
+        mock_lmodexec = os.path.join(temp_directory, "pouet")
+        __write_script(
+            mock_lmodexec,
+            """#!/bin/sh
 if [ "$2" != "foomodule/1.0" ]; then
     exit 1
 fi
 echo 'FOO="bar"'
-''')
-        resolver = Bunch(lmodexec=mock_lmodexec, settargexec=None, modulepath='/path/to/modulefiles')
+""",
+        )
+        resolver = Bunch(lmodexec=mock_lmodexec, settargexec=None, modulepath="/path/to/modulefiles")
         dependency = LmodDependency(resolver, "foomodule", "1.0")
         __assert_foo_exported(dependency.shell_commands())
 
 
 def __write_script(path, contents):
-    with open(path, 'w') as f:
+    with open(path, "w") as f:
         f.write(contents)
     st = stat(path)
     chmod(path, st.st_mode | S_IXUSR)
@@ -438,8 +525,10 @@ def test_galaxy_dependency_object_script():
     with __test_base_path() as base_path:
         # Create env.sh file that just exports variable FOO and verify it
         # shell_commands export it correctly.
-        env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION, "export FOO=\"bar\"")
-        dependency = GalaxyPackageDependency(env_path, os.path.dirname(env_path), TEST_REPO_NAME, 'package', TEST_VERSION)
+        env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION, 'export FOO="bar"')
+        dependency = GalaxyPackageDependency(
+            env_path, os.path.dirname(env_path), TEST_REPO_NAME, "package", TEST_VERSION
+        )
         __assert_foo_exported(dependency.shell_commands())
 
 
@@ -448,17 +537,17 @@ def test_shell_commands_built():
     # requirements.
     with __test_base_path() as base_path:
         dm = __dependency_manager_for_base_path(default_base_path=base_path)
-        __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION, contents="export FOO=\"bar\"")
-        mock_requirements = ToolRequirements([{'type': 'package', 'version': TEST_VERSION, 'name': TEST_REPO_NAME}])
+        __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION, contents='export FOO="bar"')
+        mock_requirements = ToolRequirements([{"type": "package", "version": TEST_VERSION, "name": TEST_REPO_NAME}])
         commands = dm.dependency_shell_commands(mock_requirements)
         __assert_foo_exported(commands)
 
 
 def __assert_foo_exported(commands):
-    command = ["bash", "-c", "%s; echo \"$FOO\"" % "".join(commands)]
+    command = ["bash", "-c", '%s; echo "$FOO"' % "".join(commands)]
     process = Popen(command, stdout=PIPE)
     output = process.communicate()[0].strip()
-    assert output == b'bar', f"Command {command} exports FOO as {unicodify(output)}, not bar"
+    assert output == b"bar", f"Command {command} exports FOO as {unicodify(output)}, not bar"
 
 
 def __setup_galaxy_package_dep(base_path, name, version, contents=""):
@@ -472,7 +561,7 @@ def __touch(fname, data=None):
     dirname = os.path.dirname(fname)
     if not os.path.exists(dirname):
         makedirs(dirname)
-    f = open(fname, 'w')
+    f = open(fname, "w")
     try:
         if data:
             f.write(data)
@@ -487,10 +576,8 @@ def __build_test_repo(type, version=None):
         type=type,
         version=version,
         tool_shed_repository=Bunch(
-            owner=TEST_REPO_USER,
-            name=TEST_REPO_NAME,
-            installed_changeset_revision=TEST_REPO_CHANGESET
-        )
+            owner=TEST_REPO_USER, name=TEST_REPO_NAME, installed_changeset_revision=TEST_REPO_CHANGESET
+        ),
     )
 
 
@@ -504,37 +591,45 @@ def __test_base_path():
 
 
 def test_parse():
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <tool_shed_packages />
   <galaxy_packages />
 </dependency_resolvers>
-''') as dependency_resolvers:
-        assert 'ToolShed' in dependency_resolvers[0].__class__.__name__
-        assert 'Galaxy' in dependency_resolvers[1].__class__.__name__
+"""
+    ) as dependency_resolvers:
+        assert "ToolShed" in dependency_resolvers[0].__class__.__name__
+        assert "Galaxy" in dependency_resolvers[1].__class__.__name__
 
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <galaxy_packages />
   <tool_shed_packages />
 </dependency_resolvers>
-''') as dependency_resolvers:
-        assert 'Galaxy' in dependency_resolvers[0].__class__.__name__
-        assert 'ToolShed' in dependency_resolvers[1].__class__.__name__
+"""
+    ) as dependency_resolvers:
+        assert "Galaxy" in dependency_resolvers[0].__class__.__name__
+        assert "ToolShed" in dependency_resolvers[1].__class__.__name__
 
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <galaxy_packages />
   <tool_shed_packages />
   <galaxy_packages versionless="true" />
 </dependency_resolvers>
-''') as dependency_resolvers:
+"""
+    ) as dependency_resolvers:
         assert not dependency_resolvers[0].versionless
         assert dependency_resolvers[2].versionless
 
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <galaxy_packages />
   <tool_shed_packages />
   <galaxy_packages base_path="/opt/galaxy/legacy/"/>
 </dependency_resolvers>
-''') as dependency_resolvers:
+"""
+    ) as dependency_resolvers:
         # Unspecified base_paths are both default_base_paths
         assert dependency_resolvers[0].base_path == dependency_resolvers[1].base_path
         # Can specify custom base path...
@@ -544,70 +639,93 @@ def test_parse():
 
 
 def test_uses_tool_shed_dependencies():
-    with __dependency_manager('''<dependency_resolvers>
+    with __dependency_manager(
+        """<dependency_resolvers>
   <galaxy_packages />
 </dependency_resolvers>
-''') as dm:
+"""
+    ) as dm:
         assert not dm.uses_tool_shed_dependencies()
 
-    with __dependency_manager('''<dependency_resolvers>
+    with __dependency_manager(
+        """<dependency_resolvers>
   <tool_shed_packages />
 </dependency_resolvers>
-''') as dm:
+"""
+    ) as dm:
         assert dm.uses_tool_shed_dependencies()
 
 
 def test_config_module_defaults():
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <modules prefetch="false" />
 </dependency_resolvers>
-''') as dependency_resolvers:
+"""
+    ) as dependency_resolvers:
         module_resolver = dependency_resolvers[0]
         assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker"
 
-    with __parse_resolvers('''
+    with __parse_resolvers(
+        """
 -  type: modules
    prefetch: false
-''', extension=".yml") as dependency_resolvers:
+""",
+        extension=".yml",
+    ) as dependency_resolvers:
         module_resolver = dependency_resolvers[0]
         assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker"
 
 
 def test_config_modulepath():
     # Test reads and splits MODULEPATH if modulepath is not specified.
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <modules find_by="directory" modulepath="/opt/modules/modulefiles:/usr/local/modules/modulefiles" />
 </dependency_resolvers>
-''') as dependency_resolvers:
-        assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles", "/usr/local/modules/modulefiles"]
+"""
+    ) as dependency_resolvers:
+        assert dependency_resolvers[0].module_checker.directories == [
+            "/opt/modules/modulefiles",
+            "/usr/local/modules/modulefiles",
+        ]
 
 
 def test_config_MODULEPATH():
     # Test reads and splits MODULEPATH if modulepath is not specified.
     with modify_environ({"MODULEPATH": "/opt/modules/modulefiles:/usr/local/modules/modulefiles"}):
-        with __parse_resolvers('''<dependency_resolvers>
+        with __parse_resolvers(
+            """<dependency_resolvers>
   <modules find_by="directory" />
 </dependency_resolvers>
-''') as dependency_resolvers:
-            assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles", "/usr/local/modules/modulefiles"]
+"""
+        ) as dependency_resolvers:
+            assert dependency_resolvers[0].module_checker.directories == [
+                "/opt/modules/modulefiles",
+                "/usr/local/modules/modulefiles",
+            ]
 
 
 def test_config_MODULESHOME():
     # Test fallbacks to read MODULESHOME if modulepath is not specified and
     # neither is MODULEPATH.
     with modify_environ({"MODULESHOME": "/opt/modules"}, keys_to_remove=["MODULEPATH"]):
-        with __parse_resolvers('''<dependency_resolvers>
+        with __parse_resolvers(
+            """<dependency_resolvers>
   <modules find_by="directory" />
 </dependency_resolvers>
-''') as dependency_resolvers:
+"""
+        ) as dependency_resolvers:
             assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles"]
 
 
 def test_config_module_directory_searcher():
-    with __parse_resolvers('''<dependency_resolvers>
+    with __parse_resolvers(
+        """<dependency_resolvers>
   <modules find_by="directory" modulepath="/opt/Modules/modulefiles" />
 </dependency_resolvers>
-''') as dependency_resolvers:
+"""
+    ) as dependency_resolvers:
         module_resolver = dependency_resolvers[0]
         assert module_resolver.module_checker.directories == ["/opt/Modules/modulefiles"]
 
@@ -730,7 +848,7 @@ def __parse_resolvers(file_content, extension=".xml"):
 @contextmanager
 def __dependency_manager(file_content, extension=".xml"):
     with __test_base_path() as base_path:
-        with tempfile.NamedTemporaryFile('w+', suffix=extension) as tmp:
+        with tempfile.NamedTemporaryFile("w+", suffix=extension) as tmp:
             tmp.write(file_content)
             tmp.flush()
             dm = __dependency_manager_for_base_path(default_base_path=base_path, conf_file=tmp.name)
@@ -738,7 +856,9 @@ def __dependency_manager(file_content, extension=".xml"):
 
 
 def __dependency_manager_for_base_path(default_base_path, conf_file=None):
-    dm = DependencyManager(default_base_path=default_base_path, conf_file=conf_file, app_config={"conda_auto_init": False})
+    dm = DependencyManager(
+        default_base_path=default_base_path, conf_file=conf_file, app_config={"conda_auto_init": False}
+    )
     if ROUND_TRIP_TEST_DEPENDENCY_MANAGER_SERIALIZATION:
         as_dict = dm.to_dict()
         dm = build_dependency_manager(resolution_config_dict=as_dict)
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 78dc4a7549a..10b4130250d 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -3,7 +3,12 @@ import tempfile
 
 import pytest
 
-from galaxy.tool_util.lint import lint_tool_source_with, LintContext, XMLLintMessageLine, XMLLintMessageXPath
+from galaxy.tool_util.lint import (
+    lint_tool_source_with,
+    LintContext,
+    XMLLintMessageLine,
+    XMLLintMessageXPath,
+)
 from galaxy.tool_util.linters import (
     citations,
     command,
@@ -622,12 +627,12 @@ XML_ORDER = """
 
 @pytest.fixture()
 def lint_ctx():
-    return LintContext('all', lint_message_class=XMLLintMessageLine)
+    return LintContext("all", lint_message_class=XMLLintMessageLine)
 
 
 @pytest.fixture()
 def lint_ctx_xpath():
-    return LintContext('all', lint_message_class=XMLLintMessageXPath)
+    return LintContext("all", lint_message_class=XMLLintMessageXPath)
 
 
 def get_xml_tool_source(xml_string):
@@ -679,8 +684,8 @@ def test_citations_errors(lint_ctx):
     run_lint(lint_ctx, citations.lint_citations, tool_source)
     assert "Unknown tag discovered in citations block [nonsense], will be ignored." in lint_ctx.warn_messages
     assert "Unknown citation type discovered [hoerensagen], will be ignored." in lint_ctx.warn_messages
-    assert 'Empty doi citation.' in lint_ctx.error_messages
-    assert 'Found no valid citations.' in lint_ctx.warn_messages
+    assert "Empty doi citation." in lint_ctx.error_messages
+    assert "Found no valid citations." in lint_ctx.warn_messages
     assert len(lint_ctx.warn_messages) == 3
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
@@ -689,7 +694,7 @@ def test_citations_errors(lint_ctx):
 def test_citations_valid(lint_ctx):
     tool_source = get_xml_tool_source(CITATIONS_VALID)
     run_lint(lint_ctx, citations.lint_citations, tool_source)
-    assert 'Found 1 likely valid citations.' in lint_ctx.valid_messages
+    assert "Found 1 likely valid citations." in lint_ctx.valid_messages
     assert len(lint_ctx.valid_messages) == 1
     assert not lint_ctx.info_messages
     assert not lint_ctx.error_messages
@@ -698,7 +703,7 @@ def test_citations_valid(lint_ctx):
 def test_command_multiple(lint_ctx):
     tool_source = get_xml_tool_source(COMMAND_MULTIPLE)
     run_lint(lint_ctx, command.lint_command, tool_source)
-    assert 'More than one command tag found, behavior undefined.' in lint_ctx.error_messages
+    assert "More than one command tag found, behavior undefined." in lint_ctx.error_messages
     assert len(lint_ctx.error_messages) == 1
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
@@ -708,32 +713,32 @@ def test_command_multiple(lint_ctx):
 def test_command_missing(lint_ctx):
     tool_source = get_xml_tool_source(COMMAND_MISSING)
     run_lint(lint_ctx, command.lint_command, tool_source)
-    assert 'No command tag found, must specify a command template to execute.' in lint_ctx.error_messages
+    assert "No command tag found, must specify a command template to execute." in lint_ctx.error_messages
 
 
 def test_command_todo(lint_ctx):
     tool_source = get_xml_tool_source(COMMAND_TODO)
     run_lint(lint_ctx, command.lint_command, tool_source)
-    assert 'Tool contains a command.' in lint_ctx.info_messages
-    assert 'Command template contains TODO text.' in lint_ctx.warn_messages
+    assert "Tool contains a command." in lint_ctx.info_messages
+    assert "Command template contains TODO text." in lint_ctx.warn_messages
 
 
 def test_command_detect_errors_interpreter(lint_ctx):
     tool_source = get_xml_tool_source(COMMAND_DETECT_ERRORS_INTERPRETER)
     run_lint(lint_ctx, command.lint_command, tool_source)
     assert "Command uses deprecated 'interpreter' attribute." in lint_ctx.warn_messages
-    assert 'Tool contains a command with interpreter of type [python].' in lint_ctx.info_messages
-    assert 'Unknown detect_errors attribute [nonsense]' in lint_ctx.warn_messages
-    assert 'Command is empty.' in lint_ctx.error_messages
+    assert "Tool contains a command with interpreter of type [python]." in lint_ctx.info_messages
+    assert "Unknown detect_errors attribute [nonsense]" in lint_ctx.warn_messages
+    assert "Command is empty." in lint_ctx.error_messages
 
 
 def test_general_missing_tool_id_name_version(lint_ctx):
     tool_source = get_xml_tool_source(GENERAL_MISSING_TOOL_ID_NAME_VERSION)
     run_lint(lint_ctx, general.lint_general, XmlToolSource(tool_source))
-    assert 'Tool version is missing or empty.' in lint_ctx.error_messages
-    assert 'Tool name is missing or empty.' in lint_ctx.error_messages
-    assert 'Tool does not define an id attribute.' in lint_ctx.error_messages
-    assert 'Tool specifies an invalid profile version [2109].' in lint_ctx.error_messages
+    assert "Tool version is missing or empty." in lint_ctx.error_messages
+    assert "Tool name is missing or empty." in lint_ctx.error_messages
+    assert "Tool does not define an id attribute." in lint_ctx.error_messages
+    assert "Tool specifies an invalid profile version [2109]." in lint_ctx.error_messages
 
 
 def test_general_whitespace_in_versions_and_names(lint_ctx):
@@ -749,7 +754,7 @@ def test_general_whitespace_in_versions_and_names(lint_ctx):
 def test_general_requirement_without_version(lint_ctx):
     tool_source = get_xml_tool_source(GENERAL_REQUIREMENT_WO_VERSION)
     run_lint(lint_ctx, general.lint_general, XmlToolSource(tool_source))
-    assert 'Tool version [1.0.1blah] is not compliant with PEP 440.' in lint_ctx.warn_messages
+    assert "Tool version [1.0.1blah] is not compliant with PEP 440." in lint_ctx.warn_messages
     assert "Requirement bwa defines no version" in lint_ctx.warn_messages
     assert "Requirement without name found" in lint_ctx.error_messages
     assert "Tool specifies profile version [20.09]." in lint_ctx.valid_messages
@@ -764,7 +769,7 @@ def test_general_requirement_without_version(lint_ctx):
 def test_general_valid(lint_ctx):
     tool_source = get_xml_tool_source(GENERAL_VALID)
     run_lint(lint_ctx, general.lint_general, XmlToolSource(tool_source))
-    assert 'Tool defines a version [1.0+galaxy1].' in lint_ctx.valid_messages
+    assert "Tool defines a version [1.0+galaxy1]." in lint_ctx.valid_messages
     assert "Tool specifies profile version [21.09]." in lint_ctx.valid_messages
     assert "Tool defines an id [valid_id]." in lint_ctx.valid_messages
     assert "Tool defines a name [valid name]." in lint_ctx.valid_messages
@@ -777,7 +782,7 @@ def test_general_valid(lint_ctx):
 def test_help_multiple(lint_ctx):
     tool_source = get_xml_tool_source(HELP_MULTIPLE)
     run_lint(lint_ctx, help.lint_help, tool_source)
-    assert 'More than one help section found, behavior undefined.' in lint_ctx.error_messages
+    assert "More than one help section found, behavior undefined." in lint_ctx.error_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -787,7 +792,7 @@ def test_help_multiple(lint_ctx):
 def test_help_absent(lint_ctx):
     tool_source = get_xml_tool_source(HELP_ABSENT)
     run_lint(lint_ctx, help.lint_help, tool_source)
-    assert 'No help section found, consider adding a help section to your tool.' in lint_ctx.warn_messages
+    assert "No help section found, consider adding a help section to your tool." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -797,7 +802,7 @@ def test_help_absent(lint_ctx):
 def test_help_empty(lint_ctx):
     tool_source = get_xml_tool_source(HELP_EMPTY)
     run_lint(lint_ctx, help.lint_help, tool_source)
-    assert 'Help section appears to be empty.' in lint_ctx.warn_messages
+    assert "Help section appears to be empty." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -807,8 +812,8 @@ def test_help_empty(lint_ctx):
 def test_help_todo(lint_ctx):
     tool_source = get_xml_tool_source(HELP_TODO)
     run_lint(lint_ctx, help.lint_help, tool_source)
-    assert 'Tool contains help section.' in lint_ctx.valid_messages
-    assert 'Help contains valid reStructuredText.' in lint_ctx.valid_messages
+    assert "Tool contains help section." in lint_ctx.valid_messages
+    assert "Help contains valid reStructuredText." in lint_ctx.valid_messages
     assert "Help contains TODO text." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert len(lint_ctx.valid_messages) == 2
@@ -819,8 +824,11 @@ def test_help_todo(lint_ctx):
 def test_help_invalid_rst(lint_ctx):
     tool_source = get_xml_tool_source(HELP_INVALID_RST)
     run_lint(lint_ctx, help.lint_help, tool_source)
-    assert 'Tool contains help section.' in lint_ctx.valid_messages
-    assert "Invalid reStructuredText found in help - [<string>:2: (WARNING/2) Inline strong start-string without end-string.\n]." in lint_ctx.warn_messages
+    assert "Tool contains help section." in lint_ctx.valid_messages
+    assert (
+        "Invalid reStructuredText found in help - [<string>:2: (WARNING/2) Inline strong start-string without end-string.\n]."
+        in lint_ctx.warn_messages
+    )
     assert not lint_ctx.info_messages
     assert len(lint_ctx.valid_messages) == 1
     assert len(lint_ctx.warn_messages) == 1
@@ -830,7 +838,7 @@ def test_help_invalid_rst(lint_ctx):
 def test_inputs_no_inputs(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_NO_INPUTS)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found no input parameters.' in lint_ctx.warn_messages
+    assert "Found no input parameters." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -840,9 +848,9 @@ def test_inputs_no_inputs(lint_ctx):
 def test_inputs_no_inputs_datasource(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_NO_INPUTS_DATASOURCE)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'No input parameters, OK for data sources' in lint_ctx.info_messages
-    assert 'display tag usually present in data sources' in lint_ctx.info_messages
-    assert 'uihints tag usually present in data sources' in lint_ctx.info_messages
+    assert "No input parameters, OK for data sources" in lint_ctx.info_messages
+    assert "display tag usually present in data sources" in lint_ctx.info_messages
+    assert "uihints tag usually present in data sources" in lint_ctx.info_messages
     assert len(lint_ctx.info_messages) == 3
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -863,10 +871,13 @@ def test_inputs_param_name(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_PARAM_NAME)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
     assert "Found 5 input parameters." in lint_ctx.info_messages
-    assert 'Param input [2] is not a valid Cheetah placeholder.' in lint_ctx.warn_messages
-    assert 'Found param input with no name specified.' in lint_ctx.error_messages
-    assert 'Param input with empty name.' in lint_ctx.error_messages
-    assert "Param input [param_name] 'name' attribute is redundant if argument implies the same name." in lint_ctx.warn_messages
+    assert "Param input [2] is not a valid Cheetah placeholder." in lint_ctx.warn_messages
+    assert "Found param input with no name specified." in lint_ctx.error_messages
+    assert "Param input with empty name." in lint_ctx.error_messages
+    assert (
+        "Param input [param_name] 'name' attribute is redundant if argument implies the same name."
+        in lint_ctx.warn_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 2
@@ -877,8 +888,8 @@ def test_inputs_param_type(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_PARAM_TYPE)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
     assert "Found 2 input parameters." in lint_ctx.info_messages
-    assert 'Param input [valid_name] input with no type specified.' in lint_ctx.error_messages
-    assert 'Param input [another_valid_name] with empty type specified.' in lint_ctx.error_messages
+    assert "Param input [valid_name] input with no type specified." in lint_ctx.error_messages
+    assert "Param input [another_valid_name] with empty type specified." in lint_ctx.error_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -889,7 +900,9 @@ def test_inputs_data_param(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_DATA_PARAM)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
     assert "Found 1 input parameters." in lint_ctx.info_messages
-    assert "Param input [valid_name] with no format specified - 'data' format will be assumed." in lint_ctx.warn_messages
+    assert (
+        "Param input [valid_name] with no format specified - 'data' format will be assumed." in lint_ctx.warn_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -899,13 +912,19 @@ def test_inputs_data_param(lint_ctx):
 def test_inputs_conditional(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_CONDITIONAL)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 10 input parameters.' in lint_ctx.info_messages
+    assert "Found 10 input parameters." in lint_ctx.info_messages
     assert "Conditional without a name" in lint_ctx.error_messages
-    assert "Select parameter of a conditional [select] options have to be defined by 'option' children elements." in lint_ctx.error_messages
-    assert 'Conditional [cond_wo_param] needs exactly one child <param> found 0' in lint_ctx.error_messages
-    assert 'Conditional [cond_w_mult_param] needs exactly one child <param> found 2' in lint_ctx.error_messages
+    assert (
+        "Select parameter of a conditional [select] options have to be defined by 'option' children elements."
+        in lint_ctx.error_messages
+    )
+    assert "Conditional [cond_wo_param] needs exactly one child <param> found 0" in lint_ctx.error_messages
+    assert "Conditional [cond_w_mult_param] needs exactly one child <param> found 2" in lint_ctx.error_messages
     assert 'Conditional [cond_text] first param should have type="select"' in lint_ctx.error_messages
-    assert 'Conditional [cond_boolean] first param of type="boolean" is discouraged, use a select' in lint_ctx.warn_messages
+    assert (
+        'Conditional [cond_boolean] first param of type="boolean" is discouraged, use a select'
+        in lint_ctx.warn_messages
+    )
     assert "Conditional [cond_boolean] no truevalue/falsevalue found for when block 'False'" in lint_ctx.warn_messages
     assert 'Conditional [cond_w_optional_select] test parameter cannot be optional="true"' in lint_ctx.warn_messages
     assert 'Conditional [cond_w_multiple_select] test parameter cannot be multiple="true"' in lint_ctx.warn_messages
@@ -920,11 +939,17 @@ def test_inputs_conditional(lint_ctx):
 def test_inputs_select_incompatible_display(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_SELECT_INCOMPATIBLE_DISPLAY)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 3 input parameters.' in lint_ctx.info_messages
+    assert "Found 3 input parameters." in lint_ctx.info_messages
     assert 'Select [radio_select] display="radio" is incompatible with optional="true"' in lint_ctx.error_messages
     assert 'Select [radio_select] display="radio" is incompatible with multiple="true"' in lint_ctx.error_messages
-    assert 'Select [checkboxes_select] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute' in lint_ctx.error_messages
-    assert 'Select [checkboxes_select] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute' in lint_ctx.error_messages
+    assert (
+        'Select [checkboxes_select] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute'
+        in lint_ctx.error_messages
+    )
+    assert (
+        'Select [checkboxes_select] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute'
+        in lint_ctx.error_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -934,9 +959,9 @@ def test_inputs_select_incompatible_display(lint_ctx):
 def test_inputs_duplicated_options(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_SELECT_DUPLICATED_OPTIONS)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 1 input parameters.' in lint_ctx.info_messages
-    assert 'Select parameter [select] has multiple options with the same text content' in lint_ctx.error_messages
-    assert 'Select parameter [select] has multiple options with the same value' in lint_ctx.error_messages
+    assert "Found 1 input parameters." in lint_ctx.info_messages
+    assert "Select parameter [select] has multiple options with the same text content" in lint_ctx.error_messages
+    assert "Select parameter [select] has multiple options with the same value" in lint_ctx.error_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -953,12 +978,15 @@ def test_inputs_duplicated_options_with_different_select(lint_ctx):
 def test_inputs_select_deprections(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_SELECT_DEPRECATIONS)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 3 input parameters.' in lint_ctx.info_messages
+    assert "Found 3 input parameters." in lint_ctx.info_messages
     assert "Select parameter [select_do] uses deprecated 'dynamic_options' attribute." in lint_ctx.warn_messages
     assert "Select parameter [select_ff] options uses deprecated 'from_file' attribute." in lint_ctx.warn_messages
     assert "Select parameter [select_fp] options uses deprecated 'from_parameter' attribute." in lint_ctx.warn_messages
     assert "Select parameter [select_ff] options uses deprecated 'transform_lines' attribute." in lint_ctx.warn_messages
-    assert "Select parameter [select_fp] options uses deprecated 'options_filter_attribute' attribute." in lint_ctx.warn_messages
+    assert (
+        "Select parameter [select_fp] options uses deprecated 'options_filter_attribute' attribute."
+        in lint_ctx.warn_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 5
@@ -968,15 +996,30 @@ def test_inputs_select_deprections(lint_ctx):
 def test_inputs_select_option_definitions(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_SELECT_OPTION_DEFINITIONS)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 6 input parameters.' in lint_ctx.info_messages
-    assert "Select parameter [select_noopt] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute." in lint_ctx.error_messages
-    assert "Select parameter [select_noopts] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values." in lint_ctx.error_messages
-    assert "Select parameter [select_fd_op] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute." in lint_ctx.error_messages
+    assert "Found 6 input parameters." in lint_ctx.info_messages
+    assert (
+        "Select parameter [select_noopt] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute."
+        in lint_ctx.error_messages
+    )
+    assert (
+        "Select parameter [select_noopts] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values."
+        in lint_ctx.error_messages
+    )
+    assert (
+        "Select parameter [select_fd_op] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute."
+        in lint_ctx.error_messages
+    )
     assert "Select parameter [select_fd_op] contains multiple options elements." in lint_ctx.error_messages
-    assert "Select parameter [select_fd_fdt] options uses 'from_dataset' and 'from_data_table' attribute." in lint_ctx.error_messages
+    assert (
+        "Select parameter [select_fd_fdt] options uses 'from_dataset' and 'from_data_table' attribute."
+        in lint_ctx.error_messages
+    )
     assert "Select parameter [select_noval_notext] has option without value" in lint_ctx.error_messages
     assert "Select parameter [select_noval_notext] has option without text" in lint_ctx.warn_messages
-    assert "Select parameter [select_meta_file_key_incomp] 'meta_file_key' is only compatible with 'from_dataset'." in lint_ctx.error_messages
+    assert (
+        "Select parameter [select_meta_file_key_incomp] 'meta_file_key' is only compatible with 'from_dataset'."
+        in lint_ctx.error_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -986,9 +1029,12 @@ def test_inputs_select_option_definitions(lint_ctx):
 def test_inputs_select_filter(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_SELECT_FILTER)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 1 input parameters.' in lint_ctx.info_messages
+    assert "Found 1 input parameters." in lint_ctx.info_messages
     assert "Select parameter [select_filter_types] contains filter without type." in lint_ctx.error_messages
-    assert "Select parameter [select_filter_types] contains filter with unknown type 'unknown_filter_type'." in lint_ctx.error_messages
+    assert (
+        "Select parameter [select_filter_types] contains filter with unknown type 'unknown_filter_type'."
+        in lint_ctx.error_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -998,15 +1044,33 @@ def test_inputs_select_filter(lint_ctx):
 def test_inputs_validator_incompatibilities(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_VALIDATOR_INCOMPATIBILITIES)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 2 input parameters.' in lint_ctx.info_messages
-    assert "Parameter [param_name]: 'in_range' validators are not expected to contain text (found 'TEXT')" in lint_ctx.warn_messages
+    assert "Found 2 input parameters." in lint_ctx.info_messages
+    assert (
+        "Parameter [param_name]: 'in_range' validators are not expected to contain text (found 'TEXT')"
+        in lint_ctx.warn_messages
+    )
     assert "Parameter [param_name]: validator with an incompatible type 'in_range'" in lint_ctx.error_messages
-    assert "Parameter [param_name]: 'in_range' validators need to define the 'min' or 'max' attribute(s)" in lint_ctx.error_messages
-    assert "Parameter [param_name]: attribute 'filename' is incompatible with validator of type 'regex'" in lint_ctx.error_messages
+    assert (
+        "Parameter [param_name]: 'in_range' validators need to define the 'min' or 'max' attribute(s)"
+        in lint_ctx.error_messages
+    )
+    assert (
+        "Parameter [param_name]: attribute 'filename' is incompatible with validator of type 'regex'"
+        in lint_ctx.error_messages
+    )
     assert "Parameter [param_name]: expression validators are expected to contain text" in lint_ctx.error_messages
-    assert "Parameter [param_name]: '[' is no valid regular expression: unterminated character set at position 0" in lint_ctx.error_messages
-    assert "Parameter [another_param_name]: 'metadata' validators need to define the 'check' or 'skip' attribute(s)" in lint_ctx.error_messages
-    assert "Parameter [param_name]: 'value_in_data_table' validators need to define the 'table_name' attribute" in lint_ctx.error_messages
+    assert (
+        "Parameter [param_name]: '[' is no valid regular expression: unterminated character set at position 0"
+        in lint_ctx.error_messages
+    )
+    assert (
+        "Parameter [another_param_name]: 'metadata' validators need to define the 'check' or 'skip' attribute(s)"
+        in lint_ctx.error_messages
+    )
+    assert (
+        "Parameter [param_name]: 'value_in_data_table' validators need to define the 'table_name' attribute"
+        in lint_ctx.error_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1016,7 +1080,7 @@ def test_inputs_validator_incompatibilities(lint_ctx):
 def test_inputs_validator_correct(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_VALIDATOR_CORRECT)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
-    assert 'Found 5 input parameters.' in lint_ctx.info_messages
+    assert "Found 5 input parameters." in lint_ctx.info_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -1037,7 +1101,7 @@ def test_inputs_repeats(lint_ctx):
 def test_outputs_missing(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_MISSING)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert 'Tool contains no outputs section, most tools should produce outputs.' in lint_ctx.warn_messages
+    assert "Tool contains no outputs section, most tools should produce outputs." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1047,8 +1111,8 @@ def test_outputs_missing(lint_ctx):
 def test_outputs_multiple(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_MULTIPLE)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert '0 outputs found.' in lint_ctx.info_messages
-    assert 'Tool contains multiple output sections, behavior undefined.' in lint_ctx.warn_messages
+    assert "0 outputs found." in lint_ctx.info_messages
+    assert "Tool contains multiple output sections, behavior undefined." in lint_ctx.warn_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1058,8 +1122,8 @@ def test_outputs_multiple(lint_ctx):
 def test_outputs_unknown_tag(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_UNKNOWN_TAG)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert '0 outputs found.' in lint_ctx.info_messages
-    assert 'Unknown element found in outputs [output]' in lint_ctx.warn_messages
+    assert "0 outputs found." in lint_ctx.info_messages
+    assert "Unknown element found in outputs [output]" in lint_ctx.warn_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1069,10 +1133,10 @@ def test_outputs_unknown_tag(lint_ctx):
 def test_outputs_unnamed_invalid_name(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_UNNAMED_INVALID_NAME)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert '2 outputs found.' in lint_ctx.info_messages
+    assert "2 outputs found." in lint_ctx.info_messages
     assert "Tool output doesn't define a name - this is likely a problem." in lint_ctx.warn_messages
     assert "Tool data output with missing name doesn't define an output format." in lint_ctx.warn_messages
-    assert 'Tool output name [2output] is not a valid Cheetah placeholder.' in lint_ctx.warn_messages
+    assert "Tool output name [2output] is not a valid Cheetah placeholder." in lint_ctx.warn_messages
     assert "Collection output with undefined 'type' found." in lint_ctx.warn_messages
     assert "Tool collection output 2output doesn't define an output format." in lint_ctx.warn_messages
     assert len(lint_ctx.info_messages) == 1
@@ -1084,8 +1148,11 @@ def test_outputs_unnamed_invalid_name(lint_ctx):
 def test_outputs_format_input(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_FORMAT_INPUT)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert '1 outputs found.' in lint_ctx.info_messages
-    assert "Using format='input' on data, format_source attribute is less ambiguous and should be used instead." in lint_ctx.warn_messages
+    assert "1 outputs found." in lint_ctx.info_messages
+    assert (
+        "Using format='input' on data, format_source attribute is less ambiguous and should be used instead."
+        in lint_ctx.warn_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1105,7 +1172,7 @@ def test_outputs_collection_format_source(lint_ctx):
 def test_outputs_discover_tool_provided_metadata(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA)
     run_lint(lint_ctx, outputs.lint_output, tool_source)
-    assert '1 outputs found.' in lint_ctx.info_messages
+    assert "1 outputs found." in lint_ctx.info_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -1115,7 +1182,10 @@ def test_outputs_discover_tool_provided_metadata(lint_ctx):
 def test_stdio_default_for_default_profile(lint_ctx):
     tool_source = get_xml_tool_source(STDIO_DEFAULT_FOR_DEFAULT_PROFILE)
     run_lint(lint_ctx, stdio.lint_stdio, XmlToolSource(tool_source))
-    assert "No stdio definition found, tool indicates error conditions with output written to stderr." in lint_ctx.info_messages
+    assert (
+        "No stdio definition found, tool indicates error conditions with output written to stderr."
+        in lint_ctx.info_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -1125,7 +1195,9 @@ def test_stdio_default_for_default_profile(lint_ctx):
 def test_stdio_default_for_nonlegacy_profile(lint_ctx):
     tool_source = get_xml_tool_source(STDIO_DEFAULT_FOR_NONLEGACY_PROFILE)
     run_lint(lint_ctx, stdio.lint_stdio, XmlToolSource(tool_source))
-    assert "No stdio definition found, tool indicates error conditions with non-zero exit codes." in lint_ctx.info_messages
+    assert (
+        "No stdio definition found, tool indicates error conditions with non-zero exit codes." in lint_ctx.info_messages
+    )
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -1145,7 +1217,9 @@ def test_stdio_multiple_stdio(lint_ctx):
 def test_stdio_invalid_child_or_attrib(lint_ctx):
     tool_source = get_xml_tool_source(STDIO_INVALID_CHILD_OR_ATTRIB)
     run_lint(lint_ctx, stdio.lint_stdio, XmlToolSource(tool_source))
-    assert "Unknown stdio child tag discovered [reqex]. Valid options are exit_code and regex." in lint_ctx.warn_messages
+    assert (
+        "Unknown stdio child tag discovered [reqex]. Valid options are exit_code and regex." in lint_ctx.warn_messages
+    )
     assert "Unknown attribute [descriptio] encountered on exit_code tag." in lint_ctx.warn_messages
     assert "Unknown attribute [descriptio] encountered on regex tag." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
@@ -1157,7 +1231,9 @@ def test_stdio_invalid_child_or_attrib(lint_ctx):
 def test_stdio_invalid_match(lint_ctx):
     tool_source = get_xml_tool_source(STDIO_INVALID_MATCH)
     run_lint(lint_ctx, stdio.lint_stdio, XmlToolSource(tool_source))
-    assert "Match '[' is no valid regular expression: unterminated character set at position 0" in lint_ctx.error_messages
+    assert (
+        "Match '[' is no valid regular expression: unterminated character set at position 0" in lint_ctx.error_messages
+    )
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -1167,7 +1243,7 @@ def test_stdio_invalid_match(lint_ctx):
 def test_tests_absent(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_ABSENT)
     run_lint(lint_ctx, tests.lint_tsts, tool_source)
-    assert 'No tests found, most tools should define test cases.' in lint_ctx.warn_messages
+    assert "No tests found, most tools should define test cases." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1177,7 +1253,7 @@ def test_tests_absent(lint_ctx):
 def test_tests_data_source(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_ABSENT_DATA_SOURCE)
     run_lint(lint_ctx, tests.lint_tsts, tool_source)
-    assert 'No tests found, that should be OK for data_sources.' in lint_ctx.info_messages
+    assert "No tests found, that should be OK for data_sources." in lint_ctx.info_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
@@ -1187,13 +1263,19 @@ def test_tests_data_source(lint_ctx):
 def test_tests_param_output_names(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_PARAM_OUTPUT_NAMES)
     run_lint(lint_ctx, tests.lint_tsts, tool_source)
-    assert '1 test(s) found.' in lint_ctx.valid_messages
+    assert "1 test(s) found." in lint_ctx.valid_messages
     assert "Test 1: Found test param tag without a name defined." in lint_ctx.error_messages
     assert "Test 1: Test param non_existent_test_name not found in the inputs" in lint_ctx.error_messages
     assert "Test 1: Found output tag without a name defined." in lint_ctx.error_messages
-    assert "Test 1: Found output tag with unknown name [nonexistent_output], valid names [['existent_output']]" in lint_ctx.error_messages
+    assert (
+        "Test 1: Found output tag with unknown name [nonexistent_output], valid names [['existent_output']]"
+        in lint_ctx.error_messages
+    )
     assert "Test 1: Found output_collection tag without a name defined." in lint_ctx.error_messages
-    assert "Test 1: Found output_collection tag with unknown name [nonexistent_collection], valid names [['existent_collection']]" in lint_ctx.error_messages
+    assert (
+        "Test 1: Found output_collection tag with unknown name [nonexistent_collection], valid names [['existent_collection']]"
+        in lint_ctx.error_messages
+    )
     assert not lint_ctx.info_messages
     assert len(lint_ctx.valid_messages) == 1
     assert not lint_ctx.warn_messages
@@ -1203,7 +1285,7 @@ def test_tests_param_output_names(lint_ctx):
 def test_tests_expect_failure_output(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_EXPECT_FAILURE_OUTPUT)
     run_lint(lint_ctx, tests.lint_tsts, tool_source)
-    assert 'No valid test(s) found.' in lint_ctx.warn_messages
+    assert "No valid test(s) found." in lint_ctx.warn_messages
     assert "Test 1: Cannot specify outputs in a test expecting failure." in lint_ctx.error_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
@@ -1214,8 +1296,10 @@ def test_tests_expect_failure_output(lint_ctx):
 def test_tests_without_expectations(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_WO_EXPECTATIONS)
     run_lint(lint_ctx, tests.lint_tsts, tool_source)
-    assert 'Test 1: No outputs or expectations defined for tests, this test is likely invalid.' in lint_ctx.warn_messages
-    assert 'No valid test(s) found.' in lint_ctx.warn_messages
+    assert (
+        "Test 1: No outputs or expectations defined for tests, this test is likely invalid." in lint_ctx.warn_messages
+    )
+    assert "No valid test(s) found." in lint_ctx.warn_messages
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 2
@@ -1240,7 +1324,10 @@ def test_tests_asserts(lint_ctx):
     assert "Test 1: missing attribute 'text' for 'has_text'" in lint_ctx.error_messages
     assert "Test 1: attribute 'value' for 'has_size' needs to be 'int' got '500k'" in lint_ctx.error_messages
     assert "Test 1: attribute 'delta' for 'has_size' needs to be 'int' got '1O'" in lint_ctx.error_messages
-    assert "Test 1: unknown attribute 'invalid_attrib_also_checked_in_nested_asserts' for 'not_has_text'" in lint_ctx.error_messages
+    assert (
+        "Test 1: unknown attribute 'invalid_attrib_also_checked_in_nested_asserts' for 'not_has_text'"
+        in lint_ctx.error_messages
+    )
     assert "Test 1: 'has_size' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
     assert "Test 1: 'has_n_columns' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
     assert "Test 1: 'has_n_lines' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
@@ -1251,8 +1338,8 @@ def test_tests_asserts(lint_ctx):
 def test_xml_order(lint_ctx):
     tool_source = get_xml_tool_source(XML_ORDER)
     run_lint(lint_ctx, xml_order.lint_xml_order, tool_source)
-    assert 'Unknown tag [wrong_tag] encountered, this may result in a warning in the future.' in lint_ctx.info_messages
-    assert 'Best practice violation [stdio] elements should come before [command]' in lint_ctx.warn_messages
+    assert "Unknown tag [wrong_tag] encountered, this may result in a warning in the future." in lint_ctx.info_messages
+    assert "Best practice violation [stdio] elements should come before [command]" in lint_ctx.warn_messages
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.valid_messages
     assert len(lint_ctx.warn_messages) == 1
@@ -1309,7 +1396,7 @@ def test_tool_and_macro_xml(lint_ctx_xpath):
     asserts = (
         ("Select parameter [select] has multiple options with the same value", "tool.xml", 5, "/tool/inputs/param[1]"),
         ("Found param input with no name specified.", "tool.xml", 13, "/tool/inputs/param[2]"),
-        ("Param input [No_type] input with no type specified.", "macros.xml", 3, "/tool/inputs/param[3]")
+        ("Param input [No_type] input with no type specified.", "macros.xml", 3, "/tool/inputs/param[3]"),
     )
     for a in asserts:
         message, fname, line, xpath = a
diff --git a/test/unit/tool_util/test_tool_loader.py b/test/unit/tool_util/test_tool_loader.py
index b1cce14ce4e..4bc997ae064 100644
--- a/test/unit/tool_util/test_tool_loader.py
+++ b/test/unit/tool_util/test_tool_loader.py
@@ -3,9 +3,18 @@ import re
 from shutil import rmtree
 from tempfile import mkdtemp
 
-from galaxy.tool_util.loader import load_tool, template_macro_params
-from galaxy.tool_util.unittest_utils.sample_data import SIMPLE_MACRO, SIMPLE_TOOL_WITH_MACRO
-from galaxy.util import parse_xml, xml_to_string
+from galaxy.tool_util.loader import (
+    load_tool,
+    template_macro_params,
+)
+from galaxy.tool_util.unittest_utils.sample_data import (
+    SIMPLE_MACRO,
+    SIMPLE_TOOL_WITH_MACRO,
+)
+from galaxy.util import (
+    parse_xml,
+    xml_to_string,
+)
 
 
 class TestToolDirectory:
@@ -36,7 +45,7 @@ def test_no_macros():
     Test tool loaded in absence of a macros node.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('<tool/>')
+        tool_dir.write("<tool/>")
         tool_dir.load(preprocess=True)
 
 
@@ -45,7 +54,8 @@ def test_loader_simple():
     Test simple macro replacement.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs" />
     <macros>
@@ -53,7 +63,8 @@ def test_loader_simple():
             <inputs />
         </macro>
     </macros>
-</tool>''')
+</tool>"""
+        )
         xml = tool_dir.load(preprocess=False)
         assert xml.find("inputs") is None
         xml = tool_dir.load(preprocess=True)
@@ -77,7 +88,8 @@ def test_loader_external():
 def test_loader_unnamed_yield():
     # Test macros with unnamed yield statements.
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs">
         <input name="first_input" />
@@ -100,7 +112,8 @@ def test_loader_unnamed_yield():
             </inputs>
         </macro>
     </macros>
-</tool>''')
+</tool>"""
+        )
         xml = tool_dir.load()
         assert xml.find("/inputs[1]/input").get("name") == "first_input"
         assert xml.find("/inputs[2]/input").get("name") == "second_input"
@@ -112,7 +125,8 @@ def test_loader_unnamed_yield_nested():
     Test nested macro with yield statements
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write("""
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <macro name="paired_options">
@@ -137,11 +151,15 @@ def test_loader_unnamed_yield_nested():
         </expand>
     </inputs>
 </tool>
-""")
+"""
+        )
         xml = tool_dir.load()
         # assert the both yields in the inner macro (paired_options) are expanded
         assert xml.find('/inputs/conditional[@name="library"]/when[@value="paired"]/param[@name="test"]') is not None
-        assert xml.find('/inputs/conditional[@name="library"]/when[@value="paired_collection"]/param[@name="test"]') is not None
+        assert (
+            xml.find('/inputs/conditional[@name="library"]/when[@value="paired_collection"]/param[@name="test"]')
+            is not None
+        )
 
 
 def test_loader_recursive():
@@ -149,7 +167,8 @@ def test_loader_recursive():
     Test recursive macro applications.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs">
         <input name="first_input" />
@@ -166,7 +185,8 @@ def test_loader_recursive():
             <input name="second_input" />
         </macro>
     </macros>
-</tool>''')
+</tool>"""
+        )
         xml = tool_dir.load()
         assert xml.find("/inputs/input[1]").get("name") == "first_input"
         assert xml.find("/inputs/input[2]").get("name") == "second_input"
@@ -178,7 +198,8 @@ def test_loader_recursive2():
     Test recursive macro applications.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs">
         <input name="first_input" />
@@ -198,7 +219,8 @@ def test_loader_recursive2():
             <input name="second_input" />
         </macro>
     </macros>
-</tool>''')
+</tool>"""
+        )
         xml = tool_dir.load()
         assert xml.find("/inputs/input[1]").get("name") == "first_input"
         assert xml.find("/inputs/input[2]").get("name") == "second_input"
@@ -210,7 +232,8 @@ def test_loader_toplevel_yield():
     test expansion of top level (ie child of <macro>) yields
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool id="issue_647">
     <macros>
         <macro name="a">
@@ -223,7 +246,8 @@ def test_loader_toplevel_yield():
             <param name="b" type="text" value="b" label="b" />
         </expand>
     </inputs>
-</tool>''')
+</tool>"""
+        )
         xml = tool_dir.load()
         assert xml.find("/inputs/param[1]").get("name") == "a1"
         assert xml.find("/inputs/param[2]").get("name") == "b"
@@ -234,7 +258,8 @@ def test_loader_shortcut():
     Test <xml> is shortcut for macro type="xml"
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs" />
     <macros>
@@ -242,14 +267,16 @@ def test_loader_shortcut():
             <inputs />
         </xml>
     </macros>
-</tool>''')
+</tool>"""
+        )
         xml = tool_dir.load()
         assert xml.find("inputs") is not None
 
 
 def test_loader_template():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <command interpreter="python">tool_wrapper.py
     #include source=$tool_params
@@ -258,15 +285,17 @@ def test_loader_template():
         <template name="tool_params">-a 1 -b 2</template>
     </macros>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         params_dict = template_macro_params(xml.getroot())
-        assert params_dict['tool_params'] == "-a 1 -b 2"
+        assert params_dict["tool_params"] == "-a 1 -b 2"
 
 
 def test_loader_token_text():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <token name="@CITATION@">The citation.</token>
@@ -276,7 +305,8 @@ def test_loader_token_text():
         <tag />
     </another>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         help_el = xml.find("help")
         assert help_el.text == "The citation.", help_el.text
@@ -284,7 +314,8 @@ def test_loader_token_text():
 
 def test_loader_token_nested():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <token name="@WIZARD@">Ab@HELPER@ra</token>
@@ -296,7 +327,8 @@ def test_loader_token_nested():
         <tag />
     </another>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         help_el = xml.find("help")
         assert help_el.text == "Abracadabra", help_el.text
@@ -307,7 +339,8 @@ def test_loader_token_cycle():
     test if cycles in nested tokens are detected
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <token name="@A@">a @ROSE@</token>
@@ -319,7 +352,8 @@ def test_loader_token_cycle():
         <tag />
     </another>
 </tool>
-''')
+"""
+        )
         try:
             tool_dir.load()
         except Exception as e:
@@ -333,7 +367,8 @@ def test_loader_token_attribute_name():
     test the repacement of an attribute name by a token
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <token name="__ATTR_NAME">name</token>
@@ -342,7 +377,8 @@ def test_loader_token_attribute_name():
         <tag __ATTR_NAME="blah" />
     </another>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         assert xml.find('/another/tag[@name="blah"]') is not None
 
@@ -352,7 +388,8 @@ def test_loader_token_attribute_value():
     test the repacement of an attribute value by a token
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <token name="@TAG_VAL@">The value.</token>
@@ -361,14 +398,16 @@ def test_loader_token_attribute_value():
         <tag value="@TAG_VAL@" />
     </another>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         assert xml.find('/another/tag[@value="The value."]') is not None
 
 
 def test_loader_token_empty():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <token name="@TAG_VAL@"><![CDATA[]]></token>
@@ -377,7 +416,8 @@ def test_loader_token_empty():
         <tag value="@TAG_VAL@" />
     </another>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         assert xml.find('/another/tag[@value=""]') is not None
 
@@ -387,7 +427,8 @@ def test_loader_macro_token_quote():
     Test macros XML macros with $$ expansions in attributes
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs" bar="hello" />
     <expand macro="inputs" bar="my awesome" />
@@ -398,7 +439,8 @@ def test_loader_macro_token_quote():
         </xml>
     </macros>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
         assert len(input_els) == 3
@@ -412,7 +454,8 @@ def test_loader_macro_token():
     Test macros XML macros with @ expansions in text
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs" foo="hello" />
     <expand macro="inputs" foo="world" />
@@ -423,7 +466,8 @@ def test_loader_macro_token():
         </xml>
     </macros>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
         assert len(input_els) == 3
@@ -437,7 +481,8 @@ def test_loader_macro_token_recursive():
     Test macros XML macros with @ expansions and recursive
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <expand macro="inputs" foo="hello" />
     <expand macro="inputs" foo="world" />
@@ -451,7 +496,8 @@ def test_loader_macro_token_recursive():
         </xml>
     </macros>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
         assert len(input_els) == 3
@@ -467,7 +513,8 @@ def test_loader_macro_named_yield():
     - unnamed yields are replaced by all non-token elements of the expand tag
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <xml name="test">
@@ -494,9 +541,12 @@ def test_loader_macro_named_yield():
         <sub_of_expand_2/>
     </expand>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
-        assert xml_to_string(xml, pretty=True) == '''<?xml version="1.0" ?>
+        assert (
+            xml_to_string(xml, pretty=True)
+            == """<?xml version="1.0" ?>
 <tool>
     <macros/>
     <A>
@@ -511,7 +561,8 @@ def test_loader_macro_named_yield():
         <content_of_token2/>
         <more_content_of_token2/>
     </B>
-</tool>'''
+</tool>"""
+        )
 
 
 def test_loader_macro_multiple_toplevel_yield():
@@ -519,7 +570,8 @@ def test_loader_macro_multiple_toplevel_yield():
     test replacement of multiple top level yield
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <xml name="test">
@@ -544,9 +596,12 @@ def test_loader_macro_multiple_toplevel_yield():
         <sub_of_expand_2/>
     </expand>
 </tool>
-''')
+"""
+        )
         xml = tool_dir.load()
-        assert xml_to_string(xml, pretty=True) == '''<?xml version="1.0" ?>
+        assert (
+            xml_to_string(xml, pretty=True)
+            == """<?xml version="1.0" ?>
 <tool>
     <macros/>
     <blah/>
@@ -558,7 +613,8 @@ def test_loader_macro_multiple_toplevel_yield():
     </blah>
     <content_of_token2/>
     <more_content_of_token2/>
-</tool>'''
+</tool>"""
+        )
 
 
 def test_loader_macro_recursive_named_yield():
@@ -571,7 +627,8 @@ def test_loader_macro_recursive_named_yield():
     - replacing unnamed yield gives the only non-token element of the expand
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <xml name="test">
@@ -593,10 +650,13 @@ def test_loader_macro_recursive_named_yield():
         </token>
         <T/>
     </expand>
-</tool>''')
+</tool>"""
+        )
 
         xml = tool_dir.load()
-        assert xml_to_string(xml, pretty=True) == '''<?xml version="1.0" ?>
+        assert (
+            xml_to_string(xml, pretty=True)
+            == """<?xml version="1.0" ?>
 <tool>
     <macros/>
     <A>
@@ -606,7 +666,8 @@ def test_loader_macro_recursive_named_yield():
             </T2>
         </T1>
     </A>
-</tool>'''
+</tool>"""
+        )
 
 
 def test_loader_specify_nested_macro_by_token():
@@ -616,15 +677,18 @@ def test_loader_specify_nested_macro_by_token():
     of the outer macro
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <import>external.xml</import>
     </macros>
     <expand macro="testp" token_name="a"/>
     <expand macro="testp" token_name="b"/>
-</tool>''')
-        tool_dir.write('''
+</tool>"""
+        )
+        tool_dir.write(
+            """
 <macros>
     <xml name="a">
         <A/>
@@ -636,18 +700,24 @@ def test_loader_specify_nested_macro_by_token():
         <expand macro="@TOKEN_NAME@"/>
     </xml>
 </macros>
-''', name="external.xml")
+""",
+            name="external.xml",
+        )
 
         xml = tool_dir.load()
         # test with re because loading from external macros
         # adds a xml:base property (containing the source path)
         # to the node which is printed
-        assert re.match(r"""<\?xml version="1\.0" \?>
+        assert re.match(
+            r"""<\?xml version="1\.0" \?>
 <tool>
     <macros/>
     <A xml:base=".*/external.xml"/>
     <B xml:base=".*/external.xml"/>
-</tool>""", xml_to_string(xml, pretty=True), re.MULTILINE)
+</tool>""",
+            xml_to_string(xml, pretty=True),
+            re.MULTILINE,
+        )
 
 
 def test_loader_circular_macros():
@@ -655,7 +725,8 @@ def test_loader_circular_macros():
     check the cycles in nested macros are detected
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write('''
+        tool_dir.write(
+            """
 <tool>
     <macros>
         <xml name="a">
@@ -670,7 +741,8 @@ def test_loader_circular_macros():
         </xml>
     </macros>
     <expand macro="a"/>
-</tool>''')
+</tool>"""
+        )
         try:
             tool_dir.load()
         except AssertionError as a:
diff --git a/test/unit/tool_util/test_toolbox_view_parsing.py b/test/unit/tool_util/test_toolbox_view_parsing.py
index 7c8ffd9468b..cb26c3b2674 100644
--- a/test/unit/tool_util/test_toolbox_view_parsing.py
+++ b/test/unit/tool_util/test_toolbox_view_parsing.py
@@ -1,6 +1,9 @@
 import pydantic
 
-from galaxy.tool_util.toolbox.views.definitions import StaticToolBoxView, StaticToolBoxViewTypeEnum
+from galaxy.tool_util.toolbox.views.definitions import (
+    StaticToolBoxView,
+    StaticToolBoxViewTypeEnum,
+)
 
 EXAMPLE_1 = {
     "id": "rna",
@@ -54,32 +57,8 @@ def test_root_parsing():
 
 
 def test_section_parsing():
-    view = StaticToolBoxView.from_dict({
-        "id": "rna",
-        "name": "RNA Seq",
-        "type": "activity",
-        "items": [
-            {
-                "type": "section",
-                "name": "My Cool Section",
-                "items": [
-                    {
-                        "type": "workflow",
-                        "id": "123456",
-                    }
-                ],
-            },
-        ],
-    })
-    section_item = view.items[0]
-    assert len(section_item.items) == 1
-    assert section_item.items[0].content_type == "workflow"
-
-
-def test_no_nested_sections():
-    exception_raised = False
-    try:
-        StaticToolBoxView.from_dict({
+    view = StaticToolBoxView.from_dict(
+        {
             "id": "rna",
             "name": "RNA Seq",
             "type": "activity",
@@ -89,13 +68,41 @@ def test_no_nested_sections():
                     "name": "My Cool Section",
                     "items": [
                         {
-                            "type": "section",
-                            "name": "My Cool Inner Section",
-                        },
+                            "type": "workflow",
+                            "id": "123456",
+                        }
                     ],
                 },
             ],
-        })
+        }
+    )
+    section_item = view.items[0]
+    assert len(section_item.items) == 1
+    assert section_item.items[0].content_type == "workflow"
+
+
+def test_no_nested_sections():
+    exception_raised = False
+    try:
+        StaticToolBoxView.from_dict(
+            {
+                "id": "rna",
+                "name": "RNA Seq",
+                "type": "activity",
+                "items": [
+                    {
+                        "type": "section",
+                        "name": "My Cool Section",
+                        "items": [
+                            {
+                                "type": "section",
+                                "name": "My Cool Inner Section",
+                            },
+                        ],
+                    },
+                ],
+            }
+        )
     except pydantic.ValidationError:
         exception_raised = True
     assert exception_raised
diff --git a/test/unit/tool_util/test_toolbox_view_sources.py b/test/unit/tool_util/test_toolbox_view_sources.py
index 9b608f7a7aa..72479548733 100644
--- a/test/unit/tool_util/test_toolbox_view_sources.py
+++ b/test/unit/tool_util/test_toolbox_view_sources.py
@@ -9,9 +9,7 @@ from .test_toolbox_view_parsing import EXAMPLE_1
 
 
 def test_from_dicts():
-    sources = StaticToolBoxViewSources(
-        view_dicts=[EXAMPLE_1]
-    )
+    sources = StaticToolBoxViewSources(view_dicts=[EXAMPLE_1])
     defs = sources.get_definitions()
     assert len(defs) == 1
     assert defs[0].id == "rna"
@@ -26,13 +24,15 @@ def test_from_directory():
     with open(os.path.join(dir_1, "foo.json"), "w") as f:
         json.dump(EXAMPLE_1, f)
     with open(os.path.join(dir_2, "seqanalysis.yml"), "w") as f:
-        f.write("""
+        f.write(
+            """
 name: Sequence Analysis
 type: generic
 items:
 - type: workflow
   id: 12345abcd
-""")
+"""
+        )
 
     config_param = f"{os.path.abspath(dir_1)},{os.path.abspath(dir_2)}"
     try:
diff --git a/test/unit/tool_util/test_util.py b/test/unit/tool_util/test_util.py
index 0071df4dc36..2a1de73abd5 100644
--- a/test/unit/tool_util/test_util.py
+++ b/test/unit/tool_util/test_util.py
@@ -13,7 +13,7 @@ def load_keyval(request):
     """
     keys = []  # preserve keys for teardown
 
-    def _load_keyval(key='a unique key', val='a value'):
+    def _load_keyval(key="a unique key", val="a value"):
         # If this is called twice with default values within the same test function,
         #   it will raise a KeyError. This is intentional: os.environ cannot have duplicate keys.
         keys.append(key)
@@ -37,7 +37,7 @@ def test_modify_environ__restore(load_keyval):
 
 def test_modify_environ__add_and_restore(load_keyval):
     key1, val1 = load_keyval()
-    key2, val2 = 'key to add', 'value to add'
+    key2, val2 = "key to add", "value to add"
     to_update = {key2: val2}
 
     assert key2 not in environ  # ensure key to add does not exist
@@ -45,13 +45,13 @@ def test_modify_environ__add_and_restore(load_keyval):
         assert environ[key1] == val1  # key/val unchanged
         assert environ[key2] == val2  # new key/val added
     assert environ[key1] == val1  # key/val unchanged
-    assert key2 not in environ   # new key removed
+    assert key2 not in environ  # new key removed
 
 
 def test_modify_environ__update_and_restore(load_keyval):
     key1, val1 = load_keyval()
-    key2, val2 = load_keyval('key to update', 'value to update')
-    val2_updated = 'updated'
+    key2, val2 = load_keyval("key to update", "value to update")
+    val2_updated = "updated"
     to_update = {key2: val2_updated}
 
     with modify_environ(to_update):
@@ -63,7 +63,7 @@ def test_modify_environ__update_and_restore(load_keyval):
 
 def test_modify_environ__remove_and_restore(load_keyval):
     key1, val1 = load_keyval()
-    key2, val2 = load_keyval('key to remove', 'value to remove')
+    key2, val2 = load_keyval("key to remove", "value to remove")
     to_update: Dict[str, str] = {}
     to_remove = [key2]
 
@@ -77,7 +77,7 @@ def test_modify_environ__remove_and_restore(load_keyval):
 def test_modify_environ__remove_nonexistant_key(load_keyval):
     # Test that removing wrong key does not raise an error
     key1, val1 = load_keyval()
-    key_nonexistant = 'no such key'
+    key_nonexistant = "no such key"
     to_update: Dict[str, str] = {}
     to_remove = [key_nonexistant]
 
diff --git a/test/unit/tool_util/test_verify.py b/test/unit/tool_util/test_verify.py
index 48fec30b9c1..03515accfce 100644
--- a/test/unit/tool_util/test_verify.py
+++ b/test/unit/tool_util/test_verify.py
@@ -1,7 +1,14 @@
 import collections
 import gzip
 import tempfile
-from typing import Any, Dict, List, Optional, Tuple, Type
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Type,
+)
 
 import pytest
 
@@ -13,22 +20,21 @@ from galaxy.tool_util.verify import (
     files_re_match_multiline,
 )
 
-
 F1 = b"A\nB\nC"
 F2 = b"A\nB\nD\nE" * 61
 F3 = b"A\nB\n\xfc"
 F4 = b"A\r\nB\nC"
 MULTILINE_MATCH = b".*"
-TestFile = collections.namedtuple('TestFile', 'value path')
+TestFile = collections.namedtuple("TestFile", "value path")
 
 TestDef = Tuple[bytes, bytes, Optional[Dict[str, Any]], Optional[Type[AssertionError]]]
 
 
 def test_file_list():
     files = []
-    for b, ext in [(F1, '.txt'), (F2, '.txt'), (F3, '.pdf'), (F4, '.txt'), (MULTILINE_MATCH, '.txt'), (F1, '.txt.gz')]:
-        with tempfile.NamedTemporaryFile(mode='wb', suffix=ext, delete=False) as out:
-            if ext == '.txt.gz':
+    for b, ext in [(F1, ".txt"), (F2, ".txt"), (F3, ".pdf"), (F4, ".txt"), (MULTILINE_MATCH, ".txt"), (F1, ".txt.gz")]:
+        with tempfile.NamedTemporaryFile(mode="wb", suffix=ext, delete=False) as out:
+            if ext == ".txt.gz":
                 b = gzip.compress(b)
             out.write(b)
         files.append(TestFile(b, out.name))
@@ -39,15 +45,17 @@ def generate_tests(multiline=False):
     f1, f2, f3, f4, multiline_match, f5 = test_file_list()
     tests: List[TestDef]
     if multiline:
-        tests = [(multiline_match, f1, {'lines_diff': 0, 'sort': True}, None)]
+        tests = [(multiline_match, f1, {"lines_diff": 0, "sort": True}, None)]
     else:
-        tests = [(f1, f1, {'lines_diff': 0, 'sort': True}, None)]
-    tests.extend([
-        (f1, f2, {'lines_diff': 0, 'sort': True}, AssertionError),
-        (f1, f3, None, AssertionError),
-        (f1, f4, None, None),
-        (f1, f5, {'decompress': True}, None),
-    ])
+        tests = [(f1, f1, {"lines_diff": 0, "sort": True}, None)]
+    tests.extend(
+        [
+            (f1, f2, {"lines_diff": 0, "sort": True}, AssertionError),
+            (f1, f3, None, AssertionError),
+            (f1, f4, None, None),
+            (f1, f5, {"decompress": True}, None),
+        ]
+    )
     return tests
 
 
@@ -56,21 +64,28 @@ def generate_tests_sim_size():
     # tests for equal files
     tests: List[TestDef] = [
         (f1, f1, None, None),  # pass default values
-        (f1, f1, {'delta': 0}, None),  # pass for values that should always pass
-        (f1, f1, {'delta_frac': 0.0}, None),
+        (f1, f1, {"delta": 0}, None),  # pass for values that should always pass
+        (f1, f1, {"delta_frac": 0.0}, None),
     ]
     # tests for two different file (diff is 422 lines, 0.011709602)
-    tests += [(f1, f2, None, None),  # pass default values
-             (f1, f2, {'delta': 422}, None),  # test around the actual difference of two different
-             (f1, f2, {'delta_frac': 84.4}, None),
-             (f1, f2, {'delta': 421}, AssertionError),
-             (f1, f2, {'delta_frac': 84.3}, AssertionError),
-             (f1, f2, {'delta': 422, 'delta_frac': 84.3}, AssertionError),  # test with combination where at least one leads to an assertion
-             (f1, f2, {'delta': 421, 'delta_frac': 84.4}, AssertionError)]
+    tests += [
+        (f1, f2, None, None),  # pass default values
+        (f1, f2, {"delta": 422}, None),  # test around the actual difference of two different
+        (f1, f2, {"delta_frac": 84.4}, None),
+        (f1, f2, {"delta": 421}, AssertionError),
+        (f1, f2, {"delta_frac": 84.3}, AssertionError),
+        (
+            f1,
+            f2,
+            {"delta": 422, "delta_frac": 84.3},
+            AssertionError,
+        ),  # test with combination where at least one leads to an assertion
+        (f1, f2, {"delta": 421, "delta_frac": 84.4}, AssertionError),
+    ]
     return tests
 
 
-@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests())
+@pytest.mark.parametrize("file1,file2,attributes,expect", generate_tests())
 def test_files_contains(file1, file2, attributes, expect):
     if expect is not None:
         with pytest.raises(expect):
@@ -79,7 +94,7 @@ def test_files_contains(file1, file2, attributes, expect):
         files_contains(file2.path, file2.path, attributes)
 
 
-@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests_sim_size())
+@pytest.mark.parametrize("file1,file2,attributes,expect", generate_tests_sim_size())
 def test_files_delta(file1, file2, attributes, expect):
     if expect is not None:
         with pytest.raises(expect):
@@ -88,7 +103,7 @@ def test_files_delta(file1, file2, attributes, expect):
         files_delta(file1.path, file2.path, attributes)
 
 
-@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests())
+@pytest.mark.parametrize("file1,file2,attributes,expect", generate_tests())
 def test_files_diff(file1, file2, attributes, expect):
     if expect is not None:
         with pytest.raises(expect):
@@ -97,7 +112,7 @@ def test_files_diff(file1, file2, attributes, expect):
         files_diff(file1.path, file2.path, attributes)
 
 
-@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests())
+@pytest.mark.parametrize("file1,file2,attributes,expect", generate_tests())
 def test_files_re_match(file1, file2, attributes, expect):
     if expect is not None:
         with pytest.raises(expect):
@@ -106,7 +121,7 @@ def test_files_re_match(file1, file2, attributes, expect):
         files_re_match(file1.path, file2.path, attributes)
 
 
-@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests(multiline=True))
+@pytest.mark.parametrize("file1,file2,attributes,expect", generate_tests(multiline=True))
 def test_files_re_match_multiline(file1, file2, attributes, expect):
     if expect is not None:
         with pytest.raises(expect):
diff --git a/test/unit/tool_util/test_verify_script.py b/test/unit/tool_util/test_verify_script.py
index 224c88fe7bf..1faed80db19 100644
--- a/test/unit/tool_util/test_verify_script.py
+++ b/test/unit/tool_util/test_verify_script.py
@@ -7,14 +7,14 @@ from galaxy.tool_util.verify.script import (
     arg_parser,
     build_case_references,
     Results,
-    test_tools as run,
-    TestReference,
 )
+from galaxy.tool_util.verify.script import test_tools as run
+from galaxy.tool_util.verify.script import TestReference
 
-VT_PATH = 'galaxy.tool_util.verify.script.verify_tool'
+VT_PATH = "galaxy.tool_util.verify.script.verify_tool"
 NEW_HISTORY = object()
-NEW_HISTORY_ID = 'new'
-EXISTING_HISTORY = {'id': 'existing'}
+NEW_HISTORY_ID = "new"
+EXISTING_HISTORY = {"id": "existing"}
 EXISTING_SUITE_NAME = "existing suite"
 EXISTING_HISTORY_NAME = f"History for {EXISTING_SUITE_NAME}"
 
@@ -125,7 +125,7 @@ def test_test_tools_history_reuse():
         assert len(calls) == 1
         assert len(results.test_exceptions) == 0
         assert_results_written(results)
-        assert interactor.history_id == EXISTING_HISTORY['id']
+        assert interactor.history_id == EXISTING_HISTORY["id"]
         assert interactor.history_name == EXISTING_HISTORY_NAME
         assert not interactor.history_created
         assert not interactor.history_deleted
@@ -297,32 +297,32 @@ def test_build_references():
     test_references = build_case_references(interactor)
     assert len(test_references) == 6
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="*")
+    test_references = build_case_references(interactor, "cat1", tool_version="*")
     assert len(test_references) == 6
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="*", page_size=3, page_number=1)
+    test_references = build_case_references(interactor, "cat1", tool_version="*", page_size=3, page_number=1)
     assert len(test_references) == 3
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="*", page_size=3, page_number=2)
+    test_references = build_case_references(interactor, "cat1", tool_version="*", page_size=3, page_number=2)
     assert len(test_references) == 0
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="*", page_size=3, page_number=3)
+    test_references = build_case_references(interactor, "cat1", tool_version="*", page_size=3, page_number=3)
     assert len(test_references) == 0
 
-    test_references = build_case_references(interactor, 'cat1', tool_version=None)
+    test_references = build_case_references(interactor, "cat1", tool_version=None)
     assert len(test_references) == 4
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="0.2.0")
+    test_references = build_case_references(interactor, "cat1", tool_version="0.2.0")
     assert len(test_references) == 4
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="0.1.0")
+    test_references = build_case_references(interactor, "cat1", tool_version="0.1.0")
     assert len(test_references) == 2
 
-    test_references = build_case_references(interactor, 'cat1', tool_version="0.1.0", test_index=1)
+    test_references = build_case_references(interactor, "cat1", tool_version="0.1.0", test_index=1)
     assert len(test_references) == 1
 
     # Specifying an index but not a version, grabs latest version and fills it in.
-    test_references = build_case_references(interactor, 'cat1', test_index=2)
+    test_references = build_case_references(interactor, "cat1", test_index=2)
     assert len(test_references) == 1
     test_reference = test_references[0]
     assert test_reference.tool_id == "cat1"
@@ -341,7 +341,6 @@ def assert_results_written(results):
 
 
 class MockGalaxyInteractor:
-
     def __init__(self):
         self.history_deleted = False
         self.history_created = False
@@ -351,7 +350,7 @@ class MockGalaxyInteractor:
     def get_history(self, history_name=""):
         if history_name == EXISTING_HISTORY_NAME:
             self.history_name = history_name
-            self.history_id = EXISTING_HISTORY['id']
+            self.history_id = EXISTING_HISTORY["id"]
             return EXISTING_HISTORY
         else:
             return None
@@ -367,12 +366,12 @@ class MockGalaxyInteractor:
 
     def get_tests_summary(self):
         return {
-            'cat1': {
-                '0.2.0': {
-                    'count': 4,
+            "cat1": {
+                "0.2.0": {
+                    "count": 4,
                 },
-                '0.1.0': {
-                    'count': 2,
+                "0.1.0": {
+                    "count": 2,
                 },
             },
         }
@@ -384,11 +383,11 @@ class MockGalaxyInteractor:
             if tool_version is not None and tool_version != "*" and this_tool_version != tool_version:
                 continue
 
-            count = version_defs['count']
+            count = version_defs["count"]
             for _ in range(count):
                 test_def = {
-                    'tool_id': tool_id,
-                    'tool_version': this_tool_version or '0.1.1-default',
+                    "tool_id": tool_id,
+                    "tool_version": this_tool_version or "0.1.1-default",
                 }
                 test_defs.append(test_def)
 
diff --git a/test/unit/tool_util/test_wait.py b/test/unit/tool_util/test_wait.py
index 14f69ed4fcd..8c94f2f6a95 100644
--- a/test/unit/tool_util/test_wait.py
+++ b/test/unit/tool_util/test_wait.py
@@ -1,8 +1,10 @@
-from galaxy.tool_util.verify.wait import TimeoutAssertionError, wait_on
+from galaxy.tool_util.verify.wait import (
+    TimeoutAssertionError,
+    wait_on,
+)
 
 
 class Sleeper:
-
     def __init__(self):
         self.sleeps = []
 
@@ -11,7 +13,6 @@ class Sleeper:
 
 
 class WaitCondition:
-
     def __init__(self, after_call_count=0, return_value=True):
         self.after_call_count = after_call_count
         self.call_count = 0
diff --git a/test/unit/tool_util/toolbox/test_tool_panel.py b/test/unit/tool_util/toolbox/test_tool_panel.py
index 3beca3b57be..5439917e443 100644
--- a/test/unit/tool_util/toolbox/test_tool_panel.py
+++ b/test/unit/tool_util/toolbox/test_tool_panel.py
@@ -3,19 +3,16 @@ from galaxy.util import etree
 
 
 def test_tool_section():
-    elem = etree.Element('section')
-    elem.attrib['name'] = "Cool Tools"
-    elem.attrib['id'] = "cool1"
+    elem = etree.Element("section")
+    elem.attrib["name"] = "Cool Tools"
+    elem.attrib["id"] = "cool1"
 
     section = ToolSection(elem)
     assert section.id == "cool1"
     assert section.name == "Cool Tools"
     assert section.version == ""
 
-    section = ToolSection(dict(
-        id="cool1",
-        name="Cool Tools"
-    ))
+    section = ToolSection(dict(id="cool1", name="Cool Tools"))
     assert section.id == "cool1"
     assert section.name == "Cool Tools"
     assert section.version == ""
diff --git a/test/unit/tool_util/toolbox/test_toolbox_filters.py b/test/unit/tool_util/toolbox/test_toolbox_filters.py
index ff1d4cdd8c4..c6f9acf37e9 100644
--- a/test/unit/tool_util/toolbox/test_toolbox_filters.py
+++ b/test/unit/tool_util/toolbox/test_toolbox_filters.py
@@ -5,25 +5,25 @@ from galaxy.util.bunch import Bunch
 
 def test_stock_filtering_requires_login_tools():
     anonymous_user_trans = mock_trans(has_user=False)
-    filters = filter_factory({}).build_filters(mock_trans())['tool']
+    filters = filter_factory({}).build_filters(mock_trans())["tool"]
     assert not is_filtered(filters, anonymous_user_trans, mock_tool(require_login=False))
     assert is_filtered(filters, anonymous_user_trans, mock_tool(require_login=True))
 
     logged_in_trans = mock_trans(has_user=True)
-    filters = filter_factory({}).build_filters(logged_in_trans)['tool']
+    filters = filter_factory({}).build_filters(logged_in_trans)["tool"]
     assert not is_filtered(filters, logged_in_trans, mock_tool(require_login=True))
 
 
 def test_stock_filtering_hidden_tools():
     trans = mock_trans()
-    filters = filter_factory({}).build_filters(trans)['tool']
+    filters = filter_factory({}).build_filters(trans)["tool"]
     assert not is_filtered(filters, trans, mock_tool(hidden=False))
     assert is_filtered(filters, trans, mock_tool(hidden=True))
 
 
 def test_trackster_filtering():
     trans = mock_trans()
-    filters = filter_factory({}).build_filters(trans, trackster=True)['tool']
+    filters = filter_factory({}).build_filters(trans, trackster=True)["tool"]
     assert is_filtered(filters, trans, mock_tool(trackster_conf=False))
     assert not is_filtered(filters, trans, mock_tool(trackster_conf=True))
 
@@ -50,7 +50,7 @@ def filter_factory(config_dict=None):
             tool_section_filters=["filtermod:filter_section"],
             tool_label_filters=["filtermod:filter_label_1", "filtermod:filter_label_2"],
         )
-    parent_module_name = '.'.join(__name__.split('.')[:-1])
+    parent_module_name = ".".join(__name__.split(".")[:-1])
     config_dict["toolbox_filter_base_modules"] = f"galaxy.tool_util.toolbox.filters,{parent_module_name}.filter_modules"
     config = Bunch(**config_dict)
     app = Bunch(config=config)
diff --git a/test/unit/tool_util/toolbox/test_watcher.py b/test/unit/tool_util/toolbox/test_watcher.py
index 827113c2217..f735c693706 100644
--- a/test/unit/tool_util/toolbox/test_watcher.py
+++ b/test/unit/tool_util/toolbox/test_watcher.py
@@ -17,9 +17,7 @@ def test_watcher():
         toolbox = Toolbox()
         with open(tool_path, "w") as f:
             f.write("a")
-        tool_watcher = watcher.get_tool_watcher(toolbox, bunch.Bunch(
-            watch_tools=True
-        ))
+        tool_watcher = watcher.get_tool_watcher(toolbox, bunch.Bunch(watch_tools=True))
         tool_watcher.start()
         tool_watcher.watch_file(tool_path, "cool_tool")
         time.sleep(2)
@@ -56,12 +54,11 @@ def wait_for_reload(check):
         reloaded = check()
         if reloaded:
             break
-        time.sleep(.2)
+        time.sleep(0.2)
     assert reloaded
 
 
 class Toolbox:
-
     def __init__(self):
         self.reloaded = {}
 
@@ -73,7 +70,6 @@ class Toolbox:
 
 
 class CallbackRecorder:
-
     def __init__(self):
         self.called = False
 
diff --git a/test/unit/tool_util/util.py b/test/unit/tool_util/util.py
index 5d2e0f0c587..0ccf6b1ecd8 100644
--- a/test/unit/tool_util/util.py
+++ b/test/unit/tool_util/util.py
@@ -4,8 +4,7 @@ from os import environ
 import pytest
 
 external_dependency_management = pytest.mark.skipif(
-    not environ.get('GALAXY_TEST_INCLUDE_SLOW'),
-    reason="GALAXY_TEST_INCLUDE_SLOW not set"
+    not environ.get("GALAXY_TEST_INCLUDE_SLOW"), reason="GALAXY_TEST_INCLUDE_SLOW not set"
 )
 
 
diff --git a/test/unit/tool_util/verify/test_asserts.py b/test/unit/tool_util/verify/test_asserts.py
index 6e0889b0758..6806f4cba37 100644
--- a/test/unit/tool_util/verify/test_asserts.py
+++ b/test/unit/tool_util/verify/test_asserts.py
@@ -216,7 +216,7 @@ XML_XML_ELEMENT = """
     </assert_contents>
 """
 
-VALID_XML = '''<root>
+VALID_XML = """<root>
     <elem name="foo">
         <more name="bar">BAR</more>
         <more name="baz">BAZ</more>
@@ -224,21 +224,21 @@ VALID_XML = '''<root>
     </elem>
     <elem name="baz"/>
 </root>
-'''
+"""
 INVALID_XML = '<root><elem name="foo"></root>'
 
 if h5py is not None:
     with tempfile.NamedTemporaryFile(delete=False) as tmp:
         h5name = tmp.name
         with h5py.File(tmp.name, "w") as h5fh:
-            h5fh.attrs['myfileattr'] = "myfileattrvalue"
-            h5fh.attrs['myfileattrint'] = 1
-            dset = h5fh.create_dataset("myint", (100,), dtype='i')
-            dset.attrs['myintattr'] = "myintattrvalue"
+            h5fh.attrs["myfileattr"] = "myfileattrvalue"
+            h5fh.attrs["myfileattrint"] = 1
+            dset = h5fh.create_dataset("myint", (100,), dtype="i")
+            dset.attrs["myintattr"] = "myintattrvalue"
             grp = h5fh.create_group("mygroup")
-            grp.attrs['mygroupattr'] = "mygroupattrvalue"
-            grp.create_dataset("myfloat", (50,), dtype='f')
-            dset.attrs['myfloatattr'] = "myfloatattrvalue"
+            grp.attrs["mygroupattr"] = "mygroupattrvalue"
+            grp.create_dataset("myfloat", (50,), dtype="f")
+            dset.attrs["myfloatattr"] = "myfloatattrvalue"
     with open(h5name, "rb") as h5fh:
         H5BYTES = h5fh.read()
     os.remove(h5name)
@@ -323,683 +323,709 @@ ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX = """
 
 TESTS = [
     # test successful assertion
-    (
-        TABULAR_ASSERTION, TABULAR_DATA_POS,
-        lambda x: len(x) == 0
-    ),
+    (TABULAR_ASSERTION, TABULAR_DATA_POS, lambda x: len(x) == 0),
     # test wrong number of columns
-    (
-        TABULAR_ASSERTION, TABULAR_DATA_NEG,
-        lambda x: 'Expected 3+-0 columns in output found 4' in x
-    ),
+    (TABULAR_ASSERTION, TABULAR_DATA_NEG, lambda x: "Expected 3+-0 columns in output found 4" in x),
     # test wrong number of columns for csv data
     (
-        TABULAR_CSV_ASSERTION, TABULAR_CSV_DATA,
-        lambda x: 'Expected the number of columns in output to be in [3:inf] found 2' in x
+        TABULAR_CSV_ASSERTION,
+        TABULAR_CSV_DATA,
+        lambda x: "Expected the number of columns in output to be in [3:inf] found 2" in x,
     ),
     # test tabular data with comments
-    (
-        TABULAR_ASSERTION_COMMENT, TABULAR_DATA_COMMENT,
-        lambda x: len(x) == 0
-    ),
+    (TABULAR_ASSERTION_COMMENT, TABULAR_DATA_COMMENT, lambda x: len(x) == 0),
     # test has_text
-    (
-        TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_text .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_HAS_TEXT_NEG,
-        lambda x: "Expected text 'test text' in output ('desired content\nis not here\n')" in x
+        TEXT_HAS_TEXT_ASSERTION,
+        TEXT_DATA_HAS_TEXT_NEG,
+        lambda x: "Expected text 'test text' in output ('desired content\nis not here\n')" in x,
     ),
     # test has_text with None output
-    (
-        TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_NONE,
-        lambda x: "Checking has_text assertion on empty output (None)" in x
-    ),
+    (TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_NONE, lambda x: "Checking has_text assertion on empty output (None)" in x),
     # test has_text with empty output
-    (
-        TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_EMPTY,
-        lambda x: "Expected text 'test text' in output ('')" in x
-    ),
+    (TEXT_HAS_TEXT_ASSERTION, TEXT_DATA_EMPTY, lambda x: "Expected text 'test text' in output ('')" in x),
     # test has_text with n
-    (
-        TEXT_HAS_TEXT_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_text with n .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_N, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 2+-0 occurences of 'test text' in output ('test text\n') found 1" in x
+        TEXT_HAS_TEXT_ASSERTION_N,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 2+-0 occurences of 'test text' in output ('test text\n') found 1" in x,
     ),
     # test has_text with n and delta
-    (
-        TEXT_HAS_TEXT_ASSERTION_N_DELTA, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_N_DELTA, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_text with n and delta .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_N_DELTA, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 3+-1 occurences of 'test text' in output ('test text\n') found 1" in x
+        TEXT_HAS_TEXT_ASSERTION_N_DELTA,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 3+-1 occurences of 'test text' in output ('test text\n') found 1" in x,
     ),
     # test has_text with min max
-    (
-        TEXT_HAS_TEXT_ASSERTION_MIN_MAX, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_MIN_MAX, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_text with min max .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_MIN_MAX, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected that the number of occurences of 'test text' in output is in [2:4] ('test text\n') found 1" in x
+        TEXT_HAS_TEXT_ASSERTION_MIN_MAX,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected that the number of occurences of 'test text' in output is in [2:4] ('test text\n') found 1"
+        in x,
     ),
-
-
     # test has_text negate
-    (
-        TEXT_HAS_TEXT_ASSERTION_NEGATE, TEXT_DATA_HAS_TEXT_NEG,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_NEGATE, TEXT_DATA_HAS_TEXT_NEG, lambda x: len(x) == 0),
     # test has_text negate .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_NEGATE, TEXT_DATA_HAS_TEXT,
-        lambda x: "Did not expect text 'test text' in output ('test text\n')" in x
+        TEXT_HAS_TEXT_ASSERTION_NEGATE,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Did not expect text 'test text' in output ('test text\n')" in x,
     ),
     # test has_text negate with None output .. should have the same output as with negate="false"
     (
-        TEXT_HAS_TEXT_ASSERTION_NEGATE, TEXT_DATA_NONE,
-        lambda x: "Checking has_text assertion on empty output (None)" in x
+        TEXT_HAS_TEXT_ASSERTION_NEGATE,
+        TEXT_DATA_NONE,
+        lambda x: "Checking has_text assertion on empty output (None)" in x,
     ),
     # test has_text negate with empty output
-    (
-        TEXT_HAS_TEXT_ASSERTION_NEGATE, TEXT_DATA_EMPTY,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_NEGATE, TEXT_DATA_EMPTY, lambda x: len(x) == 0),
     # test has_text negate with n
-    (
-        TEXT_HAS_TEXT_ASSERTION_N_NEGATE, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_N_NEGATE, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_text negate with n .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_N_NEGATE, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: "Did not expect 2+-0 occurences of 'test text' in output ('test text\ntest text\n') found 2" in x
+        TEXT_HAS_TEXT_ASSERTION_N_NEGATE,
+        TEXT_DATA_HAS_TEXT * 2,
+        lambda x: "Did not expect 2+-0 occurences of 'test text' in output ('test text\ntest text\n') found 2" in x,
     ),
     # test has_text negate with n and delta
-    (
-        TEXT_HAS_TEXT_ASSERTION_N_DELTA_NEGATE, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_N_DELTA_NEGATE, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_text negate with n and delta .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_N_DELTA_NEGATE, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: "Did not expect 3+-1 occurences of 'test text' in output ('test text\ntest text\n') found 2" in x
+        TEXT_HAS_TEXT_ASSERTION_N_DELTA_NEGATE,
+        TEXT_DATA_HAS_TEXT * 2,
+        lambda x: "Did not expect 3+-1 occurences of 'test text' in output ('test text\ntest text\n') found 2" in x,
     ),
     # test has_text negate with min max
-    (
-        TEXT_HAS_TEXT_ASSERTION_MIN_MAX_NEGATE, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_ASSERTION_MIN_MAX_NEGATE, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_text negate with min max .. negative test
     (
-        TEXT_HAS_TEXT_ASSERTION_MIN_MAX_NEGATE, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: "Did not expect that the number of occurences of 'test text' in output is in [2:4] ('test text\ntest text\n') found 2" in x
+        TEXT_HAS_TEXT_ASSERTION_MIN_MAX_NEGATE,
+        TEXT_DATA_HAS_TEXT * 2,
+        lambda x: "Did not expect that the number of occurences of 'test text' in output is in [2:4] ('test text\ntest text\n') found 2"
+        in x,
     ),
-
-
     # test not_has_text
-    (
-        TEXT_NOT_HAS_TEXT_ASSERTION, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_NOT_HAS_TEXT_ASSERTION, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test not_has_text .. negative test
     (
-        TEXT_NOT_HAS_TEXT_ASSERTION, TEXT_DATA_HAS_TEXT_NEG,
-        lambda x: "Output file contains unexpected text 'not here'" in x
+        TEXT_NOT_HAS_TEXT_ASSERTION,
+        TEXT_DATA_HAS_TEXT_NEG,
+        lambda x: "Output file contains unexpected text 'not here'" in x,
     ),
     # test not_has_text with None output
     (
-        TEXT_NOT_HAS_TEXT_ASSERTION, TEXT_DATA_NONE,
-        lambda x: "Checking not_has_text assertion on empty output (None)" in x
+        TEXT_NOT_HAS_TEXT_ASSERTION,
+        TEXT_DATA_NONE,
+        lambda x: "Checking not_has_text assertion on empty output (None)" in x,
     ),
     # test not_has_text with empty output
-    (
-        TEXT_NOT_HAS_TEXT_ASSERTION, TEXT_DATA_EMPTY,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_NOT_HAS_TEXT_ASSERTION, TEXT_DATA_EMPTY, lambda x: len(x) == 0),
     # test has_text_matching
-    (
-        TEXT_HAS_TEXT_MATCHING_ASSERTION, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_MATCHING_ASSERTION, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_text_matching .. negative test
     (
-        TEXT_HAS_TEXT_MATCHING_ASSERTION, TEXT_DATA_HAS_TEXT_NEG,
-        lambda x: "Expected text matching expression 'te[sx]t' in output ('desired content\nis not here\n')" in x
+        TEXT_HAS_TEXT_MATCHING_ASSERTION,
+        TEXT_DATA_HAS_TEXT_NEG,
+        lambda x: "Expected text matching expression 'te[sx]t' in output ('desired content\nis not here\n')" in x,
     ),
     # test has_text_matching with n
-    (
-        TEXT_HAS_TEXT_MATCHING_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_MATCHING_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_text_matching with n .. negative test (using the test text where "te[sx]st" appears twice)
     (
-        TEXT_HAS_TEXT_MATCHING_ASSERTION_N, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 4+-0 (non-overlapping) matches for 'te[sx]t' in output ('test text\n') found 2" in x
+        TEXT_HAS_TEXT_MATCHING_ASSERTION_N,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 4+-0 (non-overlapping) matches for 'te[sx]t' in output ('test text\n') found 2" in x,
     ),
     # test has_text_matching with n
-    (
-        TEXT_HAS_TEXT_MATCHING_ASSERTION_MINMAX, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_TEXT_MATCHING_ASSERTION_MINMAX, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_text_matching with n .. negative test (using the test text where "te[sx]st" appears twice)
     (
-        TEXT_HAS_TEXT_MATCHING_ASSERTION_MINMAX, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected that the number of (non-overlapping) matches for 'te[sx]t' in output is in [3:5] ('test text\n') found 2" in x
+        TEXT_HAS_TEXT_MATCHING_ASSERTION_MINMAX,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected that the number of (non-overlapping) matches for 'te[sx]t' in output is in [3:5] ('test text\n') found 2"
+        in x,
     ),
     # test has_line
-    (
-        TEXT_HAS_LINE_ASSERTION, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_LINE_ASSERTION, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_line .. negative test
     (
-        TEXT_HAS_LINE_ASSERTION, TEXT_DATA_HAS_TEXT_NEG,
-        lambda x: "Expected line 'test text' in output ('desired content\nis not here\n')" in x
+        TEXT_HAS_LINE_ASSERTION,
+        TEXT_DATA_HAS_TEXT_NEG,
+        lambda x: "Expected line 'test text' in output ('desired content\nis not here\n')" in x,
     ),
     # test has_line with n
-    (
-        TEXT_HAS_LINE_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_LINE_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_line with n .. negative test
     (
-        TEXT_HAS_LINE_ASSERTION_N, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 2+-0 lines 'test text' in output ('test text\n') found 1" in x
+        TEXT_HAS_LINE_ASSERTION_N,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 2+-0 lines 'test text' in output ('test text\n') found 1" in x,
     ),
     # test has_n_lines
-    (
-        TEXT_HAS_N_LINES_ASSERTION.format(n="2"), TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_N_LINES_ASSERTION.format(n="2"), TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_n_lines .. bytes
-    (
-        TEXT_HAS_N_LINES_ASSERTION.format(n="2ki"), TEXT_DATA_HAS_TEXT * 2048,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_N_LINES_ASSERTION.format(n="2ki"), TEXT_DATA_HAS_TEXT * 2048, lambda x: len(x) == 0),
     # test has_n_lines .. negative test
     (
-        TEXT_HAS_N_LINES_ASSERTION.format(n="2"), TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 2+-0 lines in the output found 1" in x
+        TEXT_HAS_N_LINES_ASSERTION.format(n="2"),
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 2+-0 lines in the output found 1" in x,
     ),
     # test has_n_lines ..delta
     (
-        TEXT_HAS_N_LINES_ASSERTION_DELTA.format(n="3", delta="1"), TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 3+-1 lines in the output found 1" in x
+        TEXT_HAS_N_LINES_ASSERTION_DELTA.format(n="3", delta="1"),
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 3+-1 lines in the output found 1" in x,
     ),
     # test has_line_matching
-    (
-        TEXT_HAS_LINE_MATCHING_ASSERTION, TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_LINE_MATCHING_ASSERTION, TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_line_matching .. negative test
     (
-        TEXT_HAS_LINE_MATCHING_ASSERTION, TEXT_DATA_HAS_TEXT_NEG,
-        lambda x: "Expected line matching expression 'te[sx]t te[sx]t' in output ('desired content\nis not here\n')" in x
+        TEXT_HAS_LINE_MATCHING_ASSERTION,
+        TEXT_DATA_HAS_TEXT_NEG,
+        lambda x: "Expected line matching expression 'te[sx]t te[sx]t' in output ('desired content\nis not here\n')"
+        in x,
     ),
     # test has_line_matching n
-    (
-        TEXT_HAS_LINE_MATCHING_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (TEXT_HAS_LINE_MATCHING_ASSERTION_N, TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_line_matching n .. negative test
     (
-        TEXT_HAS_LINE_MATCHING_ASSERTION_N, TEXT_DATA_HAS_TEXT,
-        lambda x: "Expected 2+-0 lines matching for 'te[sx]t te[sx]t' in output ('test text\n') found 1" in x
+        TEXT_HAS_LINE_MATCHING_ASSERTION_N,
+        TEXT_DATA_HAS_TEXT,
+        lambda x: "Expected 2+-0 lines matching for 'te[sx]t te[sx]t' in output ('test text\n') found 1" in x,
     ),
     # test has_size
-    (
-        SIZE_HAS_SIZE_ASSERTION.format(value=10), TEXT_DATA_HAS_TEXT,
-        lambda x: len(x) == 0
-    ),
+    (SIZE_HAS_SIZE_ASSERTION.format(value=10), TEXT_DATA_HAS_TEXT, lambda x: len(x) == 0),
     # test has_size .. negative test
     (
-        SIZE_HAS_SIZE_ASSERTION.format(value="10"), TEXT_DATA_HAS_TEXT * 2,
-        lambda x: "Expected file size of 10+-0 found 20" in x
+        SIZE_HAS_SIZE_ASSERTION.format(value="10"),
+        TEXT_DATA_HAS_TEXT * 2,
+        lambda x: "Expected file size of 10+-0 found 20" in x,
     ),
     # test has_size .. delta
-    (
-        SIZE_HAS_SIZE_ASSERTION_DELTA.format(value="10", delta="10"), TEXT_DATA_HAS_TEXT * 2,
-        lambda x: len(x) == 0
-    ),
+    (SIZE_HAS_SIZE_ASSERTION_DELTA.format(value="10", delta="10"), TEXT_DATA_HAS_TEXT * 2, lambda x: len(x) == 0),
     # test has_size .. bytes suffix
-    (
-        SIZE_HAS_SIZE_ASSERTION_DELTA.format(value="1k", delta="0"), TEXT_DATA_HAS_TEXT * 100,
-        lambda x: len(x) == 0
-    ),
+    (SIZE_HAS_SIZE_ASSERTION_DELTA.format(value="1k", delta="0"), TEXT_DATA_HAS_TEXT * 100, lambda x: len(x) == 0),
     # test has_size .. bytes suffix .. negative
     (
-        SIZE_HAS_SIZE_ASSERTION_DELTA.format(value="1Mi", delta="10k"), TEXT_DATA_HAS_TEXT * 100,
-        lambda x: 'Expected file size of 1Mi+-10k found 1000' in x
+        SIZE_HAS_SIZE_ASSERTION_DELTA.format(value="1Mi", delta="10k"),
+        TEXT_DATA_HAS_TEXT * 100,
+        lambda x: "Expected file size of 1Mi+-10k found 1000" in x,
     ),
     # test is_valid_xml
-    (
-        XML_IS_VALID_XML_ASSERTION, VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_IS_VALID_XML_ASSERTION, VALID_XML, lambda x: len(x) == 0),
     # test is_valid_xml .. negative test
     (
-        XML_IS_VALID_XML_ASSERTION, INVALID_XML,
-        lambda x: 'Expected valid XML, but could not parse output. Opening and ending tag mismatch: elem line 1 and root, line 1, column 31 (<string>, line 1)' in x
+        XML_IS_VALID_XML_ASSERTION,
+        INVALID_XML,
+        lambda x: "Expected valid XML, but could not parse output. Opening and ending tag mismatch: elem line 1 and root, line 1, column 31 (<string>, line 1)"
+        in x,
     ),
     # test has_element_with_path
-    (
-        XML_HAS_ELEMENT_WITH_PATH.format(path="./elem[1]/more"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
-    (
-        XML_HAS_ELEMENT_WITH_PATH.format(path="./elem[@name='foo']"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
-    (
-        XML_HAS_ELEMENT_WITH_PATH.format(path=".//more[@name]"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_HAS_ELEMENT_WITH_PATH.format(path="./elem[1]/more"), VALID_XML, lambda x: len(x) == 0),
+    (XML_HAS_ELEMENT_WITH_PATH.format(path="./elem[@name='foo']"), VALID_XML, lambda x: len(x) == 0),
+    (XML_HAS_ELEMENT_WITH_PATH.format(path=".//more[@name]"), VALID_XML, lambda x: len(x) == 0),
     # test has_element_with_path .. negative test
-    (
-        XML_HAS_ELEMENT_WITH_PATH.format(path="./blah"), VALID_XML,
-        lambda x: "Expected path './blah' in xml" in x
-    ),
+    (XML_HAS_ELEMENT_WITH_PATH.format(path="./blah"), VALID_XML, lambda x: "Expected path './blah' in xml" in x),
     # test has_n_elements_with_path
-    (
-        XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem", n="2"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem", n="2"), VALID_XML, lambda x: len(x) == 0),
     # test has_n_elements_with_path
-    (
-        XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem[1]/more", n="3"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem[1]/more", n="3"), VALID_XML, lambda x: len(x) == 0),
     # test has_n_elements_with_path
-    (
-        XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem[@name='foo']/more", n="3"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem[@name='foo']/more", n="3"), VALID_XML, lambda x: len(x) == 0),
     # test has_n_elements_with_path
-    (
-        XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem[2]/more", n="0"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem[2]/more", n="0"), VALID_XML, lambda x: len(x) == 0),
     # test has_n_elements_with_path .. negative test
     (
-        XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem", n="1"), VALID_XML,
-        lambda x: "Expected 1+-0 occurrences of path './elem' in xml found 2" in x
+        XML_HAS_N_ELEMENTS_WITH_PATH.format(path="./elem", n="1"),
+        VALID_XML,
+        lambda x: "Expected 1+-0 occurrences of path './elem' in xml found 2" in x,
     ),
     # test element_text_matches
-    (
-        XML_ELEMENT_TEXT_MATCHES.format(path="./elem/more", expression="BA(R|Z)"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_ELEMENT_TEXT_MATCHES.format(path="./elem/more", expression="BA(R|Z)"), VALID_XML, lambda x: len(x) == 0),
     # test element_text_matches more specific path
-    (
-        XML_ELEMENT_TEXT_MATCHES.format(path="./elem/more[2]", expression="BA(R|Z)"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_ELEMENT_TEXT_MATCHES.format(path="./elem/more[2]", expression="BA(R|Z)"), VALID_XML, lambda x: len(x) == 0),
     # test element_text_matches .. negative test
     (
-        XML_ELEMENT_TEXT_MATCHES.format(path="./elem/more", expression="QU(X|Y)"), VALID_XML,
-        lambda x: "Text of element with path './elem/more': Expected text matching expression 'QU(X|Y)' in output ('BAR')" in x
+        XML_ELEMENT_TEXT_MATCHES.format(path="./elem/more", expression="QU(X|Y)"),
+        VALID_XML,
+        lambda x: "Text of element with path './elem/more': Expected text matching expression 'QU(X|Y)' in output ('BAR')"
+        in x,
     ),
     # test element_text_is
-    (
-        XML_ELEMENT_TEXT_IS.format(path="./elem/more", text="BAR"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_ELEMENT_TEXT_IS.format(path="./elem/more", text="BAR"), VALID_XML, lambda x: len(x) == 0),
     # test element_text_is with more specific path
-    (
-        XML_ELEMENT_TEXT_IS.format(path="./elem/more[@name='baz']", text="BAZ"), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_ELEMENT_TEXT_IS.format(path="./elem/more[@name='baz']", text="BAZ"), VALID_XML, lambda x: len(x) == 0),
     # test element_text_is .. negative test testing that prefix is not accepted
     (
-        XML_ELEMENT_TEXT_IS.format(path="./elem/more", text="BA"), VALID_XML,
-        lambda x: "Text of element with path './elem/more': Expected text matching expression 'BA$' in output ('BAR')" in x
+        XML_ELEMENT_TEXT_IS.format(path="./elem/more", text="BA"),
+        VALID_XML,
+        lambda x: "Text of element with path './elem/more': Expected text matching expression 'BA$' in output ('BAR')"
+        in x,
     ),
     # test element_attribute_matches
     (
-        XML_ATTRIBUTE_MATCHES.format(path="./elem/more", attribute="name", expression="ba(r|z)"), VALID_XML,
-        lambda x: len(x) == 0
+        XML_ATTRIBUTE_MATCHES.format(path="./elem/more", attribute="name", expression="ba(r|z)"),
+        VALID_XML,
+        lambda x: len(x) == 0,
     ),
     # test element_attribute_matches with more specific path
     (
-        XML_ATTRIBUTE_MATCHES.format(path="./elem/more[2]", attribute="name", expression="ba(r|z)"), VALID_XML,
-        lambda x: len(x) == 0
+        XML_ATTRIBUTE_MATCHES.format(path="./elem/more[2]", attribute="name", expression="ba(r|z)"),
+        VALID_XML,
+        lambda x: len(x) == 0,
     ),
     # test element_attribute_matches .. negative test
     (
-        XML_ATTRIBUTE_MATCHES.format(path="./elem/more", attribute="name", expression="qu(x|y)"), VALID_XML,
-        lambda x: "Attribute 'name' on element with path './elem/more': Expected text matching expression 'qu(x|y)' in output ('bar')" in x
+        XML_ATTRIBUTE_MATCHES.format(path="./elem/more", attribute="name", expression="qu(x|y)"),
+        VALID_XML,
+        lambda x: "Attribute 'name' on element with path './elem/more': Expected text matching expression 'qu(x|y)' in output ('bar')"
+        in x,
     ),
     # test element_text
-    (
-        XML_ELEMENT_TEXT.format(path="./elem/more", content_assert=''), VALID_XML,
-        lambda x: len(x) == 0
-    ),
+    (XML_ELEMENT_TEXT.format(path="./elem/more", content_assert=""), VALID_XML, lambda x: len(x) == 0),
     # test element_text .. negative
     (
-        XML_ELEMENT_TEXT.format(path="./absent", content_assert=''), VALID_XML,
-        lambda x: "Expected path './absent' in xml" in x
+        XML_ELEMENT_TEXT.format(path="./absent", content_assert=""),
+        VALID_XML,
+        lambda x: "Expected path './absent' in xml" in x,
     ),
     # test element_text with sub-assertion
     (
-        XML_ELEMENT_TEXT.format(path="./elem/more", content_assert='<has_text text="BAR"/>'), VALID_XML,
-        lambda x: len(x) == 0
+        XML_ELEMENT_TEXT.format(path="./elem/more", content_assert='<has_text text="BAR"/>'),
+        VALID_XML,
+        lambda x: len(x) == 0,
     ),
     # test element_text with sub-assertion .. negative
     (
-        XML_ELEMENT_TEXT.format(path="./elem/more", content_assert='<has_text text="NOTBAR"/>'), VALID_XML,
-        lambda x: "Text of element with path './elem/more': Expected text 'NOTBAR' in output ('BAR')" in x
+        XML_ELEMENT_TEXT.format(path="./elem/more", content_assert='<has_text text="NOTBAR"/>'),
+        VALID_XML,
+        lambda x: "Text of element with path './elem/more': Expected text 'NOTBAR' in output ('BAR')" in x,
     ),
     # note that xml_element is also tested indirectly by the other xml
     # assertions which are all implemented by xml_element
     # test xml_element
     (
-        XML_XML_ELEMENT.format(path=".//more", n="2", delta="1", min="1", max="3", attribute="", all="false", content_assert='<has_text_matching expression="(BA[RZ]|QUX)$"/>', negate="false"), VALID_XML,
-        lambda x: len(x) == 0
+        XML_XML_ELEMENT.format(
+            path=".//more",
+            n="2",
+            delta="1",
+            min="1",
+            max="3",
+            attribute="",
+            all="false",
+            content_assert='<has_text_matching expression="(BA[RZ]|QUX)$"/>',
+            negate="false",
+        ),
+        VALID_XML,
+        lambda x: len(x) == 0,
     ),
     # test xml_element testing attribute matching on all matching elements
     (
-        XML_XML_ELEMENT.format(path=".//more", n="2", delta="1", min="1", max="3", attribute="name", all="true", content_assert='<has_text_matching expression="(ba[rz]|qux)$"/>', negate="false"), VALID_XML,
-        lambda x: len(x) == 0
+        XML_XML_ELEMENT.format(
+            path=".//more",
+            n="2",
+            delta="1",
+            min="1",
+            max="3",
+            attribute="name",
+            all="true",
+            content_assert='<has_text_matching expression="(ba[rz]|qux)$"/>',
+            negate="false",
+        ),
+        VALID_XML,
+        lambda x: len(x) == 0,
     ),
     # test xml_element .. failing because of n
     (
-        XML_XML_ELEMENT.format(path=".//more", n="2", delta="0", min="1", max="3", attribute="", all="false", content_assert='', negate="false"), VALID_XML,
-        lambda x: "Expected 2+-0 occurrences of path './/more' in xml found 3" in x
+        XML_XML_ELEMENT.format(
+            path=".//more",
+            n="2",
+            delta="0",
+            min="1",
+            max="3",
+            attribute="",
+            all="false",
+            content_assert="",
+            negate="false",
+        ),
+        VALID_XML,
+        lambda x: "Expected 2+-0 occurrences of path './/more' in xml found 3" in x,
     ),
     # test xml_element .. failing because of n
     (
-        XML_XML_ELEMENT.format(path=".//more", n="10000", delta="1", min="1", max="3", attribute="", all="false", content_assert='', negate="true"), VALID_XML,
-        lambda x: "Did not expect that the number of occurences of path './/more' in xml is in [1:3] found 3" in x
+        XML_XML_ELEMENT.format(
+            path=".//more",
+            n="10000",
+            delta="1",
+            min="1",
+            max="3",
+            attribute="",
+            all="false",
+            content_assert="",
+            negate="true",
+        ),
+        VALID_XML,
+        lambda x: "Did not expect that the number of occurences of path './/more' in xml is in [1:3] found 3" in x,
     ),
     # test xml_element .. failing because of sub assertion
     (
-        XML_XML_ELEMENT.format(path=".//more", n="2", delta="1", min="1", max="3", attribute="", all="false", content_assert='<has_text_matching expression="(BA[RZ]|QUX)$" negate="true"/>', negate="false"), VALID_XML,
-        lambda x: "Text of element with path './/more': Did not expect text matching expression '(BA[RZ]|QUX)$' in output ('BAR')" in x
+        XML_XML_ELEMENT.format(
+            path=".//more",
+            n="2",
+            delta="1",
+            min="1",
+            max="3",
+            attribute="",
+            all="false",
+            content_assert='<has_text_matching expression="(BA[RZ]|QUX)$" negate="true"/>',
+            negate="false",
+        ),
+        VALID_XML,
+        lambda x: "Text of element with path './/more': Did not expect text matching expression '(BA[RZ]|QUX)$' in output ('BAR')"
+        in x,
     ),
-
     # test has_archive_member with zip
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/file1.txt", content_assert="", all="false"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/file1.txt", content_assert="", all="false"),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/file1.txt", content_assert="", all="false"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/file1.txt", content_assert="", all="false"),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with non archive
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="irrelevant", content_assert="", all="false"), NONARCHIVE,
-        lambda x: "Expected path 'irrelevant' to be an archive" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="irrelevant", content_assert="", all="false"),
+        NONARCHIVE,
+        lambda x: "Expected path 'irrelevant' to be an archive" in x,
     ),
     # test has_archive_member with zip on absent member
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="absent", content_assert="", all="false"), ZIPBYTES,
-        lambda x: "Expected path 'absent' in archive" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="absent", content_assert="", all="false"),
+        ZIPBYTES,
+        lambda x: "Expected path 'absent' in archive" in x,
     ),
     # test has_archive_member with tar on absent member
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="absent", content_assert="", all="false"), TARBYTES,
-        lambda x: "Expected path 'absent' in archive" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="absent", content_assert="", all="false"),
+        TARBYTES,
+        lambda x: "Expected path 'absent' in archive" in x,
     ),
     # test has_archive_member with zip on symlink
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?symlink", content_assert='<has_text text="testdir/file1.txt"/>', all="false"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path="(\\./)?symlink", content_assert='<has_text text="testdir/file1.txt"/>', all="false"
+        ),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar on symlink
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?symlink", content_assert='<has_text text="testdir/file1.txt"/>', all="false"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path="(\\./)?symlink", content_assert='<has_text text="testdir/file1.txt"/>', all="false"
+        ),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with zip on a dir member (which are treated like empty files)
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/", content_assert='<has_size value="0"/>', all="false"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/", content_assert='<has_size value="0"/>', all="false"),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar on a dir member (which are treated like empty files)
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/", content_assert='<has_size value="0"/>', all="false"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/", content_assert='<has_size value="0"/>', all="false"),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with zip with subassertion (note that archive members are sorted therefor file1 in dir2 is tested)
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/.*\\.txt", content_assert='<has_text text="testdir/dir2/file1.txt"/>', all="false"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path="(\\./)?testdir/.*\\.txt", content_assert='<has_text text="testdir/dir2/file1.txt"/>', all="false"
+        ),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar with subassertion (note that archive members are sorted therefor file1 in dir2 is tested)
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/.*\\.txt", content_assert='<has_text text="testdir/dir2/file1.txt"/>', all="false"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path="(\\./)?testdir/.*\\.txt", content_assert='<has_text text="testdir/dir2/file1.txt"/>', all="false"
+        ),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with zip with failing subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/file1.txt", content_assert='<has_text text="ABSENT"/>', all="false"), ZIPBYTES,
-        lambda x: "Archive member '(\\./)?testdir/file1.txt': Expected text 'ABSENT' in output ('testdir/file1.txt')" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path="(\\./)?testdir/file1.txt", content_assert='<has_text text="ABSENT"/>', all="false"
+        ),
+        ZIPBYTES,
+        lambda x: "Archive member '(\\./)?testdir/file1.txt': Expected text 'ABSENT' in output ('testdir/file1.txt')"
+        in x,
     ),
     # test has_archive_member with tar with failing subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path="(\\./)?testdir/file1.txt", content_assert='<has_text text="ABSENT"/>', all="false"), TARBYTES,
-        lambda x: "Archive member '(\\./)?testdir/file1.txt': Expected text 'ABSENT' in output ('testdir/file1.txt')" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path="(\\./)?testdir/file1.txt", content_assert='<has_text text="ABSENT"/>', all="false"
+        ),
+        TARBYTES,
+        lambda x: "Archive member '(\\./)?testdir/file1.txt': Expected text 'ABSENT' in output ('testdir/file1.txt')"
+        in x,
     ),
     # test has_archive_member with zip checking all matches with subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', all="true"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', all="true"
+        ),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar checking all matches with subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', all="true"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', all="true"
+        ),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with zip checking all matches with failing subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file1\\.txt"/>', all="true"), ZIPBYTES,
-        lambda x: "Expected text matching expression 'file1\\.txt' in output ('testdir/file2.txt')"
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file1\\.txt"/>', all="true"
+        ),
+        ZIPBYTES,
+        lambda x: "Expected text matching expression 'file1\\.txt' in output ('testdir/file2.txt')",
     ),
     # test has_archive_member with tar checking all matches with failing subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file1\\.txt"/>', all="true"), TARBYTES,
-        lambda x: "Expected text matching expression 'file1\\.txt' in output ('testdir/file2.txt')"
+        ARCHIVE_HAS_ARCHIVE_MEMBER.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file1\\.txt"/>', all="true"
+        ),
+        TARBYTES,
+        lambda x: "Expected text matching expression 'file1\\.txt' in output ('testdir/file2.txt')",
     ),
-
     # test has_archive_member with zip n+delta with subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="3", delta="1"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="3", delta="1"
+        ),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with zip n+delta with subassertion .. negative
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="1", delta="1"), ZIPBYTES,
-        lambda x: "Expected 1+-1 matches for path '.*file.\\.txt' in archive found 4" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="1", delta="1"
+        ),
+        ZIPBYTES,
+        lambda x: "Expected 1+-1 matches for path '.*file.\\.txt' in archive found 4" in x,
     ),
     # test has_archive_member with tar n+delta with subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="3", delta="1"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="3", delta="1"
+        ),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar n+delta with subassertion .. negative
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="1", delta="1"), TARBYTES,
-        lambda x: "Expected 1+-1 matches for path '.*file.\\.txt' in archive found 4" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER_N.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', n="1", delta="1"
+        ),
+        TARBYTES,
+        lambda x: "Expected 1+-1 matches for path '.*file.\\.txt' in archive found 4" in x,
     ),
     # test has_archive_member with zip min+max with subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="2", max="4"), ZIPBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="2", max="4"
+        ),
+        ZIPBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with zip min+max with subassertion .. negative
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="0", max="2"), ZIPBYTES,
-        lambda x: "Expected that the number of matches for path '.*file.\\.txt' in archive is in [0:2] found 4" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="0", max="2"
+        ),
+        ZIPBYTES,
+        lambda x: "Expected that the number of matches for path '.*file.\\.txt' in archive is in [0:2] found 4" in x,
     ),
     # test has_archive_member with tar min+max with subassertion
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="2", max="4"), TARBYTES,
-        lambda x: len(x) == 0
+        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="2", max="4"
+        ),
+        TARBYTES,
+        lambda x: len(x) == 0,
     ),
     # test has_archive_member with tar min+max with subassertion .. negative
     (
-        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="0", max="2"), TARBYTES,
-        lambda x: "Expected that the number of matches for path '.*file.\\.txt' in archive is in [0:2] found 4" in x
+        ARCHIVE_HAS_ARCHIVE_MEMBER_MINMAX.format(
+            path=".*file.\\.txt", content_assert='<has_text_matching expression="file.\\.txt"/>', min="0", max="2"
+        ),
+        TARBYTES,
+        lambda x: "Expected that the number of matches for path '.*file.\\.txt' in archive is in [0:2] found 4" in x,
     ),
 ]
 
 if h5py is not None:
     H5PY_TESTS = [
         # test has_h5_keys
-        (
-            H5_HAS_H5_KEYS, H5BYTES,
-            lambda x: len(x) == 0
-        ),
+        (H5_HAS_H5_KEYS, H5BYTES, lambda x: len(x) == 0),
         # test has_h5_keys .. negative
         (
-            H5_HAS_H5_KEYS_NEGATIVE, H5BYTES,
-            lambda x: "Not a HDF5 file or H5 keys missing:\n\t['mygroup', 'mygroup/myfloat', 'myint']\n\t['absent']" in x
+            H5_HAS_H5_KEYS_NEGATIVE,
+            H5BYTES,
+            lambda x: "Not a HDF5 file or H5 keys missing:\n\t['mygroup', 'mygroup/myfloat', 'myint']\n\t['absent']"
+            in x,
         ),
         # test has_attribute
-        (
-            H5_HAS_ATTRIBUTE, H5BYTES,
-            lambda x: len(x) == 0
-        ),
+        (H5_HAS_ATTRIBUTE, H5BYTES, lambda x: len(x) == 0),
         # test has_attribute .. negative
         (
-            H5_HAS_ATTRIBUTE_NEGATIVE, H5BYTES,
-            lambda x: "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', 1)]\n\n\t(myfileattr : wrong)" in x
+            H5_HAS_ATTRIBUTE_NEGATIVE,
+            H5BYTES,
+            lambda x: "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', 1)]\n\n\t(myfileattr : wrong)"
+            in x,
         ),
     ]
     TESTS.extend(H5PY_TESTS)
 
 
 TEST_IDS = [
-    'has_n_columns success',
-    'has_n_columns failure',
-    'has_n_columns for csv',
-    'has_n_columns with comments',
-    'has_text success',
-    'has_text failure',
-    'has_text None output',
-    'has_text empty output',
-    'has_text n success',
-    'has_text n failure',
-    'has_text n delta success',
-    'has_text n delta failure',
-    'has_text min/max delta success',
-    'has_text min/max delta failure',
-    'has_text negate success',
-    'has_text negate failure',
-    'has_text negate None output',
-    'has_text negate empty output',
-    'has_text negate n success',
-    'has_text negate n failure',
-    'has_text negate n delta success',
-    'has_text negate n delta failure',
-    'has_text negate min/max delta success',
-    'has_text negate min/max delta failure',
-    'not_has_text success',
-    'not_has_text failure',
-    'not_has_text None output',
-    'not_has_text empty output',
-    'has_text_matching success',
-    'has_text_matching failure',
-    'has_text_matching n success',
-    'has_text_matching n failure',
-    'has_text_matching min/max success',
-    'has_text_matching min/max failure',
-    'has_line success',
-    'has_line failure',
-    'has_line n success',
-    'has_line n failure',
-    'has_n_lines success',
-    'has_n_lines n as bytes success',
-    'has_n_lines failure',
-    'has_n_lines delta',
-    'has_line_matching success',
-    'has_line_matching failure',
-    'has_line_matching n success',
-    'has_line_matching n failure',
-    'has_size success',
-    'has_size failure',
-    'has_size delta',
-    'has_size with bytes suffix',
-    'has_size with bytes suffix failure',
-    'is_valid_xml success',
-    'is_valid_xml failure',
-    'has_element_with_path success 1',
-    'has_element_with_path success 2',
-    'has_element_with_path success 3',
-    'has_element_with_path failure',
-    'has_n_elements_with_path success 1',
-    'has_n_elements_with_path success 2',
-    'has_n_elements_with_path success 3',
-    'has_n_elements_with_path success 4',
-    'has_n_elements_with_path failure',
-    'element_text_matches sucess',
-    'element_text_matches sucess (with more specific path)',
-    'element_text_matches failure',
-    'element_text_is sucess',
-    'element_text_is sucess (with more specific path)',
-    'element_text_is failure',
-    'attribute_matches sucess',
-    'attribute_matches sucess (with more specific path)',
-    'attribute_matches failure',
-    'element_text success',
-    'element_text failure',
-    'element_text with subassertion sucess',
-    'element_text with subassertion failure',
-    'xml_element matching text success',
-    'xml_element matching attribute success',
-    'xml_element failure (due to n)',
-    'xml_element failure (due to min/max in combination with negate)',
-    'xml_element failure (due to subassertion)',
-    'has_archive_member zip',
-    'has_archive_member tar',
-    'has_archive_member non-archive',
-    'has_archive_member zip absent member',
-    'has_archive_member tar absent member',
-    'has_archive_member zip symlink member',
-    'has_archive_member tar symlink member',
-    'has_archive_member zip non-file member',
-    'has_archive_member tar non-file member',
-    'has_archive_member zip with content assertion',
-    'has_archive_member tar with content assertion',
-    'has_archive_member zip with failing content assertion',
-    'has_archive_member tar with failing content assertion',
-    'has_archive_member zip all matching with content assertion',
-    'has_archive_member tar all matching with content assertion',
-    'has_archive_member zip all matching with failing content assertion',
-    'has_archive_member tar all matching with failing content assertion',
-    'has_archive_member zip n + delta and content assertion',
-    'has_archive_member zip n + delta failing  and content assertion',
-    'has_archive_member tar n + delta and content assertion',
-    'has_archive_member tar n + delta failing and content assertion',
-    'has_archive_member zip min max and content assertion',
-    'has_archive_member zip min max failing  and content assertion',
-    'has_archive_member tar min max and content assertion',
-    'has_archive_member tar min max failing and content assertion',
+    "has_n_columns success",
+    "has_n_columns failure",
+    "has_n_columns for csv",
+    "has_n_columns with comments",
+    "has_text success",
+    "has_text failure",
+    "has_text None output",
+    "has_text empty output",
+    "has_text n success",
+    "has_text n failure",
+    "has_text n delta success",
+    "has_text n delta failure",
+    "has_text min/max delta success",
+    "has_text min/max delta failure",
+    "has_text negate success",
+    "has_text negate failure",
+    "has_text negate None output",
+    "has_text negate empty output",
+    "has_text negate n success",
+    "has_text negate n failure",
+    "has_text negate n delta success",
+    "has_text negate n delta failure",
+    "has_text negate min/max delta success",
+    "has_text negate min/max delta failure",
+    "not_has_text success",
+    "not_has_text failure",
+    "not_has_text None output",
+    "not_has_text empty output",
+    "has_text_matching success",
+    "has_text_matching failure",
+    "has_text_matching n success",
+    "has_text_matching n failure",
+    "has_text_matching min/max success",
+    "has_text_matching min/max failure",
+    "has_line success",
+    "has_line failure",
+    "has_line n success",
+    "has_line n failure",
+    "has_n_lines success",
+    "has_n_lines n as bytes success",
+    "has_n_lines failure",
+    "has_n_lines delta",
+    "has_line_matching success",
+    "has_line_matching failure",
+    "has_line_matching n success",
+    "has_line_matching n failure",
+    "has_size success",
+    "has_size failure",
+    "has_size delta",
+    "has_size with bytes suffix",
+    "has_size with bytes suffix failure",
+    "is_valid_xml success",
+    "is_valid_xml failure",
+    "has_element_with_path success 1",
+    "has_element_with_path success 2",
+    "has_element_with_path success 3",
+    "has_element_with_path failure",
+    "has_n_elements_with_path success 1",
+    "has_n_elements_with_path success 2",
+    "has_n_elements_with_path success 3",
+    "has_n_elements_with_path success 4",
+    "has_n_elements_with_path failure",
+    "element_text_matches sucess",
+    "element_text_matches sucess (with more specific path)",
+    "element_text_matches failure",
+    "element_text_is sucess",
+    "element_text_is sucess (with more specific path)",
+    "element_text_is failure",
+    "attribute_matches sucess",
+    "attribute_matches sucess (with more specific path)",
+    "attribute_matches failure",
+    "element_text success",
+    "element_text failure",
+    "element_text with subassertion sucess",
+    "element_text with subassertion failure",
+    "xml_element matching text success",
+    "xml_element matching attribute success",
+    "xml_element failure (due to n)",
+    "xml_element failure (due to min/max in combination with negate)",
+    "xml_element failure (due to subassertion)",
+    "has_archive_member zip",
+    "has_archive_member tar",
+    "has_archive_member non-archive",
+    "has_archive_member zip absent member",
+    "has_archive_member tar absent member",
+    "has_archive_member zip symlink member",
+    "has_archive_member tar symlink member",
+    "has_archive_member zip non-file member",
+    "has_archive_member tar non-file member",
+    "has_archive_member zip with content assertion",
+    "has_archive_member tar with content assertion",
+    "has_archive_member zip with failing content assertion",
+    "has_archive_member tar with failing content assertion",
+    "has_archive_member zip all matching with content assertion",
+    "has_archive_member tar all matching with content assertion",
+    "has_archive_member zip all matching with failing content assertion",
+    "has_archive_member tar all matching with failing content assertion",
+    "has_archive_member zip n + delta and content assertion",
+    "has_archive_member zip n + delta failing  and content assertion",
+    "has_archive_member tar n + delta and content assertion",
+    "has_archive_member tar n + delta failing and content assertion",
+    "has_archive_member zip min max and content assertion",
+    "has_archive_member zip min max failing  and content assertion",
+    "has_archive_member tar min max and content assertion",
+    "has_archive_member tar min max failing and content assertion",
 ]
 
 if h5py is not None:
     H5PY_TEST_IDS = [
-        'has_h5_keys',
-        'has_h5_keys failure',
-        'has_h5_attribute',
-        'has_h5_attribute failure',
+        "has_h5_keys",
+        "has_h5_keys failure",
+        "has_h5_attribute",
+        "has_h5_attribute failure",
     ]
     TEST_IDS.extend(H5PY_TEST_IDS)
 
 
-@pytest.mark.parametrize('assertion_xml,data,assert_func', TESTS, ids=TEST_IDS)
+@pytest.mark.parametrize("assertion_xml,data,assert_func", TESTS, ids=TEST_IDS)
 def test_assertions(assertion_xml, data, assert_func):
     assertion = etree.fromstring(assertion_xml)
     assertion_description = __parse_assert_list_from_elem(assertion)
diff --git a/test/unit/util/test_bool_expressions.py b/test/unit/util/test_bool_expressions.py
index 71fa13cf366..fff6757090d 100644
--- a/test/unit/util/test_bool_expressions.py
+++ b/test/unit/util/test_bool_expressions.py
@@ -41,7 +41,7 @@ INVALID_EXPRESSIONS_TESTS = [
 ]
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def contained_evaluator() -> BooleanExpressionEvaluator:
     """Boolean expression evaluator using the TokenContainedEvaluator.
 
@@ -52,25 +52,25 @@ def contained_evaluator() -> BooleanExpressionEvaluator:
     return evaluator
 
 
-@pytest.mark.parametrize('expr, expected', VALID_EXPRESSIONS_TESTS)
+@pytest.mark.parametrize("expr, expected", VALID_EXPRESSIONS_TESTS)
 def test_expression_evaluates_as_expected(expr: str, expected: bool, contained_evaluator: BooleanExpressionEvaluator):
     actual = contained_evaluator.evaluate_expression(expr)
     assert actual == expected
 
 
-@pytest.mark.parametrize('expr', INVALID_EXPRESSIONS_TESTS)
+@pytest.mark.parametrize("expr", INVALID_EXPRESSIONS_TESTS)
 def test_invalid_expression_raises_exception(expr: str, contained_evaluator: BooleanExpressionEvaluator):
     with pytest.raises(Exception):
         contained_evaluator.evaluate_expression(expr)
 
 
-@pytest.mark.parametrize('expr, _', VALID_EXPRESSIONS_TESTS)
+@pytest.mark.parametrize("expr, _", VALID_EXPRESSIONS_TESTS)
 def test_is_valid_expression_return_true_when_valid(expr: str, _: bool):
     result = BooleanExpressionEvaluator.is_valid_expression(expr)
     assert result is True
 
 
-@pytest.mark.parametrize('expr', INVALID_EXPRESSIONS_TESTS)
+@pytest.mark.parametrize("expr", INVALID_EXPRESSIONS_TESTS)
 def test_is_valid_expression_return_false_when_invalid(expr: str):
     result = BooleanExpressionEvaluator.is_valid_expression(expr)
     assert result is False
diff --git a/test/unit/util/test_checkers.py b/test/unit/util/test_checkers.py
index c6ccc1227bb..1e30d25656c 100644
--- a/test/unit/util/test_checkers.py
+++ b/test/unit/util/test_checkers.py
@@ -7,13 +7,13 @@ def test_check_html():
     html_text = '<p>\n<a href="url">Link</a>\n</p>\n'
     assert check_html(html_text, file_path=False)
     # Test a non-HTML binary string
-    assert not check_html(b'No HTML here\nSecond line\n', file_path=False)
-    with tempfile.NamedTemporaryFile(mode='w') as tmp:
+    assert not check_html(b"No HTML here\nSecond line\n", file_path=False)
+    with tempfile.NamedTemporaryFile(mode="w") as tmp:
         tmp.write(html_text)
         tmp.flush()
         assert check_html(tmp.name)
     # Test a non-UTF8 binary file
-    with tempfile.NamedTemporaryFile(mode='wb') as tmpb:
-        tmpb.write(b'\x1f\x8b')
+    with tempfile.NamedTemporaryFile(mode="wb") as tmpb:
+        tmpb.write(b"\x1f\x8b")
         tmpb.flush()
         assert not check_html(tmpb.name)
diff --git a/test/unit/util/test_compression_util.py b/test/unit/util/test_compression_util.py
index c20d3fcc971..ee52d6eb004 100644
--- a/test/unit/util/test_compression_util.py
+++ b/test/unit/util/test_compression_util.py
@@ -4,12 +4,11 @@ import unittest
 
 from galaxy.util.compression_utils import (
     CompressedFile,
-    get_fileobj_raw
+    get_fileobj_raw,
 )
 
 
 class CompressionUtilTestCase(unittest.TestCase):
-
     def test_compression_safety(self):
         self.assert_safety("test-data/unsafe.tar", False)
         self.assert_safety("test-data/unsafe_relative_symlink.tar", False)
@@ -21,17 +20,11 @@ class CompressionUtilTestCase(unittest.TestCase):
 
     def test_get_fileobj_raw(self):
         self.assert_format_detected("test-data/4.bed.zip", "zip")
-        self.assert_format_detected(
-            "test-data/4.bed.zip", None, ["bz2", "gzip"]
-        )
+        self.assert_format_detected("test-data/4.bed.zip", None, ["bz2", "gzip"])
         self.assert_format_detected("test-data/4.bed.gz", "gzip")
-        self.assert_format_detected(
-            "test-data/4.bed.gz", None, ["bz2", "zip"]
-        )
+        self.assert_format_detected("test-data/4.bed.gz", None, ["bz2", "zip"])
         self.assert_format_detected("test-data/4.bed.bz2", "bz2")
-        self.assert_format_detected(
-            "test-data/4.bed.bz2", None, ["gzip", "zip"]
-        )
+        self.assert_format_detected("test-data/4.bed.bz2", None, ["gzip", "zip"])
 
     def assert_safety(self, path, expected_to_be_safe):
         temp_dir = tempfile.mkdtemp()
@@ -46,8 +39,8 @@ class CompressionUtilTestCase(unittest.TestCase):
 
     def assert_format_detected(self, path, expected_fmt, allowed_fmts=None):
         expected_type: type
-        for mode in ['r', 'rb', 'rt', 'U']:
-            if 'b' in mode:
+        for mode in ["r", "rb", "rt", "U"]:
+            if "b" in mode:
                 expected_type = bytes
             else:
                 expected_type = str
diff --git a/test/unit/util/test_fill_template.py b/test/unit/util/test_fill_template.py
index 8d2d0594707..883040b8677 100644
--- a/test/unit/util/test_fill_template.py
+++ b/test/unit/util/test_fill_template.py
@@ -43,7 +43,7 @@ INVALID_CHEETAH_SYNTAX = """#if 1 <> 1
 
 
 def test_fill_simple_template():
-    template_str = str(fill_template(SIMPLE_TEMPLATE, {'a_list': [1, 2]}))
+    template_str = str(fill_template(SIMPLE_TEMPLATE, {"a_list": [1, 2]}))
     assert template_str == FILLED_SIMPLE_TEMPLATE
 
 
@@ -53,8 +53,8 @@ def test_fill_list_comprehension_template():
 
 
 def test_fill_list_comprehension_template_2():
-    template_str = fill_template(LIST_COMPREHENSION_TEMPLATE, python_template_version='2', retry=1)
-    assert template_str == 'echo 1\n'
+    template_str = fill_template(LIST_COMPREHENSION_TEMPLATE, python_template_version="2", retry=1)
+    assert template_str == "echo 1\n"
 
 
 def test_fill_dict_comprehension():
@@ -73,10 +73,10 @@ def test_gen_expr():
 
 
 def test_fix_template_two_to_three():
-    template_str = fill_template(TWO_TO_THREE_TEMPLATE, python_template_version='2', retry=1)
-    assert template_str == 'a a 1'
+    template_str = fill_template(TWO_TO_THREE_TEMPLATE, python_template_version="2", retry=1)
+    assert template_str == "a a 1"
 
 
 def test_fix_template_invalid_cheetah():
-    template_str = fill_template(INVALID_CHEETAH_SYNTAX, python_template_version='2', retry=1)
+    template_str = fill_template(INVALID_CHEETAH_SYNTAX, python_template_version="2", retry=1)
     assert template_str == "1 is 1\n"
diff --git a/test/unit/util/test_fix_type_error.py b/test/unit/util/test_fix_type_error.py
index ca9e415ebc7..9ffdf03024f 100644
--- a/test/unit/util/test_fix_type_error.py
+++ b/test/unit/util/test_fix_type_error.py
@@ -1,7 +1,9 @@
 from galaxy.util.pastescript.loadwsgi import fix_type_error
 
-argtype = ''
-EXP_STRING = "a_func() got multiple values for%s argument 'kwarg'; got (1, 2, kwarg=...), wanted (argone, kwarg=True)" % argtype
+argtype = ""
+EXP_STRING = (
+    "a_func() got multiple values for%s argument 'kwarg'; got (1, 2, kwarg=...), wanted (argone, kwarg=True)" % argtype
+)
 
 
 def a_func(argone, kwarg=True):
@@ -10,7 +12,7 @@ def a_func(argone, kwarg=True):
 
 def test_fix_type_error():
     args = [1, 2]
-    kwargs = {'kwarg': False}
+    kwargs = {"kwarg": False}
     try:
         a_func(*args, **kwargs)
     except TypeError:
diff --git a/test/unit/util/test_get_url.py b/test/unit/util/test_get_url.py
index 299e405cab1..7534264d3dd 100644
--- a/test/unit/util/test_get_url.py
+++ b/test/unit/util/test_get_url.py
@@ -7,27 +7,25 @@ from galaxy.util import url_get
 
 @responses.activate
 def test_get_url_ok():
-    url = 'https://toolshed.g2.bx.psu.edu/'
-    responses.add(responses.GET, url,
-                  body='OK', status=200)
+    url = "https://toolshed.g2.bx.psu.edu/"
+    responses.add(responses.GET, url, body="OK", status=200)
     text = url_get(url)
-    assert text == 'OK'
+    assert text == "OK"
 
 
 @responses.activate
 def test_get_url_forbidden():
-    url = 'https://toolshed.g2.bx.psu.edu/'
-    responses.add(responses.GET, url,
-                  body='Forbidden', status=403)
+    url = "https://toolshed.g2.bx.psu.edu/"
+    responses.add(responses.GET, url, body="Forbidden", status=403)
     with pytest.raises(requests.exceptions.HTTPError) as excinfo:
         url_get(url)
-    assert '403 Client Error: Forbidden for url: https://toolshed.g2.bx.psu.edu/' in str(excinfo)
+    assert "403 Client Error: Forbidden for url: https://toolshed.g2.bx.psu.edu/" in str(excinfo)
 
 
 def test_get_url_retry_after():
     # This test is not ideal since it contacts an external resource
     # and doesn't acutally verify multiple attempts have been made.
     # responses doesn't mock the right place to fully simulate this.
-    url = 'https://httpbin.org/status/429'
+    url = "https://httpbin.org/status/429"
     with pytest.raises(requests.exceptions.RetryError):
         url_get(url, max_retries=2, backoff_factor=0.01)
diff --git a/test/unit/util/test_inflection.py b/test/unit/util/test_inflection.py
index 4a0e33bff8f..4e983edc2a9 100644
--- a/test/unit/util/test_inflection.py
+++ b/test/unit/util/test_inflection.py
@@ -2,7 +2,6 @@ import pytest
 
 from galaxy.util.inflection import Inflector
 
-
 SINGULAR_TO_PLURAL = {
     "search": "searches",
     "switch": "switches",
@@ -72,7 +71,7 @@ SINGULAR_TO_PLURAL = {
     "shoe": "shoes",
     "horse": "horses",
     "prize": "prizes",
-    "edge": "edges"
+    "edge": "edges",
 }
 
 
@@ -81,18 +80,18 @@ def inflector():
     return Inflector()
 
 
-@pytest.mark.parametrize('test_data', SINGULAR_TO_PLURAL.items())
+@pytest.mark.parametrize("test_data", SINGULAR_TO_PLURAL.items())
 def test_pluralize_rules(test_data, inflector):
     assert test_data[1] == inflector.pluralize(test_data[0])
 
 
-@pytest.mark.parametrize('test_data', SINGULAR_TO_PLURAL.items())
+@pytest.mark.parametrize("test_data", SINGULAR_TO_PLURAL.items())
 def test_singularize_rules(test_data, inflector):
     assert test_data[0] == inflector.singularize(test_data[1])
 
 
 def test_cond_plural(inflector):
-    assert 'edge' == inflector.cond_plural(1, 'edge')
-    assert 'edges' == inflector.cond_plural(-1, 'edge')
-    assert 'edges' == inflector.cond_plural(0, 'edge')
-    assert 'edges' == inflector.cond_plural(2, 'edge')
+    assert "edge" == inflector.cond_plural(1, "edge")
+    assert "edges" == inflector.cond_plural(-1, "edge")
+    assert "edges" == inflector.cond_plural(0, "edge")
+    assert "edges" == inflector.cond_plural(2, "edge")
diff --git a/test/unit/util/test_lazy_process.py b/test/unit/util/test_lazy_process.py
index 108846450bc..b3e41979c64 100644
--- a/test/unit/util/test_lazy_process.py
+++ b/test/unit/util/test_lazy_process.py
@@ -14,7 +14,7 @@ def test_lazy_process():
     assert not os.path.exists(t.name)
     lazy_process.start_process()
     while not os.path.exists(t.name):
-        time.sleep(.01)
+        time.sleep(0.01)
     assert lazy_process.process
     assert lazy_process.process.poll() is None
     lazy_process.shutdown()
@@ -23,5 +23,5 @@ def test_lazy_process():
         ret_val = lazy_process.process.poll()
         if ret_val is not None:
             break
-        time.sleep(.01)
+        time.sleep(0.01)
     assert ret_val is not None
diff --git a/test/unit/util/test_properties.py b/test/unit/util/test_properties.py
index 6a0cfc61bd6..22e792a55fb 100644
--- a/test/unit/util/test_properties.py
+++ b/test/unit/util/test_properties.py
@@ -4,9 +4,9 @@ from galaxy.exceptions import InvalidFileFormatError
 from galaxy.util import properties
 from galaxy.util.properties import read_properties_from_file
 
-KEY1, KEY2, KEY3, KEY4, KEY5, KEY6 = 'k1', 'k2', 'k3', 'k4', 'k5', 'k6'
+KEY1, KEY2, KEY3, KEY4, KEY5, KEY6 = "k1", "k2", "k3", "k4", "k5", "k6"
 VAL1, VAL2, VAL3, VAL4, VAL5, VAL6 = 1, 2, 3, 4, 5, 6
-OTHER_SECTION = 'other'
+OTHER_SECTION = "other"
 
 
 @pytest.fixture
@@ -18,17 +18,11 @@ def mock_properties(monkeypatch):
         return {KEY1: VAL1, KEY2: VAL2}
 
     def mock_read_from_yaml(path):
-        return {
-            'galaxy': {KEY3: VAL3, KEY4: VAL4},
-            OTHER_SECTION: {KEY5: VAL5, KEY6: VAL6}
-        }
+        return {"galaxy": {KEY3: VAL3, KEY4: VAL4}, OTHER_SECTION: {KEY5: VAL5, KEY6: VAL6}}
 
-    class MockConfigParser():
+    class MockConfigParser:
         def __init__(self):
-            self._items = {
-                'app:main': [(KEY3, VAL3), (KEY4, VAL4)],
-                OTHER_SECTION: [(KEY5, VAL5), (KEY6, VAL6)]
-            }
+            self._items = {"app:main": [(KEY3, VAL3), (KEY4, VAL4)], OTHER_SECTION: [(KEY5, VAL5), (KEY6, VAL6)]}
 
         def has_section(self, section):
             return section in self._items.keys()
@@ -42,13 +36,13 @@ def mock_properties(monkeypatch):
     def mock_nice_config_parser(path):
         return MockConfigParser()
 
-    monkeypatch.setattr(properties, '_read_from_yaml_file', mock_read_from_yaml)
-    monkeypatch.setattr(properties, 'nice_config_parser', mock_nice_config_parser)
-    monkeypatch.setattr(properties, '__default_properties', mock_default_properties)
+    monkeypatch.setattr(properties, "_read_from_yaml_file", mock_read_from_yaml)
+    monkeypatch.setattr(properties, "nice_config_parser", mock_nice_config_parser)
+    monkeypatch.setattr(properties, "__default_properties", mock_default_properties)
 
 
 def test_read_galaxy_properties_from_yaml(mock_properties):
-    file = 'foo.yaml'
+    file = "foo.yaml"
     result = read_properties_from_file(file)
 
     assert len(result) == 4
@@ -59,7 +53,7 @@ def test_read_galaxy_properties_from_yaml(mock_properties):
 
 
 def test_read_other_properties_from_yaml(mock_properties):
-    file = 'foo.yaml'
+    file = "foo.yaml"
     result = read_properties_from_file(file, config_section=OTHER_SECTION)
 
     assert len(result) == 4
@@ -70,7 +64,7 @@ def test_read_other_properties_from_yaml(mock_properties):
 
 
 def test_get_default_properties_from_yaml(mock_properties):
-    file = 'foo.yaml'
+    file = "foo.yaml"
     result = read_properties_from_file(file, config_section="section's not here, man")
 
     assert len(result) == 2
@@ -79,7 +73,7 @@ def test_get_default_properties_from_yaml(mock_properties):
 
 
 def test_read_galaxy_properties_from_ini(mock_properties):
-    file = 'foo.ini'
+    file = "foo.ini"
     result = read_properties_from_file(file)
 
     assert len(result) == 4
@@ -90,7 +84,7 @@ def test_read_galaxy_properties_from_ini(mock_properties):
 
 
 def test_read_other_properties_from_ini(mock_properties):
-    file = 'foo.ini'
+    file = "foo.ini"
     result = read_properties_from_file(file, config_section=OTHER_SECTION)
 
     assert len(result) == 4
@@ -101,7 +95,7 @@ def test_read_other_properties_from_ini(mock_properties):
 
 
 def test_get_default_properties_from_ini(mock_properties):
-    file = 'foo.ini'
+    file = "foo.ini"
     result = read_properties_from_file(file, config_section="section's not here, man")
 
     assert len(result) == 2
@@ -110,6 +104,6 @@ def test_get_default_properties_from_ini(mock_properties):
 
 
 def test_dont_read_properties_from_other_format(mock_properties):
-    file = 'invalid'
+    file = "invalid"
     with pytest.raises(InvalidFileFormatError):
         read_properties_from_file(file)
diff --git a/test/unit/util/test_sockets.py b/test/unit/util/test_sockets.py
index 13a5bcd0a21..666921613f7 100644
--- a/test/unit/util/test_sockets.py
+++ b/test/unit/util/test_sockets.py
@@ -8,5 +8,5 @@ def test_unused_free_port_unconstrained():
 
     s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
     # would throw exception if port was not free.
-    s.bind(('localhost', port))
+    s.bind(("localhost", port))
     s.close()
diff --git a/test/unit/util/test_utils.py b/test/unit/util/test_utils.py
index 125f6410e21..8009ab6a186 100644
--- a/test/unit/util/test_utils.py
+++ b/test/unit/util/test_utils.py
@@ -20,8 +20,8 @@ SECTION_XML = """<?xml version="1.0" ?>
 
 
 def test_strip_control_characters():
-    s = '\x00bla'
-    assert util.strip_control_characters(s) == 'bla'
+    s = "\x00bla"
+    assert util.strip_control_characters(s) == "bla"
 
 
 def test_parse_xml_string():
@@ -30,7 +30,7 @@ def test_parse_xml_string():
 
 
 def test_parse_xml_file():
-    with tempfile.NamedTemporaryFile(mode='w') as tmp:
+    with tempfile.NamedTemporaryFile(mode="w") as tmp:
         tmp.write(SECTION_XML)
         tmp.flush()
         section = util.parse_xml(tmp.name).getroot()
@@ -40,18 +40,19 @@ def test_parse_xml_file():
 def _verify_section(section):
     tool = next(iter(section))
     assert sorted(tool.items()) == [
-        ('file',
-         'toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/fb1313d79396/seq_filter_by_id/tools/seq_filter_by_id/seq_filter_by_id.xml'),
-        ('guid',
-         'toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.5')
+        (
+            "file",
+            "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/fb1313d79396/seq_filter_by_id/tools/seq_filter_by_id/seq_filter_by_id.xml",
+        ),
+        ("guid", "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.5"),
     ]
-    assert next(iter(tool)).text == 'toolshed.g2.bx.psu.edu'
+    assert next(iter(tool)).text == "toolshed.g2.bx.psu.edu"
 
 
 def test_xml_to_string():
     section = util.parse_xml_string(SECTION_XML)
     s = util.xml_to_string(section)
-    assert len(s.split('\n')) == 1
+    assert len(s.split("\n")) == 1
 
 
 def test_xml_to_string_pretty():
@@ -75,11 +76,13 @@ def test_parse_xml_enoent():
 
 
 def test_clean_multiline_string():
-    x = util.clean_multiline_string("""
+    x = util.clean_multiline_string(
+        """
         a
         b
         c
-""")
+"""
+    )
     assert x == "a\nb\nc\n"
 
 
@@ -92,7 +95,7 @@ def test_safe_loads():
     rval = safe_loads(d)
     assert rval == d
     assert rval is not d
-    rval['foo'] = 'bar'
-    assert 'foo' not in d
+    rval["foo"] = "bar"
+    assert "foo" not in d
     s = '{"foo": "bar"}'
     assert safe_loads(s) == {"foo": "bar"}
diff --git a/test/unit/web_framework/framework/test_framework_base.py b/test/unit/web_framework/framework/test_framework_base.py
index bba5aa540d2..495b6ec9bba 100644
--- a/test/unit/web_framework/framework/test_framework_base.py
+++ b/test/unit/web_framework/framework/test_framework_base.py
@@ -2,7 +2,6 @@ from galaxy.web.framework.base import WebApplication
 
 
 class TestWebapp(WebApplication):
-
     def assert_maps(self, url, method="GET", **parts):
         map_result = self.mapper.match(url, environ={"REQUEST_METHOD": method})
         for key, expected_value in parts.items():
@@ -14,5 +13,5 @@ class TestWebapp(WebApplication):
 
 def test_add_route():
     test_webapp = TestWebapp()
-    test_webapp.add_route('/authnz/', controller='authnz', action='index', provider=None)
+    test_webapp.add_route("/authnz/", controller="authnz", action="index", provider=None)
     test_webapp.assert_maps("/authnz/", controller="authnz", action="index")
diff --git a/test/unit/web_stack/test_message.py b/test/unit/web_stack/test_message.py
index 56c8d9d7121..2e5a3479e96 100644
--- a/test/unit/web_stack/test_message.py
+++ b/test/unit/web_stack/test_message.py
@@ -5,10 +5,10 @@ from galaxy.web_stack.message import (
 
 
 def test_validate_job_handler_message():
-    message = JobHandlerMessage(task='setup', job_id=42)
+    message = JobHandlerMessage(task="setup", job_id=42)
     message.validate()
 
-    message = JobHandlerMessage(task='setup')
+    message = JobHandlerMessage(task="setup")
     error = None
     try:
         message.validate()
@@ -18,10 +18,10 @@ def test_validate_job_handler_message():
 
 
 def test_validate_workflow_handler_message():
-    message = WorkflowSchedulingMessage(task='setup', workflow_invocation_id=42)
+    message = WorkflowSchedulingMessage(task="setup", workflow_invocation_id=42)
     message.validate()
 
-    message = WorkflowSchedulingMessage(task='setup')
+    message = WorkflowSchedulingMessage(task="setup")
     error = None
     try:
         message.validate()
diff --git a/test/unit/webapps/api/test_configuration.py b/test/unit/webapps/api/test_configuration.py
index c1fe35e0c55..a653cd4d670 100644
--- a/test/unit/webapps/api/test_configuration.py
+++ b/test/unit/webapps/api/test_configuration.py
@@ -2,16 +2,16 @@ from galaxy.webapps.galaxy.api.configuration import parse_serialization_params
 
 
 def test_parse_serialization_params():
-    view, default_view = 'a', 'b'
-    keys = 'foo'
+    view, default_view = "a", "b"
+    keys = "foo"
     serialized = parse_serialization_params(view, keys, default_view)
     assert serialized.view == view
     assert serialized.default_view == default_view
     assert serialized.keys == [keys]
 
-    keys = 'foo,bar,baz'
+    keys = "foo,bar,baz"
     serialized = parse_serialization_params(view, keys, default_view)
-    assert serialized.keys == ['foo', 'bar', 'baz']
+    assert serialized.keys == ["foo", "bar", "baz"]
 
     serialized = parse_serialization_params(default_view=default_view)
     assert serialized.view is None
diff --git a/test/unit/webapps/api/test_id_fields.py b/test/unit/webapps/api/test_id_fields.py
index b69407ff30f..6a926f41465 100644
--- a/test/unit/webapps/api/test_id_fields.py
+++ b/test/unit/webapps/api/test_id_fields.py
@@ -25,12 +25,12 @@ def security() -> IdEncodingHelper:
 
 def test_decoded_id_schema_override():
     schema = DecodedIdModel.schema()
-    assert schema['properties']['id']['type'] == 'string', schema
+    assert schema["properties"]["id"]["type"] == "string", schema
 
 
 def test_encoded_id_schema_override():
     schema = EncodedIdModel.schema()
-    assert schema['properties']['id']['type'] == 'string', schema
+    assert schema["properties"]["id"]["type"] == "string", schema
 
 
 def test_decoded_database_id_field(security: IdEncodingHelper):
diff --git a/test/unit/webapps/services/test_history_contents.py b/test/unit/webapps/services/test_history_contents.py
index dc453d2dfe8..25bb53df8cf 100644
--- a/test/unit/webapps/services/test_history_contents.py
+++ b/test/unit/webapps/services/test_history_contents.py
@@ -5,7 +5,7 @@ from galaxy.webapps.galaxy.services.history_contents import HistoriesContentsSer
 
 @pytest.fixture
 def mock_init(monkeypatch):
-    monkeypatch.setattr(HistoriesContentsService, '__init__', lambda _: None)
+    monkeypatch.setattr(HistoriesContentsService, "__init__", lambda _: None)
 
 
 class TestSetItemCounts:
@@ -38,16 +38,17 @@ class TestSetItemCounts:
         down = 10
         total_up = 90
         total_down = 100
-        counts = service._set_item_counts(matches_up=up, matches_down=down, total_matches_up=total_up,
-            total_matches_down=total_down)
+        counts = service._set_item_counts(
+            matches_up=up, matches_down=down, total_matches_up=total_up, total_matches_down=total_down
+        )
         self._verify_counts(counts, up=up, down=down, total_up=total_up, total_down=total_down)
 
     def _verify_counts(self, counts, up=0, total_up=0, down=0, total_down=0):
         # counts of displayed items
-        assert counts['matches'] == up + down
-        assert counts['matches_up'] == up
-        assert counts['matches_down'] == down
+        assert counts["matches"] == up + down
+        assert counts["matches_up"] == up
+        assert counts["matches_down"] == down
         # total counts of matching items
-        assert counts['total_matches'] == total_up + total_down + 1
-        assert counts['total_matches_up'] == total_up
-        assert counts['total_matches_down'] == total_down
+        assert counts["total_matches"] == total_up + total_down + 1
+        assert counts["total_matches_up"] == total_up
+        assert counts["total_matches_down"] == total_down
diff --git a/test/unit/webapps/test_login.py b/test/unit/webapps/test_login.py
index 8ebfdb5784b..e444f5341c3 100644
--- a/test/unit/webapps/test_login.py
+++ b/test/unit/webapps/test_login.py
@@ -1,5 +1,8 @@
 import json
-from datetime import datetime, timedelta
+from datetime import (
+    datetime,
+    timedelta,
+)
 from unittest import TestCase
 
 from galaxy import model
@@ -8,23 +11,22 @@ from galaxy.managers.users import UserManager
 from galaxy.security.passwords import check_password
 from galaxy.webapps.galaxy.controllers.user import User
 
-admin_email = 'admin@admin.admin'
+admin_email = "admin@admin.admin"
 admin_users = admin_email
-default_password = '123456'
-changed_password = '654321'
-user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
+default_password = "123456"
+changed_password = "654321"
+user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
 
 
 class LoginControllerTestCase(TestCase):
-
     def setUp(self):
-        admin_users_list = [u for u in admin_users.split(',') if u]
+        admin_users_list = [u for u in admin_users.split(",") if u]
         self.trans = galaxy_mock.MockTrans(admin_users=admin_users, admin_users_list=admin_users_list)
         self.app = self.trans.app
 
         self.user_manager = self.app[UserManager]
 
-        self.admin_user = self.user_manager.create(email=admin_email, username='admin', password=default_password)
+        self.admin_user = self.user_manager.create(email=admin_email, username="admin", password=default_password)
         self.trans.set_user(self.admin_user)
         self.trans.set_history(None)
 
@@ -39,26 +41,46 @@ class LoginControllerTestCase(TestCase):
         controller = User(self.app)
         response = json.loads(controller.login(self.trans))
         self.assertEqual(response["err_msg"], "Please specify a username and password.")
-        response = json.loads(controller.login(self.trans, payload={"login": user2.email, "password": changed_password}))
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.email, "password": changed_password})
+        )
         self.assertEqual(response["err_msg"], "Invalid password.")
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": changed_password}))
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.username, "password": changed_password})
+        )
         self.assertEqual(response["err_msg"], "Invalid password.")
         user2.deleted = True
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["err_msg"], "This account has been marked deleted, contact your local Galaxy administrator to restore the account. Contact: admin@email.to.")
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.username, "password": default_password})
+        )
+        self.assertEqual(
+            response["err_msg"],
+            "This account has been marked deleted, contact your local Galaxy administrator to restore the account. Contact: admin@email.to.",
+        )
         user2.deleted = False
         user2.external = True
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["err_msg"], "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it. Contact: admin@email.to.")
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.username, "password": default_password})
+        )
+        self.assertEqual(
+            response["err_msg"],
+            "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it. Contact: admin@email.to.",
+        )
         user2.external = False
         self.trans.app.config.password_expiration_period = timedelta(days=1)
         user2.last_password_change = datetime.today() - timedelta(days=1)
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.username, "password": default_password})
+        )
         self.assertEqual(response["message"], "Your password has expired. Please reset or change it to access Galaxy.")
         self.assertEqual(response["expired_user"], self.trans.security.encode_id(user2.id))
         self.trans.app.config.password_expiration_period = timedelta(days=10)
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.username, "password": default_password})
+        )
         self.assertEqual(response["message"], "Your password will expire in 11 day(s).")
         self.trans.app.config.password_expiration_period = timedelta(days=100)
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
+        response = json.loads(
+            controller.login(self.trans, payload={"login": user2.username, "password": default_password})
+        )
         self.assertEqual(response["message"], "Success.")
diff --git a/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py b/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
index c4ea6e26fea..d7eb3ad7b90 100644
--- a/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
+++ b/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
@@ -36,7 +36,7 @@ async def _get_app():
         GX_APP = MockApp()
         GX_APP.stop = False
     app = GX_APP
-    request_id = request_context.data['X-Request-ID']
+    request_id = request_context.data["X-Request-ID"]
     app.model.set_request_id(request_id)
     try:
         yield app
@@ -58,17 +58,17 @@ async def read_main(app=Depends(get_app)):
     return {"msg": "Hello World"}
 
 
-@app.get('/internal_server_error')
+@app.get("/internal_server_error")
 def error(app=Depends(get_app)):
     assert app.model.scoped_registry.registry == {}
     app.model.session()
     assert len(app.model.scoped_registry.registry) == 1
     request_id = app.model.request_scopefunc()
     assert is_valid_uuid(request_id)
-    raise UnexpectedException('Oh noes!')
+    raise UnexpectedException("Oh noes!")
 
 
-@app.get('/sync_wait')
+@app.get("/sync_wait")
 def sync_wait(app=Depends(get_app)):
     app.model.session()
     time.sleep(0.2)
@@ -77,7 +77,7 @@ def sync_wait(app=Depends(get_app)):
     return request_id
 
 
-@app.get('/async_wait')
+@app.get("/async_wait")
 async def async_wait(app=Depends(get_app)):
     app.model.session()
     await asyncio.sleep(0.2)
@@ -118,7 +118,7 @@ async def test_request_scoped_sa_session_exception():
 async def test_request_scoped_sa_session_concurrent_requests_sync():
     add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
-        awaitables = (client.get('/sync_wait') for _ in range(10))
+        awaitables = (client.get("/sync_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
         uuids = []
         for r in result:
@@ -133,7 +133,7 @@ async def test_request_scoped_sa_session_concurrent_requests_sync():
 async def test_request_scoped_sa_session_concurrent_requests_async():
     add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
-        awaitables = (client.get('/async_wait') for _ in range(10))
+        awaitables = (client.get("/async_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
         uuids = []
         for r in result:
@@ -152,7 +152,7 @@ async def test_request_scoped_sa_session_concurrent_requests_and_background_thre
     with concurrent.futures.ThreadPoolExecutor() as pool:
         background_pool = loop.run_in_executor(pool, target)
         async with AsyncClient(app=app, base_url="http://test") as client:
-            awaitables = (client.get('/async_wait') for _ in range(10))
+            awaitables = (client.get("/async_wait") for _ in range(10))
             result = await asyncio.gather(*awaitables)
             uuids = []
             for r in result:
diff --git a/test/unit/webapps/test_routes.py b/test/unit/webapps/test_routes.py
index 7fe1485395a..6f478b8a736 100644
--- a/test/unit/webapps/test_routes.py
+++ b/test/unit/webapps/test_routes.py
@@ -7,7 +7,6 @@ from galaxy.webapps.galaxy import buildapp as galaxy_buildapp
 
 
 class TestWebapp(WebApplication):
-
     def _instantiate_controller(self, type, app):
         # Stub out all actual controllers - just want to test routes.
         return object()
@@ -37,20 +36,12 @@ def test_galaxy_routes():
     test_webapp.assert_maps(
         "/api/tools/testtoolshed.g2.bx.psu.edu/devteam/tool1",
         controller="tools",
-        id="testtoolshed.g2.bx.psu.edu/devteam/tool1"
+        id="testtoolshed.g2.bx.psu.edu/devteam/tool1",
     )
 
-    test_webapp.assert_maps(
-        "/api/datatypes/sniffers",
-        controller="datatypes",
-        action="sniffers"
-    )
+    test_webapp.assert_maps("/api/datatypes/sniffers", controller="datatypes", action="sniffers")
 
-    test_webapp.assert_maps(
-        "/api/histories/123/contents/456",
-        controller="history_contents",
-        action="show"
-    )
+    test_webapp.assert_maps("/api/histories/123/contents/456", controller="history_contents", action="show")
 
     test_webapp.assert_maps(
         "/api/histories/123/contents/456",
@@ -66,7 +57,7 @@ def test_galaxy_routes():
         method="PUT",
         controller="history_contents",
         action="update",
-        type="dataset"
+        type="dataset",
     )
 
     test_webapp.assert_maps(
@@ -74,41 +65,26 @@ def test_galaxy_routes():
         method="PUT",
         controller="history_contents",
         action="update",
-        type="dataset_collection"
+        type="dataset_collection",
     )
 
-    assert_url_is(
-        url_for("history_content", history_id="123", id="456"),
-        "/api/histories/123/contents/456"
-    )
+    assert_url_is(url_for("history_content", history_id="123", id="456"), "/api/histories/123/contents/456")
 
     assert_url_is(
         url_for("history_content_typed", history_id="123", id="456", type="dataset"),
-        "/api/histories/123/contents/datasets/456"
+        "/api/histories/123/contents/datasets/456",
     )
 
-    test_webapp.assert_maps(
-        "/api/dependency_resolvers",
-        controller="tool_dependencies",
-        action="index"
-    )
+    test_webapp.assert_maps("/api/dependency_resolvers", controller="tool_dependencies", action="index")
 
     test_webapp.assert_maps(
-        "/api/dependency_resolvers/dependency",
-        controller="tool_dependencies",
-        action="manager_dependency"
+        "/api/dependency_resolvers/dependency", controller="tool_dependencies", action="manager_dependency"
     )
 
-    test_webapp.assert_maps(
-        "/api/dependency_resolvers/0",
-        controller="tool_dependencies",
-        action="show"
-    )
+    test_webapp.assert_maps("/api/dependency_resolvers/0", controller="tool_dependencies", action="show")
 
     test_webapp.assert_maps(
-        "/api/dependency_resolvers/0/dependency",
-        controller="tool_dependencies",
-        action="resolver_dependency"
+        "/api/dependency_resolvers/0/dependency", controller="tool_dependencies", action="resolver_dependency"
     )
 
 
diff --git a/test/unit/webapps/test_send_file.py b/test/unit/webapps/test_send_file.py
index 2ee0bdd248c..45e92093251 100644
--- a/test/unit/webapps/test_send_file.py
+++ b/test/unit/webapps/test_send_file.py
@@ -11,22 +11,23 @@ from galaxy.web.framework.base import (
     send_file,
 )
 
-CONTENT = 'content'
+CONTENT = "content"
 
 
 def setup_fastAPI(fh, nginx_x_accel_redirect_base=None, apache_xsendfile=None):
-
     def wsgi_application(env, start_response):
         trans = Bunch(
             response=Response(),
-            app=Bunch(config=Bunch(nginx_x_accel_redirect_base=nginx_x_accel_redirect_base, apache_xsendfile=apache_xsendfile))
+            app=Bunch(
+                config=Bunch(nginx_x_accel_redirect_base=nginx_x_accel_redirect_base, apache_xsendfile=apache_xsendfile)
+            ),
         )
-        trans.response.headers['content-length'] = len(CONTENT)
-        trans.response.set_content_type('application/octet-stream')
+        trans.response.headers["content-length"] = len(CONTENT)
+        trans.response.set_content_type("application/octet-stream")
         return send_file(start_response, trans, fh)
 
     app = FastAPI()
-    app.mount('/test/send_file', WSGIMiddleware(wsgi_application))
+    app.mount("/test/send_file", WSGIMiddleware(wsgi_application))
     return app
 
 
@@ -40,22 +41,22 @@ def test_file_handle():
 
 
 def test_sendfile_nginx(test_file_handle):
-    app = setup_fastAPI(test_file_handle, nginx_x_accel_redirect_base='/base')
+    app = setup_fastAPI(test_file_handle, nginx_x_accel_redirect_base="/base")
     client = TestClient(app)
     response = client.get("/test/send_file")
     assert response.status_code == 200
-    assert response.headers['x-accel-redirect'] == f"/base{test_file_handle.name}"
-    assert 'content-length' not in response.headers
+    assert response.headers["x-accel-redirect"] == f"/base{test_file_handle.name}"
+    assert "content-length" not in response.headers
     assert not response.content
 
 
 def test_sendfile_apache(test_file_handle):
-    app = setup_fastAPI(test_file_handle, apache_xsendfile='/base')
+    app = setup_fastAPI(test_file_handle, apache_xsendfile="/base")
     client = TestClient(app)
     response = client.get("/test/send_file")
     assert response.status_code == 200
-    assert response.headers['X-Sendfile'] == test_file_handle.name
-    assert 'content-length' not in response.headers
+    assert response.headers["X-Sendfile"] == test_file_handle.name
+    assert "content-length" not in response.headers
     assert not response.content
 
 
@@ -64,7 +65,7 @@ def test_sendfile_in_process(test_file_handle):
     client = TestClient(app)
     response = client.get("/test/send_file")
     assert response.status_code == 200
-    assert 'X-Sendfile' not in response.headers
-    assert 'x-accel-redirect' not in response.headers
-    assert response.headers['content-length'] == str(len(CONTENT))
-    assert response.content.decode() == 'content'
+    assert "X-Sendfile" not in response.headers
+    assert "x-accel-redirect" not in response.headers
+    assert response.headers["content-length"] == str(len(CONTENT))
+    assert response.content.decode() == "content"
diff --git a/test/unit/webapps/test_tool_validation.py b/test/unit/webapps/test_tool_validation.py
index 0d4a3a9a284..02326c67e39 100644
--- a/test/unit/webapps/test_tool_validation.py
+++ b/test/unit/webapps/test_tool_validation.py
@@ -9,16 +9,17 @@ from galaxy.tools.repositories import ValidationContext
 from galaxy.util import galaxy_directory
 from tool_shed.tools.tool_validator import ToolValidator
 
-BISMARK_TAR = os.path.join(galaxy_directory(), 'lib/tool_shed/test/test_data/bismark/bismark.tar')
-BOWTIE2_INDICES = os.path.join(galaxy_directory(), 'lib/tool_shed/test/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample')
+BISMARK_TAR = os.path.join(galaxy_directory(), "lib/tool_shed/test/test_data/bismark/bismark.tar")
+BOWTIE2_INDICES = os.path.join(
+    galaxy_directory(), "lib/tool_shed/test/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample"
+)
 
 
 def test_validate_valid_tool():
     with get_tool_validator() as tv, setup_bismark() as repo_dir:
-        full_path = os.path.join(repo_dir, 'bismark_methylation_extractor.xml')
-        tool, valid, message = tv.load_tool_from_config(repository_id=None,
-                                                        full_path=full_path)
-        assert tool.name == 'Bismark'
+        full_path = os.path.join(repo_dir, "bismark_methylation_extractor.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
+        assert tool.name == "Bismark"
         assert not tool.params_with_missing_data_table_entry
         assert not tool.params_with_missing_index_file
         assert valid is True
@@ -27,37 +28,35 @@ def test_validate_valid_tool():
 
 def test_tool_validation_denies_allow_codefile():
     with get_tool_validator() as tv, setup_bismark() as repo_dir:
-        full_path = os.path.join(repo_dir, 'bismark_methylation_extractor.xml')
-        tool, valid, message = tv.load_tool_from_config(repository_id=None,
-                                                        full_path=full_path)
+        full_path = os.path.join(repo_dir, "bismark_methylation_extractor.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
         assert tool._allow_code_files is False
 
 
 def test_validate_tool_without_index():
     with get_tool_validator() as tv, setup_bismark() as repo_dir:
-        full_path = os.path.join(repo_dir, 'bismark_bowtie2_wrapper.xml')
-        tool, valid, message = tv.load_tool_from_config(repository_id=None,
-                                                        full_path=full_path)
+        full_path = os.path.join(repo_dir, "bismark_bowtie2_wrapper.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
         assert valid is True
         # tool is missing a data table
         assert tool.params_with_missing_data_table_entry
         # check input parameters, which will set up the missing data table (if present in repo_dir)
-        invalid_files_and_errors_tups = tv.check_tool_input_params(repo_dir=os.path.dirname(full_path),
-                                                                   tool_config_name=full_path,
-                                                                   tool=tool,
-                                                                   sample_files=[])
+        invalid_files_and_errors_tups = tv.check_tool_input_params(
+            repo_dir=os.path.dirname(full_path), tool_config_name=full_path, tool=tool, sample_files=[]
+        )
         # tool is invalid because loc file is not present, but data table is present now
         assert len(invalid_files_and_errors_tups) == 1
-        assert invalid_files_and_errors_tups[0][1].startswith('This file refers to a file named')
+        assert invalid_files_and_errors_tups[0][1].startswith("This file refers to a file named")
         assert not tool.params_with_missing_data_table_entry
         assert tool.params_with_missing_index_file
         # copy a loc file
         shutil.copy(BOWTIE2_INDICES, repo_dir)
-        tool, valid, message, sample_files = tv.handle_sample_files_and_load_tool_from_disk(repo_dir, None, full_path, repo_dir)
-        invalid_files_and_errors_tups = tv.check_tool_input_params(repo_dir=repo_dir,
-                                                                   tool_config_name=full_path,
-                                                                   tool=tool,
-                                                                   sample_files=sample_files)
+        tool, valid, message, sample_files = tv.handle_sample_files_and_load_tool_from_disk(
+            repo_dir, None, full_path, repo_dir
+        )
+        invalid_files_and_errors_tups = tv.check_tool_input_params(
+            repo_dir=repo_dir, tool_config_name=full_path, tool=tool, sample_files=sample_files
+        )
         # no parameters should be missing
         assert len(invalid_files_and_errors_tups) == 0
         assert not tool.params_with_missing_data_table_entry
diff --git a/test/unit/webapps/test_webapp_base.py b/test/unit/webapps/test_webapp_base.py
index 05f93634be9..66679907016 100644
--- a/test/unit/webapps/test_webapp_base.py
+++ b/test/unit/webapps/test_webapp_base.py
@@ -24,41 +24,36 @@ class CORSParsingMockConfig(galaxy_mock.MockAppConfig):
 
     @staticmethod
     def _parse_allowed_origin_hostnames(kwargs):
-        hostnames = kwargs.get('allowed_origin_hostnames')
+        hostnames = kwargs.get("allowed_origin_hostnames")
         return galaxy.config.Configuration._parse_allowed_origin_hostnames(hostnames)
 
 
 class GalaxyWebTransaction_Headers_TestCase(unittest.TestCase):
-
     def _new_trans(self, allowed_origin_hostnames=None):
         app = galaxy_mock.MockApp()
-        app.config = CORSParsingMockConfig(
-            allowed_origin_hostnames=allowed_origin_hostnames
-        )
+        app.config = CORSParsingMockConfig(allowed_origin_hostnames=allowed_origin_hostnames)
         webapp = galaxy_mock.MockWebapp(app.security)
         environ = galaxy_mock.buildMockEnviron()
         trans = StubGalaxyWebTransaction(environ, app, webapp)
         return trans
 
     def assert_cors_header_equals(self, headers, should_be):
-        self.assertEqual(headers.get('access-control-allow-origin', None), should_be)
+        self.assertEqual(headers.get("access-control-allow-origin", None), should_be)
 
     def assert_cors_header_missing(self, headers):
-        self.assertFalse('access-control-allow-origin' in headers)
+        self.assertFalse("access-control-allow-origin" in headers)
 
     def test_parse_allowed_origin_hostnames(self):
         """Should return a list of (possibly) mixed strings and regexps"""
         config = CORSParsingMockConfig()
 
         # falsy listify value should return None
-        self.assertEqual(config._parse_allowed_origin_hostnames({
-            "allowed_origin_hostnames": ""
-        }), None)
+        self.assertEqual(config._parse_allowed_origin_hostnames({"allowed_origin_hostnames": ""}), None)
 
         # should parse regex if using fwd slashes, string otherwise
-        hostnames = config._parse_allowed_origin_hostnames({
-            "allowed_origin_hostnames": r"/host\d{2}/,geocities.com,miskatonic.edu"
-        })
+        hostnames = config._parse_allowed_origin_hostnames(
+            {"allowed_origin_hostnames": r"/host\d{2}/,geocities.com,miskatonic.edu"}
+        )
         self.assertTrue(isinstance(hostnames[0], re.Pattern))
         self.assertTrue(isinstance(hostnames[1], str))
         self.assertTrue(isinstance(hostnames[2], str))
@@ -68,50 +63,48 @@ class GalaxyWebTransaction_Headers_TestCase(unittest.TestCase):
         trans = self._new_trans(allowed_origin_hostnames=None)
         self.assertTrue(isinstance(trans, Webapp.GalaxyWebTransaction))
 
-        trans.request.headers['Origin'] = 'http://lisaskelprecipes.pinterest.com?id=kelpcake'
+        trans.request.headers["Origin"] = "http://lisaskelprecipes.pinterest.com?id=kelpcake"
         trans.set_cors_headers()
         self.assert_cors_header_missing(trans.response.headers)
 
     def test_set_cors_headers(self):
         """Origin should be echo'd when it matches an allowed hostname"""
         # an asterisk is a special 'allow all' string
-        trans = self._new_trans(allowed_origin_hostnames='*,beep.com')
-        trans.request.headers['Origin'] = 'http://xxdarkhackerxx.disney.com'
+        trans = self._new_trans(allowed_origin_hostnames="*,beep.com")
+        trans.request.headers["Origin"] = "http://xxdarkhackerxx.disney.com"
         trans.set_cors_headers()
-        self.assert_cors_header_equals(trans.response.headers, 'http://xxdarkhackerxx.disney.com')
+        self.assert_cors_header_equals(trans.response.headers, "http://xxdarkhackerxx.disney.com")
 
         # subdomains should pass
-        trans = self._new_trans(allowed_origin_hostnames=r'something.com,/^[\w\.]*beep\.com/')
-        trans.request.headers['Origin'] = 'http://boop.beep.com'
+        trans = self._new_trans(allowed_origin_hostnames=r"something.com,/^[\w\.]*beep\.com/")
+        trans.request.headers["Origin"] = "http://boop.beep.com"
         trans.set_cors_headers()
-        self.assert_cors_header_equals(trans.response.headers, 'http://boop.beep.com')
+        self.assert_cors_header_equals(trans.response.headers, "http://boop.beep.com")
 
         # ports should work
-        trans = self._new_trans(allowed_origin_hostnames=r'somethingelse.com,/^[\w\.]*beep\.com/')
-        trans.request.headers['Origin'] = 'http://boop.beep.com:8080'
+        trans = self._new_trans(allowed_origin_hostnames=r"somethingelse.com,/^[\w\.]*beep\.com/")
+        trans.request.headers["Origin"] = "http://boop.beep.com:8080"
         trans.set_cors_headers()
-        self.assert_cors_header_equals(trans.response.headers, 'http://boop.beep.com:8080')
+        self.assert_cors_header_equals(trans.response.headers, "http://boop.beep.com:8080")
 
         # localhost should work
-        trans = self._new_trans(allowed_origin_hostnames='/localhost/')
-        trans.request.headers['Origin'] = 'http://localhost:8080'
+        trans = self._new_trans(allowed_origin_hostnames="/localhost/")
+        trans.request.headers["Origin"] = "http://localhost:8080"
         trans.set_cors_headers()
-        self.assert_cors_header_equals(trans.response.headers, 'http://localhost:8080')
+        self.assert_cors_header_equals(trans.response.headers, "http://localhost:8080")
 
         # spoofing shouldn't be easy
         trans.response.headers = {}
-        trans.request.headers['Origin'] = 'http://localhost.badstuff.tv'
+        trans.request.headers["Origin"] = "http://localhost.badstuff.tv"
         trans.set_cors_headers()
         self.assert_cors_header_missing(trans.response.headers)
 
         # unicode should work
-        trans = self._new_trans(allowed_origin_hostnames=r'/öbb\.at/')
-        trans.request.headers['Origin'] = 'http://öbb.at'
+        trans = self._new_trans(allowed_origin_hostnames=r"/öbb\.at/")
+        trans.request.headers["Origin"] = "http://öbb.at"
         trans.set_cors_headers()
-        self.assertEqual(
-            trans.response.headers['access-control-allow-origin'], 'http://öbb.at'
-        )
+        self.assertEqual(trans.response.headers["access-control-allow-origin"], "http://öbb.at")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()
diff --git a/test/unit/workflows/test_extract_summary.py b/test/unit/workflows/test_extract_summary.py
index 0f0adb04182..ec096f89690 100644
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -7,7 +7,6 @@ UNDEFINED_JOB = object()
 
 
 class TestWorkflowExtractSummary(unittest.TestCase):
-
     def setUp(self):
         self.history = MockHistory()
         self.trans = MockTrans(self.history)
@@ -30,8 +29,8 @@ class TestWorkflowExtractSummary(unittest.TestCase):
         job_dict, warnings = extract.summarize(trans=self.trans)
         assert len(job_dict) == 2
         assert not warnings
-        self.assertEqual(job_dict[hda1.job], [('out1', hda1), ('out2', hda2)])
-        self.assertEqual(job_dict[hda3.job], [('out3', hda3)])
+        self.assertEqual(job_dict[hda1.job], [("out1", hda1), ("out2", hda2)])
+        self.assertEqual(job_dict[hda3.job], [("out3", hda3)])
 
     def test_finds_original_job_if_copied(self):
         hda = MockHda()
@@ -43,11 +42,10 @@ class TestWorkflowExtractSummary(unittest.TestCase):
         job_dict, warnings = extract.summarize(trans=self.trans)
         assert not warnings
         assert len(job_dict) == 1
-        self.assertEqual(job_dict[hda.job], [('out1', derived_hda_2)])
+        self.assertEqual(job_dict[hda.job], [("out1", derived_hda_2)])
 
     def test_fake_job_hda(self):
-        """ Fakes job if creating_job_associations is empty.
-        """
+        """Fakes job if creating_job_associations is empty."""
         hda = MockHda(job=UNDEFINED_JOB)
         self.history.active_datasets.append(hda)
         job_dict, warnings = extract.summarize(trans=self.trans)
@@ -101,7 +99,7 @@ class TestWorkflowExtractSummary(unittest.TestCase):
         assert job is creating_job
 
     def test_warns_and_skips_datasets_if_not_finished(self):
-        hda = MockHda(state='queued')
+        hda = MockHda(state="queued")
         self.history.active_datasets.append(hda)
         job_dict, warnings = extract.summarize(trans=self.trans)
         assert warnings
@@ -117,7 +115,6 @@ class MockJobToOutputDatasetAssociation:
 
 
 class MockHistory:
-
     def __init__(self):
         self.active_datasets = []
 
@@ -127,7 +124,6 @@ class MockHistory:
 
 
 class MockTrans:
-
     def __init__(self, history):
         self.history = history
 
@@ -136,8 +132,7 @@ class MockTrans:
 
 
 class MockHda:
-
-    def __init__(self, state='ok', output_name='out1', job=None):
+    def __init__(self, state="ok", output_name="out1", job=None):
         self.hid = 1
         self.id = 123
         self.state = state
@@ -156,7 +151,6 @@ class MockHda:
 
 
 class MockHdca:
-
     def __init__(self, implicit_output_name=None, job=None, hid=1):
         self.id = 124
         self.copied_from_history_dataset_collection_association = None
diff --git a/test/unit/workflows/test_modules.py b/test/unit/workflows/test_modules.py
index d926262b216..77ad7802146 100644
--- a/test/unit/workflows/test_modules.py
+++ b/test/unit/workflows/test_modules.py
@@ -16,7 +16,10 @@ from galaxy import model
 from galaxy.managers.workflows import WorkflowContentsManager
 from galaxy.util import bunch
 from galaxy.workflow import modules
-from .workflow_support import MockTrans, yaml_to_model
+from .workflow_support import (
+    MockTrans,
+    yaml_to_model,
+)
 
 
 def test_input_has_no_errors():
@@ -63,7 +66,9 @@ def test_data_input_compute_runtime_state_args():
     hda = model.HistoryDatasetAssociation()
     with mock.patch("galaxy.workflow.modules.check_param") as check_method:
         check_method.return_value = (hda, None)
-        state, errors = module.compute_runtime_state(module.trans, module.test_step, {"input": 4, "tool_state": tool_state})
+        state, errors = module.compute_runtime_state(
+            module.trans, module.test_step, {"input": 4, "tool_state": tool_state}
+        )
     assert not errors
     assert "input" in state.inputs
     assert state.inputs["input"] is hda
@@ -81,16 +86,20 @@ def test_data_input_connections():
 
 def test_data_collection_input_default_state():
     trans = MockTrans()
-    module = modules.module_factory.from_dict(trans, {"type": "data_collection_input", "label": "Input Dataset Collection"})
+    module = modules.module_factory.from_dict(
+        trans, {"type": "data_collection_input", "label": "Input Dataset Collection"}
+    )
     __assert_has_runtime_input(module, label="Input Dataset Collection", collection_type="list")
 
 
 def test_data_input_collection_modified_state():
-    module = __from_state({
-        "type": "data_collection_input",
-        "label": "Cool Input Collection",
-        "tool_state": json.dumps({"collection_type": "list:paired"}),
-    })
+    module = __from_state(
+        {
+            "type": "data_collection_input",
+            "label": "Cool Input Collection",
+            "tool_state": json.dumps({"collection_type": "list:paired"}),
+        }
+    )
     __assert_has_runtime_input(module, label="Cool Input Collection", collection_type="list:paired")
 
 
@@ -106,12 +115,7 @@ def test_data_input_collection_step_modified_state():
 
 
 def test_data_collection_input_connections():
-    module = __from_step(
-        type="data_collection_input",
-        tool_inputs={
-            "collection_type": "list:paired"
-        }
-    )
+    module = __from_step(type="data_collection_input", tool_inputs={"collection_type": "list:paired"})
     assert len(module.get_data_inputs()) == 0
     outputs = module.get_data_outputs()
     assert len(outputs) == 1
@@ -126,7 +130,7 @@ def test_data_collection_input_config_form():
         type="data_collection_input",
         tool_inputs={
             "collection_type": "list:paired",
-        }
+        },
     )
     result = module.get_config_form()
     assert result["inputs"][0]["value"], "list:paired"
@@ -232,7 +236,7 @@ def test_subworkflow_new_inputs():
 def test_subworkflow_new_inputs_collection_type():
     subworkflow_module = __new_subworkflow_module(COLLECTION_TYPE_WORKLFOW_YAML)
     inputs = subworkflow_module.get_data_inputs()
-    assert inputs[0]['collection_type'] == 'list:list'
+    assert inputs[0]["collection_type"] == "list:list"
 
 
 def test_subworkflow_new_outputs():
@@ -262,12 +266,12 @@ def _construct_steps_for_map_over():
     # list(itertools.product(data_input, step_input_definition, step_output_definition, [None])),
     # with the last item filled in manually
     test_case_args: List[Tuple[str, Union[str, List[str]], str, Optional[str]]] = [
-        ('dataset', 'dataset', 'dataset', None),
-        ('dataset', 'dataset', 'list', 'list'),
-        ('dataset', 'dataset', 'list:list', 'list:list'),
-        ('dataset', 'dataset_multiple', 'dataset', None),
-        ('dataset', 'dataset_multiple', 'list', 'list'),
-        ('dataset', 'dataset_multiple', 'list:list', 'list:list'),
+        ("dataset", "dataset", "dataset", None),
+        ("dataset", "dataset", "list", "list"),
+        ("dataset", "dataset", "list:list", "list:list"),
+        ("dataset", "dataset_multiple", "dataset", None),
+        ("dataset", "dataset_multiple", "list", "list"),
+        ("dataset", "dataset_multiple", "list:list", "list:list"),
         # Can't feed a dataset into a list or pair input
         # ('dataset', 'list', 'dataset', None),
         # ('dataset', 'list', 'list', None),
@@ -275,21 +279,21 @@ def _construct_steps_for_map_over():
         # ('dataset', ['list', 'pair'], 'dataset', None),
         # ('dataset', ['list', 'pair'], 'list', None),
         # ('dataset', ['list', 'pair'], 'list:list', None),
-        ('list', 'dataset', 'dataset', 'list'),
-        ('list', 'dataset', 'list', 'list:list'),
-        ('list', 'dataset', 'list:list', 'list:list:list'),
-        ('list', 'dataset_multiple', 'dataset', None),
-        ('list', 'dataset_multiple', 'list', 'list'),
-        ('list', 'dataset_multiple', 'list:list', 'list:list'),
-        ('list', 'list', 'dataset', None),
-        ('list', 'list', 'list', 'list'),
-        ('list', 'list', 'list:list', 'list:list'),
-        ('list', ['list', 'pair'], 'dataset', None),
-        ('list', ['list', 'pair'], 'list', 'list'),
-        ('list', ['list', 'pair'], 'list:list', 'list:list'),
-        ('list:pair', 'dataset', 'dataset', 'list:pair'),
-        ('list:pair', 'dataset', 'list', 'list:pair:list'),
-        ('list:pair', 'dataset', 'list:list', 'list:pair:list:list'),
+        ("list", "dataset", "dataset", "list"),
+        ("list", "dataset", "list", "list:list"),
+        ("list", "dataset", "list:list", "list:list:list"),
+        ("list", "dataset_multiple", "dataset", None),
+        ("list", "dataset_multiple", "list", "list"),
+        ("list", "dataset_multiple", "list:list", "list:list"),
+        ("list", "list", "dataset", None),
+        ("list", "list", "list", "list"),
+        ("list", "list", "list:list", "list:list"),
+        ("list", ["list", "pair"], "dataset", None),
+        ("list", ["list", "pair"], "list", "list"),
+        ("list", ["list", "pair"], "list:list", "list:list"),
+        ("list:pair", "dataset", "dataset", "list:pair"),
+        ("list:pair", "dataset", "list", "list:pair:list"),
+        ("list:pair", "dataset", "list:list", "list:pair:list:list"),
         # Pair into multiple="True" is not allowed
         # ('list:pair', 'dataset_multiple', 'dataset', None),
         # ('list:pair', 'dataset_multiple', 'list', None),
@@ -298,27 +302,27 @@ def _construct_steps_for_map_over():
         # ('list:pair', 'list', 'dataset', None),
         # ('list:pair', 'list', 'list', None),
         # ('list:pair', 'list', 'list:list', None),
-        ('list:pair', ['list', 'pair'], 'dataset', 'list'),
-        ('list:pair', ['list', 'pair'], 'list', 'list:list'),
-        ('list:pair', ['list', 'pair'], 'list:list', 'list:list:list'),
-        ('list:list', 'dataset', 'dataset', 'list:list'),
-        ('list:list', 'dataset', 'list', 'list:list:list'),
-        ('list:list', 'dataset', 'list:list', 'list:list:list:list'),
-        ('list:list', 'dataset_multiple', 'dataset', 'list'),
-        ('list:list', 'dataset_multiple', 'list', 'list:list'),
-        ('list:list', 'dataset_multiple', 'list:list', 'list:list:list'),
-        ('list:list', 'list', 'dataset', 'list'),
-        ('list:list', 'list', 'list', 'list:list'),
-        ('list:list', 'list', 'list:list', 'list:list:list'),
-        ('list:list', ['list', 'pair'], 'dataset', 'list'),
-        ('list:list', ['list', 'pair'], 'list', 'list:list'),
-        ('list:list', ['list', 'pair'], 'list:list', 'list:list:list')
+        ("list:pair", ["list", "pair"], "dataset", "list"),
+        ("list:pair", ["list", "pair"], "list", "list:list"),
+        ("list:pair", ["list", "pair"], "list:list", "list:list:list"),
+        ("list:list", "dataset", "dataset", "list:list"),
+        ("list:list", "dataset", "list", "list:list:list"),
+        ("list:list", "dataset", "list:list", "list:list:list:list"),
+        ("list:list", "dataset_multiple", "dataset", "list"),
+        ("list:list", "dataset_multiple", "list", "list:list"),
+        ("list:list", "dataset_multiple", "list:list", "list:list:list"),
+        ("list:list", "list", "dataset", "list"),
+        ("list:list", "list", "list", "list:list"),
+        ("list:list", "list", "list:list", "list:list:list"),
+        ("list:list", ["list", "pair"], "dataset", "list"),
+        ("list:list", ["list", "pair"], "list", "list:list"),
+        ("list:list", ["list", "pair"], "list:list", "list:list:list"),
     ]
     test_cases = []
     for (data_input, step_input_def, step_output_def, expected_collection_type) in test_case_args:
         steps: Dict[int, Dict[str, Any]] = {
             0: _input_step(collection_type=data_input),
-            1: _output_step(step_input_def=step_input_def, step_output_def=step_output_def)
+            1: _output_step(step_input_def=step_input_def, step_output_def=step_output_def),
         }
         test_cases.append(
             test_case(
@@ -333,67 +337,69 @@ def _construct_steps_for_map_over():
 
 
 def _input_step(collection_type) -> Dict[str, Any]:
-    output: Dict[str, Any] = {'name': 'output', 'extensions': ['input_collection']}
-    if collection_type != 'dataset':
-        output['collection'] = True
-        output['collection_type'] = collection_type
-    step_type = 'data_colletion_input' if collection_type == 'dataset' else 'data_input'
+    output: Dict[str, Any] = {"name": "output", "extensions": ["input_collection"]}
+    if collection_type != "dataset":
+        output["collection"] = True
+        output["collection_type"] = collection_type
+    step_type = "data_colletion_input" if collection_type == "dataset" else "data_input"
     return {
-        'id': 0,
-        'type': step_type,
-        'inputs': [],
-        'outputs': [output],
-        'workflow_outputs': [],
-        'input_connections': {},
+        "id": 0,
+        "type": step_type,
+        "inputs": [],
+        "outputs": [output],
+        "workflow_outputs": [],
+        "input_connections": {},
     }
 
 
 def _output_step(step_input_def, step_output_def) -> Dict[str, Any]:
     multiple = False
-    if step_input_def in ['dataset', 'dataset_multiple']:
-        input_type = 'dataset'
+    if step_input_def in ["dataset", "dataset_multiple"]:
+        input_type = "dataset"
         collection_types = None
-        if step_input_def == 'dataset_multiple':
+        if step_input_def == "dataset_multiple":
             multiple = True
     else:
-        input_type = 'dataset_collection'
+        input_type = "dataset_collection"
         collection_types = step_input_def if isinstance(step_input_def, list) else [step_input_def]
-    output: Dict[str, Any] = {'name': 'output', 'extensions': ['data']}
-    if step_output_def != 'dataset':
-        output['collection'] = True
-        output['collection_type'] = step_output_def
-    input_connection_input: Any = [{'id': 0, 'output_name': 'output', 'input_type': input_type}]
-    if step_input_def == 'dataset':
+    output: Dict[str, Any] = {"name": "output", "extensions": ["data"]}
+    if step_output_def != "dataset":
+        output["collection"] = True
+        output["collection_type"] = step_output_def
+    input_connection_input: Any = [{"id": 0, "output_name": "output", "input_type": input_type}]
+    if step_input_def == "dataset":
         # For whatever reason multiple = False inputs are not wrapped in a list.
         input_connection_input = input_connection_input[0]
     return {
-        'id': 1,
-        'type': 'tool',
-        'inputs': [
-            {'name': 'input',
-             'multiple': multiple,
-             'input_type': input_type,
-             'collection_types': collection_types,
-             'extensions': ['data']
-             }
+        "id": 1,
+        "type": "tool",
+        "inputs": [
+            {
+                "name": "input",
+                "multiple": multiple,
+                "input_type": input_type,
+                "collection_types": collection_types,
+                "extensions": ["data"],
+            }
         ],
-        'input_connections': {'input': input_connection_input},
-        'outputs': [output],
-        'workflow_outputs': [{'output_name': 'output'}]
+        "input_connections": {"input": input_connection_input},
+        "outputs": [output],
+        "workflow_outputs": [{"output_name": "output"}],
     }
 
 
-@pytest.mark.parametrize('test_case', _construct_steps_for_map_over())
+@pytest.mark.parametrize("test_case", _construct_steps_for_map_over())
 def test_subworkflow_map_over_type(test_case):
     trans = MockTrans()
     new_steps = WorkflowContentsManager(app=trans.app)._resolve_collection_type(test_case.steps)
-    assert new_steps[1]['outputs'][0].get('collection_type') == test_case.expected_collection_type, \
-        "Expected collection_type '{}' for a '{}' input module, a '{}' input and a '{}' output, got collection_type '{}' instead".format(
-            test_case.expected_collection_type,
-            test_case.data_input,
-            test_case.step_input_def,
-            test_case.step_output_def,
-            new_steps[1]['outputs'][0].get('collection_type'),
+    assert (
+        new_steps[1]["outputs"][0].get("collection_type") == test_case.expected_collection_type
+    ), "Expected collection_type '{}' for a '{}' input module, a '{}' input and a '{}' output, got collection_type '{}' instead".format(
+        test_case.expected_collection_type,
+        test_case.data_input,
+        test_case.step_input_def,
+        test_case.step_output_def,
+        new_steps[1]["outputs"][0].get("collection_type"),
     )
 
 
@@ -432,9 +438,7 @@ def __from_step(**kwds):
         del kwds["trans"]
     else:
         trans = MockTrans()
-    step = __step(
-        **kwds
-    )
+    step = __step(**kwds)
     injector = modules.WorkflowModuleInjector(trans)
     injector.inject(step, exact_tools=False)
     module = step.module
@@ -461,13 +465,17 @@ def __mock_tool(
         version=version,
         name=id,
         inputs={},
-        outputs={'out_file1': bunch.Bunch(collection=None,
-                                          format='input',
-                                          format_source=None,
-                                          change_format=[],
-                                          filters=[],
-                                          label=None,
-                                          output_type='data')},
+        outputs={
+            "out_file1": bunch.Bunch(
+                collection=None,
+                format="input",
+                format_source=None,
+                change_format=[],
+                filters=[],
+                label=None,
+                output_type="data",
+            )
+        },
         params_from_strings=mock.Mock(),
         check_and_update_param_values=mock.Mock(),
         to_json=_to_json,
diff --git a/test/unit/workflows/test_refactor_models.py b/test/unit/workflows/test_refactor_models.py
index 230e9aa2465..cae3db742c9 100644
--- a/test/unit/workflows/test_refactor_models.py
+++ b/test/unit/workflows/test_refactor_models.py
@@ -11,7 +11,11 @@ def test_root_list():
             {"action_type": "update_step_label", "label": "new_label", "step": {"order_index": 5}},
             {"action_type": "update_step_label", "label": "new_label", "step": {"label": "cool_label"}},
             {"action_type": "connect", "input": {"input_name": "foobar", "order_index": 6}, "output": {"label": "cow"}},
-            {"action_type": "disconnect", "input": {"input_name": "foobar2", "label": "foolabel"}, "output": {"order_index": 7, "output_name": "o_name"}},
+            {
+                "action_type": "disconnect",
+                "input": {"input_name": "foobar2", "label": "foolabel"},
+                "output": {"order_index": 7, "output_name": "o_name"},
+            },
             {"action_type": "add_input", "type": "data"},
             {"action_type": "add_input", "type": "integer", "optional": True, "default": 5},
             {"action_type": "extract_input", "input": {"order_index": 5, "input_name": "foobar"}},
@@ -63,9 +67,7 @@ def test_root_list():
 
 
 def test_executions():
-    ar = RefactorActions(actions=[
-        {"action_type": "extract_untyped_parameter", "name": "foo"}
-    ])
+    ar = RefactorActions(actions=[{"action_type": "extract_untyped_parameter", "name": "foo"}])
     execution = RefactorActionExecution(action={"action_type": "extract_untyped_parameter", "name": "foo"}, messages=[])
     assert isinstance(execution.messages, (list,))
     execution = RefactorActionExecution(action=ar.actions[0].dict(), messages=[])
diff --git a/test/unit/workflows/test_render.py b/test/unit/workflows/test_render.py
index 04ee10c791c..0eaed671afa 100644
--- a/test/unit/workflows/test_render.py
+++ b/test/unit/workflows/test_render.py
@@ -53,16 +53,10 @@ def test_render():
         [{"name": "di1"}],
     )
     workflow_canvas.populate_data_for_step(
-        step_2,
-        "cat wrapper",
-        [{"name": "input1", "label": "i1"}],
-        [{"name": "out1"}]
+        step_2, "cat wrapper", [{"name": "input1", "label": "i1"}], [{"name": "out1"}]
     )
     workflow_canvas.populate_data_for_step(
-        step_3,
-        "cat wrapper",
-        [{"name": "input1", "label": "i1"}],
-        [{"name": "out1"}]
+        step_3, "cat wrapper", [{"name": "input1", "label": "i1"}], [{"name": "out1"}]
     )
     workflow_canvas.add_steps()
     workflow_canvas.finish()
diff --git a/test/unit/workflows/test_run_parameters.py b/test/unit/workflows/test_run_parameters.py
index 93eea6c936b..4fb5a22ca64 100644
--- a/test/unit/workflows/test_run_parameters.py
+++ b/test/unit/workflows/test_run_parameters.py
@@ -1,7 +1,7 @@
 from galaxy import model
 from galaxy.workflow.run_request import (
     _normalize_inputs,
-    _normalize_step_parameters
+    _normalize_step_parameters,
 )
 from .workflow_support import MockTrans
 
@@ -14,62 +14,51 @@ def test_normalize_parameters_empty():
 
 
 def test_normalize_parameters_by_tool():
-    normalized_params = __normalize_parameters_against_fixture({
-        'cat1': {'foo': 'bar'}
-    })
+    normalized_params = __normalize_parameters_against_fixture({"cat1": {"foo": "bar"}})
     # Tool specified parameters are expanded out.
-    assert normalized_params[STEP_ID_OFFSET + 3] == {'foo': 'bar'}
-    assert normalized_params[STEP_ID_OFFSET + 4] == {'foo': 'bar'}
+    assert normalized_params[STEP_ID_OFFSET + 3] == {"foo": "bar"}
+    assert normalized_params[STEP_ID_OFFSET + 4] == {"foo": "bar"}
     assert len(normalized_params.keys()) == 2
 
 
 def test_step_parameters():
-    normalized_params = __normalize_parameters_against_fixture({
-        str(STEP_ID_OFFSET + 1): {'foo': 'bar'}
-    })
-    assert normalized_params[STEP_ID_OFFSET + 1] == {'foo': 'bar'}
+    normalized_params = __normalize_parameters_against_fixture({str(STEP_ID_OFFSET + 1): {"foo": "bar"}})
+    assert normalized_params[STEP_ID_OFFSET + 1] == {"foo": "bar"}
     assert len(normalized_params.keys()) == 1
 
 
 def test_step_parameters_legacy():
-    normalized_params = __normalize_parameters_against_fixture({
-        str(STEP_ID_OFFSET + 1): {'param': 'foo', 'value': 'bar'}
-    })
-    assert normalized_params[STEP_ID_OFFSET + 1] == {'foo': 'bar'}, normalized_params
+    normalized_params = __normalize_parameters_against_fixture(
+        {str(STEP_ID_OFFSET + 1): {"param": "foo", "value": "bar"}}
+    )
+    assert normalized_params[STEP_ID_OFFSET + 1] == {"foo": "bar"}, normalized_params
     assert len(normalized_params.keys()) == 1
 
 
 def test_inputs_by_step_id():
     input1 = __new_input()
     input2 = __new_input()
-    normalized_inputs = __normalize_inputs_against_fixture({
-        str(STEP_ID_OFFSET + 1): input1,
-        str(STEP_ID_OFFSET + 2): input2
-    }, inputs_by="step_id")
-    assert normalized_inputs[STEP_ID_OFFSET + 1]['content'] == input1['content']
-    assert normalized_inputs[STEP_ID_OFFSET + 2]['content'] == input2['content']
+    normalized_inputs = __normalize_inputs_against_fixture(
+        {str(STEP_ID_OFFSET + 1): input1, str(STEP_ID_OFFSET + 2): input2}, inputs_by="step_id"
+    )
+    assert normalized_inputs[STEP_ID_OFFSET + 1]["content"] == input1["content"]
+    assert normalized_inputs[STEP_ID_OFFSET + 2]["content"] == input2["content"]
 
 
 def test_inputs_by_step_index():
     input1 = __new_input()
     input2 = __new_input()
-    normalized_inputs = __normalize_inputs_against_fixture({
-        str(0): input1,
-        str(1): input2
-    }, inputs_by="step_index")
-    assert normalized_inputs[STEP_ID_OFFSET + 1]['content'] == input1['content']
-    assert normalized_inputs[STEP_ID_OFFSET + 2]['content'] == input2['content']
+    normalized_inputs = __normalize_inputs_against_fixture({str(0): input1, str(1): input2}, inputs_by="step_index")
+    assert normalized_inputs[STEP_ID_OFFSET + 1]["content"] == input1["content"]
+    assert normalized_inputs[STEP_ID_OFFSET + 2]["content"] == input2["content"]
 
 
 def test_inputs_by_name():
     input1 = __new_input()
     input2 = __new_input()
-    normalized_inputs = __normalize_inputs_against_fixture({
-        "input1": input1,
-        "input2": input2
-    }, inputs_by="name")
-    assert normalized_inputs[STEP_ID_OFFSET + 1]['content'] == input1['content']
-    assert normalized_inputs[STEP_ID_OFFSET + 2]['content'] == input2['content']
+    normalized_inputs = __normalize_inputs_against_fixture({"input1": input1, "input2": input2}, inputs_by="name")
+    assert normalized_inputs[STEP_ID_OFFSET + 1]["content"] == input1["content"]
+    assert normalized_inputs[STEP_ID_OFFSET + 2]["content"] == input2["content"]
 
 
 def __normalize_parameters_against_fixture(params):
@@ -99,10 +88,7 @@ def __new_input():
 
 
 def __workflow_fixure(trans):
-    user = model.User(
-        email="testworkflow_params@bx.psu.edu",
-        password="pass"
-    )
+    user = model.User(email="testworkflow_params@bx.psu.edu", password="pass")
     stored_workflow = model.StoredWorkflow()
     stored_workflow.user = user
     workflow = model.Workflow()
@@ -118,16 +104,8 @@ def __workflow_fixure(trans):
         workflow,
     )
 
-    add_step(
-        type="data_input",
-        order_index=0,
-        tool_inputs={"name": "input1"}
-    )
-    add_step(
-        type="data_input",
-        order_index=1,
-        tool_inputs={"name": "input2"}
-    )
+    add_step(type="data_input", order_index=0, tool_inputs={"name": "input1"})
+    add_step(type="data_input", order_index=1, tool_inputs={"name": "input2"})
     add_step(
         type="tool",
         tool_id="cat1",
diff --git a/test/unit/workflows/test_trs_proxy.py b/test/unit/workflows/test_trs_proxy.py
index 0210ac5c562..844b8599ef1 100644
--- a/test/unit/workflows/test_trs_proxy.py
+++ b/test/unit/workflows/test_trs_proxy.py
@@ -13,15 +13,14 @@ from galaxy.workflow.trs_proxy import (
 # search test is very brittle (depends on production values) and is very slow.
 # still good to know search is working though - even if manually
 search_test = pytest.mark.skipif(
-    not environ.get('GALAXY_TEST_INCLUDE_DOCKSTORE_SEARCH'),
-    reason="GALAXY_TEST_INCLUDE_DOCKSTORE_SEARCH not set"
+    not environ.get("GALAXY_TEST_INCLUDE_DOCKSTORE_SEARCH"), reason="GALAXY_TEST_INCLUDE_DOCKSTORE_SEARCH not set"
 )
 
 
 def test_proxy():
     proxy = TrsProxy()
 
-    assert 'dockstore' == proxy.get_servers()[0]["id"]
+    assert "dockstore" == proxy.get_servers()[0]["id"]
 
     tool_id = "#workflow/github.com/jmchilton/galaxy-workflow-dockstore-example-1/mycoolworkflow"
     tool = proxy.get_tool("dockstore", tool_id)
diff --git a/test/unit/workflows/test_workflow_markdown.py b/test/unit/workflows/test_workflow_markdown.py
index 262b78650c5..74ce3576aea 100644
--- a/test/unit/workflows/test_workflow_markdown.py
+++ b/test/unit/workflows/test_workflow_markdown.py
@@ -1,7 +1,13 @@
 from galaxy import model
-from galaxy.managers.markdown_util import resolve_invocation_markdown, validate_galaxy_markdown
+from galaxy.managers.markdown_util import (
+    resolve_invocation_markdown,
+    validate_galaxy_markdown,
+)
 from .test_workflow_progress import TEST_WORKFLOW_YAML
-from .workflow_support import MockTrans, yaml_to_model
+from .workflow_support import (
+    MockTrans,
+    yaml_to_model,
+)
 
 
 def test_workflow_section_expansion():
diff --git a/test/unit/workflows/test_workflow_progress.py b/test/unit/workflows/test_workflow_progress.py
index 6fafabac742..3b173c886cf 100644
--- a/test/unit/workflows/test_workflow_progress.py
+++ b/test/unit/workflows/test_workflow_progress.py
@@ -2,7 +2,10 @@ import unittest
 
 from galaxy import model
 from galaxy.workflow.run import WorkflowProgress
-from .workflow_support import MockApp, yaml_to_model
+from .workflow_support import (
+    MockApp,
+    yaml_to_model,
+)
 
 TEST_WORKFLOW_YAML = """
 steps:
@@ -62,7 +65,6 @@ UNSCHEDULED_STEP = object()
 
 
 class WorkflowProgressTestCase(unittest.TestCase):
-
     def setUp(self):
         self.app = MockApp()
         self.inputs_by_step_id = {}
@@ -74,9 +76,7 @@ class WorkflowProgressTestCase(unittest.TestCase):
         self.invocation.workflow = workflow
 
     def _new_workflow_progress(self):
-        return WorkflowProgress(
-            self.invocation, self.inputs_by_step_id, MockModuleInjector(self.progress), {}
-        )
+        return WorkflowProgress(self.invocation, self.inputs_by_step_id, MockModuleInjector(self.progress), {})
 
     def _set_previous_progress(self, outputs):
         for i, (step_id, step_value) in enumerate(outputs):
@@ -85,7 +85,7 @@ class WorkflowProgressTestCase(unittest.TestCase):
 
                 workflow_invocation_step = model.WorkflowInvocationStep()
                 workflow_invocation_step.workflow_step_id = step_id
-                workflow_invocation_step.state = 'scheduled'
+                workflow_invocation_step.state = "scheduled"
                 workflow_invocation_step.workflow_step = self._step(i)
                 self.assertEqual(step_id, self._step(i).id)
                 # workflow_invocation_step.workflow_invocation = self.invocation
@@ -150,13 +150,15 @@ class WorkflowProgressTestCase(unittest.TestCase):
     def test_remaining_steps_with_progress(self):
         self._setup_workflow(TEST_WORKFLOW_YAML)
         hda3 = model.HistoryDatasetAssociation()
-        self._set_previous_progress([
-            (100, {"output": model.HistoryDatasetAssociation()}),
-            (101, {"output": model.HistoryDatasetAssociation()}),
-            (102, {"out_file1": hda3}),
-            (103, {"out_file1": model.HistoryDatasetAssociation()}),
-            (104, UNSCHEDULED_STEP),
-        ])
+        self._set_previous_progress(
+            [
+                (100, {"output": model.HistoryDatasetAssociation()}),
+                (101, {"output": model.HistoryDatasetAssociation()}),
+                (102, {"out_file1": hda3}),
+                (103, {"out_file1": model.HistoryDatasetAssociation()}),
+                (104, UNSCHEDULED_STEP),
+            ]
+        )
         progress = self._new_workflow_progress()
         steps = progress.remaining_steps()
         assert len(steps) == 1, steps
@@ -178,10 +180,12 @@ class WorkflowProgressTestCase(unittest.TestCase):
     def test_subworkflow_progress(self):
         self._setup_workflow(TEST_SUBWORKFLOW_YAML)
         hda = model.HistoryDatasetAssociation()
-        self._set_previous_progress([
-            (100, {"output": hda}),
-            (101, UNSCHEDULED_STEP),
-        ])
+        self._set_previous_progress(
+            [
+                (100, {"output": hda}),
+                (101, UNSCHEDULED_STEP),
+            ]
+        )
         subworkflow_invocation = self.invocation.create_subworkflow_invocation_for_step(
             self.invocation.workflow.step_by_index(1)
         )
@@ -196,7 +200,7 @@ class WorkflowProgressTestCase(unittest.TestCase):
         subworkflow_input_step = subworkflow.step_by_index(0)
         subworkflow_invocation_step = model.WorkflowInvocationStep()
         subworkflow_invocation_step.workflow_step_id = subworkflow_input_step.id
-        subworkflow_invocation_step.state = 'new'
+        subworkflow_invocation_step.state = "new"
         subworkflow_invocation_step.workflow_step = subworkflow_input_step
 
         subworkflow_progress.set_outputs_for_input(subworkflow_invocation_step)
@@ -214,7 +218,6 @@ class WorkflowProgressTestCase(unittest.TestCase):
 
 
 class MockModuleInjector:
-
     def __init__(self, progress):
         self.progress = progress
 
@@ -223,7 +226,6 @@ class MockModuleInjector:
 
 
 class MockModule:
-
     def __init__(self, progress):
         self.progress = progress
 
diff --git a/test/unit/workflows/workflow_support.py b/test/unit/workflows/workflow_support.py
index 9d41856ba0d..c35cef2b12a 100644
--- a/test/unit/workflows/workflow_support.py
+++ b/test/unit/workflows/workflow_support.py
@@ -11,7 +11,6 @@ from galaxy.workflow.modules import module_factory
 
 
 class MockTrans:
-
     def __init__(self):
         self.app = MockApp()
         self.sa_session = self.app.model.context
@@ -29,24 +28,16 @@ class MockTrans:
     @property
     def user(self):
         if self._user is None:
-            self._user = model.User(
-                email="testworkflows@bx.psu.edu",
-                password="password"
-            )
+            self._user = model.User(email="testworkflows@bx.psu.edu", password="password")
         return self._user
 
 
 class MockApp:
-
     def __init__(self):
         self.config = bunch.Bunch(
             tool_secret="awesome_secret",
         )
-        self.model = mapping.init(
-            "/tmp",
-            "sqlite:///:memory:",
-            create_tables=True
-        )
+        self.model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True)
         self.toolbox = MockToolbox()
         self.datatypes_registry = MockDatatypesRegistry()
         self.security = IdEncodingHelper(id_secret="testing")
@@ -54,7 +45,6 @@ class MockApp:
 
 
 class MockDatatypesRegistry:
-
     def __init__(self):
         pass
 
@@ -67,7 +57,6 @@ class MockDatatypesRegistry:
 
 
 class MockToolbox:
-
     def __init__(self):
         self.tools = {}
 
@@ -128,11 +117,11 @@ def yaml_to_model(has_dict, id_offset=100):
                 value = inputs
             if key == "workflow_outputs":
                 value = [partial(_dict_to_workflow_output, workflow_step)(_) for _ in value]
-            if key == 'collection_type':
-                key = 'tool_inputs'
-                value = {'collection_type': value}
+            if key == "collection_type":
+                key = "tool_inputs"
+                value = {"collection_type": value}
             setattr(workflow_step, key, value)
-        if workflow_step.type != 'tool':
+        if workflow_step.type != "tool":
             module = module_factory.from_workflow_step(trans, workflow_step)
             module.save_to_step(workflow_step)
         workflow.steps.append(workflow_step)
diff --git a/tool_list.py b/tool_list.py
index 9faa151f6c5..d335805d1fc 100644
--- a/tool_list.py
+++ b/tool_list.py
@@ -4,10 +4,10 @@ import sys
 # read tool_conf.xml to get all the tool xml file names
 onoff = 1
 tool_list = []
-tool_conf_file = os.environ.get('GALAXY_TEST_TOOL_CONF', None)
+tool_conf_file = os.environ.get("GALAXY_TEST_TOOL_CONF", None)
 
 if tool_conf_file is None:
-    for possible_tool_file in ['config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample']:
+    for possible_tool_file in ["config/tool_conf.xml", "tool_conf.xml", "config/tool_conf.xml.sample"]:
         tool_conf_file = possible_tool_file
         if os.path.isfile(possible_tool_file):
             break
@@ -20,10 +20,10 @@ for line in open(tool_conf_file):
     if line.find("<!--") != -1:
         onoff = 0
     if line.find("file") != -1 and onoff == 1:
-        strs = line.split('\"')
+        strs = line.split('"')
         tool_list.append(strs[1])
     if line.find("<section") != -1 and onoff == 1:
-        keys = line.strip().split('\"')
+        keys = line.strip().split('"')
         n = 0
         strtmp = "section::"
         while n < len(keys):
@@ -32,7 +32,7 @@ for line in open(tool_conf_file):
             if keys[n].find("name") != -1:
                 strtmp = strtmp + keys[n + 1] + "-"
             n = n + 1
-        tool_list.append(strtmp.replace(' ', '_'))
+        tool_list.append(strtmp.replace(" ", "_"))
     if line.find("-->") != -1:
         onoff = 1
 
@@ -49,12 +49,12 @@ for tool in tool_list:
     if os.path.exists("tools/" + tool):
         for line in open("tools/" + tool):
             if line.find("<tool ") != -1 and line.find("id") != -1:
-                keys = line.strip().split('\"')
+                keys = line.strip().split('"')
                 tool_info = dict()
-                tool_info["desc"] = ''
+                tool_info["desc"] = ""
                 for n in range(len(keys) - 1):
                     if " id=" in keys[n]:
-                        tool_info["id"] = keys[n + 1].replace(' ', '_')
+                        tool_info["id"] = keys[n + 1].replace(" ", "_")
                     if " name=" in keys[n]:
                         tool_info["name"] = keys[n + 1]
                     if " description=" in keys[n]:
@@ -66,9 +66,13 @@ flag = 0
 if len(sys.argv) == 1:
     for tool_info in tool_infos:
         if tool_info["id"].find("section") != -1:
-            print("===========================================================================================================================================")
+            print(
+                "==========================================================================================================================================="
+            )
             print("{:<45}\t{:<40}\t{}".format("id", "name", tool_info["id"]))
-            print("- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -")
+            print(
+                "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -"
+            )
         else:
             print("{:<45}\t{:<40}".format(tool_info["id"], tool_info["name"]))
 else:
@@ -76,6 +80,6 @@ else:
         if tool_info["id"].find("section") != -1:
             flag = 0
         elif flag == 1:
-            print(" functional.test_toolbox:TestForTool_%s" % tool_info["id"], end=' ')
-        if tool_info["id"].replace('section::', '') == sys.argv[1]:
+            print(" functional.test_toolbox:TestForTool_%s" % tool_info["id"], end=" ")
+        if tool_info["id"].replace("section::", "") == sys.argv[1]:
             flag = 1
diff --git a/tools/data_export/send.py b/tools/data_export/send.py
index aef9e77b24f..3662822f8b2 100644
--- a/tools/data_export/send.py
+++ b/tools/data_export/send.py
@@ -19,9 +19,11 @@ import time
 from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.cloud import CloudManager
 
-
 try:
-    from cloudbridge.factory import CloudProviderFactory, ProviderList
+    from cloudbridge.factory import (
+        CloudProviderFactory,
+        ProviderList,
+    )
 except ImportError:
     CloudProviderFactory = None
     ProviderList = None
diff --git a/tools/data_source/data_source.py b/tools/data_source/data_source.py
index 7c1b9bca463..a90504f2036 100644
--- a/tools/data_source/data_source.py
+++ b/tools/data_source/data_source.py
@@ -3,8 +3,14 @@
 # Data source application parameters are temporarily stored in the dataset file.
 import os
 import sys
-from json import dumps, loads
-from urllib.parse import urlencode, urlparse
+from json import (
+    dumps,
+    loads,
+)
+from urllib.parse import (
+    urlencode,
+    urlparse,
+)
 from urllib.request import urlopen
 
 from galaxy.datatypes import sniff
@@ -12,7 +18,7 @@ from galaxy.datatypes.registry import Registry
 from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
-    get_charset_from_http_headers
+    get_charset_from_http_headers,
 )
 
 GALAXY_PARAM_PREFIX = 'GALAXY'
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 174fe412a35..0e68d5689e4 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -9,17 +9,24 @@ import errno
 import os
 import shutil
 import sys
-from json import dump, load, loads
+from json import (
+    dump,
+    load,
+    loads,
+)
 from typing import Dict
 
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
-from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
+from galaxy.datatypes.upload_util import (
+    handle_upload,
+    UploadProblemException,
+)
 from galaxy.util import (
     bunch,
     is_url,
     safe_makedirs,
-    unicodify
+    unicodify,
 )
 from galaxy.util.compression_utils import CompressedFile
 
diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py
index 643dc4ffc15..bf346aa5faf 100755
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -19,7 +19,10 @@ import tempfile
 import bx.seq.nib
 import bx.seq.twobit
 from bx.cookbook import doc_optparse
-from bx.tabular.io import Comment, Header
+from bx.tabular.io import (
+    Comment,
+    Header,
+)
 
 from galaxy.datatypes.util import gff_util
 from galaxy.tools.util.galaxyops import parse_cols_arg
diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py
index e8216ebd9e3..abc2a5011aa 100644
--- a/tools/filters/gff/gff_filter_by_attribute.py
+++ b/tools/filters/gff/gff_filter_by_attribute.py
@@ -3,10 +3,17 @@
 # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
 # TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats/). The commonalities should be
 # abstracted and leveraged in each filtering tool.
-from __future__ import division, print_function
+from __future__ import (
+    division,
+    print_function,
+)
 
 import sys
-from ast import Module, parse, walk
+from ast import (
+    Module,
+    parse,
+    walk,
+)
 from json import loads
 
 AST_NODE_TYPE_WHITELIST = [
diff --git a/tools/filters/gff/gff_filter_by_feature_count.py b/tools/filters/gff/gff_filter_by_feature_count.py
index 7a32432b6a8..51ac1a4b7af 100644
--- a/tools/filters/gff/gff_filter_by_feature_count.py
+++ b/tools/filters/gff/gff_filter_by_feature_count.py
@@ -8,7 +8,11 @@ Usage:
 from __future__ import print_function
 
 import sys
-from ast import Module, parse, walk
+from ast import (
+    Module,
+    parse,
+    walk,
+)
 
 from bx.intervals.io import GenomicInterval
 
diff --git a/tools/filters/grep.py b/tools/filters/grep.py
index fad39281aac..98c4aff39b0 100644
--- a/tools/filters/grep.py
+++ b/tools/filters/grep.py
@@ -17,7 +17,10 @@ import os
 import re
 import subprocess
 import sys
-from subprocess import PIPE, Popen
+from subprocess import (
+    PIPE,
+    Popen,
+)
 from tempfile import NamedTemporaryFile
 
 
diff --git a/tools/filters/random_lines_two_pass.py b/tools/filters/random_lines_two_pass.py
index 264fe9e74c5..d00826b7f6e 100644
--- a/tools/filters/random_lines_two_pass.py
+++ b/tools/filters/random_lines_two_pass.py
@@ -9,7 +9,7 @@ import optparse
 import random
 from math import (
     ceil,
-    log
+    log,
 )
 
 
diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py
index ddc3c8fd280..bed37395c23 100644
--- a/tools/filters/sff_extract.py
+++ b/tools/filters/sff_extract.py
@@ -31,7 +31,10 @@ import struct
 import subprocess
 import sys
 import tempfile
-from typing import Dict, List
+from typing import (
+    Dict,
+    List,
+)
 
 __author__ = 'Jose Blanca and Bastien Chevreux'
 __copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux'
@@ -1219,7 +1222,10 @@ def version_string():
 def read_config():
     '''It reads the configuration options from the command line arguments and
     it returns a dict with them.'''
-    from optparse import OptionParser, OptionGroup
+    from optparse import (
+        OptionGroup,
+        OptionParser,
+    )
     usage = "usage: %prog [options] sff1 sff2 ..."
     desc = "Extract sequences from 454 SFF files into FASTA, FASTA quality"\
            " and XML traceinfo format. When a paired-end linker sequence"\
diff --git a/tools/filters/wiggle_to_simple.py b/tools/filters/wiggle_to_simple.py
index d619a8dc3f7..eb911108e55 100755
--- a/tools/filters/wiggle_to_simple.py
+++ b/tools/filters/wiggle_to_simple.py
@@ -12,7 +12,7 @@ import bx.wiggle
 
 from galaxy.util.ucsc import (
     UCSCLimitException,
-    UCSCOutWrapper
+    UCSCOutWrapper,
 )
 
 
diff --git a/tools/maf/maf_thread_for_species.py b/tools/maf/maf_thread_for_species.py
index 342efbb6fa2..d60cee22544 100644
--- a/tools/maf/maf_thread_for_species.py
+++ b/tools/maf/maf_thread_for_species.py
@@ -14,7 +14,10 @@ import sys
 
 import bx.align.maf
 from bx.align.tools.fuse import FusingAlignmentWriter
-from bx.align.tools.thread import get_components_for_species, remove_all_gap_columns
+from bx.align.tools.thread import (
+    get_components_for_species,
+    remove_all_gap_columns,
+)
 
 
 def main():
diff --git a/tools/phenotype_association/pagetag.py b/tools/phenotype_association/pagetag.py
index 1b558d7b293..5490b6b63a7 100755
--- a/tools/phenotype_association/pagetag.py
+++ b/tools/phenotype_association/pagetag.py
@@ -39,8 +39,15 @@ that exceed the rsquare threshold with the first SNP.
 """
 from __future__ import print_function
 
-from getopt import getopt, GetoptError
-from sys import argv, exit, stderr
+from getopt import (
+    getopt,
+    GetoptError,
+)
+from sys import (
+    argv,
+    exit,
+    stderr,
+)
 
 __author__ = "Aakrosh Ratan"
 __email__ = "ratan@bx.psu.edu"
diff --git a/tools/phenotype_association/senatag.py b/tools/phenotype_association/senatag.py
index 04834b29277..74f4b107f24 100755
--- a/tools/phenotype_association/senatag.py
+++ b/tools/phenotype_association/senatag.py
@@ -26,8 +26,15 @@ from __future__ import print_function
 import heapq
 import os
 from functools import total_ordering
-from getopt import getopt, GetoptError
-from sys import argv, exit, stderr
+from getopt import (
+    getopt,
+    GetoptError,
+)
+from sys import (
+    argv,
+    exit,
+    stderr,
+)
 
 __author__ = "Aakrosh Ratan"
 __email__ = "ratan@bx.psu.edu"
diff --git a/tools/stats/aggregate_scores_in_intervals.py b/tools/stats/aggregate_scores_in_intervals.py
index 2c5e8d7ad45..bca1a79c7eb 100755
--- a/tools/stats/aggregate_scores_in_intervals.py
+++ b/tools/stats/aggregate_scores_in_intervals.py
@@ -7,7 +7,10 @@ usage: %prog score_file interval_file chrom start stop [out_file] [options]
     -c, --chrom_buffer=INT: number of chromosomes (default is 3) to keep in memory when using a user supplied score file
 """
 
-from __future__ import division, print_function
+from __future__ import (
+    division,
+    print_function,
+)
 
 import os
 import os.path
@@ -18,11 +21,17 @@ from collections import Mapping
 from math import isnan
 
 import bx.wiggle
-from bx.binned_array import BinnedArray, FileBinnedArray
+from bx.binned_array import (
+    BinnedArray,
+    FileBinnedArray,
+)
 from bx.bitset_builders import binned_bitsets_from_file
 from bx.cookbook import doc_optparse
 
-from galaxy.util.ucsc import UCSCLimitException, UCSCOutWrapper
+from galaxy.util.ucsc import (
+    UCSCLimitException,
+    UCSCOutWrapper,
+)
 
 
 class PositionalScoresOnDisk(object):
diff --git a/tools/stats/filtering.py b/tools/stats/filtering.py
index bbd0f42826b..4bcae7c9b99 100644
--- a/tools/stats/filtering.py
+++ b/tools/stats/filtering.py
@@ -1,12 +1,19 @@
 #!/usr/bin/env python
 # This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties.
 # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
-from __future__ import division, print_function
+from __future__ import (
+    division,
+    print_function,
+)
 
 import json
 import re
 import sys
-from ast import Module, parse, walk
+from ast import (
+    Module,
+    parse,
+    walk,
+)
 
 AST_NODE_TYPE_WHITELIST = [
     'Expr', 'Load', 'Str', 'Num', 'BoolOp', 'Compare', 'And', 'Eq', 'NotEq',
diff --git a/tools/stats/gsummary.py b/tools/stats/gsummary.py
index d7f887c7a65..077d9dd1671 100755
--- a/tools/stats/gsummary.py
+++ b/tools/stats/gsummary.py
@@ -4,11 +4,24 @@ from __future__ import print_function
 import re
 import sys
 import tempfile
+
 try:
-    from rpy2.rpy_classic import BASIC_CONVERSION, NO_CONVERSION, r, RException, set_default_mode
+    from rpy2.rpy_classic import (
+        BASIC_CONVERSION,
+        NO_CONVERSION,
+        r,
+        RException,
+        set_default_mode,
+    )
 except ImportError:
     # RPy isn't maintained, and doesn't work with R>3.0, use it as a fallback
-    from rpy import BASIC_CONVERSION, NO_CONVERSION, r, RException, set_default_mode
+    from rpy import (
+        BASIC_CONVERSION,
+        NO_CONVERSION,
+        r,
+        RException,
+        set_default_mode,
+    )
 
 
 def stop_err(msg):